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	A	T	G	C	Cg	cG	tCw	wGa	tCa	tGa	tCt	aGa	tC	Ga	tCh	dGa	cC	Gg	wrC	Gyw	Cc	gG	wA	Tw	tC_mutation	tC_mutation_to_G	tC_mutation_to_T	APOBEC_mutation	APOBEC_mutation_to_G	APOBEC_mutation_to_T	"CONTEXT(+/-20)"	a_counts	t_counts	g_counts	c_counts	cg_counts	tcw_counts	wga_counts	tca_counts	tga_counts	tct_counts	aga_counts	tc_counts	ga_counts	tch_counts	dga_counts	cc_counts	gg_counts	wrc_counts	gyw_counts	cc_counts	gg_counts	wa_counts	tw_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_Confidence	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_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	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_dbSNP_AF	i_dbSNP_PopFreq	i_dbSNP_Strength	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
ZBTB17	7709	hgsc.bcm.edu	37	chr1	16272337	16272337	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctctgtctgctctgcaccTgggtgggggaagcaccggag	5	10	15	11	1	3	0	0	0	3	0	4	2	3	2	2	4	3	3	2	4	1	1			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:16272337T>A	ENST00000375743.4	-	6	768		c.e6-2		ZBTB17_ENST00000375733.2_Splice_Site|ZBTB17_ENST00000537142.1_Splice_Site|ZBTB17_ENST00000448462.2_Splice_Site|ZBTB17_ENST00000479282.1_5'Flank	NM_003443.2	NP_003434.2	Q13105	ZBT17_HUMAN	zinc finger and BTB domain containing 17						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)		GCTCTGCACCTGGGTGGGGGA	0.672																																					.		Atlas-SNP	.											.	ZBTB17	45	.	0			c.536-2A>T						PASS	.						41	48	46					1																	16272337		2203	4300	6503	SO:0001630	splice_region_variant	7709	exon7			TGCACCTGGGTGG	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.536-2A>T	1.37:g.16272337T>A		16	0	0		16	5	0.3125	NM_003443	A0AV07|B4DXB4|B7ZLQ9|F5H411|Q15932|Q5JYB2|Q9NUC9	Splice_Site	SNP	ENST00000375743.4	37	CCDS165.1	.	.	.	.	.	.	.	.	.	.	T	13.78	2.340713	0.41498	.	.	ENSG00000116809	ENST00000375743;ENST00000375733;ENST00000537142;ENST00000448462	.	.	.	4.39	4.39	0.52855	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.584	0.33646	0.0:0.0:0.1946:0.8054	.	.	.	.	.	-1	.	.	.	-	.	.	ZBTB17	16144924	1.000000	0.71417	0.910000	0.35882	0.676000	0.39594	3.477000	0.53151	1.918000	0.55548	0.379000	0.24179	.	.	.	none		0.672	ZBTB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025998.1	NM_003443	Intron	A	16272337	T	A	16272337	5	1	1	1	0	0	0	0	0	0	1	0	17542	1594	55	5	1921	5	ZBTB17	1	16272337	Splice_Site	SNP	T	TCGA-FA-8693-01A-11D-2397-10		16272337	232978284	1	1											
GNL2	29889	hgsc.bcm.edu	37	chr1	38032563	38032563	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gttgtgtgtttcatagtagcGcacaccaacttttttcggcc	7	15	9	10	2	1	0	1	0	0	0	2	0	1	0	2	1	2	4	2	1	3	7			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:38032563G>A	ENST00000373062.3	-	16	2187	c.2089C>T	c.(2089-2091)Cgc>Tgc	p.R697C	GNL2_ENST00000462812.1_5'UTR	NM_013285.2	NP_037417.1	Q13823	NOG2_HUMAN	guanine nucleotide binding protein-like 2 (nucleolar)	697					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)				TCATAGTAGCGCACACCAACT	0.403																																					p.R697C		Atlas-SNP	.											.	GNL2	58	.	0			c.C2089T						PASS	.						188	170	176					1																	38032563		2203	4300	6503	SO:0001583	missense	29889	exon16			AGTAGCGCACACC	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.2089C>T	1.37:g.38032563G>A	ENSP00000362153:p.Arg697Cys	142	0	0		133	27	0.203008	NM_013285	Q9BWN7	Missense_Mutation	SNP	ENST00000373062.3	37	CCDS421.1	.	.	.	.	.	.	.	.	.	.	G	32	5.138938	0.94560	.	.	ENSG00000134697	ENST00000373062	T	0.25579	1.79	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.52386	0.1731	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.52503	-0.8567	10	0.72032	D	0.01	-9.6294	19.4985	0.95083	0.0:0.0:1.0:0.0	.	697	Q13823	NOG2_HUMAN	C	697	ENSP00000362153:R697C	ENSP00000362153:R697C	R	-	1	0	GNL2	37805150	1.000000	0.71417	0.994000	0.49952	0.963000	0.63663	7.721000	0.84768	2.698000	0.92095	0.561000	0.74099	CGC	.	.	none		0.403	GNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012478.1	NM_013285		A	38032563	G	A	38032563	3	1	1	1	0	0	0	0	1	0	0	0	6544	1087	38	1	110	1	GNL2	1	38032563	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	21760226	38032563	211218058	2	2											
FGGY	55277	hgsc.bcm.edu	37	chr1	60223665	60223665	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccgagactacaggataaaaaGtaagtgtgtattttttatat	15	14	8	4	1	0	1	0	0	0	1	0	3	0	2	1	1	1	2	1	1	8	8			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:60223665G>T	ENST00000303721.7	+	15	1748		c.e15+1		FGGY_ENST00000371210.1_Splice_Site|FGGY_ENST00000371212.1_Splice_Site|RP4-782L23.2_ENST00000443012.1_RNA|FGGY_ENST00000371218.4_Splice_Site	NM_018291.3	NP_060761.3	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing						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)					AGGATAAAAAGTAAGTGTGTA	0.378																																					.		Atlas-SNP	.											.	FGGY	99	.	0			c.1646+1G>T						PASS	.						95	91	92					1																	60223665		2203	4300	6503	SO:0001630	splice_region_variant	55277	exon16			TAAAAAGTAAGTG		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.1574+1G>T	1.37:g.60223665G>T		80	0	0		73	9	0.123288	NM_001113411	B1AK92|B1AK93|B1AK94|B2RDR8|D3DQ56|Q9HA63|Q9NV20	Splice_Site	SNP	ENST00000303721.7	37	CCDS611.2	.	.	.	.	.	.	.	.	.	.	G	11.53	1.665493	0.29604	.	.	ENSG00000172456	ENST00000371218;ENST00000303721;ENST00000371212;ENST00000371210	.	.	.	5.09	5.09	0.68999	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3446	0.74327	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FGGY	59996253	1.000000	0.71417	1.000000	0.80357	0.229000	0.25112	5.100000	0.64560	2.646000	0.89796	0.563000	0.77884	.	.	.	none		0.378	FGGY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023210.2	NM_001113411	Intron	T	60223665	G	T	60223665	5	4	1	1	0	0	0	0	0	0	1	0	5879	1043	36	4	1705	4	FGGY	1	60223665	Splice_Site	SNP	G	TCGA-FA-8693-01A-11D-2397-10	22191102	60223665	189026956	3	3											
C1orf87	127795	hgsc.bcm.edu	37	chr1	60491072	60491072	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcttaataagagttgacttaCtttatttcattttggtaacc	11	19	5	6	0	2	2	1	1	1	1	2	2	2	2	1	1	2	2	1	1	5	10			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:60491072C>G	ENST00000371201.3	-	8	1235		c.e8+1		C1orf87_ENST00000450089.2_Splice_Site	NM_152377.2	NP_689590.1	Q8N0U7	CA087_HUMAN	chromosome 1 open reading frame 87								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						AGTTGACTTACTTTATTTCAT	0.388																																					.	NSCLC(75;811 1386 4923 13371 51772)	Atlas-SNP	.											.	C1orf87	55	.	0			c.1127+1G>C						PASS	.						120	121	121					1																	60491072		2203	4300	6503	SO:0001630	splice_region_variant	127795	exon9			GACTTACTTTATT	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.1127+1G>C	1.37:g.60491072C>G		77	0	0		79	20	0.253165	NM_152377	Q6ZU07|Q8IVS0	Splice_Site	SNP	ENST00000371201.3	37	CCDS614.1	.	.	.	.	.	.	.	.	.	.	C	16.22	3.060848	0.55432	.	.	ENSG00000162598	ENST00000371201;ENST00000450089	.	.	.	5.09	5.09	0.68999	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.851	0.63496	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C1orf87	60263660	1.000000	0.71417	1.000000	0.80357	0.715000	0.41141	3.775000	0.55349	2.648000	0.89879	0.555000	0.69702	.	.	.	none		0.388	C1orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024943.1	NM_152377	Intron	G	60491072	C	G	60491072	5	3	1	1	0	0	0	0	0	0	1	0	2066	579	20	4	532	4	C1orf87	1	60491072	Splice_Site	SNP	C	TCGA-FA-8693-01A-11D-2397-10	267407	60491072	188759549	4	4											
PGM1	5236	hgsc.bcm.edu	37	chr1	64104389	64104389	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acaaagattgctttgtatgaGaccccaactggctggaagtt	12	11	10	8	0	0	2	0	1	0	2	0	4	0	3	2	2	2	4	2	2	4	4			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:64104389G>A	ENST00000371084.3	+	7	1275	c.1062G>A	c.(1060-1062)gaG>gaA	p.E354E	PGM1_ENST00000540265.1_Silent_p.E157E|PGM1_ENST00000371083.4_Silent_p.E372E	NM_002633.2	NP_002624.2	P36871	PGM1_HUMAN	phosphoglucomutase 1	354					carbohydrate metabolic process (GO:0005975)|galactose catabolic process (GO:0019388)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20						CTTTGTATGAGACCCCAACTG	0.502																																					p.E372E		Atlas-SNP	.											.	PGM1	75	.	0			c.G1116A						PASS	.						179	169	172					1																	64104389		2203	4300	6503	SO:0001819	synonymous_variant	5236	exon7			GTATGAGACCCCA	BC019920	CCDS625.1, CCDS53323.1, CCDS53324.1	1p22.1	2012-10-02			ENSG00000079739	ENSG00000079739	5.4.2.2		8905	protein-coding gene	gene with protein product		171900				4517931, 1530890	Standard	NM_002633		Approved		uc010ooz.2	P36871	OTTHUMG00000008968	ENST00000371084.3:c.1062G>A	1.37:g.64104389G>A		368	0	0		302	18	0.0596026	NM_001172818	B2R5N9|B4DPV0|Q16105|Q16106|Q5BKZ9|Q6NW22|Q86U74|Q96J40|Q9NTY4	Silent	SNP	ENST00000371084.3	37	CCDS625.1																																																																																			.	.	none		0.502	PGM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024868.1	NM_002633		A	64104389	G	A	64104389	2	1	1	1	0	0	0	0	0	0	0	1	11806	933	33	2		2	PGM1	1	64104389	Silent	SNP	G	TCGA-FA-8693-01A-11D-2397-10	3613317	64104389	185146232	5	5											
GBP3	2635	hgsc.bcm.edu	37	chr1	89476646	89476646	+	Missense_Mutation	SNP	T	T	C																															caggtcttgtagcttctgaaTaaagagacaatagccccctg																										TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:89476646T>C	ENST00000370481.4	-	8	1523	c.1303A>G	c.(1303-1305)Att>Gtt	p.I435V		NM_018284.2	NP_060754.2	Q8WXF7	ATLA1_HUMAN	guanylate binding protein 3	0					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)			breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(277;0.123)		all cancers(265;0.0103)|Epithelial(280;0.0293)		AGCTTCTGAATAAAGAGACAA	0.433																																					p.I435V		Atlas-SNP	.											.	GBP3	53	.	0			c.A1303G						PASS	.						203	170	182					1																	89476646		2191	3984	6175	SO:0001583	missense	2635	exon8			TCTGAATAAAGAG	BC063819	CCDS717.2	1p22.2	2008-02-05			ENSG00000117226	ENSG00000117226			4184	protein-coding gene	gene with protein product		600413				7518790	Standard	NM_018284		Approved	FLJ10961	uc001dmt.3	Q9H0R5	OTTHUMG00000010616	ENST00000370481.4:c.1303A>G	1.37:g.89476646T>C	ENSP00000359512:p.Ile435Val	321	0	0		341	73	0.214076	NM_018284	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Missense_Mutation	SNP	ENST00000370481.4	37	CCDS717.2	.	.	.	.	.	.	.	.	.	.	T	7.103	0.574507	0.13623	.	.	ENSG00000117226	ENST00000370482;ENST00000370481;ENST00000235878	T	0.01887	4.58	3.57	-1.8	0.07907	Guanylate-binding protein, C-terminal (3);	1.033460	0.07626	N	0.927902	T	0.00412	0.0013	N	0.16478	0.41	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.12837	0.008;0.006	T	0.47235	-0.9133	10	0.20519	T	0.43	.	0.9257	0.01324	0.1662:0.3148:0.1708:0.3482	.	301;435	F6X827;Q9H0R5	.;GBP3_HUMAN	V	403;435;435	ENSP00000359512:I435V	ENSP00000235878:I435V	I	-	1	0	GBP3	89249234	0.000000	0.05858	0.000000	0.03702	0.128000	0.20619	-2.842000	0.00737	-0.211000	0.10124	0.491000	0.48974	ATT	.	.	none		0.433	GBP3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313541.3	NM_018284		C	89476646	T	C	89476646	3	2	1	1	0	0	0	0	1	0	0	0	6283	1406	49	3	500	3	GBP3	1	89476646	Missense_Mutation	SNP	T	TCGA-FA-8693-01A-11D-2397-10	25372257	89476646	159773975	6	6	1	2									
GBP3	2635	hgsc.bcm.edu	37	chr1	89476655	89476655	+	Missense_Mutation	SNP	A	A	G																															tagcttctgaataaagagacAatagccccctggtttcgaat																										TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:89476655A>G	ENST00000370481.4	-	8	1514	c.1294T>C	c.(1294-1296)Tgt>Cgt	p.C432R		NM_018284.2	NP_060754.2	Q8WXF7	ATLA1_HUMAN	guanylate binding protein 3	0					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)			breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(277;0.123)		all cancers(265;0.0103)|Epithelial(280;0.0293)		ATAAAGAGACAATAGCCCCCT	0.423																																					p.C432R		Atlas-SNP	.											.	GBP3	53	.	0			c.T1294C						PASS	.						202	169	181					1																	89476655		2191	3988	6179	SO:0001583	missense	2635	exon8			AGAGACAATAGCC	BC063819	CCDS717.2	1p22.2	2008-02-05			ENSG00000117226	ENSG00000117226			4184	protein-coding gene	gene with protein product		600413				7518790	Standard	NM_018284		Approved	FLJ10961	uc001dmt.3	Q9H0R5	OTTHUMG00000010616	ENST00000370481.4:c.1294T>C	1.37:g.89476655A>G	ENSP00000359512:p.Cys432Arg	339	0	0		333	64	0.192192	NM_018284	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Missense_Mutation	SNP	ENST00000370481.4	37	CCDS717.2	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.185169	0.00305	.	.	ENSG00000117226	ENST00000370482;ENST00000370481;ENST00000235878	T	0.01821	4.62	3.79	-1.98	0.07480	Guanylate-binding protein, C-terminal (3);	0.843353	0.10841	N	0.628203	T	0.00109	0.0003	N	0.00258	-1.755	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31223	-0.9951	10	0.02654	T	1	.	5.3138	0.15845	0.2643:0.0:0.5065:0.2292	.	298;432	F6X827;Q9H0R5	.;GBP3_HUMAN	R	400;432;432	ENSP00000359512:C432R	ENSP00000235878:C432R	C	-	1	0	GBP3	89249243	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.521000	0.02239	-0.900000	0.03896	-2.405000	0.00223	TGT	.	.	none		0.423	GBP3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313541.3	NM_018284		G	89476655	A	G	89476655	3	3	1	1	0	0	0	0	1	0	0	0	6283	130	5	3	509	3	GBP3	1	89476655	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10	9	89476655	159773966	7	7	1	2									
ARHGAP29	9411	hgsc.bcm.edu	37	chr1	94670633	94670633	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcacccaagttaagctttttTtcaacccatgaaactatgtt	12	15	4	10	0	2	1	2	1	0	0	2	1	2	1	2	0	3	3	2	0	5	6	rs201001778		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:94670633T>G	ENST00000260526.6	-	7	863	c.681A>C	c.(679-681)gaA>gaC	p.E227D	ARHGAP29_ENST00000370217.3_Missense_Mutation_p.E227D	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	227					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)		TAAGCTTTTTTTCAACCCATG	0.318																																					p.E227D		Atlas-SNP	.											.	ARHGAP29	132	.	0			c.A681C						PASS	.						83	84	83					1																	94670633		2202	4298	6500	SO:0001583	missense	9411	exon7			CTTTTTTTCAACC		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.681A>C	1.37:g.94670633T>G	ENSP00000260526:p.Glu227Asp	133	0	0		140	18	0.128571	NM_004815	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Missense_Mutation	SNP	ENST00000260526.6	37	CCDS748.1	.	.	.	.	.	.	.	.	.	.	T	19.12	3.766355	0.69878	.	.	ENSG00000137962	ENST00000260526;ENST00000370217	T;T	0.46451	0.87;0.87	5.87	2.48	0.30137	.	0.000000	0.37053	N	0.002263	T	0.25531	0.0621	L	0.53671	1.685	0.45066	D	0.998081	P;P	0.46784	0.884;0.849	P;B	0.45610	0.487;0.318	T	0.02975	-1.1087	10	0.45353	T	0.12	-29.8012	8.1775	0.31292	0.0:0.3743:0.0:0.6257	.	227;227	Q52LW3-2;Q52LW3	.;RHG29_HUMAN	D	227	ENSP00000260526:E227D;ENSP00000359237:E227D	ENSP00000260526:E227D	E	-	3	2	ARHGAP29	94443221	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.684000	0.25364	0.603000	0.29913	0.533000	0.62120	GAA	T|1.000;C|0.000	.	alt		0.318	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815		G	94670633	T	G	94670633	3	3	1	1	0	0	0	0	1	0	0	0	878	1838	64	5	3172	5	ARHGAP29	1	94670633	Missense_Mutation	SNP	T	TCGA-FA-8693-01A-11D-2397-10	5193978	94670633	154579988	8	8											
CEPT1	10390	hgsc.bcm.edu	37	chr1	111724864	111724864	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgcactttgtactgtagcagGgaccatattttcctgtacaa	10	14	8	9	0	0	0	0	0	0	0	1	1	1	1	2	1	4	5	2	1	5	7			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:111724864G>A	ENST00000545121.1	+	6	978	c.770G>A	c.(769-771)gGg>gAg	p.G257E	RP5-1180E21.4_ENST00000607951.1_RNA|CEPT1_ENST00000467362.1_3'UTR|RP5-1180E21.5_ENST00000610049.1_RNA|CEPT1_ENST00000357172.4_Missense_Mutation_p.G257E	NM_001007794.1	NP_001007795.1	Q9Y6K0	CEPT1_HUMAN	choline/ethanolamine phosphotransferase 1	257					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)	ACTGTAGCAGGGACCATATTT	0.333																																					p.G257E		Atlas-SNP	.											.	CEPT1	25	.	0			c.G770A						PASS	.						84	80	82					1																	111724864		2203	4300	6503	SO:0001583	missense	10390	exon6			TAGCAGGGACCAT	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.770G>A	1.37:g.111724864G>A	ENSP00000441980:p.Gly257Glu	137	0	0		137	36	0.262774	NM_006090	Q69YJ9|Q9P0Y8	Missense_Mutation	SNP	ENST00000545121.1	37	CCDS830.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.039564	0.93630	.	.	ENSG00000134255	ENST00000545121;ENST00000357172	T;T	0.51325	0.71;0.71	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.67249	0.2873	M	0.85462	2.755	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.63139	-0.6704	10	0.30854	T	0.27	-5.595	18.3537	0.90348	0.0:0.0:1.0:0.0	.	257	Q9Y6K0	CEPT1_HUMAN	E	257	ENSP00000441980:G257E;ENSP00000349696:G257E	ENSP00000349696:G257E	G	+	2	0	CEPT1	111526387	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.434000	0.97515	2.937000	0.99478	0.650000	0.86243	GGG	.	.	none		0.333	CEPT1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034462.2	NM_006090		A	111724864	G	A	111724864	3	1	1	1	0	0	0	0	1	0	0	0	3266	1232	43	2	788	2	CEPT1	1	111724864	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	17054231	111724864	137525757	9	9											
ST7L	54879	hgsc.bcm.edu	37	chr1	113153627	113153627	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtaccaccattcaaatatcTatgacaaacagaaaatatcc	19	9	3	10	0	2	2	1	1	1	1	3	2	3	2	3	0	2	1	3	0	8	5			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:113153627T>C	ENST00000358039.4	-	3	593		c.e3-2		ST7L_ENST00000544629.1_Splice_Site|ST7L_ENST00000543570.1_Splice_Site|ST7L_ENST00000360743.4_Splice_Site|ST7L_ENST00000369668.2_Splice_Site|ST7L_ENST00000369666.1_Splice_Site|ST7L_ENST00000369669.1_Splice_Site|ST7L_ENST00000490067.1_Splice_Site|ST7L_ENST00000463235.1_Splice_Site|ST7L_ENST00000538187.1_Splice_Site|ST7L_ENST00000343210.7_Splice_Site	NM_017744.4|NM_138727.3	NP_060214.2|NP_620055.1	Q8TDW4	ST7L_HUMAN	suppression of tumorigenicity 7 like						negative regulation of cell growth (GO:0030308)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(4)|large_intestine(3)|lung(1)|prostate(2)|stomach(1)|urinary_tract(3)	15	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)		TTCAAATATCTATGACAAACA	0.383																																					.		Atlas-SNP	.											.	ST7L	31	.	0			c.289-2A>G						PASS	.						93	88	90					1																	113153627		2203	4300	6503	SO:0001630	splice_region_variant	54879	exon4			AATATCTATGACA	AB081317	CCDS848.1, CCDS849.1, CCDS850.1, CCDS852.1	1p13.1	2008-06-06			ENSG00000007341	ENSG00000007341			18441	protein-coding gene	gene with protein product						12012006	Standard	NM_138729		Approved	FLJ20284, STLR, ST7R, FAM4B	uc001ecd.3	Q8TDW4	OTTHUMG00000011753	ENST00000358039.4:c.289-2A>G	1.37:g.113153627T>C		85	0	0		92	20	0.217391	NM_138728	A8K4S7|Q49AH6|Q5TEI4|Q5U5K6|Q6N067|Q7Z2Z0|Q7Z3C2|Q8N7P8|Q8TDW1|Q8TDW2|Q8TDW3|Q9NXF3	Splice_Site	SNP	ENST00000358039.4	37	CCDS848.1	.	.	.	.	.	.	.	.	.	.	T	19.02	3.746023	0.69418	.	.	ENSG00000007341	ENST00000358039;ENST00000360743;ENST00000544629;ENST00000490067;ENST00000369668;ENST00000343210;ENST00000369666;ENST00000538187;ENST00000543570;ENST00000369664	.	.	.	5.9	5.9	0.94986	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3058	0.73990	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	ST7L	112955150	1.000000	0.71417	0.970000	0.41538	0.839000	0.47603	7.606000	0.82863	2.254000	0.74563	0.482000	0.46254	.	.	.	none		0.383	ST7L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032504.3		Intron	C	113153627	T	C	113153627	5	2	1	1	0	0	0	0	0	0	1	0	15245	1536	53	3	1531	3	ST7L	1	113153627	Splice_Site	SNP	T	TCGA-FA-8693-01A-11D-2397-10	1428763	113153627	136096994	10	10											
HIPK1	204851	hgsc.bcm.edu	37	chr1	114495495	114495495	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atggcctctttatcctggtgCttcagaatatgatcaggtaa	10	14	9	8	0	3	2	2	1	1	1	4	2	4	2	2	3	1	2	2	3	4	5			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:114495495C>G	ENST00000369558.1	+	3	1416	c.1184C>G	c.(1183-1185)gCt>gGt	p.A395G	HIPK1_ENST00000369553.1_5'Flank|HIPK1_ENST00000369554.2_Missense_Mutation_p.A395G|HIPK1_ENST00000406344.1_5'Flank|HIPK1_ENST00000369561.4_Missense_Mutation_p.A395G|HIPK1_ENST00000369555.2_Missense_Mutation_p.A395G|HIPK1_ENST00000426820.2_Missense_Mutation_p.A395G|HIPK1_ENST00000340480.4_Missense_Mutation_p.A21G|HIPK1_ENST00000369559.4_Missense_Mutation_p.A395G			Q86Z02	HIPK1_HUMAN	homeodomain interacting protein kinase 1	395	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)		TATCCTGGTGCTTCAGAATAT	0.373																																					p.A395G		Atlas-SNP	.											.	HIPK1	195	.	0			c.C1184G						PASS	.						178	164	169					1																	114495495		2203	4300	6503	SO:0001583	missense	204851	exon3			CTGGTGCTTCAGA	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.1184C>G	1.37:g.114495495C>G	ENSP00000358571:p.Ala395Gly	165	0	0		144	27	0.1875	NM_198268	A6NJ34|O75125|Q5SQL2|Q5SQL4|Q5SQL5|Q8IYD7|Q8NDN5|Q8NEB6|Q8TBZ1	Missense_Mutation	SNP	ENST00000369558.1	37	CCDS867.1	.	.	.	.	.	.	.	.	.	.	C	32	5.145198	0.94603	.	.	ENSG00000163349	ENST00000426820;ENST00000369559;ENST00000443627;ENST00000369554;ENST00000369555;ENST00000369558;ENST00000369561;ENST00000340480	T;T;T;T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;-0.2	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	0.64402	D	0.000003	T	0.60431	0.2268	N	0.17800	0.525	0.80722	D	1	D;D	0.57571	0.98;0.975	D;P	0.63488	0.915;0.904	T	0.67348	-0.5693	10	0.66056	D	0.02	.	19.0806	0.93180	0.0:1.0:0.0:0.0	.	395;395	Q86Z02;Q86Z02-2	HIPK1_HUMAN;.	G	466;395;395;395;395;395;395;21	ENSP00000407442:A466G;ENSP00000358572:A395G;ENSP00000409673:A395G;ENSP00000358567:A395G;ENSP00000358568:A395G;ENSP00000358571:A395G;ENSP00000358574:A395G;ENSP00000340956:A21G	ENSP00000340956:A21G	A	+	2	0	HIPK1	114297018	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.792000	0.85828	2.509000	0.84616	0.650000	0.86243	GCT	.	.	none		0.373	HIPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033127.1	NM_198268		G	114495495	C	G	114495495	3	3	1	1	0	0	0	0	1	0	0	0	7125	797	28	4	1190	4	HIPK1	1	114495495	Missense_Mutation	SNP	C	TCGA-FA-8693-01A-11D-2397-10	1341868	114495495	134755126	11	11											
FLG2	388698	hgsc.bcm.edu	37	chr1	152328295	152328295	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgagcctgatccatattggCcaaagccagtggattgactt	10	11	10	10	0	0	3	0	3	0	0	1	4	1	4	4	2	2	0	4	2	2	4			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:152328295C>G	ENST00000388718.5	-	3	2039	c.1967G>C	c.(1966-1968)gGc>gCc	p.G656A	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	656	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)			TCCATATTGGCCAAAGCCAGT	0.498																																					p.G656A		Atlas-SNP	.											.	FLG2	431	.	0			c.G1967C						PASS	.						213	228	223					1																	152328295		2203	4300	6503	SO:0001583	missense	388698	exon3			TATTGGCCAAAGC	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.1967G>C	1.37:g.152328295C>G	ENSP00000373370:p.Gly656Ala	177	0	0		185	10	0.0540541	NM_001014342	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	c	10.12	1.261737	0.23051	.	.	ENSG00000143520	ENST00000388718	T	0.17213	2.29	4.55	3.56	0.40772	.	.	.	.	.	T	0.11281	0.0275	M	0.73962	2.25	0.09310	N	1	D	0.56968	0.978	P	0.52856	0.711	T	0.17258	-1.0375	9	0.08599	T	0.76	-1.6533	4.9448	0.13984	0.2112:0.6799:0.0:0.109	.	656	Q5D862	FILA2_HUMAN	A	656	ENSP00000373370:G656A	ENSP00000373370:G656A	G	-	2	0	FLG2	150594919	0.004000	0.15560	0.014000	0.15608	0.046000	0.14306	1.621000	0.36986	2.083000	0.62718	0.561000	0.74099	GGC	.	.	none		0.498	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		G	152328295	C	G	152328295	3	3	1	1	0	0	0	0	1	0	0	0	5931	739	26	4	5212	4	FLG2	1	152328295	Missense_Mutation	SNP	C	TCGA-FA-8693-01A-11D-2397-10	37832800	152328295	96922326	12	12											
IVL	3713	hgsc.bcm.edu	37	chr1	152883856	152883856	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	acatctggagcagcaggaggGgcagctgaaggacctggagc	11	4	17	9	0	1	1	0	1	1	0	1	5	1	5	1	6	4	4	1	6	1	0			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:152883856G>A	ENST00000368764.3	+	2	1647	c.1583G>A	c.(1582-1584)gGg>gAg	p.G528E	IVL_ENST00000392667.2_Missense_Mutation_p.G382E			P07476	INVO_HUMAN	involucrin	528	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)			cagcaggaggggcagctgaag	0.597																																					p.G528E		Atlas-SNP	.											.	IVL	100	.	0			c.G1583A						PASS	.						70	66	67					1																	152883856		2203	4300	6503	SO:0001583	missense	3713	exon2			AGGAGGGGCAGCT	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.1583G>A	1.37:g.152883856G>A	ENSP00000357753:p.Gly528Glu	77	0	0		96	21	0.21875	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	37	CCDS1030.1	.	.	.	.	.	.	.	.	.	.	G	12.88	2.070892	0.36566	.	.	ENSG00000163207	ENST00000368764;ENST00000392667	T;T	0.47177	1.77;0.85	3.34	-1.01	0.10169	.	.	.	.	.	T	0.07234	0.0183	N	0.21545	0.675	0.09310	N	1	B	0.21905	0.062	B	0.18561	0.022	T	0.34403	-0.9830	9	0.02654	T	1	.	3.2393	0.06776	0.3377:0.0:0.447:0.2153	.	528	P07476	INVO_HUMAN	E	528;382	ENSP00000357753:G528E;ENSP00000376435:G382E	ENSP00000357753:G528E	G	+	2	0	IVL	151150480	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-0.649000	0.05384	-0.022000	0.13986	-0.274000	0.10170	GGG	.	.	none		0.597	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547		A	152883856	G	A	152883856	3	1	1	1	0	0	0	0	1	0	0	0	7938	1232	43	2	1585	2	IVL	1	152883856	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	555561	152883856	96366765	13	13											
MPZL1	9019	hgsc.bcm.edu	37	chr1	167741720	167741720	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattaggctctatgtcgtagAaaaaggtacttccttgagta	12	13	9	7	1	1	2	0	1	1	1	3	2	2	2	1	2	1	4	1	2	7	7			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:167741720A>G	ENST00000359523.2	+	3	669	c.467A>G	c.(466-468)gAa>gGa	p.E156G	MPZL1_ENST00000474859.1_Missense_Mutation_p.E156G|MPZL1_ENST00000392121.3_Intron	NM_003953.5|NM_024569.4	NP_003944.1|NP_078845.3	O95297	MPZL1_HUMAN	myelin protein zero-like 1	156					cell-cell signaling (GO:0007267)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	structural molecule activity (GO:0005198)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(2)	15	all_hematologic(923;0.215)					TATGTCGTAGAAAAAGGTACT	0.408																																					p.E156G		Atlas-SNP	.											.	MPZL1	25	.	0			c.A467G						PASS	.						83	74	77					1																	167741720		2203	4300	6503	SO:0001583	missense	9019	exon3			TCGTAGAAAAAGG	AF087020	CCDS1264.1, CCDS44273.1, CCDS53425.1	1q24.2	2013-01-11			ENSG00000197965	ENSG00000197965		"Immunoglobulin superfamily / V-set domain containing"	7226	protein-coding gene	gene with protein product		604376				9792637	Standard	NM_003953		Approved	PZR, FLJ21047	uc001geo.3	O95297	OTTHUMG00000034571	ENST00000359523.2:c.467A>G	1.37:g.167741720A>G	ENSP00000352513:p.Glu156Gly	160	0	0		186	30	0.16129	NM_024569	B2REB9|B2REC0|Q5R332|Q8IX11|Q9BWZ3|Q9NYK4|Q9UL20	Missense_Mutation	SNP	ENST00000359523.2	37	CCDS1264.1	.	.	.	.	.	.	.	.	.	.	A	19.55	3.848702	0.71603	.	.	ENSG00000197965	ENST00000359523;ENST00000474859;ENST00000367853	D;D;D	0.97850	-4.15;-4.57;-4.55	4.81	4.81	0.61882	.	0.224105	0.45867	D	0.000339	D	0.95236	0.8455	L	0.32530	0.975	0.35992	D	0.836794	D;P	0.53462	0.96;0.651	P;B	0.51229	0.663;0.273	D	0.94779	0.7952	9	0.34782	T	0.22	.	15.0743	0.72066	1.0:0.0:0.0:0.0	.	156;156	O95297-3;O95297	.;MPZL1_HUMAN	G	156;156;130	ENSP00000352513:E156G;ENSP00000420455:E156G;ENSP00000356827:E130G	ENSP00000352513:E156G	E	+	2	0	MPZL1	166008344	1.000000	0.71417	0.995000	0.50966	0.910000	0.53928	2.674000	0.46867	2.116000	0.64780	0.455000	0.32223	GAA	.	.	none		0.408	MPZL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083655.2	NM_024569		G	167741720	A	G	167741720	3	3	1	1	0	0	0	0	1	0	0	0	9758	246	9	3	477	3	MPZL1	1	167741720	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10	14857864	167741720	81508901	14	14											
ASPM	259266	hgsc.bcm.edu	37	chr1	197070009	197070009	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	accactcttgaatcataacaCcttcactttgaacagcttca	13	12	3	13	0	4	2	3	2	1	0	4	2	4	2	2	0	3	1	2	0	3	5			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:197070009C>A	ENST00000367409.4	-	18	8628	c.8372G>T	c.(8371-8373)gGt>gTt	p.G2791V	ASPM_ENST00000367408.1_Intron|ASPM_ENST00000294732.7_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2791					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						AATCATAACACCTTCACTTTG	0.393																																					p.G2791V		Atlas-SNP	.											ASPM,right_upper_lobe,carcinoma,0,1	ASPM	444	1	0			c.G8372T						PASS	.						133	133	133					1																	197070009		2203	4300	6503	SO:0001583	missense	259266	exon18			ATAACACCTTCAC	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.8372G>T	1.37:g.197070009C>A	ENSP00000356379:p.Gly2791Val	115	0	0		157	33	0.210191	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	37	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	C	10.19	1.280914	0.23392	.	.	ENSG00000066279	ENST00000367409;ENST00000367406	T	0.56611	0.45	4.66	-1.47	0.08772	.	1.296170	0.05105	N	0.487807	T	0.55689	0.1936	L	0.36672	1.1	0.09310	N	1	D;B	0.89917	1.0;0.112	D;B	0.87578	0.998;0.057	T	0.46034	-0.9220	10	0.23891	T	0.37	.	2.4063	0.04414	0.1324:0.1431:0.3433:0.3813	.	777;2791	E7EQ84;Q8IZT6	.;ASPM_HUMAN	V	2791;777	ENSP00000356379:G2791V	ENSP00000356376:G777V	G	-	2	0	ASPM	195336632	0.001000	0.12720	0.000000	0.03702	0.073000	0.16967	0.619000	0.24388	-0.532000	0.06332	-0.379000	0.06801	GGT	.	.	none		0.393	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		A	197070009	C	A	197070009	3	1	1	1	0	0	0	0	1	0	0	0	1056	507	18	4	2105	4	ASPM	1	197070009	Missense_Mutation	SNP	C	TCGA-FA-8693-01A-11D-2397-10	29328289	197070009	52180612	15	15											
NFASC	23114	hgsc.bcm.edu	37	chr1	204943936	204943936	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaaagctgaaaaccaagtcCgcctggaggtcaaaggtaaa	16	5	11	9	1	1	1	1	1	0	0	2	2	2	2	3	3	2	3	3	3	7	1	rs149731085		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:204943936C>T	ENST00000401399.1	+	13	1742	c.1543C>T	c.(1543-1545)Cgc>Tgc	p.R515C	NFASC_ENST00000367170.4_Missense_Mutation_p.R515C|NFASC_ENST00000367169.4_Missense_Mutation_p.R515C|NFASC_ENST00000339876.6_Missense_Mutation_p.R515C|NFASC_ENST00000367171.4_Missense_Mutation_p.R515C|NFASC_ENST00000338515.6_Missense_Mutation_p.R515C|NFASC_ENST00000404907.1_Missense_Mutation_p.R526C|NFASC_ENST00000539706.1_Missense_Mutation_p.R526C|NFASC_ENST00000338586.6_Missense_Mutation_p.R515C|NFASC_ENST00000404076.1_Missense_Mutation_p.R509C|NFASC_ENST00000513543.1_Missense_Mutation_p.R526C|NFASC_ENST00000367172.4_Missense_Mutation_p.R515C|NFASC_ENST00000403080.1_Missense_Mutation_p.R515C|NFASC_ENST00000360049.4_Missense_Mutation_p.R526C			O94856	NFASC_HUMAN	neurofascin	515	Ig-like C2-type 5.				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)			AAACCAAGTCCGCCTGGAGGT	0.512													C|||	1	0.000199681	0.0	0.0	5008	,	,		21343	0.0		0.001	False		,,,				2504	0.0				p.R526C		Atlas-SNP	.											.	NFASC	396	.	0			c.C1576T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	0,4406		0,0,2203	99	92	95		1543,1543,1576,1576,1525,1576	5.8	1	1	dbSNP_134	95	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense,missense,missense,missense	NFASC	NM_001005388.2,NM_001005389.1,NM_001160331.1,NM_001160332.1,NM_001160333.1,NM_015090.3	180,180,180,180,180,180	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	515/1241,515/620,526/1190,526/1175,509/614,526/1170	204943936	2,13004	2203	4300	6503	SO:0001583	missense	23114	exon14			CAAGTCCGCCTGG	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.1543C>T	1.37:g.204943936C>T	ENSP00000385637:p.Arg515Cys	131	0	0		116	30	0.258621	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	37	CCDS53460.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	34	5.399757	0.96030	0.0	2.33E-4	ENSG00000163531	ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000403080;ENST00000404076;ENST00000401399;ENST00000404907;ENST00000513543;ENST00000430393	T;T;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;-0.3;-0.3	5.8	5.8	0.92144	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.237674	0.29822	N	0.011105	T	0.80105	0.4562	L	0.61387	1.9	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;0.962;0.999;1.0;1.0;0.998;0.995	D;P;P;D;P;P;P	0.66497	0.943;0.501;0.905;0.944;0.648;0.814;0.804	T	0.78816	-0.2055	10	0.49607	T	0.09	.	19.7118	0.96099	0.0:1.0:0.0:0.0	.	515;526;526;515;515;526;515	O94856;O94856-11;O94856-8;F8W791;O94856-9;O94856-3;O94856-2	NFASC_HUMAN;.;.;.;.;.;.	C	515;515;515;515;515;515;526;526;526;515;515;509;515;526;526;502	ENSP00000356140:R515C;ENSP00000356139:R515C;ENSP00000356138:R515C;ENSP00000342128:R515C;ENSP00000344786:R515C;ENSP00000343509:R515C;ENSP00000438614:R526C;ENSP00000353154:R526C;ENSP00000356137:R515C;ENSP00000384875:R515C;ENSP00000385676:R509C;ENSP00000385637:R515C;ENSP00000384061:R526C;ENSP00000425908:R526C;ENSP00000415031:R502C	ENSP00000295776:R526C	R	+	1	0	NFASC	203210559	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.975000	0.70475	2.764000	0.94973	0.485000	0.47835	CGC	C|1.000;T|0.000	0.000	strong		0.512	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388		T	204943936	C	T	204943936	3	4	1	1	0	0	0	0	1	0	0	0	10368	652	23	1	1644	1	NFASC	1	204943936	Missense_Mutation	SNP	C	TCGA-FA-8693-01A-11D-2397-10	7873927	204943936	44306685	16	16											
PROX1	5629	hgsc.bcm.edu	37	chr1	214171399	214171399	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccggctccttctctggaaaAgacagagcctctcctgaatc	9	10	8	14	1	2	3	0	1	2	2	7	4	4	4	4	2	1	1	4	2	3	1			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:214171399A>C	ENST00000366958.4	+	2	2129	c.1521A>C	c.(1519-1521)aaA>aaC	p.K507N	PROX1_ENST00000435016.1_Missense_Mutation_p.K507N|PROX1_ENST00000498508.2_Missense_Mutation_p.K507N|PROX1_ENST00000261454.4_Missense_Mutation_p.K507N	NM_001270616.1	NP_001257545.1	Q92786	PROX1_HUMAN	prospero homeobox 1	507					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)		TCTCTGGAAAAGACAGAGCCT	0.552																																					p.K507N		Atlas-SNP	.											.	PROX1	124	.	0			c.A1521C						PASS	.						78	85	82					1																	214171399		2203	4300	6503	SO:0001583	missense	5629	exon2			TGGAAAAGACAGA	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.1521A>C	1.37:g.214171399A>C	ENSP00000355925:p.Lys507Asn	49	0	0		65	18	0.276923	NM_001270616	A6NK29|A8K2B1|Q5SW76|Q8TB91	Missense_Mutation	SNP	ENST00000366958.4	37	CCDS31021.1	.	.	.	.	.	.	.	.	.	.	A	11.80	1.748020	0.30955	.	.	ENSG00000117707	ENST00000541470;ENST00000498508;ENST00000366958;ENST00000435016;ENST00000261454	T;T;T;T	0.48836	0.81;0.8;0.81;0.81	5.71	1.66	0.24008	.	0.000000	0.85682	D	0.000000	T	0.59032	0.2164	M	0.62723	1.935	0.52501	D	0.999953	D	0.76494	0.999	D	0.85130	0.997	T	0.52223	-0.8604	10	0.22109	T	0.4	-5.3341	9.702	0.40192	0.6316:0.0:0.3684:0.0	.	507	Q92786	PROX1_HUMAN	N	79;507;507;507;507	ENSP00000420283:K507N;ENSP00000355925:K507N;ENSP00000400694:K507N;ENSP00000261454:K507N	ENSP00000261454:K507N	K	+	3	2	PROX1	212238022	1.000000	0.71417	0.995000	0.50966	0.997000	0.91878	1.513000	0.35823	0.026000	0.15269	0.533000	0.62120	AAA	.	.	none		0.552	PROX1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089727.6	NM_002763		C	214171399	A	C	214171399	3	2	1	1	0	0	0	0	1	0	0	0	12572	69	3	5	1523	5	PROX1	1	214171399	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10	9227463	214171399	35079222	17	17											
USH2A	7399	hgsc.bcm.edu	37	chr1	216221971	216221971	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgcatagtttttgaagggtAgcaagcctgtcaatatgcct	10	13	10	8	0	1	1	1	1	0	0	1	1	1	1	2	1	4	4	2	1	6	5			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:216221971A>G	ENST00000307340.3	-	31	6454	c.6068T>C	c.(6067-6069)cTa>cCa	p.L2023P	USH2A_ENST00000366943.2_Missense_Mutation_p.L2023P	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2023	Fibronectin type-III 6. {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)		TTTGAAGGGTAGCAAGCCTGT	0.413										HNSCC(13;0.011)																											p.L2023P		Atlas-SNP	.											.	USH2A	1168	.	0			c.T6068C						PASS	.						161	158	159					1																	216221971		2203	4300	6503	SO:0001583	missense	7399	exon31			AAGGGTAGCAAGC	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.6068T>C	1.37:g.216221971A>G	ENSP00000305941:p.Leu2023Pro	167	0	0		175	50	0.285714	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	A	11.46	1.644095	0.29246	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.57907	0.37;0.37	6.16	3.75	0.43078	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.558741	0.13626	N	0.374070	T	0.64000	0.2559	M	0.70275	2.135	0.34933	D	0.749578	D	0.53885	0.963	P	0.60541	0.876	T	0.65010	-0.6272	10	0.30854	T	0.27	.	6.883	0.24183	0.4969:0.1739:0.0:0.3292	.	2023	O75445	USH2A_HUMAN	P	2023	ENSP00000305941:L2023P;ENSP00000355910:L2023P	ENSP00000305941:L2023P	L	-	2	0	USH2A	214288594	0.218000	0.23608	0.304000	0.25085	0.998000	0.95712	0.502000	0.22594	0.491000	0.27793	0.528000	0.53228	CTA	.	.	none		0.413	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		G	216221971	A	G	216221971	3	3	1	1	0	0	0	0	1	0	0	0	17051	420	15	3	9708	3	USH2A	1	216221971	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10	2050572	216221971	33028650	18	18											
ITPKB	3707	hgsc.bcm.edu	37	chr1	226836447	226836447	+	Frame_Shift_Del	DEL	T	T	-																															agggagaccagtgcaccatgTtttttatcttcctccatgat																										TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:226836447delT	ENST00000272117.3	-	2	1957	c.1958delA	c.(1957-1959)aacfs	p.N653fs	ITPKB_ENST00000429204.1_Frame_Shift_Del_p.N653fs			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	653					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)				GTGCACCATGTTTTTTATCTT	0.438																																					p.N653fs	Colon(84;110 1851 5306 33547)	Pindel,Atlas-Indel	.											.	ITPKB	158	.	0			c.1959delC						PASS	.						164	163	164					1																	226836447		2203	4300	6503	SO:0001589	frameshift_variant	3707	exon3			.	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.1958delA	1.37:g.226836447delT	ENSP00000272117:p.Asn653fs	171	0	.		169	32	0.189	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Frame_Shift_Del	DEL	ENST00000272117.3	37	CCDS1555.1																																																																																			.	.	none		0.438	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221		-	226836447	T	-	226836447	7	5	1	1	0	1	0	1	0	0	0	0	7927	1725	60	0	906	0	ITPKB	1	226836447	Frame_Shift_Del	DEL	T	TCGA-FA-8693-01A-11D-2397-10	10614476	226836447	22414174	19	19											
CHRM3	1131	hgsc.bcm.edu	37	chr1	240071117	240071117	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attatcggggtcatttcaatGaatctgtttacgacctacat	11	15	7	8	2	3	1	2	1	1	0	4	2	3	1	1	2	2	1	1	2	5	5			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:240071117G>T	ENST00000255380.4	+	5	1145	c.366G>T	c.(364-366)atG>atT	p.M122I		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	122					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)	p.M122I(1)		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)	TCATTTCAATGAATCTGTTTA	0.473																																					p.M122I		Atlas-SNP	.											CHRM3,NS,carcinoma,0,1	CHRM3	118	1	1	Substitution - Missense(1)	breast(1)	c.G366T						scavenged	.						106	91	96					1																	240071117		2203	4300	6503	SO:0001583	missense	1131	exon5			TTCAATGAATCTG	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.366G>T	1.37:g.240071117G>T	ENSP00000255380:p.Met122Ile	377	1	0.00265252		349	58	0.166189	NM_000740	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Missense_Mutation	SNP	ENST00000255380.4	37	CCDS1616.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.331523	0.81690	.	.	ENSG00000133019	ENST00000255380	T	0.17213	2.29	5.9	5.9	0.94986	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.40522	0.1120	L	0.52126	1.63	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.05338	-1.0891	10	0.87932	D	0	-30.8099	20.2789	0.98501	0.0:0.0:1.0:0.0	.	122	P20309	ACM3_HUMAN	I	122	ENSP00000255380:M122I	ENSP00000255380:M122I	M	+	3	0	CHRM3	238137740	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	9.869000	0.99810	2.788000	0.95919	0.650000	0.86243	ATG	.	.	none		0.473	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740		T	240071117	G	T	240071117	3	4	1	1	0	0	0	0	1	0	0	0	3380	1290	45	4	368	4	CHRM3	1	240071117	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	13234670	240071117	9179504	20	20											
BIRC6	57448	hgsc.bcm.edu	37	chr2	32724813	32724813	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cagatagctccgtgggtgctCgagcatgctttgggggactc	6	10	15	10	2	0	1	0	0	0	1	3	3	1	2	1	3	4	4	1	3	1	2			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:32724813C>T	ENST00000421745.2	+	46	8802	c.8668C>T	c.(8668-8670)Cga>Tga	p.R2890*		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	2890					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)					CGTGGGTGCTCGAGCATGCTT	0.438																																					p.R2890X	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											BIRC6_ENST00000421745,NS,carcinoma,-1,4	BIRC6	838	4	0			c.C8668T						scavenged	.						216	211	213					2																	32724813		2203	4300	6503	SO:0001587	stop_gained	57448	exon46			GGTGCTCGAGCAT	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.8668C>T	2.37:g.32724813C>T	ENSP00000393596:p.Arg2890*	210	2	0.00952381		286	65	0.227273	NM_016252	Q9ULD1	Nonsense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	C	51	17.445868	0.99886	.	.	ENSG00000115760	ENST00000421745	.	.	.	5.42	4.53	0.55603	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	.	14.7907	0.69841	0.2614:0.7386:0.0:0.0	.	.	.	.	X	2890	.	ENSP00000393596:R2890X	R	+	1	2	BIRC6	32578317	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.557000	0.45871	1.370000	0.46153	0.655000	0.94253	CGA	.	.	none		0.438	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		T	32724813	C	T	32724813	4	4	1	1	0	0	0	0	0	1	0	0	1438	876	31	1	8850	1	BIRC6	2	32724813	Nonsense_Mutation	SNP	C	TCGA-FA-8693-01A-11D-2397-10		32724813	210474560	21	21											
LOXL3	84695	hgsc.bcm.edu	37	chr2	74761669	74761669	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctctcacccatggcactcGtgccacacccaggagtggcg	7	6	10	18	2	1	0	1	0	1	0	3	1	1	1	4	3	1	1	4	3	0	0			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:74761669G>A	ENST00000264094.3	-	10	1883	c.1812C>T	c.(1810-1812)caC>caT	p.H604H	LOXL3_ENST00000393937.2_Silent_p.H459H|LOXL3_ENST00000409549.1_Silent_p.H548H|LOXL3_ENST00000409986.1_Silent_p.H459H|LOXL3_ENST00000409249.1_Intron	NM_032603.2	NP_115992.1	P58215	LOXL3_HUMAN	lysyl oxidase-like 3	604	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						CATGGCACTCGTGCCACACCC	0.607																																					p.H604H		Atlas-SNP	.											.	LOXL3	73	.	0			c.C1812T						PASS	.						41	42	42					2																	74761669		2203	4300	6503	SO:0001819	synonymous_variant	84695	exon10			GCACTCGTGCCAC	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.1812C>T	2.37:g.74761669G>A		153	0	0		114	6	0.0526316	NM_032603	D6W5J1|Q2EHP2|Q6IPL7|Q96RS1	Silent	SNP	ENST00000264094.3	37	CCDS1953.1																																																																																			.	.	none		0.607	LOXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252215.1	NM_032603		A	74761669	G	A	74761669	2	1	1	1	0	0	0	0	0	0	0	1	8910	1136	40	1		1	LOXL3	2	74761669	Silent	SNP	G	TCGA-FA-8693-01A-11D-2397-10	42036856	74761669	168437704	22	22											
PDCL3	79031	hgsc.bcm.edu	37	chr2	101188050	101188050	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttttctatgtgtgttttatAgaattcccctctgtgccctg	5	19	8	9	0	2	1	0	0	2	1	3	1	3	1	3	0	1	2	3	0	4	7			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:101188050A>G	ENST00000264254.6	+	5	746		c.e5-1			NM_024065.4	NP_076970.1	Q9H2J4	PDCL3_HUMAN	phosducin-like 3						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)	p.?(1)		endometrium(3)|large_intestine(2)|liver(1)|lung(6)	12						TGTGTTTTATAGAATTCCCCT	0.388																																					.		Atlas-SNP	.											PDCL3,NS,carcinoma,0,1	PDCL3	27	1	1	Unknown(1)	lung(1)	c.369-2A>G						PASS	.						129	129	129					2																	101188050		2203	4300	6503	SO:0001630	splice_region_variant	79031	exon5			TTTTATAGAATTC	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.369-1A>G	2.37:g.101188050A>G		45	0	0		29	7	0.241379	NM_024065	B2RA00|Q53S68	Splice_Site	SNP	ENST00000264254.6	37	CCDS33261.1	.	.	.	.	.	.	.	.	.	.	a	17.13	3.311619	0.60414	.	.	ENSG00000115539	ENST00000264254;ENST00000416255;ENST00000450127	.	.	.	5.59	5.59	0.84812	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8181	0.78621	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PDCL3	100554482	1.000000	0.71417	0.985000	0.45067	0.633000	0.38033	8.950000	0.93019	2.150000	0.67090	0.514000	0.50259	.	.	.	none		0.388	PDCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329734.1	NM_024065	Intron	G	101188050	A	G	101188050	5	3	1	1	0	0	0	0	0	0	1	0	11637	434	15	3	385	3	PDCL3	2	101188050	Splice_Site	SNP	A	TCGA-FA-8693-01A-11D-2397-10	26426381	101188050	142011323	23	23											
EPB41L5	57669	hgsc.bcm.edu	37	chr2	120799656	120799656	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgaaagcgactattttggTctgagatttatggattcagc	11	15	10	5	1	2	2	1	2	1	1	2	5	2	3	0	2	2	0	0	2	3	7			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:120799656T>G	ENST00000263713.5	+	3	469	c.255T>G	c.(253-255)ggT>ggG	p.G85G	EPB41L5_ENST00000452780.1_Silent_p.G85G|EPB41L5_ENST00000331393.4_Silent_p.G85G|EPB41L5_ENST00000443124.1_Silent_p.G85G|EPB41L5_ENST00000443902.2_Silent_p.G85G	NM_020909.3	NP_065960.2	Q9HCM4	E41L5_HUMAN	erythrocyte membrane protein band 4.1 like 5	85	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						ACTATTTTGGTCTGAGATTTA	0.343																																					p.G85G		Atlas-SNP	.											.	EPB41L5	98	.	0			c.T255G						PASS	.						156	147	150					2																	120799656		2203	4300	6503	SO:0001819	synonymous_variant	57669	exon3			TTTTGGTCTGAGA	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.255T>G	2.37:g.120799656T>G		219	0	0		241	36	0.149378	NM_020909	Q7Z5S1|Q8IZ12|Q9H975	Silent	SNP	ENST00000263713.5	37	CCDS2130.1																																																																																			.	.	none		0.343	EPB41L5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254230.2	NM_020909		G	120799656	T	G	120799656	2	3	1	1	0	0	0	0	0	0	0	1	5159	1654	58	5		5	EPB41L5	2	120799656	Silent	SNP	T	TCGA-FA-8693-01A-11D-2397-10	19611606	120799656	122399717	24	24											
GLI2	2736	hgsc.bcm.edu	37	chr2	121708820	121708820	+	Splice_Site	DEL	C	C	-																															ctgcccattgtctctgcaggCcccctgccctcagcggcagc																										TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:121708820delC	ENST00000452319.1	+	4	316	c.256delC	c.(256-258)ccc>cc	p.P87fs	GLI2_ENST00000361492.4_Splice_Site_p.P87fs|GLI2_ENST00000314490.11_5'UTR|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)				TCTCTGCAGGCCCCCTGCCCT	0.622																																					p.G85fs		Pindel,Atlas-Indel	.											.	GLI2	187	.	0			c.255delG						PASS	.						99	112	107					2																	121708820		2203	4299	6502	SO:0001630	splice_region_variant	2736	exon3			.		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.255-1C>-	2.37:g.121708820delC		241	0	.		221	36	0.163	NM_005270		Frame_Shift_Del	DEL	ENST00000452319.1	37	CCDS33283.1																																																																																			.	.	none		0.622	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270	Frame_Shift_Del	-	121708820	C	-	121708820	8	5	1	1	0	1	0	1	0	0	1	0	6446	753	26	0	266	0	GLI2	2	121708820	Splice_Site	DEL	C	TCGA-FA-8693-01A-11D-2397-10	909164	121708820	121490553	25	25											
GLI2	2736	hgsc.bcm.edu	37	chr2	121747495	121747495	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcagcctccatgagccaggaGggctaccaccaggtccccag	9	4	12	16	0	0	1	0	1	0	0	2	2	2	2	7	3	3	2	7	3	1	1	rs570401582		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:121747495G>C	ENST00000452319.1	+	14	4065	c.4005G>C	c.(4003-4005)gaG>gaC	p.E1335D	GLI2_ENST00000361492.4_Missense_Mutation_p.E1335D|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)				TGAGCCAGGAGGGCTACCACC	0.657																																					p.E1335D		Atlas-SNP	.											.	GLI2	187	.	0			c.G4005C						PASS	.						17	18	18					2																	121747495		2200	4295	6495	SO:0001583	missense	2736	exon13			CCAGGAGGGCTAC		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.4005G>C	2.37:g.121747495G>C	ENSP00000390436:p.Glu1335Asp	86	0	0		79	19	0.240506	NM_005270		Missense_Mutation	SNP	ENST00000452319.1	37	CCDS33283.1	.	.	.	.	.	.	.	.	.	.	G	6.282	0.420101	0.11928	.	.	ENSG00000074047	ENST00000452319;ENST00000361492	T;T	0.14516	2.5;2.5	4.55	-0.643	0.11482	.	0.579611	0.18288	N	0.145806	T	0.06508	0.0167	N	0.25647	0.755	0.09310	N	0.999998	B;B	0.09022	0.0;0.002	B;B	0.06405	0.001;0.002	T	0.32134	-0.9918	9	.	.	.	.	1.8185	0.03105	0.2117:0.2668:0.3922:0.1293	.	1335;990	P10070;P10070-2	GLI2_HUMAN;.	D	1335	ENSP00000390436:E1335D;ENSP00000354586:E1335D	.	E	+	3	2	GLI2	121463965	0.923000	0.31300	0.210000	0.23637	0.895000	0.52256	0.437000	0.21543	-0.051000	0.13334	0.455000	0.32223	GAG	.	.	none		0.657	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		C	121747495	G	C	121747495	3	2	1	1	0	0	0	0	1	0	0	0	6446	991	35	4	4055	4	GLI2	2	121747495	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	38675	121747495	121451878	26	26											
LRP1B	53353	hgsc.bcm.edu	37	chr2	141356256	141356256	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttcctagactgccatctgAgaaatacagcttctctgcac	10	13	6	12	0	2	2	0	1	2	2	4	3	3	2	2	0	4	2	2	0	3	5			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:141356256A>G	ENST00000389484.3	-	43	8109	c.7138T>C	c.(7138-7140)Tca>Cca	p.S2380P		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2380					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)		CTGCCATCTGAGAAATACAGC	0.398										TSP Lung(27;0.18)																											p.S2380P	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											LRP1B,NS,carcinoma,+1,3	LRP1B	1315	3	0			c.T7138C						PASS	.						165	147	153					2																	141356256		2203	4300	6503	SO:0001583	missense	53353	exon43			CATCTGAGAAATA	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.7138T>C	2.37:g.141356256A>G	ENSP00000374135:p.Ser2380Pro	246	0	0		295	58	0.19661	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	A	19.53	3.845113	0.71603	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.92249	-3.0	5.64	4.42	0.53409	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	U	0.000003	D	0.94594	0.8258	M	0.88570	2.965	0.51233	D	0.999919	D	0.57899	0.981	P	0.52109	0.69	D	0.94914	0.8067	10	0.56958	D	0.05	.	12.4181	0.55504	0.8599:0.1401:0.0:0.0	.	2380	Q9NZR2	LRP1B_HUMAN	P	2380;2318	ENSP00000374135:S2380P	ENSP00000374135:S2380P	S	-	1	0	LRP1B	141072726	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.291000	0.78721	2.156000	0.67533	0.377000	0.23210	TCA	.	.	none		0.398	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		G	141356256	A	G	141356256	3	3	1	1	0	0	0	0	1	0	0	0	8964	304	11	3	6857	3	LRP1B	2	141356256	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10	19608761	141356256	101843117	27	27											
SCN1A	6323	hgsc.bcm.edu	37	chr2	166847770	166847770	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcatttatttccctttggcTttttcatctttgccttcttg	3	24	4	10	0	4	0	2	0	2	0	5	0	5	0	2	1	1	1	2	1	1	10			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:166847770T>G	ENST00000303395.4	-	26	6014	c.6015A>C	c.(6013-6015)aaA>aaC	p.K2005N	SCN1A_ENST00000423058.2_Missense_Mutation_p.K2005N|AC010127.3_ENST00000597623.1_RNA|SCN1A_ENST00000375405.3_Missense_Mutation_p.K1994N|SCN1A_ENST00000409050.1_Missense_Mutation_p.K1977N|AC010127.3_ENST00000595647.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	2005					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)	tCCCTTTGGCTTTTTCATCTT	0.383																																					p.K2005N		Atlas-SNP	.											SCN1A_ENST00000303395,NS,carcinoma,-1,2	SCN1A	641	2	0			c.A6015C						PASS	.						75	70	72					2																	166847770		2201	4300	6501	SO:0001583	missense	6323	exon26			TTTGGCTTTTTCA	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.6015A>C	2.37:g.166847770T>G	ENSP00000303540:p.Lys2005Asn	45	0	0		55	16	0.290909	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	37	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	T	9.523	1.108698	0.20714	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.96168	-3.93;-3.93;-3.89;-3.86	5.67	3.33	0.38152	.	0.462954	0.22275	N	0.062216	D	0.86535	0.5956	N	0.08118	0	0.34054	D	0.656484	B	0.15473	0.013	B	0.19391	0.025	T	0.81959	-0.0694	10	0.62326	D	0.03	.	2.4206	0.04447	0.2292:0.3772:0.0:0.3937	.	1994	P35498-2	.	N	2005;2005;1994;1977	ENSP00000407030:K2005N;ENSP00000303540:K2005N;ENSP00000364554:K1994N;ENSP00000386312:K1977N	ENSP00000303540:K2005N	K	-	3	2	SCN1A	166556016	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	1.969000	0.40510	0.980000	0.38523	0.397000	0.26171	AAA	.	.	none		0.383	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		G	166847770	T	G	166847770	3	3	1	1	0	0	0	0	1	0	0	0	13929	1606	56	5	18	5	SCN1A	2	166847770	Missense_Mutation	SNP	T	TCGA-FA-8693-01A-11D-2397-10	25491514	166847770	76351603	28	28											
SCN9A	6335	hgsc.bcm.edu	37	chr2	167168208	167168208	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgcgttgttcaatgagggcaAgagactgttttgtgaaatgg	10	13	14	4	1	1	3	1	2	0	1	1	4	1	3	0	2	1	4	0	2	3	4			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:167168208A>G	ENST00000409435.1	-	1	58	c.59T>C	c.(58-60)cTt>cCt	p.L20P	SCN9A_ENST00000303354.6_Missense_Mutation_p.L20P|SCN9A_ENST00000375387.4_Missense_Mutation_p.L20P|SCN9A_ENST00000409672.1_Missense_Mutation_p.L20P			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	20					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)	AATGAGGGCAAGAGACTGTTT	0.428																																					p.L20P		Atlas-SNP	.											SCN9A,colon,carcinoma,+1,2	SCN9A	296	2	0			c.T59C						PASS	.						97	95	96					2																	167168208		1908	4140	6048	SO:0001583	missense	6335	exon2			AGGGCAAGAGACT	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.59T>C	2.37:g.167168208A>G	ENSP00000386330:p.Leu20Pro	90	0	0		81	19	0.234568	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Missense_Mutation	SNP	ENST00000409435.1	37	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	a	22.4	4.283973	0.80803	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435	D;D;D;D	0.98012	-4.65;-4.66;-4.66;-4.66	5.43	5.43	0.79202	.	0.235814	0.30227	N	0.010109	D	0.99180	0.9716	H	0.96943	3.91	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.99100	1.0843	10	0.87932	D	0	.	15.1326	0.72536	1.0:0.0:0.0:0.0	.	20	E7EUN6	.	P	20	ENSP00000386306:L20P;ENSP00000364536:L20P;ENSP00000304748:L20P;ENSP00000386330:L20P	ENSP00000304748:L20P	L	-	2	0	SCN9A	166876454	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.307000	0.96226	2.055000	0.61198	0.533000	0.62120	CTT	.	.	none		0.428	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		G	167168208	A	G	167168208	3	3	1	1	0	0	0	0	1	0	0	0	13940	72	3	3	5978	3	SCN9A	2	167168208	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10	320438	167168208	76031165	29	29											
COL4A3	1285	hgsc.bcm.edu	37	chr2	228173618	228173618	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtctgatgtttcattaggaaCtcttggcagctgcctgcagc	7	13	11	10	0	3	1	1	1	2	0	3	2	3	2	1	2	5	4	1	2	2	3	rs200818438		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:228173618C>A	ENST00000396578.3	+	49	4628	c.4466C>A	c.(4465-4467)aCt>aAt	p.T1489N	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)	1489	Collagen IV NC1. {ECO:0000255|PROSITE- ProRule:PRU00736}.|Required for the anti-angiogenic activity of tumstatin.				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)		TCATTAGGAACTCTTGGCAGC	0.363																																					p.T1489N		Atlas-SNP	.											.	COL4A3	293	.	0			c.C4466A						PASS	.						104	93	97					2																	228173618		1903	4123	6026	SO:0001583	missense	1285	exon49			TAGGAACTCTTGG		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.4466C>A	2.37:g.228173618C>A	ENSP00000379823:p.Thr1489Asn	103	0	0		105	33	0.314286	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Missense_Mutation	SNP	ENST00000396578.3	37	CCDS42829.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.948596	0.73787	.	.	ENSG00000169031	ENST00000396578;ENST00000328380	D	0.94280	-3.39	5.97	5.97	0.96955	C-type lectin fold (1);	0.102311	0.43260	D	0.000584	D	0.96756	0.8941	M	0.86178	2.8	0.80722	D	1	D;D	0.63046	0.992;0.979	P;P	0.62740	0.906;0.884	D	0.95139	0.8262	10	0.31617	T	0.26	.	20.4388	0.99107	0.0:1.0:0.0:0.0	.	1489;1489	Q01955-2;Q01955	.;CO4A3_HUMAN	N	1489	ENSP00000379823:T1489N	ENSP00000327594:T1489N	T	+	2	0	COL4A3	227881862	1.000000	0.71417	0.998000	0.56505	0.927000	0.56198	7.487000	0.81328	2.836000	0.97738	0.655000	0.94253	ACT	.	.	alt		0.363	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091		A	228173618	C	A	228173618	3	1	1	1	0	0	0	0	1	0	0	0	3693	565	20	4	4660	4	COL4A3	2	228173618	Missense_Mutation	SNP	C	TCGA-FA-8693-01A-11D-2397-10	61005410	228173618	15025755	30	30											
AGAP1	116987	hgsc.bcm.edu	37	chr2	236715883	236715883	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actttccttttgctttgcagTctcggaaagggagcgaccca	8	12	10	11	2	1	0	0	0	1	0	3	3	2	2	2	2	3	2	2	2	1	4	rs202230563	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:236715883T>C	ENST00000304032.8	+	9	1538	c.958T>C	c.(958-960)Tct>Cct	p.S320P	AGAP1_ENST00000409457.1_Splice_Site_p.S320P|AGAP1_ENST00000428334.2_Splice_Site_p.S159P|AGAP1_ENST00000409538.1_Splice_Site_p.S585P|AGAP1_ENST00000336665.5_Splice_Site_p.S320P	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	320					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						TGCTTTGCAGTCTCGGAAAGG	0.532																																					p.S320P		Atlas-SNP	.											.	AGAP1	95	.	0			c.T958C						PASS	.	T	PRO/SER,PRO/SER	0,4406		0,0,2203	80	88	86		958,958	5.1	1	2		86	4,8596	3.7+/-12.6	0,4,4296	yes	missense-near-splice,missense-near-splice	AGAP1	NM_001037131.2,NM_014914.4	74,74	0,4,6499	CC,CT,TT		0.0465,0.0,0.0308	probably-damaging,probably-damaging	320/858,320/805	236715883	4,13002	2203	4300	6503	SO:0001630	splice_region_variant	116987	exon9			TTGCAGTCTCGGA	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.958-1T>C	2.37:g.236715883T>C		38	0	0		57	5	0.0877193	NM_014914	B2RTX7|Q541S5|Q6P9D7|Q9NV93	Missense_Mutation	SNP	ENST00000304032.8	37	CCDS33408.1	.	.	.	.	.	.	.	.	.	.	T	13.77	2.336551	0.41398	0.0	4.65E-4	ENSG00000157985	ENST00000409457;ENST00000304032;ENST00000336665;ENST00000409538;ENST00000428334	T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.48003	0.1476	L	0.46157	1.445	0.80722	D	1	D;D	0.69078	0.997;0.992	D;D	0.78314	0.991;0.98	T	0.36456	-0.9747	9	.	.	.	.	15.2676	0.73675	0.0:0.0:0.0:1.0	.	320;320	Q9UPQ3-2;Q9UPQ3	.;AGAP1_HUMAN	P	320;320;320;585;159	ENSP00000387174:S320P;ENSP00000307634:S320P;ENSP00000338378:S320P;ENSP00000386897:S585P;ENSP00000411824:S159P	.	S	+	1	0	AGAP1	236380622	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.731000	0.84895	2.064000	0.61679	0.533000	0.62120	TCT	T|0.998;C|0.002	0.002	strong		0.532	AGAP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257076.2	NM_014914	Missense_Mutation	C	236715883	T	C	236715883	5	2	1	1	0	0	0	0	0	0	1	0	366	1681	58	3	992	3	AGAP1	2	236715883	Splice_Site	SNP	T	TCGA-FA-8693-01A-11D-2397-10	8542265	236715883	6483490	31	31											
TOP2B	7155	hgsc.bcm.edu	37	chr3	25674218	25674218	+	Frame_Shift_Del	DEL	T	T	-																															ctgatacaccagctttgttcTttttcttaactacttcaatc																										TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:25674218delT	ENST00000264331.4	-	9	1093	c.1094delA	c.(1093-1095)aagfs	p.K365fs	TOP2B_ENST00000435706.2_Frame_Shift_Del_p.K360fs	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	365	Interaction with DNA. {ECO:0000250}.				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)	AGCTTTGTTCTTTTTCTTAAC	0.313																																					p.K360fs		Pindel,Atlas-Indel	.											.	TOP2B	98	.	0			c.1080delG						PASS	.						141	142	141					3																	25674218		1859	4100	5959	SO:0001589	frameshift_variant	7155	exon9			.	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.1094delA	3.37:g.25674218delT	ENSP00000264331:p.Lys365fs	204	0	.		261	42	0.161	NM_001068	Q13600|Q9UMG8|Q9UQP8	Frame_Shift_Del	DEL	ENST00000264331.4	37																																																																																				.	.	none		0.313	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding				-	25674218	T	-	25674218	7	5	1	1	0	1	0	1	0	0	0	0	16381	1609	56	0	3898	0	TOP2B	3	25674218	Frame_Shift_Del	DEL	T	TCGA-FA-8693-01A-11D-2397-10		25674218	172348212	32	32											
GOLGA4	2803	hgsc.bcm.edu	37	chr3	37368928	37368928	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaggaactaacctgtcagAttttggagcaaaagataaaa	19	8	9	5	0	1	3	1	0	0	3	1	5	1	5	1	2	3	1	1	2	7	4			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:37368928A>T	ENST00000361924.2	+	14	5925	c.5551A>T	c.(5551-5553)Att>Ttt	p.I1851F	GOLGA4_ENST00000444882.1_Intron|GOLGA4_ENST00000356847.4_Missense_Mutation_p.I1873F	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1851	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						AACCTGTCAGATTTTGGAGCA	0.368																																					p.I1873F		Atlas-SNP	.											.	GOLGA4	173	.	0			c.A5617T						PASS	.						56	58	57					3																	37368928		2203	4298	6501	SO:0001583	missense	2803	exon15			TGTCAGATTTTGG	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.5551A>T	3.37:g.37368928A>T	ENSP00000354486:p.Ile1851Phe	75	0	0		71	18	0.253521	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	37	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	A	10.50	1.367946	0.24771	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000437131	T;T;T	0.23147	1.92;1.92;1.92	4.81	-1.98	0.07480	.	1.321480	0.05575	N	0.571778	T	0.23492	0.0568	L	0.57536	1.79	0.09310	N	1	B;B;B;B	0.26744	0.001;0.001;0.001;0.158	B;B;B;B	0.23574	0.003;0.002;0.002;0.047	T	0.39860	-0.9593	10	0.56958	D	0.05	.	5.1342	0.14926	0.445:0.0:0.36:0.1949	.	1851;1851;1873;1851	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	F	1851;1873;1722	ENSP00000354486:I1851F;ENSP00000349305:I1873F;ENSP00000405842:I1722F	ENSP00000349305:I1873F	I	+	1	0	GOLGA4	37343932	0.000000	0.05858	0.452000	0.26994	0.653000	0.38743	-0.420000	0.07062	0.009000	0.14813	-0.463000	0.05309	ATT	.	.	none		0.368	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		T	37368928	A	T	37368928	3	4	1	1	0	0	0	0	1	0	0	0	6563	333	12	5	5675	5	GOLGA4	3	37368928	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10	11694710	37368928	160653502	33	33											
RHOA	387	hgsc.bcm.edu	37	chr3	49413009	49413009	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caacaatcaccagtttcttcCggatggcagccattgctgaa	11	10	8	12	1	2	1	1	1	1	0	3	2	3	2	3	2	3	3	3	2	3	3	rs11552758		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:49413009C>T	ENST00000418115.1	-	2	398	c.14G>A	c.(13-15)cGg>cAg	p.R5Q	RHOA_ENST00000422781.1_Missense_Mutation_p.R5Q|RHOA_ENST00000454011.2_Missense_Mutation_p.R5Q	NM_001664.2	NP_001655.1	P61586	RHOA_HUMAN	ras homolog family member A	5					actin cytoskeleton organization (GO:0030036)|androgen receptor signaling pathway (GO:0030521)|apical junction assembly (GO:0043297)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cerebral cortex cell migration (GO:0021795)|cleavage furrow formation (GO:0036089)|forebrain radial glial cell differentiation (GO:0021861)|negative chemotaxis (GO:0050919)|negative regulation of axonogenesis (GO:0050771)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron differentiation (GO:0045665)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification involved in bone maturation (GO:0043931)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of axonogenesis (GO:0050772)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytokinesis (GO:0032467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of podosome assembly (GO:0071803)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of translation (GO:0045727)|positive regulation of vasoconstriction (GO:0045907)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion transport (GO:0051924)|regulation of cell migration (GO:0030334)|regulation of dendrite development (GO:0050773)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of osteoblast proliferation (GO:0033688)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|Rho protein signal transduction (GO:0007266)|skeletal muscle tissue development (GO:0007519)|small GTPase mediated signal transduction (GO:0007264)|spindle assembly involved in mitosis (GO:0090307)|stress fiber assembly (GO:0043149)|stress-activated protein kinase signaling cascade (GO:0031098)|substantia nigra development (GO:0021762)|trabecula morphogenesis (GO:0061383)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	apical junction complex (GO:0043296)|axon (GO:0030424)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin binding (GO:0017022)	p.R5Q(1)		cervix(1)|kidney(1)|large_intestine(5)|lung(1)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	12				BRCA - Breast invasive adenocarcinoma(193;8.58e-05)|Kidney(197;0.0023)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		CAGTTTCTTCCGGATGGCAGC	0.473																																					p.R5Q		Atlas-SNP	.											RHOA,NS,lymphoid_neoplasm,0,7	RHOA	46	7	1	Substitution - Missense(1)	large_intestine(1)	c.G14A						PASS	.						106	97	100					3																	49413009		2203	4300	6503	SO:0001583	missense	387	exon2			TTCTTCCGGATGG	BC001360	CCDS2795.1	3p21.3	2012-02-27	2012-02-27	2004-03-23	ENSG00000067560	ENSG00000067560			667	protein-coding gene	gene with protein product		165390	"ras homolog gene family, member A"	ARH12, ARHA		9605859	Standard	NM_001664		Approved	RhoA, Rho12, RHOH12	uc003cwu.3	P61586	OTTHUMG00000156838	ENST00000418115.1:c.14G>A	3.37:g.49413009C>T	ENSP00000400175:p.Arg5Gln	233	0	0		171	51	0.298246	NM_001664	P06749|Q53HM4|Q5U024|Q9UDJ0|Q9UEJ4	Missense_Mutation	SNP	ENST00000418115.1	37	CCDS2795.1	.	.	.	.	.	.	.	.	.	.	C	33	5.291209	0.95546	.	.	ENSG00000067560	ENST00000418115;ENST00000454011;ENST00000422781;ENST00000445425;ENST00000431929	T;T;T;T;T	0.70399	-0.3;1.78;-0.33;-0.48;2.14	5.89	5.89	0.94794	Small GTP-binding protein domain (1);	0.000000	0.64402	D	0.000001	T	0.65943	0.2740	L	0.38175	1.15	0.80722	D	1	B	0.18166	0.026	B	0.20184	0.028	T	0.61926	-0.6962	10	0.87932	D	0	.	18.8947	0.92419	0.0:1.0:0.0:0.0	.	5	P61586	RHOA_HUMAN	Q	5	ENSP00000400175:R5Q;ENSP00000394483:R5Q;ENSP00000413587:R5Q;ENSP00000408402:R5Q;ENSP00000400747:R5Q	ENSP00000400175:R5Q	R	-	2	0	RHOA	49388013	1.000000	0.71417	0.999000	0.59377	0.896000	0.52359	7.652000	0.83633	2.809000	0.96659	0.558000	0.71614	CGG	.	.	weak		0.473	RHOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346157.3	NM_001664		T	49413009	C	T	49413009	3	4	1	1	0	0	0	0	1	0	0	0	13346	652	23	1	583	1	RHOA	3	49413009	Missense_Mutation	SNP	C	TCGA-FA-8693-01A-11D-2397-10	12044081	49413009	148609421	34	34											
VGLL3	389136	hgsc.bcm.edu	37	chr3	87018229	87018229	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctggtaagagctggtccaaaAggaagttgggaaactattcc	13	9	12	7	0	0	1	0	0	0	1	2	3	2	3	2	4	2	3	2	4	6	4			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:87018229A>C	ENST00000398399.2	-	3	811	c.448T>G	c.(448-450)Ttt>Gtt	p.F150V	VGLL3_ENST00000383698.3_Missense_Mutation_p.F150V	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)		CTGGTCCAAAAGGAAGTTGGG	0.483																																					p.F150V		Atlas-SNP	.											.	VGLL3	62	.	0			c.T448G						PASS	.						85	86	86					3																	87018229		1910	4132	6042	SO:0001583	missense	389136	exon3			TCCAAAAGGAAGT	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.448T>G	3.37:g.87018229A>C	ENSP00000381436:p.Phe150Val	32	0	0		58	14	0.241379	NM_016206		Missense_Mutation	SNP	ENST00000398399.2	37	CCDS43110.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.4|20.4	3.991213|3.991213	0.74703|0.74703	.|.	.|.	ENSG00000206538|ENSG00000206538	ENST00000398399;ENST00000383698|ENST00000494229	T;T|.	0.50277|.	0.76;0.75|.	5.88|5.88	5.88|5.88	0.94601|0.94601	.|.	0.204155|.	0.43260|.	D|.	0.000595|.	T|T	0.68026|0.68026	0.2956|0.2956	M|M	0.74881|0.74881	2.28|2.28	0.41670|0.41670	D|D	0.989238|0.989238	B|.	0.23806|.	0.091|.	B|.	0.17098|.	0.017|.	T|T	0.69892|0.69892	-0.5022|-0.5022	10|5	0.52906|.	T|.	0.07|.	-8.6808|-8.6808	10.3235|10.3235	0.43780|0.43780	0.9261:0.0:0.0739:0.0|0.9261:0.0:0.0739:0.0	.|.	150|.	A8MV65|.	VGLL3_HUMAN|.	V|R	150|83	ENSP00000381436:F150V;ENSP00000373199:F150V|.	ENSP00000373199:F150V|.	F|L	-|-	1|2	0|0	VGLL3|VGLL3	87100919|87100919	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	5.414000|5.414000	0.66405|0.66405	2.252000|2.252000	0.74401|0.74401	0.459000|0.459000	0.35465|0.35465	TTT|CTT	.	.	none		0.483	VGLL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352805.1	NM_016206		C	87018229	A	C	87018229	3	2	1	1	0	0	0	0	1	0	0	0	17175	72	3	5	540	5	VGLL3	3	87018229	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10	37605220	87018229	111004201	35	35											
KALRN	8997	hgsc.bcm.edu	37	chr3	124103697	124103697	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgttgttgctggcagaatacGtacaccaatgcggacaagct	11	10	11	9	2	0	1	0	0	0	1	0	2	0	2	1	2	5	6	1	2	5	4	rs574174504	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:124103697G>A	ENST00000240874.3	+	11	1927	c.1770G>A	c.(1768-1770)acG>acA	p.T590T	KALRN_ENST00000460856.1_Silent_p.T590T|KALRN_ENST00000360013.3_Silent_p.T590T	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	590					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						GGCAGAATACGTACACCAATG	0.612													G|||	2	0.000399361	0.0	0.0029	5008	,	,		17008	0.0		0.0	False		,,,				2504	0.0				p.T590T		Atlas-SNP	.											KALRN_ENST00000360013,NS,carcinoma,+1,4	KALRN	556	4	0			c.G1770A						PASS	.						83	71	75					3																	124103697		2203	4300	6503	SO:0001819	synonymous_variant	8997	exon11			GAATACGTACACC	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.1770G>A	3.37:g.124103697G>A		277	0	0		279	52	0.18638	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	37	CCDS3027.1	.	.	.	.	.	.	.	.	.	.	G	7.665	0.685732	0.14973	.	.	ENSG00000160145	ENST00000354186	.	.	.	5.35	-10.7	0.00240	.	.	.	.	.	T	0.40398	0.1115	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50816	-0.8783	4	.	.	.	.	4.2215	0.10559	0.1084:0.3716:0.3202:0.1998	.	.	.	.	H	568	.	.	R	+	2	0	KALRN	125586387	0.000000	0.05858	0.080000	0.20451	0.960000	0.62799	-4.083000	0.00298	-3.444000	0.00162	-0.878000	0.02970	CGT	.	.	none		0.612	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		A	124103697	G	A	124103697	2	1	1	1	0	0	0	0	0	0	0	1	7984	1132	40	1		1	KALRN	3	124103697	Silent	SNP	G	TCGA-FA-8693-01A-11D-2397-10	37085468	124103697	73918733	36	36											
ROPN1B	152015	hgsc.bcm.edu	37	chr3	125702141	125702141	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtgaatgactttacccaaaAccccagggtttggctggagt	10	10	12	9	0	0	2	0	2	0	0	0	3	0	3	3	4	2	2	3	4	4	3			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:125702141A>G	ENST00000514116.1	+	7	932	c.617A>G	c.(616-618)aAc>aGc	p.N206S	ROPN1B_ENST00000251776.4_Missense_Mutation_p.N206S|ROPN1B_ENST00000505382.1_Missense_Mutation_p.N114S|ROPN1B_ENST00000511082.1_Missense_Mutation_p.N114S			Q9BZX4	ROP1B_HUMAN	rhophilin associated tail protein 1B	206					acrosome reaction (GO:0007340)|cytokinesis (GO:0000910)|fusion of sperm to egg plasma membrane (GO:0007342)|Rho protein signal transduction (GO:0007266)|single organismal cell-cell adhesion (GO:0016337)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor signaling complex scaffold activity (GO:0030159)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)	8				GBM - Glioblastoma multiforme(114;0.151)		TTTACCCAAAACCCCAGGGTT	0.373																																					p.N206S		Atlas-SNP	.											.	ROPN1B	16	.	0			c.A617G						PASS	.						119	110	113					3																	125702141		2203	4300	6503	SO:0001583	missense	152015	exon6			CCCAAAACCCCAG	AF231410	CCDS33841.1	3q21.2	2011-01-20	2011-01-20		ENSG00000114547	ENSG00000114547			31927	protein-coding gene	gene with protein product			"ropporin, rhophilin associated protein 1B"				Standard	XM_005247137		Approved		uc003eih.3	Q9BZX4	OTTHUMG00000162651	ENST00000514116.1:c.617A>G	3.37:g.125702141A>G	ENSP00000426271:p.Asn206Ser	114	0	0		137	19	0.138686	NM_001012337	D3DNA6|Q96BM7	Missense_Mutation	SNP	ENST00000514116.1	37	CCDS33841.1	.	.	.	.	.	.	.	.	.	.	A	11.26	1.585762	0.28268	.	.	ENSG00000114547	ENST00000514116;ENST00000251776;ENST00000505382;ENST00000511082	T;T;T;T	0.22539	1.95;1.95;1.96;1.96	2.16	2.16	0.27623	.	0.000000	0.85682	D	0.000000	T	0.20941	0.0504	N	0.22421	0.69	0.27471	N	0.95288	D	0.56035	0.974	D	0.67725	0.953	T	0.10636	-1.0621	10	0.07990	T	0.79	-14.4117	6.3386	0.21310	1.0:0.0:0.0:0.0	.	206	Q9BZX4	ROP1B_HUMAN	S	206;206;114;114	ENSP00000426271:N206S;ENSP00000251776:N206S;ENSP00000421662:N114S;ENSP00000424447:N114S	ENSP00000251776:N206S	N	+	2	0	ROPN1B	127184831	1.000000	0.71417	0.999000	0.59377	0.750000	0.42670	4.669000	0.61575	1.241000	0.43820	0.373000	0.22412	AAC	.	.	none		0.373	ROPN1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369931.1	NM_001012337		G	125702141	A	G	125702141	3	3	1	1	0	0	0	0	1	0	0	0	13539	43	2	3	635	3	ROPN1B	3	125702141	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10	1598444	125702141	72320289	37	37											
COL6A5	256076	hgsc.bcm.edu	37	chr3	130128909	130128909	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagggctccaaaggagaacaAggaagacaagtaatttgatc	18	6	11	6	0	0	3	0	1	0	2	2	5	1	4	1	3	1	2	1	3	7	2			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:130128909A>T	ENST00000432398.2	+	19	5093	c.4599A>T	c.(4597-4599)caA>caT	p.Q1533H	COL6A5_ENST00000265379.6_Missense_Mutation_p.Q1533H	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1533	Triple-helical 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						AAGGAGAACAAGGAAGACAAG	0.308																																					p.Q1533H		Atlas-SNP	.											.	COL6A5	205	.	0			c.A4599T						PASS	.						209	209	209					3																	130128909		692	1591	2283	SO:0001583	missense	256076	exon19			AGAACAAGGAAGA	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.4599A>T	3.37:g.130128909A>T	ENSP00000390895:p.Gln1533His	65	0	0		78	16	0.205128	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		.	.	.	.	.	.	.	.	.	.	A	12.46	1.945999	0.34377	.	.	ENSG00000172752	ENST00000432398;ENST00000265379	D;D	0.93307	-3.2;-3.2	5.52	5.52	0.82312	.	.	.	.	.	D	0.92192	0.7524	M	0.68728	2.09	0.27514	N	0.951595	B	0.23540	0.087	B	0.23852	0.049	D	0.86368	0.1721	9	0.45353	T	0.12	.	13.4845	0.61357	1.0:0.0:0.0:0.0	.	1533	A8TX70-2	.	H	1533	ENSP00000390895:Q1533H;ENSP00000265379:Q1533H	ENSP00000265379:Q1533H	Q	+	3	2	COL6A5	131611599	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.344000	0.44010	2.236000	0.73375	0.528000	0.53228	CAA	.	.	none		0.308	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		T	130128909	A	T	130128909	3	4	1	1	0	0	0	0	1	0	0	0	3704	69	3	5	4669	5	COL6A5	3	130128909	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10	4426768	130128909	67893521	38	38											
PLOD2	5352	hgsc.bcm.edu	37	chr3	145841964	145841964	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatttggctgactgcataaaTcgatggaatccatcactttc	11	14	7	9	1	1	1	1	1	0	0	4	3	2	2	1	2	1	2	1	2	4	4			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:145841964T>G	ENST00000360060.3	-	2	339	c.162A>C	c.(160-162)cgA>cgC	p.R54R	PLOD2_ENST00000494950.1_5'UTR|PLOD2_ENST00000282903.5_Silent_p.R54R	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	54					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)	ACTGCATAAATCGATGGAATC	0.313																																					p.R54R		Atlas-SNP	.											PLOD2,colon,carcinoma,-2,5	PLOD2	81	5	0			c.A162C						PASS	.						154	151	152					3																	145841964		2202	4299	6501	SO:0001819	synonymous_variant	5352	exon2			CATAAATCGATGG	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.162A>C	3.37:g.145841964T>G		85	0	0		97	16	0.164948	NM_182943	B3KWS3|Q59ED2|Q8N170	Silent	SNP	ENST00000360060.3	37	CCDS3131.1																																																																																			.	.	none		0.313	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935		G	145841964	T	G	145841964	2	3	1	1	0	0	0	0	0	0	0	1	12111	1422	50	5		5	PLOD2	3	145841964	Silent	SNP	T	TCGA-FA-8693-01A-11D-2397-10	15713055	145841964	52180466	39	39											
ZBBX	79740	hgsc.bcm.edu	37	chr3	167023655	167023655	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttaaatttctttcaaaggAggtgctttcctcaatttttt	9	20	5	7	0	3	0	2	0	1	0	4	1	4	1	1	2	1	1	1	2	4	8			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:167023655A>G	ENST00000392766.2	-	17	1841	c.1501T>C	c.(1501-1503)Tcc>Ccc	p.S501P	ZBBX_ENST00000455345.2_Missense_Mutation_p.S501P|ZBBX_ENST00000392764.1_Missense_Mutation_p.S472P|ZBBX_ENST00000307529.5_Missense_Mutation_p.S501P|ZBBX_ENST00000392767.2_Missense_Mutation_p.S501P	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	501						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						CTTTCAAAGGAGGTGCTTTCC	0.348																																					p.S501P		Atlas-SNP	.											.	ZBBX	299	.	0			c.T1501C						PASS	.						54	48	49					3																	167023655		1798	4072	5870	SO:0001583	missense	79740	exon17			CAAAGGAGGTGCT	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.1501T>C	3.37:g.167023655A>G	ENSP00000376519:p.Ser501Pro	54	0	0		42	9	0.214286	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	37	CCDS3199.2	.	.	.	.	.	.	.	.	.	.	A	10.90	1.480260	0.26598	.	.	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764	T;T;T;T;T	0.10573	3.03;3.03;3.03;3.03;2.86	5.54	-3.07	0.05363	.	1.376370	0.04080	N	0.309527	T	0.05868	0.0153	N	0.19112	0.55	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.0	T	0.36040	-0.9764	10	0.33141	T	0.24	0.0641	0.6	0.00743	0.3168:0.135:0.1556:0.3926	.	501;501	A8MT70-2;A8MT70	.;ZBBX_HUMAN	P	501;501;501;501;472	ENSP00000376519:S501P;ENSP00000376520:S501P;ENSP00000390232:S501P;ENSP00000305065:S501P;ENSP00000376517:S472P	ENSP00000305065:S501P	S	-	1	0	ZBBX	168506349	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.094000	0.15107	-0.425000	0.07371	-1.159000	0.01794	TCC	.	.	none		0.348	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687		G	167023655	A	G	167023655	3	3	1	1	0	0	0	0	1	0	0	0	17531	304	11	3	921	3	ZBBX	3	167023655	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10	21181691	167023655	30998775	40	40											
NLGN1	22871	hgsc.bcm.edu	37	chr3	173322630	173322630	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggggcctgttattcaatttcTtggggttccatatgcagccc	6	14	11	10	0	2	0	1	0	1	0	3	0	3	0	3	4	2	3	3	4	3	6			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:173322630T>C	ENST00000457714.1	+	3	671	c.242T>C	c.(241-243)cTt>cCt	p.L81P	NLGN1_ENST00000401917.3_Missense_Mutation_p.L81P|NLGN1_ENST00000545397.1_Missense_Mutation_p.L81P|NLGN1_ENST00000361589.4_Missense_Mutation_p.L81P	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	81					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)			ATTCAATTTCTTGGGGTTCCA	0.458																																					p.L81P		Atlas-SNP	.											NLGN1,NS,carcinoma,+1,1	NLGN1	209	1	0			c.T242C						PASS	.						102	108	106					3																	173322630		2203	4300	6503	SO:0001583	missense	22871	exon3			AATTTCTTGGGGT	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.242T>C	3.37:g.173322630T>C	ENSP00000392500:p.Leu81Pro	56	0	0		64	11	0.171875	NM_014932	Q9UPT2	Missense_Mutation	SNP	ENST00000457714.1	37	CCDS3222.1	.	.	.	.	.	.	.	.	.	.	T	18.42	3.620055	0.66787	.	.	ENSG00000169760	ENST00000457714;ENST00000361589;ENST00000415045;ENST00000545397;ENST00000401917	T;T;T;T;T	0.71934	-0.08;-0.08;-0.61;-0.08;-0.08	5.62	5.62	0.85841	.	0.000000	0.64402	D	0.000005	D	0.90202	0.6937	H	0.98089	4.145	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.992;0.997	D	0.93761	0.7067	10	0.87932	D	0	.	16.1135	0.81278	0.0:0.0:0.0:1.0	.	81;81	D2X2H5;Q8N2Q7-2	.;.	P	81	ENSP00000392500:L81P;ENSP00000354541:L81P;ENSP00000410374:L81P;ENSP00000441108:L81P;ENSP00000385750:L81P	ENSP00000354541:L81P	L	+	2	0	NLGN1	174805324	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.655000	0.83696	2.267000	0.75376	0.383000	0.25322	CTT	.	.	none		0.458	NLGN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347054.3	NM_014932		C	173322630	T	C	173322630	3	2	1	1	0	0	0	0	1	0	0	0	10470	1609	56	3	244	3	NLGN1	3	173322630	Missense_Mutation	SNP	T	TCGA-FA-8693-01A-11D-2397-10	6298975	173322630	24699800	41	41											
WHSC1	7468	hgsc.bcm.edu	37	chr4	1957912	1957912	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggatcggaagagtcttcaaaAacggtacggagatattcaga	15	8	12	6	3	3	3	2	0	1	3	4	6	3	5	0	4	2	1	0	4	5	4			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:1957912A>C	ENST00000382895.3	+	17	3309	c.2878A>C	c.(2878-2880)Aac>Cac	p.N960H	WHSC1_ENST00000382891.5_Missense_Mutation_p.N960H|WHSC1_ENST00000508803.1_Missense_Mutation_p.N960H|WHSC1_ENST00000382888.3_Missense_Mutation_p.N308H|WHSC1_ENST00000382892.2_Missense_Mutation_p.N960H|WHSC1_ENST00000482415.2_3'UTR	NM_133330.2	NP_579877.1	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1	960					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)		AGTCTTCAAAAACGGTACGGA	0.458			T	IGH@	MM																																p.N960H		Atlas-SNP	.		Dom	yes		4	4p16.3	7468	Wolf-Hirschhorn syndrome candidate 1(MMSET)		L	.	WHSC1	180	.	0			c.A2878C						PASS	.						54	64	61					4																	1957912		2199	4300	6499	SO:0001583	missense	7468	exon15			TTCAAAAACGGTA	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.2878A>C	4.37:g.1957912A>C	ENSP00000372351:p.Asn960His	18	0	0		18	6	0.333333	NM_133335	A2A2T2|A2A2T3|A2A2T4|A7MCZ1|D3DVQ2|O96031|Q4VBY8|Q672J1|Q6IS00|Q86V01|Q9BZB4|Q9UI92|Q9UPR2	Missense_Mutation	SNP	ENST00000382895.3	37	CCDS33940.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.80|14.80	2.643251|2.643251	0.47153|0.47153	.|.	.|.	ENSG00000109685|ENSG00000109685	ENST00000514329|ENST00000508803;ENST00000382891;ENST00000382892;ENST00000382895;ENST00000382888	D|T;T;T;T;T	0.98105|0.70749	-4.72|-0.51;-0.51;-0.51;-0.51;-0.51	5.43|5.43	5.43|5.43	0.79202|0.79202	.|.	.|0.000000	.|0.64402	.|D	.|0.000017	T|T	0.56093|0.56093	0.1962|0.1962	N|N	0.15975|0.15975	0.35|0.35	0.80722|0.80722	D|D	1|1	.|B;B	.|0.25850	.|0.005;0.136	.|B;B	.|0.22753	.|0.006;0.041	T|T	0.57505|0.57505	-0.7800|-0.7800	7|10	0.87932|0.62326	D|D	0|0.03	.|.	15.4756|15.4756	0.75478|0.75478	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|308;960	.|A2A2T2;O96028	.|.;NSD2_HUMAN	T|H	283|960;960;960;960;308	ENSP00000425094:K283T|ENSP00000423972:N960H;ENSP00000372347:N960H;ENSP00000372348:N960H;ENSP00000372351:N960H;ENSP00000372344:N308H	ENSP00000425094:K283T|ENSP00000372344:N308H	K|N	+|+	2|1	0|0	WHSC1|WHSC1	1927710|1927710	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.949000|0.949000	0.60115|0.60115	5.838000|5.838000	0.69388|0.69388	2.062000|2.062000	0.61559|0.61559	0.533000|0.533000	0.62120|0.62120	AAA|AAC	.	.	none		0.458	WHSC1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366269.2	NM_133330		C	1957912	A	C	1957912	3	2	1	1	0	0	0	0	1	0	0	0	17377	14	1	5	3008	5	WHSC1	4	1957912	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10		1957912	189196364	42	42											
TBC1D14	57533	hgsc.bcm.edu	37	chr4	7008366	7008366	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catcttttgacagatgctggTttttcagcagcagacagaga	11	12	10	8	0	2	4	1	1	1	3	2	5	2	4	0	1	3	4	0	1	0	4			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:7008366T>C	ENST00000409757.4	+	9	1483	c.1359T>C	c.(1357-1359)ggT>ggC	p.G453G	TBC1D14_ENST00000451522.2_Silent_p.G173G|TBC1D14_ENST00000448507.1_Silent_p.G453G|TBC1D14_ENST00000410031.1_Silent_p.G225G|TBC1D14_ENST00000446947.2_Silent_p.G66G	NM_020773.2	NP_065824.2	Q9P2M4	TBC14_HUMAN	TBC1 domain family, member 14	453	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						CAGATGCTGGTTTTTCAGCAG	0.403																																					p.G453G		Atlas-SNP	.											.	TBC1D14	110	.	0			c.T1359C						PASS	.						90	89	90					4																	7008366		2203	4300	6503	SO:0001819	synonymous_variant	57533	exon9			TGCTGGTTTTTCA	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.1359T>C	4.37:g.7008366T>C		98	0	0		125	26	0.208	NM_001113361	B9A6L5|D3DVT4|E9PAZ6|Q8IW15|Q8NDK3	Silent	SNP	ENST00000409757.4	37	CCDS3394.2																																																																																			.	.	none		0.403	TBC1D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206981.3	NM_020773		C	7008366	T	C	7008366	2	2	1	1	0	0	0	0	0	0	0	1	15618	1712	60	3		3	TBC1D14	4	7008366	Silent	SNP	T	TCGA-FA-8693-01A-11D-2397-10	5050454	7008366	184145910	43	43											
SLIT2	9353	hgsc.bcm.edu	37	chr4	20619095	20619095	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acctgcttgcccatcaatgcGttctcctacagctgtaagtg	8	12	8	13	1	2	0	1	0	1	0	3	0	2	0	3	0	5	4	3	0	3	4	rs61746361	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:20619095G>A	ENST00000504154.1	+	36	4422	c.4170G>A	c.(4168-4170)gcG>gcA	p.A1390A	SLIT2_ENST00000273739.5_Silent_p.A1403A|SLIT2_ENST00000503823.1_Silent_p.A1382A|SLIT2_ENST00000503837.1_Silent_p.A1386A	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	1390					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						CCATCAATGCGTTCTCCTACA	0.522													G|||	22	0.00439297	0.0166	0.0	5008	,	,		16502	0.0		0.0	False		,,,				2504	0.0				p.A1390A		Atlas-SNP	.											.	SLIT2	290	.	0			c.G4170A						PASS	.	G		54,4352	54.9+/-90.9	0,54,2149	106	92	97		4170	-11.8	0	4	dbSNP_129	97	0,8600		0,0,4300	no	coding-synonymous	SLIT2	NM_004787.1		0,54,6449	AA,AG,GG		0.0,1.2256,0.4152		1390/1530	20619095	54,12952	2203	4300	6503	SO:0001819	synonymous_variant	9353	exon36			CAATGCGTTCTCC	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.4170G>A	4.37:g.20619095G>A		330	0	0		261	54	0.206897	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Silent	SNP	ENST00000504154.1	37	CCDS3426.1																																																																																			G|0.996;A|0.004	0.004	strong		0.522	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			A	20619095	G	A	20619095	2	1	1	1	0	0	0	0	0	0	0	1	14755	1132	40	1		1	SLIT2	4	20619095	Silent	SNP	G	TCGA-FA-8693-01A-11D-2397-10	13610729	20619095	170535181	44	44											
SEL1L3	23231	hgsc.bcm.edu	37	chr4	25783964	25783964	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttcttctgcttttaaccagTactttgctgctttggcgtaa	6	19	7	9	1	2	0	0	0	2	0	2	0	2	0	1	1	5	5	1	1	3	8			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:25783964T>A	ENST00000399878.3	-	15	2479	c.2357A>T	c.(2356-2358)tAc>tTc	p.Y786F	SEL1L3_ENST00000264868.5_Missense_Mutation_p.Y751F|SEL1L3_ENST00000502949.1_Missense_Mutation_p.Y633F	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	786						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						TTTTAACCAGTACTTTGCTGC	0.433																																					p.Y786F		Atlas-SNP	.											SEL1L3,NS,carcinoma,+1,2	SEL1L3	62	2	0			c.A2357T						scavenged	.						207	190	195					4																	25783964		1870	4113	5983	SO:0001583	missense	23231	exon15			AACCAGTACTTTG	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.2357A>T	4.37:g.25783964T>A	ENSP00000382767:p.Tyr786Phe	184	1	0.00543478		175	45	0.257143	NM_015187	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Missense_Mutation	SNP	ENST00000399878.3	37	CCDS47037.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.316857	0.81469	.	.	ENSG00000091490	ENST00000399878;ENST00000264868;ENST00000502949	T;T;T	0.55930	0.49;0.49;0.49	5.66	5.66	0.87406	Tetratricopeptide-like helical (1);	0.414434	0.25291	N	0.031738	T	0.60573	0.2279	L	0.27053	0.805	0.43103	D	0.99479	P;D	0.67145	0.924;0.996	P;D	0.67725	0.652;0.953	T	0.65274	-0.6208	10	0.72032	D	0.01	-18.4383	15.9017	0.79384	0.0:0.0:0.0:1.0	.	193;786	B4DTH5;Q68CR1	.;SE1L3_HUMAN	F	786;751;633	ENSP00000382767:Y786F;ENSP00000264868:Y751F;ENSP00000425438:Y633F	ENSP00000264868:Y751F	Y	-	2	0	SEL1L3	25393062	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.721000	0.61951	2.153000	0.67306	0.460000	0.39030	TAC	.	.	none		0.433	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187		A	25783964	T	A	25783964	3	1	1	1	0	0	0	0	1	0	0	0	14027	1638	57	5	1081	5	SEL1L3	4	25783964	Missense_Mutation	SNP	T	TCGA-FA-8693-01A-11D-2397-10	5164869	25783964	165370312	45	45											
PCDH7	5099	hgsc.bcm.edu	37	chr4	30723952	30723952	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcatcaccgacgtgaacgAcaacagcccccgcttcgaga	11	5	8	17	5	2	2	2	1	0	1	3	5	2	2	4	0	3	1	4	0	2	1			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:30723952A>C	ENST00000361762.2	+	1	1916	c.908A>C	c.(907-909)gAc>gCc	p.D303A	PCDH7_ENST00000543491.1_Missense_Mutation_p.D303A	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	303	Cadherin 2. {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						GACGTGAACGACAACAGCCCC	0.682																																					p.D303A		Atlas-SNP	.											.	PCDH7	215	.	0			c.A908C						PASS	.						11	14	13					4																	30723952		2196	4284	6480	SO:0001583	missense	5099	exon1			TGAACGACAACAG	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.908A>C	4.37:g.30723952A>C	ENSP00000355243:p.Asp303Ala	78	0	0		64	6	0.09375	NM_032457	O60246|O60247|Q4W5C4	Missense_Mutation	SNP	ENST00000361762.2	37	CCDS33971.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.270608	0.80469	.	.	ENSG00000169851	ENST00000361762;ENST00000543491	T;T	0.71579	-0.58;-0.58	5.18	5.18	0.71444	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	D	0.88250	0.6386	H	0.94964	3.605	0.54753	D	0.999988	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	D	0.91602	0.5296	9	0.87932	D	0	.	15.0142	0.71570	1.0:0.0:0.0:0.0	.	303;303	F5GWJ1;O60245	.;PCDH7_HUMAN	A	303	ENSP00000355243:D303A;ENSP00000441802:D303A	ENSP00000355243:D303A	D	+	2	0	PCDH7	30333050	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.322000	0.96357	1.934000	0.56057	0.459000	0.35465	GAC	.	.	none		0.682	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589		C	30723952	A	C	30723952	3	2	1	1	0	0	0	0	1	0	0	0	11525	275	10	5	910	5	PCDH7	4	30723952	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10	4939988	30723952	160430324	46	46											
REST	5978	hgsc.bcm.edu	37	chr4	57777675	57777676	+	Frame_Shift_Ins	INS	-	-	A																															ttcagacagaaaaaacaattINSatgttcagcatgttagaact																										TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:57777675_57777676insA	ENST00000309042.7	+	2	1185_1186	c.871_872insA	c.(871-873)tatfs	p.Y291fs	REST_ENST00000514063.1_3'UTR	NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	291					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)					AAAAAACAATTATGTTCAGCAT	0.351																																					p.Y291_V292delinsX		Pindel,Atlas-Indel	.											.	REST	104	.	0			c.871_872insA						PASS	.																																			SO:0001589	frameshift_variant	5978	exon2			.	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.872dupA	4.37:g.57777676_57777676dupA	ENSP00000311816:p.Tyr291fs	97	0	.		89	14	0.157	NM_001193508	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Frame_Shift_Ins	INS	ENST00000309042.7	37	CCDS3509.1																																																																																			.	.	none		0.351	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612		A	57777676	-	A	57777675	7	5	1	1	0	1	1	0	0	0	0	0	13249	1754	61	0	873	0	REST	4	57777675	Frame_Shift_Ins	INS	-	TCGA-FA-8693-01A-11D-2397-10	27053723	57777675	133376601	47	47											
UBA6	55236	hgsc.bcm.edu	37	chr4	68514904	68514904	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcagtccaagagagccaaTgcacaatgtcagcatttaca	14	7	10	10	0	1	1	1	0	0	1	2	2	2	1	2	1	4	3	2	1	4	2			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:68514904T>C	ENST00000322244.5	-	14	1189	c.1130A>G	c.(1129-1131)cAt>cGt	p.H377R		NM_018227.5	NP_060697.4	A0AVT1	UBA6_HUMAN	ubiquitin-like modifier activating enzyme 6	377					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						AGAGAGCCAATGCACAATGTC	0.388																																					p.H377R		Atlas-SNP	.											.	UBA6	98	.	0			c.A1130G						PASS	.						94	95	95					4																	68514904		2203	4300	6503	SO:0001583	missense	55236	exon14			AGCCAATGCACAA	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.1130A>G	4.37:g.68514904T>C	ENSP00000313454:p.His377Arg	205	0	0		197	55	0.279188	NM_018227	A6N8M7|B2RAV3|Q4W5K0|Q6UV21|Q86T78|Q86TC7|Q8N5T3|Q8N9E4|Q9H3T7|Q9NVC9	Missense_Mutation	SNP	ENST00000322244.5	37	CCDS3516.1	.	.	.	.	.	.	.	.	.	.	T	0.007	-1.995347	0.00435	.	.	ENSG00000033178	ENST00000322244	T	0.54866	0.55	5.08	-3.06	0.05379	Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.635180	0.16937	N	0.193439	T	0.13500	0.0327	N	0.00272	-1.73	0.58432	D	0.999998	B	0.02656	0.0	B	0.01281	0.0	T	0.46665	-0.9175	10	0.02654	T	1	-0.5102	14.018	0.64536	0.0:0.1147:0.0:0.8853	.	377	A0AVT1	UBA6_HUMAN	R	377	ENSP00000313454:H377R	ENSP00000313454:H377R	H	-	2	0	UBA6	68197499	0.396000	0.25262	0.545000	0.28153	0.083000	0.17756	0.448000	0.21726	-0.758000	0.04690	-0.425000	0.05940	CAT	.	.	none		0.388	UBA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251429.2	NM_018227		C	68514904	T	C	68514904	3	2	1	1	0	0	0	0	1	0	0	0	16847	1464	51	3	2108	3	UBA6	4	68514904	Missense_Mutation	SNP	T	TCGA-FA-8693-01A-11D-2397-10	10737229	68514904	122639372	48	48											
FRAS1	80144	hgsc.bcm.edu	37	chr4	79399181	79399181	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atctactgggttaacgagagCgctggttttctgtttgcacc	7	14	11	9	2	2	1	0	0	2	1	2	2	2	1	1	2	4	5	1	2	2	5	rs371145937		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:79399181C>T	ENST00000264895.6	+	55	8504	c.8064C>T	c.(8062-8064)agC>agT	p.S2688S		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	2684	Calx-beta 2.				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						TTAACGAGAGCGCTGGTTTTC	0.418													C|||	1	0.000199681	0.0	0.0	5008	,	,		21744	0.0		0.001	False		,,,				2504	0.0				p.S2688S		Atlas-SNP	.											.	FRAS1	779	.	0			c.C8064T						PASS	.	C		1,3763		0,1,1881	79	79	79		8064	-9	0.8	4		79	0,8244		0,0,4122	no	coding-synonymous	FRAS1	NM_025074.6		0,1,6003	TT,TC,CC		0.0,0.0266,0.0083		2688/4013	79399181	1,12007	1882	4122	6004	SO:0001819	synonymous_variant	80144	exon55			CGAGAGCGCTGGT	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.8064C>T	4.37:g.79399181C>T		274	0	0		322	80	0.248447	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	.	.	.	.	.	.	.	.	.	.	C	0.046	-1.265514	0.01433	2.66E-4	0.0	ENSG00000138759	ENST00000512123	.	.	.	5.69	-8.98	0.00754	.	.	.	.	.	T	0.63414	0.2509	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.71300	-0.4634	4	.	.	.	.	17.9308	0.88996	0.0:0.524:0.0:0.476	.	.	.	.	C	917	.	.	R	+	1	0	FRAS1	79618205	0.024000	0.19004	0.770000	0.31555	0.041000	0.13682	-0.890000	0.04140	-1.654000	0.01499	-1.152000	0.01820	CGC	.	.	weak		0.418	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	79399181	C	T	79399181	2	4	1	1	0	0	0	0	0	0	0	1	6050	767	27	1		1	FRAS1	4	79399181	Silent	SNP	C	TCGA-FA-8693-01A-11D-2397-10	10884277	79399181	111755095	49	49											
TET2	54790	hgsc.bcm.edu	37	chr4	106196908	106196908	+	Frame_Shift_Del	DEL	A	A	-																															ccacccaatctgagcaatccAaacatggactataaaaatgg																										TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:106196908delA	ENST00000540549.1	+	11	6101	c.5241delA	c.(5239-5241)ccafs	p.P1747fs	TET2_ENST00000380013.4_Frame_Shift_Del_p.P1747fs|TET2_ENST00000545826.1_3'UTR|TET2_ENST00000513237.1_Frame_Shift_Del_p.P1768fs			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1747					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)		TGAGCAATCCAAACATGGACT	0.458			"Mis N, F"		MDS																																p.P1747fs		Atlas-Indel	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	0			c.5240delC						PASS	.						37	29	31					4																	106196908		692	1591	2283	SO:0001589	frameshift_variant	54790	exon11			.	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.5241delA	4.37:g.106196908delA	ENSP00000442788:p.Pro1747fs	91	0	0		110	18	0.163636	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Frame_Shift_Del	DEL	ENST00000540549.1	37	CCDS47120.1																																																																																			.	.	none		0.458	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		-	106196908	A	-	106196908	7	5	1	1	0	1	0	1	0	0	0	0	15785	117	5	0	5364	0	TET2	4	106196908	Frame_Shift_Del	DEL	A	TCGA-FA-8693-01A-11D-2397-10	26797727	106196908	84957368	50	50											
ENPEP	2028	hgsc.bcm.edu	37	chr4	111397599	111397599	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgcggagagagagggctctaAgagatactgcattcaaacga	14	7	13	7	2	2	3	1	0	1	3	2	7	2	3	0	2	4	2	0	2	3	3	rs564550794		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:111397599A>C	ENST00000265162.5	+	1	371	c.29A>C	c.(28-30)aAg>aCg	p.K10T		NM_001977.3	NP_001968.3	Q07075	AMPE_HUMAN	glutamyl aminopeptidase (aminopeptidase A)	10					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)		GAGGGCTCTAAGAGATACTGC	0.438																																					p.K10T		Atlas-SNP	.											.	ENPEP	149	.	0			c.A29C						PASS	.						171	163	166					4																	111397599		2203	4300	6503	SO:0001583	missense	2028	exon1			GCTCTAAGAGATA	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.29A>C	4.37:g.111397599A>C	ENSP00000265162:p.Lys10Thr	184	0	0		212	31	0.146226	NM_001977	Q504U2	Missense_Mutation	SNP	ENST00000265162.5	37	CCDS3691.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.679199	0.88542	.	.	ENSG00000138792	ENST00000265162	T	0.01347	4.99	5.42	3.04	0.35103	.	0.352416	0.31279	N	0.007939	T	0.02848	0.0085	M	0.66939	2.045	0.48040	D	0.99957	D	0.57899	0.981	P	0.46629	0.522	T	0.55685	-0.8102	10	0.51188	T	0.08	.	9.0788	0.36538	0.8513:0.0:0.1487:0.0	.	10	Q07075	AMPE_HUMAN	T	10	ENSP00000265162:K10T	ENSP00000265162:K10T	K	+	2	0	ENPEP	111617048	1.000000	0.71417	0.278000	0.24718	0.723000	0.41478	4.877000	0.63086	0.912000	0.36772	0.260000	0.18958	AAG	.	.	none		0.438	ENPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255747.2			C	111397599	A	C	111397599	3	2	1	1	0	0	0	0	1	0	0	0	5130	72	3	5	31	5	ENPEP	4	111397599	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10	5200691	111397599	79756677	51	51											
TRPC3	7222	hgsc.bcm.edu	37	chr4	122846198	122846198	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgacttcatacttaatggcaAgtttgacacgacttaatgaa	14	13	7	7	1	1	3	1	3	0	0	1	4	1	3	0	1	1	2	0	1	5	5			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:122846198A>C	ENST00000379645.3	-	3	1224	c.1151T>G	c.(1150-1152)cTt>cGt	p.L384R	TRPC3_ENST00000513531.1_Missense_Mutation_p.L311R|TRPC3_ENST00000264811.5_Missense_Mutation_p.L311R	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	299					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						CTTAATGGCAAGTTTGACACG	0.418																																					p.L384R		Atlas-SNP	.											.	TRPC3	201	.	0			c.T1151G						PASS	.						208	185	192					4																	122846198		2203	4300	6503	SO:0001583	missense	7222	exon3			ATGGCAAGTTTGA	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.1151T>G	4.37:g.122846198A>C	ENSP00000368966:p.Leu384Arg	205	0	0		212	11	0.0518868	NM_001130698	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Missense_Mutation	SNP	ENST00000379645.3	37	CCDS47130.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.923161	0.92319	.	.	ENSG00000138741	ENST00000264811;ENST00000379645;ENST00000513531	T;T;T	0.71103	-0.54;-0.54;-0.54	5.92	5.92	0.95590	.	0.141093	0.39341	N	0.001390	D	0.85682	0.5753	M	0.87456	2.885	0.30473	N	0.773102	P;D;P	0.71674	0.852;0.998;0.911	P;D;P	0.67725	0.736;0.953;0.821	D	0.86427	0.1758	10	0.87932	D	0	-16.0118	16.3526	0.83220	1.0:0.0:0.0:0.0	.	299;311;384	Q13507;E9PCJ9;Q5G1L5	TRPC3_HUMAN;.;.	R	311;384;311	ENSP00000264811:L311R;ENSP00000368966:L384R;ENSP00000426899:L311R	ENSP00000264811:L311R	L	-	2	0	TRPC3	123065648	1.000000	0.71417	0.990000	0.47175	0.998000	0.95712	9.262000	0.95591	2.255000	0.74692	0.533000	0.62120	CTT	.	.	none		0.418	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305		C	122846198	A	C	122846198	3	2	1	1	0	0	0	0	1	0	0	0	16594	72	3	5	1654	5	TRPC3	4	122846198	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10	11448599	122846198	68308078	52	52											
ABCE1	6059	hgsc.bcm.edu	37	chr4	146033391	146033391	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttttttttttttttcatagTttcatgtttgatgagccttc	5	26	5	5	0	2	2	2	2	0	0	3	2	2	2	1	0	1	2	1	0	1	11			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:146033391T>C	ENST00000296577.4	+	9	1226	c.711T>C	c.(709-711)atT>atC	p.I237I	OTUD4_ENST00000455611.2_Intron|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	237	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)					TTTTTCATAGTTTCATGTTTG	0.313																																					p.I237I		Atlas-SNP	.											.	ABCE1	47	.	0			c.T711C						PASS	.						30	29	29					4																	146033391		2202	4297	6499	SO:0001630	splice_region_variant	6059	exon9			TCATAGTTTCATG	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.711-1T>C	4.37:g.146033391T>C		96	0	0		101	12	0.118812	NM_002940	O88793|Q13181|Q13864|Q6NR76|Q96AL0|Q96B10|Q99K66	Silent	SNP	ENST00000296577.4	37	CCDS34071.1																																																																																			.	.	none		0.313	ABCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365104.1	NM_002940	Silent	C	146033391	T	C	146033391	5	2	1	1	0	0	0	0	0	0	1	0	64	1739	60	3	741	3	ABCE1	4	146033391	Splice_Site	SNP	T	TCGA-FA-8693-01A-11D-2397-10	23187193	146033391	45120885	53	53											
GRIA2	2891	hgsc.bcm.edu	37	chr4	158254497	158254497	+	Frame_Shift_Del	DEL	C	C	-																															tggagctcaaaactaatgggCcccggaaggtaaatccttag																										TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:158254497delC	ENST00000264426.9	+	8	1426	c.1147delC	c.(1147-1149)cccfs	p.P383fs	GRIA2_ENST00000393815.2_Frame_Shift_Del_p.P336fs|GRIA2_ENST00000449365.1_Frame_Shift_Del_p.P336fs|GRIA2_ENST00000296526.7_Frame_Shift_Del_p.P383fs|GRIA2_ENST00000507898.1_Frame_Shift_Del_p.P336fs	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	383					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)	AACTAATGGGCCCCGGAAGGT	0.398																																					p.G382fs		Atlas-Indel	.											.	GRIA2	358	.	0			c.1146delG						PASS	.						34	36	35					4																	158254497		2198	4294	6492	SO:0001589	frameshift_variant	2891	exon8			.		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.1147delC	4.37:g.158254497delC	ENSP00000264426:p.Pro383fs	49	0	0		68	11	0.161765	NM_001083619	A8MT92|I6L997|Q96FP6	Frame_Shift_Del	DEL	ENST00000264426.9	37	CCDS43274.1																																																																																			.	.	none		0.398	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2			-	158254497	C	-	158254497	7	5	1	1	0	1	0	1	0	0	0	0	6777	739	26	0	1177	0	GRIA2	4	158254497	Frame_Shift_Del	DEL	C	TCGA-FA-8693-01A-11D-2397-10	12221106	158254497	32899779	54	54											
MTNR1A	4543	hgsc.bcm.edu	37	chr4	187455075	187455075	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aactggccacaaacagccacTctgggatcctaggcaccatg	12	6	9	14	0	1	0	0	0	1	0	2	1	2	1	4	3	3	1	4	3	3	1			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:187455075T>C	ENST00000307161.5	-	2	1022	c.821A>G	c.(820-822)gAg>gGg	p.E274G	RP11-215A19.2_ENST00000509111.1_Intron	NM_005958.3	NP_005949.1	P48039	MTR1A_HUMAN	melatonin receptor 1A	274					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)	AAACAGCCACTCTGGGATCCT	0.502																																					p.E274G		Atlas-SNP	.											.	MTNR1A	46	.	0			c.A821G						PASS	.						73	79	77					4																	187455075		2203	4300	6503	SO:0001583	missense	4543	exon2			AGCCACTCTGGGA		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.821A>G	4.37:g.187455075T>C	ENSP00000302811:p.Glu274Gly	131	0	0		137	14	0.10219	NM_005958	A0AVC5|B0M0L2	Missense_Mutation	SNP	ENST00000307161.5	37	CCDS3848.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.224502	0.79576	.	.	ENSG00000168412	ENST00000307161	T	0.73047	-0.71	4.96	4.96	0.65561	GPCR, rhodopsin-like superfamily (1);	0.049677	0.85682	D	0.000000	T	0.77398	0.4124	M	0.89353	3.025	0.80722	D	1	B	0.29909	0.261	B	0.36378	0.223	T	0.76963	-0.2764	10	0.33940	T	0.23	-23.224	14.6218	0.68592	0.0:0.0:0.0:1.0	.	274	P48039	MTR1A_HUMAN	G	274	ENSP00000302811:E274G	ENSP00000302811:E274G	E	-	2	0	MTNR1A	187692069	1.000000	0.71417	1.000000	0.80357	0.713000	0.41058	6.145000	0.71769	1.860000	0.53959	0.533000	0.62120	GAG	.	.	none		0.502	MTNR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360189.1			C	187455075	T	C	187455075	3	2	1	1	0	0	0	0	1	0	0	0	9960	1551	54	3	235	3	MTNR1A	4	187455075	Missense_Mutation	SNP	T	TCGA-FA-8693-01A-11D-2397-10	29200578	187455075	3699201	55	55											
VCAN	1462	hgsc.bcm.edu	37	chr5	82816658	82816658	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaaaggataaagacatcccaAgtttcactgaagatggagca	17	7	10	7	0	1	3	1	1	0	2	2	6	2	5	1	2	1	2	1	2	5	2			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr5:82816658A>C	ENST00000265077.3	+	7	3098	c.2533A>C	c.(2533-2535)Agt>Cgt	p.S845R	VCAN_ENST00000342785.4_Missense_Mutation_p.S845R|VCAN_ENST00000512590.2_Missense_Mutation_p.S797R|VCAN_ENST00000343200.5_Intron|VCAN_ENST00000502527.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	845	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)	AGACATCCCAAGTTTCACTGA	0.428																																					p.S845R		Atlas-SNP	.											.	VCAN	498	.	0			c.A2533C						PASS	.						105	105	105					5																	82816658		2203	4300	6503	SO:0001583	missense	1462	exon7			ATCCCAAGTTTCA	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.2533A>C	5.37:g.82816658A>C	ENSP00000265077:p.Ser845Arg	63	0	0		84	22	0.261905	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	A	2.468	-0.322533	0.05350	.	.	ENSG00000038427	ENST00000265077;ENST00000342785;ENST00000512590	T;T;T	0.24538	1.85;1.85;1.85	5.76	-2.5	0.06384	.	0.320753	0.31589	N	0.007394	T	0.17023	0.0409	L	0.48362	1.52	0.20926	N	0.999821	B;B	0.12630	0.005;0.006	B;B	0.12156	0.007;0.006	T	0.15037	-1.0451	10	0.44086	T	0.13	.	6.2271	0.20714	0.4327:0.1508:0.4164:0.0	.	845;845	P13611-3;P13611	.;CSPG2_HUMAN	R	845;845;797	ENSP00000265077:S845R;ENSP00000342768:S845R;ENSP00000425959:S797R	ENSP00000265077:S845R	S	+	1	0	VCAN	82852414	0.073000	0.21202	0.880000	0.34516	0.109000	0.19521	0.804000	0.27098	-0.051000	0.13334	0.528000	0.53228	AGT	.	.	none		0.428	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		C	82816658	A	C	82816658	3	2	1	1	0	0	0	0	1	0	0	0	17153	72	3	5	2555	5	VCAN	5	82816658	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10		82816658	98098602	56	56											
VCAN	1462	hgsc.bcm.edu	37	chr5	82833506	82833506	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagaatctcagaaaatagccTttgcaagggctacagaagta	17	8	9	7	0	1	3	1	0	1	3	2	3	1	3	1	1	3	3	1	1	9	4			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr5:82833506T>G	ENST00000265077.3	+	8	5249	c.4684T>G	c.(4684-4686)Ttt>Gtt	p.F1562V	VCAN_ENST00000342785.4_Intron|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000343200.5_Missense_Mutation_p.F575V|VCAN_ENST00000502527.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1562	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)	GAAAATAGCCTTTGCAAGGGC	0.413																																					p.F1562V		Atlas-SNP	.											.	VCAN	498	.	0			c.T4684G						PASS	.						72	74	73					5																	82833506		2203	4300	6503	SO:0001583	missense	1462	exon8			ATAGCCTTTGCAA	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.4684T>G	5.37:g.82833506T>G	ENSP00000265077:p.Phe1562Val	51	0	0		73	16	0.219178	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	T	5.696	0.312954	0.10789	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000513960	D;D;T	0.86769	-2.17;-2.17;2.95	5.78	1.85	0.25348	.	0.656922	0.14873	N	0.293408	T	0.81503	0.4836	M	0.61703	1.905	0.09310	N	0.999999	B;B	0.23806	0.091;0.055	B;B	0.19946	0.027;0.012	T	0.64334	-0.6432	10	0.18276	T	0.48	.	6.8329	0.23921	0.2407:0.0:0.2497:0.5096	.	575;1562	P13611-2;P13611	.;CSPG2_HUMAN	V	1562;575;575	ENSP00000265077:F1562V;ENSP00000340062:F575V;ENSP00000426251:F575V	ENSP00000265077:F1562V	F	+	1	0	VCAN	82869262	0.055000	0.20627	0.001000	0.08648	0.056000	0.15407	1.323000	0.33701	0.436000	0.26393	0.533000	0.62120	TTT	.	.	none		0.413	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		G	82833506	T	G	82833506	3	3	1	1	0	0	0	0	1	0	0	0	17153	1609	56	5	4710	5	VCAN	5	82833506	Missense_Mutation	SNP	T	TCGA-FA-8693-01A-11D-2397-10	16848	82833506	98081754	57	57											
GPR98	84059	hgsc.bcm.edu	37	chr5	89948249	89948249	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctttgcagcctgggcaggAgttctatgaaacttcaggaa	10	11	12	8	0	2	1	1	1	1	0	2	3	2	3	1	3	4	4	1	3	3	4			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr5:89948249A>T	ENST00000405460.2	+	19	3599	c.3503A>T	c.(3502-3504)gAg>gTg	p.E1168V		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1168	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)		CCTGGGCAGGAGTTCTATGAA	0.388																																					p.E1168V		Atlas-SNP	.											.	GPR98	605	.	0			c.A3503T						PASS	.						134	128	130					5																	89948249		1908	4144	6052	SO:0001583	missense	84059	exon19			GGCAGGAGTTCTA	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.3503A>T	5.37:g.89948249A>T	ENSP00000384582:p.Glu1168Val	168	0	0		153	31	0.202614	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	33	5.230671	0.95207	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000399043	T	0.29917	1.55	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.47637	0.1456	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.45789	-0.9237	10	0.87932	D	0	.	16.635	0.85050	1.0:0.0:0.0:0.0	.	1168	Q8WXG9	GPR98_HUMAN	V	1168	ENSP00000384582:E1168V	ENSP00000296619:E1168V	E	+	2	0	GPR98	89984005	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.078000	0.94023	2.330000	0.79161	0.477000	0.44152	GAG	.	.	none		0.388	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		T	89948249	A	T	89948249	3	4	1	1	0	0	0	0	1	0	0	0	6730	304	11	5	3577	5	GPR98	5	89948249	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10	7114743	89948249	90967011	58	58											
ZNF454	285676	hgsc.bcm.edu	37	chr5	178392474	178392474	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acactggagagaaaccctttGaatgtaatgaatgtgggaag	15	9	12	5	0	0	3	0	2	0	1	0	6	0	5	1	2	1	1	1	2	5	2			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr5:178392474G>A	ENST00000320129.3	+	5	1372	c.1069G>A	c.(1069-1071)Gaa>Aaa	p.E357K	ZNF454_ENST00000519564.1_Missense_Mutation_p.E357K	NM_001178090.1|NM_182594.2	NP_001171561.1|NP_872400.2	Q8N9F8	ZN454_HUMAN	zinc finger protein 454	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)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(11)|lung(18)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	46	all_cancers(89;0.000904)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.225)|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;0.234)		GAAACCCTTTGAATGTAATGA	0.393																																					p.E357K		Atlas-SNP	.											.	ZNF454	99	.	0			c.G1069A						PASS	.						40	44	43					5																	178392474		2203	4300	6503	SO:0001583	missense	285676	exon5			CCCTTTGAATGTA	AK094763	CCDS4441.1	5q35.3	2013-01-08			ENSG00000178187	ENSG00000178187		"Zinc fingers, C2H2-type", "-"	21200	protein-coding gene	gene with protein product							Standard	NM_182594		Approved	FLJ37444	uc021yjc.1	Q8N9F8	OTTHUMG00000130891	ENST00000320129.3:c.1069G>A	5.37:g.178392474G>A	ENSP00000326249:p.Glu357Lys	63	0	0		49	5	0.102041	NM_001178089	Q2M1P2|Q2M323	Missense_Mutation	SNP	ENST00000320129.3	37	CCDS4441.1	.	.	.	.	.	.	.	.	.	.	G	15.05	2.716785	0.48622	.	.	ENSG00000178187	ENST00000320129;ENST00000519564	T;T	0.06608	3.28;3.28	4.21	4.21	0.49690	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.40818	N	0.001005	T	0.04452	0.0122	N	0.01188	-0.97	0.28822	N	0.897625	P	0.51791	0.948	P	0.51866	0.682	T	0.44050	-0.9353	10	0.34782	T	0.22	-18.4194	14.4348	0.67274	0.0:0.0:1.0:0.0	.	357	Q8N9F8	ZN454_HUMAN	K	357	ENSP00000326249:E357K;ENSP00000430354:E357K	ENSP00000326249:E357K	E	+	1	0	ZNF454	178325080	0.000000	0.05858	1.000000	0.80357	0.992000	0.81027	-0.128000	0.10531	2.344000	0.79699	0.650000	0.86243	GAA	.	.	none		0.393	ZNF454-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253476.2	XM_209718		A	178392474	G	A	178392474	3	1	1	1	0	0	0	0	1	0	0	0	17938	1291	45	2	1083	2	ZNF454	5	178392474	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	88444225	178392474	2522786	59	59											
HIST1H1E	3008	hgsc.bcm.edu	37	chr6	26157012	26157012	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cggccaaggccaagaagccaGcaggagcggcgaagaagccc	13	0	15	13	3	0	2	0	0	0	2	0	4	0	3	4	4	4	1	4	4	5	0			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:26157012G>A	ENST00000304218.3	+	1	454	c.394G>A	c.(394-396)Gca>Aca	p.A132T	HIST1H2BD_ENST00000289316.2_5'Flank|HIST1H2BD_ENST00000377777.4_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	132					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						CAAGAAGCCAGCAGGAGCGGC	0.637																																					p.A132T		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.G394A						PASS	.						15	22	19					6																	26157012		2201	4297	6498	SO:0001583	missense	3008	exon1			AAGCCAGCAGGAG	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.394G>A	6.37:g.26157012G>A	ENSP00000307705:p.Ala132Thr	103	0	0		73	15	0.205479	NM_005321	Q4VB25	Missense_Mutation	SNP	ENST00000304218.3	37	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	5.354	0.250648	0.10130	.	.	ENSG00000168298	ENST00000304218	T	0.26957	1.7	5.51	1.63	0.23807	.	0.267468	0.34628	N	0.003817	T	0.05135	0.0137	L	0.27053	0.805	0.32693	N	0.513953	B	0.02656	0.0	B	0.04013	0.001	T	0.40194	-0.9576	10	0.14656	T	0.56	-0.2098	9.6047	0.39626	0.1402:0.0:0.7406:0.1192	.	132	P10412	H14_HUMAN	T	132	ENSP00000307705:A132T	ENSP00000307705:A132T	A	+	1	0	HIST1H1E	26264991	0.944000	0.32072	0.001000	0.08648	0.032000	0.12392	2.034000	0.41145	0.070000	0.16634	-1.300000	0.01332	GCA	.	.	none		0.637	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321		A	26157012	G	A	26157012	3	1	1	1	0	0	0	0	1	0	0	0	7135	971	34	2	396	2	HIST1H1E	6	26157012	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10		26157012	144958055	60	60											
HIST1H2BL	8340	hgsc.bcm.edu	37	chr6	27775641	27775641	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ccttggtcaccgccttcttgGagcccttcttcggggcggga	3	11	13	14	3	3	0	1	0	2	0	4	2	3	2	4	5	1	0	4	5	0	5			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:27775641G>A	ENST00000377401.2	-	1	68	c.44C>T	c.(43-45)tCc>tTc	p.S15F	HIST1H2AI_ENST00000358739.3_5'Flank|HIST1H3H_ENST00000369163.2_5'Flank	NM_003519.3	NP_003510.1	Q99880	H2B1L_HUMAN	histone cluster 1, H2bl	15					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						CGCCTTCTTGGAGCCCTTCTT	0.527																																					p.S15F		Atlas-SNP	.											.	HIST1H2BL	48	.	0			c.C44T						PASS	.						98	99	99					6																	27775641		2203	4300	6503	SO:0001583	missense	8340	exon1			TTCTTGGAGCCCT	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.44C>T	6.37:g.27775641G>A	ENSP00000366618:p.Ser15Phe	272	0	0		286	71	0.248252	NM_003519	B2R5A3|Q52LW9	Missense_Mutation	SNP	ENST00000377401.2	37	CCDS4625.1	.	.	.	.	.	.	.	.	.	.	.	24.0	4.484608	0.84854	.	.	ENSG00000185130	ENST00000377401	T	0.22945	1.93	4.35	4.35	0.52113	Histone-fold (2);	.	.	.	.	T	0.33177	0.0854	L	0.45228	1.405	0.58432	D	0.999991	D	0.69078	0.997	D	0.71656	0.974	T	0.05022	-1.0911	9	0.46703	T	0.11	.	16.7381	0.85452	0.0:0.0:1.0:0.0	.	15	Q99880	H2B1L_HUMAN	F	15	ENSP00000366618:S15F	ENSP00000366618:S15F	S	-	2	0	HIST1H2BL	27883620	1.000000	0.71417	0.997000	0.53966	0.633000	0.38033	4.668000	0.61568	2.331000	0.79229	0.650000	0.86243	TCC	.	.	none		0.527	HIST1H2BL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040153.1	NM_003519		A	27775641	G	A	27775641	3	1	1	1	0	0	0	0	1	0	0	0	7160	1174	41	2	340	2	HIST1H2BL	6	27775641	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	1618629	27775641	143339426	61	61											
LTB	4050	hgsc.bcm.edu	37	chr6	31549632	31549632	+	Missense_Mutation	SNP	G	G	A																															ccccggggtcggccgtctccGttacctggttgggtggggtc																										TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:31549632G>A	ENST00000429299.2	-	2	174	c.167C>T	c.(166-168)aCg>aTg	p.T56M	LTB_ENST00000446745.2_Intron|LTB_ENST00000483972.1_Intron	NM_002341.1	NP_002332.1	Q06643	TNFC_HUMAN	lymphotoxin beta (TNF superfamily, member 3)	56					cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|signal transduction (GO:0007165)|skin development (GO:0043588)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	9						GGCCGTCTCCGTTACCTGGTT	0.627																																					p.T56M		Atlas-SNP	.											.	LTB	19	.	0			c.C167T						PASS	.						80	89	86					6																	31549632		1509	2709	4218	SO:0001583	missense	4050	exon2			GTCTCCGTTACCT	L11015	CCDS4703.1, CCDS4704.1	6p21.3	2013-05-22			ENSG00000227507	ENSG00000227507		"Tumor necrosis factor (ligand) superfamily"	6711	protein-coding gene	gene with protein product		600978		TNFC		7916655, 1714477	Standard	NM_002341		Approved	p33, TNFSF3	uc003nuk.3	Q06643	OTTHUMG00000031136	ENST00000429299.2:c.167C>T	6.37:g.31549632G>A	ENSP00000410481:p.Thr56Met	99	0	0		82	13	0.158537	NM_002341	P78370|Q52LU8|Q99761	Missense_Mutation	SNP	ENST00000429299.2	37	CCDS4703.1	.	.	.	.	.	.	.	.	.	.	G	11.08	1.534745	0.27475	.	.	ENSG00000227507	ENST00000429299	T	0.21932	1.98	5.45	-0.999	0.10208	.	1.156080	0.06349	N	0.709538	T	0.03871	0.0109	N	0.22421	0.69	0.09310	N	0.999997	B	0.13145	0.007	B	0.08055	0.003	T	0.42732	-0.9434	10	0.44086	T	0.13	-0.0223	3.3408	0.07118	0.3298:0.0:0.3705:0.2997	.	56	Q06643	TNFC_HUMAN	M	56	ENSP00000410481:T56M	ENSP00000410481:T56M	T	-	2	0	LTB	31657611	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.359000	0.20233	-0.203000	0.10251	-0.742000	0.03525	ACG	.	.	none		0.627	LTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076239.3			A	31549632	G	A	31549632	3	1	1	1	0	0	0	0	1	0	0	0	9079	1145	40	1	579	1	LTB	6	31549632	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	3773991	31549632	139565435	62	62	2	2									
LTB	4050	hgsc.bcm.edu	37	chr6	31549636	31549636	+	Splice_Site	SNP	C	C	G																															ggggtcggccgtctccgttaCctggttgggtggggtcacag																								rs571318566	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:31549636C>G	ENST00000429299.2	-	2	170	c.163G>C	c.(163-165)Gta>Cta	p.V55L	LTB_ENST00000446745.2_Intron|LTB_ENST00000483972.1_Intron	NM_002341.1	NP_002332.1	Q06643	TNFC_HUMAN	lymphotoxin beta (TNF superfamily, member 3)	55					cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|signal transduction (GO:0007165)|skin development (GO:0043588)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	9						GTCTCCGTTACCTGGTTGGGT	0.622																																					p.V55L		Atlas-SNP	.											.	LTB	19	.	0			c.G163C						PASS	.						78	87	84					6																	31549636		1509	2709	4218	SO:0001630	splice_region_variant	4050	exon2			CCGTTACCTGGTT	L11015	CCDS4703.1, CCDS4704.1	6p21.3	2013-05-22			ENSG00000227507	ENSG00000227507		"Tumor necrosis factor (ligand) superfamily"	6711	protein-coding gene	gene with protein product		600978		TNFC		7916655, 1714477	Standard	NM_002341		Approved	p33, TNFSF3	uc003nuk.3	Q06643	OTTHUMG00000031136	ENST00000429299.2:c.163-1G>C	6.37:g.31549636C>G		100	0	0		79	11	0.139241	NM_002341	P78370|Q52LU8|Q99761	Missense_Mutation	SNP	ENST00000429299.2	37	CCDS4703.1	.	.	.	.	.	.	.	.	.	.	C	17.12	3.307743	0.60305	.	.	ENSG00000227507	ENST00000429299	T	0.21361	2.01	5.45	5.45	0.79879	.	0.715933	0.12594	N	0.455328	T	0.22627	0.0546	L	0.49126	1.545	0.80722	D	1	D	0.67145	0.996	P	0.55161	0.77	T	0.00915	-1.1516	10	0.27082	T	0.32	-17.783	14.7884	0.69821	0.0:1.0:0.0:0.0	.	55	Q06643	TNFC_HUMAN	L	55	ENSP00000410481:V55L	ENSP00000410481:V55L	V	-	1	0	LTB	31657615	0.998000	0.40836	0.993000	0.49108	0.049000	0.14656	1.506000	0.35747	2.555000	0.86185	0.655000	0.94253	GTA	.	.	none		0.622	LTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076239.3		Missense_Mutation	G	31549636	C	G	31549636	5	3	1	1	0	0	0	0	0	0	1	0	9079	521	18	4	583	4	LTB	6	31549636	Splice_Site	SNP	C	TCGA-FA-8693-01A-11D-2397-10	4	31549636	139565431	63	63	2	2									
TNXB	7148	hgsc.bcm.edu	37	chr6	32020562	32020562	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acggtgacctcgctctcctcGcccctgacacgcaccacctg	6	7	8	20	4	1	2	0	2	1	0	4	2	1	2	6	1	0	2	6	1	0	0	rs375459891		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:32020562G>A	ENST00000375244.3	-	26	9201	c.9000C>T	c.(8998-9000)ggC>ggT	p.G3000G	TNXB_ENST00000375247.2_Silent_p.G2998G			P22105	TENX_HUMAN	tenascin XB	3045	Fibronectin type-III 22. {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						CGCTCTCCTCGCCCCTGACAC	0.687													g|||	1	0.000199681	0.0	0.0	5008	,	,		14923	0.001		0.0	False		,,,				2504	0.0				p.G2998G		Atlas-SNP	.											.	TNXB	553	.	0			c.C8994T						PASS	.						40	44	43					6																	32020562		1251	2548	3799	SO:0001819	synonymous_variant	7148	exon26			CTCCTCGCCCCTG	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.9000C>T	6.37:g.32020562G>A		58	0	0		41	5	0.121951	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	37																																																																																				.	.	weak		0.687	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		A	32020562	G	A	32020562	2	1	1	1	0	0	0	0	0	0	0	1	16361	1074	38	1		1	TNXB	6	32020562	Silent	SNP	G	TCGA-FA-8693-01A-11D-2397-10	470926	32020562	139094505	64	64											
PRPH2	5961	hgsc.bcm.edu	37	chr6	42690015	42690015	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaccagttcatgagccagaGcccttgggccaacttgaccc	10	7	10	14	0	1	3	1	2	0	1	1	4	1	3	5	1	4	1	5	1	2	3			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:42690015G>T	ENST00000230381.5	-	1	297	c.58C>A	c.(58-60)Ctc>Atc	p.L20I		NM_000322.4	NP_000313.2	P23942	PRPH2_HUMAN	peripherin 2 (retinal degeneration, slow)	20					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)			ATGAGCCAGAGCCCTTGGGCC	0.527																																					p.L20I		Atlas-SNP	.											.	PRPH2	47	.	0			c.C58A						PASS	.						81	78	79					6																	42690015		2203	4300	6503	SO:0001583	missense	5961	exon1			GCCAGAGCCCTTG		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.58C>A	6.37:g.42690015G>T	ENSP00000230381:p.Leu20Ile	116	0	0		133	38	0.285714	NM_000322	Q5TFH5|Q6DK65	Missense_Mutation	SNP	ENST00000230381.5	37	CCDS4871.1	.	.	.	.	.	.	.	.	.	.	G	19.18	3.778382	0.70107	.	.	ENSG00000112619	ENST00000230381	D	0.82526	-1.62	5.61	5.61	0.85477	.	0.057622	0.64402	D	0.000001	D	0.89203	0.6648	M	0.84585	2.705	0.51233	D	0.999911	P	0.51791	0.948	P	0.56700	0.804	D	0.88512	0.3090	10	0.44086	T	0.13	.	19.6248	0.95674	0.0:0.0:1.0:0.0	.	20	P23942	PRPH2_HUMAN	I	20	ENSP00000230381:L20I	ENSP00000230381:L20I	L	-	1	0	PRPH2	42797993	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.685000	0.54678	2.631000	0.89168	0.655000	0.94253	CTC	.	.	none		0.527	PRPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040556.1	NM_000322		T	42690015	G	T	42690015	3	4	1	1	0	0	0	0	1	0	0	0	12589	971	34	4	994	4	PRPH2	6	42690015	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	10669453	42690015	128425052	65	65											
HDDC2	51020	hgsc.bcm.edu	37	chr6	125621684	125621684	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caaagtccagctcagcttacCggtctttgttaagacggtca	10	11	9	11	2	3	1	2	0	1	1	4	1	4	1	2	2	3	3	2	2	3	3			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:125621684C>T	ENST00000398153.2	-	2	248	c.206G>A	c.(205-207)cGa>cAa	p.R69Q	HDDC2_ENST00000608284.1_Splice_Site_p.R69Q|HDDC2_ENST00000368377.4_Splice_Site_p.R69Q|HDDC2_ENST00000608295.1_Splice_Site_p.R69Q	NM_016063.2	NP_057147.2	Q7Z4H3	HDDC2_HUMAN	HD domain containing 2	69	HD.			R -> P (in Ref. 2; AAD34125). {ECO:0000305}.		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)		CTCAGCTTACCGGTCTTTGTT	0.468																																					p.R69Q		Atlas-SNP	.											.	HDDC2	21	.	0			c.G206A						PASS	.						87	93	91					6																	125621684		1978	4164	6142	SO:0001630	splice_region_variant	51020	exon2			GCTTACCGGTCTT	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.206+1G>A	6.37:g.125621684C>T		193	0	0		186	40	0.215054	NM_016063	Q5TDQ4|Q6NZ49|Q9BTT2|Q9BV31|Q9Y3D1	Missense_Mutation	SNP	ENST00000398153.2	37	CCDS43503.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.402058	0.83120	.	.	ENSG00000111906	ENST00000318787;ENST00000398153;ENST00000368377	T;T;T	0.53857	1.01;0.6;1.01	5.53	5.53	0.82687	Metal-dependent phosphohydrolase, HD domain (1);Metal-dependent phosphohydrolase, HD subdomain (1);HD domain (1);	0.045026	0.85682	D	0.000000	T	0.63640	0.2528	M	0.87682	2.9	0.42936	D	0.994335	D	0.62365	0.991	P	0.56612	0.802	T	0.63659	-0.6587	10	0.19147	T	0.46	.	18.2254	0.89915	0.0:1.0:0.0:0.0	.	69	Q7Z4H3	HDDC2_HUMAN	Q	69	ENSP00000316242:R69Q;ENSP00000381220:R69Q;ENSP00000357361:R69Q	ENSP00000316242:R69Q	R	-	2	0	HDDC2	125663383	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	5.636000	0.67848	2.593000	0.87608	0.655000	0.94253	CGG;CGA;CGA	.	.	none		0.468	HDDC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472493.1	NM_016063	Missense_Mutation	T	125621684	C	T	125621684	5	4	1	1	0	0	0	0	0	0	1	0	7025	666	23	1	428	1	HDDC2	6	125621684	Splice_Site	SNP	C	TCGA-FA-8693-01A-11D-2397-10	82931669	125621684	45493383	66	66											
SGK1	6446	hgsc.bcm.edu	37	chr6	134494703	134494703	+	Splice_Site	DEL	G	G	-																															tgatttgctgagaaggacttGgctagaaaaaaaaaaaaaga																										TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:134494703delG	ENST00000237305.7	-	4	318	c.230delC	c.(229-231)cca>ca	p.P77fs	SGK1_ENST00000475719.2_Splice_Site_p.P77fs|SGK1_ENST00000367858.5_Splice_Site_p.P172fs|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000413996.3_Splice_Site_p.P91fs|SGK1_ENST00000528577.1_Splice_Site_p.P105fs|SGK1_ENST00000367857.5_Splice_Site_p.P67fs	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	77					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)		AGAAGGACTTGGCTAGAAAAA	0.368																																					p.P172fs		Atlas-Indel	.											SGK1_ENST00000528577,NS,lymphoid_neoplasm,-2,6	SGK1	387	6	0			c.516delA						PASS	.						46	49	48					6																	134494703		2203	4300	6503	SO:0001630	splice_region_variant	6446	exon6			.	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.229-1C>-	6.37:g.134494703delG		56	0	0		68	13	0.191176	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Frame_Shift_Del	DEL	ENST00000237305.7	37	CCDS5170.1																																																																																			.	.	none		0.368	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		Frame_Shift_Del	-	134494703	G	-	134494703	8	5	1	1	0	1	0	1	0	0	1	0	14222	1362	47	0	1101	0	SGK1	6	134494703	Splice_Site	DEL	G	TCGA-FA-8693-01A-11D-2397-10	8873019	134494703	36620364	67	67	3	2	1	1		4	3	956	N	G	1.337001e-05
SGK1	6446	hgsc.bcm.edu	37	chr6	134494704	134494704	+	Splice_Site	SNP	G	G	C																															gatttgctgagaaggacttgGctagaaaaaaaaaaaaagaa																										TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:134494704G>C	ENST00000237305.7	-	4	317	c.229C>G	c.(229-231)Cca>Gca	p.P77A	SGK1_ENST00000475719.2_Splice_Site_p.P77A|SGK1_ENST00000367858.5_Splice_Site_p.P172A|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000413996.3_Splice_Site_p.P91A|SGK1_ENST00000528577.1_Splice_Site_p.P105A|SGK1_ENST00000367857.5_Splice_Site_p.P67A	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	77					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)	p.P172S(1)|p.P77S(1)		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)		GAAGGACTTGGCTAGAAAAAA	0.368																																					p.P172A		Atlas-SNP	.											SGK1_ENST00000528577,NS,lymphoid_neoplasm,0,6	SGK1	387	6	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.C514G						PASS	.						44	48	47					6																	134494704		2203	4300	6503	SO:0001630	splice_region_variant	6446	exon6			GACTTGGCTAGAA	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.229-1C>G	6.37:g.134494704G>C		51	0	0		50	5	0.1	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	14.64	2.594913	0.46318	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T	0.72394	3.18;3.18;3.18;3.18;3.18;-0.65	6.02	6.02	0.97574	Protein kinase-like domain (1);	0.050195	0.85682	D	0.000000	T	0.56558	0.1993	M	0.62723	1.935	0.80722	D	1	B;P;B;B;B;B	0.42871	0.065;0.792;0.014;0.05;0.232;0.008	B;B;B;B;B;B	0.34138	0.064;0.121;0.028;0.061;0.176;0.011	T	0.59359	-0.7469	10	0.21014	T	0.42	.	20.5407	0.99260	0.0:0.0:1.0:0.0	.	105;91;77;67;172;77	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	A	172;91;77;67;105;77;141	ENSP00000356832:P172A;ENSP00000396242:P91A;ENSP00000237305:P77A;ENSP00000356831:P67A;ENSP00000434450:P105A;ENSP00000434302:P77A	ENSP00000237305:P77A	P	-	1	0	SGK1	134536397	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.563000	0.82314	2.865000	0.98341	0.655000	0.94253	CCA	.	.	none		0.368	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		Missense_Mutation	C	134494704	G	C	134494704	5	2	1	1	0	0	0	0	0	0	1	0	14222	1217	42	4	1102	4	SGK1	6	134494704	Splice_Site	SNP	G	TCGA-FA-8693-01A-11D-2397-10	1	134494704	36620363	68	68	3	2	1	1		4	3	956	N	G	1.337001e-05
SGK1	6446	hgsc.bcm.edu	37	chr6	134495169	134495169	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agaagggttggcattcataaGctcaggctcctgaggttggg	9	10	15	7	0	2	2	2	1	0	1	3	2	3	2	1	5	1	5	1	5	2	4	rs141028225		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:134495169G>C	ENST00000237305.7	-	3	290	c.202C>G	c.(202-204)Ctt>Gtt	p.L68V	SGK1_ENST00000475719.2_Missense_Mutation_p.L68V|SGK1_ENST00000367858.5_Missense_Mutation_p.L163V|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000413996.3_Missense_Mutation_p.L82V|SGK1_ENST00000528577.1_Missense_Mutation_p.L96V|SGK1_ENST00000367857.5_Missense_Mutation_p.L58V	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	68					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)		GCATTCATAAGCTCAGGCTCC	0.478																																					p.L163V		Atlas-SNP	.											.	SGK1	387	.	0			c.C487G						PASS	.	G	VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU	0,4406		0,0,2203	151	144	146		487,286,244,202	5	1	6	dbSNP_134	146	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	SGK1	NM_001143676.1,NM_001143677.1,NM_001143678.1,NM_005627.3	32,32,32,32	0,1,6502	CC,CG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	163/527,96/460,82/446,68/432	134495169	1,13005	2203	4300	6503	SO:0001583	missense	6446	exon5			TCATAAGCTCAGG	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.202C>G	6.37:g.134495169G>C	ENSP00000237305:p.Leu68Val	109	0	0		110	22	0.2	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	12.84	2.057170	0.36277	0.0	1.16E-4	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T	0.72282	-0.64;-0.63;-0.62;-0.62;-0.62;-0.63	5.99	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.51210	0.1661	L	0.54323	1.7	0.80722	D	1	B;B;B;B;B;B	0.28605	0.008;0.008;0.0;0.073;0.217;0.002	B;B;B;B;B;B	0.31946	0.012;0.002;0.001;0.088;0.138;0.004	T	0.53092	-0.8487	10	0.30854	T	0.27	.	11.0283	0.47757	0.1506:0.0:0.8494:0.0	.	96;82;68;58;163;68	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	V	163;82;68;58;96;68;132	ENSP00000356832:L163V;ENSP00000396242:L82V;ENSP00000237305:L68V;ENSP00000356831:L58V;ENSP00000434450:L96V;ENSP00000434302:L68V	ENSP00000237305:L68V	L	-	1	0	SGK1	134536862	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.307000	0.51888	1.377000	0.46286	0.655000	0.94253	CTT	G|1.000;C|0.000	0.000	weak		0.478	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			C	134495169	G	C	134495169	3	2	1	1	0	0	0	0	1	0	0	0	14222	971	34	4	1133	4	SGK1	6	134495169	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	465	134495169	36619898	69	69			1	1		4	3	956	N	G	1.337001e-05
SGK1	6446	hgsc.bcm.edu	37	chr6	134495658	134495658	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcaaacttactgtttgcatGcataggagttattggcaatc	11	14	9	7	0	1	0	1	0	0	0	2	1	1	1	0	2	4	5	0	2	5	5	rs375777416		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:134495658G>A	ENST00000237305.7	-	2	231	c.143C>T	c.(142-144)gCa>gTa	p.A48V	SGK1_ENST00000475719.2_Missense_Mutation_p.A48V|SGK1_ENST00000367858.5_Missense_Mutation_p.A143V|SGK1_ENST00000489458.2_5'Flank|SGK1_ENST00000413996.3_Missense_Mutation_p.A62V|SGK1_ENST00000528577.1_Missense_Mutation_p.A76V|SGK1_ENST00000367857.5_Missense_Mutation_p.A38V	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	48	Necessary for localization to the mitochondria.				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)		CTGTTTGCATGCATAGGAGTT	0.413											OREG0017675	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A143V		Atlas-SNP	.											.	SGK1	387	.	0			c.C428T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	0,4406		0,0,2203	88	85	86		143,185,227,428	5.9	1	6		86	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	SGK1	NM_005627.3,NM_001143678.1,NM_001143677.1,NM_001143676.1	64,64,64,64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign,benign	48/432,62/446,76/460,143/527	134495658	1,13005	2203	4300	6503	SO:0001583	missense	6446	exon4			TTGCATGCATAGG	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.143C>T	6.37:g.134495658G>A	ENSP00000237305:p.Ala48Val	86	0	0	1611	88	14	0.159091	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	11.90	1.778015	0.31502	0.0	1.16E-4	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T;T	0.38240	1.67;1.67;1.67;1.67;1.67;1.67;1.15	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.19005	0.0456	L	0.42245	1.32	0.80722	D	1	B;B;B;B;B;B	0.29988	0.001;0.264;0.0;0.004;0.013;0.001	B;B;B;B;B;B	0.24269	0.004;0.052;0.001;0.005;0.022;0.002	T	0.06267	-1.0836	10	0.15066	T	0.55	.	20.2576	0.98430	0.0:0.0:1.0:0.0	.	76;62;48;38;143;48	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	V	143;62;48;38;76;48;112	ENSP00000356832:A143V;ENSP00000396242:A62V;ENSP00000237305:A48V;ENSP00000356831:A38V;ENSP00000434450:A76V;ENSP00000434302:A48V;ENSP00000435577:A112V	ENSP00000237305:A48V	A	-	2	0	SGK1	134537351	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	8.062000	0.89475	2.783000	0.95769	0.655000	0.94253	GCA	.	.	weak		0.413	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			A	134495658	G	A	134495658	3	1	1	1	0	0	0	0	1	0	0	0	14222	1319	46	2	1196	2	SGK1	6	134495658	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	489	134495658	36619409	70	70			1	1		4	3	956	N	G	1.337001e-05
NMBR	4829	hgsc.bcm.edu	37	chr6	142399929	142399929	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccacttctgaaaacaccgcTtcgggaactgccagcaacac	12	6	8	15	2	1	1	0	1	1	0	2	2	1	2	3	1	5	2	3	1	4	2			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:142399929T>C	ENST00000258042.1	-	2	674	c.534A>G	c.(532-534)gaA>gaG	p.E178E	NMBR_ENST00000480652.1_5'Flank	NM_002511.2	NP_002502.2	P28336	NMBR_HUMAN	neuromedin B receptor	178					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)		AAAACACCGCTTCGGGAACTG	0.512																																					p.E178E		Atlas-SNP	.											NMBR,NS,carcinoma,-2,1	NMBR	62	1	0			c.A534G						PASS	.						117	107	110					6																	142399929		2203	4300	6503	SO:0001819	synonymous_variant	4829	exon2			CACCGCTTCGGGA		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.534A>G	6.37:g.142399929T>C		145	0	0		176	37	0.210227	NM_002511	E9KL38|Q5VUK8	Silent	SNP	ENST00000258042.1	37	CCDS5196.1																																																																																			.	.	none		0.512	NMBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042479.1			C	142399929	T	C	142399929	2	2	1	1	0	0	0	0	0	0	0	1	10496	1606	56	3		3	NMBR	6	142399929	Silent	SNP	T	TCGA-FA-8693-01A-11D-2397-10	7904271	142399929	28715138	71	71											
RNF216	54476	hgsc.bcm.edu	37	chr7	5662542	5662542	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcatgggcaggttgtgctcCaggggcatgtggatgggacc	6	9	18	8	0	0	0	0	0	0	0	1	2	1	2	2	6	2	5	2	6	0	1			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr7:5662542C>T	ENST00000425013.2	-	17	2774	c.2550G>A	c.(2548-2550)ctG>ctA	p.L850L	RNF216_ENST00000389902.3_Silent_p.L907L|RNF216_ENST00000469375.1_5'Flank	NM_207111.3|NM_207116.2	NP_996994.1|NP_996999.1	Q9NWF9	RN216_HUMAN	ring finger protein 216	850	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)		GGTTGTGCTCCAGGGGCATGT	0.617																																					p.L907L		Atlas-SNP	.											.	RNF216	71	.	0			c.G2721A						PASS	.						108	118	114					7																	5662542		2203	4300	6503	SO:0001819	synonymous_variant	54476	exon17			GTGCTCCAGGGGC	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.2550G>A	7.37:g.5662542C>T		47	0	0		51	8	0.156863	NM_207111	Q6Y691|Q75ML7|Q7Z2H7|Q7Z7C1|Q8NHW7|Q9NYT1	Silent	SNP	ENST00000425013.2	37	CCDS34595.1																																																																																			.	.	none		0.617	RNF216-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000340374.1	NM_207111		T	5662542	C	T	5662542	2	4	1	1	0	0	0	0	0	0	0	1	13495	581	21	2		2	RNF216	7	5662542	Silent	SNP	C	TCGA-FA-8693-01A-11D-2397-10		5662542	153476121	72	72											
DTX2	113878	hgsc.bcm.edu	37	chr7	76132841	76132841	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtattacggttccagatgtcGctccccggccacgaggactg	7	9	12	13	4	0	1	0	0	0	1	3	3	2	2	4	3	1	3	4	3	2	3			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr7:76132841G>A	ENST00000324432.5	+	10	1998	c.1488G>A	c.(1486-1488)tcG>tcA	p.S496S	DTX2_ENST00000307569.8_Silent_p.S449S|DTX2_ENST00000446820.2_Silent_p.S449S|DTX2_ENST00000413936.2_Silent_p.S496S|DTX2_ENST00000446600.1_Silent_p.S405S|DTX2_ENST00000430490.2_Silent_p.S496S	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	496					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						TCCAGATGTCGCTCCCCGGCC	0.577																																					p.S496S		Atlas-SNP	.											.	DTX2	64	.	0			c.G1488A						PASS	.						68	61	63					7																	76132841		2199	4293	6492	SO:0001819	synonymous_variant	113878	exon9			GATGTCGCTCCCC		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.1488G>A	7.37:g.76132841G>A		203	0	0		219	51	0.232877	NM_001102594	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Silent	SNP	ENST00000324432.5	37	CCDS5587.1																																																																																			.	.	none		0.577	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2			A	76132841	G	A	76132841	2	1	1	1	0	0	0	0	0	0	0	1	4796	1074	38	1		1	DTX2	7	76132841	Silent	SNP	G	TCGA-FA-8693-01A-11D-2397-10	70470299	76132841	83005822	73	73											
MAGI2	9863	hgsc.bcm.edu	37	chr7	78636484	78636484	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaacccttttgaaatcgtaAgttgaggtagtgacgaaggt	13	11	12	5	2	0	4	0	3	0	1	1	5	0	4	1	2	1	3	1	2	5	5			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr7:78636484A>C	ENST00000354212.4	-	2	593	c.340T>G	c.(340-342)Tta>Gta	p.L114V	MAGI2_ENST00000419488.1_Missense_Mutation_p.L114V|MAGI2_ENST00000522391.1_Missense_Mutation_p.L114V|MAGI2-AS2_ENST00000411616.1_RNA	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	114	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				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)	p.L114V(1)		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)				TGAAATCGTAAGTTGAGGTAG	0.388																																					p.L114V		Atlas-SNP	.											MAGI2,caecum,carcinoma,0,1	MAGI2	246	1	1	Substitution - Missense(1)	large_intestine(1)	c.T340G						PASS	.						147	126	133					7																	78636484		2203	4300	6503	SO:0001583	missense	9863	exon2			ATCGTAAGTTGAG	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.340T>G	7.37:g.78636484A>C	ENSP00000346151:p.Leu114Val	107	0	0		148	22	0.148649	NM_012301	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Missense_Mutation	SNP	ENST00000354212.4	37	CCDS5594.1	.	.	.	.	.	.	.	.	.	.	A	20.5	3.994850	0.74703	.	.	ENSG00000187391	ENST00000419488;ENST00000354212;ENST00000536298;ENST00000522391	T;T;T	0.11277	2.89;2.89;2.79	5.29	4.1	0.47936	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (1);	.	.	.	.	T	0.23492	0.0568	L	0.52573	1.65	0.80722	D	1	D;D	0.89917	1.0;0.996	D;P	0.91635	0.999;0.82	T	0.00647	-1.1628	9	0.35671	T	0.21	.	9.4432	0.38681	0.8477:0.0:0.1523:0.0	.	114;114	Q86UL8-2;Q86UL8	.;MAGI2_HUMAN	V	114	ENSP00000405766:L114V;ENSP00000346151:L114V;ENSP00000428389:L114V	ENSP00000346151:L114V	L	-	1	2	MAGI2	78474420	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.746000	0.55127	0.802000	0.34089	0.519000	0.50382	TTA	.	.	none		0.388	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		C	78636484	A	C	78636484	3	2	1	1	0	0	0	0	1	0	0	0	9200	69	3	5	4111	5	MAGI2	7	78636484	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10	2503643	78636484	80502179	74	74											
GNAT3	346562	hgsc.bcm.edu	37	chr7	80117974	80117974	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgcattcttgctcactgtaAccattcttatggatgatcct	9	16	6	10	0	3	1	1	1	2	0	4	2	4	2	2	1	3	3	2	1	2	5			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr7:80117974A>C	ENST00000398291.3	-	3	273	c.180T>G	c.(178-180)ggT>ggG	p.G60G	CD36_ENST00000435819.1_Intron	NM_001102386.1	NP_001095856.1	A8MTJ3	GNAT3_HUMAN	guanine nucleotide binding protein, alpha transducing 3	60					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						GCTCACTGTAACCATTCTTAT	0.343																																					p.G60G		Atlas-SNP	.											.	GNAT3	65	.	0			c.T180G						PASS	.						119	100	106					7																	80117974		1847	4095	5942	SO:0001819	synonymous_variant	346562	exon3			ACTGTAACCATTC		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.180T>G	7.37:g.80117974A>C		113	0	0		143	26	0.181818	NM_001102386	A4D1B2|A4D1B3|B9EJG5	Silent	SNP	ENST00000398291.3	37	CCDS47625.1																																																																																			.	.	none		0.343	GNAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339909.3	XM_294370		C	80117974	A	C	80117974	2	2	1	1	0	0	0	0	0	0	0	1	6521	30	2	5		5	GNAT3	7	80117974	Silent	SNP	A	TCGA-FA-8693-01A-11D-2397-10	1481490	80117974	79020689	75	75											
ABCB1	5243	hgsc.bcm.edu	37	chr7	87195445	87195445	+	Frame_Shift_Del	DEL	T	T	-																															gatggccaaaatcacaagggTtagcttccaaccacgtgtaa																										TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr7:87195445delT	ENST00000265724.3	-	8	1060	c.643delA	c.(643-645)accfs	p.T215fs	ABCB1_ENST00000543898.1_Frame_Shift_Del_p.T151fs	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	215	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)	ATCACAAGGGTTAGCTTCCAA	0.428																																					p.T215fs		Pindel,Atlas-Indel	.											.	ABCB1	263	.	0			c.644delC						PASS	.						150	134	139					7																	87195445		2203	4300	6503	SO:0001589	frameshift_variant	5243	exon8			.	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.643delA	7.37:g.87195445delT	ENSP00000265724:p.Thr215fs	144	0	.		198	33	0.167	NM_000927	A8K294|B5AK60|Q12755|Q14812	Frame_Shift_Del	DEL	ENST00000265724.3	37	CCDS5608.1																																																																																			.	.	none		0.428	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927		-	87195445	T	-	87195445	7	5	1	1	0	1	0	1	0	0	0	0	40	1725	60	0	3287	0	ABCB1	7	87195445	Frame_Shift_Del	DEL	T	TCGA-FA-8693-01A-11D-2397-10	7077471	87195445	71943218	76	76											
CTTNBP2	83992	hgsc.bcm.edu	37	chr7	117368154	117368154	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggcacttacttcactgtcacTtgggcatgcccaggaactac	9	10	9	13	0	2	0	2	0	0	0	2	1	2	1	1	3	4	2	1	3	3	4			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr7:117368154T>C	ENST00000160373.3	-	17	4135	c.4044A>G	c.(4042-4044)caA>caG	p.Q1348Q		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1348					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)		TCACTGTCACTTGGGCATGCC	0.498																																					p.Q1348Q		Atlas-SNP	.											.	CTTNBP2	200	.	0			c.A4044G						PASS	.						78	83	82					7																	117368154		2203	4300	6503	SO:0001819	synonymous_variant	83992	exon17			TGTCACTTGGGCA		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.4044A>G	7.37:g.117368154T>C		182	0	0		177	33	0.186441	NM_033427	O43389|Q7LG11|Q9C0A5	Silent	SNP	ENST00000160373.3	37	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	T	8.983	0.975850	0.18736	.	.	ENSG00000077063	ENST00000446636	.	.	.	5.43	0.0764	0.14403	.	.	.	.	.	T	0.44623	0.1302	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.28554	-1.0040	4	.	.	.	3.8122	4.251	0.10695	0.2507:0.22:0.0:0.5293	.	.	.	.	G	836	.	.	S	-	1	0	CTTNBP2	117155390	0.004000	0.15560	0.997000	0.53966	0.975000	0.68041	-0.307000	0.08167	0.414000	0.25790	0.528000	0.53228	AGT	.	.	none		0.498	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		C	117368154	T	C	117368154	2	2	1	1	0	0	0	0	0	0	0	1	4047	1606	56	3		3	CTTNBP2	7	117368154	Silent	SNP	T	TCGA-FA-8693-01A-11D-2397-10	30172709	117368154	41770509	77	77											
BRAF	673	hgsc.bcm.edu	37	chr7	140453134	140453134	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacccactccatcgagattTcactgtagctagaccaaaat	13	9	7	12	1	1	2	1	0	0	2	3	4	2	3	3	1	1	2	3	1	4	3	rs397516897|rs121913364|rs121913226|rs121913377		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr7:140453134T>C	ENST00000288602.6	-	15	1861	c.1801A>G	c.(1801-1803)Aaa>Gaa	p.K601E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	601	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		K -> E (in CRC). {ECO:0000269|PubMed:12198537}.|K -> Q (in CFC1). {ECO:0000269|PubMed:19206169}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|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 stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.K601E(40)|p.V600_K601>E(12)|p.T599_R603>I(2)|p.K601del(1)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	CATCGAGATTTCACTGTAGCT	0.368		61	"Mis, T, O"	"AKAP9, KIAA1549"	"melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												p.K601E	Colon(40;35 892 2973 5743 27438)	Atlas-SNP	.		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	BRAF,NS,malignant_melanoma,0,81	BRAF	36346	81	58	Substitution - Missense(40)|Complex - deletion inframe(17)|Deletion - In frame(1)	thyroid(30)|skin(15)|large_intestine(5)|ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|endometrium(1)|lung(1)|NS(1)	c.A1801G						PASS	.						111	103	106					7																	140453134		2203	4300	6503	SO:0001583	missense	673	exon15	Familial Cancer Database	CFC, CFCS	GAGATTTCACTGT	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1801A>G	7.37:g.140453134T>C	ENSP00000288602:p.Lys601Glu	87	0	0		115	19	0.165217	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.8|23.8	4.454487|4.454487	0.84209|0.84209	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.82711|.	-1.64|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.54464|.	0.1860|.	N|N	0.25380|0.25380	0.74|0.74	0.80722|0.80722	D|D	1|1	P|.	0.42584|.	0.784|.	P|.	0.49922|.	0.626|.	T|.	0.51108|.	-0.8747|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	601|.	P15056|.	BRAF_HUMAN|.	E|W	601|208	ENSP00000288602:K601E|.	ENSP00000288602:K601E|.	K|X	-|-	1|3	0|0	BRAF|BRAF	140099603|140099603	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.921000|7.921000	0.87530|0.87530	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	AAA|TGA	.	.	weak		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		C	140453134	T	C	140453134	3	2	1	1	0	0	0	0	1	0	0	0	1498	1792	62	3	515	3	BRAF	7	140453134	Missense_Mutation	SNP	T	TCGA-FA-8693-01A-11D-2397-10	23084980	140453134	18685529	78	78											
SLC18A1	6570	hgsc.bcm.edu	37	chr8	20031913	20031913	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atccaatgccttgaagggttCgggccacaaagagtagagta	13	8	12	8	1	0	3	0	1	0	2	2	3	1	3	3	2	1	3	3	2	5	4			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr8:20031913C>T	ENST00000276373.5	-	5	856	c.590G>A	c.(589-591)cGa>cAa	p.R197Q	SLC18A1_ENST00000437980.1_Missense_Mutation_p.R197Q|SLC18A1_ENST00000524272.1_5'UTR|SLC18A1_ENST00000381608.4_Missense_Mutation_p.R197Q|SLC18A1_ENST00000440926.1_Missense_Mutation_p.R197Q|SLC18A1_ENST00000265808.7_Missense_Mutation_p.R197Q|SLC18A1_ENST00000519026.1_Missense_Mutation_p.R197Q	NM_003053.3	NP_003044.1	P54219	VMAT1_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 1	197					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)	TTGAAGGGTTCGGGCCACAAA	0.468																																					p.R197Q		Atlas-SNP	.											SLC18A1,NS,carcinoma,-1,1	SLC18A1	68	1	0			c.G590A						PASS	.						159	137	145					8																	20031913		2203	4300	6503	SO:0001583	missense	6570	exon6			AGGGTTCGGGCCA		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.590G>A	8.37:g.20031913C>T	ENSP00000276373:p.Arg197Gln	144	0	0		139	24	0.172662	NM_001142324	E9PDJ5|Q9BRE4	Missense_Mutation	SNP	ENST00000276373.5	37	CCDS6013.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.107635	0.77096	.	.	ENSG00000036565	ENST00000265808;ENST00000276373;ENST00000440926;ENST00000437980;ENST00000519026;ENST00000381608	T;T;T;T;T;T	0.70164	-0.46;-0.46;-0.46;-0.46;-0.46;-0.46	5.6	4.73	0.59995	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.054237	0.85682	N	0.000000	D	0.85974	0.5822	H	0.94345	3.525	0.58432	D	0.999995	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.89609	0.3840	10	0.87932	D	0	-8.6207	13.4319	0.61059	0.0:0.9232:0.0:0.0768	.	197;197;197	E9PB33;E9PDJ5;P54219	.;.;VMAT1_HUMAN	Q	197	ENSP00000265808:R197Q;ENSP00000276373:R197Q;ENSP00000387549:R197Q;ENSP00000413361:R197Q;ENSP00000429664:R197Q;ENSP00000371021:R197Q	ENSP00000265808:R197Q	R	-	2	0	SLC18A1	20076193	0.965000	0.33210	0.695000	0.30226	0.332000	0.28634	5.733000	0.68571	1.487000	0.48415	0.655000	0.94253	CGA	.	.	none		0.468	SLC18A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214106.1			T	20031913	C	T	20031913	3	4	1	1	0	0	0	0	1	0	0	0	14440	884	31	1	1035	1	SLC18A1	8	20031913	Missense_Mutation	SNP	C	TCGA-FA-8693-01A-11D-2397-10		20031913	126332109	79	79											
DOCK5	80005	hgsc.bcm.edu	37	chr8	25198452	25198452	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcaattcgccagttatttcTtgctttcaatatgctgatgg	8	18	7	8	1	3	1	2	1	1	0	4	1	3	1	1	1	2	3	1	1	4	7			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr8:25198452T>C	ENST00000276440.7	+	23	2431	c.2387T>C	c.(2386-2388)cTt>cCt	p.L796P		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	796					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)		CAGTTATTTCTTGCTTTCAAT	0.423																																					p.L796P	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											.	DOCK5	167	.	0			c.T2387C						PASS	.						85	81	82					8																	25198452		2203	4300	6503	SO:0001583	missense	80005	exon23			TATTTCTTGCTTT		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.2387T>C	8.37:g.25198452T>C	ENSP00000276440:p.Leu796Pro	77	0	0		87	13	0.149425	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Missense_Mutation	SNP	ENST00000276440.7	37	CCDS6047.1	.	.	.	.	.	.	.	.	.	.	T	11.20	1.567446	0.28003	.	.	ENSG00000147459	ENST00000276440	T	0.27890	1.64	4.99	4.99	0.66335	Armadillo-type fold (1);	0.222771	0.39210	N	0.001427	T	0.28665	0.0710	L	0.40543	1.245	0.80722	D	1	B;B;B	0.30664	0.186;0.289;0.186	B;B;B	0.33339	0.162;0.162;0.162	T	0.05954	-1.0854	10	0.36615	T	0.2	.	14.8781	0.70510	0.0:0.0:0.0:1.0	.	786;571;796	D3DSS6;Q68DL4;Q9H7D0	.;.;DOCK5_HUMAN	P	796	ENSP00000276440:L796P	ENSP00000276440:L796P	L	+	2	0	DOCK5	25254369	1.000000	0.71417	0.892000	0.35008	0.266000	0.26442	7.525000	0.81892	2.095000	0.63458	0.528000	0.53228	CTT	.	.	none		0.423	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940		C	25198452	T	C	25198452	3	2	1	1	0	0	0	0	1	0	0	0	4692	1609	56	3	2477	3	DOCK5	8	25198452	Missense_Mutation	SNP	T	TCGA-FA-8693-01A-11D-2397-10	5166539	25198452	121165570	80	80											
LYN	4067	hgsc.bcm.edu	37	chr8	56910951	56910951	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcggaagaactacattcaccGggacctgcgagcagctaatg	12	6	12	11	3	1	1	1	0	0	1	1	4	1	3	2	2	5	2	2	2	4	3			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr8:56910951G>A	ENST00000519728.1	+	11	1393	c.1097G>A	c.(1096-1098)cGg>cAg	p.R366Q	LYN_ENST00000520220.2_Missense_Mutation_p.R345Q|LYN_ENST00000420292.1_3'UTR	NM_002350.3	NP_002341.1	P07948	LYN_HUMAN	LYN proto-oncogene, Src family tyrosine kinase	366	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to extracellular stimulus (GO:0031668)|cellular response to heat (GO:0034605)|cellular response to retinoic acid (GO:0071300)|cytokine secretion (GO:0050663)|dendritic cell differentiation (GO:0097028)|erythrocyte differentiation (GO:0030218)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|Fc receptor mediated stimulatory signaling pathway (GO:0002431)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|histamine secretion by mast cell (GO:0002553)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|leukocyte migration (GO:0050900)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of immune response (GO:0050777)|negative regulation of intracellular signal transduction (GO:1902532)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mast cell proliferation (GO:0070667)|negative regulation of myeloid leukocyte differentiation (GO:0002762)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|neuron projection development (GO:0031175)|oligodendrocyte development (GO:0014003)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of B cell receptor signaling pathway (GO:0050861)|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 dendritic cell apoptotic process (GO:2000670)|positive regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060369)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oligodendrocyte progenitor proliferation (GO:0070447)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of stress-activated protein kinase signaling cascade (GO:0070304)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of B cell apoptotic process (GO:0002902)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cytokine production (GO:0001817)|regulation of cytokine secretion (GO:0050707)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of erythrocyte differentiation (GO:0045646)|regulation of inflammatory response (GO:0050727)|regulation of mast cell activation (GO:0033003)|regulation of mast cell degranulation (GO:0043304)|regulation of monocyte chemotaxis (GO:0090025)|regulation of platelet aggregation (GO:0090330)|regulation of protein phosphorylation (GO:0001932)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to amino acid (GO:0043200)|response to axon injury (GO:0048678)|response to carbohydrate (GO:0009743)|response to drug (GO:0042493)|response to hormone (GO:0009725)|response to insulin (GO:0032868)|response to organic cyclic compound (GO:0014070)|response to sterol depletion (GO:0006991)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|T cell costimulation (GO:0031295)|tolerance induction to self antigen (GO:0002513)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integrin alpha2-beta1 complex (GO:0034666)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|mitochondrial crista (GO:0030061)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycosphingolipid binding (GO:0043208)|ion channel binding (GO:0044325)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22		all_lung(136;0.0555)|Lung NSC(129;0.0726)|all_epithelial(80;0.0772)	Epithelial(17;0.000834)|all cancers(17;0.00598)		Bosutinib(DB06616)|Ponatinib(DB08901)	TACATTCACCGGGACCTGCGA	0.448																																					p.R366Q		Atlas-SNP	.											.	LYN	54	.	0			c.G1097A						PASS	.						115	110	112					8																	56910951		2203	4300	6503	SO:0001583	missense	4067	exon11			TTCACCGGGACCT	M16038	CCDS6162.1, CCDS47859.1	8q13	2014-06-25	2014-06-25		ENSG00000254087	ENSG00000254087		"SH2 domain containing"	6735	protein-coding gene	gene with protein product		165120	"v-yes-1 Yamaguchi sarcoma viral related oncogene homolog"			3561390	Standard	NM_002350		Approved	JTK8	uc003xsk.4	P07948	OTTHUMG00000044345	ENST00000519728.1:c.1097G>A	8.37:g.56910951G>A	ENSP00000428924:p.Arg366Gln	227	0	0		287	73	0.254355	NM_002350	A0AVQ5	Missense_Mutation	SNP	ENST00000519728.1	37	CCDS6162.1	.	.	.	.	.	.	.	.	.	.	G	36	5.851905	0.97023	.	.	ENSG00000254087	ENST00000519728;ENST00000520220	D;D	0.88354	-2.37;-2.37	5.52	5.52	0.82312	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	0.97099	0.9052	H	0.98507	4.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.99	D	0.98468	1.0599	10	0.87932	D	0	.	19.4505	0.94865	0.0:0.0:1.0:0.0	.	436;366	Q6NUK7;P07948	.;LYN_HUMAN	Q	366;345	ENSP00000428924:R366Q;ENSP00000428424:R345Q	ENSP00000428924:R366Q	R	+	2	0	LYN	57073505	1.000000	0.71417	0.688000	0.30117	0.945000	0.59286	9.869000	0.99810	2.597000	0.87782	0.655000	0.94253	CGG	.	.	none		0.448	LYN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378155.1	NM_002350		A	56910951	G	A	56910951	3	1	1	1	0	0	0	0	1	0	0	0	9116	1116	39	1	1135	1	LYN	8	56910951	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	31712499	56910951	89453071	81	81											
PENK	5179	hgsc.bcm.edu	37	chr8	57354094	57354094	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cccatatctcttgctcacttCttcctcattatcactgccat	7	16	2	16	0	5	0	3	0	2	0	7	0	6	0	3	0	2	1	3	0	2	5			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr8:57354094C>T	ENST00000314922.3	-	2	617	c.541G>A	c.(541-543)Gaa>Aaa	p.E181K	PENK_ENST00000451791.2_Missense_Mutation_p.E181K|PENK_ENST00000523274.1_5'UTR	NM_006211.3	NP_006202.1	P01210	PENK_HUMAN	proenkephalin	181					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)	p.E181K(1)		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)			TTGCTCACTTCTTCCTCATTA	0.522																																					p.E181K		Atlas-SNP	.											PENK,NS,carcinoma,0,1	PENK	59	1	1	Substitution - Missense(1)	lung(1)	c.G541A						PASS	.						136	140	138					8																	57354094		2203	4300	6503	SO:0001583	missense	5179	exon4			TCACTTCTTCCTC		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.541G>A	8.37:g.57354094C>T	ENSP00000324248:p.Glu181Lys	104	0	0		116	20	0.172414	NM_001135690	B2RC23|Q6FHC6|Q6FHE6	Missense_Mutation	SNP	ENST00000314922.3	37	CCDS6168.1	.	.	.	.	.	.	.	.	.	.	C	18.30	3.593512	0.66219	.	.	ENSG00000181195	ENST00000539312;ENST00000314922;ENST00000451791	T;T	0.17691	2.26;2.26	5.81	4.92	0.64577	.	0.472244	0.22308	N	0.061779	T	0.19967	0.0480	L	0.55990	1.75	0.80722	D	1	P	0.42078	0.77	B	0.38803	0.282	T	0.01630	-1.1308	10	0.41790	T	0.15	-3.0444	15.9707	0.80013	0.0:0.8651:0.1349:0.0	.	181	P01210	PENK_HUMAN	K	181	ENSP00000324248:E181K;ENSP00000400894:E181K	ENSP00000324248:E181K	E	-	1	0	PENK	57516648	0.997000	0.39634	0.064000	0.19789	0.904000	0.53231	7.035000	0.76517	1.429000	0.47314	0.655000	0.94253	GAA	.	.	none		0.522	PENK-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378645.1			T	57354094	C	T	57354094	3	4	1	1	0	0	0	0	1	0	0	0	11736	922	32	2	266	2	PENK	8	57354094	Missense_Mutation	SNP	C	TCGA-FA-8693-01A-11D-2397-10	443143	57354094	89009928	82	82											
CD274	29126	hgsc.bcm.edu	37	chr9	5457196	5457196	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggctgcactaattgtctattGggaaatggaggataagaaca	14	10	12	5	0	1	1	0	0	1	1	1	4	1	4	0	4	2	2	0	4	5	5			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr9:5457196G>A	ENST00000381577.3	+	3	256	c.170G>A	c.(169-171)tGg>tAg	p.W57*	CD274_ENST00000498261.1_3'UTR|CD274_ENST00000381573.4_Intron	NM_014143.3	NP_054862.1	Q9NZQ7	PD1L1_HUMAN	CD274 molecule	57	Ig-like V-type.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-10 secretion (GO:2001181)|positive regulation of T cell proliferation (GO:0042102)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)	11	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000742)|Lung(218;0.111)		ATTGTCTATTGGGAAATGGAG	0.428			T	CIITA	"PMBL, Hodgkin Lymphona, "																																p.W57X		Atlas-SNP	.		Dom	yes		9	9p24	29126	CD274 molecule		L	CD274,spleen,lymphoid_neoplasm,-1,1	CD274	26	1	0			c.G170A						PASS	.						94	94	94					9																	5457196		2203	4300	6503	SO:0001587	stop_gained	29126	exon3			TCTATTGGGAAAT	AF177937	CCDS6464.1, CCDS59118.1	9p24.1	2014-01-30	2006-03-28	2005-02-25	ENSG00000120217	ENSG00000120217		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Endogenous ligands"	17635	protein-coding gene	gene with protein product	"B7 homolog 1"	605402	"programmed cell death 1 ligand 1", "CD274 antigen"	PDCD1LG1		11015443, 10581077	Standard	NM_014143		Approved	B7-H, B7H1, PD-L1, PDL1, B7-H1	uc003zje.3	Q9NZQ7	OTTHUMG00000019503	ENST00000381577.3:c.170G>A	9.37:g.5457196G>A	ENSP00000370989:p.Trp57*	93	0	0		130	20	0.153846	NM_014143	B2RBA2|B4DU27|Q14CJ2|Q2V8D5|Q66RK1|Q6WEX4|Q9NUZ5	Nonsense_Mutation	SNP	ENST00000381577.3	37	CCDS6464.1	.	.	.	.	.	.	.	.	.	.	G	37	6.439266	0.97568	.	.	ENSG00000120217	ENST00000381577	.	.	.	5.87	5.87	0.94306	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	-5.8249	18.3892	0.90477	0.0:0.0:1.0:0.0	.	.	.	.	X	57	.	ENSP00000370989:W57X	W	+	2	0	CD274	5447196	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	6.301000	0.72782	2.791000	0.96007	0.655000	0.94253	TGG	.	.	none		0.428	CD274-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051631.2	NM_014143		A	5457196	G	A	5457196	4	1	1	1	0	0	0	0	0	1	0	0	2993	1357	47	2	176	2	CD274	9	5457196	Nonsense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10		5457196	135756235	83	83											
FREM1	158326	hgsc.bcm.edu	37	chr9	14859353	14859353	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgagcagatttttatcaatCgcttgggacaagccattgaa	12	12	9	8	1	1	3	1	2	0	1	2	4	1	4	1	1	2	2	1	1	4	5	rs562673690	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr9:14859353C>T	ENST00000380880.3	-	4	1242	c.459G>A	c.(457-459)gcG>gcA	p.A153A	FREM1_ENST00000422223.2_Silent_p.A153A|FREM1_ENST00000380881.4_Silent_p.A153A			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	153					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)		TTTTATCAATCGCTTGGGACA	0.488																																					p.A153A		Atlas-SNP	.											.	FREM1	261	.	0			c.G459A						PASS	.						132	130	131					9																	14859353		1898	4126	6024	SO:0001819	synonymous_variant	158326	exon5			ATCAATCGCTTGG	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.459G>A	9.37:g.14859353C>T		125	0	0		130	25	0.192308	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	37	CCDS47952.1																																																																																			.	.	none		0.488	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		T	14859353	C	T	14859353	2	4	1	1	0	0	0	0	0	0	0	1	6052	871	31	1		1	FREM1	9	14859353	Silent	SNP	C	TCGA-FA-8693-01A-11D-2397-10	9402157	14859353	126354078	84	84											
BNC2	54796	hgsc.bcm.edu	37	chr9	16436374	16436375	+	Frame_Shift_Ins	INS	-	-	G																															ctactggctcagagggtggcINSggggggtgctgctctatggt																								rs116528562|rs142872531	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr9:16436374_16436375insG	ENST00000380672.4	-	6	1874_1875	c.1817_1818insC	c.(1816-1818)ccgfs	p.P606fs	BNC2_ENST00000380666.2_Frame_Shift_Ins_p.P606fs|BNC2_ENST00000380667.2_Frame_Shift_Ins_p.P539fs|BNC2_ENST00000545497.1_Frame_Shift_Ins_p.P511fs	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)		CAGAGGGTGGCGGGGGGTGCTG	0.564																																					p.P606fs		Pindel,Atlas-Indel	.											.	BNC2	166	.	0			c.1818_1819insC						PASS	.																																			SO:0001589	frameshift_variant	54796	exon6			.	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.1818dupC	9.37:g.16436380_16436380dupG	ENSP00000370047:p.Pro606fs	99	0	.		96	17	0.177	NM_017637		Frame_Shift_Ins	INS	ENST00000380672.4	37	CCDS6482.2																																																																																			.	.	none		0.564	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637		G	16436375	-	G	16436374	7	5	1	1	0	1	1	0	0	0	0	0	1475	755	27	0	1489	0	BNC2	9	16436374	Frame_Shift_Ins	INS	-	TCGA-FA-8693-01A-11D-2397-10	1577021	16436374	124777057	85	85											
C9orf79	286234	hgsc.bcm.edu	37	chr9	90499849	90499849	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacctgaggaagctcgctggCgaaggcagctcccacctgcc	8	5	12	16	2	0	1	0	1	0	0	2	3	1	2	4	3	3	4	4	3	2	0	rs148586576		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr9:90499849C>T	ENST00000325643.5	+	4	513	c.447C>T	c.(445-447)ggC>ggT	p.G149G		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	149					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.G149G(1)									AGCTCGCTGGCGAAGGCAGCT	0.657																																					p.G149G		Atlas-SNP	.											C9orf79,colon,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C447T						PASS	.	C		7,4399		0,7,2196	28	29	29		447	-1	0	9	dbSNP_134	29	1,8597		0,1,4298	no	coding-synonymous	C9orf79	NM_178828.4		0,8,6494	TT,TC,CC		0.0116,0.1589,0.0615		149/1446	90499849	8,12996	2203	4299	6502	SO:0001819	synonymous_variant	286234	exon4			CGCTGGCGAAGGC	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.447C>T	9.37:g.90499849C>T		86	0	0		71	8	0.112676	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Silent	SNP	ENST00000325643.5	37	CCDS6676.1																																																																																			C|1.000;T|0.000	0.000	weak		0.657	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828		T	90499849	C	T	90499849	2	4	1	1	0	0	0	0	0	0	0	1	2499	755	27	1		1	C9orf79	9	90499849	Silent	SNP	C	TCGA-FA-8693-01A-11D-2397-10	74063475	90499849	50713582	86	86											
FCN2	2220	hgsc.bcm.edu	37	chr9	137779176	137779176	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctcagggggactcatggcaGctttgcaaatggcatcaact	10	9	11	11	0	3	0	3	0	0	0	3	1	3	1	1	4	3	4	1	4	2	1			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr9:137779176G>A	ENST00000291744.6	+	8	867	c.857G>A	c.(856-858)aGc>aAc	p.S286N	FCN2_ENST00000350339.2_Missense_Mutation_p.S248N	NM_004108.2	NP_004099.2	Q15485	FCN2_HUMAN	ficolin (collagen/fibrinogen domain containing lectin) 2	286	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|opsonization (GO:0008228)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	20		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.58e-08)|Epithelial(140;6.41e-08)|all cancers(34;3.96e-07)		ACTCATGGCAGCTTTGCAAAT	0.512																																					p.S286N		Atlas-SNP	.											.	FCN2	55	.	0			c.G857A						PASS	.						85	83	83					9																	137779176		2203	4300	6503	SO:0001583	missense	2220	exon8			ATGGCAGCTTTGC	D49353	CCDS6983.1	9q34	2013-09-12	2013-09-12		ENSG00000160339	ENSG00000160339		"Fibrinogen C domain containing"	3624	protein-coding gene	gene with protein product	"hucolin", "collagen/fibrinogen domain-containing protein 2", "ficolin B", "serum lectin p35", "L-ficolin"	601624	"ficolin (collagen/fibrinogen domain-containing lectin) 2 (hucolin)"			8884275	Standard	XM_006717015		Approved	P35, FCNL, EBP-37, ficolin-2	uc004cfg.1	Q15485	OTTHUMG00000020892	ENST00000291744.6:c.857G>A	9.37:g.137779176G>A	ENSP00000291744:p.Ser286Asn	149	0	0		164	19	0.115854	NM_004108	A6NFG7|A8K478|Q6IS69|Q7M4P4|Q9UC57	Missense_Mutation	SNP	ENST00000291744.6	37	CCDS6983.1	.	.	.	.	.	.	.	.	.	.	G	16.19	3.052816	0.55218	.	.	ENSG00000160339	ENST00000350339;ENST00000291744	T;T	0.21361	2.01;2.01	4.05	4.05	0.47172	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2 (1);	0.000000	0.50627	D	0.000110	T	0.26304	0.0642	M	0.66297	2.02	0.22796	N	0.998726	B;B	0.29835	0.258;0.144	B;B	0.32724	0.064;0.151	T	0.19976	-1.0289	10	0.52906	T	0.07	.	13.7007	0.62606	0.0:0.0:1.0:0.0	.	248;286	Q15485-2;Q15485	.;FCN2_HUMAN	N	248;286	ENSP00000291741:S248N;ENSP00000291744:S286N	ENSP00000291744:S286N	S	+	2	0	FCN2	136918997	0.171000	0.23029	0.279000	0.24732	0.456000	0.32438	0.609000	0.24238	1.791000	0.52520	0.563000	0.77884	AGC	.	.	none		0.512	FCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054960.1	NM_004108		A	137779176	G	A	137779176	3	1	1	1	0	0	0	0	1	0	0	0	5800	971	34	2	887	2	FCN2	9	137779176	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	47279327	137779176	3434255	87	87											
SFTPD	6441	hgsc.bcm.edu	37	chr10	81702260	81702260	+	Splice_Site	SNP	C	C	T																															caccgggaggtcctggaggtCctgagcaaaagcaccagccc																										TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr10:81702260C>T	ENST00000372292.3	-	4	357	c.317G>A	c.(316-318)gGa>gAa	p.G106E		NM_003019.4	NP_003010.4	P35247	SFTPD_HUMAN	surfactant protein D	106	Collagen-like.				defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|lung alveolus development (GO:0048286)|macrophage chemotaxis (GO:0048246)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of phagocytosis (GO:0050766)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|regulation of cytokine production (GO:0001817)|respiratory gaseous exchange (GO:0007585)|surfactant homeostasis (GO:0043129)	collagen trimer (GO:0005581)|endocytic vesicle (GO:0030139)|extracellular region (GO:0005576)|lysosome (GO:0005764)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)			endometrium(1)|kidney(3)|large_intestine(5)|lung(3)|skin(4)|urinary_tract(1)	17	Breast(12;0.000615)|Prostate(51;0.0095)|all_epithelial(25;0.027)		Epithelial(14;0.0244)|all cancers(16;0.0558)|Colorectal(32;0.109)			TCCTGGAGGTCCTGAGCAAAA	0.567																																					p.G106E		Atlas-SNP	.											.	SFTPD	43	.	0			c.G317A						PASS	.						58	57	57					10																	81702260		2203	4300	6503	SO:0001630	splice_region_variant	6441	exon4			GGAGGTCCTGAGC	L05485	CCDS7362.1	10q22.2-q23.1	2012-11-02	2008-08-26		ENSG00000133661	ENSG00000133661		"Collectins"	10803	protein-coding gene	gene with protein product		178635	"surfactant, pulmonary-associated protein D"	SFTP4		1898081, 1339284	Standard	NM_003019		Approved	SP-D, COLEC7	uc001kbh.3	P35247	OTTHUMG00000018590	ENST00000372292.3:c.317-1G>A	10.37:g.81702260C>T		62	0	0		61	8	0.131148	NM_003019	Q5T0M3|Q6FH08|Q86YK9|Q8TCD8|Q9UCJ2|Q9UCJ3	Missense_Mutation	SNP	ENST00000372292.3	37	CCDS7362.1	.	.	.	.	.	.	.	.	.	.	C	15.84	2.951636	0.53186	.	.	ENSG00000133661	ENST00000372292;ENST00000444384	D;D	0.99353	-4.61;-5.77	5.02	4.1	0.47936	.	0.000000	0.56097	D	0.000031	D	0.98883	0.9622	H	0.96889	3.9	0.39145	D	0.96211	P	0.38711	0.643	B	0.34489	0.184	D	0.98750	1.0720	10	0.87932	D	0	.	9.683	0.40080	0.0:0.9007:0.0:0.0993	.	106	P35247	SFTPD_HUMAN	E	106;119	ENSP00000361366:G106E;ENSP00000394325:G119E	ENSP00000361366:G106E	G	-	2	0	SFTPD	81692240	1.000000	0.71417	0.948000	0.38648	0.427000	0.31564	2.235000	0.43044	1.068000	0.40764	0.457000	0.33378	GGA	.	.	none		0.567	SFTPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049011.1		Missense_Mutation	T	81702260	C	T	81702260	5	4	1	1	0	0	0	0	0	0	1	0	14208	869	30	2	830	2	SFTPD	10	81702260	Splice_Site	SNP	C	TCGA-FA-8693-01A-11D-2397-10		81702260	53832487	88	88	4	2									
SFTPD	6441	hgsc.bcm.edu	37	chr10	81702261	81702261	+	Splice_Site	SNP	C	C	A																															accgggaggtcctggaggtcCtgagcaaaagcaccagcccg																										TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr10:81702261C>A	ENST00000372292.3	-	4	357		c.e4-1			NM_003019.4	NP_003010.4	P35247	SFTPD_HUMAN	surfactant protein D						defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|lung alveolus development (GO:0048286)|macrophage chemotaxis (GO:0048246)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of phagocytosis (GO:0050766)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|regulation of cytokine production (GO:0001817)|respiratory gaseous exchange (GO:0007585)|surfactant homeostasis (GO:0043129)	collagen trimer (GO:0005581)|endocytic vesicle (GO:0030139)|extracellular region (GO:0005576)|lysosome (GO:0005764)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)			endometrium(1)|kidney(3)|large_intestine(5)|lung(3)|skin(4)|urinary_tract(1)	17	Breast(12;0.000615)|Prostate(51;0.0095)|all_epithelial(25;0.027)		Epithelial(14;0.0244)|all cancers(16;0.0558)|Colorectal(32;0.109)			CCTGGAGGTCCTGAGCAAAAG	0.572																																					.		Atlas-SNP	.											.	SFTPD	43	.	0			c.317-1G>T						PASS	.						57	56	56					10																	81702261		2203	4300	6503	SO:0001630	splice_region_variant	6441	exon5			GAGGTCCTGAGCA	L05485	CCDS7362.1	10q22.2-q23.1	2012-11-02	2008-08-26		ENSG00000133661	ENSG00000133661		"Collectins"	10803	protein-coding gene	gene with protein product		178635	"surfactant, pulmonary-associated protein D"	SFTP4		1898081, 1339284	Standard	NM_003019		Approved	SP-D, COLEC7	uc001kbh.3	P35247	OTTHUMG00000018590	ENST00000372292.3:c.317-1G>T	10.37:g.81702261C>A		63	0	0		61	8	0.131148	NM_003019	Q5T0M3|Q6FH08|Q86YK9|Q8TCD8|Q9UCJ2|Q9UCJ3	Splice_Site	SNP	ENST00000372292.3	37	CCDS7362.1	.	.	.	.	.	.	.	.	.	.	c	13.45	2.241591	0.39598	.	.	ENSG00000133661	ENST00000372292;ENST00000444384	.	.	.	5.02	5.02	0.67125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8133	0.63276	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SFTPD	81692241	1.000000	0.71417	0.938000	0.37757	0.374000	0.29953	4.668000	0.61568	2.311000	0.77944	0.457000	0.33378	.	.	.	none		0.572	SFTPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049011.1		Intron	A	81702261	C	A	81702261	5	1	1	1	0	0	0	0	0	0	1	0	14208	695	24	4	831	4	SFTPD	10	81702261	Splice_Site	SNP	C	TCGA-FA-8693-01A-11D-2397-10	1	81702261	53832486	89	89	4	2									
SH2D4B	387694	hgsc.bcm.edu	37	chr10	82329986	82329986	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggatcatgggagaaggcccTggtgacaagccctacgaaga	12	6	14	9	1	1	3	1	1	0	2	1	6	1	4	2	4	2	0	2	4	4	1	rs192169537		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr10:82329986T>C	ENST00000470604.2	+	2	258	c.258T>C	c.(256-258)ccT>ccC	p.P86P	SH2D4B_ENST00000339284.2_Silent_p.P87P|SH2D4B_ENST00000313455.4_Silent_p.P38P			Q5SQS7	SH24B_HUMAN	SH2 domain containing 4B	86										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(6)	13			Colorectal(32;0.229)			GAGAAGGCCCTGGTGACAAGC	0.572																																					p.P87P		Atlas-SNP	.											.	SH2D4B	44	.	0			c.T261C						PASS	.						99	97	98					10																	82329986		2203	4300	6503	SO:0001819	synonymous_variant	387694	exon2			AGGCCCTGGTGAC		CCDS7370.1, CCDS44449.1	10q23.1	2013-02-14			ENSG00000178217	ENSG00000178217		"SH2 domain containing"	31440	protein-coding gene	gene with protein product							Standard	NM_207372		Approved		uc001kck.1	Q5SQS7	OTTHUMG00000018617	ENST00000470604.2:c.258T>C	10.37:g.82329986T>C		135	0	0		127	22	0.173228	NM_207372	Q5SQS5|Q6ZVW9|Q6ZVZ3	Silent	SNP	ENST00000470604.2	37																																																																																				T|1.000;A|0.000	.	alt		0.572	SH2D4B-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_351984		C	82329986	T	C	82329986	2	2	1	1	0	0	0	0	0	0	0	1	14251	1567	55	3		3	SH2D4B	10	82329986	Silent	SNP	T	TCGA-FA-8693-01A-11D-2397-10	627725	82329986	53204761	90	90											
NRG3	10718	hgsc.bcm.edu	37	chr10	84498369	84498369	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaggagtccgttgtgatcaAtttctgccgaaaactgattc	11	12	9	9	2	2	2	1	2	1	0	4	4	3	3	2	1	2	1	2	1	4	3			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr10:84498369A>G	ENST00000404547.1	+	3	990	c.990A>G	c.(988-990)caA>caG	p.Q330Q	NRG3_ENST00000404576.2_Silent_p.Q134Q|NRG3_ENST00000556918.1_Silent_p.Q160Q|NRG3_ENST00000372142.2_Silent_p.Q109Q|NRG3_ENST00000372141.2_Silent_p.Q330Q			P56975	NRG3_HUMAN	neuregulin 3	330					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)		GTTGTGATCAATTTCTGCCGA	0.398																																					p.Q330Q		Atlas-SNP	.											.	NRG3	301	.	0			c.A990G						PASS	.						161	142	149					10																	84498369		2203	4300	6503	SO:0001819	synonymous_variant	10718	exon3			TGATCAATTTCTG	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.990A>G	10.37:g.84498369A>G		191	0	0		213	40	0.187793	NM_001165972	A4D7U1|Q0PEH2|Q5VYH3	Silent	SNP	ENST00000404547.1	37	CCDS31233.1																																																																																			.	.	none		0.398	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1	XM_166086		G	84498369	A	G	84498369	2	3	1	1	0	0	0	0	0	0	0	1	10658	98	4	3		3	NRG3	10	84498369	Silent	SNP	A	TCGA-FA-8693-01A-11D-2397-10	2168383	84498369	51036378	91	91											
PDLIM1	9124	hgsc.bcm.edu	37	chr10	96998439	96998439	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcctgagggcttgttgggaTcccctgaaatgaggaaaaca	12	9	12	8	0	0	3	0	3	0	0	2	5	2	5	3	3	1	2	3	3	3	2			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr10:96998439T>C	ENST00000329399.6	-	6	797	c.689A>G	c.(688-690)gAt>gGt	p.D230G	PDLIM1_ENST00000477757.1_5'UTR	NM_020992.2	NP_066272.1	O00151	PDLI1_HUMAN	PDZ and LIM domain 1	230					regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(5)|lung(1)|ovary(1)|skin(2)	10		Colorectal(252;0.083)		Epithelial(162;1.64e-06)|all cancers(201;3.71e-05)		CTTGTTGGGATCCCCTGAAAT	0.433																																					p.D230G		Atlas-SNP	.											.	PDLIM1	33	.	0			c.A689G						PASS	.						80	72	74					10																	96998439		2203	4300	6503	SO:0001583	missense	9124	exon6			TTGGGATCCCCTG	U90878	CCDS7441.1	10q23.1	2008-07-29	2008-07-29		ENSG00000107438	ENSG00000107438			2067	protein-coding gene	gene with protein product	"carboxyl terminal LIM domain protein 1", "elfin"	605900	"PDZ and LIM domain 1 (elfin)"	CLIM1		10861853	Standard	NM_020992		Approved	CLP-36, hCLIM1, CLP36	uc001kkh.4	O00151	OTTHUMG00000018810	ENST00000329399.6:c.689A>G	10.37:g.96998439T>C	ENSP00000360305:p.Asp230Gly	248	0	0		225	46	0.204444	NM_020992	B2RBS6|Q5VZH5|Q9BPZ9	Missense_Mutation	SNP	ENST00000329399.6	37	CCDS7441.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.399588	0.83120	.	.	ENSG00000107438	ENST00000329399	T	0.21734	1.99	5.23	5.23	0.72850	.	0.088256	0.85682	D	0.000000	T	0.37183	0.0994	M	0.68317	2.08	0.80722	D	1	D	0.61080	0.989	P	0.55749	0.783	T	0.09907	-1.0653	10	0.37606	T	0.19	-18.4018	14.2967	0.66318	0.0:0.0:0.0:1.0	.	230	O00151	PDLI1_HUMAN	G	230	ENSP00000360305:D230G	ENSP00000360305:D230G	D	-	2	0	PDLIM1	96988429	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.491000	0.81471	1.978000	0.57642	0.454000	0.30748	GAT	.	.	none		0.433	PDLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049508.1			C	96998439	T	C	96998439	3	2	1	1	0	0	0	0	1	0	0	0	11688	1435	50	3	308	3	PDLIM1	10	96998439	Missense_Mutation	SNP	T	TCGA-FA-8693-01A-11D-2397-10	12500070	96998439	38536308	92	92											
DMBT1	1755	hgsc.bcm.edu	37	chr10	124340397	124340397	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacagctccccagtcccggcCgacacccagcccaggtaggt	8	4	10	19	2	0	0	0	0	0	0	2	1	2	0	6	3	2	2	6	3	1	1			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr10:124340397C>T	ENST00000338354.3	+	11	1125	c.1019C>T	c.(1018-1020)cCg>cTg	p.P340L	DMBT1_ENST00000344338.3_Missense_Mutation_p.P340L|DMBT1_ENST00000368955.3_Missense_Mutation_p.P340L|DMBT1_ENST00000330163.4_Missense_Mutation_p.P340L|DMBT1_ENST00000368909.3_Missense_Mutation_p.P340L|DMBT1_ENST00000359586.6_Missense_Mutation_p.P208L|DMBT1_ENST00000368956.2_Missense_Mutation_p.P340L			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	340					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)				CAGTCCCGGCCGACACCCAGC	0.532																																					p.P340L	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											DMBT1_ENST00000368915,NS,carcinoma,-1,13	DMBT1	677	13	0			c.C1019T						scavenged	.						449	390	409					10																	124340397		1913	4113	6026	SO:0001583	missense	1755	exon11			CCCGGCCGACACC		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.1019C>T	10.37:g.124340397C>T	ENSP00000342210:p.Pro340Leu	726	2	0.00275482		784	158	0.201531	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	37		.	.	.	.	.	.	.	.	.	.	C	5.419	0.262446	0.10294	.	.	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956;ENST00000359586	T;T;T;T;T;T;T	0.25579	1.82;1.83;1.81;1.82;1.83;1.81;1.79	1.45	1.45	0.22620	Speract/scavenger receptor-related (1);	.	.	.	.	T	0.12008	0.0292	N	0.08118	0	0.09310	N	1	B;B;P;B;D;B	0.55800	0.11;0.036;0.704;0.001;0.973;0.293	B;B;B;B;P;B	0.45343	0.018;0.004;0.041;0.001;0.477;0.034	T	0.08106	-1.0738	9	0.11182	T	0.66	.	6.398	0.21622	0.0:1.0:0.0:0.0	.	208;340;340;340;340;340	F8WEF7;Q9UGM3-4;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;.;DMBT1_HUMAN	L	340;340;340;340;340;340;340;340;340;340;340;340;340;208	ENSP00000342210:P340L;ENSP00000343175:P340L;ENSP00000327747:P340L;ENSP00000357905:P340L;ENSP00000357951:P340L;ENSP00000357952:P340L;ENSP00000352593:P208L	ENSP00000331522:P340L	P	+	2	0	DMBT1	124330387	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	0.841000	0.27613	1.165000	0.42670	0.194000	0.17425	CCG	.	.	none		0.532	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		T	124340397	C	T	124340397	3	4	1	1	0	0	0	0	1	0	0	0	4579	652	23	1	1061	1	DMBT1	10	124340397	Missense_Mutation	SNP	C	TCGA-FA-8693-01A-11D-2397-10	27341958	124340397	11194350	93	93											
DOCK1	1793	hgsc.bcm.edu	37	chr10	128807004	128807004	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttttgtctccagtgatggatGtaacagatataataaatgga	14	14	9	4	0	1	2	0	1	1	1	2	4	1	4	1	2	1	1	1	2	5	6			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr10:128807004G>A	ENST00000280333.6	+	11	1103	c.994G>A	c.(994-996)Gta>Ata	p.V332I	RP11-223P11.3_ENST00000595456.1_RNA|RP11-223P11.3_ENST00000601242.1_RNA|RP11-223P11.3_ENST00000601826.1_RNA|RP11-223P11.3_ENST00000594614.1_RNA|RP11-223P11.3_ENST00000594559.1_RNA	NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	332					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)		AGTGATGGATGTAACAGATAT	0.353																																					p.V332I		Atlas-SNP	.											.	DOCK1	188	.	0			c.G994A						PASS	.						77	76	76					10																	128807004		1953	4194	6147	SO:0001583	missense	1793	exon11			ATGGATGTAACAG	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.994G>A	10.37:g.128807004G>A	ENSP00000280333:p.Val332Ile	141	0	0		107	14	0.130841	NM_001380	A9Z1Z5	Missense_Mutation	SNP	ENST00000280333.6	37		.	.	.	.	.	.	.	.	.	.	G	7.557	0.663827	0.14710	.	.	ENSG00000150760	ENST00000280333	T	0.16457	2.34	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.04363	0.0120	N	0.00280	-1.71	0.54753	D	0.999984	B;B	0.16166	0.008;0.016	B;B	0.14023	0.01;0.01	T	0.40905	-0.9538	10	0.02654	T	1	.	18.5603	0.91097	0.0:0.0:1.0:0.0	.	332;332	B2RUU3;Q14185	.;DOCK1_HUMAN	I	332	ENSP00000280333:V332I	ENSP00000280333:V332I	V	+	1	0	DOCK1	128696994	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.530000	0.81962	2.624000	0.88883	0.650000	0.86243	GTA	.	.	none		0.353	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380		A	128807004	G	A	128807004	3	1	1	1	0	0	0	0	1	0	0	0	4686	1377	48	2	1036	2	DOCK1	10	128807004	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	4466607	128807004	6727743	94	94											
OR52I2	143502	hgsc.bcm.edu	37	chr11	4608396	4608396	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgagcatcttctgctcaggAgacagctcaatcagctttag	10	11	10	10	0	5	2	3	1	2	1	5	3	5	2	0	1	4	4	0	1	2	3			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:4608396A>C	ENST00000312614.4	+	1	376	c.354A>C	c.(352-354)ggA>ggC	p.G118G		NM_001005170.2	NP_001005170.1	Q8NH67	O52I2_HUMAN	olfactory receptor, family 52, subfamily I, member 2	118						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(2)|lung(11)|pancreas(1)|skin(1)	19		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)		TCTGCTCAGGAGACAGCTCAA	0.512																																					p.G118G		Atlas-SNP	.											.	OR52I2	50	.	0			c.A354C						PASS	.						201	189	193					11																	4608396		2201	4298	6499	SO:0001819	synonymous_variant	143502	exon1			CTCAGGAGACAGC	BK004264	CCDS31355.1	11p15.4	2012-08-09			ENSG00000226288	ENSG00000226288		"GPCR / Class A : Olfactory receptors"	15221	protein-coding gene	gene with protein product							Standard	NM_001005170		Approved		uc010qyh.2	Q8NH67	OTTHUMG00000165721	ENST00000312614.4:c.354A>C	11.37:g.4608396A>C		503	1	0.00198807		572	149	0.26049	NM_001005170	B2RNJ5|B9EKV8|Q6IFJ8	Silent	SNP	ENST00000312614.4	37	CCDS31355.1																																																																																			.	.	none		0.512	OR52I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385946.1	NM_001005170		C	4608396	A	C	4608396	2	2	1	1	0	0	0	0	0	0	0	1	11130	291	11	5		5	OR52I2	11	4608396	Silent	SNP	A	TCGA-FA-8693-01A-11D-2397-10		4608396	130398120	95	95											
RBMXL2	27288	hgsc.bcm.edu	37	chr11	7111451	7111451	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccagcgtgattcttacagccGgtcaggctgcagggtgccca	7	8	13	13	2	2	1	1	1	1	0	2	1	2	1	3	3	5	2	3	3	1	2			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:7111451G>T	ENST00000306904.5	+	1	1287	c.1100G>T	c.(1099-1101)cGg>cTg	p.R367L		NM_014469.4	NP_055284.3	O75526	RMXL2_HUMAN	RNA binding motif protein, X-linked-like 2	367	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)		TCTTACAGCCGGTCAGGCTGC	0.652																																					p.R367L		Atlas-SNP	.											.	RBMXL2	47	.	0			c.G1100T						PASS	.						12	14	14					11																	7111451		2198	4295	6493	SO:0001583	missense	27288	exon1			ACAGCCGGTCAGG	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.1100G>T	11.37:g.7111451G>T	ENSP00000304139:p.Arg367Leu	68	0	0		67	14	0.208955	NM_014469	Q6PEZ2|Q9NQU0	Missense_Mutation	SNP	ENST00000306904.5	37	CCDS7777.1	.	.	.	.	.	.	.	.	.	.	G	13.21	2.170468	0.38315	.	.	ENSG00000170748	ENST00000306904	T	0.76448	-1.02	3.97	3.97	0.46021	.	0.162448	0.51477	U	0.000087	T	0.69931	0.3166	L	0.47716	1.5	0.29826	N	0.830395	P	0.48764	0.915	B	0.38712	0.28	T	0.74509	-0.3642	10	0.66056	D	0.02	.	14.3415	0.66630	0.0:0.0:1.0:0.0	.	367	O75526	HNRGT_HUMAN	L	367	ENSP00000304139:R367L	ENSP00000304139:R367L	R	+	2	0	RBMXL2	7068027	1.000000	0.71417	0.920000	0.36463	0.112000	0.19704	6.007000	0.70731	2.492000	0.84095	0.655000	0.94253	CGG	.	.	none		0.652	RBMXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384552.1	NM_014469		T	7111451	G	T	7111451	3	4	1	1	0	0	0	0	1	0	0	0	13169	1116	39	4	1102	4	RBMXL2	11	7111451	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	2503055	7111451	127895065	96	96											
INSC	387755	hgsc.bcm.edu	37	chr11	15267551	15267551	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcggctggtggactccttcTtactctgcagcaacatggag	7	11	11	12	1	2	0	0	0	2	0	4	2	3	2	1	4	4	3	1	4	2	2			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:15267551T>G	ENST00000379554.3	+	13	1751	c.1705T>G	c.(1705-1707)Tta>Gta	p.L569V	INSC_ENST00000379556.3_Missense_Mutation_p.L522V|INSC_ENST00000530161.1_Missense_Mutation_p.L522V|INSC_ENST00000447214.2_3'UTR|INSC_ENST00000528567.1_3'UTR|INSC_ENST00000424273.1_Missense_Mutation_p.L480V|INSC_ENST00000525218.1_Missense_Mutation_p.L480V	NM_001031853.3	NP_001027024.3	Q1MX18	INSC_HUMAN	inscuteable homolog (Drosophila)	569					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						GGACTCCTTCTTACTCTGCAG	0.547																																					p.L569V		Atlas-SNP	.											.	INSC	104	.	0			c.T1705G						PASS	.						122	124	123					11																	15267551		1986	4160	6146	SO:0001583	missense	387755	exon13			TCCTTCTTACTCT	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.1705T>G	11.37:g.15267551T>G	ENSP00000368872:p.Leu569Val	199	0	0		214	40	0.186916	NM_001031853	A0PJX5|Q1MX19|Q3C1V6|Q4AC95|Q4AC96|Q4AC97|Q4AC98	Missense_Mutation	SNP	ENST00000379554.3	37	CCDS41621.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.320930	0.81580	.	.	ENSG00000188487	ENST00000379554;ENST00000379556;ENST00000424273;ENST00000530161;ENST00000525218	T;T;T;T;T	0.50277	0.75;0.79;0.94;0.79;0.94	6.17	3.57	0.40892	Armadillo-type fold (1);	0.000000	0.64402	D	0.000004	T	0.58566	0.2131	L	0.53249	1.67	0.38663	D	0.952138	D;D;D	0.89917	1.0;0.996;1.0	D;D;D	0.87578	0.998;0.986;0.996	T	0.61950	-0.6957	10	0.66056	D	0.02	-7.5535	6.8426	0.23971	0.0:0.2948:0.0:0.7052	.	557;480;569	Q1MX18-5;Q1MX18-4;Q1MX18	.;.;INSC_HUMAN	V	569;522;480;522;480	ENSP00000368872:L569V;ENSP00000368874:L522V;ENSP00000389161:L480V;ENSP00000436194:L522V;ENSP00000436113:L480V	ENSP00000368872:L569V	L	+	1	2	INSC	15224127	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.660000	0.37397	1.158000	0.42547	0.533000	0.62120	TTA	.	.	none		0.547	INSC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386590.1	NM_001031853		G	15267551	T	G	15267551	3	3	1	1	0	0	0	0	1	0	0	0	7773	1606	56	5	1755	5	INSC	11	15267551	Missense_Mutation	SNP	T	TCGA-FA-8693-01A-11D-2397-10	8156100	15267551	119738965	97	97											
OR4C3	256144	hgsc.bcm.edu	37	chr11	48347041	48347041	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcttcctgcattcattggtTcagctcctcctggtcctttg	3	16	9	13	0	2	0	2	0	0	0	6	0	6	0	4	3	2	4	4	3	0	5			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:48347041T>C	ENST00000319856.4	+	1	570	c.549T>C	c.(547-549)gtT>gtC	p.V183V		NM_001004702.1	NP_001004702.1	Q8NH37	OR4C3_HUMAN	olfactory receptor, family 4, subfamily C, member 3	156						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						ATTCATTGGTTCAGCTCCTCC	0.527																																					p.V183V		Atlas-SNP	.											.	OR4C3	75	.	0			c.T549C						PASS	.						155	144	148					11																	48347041		2201	4298	6499	SO:0001819	synonymous_variant	256144	exon1			ATTGGTTCAGCTC	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.549T>C	11.37:g.48347041T>C		347	0	0		361	26	0.0720222	NM_001004702	B2RNF2|Q6IFB3	Silent	SNP	ENST00000319856.4	37	CCDS31489.1																																																																																			.	.	none		0.527	OR4C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390557.1	NM_001004702		C	48347041	T	C	48347041	2	2	1	1	0	0	0	0	0	0	0	1	11059	1770	62	3		3	OR4C3	11	48347041	Silent	SNP	T	TCGA-FA-8693-01A-11D-2397-10	33079490	48347041	86659475	98	98											
OR5AP2	338675	hgsc.bcm.edu	37	chr11	56409697	56409697	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagtaagaggcatctacaaaAgagaggctactgagaaagaa	19	5	12	5	0	1	4	0	1	1	4	1	7	1	4	0	2	2	3	0	2	7	3			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:56409697A>C	ENST00000302981.1	-	1	218	c.219T>G	c.(217-219)tcT>tcG	p.S73S	OR5AP2_ENST00000544374.1_Silent_p.S74S	NM_001002925.1	NP_001002925.1	Q8NGF4	O5AP2_HUMAN	olfactory receptor, family 5, subfamily AP, member 2	73						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						CATCTACAAAAGAGAGGCTAC	0.443																																					p.S73S		Atlas-SNP	.											.	OR5AP2	69	.	0			c.T219G						PASS	.						65	64	65					11																	56409697		2201	4296	6497	SO:0001819	synonymous_variant	338675	exon1			TACAAAAGAGAGG	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.219T>G	11.37:g.56409697A>C		82	0	0		102	15	0.147059	NM_001002925	B2RNM8	Silent	SNP	ENST00000302981.1	37	CCDS31534.1																																																																																			.	.	none		0.443	OR5AP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391613.1	NM_001002925		C	56409697	A	C	56409697	2	2	1	1	0	0	0	0	0	0	0	1	11153	59	3	5		5	OR5AP2	11	56409697	Silent	SNP	A	TCGA-FA-8693-01A-11D-2397-10	8062656	56409697	78596819	99	99											
SLC22A25	387601	hgsc.bcm.edu	37	chr11	62997098	62997098	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatctccccaggcctccaacTtgatctaggaggtcctgaaa	11	9	8	13	0	2	2	0	2	2	0	5	3	4	3	5	3	1	0	5	3	4	2			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:62997098T>G	ENST00000306494.6	-	1	26	c.27A>C	c.(25-27)caA>caC	p.Q9H	SLC22A25_ENST00000403374.2_5'Flank|SLC22A10_ENST00000535888.1_Intron|SLC22A10_ENST00000525620.1_Intron	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						GGCCTCCAACTTGATCTAGGA	0.438																																					p.Q9H		Atlas-SNP	.											SLC22A25,right_upper_lobe,carcinoma,-2,1	SLC22A25	87	1	0			c.A27C						PASS	.						47	51	50					11																	62997098		2201	4298	6499	SO:0001583	missense	387601	exon1			TCCAACTTGATCT	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.27A>C	11.37:g.62997098T>G	ENSP00000307443:p.Gln9His	42	0	0		54	13	0.240741	NM_199352		Missense_Mutation	SNP	ENST00000306494.6	37	CCDS31592.1	.	.	.	.	.	.	.	.	.	.	T	2.589	-0.295687	0.05532	.	.	ENSG00000196600	ENST00000306494;ENST00000451441	T	0.36157	1.27	3.98	0.0938	0.14478	.	0.474947	0.22983	N	0.053281	T	0.28995	0.0720	M	0.65677	2.01	0.24828	N	0.992545	B;B	0.20671	0.01;0.047	B;B	0.23419	0.019;0.046	T	0.17531	-1.0366	10	0.30854	T	0.27	.	3.2687	0.06874	0.1778:0.3193:0.0:0.503	.	7;9	A4IF29;Q6T423	.;S22AP_HUMAN	H	9	ENSP00000307443:Q9H	ENSP00000307443:Q9H	Q	-	3	2	SLC22A25	62753674	0.256000	0.24012	0.031000	0.17742	0.131000	0.20780	1.426000	0.34870	0.062000	0.16340	0.386000	0.25728	CAA	.	.	none		0.438	SLC22A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383519.3	NM_199352		G	62997098	T	G	62997098	3	3	1	1	0	0	0	0	1	0	0	0	14469	1606	56	5	1652	5	SLC22A25	11	62997098	Missense_Mutation	SNP	T	TCGA-FA-8693-01A-11D-2397-10	6587401	62997098	72009418	100	100											
PPFIA1	8500	hgsc.bcm.edu	37	chr11	70171055	70171055	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctccagcaggcgtgtccagcGaagtggaagtgctgaaagca	11	6	14	10	2	0	1	0	1	0	0	2	3	2	2	2	2	4	3	2	2	3	0			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:70171055G>A	ENST00000253925.7	+	4	684	c.469G>A	c.(469-471)Gaa>Aaa	p.E157K	AP000487.6_ENST00000528607.1_RNA|PPFIA1_ENST00000389547.3_Missense_Mutation_p.E157K|CTA-797E19.2_ENST00000526017.1_RNA	NM_003626.3	NP_003617.1	Q13136	LIPA1_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	157					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)			CGTGTCCAGCGAAGTGGAAGT	0.507																																					p.E157K		Atlas-SNP	.											.	PPFIA1	114	.	0			c.G469A						PASS	.						95	96	96					11																	70171055		2200	4294	6494	SO:0001583	missense	8500	exon4			TCCAGCGAAGTGG	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.469G>A	11.37:g.70171055G>A	ENSP00000253925:p.Glu157Lys	93	0	0		95	22	0.231579	NM_177423	A6NLE3|Q13135|Q14567|Q8N4I2	Missense_Mutation	SNP	ENST00000253925.7	37	CCDS31627.1	.	.	.	.	.	.	.	.	.	.	G	36	5.665691	0.96745	.	.	ENSG00000131626	ENST00000253925;ENST00000389547;ENST00000530746	T;T;T	0.46451	0.87;0.87;0.87	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.56702	0.2003	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	T	0.59804	-0.7385	10	0.87932	D	0	.	19.2525	0.93930	0.0:0.0:1.0:0.0	.	157;157	Q13136;Q13136-2	LIPA1_HUMAN;.	K	157	ENSP00000253925:E157K;ENSP00000374198:E157K;ENSP00000432722:E157K	ENSP00000253925:E157K	E	+	1	0	PPFIA1	69848703	1.000000	0.71417	0.791000	0.31998	0.687000	0.40016	9.522000	0.98032	2.617000	0.88574	0.650000	0.86243	GAA	.	.	none		0.507	PPFIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393905.1	NM_003626		A	70171055	G	A	70171055	3	1	1	1	0	0	0	0	1	0	0	0	12318	1059	37	1	479	1	PPFIA1	11	70171055	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	7173957	70171055	64835461	101	101											
NOX4	50507	hgsc.bcm.edu	37	chr11	89182653	89182653	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaggtaatatggaatgttcTgcttttatccaacaatctcc	12	14	6	9	0	2	0	0	0	2	0	4	1	3	1	2	2	2	3	2	2	6	5			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:89182653T>C	ENST00000263317.4	-	4	542	c.304A>G	c.(304-306)Aga>Gga	p.R102G	NOX4_ENST00000535633.1_Missense_Mutation_p.R78G|NOX4_ENST00000413594.2_Missense_Mutation_p.R123G|NOX4_ENST00000343727.5_Missense_Mutation_p.R78G|NOX4_ENST00000527956.1_Missense_Mutation_p.R78G|NOX4_ENST00000531342.1_Intron|NOX4_ENST00000532825.1_Missense_Mutation_p.R78G|NOX4_ENST00000375979.3_Intron|NOX4_ENST00000424319.1_Missense_Mutation_p.R78G|NOX4_ENST00000527626.1_Intron|NOX4_ENST00000528341.1_Missense_Mutation_p.R77G|NOX4_ENST00000542487.1_Missense_Mutation_p.R78G|NOX4_ENST00000525196.1_Missense_Mutation_p.R102G|NOX4_ENST00000534731.1_Missense_Mutation_p.R102G			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4	102	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)				TGGAATGTTCTGCTTTTATCC	0.299																																					p.R102G		Atlas-SNP	.											.	NOX4	101	.	0			c.A304G						PASS	.						88	85	86					11																	89182653		2201	4295	6496	SO:0001583	missense	50507	exon4			ATGTTCTGCTTTT	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.304A>G	11.37:g.89182653T>C	ENSP00000263317:p.Arg102Gly	140	0	0		120	28	0.233333	NM_001143836	A8K715|B7Z520|E7EMD7|Q5K3R4|Q5K3R5|Q5K3R6|Q5K3R8|Q7Z7G3|Q86V92	Missense_Mutation	SNP	ENST00000263317.4	37	CCDS8285.1	.	.	.	.	.	.	.	.	.	.	T	14.99	2.701251	0.48307	.	.	ENSG00000086991	ENST00000424319;ENST00000535633;ENST00000343727;ENST00000534731;ENST00000525196;ENST00000263317;ENST00000532825;ENST00000527956;ENST00000542487;ENST00000528341;ENST00000413594	D;D;D;D;D;D;D;D;D;D;D	0.90955	-2.76;-2.76;-2.76;-2.76;-2.76;-2.76;-2.76;-2.76;-2.76;-2.76;-2.76	5.42	4.22	0.49857	Flavoprotein transmembrane component (1);	0.105540	0.64402	D	0.000010	D	0.88321	0.6405	L	0.47716	1.5	0.29673	N	0.842284	B;P;B;B;B	0.43287	0.154;0.802;0.049;0.077;0.154	B;P;B;B;B	0.45577	0.102;0.486;0.025;0.259;0.175	D	0.84793	0.0780	9	.	.	.	-8.7869	11.2298	0.48905	0.0:0.0:0.1532:0.8468	.	78;77;102;102;102	E9PMY6;E9PPP2;E9PI95;Q9NPH5-6;Q9NPH5	.;.;.;.;NOX4_HUMAN	G	78;78;78;102;102;102;78;78;78;77;123	ENSP00000412446:R78G;ENSP00000440172:R78G;ENSP00000344747:R78G;ENSP00000436892:R102G;ENSP00000436716:R102G;ENSP00000263317:R102G;ENSP00000434924:R78G;ENSP00000433797:R78G;ENSP00000439373:R78G;ENSP00000436970:R77G;ENSP00000405705:R123G	.	R	-	1	2	NOX4	88822301	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.714000	0.47202	2.043000	0.60533	0.533000	0.62120	AGA	.	.	none		0.299	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	NM_016931		C	89182653	T	C	89182653	3	2	1	1	0	0	0	0	1	0	0	0	10567	1588	55	3	1492	3	NOX4	11	89182653	Missense_Mutation	SNP	T	TCGA-FA-8693-01A-11D-2397-10	19011598	89182653	45823863	102	102											
FAT3	120114	hgsc.bcm.edu	37	chr11	92577819	92577819	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcttgtcactcgattcccaCgcgctcatgacctacagcac	8	9	8	16	3	2	1	2	1	0	0	4	2	3	1	2	1	2	3	2	1	1	3			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:92577819C>T	ENST00000298047.6	+	18	11303	c.11286C>T	c.(11284-11286)caC>caT	p.H3762H	FAT3_ENST00000409404.2_Silent_p.H3762H|FAT3_ENST00000533797.1_Silent_p.H97H|FAT3_ENST00000525166.1_Silent_p.H3612H			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3762					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)				TCGATTCCCACGCGCTCATGA	0.527										TCGA Ovarian(4;0.039)																											p.H3762H		Atlas-SNP	.											FAT3_ENST00000409404,colon,carcinoma,0,6	FAT3	1822	6	0			c.C11286T						PASS	.						101	100	101					11																	92577819		2143	4249	6392	SO:0001819	synonymous_variant	120114	exon18			TTCCCACGCGCTC	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.11286C>T	11.37:g.92577819C>T		399	0	0		451	80	0.177384	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				.	.	none		0.527	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92577819	C	T	92577819	2	4	1	1	0	0	0	0	0	0	0	1	5699	535	19	1		1	FAT3	11	92577819	Silent	SNP	C	TCGA-FA-8693-01A-11D-2397-10	3395166	92577819	42428697	103	103											
MAML2	84441	hgsc.bcm.edu	37	chr11	95825407	95825407	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgctgctgctgctgctgctgCtgctgctgttgctgctgttg	0	16	14	11	0	0	0	0	0	0	0	0	0	0	0	0	0	11	13	0	0	0	2	rs61901862		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:95825407C>T	ENST00000524717.1	-	2	3072	c.1788G>A	c.(1786-1788)caG>caA	p.Q596Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	596					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)	p.Q596Q(1)	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)				gctgctgctgctgctgctgtt	0.532			T	"MECT1, CRTC3"	salivary gland mucoepidermoid																																p.Q596Q		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	MAML2,rectum,carcinoma,0,2	MAML2	94	2	1	Substitution - coding silent(1)	kidney(1)	c.G1788A						PASS	.						28	35	33					11																	95825407		2119	4148	6267	SO:0001819	synonymous_variant	84441	exon2			CTGCTGCTGCTGC	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.1788G>A	11.37:g.95825407C>T		192	0	0		180	23	0.127778	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																			C|0.250;T|0.750	0.750	weak		0.532	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			T	95825407	C	T	95825407	2	4	1	1	0	0	0	0	0	0	0	1	9215	796	28	2		2	MAML2	11	95825407	Silent	SNP	C	TCGA-FA-8693-01A-11D-2397-10	3247588	95825407	39181109	104	104											
POU2AF1	5450	hgsc.bcm.edu	37	chr11	111249896	111249896	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaccacttacgtttttgccAgagcatggcctgtgacagga	11	10	10	10	1	0	2	0	1	0	1	0	3	0	3	3	2	4	2	3	2	2	3			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:111249896A>G	ENST00000393067.3	-	1	521	c.7T>C	c.(7-9)Tgg>Cgg	p.W3R		NM_006235.2	NP_006226.2	Q16633	OBF1_HUMAN	POU class 2 associating factor 1	3					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)		CGTTTTTGCCAGAGCATGGCC	0.557			T	BCL6	NHL																																p.W3R		Atlas-SNP	.		Dom	yes		11	11q23.1	5450	"POU domain, class 2, associating factor 1 (OBF1)"		L	.	POU2AF1	23	.	0			c.T7C						PASS	.						211	202	205					11																	111249896		2201	4297	6498	SO:0001583	missense	5450	exon1			TTTGCCAGAGCAT		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.7T>C	11.37:g.111249896A>G	ENSP00000376786:p.Trp3Arg	313	0	0		366	82	0.224044	NM_006235	B2R8Z9|Q14983	Missense_Mutation	SNP	ENST00000393067.3	37	CCDS31675.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.211438	0.79240	.	.	ENSG00000110777	ENST00000393067	T	0.31510	1.49	5.3	5.3	0.74995	.	0.572674	0.16592	N	0.207726	T	0.46073	0.1374	L	0.38175	1.15	0.45118	D	0.998132	D	0.76494	0.999	D	0.87578	0.998	T	0.40403	-0.9565	10	0.87932	D	0	.	13.2379	0.59979	1.0:0.0:0.0:0.0	.	3	Q16633	OBF1_HUMAN	R	3	ENSP00000376786:W3R	ENSP00000376786:W3R	W	-	1	0	POU2AF1	110755106	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.293000	0.65680	2.225000	0.72522	0.533000	0.62120	TGG	.	.	none		0.557	POU2AF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391002.1	NM_006235		G	111249896	A	G	111249896	3	3	1	1	0	0	0	0	1	0	0	0	12279	188	7	3	783	3	POU2AF1	11	111249896	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10	15424489	111249896	23756620	105	105											
AMICA1	120425	hgsc.bcm.edu	37	chr11	118085545	118085545	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tagcttctacttacccagtaAcactggcagcaggatgagtt	11	11	9	10	0	1	1	0	1	1	0	1	2	1	2	1	2	5	5	1	2	4	6	rs553861053	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:118085545A>G	ENST00000356289.5	-	2	210	c.37T>C	c.(37-39)Tta>Cta	p.L13L	AMICA1_ENST00000292067.7_5'Flank|AMICA1_ENST00000526620.1_Intron|AMICA1_ENST00000533261.1_Silent_p.L13L	NM_001098526.1	NP_001091996.1	Q86YT9	JAML1_HUMAN	adhesion molecule, interacts with CXADR antigen 1	13					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)		TTACCCAGTAACACTGGCAGC	0.383													A|||	12	0.00239617	0.0	0.0	5008	,	,		20342	0.0		0.0	False		,,,				2504	0.0123				p.L13L		Atlas-SNP	.											.	AMICA1	49	.	0			c.T37C						PASS	.						124	119	120					11																	118085545		1843	4089	5932	SO:0001819	synonymous_variant	120425	exon2			CCAGTAACACTGG	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.37T>C	11.37:g.118085545A>G		37	0	0		46	7	0.152174	NM_001098526	B0YIV1|B0YIV2|Q496M1|Q5DTC6|Q7Z499|Q8N9I7|Q8NF70	Silent	SNP	ENST00000356289.5	37	CCDS41723.1																																																																																			.	.	none		0.383	AMICA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392105.2	NM_153206		G	118085545	A	G	118085545	2	3	1	1	0	0	0	0	0	0	0	1	574	40	2	3		3	AMICA1	11	118085545	Silent	SNP	A	TCGA-FA-8693-01A-11D-2397-10	6835649	118085545	16920971	106	106											
KIRREL3	84623	hgsc.bcm.edu	37	chr11	126294687	126294687	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggagcctctctggaactcccGctcacaaagctcgatggacg	9	7	11	14	3	2	0	1	0	1	0	5	4	3	3	2	3	3	2	2	3	2	0			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:126294687G>A	ENST00000525144.2	-	17	2374	c.2125C>T	c.(2125-2127)Cgg>Tgg	p.R709W	KIRREL3_ENST00000529097.2_Missense_Mutation_p.R697W|KIRREL3_ENST00000416561.2_Missense_Mutation_p.R176W	NM_032531.3	NP_115920.1	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 (Drosophila)	709	Ser-rich.				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)		TGGAACTCCCGCTCACAAAGC	0.627																																					p.R709W		Atlas-SNP	.											KIRREL3_ENST00000525144,NS,carcinoma,0,2	KIRREL3	183	2	0			c.C2125T						PASS	.						64	72	69					11																	126294687		2161	4274	6435	SO:0001583	missense	84623	exon17			ACTCCCGCTCACA	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.2125C>T	11.37:g.126294687G>A	ENSP00000435466:p.Arg709Trp	144	0	0		122	31	0.254098	NM_032531	Q3MIJ7|Q6UWJ9|Q6UWL5|Q96JG0	Missense_Mutation	SNP	ENST00000525144.2	37	CCDS53723.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.353005	0.82132	.	.	ENSG00000149571	ENST00000525144;ENST00000529097;ENST00000416561	T;T;T	0.53423	0.62;0.62;0.62	4.88	3.96	0.45880	.	0.000000	0.85682	D	0.000000	T	0.57961	0.2089	L	0.36672	1.1	0.58432	D	0.999993	D;D	0.89917	1.0;1.0	D;D	0.74023	0.982;0.982	T	0.62115	-0.6922	10	0.72032	D	0.01	-11.0324	14.353	0.66716	0.0:0.0:0.8508:0.1492	.	697;709	E9PRX9;Q8IZU9	.;KIRR3_HUMAN	W	709;697;176	ENSP00000435466:R709W;ENSP00000434081:R697W;ENSP00000408692:R176W	ENSP00000408692:R176W	R	-	1	2	KIRREL3	125799897	1.000000	0.71417	0.987000	0.45799	0.993000	0.82548	6.135000	0.71696	1.271000	0.44313	0.655000	0.94253	CGG	.	.	none		0.627	KIRREL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386479.2	NM_032531		A	126294687	G	A	126294687	3	1	1	1	0	0	0	0	1	0	0	0	8335	1086	38	1	215	1	KIRREL3	11	126294687	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	8209142	126294687	8711829	107	107											
KIRREL3	84623	hgsc.bcm.edu	37	chr11	126299148	126299148	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttgtggacaatttccactcGgatatcatttttggctgaca	9	15	8	9	1	1	1	1	1	0	0	3	3	2	3	1	3	0	1	1	3	2	5			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:126299148G>A	ENST00000525144.2	-	15	1981	c.1732C>T	c.(1732-1734)Cga>Tga	p.R578*	KIRREL3_ENST00000529097.2_Nonsense_Mutation_p.R566*|KIRREL3_ENST00000416561.2_Nonsense_Mutation_p.R45*	NM_032531.3	NP_115920.1	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 (Drosophila)	578					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)		ATTTCCACTCGGATATCATTT	0.458																																					p.R578X		Atlas-SNP	.											.	KIRREL3	183	.	0			c.C1732T						PASS	.						96	99	98					11																	126299148		1942	4138	6080	SO:0001587	stop_gained	84623	exon15			CCACTCGGATATC	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.1732C>T	11.37:g.126299148G>A	ENSP00000435466:p.Arg578*	158	0	0		108	36	0.333333	NM_032531	Q3MIJ7|Q6UWJ9|Q6UWL5|Q96JG0	Nonsense_Mutation	SNP	ENST00000525144.2	37	CCDS53723.1	.	.	.	.	.	.	.	.	.	.	G	37	6.421659	0.97555	.	.	ENSG00000149571	ENST00000525144;ENST00000529097;ENST00000416561	.	.	.	5.66	4.71	0.59529	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.7594	15.9821	0.80116	0.0:0.0:0.8647:0.1353	.	.	.	.	X	578;566;45	.	ENSP00000408692:R45X	R	-	1	2	KIRREL3	125804358	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	5.330000	0.65899	2.668000	0.90789	0.561000	0.74099	CGA	.	.	none		0.458	KIRREL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386479.2	NM_032531		A	126299148	G	A	126299148	4	1	1	1	0	0	0	0	0	1	0	0	8335	1124	39	1	616	1	KIRREL3	11	126299148	Nonsense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	4461	126299148	8707368	108	108											
IGSF9B	22997	hgsc.bcm.edu	37	chr11	133790483	133790483	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gggtctccagccccccgaagGggaattctggccggccccag	6	5	14	16	2	2	0	0	0	2	0	3	2	2	1	7	5	1	0	7	5	2	1			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:133790483G>A	ENST00000321016.8	-	18	3367	c.3137C>T	c.(3136-3138)cCc>cTc	p.P1046L	IGSF9B_ENST00000533871.2_Missense_Mutation_p.P1046L			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	1046	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)		CCCCCCGAAGGGGAATTCTGG	0.662																																					p.P1046L		Atlas-SNP	.											.	IGSF9B	290	.	0			c.C3137T						PASS	.						45	54	51					11																	133790483		1935	4142	6077	SO:0001583	missense	22997	exon18			CCGAAGGGGAATT	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.3137C>T	11.37:g.133790483G>A	ENSP00000317980:p.Pro1046Leu	113	0	0		151	39	0.258278	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	37		.	.	.	.	.	.	.	.	.	.	G	17.22	3.335293	0.60853	.	.	ENSG00000080854	ENST00000321016;ENST00000533871	T;T	0.69561	-0.09;-0.41	4.82	4.82	0.62117	.	0.159476	0.29737	N	0.011322	T	0.71341	0.3328	N	0.19112	0.55	0.58432	D	0.999997	D	0.89917	1.0	D	0.80764	0.994	T	0.75045	-0.3456	10	0.51188	T	0.08	.	17.5246	0.87796	0.0:0.0:1.0:0.0	.	1046	Q9UPX0	TUTLB_HUMAN	L	1046;888	ENSP00000317980:P1046L;ENSP00000436552:P888L	ENSP00000317980:P1046L	P	-	2	0	IGSF9B	133295693	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	7.551000	0.82182	2.220000	0.72140	0.455000	0.32223	CCC	.	.	none		0.662	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		A	133790483	G	A	133790483	3	1	1	1	0	0	0	0	1	0	0	0	7615	1232	43	2	920	2	IGSF9B	11	133790483	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	7491335	133790483	1216033	109	109											
NCAPD3	23310	hgsc.bcm.edu	37	chr11	134076494	134076494	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacgatttgtgtgcttcacCtgataaactggaccgcctgg	8	12	10	11	2	2	1	2	1	0	0	2	3	2	2	3	2	2	1	3	2	2	3			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:134076494C>T	ENST00000534548.2	-	8	1080	c.1016G>A	c.(1015-1017)aGc>aAc	p.S339N		NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	339					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)		TGTGCTTCACCTGATAAACTG	0.453																																					p.S339N		Atlas-SNP	.											.	NCAPD3	141	.	0			c.G1016A						PASS	.						136	122	127					11																	134076494		2201	4297	6498	SO:0001630	splice_region_variant	23310	exon8			CTTCACCTGATAA	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.1016+1G>A	11.37:g.134076494C>T		259	0	0		284	63	0.221831	NM_015261	A6NFS2|Q4KMQ9	Missense_Mutation	SNP	ENST00000534548.2	37	CCDS31723.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.240992	0.79912	.	.	ENSG00000151503	ENST00000534548	T	0.08546	3.08	5.67	5.67	0.87782	Armadillo-type fold (1);	0.116016	0.85682	D	0.000000	T	0.18467	0.0443	M	0.66939	2.045	0.80722	D	1	P	0.48764	0.915	P	0.47251	0.542	T	0.00206	-1.1920	9	.	.	.	-11.7273	20.1313	0.98000	0.0:1.0:0.0:0.0	.	339	P42695	CNDD3_HUMAN	N	339	ENSP00000433681:S339N	.	S	-	2	0	NCAPD3	133581704	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	5.469000	0.66749	2.837000	0.97791	0.655000	0.94253	AGC	.	.	none		0.453	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261	Missense_Mutation	T	134076494	C	T	134076494	5	4	1	1	0	0	0	0	0	0	1	0	10215	695	24	2	3592	2	NCAPD3	11	134076494	Splice_Site	SNP	C	TCGA-FA-8693-01A-11D-2397-10	286011	134076494	930022	110	110											
NECAP1	25977	hgsc.bcm.edu	37	chr12	8245311	8245311	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagatttccaaggaatctcaAgaaatggatgctcgtcctaa	14	10	9	8	1	1	2	1	0	1	2	5	5	3	4	2	2	1	1	2	2	5	2			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:8245311A>G	ENST00000339754.5	+	5	501	c.423A>G	c.(421-423)caA>caG	p.Q141Q		NM_015509.3	NP_056324.2	Q8NC96	NECP1_HUMAN	NECAP endocytosis associated 1	141					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)		AGGAATCTCAAGAAATGGATG	0.408																																					p.Q141Q		Atlas-SNP	.											.	NECAP1	21	.	0			c.A423G						PASS	.						70	71	71					12																	8245311		2203	4300	6503	SO:0001819	synonymous_variant	25977	exon5			ATCTCAAGAAATG	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.423A>G	12.37:g.8245311A>G		104	0	0		138	40	0.289855	NM_015509	Q2NL73|Q5XG95|Q6NWY6|Q8N153|Q8NCB0|Q9BU52|Q9Y407	Silent	SNP	ENST00000339754.5	37	CCDS8589.1																																																																																			.	.	none		0.408	NECAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400244.1	NM_015509		G	8245311	A	G	8245311	2	3	1	1	0	0	0	0	0	0	0	1	10316	69	3	3		3	NECAP1	12	8245311	Silent	SNP	A	TCGA-FA-8693-01A-11D-2397-10		8245311	125606584	111	111											
C12orf11	55726	hgsc.bcm.edu	37	chr12	27070328	27070328	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caggaggaaggtctactattTacatctacaggtgaaatccg	13	10	10	8	1	2	1	0	1	2	0	3	3	3	3	1	4	3	0	1	4	6	5			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:27070328T>G	ENST00000261191.7	-	10	1562	c.1026A>C	c.(1024-1026)gtA>gtC	p.V342V	ASUN_ENST00000539625.1_Silent_p.V241V	NM_018164.2	NP_060634.2	Q9NVM9	ASUN_HUMAN	asunder spermatogenesis regulator	342					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)											GTCTACTATTTACATCTACAG	0.269																																					p.V342V		Atlas-SNP	.											.	.	.	.	0			c.A1026C						PASS	.						47	50	49					12																	27070328		2199	4289	6488	SO:0001819	synonymous_variant	55726	exon10			ACTATTTACATCT	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.1026A>C	12.37:g.27070328T>G		117	0	0		168	40	0.238095	NM_018164	B4DNK1|Q86WE2|Q96HM2|Q9BTX2|Q9NTB6|Q9NVM5	Silent	SNP	ENST00000261191.7	37	CCDS8708.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.949|9.949	1.219491|1.219491	0.22373|0.22373	.|.	.|.	ENSG00000064102|ENSG00000064102	ENST00000542392|ENST00000536232	.|.	.|.	.|.	5.39|5.39	2.92|2.92	0.33932|0.33932	.|.	.|.	.|.	.|.	.|.	T|.	0.56645|.	0.1999|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.51608|.	-0.8684|.	4|.	.|.	.|.	.|.	-15.2582|-15.2582	8.0783|8.0783	0.30729|0.30729	0.0:0.0698:0.2529:0.6773|0.0:0.0698:0.2529:0.6773	.|.	.|.	.|.	.|.	Q|S	56|70	.|.	.|.	K|X	-|-	1|2	0|2	C12orf11|C12orf11	26961595|26961595	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	1.034000|1.034000	0.30204|0.30204	0.948000|0.948000	0.37687|0.37687	0.477000|0.477000	0.44152|0.44152	AAA|TAA	.	.	none		0.269	ASUN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402819.1	NM_018164		G	27070328	T	G	27070328	2	3	1	1	0	0	0	0	0	0	0	1	1677	1741	61	5		5	C12orf11	12	27070328	Silent	SNP	T	TCGA-FA-8693-01A-11D-2397-10	18825017	27070328	106781567	112	112											
MAP3K12	7786	hgsc.bcm.edu	37	chr12	53880795	53880795	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	atggtccagacagggcgcagGcagccaaagaggccctcaag	12	3	14	12	1	1	2	1	0	0	2	2	2	2	2	3	4	1	2	3	4	2	0			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:53880795G>A	ENST00000267079.2	-	3	507	c.282C>T	c.(280-282)tgC>tgT	p.C94C	MAP3K12_ENST00000547151.1_5'UTR|MAP3K12_ENST00000547035.1_Silent_p.C127C|MAP3K12_ENST00000547488.1_Silent_p.C127C	NM_001193511.1|NM_006301.3	NP_001180440.1|NP_006292.3	Q12852	M3K12_HUMAN	mitogen-activated protein kinase kinase kinase 12	94					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						CAGGGCGCAGGCAGCCAAAGA	0.602																																					p.C127C		Atlas-SNP	.											.	MAP3K12	160	.	0			c.C381T						PASS	.						80	66	71					12																	53880795		2203	4300	6503	SO:0001819	synonymous_variant	7786	exon2			GCGCAGGCAGCCA	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.282C>T	12.37:g.53880795G>A		149	0	0		147	39	0.265306	NM_001193511	B3KSS9|G3V1Y2|Q86VQ5|Q8WY25	Silent	SNP	ENST00000267079.2	37	CCDS8860.1	.	.	.	.	.	.	.	.	.	.	G	7.742	0.701512	0.15172	.	.	ENSG00000139625	ENST00000547151	.	.	.	4.73	1.91	0.25777	.	.	.	.	.	T	0.63177	0.2489	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61681	-0.7013	5	0.87932	D	0	.	7.939	0.29946	0.3359:0.0:0.6641:0.0	.	.	.	.	V	91	.	ENSP00000446800:A91V	A	-	2	0	MAP3K12	52167062	0.968000	0.33430	1.000000	0.80357	0.987000	0.75469	0.040000	0.13905	0.183000	0.20059	-0.448000	0.05591	GCC	.	.	none		0.602	MAP3K12-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406267.1	NM_006301		A	53880795	G	A	53880795	2	1	1	1	0	0	0	0	0	0	0	1	9255	1195	42	2		2	MAP3K12	12	53880795	Silent	SNP	G	TCGA-FA-8693-01A-11D-2397-10	26810467	53880795	79971100	113	113											
ZFC3H1	196441	hgsc.bcm.edu	37	chr12	72022729	72022729	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtcctgtagactgttcctcAtcactactgaagctattatc	9	14	7	11	0	2	2	2	1	0	1	5	2	4	2	2	1	2	3	2	1	5	5			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:72022729A>G	ENST00000378743.3	-	20	4273	c.3915T>C	c.(3913-3915)gaT>gaC	p.D1305D		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	1305					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						ACTGTTCCTCATCACTACTGA	0.323																																					p.D1305D		Atlas-SNP	.											.	ZFC3H1	172	.	0			c.T3915C						PASS	.						147	134	138					12																	72022729		1824	4077	5901	SO:0001819	synonymous_variant	196441	exon20			TTCCTCATCACTA	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.3915T>C	12.37:g.72022729A>G		70	0	0		87	36	0.413793	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Silent	SNP	ENST00000378743.3	37	CCDS41813.1																																																																																			.	.	none		0.323	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982		G	72022729	A	G	72022729	2	3	1	1	0	0	0	0	0	0	0	1	17648	214	8	3		3	ZFC3H1	12	72022729	Silent	SNP	A	TCGA-FA-8693-01A-11D-2397-10	18141934	72022729	61829166	114	114											
TSPAN19	144448	hgsc.bcm.edu	37	chr12	85421763	85421763	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaagatcccattccaatcaAaatttgagaaataggtacta	18	10	6	7	0	1	3	1	1	0	3	3	4	3	3	2	1	1	1	2	1	8	5			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:85421763A>C	ENST00000532498.2	-	4	258	c.178T>G	c.(178-180)Ttg>Gtg	p.L60V	TSPAN19_ENST00000547403.2_Intron	NM_001100917.1	NP_001094387.1	P0C672	TSN19_HUMAN	tetraspanin 19	60						integral component of membrane (GO:0016021)				ovary(1)	1						ATTCCAATCAAAATTTGAGAA	0.294																																					p.L60V		Atlas-SNP	.											TSPAN19_ENST00000532498,NS,carcinoma,+2,2	TSPAN19	23	2	0			c.T178G						PASS	.						58	54	55					12																	85421763		1806	4063	5869	SO:0001583	missense	144448	exon4			CAATCAAAATTTG		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.178T>G	12.37:g.85421763A>C	ENSP00000433816:p.Leu60Val	108	0	0		119	22	0.184874	NM_001100917		Missense_Mutation	SNP	ENST00000532498.2	37	CCDS44949.1	.	.	.	.	.	.	.	.	.	.	A	10.04	1.241688	0.22711	.	.	ENSG00000231738	ENST00000532498;ENST00000547836	T;T	0.80738	-1.41;-1.41	4.4	0.887	0.19200	.	.	.	.	.	T	0.70885	0.3275	L	0.29908	0.895	0.09310	N	1	P	0.45348	0.856	P	0.45753	0.492	T	0.60342	-0.7282	9	0.51188	T	0.08	.	5.6138	0.17420	0.5677:0.0:0.4323:0.0	.	60	P0C672	TSN19_HUMAN	V	60	ENSP00000433816:L60V;ENSP00000446898:L60V	ENSP00000433816:L60V	L	-	1	2	TSPAN19	83945894	0.109000	0.22037	0.001000	0.08648	0.131000	0.20780	0.497000	0.22514	0.302000	0.22762	0.533000	0.62120	TTG	.	.	none		0.294	TSPAN19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388240.2	NM_001100917		C	85421763	A	C	85421763	3	2	1	1	0	0	0	0	1	0	0	0	16658	11	1	5	592	5	TSPAN19	12	85421763	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10	13399034	85421763	48430132	115	115											
ALX1	8092	hgsc.bcm.edu	37	chr12	85674196	85674196	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caggcaaatgcgtgcaggccTtcggacccctgccccgcgcc	6	5	12	18	4	0	0	0	0	0	0	1	1	0	1	6	3	3	2	6	3	1	1			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:85674196T>G	ENST00000316824.3	+	1	312	c.157T>G	c.(157-159)Ttc>Gtc	p.F53V		NM_006982.2	NP_008913.2	Q15699	ALX1_HUMAN	ALX homeobox 1	53					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)		CGTGCAGGCCTTCGGACCCCT	0.637																																					p.F53V		Atlas-SNP	.											ALX1,lower_third,carcinoma,-2,1	ALX1	61	1	0			c.T157G						scavenged	.						43	44	44					12																	85674196		2203	4300	6503	SO:0001583	missense	8092	exon1			CAGGCCTTCGGAC	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.157T>G	12.37:g.85674196T>G	ENSP00000315417:p.Phe53Val	73	1	0.0136986		66	12	0.181818	NM_006982	Q546C8|Q96FH4	Missense_Mutation	SNP	ENST00000316824.3	37	CCDS9028.1	.	.	.	.	.	.	.	.	.	.	T	17.81	3.481878	0.63849	.	.	ENSG00000180318	ENST00000316824	D	0.91843	-2.92	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	D	0.91794	0.7404	N	0.24115	0.695	0.80722	D	1	D	0.57899	0.981	D	0.65140	0.932	D	0.90594	0.4539	10	0.27082	T	0.32	.	14.7384	0.69434	0.0:0.0:0.0:1.0	.	53	Q15699	ALX1_HUMAN	V	53	ENSP00000315417:F53V	ENSP00000315417:F53V	F	+	1	0	ALX1	84198327	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.290000	0.65661	2.069000	0.61940	0.528000	0.53228	TTC	.	.	none		0.637	ALX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406072.1	NM_006982		G	85674196	T	G	85674196	3	3	1	1	0	0	0	0	1	0	0	0	556	1609	56	5	159	5	ALX1	12	85674196	Missense_Mutation	SNP	T	TCGA-FA-8693-01A-11D-2397-10	252433	85674196	48177699	116	116											
USP44	84101	hgsc.bcm.edu	37	chr12	95926864	95926864	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actttccagaccacatgactTggaacaaagtatgcaattca	15	10	6	10	0	1	2	1	1	0	1	2	3	2	3	2	1	2	2	2	1	4	4			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:95926864T>C	ENST00000258499.3	-	2	1457	c.1169A>G	c.(1168-1170)cAa>cGa	p.Q390R	USP44_ENST00000552440.1_Missense_Mutation_p.Q390R|USP44_ENST00000393091.2_Missense_Mutation_p.Q390R|USP44_ENST00000537435.2_Missense_Mutation_p.Q390R	NM_001278393.1|NM_032147.2	NP_001265322.1|NP_115523.2	Q9H0E7	UBP44_HUMAN	ubiquitin specific peptidase 44	390	USP.				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						CCACATGACTTGGAACAAAGT	0.453																																					p.Q390R		Atlas-SNP	.											.	USP44	83	.	0			c.A1169G						PASS	.						140	127	131					12																	95926864		2203	4300	6503	SO:0001583	missense	84101	exon2			ATGACTTGGAACA	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.1169A>G	12.37:g.95926864T>C	ENSP00000258499:p.Gln390Arg	195	0	0		250	62	0.248	NM_032147	B2RDW3	Missense_Mutation	SNP	ENST00000258499.3	37	CCDS9053.1	.	.	.	.	.	.	.	.	.	.	T	1.962	-0.438603	0.04636	.	.	ENSG00000136014	ENST00000258499;ENST00000393091;ENST00000552440;ENST00000537435	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	5.1	5.1	0.69264	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.100708	0.64402	D	0.000001	T	0.14270	0.0345	N	0.04090	-0.28	0.53688	D	0.999972	B	0.11235	0.004	B	0.18871	0.023	T	0.08973	-1.0696	10	0.05833	T	0.94	.	15.189	0.73028	0.0:0.0:0.0:1.0	.	390	Q9H0E7	UBP44_HUMAN	R	390	ENSP00000258499:Q390R;ENSP00000376806:Q390R;ENSP00000448670:Q390R;ENSP00000442629:Q390R	ENSP00000258499:Q390R	Q	-	2	0	USP44	94450995	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.495000	0.53280	2.049000	0.60858	0.454000	0.30748	CAA	.	.	none		0.453	USP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408312.1	NM_032147		C	95926864	T	C	95926864	3	2	1	1	0	0	0	0	1	0	0	0	17090	1812	63	3	989	3	USP44	12	95926864	Missense_Mutation	SNP	T	TCGA-FA-8693-01A-11D-2397-10	10252668	95926864	37925031	117	117											
LTA4H	4048	hgsc.bcm.edu	37	chr12	96409429	96409429	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttttcaccaaacaatcgtcCgcaaatgtggcgttccaagt	11	11	7	12	3	1	0	1	0	0	0	4	0	3	0	3	1	1	2	3	1	4	3	rs138184255	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:96409429C>A	ENST00000228740.2	-	11	1132	c.991G>T	c.(991-993)Gga>Tga	p.G331*	LTA4H_ENST00000548375.1_5'Flank|LTA4H_ENST00000413268.2_Nonsense_Mutation_p.G307*|LTA4H_ENST00000552789.1_Nonsense_Mutation_p.G307*	NM_000895.2	NP_000886.1	P09960	LKHA4_HUMAN	leukotriene A4 hydrolase	331					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)	AACAATCGTCCGCAAATGTGG	0.373											OREG0022040	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G331X		Atlas-SNP	.											.	LTA4H	38	.	0			c.G991T						PASS	.						130	126	127					12																	96409429		2203	4300	6503	SO:0001587	stop_gained	4048	exon11			ATCGTCCGCAAAT	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.991G>T	12.37:g.96409429C>A	ENSP00000228740:p.Gly331*	61	0	0	1320	73	4	0.0547945	NM_000895	B4DNQ9|F8VV40|Q6IAT6|Q9UCT7	Nonsense_Mutation	SNP	ENST00000228740.2	37	CCDS9059.1	.	.	.	.	.	.	.	.	.	.	C	39	7.747344	0.98468	.	.	ENSG00000111144	ENST00000228740;ENST00000552789;ENST00000413268	.	.	.	6.17	6.17	0.99709	.	0.044184	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	-23.289	20.8794	0.99867	0.0:1.0:0.0:0.0	.	.	.	.	X	331;307;307	.	ENSP00000228740:G331X	G	-	1	0	LTA4H	94933560	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.426000	0.59882	2.941000	0.99782	0.655000	0.94253	GGA	C|0.999;T|0.001	.	alt		0.373	LTA4H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408655.1	NM_000895		A	96409429	C	A	96409429	4	1	1	1	0	0	0	0	0	1	0	0	9078	661	23	4	880	4	LTA4H	12	96409429	Nonsense_Mutation	SNP	C	TCGA-FA-8693-01A-11D-2397-10	482565	96409429	37442466	118	118											
RFC5	5985	hgsc.bcm.edu	37	chr12	118458748	118458748	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccgaggaatagacatcattcGaggaccgatcctgagctttg	11	9	11	10	3	1	2	1	1	0	1	3	7	2	4	3	2	1	1	3	2	2	3			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:118458748G>A	ENST00000454402.2	+	4	423	c.305G>A	c.(304-306)cGa>cAa	p.R102Q	RFC5_ENST00000392542.2_Missense_Mutation_p.R81Q|RFC5_ENST00000229043.3_Missense_Mutation_p.R17Q	NM_001206801.1|NM_007370.5	NP_001193730.1|NP_031396.1	P40937	RFC5_HUMAN	replication factor C (activator 1) 5, 36.5kDa	102					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)|enzyme binding (GO:0019899)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(3)	9	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GACATCATTCGAGGACCGATC	0.388																																					p.R102Q		Atlas-SNP	.											.	RFC5	35	.	0			c.G305A						PASS	.						149	135	140					12																	118458748		2203	4300	6503	SO:0001583	missense	5985	exon4			TCATTCGAGGACC		CCDS9185.1, CCDS41843.2	12q24.3	2010-04-21	2002-08-29		ENSG00000111445	ENSG00000111445		"ATPases / AAA-type"	9973	protein-coding gene	gene with protein product		600407	"replication factor C (activator 1) 5 (36.5kD)"			7774928	Standard	NM_007370		Approved	RFC36	uc001twq.3	P40937	OTTHUMG00000156438	ENST00000454402.2:c.305G>A	12.37:g.118458748G>A	ENSP00000408295:p.Arg102Gln	84	0	0		83	19	0.228916	NM_007370	A8MZ62|B3KSX8	Missense_Mutation	SNP	ENST00000454402.2	37	CCDS9185.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.488169	0.84854	.	.	ENSG00000111445	ENST00000449641;ENST00000537315;ENST00000229043;ENST00000484086;ENST00000420967;ENST00000454402;ENST00000392542	T;T;T;T;T	0.51817	0.96;0.69;0.69;0.69;1.39	5.38	4.49	0.54785	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.69459	0.3113	M	0.83774	2.66	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.75020	0.978;0.985;0.985	T	0.74751	-0.3559	10	0.87932	D	0	0.7778	13.1853	0.59677	0.0783:0.0:0.9217:0.0	.	81;116;102	A8MZ62;Q59GW7;P40937	.;.;RFC5_HUMAN	Q	17;17;17;134;81;102;81	ENSP00000229043:R17Q;ENSP00000445917:R134Q;ENSP00000390340:R81Q;ENSP00000408295:R102Q;ENSP00000376325:R81Q	ENSP00000229043:R17Q	R	+	2	0	RFC5	116943131	1.000000	0.71417	0.998000	0.56505	0.461000	0.32589	9.691000	0.98679	1.270000	0.44297	-0.150000	0.13652	CGA	.	.	none		0.388	RFC5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344196.2	NM_007370		A	118458748	G	A	118458748	3	1	1	1	0	0	0	0	1	0	0	0	13263	1058	37	1	325	1	RFC5	12	118458748	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	22049319	118458748	15393147	119	119											
PIWIL1	9271	hgsc.bcm.edu	37	chr12	130855827	130855827	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgaagccagaccacatacagCgcttgacctacaagctgtgc	12	7	9	13	1	0	3	0	2	0	1	0	3	0	3	3	0	6	2	3	0	4	3			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:130855827C>T	ENST00000245255.3	+	20	2700	c.2428C>T	c.(2428-2430)Cgc>Tgc	p.R810C	PIWIL1_ENST00000541480.1_3'UTR	NM_001190971.1|NM_004764.4	NP_001177900.1|NP_004755.2	Q96J94	PIWL1_HUMAN	piwi-like RNA-mediated gene silencing 1	810	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)		CCACATACAGCGCTTGACCTA	0.428																																					p.R810C		Atlas-SNP	.											.	PIWIL1	157	.	0			c.C2428T						PASS	.						192	164	174					12																	130855827		2203	4300	6503	SO:0001583	missense	9271	exon20			ATACAGCGCTTGA	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.2428C>T	12.37:g.130855827C>T	ENSP00000245255:p.Arg810Cys	187	0	0		202	39	0.193069	NM_004764	A4F266|O95404|Q8NA60|Q8TBY5|Q96JD5	Missense_Mutation	SNP	ENST00000245255.3	37	CCDS9268.1	.	.	.	.	.	.	.	.	.	.	C	17.89	3.499927	0.64298	.	.	ENSG00000125207	ENST00000245255	T	0.32515	1.45	5.45	3.49	0.39957	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.053233	0.85682	D	0.000000	T	0.52108	0.1714	M	0.81112	2.525	0.80722	D	1	P;D	0.89917	0.602;1.0	B;D	0.87578	0.178;0.998	T	0.52946	-0.8507	10	0.59425	D	0.04	-29.512	7.1092	0.25380	0.3786:0.5358:0.0:0.0856	.	810;810	Q96J94;Q96J94-2	PIWL1_HUMAN;.	C	810	ENSP00000245255:R810C	ENSP00000245255:R810C	R	+	1	0	PIWIL1	129421780	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	2.059000	0.41384	1.154000	0.42482	0.561000	0.74099	CGC	.	.	none		0.428	PIWIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399510.1			T	130855827	C	T	130855827	3	4	1	1	0	0	0	0	1	0	0	0	11966	768	27	1	2502	1	PIWIL1	12	130855827	Missense_Mutation	SNP	C	TCGA-FA-8693-01A-11D-2397-10	12397079	130855827	2996068	120	120											
SACS	26278	hgsc.bcm.edu	37	chr13	23907902	23907902	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttttctgctctaaatgttgaAgtttggaccatataatgtag	11	17	8	5	0	2	1	0	1	2	0	2	2	2	2	1	1	1	4	1	1	6	8			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr13:23907902A>C	ENST00000382292.3	-	9	10386	c.10113T>G	c.(10111-10113)acT>acG	p.T3371T	SACS_ENST00000382298.3_Silent_p.T3371T|SACS_ENST00000402364.1_Silent_p.T2621T			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3371					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)		TAAATGTTGAAGTTTGGACCA	0.353																																					p.T3371T		Atlas-SNP	.											SACS_ENST00000382298,NS,carcinoma,0,2	SACS	871	2	0			c.T10113G						PASS	.						75	73	74					13																	23907902		2203	4299	6502	SO:0001819	synonymous_variant	26278	exon10			TGTTGAAGTTTGG	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.10113T>G	13.37:g.23907902A>C		90	0	0		96	20	0.208333	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2																																																																																			.	.	none		0.353	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		C	23907902	A	C	23907902	2	2	1	1	0	0	0	0	0	0	0	1	13819	59	3	5		5	SACS	13	23907902	Silent	SNP	A	TCGA-FA-8693-01A-11D-2397-10		23907902	91261976	121	121											
WASF3	10810	hgsc.bcm.edu	37	chr13	27239258	27239258	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcaagacagaattgatcgccTtgctgtcaaagtcacccagc	12	9	8	12	1	3	3	3	1	0	2	4	3	3	3	2	0	2	1	2	0	3	2			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr13:27239258T>C	ENST00000335327.5	+	4	405	c.227T>C	c.(226-228)cTt>cCt	p.L76P	WASF3_ENST00000361042.4_Missense_Mutation_p.L76P|WASF3_ENST00000496788.1_3'UTR	NM_006646.5	NP_006637.2	Q9UPY6	WASF3_HUMAN	WAS protein family, member 3	76					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)		ATTGATCGCCTTGCTGTCAAA	0.413																																					p.L76P		Atlas-SNP	.											.	WASF3	68	.	0			c.T227C						PASS	.						92	85	88					13																	27239258		2203	4300	6503	SO:0001583	missense	10810	exon4			ATCGCCTTGCTGT	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.227T>C	13.37:g.27239258T>C	ENSP00000335055:p.Leu76Pro	79	0	0		110	34	0.309091	NM_006646	O94974|Q86VQ2	Missense_Mutation	SNP	ENST00000335327.5	37	CCDS9318.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.230247	0.79688	.	.	ENSG00000132970	ENST00000361042;ENST00000335327	T;T	0.69040	-0.37;-0.37	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	D	0.85062	0.5611	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	0.88329	0.2967	10	0.87932	D	0	-27.7935	15.8529	0.78947	0.0:0.0:0.0:1.0	.	76;76	Q86VQ2;Q9UPY6	.;WASF3_HUMAN	P	76	ENSP00000354325:L76P;ENSP00000335055:L76P	ENSP00000335055:L76P	L	+	2	0	WASF3	26137258	1.000000	0.71417	0.922000	0.36590	0.865000	0.49528	7.562000	0.82300	2.147000	0.66899	0.528000	0.53228	CTT	.	.	none		0.413	WASF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044258.1			C	27239258	T	C	27239258	3	2	1	1	0	0	0	0	1	0	0	0	17269	1609	56	3	233	3	WASF3	13	27239258	Missense_Mutation	SNP	T	TCGA-FA-8693-01A-11D-2397-10	3331356	27239258	87930620	122	122											
FREM2	341640	hgsc.bcm.edu	37	chr13	39262561	39262561	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgttgatcttcaaccttacTtctccattccagcctggcca	7	14	5	15	0	3	1	1	1	2	0	5	1	4	1	5	1	3	1	5	1	2	5			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr13:39262561T>C	ENST00000280481.7	+	1	1296	c.1080T>C	c.(1078-1080)acT>acC	p.T360T		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	360					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)		TCAACCTTACTTCTCCATTCC	0.572																																					p.T360T		Atlas-SNP	.											.	FREM2	385	.	0			c.T1080C						PASS	.						124	113	117					13																	39262561		2203	4300	6503	SO:0001819	synonymous_variant	341640	exon1			CCTTACTTCTCCA	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.1080T>C	13.37:g.39262561T>C		109	0	0		132	28	0.212121	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																			.	.	none		0.572	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		C	39262561	T	C	39262561	2	2	1	1	0	0	0	0	0	0	0	1	6053	1596	56	3		3	FREM2	13	39262561	Silent	SNP	T	TCGA-FA-8693-01A-11D-2397-10	12023303	39262561	75907317	123	123											
PCDH17	27253	hgsc.bcm.edu	37	chr13	58208119	58208119	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaagggctctacgtgcttcAggtgcacgagaacaacatcc	12	7	10	12	2	2	1	1	0	1	1	3	2	3	1	1	2	5	3	1	2	4	2			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr13:58208119A>G	ENST00000377918.3	+	1	1465	c.1439A>G	c.(1438-1440)cAg>cGg	p.Q480R		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	480	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)|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)		TACGTGCTTCAGGTGCACGAG	0.602																																					p.Q480R	Melanoma(72;952 1291 1619 12849 33676)	Atlas-SNP	.											.	PCDH17	304	.	0			c.A1439G						PASS	.						48	44	46					13																	58208119		2203	4300	6503	SO:0001583	missense	27253	exon1			TGCTTCAGGTGCA	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.1439A>G	13.37:g.58208119A>G	ENSP00000367151:p.Gln480Arg	90	0	0		94	12	0.12766	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Missense_Mutation	SNP	ENST00000377918.3	37	CCDS31986.1	.	.	.	.	.	.	.	.	.	.	A	19.56	3.850826	0.71719	.	.	ENSG00000118946	ENST00000377918	T	0.51071	0.72	5.68	5.68	0.88126	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.55097	0.1899	L	0.31065	0.9	0.58432	D	0.999996	D;D	0.61697	0.988;0.99	P;D	0.64877	0.775;0.93	T	0.52155	-0.8613	9	.	.	.	.	15.9249	0.79609	1.0:0.0:0.0:0.0	.	480;480	O14917-2;O14917	.;PCD17_HUMAN	R	480	ENSP00000367151:Q480R	.	Q	+	2	0	PCDH17	57106120	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.576000	0.82467	2.170000	0.68504	0.459000	0.35465	CAG	.	.	none		0.602	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		G	58208119	A	G	58208119	3	3	1	1	0	0	0	0	1	0	0	0	11521	188	7	3	1441	3	PCDH17	13	58208119	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10	18945558	58208119	56961759	124	124											
CPNE6	9362	hgsc.bcm.edu	37	chr14	24544773	24544773	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaagaattacaagagctcAgggacggtagtgctggccca	14	6	13	8	1	1	3	1	0	0	3	1	4	1	4	1	3	3	3	1	3	6	2			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr14:24544773A>C	ENST00000397016.2	+	10	1148	c.837A>C	c.(835-837)tcA>tcC	p.S279S	CPNE6_ENST00000537691.1_Silent_p.S334S|CPNE6_ENST00000216775.2_Silent_p.S279S	NM_001280558.1	NP_001267487.1	O95741	CPNE6_HUMAN	copine VI (neuronal)	279					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)		ACAAGAGCTCAGGGACGGTAG	0.552																																					p.S279S		Atlas-SNP	.											CPNE6,mouth,carcinoma,+1,1	CPNE6	40	1	0			c.A837C						PASS	.						104	89	94					14																	24544773		2203	4300	6503	SO:0001819	synonymous_variant	9362	exon9			GAGCTCAGGGACG	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.837A>C	14.37:g.24544773A>C		162	0	0		191	32	0.167539	NM_006032	B2RAG6|B7Z1M3|D3DS55|F5GXN1|Q53HA6|Q8WVG1	Silent	SNP	ENST00000397016.2	37	CCDS9607.1																																																																																			.	.	none		0.552	CPNE6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071869.5			C	24544773	A	C	24544773	2	2	1	1	0	0	0	0	0	0	0	1	3818	175	7	5		5	CPNE6	14	24544773	Silent	SNP	A	TCGA-FA-8693-01A-11D-2397-10		24544773	82804767	125	125											
NYNRIN	57523	hgsc.bcm.edu	37	chr14	24878537	24878537	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agggactggaagagggacccGctccagtgctgccaacaggg	10	4	16	11	1	0	1	0	0	0	1	1	4	1	4	3	4	3	2	3	4	2	0			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr14:24878537G>A	ENST00000382554.3	+	4	1855	c.1537G>A	c.(1537-1539)Gct>Act	p.A513T		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	513					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						AGAGGGACCCGCTCCAGTGCT	0.572																																					p.A513T		Atlas-SNP	.											.	NYNRIN	120	.	0			c.G1537A						PASS	.						39	42	41					14																	24878537		1934	4128	6062	SO:0001583	missense	57523	exon4			GGACCCGCTCCAG	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.1537G>A	14.37:g.24878537G>A	ENSP00000371994:p.Ala513Thr	110	0	0		102	13	0.127451	NM_025081	Q6P153|Q86TR3|Q9HAC4	Missense_Mutation	SNP	ENST00000382554.3	37	CCDS45090.1	.	.	.	.	.	.	.	.	.	.	g	7.747	0.702554	0.15172	.	.	ENSG00000205978	ENST00000382554	T	0.09817	2.94	4.63	-3.59	0.04583	.	.	.	.	.	T	0.03348	0.0097	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.44314	-0.9336	9	0.07990	T	0.79	.	2.4094	0.04420	0.2503:0.0823:0.4134:0.2539	.	513	Q9P2P1	NYNRI_HUMAN	T	513	ENSP00000371994:A513T	ENSP00000371994:A513T	A	+	1	0	NYNRIN	23948377	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.413000	0.07123	-0.640000	0.05495	-2.194000	0.00310	GCT	.	.	none		0.572	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1			A	24878537	G	A	24878537	3	1	1	1	0	0	0	0	1	0	0	0	10805	1087	38	1	1547	1	NYNRIN	14	24878537	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	333764	24878537	82471003	126	126											
SYT16	83851	hgsc.bcm.edu	37	chr14	62536400	62536400	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atcaaacaatttgagatttcCgtgtcccggtcccagagttt	10	13	8	10	2	1	2	1	1	0	2	4	3	4	2	3	1	1	1	3	1	2	3			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr14:62536400C>T	ENST00000430451.2	+	2	800	c.603C>T	c.(601-603)tcC>tcT	p.S201S	RP11-355I22.5_ENST00000553990.1_lincRNA|SYT16_ENST00000446982.2_Silent_p.S201S	NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	201					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)		TTGAGATTTCCGTGTCCCGGT	0.483																																					p.S201S		Atlas-SNP	.											.	SYT16	144	.	0			c.C603T						PASS	.						169	159	162					14																	62536400		1932	4125	6057	SO:0001819	synonymous_variant	83851	exon2			GATTTCCGTGTCC	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.603C>T	14.37:g.62536400C>T		212	0	0		227	50	0.220264	NM_031914	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Silent	SNP	ENST00000430451.2	37	CCDS45121.1																																																																																			.	.	none		0.483	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914		T	62536400	C	T	62536400	2	4	1	1	0	0	0	0	0	0	0	1	15487	639	23	1		1	SYT16	14	62536400	Silent	SNP	C	TCGA-FA-8693-01A-11D-2397-10	37657863	62536400	44813140	127	127											
LTBP2	4053	hgsc.bcm.edu	37	chr14	74971792	74971792	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaggacactggagcagggCgcatggcccttctgcccgga	7	5	14	15	2	1	0	0	0	1	0	1	3	1	3	3	5	2	2	3	5	0	1	rs61738017	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr14:74971792C>T	ENST00000261978.4	-	29	4649	c.4263G>A	c.(4261-4263)gcG>gcA	p.A1421A	LTBP2_ENST00000556690.1_Silent_p.A1377A	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	1421	TB 3.				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)		TGGAGCAGGGCGCATGGCCCT	0.662													C|||	101	0.0201677	0.0703	0.0101	5008	,	,		17322	0.0		0.0	False		,,,				2504	0.001				p.A1421A		Atlas-SNP	.											LTBP2,colon,carcinoma,-1,1	LTBP2	158	1	0			c.G4263A						PASS	.	C		268,4138	150.7+/-184.7	12,244,1947	48	48	48		4263	-7.4	0	14	dbSNP_129	48	12,8588	9.1+/-34.3	0,12,4288	no	coding-synonymous	LTBP2	NM_000428.2		12,256,6235	TT,TC,CC		0.1395,6.0826,2.1529		1421/1822	74971792	280,12726	2203	4300	6503	SO:0001819	synonymous_variant	4053	exon29			GCAGGGCGCATGG		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.4263G>A	14.37:g.74971792C>T		38	0	0		49	22	0.44898	NM_000428	Q99907|Q9NS51	Silent	SNP	ENST00000261978.4	37	CCDS9831.1																																																																																			C|0.979;T|0.021	0.021	strong		0.662	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428		T	74971792	C	T	74971792	2	4	1	1	0	0	0	0	0	0	0	1	9083	755	27	1		1	LTBP2	14	74971792	Silent	SNP	C	TCGA-FA-8693-01A-11D-2397-10	12435392	74971792	32377748	128	128											
ATG2B	55102	hgsc.bcm.edu	37	chr14	96771961	96771961	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagaagtgggagggactatTccaaaatcctttcctccata	12	10	10	9	0	0	1	0	0	0	1	4	4	4	3	4	3	0	0	4	3	5	4			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr14:96771961T>A	ENST00000359933.4	-	31	5591	c.4698A>T	c.(4696-4698)ggA>ggT	p.G1566G	ATG2B_ENST00000261834.5_5'UTR	NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	1566					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)		GAGGGACTATTCCAAAATCCT	0.383																																					p.G1566G		Atlas-SNP	.											.	ATG2B	169	.	0			c.A4698T						PASS	.						67	63	64					14																	96771961		2203	4300	6503	SO:0001819	synonymous_variant	55102	exon31			GACTATTCCAAAA	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.4698A>T	14.37:g.96771961T>A		65	0	0		51	18	0.352941	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Silent	SNP	ENST00000359933.4	37	CCDS9944.2																																																																																			.	.	none		0.383	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		A	96771961	T	A	96771961	2	1	1	1	0	0	0	0	0	0	0	1	1094	1770	62	5		5	ATG2B	14	96771961	Silent	SNP	T	TCGA-FA-8693-01A-11D-2397-10	21800169	96771961	10577579	129	129											
HSP90AA1	3320	hgsc.bcm.edu	37	chr14	102552577	102552577	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgatgaatttgaaatgagctCtctcagaaagatctctttgt	12	15	8	6	0	3	6	1	4	2	2	5	6	3	6	0	0	1	1	0	0	3	2			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr14:102552577C>G	ENST00000216281.8	-	2	344	c.139G>C	c.(139-141)Gag>Cag	p.E47Q	HSP90AA1_ENST00000441629.2_5'UTR|HSP90AA1_ENST00000334701.7_Missense_Mutation_p.E169Q	NM_005348.3	NP_005339.3	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 1	47					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)	GAAATGAGCTCTCTCAGAAAG	0.403																																					p.E169Q		Atlas-SNP	.											.	HSP90AA1	65	.	0			c.G505C						PASS	.						51	53	52					14																	102552577		2203	4300	6503	SO:0001583	missense	3320	exon3			TGAGCTCTCTCAG	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.139G>C	14.37:g.102552577C>G	ENSP00000216281:p.Glu47Gln	125	0	0		117	30	0.25641	NM_001017963	A8K500|B3KPJ9|Q2PP14|Q5CAQ6|Q5CAQ7|Q9BVQ5	Missense_Mutation	SNP	ENST00000216281.8	37	CCDS9967.1	.	.	.	.	.	.	.	.	.	.	C	8.396	0.840777	0.16891	.	.	ENSG00000080824	ENST00000216281;ENST00000334701;ENST00000553585	D;D;D	0.85411	-1.98;-1.98;-1.98	3.79	2.88	0.33553	Heat shock protein Hsp90, conserved site (1);Heat shock protein Hsp90, N-terminal (1);ATPase-like, ATP-binding domain (4);	0.000000	0.85682	U	0.000000	D	0.96522	0.8865	H	0.99993	5.365	0.80722	D	1	D;D	0.69078	0.997;0.992	D;D	0.78314	0.99;0.991	D	0.96129	0.9091	10	0.87932	D	0	.	12.6451	0.56729	0.1672:0.8328:0.0:0.0	.	169;47	P07900-2;P07900	.;HS90A_HUMAN	Q	47;169;47	ENSP00000216281:E47Q;ENSP00000335153:E169Q;ENSP00000450712:E47Q	ENSP00000216281:E47Q	E	-	1	0	HSP90AA1	101622330	1.000000	0.71417	0.999000	0.59377	0.175000	0.22909	7.473000	0.81007	0.694000	0.31654	-0.312000	0.09012	GAG	.	.	none		0.403	HSP90AA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414952.2	NM_005348		G	102552577	C	G	102552577	3	3	1	1	0	0	0	0	1	0	0	0	7410	922	32	4	2099	4	HSP90AA1	14	102552577	Missense_Mutation	SNP	C	TCGA-FA-8693-01A-11D-2397-10	5780616	102552577	4796963	130	130											
GABRG3	2567	hgsc.bcm.edu	37	chr15	27765242	27765242	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtgtcattttggatcaaaaaAgatgctacgccagcaagaac	15	9	9	8	1	2	2	2	0	0	2	2	3	2	3	1	1	4	2	1	1	6	3			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr15:27765242A>C	ENST00000333743.6	+	7	1091	c.837A>C	c.(835-837)aaA>aaC	p.K279N	RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	279					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)	GGATCAAAAAAGATGCTACGC	0.348																																					p.K279N	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											.	GABRG3	115	.	0			c.A837C						PASS	.						65	61	62					15																	27765242		1844	4105	5949	SO:0001583	missense	2567	exon7			CAAAAAAGATGCT		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.837A>C	15.37:g.27765242A>C	ENSP00000331912:p.Lys279Asn	112	0	0		124	26	0.209677	NM_033223	G3V594|Q9HD46|Q9NYT2	Missense_Mutation	SNP	ENST00000333743.6	37	CCDS45195.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.47|18.47	3.630222|3.630222	0.67015|0.67015	.|.	.|.	ENSG00000182256|ENSG00000182256	ENST00000333743;ENST00000554696|ENST00000451330	D;D|D	0.86097|0.86030	-2.07;-2.07|-2.06	5.3|5.3	1.55|1.55	0.23275|0.23275	Neurotransmitter-gated ion-channel transmembrane domain (2);|.	0.208504|0.208504	0.49916|0.49916	D|D	0.000133|0.000133	D|D	0.83982|0.83982	0.5372|0.5372	L|L	0.49350|0.49350	1.555|1.555	0.80722|0.80722	D|D	1|1	D|.	0.56521|.	0.976|.	P|.	0.62560|.	0.904|.	T|T	0.80908|0.80908	-0.1172|-0.1172	10|8	0.66056|0.54805	D|T	0.02|0.06	.|.	8.4792|8.4792	0.33032|0.33032	0.6971:0.0:0.3029:0.0|0.6971:0.0:0.3029:0.0	.|.	279|.	Q99928|.	GBRG3_HUMAN|.	N|T	279;221|42	ENSP00000331912:K279N;ENSP00000451862:K221N|ENSP00000390708:K42T	ENSP00000331912:K279N|ENSP00000390708:K88T	K|K	+|+	3|2	2|0	GABRG3|GABRG3	25438837|25438837	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	1.094000|1.094000	0.30951|0.30951	0.430000|0.430000	0.26230|0.26230	0.528000|0.528000	0.53228|0.53228	AAA|AAG	.	.	none		0.348	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2			C	27765242	A	C	27765242	3	2	1	1	0	0	0	0	1	0	0	0	6181	69	3	5	863	5	GABRG3	15	27765242	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10		27765242	74766150	131	131											
ZNF592	9640	hgsc.bcm.edu	37	chr15	85328068	85328068	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgaatgtcacaagcagatgcGggactacatggtcctggctg	10	9	13	9	1	1	2	1	1	0	1	2	3	2	3	1	3	3	2	1	3	3	1	rs549731730		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr15:85328068G>A	ENST00000560079.2	+	4	2450	c.2162G>A	c.(2161-2163)cGg>cAg	p.R721Q	ZNF592_ENST00000299927.3_Missense_Mutation_p.R721Q	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	721					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)			AAGCAGATGCGGGACTACATG	0.582																																					p.R721Q		Atlas-SNP	.											.	ZNF592	95	.	0			c.G2162A						PASS	.						77	71	73					15																	85328068		2203	4299	6502	SO:0001583	missense	9640	exon4			AGATGCGGGACTA	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.2162G>A	15.37:g.85328068G>A	ENSP00000452877:p.Arg721Gln	250	0	0		286	54	0.188811	NM_014630	Q2M1T2|Q504Y9	Missense_Mutation	SNP	ENST00000560079.2	37	CCDS32317.1	.	.	.	.	.	.	.	.	.	.	G	5.267	0.234764	0.09969	.	.	ENSG00000166716	ENST00000299927	T	0.28454	1.61	6.07	1.72	0.24424	Zinc finger, C2H2-like (1);	0.573110	0.19945	N	0.102543	T	0.19127	0.0459	L	0.45581	1.43	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.35475	-0.9787	10	0.02654	T	1	-6.9559	6.7387	0.23422	0.4709:0.0:0.5291:0.0	.	721	Q92610	ZN592_HUMAN	Q	721	ENSP00000299927:R721Q	ENSP00000299927:R721Q	R	+	2	0	ZNF592	83129072	0.011000	0.17503	0.647000	0.29507	0.998000	0.95712	0.820000	0.27323	0.467000	0.27218	0.655000	0.94253	CGG	.	.	none		0.582	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2	NM_014630		A	85328068	G	A	85328068	3	1	1	1	0	0	0	0	1	0	0	0	18037	1116	39	1	2164	1	ZNF592	15	85328068	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	57562826	85328068	17203324	132	132											
CHTF18	63922	hgsc.bcm.edu	37	chr16	847932	847932	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	ccgcttcaacgagggtgtctCcaacgccgtgcggcgcagcc	6	6	13	16	6	2	0	1	0	1	0	3	1	2	0	4	2	4	2	4	2	2	1			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr16:847932C>G	ENST00000262315.9	+	22	2948	c.2885C>G	c.(2884-2886)tCc>tGc	p.S962C	CHTF18_ENST00000455171.2_Missense_Mutation_p.S990C|CHTF18_ENST00000317063.6_Missense_Mutation_p.S1171C	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	962					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)				GAGGGTGTCTCCAACGCCGTG	0.657																																					p.S962C		Atlas-SNP	.											.	CHTF18	52	.	0			c.C2885G						PASS	.						33	40	38					16																	847932		2120	4231	6351	SO:0001583	missense	63922	exon22			GTGTCTCCAACGC	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.2885C>G	16.37:g.847932C>G	ENSP00000262315:p.Ser962Cys	88	0	0		81	7	0.0864198	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Missense_Mutation	SNP	ENST00000262315.9	37	CCDS45371.1	.	.	.	.	.	.	.	.	.	.	C	16.70	3.196489	0.58126	.	.	ENSG00000127586	ENST00000317063;ENST00000455171;ENST00000262315	T;T;T	0.22134	1.97;2.11;2.08	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.51890	0.1701	M	0.82323	2.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.57711	-0.7764	10	0.87932	D	0	-42.161	17.6563	0.88179	0.0:1.0:0.0:0.0	.	990;962	Q8WVB6-2;Q8WVB6	.;CTF18_HUMAN	C	1171;990;962	ENSP00000313029:S1171C;ENSP00000406252:S990C;ENSP00000262315:S962C	ENSP00000262315:S962C	S	+	2	0	CHTF18	787933	1.000000	0.71417	0.996000	0.52242	0.334000	0.28698	7.419000	0.80179	2.529000	0.85273	0.561000	0.74099	TCC	.	.	none		0.657	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092		G	847932	C	G	847932	3	3	1	1	0	0	0	0	1	0	0	0	3416	855	30	4	2971	4	CHTF18	16	847932	Missense_Mutation	SNP	C	TCGA-FA-8693-01A-11D-2397-10		847932	89506821	133	133											
GLYR1	84656	hgsc.bcm.edu	37	chr16	4882161	4882161	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcatcacctgagtttggcCtacttctctcctcactggaa	7	14	6	14	0	4	1	3	1	2	0	7	2	5	2	3	2	1	1	3	2	2	3			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr16:4882161C>T	ENST00000321919.9	-	5	432	c.356G>A	c.(355-357)aGg>aAg	p.R119K	GLYR1_ENST00000436648.5_Intron|GLYR1_ENST00000586901.1_5'UTR|GLYR1_ENST00000591451.1_Missense_Mutation_p.R119K|GLYR1_ENST00000381983.3_Missense_Mutation_p.R119K	NM_032569.3	NP_115958	Q49A26	GLYR1_HUMAN	glyoxylate reductase 1 homolog (Arabidopsis)	119					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						TGAGTTTGGCCTACTTCTCTC	0.433																																					p.R119K		Atlas-SNP	.											.	GLYR1	49	.	0			c.G356A						PASS	.						177	156	163					16																	4882161		2197	4300	6497	SO:0001583	missense	84656	exon5			TTTGGCCTACTTC	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.356G>A	16.37:g.4882161C>T	ENSP00000322716:p.Arg119Lys	257	0	0		255	43	0.168627	NM_032569	B4DL47|C9JJ40|C9JJ60|Q5U632|Q6P1Q2|Q6V3W7|Q9BTI1|Q9BXK2	Missense_Mutation	SNP	ENST00000321919.9	37	CCDS10524.1	.	.	.	.	.	.	.	.	.	.	C	11.48	1.651816	0.29336	.	.	ENSG00000140632	ENST00000321919;ENST00000381983	T;T	0.61742	0.08;0.08	5.29	4.32	0.51571	.	0.300170	0.38326	N	0.001739	T	0.33673	0.0871	N	0.08118	0	0.28988	N	0.888228	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.13045	-1.0524	10	0.37606	T	0.19	-24.4605	8.8028	0.34918	0.0:0.8427:0.0:0.1573	.	119;119;119	Q49A26-3;Q49A26-2;Q49A26	.;.;GLYR1_HUMAN	K	119	ENSP00000322716:R119K;ENSP00000371413:R119K	ENSP00000322716:R119K	R	-	2	0	GLYR1	4822162	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.203000	0.42752	2.634000	0.89283	0.650000	0.86243	AGG	.	.	none		0.433	GLYR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251717.2	NM_032569		T	4882161	C	T	4882161	3	4	1	1	0	0	0	0	1	0	0	0	6491	681	24	2	1353	2	GLYR1	16	4882161	Missense_Mutation	SNP	C	TCGA-FA-8693-01A-11D-2397-10	4034229	4882161	85472592	134	134											
USP31	57478	hgsc.bcm.edu	37	chr16	23117736	23117736	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atacctgtattgcgcttgaaAgagttcttgtacaaaagtgc	12	13	9	7	1	1	2	0	1	1	1	1	2	1	2	1	0	4	4	1	0	6	7			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr16:23117736A>C	ENST00000219689.7	-	3	843	c.844T>G	c.(844-846)Ttt>Gtt	p.F282V		NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	213	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)		TGCGCTTGAAAGAGTTCTTGT	0.388																																					p.F282V		Atlas-SNP	.											.	USP31	122	.	0			c.T844G						PASS	.						79	72	75					16																	23117736		2197	4300	6497	SO:0001583	missense	57478	exon3			CTTGAAAGAGTTC	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.844T>G	16.37:g.23117736A>C	ENSP00000219689:p.Phe282Val	201	0	0		249	40	0.160643	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000219689.7	37	CCDS10607.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.559863	0.86335	.	.	ENSG00000103404	ENST00000219689	T	0.48522	0.81	5.5	5.5	0.81552	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.060995	0.64402	D	0.000003	T	0.74824	0.3767	M	0.92026	3.265	0.80722	D	1	D	0.69078	0.997	D	0.79108	0.992	T	0.81360	-0.0968	10	0.87932	D	0	-20.3252	15.0849	0.72145	1.0:0.0:0.0:0.0	.	282	Q70CQ4	UBP31_HUMAN	V	282	ENSP00000219689:F282V	ENSP00000219689:F282V	F	-	1	0	USP31	23025237	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.851000	0.92205	2.214000	0.71695	0.523000	0.50628	TTT	.	.	none		0.388	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718		C	23117736	A	C	23117736	3	2	1	1	0	0	0	0	1	0	0	0	17077	72	3	5	3270	5	USP31	16	23117736	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10	18235575	23117736	67237017	135	135											
RABEP2	79874	hgsc.bcm.edu	37	chr16	28935738	28935738	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcacctttcaggatggccTgcagcgaggccacctcctct	6	10	9	16	1	3	0	2	0	2	0	5	2	4	1	5	3	2	1	5	3	0	1			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr16:28935738T>C	ENST00000358201.4	-	2	848	c.260A>G	c.(259-261)cAg>cGg	p.Q87R	RABEP2_ENST00000544477.1_Intron|RABEP2_ENST00000357573.6_Missense_Mutation_p.Q87R|RABEP2_ENST00000561803.1_5'UTR	NM_024816.2	NP_079092.2	Q9H5N1	RABE2_HUMAN	rabaptin, RAB GTPase binding effector protein 2	87					endocytosis (GO:0006897)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	16						CAGGATGGCCTGCAGCGAGGC	0.607																																					p.Q87R	Pancreas(66;639 1284 10093 31061 49099)	Atlas-SNP	.											.	RABEP2	48	.	0			c.A260G						PASS	.						47	49	48					16																	28935738		2102	4240	6342	SO:0001583	missense	79874	exon2			ATGGCCTGCAGCG	AK026935	CCDS42140.1	16p11.2	2014-09-11			ENSG00000177548	ENSG00000177548			24817	protein-coding gene	gene with protein product		611869				12477932	Standard	NM_024816		Approved	FRA, FLJ23282	uc002drq.3	Q9H5N1	OTTHUMG00000176593	ENST00000358201.4:c.260A>G	16.37:g.28935738T>C	ENSP00000350934:p.Gln87Arg	73	0	0		81	10	0.123457	NM_024816		Missense_Mutation	SNP	ENST00000358201.4	37	CCDS42140.1	.	.	.	.	.	.	.	.	.	.	T	14.78	2.637917	0.47049	.	.	ENSG00000177548	ENST00000358201;ENST00000357573	T;T	0.58210	0.39;0.35	4.29	4.29	0.51040	Rabaptin coiled-coil domain (1);	0.000000	0.85682	D	0.000000	T	0.67097	0.2857	L	0.58810	1.83	0.80722	D	1	D;D;D	0.69078	0.992;0.997;0.994	D;D;D	0.81914	0.979;0.995;0.988	T	0.70461	-0.4865	10	0.72032	D	0.01	-26.7142	12.7364	0.57228	0.0:0.0:0.0:1.0	.	87;87;87	Q9H5N1-2;Q49AT6;Q9H5N1	.;.;RABE2_HUMAN	R	87	ENSP00000350934:Q87R;ENSP00000350186:Q87R	ENSP00000350186:Q87R	Q	-	2	0	RABEP2	28843239	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	7.284000	0.78650	1.711000	0.51337	0.454000	0.30748	CAG	.	.	none		0.607	RABEP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432691.1	NM_024816		C	28935738	T	C	28935738	3	2	1	1	0	0	0	0	1	0	0	0	12977	1580	55	3	1497	3	RABEP2	16	28935738	Missense_Mutation	SNP	T	TCGA-FA-8693-01A-11D-2397-10	5818002	28935738	61419015	136	136											
ZNF629	23361	hgsc.bcm.edu	37	chr16	30795076	30795076	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgctggtgctgcaccaggtgCgagctctgcgtgaagctctt	5	10	14	12	3	2	1	0	1	2	0	2	2	2	1	1	2	6	5	1	2	1	1			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr16:30795076C>T	ENST00000262525.4	-	3	780	c.573G>A	c.(571-573)tcG>tcA	p.S191S		NM_001080417.1	NP_001073886.1	Q9UEG4	ZN629_HUMAN	zinc finger protein 629	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)|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)			GCACCAGGTGCGAGCTCTGCG	0.662																																					p.S191S		Atlas-SNP	.											ZNF629,colon,carcinoma,-1,1	ZNF629	44	1	0			c.G573A						PASS	.						45	47	46					16																	30795076		2197	4300	6497	SO:0001819	synonymous_variant	23361	exon3			CAGGTGCGAGCTC	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.573G>A	16.37:g.30795076C>T		16	0	0		20	7	0.35	NM_001080417	Q15938	Silent	SNP	ENST00000262525.4	37	CCDS45463.1																																																																																			.	.	none		0.662	ZNF629-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434291.1	NM_015309		T	30795076	C	T	30795076	2	4	1	1	0	0	0	0	0	0	0	1	18068	755	27	1		1	ZNF629	16	30795076	Silent	SNP	C	TCGA-FA-8693-01A-11D-2397-10	1859338	30795076	59559677	137	137											
HSD3B7	80270	hgsc.bcm.edu	37	chr16	30997460	30997460	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcccatgtggtcatccacaCggctgggctggtagacgtgt	7	9	14	11	2	1	1	1	0	0	1	2	1	2	1	2	4	1	3	2	4	1	1	rs371576756		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr16:30997460C>T	ENST00000297679.5	+	3	350	c.257C>T	c.(256-258)aCg>aTg	p.T86M	HSD3B7_ENST00000262520.6_Missense_Mutation_p.T86M|HSD3B7_ENST00000353250.5_Missense_Mutation_p.T86M|AC135048.1_ENST00000602217.1_Missense_Mutation_p.R25H	NM_025193.3	NP_079469.2	Q9H2F3	3BHS7_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7	86					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|cholest-5-ene-3-beta,7-alpha-diol 3-beta-dehydrogenase activity (GO:0047016)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						GTCATCCACACGGCTGGGCTG	0.652																																					p.T86M		Atlas-SNP	.											.	HSD3B7	33	.	0			c.C257T						PASS	.	C	MET/THR,MET/THR,MET/THR	1,4393	2.1+/-5.4	0,1,2196	56	48	51		257,257,257	0.2	0.9	16		51	0,8600		0,0,4300	no	missense,missense,missense	HSD3B7	NM_001142777.1,NM_001142778.1,NM_025193.3	81,81,81	0,1,6496	TT,TC,CC		0.0,0.0228,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	86/197,86/197,86/370	30997460	1,12993	2197	4300	6497	SO:0001583	missense	80270	exon3			TCCACACGGCTGG	AF277719	CCDS10698.1, CCDS45466.1	16p11.2	2011-09-14			ENSG00000099377	ENSG00000099377	1.1.1.-	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	18324	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 11E, member 3"	607764				11067870, 19027726	Standard	NM_001142777		Approved	C(27)-3BETA-HSD, SDR11E3	uc002eaf.2	Q9H2F3	OTTHUMG00000132417	ENST00000297679.5:c.257C>T	16.37:g.30997460C>T	ENSP00000297679:p.Thr86Met	318	0	0		355	74	0.208451	NM_025193	Q96M28|Q9BSN9	Missense_Mutation	SNP	ENST00000297679.5	37	CCDS10698.1	.	.	.	.	.	.	.	.	.	.	C	17.65	3.442073	0.63067	2.28E-4	0.0	ENSG00000099377	ENST00000262520;ENST00000353250;ENST00000297679	D;D;D	0.88586	-2.4;-2.4;-2.03	4.84	0.206	0.15208	3-beta hydroxysteroid dehydrogenase/isomerase (1);NAD(P)-binding domain (1);	0.448337	0.25391	N	0.031012	D	0.86222	0.5881	L	0.53617	1.68	0.27401	N	0.954856	P;P	0.51057	0.941;0.895	P;P	0.46850	0.473;0.529	T	0.80193	-0.1484	10	0.62326	D	0.03	-0.1907	9.4723	0.38851	0.0:0.6139:0.0:0.3861	.	86;86	Q96M28;Q9H2F3	.;3BHS7_HUMAN	M	86	ENSP00000262520:T86M;ENSP00000370662:T86M;ENSP00000297679:T86M	ENSP00000262520:T86M	T	+	2	0	HSD3B7	30904961	0.025000	0.19082	0.859000	0.33776	0.922000	0.55478	1.024000	0.30077	0.198000	0.20407	-0.377000	0.06932	ACG	.	.	weak		0.652	HSD3B7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255554.2			T	30997460	C	T	30997460	3	4	1	1	0	0	0	0	1	0	0	0	7401	536	19	1	263	1	HSD3B7	16	30997460	Missense_Mutation	SNP	C	TCGA-FA-8693-01A-11D-2397-10	202384	30997460	59357293	138	138											
TOX3	27324	hgsc.bcm.edu	37	chr16	52478202	52478202	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttaccttagaaacgaggcTggccctgtatgccgccaggg	8	9	13	11	2	0	1	0	0	0	1	0	2	0	1	4	3	3	3	4	3	4	4			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr16:52478202T>C	ENST00000219746.9	-	6	1257	c.973A>G	c.(973-975)Agc>Ggc	p.S325G	TOX3_ENST00000407228.3_Missense_Mutation_p.S320G	NM_001080430.2	NP_001073899.2	O15405	TOX3_HUMAN	TOX high mobility group box family member 3	325					apoptotic process (GO:0006915)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|estrogen response element binding (GO:0034056)|phosphoprotein binding (GO:0051219)|protein homodimerization activity (GO:0042803)			NS(2)|endometrium(6)|kidney(1)|lung(8)|prostate(3)|stomach(3)|upper_aerodigestive_tract(1)	24						GAAACGAGGCTGGCCCTGTAT	0.478																																					p.S325G		Atlas-SNP	.											.	TOX3	121	.	0			c.A973G						PASS	.						44	43	43					16																	52478202		1826	4090	5916	SO:0001583	missense	27324	exon6			CGAGGCTGGCCCT	U80736	CCDS54008.1, CCDS54009.1	16q12.1	2008-02-05	2007-03-20	2007-03-20		ENSG00000103460		"Trinucleotide (CAG) repeat containing"	11972	protein-coding gene	gene with protein product		611416	"trinucleotide repeat containing 9"	TNRC9		9225980	Standard	NM_001080430		Approved	CAGF9	uc002egw.2	O15405		ENST00000219746.9:c.973A>G	16.37:g.52478202T>C	ENSP00000219746:p.Ser325Gly	64	0	0		63	7	0.111111	NM_001080430	B4DRD0|B5MCW4	Missense_Mutation	SNP	ENST00000219746.9	37	CCDS54009.1	.	.	.	.	.	.	.	.	.	.	T	19.68	3.873421	0.72180	.	.	ENSG00000103460	ENST00000219746;ENST00000407228	T;T	0.45668	0.89;0.89	5.35	5.35	0.76521	High mobility group, HMG1/HMG2, subgroup (1);High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (1);	0.000000	0.85682	D	0.000000	T	0.39627	0.1085	L	0.27053	0.805	0.58432	D	0.999997	P;P	0.35612	0.512;0.512	B;B	0.42522	0.39;0.39	T	0.37865	-0.9687	10	0.59425	D	0.04	.	15.6388	0.76977	0.0:0.0:0.0:1.0	.	320;325	B4DRD0;O15405	.;TOX3_HUMAN	G	325;320	ENSP00000219746:S325G;ENSP00000385705:S320G	ENSP00000219746:S325G	S	-	1	0	TOX3	51035703	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.232000	0.72313	2.169000	0.68431	0.528000	0.53228	AGC	.	.	none		0.478	TOX3-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000422534.1	XM_049037		C	52478202	T	C	52478202	3	2	1	1	0	0	0	0	1	0	0	0	16394	1580	55	3	765	3	TOX3	16	52478202	Missense_Mutation	SNP	T	TCGA-FA-8693-01A-11D-2397-10	21480742	52478202	37876551	139	139											
ABR	29	hgsc.bcm.edu	37	chr17	970326	970326	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gctctgctcacctccttctgGatttcactcttgagggcaga	6	13	9	13	0	5	2	2	1	3	1	6	3	6	3	2	2	1	3	2	2	0	3			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:970326G>A	ENST00000302538.5	-	10	1319	c.1173C>T	c.(1171-1173)atC>atT	p.I391I	ABR_ENST00000536794.2_Silent_p.I173I|ABR_ENST00000544583.2_Silent_p.I345I|ABR_ENST00000291107.2_Silent_p.I354I|ABR_ENST00000574437.1_Silent_p.I345I	NM_001282149.1|NM_021962.3	NP_001269078.1|NP_068781.2	Q12979	ABR_HUMAN	active BCR-related	391	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)		CCTCCTTCTGGATTTCACTCT	0.572																																					p.I391I	Esophageal Squamous(197;2016 2115 4129 29033 46447)	Atlas-SNP	.											.	ABR	119	.	0			c.C1173T						PASS	.						55	43	47					17																	970326		2203	4300	6503	SO:0001819	synonymous_variant	29	exon10			CTTCTGGATTTCA	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.1173C>T	17.37:g.970326G>A		110	0	0		76	21	0.276316	NM_021962	B3KW89|B7Z6H7|D3DTH3|D3DTH4|F5H3S2|F5H8B3|Q13693|Q13694	Silent	SNP	ENST00000302538.5	37	CCDS10999.1																																																																																			.	.	none		0.572	ABR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206675.4			A	970326	G	A	970326	2	1	1	1	0	0	0	0	0	0	0	1	99	1164	41	2		2	ABR	17	970326	Silent	SNP	G	TCGA-FA-8693-01A-11D-2397-10		970326	80224884	140	140											
MYH1	4619	hgsc.bcm.edu	37	chr17	10409204	10409204	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggatgccttccagcacaccgTtacacctcagctgatgcagg	9	8	10	14	1	1	1	1	1	0	0	2	2	2	2	4	2	5	4	4	2	1	2			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:10409204T>G	ENST00000226207.5	-	19	2193	c.2099A>C	c.(2098-2100)aAc>aCc	p.N700T	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	700	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						CAGCACACCGTTACACCTCAG	0.468																																					p.N700T		Atlas-SNP	.											MYH1,NS,carcinoma,+1,1	MYH1	403	1	0			c.A2099C						PASS	.						76	64	68					17																	10409204		2203	4298	6501	SO:0001583	missense	4619	exon19			ACACCGTTACACC		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.2099A>C	17.37:g.10409204T>G	ENSP00000226207:p.Asn700Thr	490	0	0		521	88	0.168906	NM_005963	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	37	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	T	17.41	3.381448	0.61845	.	.	ENSG00000109061	ENST00000226207	T	0.71579	-0.58	4.94	4.94	0.65067	Myosin head, motor domain (2);	0.000000	0.46442	U	0.000282	T	0.77418	0.4127	M	0.82132	2.575	0.58432	D	0.999997	P	0.38078	0.617	B	0.44085	0.44	T	0.81516	-0.0897	10	0.87932	D	0	.	15.0655	0.71992	0.0:0.0:0.0:1.0	.	700	P12882	MYH1_HUMAN	T	700	ENSP00000226207:N700T	ENSP00000226207:N700T	N	-	2	0	MYH1	10349929	1.000000	0.71417	0.896000	0.35187	0.920000	0.55202	7.698000	0.84413	2.216000	0.71823	0.528000	0.53228	AAC	.	.	none		0.468	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		G	10409204	T	G	10409204	3	3	1	1	0	0	0	0	1	0	0	0	10038	1725	60	5	3808	5	MYH1	17	10409204	Missense_Mutation	SNP	T	TCGA-FA-8693-01A-11D-2397-10	9438878	10409204	70786006	141	141											
RICH2	9912	hgsc.bcm.edu	37	chr17	12859254	12859254	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agatgactcccagtaatatgGcaattgttttaggacccaac	13	11	8	9	0	0	2	0	1	0	1	1	3	1	3	2	2	1	3	2	2	5	5			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:12859254G>A	ENST00000379672.5	+	14	1507	c.1207G>A	c.(1207-1209)Gca>Aca	p.A403T	ARHGAP44_ENST00000340825.3_Missense_Mutation_p.A403T|ARHGAP44_ENST00000262444.9_Missense_Mutation_p.A403T	NM_014859.4	NP_055674.4	Q17R89	RHG44_HUMAN	Rho GTPase activating protein 44	403	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						CAGTAATATGGCAATTGTTTT	0.428																																					p.A403T		Atlas-SNP	.											.	ARHGAP44	55	.	0			c.G1207A						PASS	.						72	69	70					17																	12859254		1959	4140	6099	SO:0001583	missense	9912	exon14			AATATGGCAATTG		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.1207G>A	17.37:g.12859254G>A	ENSP00000368994:p.Ala403Thr	236	0	0		210	38	0.180952	NM_014859	A6NCP5|A8MQB2|O75160|Q7Z5Z7|Q9Y4Q4	Missense_Mutation	SNP	ENST00000379672.5	37	CCDS45616.1	.	.	.	.	.	.	.	.	.	.	G	17.50	3.406245	0.62288	.	.	ENSG00000006740	ENST00000379672;ENST00000544416;ENST00000340825	T;T	0.25250	1.81;1.81	5.89	5.89	0.94794	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.67906	0.2943	H	0.97564	4.03	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;0.998;0.997;0.992	T	0.79415	-0.1813	10	0.87932	D	0	.	17.7556	0.88447	0.0:0.0:1.0:0.0	.	403;48;65;403	A6NCP5;Q9Y4Q4;F5H6L3;Q17R89	.;.;.;RHG44_HUMAN	T	403;65;403	ENSP00000368994:A403T;ENSP00000342566:A403T	ENSP00000342566:A403T	A	+	1	0	ARHGAP44	12799979	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.420000	0.97426	2.793000	0.96121	0.655000	0.94253	GCA	.	.	none		0.428	ARHGAP44-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441566.1	NM_014859		A	12859254	G	A	12859254	3	1	1	1	0	0	0	0	1	0	0	0	13372	1203	42	2	1261	2	RICH2	17	12859254	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	2450050	12859254	68335956	142	142											
MAP2K3	5606	hgsc.bcm.edu	37	chr17	21206529	21206529	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagcatctgcacagcaagcTgtcggtgatccacagaggtc	10	7	13	11	1	1	2	0	1	1	1	4	3	2	3	1	3	4	4	1	3	1	0			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:21206529T>C	ENST00000342679.4	+	7	800	c.551T>C	c.(550-552)cTg>cCg	p.L184P	MAP2K3_ENST00000316920.6_Missense_Mutation_p.L155P|MAP2K3_ENST00000361818.5_Missense_Mutation_p.L155P	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	184	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		CACAGCAAGCTGTCGGTGATC	0.632																																					p.L184P		Atlas-SNP	.											.	MAP2K3	135	.	0			c.T551C						PASS	.						50	42	45					17																	21206529		2203	4300	6503	SO:0001583	missense	5606	exon7			GCAAGCTGTCGGT	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.551T>C	17.37:g.21206529T>C	ENSP00000345083:p.Leu184Pro	89	0	0		98	12	0.122449	NM_145109	B3KSK7|Q99441|Q9UE71|Q9UE72	Missense_Mutation	SNP	ENST00000342679.4	37	CCDS11217.1	.	.	.	.	.	.	.	.	.	.	T	14.32	2.501712	0.44455	.	.	ENSG00000034152	ENST00000342679;ENST00000395491;ENST00000361818;ENST00000316920	T;T	0.40756	1.02;1.02	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	0.52532	D	0.000069	T	0.63534	0.2519	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.67325	-0.5699	10	0.87932	D	0	-29.8457	15.5058	0.75739	0.0:0.0:0.0:1.0	.	184	P46734	MP2K3_HUMAN	P	184;155;155;188	ENSP00000345083:L184P;ENSP00000355081:L155P	ENSP00000319139:L188P	L	+	2	0	MAP2K3	21147122	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.679000	0.84048	2.077000	0.62373	0.459000	0.35465	CTG	.	.	none		0.632	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259374.2	NM_145109		C	21206529	T	C	21206529	3	2	1	1	0	0	0	0	1	0	0	0	9247	1580	55	3	577	3	MAP2K3	17	21206529	Missense_Mutation	SNP	T	TCGA-FA-8693-01A-11D-2397-10	8347275	21206529	59988681	143	143											
NF1	4763	hgsc.bcm.edu	37	chr17	29661926	29661927	+	Frame_Shift_Ins	INS	-	-	C																															atctagttcgtttttgcaagINScataatgatgatgccaaacg																								rs144808600	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:29661926_29661927insC	ENST00000358273.4	+	40	6266_6267	c.5883_5884insC	c.(5884-5886)catfs	p.H1962fs	NF1_ENST00000417592.2_5'Flank|NF1_ENST00000581113.2_3'UTR|NF1_ENST00000356175.3_Frame_Shift_Ins_p.H1941fs|NF1_ENST00000444181.2_5'Flank	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1962					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)		GTTTTTGCAAGCATAATGATGA	0.351			"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.K1961fs		Pindel,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.5883_5884insC						PASS	.																																			SO:0001589	frameshift_variant	4763	exon40	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.5884dupC	17.37:g.29661927_29661927dupC	ENSP00000351015:p.His1962fs	125	0	.		145	24	0.166	NM_001042492	O00662|Q14284|Q14930|Q14931|Q9UMK3	Frame_Shift_Ins	INS	ENST00000358273.4	37	CCDS42292.1																																																																																			.	.	none		0.351	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		C	29661927	-	C	29661926	7	5	1	1	0	1	1	0	0	0	0	0	10365	962	34	0	6102	0	NF1	17	29661926	Frame_Shift_Ins	INS	-	TCGA-FA-8693-01A-11D-2397-10	8455397	29661926	51533284	144	144											
UNC45B	146862	hgsc.bcm.edu	37	chr17	33497208	33497208	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggcctacctcacgctggaCgctgatgtgaaggacgactt	8	9	12	12	3	1	2	1	2	0	0	1	5	1	4	2	3	1	2	2	3	2	2	rs531660473		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:33497208C>T	ENST00000268876.5	+	12	1720	c.1623C>T	c.(1621-1623)gaC>gaT	p.D541D	UNC45B_ENST00000591048.1_Intron|UNC45B_ENST00000433649.1_Silent_p.D541D|UNC45B_ENST00000394570.2_Silent_p.D541D|UNC45B_ENST00000378449.1_Intron	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	541					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)				TCACGCTGGACGCTGATGTGA	0.617													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18902	0.0		0.0	False		,,,				2504	0.0				p.D541D		Atlas-SNP	.											.	UNC45B	133	.	0			c.C1623T						PASS	.						77	62	67					17																	33497208		2203	4300	6503	SO:0001819	synonymous_variant	146862	exon12			GCTGGACGCTGAT	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.1623C>T	17.37:g.33497208C>T		169	0	0		150	23	0.153333	NM_001267052	Q495Q8|Q495Q9	Silent	SNP	ENST00000268876.5	37	CCDS11292.1																																																																																			.	.	none		0.617	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2	NM_173167		T	33497208	C	T	33497208	2	4	1	1	0	0	0	0	0	0	0	1	17004	535	19	1		1	UNC45B	17	33497208	Silent	SNP	C	TCGA-FA-8693-01A-11D-2397-10	3835282	33497208	47698002	145	145											
GSDMA	284110	hgsc.bcm.edu	37	chr17	38122591	38122591	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatgtggatgtaccaaagaCggtgaaggtgaagggaacgg	14	6	17	4	2	0	4	0	2	0	2	0	6	0	6	1	5	2	1	1	5	5	1	rs140044904	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:38122591C>T	ENST00000301659.4	+	3	411	c.293C>T	c.(292-294)aCg>aTg	p.T98M		NM_178171.4	NP_835465.2	Q96QA5	GSDMA_HUMAN	gasdermin A	98					apoptotic process (GO:0006915)	perinuclear region of cytoplasm (GO:0048471)				NS(1)|endometrium(2)|large_intestine(3)|lung(1)	7						GTACCAAAGACGGTGAAGGTG	0.552													C|||	33	0.00658946	0.0242	0.0014	5008	,	,		18543	0.0		0.0	False		,,,				2504	0.0				p.T98M		Atlas-SNP	.											.	GSDMA	26	.	0			c.C293T						PASS	.	C	MET/THR	42,3964		0,42,1961	107	111	110		293	5.5	1	17	dbSNP_134	110	0,8332		0,0,4166	yes	missense	GSDMA	NM_178171.4	81	0,42,6127	TT,TC,CC		0.0,1.0484,0.3404	benign	98/446	38122591	42,12296	2003	4166	6169	SO:0001583	missense	284110	exon3			CAAAGACGGTGAA	AB093591	CCDS45669.1	17q21.2	2008-07-31	2008-07-31	2008-07-31		ENSG00000167914			13311	protein-coding gene	gene with protein product		611218	"gasdermin", "gasdermin 1"	GSDM, GSDM1		12883658, 15010812, 17350798	Standard	NM_178171		Approved	FLJ39120	uc002htl.1	Q96QA5		ENST00000301659.4:c.293C>T	17.37:g.38122591C>T	ENSP00000301659:p.Thr98Met	298	0	0		278	54	0.194245	NM_178171	Q32MC5|Q86VE7|Q8N1M6	Missense_Mutation	SNP	ENST00000301659.4	37	CCDS45669.1	20	0.009157509157509158	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	0	0.0	C	11.66	1.704373	0.30232	0.010484	0.0	ENSG00000167914	ENST00000301659	T	0.23147	1.92	5.5	5.5	0.81552	.	0.442749	0.21282	N	0.077127	T	0.04318	0.0119	L	0.36672	1.1	0.35397	D	0.791245	P	0.39404	0.672	B	0.27887	0.084	T	0.14531	-1.0469	10	0.48119	T	0.1	-0.926	14.8824	0.70542	0.0:1.0:0.0:0.0	.	98	Q96QA5	GSDMA_HUMAN	M	98	ENSP00000301659:T98M	ENSP00000301659:T98M	T	+	2	0	GSDMA	35376117	0.987000	0.35691	0.972000	0.41901	0.744000	0.42396	3.521000	0.53472	2.581000	0.87130	0.563000	0.77884	ACG	C|0.991;T|0.009	0.009	strong		0.552	GSDMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446847.1	NM_178171		T	38122591	C	T	38122591	3	4	1	1	0	0	0	0	1	0	0	0	6825	536	19	1	299	1	GSDMA	17	38122591	Missense_Mutation	SNP	C	TCGA-FA-8693-01A-11D-2397-10	4625383	38122591	43072619	146	146											
SFRS1	6426	hgsc.bcm.edu	37	chr17	56083867	56083867	+	Nonsense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taatcatagccgtcgcgaccAtacaccgcgtcttccgcgtc	8	9	8	16	7	2	0	1	0	1	0	5	1	3	0	4	0	2	0	4	0	3	4			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:56083867A>C	ENST00000258962.4	-	2	424	c.216T>G	c.(214-216)taT>taG	p.Y72*	SRSF1_ENST00000582730.2_Nonsense_Mutation_p.Y72*|RP11-159D12.5_ENST00000578794.1_5'Flank|SRSF1_ENST00000581497.1_5'Flank|SRSF1_ENST00000584773.1_Nonsense_Mutation_p.Y72*|SRSF1_ENST00000585096.1_Intron	NM_006924.4	NP_008855.1	Q07955	SRSF1_HUMAN	serine/arginine-rich splicing factor 1	72	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				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						CGTCGCGACCATACACCGCGT	0.627																																					p.Y72X		Atlas-SNP	.											.	SRSF1	41	.	0			c.T216G						PASS	.						28	25	26					17																	56083867		2202	4288	6490	SO:0001587	stop_gained	6426	exon2			GCGACCATACACC		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.216T>G	17.37:g.56083867A>C	ENSP00000258962:p.Tyr72*	149	0	0		174	42	0.241379	NM_006924	B2R6Z7|D3DTZ3|Q13809	Nonsense_Mutation	SNP	ENST00000258962.4	37	CCDS11600.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.381974	0.82792	.	.	ENSG00000136450	ENST00000258962	.	.	.	5.96	-3.56	0.04626	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.7599	0.62959	0.5977:0.0:0.4023:0.0	.	.	.	.	X	72	.	ENSP00000258962:Y72X	Y	-	3	2	SRSF1	53438866	0.877000	0.30153	0.866000	0.34008	0.984000	0.73092	0.001000	0.13038	-0.941000	0.03700	-0.899000	0.02877	TAT	.	.	none		0.627	SRSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443335.1	NM_006924		C	56083867	A	C	56083867	4	2	1	1	0	0	0	0	0	1	0	0	14180	224	8	5	596	5	SFRS1	17	56083867	Nonsense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10	17961276	56083867	25111343	147	147											
DDX42	11325	hgsc.bcm.edu	37	chr17	61895140	61895140	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggcaagtgggtggactagTgcagggagcttgaattctgt	8	10	18	5	0	1	1	0	1	1	0	1	3	1	3	0	5	2	3	0	5	3	3			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:61895140T>C	ENST00000578681.1	+	19	2800	c.2199T>C	c.(2197-2199)agT>agC	p.S733S	DDX42_ENST00000457800.2_Silent_p.S733S|DDX42_ENST00000583590.1_Silent_p.S733S|DDX42_ENST00000359353.5_Silent_p.S614S|DDX42_ENST00000582985.1_Intron|DDX42_ENST00000389924.2_Silent_p.S733S	NM_007372.2	NP_031398.2	Q86XP3	DDX42_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 42	733					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						GGTGGACTAGTGCAGGGAGCT	0.517																																					p.S733S		Atlas-SNP	.											.	DDX42	86	.	0			c.T2199C						PASS	.						105	98	100					17																	61895140		2203	4300	6503	SO:0001819	synonymous_variant	11325	exon18			GACTAGTGCAGGG	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.2199T>C	17.37:g.61895140T>C		208	0	0		215	44	0.204651	NM_203499	A6NML1|A8KA43|O75619|Q68G51|Q96BK1|Q96HR7|Q9Y3V8	Silent	SNP	ENST00000578681.1	37	CCDS32704.1																																																																																			.	.	none		0.517	DDX42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444368.1	NM_007372		C	61895140	T	C	61895140	2	2	1	1	0	0	0	0	0	0	0	1	4364	1693	59	3		3	DDX42	17	61895140	Silent	SNP	T	TCGA-FA-8693-01A-11D-2397-10	5811273	61895140	19300070	148	148											
CD300LB	124599	hgsc.bcm.edu	37	chr17	72522004	72522004	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	catggtcacagtgaacgtgcGgtctttctgattgtccttga	7	14	11	9	2	3	3	1	3	2	0	4	3	4	3	1	2	2	0	1	2	1	3			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:72522004G>A	ENST00000392621.1	-	2	368	c.364C>T	c.(364-366)Cgc>Tgc	p.R122C	CD300LB_ENST00000314401.3_Missense_Mutation_p.R122C	NM_174892.2	NP_777552	A8K4G0	CLM7_HUMAN	CD300 molecule-like family member b	85					cellular response to lipopolysaccharide (GO:0071222)|innate immune response (GO:0045087)|neutrophil mediated immunity (GO:0002446)|positive regulation of mast cell activation (GO:0033005)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(1)	21						GTGAACGTGCGGTCTTTCTGA	0.527																																					p.R122C		Atlas-SNP	.											CD300LB,lower_third,carcinoma,0,1	CD300LB	38	1	0			c.C364T						PASS	.						256	225	235					17																	72522004		2203	4300	6503	SO:0001583	missense	124599	exon2			ACGTGCGGTCTTT	AF427618	CCDS11700.1, CCDS11700.2	17q25.1	2013-01-11	2006-03-29		ENSG00000178789	ENSG00000178789		"Immunoglobulin superfamily / V-set domain containing"	30811	protein-coding gene	gene with protein product	"triggering receptor expressed on myeloid cells 5"	610705	"CD300 antigen like family member B"			12975309	Standard	NM_174892		Approved	TREM5, CLM7	uc002jkx.2	A8K4G0	OTTHUMG00000067606	ENST00000392621.1:c.364C>T	17.37:g.72522004G>A	ENSP00000376397:p.Arg122Cys	248	0	0		280	64	0.228571	NM_174892	Q1EG73|Q8IX40|Q8N6D1	Missense_Mutation	SNP	ENST00000392621.1	37	CCDS11700.1	.	.	.	.	.	.	.	.	.	.	G	6.311	0.425440	0.11987	.	.	ENSG00000178789	ENST00000392621;ENST00000314401	T	0.04502	3.61	5.17	2.03	0.26663	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.216860	0.05978	N	0.643733	T	0.07324	0.0185	M	0.73319	2.225	0.09310	N	1	B;P	0.35242	0.077;0.492	B;B	0.23716	0.019;0.048	T	0.40961	-0.9535	10	0.38643	T	0.18	-16.1436	8.9441	0.35747	0.1487:0.0:0.7281:0.1232	.	122;85	B4DQ71;A8K4G0	.;CLM7_HUMAN	C	85;122	ENSP00000317337:R122C	ENSP00000317337:R122C	R	-	1	0	CD300LB	70033599	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.013000	0.13310	0.022000	0.15160	-1.119000	0.02030	CGC	.	.	none		0.527	CD300LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145082.2	NM_174892		A	72522004	G	A	72522004	3	1	1	1	0	0	0	0	1	0	0	0	3001	1116	39	1	364	1	CD300LB	17	72522004	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	10626864	72522004	8673206	149	149											
SOCS3	9021	hgsc.bcm.edu	37	chr17	76354959	76354959	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agaagtggcgctggtccgagCtgtcgcggatcagaaaggtg	9	7	17	8	4	1	2	1	0	0	2	3	4	2	3	1	4	1	2	1	4	2	0			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:76354959C>T	ENST00000330871.2	-	2	633	c.218G>A	c.(217-219)aGc>aAc	p.S73N	RP11-806H10.4_ENST00000592569.1_lincRNA	NM_003955.3	NP_003946.3	O14543	SOCS3_HUMAN	suppressor of cytokine signaling 3	73	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)			CTGGTCCGAGCTGTCGCGGAT	0.647																																					p.S73N		Atlas-SNP	.											.	SOCS3	16	.	0			c.G218A						PASS	.						31	28	29					17																	76354959		2203	4300	6503	SO:0001583	missense	9021	exon2			TCCGAGCTGTCGC	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.218G>A	17.37:g.76354959C>T	ENSP00000330341:p.Ser73Asn	62	0	0		84	20	0.238095	NM_003955	O14509	Missense_Mutation	SNP	ENST00000330871.2	37	CCDS11756.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.046512	0.75846	.	.	ENSG00000184557	ENST00000330871	D	0.95069	-3.6	4.13	4.13	0.48395	SH2 motif (4);	0.200591	0.51477	D	0.000091	D	0.98140	0.9386	H	0.96208	3.785	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.99847	1.1067	10	0.87932	D	0	-16.133	16.3864	0.83505	0.0:1.0:0.0:0.0	.	73	O14543	SOCS3_HUMAN	N	73	ENSP00000330341:S73N	ENSP00000330341:S73N	S	-	2	0	SOCS3	73866554	1.000000	0.71417	1.000000	0.80357	0.629000	0.37895	3.837000	0.55820	1.845000	0.53610	0.313000	0.20887	AGC	.	.	none		0.647	SOCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437300.1			T	76354959	C	T	76354959	3	4	1	1	0	0	0	0	1	0	0	0	14930	797	28	2	463	2	SOCS3	17	76354959	Missense_Mutation	SNP	C	TCGA-FA-8693-01A-11D-2397-10	3832955	76354959	4840251	150	150											
CHST9	83539	hgsc.bcm.edu	37	chr18	24496569	24496569	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtggataaactctttgaacTtgactccagatccattaatt	13	14	6	8	0	1	3	0	2	1	1	3	4	3	4	2	1	2	0	2	1	4	5			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr18:24496569T>C	ENST00000284224.8	-	6	1263	c.986A>G	c.(985-987)aAg>aGg	p.K329R	AQP4-AS1_ENST00000578701.1_RNA|AQP4-AS1_ENST00000579964.1_RNA|AQP4-AS1_ENST00000568797.1_RNA|AQP4-AS1_ENST00000582605.1_RNA|CHST9_ENST00000581714.1_Missense_Mutation_p.K329R|CHST9_ENST00000580774.1_3'UTR	NM_031422.5	NP_113610.2	Q7L1S5	CHST9_HUMAN	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	329					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)|hormone biosynthetic process (GO:0042446)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|skin(3)	28	all_lung(6;0.0145)|Ovarian(20;0.124)					CTCTTTGAACTTGACTCCAGA	0.418																																					p.K329R		Atlas-SNP	.											CHST9_ENST00000284224,NS,carcinoma,0,2	CHST9	114	2	0			c.A986G						scavenged	.						142	137	138					18																	24496569		1904	4110	6014	SO:0001583	missense	83539	exon6			TTGAACTTGACTC	AF239821	CCDS42422.1, CCDS58618.1	18q11.2	2011-04-28			ENSG00000154080	ENSG00000154080		"Sulfotransferases, membrane-bound"	19898	protein-coding gene	gene with protein product		610191				11139592, 11445554	Standard	NM_031422		Approved	GALNAC4ST-2, GALNAC-4-ST2	uc002kwe.4	Q7L1S5		ENST00000284224.8:c.986A>G	18.37:g.24496569T>C	ENSP00000284224:p.Lys329Arg	148	1	0.00675676		209	47	0.22488	NM_031422	Q6UX69|Q9BXH3|Q9BXH4|Q9BZW9	Missense_Mutation	SNP	ENST00000284224.8	37	CCDS42422.1	.	.	.	.	.	.	.	.	.	.	T	1.905	-0.452082	0.04540	.	.	ENSG00000154080	ENST00000284224	T	0.73258	-0.73	6.17	2.49	0.30216	.	0.214382	0.41938	N	0.000787	T	0.49321	0.1550	N	0.13043	0.29	0.80722	D	1	B	0.06786	0.001	B	0.15052	0.012	T	0.30119	-0.9989	10	0.07813	T	0.8	-12.2193	13.2521	0.60057	0.0:0.1491:0.0:0.8509	.	329	Q7L1S5	CHST9_HUMAN	R	329	ENSP00000284224:K329R	ENSP00000284224:K329R	K	-	2	0	CHST9	22750567	0.999000	0.42202	0.993000	0.49108	0.700000	0.40528	1.620000	0.36976	-0.021000	0.14009	-1.715000	0.00711	AAG	.	.	none		0.418	CHST9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446549.1	NM_031422		C	24496569	T	C	24496569	3	2	1	1	0	0	0	0	1	0	0	0	3413	1609	56	3	349	3	CHST9	18	24496569	Missense_Mutation	SNP	T	TCGA-FA-8693-01A-11D-2397-10		24496569	53580679	151	151											
CDH20	28316	hgsc.bcm.edu	37	chr18	59195219	59195219	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcccctgagttttgaaagcaAgaaaagctacaccttaaagg	15	8	9	9	0	0	3	0	2	0	1	0	3	0	3	3	1	3	3	3	1	7	4			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr18:59195219A>G	ENST00000262717.4	+	7	1435	c.1037A>G	c.(1036-1038)aAg>aGg	p.K346R	CDH20_ENST00000536675.2_Missense_Mutation_p.K346R|CDH20_ENST00000538374.1_Missense_Mutation_p.K346R			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	346	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)				TTTGAAAGCAAGAAAAGCTAC	0.438																																					p.K346R		Atlas-SNP	.											.	CDH20	117	.	0			c.A1037G						PASS	.						73	69	70					18																	59195219		2203	4300	6503	SO:0001583	missense	28316	exon6			AAAGCAAGAAAAG	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.1037A>G	18.37:g.59195219A>G	ENSP00000262717:p.Lys346Arg	180	0	0		179	28	0.156425	NM_031891	Q495S3	Missense_Mutation	SNP	ENST00000262717.4	37	CCDS11977.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.104904	0.77096	.	.	ENSG00000101542	ENST00000536675;ENST00000538374;ENST00000262717	T;T;T	0.49720	0.77;0.77;0.77	5.92	5.92	0.95590	Cadherin (5);Cadherin-like (1);	0.190290	0.53938	D	0.000052	T	0.54919	0.1888	L	0.45422	1.42	0.58432	D	0.999996	P	0.40476	0.718	P	0.51415	0.669	T	0.49952	-0.8884	10	0.35671	T	0.21	.	16.3526	0.83220	1.0:0.0:0.0:0.0	.	346	Q9HBT6	CAD20_HUMAN	R	346	ENSP00000444767:K346R;ENSP00000442226:K346R;ENSP00000262717:K346R	ENSP00000262717:K346R	K	+	2	0	CDH20	57346199	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.932000	0.92897	2.255000	0.74692	0.533000	0.62120	AAG	.	.	none		0.438	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891		G	59195219	A	G	59195219	3	3	1	1	0	0	0	0	1	0	0	0	3108	72	3	3	1059	3	CDH20	18	59195219	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10	34698650	59195219	18882029	152	152											
ZNF181	339318	hgsc.bcm.edu	37	chr19	35232469	35232469	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagctcacaccttactcgaCatcaaagaattcacactatg	14	10	5	12	1	3	1	3	0	0	1	4	2	3	1	1	0	2	2	1	0	5	4			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:35232469C>T	ENST00000492450.1	+	4	1272	c.1183C>T	c.(1183-1185)Cat>Tat	p.H395Y	ZNF181_ENST00000392232.3_Missense_Mutation_p.H439Y|ZNF181_ENST00000459757.2_Missense_Mutation_p.H394Y			Q2M3W8	ZN181_HUMAN	zinc finger protein 181	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)			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)			CCTTACTCGACATCAAAGAAT	0.388																																					p.H395Y		Atlas-SNP	.											.	ZNF181	65	.	0			c.C1183T						PASS	.						72	67	68					19																	35232469		2203	4298	6501	SO:0001583	missense	339318	exon4			ACTCGACATCAAA	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.1183C>T	19.37:g.35232469C>T	ENSP00000420727:p.His395Tyr	137	0	0		122	19	0.155738	NM_001029997	B7ZKX3|Q49A75	Missense_Mutation	SNP	ENST00000492450.1	37	CCDS32990.2	.	.	.	.	.	.	.	.	.	.	C	17.03	3.285590	0.59867	.	.	ENSG00000197841	ENST00000392232;ENST00000425140;ENST00000492450;ENST00000459757	D;D;D	0.86769	-2.17;-2.17;-2.17	2.84	2.84	0.33178	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.95098	0.8412	H	0.97611	4.04	0.34829	D	0.739442	D;P	0.71674	0.998;0.95	D;D	0.66847	0.944;0.947	D	0.97572	1.0105	9	0.87932	D	0	.	11.88	0.52568	0.0:1.0:0.0:0.0	.	394;395	B7ZKX3;Q2M3W8	.;ZN181_HUMAN	Y	439;394;395;394	ENSP00000376065:H439Y;ENSP00000420727:H395Y;ENSP00000419435:H394Y	ENSP00000376065:H439Y	H	+	1	0	ZNF181	39924309	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.481000	0.73608	1.876000	0.54355	0.561000	0.74099	CAT	.	.	none		0.388	ZNF181-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349005.3	NM_001029997		T	35232469	C	T	35232469	3	4	1	1	0	0	0	0	1	0	0	0	17764	478	17	2	1197	2	ZNF181	19	35232469	Missense_Mutation	SNP	C	TCGA-FA-8693-01A-11D-2397-10		35232469	23896514	153	153											
ZNF546	339327	hgsc.bcm.edu	37	chr19	40504295	40504295	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcatttttcaaatcattcCtctgcactcactttctataa	10	18	1	12	0	6	0	4	0	3	0	8	0	7	0	1	0	1	1	1	0	3	6	rs139751800	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:40504295C>T	ENST00000347077.4	+	3	278	c.62C>T	c.(61-63)cCt>cTt	p.P21L	ZNF546_ENST00000600094.1_Intron|ZNF546_ENST00000596894.1_Intron	NM_178544.3	NP_848639.2	Q86UE3	ZN546_HUMAN	zinc finger protein 546	21					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(15)|lung(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)	34	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					CAAATCATTCCTCTGCACTCA	0.403													C|||	2	0.000399361	0.0015	0.0	5008	,	,		18331	0.0		0.0	False		,,,				2504	0.0				p.P21L		Atlas-SNP	.											.	ZNF546	93	.	0			c.C62T						PASS	.	C	LEU/PRO	4,4402	8.1+/-20.4	0,4,2199	95	92	93		62	-0.7	0	19	dbSNP_134	93	0,8600		0,0,4300	no	missense	ZNF546	NM_178544.3	98	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	benign	21/837	40504295	4,13002	2203	4300	6503	SO:0001583	missense	339327	exon3			TCATTCCTCTGCA	BC045649	CCDS12548.1	19q13.2	2013-01-08				ENSG00000187187		"Zinc fingers, C2H2-type", "-"	28671	protein-coding gene	gene with protein product				ZNF49		12477932	Standard	XM_005258853		Approved	MGC43537	uc002oms.2	Q86UE3		ENST00000347077.4:c.62C>T	19.37:g.40504295C>T	ENSP00000339823:p.Pro21Leu	107	0	0		103	31	0.300971	NM_178544	A8K913	Missense_Mutation	SNP	ENST00000347077.4	37	CCDS12548.1	.	.	.	.	.	.	.	.	.	.	c	6.834	0.523083	0.13066	9.08E-4	0.0	ENSG00000187187	ENST00000347077	T	0.06528	3.29	1.66	-0.677	0.11357	.	.	.	.	.	T	0.02807	0.0084	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43048	-0.9415	9	0.49607	T	0.09	.	2.2331	0.04002	0.3012:0.5036:0.0:0.1953	.	21	Q86UE3	ZN546_HUMAN	L	21	ENSP00000339823:P21L	ENSP00000339823:P21L	P	+	2	0	ZNF546	45196135	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.414000	0.07114	-0.099000	0.12263	-0.145000	0.13849	CCT	C|1.000;T|0.000	0.000	weak		0.403	ZNF546-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462495.2	NM_178544		T	40504295	C	T	40504295	3	4	1	1	0	0	0	0	1	0	0	0	17993	681	24	2	64	2	ZNF546	19	40504295	Missense_Mutation	SNP	C	TCGA-FA-8693-01A-11D-2397-10	5271826	40504295	18624688	154	154											
BIRC8	112401	hgsc.bcm.edu	37	chr19	53793122	53793122	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgatttctctctgcaatGaagtctgattcaattcattt	9	17	7	8	0	5	3	2	3	3	0	6	3	5	3	0	1	1	2	0	1	3	4			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:53793122G>T	ENST00000426466.1	-	1	1753	c.506C>A	c.(505-507)tCa>tAa	p.S169*		NM_033341.4	NP_203127.3	Q96P09	BIRC8_HUMAN	baculoviral IAP repeat containing 8	169					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)		TCTCTGCAATGAAGTCTGATT	0.418																																					p.S169X		Atlas-SNP	.											.	BIRC8	54	.	0			c.C506A						PASS	.						87	86	86					19																	53793122		2203	4300	6503	SO:0001587	stop_gained	112401	exon1			TGCAATGAAGTCT	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.506C>A	19.37:g.53793122G>T	ENSP00000412957:p.Ser169*	116	0	0		110	17	0.154545	NM_033341	Q6IPY1|Q96RW5	Nonsense_Mutation	SNP	ENST00000426466.1	37	CCDS12863.1	.	.	.	.	.	.	.	.	.	.	G	43	10.235541	0.99365	.	.	ENSG00000163098	ENST00000426466	.	.	.	0.637	-0.588	0.11687	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.1522	4.9292	0.13909	0.2589:0.0:0.7411:0.0	.	.	.	.	X	169	.	ENSP00000412957:S169X	S	-	2	0	BIRC8	58484934	0.007000	0.16637	0.010000	0.14722	0.003000	0.03518	0.299000	0.19138	-0.140000	0.11394	-0.347000	0.07816	TCA	.	.	none		0.418	BIRC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464357.1	NM_033341		T	53793122	G	T	53793122	4	4	1	1	0	0	0	0	0	1	0	0	1440	1294	45	4	208	4	BIRC8	19	53793122	Nonsense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	13288827	53793122	5335861	155	155											
ZNF471	57573	hgsc.bcm.edu	37	chr19	57036891	57036891	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaattcatactggtgaaaaAccctatgaatgtaaagaatg	18	10	8	5	0	1	4	1	2	0	2	1	4	1	4	1	1	2	1	1	1	9	4			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:57036891A>C	ENST00000308031.5	+	5	1588	c.1455A>C	c.(1453-1455)aaA>aaC	p.K485N	ZNF471_ENST00000593197.1_Intron|ZNF471_ENST00000591537.1_3'UTR	NM_020813.2	NP_065864.2	Q9BX82	ZN471_HUMAN	zinc finger protein 471	485					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)		CTGGTGAAAAACCCTATGAAT	0.383																																					p.K485N	Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)	Atlas-SNP	.											.	ZNF471	99	.	0			c.A1455C						PASS	.						55	56	55					19																	57036891		2203	4300	6503	SO:0001583	missense	57573	exon5			TGAAAAACCCTAT	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.1455A>C	19.37:g.57036891A>C	ENSP00000309161:p.Lys485Asn	64	0	0		61	7	0.114754	NM_020813	B4DF32|O75260|Q08AD6|Q08AD7|Q8N3V1|Q9P2F1	Missense_Mutation	SNP	ENST00000308031.5	37	CCDS12945.1	.	.	.	.	.	.	.	.	.	.	A	15.71	2.913227	0.52439	.	.	ENSG00000196263	ENST00000308031	T	0.26067	1.76	3.66	2.59	0.31030	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.43166	0.1235	M	0.76727	2.345	0.80722	D	1	D	0.76494	0.999	D	0.65684	0.937	T	0.27434	-1.0074	9	0.72032	D	0.01	.	5.8421	0.18639	0.8355:0.0:0.1645:0.0	.	485	Q9BX82	ZN471_HUMAN	N	485	ENSP00000309161:K485N	ENSP00000309161:K485N	K	+	3	2	ZNF471	61728703	0.004000	0.15560	0.997000	0.53966	0.985000	0.73830	-0.726000	0.04936	0.497000	0.27926	0.379000	0.24179	AAA	.	.	none		0.383	ZNF471-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458405.1	NM_020813		C	57036891	A	C	57036891	3	2	1	1	0	0	0	0	1	0	0	0	17945	40	2	5	1469	5	ZNF471	19	57036891	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10	3243769	57036891	2092092	156	156											
TMX4	56255	hgsc.bcm.edu	37	chr20	8000141	8000141	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagttggaggcggtcatgggCtggacccggctctgctccgg	4	8	17	12	3	2	0	1	0	1	0	3	2	3	2	2	7	1	4	2	7	0	1			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr20:8000141C>T	ENST00000246024.2	-	1	335	c.120G>A	c.(118-120)caG>caA	p.Q40Q	RP5-971N18.3_ENST00000607924.1_RNA|RP5-971N18.3_ENST00000457707.1_RNA	NM_021156.2	NP_066979.2	Q9H1E5	TMX4_HUMAN	thioredoxin-related transmembrane protein 4	40	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|oxidation-reduction process (GO:0055114)|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(2)|lung(11)|skin(1)	17						CGGTCATGGGCTGGACCCGGC	0.736																																					p.Q40Q		Atlas-SNP	.											.	TMX4	39	.	0			c.G120A						PASS	.						13	14	14					20																	8000141		1935	3764	5699	SO:0001819	synonymous_variant	56255	exon1			CATGGGCTGGACC		CCDS13101.1	20p12	2011-10-19	2009-02-23	2009-02-23	ENSG00000125827	ENSG00000125827		"Protein disulfide isomerases"	25237	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 14"		"thioredoxin domain containing 13"	TXNDC13			Standard	NM_021156		Approved	DJ971N18.2, KIAA1162, PDIA14	uc002wmx.1	Q9H1E5	OTTHUMG00000031843	ENST00000246024.2:c.120G>A	20.37:g.8000141C>T		14	0	0		40	11	0.275	NM_021156	Q8N4P7|Q8NCC1|Q9UJA1|Q9ULQ8	Silent	SNP	ENST00000246024.2	37	CCDS13101.1																																																																																			.	.	none		0.736	TMX4-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000077928.2	NM_021156		T	8000141	C	T	8000141	2	4	1	1	0	0	0	0	0	0	0	1	16284	796	28	2		2	TMX4	20	8000141	Silent	SNP	C	TCGA-FA-8693-01A-11D-2397-10		8000141	55025379	157	157											
C20orf103	24141	hgsc.bcm.edu	37	chr20	9498795	9498795	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcactggcctctagtgatcCgcagaagacggtcaccatga	10	9	10	12	2	3	4	2	2	1	2	4	4	4	4	3	2	0	1	3	2	2	2	rs137866690		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr20:9498795C>T	ENST00000246070.2	+	5	1076	c.584C>T	c.(583-585)cCg>cTg	p.P195L	LAMP5_ENST00000427562.2_Missense_Mutation_p.P151L	NM_012261.3	NP_036393.1	Q9UJQ1	LAMP5_HUMAN	lysosomal-associated membrane protein family, member 5	195						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)											TCTAGTGATCCGCAGAAGACG	0.512																																					p.P195L		Atlas-SNP	.											.	.	.	.	0			c.C584T						PASS	.	T	LEU/PRO,LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	129	104	112		452,584	2.6	0.3	20	dbSNP_134	112	0,8600		0,0,4300	no	missense,missense	C20orf103	NM_001199897.1,NM_012261.3	98,98	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	151/237,195/281	9498795	1,13005	2203	4300	6503	SO:0001583	missense	24141	exon5			GTGATCCGCAGAA	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.584C>T	20.37:g.9498795C>T	ENSP00000246070:p.Pro195Leu	272	0	0		303	72	0.237624	NM_012261	B4DHZ7|B7Z9Z9	Missense_Mutation	SNP	ENST00000246070.2	37	CCDS13106.1	.	.	.	.	.	.	.	.	.	.	c	10.44	1.351081	0.24512	2.27E-4	0.0	ENSG00000125869	ENST00000246070;ENST00000427562	T;T	0.31510	1.49;1.49	5.84	2.59	0.31030	.	0.274631	0.40908	N	0.000994	T	0.12646	0.0307	N	0.14661	0.345	0.42298	D	0.992169	P;B	0.35192	0.489;0.004	B;B	0.22152	0.038;0.002	T	0.13764	-1.0497	9	.	.	.	-2.5454	7.7449	0.28862	0.5288:0.3877:0.0:0.0835	.	151;195	Q9UJQ1-2;Q9UJQ1	.;CT103_HUMAN	L	195;151	ENSP00000246070:P195L;ENSP00000406360:P151L	.	P	+	2	0	C20orf103	9446795	0.999000	0.42202	0.335000	0.25508	0.363000	0.29612	4.323000	0.59221	0.800000	0.34041	-0.119000	0.15052	CCG	C|1.000;T|0.000	0.000	weak		0.512	LAMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077946.2	NM_012261		T	9498795	C	T	9498795	3	4	1	1	0	0	0	0	1	0	0	0	2077	652	23	1	602	1	C20orf103	20	9498795	Missense_Mutation	SNP	C	TCGA-FA-8693-01A-11D-2397-10	1498654	9498795	53526725	158	158											
C20orf94	128710	hgsc.bcm.edu	37	chr20	10603706	10603706	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgcaggaactgcagctctgcGgaagacttcgaccaccacgg	10	5	12	14	4	1	1	0	0	1	1	2	4	1	3	2	3	4	3	2	3	2	1			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr20:10603706G>A	ENST00000334534.5	+	8	1086	c.906G>A	c.(904-906)gcG>gcA	p.A302A		NM_001009608.1	NP_001009608.1	Q5VYV7	SLX4I_HUMAN	SLX4 interacting protein	302																	GCAGCTCTGCGGAAGACTTCG	0.507																																					p.A302A		Atlas-SNP	.											.	.	.	.	0			c.G906A						PASS	.						89	99	96					20																	10603706		2203	4300	6503	SO:0001819	synonymous_variant	128710	exon8			CTCTGCGGAAGAC	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.906G>A	20.37:g.10603706G>A		77	0	0		71	11	0.15493	NM_001009608	Q05CG2|Q05CT9	Silent	SNP	ENST00000334534.5	37	CCDS33439.1																																																																																			.	.	none		0.507	SLX4IP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078000.3	NM_001009608		A	10603706	G	A	10603706	2	1	1	1	0	0	0	0	0	0	0	1	2123	1103	39	1		1	C20orf94	20	10603706	Silent	SNP	G	TCGA-FA-8693-01A-11D-2397-10	1104911	10603706	52421814	159	159											
PAX1	5075	hgsc.bcm.edu	37	chr20	21687153	21687153	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgcccaacgccatccgcttgCgcattgtggagctggcgcag	6	8	13	14	4	0	0	0	0	0	0	1	1	1	1	3	2	4	4	3	2	1	2			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr20:21687153C>T	ENST00000398485.2	+	2	418	c.364C>T	c.(364-366)Cgc>Tgc	p.R122C	PAX1_ENST00000460221.1_Intron|PAX1_ENST00000444366.2_Missense_Mutation_p.R98C	NM_001257096.1|NM_006192.4	NP_001244025.1|NP_006183.2	P15863	PAX1_HUMAN	paired box 1	122	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						CATCCGCTTGCGCATTGTGGA	0.647																																					p.R122C		Atlas-SNP	.											.	PAX1	152	.	0			c.C364T						PASS	.						32	35	34					20																	21687153		2203	4299	6502	SO:0001583	missense	5075	exon2			CGCTTGCGCATTG		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.364C>T	20.37:g.21687153C>T	ENSP00000381499:p.Arg122Cys	22	0	0		27	8	0.296296	NM_006192	B4E0D6|Q642X9|Q6NTC0|Q9Y558	Missense_Mutation	SNP	ENST00000398485.2	37	CCDS13146.2	.	.	.	.	.	.	.	.	.	.	C	15.94	2.981240	0.53827	.	.	ENSG00000125813	ENST00000398485;ENST00000444366	D;D	0.99479	-5.98;-5.98	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	0.99510	0.9825	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;1.0;1.0	D	0.98521	1.0623	10	0.87932	D	0	.	18.2175	0.89890	0.0:1.0:0.0:0.0	.	98;28;122	P15863-2;C9J775;P15863	.;.;PAX1_HUMAN	C	122;98	ENSP00000381499:R122C;ENSP00000410355:R98C	ENSP00000381499:R122C	R	+	1	0	PAX1	21635153	1.000000	0.71417	0.998000	0.56505	0.015000	0.08874	2.369000	0.44231	2.382000	0.81193	0.655000	0.94253	CGC	.	.	none		0.647	PAX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078282.3			T	21687153	C	T	21687153	3	4	1	1	0	0	0	0	1	0	0	0	11487	768	27	1	370	1	PAX1	20	21687153	Missense_Mutation	SNP	C	TCGA-FA-8693-01A-11D-2397-10	11083447	21687153	41338367	160	160											
PTPRT	11122	hgsc.bcm.edu	37	chr20	40709537	40709537	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agctaaaaggagcttaaataTtccagtgccacctcgtatac	14	10	7	10	1	0	0	0	0	0	0	2	1	1	1	3	1	4	3	3	1	7	6			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr20:40709537T>A	ENST00000373187.1	-	31	4307	c.4308A>T	c.(4306-4308)gaA>gaT	p.E1436D	PTPRT_ENST00000373190.1_Missense_Mutation_p.E1435D|PTPRT_ENST00000373198.4_Missense_Mutation_p.E1455D|PTPRT_ENST00000373201.1_Missense_Mutation_p.E1426D|PTPRT_ENST00000373184.1_Missense_Mutation_p.E1446D|PTPRT_ENST00000356100.2_Missense_Mutation_p.E1445D|PTPRT_ENST00000373193.3_Missense_Mutation_p.E1439D			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	1436	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)				AGCTTAAATATTCCAGTGCCA	0.507																																					p.E1455D		Atlas-SNP	.											PTPRT,upper_back,malignant_melanoma,-2,1	PTPRT	372	1	0			c.A4365T						PASS	.						56	60	59					20																	40709537		2084	4243	6327	SO:0001583	missense	11122	exon32			TAAATATTCCAGT	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.4308A>T	20.37:g.40709537T>A	ENSP00000362283:p.Glu1436Asp	39	0	0		31	7	0.225806	NM_133170	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Missense_Mutation	SNP	ENST00000373187.1	37	CCDS42874.1	.	.	.	.	.	.	.	.	.	.	T	26.5	4.740476	0.89573	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	D;D;D;D;D;D;D	0.84516	-1.86;-1.86;-1.86;-1.86;-1.86;-1.86;-1.86	6.08	6.08	0.98989	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	D	0.92047	0.7480	M	0.83012	2.62	0.58432	D	0.999999	D;D	0.76494	0.999;0.999	D;D	0.87578	0.997;0.998	D	0.92777	0.6237	10	0.87932	D	0	.	10.9027	0.47062	0.0:0.0695:0.0:0.9305	.	1458;1436	O14522-1;O14522	.;PTPRT_HUMAN	D	1435;1436;1439;1445;1458;1446;1426	ENSP00000362286:E1435D;ENSP00000362283:E1436D;ENSP00000362289:E1439D;ENSP00000348408:E1445D;ENSP00000362294:E1458D;ENSP00000362280:E1446D;ENSP00000362297:E1426D	ENSP00000348408:E1445D	E	-	3	2	PTPRT	40142951	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.782000	0.47758	2.333000	0.79357	0.533000	0.62120	GAA	.	.	none		0.507	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			A	40709537	T	A	40709537	3	1	1	1	0	0	0	0	1	0	0	0	12827	1490	52	5	21	5	PTPRT	20	40709537	Missense_Mutation	SNP	T	TCGA-FA-8693-01A-11D-2397-10	19022384	40709537	22315983	161	161											
TIAM1	7074	hgsc.bcm.edu	37	chr21	32554842	32554842	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ccactccttcctccagctcgGggtaggtcctcaccaggagg	6	8	11	16	1	1	0	1	0	0	0	6	1	5	1	6	5	1	2	6	5	1	2			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr21:32554842G>T	ENST00000286827.3	-	16	3254	c.2783C>A	c.(2782-2784)cCc>cAc	p.P928H	TIAM1_ENST00000541036.1_Missense_Mutation_p.P868H	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	928					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						CTCCAGCTCGGGGTAGGTCCT	0.602																																					p.P928H		Atlas-SNP	.											.	TIAM1	522	.	0			c.C2783A						PASS	.						43	43	43					21																	32554842		2203	4300	6503	SO:0001583	missense	7074	exon16			AGCTCGGGGTAGG		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.2783C>A	21.37:g.32554842G>T	ENSP00000286827:p.Pro928His	111	0	0		95	25	0.263158	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	37	CCDS13609.1	.	.	.	.	.	.	.	.	.	.	G	19.69	3.873912	0.72180	.	.	ENSG00000156299	ENST00000286827;ENST00000399841;ENST00000541036	T;T	0.49139	0.79;0.82	4.24	4.24	0.50183	PDZ/DHR/GLGF (1);	0.000000	0.85682	D	0.000000	T	0.62624	0.2443	L	0.55481	1.735	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	T	0.64807	-0.6320	10	0.56958	D	0.05	.	13.6799	0.62476	0.0:0.0:1.0:0.0	.	868;868;928	F5GZ53;B7ZLR6;Q13009	.;.;TIAM1_HUMAN	H	928;769;868	ENSP00000286827:P928H;ENSP00000441570:P868H	ENSP00000286827:P928H	P	-	2	0	TIAM1	31476713	1.000000	0.71417	0.937000	0.37676	0.985000	0.73830	5.349000	0.66010	2.193000	0.70182	0.555000	0.69702	CCC	.	.	none		0.602	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		T	32554842	G	T	32554842	3	4	1	1	0	0	0	0	1	0	0	0	15905	1232	43	4	2048	4	TIAM1	21	32554842	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10		32554842	15575053	162	162											
TMPRSS2	7113	hgsc.bcm.edu	37	chr21	42851153	42851153	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcacttgtgttcagtttcAtaaagctggtggatccgctg	7	13	12	9	2	2	0	2	0	0	0	3	1	3	1	1	3	1	5	1	3	2	4			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr21:42851153A>T	ENST00000332149.5	-	7	763	c.629T>A	c.(628-630)aTg>aAg	p.M210K	TMPRSS2_ENST00000398585.3_Missense_Mutation_p.M247K|TMPRSS2_ENST00000458356.1_Missense_Mutation_p.M210K	NM_005656.3	NP_005647.3	O15393	TMPS2_HUMAN	transmembrane protease, serine 2	210	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)				GTTCAGTTTCATAAAGCTGGT	0.353			T	"ERG, ETV1, ETV4, ETV5"	prostate																																p.M247K		Atlas-SNP	.		Dom	yes		21	21q22.3	7113	"transmembrane protease, serine 2"		E	.	TMPRSS2	148	.	0			c.T740A						PASS	.						146	145	146					21																	42851153		2203	4300	6503	SO:0001583	missense	7113	exon7			AGTTTCATAAAGC	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.629T>A	21.37:g.42851153A>T	ENSP00000330330:p.Met210Lys	102	0	0		88	4	0.0454545	NM_001135099	A8K6Z8|B2R8E5|B7Z459|D3DSJ2|F8WES1|Q6GTK7|Q9BXX1	Missense_Mutation	SNP	ENST00000332149.5	37	CCDS33564.1	.	.	.	.	.	.	.	.	.	.	A	13.10	2.137229	0.37728	.	.	ENSG00000184012	ENST00000332149;ENST00000398585;ENST00000458356;ENST00000454499;ENST00000424093	T;T;T;T;T	0.60171	0.21;0.21;0.21;0.21;0.21	5.43	4.25	0.50352	Speract/scavenger receptor (1);Speract/scavenger receptor-related (2);	0.065677	0.64402	D	0.000007	T	0.62527	0.2435	M	0.72479	2.2	0.39156	D	0.962314	D;P	0.55800	0.973;0.85	P;P	0.54174	0.735;0.744	T	0.62324	-0.6878	10	0.12766	T	0.61	.	9.4178	0.38532	0.8205:0.1795:0.0:0.0	.	247;210	F8WES1;O15393	.;TMPS2_HUMAN	K	210;247;210;210;170	ENSP00000330330:M210K;ENSP00000381588:M247K;ENSP00000391216:M210K;ENSP00000389006:M210K;ENSP00000397846:M170K	ENSP00000330330:M210K	M	-	2	0	TMPRSS2	41773023	1.000000	0.71417	0.597000	0.28824	0.032000	0.12392	4.796000	0.62496	0.872000	0.35775	0.448000	0.29417	ATG	.	.	none		0.353	TMPRSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195189.1			T	42851153	A	T	42851153	3	4	1	1	0	0	0	0	1	0	0	0	16262	217	8	5	881	5	TMPRSS2	21	42851153	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10	10296311	42851153	5278742	163	163											
KRTAP10-2	386679	hgsc.bcm.edu	37	chr21	45970771	45970771	+	Missense_Mutation	SNP	C	C	T																															gcagatggacttgcagcagaCaggcttgcagcagacggaca																								rs200215960|rs67692969|rs71199610	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr21:45970771C>T	ENST00000391621.1	-	1	617	c.571G>A	c.(571-573)Gtc>Atc	p.V191I	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron|KRTAP10-2_ENST00000498210.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	191	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						TTGCAGCAGACAGGCTTGCAG	0.612																																					p.V191I		Atlas-SNP	.											.	KRTAP10-2	21	.	0			c.G571A						PASS	.						114	116	115					21																	45970771		2203	4299	6502	SO:0001583	missense	386679	exon1			AGCAGACAGGCTT	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"Keratin associated proteins"	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.571G>A	21.37:g.45970771C>T	ENSP00000375479:p.Val191Ile	100	0	0		125	12	0.096	NM_198693	Q70LJ5	Missense_Mutation	SNP	ENST00000391621.1	37	CCDS42955.1	.	.	.	.	.	.	.	.	.	.	c	9.177	1.022646	0.19433	.	.	ENSG00000205445	ENST00000391621	T	0.01430	4.9	3.28	-6.57	0.01842	.	.	.	.	.	T	0.01627	0.0052	L	0.60904	1.88	0.09310	N	1	B	0.22604	0.072	B	0.26614	0.071	T	0.44697	-0.9311	9	0.62326	D	0.03	.	3.2055	0.06665	0.2595:0.2667:0.3822:0.0916	.	191	P60368	KR102_HUMAN	I	191	ENSP00000375479:V191I	ENSP00000375479:V191I	V	-	1	0	KRTAP10-2	44795199	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.395000	0.02516	-1.216000	0.02607	0.462000	0.41574	GTC	C|0.956;T|0.044	0.044	strong		0.612	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1			T	45970771	C	T	45970771	3	4	1	1	0	0	0	0	1	0	0	0	8518	478	17	2	200	2	KRTAP10-2	21	45970771	Missense_Mutation	SNP	C	TCGA-FA-8693-01A-11D-2397-10	3119618	45970771	2159124	164	164	5	3									
KRTAP10-2	386679	hgsc.bcm.edu	37	chr21	45970772	45970772	+	Silent	SNP	A	A	G																															cagatggacttgcagcagacAggcttgcagcagacggacac																								rs76021731|rs67692969|rs71199610	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr21:45970772A>G	ENST00000391621.1	-	1	616	c.570T>C	c.(568-570)ccT>ccC	p.P190P	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron|KRTAP10-2_ENST00000498210.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	190	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						TGCAGCAGACAGGCTTGCAGC	0.607																																					p.P190P		Atlas-SNP	.											.	KRTAP10-2	21	.	0			c.T570C						PASS	.						111	112	112					21																	45970772		2192	4282	6474	SO:0001819	synonymous_variant	386679	exon1			GCAGACAGGCTTG	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"Keratin associated proteins"	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.570T>C	21.37:g.45970772A>G		96	0	0		120	14	0.116667	NM_198693	Q70LJ5	Silent	SNP	ENST00000391621.1	37	CCDS42955.1																																																																																			A|0.908;G|0.092	0.092	strong		0.607	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1			G	45970772	A	G	45970772	2	3	1	1	0	0	0	0	0	0	0	1	8518	175	7	3		3	KRTAP10-2	21	45970772	Silent	SNP	A	TCGA-FA-8693-01A-11D-2397-10	1	45970772	2159123	165	165	5	3									
KRTAP10-2	386679	hgsc.bcm.edu	37	chr21	45970774	45970774	+	Missense_Mutation	SNP	G	G	A																															gatggacttgcagcagacagGcttgcagcagacggacacac																								rs76536096|rs67692969|rs71199610	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr21:45970774G>A	ENST00000391621.1	-	1	614	c.568C>T	c.(568-570)Cct>Tct	p.P190S	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron|KRTAP10-2_ENST00000498210.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	190	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						CAGCAGACAGGCTTGCAGCAG	0.607																																					p.P190S		Atlas-SNP	.											.	KRTAP10-2	21	.	0			c.C568T						PASS	.						110	112	111					21																	45970774		2192	4279	6471	SO:0001583	missense	386679	exon1			AGACAGGCTTGCA	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"Keratin associated proteins"	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.568C>T	21.37:g.45970774G>A	ENSP00000375479:p.Pro190Ser	94	0	0		119	12	0.10084	NM_198693	Q70LJ5	Missense_Mutation	SNP	ENST00000391621.1	37	CCDS42955.1	.	.	.	.	.	.	.	.	.	.	g	9.523	1.108901	0.20714	.	.	ENSG00000205445	ENST00000391621	T	0.01705	4.68	3.28	0.222	0.15288	.	.	.	.	.	T	0.02083	0.0065	L	0.49455	1.56	0.09310	N	1	B	0.26672	0.156	B	0.24394	0.053	T	0.42310	-0.9459	9	0.62326	D	0.03	.	4.9369	0.13944	0.2108:0.1755:0.6137:0.0	.	190	P60368	KR102_HUMAN	S	190	ENSP00000375479:P190S	ENSP00000375479:P190S	P	-	1	0	KRTAP10-2	44795202	0.105000	0.21958	0.000000	0.03702	0.002000	0.02628	1.284000	0.33249	-0.177000	0.10690	0.462000	0.41574	CCT	G|0.917;A|0.083	0.083	strong		0.607	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1			A	45970774	G	A	45970774	3	1	1	1	0	0	0	0	1	0	0	0	8518	1203	42	2	203	2	KRTAP10-2	21	45970774	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	2	45970774	2159121	166	166	5	3									
SLC19A1	6573	hgsc.bcm.edu	37	chr21	46935613	46935613	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	accgtcgcttggaagacactGcaaacccagcttgctgacac	11	7	9	14	2	0	2	0	1	0	1	1	3	0	3	2	1	4	4	2	1	2	2			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr21:46935613G>A	ENST00000311124.4	-	6	1887	c.1735C>T	c.(1735-1737)Cag>Tag	p.Q579*	SLC19A1_ENST00000468508.1_5'Flank|SLC19A1_ENST00000380010.4_Intron|SLC19A1_ENST00000567670.1_Intron|SLC19A1_ENST00000485649.2_Nonsense_Mutation_p.Q539*	NM_194255.2	NP_919231.1	P41440	S19A1_HUMAN	solute carrier family 19 (folate transporter), member 1	579					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)	GGAAGACACTGCAAACCCAGC	0.612																																					p.Q579X		Atlas-SNP	.											.	SLC19A1	53	.	0			c.C1735T						PASS	.						68	65	66					21																	46935613		2203	4300	6503	SO:0001587	stop_gained	6573	exon6			GACACTGCAAACC	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.1735C>T	21.37:g.46935613G>A	ENSP00000308895:p.Gln579*	90	0	0		86	4	0.0465116	NM_194255	B2R7U8|B7Z8C3|E9PFY4|O00553|O60227|Q13026|Q9BTX8	Nonsense_Mutation	SNP	ENST00000311124.4	37	CCDS13725.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.905088	0.92035	.	.	ENSG00000173638	ENST00000311124;ENST00000485649	.	.	.	2.8	-1.34	0.09143	.	.	.	.	.	.	.	.	.	.	.	0.30402	N	0.779886	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	6.3474	0.21357	0.5305:0.0:0.4695:0.0	.	.	.	.	X	579;539	.	ENSP00000308895:Q579X	Q	-	1	0	SLC19A1	45760041	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-1.359000	0.02602	-0.337000	0.08426	0.467000	0.42956	CAG	.	.	none		0.612	SLC19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206796.1			A	46935613	G	A	46935613	4	1	1	1	0	0	0	0	0	1	0	0	14443	1328	46	2	44	2	SLC19A1	21	46935613	Nonsense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	964839	46935613	1194282	167	167											
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230283	23230283	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgagacccctgaggagctggGccctggtcccaggcagcgct	6	6	15	14	1	0	2	0	2	0	1	1	4	1	3	4	4	2	3	4	4	0	0			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr22:23230283G>A	ENST00000526893.1	+	1	324	c.50G>A	c.(49-51)gGc>gAc	p.G17D	IGLL5_ENST00000532223.2_Missense_Mutation_p.G17D|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000531372.1_Missense_Mutation_p.G17D	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	17						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GAGGAGCTGGGCCCTGGTCCC	0.672																																					p.G17D		Atlas-SNP	.											.	IGLL5	26	.	0			c.G50A						PASS	.																																			SO:0001583	missense	100423062	exon1			AGCTGGGCCCTGG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.50G>A	22.37:g.23230283G>A	ENSP00000431254:p.Gly17Asp	107	0	0		142	38	0.267606	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	10.81	1.455202	0.26161	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00614	6.21;6.22	3.24	-0.78	0.10969	.	.	.	.	.	T	0.00580	0.0019	L	0.29908	0.895	0.09310	N	1	B	0.15930	0.015	B	0.10450	0.005	T	0.45425	-0.9262	9	0.52906	T	0.07	.	3.2568	0.06835	0.325:0.2123:0.4627:0.0	.	17	B9A064	IGLL5_HUMAN	D	17	ENSP00000436353:G17D;ENSP00000431254:G17D	ENSP00000431254:G17D	G	+	2	0	IGLL5	21560283	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.154000	0.16343	-0.051000	0.13334	0.643000	0.83706	GGC	.	.	none		0.672	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		A	23230283	G	A	23230283	3	1	1	1	0	0	0	0	1	0	0	0	7603	1203	42	2	52	2	IGLL5	22	23230283	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10		23230283	28074283	168	168			2	2		4	3	122	N	G_C_A	2.137257e-07
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230315	23230315	+	Silent	SNP	C	C	T																															ggcagcgctggcccctgctgCtgctgggtctggccatggtc																								rs148489860	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr22:23230315C>T	ENST00000526893.1	+	1	356	c.82C>T	c.(82-84)Ctg>Ttg	p.L28L	IGLL5_ENST00000532223.2_Silent_p.L28L|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000531372.1_Silent_p.L28L	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	28						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GCCCCTGCTGCTGCTGGGTCT	0.662													C|||	11	0.00219649	0.0045	0.0	5008	,	,		12566	0.003		0.001	False		,,,				2504	0.001				p.L28L		Atlas-SNP	.											.	IGLL5	26	.	0			c.C82T						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			CTGCTGCTGCTGG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.82C>T	22.37:g.23230315C>T		45	0	0		68	20	0.294118	NM_001178126		Silent	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			C|1.000;T|0.000	0.000	strong		0.662	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		T	23230315	C	T	23230315	2	4	1	1	0	0	0	0	0	0	0	1	7603	796	28	2		2	IGLL5	22	23230315	Silent	SNP	C	TCGA-FA-8693-01A-11D-2397-10	32	23230315	28074251	169	169	6	2	2	2		4	3	122	N	G_C_A	2.137257e-07
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230318	23230318	+	Missense_Mutation	SNP	C	C	G																															agcgctggcccctgctgctgCtgggtctggccatggtcgcc																								rs567537853		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr22:23230318C>G	ENST00000526893.1	+	1	359	c.85C>G	c.(85-87)Ctg>Gtg	p.L29V	IGLL5_ENST00000532223.2_Missense_Mutation_p.L29V|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000531372.1_Missense_Mutation_p.L29V	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	29						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CCTGCTGCTGCTGGGTCTGGC	0.657																																					p.L29V		Atlas-SNP	.											.	IGLL5	26	.	0			c.C85G						PASS	.																																			SO:0001583	missense	100423062	exon1			CTGCTGCTGGGTC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.85C>G	22.37:g.23230318C>G	ENSP00000431254:p.Leu29Val	39	0	0		62	18	0.290323	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	C	17.27	3.347544	0.61183	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00717	5.79;5.8	3.82	3.82	0.43975	.	.	.	.	.	T	0.02193	0.0068	L	0.32530	0.975	0.24893	N	0.992151	D	0.76494	0.999	D	0.75484	0.986	T	0.54159	-0.8335	9	0.66056	D	0.02	.	11.5007	0.50435	0.0:1.0:0.0:0.0	.	29	B9A064	IGLL5_HUMAN	V	29	ENSP00000436353:L29V;ENSP00000431254:L29V	ENSP00000431254:L29V	L	+	1	2	IGLL5	21560318	0.000000	0.05858	0.815000	0.32552	0.079000	0.17450	0.026000	0.13599	2.423000	0.82170	0.643000	0.83706	CTG	.	.	none		0.657	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		G	23230318	C	G	23230318	3	3	1	1	0	0	0	0	1	0	0	0	7603	796	28	4	87	4	IGLL5	22	23230318	Missense_Mutation	SNP	C	TCGA-FA-8693-01A-11D-2397-10	3	23230318	28074248	170	170	6	2	2	2		4	3	122	N	G_C_A	2.137257e-07
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230404	23230404	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccctggagcctcagttggAagcagccgatccagcctgcg	8	6	13	14	2	1	0	1	0	0	0	2	4	2	2	5	2	5	2	5	2	1	1	rs115653109	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr22:23230404A>G	ENST00000526893.1	+	1	445	c.171A>G	c.(169-171)ggA>ggG	p.G57G	IGLL5_ENST00000532223.2_Silent_p.G57G|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000531372.1_Silent_p.G57G	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	57						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CCTCAGTTGGAAGCAGCCGAT	0.662													A|||	2	0.000399361	0.0015	0.0	5008	,	,		10542	0.0		0.0	False		,,,				2504	0.0				p.E22G		Atlas-SNP	.											.	IGLL5	26	.	0			c.A65G						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			AGTTGGAAGCAGC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.171A>G	22.37:g.23230404A>G		97	0	0		59	14	0.237288	NM_001256296		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			A|0.999;G|0.001	0.001	strong		0.662	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		G	23230404	A	G	23230404	2	3	1	1	0	0	0	0	0	0	0	1	7603	233	9	3		3	IGLL5	22	23230404	Silent	SNP	A	TCGA-FA-8693-01A-11D-2397-10	86	23230404	28074162	171	171			2	2		4	3	122	N	G_C_A	2.137257e-07
C22orf43	51233	hgsc.bcm.edu	37	chr22	23956338	23956340	+	In_Frame_Del	DEL	TCT	TCT	-																															ttacgtggatgtcatcatcaTcttcttcttcttcatctttg																								rs117546628	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr22:23956338_23956340delTCT	ENST00000317749.5	-	9	900_902	c.603_605delAGA	c.(601-606)gaagat>gat	p.E201del		NM_016449.3	NP_057533.2	Q6PGQ1	DRIC1_HUMAN		201	Asp-rich.									endometrium(1)|large_intestine(3)|lung(5)|pancreas(1)|skin(1)	11						GTCATCATCATCTTCTTCTTCTT	0.384																																					p.202_202del		Pindel,Atlas-Indel	.											.	C22orf43	18	.	0			c.604_606del						PASS	.																																			SO:0001651	inframe_deletion	51233	exon9			.																												ENST00000317749.5:c.603_605delAGA	22.37:g.23956347_23956349delTCT	ENSP00000316137:p.Glu201del	236	0	.		306	52	0.17	NM_016449	Q6ICJ8|Q6P4I3|Q9NU31	In_Frame_Del	DEL	ENST00000317749.5	37	CCDS42985.1																																																																																			.	.	none		0.384	C22orf43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319708.2			-	23956340	TCT	-	23956338	7	5	1	1	0	1	0	1	0	0	0	0	2152	1435	50	0	100	0	C22orf43	22	23956338	In_Frame_Del	DEL	TCT	TCGA-FA-8693-01A-11D-2397-10	725934	23956338	27348228	172	172											
SCUBE1	80274	hgsc.bcm.edu	37	chr22	43600118	43600118	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagtagttctggggatgcGccagcacgtcgaagagggcc	9	7	16	9	3	1	2	0	1	1	1	2	4	1	3	2	3	2	3	2	3	3	2			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr22:43600118G>A	ENST00000360835.4	-	22	2978	c.2852C>T	c.(2851-2853)gCg>gTg	p.A951V		NM_173050.3	NP_766638.2	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	951					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)				CTGGGGATGCGCCAGCACGTC	0.567																																					p.A951V		Atlas-SNP	.											.	SCUBE1	105	.	0			c.C2852T						PASS	.						157	140	146					22																	43600118		2203	4300	6503	SO:0001583	missense	80274	exon22			GGATGCGCCAGCA		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.2852C>T	22.37:g.43600118G>A	ENSP00000354080:p.Ala951Val	212	0	0		192	46	0.239583	NM_173050	Q5R336	Missense_Mutation	SNP	ENST00000360835.4	37	CCDS14048.1	.	.	.	.	.	.	.	.	.	.	G	31	5.082468	0.94050	.	.	ENSG00000159307	ENST00000360835;ENST00000381243	D	0.88586	-2.4	3.95	3.95	0.45737	.	0.000000	0.85682	D	0.000000	D	0.90584	0.7048	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92328	0.5871	10	0.87932	D	0	.	16.5437	0.84408	0.0:0.0:1.0:0.0	.	951	Q8IWY4	SCUB1_HUMAN	V	951;581	ENSP00000354080:A951V	ENSP00000354080:A951V	A	-	2	0	SCUBE1	41930062	1.000000	0.71417	0.948000	0.38648	0.976000	0.68499	9.514000	0.98013	2.204000	0.70986	0.591000	0.81541	GCG	.	.	none		0.567	SCUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319582.3	NM_173050		A	43600118	G	A	43600118	3	1	1	1	0	0	0	0	1	0	0	0	13959	1087	38	1	118	1	SCUBE1	22	43600118	Missense_Mutation	SNP	G	TCGA-FA-8693-01A-11D-2397-10	19643780	43600118	7704448	173	173											
EGFL6	25975	hgsc.bcm.edu	37	chrX	13636081	13636082	+	Frame_Shift_Ins	INS	-	-	A																															gtaaaaaagggaatgaagagINSaaaatgaaagaggggcttga																										TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chrX:13636081_13636082insA	ENST00000361306.1	+	8	1268_1269	c.1011_1012insA	c.(1012-1014)aaafs	p.K338fs	EGFL6_ENST00000380602.3_Frame_Shift_Ins_p.K338fs	NM_001167890.1|NM_015507.3	NP_001161362.1|NP_056322.2	Q8IUX8	EGFL6_HUMAN	EGF-like-domain, multiple 6	338					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						GGAATGAAGAGAAAATGAAAGA	0.465																																					p.E337fs		Pindel,Atlas-Indel	.											.	EGFL6	111	.	0			c.1011_1012insA						PASS	.																																			SO:0001589	frameshift_variant	25975	exon8			.	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.1015dupA	X.37:g.13636085_13636085dupA	ENSP00000355126:p.Lys338fs	74	0	.		79	22	0.278	NM_001167890	B2RCB1|Q6UXJ1|Q8NBV0|Q8WYG3|Q9NY67|Q9NZL7|Q9UFK6	Frame_Shift_Ins	INS	ENST00000361306.1	37	CCDS14155.1																																																																																			.	.	none		0.465	EGFL6-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055800.1	NM_015507		A	13636082	-	A	13636081	7	5	1	1	0	1	1	0	0	0	0	0	4965	933	33	0	1041	0	EGFL6	23	13636081	Frame_Shift_Ins	INS	-	TCGA-FA-8693-01A-11D-2397-10		13636081	141634479	174	174											
CPXCR1	53336	hgsc.bcm.edu	37	chrX	88008609	88008609	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggaagatgttgttcctcAagcagcagaaaacagcgagc	14	6	11	10	1	1	2	1	0	0	2	2	4	2	3	2	1	5	4	2	1	4	2			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chrX:88008609A>G	ENST00000276127.4	+	3	453	c.194A>G	c.(193-195)cAa>cGa	p.Q65R	CPXCR1_ENST00000373111.1_Missense_Mutation_p.Q65R	NM_033048.5	NP_149037	Q8N123	CPXCR_HUMAN	CPX chromosome region, candidate 1	65							metal ion binding (GO:0046872)			NS(1)|cervix(1)|kidney(1)|large_intestine(11)|liver(1)|lung(20)|ovary(3)|upper_aerodigestive_tract(2)	40						GTTGTTCCTCAAGCAGCAGAA	0.463																																					p.Q65R		Atlas-SNP	.											.	CPXCR1	83	.	0			c.A194G						PASS	.						44	42	43					X																	88008609		2203	4300	6503	SO:0001583	missense	53336	exon3			TTCCTCAAGCAGC	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.194A>G	X.37:g.88008609A>G	ENSP00000276127:p.Gln65Arg	82	0	0		57	17	0.298246	NM_001184771	B2R9F9|D3DTE7|Q96RS3	Missense_Mutation	SNP	ENST00000276127.4	37	CCDS14458.1	.	.	.	.	.	.	.	.	.	.	A	9.947	1.219144	0.22373	.	.	ENSG00000147183	ENST00000276127;ENST00000373111	T;T	0.32515	1.45;1.45	3.43	2.22	0.28083	.	0.415062	0.17767	N	0.162708	T	0.28699	0.0711	L	0.29908	0.895	0.09310	N	1	D	0.61697	0.99	P	0.54174	0.744	T	0.06092	-1.0846	9	.	.	.	.	5.9873	0.19442	0.7342:0.2658:0.0:0.0	.	65	Q8N123	CPXCR_HUMAN	R	65	ENSP00000276127:Q65R;ENSP00000362203:Q65R	.	Q	+	2	0	CPXCR1	87895265	0.000000	0.05858	0.004000	0.12327	0.089000	0.18198	-0.008000	0.12788	0.511000	0.28236	-0.387000	0.06579	CAA	.	.	none		0.463	CPXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057418.1	NM_033048		G	88008609	A	G	88008609	3	3	1	1	0	0	0	0	1	0	0	0	3838	130	5	3	196	3	CPXCR1	23	88008609	Missense_Mutation	SNP	A	TCGA-FA-8693-01A-11D-2397-10	74372528	88008609	67261951	175	175											
TNFRSF14	8764	hgsc.bcm.edu	37	chr1	2494626	2494626	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aaggtgaggccacagtcattGaggccctgcaggcccctccg	8	6	13	14	1	1	2	1	2	0	0	2	2	2	2	5	4	1	1	5	4	1	1			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr1:2494626G>C	ENST00000355716.4	+	8	1065	c.766G>C	c.(766-768)Gag>Cag	p.E256Q		NM_003820.2	NP_003811.2	Q92956	TNR14_HUMAN	tumor necrosis factor receptor superfamily, member 14	256					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)		CACAGTCATTGAGGCCCTGCA	0.627			"Mis, N, F"		follicular lymphoma																																p.E256Q		Atlas-SNP	.		Rec	yes		1	1p36.32	8764	"tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)"		L	.	TNFRSF14	89	.	0			c.G766C						PASS	.						120	103	109					1																	2494626		2203	4300	6503	SO:0001583	missense	8764	exon8			GTCATTGAGGCCC	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.766G>C	1.37:g.2494626G>C	ENSP00000347948:p.Glu256Gln	60	0	0		65	13	0.2	NM_003820	B3KW30|B9DI89|Q6IB95|Q8N634|Q8WXR1|Q96J31|Q9UM65	Missense_Mutation	SNP	ENST00000355716.4	37	CCDS44046.1	.	.	.	.	.	.	.	.	.	.	G	0.012	-1.662888	0.00772	.	.	ENSG00000157873	ENST00000355716	D	0.86865	-2.18	1.85	-0.23	0.13090	.	.	.	.	.	T	0.68384	0.2995	N	0.04508	-0.205	0.09310	N	1	B	0.24576	0.106	B	0.10450	0.005	T	0.54944	-0.8217	9	0.26408	T	0.33	1.2888	7.7934	0.29133	0.0:0.6123:0.3877:0.0	.	256	Q92956	TNR14_HUMAN	Q	256	ENSP00000347948:E256Q	ENSP00000347948:E256Q	E	+	1	0	TNFRSF14	2479792	0.011000	0.17503	0.000000	0.03702	0.002000	0.02628	0.441000	0.21611	-0.044000	0.13491	-0.304000	0.09214	GAG	.	.	none		0.627	TNFRSF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002088.1			C	2494626	G	C	2494626	3	2	2	1	0	0	0	0	1	0	0	0	16304	1291	45	4	796	4	TNFRSF14	1	2494626	Missense_Mutation	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10		2494626	246755995	1	176											
CLCN6	1185	hgsc.bcm.edu	37	chr1	11879572	11879572	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tctttgtggacttttttgtgCgactcttcacccaactcaag	7	16	7	11	1	4	0	2	0	2	0	4	2	4	1	1	1	2	0	1	1	2	5			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr1:11879572C>T	ENST00000346436.6	+	5	359	c.307C>T	c.(307-309)Cga>Tga	p.R103*	CLCN6_ENST00000376492.3_3'UTR|CLCN6_ENST00000376496.3_Nonsense_Mutation_p.R103*|CLCN6_ENST00000376487.3_Nonsense_Mutation_p.R81*|CLCN6_ENST00000376497.3_Nonsense_Mutation_p.R103*|CLCN6_ENST00000312413.6_Nonsense_Mutation_p.R103*	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6	103					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)		CTTTTTTGTGCGACTCTTCAC	0.463																																					p.R103X		Atlas-SNP	.											CLCN6,NS,carcinoma,-1,1	CLCN6	77	1	0			c.C307T						scavenged	.						297	249	266					1																	11879572		2203	4300	6503	SO:0001587	stop_gained	1185	exon5			TTTGTGCGACTCT	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.307C>T	1.37:g.11879572C>T	ENSP00000234488:p.Arg103*	96	1	0.0104167		98	7	0.0714286	NM_001286	A8K1T4|B4DGT7|F8W9R3|O60818|O60819|O60820|O60821|P78520|P78521|Q17R81|Q5SNW2|Q5SNW3|Q5SNX1|Q5SNX2|Q5SNX3|Q99427|Q99428|Q99429	Nonsense_Mutation	SNP	ENST00000346436.6	37	CCDS138.1	.	.	.	.	.	.	.	.	.	.	C	35	5.418281	0.96092	.	.	ENSG00000011021	ENST00000312413;ENST00000346436;ENST00000376497;ENST00000376487;ENST00000376496;ENST00000376490;ENST00000376491;ENST00000376492	.	.	.	5.34	5.34	0.76211	.	0.222897	0.47852	D	0.000215	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	-6.8753	18.3846	0.90463	0.0:1.0:0.0:0.0	.	.	.	.	X	103;103;103;81;103;103;103;103	.	ENSP00000308367:R103X	R	+	1	2	CLCN6	11802159	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.617000	0.67716	2.651000	0.90000	0.655000	0.94253	CGA	.	.	none		0.463	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2	NM_001286		T	11879572	C	T	11879572	4	4	2	1	0	0	0	0	0	1	0	0	3469	760	27	1	325	1	CLCN6	1	11879572	Nonsense_Mutation	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10	9384946	11879572	237371049	2	177											
SPEN	23013	hgsc.bcm.edu	37	chr1	16235856	16235856	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caagtgatgattctccagctCgatcagttcagtctgcagca	10	11	9	11	1	4	2	2	2	2	0	6	3	4	2	1	0	3	4	1	0	1	2			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr1:16235856C>T	ENST00000375759.3	+	4	1126	c.922C>T	c.(922-924)Cga>Tga	p.R308*	snoU13_ENST00000459258.1_RNA	NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	308	Ser-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)		TTCTCCAGCTCGATCAGTTCA	0.443																																					p.R308X		Atlas-SNP	.											SPEN,NS,carcinoma,0,2	SPEN	374	2	0			c.C922T						PASS	.						147	147	147					1																	16235856		2203	4300	6503	SO:0001587	stop_gained	23013	exon4			CCAGCTCGATCAG		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.922C>T	1.37:g.16235856C>T	ENSP00000364912:p.Arg308*	117	0	0		96	23	0.239583	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Nonsense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.154147	0.78114	.	.	ENSG00000065526	ENST00000375759;ENST00000438066;ENST00000375753	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.8431	17.6753	0.88229	0.0:1.0:0.0:0.0	.	.	.	.	X	308;267;267	.	ENSP00000364906:R267X	R	+	1	2	SPEN	16108443	0.997000	0.39634	0.999000	0.59377	0.826000	0.46750	3.632000	0.54287	2.615000	0.88500	0.655000	0.94253	CGA	.	.	none		0.443	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		T	16235856	C	T	16235856	4	4	2	1	0	0	0	0	0	1	0	0	15053	876	31	1	936	1	SPEN	1	16235856	Nonsense_Mutation	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10	4356284	16235856	233014765	3	178											
LRIG2	9860	hgsc.bcm.edu	37	chr1	113655236	113655236	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggtggtactgactttcctgCggctcgagaaagacgcatgc	8	10	13	10	3	0	3	0	1	0	2	2	4	1	3	1	3	3	3	1	3	2	2			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr1:113655236C>T	ENST00000361127.5	+	14	2132	c.1934C>T	c.(1933-1935)gCg>gTg	p.A645V	LRIG2_ENST00000492207.1_3'UTR	NM_014813.1	NP_055628.1	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like domains 2	645	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)		GACTTTCCTGCGGCTCGAGAA	0.493																																					p.A645V		Atlas-SNP	.											LRIG2,NS,lymphoid_neoplasm,0,1	LRIG2	67	1	0			c.C1934T						scavenged	.						140	125	130					1																	113655236		2203	4300	6503	SO:0001583	missense	9860	exon14			TTCCTGCGGCTCG	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.1934C>T	1.37:g.113655236C>T	ENSP00000355396:p.Ala645Val	115	1	0.00869565		70	3	0.0428571	NM_014813	Q9NSN2	Missense_Mutation	SNP	ENST00000361127.5	37	CCDS30808.1	.	.	.	.	.	.	.	.	.	.	C	35	5.577687	0.96565	.	.	ENSG00000198799	ENST00000361127	T	0.77620	-1.11	5.45	5.45	0.79879	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.73837	0.3638	N	0.10629	0.01	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80986	-0.1137	10	0.56958	D	0.05	.	19.2881	0.94087	0.0:1.0:0.0:0.0	.	645	O94898	LRIG2_HUMAN	V	645	ENSP00000355396:A645V	ENSP00000355396:A645V	A	+	2	0	LRIG2	113456759	1.000000	0.71417	0.962000	0.40283	0.988000	0.76386	7.818000	0.86416	2.560000	0.86352	0.591000	0.81541	GCG	.	.	none		0.493	LRIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033549.2	NM_014813		T	113655236	C	T	113655236	3	4	2	1	0	0	0	0	1	0	0	0	8954	768	27	1	1988	1	LRIG2	1	113655236	Missense_Mutation	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10	97419380	113655236	135595385	4	179											
NOTCH2	4853	hgsc.bcm.edu	37	chr1	120458147	120458147	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	accactgtgactgggtgttcGctcagcagcatttgaggaag	9	10	13	9	1	1	2	1	2	0	0	2	3	1	3	1	2	2	4	1	2	1	2			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr1:120458147G>A	ENST00000256646.2	-	34	7417	c.7198C>T	c.(7198-7200)Cga>Tga	p.R2400*		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	2400					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.R2400*(4)		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)		CTGGGTGTTCGCTCAGCAGCA	0.562			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome																												p.R2400X		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	NOTCH2,NS,lymphoid_neoplasm,0,26	NOTCH2	348	26	4	Substitution - Nonsense(4)	haematopoietic_and_lymphoid_tissue(3)|breast(1)	c.C7198T						scavenged	.						126	109	115					1																	120458147		2203	4300	6503	SO:0001587	stop_gained	4853	exon34	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	GTGTTCGCTCAGC	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.7198C>T	1.37:g.120458147G>A	ENSP00000256646:p.Arg2400*	64	1	0.015625		53	17	0.320755	NM_024408	Q5T3X7|Q99734|Q9H240	Nonsense_Mutation	SNP	ENST00000256646.2	37	CCDS908.1	.	.	.	.	.	.	.	.	.	.	G	48	14.010061	0.99775	.	.	ENSG00000134250	ENST00000256646	.	.	.	5.35	4.43	0.53597	.	0.000000	0.30695	U	0.009069	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10902	T	0.67	.	12.2534	0.54611	0.0:0.0:0.6765:0.3235	.	.	.	.	X	2400	.	ENSP00000256646:R2400X	R	-	1	2	NOTCH2	120259670	0.616000	0.27035	1.000000	0.80357	0.996000	0.88848	0.360000	0.20250	1.224000	0.43551	0.591000	0.81541	CGA	.	.	none		0.562	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		A	120458147	G	A	120458147	4	1	2	1	0	0	0	0	0	1	0	0	10557	1095	38	1	221	1	NOTCH2	1	120458147	Nonsense_Mutation	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10	6802911	120458147	128792474	5	180											
MTMR11	10903	hgsc.bcm.edu	37	chr1	149906097	149906097	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggatcacctggtggctacgtCgaacctctcgttgaccgtgc	6	10	12	13	4	2	1	1	1	1	0	4	3	2	2	3	3	3	2	3	3	2	2	rs143590446	byFrequency	TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr1:149906097C>T	ENST00000439741.2	-	7	920	c.670G>A	c.(670-672)Gac>Aac	p.D224N	MTMR11_ENST00000369140.3_Missense_Mutation_p.D152N|MTMR11_ENST00000406732.3_Missense_Mutation_p.D196N|MTMR11_ENST00000361405.6_Missense_Mutation_p.D224N|MTMR11_ENST00000492824.1_5'UTR	NM_001145862.1	NP_001139334.1	A4FU01	MTMRB_HUMAN	myotubularin related protein 11	224	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)			GTGGCTACGTCGAACCTCTCG	0.567													C|||	2	0.000399361	0.0	0.0	5008	,	,		18552	0.002		0.0	False		,,,				2504	0.0				p.D224N		Atlas-SNP	.											.	MTMR11	136	.	0			c.G670A						PASS	.	C	ASN/ASP,ASN/ASP	1,4405	2.1+/-5.4	0,1,2202	100	95	97		670,454	6.1	1	1	dbSNP_134	97	0,8600		0,0,4300	yes	missense,missense	MTMR11	NM_001145862.1,NM_181873.3	23,23	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	224/710,152/641	149906097	1,13005	2203	4300	6503	SO:0001583	missense	10903	exon7			CTACGTCGAACCT	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.670G>A	1.37:g.149906097C>T	ENSP00000391668:p.Asp224Asn	48	0	0		52	11	0.211538	NM_001145862	B3KUE4|B4DJI6|B4DQF5|B4E3Q6|Q3ZCP7|Q5SZ62|Q6P2Q8|Q99752|Q99753	Missense_Mutation	SNP	ENST00000439741.2	37	CCDS53360.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	24.0	4.483644	0.84854	2.27E-4	0.0	ENSG00000014914	ENST00000369140;ENST00000439741;ENST00000361405;ENST00000406732;ENST00000405710	D;D;T;D	0.92595	-3.07;-2.67;0.88;-3.07	6.07	6.07	0.98685	Myotubularin phosphatase domain (1);Myotubularin-related (1);	0.054950	0.64402	D	0.000001	D	0.91788	0.7402	N	0.24115	0.695	0.53005	D	0.999965	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.78314	0.977;0.984;0.984;0.991	D	0.91383	0.5129	10	0.40728	T	0.16	.	18.1378	0.89627	0.0:1.0:0.0:0.0	.	66;196;152;224	F8W8W0;A4FU01-6;A4FU01-4;A4FU01	.;.;.;MTMRB_HUMAN	N	152;224;224;196;66	ENSP00000358136:D152N;ENSP00000391668:D224N;ENSP00000354941:D224N;ENSP00000383948:D196N	ENSP00000354941:D224N	D	-	1	0	MTMR11	148172721	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.244000	0.72391	2.884000	0.98904	0.655000	0.94253	GAC	C|1.000;T|0.000	0.000	strong		0.567	MTMR11-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_181873		T	149906097	C	T	149906097	3	4	2	1	0	0	0	0	1	0	0	0	9949	884	31	1	1542	1	MTMR11	1	149906097	Missense_Mutation	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10	29447950	149906097	99344524	6	181											
FLG	2312	hgsc.bcm.edu	37	chr1	152278749	152278749	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gattgtccctggactgcctgTgagtgtctagagatgtcggc	6	12	14	9	1	1	2	0	1	1	1	3	5	2	3	2	2	1	0	2	2	1	2			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr1:152278749T>G	ENST00000368799.1	-	3	8648	c.8613A>C	c.(8611-8613)tcA>tcC	p.S2871S	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2871	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)			GGACTGCCTGTGAGTGTCTAG	0.562									Ichthyosis																												p.S2871S		Atlas-SNP	.											.	FLG	900	.	0			c.A8613C						PASS	.						174	278	244					1																	152278749		2116	4297	6413	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGCCTGTGAGTGT	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.8613A>C	1.37:g.152278749T>G		110	0	0		110	11	0.1	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			.	.	none		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		G	152278749	T	G	152278749	2	3	2	1	0	0	0	0	0	0	0	1	5930	1683	59	5		5	FLG	1	152278749	Silent	SNP	T	TCGA-FA-A4BB-01A-11D-A31X-10	2372652	152278749	96971872	7	182											
INTS3	65123	hgsc.bcm.edu	37	chr1	153719499	153719499	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctgaataaaatcaaccagAtacttatggagaagtacctg	16	10	7	8	0	1	3	1	1	0	2	2	4	2	3	3	1	3	1	3	1	8	4			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr1:153719499A>G	ENST00000318967.2	+	4	953	c.385A>G	c.(385-387)Ata>Gta	p.I129V	INTS3_ENST00000435409.2_Missense_Mutation_p.I129V|RP11-216N14.8_ENST00000453778.1_RNA|INTS3_ENST00000456435.1_5'UTR	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	129					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)			AATCAACCAGATACTTATGGA	0.448																																					p.I129V		Atlas-SNP	.											INTS3,NS,carcinoma,0,1	INTS3	83	1	0			c.A385G						PASS	.						104	105	105					1																	153719499		2203	4300	6503	SO:0001583	missense	65123	exon4			AACCAGATACTTA	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.385A>G	1.37:g.153719499A>G	ENSP00000318641:p.Ile129Val	87	0	0		87	11	0.126437	NM_023015	A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Missense_Mutation	SNP	ENST00000318967.2	37	CCDS1052.1	.	.	.	.	.	.	.	.	.	.	A	15.16	2.750433	0.49257	.	.	ENSG00000143624	ENST00000318967;ENST00000435409	.	.	.	4.82	3.68	0.42216	.	0.111158	0.64402	D	0.000015	T	0.31009	0.0783	L	0.43152	1.355	0.80722	D	1	B	0.25312	0.123	B	0.21917	0.037	T	0.28106	-1.0054	9	0.66056	D	0.02	.	9.0006	0.36079	0.6135:0.3865:0.0:0.0	.	129	Q68E01-2	.	V	129	.	ENSP00000318641:I129V	I	+	1	0	INTS3	151986123	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.853000	0.48317	0.855000	0.35359	0.459000	0.35465	ATA	.	.	none		0.448	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015		G	153719499	A	G	153719499	3	3	2	1	0	0	0	0	1	0	0	0	7788	333	12	3	399	3	INTS3	1	153719499	Missense_Mutation	SNP	A	TCGA-FA-A4BB-01A-11D-A31X-10	1440750	153719499	95531122	8	183											
FCRLB	127943	hgsc.bcm.edu	37	chr1	161695618	161695618	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtgtctgtcgcagattggctGattctgcaagtgccctatgc	6	13	12	10	1	2	2	0	1	2	1	3	2	2	2	1	1	3	3	1	1	2	3			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr1:161695618G>A	ENST00000367948.2	+	6	530	c.315G>A	c.(313-315)ctG>ctA	p.L105L	FCRLB_ENST00000367946.3_Silent_p.L105L|FCRLB_ENST00000367944.3_Silent_p.L98L|FCRLB_ENST00000392158.1_Silent_p.L105L|FCRLB_ENST00000367945.1_Silent_p.L98L|FCRLB_ENST00000336830.5_Silent_p.L105L			Q6BAA4	FCRLB_HUMAN	Fc receptor-like B	105	Ig-like C2-type 2.				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)			CAGATTGGCTGATTCTGCAAG	0.567																																					p.L105L		Atlas-SNP	.											.	FCRLB	35	.	0			c.G315A						PASS	.						118	111	113					1																	161695618		2203	4300	6503	SO:0001819	synonymous_variant	127943	exon4			TTGGCTGATTCTG	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.315G>A	1.37:g.161695618G>A		67	0	0		56	4	0.0714286	NM_001002901	A2A3J5|A2A3J7|Q5VXA6|Q6BAA0|Q6BAA1|Q6BAA2|Q6BAA3|Q8IXZ7	Silent	SNP	ENST00000367948.2	37	CCDS30927.1																																																																																			.	.	none		0.567	FCRLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083585.1	NM_152378		A	161695618	G	A	161695618	2	1	2	1	0	0	0	0	0	0	0	1	5809	1277	45	2		2	FCRLB	1	161695618	Silent	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10	7976119	161695618	87555003	9	184											
BTG2	7832	hgsc.bcm.edu	37	chr1	203276375	203276375	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agccccagctgcaccagctgCtgcccagcgagctgaccctg	7	5	11	18	1	0	1	0	1	0	0	0	2	0	1	5	0	8	5	5	0	0	0			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr1:203276375C>T	ENST00000290551.4	+	2	357	c.286C>T	c.(286-288)Ctg>Ttg	p.L96L	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	96					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			GCACCAGCTGCTGCCCAGCGA	0.642																																					p.L96L		Atlas-SNP	.											.	BTG2	16	.	0			c.C286T						PASS	.						47	49	48					1																	203276375		2203	4300	6503	SO:0001819	synonymous_variant	7832	exon2			CAGCTGCTGCCCA		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.286C>T	1.37:g.203276375C>T		52	0	0		57	11	0.192982	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Silent	SNP	ENST00000290551.4	37	CCDS1437.1																																																																																			.	.	none		0.642	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		T	203276375	C	T	203276375	2	4	2	1	0	0	0	0	0	0	0	1	1556	796	28	2		2	BTG2	1	203276375	Silent	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10	41580757	203276375	45974246	10	185											
KCTD3	51133	hgsc.bcm.edu	37	chr1	215759865	215759865	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaatcttcaggatggcagcaAgtgtttacgagcccatattt	11	12	10	8	1	2	0	1	0	1	0	2	3	2	1	1	2	3	3	1	2	4	5			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr1:215759865A>G	ENST00000259154.4	+	9	948	c.654A>G	c.(652-654)caA>caG	p.Q218Q		NM_016121.3	NP_057205.2	Q9Y597	KCTD3_HUMAN	potassium channel tetramerization domain containing 3	218					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)		GATGGCAGCAAGTGTTTACGA	0.438																																					p.Q218Q		Atlas-SNP	.											.	KCTD3	101	.	0			c.A654G						PASS	.						145	138	140					1																	215759865		2203	4300	6503	SO:0001819	synonymous_variant	51133	exon9			GCAGCAAGTGTTT	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.654A>G	1.37:g.215759865A>G		123	0	0		98	8	0.0816327	NM_016121	A0AV15|D3DTA6|Q49AG7|Q504Q9|Q6PJN6|Q8ND58|Q8NDJ0|Q8WX16	Silent	SNP	ENST00000259154.4	37	CCDS1515.1																																																																																			.	.	none		0.438	KCTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089871.2	NM_016121		G	215759865	A	G	215759865	2	3	2	1	0	0	0	0	0	0	0	1	8119	69	3	3		3	KCTD3	1	215759865	Silent	SNP	A	TCGA-FA-A4BB-01A-11D-A31X-10	12483490	215759865	33490756	11	186											
NRXN1	9378	hgsc.bcm.edu	37	chr2	51254998	51254998	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcgcttggacttgacctcCacccacttggcctccacctg	5	10	8	18	1	0	1	0	1	0	0	2	2	2	2	6	2	1	1	6	2	0	3			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr2:51254998C>T	ENST00000406316.2	-	2	1890	c.414G>A	c.(412-414)gtG>gtA	p.V138V	NRXN1_ENST00000406859.3_Silent_p.V138V|NRXN1_ENST00000405581.1_Silent_p.V138V|NRXN1_ENST00000402717.3_Silent_p.V138V|NRXN1_ENST00000401669.2_Silent_p.V138V|NRXN1_ENST00000405472.3_Silent_p.V138V|NRXN1_ENST00000404971.1_Silent_p.V138V	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	138	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)			ACTTGACCTCCACCCACTTGG	0.682																																					p.V138V		Atlas-SNP	.											.	NRXN1	1118	.	0			c.G414A						PASS	.						29	34	33					2																	51254998		2139	4250	6389	SO:0001819	synonymous_variant	9378	exon2			GACCTCCACCCAC	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.414G>A	2.37:g.51254998C>T		50	0	0		53	8	0.150943	NM_004801	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	37	CCDS54360.1																																																																																			.	.	none		0.682	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			T	51254998	C	T	51254998	2	4	2	1	0	0	0	0	0	0	0	1	10674	581	21	2		2	NRXN1	2	51254998	Silent	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10		51254998	191944375	12	187											
DUSP2	1844	hgsc.bcm.edu	37	chr2	96810531	96810531	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caggagccctggagtcggagCggctggttttgtcccctgtt	4	11	15	11	2	0	0	0	0	0	0	2	3	1	3	3	5	2	3	3	5	0	3			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr2:96810531C>T	ENST00000288943.4	-	2	564	c.479G>A	c.(478-480)cGc>cAc	p.R160H	AC012307.2_ENST00000449242.1_lincRNA	NM_004418.3	NP_004409.1	Q05923	DUS2_HUMAN	dual specificity phosphatase 2	160					endoderm formation (GO:0001706)|inactivation of MAPK activity (GO:0000188)|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)|protein tyrosine/threonine phosphatase activity (GO:0008330)			NS(1)|breast(1)|lung(2)|skin(1)	5		Ovarian(717;0.0228)				GGAGTCGGAGCGGCTGGTTTT	0.677																																					p.R160H		Atlas-SNP	.											.	DUSP2	20	.	0			c.G479A						PASS	.						12	17	15					2																	96810531		2184	4285	6469	SO:0001583	missense	1844	exon2			TCGGAGCGGCTGG	L11329	CCDS2016.1	2q11	2011-06-09			ENSG00000158050	ENSG00000158050		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3068	protein-coding gene	gene with protein product		603068				7806236, 7590752, 12673251	Standard	NM_004418		Approved	PAC-1	uc002svk.4	Q05923	OTTHUMG00000130456	ENST00000288943.4:c.479G>A	2.37:g.96810531C>T	ENSP00000288943:p.Arg160His	84	0	0		51	6	0.117647	NM_004418	Q53T45	Missense_Mutation	SNP	ENST00000288943.4	37	CCDS2016.1	.	.	.	.	.	.	.	.	.	.	c	13.14	2.148441	0.37923	.	.	ENSG00000158050	ENST00000288943	T	0.02498	4.27	4.0	-3.73	0.04398	.	1.159010	0.06242	N	0.690580	T	0.02888	0.0086	L	0.51422	1.61	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.46582	-0.9181	10	0.44086	T	0.13	.	1.8718	0.03210	0.1343:0.4233:0.1327:0.3096	.	160	Q05923	DUS2_HUMAN	H	160	ENSP00000288943:R160H	ENSP00000288943:R160H	R	-	2	0	DUSP2	96174258	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.775000	0.04679	-0.898000	0.03906	0.450000	0.29827	CGC	.	.	none		0.677	DUSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252847.1	NM_004418		T	96810531	C	T	96810531	3	4	2	1	0	0	0	0	1	0	0	0	4821	768	27	1	477	1	DUSP2	2	96810531	Missense_Mutation	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10	45555533	96810531	146388842	13	188											
NUP210	23225	hgsc.bcm.edu	37	chr3	13427859	13427859	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gacgtcataggccgggttcaGaaggatgttttccaaaatca	12	10	11	8	2	3	1	3	0	0	1	4	3	4	2	2	3	0	2	2	3	4	4			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr3:13427859G>A	ENST00000254508.5	-	6	815	c.733C>T	c.(733-735)Ctg>Ttg	p.L245L		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	245					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)					GCCGGGTTCAGAAGGATGTTT	0.493																																					p.L245L		Atlas-SNP	.											.	NUP210	182	.	0			c.C733T						PASS	.						184	165	172					3																	13427859		2203	4300	6503	SO:0001819	synonymous_variant	23225	exon6			GGTTCAGAAGGAT	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.733C>T	3.37:g.13427859G>A		87	0	0		64	10	0.15625	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Silent	SNP	ENST00000254508.5	37	CCDS33704.1																																																																																			.	.	none		0.493	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923		A	13427859	G	A	13427859	2	1	2	1	0	0	0	0	0	0	0	1	10769	933	33	2		2	NUP210	3	13427859	Silent	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10		13427859	184594571	14	189											
RBM5	10181	hgsc.bcm.edu	37	chr3	50154752	50154752	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aacaagatgctgcaggccatGggctggcgggaaggctctgg	9	6	17	9	1	1	1	0	0	1	1	1	2	1	2	1	6	3	4	1	6	3	0			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr3:50154752G>A	ENST00000347869.3	+	24	2437	c.2262G>A	c.(2260-2262)atG>atA	p.M754I	RP11-493K19.3_ENST00000425674.1_RNA|RP11-493K19.3_ENST00000437204.1_RNA	NM_005778.3	NP_005769.1	P52756	RBM5_HUMAN	RNA binding motif protein 5	754	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.|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)		TGCAGGCCATGGGCTGGCGGG	0.517																																					p.M754I		Atlas-SNP	.											.	RBM5	76	.	0			c.G2262A						PASS	.						171	164	167					3																	50154752		2203	4300	6503	SO:0001583	missense	10181	exon24			GGCCATGGGCTGG	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.2262G>A	3.37:g.50154752G>A	ENSP00000343054:p.Met754Ile	101	0	0		88	8	0.0909091	NM_005778	B2RA45|B4DM16|B4DMF9|B4DZ63|Q93021|Q9BU14|Q9HDA6|Q9UKY8|Q9UL24	Missense_Mutation	SNP	ENST00000347869.3	37	CCDS2810.1	.	.	.	.	.	.	.	.	.	.	G	34	5.322192	0.95708	.	.	ENSG00000003756	ENST00000347869;ENST00000543047;ENST00000544851	T	0.50001	0.76	5.48	5.48	0.80851	D111/G-patch (3);	0.000000	0.85682	D	0.000000	D	0.83266	0.5217	H	0.99487	4.59	0.80722	D	1	D;D	0.63046	0.992;0.981	D;D	0.70227	0.968;0.966	D	0.90805	0.4697	10	0.87932	D;D	0;0	-14.2084	19.3354	0.94316	0.0:0.0:1.0:0.0	.	444;754	Q59HE6;P52756	.;RBM5_HUMAN	I	754;753;444	ENSP00000343054:M754I	ENSP00000343054:M754I;ENSP00000343054:M754I	M	+	3	0	RBM5	50129756	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.532000	0.98057	2.571000	0.86741	0.650000	0.86243	ATG	.	.	none		0.517	RBM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345797.3	NM_005778		A	50154752	G	A	50154752	3	1	2	1	0	0	0	0	1	0	0	0	13158	1348	47	2	2352	2	RBM5	3	50154752	Missense_Mutation	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10	36726893	50154752	147867678	15	190											
CBLB	868	hgsc.bcm.edu	37	chr3	105495385	105495385	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacagttttgtgagatttcGtctgtaggcacaagggaaaa	12	11	13	5	1	1	1	0	1	1	1	2	4	1	3	0	3	0	3	0	3	4	4	rs369966206		TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr3:105495385G>A	ENST00000264122.4	-	4	742	c.421C>T	c.(421-423)Cga>Tga	p.R141*	CBLB_ENST00000545639.1_Intron|CBLB_ENST00000405772.1_Splice_Site_p.R141*|CBLB_ENST00000394027.3_Splice_Site_p.R163*|CBLB_ENST00000403724.1_Splice_Site_p.R141*	NM_170662.3	NP_733762.2	Q13191	CBLB_HUMAN	Cbl proto-oncogene B, E3 ubiquitin protein ligase	141	4H.|Cbl-PTB. {ECO:0000255|PROSITE- ProRule:PRU00839}.				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)	p.R141*(1)		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						GTGAGATTTCGTCTGTAGGCA	0.348			Mis S		AML																																p.R141X	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,NS,carcinoma,+1,3	CBLB	118	3	1	Substitution - Nonsense(1)	lung(1)	c.C421T						PASS	.	G	stop/ARG	0,4406		0,0,2203	103	100	101		421	3.9	0.8	3		101	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained-near-splice	CBLB	NM_170662.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		141/983	105495385	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	868	exon4			GATTTCGTCTGTA	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.420-1C>T	3.37:g.105495385G>A		90	0	0		64	12	0.1875	NM_170662	A8K9S7|B7WNM4|Q13192|Q13193|Q3LIC0|Q63Z43|Q8IVC5	Nonsense_Mutation	SNP	ENST00000264122.4	37	CCDS2948.1	.	.	.	.	.	.	.	.	.	.	G	39	7.302140	0.98196	0.0	1.16E-4	ENSG00000114423	ENST00000264122;ENST00000394027;ENST00000403724;ENST00000405772	.	.	.	5.79	3.86	0.44501	.	0.057808	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-11.1062	9.6351	0.39802	0.0697:0.0:0.6249:0.3054	.	.	.	.	X	141;163;141;141	.	ENSP00000264122:R141X	R	-	1	2	CBLB	106978075	1.000000	0.71417	0.802000	0.32245	0.896000	0.52359	2.245000	0.43133	0.728000	0.32382	0.557000	0.71058	CGA	.	.	weak		0.348	CBLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319417.2	NM_170662	Nonsense_Mutation	A	105495385	G	A	105495385	5	1	2	1	0	0	0	0	0	0	1	0	2703	1159	40	1	2591	1	CBLB	3	105495385	Splice_Site	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10	55340633	105495385	92527045	16	191											
GP9	2815	hgsc.bcm.edu	37	chr3	128780664	128780664	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagcccatgtacctgccgcGccctggaaaccatggggctg	7	6	12	16	2	0	0	0	0	0	0	0	1	0	1	6	3	4	2	6	3	2	1			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr3:128780664G>A	ENST00000307395.4	+	3	304	c.82G>A	c.(82-84)Gcc>Acc	p.A28T		NM_000174.3	NP_000165.1	P14770	GPIX_HUMAN	glycoprotein IX (platelet)	28	LRRNT.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|lung(4)	6					Quinine(DB00468)	TACCTGCCGCGCCCTGGAAAC	0.697																																					p.A28T		Atlas-SNP	.											GP9,colon,carcinoma,-1,1	GP9	10	1	0			c.G82A						scavenged	.						20	21	20					3																	128780664		2202	4296	6498	SO:0001583	missense	2815	exon3			TGCCGCGCCCTGG		CCDS3055.1	3q21.3	2014-09-17				ENSG00000169704		"CD molecules"	4444	protein-coding gene	gene with protein product		173515				2253772	Standard	XM_005247374		Approved	CD42a, GPIX	uc003elm.2	P14770		ENST00000307395.4:c.82G>A	3.37:g.128780664G>A	ENSP00000303942:p.Ala28Thr	75	1	0.0133333		75	19	0.253333	NM_000174	Q14445|Q8N1D1|Q92525	Missense_Mutation	SNP	ENST00000307395.4	37	CCDS3055.1	.	.	.	.	.	.	.	.	.	.	G	0.018	-1.484390	0.01027	.	.	ENSG00000169704	ENST00000307395	T	0.79141	-1.24	4.17	-2.72	0.05968	Leucine-rich repeat-containing N-terminal (2);	0.533187	0.17413	N	0.175135	T	0.47820	0.1466	N	0.17474	0.49	0.09310	N	1	B	0.33000	0.393	B	0.22601	0.04	T	0.38693	-0.9649	10	0.29301	T	0.29	-0.5344	0.6074	0.00755	0.3136:0.2824:0.2313:0.1728	.	28	P14770	GPIX_HUMAN	T	28	ENSP00000303942:A28T	ENSP00000303942:A28T	A	+	1	0	GP9	130263354	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-2.698000	0.00826	-0.879000	0.04002	0.462000	0.41574	GCC	.	.	none		0.697	GP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358428.1			A	128780664	G	A	128780664	3	1	2	1	0	0	0	0	1	0	0	0	6593	1087	38	1	84	1	GP9	3	128780664	Missense_Mutation	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10	23285279	128780664	69241766	17	192											
HPS3	84343	hgsc.bcm.edu	37	chr3	148863160	148863160	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttctcttacatctgatggAaaaaatttgtctcaggaaaa	14	13	8	6	0	3	1	1	1	3	0	5	3	3	3	0	3	1	1	0	3	6	3			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr3:148863160A>G	ENST00000296051.2	+	5	1130	c.990A>G	c.(988-990)ggA>ggG	p.G330G	HPS3_ENST00000460120.1_Silent_p.G165G	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	330					organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)		p.N332fs*31(1)		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)			CATCTGATGGAAAAAATTTGT	0.343									Hermansky-Pudlak syndrome																												p.G330G		Atlas-SNP	.											.	HPS3	104	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.A990G						PASS	.						96	103	101					3																	148863160		2203	4300	6503	SO:0001819	synonymous_variant	84343	exon5	Familial Cancer Database	HPS, HPS1-8	TGATGGAAAAAAT	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.990A>G	3.37:g.148863160A>G		74	0	0		83	7	0.0843373	NM_032383	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Silent	SNP	ENST00000296051.2	37	CCDS3140.1																																																																																			.	.	none		0.343	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383		G	148863160	A	G	148863160	2	3	2	1	0	0	0	0	0	0	0	1	7349	233	9	3		3	HPS3	3	148863160	Silent	SNP	A	TCGA-FA-A4BB-01A-11D-A31X-10	20082496	148863160	49159270	18	193											
IQCJ	654502	hgsc.bcm.edu	37	chr3	158980510	158980510	+	Intron	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttctatgtcctgacttgaCattcaactgaaagcctagac	11	14	6	10	0	2	4	1	3	1	1	3	4	3	4	2	0	2	0	2	0	4	6			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr3:158980510C>A	ENST00000451172.1	+	4	396				IQCJ-SCHIP1_ENST00000485419.1_Intron|IQCJ_ENST00000397832.2_Missense_Mutation_p.T110K|IQCJ_ENST00000482126.1_Intron|IQCJ-SCHIP1_ENST00000476809.1_Intron|IQCJ-SCHIP1_ENST00000467442.1_Intron	NM_001042705.2	NP_001036170.1	Q1A5X6	IQCJ_HUMAN	IQ motif containing J											cervix(1)|endometrium(2)|large_intestine(2)|lung(10)	15			LUSC - Lung squamous cell carcinoma(72;0.00523)|Lung(72;0.00534)			CCTGACTTGACATTCAACTGA	0.458																																					p.T110K		Atlas-SNP	.											.	IQCJ	28	.	0			c.C329A						PASS	.						109	103	105					3																	158980510		1953	4159	6112	SO:0001627	intron_variant	654502	exon4			ACTTGACATTCAA	DQ309553, DQ309554	CCDS46946.1, CCDS46947.1, CCDS56290.1	3q25.32	2011-03-24			ENSG00000214216	ENSG00000214216			32406	protein-coding gene	gene with protein product		611622				17045569	Standard	NM_001042705		Approved			Q1A5X6	OTTHUMG00000166440	ENST00000451172.1:c.291+38C>A	3.37:g.158980510C>A		134	0	0		109	9	0.0825688	NM_001042706	B7ZMM2|B9EH97|Q1A5X5	Missense_Mutation	SNP	ENST00000451172.1	37	CCDS46946.1	.	.	.	.	.	.	.	.	.	.	C	11.01	1.514430	0.27123	.	.	ENSG00000214216	ENST00000397832	.	.	.	4.84	2.84	0.33178	.	.	.	.	.	T	0.27798	0.0684	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.15867	-1.0422	6	.	.	.	.	10.9941	0.47565	0.4198:0.5802:0.0:0.0	.	110	Q1A5X6-2	.	K	110	.	.	T	+	2	0	IQCJ	160463204	0.000000	0.05858	0.001000	0.08648	0.019000	0.09904	-0.252000	0.08806	1.102000	0.41551	0.655000	0.94253	ACA	.	.	none		0.458	IQCJ-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352395.1	NM_001042705.1		A	158980510	C	A	158980510	1	1	2	0	1	0	0	0	0	0	0	0	7821	478	17	4		4	IQCJ	3	158980510	Intron	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10	10117350	158980510	39041920	19	194											
IFT80	57560	hgsc.bcm.edu	37	chr3	159998476	159998476	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttgcatccctttcatataatGttttaggcaaaatgtctctg	10	17	6	8	0	2	0	1	0	1	0	4	0	3	0	1	1	1	3	1	1	5	6			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr3:159998476G>A	ENST00000326448.7	-	15	2075	c.1643C>T	c.(1642-1644)aCa>aTa	p.T548I	IFT80_ENST00000483465.1_Missense_Mutation_p.T411I|IFT80_ENST00000496589.1_Missense_Mutation_p.T411I|RP11-432B6.3_ENST00000483754.1_Missense_Mutation_p.T719I	NM_020800.2	NP_065851.1	Q9P2H3	IFT80_HUMAN	intraflagellar transport 80	548					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)		p.T548I(1)		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)			TTCATATAATGTTTTAGGCAA	0.323																																					p.T548I		Atlas-SNP	.											IFT80,colon,carcinoma,0,1	IFT80	68	1	1	Substitution - Missense(1)	large_intestine(1)	c.C1643T						PASS	.						122	111	115					3																	159998476		2203	4300	6503	SO:0001583	missense	57560	exon15			TATAATGTTTTAG	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.1643C>T	3.37:g.159998476G>A	ENSP00000312778:p.Thr548Ile	127	0	0		119	12	0.10084	NM_020800	B4E0K1|C9J8I0|Q3MJC4|Q86YF4|Q9UIX1	Missense_Mutation	SNP	ENST00000326448.7	37	CCDS3188.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.327407	0.81690	.	.	ENSG00000068885	ENST00000326448;ENST00000483465;ENST00000496589	T;T;T	0.78481	-0.08;-1.18;-1.18	5.6	5.6	0.85130	.	0.000000	0.64402	U	0.000014	D	0.83936	0.5362	M	0.87456	2.885	0.80722	D	1	D	0.53312	0.959	P	0.46076	0.503	D	0.84821	0.0796	10	0.36615	T	0.2	.	19.6123	0.95613	0.0:0.0:1.0:0.0	.	548	Q9P2H3	IFT80_HUMAN	I	548;411;411	ENSP00000312778:T548I;ENSP00000418196:T411I;ENSP00000420646:T411I	ENSP00000312778:T548I	T	-	2	0	IFT80	161481170	1.000000	0.71417	0.982000	0.44146	0.965000	0.64279	9.074000	0.93998	2.640000	0.89533	0.467000	0.42956	ACA	.	.	none		0.323	IFT80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352651.2	NM_020800		A	159998476	G	A	159998476	3	1	2	1	0	0	0	0	1	0	0	0	7573	1377	48	2	714	2	IFT80	3	159998476	Missense_Mutation	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10	1017966	159998476	38023954	20	195											
CXCL3	2921	hgsc.bcm.edu	37	chr4	74904067	74904067	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cattcacactttggatgttcTtgaggtgaattccctgcagt	8	15	9	9	0	2	2	1	2	1	0	3	3	3	3	1	2	1	2	1	2	1	5			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr4:74904067T>C	ENST00000296026.4	-	2	241	c.164A>G	c.(163-165)aAg>aGg	p.K55R	CXCL3_ENST00000511669.1_5'UTR	NM_002090.2	NP_002081.2	P19876	CXCL3_HUMAN	chemokine (C-X-C motif) ligand 3	55					immune response (GO:0006955)|inflammatory response (GO:0006954)|neutrophil chemotaxis (GO:0030593)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)			central_nervous_system(1)|endometrium(1)	2	Breast(15;0.00612)		all cancers(17;0.00273)|Lung(101;0.196)			TTGGATGTTCTTGAGGTGAAT	0.597																																					p.K55R		Atlas-SNP	.											.	CXCL3	9	.	0			c.A164G						PASS	.						93	101	98					4																	74904067		2203	4300	6503	SO:0001583	missense	2921	exon2			ATGTTCTTGAGGT	M36821	CCDS34007.1	4q21	2013-02-25	2002-08-22	2002-08-23		ENSG00000163734		"Endogenous ligands"	4604	protein-coding gene	gene with protein product		139111	"GRO3 oncogene"	GRO3		2217207	Standard	NM_002090		Approved	SCYB3, GROg, MIP-2b, CINC-2b	uc003hhl.3	P19876		ENST00000296026.4:c.164A>G	4.37:g.74904067T>C	ENSP00000296026:p.Lys55Arg	187	0	0		155	14	0.0903226	NM_002090	Q4W5H9	Missense_Mutation	SNP	ENST00000296026.4	37	CCDS34007.1	.	.	.	.	.	.	.	.	.	.	T	15.82	2.946577	0.53186	.	.	ENSG00000163734	ENST00000296026	T	0.04406	3.63	3.45	0.597	0.17504	CXC chemokine, conserved site (1);Chemokine interleukin-8-like domain (3);	0.477746	0.24341	N	0.039377	T	0.07728	0.0194	L	0.58583	1.82	0.09310	N	1	P	0.40066	0.701	P	0.50109	0.631	T	0.19844	-1.0293	10	0.23891	T	0.37	.	3.2866	0.06934	0.0:0.1382:0.2414:0.6204	.	55	P19876	CXCL3_HUMAN	R	55	ENSP00000296026:K55R	ENSP00000296026:K55R	K	-	2	0	CXCL3	75122931	0.014000	0.17966	0.064000	0.19789	0.282000	0.26991	0.231000	0.17872	0.355000	0.24131	0.254000	0.18369	AAG	.	.	none		0.597	CXCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362721.1			C	74904067	T	C	74904067	3	2	2	1	0	0	0	0	1	0	0	0	4088	1609	56	3	171	3	CXCL3	4	74904067	Missense_Mutation	SNP	T	TCGA-FA-A4BB-01A-11D-A31X-10		74904067	116250209	21	196											
CLCN3	1182	hgsc.bcm.edu	37	chr4	170616831	170616831	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccaattggaggagttcttttTagcctggaagaggtaggtga	10	12	14	5	0	1	2	0	1	1	1	1	5	1	5	2	5	1	2	2	5	4	6			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr4:170616831T>G	ENST00000513761.1	+	8	1564	c.1005T>G	c.(1003-1005)ttT>ttG	p.F335L	CLCN3_ENST00000347613.4_Missense_Mutation_p.F335L|CLCN3_ENST00000504131.2_Missense_Mutation_p.F318L|CLCN3_ENST00000360642.3_Intron	NM_001829.3	NP_001820.2	P51790	CLCN3_HUMAN	chloride channel, voltage-sensitive 3	335					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)		GAGTTCTTTTTAGCCTGGAAG	0.348																																					p.F335L		Atlas-SNP	.											.	CLCN3	85	.	0			c.T1005G						PASS	.						82	87	85					4																	170616831		2203	4300	6503	SO:0001583	missense	1182	exon8			TCTTTTTAGCCTG	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.1005T>G	4.37:g.170616831T>G	ENSP00000424603:p.Phe335Leu	72	0	0		55	8	0.145455	NM_001829	B7Z932|B9EGJ9|D3DP34|E9PB97|O14918|Q86Z21	Missense_Mutation	SNP	ENST00000513761.1	37	CCDS34101.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.13|18.13	3.554513|3.554513	0.65425|0.65425	.|.	.|.	ENSG00000109572|ENSG00000109572	ENST00000513761;ENST00000347613;ENST00000504131;ENST00000507875|ENST00000515420	D;D;D;D|.	0.96885|.	-4.16;-4.16;-4.16;-4.16|.	5.9|5.9	0.483|0.483	0.16820|0.16820	Chloride channel, core (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.85431|.	0.5695|.	H|H	0.97682|0.97682	4.055|4.055	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;0.998;1.0;0.999|.	D|.	0.85847|.	0.1401|.	10|.	0.87932|.	D|.	0|.	-12.0339|-12.0339	10.6439|10.6439	0.45608|0.45608	0.0:0.3784:0.0:0.6216|0.0:0.3784:0.0:0.6216	.|.	318;308;335;335|.	B9EGJ9;E9PE15;P51790;P51790-2|.	.;.;CLCN3_HUMAN;.|.	L|X	335;335;318;308|17	ENSP00000424603:F335L;ENSP00000261514:F335L;ENSP00000424540:F318L;ENSP00000425323:F308L|.	ENSP00000261514:F335L|.	F|L	+|+	3|2	2|0	CLCN3|CLCN3	170853406|170853406	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.671000|0.671000	0.39405|0.39405	0.955000|0.955000	0.29188|0.29188	-0.106000|-0.106000	0.12110|0.12110	-0.973000|-0.973000	0.02599|0.02599	TTT|TTA	.	.	none		0.348	CLCN3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363210.2			G	170616831	T	G	170616831	3	3	2	1	0	0	0	0	1	0	0	0	3466	1751	61	5	1031	5	CLCN3	4	170616831	Missense_Mutation	SNP	T	TCGA-FA-A4BB-01A-11D-A31X-10	95712764	170616831	20537445	22	197											
PCDH12	51294	hgsc.bcm.edu	37	chr5	141324966	141324966	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacaggcacctgctgctgcTgctgctgcctctgctcttgc	3	12	10	16	0	3	0	1	0	2	0	3	0	3	0	2	1	8	7	2	1	0	1	rs62380003|rs532090538	byFrequency	TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr5:141324966T>C	ENST00000231484.3	-	4	4745	c.3535A>G	c.(3535-3537)Agc>Ggc	p.S1179G		NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	1179	Poly-Ser.				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)			ctgctgctgctgctgctgcct	0.557																																					p.S1179G		Atlas-SNP	.											.	PCDH12	133	.	0			c.A3535G						PASS	.						22	24	23					5																	141324966		2203	4295	6498	SO:0001583	missense	51294	exon4			TGCTGCTGCTGCT	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.3535A>G	5.37:g.141324966T>C	ENSP00000231484:p.Ser1179Gly	35	0	0		51	14	0.27451	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	37	CCDS4269.1	26	0.011904761904761904	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	22	0.029023746701846966	T	8.193	0.796523	0.16327	.	.	ENSG00000113555	ENST00000231484	T	0.53640	0.61	5.24	-0.821	0.10822	.	0.585786	0.17591	N	0.168779	T	0.12347	0.0300	L	0.31294	0.92	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.14924	-1.0455	10	0.87932	D	0	.	8.4335	0.32773	0.0:0.4561:0.0:0.5439	rs62380003	1179	Q9NPG4	PCD12_HUMAN	G	1179	ENSP00000231484:S1179G	ENSP00000231484:S1179G	S	-	1	0	PCDH12	141305150	1.000000	0.71417	0.027000	0.17364	0.001000	0.01503	0.556000	0.23438	-0.256000	0.09473	-0.353000	0.07706	AGC	T|0.988;C|0.012	0.012	strong		0.557	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		C	141324966	T	C	141324966	3	2	2	1	0	0	0	0	1	0	0	0	11519	1580	55	3	23	3	PCDH12	5	141324966	Missense_Mutation	SNP	T	TCGA-FA-A4BB-01A-11D-A31X-10		141324966	39590294	23	198											
EBF1	1879	hgsc.bcm.edu	37	chr5	158267047	158267047	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagacccacctggaatctcCgcatgtcacgtgggtttccc	7	10	9	15	2	3	1	2	0	1	1	5	2	4	2	4	2	0	2	4	2	1	1			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr5:158267047C>A	ENST00000313708.6	-	7	908	c.626G>T	c.(625-627)cGg>cTg	p.R209L	EBF1_ENST00000517373.1_Missense_Mutation_p.R209L|EBF1_ENST00000518836.1_5'UTR|EBF1_ENST00000380654.4_Missense_Mutation_p.R186L	NM_024007.3	NP_076870.1	Q9UH73	COE1_HUMAN	early B-cell factor 1	209					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)			CTGGAATCTCCGCATGTCACG	0.388			T	HMGA2	lipoma																																p.R209L		Atlas-SNP	.		Dom	yes		5	5q34	1879	early B-cell factor 1		M	EBF1,colon,carcinoma,-1,1	EBF1	110	1	0			c.G626T						PASS	.						115	122	119					5																	158267047		2203	4300	6503	SO:0001583	missense	1879	exon7			AATCTCCGCATGT	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.626G>T	5.37:g.158267047C>A	ENSP00000322898:p.Arg209Leu	123	0	0		127	21	0.165354	NM_024007	Q8IW11	Missense_Mutation	SNP	ENST00000313708.6	37	CCDS4343.1	.	.	.	.	.	.	.	.	.	.	C	30	5.056361	0.93793	.	.	ENSG00000164330	ENST00000318060;ENST00000313708;ENST00000380654;ENST00000517373	T;T;T	0.60171	0.21;0.46;0.36	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.77398	0.4124	M	0.75884	2.315	0.58432	D	0.999999	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.91635	0.994;0.972;0.998;0.999	T	0.79897	-0.1609	10	0.87932	D	0	-5.0542	19.1382	0.93436	0.0:1.0:0.0:0.0	.	209;195;209;186	A8K0Z7;B4E2U8;Q9UH73;Q9UH73-2	.;.;COE1_HUMAN;.	L	209;209;186;209	ENSP00000322898:R209L;ENSP00000370029:R186L;ENSP00000428020:R209L	ENSP00000322898:R209L	R	-	2	0	EBF1	158199625	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.277000	0.78572	2.505000	0.84491	0.655000	0.94253	CGG	.	.	none		0.388	EBF1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000252649.1	NM_024007		A	158267047	C	A	158267047	3	1	2	1	0	0	0	0	1	0	0	0	4882	652	23	4	1189	4	EBF1	5	158267047	Missense_Mutation	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10	16942081	158267047	22648213	24	199											
HIST1H2BK	85236	hgsc.bcm.edu	37	chr6	27114250	27114250	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggtgccctcggacacggcgtGcttggccaactccccgggca	5	6	14	16	4	0	0	0	0	0	0	2	1	1	1	4	5	3	2	4	5	1	1			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr6:27114250G>A	ENST00000356950.1	-	1	327	c.328C>T	c.(328-330)Cac>Tac	p.H110Y	HIST1H2BK_ENST00000396891.4_Missense_Mutation_p.H110Y|HIST1H2AH_ENST00000377459.1_5'Flank|MIR3143_ENST00000584253.1_RNA			O60814	H2B1K_HUMAN	histone cluster 1, H2bk	110					antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)	extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	13						GACACGGCGTGCTTGGCCAAC	0.597																																					p.H110Y		Atlas-SNP	.											.	HIST1H2BK	68	.	0			c.C328T						PASS	.						59	65	63					6																	27114250		2203	4292	6495	SO:0001583	missense	85236	exon1			CGGCGTGCTTGGC	AJ223352	CCDS4621.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000197903	ENSG00000197903		"Histones / Replication-dependent"	13954	protein-coding gene	gene with protein product		615045	"H2B histone family, member T", "histone 1, H2bk"	H2BFT		12408966	Standard	NM_080593		Approved	H2BFAiii	uc003nix.2	O60814	OTTHUMG00000014473	ENST00000356950.1:c.328C>T	6.37:g.27114250G>A	ENSP00000349430:p.His110Tyr	110	0	0		81	9	0.111111	NM_080593	A8K7P7|Q2VPI7	Missense_Mutation	SNP	ENST00000356950.1	37	CCDS4621.1	.	.	.	.	.	.	.	.	.	.	.	19.40	3.820178	0.71028	.	.	ENSG00000197903	ENST00000396891;ENST00000356950	T;T	0.51574	0.7;0.7	4.05	4.05	0.47172	Histone-fold (2);	0.000000	0.40469	U	0.001098	T	0.67850	0.2937	M	0.92738	3.34	0.40826	D	0.983549	D	0.71674	0.998	D	0.63957	0.92	T	0.77773	-0.2462	10	0.87932	D	0	.	14.5252	0.67884	0.0:0.0:1.0:0.0	.	110	O60814	H2B1K_HUMAN	Y	110	ENSP00000380100:H110Y;ENSP00000349430:H110Y	ENSP00000349430:H110Y	H	-	1	0	HIST1H2BK	27222229	1.000000	0.71417	1.000000	0.80357	0.530000	0.34684	5.915000	0.69973	2.196000	0.70406	0.650000	0.86243	CAC	.	.	none		0.597	HIST1H2BK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040141.1	NM_080593		A	27114250	G	A	27114250	3	1	2	1	0	0	0	0	1	0	0	0	7159	1319	46	2	56	2	HIST1H2BK	6	27114250	Missense_Mutation	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10		27114250	144000817	25	200											
HLA-C	3107	hgsc.bcm.edu	37	chr6	31238202	31238202	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggtagaagcccagggcccagCacctcagggtggcctcatgg	8	5	15	13	0	2	1	2	0	0	1	2	1	2	1	4	5	2	2	4	5	2	1			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr6:31238202C>T	ENST00000376228.5	-	4	694	c.680G>A	c.(679-681)tGc>tAc	p.C227Y	HLA-C_ENST00000383329.3_Missense_Mutation_p.C227Y	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	227	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)|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)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						CAGGGCCCAGCACCTCAGGGT	0.607																																					p.C227Y		Atlas-SNP	.											.	HLA-C	92	.	0			c.G680A						PASS	.						46	49	48					6																	31238202		2203	4295	6498	SO:0001583	missense	3107	exon4			GCCCAGCACCTCA	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4933	protein-coding gene	gene with protein product		142840	"psoriasis susceptibility 1"	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.680G>A	6.37:g.31238202C>T	ENSP00000365402:p.Cys227Tyr	76	0	0		58	5	0.0862069	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.	.	.	.	.	.	.	.	.	.	.	10.47	1.359977	0.24598	.	.	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	D;D	0.93488	-3.23;-3.23	2.65	2.65	0.31530	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.000000	0.45867	U	0.000326	D	0.97414	0.9154	H	0.99312	4.51	0.29781	N	0.833962	D;D;D;D	0.89917	0.999;0.999;0.999;1.0	D;D;D;D	0.97110	0.999;0.999;0.999;1.0	D	0.92277	0.5830	10	0.87932	D	0	.	8.9782	0.35948	0.0:1.0:0.0:0.0	.	227;227;227;227	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	Y	227;227;227;264	ENSP00000365402:C227Y;ENSP00000372819:C227Y	ENSP00000365402:C227Y	C	-	2	0	HLA-C	31346181	1.000000	0.71417	1.000000	0.80357	0.696000	0.40369	2.210000	0.42816	1.812000	0.52913	0.281000	0.19383	TGC	.	.	none		0.607	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117		T	31238202	C	T	31238202	3	4	2	1	0	0	0	0	1	0	0	0	7206	710	25	2	440	2	HLA-C	6	31238202	Missense_Mutation	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10	4123952	31238202	139876865	26	201											
TNXB	7148	hgsc.bcm.edu	37	chr6	32017196	32017196	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacctggggctgcccgtccCtgtccttgtactgcacggtg	3	10	12	16	2	0	0	0	0	0	0	2	0	2	0	5	3	3	3	5	3	1	2			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr6:32017196C>T	ENST00000375244.3	-	28	9809	c.9608G>A	c.(9607-9609)aGg>aAg	p.R3203K	TNXB_ENST00000375247.2_Missense_Mutation_p.R3201K			P22105	TENX_HUMAN	tenascin XB	3248					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						CTGCCCGTCCCTGTCCTTGTA	0.662																																					p.R3201K		Atlas-SNP	.											.	TNXB	553	.	0			c.G9602A						PASS	.						68	73	71					6																	32017196		1278	2543	3821	SO:0001583	missense	7148	exon28			CCGTCCCTGTCCT	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.9608G>A	6.37:g.32017196C>T	ENSP00000364393:p.Arg3203Lys	109	0	0		85	4	0.0470588	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		.	.	.	.	.	.	.	.	.	.	C	2.339	-0.351566	0.05173	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.54866	0.55;0.55	4.39	2.57	0.30868	.	0.368597	0.23524	N	0.047242	T	0.12518	0.0304	L	0.41573	1.285	0.09310	N	0.999998	B	0.02656	0.0	B	0.01281	0.0	T	0.32402	-0.9908	10	0.02654	T	1	.	4.1787	0.10365	0.1809:0.6141:0.0:0.205	.	3201	P22105-3	.	K	3203;3201	ENSP00000364393:R3203K;ENSP00000364396:R3201K	ENSP00000364393:R3203K	R	-	2	0	TNXB	32125174	0.000000	0.05858	0.656000	0.29637	0.211000	0.24417	0.021000	0.13489	0.848000	0.35191	0.306000	0.20318	AGG	.	.	none		0.662	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		T	32017196	C	T	32017196	3	4	2	1	0	0	0	0	1	0	0	0	16361	681	24	2	5179	2	TNXB	6	32017196	Missense_Mutation	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10	778994	32017196	139097871	27	202											
DEFB114	245928	hgsc.bcm.edu	37	chr6	49928117	49928117	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtctcttttacaacgaccgTaacgtttggtgcaacgatca	11	12	8	10	4	2	0	1	0	1	0	3	2	2	0	1	1	5	3	1	1	4	4			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr6:49928117T>A	ENST00000322066.3	-	2	97	c.98A>T	c.(97-99)tAc>tTc	p.Y33F		NM_001037499.1	NP_001032588.1	Q30KQ6	DB114_HUMAN	defensin, beta 114	33					defense response to bacterium (GO:0042742)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)	extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)			kidney(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	8	Lung NSC(77;0.042)					ACAACGACCGTAACGTTTGGT	0.353																																					p.Y33F		Atlas-SNP	.											.	DEFB114	12	.	0			c.A98T						PASS	.						108	98	101					6																	49928117		2203	4299	6502	SO:0001583	missense	245928	exon2			CGACCGTAACGTT	DQ012018	CCDS34474.1	6p12.3	2010-03-30			ENSG00000177684	ENSG00000177684		"Defensins, beta"	18095	protein-coding gene	gene with protein product		615243				11854508, 16033865	Standard	NM_001037499		Approved	DEFB-14	uc011dwp.2	Q30KQ6	OTTHUMG00000160209	ENST00000322066.3:c.98A>T	6.37:g.49928117T>A	ENSP00000312702:p.Tyr33Phe	107	0	0		97	18	0.185567	NM_001037499	Q8NES9	Missense_Mutation	SNP	ENST00000322066.3	37	CCDS34474.1	.	.	.	.	.	.	.	.	.	.	T	10.48	1.363120	0.24684	.	.	ENSG00000177684	ENST00000322066	T	0.11495	2.77	3.55	1.08	0.20341	.	2.144620	0.02476	N	0.088045	T	0.01627	0.0052	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.40776	-0.9545	8	.	.	.	-2.5461	2.8936	0.05684	0.2578:0.131:0.0:0.6112	.	33	Q30KQ6	DB114_HUMAN	F	33	ENSP00000312702:Y33F	.	Y	-	2	0	DEFB114	50036076	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	0.082000	0.14847	0.227000	0.20999	0.528000	0.53228	TAC	.	.	none		0.353	DEFB114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359665.1	NM_001037499		A	49928117	T	A	49928117	3	1	2	1	0	0	0	0	1	0	0	0	4405	1638	57	5	114	5	DEFB114	6	49928117	Missense_Mutation	SNP	T	TCGA-FA-A4BB-01A-11D-A31X-10	17910921	49928117	121186950	28	203											
C6orf97	80129	hgsc.bcm.edu	37	chr6	151914338	151914338	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggctggacgtggttttagctCgaacagagcagctggttcgt	7	11	15	8	3	0	1	0	0	0	1	2	3	0	2	0	4	4	6	0	4	2	3	rs201819308		TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr6:151914338C>T	ENST00000239374.7	+	8	1489	c.1390C>T	c.(1390-1392)Cga>Tga	p.R464*	CCDC170_ENST00000367290.5_Nonsense_Mutation_p.R464*	NM_025059.3	NP_079335.2	Q8IYT3	CC170_HUMAN	coiled-coil domain containing 170	464																	GGTTTTAGCTCGAACAGAGCA	0.443													C|||	1	0.000199681	0.0	0.0	5008	,	,		18393	0.0		0.001	False		,,,				2504	0.0				p.R464X		Atlas-SNP	.											.	.	.	.	0			c.C1390T						PASS	.	C	stop/ARG	0,3844		0,0,1922	96	90	92		1390	5.7	1	6		92	3,8273		0,3,4135	yes	stop-gained	C6orf97	NM_025059.3		0,3,6057	TT,TC,CC		0.0362,0.0,0.0248		464/716	151914338	3,12117	1922	4138	6060	SO:0001587	stop_gained	80129	exon8			TTAGCTCGAACAG	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.1390C>T	6.37:g.151914338C>T	ENSP00000239374:p.Arg464*	87	0	0		62	8	0.129032	NM_025059	Q5VXB7|Q6P9E4|Q96KA9|Q9H5M3	Nonsense_Mutation	SNP	ENST00000239374.7	37	CCDS43515.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	40	8.013174	0.98610	0.0	3.62E-4	ENSG00000120262	ENST00000239374;ENST00000367290	.	.	.	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.6122	20.2602	0.98440	0.0:1.0:0.0:0.0	.	.	.	.	X	464	.	ENSP00000239374:R464X	R	+	1	2	C6orf97	151956031	1.000000	0.71417	1.000000	0.80357	0.512000	0.34134	3.649000	0.54417	2.861000	0.98227	0.655000	0.94253	CGA	C|1.000;T|0.000	0.000	strong		0.443	CCDC170-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042727.2	NM_025059		T	151914338	C	T	151914338	4	4	2	1	0	0	0	0	0	1	0	0	2376	876	31	1	1420	1	C6orf97	6	151914338	Nonsense_Mutation	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10	101986221	151914338	19200729	29	204											
THSD7A	221981	hgsc.bcm.edu	37	chr7	11676123	11676123	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgggggcgccaccacatgaCgcgtccggtgctggagcccg	5	4	17	15	6	0	1	0	1	0	0	1	2	1	2	4	4	2	1	4	4	0	0			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr7:11676123C>T	ENST00000423059.4	-	2	907	c.656G>A	c.(655-657)cGt>cAt	p.R219H	THSD7A_ENST00000480061.1_5'Flank	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	219	TSP type-1 2. {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)		CACCACATGACGCGTCCGGTG	0.617										HNSCC(18;0.044)																											p.R219H		Atlas-SNP	.											.	THSD7A	219	.	0			c.G656A						PASS	.						28	29	29					7																	11676123		2016	4187	6203	SO:0001583	missense	221981	exon2			ACATGACGCGTCC		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.656G>A	7.37:g.11676123C>T	ENSP00000406482:p.Arg219His	40	0	0		53	7	0.132075	NM_015204		Missense_Mutation	SNP	ENST00000423059.4	37	CCDS47543.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.337694	0.81911	.	.	ENSG00000005108	ENST00000262042;ENST00000423059	T	0.65364	-0.15	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.89294	0.6674	H	0.99391	4.545	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.93148	0.6547	10	0.62326	D	0.03	.	20.0333	0.97547	0.0:1.0:0.0:0.0	.	219	Q9UPZ6	THS7A_HUMAN	H	219	ENSP00000406482:R219H	ENSP00000262042:R219H	R	-	2	0	THSD7A	11642648	1.000000	0.71417	0.086000	0.20670	0.358000	0.29455	7.776000	0.85560	2.810000	0.96702	0.585000	0.79938	CGT	.	.	none		0.617	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		T	11676123	C	T	11676123	3	4	2	1	0	0	0	0	1	0	0	0	15894	536	19	1	4421	1	THSD7A	7	11676123	Missense_Mutation	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10		11676123	147462540	30	205											
TMEM130	222865	hgsc.bcm.edu	37	chr7	98449156	98449156	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaggtgtgggtcaggttgtaCgctgtgctggccacggacac	7	9	16	9	2	1	0	1	0	0	0	1	1	1	1	1	5	2	4	1	5	2	2			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr7:98449156C>G	ENST00000416379.2	-	6	898	c.894G>C	c.(892-894)gcG>gcC	p.A298A	TMEM130_ENST00000339375.4_Silent_p.A298A|TMEM130_ENST00000450876.1_Silent_p.A214A|TMEM130_ENST00000546258.1_Silent_p.A279A|TMEM130_ENST00000345589.4_Silent_p.A196A			Q8N3G9	TM130_HUMAN	transmembrane protein 130	298						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)			TCAGGTTGTACGCTGTGCTGG	0.602																																					p.A298A		Atlas-SNP	.											TMEM130,NS,carcinoma,0,1	TMEM130	54	1	0			c.G894C						scavenged	.						123	88	100					7																	98449156		2203	4300	6503	SO:0001819	synonymous_variant	222865	exon6			GTTGTACGCTGTG		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.894G>C	7.37:g.98449156C>G		66	2	0.030303		46	5	0.108696	NM_152913	A4D266|B7Z364|Q8IY46|Q8N0W9|Q8N3R2	Silent	SNP	ENST00000416379.2	37	CCDS47650.1																																																																																			.	.	none		0.602	TMEM130-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000380713.1	NM_152913		G	98449156	C	G	98449156	2	3	2	1	0	0	0	0	0	0	0	1	16058	523	19	4		4	TMEM130	7	98449156	Silent	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10	86773033	98449156	60689507	31	206											
TAS2R16	50833	hgsc.bcm.edu	37	chr7	122634960	122634960	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtacctataatggtgatgagTatggttagaaagtaagaggt	14	12	13	2	0	0	4	0	2	0	2	0	4	0	4	1	3	1	4	1	3	7	6			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr7:122634960T>C	ENST00000249284.2	-	1	794	c.729A>G	c.(727-729)atA>atG	p.I243M		NM_016945.2	NP_058641.1	Q9NYV7	T2R16_HUMAN	taste receptor, type 2, member 16	243					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						TGGTGATGAGTATGGTTAGAA	0.418																																					p.I243M		Atlas-SNP	.											.	TAS2R16	57	.	0			c.A729G						PASS	.						135	124	128					7																	122634960		2203	4300	6503	SO:0001583	missense	50833	exon1			GATGAGTATGGTT	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.729A>G	7.37:g.122634960T>C	ENSP00000249284:p.Ile243Met	123	0	0		102	8	0.0784314	NM_016945	A4D0X2|Q502V3|Q549U8|Q645W1	Missense_Mutation	SNP	ENST00000249284.2	37	CCDS5785.1	.	.	.	.	.	.	.	.	.	.	T	14.07	2.426121	0.43020	.	.	ENSG00000128519	ENST00000249284	T	0.38077	1.16	4.67	1.06	0.20224	.	1.003370	0.08035	N	0.994197	T	0.43144	0.1234	L	0.53249	1.67	0.09310	N	1	D	0.57571	0.98	P	0.54270	0.747	T	0.27262	-1.0079	10	0.39692	T	0.17	.	6.0768	0.19919	0.0:0.3142:0.0:0.6858	.	243	Q9NYV7	T2R16_HUMAN	M	243	ENSP00000249284:I243M	ENSP00000249284:I243M	I	-	3	3	TAS2R16	122422196	0.001000	0.12720	0.000000	0.03702	0.013000	0.08279	0.432000	0.21461	0.384000	0.24942	0.533000	0.62120	ATA	.	.	none		0.418	TAS2R16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347409.1	NM_016945		C	122634960	T	C	122634960	3	2	2	1	0	0	0	0	1	0	0	0	15584	1628	57	3	150	3	TAS2R16	7	122634960	Missense_Mutation	SNP	T	TCGA-FA-A4BB-01A-11D-A31X-10	24185804	122634960	36503703	32	207											
AHCYL2	23382	hgsc.bcm.edu	37	chr7	129064932	129064932	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttgatagagctttacaatgCtcctgagggtcgctataagc	10	12	10	9	1	0	3	0	2	0	1	2	3	1	3	1	1	4	3	1	1	5	6			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr7:129064932C>T	ENST00000325006.3	+	15	1712	c.1658C>T	c.(1657-1659)gCt>gTt	p.A553V	AHCYL2_ENST00000446212.1_Missense_Mutation_p.A451V|AHCYL2_ENST00000446544.2_Missense_Mutation_p.A552V|AHCYL2_ENST00000490911.1_Missense_Mutation_p.A450V|AHCYL2_ENST00000474594.1_Missense_Mutation_p.A450V|AHCYL2_ENST00000531335.2_Missense_Mutation_p.A472V	NM_001130720.2|NM_015328.3	NP_001124192.1|NP_056143.1	Q96HN2	SAHH3_HUMAN	adenosylhomocysteinase-like 2	553					one-carbon metabolic process (GO:0006730)		adenosylhomocysteinase activity (GO:0004013)			breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	22						CTTTACAATGCTCCTGAGGGT	0.463																																					p.A553V	Pancreas(160;1736 1964 29875 40941 45605)	Atlas-SNP	.											.	AHCYL2	79	.	0			c.C1658T						PASS	.						171	153	159					7																	129064932		2203	4300	6503	SO:0001583	missense	23382	exon15			ACAATGCTCCTGA	AB020635	CCDS5812.1, CCDS47706.1, CCDS47707.1, CCDS47708.1, CCDS47707.2	7q32.1	2009-06-12	2009-06-12		ENSG00000158467	ENSG00000158467			22204	protein-coding gene	gene with protein product			"S-adenosylhomocysteine hydrolase-like 2"				Standard	NM_001130720		Approved	KIAA0828	uc011kov.2	Q96HN2	OTTHUMG00000157677	ENST00000325006.3:c.1658C>T	7.37:g.129064932C>T	ENSP00000315931:p.Ala553Val	48	0	0		66	14	0.212121	NM_015328	B4DIZ5|D9N155|O94917	Missense_Mutation	SNP	ENST00000325006.3	37	CCDS5812.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.439306|5.439306	0.96168|0.96168	.|.	.|.	ENSG00000158467|ENSG00000158467	ENST00000325006;ENST00000446544;ENST00000531335;ENST00000474594;ENST00000446212;ENST00000490911|ENST00000466924	T;T;T;T;T;T|.	0.77489|.	-1.1;-1.1;-1.1;-1.1;-1.1;-1.1|.	5.46|5.46	5.46|5.46	0.80206|0.80206	.|.	0.046797|.	0.85682|.	D|.	0.000000|.	T|T	0.78572|0.78572	0.4304|0.4304	M|M	0.81802|0.81802	2.56|2.56	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.71674|.	0.987;0.978;0.998;0.978;0.997|.	P;P;D;P;P|.	0.65773|.	0.861;0.806;0.938;0.806;0.897|.	T|T	0.79438|0.79438	-0.1803|-0.1803	10|5	0.48119|.	T|.	0.1|.	-12.0409|-12.0409	17.8694|17.8694	0.88807|0.88807	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	450;451;553;450;552|.	B4DIZ5;D7UEQ7;Q96HN2;D9N155;Q96HN2-2|.	.;.;SAHH3_HUMAN;.;.|.	V|F	553;552;472;450;451;450|460	ENSP00000315931:A553V;ENSP00000413639:A552V;ENSP00000431787:A472V;ENSP00000420459:A450V;ENSP00000405267:A451V;ENSP00000420801:A450V|.	ENSP00000315931:A553V|.	A|L	+|+	2|1	0|0	AHCYL2|AHCYL2	128852168|128852168	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.796000|7.796000	0.85898|0.85898	2.565000|2.565000	0.86533|0.86533	0.650000|0.650000	0.86243|0.86243	GCT|CTC	.	.	none		0.463	AHCYL2-012	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354065.1			T	129064932	C	T	129064932	3	4	2	1	0	0	0	0	1	0	0	0	411	797	28	2	1838	2	AHCYL2	7	129064932	Missense_Mutation	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10	6429972	129064932	30073731	33	208											
KIAA1549	57670	hgsc.bcm.edu	37	chr7	138603173	138603173	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gagtgttgtccacaggaccgGggagggctgaattgctatgc	8	9	16	8	1	0	1	0	1	0	0	1	4	1	3	2	4	2	3	2	4	2	3			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr7:138603173G>A	ENST00000422774.1	-	2	1247	c.1199C>T	c.(1198-1200)cCc>cTc	p.P400L	KIAA1549_ENST00000242365.4_Missense_Mutation_p.P350L|KIAA1549_ENST00000440172.1_Missense_Mutation_p.P400L			Q9HCM3	K1549_HUMAN	KIAA1549	400						integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						CACAGGACCGGGGAGGGCTGA	0.527			O	BRAF	pilocytic astrocytoma																																p.P400L	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549	314	.	0			c.C1199T						PASS	.						98	98	98					7																	138603173		2015	4181	6196	SO:0001583	missense	57670	exon2			GGACCGGGGAGGG		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.1199C>T	7.37:g.138603173G>A	ENSP00000416040:p.Pro400Leu	82	0	0		91	9	0.0989011	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	37	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	G	13.66	2.303705	0.40795	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.25414	1.8;1.81;1.81	4.73	4.73	0.59995	.	0.299915	0.24303	N	0.039706	T	0.24890	0.0604	L	0.29908	0.895	0.30414	N	0.778801	P;P	0.44946	0.761;0.846	B;P	0.44811	0.272;0.461	T	0.09487	-1.0672	10	0.56958	D	0.05	.	15.023	0.71647	0.0:0.0:1.0:0.0	.	400;400	Q9HCM3;Q9HCM3-2	K1549_HUMAN;.	L	400;350;400	ENSP00000406661:P400L;ENSP00000242365:P350L;ENSP00000416040:P400L	ENSP00000242365:P350L	P	-	2	0	KIAA1549	138253713	0.746000	0.28272	0.227000	0.23927	0.010000	0.07245	2.470000	0.45119	2.459000	0.83118	0.650000	0.86243	CCC	.	.	none		0.527	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			A	138603173	G	A	138603173	3	1	2	1	0	0	0	0	1	0	0	0	8253	1232	43	2	4729	2	KIAA1549	7	138603173	Missense_Mutation	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10	9538241	138603173	20535490	34	209											
SLC37A3	84255	hgsc.bcm.edu	37	chr7	140055490	140055490	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cataaccatactgaagaacaGaagaagctaggcacgctccc	16	5	8	12	1	0	4	0	1	0	3	1	4	1	4	2	1	4	3	2	1	7	3			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr7:140055490G>T	ENST00000326232.9	-	7	799	c.596C>A	c.(595-597)tCt>tAt	p.S199Y	SLC37A3_ENST00000447932.2_Missense_Mutation_p.S199Y|SLC37A3_ENST00000429996.2_Missense_Mutation_p.F150L|SLC37A3_ENST00000340308.3_Missense_Mutation_p.S199Y|SLC37A3_ENST00000461089.1_5'Flank	NM_207113.1	NP_996996.1	Q8NCC5	SPX3_HUMAN	solute carrier family 37, member 3	199					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)					CTGAAGAACAGAAGAAGCTAG	0.438																																					p.S199Y	Esophageal Squamous(133;211 1716 4665 11387 37873)	Atlas-SNP	.											.	SLC37A3	80	.	0			c.C596A						PASS	.						177	145	156					7																	140055490		2203	4300	6503	SO:0001583	missense	84255	exon7			AGAACAGAAGAAG	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.596C>A	7.37:g.140055490G>T	ENSP00000321498:p.Ser199Tyr	50	0	0		48	6	0.125	NM_207113	Q6PIU7|Q86SS4|Q9BQG7	Missense_Mutation	SNP	ENST00000326232.9	37	CCDS5859.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	g|g|g	0.599|0.599|0.599	-0.830008|-0.830008|-0.830008	0.02734|0.02734|0.02734	.|.|.	.|.|.	ENSG00000157800|ENSG00000157800|ENSG00000157800	ENST00000429996|ENST00000485861|ENST00000340308;ENST00000447932;ENST00000326232;ENST00000539816	T|.|T;T;T	0.38401|.|0.55760	1.14|.|0.5;0.5;0.5	5.28|5.28|5.28	4.34|4.34|4.34	0.51931|0.51931|0.51931	.|.|Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	.|.|0.157131	.|.|0.56097	.|.|D	.|.|0.000027	T|T|T	0.33147|0.33147|0.33147	0.0853|0.0853|0.0853	N|N|N	0.16708|0.16708|0.16708	0.43|0.43|0.43	0.22468|0.22468|0.22468	N|N|N	0.99907|0.99907|0.99907	.|.|B;B;B;B;B	.|.|0.20550	.|.|0.011;0.005;0.009;0.046;0.012	.|.|B;B;B;B;B	.|.|0.19666	.|.|0.026;0.015;0.015;0.022;0.026	T|T|T	0.08351|0.08351|0.08351	-1.0726|-1.0726|-1.0726	7|5|10	0.27785|.|0.02654	T|.|T	0.31|.|1	-20.8037|-20.8037|-20.8037	15.9284|15.9284|15.9284	0.79639|0.79639|0.79639	0.0:0.2129:0.7871:0.0|0.0:0.2129:0.7871:0.0|0.0:0.2129:0.7871:0.0	.|.|.	.|.|171;199;199;199;199	.|.|B4DKF5;F5H743;Q8NCC5-2;Q8NCC5-3;Q8NCC5	.|.|.;.;.;.;SPX3_HUMAN	L|M|Y	150|124|199	ENSP00000412208:F150L|.|ENSP00000343358:S199Y;ENSP00000397481:S199Y;ENSP00000321498:S199Y	ENSP00000412208:F150L|.|ENSP00000321498:S199Y	F|L|S	-|-|-	3|1|2	2|2|0	SLC37A3|SLC37A3|SLC37A3	139701959|139701959|139701959	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.610000|0.610000|0.610000	0.28997|0.28997|0.28997	0.166000|0.166000|0.166000	0.22503|0.22503|0.22503	4.226000|4.226000|4.226000	0.58606|0.58606|0.58606	2.616000|2.616000|2.616000	0.88540|0.88540|0.88540	0.639000|0.639000|0.639000	0.83563|0.83563|0.83563	TTC|CTG|TCT	.	.	none		0.438	SLC37A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348492.1	NM_032295		T	140055490	G	T	140055490	3	4	2	1	0	0	0	0	1	0	0	0	14614	942	33	4	1073	4	SLC37A3	7	140055490	Missense_Mutation	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10	1452317	140055490	19083173	35	210											
EPHB6	2051	hgsc.bcm.edu	37	chr7	142564346	142564346	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acatcctggactatcagctcCgctactatgaccaggtgcgc	9	9	9	14	2	1	1	1	1	0	0	3	2	3	2	3	2	3	2	3	2	3	3			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr7:142564346C>T	ENST00000392957.2	+	10	2357	c.1570C>T	c.(1570-1572)Cgc>Tgc	p.R524C	EPHB6_ENST00000411471.2_Missense_Mutation_p.R247C|EPHB6_ENST00000442129.1_Missense_Mutation_p.R524C	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	524	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)					CTATCAGCTCCGCTACTATGA	0.627																																					p.R524C		Atlas-SNP	.											EPHB6,NS,carcinoma,0,1	EPHB6	168	1	0			c.C1570T						scavenged	.						78	79	78					7																	142564346		2203	4300	6503	SO:0001583	missense	2051	exon10			CAGCTCCGCTACT	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.1570C>T	7.37:g.142564346C>T	ENSP00000376684:p.Arg524Cys	55	0	0		57	6	0.105263	NM_004445	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Missense_Mutation	SNP	ENST00000392957.2	37	CCDS5873.2	.	.	.	.	.	.	.	.	.	.	C	20.7	4.030264	0.75504	.	.	ENSG00000106123	ENST00000392957;ENST00000442129;ENST00000411471	T;T;T	0.58652	0.32;0.32;0.32	4.95	4.95	0.65309	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.47455	D	0.000230	T	0.68622	0.3021	M	0.65320	2	0.58432	D	0.999999	D	0.61697	0.99	P	0.59643	0.861	T	0.72060	-0.4404	10	0.87932	D	0	.	12.6742	0.56884	0.165:0.835:0.0:0.0	.	524	O15197	EPHB6_HUMAN	C	524;524;247	ENSP00000376684:R524C;ENSP00000410789:R524C;ENSP00000409061:R247C	ENSP00000376684:R524C	R	+	1	0	EPHB6	142274468	0.322000	0.24634	1.000000	0.80357	0.995000	0.86356	0.846000	0.27682	2.451000	0.82905	0.556000	0.70494	CGC	.	.	none		0.627	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			T	142564346	C	T	142564346	3	4	2	1	0	0	0	0	1	0	0	0	5180	652	23	1	1592	1	EPHB6	7	142564346	Missense_Mutation	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10	2508856	142564346	16574317	36	211											
NOM1	64434	hgsc.bcm.edu	37	chr7	156743222	156743222	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaaagtgaggaggaggaggAgggagacgtagaaaaggaaa	18	2	19	2	2	0	3	0	1	0	2	0	10	0	8	0	6	0	1	0	6	5	1			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr7:156743222A>G	ENST00000275820.3	+	1	806	c.791A>G	c.(790-792)gAg>gGg	p.E264G		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	264	Glu-rich.|Necessary for nucleolar localization and for targeting PPP1CA to the nucleolus.					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)		gaggaggaggagggagacgta	0.542																																					p.E264G		Atlas-SNP	.											NOM1,NS,carcinoma,+1,1	NOM1	73	1	0			c.A791G						scavenged	.						64	46	52					7																	156743222		2203	4300	6503	SO:0001583	missense	64434	exon1			AGGAGGAGGGAGA	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.791A>G	7.37:g.156743222A>G	ENSP00000275820:p.Glu264Gly	73	2	0.0273973		72	3	0.0416667	NM_138400	Q96I08	Missense_Mutation	SNP	ENST00000275820.3	37	CCDS34787.1	.	.	.	.	.	.	.	.	.	.	A	11.47	1.648378	0.29336	.	.	ENSG00000146909	ENST00000275820	T	0.13901	2.55	3.07	-6.13	0.02118	.	2.984370	0.01388	N	0.013164	T	0.05686	0.0149	N	0.08118	0	0.09310	N	1	B	0.22003	0.063	B	0.17098	0.017	T	0.25710	-1.0124	10	0.18710	T	0.47	0.0073	4.0147	0.09639	0.36:0.4427:0.0802:0.1172	.	264	Q5C9Z4	NOM1_HUMAN	G	264	ENSP00000275820:E264G	ENSP00000275820:E264G	E	+	2	0	NOM1	156435983	0.146000	0.22672	0.000000	0.03702	0.139000	0.21198	0.678000	0.25277	-1.661000	0.01484	0.456000	0.33151	GAG	.	.	none		0.542	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400		G	156743222	A	G	156743222	3	3	2	1	0	0	0	0	1	0	0	0	10539	304	11	3	793	3	NOM1	7	156743222	Missense_Mutation	SNP	A	TCGA-FA-A4BB-01A-11D-A31X-10	14178876	156743222	2395441	37	212											
PEX2	5828	hgsc.bcm.edu	37	chr8	77896279	77896279	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aaagcgagctaacagcccagGtttaaatccatgaaagcact	16	7	8	10	1	0	1	0	1	0	0	1	2	1	1	2	1	5	3	2	1	5	3			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr8:77896279G>A	ENST00000419564.2	-	4	600	c.136C>T	c.(136-138)Cct>Tct	p.P46S	PEX2_ENST00000520103.1_Missense_Mutation_p.P46S|PEX2_ENST00000357039.4_Missense_Mutation_p.P46S|PEX2_ENST00000522527.1_Missense_Mutation_p.P46S	NM_001172087.1	NP_001165558.1	P28328	PEX2_HUMAN	peroxisomal biogenesis factor 2	46					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						AACAGCCCAGGTTTAAATCCA	0.473																																					p.P46S		Atlas-SNP	.											.	PEX2	44	.	0			c.C136T						PASS	.						91	90	90					8																	77896279		2203	4300	6503	SO:0001583	missense	5828	exon4			GCCCAGGTTTAAA	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.136C>T	8.37:g.77896279G>A	ENSP00000400984:p.Pro46Ser	89	0	0		102	8	0.0784314	NM_000318	Q567S6|Q9BW41	Missense_Mutation	SNP	ENST00000419564.2	37	CCDS6221.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.531768	0.85706	.	.	ENSG00000164751	ENST00000357039;ENST00000419564;ENST00000520103;ENST00000522527;ENST00000518986	D;D;D;D;D	0.82081	-1.57;-1.57;-1.57;-1.57;-1.57	5.74	5.74	0.90152	Pex, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.90133	0.6917	M	0.64404	1.975	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	D	0.88246	0.2913	10	0.38643	T	0.18	-14.1507	19.9336	0.97129	0.0:0.0:1.0:0.0	.	46	P28328	PEX2_HUMAN	S	46	ENSP00000349543:P46S;ENSP00000400984:P46S;ENSP00000428590:P46S;ENSP00000428638:P46S;ENSP00000429304:P46S	ENSP00000349543:P46S	P	-	1	0	PEX2	78058834	1.000000	0.71417	1.000000	0.80357	0.813000	0.45954	9.434000	0.97515	2.717000	0.92951	0.563000	0.77884	CCT	.	.	none		0.473	PEX2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379122.1	NM_000318		A	77896279	G	A	77896279	3	1	2	1	0	0	0	0	1	0	0	0	11754	1261	44	2	785	2	PEX2	8	77896279	Missense_Mutation	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10		77896279	68467743	38	213											
RIMS2	9699	hgsc.bcm.edu	37	chr8	105263836	105263836	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tattttgccaacagatcatcGtctggggagattatggccgc	9	12	11	9	2	2	2	1	0	1	2	3	3	2	2	2	3	2	0	2	3	3	4			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr8:105263836G>A	ENST00000436393.2	+	28	4133	c.3892G>A	c.(3892-3894)Gtc>Atc	p.V1298I	RIMS2_ENST00000339750.2_Missense_Mutation_p.V216I|RIMS2_ENST00000507740.1_Missense_Mutation_p.V1094I|RIMS2_ENST00000262231.10_Missense_Mutation_p.V1119I|RIMS2_ENST00000406091.3_Missense_Mutation_p.V1280I			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	1342	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				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)			ACAGATCATCGTCTGGGGAGA	0.358										HNSCC(12;0.0054)																											p.V1280I		Atlas-SNP	.											RIMS2_ENST00000507740,NS,carcinoma,-2,4	RIMS2	1357	4	0			c.G3838A						PASS	.						118	115	116					8																	105263836		1880	4138	6018	SO:0001583	missense	9699	exon24			ATCATCGTCTGGG	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.3892G>A	8.37:g.105263836G>A	ENSP00000390665:p.Val1298Ile	105	0	0		100	12	0.12	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Missense_Mutation	SNP	ENST00000436393.2	37		.	.	.	.	.	.	.	.	.	.	G	22.0	4.231635	0.79688	.	.	ENSG00000176406	ENST00000329869;ENST00000406091;ENST00000402998;ENST00000262231;ENST00000507740;ENST00000436393;ENST00000523362;ENST00000339750	D;D;D;D;D;D	0.84800	-1.9;-1.9;-1.9;-1.9;-1.9;-1.9	5.64	5.64	0.86602	.	.	.	.	.	D	0.92564	0.7638	M	0.79614	2.46	0.80722	D	1	D;D;D;D	0.71674	0.984;0.995;0.995;0.998	D;D;D;D	0.69824	0.925;0.95;0.95;0.966	D	0.92842	0.6289	9	0.72032	D	0.01	.	19.6939	0.96016	0.0:0.0:1.0:0.0	.	1298;1119;1094;1280	D6RA03;Q9UQ26-1;Q9UQ26-3;F8WD47	.;.;.;.	I	1317;1280;1342;1119;1094;1298;216;216	ENSP00000384892:V1280I;ENSP00000262231:V1119I;ENSP00000423559:V1094I;ENSP00000390665:V1298I;ENSP00000428478:V216I;ENSP00000342051:V216I	ENSP00000262231:V1119I	V	+	1	0	RIMS2	105333012	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	9.857000	0.99534	2.660000	0.90430	0.655000	0.94253	GTC	.	.	none		0.358	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117		A	105263836	G	A	105263836	3	1	2	1	0	0	0	0	1	0	0	0	13383	1145	40	1	4128	1	RIMS2	8	105263836	Missense_Mutation	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10	27367557	105263836	41100186	39	214											
TRPM6	140803	hgsc.bcm.edu	37	chr9	77427256	77427256	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcgagggatggtaagaaagcGatggaggttcactccatatt	12	10	13	6	2	1	1	1	0	0	1	3	5	2	3	1	4	1	2	1	4	3	4			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr9:77427256G>A	ENST00000360774.1	-	12	1639	c.1402C>T	c.(1402-1404)Cgc>Tgc	p.R468C	TRPM6_ENST00000376872.3_Missense_Mutation_p.R468C|TRPM6_ENST00000361255.3_Missense_Mutation_p.R463C|TRPM6_ENST00000376871.3_Missense_Mutation_p.R468C|TRPM6_ENST00000449912.2_Missense_Mutation_p.R463C|TRPM6_ENST00000451710.3_Missense_Mutation_p.R468C|TRPM6_ENST00000376864.4_Missense_Mutation_p.R468C	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	468					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						GTAAGAAAGCGATGGAGGTTC	0.433																																					p.R468C		Atlas-SNP	.											TRPM6,NS,carcinoma,0,1	TRPM6	377	1	0			c.C1402T						scavenged	.						127	114	119					9																	77427256		2203	4300	6503	SO:0001583	missense	140803	exon12			GAAAGCGATGGAG	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.1402C>T	9.37:g.77427256G>A	ENSP00000354006:p.Arg468Cys	74	0	0		61	5	0.0819672	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	37	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	G	18.24	3.579285	0.65878	.	.	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000376872;ENST00000376871;ENST00000449912;ENST00000361255;ENST00000376864;ENST00000312449;ENST00000448641	T;T;T;T;T;T;T	0.36520	1.25;1.25;1.25;1.25;1.25;1.25;1.25	5.7	3.82	0.43975	.	0.258733	0.45867	N	0.000333	T	0.60843	0.2300	M	0.80616	2.505	0.46981	D	0.999271	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.79784	0.917;0.917;0.993;0.988	T	0.62558	-0.6829	10	0.59425	D	0.04	.	13.5144	0.61533	0.0634:0.0:0.823:0.1135	.	468;468;468;463	Q9BX84-6;Q9BX84-5;Q9BX84;Q9BX84-3	.;.;TRPM6_HUMAN;.	C	468;468;468;468;463;463;468;131;131	ENSP00000354006:R468C;ENSP00000407341:R468C;ENSP00000366068:R468C;ENSP00000366067:R468C;ENSP00000396672:R463C;ENSP00000354962:R463C;ENSP00000366060:R468C	ENSP00000309693:R131C	R	-	1	0	TRPM6	76617076	1.000000	0.71417	0.995000	0.50966	0.973000	0.67179	3.439000	0.52878	0.332000	0.23536	-0.813000	0.03139	CGC	.	.	none		0.433	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		A	77427256	G	A	77427256	3	1	2	1	0	0	0	0	1	0	0	0	16605	1058	37	1	4778	1	TRPM6	9	77427256	Missense_Mutation	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10		77427256	63786175	40	215											
MUC2	4583	hgsc.bcm.edu	37	chr11	1092971	1092971	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tacggtgaccccaaccccaaCacccaccggcacacagaccc	12	2	6	21	2	0	2	0	1	0	1	0	2	0	2	7	2	3	1	7	2	3	1			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr11:1092971C>T	ENST00000441003.2	+	30	4817	c.4790C>T	c.(4789-4791)aCa>aTa	p.T1597I	MUC2_ENST00000359061.5_Intron|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)	ccaaccccaacacccaccggc	0.632																																					p.T1597I		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,1	MUC2	614	1	0			c.C4790T						scavenged	.						47	82	70					11																	1092971		1782	3233	5015	SO:0001583	missense	4583	exon30			CCCCAACACCCAC	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.4790C>T	11.37:g.1092971C>T	ENSP00000415183:p.Thr1597Ile	34	2	0.0588235		43	6	0.139535	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	2.395	-0.338980	0.05243	.	.	ENSG00000198788	ENST00000441003	T	0.14640	2.49	1.75	0.762	0.18454	.	.	.	.	.	T	0.07143	0.0181	.	.	.	0.09310	N	1	B	0.13145	0.007	B	0.04013	0.001	T	0.41520	-0.9504	8	0.22109	T	0.4	.	4.3366	0.11089	0.0:0.6142:0.0:0.3858	.	1597	E7EUV1	.	I	1597	ENSP00000415183:T1597I	ENSP00000415183:T1597I	T	+	2	0	MUC2	1082971	0.029000	0.19370	0.001000	0.08648	0.134000	0.20937	1.107000	0.31110	0.104000	0.17725	0.121000	0.15741	ACA	.	.	none		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1092971	C	T	1092971	3	4	2	1	0	0	0	0	1	0	0	0	9984	478	17	2	4908	2	MUC2	11	1092971	Missense_Mutation	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10		1092971	133913545	41	216											
MPEG1	219972	hgsc.bcm.edu	37	chr11	58978341	58978341	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgataacaacagccagaatGgtggtgacccccactgtgac	12	7	11	11	0	0	4	0	3	0	1	0	4	0	4	3	2	3	0	3	2	3	1			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr11:58978341G>A	ENST00000361050.3	-	1	2083	c.1998C>T	c.(1996-1998)acC>acT	p.T666T		NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	666						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)				CAGCCAGAATGGTGGTGACCC	0.552																																					p.T666T		Atlas-SNP	.											.	MPEG1	72	.	0			c.C1998T						PASS	.						119	125	123					11																	58978341		2046	4179	6225	SO:0001819	synonymous_variant	219972	exon1			CAGAATGGTGGTG	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.1998C>T	11.37:g.58978341G>A		70	0	0		138	11	0.0797101	NM_001039396	Q2M1T6|Q8TEF8	Silent	SNP	ENST00000361050.3	37	CCDS41650.1																																																																																			.	.	none		0.552	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396		A	58978341	G	A	58978341	2	1	2	1	0	0	0	0	0	0	0	1	9732	1335	47	2		2	MPEG1	11	58978341	Silent	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10	57885370	58978341	76028175	42	217			1	3		3	3	400	G		5.703778e-07
MPEG1	219972	hgsc.bcm.edu	37	chr11	58978525	58978525	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctatgacagtattggtggcaGcctgactcatgaggggtggc	8	10	15	8	0	1	3	1	3	0	0	1	3	1	3	1	5	1	2	1	5	2	3			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr11:58978525G>A	ENST00000361050.3	-	1	1899	c.1814C>T	c.(1813-1815)gCt>gTt	p.A605V		NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	605						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)				ATTGGTGGCAGCCTGACTCAT	0.572																																					p.A605V		Atlas-SNP	.											.	MPEG1	72	.	0			c.C1814T						PASS	.						103	110	108					11																	58978525		1949	4129	6078	SO:0001583	missense	219972	exon1			GTGGCAGCCTGAC	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.1814C>T	11.37:g.58978525G>A	ENSP00000354335:p.Ala605Val	67	0	0		108	43	0.398148	NM_001039396	Q2M1T6|Q8TEF8	Missense_Mutation	SNP	ENST00000361050.3	37	CCDS41650.1	.	.	.	.	.	.	.	.	.	.	G	0.041	-1.285390	0.01387	.	.	ENSG00000197629	ENST00000361050	T	0.23147	1.92	5.69	2.76	0.32466	.	0.496999	0.22900	N	0.054275	T	0.12860	0.0312	N	0.21142	0.635	0.23559	N	0.997413	B	0.10296	0.003	B	0.08055	0.003	T	0.32402	-0.9908	10	0.13108	T	0.6	-5.3059	4.8432	0.13501	0.2569:0.1569:0.5862:0.0	.	605	Q2M385	MPEG1_HUMAN	V	605	ENSP00000354335:A605V	ENSP00000354335:A605V	A	-	2	0	MPEG1	58735101	0.011000	0.17503	1.000000	0.80357	0.389000	0.30415	0.242000	0.18087	0.316000	0.23135	0.655000	0.94253	GCT	.	.	none		0.572	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396		A	58978525	G	A	58978525	3	1	2	1	0	0	0	0	1	0	0	0	9732	971	34	2	340	2	MPEG1	11	58978525	Missense_Mutation	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10	184	58978525	76027991	43	218			1	3		3	3	400	G		5.703778e-07
MPEG1	219972	hgsc.bcm.edu	37	chr11	58978740	58978740	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agggggttcccaactgtgcaGctaaagaacccgccaaaggg	12	5	13	11	1	0	1	0	0	0	1	1	1	1	1	3	3	4	3	3	3	5	2			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr11:58978740G>A	ENST00000361050.3	-	1	1684	c.1599C>T	c.(1597-1599)agC>agT	p.S533S		NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	533						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)				CAACTGTGCAGCTAAAGAACC	0.537																																					p.S533S		Atlas-SNP	.											MPEG1,NS,lymphoid_neoplasm,0,2	MPEG1	72	2	0			c.C1599T						PASS	.						40	43	42					11																	58978740		1837	4086	5923	SO:0001819	synonymous_variant	219972	exon1			TGTGCAGCTAAAG	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.1599C>T	11.37:g.58978740G>A		67	0	0		99	6	0.0606061	NM_001039396	Q2M1T6|Q8TEF8	Silent	SNP	ENST00000361050.3	37	CCDS41650.1																																																																																			.	.	none		0.537	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396		A	58978740	G	A	58978740	2	1	2	1	0	0	0	0	0	0	0	1	9732	962	34	2		2	MPEG1	11	58978740	Silent	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10	215	58978740	76027776	44	219			1	3		3	3	400	G		5.703778e-07
ARAP1	116985	hgsc.bcm.edu	37	chr11	72408662	72408662	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cctccttcgctccaccagcaCcagcacctggttctcactgt	6	10	6	19	1	1	0	1	0	1	0	5	0	3	0	6	1	2	4	6	1	0	2			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr11:72408662C>T	ENST00000393609.3	-	20	2972	c.2770G>A	c.(2770-2772)Gtg>Atg	p.V924M	ARAP1_ENST00000393605.3_Missense_Mutation_p.V684M|ARAP1_ENST00000495878.1_5'UTR|ARAP1_ENST00000359373.5_Missense_Mutation_p.V924M|ARAP1_ENST00000426523.1_Missense_Mutation_p.V679M|ARAP1_ENST00000455638.2_Missense_Mutation_p.V924M|ARAP1-AS2_ENST00000500163.2_RNA|ARAP1_ENST00000334211.8_Missense_Mutation_p.V679M|ARAP1_ENST00000429686.1_Missense_Mutation_p.V618M	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	924					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						TCCACCAGCACCAGCACCTGG	0.637																																					p.V924M	Ovarian(102;1198 1520 13195 17913 37529)	Atlas-SNP	.											.	ARAP1	168	.	0			c.G2770A						PASS	.						108	94	99					11																	72408662		2200	4293	6493	SO:0001583	missense	116985	exon20			CCAGCACCAGCAC	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.2770G>A	11.37:g.72408662C>T	ENSP00000377233:p.Val924Met	75	0	0		87	7	0.0804598	NM_001040118	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Missense_Mutation	SNP	ENST00000393609.3	37	CCDS41687.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.694061	0.88735	.	.	ENSG00000186635	ENST00000359373;ENST00000455638;ENST00000393605;ENST00000334211;ENST00000393609;ENST00000426523;ENST00000429686;ENST00000427971;ENST00000452383	T;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;1.53	4.93	4.93	0.64822	Pleckstrin homology domain (1);	0.133016	0.49916	D	0.000132	T	0.48926	0.1527	L	0.54323	1.7	0.41335	D	0.987265	P;D;P;P;P	0.69078	0.843;0.997;0.881;0.843;0.903	P;P;P;P;P	0.61533	0.779;0.845;0.746;0.677;0.89	T	0.52019	-0.8631	10	0.87932	D	0	.	17.0897	0.86618	0.0:1.0:0.0:0.0	.	679;618;924;924;684	E7EU13;B2RTS2;Q96P48-3;Q96P48;Q96P48-1	.;.;.;ARAP1_HUMAN;.	M	924;924;684;679;924;679;618;212;212	ENSP00000352332:V924M;ENSP00000390461:V924M;ENSP00000377230:V684M;ENSP00000335506:V679M;ENSP00000377233:V924M;ENSP00000392264:V679M;ENSP00000403127:V618M;ENSP00000411452:V212M;ENSP00000399118:V212M	ENSP00000335506:V679M	V	-	1	0	ARAP1	72086310	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.823000	0.48081	2.435000	0.82474	0.563000	0.77884	GTG	.	.	none		0.637	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118		T	72408662	C	T	72408662	3	4	2	1	0	0	0	0	1	0	0	0	838	507	18	2	1646	2	ARAP1	11	72408662	Missense_Mutation	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10	13429922	72408662	62597854	45	220											
TMPRSS13	84000	hgsc.bcm.edu	37	chr11	117789317	117789317	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagccggagatgcccgggcTggagatgcctgggctggaga	8	5	19	9	2	0	4	0	0	0	4	0	7	0	4	3	5	3	2	3	5	0	0	rs201746372|rs58754377|rs201369736		TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr11:117789317T>C	ENST00000430170.2	-	2	345	c.258A>G	c.(256-258)ccA>ccG	p.P86P	TMPRSS13_ENST00000526090.1_Silent_p.P86P|TMPRSS13_ENST00000445164.2_Silent_p.P86P|TMPRSS13_ENST00000528626.1_Silent_p.P86P|TMPRSS13_ENST00000524993.1_Silent_p.P86P	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	86	13 X 5 AA repeats of A-S-P-A-[GLQR].|Ala-rich.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.Q83_A87delQASPA(1)		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)		ATGCCCGGGCTGGAGATGCCT	0.652																																					p.P86P		Atlas-SNP	.											TMPRSS13,caecum,carcinoma,0,1	TMPRSS13	75	1	1	Deletion - In frame(1)	urinary_tract(1)	c.A258G						scavenged	.						34	41	38					11																	117789317		1955	4135	6090	SO:0001819	synonymous_variant	84000	exon2			CCGGGCTGGAGAT	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.258A>G	11.37:g.117789317T>C		57	1	0.0175439		56	4	0.0714286	NM_001206790	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Silent	SNP	ENST00000430170.2	37	CCDS58185.1																																																																																			.	.	weak		0.652	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046		C	117789317	T	C	117789317	2	2	2	1	0	0	0	0	0	0	0	1	16260	1567	55	3		3	TMPRSS13	11	117789317	Silent	SNP	T	TCGA-FA-A4BB-01A-11D-A31X-10	45380655	117789317	17217199	46	221											
CXCR5	643	hgsc.bcm.edu	37	chr11	118765330	118765331	+	Frame_Shift_Del	DEL	TC	TC	-																															cctagctggcgcaggagcagTctctctgagtcagagaatgc																										TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr11:118765330_118765331delTC	ENST00000292174.4	+	2	1253_1254	c.1077_1078delTC	c.(1075-1080)agtctcfs	p.L360fs	BCL9L_ENST00000334801.3_3'UTR	NM_001716.4|NM_032966.2	NP_001707.1|NP_116743.1	P32302	CXCR5_HUMAN	chemokine (C-X-C motif) receptor 5	360					B cell activation (GO:0042113)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of cytokinesis (GO:0032467)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|G-protein coupled receptor activity (GO:0004930)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(5)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	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)		GCAGGAGCAGTCTCTCTGAGTC	0.599																																					p.359_359del		Atlas-Indel	.											.	CXCR5	34	.	0			c.1076_1077del						PASS	.																																			SO:0001589	frameshift_variant	643	exon2			.	X68829	CCDS8402.1	11q23.3	2012-08-08	2008-01-22	2008-01-22	ENSG00000160683	ENSG00000160683		"CD molecules", "GPCR / Class A : Chemokine receptors : C-X-C motif"	1060	protein-coding gene	gene with protein product		601613	"Burkitt lymphoma receptor 1, GTP-binding protein", "Burkitt lymphoma receptor 1, GTP binding protein (chemokine (C-X-C motif) receptor 5)"	BLR1		1425907	Standard	NM_001716		Approved	MDR15, CD185	uc001pue.4	P32302	OTTHUMG00000166345	ENST00000292174.4:c.1077_1078delTC	11.37:g.118765334_118765335delTC	ENSP00000292174:p.Leu360fs	31	0	0		34	11	0.323529	NM_001716	Q14811	Frame_Shift_Del	DEL	ENST00000292174.4	37	CCDS8402.1																																																																																			.	.	none		0.599	CXCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389309.1	NM_001716		-	118765331	TC	-	118765330	7	5	2	1	0	1	0	1	0	0	0	0	4096	1664	58	0	1083	0	CXCR5	11	118765330	Frame_Shift_Del	DEL	TC	TCGA-FA-A4BB-01A-11D-A31X-10	976013	118765330	16241186	47	222											
ATN1	1822	hgsc.bcm.edu	37	chr12	7045924	7045924	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagcagcagcagcagcagcaGcagcagcagcagcatcacgg	13	1	13	14	1	1	0	1	0	0	0	1	0	1	0	0	1	11	11	0	1	0	0	rs199988271		TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr12:7045924G>T	ENST00000356654.4	+	5	1731	c.1494G>T	c.(1492-1494)caG>caT	p.Q498H	ATN1_ENST00000396684.2_Missense_Mutation_p.Q498H	NM_001007026.1	NP_001007027.1	P54259	ATN1_HUMAN	atrophin 1	498	Poly-Gln.				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						agcagcagcagcagcagcagc	0.637																																					p.Q498H		Atlas-SNP	.											ATN1,colon,carcinoma,0,1	ATN1	95	1	0			c.G1494T						scavenged	.						43	53	49					12																	7045924		2201	4297	6498	SO:0001583	missense	1822	exon5			GCAGCAGCAGCAG	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.1494G>T	12.37:g.7045924G>T	ENSP00000349076:p.Gln498His	41	2	0.0487805		36	3	0.0833333	NM_001007026	Q99495|Q99621|Q9UEK7	Missense_Mutation	SNP	ENST00000356654.4	37	CCDS31734.1	.	.	.	.	.	.	.	.	.	.	g	0.004	-2.273578	0.00257	.	.	ENSG00000111676	ENST00000356654;ENST00000396684;ENST00000544325;ENST00000229279	T;T;T	0.56776	0.44;0.44;0.44	1.44	-2.88	0.05682	.	.	.	.	.	T	0.24392	0.0591	N	0.22421	0.69	0.09310	N	1	P	0.40970	0.734	B	0.30401	0.115	T	0.19353	-1.0308	9	0.17832	T	0.49	.	3.3676	0.07208	0.2981:0.2446:0.4573:0.0	.	498	P54259	ATN1_HUMAN	H	498;498;498;83	ENSP00000349076:Q498H;ENSP00000379915:Q498H;ENSP00000441744:Q498H	ENSP00000229279:Q83H	Q	+	3	2	ATN1	6916185	0.175000	0.23083	0.269000	0.24586	0.334000	0.28698	-0.489000	0.06490	-0.760000	0.04677	0.109000	0.15622	CAG	G|0.999;A|0.001	.	alt		0.637	ATN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401948.2	NM_001940		T	7045924	G	T	7045924	3	4	2	1	0	0	0	0	1	0	0	0	1111	962	34	4	1508	4	ATN1	12	7045924	Missense_Mutation	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10		7045924	126805971	48	223											
PIK3C2G	5288	hgsc.bcm.edu	37	chr12	18691191	18691191	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttgtggaactttgctgtcGtgcttataatattatcagaa	10	18	8	5	1	1	1	1	0	0	1	2	2	1	2	0	1	3	2	0	1	6	7			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr12:18691191G>A	ENST00000266497.5	+	23	3340	c.3302G>A	c.(3301-3303)cGt>cAt	p.R1101H	PIK3C2G_ENST00000433979.1_Missense_Mutation_p.R1101H|PIK3C2G_ENST00000538779.1_Missense_Mutation_p.R1142H			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	1101	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				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)	p.R1101H(2)		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)				CTTTGCTGTCGTGCTTATAAT	0.373																																					p.R1101H		Atlas-SNP	.											PIK3C2G_ENST00000433979,colon,carcinoma,0,2	PIK3C2G	315	2	2	Substitution - Missense(2)	large_intestine(2)	c.G3302A						scavenged	.						79	76	77					12																	18691191		1807	4067	5874	SO:0001583	missense	5288	exon24			GCTGTCGTGCTTA	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.3302G>A	12.37:g.18691191G>A	ENSP00000266497:p.Arg1101His	109	1	0.00917431		110	15	0.136364	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	37	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	G	12.00	1.806365	0.31961	.	.	ENSG00000139144	ENST00000433979;ENST00000266497;ENST00000538779	T;T;T	0.75821	-0.97;-0.97;-0.97	4.21	1.45	0.22620	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.650248	0.14461	N	0.318218	T	0.65048	0.2654	L	0.48935	1.535	0.39991	D	0.975043	B;B;B	0.21071	0.051;0.042;0.015	B;B;B	0.19391	0.025;0.014;0.015	T	0.61178	-0.7115	10	0.72032	D	0.01	-8.2819	7.7154	0.28702	0.339:0.0:0.661:0.0	.	1141;1142;1101	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	H	1101;1101;1142	ENSP00000404845:R1101H;ENSP00000266497:R1101H;ENSP00000445381:R1142H	ENSP00000266497:R1101H	R	+	2	0	PIK3C2G	18582458	1.000000	0.71417	0.999000	0.59377	0.933000	0.57130	2.304000	0.43655	0.346000	0.23899	-0.899000	0.02877	CGT	.	.	none		0.373	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570		A	18691191	G	A	18691191	3	1	2	1	0	0	0	0	1	0	0	0	11920	1145	40	1	3392	1	PIK3C2G	12	18691191	Missense_Mutation	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10	11645267	18691191	115160704	49	224											
MLL2	8085	hgsc.bcm.edu	37	chr12	49427102	49427102	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagcatgccctggggcccctGgggtggttgaggggacagct	5	7	18	11	0	0	1	0	1	0	0	0	2	0	2	3	7	3	3	3	7	0	1			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr12:49427102G>A	ENST00000301067.7	-	39	11385	c.11386C>T	c.(11386-11388)Cag>Tag	p.Q3796*	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3796	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)										TGGGGCCCCTGGGGTGGTTGA	0.657																																					p.Q3796X		Atlas-SNP	.											.	MLL2	1173	.	0			c.C11386T						PASS	.						12	14	14					12																	49427102		1930	4119	6049	SO:0001587	stop_gained	8085	exon39			GCCCCTGGGGTGG	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.11386C>T	12.37:g.49427102G>A	ENSP00000301067:p.Gln3796*	43	0	0		41	7	0.170732	NM_003482	O14687	Nonsense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	51	18.491664	0.99906	.	.	ENSG00000167548	ENST00000301067	.	.	.	5.02	5.02	0.67125	.	0.258092	0.20680	N	0.087663	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.4938	0.87712	0.0:0.0:1.0:0.0	.	.	.	.	X	3796	.	ENSP00000301067:Q3796X	Q	-	1	0	MLL2	47713369	0.995000	0.38212	1.000000	0.80357	0.911000	0.54048	3.379000	0.52440	2.505000	0.84491	0.462000	0.41574	CAG	.	.	none		0.657	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49427102	G	A	49427102	4	1	2	1	0	0	0	0	0	1	0	0	9630	1357	47	2	5291	2	MLL2	12	49427102	Nonsense_Mutation	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10	30735911	49427102	84424793	50	225											
BAZ2A	11176	hgsc.bcm.edu	37	chr12	56992706	56992706	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatccataggatttttgatgAtgcgccggtacccactcacc	10	11	8	12	2	1	2	1	2	0	0	2	3	2	3	4	2	2	1	4	2	3	4			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr12:56992706A>C	ENST00000551812.1	-	28	5691	c.5498T>G	c.(5497-5499)aTc>aGc	p.I1833S	BAZ2A_ENST00000549884.1_Missense_Mutation_p.I1831S|BAZ2A_ENST00000379441.3_Missense_Mutation_p.I1803S|BAZ2A_ENST00000553222.1_5'Flank|BAZ2A_ENST00000179765.5_Missense_Mutation_p.I1801S	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	1833	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				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						ATTTTTGATGATGCGCCGGTA	0.532																																					p.I1833S		Atlas-SNP	.											.	BAZ2A	263	.	0			c.T5498G						PASS	.						28	30	30					12																	56992706		1892	4125	6017	SO:0001583	missense	11176	exon28			TTGATGATGCGCC	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.5498T>G	12.37:g.56992706A>C	ENSP00000446880:p.Ile1833Ser	39	0	0		35	5	0.142857	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Missense_Mutation	SNP	ENST00000551812.1	37	CCDS44924.1	.	.	.	.	.	.	.	.	.	.	A	19.37	3.815359	0.70912	.	.	ENSG00000076108	ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549787;ENST00000549884	T;T;T;T;T	0.37411	1.2;1.2;1.2;1.2;1.2	5.81	5.81	0.92471	Bromodomain (6);Bromodomain, conserved site (1);	0.117336	0.53938	D	0.000055	T	0.67363	0.2885	H	0.97564	4.03	0.58432	D	0.999999	P;P;P;P	0.49783	0.879;0.609;0.661;0.928	P;P;P;P	0.52343	0.572;0.521;0.653;0.696	T	0.80049	-0.1545	10	0.87932	D	0	-8.6423	15.5128	0.75798	1.0:0.0:0.0:0.0	.	1831;1829;1833;1806	F8VU39;Q9UIF9-3;Q9UIF9;Q9UIF9-2	.;.;BAZ2A_HUMAN;.	S	1803;1801;1833;765;1831	ENSP00000368754:I1803S;ENSP00000179765:I1801S;ENSP00000446880:I1833S;ENSP00000448760:I765S;ENSP00000447941:I1831S	ENSP00000179765:I1801S	I	-	2	0	BAZ2A	55278973	1.000000	0.71417	0.992000	0.48379	0.918000	0.54935	8.604000	0.90877	2.367000	0.80283	0.529000	0.55759	ATC	.	.	none		0.532	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449		C	56992706	A	C	56992706	3	2	2	1	0	0	0	0	1	0	0	0	1331	333	12	5	227	5	BAZ2A	12	56992706	Missense_Mutation	SNP	A	TCGA-FA-A4BB-01A-11D-A31X-10	7565604	56992706	76859189	51	226											
ZDHHC17	23390	hgsc.bcm.edu	37	chr12	77242136	77242136	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagtgttttccacttcatgtGggtggctgtattactcatgt	6	17	10	8	0	2	0	2	0	0	0	3	0	3	0	1	2	1	3	1	2	2	5			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr12:77242136G>T	ENST00000426126.2	+	15	2280	c.1631G>T	c.(1630-1632)tGg>tTg	p.W544L	ZDHHC17_ENST00000550789.1_3'UTR|ZDHHC17_ENST00000334822.5_Missense_Mutation_p.W544L	NM_015336.2	NP_056151.2	Q8IUH5	ZDH17_HUMAN	zinc finger, DHHC-type containing 17	544					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						CACTTCATGTGGGTGGCTGTA	0.403																																					p.W544L		Atlas-SNP	.											.	ZDHHC17	45	.	0			c.G1631T						PASS	.						205	200	202					12																	77242136		2005	4162	6167	SO:0001583	missense	23390	exon15			TCATGTGGGTGGC	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.1631G>T	12.37:g.77242136G>T	ENSP00000403397:p.Trp544Leu	104	0	0		90	4	0.0444444	NM_015336	B4DR39|O75407|Q7Z2I0|Q86W89|Q86YK0|Q9P088|Q9UPZ8	Missense_Mutation	SNP	ENST00000426126.2	37	CCDS44946.1	.	.	.	.	.	.	.	.	.	.	G	35	5.460578	0.96240	.	.	ENSG00000186908	ENST00000426126;ENST00000334822	T;T	0.20463	2.07;2.07	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.44414	0.1292	L	0.50333	1.59	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.28902	-1.0029	10	0.87932	D	0	-5.0867	19.5662	0.95393	0.0:0.0:1.0:0.0	.	544	Q8IUH5	ZDH17_HUMAN	L	544	ENSP00000403397:W544L;ENSP00000334868:W544L	ENSP00000334868:W544L	W	+	2	0	ZDHHC17	75766267	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	2.608000	0.88229	0.655000	0.94253	TGG	.	.	none		0.403	ZDHHC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406555.1	NM_015336		T	77242136	G	T	77242136	3	4	2	1	0	0	0	0	1	0	0	0	17622	1357	47	4	1689	4	ZDHHC17	12	77242136	Missense_Mutation	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10	20249430	77242136	56609759	52	227											
DTX1	1840	hgsc.bcm.edu	37	chr12	113496044	113496044	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gatgcctgtgaatggtctggGcttcccaccgcagaacgtgg	7	9	14	11	2	1	2	0	1	1	1	2	3	2	2	3	3	2	2	3	3	2	1			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr12:113496044G>A	ENST00000257600.3	+	1	550	c.47G>A	c.(46-48)gGc>gAc	p.G16D		NM_004416.2	NP_004407.2	Q86Y01	DTX1_HUMAN	deltex 1, E3 ubiquitin ligase	16	WWE 1. {ECO:0000255|PROSITE- ProRule:PRU00248}.				cell surface receptor signaling pathway (GO:0007166)|glial cell differentiation (GO:0010001)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of T cell differentiation (GO:0045581)|Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)|regulation of Notch signaling pathway (GO:0008593)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Notch binding (GO:0005112)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	32						AATGGTCTGGGCTTCCCACCG	0.677																																					p.G16D		Atlas-SNP	.											DTX1,NS,lymphoid_neoplasm,0,1	DTX1	83	1	0			c.G47A						PASS	.						63	52	55					12																	113496044		2202	4299	6501	SO:0001583	missense	1840	exon1			GTCTGGGCTTCCC	AF053700	CCDS9164.1	12q24	2014-01-28	2014-01-28			ENSG00000135144			3060	protein-coding gene	gene with protein product		602582	"deltex homolog 1 (Drosophila)"			9590294, 12670957	Standard	NM_004416		Approved	hDx-1	uc001tuk.1	Q86Y01	OTTHUMG00000169610	ENST00000257600.3:c.47G>A	12.37:g.113496044G>A	ENSP00000257600:p.Gly16Asp	153	0	0		111	9	0.0810811	NM_004416	O60630|Q9BS04	Missense_Mutation	SNP	ENST00000257600.3	37	CCDS9164.1	.	.	.	.	.	.	.	.	.	.	G	19.62	3.862540	0.71949	.	.	ENSG00000135144	ENST00000257600	T	0.12879	2.64	3.89	3.89	0.44902	WWE domain (1);	0.178522	0.35151	U	0.003402	T	0.11495	0.0280	L	0.44542	1.39	0.41096	D	0.985633	P	0.42908	0.793	B	0.38225	0.268	T	0.03728	-1.1009	10	0.51188	T	0.08	-13.5407	8.7963	0.34881	0.107:0.0:0.893:0.0	.	16	Q86Y01	DTX1_HUMAN	D	16	ENSP00000257600:G16D	ENSP00000257600:G16D	G	+	2	0	DTX1	111980427	1.000000	0.71417	1.000000	0.80357	0.635000	0.38103	6.846000	0.75399	2.017000	0.59298	0.549000	0.68633	GGC	.	.	none		0.677	DTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405045.2			A	113496044	G	A	113496044	3	1	2	1	0	0	0	0	1	0	0	0	4795	1203	42	2	49	2	DTX1	12	113496044	Missense_Mutation	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10	36253908	113496044	20355851	53	228											
SIRT4	23409	hgsc.bcm.edu	37	chr12	120750455	120750455	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccatctgaaaccagatgtcGttttcttcggggacacagtg	9	11	11	10	2	2	2	0	1	2	1	4	3	2	3	2	2	1	1	2	2	1	3	rs557152464		TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr12:120750455G>A	ENST00000202967.4	+	3	753	c.694G>A	c.(694-696)Gtt>Att	p.V232I	SIRT4_ENST00000537892.1_3'UTR|RNU6-1088P_ENST00000516850.1_RNA	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)					ACCAGATGTCGTTTTCTTCGG	0.527													G|||	1	0.000199681	0.0	0.0	5008	,	,		19764	0.0		0.0	False		,,,				2504	0.001				p.V232I		Atlas-SNP	.											SIRT4,colon,carcinoma,0,1	SIRT4	29	1	0			c.G694A						PASS	.						73	67	69					12																	120750455		2203	4300	6503	SO:0001583	missense	23409	exon3			GATGTCGTTTTCT	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.694G>A	12.37:g.120750455G>A	ENSP00000202967:p.Val232Ile	94	0	0		70	9	0.128571	NM_012240		Missense_Mutation	SNP	ENST00000202967.4	37	CCDS9194.1	.	.	.	.	.	.	.	.	.	.	G	17.15	3.315918	0.60524	.	.	ENSG00000089163	ENST00000202967	T	0.53857	0.6	4.5	1.39	0.22231	.	0.235849	0.41712	N	0.000829	T	0.51500	0.1678	M	0.69358	2.11	0.29480	N	0.856439	P	0.48589	0.912	P	0.46850	0.529	T	0.51694	-0.8673	10	0.46703	T	0.11	-7.8021	7.933	0.29914	0.4701:0.0:0.5299:0.0	.	232	Q9Y6E7	SIRT4_HUMAN	I	232	ENSP00000202967:V232I	ENSP00000202967:V232I	V	+	1	0	SIRT4	119234838	0.999000	0.42202	0.313000	0.25210	0.655000	0.38815	3.571000	0.53841	0.196000	0.20367	-0.201000	0.12746	GTT	.	.	none		0.527	SIRT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402003.1	NM_012240		A	120750455	G	A	120750455	3	1	2	1	0	0	0	0	1	0	0	0	14355	1145	40	1	700	1	SIRT4	12	120750455	Missense_Mutation	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10	7254411	120750455	13101440	54	229											
KDM2B	84678	hgsc.bcm.edu	37	chr12	121882313	121882313	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagcagtttggaagctcgtcGttgaccacaccctctgactc	8	10	9	14	2	1	2	0	2	1	0	4	3	1	3	2	1	2	4	2	1	1	2	rs34911648	byFrequency	TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr12:121882313G>A	ENST00000377071.4	-	15	2202	c.2130C>T	c.(2128-2130)aaC>aaT	p.N710N	KDM2B_ENST00000542973.1_Silent_p.N78N|KDM2B_ENST00000377069.4_Silent_p.N679N|KDM2B_ENST00000536437.1_Intron	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	710					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						GAAGCTCGTCGTTGACCACAC	0.617													G|||	75	0.014976	0.0567	0.0	5008	,	,		17551	0.0		0.0	False		,,,				2504	0.0				p.N710N		Atlas-SNP	.											.	KDM2B	218	.	0			c.C2130T						PASS	.	G	,	234,4058		6,222,1918	85	90	88		2037,2130	3	1	12	dbSNP_126	88	1,8465		0,1,4232	no	coding-synonymous,coding-synonymous	KDM2B	NM_001005366.1,NM_032590.4	,	6,223,6150	AA,AG,GG		0.0118,5.452,1.842	,	679/1266,710/1337	121882313	235,12523	2146	4233	6379	SO:0001819	synonymous_variant	84678	exon15			CTCGTCGTTGACC	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.2130C>T	12.37:g.121882313G>A		58	0	0		52	11	0.211538	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Silent	SNP	ENST00000377071.4	37	CCDS41850.1																																																																																			G|0.990;A|0.010	0.010	strong		0.617	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590		A	121882313	G	A	121882313	2	1	2	1	0	0	0	0	0	0	0	1	8134	1136	40	1		1	KDM2B	12	121882313	Silent	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10	1131858	121882313	11969582	55	230											
BAZ1A	11177	hgsc.bcm.edu	37	chr14	35231204	35231204	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccatgactgtggcgagtagaAcgactggcaattcttaaaga	13	9	11	8	2	1	3	0	1	1	2	1	5	1	3	1	2	1	2	1	2	5	3			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr14:35231204A>G	ENST00000382422.2	-	23	4329	c.4002T>C	c.(4000-4002)cgT>cgC	p.R1334R	BAZ1A_ENST00000358716.4_Silent_p.R1302R|BAZ1A_ENST00000360310.1_Silent_p.R1334R			Q9NRL2	BAZ1A_HUMAN	bromodomain adjacent to zinc finger domain, 1A	1334					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)		GGCGAGTAGAACGACTGGCAA	0.423																																					p.R1334R		Atlas-SNP	.											.	BAZ1A	128	.	0			c.T4002C						PASS	.						188	179	182					14																	35231204		2203	4300	6503	SO:0001819	synonymous_variant	11177	exon24			AGTAGAACGACTG	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.4002T>C	14.37:g.35231204A>G		106	0	0		140	12	0.0857143	NM_013448	Q9NZ15|Q9P065|Q9UIG1|Q9Y3V3	Silent	SNP	ENST00000382422.2	37	CCDS9651.1																																																																																			.	.	none		0.423	BAZ1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276646.1			G	35231204	A	G	35231204	2	3	2	1	0	0	0	0	0	0	0	1	1329	30	2	3		3	BAZ1A	14	35231204	Silent	SNP	A	TCGA-FA-A4BB-01A-11D-A31X-10		35231204	72118336	56	231											
SEMA6D	80031	hgsc.bcm.edu	37	chr15	48058789	48058791	+	Intron	DEL	CTT	CTT	-																															tgaaggctgttaaccgaagaCttctttgctttccataacca																										TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr15:48058789_48058791delCTT	ENST00000316364.5	+	16	2085				SEMA6D_ENST00000536845.2_Intron|SEMA6D_ENST00000558014.1_In_Frame_Del_p.F556del|SEMA6D_ENST00000389428.3_Intron|SEMA6D_ENST00000354744.4_Intron|SEMA6D_ENST00000537942.1_In_Frame_Del_p.F556del|SEMA6D_ENST00000389432.2_In_Frame_Del_p.F556del|SEMA6D_ENST00000389433.2_Intron|SEMA6D_ENST00000355997.3_Intron|SEMA6D_ENST00000558816.1_Intron|SEMA6D_ENST00000358066.4_In_Frame_Del_p.F556del	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D						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)		TAACCGAAGACTTCTTTGCTTTC	0.429																																					p.554_555del		Atlas-Indel	.											.	SEMA6D	322	.	0			c.1661_1663del						PASS	.																																			SO:0001627	intron_variant	80031	exon16			.	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.1647-22CTT>-	15.37:g.48058792_48058794delCTT		118	0	0		116	11	0.0948276	NM_020858	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	In_Frame_Del	DEL	ENST00000316364.5	37	CCDS32225.1																																																																																			.	.	none		0.429	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		-	48058791	CTT	-	48058789	6	5	2	0	1	1	0	1	0	0	0	0	14057	564	20	0		0	SEMA6D	15	48058789	Intron	DEL	CTT	TCGA-FA-A4BB-01A-11D-A31X-10		48058789	54472603	57	232											
HERC1	8925	hgsc.bcm.edu	37	chr15	63970537	63970537	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtaagtctcggggtgtgcCacgcatctgcatatcacaaa	12	9	10	10	2	3	0	1	0	2	0	4	0	3	0	1	2	2	3	1	2	4	2			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr15:63970537C>T	ENST00000443617.2	-	37	6664	c.6577G>A	c.(6577-6579)Ggc>Agc	p.G2193S	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	2193	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				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						CGGGGTGTGCCACGCATCTGC	0.433																																					p.G2193S		Atlas-SNP	.											.	HERC1	624	.	0			c.G6577A						PASS	.						29	27	28					15																	63970537		1945	4132	6077	SO:0001583	missense	8925	exon37			GTGTGCCACGCAT	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.6577G>A	15.37:g.63970537C>T	ENSP00000390158:p.Gly2193Ser	79	0	0		79	10	0.126582	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	37	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.012108	0.93346	.	.	ENSG00000103657	ENST00000443617	T	0.59224	0.28	5.7	5.7	0.88788	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	0.000000	0.85682	D	0.000000	T	0.65647	0.2711	N	0.20685	0.6	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.66881	-0.5811	10	0.46703	T	0.11	.	19.8247	0.96612	0.0:1.0:0.0:0.0	.	2193	Q15751	HERC1_HUMAN	S	2193	ENSP00000390158:G2193S	ENSP00000390158:G2193S	G	-	1	0	HERC1	61757590	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.818000	0.86416	2.696000	0.92011	0.655000	0.94253	GGC	.	.	none		0.433	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		T	63970537	C	T	63970537	3	4	2	1	0	0	0	0	1	0	0	0	7066	594	21	2	8176	2	HERC1	15	63970537	Missense_Mutation	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10	15911748	63970537	38560855	58	233											
CTSH	1512	hgsc.bcm.edu	37	chr15	79215405	79215405	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatcccatttttttctccatAcccaacagccagtactgcat	10	13	4	14	0	1	0	0	0	1	0	3	1	2	0	4	0	5	2	4	0	3	5			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr15:79215405A>G	ENST00000220166.5	-	11	971	c.862T>C	c.(862-864)Tat>Cat	p.Y288H	CTSH_ENST00000534533.1_5'UTR	NM_004390.3	NP_004381.2	P09668	CATH_HUMAN	cathepsin H	288					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						TTTTCTCCATACCCAACAGCC	0.453																																					p.Y288H		Atlas-SNP	.											.	CTSH	23	.	0			c.T862C						PASS	.						94	95	95					15																	79215405		2196	4293	6489	SO:0001583	missense	1512	exon11			CTCCATACCCAAC	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.862T>C	15.37:g.79215405A>G	ENSP00000220166:p.Tyr288His	95	0	0		104	14	0.134615	NM_004390	B2RBK0|Q96NY6|Q9BUM7	Missense_Mutation	SNP	ENST00000220166.5	37	CCDS10308.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.284657	0.80803	.	.	ENSG00000103811	ENST00000220166;ENST00000394758	T	0.37411	1.2	4.65	4.65	0.58169	Peptidase C1A, papain C-terminal (3);	0.000000	0.85682	D	0.000000	T	0.71676	0.3368	H	0.97783	4.075	0.53005	D	0.999967	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.80491	-0.1359	10	0.87932	D	0	.	10.3628	0.44006	1.0:0.0:0.0:0.0	.	288;276	P09668;E9PBP2	CATH_HUMAN;.	H	288;276	ENSP00000220166:Y288H	ENSP00000220166:Y288H	Y	-	1	0	CTSH	77002460	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.492000	0.81482	1.959000	0.56917	0.402000	0.26972	TAT	.	.	none		0.453	CTSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291370.1	NM_004390		G	79215405	A	G	79215405	3	3	2	1	0	0	0	0	1	0	0	0	4038	391	14	3	153	3	CTSH	15	79215405	Missense_Mutation	SNP	A	TCGA-FA-A4BB-01A-11D-A31X-10	15244868	79215405	23315987	59	234											
HYDIN	54768	hgsc.bcm.edu	37	chr16	71004449	71004449	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctatgagatactgctgatCaaattctaaggaataaaact	16	13	6	6	0	3	2	1	2	2	1	3	4	3	3	0	1	3	1	0	1	7	6			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr16:71004449C>A	ENST00000393567.2	-	36	5743	c.5593G>T	c.(5593-5595)Gat>Tat	p.D1865Y		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	1865					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)		p.D1816H(1)		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)				TACTGCTGATCAAATTCTAAG	0.443																																					p.D1865Y		Atlas-SNP	.											LOC652153,NS,carcinoma,0,1	HYDIN	788	1	1	Substitution - Missense(1)	ovary(1)	c.G5593T						scavenged	.						37	37	37					16																	71004449		1803	4051	5854	SO:0001583	missense	54768	exon36			GCTGATCAAATTC	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.5593G>T	16.37:g.71004449C>A	ENSP00000377197:p.Asp1865Tyr	51	0	0		51	5	0.0980392	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.398623	0.83120	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.42900	0.96	4.65	4.65	0.58169	.	0.000000	0.34411	U	0.003995	T	0.67961	0.2949	M	0.83953	2.67	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.72988	-0.4124	10	0.54805	T	0.06	.	17.4637	0.87626	0.0:1.0:0.0:0.0	.	1864	F8WD23	.	Y	1865;1864	ENSP00000377197:D1865Y	ENSP00000310485:D156Y	D	-	1	0	HYDIN	69561950	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.484000	0.81180	2.311000	0.77944	0.505000	0.49811	GAT	.	.	none		0.443	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			A	71004449	C	A	71004449	3	1	2	1	0	0	0	0	1	0	0	0	7476	826	29	4	9976	4	HYDIN	16	71004449	Missense_Mutation	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10		71004449	19350304	60	235											
AURKB	9212	hgsc.bcm.edu	37	chr17	8108196	8108196	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgacagggaccatcaggcgAcagattgaagggcagaggga	14	4	16	7	1	1	4	1	2	0	2	1	7	1	6	1	4	0	1	1	4	1	1			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr17:8108196A>G	ENST00000585124.1	-	9	1121	c.1028T>C	c.(1027-1029)gTc>gCc	p.V343A	AURKB_ENST00000316199.6_Missense_Mutation_p.V344A|AURKB_ENST00000578549.1_Missense_Mutation_p.V311A|AURKB_ENST00000535053.1_3'UTR|AURKB_ENST00000534871.1_Missense_Mutation_p.V302A	NM_004217.3	NP_004208.2	Q96GD4	AURKB_HUMAN	aurora kinase B	343					abscission (GO:0009838)|aging (GO:0007568)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|attachment of spindle microtubules to kinetochore (GO:0008608)|cell proliferation (GO:0008283)|cellular response to UV (GO:0034644)|cleavage furrow formation (GO:0036089)|cytokinesis checkpoint (GO:0031565)|histone H3-S28 phosphorylation (GO:0043988)|histone modification (GO:0016570)|mitotic cell cycle (GO:0000278)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cytokinesis (GO:0032467)|protein autophosphorylation (GO:0046777)|protein localization to kinetochore (GO:0034501)|protein phosphorylation (GO:0006468)|regulation of chromosome segregation (GO:0051983)|spindle checkpoint (GO:0031577)|spindle midzone assembly involved in mitosis (GO:0051256)|spindle stabilization (GO:0043146)	chromocenter (GO:0010369)|chromosome passenger complex (GO:0032133)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			breast(1)|central_nervous_system(1)|lung(2)	4						CCATCAGGCGACAGATTGAAG	0.572																																					p.V343A	NSCLC(134;1161 2470 43664 51568)	Atlas-SNP	.											.	AURKB	47	.	0			c.T1028C						PASS	.						70	70	70					17																	8108196		2203	4300	6503	SO:0001583	missense	9212	exon9			CAGGCGACAGATT	AF004022	CCDS11134.1, CCDS58514.1, CCDS67162.1	17p13.1	2013-01-17	2003-07-21	2003-07-23	ENSG00000178999	ENSG00000178999		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	11390	protein-coding gene	gene with protein product	"aurora-B", "aurora-1", "protein phosphatase 1, regulatory subunit 48"	604970	"serine/threonine kinase 12"	STK12		9858806	Standard	NM_001256834		Approved	Aik2, IPL1, AurB, AIM-1, ARK2, STK5, PPP1R48	uc002gkm.4	Q96GD4	OTTHUMG00000108189	ENST00000585124.1:c.1028T>C	17.37:g.8108196A>G	ENSP00000463999:p.Val343Ala	40	0	0		42	6	0.142857	NM_004217	B4DNM4|C7G533|C7G534|C7G535|D3DTR4|J9JID1|O14630|O60446|O95083|Q96DV5|Q9UQ46	Missense_Mutation	SNP	ENST00000585124.1	37	CCDS11134.1	.	.	.	.	.	.	.	.	.	.	A	9.318	1.057435	0.19907	.	.	ENSG00000178999	ENST00000316199;ENST00000534871	T	0.70399	-0.48	5.03	0.173	0.15036	.	1.328900	0.05074	N	0.482223	T	0.51584	0.1683	N	0.14661	0.345	0.30620	N	0.758543	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44651	-0.9314	10	0.33940	T	0.23	-10.2184	5.6234	0.17469	0.3103:0.1898:0.4999:0.0	.	343;343	C7G533;Q96GD4	.;AURKB_HUMAN	A	343;302	ENSP00000443869:V302A	ENSP00000313950:V343A	V	-	2	0	AURKB	8048921	0.000000	0.05858	0.026000	0.17262	0.280000	0.26924	-1.102000	0.03332	0.117000	0.18138	0.533000	0.62120	GTC	.	.	none		0.572	AURKB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000226995.2	NM_004217		G	8108196	A	G	8108196	3	3	2	1	0	0	0	0	1	0	0	0	1223	275	10	3	10	3	AURKB	17	8108196	Missense_Mutation	SNP	A	TCGA-FA-A4BB-01A-11D-A31X-10		8108196	73087014	61	236											
MYH13	8735	hgsc.bcm.edu	37	chr17	10267752	10267752	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aagcaggctttcttggaatcGaatggacgattttgagcctc	10	12	11	8	2	1	1	0	1	1	0	3	5	1	3	1	3	2	2	1	3	3	4	rs189377998		TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr17:10267752G>A	ENST00000418404.3	-	2	259	c.96C>T	c.(94-96)ttC>ttT	p.F32F	MYH13_ENST00000252172.4_Silent_p.F32F			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	32					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						TCTTGGAATCGAATGGACGAT	0.463													G|||	1	0.000199681	0.0	0.0	5008	,	,		19558	0.001		0.0	False		,,,				2504	0.0				p.F32F		Atlas-SNP	.											MYH13_ENST00000252172,NS,carcinoma,0,2	MYH13	533	2	0			c.C96T						PASS	.						121	113	115					17																	10267752		1920	4138	6058	SO:0001819	synonymous_variant	8735	exon3			GGAATCGAATGGA	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.96C>T	17.37:g.10267752G>A		193	0	0		159	19	0.119497	NM_003802	O95252|Q9P0U8	Silent	SNP	ENST00000418404.3	37	CCDS45613.1																																																																																			G|1.000;A|0.000	0.000	strong		0.463	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	10267752	G	A	10267752	2	1	2	1	0	0	0	0	0	0	0	1	10041	1049	37	1		1	MYH13	17	10267752	Silent	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10	2159556	10267752	70927458	62	237											
NF1	4763	hgsc.bcm.edu	37	chr17	29528446	29528446	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tagatctgcctggctcagaaTtcaccttctacatttcacta	10	14	5	12	0	5	2	3	0	2	2	5	2	5	2	2	1	2	1	2	1	4	6			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr17:29528446T>A	ENST00000358273.4	+	11	1586	c.1203T>A	c.(1201-1203)aaT>aaA	p.N401K	NF1_ENST00000431387.4_Missense_Mutation_p.N401K|NF1_ENST00000356175.3_Missense_Mutation_p.N401K	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	401					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.?(6)	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)		TGGCTCAGAATTCACCTTCTA	0.303			"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.N401K		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	14	Whole gene deletion(8)|Unknown(6)	soft_tissue(7)|autonomic_ganglia(3)|central_nervous_system(3)|lung(1)	c.T1203A						PASS	.						80	89	86					17																	29528446		2203	4295	6498	SO:0001583	missense	4763	exon11	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	TCAGAATTCACCT		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.1203T>A	17.37:g.29528446T>A	ENSP00000351015:p.Asn401Lys	276	0	0		312	30	0.0961538	NM_001128147	O00662|Q14284|Q14930|Q14931|Q9UMK3	Missense_Mutation	SNP	ENST00000358273.4	37	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	T	13.39	2.223593	0.39300	.	.	ENSG00000196712	ENST00000431387;ENST00000358273;ENST00000356175;ENST00000456735	T;T;T;T	0.80909	-1.43;-1.43;-1.43;-1.43	5.17	3.87	0.44632	Armadillo-type fold (1);	0.167666	0.56097	D	0.000026	T	0.69797	0.3151	L	0.42245	1.32	0.80722	D	1	B;B;B;B;B	0.33413	0.411;0.013;0.031;0.161;0.161	B;B;B;B;B	0.30495	0.08;0.017;0.034;0.116;0.073	T	0.71159	-0.4674	10	0.59425	D	0.04	.	6.7182	0.23314	0.139:0.0845:0.0:0.7765	.	401;401;401;401;401	E1P657;P21359-2;P21359;Q14931;P21359-3	.;.;NF1_HUMAN;.;.	K	401;401;401;67	ENSP00000412921:N401K;ENSP00000351015:N401K;ENSP00000348498:N401K;ENSP00000389907:N67K	ENSP00000348498:N401K	N	+	3	2	NF1	26552572	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.032000	0.41127	1.953000	0.56701	0.402000	0.26972	AAT	.	.	none		0.303	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		A	29528446	T	A	29528446	3	1	2	1	0	0	0	0	1	0	0	0	10365	1490	52	5	1245	5	NF1	17	29528446	Missense_Mutation	SNP	T	TCGA-FA-A4BB-01A-11D-A31X-10	19260694	29528446	51666764	63	238											
C17orf79	55352	hgsc.bcm.edu	37	chr17	30179882	30179882	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgagtcccagtcctcattaaAaagatcgccaggctgttcct	10	10	8	13	2	1	1	1	0	0	1	5	2	4	1	4	1	0	2	4	1	3	2			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr17:30179882A>C	ENST00000302362.6	-	3	471	c.334T>G	c.(334-336)Ttt>Gtt	p.F112V	COPRS_ENST00000378634.2_Missense_Mutation_p.F100V	NM_018405.3	NP_060875.2	Q9NQ92	COPRS_HUMAN	coordinator of PRMT5, differentiation stimulator	112					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)										TCCTCATTAAAAAGATCGCCA	0.517																																					p.F112V		Atlas-SNP	.											C17orf79,colon,carcinoma,+1,1	.	.	1	0			c.T334G						scavenged	.						180	185	183					17																	30179882		2203	4300	6503	SO:0001583	missense	55352	exon3			CATTAAAAAGATC	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.334T>G	17.37:g.30179882A>C	ENSP00000304327:p.Phe112Val	94	2	0.0212766		84	16	0.190476	NM_018405	A6NP14|E1P656|Q96EF5|Q96P75	Missense_Mutation	SNP	ENST00000302362.6	37	CCDS11268.1	.	.	.	.	.	.	.	.	.	.	A	14.24	2.476405	0.44044	.	.	ENSG00000172301	ENST00000302362;ENST00000378634	T;T	0.40756	1.02;1.02	5.37	4.26	0.50523	.	0.378221	0.22871	N	0.054628	T	0.23210	0.0561	N	0.20986	0.625	0.09310	N	0.999999	P	0.36535	0.557	B	0.34242	0.178	T	0.07558	-1.0766	10	0.27082	T	0.32	-5.3289	4.8505	0.13535	0.8376:0.0:0.1624:0.0	.	112	Q9NQ92	COPR5_HUMAN	V	112;100	ENSP00000304327:F112V;ENSP00000367901:F100V	ENSP00000304327:F112V	F	-	1	0	C17orf79	27203995	0.961000	0.32948	0.156000	0.22583	0.316000	0.28119	2.353000	0.44089	2.030000	0.59900	0.383000	0.25322	TTT	.	.	none		0.517	COPRS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256257.2	NM_018405		C	30179882	A	C	30179882	3	2	2	1	0	0	0	0	1	0	0	0	1886	14	1	5	228	5	C17orf79	17	30179882	Missense_Mutation	SNP	A	TCGA-FA-A4BB-01A-11D-A31X-10	651436	30179882	51015328	64	239											
DDX52	11056	hgsc.bcm.edu	37	chr17	35993354	35993354	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttctccaactttccggaagtTagtttactttctctctgaac	8	17	5	11	1	3	1	0	1	3	0	6	2	4	2	2	1	3	2	2	1	5	6			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr17:35993354T>G	ENST00000349699.2	-	3	424	c.381A>C	c.(379-381)ctA>ctC	p.L127L	DDX52_ENST00000394367.3_Silent_p.L19L	NM_007010.3	NP_008941.2	Q9Y2R4	DDX52_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52	127						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)				TTCCGGAAGTTAGTTTACTTT	0.348																																					p.L127L		Atlas-SNP	.											.	DDX52	40	.	0			c.A381C						PASS	.						93	95	94					17																	35993354		2202	4298	6500	SO:0001819	synonymous_variant	11056	exon3			GGAAGTTAGTTTA	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.381A>C	17.37:g.35993354T>G		70	0	0		60	9	0.15	NM_007010	Q86YG1|Q8N213|Q9NVE0|Q9Y482	Silent	SNP	ENST00000349699.2	37	CCDS11323.1																																																																																			.	.	none		0.348	DDX52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256795.1	NM_152300		G	35993354	T	G	35993354	2	3	2	1	0	0	0	0	0	0	0	1	4372	1741	61	5		5	DDX52	17	35993354	Silent	SNP	T	TCGA-FA-A4BB-01A-11D-A31X-10	5813472	35993354	45201856	65	240											
KRT37	8688	hgsc.bcm.edu	37	chr17	39580747	39580747	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatggtgcaacccagagggCatgaggaggtgctgtagaag	11	6	16	8	0	0	3	0	1	0	2	0	4	0	4	2	4	3	4	2	4	3	1			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr17:39580747C>A	ENST00000225550.3	-	1	28	c.29G>T	c.(28-30)tGc>tTc	p.C10F	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	10	Head.					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)				ACCCAGAGGGCATGAGGAGGT	0.572																																					p.C10F		Atlas-SNP	.											.	KRT37	61	.	0			c.G29T						PASS	.						66	70	68					17																	39580747		2203	4300	6503	SO:0001583	missense	8688	exon1			AGAGGGCATGAGG	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.29G>T	17.37:g.39580747C>A	ENSP00000225550:p.Cys10Phe	78	0	0		71	6	0.084507	NM_003770		Missense_Mutation	SNP	ENST00000225550.3	37	CCDS32653.1	.	.	.	.	.	.	.	.	.	.	.	3.388	-0.124847	0.06795	.	.	ENSG00000108417	ENST00000225550	D	0.81739	-1.53	4.0	-5.2	0.02823	.	1.694370	0.03249	N	0.181556	T	0.50769	0.1635	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.54016	-0.8356	10	0.06365	T	0.9	.	3.0653	0.06212	0.1093:0.34:0.3573:0.1934	.	10	O76014	KRT37_HUMAN	F	10	ENSP00000225550:C10F	ENSP00000225550:C10F	C	-	2	0	KRT37	36834273	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-1.529000	0.02223	-0.991000	0.03476	0.655000	0.94253	TGC	.	.	none		0.572	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770		A	39580747	C	A	39580747	3	1	2	1	0	0	0	0	1	0	0	0	8483	710	25	4	1348	4	KRT37	17	39580747	Missense_Mutation	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10	3587393	39580747	41614463	66	241											
SFRS1	6426	hgsc.bcm.edu	37	chr17	56083716	56083717	+	Frame_Shift_Del	DEL	CT	CT	-																															acactcaccagagacaaccaCtctgttttcagaccgcctgg																										TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr17:56083716_56083717delCT	ENST00000258962.4	-	2	574_575	c.366_367delAG	c.(364-369)agagtgfs	p.RV122fs	SRSF1_ENST00000584773.1_Frame_Shift_Del_p.RV122fs|SRSF1_ENST00000585096.1_Intron|SRSF1_ENST00000581497.1_5'Flank|SRSF1_ENST00000582730.2_Frame_Shift_Del_p.RV122fs|RP11-159D12.5_ENST00000578794.1_5'Flank	NM_006924.4	NP_008855.1	Q07955	SRSF1_HUMAN	serine/arginine-rich splicing factor 1	122	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				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)	p.V123L(1)		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						GAGACAACCACTCTGTTTTCAG	0.554																																					p.123_123del		Pindel,Atlas-Indel	.											SRSF1,NS,carcinoma,-1,1	SRSF1	41	1	1	Substitution - Missense(1)	lung(1)	c.367_368del						PASS	.																																			SO:0001589	frameshift_variant	6426	exon2			.		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.366_367delAG	17.37:g.56083718_56083719delCT	ENSP00000258962:p.Arg122fs	0	0	.		11	11	1	NM_001078166	B2R6Z7|D3DTZ3|Q13809	Frame_Shift_Del	DEL	ENST00000258962.4	37	CCDS11600.1																																																																																			.	.	none		0.554	SRSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443335.1	NM_006924		-	56083717	CT	-	56083716	7	5	2	1	0	1	0	1	0	0	0	0	14180	565	20	0	445	0	SFRS1	17	56083716	Frame_Shift_Del	DEL	CT	TCGA-FA-A4BB-01A-11D-A31X-10	16502969	56083716	25111494	67	242											
UNK	85451	hgsc.bcm.edu	37	chr17	73780999	73780999	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gcccggcggctccgcagcttCctcggcgcccccggccgcta	2	5	13	21	7	0	0	0	0	0	0	3	0	2	0	6	4	1	4	6	4	1	2			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr17:73780999C>T	ENST00000589666.1	+	1	148	c.38C>T	c.(37-39)tCc>tTc	p.S13F	H3F3B_ENST00000586607.1_Intron|MIR4738_ENST00000579134.1_RNA|UNK_ENST00000293218.3_Missense_Mutation_p.S89F	NM_001080419.2	NP_001073888.2	Q9C0B0	UNK_HUMAN	unkempt family zinc finger	13							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)			TCCGCAGCTTCCTCGGCGCCC	0.711																																					p.S13F		Atlas-SNP	.											.	UNK	87	.	0			c.C38T						PASS	.						6	10	9					17																	73780999		1748	3892	5640	SO:0001583	missense	85451	exon1			CAGCTTCCTCGGC	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.38C>T	17.37:g.73780999C>T	ENSP00000464893:p.Ser13Phe	57	0	0		51	8	0.156863	NM_001080419		Missense_Mutation	SNP	ENST00000589666.1	37	CCDS45778.2	.	.	.	.	.	.	.	.	.	.	C	19.42	3.823706	0.71143	.	.	ENSG00000132478	ENST00000293218	.	.	.	5.88	4.91	0.64330	.	0.228714	0.47093	N	0.000253	T	0.56108	0.1963	L	0.51422	1.61	0.51767	D	0.999932	D	0.55385	0.971	B	0.44278	0.445	T	0.62348	-0.6873	9	0.72032	D	0.01	-19.3886	14.8103	0.69989	0.0:0.855:0.145:0.0	.	13	Q9C0B0	UNK_HUMAN	F	89	.	ENSP00000293218:S89F	S	+	2	0	UNK	71292594	1.000000	0.71417	1.000000	0.80357	0.306000	0.27790	3.612000	0.54142	1.473000	0.48159	-0.175000	0.13238	TCC	.	.	none		0.711	UNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448835.1	NM_001080419		T	73780999	C	T	73780999	3	4	2	1	0	0	0	0	1	0	0	0	17015	855	30	2	272	2	UNK	17	73780999	Missense_Mutation	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10	17697283	73780999	7414211	68	243											
LAMA1	284217	hgsc.bcm.edu	37	chr18	7049165	7049165	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcgttctaatgcgttgcaagCgaaggcgaatatatcgtgca	11	10	12	8	5	1	0	0	0	1	0	2	2	1	0	0	1	4	4	0	1	6	5			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr18:7049165C>T	ENST00000389658.3	-	5	773	c.680G>A	c.(679-681)cGc>cAc	p.R227H		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	227	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)				GCGTTGCAAGCGAAGGCGAAT	0.468																																					p.R227H		Atlas-SNP	.											.	LAMA1	458	.	0			c.G680A						PASS	.						148	123	131					18																	7049165		2203	4300	6503	SO:0001583	missense	284217	exon5			TGCAAGCGAAGGC	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.680G>A	18.37:g.7049165C>T	ENSP00000374309:p.Arg227His	123	0	0		113	14	0.123894	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.623061	0.87460	.	.	ENSG00000101680	ENST00000389658	T	0.76709	-1.04	5.85	4.95	0.65309	Laminin, N-terminal (3);	0.000000	0.85682	D	0.000000	D	0.87334	0.6151	M	0.82517	2.595	0.48395	D	0.999643	D	0.89917	1.0	D	0.75484	0.986	D	0.87835	0.2647	10	0.62326	D	0.03	.	11.2793	0.49184	0.0:0.8035:0.128:0.0684	.	227	P25391	LAMA1_HUMAN	H	227	ENSP00000374309:R227H	ENSP00000374309:R227H	R	-	2	0	LAMA1	7039165	1.000000	0.71417	0.866000	0.34008	0.886000	0.51366	2.476000	0.45171	2.767000	0.95098	0.557000	0.71058	CGC	.	.	none		0.468	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		T	7049165	C	T	7049165	3	4	2	1	0	0	0	0	1	0	0	0	8614	768	27	1	8783	1	LAMA1	18	7049165	Missense_Mutation	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10		7049165	71028083	69	244											
DSEL	92126	hgsc.bcm.edu	37	chr18	65180409	65180409	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaaacaaatacttgtccattGggggcaaaagtaaatgagtt	16	10	10	5	0	0	1	0	1	0	0	1	2	1	1	1	2	2	3	1	2	7	5			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr18:65180409G>T	ENST00000310045.7	-	2	2940	c.1467C>A	c.(1465-1467)ccC>ccA	p.P489P	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	479					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)				CTTGTCCATTGGGGGCAAAAG	0.423																																					p.P489P		Atlas-SNP	.											.	DSEL	196	.	0			c.C1467A						PASS	.						103	99	101					18																	65180409		2203	4300	6503	SO:0001819	synonymous_variant	92126	exon2			TCCATTGGGGGCA	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.1467C>A	18.37:g.65180409G>T		121	0	0		113	11	0.0973451	NM_032160	Q17RH1|Q6P5Z3	Silent	SNP	ENST00000310045.7	37	CCDS11995.1																																																																																			.	.	none		0.423	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160		T	65180409	G	T	65180409	2	4	2	1	0	0	0	0	0	0	0	1	4777	1335	47	4		4	DSEL	18	65180409	Silent	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10	58131244	65180409	12896839	70	245											
LPHN1	22859	hgsc.bcm.edu	37	chr19	14266282	14266282	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttgttgatgaagaggaggccGaaagcccaggtgaggcccag	11	6	16	8	1	0	4	0	3	0	1	0	6	0	5	3	4	1	1	3	4	2	2			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr19:14266282G>A	ENST00000340736.6	-	19	3495	c.3198C>T	c.(3196-3198)ttC>ttT	p.F1066F	LPHN1_ENST00000361434.3_Silent_p.F1061F|CTB-55O6.12_ENST00000588387.1_RNA|CTB-55O6.12_ENST00000588658.1_RNA|CTB-55O6.12_ENST00000592086.1_RNA	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	1066					calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|heterophilic cell-cell adhesion (GO:0007157)|neuropeptide signaling pathway (GO:0007218)|positive regulation of synapse maturation (GO:0090129)	axon (GO:0030424)|cell junction (GO:0030054)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						AGAGGAGGCCGAAAGCCCAGG	0.622																																					p.F1066F		Atlas-SNP	.											.	LPHN1	107	.	0			c.C3198T						PASS	.						90	86	87					19																	14266282		2203	4300	6503	SO:0001819	synonymous_variant	22859	exon19			GAGGCCGAAAGCC	AB020628	CCDS12307.1, CCDS32928.1	19p13.2	2014-08-08				ENSG00000072071		"-", "GPCR / Class B : Orphans"	20973	protein-coding gene	gene with protein product						10994649	Standard	NM_014921		Approved	KIAA0821, CIRL1, LEC2	uc010xnn.2	O94910		ENST00000340736.6:c.3198C>T	19.37:g.14266282G>A		101	0	0		88	17	0.193182	NM_001008701	Q96IE7|Q9BU07|Q9HAR3	Silent	SNP	ENST00000340736.6	37	CCDS32928.1																																																																																			.	.	none		0.622	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921		A	14266282	G	A	14266282	2	1	2	1	0	0	0	0	0	0	0	1	8924	1049	37	1		1	LPHN1	19	14266282	Silent	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10		14266282	44862701	71	246											
LPHN1	22859	hgsc.bcm.edu	37	chr19	14288465	14288465	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcattctccaccatgatgacGtcgctgccggggcaccgcag	7	7	12	15	4	1	2	0	2	1	0	3	2	1	2	4	2	1	4	4	2	0	1			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr19:14288465G>A	ENST00000340736.6	-	3	459	c.162C>T	c.(160-162)gaC>gaT	p.D54D	LPHN1_ENST00000361434.3_Silent_p.D54D	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	54	SUEL-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00260}.				calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|heterophilic cell-cell adhesion (GO:0007157)|neuropeptide signaling pathway (GO:0007218)|positive regulation of synapse maturation (GO:0090129)	axon (GO:0030424)|cell junction (GO:0030054)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						CCATGATGACGTCGCTGCCGG	0.652																																					p.D54D		Atlas-SNP	.											LPHN1,NS,carcinoma,-1,1	LPHN1	107	1	0			c.C162T						PASS	.						114	91	99					19																	14288465		2203	4300	6503	SO:0001819	synonymous_variant	22859	exon3			GATGACGTCGCTG	AB020628	CCDS12307.1, CCDS32928.1	19p13.2	2014-08-08				ENSG00000072071		"-", "GPCR / Class B : Orphans"	20973	protein-coding gene	gene with protein product						10994649	Standard	NM_014921		Approved	KIAA0821, CIRL1, LEC2	uc010xnn.2	O94910		ENST00000340736.6:c.162C>T	19.37:g.14288465G>A		78	0	0		48	7	0.145833	NM_001008701	Q96IE7|Q9BU07|Q9HAR3	Silent	SNP	ENST00000340736.6	37	CCDS32928.1																																																																																			.	.	none		0.652	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921		A	14288465	G	A	14288465	2	1	2	1	0	0	0	0	0	0	0	1	8924	1136	40	1		1	LPHN1	19	14288465	Silent	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10	22183	14288465	44840518	72	247											
ZNF575	284346	hgsc.bcm.edu	37	chr19	44039461	44039461	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcggcgcccgcccgcacccGtgcccacactgcccgaagtc	6	3	11	21	6	0	0	0	0	0	0	1	1	0	0	5	1	3	1	5	1	1	0			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr19:44039461G>T	ENST00000314228.5	+	4	872	c.360G>T	c.(358-360)ccG>ccT	p.P120P	ZNF575_ENST00000458714.2_Silent_p.P219P|ZNF575_ENST00000601282.1_Silent_p.P120P	NM_174945.2	NP_777605.1	Q86XF7	ZN575_HUMAN	zinc finger protein 575	120					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)|prostate(1)|urinary_tract(1)	4		Prostate(69;0.0199)				GCCCGCACCCGTGCCCACACT	0.731																																					p.P120P		Atlas-SNP	.											ZNF575,NS,carcinoma,+1,1	ZNF575	14	1	0			c.G360T						scavenged	.						23	24	24					19																	44039461		2199	4297	6496	SO:0001819	synonymous_variant	284346	exon4			GCACCCGTGCCCA	BC043611	CCDS12623.1	19q13.31	2013-09-20			ENSG00000176472	ENSG00000176472		"Zinc fingers, C2H2-type"	27606	protein-coding gene	gene with protein product							Standard	NM_174945		Approved	FLJ32567	uc002ows.3	Q86XF7	OTTHUMG00000182698	ENST00000314228.5:c.360G>T	19.37:g.44039461G>T		90	1	0.0111111		76	5	0.0657895	NM_174945	B4DX54	Silent	SNP	ENST00000314228.5	37	CCDS12623.1																																																																																			.	.	none		0.731	ZNF575-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463191.1	NM_174945		T	44039461	G	T	44039461	2	4	2	1	0	0	0	0	0	0	0	1	18022	1132	40	4		4	ZNF575	19	44039461	Silent	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10	29750996	44039461	15089522	73	248											
NLRP9	338321	hgsc.bcm.edu	37	chr19	56244558	56244558	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggctgggaaaaaatgtcttcGatcttctctgaagactccgg	10	11	11	9	2	3	2	0	1	3	1	6	4	4	3	1	3	0	1	1	3	4	2			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr19:56244558G>A	ENST00000332836.2	-	2	666	c.639C>T	c.(637-639)atC>atT	p.I213I		NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	213	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)		AAATGTCTTCGATCTTCTCTG	0.443																																					p.I213I		Atlas-SNP	.											NLRP9,NS,carcinoma,0,1	NLRP9	163	1	0			c.C639T						PASS	.						33	32	32					19																	56244558		2203	4300	6503	SO:0001819	synonymous_variant	338321	exon2			GTCTTCGATCTTC	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.639C>T	19.37:g.56244558G>A		102	0	0		84	11	0.130952	NM_176820	B2RN12|Q86W27	Silent	SNP	ENST00000332836.2	37	CCDS12934.1																																																																																			.	.	none		0.443	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453653.1	NM_176820		A	56244558	G	A	56244558	2	1	2	1	0	0	0	0	0	0	0	1	10493	1048	37	1		1	NLRP9	19	56244558	Silent	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10	12205097	56244558	2884425	74	249											
ZNF324	25799	hgsc.bcm.edu	37	chr19	58983107	58983107	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcgctctttaagcaccaGcgcgtgcacacaggcgagaa	10	7	10	14	4	1	1	0	0	1	1	3	2	2	1	2	1	3	3	2	1	2	2			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr19:58983107G>A	ENST00000536459.2	+	4	1957	c.1248G>A	c.(1246-1248)caG>caA	p.Q416Q	ZNF324_ENST00000535298.1_Silent_p.Q193Q|ZNF446_ENST00000596341.1_5'Flank|ZNF324_ENST00000196482.3_Silent_p.Q416Q			O75467	Z324A_HUMAN	zinc finger protein 324	416					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(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(2)|prostate(2)|urinary_tract(2)	16		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)		TTAAGCACCAGCGCGTGCACA	0.662																																					p.Q416Q		Atlas-SNP	.											.	ZNF324	46	.	0			c.G1248A						PASS	.						41	41	41					19																	58983107		2203	4299	6502	SO:0001819	synonymous_variant	25799	exon4			GCACCAGCGCGTG	AF060503	CCDS12981.1	19q13.43	2013-01-08				ENSG00000083812		"Zinc fingers, C2H2-type", "-"	14096	protein-coding gene	gene with protein product							Standard	NM_014347		Approved	ZF5128, ZNF324A	uc002qsw.2	O75467		ENST00000536459.2:c.1248G>A	19.37:g.58983107G>A		105	0	0		77	9	0.116883	NM_014347	B3KRX1	Silent	SNP	ENST00000536459.2	37	CCDS12981.1																																																																																			.	.	none		0.662	ZNF324-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467044.1	NM_014347		A	58983107	G	A	58983107	2	1	2	1	0	0	0	0	0	0	0	1	17859	962	34	2		2	ZNF324	19	58983107	Silent	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10	2738549	58983107	145876	75	250											
ANGPT4	51378	hgsc.bcm.edu	37	chr20	865839	865839	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcctgacaccgcgcaggccGcgctcgatgttggtgagggc	5	7	16	13	5	0	2	0	2	0	0	1	3	0	2	3	3	1	3	3	3	0	1			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr20:865839G>A	ENST00000381922.3	-	4	819	c.717C>T	c.(715-717)cgC>cgT	p.R239R	ANGPT4_ENST00000546022.1_Silent_p.R239R	NM_015985.2	NP_057069.1	Q9Y264	ANGP4_HUMAN	angiopoietin 4	239					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						CGCGCAGGCCGCGCTCGATGT	0.652																																					p.R239R	Pancreas(181;481 2077 3259 31286 49856)	Atlas-SNP	.											.	ANGPT4	77	.	0			c.C717T						PASS	.						22	20	21					20																	865839		2197	4295	6492	SO:0001819	synonymous_variant	51378	exon4			CAGGCCGCGCTCG	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.717C>T	20.37:g.865839G>A		88	0	0		65	9	0.138462	NM_015985	B4E3J9|Q5TFF4|Q9H4Z4	Silent	SNP	ENST00000381922.3	37	CCDS13009.1																																																																																			.	.	none		0.652	ANGPT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077493.1	NM_015985		A	865839	G	A	865839	2	1	2	1	0	0	0	0	0	0	0	1	612	1074	38	1		1	ANGPT4	20	865839	Silent	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10		865839	62159681	76	251											
KCNJ6	3763	hgsc.bcm.edu	37	chr21	39087049	39087049	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaaaaagcagagacgaacccGttgaggttggtaacacaagg	17	5	12	7	2	0	2	0	1	0	1	0	4	0	2	1	3	3	4	1	3	6	3			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr21:39087049G>A	ENST00000609713.1	-	3	1000	c.411C>T	c.(409-411)aaC>aaT	p.N137N	KCNJ6_ENST00000288309.6_Silent_p.N137N|KCNJ6-IT1_ENST00000435001.1_RNA	NM_002240.3	NP_002231.1	P48051	KCNJ6_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 6	137					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)	AGACGAACCCGTTGAGGTTGG	0.468																																					p.N137N	Pancreas(48;379 1118 2936 19024 28214)	Atlas-SNP	.											.	KCNJ6	58	.	0			c.C411T						PASS	.						109	112	111					21																	39087049		1857	4106	5963	SO:0001819	synonymous_variant	3763	exon3			GAACCCGTTGAGG	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.411C>T	21.37:g.39087049G>A		110	0	0		79	9	0.113924	NM_002240	Q3MJ74|Q53WW6	Silent	SNP	ENST00000609713.1	37	CCDS42927.1																																																																																			.	.	none		0.468	KCNJ6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194828.2	NM_002240		A	39087049	G	A	39087049	2	1	2	1	0	0	0	0	0	0	0	1	8064	1136	40	1		1	KCNJ6	21	39087049	Silent	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10		39087049	9042846	77	252											
ADARB1	104	hgsc.bcm.edu	37	chr21	46595934	46595934	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagactgggcccgtgcacgcGcctttgtttgtcatgtctgt	4	13	12	12	3	2	1	1	0	1	1	2	1	2	1	2	1	1	2	2	1	0	2	rs201356458		TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr21:46595934G>A	ENST00000360697.3	+	2	333	c.318G>A	c.(316-318)gcG>gcA	p.A106A	ADARB1_ENST00000539173.1_Silent_p.A106A|ADARB1_ENST00000389863.4_Silent_p.A106A|ADARB1_ENST00000437626.1_Intron|ADARB1_ENST00000348831.4_Silent_p.A106A			P78563	RED1_HUMAN	adenosine deaminase, RNA-specific, B1	106	DRBM 1. {ECO:0000255|PROSITE- ProRule:PRU00266}.				adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|positive regulation of viral genome replication (GO:0045070)|regulation of cell cycle (GO:0051726)|RNA processing (GO:0006396)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA adenosine deaminase activity (GO:0003726)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.A106A(2)		endometrium(4)|kidney(1)|large_intestine(3)|lung(8)|skin(1)	17				Colorectal(79;0.115)		CCGTGCACGCGCCTTTGTTTG	0.557																																					p.A106A		Atlas-SNP	.											ADARB1_ENST00000389863,NS,carcinoma,0,4	ADARB1	81	4	2	Substitution - coding silent(2)	large_intestine(2)	c.G318A						PASS	.						113	118	116					21																	46595934		2203	4300	6503	SO:0001819	synonymous_variant	104	exon4			GCACGCGCCTTTG	U76420	CCDS33589.1, CCDS33590.1, CCDS42970.1	21q22.3	2012-03-22	2010-06-24		ENSG00000197381	ENSG00000197381	3.5.-.-		226	protein-coding gene	gene with protein product	"RED1 homolog (rat)"	601218	"adenosine deaminase, RNA-specific, B1 (homolog of rat RED1)"			9143496, 14759252	Standard	NR_027672		Approved	ADAR2, DRADA2, ADAR2g, DRABA2, RED1, hRED1, ADAR2a-L1, ADAR2a-L2, ADAR2a-L3, ADAR2a, ADAR2b, ADAR2c, ADAR2d	uc002zgy.2	P78563	OTTHUMG00000090295	ENST00000360697.3:c.318G>A	21.37:g.46595934G>A		137	0	0		124	16	0.129032	NM_001160230	A6NFK8|A6NJ84|C3TTQ1|C3TTQ2|C9JUP4|G5E9B4|O00395|O00465|O00691|O00692|P78555|Q4AE79|Q6P0M9|Q8NFD1	Silent	SNP	ENST00000360697.3	37	CCDS33589.1																																																																																			G|0.999;A|0.001	0.001	weak		0.557	ADARB1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206648.2	NM_015833		A	46595934	G	A	46595934	2	1	2	1	0	0	0	0	0	0	0	1	282	1074	38	1		1	ADARB1	21	46595934	Silent	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10	7508885	46595934	1533961	78	253											
PRMT2	3275	hgsc.bcm.edu	37	chr21	48069615	48069615	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgctgcccgagaaggtggaCgtgctggtgtctgagtggat	6	10	18	7	2	1	2	0	1	1	1	1	5	1	4	1	4	3	2	1	4	1	0	rs111614078		TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr21:48069615C>T	ENST00000397637.1	+	6	1572	c.618C>T	c.(616-618)gaC>gaT	p.D206D	PRMT2_ENST00000291705.6_Silent_p.D206D|PRMT2_ENST00000397628.1_Silent_p.D206D|PRMT2_ENST00000458387.2_Silent_p.D206D|PRMT2_ENST00000491389.1_3'UTR|PRMT2_ENST00000334494.4_Silent_p.D206D|PRMT2_ENST00000440086.1_Silent_p.D206D|PRMT2_ENST00000397638.2_Silent_p.D206D|PRMT2_ENST00000355680.3_Silent_p.D206D|PRMT2_ENST00000451211.2_Silent_p.D206D			P55345	ANM2_HUMAN	protein arginine methyltransferase 2	206	Interaction with ESR1.|Interaction with RB1. {ECO:0000250}.|SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				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)		AGAAGGTGGACGTGCTGGTGT	0.667													C|||	1	0.000199681	0.0	0.0	5008	,	,		14573	0.0		0.001	False		,,,				2504	0.0				p.D206D		Atlas-SNP	.											.	PRMT2	48	.	0			c.C618T						PASS	.	C	,,,,	2,4404		0,2,2201	115	76	89		618,618,618,618,618	-5.5	1	21	dbSNP_132	89	6,8594		0,6,4294	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRMT2	NM_001242864.1,NM_001242865.1,NM_001242866.1,NM_001535.3,NM_206962.2	,,,,	0,8,6495	TT,TC,CC		0.0698,0.0454,0.0615	,,,,	206/332,206/285,206/278,206/434,206/434	48069615	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	3275	exon6			GGTGGACGTGCTG	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.618C>T	21.37:g.48069615C>T		128	0	0		164	22	0.134146	NM_001242864	B7U630|B7U631|B7U632|P78350|Q498Y5|Q5U7D4|Q6FHF0|Q99781|Q9BW15|Q9UMC2	Silent	SNP	ENST00000397637.1	37	CCDS13737.1	.	.	.	.	.	.	.	.	.	.	.	10.28	1.307050	0.23821	4.54E-4	6.98E-4	ENSG00000160310	ENST00000455177	.	.	.	4.97	-5.54	0.02544	.	.	.	.	.	T	0.60130	0.2245	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61884	-0.6971	4	.	.	.	-7.4869	12.8764	0.57991	0.0:0.4715:0.0:0.5285	.	.	.	.	M	146	.	.	T	+	2	0	PRMT2	46894043	0.012000	0.17670	0.962000	0.40283	0.964000	0.63967	-2.105000	0.01339	-0.813000	0.04357	-1.021000	0.02439	ACG	C|1.000;T|0.000	0.000	strong		0.667	PRMT2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207401.1	NM_001535		T	48069615	C	T	48069615	2	4	2	1	0	0	0	0	0	0	0	1	12549	535	19	1		1	PRMT2	21	48069615	Silent	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10	1473681	48069615	60280	79	254											
PISD	23761	hgsc.bcm.edu	37	chr22	32015667	32015667	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agctggaaattgaagtccttGggggcctcgaagatgagcac	11	8	14	8	1	0	3	0	2	0	1	2	5	1	4	2	3	2	2	2	3	3	2			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr22:32015667G>A	ENST00000439502.2	-	8	1384	c.1161C>T	c.(1159-1161)ccC>ccT	p.P387P	PISD_ENST00000382151.2_Silent_p.P353P|PISD_ENST00000266095.5_Silent_p.P353P|PISD_ENST00000478893.1_5'Flank|PISD_ENST00000397500.1_3'UTR|PISD_ENST00000336566.4_Silent_p.P386P			Q9UG56	PISD_HUMAN	phosphatidylserine decarboxylase	387					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)	TGAAGTCCTTGGGGGCCTCGA	0.562																																					p.P353P		Atlas-SNP	.											.	PISD	53	.	0			c.C1059T						PASS	.						89	84	86					22																	32015667		2203	4300	6503	SO:0001819	synonymous_variant	23761	exon9			GTCCTTGGGGGCC		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.1161C>T	22.37:g.32015667G>A		91	0	0		90	13	0.144444	NM_014338	B1AKM7|O43207|O95535|Q6IC28|Q96GQ2|Q9UGA9	Silent	SNP	ENST00000439502.2	37		.	.	.	.	.	.	.	.	.	.	G	7.019	0.558312	0.13436	.	.	ENSG00000241878	ENST00000435900	.	.	.	5.29	3.17	0.36434	.	0.000000	0.85682	D	0.000000	T	0.62454	0.2429	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62039	-0.6938	6	0.87932	D	0	-35.6684	6.5047	0.22188	0.1533:0.0:0.7027:0.144	.	.	.	.	L	340	.	ENSP00000414395:P340L	P	-	2	0	PISD	30345667	0.985000	0.35326	1.000000	0.80357	0.659000	0.38960	0.069000	0.14552	0.593000	0.29745	-0.216000	0.12614	CCA	.	.	none		0.562	PISD-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000075106.4			A	32015667	G	A	32015667	2	1	2	1	0	0	0	0	0	0	0	1	11955	1335	47	2		2	PISD	22	32015667	Silent	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10		32015667	19288899	80	255											
SBF1	6305	hgsc.bcm.edu	37	chr22	50887015	50887015	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgctgtgcagccttcaccCggtcccaggtgtccttccag	4	9	12	16	2	1	0	1	0	0	0	4	0	4	0	5	3	2	2	5	3	0	2	rs367954544		TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chr22:50887015C>T	ENST00000390679.3	-	36	5214	c.5030G>A	c.(5029-5031)cGg>cAg	p.R1677Q	SBF1_ENST00000380817.3_Missense_Mutation_p.R1703Q|SBF1_ENST00000348911.6_Missense_Mutation_p.R1678Q			O95248	MTMR5_HUMAN	SET binding factor 1	1677					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)		AGCCTTCACCCGGTCCCAGGT	0.622																																					p.R1703Q		Atlas-SNP	.											.	SBF1	211	.	0			c.G5108A						PASS	.						37	45	42					22																	50887015		2039	4208	6247	SO:0001583	missense	6305	exon37			TTCACCCGGTCCC	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.5030G>A	22.37:g.50887015C>T	ENSP00000375097:p.Arg1677Gln	18	0	0		33	4	0.121212	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Missense_Mutation	SNP	ENST00000390679.3	37		.	.	.	.	.	.	.	.	.	.	C	19.07	3.755100	0.69648	.	.	ENSG00000100241	ENST00000380817;ENST00000348911;ENST00000337034;ENST00000390679	T;T;T	0.11604	2.76;2.76;2.76	4.57	4.57	0.56435	.	0.367621	0.27406	N	0.019512	T	0.07188	0.0182	N	0.14661	0.345	0.35309	D	0.783682	P;P;P	0.52061	0.95;0.948;0.95	P;B;B	0.44422	0.449;0.182;0.382	T	0.21484	-1.0244	10	0.45353	T	0.12	.	7.4391	0.27172	0.0:0.8096:0.0:0.1904	.	1677;1703;224	O95248;O95248-4;A6PVG7	MTMR5_HUMAN;.;.	Q	1703;1678;1713;1677	ENSP00000370196:R1703Q;ENSP00000252027:R1678Q;ENSP00000375097:R1677Q	ENSP00000336522:R1713Q	R	-	2	0	SBF1	49233881	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.230000	0.58632	2.285000	0.76669	0.491000	0.48974	CGG	.	.	weak		0.622	SBF1-201	KNOWN	basic	protein_coding	protein_coding				T	50887015	C	T	50887015	3	4	2	1	0	0	0	0	1	0	0	0	13873	652	23	1	593	1	SBF1	22	50887015	Missense_Mutation	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10	18871348	50887015	417551	81	256											
PHKA1	5255	hgsc.bcm.edu	37	chrX	71855062	71855062	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctggcctgtcatccgccagcGgctacagaggtaggagaggt	8	7	15	11	2	1	2	1	0	0	2	2	3	2	2	3	5	2	2	3	5	2	2			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chrX:71855062G>A	ENST00000373542.4	-	16	1816	c.1657C>T	c.(1657-1659)Cgc>Tgc	p.R553C	PHKA1_ENST00000373539.3_Missense_Mutation_p.R553C|PHKA1_ENST00000373545.3_Missense_Mutation_p.R553C|PHKA1_ENST00000339490.3_Missense_Mutation_p.R553C|PHKA1_ENST00000541944.1_Missense_Mutation_p.R553C	NM_002637.3	NP_002628.2	P46020	KPB1_HUMAN	phosphorylase kinase, alpha 1 (muscle)	553					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)					ATCCGCCAGCGGCTACAGAGG	0.483																																					p.R553C		Atlas-SNP	.											.	PHKA1	129	.	0			c.C1657T						PASS	.						106	84	92					X																	71855062		2203	4300	6503	SO:0001583	missense	5255	exon16			GCCAGCGGCTACA		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.1657C>T	X.37:g.71855062G>A	ENSP00000362643:p.Arg553Cys	49	0	0		55	17	0.309091	NM_001172436	B7ZL05|B7ZL07|Q2M3D7	Missense_Mutation	SNP	ENST00000373542.4	37	CCDS14421.1	.	.	.	.	.	.	.	.	.	.	G	6.750	0.507139	0.12883	.	.	ENSG00000067177	ENST00000373545;ENST00000373542;ENST00000541944;ENST00000339490;ENST00000373539	D;D;D;D;D	0.88124	-2.34;-2.34;-2.34;-2.34;-2.34	4.33	4.33	0.51752	Glycoside hydrolase 15-related (1);	0.000000	0.85682	D	0.000000	D	0.84106	0.5399	N	0.05351	-0.065	0.80722	D	1	D;B;B	0.89917	1.0;0.005;0.021	D;B;B	0.66351	0.943;0.008;0.021	T	0.82908	-0.0224	10	0.23891	T	0.37	-5.103	13.7081	0.62653	0.0:0.0:1.0:0.0	.	553;553;553	B7ZL07;P46020-2;P46020	.;.;KPB1_HUMAN	C	553	ENSP00000362646:R553C;ENSP00000362643:R553C;ENSP00000441251:R553C;ENSP00000342469:R553C;ENSP00000362640:R553C	ENSP00000342469:R553C	R	-	1	0	PHKA1	71771787	1.000000	0.71417	1.000000	0.80357	0.227000	0.25037	2.565000	0.45939	1.890000	0.54733	0.415000	0.27848	CGC	.	.	none		0.483	PHKA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058896.1			A	71855062	G	A	71855062	3	1	2	1	0	0	0	0	1	0	0	0	11852	1116	39	1	2082	1	PHKA1	23	71855062	Missense_Mutation	SNP	G	TCGA-FA-A4BB-01A-11D-A31X-10		71855062	83415498	82	257											
COL4A5	1287	hgsc.bcm.edu	37	chrX	107923951	107923951	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcaatggaatgaaaggagatCctggtctccctggtgttcca	10	11	11	9	0	2	2	1	1	1	1	5	4	4	3	3	4	0	1	3	4	3	1			TCGA-FA-A4BB-01A-11D-A31X-10	TCGA-FA-A4BB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	698b2e1b-0389-4dd2-a8bd-1499e0912f11	c1a1aa05-7d9f-41a8-b682-776d11b54183	g.chrX:107923951C>A	ENST00000361603.2	+	43	4211	c.3967C>A	c.(3967-3969)Cct>Act	p.P1323T	COL4A5_ENST00000328300.6_Missense_Mutation_p.P1329T	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	1323	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						GAAAGGAGATCCTGGTCTCCC	0.428									Alport syndrome with Diffuse Leiomyomatosis																												p.P1323T		Atlas-SNP	.											.	COL4A5	262	.	0			c.C3967A						PASS	.						89	84	86					X																	107923951		2203	4300	6503	SO:0001583	missense	1287	exon43	Familial Cancer Database		GGAGATCCTGGTC	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.3967C>A	X.37:g.107923951C>A	ENSP00000354505:p.Pro1323Thr	109	0	0		102	22	0.215686	NM_000495	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Missense_Mutation	SNP	ENST00000361603.2	37	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	C	13.12	2.142734	0.37825	.	.	ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186	D;D	0.96651	-4.08;-4.08	5.32	4.43	0.53597	.	0.407150	0.28047	N	0.016807	D	0.94023	0.8085	M	0.63428	1.95	0.41880	D	0.990319	B;B	0.14012	0.009;0.004	B;B	0.11329	0.006;0.001	D	0.91307	0.5071	10	0.11794	T	0.64	.	14.5286	0.67909	0.1468:0.8532:0.0:0.0	.	1326;1323	E7EVY4;P29400	.;CO4A5_HUMAN	T	1329;1323;1329	ENSP00000331902:P1329T;ENSP00000354505:P1323T	ENSP00000331902:P1329T	P	+	1	0	COL4A5	107810607	0.883000	0.30277	1.000000	0.80357	0.993000	0.82548	1.094000	0.30951	2.212000	0.71576	0.523000	0.50628	CCT	.	.	none		0.428	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2			A	107923951	C	A	107923951	3	1	2	1	0	0	0	0	1	0	0	0	3696	855	30	4	4148	4	COL4A5	23	107923951	Missense_Mutation	SNP	C	TCGA-FA-A4BB-01A-11D-A31X-10	36068889	107923951	47346609	83	258											
VPS13D	55187	hgsc.bcm.edu	37	chr1	12387807	12387807	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tagcccaggggctgtggcagCgccattgatctctggcgtgg	5	9	16	11	2	1	1	0	1	1	0	2	1	1	1	2	5	2	2	2	5	1	2	rs143572864		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr1:12387807C>T	ENST00000358136.3	+	36	8223	c.8093C>T	c.(8092-8094)gCg>gTg	p.A2698V	VPS13D_ENST00000356315.4_Missense_Mutation_p.A2698V	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)		GCTGTGGCAGCGCCATTGATC	0.502																																					p.A2698V		Atlas-SNP	.											VPS13D,NS,carcinoma,+1,1	VPS13D	316	1	0			c.C8093T						PASS	.	C	VAL/ALA,VAL/ALA	0,4406		0,0,2203	155	149	151		8093,8093	5.5	0.1	1	dbSNP_134	151	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	VPS13D	NM_015378.2,NM_018156.2	64,64	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	2698/4389,2698/4364	12387807	1,13005	2203	4300	6503	SO:0001583	missense	55187	exon36			TGGCAGCGCCATT	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.8093C>T	1.37:g.12387807C>T	ENSP00000350854:p.Ala2698Val	127	0	0		120	51	0.425	NM_015378		Missense_Mutation	SNP	ENST00000358136.3	37	CCDS30588.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.04|13.04	2.119674|2.119674	0.37436|0.37436	0.0|0.0	1.16E-4|1.16E-4	ENSG00000048707|ENSG00000048707	ENST00000356315;ENST00000358136|ENST00000011700	T;T|.	0.46451|.	0.87;0.87|.	5.51|5.51	5.51|5.51	0.81932|0.81932	.|.	0.368669|.	0.31290|.	N|.	0.007902|.	T|T	0.40423|0.40423	0.1116|0.1116	L|L	0.44542|0.44542	1.39|1.39	0.29599|0.29599	N|N	0.847863|0.847863	B;B;B|.	0.33857|.	0.041;0.429;0.303|.	B;B;B|.	0.27380|.	0.003;0.079;0.054|.	T|T	0.36744|0.36744	-0.9735|-0.9735	10|5	0.24483|.	T|.	0.36|.	.|.	7.5184|7.5184	0.27614|0.27614	0.0:0.8005:0.0:0.1995|0.0:0.8005:0.0:0.1995	.|.	605;2698;2698|.	B1AJZ2;Q5THJ4-2;Q5THJ4|.	.;.;VP13D_HUMAN|.	V|C	2698|1521	ENSP00000348666:A2698V;ENSP00000350854:A2698V|.	ENSP00000348666:A2698V|.	A|R	+|+	2|1	0|0	VPS13D|VPS13D	12310394|12310394	0.143000|0.143000	0.22626|0.22626	0.058000|0.058000	0.19502|0.19502	0.510000|0.510000	0.34073|0.34073	3.538000|3.538000	0.53597|0.53597	2.750000|2.750000	0.94351|0.94351	0.655000|0.655000	0.94253|0.94253	GCG|CGC	C|1.000;T|0.000	0.000	weak		0.502	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		T	12387807	C	T	12387807	3	4	3	1	0	0	0	0	1	0	0	0	17207	768	27	1	8231	1	VPS13D	1	12387807	Missense_Mutation	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10		12387807	236862814	1	259											
INTS3	65123	hgsc.bcm.edu	37	chr1	153719461	153719461	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacttagctctggtgagtcGtgatggcatgaatattgtcc	8	13	13	7	1	1	3	0	3	1	0	3	4	2	4	1	3	1	2	1	3	3	3			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr1:153719461G>A	ENST00000318967.2	+	4	915	c.347G>A	c.(346-348)cGt>cAt	p.R116H	INTS3_ENST00000456435.1_5'UTR|RP11-216N14.8_ENST00000453778.1_RNA|INTS3_ENST00000435409.2_Missense_Mutation_p.R116H	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	116					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)			CTGGTGAGTCGTGATGGCATG	0.488																																					p.R116H		Atlas-SNP	.											.	INTS3	83	.	0			c.G347A						PASS	.						109	108	108					1																	153719461		2203	4300	6503	SO:0001583	missense	65123	exon4			TGAGTCGTGATGG	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.347G>A	1.37:g.153719461G>A	ENSP00000318641:p.Arg116His	105	0	0		100	34	0.34	NM_023015	A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Missense_Mutation	SNP	ENST00000318967.2	37	CCDS1052.1	.	.	.	.	.	.	.	.	.	.	G	33	5.246806	0.95305	.	.	ENSG00000143624	ENST00000318967;ENST00000435409	.	.	.	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.70500	0.3231	L	0.59436	1.845	0.80722	D	1	D	0.76494	0.999	D	0.74674	0.984	T	0.72235	-0.4352	9	0.59425	D	0.04	.	15.856	0.78977	0.0:0.0:1.0:0.0	.	116	Q68E01-2	.	H	116	.	ENSP00000318641:R116H	R	+	2	0	INTS3	151986085	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.867000	0.92314	2.608000	0.88229	0.561000	0.74099	CGT	.	.	none		0.488	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015		A	153719461	G	A	153719461	3	1	3	1	0	0	0	0	1	0	0	0	7788	1145	40	1	361	1	INTS3	1	153719461	Missense_Mutation	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10	141331654	153719461	95531160	2	260											
GBA	2629	hgsc.bcm.edu	37	chr1	155207245	155207245	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcacgggcaatgaagtctcGctgatgttcaggggtgaagc	9	9	15	8	2	3	3	2	3	1	0	4	3	3	3	0	3	1	3	0	3	3	1			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr1:155207245G>A	ENST00000327247.5	-	8	1118	c.886C>T	c.(886-888)Cga>Tga	p.R296*	GBA_ENST00000536770.1_Nonsense_Mutation_p.R183*|GBA_ENST00000493842.1_5'Flank|GBA_ENST00000428024.3_Nonsense_Mutation_p.R209*|AL713999.1_ENST00000401290.1_RNA|GBA_ENST00000368373.3_Nonsense_Mutation_p.R296*|GBA_ENST00000427500.3_Nonsense_Mutation_p.R247*	NM_001005741.2|NM_001005742.2	NP_001005741.1|NP_001005742.1	P04062	GLCM_HUMAN	glucosidase, beta, acid	296			R -> Q (in GD; type 2; also found in a patient with Parkinson disease). {ECO:0000269|PubMed:10796875, ECO:0000269|PubMed:19286695, ECO:0000269|PubMed:8790604}.		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)	ATGAAGTCTCGCTGATGTTCA	0.557									Gaucher disease type I																												p.R296X		Atlas-SNP	.											GBA,NS,carcinoma,+1,1	GBA	46	1	0			c.C886T	GRCh37	CM980835	GBA	M		PASS	.						94	77	83					1																	155207245		2203	4300	6503	SO:0001587	stop_gained	2629	exon8	Familial Cancer Database	glucocerebrosidase insufficiency	AGTCTCGCTGATG	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.886C>T	1.37:g.155207245G>A	ENSP00000314508:p.Arg296*	221	0	0		160	49	0.30625	NM_001005742	A8K796|B7Z5G2|B7Z6S1|J3KQG4|J3KQK9|Q16545|Q4VX22|Q6I9R6|Q9UMJ8	Nonsense_Mutation	SNP	ENST00000327247.5	37	CCDS1102.1	.	.	.	.	.	.	.	.	.	.	.	16.64	3.180530	0.57800	.	.	ENSG00000177628	ENST00000427500;ENST00000428024;ENST00000368373;ENST00000327247;ENST00000536770;ENST00000536555;ENST00000402928	.	.	.	3.51	1.41	0.22369	.	0.000000	0.64402	D	0.000011	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.3734	8.0076	0.30334	0.0:0.0:0.5612:0.4388	.	.	.	.	X	247;209;296;296;183;253;281	.	ENSP00000314508:R296X	R	-	1	2	GBA	153473869	1.000000	0.71417	1.000000	0.80357	0.647000	0.38526	2.133000	0.42093	0.216000	0.20781	0.313000	0.20887	CGA	.	.	none		0.557	GBA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087204.1	NM_000157		A	155207245	G	A	155207245	4	1	3	1	0	0	0	0	0	1	0	0	6274	1095	38	1	744	1	GBA	1	155207245	Nonsense_Mutation	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10	1487784	155207245	94043376	3	261											
BTG2	7832	hgsc.bcm.edu	37	chr1	203274847	203274847	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgagcagaggcttaaggtctTcagcggggcgctccaggagg	8	6	17	10	3	2	1	1	0	1	1	3	3	3	2	1	6	2	3	1	6	1	2			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr1:203274847T>G	ENST00000290551.4	+	1	184	c.113T>G	c.(112-114)tTc>tGc	p.F38C	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	38					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			CTTAAGGTCTTCAGCGGGGCG	0.692																																					p.F38C		Atlas-SNP	.											.	BTG2	16	.	0			c.T113G						PASS	.						14	15	15					1																	203274847		2115	4145	6260	SO:0001583	missense	7832	exon1			AGGTCTTCAGCGG		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.113T>G	1.37:g.203274847T>G	ENSP00000290551:p.Phe38Cys	119	0	0		95	38	0.4	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.936706	0.92458	.	.	ENSG00000159388	ENST00000290551	T	0.42513	0.97	4.65	4.65	0.58169	Anti-proliferative protein (3);	0.000000	0.85682	D	0.000000	T	0.73313	0.3571	H	0.95679	3.705	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.81814	-0.0760	10	0.87932	D	0	-41.2615	13.0222	0.58794	0.0:0.0:0.0:1.0	.	38	P78543	BTG2_HUMAN	C	38	ENSP00000290551:F38C	ENSP00000290551:F38C	F	+	2	0	BTG2	201541470	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.827000	0.75303	1.958000	0.56883	0.386000	0.25728	TTC	.	.	none		0.692	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		G	203274847	T	G	203274847	3	3	3	1	0	0	0	0	1	0	0	0	1556	1783	62	5	115	5	BTG2	1	203274847	Missense_Mutation	SNP	T	TCGA-FA-A4XK-01A-11D-A31X-10	48067602	203274847	45975774	4	262											
KCNH1	3756	hgsc.bcm.edu	37	chr1	211256200	211256200	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgctgcaggacacccctgctGcttgtcagtgctcttgtcag	5	12	11	13	0	3	0	2	0	1	0	3	1	3	1	2	1	5	5	2	1	0	2			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr1:211256200G>T	ENST00000271751.4	-	5	507	c.480C>A	c.(478-480)agC>agA	p.S160R	KCNH1_ENST00000367007.4_Missense_Mutation_p.S160R			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	160					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)		CACCCCTGCTGCTTGTCAGTG	0.557																																					p.S160R		Atlas-SNP	.											KCNH1,NS,carcinoma,0,1	KCNH1	199	1	0			c.C480A						PASS	.						95	77	84					1																	211256200		2203	4300	6503	SO:0001583	missense	3756	exon5			CCTGCTGCTTGTC	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.480C>A	1.37:g.211256200G>T	ENSP00000271751:p.Ser160Arg	49	0	0		43	18	0.418605	NM_172362	B1AQ26|O76035|Q14CL3	Missense_Mutation	SNP	ENST00000271751.4	37	CCDS1496.1	.	.	.	.	.	.	.	.	.	.	G	9.983	1.228687	0.22542	.	.	ENSG00000143473	ENST00000271751;ENST00000367007	D;D	0.98617	-5.01;-5.03	5.1	4.18	0.49190	.	0.075279	0.85682	D	0.000000	D	0.91469	0.7307	N	0.01009	-1.055	0.80722	D	1	B;B	0.09022	0.001;0.002	B;B	0.09377	0.004;0.004	D	0.88309	0.2955	10	0.02654	T	1	.	14.3963	0.67013	0.0:0.0:0.8514:0.1486	.	160;160	Q14CL3;O95259	.;KCNH1_HUMAN	R	160	ENSP00000271751:S160R;ENSP00000355974:S160R	ENSP00000271751:S160R	S	-	3	2	KCNH1	209322823	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.252000	0.72447	1.275000	0.44379	0.655000	0.94253	AGC	.	.	none		0.557	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238		T	211256200	G	T	211256200	3	4	3	1	0	0	0	0	1	0	0	0	8040	1310	46	4	2517	4	KCNH1	1	211256200	Missense_Mutation	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10	7981353	211256200	37994421	5	263											
TPO	7173	hgsc.bcm.edu	37	chr2	1459995	1459995	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcaccagcaaagctgccttcGggggaggggctgactgccag	8	5	16	12	1	0	1	0	1	0	0	1	2	0	2	3	4	4	4	3	4	1	1	rs371917329		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr2:1459995G>A	ENST00000345913.4	+	7	851	c.760G>A	c.(760-762)Ggg>Agg	p.G254R	TPO_ENST00000329066.4_Missense_Mutation_p.G254R|TPO_ENST00000497517.2_Intron|TPO_ENST00000349624.3_Missense_Mutation_p.G254R|TPO_ENST00000382201.3_Missense_Mutation_p.G254R|TPO_ENST00000346956.3_Missense_Mutation_p.G254R|TPO_ENST00000382198.1_Missense_Mutation_p.G254R|TPO_ENST00000337415.3_Missense_Mutation_p.G254R	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	254					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)	AGCTGCCTTCGGGGGAGGGGC	0.473													G|||	1	0.000199681	0.0008	0.0	5008	,	,		21539	0.0		0.0	False		,,,				2504	0.0				p.G254R		Atlas-SNP	.											TPO,NS,carcinoma,-2,1	TPO	224	1	0			c.G760A						PASS	.	G	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	0,4406		0,0,2203	80	71	74		760,760,760,760,760,760	-8.7	0	2		74	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense	TPO	NM_000547.5,NM_001206744.1,NM_001206745.1,NM_175719.3,NM_175721.3,NM_175722.3	125,125,125,125,125,125	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign,benign,benign,benign	254/934,254/934,254/877,254/877,254/890,254/761	1459995	1,13005	2203	4300	6503	SO:0001583	missense	7173	exon7			GCCTTCGGGGGAG		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.760G>A	2.37:g.1459995G>A	ENSP00000318820:p.Gly254Arg	129	0	0		96	36	0.375	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	37	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	G	0.071	-1.202813	0.01581	0.0	1.16E-4	ENSG00000115705	ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000329066;ENST00000382201;ENST00000382198;ENST00000422464	T;T;T;T;T;T;T;T	0.68025	-0.26;-0.27;-0.23;0.0;-0.27;-0.2;0.0;-0.3	4.81	-8.66	0.00866	.	1.631860	0.02746	N	0.116912	T	0.40473	0.1118	N	0.21142	0.635	0.09310	N	1	B;B;B;B	0.19073	0.011;0.008;0.027;0.033	B;B;B;B	0.14578	0.006;0.002;0.006;0.011	T	0.26950	-1.0088	10	0.15952	T	0.53	-0.1794	0.5679	0.00690	0.2306:0.1941:0.2969:0.2783	.	254;254;254;254	P07202-4;P07202-5;P07202-2;P07202	.;.;.;PERT_HUMAN	R	254;254;254;254;254;254;254;183	ENSP00000337263:G254R;ENSP00000318820:G254R;ENSP00000263886:G254R;ENSP00000332044:G254R;ENSP00000329869:G254R;ENSP00000371636:G254R;ENSP00000371633:G254R;ENSP00000405788:G183R	ENSP00000329869:G254R	G	+	1	0	TPO	1439002	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.061000	0.03472	-1.603000	0.01597	-1.571000	0.00872	GGG	.	.	weak		0.473	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		A	1459995	G	A	1459995	3	1	3	1	0	0	0	0	1	0	0	0	16425	1116	39	1	782	1	TPO	2	1459995	Missense_Mutation	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10		1459995	241739378	6	264											
PLEK	5341	hgsc.bcm.edu	37	chr2	68592512	68592512	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaagcggatcagagagggctAccttgtgaagaaggtgagcg	13	6	16	6	2	1	4	1	2	0	2	1	6	1	5	1	3	3	1	1	3	4	2			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr2:68592512A>T	ENST00000234313.7	+	1	208	c.29A>T	c.(28-30)tAc>tTc	p.Y10F	AC015969.3_ENST00000366218.2_RNA	NM_002664.2	NP_002655.2	P08567	PLEK_HUMAN	pleckstrin	10	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cell projection organization (GO:0030030)|cortical actin cytoskeleton organization (GO:0030866)|hematopoietic progenitor cell differentiation (GO:0002244)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of calcium-mediated signaling (GO:0050849)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of inositol phosphate biosynthetic process (GO:0010920)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-inhibiting G-protein coupled receptor signaling pathway (GO:0030845)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of inositol-polyphosphate 5-phosphatase activity (GO:0010925)|positive regulation of integrin activation (GO:0033625)|positive regulation of platelet activation (GO:0010572)|protein kinase C signaling (GO:0070528)|protein secretion by platelet (GO:0070560)|regulation of cell diameter (GO:0060305)|ruffle organization (GO:0031529)|thrombin receptor signaling pathway (GO:0070493)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|membrane (GO:0016020)|ruffle membrane (GO:0032587)	phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)			autonomic_ganglia(1)|endometrium(3)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	24		Ovarian(717;0.0129)		STAD - Stomach adenocarcinoma(1183;0.00159)|READ - Rectum adenocarcinoma(193;0.0419)		AGAGAGGGCTACCTTGTGAAG	0.577																																					p.Y10F		Atlas-SNP	.											.	PLEK	64	.	0			c.A29T						PASS	.						136	114	122					2																	68592512		2203	4300	6503	SO:0001583	missense	5341	exon1			AGGGCTACCTTGT	X07743	CCDS1887.1	2p13.3	2013-01-10			ENSG00000115956	ENSG00000115956		"Pleckstrin homology (PH) domain containing"	9070	protein-coding gene	gene with protein product		173570				2897630, 12054651	Standard	NM_002664		Approved	P47	uc002sen.4	P08567	OTTHUMG00000129562	ENST00000234313.7:c.29A>T	2.37:g.68592512A>T	ENSP00000234313:p.Tyr10Phe	77	0	0		91	25	0.274725	NM_002664	B2R9E8|Q53SU8|Q6FGM8|Q6FGQ1|Q8WV81	Missense_Mutation	SNP	ENST00000234313.7	37	CCDS1887.1	.	.	.	.	.	.	.	.	.	.	A	10.81	1.454506	0.26161	.	.	ENSG00000115956	ENST00000234313	T	0.14640	2.49	5.85	5.85	0.93711	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.14056	0.0340	L	0.52573	1.65	0.58432	D	0.999999	B;B	0.02656	0.0;0.0	B;B	0.12837	0.008;0.003	T	0.08046	-1.0741	10	0.19590	T	0.45	.	12.6189	0.56592	1.0:0.0:0.0:0.0	.	28;10	Q59GZ2;P08567	.;PLEK_HUMAN	F	10	ENSP00000234313:Y10F	ENSP00000234313:Y10F	Y	+	2	0	PLEK	68446016	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.687000	0.61708	2.234000	0.73211	0.460000	0.39030	TAC	.	.	none		0.577	PLEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251755.1	NM_002664		T	68592512	A	T	68592512	3	4	3	1	0	0	0	0	1	0	0	0	12062	391	14	5	31	5	PLEK	2	68592512	Missense_Mutation	SNP	A	TCGA-FA-A4XK-01A-11D-A31X-10	67132517	68592512	174606861	7	265											
SMYD1	150572	hgsc.bcm.edu	37	chr2	88387391	88387391	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcccacaggctggcggcgCgcatcatgtggcgggtggag	5	7	17	12	4	1	0	1	0	0	0	2	1	2	1	1	6	0	2	1	6	0	1			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr2:88387391C>T	ENST00000419482.2	+	3	410	c.325C>T	c.(325-327)Cgc>Tgc	p.R109C	SMYD1_ENST00000468008.1_3'UTR|SMYD1_ENST00000444564.2_Missense_Mutation_p.R109C|SMYD1_ENST00000438570.1_Intron	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	109	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				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						GCTGGCGGCGCGCATCATGTG	0.607																																					p.R109C		Atlas-SNP	.											.	SMYD1	95	.	0			c.C325T						PASS	.						28	25	26					2																	88387391		2197	4297	6494	SO:0001583	missense	150572	exon3			GCGGCGCGCATCA	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.325C>T	2.37:g.88387391C>T	ENSP00000393453:p.Arg109Cys	148	0	0		142	48	0.338028	NM_198274	A0AV30|A6NE13	Missense_Mutation	SNP	ENST00000419482.2	37	CCDS33240.1	.	.	.	.	.	.	.	.	.	.	C	18.98	3.737350	0.69304	.	.	ENSG00000115593	ENST00000419482;ENST00000444564	T;T	0.36520	1.25;1.27	4.82	3.88	0.44766	SET domain (2);	0.000000	0.85682	D	0.000000	T	0.58878	0.2153	M	0.77406	2.37	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.64007	-0.6508	10	0.87932	D	0	-22.6609	12.1981	0.54309	0.284:0.716:0.0:0.0	.	109	Q8NB12	SMYD1_HUMAN	C	109	ENSP00000393453:R109C;ENSP00000407888:R109C	ENSP00000393453:R109C	R	+	1	0	SMYD1	88168506	0.988000	0.35896	0.938000	0.37757	0.765000	0.43378	2.757000	0.47557	2.363000	0.80096	0.561000	0.74099	CGC	.	.	none		0.607	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915		T	88387391	C	T	88387391	3	4	3	1	0	0	0	0	1	0	0	0	14836	768	27	1	335	1	SMYD1	2	88387391	Missense_Mutation	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10	19794879	88387391	154811982	8	266											
ANKRD23	200539	hgsc.bcm.edu	37	chr2	97507820	97507821	+	Frame_Shift_Ins	INS	-	-	G																															accaggggctcaggtttcctINSgggggggactctgtgtctca																										TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr2:97507820_97507821insG	ENST00000318357.4	-	3	317_318	c.276_277insC	c.(274-279)cccaggfs	p.R93fs	ANKRD23_ENST00000331001.2_Frame_Shift_Ins_p.R93fs|ANKRD23_ENST00000476975.1_5'UTR|ANKRD23_ENST00000418232.1_Frame_Shift_Ins_p.R93fs	NM_144994.7	NP_659431.5	Q86SG2	ANR23_HUMAN	ankyrin repeat domain 23	93					fatty acid metabolic process (GO:0006631)|response to mechanical stimulus (GO:0009612)	I band (GO:0031674)|intercalated disc (GO:0014704)|nucleus (GO:0005634)	titin binding (GO:0031432)			endometrium(2)|kidney(1)|lung(4)|ovary(1)|prostate(1)	9						TCAGGTTTCCTGGGGGGGACTC	0.53																																					p.R93fs		Pindel,Atlas-Indel	.											.	ANKRD23	28	.	0			c.277_278insC						PASS	.			3,4263		0,3,2130						4.5	1			89	6,8248		0,6,4121	no	frameshift	ANKRD23	NM_144994.7		0,9,6251	A1A1,A1R,RR		0.0727,0.0703,0.0719				9,12511				SO:0001589	frameshift_variant	200539	exon3			.		CCDS2027.1	2q11.2	2013-01-10			ENSG00000163126	ENSG00000163126		"Ankyrin repeat domain containing"	24470	protein-coding gene	gene with protein product	"diabetes related ankyrin repeat protein"	610736				12456686	Standard	NM_144994		Approved	DARP, FLJ32449, MARP3	uc002sxa.3	Q86SG2	OTTHUMG00000130534	ENST00000318357.4:c.277dupC	2.37:g.97507827_97507827dupG	ENSP00000321679:p.Arg93fs	0	0	.		20	20	1	NM_144994	Q711K7|Q8NAJ7	Frame_Shift_Ins	INS	ENST00000318357.4	37	CCDS2027.1																																																																																			.	.	none		0.53	ANKRD23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252956.1	NM_144994		G	97507821	-	G	97507820	7	5	3	1	0	1	1	0	0	0	0	0	652	1579	55	0	668	0	ANKRD23	2	97507820	Frame_Shift_Ins	INS	-	TCGA-FA-A4XK-01A-11D-A31X-10	9120429	97507820	145691553	9	267											
HOXD11	3237	hgsc.bcm.edu	37	chr2	176972104	176972104	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atgaacgactttgacgagtgCggccagagcgcagccagcat	11	6	13	11	4	0	3	0	2	0	1	0	5	0	3	2	1	5	2	2	1	1	1			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr2:176972104C>T	ENST00000249504.5	+	1	91	c.21C>T	c.(19-21)tgC>tgT	p.C7C	HOXD11_ENST00000498438.1_Intron|AC009336.1_ENST00000401374.2_RNA	NM_021192.2	NP_067015.2	P31277	HXD11_HUMAN	homeobox D11	7					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 skeletal joint morphogenesis (GO:0060272)|metanephros development (GO:0001656)|organ induction (GO:0001759)|positive regulation of cell development (GO:0010720)|positive regulation of chondrocyte differentiation (GO:0032332)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|single fertilization (GO:0007338)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)							OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0521)|READ - Rectum adenocarcinoma(9;0.0678)		TTGACGAGTGCGGCCAGAGCG	0.642			T	NUP98	AML																																p.C7C		Atlas-SNP	.		Dom	yes		2	2q31-q32	3237	homeo box D11		L	.	HOXD11	26	.	0			c.C21T						PASS	.						22	19	20					2																	176972104		2190	4275	6465	SO:0001819	synonymous_variant	3237	exon1			CGAGTGCGGCCAG		CCDS2265.1	2q31.1	2011-06-20	2005-12-22		ENSG00000128713	ENSG00000128713		"Homeoboxes / ANTP class : HOXL subclass"	5134	protein-coding gene	gene with protein product		142986	"homeo box D11"	HOX4, HOX4F		1973146, 1358459	Standard	NM_021192		Approved		uc002uki.3	P31277	OTTHUMG00000132510	ENST00000249504.5:c.21C>T	2.37:g.176972104C>T		100	0	0		124	34	0.274194	NM_021192	A6NIS4|Q9NS02	Silent	SNP	ENST00000249504.5	37	CCDS2265.1																																																																																			.	.	none		0.642	HOXD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359250.2			T	176972104	C	T	176972104	2	4	3	1	0	0	0	0	0	0	0	1	7329	776	27	1		1	HOXD11	2	176972104	Silent	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10	79464284	176972104	66227269	10	268											
TTN	7273	hgsc.bcm.edu	37	chr2	179400129	179400129	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctcgggcctgtcctacaCggagccatctttctgcagta	6	13	9	13	2	3	0	0	0	3	0	5	1	4	1	3	2	3	2	3	2	2	4	rs192391568	byFrequency	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr2:179400129C>T	ENST00000591111.1	-	308	96514	c.96290G>A	c.(96289-96291)cGt>cAt	p.R32097H	TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.R33738H|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R24673H|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R31170H|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R24865H|TTN_ENST00000359218.5_Missense_Mutation_p.R24798H|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000589842.1_RNA			Q8WZ42	TITIN_HUMAN	titin	32097	Fibronectin type-III 132. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> C. {ECO:0000269|PubMed:17344846}.		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)			CTGTCCTACACGGAGCCATCT	0.433													C|||	2	0.000399361	0.0008	0.0014	5008	,	,		23700	0.0		0.0	False		,,,				2504	0.0				p.R33738H		Atlas-SNP	.											.	TTN	18412	.	0			c.G101213A						PASS	.						98	96	97					2																	179400129		1951	4152	6103	SO:0001583	missense	7273	exon358			CCTACACGGAGCC	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.96290G>A	2.37:g.179400129C>T	ENSP00000465570:p.Arg32097His	67	0	0		69	38	0.550725	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	37		1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	18.13	3.556169	0.65425	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56103	0.48;0.48;0.48;0.48	5.52	5.52	0.82312	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.68165	0.2971	L	0.45285	1.41	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	0.69405	-0.5154	9	0.87932	D	0	.	19.8108	0.96545	0.0:1.0:0.0:0.0	.	24673;24798;24865;32097	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	H	31170;24673;24865;24798;24670	ENSP00000343764:R31170H;ENSP00000434586:R24673H;ENSP00000340554:R24865H;ENSP00000352154:R24798H	ENSP00000340554:R24865H	R	-	2	0	TTN	179108375	1.000000	0.71417	0.971000	0.41717	0.961000	0.63080	7.776000	0.85560	2.754000	0.94517	0.557000	0.71058	CGT	C|1.000;T|0.000	0.000	strong		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179400129	C	T	179400129	3	4	3	1	0	0	0	0	1	0	0	0	16750	536	19	1	6786	1	TTN	2	179400129	Missense_Mutation	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10	2428025	179400129	63799244	11	269											
MFSD6	54842	hgsc.bcm.edu	37	chr2	191300917	191300917	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctattcctgaggaggaaatAgactggatagagaaacattg	15	9	12	5	0	0	3	0	1	0	2	1	7	1	6	1	3	1	1	1	3	5	5			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr2:191300917A>C	ENST00000392328.1	+	3	486	c.162A>C	c.(160-162)atA>atC	p.I54I	MFSD6_ENST00000281416.7_Silent_p.I54I	NM_017694.3	NP_060164.3	Q6ZSS7	MFSD6_HUMAN	major facilitator superfamily domain containing 6	54					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						AGGAGGAAATAGACTGGATAG	0.403																																					p.I54I		Atlas-SNP	.											.	MFSD6	58	.	0			c.A162C						PASS	.						108	110	109					2																	191300917		2203	4300	6503	SO:0001819	synonymous_variant	54842	exon3			GGAAATAGACTGG		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.162A>C	2.37:g.191300917A>C		168	0	0		188	84	0.446809	NM_017694	D3KSZ4|Q86TH2|Q9NXM3	Silent	SNP	ENST00000392328.1	37	CCDS2306.1																																																																																			.	.	none		0.403	MFSD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255931.1			C	191300917	A	C	191300917	2	2	3	1	0	0	0	0	0	0	0	1	9544	410	15	5		5	MFSD6	2	191300917	Silent	SNP	A	TCGA-FA-A4XK-01A-11D-A31X-10	11900788	191300917	51898456	12	270											
ZCWPW2	152098	hgsc.bcm.edu	37	chr3	28476649	28476649	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttaaagggaaatatgtaacTtatgacccggatggaaatgt	15	12	10	4	1	0	1	0	1	0	0	0	4	0	4	1	3	1	1	1	3	7	5			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr3:28476649T>G	ENST00000383768.2	+	4	569	c.381T>G	c.(379-381)acT>acG	p.T127T	ZCWPW2_ENST00000421010.1_Silent_p.T127T			Q504Y3	ZCPW2_HUMAN	zinc finger, CW type with PWWP domain 2	127	PWWP. {ECO:0000255|PROSITE- ProRule:PRU00162}.						zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(6)|ovary(2)	17						AATATGTAACTTATGACCCGG	0.358																																					p.T127T		Atlas-SNP	.											.	ZCWPW2	49	.	0			c.T381G						PASS	.						96	97	97					3																	28476649		2203	4300	6503	SO:0001819	synonymous_variant	152098	exon3			TGTAACTTATGAC	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.381T>G	3.37:g.28476649T>G		364	1	0.00274725		363	129	0.355372	NM_001040432		Silent	SNP	ENST00000383768.2	37	CCDS33723.1	.	.	.	.	.	.	.	.	.	.	T	5.612	0.297711	0.10622	.	.	ENSG00000206559	ENST00000428875	.	.	.	6.06	1.1	0.20463	.	.	.	.	.	T	0.50565	0.1623	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33394	-0.9870	4	.	.	.	1.5734	4.335	0.11081	0.1458:0.5228:0.0:0.3314	.	.	.	.	V	111	.	.	L	+	1	2	ZCWPW2	28451653	0.463000	0.25799	0.677000	0.29947	0.479000	0.33129	-0.481000	0.06552	-0.073000	0.12842	-0.859000	0.03014	TTA	.	.	none		0.358	ZCWPW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341318.1	XM_087384		G	28476649	T	G	28476649	2	3	3	1	0	0	0	0	0	0	0	1	17613	1596	56	5		5	ZCWPW2	3	28476649	Silent	SNP	T	TCGA-FA-A4XK-01A-11D-A31X-10		28476649	169545781	13	271											
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113376116	113376116	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgttgttgttgctgttgctgCtgctgctgctgctgctgctg	0	18	14	9	0	0	0	0	0	0	0	0	0	0	0	0	0	9	13	0	0	0	4	rs112313093|rs59601191		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr3:113376116C>T	ENST00000478658.1	-	5	4430	c.4413G>A	c.(4411-4413)caG>caA	p.Q1471Q	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Silent_p.Q1471Q			Q68DE3	K2018_HUMAN	KIAA2018	1471	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						gctgttgctgctgctgctgct	0.498																																					p.Q1471Q		Atlas-SNP	.											.	KIAA2018	180	.	0			c.G4413A						PASS	.						63	72	69					3																	113376116		2187	4278	6465	SO:0001819	synonymous_variant	205717	exon7			TTGCTGCTGCTGC	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.4413G>A	3.37:g.113376116C>T		36	0	0		28	10	0.357143	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	37	CCDS43133.1																																																																																			.	.	none		0.498	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		T	113376116	C	T	113376116	2	4	3	1	0	0	0	0	0	0	0	1	8277	796	28	2		2	KIAA2018	3	113376116	Silent	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10	84899467	113376116	84646314	14	272											
GPR156	165829	hgsc.bcm.edu	37	chr3	119892302	119892302	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttggttttcctcttcaaatgCcttccattgcttcagctgtt	5	19	6	11	0	3	0	2	0	1	0	5	0	5	0	3	1	3	4	3	1	1	8			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr3:119892302C>A	ENST00000464295.1	-	9	1394	c.949G>T	c.(949-951)Gca>Tca	p.A317S	GPR156_ENST00000315843.3_Missense_Mutation_p.A317S|GPR156_ENST00000461057.1_Missense_Mutation_p.A313S			Q8NFN8	GP156_HUMAN	G protein-coupled receptor 156	317						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled GABA receptor activity (GO:0004965)	p.A317S(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|prostate(1)|skin(1)	32				GBM - Glioblastoma multiforme(114;0.19)		TCTTCAAATGCCTTCCATTGC	0.398																																					p.A317S		Atlas-SNP	.											GPR156,rectum,carcinoma,0,1	GPR156	85	1	1	Substitution - Missense(1)	large_intestine(1)	c.G949T						PASS	.						203	183	189					3																	119892302		2203	4300	6503	SO:0001583	missense	165829	exon8			CAAATGCCTTCCA	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.949G>T	3.37:g.119892302C>A	ENSP00000417261:p.Ala317Ser	119	0	0		109	36	0.330275	NM_153002	B7ZL66|E9PFZ4|Q14CM1|Q86SN6	Missense_Mutation	SNP	ENST00000464295.1	37	CCDS2997.1	.	.	.	.	.	.	.	.	.	.	C	12.20	1.866726	0.32977	.	.	ENSG00000175697	ENST00000464295;ENST00000315843;ENST00000461057	T;T;T	0.23348	1.91;1.91;1.91	5.48	3.58	0.41010	.	0.317821	0.27792	N	0.017826	T	0.23806	0.0576	M	0.67953	2.075	0.27786	N	0.942993	P;P	0.35077	0.483;0.483	B;B	0.30943	0.122;0.122	T	0.13019	-1.0525	9	.	.	.	-5.8605	8.9517	0.35792	0.0:0.6408:0.2041:0.1551	.	313;317	E9PFZ4;Q8NFN8	.;GP156_HUMAN	S	317;317;313	ENSP00000417261:A317S;ENSP00000324553:A317S;ENSP00000418758:A313S	.	A	-	1	0	GPR156	121374992	0.999000	0.42202	1.000000	0.80357	0.996000	0.88848	0.641000	0.24720	1.324000	0.45282	0.462000	0.41574	GCA	.	.	none		0.398	GPR156-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355139.1	NM_153002		A	119892302	C	A	119892302	3	1	3	1	0	0	0	0	1	0	0	0	6669	739	26	4	1503	4	GPR156	3	119892302	Missense_Mutation	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10	6516186	119892302	78130128	15	273											
PARP9	83666	hgsc.bcm.edu	37	chr3	122247336	122247347	+	In_Frame_Del	DEL	TAGCCTGCATGC	TAGCCTGCATGC	-																															tgtccacaaatactgaggtaTagcctgcatgccactaaaaa																										TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	TAGCCTGCATGC	TAGCCTGCATGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr3:122247336_122247347delTAGCCTGCATGC	ENST00000360356.2	-	11	2656_2667	c.2429_2440delGCATGCAGGCTA	c.(2428-2442)ggcatgcaggctata>gta	p.810_814GMQAI>V	PARP9_ENST00000492382.1_In_Frame_Del_p.355_359GMQAI>V|PARP9_ENST00000477522.2_In_Frame_Del_p.775_779GMQAI>V|PARP9_ENST00000471785.1_In_Frame_Del_p.775_779GMQAI>V	NM_001146102.1|NM_031458.2	NP_001139574.1|NP_113646.2	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	810	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				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)		TACTGAGGTATAGCCTGCATGCCACTAAAAAT	0.453																																					p.810_814del		Pindel	.											.	PARP9	72	.	0			c.2430_2441del						PASS	.																																			SO:0001651	inframe_deletion	83666	exon11			.	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.2429_2440delGCATGCAGGCTA	3.37:g.122247336_122247347delTAGCCTGCATGC	ENSP00000353512:p.Gly810_Ile814delinsVal	0	0	.		26	26	1	NM_001146102	A8KA94|B2R8S9|E9PFM7|Q8TCP3|Q9BZL8|Q9BZL9	In_Frame_Del	DEL	ENST00000360356.2	37	CCDS3014.1																																																																																			.	.	none		0.453	PARP9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355957.1	NM_031458		-	122247347	TAGCCTGCATGC	-	122247336	7	5	3	1	0	1	0	1	0	0	0	0	11475	1406	49	0	128	0	PARP9	3	122247336	In_Frame_Del	DEL	TAGCCTGCATGC	TCGA-FA-A4XK-01A-11D-A31X-10	2355034	122247336	75775094	16	274	7	3									
PARP9	83666	hgsc.bcm.edu	37	chr3	122247338	122247343	+	In_Frame_Del	DEL	GCCTGC	GCCTGC	-																															tccacaaatactgaggtataGcctgcatgccactaaaaata																										TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	GCCTGC	GCCTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr3:122247338_122247343delGCCTGC	ENST00000360356.2	-	11	2660_2665	c.2433_2438delGCAGGC	c.(2431-2439)atgcaggct>att	p.811_813MQA>I	PARP9_ENST00000492382.1_In_Frame_Del_p.356_358MQA>I|PARP9_ENST00000477522.2_In_Frame_Del_p.776_778MQA>I|PARP9_ENST00000471785.1_In_Frame_Del_p.776_778MQA>I	NM_001146102.1|NM_031458.2	NP_001139574.1|NP_113646.2	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	811	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				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)		CTGAGGTATAGCCTGCATGCCACTAA	0.466																																					p.812_813del		Atlas-Indel	.											.	PARP9	72	.	0			c.2434_2439del						PASS	.																																			SO:0001651	inframe_deletion	83666	exon11			.	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.2433_2438delGCAGGC	3.37:g.122247338_122247343delGCCTGC	ENSP00000353512:p.Met811_Ala813delinsIle	149	0	0		115	26	0.226087	NM_001146102	A8KA94|B2R8S9|E9PFM7|Q8TCP3|Q9BZL8|Q9BZL9	In_Frame_Del	DEL	ENST00000360356.2	37	CCDS3014.1																																																																																			.	.	none		0.466	PARP9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355957.1	NM_031458		-	122247343	GCCTGC	-	122247338	7	5	3	1	0	1	0	1	0	0	0	0	11475	971	34	0	130	0	PARP9	3	122247338	In_Frame_Del	DEL	GCCTGC	TCGA-FA-A4XK-01A-11D-A31X-10	2	122247338	75775092	17	275	7	3									
PARP9	83666	hgsc.bcm.edu	37	chr3	122247346	122247346	+	Frame_Shift_Del	DEL	G	G	-																															tactgaggtatagcctgcatGccactaaaaataacaaaggt																										TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr3:122247346delG	ENST00000360356.2	-	11	2657	c.2430delC	c.(2428-2430)ggcfs	p.G810fs	PARP9_ENST00000492382.1_Frame_Shift_Del_p.G355fs|PARP9_ENST00000477522.2_Frame_Shift_Del_p.G775fs|PARP9_ENST00000471785.1_Frame_Shift_Del_p.G775fs	NM_001146102.1|NM_031458.2	NP_001139574.1|NP_113646.2	Q8IXQ6	PARP9_HUMAN	poly (ADP-ribose) polymerase family, member 9	810	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				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)		TAGCCTGCATGCCACTAAAAA	0.448																																					p.M811fs		Atlas-Indel	.											.	PARP9	72	.	0			c.2431delA						PASS	.						125	111	116					3																	122247346		2203	4300	6503	SO:0001589	frameshift_variant	83666	exon11			.	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.2430delC	3.37:g.122247346delG	ENSP00000353512:p.Gly810fs	144	0	0		120	28	0.233333	NM_001146102	A8KA94|B2R8S9|E9PFM7|Q8TCP3|Q9BZL8|Q9BZL9	Frame_Shift_Del	DEL	ENST00000360356.2	37	CCDS3014.1																																																																																			.	.	none		0.448	PARP9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355957.1	NM_031458		-	122247346	G	-	122247346	7	5	3	1	0	1	0	1	0	0	0	0	11475	1306	46	0	138	0	PARP9	3	122247346	Frame_Shift_Del	DEL	G	TCGA-FA-A4XK-01A-11D-A31X-10	8	122247346	75775084	18	276	7	3									
PRR23C	389152	hgsc.bcm.edu	37	chr3	138762875	138762875	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ttgggggccagagcacagggCcctcggatggggccctcccg	5	5	17	14	2	0	1	0	0	0	1	2	2	1	2	4	6	1	1	4	6	0	1			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr3:138762875C>T	ENST00000413199.1	-	1	859	c.588G>A	c.(586-588)ggG>ggA	p.G196G	MRPS22_ENST00000495075.1_Intron|PRR23C_ENST00000502927.2_Silent_p.G196G	NM_001134657.1	NP_001128129.1	Q6ZRP0	PR23C_HUMAN	proline rich 23C	196	Pro-rich.									breast(2)|lung(7)|skin(2)	11						GAGCACAGGGCCCTCGGATGG	0.652																																					p.G196G		Atlas-SNP	.											.	PRR23C	31	.	0			c.G588A						PASS	.						37	44	42					3																	138762875		692	1591	2283	SO:0001819	synonymous_variant	389152	exon1			ACAGGGCCCTCGG		CCDS46924.1	3q22.3	2014-06-03				ENSG00000233701			37173	protein-coding gene	gene with protein product							Standard	NM_001134657		Approved	FLJ46210	uc011bmt.1	Q6ZRP0		ENST00000413199.1:c.588G>A	3.37:g.138762875C>T		111	0	0		94	39	0.414894	NM_001134657		Silent	SNP	ENST00000413199.1	37	CCDS46924.1																																																																																			.	.	none		0.652	PRR23C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361502.1	NM_001134657		T	138762875	C	T	138762875	2	4	3	1	0	0	0	0	0	0	0	1	12608	726	26	2		2	PRR23C	3	138762875	Silent	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10	16515529	138762875	59259555	19	277											
SPATA18	132671	hgsc.bcm.edu	37	chr4	52938302	52938302	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atagctgttctgtctgctgaGaaaagtgcactccaaggaag	12	10	11	8	0	2	1	0	1	2	1	3	3	3	2	1	1	3	4	1	1	5	2			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr4:52938302G>T	ENST00000295213.4	+	6	1112	c.738G>T	c.(736-738)gaG>gaT	p.E246D	SPATA18_ENST00000419395.2_Missense_Mutation_p.E214D|SPATA18_ENST00000506829.1_3'UTR	NM_145263.2	NP_660306.1	Q8TC71	MIEAP_HUMAN	spermatogenesis associated 18	246					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)		p.E246E(1)		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)			TGTCTGCTGAGAAAAGTGCAC	0.453																																					p.E246D		Atlas-SNP	.											SPATA18_ENST00000295213,colon,carcinoma,+2,5	SPATA18	222	5	1	Substitution - coding silent(1)	ovary(1)	c.G738T						PASS	.						79	75	76					4																	52938302		2203	4300	6503	SO:0001583	missense	132671	exon6			TGCTGAGAAAAGT	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.738G>T	4.37:g.52938302G>T	ENSP00000295213:p.Glu246Asp	203	0	0		203	78	0.384236	NM_145263	B4E2R0|E5RLK1|Q8IY48|Q8N7D7	Missense_Mutation	SNP	ENST00000295213.4	37	CCDS3489.1	.	.	.	.	.	.	.	.	.	.	G	10.99	1.507772	0.27036	.	.	ENSG00000163071	ENST00000295213;ENST00000419395	T;D	0.88354	0.43;-2.37	4.97	-1.64	0.08318	.	0.047408	0.85682	D	0.000000	D	0.92499	0.7618	M	0.78049	2.395	0.43080	D	0.994736	D;D;D	0.76494	0.999;0.999;0.998	D;D;D	0.80764	0.994;0.994;0.99	D	0.90626	0.4563	10	0.72032	D	0.01	-26.6162	11.075	0.48025	0.3755:0.0:0.6245:0.0	.	214;246;246	Q8TC71-2;Q8TC71;Q96M13	.;MIEAP_HUMAN;.	D	246;214	ENSP00000295213:E246D;ENSP00000415309:E214D	ENSP00000295213:E246D	E	+	3	2	SPATA18	52633059	1.000000	0.71417	0.464000	0.27143	0.008000	0.06430	0.397000	0.20883	-0.461000	0.06993	-0.355000	0.07637	GAG	.	.	none		0.453	SPATA18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250597.2	NM_145263		T	52938302	G	T	52938302	3	4	3	1	0	0	0	0	1	0	0	0	15018	933	33	4	760	4	SPATA18	4	52938302	Missense_Mutation	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10		52938302	138215974	20	278											
EPHA5	2044	hgsc.bcm.edu	37	chr4	66467586	66467586	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagggcattttttatagtatAcacgcacagaaaccagagca	16	9	8	8	1	0	2	0	0	0	2	0	2	0	2	1	1	3	4	1	1	6	6			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr4:66467586A>G	ENST00000273854.3	-	3	1283	c.683T>C	c.(682-684)gTa>gCa	p.V228A	EPHA5_ENST00000354839.4_Missense_Mutation_p.V228A|EPHA5_ENST00000432638.2_Missense_Mutation_p.V228A|EPHA5_ENST00000511294.1_Missense_Mutation_p.V228A	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	228	Cys-rich.|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						TTTATAGTATACACGCACAGA	0.453										TSP Lung(17;0.13)																											p.V228A		Atlas-SNP	.											EPHA5,colon,carcinoma,0,1	EPHA5	315	1	0			c.T683C						PASS	.						70	67	68					4																	66467586		2203	4300	6503	SO:0001583	missense	2044	exon3			TAGTATACACGCA	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.683T>C	4.37:g.66467586A>G	ENSP00000273854:p.Val228Ala	102	0	0		110	39	0.354545	NM_004439	Q7Z3F2	Missense_Mutation	SNP	ENST00000273854.3	37	CCDS3513.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.044907	0.75732	.	.	ENSG00000145242	ENST00000273854;ENST00000432638;ENST00000354839;ENST00000511294	T;T;T;T	0.07327	3.2;3.2;3.2;3.2	5.83	5.83	0.93111	Tyrosine-protein kinase, receptor class V, conserved site (1);Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.56097	D	0.000038	T	0.33118	0.0852	M	0.84326	2.69	0.58432	D	0.999998	D;D;D;D	0.89917	0.999;1.0;0.998;0.999	D;D;D;D	0.91635	0.998;0.999;0.997;0.997	T	0.06303	-1.0834	10	0.52906	T	0.07	.	16.1982	0.82046	1.0:0.0:0.0:0.0	.	228;228;228;228	B7ZKW7;B7ZKJ3;P54756-2;P54756	.;.;.;EPHA5_HUMAN	A	228	ENSP00000273854:V228A;ENSP00000389208:V228A;ENSP00000346899:V228A;ENSP00000427638:V228A	ENSP00000273854:V228A	V	-	2	0	EPHA5	66150181	1.000000	0.71417	0.997000	0.53966	0.941000	0.58515	9.339000	0.96797	2.226000	0.72624	0.533000	0.62120	GTA	.	.	none		0.453	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		G	66467586	A	G	66467586	3	3	3	1	0	0	0	0	1	0	0	0	5172	391	14	3	2494	3	EPHA5	4	66467586	Missense_Mutation	SNP	A	TCGA-FA-A4XK-01A-11D-A31X-10	13529284	66467586	124686690	21	279											
AMBN	258	hgsc.bcm.edu	37	chr4	71468348	71468348	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	atctgtgatatagctcccagGagtagattttgctgatccac	10	13	9	9	0	1	3	0	2	1	1	3	4	3	4	2	1	2	3	2	1	3	5	rs368655454|rs141384720|rs199556863	byFrequency	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr4:71468348G>T	ENST00000322937.6	+	7	642	c.539G>T	c.(538-540)gGa>gTa	p.G180V	AMBN_ENST00000449493.2_Missense_Mutation_p.G165V	NM_016519.5	NP_057603.1	Q9NP70	AMBN_HUMAN	ameloblastin (enamel matrix protein)	180				G -> R (in Ref. 3; AAG35772 and 4; AAG27036). {ECO:0000305}.	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)			TAGCTCCCAGGAGTAGATTTT	0.264																																					p.G180V		Atlas-SNP	.											.	AMBN	73	.	0			c.G539T						PASS	.						42	49	47					4																	71468348		2161	4276	6437	SO:0001583	missense	258	exon7			TCCCAGGAGTAGA	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.539G>T	4.37:g.71468348G>T	ENSP00000313809:p.Gly180Val	303	0	0		381	17	0.0446194	NM_016519	Q3B862|Q9H2X1|Q9H4L1	Missense_Mutation	SNP	ENST00000322937.6	37	CCDS3543.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.097|0.097	-1.157535|-1.157535	0.01686|0.01686	.|.	.|.	ENSG00000178522|ENSG00000178522	ENST00000322937;ENST00000449493|ENST00000538728	T;T|.	0.27890|.	1.64;1.64|.	3.34|3.34	-2.84|-2.84	0.05751|0.05751	.|.	2.543920|.	0.02234|.	U|.	0.065161|.	T|T	0.18002|0.18002	0.0432|0.0432	N|N	0.22421|0.22421	0.69|0.69	0.19575|0.19575	N|N	0.999964|0.999964	B|.	0.17268|.	0.021|.	B|.	0.12837|.	0.008|.	T|T	0.24190|0.24190	-1.0167|-1.0167	10|6	0.22706|0.29301	T|T	0.39|0.29	.|.	0.3396|0.3396	0.00331|0.00331	0.3712:0.1546:0.2472:0.227|0.3712:0.1546:0.2472:0.227	.|.	180|.	Q9NP70|.	AMBN_HUMAN|.	V|L	180;165|179	ENSP00000313809:G180V;ENSP00000391234:G165V|.	ENSP00000313809:G180V|ENSP00000445605:R179L	G|R	+|+	2|2	0|0	AMBN|AMBN	71502937|71502937	0.095000|0.095000	0.21747|0.21747	0.002000|0.002000	0.10522|0.10522	0.194000|0.194000	0.23727|0.23727	-0.066000|-0.066000	0.11598|0.11598	-0.545000|-0.545000	0.06224|0.06224	0.305000|0.305000	0.20034|0.20034	GGA|CGA	.	.	weak		0.264	AMBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252165.1	NM_016519		T	71468348	G	T	71468348	3	4	3	1	0	0	0	0	1	0	0	0	563	1174	41	4	565	4	AMBN	4	71468348	Missense_Mutation	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10	5000762	71468348	119685928	22	280											
ADAMTS3	9508	hgsc.bcm.edu	37	chr4	73205310	73205310	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agtacctcgatattgtaatcGttttctcccgcgtgtctgcg	6	15	9	11	5	2	0	0	0	2	0	5	1	2	0	2	0	2	3	2	0	3	6			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr4:73205310G>A	ENST00000286657.4	-	5	798	c.762C>T	c.(760-762)aaC>aaT	p.N254N		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	254					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)			TATTGTAATCGTTTTCTCCCG	0.498																																					p.N254N	NSCLC(168;1941 2048 2918 13048 43078)	Atlas-SNP	.											.	ADAMTS3	164	.	0			c.C762T						PASS	.						284	272	276					4																	73205310		2203	4300	6503	SO:0001819	synonymous_variant	9508	exon5			GTAATCGTTTTCT	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.762C>T	4.37:g.73205310G>A		88	0	0		108	41	0.37963	NM_014243	A1L3U9|Q9BXZ8	Silent	SNP	ENST00000286657.4	37	CCDS3553.1																																																																																			.	.	none		0.498	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2			A	73205310	G	A	73205310	2	1	3	1	0	0	0	0	0	0	0	1	267	1136	40	1		1	ADAMTS3	4	73205310	Silent	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10	1736962	73205310	117948966	23	281											
BBS12	166379	hgsc.bcm.edu	37	chr4	123664881	123664881	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acactgccaattactcatcaGaatttgaagccagcacatac	15	9	5	12	0	2	2	2	1	0	1	2	2	2	2	2	0	5	1	2	0	5	3			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr4:123664881G>T	ENST00000314218.3	+	2	2027	c.1834G>T	c.(1834-1836)Gaa>Taa	p.E612*	BBS12_ENST00000542236.1_Nonsense_Mutation_p.E612*	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	612					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						TTACTCATCAGAATTTGAAGC	0.378									Bardet-Biedl syndrome																												p.E612X		Atlas-SNP	.											.	BBS12	63	.	0			c.G1834T						PASS	.						85	83	83					4																	123664881		2203	4300	6503	SO:0001587	stop_gained	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	TCATCAGAATTTG	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.1834G>T	4.37:g.123664881G>T	ENSP00000319062:p.Glu612*	94	0	0		91	5	0.0549451	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Nonsense_Mutation	SNP	ENST00000314218.3	37	CCDS3728.1	.	.	.	.	.	.	.	.	.	.	G	40	8.505213	0.98841	.	.	ENSG00000181004	ENST00000314218;ENST00000542236	.	.	.	5.81	4.97	0.65823	.	0.282205	0.39274	N	0.001417	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	-34.5508	16.4957	0.84242	0.0:0.1415:0.8585:0.0	.	.	.	.	X	612	.	ENSP00000319062:E612X	E	+	1	0	BBS12	123884331	1.000000	0.71417	0.698000	0.30274	0.872000	0.50106	3.556000	0.53734	1.427000	0.47276	0.591000	0.81541	GAA	.	.	none		0.378	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618		T	123664881	G	T	123664881	4	4	3	1	0	0	0	0	0	1	0	0	1337	943	33	4	1836	4	BBS12	4	123664881	Nonsense_Mutation	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10	50459571	123664881	67489395	24	282											
TLR2	7097	hgsc.bcm.edu	37	chr4	154625039	154625039	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggttttacttattttatgAtctgagcactttatattcac	11	19	5	6	0	2	2	1	2	1	0	2	2	2	2	0	1	2	2	0	1	6	9			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr4:154625039A>T	ENST00000260010.6	+	1	2388	c.980A>T	c.(979-981)gAt>gTt	p.D327V		NM_003264.3	NP_003255.2	O60603	TLR2_HUMAN	toll-like receptor 2	327					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)	p.D327V(2)		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)	TTATTTTATGATCTGAGCACT	0.318																																					p.D327V		Atlas-SNP	.											TLR2,NS,lymphoid_neoplasm,0,3	TLR2	84	3	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.A980T						PASS	.						58	63	62					4																	154625039		2203	4299	6502	SO:0001583	missense	7097	exon3			TTTATGATCTGAG	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.980A>T	4.37:g.154625039A>T	ENSP00000260010:p.Asp327Val	99	0	0		109	41	0.376147	NM_003264	B3Y612|D1CS45|D1CS48|D1CS49|O15454|Q8NI00	Missense_Mutation	SNP	ENST00000260010.6	37	CCDS3784.1	.	.	.	.	.	.	.	.	.	.	A	16.40	3.112000	0.56398	.	.	ENSG00000137462	ENST00000260010	T	0.16457	2.34	6.06	6.06	0.98353	.	0.366671	0.29165	N	0.012947	T	0.36635	0.0974	M	0.67397	2.05	0.28454	N	0.916221	D	0.61697	0.99	D	0.63113	0.911	T	0.35101	-0.9802	10	0.87932	D	0	.	11.615	0.51083	0.9314:0.0:0.0686:0.0	.	327	O60603	TLR2_HUMAN	V	327	ENSP00000260010:D327V	ENSP00000260010:D327V	D	+	2	0	TLR2	154844489	0.991000	0.36638	0.150000	0.22450	0.033000	0.12548	3.108000	0.50337	2.324000	0.78689	0.533000	0.62120	GAT	.	.	none		0.318	TLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365205.1			T	154625039	A	T	154625039	3	4	3	1	0	0	0	0	1	0	0	0	15966	333	12	5	982	5	TLR2	4	154625039	Missense_Mutation	SNP	A	TCGA-FA-A4XK-01A-11D-A31X-10	30960158	154625039	36529237	25	283											
VCAN	1462	hgsc.bcm.edu	37	chr5	82834316	82834316	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cacgtagtcctgcctctgtcTttatggagcagggctctgga	6	12	12	11	1	3	0	0	0	3	0	4	2	4	2	2	3	2	3	2	3	2	3			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr5:82834316T>C	ENST00000265077.3	+	8	6059	c.5494T>C	c.(5494-5496)Ttt>Ctt	p.F1832L	VCAN_ENST00000512590.2_Intron|VCAN-AS1_ENST00000512090.1_RNA|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000343200.5_Missense_Mutation_p.F845L	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1832	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)	TGCCTCTGTCTTTATGGAGCA	0.498																																					p.F1832L		Atlas-SNP	.											.	VCAN	498	.	0			c.T5494C						PASS	.						78	86	83					5																	82834316		2203	4299	6502	SO:0001583	missense	1462	exon8			TCTGTCTTTATGG	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.5494T>C	5.37:g.82834316T>C	ENSP00000265077:p.Phe1832Leu	122	0	0		89	34	0.382022	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	T	14.64	2.596304	0.46318	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000513960	D;D;T	0.85484	-1.98;-1.99;3.27	5.82	3.13	0.36017	.	0.288191	0.30547	N	0.009390	T	0.79263	0.4416	L	0.49350	1.555	0.18873	N	0.999989	B;B	0.25390	0.037;0.125	B;B	0.22386	0.039;0.028	T	0.66532	-0.5900	10	0.31617	T	0.26	.	10.9593	0.47376	0.0:0.1464:0.0:0.8536	.	845;1832	P13611-2;P13611	.;CSPG2_HUMAN	L	1832;845;845	ENSP00000265077:F1832L;ENSP00000340062:F845L;ENSP00000426251:F845L	ENSP00000265077:F1832L	F	+	1	0	VCAN	82870072	0.111000	0.22076	0.003000	0.11579	0.350000	0.29205	2.000000	0.40816	1.035000	0.39972	0.533000	0.62120	TTT	.	.	none		0.498	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		C	82834316	T	C	82834316	3	2	3	1	0	0	0	0	1	0	0	0	17153	1609	56	3	5520	3	VCAN	5	82834316	Missense_Mutation	SNP	T	TCGA-FA-A4XK-01A-11D-A31X-10		82834316	98080944	26	284											
SLC22A23	63027	hgsc.bcm.edu	37	chr6	3284179	3284179	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ccacgatggaaaacgcgatgGaaaatttgtccttgacgctg	12	9	11	9	4	0	1	0	1	0	0	1	5	1	3	2	2	1	1	2	2	4	2			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr6:3284179G>A	ENST00000406686.3	-	9	1609	c.1610C>T	c.(1609-1611)tCc>tTc	p.S537F	SLC22A23_ENST00000490273.1_Missense_Mutation_p.S256F|SLC22A23_ENST00000380302.4_Missense_Mutation_p.S256F|SLC22A23_ENST00000436008.2_Missense_Mutation_p.S545F|PSMG4_ENST00000451246.2_Intron	NM_015482.1	NP_056297.1	A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23	537					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)				AAACGCGATGGAAAATTTGTC	0.597																																					p.S537F		Atlas-SNP	.											SLC22A23_ENST00000406686,NS,carcinoma,-1,2	SLC22A23	89	2	0			c.C1610T						scavenged	.						103	90	95					6																	3284179		2203	4300	6503	SO:0001583	missense	63027	exon9			GCGATGGAAAATT	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.1610C>T	6.37:g.3284179G>A	ENSP00000385028:p.Ser537Phe	96	1	0.0104167		83	37	0.445783	NM_015482	A1A5C8|Q5T8B8|Q6ZMH3|Q8IW73	Missense_Mutation	SNP	ENST00000406686.3	37	CCDS47363.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.681253	0.88542	.	.	ENSG00000137266	ENST00000436008;ENST00000406686;ENST00000380302;ENST00000490273;ENST00000485307;ENST00000467177	T;T;T;T;T;T	0.74526	-0.85;-0.85;-0.85;-0.85;-0.85;-0.85	5.35	5.35	0.76521	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.054601	0.85682	D	0.000000	T	0.78336	0.4267	L	0.39898	1.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.987	T	0.79818	-0.1643	10	0.56958	D	0.05	-37.9193	18.0651	0.89388	0.0:0.0:1.0:0.0	.	545;537	C9J4Z0;A1A5C7	.;S22AN_HUMAN	F	545;537;256;256;365;363	ENSP00000410245:S545F;ENSP00000385028:S537F;ENSP00000369657:S256F;ENSP00000419463:S256F;ENSP00000418134:S365F;ENSP00000418985:S363F	ENSP00000369657:S256F	S	-	2	0	SLC22A23	3229178	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.303000	0.96183	2.491000	0.84063	0.655000	0.94253	TCC	.	.	none		0.597	SLC22A23-006	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353059.1	NM_021945		A	3284179	G	A	3284179	3	1	3	1	0	0	0	0	1	0	0	0	14467	1174	41	2	458	2	SLC22A23	6	3284179	Missense_Mutation	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10		3284179	167830888	27	285											
HIST1H2AE	3012	hgsc.bcm.edu	37	chr6	26217398	26217398	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgacggccgagatcttagagCtagctggcaacgcggctcgc	8	7	14	12	5	1	3	0	1	1	2	2	4	1	3	1	3	3	4	1	3	3	2			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr6:26217398C>G	ENST00000303910.2	+	1	234	c.196C>G	c.(196-198)Cta>Gta	p.L66V	HIST1H2BG_ENST00000244601.3_5'Flank	NM_021052.2	NP_066390.1	P04908	H2A1B_HUMAN	histone cluster 1, H2ae	66						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)				GATCTTAGAGCTAGCTGGCAA	0.607																																					p.L66V		Atlas-SNP	.											.	HIST1H2AE	25	.	0			c.C196G						PASS	.						57	57	57					6																	26217398		2203	4300	6503	SO:0001583	missense	3012	exon1			TTAGAGCTAGCTG	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.196C>G	6.37:g.26217398C>G	ENSP00000303373:p.Leu66Val	127	0	0		124	52	0.419355	NM_021052	P28001|Q76P63	Missense_Mutation	SNP	ENST00000303910.2	37	CCDS4595.1	.	.	.	.	.	.	.	.	.	.	.	10.95	1.494701	0.26774	.	.	ENSG00000168274	ENST00000303910	T	0.70631	-0.5	4.07	4.07	0.47477	.	0.000000	0.27886	U	0.017441	D	0.84311	0.5444	H	0.95884	3.735	0.38725	D	0.953543	.	.	.	.	.	.	D	0.87649	0.2527	8	0.87932	D	0	.	9.5775	0.39468	0.0:0.9023:0.0:0.0977	.	.	.	.	V	66	ENSP00000303373:L66V	ENSP00000303373:L66V	L	+	1	2	HIST1H2AE	26325377	0.997000	0.39634	1.000000	0.80357	0.029000	0.11900	0.500000	0.22562	2.263000	0.75096	0.650000	0.86243	CTA	.	.	none		0.607	HIST1H2AE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040103.1	NM_021052		G	26217398	C	G	26217398	3	3	3	1	0	0	0	0	1	0	0	0	7141	796	28	4	198	4	HIST1H2AE	6	26217398	Missense_Mutation	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10	22933219	26217398	144897669	28	286											
CSNK2B	1460	hgsc.bcm.edu	37	chr6	31637636	31637636	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctacggtttcaagatccatcCgatggcctaccagctgcagc	9	9	9	14	2	1	1	1	0	0	1	3	2	3	1	4	2	5	3	4	2	3	3			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr6:31637636C>T	ENST00000375882.2	+	7	737	c.581C>T	c.(580-582)cCg>cTg	p.P194L	LY6G5B_ENST00000409525.1_5'Flank|CSNK2B_ENST00000375865.2_Missense_Mutation_p.P194L|CSNK2B-LY6G5B-1181_ENST00000375880.2_Intron|CSNK2B_ENST00000375885.4_Missense_Mutation_p.P213L|CSNK2B_ENST00000375866.2_Missense_Mutation_p.P194L|LY6G5B_ENST00000375864.4_5'Flank	NM_001282385.1|NM_001320.5	NP_001269314.1|NP_001311.3	P67870	CSK2B_HUMAN	casein kinase 2, beta polypeptide	194				P -> A (in Ref. 3; AAA52123). {ECO:0000305}.	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						AAGATCCATCCGATGGCCTAC	0.597																																					p.P194L		Atlas-SNP	.											.	CSNK2B	15	.	0			c.C581T						PASS	.						117	84	96					6																	31637636		1511	2709	4220	SO:0001583	missense	1460	exon7			TCCATCCGATGGC	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.581C>T	6.37:g.31637636C>T	ENSP00000365042:p.Pro194Leu	38	0	0		23	11	0.478261	NM_001320	B0UXA9|P07312|P13862|Q4VX47	Missense_Mutation	SNP	ENST00000375882.2	37	CCDS4712.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.467278	0.84533	.	.	ENSG00000204435	ENST00000375885;ENST00000375882;ENST00000375865;ENST00000375866	.	.	.	5.52	5.52	0.82312	.	0.119582	0.56097	D	0.000022	T	0.52468	0.1736	M	0.84326	2.69	0.49051	D	0.999744	D	0.53462	0.96	B	0.40982	0.345	T	0.63166	-0.6698	8	0.41790	T	0.15	-20.7702	16.978	0.86319	0.0:1.0:0.0:0.0	.	194	P67870	CSK2B_HUMAN	L	213;194;194;194	.	ENSP00000365025:P194L	P	+	2	0	CSNK2B	31745615	1.000000	0.71417	0.997000	0.53966	0.983000	0.72400	6.664000	0.74437	2.873000	0.98535	0.563000	0.77884	CCG	.	.	none		0.597	CSNK2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076063.8	NM_001320		T	31637636	C	T	31637636	3	4	3	1	0	0	0	0	1	0	0	0	3961	652	23	1	603	1	CSNK2B	6	31637636	Missense_Mutation	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10	5420238	31637636	139477431	29	287											
MEP1A	4224	hgsc.bcm.edu	37	chr6	46766884	46766884	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gacccaaacaccaggtggacGttccccattccttacatctt	10	10	6	15	1	1	0	0	0	1	0	3	2	3	1	5	2	2	1	5	2	2	4			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr6:46766884G>T	ENST00000230588.4	+	5	237	c.228G>T	c.(226-228)acG>acT	p.T76T		NM_005588.2	NP_005579.2	Q16819	MEP1A_HUMAN	meprin A, alpha (PABA peptide hydrolase)	76	Metalloprotease.				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)			CCAGGTGGACGTTCCCCATTC	0.438																																					p.T76T		Atlas-SNP	.											.	MEP1A	93	.	0			c.G228T						PASS	.						162	152	155					6																	46766884		2203	4300	6503	SO:0001819	synonymous_variant	4224	exon5			GTGGACGTTCCCC		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.228G>T	6.37:g.46766884G>T		139	0	0		135	43	0.318519	NM_005588	A2RRM4|B0AZP9|B2RCS2|Q8TDC9|Q9H1R1	Silent	SNP	ENST00000230588.4	37	CCDS4918.1																																																																																			.	.	none		0.438	MEP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040803.1	NM_005588		T	46766884	G	T	46766884	2	4	3	1	0	0	0	0	0	0	0	1	9484	1132	40	4		4	MEP1A	6	46766884	Silent	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10	15129248	46766884	124348183	30	288											
BAI3	577	hgsc.bcm.edu	37	chr6	70042873	70042873	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtttccagagatggaatccTagataaaaagctcaaacaca	17	9	7	8	0	1	2	1	0	0	2	3	4	3	3	2	1	2	2	2	1	6	3			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr6:70042873T>C	ENST00000370598.1	+	24	3982	c.3161T>C	c.(3160-3162)cTa>cCa	p.L1054P	BAI3_ENST00000238918.8_Missense_Mutation_p.L260P|BAI3_ENST00000546190.1_Missense_Mutation_p.L18P	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1054					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.L1054R(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)				GATGGAATCCTAGATAAAAAG	0.373																																					p.L1054P		Atlas-SNP	.											BAI3,NS,carcinoma,+1,2	BAI3	451	2	1	Substitution - Missense(1)	liver(1)	c.T3161C						PASS	.						105	105	105					6																	70042873		2203	4299	6502	SO:0001583	missense	577	exon24			GAATCCTAGATAA	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.3161T>C	6.37:g.70042873T>C	ENSP00000359630:p.Leu1054Pro	151	0	0		134	41	0.30597	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	37	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	T	19.52	3.842563	0.71488	.	.	ENSG00000135298	ENST00000370598;ENST00000238918;ENST00000546190	T;T;T	0.40476	1.03;1.03;1.03	5.28	5.28	0.74379	GPCR, family 2-like (1);	0.000000	0.64402	D	0.000001	T	0.48696	0.1514	L	0.52011	1.625	0.80722	D	1	B;B;D	0.71674	0.098;0.004;0.998	B;B;D	0.66351	0.114;0.01;0.943	T	0.51180	-0.8738	10	0.56958	D	0.05	.	15.5917	0.76534	0.0:0.0:0.0:1.0	.	260;1054;1054	B7Z356;A8K0Y1;O60242	.;.;BAI3_HUMAN	P	1054;260;18	ENSP00000359630:L1054P;ENSP00000238918:L260P;ENSP00000441821:L18P	ENSP00000238918:L260P	L	+	2	0	BAI3	70099594	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.147000	0.58078	2.138000	0.66242	0.524000	0.50904	CTA	.	.	none		0.373	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			C	70042873	T	C	70042873	3	2	3	1	0	0	0	0	1	0	0	0	1300	1522	53	3	3247	3	BAI3	6	70042873	Missense_Mutation	SNP	T	TCGA-FA-A4XK-01A-11D-A31X-10	23275989	70042873	101072194	31	289											
PRDM1	639	hgsc.bcm.edu	37	chr6	106543518	106543518	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtgatgagtaaagaatacaTaccaaagggcacacgttttg	16	9	10	6	1	0	3	0	2	0	1	0	3	0	3	1	1	2	3	1	1	6	5			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr6:106543518T>A	ENST00000369096.4	+	3	554	c.320T>A	c.(319-321)aTa>aAa	p.I107K	PRDM1_ENST00000369091.2_Missense_Mutation_p.I71K	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	107	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				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)		AAAGAATACATACCAAAGGGC	0.343			"D, N, Mis, F, S"		DLBCL																																p.I107K		Atlas-SNP	.		Rec	yes		6	6q21	639	"PR domain containing 1, with ZNF domain"		L	.	PRDM1	195	.	0			c.T320A						PASS	.						94	89	91					6																	106543518		2203	4300	6503	SO:0001583	missense	639	exon3			AATACATACCAAA		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.320T>A	6.37:g.106543518T>A	ENSP00000358092:p.Ile107Lys	123	0	0		61	30	0.491803	NM_001198	B2REA6|E1P5E0|Q86WM7	Missense_Mutation	SNP	ENST00000369096.4	37	CCDS5054.2	.	.	.	.	.	.	.	.	.	.	T	31	5.093722	0.94149	.	.	ENSG00000057657	ENST00000369091;ENST00000369096;ENST00000456278	D;D	0.89196	-2.48;-2.48	6.06	6.06	0.98353	SET domain (3);	0.000000	0.85682	D	0.000000	D	0.95671	0.8592	H	0.94582	3.555	0.80722	D	1	D	0.61697	0.99	D	0.69824	0.966	D	0.96716	0.9529	10	0.87932	D	0	-24.395	16.6093	0.84858	0.0:0.0:0.0:1.0	.	107	O75626	PRDM1_HUMAN	K	71;107;71	ENSP00000358087:I71K;ENSP00000358092:I107K	ENSP00000358087:I71K	I	+	2	0	PRDM1	106650211	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.040000	0.89188	2.324000	0.78689	0.533000	0.62120	ATA	.	.	none		0.343	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3			A	106543518	T	A	106543518	3	1	3	1	0	0	0	0	1	0	0	0	12462	1406	49	5	330	5	PRDM1	6	106543518	Missense_Mutation	SNP	T	TCGA-FA-A4XK-01A-11D-A31X-10	36500645	106543518	64571549	32	290											
ADCYAP1R1	117	hgsc.bcm.edu	37	chr7	31132339	31132339	+	Missense_Mutation	SNP	A	A	G																															acatgggaggcaatgagtccAgcatctacttgtaagtacca																										TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr7:31132339A>G	ENST00000304166.4	+	13	1325	c.1036A>G	c.(1036-1038)Agc>Ggc	p.S346G	ADCYAP1R1_ENST00000396211.2_Missense_Mutation_p.S346G|ADCYAP1R1_ENST00000409489.1_Missense_Mutation_p.S346G|ADCYAP1R1_ENST00000409363.1_Missense_Mutation_p.S325G	NM_001118.4|NM_001199635.1|NM_001199636.1	NP_001109.2|NP_001186564.1|NP_001186565.1	P41586	PACR_HUMAN	adenylate cyclase activating polypeptide 1 (pituitary) receptor type I	346					activation of adenylate cyclase activity (GO:0007190)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)|vasoactive intestinal polypeptide receptor activity (GO:0004999)			endometrium(1)|large_intestine(4)|liver(2)|lung(24)|ovary(1)|skin(2)|stomach(1)	35						CAATGAGTCCAGCATCTACTT	0.488																																					p.S346G	Ovarian(44;225 1186 2158 11092)	Atlas-SNP	.											.	ADCYAP1R1	78	.	0			c.A1036G						PASS	.						96	90	92					7																	31132339		2203	4300	6503	SO:0001583	missense	117	exon13			GAGTCCAGCATCT		CCDS5433.1, CCDS56480.1, CCDS56481.1	7p14.3	2012-09-20			ENSG00000078549	ENSG00000078549		"GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"	242	protein-coding gene	gene with protein product	"PACAP receptor 1"	102981				7902709	Standard	NM_001199635		Approved	PAC1, PACAPR, PAC1R	uc003tcg.3	P41586	OTTHUMG00000023884	ENST00000304166.4:c.1036A>G	7.37:g.31132339A>G	ENSP00000306620:p.Ser346Gly	49	0	0		41	27	0.658537	NM_001118	A8K1Y1|B7ZLA7|B8ZZK3|Q17S10	Missense_Mutation	SNP	ENST00000304166.4	37	CCDS5433.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.07|18.07	3.541658|3.541658	0.65085|0.65085	.|.	.|.	ENSG00000078549|ENSG00000078549	ENST00000436116|ENST00000304166;ENST00000381667;ENST00000409363;ENST00000396211;ENST00000409489	.|T;T;T;T	.|0.46063	.|1.15;1.17;0.88;1.09	5.72|5.72	5.72|5.72	0.89469|0.89469	.|GPCR, family 2-like (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.57242|0.57242	0.2040|0.2040	L|L	0.52266|0.52266	1.64|1.64	0.80722|0.80722	D|D	1|1	.|P;B;D;B;B	.|0.71674	.|0.952;0.118;0.998;0.02;0.056	.|P;B;D;B;B	.|0.71184	.|0.792;0.082;0.972;0.033;0.056	T|T	0.54944|0.54944	-0.8217|-0.8217	5|10	.|0.41790	.|T	.|0.15	.|.	14.2607|14.2607	0.66083|0.66083	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|346;346;346;325;346	.|B7ZLA7;Q17S10;E9PFU5;B8ZZK3;P41586	.|.;.;.;.;PACR_HUMAN	R|G	62|346;117;325;346;346	.|ENSP00000306620:S346G;ENSP00000387335:S325G;ENSP00000379514:S346G;ENSP00000386395:S346G	.|ENSP00000306620:S346G	Q|S	+|+	2|1	0|0	ADCYAP1R1|ADCYAP1R1	31098864|31098864	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.748000|8.748000	0.91615|0.91615	2.317000|2.317000	0.78254|0.78254	0.460000|0.460000	0.39030|0.39030	CAG|AGC	.	.	none		0.488	ADCYAP1R1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215041.3	NM_001118		G	31132339	A	G	31132339	3	3	3	1	0	0	0	0	1	0	0	0	303	188	7	3	1082	3	ADCYAP1R1	7	31132339	Missense_Mutation	SNP	A	TCGA-FA-A4XK-01A-11D-A31X-10		31132339	128006324	33	291	8	2									
ADCYAP1R1	117	hgsc.bcm.edu	37	chr7	31132340	31132340	+	Missense_Mutation	SNP	G	G	C																															catgggaggcaatgagtccaGcatctacttgtaagtaccat																										TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr7:31132340G>C	ENST00000304166.4	+	13	1326	c.1037G>C	c.(1036-1038)aGc>aCc	p.S346T	ADCYAP1R1_ENST00000396211.2_Missense_Mutation_p.S346T|ADCYAP1R1_ENST00000409489.1_Missense_Mutation_p.S346T|ADCYAP1R1_ENST00000409363.1_Missense_Mutation_p.S325T	NM_001118.4|NM_001199635.1|NM_001199636.1	NP_001109.2|NP_001186564.1|NP_001186565.1	P41586	PACR_HUMAN	adenylate cyclase activating polypeptide 1 (pituitary) receptor type I	346					activation of adenylate cyclase activity (GO:0007190)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)|vasoactive intestinal polypeptide receptor activity (GO:0004999)			endometrium(1)|large_intestine(4)|liver(2)|lung(24)|ovary(1)|skin(2)|stomach(1)	35						AATGAGTCCAGCATCTACTTG	0.488																																					p.S346T	Ovarian(44;225 1186 2158 11092)	Atlas-SNP	.											.	ADCYAP1R1	78	.	0			c.G1037C						PASS	.						95	88	91					7																	31132340		2203	4300	6503	SO:0001583	missense	117	exon13			AGTCCAGCATCTA		CCDS5433.1, CCDS56480.1, CCDS56481.1	7p14.3	2012-09-20			ENSG00000078549	ENSG00000078549		"GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"	242	protein-coding gene	gene with protein product	"PACAP receptor 1"	102981				7902709	Standard	NM_001199635		Approved	PAC1, PACAPR, PAC1R	uc003tcg.3	P41586	OTTHUMG00000023884	ENST00000304166.4:c.1037G>C	7.37:g.31132340G>C	ENSP00000306620:p.Ser346Thr	48	0	0		40	27	0.675	NM_001118	A8K1Y1|B7ZLA7|B8ZZK3|Q17S10	Missense_Mutation	SNP	ENST00000304166.4	37	CCDS5433.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.4|24.4	4.524258|4.524258	0.85600|0.85600	.|.	.|.	ENSG00000078549|ENSG00000078549	ENST00000436116|ENST00000304166;ENST00000381667;ENST00000409363;ENST00000396211;ENST00000409489	.|T;T;T;T	.|0.42900	.|1.13;1.23;0.96;1.15	5.72|5.72	5.72|5.72	0.89469|0.89469	.|GPCR, family 2-like (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.48572|0.48572	0.1507|0.1507	L|L	0.37561|0.37561	1.115|1.115	0.80722|0.80722	D|D	1|1	.|P;P;P;B;B	.|0.46395	.|0.78;0.624;0.877;0.205;0.425	.|P;B;P;B;B	.|0.52646	.|0.604;0.42;0.705;0.215;0.324	T|T	0.29971|0.29971	-0.9994|-0.9994	5|10	.|0.44086	.|T	.|0.13	.|.	17.7518|17.7518	0.88436|0.88436	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|346;346;346;325;346	.|B7ZLA7;Q17S10;E9PFU5;B8ZZK3;P41586	.|.;.;.;.;PACR_HUMAN	H|T	62|346;117;325;346;346	.|ENSP00000306620:S346T;ENSP00000387335:S325T;ENSP00000379514:S346T;ENSP00000386395:S346T	.|ENSP00000306620:S346T	Q|S	+|+	3|2	2|0	ADCYAP1R1|ADCYAP1R1	31098865|31098865	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.248000|9.248000	0.95456|0.95456	2.873000|2.873000	0.98535|0.98535	0.563000|0.563000	0.77884|0.77884	CAG|AGC	.	.	none		0.488	ADCYAP1R1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215041.3	NM_001118		C	31132340	G	C	31132340	3	2	3	1	0	0	0	0	1	0	0	0	303	971	34	4	1083	4	ADCYAP1R1	7	31132340	Missense_Mutation	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10	1	31132340	128006323	34	292	8	2									
SEMA3C	10512	hgsc.bcm.edu	37	chr7	80433481	80433481	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctcctgttattgtcagtcaGtttttctttgaagaagaagt	9	17	9	6	0	3	3	2	1	1	2	4	3	4	3	1	0	0	3	1	0	4	5	rs143347984		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr7:80433481G>T	ENST00000265361.3	-	8	1303	c.742C>A	c.(742-744)Ctg>Atg	p.L248M	SEMA3C_ENST00000419255.2_Missense_Mutation_p.L248M|SEMA3C_ENST00000536800.1_Missense_Mutation_p.L100M|SEMA3C_ENST00000544525.1_Missense_Mutation_p.L266M	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	248	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						TTGTCAGTCAGTTTTTCTTTG	0.368																																					p.L248M		Atlas-SNP	.											.	SEMA3C	106	.	0			c.C742A						PASS	.	G	MET/LEU	0,4406		0,0,2203	160	150	153		742	3.7	1	7	dbSNP_134	153	1,8599	1.2+/-3.3	0,1,4299	no	missense	SEMA3C	NM_006379.3	15	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	benign	248/752	80433481	1,13005	2203	4300	6503	SO:0001583	missense	10512	exon8			CAGTCAGTTTTTC	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.742C>A	7.37:g.80433481G>T	ENSP00000265361:p.Leu248Met	93	0	0		147	48	0.326531	NM_006379	B4DRL8	Missense_Mutation	SNP	ENST00000265361.3	37	CCDS5596.1	.	.	.	.	.	.	.	.	.	.	G	14.11	2.437638	0.43224	0.0	1.16E-4	ENSG00000075223	ENST00000265361;ENST00000419255;ENST00000544525;ENST00000536800	T;T;T;T	0.10860	2.83;2.83;2.83;2.83	5.62	3.68	0.42216	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.064498	0.64402	D	0.000005	T	0.11452	0.0279	L	0.51422	1.61	0.52099	D	0.999948	B;B;B	0.16396	0.017;0.008;0.01	B;B;B	0.25614	0.016;0.037;0.062	T	0.05533	-1.0879	10	0.72032	D	0.01	.	7.7762	0.29039	0.1417:0.0:0.7252:0.1332	.	100;266;248	B4DRL8;F5H1Z7;Q99985	.;.;SEM3C_HUMAN	M	248;248;266;100	ENSP00000265361:L248M;ENSP00000411193:L248M;ENSP00000445649:L266M;ENSP00000438258:L100M	ENSP00000265361:L248M	L	-	1	2	SEMA3C	80271417	1.000000	0.71417	0.999000	0.59377	0.861000	0.49209	3.527000	0.53517	1.334000	0.45468	0.585000	0.79938	CTG	G|1.000;T|0.000	0.000	weak		0.368	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379		T	80433481	G	T	80433481	3	4	3	1	0	0	0	0	1	0	0	0	14041	1020	36	4	1557	4	SEMA3C	7	80433481	Missense_Mutation	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10	49301141	80433481	78705182	35	293											
CACNA2D1	781	hgsc.bcm.edu	37	chr7	81601100	81601100	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacaaatacttacatattttTctgcttactccagtaatttt	13	18	2	8	0	1	0	0	0	1	0	2	0	2	0	1	0	5	2	1	0	7	9			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr7:81601100T>C	ENST00000356253.5	-	26	2425	c.2170A>G	c.(2170-2172)Aaa>Gaa	p.K724E	CACNA2D1_ENST00000535308.1_5'Flank|CACNA2D1_ENST00000356860.3_Missense_Mutation_p.K712E			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	724					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)	TACATATTTTTCTGCTTACTC	0.303																																					p.K712E		Atlas-SNP	.											.	CACNA2D1	191	.	0			c.A2134G						PASS	.						58	61	60					7																	81601100		2202	4293	6495	SO:0001583	missense	781	exon26			TATTTTTCTGCTT	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.2170A>G	7.37:g.81601100T>C	ENSP00000348589:p.Lys724Glu	259	0	0		330	70	0.212121	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Missense_Mutation	SNP	ENST00000356253.5	37		.	.	.	.	.	.	.	.	.	.	T	2.518	-0.311456	0.05422	.	.	ENSG00000153956	ENST00000356860;ENST00000284088;ENST00000356253	T;T	0.71698	-0.59;-0.59	4.69	4.69	0.59074	.	0.258919	0.39407	N	0.001374	T	0.45498	0.1345	N	0.19112	0.55	0.80722	D	1	B	0.10296	0.003	B	0.11329	0.006	T	0.40924	-0.9537	10	0.02654	T	1	-19.5396	4.1471	0.10220	0.1938:0.0948:0.0:0.7114	.	712	P54289-2	.	E	712;731;724	ENSP00000349320:K712E;ENSP00000348589:K724E	ENSP00000284088:K731E	K	-	1	0	CACNA2D1	81439036	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	0.983000	0.29552	1.953000	0.56701	0.477000	0.44152	AAA	.	.	none		0.303	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding				C	81601100	T	C	81601100	3	2	3	1	0	0	0	0	1	0	0	0	2550	1792	62	3	1197	3	CACNA2D1	7	81601100	Missense_Mutation	SNP	T	TCGA-FA-A4XK-01A-11D-A31X-10	1167619	81601100	77537563	36	294											
RABL5	64792	hgsc.bcm.edu	37	chr7	100958542	100958542	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccaggtttgagtgcaccagcTtcagcttgttcaagggtggc	7	11	13	10	0	2	1	2	1	0	0	2	1	2	1	2	3	3	5	2	3	1	4			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr7:100958542T>G	ENST00000315322.4	-	5	524	c.431A>C	c.(430-432)aAg>aCg	p.K144T	RABL5_ENST00000437644.2_Missense_Mutation_p.K114T|RABL5_ENST00000517481.1_Missense_Mutation_p.K67T|RABL5_ENST00000495166.1_5'UTR|RABL5_ENST00000498704.2_Missense_Mutation_p.K67T	NM_022777.2	NP_073614.1	Q9H7X7	IFT22_HUMAN		144					small GTPase mediated signal transduction (GO:0007264)	centrosome (GO:0005813)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)	GTP binding (GO:0005525)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	7	Lung NSC(181;0.215)					GTGCACCAGCTTCAGCTTGTT	0.423											OREG0018221	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K144T		Atlas-SNP	.											.	RABL5	15	.	0			c.A431C						PASS	.						86	83	84					7																	100958542		2203	4300	6503	SO:0001583	missense	64792	exon5			ACCAGCTTCAGCT																												ENST00000315322.4:c.431A>C	7.37:g.100958542T>G	ENSP00000320359:p.Lys144Thr	90	0	0	1355	99	36	0.363636	NM_022777	Q49AG1|Q69YV5|Q9BSW4	Missense_Mutation	SNP	ENST00000315322.4	37	CCDS5719.1	.	.	.	.	.	.	.	.	.	.	T	8.424	0.846993	0.17034	.	.	ENSG00000128581	ENST00000517481;ENST00000315322;ENST00000498704;ENST00000437644	T	0.46451	0.87	5.41	3.03	0.35002	.	0.473361	0.23614	N	0.046303	T	0.24275	0.0588	L	0.27053	0.805	0.28871	N	0.894977	B;B	0.14438	0.01;0.004	B;B	0.12156	0.007;0.003	T	0.16070	-1.0415	10	0.21540	T	0.41	-21.9243	4.6961	0.12804	0.0:0.1701:0.1616:0.6684	.	114;144	Q9H7X7-2;Q9H7X7	.;RABL5_HUMAN	T	67;144;67;114	ENSP00000320359:K144T	ENSP00000320359:K144T	K	-	2	0	RABL5	100745262	0.995000	0.38212	1.000000	0.80357	0.998000	0.95712	0.568000	0.23623	0.360000	0.24265	0.533000	0.62120	AAG	.	.	none		0.423	RABL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347565.1			G	100958542	T	G	100958542	3	3	3	1	0	0	0	0	1	0	0	0	12988	1609	56	5	130	5	RABL5	7	100958542	Missense_Mutation	SNP	T	TCGA-FA-A4XK-01A-11D-A31X-10	19357442	100958542	58180121	37	295											
MGAM	8972	hgsc.bcm.edu	37	chr7	141756637	141756637	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tctttattttcagatgtgacGttccagcccctgcctgcctt	5	16	7	13	1	2	2	1	1	1	1	3	2	3	2	5	0	3	1	5	0	1	6	rs181422456	byFrequency	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr7:141756637G>A	ENST00000549489.2	+	30	3683	c.3588G>A	c.(3586-3588)acG>acA	p.T1196T	MGAM_ENST00000475668.2_Silent_p.T1196T	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1196	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)	CAGATGTGACGTTCCAGCCCC	0.522													g|||	3	0.000599042	0.0008	0.0029	5008	,	,		14732	0.0		0.0	False		,,,				2504	0.0				p.T1196T		Atlas-SNP	.											.	MGAM	767	.	0			c.G3588A						PASS	.						78	77	77					7																	141756637		1990	4160	6150	SO:0001819	synonymous_variant	8972	exon30			TGTGACGTTCCAG	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.3588G>A	7.37:g.141756637G>A		58	0	0		69	15	0.217391	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000549489.2	37	CCDS47727.1																																																																																			G|1.000;A|0.000	0.000	strong		0.522	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			A	141756637	G	A	141756637	2	1	3	1	0	0	0	0	0	0	0	1	9550	1132	40	1		1	MGAM	7	141756637	Silent	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10	40798095	141756637	17382026	38	296											
OPRK1	4986	hgsc.bcm.edu	37	chr8	54142312	54142312	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacgaaggcaaagatgaagaCgcagatcttcatgaagaggt	16	6	12	7	2	2	6	1	2	1	4	2	7	2	6	0	2	0	2	0	2	4	1	rs186551684		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr8:54142312C>T	ENST00000265572.3	-	4	985	c.688G>A	c.(688-690)Gtc>Atc	p.V230I	OPRK1_ENST00000524278.1_Missense_Mutation_p.V141I|RP11-162D9.3_ENST00000524425.1_RNA|OPRK1_ENST00000520287.1_Missense_Mutation_p.V230I	NM_000912.3	NP_000903.2	P41145	OPRK_HUMAN	opioid receptor, kappa 1	230					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)	AAGATGAAGACGCAGATCTTC	0.527													C|||	1	0.000199681	0.0	0.0014	5008	,	,		19957	0.0		0.0	False		,,,				2504	0.0				p.V230I		Atlas-SNP	.											OPRK1,colon,carcinoma,0,1	OPRK1	90	1	0			c.G688A						PASS	.	C	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	76	82	80		688	5.7	1	8		80	0,8600		0,0,4300	no	missense	OPRK1	NM_000912.3	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	230/381	54142312	1,13005	2203	4300	6503	SO:0001583	missense	4986	exon4			TGAAGACGCAGAT		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.688G>A	8.37:g.54142312C>T	ENSP00000265572:p.Val230Ile	125	0	0		122	41	0.336066	NM_000912	E5RHC9|Q499G4	Missense_Mutation	SNP	ENST00000265572.3	37	CCDS6152.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	21.7	4.189259	0.78789	2.27E-4	0.0	ENSG00000082556	ENST00000265572;ENST00000524278;ENST00000520287;ENST00000396798	T;T;T	0.71817	-0.6;-0.6;-0.6	5.7	5.7	0.88788	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.76681	0.4021	L	0.31664	0.95	0.80722	D	1	D	0.76494	0.999	D	0.64595	0.927	T	0.75572	-0.3271	10	0.41790	T	0.15	.	19.8351	0.96655	0.0:1.0:0.0:0.0	.	230	P41145	OPRK_HUMAN	I	230;141;230;216	ENSP00000265572:V230I;ENSP00000430923:V141I;ENSP00000429706:V230I	ENSP00000265572:V230I	V	-	1	0	OPRK1	54304865	1.000000	0.71417	0.973000	0.42090	0.620000	0.37586	7.818000	0.86416	2.693000	0.91896	0.650000	0.86243	GTC	C|1.000;T|0.000	0.000	strong		0.527	OPRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378048.1			T	54142312	C	T	54142312	3	4	3	1	0	0	0	0	1	0	0	0	10894	536	19	1	458	1	OPRK1	8	54142312	Missense_Mutation	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10		54142312	92221710	39	297											
SOX17	64321	hgsc.bcm.edu	37	chr8	55372347	55372347	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgccctgccgggacggcaCggaccccagtcagcccgccg	6	3	13	19	5	1	0	1	0	0	0	1	2	1	2	6	3	3	1	6	3	0	0			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr8:55372347C>T	ENST00000297316.4	+	2	1241	c.1037C>T	c.(1036-1038)aCg>aTg	p.T346M		NM_022454.3	NP_071899.1	Q9H6I2	SOX17_HUMAN	SRY (sex determining region Y)-box 17	346	Gln/Pro-rich.|Sox C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00849}.				angiogenesis (GO:0001525)|canonical Wnt signaling pathway (GO:0060070)|cardiac cell fate determination (GO:0060913)|cardiogenic plate morphogenesis (GO:0003142)|cell migration involved in gastrulation (GO:0042074)|common bile duct development (GO:0061009)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube development (GO:0035050)|embryonic heart tube morphogenesis (GO:0003143)|endocardial cell differentiation (GO:0060956)|endocardium formation (GO:0060214)|endoderm formation (GO:0001706)|endodermal cell fate determination (GO:0007493)|endodermal digestive tract morphogenesis (GO:0061031)|gall bladder development (GO:0061010)|heart formation (GO:0060914)|heart looping (GO:0001947)|inner cell mass cellular morphogenesis (GO:0001828)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell growth (GO:0030308)|negative regulation of mesodermal cell fate specification (GO:0042662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway involved in heart development (GO:0003308)|outflow tract morphogenesis (GO:0003151)|positive regulation of cell differentiation (GO:0045597)|positive regulation of protein catabolic process (GO:0045732)|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)|protein destabilization (GO:0031648)|protein stabilization (GO:0050821)|regulation of cardiac cell fate specification (GO:2000043)|regulation of embryonic development (GO:0045995)|regulation of stem cell division (GO:2000035)|regulation of stem cell proliferation (GO:0072091)|regulation of transcription from RNA polymerase II promoter involved in definitive endodermal cell fate specification (GO:0060807)|regulation of transcription, DNA-templated (GO:0006355)|renal system development (GO:0072001)|rostrocaudal neural tube patterning (GO:0021903)|signal transduction involved in regulation of gene expression (GO:0023019)|spermatogenesis (GO:0007283)|stem cell fate specification (GO:0048866)|vasculogenesis (GO:0001570)	nuclear transcription factor complex (GO:0044798)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			endometrium(6)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)	18		Lung NSC(129;0.109)|all_epithelial(80;0.176)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;1.9e-07)|Epithelial(17;1.7e-05)|all cancers(17;0.000159)			CGGGACGGCACGGACCCCAGT	0.692																																					p.T346M		Atlas-SNP	.											.	SOX17	37	.	0			c.C1037T						PASS	.						17	20	19					8																	55372347		2201	4297	6498	SO:0001583	missense	64321	exon2			ACGGCACGGACCC	AB073988	CCDS6159.1	8q11.23	2014-09-04			ENSG00000164736	ENSG00000164736		"SRY (sex determining region Y)-boxes"	18122	protein-coding gene	gene with protein product		610928				11786926	Standard	NM_022454		Approved		uc003xsb.4	Q9H6I2	OTTHUMG00000164377	ENST00000297316.4:c.1037C>T	8.37:g.55372347C>T	ENSP00000297316:p.Thr346Met	32	0	0		18	9	0.5	NM_022454		Missense_Mutation	SNP	ENST00000297316.4	37	CCDS6159.1	.	.	.	.	.	.	.	.	.	.	C	12.98	2.100586	0.37048	.	.	ENSG00000164736	ENST00000297316	T	0.75938	-0.98	4.72	1.31	0.21738	.	0.746294	0.12225	N	0.487973	T	0.52240	0.1722	N	0.14661	0.345	0.27685	N	0.946303	B	0.18310	0.027	B	0.14023	0.01	T	0.41645	-0.9497	10	0.44086	T	0.13	.	3.8408	0.08914	0.0:0.4588:0.2057:0.3356	.	346	Q9H6I2	SOX17_HUMAN	M	346	ENSP00000297316:T346M	ENSP00000297316:T346M	T	+	2	0	SOX17	55534900	0.971000	0.33674	0.666000	0.29783	0.578000	0.36192	1.665000	0.37449	0.392000	0.25172	0.455000	0.32223	ACG	.	.	none		0.692	SOX17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378526.2			T	55372347	C	T	55372347	3	4	3	1	0	0	0	0	1	0	0	0	14962	536	19	1	1043	1	SOX17	8	55372347	Missense_Mutation	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10	1230035	55372347	90991675	40	298											
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77690572	77690572	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcggtgaagcatcagcagacTgagggcctacggaagctcca	11	6	13	11	2	1	3	1	2	0	1	3	4	2	4	2	3	4	3	2	3	3	1			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr8:77690572T>C	ENST00000521891.2	+	4	3670	c.3222T>C	c.(3220-3222)acT>acC	p.T1074T	ZFHX4_ENST00000050961.6_Silent_p.T1048T|ZFHX4_ENST00000517683.1_3'UTR|ZFHX4_ENST00000455469.2_Silent_p.T1048T|ZFHX4_ENST00000518282.1_Silent_p.T1048T	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	1048					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)			ATCAGCAGACTGAGGGCCTAC	0.507										HNSCC(33;0.089)																											p.T1074T		Atlas-SNP	.											.	ZFHX4	878	.	0			c.T3222C						PASS	.						148	158	154					8																	77690572		2068	4205	6273	SO:0001819	synonymous_variant	79776	exon4			GCAGACTGAGGGC		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.3222T>C	8.37:g.77690572T>C		74	0	0		80	29	0.3625	NM_024721	G3V138|Q18PS0|Q6ZN20	Silent	SNP	ENST00000521891.2	37	CCDS47878.2																																																																																			.	.	none		0.507	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		C	77690572	T	C	77690572	2	2	3	1	0	0	0	0	0	0	0	1	17650	1567	55	3		3	ZFHX4	8	77690572	Silent	SNP	T	TCGA-FA-A4XK-01A-11D-A31X-10	22318225	77690572	68673450	41	299											
MYC	4609	hgsc.bcm.edu	37	chr8	128750844	128750844	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctgggaggagacatggtgaaCcagagtttcatctgcgaccc	10	8	13	10	1	2	3	1	1	1	2	2	6	2	4	2	3	2	1	2	3	1	1			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr8:128750844C>T	ENST00000259523.6	+	2	1541	c.336C>T	c.(334-336)aaC>aaT	p.N112N	MYC_ENST00000377970.2_Silent_p.N127N|MYC_ENST00000524013.1_Silent_p.N126N			P01106	MYC_HUMAN	v-myc avian myelocytomatosis viral oncogene homolog	112					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)	ACATGGTGAACCAGAGTTTCA	0.607		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.N127N		Atlas-SNP	.		Dom	yes		8	8q24.12-q24.13	4609	v-myc myelocytomatosis viral oncogene homolog (avian)		"L, E"	.	MYC	168	.	0			c.C381T						PASS	.						65	65	65					8																	128750844		2203	4300	6503	SO:0001819	synonymous_variant	4609	exon2			GGTGAACCAGAGT		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.336C>T	8.37:g.128750844C>T		118	0	0	1567	90	36	0.4	NM_002467	A8WFE7|P01107|Q14026	Silent	SNP	ENST00000259523.6	37																																																																																				.	.	none		0.607	MYC-002	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000250278.1			T	128750844	C	T	128750844	2	4	3	1	0	0	0	0	0	0	0	1	10025	506	18	2		2	MYC	8	128750844	Silent	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10	51060272	128750844	17613178	42	300											
ZNF782	158431	hgsc.bcm.edu	37	chr9	99581542	99581542	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggaataataaaggttgattTatcatatttgttttccccaa	14	16	6	5	0	1	1	1	1	0	0	2	2	2	2	2	2	0	2	2	2	7	9			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr9:99581542T>C	ENST00000481138.1	-	6	1424	c.763A>G	c.(763-765)Aaa>Gaa	p.K255E	ZNF782_ENST00000466833.1_5'Flank|ZNF782_ENST00000535338.1_Missense_Mutation_p.K123E	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	255					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)				AAGGTTGATTTATCATATTTG	0.328																																					p.K255E		Atlas-SNP	.											.	ZNF782	64	.	0			c.A763G						PASS	.						81	86	84					9																	99581542		2202	4299	6501	SO:0001583	missense	158431	exon6			TTGATTTATCATA	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.763A>G	9.37:g.99581542T>C	ENSP00000419397:p.Lys255Glu	67	0	0		79	22	0.278481	NM_001001662	B2RNR0	Missense_Mutation	SNP	ENST00000481138.1	37	CCDS35075.1	.	.	.	.	.	.	.	.	.	.	T	11.88	1.770680	0.31320	.	.	ENSG00000196597	ENST00000481138;ENST00000535338	T;T	0.07021	3.44;3.23	3.53	2.39	0.29439	.	0.000000	0.35708	N	0.003027	T	0.05914	0.0154	L	0.48362	1.52	0.09310	N	1	B	0.32203	0.36	B	0.24269	0.052	T	0.31752	-0.9932	10	0.41790	T	0.15	.	3.0506	0.06168	0.2109:0.1157:0.0:0.6734	.	255	Q6ZMW2	ZN782_HUMAN	E	255;123	ENSP00000419397:K255E;ENSP00000440624:K123E	ENSP00000419397:K255E	K	-	1	0	ZNF782	98621363	0.009000	0.17119	0.003000	0.11579	0.035000	0.12851	0.984000	0.29565	0.730000	0.32425	0.529000	0.55759	AAA	.	.	none		0.328	ZNF782-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356810.1	NM_001001662		C	99581542	T	C	99581542	3	2	3	1	0	0	0	0	1	0	0	0	18170	1763	61	3	1340	3	ZNF782	9	99581542	Missense_Mutation	SNP	T	TCGA-FA-A4XK-01A-11D-A31X-10		99581542	41631889	43	301											
LPPR1	54886	hgsc.bcm.edu	37	chr9	104079734	104079734	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cccgtggagtacccctaatgGctttcccaaggatagaaagc	11	8	10	12	1	0	1	0	0	0	1	1	3	1	3	4	3	2	2	4	3	5	4			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr9:104079734G>T	ENST00000374874.3	+	7	1340	c.901G>T	c.(901-903)Gct>Tct	p.A301S	LPPR1_ENST00000395056.2_Missense_Mutation_p.A301S	NM_207299.1	NP_997182.1	Q8TBJ4	LPPR1_HUMAN		301					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)										ACCCCTAATGGCTTTCCCAAG	0.493																																					p.A301S		Atlas-SNP	.											.	.	.	.	0			c.G901T						PASS	.						115	121	119					9																	104079734		2203	4300	6503	SO:0001583	missense	0	exon7			CTAATGGCTTTCC																												ENST00000374874.3:c.901G>T	9.37:g.104079734G>T	ENSP00000364008:p.Ala301Ser	108	0	0		134	41	0.30597	NM_207299	Q5VX23|Q9NXE2	Missense_Mutation	SNP	ENST00000374874.3	37	CCDS6751.1	.	.	.	.	.	.	.	.	.	.	G	8.333	0.826970	0.16749	.	.	ENSG00000148123	ENST00000374874;ENST00000374871;ENST00000395056	T;T	0.28454	1.61;1.61	5.79	5.79	0.91817	.	0.062463	0.64402	D	0.000004	T	0.19167	0.0460	N	0.19112	0.55	0.53688	D	0.999973	B;B	0.29378	0.004;0.243	B;B	0.21917	0.005;0.037	T	0.06267	-1.0836	10	0.02654	T	1	-36.4594	19.0195	0.92908	0.0:0.0:1.0:0.0	.	285;301	B7Z8P4;Q8TBJ4	.;LPPR1_HUMAN	S	301	ENSP00000364008:A301S;ENSP00000378496:A301S	ENSP00000364005:A301S	A	+	1	0	RP11-35N6.1	103119555	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.250000	0.78287	2.746000	0.94184	0.655000	0.94253	GCT	.	.	none		0.493	LPPR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053425.1			T	104079734	G	T	104079734	3	4	3	1	0	0	0	0	1	0	0	0	8933	1203	42	4	923	4	LPPR1	9	104079734	Missense_Mutation	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10	4498192	104079734	37133697	44	302											
SARDH	1757	hgsc.bcm.edu	37	chr9	136577806	136577806	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	atccagtgggccagctcctgCccacagccaccacccagcat	9	5	8	19	0	0	0	0	0	0	0	2	0	2	0	7	1	4	2	7	1	0	0			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr9:136577806C>T	ENST00000371872.4	-	10	1520	c.1263G>A	c.(1261-1263)ggG>ggA	p.G421G	SARDH_ENST00000422262.2_Silent_p.G253G|SARDH_ENST00000439388.1_Silent_p.G421G	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	421					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)		CCAGCTCCTGCCCACAGCCAC	0.637																																					p.G421G		Atlas-SNP	.											.	SARDH	112	.	0			c.G1263A						PASS	.						55	56	55					9																	136577806		2203	4300	6503	SO:0001819	synonymous_variant	1757	exon10			CTCCTGCCCACAG		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.1263G>A	9.37:g.136577806C>T		34	0	0		24	11	0.458333	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Silent	SNP	ENST00000371872.4	37	CCDS6978.1																																																																																			.	.	none		0.637	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1			T	136577806	C	T	136577806	2	4	3	1	0	0	0	0	0	0	0	1	13856	726	26	2		2	SARDH	9	136577806	Silent	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10	32498072	136577806	4635625	45	303											
CSGALNACT2	55454	hgsc.bcm.edu	37	chr10	43659419	43659419	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggacaagggagaggtcttGatgtttttctgtgatgttga	8	15	15	3	0	2	4	0	3	2	1	2	6	2	5	0	3	0	2	0	3	1	4	rs79064394		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr10:43659419G>T	ENST00000374466.3	+	5	1421	c.1086G>T	c.(1084-1086)ttG>ttT	p.L362F		NM_018590.3	NP_061060.3	Q8N6G5	CGAT2_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 2	362					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)	p.L362F(5)		endometrium(12)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						GAGAGGTCTTGATGTTTTTCT	0.433																																					p.L362F		Atlas-SNP	.											CSGALNACT2,NS,carcinoma,0,5	CSGALNACT2	67	5	5	Substitution - Missense(5)	endometrium(4)|kidney(1)	c.G1086T						scavenged	.						223	221	222					10																	43659419		2203	4300	6503	SO:0001583	missense	55454	exon5			GGTCTTGATGTTT	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.1086G>T	10.37:g.43659419G>T	ENSP00000363590:p.Leu362Phe	162	1	0.00617284		126	6	0.047619	NM_018590	B3KWL7|Q6MZJ5|Q6MZP6|Q8TCH4|Q9P1I6	Missense_Mutation	SNP	ENST00000374466.3	37	CCDS7201.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.499782	0.85176	.	.	ENSG00000169826	ENST00000374466	T	0.27256	1.68	6.08	5.17	0.71159	.	0.064535	0.64402	D	0.000004	T	0.57359	0.2048	M	0.89095	3.005	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.63721	-0.6573	10	0.87932	D	0	-11.7375	14.8306	0.70146	0.0683:0.0:0.9317:0.0	.	362	Q8N6G5	CGAT2_HUMAN	F	362	ENSP00000363590:L362F	ENSP00000363590:L362F	L	+	3	2	CSGALNACT2	42979425	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.683000	0.37638	2.894000	0.99253	0.591000	0.81541	TTG	.	.	weak		0.433	CSGALNACT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047693.1	NM_018590		T	43659419	G	T	43659419	3	4	3	1	0	0	0	0	1	0	0	0	3941	1281	45	4	1100	4	CSGALNACT2	10	43659419	Missense_Mutation	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10		43659419	91875328	46	304											
ZNF503	84858	hgsc.bcm.edu	37	chr10	77161102	77161102	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggcagggtctgcaccgcCgcctccgcctccgccgccgc	3	4	12	22	6	1	0	0	0	1	0	3	0	3	0	9	2	1	2	9	2	0	0	rs533859340|rs374168185	byFrequency	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr10:77161102C>T	ENST00000372524.4	-	1	562	c.76G>A	c.(76-78)Ggc>Agc	p.G26S	ZNF503-AS2_ENST00000466942.2_RNA|ZNF503-AS2_ENST00000486015.1_RNA|ZNF503_ENST00000535216.1_Missense_Mutation_p.G26S|ZNF503-AS2_ENST00000425916.3_RNA|RP11-399K21.11_ENST00000418818.2_lincRNA	NM_032772.4	NP_116161.2	Q96F45	ZN503_HUMAN	zinc finger protein 503	26	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)					TCTGCAccgccgcctccgcct	0.711																																					p.G26S		Atlas-SNP	.											.	ZNF503	25	.	0			c.G76A						PASS	.						3	4	4					10																	77161102		1704	3476	5180	SO:0001583	missense	84858	exon1			CACCGCCGCCTCC	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.76G>A	10.37:g.77161102C>T	ENSP00000361602:p.Gly26Ser	31	0	0		18	9	0.5	NM_032772	Q8NAC5|Q96E25|Q96IJ0	Missense_Mutation	SNP	ENST00000372524.4	37	CCDS7350.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.061|0.061	-1.224407|-1.224407	0.01530|0.01530	.|.	.|.	ENSG00000165655|ENSG00000233745	ENST00000372524;ENST00000535216;ENST00000372516|ENST00000438638	D;D|.	0.87334|.	-2.24;-2.24|.	1.32|1.32	-2.14|-2.14	0.07123|0.07123	.|.	1.267280|.	0.06383|.	N|.	0.715644|.	T|T	0.17023|0.17023	0.0409|0.0409	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	0.999992|0.999992	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.25779|0.25779	-1.0122|-1.0122	9|6	.|0.87932	.|D	.|0	-4.8545|-4.8545	3.8606|3.8606	0.08994|0.08994	0.0:0.3276:0.2147:0.4577|0.0:0.3276:0.2147:0.4577	.|.	26|.	Q96F45|.	ZN503_HUMAN|.	S|L	26|115	ENSP00000361602:G26S;ENSP00000438988:G26S|.	.|ENSP00000391835:P115L	G|P	-|+	1|2	0|0	ZNF503|AC010997.1	76831108|76831108	0.437000|0.437000	0.25593|0.25593	0.723000|0.723000	0.30687|0.30687	0.115000|0.115000	0.19883|0.19883	-0.115000|-0.115000	0.10741|0.10741	-0.181000|-0.181000	0.10619|0.10619	0.000000|0.000000	0.15137|0.15137	GGC|CCG	.	.	none		0.711	ZNF503-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048826.1	NM_032772		T	77161102	C	T	77161102	3	4	3	1	0	0	0	0	1	0	0	0	17966	652	23	1	1872	1	ZNF503	10	77161102	Missense_Mutation	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10	33501683	77161102	58373645	47	305											
DLG5	9231	hgsc.bcm.edu	37	chr10	79565519	79565520	+	Frame_Shift_Ins	INS	-	-	A																															ttgtgcttgtgtttcctccgINSaaaaaaggaccggcgtgcag																										TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr10:79565519_79565520insA	ENST00000372391.2	-	27	5072_5073	c.5067_5068insT	c.(5065-5070)tttcggfs	p.R1690fs	DLG5_ENST00000372388.2_Frame_Shift_Ins_p.R1350fs|DLG5_ENST00000459739.1_5'UTR	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	1690					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)			TGTTTCCTCCGAAAAAAGGACC	0.535																																					p.R1690fs		Pindel,Atlas-Indel	.											.	DLG5	154	.	0			c.5068_5069insT						PASS	.																																			SO:0001589	frameshift_variant	9231	exon27			.	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.5068dupT	10.37:g.79565525_79565525dupA	ENSP00000361467:p.Arg1690fs	0	0	.		17	17	1	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Frame_Shift_Ins	INS	ENST00000372391.2	37	CCDS7353.2																																																																																			.	.	none		0.535	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2			A	79565520	-	A	79565519	7	5	3	1	0	1	1	0	0	0	0	0	4560	1057	37	0	715	0	DLG5	10	79565519	Frame_Shift_Ins	INS	-	TCGA-FA-A4XK-01A-11D-A31X-10	2404417	79565519	55969228	48	306											
CYP26C1	340665	hgsc.bcm.edu	37	chr10	94824263	94824263	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	attcacagtgcaagggagctGggccatgagccctccatgca	10	7	12	12	0	1	1	1	1	0	0	2	2	2	2	3	2	4	3	3	2	1	1			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr10:94824263G>T	ENST00000285949.5	+	4	831	c.831G>T	c.(829-831)ctG>ctT	p.L277L		NM_183374.2	NP_899230.2	Q6V0L0	CP26C_HUMAN	cytochrome P450, family 26, subfamily C, polypeptide 1	277					anterior/posterior pattern specification (GO:0009952)|central nervous system development (GO:0007417)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|neural crest cell development (GO:0014032)|organelle fusion (GO:0048284)|oxidation-reduction process (GO:0055114)|retinoic acid catabolic process (GO:0034653)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|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)|retinoic acid 4-hydroxylase activity (GO:0008401)|retinoic acid binding (GO:0001972)			central_nervous_system(1)|lung(3)|ovary(1)	5		Colorectal(252;0.122)				CAAGGGAGCTGGGCCATGAGC	0.587																																					p.L277L		Atlas-SNP	.											.	CYP26C1	25	.	0			c.G831T						PASS	.						96	90	92					10																	94824263		2203	4300	6503	SO:0001819	synonymous_variant	340665	exon4			GGAGCTGGGCCAT		CCDS7425.1	10q23.33	2003-11-20			ENSG00000187553	ENSG00000187553		"Cytochrome P450s"	20577	protein-coding gene	gene with protein product		608428					Standard	XR_246086		Approved		uc010qns.2	Q6V0L0	OTTHUMG00000018766	ENST00000285949.5:c.831G>T	10.37:g.94824263G>T		129	0	0		97	5	0.0515464	NM_183374	Q5VXH6	Silent	SNP	ENST00000285949.5	37	CCDS7425.1																																																																																			.	.	none		0.587	CYP26C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049409.2	NM_183374		T	94824263	G	T	94824263	2	4	3	1	0	0	0	0	0	0	0	1	4159	1335	47	4		4	CYP26C1	10	94824263	Silent	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10	15258744	94824263	40710484	49	307											
DMBT1	1755	hgsc.bcm.edu	37	chr10	124352028	124352028	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgcgctgctcaggacacgAgtcctacctgtggagctgcc	6	9	13	13	2	1	0	1	0	0	0	2	3	2	2	3	2	5	3	3	2	1	1			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr10:124352028A>G	ENST00000338354.3	+	20	2523	c.2417A>G	c.(2416-2418)gAg>gGg	p.E806G	DMBT1_ENST00000330163.4_Intron|DMBT1_ENST00000344338.3_Missense_Mutation_p.E796G|DMBT1_ENST00000368909.3_Missense_Mutation_p.E806G|DMBT1_ENST00000368956.2_Intron|DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000368955.3_Missense_Mutation_p.E796G			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	806	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)				TCAGGACACGAGTCCTACCTG	0.617																																					p.E806G	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.A2417G						PASS	.						144	104	117					10																	124352028		2018	4109	6127	SO:0001583	missense	1755	exon20			GACACGAGTCCTA		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.2417A>G	10.37:g.124352028A>G	ENSP00000342210:p.Glu806Gly	25	0	0		15	14	0.933333	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	37		.	.	.	.	.	.	.	.	.	.	A	10.04	1.242226	0.22796	.	.	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000344338;ENST00000368909;ENST00000368955	T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04	3.75	2.6	0.31112	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	.	.	.	.	D	0.84365	0.5456	H	0.97852	4.09	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;0.996;0.998	D	0.84836	0.0805	9	0.87932	D	0	.	8.8898	0.35425	0.9078:0.0:0.0922:0.0	.	567;806;796;806	Q9UGM3-4;Q9UGM3-6;Q9UGM3-3;Q9UGM3	.;.;.;DMBT1_HUMAN	G	806;806;806;806;806;806;796;806;796	ENSP00000342210:E806G;ENSP00000343175:E796G;ENSP00000357905:E806G;ENSP00000357951:E796G	ENSP00000342210:E806G	E	+	2	0	DMBT1	124342018	1.000000	0.71417	0.022000	0.16811	0.047000	0.14425	6.948000	0.75965	0.438000	0.26450	0.460000	0.39030	GAG	.	.	none		0.617	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		G	124352028	A	G	124352028	3	3	3	1	0	0	0	0	1	0	0	0	4579	304	11	3	2495	3	DMBT1	10	124352028	Missense_Mutation	SNP	A	TCGA-FA-A4XK-01A-11D-A31X-10	29527765	124352028	11182719	50	308											
CPXM2	119587	hgsc.bcm.edu	37	chr10	125557598	125557598	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gccaccatggggacgggtagCtcattgagaacagggatctc	10	7	14	10	1	2	1	1	1	1	1	3	4	2	3	2	4	2	2	2	4	2	2			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr10:125557598C>T	ENST00000241305.3	-	6	937	c.783G>A	c.(781-783)gaG>gaA	p.E261E	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.E261E		Atlas-SNP	.											.	CPXM2	120	.	0			c.G783A						PASS	.						130	111	118					10																	125557598		2203	4300	6503	SO:0001819	synonymous_variant	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>A	10.37:g.125557598C>T		99	0	0		100	29	0.29	NM_198148	B4E3Q2	Silent	SNP	ENST00000241305.3	37	CCDS7637.1																																																																																			.	.	none		0.473	CPXM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050853.1	NM_198148		T	125557598	C	T	125557598	2	4	3	1	0	0	0	0	0	0	0	1	3840	796	28	2		2	CPXM2	10	125557598	Silent	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10	1205570	125557598	9977149	51	309											
C10orf90	118611	hgsc.bcm.edu	37	chr10	128193433	128193433	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaggtcctcgctcatctgaCggtgccgggattcctaatct	6	12	10	13	3	4	1	2	1	2	0	7	2	6	2	3	3	1	1	3	3	1	2			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr10:128193433C>T	ENST00000284694.7	-	3	456	c.336G>A	c.(334-336)ccG>ccA	p.P112P	C10orf90_ENST00000392694.1_Silent_p.P65P|C10orf90_ENST00000454341.1_Silent_p.P112P|C10orf90_ENST00000368674.1_5'UTR|C10orf90_ENST00000356858.3_Silent_p.P65P|C10orf90_ENST00000544758.1_Silent_p.P209P	NM_001004298.2	NP_001004298.2	Q96M02	CJ090_HUMAN	chromosome 10 open reading frame 90	112					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)		GCTCATCTGACGGTGCCGGGA	0.597											OREG0020616	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P112P		Atlas-SNP	.											C10orf90,NS,carcinoma,-1,1	C10orf90	121	1	0			c.G336A						PASS	.						81	65	70					10																	128193433		2203	4300	6503	SO:0001819	synonymous_variant	118611	exon3			ATCTGACGGTGCC	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.336G>A	10.37:g.128193433C>T		115	0	0	1563	98	39	0.397959	NM_001004298	B9EIQ9|Q5JRP6|Q5T023|Q8NCV5|Q8WU75	Silent	SNP	ENST00000284694.7	37	CCDS31310.1																																																																																			.	.	none		0.597	C10orf90-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004298		T	128193433	C	T	128193433	2	4	3	1	0	0	0	0	0	0	0	1	1625	523	19	1		1	C10orf90	10	128193433	Silent	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10	2635835	128193433	7341314	52	310											
VWCE	220001	hgsc.bcm.edu	37	chr11	61048187	61048187	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttcacaggtcaccttcccGtcctagaagcacaagcagga	11	9	8	13	1	2	1	2	0	0	1	4	2	4	2	3	2	2	2	3	2	3	4	rs375996793		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr11:61048187G>A	ENST00000335613.5	-	9	1619	c.1233C>T	c.(1231-1233)gaC>gaT	p.D411D		NM_152718.2	NP_689931.2	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	411	VWFC 1. {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						TCACCTTCCCGTCCTAGAAGC	0.592																																					p.D411D		Atlas-SNP	.											.	VWCE	84	.	0			c.C1233T						PASS	.	G		0,4406		0,0,2203	96	79	85		1233	-6	0.5	11		85	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	VWCE	NM_152718.2		0,1,6501	AA,AG,GG		0.0116,0.0,0.0077		411/956	61048187	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	220001	exon9			CTTCCCGTCCTAG	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.1233C>T	11.37:g.61048187G>A		64	0	0		67	34	0.507463	NM_152718	A5PKV0|Q7Z7L6|Q86WK8	Silent	SNP	ENST00000335613.5	37	CCDS8002.1																																																																																			.	.	weak		0.592	VWCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398811.1	NM_152718		A	61048187	G	A	61048187	2	1	3	1	0	0	0	0	0	0	0	1	17260	1136	40	1		1	VWCE	11	61048187	Silent	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10		61048187	73958329	53	311											
ME3	10873	hgsc.bcm.edu	37	chr11	86198437	86198437	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcgtatgccttcccgtgcaCgcgctggtgtttcaggccga	5	11	12	13	5	1	0	1	0	0	0	3	1	2	0	3	2	2	4	3	2	1	3			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr11:86198437C>T	ENST00000393324.3	-	6	1004	c.751G>A	c.(751-753)Gtg>Atg	p.V251M	ME3_ENST00000543262.1_Missense_Mutation_p.V251M|ME3_ENST00000359636.2_Missense_Mutation_p.V251M|ME3_ENST00000323418.6_Missense_Mutation_p.V189M|RP11-317J19.1_ENST00000524610.1_RNA|ME3_ENST00000525957.1_5'UTR	NM_001014811.1	NP_001014811.1	Q16798	MAON_HUMAN	malic enzyme 3, NADP(+)-dependent, mitochondrial	251					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)				TTCCCGTGCACGCGCTGGTGT	0.512																																					p.V251M		Atlas-SNP	.											.	ME3	70	.	0			c.G751A						PASS	.						132	106	115					11																	86198437		2202	4299	6501	SO:0001583	missense	10873	exon7			CGTGCACGCGCTG	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.751G>A	11.37:g.86198437C>T	ENSP00000376998:p.Val251Met	82	0	0		92	58	0.630435	NM_006680	B7Z6V0|Q8TBJ0	Missense_Mutation	SNP	ENST00000393324.3	37	CCDS8277.1	.	.	.	.	.	.	.	.	.	.	C	14.64	2.596022	0.46318	.	.	ENSG00000151376	ENST00000359636;ENST00000543262;ENST00000393324;ENST00000524826;ENST00000545395;ENST00000323418	T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8	5.44	4.53	0.55603	Malic enzyme, N-terminal (2);	0.187074	0.46442	N	0.000290	T	0.69169	0.3081	M	0.87547	2.89	0.58432	D	0.999995	D	0.76494	0.999	D	0.63877	0.919	T	0.74423	-0.3670	9	.	.	.	.	12.7938	0.57549	0.0:0.92:0.0:0.08	.	251	Q16798	MAON_HUMAN	M	251;251;251;251;189;189	ENSP00000352657:V251M;ENSP00000440246:V251M;ENSP00000376998:V251M;ENSP00000431182:V251M;ENSP00000315255:V189M	.	V	-	1	0	ME3	85876085	0.978000	0.34361	0.230000	0.23976	0.322000	0.28314	2.358000	0.44134	1.287000	0.44583	0.655000	0.94253	GTG	.	.	none		0.512	ME3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393767.2			T	86198437	C	T	86198437	3	4	3	1	0	0	0	0	1	0	0	0	9428	536	19	1	1099	1	ME3	11	86198437	Missense_Mutation	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10	25150250	86198437	48808079	54	312											
OR4D5	219875	hgsc.bcm.edu	37	chr11	123811056	123811056	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctacctgtgcctctcacattGctgtggtgaccttaatcttt	6	16	7	12	0	2	1	1	1	2	0	3	1	2	1	3	1	3	1	3	1	2	4			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr11:123811056G>A	ENST00000307033.2	+	1	807	c.733G>A	c.(733-735)Gct>Act	p.A245T		NM_001001965.1	NP_001001965.1	Q8NGN0	OR4D5_HUMAN	olfactory receptor, family 4, subfamily D, member 5	245						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)		CTCTCACATTGCTGTGGTGAC	0.532																																					p.A245T		Atlas-SNP	.											.	OR4D5	94	.	0			c.G733A						PASS	.						235	188	204					11																	123811056		2202	4299	6501	SO:0001583	missense	219875	exon1			CACATTGCTGTGG	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.733G>A	11.37:g.123811056G>A	ENSP00000305970:p.Ala245Thr	75	0	0		139	35	0.251799	NM_001001965	B9EGZ4|Q6IFE6	Missense_Mutation	SNP	ENST00000307033.2	37	CCDS31699.1	.	.	.	.	.	.	.	.	.	.	G	2.022	-0.424500	0.04734	.	.	ENSG00000171014	ENST00000307033	T	0.36520	1.25	4.96	4.03	0.46877	GPCR, rhodopsin-like superfamily (1);	0.437967	0.19315	N	0.117284	T	0.08891	0.0220	N	0.00462	-1.47	0.22521	N	0.999028	B	0.02656	0.0	B	0.06405	0.002	T	0.28586	-1.0039	10	0.02654	T	1	-6.2297	9.8887	0.41276	0.1608:0.0:0.8392:0.0	.	245	Q8NGN0	OR4D5_HUMAN	T	245	ENSP00000305970:A245T	ENSP00000305970:A245T	A	+	1	0	OR4D5	123316266	0.000000	0.05858	1.000000	0.80357	0.983000	0.72400	0.241000	0.18065	1.275000	0.44379	0.650000	0.86243	GCT	.	.	none		0.532	OR4D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387263.1	NM_001001965		A	123811056	G	A	123811056	3	1	3	1	0	0	0	0	1	0	0	0	11066	1319	46	2	735	2	OR4D5	11	123811056	Missense_Mutation	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10	37612619	123811056	11195460	55	313											
ANKRD33	341405	hgsc.bcm.edu	37	chr12	52284586	52284586	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgccccttcactcctagaaCggctgcaggctaccttgagc	7	10	9	15	1	1	2	1	1	0	1	2	2	2	2	4	2	5	3	4	2	3	5	rs200291062		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr12:52284586C>T	ENST00000340970.4	+	5	852	c.481C>T	c.(481-483)Cgg>Tgg	p.R161W	ANKRD33_ENST00000538991.1_Missense_Mutation_p.R92W|ANKRD33_ENST00000547119.1_3'UTR|ANKRD33_ENST00000301190.6_Missense_Mutation_p.R286W			Q7Z3H0	ANR33_HUMAN	ankyrin repeat domain 33	161					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|skeletal muscle cell differentiation (GO:0035914)	cytosol (GO:0005829)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	22				BRCA - Breast invasive adenocarcinoma(357;0.0969)		ACTCCTAGAACGGCTGCAGGC	0.662																																					p.R286W		Atlas-SNP	.											.	ANKRD33	33	.	0			c.C856T						PASS	.	C	TRP/ARG,TRP/ARG	0,4406		0,0,2203	25	24	24		481,856	0.1	0.6	12		24	4,8590		0,4,4293	yes	missense,missense	ANKRD33	NM_001130015.1,NM_182608.3	101,101	0,4,6496	TT,TC,CC		0.0465,0.0,0.0308	probably-damaging,probably-damaging	161/273,286/453	52284586	4,12996	2203	4297	6500	SO:0001583	missense	341405	exon5			CTAGAACGGCTGC		CCDS8815.1, CCDS44892.1	12q13.13	2013-01-10	2005-01-07	2005-01-07		ENSG00000167612		"Ankyrin repeat domain containing"	13788	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 7"	C12orf7		20026326	Standard	NM_182608		Approved	DKFZp686O1689, PANKY	uc001rzd.3	Q7Z3H0	OTTHUMG00000169506	ENST00000340970.4:c.481C>T	12.37:g.52284586C>T	ENSP00000344690:p.Arg161Trp	42	0	0		44	19	0.431818	NM_182608	Q0VAA7|Q5K619|Q5K621|Q5K622|Q5K623|Q5K624|Q6ZUN0	Missense_Mutation	SNP	ENST00000340970.4	37	CCDS44892.1	.	.	.	.	.	.	.	.	.	.	C	14.05	2.419121	0.42918	0.0	4.65E-4	ENSG00000167612	ENST00000301190;ENST00000538991;ENST00000340970	T;T;T	0.24908	1.93;1.83;2.28	4.7	0.0507	0.14294	.	0.080339	0.47455	D	0.000234	T	0.39655	0.1086	L	0.55481	1.735	0.21473	N	0.999672	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74674	0.965;0.984;0.977	T	0.22836	-1.0205	10	0.37606	T	0.19	-7.9632	11.629	0.51162	0.7308:0.2692:0.0:0.0	.	161;92;286	Q7Z3H0;Q0VAA8;Q7Z3H0-2	ANR33_HUMAN;.;.	W	286;92;161	ENSP00000301190:R286W;ENSP00000443722:R92W;ENSP00000344690:R161W	ENSP00000301190:R286W	R	+	1	2	ANKRD33	50570853	0.279000	0.24239	0.605000	0.28930	0.607000	0.37147	0.456000	0.21859	0.192000	0.20272	0.561000	0.74099	CGG	.	.	weak		0.662	ANKRD33-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404515.1	NM_182608		T	52284586	C	T	52284586	3	4	3	1	0	0	0	0	1	0	0	0	661	527	19	1	904	1	ANKRD33	12	52284586	Missense_Mutation	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10		52284586	81567309	56	314											
B3GALTL	145173	hgsc.bcm.edu	37	chr13	31891810	31891810	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtggctacagctacatcaCgggaggaggagggtaactat	11	8	15	7	1	1	0	1	0	0	0	1	3	1	3	0	6	4	3	0	6	4	4	rs144117014		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr13:31891810C>T	ENST00000343307.4	+	13	1321	c.1172C>T	c.(1171-1173)aCg>aTg	p.T391M		NM_194318.3	NP_919299.3	Q6Y288	B3GLT_HUMAN	beta 1,3-galactosyltransferase-like	391					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)		AGCTACATCACGGGAGGAGGA	0.522																																					p.T391M		Atlas-SNP	.											.	B3GALTL	48	.	0			c.C1172T						PASS	.	C	MET/THR	0,4406		0,0,2203	107	100	102		1172	4.9	0.9	13	dbSNP_134	102	2,8598	2.2+/-6.3	0,2,4298	no	missense	B3GALTL	NM_194318.3	81	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	391/499	31891810	2,13004	2203	4300	6503	SO:0001583	missense	145173	exon13			ACATCACGGGAGG	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.1172C>T	13.37:g.31891810C>T	ENSP00000343002:p.Thr391Met	63	0	0		39	14	0.358974	NM_194318	A8K5F8|Q5W0H2|Q6NUI3	Missense_Mutation	SNP	ENST00000343307.4	37	CCDS9341.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.700733	0.88924	0.0	2.33E-4	ENSG00000187676	ENST00000343307	T	0.72394	-0.65	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	T	0.82250	0.4996	M	0.64630	1.985	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.81430	-0.0936	10	0.39692	T	0.17	-18.4961	18.5122	0.90921	0.0:1.0:0.0:0.0	.	391	Q6Y288	B3GLT_HUMAN	M	391	ENSP00000343002:T391M	ENSP00000343002:T391M	T	+	2	0	B3GALTL	30789810	1.000000	0.71417	0.922000	0.36590	0.873000	0.50193	7.264000	0.78432	2.432000	0.82394	0.650000	0.86243	ACG	C|1.000;T|0.000	0.000	weak		0.522	B3GALTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044396.3	NM_194318		T	31891810	C	T	31891810	3	4	3	1	0	0	0	0	1	0	0	0	1252	536	19	1	1222	1	B3GALTL	13	31891810	Missense_Mutation	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10		31891810	83278068	57	315											
SLC38A6	145389	hgsc.bcm.edu	37	chr14	61550378	61550378	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcctcaggagaaccaaacGtgtccacaccttgatcttgc	11	8	9	13	1	2	2	1	1	1	1	3	3	3	2	4	2	3	0	4	2	2	2			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr14:61550378G>A	ENST00000354886.2	+	17	1678	c.1514G>A	c.(1513-1515)cGt>cAt	p.R505H	SLC38A6_ENST00000456840.2_Missense_Mutation_p.V484M	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)		agaaccaaacgtgtccacacc	0.478																																					p.R505H		Atlas-SNP	.											.	SLC38A6	87	.	0			c.G1514A						PASS	.																																			SO:0001583	missense	145389	exon17			CCAAACGTGTCCA	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.1514G>A	14.37:g.61550378G>A	ENSP00000346959:p.Arg505His	47	0	0		24	15	0.625	NM_001172702	C9JWA6|Q86SY5	Missense_Mutation	SNP	ENST00000354886.2	37	CCDS53900.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.89|14.89	2.670972|2.670972	0.47781|0.47781	.|.	.|.	ENSG00000139974|ENSG00000139974	ENST00000354886;ENST00000451406|ENST00000456840	T;T|T	0.06294|0.06608	3.32;3.32|3.28	2.8|2.8	-0.176|-0.176	0.13311|0.13311	.|.	.|.	.|.	.|.	.|.	T|T	0.04137|0.04137	0.0115|0.0115	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	B|B	0.02656|0.02656	0.0|0.0	B|B	0.01281|0.01281	0.0|0.0	T|T	0.44298|0.44298	-0.9337|-0.9337	8|8	0.87932|0.56958	D|D	0|0.05	.|.	0.479|0.479	0.00544|0.00544	0.2013:0.35:0.1969:0.2518|0.2013:0.35:0.1969:0.2518	.|.	505|484	Q8IZM9-2|E7ETF2	.|.	H|M	505;500|484	ENSP00000346959:R505H;ENSP00000395851:R500H|ENSP00000413863:V484M	ENSP00000346959:R505H|ENSP00000413863:V484M	R|V	+|+	2|1	0|0	SLC38A6|SLC38A6	60620131|60620131	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-0.119000|-0.119000	0.10676|0.10676	-0.303000|-0.303000	0.08856|0.08856	-1.816000|-1.816000	0.00601|0.00601	CGT|GTG	.	.	none		0.478	SLC38A6-201	KNOWN	basic|CCDS	protein_coding	protein_coding				A	61550378	G	A	61550378	3	1	3	1	0	0	0	0	1	0	0	0	14623	1145	40	1	1665	1	SLC38A6	14	61550378	Missense_Mutation	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10		61550378	45799162	58	316											
LGMN	5641	hgsc.bcm.edu	37	chr14	93171022	93171022	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttctcacaaaggttgaccaGcacgtacaaatgtctcaacg	13	9	7	12	2	2	1	2	1	2	0	4	1	2	1	1	1	3	3	1	1	4	3			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr14:93171022G>A	ENST00000393218.2	-	14	1559	c.1222C>T	c.(1222-1224)Ctg>Ttg	p.L408L	LGMN_ENST00000555699.1_Intron|LGMN_ENST00000557434.1_Silent_p.L351L|LGMN_ENST00000334869.4_Silent_p.L408L	NM_001008530.2	NP_001008530.1	Q99538	LGMN_HUMAN	legumain	408					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|innate immune response (GO:0045087)|negative regulation of ERBB signaling pathway (GO:1901185)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of neuron apoptotic process (GO:0043524)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|receptor catabolic process (GO:0032801)|renal system process (GO:0003014)|response to acidic pH (GO:0010447)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|toll-like receptor signaling pathway (GO:0002224)|vitamin D metabolic process (GO:0042359)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(5)|skin(2)	18		all_cancers(154;0.0706)		COAD - Colon adenocarcinoma(157;0.224)		AGGTTGACCAGCACGTACAAA	0.468																																					p.L408L		Atlas-SNP	.											.	LGMN	28	.	0			c.C1222T						PASS	.						183	172	175					14																	93171022		2203	4300	6503	SO:0001819	synonymous_variant	5641	exon13			TGACCAGCACGTA	D55696	CCDS9904.1	14q32.12	2011-04-08		2002-01-18	ENSG00000100600	ENSG00000100600			9472	protein-coding gene	gene with protein product		602620	"protease, cysteine, 1 (legumain)"	PRSC1		8893817, 9065484	Standard	NM_001008530		Approved	LGMN1	uc001yaw.3	Q99538		ENST00000393218.2:c.1222C>T	14.37:g.93171022G>A		119	0	0		125	8	0.064	NM_005606	O00123|Q86TV2|Q86TV3|Q9BTY1	Silent	SNP	ENST00000393218.2	37	CCDS9904.1																																																																																			.	.	none		0.468	LGMN-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412288.1	NM_005606		A	93171022	G	A	93171022	2	1	3	1	0	0	0	0	0	0	0	1	8764	962	34	2		2	LGMN	14	93171022	Silent	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10	31620644	93171022	14178518	59	317											
BCL11B	64919	hgsc.bcm.edu	37	chr14	99642463	99642463	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgtgttctgcgcgtgctgcAgcaggaaccacgcgctgttg	5	9	15	12	5	1	0	0	0	1	0	1	1	1	1	1	1	5	6	1	1	1	2			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr14:99642463A>G	ENST00000357195.3	-	4	719	c.710T>C	c.(709-711)cTg>cCg	p.L237P	BCL11B_ENST00000345514.2_Missense_Mutation_p.L166P|BCL11B_ENST00000443726.2_Missense_Mutation_p.L43P	NM_001282237.1|NM_138576.2	NP_001269166.1|NP_612808.1	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B (zinc finger protein)	237					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)		CGCGTGCTGCAGCAGGAACCA	0.637			T	TLX3	T-ALL																																p.L237P		Atlas-SNP	.		Dom	yes		14	14q32.1	64919	B-cell CLL/lymphoma 11B  (CTIP2)		L	.	BCL11B	108	.	0			c.T710C						PASS	.						33	32	32					14																	99642463		2199	4298	6497	SO:0001583	missense	64919	exon4			TGCTGCAGCAGGA	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.710T>C	14.37:g.99642463A>G	ENSP00000349723:p.Leu237Pro	35	0	0		43	14	0.325581	NM_138576	Q9H162	Missense_Mutation	SNP	ENST00000357195.3	37	CCDS9950.1	.	.	.	.	.	.	.	.	.	.	A	18.53	3.643442	0.67244	.	.	ENSG00000127152	ENST00000357195;ENST00000345514;ENST00000443726	T;T;T	0.26223	1.81;1.75;1.8	4.68	4.68	0.58851	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.103621	0.38548	N	0.001653	T	0.48059	0.1479	M	0.64170	1.965	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.50303	-0.8844	10	0.66056	D	0.02	-12.3029	14.4247	0.67207	1.0:0.0:0.0:0.0	.	166;237	Q9C0K0-2;Q9C0K0	.;BC11B_HUMAN	P	237;166;43	ENSP00000349723:L237P;ENSP00000280435:L166P;ENSP00000387419:L43P	ENSP00000280435:L166P	L	-	2	0	BCL11B	98712216	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	9.163000	0.94750	1.883000	0.54544	0.533000	0.62120	CTG	.	.	none		0.637	BCL11B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000072332.2	NM_138576		G	99642463	A	G	99642463	3	3	3	1	0	0	0	0	1	0	0	0	1364	188	7	3	1978	3	BCL11B	14	99642463	Missense_Mutation	SNP	A	TCGA-FA-A4XK-01A-11D-A31X-10	6471441	99642463	7707077	60	318											
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105412163	105412163	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggccctctgggagcttcaCgtccacctggccagcctgga	5	8	13	15	1	2	0	1	0	1	0	3	2	3	2	5	4	2	1	5	4	0	1	rs201181175		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr14:105412163C>G	ENST00000333244.5	-	7	9744	c.9625G>C	c.(9625-9627)Gtg>Ctg	p.V3209L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3209						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)			GGGAGCTTCACGTCCACCTGG	0.607																																					p.V3209L		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	0			c.G9625C						scavenged	.						108	70	83					14																	105412163		1920	3847	5767	SO:0001583	missense	113146	exon7			GCTTCACGTCCAC	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.9625G>C	14.37:g.105412163C>G	ENSP00000353114:p.Val3209Leu	134	2	0.0149254		105	6	0.0571429	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	c	9.043	0.990179	0.18966	.	.	ENSG00000185567	ENST00000333244	T	0.01119	5.31	2.98	-2.26	0.06867	.	.	.	.	.	T	0.00906	0.0030	L	0.35723	1.085	0.09310	N	1	B	0.13594	0.008	B	0.12156	0.007	T	0.48875	-0.8996	9	0.22109	T	0.4	.	0.8864	0.01245	0.2903:0.3589:0.1435:0.2074	.	3209	Q8IVF2	AHNK2_HUMAN	L	3209	ENSP00000353114:V3209L	ENSP00000353114:V3209L	V	-	1	0	AHNAK2	104483208	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.193000	0.00564	-0.054000	0.13266	0.313000	0.20887	GTG	.	.	weak		0.607	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		G	105412163	C	G	105412163	3	3	3	1	0	0	0	0	1	0	0	0	415	536	19	4	7766	4	AHNAK2	14	105412163	Missense_Mutation	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10	5769700	105412163	1937377	61	319											
RPAP1	26015	hgsc.bcm.edu	37	chr15	41826971	41826971	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcaggagccatggcctgcAgtcttgctatgttctcttca	6	13	9	13	0	4	0	2	0	2	0	5	1	4	1	3	2	3	3	3	2	1	4			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr15:41826971A>G	ENST00000304330.4	-	6	820	c.704T>C	c.(703-705)cTg>cCg	p.L235P	RPAP1_ENST00000568413.1_5'Flank|RPAP1_ENST00000561603.1_Missense_Mutation_p.L235P	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	235						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)		CATGGCCTGCAGTCTTGCTAT	0.572																																					p.L235P		Atlas-SNP	.											.	RPAP1	111	.	0			c.T704C						PASS	.						123	98	107					15																	41826971		2203	4300	6503	SO:0001583	missense	26015	exon6			GCCTGCAGTCTTG	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.704T>C	15.37:g.41826971A>G	ENSP00000306123:p.Leu235Pro	58	0	0		43	15	0.348837	NM_015540	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Missense_Mutation	SNP	ENST00000304330.4	37	CCDS10079.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.463125	0.84425	.	.	ENSG00000103932	ENST00000304330	T	0.35048	1.33	5.22	5.22	0.72569	RNA polymerase II-associated protein 1, N-terminal (1);	0.157253	0.43416	D	0.000570	T	0.67439	0.2893	M	0.92026	3.265	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.76000	-0.3119	10	0.87932	D	0	-14.2976	14.084	0.64944	1.0:0.0:0.0:0.0	.	235	Q9BWH6	RPAP1_HUMAN	P	235	ENSP00000306123:L235P	ENSP00000306123:L235P	L	-	2	0	RPAP1	39614263	1.000000	0.71417	0.743000	0.31040	0.974000	0.67602	8.707000	0.91367	1.977000	0.57605	0.402000	0.26972	CTG	.	.	none		0.572	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540		G	41826971	A	G	41826971	3	3	3	1	0	0	0	0	1	0	0	0	13556	188	7	3	3557	3	RPAP1	15	41826971	Missense_Mutation	SNP	A	TCGA-FA-A4XK-01A-11D-A31X-10		41826971	60704421	62	320											
CHRNA3	1136	hgsc.bcm.edu	37	chr15	78894447	78894447	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcgccttatcgtaggaccaGgaaccgaacttcatggtaca	11	10	9	11	3	1	0	1	0	0	0	3	3	1	2	3	3	3	2	3	3	5	5			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr15:78894447G>A	ENST00000326828.5	-	5	921	c.537C>T	c.(535-537)tcC>tcT	p.S179S	CHRNA3_ENST00000348639.3_Silent_p.S179S	NM_000743.4	NP_000734.2	P32297	ACHA3_HUMAN	cholinergic receptor, nicotinic, alpha 3 (neuronal)	179					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|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)|nervous system development (GO:0007399)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane potential (GO:0042391)|regulation of smooth muscle contraction (GO:0006940)|signal transduction (GO:0007165)|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)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|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)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18					Bupropion(DB01156)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Levomethadyl Acetate(DB01227)|Nicotine(DB00184)|Pentolinium(DB01090)|Varenicline(DB01273)	CGTAGGACCAGGAACCGAACT	0.502																																					p.S179S		Atlas-SNP	.											.	CHRNA3	56	.	0			c.C537T						PASS	.						187	169	175					15																	78894447		2196	4293	6489	SO:0001819	synonymous_variant	1136	exon5			GGACCAGGAACCG		CCDS10305.1, CCDS53964.1	15q24	2012-02-11	2012-02-07		ENSG00000080644	ENSG00000080644		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1957	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 3 (neuronal)"	118503	"cholinergic receptor, nicotinic, alpha polypeptide 3"			2004777	Standard	NM_000743		Approved		uc002bec.3	P32297	OTTHUMG00000143863	ENST00000326828.5:c.537C>T	15.37:g.78894447G>A		123	0	0		107	38	0.35514	NM_000743	Q15823|Q4KMN8|Q86U77|Q96RH3|Q99553|Q9BQ93|Q9BRR4	Silent	SNP	ENST00000326828.5	37	CCDS10305.1																																																																																			.	.	none		0.502	CHRNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290111.3			A	78894447	G	A	78894447	2	1	3	1	0	0	0	0	0	0	0	1	3386	987	35	2		2	CHRNA3	15	78894447	Silent	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10	37067476	78894447	23636945	63	321											
ABCC6	368	hgsc.bcm.edu	37	chr16	16248757	16248757	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgatgctgatcctggagcgCagtgtgtgcagccccacgtg	7	9	14	11	2	0	2	0	2	0	0	1	3	1	3	3	1	4	3	3	1	0	0			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr16:16248757C>T	ENST00000205557.7	-	28	4043	c.4014G>A	c.(4012-4014)ctG>ctA	p.L1338L		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1338	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)	TCCTGGAGCGCAGTGTGTGCA	0.687																																					p.L1338L		Atlas-SNP	.											.	ABCC6	110	.	0			c.G4014A						PASS	.						29	27	28					16																	16248757		2197	4299	6496	SO:0001819	synonymous_variant	368	exon28			GGAGCGCAGTGTG	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.4014G>A	16.37:g.16248757C>T		98	0	0		93	33	0.354839	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Silent	SNP	ENST00000205557.7	37	CCDS10568.1																																																																																			.	.	none		0.687	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2			T	16248757	C	T	16248757	2	4	3	1	0	0	0	0	0	0	0	1	57	697	25	2		2	ABCC6	16	16248757	Silent	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10		16248757	74105996	64	322											
CES7	221223	hgsc.bcm.edu	37	chr16	55890347	55890347	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggagccactgaggatctcaGgagcctccttctgtggagag	8	9	14	10	0	2	2	1	1	2	1	4	6	3	5	3	4	2	0	3	4	0	1			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr16:55890347G>A	ENST00000290567.9	-	9	1188	c.1067C>T	c.(1066-1068)cCt>cTt	p.P356L	CES5A_ENST00000521992.1_Missense_Mutation_p.P385L|CES5A_ENST00000541580.1_5'UTR|CES5A_ENST00000319165.9_Missense_Mutation_p.P356L|CES5A_ENST00000518005.1_Missense_Mutation_p.P250L|CES5A_ENST00000520435.1_Missense_Mutation_p.P326L	NM_001143685.1	NP_001137157.1	Q6NT32	EST5A_HUMAN	carboxylesterase 5A	356						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						GAGGATCTCAGGAGCCTCCTT	0.547																																					p.P385L		Atlas-SNP	.											.	CES5A	206	.	0			c.C1154T						PASS	.						135	115	122					16																	55890347		2198	4300	6498	SO:0001583	missense	221223	exon10			ATCTCAGGAGCCT	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.1067C>T	16.37:g.55890347G>A	ENSP00000290567:p.Pro356Leu	48	0	0		60	42	0.7	NM_001190158	B7Z252|B7ZLB6|Q8NBC8|Q96DN9	Missense_Mutation	SNP	ENST00000290567.9	37	CCDS45490.1	.	.	.	.	.	.	.	.	.	.	G	4.176	0.031232	0.08101	.	.	ENSG00000159398	ENST00000521992;ENST00000319165;ENST00000518005;ENST00000290567;ENST00000520435;ENST00000541580	T;T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19;-0.19	3.18	3.18	0.36537	Carboxylesterase, type B (1);	0.794542	0.10319	N	0.688955	T	0.51669	0.1688	L	0.33753	1.03	0.30761	N	0.744061	B;B	0.32245	0.1;0.361	B;B	0.34242	0.066;0.178	T	0.54794	-0.8240	10	0.42905	T	0.14	.	10.1997	0.43075	0.0:0.0:1.0:0.0	.	356;356	Q6NT32;Q6NT32-2	EST5A_HUMAN;.	L	385;356;250;356;326;136	ENSP00000428864:P385L;ENSP00000324271:P356L;ENSP00000428571:P250L;ENSP00000290567:P356L;ENSP00000428887:P326L	ENSP00000290567:P356L	P	-	2	0	CES5A	54447848	0.998000	0.40836	0.399000	0.26333	0.068000	0.16541	3.777000	0.55364	2.100000	0.63781	0.449000	0.29647	CCT	.	.	none		0.547	CES5A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256975.3	NM_145024		A	55890347	G	A	55890347	3	1	3	1	0	0	0	0	1	0	0	0	3274	1000	35	2	680	2	CES7	16	55890347	Missense_Mutation	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10	39641590	55890347	34464406	65	323											
PFN1	5216	hgsc.bcm.edu	37	chr17	4851557	4851557	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	accgcgcaggcctcgcagtaCcgtgatgttgacgaacgttt	8	9	12	12	6	0	2	0	2	0	0	1	3	0	2	3	1	2	5	3	1	2	3			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr17:4851557C>T	ENST00000225655.5	-	1	752		c.e1+1		ENO3_ENST00000519584.1_5'Flank|ENO3_ENST00000323997.6_5'Flank|PFN1_ENST00000574872.1_5'Flank	NM_005022.3	NP_005013.1	P07737	PROF1_HUMAN	profilin 1						actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cell death (GO:0008219)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of ATPase activity (GO:0032781)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of ruffle assembly (GO:1900029)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	actin binding (GO:0003779)|adenyl-nucleotide exchange factor activity (GO:0000774)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|poly(A) RNA binding (GO:0044822)|proline-rich region binding (GO:0070064)			NS(1)|endometrium(1)|lung(2)|upper_aerodigestive_tract(1)	5						CCTCGCAGTACCGTGATGTTG	0.706																																					.		Atlas-SNP	.											.	PFN1	6	.	0			c.132+1G>A						PASS	.						50	46	48					17																	4851557		2203	4300	6503	SO:0001630	splice_region_variant	5216	exon2			GCAGTACCGTGAT	BC057828	CCDS11061.1	17p13.2	2010-07-09			ENSG00000108518	ENSG00000108518			8881	protein-coding gene	gene with protein product		176610				3356709, 1968707	Standard	NM_005022		Approved		uc002gaa.4	P07737	OTTHUMG00000099396	ENST00000225655.5:c.132+1G>A	17.37:g.4851557C>T		34	0	0		23	10	0.434783	NM_005022	Q53Y44	Splice_Site	SNP	ENST00000225655.5	37	CCDS11061.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.986323	0.74589	.	.	ENSG00000108518	ENST00000225655	.	.	.	3.79	3.79	0.43588	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1965	0.59740	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PFN1	4792302	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.338000	0.59316	1.953000	0.56701	0.563000	0.77884	.	.	.	none		0.706	PFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216853.1	NM_005022	Intron	T	4851557	C	T	4851557	5	4	3	1	0	0	0	0	0	0	1	0	11776	521	18	2	301	2	PFN1	17	4851557	Splice_Site	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10		4851557	76343653	66	324											
KRT13	3860	hgsc.bcm.edu	37	chr17	39661359	39661359	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taggggctgtagtcccgctcAgggctagctgggctctgctt	4	11	15	11	1	2	0	1	0	1	0	3	0	3	0	1	4	2	7	1	4	3	4			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr17:39661359A>G	ENST00000246635.3	-	1	490	c.444T>C	c.(442-444)ccT>ccC	p.P148P	KRT13_ENST00000587118.1_5'Flank|KRT13_ENST00000587544.1_Silent_p.P148P|AC019349.5_ENST00000411759.1_RNA|KRT13_ENST00000336861.3_Silent_p.P148P	NM_153490.2	NP_705694	P13646	K1C13_HUMAN	keratin 13	148	Linker 1.|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)				AGTCCCGCTCAGGGCTAGCTG	0.617																																					p.P148P		Atlas-SNP	.											.	KRT13	72	.	0			c.T444C						PASS	.						100	92	94					17																	39661359		2203	4300	6503	SO:0001819	synonymous_variant	3860	exon1			CCGCTCAGGGCTA		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.444T>C	17.37:g.39661359A>G		75	0	0		58	20	0.344828	NM_002274	Q53G54|Q6AZK5|Q8N240	Silent	SNP	ENST00000246635.3	37	CCDS11396.1																																																																																			.	.	none		0.617	KRT13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257297.1	NM_153490		G	39661359	A	G	39661359	2	3	3	1	0	0	0	0	0	0	0	1	8459	175	7	3		3	KRT13	17	39661359	Silent	SNP	A	TCGA-FA-A4XK-01A-11D-A31X-10	34809802	39661359	41533851	67	325											
CACNA1G	8913	hgsc.bcm.edu	37	chr17	48674136	48674136	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcggaagagcctgctgcCgcctctcatcatccacacgg	7	7	11	16	3	2	1	2	0	1	1	4	2	3	2	4	2	4	2	4	2	1	0	rs573756072		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr17:48674136C>T	ENST00000359106.5	+	16	3110	c.3110C>T	c.(3109-3111)cCg>cTg	p.P1037L	CACNA1G_ENST00000512389.1_Missense_Mutation_p.P1037L|CACNA1G_ENST00000505165.1_Missense_Mutation_p.P1037L|CACNA1G_ENST00000515165.1_Missense_Mutation_p.P1037L|CACNA1G_ENST00000515411.1_Missense_Mutation_p.P1037L|CACNA1G_ENST00000513964.1_Missense_Mutation_p.P1037L|CACNA1G_ENST00000354983.4_Missense_Mutation_p.P1014L|CACNA1G_ENST00000510366.1_Missense_Mutation_p.P1037L|CACNA1G_ENST00000514717.1_Missense_Mutation_p.P1014L|CACNA1G_ENST00000515765.1_Missense_Mutation_p.P1037L|CACNA1G_ENST00000352832.5_Missense_Mutation_p.P1014L|CACNA1G_ENST00000514181.1_Missense_Mutation_p.P1037L|CACNA1G_ENST00000429973.2_Missense_Mutation_p.P1037L|CACNA1G_ENST00000514079.1_Missense_Mutation_p.P1037L|CACNA1G_ENST00000442258.2_Missense_Mutation_p.P1014L|CACNA1G_ENST00000507896.1_Missense_Mutation_p.P1037L|CACNA1G_ENST00000507609.1_Missense_Mutation_p.P1037L|CACNA1G_ENST00000513689.2_Missense_Mutation_p.P1037L|CACNA1G_ENST00000507336.1_Missense_Mutation_p.P1037L|CACNA1G_ENST00000503485.1_Missense_Mutation_p.P1037L|CACNA1G_ENST00000502264.1_Missense_Mutation_p.P1014L|CACNA1G_ENST00000510115.1_Missense_Mutation_p.P1014L|CACNA1G_ENST00000360761.4_Missense_Mutation_p.P1014L|CACNA1G_ENST00000507510.2_Missense_Mutation_p.P1037L|CACNA1G_ENST00000358244.5_Missense_Mutation_p.P1014L|CACNA1G_ENST00000416767.4_Missense_Mutation_p.P1037L	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	1037					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)	AGCCTGCTGCCGCCTCTCATC	0.711													C|||	1	0.000199681	0.0	0.0	5008	,	,		13405	0.0		0.001	False		,,,				2504	0.0				p.P1037L		Atlas-SNP	.											.	CACNA1G	659	.	0			c.C3110T						PASS	.						17	21	20					17																	48674136		2090	4220	6310	SO:0001583	missense	8913	exon16			TGCTGCCGCCTCT	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.3110C>T	17.37:g.48674136C>T	ENSP00000352011:p.Pro1037Leu	39	0	0		37	13	0.351351	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	37	CCDS45730.1	.	.	.	.	.	.	.	.	.	.	c	22.2	4.262675	0.80358	.	.	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	0.90563	-2.69;-2.69;-2.69;-2.69;-2.69;-2.69;-2.69;-2.69;-2.69;-2.69;-2.69;-2.69;-2.69;-2.69;-2.69;-2.69;-2.69;-2.69;-2.69;-2.69;-2.69;-2.69;-2.69;-2.69;-2.69;-2.69	4.78	4.78	0.61160	.	0.494671	0.21871	N	0.067899	D	0.92971	0.7763	L	0.47716	1.5	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;P;P;D;D;D;P;D;D;D;P	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.998;1.0;0.99;1.0;0.999;0.627;0.827;0.995;1.0;1.0;0.953;1.0;0.98;0.982;0.744	D;D;D;D;D;D;D;D;D;D;D;D;D;P;D;D;B;B;P;D;D;P;D;P;P;B	0.91635	0.994;0.957;0.999;0.997;0.999;0.999;0.996;0.999;0.996;0.957;0.999;0.926;0.971;0.87;0.999;0.952;0.053;0.18;0.867;0.995;0.992;0.481;0.999;0.579;0.459;0.115	D	0.93116	0.6521	10	0.62326	D	0.03	.	12.8738	0.57980	0.1627:0.8373:0.0:0.0	.	1014;1037;1037;1037;1037;1037;1037;1037;1037;1037;1037;1014;1037;1037;1037;1037;1037;1014;1037;1014;1014;1014;1014;1037;1014;1037	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;.;.	L	1014;1014;1037;1014;1014;1014;1037;1037;1014;1037;1037;1037;1037;1037;1037;1014;1037;1037;1037;1037;1014;1037;1037;1037;1037;1037	ENSP00000353990:P1014L;ENSP00000339302:P1014L;ENSP00000392390:P1037L;ENSP00000347078:P1014L;ENSP00000409759:P1014L;ENSP00000425522:P1014L;ENSP00000426261:P1037L;ENSP00000425451:P1037L;ENSP00000422407:P1014L;ENSP00000426814:P1037L;ENSP00000427238:P1037L;ENSP00000423112:P1037L;ENSP00000420918:P1037L;ENSP00000426172:P1037L;ENSP00000423045:P1037L;ENSP00000427173:P1014L;ENSP00000426098:P1037L;ENSP00000425698:P1037L;ENSP00000426232:P1037L;ENSP00000423317:P1037L;ENSP00000350979:P1014L;ENSP00000352011:P1037L;ENSP00000414388:P1037L;ENSP00000423155:P1037L;ENSP00000422268:P1037L;ENSP00000421518:P1037L	ENSP00000339302:P1014L	P	+	2	0	CACNA1G	46029135	1.000000	0.71417	0.592000	0.28758	0.943000	0.58893	7.487000	0.81328	2.210000	0.71456	0.491000	0.48974	CCG	.	.	none		0.711	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		T	48674136	C	T	48674136	3	4	3	1	0	0	0	0	1	0	0	0	2546	652	23	1	3172	1	CACNA1G	17	48674136	Missense_Mutation	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10	9012777	48674136	32521074	68	326											
RECQL5	9400	hgsc.bcm.edu	37	chr17	73654377	73654377	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cttctactgcccaagccttaCctggagttttgctacttcct	6	15	6	14	0	1	0	0	0	1	0	2	1	2	1	4	1	6	2	4	1	4	7			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr17:73654377C>T	ENST00000317905.5	-	7	1309		c.e7+1		RECQL5_ENST00000420326.2_Splice_Site|RECQL5_ENST00000423245.2_Splice_Site|RECQL5_ENST00000340830.5_Splice_Site|RECQL5_ENST00000584999.1_Splice_Site	NM_004259.6	NP_004250.4	O94762	RECQ5_HUMAN	RecQ protein-like 5						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)			CCAAGCCTTACCTGGAGTTTT	0.502								Other identified genes with known or suspected DNA repair function																													.		Atlas-SNP	.											.	RECQL5	77	.	0			c.1149+1G>A						PASS	.						196	185	189					17																	73654377		2203	4300	6503	SO:0001630	splice_region_variant	9400	exon8			GCCTTACCTGGAG	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.1149+1G>A	17.37:g.73654377C>T		60	0	0		55	18	0.327273	NM_004259	Q9H0B1|Q9P1W7|Q9UNC8	Splice_Site	SNP	ENST00000317905.5	37	CCDS42380.1	.	.	.	.	.	.	.	.	.	.	C	14.92	2.679018	0.47886	.	.	ENSG00000108469	ENST00000423245;ENST00000317905;ENST00000420326;ENST00000340830	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.1346	0.98019	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RECQL5	71165972	1.000000	0.71417	0.999000	0.59377	0.594000	0.36715	7.003000	0.76310	2.765000	0.95021	0.655000	0.94253	.	.	.	none		0.502	RECQL5-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448207.1	NM_004259	Intron	T	73654377	C	T	73654377	5	4	3	1	0	0	0	0	0	0	1	0	13218	521	18	2	1968	2	RECQL5	17	73654377	Splice_Site	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10	24980241	73654377	7540833	69	327											
SOCS3	9021	hgsc.bcm.edu	37	chr17	76354835	76354835	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcacgcagtcgaagcggggCacgggctgcgtgctccgggg	6	4	19	12	6	0	0	0	0	0	0	2	1	1	0	1	5	4	5	1	5	1	0			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr17:76354835C>A	ENST00000330871.2	-	2	757	c.342G>T	c.(340-342)gtG>gtT	p.V114V	RP11-806H10.4_ENST00000592569.1_lincRNA	NM_003955.3	NP_003946.3	O14543	SOCS3_HUMAN	suppressor of cytokine signaling 3	114	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)			CGAAGCGGGGCACGGGCTGCG	0.667																																					p.V114V		Atlas-SNP	.											.	SOCS3	16	.	0			c.G342T						PASS	.						29	30	30					17																	76354835		2201	4298	6499	SO:0001819	synonymous_variant	9021	exon2			GCGGGGCACGGGC	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.342G>T	17.37:g.76354835C>A		79	0	0		64	34	0.53125	NM_003955	O14509	Silent	SNP	ENST00000330871.2	37	CCDS11756.1																																																																																			.	.	none		0.667	SOCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437300.1			A	76354835	C	A	76354835	2	1	3	1	0	0	0	0	0	0	0	1	14930	697	25	4		4	SOCS3	17	76354835	Silent	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10	2700458	76354835	4840375	70	328											
AATK	9625	hgsc.bcm.edu	37	chr17	79098602	79098602	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaccagctctggcgcgatcCagcgcagaggcacccacagc	9	3	11	18	3	1	1	0	0	1	1	2	2	2	1	4	2	3	3	4	2	0	0			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr17:79098602C>T	ENST00000326724.4	-	9	911	c.887G>A	c.(886-888)tGg>tAg	p.W296*	MIR338_ENST00000390137.2_RNA|MIR657_ENST00000385003.1_RNA|AATK_ENST00000417379.1_Nonsense_Mutation_p.W193*|AATK_ENST00000572339.1_5'Flank	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	296	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)			TGGCGCGATCCAGCGCAGAGG	0.667																																					p.W296X		Atlas-SNP	.											.	AATK	102	.	0			c.G887A						PASS	.						36	43	40					17																	79098602		2171	4255	6426	SO:0001587	stop_gained	9625	exon9			GCGATCCAGCGCA	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.887G>A	17.37:g.79098602C>T	ENSP00000324196:p.Trp296*	146	0	0		92	5	0.0543478	NM_001080395	O75136|Q6ZN31|Q86X28	Nonsense_Mutation	SNP	ENST00000326724.4	37	CCDS45807.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	38|38	6.718074|6.718074	0.97784|0.97784	.|.	.|.	ENSG00000181409|ENSG00000181409	ENST00000417379|ENST00000326724;ENST00000374792	.|.	.|.	.|.	3.86|3.86	3.86|3.86	0.44501|0.44501	.|.	.|0.000000	.|0.64402	.|D	.|0.000001	T|.	0.34571|.	0.0902|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.33317|.	-0.9873|.	3|.	.|0.02654	.|T	.|1	.|.	14.7321|14.7321	0.69388|0.69388	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	R|X	249|296	.|.	.|ENSP00000324196:W296X	G|W	-|-	1|2	0|0	AATK|AATK	76713197|76713197	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.907000|0.907000	0.53573|0.53573	5.431000|5.431000	0.66507|0.66507	1.982000|1.982000	0.57802|0.57802	0.591000|0.591000	0.81541|0.81541	GGA|TGG	.	.	none		0.667	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920		T	79098602	C	T	79098602	4	4	3	1	0	0	0	0	0	1	0	0	26	595	21	2	3261	2	AATK	17	79098602	Nonsense_Mutation	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10	2743767	79098602	2096608	71	329											
ABCA7	10347	hgsc.bcm.edu	37	chr19	1046827	1046827	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgtgtgctgagccggtcgcTgccgctcttcctgacgctgg	2	10	15	14	5	1	2	0	2	1	0	3	2	2	2	3	2	3	4	3	2	0	1			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr19:1046827T>C	ENST00000263094.6	+	14	1880	c.1649T>C	c.(1648-1650)cTg>cCg	p.L550P	ABCA7_ENST00000433129.1_Missense_Mutation_p.L550P|ABCA7_ENST00000533574.1_Intron|ABCA7_ENST00000435683.2_Missense_Mutation_p.L412P	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	550					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)		AGCCGGTCGCTGCCGCTCTTC	0.697																																					p.L550P		Atlas-SNP	.											.	ABCA7	174	.	0			c.T1649C						PASS	.						18	16	17					19																	1046827		2119	4178	6297	SO:0001583	missense	10347	exon14			GGTCGCTGCCGCT	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.1649T>C	19.37:g.1046827T>C	ENSP00000263094:p.Leu550Pro	23	0	0		23	6	0.26087	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	t	24.2	4.506096	0.85282	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.89270	-2.49;-2.49	5.06	5.06	0.68205	.	.	.	.	.	D	0.94988	0.8378	M	0.90483	3.12	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.79784	0.993;0.992	D	0.95706	0.8753	9	0.87932	D	0	.	12.7496	0.57300	0.0:0.0:0.0:1.0	.	412;550	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	P	550	ENSP00000263094:L550P;ENSP00000414062:L550P	ENSP00000263094:L550P	L	+	2	0	ABCA7	997827	1.000000	0.71417	0.999000	0.59377	0.857000	0.48899	7.824000	0.86668	1.915000	0.55452	0.454000	0.30748	CTG	.	.	none		0.697	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		C	1046827	T	C	1046827	3	2	3	1	0	0	0	0	1	0	0	0	37	1580	55	3	1699	3	ABCA7	19	1046827	Missense_Mutation	SNP	T	TCGA-FA-A4XK-01A-11D-A31X-10		1046827	58082156	72	330											
MUC16	94025	hgsc.bcm.edu	37	chr19	9047271	9047271	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cagcatctttgatgcaccagGggagacagggagagttggaa	12	7	15	7	0	1	3	0	1	1	2	1	6	1	4	1	4	2	3	1	4	1	2			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr19:9047271G>A	ENST00000397910.4	-	5	34563	c.34360C>T	c.(34360-34362)Cct>Tct	p.P11454S		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	11456	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						GATGCACCAGGGGAGACAGGG	0.493																																					p.P11454S		Atlas-SNP	.											.	MUC16	4315	.	0			c.C34360T						PASS	.						173	169	170					19																	9047271		2012	4170	6182	SO:0001583	missense	94025	exon5			CACCAGGGGAGAC	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.34360C>T	19.37:g.9047271G>A	ENSP00000381008:p.Pro11454Ser	76	0	0		81	31	0.382716	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	5.483	0.274203	0.10403	.	.	ENSG00000181143	ENST00000397910	T	0.01947	4.54	3.21	-3.54	0.04653	.	.	.	.	.	T	0.02455	0.0075	L	0.55481	1.735	.	.	.	B	0.27166	0.17	B	0.28709	0.093	T	0.43475	-0.9389	8	0.87932	D	0	.	2.7963	0.05402	0.3391:0.0:0.2952:0.3658	.	11454	B5ME49	.	S	11454	ENSP00000381008:P11454S	ENSP00000381008:P11454S	P	-	1	0	MUC16	8908271	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-2.871000	0.00720	-0.590000	0.05866	-1.173000	0.01734	CCT	.	.	none		0.493	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9047271	G	A	9047271	3	1	3	1	0	0	0	0	1	0	0	0	9982	1232	43	2	9483	2	MUC16	19	9047271	Missense_Mutation	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10	8000444	9047271	50081712	73	331											
NWD1	284434	hgsc.bcm.edu	37	chr19	16860860	16860860	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cacctcatcctctcagcttgCtcgggggcactgggggtttt	4	12	12	13	1	2	0	2	0	1	0	5	0	3	0	2	4	2	4	2	4	0	3			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr19:16860860C>T	ENST00000552788.1	+	4	1407	c.1407C>T	c.(1405-1407)tgC>tgT	p.C469C	NWD1_ENST00000549814.1_Silent_p.C469C|NWD1_ENST00000339803.6_Silent_p.C334C|NWD1_ENST00000379808.3_Silent_p.C469C|NWD1_ENST00000524140.2_Silent_p.C469C|NWD1_ENST00000523826.1_Silent_p.C263C			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	469	NACHT.						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						TCTCAGCTTGCTCGGGGGCAC	0.637																																					p.C469C		Atlas-SNP	.											NWD1_ENST00000524140,NS,neuroblastoma,+2,2	NWD1	303	2	0			c.C1407T						PASS	.						65	68	67					19																	16860860		2203	4300	6503	SO:0001819	synonymous_variant	284434	exon6			AGCTTGCTCGGGG	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.1407C>T	19.37:g.16860860C>T		84	0	0		82	22	0.268293	NM_001007525	C9J021|Q68CT3	Silent	SNP	ENST00000552788.1	37																																																																																				.	.	none		0.637	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525		T	16860860	C	T	16860860	2	4	3	1	0	0	0	0	0	0	0	1	10790	805	28	2		2	NWD1	19	16860860	Silent	SNP	C	TCGA-FA-A4XK-01A-11D-A31X-10	7813589	16860860	42268123	74	332											
B3GNT8	593	hgsc.bcm.edu	37	chr19	41932420	41932420	+	IGR	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggcagccccccgtttcagtGctgtccccactgggcaggga	5	8	13	15	1	1	0	1	0	0	0	2	1	2	1	5	3	2	4	5	3	0	1			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr19:41932420G>A	ENST00000269980.2	+	0	2103				B3GNT8_ENST00000321702.2_Silent_p.S88S|B3GNT8_ENST00000601379.1_Intron|CTC-435M10.6_ENST00000598887.1_RNA	NM_000709.3|NM_001164783.1	NP_000700.1|NP_001158255.1	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha polypeptide						branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity (GO:0003863)|alpha-ketoacid dehydrogenase activity (GO:0003826)|carboxy-lyase activity (GO:0016831)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	10						CCGTTTCAGTGCTGTCCCCAC	0.682																																					p.S88S		Atlas-SNP	.											.	B3GNT8	20	.	0			c.C264T						PASS	.						11	11	11					19																	41932420		2181	4275	6456	SO:0001628	intergenic_variant	374907	exon3			TTCAGTGCTGTCC	J04474	CCDS12581.1	19q13.1-q13.2	2008-07-09	2005-11-29		ENSG00000248098	ENSG00000248098			986	protein-coding gene	gene with protein product	"maple syrup urine disease"	608348	"branched chain keto acid dehydrogenase E1, alpha polypeptide (maple syrup urine disease)", "2-oxoisovalerate dehydrogenase (lipoamide)"	OVD1A			Standard	NM_000709		Approved	MSU	uc002oqq.3	P12694	OTTHUMG00000168128		19.37:g.41932420G>A		53	0	0		52	13	0.25	NM_198540	B4DP47|E7EW46|Q16034|Q16472	Silent	SNP	ENST00000269980.2	37	CCDS12581.1																																																																																			.	.	none		0.682	BCKDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398313.3	NM_000709		A	41932420	G	A	41932420	1	1	3	0	1	0	0	0	0	0	0	0	1263	1310	46	2		2	B3GNT8	19	41932420	IGR	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10	25071560	41932420	17196563	75	333											
CD79A	973	hgsc.bcm.edu	37	chr19	42384803	42384803	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgaagatgaaaacctttatGaagtgagtgaagggtgggga	15	9	15	2	0	0	6	0	5	0	1	0	7	0	7	1	3	1	0	1	3	6	2			TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr19:42384803G>T	ENST00000221972.3	+	4	750	c.565G>T	c.(565-567)Gaa>Taa	p.E189*	ARHGEF1_ENST00000354532.3_5'Flank|CD79A_ENST00000444740.2_Nonsense_Mutation_p.E151*|ARHGEF1_ENST00000347545.4_5'Flank|ARHGEF1_ENST00000599846.1_5'Flank	NM_001783.3|NM_021601.3	NP_001774.1|NP_067612.1	P11912	CD79A_HUMAN	CD79a molecule, immunoglobulin-associated alpha	189	ITAM. {ECO:0000255|PROSITE- ProRule:PRU00379}.			E -> G (in Ref. 10; BAD97091). {ECO:0000305}.	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						AAACCTTTATGAAGTGAGTGA	0.597			"O, S"		DLBCL																																p.E189X		Atlas-SNP	.		Dom	yes		19	19q13.2	973	"CD79a molecule, immunoglobulin-associated alpha"		L	.	CD79A	25	.	0			c.G565T						PASS	.						17	17	17					19																	42384803		2059	4062	6121	SO:0001587	stop_gained	973	exon4			CTTTATGAAGTGA	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.565G>T	19.37:g.42384803G>T	ENSP00000221972:p.Glu189*	78	0	0		51	20	0.392157	NM_001783	A0N775|Q53FB8	Nonsense_Mutation	SNP	ENST00000221972.3	37	CCDS12589.1	.	.	.	.	.	.	.	.	.	.	G	15.17	2.752565	0.49362	.	.	ENSG00000105369	ENST00000221972;ENST00000444740	.	.	.	3.89	3.89	0.44902	.	0.222714	0.28125	N	0.016501	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-31.5868	12.151	0.54050	0.0:0.0:1.0:0.0	.	.	.	.	X	189;151	.	ENSP00000221972:E189X	E	+	1	0	CD79A	47076643	1.000000	0.71417	0.983000	0.44433	0.048000	0.14542	4.749000	0.62155	2.135000	0.66039	0.449000	0.29647	GAA	.	.	none		0.597	CD79A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463058.1			T	42384803	G	T	42384803	4	4	3	1	0	0	0	0	0	1	0	0	3038	1291	45	4	579	4	CD79A	19	42384803	Nonsense_Mutation	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10	452383	42384803	16744180	76	334											
PSG3	5671	hgsc.bcm.edu	37	chr19	43234049	43234049	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaatgaggatcctgttttcaAtgggtcgctttaccctggga	8	13	12	8	1	1	1	1	1	0	0	3	4	2	3	2	3	1	2	2	3	3	4	rs28698193	byFrequency	TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr19:43234049A>T	ENST00000327495.5	-	4	1053	c.869T>A	c.(868-870)aTt>aAt	p.I290N	PSG3_ENST00000595140.1_Missense_Mutation_p.I290N	NM_021016.3	NP_066296.2	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	290	Ig-like C2-type 2.		I -> N (in dbSNP:rs28698193).		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)				CCTGTTTTCAATGGGTCGCTT	0.488													.|||	690	0.13778	0.3116	0.1225	5008	,	,		21813	0.0248		0.0706	False		,,,				2504	0.0992				p.I290N		Atlas-SNP	.											.	PSG3	82	.	0			c.T869A						PASS	.	T	ASN/ILE	845,2175		128,589,793	84	85	85		869	-2.2	0	19	dbSNP_125	85	372,5032		10,352,2340	no	missense	PSG3	NM_021016.3	149	138,941,3133	TT,TA,AA		6.8838,27.9801,14.4468	possibly-damaging	290/429	43234049	1217,7207	1510	2702	4212	SO:0001583	missense	5671	exon4			TTTTCAATGGGTC		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.869T>A	19.37:g.43234049A>T	ENSP00000332215:p.Ile290Asn	54	0	0		53	5	0.0943396	NM_021016	Q08265|Q9BRW2|Q9UPL4|Q9UQ77	Missense_Mutation	SNP	ENST00000327495.5	37	CCDS12611.1	273	0.125	154	0.3130081300813008	52	0.143646408839779	8	0.013986013986013986	59	0.07783641160949868	t	0.001	-3.244528	0.00022	0.279801	0.068838	ENSG00000221826	ENST00000327495	T	0.09255	3.0	1.1	-2.21	0.06973	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.00077	-2.24	0.80722	P	0.0	B;B	0.14012	0.009;0.001	B;B	0.17979	0.02;0.004	T	0.31752	-0.9932	8	0.12103	T	0.63	.	0.3073	0.00282	0.2656:0.215:0.3044:0.2151	rs28698193;rs60112374	268;290	Q08266;Q16557	.;PSG3_HUMAN	N	290	ENSP00000332215:I290N	ENSP00000332215:I290N	I	-	2	0	PSG3	47925889	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.576000	0.00112	-4.294000	0.00058	-4.092000	0.00011	ATT	A|0.879;T|0.121	0.121	strong		0.488	PSG3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321423.2	NM_021016		T	43234049	A	T	43234049	3	4	3	1	0	0	0	0	1	0	0	0	12668	101	4	5	429	5	PSG3	19	43234049	Missense_Mutation	SNP	A	TCGA-FA-A4XK-01A-11D-A31X-10	849246	43234049	15894934	77	335											
NCOA3	8202	hgsc.bcm.edu	37	chr20	46279884	46279884	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caacagcaacagcaacagcaAcagcagcaacagcagcaaac	20	0	7	14	0	0	0	0	0	0	0	0	0	0	0	0	0	13	7	0	0	6	0	rs112355546		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr20:46279884A>G	ENST00000371998.3	+	20	4001	c.3810A>G	c.(3808-3810)caA>caG	p.Q1270Q	NCOA3_ENST00000341724.6_Silent_p.Q1196Q|NCOA3_ENST00000372004.3_Silent_p.Q1266Q|NCOA3_ENST00000371997.3_Silent_p.Q1261Q			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	1270	Acetyltransferase.|Poly-Gln.				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						agcaacagcaacagcagcaac	0.572																																					p.Q1270Q		Atlas-SNP	.											.	NCOA3	156	.	0			c.A3810G						PASS	.						92	92	92					20																	46279884		2203	4300	6503	SO:0001819	synonymous_variant	8202	exon20			ACAGCAACAGCAG	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.3810A>G	20.37:g.46279884A>G		68	0	0		61	4	0.0655738	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Silent	SNP	ENST00000371998.3	37	CCDS13407.1																																																																																			A|0.500;G|0.500	0.500	weak		0.572	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		G	46279884	A	G	46279884	2	3	3	1	0	0	0	0	0	0	0	1	10239	40	2	3		3	NCOA3	20	46279884	Silent	SNP	A	TCGA-FA-A4XK-01A-11D-A31X-10		46279884	16745636	78	336											
MOCS3	8813	hgsc.bcm.edu	37	chr20	49575719	49575719	+	5'Flank	SNP	T	T	A																															gccgccttggccttgtggacTatgacgtggtagagatgagc																										TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr20:49575719T>A	ENST00000371588.5	-	0	0				MOCS3_ENST00000244051.1_Missense_Mutation_p.Y114N|DPM1_ENST00000371583.5_5'Flank|DPM1_ENST00000466152.1_5'Flank|DPM1_ENST00000371582.4_5'Flank	NM_003859.1	NP_003850.1	O60762	DPM1_HUMAN	dolichyl-phosphate mannosyltransferase polypeptide 1, catalytic subunit						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						CCTTGTGGACTATGACGTGGT	0.692																																					p.Y114N		Atlas-SNP	.											.	MOCS3	44	.	0			c.T340A						PASS	.						46	56	53					20																	49575719		2192	4285	6477	SO:0001631	upstream_gene_variant	27304	exon1			GTGGACTATGACG	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		20.37:g.49575719T>A	Exception_encountered	62	0	0		51	17	0.333333	NM_014484	O15157|Q6IB78|Q96HK0	Missense_Mutation	SNP	ENST00000371588.5	37	CCDS13434.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.975590	0.74360	.	.	ENSG00000124217	ENST00000244051	T	0.28069	1.63	6.08	2.51	0.30379	UBA/THIF-type NAD/FAD binding fold (1);Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.272984	0.37955	N	0.001868	T	0.27731	0.0682	L	0.37561	1.115	0.50039	D	0.99984	P	0.42409	0.779	P	0.49683	0.619	T	0.04360	-1.0957	9	.	.	.	-10.1451	4.0058	0.09600	0.0:0.4057:0.2107:0.3836	.	114	O95396	MOCS3_HUMAN	N	114	ENSP00000244051:Y114N	.	Y	+	1	0	MOCS3	49009126	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.110000	0.41873	0.550000	0.28991	0.533000	0.62120	TAT	.	.	none		0.692	DPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079716.1	NM_003859		A	49575719	T	A	49575719	1	1	3	0	1	0	0	0	0	0	0	0	9701	1522	53	5		5	MOCS3	20	49575719	5'Flank	SNP	T	TCGA-FA-A4XK-01A-11D-A31X-10	3295835	49575719	13449801	79	337	9	2									
MOCS3	8813	hgsc.bcm.edu	37	chr20	49575721	49575721	+	5'Flank	SNP	T	T	C																															cgccttggccttgtggactaTgacgtggtagagatgagcaa																										TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr20:49575721T>C	ENST00000371588.5	-	0	0				MOCS3_ENST00000244051.1_Silent_p.Y114Y|DPM1_ENST00000371583.5_5'Flank|DPM1_ENST00000466152.1_5'Flank|DPM1_ENST00000371582.4_5'Flank	NM_003859.1	NP_003850.1	O60762	DPM1_HUMAN	dolichyl-phosphate mannosyltransferase polypeptide 1, catalytic subunit						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						TTGTGGACTATGACGTGGTAG	0.692																																					p.Y114Y		Atlas-SNP	.											.	MOCS3	44	.	0			c.T342C						PASS	.						46	57	53					20																	49575721		2192	4282	6474	SO:0001631	upstream_gene_variant	27304	exon1			GGACTATGACGTG	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		20.37:g.49575721T>C	Exception_encountered	59	0	0		52	17	0.326923	NM_014484	O15157|Q6IB78|Q96HK0	Silent	SNP	ENST00000371588.5	37	CCDS13434.1																																																																																			.	.	none		0.692	DPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079716.1	NM_003859		C	49575721	T	C	49575721	1	2	3	0	1	0	0	0	0	0	0	0	9701	1471	51	3		3	MOCS3	20	49575721	5'Flank	SNP	T	TCGA-FA-A4XK-01A-11D-A31X-10	2	49575721	13449799	80	338	9	2									
MYT1	4661	hgsc.bcm.edu	37	chr20	62839368	62839368	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggaagaggaggaggaggaGgatgaagaagaggaagagga	18	1	22	0	0	0	5	0	1	0	4	0	14	0	13	0	8	0	0	0	8	4	0	rs369047925		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr20:62839368G>T	ENST00000328439.1	+	7	1183	c.819G>T	c.(817-819)gaG>gaT	p.E273D	MYT1_ENST00000536311.1_Missense_Mutation_p.E273D|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)	p.E273D(1)		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)					aggaggaggaggatgaagaag	0.572																																					p.E273D	GBM(59;481 1041 20555 21139 33705)	Atlas-SNP	.											MYT1,NS,carcinoma,0,1	MYT1	152	1	1	Substitution - Missense(1)	endometrium(1)	c.G819T						scavenged	.						21	21	21					20																	62839368		2203	4299	6502	SO:0001583	missense	4661	exon7			GGAGGAGGATGAA	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.819G>T	20.37:g.62839368G>T	ENSP00000327465:p.Glu273Asp	28	0	0		22	4	0.181818	NM_004535	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000328439.1	37	CCDS13558.1	.	.	.	.	.	.	.	.	.	.	g	6.948	0.544734	0.13312	.	.	ENSG00000196132	ENST00000328439;ENST00000536311	T;T	0.74526	-0.85;-0.85	4.12	-4.11	0.03928	.	0.319667	0.24102	N	0.041536	T	0.40272	0.1110	N	0.08118	0	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.03761	-1.1006	10	0.17832	T	0.49	.	1.4958	0.02466	0.2938:0.235:0.3514:0.1198	.	273	Q01538	MYT1_HUMAN	D	273	ENSP00000327465:E273D;ENSP00000442412:E273D	ENSP00000327465:E273D	E	+	3	2	MYT1	62309812	0.048000	0.20356	0.073000	0.20177	0.034000	0.12701	-1.232000	0.02936	-0.392000	0.07751	-0.260000	0.10688	GAG	.	.	alt		0.572	MYT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080297.1	NM_004535		T	62839368	G	T	62839368	3	4	3	1	0	0	0	0	1	0	0	0	10115	991	35	4	837	4	MYT1	20	62839368	Missense_Mutation	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10	13263647	62839368	186152	81	339											
DSCAM	1826	hgsc.bcm.edu	37	chr21	41414420	41414420	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctggaggtcagactgtccGtgtactcatttgtccctgcc	5	13	11	12	1	2	1	2	0	0	1	4	2	4	2	3	2	3	2	3	2	1	2	rs200410460		TCGA-FA-A4XK-01A-11D-A31X-10	TCGA-FA-A4XK-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1c24a152-3311-444f-bda2-4612303ddc50	cbaae798-7a40-44d1-b164-ebf0f6a2b8fa	g.chr21:41414420G>A	ENST00000400454.1	-	32	6041	c.5564C>T	c.(5563-5565)aCg>aTg	p.T1855M		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1855					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)				CAGACTGTCCGTGTACTCATT	0.527																																					p.T1855M	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.C5564T						PASS	.	G	MET/THR	1,4227		0,1,2113	185	179	181		5564	5.3	1	21		181	1,8449		0,1,4224	yes	missense	DSCAM	NM_001389.3	81	0,2,6337	AA,AG,GG		0.0118,0.0237,0.0158	probably-damaging	1855/2013	41414420	2,12676	2114	4225	6339	SO:0001583	missense	1826	exon32			CTGTCCGTGTACT	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.5564C>T	21.37:g.41414420G>A	ENSP00000383303:p.Thr1855Met	67	0	0		81	31	0.382716	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	37	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	g	18.87	3.716437	0.68844	2.37E-4	1.18E-4	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.60424	0.19;0.29	5.26	5.26	0.73747	.	0.000000	0.85682	D	0.000000	T	0.64789	0.2630	L	0.27053	0.805	0.36068	D	0.841933	D	0.89917	1.0	D	0.83275	0.996	T	0.73458	-0.3976	10	0.72032	D	0.01	.	14.4825	0.67592	0.0:0.1467:0.8533:0.0	.	1855	O60469	DSCAM_HUMAN	M	1855;1607	ENSP00000383303:T1855M;ENSP00000385342:T1607M	ENSP00000383303:T1855M	T	-	2	0	DSCAM	40336290	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.419000	0.73345	2.458000	0.83093	0.655000	0.94253	ACG	.	.	weak		0.527	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		A	41414420	G	A	41414420	3	1	3	1	0	0	0	0	1	0	0	0	4770	1145	40	1	482	1	DSCAM	21	41414420	Missense_Mutation	SNP	G	TCGA-FA-A4XK-01A-11D-A31X-10		41414420	6715475	82	340											
ATAD3B	83858	hgsc.bcm.edu	37	chr1	1431048	1431048	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacctcatggagcctggccAcggacccctcctacccctgc	6	7	8	20	1	2	0	2	0	0	0	3	2	3	2	8	3	3	0	8	3	1	1	rs201429000		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr1:1431048A>G	ENST00000308647.7	+	16	1914	c.1798A>G	c.(1798-1800)Acg>Gcg	p.T600A		NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	600						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)		GAGCCTGGCCACGGACCCCTC	0.672																																					p.T600A		Atlas-SNP	.											ATAD3B,NS,neuroblastoma,0,1	ATAD3B	68	1	0			c.A1798G						scavenged	.																																			SO:0001583	missense	83858	exon16			CTGGCCACGGACC	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.1798A>G	1.37:g.1431048A>G	ENSP00000311766:p.Thr600Ala	69	1	0.0144928		56	4	0.0714286	NM_031921	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Missense_Mutation	SNP	ENST00000308647.7	37	CCDS30.1	.	.	.	.	.	.	.	.	.	.	g	0.005	-2.129716	0.00338	.	.	ENSG00000160072	ENST00000378737;ENST00000308647	D	0.93189	-3.18	1.2	-1.67	0.08238	.	0.186138	0.20546	N	0.090207	T	0.78220	0.4249	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	0.65792	-0.6082	10	0.12766	T	0.61	.	2.0444	0.03557	0.4037:0.0:0.3428:0.2535	.	554;600	Q5T9A4-3;Q5T9A4	.;ATD3B_HUMAN	A	434;600	ENSP00000311766:T600A	ENSP00000311766:T600A	T	+	1	0	ATAD3B	1420911	0.007000	0.16637	0.000000	0.03702	0.003000	0.03518	0.259000	0.18405	-1.264000	0.02452	-1.032000	0.02404	ACG	.	.	weak		0.672	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921		G	1431048	A	G	1431048	3	3	4	1	0	0	0	0	1	0	0	0	1074	159	6	3	1860	3	ATAD3B	1	1431048	Missense_Mutation	SNP	A	TCGA-FA-A6HN-01A-11D-A31X-10		1431048	247819573	1	341											
CHD5	26038	hgsc.bcm.edu	37	chr1	6189098	6189098	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtagatcatcaccttcttgTtctggccgatgcggtgggcg	5	12	14	10	3	4	1	2	0	2	1	4	2	4	1	2	4	1	2	2	4	1	4			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr1:6189098T>A	ENST00000262450.3	-	23	3518	c.3419A>T	c.(3418-3420)aAc>aTc	p.N1140I	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)		CACCTTCTTGTTCTGGCCGAT	0.642																																					p.N1140I		Atlas-SNP	.											.	CHD5	267	.	0			c.A3419T						PASS	.						53	49	50					1																	6189098		2203	4300	6503	SO:0001583	missense	26038	exon23			TTCTTGTTCTGGC	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.3419A>T	1.37:g.6189098T>A	ENSP00000262450:p.Asn1140Ile	52	0	0		43	7	0.162791	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Missense_Mutation	SNP	ENST00000262450.3	37	CCDS57.1	.	.	.	.	.	.	.	.	.	.	T	19.74	3.883183	0.72410	.	.	ENSG00000116254	ENST00000262450;ENST00000378006;ENST00000536802;ENST00000538279	T	0.75938	-0.98	4.62	4.62	0.57501	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.62060	0.2397	N	0.16201	0.385	0.80722	D	1	P	0.46512	0.879	B	0.43575	0.424	T	0.68584	-0.5370	10	0.56958	D	0.05	-42.1979	14.314	0.66434	0.0:0.0:0.0:1.0	.	1140	Q8TDI0	CHD5_HUMAN	I	1140;656;548;548	ENSP00000262450:N1140I	ENSP00000262450:N1140I	N	-	2	0	CHD5	6111685	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.606000	0.61126	1.839000	0.53478	0.459000	0.35465	AAC	.	.	none		0.642	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557		A	6189098	T	A	6189098	3	1	4	1	0	0	0	0	1	0	0	0	3330	1725	60	5	2521	5	CHD5	1	6189098	Missense_Mutation	SNP	T	TCGA-FA-A6HN-01A-11D-A31X-10	4758050	6189098	243061523	2	342											
ESPN	83715	hgsc.bcm.edu	37	chr1	6504644	6504644	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	taccacggtgtcggtccagcCgctgaactttgacctcagct	7	10	10	14	3	1	2	1	2	0	0	3	2	2	2	4	2	4	2	4	2	2	2	rs201251427		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr1:6504644C>T	ENST00000377828.1	+	6	1262	c.1094C>T	c.(1093-1095)cCg>cTg	p.P365L	RP1-202O8.2_ENST00000419034.1_RNA	NM_031475.2	NP_113663.2	B1AK53	ESPN_HUMAN	espin	365					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)		TCGGTCCAGCCGCTGAACTTT	0.617																																					p.P365L		Atlas-SNP	.											ESPN,NS,carcinoma,+1,1	ESPN	32	1	0			c.C1094T						PASS	.						134	98	110					1																	6504644		2203	4300	6503	SO:0001583	missense	83715	exon6			TCCAGCCGCTGAA	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.1094C>T	1.37:g.6504644C>T	ENSP00000367059:p.Pro365Leu	125	0	0		113	26	0.230089	NM_031475	Q6XYB2|Q9H0A2|Q9Y329	Missense_Mutation	SNP	ENST00000377828.1	37	CCDS70.1	.	.	.	.	.	.	.	.	.	.	c	9.903	1.207541	0.22205	.	.	ENSG00000187017	ENST00000377828;ENST00000418286	D;D	0.86562	-2.14;-2.14	3.77	1.77	0.24775	.	0.374614	0.20905	U	0.083577	T	0.74329	0.3702	L	0.29908	0.895	0.35234	D	0.777217	P	0.52061	0.95	B	0.35413	0.202	T	0.75542	-0.3281	10	0.59425	D	0.04	-2.8623	8.1598	0.31192	0.1648:0.5137:0.3215:0.0	.	365	B1AK53	ESPN_HUMAN	L	365;150	ENSP00000367059:P365L;ENSP00000401793:P150L	ENSP00000367059:P365L	P	+	2	0	ESPN	6427231	0.993000	0.37304	0.369000	0.25952	0.221000	0.24807	2.040000	0.41203	0.246000	0.21394	0.486000	0.48141	CCG	C|0.999;T|0.001	0.001	weak		0.617	ESPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001887.3	NM_031475		T	6504644	C	T	6504644	3	4	4	1	0	0	0	0	1	0	0	0	5256	652	23	1	1116	1	ESPN	1	6504644	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	315546	6504644	242745977	3	343											
TNFRSF8	943	hgsc.bcm.edu	37	chr1	12123708	12123708	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gttcctgggggcgctacgagCcttcccacaggtaagcgggt	6	8	15	12	3	0	0	0	0	0	0	2	1	2	0	3	4	3	3	3	4	2	4			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr1:12123708C>T	ENST00000263932.2	+	1	275	c.53C>T	c.(52-54)gCc>gTc	p.A18V	TNFRSF8_ENST00000417814.2_5'UTR	NM_001243.3|NM_001281430.1	NP_001234.2|NP_001268359.1	P28908	TNR8_HUMAN	tumor necrosis factor receptor superfamily, member 8	18					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)	GCGCTACGAGCCTTCCCACAG	0.736																																					p.A18V		Atlas-SNP	.											.	TNFRSF8	70	.	0			c.C53T						PASS	.						5	5	5					1																	12123708		1864	3572	5436	SO:0001583	missense	943	exon1			TACGAGCCTTCCC	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.53C>T	1.37:g.12123708C>T	ENSP00000263932:p.Ala18Val	101	0	0		84	20	0.238095	NM_001243	B1AN79|B9EGD9|D3YTD8|Q6P4D9	Missense_Mutation	SNP	ENST00000263932.2	37	CCDS144.1	.	.	.	.	.	.	.	.	.	.	C	11.68	1.710987	0.30322	.	.	ENSG00000120949	ENST00000263932	T	0.27256	1.68	3.03	3.03	0.35002	.	1.573450	0.04122	N	0.316409	T	0.37237	0.0996	N	0.24115	0.695	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.36504	-0.9745	10	0.28530	T	0.3	-10.4661	9.7885	0.40690	0.0:1.0:0.0:0.0	.	18	P28908	TNR8_HUMAN	V	18	ENSP00000263932:A18V	ENSP00000263932:A18V	A	+	2	0	TNFRSF8	12046295	1.000000	0.71417	0.956000	0.39512	0.581000	0.36288	3.147000	0.50639	2.000000	0.58554	0.555000	0.69702	GCC	.	.	none		0.736	TNFRSF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005130.1			T	12123708	C	T	12123708	3	4	4	1	0	0	0	0	1	0	0	0	16314	739	26	2	55	2	TNFRSF8	1	12123708	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	5619064	12123708	237126913	4	344											
FPGT	8790	hgsc.bcm.edu	37	chr1	74670119	74670119	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgcaagtgctctgggaaaaAttttcactgctttacctctt	10	15	7	9	0	3	0	1	0	2	0	3	1	3	1	1	1	4	3	1	1	4	5			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr1:74670119A>C	ENST00000609362.1	+	4	425	c.388A>C	c.(388-390)Att>Ctt	p.I130L	FPGT_ENST00000534056.1_Missense_Mutation_p.I130L|FPGT-TNNI3K_ENST00000370893.1_Intron|FPGT-TNNI3K_ENST00000533006.1_Intron|FPGT_ENST00000370894.5_Intron|FPGT_ENST00000524915.1_3'UTR|FPGT_ENST00000370898.3_Missense_Mutation_p.I143L|FPGT-TNNI3K_ENST00000557284.2_Intron|FPGT-TNNI3K_ENST00000370899.3_Intron|FPGT_ENST00000467578.2_3'UTR|TNNI3K_ENST00000370891.2_Intron|FPGT-TNNI3K_ENST00000370895.1_Intron|FPGT_ENST00000482102.2_3'UTR	NM_003838.4	NP_003829.3	O14772	FPGT_HUMAN	fucose-1-phosphate guanylyltransferase	130					fucose metabolic process (GO:0006004)	cytoplasm (GO:0005737)	catalytic activity (GO:0003824)|fucose-1-phosphate guanylyltransferase activity (GO:0047341)|GTP binding (GO:0005525)	p.I130F(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	39						TCTGGGAAAAATTTTCACTGC	0.318																																					p.I130L		Atlas-SNP	.											FPGT,NS,carcinoma,0,1	FPGT	77	1	1	Substitution - Missense(1)	ovary(1)	c.A388C						PASS	.						102	115	111					1																	74670119		2203	4300	6503	SO:0001583	missense	8790	exon4			GGAAAAATTTTCA	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.388A>C	1.37:g.74670119A>C	ENSP00000476680:p.Ile130Leu	112	0	0		86	11	0.127907	NM_001199328	A6NMH3|B4DRX2|B4E2Y7|E9PNQ2|Q8N5J7	Missense_Mutation	SNP	ENST00000609362.1	37	CCDS663.1	.	.	.	.	.	.	.	.	.	.	A	14.28	2.488872	0.44249	.	.	ENSG00000254685	ENST00000524915;ENST00000370898;ENST00000534056;ENST00000472069	T;T;T;T	0.36878	1.23;1.23;1.23;1.23	5.57	5.57	0.84162	L-fucokinase (1);	.	.	.	.	T	0.46521	0.1397	L	0.60845	1.875	0.80722	D	1	D;D;P	0.71674	0.998;0.99;0.56	D;D;B	0.74348	0.983;0.912;0.388	T	0.38478	-0.9659	9	0.38643	T	0.18	.	15.7348	0.77834	1.0:0.0:0.0:0.0	.	130;130;130	B4DH62;E9PNQ2;O14772	.;.;FPGT_HUMAN	L	130;130;130;128	ENSP00000434802:I130L;ENSP00000359935:I130L;ENSP00000432819:I130L;ENSP00000433499:I128L	ENSP00000359935:I130L	I	+	1	0	TNNI3K	74442707	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.944000	0.70219	2.116000	0.64780	0.482000	0.46254	ATT	.	.	none		0.318	FPGT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	74670119	A	C	74670119	3	2	4	1	0	0	0	0	1	0	0	0	6045	101	4	5	402	5	FPGT	1	74670119	Missense_Mutation	SNP	A	TCGA-FA-A6HN-01A-11D-A31X-10	62546411	74670119	174580502	5	345											
ACADM	34	hgsc.bcm.edu	37	chr1	76228440	76228440	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgaacacattgacaagtacAaaaattaaaaaaattactgt	21	10	5	5	0	0	2	0	2	0	0	0	2	0	2	0	0	3	1	0	0	10	4			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr1:76228440A>G	ENST00000370841.4	+	12	1695	c.1258A>G	c.(1258-1260)Aaa>Gaa	p.K420E	ACADM_ENST00000370834.5_Missense_Mutation_p.K453E|ACADM_ENST00000420607.2_Missense_Mutation_p.K424E|ACADM_ENST00000481374.1_Intron|ACADM_ENST00000543667.1_Missense_Mutation_p.K231E|ACADM_ENST00000541113.1_Missense_Mutation_p.K384E	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	420					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)	TGACAAGTACAAAAATTAAAA	0.303																																					p.K424E		Atlas-SNP	.											.	ACADM	50	.	0			c.A1270G						PASS	.						22	25	24					1																	76228440		2173	4259	6432	SO:0001583	missense	34	exon12			AAGTACAAAAATT	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.1258A>G	1.37:g.76228440A>G	ENSP00000359878:p.Lys420Glu	406	0	0		367	71	0.19346	NM_001127328	Q5T4U4|Q9NYF1	Missense_Mutation	SNP	ENST00000370841.4	37	CCDS668.1	.	.	.	.	.	.	.	.	.	.	A	13.76	2.333626	0.41297	.	.	ENSG00000117054	ENST00000370841;ENST00000370834;ENST00000541113;ENST00000543667;ENST00000420607	D;D;D;D;D	0.97731	-4.51;-4.44;-4.49;-4.09;-4.51	5.87	5.87	0.94306	Acyl-CoA dehydrogenase/oxidase C-terminal (2);	0.137380	0.64402	D	0.000005	D	0.92519	0.7624	N	0.22421	0.69	0.54753	D	0.999987	B;B;B;B	0.20671	0.0;0.047;0.013;0.004	B;B;B;B	0.18561	0.001;0.022;0.008;0.003	D	0.90629	0.4565	10	0.87932	D	0	.	15.0981	0.72250	1.0:0.0:0.0:0.0	.	384;453;424;420	B7Z9I1;Q5T4U5;P11310-2;P11310	.;.;.;ACADM_HUMAN	E	420;453;384;231;424	ENSP00000359878:K420E;ENSP00000359871:K453E;ENSP00000442324:K384E;ENSP00000446176:K231E;ENSP00000409612:K424E	ENSP00000359871:K453E	K	+	1	0	ACADM	76001028	1.000000	0.71417	0.975000	0.42487	0.145000	0.21501	4.283000	0.58977	2.239000	0.73571	0.528000	0.53228	AAA	.	.	none		0.303	ACADM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026967.1			G	76228440	A	G	76228440	3	3	4	1	0	0	0	0	1	0	0	0	113	131	5	3	1316	3	ACADM	1	76228440	Missense_Mutation	SNP	A	TCGA-FA-A6HN-01A-11D-A31X-10	1558321	76228440	173022181	6	346											
LPHN2	23266	hgsc.bcm.edu	37	chr1	82415874	82415874	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcatcttttttccatagtGcctaccacagctgtgacaat	10	14	5	12	0	2	1	1	1	1	0	3	1	3	1	3	0	3	1	3	0	3	5			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr1:82415874G>T	ENST00000370728.1	+	9	1845	c.1200G>T	c.(1198-1200)gtG>gtT	p.V400V	LPHN2_ENST00000469377.2_Intron|LPHN2_ENST00000370725.1_Splice_Site_p.V400V|LPHN2_ENST00000359929.3_Splice_Site_p.V400V|LPHN2_ENST00000370721.1_Intron|LPHN2_ENST00000370713.1_Splice_Site_p.V400V|LPHN2_ENST00000370717.2_Splice_Site_p.V400V|LPHN2_ENST00000370730.1_Splice_Site_p.V400V|LPHN2_ENST00000394879.1_Splice_Site_p.V400V|LPHN2_ENST00000335786.5_Splice_Site_p.V400V|LPHN2_ENST00000271029.4_Splice_Site_p.V400V|LPHN2_ENST00000370723.1_Splice_Site_p.V400V|LPHN2_ENST00000319517.6_Splice_Site_p.V400V|LPHN2_ENST00000370727.1_Splice_Site_p.V400V|LPHN2_ENST00000370715.1_Splice_Site_p.V400V			O95490	LPHN2_HUMAN	latrophilin 2	400					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)		TTTCCATAGTGCCTACCACAG	0.418																																					p.V400V		Atlas-SNP	.											.	LPHN2	464	.	0			c.G1200T						PASS	.						161	165	163					1																	82415874		2203	4299	6502	SO:0001630	splice_region_variant	23266	exon6			CATAGTGCCTACC	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.1199-1G>T	1.37:g.82415874G>T		116	0	0		120	27	0.225	NM_012302	A5XEI2|B1ALT8|B1ALT9|B1ALU0|B1ALU2|B1ALU4|B1ALU5|B1ALU6|O94882|Q5VX76|Q9UKY5|Q9UKY6	Silent	SNP	ENST00000370728.1	37		.	.	.	.	.	.	.	.	.	.	G	11.46	1.644199	0.29246	.	.	ENSG00000117114	ENST00000449420	.	.	.	6.06	6.06	0.98353	.	.	.	.	.	T	0.72614	0.3482	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68507	-0.5390	4	.	.	.	.	20.6402	0.99549	0.0:0.0:1.0:0.0	.	.	.	.	F	268	.	.	C	+	2	0	LPHN2	82188462	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.513000	0.60476	2.885000	0.99019	0.655000	0.94253	TGC	.	.	none		0.418	LPHN2-007	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000027188.1	NM_012302	Silent	T	82415874	G	T	82415874	5	4	4	1	0	0	0	0	0	0	1	0	8925	1333	46	4	1218	4	LPHN2	1	82415874	Splice_Site	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	6187434	82415874	166834747	7	347											
ALX3	257	hgsc.bcm.edu	37	chr1	110607400	110607400	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	agggagtcccggggaaagagGaagatgcaggctggccaggc	11	3	19	8	1	0	2	0	0	0	2	1	5	1	5	2	7	1	2	2	7	2	0			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr1:110607400G>A	ENST00000369792.4	-	2	490	c.403C>T	c.(403-405)Cct>Tct	p.P135S	RP4-773N10.4_ENST00000554749.1_RNA	NM_006492.2	NP_006483.2	O95076	ALX3_HUMAN	ALX homeobox 3	135					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)		GGGGAAAGAGGAAGATGCAGG	0.632																																					p.P135S		Atlas-SNP	.											.	ALX3	16	.	0			c.C403T						PASS	.						70	78	76					1																	110607400		2203	4300	6503	SO:0001583	missense	257	exon2			AAAGAGGAAGATG	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.403C>T	1.37:g.110607400G>A	ENSP00000358807:p.Pro135Ser	150	0	0		119	26	0.218487	NM_006492	O95075|Q5T8M4	Missense_Mutation	SNP	ENST00000369792.4	37	CCDS819.1	.	.	.	.	.	.	.	.	.	.	G	13.43	2.235321	0.39498	.	.	ENSG00000156150	ENST00000369792	D	0.95447	-3.71	3.51	3.51	0.40186	Homeodomain-like (1);	0.158416	0.29806	N	0.011154	D	0.87386	0.6164	N	0.24115	0.695	0.09310	N	1	D	0.58620	0.983	P	0.51016	0.656	T	0.80659	-0.1284	10	0.24483	T	0.36	.	6.899	0.24273	0.1283:0.0:0.8717:0.0	.	135	O95076	ALX3_HUMAN	S	135	ENSP00000358807:P135S	ENSP00000358807:P135S	P	-	1	0	ALX3	110408923	0.987000	0.35691	0.899000	0.35326	0.924000	0.55760	3.339000	0.52135	1.940000	0.56252	0.462000	0.41574	CCT	.	.	none		0.632	ALX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032232.2	NM_006492		A	110607400	G	A	110607400	3	1	4	1	0	0	0	0	1	0	0	0	557	1174	41	2	640	2	ALX3	1	110607400	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	28191526	110607400	138643221	8	348											
HIST2H2BE	8349	hgsc.bcm.edu	37	chr1	149858111	149858111	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggctgcgcttgcgcttcttgCcgtctttcttctgggctttg	0	17	12	12	3	4	0	0	0	4	0	4	0	4	0	1	2	3	4	1	2	0	6			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr1:149858111C>G	ENST00000369155.2	-	1	121	c.80G>C	c.(79-81)gGc>gCc	p.G27A	BOLA1_ENST00000369153.2_5'Flank|HIST2H2AC_ENST00000331380.2_5'Flank	NM_003528.2	NP_003519.1	Q16778	H2B2E_HUMAN	histone cluster 2, H2be	27					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)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	14	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			GCGCTTCTTGCCGTCTTTCTT	0.567																																					p.G27A		Atlas-SNP	.											HIST2H2BE,NS,carcinoma,0,2	HIST2H2BE	33	2	0			c.G80C						PASS	.						136	131	133					1																	149858111		2203	4300	6503	SO:0001583	missense	8349	exon1			TTCTTGCCGTCTT	AY131979	CCDS936.1	1q21.2	2011-01-27	2006-10-11	2003-03-07	ENSG00000184678	ENSG00000184678		"Histones / Replication-dependent"	4760	protein-coding gene	gene with protein product		601831	"H2B histone family, member Q", "histone 2, H2be"	H2B, H2BFQ		1469070, 12408966	Standard	NM_003528		Approved	H2B/q, H2B.1	uc001etc.3	Q16778	OTTHUMG00000012095	ENST00000369155.2:c.80G>C	1.37:g.149858111C>G	ENSP00000358151:p.Gly27Ala	97	0	0		88	16	0.181818	NM_003528	A3KMC7|A8K110|Q4KMY1|Q5QNX0|Q9UE88	Missense_Mutation	SNP	ENST00000369155.2	37	CCDS936.1	.	.	.	.	.	.	.	.	.	.	C	17.03	3.285780	0.59867	.	.	ENSG00000184678	ENST00000369155	T	0.23348	1.91	5.99	5.99	0.97316	Histone-fold (2);	0.137618	0.47093	D	0.000241	T	0.18593	0.0446	M	0.74881	2.28	0.35748	D	0.819229	B	0.26602	0.154	B	0.10450	0.005	T	0.05517	-1.0880	10	0.66056	D	0.02	.	13.3551	0.60623	0.0:0.9245:0.0:0.0755	.	27	Q16778	H2B2E_HUMAN	A	27	ENSP00000358151:G27A	ENSP00000358151:G27A	G	-	2	0	HIST2H2BE	148124735	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.440000	0.44855	2.857000	0.98124	0.650000	0.86243	GGC	.	.	none		0.567	HIST2H2BE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033455.1	NM_003528		G	149858111	C	G	149858111	3	3	4	1	0	0	0	0	1	0	0	0	7188	739	26	4	304	4	HIST2H2BE	1	149858111	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	39250711	149858111	99392510	9	349											
LINGO4	339398	hgsc.bcm.edu	37	chr1	151774688	151774688	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cacaaataccaggtggttgtCcccaacctccagcttctgga	10	9	8	14	0	1	0	0	0	1	0	3	1	3	1	5	3	3	2	5	3	3	3	rs532798041	byFrequency	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr1:151774688C>A	ENST00000368820.3	-	2	1430	c.493G>T	c.(493-495)Gac>Tac	p.D165Y		NM_001004432.2	NP_001004432.1	Q6UY18	LIGO4_HUMAN	leucine rich repeat and Ig domain containing 4	165						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)			AGGTGGTTGTCCCCAACCTCC	0.602																																					p.D165Y		Atlas-SNP	.											.	LINGO4	51	.	0			c.G493T						PASS	.						52	59	57					1																	151774688		2203	4300	6503	SO:0001583	missense	339398	exon2			GGTTGTCCCCAAC		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.493G>T	1.37:g.151774688C>A	ENSP00000357810:p.Asp165Tyr	64	0	0		57	9	0.157895	NM_001004432		Missense_Mutation	SNP	ENST00000368820.3	37	CCDS30855.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.132137	0.77662	.	.	ENSG00000213171	ENST00000368820	T	0.58060	0.36	5.29	5.29	0.74685	.	0.000000	0.51477	D	0.000100	T	0.54532	0.1864	L	0.31476	0.935	0.58432	D	0.999994	D	0.89917	1.0	D	0.91635	0.999	T	0.55749	-0.8092	10	0.51188	T	0.08	.	16.4618	0.84059	0.0:1.0:0.0:0.0	.	165	Q6UY18	LIGO4_HUMAN	Y	165	ENSP00000357810:D165Y	ENSP00000357810:D165Y	D	-	1	0	LINGO4	150041312	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.825000	0.62708	2.757000	0.94681	0.462000	0.41574	GAC	.	.	none		0.602	LINGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036639.1	XM_291387		A	151774688	C	A	151774688	3	1	4	1	0	0	0	0	1	0	0	0	8826	855	30	4	1292	4	LINGO4	1	151774688	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	1916577	151774688	97475933	10	350											
RHBG	57127	hgsc.bcm.edu	37	chr1	156347192	156347192	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgggcttcaccttcctcctGgccgcctttgccctgcagtg	2	12	11	16	1	1	0	1	0	0	0	3	0	3	0	6	2	2	2	6	2	0	3			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr1:156347192G>A	ENST00000368249.1	+	2	326	c.288G>A	c.(286-288)ctG>ctA	p.L96L	RHBG_ENST00000537040.1_Intron|RHBG_ENST00000400992.2_Silent_p.L27L|RHBG_ENST00000368246.2_Silent_p.L96L|RHBG_ENST00000255013.3_Silent_p.L27L|RHBG_ENST00000451864.2_Silent_p.L27L	NM_001256396.1|NM_020407.4	NP_001243325.1|NP_065140.3	Q9H310	RHBG_HUMAN	Rh family, B glycoprotein (gene/pseudogene)	96					ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|transepithelial ammonium transport (GO:0070634)|transmembrane transport (GO:0055085)	anchored component of plasma membrane (GO:0046658)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|spectrin-associated cytoskeleton (GO:0014731)	ammonium transmembrane transporter activity (GO:0008519)|ankyrin binding (GO:0030506)			endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(3)|skin(2)|stomach(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					CCTTCCTCCTGGCCGCCTTTG	0.622																																					p.L96L		Atlas-SNP	.											.	RHBG	133	.	0			c.G288A						PASS	.						113	117	116					1																	156347192		2200	4300	6500	SO:0001819	synonymous_variant	57127	exon2			CCTCCTGGCCGCC	AF193807		1q22	2013-05-22	2009-01-22		ENSG00000132677	ENSG00000132677		"Solute carriers"	14572	protein-coding gene	gene with protein product		607079	"Rhesus blood group, B glycoprotein"			10852913	Standard	NM_020407		Approved	SLC42A2	uc010pho.3	Q9H310	OTTHUMG00000024057	ENST00000368249.1:c.288G>A	1.37:g.156347192G>A		90	0	0		76	12	0.157895	NM_020407	A8K475|Q5SZW4|Q5SZW6|Q5SZW7|Q6P193|Q6YJI2|Q6YJI3	Silent	SNP	ENST00000368249.1	37																																																																																				.	.	none		0.622	RHBG-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000060589.2	NM_001256395		A	156347192	G	A	156347192	2	1	4	1	0	0	0	0	0	0	0	1	13339	1335	47	2		2	RHBG	1	156347192	Silent	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	4572504	156347192	92903429	11	351											
PRCC	5546	hgsc.bcm.edu	37	chr1	156737930	156737930	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gaggccctggcctcaatctgCcccctccaattggcggtgcc	5	8	11	17	1	2	0	1	0	1	0	3	1	3	0	6	4	2	0	6	4	2	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr1:156737930C>T	ENST00000271526.4	+	1	639	c.367C>T	c.(367-369)Ccc>Tcc	p.P123S	PRCC_ENST00000491853.1_Intron|PRCC_ENST00000353233.3_Missense_Mutation_p.P123S|HDGF_ENST00000465180.1_5'Flank	NM_005973.4	NP_005964.3	Q92733	PRCC_HUMAN	papillary renal cell carcinoma (translocation-associated)	123					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)					CCTCAATCTGCCCCCTCCAAT	0.677			T	TFE3	papillary renal																																p.P123S		Atlas-SNP	.		Dom	yes		1	1q21.1	5546	papillary renal cell carcinoma (translocation-associated)		E	.	PRCC	39	.	0			c.C367T						PASS	.						7	10	9					1																	156737930		2157	4211	6368	SO:0001583	missense	5546	exon1			AATCTGCCCCCTC	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.367C>T	1.37:g.156737930C>T	ENSP00000271526:p.Pro123Ser	46	0	0		39	6	0.153846	NM_005973	A8K1F7|O00665|O00724|Q5SZ06	Missense_Mutation	SNP	ENST00000271526.4	37	CCDS1157.1	.	.	.	.	.	.	.	.	.	.	C	10.61	1.398085	0.25205	.	.	ENSG00000143294	ENST00000271526;ENST00000353233;ENST00000368201	T;T	0.66638	-0.22;-0.22	4.95	4.95	0.65309	.	0.336600	0.28766	N	0.014210	T	0.32071	0.0817	L	0.36672	1.1	0.48135	D	0.999597	B;B	0.17038	0.02;0.02	B;B	0.11329	0.006;0.006	T	0.13899	-1.0492	10	0.07030	T	0.85	-2.1728	9.1785	0.37127	0.0:0.9036:0.0:0.0964	.	123;123	A6NG79;Q92733	.;PRCC_HUMAN	S	123;123;67	ENSP00000271526:P123S;ENSP00000339300:P123S	ENSP00000271526:P123S	P	+	1	0	PRCC	155004554	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.096000	0.41738	2.576000	0.86940	0.655000	0.94253	CCC	.	.	none		0.677	PRCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098941.2	NM_005973		T	156737930	C	T	156737930	3	4	4	1	0	0	0	0	1	0	0	0	12459	739	26	2	369	2	PRCC	1	156737930	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	390738	156737930	92512691	12	352											
OR10X1	128367	hgsc.bcm.edu	37	chr1	158549535	158549535	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gattacctgcaagggtgagaAggtagagacaaaagaagacc	17	5	13	6	0	0	4	0	1	0	4	0	7	0	4	2	2	2	2	2	2	7	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr1:158549535A>G	ENST00000368150.1	-	1	154	c.155T>C	c.(154-156)cTt>cCt	p.L52P		NM_001004477.1	NP_001004477.1	Q8NGY0	O10X1_HUMAN	olfactory receptor, family 10, subfamily X, member 1 (gene/pseudogene)	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)|cervix(1)|endometrium(2)|large_intestine(6)|lung(22)|ovary(2)|skin(2)|urinary_tract(1)	37	all_hematologic(112;0.0378)					AAGGGTGAGAAGGTAGAGACA	0.443																																					p.L52P		Atlas-SNP	.											.	OR10X1	96	.	0			c.T155C						PASS	.						126	124	125					1																	158549535		2203	4300	6503	SO:0001583	missense	128367	exon1			GTGAGAAGGTAGA	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.155T>C	1.37:g.158549535A>G	ENSP00000357132:p.Leu52Pro	89	0	0		89	8	0.0898876	NM_001004477	Q6IFR8	Missense_Mutation	SNP	ENST00000368150.1	37	CCDS30900.1	.	.	.	.	.	.	.	.	.	.	A	19.93	3.918114	0.73098	.	.	ENSG00000186400	ENST00000368150	T	0.05786	3.39	5.13	5.13	0.70059	.	0.725423	0.11934	N	0.515453	T	0.14056	0.0340	M	0.87038	2.855	0.33910	D	0.639626	D	0.58620	0.983	P	0.52909	0.713	T	0.03463	-1.1034	10	0.87932	D	0	.	14.0613	0.64802	1.0:0.0:0.0:0.0	.	52	Q8NGY0	O10X1_HUMAN	P	52	ENSP00000357132:L52P	ENSP00000357132:L52P	L	-	2	0	OR10X1	156816159	0.487000	0.25988	0.233000	0.24025	0.993000	0.82548	5.407000	0.66363	2.139000	0.66308	0.528000	0.53228	CTT	.	.	none		0.443	OR10X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051850.2	NM_001004477		G	158549535	A	G	158549535	3	3	4	1	0	0	0	0	1	0	0	0	10931	72	3	3	820	3	OR10X1	1	158549535	Missense_Mutation	SNP	A	TCGA-FA-A6HN-01A-11D-A31X-10	1811605	158549535	90701086	13	353											
HMCN1	83872	hgsc.bcm.edu	37	chr1	186039858	186039858	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagcgtatgcaattccttCtgcctccctcagctggtaca	8	12	8	13	1	2	1	1	1	1	0	4	1	4	1	3	1	5	4	3	1	4	4			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr1:186039858C>A	ENST00000271588.4	+	52	8337	c.8108C>A	c.(8107-8109)tCt>tAt	p.S2703Y	HMCN1_ENST00000367492.2_Missense_Mutation_p.S2703Y	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2703	Ig-like C2-type 25.				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						GCAATTCCTTCTGCCTCCCTC	0.413																																					p.S2703Y		Atlas-SNP	.											.	HMCN1	797	.	0			c.C8108A						PASS	.						125	118	121					1																	186039858		2203	4300	6503	SO:0001583	missense	83872	exon52			TTCCTTCTGCCTC	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.8108C>A	1.37:g.186039858C>A	ENSP00000271588:p.Ser2703Tyr	126	0	0		131	23	0.175573	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	17.02	3.283237	0.59867	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.68025	-0.3;-0.3	5.71	4.8	0.61643	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.394599	0.30879	N	0.008695	T	0.72859	0.3513	L	0.42686	1.345	0.29164	N	0.877576	D	0.76494	0.999	D	0.85130	0.997	T	0.67476	-0.5661	10	0.46703	T	0.11	.	8.9824	0.35972	0.0:0.7805:0.0:0.2195	.	2703	Q96RW7	HMCN1_HUMAN	Y	2703	ENSP00000271588:S2703Y;ENSP00000356462:S2703Y	ENSP00000271588:S2703Y	S	+	2	0	HMCN1	184306481	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	3.172000	0.50832	1.410000	0.46936	0.655000	0.94253	TCT	.	.	none		0.413	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	186039858	C	A	186039858	3	1	4	1	0	0	0	0	1	0	0	0	7229	913	32	4	8314	4	HMCN1	1	186039858	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	27490323	186039858	63210763	14	354											
GPR25	2848	hgsc.bcm.edu	37	chr1	200843152	200843178	+	In_Frame_Del	DEL	GGCGCGAAGGATCAGCTCAGCCTCCTC	GGCGCGAAGGATCAGCTCAGCCTCCTC	-																															tgcgggcgcaccggccgcctGgcgcgaaggatcagctcagc																								rs367604641		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	GGCGCGAAGGATCAGCTCAGCCTCCTC	GGCGCGAAGGATCAGCTCAGCCTCCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr1:200843152_200843178delGGCGCGAAGGATCAGCTCAGCCTCCTC	ENST00000304244.2	+	1	1070_1096	c.987_1013delGGCGCGAAGGATCAGCTCAGCCTCCTC	c.(985-1014)ctggcgcgaaggatcagctcagcctcctcg>ctg	p.ARRISSASS330del		NM_005298.2	NP_005289.2	O00155	GPR25_HUMAN	G protein-coupled receptor 25	330					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			large_intestine(1)|lung(2)|ovary(1)|skin(1)	5						CCGGCCGCCTGGCGCGAAGGATCAGCTCAGCCTCCTCGCTCTCCAGG	0.718																																					p.329_338del		Atlas-Indel	.											.	GPR25	23	.	0			c.986_1012del						PASS	.																																			SO:0001651	inframe_deletion	2848	exon1			.	U91939	CCDS1405.1	1q32.1	2012-08-21			ENSG00000170128	ENSG00000170128		"GPCR / Class A : Orphans"	4480	protein-coding gene	gene with protein product		602174				9020062	Standard	NM_005298		Approved		uc001gvn.2	O00155	OTTHUMG00000035788	ENST00000304244.2:c.987_1013delGGCGCGAAGGATCAGCTCAGCCTCCTC	1.37:g.200843152_200843178delGGCGCGAAGGATCAGCTCAGCCTCCTC	ENSP00000301917:p.Ala330_Ser338del	100	0	0		99	15	0.151515	NM_005298	A0AVJ5	In_Frame_Del	DEL	ENST00000304244.2	37	CCDS1405.1																																																																																			.	.	none		0.718	GPR25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087056.1	NM_005298		-	200843178	GGCGCGAAGGATCAGCTCAGCCTCCTC	-	200843152	7	5	4	1	0	1	0	1	0	0	0	0	6691	1335	47	0	989	0	GPR25	1	200843152	In_Frame_Del	DEL	GGCGCGAAGGATCAGCTCAGCCTCCTC	TCGA-FA-A6HN-01A-11D-A31X-10	14803294	200843152	48407469	15	355											
TAF5L	27097	hgsc.bcm.edu	37	chr1	229730826	229730826	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttcatctccgtgcctgcatTatcatcctcatcatcctggg	6	14	6	15	1	5	0	4	0	1	0	8	0	7	0	4	1	2	1	4	1	1	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr1:229730826T>G	ENST00000366676.1	-	4	987	c.988A>C	c.(988-990)Aat>Cat	p.N330H	TAF5L_ENST00000258281.2_Missense_Mutation_p.N330H			O75529	TAF5L_HUMAN	TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa	330					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|transcription from RNA polymerase II promoter (GO:0006366)	STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)	11	Breast(184;0.193)|Ovarian(103;0.249)	Prostate(94;0.167)				GTGCCTGCATTATCATCCTCA	0.512																																					p.N330H		Atlas-SNP	.											.	TAF5L	76	.	0			c.A988C						PASS	.						73	69	70					1																	229730826		2202	4300	6502	SO:0001583	missense	27097	exon5			CTGCATTATCATC	AF069736	CCDS1581.1, CCDS31051.1	1q42.11-q42.3	2013-01-10	2002-08-29		ENSG00000135801	ENSG00000135801		"WD repeat domain containing"	17304	protein-coding gene	gene with protein product	"PCAF associated factor 65 beta"		"TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65 kD"			9674425, 11124703	Standard	XM_005273100		Approved	PAF65B	uc001htq.3	O75529	OTTHUMG00000039463	ENST00000366676.1:c.988A>C	1.37:g.229730826T>G	ENSP00000355636:p.Asn330His	30	0	0		37	18	0.486486	NM_014409	Q5TDI5|Q5TDI6|Q8IW31	Missense_Mutation	SNP	ENST00000366676.1	37	CCDS1581.1	.	.	.	.	.	.	.	.	.	.	T	11.66	1.704776	0.30232	.	.	ENSG00000135801	ENST00000366676;ENST00000258281	T;T	0.59638	0.25;0.25	5.8	-0.833	0.10782	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	1.250220	0.04766	N	0.427222	T	0.47783	0.1464	L	0.40543	1.245	0.09310	N	1	B	0.20164	0.042	B	0.19946	0.027	T	0.39057	-0.9632	10	0.48119	T	0.1	-0.299	6.7515	0.23489	0.0:0.3607:0.1239:0.5154	.	330	O75529	TAF5L_HUMAN	H	330	ENSP00000355636:N330H;ENSP00000258281:N330H	ENSP00000258281:N330H	N	-	1	0	TAF5L	227797449	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.085000	0.14912	-0.150000	0.11195	-0.256000	0.11100	AAT	.	.	none		0.512	TAF5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095229.1	NM_014409		G	229730826	T	G	229730826	3	3	4	1	0	0	0	0	1	0	0	0	15544	1754	61	5	785	5	TAF5L	1	229730826	Missense_Mutation	SNP	T	TCGA-FA-A6HN-01A-11D-A31X-10	28887674	229730826	19519795	16	356											
LGALS8	3964	hgsc.bcm.edu	37	chr1	236703874	236703874	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atctctctaggtggctgtaaAtggaaaacatactctgctct	11	13	8	9	0	4	0	0	0	4	0	5	1	4	1	0	3	3	3	0	3	6	3			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr1:236703874A>G	ENST00000366584.4	+	5	922	c.356A>G	c.(355-357)aAt>aGt	p.N119S	LGALS8_ENST00000526589.1_Missense_Mutation_p.N119S|LGALS8_ENST00000450372.2_Missense_Mutation_p.N119S|LGALS8_ENST00000352231.2_Missense_Mutation_p.N119S|LGALS8_ENST00000416919.2_Intron|RP11-385F5.4_ENST00000433131.1_RNA|LGALS8_ENST00000527974.1_Missense_Mutation_p.N119S|LGALS8_ENST00000525042.1_Intron|LGALS8_ENST00000323938.6_Missense_Mutation_p.N92S|LGALS8_ENST00000526634.1_Missense_Mutation_p.N119S|LGALS8_ENST00000341872.6_Missense_Mutation_p.N119S	NM_201544.2	NP_963838.1	O00214	LEG8_HUMAN	lectin, galactoside-binding, soluble, 8	119	Galectin 1. {ECO:0000255|PROSITE- ProRule:PRU00639}.				plasma cell differentiation (GO:0002317)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(5)	20	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.0253)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			GTGGCTGTAAATGGAAAACAT	0.398																																					p.N119S		Atlas-SNP	.											.	LGALS8	42	.	0			c.A356G						PASS	.						98	107	104					1																	236703874		2203	4300	6503	SO:0001583	missense	3964	exon6			CTGTAAATGGAAA	X91790	CCDS1611.1, CCDS1612.1	1q43	2011-08-04	2008-07-25		ENSG00000116977	ENSG00000116977		"Lectins, galactoside-binding"	6569	protein-coding gene	gene with protein product	"galectin 8"	606099				7852431, 8692978	Standard	NM_201545		Approved	PCTA-1	uc001hxy.2	O00214	OTTHUMG00000039953	ENST00000366584.4:c.356A>G	1.37:g.236703874A>G	ENSP00000355543:p.Asn119Ser	41	0	0		53	9	0.169811	NM_006499	O15215|Q5T3P5|Q5T3Q4|Q8TEV1|Q96B92|Q9BXC8|Q9H584|Q9H585|Q9UEZ6|Q9UP32|Q9UP33|Q9UP34	Missense_Mutation	SNP	ENST00000366584.4	37	CCDS1612.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.121846	0.77436	.	.	ENSG00000116977	ENST00000454943;ENST00000527974;ENST00000352231;ENST00000406509;ENST00000526589;ENST00000341872;ENST00000450372;ENST00000366584;ENST00000356238;ENST00000323938;ENST00000526634	T;T;T;T;T;T;T;T;T;T	0.18810	2.19;2.19;2.19;2.19;2.19;2.19;2.19;2.19;2.19;2.19	5.46	5.46	0.80206	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	0.046652	0.85682	D	0.000000	T	0.44265	0.1285	M	0.91663	3.23	0.80722	D	1	D;P	0.56746	0.977;0.67	P;B	0.49528	0.614;0.173	T	0.58618	-0.7605	10	0.62326	D	0.03	-8.8691	15.7119	0.77635	1.0:0.0:0.0:0.0	.	119;119	O00214;O00214-2	LEG8_HUMAN;.	S	119;119;119;119;119;119;119;119;119;92;119	ENSP00000405504:N119S;ENSP00000431398:N119S;ENSP00000309576:N119S;ENSP00000385999:N119S;ENSP00000435460:N119S;ENSP00000342139:N119S;ENSP00000408657:N119S;ENSP00000355543:N119S;ENSP00000434860:N92S;ENSP00000437040:N119S	ENSP00000434860:N92S	N	+	2	0	LGALS8	234770497	1.000000	0.71417	0.985000	0.45067	0.752000	0.42762	8.536000	0.90627	2.291000	0.77112	0.533000	0.62120	AAT	.	.	none		0.398	LGALS8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000096365.2	NM_006499		G	236703874	A	G	236703874	3	3	4	1	0	0	0	0	1	0	0	0	8756	101	4	3	370	3	LGALS8	1	236703874	Missense_Mutation	SNP	A	TCGA-FA-A6HN-01A-11D-A31X-10	6973048	236703874	12546747	17	357											
RGS7	6000	hgsc.bcm.edu	37	chr1	241032080	241032080	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	actcacaaggactcactttgCttgtgcttctgcttgcatga	8	14	8	11	0	3	1	2	1	1	0	3	2	3	2	0	1	4	4	0	1	1	4			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr1:241032080C>T	ENST00000407727.1	-	7	522	c.523G>A	c.(523-525)Gca>Aca	p.A175T	RGS7_ENST00000331110.7_Missense_Mutation_p.A149T|RGS7_ENST00000446183.2_Missense_Mutation_p.A91T|RGS7_ENST00000366563.1_Missense_Mutation_p.A175T|RGS7_ENST00000348120.2_Missense_Mutation_p.A122T|RGS7_ENST00000366564.1_Missense_Mutation_p.A175T|RGS7_ENST00000366562.4_Missense_Mutation_p.A175T|RGS7_ENST00000366565.1_Missense_Mutation_p.A175T|RGS7_ENST00000401882.1_Missense_Mutation_p.A122T			P49802	RGS7_HUMAN	regulator of G-protein signaling 7	175					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)			ACTCACTTTGCTTGTGCTTCT	0.443																																					p.A175T		Atlas-SNP	.											.	RGS7	308	.	0			c.G523A						PASS	.						168	169	168					1																	241032080		2203	4300	6503	SO:0001583	missense	6000	exon8			ACTTTGCTTGTGC	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.523G>A	1.37:g.241032080C>T	ENSP00000384428:p.Ala175Thr	100	0	0		88	14	0.159091	NM_002924	Q5T3H4|Q8TD66|Q8TD67|Q8WW09|Q9UNU7|Q9Y6B9	Missense_Mutation	SNP	ENST00000407727.1	37		.	.	.	.	.	.	.	.	.	.	C	23.6	4.436438	0.83885	.	.	ENSG00000182901	ENST00000331110;ENST00000366565;ENST00000366564;ENST00000366563;ENST00000440928;ENST00000348120;ENST00000446183;ENST00000366562;ENST00000407727;ENST00000401882	T;T;T;T;T;T;T;T;T;T	0.35605	1.47;1.47;1.48;1.46;1.3;1.47;1.47;1.48;1.46;1.47	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.42787	0.1218	L	0.42245	1.32	0.80722	D	1	B;P;P;P;P;P;P	0.44521	0.417;0.749;0.837;0.553;0.837;0.529;0.749	B;B;P;B;B;B;B	0.47134	0.146;0.338;0.539;0.373;0.356;0.205;0.194	T	0.10636	-1.0621	10	0.44086	T	0.13	.	19.1613	0.93533	0.0:1.0:0.0:0.0	.	91;149;122;175;175;175;175	B7Z223;B7Z257;P49802-4;P49802-2;P49802-5;P49802-3;P49802	.;.;.;.;.;.;RGS7_HUMAN	T	149;175;175;175;6;122;91;175;175;122	ENSP00000331485:A149T;ENSP00000355523:A175T;ENSP00000355522:A175T;ENSP00000355521:A175T;ENSP00000404399:A6T;ENSP00000341242:A122T;ENSP00000390138:A91T;ENSP00000355520:A175T;ENSP00000384428:A175T;ENSP00000385508:A122T	ENSP00000331485:A149T	A	-	1	0	RGS7	239098703	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.734000	0.84928	2.768000	0.95171	0.655000	0.94253	GCA	.	.	none		0.443	RGS7-204	KNOWN	basic	protein_coding	protein_coding		NM_002924		T	241032080	C	T	241032080	3	4	4	1	0	0	0	0	1	0	0	0	13325	797	28	2	984	2	RGS7	1	241032080	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	4328206	241032080	8218541	18	358											
TAF1B	9014	hgsc.bcm.edu	37	chr2	10008516	10008516	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggagtctcagtctgacatcCacactcgaaaacctttcccc	10	9	6	16	2	2	1	1	1	2	0	6	3	4	2	4	1	1	0	4	1	2	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr2:10008516C>G	ENST00000263663.5	+	6	699	c.511C>G	c.(511-513)Cac>Gac	p.H171D	TAF1B_ENST00000402170.1_3'UTR|TAF1B_ENST00000396242.3_5'UTR	NM_005680.2	NP_005671	Q53T94	TAF1B_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, B, 63kDa	171	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)					GTCTGACATCCACACTCGAAA	0.428																																					p.H171D		Atlas-SNP	.											.	TAF1B	62	.	0			c.C511G						PASS	.						93	81	85					2																	10008516		2203	4300	6503	SO:0001583	missense	9014	exon6			GACATCCACACTC	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.511C>G	2.37:g.10008516C>G	ENSP00000263663:p.His171Asp	259	0	0		269	50	0.185874	NM_005680	B4DI42|F8WD72|Q15574|Q8WVC3	Missense_Mutation	SNP	ENST00000263663.5	37	CCDS33143.1	.	.	.	.	.	.	.	.	.	.	C	4.630	0.117174	0.08881	.	.	ENSG00000115750	ENST00000263663;ENST00000402170	T	0.02552	4.25	5.41	1.22	0.21188	.	2.518540	0.00906	N	0.002413	T	0.02571	0.0078	N	0.19112	0.55	0.19575	N	0.999964	B;B;B	0.14805	0.002;0.006;0.011	B;B;B	0.18871	0.007;0.007;0.023	T	0.44221	-0.9342	9	.	.	.	0.1658	4.2181	0.10544	0.4494:0.3528:0.0:0.1978	.	171;171;171	B5MD29;Q53T94;Q53T94-2	.;TAF1B_HUMAN;.	D	171	ENSP00000263663:H171D	.	H	+	1	0	TAF1B	9925967	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.563000	0.23547	0.067000	0.16545	-0.150000	0.13652	CAC	.	.	none		0.428	TAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323426.2	NM_005680		G	10008516	C	G	10008516	3	3	4	1	0	0	0	0	1	0	0	0	15535	594	21	4	533	4	TAF1B	2	10008516	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10		10008516	233190857	19	359											
KCNK3	3777	hgsc.bcm.edu	37	chr2	26951314	26951314	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gagggggcggccgctacagcGacacgccctcgcgacgctgc	6	3	16	16	7	0	0	0	0	0	0	1	3	0	0	2	3	3	2	2	3	1	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr2:26951314G>A	ENST00000302909.3	+	2	1188	c.1063G>A	c.(1063-1065)Gac>Aac	p.D355N		NM_002246.2	NP_002237.1	O14649	KCNK3_HUMAN	potassium channel, subfamily K, member 3	355					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)	CCGCTACAGCGACACGCCCTC	0.701																																					p.D355N	GBM(80;1457 1631 27100 45946)	Atlas-SNP	.											.	KCNK3	43	.	0			c.G1063A						PASS	.						11	11	11					2																	26951314		2174	4258	6432	SO:0001583	missense	3777	exon2			TACAGCGACACGC	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.1063G>A	2.37:g.26951314G>A	ENSP00000306275:p.Asp355Asn	48	0	0		44	9	0.204545	NM_002246	Q53SU2	Missense_Mutation	SNP	ENST00000302909.3	37	CCDS1727.1	.	.	.	.	.	.	.	.	.	.	G	15.64	2.894703	0.52121	.	.	ENSG00000171303	ENST00000538762;ENST00000302909	T	0.20069	2.1	5.22	4.31	0.51392	.	1.496640	0.03451	N	0.210632	T	0.15003	0.0362	L	0.29908	0.895	0.25099	N	0.990794	P	0.42993	0.797	B	0.30572	0.117	T	0.21724	-1.0237	10	0.52906	T	0.07	.	6.4844	0.22081	0.0913:0.0:0.7263:0.1824	.	355	O14649	KCNK3_HUMAN	N	232;355	ENSP00000306275:D355N	ENSP00000306275:D355N	D	+	1	0	KCNK3	26804818	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.918000	0.40006	1.155000	0.42497	0.555000	0.69702	GAC	.	.	none		0.701	KCNK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246861.2	NM_002246		A	26951314	G	A	26951314	3	1	4	1	0	0	0	0	1	0	0	0	8076	1058	37	1	1069	1	KCNK3	2	26951314	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	16942798	26951314	216248059	20	360											
DUSP2	1844	hgsc.bcm.edu	37	chr2	96810559	96810559	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgtcccctgttggcggcaGcgcaggggcgggggcctcag	3	8	18	12	3	1	0	1	0	0	0	2	0	2	0	3	6	1	3	3	6	0	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr2:96810559G>C	ENST00000288943.4	-	2	536	c.451C>G	c.(451-453)Ctg>Gtg	p.L151V	AC012307.2_ENST00000449242.1_lincRNA	NM_004418.3	NP_004409.1	Q05923	DUS2_HUMAN	dual specificity phosphatase 2	151					endoderm formation (GO:0001706)|inactivation of MAPK activity (GO:0000188)|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)|protein tyrosine/threonine phosphatase activity (GO:0008330)			NS(1)|breast(1)|lung(2)|skin(1)	5		Ovarian(717;0.0228)				GTTGGCGGCAGCGCAGGGGCG	0.662																																					p.L151V		Atlas-SNP	.											.	DUSP2	20	.	0			c.C451G						PASS	.						11	15	14					2																	96810559		2143	4243	6386	SO:0001583	missense	1844	exon2			GCGGCAGCGCAGG	L11329	CCDS2016.1	2q11	2011-06-09			ENSG00000158050	ENSG00000158050		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3068	protein-coding gene	gene with protein product		603068				7806236, 7590752, 12673251	Standard	NM_004418		Approved	PAC-1	uc002svk.4	Q05923	OTTHUMG00000130456	ENST00000288943.4:c.451C>G	2.37:g.96810559G>C	ENSP00000288943:p.Leu151Val	54	0	0		60	10	0.166667	NM_004418	Q53T45	Missense_Mutation	SNP	ENST00000288943.4	37	CCDS2016.1	.	.	.	.	.	.	.	.	.	.	g	9.396	1.076711	0.20227	.	.	ENSG00000158050	ENST00000288943	T	0.02763	4.17	4.3	-2.2	0.06994	.	0.606495	0.16301	N	0.220447	T	0.02380	0.0073	L	0.52126	1.63	0.09310	N	1	B	0.12013	0.005	B	0.14023	0.01	T	0.43015	-0.9417	10	0.27785	T	0.31	.	2.2955	0.04149	0.1178:0.1236:0.3826:0.376	.	151	Q05923	DUS2_HUMAN	V	151	ENSP00000288943:L151V	ENSP00000288943:L151V	L	-	1	2	DUSP2	96174286	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.849000	0.27723	-0.252000	0.09528	-0.532000	0.04303	CTG	.	.	none		0.662	DUSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252847.1	NM_004418		C	96810559	G	C	96810559	3	2	4	1	0	0	0	0	1	0	0	0	4821	962	34	4	505	4	DUSP2	2	96810559	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	69859245	96810559	146388814	21	361											
CXCR4	7852	hgsc.bcm.edu	37	chr2	136872627	136872627	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagacaacagtggaagaaagCtagggcctcggtgatggaaa	15	5	14	7	1	0	3	0	1	0	2	1	5	0	5	1	4	2	1	1	4	5	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr2:136872627C>T	ENST00000241393.3	-	2	975	c.871G>A	c.(871-873)Gct>Act	p.A291T	CXCR4_ENST00000466288.1_5'UTR|CXCR4_ENST00000409817.1_Missense_Mutation_p.A295T	NM_003467.2	NP_003458.1	P61073	CXCR4_HUMAN	chemokine (C-X-C motif) receptor 4	291					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)	TGGAAGAAAGCTAGGGCCTCG	0.507																																					p.A295T		Atlas-SNP	.											.	CXCR4	51	.	0			c.G883A						PASS	.						457	435	443					2																	136872627		2203	4300	6503	SO:0001583	missense	7852	exon1			AGAAAGCTAGGGC	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.871G>A	2.37:g.136872627C>T	ENSP00000241393:p.Ala291Thr	179	0	0		151	28	0.18543	NM_001008540	B2R5N0|O60835|P30991|P56438|Q53S69|Q9BXA0|Q9UKN2	Missense_Mutation	SNP	ENST00000241393.3	37	CCDS46420.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.744707	0.89663	.	.	ENSG00000121966	ENST00000409817;ENST00000241393;ENST00000537957	T;T	0.39229	1.09;1.09	6.16	6.16	0.99307	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.72301	0.3443	M	0.86502	2.82	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.995	T	0.74668	-0.3588	10	0.87932	D	0	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	291;295	P61073;P61073-2	CXCR4_HUMAN;.	T	295;291;161	ENSP00000386884:A295T;ENSP00000241393:A291T	ENSP00000241393:A291T	A	-	1	0	CXCR4	136589097	1.000000	0.71417	0.948000	0.38648	0.985000	0.73830	7.818000	0.86416	2.937000	0.99478	0.650000	0.86243	GCT	.	.	none		0.507	CXCR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331732.1			T	136872627	C	T	136872627	3	4	4	1	0	0	0	0	1	0	0	0	4095	797	28	2	191	2	CXCR4	2	136872627	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	40062068	136872627	106326746	22	362											
LRP1B	53353	hgsc.bcm.edu	37	chr2	141819821	141819821	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tccactttggcgacattcccGtagtcagtaaagaaaagttt	12	12	8	9	2	1	1	1	0	0	1	3	2	3	1	2	1	0	3	2	1	5	5			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr2:141819821G>A	ENST00000389484.3	-	8	2006	c.1035C>T	c.(1033-1035)taC>taT	p.Y345Y		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	345					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)		CGACATTCCCGTAGTCAGTAA	0.448										TSP Lung(27;0.18)																											p.Y345Y	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.C1035T						PASS	.						92	85	87					2																	141819821		2203	4299	6502	SO:0001819	synonymous_variant	53353	exon8			ATTCCCGTAGTCA	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.1035C>T	2.37:g.141819821G>A		59	0	0		56	13	0.232143	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																			.	.	none		0.448	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141819821	G	A	141819821	2	1	4	1	0	0	0	0	0	0	0	1	8964	1140	40	1		1	LRP1B	2	141819821	Silent	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	4947194	141819821	101379552	23	363											
NEB	4703	hgsc.bcm.edu	37	chr2	152486080	152486080	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ataacgtccctggaggccttGgcagccacgatggggatggc	8	7	15	11	2	0	0	0	0	0	0	1	3	1	2	3	6	2	1	3	6	1	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr2:152486080G>T	ENST00000172853.10	-	64	9222	c.9075C>A	c.(9073-9075)gcC>gcA	p.A3025A	NEB_ENST00000604864.1_Silent_p.A3268A|NEB_ENST00000409198.1_Silent_p.A3025A|NEB_ENST00000397345.3_Silent_p.A3268A|NEB_ENST00000603639.1_Silent_p.A3268A|NEB_ENST00000427231.2_Silent_p.A3268A			P20929	NEBU_HUMAN	nebulin	3025					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)		TGGAGGCCTTGGCAGCCACGA	0.438																																					p.A3268A		Atlas-SNP	.											.	NEB	1697	.	0			c.C9804A						PASS	.						154	153	153					2																	152486080		1944	4138	6082	SO:0001819	synonymous_variant	4703	exon68			GGCCTTGGCAGCC	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.9075C>A	2.37:g.152486080G>T		62	0	0		66	13	0.19697	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				.	.	none		0.438	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152486080	G	T	152486080	2	4	4	1	0	0	0	0	0	0	0	1	10311	1335	47	4		4	NEB	2	152486080	Silent	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	10666259	152486080	90713293	24	364											
ITGA4	3676	hgsc.bcm.edu	37	chr2	182322531	182322531	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	taccagggcccccacaacacGctgttcggctactcggtcgt	7	8	10	16	4	0	0	0	0	0	0	3	0	0	0	3	3	3	3	3	3	3	3	rs546061211		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr2:182322531G>A	ENST00000397033.2	+	1	580	c.150G>A	c.(148-150)acG>acA	p.T50T	ITGA4_ENST00000339307.4_Silent_p.T50T	NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	50					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)	CCCACAACACGCTGTTCGGCT	0.647													G|||	1	0.000199681	0.0	0.0	5008	,	,		14794	0.0		0.0	False		,,,				2504	0.001				p.T50T		Atlas-SNP	.											ITGA4,colon,carcinoma,+1,1	ITGA4	142	1	0			c.G150A						PASS	.						25	31	29					2																	182322531		2104	4230	6334	SO:0001819	synonymous_variant	3676	exon1			CAACACGCTGTTC		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.150G>A	2.37:g.182322531G>A		82	0	0		70	12	0.171429	NM_000885	D3DPG4|Q7Z4L6	Silent	SNP	ENST00000397033.2	37	CCDS42788.1																																																																																			.	.	none		0.647	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1			A	182322531	G	A	182322531	2	1	4	1	0	0	0	0	0	0	0	1	7887	1074	38	1		1	ITGA4	2	182322531	Silent	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	29836451	182322531	60876842	25	365											
CLK1	1195	hgsc.bcm.edu	37	chr2	201721689	201721689	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggctttaagtctgtgtgagtCaacttattactgtgcaaaac	11	14	9	7	0	2	1	1	1	1	0	2	1	2	1	0	1	4	2	0	1	6	4			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr2:201721689C>T	ENST00000321356.4	-	8	987	c.852G>A	c.(850-852)ttG>ttA	p.L284L	CLK1_ENST00000409769.2_Silent_p.L107L|CLK1_ENST00000434813.2_Silent_p.L326L	NM_004071.3	NP_004062.2	P49759	CLK1_HUMAN	CDC-like kinase 1	284	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			NS(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(12)|ovary(1)|pancreas(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33						CTGTGTGAGTCAACTTATTAC	0.378																																					p.L326L		Atlas-SNP	.											.	CLK1	103	.	0			c.G978A						PASS	.						85	86	86					2																	201721689		2203	4300	6503	SO:0001819	synonymous_variant	1195	exon8			GTGAGTCAACTTA	L29219	CCDS2331.1, CCDS54427.1	2q33	2008-05-02			ENSG00000013441	ENSG00000013441		"CDC-like kinases"	2068	protein-coding gene	gene with protein product		601951				9856501	Standard	NM_004071		Approved		uc002uwe.2	P49759	OTTHUMG00000132784	ENST00000321356.4:c.852G>A	2.37:g.201721689C>T		64	0	0		56	16	0.285714	NM_001162407	B4DFW7|Q0P694|Q8N5V8	Silent	SNP	ENST00000321356.4	37	CCDS2331.1																																																																																			.	.	none		0.378	CLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256192.2			T	201721689	C	T	201721689	2	4	4	1	0	0	0	0	0	0	0	1	3538	825	29	2		2	CLK1	2	201721689	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	19399158	201721689	41477684	26	366											
SLC23A3	151295	hgsc.bcm.edu	37	chr2	220033469	220033469	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgggagccagcaccaggggCccacagtgggggaacacgtg	9	3	17	12	1	0	0	0	0	0	0	0	2	0	2	3	5	3	1	3	5	1	0			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr2:220033469C>T	ENST00000409878.3	-	5	611	c.579G>A	c.(577-579)ggG>ggA	p.G193G	SLC23A3_ENST00000295738.7_Silent_p.G193G|SLC23A3_ENST00000455516.2_Silent_p.G201G|SLC23A3_ENST00000396775.3_Intron	NM_001144889.1	NP_001138361.1	Q6PIS1	S23A3_HUMAN	solute carrier family 23, member 3	193					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)		GCACCAGGGGCCCACAGTGGG	0.652																																					p.G201G		Atlas-SNP	.											.	SLC23A3	60	.	0			c.G603A						PASS	.						26	30	29					2																	220033469		1952	4138	6090	SO:0001819	synonymous_variant	151295	exon5			CAGGGGCCCACAG	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.579G>A	2.37:g.220033469C>T		112	0	0		73	14	0.191781	NM_001144890	B7Z512|Q2PYN6|Q96NA6	Silent	SNP	ENST00000409878.3	37	CCDS46518.1																																																																																			.	.	none		0.652	SLC23A3-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336331.2	NM_144712		T	220033469	C	T	220033469	2	4	4	1	0	0	0	0	0	0	0	1	14479	726	26	2		2	SLC23A3	2	220033469	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	18311780	220033469	23165904	27	367											
IRS1	3667	hgsc.bcm.edu	37	chr2	227663446	227663446	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aagccatcgctctccggaggGctcgccatgctgccaccgcc	6	6	11	18	4	1	0	0	0	1	0	4	1	1	1	6	2	3	3	6	2	1	0			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr2:227663446G>A	ENST00000305123.5	-	1	1029	c.9C>T	c.(7-9)agC>agT	p.S3S	RP11-395N3.2_ENST00000607970.1_lincRNA	NM_005544.2	NP_005535.1	P35568	IRS1_HUMAN	insulin receptor substrate 1	3	Mediates interaction with PHIP. {ECO:0000250}.				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)		TCTCCGGAGGGCTCGCCATGC	0.677																																					p.S3S		Atlas-SNP	.											.	IRS1	141	.	0			c.C9T						PASS	.						12	13	13					2																	227663446		2195	4291	6486	SO:0001819	synonymous_variant	3667	exon1			CGGAGGGCTCGCC		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.9C>T	2.37:g.227663446G>A		73	0	0		74	14	0.189189	NM_005544		Silent	SNP	ENST00000305123.5	37	CCDS2463.1																																																																																			.	.	none		0.677	IRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256886.3	NM_005544		A	227663446	G	A	227663446	2	1	4	1	0	0	0	0	0	0	0	1	7849	1194	42	2		2	IRS1	2	227663446	Silent	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	7629977	227663446	15535927	28	368											
OSBPL10	114884	hgsc.bcm.edu	37	chr3	32022446	32022446	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gctgagcacgccctcgagcgCcggctccctcctgcggccgc	3	5	13	20	6	0	1	0	1	0	0	3	2	2	1	5	2	3	3	5	2	0	0			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr3:32022446C>T	ENST00000396556.2	-	1	348	c.226G>A	c.(226-228)Gcg>Acg	p.A76T	ZNF860_ENST00000360311.4_5'Flank|OSBPL10_ENST00000438237.2_Missense_Mutation_p.A76T	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	76	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)		CCCTCGAGCGCCGGCTCCCTC	0.766																																					p.A76T		Atlas-SNP	.											.	OSBPL10	160	.	0			c.G226A						PASS	.						14	15	15					3																	32022446		2192	4286	6478	SO:0001583	missense	114884	exon1			CGAGCGCCGGCTC	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.226G>A	3.37:g.32022446C>T	ENSP00000379804:p.Ala76Thr	43	0	0		50	6	0.12	NM_017784	B4E212|Q9BTU5	Missense_Mutation	SNP	ENST00000396556.2	37	CCDS2651.1	.	.	.	.	.	.	.	.	.	.	C	8.327	0.825617	0.16749	.	.	ENSG00000144645	ENST00000396556;ENST00000438237	T;T	0.22945	1.93;2.22	4.02	3.14	0.36123	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.820194	0.10442	N	0.674159	T	0.12475	0.0303	N	0.05351	-0.065	0.23577	N	0.997376	P;P	0.37914	0.611;0.611	B;B	0.40256	0.324;0.324	T	0.15694	-1.0428	10	0.09843	T	0.71	-11.5122	6.3054	0.21135	0.0:0.7736:0.0:0.2264	.	76;76	B4E212;Q9BXB5	.;OSB10_HUMAN	T	76	ENSP00000379804:A76T;ENSP00000406124:A76T	ENSP00000379804:A76T	A	-	1	0	OSBPL10	31997450	0.997000	0.39634	0.993000	0.49108	0.014000	0.08584	0.681000	0.25320	1.043000	0.40175	0.462000	0.41574	GCG	.	.	none		0.766	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2			T	32022446	C	T	32022446	3	4	4	1	0	0	0	0	1	0	0	0	11284	739	26	2	2116	2	OSBPL10	3	32022446	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10		32022446	165999984	29	369											
LRRFIP2	9209	hgsc.bcm.edu	37	chr3	37151161	37151161	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaccctgtcactcttatatgTtgccagagggtcactgtaca	10	12	8	11	0	3	1	2	0	1	1	3	1	3	1	2	1	3	2	2	1	4	4			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr3:37151161T>C	ENST00000336686.4	-	10	627	c.547A>G	c.(547-549)Aca>Gca	p.T183A	LRRFIP2_ENST00000396428.2_Intron|LRRFIP2_ENST00000421307.1_Missense_Mutation_p.T183A|LRRFIP2_ENST00000421276.2_Intron|LRRFIP2_ENST00000440230.1_Intron|LRRFIP2_ENST00000354379.4_Intron			Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting protein 2	183	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						CTCTTATATGTTGCCAGAGGG	0.368																																					p.T183A		Atlas-SNP	.											.	LRRFIP2	71	.	1	Whole gene deletion(1)	ovary(1)	c.A547G						PASS	.						109	112	111					3																	37151161		2203	4300	6503	SO:0001583	missense	9209	exon11			TATATGTTGCCAG	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.547A>G	3.37:g.37151161T>C	ENSP00000338727:p.Thr183Ala	198	0	0		218	42	0.192661	NM_006309	A8K649|A8MXR0|B4DY63|Q68CV3|Q9NXH5	Missense_Mutation	SNP	ENST00000336686.4	37	CCDS2664.1	.	.	.	.	.	.	.	.	.	.	T	12.33	1.905655	0.33628	.	.	ENSG00000093167	ENST00000421307;ENST00000336686	T;T	0.46063	0.88;0.88	5.49	4.34	0.51931	.	0.352176	0.29884	N	0.010945	T	0.23766	0.0575	N	0.08118	0	0.33957	D	0.645154	B	0.23650	0.089	B	0.23852	0.049	T	0.24621	-1.0155	10	0.39692	T	0.17	2.162	11.145	0.48426	0.0:0.0723:0.0:0.9277	.	183	Q9Y608	LRRF2_HUMAN	A	183	ENSP00000392217:T183A;ENSP00000338727:T183A	ENSP00000338727:T183A	T	-	1	0	LRRFIP2	37126165	0.998000	0.40836	0.323000	0.25347	0.646000	0.38490	2.746000	0.47467	1.106000	0.41623	-0.256000	0.11100	ACA	.	.	none		0.368	LRRFIP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253335.3	NM_006309		C	37151161	T	C	37151161	3	2	4	1	0	0	0	0	1	0	0	0	9037	1725	60	3	1694	3	LRRFIP2	3	37151161	Missense_Mutation	SNP	T	TCGA-FA-A6HN-01A-11D-A31X-10	5128715	37151161	160871269	30	370											
LIMD1	8994	hgsc.bcm.edu	37	chr3	45636656	45636656	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgttgggaagttgtgggcagCaagctgactgtggatggtgc	7	10	18	6	1	0	1	0	1	0	0	0	3	0	3	0	4	3	5	0	4	2	2	rs143647674		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr3:45636656C>T	ENST00000273317.4	+	1	306	c.285C>T	c.(283-285)agC>agT	p.S95S	AC099539.1_ENST00000516118.1_RNA|LIMD1_ENST00000440097.1_Silent_p.S95S|LIMD1_ENST00000465039.1_Intron	NM_014240.2	NP_055055.1	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1	95	Mediates nuclear export.				cell migration (GO:0016477)|cytoplasmic mRNA processing body assembly (GO:0033962)|cytoskeleton organization (GO:0007010)|gene silencing by miRNA (GO:0035195)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of hippo signaling (GO:0035331)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|phosphorylation (GO:0016310)|positive regulation of gene silencing by miRNA (GO:2000637)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|RISC complex (GO:0016442)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)		TTGTGGGCAGCAAGCTGACTG	0.677																																					p.S95S		Atlas-SNP	.											.	LIMD1	34	.	0			c.C285T						PASS	.						19	24	22					3																	45636656		2197	4292	6489	SO:0001819	synonymous_variant	8994	exon1			GGGCAGCAAGCTG	AJ132408	CCDS2729.1	3p21.31	2008-02-01			ENSG00000144791	ENSG00000144791			6612	protein-coding gene	gene with protein product		604543				10647888	Standard	NM_014240		Approved		uc003coq.3	Q9UGP4	OTTHUMG00000133453	ENST00000273317.4:c.285C>T	3.37:g.45636656C>T		39	0	0		29	6	0.206897	NM_014240	Q17RQ1|Q9BQQ9|Q9NQ47	Silent	SNP	ENST00000273317.4	37	CCDS2729.1																																																																																			C|1.000;G|0.000	.	alt		0.677	LIMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257327.1	NM_014240		T	45636656	C	T	45636656	2	4	4	1	0	0	0	0	0	0	0	1	8807	709	25	2		2	LIMD1	3	45636656	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	8485495	45636656	152385774	31	371											
HEMK1	51409	hgsc.bcm.edu	37	chr3	50609175	50609175	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gccggcactttggacccagcCcttgacctctcagcaactac	8	8	8	17	1	1	1	1	1	1	0	2	2	1	2	4	2	4	2	4	2	2	3			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr3:50609175C>T	ENST00000232854.4	+	3	815	c.263C>T	c.(262-264)cCc>cTc	p.P88L	HEMK1_ENST00000434410.1_Missense_Mutation_p.P88L|C3orf18_ENST00000449241.1_5'Flank|HEMK1_ENST00000455834.1_Missense_Mutation_p.P88L	NM_016173.3	NP_057257.1	Q9Y5R4	HEMK1_HUMAN	HemK methyltransferase family member 1	88					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)		TGGACCCAGCCCTTGACCTCT	0.572											OREG0015589	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P88L		Atlas-SNP	.											.	HEMK1	17	.	0			c.C263T						PASS	.						126	132	130					3																	50609175		2203	4300	6503	SO:0001583	missense	51409	exon3			CCCAGCCCTTGAC	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.263C>T	3.37:g.50609175C>T	ENSP00000232854:p.Pro88Leu	98	0	0	971	74	21	0.283784	NM_016173		Missense_Mutation	SNP	ENST00000232854.4	37	CCDS2830.1	.	.	.	.	.	.	.	.	.	.	c	11.65	1.703370	0.30232	.	.	ENSG00000114735	ENST00000434410;ENST00000232854;ENST00000455834	T;T;T	0.14893	2.47;2.47;2.47	5.53	4.65	0.58169	.	0.139018	0.49916	D	0.000131	T	0.17066	0.0410	L	0.52266	1.64	0.40106	D	0.976427	B	0.18166	0.026	B	0.19391	0.025	T	0.03555	-1.1025	10	0.41790	T	0.15	-7.7147	10.4992	0.44796	0.0:0.9105:0.0:0.0895	.	88	Q9Y5R4	HEMK1_HUMAN	L	88	ENSP00000404843:P88L;ENSP00000232854:P88L;ENSP00000404334:P88L	ENSP00000232854:P88L	P	+	2	0	HEMK1	50584179	0.736000	0.28164	0.993000	0.49108	0.191000	0.23601	0.979000	0.29500	1.485000	0.48380	0.651000	0.88453	CCC	.	.	none		0.572	HEMK1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346231.1	NM_016173		T	50609175	C	T	50609175	3	4	4	1	0	0	0	0	1	0	0	0	7060	623	22	2	269	2	HEMK1	3	50609175	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	4972519	50609175	147413255	32	372											
SYNPR	132204	hgsc.bcm.edu	37	chr3	63466620	63466620	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cagcatcgacatagcgtttgCctacccattcaggtagggaa	11	9	10	11	2	1	0	1	0	0	0	2	2	1	1	2	2	4	3	2	2	4	5			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr3:63466620C>T	ENST00000295894.5	+	2	506	c.137C>T	c.(136-138)gCc>gTc	p.A46V	SYNPR_ENST00000478744.1_3'UTR|SYNPR-AS1_ENST00000488201.1_RNA|SYNPR_ENST00000478300.1_Missense_Mutation_p.A66V|SYNPR_ENST00000479198.1_Missense_Mutation_p.A46V|SYNPR_ENST00000465156.1_Missense_Mutation_p.A46V|SYNPR_ENST00000460711.1_Missense_Mutation_p.A57V	NM_144642.4	NP_653243.1	Q8TBG9	SYNPR_HUMAN	synaptoporin	46	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.					cell junction (GO:0030054)|integral component of synaptic vesicle membrane (GO:0030285)|neuron projection (GO:0043005)	transporter activity (GO:0005215)	p.A66V(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	8				BRCA - Breast invasive adenocarcinoma(55;0.000918)|KIRC - Kidney renal clear cell carcinoma(15;0.0658)|Kidney(15;0.0904)		ATAGCGTTTGCCTACCCATTC	0.483																																					p.A66V	NSCLC(29;1052 1116 20025 32519)	Atlas-SNP	.											SYNPR,NS,carcinoma,+1,4	SYNPR	38	4	1	Substitution - Missense(1)	NS(1)	c.C197T						PASS	.						152	154	153					3																	63466620		1998	4164	6162	SO:0001583	missense	132204	exon3			CGTTTGCCTACCC	AF411860	CCDS46859.1, CCDS46860.1	3p14.3	2011-07-28			ENSG00000163630	ENSG00000163630			16507	protein-coding gene	gene with protein product						8034131, 12974474	Standard	NM_144642		Approved	MGC26651, SPO	uc003dlp.3	Q8TBG9	OTTHUMG00000158699	ENST00000295894.5:c.137C>T	3.37:g.63466620C>T	ENSP00000295894:p.Ala46Val	47	0	0		41	8	0.195122	NM_001130003	B2R675|G5E9W4	Missense_Mutation	SNP	ENST00000295894.5	37	CCDS46860.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.000995	0.74818	.	.	ENSG00000163630	ENST00000478300;ENST00000295894;ENST00000479198;ENST00000460711;ENST00000465156	T;T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04;-0.04	5.04	5.04	0.67666	Marvel (1);MARVEL-like domain (1);	0.000000	0.85682	D	0.000000	T	0.72479	0.3465	M	0.75264	2.295	0.80722	D	1	P;P;D	0.56521	0.939;0.856;0.976	P;P;P	0.53224	0.721;0.636;0.6	T	0.72347	-0.4321	10	0.31617	T	0.26	-21.964	17.382	0.87407	0.0:1.0:0.0:0.0	.	57;46;66	B3KVD8;Q8TBG9;G5E9W4	.;SYNPR_HUMAN;.	V	66;46;46;57;46	ENSP00000418994:A66V;ENSP00000295894:A46V;ENSP00000418929:A46V;ENSP00000418701:A57V;ENSP00000418123:A46V	ENSP00000295894:A46V	A	+	2	0	SYNPR	63441660	1.000000	0.71417	0.983000	0.44433	0.964000	0.63967	3.717000	0.54911	2.343000	0.79666	0.557000	0.71058	GCC	.	.	none		0.483	SYNPR-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351787.1			T	63466620	C	T	63466620	3	4	4	1	0	0	0	0	1	0	0	0	15474	739	26	2	235	2	SYNPR	3	63466620	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	12857445	63466620	134555810	33	373											
EPHB1	2047	hgsc.bcm.edu	37	chr3	134670283	134670283	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggtgtgcaatgtcttcgAgcccaaccagaacaattggc	11	8	10	12	1	1	1	0	0	1	1	2	2	1	1	3	2	4	1	3	2	4	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr3:134670283A>G	ENST00000398015.3	+	3	564	c.194A>G	c.(193-195)gAg>gGg	p.E65G	EPHB1_ENST00000488154.1_3'UTR	NM_004441.4	NP_004432.1	P54762	EPHB1_HUMAN	EPH receptor B1	65	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				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						AATGTCTTCGAGCCCAACCAG	0.552																																					p.E65G		Atlas-SNP	.											.	EPHB1	519	.	0			c.A194G						PASS	.						39	43	42					3																	134670283		2143	4268	6411	SO:0001583	missense	2047	exon3			TCTTCGAGCCCAA	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.194A>G	3.37:g.134670283A>G	ENSP00000381097:p.Glu65Gly	114	0	0		84	31	0.369048	NM_004441	A8K593|B3KTB2|B5A969|O43569|O95142|O95143|Q0VG87	Missense_Mutation	SNP	ENST00000398015.3	37	CCDS46921.1	.	.	.	.	.	.	.	.	.	.	A	16.34	3.096720	0.56075	.	.	ENSG00000154928	ENST00000460895;ENST00000398015;ENST00000473867;ENST00000474732	T;T;T;T	0.03920	3.76;3.76;3.76;3.76	5.55	5.55	0.83447	Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	T	0.07098	0.0180	L	0.55213	1.73	0.80722	D	1	B;B	0.18461	0.028;0.002	B;B	0.24541	0.054;0.003	T	0.12066	-1.0562	10	0.51188	T	0.08	.	10.1025	0.42513	0.9253:0.0:0.0747:0.0	.	65;65	B5A969;P54762	.;EPHB1_HUMAN	G	43;65;43;43	ENSP00000417435:E43G;ENSP00000381097:E65G;ENSP00000417216:E43G;ENSP00000418352:E43G	ENSP00000381097:E65G	E	+	2	0	EPHB1	136152973	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.574000	0.82434	2.105000	0.64084	0.528000	0.53228	GAG	.	.	none		0.552	EPHB1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357671.1	NM_004441		G	134670283	A	G	134670283	3	3	4	1	0	0	0	0	1	0	0	0	5176	304	11	3	204	3	EPHB1	3	134670283	Missense_Mutation	SNP	A	TCGA-FA-A6HN-01A-11D-A31X-10	71203663	134670283	63352147	34	374											
SMC4	10051	hgsc.bcm.edu	37	chr3	160130162	160130162	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaaaggatgccttagaaggaGagaaaaacatagctatcgaa	20	6	10	5	1	0	2	0	0	0	2	1	6	0	4	1	2	3	1	1	2	9	3			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr3:160130162G>A	ENST00000357388.3	+	7	1352	c.901G>A	c.(901-903)Gag>Aag	p.E301K	SMC4_ENST00000462787.1_Missense_Mutation_p.E301K|SMC4_ENST00000469762.1_Missense_Mutation_p.E276K|SMC4_ENST00000360111.2_Missense_Mutation_p.E301K|SMC4_ENST00000344722.5_Missense_Mutation_p.E301K|RP11-432B6.3_ENST00000483754.1_Intron|SMC4_ENST00000470240.1_Intron	NM_001002800.1	NP_001002800.1	Q9NTJ3	SMC4_HUMAN	structural maintenance of chromosomes 4	301					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)	p.E301K(1)		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)			CTTAGAAGGAGAGAAAAACAT	0.289																																					p.E301K		Atlas-SNP	.											SMC4,mouth,carcinoma,0,1	SMC4	135	1	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.G901A						PASS	.						54	56	56					3																	160130162		2202	4292	6494	SO:0001583	missense	10051	exon6			GAAGGAGAGAAAA	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.901G>A	3.37:g.160130162G>A	ENSP00000349961:p.Glu301Lys	294	0	0		312	118	0.378205	NM_005496	A6NLT9|D3DNL8|O95752|Q8NDL4|Q9UNT9	Missense_Mutation	SNP	ENST00000357388.3	37	CCDS3189.1	.	.	.	.	.	.	.	.	.	.	G	35	5.413422	0.96072	.	.	ENSG00000113810	ENST00000357388;ENST00000360111;ENST00000392788;ENST00000469762;ENST00000489573;ENST00000462787;ENST00000344722	T;T;T;T;T;T	0.78003	-1.12;-1.14;-1.11;0.07;-1.14;-1.12	5.57	5.57	0.84162	RecF/RecN/SMC (1);	0.046370	0.85682	D	0.000000	T	0.77232	0.4100	N	0.20986	0.625	0.80722	D	1	P;D;P	0.56746	0.692;0.977;0.737	B;P;P	0.55011	0.295;0.766;0.524	T	0.74595	-0.3613	10	0.27082	T	0.32	-18.5462	19.1507	0.93487	0.0:0.0:1.0:0.0	.	301;276;301	Q9NTJ3-2;E9PD53;Q9NTJ3	.;.;SMC4_HUMAN	K	301;301;301;276;301;301;301	ENSP00000349961:E301K;ENSP00000353225:E301K;ENSP00000417964:E276K;ENSP00000420121:E301K;ENSP00000420734:E301K;ENSP00000341382:E301K	ENSP00000341382:E301K	E	+	1	0	SMC4	161612856	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.247000	0.95444	2.628000	0.89032	0.585000	0.79938	GAG	.	.	none		0.289	SMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352862.1			A	160130162	G	A	160130162	3	1	4	1	0	0	0	0	1	0	0	0	14800	943	33	2	923	2	SMC4	3	160130162	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	25459879	160130162	37892268	35	375											
EIF2B5	8893	hgsc.bcm.edu	37	chr3	183855505	183855505	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtcctccgtgatgttgatGccaaggctttggtgcgctct	5	14	12	10	2	1	2	0	2	1	0	3	2	3	2	3	2	2	3	3	2	1	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr3:183855505G>T	ENST00000273783.3	+	3	540	c.418G>T	c.(418-420)Gcc>Tcc	p.A140S	EIF2B5_ENST00000444495.1_Missense_Mutation_p.A140S|EIF2B5_ENST00000498831.1_3'UTR|RP11-778D9.12_ENST00000608135.1_RNA|RP11-778D9.12_ENST00000608232.1_RNA	NM_003907.2	NP_003898.2	Q13144	EI2BE_HUMAN	eukaryotic translation initiation factor 2B, subunit 5 epsilon, 82kDa	140					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)			TGATGTTGATGCCAAGGCTTT	0.483																																					p.A140S		Atlas-SNP	.											.	EIF2B5	62	.	0			c.G418T						PASS	.						195	163	174					3																	183855505		2203	4300	6503	SO:0001583	missense	8893	exon3			GTTGATGCCAAGG	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.418G>T	3.37:g.183855505G>T	ENSP00000273783:p.Ala140Ser	117	0	0		88	25	0.284091	NM_003907	Q541Z1|Q96D04	Missense_Mutation	SNP	ENST00000273783.3	37	CCDS3252.1	.	.	.	.	.	.	.	.	.	.	g	17.74	3.463615	0.63513	.	.	ENSG00000145191	ENST00000273783;ENST00000444495	D;D	0.93763	-3.28;-3.28	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	D	0.94555	0.8246	L	0.38733	1.17	0.80722	D	1	D	0.76494	0.999	D	0.78314	0.991	D	0.91422	0.5159	10	0.14252	T	0.57	-19.8346	20.051	0.97627	0.0:0.0:1.0:0.0	.	140	Q13144	EI2BE_HUMAN	S	140	ENSP00000273783:A140S;ENSP00000409142:A140S	ENSP00000273783:A140S	A	+	1	0	EIF2B5	185338199	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.740000	0.93945	0.650000	0.86243	GCC	.	.	none		0.483	EIF2B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346168.1			T	183855505	G	T	183855505	3	4	4	1	0	0	0	0	1	0	0	0	5006	1319	46	4	428	4	EIF2B5	3	183855505	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	23725343	183855505	14166925	36	376											
EIF4A2	1974	hgsc.bcm.edu	37	chr3	186502355	186502355	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	attttttctaacttacagagCaactggaatgagattgttga	13	15	8	5	0	1	3	0	2	1	2	1	5	1	4	0	1	4	2	0	1	4	7	rs371691662		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr3:186502355C>G	ENST00000323963.5	+	3	142	c.78C>G	c.(76-78)agC>agG	p.S26R	SNORD2_ENST00000459163.1_RNA|EIF4A2_ENST00000356531.5_5'UTR|RP11-573D15.9_ENST00000577781.1_RNA|EIF4A2_ENST00000440191.2_Missense_Mutation_p.S27R|SNORA63_ENST00000363548.1_RNA|SNORA81_ENST00000408493.2_RNA|SNORA63_ENST00000363450.1_RNA			Q14240	IF4A2_HUMAN	eukaryotic translation initiation factor 4A2	26					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)		ACTTACAGAGCAACTGGAATG	0.398			T	BCL6	NHL																																p.S26R		Atlas-SNP	.		Dom	yes		3	3q27.3	1974	"eukaryotic translation initiation factor 4A, isoform 2"		L	.	EIF4A2	55	.	0			c.C78G						PASS	.						184	188	187					3																	186502355		2203	4300	6503	SO:0001583	missense	1974	exon3			ACAGAGCAACTGG	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.78C>G	3.37:g.186502355C>G	ENSP00000326381:p.Ser26Arg	151	0	0		109	21	0.192661	NM_001967	D3DNU9|Q53XJ6|Q96B90|Q96EA8	Missense_Mutation	SNP	ENST00000323963.5	37	CCDS3282.1	.	.	.	.	.	.	.	.	.	.	C	18.59	3.656454	0.67586	.	.	ENSG00000156976	ENST00000441007;ENST00000445596;ENST00000323963;ENST00000440191	T;T;T	0.32753	1.44;1.64;1.65	4.16	3.29	0.37713	.	0.043514	0.85682	D	0.000000	T	0.37237	0.0996	M	0.82517	2.595	0.80722	D	1	B;B	0.15473	0.013;0.005	B;B	0.19391	0.012;0.025	T	0.42666	-0.9438	10	0.87932	D	0	-14.8241	10.5715	0.45202	0.0:0.9034:0.0:0.0966	.	27;26	Q14240-2;Q14240	.;IF4A2_HUMAN	R	26;26;26;27	ENSP00000415878:S26R;ENSP00000326381:S26R;ENSP00000398370:S27R	ENSP00000326381:S26R	S	+	3	2	EIF4A2	187985049	1.000000	0.71417	1.000000	0.80357	0.827000	0.46813	2.929000	0.48916	1.345000	0.45676	0.585000	0.79938	AGC	.	.	alt		0.398	EIF4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344609.1	NM_001967		G	186502355	C	G	186502355	3	3	4	1	0	0	0	0	1	0	0	0	5027	709	25	4	88	4	EIF4A2	3	186502355	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	2646850	186502355	11520075	37	377											
EIF4A2	1974	hgsc.bcm.edu	37	chr3	186502430	186502430	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttcgtggcatctatgcttaCggttttgagaagccttccgc	6	14	10	11	3	1	1	0	1	1	1	3	2	2	1	2	2	3	3	2	2	3	6			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr3:186502430C>T	ENST00000323963.5	+	3	217	c.153C>T	c.(151-153)taC>taT	p.Y51Y	SNORA4_ENST00000584302.1_RNA|SNORD2_ENST00000459163.1_RNA|EIF4A2_ENST00000356531.5_Missense_Mutation_p.T3M|RP11-573D15.9_ENST00000577781.1_RNA|EIF4A2_ENST00000440191.2_Silent_p.Y52Y|SNORA63_ENST00000363548.1_RNA|SNORA81_ENST00000408493.2_RNA|SNORA63_ENST00000363450.1_RNA			Q14240	IF4A2_HUMAN	eukaryotic translation initiation factor 4A2	51					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)		TCTATGCTTACGGTTTTGAGA	0.358			T	BCL6	NHL																																p.Y51Y		Atlas-SNP	.		Dom	yes		3	3q27.3	1974	"eukaryotic translation initiation factor 4A, isoform 2"		L	.	EIF4A2	55	.	0			c.C153T						PASS	.						124	130	128					3																	186502430		2203	4300	6503	SO:0001819	synonymous_variant	1974	exon3			TGCTTACGGTTTT	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.153C>T	3.37:g.186502430C>T		110	0	0		95	20	0.210526	NM_001967	D3DNU9|Q53XJ6|Q96B90|Q96EA8	Silent	SNP	ENST00000323963.5	37	CCDS3282.1	.	.	.	.	.	.	.	.	.	.	C	13.35	2.211860	0.39102	.	.	ENSG00000156976	ENST00000356531	T	0.34275	1.37	4.6	-3.99	0.04069	.	.	.	.	.	T	0.23532	0.0569	.	.	.	0.24291	N	0.99516	B	0.06786	0.001	B	0.01281	0.0	T	0.34527	-0.9825	8	0.87932	D	0	-2.7687	7.1768	0.25749	0.0:0.4534:0.1318:0.4148	.	3	Q9NZE6	.	M	3	ENSP00000348925:T3M	ENSP00000348925:T3M	T	+	2	0	EIF4A2	187985124	0.974000	0.33945	0.990000	0.47175	0.994000	0.84299	0.071000	0.14594	-0.466000	0.06943	-0.237000	0.12165	ACG	.	.	none		0.358	EIF4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344609.1	NM_001967		T	186502430	C	T	186502430	2	4	4	1	0	0	0	0	0	0	0	1	5027	547	19	1		1	EIF4A2	3	186502430	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	75	186502430	11520000	38	378											
RPL35A	6165	hgsc.bcm.edu	37	chr3	197678057	197678057	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaaggccatttttgctggCtataagcggggtctccggaa	8	11	12	10	2	1	0	0	0	1	0	3	1	2	1	3	5	2	2	3	5	4	4			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr3:197678057C>T	ENST00000464167.1	+	3	306	c.39C>T	c.(37-39)ggC>ggT	p.G13G	IQCG_ENST00000480302.1_Intron|RPL35A_ENST00000329092.8_3'UTR|IQCG_ENST00000455191.1_5'Flank|IQCG_ENST00000453254.1_5'Flank|RPL35A_ENST00000448864.1_Silent_p.G13G|IQCG_ENST00000265239.6_Intron	NM_000996.2	NP_000987.2	P18077	RL35A_HUMAN	ribosomal protein L35a	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)|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)		TTTTTGCTGGCTATAAGCGGG	0.443																																					p.G13G		Atlas-SNP	.											.	RPL35A	9	.	0			c.C39T						PASS	.						73	74	73					3																	197678057		2202	4298	6500	SO:0001819	synonymous_variant	6165	exon3			TGCTGGCTATAAG	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.39C>T	3.37:g.197678057C>T		88	0	0		70	15	0.214286	NM_000996	Q08ES9|Q9BVN7	Silent	SNP	ENST00000464167.1	37	CCDS33930.1																																																																																			.	.	none		0.443	RPL35A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339788.1	NM_000996		T	197678057	C	T	197678057	2	4	4	1	0	0	0	0	0	0	0	1	13600	784	28	2		2	RPL35A	3	197678057	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	11175627	197678057	344373	39	379											
NAT8L	339983	hgsc.bcm.edu	37	chr4	2062888	2062888	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtactacatgaagccgccCggtgagtcccgctcccgccg	7	6	11	17	5	0	2	0	2	0	0	2	2	2	2	5	1	3	2	5	1	3	2	rs376253416		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr4:2062888C>T	ENST00000423729.2	+	2	540	c.540C>T	c.(538-540)ccC>ccT	p.P180P	NAT8L_ENST00000331662.3_Splice_Site_p.P12P	NM_178557.3	NP_848652.2	Q8N9F0	NAT8L_HUMAN	N-acetyltransferase 8-like (GCN5-related, putative)	180	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				metabolic process (GO:0008152)|positive regulation of dopamine uptake involved in synaptic transmission (GO:0051586)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)	aspartate N-acetyltransferase activity (GO:0017188)			haematopoietic_and_lymphoid_tissue(1)|lung(1)	2			OV - Ovarian serous cystadenocarcinoma(23;0.0315)			TGAAGCCGCCCGGTGAGTCCC	0.706																																					p.P180P		Atlas-SNP	.											.	NAT8L	23	.	0			c.C540T						PASS	.	C		0,4366		0,0,2183	23	23	23		540	-8.1	0.1	4		23	1,8573		0,1,4286	no	coding-synonymous-near-splice	NAT8L	NM_178557.3		0,1,6469	TT,TC,CC		0.0117,0.0,0.0077		180/303	2062888	1,12939	2183	4287	6470	SO:0001630	splice_region_variant	339983	exon2			GCCGCCCGGTGAG	AK094797	CCDS3359.1, CCDS3359.2	4p16.3	2011-11-16	2008-09-24		ENSG00000185818	ENSG00000185818			26742	protein-coding gene	gene with protein product		610647	"N-acetyltransferase 8-like"			11397015	Standard	NM_178557		Approved	FLJ37478, Hcml3	uc003geq.2	Q8N9F0	OTTHUMG00000121151	ENST00000423729.2:c.541+1C>T	4.37:g.2062888C>T		125	0	0		115	19	0.165217	NM_178557		Silent	SNP	ENST00000423729.2	37	CCDS3359.2																																																																																			.	.	weak		0.706	NAT8L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178557	Silent	T	2062888	C	T	2062888	5	4	4	1	0	0	0	0	0	0	1	0	10190	666	23	1	546	1	NAT8L	4	2062888	Splice_Site	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10		2062888	189091388	40	380											
HNRNPD	3184	hgsc.bcm.edu	37	chr4	83294756	83294756	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgccaccatggctccctcctGctcgcccgccgagccgccta	4	6	9	22	5	0	0	0	0	0	0	3	1	2	0	8	1	2	2	8	1	1	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr4:83294756G>A	ENST00000313899.7	-	1	353	c.76C>T	c.(76-78)Cag>Tag	p.Q26*	HNRNPD_ENST00000541060.1_5'UTR|RP11-127B20.3_ENST00000609552.1_RNA|HNRNPD_ENST00000353341.4_Nonsense_Mutation_p.Q26*|HNRNPD_ENST00000543098.1_Intron|HNRNPD_ENST00000352301.4_Nonsense_Mutation_p.Q26*|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)	26	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						gctccctcctgctcgcccgcc	0.771																																					p.Q26X		Atlas-SNP	.											.	HNRNPD	23	.	0			c.C76T						PASS	.						2	2	2					4																	83294756		1399	2648	4047	SO:0001587	stop_gained	3184	exon1			CCTCCTGCTCGCC	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.76C>T	4.37:g.83294756G>A	ENSP00000313199:p.Gln26*	18	0	0		23	6	0.26087	NM_031370	A8K9J2|P07029|Q01858|Q14100|Q14101|Q14102|Q4W5A1|Q9UCE8|Q9UCE9	Nonsense_Mutation	SNP	ENST00000313899.7	37	CCDS3592.1	.	.	.	.	.	.	.	.	.	.	G	40	8.250992	0.98727	.	.	ENSG00000138668	ENST00000313899;ENST00000353341;ENST00000352301;ENST00000307213;ENST00000507010;ENST00000503822	.	.	.	3.59	3.59	0.41128	.	0.717750	0.12547	N	0.459378	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	.	12.5691	0.56326	0.0:0.0:1.0:0.0	.	.	.	.	X	26;26;26;23;26;26	.	ENSP00000307544:Q23X	Q	-	1	0	HNRNPD	83513780	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.805000	0.55575	2.009000	0.58944	0.430000	0.28490	CAG	.	.	none		0.771	HNRNPD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252630.2	NM_031370		A	83294756	G	A	83294756	4	1	4	1	0	0	0	0	0	1	0	0	7273	1328	46	2	1023	2	HNRNPD	4	83294756	Nonsense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	81231868	83294756	107859520	41	381											
DSPP	1834	hgsc.bcm.edu	37	chr4	88537205	88537213	+	In_Frame_Del	DEL	GACAGCAGT	GACAGCAGT	-																															gtgacagcagtgacagcagcGacagcagtgatagcagtgac																								rs143067236|rs151217478|rs551655835	byFrequency	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	GACAGCAGT	GACAGCAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr4:88537205_88537213delGACAGCAGT	ENST00000282478.7	+	4	3424_3432	c.3391_3399delGACAGCAGT	c.(3391-3399)gacagcagtdel	p.DSS1137del	DSPP_ENST00000399271.1_In_Frame_Del_p.DSS1137del|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1137	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)		tgacagcagcgacagcagtgatagcagtg	0.569																																					p.1130_1133del		Atlas-Indel	.											.	DSPP	174	.	0			c.3390_3398del						PASS	.			357,1999		74,209,895						-1.1	0			19	1005,3537		137,731,1403	no	coding	DSPP	NM_014208.3		211,940,2298	A1A1,A1R,RR		22.1268,15.1528,19.7449				1362,5536				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.3391_3399delGACAGCAGT	4.37:g.88537205_88537213delGACAGCAGT	ENSP00000282478:p.Asp1137_Ser1139del	71	0	0		87	77	0.885057	NM_014208	A8MUI0|O95815	In_Frame_Del	DEL	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	none		0.569	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		-	88537213	GACAGCAGT	-	88537205	7	5	4	1	0	1	0	1	0	0	0	0	4784	1058	37	0	3405	0	DSPP	4	88537205	In_Frame_Del	DEL	GACAGCAGT	TCGA-FA-A6HN-01A-11D-A31X-10	5242449	88537205	102617071	42	382											
ANK2	287	hgsc.bcm.edu	37	chr4	114290944	114290944	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctgtgaaagactcgatgaaGatgcagcttttgaaaaggta	14	10	11	6	1	0	5	0	3	0	2	1	6	0	5	1	1	2	3	1	1	5	3			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr4:114290944G>A	ENST00000357077.4	+	43	11646	c.11593G>A	c.(11593-11595)Gat>Aat	p.D3865N	ANK2_ENST00000394537.3_Missense_Mutation_p.D1780N|ANK2_ENST00000506722.1_Missense_Mutation_p.D1771N|ANK2_ENST00000264366.6_Missense_Mutation_p.D3832N|ANK2_ENST00000509550.1_Missense_Mutation_p.D956N|ANK2_ENST00000510275.2_Missense_Mutation_p.D432N	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	3865					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)		ACTCGATGAAGATGCAGCTTT	0.468																																					p.D3865N		Atlas-SNP	.											.	ANK2	576	.	0			c.G11593A						PASS	.						91	83	86					4																	114290944		2203	4300	6503	SO:0001583	missense	287	exon43			GATGAAGATGCAG	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.11593G>A	4.37:g.114290944G>A	ENSP00000349588:p.Asp3865Asn	90	0	0		84	15	0.178571	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.40|16.40	3.114027|3.114027	0.56398|0.56398	.|.	.|.	ENSG00000145362|ENSG00000145362	ENST00000506722;ENST00000431447;ENST00000394537;ENST00000357077;ENST00000264366;ENST00000343056;ENST00000509550;ENST00000510275;ENST00000505342|ENST00000514960	T;T;T;T;T;D;D|.	0.96300|.	-0.27;-0.25;-0.32;-0.33;-1.04;-2.0;-3.97|.	5.63|5.63	4.79|4.79	0.61399|0.61399	.|.	0.328121|.	0.25631|.	N|.	0.029352|.	T|T	0.53965|0.53965	0.1829|0.1829	L|L	0.54323|0.54323	1.7|1.7	0.25795|0.25795	N|N	0.984572|0.984572	B;B;B;B;P;B|.	0.48503|.	0.321;0.01;0.094;0.0;0.911;0.016|.	B;B;B;B;P;B|.	0.52646|.	0.101;0.01;0.054;0.001;0.705;0.04|.	T|T	0.48559|0.48559	-0.9025|-0.9025	10|5	0.44086|.	T|.	0.13|.	.|.	15.041|15.041	0.71791|0.71791	0.0689:0.0:0.9311:0.0|0.0689:0.0:0.9311:0.0	.|.	956;815;781;1780;3865;1771|.	E9PCH6;F8W694;Q7Z344;Q01484-2;Q01484-4;Q01484-5|.	.;.;.;.;.;.|.	N|K	1771;815;1780;3865;3832;1771;956;432;875|781	ENSP00000421067:D1771N;ENSP00000378044:D1780N;ENSP00000349588:D3865N;ENSP00000264366:D3832N;ENSP00000426944:D956N;ENSP00000421023:D432N;ENSP00000422498:D875N|.	ENSP00000264366:D3832N|.	D|R	+|+	1|2	0|0	ANK2|ANK2	114510393|114510393	1.000000|1.000000	0.71417|0.71417	0.042000|0.042000	0.18584|0.18584	0.149000|0.149000	0.21700|0.21700	4.966000|4.966000	0.63715|0.63715	1.517000|1.517000	0.48917|0.48917	-0.157000|-0.157000	0.13467|0.13467	GAT|AGA	.	.	none		0.468	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		A	114290944	G	A	114290944	3	1	4	1	0	0	0	0	1	0	0	0	621	942	33	2	11828	2	ANK2	4	114290944	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	25753739	114290944	76863332	43	383											
SMARCA5	8467	hgsc.bcm.edu	37	chr4	144467950	144467950	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatttaccaattggaataagAgagattttaaccagtttatc	15	14	7	5	0	0	2	0	0	0	2	1	5	0	3	2	1	2	1	2	1	6	8			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr4:144467950A>C	ENST00000283131.3	+	20	3004	c.2542A>C	c.(2542-2544)Aga>Cga	p.R848R		NM_003601.3	NP_003592.3	O60264	SMCA5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	848	SANT 1. {ECO:0000255|PROSITE- ProRule:PRU00624}.				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)					TTGGAATAAGAGAGATTTTAA	0.333																																					p.R848R		Atlas-SNP	.											SMARCA5,rectum,carcinoma,-1,1	SMARCA5	73	1	0			c.A2542C						PASS	.						82	85	84					4																	144467950		2203	4299	6502	SO:0001819	synonymous_variant	8467	exon20			AATAAGAGAGATT	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.2542A>C	4.37:g.144467950A>C		141	0	0		101	27	0.267327	NM_003601		Silent	SNP	ENST00000283131.3	37	CCDS3761.1																																																																																			.	.	none		0.333	SMARCA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365077.3			C	144467950	A	C	144467950	2	2	4	1	0	0	0	0	0	0	0	1	14786	296	11	5		5	SMARCA5	4	144467950	Silent	SNP	A	TCGA-FA-A6HN-01A-11D-A31X-10	30177006	144467950	46686326	44	384											
PRMT10	90826	hgsc.bcm.edu	37	chr4	148594981	148594981	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaaatcagggtttagcttcActgctttatgaaaataccca	13	13	7	8	0	2	2	2	2	0	0	2	2	2	2	1	1	3	3	1	1	6	6			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr4:148594981A>C	ENST00000322396.6	-	3	625	c.383T>G	c.(382-384)gTg>gGg	p.V128G	PRMT10_ENST00000541232.1_Missense_Mutation_p.V15G	NM_138364.2	NP_612373.2	Q6P2P2	ANM9_HUMAN		128						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						GTTTAGCTTCACTGCTTTATG	0.383																																					p.V128G		Atlas-SNP	.											.	PRMT10	68	.	0			c.T383G						PASS	.						81	81	81					4																	148594981		2203	4300	6503	SO:0001583	missense	90826	exon3			AGCTTCACTGCTT																												ENST00000322396.6:c.383T>G	4.37:g.148594981A>C	ENSP00000314396:p.Val128Gly	102	0	0		108	21	0.194444	NM_138364	A8KA39|B3KU92|Q6ZR58|Q8N383|Q9BT55|Q9NT98	Missense_Mutation	SNP	ENST00000322396.6	37	CCDS3771.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.425487	0.83667	.	.	ENSG00000164169	ENST00000322396;ENST00000541232	D;T	0.89123	-2.47;1.7	5.37	5.37	0.77165	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.064517	0.64402	D	0.000007	D	0.89322	0.6682	N	0.19112	0.55	0.80722	D	1	D	0.76494	0.999	D	0.64506	0.926	D	0.90662	0.4591	10	0.54805	T	0.06	.	15.3765	0.74610	1.0:0.0:0.0:0.0	.	128	Q6P2P2	ANM10_HUMAN	G	128;15	ENSP00000314396:V128G;ENSP00000439508:V15G	ENSP00000314396:V128G	V	-	2	0	PRMT10	148814431	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.948000	0.93006	2.045000	0.60652	0.533000	0.62120	GTG	.	.	none		0.383	PRMT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364650.1			C	148594981	A	C	148594981	3	2	4	1	0	0	0	0	1	0	0	0	12548	159	6	5	2194	5	PRMT10	4	148594981	Missense_Mutation	SNP	A	TCGA-FA-A6HN-01A-11D-A31X-10	4127031	148594981	42559295	45	385											
PDE4D	5144	hgsc.bcm.edu	37	chr5	58334737	58334737	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctggtctgtagggtctctagCtggtccagacaccagtccag	7	10	12	12	0	2	1	0	0	2	1	5	1	4	1	3	3	1	2	3	3	2	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr5:58334737C>T	ENST00000340635.6	-	6	1045	c.870G>A	c.(868-870)caG>caA	p.Q290Q	PDE4D_ENST00000358923.6_5'UTR|PDE4D_ENST00000405755.2_Silent_p.Q168Q|PDE4D_ENST00000360047.5_Silent_p.Q154Q|PDE4D_ENST00000546160.1_Silent_p.Q229Q|PDE4D_ENST00000503258.1_Silent_p.Q160Q|PDE4D_ENST00000507116.1_Silent_p.Q226Q|RP11-266N13.2_ENST00000500224.2_RNA|PDE4D_ENST00000502484.2_Silent_p.Q229Q	NM_001104631.1	NP_001098101.1	Q08499	PDE4D_HUMAN	phosphodiesterase 4D, cAMP-specific	290					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)	GGGTCTCTAGCTGGTCCAGAC	0.602																																					p.Q290Q		Atlas-SNP	.											.	PDE4D	345	.	0			c.G870A						PASS	.						48	54	52					5																	58334737		2043	4208	6251	SO:0001819	synonymous_variant	5144	exon6			CTCTAGCTGGTCC		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.870G>A	5.37:g.58334737C>T		87	0	0		72	13	0.180556	NM_001104631	O43433|Q13549|Q13550|Q13551|Q7Z2L8|Q8IV84|Q8IVA9|Q8IVD2|Q8IVD3|Q96HL4|Q9HCX7	Silent	SNP	ENST00000340635.6	37	CCDS47213.1																																																																																			.	.	none		0.602	PDE4D-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367940.3			T	58334737	C	T	58334737	2	4	4	1	0	0	0	0	0	0	0	1	11651	796	28	2		2	PDE4D	5	58334737	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10		58334737	122580523	46	386											
ZNF474	133923	hgsc.bcm.edu	37	chr5	121488255	121488255	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacagaagctgcaagccaaaGggtgagggtcccagagcacc	13	3	13	12	0	0	3	0	1	0	2	1	3	1	3	3	2	4	3	3	2	3	0			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr5:121488255G>T	ENST00000296600.4	+	2	953	c.570G>T	c.(568-570)aaG>aaT	p.K190N	CTC-441N14.1_ENST00000505209.1_RNA|ZNF474_ENST00000514925.1_Intron|CTC-441N14.2_ENST00000504829.1_RNA	NM_207317.1	NP_997200.1	Q6S9Z5	ZN474_HUMAN	zinc finger protein 474	190							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)		GCAAGCCAAAGGGTGAGGGTC	0.522																																					p.K190N		Atlas-SNP	.											.	ZNF474	43	.	0			c.G570T						PASS	.						89	85	86					5																	121488255		2203	4300	6503	SO:0001583	missense	133923	exon2			GCCAAAGGGTGAG	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.570G>T	5.37:g.121488255G>T	ENSP00000296600:p.Lys190Asn	74	0	0		70	17	0.242857	NM_207317	A8K4M0|Q96M07	Missense_Mutation	SNP	ENST00000296600.4	37	CCDS4130.1	.	.	.	.	.	.	.	.	.	.	G	6.459	0.452915	0.12283	.	.	ENSG00000164185	ENST00000296600	T	0.51574	0.7	5.26	3.44	0.39384	Zinc finger, C2H2 (1);	0.638340	0.13037	N	0.418838	T	0.33381	0.0861	L	0.32530	0.975	0.25703	N	0.985565	B	0.10296	0.003	B	0.12837	0.008	T	0.15235	-1.0444	10	0.31617	T	0.26	-6.7594	6.1089	0.20090	0.0771:0.1358:0.6472:0.14	.	190	Q6S9Z5	ZN474_HUMAN	N	190	ENSP00000296600:K190N	ENSP00000296600:K190N	K	+	3	2	ZNF474	121516154	1.000000	0.71417	0.857000	0.33713	0.123000	0.20343	1.969000	0.40510	1.372000	0.46190	-0.122000	0.15005	AAG	.	.	none		0.522	ZNF474-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250883.2	NM_207317		T	121488255	G	T	121488255	3	4	4	1	0	0	0	0	1	0	0	0	17947	991	35	4	572	4	ZNF474	5	121488255	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	63153518	121488255	59427005	47	387											
PCDHA9	9752	hgsc.bcm.edu	37	chr5	140229745	140229745	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgacgctgcaggtgttcgtGctggacgagaacgacaatgc	9	8	15	9	4	0	2	0	1	0	1	1	5	0	3	0	2	4	4	0	2	2	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr5:140229745G>A	ENST00000532602.1	+	1	2698	c.1665G>A	c.(1663-1665)gtG>gtA	p.V555V	PCDHA3_ENST00000522353.2_Intron|PCDHA9_ENST00000378122.3_Silent_p.V555V|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000394633.3_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	555	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(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)			AGGTGTTCGTGCTGGACGAGA	0.692																																					p.V555V	Melanoma(55;1800 1972 14909)	Atlas-SNP	.											.	PCDHA9	373	.	0			c.G1665A						PASS	.						63	68	66					5																	140229745		2196	4270	6466	SO:0001819	synonymous_variant	9752	exon1			GTTCGTGCTGGAC	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.1665G>A	5.37:g.140229745G>A		122	0	0		92	15	0.163043	NM_031857	O15053|Q2M3S5	Silent	SNP	ENST00000532602.1	37	CCDS54920.1																																																																																			.	.	none		0.692	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		A	140229745	G	A	140229745	2	1	4	1	0	0	0	0	0	0	0	1	11540	1306	46	2		2	PCDHA9	5	140229745	Silent	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	18741490	140229745	40685515	48	388											
PCDHGA12	26025	hgsc.bcm.edu	37	chr5	140810511	140810511	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccccgggagctcgcggagcGcggagtccgcatcatcccca	6	4	14	17	6	1	0	1	0	0	0	4	3	3	3	5	3	2	2	5	3	0	0			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr5:140810511G>A	ENST00000252085.3	+	1	327	c.185G>A	c.(184-186)cGc>cAc	p.R62H	PCDHGA10_ENST00000398610.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB8P_ENST00000502926.1_RNA|PCDHGA3_ENST00000253812.6_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA2_ENST00000394576.2_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	62	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)|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)			CTCGCGGAGCGCGGAGTCCGC	0.652																																					p.R62H		Atlas-SNP	.											PCDHGA12_ENST00000252085,NS,carcinoma,+1,4	PCDHGA12	271	4	0			c.G185A						PASS	.						58	72	67					5																	140810511		2202	4300	6502	SO:0001583	missense	26025	exon1			CGGAGCGCGGAGT	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.185G>A	5.37:g.140810511G>A	ENSP00000252085:p.Arg62His	109	0	0		102	12	0.117647	NM_032094	O15100|Q6UW70|Q9Y5D7	Missense_Mutation	SNP	ENST00000252085.3	37	CCDS4260.1	.	.	.	.	.	.	.	.	.	.	g	10.60	1.395216	0.25205	.	.	ENSG00000253159	ENST00000252085	T	0.41400	1.0	5.55	3.74	0.42951	Cadherin, N-terminal (1);Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.48822	0.1521	M	0.84433	2.695	0.09310	N	1	B;B	0.26809	0.16;0.1	B;B	0.27170	0.062;0.077	T	0.47995	-0.9073	9	0.52906	T	0.07	.	11.4063	0.49900	0.07:0.1252:0.8048:0.0	.	62;62	O60330-2;O60330	.;PCDGC_HUMAN	H	62	ENSP00000252085:R62H	ENSP00000252085:R62H	R	+	2	0	PCDHGA12	140790695	1.000000	0.71417	0.908000	0.35775	0.194000	0.23727	5.368000	0.66133	1.333000	0.45449	0.555000	0.69702	CGC	.	.	none		0.652	PCDHGA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251806.2	NM_003735		A	140810511	G	A	140810511	3	1	4	1	0	0	0	0	1	0	0	0	11562	1087	38	1	187	1	PCDHGA12	5	140810511	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	580766	140810511	40104749	49	389											
PCDH1	5097	hgsc.bcm.edu	37	chr5	141248200	141248200	+	Frame_Shift_Del	DEL	C	C	-																															tcataggagggccgctcaaaCttgggggcgttgtcattggt																										TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr5:141248200delC	ENST00000394536.3	-	2	976	c.837delG	c.(835-837)aagfs	p.K279fs	PCDH1_ENST00000503492.1_Frame_Shift_Del_p.K279fs|PCDH1_ENST00000287008.3_Frame_Shift_Del_p.K279fs|PCDH1_ENST00000511044.1_5'Flank|PCDH1_ENST00000536585.1_Frame_Shift_Del_p.K257fs|PCDH1_ENST00000456271.1_Frame_Shift_Del_p.K267fs	NM_001278613.1|NM_001278615.1	NP_001265542.1|NP_001265544.1	Q08174	PCDH1_HUMAN	protocadherin 1	279	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)		GCCGCTCAAACTTGGGGGCGT	0.607																																					p.F280fs	Ovarian(132;1609 1739 4190 14731 45037)	Pindel,Atlas-Indel	.											.	PCDH1	119	.	0			c.838delT						PASS	.						40	41	41					5																	141248200		2203	4300	6503	SO:0001589	frameshift_variant	5097	exon2			.	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.837delG	5.37:g.141248200delC	ENSP00000378043:p.Lys279fs	84	0	.		62	10	0.161	NM_032420	Q8IUP2	Frame_Shift_Del	DEL	ENST00000394536.3	37	CCDS43375.1																																																																																			.	.	none		0.607	PCDH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251862.1	NM_032420		-	141248200	C	-	141248200	7	5	4	1	0	1	0	1	0	0	0	0	11515	564	20	0	2976	0	PCDH1	5	141248200	Frame_Shift_Del	DEL	C	TCGA-FA-A6HN-01A-11D-A31X-10	437689	141248200	39667060	50	390											
SPRY4	81848	hgsc.bcm.edu	37	chr5	141694497	141694497	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cgctttgggccggtggtcagGgccaggctagggttgtctat	4	11	17	9	2	2	0	1	0	1	0	2	0	2	0	2	6	0	3	2	6	2	4			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr5:141694497G>A	ENST00000434127.2	-	2	420	c.177C>T	c.(175-177)gcC>gcT	p.A59A	SPRY4_ENST00000344120.4_Silent_p.A82A|SPRY4_ENST00000503582.1_5'Flank	NM_001127496.1	NP_001120968.1	Q9C004	SPY4_HUMAN	sprouty homolog 4 (Drosophila)	59					multicellular organismal development (GO:0007275)|negative regulation of MAP kinase activity (GO:0043407)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(1)	18		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGTGGTCAGGGCCAGGCTAG	0.642									Testicular Cancer, Familial Clustering of																												p.A82A		Atlas-SNP	.											.	SPRY4	31	.	0			c.C246T						PASS	.						29	32	31					5																	141694497		2198	4294	6492	SO:0001819	synonymous_variant	81848	exon3	Familial Cancer Database		GGTCAGGGCCAGG	AF227516	CCDS4274.1, CCDS47296.1	5q31.3	2010-08-05			ENSG00000187678	ENSG00000187678			15533	protein-coding gene	gene with protein product		607984				16465403	Standard	NM_030964		Approved		uc010jgi.1	Q9C004	OTTHUMG00000129663	ENST00000434127.2:c.177C>T	5.37:g.141694497G>A		117	0	0		96	22	0.229167	NM_030964	A4FVB2|A4FVB3|Q6QIX2|Q9C003	Silent	SNP	ENST00000434127.2	37	CCDS47296.1																																																																																			.	.	none		0.642	SPRY4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370652.1			A	141694497	G	A	141694497	2	1	4	1	0	0	0	0	0	0	0	1	15123	1219	43	2		2	SPRY4	5	141694497	Silent	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	446297	141694497	39220763	51	391											
C5orf46	389336	hgsc.bcm.edu	37	chr5	147286021	147286021	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcaggtcaggaataagacaAgcagtcccaggacaactgtc	15	5	11	10	0	1	1	1	0	0	1	3	3	2	3	1	3	3	2	1	3	4	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr5:147286021A>C	ENST00000318315.4	-	1	44	c.44T>G	c.(43-45)cTt>cGt	p.L15R	C5orf46_ENST00000510432.1_5'UTR|C5orf46_ENST00000515291.1_Missense_Mutation_p.L15R	NM_206966.2	NP_996849.2	Q6UWT4	CE046_HUMAN	chromosome 5 open reading frame 46	15						extracellular vesicular exosome (GO:0070062)				NS(1)|lung(1)|prostate(1)	3						GAATAAGACAAGCAGTCCCAG	0.458																																					p.L15R		Atlas-SNP	.											.	C5orf46	8	.	0			c.T44G						PASS	.						103	89	94					5																	147286021		2203	4300	6503	SO:0001583	missense	389336	exon1			AAGACAAGCAGTC		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.44T>G	5.37:g.147286021A>C	ENSP00000315370:p.Leu15Arg	293	0	0		281	42	0.149466	NM_206966	A8K038|Q8WU04	Missense_Mutation	SNP	ENST00000318315.4	37	CCDS34267.1	.	.	.	.	.	.	.	.	.	.	A	12.94	2.087544	0.36855	.	.	ENSG00000178776	ENST00000318315;ENST00000515291	T;T	0.52057	0.68;0.68	4.88	2.47	0.30058	.	0.338031	0.21758	N	0.069580	T	0.54679	0.1873	.	.	.	0.20307	N	0.999918	D	0.57257	0.979	P	0.59487	0.858	T	0.44406	-0.9330	9	0.59425	D	0.04	-2.2362	4.8194	0.13383	0.7:0.2008:0.0991:0.0	.	15	Q6UWT4	CE046_HUMAN	R	15	ENSP00000315370:L15R;ENSP00000425984:L15R	ENSP00000315370:L15R	L	-	2	0	C5orf46	147266214	0.078000	0.21339	0.294000	0.24946	0.995000	0.86356	1.064000	0.30579	0.449000	0.26747	0.533000	0.62120	CTT	.	.	none		0.458	C5orf46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373314.1	NM_206966		C	147286021	A	C	147286021	3	2	4	1	0	0	0	0	1	0	0	0	2307	72	3	5	231	5	C5orf46	5	147286021	Missense_Mutation	SNP	A	TCGA-FA-A6HN-01A-11D-A31X-10	5591524	147286021	33629239	52	392											
C5orf46	389336	hgsc.bcm.edu	37	chr5	147286047	147286047	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaggacaactgtcaggcgAagtactgagacagccattct	12	7	10	12	1	2	1	1	1	1	1	2	4	2	2	2	2	3	1	2	2	3	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr5:147286047A>G	ENST00000318315.4	-	1	18	c.18T>C	c.(16-18)ctT>ctC	p.L6L	C5orf46_ENST00000510432.1_5'UTR|C5orf46_ENST00000515291.1_Silent_p.L6L	NM_206966.2	NP_996849.2	Q6UWT4	CE046_HUMAN	chromosome 5 open reading frame 46	6						extracellular vesicular exosome (GO:0070062)				NS(1)|lung(1)|prostate(1)	3						CTGTCAGGCGAAGTACTGAGA	0.453																																					p.L6L		Atlas-SNP	.											.	C5orf46	8	.	0			c.T18C						PASS	.						102	88	93					5																	147286047		2203	4300	6503	SO:0001819	synonymous_variant	389336	exon1			CAGGCGAAGTACT		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.18T>C	5.37:g.147286047A>G		284	0	0		271	39	0.143911	NM_206966	A8K038|Q8WU04	Silent	SNP	ENST00000318315.4	37	CCDS34267.1																																																																																			.	.	none		0.453	C5orf46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373314.1	NM_206966		G	147286047	A	G	147286047	2	3	4	1	0	0	0	0	0	0	0	1	2307	233	9	3		3	C5orf46	5	147286047	Silent	SNP	A	TCGA-FA-A6HN-01A-11D-A31X-10	26	147286047	33629213	53	393											
IRF4	3662	hgsc.bcm.edu	37	chr6	393209	393209	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggcatgagcgcggtgagctgCggcaacgggaagctccgcca	8	4	17	12	5	0	2	0	2	0	0	1	3	1	3	2	4	5	4	2	4	2	0			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:393209C>T	ENST00000380956.4	+	2	183	c.57C>T	c.(55-57)tgC>tgT	p.C19C	IRF4_ENST00000495137.1_Intron	NM_001195286.1|NM_002460.3	NP_001182215.1|NP_002451.2	Q15306	IRF4_HUMAN	interferon regulatory factor 4	19					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)		CGGTGAGCTGCGGCAACGGGA	0.711			T	IGH@	MM																																p.C19C		Atlas-SNP	.		Dom	yes		6	6p25-p23	3662	interferon regulatory factor 4		L	.	IRF4	65	.	0			c.C57T						PASS	.						29	32	31					6																	393209		2181	4272	6453	SO:0001819	synonymous_variant	3662	exon2			GAGCTGCGGCAAC	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.57C>T	6.37:g.393209C>T		135	0	0		180	73	0.405556	NM_001195286	Q5VUI7|Q99660	Silent	SNP	ENST00000380956.4	37	CCDS4469.1																																																																																			.	.	none		0.711	IRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043638.1			T	393209	C	T	393209	2	4	4	1	0	0	0	0	0	0	0	1	7841	776	27	1		1	IRF4	6	393209	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10		393209	170721858	54	394			1	4		3	3	140	N	G_C	3.960989e-07
IRF4	3662	hgsc.bcm.edu	37	chr6	393222	393222	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgagctgcggcaacgggaagCtccgccagtggctgatcgac	8	6	15	12	4	0	2	0	2	0	0	2	4	1	3	2	3	4	4	2	3	2	0			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:393222C>G	ENST00000380956.4	+	2	196	c.70C>G	c.(70-72)Ctc>Gtc	p.L24V	IRF4_ENST00000495137.1_Intron	NM_001195286.1|NM_002460.3	NP_001182215.1|NP_002451.2	Q15306	IRF4_HUMAN	interferon regulatory factor 4	24					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)		CAACGGGAAGCTCCGCCAGTG	0.701			T	IGH@	MM																																p.L24V		Atlas-SNP	.		Dom	yes		6	6p25-p23	3662	interferon regulatory factor 4		L	.	IRF4	65	.	0			c.C70G						PASS	.						31	32	32					6																	393222		2192	4286	6478	SO:0001583	missense	3662	exon2			GGGAAGCTCCGCC	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.70C>G	6.37:g.393222C>G	ENSP00000370343:p.Leu24Val	155	0	0		205	79	0.385366	NM_001195286	Q5VUI7|Q99660	Missense_Mutation	SNP	ENST00000380956.4	37	CCDS4469.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.123443	0.77436	.	.	ENSG00000137265	ENST00000380956;ENST00000412334	D	0.98747	-5.11	4.58	4.58	0.56647	Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (4);	0.134094	0.50627	N	0.000102	D	0.99202	0.9723	M	0.87682	2.9	0.80722	D	1	D;D;D	0.89917	0.996;0.995;1.0	D;D;D	0.91635	0.997;0.994;0.999	D	0.99449	1.0940	10	0.72032	D	0.01	-24.4797	17.6301	0.88104	0.0:1.0:0.0:0.0	.	24;24;24	F2Z3D5;Q15306-2;Q15306	.;.;IRF4_HUMAN	V	24;54	ENSP00000370343:L24V	ENSP00000370343:L24V	L	+	1	0	IRF4	338222	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.118000	0.57884	2.399000	0.81585	0.306000	0.20318	CTC	.	.	none		0.701	IRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043638.1			G	393222	C	G	393222	3	3	4	1	0	0	0	0	1	0	0	0	7841	797	28	4	72	4	IRF4	6	393222	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	13	393222	170721845	55	395			1	4		3	3	140	N	G_C	3.960989e-07
IRF4	3662	hgsc.bcm.edu	37	chr6	393348	393348	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	agcaggactacaaccgcgagGaggacgccgcgctcttcaag	11	4	13	13	5	2	0	1	0	1	0	2	4	2	3	2	3	3	2	2	3	3	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:393348G>A	ENST00000380956.4	+	2	322	c.196G>A	c.(196-198)Gag>Aag	p.E66K	IRF4_ENST00000495137.1_Intron	NM_001195286.1|NM_002460.3	NP_001182215.1|NP_002451.2	Q15306	IRF4_HUMAN	interferon regulatory factor 4	66					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)		CAACCGCGAGGAGGACGCCGC	0.721			T	IGH@	MM																																p.E66K		Atlas-SNP	.		Dom	yes		6	6p25-p23	3662	interferon regulatory factor 4		L	.	IRF4	65	.	0			c.G196A						PASS	.						22	20	21					6																	393348		2199	4300	6499	SO:0001583	missense	3662	exon2			CGCGAGGAGGACG	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.196G>A	6.37:g.393348G>A	ENSP00000370343:p.Glu66Lys	96	0	0		117	49	0.418803	NM_001195286	Q5VUI7|Q99660	Missense_Mutation	SNP	ENST00000380956.4	37	CCDS4469.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.466289	0.84425	.	.	ENSG00000137265	ENST00000380956;ENST00000412334	D	0.97731	-4.51	4.58	4.58	0.56647	Interferon regulatory factor, conserved site (1);Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (3);	0.099647	0.64402	D	0.000002	D	0.96870	0.8978	L	0.33189	0.99	0.80722	D	1	P;B;D	0.65815	0.798;0.379;0.995	P;P;D	0.74348	0.889;0.612;0.983	D	0.95508	0.8583	10	0.20046	T	0.44	-25.9593	17.6301	0.88104	0.0:0.0:1.0:0.0	.	66;66;66	F2Z3D5;Q15306-2;Q15306	.;.;IRF4_HUMAN	K	66;96	ENSP00000370343:E66K	ENSP00000370343:E66K	E	+	1	0	IRF4	338348	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.728000	0.91484	2.399000	0.81585	0.306000	0.20318	GAG	.	.	none		0.721	IRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043638.1			A	393348	G	A	393348	3	1	4	1	0	0	0	0	1	0	0	0	7841	1175	41	2	198	2	IRF4	6	393348	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	126	393348	170721719	56	396			1	4		3	3	140	N	G_C	3.960989e-07
HIST1H1C	3006	hgsc.bcm.edu	37	chr6	26056391	26056391	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttgcaccagagtgcccttgCtcaccaggctcttgagacca	8	10	9	14	0	2	2	1	1	1	2	2	3	2	2	4	1	3	3	4	1	0	3	rs370479531		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:26056391C>T	ENST00000343677.2	-	1	308	c.266G>A	c.(265-267)aGc>aAc	p.S89N		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	89	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				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						AGTGCCCTTGCTCACCAGGCT	0.527																																					p.S89N		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.G266A						PASS	.						112	117	115					6																	26056391		2203	4300	6503	SO:0001583	missense	3006	exon1			CCCTTGCTCACCA	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.266G>A	6.37:g.26056391C>T	ENSP00000339566:p.Ser89Asn	114	0	0		83	12	0.144578	NM_005319	A8K4I2	Missense_Mutation	SNP	ENST00000343677.2	37	CCDS4577.1	.	.	.	.	.	.	.	.	.	.	C	11.24	1.581681	0.28180	.	.	ENSG00000187837	ENST00000343677	T	0.09538	2.97	5.63	3.74	0.42951	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.448135	0.25625	N	0.029383	T	0.04092	0.0114	L	0.48260	1.515	0.38874	D	0.956758	B	0.32968	0.392	B	0.33960	0.173	T	0.33111	-0.9881	10	0.25106	T	0.35	-23.6919	9.0651	0.36458	0.0:0.661:0.263:0.076	.	89	P16403	H12_HUMAN	N	89	ENSP00000339566:S89N	ENSP00000339566:S89N	S	-	2	0	HIST1H1C	26164370	0.006000	0.16342	1.000000	0.80357	0.345000	0.29048	-0.967000	0.03821	1.521000	0.48983	0.655000	0.94253	AGC	.	.	alt		0.527	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319		T	26056391	C	T	26056391	3	4	4	1	0	0	0	0	1	0	0	0	7133	797	28	2	379	2	HIST1H1C	6	26056391	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	25663043	26056391	145058676	57	397											
HIST1H1C	3006	hgsc.bcm.edu	37	chr6	26056512	26056513	+	Frame_Shift_Ins	INS	-	-	CA																															ctacgctctttagaggcggcINScacagccttggtgatgagct																								rs201575715		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:26056512_26056513insCA	ENST00000343677.2	-	1	186_187	c.144_145insTG	c.(142-147)gtggccfs	p.A49fs		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	49	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				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						TTAGAGGCGGCCACAGCCTTGG	0.569																																					p.A49fs		Atlas-Indel	.											.	HIST1H1C	80	.	0			c.145_146insTG						PASS	.																																			SO:0001589	frameshift_variant	3006	exon1			.	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.143_144dupTG	6.37:g.26056515_26056516dupCA	ENSP00000339566:p.Ala49fs	76	0	0		73	12	0.164384	NM_005319	A8K4I2	Frame_Shift_Ins	INS	ENST00000343677.2	37	CCDS4577.1																																																																																			.	.	none		0.569	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319		CA	26056513	-	CA	26056512	7	5	4	1	0	1	1	0	0	0	0	0	7133	739	26	0	500	0	HIST1H1C	6	26056512	Frame_Shift_Ins	INS	-	TCGA-FA-A6HN-01A-11D-A31X-10	121	26056512	145058555	58	398											
HIST1H2BC	8347	hgsc.bcm.edu	37	chr6	26123770	26123770	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtttacttggagctggtgtaCttggtgacggccttggtgcc	4	14	15	8	1	0	1	0	1	0	0	0	2	0	2	2	5	4	3	2	5	2	6			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:26123770C>T	ENST00000314332.5	-	1	368	c.363G>A	c.(361-363)aaG>aaA	p.K121K	HIST1H2BC_ENST00000396984.1_Silent_p.K121K|HIST1H2AC_ENST00000602637.1_5'Flank|HIST1H2AC_ENST00000377791.2_5'Flank			P62807	H2B1C_HUMAN	histone cluster 1, H2bc	121					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)			NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)	16						AGCTGGTGTACTTGGTGACGG	0.577																																					p.K121K		Atlas-SNP	.											.	HIST1H2BC	35	.	0			c.G363A						PASS	.						85	88	87					6																	26123770		2203	4300	6503	SO:0001819	synonymous_variant	8347	exon1			GGTGTACTTGGTG	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.363G>A	6.37:g.26123770C>T		106	0	0		107	20	0.186916	NM_003526	P02278|Q3B872|Q4VB69|Q93078|Q93080	Silent	SNP	ENST00000314332.5	37	CCDS4584.1																																																																																			.	.	none		0.577	HIST1H2BC-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468022.1	NM_003526		T	26123770	C	T	26123770	2	4	4	1	0	0	0	0	0	0	0	1	7151	564	20	2		2	HIST1H2BC	6	26123770	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	67258	26123770	144991297	59	399											
HIST1H2AC	8334	hgsc.bcm.edu	37	chr6	26124565	26124565	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggccgagtgcaccgcctgctCcgtaaaggcaactacgcaga	10	5	12	14	4	0	1	0	0	0	1	1	2	1	1	4	2	4	5	4	2	4	2	rs531071869		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:26124565C>A	ENST00000602637.1	+	1	135	c.105C>A	c.(103-105)ctC>ctA	p.L35L	HIST1H2BC_ENST00000314332.5_5'Flank|HIST1H2BC_ENST00000396984.1_5'Flank|HIST1H2AC_ENST00000377791.2_Silent_p.L35L			Q93077	H2A1C_HUMAN	histone cluster 1, H2ac	35						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(5)	12						ACCGCCTGCTCCGTAAAGGCA	0.657																																					p.L35L		Atlas-SNP	.											.	HIST1H2AC	29	.	0			c.C105A						PASS	.						43	45	44					6																	26124565		2203	4300	6503	SO:0001819	synonymous_variant	8334	exon1			CCTGCTCCGTAAA	Z80778	CCDS4585.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000180573	ENSG00000180573		"Histones / Replication-dependent"	4733	protein-coding gene	gene with protein product		602794	"H2A histone family, member L", "histone 1, H2ac"	H2AFL		9119399, 12408966	Standard	NM_003512		Approved		uc003ngm.3	Q93077	OTTHUMG00000014428	ENST00000602637.1:c.105C>A	6.37:g.26124565C>A		121	0	0		81	12	0.148148	NM_003512	B2R4F7|O00775|O00776|O00777|O00778|Q540R1	Silent	SNP	ENST00000602637.1	37	CCDS4585.1																																																																																			.	.	none		0.657	HIST1H2AC-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468023.1	NM_003512		A	26124565	C	A	26124565	2	1	4	1	0	0	0	0	0	0	0	1	7139	842	30	4		4	HIST1H2AC	6	26124565	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	795	26124565	144990502	60	400											
HIST1H4E	8367	hgsc.bcm.edu	37	chr6	26204831	26204967	+	Start_Codon_Del	DEL	GTTTTTCAGATTTTTGCGGCTATTTTCGTTGGTGTGTTGGTCATGTCTGGTCGCGGCAAAGGCGGAAAGGGACTGGGTAAAGGAGGCGCTAAGCGTCACCGTAAGGTCCTGCGAGATAACATCCAGGGCATTACCAA	GTTTTTCAGATTTTTGCGGCTATTTTCGTTGGTGTGTTGGTCATGTCTGGTCGCGGCAAAGGCGGAAAGGGACTGGGTAAAGGAGGCGCTAAGCGTCACCGTAAGGTCCTGCGAGATAACATCCAGGGCATTACCAA	-																															taagaatactaccgtcgcttGtttttcagatttttgcggct																								rs371154912|rs368144763|rs143652738|rs370851019|rs372764747|rs140853277|rs199914113|rs572544472|rs201304438|rs368355176|rs533676183|rs374139942|rs147263244|rs201324703|rs532184358|rs540442619|rs139616312|rs368745174|rs145699171|rs377601396|rs376058980|rs184503150|rs144621549|rs144595768|rs376989143|rs61742995|rs202183095|rs61742993|rs201319649|rs372683763	byFrequency	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	GTTTTTCAGATTTTTGCGGCTATTTTCGTTGGTGTGTTGGTCATGTCTGGTCGCGGCAAAGGCGGAAAGGGACTGGGTAAAGGAGGCGCTAAGCGTCACCGTAAGGTCCTGCGAGATAACATCCAGGGCATTACCAA	GTTTTTCAGATTTTTGCGGCTATTTTCGTTGGTGTGTTGGTCATGTCTGGTCGCGGCAAAGGCGGAAAGGGACTGGGTAAAGGAGGCGCTAAGCGTCACCGTAAGGTCCTGCGAGATAACATCCAGGGCATTACCAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:26204831_26204967delGTTTTTCAGATTTTTGCGGCTATTTTCGTTGGTGTGTTGGTCATGTCTGGTCGCGGCAAAGGCGGAAAGGGACTGGGTAAAGGAGGCGCTAAGCGTCACCGTAAGGTCCTGCGAGATAACATCCAGGGCATTACCAA	ENST00000360441.4	+	0	0_110					NM_003545.3	NP_003536.1	P62805	H4_HUMAN	histone cluster 1, H4e						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)	p.R20S(2)|p.G5C(1)|p.N26I(1)|p.G5D(1)		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)				ACCGTCGCTTGTTTTTCAGATTTTTGCGGCTATTTTCGTTGGTGTGTTGGTCATGTCTGGTCGCGGCAAAGGCGGAAAGGGACTGGGTAAAGGAGGCGCTAAGCGTCACCGTAAGGTCCTGCGAGATAACATCCAGGGCATTACCAAGCCTGCCATC	0.537											OREG0017239	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Pindel	.											.	HIST1H4E	22	.	5	Substitution - Missense(5)	lung(3)|upper_aerodigestive_tract(1)|breast(1)	.						PASS	.																																			SO:0001582	initiator_codon_variant	8367	wholegene			.	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		6.37:g.26204831_26204967delGTTTTTCAGATTTTTGCGGCTATTTTCGTTGGTGTGTTGGTCATGTCTGGTCGCGGCAAAGGCGGAAAGGGACTGGGTAAAGGAGGCGCTAAGCGTCACCGTAAGGTCCTGCGAGATAACATCCAGGGCATTACCAA		69	0	.	784	56	12	0.214	NM_003545	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Frame_Shift_Del	DEL	ENST00000360441.4	37	CCDS4593.1																																																																																			.	.	none		0.537	HIST1H4E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040104.1	NM_003545		-	26204967	GTTTTTCAGATTTTTGCGGCTATTTTCGTTGGTGTGTTGGTCATGTCTGGTCGCGGCAAAGGCGGAAAGGGACTGGGTAAAGGAGGCGCTAAGCGTCACCGTAAGGTCCTGCGAGATAACATCCAGGGCATTACCAA	-	26204831	7	5	4	1	0	1	0	1	0	0	0	0	7178	1392	48	0		0	HIST1H4E	6	26204831	Start_Codon_Del	DEL	GTTTTTCAGATTTTTGCGGCTATTTTCGTTGGTGTGTTGGTCATGTCTGGTCGCGGCAAAGGCGGAAAGGGACTGGGTAAAGGAGGCGCTAAGCGTCACCGTAAGGTCCTGCGAGATAACATCCAGGGCATTACCAA	TCGA-FA-A6HN-01A-11D-A31X-10	80266	26204831	144910236	61	401											
HIST1H2BG	8339	hgsc.bcm.edu	37	chr6	26216544	26216544	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggtaccttcggacactgcgtGcttggccagctctccgggaa	6	9	13	13	3	1	0	0	0	1	0	3	2	1	2	3	4	4	3	3	4	2	3			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:26216544G>A	ENST00000244601.3	-	1	328	c.328C>T	c.(328-330)Cac>Tac	p.H110Y	HIST1H2AE_ENST00000303910.2_5'Flank	NM_003518.3	NP_003509.1	P62807	H2B1C_HUMAN	histone cluster 1, H2bg	110					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)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	8		all_hematologic(11;0.196)				GACACTGCGTGCTTGGCCAGC	0.552																																					p.H110Y		Atlas-SNP	.											.	HIST1H2BG	25	.	0			c.C328T						PASS	.						96	96	96					6																	26216544		2203	4300	6503	SO:0001583	missense	8339	exon1			CTGCGTGCTTGGC	M60750	CCDS4594.1	6p21.3	2011-01-27	2006-10-11	2003-02-14	ENSG00000187990	ENSG00000273802		"Histones / Replication-dependent"	4746	protein-coding gene	gene with protein product		602798	"H2B histone family, member A", "histone 1, H2bg"	H2BFA		1916825, 12408966	Standard	NM_003518		Approved	H2B/a, H2B.1A	uc003ngz.2	P62807	OTTHUMG00000014446	ENST00000244601.3:c.328C>T	6.37:g.26216544G>A	ENSP00000244601:p.His110Tyr	69	0	0		76	7	0.0921053	NM_003518	P02278|Q3B872|Q4VB69|Q93078|Q93080	Missense_Mutation	SNP	ENST00000244601.3	37	CCDS4594.1	.	.	.	.	.	.	.	.	.	.	.	17.25	3.343011	0.61073	.	.	ENSG00000187990	ENST00000244601	T	0.51574	0.7	3.89	3.89	0.44902	.	0.000000	0.35124	U	0.003433	T	0.55033	0.1895	.	.	.	0.38755	D	0.954201	.	.	.	.	.	.	T	0.63193	-0.6692	7	0.87932	D	0	.	15.3699	0.74554	0.0:0.0:1.0:0.0	.	.	.	.	Y	110	ENSP00000244601:H110Y	ENSP00000244601:H110Y	H	-	1	0	HIST1H2BG	26324523	1.000000	0.71417	1.000000	0.80357	0.162000	0.22319	7.631000	0.83237	2.172000	0.68678	0.561000	0.74099	CAC	.	.	none		0.552	HIST1H2BG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040109.2	NM_003518		A	26216544	G	A	26216544	3	1	4	1	0	0	0	0	1	0	0	0	7155	1319	46	2	56	2	HIST1H2BG	6	26216544	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	11713	26216544	144898523	62	402											
HIST1H1D	3007	hgsc.bcm.edu	37	chr6	26234570	26234570	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cttaggcttggccgccttggGcttaggggctttggccttag	3	13	15	10	1	0	0	0	0	0	0	0	0	0	0	3	6	0	3	3	6	3	6			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:26234570G>A	ENST00000244534.5	-	1	646	c.592C>T	c.(592-594)Ccc>Tcc	p.P198S		NM_005320.2	NP_005311.1	P16402	H13_HUMAN	histone cluster 1, H1d	198					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				GCCGCCTTGGGCTTAGGGGCT	0.532																																					p.P198S		Atlas-SNP	.											.	HIST1H1D	40	.	0			c.C592T						PASS	.						82	89	86					6																	26234570		2203	4300	6503	SO:0001583	missense	3007	exon1			CCTTGGGCTTAGG	M60747	CCDS4597.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000124575	ENSG00000124575		"Histones / Replication-dependent"	4717	protein-coding gene	gene with protein product		142210	"H1 histone family, member 3", "histone 1, H1d"	H1F3		1916825, 12408966	Standard	NM_005320		Approved	H1.3, H1d, H1s-2	uc003nhd.3	P16402	OTTHUMG00000014432	ENST00000244534.5:c.592C>T	6.37:g.26234570G>A	ENSP00000244534:p.Pro198Ser	98	0	0		117	35	0.299145	NM_005320	B2R751|Q2M2I2	Missense_Mutation	SNP	ENST00000244534.5	37	CCDS4597.1	.	.	.	.	.	.	.	.	.	.	.	6.207	0.406380	0.11754	.	.	ENSG00000124575	ENST00000244534	T	0.23147	1.92	5.12	2.17	0.27698	.	0.556195	0.18052	N	0.153226	T	0.05823	0.0152	N	0.08118	0	0.40794	D	0.98328	B	0.27853	0.191	B	0.30943	0.122	T	0.24905	-1.0147	10	0.21014	T	0.42	-9.1084	15.3281	0.74182	0.0:0.399:0.601:0.0	.	198	P16402	H13_HUMAN	S	198	ENSP00000244534:P198S	ENSP00000244534:P198S	P	-	1	0	HIST1H1D	26342549	1.000000	0.71417	0.919000	0.36401	0.065000	0.16274	3.426000	0.52778	0.213000	0.20722	0.650000	0.86243	CCC	.	.	none		0.532	HIST1H1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040095.1	NM_005320		A	26234570	G	A	26234570	3	1	4	1	0	0	0	0	1	0	0	0	7134	1203	42	2	77	2	HIST1H1D	6	26234570	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	18026	26234570	144880497	63	403			2	5	25841222	6	6	15937	N	GCATGATAGTC_G_C	8.628033e-08
HIST1H1D	3007	hgsc.bcm.edu	37	chr6	26234687	26234687	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agcggttgctggcttctttaCcttcttaggagtctttttga	5	18	10	8	1	3	1	0	1	3	0	3	2	3	2	1	3	3	3	1	3	2	8			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:26234687C>A	ENST00000244534.5	-	1	529	c.475G>T	c.(475-477)Gta>Tta	p.V159L		NM_005320.2	NP_005311.1	P16402	H13_HUMAN	histone cluster 1, H1d	159					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)	p.V159I(1)		breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				GGCTTCTTTACCTTCTTAGGA	0.537																																					p.V159L		Atlas-SNP	.											HIST1H1D,NS,carcinoma,0,1	HIST1H1D	40	1	1	Substitution - Missense(1)	breast(1)	c.G475T						PASS	.						93	98	96					6																	26234687		2203	4300	6503	SO:0001583	missense	3007	exon1			TCTTTACCTTCTT	M60747	CCDS4597.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000124575	ENSG00000124575		"Histones / Replication-dependent"	4717	protein-coding gene	gene with protein product		142210	"H1 histone family, member 3", "histone 1, H1d"	H1F3		1916825, 12408966	Standard	NM_005320		Approved	H1.3, H1d, H1s-2	uc003nhd.3	P16402	OTTHUMG00000014432	ENST00000244534.5:c.475G>T	6.37:g.26234687C>A	ENSP00000244534:p.Val159Leu	82	0	0		87	12	0.137931	NM_005320	B2R751|Q2M2I2	Missense_Mutation	SNP	ENST00000244534.5	37	CCDS4597.1	.	.	.	.	.	.	.	.	.	.	.	10.31	1.315837	0.23908	.	.	ENSG00000124575	ENST00000244534	T	0.13901	2.55	5.22	3.42	0.39159	.	0.381500	0.28349	N	0.015665	T	0.02230	0.0069	N	0.08118	0	0.09310	N	0.999998	B	0.17038	0.02	B	0.14023	0.01	T	0.42498	-0.9448	10	0.41790	T	0.15	-0.0274	10.3773	0.44090	0.0:0.7912:0.1347:0.074	.	159	P16402	H13_HUMAN	L	159	ENSP00000244534:V159L	ENSP00000244534:V159L	V	-	1	0	HIST1H1D	26342666	0.543000	0.26434	0.026000	0.17262	0.002000	0.02628	3.715000	0.54897	0.691000	0.31592	0.650000	0.86243	GTA	.	.	none		0.537	HIST1H1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040095.1	NM_005320		A	26234687	C	A	26234687	3	1	4	1	0	0	0	0	1	0	0	0	7134	507	18	4	194	4	HIST1H1D	6	26234687	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	117	26234687	144880380	64	404			2	5	25841222	6	6	15937	N	GCATGATAGTC_G_C	8.628033e-08
HIST1H1D	3007	hgsc.bcm.edu	37	chr6	26234812	26234812	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cctttttggccttgggtttgCcttccccggaagccgctttc	2	15	10	14	2	0	0	0	0	0	0	2	1	1	1	6	3	2	2	6	3	1	6			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:26234812C>T	ENST00000244534.5	-	1	404	c.350G>A	c.(349-351)gGc>gAc	p.G117D		NM_005320.2	NP_005311.1	P16402	H13_HUMAN	histone cluster 1, H1d	117					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				CTTGGGTTTGCCTTCCCCGGA	0.587																																					p.G117D		Atlas-SNP	.											.	HIST1H1D	40	.	0			c.G350A						PASS	.						61	68	65					6																	26234812		2203	4300	6503	SO:0001583	missense	3007	exon1			GGTTTGCCTTCCC	M60747	CCDS4597.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000124575	ENSG00000124575		"Histones / Replication-dependent"	4717	protein-coding gene	gene with protein product		142210	"H1 histone family, member 3", "histone 1, H1d"	H1F3		1916825, 12408966	Standard	NM_005320		Approved	H1.3, H1d, H1s-2	uc003nhd.3	P16402	OTTHUMG00000014432	ENST00000244534.5:c.350G>A	6.37:g.26234812C>T	ENSP00000244534:p.Gly117Asp	70	0	0		80	20	0.25	NM_005320	B2R751|Q2M2I2	Missense_Mutation	SNP	ENST00000244534.5	37	CCDS4597.1	.	.	.	.	.	.	.	.	.	.	.	4.798	0.148320	0.09134	.	.	ENSG00000124575	ENST00000244534	T	0.10668	2.85	5.23	3.34	0.38264	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.673705	0.14516	N	0.314786	T	0.01287	0.0042	N	0.08118	0	0.09310	N	0.999992	B	0.02656	0.0	B	0.04013	0.001	T	0.45760	-0.9239	10	0.07325	T	0.83	-14.8326	9.3036	0.37861	0.0824:0.3818:0.5358:0.0	.	117	P16402	H13_HUMAN	D	117	ENSP00000244534:G117D	ENSP00000244534:G117D	G	-	2	0	HIST1H1D	26342791	0.999000	0.42202	0.915000	0.36163	0.006000	0.05464	2.678000	0.46900	1.354000	0.45846	-0.147000	0.13772	GGC	.	.	none		0.587	HIST1H1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040095.1	NM_005320		T	26234812	C	T	26234812	3	4	4	1	0	0	0	0	1	0	0	0	7134	739	26	2	319	2	HIST1H1D	6	26234812	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	125	26234812	144880255	65	405			2	5	25841222	6	6	15937	N	GCATGATAGTC_G_C	8.628033e-08
HIST1H4F	8361	hgsc.bcm.edu	37	chr6	26240823	26240823	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	catttatgaggagacccgcgGtgttcttaaggtgttcctgg	7	13	13	8	2	1	2	0	1	1	1	2	3	2	2	2	4	0	2	2	4	2	5			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:26240823G>A	ENST00000377745.2	+	1	263	c.170G>A	c.(169-171)gGt>gAt	p.G57D		NM_003540.3	NP_003531.1	P62805	H4_HUMAN	histone cluster 1, H4f	57					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)	p.G57D(1)		cervix(1)|endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				GAGACCCGCGGTGTTCTTAAG	0.577																																					p.G57D		Atlas-SNP	.											HIST1H4F,colon,carcinoma,0,1	HIST1H4F	9	1	1	Substitution - Missense(1)	large_intestine(1)	c.G170A						PASS	.						76	67	70					6																	26240823		2203	4300	6503	SO:0001583	missense	8361	exon1			CCCGCGGTGTTCT	M60749	CCDS4598.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000198327			"Histones / Replication-dependent"	4783	protein-coding gene	gene with protein product		602824	"H4 histone family, member C", "histone 1, H4f"	H4FC		1916825, 9119399, 12408966	Standard	NM_003540		Approved	H4/c, H4	uc003nhe.1	P62805	OTTHUMG00000014443	ENST00000377745.2:c.170G>A	6.37:g.26240823G>A	ENSP00000366974:p.Gly57Asp	128	0	0		103	15	0.145631	NM_003540	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000377745.2	37	CCDS4598.1	.	.	.	.	.	.	.	.	.	.	.	14.99	2.700370	0.48307	.	.	ENSG00000198327	ENST00000377745	T	0.67523	-0.27	4.36	4.36	0.52297	.	0.000000	0.85682	D	0.000000	T	0.74374	0.3708	.	.	.	0.51233	D	0.999914	.	.	.	.	.	.	T	0.78013	-0.2370	7	0.66056	D	0.02	.	16.4132	0.83726	0.0:0.0:1.0:0.0	.	.	.	.	D	57	ENSP00000366974:G57D	ENSP00000366974:G57D	G	+	2	0	HIST1H4F	26348802	1.000000	0.71417	0.993000	0.49108	0.003000	0.03518	9.222000	0.95196	2.430000	0.82344	0.563000	0.77884	GGT	.	.	none		0.577	HIST1H4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040106.1	NM_003540		A	26240823	G	A	26240823	3	1	4	1	0	0	0	0	1	0	0	0	7179	1261	44	2	172	2	HIST1H4F	6	26240823	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	6011	26240823	144874244	66	406			2	5	25841222	6	6	15937	N	GCATGATAGTC_G_C	8.628033e-08
HIST1H3F	8968	hgsc.bcm.edu	37	chr6	26250470	26250480	+	Frame_Shift_Del	DEL	GCATGATAGTC	GCATGATAGTC	-																															agcgagctggatgtccttggGcatgatagtcactcgcttgg																										TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	GCATGATAGTC	GCATGATAGTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:26250470_26250480delGCATGATAGTC	ENST00000446824.2	-	1	355_365	c.354_364delGACTATCATGC	c.(352-366)gtgactatcatgcccfs	p.TIMP119fs	HIST1H2BH_ENST00000356350.2_5'Flank	NM_021018.2	NP_066298.1	P68431	H31_HUMAN	histone cluster 1, H3f	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)			lung(6)|urinary_tract(1)	7						ATGTCCTTGGGCATGATAGTCACTCGCTTGG	0.583											OREG0017241	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.119_122del		Pindel,Atlas-Indel	.											.	HIST1H3F	16	.	0			c.355_365del						PASS	.																																			SO:0001589	frameshift_variant	8968	exon1			.	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.354_364delGACTATCATGC	6.37:g.26250470_26250480delGCATGATAGTC	ENSP00000444823:p.Thr119fs	94	0	.	785	69	14	0.203	NM_021018	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Frame_Shift_Del	DEL	ENST00000446824.2	37	CCDS4600.1																																																																																			.	.	none		0.583	HIST1H3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040098.1	NM_021018		-	26250480	GCATGATAGTC	-	26250470	7	5	4	1	0	1	0	1	0	0	0	0	7169	1203	42	0	50	0	HIST1H3F	6	26250470	Frame_Shift_Del	DEL	GCATGATAGTC	TCGA-FA-A6HN-01A-11D-A31X-10	9647	26250470	144864597	67	407			2	5	25841222	6	6	15937	N	GCATGATAGTC_G_C	8.628033e-08
HIST1H3F	8968	hgsc.bcm.edu	37	chr6	26250506	26250506	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttggcgtggatagcacacaGgttggtgtcctcaaagagcc	9	9	13	10	1	1	1	1	0	0	1	2	2	2	2	2	4	2	2	2	4	2	3			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:26250506G>A	ENST00000446824.2	-	1	329	c.328C>T	c.(328-330)Ctg>Ttg	p.L110L	HIST1H2BH_ENST00000356350.2_5'Flank	NM_021018.2	NP_066298.1	P68431	H31_HUMAN	histone cluster 1, H3f	110					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						ATAGCACACAGGTTGGTGTCC	0.602											OREG0017241	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L110L		Atlas-SNP	.											.	HIST1H3F	16	.	0			c.C328T						PASS	.						102	99	100					6																	26250506		2203	4300	6503	SO:0001819	synonymous_variant	8968	exon1			CACACAGGTTGGT	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.328C>T	6.37:g.26250506G>A		87	0	0	785	75	18	0.24	NM_021018	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000446824.2	37	CCDS4600.1																																																																																			.	.	none		0.602	HIST1H3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040098.1	NM_021018		A	26250506	G	A	26250506	2	1	4	1	0	0	0	0	0	0	0	1	7169	991	35	2		2	HIST1H3F	6	26250506	Silent	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	36	26250506	144864561	68	408			2	5	25841222	6	6	15937	N	GCATGATAGTC_G_C	8.628033e-08
HIST1H4H	8365	hgsc.bcm.edu	37	chr6	26285420	26285420	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gcagcaagcaggagccttagCcaccgaagccgtaaagagtg	13	4	13	11	2	0	1	0	0	0	1	0	3	0	2	4	1	5	4	4	1	5	2	rs377418572		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:26285420C>T	ENST00000377727.1	-	1	317	c.308G>A	c.(307-309)gGc>gAc	p.G103D	HIST1H4H_ENST00000289352.1_Missense_Mutation_p.G103D	NM_003543.3	NP_003534.1	P62805	H4_HUMAN	histone cluster 1, H4h	103					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						GGAGCCTTAGCCACCGAAGCC	0.507										HNSCC(76;0.23)																											p.G103D		Atlas-SNP	.											.	HIST1H4H	16	.	0			c.G308A						PASS	.						118	103	108					6																	26285420		2203	4300	6503	SO:0001583	missense	8365	exon1			CCTTAGCCACCGA	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.308G>A	6.37:g.26285420C>T	ENSP00000366956:p.Gly103Asp	89	0	0		95	38	0.4	NM_003543	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000377727.1	37	CCDS4604.1	.	.	.	.	.	.	.	.	.	.	.	17.75	3.466993	0.63625	.	.	ENSG00000158406	ENST00000289352;ENST00000377727	.	.	.	4.13	4.13	0.48395	.	0.000000	0.52532	U	0.000072	T	0.67173	0.2865	.	.	.	0.39431	D	0.967073	.	.	.	.	.	.	T	0.73436	-0.3983	6	0.87932	D	0	.	14.2671	0.66126	0.0:1.0:0.0:0.0	.	.	.	.	D	103	.	ENSP00000289352:G103D	G	-	2	0	HIST1H4H	26393399	1.000000	0.71417	0.878000	0.34440	0.015000	0.08874	7.702000	0.84576	2.034000	0.60081	0.313000	0.20887	GGC	.	.	alt		0.507	HIST1H4H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040119.1	NM_003543		T	26285420	C	T	26285420	3	4	4	1	0	0	0	0	1	0	0	0	7181	739	26	2	7	2	HIST1H4H	6	26285420	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	34914	26285420	144829647	69	409											
HIST1H2AG	8969	hgsc.bcm.edu	37	chr6	27100963	27100963	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gcaccgcctgctccgcaaagGcaactatgccgagcgggtcg	8	5	13	15	5	0	0	0	0	0	0	2	1	1	0	4	2	4	4	4	2	3	1	rs201426448		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:27100963G>A	ENST00000359193.2	+	1	132	c.113G>A	c.(112-114)gGc>gAc	p.G38D	HIST1H2BJ_ENST00000339812.2_5'Flank|HIST1H2BJ_ENST00000541790.1_5'Flank|HIST1H2BJ_ENST00000607124.1_5'Flank	NM_021064.4	NP_066408.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2ag	38						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						CTCCGCAAAGGCAACTATGCC	0.692																																					p.G38D		Atlas-SNP	.											.	HIST1H2AG	37	.	0			c.G113A						PASS	.						32	37	35					6																	27100963		2203	4300	6503	SO:0001583	missense	8969	exon1			GCAAAGGCAACTA	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.113G>A	6.37:g.27100963G>A	ENSP00000352119:p.Gly38Asp	95	0	0		111	21	0.189189	NM_021064	P02261|Q2M1R2|Q76PA6	Missense_Mutation	SNP	ENST00000359193.2	37	CCDS4619.1	.	.	.	.	.	.	.	.	.	.	G	16.01	3.000701	0.54254	.	.	ENSG00000196787	ENST00000359193	T	0.68025	-0.3	4.08	4.08	0.47627	Histone-fold (2);Histone core (1);Histone H2A (1);	0.000000	0.40908	D	0.000983	T	0.70325	0.3211	.	.	.	0.43255	D	0.995186	P	0.50819	0.939	P	0.55112	0.769	T	0.75897	-0.3155	9	0.87932	D	0	.	14.6102	0.68510	0.0:0.0:1.0:0.0	.	38	P0C0S8	H2A1_HUMAN	D	38	ENSP00000352119:G38D	ENSP00000352119:G38D	G	+	2	0	HIST1H2AG	27208942	1.000000	0.71417	1.000000	0.80357	0.200000	0.23975	8.818000	0.91991	2.217000	0.71921	0.655000	0.94253	GGC	G|0.999;A|0.001	0.001	weak		0.692	HIST1H2AG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040137.1	NM_021064		A	27100963	G	A	27100963	3	1	4	1	0	0	0	0	1	0	0	0	7142	1203	42	2	115	2	HIST1H2AG	6	27100963	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	815543	27100963	144014104	70	410											
HIST1H4I	8294	hgsc.bcm.edu	37	chr6	27107282	27107282	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgaaggtgttcctggagaaCgtgatccgggacgccgtgac	8	9	15	9	4	0	4	0	3	0	1	2	6	2	5	3	3	1	1	3	3	2	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:27107282C>T	ENST00000354348.2	+	1	207	c.195C>T	c.(193-195)aaC>aaT	p.N65N	HIST1H2BK_ENST00000396891.4_Intron	NM_003495.2	NP_003486.1	P62805	H4_HUMAN	histone cluster 1, H4i	65					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						TCCTGGAGAACGTGATCCGGG	0.652			T	BCL6	NHL																																p.N65N		Atlas-SNP	.		Dom	yes		6	6p21.3	8294	"histone 1, H4i (H4FM)"		L	.	HIST1H4I	26	.	0			c.C195T						PASS	.						81	74	76					6																	27107282		2203	4300	6503	SO:0001819	synonymous_variant	8294	exon1			GGAGAACGTGATC	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.195C>T	6.37:g.27107282C>T		132	0	0		140	49	0.35	NM_003495	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Silent	SNP	ENST00000354348.2	37	CCDS4620.1																																																																																			.	.	none		0.652	HIST1H4I-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040139.1	NM_003495		T	27107282	C	T	27107282	2	4	4	1	0	0	0	0	0	0	0	1	7182	535	19	1		1	HIST1H4I	6	27107282	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	6319	27107282	144007785	71	411											
HIST1H2AK	8330	hgsc.bcm.edu	37	chr6	27805883	27805883	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcaagtggcgcgggatgaTgcgggtcttcttgttgtcgc	4	12	16	9	4	2	1	0	1	2	0	3	2	2	2	0	3	2	2	0	3	1	3			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:27805883T>C	ENST00000330180.2	-	1	234	c.235A>G	c.(235-237)Atc>Gtc	p.I79V	HIST1H2BN_ENST00000606613.1_5'Flank|HIST1H2BN_ENST00000396980.3_5'Flank	NM_003510.2	NP_003501.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2ak	79						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)	p.I79L(1)		breast(2)|endometrium(2)|kidney(1)|lung(3)|upper_aerodigestive_tract(2)	10						CGCGGGATGATGCGGGTCTTC	0.627																																					p.I79V		Atlas-SNP	.											HIST1H2AK,NS,carcinoma,0,1	HIST1H2AK	28	1	1	Substitution - Missense(1)	kidney(1)	c.A235G						PASS	.						108	110	109					6																	27805883		2203	4300	6503	SO:0001583	missense	8330	exon1			GGATGATGCGGGT	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.235A>G	6.37:g.27805883T>C	ENSP00000330307:p.Ile79Val	148	0	0		149	22	0.147651	NM_003510	P02261|Q2M1R2|Q76PA6	Missense_Mutation	SNP	ENST00000330180.2	37	CCDS4632.1	.	.	.	.	.	.	.	.	.	.	.	19.08	3.757723	0.69648	.	.	ENSG00000184348	ENST00000330180	T	0.73897	-0.79	4.28	4.28	0.50868	.	0.000000	0.31507	U	0.007535	T	0.73644	0.3613	.	.	.	0.32741	N	0.507672	.	.	.	.	.	.	T	0.77308	-0.2636	7	0.87932	D	0	.	13.277	0.60191	0.0:0.0:0.0:1.0	.	.	.	.	V	79	ENSP00000330307:I79V	ENSP00000330307:I79V	I	-	1	0	HIST1H2AK	27913862	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.949000	0.70257	1.860000	0.53959	0.454000	0.30748	ATC	.	.	none		0.627	HIST1H2AK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043814.1	NM_003510		C	27805883	T	C	27805883	3	2	4	1	0	0	0	0	1	0	0	0	7146	1464	51	3	161	3	HIST1H2AK	6	27805883	Missense_Mutation	SNP	T	TCGA-FA-A6HN-01A-11D-A31X-10	698601	27805883	143309184	72	412											
HIST1H2BN	8341	hgsc.bcm.edu	37	chr6	27806574	27806574	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tccgtgtacgtgtacaaggtGctgaagcaggtccaccccga	9	8	12	12	3	0	1	0	1	0	0	2	2	2	1	4	2	4	4	4	2	4	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:27806574G>A	ENST00000396980.3	+	1	135	c.135G>A	c.(133-135)gtG>gtA	p.V45V	HIST1H2AK_ENST00000330180.2_5'Flank|HIST1H2BN_ENST00000606613.1_Silent_p.V45V	NM_003520.3	NP_003511.1	Q99877	H2B1N_HUMAN	histone cluster 1, H2bn	45					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)			central_nervous_system(1)|endometrium(3)|lung(3)|prostate(1)	8						TGTACAAGGTGCTGAAGCAGG	0.577																																					p.V45V		Atlas-SNP	.											.	HIST1H2BN	11	.	0			c.G135A						PASS	.						227	205	212					6																	27806574		2203	4298	6501	SO:0001819	synonymous_variant	8341	exon1			CAAGGTGCTGAAG	Z83336	CCDS4633.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000233822	ENSG00000233822		"Histones / Replication-dependent"	4749	protein-coding gene	gene with protein product		602801	"H2B histone family, member D", "histone 1, H2bn"	H2BFD		9439656, 12408966	Standard	NM_003520		Approved	H2B/d	uc003njv.3	Q99877	OTTHUMG00000016397	ENST00000396980.3:c.135G>A	6.37:g.27806574G>A		108	0	0		113	22	0.19469	NM_003520	B2R5L4|Q494S8|Q96FB7	Silent	SNP	ENST00000396980.3	37	CCDS4633.1																																																																																			.	.	none		0.577	HIST1H2BN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043840.2	NM_003520		A	27806574	G	A	27806574	2	1	4	1	0	0	0	0	0	0	0	1	7162	1306	46	2		2	HIST1H2BN	6	27806574	Silent	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	691	27806574	143308493	73	413											
HIST1H3I	8354	hgsc.bcm.edu	37	chr6	27839875	27839875	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ttaaagtcctgtgcgatctcCcgtaccaagcgctgaaaagg	11	9	10	11	3	1	1	0	1	1	0	3	2	2	1	3	1	3	2	3	1	6	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:27839875C>T	ENST00000328488.2	-	1	224	c.219G>A	c.(217-219)cgG>cgA	p.R73R		NM_003533.2	NP_003524.1	P68431	H31_HUMAN	histone cluster 1, H3i	73					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						GTGCGATCTCCCGTACCAAGC	0.632																																					p.R73R		Atlas-SNP	.											.	HIST1H3I	28	.	0			c.G219A						PASS	.						82	87	85					6																	27839875		2203	4300	6503	SO:0001819	synonymous_variant	8354	exon1			GATCTCCCGTACC	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.219G>A	6.37:g.27839875C>T		151	0	0		154	60	0.38961	NM_003533	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000328488.2	37	CCDS4636.1																																																																																			.	.	none		0.632	HIST1H3I-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043452.1	NM_003533		T	27839875	C	T	27839875	2	4	4	1	0	0	0	0	0	0	0	1	7172	610	22	2		2	HIST1H3I	6	27839875	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	33301	27839875	143275192	74	414											
HIST1H2AM	8336	hgsc.bcm.edu	37	chr6	27860749	27860749	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccagctccaggatctcggcaGttaggtactccagcaccgcc	8	7	10	16	2	1	0	0	0	1	0	4	1	3	1	5	3	3	5	5	3	2	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:27860749G>A	ENST00000359611.2	-	1	214	c.179C>T	c.(178-180)aCt>aTt	p.T60I	HIST1H3J_ENST00000359303.2_5'Flank|HIST1H2BO_ENST00000303806.4_5'Flank|HIST1H3J_ENST00000479986.1_5'UTR	NM_003514.2	NP_003505.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2am	60						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						GATCTCGGCAGTTAGGTACTC	0.672																																					p.T60I		Atlas-SNP	.											.	HIST1H2AM	27	.	0			c.C179T						PASS	.						66	72	70					6																	27860749		2202	4300	6502	SO:0001583	missense	8336	exon1			TCGGCAGTTAGGT	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.179C>T	6.37:g.27860749G>A	ENSP00000352627:p.Thr60Ile	135	0	0		161	32	0.198758	NM_003514	P02261|Q2M1R2|Q76PA6	Missense_Mutation	SNP	ENST00000359611.2	37	CCDS4639.1	.	.	.	.	.	.	.	.	.	.	G	19.87	3.907441	0.72868	.	.	ENSG00000233224	ENST00000359611	T	0.66995	-0.24	4.06	4.06	0.47325	.	0.000000	0.30911	U	0.008621	T	0.76856	0.4046	M	0.83774	2.66	0.35595	D	0.807403	.	.	.	.	.	.	T	0.81680	-0.0823	8	0.87932	D	0	.	16.02	0.80473	0.0:0.0:1.0:0.0	.	.	.	.	I	60	ENSP00000352627:T60I	ENSP00000352627:T60I	T	-	2	0	HIST1H2AM	27968728	1.000000	0.71417	0.999000	0.59377	0.959000	0.62525	7.384000	0.79751	2.545000	0.85829	0.655000	0.94253	ACT	.	.	none		0.672	HIST1H2AM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040162.1	NM_003514		A	27860749	G	A	27860749	3	1	4	1	0	0	0	0	1	0	0	0	7148	1029	36	2	217	2	HIST1H2AM	6	27860749	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	20874	27860749	143254318	75	415											
HLA-C	3107	hgsc.bcm.edu	37	chr6	31239047	31239047	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgtaatccttgccgtcgtagGcggactggtcatacccgcgg	6	10	13	12	5	1	0	1	0	0	0	3	1	2	1	3	4	2	2	3	4	3	4	rs281860470		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:31239047G>A	ENST00000376228.5	-	3	436	c.422C>T	c.(421-423)gCc>gTc	p.A141V	HLA-C_ENST00000383329.3_Missense_Mutation_p.A141V	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	141	Alpha-2.				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)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GCCGTCGTAGGCGGACTGGTC	0.706													g|||	1	0.000199681	0.0	0.0	5008	,	,		12845	0.0		0.0	False		,,,				2504	0.001				p.A141V		Atlas-SNP	.											.	HLA-C	92	.	0			c.C422T						PASS	.						35	27	30					6																	31239047		2182	4253	6435	SO:0001583	missense	3107	exon3			TCGTAGGCGGACT	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4933	protein-coding gene	gene with protein product		142840	"psoriasis susceptibility 1"	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.422C>T	6.37:g.31239047G>A	ENSP00000365402:p.Ala141Val	133	0	0		150	23	0.153333	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.	.	.	.	.	.	.	.	.	.	.	13.97	2.394451	0.42410	.	.	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.00018	9.08;9.08	2.59	2.59	0.31030	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.229535	0.21218	U	0.078193	T	0.00328	0.0010	H	0.99914	4.94	0.20196	N	0.999921	D;P;P;P	0.58970	0.984;0.878;0.878;0.939	P;P;P;P	0.58391	0.838;0.482;0.61;0.662	T	0.46830	-0.9163	10	0.87932	D	0	.	7.4947	0.27481	0.0:0.2697:0.7303:0.0	.	141;141;141;141	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	V	141;141;141;178	ENSP00000365402:A141V;ENSP00000372819:A141V	ENSP00000365402:A141V	A	-	2	0	HLA-C	31347026	0.028000	0.19301	0.011000	0.14972	0.023000	0.10783	0.934000	0.28910	1.768000	0.52137	0.305000	0.20034	GCC	.	.	weak		0.706	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117		A	31239047	G	A	31239047	3	1	4	1	0	0	0	0	1	0	0	0	7206	1203	42	2	702	2	HLA-C	6	31239047	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	3378298	31239047	139876020	76	416											
EHMT2	10919	hgsc.bcm.edu	37	chr6	31856190	31856190	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcagtggtgtttgaccatgcGggcgcggtgggtctcacaga	6	9	17	9	3	1	2	1	1	1	1	2	2	1	2	1	4	1	2	1	4	0	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:31856190G>T	ENST00000375537.4	-	12	1465	c.1459C>A	c.(1459-1461)Cgc>Agc	p.R487S	EHMT2_ENST00000395728.3_Missense_Mutation_p.R544S|EHMT2_ENST00000480912.1_5'UTR|EHMT2_ENST00000375528.4_Missense_Mutation_p.R510S|EHMT2_ENST00000375530.4_Missense_Mutation_p.R453S	NM_006709.3	NP_006700.3	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	487					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						TTGACCATGCGGGCGCGGTGG	0.662																																					p.R487S		Atlas-SNP	.											.	EHMT2	45	.	0			c.C1459A						PASS	.						30	29	29					6																	31856190		1511	2708	4219	SO:0001583	missense	10919	exon12			CCATGCGGGCGCG	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.1459C>A	6.37:g.31856190G>T	ENSP00000364687:p.Arg487Ser	66	0	0		83	5	0.060241	NM_006709	B0UZY2|Q14349|Q5JP83|Q5JQ92|Q5JQA1|Q5JQG3|Q6PK06|Q96MH5|Q96QD0|Q9UQL8|Q9Y331	Missense_Mutation	SNP	ENST00000375537.4	37	CCDS4725.1	.	.	.	.	.	.	.	.	.	.	G	18.18	3.567273	0.65651	.	.	ENSG00000204371	ENST00000395728;ENST00000375528;ENST00000375530;ENST00000375537;ENST00000442298	T;T;T;T	0.72282	-0.64;-0.52;-0.47;-0.64	4.62	4.62	0.57501	.	0.074232	0.56097	D	0.000039	T	0.64897	0.2640	L	0.43152	1.355	0.36772	D	0.883846	D;D;D;D	0.64830	0.975;0.994;0.989;0.978	P;P;P;P	0.60473	0.735;0.875;0.753;0.753	T	0.72104	-0.4391	10	0.87932	D	0	.	5.8076	0.18448	0.0967:0.0:0.7103:0.1931	.	510;453;487;301	A2ABF8;Q96KQ7-2;Q96KQ7;Q59FM7	.;.;EHMT2_HUMAN;.	S	544;510;453;487;301	ENSP00000379078:R544S;ENSP00000364678:R510S;ENSP00000364680:R453S;ENSP00000364687:R487S	ENSP00000364678:R510S	R	-	1	0	EHMT2	31964169	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	2.094000	0.41719	2.394000	0.81467	0.555000	0.69702	CGC	.	.	none		0.662	EHMT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076355.5	NM_006709		T	31856190	G	T	31856190	3	4	4	1	0	0	0	0	1	0	0	0	4986	1116	39	4	2241	4	EHMT2	6	31856190	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	617143	31856190	139258877	77	417											
CFB	629	hgsc.bcm.edu	37	chr6	31918104	31918104	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgtatgggggctgtggtGtctgagtactttgtgctgac	5	14	16	6	0	1	2	0	2	1	0	1	2	1	2	0	3	3	5	0	3	2	3	rs553118090		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:31918104G>A	ENST00000425368.2	+	12	2061	c.1548G>A	c.(1546-1548)gtG>gtA	p.V516V	CFB_ENST00000477310.1_Silent_p.V867V|CFB_ENST00000556679.1_Silent_p.V1018V|CFB_ENST00000456570.1_Silent_p.V1018V	NM_001710.5	NP_001701.2	P00751	CFAB_HUMAN	complement factor B	516	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						GGGCTGTGGTGTCTGAGTACT	0.502													G|||	1	0.000199681	0.0	0.0014	5008	,	,		24111	0.0		0.0	False		,,,				2504	0.0				p.V516V		Atlas-SNP	.											.	CFB	33	.	0			c.G1548A						PASS	.						128	90	104					6																	31918104		1511	2709	4220	SO:0001819	synonymous_variant	629	exon12			TGTGGTGTCTGAG	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.1548G>A	6.37:g.31918104G>A		66	0	0		67	5	0.0746269	NM_001710	B0QZQ6|O15006|Q29944|Q53F89|Q5JP67|Q5ST50|Q96HX6|Q9BTF5|Q9BX92	Silent	SNP	ENST00000425368.2	37	CCDS4729.1																																																																																			.	.	none		0.502	CFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076395.3	NM_001710		A	31918104	G	A	31918104	2	1	4	1	0	0	0	0	0	0	0	1	3280	1364	48	2		2	CFB	6	31918104	Silent	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	61914	31918104	139196963	78	418											
ANKS1A	23294	hgsc.bcm.edu	37	chr6	34857318	34857318	+	Missense_Mutation	SNP	A	A	G																															ctgggggcggcggcggcggcAgcggcggcggcggcggcggc																										TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:34857318A>G	ENST00000360359.3	+	1	277	c.139A>G	c.(139-141)Agc>Ggc	p.S47G	TAF11_ENST00000420584.2_5'Flank|ANKS1A_ENST00000535627.1_Missense_Mutation_p.S47G|TAF11_ENST00000361288.4_5'Flank	NM_015245.2	NP_056060.2	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1A	47	Gly-rich.				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						cggcggcggcagcggcggcgg	0.771																																					p.S47G		Atlas-SNP	.											ANKS1A,NS,carcinoma,0,1	ANKS1A	123	1	0			c.A139G						scavenged	.						2	2	2					6																	34857318		328	1149	1477	SO:0001583	missense	23294	exon1			GGCGGCAGCGGCG	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.139A>G	6.37:g.34857318A>G	ENSP00000353518:p.Ser47Gly	6	0	0		12	10	0.833333	NM_015245	A2RUC1|B4DQW8|Q5JYI9|Q5SYR2|Q86WQ7	Missense_Mutation	SNP	ENST00000360359.3	37	CCDS4798.1	.	.	.	.	.	.	.	.	.	.	A	0.001	-3.186111	0.00026	.	.	ENSG00000064999	ENST00000544150;ENST00000360359;ENST00000535627	T;D	0.88046	1.12;-2.33	0.892	-1.78	0.07957	Ankyrin repeat-containing domain (1);	.	.	.	.	T	0.39253	0.1071	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36480	-0.9746	9	0.08381	T	0.77	-3.6165	5.4862	0.16751	0.2218:0.0:0.7782:0.0	.	47;47	B4DQW8;Q92625	.;ANS1A_HUMAN	G	47	ENSP00000353518:S47G;ENSP00000438752:S47G	ENSP00000353518:S47G	S	+	1	0	ANKS1A	34965296	0.056000	0.20664	0.088000	0.20740	0.019000	0.09904	0.065000	0.14466	-1.299000	0.02344	-1.288000	0.01363	AGC	.	.	none		0.771	ANKS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040262.1	XM_166478		G	34857318	A	G	34857318	3	3	4	1	0	0	0	0	1	0	0	0	688	188	7	3	141	3	ANKS1A	6	34857318	Missense_Mutation	SNP	A	TCGA-FA-A6HN-01A-11D-A31X-10	2939214	34857318	136257749	79	419	10	2									
ANKS1A	23294	hgsc.bcm.edu	37	chr6	34857324	34857324	+	Missense_Mutation	SNP	G	G	A																															gcggcggcggcggcagcggcGgcggcggcggcggcctcggc																										TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:34857324G>A	ENST00000360359.3	+	1	283	c.145G>A	c.(145-147)Ggc>Agc	p.G49S	TAF11_ENST00000420584.2_5'Flank|ANKS1A_ENST00000535627.1_Missense_Mutation_p.G49S|TAF11_ENST00000361288.4_5'Flank	NM_015245.2	NP_056060.2	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1A	49	Gly-rich.				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						cggcagcggcggcggcggcgg	0.771																																					p.G49S		Atlas-SNP	.											ANKS1A,NS,carcinoma,0,1	ANKS1A	123	1	0			c.G145A						scavenged	.						2	2	2					6																	34857324		382	1194	1576	SO:0001583	missense	23294	exon1			AGCGGCGGCGGCG	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.145G>A	6.37:g.34857324G>A	ENSP00000353518:p.Gly49Ser	4	0	0		10	7	0.7	NM_015245	A2RUC1|B4DQW8|Q5JYI9|Q5SYR2|Q86WQ7	Missense_Mutation	SNP	ENST00000360359.3	37	CCDS4798.1	.	.	.	.	.	.	.	.	.	.	G	16.03	3.008376	0.54361	.	.	ENSG00000064999	ENST00000544150;ENST00000360359;ENST00000535627	T;D	0.98649	1.19;-5.05	4.58	1.53	0.23141	Ankyrin repeat-containing domain (1);	1.264600	0.06451	N	0.727796	D	0.90783	0.7106	N	0.19112	0.55	0.25322	N	0.989108	P;B	0.49090	0.919;0.003	B;B	0.38655	0.278;0.002	D	0.88474	0.3064	10	0.17832	T	0.49	-4.009	8.7007	0.34323	0.0795:0.0:0.6816:0.2389	.	49;49	B4DQW8;Q92625	.;ANS1A_HUMAN	S	49	ENSP00000353518:G49S;ENSP00000438752:G49S	ENSP00000353518:G49S	G	+	1	0	ANKS1A	34965302	1.000000	0.71417	0.794000	0.32065	0.327000	0.28475	2.586000	0.46119	0.389000	0.25086	0.471000	0.43371	GGC	.	.	none		0.771	ANKS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040262.1	XM_166478		A	34857324	G	A	34857324	3	1	4	1	0	0	0	0	1	0	0	0	688	1116	39	1	147	1	ANKS1A	6	34857324	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	6	34857324	136257743	80	420	10	2									
BTBD9	114781	hgsc.bcm.edu	37	chr6	38545397	38545397	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgcagacacgggctggaaaaTataatttctgccaagaacga	15	8	10	8	2	1	2	0	0	1	2	1	4	1	3	1	2	3	2	1	2	6	3	rs373363401		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:38545397T>C	ENST00000481247.1	-	6	1284	c.1133A>G	c.(1132-1134)tAt>tGt	p.Y378C	BTBD9_ENST00000314100.6_Missense_Mutation_p.Y310C|BTBD9_ENST00000408958.1_Missense_Mutation_p.Y310C|BTBD9_ENST00000403056.1_Missense_Mutation_p.Y378C|BTBD9_ENST00000419706.2_Missense_Mutation_p.Y319C	NM_001099272.1|NM_052893.1	NP_001092742.1|NP_443125.1	Q96Q07	BTBD9_HUMAN	BTB (POZ) domain containing 9	378					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						GGCTGGAAAATATAATTTCTG	0.358																																					p.Y378C		Atlas-SNP	.											.	BTBD9	85	.	0			c.A1133G						PASS	.	T	CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR	0,3730		0,0,1865	102	97	99		1133,956,1133,929	5.7	1	6		99	2,8190		0,2,4094	no	missense,missense,missense,missense	BTBD9	NM_001099272.1,NM_001172418.1,NM_052893.1,NM_152733.2	194,194,194,194	0,2,5959	CC,CT,TT		0.0244,0.0,0.0168	probably-damaging,probably-damaging,probably-damaging,probably-damaging	378/613,319/583,378/613,310/545	38545397	2,11920	1865	4096	5961	SO:0001583	missense	114781	exon7			GGAAAATATAATT		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.1133A>G	6.37:g.38545397T>C	ENSP00000418751:p.Tyr378Cys	54	0	0		51	21	0.411765	NM_052893	Q494V9|Q494W1|Q96M00	Missense_Mutation	SNP	ENST00000481247.1	37	CCDS47418.1	.	.	.	.	.	.	.	.	.	.	T	17.04	3.288377	0.59976	0.0	2.44E-4	ENSG00000183826	ENST00000314100;ENST00000481247;ENST00000419706;ENST00000403056;ENST00000408958	D;D;T;D;D	0.98135	-4.74;-4.74;-0.95;-4.74;-4.74	5.71	5.71	0.89125	Coagulation factor 5/8 C-terminal type domain (1);Galactose-binding domain-like (1);	0.124631	0.56097	D	0.000033	D	0.98298	0.9436	M	0.69523	2.12	0.80722	D	1	B;D	0.89917	0.07;1.0	B;D	0.87578	0.078;0.998	D	0.99437	1.0937	10	0.59425	D	0.04	.	15.9738	0.80044	0.0:0.0:0.0:1.0	.	319;378	Q494V9;Q96Q07	.;BTBD9_HUMAN	C	310;378;319;378;310	ENSP00000323408:Y310C;ENSP00000418751:Y378C;ENSP00000415365:Y319C;ENSP00000386121:Y378C;ENSP00000386211:Y310C	ENSP00000323408:Y310C	Y	-	2	0	BTBD9	38653375	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.854000	0.86942	2.179000	0.69175	0.528000	0.53228	TAT	.	.	weak		0.358	BTBD9-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040433.2	NM_152733		C	38545397	T	C	38545397	3	2	4	1	0	0	0	0	1	0	0	0	1550	1406	49	3	820	3	BTBD9	6	38545397	Missense_Mutation	SNP	T	TCGA-FA-A6HN-01A-11D-A31X-10	3688073	38545397	132569670	81	421											
ABCC10	89845	hgsc.bcm.edu	37	chr6	43399895	43399895	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cccaggagtccagattacatCctaccctgcagtcctggatg	9	9	9	14	0	0	1	0	0	0	1	3	3	3	3	5	2	3	1	5	2	2	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:43399895C>T	ENST00000372530.4	+	3	392	c.177C>T	c.(175-177)atC>atT	p.I59I	ABCC10_ENST00000244533.3_Silent_p.I16I|ABCC10_ENST00000443426.2_Intron	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	59					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)	CAGATTACATCCTACCCTGCA	0.567																																					p.I59I		Atlas-SNP	.											.	ABCC10	118	.	0			c.C177T						PASS	.						119	105	110					6																	43399895		2203	4300	6503	SO:0001819	synonymous_variant	89845	exon3			TTACATCCTACCC	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.177C>T	6.37:g.43399895C>T		48	0	0		46	6	0.130435	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Silent	SNP	ENST00000372530.4	37	CCDS56430.1																																																																																			.	.	none		0.567	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450		T	43399895	C	T	43399895	2	4	4	1	0	0	0	0	0	0	0	1	50	845	30	2		2	ABCC10	6	43399895	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	4854498	43399895	127715172	82	422											
TFAP2D	83741	hgsc.bcm.edu	37	chr6	50712940	50712940	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaaagaacagacagcaagaaAaaagatgatcctggcgacca	20	3	10	8	1	0	5	0	1	0	4	1	7	1	5	2	1	2	1	2	1	6	0	rs201424626		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:50712940A>G	ENST00000008391.3	+	6	1232	c.1004A>G	c.(1003-1005)aAa>aGa	p.K335R	TFAP2D_ENST00000492804.1_3'UTR	NM_172238.3	NP_758438.2			transcription factor AP-2 delta (activating enhancer binding protein 2 delta)											NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(26)|ovary(6)|pancreas(1)|prostate(5)|stomach(1)	60	Lung NSC(77;0.0334)					ACAGCAAGAAAAAAGATGATC	0.403													A|||	1	0.000199681	0.0008	0.0	5008	,	,		20233	0.0		0.0	False		,,,				2504	0.0				p.K335R		Atlas-SNP	.											TFAP2D,NS,carcinoma,0,1	TFAP2D	144	1	0			c.A1004G						scavenged	.						121	117	119					6																	50712940		2203	4300	6503	SO:0001583	missense	83741	exon6			CAAGAAAAAAGAT	AY028376	CCDS4933.1	6p12.3	2008-02-05	2004-10-26	2004-10-27		ENSG00000008197			15581	protein-coding gene	gene with protein product		610161	"transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)-like 1"	TFAP2BL1		11733187	Standard	NM_172238		Approved		uc003paf.3	Q7Z6R9		ENST00000008391.3:c.1004A>G	6.37:g.50712940A>G	ENSP00000008391:p.Lys335Arg	198	1	0.00505051		182	39	0.214286	NM_172238		Missense_Mutation	SNP	ENST00000008391.3	37	CCDS4933.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	17.94	3.512600	0.64522	.	.	ENSG00000008197	ENST00000008391	D	0.96992	-4.2	5.77	5.77	0.91146	Transcription factor AP-2, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.92001	0.7466	L	0.39898	1.24	0.80722	D	1	P	0.37207	0.587	B	0.37091	0.241	D	0.93015	0.6435	10	0.54805	T	0.06	-8.0383	16.0828	0.81017	1.0:0.0:0.0:0.0	.	335	Q7Z6R9	AP2D_HUMAN	R	335	ENSP00000008391:K335R	ENSP00000008391:K335R	K	+	2	0	TFAP2D	50820899	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.576000	0.82467	2.206000	0.71126	0.477000	0.44152	AAA	A|1.000;G|0.000	0.000	strong		0.403	TFAP2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040881.1	NM_172238		G	50712940	A	G	50712940	3	3	4	1	0	0	0	0	1	0	0	0	15805	14	1	3	1026	3	TFAP2D	6	50712940	Missense_Mutation	SNP	A	TCGA-FA-A6HN-01A-11D-A31X-10	7313045	50712940	120402127	83	423											
EFHC1	114327	hgsc.bcm.edu	37	chr6	52344443	52344443	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctaccttctctccagtgtttGgtcaccggttcatcatcctt	5	16	6	14	1	4	0	3	0	1	0	7	0	6	0	4	2	1	2	4	2	1	5			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:52344443G>T	ENST00000371068.5	+	9	1601	c.1498G>T	c.(1498-1500)Ggt>Tgt	p.G500C	EFHC1_ENST00000538167.1_Missense_Mutation_p.G481C|EFHC1_ENST00000433625.2_Missense_Mutation_p.G409C	NM_018100.3	NP_060570.2	Q5JVL4	EFHC1_HUMAN	EF-hand domain (C-terminal) containing 1	500	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)					TCCAGTGTTTGGTCACCGGTT	0.433																																					p.G500C		Atlas-SNP	.											.	EFHC1	68	.	0			c.G1498T						PASS	.						184	187	186					6																	52344443		2203	4300	6503	SO:0001583	missense	114327	exon9			GTGTTTGGTCACC	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.1498G>T	6.37:g.52344443G>T	ENSP00000360107:p.Gly500Cys	96	0	0		98	17	0.173469	NM_018100	B4DMU3|F5GZD8|Q5XKM4|Q6E1U7|Q6E1U8|Q8WUL2|Q9NVW6	Missense_Mutation	SNP	ENST00000371068.5	37	CCDS4942.1	.	.	.	.	.	.	.	.	.	.	G	17.30	3.354583	0.61293	.	.	ENSG00000096093	ENST00000371068;ENST00000433625;ENST00000538167	T;T;T	0.70869	-0.27;-0.52;-0.48	5.62	4.76	0.60689	Uncharacterised domain DM10 (2);	0.049564	0.85682	D	0.000000	T	0.80819	0.4696	M	0.89163	3.01	0.48341	D	0.999637	D;B;P	0.89917	1.0;0.37;0.873	D;B;P	0.74023	0.982;0.311;0.583	D	0.84095	0.0392	10	0.66056	D	0.02	-6.5516	9.8614	0.41116	0.1553:0.0:0.8447:0.0	.	481;409;500	F5GZD8;B7Z2S4;Q5JVL4	.;.;EFHC1_HUMAN	C	500;409;481	ENSP00000360107:G500C;ENSP00000416492:G409C;ENSP00000444521:G481C	ENSP00000360107:G500C	G	+	1	0	EFHC1	52452402	1.000000	0.71417	1.000000	0.80357	0.717000	0.41224	3.224000	0.51238	1.382000	0.46385	0.555000	0.69702	GGT	.	.	none		0.433	EFHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040905.2	NM_018100		T	52344443	G	T	52344443	3	4	4	1	0	0	0	0	1	0	0	0	4948	1348	47	4	1542	4	EFHC1	6	52344443	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	1631503	52344443	118770624	84	424											
HTR1B	3351	hgsc.bcm.edu	37	chr6	78172576	78172576	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacgccagaagaagggcggcAgcgagatagagatggagaag	15	2	18	6	3	0	5	0	0	0	5	0	9	0	5	1	3	1	1	1	3	4	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:78172576A>G	ENST00000369947.2	-	1	914	c.545T>C	c.(544-546)cTg>cCg	p.L182P		NM_000863.1	NP_000854.1	P28222	5HT1B_HUMAN	5-hydroxytryptamine (serotonin) receptor 1B, G protein-coupled	182					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)	GAAGGGCGGCAGCGAGATAGA	0.602																																					p.L182P		Atlas-SNP	.											.	HTR1B	55	.	0			c.T545C						PASS	.						71	76	75					6																	78172576		2203	4300	6503	SO:0001583	missense	3351	exon1			GGCGGCAGCGAGA	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.545T>C	6.37:g.78172576A>G	ENSP00000358963:p.Leu182Pro	92	0	0		95	14	0.147368	NM_000863	Q4VAY7	Missense_Mutation	SNP	ENST00000369947.2	37	CCDS4986.1	.	.	.	.	.	.	.	.	.	.	A	18.96	3.733478	0.69189	.	.	ENSG00000135312	ENST00000369947	T	0.75704	-0.96	5.09	5.09	0.68999	GPCR, rhodopsin-like superfamily (1);	0.137678	0.47455	D	0.000229	T	0.80618	0.4657	M	0.76328	2.33	0.80722	D	1	D	0.56521	0.976	D	0.63703	0.917	T	0.81895	-0.0723	9	.	.	.	.	14.1973	0.65679	1.0:0.0:0.0:0.0	.	182	P28222	5HT1B_HUMAN	P	182	ENSP00000358963:L182P	.	L	-	2	0	HTR1B	78229295	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.995000	0.93534	2.138000	0.66242	0.454000	0.30748	CTG	.	.	none		0.602	HTR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041292.1	NM_000863		G	78172576	A	G	78172576	3	3	4	1	0	0	0	0	1	0	0	0	7446	188	7	3	631	3	HTR1B	6	78172576	Missense_Mutation	SNP	A	TCGA-FA-A6HN-01A-11D-A31X-10	25828133	78172576	92942491	85	425											
PHIP	55023	hgsc.bcm.edu	37	chr6	79671508	79671508	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttgcagatccacgggggcCacaaatgctgaggcaatatc	11	7	12	11	1	0	2	0	1	0	1	2	2	1	2	2	3	2	4	2	3	3	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:79671508C>T	ENST00000275034.4	-	31	3722	c.3555G>A	c.(3553-3555)gtG>gtA	p.V1185V	PHIP_ENST00000479165.1_5'UTR|AL356776.1_ENST00000516160.2_RNA	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	1185	Bromo 1. {ECO:0000255|PROSITE- ProRule:PRU00035}.				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)		CCACGGGGGCCACAAATGCTG	0.343																																					p.V1185V		Atlas-SNP	.											.	PHIP	177	.	0			c.G3555A						PASS	.						71	66	68					6																	79671508		2203	4300	6503	SO:0001819	synonymous_variant	55023	exon31			GGGGGCCACAAAT	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.3555G>A	6.37:g.79671508C>T		271	0	0		245	11	0.044898	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000275034.4	37	CCDS4987.1																																																																																			.	.	none		0.343	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			T	79671508	C	T	79671508	2	4	4	1	0	0	0	0	0	0	0	1	11851	581	21	2		2	PHIP	6	79671508	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	1498932	79671508	91443559	86	426											
CYB5R4	51167	hgsc.bcm.edu	37	chr6	84569547	84569547	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcccggcccccaggtcgcagCagcgtgtcgcctccgggggg	3	5	16	17	5	0	0	0	0	0	0	4	0	2	0	5	5	2	2	5	5	0	0			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:84569547C>G	ENST00000369681.5	+	1	186	c.46C>G	c.(46-48)Cag>Gag	p.Q16E	CYB5R4_ENST00000369679.4_5'UTR	NM_016230.3	NP_057314.2	Q7L1T6	NB5R4_HUMAN	cytochrome b5 reductase 4	16					cell development (GO:0048468)|detection of oxygen (GO:0003032)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|NADP metabolic process (GO:0006739)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|superoxide metabolic process (GO:0006801)	endoplasmic reticulum (GO:0005783)|perinuclear region of cytoplasm (GO:0048471)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|NAD(P)H oxidase activity (GO:0016174)|NADPH-hemoprotein reductase activity (GO:0003958)|oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor (GO:0016653)			breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	23		all_cancers(76;7e-07)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00128)		BRCA - Breast invasive adenocarcinoma(397;0.0871)		CAGGTCGCAGCAGCGTGTCGC	0.677											OREG0017553	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q16E	Esophageal Squamous(86;1289 1332 25971 40349 52675)	Atlas-SNP	.											.	CYB5R4	72	.	0			c.C46G						PASS	.						21	25	24					6																	84569547		2202	4300	6502	SO:0001583	missense	51167	exon1			TCGCAGCAGCGTG	AF169803	CCDS5000.2	6q14.2	2012-09-19		2005-07-13	ENSG00000065615	ENSG00000065615	1.6.2.2		20147	protein-coding gene	gene with protein product		608343	"NADPH cytochrome B5 oxidoreductase"	NCB5OR		10611283	Standard	NM_016230		Approved	b5+b5R, dJ676J13.1	uc003pkf.3	Q7L1T6	OTTHUMG00000015118	ENST00000369681.5:c.46C>G	6.37:g.84569547C>G	ENSP00000358695:p.Gln16Glu	84	0	0	1230	76	14	0.184211	NM_016230	B1AEM2|Q5TGI9|Q9NUE4|Q9UHI9	Missense_Mutation	SNP	ENST00000369681.5	37	CCDS5000.2	.	.	.	.	.	.	.	.	.	.	C	20.7	4.031288	0.75504	.	.	ENSG00000065615	ENST00000369681	T	0.44482	0.92	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.40222	0.1108	L	0.53249	1.67	0.80722	D	1	P	0.49185	0.92	P	0.48304	0.573	T	0.09509	-1.0671	10	0.40728	T	0.16	-26.7412	19.2909	0.94098	0.0:1.0:0.0:0.0	.	16	Q7L1T6	NB5R4_HUMAN	E	16	ENSP00000358695:Q16E	ENSP00000358695:Q16E	Q	+	1	0	CYB5R4	84626266	1.000000	0.71417	1.000000	0.80357	0.026000	0.11368	6.502000	0.73695	2.894000	0.99253	0.655000	0.94253	CAG	.	.	none		0.677	CYB5R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041362.4	NM_016230		G	84569547	C	G	84569547	3	3	4	1	0	0	0	0	1	0	0	0	4131	711	25	4	48	4	CYB5R4	6	84569547	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	4898039	84569547	86545520	87	427											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152671306	152671306	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaaaggtcaggggtaccttGtggtgggccaattgctgggt	7	12	16	6	0	1	0	1	0	0	0	1	0	1	0	2	6	2	2	2	6	4	4			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:152671306G>C	ENST00000367255.5	-	72	12499	c.11898C>G	c.(11896-11898)caC>caG	p.H3966Q	SYNE1_ENST00000423061.1_Intron|SYNE1_ENST00000448038.1_Intron|SYNE1_ENST00000341594.5_Missense_Mutation_p.H3890Q|SYNE1_ENST00000265368.4_Missense_Mutation_p.H3966Q	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	3966					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)		GGGGTACCTTGTGGTGGGCCA	0.562										HNSCC(10;0.0054)																											p.H3966Q		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C11898G						PASS	.						98	87	91					6																	152671306		2203	4300	6503	SO:0001583	missense	23345	exon72			TACCTTGTGGTGG	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.11898C>G	6.37:g.152671306G>C	ENSP00000356224:p.His3966Gln	83	0	0		61	13	0.213115	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	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	12.72	2.022767	0.35701	.	.	ENSG00000131018	ENST00000367255;ENST00000265368;ENST00000341594	T;T;T	0.43294	0.95;0.95;0.95	5.61	2.8	0.32819	.	0.089810	0.48767	N	0.000173	T	0.20210	0.0486	M	0.64997	1.995	0.80722	D	1	P;P;P	0.44478	0.836;0.836;0.836	B;B;B	0.42138	0.377;0.377;0.377	T	0.10497	-1.0627	10	0.12766	T	0.61	.	9.0358	0.36287	0.0673:0.0:0.5578:0.3749	.	3966;3966;3966	B7ZBC3;Q8NF91;E7EQI5	.;SYNE1_HUMAN;.	Q	3966;3966;3890	ENSP00000356224:H3966Q;ENSP00000265368:H3966Q;ENSP00000341887:H3890Q	ENSP00000265368:H3966Q	H	-	3	2	SYNE1	152712999	1.000000	0.71417	0.987000	0.45799	0.958000	0.62258	3.159000	0.50731	0.288000	0.22398	0.561000	0.74099	CAC	.	.	none		0.562	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		C	152671306	G	C	152671306	3	2	4	1	0	0	0	0	1	0	0	0	15460	1368	48	4	14868	4	SYNE1	6	152671306	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	68101759	152671306	18443761	88	428											
TAGAP	117289	hgsc.bcm.edu	37	chr6	159463199	159463199	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tttcaagtctgtctccaaagCcccagaaaaatctgatgcag	13	10	7	11	0	4	2	1	1	3	1	5	2	4	2	3	0	2	1	3	0	4	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:159463199C>T	ENST00000367066.3	-	5	557	c.226G>A	c.(226-228)Gct>Act	p.A76T	RP1-111C20.4_ENST00000607391.1_RNA|RP1-111C20.4_ENST00000606466.1_RNA|RP1-111C20.4_ENST00000606470.1_RNA|TAGAP_ENST00000326965.6_Intron|RP1-111C20.4_ENST00000607796.1_RNA|TAGAP_ENST00000338313.5_Missense_Mutation_p.A76T	NM_001278733.1|NM_054114.3	NP_001265662.1|NP_473455.2	Q8N103	TAGAP_HUMAN	T-cell activation RhoGTPase activating protein	76					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)		GTCTCCAAAGCCCCAGAAAAA	0.493																																					p.A76T		Atlas-SNP	.											TAGAP,NS,carcinoma,+1,1	TAGAP	75	1	0			c.G226A						scavenged	.						175	184	181					6																	159463199		2203	4300	6503	SO:0001583	missense	117289	exon5			CCAAAGCCCCAGA	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.226G>A	6.37:g.159463199C>T	ENSP00000356033:p.Ala76Thr	89	1	0.011236		78	11	0.141026	NM_138810	Q2NKM8|Q8NI40|Q96KZ2|Q96QA2	Missense_Mutation	SNP	ENST00000367066.3	37	CCDS5261.1	.	.	.	.	.	.	.	.	.	.	C	10.46	1.357352	0.24598	.	.	ENSG00000164691	ENST00000367066;ENST00000338313	T;T	0.20598	2.24;2.06	6.08	-1.9	0.07665	.	0.809387	0.11245	N	0.584227	T	0.04724	0.0128	L	0.51422	1.61	0.09310	N	1	B;B	0.14805	0.002;0.011	B;B	0.12837	0.003;0.008	T	0.39901	-0.9591	10	0.28530	T	0.3	-5.3104	1.843	0.03153	0.3909:0.1811:0.2861:0.142	.	76;76	Q8N103-4;Q8N103	.;TAGAP_HUMAN	T	76	ENSP00000356033:A76T;ENSP00000340217:A76T	ENSP00000340217:A76T	A	-	1	0	TAGAP	159383187	0.000000	0.05858	0.003000	0.11579	0.528000	0.34623	-0.055000	0.11807	-0.195000	0.10382	0.591000	0.81541	GCT	.	.	none		0.493	TAGAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042890.1	NM_054114		T	159463199	C	T	159463199	3	4	4	1	0	0	0	0	1	0	0	0	15552	739	26	2	2011	2	TAGAP	6	159463199	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	6791893	159463199	11651868	89	429											
PLG	5340	hgsc.bcm.edu	37	chr6	161173935	161173935	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tctctccctctgtatagggtGacagtggaggtcctctggtt	5	14	12	10	0	3	1	0	1	3	0	6	2	5	2	2	4	0	2	2	4	2	3			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr6:161173935G>A	ENST00000308192.9	+	19	2338	c.2275G>A	c.(2275-2277)Gac>Aac	p.D759N		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	759	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				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)	TGTATAGGGTGACAGTGGAGG	0.468																																					p.D759N		Atlas-SNP	.											.	PLG	150	.	0			c.G2275A						PASS	.						95	89	91					6																	161173935		2203	4300	6503	SO:0001583	missense	5340	exon19			TAGGGTGACAGTG	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.2275G>A	6.37:g.161173935G>A	ENSP00000308938:p.Asp759Asn	352	0	0		283	58	0.204947	NM_000301	Q15146|Q5TEH4|Q6PA00	Missense_Mutation	SNP	ENST00000308192.9	37	CCDS5279.1	.	.	.	.	.	.	.	.	.	.	.	20.6	4.023041	0.75275	.	.	ENSG00000122194	ENST00000308192;ENST00000316325	D	0.94457	-3.43	3.44	3.44	0.39384	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.41097	U	0.000956	D	0.97676	0.9238	H	0.94658	3.565	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98936	1.0789	10	0.87932	D	0	.	14.7974	0.69886	0.0:0.0:1.0:0.0	.	759	P00747	PLMN_HUMAN	N	759;159	ENSP00000308938:D759N	ENSP00000308938:D759N	D	+	1	0	PLG	161093925	1.000000	0.71417	1.000000	0.80357	0.733000	0.41908	8.934000	0.92915	1.614000	0.50241	0.460000	0.39030	GAC	.	.	none		0.468	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301		A	161173935	G	A	161173935	3	1	4	1	0	0	0	0	1	0	0	0	12095	1290	45	2	2353	2	PLG	6	161173935	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	1710736	161173935	9941132	90	430											
ACTB	60	hgsc.bcm.edu	37	chr7	5568064	5568064	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgaagtccagggcgacgtagCacagcttctccttaatgtca	10	9	10	12	3	2	0	1	0	1	0	4	2	3	0	2	1	2	3	2	1	3	3			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr7:5568064C>T	ENST00000331789.5	-	4	841	c.650G>A	c.(649-651)tGc>tAc	p.C217Y	ACTB_ENST00000464611.1_5'Flank|AC006483.1_ENST00000579427.1_RNA	NM_001101.3	NP_001092.1	P63261	ACTG_HUMAN	actin, beta	217					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)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(2)	8		Ovarian(82;0.0606)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)|OV - Ovarian serous cystadenocarcinoma(56;4.24e-37)		GGCGACGTAGCACAGCTTCTC	0.592																																					p.C217Y		Atlas-SNP	.											.	ACTB	45	.	0			c.G650A						PASS	.						68	69	69					7																	5568064		2203	4300	6503	SO:0001583	missense	60	exon4			ACGTAGCACAGCT	M28424	CCDS5341.1	7p22	2014-09-17			ENSG00000075624	ENSG00000075624			132	protein-coding gene	gene with protein product		102630				1505215	Standard	NM_001101		Approved		uc003sot.4	P60709	OTTHUMG00000023268	ENST00000331789.5:c.650G>A	7.37:g.5568064C>T	ENSP00000349960:p.Cys217Tyr	99	0	0		69	14	0.202899	NM_001101	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000331789.5	37	CCDS5341.1	.	.	.	.	.	.	.	.	.	.	C	17.73	3.460810	0.63513	.	.	ENSG00000075624	ENST00000331789;ENST00000445914;ENST00000400179;ENST00000320713	D	0.95788	-3.81	5.55	5.55	0.83447	.	0.086725	0.49916	D	0.000140	D	0.99052	0.9675	H	0.99689	4.705	0.58432	D	0.999999	P	0.44044	0.825	D	0.72338	0.977	D	0.98548	1.0635	10	0.87932	D	0	.	18.1418	0.89642	0.0:1.0:0.0:0.0	.	217	P60709	ACTB_HUMAN	Y	217;193;189;136	ENSP00000349960:C217Y	ENSP00000440549:C136Y	C	-	2	0	ACTB	5534590	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.533000	0.81994	2.617000	0.88574	0.650000	0.86243	TGC	.	.	none		0.592	ACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059589.4	NM_001101		T	5568064	C	T	5568064	3	4	4	1	0	0	0	0	1	0	0	0	193	710	25	2	489	2	ACTB	7	5568064	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10		5568064	153570599	91	431											
HIBADH	11112	hgsc.bcm.edu	37	chr7	27702327	27702327	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggtccttacccgctgcaaaGctgccggctgccggccgcag	6	6	13	16	4	0	0	0	0	0	0	1	0	1	0	5	3	5	5	5	3	2	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr7:27702327G>A	ENST00000265395.2	-	1	287	c.81C>T	c.(79-81)agC>agT	p.S27S		NM_152740.3	NP_689953.1	P31937	3HIDH_HUMAN	3-hydroxyisobutyrate dehydrogenase	27					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)			CCGCTGCAAAGCTGCCGGCTG	0.682																																					p.S27S		Atlas-SNP	.											.	HIBADH	28	.	0			c.C81T						PASS	.						3	3	3					7																	27702327		1444	2917	4361	SO:0001819	synonymous_variant	11112	exon1			TGCAAAGCTGCCG	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.81C>T	7.37:g.27702327G>A		158	0	0		135	25	0.185185	NM_152740	Q546Z2|Q9UDN3	Silent	SNP	ENST00000265395.2	37	CCDS5414.1																																																																																			.	.	none		0.682	HIBADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214132.1	NM_152740		A	27702327	G	A	27702327	2	1	4	1	0	0	0	0	0	0	0	1	7108	962	34	2		2	HIBADH	7	27702327	Silent	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	22134263	27702327	131436336	92	432											
SEMA3D	223117	hgsc.bcm.edu	37	chr7	84629120	84629120	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatacatcccagaatccttcTtctgcaaacttcgaatcagt	13	12	4	12	1	3	1	1	0	2	1	6	2	5	1	2	0	3	1	2	0	5	4			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr7:84629120T>C	ENST00000284136.6	-	17	2013	c.1970A>G	c.(1969-1971)aAg>aGg	p.K657R	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	657	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						AGAATCCTTCTTCTGCAAACT	0.393																																					p.K657R	Ovarian(63;442 1191 17318 29975 31528)	Atlas-SNP	.											.	SEMA3D	177	.	0			c.A1970G						PASS	.						67	60	62					7																	84629120		2203	4300	6503	SO:0001583	missense	223117	exon17			TCCTTCTTCTGCA	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.1970A>G	7.37:g.84629120T>C	ENSP00000284136:p.Lys657Arg	89	0	0		62	12	0.193548	NM_152754	A6NK46|Q6UW77|Q8NCQ1	Missense_Mutation	SNP	ENST00000284136.6	37	CCDS34676.1	.	.	.	.	.	.	.	.	.	.	T	1.767	-0.485356	0.04352	.	.	ENSG00000153993	ENST00000284136	T	0.64438	-0.1	5.83	4.68	0.58851	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.467996	0.26895	N	0.021959	T	0.30854	0.0778	N	0.03238	-0.38	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.22277	-1.0221	10	0.02654	T	1	.	7.8504	0.29451	0.0:0.2012:0.0:0.7988	.	657	O95025	SEM3D_HUMAN	R	657	ENSP00000284136:K657R	ENSP00000284136:K657R	K	-	2	0	SEMA3D	84467056	0.430000	0.25538	1.000000	0.80357	0.991000	0.79684	0.597000	0.24059	1.043000	0.40175	0.533000	0.62120	AAG	.	.	none		0.393	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754		C	84629120	T	C	84629120	3	2	4	1	0	0	0	0	1	0	0	0	14042	1609	56	3	367	3	SEMA3D	7	84629120	Missense_Mutation	SNP	T	TCGA-FA-A6HN-01A-11D-A31X-10	56926793	84629120	74509543	93	433											
ZNF804B	219578	hgsc.bcm.edu	37	chr7	88956767	88956767	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgacttcatcagctggctgAgttaaggcagcaatctgaat	12	10	10	9	1	3	2	2	2	1	0	3	3	3	2	0	2	2	5	0	2	3	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr7:88956767A>C	ENST00000333190.4	+	3	968	c.359A>C	c.(358-360)gAg>gCg	p.E120A		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	120							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)			CAGCTGGCTGAGTTAAGGCAG	0.383										HNSCC(36;0.09)																											p.E120A		Atlas-SNP	.											.	ZNF804B	322	.	0			c.A359C						PASS	.						95	95	95					7																	88956767		2203	4300	6503	SO:0001583	missense	219578	exon3			TGGCTGAGTTAAG	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.359A>C	7.37:g.88956767A>C	ENSP00000329638:p.Glu120Ala	90	0	0		94	12	0.12766	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	.	.	.	.	.	.	.	.	.	.	A	26.8	4.776991	0.90195	.	.	ENSG00000182348	ENST00000333190	T	0.23348	1.91	5.04	5.04	0.67666	.	0.095683	0.45126	D	0.000385	T	0.42314	0.1197	M	0.77486	2.375	0.41418	D	0.987787	D	0.59767	0.986	P	0.50659	0.647	T	0.50533	-0.8817	10	0.72032	D	0.01	-12.1328	15.2309	0.73386	1.0:0.0:0.0:0.0	.	120	A4D1E1	Z804B_HUMAN	A	120	ENSP00000329638:E120A	ENSP00000329638:E120A	E	+	2	0	ZNF804B	88794703	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.105000	0.77031	2.239000	0.73571	0.528000	0.53228	GAG	.	.	none		0.383	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		C	88956767	A	C	88956767	3	2	4	1	0	0	0	0	1	0	0	0	18186	304	11	5	369	5	ZNF804B	7	88956767	Missense_Mutation	SNP	A	TCGA-FA-A6HN-01A-11D-A31X-10	4327647	88956767	70181896	94	434											
CPA2	1358	hgsc.bcm.edu	37	chr7	129916536	129916536	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccctggatatcttcctcctGccagtcacaaaccctgatgg	8	10	8	15	0	2	1	1	1	1	0	4	2	4	2	5	2	2	0	5	2	2	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr7:129916536G>A	ENST00000222481.4	+	7	709	c.654G>A	c.(652-654)ctG>ctA	p.L218L		NM_001869.2	NP_001860.2	P48052	CBPA2_HUMAN	carboxypeptidase A2 (pancreatic)	218					protein catabolic process in the vacuole (GO:0007039)	extracellular region (GO:0005576)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.L216L(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	Melanoma(18;0.0435)					TCTTCCTCCTGCCAGTCACAA	0.443																																					p.L218L		Atlas-SNP	.											CPA2,NS,carcinoma,0,1	CPA2	36	1	1	Substitution - coding silent(1)	endometrium(1)	c.G654A						PASS	.						212	192	199					7																	129916536		2203	4300	6503	SO:0001819	synonymous_variant	1358	exon7			CCTCCTGCCAGTC	U19977	CCDS5817.2	7q32	2012-02-10			ENSG00000158516	ENSG00000158516	3.4.17.15		2297	protein-coding gene	gene with protein product		600688				7896805, 10860668	Standard	NM_001869		Approved		uc003vpq.3	P48052	OTTHUMG00000157019	ENST00000222481.4:c.654G>A	7.37:g.129916536G>A		115	0	0		88	5	0.0568182	NM_001869	A4D1M4|C9JIK1|Q53XS1|Q96A12|Q96QN3|Q9UCF1	Silent	SNP	ENST00000222481.4	37	CCDS5817.2																																																																																			.	.	none		0.443	CPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347124.2	NM_001869		A	129916536	G	A	129916536	2	1	4	1	0	0	0	0	0	0	0	1	3792	1306	46	2		2	CPA2	7	129916536	Silent	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	40959769	129916536	29222127	95	435											
DGKI	9162	hgsc.bcm.edu	37	chr7	137080402	137080402	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagaagctggcacacagccCggttccgctggcaggcagcc	8	4	13	16	2	0	1	0	0	0	1	1	1	1	1	4	4	3	6	4	4	1	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr7:137080402C>A	ENST00000288490.5	-	33	3023	c.3023G>T	c.(3022-3024)cGg>cTg	p.R1008L	DGKI_ENST00000424189.2_Missense_Mutation_p.R1021L|DGKI_ENST00000494390.1_5'UTR|DGKI_ENST00000446122.1_Missense_Mutation_p.R990L|DGKI_ENST00000453654.2_Missense_Mutation_p.R677L	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	1008					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						GCACACAGCCCGGTTCCGCTG	0.562																																					p.R1008L		Atlas-SNP	.											DGKI_ENST00000288490,NS,carcinoma,-1,2	DGKI	335	2	0			c.G3023T						PASS	.						76	67	70					7																	137080402		2203	4300	6503	SO:0001583	missense	9162	exon33			ACAGCCCGGTTCC	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.3023G>T	7.37:g.137080402C>A	ENSP00000288490:p.Arg1008Leu	55	0	0		62	9	0.145161	NM_004717	A4D1Q9|Q9NZ49	Missense_Mutation	SNP	ENST00000288490.5	37	CCDS5845.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.613227	0.87359	.	.	ENSG00000157680	ENST00000453654;ENST00000540376;ENST00000424189;ENST00000288490;ENST00000446122	T;T;T	0.60424	0.19;0.19;0.19	5.35	5.35	0.76521	Ankyrin repeat-containing domain (3);	0.061139	0.64402	D	0.000002	T	0.48750	0.1517	N	0.01640	-0.785	0.58432	D	0.999999	P;P	0.44986	0.659;0.847	P;P	0.54706	0.494;0.759	T	0.67845	-0.5565	10	0.87932	D	0	.	19.4396	0.94813	0.0:1.0:0.0:0.0	.	677;1008	E9PFX6;O75912	.;DGKI_HUMAN	L	677;925;1011;1008;990	ENSP00000392161:R677L;ENSP00000288490:R1008L;ENSP00000399131:R990L	ENSP00000288490:R1008L	R	-	2	0	DGKI	136730942	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	5.491000	0.66887	2.652000	0.90054	0.650000	0.86243	CGG	.	.	none		0.562	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717		A	137080402	C	A	137080402	3	1	4	1	0	0	0	0	1	0	0	0	4473	652	23	4	182	4	DGKI	7	137080402	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	7163866	137080402	22058261	96	436											
KCNU1	157855	hgsc.bcm.edu	37	chr8	36694417	36694417	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ccaaggctgtttggtgccagGcttgtgtaccttcctaacat	7	13	10	11	0	0	0	0	0	0	0	1	0	1	0	4	3	3	4	4	3	3	5			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr8:36694417G>A	ENST00000399881.3	+	14	1509	c.1472G>A	c.(1471-1473)gGc>gAc	p.G491D		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	491	Segment S7.				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)		TTGGTGCCAGGCTTGTGTACC	0.428																																					p.G491D		Atlas-SNP	.											.	KCNU1	359	.	0			c.G1472A						PASS	.						188	187	188					8																	36694417		1879	4107	5986	SO:0001583	missense	157855	exon14			TGCCAGGCTTGTG	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.1472G>A	8.37:g.36694417G>A	ENSP00000382770:p.Gly491Asp	88	0	0		86	16	0.186047	NM_001031836		Missense_Mutation	SNP	ENST00000399881.3	37	CCDS55220.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.985327	0.93044	.	.	ENSG00000215262	ENST00000399881	T	0.66995	-0.24	5.34	5.34	0.76211	Potassium channel, calcium-activated, BK, alpha subunit (2);NAD(P)-binding domain (1);	0.000000	0.38837	U	0.001555	D	0.83746	0.5321	M	0.82193	2.58	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.85851	0.1404	10	0.87932	D	0	-7.8102	18.9859	0.92769	0.0:0.0:1.0:0.0	.	491	A8MYU2	KCNU1_HUMAN	D	491	ENSP00000382770:G491D	ENSP00000382770:G491D	G	+	2	0	KCNU1	36813575	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.234000	0.95347	2.657000	0.90304	0.585000	0.79938	GGC	.	.	none		0.428	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836		A	36694417	G	A	36694417	3	1	4	1	0	0	0	0	1	0	0	0	8102	1203	42	2	1526	2	KCNU1	8	36694417	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10		36694417	109669605	97	437											
ADAM9	8754	hgsc.bcm.edu	37	chr8	38899582	38899582	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagcctatagtgctccctcCtgtggtaataagttggtgga	9	12	12	8	0	0	0	0	0	0	0	2	2	2	1	3	3	2	3	3	3	5	5			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr8:38899582C>A	ENST00000487273.2	+	12	1326	c.1248C>A	c.(1246-1248)tcC>tcA	p.S416S		NM_003816.2	NP_003807.1	Q13443	ADAM9_HUMAN	ADAM metallopeptidase domain 9	416	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)			GTGCTCCCTCCTGTGGTAATA	0.413																																					p.S416S		Atlas-SNP	.											.	ADAM9	66	.	0			c.C1248A						PASS	.						96	95	95					8																	38899582		2203	4300	6503	SO:0001819	synonymous_variant	8754	exon12			TCCCTCCTGTGGT	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.1248C>A	8.37:g.38899582C>A		212	0	0		194	45	0.231959	NM_003816	B7ZLN7|Q10718|Q8NFM6	Silent	SNP	ENST00000487273.2	37	CCDS6112.1																																																																																			.	.	none		0.413	ADAM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357291.2			A	38899582	C	A	38899582	2	1	4	1	0	0	0	0	0	0	0	1	253	668	24	4		4	ADAM9	8	38899582	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	2205165	38899582	107464440	98	438											
MCM4	4173	hgsc.bcm.edu	37	chr8	48889332	48889332	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	actgggaagaccgtgcgcttGctctgaagccttgtgagcaa	9	9	13	10	2	1	3	0	2	1	1	1	4	1	4	2	1	4	3	2	1	3	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr8:48889332G>A	ENST00000262105.2	+	16	2795	c.2586G>A	c.(2584-2586)ttG>ttA	p.L862L	MCM4_ENST00000523944.1_Silent_p.L862L|RNU6-519P_ENST00000410590.1_RNA	NM_005914.3	NP_005905.2	P33991	MCM4_HUMAN	minichromosome maintenance complex component 4	862					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)				CCGTGCGCTTGCTCTGAAGCC	0.527																																					p.L862L		Atlas-SNP	.											.	MCM4	97	.	0			c.G2586A						PASS	.						128	115	120					8																	48889332		2203	4300	6503	SO:0001819	synonymous_variant	4173	exon17			GCGCTTGCTCTGA		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.2586G>A	8.37:g.48889332G>A		48	0	0		51	10	0.196078	NM_182746	Q8NEH1|Q99658	Silent	SNP	ENST00000262105.2	37	CCDS6143.1																																																																																			.	.	none		0.527	MCM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377791.1	NM_005914		A	48889332	G	A	48889332	2	1	4	1	0	0	0	0	0	0	0	1	9398	1310	46	2		2	MCM4	8	48889332	Silent	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	9989750	48889332	97474690	99	439											
FAM164A	51101	hgsc.bcm.edu	37	chr8	79629693	79629693	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtagaatgggccaaatttTgctgtgaatgtggcattcga	10	13	12	6	1	0	2	0	1	0	1	1	3	0	2	1	2	1	3	1	2	4	4			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr8:79629693T>C	ENST00000263849.4	+	9	1045	c.943T>C	c.(943-945)Tgc>Cgc	p.C315R	IL7_ENST00000519833.1_5'Flank	NM_016010.2	NP_057094.2	Q96GY0	ZC21A_HUMAN	zinc finger, C2HC-type containing 1A	315							metal ion binding (GO:0046872)										GGCCAAATTTTGCTGTGAATG	0.368																																					p.C315R		Atlas-SNP	.											.	.	.	.	0			c.T943C						PASS	.						145	145	145					8																	79629693		2203	4300	6503	SO:0001583	missense	51101	exon9			AAATTTTGCTGTG		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.943T>C	8.37:g.79629693T>C	ENSP00000263849:p.Cys315Arg	80	0	0		80	17	0.2125	NM_016010	Q9Y372	Missense_Mutation	SNP	ENST00000263849.4	37	CCDS6223.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.88|18.88	3.717860|3.717860	0.68844|0.68844	.|.	.|.	ENSG00000104427|ENSG00000104427	ENST00000263849|ENST00000519307	D|.	0.82984|.	-1.67|.	5.14|5.14	5.14|5.14	0.70334|0.70334	.|.	0.085531|.	0.85682|.	D|.	0.000000|.	T|T	0.78610|0.78610	0.4310|0.4310	M|M	0.84511|0.84511	2.7|2.7	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.87578|.	0.998|.	T|T	0.81437|0.81437	-0.0933|-0.0933	9|5	.|.	.|.	.|.	-8.3283|-8.3283	15.2358|15.2358	0.73430|0.73430	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	315|.	Q96GY0|.	F164A_HUMAN|.	R|S	315|186	ENSP00000263849:C315R|.	.|.	C|L	+|+	1|2	0|0	FAM164A|FAM164A	79792248|79792248	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.975000|0.975000	0.68041|0.68041	6.025000|6.025000	0.70864|0.70864	2.060000|2.060000	0.61445|0.61445	0.482000|0.482000	0.46254|0.46254	TGC|TTG	.	.	none		0.368	ZC2HC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379423.2	NM_016010		C	79629693	T	C	79629693	3	2	4	1	0	0	0	0	1	0	0	0	5483	1812	63	3	977	3	FAM164A	8	79629693	Missense_Mutation	SNP	T	TCGA-FA-A6HN-01A-11D-A31X-10	30740361	79629693	66734329	100	440											
RIMS2	9699	hgsc.bcm.edu	37	chr8	105263908	105263908	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agatacttttagatgaactaGagctatccaatatggtgatc	14	13	8	6	0	0	5	0	2	0	3	2	5	1	5	1	1	3	1	1	1	7	6			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr8:105263908G>C	ENST00000436393.2	+	28	4205	c.3964G>C	c.(3964-3966)Gag>Cag	p.E1322Q	RIMS2_ENST00000339750.2_Missense_Mutation_p.E240Q|RIMS2_ENST00000507740.1_Missense_Mutation_p.E1118Q|RIMS2_ENST00000406091.3_Missense_Mutation_p.E1304Q|RIMS2_ENST00000262231.10_Missense_Mutation_p.E1143Q			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	1366	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				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)			AGATGAACTAGAGCTATCCAA	0.448										HNSCC(12;0.0054)																											p.E1304Q		Atlas-SNP	.											.	RIMS2	1357	.	0			c.G3910C						PASS	.						166	164	165					8																	105263908		1887	4136	6023	SO:0001583	missense	9699	exon24			GAACTAGAGCTAT	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.3964G>C	8.37:g.105263908G>C	ENSP00000390665:p.Glu1322Gln	125	0	0		130	23	0.176923	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Missense_Mutation	SNP	ENST00000436393.2	37		.	.	.	.	.	.	.	.	.	.	G	15.52	2.857994	0.51376	.	.	ENSG00000176406	ENST00000329869;ENST00000406091;ENST00000402998;ENST00000262231;ENST00000507740;ENST00000436393;ENST00000523362;ENST00000339750	T;T;T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03;-1.03;-1.03	5.64	5.64	0.86602	.	.	.	.	.	T	0.65502	0.2697	N	0.14661	0.345	0.58432	D	0.999992	P;B;B;P	0.39480	0.534;0.241;0.241;0.675	B;B;B;B	0.37888	0.107;0.192;0.192;0.26	T	0.64257	-0.6450	9	0.23302	T	0.38	.	19.6939	0.96016	0.0:0.0:1.0:0.0	.	1322;1143;1118;1304	D6RA03;Q9UQ26-1;Q9UQ26-3;F8WD47	.;.;.;.	Q	1341;1304;1366;1143;1118;1322;240;240	ENSP00000384892:E1304Q;ENSP00000262231:E1143Q;ENSP00000423559:E1118Q;ENSP00000390665:E1322Q;ENSP00000428478:E240Q;ENSP00000342051:E240Q	ENSP00000262231:E1143Q	E	+	1	0	RIMS2	105333084	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.857000	0.99534	2.660000	0.90430	0.655000	0.94253	GAG	.	.	none		0.448	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117		C	105263908	G	C	105263908	3	2	4	1	0	0	0	0	1	0	0	0	13383	943	33	4	4200	4	RIMS2	8	105263908	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	25634215	105263908	41100114	101	441											
MYC	4609	hgsc.bcm.edu	37	chr8	128751032	128751032	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagcgtctgctccacctccaGcttgtacctgcaggatctga	7	10	9	15	1	2	1	0	1	2	0	4	2	4	2	4	1	5	4	4	1	1	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr8:128751032G>A	ENST00000259523.6	+	2	1729	c.524G>A	c.(523-525)aGc>aAc	p.S175N	MYC_ENST00000524013.1_Missense_Mutation_p.S189N|MYC_ENST00000377970.2_Missense_Mutation_p.S190N			P01106	MYC_HUMAN	v-myc avian myelocytomatosis viral oncogene homolog	175					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)	TCCACCTCCAGCTTGTACCTG	0.667		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.S190N		Atlas-SNP	.		Dom	yes		8	8q24.12-q24.13	4609	v-myc myelocytomatosis viral oncogene homolog (avian)		"L, E"	MYC_ENST00000377970,NS,lymphoid_neoplasm,0,2	MYC	168	2	0			c.G569A						PASS	.						23	24	24					8																	128751032		2202	4299	6501	SO:0001583	missense	4609	exon2			CCTCCAGCTTGTA		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.524G>A	8.37:g.128751032G>A	ENSP00000259523:p.Ser175Asn	69	0	0	1567	52	10	0.192308	NM_002467	A8WFE7|P01107|Q14026	Missense_Mutation	SNP	ENST00000259523.6	37		.	.	.	.	.	.	.	.	.	.	G	15.78	2.935198	0.52866	.	.	ENSG00000136997	ENST00000259523;ENST00000377970;ENST00000524013;ENST00000454617	T;T;T	0.18174	2.23;2.23;2.23	4.78	3.89	0.44902	Transcription regulator Myc, N-terminal (1);	0.540883	0.20177	N	0.097620	T	0.35008	0.0917	L	0.57536	1.79	0.32900	D	0.512998	D	0.58970	0.984	P	0.62491	0.903	T	0.50642	-0.8804	10	0.62326	D	0.03	-20.4131	14.2765	0.66184	0.0:0.1501:0.8499:0.0	.	175	P01106	MYC_HUMAN	N	175;190;189;156	ENSP00000259523:S175N;ENSP00000367207:S190N;ENSP00000430235:S189N	ENSP00000259523:S175N	S	+	2	0	MYC	128820214	1.000000	0.71417	0.998000	0.56505	0.893000	0.52053	5.074000	0.64401	1.102000	0.41551	0.561000	0.74099	AGC	.	.	none		0.667	MYC-002	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000250278.1			A	128751032	G	A	128751032	3	1	4	1	0	0	0	0	1	0	0	0	10025	971	34	2	575	2	MYC	8	128751032	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	23487124	128751032	17612990	102	442											
FANCG	2189	hgsc.bcm.edu	37	chr9	35077020	35077020	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acacctggaccaacacaggcCgtggacacaggcctgaggcc	11	3	12	15	1	0	1	0	1	0	0	0	3	0	3	5	5	1	0	5	5	1	0			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr9:35077020C>T	ENST00000378643.3	-	6	1216	c.725G>A	c.(724-726)cGg>cAg	p.R242Q	FANCG_ENST00000476212.1_5'Flank	NM_004629.1	NP_004620.1	O15287	FANCG_HUMAN	Fanconi anemia, complementation group G	242					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)			CAACACAGGCCGTGGACACAG	0.552			"Mis, N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks																													p.R242Q		Atlas-SNP	.	yes	Rec		Fanconi anaemia G	9	9p13	2189	"Fanconi anemia, complementation group G"		L	.	FANCG	56	.	0			c.G725A						PASS	.						88	92	91					9																	35077020		2203	4300	6503	SO:0001583	missense	2189	exon6			ACAGGCCGTGGAC	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.725G>A	9.37:g.35077020C>T	ENSP00000367910:p.Arg242Gln	85	0	0		80	19	0.2375	NM_004629		Missense_Mutation	SNP	ENST00000378643.3	37	CCDS6574.1	.	.	.	.	.	.	.	.	.	.	C	13.15	2.152449	0.38021	.	.	ENSG00000221829	ENST00000378643;ENST00000543657	T	0.37235	1.21	6.07	3.23	0.37069	Tetratricopeptide-like helical (1);	.	.	.	.	T	0.18467	0.0443	L	0.27053	0.805	0.09310	N	0.999999	P	0.36438	0.553	B	0.20955	0.032	T	0.10800	-1.0614	9	0.26408	T	0.33	-8.4425	6.3483	0.21361	0.0:0.6801:0.1565:0.1633	.	242	O15287	FANCG_HUMAN	Q	242	ENSP00000367910:R242Q	ENSP00000367910:R242Q	R	-	2	0	FANCG	35067020	0.334000	0.24739	0.327000	0.25402	0.992000	0.81027	0.672000	0.25187	0.442000	0.26555	0.655000	0.94253	CGG	.	.	none		0.552	FANCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052269.1	NM_004629		T	35077020	C	T	35077020	3	4	4	1	0	0	0	0	1	0	0	0	5676	652	23	1	1179	1	FANCG	9	35077020	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10		35077020	106136411	103	443											
PAX5	5079	hgsc.bcm.edu	37	chr9	37002696	37002696	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgggggacgtgatgcccaGgatgccgctgatggagtacg	7	7	18	9	3	0	2	0	2	0	0	0	5	0	5	2	4	3	3	2	4	1	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr9:37002696G>C	ENST00000358127.4	-	5	627	c.553C>G	c.(553-555)Ctg>Gtg	p.L185V	PAX5_ENST00000377853.2_Missense_Mutation_p.L185V|RP11-297B17.3_ENST00000509911.2_RNA|PAX5_ENST00000446742.1_Missense_Mutation_p.L119V|PAX5_ENST00000523145.1_Missense_Mutation_p.L77V|PAX5_ENST00000523241.1_Missense_Mutation_p.L185V|PAX5_ENST00000520281.1_Intron|PAX5_ENST00000377852.2_Missense_Mutation_p.L185V|PAX5_ENST00000377847.2_Missense_Mutation_p.L185V|PAX5_ENST00000520154.1_Missense_Mutation_p.L185V|PAX5_ENST00000522003.1_Missense_Mutation_p.L77V|PAX5_ENST00000414447.1_Intron	NM_001280554.1|NM_001280556.1|NM_016734.1	NP_001267483.1|NP_001267485.1|NP_057953.1	Q02548	PAX5_HUMAN	paired box 5	185					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)		GTGATGCCCAGGATGCCGCTG	0.672			"T, Mis, D, F, S"	"IGH@, ETV6, PML, FOXP1, ZNF521, ELN"	"NHL, ALL, B-ALL"																																p.L185V		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.C553G						PASS	.						48	37	41					9																	37002696		2201	4296	6497	SO:0001583	missense	5079	exon5			TGCCCAGGATGCC		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.553C>G	9.37:g.37002696G>C	ENSP00000350844:p.Leu185Val	169	0	0		159	32	0.201258	NM_016734	A3QVP6|A3QVP7|A3QVP8|C0KTF6|C0KTF7|C0KTF8|C0KTF9|C0KTG0|O75933|Q5SFM2|Q6S728|Q6S729|Q6S730|Q6S731|Q6S732	Missense_Mutation	SNP	ENST00000358127.4	37	CCDS6607.1	.	.	.	.	.	.	.	.	.	.	G	16.28	3.077844	0.55753	.	.	ENSG00000196092	ENST00000358127;ENST00000377849;ENST00000377853;ENST00000377852;ENST00000523241;ENST00000520154;ENST00000446742;ENST00000522003;ENST00000523145;ENST00000377847	D;D;D;D;D;D;D;D;D	0.98164	-4.26;-4.27;-4.26;-4.76;-4.73;-4.37;-2.1;-2.68;-4.75	5.15	5.15	0.70609	.	0.369945	0.24325	N	0.039514	D	0.98767	0.9585	M	0.83012	2.62	0.50313	D	0.999869	D;P;B;D;D;P;P	0.65815	0.989;0.956;0.213;0.995;0.993;0.956;0.956	D;P;B;P;D;P;P	0.72338	0.977;0.899;0.222;0.885;0.952;0.899;0.899	D	0.98703	1.0701	10	0.44086	T	0.13	.	13.3201	0.60428	0.0769:0.0:0.9231:0.0	.	119;185;185;185;185;185;185	C0KTF9;C0KTF6;E7ERW5;E7EQT0;Q6S730;Q6S731;Q02548	.;.;.;.;.;.;PAX5_HUMAN	V	185;77;185;185;185;185;119;77;77;185	ENSP00000350844:L185V;ENSP00000367084:L185V;ENSP00000367083:L185V;ENSP00000429637:L185V;ENSP00000429291:L185V;ENSP00000404687:L119V;ENSP00000429359:L77V;ENSP00000429197:L77V;ENSP00000367078:L185V	ENSP00000350844:L185V	L	-	1	2	PAX5	36992696	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	5.768000	0.68858	2.553000	0.86117	0.555000	0.69702	CTG	.	.	none		0.672	PAX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052433.1			C	37002696	G	C	37002696	3	2	4	1	0	0	0	0	1	0	0	0	11491	991	35	4	646	4	PAX5	9	37002696	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	1925676	37002696	104210735	104	444											
TRPM6	140803	hgsc.bcm.edu	37	chr9	77400960	77400960	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	agctgaaaacaggccaatggCcacagtttctgttaagttcc	12	10	9	10	0	1	1	0	1	1	0	2	1	2	1	3	2	2	4	3	2	4	3			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr9:77400960C>G	ENST00000360774.1	-	21	2986	c.2749G>C	c.(2749-2751)Gcc>Ccc	p.A917P	TRPM6_ENST00000451710.3_Missense_Mutation_p.A917P|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000361255.3_Missense_Mutation_p.A912P|TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000376864.4_Missense_Mutation_p.A917P|TRPM6_ENST00000449912.2_Missense_Mutation_p.A912P	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	917					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						AGGCCAATGGCCACAGTTTCT	0.448																																					p.A917P		Atlas-SNP	.											TRPM6_ENST00000451710,axilla,malignant_melanoma,+1,2	TRPM6	377	2	0			c.G2749C						PASS	.						178	163	168					9																	77400960		2203	4300	6503	SO:0001583	missense	140803	exon21			CAATGGCCACAGT	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.2749G>C	9.37:g.77400960C>G	ENSP00000354006:p.Ala917Pro	158	0	0		132	27	0.204545	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	37	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	C	18.55	3.648930	0.67358	.	.	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000449912;ENST00000361255;ENST00000376864;ENST00000312449;ENST00000448641	T;T;T;T;T	0.71103	-0.54;-0.54;-0.54;-0.54;-0.54	5.14	5.14	0.70334	Ion transport (1);	0.144833	0.64402	D	0.000008	D	0.87771	0.6261	M	0.91612	3.225	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.999	D;D;D	0.80764	0.994;0.988;0.99	D	0.90238	0.4284	10	0.87932	D	0	.	18.7871	0.91960	0.0:1.0:0.0:0.0	.	580;917;912	F5H7D1;Q9BX84;Q9BX84-3	.;TRPM6_HUMAN;.	P	917;917;912;912;917;580;580	ENSP00000354006:A917P;ENSP00000407341:A917P;ENSP00000396672:A912P;ENSP00000354962:A912P;ENSP00000366060:A917P	ENSP00000309693:A580P	A	-	1	0	TRPM6	76590780	1.000000	0.71417	0.999000	0.59377	0.077000	0.17291	7.602000	0.82796	2.669000	0.90835	0.549000	0.68633	GCC	.	.	none		0.448	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		G	77400960	C	G	77400960	3	3	4	1	0	0	0	0	1	0	0	0	16605	739	26	4	3395	4	TRPM6	9	77400960	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	40398264	77400960	63812471	105	445											
NINJ1	4814	hgsc.bcm.edu	37	chr9	95887259	95887259	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgatgaagatgttgactacCacgatgatgaacaccaggcc	13	8	11	9	1	0	6	0	5	0	1	0	7	0	6	3	1	2	1	3	1	3	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr9:95887259C>A	ENST00000375446.4	-	3	460	c.390G>T	c.(388-390)gtG>gtT	p.V130V	NINJ1_ENST00000489274.1_5'UTR	NM_004148.3	NP_004139.2	Q92982	NINJ1_HUMAN	ninjurin 1	130					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						TGTTGACTACCACGATGATGA	0.597																																					p.V130V		Atlas-SNP	.											.	NINJ1	7	.	0			c.G390T						PASS	.						158	130	139					9																	95887259		2203	4300	6503	SO:0001819	synonymous_variant	4814	exon3			GACTACCACGATG	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.390G>T	9.37:g.95887259C>A		65	0	0		54	10	0.185185	NM_004148	Q6GU89|Q8WUV5|Q9BT07	Silent	SNP	ENST00000375446.4	37	CCDS6703.1																																																																																			.	.	none		0.597	NINJ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053123.2	NM_004148		A	95887259	C	A	95887259	2	1	4	1	0	0	0	0	0	0	0	1	10427	581	21	4		4	NINJ1	9	95887259	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	18486299	95887259	45326172	106	446											
ZNF367	195828	hgsc.bcm.edu	37	chr9	99180102	99180102	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgtgcgttctcgccccagcgCcacgggtacaccatgaagtc	7	8	11	15	4	1	1	0	1	1	0	3	1	1	1	4	1	3	2	4	1	2	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr9:99180102C>T	ENST00000375256.4	-	1	509	c.213G>A	c.(211-213)tgG>tgA	p.W71*		NM_153695.3	NP_710162.1	Q7RTV3	ZN367_HUMAN	zinc finger protein 367	71					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)			cervix(1)|endometrium(4)|large_intestine(3)|lung(3)|prostate(1)	12		Acute lymphoblastic leukemia(62;0.0167)				CGCCCCAGCGCCACGGGTACA	0.756																																					p.W71X		Atlas-SNP	.											.	ZNF367	27	.	0			c.G213A						PASS	.						6	7	7					9																	99180102		2098	4155	6253	SO:0001587	stop_gained	195828	exon1			CCAGCGCCACGGG	AK091289	CCDS6718.1	9q22	2008-05-02			ENSG00000165244	ENSG00000165244		"Zinc fingers, C2H2-type"	18320	protein-coding gene	gene with protein product		610160					Standard	NM_153695		Approved	FLJ33970	uc004awf.3	Q7RTV3	OTTHUMG00000020295	ENST00000375256.4:c.213G>A	9.37:g.99180102C>T	ENSP00000364405:p.Trp71*	59	0	0		46	6	0.130435	NM_153695	Q6Q7C8	Nonsense_Mutation	SNP	ENST00000375256.4	37	CCDS6718.1	.	.	.	.	.	.	.	.	.	.	C	40	8.166298	0.98686	.	.	ENSG00000165244	ENST00000375256	.	.	.	3.45	3.45	0.39498	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.4595	15.072	0.72046	0.0:1.0:0.0:0.0	.	.	.	.	X	71	.	ENSP00000364405:W71X	W	-	3	0	ZNF367	98219923	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.458000	0.73509	1.758000	0.51981	0.313000	0.20887	TGG	.	.	none		0.756	ZNF367-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053266.1			T	99180102	C	T	99180102	4	4	4	1	0	0	0	0	0	1	0	0	17886	740	26	2	859	2	ZNF367	9	99180102	Nonsense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	3292843	99180102	42033329	107	447											
ANKS6	203286	hgsc.bcm.edu	37	chr9	101518730	101518730	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgatggtgccactgctggaGcccccactgctcttggactg	5	10	13	13	0	1	1	0	1	1	0	1	3	1	3	3	3	4	2	3	3	0	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr9:101518730G>T	ENST00000353234.4	-	12	2345	c.2298C>A	c.(2296-2298)ggC>ggA	p.G766G	ANKS6_ENST00000375018.1_Silent_p.G767G|ANKS6_ENST00000375019.2_Silent_p.G465G|ANKS6_ENST00000540940.1_Silent_p.G571G			Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain containing 6	766	Ser-rich.					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)				CACTGCTGGAGCCCCCACTGC	0.602																																					p.G766G		Atlas-SNP	.											.	ANKS6	59	.	0			c.C2298A						PASS	.						83	84	83					9																	101518730		2056	4201	6257	SO:0001819	synonymous_variant	203286	exon12			GCTGGAGCCCCCA	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.2298C>A	9.37:g.101518730G>T		69	0	0		42	6	0.142857	NM_173551	A0SE62|Q5VSL0|Q5VSL2|Q5VSL3|Q5VSL4|Q68DB8|Q6P2R2|Q8N9L6|Q96D62	Silent	SNP	ENST00000353234.4	37	CCDS43856.1	.	.	.	.	.	.	.	.	.	.	G	9.761	1.169977	0.21621	.	.	ENSG00000165138	ENST00000444472	.	.	.	5.27	2.18	0.27775	.	.	.	.	.	T	0.46541	0.1398	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37103	-0.9720	4	.	.	.	-27.5593	3.861	0.08996	0.2675:0.0:0.5604:0.1721	.	.	.	.	I	236	.	.	L	-	1	0	ANKS6	100558551	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	1.132000	0.31418	1.239000	0.43787	0.484000	0.47621	CTC	.	.	none		0.602	ANKS6-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277053.1	NM_173551		T	101518730	G	T	101518730	2	4	4	1	0	0	0	0	0	0	0	1	692	958	34	4		4	ANKS6	9	101518730	Silent	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	2338628	101518730	39694701	108	448											
IL2RA	3559	hgsc.bcm.edu	37	chr10	6104051	6104051	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcacccacaggcccttacCtgcctggcagccaggcacca	8	4	11	18	0	0	0	0	0	0	0	0	0	0	0	6	4	3	3	6	4	1	1	rs267602536		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr10:6104051C>T	ENST00000379959.3	-	1	237	c.64G>A	c.(64-66)Gag>Aag	p.E22K	IL2RA_ENST00000256876.6_Splice_Site_p.E22K|IL2RA_ENST00000379954.1_Splice_Site_p.E22K	NM_000417.2	NP_000408.1	P01589	IL2RA_HUMAN	interleukin 2 receptor, alpha	22	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				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)	AGGCCCTTACCTGCCTGGCAG	0.612																																					p.E22K		Atlas-SNP	.											.	IL2RA	37	.	0			c.G64A						PASS	.						65	63	64					10																	6104051		2203	4300	6503	SO:0001630	splice_region_variant	3559	exon1			CCTTACCTGCCTG	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.64+1G>A	10.37:g.6104051C>T		113	0	0		93	16	0.172043	NM_000417	Q5W007	Missense_Mutation	SNP	ENST00000379959.3	37	CCDS7076.1	.	.	.	.	.	.	.	.	.	.	C	19.32	3.805459	0.70682	.	.	ENSG00000134460	ENST00000379959;ENST00000397240;ENST00000379954;ENST00000256876	T;T;T	0.52526	1.26;0.66;1.32	5.24	5.24	0.73138	Complement control module (1);Sushi/SCR/CCP (1);	0.606025	0.15011	N	0.285558	T	0.52629	0.1746	L	0.58101	1.795	0.43462	D	0.995663	D;P	0.54047	0.964;0.956	P;P	0.48270	0.538;0.572	T	0.51052	-0.8754	9	.	.	.	-19.9974	14.3538	0.66722	0.0:1.0:0.0:0.0	.	22;22	Q5W005;P01589	.;IL2RA_HUMAN	K	22;8;22;22	ENSP00000369293:E22K;ENSP00000369287:E22K;ENSP00000256876:E22K	.	E	-	1	0	IL2RA	6144057	1.000000	0.71417	1.000000	0.80357	0.163000	0.22366	1.983000	0.40648	2.436000	0.82500	0.563000	0.77884	GAG	.	.	none		0.612	IL2RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046627.1	NM_000417	Missense_Mutation	T	6104051	C	T	6104051	5	4	4	1	0	0	0	0	0	0	1	0	7695	695	24	2	786	2	IL2RA	10	6104051	Splice_Site	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10		6104051	129430696	109	449											
CUBN	8029	hgsc.bcm.edu	37	chr10	16883024	16883024	+	Frame_Shift_Del	DEL	T	T	-																															acgttccagccaagttcgcaTtttcactatccccatcatat																										TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr10:16883024delT	ENST00000377833.4	-	61	9751	c.9686delA	c.(9685-9687)aatfs	p.N3229fs		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	3229	CUB 24. {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)	CAAGTTCGCATTTTCACTATC	0.363																																					p.N3229fs		Atlas-Indel	.											.	CUBN	515	.	0			c.9687delT						PASS	.						84	76	78					10																	16883024		2203	4300	6503	SO:0001589	frameshift_variant	8029	exon61			.	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.9686delA	10.37:g.16883024delT	ENSP00000367064:p.Asn3229fs	73	0	0		75	10	0.133333	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Frame_Shift_Del	DEL	ENST00000377833.4	37	CCDS7113.1																																																																																			.	.	none		0.363	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		-	16883024	T	-	16883024	7	5	4	1	0	1	0	1	0	0	0	0	4053	1493	52	0	1213	0	CUBN	10	16883024	Frame_Shift_Del	DEL	T	TCGA-FA-A6HN-01A-11D-A31X-10	10778973	16883024	118651723	110	450											
ARHGAP21	57584	hgsc.bcm.edu	37	chr10	24909112	24909112	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccactcctctaccactcattCgcctgttatcagaattaaca	11	12	3	15	1	3	1	2	0	1	1	5	1	4	1	4	0	2	1	4	0	4	4			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr10:24909112C>T	ENST00000396432.2	-	9	2198	c.1712G>A	c.(1711-1713)cGa>cAa	p.R571Q	ARHGAP21_ENST00000320481.6_Missense_Mutation_p.R358Q	NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	570					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						ACCACTCATTCGCCTGTTATC	0.393																																					p.R571Q		Atlas-SNP	.											.	ARHGAP21	185	.	0			c.G1712A						PASS	.						74	75	75					10																	24909112		2203	4300	6503	SO:0001583	missense	57584	exon9			CTCATTCGCCTGT	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.1712G>A	10.37:g.24909112C>T	ENSP00000379709:p.Arg571Gln	93	0	0		87	20	0.229885	NM_020824	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000396432.2	37	CCDS7144.2	.	.	.	.	.	.	.	.	.	.	c	11.85	1.760900	0.31137	.	.	ENSG00000107863	ENST00000396432;ENST00000447364;ENST00000320481;ENST00000376410;ENST00000446003;ENST00000445703	T;T;T;T	0.54675	2.52;2.63;0.56;0.58	5.5	4.6	0.57074	.	0.207171	0.40064	N	0.001187	T	0.62527	0.2435	M	0.70595	2.14	0.09310	N	0.999999	D;D	0.76494	0.981;0.999	B;P	0.57960	0.405;0.83	T	0.55354	-0.8154	10	0.23891	T	0.37	.	10.5329	0.44988	0.1326:0.7983:0.0:0.0691	.	561;570	F8W9U9;Q5T5U3	.;RHG21_HUMAN	Q	571;560;358;561;571;406	ENSP00000379709:R571Q;ENSP00000365604:R358Q;ENSP00000365592:R561Q;ENSP00000405018:R571Q	ENSP00000365604:R358Q	R	-	2	0	ARHGAP21	24949118	0.989000	0.36119	0.027000	0.17364	0.013000	0.08279	3.061000	0.49963	1.464000	0.47987	-0.127000	0.14921	CGA	.	.	none		0.393	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824		T	24909112	C	T	24909112	3	4	4	1	0	0	0	0	1	0	0	0	871	884	31	1	4236	1	ARHGAP21	10	24909112	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	8026088	24909112	110625635	111	451											
PARD3	56288	hgsc.bcm.edu	37	chr10	34626206	34626206	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atggagattgtactcactacCtaaatccatgctttttgatt	11	16	6	8	0	1	2	1	1	0	1	2	3	2	2	2	1	3	2	2	1	4	7			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr10:34626206C>T	ENST00000374789.3	-	17	2891	c.2566G>A	c.(2566-2568)Ggt>Agt	p.G856S	PARD3_ENST00000374776.1_Intron|PARD3_ENST00000374790.3_Missense_Mutation_p.G796S|PARD3_ENST00000545693.1_Missense_Mutation_p.G840S|PARD3_ENST00000340077.5_Missense_Mutation_p.G853S|PARD3_ENST00000466092.1_5'Flank|PARD3_ENST00000374788.3_Missense_Mutation_p.G853S|PARD3_ENST00000545260.1_Intron|PARD3_ENST00000544292.1_Splice_Site_p.V570I|PARD3_ENST00000350537.4_Intron|PARD3_ENST00000346874.4_Missense_Mutation_p.G856S|PARD3_ENST00000374794.3_Missense_Mutation_p.G796S|PARD3_ENST00000374773.1_Intron	NM_019619.3	NP_062565.2	Q8TEW0	PARD3_HUMAN	par-3 family cell polarity regulator	856	Interacts with PRKCI and PRKCZ. {ECO:0000250}.				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)				TACTCACTACCTAAATCCATG	0.343																																					p.G856S		Atlas-SNP	.											.	PARD3	131	.	0			c.G2566A						PASS	.						96	87	90					10																	34626206		2203	4298	6501	SO:0001583	missense	56288	exon17			CACTACCTAAATC	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.2566G>A	10.37:g.34626206C>T	ENSP00000363921:p.Gly856Ser	78	0	0		62	10	0.16129	NM_001184787	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	37	CCDS7178.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.4|23.4	4.415053|4.415053	0.83449|0.83449	.|.	.|.	ENSG00000148498|ENSG00000148498	ENST00000545693;ENST00000374789;ENST00000374788;ENST00000346874;ENST00000374794;ENST00000374790;ENST00000340077|ENST00000544292	T;T;T;T;T;T;T|T	0.28666|0.29917	1.73;1.73;1.73;1.73;1.6;1.73;1.73|1.55	5.83|5.83	5.83|5.83	0.93111|0.93111	.|.	0.130941|.	0.49305|.	D|.	0.000158|.	T|T	0.26376|0.26376	0.0644|0.0644	L|L	0.29908|0.29908	0.895|0.895	0.32905|0.32905	D|D	0.513695|0.513695	D;D;P;D;D;P;D|B	0.89917|0.02656	0.982;1.0;0.847;0.995;0.973;0.833;0.98|0.0	P;D;B;P;P;B;P|B	0.85130|0.06405	0.676;0.997;0.36;0.853;0.576;0.267;0.758|0.002	T|T	0.16600|0.16600	-1.0397|-1.0397	10|9	0.27082|0.15066	T|T	0.32|0.55	.|.	20.1237|20.1237	0.97972|0.97972	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	796;840;856;853;856;840;853|570	Q8TEW0-5;F5H5T0;Q8TEW0-4;Q8TEW0-2;Q8TEW0;Q6IQ47;Q8TEW0-8|F5GZI3	.;.;.;.;PARD3_HUMAN;.;.|.	S|I	840;856;853;856;796;796;853|570	ENSP00000443147:G840S;ENSP00000363921:G856S;ENSP00000363920:G853S;ENSP00000340591:G856S;ENSP00000363926:G796S;ENSP00000363922:G796S;ENSP00000341844:G853S|ENSP00000444429:V570I	ENSP00000341844:G853S|ENSP00000444429:V570I	G|V	-|-	1|1	0|0	PARD3|PARD3	34666212|34666212	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.089000|6.089000	0.71384|0.71384	2.759000|2.759000	0.94783|0.94783	0.561000|0.561000	0.74099|0.74099	GGT|GTA	.	.	none		0.343	PARD3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047527.1	NM_019619		T	34626206	C	T	34626206	3	4	4	1	0	0	0	0	1	0	0	0	11452	681	24	2	1575	2	PARD3	10	34626206	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	9717094	34626206	100908541	112	452											
PCDH15	65217	hgsc.bcm.edu	37	chr10	55698632	55698632	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cagggaatcagcttggactcGaagtacatagcttgtcctgg	10	10	12	9	1	1	0	1	0	0	0	3	3	2	2	1	3	3	3	1	3	4	4	rs202033121		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr10:55698632G>A	ENST00000320301.6	-	25	3710	c.3316C>T	c.(3316-3318)Cga>Tga	p.R1106*	PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000409834.1_Nonsense_Mutation_p.R717*|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000361849.3_Nonsense_Mutation_p.R1106*|PCDH15_ENST00000414778.1_Nonsense_Mutation_p.R1111*|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000373965.2_Nonsense_Mutation_p.R1113*|PCDH15_ENST00000395438.1_Nonsense_Mutation_p.R1106*|PCDH15_ENST00000395433.1_Nonsense_Mutation_p.R1084*|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000437009.1_Nonsense_Mutation_p.R1035*|PCDH15_ENST00000395432.2_Nonsense_Mutation_p.R1069*|PCDH15_ENST00000395430.1_Nonsense_Mutation_p.R1106*|PCDH15_ENST00000395445.1_Nonsense_Mutation_p.R1113*	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1106	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)				GCTTGGACTCGAAGTACATAG	0.373										HNSCC(58;0.16)																											p.R1111X		Atlas-SNP	.											PCDH15_ENST00000417177,NS,malignant_melanoma,0,8	PCDH15	1715	8	0			c.C3331T						PASS	.	G	stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG,stop/ARG	0,4406		0,0,2203	119	110	113		3331,3316,3103,3316,3205,3250,3352,3316,3331,3316,3250,3316	4.8	1	10		113	1,8597	1.2+/-3.3	0,1,4298	yes	stop-gained,stop-gained,stop-gained,stop-gained,stop-gained,stop-gained,stop-gained,stop-gained,stop-gained,stop-gained,stop-gained,stop-gained	PCDH15	NM_001142763.1,NM_001142764.1,NM_001142765.1,NM_001142766.1,NM_001142767.1,NM_001142768.1,NM_001142769.1,NM_001142770.1,NM_001142771.1,NM_001142772.1,NM_001142773.1,NM_033056.3	,,,,,,,,,,,	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	,,,,,,,,,,,	1111/1963,1106/1958,1035/1887,1106/1953,1069/1916,1084/1936,1118/1791,1106/1540,1111/1683,1106/1678,1084/1933,1106/1956	55698632	1,13003	2203	4299	6502	SO:0001587	stop_gained	65217	exon26			GGACTCGAAGTAC	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.3316C>T	10.37:g.55698632G>A	ENSP00000322604:p.Arg1106*	44	0	0		43	10	0.232558	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Nonsense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	G	45	11.791944	0.99603	0.0	1.16E-4	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009	.	.	.	5.77	4.85	0.62838	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.6969	0.57010	0.0:0.0:0.7007:0.2993	.	.	.	.	X	1113;1111;1106;1106;717;1113;1069;1106;1084;1106;1106;1111;1035	.	ENSP00000322604:R1106X	R	-	1	2	PCDH15	55368638	1.000000	0.71417	0.986000	0.45419	0.968000	0.65278	2.995000	0.49441	1.380000	0.46344	0.655000	0.94253	CGA	.	.	weak		0.373	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		A	55698632	G	A	55698632	4	1	4	1	0	0	0	0	0	1	0	0	11520	1066	37	1	4206	1	PCDH15	10	55698632	Nonsense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	21072426	55698632	79836115	113	453											
AIFM2	84883	hgsc.bcm.edu	37	chr10	71880315	71880315	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgccatctccactccagccGagcctcctcccaccaccacg	7	6	5	23	2	1	0	0	0	1	0	5	1	4	0	9	0	3	0	9	0	0	0			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr10:71880315G>A	ENST00000307864.1	-	5	668	c.455C>T	c.(454-456)tCg>tTg	p.S152L	AIFM2_ENST00000482166.1_5'Flank|AIFM2_ENST00000373248.1_Missense_Mutation_p.S152L	NM_001198696.1|NM_032797.5	NP_001185625.1|NP_116186.1	Q9BRQ8	AIFM2_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 2	152					apoptotic mitochondrial changes (GO:0008637)|positive regulation of apoptotic process (GO:0043065)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|electron-transferring-flavoprotein dehydrogenase activity (GO:0004174)|flavin adenine dinucleotide binding (GO:0050660)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)|skin(2)|urinary_tract(2)	16						CACTCCAGCCGAGCCTCCTCC	0.522																																					p.S152L		Atlas-SNP	.											.	AIFM2	33	.	0			c.C455T						PASS	.						155	144	148					10																	71880315		2203	4300	6503	SO:0001583	missense	84883	exon5			CCAGCCGAGCCTC	AK027403	CCDS7297.1	10q22.2	2006-11-16	2006-11-16	2006-11-16	ENSG00000042286	ENSG00000042286			21411	protein-coding gene	gene with protein product		605159	"apoptosis-inducing factor (AIF)-like mitochondrion-associated inducer of death"	AMID		12135761, 11980907, 15958387	Standard	NM_001198696		Approved	FLJ14497, PRG3	uc001jqp.2	Q9BRQ8	OTTHUMG00000018398	ENST00000307864.1:c.455C>T	10.37:g.71880315G>A	ENSP00000312370:p.Ser152Leu	63	0	0		50	7	0.14	NM_001198696	B3KXI0|Q63Z39	Missense_Mutation	SNP	ENST00000307864.1	37	CCDS7297.1	.	.	.	.	.	.	.	.	.	.	G	35	5.425664	0.96131	.	.	ENSG00000042286	ENST00000373248;ENST00000307864;ENST00000395039	T;T	0.54675	0.56;0.56	5.05	5.05	0.67936	Pyridine nucleotide-disulphide oxidoreductase, NAD-binding domain (1);Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (1);	0.056297	0.64402	D	0.000001	T	0.39655	0.1086	N	0.10837	0.055	0.53688	D	0.99997	P	0.51653	0.947	P	0.44561	0.453	T	0.38415	-0.9662	10	0.38643	T	0.18	-14.083	18.2036	0.89847	0.0:0.0:1.0:0.0	.	152	Q9BRQ8	AIFM2_HUMAN	L	152;152;112	ENSP00000362345:S152L;ENSP00000312370:S152L	ENSP00000312370:S152L	S	-	2	0	AIFM2	71550321	1.000000	0.71417	0.969000	0.41365	0.996000	0.88848	8.832000	0.92079	2.645000	0.89757	0.655000	0.94253	TCG	.	.	none		0.522	AIFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048487.1	NM_032797		A	71880315	G	A	71880315	3	1	4	1	0	0	0	0	1	0	0	0	427	1059	37	1	686	1	AIFM2	10	71880315	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	16181683	71880315	63654432	114	454											
ANXA11	311	hgsc.bcm.edu	37	chr10	81930597	81930597	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgaactgccccgcataggTggccacgttatccagcccga	8	8	11	14	3	0	1	0	1	0	0	1	2	1	1	5	2	3	3	5	2	3	3	rs539258237		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr10:81930597T>A	ENST00000438331.1	-	5	612	c.130A>T	c.(130-132)Acc>Tcc	p.T44S	ANXA11_ENST00000422982.3_Missense_Mutation_p.T44S|ANXA11_ENST00000463657.1_5'Flank|ANXA11_ENST00000537102.1_Missense_Mutation_p.T11S|ANXA11_ENST00000360615.4_Missense_Mutation_p.T44S|ANXA11_ENST00000265447.4_Missense_Mutation_p.T44S|ANXA11_ENST00000372231.3_Missense_Mutation_p.T44S|ANXA11_ENST00000535999.1_Missense_Mutation_p.T44S	NM_145869.1	NP_665876.1	P50995	ANX11_HUMAN	annexin A11	44					cytokinesis, completion of separation (GO:0007109)|phagocytosis (GO:0006909)|response to calcium ion (GO:0051592)	azurophil granule (GO:0042582)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|specific granule (GO:0042581)|spindle (GO:0005819)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|MHC class II protein complex binding (GO:0023026)|phosphatidylethanolamine binding (GO:0008429)|poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)			endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|urinary_tract(1)	17	Prostate(51;0.00985)|all_epithelial(25;0.0951)		Colorectal(32;0.109)			CCCGCATAGGTGGCCACGTTA	0.632																																					p.T44S		Atlas-SNP	.											ANXA11,right_upper_lobe,carcinoma,0,1	ANXA11	32	1	0			c.A130T						scavenged	.						78	67	71					10																	81930597		2203	4300	6503	SO:0001583	missense	311	exon4			CATAGGTGGCCAC	L19605	CCDS7364.1, CCDS60576.1	10q22.3	2005-11-09			ENSG00000122359	ENSG00000122359		"Annexins"	535	protein-coding gene	gene with protein product		602572		ANX11		7508441, 9503022	Standard	NM_001157		Approved		uc001kbt.1	P50995	OTTHUMG00000018604	ENST00000438331.1:c.130A>T	10.37:g.81930597T>A	ENSP00000398610:p.Thr44Ser	68	1	0.0147059		42	13	0.309524	NM_145868	B4DVE7	Missense_Mutation	SNP	ENST00000438331.1	37	CCDS7364.1	.	.	.	.	.	.	.	.	.	.	.	11.12	1.544761	0.27563	.	.	ENSG00000122359	ENST00000372231;ENST00000422982;ENST00000438331;ENST00000372234;ENST00000360615;ENST00000265447;ENST00000535999;ENST00000537102;ENST00000445524;ENST00000437799	T;T;T;T;T;T;T	0.01725	4.67;4.67;4.67;4.67;4.67;4.67;4.67	4.69	3.55	0.40652	.	2.338380	0.01769	N	0.031065	T	0.01558	0.0050	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	0.31420	-0.9944	10	0.30078	T	0.28	.	8.0097	0.30347	0.0:0.0986:0.0:0.9014	.	144;44;44	B7Z6L0;Q5T0G8;P50995	.;.;ANX11_HUMAN	S	44;44;44;44;44;44;44;11;44;44	ENSP00000361305:T44S;ENSP00000404412:T44S;ENSP00000398610:T44S;ENSP00000353827:T44S;ENSP00000265447:T44S;ENSP00000441748:T44S;ENSP00000441400:T11S	ENSP00000265447:T44S	T	-	1	0	ANXA11	81920577	0.998000	0.40836	0.969000	0.41365	0.033000	0.12548	1.684000	0.37649	1.886000	0.54624	0.364000	0.22116	ACC	.	.	none		0.632	ANXA11-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049044.1	NM_145869		A	81930597	T	A	81930597	3	1	4	1	0	0	0	0	1	0	0	0	716	1696	59	5	1439	5	ANXA11	10	81930597	Missense_Mutation	SNP	T	TCGA-FA-A6HN-01A-11D-A31X-10	10050282	81930597	53604150	115	455											
LIPN	643418	hgsc.bcm.edu	37	chr10	90537944	90537944	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgattttgtctggggcctcgAtgcccctcaacggatgtaca	7	12	11	11	2	2	1	1	1	1	0	3	3	2	2	3	3	3	1	3	3	2	3			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr10:90537944A>G	ENST00000404459.1	+	9	1142	c.1142A>G	c.(1141-1143)gAt>gGt	p.D381G		NM_001102469.1	NP_001095939.1	Q5VXI9	LIPN_HUMAN	lipase, family member N	381					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	hydrolase activity, acting on ester bonds (GO:0016788)			endometrium(1)|kidney(1)|large_intestine(5)|lung(1)|skin(1)	9		Colorectal(252;0.0161)		Colorectal(12;4.83e-05)|COAD - Colon adenocarcinoma(12;6.5e-05)		TGGGGCCTCGATGCCCCTCAA	0.418																																					p.D381G		Atlas-SNP	.											.	LIPN	28	.	0			c.A1142G						PASS	.						78	73	74					10																	90537944		1878	4099	5977	SO:0001583	missense	643418	exon9			GCCTCGATGCCCC		CCDS44456.1	10q23.31	2013-09-20	2007-02-27	2007-02-27	ENSG00000204020	ENSG00000204020			23452	protein-coding gene	gene with protein product		613924	"lipase-like, ab-hydrolase domain containing 4"	LIPL4			Standard	NM_001102469		Approved	bA186O14.3	uc010qmw.2	Q5VXI9	OTTHUMG00000018694	ENST00000404459.1:c.1142A>G	10.37:g.90537944A>G	ENSP00000383923:p.Asp381Gly	98	0	0		95	21	0.221053	NM_001102469	A7KIH9	Missense_Mutation	SNP	ENST00000404459.1	37	CCDS44456.1	.	.	.	.	.	.	.	.	.	.	A	17.74	3.464544	0.63513	.	.	ENSG00000204020	ENST00000404459	T	0.64618	-0.11	5.21	4.07	0.47477	Alpha/beta hydrolase fold-1 (1);	.	.	.	.	T	0.76499	0.3996	M	0.80028	2.48	0.33987	D	0.648718	D	0.89917	1.0	D	0.81914	0.995	T	0.82043	-0.0653	8	.	.	.	-23.3114	8.0083	0.30338	0.8345:0.0:0.1655:0.0	.	381	Q5VXI9	LIPN_HUMAN	G	381	ENSP00000383923:D381G	.	D	+	2	0	LIPN	90527924	1.000000	0.71417	0.951000	0.38953	0.983000	0.72400	4.688000	0.61715	1.114000	0.41781	0.523000	0.50628	GAT	.	.	none		0.418	LIPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049254.2	XM_926751		G	90537944	A	G	90537944	3	3	4	1	0	0	0	0	1	0	0	0	8837	333	12	3	1176	3	LIPN	10	90537944	Missense_Mutation	SNP	A	TCGA-FA-A6HN-01A-11D-A31X-10	8607347	90537944	44996803	116	456											
NFKB2	4791	hgsc.bcm.edu	37	chr10	104157819	104157819	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtggagatgaagtttatcTgctttgtgacaaggtgcaga	10	12	15	4	0	1	4	0	2	1	2	1	5	1	4	0	3	2	3	0	3	3	3			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr10:104157819T>A	ENST00000369966.3	+	9	993	c.743T>A	c.(742-744)cTg>cAg	p.L248Q	NFKB2_ENST00000189444.6_Missense_Mutation_p.L248Q|NFKB2_ENST00000428099.1_Missense_Mutation_p.L248Q	NM_001077494.2	NP_001070962.1	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)	248	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)	GAAGTTTATCTGCTTTGTGAC	0.517			T	IGH@	B-NHL																																p.L248Q		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.T743A						PASS	.						119	120	120					10																	104157819		1979	4177	6156	SO:0001583	missense	4791	exon9			TTTATCTGCTTTG	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.743T>A	10.37:g.104157819T>A	ENSP00000358983:p.Leu248Gln	143	0	0		114	16	0.140351	NM_001077494	A8K9D9|D3DR83|Q04860|Q9BU75|Q9H471|Q9H472	Missense_Mutation	SNP	ENST00000369966.3	37	CCDS41564.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.245955	0.80024	.	.	ENSG00000077150	ENST00000428099;ENST00000369966;ENST00000336486;ENST00000189444	T;T;T	0.57752	0.38;0.38;0.38	5.21	5.21	0.72293	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	T	0.78811	0.4342	M	0.92833	3.35	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	0.84653	0.0702	10	0.87932	D	0	.	15.1176	0.72416	0.0:0.0:0.0:1.0	.	248;248;248	D3DR86;Q00653;A8K9D9	.;NFKB2_HUMAN;.	Q	248	ENSP00000410256:L248Q;ENSP00000358983:L248Q;ENSP00000189444:L248Q	ENSP00000189444:L248Q	L	+	2	0	NFKB2	104147809	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.984000	0.88150	1.972000	0.57404	0.459000	0.35465	CTG	.	.	none		0.517	NFKB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050080.2			A	104157819	T	A	104157819	3	1	4	1	0	0	0	0	1	0	0	0	10385	1580	55	5	773	5	NFKB2	10	104157819	Missense_Mutation	SNP	T	TCGA-FA-A6HN-01A-11D-A31X-10	13619875	104157819	31376928	117	457											
C10orf79	80217	hgsc.bcm.edu	37	chr10	105923874	105923874	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctcatcttgcacaacaagcGttctctctggcttctcacag	8	12	6	15	1	5	0	2	0	4	0	7	0	5	0	1	1	3	3	1	1	2	3	rs146455280		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr10:105923874G>A	ENST00000357060.3	-	24	3339	c.3224C>T	c.(3223-3225)aCg>aTg	p.T1075M	WDR96_ENST00000428666.1_Missense_Mutation_p.T1076M	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						CACAACAAGCGTTCTCTCTGG	0.428																																					p.T1075M		Atlas-SNP	.											.	WDR96	183	.	0			c.C3224T						PASS	.						151	134	140					10																	105923874		2203	4300	6503	SO:0001583	missense	80217	exon24			ACAAGCGTTCTCT																												ENST00000357060.3:c.3224C>T	10.37:g.105923874G>A	ENSP00000349568:p.Thr1075Met	80	0	0		71	22	0.309859	NM_025145		Missense_Mutation	SNP	ENST00000357060.3	37	CCDS31281.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	4.355|4.355	0.065353|0.065353	0.08388|0.08388	.|.	.|.	ENSG00000197748|ENSG00000197748	ENST00000434629|ENST00000357060;ENST00000428666	.|T;T	.|0.13778	.|2.56;2.56	6.06|6.06	1.42|1.42	0.22433|0.22433	.|.	.|0.338170	.|0.28589	.|N	.|0.014819	T|T	0.07324|0.07324	0.0185|0.0185	L|L	0.33485|0.33485	1.01|1.01	0.09310|0.09310	N|N	1|1	.|B;B	.|0.33171	.|0.241;0.4	.|B;B	.|0.25987	.|0.065;0.05	T|T	0.24440|0.24440	-1.0160|-1.0160	5|10	.|0.33141	.|T	.|0.24	.|.	3.9695|3.9695	0.09447|0.09447	0.1936:0.1251:0.5536:0.1277|0.1936:0.1251:0.5536:0.1277	.|.	.|1076;1075	.|G5E9L1;Q8NDM7	.|.;WDR96_HUMAN	C|M	436|1075;1076	.|ENSP00000349568:T1075M;ENSP00000400289:T1076M	.|ENSP00000349568:T1075M	R|T	-|-	1|2	0|0	WDR96|WDR96	105913864|105913864	0.781000|0.781000	0.28676|0.28676	0.590000|0.590000	0.28732|0.28732	0.048000|0.048000	0.14542|0.14542	1.142000|1.142000	0.31540|0.31540	0.894000|0.894000	0.36317|0.36317	-0.127000|-0.127000	0.14921|0.14921	CGC|ACG	G|1.000;T|0.000	.	alt		0.428	WDR96-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	105923874	G	A	105923874	3	1	4	1	0	0	0	0	1	0	0	0	1620	1145	40	1	1833	1	C10orf79	10	105923874	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	1766055	105923874	29610873	118	458											
KRTAP5-2	440021	hgsc.bcm.edu	37	chr11	1619234	1619234	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gccacagccccccttggagcCcccacaggagccacagctgg	8	3	11	19	0	0	0	0	0	0	0	0	2	0	2	7	3	4	1	7	3	0	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr11:1619234C>T	ENST00000412090.1	-	1	290	c.247G>A	c.(247-249)Ggc>Agc	p.G83S	KRTAP5-AS1_ENST00000532922.1_RNA|KRTAP5-AS1_ENST00000424148.1_RNA|KRTAP5-AS1_ENST00000534077.1_RNA|KRTAP5-AS1_ENST00000524947.1_RNA	NM_001004325.1	NP_001004325.1	Q701N4	KRA52_HUMAN	keratin associated protein 5-2	83	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)		CCCTTGGAGCCCCCACAGGAG	0.662																																					p.G83S		Atlas-SNP	.											.	KRTAP5-2	38	.	0			c.G247A						PASS	.						60	83	75					11																	1619234		2202	4297	6499	SO:0001583	missense	440021	exon1			TGGAGCCCCCACA	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.247G>A	11.37:g.1619234C>T	ENSP00000400041:p.Gly83Ser	118	0	0		102	19	0.186275	NM_001004325	A9JTZ1	Missense_Mutation	SNP	ENST00000412090.1	37	CCDS31331.1	.	.	.	.	.	.	.	.	.	.	c	13.71	2.319352	0.41096	.	.	ENSG00000205867	ENST00000412090	T	0.00864	5.6	3.88	2.92	0.33932	.	.	.	.	.	T	0.00967	0.0032	L	0.33189	0.99	0.24258	N	0.995291	P	0.51791	0.948	B	0.41332	0.354	T	0.56360	-0.7992	9	0.23891	T	0.37	.	8.6816	0.34212	0.2552:0.7448:0.0:0.0	.	83	Q701N4	KRA52_HUMAN	S	83	ENSP00000400041:G83S	ENSP00000400041:G83S	G	-	1	0	KRTAP5-2	1575810	0.042000	0.20092	0.984000	0.44739	0.843000	0.47879	0.460000	0.21924	0.712000	0.32039	0.447000	0.29281	GGC	.	.	none		0.662	KRTAP5-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384775.1	NM_001004325		T	1619234	C	T	1619234	3	4	4	1	0	0	0	0	1	0	0	0	8570	623	22	2	290	2	KRTAP5-2	11	1619234	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10		1619234	133387282	119	459											
KRTAP5-3	387266	hgsc.bcm.edu	37	chr11	1629430	1629431	+	Frame_Shift_Ins	INS	-	-	C																															agccacagacccccttggagINScccccacaggagccacagct																										TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr11:1629430_1629431insC	ENST00000399685.1	-	1	262_263	c.185_186insG	c.(184-186)ggcfs	p.G62fs		NM_001012708.2	NP_001012726.1	Q6L8H2	KRA53_HUMAN	keratin associated protein 5-3	62	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)		CCCCCTTGGAGCCCCCACAGGA	0.678																																					p.G62fs		Atlas-Indel	.											.	KRTAP5-3	33	.	0			c.186_187insG						PASS	.																																			SO:0001589	frameshift_variant	387266	exon1			.	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.186dupG	11.37:g.1629435_1629435dupC	ENSP00000382592:p.Gly62fs	199	0	0		136	25	0.183824	NM_001012708	Q6PL44|Q701N3	Frame_Shift_Ins	INS	ENST00000399685.1	37	CCDS41591.1																																																																																			.	.	none		0.678	KRTAP5-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127924.1			C	1629431	-	C	1629430	7	5	4	1	0	1	1	0	0	0	0	0	8571	958	34	0	534	0	KRTAP5-3	11	1629430	Frame_Shift_Ins	INS	-	TCGA-FA-A6HN-01A-11D-A31X-10	10196	1629430	133377086	120	460											
OR51G2	81282	hgsc.bcm.edu	37	chr11	4936072	4936072	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atgaccacctggaccaggtgGggtgcctgctttccaaagcg	8	8	13	12	1	0	1	0	1	0	0	1	2	1	2	5	4	3	1	5	4	1	1	rs199760109		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr11:4936072G>A	ENST00000322013.3	-	1	850	c.822C>T	c.(820-822)ccC>ccT	p.P274P	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	274						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)		GGACCAGGTGGGGTGCCTGCT	0.512													G|||	1	0.000199681	0.0	0.0	5008	,	,		21041	0.001		0.0	False		,,,				2504	0.0				p.P274P		Atlas-SNP	.											.	OR51G2	70	.	0			c.C822T						PASS	.						111	100	104					11																	4936072		2201	4298	6499	SO:0001819	synonymous_variant	81282	exon1			CAGGTGGGGTGCC	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.822C>T	11.37:g.4936072G>A		83	0	0		79	22	0.278481	NM_001005238	Q6IFH7	Silent	SNP	ENST00000322013.3	37	CCDS31365.1																																																																																			G|1.000;A|0.000	0.000	strong		0.512	OR51G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142174.1	NM_001005238		A	4936072	G	A	4936072	2	1	4	1	0	0	0	0	0	0	0	1	11108	1219	43	2		2	OR51G2	11	4936072	Silent	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	3306642	4936072	130070444	121	461											
OR51M1	390059	hgsc.bcm.edu	37	chr11	5410941	5410941	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtttaactcccatagtatcTactttggagcgtgtcaaatc	10	14	8	9	1	2	0	1	0	1	0	4	1	3	1	1	2	3	2	1	2	5	6			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr11:5410941T>C	ENST00000328611.3	+	1	335	c.313T>C	c.(313-315)Tac>Cac	p.Y105H	AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001004756.2	NP_001004756.2	Q9H341	O51M1_HUMAN	olfactory receptor, family 51, subfamily M, member 1	105					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(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|upper_aerodigestive_tract(1)	30		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.98e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCATAGTATCTACTTTGGAGC	0.502																																					p.Y105H		Atlas-SNP	.											.	OR51M1	60	.	0			c.T313C						PASS	.						195	184	188					11																	5410941		2001	4189	6190	SO:0001583	missense	390059	exon1			AGTATCTACTTTG	BK004382	CCDS53596.1	11p15.4	2012-08-09			ENSG00000184698	ENSG00000184698		"GPCR / Class A : Olfactory receptors"	14847	protein-coding gene	gene with protein product							Standard	NM_001004756		Approved		uc010qzc.2	Q9H341	OTTHUMG00000066680	ENST00000328611.3:c.313T>C	11.37:g.5410941T>C	ENSP00000333196:p.Tyr105His	53	0	0		41	8	0.195122	NM_001004756	Q6IF80	Missense_Mutation	SNP	ENST00000328611.3	37	CCDS53596.1	.	.	.	.	.	.	.	.	.	.	T	5.448	0.267790	0.10349	.	.	ENSG00000184698	ENST00000328611	T	0.37411	1.2	5.15	2.72	0.32119	GPCR, rhodopsin-like superfamily (1);	0.269998	0.19621	U	0.109920	T	0.24236	0.0587	L	0.35542	1.07	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.18366	-1.0339	10	0.66056	D	0.02	.	5.5623	0.17150	0.1898:0.0899:0.0:0.7204	.	94	Q9H341	O51M1_HUMAN	H	105	ENSP00000333196:Y105H	ENSP00000333196:Y105H	Y	+	1	0	OR51M1	5367517	0.000000	0.05858	0.767000	0.31495	0.054000	0.15201	-0.695000	0.05109	0.995000	0.38917	0.528000	0.53228	TAC	.	.	none		0.502	OR51M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142981.1	NM_001004756		C	5410941	T	C	5410941	3	2	4	1	0	0	0	0	1	0	0	0	11112	1522	53	3	315	3	OR51M1	11	5410941	Missense_Mutation	SNP	T	TCGA-FA-A6HN-01A-11D-A31X-10	474869	5410941	129595575	122	462											
PIK3C2A	5286	hgsc.bcm.edu	37	chr11	17167456	17167456	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctatttgatacaggtgttTgtttaaatccacgggtgttt	8	19	9	5	1	1	1	0	1	1	0	2	1	2	1	1	2	1	3	1	2	4	8			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr11:17167456T>G	ENST00000265970.7	-	6	1593	c.1594A>C	c.(1594-1596)Aaa>Caa	p.K532Q	PIK3C2A_ENST00000540361.1_Missense_Mutation_p.K152Q|PIK3C2A_ENST00000531428.1_Intron	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	532					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						TACAGGTGTTTGTTTAAATCC	0.333																																					p.K532Q		Atlas-SNP	.											.	PIK3C2A	148	.	0			c.A1594C						PASS	.						133	141	138					11																	17167456		2200	4293	6493	SO:0001583	missense	5286	exon6			GGTGTTTGTTTAA	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.1594A>C	11.37:g.17167456T>G	ENSP00000265970:p.Lys532Gln	83	0	0		75	15	0.2	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	37	CCDS7824.1	.	.	.	.	.	.	.	.	.	.	T	16.35	3.099125	0.56183	.	.	ENSG00000011405	ENST00000265970;ENST00000540361;ENST00000544896	T;T	0.63744	-0.06;0.37	5.32	5.32	0.75619	.	0.091731	0.64402	D	0.000001	T	0.75213	0.3819	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.994	T	0.71368	-0.4614	10	0.14656	T	0.56	-12.0604	15.5669	0.76300	0.0:0.0:0.0:1.0	.	532;532	F5H5W9;O00443	.;P3C2A_HUMAN	Q	532;152;532	ENSP00000265970:K532Q;ENSP00000438687:K152Q	ENSP00000265970:K532Q	K	-	1	0	PIK3C2A	17124032	1.000000	0.71417	0.997000	0.53966	0.601000	0.36947	5.361000	0.66092	2.140000	0.66376	0.482000	0.46254	AAA	.	.	none		0.333	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		G	17167456	T	G	17167456	3	3	4	1	0	0	0	0	1	0	0	0	11918	1821	63	5	3574	5	PIK3C2A	11	17167456	Missense_Mutation	SNP	T	TCGA-FA-A6HN-01A-11D-A31X-10	11756515	17167456	117839060	123	463											
TMEM132A	54972	hgsc.bcm.edu	37	chr11	60699343	60699343	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgggacatcagagcccttaTcccactggccaaggtaagga	11	6	12	12	1	1	1	1	0	0	1	2	3	2	3	3	4	1	1	3	4	3	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr11:60699343T>C	ENST00000453848.2	+	6	1357	c.1199T>C	c.(1198-1200)aTc>aCc	p.I400T	TMEM132A_ENST00000005286.4_Missense_Mutation_p.I401T			Q24JP5	T132A_HUMAN	transmembrane protein 132A	400						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						AGAGCCCTTATCCCACTGGCC	0.622																																					p.I401T		Atlas-SNP	.											.	TMEM132A	135	.	0			c.T1202C						PASS	.						78	79	79					11																	60699343		2203	4299	6502	SO:0001583	missense	54972	exon6			CCCTTATCCCACT	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.1199T>C	11.37:g.60699343T>C	ENSP00000405823:p.Ile400Thr	137	0	0		104	20	0.192308	NM_017870	Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Missense_Mutation	SNP	ENST00000453848.2	37	CCDS44618.1	.	.	.	.	.	.	.	.	.	.	T	13.06	2.125456	0.37533	.	.	ENSG00000006118	ENST00000444690;ENST00000453848;ENST00000005286	T;T	0.16457	2.34;2.34	4.61	4.61	0.57282	.	0.392434	0.20638	N	0.088449	T	0.15478	0.0373	L	0.42245	1.32	0.32827	D	0.503569	B;P;B;B	0.35272	0.417;0.493;0.277;0.277	B;B;B;B	0.28011	0.085;0.085;0.053;0.053	T	0.19910	-1.0291	10	0.87932	D	0	.	14.0171	0.64531	0.0:0.0:0.0:1.0	.	389;151;400;401	Q24JP5-3;Q24JP5-4;Q24JP5;Q24JP5-2	.;.;T132A_HUMAN;.	T	151;400;401	ENSP00000405823:I400T;ENSP00000005286:I401T	ENSP00000005286:I401T	I	+	2	0	TMEM132A	60455919	0.622000	0.27085	0.808000	0.32385	0.726000	0.41606	3.959000	0.56744	1.859000	0.53934	0.374000	0.22700	ATC	.	.	none		0.622	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870		C	60699343	T	C	60699343	3	2	4	1	0	0	0	0	1	0	0	0	16060	1435	50	3	1224	3	TMEM132A	11	60699343	Missense_Mutation	SNP	T	TCGA-FA-A6HN-01A-11D-A31X-10	43531887	60699343	74307173	124	464											
EHD1	10938	hgsc.bcm.edu	37	chr11	64645661	64645661	+	Frame_Shift_Del	DEL	G	G	-																															gcgatgaaggagtcggtggtGggctcgggcccgatgcgcat																										TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr11:64645661delG	ENST00000320631.3	-	1	530	c.276delC	c.(274-276)cccfs	p.P92fs	EHD1_ENST00000359393.2_Frame_Shift_Del_p.P92fs	NM_001282445.1|NM_006795.2	NP_001269374.1|NP_006786.2	Q9H4M9	EHD1_HUMAN	EH-domain containing 1	92	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						AGTCGGTGGTGGGCTCGGGCC	0.682																																					p.T93fs		Atlas-Indel	.											.	EHD1	31	.	0			c.277delA						PASS	.						98	76	83					11																	64645661		2201	4297	6498	SO:0001589	frameshift_variant	10938	exon1			.	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.276delC	11.37:g.64645661delG	ENSP00000320516:p.Pro92fs	82	0	0		67	12	0.179104	NM_006795	O14611|Q2M3Q4|Q9UNR3	Frame_Shift_Del	DEL	ENST00000320631.3	37	CCDS8084.1																																																																																			.	.	none		0.682	EHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143229.2	NM_006795		-	64645661	G	-	64645661	7	5	4	1	0	1	0	1	0	0	0	0	4979	1335	47	0	1348	0	EHD1	11	64645661	Frame_Shift_Del	DEL	G	TCGA-FA-A6HN-01A-11D-A31X-10	3946318	64645661	70360855	125	465											
SIPA1	6494	hgsc.bcm.edu	37	chr11	65416900	65416900	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tccagggcctggggatctggCcgaggagaggactgagttcc	7	7	17	10	1	1	2	0	1	1	1	3	6	3	4	4	6	0	1	4	6	0	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr11:65416900C>T	ENST00000394224.3	+	10	2770	c.2474C>T	c.(2473-2475)gCc>gTc	p.A825V	MIR4489_ENST00000578869.1_RNA|SIPA1_ENST00000527525.1_Missense_Mutation_p.A723V|SIPA1_ENST00000534313.1_Missense_Mutation_p.A825V|SIPA1_ENST00000394227.3_Missense_Mutation_p.A723V	NM_153253.29	NP_694985.29	Q96FS4	SIPA1_HUMAN	signal-induced proliferation-associated 1	825					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						GGGGATCTGGCCGAGGAGAGG	0.637																																					p.A825V		Atlas-SNP	.											.	SIPA1	45	.	0			c.C2474T						PASS	.						41	36	38					11																	65416900		2197	4292	6489	SO:0001583	missense	6494	exon10			ATCTGGCCGAGGA	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.2474C>T	11.37:g.65416900C>T	ENSP00000377771:p.Ala825Val	78	0	0		59	12	0.20339	NM_006747	O14518|O60484|O60618|Q2YD83	Missense_Mutation	SNP	ENST00000394224.3	37	CCDS8108.1	.	.	.	.	.	.	.	.	.	.	C	15.08	2.728042	0.48833	.	.	ENSG00000213445	ENST00000534313;ENST00000527525;ENST00000394224;ENST00000394227	D;D;D;D	0.82344	-1.6;-1.59;-1.6;-1.59	4.77	3.86	0.44501	.	1.724340	0.04463	N	0.374696	T	0.75583	0.3869	L	0.27053	0.805	0.09310	N	0.999998	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.59375	-0.7466	10	0.33940	T	0.23	-1.6822	9.3108	0.37903	0.0:0.899:0.0:0.101	.	723;825	F6RY50;Q96FS4	.;SIPA1_HUMAN	V	825;723;825;723	ENSP00000436269:A825V;ENSP00000433686:A723V;ENSP00000377771:A825V;ENSP00000377774:A723V	ENSP00000377771:A825V	A	+	2	0	SIPA1	65173476	0.672000	0.27530	0.445000	0.26908	0.419000	0.31324	1.953000	0.40352	1.152000	0.42452	0.462000	0.41574	GCC	.	.	none		0.637	SIPA1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390356.1	NM_006747		T	65416900	C	T	65416900	3	4	4	1	0	0	0	0	1	0	0	0	14343	739	26	2	2508	2	SIPA1	11	65416900	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	771239	65416900	69589616	126	466											
TMEM135	65084	hgsc.bcm.edu	37	chr11	87024484	87024484	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagggtactagttgcttcctGcgctggatcagaaacttaga	10	12	11	8	1	1	2	1	0	0	2	2	3	2	3	1	2	4	4	1	2	5	6			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr11:87024484G>A	ENST00000305494.5	+	11	993	c.954G>A	c.(952-954)ctG>ctA	p.L318L	TMEM135_ENST00000532959.1_Silent_p.L189L|TMEM135_ENST00000535167.1_Silent_p.L179L|TMEM135_ENST00000340353.7_Silent_p.L296L	NM_022918.3	NP_075069.3	Q86UB9	TM135_HUMAN	transmembrane protein 135	318					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)				GTTGCTTCCTGCGCTGGATCA	0.289																																					p.L318L		Atlas-SNP	.											.	TMEM135	40	.	0			c.G954A						PASS	.						94	97	96					11																	87024484		2201	4297	6498	SO:0001819	synonymous_variant	65084	exon11			CTTCCTGCGCTGG	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.954G>A	11.37:g.87024484G>A		260	0	0		227	46	0.202643	NM_022918	Q6AW91|Q8ND01|Q9H6M3	Silent	SNP	ENST00000305494.5	37	CCDS8280.1																																																																																			.	.	none		0.289	TMEM135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393875.1	NM_022918		A	87024484	G	A	87024484	2	1	4	1	0	0	0	0	0	0	0	1	16066	1306	46	2		2	TMEM135	11	87024484	Silent	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	21607584	87024484	47982032	127	467											
TMEM135	65084	hgsc.bcm.edu	37	chr11	87024503	87024503	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgcgctggatcagaaacttaGatgatgaactacatgctatt	13	12	9	7	1	1	4	1	2	0	2	1	5	1	5	0	1	5	2	0	1	5	4			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr11:87024503G>A	ENST00000305494.5	+	11	1012	c.973G>A	c.(973-975)Gat>Aat	p.D325N	TMEM135_ENST00000532959.1_Missense_Mutation_p.D196N|TMEM135_ENST00000535167.1_Missense_Mutation_p.D186N|TMEM135_ENST00000340353.7_Missense_Mutation_p.D303N	NM_022918.3	NP_075069.3	Q86UB9	TM135_HUMAN	transmembrane protein 135	325					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)				CAGAAACTTAGATGATGAACT	0.308																																					p.D325N		Atlas-SNP	.											.	TMEM135	40	.	0			c.G973A						PASS	.						91	96	94					11																	87024503		2201	4297	6498	SO:0001583	missense	65084	exon11			AACTTAGATGATG	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.973G>A	11.37:g.87024503G>A	ENSP00000306344:p.Asp325Asn	265	0	0		231	41	0.177489	NM_022918	Q6AW91|Q8ND01|Q9H6M3	Missense_Mutation	SNP	ENST00000305494.5	37	CCDS8280.1	.	.	.	.	.	.	.	.	.	.	G	33	5.224353	0.95139	.	.	ENSG00000166575	ENST00000340353;ENST00000544294;ENST00000532959;ENST00000305494;ENST00000535167	T;T;T;T	0.57752	0.38;0.38;0.38;0.38	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.72795	0.3505	M	0.73598	2.24	0.80722	D	1	P;D	0.76494	0.663;0.999	B;D	0.73380	0.321;0.98	T	0.72769	-0.4193	9	.	.	.	-30.6207	18.3398	0.90302	0.0:0.0:1.0:0.0	.	303;325	Q86UB9-2;Q86UB9	.;TM135_HUMAN	N	303;162;196;325;186	ENSP00000345513:D303N;ENSP00000436179:D196N;ENSP00000306344:D325N;ENSP00000439525:D186N	.	D	+	1	0	TMEM135	86702151	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.066000	0.93949	2.579000	0.87056	0.655000	0.94253	GAT	.	.	none		0.308	TMEM135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393875.1	NM_022918		A	87024503	G	A	87024503	3	1	4	1	0	0	0	0	1	0	0	0	16066	942	33	2	1015	2	TMEM135	11	87024503	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	19	87024503	47982013	128	468											
NOX4	50507	hgsc.bcm.edu	37	chr11	89059934	89059934	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaaaagttttcagctgaaaGactctttattgtattcaaat	14	15	6	6	0	3	2	2	1	1	1	3	2	3	2	0	0	1	4	0	0	6	7			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr11:89059934G>T	ENST00000263317.4	-	18	1965	c.1727C>A	c.(1726-1728)tCt>tAt	p.S576Y	NOX4_ENST00000527626.1_Missense_Mutation_p.S389Y|NOX4_ENST00000413594.2_Missense_Mutation_p.S597Y|NOX4_ENST00000375979.3_Missense_Mutation_p.S269Y|NOX4_ENST00000532825.1_Missense_Mutation_p.S512Y|NOX4_ENST00000424319.1_Missense_Mutation_p.S552Y|NOX4_ENST00000531342.1_Missense_Mutation_p.S229Y|NOX4_ENST00000527956.1_Missense_Mutation_p.S552Y|NOX4_ENST00000343727.5_Missense_Mutation_p.S552Y|NOX4_ENST00000542487.1_Missense_Mutation_p.S552Y|NOX4_ENST00000535633.1_Missense_Mutation_p.S552Y|NOX4_ENST00000534731.1_Missense_Mutation_p.S536Y|NOX4_ENST00000525196.1_Missense_Mutation_p.S340Y|NOX4_ENST00000528341.1_Missense_Mutation_p.S551Y			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4	576					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)				TCAGCTGAAAGACTCTTTATT	0.383																																					p.S576Y		Atlas-SNP	.											.	NOX4	101	.	0			c.C1727A						PASS	.						93	94	93					11																	89059934		2201	4299	6500	SO:0001583	missense	50507	exon18			CTGAAAGACTCTT	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.1727C>A	11.37:g.89059934G>T	ENSP00000263317:p.Ser576Tyr	128	0	0		101	21	0.207921	NM_016931	A8K715|B7Z520|E7EMD7|Q5K3R4|Q5K3R5|Q5K3R6|Q5K3R8|Q7Z7G3|Q86V92	Missense_Mutation	SNP	ENST00000263317.4	37	CCDS8285.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.774968	0.49786	.	.	ENSG00000086991	ENST00000424319;ENST00000535633;ENST00000343727;ENST00000534731;ENST00000525196;ENST00000263317;ENST00000532825;ENST00000527956;ENST00000542487;ENST00000527626;ENST00000528341;ENST00000413594;ENST00000531342;ENST00000375979	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.95377	-3.64;-3.64;-3.64;-3.6;-3.63;-3.56;-3.69;-3.64;-3.64;-3.41;-3.61;-3.67;-3.05;-3.0	4.1	4.1	0.47936	.	0.067280	0.64402	D	0.000010	D	0.95778	0.8626	L	0.31845	0.965	0.49798	D	0.999821	B;P;D;D;D;D;D;B	0.76494	0.367;0.885;0.999;0.999;0.997;0.998;0.968;0.242	B;P;D;D;D;D;P;B	0.78314	0.097;0.513;0.979;0.988;0.991;0.935;0.693;0.186	D	0.95144	0.8266	9	.	.	.	-10.1463	16.6923	0.85325	0.0:0.0:1.0:0.0	.	512;389;551;340;229;269;536;576	E9PMY6;E9PR43;E9PPP2;E9PI95;Q9NPH5-3;Q9NPH5-4;Q9NPH5-6;Q9NPH5	.;.;.;.;.;.;.;NOX4_HUMAN	Y	552;552;552;536;340;576;512;552;552;389;551;597;229;269	ENSP00000412446:S552Y;ENSP00000440172:S552Y;ENSP00000344747:S552Y;ENSP00000436892:S536Y;ENSP00000436716:S340Y;ENSP00000263317:S576Y;ENSP00000434924:S512Y;ENSP00000433797:S552Y;ENSP00000439373:S552Y;ENSP00000436093:S389Y;ENSP00000436970:S551Y;ENSP00000405705:S597Y;ENSP00000435039:S229Y;ENSP00000365146:S269Y	.	S	-	2	0	NOX4	88699582	1.000000	0.71417	1.000000	0.80357	0.510000	0.34073	8.051000	0.89446	1.991000	0.58162	0.467000	0.42956	TCT	.	.	none		0.383	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	NM_016931		T	89059934	G	T	89059934	3	4	4	1	0	0	0	0	1	0	0	0	10567	942	33	4	13	4	NOX4	11	89059934	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	2035431	89059934	45946582	129	469											
NOX4	50507	hgsc.bcm.edu	37	chr11	89069055	89069055	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	catcaaacaaaagtttccacCgaggacgtcctataaacagt	16	8	6	11	2	1	0	1	0	0	0	3	2	3	1	3	1	2	1	3	1	6	3	rs147166939		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr11:89069055C>A	ENST00000263317.4	-	17	1812	c.1574G>T	c.(1573-1575)cGg>cTg	p.R525L	NOX4_ENST00000527626.1_Missense_Mutation_p.R338L|NOX4_ENST00000413594.2_Missense_Mutation_p.R546L|NOX4_ENST00000375979.3_Missense_Mutation_p.R218L|NOX4_ENST00000532825.1_Missense_Mutation_p.R461L|NOX4_ENST00000424319.1_Missense_Mutation_p.R501L|NOX4_ENST00000531342.1_Missense_Mutation_p.R178L|NOX4_ENST00000527956.1_Missense_Mutation_p.R501L|NOX4_ENST00000343727.5_Missense_Mutation_p.R501L|NOX4_ENST00000542487.1_Missense_Mutation_p.R501L|NOX4_ENST00000535633.1_Missense_Mutation_p.R501L|NOX4_ENST00000534731.1_Missense_Mutation_p.R485L|NOX4_ENST00000525196.1_Missense_Mutation_p.R289L|NOX4_ENST00000528341.1_Missense_Mutation_p.R500L			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4	525	Mediates interaction with TLR4.				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)				AAGTTTCCACCGAGGACGTCC	0.294																																					p.R525L		Atlas-SNP	.											NOX4,colon,carcinoma,0,1	NOX4	101	1	0			c.G1574T						PASS	.						71	72	72					11																	89069055		2201	4296	6497	SO:0001583	missense	50507	exon17			TTCCACCGAGGAC	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.1574G>T	11.37:g.89069055C>A	ENSP00000263317:p.Arg525Leu	523	0	0		445	92	0.206742	NM_016931	A8K715|B7Z520|E7EMD7|Q5K3R4|Q5K3R5|Q5K3R6|Q5K3R8|Q7Z7G3|Q86V92	Missense_Mutation	SNP	ENST00000263317.4	37	CCDS8285.1	.	.	.	.	.	.	.	.	.	.	C	16.56	3.156311	0.57259	.	.	ENSG00000086991	ENST00000424319;ENST00000535633;ENST00000343727;ENST00000534731;ENST00000525196;ENST00000263317;ENST00000532825;ENST00000527956;ENST00000542487;ENST00000527626;ENST00000528341;ENST00000413594;ENST00000531342;ENST00000375979	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.94931	-3.56;-3.56;-3.56;-3.56;-3.56;-3.56;-3.56;-3.56;-3.56;-3.56;-3.56;-3.56;-3.56;-3.56	4.33	1.36	0.22044	Ferric reductase, NAD binding (1);	0.394426	0.27323	N	0.019884	D	0.92688	0.7676	L	0.33485	1.01	0.35831	D	0.825349	B;P;P;D;B;P;B;B	0.63880	0.091;0.51;0.655;0.993;0.065;0.807;0.186;0.16	B;B;P;P;B;B;B;B	0.58820	0.112;0.319;0.559;0.846;0.045;0.242;0.127;0.112	D	0.90439	0.4430	9	.	.	.	-2.1831	7.9501	0.30010	0.0:0.6701:0.0:0.3299	.	461;338;500;289;178;218;485;525	E9PMY6;E9PR43;E9PPP2;E9PI95;Q9NPH5-3;Q9NPH5-4;Q9NPH5-6;Q9NPH5	.;.;.;.;.;.;.;NOX4_HUMAN	L	501;501;501;485;289;525;461;501;501;338;500;546;178;218	ENSP00000412446:R501L;ENSP00000440172:R501L;ENSP00000344747:R501L;ENSP00000436892:R485L;ENSP00000436716:R289L;ENSP00000263317:R525L;ENSP00000434924:R461L;ENSP00000433797:R501L;ENSP00000439373:R501L;ENSP00000436093:R338L;ENSP00000436970:R500L;ENSP00000405705:R546L;ENSP00000435039:R178L;ENSP00000365146:R218L	.	R	-	2	0	NOX4	88708703	0.001000	0.12720	0.994000	0.49952	0.974000	0.67602	-0.169000	0.09911	0.067000	0.16545	0.563000	0.77884	CGG	C|1.000;T|0.000	.	alt		0.294	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	NM_016931		A	89069055	C	A	89069055	3	1	4	1	0	0	0	0	1	0	0	0	10567	652	23	4	170	4	NOX4	11	89069055	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	9121	89069055	45937461	130	470											
FUT4	2526	hgsc.bcm.edu	37	chr11	94278849	94278849	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtacagagggctggggaccGgcccaagagcatacggaact	11	5	15	10	2	0	2	0	0	0	2	0	4	0	4	2	5	4	3	2	5	4	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr11:94278849G>A	ENST00000358752.2	+	1	1833	c.1550G>A	c.(1549-1551)cGg>cAg	p.R517Q	RP11-867G2.8_ENST00000536540.1_RNA|RP11-867G2.8_ENST00000537874.1_RNA	NM_002033.3	NP_002024.1	P22083	FUT4_HUMAN	fucosyltransferase 4 (alpha (1,3) fucosyltransferase, myeloid-specific)	517					carbohydrate metabolic process (GO:0005975)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	cell periphery (GO:0071944)|cell surface (GO:0009986)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			central_nervous_system(2)|endometrium(2)|lung(1)|skin(2)|upper_aerodigestive_tract(1)	8		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GCTGGGGACCGGCCCAAGAGC	0.637																																					p.R517Q		Atlas-SNP	.											.	FUT4	17	.	0			c.G1550A						PASS	.						21	22	21					11																	94278849		2201	4298	6499	SO:0001583	missense	2526	exon1			GGGACCGGCCCAA		CCDS8301.1	11q21	2013-02-26			ENSG00000196371	ENSG00000196371		"CD molecules", "Fucosyltransferases"	4015	protein-coding gene	gene with protein product	"ELAM ligand fucosyltransferase", "galactoside 3-L-fucosyltransferase"	104230		CD15, FCT3A, ELFT		1702034	Standard	NM_002033		Approved	FUC-TIV	uc001pez.3	P22083	OTTHUMG00000167795	ENST00000358752.2:c.1550G>A	11.37:g.94278849G>A	ENSP00000351602:p.Arg517Gln	39	0	0		32	7	0.21875	NM_002033	B2RMS0	Missense_Mutation	SNP	ENST00000358752.2	37	CCDS8301.1	.	.	.	.	.	.	.	.	.	.	g	11.46	1.646077	0.29246	.	.	ENSG00000196371	ENST00000358752	T	0.23552	1.9	5.18	-4.55	0.03441	.	0.420286	0.20265	N	0.095800	T	0.08447	0.0210	N	0.05230	-0.09	0.09310	N	1	B	0.14438	0.01	B	0.15052	0.012	T	0.35699	-0.9778	10	0.06891	T	0.86	.	10.9392	0.47264	0.7511:0.0:0.1487:0.1002	.	517	P22083	FUT4_HUMAN	Q	517	ENSP00000351602:R517Q	ENSP00000351602:R517Q	R	+	2	0	FUT4	93918497	0.000000	0.05858	0.000000	0.03702	0.909000	0.53808	0.063000	0.14410	-0.920000	0.03799	-0.254000	0.11334	CGG	.	.	none		0.637	FUT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396327.2	NM_002033		A	94278849	G	A	94278849	3	1	4	1	0	0	0	0	1	0	0	0	6114	1116	39	1	1552	1	FUT4	11	94278849	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	5209794	94278849	40727667	131	471											
ALG9	79796	hgsc.bcm.edu	37	chr11	111657183	111657183	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttgaggatggtgtagtttaCgtacactgtatactgatctg	9	16	11	5	1	1	2	0	2	1	0	1	3	1	3	0	2	3	4	0	2	5	7			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr11:111657183C>T	ENST00000531154.1	-	15	1754	c.1282G>A	c.(1282-1284)Gta>Ata	p.V428I	ALG9_ENST00000527228.1_5'UTR|ALG9_ENST00000398006.2_Missense_Mutation_p.V421I|ALG9_ENST00000524880.1_3'UTR	NM_024740.2	NP_079016.2	Q9H6U8	ALG9_HUMAN	ALG9, alpha-1,2-mannosyltransferase	592					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)		GTGTAGTTTACGTACACTGTA	0.428																																					p.V599I		Atlas-SNP	.											.	ALG9	77	.	0			c.G1795A						PASS	.						255	237	243					11																	111657183		1907	4122	6029	SO:0001583	missense	79796	exon16			AGTTTACGTACAC		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	ENST00000531154.1:c.1282G>A	11.37:g.111657183C>T	ENSP00000435517:p.Val428Ile	110	0	0		120	5	0.0416667	NM_024740	Q6ZMD5|Q7Z4R4|Q96GS7|Q96PB9|Q9H068	Missense_Mutation	SNP	ENST00000531154.1	37	CCDS41714.1	.	.	.	.	.	.	.	.	.	.	C	12.87	2.067398	0.36470	.	.	ENSG00000086848	ENST00000531154;ENST00000398006;ENST00000428306	T;T	0.14022	2.54;2.54	5.76	4.84	0.62591	.	0.396088	0.27754	N	0.017992	T	0.08582	0.0213	N	0.20986	0.625	0.24575	N	0.9939	B;B	0.13145	0.007;0.004	B;B	0.12837	0.008;0.003	T	0.18745	-1.0327	10	0.27785	T	0.31	-2.7151	7.7102	0.28673	0.0:0.7489:0.166:0.0851	.	599;592	Q9H6U8-3;Q9H6U8	.;ALG9_HUMAN	I	428;421;825	ENSP00000435517:V428I;ENSP00000381090:V421I	ENSP00000381090:V421I	V	-	1	0	ALG9	111162393	0.947000	0.32204	1.000000	0.80357	0.433000	0.31745	0.805000	0.27112	2.882000	0.98803	0.655000	0.94253	GTA	.	.	none		0.428	ALG9-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000391485.1	NM_024740		T	111657183	C	T	111657183	3	4	4	1	0	0	0	0	1	0	0	0	524	536	19	1	65	1	ALG9	11	111657183	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	17378334	111657183	23349333	132	472											
CCND2	894	hgsc.bcm.edu	37	chr12	4383364	4383364	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cgtgcagaaggacatccaacCctacatgcgcagaatggtgg	12	6	12	11	2	0	2	0	0	0	2	1	3	1	3	2	3	4	2	2	3	4	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr12:4383364C>T	ENST00000261254.3	+	1	427	c.158C>T	c.(157-159)cCc>cTc	p.P53L	RP11-264F23.3_ENST00000539135.1_RNA|RP11-264F23.4_ENST00000537370.1_RNA	NM_001759.3	NP_001750.1	P30279	CCND2_HUMAN	cyclin D2	53	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)			GACATCCAACCCTACATGCGC	0.657			T	IGL@	"NHL,CLL"																																p.P53L		Atlas-SNP	.		Dom	yes		12	12p13	894	cyclin D2		L	.	CCND2	50	.	0			c.C158T						PASS	.						103	91	95					12																	4383364		2203	4300	6503	SO:0001583	missense	894	exon1			TCCAACCCTACAT	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.158C>T	12.37:g.4383364C>T	ENSP00000261254:p.Pro53Leu	194	0	0		177	26	0.146893	NM_001759	A8K531|Q13955|Q5U035	Missense_Mutation	SNP	ENST00000261254.3	37	CCDS8524.1	.	.	.	.	.	.	.	.	.	.	C	18.25	3.582352	0.65992	.	.	ENSG00000118971	ENST00000261254	T	0.12039	2.72	4.17	4.17	0.49024	Cyclin, N-terminal (1);Cyclin-like (2);	0.000000	0.85682	D	0.000000	T	0.22936	0.0554	M	0.64997	1.995	0.80722	D	1	P	0.41232	0.743	P	0.46419	0.516	T	0.02269	-1.1185	10	0.87932	D	0	.	13.7742	0.63044	0.0:1.0:0.0:0.0	.	53	P30279	CCND2_HUMAN	L	53	ENSP00000261254:P53L	ENSP00000261254:P53L	P	+	2	0	CCND2	4253625	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.232000	0.78116	2.127000	0.65507	0.491000	0.48974	CCC	.	.	none		0.657	CCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398287.1	NM_001759		T	4383364	C	T	4383364	3	4	4	1	0	0	0	0	1	0	0	0	2919	623	22	2	160	2	CCND2	12	4383364	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10		4383364	129468531	133	473											
PTPN6	5777	hgsc.bcm.edu	37	chr12	7061240	7061240	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ttgcgactctgacagagctgGtggagtactacactcagcag	10	9	12	10	1	2	2	1	1	1	1	2	4	2	3	0	2	5	3	0	2	2	3			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr12:7061240G>C	ENST00000318974.9	+	3	470	c.226G>C	c.(226-228)Gtg>Ctg	p.V76L	PTPN6_ENST00000456013.1_Missense_Mutation_p.V76L|PTPN6_ENST00000399448.1_Missense_Mutation_p.V78L|PTPN6_ENST00000447931.2_Missense_Mutation_p.V37L	NM_002831.5	NP_002822.2	P29350	PTN6_HUMAN	protein tyrosine phosphatase, non-receptor type 6	76	SH2 1. {ECO:0000255|PROSITE- ProRule:PRU00191}.				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						GACAGAGCTGGTGGAGTACTA	0.567																																					p.V78L		Atlas-SNP	.											.	PTPN6	42	.	0			c.G232C						PASS	.						106	124	118					12																	7061240		2201	4298	6499	SO:0001583	missense	5777	exon3			GAGCTGGTGGAGT		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.226G>C	12.37:g.7061240G>C	ENSP00000326010:p.Val76Leu	112	0	0		83	11	0.13253	NM_080548	A8K306|G3V0F8|Q969V8|Q9UK67	Missense_Mutation	SNP	ENST00000318974.9	37	CCDS44820.1	.	.	.	.	.	.	.	.	.	.	G	34	5.389101	0.95988	.	.	ENSG00000111679	ENST00000543115;ENST00000399448;ENST00000447931;ENST00000538715;ENST00000318974;ENST00000456013;ENST00000536521;ENST00000541698;ENST00000542462	D;D;D;D;D;D;D;D;D	0.97752	-4.52;-4.52;-4.52;-4.52;-4.52;-4.52;-4.52;-4.52;-4.52	4.86	4.86	0.63082	SH2 motif (5);	0.000000	0.64402	D	0.000001	D	0.98457	0.9486	M	0.82323	2.585	0.80722	D	1	D;P;P;P;D	0.63880	0.993;0.94;0.885;0.906;0.957	P;P;P;P;P	0.59056	0.755;0.65;0.67;0.778;0.851	D	0.99133	1.0853	10	0.54805	T	0.06	.	18.0136	0.89232	0.0:0.0:1.0:0.0	.	64;37;76;76;78	B4DPS0;P29350-2;G3V0F8;P29350;Q53XS4	.;.;.;PTN6_HUMAN;.	L	97;78;37;76;76;76;76;76;35	ENSP00000443393:V97L;ENSP00000382376:V78L;ENSP00000415979:V37L;ENSP00000438740:V76L;ENSP00000326010:V76L;ENSP00000391592:V76L;ENSP00000444337:V76L;ENSP00000445646:V76L;ENSP00000440114:V35L	ENSP00000326010:V76L	V	+	1	0	PTPN6	6931501	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	9.869000	0.99810	2.253000	0.74438	0.561000	0.74099	GTG	.	.	none		0.567	PTPN6-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400023.1	NM_002831		C	7061240	G	C	7061240	3	2	4	1	0	0	0	0	1	0	0	0	12807	1261	44	4	254	4	PTPN6	12	7061240	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	2677876	7061240	126790655	134	474											
C1S	716	hgsc.bcm.edu	37	chr12	7173133	7173133	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttgttcagtttgttgcaggaGatcggcaatttggtccttac	7	16	11	7	1	1	1	1	0	0	1	3	2	2	1	1	3	2	5	1	3	2	6			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr12:7173133G>C	ENST00000406697.1	+	10	1358	c.730G>C	c.(730-732)Gat>Cat	p.D244H	C1S_ENST00000402681.3_Missense_Mutation_p.D77H|C1S_ENST00000360817.5_Missense_Mutation_p.D244H|C1S_ENST00000328916.3_Missense_Mutation_p.D244H			P09871	C1S_HUMAN	complement component 1, s subcomponent	244	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				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)	TGTTGCAGGAGATCGGCAATT	0.393																																					p.D244H	GBM(156;750 1943 12971 24779 31015)	Atlas-SNP	.											.	C1S	93	.	0			c.G730C						PASS	.						152	140	144					12																	7173133		2203	4300	6503	SO:0001583	missense	716	exon7			GCAGGAGATCGGC		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.730G>C	12.37:g.7173133G>C	ENSP00000385035:p.Asp244His	108	0	0		91	11	0.120879	NM_201442	D3DUT4|Q9UCU7|Q9UCU8|Q9UCU9|Q9UCV0|Q9UCV1|Q9UCV2|Q9UCV3|Q9UCV4|Q9UCV5|Q9UM14	Missense_Mutation	SNP	ENST00000406697.1	37	CCDS31735.1	.	.	.	.	.	.	.	.	.	.	G	12.35	1.911718	0.33721	.	.	ENSG00000182326	ENST00000406697;ENST00000328916;ENST00000360817;ENST00000382222;ENST00000402681;ENST00000542978	T;T;T;T;T	0.21543	2.0;2.0;2.0;2.0;2.0	5.75	-2.25	0.06888	CUB (5);	0.494197	0.17083	N	0.187681	T	0.26011	0.0634	L	0.46885	1.475	0.09310	N	1	P	0.45126	0.851	P	0.51055	0.657	T	0.19451	-1.0305	10	0.52906	T	0.07	.	12.5694	0.56328	0.732:0.0:0.268:0.0	.	244	P09871	C1S_HUMAN	H	244;244;244;232;77;77	ENSP00000385035:D244H;ENSP00000328173:D244H;ENSP00000354057:D244H;ENSP00000384171:D77H;ENSP00000442298:D77H	ENSP00000328173:D244H	D	+	1	0	C1S	7043394	0.002000	0.14202	0.003000	0.11579	0.432000	0.31715	-0.406000	0.07187	-0.499000	0.06623	0.561000	0.74099	GAT	.	.	none		0.393	C1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317481.1	NM_001734		C	7173133	G	C	7173133	3	2	4	1	0	0	0	0	1	0	0	0	1976	942	33	4	752	4	C1S	12	7173133	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	111893	7173133	126678762	135	475											
A2M	2	hgsc.bcm.edu	37	chr12	9266020	9266020	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cagtgaagaggctcctgtttCccctgacagactccaaggaa	11	8	10	12	0	0	4	0	2	0	2	3	5	3	5	4	2	0	2	4	2	3	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr12:9266020C>T	ENST00000318602.7	-	2	513	c.206G>A	c.(205-207)gGa>gAa	p.G69E		NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	69					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)	GCTCCTGTTTCCCCTGACAGA	0.527																																					p.G69E		Atlas-SNP	.											.	A2M	180	.	0			c.G206A						PASS	.						127	129	128					12																	9266020		2203	4300	6503	SO:0001583	missense	2	exon2			CTGTTTCCCCTGA	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.206G>A	12.37:g.9266020C>T	ENSP00000323929:p.Gly69Glu	135	0	0		144	28	0.194444	NM_000014	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Missense_Mutation	SNP	ENST00000318602.7	37	CCDS44827.1	.	.	.	.	.	.	.	.	.	.	C	1.695	-0.503106	0.04261	.	.	ENSG00000175899	ENST00000318602;ENST00000540099;ENST00000404455	T;T	0.08008	3.14;3.14	4.83	-4.86	0.03132	.	0.951065	0.08710	N	0.905052	T	0.02848	0.0085	N	0.05487	-0.04	0.09310	N	1	B	0.09022	0.002	B	0.12837	0.008	T	0.46707	-0.9172	10	0.02654	T	1	.	7.029	0.24956	0.0:0.27:0.1246:0.6054	.	69	P01023	A2MG_HUMAN	E	69;84;69	ENSP00000323929:G69E;ENSP00000385710:G69E	ENSP00000323929:G69E	G	-	2	0	A2M	9157287	0.000000	0.05858	0.002000	0.10522	0.888000	0.51559	-0.865000	0.04250	-0.510000	0.06523	-0.142000	0.14014	GGA	.	.	none		0.527	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014		T	9266020	C	T	9266020	3	4	4	1	0	0	0	0	1	0	0	0	4	855	30	2	4358	2	A2M	12	9266020	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	2092887	9266020	124585875	136	476											
HIST4H4	121504	hgsc.bcm.edu	37	chr12	14923952	14923952	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccttggatattgtcccgcaGcaccttccggtggcgcttgg	4	11	13	13	3	0	0	0	0	0	0	2	1	2	1	4	4	1	3	4	4	1	5			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr12:14923952G>T	ENST00000539745.1	-	1	113	c.67C>A	c.(67-69)Ctg>Atg	p.L23M	HIST4H4_ENST00000541592.1_5'Flank	NM_175054.2	NP_778224.1	P62805	H4_HUMAN	histone cluster 4, H4	23					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)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)	6						TTGTCCCGCAGCACCTTCCGG	0.597											OREG0021698	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L23M		Atlas-SNP	.											.	HIST4H4	13	.	0			c.C67A						PASS	.						51	57	55					12																	14923952		2203	4300	6503	SO:0001583	missense	121504	exon1			CCCGCAGCACCTT	AY128653	CCDS8665.1	12p12.3	2011-01-27	2006-10-11			ENSG00000197837		"Histones / Replication-dependent"	20510	protein-coding gene	gene with protein product		615069	"histone 4, H4"			12408966	Standard	NM_175054		Approved	MGC24116	uc001rcf.4	P62805		ENST00000539745.1:c.67C>A	12.37:g.14923952G>T	ENSP00000443017:p.Leu23Met	63	0	0	698	59	12	0.20339	NM_175054	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000539745.1	37	CCDS8665.1	.	.	.	.	.	.	.	.	.	.	G	10.68	1.418716	0.25552	.	.	ENSG00000197837	ENST00000539745	.	.	.	4.18	-7.5	0.01351	.	0.000000	0.45126	U	0.000396	T	0.60919	0.2306	.	.	.	0.23712	N	0.997046	.	.	.	.	.	.	T	0.65450	-0.6165	6	0.66056	D	0.02	.	21.8368	0.99962	0.1506:0.0:0.8494:0.0	.	.	.	.	M	23	.	ENSP00000350767:L23M	L	-	1	2	HIST4H4	14815219	0.797000	0.28877	0.000000	0.03702	0.002000	0.02628	1.140000	0.31516	-2.027000	0.00932	-1.847000	0.00572	CTG	.	.	none		0.597	HIST4H4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400844.1	NM_175054		T	14923952	G	T	14923952	3	4	4	1	0	0	0	0	1	0	0	0	7194	962	34	4	248	4	HIST4H4	12	14923952	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	5657932	14923952	118927943	137	477											
SLC16A7	9194	hgsc.bcm.edu	37	chr12	60168856	60168856	+	Frame_Shift_Del	DEL	T	T	-																															aatgtcattatgttcctaggTttttttgcccccattatatt																										TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr12:60168856delT	ENST00000261187.4	+	4	944	c.780delT	c.(778-780)ggtfs	p.G260fs	SLC16A7_ENST00000543448.1_Frame_Shift_Del_p.G161fs|SLC16A7_ENST00000552024.1_Frame_Shift_Del_p.G260fs|SLC16A7_ENST00000547379.1_Frame_Shift_Del_p.G260fs|SLC16A7_ENST00000552432.1_Frame_Shift_Del_p.G260fs	NM_004731.4	NP_004722.2	O60669	MOT2_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 7	260					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)	p.G260G(1)		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)	TGTTCCTAGGTTTTTTTGCCC	0.353																																					p.G260fs		Pindel,Atlas-Indel	.											SLC16A7,NS,carcinoma,-1,1	SLC16A7	82	1	1	Substitution - coding silent(1)	lung(1)	c.779delG						PASS	.						84	82	83					12																	60168856		2203	4300	6503	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.780delT	12.37:g.60168856delT	ENSP00000261187:p.Gly260fs	130	0	.		137	23	0.168	NM_001270623	Q8NEM3|Q9UPB3	Frame_Shift_Del	DEL	ENST00000261187.4	37	CCDS8961.1																																																																																			.	.	none		0.353	SLC16A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406587.1	NM_004731		-	60168856	T	-	60168856	7	5	4	1	0	1	0	1	0	0	0	0	14428	1712	60	0	790	0	SLC16A7	12	60168856	Frame_Shift_Del	DEL	T	TCGA-FA-A6HN-01A-11D-A31X-10	45244904	60168856	73683039	138	478											
KCNC2	3747	hgsc.bcm.edu	37	chr12	75436936	75436936	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgcctcagaggacaaggagaGttgtagggtgatgttactgg	10	9	16	6	1	1	3	1	1	0	2	1	5	1	4	1	4	1	3	1	4	3	3			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr12:75436936G>A	ENST00000549446.1	-	5	2546	c.1866C>T	c.(1864-1866)aaC>aaT	p.N622N	KCNC2_ENST00000550433.1_Intron|KCNC2_ENST00000298972.1_Intron|KCNC2_ENST00000548513.1_Intron|KCNC2_ENST00000350228.2_Intron|KCNC2_ENST00000341669.3_Intron|KCNC2_ENST00000540018.1_Silent_p.N567N|RP11-81K13.1_ENST00000550049.1_RNA|RP11-81K13.1_ENST00000547040.1_RNA|RP11-81K13.1_ENST00000549762.1_RNA	NM_001260497.1|NM_139137.3	NP_001247426.1|NP_631875.1	Q96PR1	KCNC2_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 2	622					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)	GACAAGGAGAGTTGTAGGGTG	0.433																																					p.N622N		Atlas-SNP	.											.	KCNC2	239	.	0			c.C1866T						PASS	.						167	151	156					12																	75436936		2203	4300	6503	SO:0001819	synonymous_variant	3747	exon5			AGGAGAGTTGTAG	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.1866C>T	12.37:g.75436936G>A		148	0	0		102	19	0.186275	NM_139137	B7Z231|F5H030|J3KPP5|Q4LE77|Q86W09|Q8N1V9|Q96PR0	Silent	SNP	ENST00000549446.1	37	CCDS9007.1																																																																																			.	.	none		0.433	KCNC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405581.2	NM_153748		A	75436936	G	A	75436936	2	1	4	1	0	0	0	0	0	0	0	1	8024	1020	36	2		2	KCNC2	12	75436936	Silent	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	15268080	75436936	58414959	139	479											
PPFIA2	8499	hgsc.bcm.edu	37	chr12	81769580	81769580	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acagagatactgaacctgccGcaggatagcttctttatttg	11	12	9	9	1	1	2	0	1	1	1	1	4	1	3	2	1	4	2	2	1	4	6	rs370246827		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr12:81769580G>A	ENST00000549396.1	-	10	1286	c.1126C>T	c.(1126-1128)Cgg>Tgg	p.R376W	PPFIA2_ENST00000552948.1_Missense_Mutation_p.R376W|PPFIA2_ENST00000548586.1_Missense_Mutation_p.R376W|RP11-315E17.1_ENST00000546936.1_RNA|PPFIA2_ENST00000407050.4_Missense_Mutation_p.R302W|PPFIA2_ENST00000545296.2_5'UTR|PPFIA2_ENST00000333447.7_Missense_Mutation_p.R358W|PPFIA2_ENST00000550584.2_Missense_Mutation_p.R376W|PPFIA2_ENST00000443686.3_Missense_Mutation_p.R277W|PPFIA2_ENST00000549325.1_Missense_Mutation_p.R358W|PPFIA2_ENST00000550359.2_Missense_Mutation_p.R223W	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	376	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						TGAACCTGCCGCAGGATAGCT	0.398																																					p.R376W		Atlas-SNP	.											.	PPFIA2	207	.	0			c.C1126T						PASS	.	G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,3796		0,0,1898	150	146	147		1126,1072,1126,1126,904,829,1126	5.4	1	12		147	1,8205		0,1,4102	no	missense,missense,missense,missense,missense,missense,missense	PPFIA2	NM_001220473.1,NM_001220474.1,NM_001220475.1,NM_001220476.1,NM_001220477.1,NM_001220478.1,NM_003625.3	101,101,101,101,101,101,101	0,1,6000	AA,AG,GG		0.0122,0.0,0.0083	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	376/1248,358/1233,376/1237,376/1252,302/1157,277/1153,376/1258	81769580	1,12001	1898	4103	6001	SO:0001583	missense	8499	exon9			CCTGCCGCAGGAT	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.1126C>T	12.37:g.81769580G>A	ENSP00000450337:p.Arg376Trp	105	0	0		81	12	0.148148	NM_001220476	B3KVT5|B3KXA0|B7Z2A6|B7Z3U9|B7Z663|B7ZKZ5|E7ERB8|E7ETG6|F8VP68|Q2M3G8	Missense_Mutation	SNP	ENST00000549396.1	37	CCDS55857.1	.	.	.	.	.	.	.	.	.	.	G	17.53	3.411904	0.62511	0.0	1.22E-4	ENSG00000139220	ENST00000549396;ENST00000549325;ENST00000407050;ENST00000541501;ENST00000333447;ENST00000548586;ENST00000443686;ENST00000552948	T;T;T;T;T;T;T	0.79033	1.19;1.19;1.19;-1.23;1.19;1.19;1.19	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	D	0.88020	0.6325	M	0.87682	2.9	0.80722	D	1	D;D	0.76494	0.998;0.999	P;P	0.60609	0.736;0.877	D	0.89787	0.3965	10	0.87932	D	0	-3.2321	15.3055	0.73990	0.0:0.0:0.8594:0.1406	.	276;376	B7Z4H8;O75334	.;LIPA2_HUMAN	W	376;358;302;387;358;376;277;376	ENSP00000450337:R376W;ENSP00000450298:R358W;ENSP00000385093:R302W;ENSP00000327416:R358W;ENSP00000449338:R376W;ENSP00000388373:R277W;ENSP00000447868:R376W	ENSP00000327416:R358W	R	-	1	2	PPFIA2	80293711	1.000000	0.71417	0.993000	0.49108	0.794000	0.44872	3.400000	0.52594	2.723000	0.93209	0.650000	0.86243	CGG	.	.	weak		0.398	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1			A	81769580	G	A	81769580	3	1	4	1	0	0	0	0	1	0	0	0	12319	1086	38	1	2739	1	PPFIA2	12	81769580	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	6332644	81769580	52082315	140	480											
CUX2	23316	hgsc.bcm.edu	37	chr12	111744875	111744875	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	catccgccaaccagatcgccGacctggagcggcagctcacg	9	4	11	17	5	1	1	1	0	0	1	3	3	2	2	5	2	3	2	5	2	1	0	rs201601231	byFrequency	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr12:111744875G>A	ENST00000261726.6	+	11	1163	c.1009G>A	c.(1009-1011)Gac>Aac	p.D337N		NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	337					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						CCAGATCGCCGACCTGGAGCG	0.667													G|||	2	0.000399361	0.0	0.0	5008	,	,		17073	0.002		0.0	False		,,,				2504	0.0				p.D337N		Atlas-SNP	.											.	CUX2	145	.	0			c.G1009A						PASS	.	G	ASN/ASP	0,4020		0,0,2010	20	25	23		1009	5.3	0.9	12		23	1,8323		0,1,4161	no	missense	CUX2	NM_015267.3	23	0,1,6171	AA,AG,GG		0.012,0.0,0.0081	possibly-damaging	337/1487	111744875	1,12343	2010	4162	6172	SO:0001583	missense	23316	exon11			ATCGCCGACCTGG	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.1009G>A	12.37:g.111744875G>A	ENSP00000261726:p.Asp337Asn	57	0	0		49	10	0.204082	NM_015267	A7E2Y4	Missense_Mutation	SNP	ENST00000261726.6	37	CCDS41837.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	35	5.535085	0.96460	0.0	1.2E-4	ENSG00000111249	ENST00000261726	T	0.43294	0.95	5.3	5.3	0.74995	.	0.102642	0.64402	D	0.000005	T	0.39733	0.1089	L	0.44542	1.39	0.49130	D	0.999751	D	0.59357	0.985	B	0.43155	0.41	T	0.15665	-1.0429	10	0.26408	T	0.33	-36.3562	18.5534	0.91073	0.0:0.0:1.0:0.0	.	337	O14529	CUX2_HUMAN	N	337	ENSP00000261726:D337N	ENSP00000261726:D337N	D	+	1	0	CUX2	110229258	1.000000	0.71417	0.938000	0.37757	0.742000	0.42306	6.315000	0.72853	2.483000	0.83821	0.643000	0.83706	GAC	G|1.000;A|0.000	0.000	strong		0.667	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267		A	111744875	G	A	111744875	3	1	4	1	0	0	0	0	1	0	0	0	4067	1058	37	1	1051	1	CUX2	12	111744875	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	29975295	111744875	22107020	141	481											
BRAP	8315	hgsc.bcm.edu	37	chr12	112082105	112082105	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atggcgatgttgatctgtccCtcctggatttcctgccgggt	4	14	12	11	2	1	1	0	1	1	0	4	3	4	2	4	3	1	1	4	3	0	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr12:112082105C>T	ENST00000327551.6	-	12	1727	c.1587G>A	c.(1585-1587)gaG>gaA	p.E529E	BRAP_ENST00000539060.1_Silent_p.E380E|BRAP_ENST00000419234.4_Silent_p.E559E			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						TGATCTGTCCCTCCTGGATTT	0.617																																					p.E559E	Pancreas(146;846 1904 7830 25130 26065)	Atlas-SNP	.											.	BRAP	42	.	0			c.G1677A						PASS	.						146	119	128					12																	112082105		2203	4300	6503	SO:0001819	synonymous_variant	8315	exon12			CTGTCCCTCCTGG	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.1587G>A	12.37:g.112082105C>T		79	0	0		47	12	0.255319	NM_006768	B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Silent	SNP	ENST00000327551.6	37																																																																																				.	.	none		0.617	BRAP-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404994.2			T	112082105	C	T	112082105	2	4	4	1	0	0	0	0	0	0	0	1	1499	680	24	2		2	BRAP	12	112082105	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	337230	112082105	21769790	142	482											
ZMYM2	7750	hgsc.bcm.edu	37	chr13	20641392	20641392	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tttttagctaaatcagtaaaGttaaaagaggatctactctc	15	14	6	6	0	3	1	1	0	2	1	4	2	3	2	0	1	2	3	0	1	8	7			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr13:20641392G>A	ENST00000382874.2	+	22	3505	c.3315G>A	c.(3313-3315)aaG>aaA	p.K1105K	ZMYM2_ENST00000382871.2_Silent_p.K1105K|ZMYM2_ENST00000382869.3_Silent_p.K1105K|ZMYM2_ENST00000494061.2_3'UTR	NM_001190964.1	NP_001177893.1	Q9UBW7	ZMYM2_HUMAN	zinc finger, MYM-type 2	1105					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)		AATCAGTAAAGTTAAAAGAGG	0.328																																					p.K1105K		Atlas-SNP	.											.	ZMYM2	191	.	0			c.G3315A						PASS	.						43	38	39					13																	20641392		1816	4065	5881	SO:0001819	synonymous_variant	7750	exon22			AGTAAAGTTAAAA	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.3315G>A	13.37:g.20641392G>A		78	0	0		80	19	0.2375	NM_001190964	A6NDG0|A6NI02|O43212|O43434|O60898|Q5W0Q4|Q5W0T3|Q63HP0|Q8NE39|Q9H0V5|Q9H538|Q9UEU2	Silent	SNP	ENST00000382874.2	37	CCDS45016.1																																																																																			.	.	none		0.328	ZMYM2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044051.2	NM_003453		A	20641392	G	A	20641392	2	1	4	1	0	0	0	0	0	0	0	1	17715	1020	36	2		2	ZMYM2	13	20641392	Silent	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10		20641392	94528486	143	483											
IFT88	8100	hgsc.bcm.edu	37	chr13	21237643	21237643	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	attttacaatttaggtctgcGtttcttagttcgtctctgca	7	19	7	8	2	3	0	0	0	3	0	5	0	3	0	0	1	3	3	0	1	4	7	rs143840290	byFrequency	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr13:21237643G>A	ENST00000319980.6	+	25	2429	c.2102G>A	c.(2101-2103)cGt>cAt	p.R701H	IFT88_ENST00000382778.4_Silent_p.A742A|IFT88_ENST00000351808.5_Missense_Mutation_p.R692H|IFT88_ENST00000537103.1_Missense_Mutation_p.R673H	NM_175605.3	NP_783195.2	Q13099	IFT88_HUMAN	intraflagellar transport 88	701					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)		p.R701H(1)		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)		TTAGGTCTGCGTTTCTTAGTT	0.338													G|||	6	0.00119808	0.0	0.0058	5008	,	,		18602	0.002		0.0	False		,,,				2504	0.0				p.R701H		Atlas-SNP	.											IFT88,caecum,carcinoma,0,1	IFT88	83	1	1	Substitution - Missense(1)	large_intestine(1)	c.G2102A						scavenged	.	G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	105	99	101		2075,2102	5.8	1	13	dbSNP_134	101	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	IFT88	NM_006531.3,NM_175605.3	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	692/825,701/834	21237643	1,13005	2203	4300	6503	SO:0001583	missense	8100	exon25			GTCTGCGTTTCTT	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.2102G>A	13.37:g.21237643G>A	ENSP00000323580:p.Arg701His	51	1	0.0196078		31	6	0.193548	NM_175605	A2A491|B4DUS2|Q5SZJ6|Q8N719	Missense_Mutation	SNP	ENST00000319980.6	37	CCDS31944.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.701816	0.88924	0.0	1.16E-4	ENSG00000032742	ENST00000351808;ENST00000319980;ENST00000537103	T;T;T	0.53206	0.63;0.63;0.63	5.84	5.84	0.93424	.	0.106704	0.64402	D	0.000004	T	0.72036	0.3411	M	0.79805	2.47	0.80722	D	1	D;D	0.89917	0.999;1.0	P;D	0.78314	0.855;0.991	T	0.74090	-0.3777	10	0.66056	D	0.02	-12.7827	18.9266	0.92548	0.0:0.0:1.0:0.0	.	673;701	F5H6C2;Q13099	.;IFT88_HUMAN	H	692;701;673	ENSP00000261632:R692H;ENSP00000323580:R701H;ENSP00000437719:R673H	ENSP00000323580:R701H	R	+	2	0	IFT88	20135643	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.539000	0.82063	2.760000	0.94817	0.655000	0.94253	CGT	G|1.000;A|0.000	0.000	weak		0.338	IFT88-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044075.3	NM_006531		A	21237643	G	A	21237643	3	1	4	1	0	0	0	0	1	0	0	0	7575	1145	40	1	2192	1	IFT88	13	21237643	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	596251	21237643	93932235	144	484											
RXFP2	122042	hgsc.bcm.edu	37	chr13	32376518	32376518	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacaaaataacacttggagaCagtataatgaaaccagtttc	19	9	6	7	0	0	2	0	1	0	1	1	3	0	2	1	1	3	2	1	1	7	5			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr13:32376518C>G	ENST00000298386.2	+	18	2312	c.2241C>G	c.(2239-2241)gaC>gaG	p.D747E	RXFP2_ENST00000380314.1_Missense_Mutation_p.D723E	NM_130806.3	NP_570718.1	Q8WXD0	RXFP2_HUMAN	relaxin/insulin-like family peptide receptor 2	747					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oocyte maturation (GO:0001556)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	peptide hormone binding (GO:0017046)|protein-hormone receptor activity (GO:0016500)			cervix(1)|endometrium(2)|large_intestine(15)|lung(13)|prostate(1)|stomach(1)	33		Lung SC(185;0.0262)		all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535)		CACTTGGAGACAGTATAATGA	0.368																																					p.D747E		Atlas-SNP	.											.	RXFP2	95	.	0			c.C2241G						PASS	.						170	186	181					13																	32376518		2203	4300	6503	SO:0001583	missense	122042	exon18			TGGAGACAGTATA	AF403384	CCDS9342.1, CCDS53862.1	13q12.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000133105	ENSG00000133105		"GPCR / Class A : Relaxin family peptide receptors"	17318	protein-coding gene	gene with protein product		606655	"leucine-rich repeat-containing G protein-coupled receptor 8"	LGR8		12217959, 12970298, 15956688, 16507880	Standard	NM_130806		Approved	GREAT, GPR106, INSL3R, RXFPR2	uc001utt.3	Q8WXD0	OTTHUMG00000016690	ENST00000298386.2:c.2241C>G	13.37:g.32376518C>G	ENSP00000298386:p.Asp747Glu	107	0	0		95	22	0.231579	NM_130806	B1ALE9|Q3KU23	Missense_Mutation	SNP	ENST00000298386.2	37	CCDS9342.1	.	.	.	.	.	.	.	.	.	.	C	12.46	1.945129	0.34283	.	.	ENSG00000133105	ENST00000380314;ENST00000298386	T;T	0.71698	-0.59;-0.53	5.78	2.1	0.27182	.	0.061064	0.64402	D	0.000009	T	0.56514	0.1990	L	0.40543	1.245	0.27142	N	0.96162	B;B	0.10296	0.003;0.003	B;B	0.12156	0.007;0.007	T	0.43956	-0.9359	10	0.30078	T	0.28	.	7.8028	0.29185	0.0:0.4382:0.4154:0.1463	.	723;747	Q3KU23;Q8WXD0	.;RXFP2_HUMAN	E	723;747	ENSP00000369670:D723E;ENSP00000298386:D747E	ENSP00000298386:D747E	D	+	3	2	RXFP2	31274518	0.006000	0.16342	0.996000	0.52242	0.918000	0.54935	-0.743000	0.04845	0.358000	0.24211	0.655000	0.94253	GAC	.	.	none		0.368	RXFP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044399.1	NM_130806		G	32376518	C	G	32376518	3	3	4	1	0	0	0	0	1	0	0	0	13775	477	17	4	2311	4	RXFP2	13	32376518	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	11138875	32376518	82793360	145	485											
GAS6	2621	hgsc.bcm.edu	37	chr13	114530106	114530106	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctccgttcagccagttccagCtcctcatgcagccatccaga	8	9	7	17	1	2	1	2	0	0	1	6	1	6	1	6	0	4	4	6	0	0	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr13:114530106C>T	ENST00000327773.6	-	12	1486	c.1340G>A	c.(1339-1341)aGc>aAc	p.S447N	GAS6_ENST00000355761.4_Missense_Mutation_p.S393N|GAS6_ENST00000450766.1_Missense_Mutation_p.S174N|GAS6_ENST00000357389.3_Missense_Mutation_p.S490N|GAS6-AS1_ENST00000458001.1_RNA|GAS6_ENST00000418959.3_Missense_Mutation_p.S148N	NM_000820.2	NP_000811.1	Q14393	GAS6_HUMAN	growth arrest-specific 6	490	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				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)				CCAGTTCCAGCTCCTCATGCA	0.567																																					p.S447N		Atlas-SNP	.											GAS6_ENST00000327773,colon,carcinoma,-1,2	GAS6	75	2	0			c.G1340A						PASS	.						142	115	124					13																	114530106		2203	4300	6503	SO:0001583	missense	2621	exon12			TTCCAGCTCCTCA		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.1340G>A	13.37:g.114530106C>T	ENSP00000331831:p.Ser447Asn	90	0	0		62	9	0.145161	NM_000820	B3KRQ7|B3KVL4|E9PBL7|Q6IMN1|Q7Z7N3	Missense_Mutation	SNP	ENST00000327773.6	37	CCDS45072.1	.	.	.	.	.	.	.	.	.	.	C	6.825	0.521409	0.13005	.	.	ENSG00000183087	ENST00000357389;ENST00000355761;ENST00000450766;ENST00000418959;ENST00000327773	T;T;T;T;T	0.77750	-1.12;-1.12;-1.12;-1.12;-1.12	4.55	3.7	0.42460	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	.	.	.	.	T	0.64057	0.2564	N	0.16903	0.455	0.29004	N	0.887312	P;B;B	0.48503	0.911;0.001;0.001	P;B;B	0.47402	0.546;0.002;0.002	T	0.54330	-0.8310	9	0.16896	T	0.51	-32.5518	6.1848	0.20491	0.0:0.6573:0.1674:0.1753	.	490;174;447	Q14393;B3KVL4;Q14393-2	GAS6_HUMAN;.;.	N	490;393;174;148;447	ENSP00000349962:S490N;ENSP00000348003:S393N;ENSP00000416498:S174N;ENSP00000400117:S148N;ENSP00000331831:S447N	ENSP00000331831:S447N	S	-	2	0	GAS6	113583837	1.000000	0.71417	0.889000	0.34880	0.462000	0.32619	3.448000	0.52943	0.901000	0.36495	0.462000	0.41574	AGC	.	.	none		0.567	GAS6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045946.2	NM_000820		T	114530106	C	T	114530106	3	4	4	1	0	0	0	0	1	0	0	0	6257	797	28	2	712	2	GAS6	13	114530106	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	82153588	114530106	639772	146	486											
FAM179B	23116	hgsc.bcm.edu	37	chr14	45433254	45433254	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggcatcatcaatgggctcaGgtaaaaccagcatccttttt	11	12	8	10	0	3	0	3	0	0	0	4	0	4	0	2	3	2	4	2	3	3	3			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr14:45433254G>A	ENST00000361577.3	+	1	1844	c.1630G>A	c.(1630-1632)Ggt>Agt	p.G544S	KLHL28_ENST00000396128.4_5'Flank|KLHL28_ENST00000553817.1_5'UTR|FAM179B_ENST00000361462.2_Missense_Mutation_p.G544S|KLHL28_ENST00000355081.2_5'Flank|FAM179B_ENST00000382233.2_Missense_Mutation_p.G544S	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	544										endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						AATGGGCTCAGGTAAAACCAG	0.463																																					p.G544S		Atlas-SNP	.											.	FAM179B	115	.	0			c.G1630A						PASS	.						117	116	116					14																	45433254		2203	4300	6503	SO:0001583	missense	23116	exon1			GGCTCAGGTAAAA	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.1630G>A	14.37:g.45433254G>A	ENSP00000355045:p.Gly544Ser	85	0	0		58	9	0.155172	NM_015091	Q68D66|Q6PG27	Missense_Mutation	SNP	ENST00000361577.3	37	CCDS9681.1	.	.	.	.	.	.	.	.	.	.	G	19.29	3.798793	0.70567	.	.	ENSG00000198718	ENST00000429476;ENST00000361577;ENST00000361462;ENST00000382233	T;T;T	0.54675	0.56;0.56;0.56	4.47	3.57	0.40892	Armadillo-like helical (1);Armadillo-type fold (1);	0.073488	0.53938	N	0.000058	T	0.59918	0.2229	L	0.35723	1.085	0.58432	D	0.999997	P;D;D;P	0.89917	0.715;1.0;1.0;0.715	P;D;D;P	0.91635	0.653;0.999;0.997;0.577	T	0.55679	-0.8103	10	0.30854	T	0.27	-9.2512	12.2476	0.54578	0.0837:0.0:0.9163:0.0	.	544;544;544;544	Q9Y4F4-3;G3XAE9;Q9Y4F4;Q9Y4F4-2	.;.;F179B_HUMAN;.	S	544	ENSP00000355045:G544S;ENSP00000354917:G544S;ENSP00000371668:G544S	ENSP00000354917:G544S	G	+	1	0	FAM179B	44503004	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.158000	0.64917	1.097000	0.41459	0.561000	0.74099	GGT	.	.	none		0.463	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781		A	45433254	G	A	45433254	3	1	4	1	0	0	0	0	1	0	0	0	5511	1000	35	2	1632	2	FAM179B	14	45433254	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10		45433254	61916286	147	487											
CRIP1	1396	hgsc.bcm.edu	37	chr14	105954680	105954681	+	Frame_Shift_Del	DEL	CC	CC	-																															ctttgcagcacgaaggcaaaCcctactgcaaccacccctgc																										TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr14:105954680_105954681delCC	ENST00000330233.7	+	3	1091_1092	c.148_149delCC	c.(148-150)cccfs	p.P50fs	C14orf80_ENST00000329886.7_5'Flank|CRIP1_ENST00000409393.2_Frame_Shift_Del_p.P50fs|C14orf80_ENST00000392522.3_5'Flank|C14orf80_ENST00000334656.7_5'Flank|C14orf80_ENST00000392527.1_5'Flank|CRIP1_ENST00000551180.1_Frame_Shift_Del_p.T18fs|C14orf80_ENST00000354560.6_5'Flank|C14orf80_ENST00000392523.4_5'Flank|CRIP1_ENST00000392531.3_Frame_Shift_Del_p.P50fs			P50238	CRIP1_HUMAN	cysteine-rich protein 1 (intestinal)	50	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell proliferation (GO:0008283)|cellular response to antibiotic (GO:0071236)|cellular response to UV-B (GO:0071493)|heart development (GO:0007507)|immune response (GO:0006955)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|prostate gland stromal morphogenesis (GO:0060741)|regulation of gene expression (GO:0010468)|response to organic substance (GO:0010033)|response to zinc ion (GO:0010043)	cytoplasm (GO:0005737)	AT DNA binding (GO:0003680)|DNA binding, bending (GO:0008301)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)						Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0188)	Epithelial(152;0.235)		CGAAGGCAAACCCTACTGCAAC	0.658																																					p.49_50del		Atlas-Indel	.											.	CRIP1	1	.	0			c.147_148del						PASS	.																																			SO:0001589	frameshift_variant	1396	exon4			.		CCDS10004.1	14q32.33	2004-06-18			ENSG00000213145	ENSG00000213145			2360	protein-coding gene	gene with protein product		123875				9480758	Standard	NM_001311		Approved	CRIP	uc001yri.4	P50238	OTTHUMG00000029908	ENST00000330233.7:c.148_149delCC	14.37:g.105954680_105954681delCC	ENSP00000332449:p.Pro50fs	136	0	0		101	15	0.148515	NM_001311	H3BPI2|Q13628|Q53XY7|Q96J34	Frame_Shift_Del	DEL	ENST00000330233.7	37	CCDS10004.1																																																																																			.	.	none		0.658	CRIP1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335466.2	NM_001311		-	105954681	CC	-	105954680	7	5	4	1	0	1	0	1	0	0	0	0	3876	507	18	0	158	0	CRIP1	14	105954680	Frame_Shift_Del	DEL	CC	TCGA-FA-A6HN-01A-11D-A31X-10	60521426	105954680	1394860	148	488	11	2									
CRIP1	1396	hgsc.bcm.edu	37	chr14	105954689	105954689	+	Missense_Mutation	SNP	A	A	C																															acgaaggcaaaccctactgcAaccacccctgctacgcagcc																										TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr14:105954689A>C	ENST00000330233.7	+	3	1100	c.157A>C	c.(157-159)Aac>Cac	p.N53H	C14orf80_ENST00000329886.7_5'Flank|CRIP1_ENST00000409393.2_Missense_Mutation_p.N53H|C14orf80_ENST00000392522.3_5'Flank|C14orf80_ENST00000334656.7_5'Flank|C14orf80_ENST00000392527.1_5'Flank|CRIP1_ENST00000551180.1_Missense_Mutation_p.Q21P|C14orf80_ENST00000354560.6_5'Flank|C14orf80_ENST00000392523.4_5'Flank|CRIP1_ENST00000392531.3_Missense_Mutation_p.N53H			P50238	CRIP1_HUMAN	cysteine-rich protein 1 (intestinal)	53	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell proliferation (GO:0008283)|cellular response to antibiotic (GO:0071236)|cellular response to UV-B (GO:0071493)|heart development (GO:0007507)|immune response (GO:0006955)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|prostate gland stromal morphogenesis (GO:0060741)|regulation of gene expression (GO:0010468)|response to organic substance (GO:0010033)|response to zinc ion (GO:0010043)	cytoplasm (GO:0005737)	AT DNA binding (GO:0003680)|DNA binding, bending (GO:0008301)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)						Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0188)	Epithelial(152;0.235)		ACCCTACTGCAACCACCCCTG	0.642																																					p.N53H		Atlas-SNP	.											.	CRIP1	1	.	0			c.A157C						PASS	.						46	62	57					14																	105954689		2202	4300	6502	SO:0001583	missense	1396	exon4			TACTGCAACCACC		CCDS10004.1	14q32.33	2004-06-18			ENSG00000213145	ENSG00000213145			2360	protein-coding gene	gene with protein product		123875				9480758	Standard	NM_001311		Approved	CRIP	uc001yri.4	P50238	OTTHUMG00000029908	ENST00000330233.7:c.157A>C	14.37:g.105954689A>C	ENSP00000332449:p.Asn53His	149	0	0		108	17	0.157407	NM_001311	H3BPI2|Q13628|Q53XY7|Q96J34	Missense_Mutation	SNP	ENST00000330233.7	37	CCDS10004.1	.	.	.	.	.	.	.	.	.	.	A	4.183	0.032586	0.08101	.	.	ENSG00000213145	ENST00000330233;ENST00000409393;ENST00000392531	D;D;D	0.87491	-2.26;-2.26;-2.26	4.76	4.76	0.60689	Zinc finger, LIM-type (4);	0.000000	0.53938	U	0.000044	T	0.73613	0.3609	.	.	.	0.51012	D	0.999902	B	0.06786	0.001	B	0.18263	0.021	T	0.65257	-0.6212	9	0.07482	T	0.82	-7.0094	9.4659	0.38813	0.8215:0.1785:0.0:0.0	.	53	P50238	CRIP1_HUMAN	H	53	ENSP00000332449:N53H;ENSP00000386340:N53H;ENSP00000376315:N53H	ENSP00000447493:N53H	N	+	1	0	CRIP1	105025734	1.000000	0.71417	1.000000	0.80357	0.504000	0.33889	1.736000	0.38187	1.775000	0.52247	0.528000	0.53228	AAC	.	.	none		0.642	CRIP1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335466.2	NM_001311		C	105954689	A	C	105954689	3	2	4	1	0	0	0	0	1	0	0	0	3876	130	5	5	167	5	CRIP1	14	105954689	Missense_Mutation	SNP	A	TCGA-FA-A6HN-01A-11D-A31X-10	9	105954689	1394851	149	489	11	2									
SLC12A6	9990	hgsc.bcm.edu	37	chr15	34628685	34628685	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cagttgccagcgaagtggtgGccccagacatctcactcata	10	8	10	13	1	2	1	2	0	1	1	3	2	2	1	3	2	2	1	3	2	2	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr15:34628685G>A	ENST00000354181.3	-	2	689	c.197C>T	c.(196-198)gCc>gTc	p.A66V	SLC12A6_ENST00000558667.1_Missense_Mutation_p.A66V|SLC12A6_ENST00000560611.1_Missense_Mutation_p.A66V|SLC12A6_ENST00000458406.2_Missense_Mutation_p.A7V|SLC12A6_ENST00000397707.2_Missense_Mutation_p.A66V|SLC12A6_ENST00000397702.2_Missense_Mutation_p.A7V|SLC12A6_ENST00000558589.1_Missense_Mutation_p.A57V			Q9UHW9	S12A6_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 6	66					angiogenesis (GO:0001525)|cellular hypotonic response (GO:0071476)|cellular hypotonic salinity response (GO:0071477)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|rubidium ion transport (GO:0035826)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium ion transmembrane transporter activity (GO:0015079)|potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)|rubidium ion transmembrane transporter activity (GO:0035827)			central_nervous_system(5)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|skin(3)	45		all_lung(180;2.78e-08)		all cancers(64;3.43e-17)|GBM - Glioblastoma multiforme(113;2.6e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0301)	Potassium Chloride(DB00761)	CGAAGTGGTGGCCCCAGACAT	0.562																																					p.A66V		Atlas-SNP	.											.	SLC12A6	205	.	0			c.C197T						PASS	.						63	70	68					15																	34628685		2178	4286	6464	SO:0001583	missense	9990	exon1			GTGGTGGCCCCAG	AF108831	CCDS10036.1, CCDS42010.1, CCDS42011.1, CCDS42012.1, CCDS58352.1	15q13	2014-09-17	2013-07-18		ENSG00000140199	ENSG00000140199		"Solute carriers"	10914	protein-coding gene	gene with protein product		604878	"agenesis of corpus callosum and peripheral neuropathy (Andermann syndrome)"	KCC3, ACCPN		10187864, 10347194	Standard	NM_133647		Approved		uc001zhw.3	Q9UHW9	OTTHUMG00000129441	ENST00000354181.3:c.197C>T	15.37:g.34628685G>A	ENSP00000346112:p.Ala66Val	93	0	0		76	11	0.144737	NM_133647	A0AV76|Q2VI00|Q7Z2E7|Q7Z4G5|Q8TDD4|Q9UFR2|Q9Y642|Q9Y665	Missense_Mutation	SNP	ENST00000354181.3	37	CCDS58352.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.755564	0.49362	.	.	ENSG00000140199	ENST00000397707;ENST00000354181;ENST00000397702;ENST00000458406	D;D;D	0.83992	-1.79;-1.79;-1.79	4.89	3.97	0.46021	.	0.237554	0.33938	N	0.004416	T	0.63522	0.2518	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	0.55560	-0.8122	10	0.13108	T	0.6	.	10.0434	0.42173	0.0939:0.0:0.9061:0.0	.	66;66	Q9UHW9-3;Q9UHW9	.;S12A6_HUMAN	V	66;57;7;7	ENSP00000380819:A66V;ENSP00000380814:A7V;ENSP00000387725:A7V	ENSP00000346112:A57V	A	-	2	0	SLC12A6	32415977	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.116000	0.50399	1.285000	0.44548	0.563000	0.77884	GCC	.	.	none		0.562	SLC12A6-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000417991.1	NM_005135		A	34628685	G	A	34628685	3	1	4	1	0	0	0	0	1	0	0	0	14402	1203	42	2	3477	2	SLC12A6	15	34628685	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10		34628685	67902707	150	490											
MGA	23269	hgsc.bcm.edu	37	chr15	42003386	42003386	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttagtttgcggcaggcacagCagcagcagcaacagcaacag	13	5	12	11	1	0	0	0	0	0	0	0	0	0	0	0	2	8	8	0	2	3	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr15:42003386C>T	ENST00000570161.1	+	7	2923	c.2923C>T	c.(2923-2925)Cag>Tag	p.Q975*	MGA_ENST00000545763.1_Nonsense_Mutation_p.Q975*|MGA_ENST00000389936.4_Nonsense_Mutation_p.Q975*|MGA_ENST00000219905.7_Nonsense_Mutation_p.Q975*|MGA_ENST00000566586.1_Nonsense_Mutation_p.Q975*			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	P-type 2. {ECO:0000255|PROSITE- ProRule:PRU00779}.				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)	GCAGGCACAGCAGCAGCAGCA	0.463																																					p.Q975X		Atlas-SNP	.											.	MGA	264	.	0			c.C2923T						PASS	.						56	62	60					15																	42003386		2056	4224	6280	SO:0001587	stop_gained	23269	exon8			GCACAGCAGCAGC	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.2923C>T	15.37:g.42003386C>T	ENSP00000457035:p.Gln975*	55	0	0		65	9	0.138462	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Nonsense_Mutation	SNP	ENST00000570161.1	37	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	C	38	7.045182	0.98025	.	.	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	.	.	.	4.88	3.92	0.45320	.	0.485631	0.18517	N	0.138876	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	.	14.8687	0.70437	0.1451:0.8549:0.0:0.0	.	.	.	.	X	975	.	ENSP00000219905:Q975X	Q	+	1	0	MGA	39790678	0.889000	0.30405	0.964000	0.40570	0.530000	0.34684	3.477000	0.53151	1.312000	0.45043	0.650000	0.86243	CAG	.	.	none		0.463	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		T	42003386	C	T	42003386	4	4	4	1	0	0	0	0	0	1	0	0	9549	711	25	2	2949	2	MGA	15	42003386	Nonsense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	7374701	42003386	60528006	151	491											
JMJD7-PLA2G4B	100137049	hgsc.bcm.edu	37	chr15	42139859	42139859	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccacaggggtccggcggaCacccgaggaggcggcagctg	7	3	17	14	4	0	0	0	0	0	0	2	3	2	2	3	7	1	2	3	7	0	0			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr15:42139859C>A	ENST00000452633.1	+	21	2499	c.2147C>A	c.(2146-2148)aCa>aAa	p.T716K	PLA2G4B_ENST00000542534.2_Missense_Mutation_p.T947K|JMJD7-PLA2G4B_ENST00000342159.4_Missense_Mutation_p.H885N|PLA2G4B_ENST00000458483.1_Missense_Mutation_p.T716K|JMJD7-PLA2G4B_ENST00000382448.4_Missense_Mutation_p.T947K			P0C869	PA24B_HUMAN	phospholipase A2, group IVB (cytosolic)	716	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|arachidonic acid metabolic process (GO:0019369)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|parturition (GO:0007567)|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)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|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)						all_cancers(109;1.84e-13)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		all cancers(2;1.08e-30)|Epithelial(2;1.43e-22)|OV - Ovarian serous cystadenocarcinoma(18;1.13e-17)|GBM - Glioblastoma multiforme(94;9.77e-07)|Colorectal(2;0.0129)|COAD - Colon adenocarcinoma(120;0.0371)		GTCCGGCGGACACCCGAGGAG	0.632																																					p.T947K		Atlas-SNP	.											.	JMJD7-PLA2G4B	90	.	0			c.C2840A						PASS	.						56	54	55					15																	42139859		2203	4300	6503	SO:0001583	missense	8681	exon25			GGCGGACACCCGA	AF065215	CCDS45241.1	15q11.2-q21.3	2010-08-17			ENSG00000243708	ENSG00000243708	3.1.1.4		9036	protein-coding gene	gene with protein product		606088				9705332	Standard	NM_001114633		Approved	cPLA2-beta, HsT16992		P0C869	OTTHUMG00000156809	ENST00000452633.1:c.2147C>A	15.37:g.42139859C>A	ENSP00000396045:p.Thr716Lys	87	0	0		67	19	0.283582	NM_005090	B4DRT9|O95712|Q19KD5|Q19KD6|Q59GF9|Q8TB10|Q9UKV7	Missense_Mutation	SNP	ENST00000452633.1	37	CCDS45241.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	13.47|13.47	2.246633|2.246633	0.39697|0.39697	.|.	.|.	ENSG00000168970|ENSG00000168970;ENSG00000168970;ENSG00000243708	ENST00000342159|ENST00000382448;ENST00000458483;ENST00000452633	T|T;T;T	0.01474|0.03951	4.85|3.75;3.75;3.75	4.77|4.77	1.66|1.66	0.24008|0.24008	.|Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	.|0.389650	.|0.24757	.|N	.|0.035848	T|T	0.03390|0.03390	0.0098|0.0098	.|.	.|.	.|.	0.19775|0.19775	N|N	0.99996|0.99996	B|B;B	0.19817|0.24258	0.039|0.047;0.1	B|B;B	0.13407|0.25506	0.009|0.012;0.061	T|T	0.36890|0.36890	-0.9729|-0.9729	8|9	0.87932|0.59425	D|D	0|0.04	-9.1587|-9.1587	2.3448|2.3448	0.04269|0.04269	0.2463:0.3812:0.2733:0.0992|0.2463:0.3812:0.2733:0.0992	.|.	885|716;947	P0C869-7|P0C869;P0C869-6	.|PA24B_HUMAN;.	N|K	885|947;716;716	ENSP00000342785:H885N|ENSP00000371886:T947K;ENSP00000416610:T716K;ENSP00000396045:T716K	ENSP00000342785:H885N|ENSP00000371886:T947K	H|T	+|+	1|2	0|0	JMJD7-PLA2G4B|JMJD7-PLA2G4B;PLA2G4B	39927151|39927151	0.000000|0.000000	0.05858|0.05858	0.286000|0.286000	0.24833|0.24833	0.347000|0.347000	0.29111|0.29111	-0.089000|-0.089000	0.11180|0.11180	1.155000|1.155000	0.42497|0.42497	0.491000|0.491000	0.48974|0.48974	CAC|ACA	.	.	none		0.632	PLA2G4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345969.1	NM_001114633		A	42139859	C	A	42139859	3	1	4	1	0	0	0	0	1	0	0	0	7964	478	17	4	2938	4	JMJD7-PLA2G4B	15	42139859	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	136473	42139859	60391533	152	492											
SNX1	6642	hgsc.bcm.edu	37	chr15	64410372	64410372	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataatcagaagaaggtgctaGccaaaacactcatttctctt	15	11	6	9	0	3	2	2	0	1	2	4	2	3	2	1	1	3	1	1	1	6	4			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr15:64410372G>A	ENST00000559844.1	+	3	342	c.328G>A	c.(328-330)Gcc>Acc	p.A110T	SNX1_ENST00000560829.1_5'UTR|SNX1_ENST00000353874.4_Missense_Mutation_p.A110T|SNX1_ENST00000261889.5_Missense_Mutation_p.A110T|SNX1_ENST00000561026.1_Intron			Q13596	SNX1_HUMAN	sorting nexin 1	110					early endosome to Golgi transport (GO:0034498)|intracellular protein transport (GO:0006886)|positive regulation of protein catabolic process (GO:0045732)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|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)			breast(1)|endometrium(1)|large_intestine(5)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	13						GAAGGTGCTAGCCAAAACACT	0.438																																					p.A110T		Atlas-SNP	.											.	SNX1	36	.	0			c.G328A						PASS	.						111	100	104					15																	64410372		2203	4300	6503	SO:0001583	missense	6642	exon3			GTGCTAGCCAAAA	BC000357	CCDS32266.1, CCDS32268.1, CCDS58371.1	15q22.31	2011-05-03			ENSG00000028528	ENSG00000028528		"Sorting nexins"	11172	protein-coding gene	gene with protein product		601272				8638121	Standard	NM_003099		Approved	SNX1A, MGC8664, HsT17379, Vps5	uc010uio.2	Q13596		ENST00000559844.1:c.328G>A	15.37:g.64410372G>A	ENSP00000453785:p.Ala110Thr	202	0	0		140	35	0.25	NM_003099	A6NM19|A8K6T7|H0Y2M5|O60750|O60751|Q6ZRJ8	Missense_Mutation	SNP	ENST00000559844.1	37	CCDS32266.1	.	.	.	.	.	.	.	.	.	.	G	10.72	1.429880	0.25726	.	.	ENSG00000028528	ENST00000380285;ENST00000353874	T	0.46063	0.88	5.66	4.75	0.60458	.	0.625902	0.17890	N	0.158550	T	0.32133	0.0819	N	0.19112	0.55	0.28175	N	0.928424	B;B;B;B	0.23990	0.095;0.011;0.012;0.011	B;B;B;B	0.34991	0.158;0.063;0.193;0.034	T	0.28299	-1.0048	10	0.20519	T	0.43	-11.319	12.4081	0.55451	0.0774:0.0:0.9226:0.0	.	110;110;110;110	Q6ZRJ8;Q53GY8;A6NKH4;Q13596	.;.;.;SNX1_HUMAN	T	110	ENSP00000326668:A110T	ENSP00000326668:A110T	A	+	1	0	SNX1	62197425	1.000000	0.71417	0.654000	0.29608	0.054000	0.15201	3.917000	0.56424	1.542000	0.49330	0.655000	0.94253	GCC	.	.	none		0.438	SNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418559.1	NM_003099		A	64410372	G	A	64410372	3	1	4	1	0	0	0	0	1	0	0	0	14895	971	34	2	338	2	SNX1	15	64410372	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	22270513	64410372	38121020	153	493											
UACA	55075	hgsc.bcm.edu	37	chr15	70960860	70960860	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcttattatccaaataaacTttttcaatttccttttgtag	12	19	3	7	0	1	0	1	0	0	0	3	0	3	0	2	0	2	2	2	0	7	9			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr15:70960860T>C	ENST00000322954.6	-	16	2348	c.2163A>G	c.(2161-2163)aaA>aaG	p.K721K	UACA_ENST00000560441.1_Silent_p.K706K|UACA_ENST00000539319.1_Silent_p.K612K|UACA_ENST00000379983.2_Silent_p.K708K	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	721					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						CCAAATAAACTTTTTCAATTT	0.313																																					p.K721K		Atlas-SNP	.											.	UACA	235	.	0			c.A2163G						PASS	.						97	98	97					15																	70960860		2199	4296	6495	SO:0001819	synonymous_variant	55075	exon16			ATAAACTTTTTCA	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.2163A>G	15.37:g.70960860T>C		75	0	0		55	10	0.181818	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Silent	SNP	ENST00000322954.6	37	CCDS10235.1																																																																																			.	.	none		0.313	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			C	70960860	T	C	70960860	2	2	4	1	0	0	0	0	0	0	0	1	16839	1606	56	3		3	UACA	15	70960860	Silent	SNP	T	TCGA-FA-A6HN-01A-11D-A31X-10	6550488	70960860	31570532	154	494											
ISLR2	57611	hgsc.bcm.edu	37	chr15	74426853	74426853	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgttttccaccaagaaggaGctcccatcgctgctggtcat	8	11	10	12	1	1	1	1	0	0	1	4	2	3	2	3	2	2	4	3	2	2	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr15:74426853G>T	ENST00000361742.3	+	4	2527	c.1758G>T	c.(1756-1758)gaG>gaT	p.E586D	ISLR2_ENST00000565540.1_Missense_Mutation_p.E586D|ISLR2_ENST00000419208.1_Missense_Mutation_p.E586D|ISLR2_ENST00000565159.1_Missense_Mutation_p.E586D|ISLR2_ENST00000561975.1_Intron|ISLR2_ENST00000453268.2_Missense_Mutation_p.E586D|ISLR2_ENST00000435464.1_Missense_Mutation_p.E586D|ISLR2_ENST00000445793.1_Missense_Mutation_p.E586D	NM_001130136.1|NM_020851.2	NP_001123608.1|NP_065902.1	Q6UXK2	ISLR2_HUMAN	immunoglobulin superfamily containing leucine-rich repeat 2	586					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						CCAAGAAGGAGCTCCCATCGC	0.642																																					p.E586D		Atlas-SNP	.											.	ISLR2	78	.	0			c.G1758T						PASS	.						35	31	32					15																	74426853		2198	4296	6494	SO:0001583	missense	57611	exon4			GAAGGAGCTCCCA		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.1758G>T	15.37:g.74426853G>T	ENSP00000355402:p.Glu586Asp	95	0	0		75	8	0.106667	NM_001130138	A8K352|Q9P263	Missense_Mutation	SNP	ENST00000361742.3	37	CCDS10259.1	.	.	.	.	.	.	.	.	.	.	G	15.55	2.865890	0.51588	.	.	ENSG00000167178	ENST00000445793;ENST00000361742;ENST00000435464;ENST00000453268;ENST00000395121;ENST00000419208	T;T;T;T;T	0.57907	0.37;0.37;0.37;0.37;0.37	4.73	0.492	0.16872	.	0.059441	0.64402	D	0.000003	T	0.41627	0.1167	L	0.27053	0.805	0.34021	D	0.652649	D	0.57257	0.979	P	0.49999	0.628	T	0.51371	-0.8714	10	0.27785	T	0.31	.	8.8954	0.35460	0.4526:0.0:0.5474:0.0	.	586	Q6UXK2	ISLR2_HUMAN	D	586;586;586;586;175;586	ENSP00000403244:E586D;ENSP00000355402:E586D;ENSP00000411443:E586D;ENSP00000411834:E586D;ENSP00000408872:E586D	ENSP00000355402:E586D	E	+	3	2	ISLR2	72213906	0.924000	0.31332	0.992000	0.48379	0.893000	0.52053	0.436000	0.21526	0.207000	0.20607	0.313000	0.20887	GAG	.	.	none		0.642	ISLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269046.1	NM_020851		T	74426853	G	T	74426853	3	4	4	1	0	0	0	0	1	0	0	0	7868	962	34	4	1760	4	ISLR2	15	74426853	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	3465993	74426853	28104539	155	495											
MAZ	4150	hgsc.bcm.edu	37	chr16	29819056	29819064	+	In_Frame_Del	DEL	AGCGCAAGG	AGCGCAAGG	-																															ggtgtgccagcagcgcttcaAgcgcaaggaccgcatgagct																								rs141211357	byFrequency	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	AGCGCAAGG	AGCGCAAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr16:29819056_29819064delAGCGCAAGG	ENST00000322945.6	+	2	1115_1123	c.950_958delAGCGCAAGG	c.(949-960)aagcgcaaggac>aac	p.317_320KRKD>N	AC009133.14_ENST00000563806.1_RNA|MAZ_ENST00000563402.1_Intron|MAZ_ENST00000566906.2_Intron|MAZ_ENST00000545521.1_In_Frame_Del_p.294_297KRKD>N|AC009133.14_ENST00000569981.1_RNA|MAZ_ENST00000568282.1_5'Flank|MAZ_ENST00000569978.1_5'Flank|MAZ_ENST00000219782.6_In_Frame_Del_p.317_320KRKD>N|AC009133.15_ENST00000566537.1_RNA|MAZ_ENST00000568544.1_5'Flank|AC009133.20_ENST00000569039.1_RNA|MAZ_ENST00000562337.1_Intron	NM_002383.2	NP_002374.2	P56270	MAZ_HUMAN	MYC-associated zinc finger protein (purine-binding transcription factor)	317					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						CAGCGCTTCAAGCGCAAGGACCGCATGAG	0.632																																					p.317_319del	Colon(72;875 1167 15364 30899 37091)	Atlas-Indel	.											.	MAZ	48	.	0			c.949_957del						PASS	.																																			SO:0001651	inframe_deletion	4150	exon2			.	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.950_958delAGCGCAAGG	16.37:g.29819056_29819064delAGCGCAAGG	ENSP00000313362:p.Lys317_Asp320delinsAsn	82	0	0		74	13	0.175676	NM_002383	A8QJL9|C6G496|G5E927|H3BQD6|Q15703|Q8NFN7|Q99443	In_Frame_Del	DEL	ENST00000322945.6	37	CCDS42143.1																																																																																			.	.	none		0.632	MAZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435536.1	NM_002383		-	29819064	AGCGCAAGG	-	29819056	7	5	4	1	0	1	0	1	0	0	0	0	9349	72	3	0	956	0	MAZ	16	29819056	In_Frame_Del	DEL	AGCGCAAGG	TCGA-FA-A6HN-01A-11D-A31X-10		29819056	60535697	156	496											
CORO1A	11151	hgsc.bcm.edu	37	chr16	30198463	30198463	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	atctacagtgtggactggagCcgagatggaggcctcatttg	9	10	14	8	1	2	1	1	0	1	1	2	5	2	4	2	4	2	0	2	4	1	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr16:30198463C>T	ENST00000219150.5	+	5	860	c.555C>T	c.(553-555)agC>agT	p.S185S	RP11-455F5.5_ENST00000568506.1_RNA|CORO1A_ENST00000565497.1_Silent_p.S185S|RP11-455F5.5_ENST00000567153.1_RNA|CORO1A_ENST00000570045.1_Silent_p.S185S|RP11-455F5.5_ENST00000566144.1_RNA	NM_001193333.2|NM_007074.3	NP_001180262.1|NP_009005.1	P31146	COR1A_HUMAN	coronin, actin binding protein, 1A	185					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						TGGACTGGAGCCGAGATGGAG	0.612																																					p.S185S		Atlas-SNP	.											.	CORO1A	36	.	0			c.C555T						PASS	.						89	77	81					16																	30198463		2197	4300	6497	SO:0001819	synonymous_variant	11151	exon6			CTGGAGCCGAGAT	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.555C>T	16.37:g.30198463C>T		52	0	0		46	10	0.217391	NM_001193333	B2RBL1|Q2YD73	Silent	SNP	ENST00000219150.5	37	CCDS10673.1																																																																																			.	.	none		0.612	CORO1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255195.2	NM_007074		T	30198463	C	T	30198463	2	4	4	1	0	0	0	0	0	0	0	1	3755	738	26	2		2	CORO1A	16	30198463	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	379407	30198463	60156290	157	497											
PLD2	5338	hgsc.bcm.edu	37	chr17	4711711	4711711	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagtctgctccctctggctcGgtgagggcgaccggactgct	4	9	15	13	3	2	1	0	1	2	0	4	4	3	2	2	4	2	3	2	4	0	0			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr17:4711711G>A	ENST00000263088.6	+	4	514	c.383G>A	c.(382-384)cGa>cAa	p.R128Q	RP11-81A22.5_ENST00000571067.1_lincRNA|PLD2_ENST00000572940.1_Splice_Site_p.R128Q	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2	128	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				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)	CCTCTGGCTCGGTGAGGGCGA	0.567																																					p.R128Q		Atlas-SNP	.											.	PLD2	138	.	0			c.G383A						PASS	.						131	132	132					17																	4711711		2203	4300	6503	SO:0001630	splice_region_variant	5338	exon4			TGGCTCGGTGAGG	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.383+1G>A	17.37:g.4711711G>A		62	0	0		45	13	0.288889	NM_001243108	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Missense_Mutation	SNP	ENST00000263088.6	37	CCDS11057.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.665808	0.88251	.	.	ENSG00000129219	ENST00000263088	T	0.08807	3.05	5.51	5.51	0.81932	Phox homologous domain (5);	0.110266	0.64402	D	0.000015	T	0.14056	0.0340	M	0.77103	2.36	0.80722	D	1	B;P	0.42248	0.26;0.774	B;B	0.36567	0.095;0.228	T	0.02313	-1.1178	10	0.41790	T	0.15	-22.7426	16.9089	0.86135	0.0:0.0:1.0:0.0	.	128;128	O14939-2;O14939	.;PLD2_HUMAN	Q	128	ENSP00000263088:R128Q	ENSP00000263088:R128Q	R	+	2	0	PLD2	4658675	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.337000	0.79256	2.578000	0.87016	0.561000	0.74099	CGA	.	.	none		0.567	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663	Missense_Mutation	A	4711711	G	A	4711711	5	1	4	1	0	0	0	0	0	0	1	0	12055	1130	39	1	393	1	PLD2	17	4711711	Splice_Site	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10		4711711	76483499	158	498											
SLC13A5	284111	hgsc.bcm.edu	37	chr17	6607294	6607294	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgcaatatggcctccacgatGggcaccatcatggccgtggt	8	9	12	12	2	1	0	1	0	0	0	2	1	2	0	4	4	1	2	4	4	2	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr17:6607294G>A	ENST00000433363.2	-	4	683	c.450C>T	c.(448-450)ccC>ccT	p.P150P	SLC13A5_ENST00000573648.1_Silent_p.P150P|SLC13A5_ENST00000293800.6_Silent_p.P133P|SLC13A5_ENST00000381074.4_Silent_p.P107P	NM_001284510.1|NM_177550.3	NP_001271439.1|NP_808218.1	Q86YT5	S13A5_HUMAN	solute carrier family 13 (sodium-dependent citrate transporter), member 5	150					transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	citrate transmembrane transporter activity (GO:0015137)|sodium:dicarboxylate symporter activity (GO:0017153)|succinate transmembrane transporter activity (GO:0015141)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|prostate(5)|skin(3)|urinary_tract(1)	26						CCTCCACGATGGGCACCATCA	0.637																																					p.P150P		Atlas-SNP	.											.	SLC13A5	57	.	0			c.C450T						PASS	.						54	47	49					17																	6607294		2203	4300	6503	SO:0001819	synonymous_variant	284111	exon4			CACGATGGGCACC	AJ489980	CCDS11079.1, CCDS45593.1, CCDS67136.1, CCDS67137.1	17p13.1	2013-05-22			ENSG00000141485	ENSG00000141485		"Solute carriers"	23089	protein-coding gene	gene with protein product		608305				12445824	Standard	NM_001284510		Approved	NACT	uc002gdj.3	Q86YT5	OTTHUMG00000102052	ENST00000433363.2:c.450C>T	17.37:g.6607294G>A		48	0	0		23	6	0.26087	NM_001143838	B3KXR0|B7Z4P2|B7ZLB4|F8W7N2|Q6ZMG1	Silent	SNP	ENST00000433363.2	37	CCDS11079.1																																																																																			.	.	none		0.637	SLC13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219853.2	NM_177550		A	6607294	G	A	6607294	2	1	4	1	0	0	0	0	0	0	0	1	14410	1335	47	2		2	SLC13A5	17	6607294	Silent	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	1895583	6607294	74587916	159	499											
PLD6	201164	hgsc.bcm.edu	37	chr17	17106346	17106346	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgagccagtgatgagcaccCtcttgtccacgatggcaaac	10	7	11	13	2	1	2	0	2	1	0	2	4	2	2	3	1	3	2	3	1	1	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr17:17106346C>G	ENST00000321560.3	-	2	522	c.494G>C	c.(493-495)aGg>aCg	p.R165T	RP11-45M22.4_ENST00000427497.3_3'UTR	NM_178836.3	NP_849158.2	Q8N2A8	PLD6_HUMAN	phospholipase D family, member 6	165	PLD phosphodiesterase. {ECO:0000255|PROSITE-ProRule:PRU00153}.				DNA methylation involved in gamete generation (GO:0043046)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|meiotic nuclear division (GO:0007126)|mitochondrial fusion (GO:0008053)|P granule organization (GO:0030719)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|piRNA metabolic process (GO:0034587)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)	cardiolipin hydrolase activity (GO:0035755)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)			endometrium(1)|lung(1)	2						GATGAGCACCCTCTTGTCCAC	0.532																																					p.R165T		Atlas-SNP	.											.	PLD6	9	.	0			c.G494C						PASS	.						134	105	115					17																	17106346		2203	4300	6503	SO:0001583	missense	201164	exon2			AGCACCCTCTTGT	AK090899	CCDS11182.1	17p11.2	2008-08-14			ENSG00000179598	ENSG00000179598			30447	protein-coding gene	gene with protein product		614960				12477932	Standard	NM_178836		Approved		uc002gqz.3	Q8N2A8	OTTHUMG00000059278	ENST00000321560.3:c.494G>C	17.37:g.17106346C>G	ENSP00000317177:p.Arg165Thr	161	0	0		105	21	0.2	NM_178836	Q8N5Y1	Missense_Mutation	SNP	ENST00000321560.3	37	CCDS11182.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.914|9.914	1.210336|1.210336	0.22289|0.22289	.|.	.|.	ENSG00000179598|ENSG00000179598	ENST00000427497|ENST00000321560	.|T	.|0.20881	.|2.04	5.15|5.15	2.94|2.94	0.34122|0.34122	.|Phospholipase D/Transphosphatidylase (2);	.|0.167628	.|0.50627	.|D	.|0.000117	T|T	0.13286|0.13286	0.0322|0.0322	L|L	0.35249|0.35249	1.045|1.045	0.27240|0.27240	N|N	0.959164|0.959164	.|B	.|0.22683	.|0.073	.|B	.|0.20577	.|0.03	T|T	0.19679|0.19679	-1.0298|-1.0298	6|10	0.87932|0.30854	D|T	0|0.27	-7.1851|-7.1851	5.2864|5.2864	0.15704|0.15704	0.0:0.231:0.1386:0.6304|0.0:0.231:0.1386:0.6304	.|.	.|165	.|Q8N2A8	.|PLD6_HUMAN	D|T	138|165	.|ENSP00000317177:R165T	ENSP00000394249:E138D|ENSP00000317177:R165T	E|R	-|-	3|2	2|0	PLD6|PLD6	17047071|17047071	0.962000|0.962000	0.33011|0.33011	0.997000|0.997000	0.53966|0.53966	0.623000|0.623000	0.37688|0.37688	1.395000|1.395000	0.34520|0.34520	0.395000|0.395000	0.25257|0.25257	-0.302000|-0.302000	0.09304|0.09304	GAG|AGG	.	.	none		0.532	PLD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131600.2	NM_178836		G	17106346	C	G	17106346	3	3	4	1	0	0	0	0	1	0	0	0	12059	681	24	4	268	4	PLD6	17	17106346	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	10499052	17106346	64088864	160	500											
KAT2A	2648	hgsc.bcm.edu	37	chr17	40267789	40267789	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcgtcggcgtaggtgaggaaGtagagaatgttgtgcttgat	9	12	16	4	3	0	3	0	2	0	1	2	5	0	4	0	3	1	4	0	3	4	4			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr17:40267789G>A	ENST00000225916.5	-	12	1880	c.1827C>T	c.(1825-1827)taC>taT	p.Y609Y		NM_021078.2	NP_066564.2	Q92830	KAT2A_HUMAN	K(lysine) acetyltransferase 2A	609	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				cell proliferation (GO:0008283)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|histone H3-K14 acetylation (GO:0044154)|in utero embryonic development (GO:0001701)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|positive regulation of gluconeogenesis (GO:0045722)|regulation of protein stability (GO:0031647)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|somitogenesis (GO:0001756)|telencephalon development (GO:0021537)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|extracellular space (GO:0005615)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	chromatin binding (GO:0003682)|H3 histone acetyltransferase activity (GO:0010484)|histone acetyltransferase activity (GO:0004402)|histone acetyltransferase activity (H4-K12 specific) (GO:0043997)|histone deacetylase binding (GO:0042826)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						AGGTGAGGAAGTAGAGAATGT	0.572																																					p.Y609Y		Atlas-SNP	.											.	KAT2A	54	.	0			c.C1827T						PASS	.						251	228	235					17																	40267789		2203	4300	6503	SO:0001819	synonymous_variant	2648	exon12			GAGGAAGTAGAGA	AF029777	CCDS11417.1	17q12-q21	2011-07-01	2008-07-04	2008-07-04	ENSG00000108773	ENSG00000108773		"Chromatin-modifying enzymes / K-acetyltransferases"	4201	protein-coding gene	gene with protein product		602301	"GCN5 general control of amino-acid synthesis 5-like 2 (yeast)"	GCN5L2		8552087	Standard	NM_021078		Approved	GCN5, PCAF-b	uc002hyx.2	Q92830	OTTHUMG00000133504	ENST00000225916.5:c.1827C>T	17.37:g.40267789G>A		70	0	0		52	8	0.153846	NM_021078	Q8N1A2|Q9UCW1	Silent	SNP	ENST00000225916.5	37	CCDS11417.1																																																																																			.	.	none		0.572	KAT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257458.1	NM_021078		A	40267789	G	A	40267789	2	1	4	1	0	0	0	0	0	0	0	1	7990	1024	36	2		2	KAT2A	17	40267789	Silent	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	23161443	40267789	40927421	161	501											
STAT3	6774	hgsc.bcm.edu	37	chr17	40474419	40474419	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaccaggatattggtagcaTccatgatcttatagcccatg	12	11	8	10	0	1	1	0	1	1	0	2	2	2	2	3	2	2	2	3	2	4	5			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr17:40474419T>A	ENST00000264657.5	-	21	2294	c.1982A>T	c.(1981-1983)gAt>gTt	p.D661V	STAT3_ENST00000588969.1_Missense_Mutation_p.D661V|STAT3_ENST00000389272.3_Missense_Mutation_p.D563V|STAT3_ENST00000585517.1_Missense_Mutation_p.D661V|STAT3_ENST00000404395.3_Missense_Mutation_p.D661V	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)	661	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)		ATTGGTAGCATCCATGATCTT	0.483									Hyperimmunoglobulin E Recurrent Infection Syndrome																												p.D661V		Atlas-SNP	.											STAT3,skin,lymphoid_neoplasm,-1,42	STAT3	268	42	0			c.A1982T						PASS	.						244	212	223					17																	40474419		2203	4300	6503	SO:0001583	missense	6774	exon21	Familial Cancer Database	HIES, Hyper IgE syndrome, autosomal dominant (Job syndrome) / recessive	GTAGCATCCATGA	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.1982A>T	17.37:g.40474419T>A	ENSP00000264657:p.Asp661Val	154	0	0		93	14	0.150538	NM_003150	A8K7B8|K7ENL3|O14916|Q9BW54	Missense_Mutation	SNP	ENST00000264657.5	37	CCDS32656.1	.	.	.	.	.	.	.	.	.	.	T	16.67	3.187509	0.57909	.	.	ENSG00000168610	ENST00000264657;ENST00000389272;ENST00000404395	D;D;D	0.89270	-2.49;-2.49;-2.49	4.47	4.47	0.54385	SH2 motif (4);	0.131223	0.56097	D	0.000040	D	0.89424	0.6711	N	0.24115	0.695	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.87578	0.996;0.998;0.998	D	0.88197	0.2881	10	0.30854	T	0.27	-36.2816	13.9124	0.63876	0.0:0.0:0.0:1.0	.	661;661;661	P40763-2;P40763;B5BTZ6	.;STAT3_HUMAN;.	V	661;563;661	ENSP00000264657:D661V;ENSP00000373923:D563V;ENSP00000384943:D661V	ENSP00000264657:D661V	D	-	2	0	STAT3	37727945	1.000000	0.71417	0.999000	0.59377	0.848000	0.48234	4.904000	0.63279	1.882000	0.54519	0.533000	0.62120	GAT	.	.	none		0.483	STAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319353.3	NM_139276, NM_003150		A	40474419	T	A	40474419	3	1	4	1	0	0	0	0	1	0	0	0	15281	1435	50	5	346	5	STAT3	17	40474419	Missense_Mutation	SNP	T	TCGA-FA-A6HN-01A-11D-A31X-10	206630	40474419	40720791	162	502											
SCRN2	90507	hgsc.bcm.edu	37	chr17	45915662	45915662	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctctccatcagccccagggCtgcctggtgtccacggtaga	6	9	11	15	1	2	1	1	0	1	1	5	1	4	1	5	3	2	2	5	3	1	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr17:45915662C>A	ENST00000290216.9	-	7	1218	c.1093G>T	c.(1093-1095)Gcc>Tcc	p.A365S	SCRN2_ENST00000407215.3_Missense_Mutation_p.A365S|SCRN2_ENST00000584123.1_Missense_Mutation_p.A373S	NM_001145023.1|NM_138355.3	NP_001138495.1|NP_612364.2	Q96FV2	SCRN2_HUMAN	secernin 2	365						extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)			cervix(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	14						AGCCCCAGGGCTGCCTGGTGT	0.597																																					p.A365S		Atlas-SNP	.											.	SCRN2	35	.	0			c.G1093T						PASS	.						59	60	59					17																	45915662		2203	4300	6503	SO:0001583	missense	90507	exon7			CCAGGGCTGCCTG	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.1093G>T	17.37:g.45915662C>A	ENSP00000290216:p.Ala365Ser	72	0	0		48	14	0.291667	NM_138355	A8K3N1|B7Z8S7|E9PBV5|Q96AC3|Q9BU04	Missense_Mutation	SNP	ENST00000290216.9	37	CCDS11519.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.850840	0.91277	.	.	ENSG00000141295	ENST00000290216;ENST00000407215	T;T	0.10573	3.09;2.86	5.66	5.66	0.87406	.	0.046551	0.85682	D	0.000000	T	0.39708	0.1088	M	0.85041	2.73	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.80764	0.991;0.994;0.991	T	0.24225	-1.0166	10	0.56958	D	0.05	-23.5455	18.5098	0.90911	0.0:1.0:0.0:0.0	.	365;365;365	E9PBV5;Q96FV2;B7Z8S7	.;SCRN2_HUMAN;.	S	365	ENSP00000290216:A365S;ENSP00000383935:A365S	ENSP00000290216:A365S	A	-	1	0	SCRN2	43270661	1.000000	0.71417	0.975000	0.42487	0.775000	0.43874	5.320000	0.65841	2.675000	0.91044	0.655000	0.94253	GCC	.	.	none		0.597	SCRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441383.1	NM_138355		A	45915662	C	A	45915662	3	1	4	1	0	0	0	0	1	0	0	0	13954	797	28	4	210	4	SCRN2	17	45915662	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	5441243	45915662	35279548	163	503											
MBTD1	54799	hgsc.bcm.edu	37	chr17	49281177	49281177	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggaggaacaagaggttttccGctggctgcacaccaaccaac	12	6	11	12	1	0	1	0	0	0	1	1	3	1	3	3	4	4	4	3	4	4	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr17:49281177G>A	ENST00000586178.1	-	8	1057	c.714C>T	c.(712-714)agC>agT	p.S238S	MBTD1_ENST00000415868.1_Silent_p.S238S|MBTD1_ENST00000376381.2_Silent_p.S238S	NM_017643.2	NP_060113.2	Q05BQ5	MBTD1_HUMAN	mbt domain containing 1	238					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)			GAGGTTTTCCGCTGGCTGCAC	0.363																																					p.S238S		Atlas-SNP	.											.	MBTD1	44	.	0			c.C714T						PASS	.						130	130	130					17																	49281177		2203	4300	6503	SO:0001819	synonymous_variant	54799	exon8			TTTTCCGCTGGCT	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.714C>T	17.37:g.49281177G>A		197	0	0		197	47	0.238579	NM_017643	Q6ZVU7|Q9NXU1	Silent	SNP	ENST00000586178.1	37	CCDS11581.2																																																																																			.	.	none		0.363	MBTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318124.1			A	49281177	G	A	49281177	2	1	4	1	0	0	0	0	0	0	0	1	9369	1078	38	1		1	MBTD1	17	49281177	Silent	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	3365515	49281177	31914033	164	504											
CA4	762	hgsc.bcm.edu	37	chr17	58227428	58227428	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggcgctcctggccctctcCgcggcgcggccatcggccag	2	6	14	19	6	1	0	0	0	1	0	4	0	2	0	5	5	0	1	5	5	0	0			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr17:58227428C>T	ENST00000300900.4	+	1	132	c.33C>T	c.(31-33)tcC>tcT	p.S11S		NM_000717.3	NP_000708.1	P22748	CAH4_HUMAN	carbonic anhydrase IV	11					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)	TGGCCCTCTCCGCGGCGCGGC	0.761																																					p.S11S		Atlas-SNP	.											.	CA4	20	.	0			c.C33T						PASS	.						10	12	11					17																	58227428		2156	4197	6353	SO:0001819	synonymous_variant	762	exon1			CCTCTCCGCGGCG	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.33C>T	17.37:g.58227428C>T		46	0	0		53	5	0.0943396	NM_000717	B4DQA4|Q6FHI7	Silent	SNP	ENST00000300900.4	37	CCDS11624.1																																																																																			.	.	none		0.761	CA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449189.1	NM_000717		T	58227428	C	T	58227428	2	4	4	1	0	0	0	0	0	0	0	1	2520	639	23	1		1	CA4	17	58227428	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	8946251	58227428	22967782	165	505											
SCN4A	6329	hgsc.bcm.edu	37	chr17	62045701	62045701	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgactggatcagggcccccaCgatcgtcttcagccctgacc	7	7	10	17	3	3	1	2	1	1	0	4	4	3	2	4	2	1	0	4	2	0	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr17:62045701C>T	ENST00000435607.1	-	6	794	c.718G>A	c.(718-720)Gtg>Atg	p.V240M	SCN4A_ENST00000578147.1_Missense_Mutation_p.V240M	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	240					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)	AGGGCCCCCACGATCGTCTTC	0.597																																					p.V240M		Atlas-SNP	.											.	SCN4A	205	.	0			c.G718A						PASS	.						69	70	70					17																	62045701		2092	4260	6352	SO:0001583	missense	6329	exon6			CCCCCACGATCGT	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.718G>A	17.37:g.62045701C>T	ENSP00000396320:p.Val240Met	107	0	0		80	6	0.075	NM_000334	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	37	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.275416	0.80580	.	.	ENSG00000007314	ENST00000435607	D	0.98968	-5.28	5.08	5.08	0.68730	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99309	0.9758	M	0.91090	3.175	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	D	0.99000	1.0811	10	0.87932	D	0	.	17.6345	0.88118	0.0:1.0:0.0:0.0	.	240	P35499	SCN4A_HUMAN	M	240	ENSP00000396320:V240M	ENSP00000396320:V240M	V	-	1	0	SCN4A	59399433	1.000000	0.71417	0.967000	0.41034	0.635000	0.38103	7.651000	0.83577	2.648000	0.89879	0.561000	0.74099	GTG	.	.	none		0.597	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		T	62045701	C	T	62045701	3	4	4	1	0	0	0	0	1	0	0	0	13935	536	19	1	4868	1	SCN4A	17	62045701	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	3818273	62045701	19149509	166	506											
ABCA10	10349	hgsc.bcm.edu	37	chr17	67178333	67178333	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccatttgaataagctccgtGaagttaaaaattcccataag	15	12	6	8	1	0	2	0	2	0	0	3	2	3	2	3	0	1	2	3	0	7	5			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr17:67178333G>T	ENST00000269081.4	-	23	3639	c.2730C>A	c.(2728-2730)ttC>ttA	p.F910L	ABCA10_ENST00000416101.2_3'UTR	NM_080282.3	NP_525021.3	Q8WWZ4	ABCAA_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 10	910					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)					TAAGCTCCGTGAAGTTAAAAA	0.378																																					p.F910L		Atlas-SNP	.											.	ABCA10	209	.	0			c.C2730A						PASS	.						52	50	50					17																	67178333		2203	4300	6503	SO:0001583	missense	10349	exon23			CTCCGTGAAGTTA	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.2730C>A	17.37:g.67178333G>T	ENSP00000269081:p.Phe910Leu	302	0	0		256	48	0.1875	NM_080282	C9JZH2|C9K035|Q6PIQ6|Q7Z2I9|Q7Z7P7|Q86TD2	Missense_Mutation	SNP	ENST00000269081.4	37	CCDS11684.1	.	.	.	.	.	.	.	.	.	.	G	1.793	-0.478907	0.04414	.	.	ENSG00000154263	ENST00000269081	D	0.82081	-1.57	2.76	-5.52	0.02560	.	1.124900	0.07235	U	0.863186	T	0.62319	0.2418	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	0.49986	-0.8880	10	0.11485	T	0.65	.	2.25	0.04041	0.1658:0.1157:0.3923:0.3262	.	910;910	E5RFN6;Q8WWZ4	.;ABCAA_HUMAN	L	910	ENSP00000269081:F910L	ENSP00000269081:F910L	F	-	3	2	ABCA10	64689928	0.000000	0.05858	0.000000	0.03702	0.070000	0.16714	-0.996000	0.03709	-1.060000	0.03189	0.186000	0.17326	TTC	.	.	none		0.378	ABCA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379881.4	NM_080282		T	67178333	G	T	67178333	3	4	4	1	0	0	0	0	1	0	0	0	29	1281	45	4	1973	4	ABCA10	17	67178333	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	5132632	67178333	14016877	167	507											
TNRC6C	57690	hgsc.bcm.edu	37	chr17	76045908	76045908	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tggggactgtccccaggtaaCcctgccacaggaaatagcaa	12	6	11	12	0	0	0	0	0	0	0	1	2	1	2	4	4	3	2	4	4	4	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr17:76045908C>T	ENST00000588061.1	+	5	1492	c.765C>T	c.(763-765)aaC>aaT	p.N255N	TNRC6C_ENST00000588847.1_Silent_p.N255N|TNRC6C_ENST00000544502.1_Silent_p.N255N|TNRC6C_ENST00000301624.4_Silent_p.N255N|TNRC6C_ENST00000335749.4_Silent_p.N255N|TNRC6C_ENST00000541771.1_Silent_p.N255N			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	255	Gly-rich.|Sufficient for interaction with argonaute family proteins.				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)			CCCCAGGTAACCCTGCCACAG	0.498																																					p.N255N		Atlas-SNP	.											TNRC6C,NS,carcinoma,+1,1	TNRC6C	173	1	0			c.C765T						PASS	.						70	72	71					17																	76045908		1950	4151	6101	SO:0001819	synonymous_variant	57690	exon4			AGGTAACCCTGCC	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.765C>T	17.37:g.76045908C>T		63	0	0		61	25	0.409836	NM_018996	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Silent	SNP	ENST00000588061.1	37	CCDS45798.1																																																																																			.	.	none		0.498	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996		T	76045908	C	T	76045908	2	4	4	1	0	0	0	0	0	0	0	1	16357	506	18	2		2	TNRC6C	17	76045908	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	8867575	76045908	5149302	168	508											
GZMM	3004	hgsc.bcm.edu	37	chr19	549011	549011	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcagcagggactcggtgcagCatggccggctgggggctgac	6	5	19	11	2	0	1	0	1	0	0	1	2	0	2	1	6	3	6	1	6	0	0			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr19:549011C>T	ENST00000264553.3	+	4	476	c.438C>T	c.(436-438)agC>agT	p.S146S		NM_001258351.1|NM_005317.3	NP_001245280.1|NP_005308	P51124	GRAM_HUMAN	granzyme M (lymphocyte met-ase 1)	146	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)		CTCGGTGCAGCATGGCCGGCT	0.687																																					p.S146S		Atlas-SNP	.											GZMM,bladder,carcinoma,+1,1	GZMM	11	1	0			c.C438T						PASS	.						13	15	14					19																	549011		2189	4274	6463	SO:0001819	synonymous_variant	3004	exon4			GTGCAGCATGGCC		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.438C>T	19.37:g.549011C>T		94	0	0		103	11	0.106796	NM_005317		Silent	SNP	ENST00000264553.3	37	CCDS12031.1																																																																																			.	.	none		0.687	GZMM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451895.2	NM_005317		T	549011	C	T	549011	2	4	4	1	0	0	0	0	0	0	0	1	6928	709	25	2		2	GZMM	19	549011	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10		549011	58579972	169	509											
GADD45B	4616	hgsc.bcm.edu	37	chr19	2476602	2476602	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gatcgcctcacagtgggggtGtacgagtcggccaagttgat	8	9	15	9	3	1	1	1	1	0	0	3	3	1	1	2	3	1	2	2	3	2	2	rs544016078	byFrequency	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr19:2476602G>A	ENST00000215631.4	+	2	352	c.120G>A	c.(118-120)gtG>gtA	p.V40V	GADD45B_ENST00000587345.1_Silent_p.V40V	NM_015675.3	NP_056490.2	O75293	GA45B_HUMAN	growth arrest and DNA-damage-inducible, beta	40					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)				cervix(2)|lung(1)|ovary(1)	4		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)		CAGTGGGGGTGTACGAGTCGG	0.652											OREG0025141	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2	0.000399361	0.0008	0.0	5008	,	,		14231	0.001		0.0	False		,,,				2504	0.0				p.V40V		Atlas-SNP	.											.	GADD45B	6	.	0			c.G120A						PASS	.						76	65	69					19																	2476602		2203	4300	6503	SO:0001819	synonymous_variant	4616	exon2			GGGGGTGTACGAG	AF090950	CCDS32868.1	19p13.3	2012-10-02			ENSG00000099860	ENSG00000099860			4096	protein-coding gene	gene with protein product	"myeloid differentiation primary response", "growth arrest and DNA-damage-inducible beta"	604948		MYD118		1899477, 9827804	Standard	NM_015675		Approved	GADD45BETA, DKFZP566B133	uc002lwb.2	O75293	OTTHUMG00000180434	ENST00000215631.4:c.120G>A	19.37:g.2476602G>A		76	0	0	603	66	12	0.181818	NM_015675	A8KAM2|O75960|Q17R46	Silent	SNP	ENST00000215631.4	37	CCDS32868.1																																																																																			.	.	none		0.652	GADD45B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451337.1	NM_015675		A	2476602	G	A	2476602	2	1	4	1	0	0	0	0	0	0	0	1	6190	1364	48	2		2	GADD45B	19	2476602	Silent	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	1927591	2476602	56652381	170	510											
KIAA1543	57662	hgsc.bcm.edu	37	chr19	7670117	7670117	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctatgcccccacagagcacGtgcccccggagctgtgggag	7	6	13	15	2	1	1	0	0	1	1	1	3	1	3	4	2	4	2	4	2	1	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr19:7670117G>T	ENST00000160298.4	+	2	255	c.154G>T	c.(154-156)Gtg>Ttg	p.V52L	CAMSAP3_ENST00000446248.2_Missense_Mutation_p.V52L	NM_020902.1	NP_065953.1	Q9P1Y5	CAMP3_HUMAN	calmodulin regulated spectrin-associated protein family, member 3	52					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						CACAGAGCACGTGCCCCCGGA	0.607																																					p.V52L		Atlas-SNP	.											KIAA1543,rectum,carcinoma,-2,4	CAMSAP3	131	4	0			c.G154T						PASS	.						107	117	114					19																	7670117		2016	4180	6196	SO:0001583	missense	57662	exon2			GAGCACGTGCCCC	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.154G>T	19.37:g.7670117G>T	ENSP00000160298:p.Val52Leu	83	0	0		69	4	0.057971	NM_020902	Q8NDF1	Missense_Mutation	SNP	ENST00000160298.4	37	CCDS42489.1	.	.	.	.	.	.	.	.	.	.	g	18.62	3.663861	0.67700	.	.	ENSG00000076826	ENST00000446248;ENST00000160298	T;T	0.22539	1.98;1.95	4.45	4.45	0.53987	.	0.000000	0.64402	D	0.000003	T	0.47060	0.1425	M	0.73598	2.24	0.42982	D	0.994469	D;D	0.89917	1.0;0.996	D;D	0.81914	0.995;0.989	T	0.53872	-0.8377	10	0.72032	D	0.01	-29.4892	15.8571	0.78987	0.0:0.0:1.0:0.0	.	52;52	Q9P1Y5;Q9P1Y5-2	CAMP3_HUMAN;.	L	52	ENSP00000416797:V52L;ENSP00000160298:V52L	ENSP00000160298:V52L	V	+	1	0	KIAA1543	7576117	1.000000	0.71417	1.000000	0.80357	0.569000	0.35902	5.354000	0.66040	2.005000	0.58758	0.478000	0.44815	GTG	.	.	none		0.607	CAMSAP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459300.1	XM_048362		T	7670117	G	T	7670117	3	4	4	1	0	0	0	0	1	0	0	0	8252	1145	40	4	160	4	KIAA1543	19	7670117	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	5193515	7670117	51458866	171	511											
MUC16	94025	hgsc.bcm.edu	37	chr19	9072256	9072256	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgaagtcataggagaggagaGcttatcctctggtaaggtag	12	10	14	5	0	2	3	1	1	1	2	3	5	3	3	1	4	1	3	1	4	5	4			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr19:9072256G>T	ENST00000397910.4	-	3	15393	c.15190C>A	c.(15190-15192)Ctc>Atc	p.L5064I		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5066	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						GGAGAGGAGAGCTTATCCTCT	0.478																																					p.L5064I		Atlas-SNP	.											.	MUC16	4315	.	0			c.C15190A						PASS	.						122	112	115					19																	9072256		1940	4136	6076	SO:0001583	missense	94025	exon3			AGGAGAGCTTATC	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.15190C>A	19.37:g.9072256G>T	ENSP00000381008:p.Leu5064Ile	90	0	0		67	11	0.164179	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	4.778	0.144639	0.09134	.	.	ENSG00000181143	ENST00000397910	T	0.21932	1.98	1.74	-0.916	0.10489	.	.	.	.	.	T	0.07369	0.0186	N	0.08118	0	.	.	.	P	0.46020	0.871	B	0.31751	0.135	T	0.24404	-1.0161	8	0.87932	D	0	.	5.907	0.19006	0.0:0.0:0.4445:0.5555	.	5064	B5ME49	.	I	5064	ENSP00000381008:L5064I	ENSP00000381008:L5064I	L	-	1	0	MUC16	8933256	0.000000	0.05858	0.000000	0.03702	0.150000	0.21749	-2.735000	0.00802	-0.101000	0.12219	0.282000	0.19409	CTC	.	.	none		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9072256	G	T	9072256	3	4	4	1	0	0	0	0	1	0	0	0	9982	971	34	4	28661	4	MUC16	19	9072256	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	1402139	9072256	50056727	172	512											
OR7G3	390883	hgsc.bcm.edu	37	chr19	9236917	9236917	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgacccgcagatggaaaaaGctttatactttccaccagct	12	10	8	11	1	0	2	0	1	0	1	1	3	1	3	3	1	3	3	3	1	4	4	rs61730387|rs75266995	byFrequency	TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr19:9236917G>A	ENST00000305444.2	-	1	709	c.710C>T	c.(709-711)gCt>gTt	p.A237V		NM_001001958.1	NP_001001958.1	Q8NG95	OR7G3_HUMAN	olfactory receptor, family 7, subfamily G, member 3	237						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A237fs*9(1)		NS(2)|endometrium(1)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15						GATGGAAAAAGCTTTATACTT	0.448																																					p.A237V		Atlas-SNP	.											.	OR7G3	41	.	1	Deletion - Frameshift(1)	liver(1)	c.C710T						PASS	.						93	99	97					19																	9236917		2190	4290	6480	SO:0001583	missense	390883	exon1			GAAAAAGCTTTAT		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.710C>T	19.37:g.9236917G>A	ENSP00000302867:p.Ala237Val	142	0	0		104	6	0.0576923	NM_001001958	Q6IFJ6|Q96R99	Missense_Mutation	SNP	ENST00000305444.2	37	CCDS32899.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.209809	0.79240	.	.	ENSG00000170920	ENST00000305444	T	0.00342	8.03	3.96	2.91	0.33838	GPCR, rhodopsin-like superfamily (1);	0.181685	0.25975	N	0.027104	T	0.00580	0.0019	M	0.79475	2.455	0.26503	N	0.974731	P	0.50710	0.938	P	0.57324	0.818	T	0.33111	-0.9881	10	0.66056	D	0.02	.	10.7615	0.46268	0.0964:0.0:0.9035:0.0	rs61730387	237	Q8NG95	OR7G3_HUMAN	V	237	ENSP00000302867:A237V	ENSP00000302867:A237V	A	-	2	0	OR7G3	9097917	0.979000	0.34478	0.007000	0.13788	0.341000	0.28922	3.298000	0.51818	1.038000	0.40049	0.551000	0.68910	GCT	G|0.935;A|0.065	0.065	strong		0.448	OR7G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384611.1			A	9236917	G	A	9236917	3	1	4	1	0	0	0	0	1	0	0	0	11233	971	34	2	231	2	OR7G3	19	9236917	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	164661	9236917	49892066	173	513											
ZNF846	162993	hgsc.bcm.edu	37	chr19	9868728	9868728	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaataaaagcttttccacacTccttacattcatatggcttt	12	15	4	10	0	1	0	1	0	0	0	3	1	3	0	2	1	2	2	2	1	5	7			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr19:9868728T>C	ENST00000397902.2	-	6	1438	c.1025A>G	c.(1024-1026)gAg>gGg	p.E342G	ZNF846_ENST00000592859.1_Intron|ZNF846_ENST00000588267.1_Intron|ZNF846_ENST00000586293.1_3'UTR	NM_001077624.1	NP_001071092.1	Q147U1	ZN846_HUMAN	zinc finger protein 846	342					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(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22						TTTTCCACACTCCTTACATTC	0.383																																					p.E342G		Atlas-SNP	.											.	ZNF846	61	.	0			c.A1025G						PASS	.						52	57	55					19																	9868728		2174	4292	6466	SO:0001583	missense	162993	exon6			CCACACTCCTTAC	AK097652	CCDS42496.1	19p13.2	2013-01-08			ENSG00000196605	ENSG00000196605		"Zinc fingers, C2H2-type", "-"	27260	protein-coding gene	gene with protein product							Standard	NM_001077624		Approved		uc002mmb.1	Q147U1		ENST00000397902.2:c.1025A>G	19.37:g.9868728T>C	ENSP00000380999:p.Glu342Gly	81	0	0		80	15	0.1875	NM_001077624	A8K0H1|B3KUP1	Missense_Mutation	SNP	ENST00000397902.2	37	CCDS42496.1	.	.	.	.	.	.	.	.	.	.	.	16.53	3.150075	0.57151	.	.	ENSG00000196605	ENST00000397902	T	0.07444	3.19	2.01	0.932	0.19466	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09113	0.0225	M	0.65320	2	0.09310	N	1	B	0.30793	0.295	B	0.30855	0.121	T	0.29731	-1.0002	8	.	.	.	.	5.5686	0.17184	0.2448:0.0:0.0:0.7551	.	342	Q147U1	ZN846_HUMAN	G	342	ENSP00000380999:E342G	.	E	-	2	0	ZNF846	9729728	0.000000	0.05858	0.012000	0.15200	0.932000	0.56968	-0.585000	0.05794	0.217000	0.20800	0.374000	0.22700	GAG	.	.	none		0.383	ZNF846-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450253.1	NM_001077624		C	9868728	T	C	9868728	3	2	4	1	0	0	0	0	1	0	0	0	18207	1551	54	3	580	3	ZNF846	19	9868728	Missense_Mutation	SNP	T	TCGA-FA-A6HN-01A-11D-A31X-10	631811	9868728	49260255	174	514											
AKAP8	10270	hgsc.bcm.edu	37	chr19	15484046	15484046	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aagctgccattgcggtcggaCcccaggtcgaactcatagtc	9	8	11	13	3	1	0	1	0	0	0	4	2	1	1	3	3	4	1	3	3	3	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr19:15484046C>T	ENST00000269701.2	-	5	537	c.477G>A	c.(475-477)ggG>ggA	p.G159G		NM_005858.3	NP_005849.1	O43823	AKAP8_HUMAN	A kinase (PRKA) anchor protein 8	159					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						TGCGGTCGGACCCCAGGTCGA	0.662																																					p.G159G	GBM(190;1671 2163 3274 27186 30476)	Atlas-SNP	.											.	AKAP8	68	.	0			c.G477A						PASS	.						31	36	34					19																	15484046		2203	4300	6503	SO:0001819	synonymous_variant	10270	exon5			GTCGGACCCCAGG	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.477G>A	19.37:g.15484046C>T		105	0	0		97	17	0.175258	NM_005858		Silent	SNP	ENST00000269701.2	37	CCDS12329.1																																																																																			.	.	none		0.662	AKAP8-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461293.3	NM_005858		T	15484046	C	T	15484046	2	4	4	1	0	0	0	0	0	0	0	1	457	494	18	2		2	AKAP8	19	15484046	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	5615318	15484046	43644937	175	515											
KLF2	10365	hgsc.bcm.edu	37	chr19	16436027	16436027	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cattgccctgtcgcccgcagCgctggccgcgcgccgaaccc	4	5	12	20	7	0	0	0	0	0	0	1	1	0	0	5	1	3	2	5	1	1	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr19:16436027C>T	ENST00000248071.5	+	2	183	c.76C>T	c.(76-78)Cgc>Tgc	p.R26C	CTD-2562J15.6_ENST00000588799.1_RNA|KLF2_ENST00000592003.1_Intron	NM_016270.2	NP_057354.1	Q9Y5W3	KLF2_HUMAN	Kruppel-like factor 2	26					cell morphogenesis (GO:0000902)|cellular response to cycloheximide (GO:0071409)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to peptide (GO:1901653)|cellular response to tumor necrosis factor (GO:0071356)|erythrocyte maturation (GO:0043249)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of interleukin-6 production (GO:0032715)|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 gene expression, epigenetic (GO:0040029)|transcription, DNA-templated (GO:0006351)|Type I pneumocyte differentiation (GO:0060509)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			haematopoietic_and_lymphoid_tissue(3)|lung(1)|skin(1)	5						TCGCCCGCAGCGCTGGCCGCG	0.721																																					p.R26C		Atlas-SNP	.											.	KLF2	10	.	0			c.C76T						PASS	.						2	2	2					19																	16436027		1269	2632	3901	SO:0001630	splice_region_variant	10365	exon2			CCGCAGCGCTGGC	AF123344	CCDS12343.1	19p13.11	2013-10-15	2013-10-15		ENSG00000127528	ENSG00000127528		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	6347	protein-coding gene	gene with protein product		602016	"Kruppel-like factor 2 (lung)"			10217429, 10458913	Standard	NM_016270		Approved	LKLF	uc002ndw.3	Q9Y5W3	OTTHUMG00000182330	ENST00000248071.5:c.76-1C>T	19.37:g.16436027C>T		17	0	0		35	6	0.171429	NM_016270	Q6IPC4|Q9UJS5|Q9UKR6	Missense_Mutation	SNP	ENST00000248071.5	37	CCDS12343.1	.	.	.	.	.	.	.	.	.	.	C	7.506	0.653605	0.14580	.	.	ENSG00000127528	ENST00000248071	T	0.18016	2.24	2.41	1.31	0.21738	.	.	.	.	.	T	0.15609	0.0376	M	0.64404	1.975	0.20403	N	0.99991	B	0.15473	0.013	B	0.08055	0.003	T	0.28364	-1.0046	8	.	.	.	.	4.9114	0.13823	0.0:0.6813:0.0:0.3187	.	26	Q9Y5W3	KLF2_HUMAN	C	26	ENSP00000248071:R26C	.	R	+	1	0	KLF2	16297027	1.000000	0.71417	0.987000	0.45799	0.016000	0.09150	0.844000	0.27654	0.221000	0.20879	-1.492000	0.00969	CGC	.	.	none		0.721	KLF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460562.1		Missense_Mutation	T	16436027	C	T	16436027	5	4	4	1	0	0	0	0	0	0	1	0	8355	782	27	1	82	1	KLF2	19	16436027	Splice_Site	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	951981	16436027	42692956	176	516			3	6		3	3	807	N	G_C	1.335979e-05
KLF2	10365	hgsc.bcm.edu	37	chr19	16436806	16436806	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgcggcaagacctacaccaaGagttcgcatctgaaggcgca	12	6	11	12	3	1	3	0	1	1	2	2	3	1	3	2	2	2	4	2	2	4	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr19:16436806G>C	ENST00000248071.5	+	2	962	c.855G>C	c.(853-855)aaG>aaC	p.K285N	CTD-2562J15.6_ENST00000588799.1_RNA|KLF2_ENST00000592003.1_Intron	NM_016270.2	NP_057354.1	Q9Y5W3	KLF2_HUMAN	Kruppel-like factor 2	285					cell morphogenesis (GO:0000902)|cellular response to cycloheximide (GO:0071409)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to peptide (GO:1901653)|cellular response to tumor necrosis factor (GO:0071356)|erythrocyte maturation (GO:0043249)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of interleukin-6 production (GO:0032715)|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 gene expression, epigenetic (GO:0040029)|transcription, DNA-templated (GO:0006351)|Type I pneumocyte differentiation (GO:0060509)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			haematopoietic_and_lymphoid_tissue(3)|lung(1)|skin(1)	5						CCTACACCAAGAGTTCGCATC	0.692																																					p.K285N		Atlas-SNP	.											.	KLF2	10	.	0			c.G855C						PASS	.						10	6	7					19																	16436806		2111	4164	6275	SO:0001583	missense	10365	exon2			CACCAAGAGTTCG	AF123344	CCDS12343.1	19p13.11	2013-10-15	2013-10-15		ENSG00000127528	ENSG00000127528		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	6347	protein-coding gene	gene with protein product		602016	"Kruppel-like factor 2 (lung)"			10217429, 10458913	Standard	NM_016270		Approved	LKLF	uc002ndw.3	Q9Y5W3	OTTHUMG00000182330	ENST00000248071.5:c.855G>C	19.37:g.16436806G>C	ENSP00000248071:p.Lys285Asn	35	0	0		31	9	0.290323	NM_016270	Q6IPC4|Q9UJS5|Q9UKR6	Missense_Mutation	SNP	ENST00000248071.5	37	CCDS12343.1	.	.	.	.	.	.	.	.	.	.	G	15.82	2.944729	0.53079	.	.	ENSG00000127528	ENST00000248071	T	0.36157	1.27	3.44	3.44	0.39384	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.59542	0.2201	M	0.78049	2.395	0.80722	D	1	D	0.76494	0.999	D	0.72625	0.978	T	0.67248	-0.5718	9	0.87932	D	0	.	14.2198	0.65818	0.0:0.0:1.0:0.0	.	285	Q9Y5W3	KLF2_HUMAN	N	285	ENSP00000248071:K285N	ENSP00000248071:K285N	K	+	3	2	KLF2	16297806	1.000000	0.71417	1.000000	0.80357	0.157000	0.22087	6.161000	0.71868	1.627000	0.50400	0.460000	0.39030	AAG	.	.	none		0.692	KLF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460562.1			C	16436806	G	C	16436806	3	2	4	1	0	0	0	0	1	0	0	0	8355	933	33	4	861	4	KLF2	19	16436806	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	779	16436806	42692177	177	517			3	6		3	3	807	N	G_C	1.335979e-05
KLF2	10365	hgsc.bcm.edu	37	chr19	16436833	16436833	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catctgaaggcgcatctgcgCacgcacacaggtgggcggca	9	5	14	13	4	2	1	0	1	2	0	2	1	2	1	0	4	1	4	0	4	1	0			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr19:16436833C>G	ENST00000248071.5	+	2	989	c.882C>G	c.(880-882)cgC>cgG	p.R294R	CTD-2562J15.6_ENST00000588799.1_RNA|KLF2_ENST00000592003.1_Intron	NM_016270.2	NP_057354.1	Q9Y5W3	KLF2_HUMAN	Kruppel-like factor 2	294					cell morphogenesis (GO:0000902)|cellular response to cycloheximide (GO:0071409)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to peptide (GO:1901653)|cellular response to tumor necrosis factor (GO:0071356)|erythrocyte maturation (GO:0043249)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of interleukin-6 production (GO:0032715)|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 gene expression, epigenetic (GO:0040029)|transcription, DNA-templated (GO:0006351)|Type I pneumocyte differentiation (GO:0060509)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			haematopoietic_and_lymphoid_tissue(3)|lung(1)|skin(1)	5						CGCATCTGCGCACGCACACAG	0.662																																					p.R294R		Atlas-SNP	.											.	KLF2	10	.	0			c.C882G						PASS	.						8	5	6					19																	16436833		2066	4108	6174	SO:0001819	synonymous_variant	10365	exon2			TCTGCGCACGCAC	AF123344	CCDS12343.1	19p13.11	2013-10-15	2013-10-15		ENSG00000127528	ENSG00000127528		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	6347	protein-coding gene	gene with protein product		602016	"Kruppel-like factor 2 (lung)"			10217429, 10458913	Standard	NM_016270		Approved	LKLF	uc002ndw.3	Q9Y5W3	OTTHUMG00000182330	ENST00000248071.5:c.882C>G	19.37:g.16436833C>G		33	0	0		28	9	0.321429	NM_016270	Q6IPC4|Q9UJS5|Q9UKR6	Silent	SNP	ENST00000248071.5	37	CCDS12343.1																																																																																			.	.	none		0.662	KLF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460562.1			G	16436833	C	G	16436833	2	3	4	1	0	0	0	0	0	0	0	1	8355	697	25	4		4	KLF2	19	16436833	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	27	16436833	42692150	178	518			3	6		3	3	807	N	G_C	1.335979e-05
ZNF208	7757	hgsc.bcm.edu	37	chr19	22157028	22157028	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttatgtttagtaaggattgCagattggttaaaagccttgc	11	15	10	5	0	0	1	0	0	0	1	0	2	0	2	1	2	3	4	1	2	5	8	rs202182420		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr19:22157028C>A	ENST00000397126.4	-	4	956	c.808G>T	c.(808-810)Gca>Tca	p.A270S	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	270					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)				GTAAGGATTGCAGATTGGTTA	0.363																																					p.A270S		Atlas-SNP	.											.	ZNF208	817	.	0			c.G808T						PASS	.						33	36	35					19																	22157028		2135	4261	6396	SO:0001583	missense	7757	exon4			GGATTGCAGATTG	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.808G>T	19.37:g.22157028C>A	ENSP00000380315:p.Ala270Ser	40	0	0		42	6	0.142857	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	C	0	-2.619833	0.00118	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.12465	2.68	2.89	-5.78	0.02362	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03959	0.0111	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35773	-0.9775	8	0.02654	T	1	.	5.8775	0.18836	0.3922:0.3729:0.0:0.2349	.	270	O43345	ZN208_HUMAN	S	270	ENSP00000380315:A270S	ENSP00000380315:A270S	A	-	1	0	ZNF208	21948868	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.978000	0.01494	-2.348000	0.00619	-2.562000	0.00173	GCA	C|0.996;A|0.004	0.004	weak		0.363	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		A	22157028	C	A	22157028	3	1	4	1	0	0	0	0	1	0	0	0	17781	710	25	4	3038	4	ZNF208	19	22157028	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	5720195	22157028	36971955	179	519											
ZNF570	148268	hgsc.bcm.edu	37	chr19	37975034	37975034	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaatataaatcttggggaagTtttcatcagaacccactgct	13	12	8	8	0	3	1	2	0	1	1	3	3	3	2	1	2	2	2	1	2	6	5			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr19:37975034T>C	ENST00000330173.1	+	5	1039	c.510T>C	c.(508-510)agT>agC	p.S170S	ZNF570_ENST00000388801.3_5'UTR|ZNF570_ENST00000586475.1_Silent_p.S226S	NM_144694.1	NP_653295.1	Q96NI8	ZN570_HUMAN	zinc finger protein 570	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)			endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(1)	27			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CTTGGGGAAGTTTTCATCAGA	0.363																																					p.S170S		Atlas-SNP	.											.	ZNF570	58	.	0			c.T510C						PASS	.						118	129	125					19																	37975034		2203	4300	6503	SO:0001819	synonymous_variant	148268	exon5			GGGAAGTTTTCAT	AK055353	CCDS12504.1, CCDS74355.1	19q13.12	2013-09-20			ENSG00000171827	ENSG00000171827		"Zinc fingers, C2H2-type", "-"	26416	protein-coding gene	gene with protein product							Standard	XM_005258567		Approved	FLJ30791	uc002ogk.1	Q96NI8	OTTHUMG00000048176	ENST00000330173.1:c.510T>C	19.37:g.37975034T>C		79	0	0		81	18	0.222222	NM_144694	A1L472|B4DMP1	Silent	SNP	ENST00000330173.1	37	CCDS12504.1																																																																																			.	.	none		0.363	ZNF570-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109600.1	NM_144694		C	37975034	T	C	37975034	2	2	4	1	0	0	0	0	0	0	0	1	18017	1722	60	3		3	ZNF570	19	37975034	Silent	SNP	T	TCGA-FA-A6HN-01A-11D-A31X-10	15818006	37975034	21153949	180	520											
HIF3A	64344	hgsc.bcm.edu	37	chr19	46832549	46832549	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	caacgccagcgagcagctacCcagggcctaccacagacctc	11	3	9	18	2	0	1	0	0	0	1	1	2	0	1	5	1	6	2	5	1	3	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr19:46832549C>T	ENST00000377670.4	+	12	1557	c.1526C>T	c.(1525-1527)cCc>cTc	p.P509L	HIF3A_ENST00000244303.6_Missense_Mutation_p.P440L|HIF3A_ENST00000420102.2_Missense_Mutation_p.P458L|AC007193.10_ENST00000596807.1_RNA|HIF3A_ENST00000472815.1_Intron|HIF3A_ENST00000339613.2_Missense_Mutation_p.P453L|HIF3A_ENST00000600383.1_Missense_Mutation_p.P440L|HIF3A_ENST00000300862.3_Missense_Mutation_p.P507L	NM_152795.3	NP_690008.2	Q9Y2N7	HIF3A_HUMAN	hypoxia inducible factor 3, alpha subunit	509	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)			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)		GAGCAGCTACCCAGGGCCTAC	0.647																																					p.P509L		Atlas-SNP	.											.	HIF3A	154	.	0			c.C1526T						PASS	.						58	58	58					19																	46832549		2203	4300	6503	SO:0001583	missense	64344	exon12			AGCTACCCAGGGC	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.1526C>T	19.37:g.46832549C>T	ENSP00000366898:p.Pro509Leu	109	0	0		90	18	0.2	NM_152795	B0M185|B4DNA2|Q58A43|Q66K72|Q8WXA1|Q96K34|Q9H7Z9|Q9HAI2	Missense_Mutation	SNP	ENST00000377670.4	37	CCDS12681.2	.	.	.	.	.	.	.	.	.	.	C	14.57	2.574652	0.45902	.	.	ENSG00000124440	ENST00000244302;ENST00000377670;ENST00000244303;ENST00000339613;ENST00000291300;ENST00000300862;ENST00000420102	D;D;D;D;D	0.86694	-2.16;-2.16;-2.16;-2.16;-2.16	4.82	3.72	0.42706	.	0.243027	0.21541	N	0.072885	T	0.82263	0.4999	N	0.22421	0.69	0.39731	D	0.971608	P;P;P;P;P;P	0.48089	0.782;0.905;0.573;0.77;0.626;0.626	B;B;B;P;B;B	0.48598	0.423;0.419;0.294;0.583;0.419;0.419	D	0.84495	0.0613	10	0.72032	D	0.01	.	10.954	0.47347	0.1862:0.8138:0.0:0.0	.	458;440;507;453;509;509	F5H884;B4DNA2;Q9Y2N7-2;A8MPQ1;Q9Y2N7;B0M185	.;.;.;.;HIF3A_HUMAN;.	L	509;509;440;453;453;507;458	ENSP00000366898:P509L;ENSP00000244303:P440L;ENSP00000341877:P453L;ENSP00000300862:P507L;ENSP00000407771:P458L	ENSP00000244302:P509L	P	+	2	0	HIF3A	51524389	0.975000	0.34042	0.999000	0.59377	0.999000	0.98932	2.401000	0.44513	2.394000	0.81467	0.655000	0.94253	CCC	.	.	none		0.647	HIF3A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280556.3			T	46832549	C	T	46832549	3	4	4	1	0	0	0	0	1	0	0	0	7114	623	22	2	1596	2	HIF3A	19	46832549	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	8857515	46832549	12296434	181	521											
SIGLEC5	8778	hgsc.bcm.edu	37	chr19	52131127	52131127	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaaatttgcaggaagcccagCgggtgctgagcgcggcaggt	10	6	16	9	3	0	1	0	1	0	0	0	2	0	2	1	4	5	3	1	4	3	1	rs528680868		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr19:52131127C>T	ENST00000534261.2	-	6	1356	c.957G>A	c.(955-957)ccG>ccA	p.P319P	SIGLEC5_ENST00000222107.4_Silent_p.P319P|SIGLEC5_ENST00000429354.3_Silent_p.P319P|SIGLEC5_ENST00000599649.1_Silent_p.P319P|SIGLEC5_ENST00000570106.2_Silent_p.P319P			O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5	319	Ig-like C2-type 2.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)	p.P319P(1)		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)		GGAAGCCCAGCGGGTGCTGAG	0.557													C|||	1	0.000199681	0.0	0.0	5008	,	,		17624	0.0		0.0	False		,,,				2504	0.001				p.P319P		Atlas-SNP	.											SIGLEC5,NS,carcinoma,0,2	SIGLEC5	67	2	1	Substitution - coding silent(1)	endometrium(1)	c.G957A						PASS	.						34	39	37					19																	52131127		2203	4300	6503	SO:0001819	synonymous_variant	8778	exon5			GCCCAGCGGGTGC	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.957G>A	19.37:g.52131127C>T		128	0	0		110	20	0.181818	NM_003830		Silent	SNP	ENST00000534261.2	37	CCDS33088.1																																																																																			.	.	none		0.557	SIGLEC5-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466897.2	NM_003830		T	52131127	C	T	52131127	2	4	4	1	0	0	0	0	0	0	0	1	14326	755	27	1		1	SIGLEC5	19	52131127	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	5298578	52131127	6997856	182	522											
ZNF534	147658	hgsc.bcm.edu	37	chr19	52941505	52941505	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcacaacatcagaaaattcaTactggacagaaaccttacaa	19	7	5	10	0	2	2	2	0	0	2	2	3	2	3	1	1	4	1	1	1	7	3			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr19:52941505T>C	ENST00000332323.6	+	4	892	c.831T>C	c.(829-831)caT>caC	p.H277H	ZNF534_ENST00000301085.4_Intron|ZNF534_ENST00000433050.1_Silent_p.H264H|ZNF534_ENST00000432303.2_Intron	NM_001143939.1	NP_001137411.1	Q76KX8	ZN534_HUMAN	zinc finger protein 534	277					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						AGAAAATTCATACTGGACAGA	0.383																																					p.H277H		Atlas-SNP	.											.	ZNF534	105	.	0			c.T831C						PASS	.						54	49	50					19																	52941505		1568	3582	5150	SO:0001819	synonymous_variant	147658	exon4			AATTCATACTGGA	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.831T>C	19.37:g.52941505T>C		82	0	0		65	15	0.230769	NM_001143939	Q76KX9	Silent	SNP	ENST00000332323.6	37	CCDS46165.1																																																																																			.	.	none		0.383	ZNF534-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460877.1	NM_182512		C	52941505	T	C	52941505	2	2	4	1	0	0	0	0	0	0	0	1	17988	1403	49	3		3	ZNF534	19	52941505	Silent	SNP	T	TCGA-FA-A6HN-01A-11D-A31X-10	810378	52941505	6187478	183	523											
TNNT1	7138	hgsc.bcm.edu	37	chr19	55645539	55645539	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttctccctggcagggcaggaGggctgtgatggaggcagcca	7	7	17	10	0	1	1	0	1	1	0	2	3	1	3	2	6	1	4	2	6	0	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr19:55645539G>A	ENST00000588981.1	-	12	849	c.645C>T	c.(643-645)ccC>ccT	p.P215P	TNNT1_ENST00000587758.1_Intron|TNNT1_ENST00000356783.5_Intron|TNNT1_ENST00000587465.2_Intron|TNNT1_ENST00000291901.8_Intron|TNNT1_ENST00000536926.1_Intron|TNNT1_ENST00000588426.1_Intron|TNNT1_ENST00000585321.2_Intron	NM_003283.4	NP_003274.3	P13805	TNNT1_HUMAN	troponin T type 1 (skeletal, slow)	215					muscle filament sliding (GO:0030049)|negative regulation of muscle contraction (GO:0045932)|skeletal muscle contraction (GO:0003009)|slow-twitch skeletal muscle fiber contraction (GO:0031444)	cytosol (GO:0005829)|troponin complex (GO:0005861)	tropomyosin binding (GO:0005523)			endometrium(2)|kidney(3)|lung(4)|ovary(1)	10			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.047)		CAGGGCAGGAGGGCTGTGATG	0.617																																					p.P215P		Atlas-SNP	.											.	TNNT1	28	.	0			c.C645T						PASS	.						23	21	22					19																	55645539		2199	4295	6494	SO:0001819	synonymous_variant	7138	exon12			GCAGGAGGGCTGT		CCDS12917.1, CCDS46185.1, CCDS59421.1	19q13.4	2014-09-17	2005-09-12			ENSG00000105048			11948	protein-coding gene	gene with protein product	"slow skeletal muscle troponin T", "troponin T1, skeletal, slow", "nemaline myopathy type 5"	191041	"troponin T1, skeletal, slow"			1505979	Standard	XM_006723343		Approved	ANM, STNT, TNT, TNTS, FLJ98147, MGC104241, NEM5	uc002qjb.4	P13805		ENST00000588981.1:c.645C>T	19.37:g.55645539G>A		61	0	0		40	7	0.175	NM_003283	O95472|Q16061|Q5U0E1	Silent	SNP	ENST00000588981.1	37	CCDS12917.1																																																																																			.	.	none		0.617	TNNT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451825.2	NM_003283		A	55645539	G	A	55645539	2	1	4	1	0	0	0	0	0	0	0	1	16345	987	35	2		2	TNNT1	19	55645539	Silent	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	2704034	55645539	3483444	184	524											
SUV420H2	84787	hgsc.bcm.edu	37	chr19	55853653	55853653	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttcctgaggcagcgggacCtggaggctgcgtaccgggcc	5	7	16	13	3	0	1	0	1	0	0	1	3	1	3	4	5	3	3	4	5	1	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr19:55853653C>A	ENST00000255613.3	+	3	429	c.181C>A	c.(181-183)Ctg>Atg	p.L61M	AC020922.1_ENST00000539076.1_Intron|SUV420H2_ENST00000402499.4_Intron	NM_032701.3	NP_116090.2	Q86Y97	SV422_HUMAN	suppressor of variegation 4-20 homolog 2 (Drosophila)	61					histone H4-K20 trimethylation (GO:0034773)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome, centromeric region (GO:0000780)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	histone methyltransferase activity (H4-K20 specific) (GO:0042799)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)	4	Breast(117;0.191)		BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		GCAGCGGGACCTGGAGGCTGC	0.721																																					p.L61M		Atlas-SNP	.											.	SUV420H2	20	.	0			c.C181A						PASS	.						8	9	9					19																	55853653		2173	4274	6447	SO:0001583	missense	84787	exon3			CGGGACCTGGAGG	BC005842	CCDS12922.1	19q13.42	2011-07-01			ENSG00000133247	ENSG00000133247		"Chromatin-modifying enzymes / K-methyltransferases"	28405	protein-coding gene	gene with protein product		613198				12477932	Standard	NM_032701		Approved	MGC2705, KMT5C	uc002qkj.4	Q86Y97	OTTHUMG00000150483	ENST00000255613.3:c.181C>A	19.37:g.55853653C>A	ENSP00000255613:p.Leu61Met	100	0	0		91	5	0.0549451	NM_032701	Q8WZ10|Q9BRZ6	Missense_Mutation	SNP	ENST00000255613.3	37	CCDS12922.1	.	.	.	.	.	.	.	.	.	.	C	18.15	3.559480	0.65538	.	.	ENSG00000133247	ENST00000255613	.	.	.	4.41	3.34	0.38264	.	0.183772	0.36066	N	0.002806	T	0.68906	0.3052	L	0.54323	1.7	0.40803	D	0.983356	D	0.76494	0.999	D	0.70227	0.968	T	0.71504	-0.4573	9	0.59425	D	0.04	-28.7158	12.7082	0.57073	0.1667:0.8333:0.0:0.0	.	61	Q86Y97	SV422_HUMAN	M	61	.	ENSP00000255613:L61M	L	+	1	2	SUV420H2	60545465	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.898000	0.28404	0.938000	0.37419	0.561000	0.74099	CTG	.	.	none		0.721	SUV420H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318309.2	NM_032701		A	55853653	C	A	55853653	3	1	4	1	0	0	0	0	1	0	0	0	15430	680	24	4	187	4	SUV420H2	19	55853653	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	208114	55853653	3275330	185	525											
ZNF530	348327	hgsc.bcm.edu	37	chr19	58117726	58117726	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgtgggaaatcatttagtcGcaaaactcacctaactcaac	15	10	6	10	1	3	0	3	0	0	0	4	1	3	1	1	1	3	1	1	1	6	3	rs201516823		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr19:58117726G>A	ENST00000332854.6	+	3	1053	c.833G>A	c.(832-834)cGc>cAc	p.R278H	ZNF530_ENST00000597864.1_Intron	NM_020880.3	NP_065931.3	Q6P9A1	ZN530_HUMAN	zinc finger protein 530	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(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(6)|skin(1)	20		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0443)|Breast(46;0.0848)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		TCATTTAGTCGCAAAACTCAC	0.438																																					p.R278H		Atlas-SNP	.											.	ZNF530	71	.	0			c.G833A						PASS	.						94	81	85					19																	58117726		2203	4300	6503	SO:0001583	missense	348327	exon3			TTAGTCGCAAAAC	AK096831	CCDS12955.1	19q13.43	2013-01-08				ENSG00000183647		"Zinc fingers, C2H2-type", "-"	29297	protein-coding gene	gene with protein product						10819331	Standard	NM_020880		Approved	KIAA1508	uc002qpk.2	Q6P9A1		ENST00000332854.6:c.833G>A	19.37:g.58117726G>A	ENSP00000332861:p.Arg278His	108	0	0		62	10	0.16129	NM_020880	O43340|Q9P220	Missense_Mutation	SNP	ENST00000332854.6	37	CCDS12955.1	.	.	.	.	.	.	.	.	.	.	G	5.242	0.230126	0.09969	.	.	ENSG00000183647	ENST00000332854	T	0.07327	3.2	1.51	-3.03	0.05429	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05868	0.0153	L	0.52266	1.64	0.09310	N	1	B	0.15930	0.015	B	0.04013	0.001	T	0.47262	-0.9131	9	0.11485	T	0.65	.	3.3452	0.07132	0.2697:0.0:0.4615:0.2688	.	278	Q6P9A1	ZN530_HUMAN	H	278	ENSP00000332861:R278H	ENSP00000332861:R278H	R	+	2	0	ZNF530	62809538	0.000000	0.05858	0.002000	0.10522	0.199000	0.23934	-1.220000	0.02971	-0.684000	0.05183	0.537000	0.68136	CGC	G|0.999;A|0.001	0.001	weak		0.438	ZNF530-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466797.1	NM_020880		A	58117726	G	A	58117726	3	1	4	1	0	0	0	0	1	0	0	0	17986	1087	38	1	843	1	ZNF530	19	58117726	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	2264073	58117726	1011257	186	526											
SPTLC3	55304	hgsc.bcm.edu	37	chr20	13107302	13107302	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcttcatccatgagcccacCgatagcagagcaaatcatca	13	8	7	13	1	3	2	3	1	0	1	4	3	4	2	3	0	4	3	3	0	2	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr20:13107302C>T	ENST00000399002.2	+	9	1491	c.1217C>T	c.(1216-1218)cCg>cTg	p.P406L	SPTLC3_ENST00000378194.4_3'UTR	NM_018327.2	NP_060797.2	Q9NUV7	SPTC3_HUMAN	serine palmitoyltransferase, long chain base subunit 3	406					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						ATGAGCCCACCGATAGCAGAG	0.463																																					p.P406L		Atlas-SNP	.											.	SPTLC3	78	.	0			c.C1217T						PASS	.						227	213	218					20																	13107302		1937	4135	6072	SO:0001583	missense	55304	exon9			GCCCACCGATAGC	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.1217C>T	20.37:g.13107302C>T	ENSP00000381968:p.Pro406Leu	83	0	0		82	17	0.207317	NM_018327	A2A2I4|B9EK64|Q05DQ8|Q5T1U4|Q9H1L1|Q9H1Z0	Missense_Mutation	SNP	ENST00000399002.2	37	CCDS13115.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.9|25.9	4.688150|4.688150	0.88639|0.88639	.|.	.|.	ENSG00000172296|ENSG00000172296	ENST00000399002|ENST00000431275	D|.	0.94184|.	-3.37|.	6.17|6.17	5.23|5.23	0.72850|0.72850	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);|.	0.187728|.	0.64402|.	D|.	0.000016|.	T|.	0.77458|.	0.4133|.	M|M	0.83774|0.83774	2.66|2.66	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.70935|.	0.971|.	T|.	0.79741|.	-0.1676|.	10|.	0.87932|.	D|.	0|.	-5.7364|-5.7364	14.6875|14.6875	0.69059|0.69059	0.0:0.9302:0.0:0.0698|0.0:0.9302:0.0:0.0698	.|.	406|.	Q9NUV7|.	SPTC3_HUMAN|.	L|X	406|4	ENSP00000381968:P406L|.	ENSP00000381968:P406L|.	P|R	+|+	2|1	0|2	SPTLC3|SPTLC3	13055302|13055302	0.977000|0.977000	0.34250|0.34250	0.122000|0.122000	0.21767|0.21767	0.929000|0.929000	0.56500|0.56500	6.079000|6.079000	0.71291|0.71291	1.598000|1.598000	0.50083|0.50083	0.655000|0.655000	0.94253|0.94253	CCG|CGA	.	.	none		0.463	SPTLC3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254544.1	NM_018327		T	13107302	C	T	13107302	3	4	4	1	0	0	0	0	1	0	0	0	15140	652	23	1	1251	1	SPTLC3	20	13107302	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10		13107302	49918218	187	527											
SSTR4	6754	hgsc.bcm.edu	37	chr20	23016253	23016253	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggcccggggacgcgcgggcgGcgggcatggtcgctatccag	4	4	20	13	7	0	0	0	0	0	0	2	1	1	1	2	7	0	2	2	7	1	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr20:23016253G>A	ENST00000255008.3	+	1	197	c.133G>A	c.(133-135)Gcg>Acg	p.A45T	RP4-753D10.3_ENST00000440921.1_RNA	NM_001052.2	NP_001043.2	P31391	SSR4_HUMAN	somatostatin receptor 4	45					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)					cgcgcgggcggcgggcATGGT	0.706																																					p.A45T	Esophageal Squamous(15;850 1104 16640)	Atlas-SNP	.											SSTR4,NS,carcinoma,-1,1	SSTR4	83	1	0			c.G133A						scavenged	.						34	44	40					20																	23016253		2158	4263	6421	SO:0001583	missense	6754	exon1			CGGGCGGCGGGCA		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.133G>A	20.37:g.23016253G>A	ENSP00000255008:p.Ala45Thr	59	1	0.0169492		66	20	0.30303	NM_001052	Q17RM1|Q17RM3|Q9UIY1	Missense_Mutation	SNP	ENST00000255008.3	37	CCDS42856.1	.	.	.	.	.	.	.	.	.	.	G	16.61	3.170408	0.57584	.	.	ENSG00000132671	ENST00000255008	T	0.19806	2.12	3.57	3.57	0.40892	.	0.492039	0.15989	N	0.234938	T	0.14313	0.0346	L	0.27053	0.805	0.34943	D	0.750537	B	0.14805	0.011	B	0.12837	0.008	T	0.13495	-1.0507	10	0.15066	T	0.55	.	12.452	0.55682	0.0:0.0:1.0:0.0	.	45	P31391	SSR4_HUMAN	T	45	ENSP00000255008:A45T	ENSP00000255008:A45T	A	+	1	0	SSTR4	22964253	0.002000	0.14202	0.009000	0.14445	0.327000	0.28475	1.133000	0.31430	1.806000	0.52798	0.555000	0.69702	GCG	.	.	none		0.706	SSTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078308.1			A	23016253	G	A	23016253	3	1	4	1	0	0	0	0	1	0	0	0	15215	1203	42	2	135	2	SSTR4	20	23016253	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	9908951	23016253	40009267	188	528											
SSTR4	6754	hgsc.bcm.edu	37	chr20	23016714	23016714	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggcggccaggccgtggcctgCaacctgcagtggccacaccc	6	4	14	17	2	0	0	0	0	0	0	0	0	0	0	6	5	3	2	6	5	1	0			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr20:23016714C>A	ENST00000255008.3	+	1	658	c.594C>A	c.(592-594)tgC>tgA	p.C198*	RP4-753D10.3_ENST00000440921.1_RNA	NM_001052.2	NP_001043.2	P31391	SSR4_HUMAN	somatostatin receptor 4	198					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)					CCGTGGCCTGCAACCTGCAGT	0.657																																					p.C198X	Esophageal Squamous(15;850 1104 16640)	Atlas-SNP	.											.	SSTR4	83	.	0			c.C594A						PASS	.						30	38	35					20																	23016714		2135	4242	6377	SO:0001587	stop_gained	6754	exon1			GGCCTGCAACCTG		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.594C>A	20.37:g.23016714C>A	ENSP00000255008:p.Cys198*	11	0	0		16	5	0.3125	NM_001052	Q17RM1|Q17RM3|Q9UIY1	Nonsense_Mutation	SNP	ENST00000255008.3	37	CCDS42856.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.810719	0.90707	.	.	ENSG00000132671	ENST00000255008	.	.	.	3.21	1.21	0.21127	.	0.000000	0.64402	U	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.5942	0.28037	0.0:0.7766:0.0:0.2234	.	.	.	.	X	198	.	ENSP00000255008:C198X	C	+	3	2	SSTR4	22964714	1.000000	0.71417	0.967000	0.41034	0.983000	0.72400	2.053000	0.41326	0.091000	0.17302	0.655000	0.94253	TGC	.	.	none		0.657	SSTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078308.1			A	23016714	C	A	23016714	4	1	4	1	0	0	0	0	0	1	0	0	15215	718	25	4	596	4	SSTR4	20	23016714	Nonsense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	461	23016714	40008806	189	529											
ICOSLG	23308	hgsc.bcm.edu	37	chr21	45656994	45656994	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gttttcgactcactggtttgCcaatatacgtaaacatcatt	11	15	6	9	2	2	0	2	0	0	0	3	1	2	0	1	1	3	3	1	1	5	7			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr21:45656994C>T	ENST00000407780.3	-	3	289	c.162G>A	c.(160-162)tgG>tgA	p.W54*	ICOSLG_ENST00000400377.3_Intron|ICOSLG_ENST00000400379.3_Nonsense_Mutation_p.W54*|ICOSLG_ENST00000344330.4_Nonsense_Mutation_p.W54*	NM_001283052.1	NP_001269981.1	O75144	ICOSL_HUMAN	inducible T-cell co-stimulator ligand	54	Ig-like V-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)		CACTGGTTTGCCAATATACGT	0.527																																					p.W54X		Atlas-SNP	.											.	ICOSLG	20	.	0			c.G162A						PASS	.						92	108	102					21																	45656994		2125	4233	6358	SO:0001587	stop_gained	23308	exon3			GGTTTGCCAATAT	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.162G>A	21.37:g.45656994C>T	ENSP00000384432:p.Trp54*	102	0	0		95	4	0.0421053	NM_015259	A8MUZ1|Q9HD18|Q9NRQ1	Nonsense_Mutation	SNP	ENST00000407780.3	37	CCDS42952.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.453793	0.84209	.	.	ENSG00000160223	ENST00000344330;ENST00000407780;ENST00000400379	.	.	.	5.01	5.01	0.66863	.	0.000000	0.51477	D	0.000093	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-28.5671	14.542	0.68002	0.0:1.0:0.0:0.0	.	.	.	.	X	54	.	ENSP00000339477:W54X	W	-	3	0	ICOSLG	44481422	1.000000	0.71417	1.000000	0.80357	0.253000	0.25986	3.355000	0.52262	2.713000	0.92767	0.655000	0.94253	TGG	.	.	none		0.527	ICOSLG-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000195838.1	NM_015259		T	45656994	C	T	45656994	4	4	4	1	0	0	0	0	0	1	0	0	7496	740	26	2	766	2	ICOSLG	21	45656994	Nonsense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10		45656994	2472901	190	530											
PATZ1	23598	hgsc.bcm.edu	37	chr22	31741415	31741415	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tactcgctgcaggcggccagCacggcgcggtgcgctgggaa	6	5	17	13	6	0	0	0	0	0	0	1	1	0	1	1	5	4	4	1	5	2	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr22:31741415C>T	ENST00000266269.5	-	1	803	c.174G>A	c.(172-174)gtG>gtA	p.V58V	PATZ1_ENST00000215919.3_Silent_p.V58V|PATZ1_ENST00000351933.4_Silent_p.V58V|PATZ1_ENST00000405309.3_Silent_p.V58V|AC005003.1_ENST00000504184.2_5'Flank	NM_014323.2	NP_055138.2	Q9HBE1	PATZ1_HUMAN	POZ (BTB) and AT hook containing zinc finger 1	58	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				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						AGGCGGCCAGCACGGCGCGGT	0.682																																					p.V58V		Atlas-SNP	.											.	PATZ1	24	.	0			c.G174A						PASS	.						22	22	22					22																	31741415		2203	4296	6499	SO:0001819	synonymous_variant	23598	exon1			GGCCAGCACGGCG	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.174G>A	22.37:g.31741415C>T		114	0	0		70	9	0.128571	NM_032050	Q9HBE2|Q9HBE3|Q9P1A9|Q9UDU0|Q9Y529	Silent	SNP	ENST00000266269.5	37	CCDS13894.1																																																																																			.	.	none		0.682	PATZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321932.1	NM_032052		T	31741415	C	T	31741415	2	4	4	1	0	0	0	0	0	0	0	1	11485	697	25	2		2	PATZ1	22	31741415	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10		31741415	19563151	191	531											
ATF4	468	hgsc.bcm.edu	37	chr22	39917610	39917610	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	atgggttctccagcgacaagGctaaggcgggctcctccgaa	9	7	13	12	3	1	0	0	0	1	0	4	2	3	0	3	4	1	3	3	4	3	2	rs148038848		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr22:39917610G>A	ENST00000337304.2	+	1	1042	c.160G>A	c.(160-162)Gct>Act	p.A54T	ATF4_ENST00000404241.2_Missense_Mutation_p.A54T|ATF4_ENST00000396680.1_Missense_Mutation_p.A54T	NM_001675.2	NP_001666.2	P18848	ATF4_HUMAN	activating transcription factor 4	54					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)	CAGCGACAAGGCTAAGGCGGG	0.582																																					p.A54T		Atlas-SNP	.											.	ATF4	27	.	0			c.G160A						PASS	.	G	THR/ALA,THR/ALA	1,4405		0,1,2202	50	52	51		160,160	4.2	1	22	dbSNP_134	51	0,8600		0,0,4300	no	missense,missense	ATF4	NM_001675.2,NM_182810.1	58,58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	54/352,54/352	39917610	1,13005	2203	4300	6503	SO:0001583	missense	468	exon1			GACAAGGCTAAGG	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.160G>A	22.37:g.39917610G>A	ENSP00000336790:p.Ala54Thr	118	0	0		99	23	0.232323	NM_001675	Q9UH31	Missense_Mutation	SNP	ENST00000337304.2	37	CCDS13996.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.494153	0.85069	2.27E-4	0.0	ENSG00000128272	ENST00000404241;ENST00000337304;ENST00000396680	T;T;T	0.46819	0.86;0.86;0.86	4.15	4.15	0.48705	.	0.257440	0.37669	N	0.001990	T	0.68751	0.3035	M	0.75264	2.295	0.52501	D	0.999956	D	0.89917	1.0	D	0.83275	0.996	T	0.74970	-0.3482	10	0.87932	D	0	-16.9756	16.4315	0.83847	0.0:0.0:1.0:0.0	.	54	P18848	ATF4_HUMAN	T	54	ENSP00000384587:A54T;ENSP00000336790:A54T;ENSP00000379912:A54T	ENSP00000336790:A54T	A	+	1	0	ATF4	38247556	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.442000	0.73443	1.863000	0.54032	0.561000	0.74099	GCT	G|1.000;A|0.000	0.000	weak		0.582	ATF4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321305.1	NM_001675		A	39917610	G	A	39917610	3	1	4	1	0	0	0	0	1	0	0	0	1082	1203	42	2	162	2	ATF4	22	39917610	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	8176195	39917610	11386956	192	532											
ARHGAP8	23779	hgsc.bcm.edu	37	chr22	45241156	45241156	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tctgttttctcagcctcaaaGacaaaaatcaaggcgaactc	14	10	6	11	1	4	1	3	0	2	1	6	2	4	1	1	1	2	1	1	1	5	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chr22:45241156G>C	ENST00000389774.2	+	9	838	c.697G>C	c.(697-699)Gac>Cac	p.D233H	ARHGAP8_ENST00000356099.6_Missense_Mutation_p.D202H|ARHGAP8_ENST00000336963.4_Missense_Mutation_p.D202H|ARHGAP8_ENST00000389773.5_Missense_Mutation_p.D324H|PRR5-ARHGAP8_ENST00000361473.5_Missense_Mutation_p.D333H|PRR5-ARHGAP8_ENST00000352766.7_Missense_Mutation_p.D412H|ARHGAP8_ENST00000517296.3_Missense_Mutation_p.D412H	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	233	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				positive regulation of ERK1 and ERK2 cascade (GO:0070374)|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)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(9)|prostate(1)|skin(7)	29		all_neural(38;0.00409)|Ovarian(80;0.00976)|Glioma(61;0.0649)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0204)		CAGCCTCAAAGACAAAAATCA	0.522																																					p.D324H		Atlas-SNP	.											.	PRR5-ARHGAP8	53	.	0			c.G970C						PASS	.						71	69	69					22																	45241156		2203	4300	6503	SO:0001583	missense	553158	exon11			CTCAAAGACAAAA	AF177331	CCDS14060.2, CCDS33664.1, CCDS56233.1	22q13.3	2010-05-11			ENSG00000241484	ENSG00000241484		"Rho GTPase activating proteins"	677	protein-coding gene	gene with protein product		609405				10591208	Standard	NM_001198726		Approved	FLJ20185, BPGAP1		P85298	OTTHUMG00000030234	ENST00000389774.2:c.697G>C	22.37:g.45241156G>C	ENSP00000374424:p.Asp233His	47	0	0		54	14	0.259259	NM_181334	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Missense_Mutation	SNP	ENST00000389774.2	37	CCDS33664.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.42|15.42	2.827083|2.827083	0.50739|0.50739	.|.	.|.	ENSG00000248405;ENSG00000248405;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484|ENSG00000248405	ENST00000361473;ENST00000352766;ENST00000517296;ENST00000389773;ENST00000389774;ENST00000336963;ENST00000356099|ENST00000515632	T;T;T;T;T;T;T|T	0.42131|0.42131	0.98;0.98;0.98;0.98;0.98;0.98;0.98|0.98	3.95|3.95	3.95|3.95	0.45737|0.45737	Rho GTPase-activating protein domain (2);Rho GTPase activation protein (1);|.	0.513253|.	0.14386|.	U|.	0.322816|.	T|T	0.37376|0.37376	0.1001|0.1001	L|L	0.38531|0.38531	1.155|1.155	0.36768|0.36768	D|D	0.883623|0.883623	B;B;P;B;B;D;B|.	0.52996|.	0.086;0.012;0.93;0.026;0.086;0.957;0.167|.	B;B;P;B;B;P;B|.	0.48030|.	0.025;0.009;0.564;0.014;0.035;0.525;0.042|.	T|T	0.30297|0.30297	-0.9983|-0.9983	10|7	0.46703|0.19590	T|T	0.11|0.45	.|.	9.5957|9.5957	0.39573|0.39573	0.0:0.2139:0.7861:0.0|0.0:0.2139:0.7861:0.0	.|.	238;202;238;233;243;412;333|.	B7ZMA4;A6ZJ79;A2RU51;P85298;Q6PCC7;B1AHC4;B1AHC3|.	.;.;.;RHG08_HUMAN;.;.;.|.	H|N	333;412;412;324;233;202;202|255	ENSP00000354732:D333H;ENSP00000262731:D412H;ENSP00000429240:D412H;ENSP00000374423:D324H;ENSP00000374424:D233H;ENSP00000337287:D202H;ENSP00000348407:D202H|ENSP00000425026:K255N	ENSP00000337287:D202H|ENSP00000425026:K255N	D|K	+|+	1|3	0|2	PRR5-ARHGAP8;ARHGAP8|PRR5-ARHGAP8	43619820|43619820	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.745000|0.745000	0.42441|0.42441	4.689000|4.689000	0.61723|0.61723	2.036000|2.036000	0.60181|0.60181	0.655000|0.655000	0.94253|0.94253	GAC|AAG	.	.	none		0.522	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701		C	45241156	G	C	45241156	3	2	4	1	0	0	0	0	1	0	0	0	888	942	33	4	727	4	ARHGAP8	22	45241156	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	5323546	45241156	6063410	193	533											
SFRS17A	8227	hgsc.bcm.edu	37	chrX	1718203	1718203	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atcagaagaagctggagaagCtgcaggcggaggagcagaag	15	3	17	6	1	1	4	1	0	0	4	1	7	1	6	0	4	4	4	0	4	4	0			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chrX:1718203C>G	ENST00000313871.3	+	4	1226	c.1030C>G	c.(1030-1032)Ctg>Gtg	p.L344V	AKAP17A_ENST00000381261.3_Missense_Mutation_p.L344V	NM_005088.2	NP_005079.2	Q02040	AK17A_HUMAN	A kinase (PRKA) anchor protein 17A	344					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						GCTGGAGAAGCTGCAGGCGGA	0.597																																					p.L344V		Atlas-SNP	.											.	AKAP17A	46	.	0			c.C1030G						PASS	.						74	78	76					X																	1718203		2203	4296	6499	SO:0001583	missense	8227	exon4			GAGAAGCTGCAGG	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.1030C>G	X.37:g.1718203C>G	ENSP00000324827:p.Leu344Val	93	0	0		113	20	0.176991	NM_005088	Q02832|Q2TB98|Q5JQ74|Q5JQ76|Q8N6U9	Missense_Mutation	SNP	ENST00000313871.3	37	CCDS14116.1	.	.	.	.	.	.	.	.	.	.	c	0.213	-1.034755	0.02029	.	.	ENSG00000197976	ENST00000313871;ENST00000381261	T;T	0.34667	1.44;1.35	1.74	-3.48	0.04739	.	0.366735	0.22112	U	0.064477	T	0.14960	0.0361	.	.	.	0.09310	N	1	B;B	0.16166	0.016;0.003	B;B	0.21708	0.036;0.015	T	0.20706	-1.0267	9	0.15952	T	0.53	.	4.6949	0.12799	0.4003:0.4443:0.0:0.1555	.	344;344	Q02040-3;Q02040	.;AK17A_HUMAN	V	344	ENSP00000324827:L344V;ENSP00000370660:L344V	ENSP00000324827:L344V	L	+	1	2	AKAP17A	1678203	1.000000	0.71417	0.039000	0.18376	0.497000	0.33675	0.985000	0.29578	-0.165000	0.10908	0.100000	0.15512	CTG	.	.	none		0.597	AKAP17A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055609.2	NM_005088		G	1718203	C	G	1718203	3	3	4	1	0	0	0	0	1	0	0	0	14188	796	28	4	1040	4	SFRS17A	23	1718203	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10		1718203	153552357	194	534											
TMSB4X	7114	hgsc.bcm.edu	37	chrX	12994468	12994468	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cgcaagagaaaaatccactgCcttccaaagaaagtgagctc	16	6	8	11	1	0	3	0	1	0	2	3	4	2	3	3	0	2	2	3	0	5	1			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chrX:12994468C>A	ENST00000380635.1	+	2	304	c.88C>A	c.(88-90)Cct>Act	p.P30T	TMSB4X_ENST00000380636.1_Missense_Mutation_p.P30T|TMSB4X_ENST00000451311.2_Missense_Mutation_p.P30T|TMSB4X_ENST00000380633.1_Missense_Mutation_p.P30T			P62328	TYB4_HUMAN	thymosin beta 4, X-linked	30					actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|sequestering of actin monomers (GO:0042989)	cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	poly(A) RNA binding (GO:0044822)			upper_aerodigestive_tract(1)	1						AAATCCACTGCCTTCCAAAGA	0.557																																					p.P30T		Atlas-SNP	.											.	TMSB4X	3	.	0			c.C88A						PASS	.						49	46	47					X																	12994468		2203	4300	6503	SO:0001583	missense	7114	exon2			CCACTGCCTTCCA		CCDS35202.1	Xp22.2	2013-05-14	2008-02-25		ENSG00000205542	ENSG00000205542			11881	protein-coding gene	gene with protein product		300159	"thymosin, beta 4, X chromosome"	TMSB4		2677145, 9381176	Standard	NM_021109		Approved	TB4X	uc004cvf.3	P62328	OTTHUMG00000021144	ENST00000380635.1:c.88C>A	X.37:g.12994468C>A	ENSP00000370009:p.Pro30Thr	170	0	0		146	55	0.376712	NM_021109	P01253|P01254|Q546P5|Q63576|Q9UE55	Missense_Mutation	SNP	ENST00000380635.1	37	CCDS35202.1	.	.	.	.	.	.	.	.	.	.	C	18.68	3.676205	0.67928	.	.	ENSG00000205542	ENST00000451311;ENST00000380636;ENST00000380635;ENST00000380633	D;D;D;D	0.91351	-2.83;-2.83;-2.83;-2.83	4.53	4.53	0.55603	.	0.000000	0.64402	U	0.000010	D	0.93719	0.7993	.	.	.	0.53688	D	0.999977	P	0.41597	0.756	P	0.52909	0.713	D	0.94659	0.7846	9	0.72032	D	0.01	-19.0029	16.916	0.86152	0.0:1.0:0.0:0.0	.	30	P62328	TYB4_HUMAN	T	30	ENSP00000414376:P30T;ENSP00000370010:P30T;ENSP00000370009:P30T;ENSP00000370007:P30T	ENSP00000370007:P30T	P	+	1	0	TMSB4X	12904389	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.858000	0.75461	1.999000	0.58509	0.513000	0.50165	CCT	.	.	none		0.557	TMSB4X-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000055779.1	NM_021109		A	12994468	C	A	12994468	3	1	4	1	0	0	0	0	1	0	0	0	16272	739	26	4	90	4	TMSB4X	23	12994468	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	11276265	12994468	142276092	195	535											
GPR34	2857	hgsc.bcm.edu	37	chrX	41555136	41555136	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtatttctgggtattcacCgtaaaagaaattccattcaa	14	14	6	7	1	3	1	2	0	1	1	4	1	4	1	2	1	0	3	2	1	6	7			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chrX:41555136C>T	ENST00000378142.4	+	3	534	c.250C>T	c.(250-252)Cgt>Tgt	p.R84C	GPR34_ENST00000378138.5_Missense_Mutation_p.R84C|CASK_ENST00000378154.1_Intron|CASK_ENST00000378166.4_Intron|CASK_ENST00000442742.2_Intron|CASK_ENST00000318588.9_Intron|CASK_ENST00000421587.2_Intron|CASK_ENST00000378163.1_Intron|CASK_ENST00000378158.1_Intron|CASK_ENST00000361962.4_Intron	NM_001097579.1|NM_005300.3	NP_001091048.1|NP_005291.1	Q9UPC5	GPR34_HUMAN	G protein-coupled receptor 34	84					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|large_intestine(6)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	14						GGGTATTCACCGTAAAAGAAA	0.383																																					p.R84C		Atlas-SNP	.											.	GPR34	42	.	0			c.C250T						PASS	.						112	101	105					X																	41555136		2203	4300	6503	SO:0001583	missense	2857	exon3			ATTCACCGTAAAA	AF039686	CCDS14258.1	Xp11.4	2012-08-21			ENSG00000171659	ENSG00000171659		"GPCR / Class A : Orphans"	4490	protein-coding gene	gene with protein product		300241				10395919, 10036181	Standard	NM_005300		Approved		uc004dfq.4	Q9UPC5	OTTHUMG00000021375	ENST00000378142.4:c.250C>T	X.37:g.41555136C>T	ENSP00000367384:p.Arg84Cys	110	0	0		106	44	0.415094	NM_001097579	O95853	Missense_Mutation	SNP	ENST00000378142.4	37	CCDS14258.1	.	.	.	.	.	.	.	.	.	.	C	12.38	1.922125	0.33908	.	.	ENSG00000171659	ENST00000378142;ENST00000378138;ENST00000535368	T;T	0.73575	-0.76;-0.76	5.87	5.87	0.94306	GPCR, rhodopsin-like superfamily (1);	0.199385	0.46758	D	0.000278	T	0.69788	0.3150	M	0.77103	2.36	0.41855	D	0.990198	P	0.36162	0.54	B	0.27076	0.076	T	0.74609	-0.3608	10	0.87932	D	0	-12.6129	8.3959	0.32557	0.1551:0.7665:0.0:0.0785	.	84	Q9UPC5	GPR34_HUMAN	C	84;84;37	ENSP00000367384:R84C;ENSP00000367378:R84C	ENSP00000367378:R84C	R	+	1	0	GPR34	41440080	0.961000	0.32948	1.000000	0.80357	0.995000	0.86356	1.419000	0.34793	2.466000	0.83321	0.594000	0.82650	CGT	.	.	none		0.383	GPR34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056264.1	NM_005300		T	41555136	C	T	41555136	3	4	4	1	0	0	0	0	1	0	0	0	6697	652	23	1	252	1	GPR34	23	41555136	Missense_Mutation	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	28560668	41555136	113715424	196	536											
SLC9A7	84679	hgsc.bcm.edu	37	chrX	46618168	46618168	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atggccagcccggtctcgtgCagaaagcgcacccggcggtg	7	5	15	14	5	1	1	0	0	1	1	2	1	1	1	3	4	3	2	3	4	1	0			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chrX:46618168C>T	ENST00000328306.4	-	1	322	c.297G>A	c.(295-297)ctG>ctA	p.L99L		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	99					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						CGGTCTCGTGCAGAAAGCGCA	0.677																																					p.L99L	Pancreas(118;454 1696 1930 13865 39976)	Atlas-SNP	.											.	SLC9A7	73	.	0			c.G297A						PASS	.						47	34	38					X																	46618168		2203	4300	6503	SO:0001819	synonymous_variant	84679	exon1			CTCGTGCAGAAAG	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.297G>A	X.37:g.46618168C>T		41	0	0		47	19	0.404255	NM_001257291	O75827|Q5JXP9	Silent	SNP	ENST00000328306.4	37	CCDS14269.1																																																																																			.	.	none		0.677	SLC9A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056370.1	NM_032591		T	46618168	C	T	46618168	2	4	4	1	0	0	0	0	0	0	0	1	14734	697	25	2		2	SLC9A7	23	46618168	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	5063032	46618168	108652392	197	537											
BMP15	9210	hgsc.bcm.edu	37	chrX	50659592	50659592	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagggtatgattgctgagtcTtgtacatgcagatgacagca	11	11	13	6	0	1	4	0	3	1	1	1	5	1	4	0	1	4	5	0	1	2	4			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chrX:50659592T>C	ENST00000252677.3	+	2	1164	c.1164T>C	c.(1162-1164)tcT>tcC	p.S388S		NM_005448.2	NP_005439.2	O95972	BMP15_HUMAN	bone morphogenetic protein 15	388					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)					TTGCTGAGTCTTGTACATGCA	0.418																																					p.S388S		Atlas-SNP	.											.	BMP15	62	.	0			c.T1164C						PASS	.						106	97	100					X																	50659592		2203	4299	6502	SO:0001819	synonymous_variant	9210	exon2			TGAGTCTTGTACA	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.1164T>C	X.37:g.50659592T>C		72	0	0		64	33	0.515625	NM_005448	Q17RM6|Q5JST1|Q9UMS1	Silent	SNP	ENST00000252677.3	37	CCDS14334.1																																																																																			.	.	none		0.418	BMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056572.1	NM_005448		C	50659592	T	C	50659592	2	2	4	1	0	0	0	0	0	0	0	1	1458	1596	56	3		3	BMP15	23	50659592	Silent	SNP	T	TCGA-FA-A6HN-01A-11D-A31X-10	4041424	50659592	104610968	198	538											
ANKRD58	347454	hgsc.bcm.edu	37	chrX	118893023	118893023	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgctatgaggtgctgcgggaGctgctggaggctgagccgga	6	7	19	9	3	0	2	0	2	0	0	0	5	0	5	1	5	5	5	1	5	1	1	rs373940647		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chrX:118893023G>C	ENST00000343905.3	+	1	448	c.393G>C	c.(391-393)gaG>gaC	p.E131D		NM_001105576.2	NP_001099046.1	A6NJG2	SWAHD_HUMAN	sosondowah ankyrin repeat domain family member D	131																	TGCTGCGGGAGCTGCTGGAGG	0.721																																					p.E131D		Atlas-SNP	.											.	.	.	.	0			c.G393C						PASS	.		ASP/GLU	0,3633		0,0,0,1549,535	5	7	6		393	3.8	1	X		6	1,6518		0,0,1,2390,1738	no	missense	ANKRD58	NM_001105576.2	45	0,0,1,3939,2273	CC,CG,C,GG,G		0.0153,0.0,0.0099	probably-damaging	131/316	118893023	1,10151	2084	4129	6213	SO:0001583	missense	347454	exon1			GCGGGAGCTGCTG		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.393G>C	X.37:g.118893023G>C	ENSP00000340975:p.Glu131Asp	25	0	0		26	5	0.192308	NM_001105576		Missense_Mutation	SNP	ENST00000343905.3	37	CCDS43984.1	.	.	.	.	.	.	.	.	.	.	G	15.02	2.708542	0.48517	0.0	1.53E-4	ENSG00000187808	ENST00000343905	T	0.64803	-0.12	3.84	3.84	0.44239	Ankyrin repeat-containing domain (4);	.	.	.	.	T	0.68879	0.3049	L	0.52206	1.635	0.31372	N	0.680013	D	0.61697	0.99	P	0.60286	0.872	T	0.67620	-0.5624	9	0.23302	T	0.38	-10.3977	13.7024	0.62618	0.0:0.0:1.0:0.0	.	131	A6NJG2	ANR58_HUMAN	D	131	ENSP00000340975:E131D	ENSP00000340975:E131D	E	+	3	2	ANKRD58	118777051	0.998000	0.40836	0.998000	0.56505	0.898000	0.52572	1.055000	0.30467	1.767000	0.52121	0.183000	0.17082	GAG	.	.	weak		0.721	SOWAHD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356469.1	NM_001105576		C	118893023	G	C	118893023	3	2	4	1	0	0	0	0	1	0	0	0	684	962	34	4	395	4	ANKRD58	23	118893023	Missense_Mutation	SNP	G	TCGA-FA-A6HN-01A-11D-A31X-10	68233431	118893023	36377537	199	539											
BRS3	680	hgsc.bcm.edu	37	chrX	135574270	135574270	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccatgcatttcattttcacCattttctctcgggttttggc	5	18	7	11	1	3	0	2	0	1	0	5	0	3	0	2	2	1	2	2	2	0	7	rs369993360		TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chrX:135574270C>T	ENST00000370648.3	+	3	1164	c.936C>T	c.(934-936)acC>acT	p.T312T		NM_001727.1	NP_001718.1	P32247	BRS3_HUMAN	bombesin-like receptor 3	312					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)					TCATTTTCACCATTTTCTCTC	0.448																																					p.T312T		Atlas-SNP	.											.	BRS3	62	.	0			c.C936T						PASS	.						271	237	248					X																	135574270		2203	4300	6503	SO:0001819	synonymous_variant	680	exon3			TTTCACCATTTTC		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.936C>T	X.37:g.135574270C>T		70	0	0		64	32	0.5	NM_001727		Silent	SNP	ENST00000370648.3	37	CCDS14656.1																																																																																			.	.	alt		0.448	BRS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059005.1	NM_001727		T	135574270	C	T	135574270	2	4	4	1	0	0	0	0	0	0	0	1	1524	581	21	2		2	BRS3	23	135574270	Silent	SNP	C	TCGA-FA-A6HN-01A-11D-A31X-10	16681247	135574270	19696290	200	540											
GDI1	2664	hgsc.bcm.edu	37	chrX	153670076	153670076	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tatccttagccaccccatcaAgaacaccaacgacgccaact	14	6	4	17	2	1	1	1	0	0	1	2	2	2	1	6	0	4	0	6	0	6	2			TCGA-FA-A6HN-01A-11D-A31X-10	TCGA-FA-A6HN-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	01217848-97f3-4995-89c8-3b0cf9527c40	6c06b9ec-6df2-4029-9b30-c38448f9637f	g.chrX:153670076A>G	ENST00000447750.2	+	8	1261	c.926A>G	c.(925-927)aAg>aGg	p.K309R	FAM50A_ENST00000393600.3_5'Flank	NM_001493.2	NP_001484.1	P31150	GDIA_HUMAN	GDP dissociation inhibitor 1	309					negative regulation of axonogenesis (GO:0050771)|negative regulation of protein targeting to membrane (GO:0090315)|protein transport (GO:0015031)|Rab protein signal transduction (GO:0032482)|regulation of catalytic activity (GO:0050790)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|midbody (GO:0030496)|neuron projection (GO:0043005)|protein complex (GO:0043234)	GDP-dissociation inhibitor activity (GO:0005092)|GTPase activator activity (GO:0005096)|Rab GDP-dissociation inhibitor activity (GO:0005093)			autonomic_ganglia(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	16	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)					CACCCCATCAAGAACACCAAC	0.577																																					p.K309R		Atlas-SNP	.											.	GDI1	36	.	0			c.A926G						PASS	.						166	139	148					X																	153670076		2203	4300	6503	SO:0001583	missense	2664	exon8			CCATCAAGAACAC	X79353	CCDS35452.1	Xq28	2008-08-01			ENSG00000203879	ENSG00000203879			4226	protein-coding gene	gene with protein product	"mental retardation, X-linked 41", "mental retardation, X-linked 48", "rab GDP-dissociation inhibitor, alpha"	300104		MRX48, MRX41, GDIL		7543319, 7849400	Standard	NM_001493		Approved	RABGDIA, XAP-4, OPHN2, FLJ41411	uc004fli.4	P31150	OTTHUMG00000033293	ENST00000447750.2:c.926A>G	X.37:g.153670076A>G	ENSP00000394071:p.Lys309Arg	105	0	0		137	29	0.211679	NM_001493	P50394|Q6FG50|Q7Z2G6|Q7Z2G9|Q7Z2H5|Q7Z2I6	Missense_Mutation	SNP	ENST00000447750.2	37	CCDS35452.1	.	.	.	.	.	.	.	.	.	.	A	15.70	2.912341	0.52439	.	.	ENSG00000203879	ENST00000447750;ENST00000369741	T	0.59364	0.27	5.43	3.02	0.34903	.	0.000000	0.85682	D	0.000000	T	0.45196	0.1330	L	0.39397	1.21	0.51767	D	0.999934	B	0.02656	0.0	B	0.09377	0.004	T	0.31166	-0.9953	10	0.66056	D	0.02	-30.0025	7.5464	0.27770	0.8186:0.0:0.1814:0.0	.	309	P31150	GDIA_HUMAN	R	309;293	ENSP00000394071:K309R	ENSP00000358756:K293R	K	+	2	0	GDI1	153323270	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	3.797000	0.55514	0.231000	0.21079	-0.424000	0.05967	AAG	.	.	none		0.577	GDI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081649.2	NM_001493		G	153670076	A	G	153670076	3	3	4	1	0	0	0	0	1	0	0	0	6328	72	3	3	956	3	GDI1	23	153670076	Missense_Mutation	SNP	A	TCGA-FA-A6HN-01A-11D-A31X-10	18095806	153670076	1600484	201	541											
AIM1L	55057	hgsc.bcm.edu	37	chr1	26655287	26655287	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctcggcttgcaggctccgCacctccctgctgagctcgat	4	9	10	18	3	0	1	0	1	0	0	4	2	2	1	4	2	3	6	4	2	0	1			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr1:26655287C>T	ENST00000308182.5	-	15	1686	c.1257G>A	c.(1255-1257)gtG>gtA	p.V419V	AIM1L_ENST00000527815.1_Silent_p.V590V			Q8N1P7	AIM1L_HUMAN	absent in melanoma 1-like	419	Beta/gamma crystallin 'Greek key' 9. {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)		GCAGGCTCCGCACCTCCCTGC	0.602																																					p.V1464V		Atlas-SNP	.											.	AIM1L	98	.	0			c.G4392A						PASS	.						144	122	129					1																	26655287		2203	4300	6503	SO:0001819	synonymous_variant	55057	exon16			GCTCCGCACCTCC			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.1257G>A	1.37:g.26655287C>T		61	0	0		47	12	0.255319	NM_001039775	B2RNG3|Q5T137|Q5T150	Silent	SNP	ENST00000308182.5	37																																																																																				.	.	none		0.602	AIM1L-201	KNOWN	basic	protein_coding	protein_coding		NM_001039775.2		T	26655287	C	T	26655287	2	4	5	1	0	0	0	0	0	0	0	1	431	697	25	2		2	AIM1L	1	26655287	Silent	SNP	C	TCGA-FA-A6HO-01A-11D-A31X-10		26655287	222595334	1	542											
ZC3H12A	80149	hgsc.bcm.edu	37	chr1	37948367	37948367	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacctatgggatcaagtgcCgattcttccacccagagcgg	9	8	11	13	2	2	1	1	0	1	1	3	3	3	2	4	2	2	1	4	2	2	3			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr1:37948367C>T	ENST00000373087.6	+	6	1071	c.955C>T	c.(955-957)Cga>Tga	p.R319*		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)				GATCAAGTGCCGATTCTTCCA	0.592																																					p.R319X		Atlas-SNP	.											.	ZC3H12A	58	.	0			c.C955T						PASS	.						53	58	56					1																	37948367		2203	4300	6503	SO:0001587	stop_gained	80149	exon6			AAGTGCCGATTCT		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.955C>T	1.37:g.37948367C>T	ENSP00000362179:p.Arg319*	58	0	0		36	7	0.194444	NM_025079		Nonsense_Mutation	SNP	ENST00000373087.6	37	CCDS417.1	.	.	.	.	.	.	.	.	.	.	C	37	6.207425	0.97376	.	.	ENSG00000163874	ENST00000373087;ENST00000373082	.	.	.	5.35	4.42	0.53409	.	0.056788	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	-13.4531	12.5056	0.55979	0.4622:0.5378:0.0:0.0	.	.	.	.	X	319	.	ENSP00000362174:R319X	R	+	1	2	ZC3H12A	37720954	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.551000	0.67274	1.202000	0.43218	0.563000	0.77884	CGA	.	.	none		0.592	ZC3H12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012154.2	NM_025079		T	37948367	C	T	37948367	4	4	5	1	0	0	0	0	0	1	0	0	17576	644	23	1	973	1	ZC3H12A	1	37948367	Nonsense_Mutation	SNP	C	TCGA-FA-A6HO-01A-11D-A31X-10	11293080	37948367	211302254	2	543											
SLC16A1	6566	hgsc.bcm.edu	37	chr1	113460019	113460019	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acacactccatttgcaacaaCggaagccgcaaagaaatact	17	6	6	12	2	0	1	0	0	0	1	1	2	1	2	2	1	5	2	2	1	6	2			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr1:113460019C>T	ENST00000538576.1	-	4	1840	c.1009G>A	c.(1009-1011)Gtt>Att	p.V337I	SLC16A1_ENST00000433570.4_Missense_Mutation_p.V337I|SLC16A1_ENST00000369626.3_Missense_Mutation_p.V337I	NM_001166496.1	NP_001159968.1	P53985	MOT1_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 1	337					behavioral response to nutrient (GO:0051780)|blood coagulation (GO:0007596)|cellular metabolic process (GO:0044237)|cellular response to organic cyclic compound (GO:0071407)|centrosome organization (GO:0051297)|glucose homeostasis (GO:0042593)|leukocyte migration (GO:0050900)|lipid metabolic process (GO:0006629)|mevalonate transport (GO:0015728)|monocarboxylic acid transport (GO:0015718)|plasma membrane lactate transport (GO:0035879)|pyruvate metabolic process (GO:0006090)|regulation of insulin secretion (GO:0050796)|response to food (GO:0032094)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	mevalonate transmembrane transporter activity (GO:0015130)|monocarboxylic acid transmembrane transporter activity (GO:0008028)|organic cyclic compound binding (GO:0097159)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|urinary_tract(1)	20	Lung SC(450;0.246)	all_cancers(81;7.6e-08)|all_epithelial(167;3.82e-07)|all_lung(203;3.07e-05)|Lung NSC(69;5.51e-05)|Prostate(1639;0.00232)		Epithelial(280;7.31e-13)|all cancers(265;5.1e-10)|Kidney(133;5.29e-07)|KIRC - Kidney renal clear cell carcinoma(1967;8.63e-06)|OV - Ovarian serous cystadenocarcinoma(397;1.48e-05)|BRCA - Breast invasive adenocarcinoma(282;0.003)|LUSC - Lung squamous cell carcinoma(189;0.008)|Lung(183;0.00948)|Colorectal(144;0.0325)|COAD - Colon adenocarcinoma(174;0.0643)	Acetic acid(DB03166)|Aminohippurate(DB00345)|Ampicillin(DB00415)|Foscarnet(DB00529)|Gamma Hydroxybutyric Acid(DB01440)|Methotrexate(DB00563)|Nateglinide(DB00731)|Niacin(DB00627)|Niflumic Acid(DB04552)|Pravastatin(DB00175)|Probenecid(DB01032)|Pyruvic acid(DB00119)|Salicylic acid(DB00936)|Valproic Acid(DB00313)	TTTGCAACAACGGAAGCCGCA	0.458																																					p.V337I		Atlas-SNP	.											.	SLC16A1	61	.	0			c.G1009A						PASS	.						64	52	56					1																	113460019		2203	4300	6503	SO:0001583	missense	6566	exon4			CAACAACGGAAGC	BC026317	CCDS858.1	1p12	2013-07-18	2013-07-18		ENSG00000155380	ENSG00000155380		"Solute carriers"	10922	protein-coding gene	gene with protein product		600682	"solute carrier family 16 (monocarboxylic acid transporters), member 1", "solute carrier family 16, member 1 (monocarboxylic acid transporter 1)"			8124722, 7835905	Standard	NM_003051		Approved	MCT, MCT1	uc001ecy.3	P53985	OTTHUMG00000012129	ENST00000538576.1:c.1009G>A	1.37:g.113460019C>T	ENSP00000441065:p.Val337Ile	162	0	0		113	30	0.265487	NM_001166496	Q49A45|Q5T8R6|Q9NSJ9	Missense_Mutation	SNP	ENST00000538576.1	37	CCDS858.1	.	.	.	.	.	.	.	.	.	.	C	0.510	-0.867034	0.02590	.	.	ENSG00000155380	ENST00000369626;ENST00000538576;ENST00000458229;ENST00000433570	T;T;T;T	0.54866	0.55;0.55;0.55;0.55	5.56	-8.41	0.00961	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.434923	0.25001	N	0.033909	T	0.10380	0.0254	N	0.05199	-0.095	0.09310	N	1	B;B	0.21147	0.052;0.006	B;B	0.24006	0.05;0.03	T	0.15925	-1.0420	10	0.10902	T	0.67	.	20.5631	0.99335	0.0:0.7483:0.0:0.2517	.	337;337	Q49A45;P53985	.;MOT1_HUMAN	I	337	ENSP00000358640:V337I;ENSP00000441065:V337I;ENSP00000416167:V337I;ENSP00000445061:V337I	ENSP00000358640:V337I	V	-	1	0	SLC16A1	113261542	0.000000	0.05858	0.000000	0.03702	0.080000	0.17528	-0.393000	0.07305	-1.666000	0.01475	-1.166000	0.01754	GTT	.	.	none		0.458	SLC16A1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033539.1	NM_003051		T	113460019	C	T	113460019	3	4	5	1	0	0	0	0	1	0	0	0	14417	536	19	1	501	1	SLC16A1	1	113460019	Missense_Mutation	SNP	C	TCGA-FA-A6HO-01A-11D-A31X-10	75511652	113460019	135790602	3	544											
BTG2	7832	hgsc.bcm.edu	37	chr1	203276562	203276562	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctacgtgatggcagtctccaGctaggcccttccgcccccgc	5	8	10	18	3	1	1	0	1	1	0	3	1	2	1	5	2	2	2	5	2	2	3			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr1:203276562G>A	ENST00000290551.4	+	2	544	c.473G>A	c.(472-474)aGc>aAc	p.S158N	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	158					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			GCAGTCTCCAGCTAGGCCCTT	0.627																																					p.S158N		Atlas-SNP	.											.	BTG2	16	.	0			c.G473A						PASS	.						23	24	24					1																	203276562		2196	4278	6474	SO:0001583	missense	7832	exon2			TCTCCAGCTAGGC		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.473G>A	1.37:g.203276562G>A	ENSP00000290551:p.Ser158Asn	66	0	0		50	10	0.2	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	G	15.67	2.902148	0.52227	.	.	ENSG00000159388	ENST00000290551	T	0.26373	1.74	4.76	3.85	0.44370	.	0.000000	0.85682	D	0.000000	T	0.46483	0.1395	M	0.73217	2.22	0.43338	D	0.995382	D	0.76494	0.999	D	0.66084	0.941	T	0.49021	-0.8982	10	0.87932	D	0	-21.5168	11.8943	0.52648	0.087:0.0:0.913:0.0	.	158	P78543	BTG2_HUMAN	N	158	ENSP00000290551:S158N	ENSP00000290551:S158N	S	+	2	0	BTG2	201543185	1.000000	0.71417	1.000000	0.80357	0.097000	0.18754	9.420000	0.97426	1.140000	0.42260	0.313000	0.20887	AGC	.	.	none		0.627	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		A	203276562	G	A	203276562	3	1	5	1	0	0	0	0	1	0	0	0	1556	971	34	2	479	2	BTG2	1	203276562	Missense_Mutation	SNP	G	TCGA-FA-A6HO-01A-11D-A31X-10	89816543	203276562	45974059	4	545											
ARIH2	10425	hgsc.bcm.edu	37	chr3	49017001	49017001	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaaggagaatcctgacatcGtgaaccagagccaacaagcc	16	4	9	12	1	0	4	0	2	0	2	2	5	1	4	4	1	4	0	4	1	5	0			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr3:49017001G>A	ENST00000356401.4	+	12	1387	c.1048G>A	c.(1048-1050)Gtg>Atg	p.V350M	ARIH2_ENST00000490095.1_3'UTR|RP13-131K19.1_ENST00000415982.1_RNA|ARIH2_ENST00000449376.1_Missense_Mutation_p.V350M|RP13-131K19.1_ENST00000429681.1_RNA	NM_006321.2	NP_006312.1	O95376	ARI2_HUMAN	ariadne RBR E3 ubiquitin protein ligase 2	350					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)		TCCTGACATCGTGAACCAGAG	0.498																																					p.V350M		Atlas-SNP	.											ARIH2,NS,carcinoma,0,1	ARIH2	32	1	0			c.G1048A						scavenged	.						142	120	128					3																	49017001		2203	4300	6503	SO:0001583	missense	10425	exon12			GACATCGTGAACC	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.1048G>A	3.37:g.49017001G>A	ENSP00000348769:p.Val350Met	74	1	0.0135135		84	14	0.166667	NM_006321	Q9HBZ6|Q9UEM9	Missense_Mutation	SNP	ENST00000356401.4	37	CCDS2780.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.213019	0.79352	.	.	ENSG00000177479	ENST00000356401;ENST00000449376;ENST00000444790;ENST00000395481	D;D	0.82711	-1.64;-1.64	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.86108	0.5854	N	0.24115	0.695	0.80722	D	1	D;D;P	0.76494	0.999;0.998;0.792	P;D;B	0.70935	0.813;0.971;0.154	D	0.86779	0.1978	10	0.52906	T	0.07	.	19.9097	0.97022	0.0:0.0:1.0:0.0	.	357;350;350	B3KMG5;Q53ET9;O95376	.;.;ARI2_HUMAN	M	350;350;349;174	ENSP00000348769:V350M;ENSP00000403222:V350M	ENSP00000348769:V350M	V	+	1	0	ARIH2	48992005	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.418000	0.80167	2.710000	0.92621	0.472000	0.43445	GTG	.	.	none		0.498	ARIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257525.1	NM_006321		A	49017001	G	A	49017001	3	1	5	1	0	0	0	0	1	0	0	0	924	1145	40	1	1086	1	ARIH2	3	49017001	Missense_Mutation	SNP	G	TCGA-FA-A6HO-01A-11D-A31X-10		49017001	149005429	5	546											
USP4	7375	hgsc.bcm.edu	37	chr3	49362425	49362425	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gttccagagccgtgtttcacGctccgcagggatgttgaata	8	11	12	10	3	1	2	1	1	0	1	3	3	3	3	3	1	1	5	3	1	2	4			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr3:49362425G>C	ENST00000265560.4	-	5	581	c.535C>G	c.(535-537)Cgt>Ggt	p.R179G	USP4_ENST00000351842.4_Missense_Mutation_p.R179G|USP4_ENST00000416417.1_Missense_Mutation_p.R179G|USP4_ENST00000415188.1_Missense_Mutation_p.R179G	NM_003363.3	NP_003354.2	Q13107	UBP4_HUMAN	ubiquitin specific peptidase 4 (proto-oncogene)	179	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)		CGTGTTTCACGCTCCGCAGGG	0.502																																					p.R179G		Atlas-SNP	.											USP4,mouth,carcinoma,+1,1	USP4	72	1	0			c.C535G						PASS	.						182	180	181					3																	49362425		2203	4300	6503	SO:0001583	missense	7375	exon5			TTTCACGCTCCGC	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.535C>G	3.37:g.49362425G>C	ENSP00000265560:p.Arg179Gly	87	0	0		102	10	0.0980392	NM_199443	A8K6Y0|C9IY91|O43452|O43453|Q08AK8	Missense_Mutation	SNP	ENST00000265560.4	37	CCDS2793.1	.	.	.	.	.	.	.	.	.	.	G	16.00	2.997823	0.54147	.	.	ENSG00000114316	ENST00000351842;ENST00000265560;ENST00000416417;ENST00000415188	T;T;T	0.32023	1.98;2.1;1.47	5.51	2.33	0.28932	.	0.100082	0.64402	N	0.000006	T	0.26268	0.0641	L	0.41824	1.3	0.32078	N	0.593569	P;B	0.39624	0.681;0.372	B;B	0.38755	0.281;0.095	T	0.38457	-0.9660	10	0.72032	D	0.01	-9.6545	12.7177	0.57123	0.0:0.0:0.3137:0.6863	.	179;179	Q13107-2;Q13107	.;UBP4_HUMAN	G	179	ENSP00000341028:R179G;ENSP00000265560:R179G;ENSP00000400623:R179G	ENSP00000265560:R179G	R	-	1	0	USP4	49337429	1.000000	0.71417	0.005000	0.12908	0.963000	0.63663	4.711000	0.61881	0.644000	0.30656	0.491000	0.48974	CGT	.	.	none		0.502	USP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346069.1	NM_199443		C	49362425	G	C	49362425	3	2	5	1	0	0	0	0	1	0	0	0	17086	1087	38	4	2428	4	USP4	3	49362425	Missense_Mutation	SNP	G	TCGA-FA-A6HO-01A-11D-A31X-10	345424	49362425	148660005	6	547											
ROBO2	6092	hgsc.bcm.edu	37	chr3	77147265	77147265	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acgactctgaactgcaaggcGgagggccggccaacgcccac	10	3	13	15	4	1	1	0	1	1	0	1	3	1	2	3	4	3	1	3	4	3	0			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr3:77147265G>A	ENST00000461745.1	+	2	1062	c.162G>A	c.(160-162)gcG>gcA	p.A54A	ROBO2_ENST00000487694.3_Silent_p.A70A|ROBO2_ENST00000332191.8_Silent_p.A54A	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	54	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)		ACTGCAAGGCGGAGGGCCGGC	0.617																																					p.A54A		Atlas-SNP	.											.	ROBO2	527	.	0			c.G162A						PASS	.						53	59	57					3																	77147265		1980	4165	6145	SO:0001819	synonymous_variant	6092	exon2			CAAGGCGGAGGGC	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.162G>A	3.37:g.77147265G>A		89	0	0		139	8	0.057554	NM_002942	O43608|Q19AB4|Q19AB5	Silent	SNP	ENST00000461745.1	37	CCDS43109.1																																																																																			.	.	none		0.617	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		A	77147265	G	A	77147265	2	1	5	1	0	0	0	0	0	0	0	1	13529	1117	39	1		1	ROBO2	3	77147265	Silent	SNP	G	TCGA-FA-A6HO-01A-11D-A31X-10	27784840	77147265	120875165	7	548											
TMEM108	66000	hgsc.bcm.edu	37	chr3	133099739	133099739	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tccctccagggtctcagaaaGcactatttctggagccaagg	10	9	10	12	0	2	1	1	0	2	1	5	2	4	2	3	3	2	1	3	3	3	2			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr3:133099739G>A	ENST00000321871.6	+	4	1394	c.1184G>A	c.(1183-1185)aGc>aAc	p.S395N	TMEM108_ENST00000508711.1_Intron|TMEM108_ENST00000515826.1_Missense_Mutation_p.S395N|TMEM108_ENST00000393130.3_Missense_Mutation_p.S395N	NM_001136469.1|NM_023943.2	NP_001129941.1|NP_076432.1	Q6UXF1	TM108_HUMAN	transmembrane protein 108	395						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						GTCTCAGAAAGCACTATTTCT	0.592																																					p.S395N		Atlas-SNP	.											.	TMEM108	67	.	0			c.G1184A						PASS	.						51	51	51					3																	133099739		2203	4300	6503	SO:0001583	missense	66000	exon4			CAGAAAGCACTAT	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.1184G>A	3.37:g.133099739G>A	ENSP00000324651:p.Ser395Asn	51	0	0		58	11	0.189655	NM_023943	D3DNC9|Q9BQH1|Q9BW81|Q9C0H3	Missense_Mutation	SNP	ENST00000321871.6	37	CCDS33858.1	.	.	.	.	.	.	.	.	.	.	G	14.05	2.419812	0.42918	.	.	ENSG00000144868	ENST00000321871;ENST00000393130;ENST00000515826	T;T;T	0.51325	0.77;0.77;0.71	3.66	2.78	0.32641	.	0.563192	0.16981	N	0.191688	T	0.58935	0.2157	L	0.57536	1.79	0.25499	N	0.987578	D;B	0.67145	0.996;0.023	D;B	0.78314	0.991;0.01	T	0.43653	-0.9378	10	0.45353	T	0.12	-9.2727	6.9696	0.24642	0.2917:0.0:0.7083:0.0	.	395;395	E9PB58;Q6UXF1	.;TM108_HUMAN	N	395	ENSP00000324651:S395N;ENSP00000376838:S395N;ENSP00000423338:S395N	ENSP00000324651:S395N	S	+	2	0	TMEM108	134582429	0.989000	0.36119	0.992000	0.48379	0.937000	0.57800	0.931000	0.28871	0.881000	0.35993	0.561000	0.74099	AGC	.	.	none		0.592	TMEM108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356907.2	NM_023943		A	133099739	G	A	133099739	3	1	5	1	0	0	0	0	1	0	0	0	16039	971	34	2	1190	2	TMEM108	3	133099739	Missense_Mutation	SNP	G	TCGA-FA-A6HO-01A-11D-A31X-10	55952474	133099739	64922691	8	549											
PEX5L	51555	hgsc.bcm.edu	37	chr3	179525541	179525541	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggctgaatctccagtgctcGcgtataggcctccacggctt	6	11	11	13	3	1	1	0	1	1	0	4	1	2	1	3	3	1	4	3	3	3	3			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr3:179525541G>A	ENST00000467460.1	-	14	1927	c.1597C>T	c.(1597-1599)Cga>Tga	p.R533*	PEX5L_ENST00000467440.2_5'UTR|PEX5L_ENST00000468741.1_Nonsense_Mutation_p.R341*|PEX5L_ENST00000392649.3_Nonsense_Mutation_p.R425*|PEX5L_ENST00000476138.1_Nonsense_Mutation_p.R490*|PEX5L_ENST00000485199.1_Nonsense_Mutation_p.R498*|PEX5L_ENST00000263962.8_Nonsense_Mutation_p.R531*|PEX5L_ENST00000472994.1_Nonsense_Mutation_p.R474*|PEX5L_ENST00000464614.1_Nonsense_Mutation_p.R425*|PEX5L_ENST00000465751.1_Nonsense_Mutation_p.R509*	NM_001256751.1|NM_016559.2	NP_001243680.1|NP_057643.1	Q8IYB4	PEX5R_HUMAN	peroxisomal biogenesis factor 5-like	533					maintenance of protein location (GO:0045185)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, docking (GO:0016560)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of membrane potential (GO:0042391)	cytosol (GO:0005829)|dendrite (GO:0030425)|peroxisomal membrane (GO:0005778)|receptor complex (GO:0043235)	peroxisome matrix targeting signal-1 binding (GO:0005052)|peroxisome targeting sequence binding (GO:0000268)|small GTPase binding (GO:0031267)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	all_cancers(143;3.94e-14)|Ovarian(172;0.0338)|Breast(254;0.183)		OV - Ovarian serous cystadenocarcinoma(80;1.75e-26)|GBM - Glioblastoma multiforme(14;0.000518)			TCCAGTGCTCGCGTATAGGCC	0.547																																					p.R533X		Atlas-SNP	.											.	PEX5L	104	.	0			c.C1597T						PASS	.						156	158	157					3																	179525541		2203	4300	6503	SO:0001587	stop_gained	51555	exon14			GTGCTCGCGTATA	AJ245503	CCDS3236.1, CCDS58861.1, CCDS58862.1, CCDS58863.1, CCDS58864.1, CCDS58865.1, CCDS58866.1, CCDS58867.1	3q27.1	2013-01-10			ENSG00000114757	ENSG00000114757		"Tetratricopeptide (TTC) repeat domain containing"	30024	protein-coding gene	gene with protein product		611058				11463335	Standard	NM_016559		Approved	PEX5R, PXR2	uc003fki.2	Q8IYB4	OTTHUMG00000157363	ENST00000467460.1:c.1597C>T	3.37:g.179525541G>A	ENSP00000419975:p.Arg533*	55	0	0		80	5	0.0625	NM_016559	B7Z2A5|B7Z305|B7Z318|B7Z5Z5|B7Z8P2|E7EUV8|E7EUZ0|E9PEC1|E9PH97|Q9NQD1|Q9P2U3|Q9P2U4	Nonsense_Mutation	SNP	ENST00000467460.1	37	CCDS3236.1	.	.	.	.	.	.	.	.	.	.	G	17.13	3.310115	0.60414	.	.	ENSG00000114757	ENST00000467460;ENST00000263962;ENST00000485199;ENST00000382596;ENST00000392649;ENST00000468741;ENST00000476138;ENST00000467440;ENST00000472994;ENST00000464614;ENST00000465751	.	.	.	6.07	0.263	0.15602	.	0.062097	0.64402	D	0.000005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.1829	18.2127	0.89876	0.0:0.0:0.3064:0.6936	.	.	.	.	X	533;531;498;531;425;341;490;421;474;425;509	.	ENSP00000263962:R531X	R	-	1	2	PEX5L	181008235	0.806000	0.28996	0.047000	0.18901	0.321000	0.28281	1.324000	0.33712	0.023000	0.15187	-0.291000	0.09656	CGA	.	.	none		0.547	PEX5L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348577.1	NM_016559		A	179525541	G	A	179525541	4	1	5	1	0	0	0	0	0	1	0	0	11758	1095	38	1	291	1	PEX5L	3	179525541	Nonsense_Mutation	SNP	G	TCGA-FA-A6HO-01A-11D-A31X-10	46425802	179525541	18496889	9	550											
HTT	3064	hgsc.bcm.edu	37	chr4	3184180	3184180	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tagctgacatcatcctcccaAtgttagccaaacagcaggtt	12	10	7	12	0	1	1	1	1	0	0	3	1	3	1	3	1	4	4	3	1	4	3			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr4:3184180A>G	ENST00000355072.5	+	37	4994	c.4849A>G	c.(4849-4851)Atg>Gtg	p.M1617V		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	1617					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)		CATCCTCCCAATGTTAGCCAA	0.502																																					p.M1617V		Atlas-SNP	.											.	HTT	221	.	0			c.A4849G						PASS	.						135	137	137					4																	3184180		2052	4201	6253	SO:0001583	missense	3064	exon37			CTCCCAATGTTAG	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.4849A>G	4.37:g.3184180A>G	ENSP00000347184:p.Met1617Val	88	0	0		51	16	0.313726	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	37	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	A	13.10	2.136143	0.37728	.	.	ENSG00000197386	ENST00000355072	T	0.05139	3.49	4.98	3.81	0.43845	.	0.000000	0.85682	D	0.000000	T	0.06554	0.0168	L	0.60455	1.87	0.48185	D	0.9996	P	0.35328	0.495	B	0.23852	0.049	T	0.27773	-1.0064	10	0.42905	T	0.14	.	9.3075	0.37885	0.9186:0.0:0.0814:0.0	.	1617	P42858	HD_HUMAN	V	1617	ENSP00000347184:M1617V	ENSP00000347184:M1617V	M	+	1	0	HTT	3153978	1.000000	0.71417	0.796000	0.32109	0.774000	0.43823	6.119000	0.71590	0.931000	0.37242	-0.379000	0.06801	ATG	.	.	none		0.502	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		G	3184180	A	G	3184180	3	3	5	1	0	0	0	0	1	0	0	0	7466	101	4	3	4995	3	HTT	4	3184180	Missense_Mutation	SNP	A	TCGA-FA-A6HO-01A-11D-A31X-10		3184180	187970096	10	551											
PCYOX1L	78991	hgsc.bcm.edu	37	chr5	148742308	148742308	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaagggaaccgtgggtggccGcttggccaccatctcagtca	8	7	14	12	2	2	0	2	0	1	0	3	2	2	1	4	4	1	1	4	4	2	1			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr5:148742308G>T	ENST00000274569.4	+	2	259	c.197G>T	c.(196-198)cGc>cTc	p.R66L	PCYOX1L_ENST00000514349.1_5'UTR	NM_024028.3	NP_076933.3	Q8NBM8	PCYXL_HUMAN	prenylcysteine oxidase 1 like	66					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)			GTGGGTGGCCGCTTGGCCACC	0.612																																					p.R66L	Ovarian(62;1136 1477 27277 27495)	Atlas-SNP	.											.	PCYOX1L	32	.	0			c.G197T						PASS	.						102	107	105					5																	148742308		2203	4300	6503	SO:0001583	missense	78991	exon2			GTGGCCGCTTGGC		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.197G>T	5.37:g.148742308G>T	ENSP00000274569:p.Arg66Leu	58	0	0		44	14	0.318182	NM_024028	Q7Z4S2|Q8NCY5|Q8NF69|Q9BTE8|Q9BWS3	Missense_Mutation	SNP	ENST00000274569.4	37	CCDS4296.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.532690	0.85812	.	.	ENSG00000145882	ENST00000274569	T	0.14391	2.51	5.23	4.35	0.52113	.	0.000000	0.85682	D	0.000000	T	0.36690	0.0976	M	0.67953	2.075	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.26121	-1.0112	10	0.87932	D	0	-20.8276	16.1457	0.81563	0.0:0.1339:0.8661:0.0	.	66	Q8NBM8	PCYXL_HUMAN	L	66	ENSP00000274569:R66L	ENSP00000274569:R66L	R	+	2	0	PCYOX1L	148722501	1.000000	0.71417	1.000000	0.80357	0.765000	0.43378	7.840000	0.86819	1.321000	0.45227	0.561000	0.74099	CGC	.	.	none		0.612	PCYOX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252331.2	NM_024028		T	148742308	G	T	148742308	3	4	5	1	0	0	0	0	1	0	0	0	11618	1087	38	4	203	4	PCYOX1L	5	148742308	Missense_Mutation	SNP	G	TCGA-FA-A6HO-01A-11D-A31X-10		148742308	32172952	11	552											
TNF	7124	hgsc.bcm.edu	37	chr6	31543608	31543608	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccccagggctccaggcggtgCttgttcctcagcctcttctc	3	11	10	17	1	3	0	1	0	2	0	6	0	5	0	5	3	2	3	5	3	0	3			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr6:31543608C>T	ENST00000449264.2	+	1	265	c.90C>T	c.(88-90)tgC>tgT	p.C30C		NM_000594.3	NP_000585.2	P01375	TNFA_HUMAN	tumor necrosis factor	30					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|calcium-mediated signaling (GO:0019722)|cell activation (GO:0001775)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nicotine (GO:0071316)|cellular response to organic cyclic compound (GO:0071407)|chronic inflammatory response to antigenic stimulus (GO:0002439)|defense response to Gram-positive bacterium (GO:0050830)|embryonic digestive tract development (GO:0048566)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|glucose metabolic process (GO:0006006)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|JNK cascade (GO:0007254)|leukocyte tethering or rolling (GO:0050901)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|necroptotic signaling pathway (GO:0097527)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of branching involved in lung morphogenesis (GO:0061048)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of glucose import (GO:0046325)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of L-glutamate transport (GO:0002037)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of lipid storage (GO:0010888)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein complex disassembly (GO:0043242)|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)|organ morphogenesis (GO:0009887)|osteoclast differentiation (GO:0030316)|positive regulation of apoptotic process (GO:0043065)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of chronic inflammatory response to antigenic stimulus (GO:0002876)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fever generation (GO:0031622)|positive regulation of gene expression (GO:0010628)|positive regulation of hair follicle development (GO:0051798)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|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 interferon-gamma production (GO:0032729)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mitosis (GO:0045840)|positive regulation of mononuclear cell migration (GO:0071677)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of podosome assembly (GO:0071803)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein transport (GO:0051222)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of synaptic transmission (GO:0050806)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translational initiation by iron (GO:0045994)|positive regulation of vitamin D biosynthetic process (GO:0060557)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|receptor biosynthetic process (GO:0032800)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of immunoglobulin secretion (GO:0051023)|regulation of insulin secretion (GO:0050796)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to salt stress (GO:0009651)|response to virus (GO:0009615)|sequestering of triglyceride (GO:0030730)|skeletal muscle contraction (GO:0003009)|transformed cell apoptotic process (GO:0006927)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	cytokine activity (GO:0005125)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|transcription regulatory region DNA binding (GO:0044212)|tumor necrosis factor receptor binding (GO:0005164)			large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|skin(3)	8		Ovarian(999;0.00556)			Adalimumab(DB00051)|Amrinone(DB01427)|Certolizumab pegol(DB08904)|Chloroquine(DB00608)|Clenbuterol(DB01407)|Epinephrine(DB00668)|Etanercept(DB00005)|Glucosamine(DB01296)|golimumab(DB06674)|Infliximab(DB00065)|Pomalidomide(DB08910)|Pranlukast(DB01411)|Pseudoephedrine(DB00852)|Thalidomide(DB01041)	CCAGGCGGTGCTTGTTCCTCA	0.632									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of																												p.C30C		Atlas-SNP	.											.	TNF	15	.	0			c.C90T						PASS	.						74	74	74					6																	31543608		2203	4300	6503	SO:0001819	synonymous_variant	7124	exon1	Familial Cancer Database	incl.: Familial Head and Neck Cancer	GCGGTGCTTGTTC	X02910	CCDS4702.1	6p21.3	2013-05-22	2010-05-04		ENSG00000232810	ENSG00000232810		"Tumor necrosis factor (ligand) superfamily"	11892	protein-coding gene	gene with protein product	"TNF superfamily, member 2"	191160	"tumor necrosis factor (TNF superfamily, member 2)"	TNFA		2413547, 6392892	Standard	NM_000594		Approved	TNFSF2, DIF, TNF-alpha	uc003nui.4	P01375	OTTHUMG00000031194	ENST00000449264.2:c.90C>T	6.37:g.31543608C>T		54	0	0		40	14	0.35	NM_000594	O43647|Q9P1Q2|Q9UIV3	Silent	SNP	ENST00000449264.2	37	CCDS4702.1																																																																																			.	.	none		0.632	TNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076390.2			T	31543608	C	T	31543608	2	4	5	1	0	0	0	0	0	0	0	1	16286	805	28	2		2	TNF	6	31543608	Silent	SNP	C	TCGA-FA-A6HO-01A-11D-A31X-10		31543608	139571459	12	553											
COL1A2	1278	hgsc.bcm.edu	37	chr7	94041934	94041934	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggcaggcctggcccaattggCccagctggagcaagaggaga	10	4	16	11	0	0	2	0	0	0	2	0	4	0	3	3	6	2	3	3	6	2	1			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr7:94041934C>T	ENST00000297268.6	+	25	1914	c.1443C>T	c.(1441-1443)ggC>ggT	p.G481G		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	481					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)	GCCCAATTGGCCCAGCTGGAG	0.512										HNSCC(75;0.22)																											p.G481G		Atlas-SNP	.											.	COL1A2	240	.	0			c.C1443T						PASS	.						51	50	50					7																	94041934		2203	4300	6503	SO:0001819	synonymous_variant	1278	exon25			AATTGGCCCAGCT	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.1443C>T	7.37:g.94041934C>T		41	0	0		47	8	0.170213	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Silent	SNP	ENST00000297268.6	37	CCDS34682.1																																																																																			.	.	none		0.512	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		T	94041934	C	T	94041934	2	4	5	1	0	0	0	0	0	0	0	1	3680	726	26	2		2	COL1A2	7	94041934	Silent	SNP	C	TCGA-FA-A6HO-01A-11D-A31X-10		94041934	65096729	13	554											
CUX1	1523	hgsc.bcm.edu	37	chr7	101892121	101892121	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggccccgagctccgcgccGccgcccagcaacagcagcag	7	1	13	20	6	0	0	0	0	0	0	1	1	1	0	6	1	5	4	6	1	1	0	rs410825	byFrequency	TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr7:101892121G>A	ENST00000292535.7	+	24	4355	c.4317G>A	c.(4315-4317)ccG>ccA	p.P1439P	CUX1_ENST00000547394.2_Intron|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000360264.3_Silent_p.P1450P|CUX1_ENST00000437600.4_Intron|CUX1_ENST00000549414.2_Silent_p.P1417P|CUX1_ENST00000550008.2_Silent_p.P1383P|CUX1_ENST00000560541.1_Intron|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000556210.1_Silent_p.P1281P|CUX1_ENST00000546411.2_Silent_p.P1337P|CUX1_ENST00000292538.4_Intron	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	1439					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						GCTCCGCGCCGCCGCCCAGCA	0.831													G|||	2727	0.544529	0.3147	0.5	5008	,	,		1201	0.9097		0.4901	False		,,,				2504	0.5665				p.P1450P		Atlas-SNP	.											.	CUX1	253	.	0			c.G4350A						PASS	.						1	1	1					7																	101892121		593	1623	2216	SO:0001819	synonymous_variant	1523	exon24			CGCGCCGCCGCCC	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.4317G>A	7.37:g.101892121G>A		0	0	.		5	5	1	NM_001202543	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Silent	SNP	ENST00000292535.7	37	CCDS5721.1																																																																																			G|0.460;A|0.540	0.540	strong		0.831	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913		A	101892121	G	A	101892121	2	1	5	1	0	0	0	0	0	0	0	1	4066	1074	38	1		1	CUX1	7	101892121	Silent	SNP	G	TCGA-FA-A6HO-01A-11D-A31X-10	7850187	101892121	57246542	14	555											
CSMD1	64478	hgsc.bcm.edu	37	chr8	2944669	2944669	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggtacatgccaagtgggtttCgtctacaggttgcattgctg	7	13	13	8	1	1	0	0	0	1	0	2	0	1	0	1	3	5	5	1	3	3	5			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr8:2944669C>T	ENST00000520002.1	-	50	7982	c.7427G>A	c.(7426-7428)cGa>cAa	p.R2476Q	CSMD1_ENST00000537824.1_Missense_Mutation_p.R2475Q|CSMD1_ENST00000602723.1_Missense_Mutation_p.R2476Q|CSMD1_ENST00000400186.3_Missense_Mutation_p.R2476Q|CSMD1_ENST00000542608.1_Missense_Mutation_p.R2475Q|CSMD1_ENST00000602557.1_Missense_Mutation_p.R2476Q			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	2476	Sushi 14. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)		p.R2204P(1)|p.R2204Q(1)|p.R2475P(1)|p.R2475Q(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)		AAGTGGGTTTCGTCTACAGGT	0.507																																					p.R2475Q		Atlas-SNP	.											CSMD1_ENST00000537824,NS,carcinoma,0,4	CSMD1	1469	4	4	Substitution - Missense(4)	lung(2)|skin(2)	c.G7424A						PASS	.						106	106	106					8																	2944669		2042	4187	6229	SO:0001583	missense	64478	exon49			GGGTTTCGTCTAC			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.7427G>A	8.37:g.2944669C>T	ENSP00000430733:p.Arg2476Gln	78	0	0		52	9	0.173077	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	C	7.075	0.569036	0.13560	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608	T;T;T;T	0.23950	1.88;1.88;1.88;1.88	5.81	4.93	0.64822	Complement control module (2);Sushi/SCR/CCP (3);	0.172123	0.40064	N	0.001184	T	0.19005	0.0456	L	0.27053	0.805	0.42680	D	0.993547	B;B;B	0.23442	0.015;0.066;0.085	B;B;B	0.21917	0.008;0.037;0.022	T	0.04053	-1.0981	10	0.27785	T	0.31	.	14.2967	0.66318	0.0:0.9289:0.0:0.0711	.	2476;2476;2475	E5RIG2;Q96PZ7;F5H2I8	.;CSMD1_HUMAN;.	Q	2476;2476;2337;2475;2475	ENSP00000383047:R2476Q;ENSP00000430733:R2476Q;ENSP00000441462:R2475Q;ENSP00000446243:R2475Q	ENSP00000320445:R2337Q	R	-	2	0	CSMD1	2932076	0.648000	0.27313	0.059000	0.19551	0.012000	0.07955	1.487000	0.35540	2.749000	0.94314	0.561000	0.74099	CGA	.	.	none		0.507	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		T	2944669	C	T	2944669	3	4	5	1	0	0	0	0	1	0	0	0	3946	884	31	1	3358	1	CSMD1	8	2944669	Missense_Mutation	SNP	C	TCGA-FA-A6HO-01A-11D-A31X-10		2944669	143419353	15	556											
TEX15	56154	hgsc.bcm.edu	37	chr8	30706107	30706107	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acattgccctgccatggtaaCtttattgggaggtatacagt	10	13	10	8	0	0	0	0	0	0	0	0	1	0	1	2	3	4	2	2	3	4	7			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr8:30706107C>A	ENST00000256246.2	-	1	501	c.427G>T	c.(427-429)Gtt>Ttt	p.V143F	TEX15_ENST00000523186.1_5'Flank	NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	143					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)		GCCATGGTAACTTTATTGGGA	0.423																																					p.V143F		Atlas-SNP	.											TEX15,colon,carcinoma,+1,1	TEX15	350	1	0			c.G427T						PASS	.						116	111	113					8																	30706107		2203	4300	6503	SO:0001583	missense	56154	exon1			TGGTAACTTTATT	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.427G>T	8.37:g.30706107C>A	ENSP00000256246:p.Val143Phe	103	0	0		111	7	0.0630631	NM_031271		Missense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	C	12.73	2.025481	0.35701	.	.	ENSG00000133863	ENST00000256246	T	0.13196	2.61	5.51	-1.39	0.08997	.	1.516910	0.03687	N	0.246505	T	0.10937	0.0267	N	0.08118	0	0.09310	N	1	P	0.44380	0.834	P	0.45506	0.483	T	0.41088	-0.9528	10	0.87932	D	0	.	10.4415	0.44469	0.0:0.5403:0.0:0.4597	.	143	Q9BXT5	TEX15_HUMAN	F	143	ENSP00000256246:V143F	ENSP00000256246:V143F	V	-	1	0	TEX15	30825649	0.034000	0.19679	0.002000	0.10522	0.030000	0.12068	0.067000	0.14510	-0.081000	0.12662	-0.302000	0.09304	GTT	.	.	none		0.423	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			A	30706107	C	A	30706107	3	1	5	1	0	0	0	0	1	0	0	0	15794	565	20	4	7958	4	TEX15	8	30706107	Missense_Mutation	SNP	C	TCGA-FA-A6HO-01A-11D-A31X-10	27761438	30706107	115657915	16	557											
ASPH	444	hgsc.bcm.edu	37	chr8	62430094	62430094	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agaggacccatacttggtctCgttggcacatcgaatcttgc	9	11	10	11	2	2	1	0	0	2	1	4	3	2	2	1	3	2	2	1	3	2	4			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr8:62430094C>T	ENST00000379454.4	-	24	2306	c.2119G>A	c.(2119-2121)Gag>Aag	p.E707K	ASPH_ENST00000541428.1_Missense_Mutation_p.E678K	NM_004318.3	NP_004309.2	Q12797	ASPH_HUMAN	aspartate beta-hydroxylase	707					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)	TACTTGGTCTCGTTGGCACAT	0.507																																					p.E707K		Atlas-SNP	.											.	ASPH	87	.	0			c.G2119A						PASS	.						171	121	138					8																	62430094		2203	4300	6503	SO:0001583	missense	444	exon24			TGGTCTCGTTGGC	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.2119G>A	8.37:g.62430094C>T	ENSP00000368767:p.Glu707Lys	72	0	0		77	13	0.168831	NM_004318	A6NDF4|A6NHI2|B4DIC9|B4E2K4|B7ZM95|E5RGP5|F5H667|Q6NXR7|Q8TB28|Q9H291|Q9H2C4|Q9NRI0|Q9NRI1|Q9Y4J0	Missense_Mutation	SNP	ENST00000379454.4	37	CCDS34898.1	.	.	.	.	.	.	.	.	.	.	C	15.22	2.768991	0.49680	.	.	ENSG00000198363	ENST00000541428;ENST00000379454	T;T	0.43688	0.94;0.94	5.96	4.19	0.49359	.	0.116455	0.64402	D	0.000016	T	0.43144	0.1234	M	0.80422	2.495	0.80722	D	1	B;P	0.50943	0.235;0.94	B;B	0.37346	0.092;0.247	T	0.50734	-0.8793	10	0.49607	T	0.09	-19.997	12.9723	0.58520	0.0:0.8691:0.0:0.1309	.	678;707	F5H667;Q12797	.;ASPH_HUMAN	K	678;707	ENSP00000437864:E678K;ENSP00000368767:E707K	ENSP00000368767:E707K	E	-	1	0	ASPH	62592648	0.996000	0.38824	0.678000	0.29963	0.418000	0.31294	3.084000	0.50143	0.872000	0.35775	0.650000	0.86243	GAG	.	.	none		0.507	ASPH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378510.3	NM_004318		T	62430094	C	T	62430094	3	4	5	1	0	0	0	0	1	0	0	0	1053	893	31	1	165	1	ASPH	8	62430094	Missense_Mutation	SNP	C	TCGA-FA-A6HO-01A-11D-A31X-10	31723987	62430094	83933928	17	558											
CSMD3	114788	hgsc.bcm.edu	37	chr8	113657379	113657379	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagtccatgtacaattcagaGaatttggataaaattccggg	14	11	9	7	1	1	1	1	0	0	1	3	3	3	2	2	2	1	1	2	2	5	5			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr8:113657379G>A	ENST00000297405.5	-	20	3513	c.3269C>T	c.(3268-3270)tCt>tTt	p.S1090F	MIR2053_ENST00000459295.1_RNA|CSMD3_ENST00000352409.3_Missense_Mutation_p.S1090F|CSMD3_ENST00000455883.2_Missense_Mutation_p.S986F|CSMD3_ENST00000343508.3_Missense_Mutation_p.S1050F	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1090	CUB 6. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.S1090Y(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						ACAATTCAGAGAATTTGGATA	0.363										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.S1090F		Atlas-SNP	.											CSMD3_ENST00000343508,NS,carcinoma,0,5	CSMD3	2325	5	1	Substitution - Missense(1)	large_intestine(1)	c.C3269T						PASS	.						92	92	92					8																	113657379		2203	4300	6503	SO:0001583	missense	114788	exon20			TTCAGAGAATTTG	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.3269C>T	8.37:g.113657379G>A	ENSP00000297405:p.Ser1090Phe	90	0	0		66	14	0.212121	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.979091	0.74360	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52	5.68	5.68	0.88126	CUB (5);	0.073489	0.56097	D	0.000033	T	0.54565	0.1866	M	0.62016	1.91	0.43069	D	0.994709	B;B;D	0.67145	0.016;0.02;0.996	B;B;D	0.66602	0.026;0.044;0.945	T	0.53301	-0.8458	10	0.66056	D	0.02	.	20.1553	0.98111	0.0:0.0:1.0:0.0	.	986;1090;1050	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	F	1050;1090;430;986;1090	ENSP00000345799:S1050F;ENSP00000297405:S1090F;ENSP00000341558:S430F;ENSP00000412263:S986F;ENSP00000343124:S1090F	ENSP00000297405:S1090F	S	-	2	0	CSMD3	113726555	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.677000	0.74503	2.838000	0.97847	0.591000	0.81541	TCT	.	.	none		0.363	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113657379	G	A	113657379	3	1	5	1	0	0	0	0	1	0	0	0	3948	942	33	2	8062	2	CSMD3	8	113657379	Missense_Mutation	SNP	G	TCGA-FA-A6HO-01A-11D-A31X-10	51227285	113657379	32706643	18	559											
COL22A1	169044	hgsc.bcm.edu	37	chr8	139606427	139606427	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgggggcatctgggccaggAggtaggcgagtctggctgta	6	7	19	9	2	2	0	0	0	2	0	2	2	2	1	2	7	0	4	2	7	2	2	rs72727814	byFrequency	TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr8:139606427A>G	ENST00000303045.6	-	63	4894	c.4448T>C	c.(4447-4449)cTc>cCc	p.L1483P	COL22A1_ENST00000435777.1_Missense_Mutation_p.L1463P|COL22A1_ENST00000341807.4_5'UTR	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1483	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)			CTGGGCCAGGAGGTAGGCGAG	0.577										HNSCC(7;0.00092)																											p.L1483P		Atlas-SNP	.											.	COL22A1	390	.	0			c.T4448C						PASS	.						35	39	37					8																	139606427		2203	4300	6503	SO:0001583	missense	169044	exon63			GCCAGGAGGTAGG	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.4448T>C	8.37:g.139606427A>G	ENSP00000303153:p.Leu1483Pro	155	0	0		117	11	0.0940171	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	37	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	A	15.75	2.924459	0.52653	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.90504	-2.68;-2.57	5.92	5.92	0.95590	.	0.155601	0.29783	N	0.011218	D	0.93943	0.8061	M	0.63428	1.95	0.80722	D	1	D;D	0.89917	0.996;1.0	D;D	0.77004	0.989;0.972	D	0.92409	0.5936	10	0.26408	T	0.33	.	15.5808	0.76439	1.0:0.0:0.0:0.0	.	1463;1483	Q8NFW1-2;Q8NFW1	.;COMA1_HUMAN	P	1483;1463;1176	ENSP00000303153:L1483P;ENSP00000387655:L1463P	ENSP00000303153:L1483P	L	-	2	0	COL22A1	139675609	1.000000	0.71417	1.000000	0.80357	0.740000	0.42216	7.098000	0.76974	2.275000	0.75901	0.529000	0.55759	CTC	A|0.995;T|0.005	.	alt		0.577	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		G	139606427	A	G	139606427	3	3	5	1	0	0	0	0	1	0	0	0	3683	304	11	3	444	3	COL22A1	8	139606427	Missense_Mutation	SNP	A	TCGA-FA-A6HO-01A-11D-A31X-10	25949048	139606427	6757595	19	560											
GDA	9615	hgsc.bcm.edu	37	chr9	74838127	74838127	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcaacattgctaaaacccGtgatttgcacattcaggtgg	11	10	11	9	1	1	1	1	1	0	0	1	1	1	1	1	3	4	3	1	3	3	4	rs142139311	byFrequency	TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr9:74838127G>A	ENST00000358399.3	+	7	791	c.698G>A	c.(697-699)cGt>cAt	p.R233H	GDA_ENST00000376989.3_Intron|GDA_ENST00000545168.1_Missense_Mutation_p.R159H|GDA_ENST00000376986.1_Intron|GDA_ENST00000477618.1_3'UTR|GDA_ENST00000238018.4_Missense_Mutation_p.R233H	NM_001242505.2|NM_001242506.2|NM_004293.4	NP_001229434.1|NP_001229435.1|NP_004284.1	Q9Y2T3	GUAD_HUMAN	guanine deaminase	233					guanine catabolic process (GO:0006147)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|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)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	guanine deaminase activity (GO:0008892)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|kidney(1)|large_intestine(1)|lung(20)|ovary(2)|skin(2)|urinary_tract(1)	32		Myeloproliferative disorder(762;0.0122)		Lung(182;0.0583)		GCTAAAACCCGTGATTTGCAC	0.433													G|||	2	0.000399361	0.0008	0.0	5008	,	,		18219	0.001		0.0	False		,,,				2504	0.0				p.R233H		Atlas-SNP	.											.	GDA	113	.	0			c.G698A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	174	154	161		698,476,476,698	-1.5	0.9	9	dbSNP_134	161	0,8600		0,0,4300	no	missense,missense,missense,missense	GDA	NM_001242505.1,NM_001242506.1,NM_001242507.1,NM_004293.3	29,29,29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign,benign,benign	233/472,159/381,159/381,233/455	74838127	1,13005	2203	4300	6503	SO:0001583	missense	9615	exon7			AAACCCGTGATTT	AF095286	CCDS6641.1, CCDS56576.1, CCDS56577.1	9q21.13	2008-05-14			ENSG00000119125	ENSG00000119125			4212	protein-coding gene	gene with protein product		139260				10075721, 3966794	Standard	NM_001242507		Approved		uc004air.3	Q9Y2T3	OTTHUMG00000020005	ENST00000358399.3:c.698G>A	9.37:g.74838127G>A	ENSP00000351170:p.Arg233His	100	0	0		96	5	0.0520833	NM_004293	B4DTY5|Q5SZC7|Q9H335|Q9ULG2	Missense_Mutation	SNP	ENST00000358399.3	37	CCDS6641.1	.	.	.	.	.	.	.	.	.	.	G	1.462	-0.562132	0.03939	2.27E-4	0.0	ENSG00000119125	ENST00000545168;ENST00000238018;ENST00000358399;ENST00000414671	D;D;D;D	0.90324	-2.65;-2.65;-2.65;-2.65	5.58	-1.51	0.08664	Amidohydrolase 1 (1);	0.560216	0.21401	N	0.075150	T	0.66376	0.2783	N	0.00496	-1.435	0.27209	N	0.959976	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.61402	-0.7070	10	0.15066	T	0.55	-0.897	10.6755	0.45783	0.739:0.0:0.261:0.0	.	233;233	Q9Y2T3-3;Q9Y2T3	.;GUAD_HUMAN	H	159;233;233;99	ENSP00000437972:R159H;ENSP00000238018:R233H;ENSP00000351170:R233H;ENSP00000403897:R99H	ENSP00000238018:R233H	R	+	2	0	GDA	74027947	0.001000	0.12720	0.885000	0.34714	0.643000	0.38383	0.307000	0.19296	-0.524000	0.06400	-0.783000	0.03347	CGT	G|1.000;A|0.000	0.000	weak		0.433	GDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052633.1			A	74838127	G	A	74838127	3	1	5	1	0	0	0	0	1	0	0	0	6314	1145	40	1	724	1	GDA	9	74838127	Missense_Mutation	SNP	G	TCGA-FA-A6HO-01A-11D-A31X-10		74838127	66375304	20	561											
FBP2	8789	hgsc.bcm.edu	37	chr9	97321395	97321395	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgatgtaggccacgggattgCattcatacaggagccggagc	10	8	14	9	2	1	1	1	1	0	0	1	4	1	4	2	4	4	2	2	4	2	4			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr9:97321395C>T	ENST00000375337.3	-	7	911	c.845G>A	c.(844-846)tGc>tAc	p.C282Y	PCAT7_ENST00000452148.2_RNA	NM_003837.2	NP_003828.2	O00757	F16P2_HUMAN	fructose-1,6-bisphosphatase 2	282					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)				CACGGGATTGCATTCATACAG	0.597																																					p.C282Y		Atlas-SNP	.											.	FBP2	26	.	0			c.G845A						PASS	.						56	53	54					9																	97321395		2203	4300	6503	SO:0001583	missense	8789	exon7			GGATTGCATTCAT	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.845G>A	9.37:g.97321395C>T	ENSP00000364486:p.Cys282Tyr	62	0	0		62	6	0.0967742	NM_003837	Q17R39|Q6FI53	Missense_Mutation	SNP	ENST00000375337.3	37	CCDS6711.1	.	.	.	.	.	.	.	.	.	.	.	25.5	4.645909	0.87958	.	.	ENSG00000130957	ENST00000375337	T	0.73152	-0.72	5.43	5.43	0.79202	.	0.045824	0.85682	D	0.000000	D	0.88786	0.6531	H	0.94734	3.575	0.80722	D	1	D	0.64830	0.994	D	0.69479	0.964	D	0.91262	0.5037	10	0.87932	D	0	0.263	19.4276	0.94749	0.0:1.0:0.0:0.0	.	282	O00757	F16P2_HUMAN	Y	282	ENSP00000364486:C282Y	ENSP00000364486:C282Y	C	-	2	0	FBP2	96361216	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.327000	0.79147	2.813000	0.96785	0.655000	0.94253	TGC	.	.	none		0.597	FBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053189.1	NM_003837		T	97321395	C	T	97321395	3	4	5	1	0	0	0	0	1	0	0	0	5714	710	25	2	178	2	FBP2	9	97321395	Missense_Mutation	SNP	C	TCGA-FA-A6HO-01A-11D-A31X-10	22483268	97321395	43892036	21	562											
NEBL	10529	hgsc.bcm.edu	37	chr10	21309077	21309077	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attcactttgctgcttcaggCgaagattttcaggtgtatct	8	16	9	8	1	4	1	3	0	1	1	4	2	4	1	0	2	2	3	0	2	2	6			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr10:21309077C>T	ENST00000417816.2	-	3	571	c.218G>A	c.(217-219)cGc>cAc	p.R73H	NEBL_ENST00000377159.4_Missense_Mutation_p.R39H	NM_001173484.1|NM_213569.2	NP_001166955.1|NP_998734.1	O76041	NEBL_HUMAN	nebulette	737					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						CTGCTTCAGGCGAAGATTTTC	0.413																																					p.R73H		Atlas-SNP	.											NEBL_ENST00000417816,NS,malignant_melanoma,-1,2	NEBL	199	2	0			c.G218A						PASS	.						105	99	101					10																	21309077		2203	4300	6503	SO:0001583	missense	10529	exon3			TTCAGGCGAAGAT	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	ENST00000417816.2:c.218G>A	10.37:g.21309077C>T	ENSP00000393896:p.Arg73His	96	0	0		113	8	0.0707965	NM_001173484	B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Missense_Mutation	SNP	ENST00000417816.2	37	CCDS7133.1	.	.	.	.	.	.	.	.	.	.	c	27.3	4.819770	0.90873	.	.	ENSG00000078114	ENST00000417816;ENST00000377159	T;T	0.42131	0.98;0.98	5.24	5.24	0.73138	.	.	.	.	.	T	0.61223	0.2330	L	0.53729	1.69	0.41209	D	0.986421	D	0.89917	1.0	D	0.91635	0.999	T	0.60459	-0.7259	9	0.48119	T	0.1	.	17.9579	0.89075	0.0:1.0:0.0:0.0	.	73	Q70I54	.	H	73;39	ENSP00000393896:R73H;ENSP00000366364:R39H	ENSP00000366364:R39H	R	-	2	0	NEBL	21349083	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.105000	0.71505	2.595000	0.87683	0.651000	0.88453	CGC	.	.	none		0.413	NEBL-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047112.1	NM_006393		T	21309077	C	T	21309077	3	4	5	1	0	0	0	0	1	0	0	0	10312	768	27	1	3303	1	NEBL	10	21309077	Missense_Mutation	SNP	C	TCGA-FA-A6HO-01A-11D-A31X-10		21309077	114225670	22	563											
ZNF503	84858	hgsc.bcm.edu	37	chr10	77158962	77158962	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggggtagagggggtggccggCcagggagggcggtgtggcgc	4	4	26	7	3	0	1	0	0	0	1	0	2	0	2	2	10	0	1	2	10	1	1			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr10:77158962C>T	ENST00000372524.4	-	2	1972	c.1486G>A	c.(1486-1488)Gcc>Acc	p.A496T	RP11-399K21.11_ENST00000418818.2_lincRNA|ZNF503_ENST00000535216.1_Missense_Mutation_p.A496T|ZNF503-AS2_ENST00000466942.2_RNA	NM_032772.4	NP_116161.2	Q96F45	ZN503_HUMAN	zinc finger protein 503	496					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)					GGGTGGCCGGCCAGGGAGGGC	0.687																																					p.A496T		Atlas-SNP	.											.	ZNF503	25	.	0			c.G1486A						PASS	.						14	16	15					10																	77158962		2197	4291	6488	SO:0001583	missense	84858	exon2			GGCCGGCCAGGGA	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.1486G>A	10.37:g.77158962C>T	ENSP00000361602:p.Ala496Thr	21	0	0		21	10	0.47619	NM_032772	Q8NAC5|Q96E25|Q96IJ0	Missense_Mutation	SNP	ENST00000372524.4	37	CCDS7350.1	.	.	.	.	.	.	.	.	.	.	C	9.686	1.150705	0.21371	.	.	ENSG00000165655	ENST00000372524;ENST00000535216;ENST00000372516	T;T	0.49720	0.77;0.77	4.04	4.04	0.47022	.	0.331694	0.32918	N	0.005493	T	0.31263	0.0791	N	0.24115	0.695	0.35873	D	0.828373	B	0.18863	0.031	B	0.13407	0.009	T	0.29822	-0.9999	10	0.19590	T	0.45	-16.1824	11.987	0.53153	0.0:0.8248:0.1752:0.0	.	496	Q96F45	ZN503_HUMAN	T	496;496;459	ENSP00000361602:A496T;ENSP00000438988:A496T	ENSP00000361594:A459T	A	-	1	0	ZNF503	76828968	0.999000	0.42202	1.000000	0.80357	0.994000	0.84299	0.688000	0.25422	2.084000	0.62774	0.551000	0.68910	GCC	.	.	none		0.687	ZNF503-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048826.1	NM_032772		T	77158962	C	T	77158962	3	4	5	1	0	0	0	0	1	0	0	0	17966	739	26	2	458	2	ZNF503	10	77158962	Missense_Mutation	SNP	C	TCGA-FA-A6HO-01A-11D-A31X-10	55849885	77158962	58375785	23	564											
CCDC81	60494	hgsc.bcm.edu	37	chr11	86131001	86131001	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acagaaccgctgagctggagCgagtaaatagagtcaaccaa	16	5	11	9	2	1	3	1	1	0	2	1	5	1	4	2	1	4	3	2	1	6	2			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr11:86131001C>T	ENST00000445632.2	+	14	1995	c.1723C>T	c.(1723-1725)Cga>Tga	p.R575*	CCDC81_ENST00000278487.3_Nonsense_Mutation_p.R310*|CCDC81_ENST00000528728.1_Nonsense_Mutation_p.R310*|CCDC81_ENST00000354755.1_Nonsense_Mutation_p.R485*	NM_001156474.1	NP_001149946.1	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81	575										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)				TGAGCTGGAGCGAGTAAATAG	0.507																																					p.R575X		Atlas-SNP	.											.	CCDC81	89	.	0			c.C1723T						PASS	.						87	75	79					11																	86131001		2202	4299	6501	SO:0001587	stop_gained	60494	exon14			CTGGAGCGAGTAA	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.1723C>T	11.37:g.86131001C>T	ENSP00000415528:p.Arg575*	72	0	0		74	16	0.216216	NM_001156474	A0AVL7|Q53FW3|Q9H5E5	Nonsense_Mutation	SNP	ENST00000445632.2	37	CCDS53691.1	.	.	.	.	.	.	.	.	.	.	C	44	10.710250	0.99454	.	.	ENSG00000149201	ENST00000354755;ENST00000278487;ENST00000445632;ENST00000528728	.	.	.	5.16	1.89	0.25635	.	0.306262	0.25236	N	0.032136	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-5.9965	10.4293	0.44398	0.5496:0.4504:0.0:0.0	.	.	.	.	X	485;310;575;310	.	.	R	+	1	2	CCDC81	85808649	0.100000	0.21855	0.007000	0.13788	0.208000	0.24298	0.133000	0.15912	0.683000	0.31428	0.555000	0.69702	CGA	.	.	none		0.507	CCDC81-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393756.1	NM_021827		T	86131001	C	T	86131001	4	4	5	1	0	0	0	0	0	1	0	0	2857	760	27	1	1777	1	CCDC81	11	86131001	Nonsense_Mutation	SNP	C	TCGA-FA-A6HO-01A-11D-A31X-10		86131001	48875515	24	565											
TRPC6	7225	hgsc.bcm.edu	37	chr11	101375357	101375357	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcattcttctaacatcttccGcaccactgggatgttaccat	9	13	6	13	1	3	0	0	0	3	0	4	1	4	1	3	1	2	3	3	1	2	5	rs199884871		TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr11:101375357G>A	ENST00000344327.3	-	2	767	c.343C>T	c.(343-345)Cgg>Tgg	p.R115W	TRPC6_ENST00000532133.1_Missense_Mutation_p.R115W|TRPC6_ENST00000348423.4_Missense_Mutation_p.R115W|TRPC6_ENST00000360497.4_Missense_Mutation_p.R115W|TRPC6_ENST00000526713.1_5'Flank	NM_004621.5	NP_004612.2	Q9Y210	TRPC6_HUMAN	transient receptor potential cation channel, subfamily C, member 6	115					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)		AACATCTTCCGCACCACTGGG	0.473																																					p.R115W	Colon(166;1315 1927 11094 12848 34731)	Atlas-SNP	.											TRPC6,NS,carcinoma,+1,1	TRPC6	132	1	0			c.C343T						PASS	.	G	TRP/ARG	0,4406		0,0,2203	156	142	147		343	4	1	11		147	1,8597	1.2+/-3.3	0,1,4298	no	missense	TRPC6	NM_004621.5	101	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	benign	115/932	101375357	1,13003	2203	4299	6502	SO:0001583	missense	7225	exon2			TCTTCCGCACCAC	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.343C>T	11.37:g.101375357G>A	ENSP00000340913:p.Arg115Trp	93	0	0		72	6	0.0833333	NM_004621	Q52M59|Q9HCW3|Q9NQA8|Q9NQA9	Missense_Mutation	SNP	ENST00000344327.3	37	CCDS8311.1	.	.	.	.	.	.	.	.	.	.	G	18.36	3.607032	0.66558	0.0	1.16E-4	ENSG00000137672	ENST00000344327;ENST00000532133;ENST00000348423;ENST00000360497	T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27	5.96	3.95	0.45737	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.82130	0.4970	M	0.83692	2.655	0.51233	D	0.999918	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.986;0.999;0.992	D	0.83852	0.0263	10	0.72032	D	0.01	-15.8714	13.7254	0.62754	0.0:0.0:0.6021:0.3979	.	115;115;115	Q9Y210-3;Q9Y210-2;Q9Y210	.;.;TRPC6_HUMAN	W	115	ENSP00000340913:R115W;ENSP00000435574:R115W;ENSP00000343672:R115W;ENSP00000353687:R115W	ENSP00000340913:R115W	R	-	1	2	TRPC6	100880567	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.284000	0.43478	0.673000	0.31224	0.655000	0.94253	CGG	.	.	weak		0.473	TRPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394770.1	NM_004621		A	101375357	G	A	101375357	3	1	5	1	0	0	0	0	1	0	0	0	16598	1086	38	1	2500	1	TRPC6	11	101375357	Missense_Mutation	SNP	G	TCGA-FA-A6HO-01A-11D-A31X-10	15244356	101375357	33631159	25	566											
GDF3	9573	hgsc.bcm.edu	37	chr12	7848214	7848214	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aacttctggggtgaaggcgcCttatctaagcccagaaattg	11	10	11	9	1	2	2	0	1	2	1	2	2	2	2	2	3	2	0	2	3	5	4	rs376751766		TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr12:7848214C>T	ENST00000329913.3	-	1	158	c.111G>A	c.(109-111)aaG>aaA	p.K37K		NM_020634.1	NP_065685.1	Q9NR23	GDF3_HUMAN	growth differentiation factor 3	37					endoderm development (GO:0007492)|eye development (GO:0001654)|formation of anatomical boundary (GO:0048859)|growth (GO:0040007)|in utero embryonic development (GO:0001701)|mesoderm development (GO:0007498)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of epidermal cell differentiation (GO:0045605)|notochord development (GO:0030903)|primitive streak formation (GO:0090009)|regulation of cell fate commitment (GO:0010453)|response to dietary excess (GO:0002021)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	28						GTGAAGGCGCCTTATCTAAGC	0.478																																					p.K37K		Atlas-SNP	.											.	GDF3	68	.	0			c.G111A						PASS	.	C		0,4406		0,0,2203	47	48	48		111	-1.4	0	12		48	1,8599		0,1,4299	no	coding-synonymous	GDF3	NM_020634.1		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		37/365	7848214	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9573	exon1			AGGCGCCTTATCT	AF263538	CCDS8581.1	12p13.1	2014-01-30			ENSG00000184344	ENSG00000184344		"Endogenous ligands"	4218	protein-coding gene	gene with protein product		606522				9467948	Standard	NM_020634		Approved		uc001qte.3	Q9NR23	OTTHUMG00000168433	ENST00000329913.3:c.111G>A	12.37:g.7848214C>T		119	0	0		82	13	0.158537	NM_020634	Q8NEJ4	Silent	SNP	ENST00000329913.3	37	CCDS8581.1																																																																																			.	.	weak		0.478	GDF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399717.1			T	7848214	C	T	7848214	2	4	5	1	0	0	0	0	0	0	0	1	6323	680	24	2		2	GDF3	12	7848214	Silent	SNP	C	TCGA-FA-A6HO-01A-11D-A31X-10		7848214	126003681	26	567											
BTG1	694	hgsc.bcm.edu	37	chr12	92539200	92539200	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caggctctggctgaaggtctGcagctgtcgctcgctcgtga	5	10	14	12	3	2	2	0	2	2	0	5	2	2	2	0	3	2	6	0	3	1	0			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr12:92539200G>A	ENST00000256015.3	-	1	473	c.112C>T	c.(112-114)Cag>Tag	p.Q38*	RP11-796E2.4_ENST00000499685.2_RNA|C12orf79_ENST00000551563.2_5'Flank|RP11-796E2.4_ENST00000501008.2_RNA|C12orf79_ENST00000549802.1_5'Flank|C12orf79_ENST00000546975.1_5'Flank	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	38					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)	p.Q38E(1)		haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				CTGAAGGTCTGCAGCTGTCGC	0.682			T	MYC	BCLL																																p.Q38X		Atlas-SNP	.		Dom	yes		12	12q22	694	"B-cell translocation gene 1, anti-proliferative"		L	BTG1,NS,lymphoid_neoplasm,0,1	BTG1	30	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C112T						scavenged	.						37	40	39					12																	92539200		2203	4300	6503	SO:0001587	stop_gained	694	exon1			AGGTCTGCAGCTG		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.112C>T	12.37:g.92539200G>A	ENSP00000256015:p.Gln38*	123	1	0.00813008		85	12	0.141176	NM_001731	P31607	Nonsense_Mutation	SNP	ENST00000256015.3	37	CCDS9043.1	.	.	.	.	.	.	.	.	.	.	G	39	7.775086	0.98483	.	.	ENSG00000133639	ENST00000256015	.	.	.	3.92	1.83	0.25207	.	0.185973	0.48286	D	0.000200	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	-3.618	9.7333	0.40374	0.0:0.1525:0.6897:0.1579	.	.	.	.	X	38	.	ENSP00000256015:Q38X	Q	-	1	0	BTG1	91063331	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.272000	0.89885	0.765000	0.33221	0.455000	0.32223	CAG	.	.	none		0.682	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1			A	92539200	G	A	92539200	4	1	5	1	0	0	0	0	0	1	0	0	1555	1328	46	2	411	2	BTG1	12	92539200	Nonsense_Mutation	SNP	G	TCGA-FA-A6HO-01A-11D-A31X-10	84690986	92539200	41312695	27	568											
RNF10	9921	hgsc.bcm.edu	37	chr12	121014414	121014414	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agagaaaggaggaaagaaaaGaaaaaaacagaaacagaagc	27	0	11	3	0	0	5	0	0	0	5	0	8	0	7	0	2	3	0	0	2	9	0			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr12:121014414G>C	ENST00000325954.4	+	17	2842	c.2381G>C	c.(2380-2382)aGa>aCa	p.R794T	POP5_ENST00000542776.1_5'Flank|RNF10_ENST00000542701.1_3'UTR|RNF10_ENST00000413266.2_Missense_Mutation_p.R799T	NM_014868.4	NP_055683.3	Q8N5U6	RNF10_HUMAN	ring finger protein 10	794					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)					ggaaagaaaagaaaaaaacag	0.443																																					p.R794T		Atlas-SNP	.											.	RNF10	75	.	0			c.G2381C						PASS	.						84	80	81					12																	121014414		2203	4300	6503	SO:0001583	missense	9921	exon17			AGAAAAGAAAAAA	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.2381G>C	12.37:g.121014414G>C	ENSP00000322242:p.Arg794Thr	113	0	0		77	14	0.181818	NM_014868	Q92550|Q9NPP8|Q9ULW4	Missense_Mutation	SNP	ENST00000325954.4	37	CCDS9201.1	.	.	.	.	.	.	.	.	.	.	G	17.36	3.368859	0.61624	.	.	ENSG00000022840	ENST00000325954;ENST00000458409;ENST00000413266;ENST00000538254	D;D	0.89415	-2.51;-2.51	6.09	6.09	0.99107	.	0.204155	0.51477	D	0.000100	D	0.82554	0.5062	L	0.36672	1.1	0.50813	D	0.999892	B;P	0.48764	0.277;0.915	B;B	0.36922	0.068;0.236	D	0.84750	0.0756	10	0.72032	D	0.01	.	12.9234	0.58245	0.0733:0.0:0.9267:0.0	.	799;794	Q8N5U6-2;Q8N5U6	.;RNF10_HUMAN	T	794;794;799;129	ENSP00000322242:R794T;ENSP00000415682:R799T	ENSP00000322242:R794T	R	+	2	0	RNF10	119498797	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.030000	0.64128	2.899000	0.99337	0.655000	0.94253	AGA	.	.	none		0.443	RNF10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401898.4			C	121014414	G	C	121014414	3	2	5	1	0	0	0	0	1	0	0	0	13437	942	33	4	2447	4	RNF10	12	121014414	Missense_Mutation	SNP	G	TCGA-FA-A6HO-01A-11D-A31X-10	28475214	121014414	12837481	28	569											
GOLGA3	2802	hgsc.bcm.edu	37	chr12	133389993	133389993	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttctccaggggcaggggaGaatctgtagagcctgcagtg	8	8	15	10	0	2	2	0	0	2	2	3	3	2	2	3	4	2	3	3	4	2	2			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr12:133389993G>T	ENST00000450791.2	-	3	602	c.419C>A	c.(418-420)tCt>tAt	p.S140Y	GOLGA3_ENST00000545875.1_Missense_Mutation_p.S140Y|GOLGA3_ENST00000204726.3_Missense_Mutation_p.S140Y|GOLGA3_ENST00000456883.2_Missense_Mutation_p.S140Y|GOLGA3_ENST00000537452.1_Missense_Mutation_p.S140Y			Q08378	GOGA3_HUMAN	golgin A3	140	Interaction with GOPC.	Cleavage; by caspase-3.			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)		GGGCAGGGGAGAATCTGTAGA	0.512																																					p.S140Y		Atlas-SNP	.											.	GOLGA3	234	.	0			c.C419A						PASS	.						51	46	48					12																	133389993		2203	4300	6503	SO:0001583	missense	2802	exon4			AGGGGAGAATCTG	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.419C>A	12.37:g.133389993G>T	ENSP00000410378:p.Ser140Tyr	35	0	0		43	7	0.162791	NM_001172557	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Missense_Mutation	SNP	ENST00000450791.2	37	CCDS9281.1	.	.	.	.	.	.	.	.	.	.	G	13.04	2.118729	0.37436	.	.	ENSG00000090615	ENST00000204726;ENST00000450791;ENST00000456883;ENST00000537452;ENST00000545875	T;T;T;T;T	0.35236	1.75;1.75;1.75;1.32;1.32	5.21	5.21	0.72293	.	0.414396	0.28665	N	0.014554	T	0.36026	0.0952	L	0.43152	1.355	0.80722	D	1	P;B;P	0.45078	0.85;0.432;0.492	B;B;B	0.40534	0.246;0.246;0.332	T	0.32587	-0.9901	10	0.72032	D	0.01	.	18.3644	0.90385	0.0:0.0:1.0:0.0	.	140;140;140	Q08378-4;Q08378-2;Q08378	.;.;GOGA3_HUMAN	Y	140	ENSP00000204726:S140Y;ENSP00000410378:S140Y;ENSP00000409303:S140Y;ENSP00000442143:S140Y;ENSP00000442603:S140Y	ENSP00000204726:S140Y	S	-	2	0	GOLGA3	131900066	1.000000	0.71417	0.069000	0.20011	0.265000	0.26407	8.069000	0.89491	2.414000	0.81942	0.462000	0.41574	TCT	.	.	none		0.512	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	NM_005895		T	133389993	G	T	133389993	3	4	5	1	0	0	0	0	1	0	0	0	6562	942	33	4	4299	4	GOLGA3	12	133389993	Missense_Mutation	SNP	G	TCGA-FA-A6HO-01A-11D-A31X-10	12375579	133389993	461902	29	570											
AKAP11	11215	hgsc.bcm.edu	37	chr13	42877901	42877901	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagtaccagcctggcagcCgacagtgggatcggacagga	11	4	15	11	2	0	0	0	0	0	0	1	4	0	3	3	4	4	3	3	4	1	1	rs201525107	byFrequency	TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr13:42877901C>T	ENST00000025301.2	+	8	5194	c.5019C>T	c.(5017-5019)gcC>gcT	p.A1673A		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	1673					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)		GCCTGGCAGCCGACAGTGGGA	0.507													C|||	3	0.000599042	0.0	0.0	5008	,	,		18914	0.003		0.0	False		,,,				2504	0.0				p.A1673A		Atlas-SNP	.											.	AKAP11	146	.	0			c.C5019T						PASS	.						37	35	36					13																	42877901		2203	4300	6503	SO:0001819	synonymous_variant	11215	exon8			GGCAGCCGACAGT	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.5019C>T	13.37:g.42877901C>T		110	0	0		96	24	0.25	NM_016248	O75124|Q9NUK7	Silent	SNP	ENST00000025301.2	37	CCDS9383.1																																																																																			C|1.000;T|0.000	0.000	strong		0.507	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248		T	42877901	C	T	42877901	2	4	5	1	0	0	0	0	0	0	0	1	447	639	23	1		1	AKAP11	13	42877901	Silent	SNP	C	TCGA-FA-A6HO-01A-11D-A31X-10		42877901	72291977	30	571											
EPSTI1	94240	hgsc.bcm.edu	37	chr13	43474489	43474489	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tttggctctttcttgctcttGctgctgccgtttcagttcca	2	19	8	12	1	4	0	1	0	3	0	5	0	5	0	2	1	4	6	2	1	0	6			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr13:43474489G>T	ENST00000398762.3	-	10	804	c.805C>A	c.(805-807)Caa>Aaa	p.Q269K	EPSTI1_ENST00000313640.7_Missense_Mutation_p.Q269K|EPSTI1_ENST00000313624.7_Missense_Mutation_p.Q258K			Q96J88	ESIP1_HUMAN	epithelial stromal interaction 1 (breast)	269										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)		TCTTGCTCTTGCTGCTGCCGT	0.353																																					p.Q269K		Atlas-SNP	.											.	EPSTI1	47	.	0			c.C805A						PASS	.						210	180	191					13																	43474489		2202	4300	6502	SO:0001583	missense	94240	exon10			GCTCTTGCTGCTG	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.805C>A	13.37:g.43474489G>T	ENSP00000381746:p.Gln269Lys	77	0	0		65	4	0.0615385	NM_001002264	Q8IVC7|Q8NDQ7	Missense_Mutation	SNP	ENST00000398762.3	37	CCDS9387.1	.	.	.	.	.	.	.	.	.	.	G	13.28	2.189527	0.38707	.	.	ENSG00000133106	ENST00000313640;ENST00000313624;ENST00000398762	T	0.21191	2.02	5.15	3.42	0.39159	.	0.315322	0.27535	N	0.018925	T	0.27629	0.0679	M	0.67953	2.075	0.27333	N	0.956715	P;P	0.51537	0.946;0.946	P;P	0.48840	0.592;0.592	T	0.10064	-1.0646	10	0.49607	T	0.09	-9.5038	7.5873	0.27999	0.085:0.3183:0.5966:0.0	.	258;269	Q96J88-2;Q96J88-3	.;.	K	269;258;269	ENSP00000318982:Q269K	ENSP00000318643:Q258K	Q	-	1	0	EPSTI1	42372489	0.720000	0.27996	0.948000	0.38648	0.158000	0.22134	0.469000	0.22067	0.869000	0.35703	0.650000	0.86243	CAA	.	.	none		0.353	EPSTI1-010	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400321.1	NM_001002264		T	43474489	G	T	43474489	3	4	5	1	0	0	0	0	1	0	0	0	5200	1328	46	4	443	4	EPSTI1	13	43474489	Missense_Mutation	SNP	G	TCGA-FA-A6HO-01A-11D-A31X-10	596588	43474489	71695389	31	572											
DCT	1638	hgsc.bcm.edu	37	chr13	95092324	95092324	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gccaacctggagtttcttcaActgaaactaaagcagaagag	15	8	9	9	0	2	3	1	1	1	2	2	4	2	4	2	1	4	2	2	1	6	3	rs138244474		TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr13:95092324A>G	ENST00000377028.5	-	8	1801	c.1388T>C	c.(1387-1389)gTt>gCt	p.V463A	DCT_ENST00000446125.1_Missense_Mutation_p.V496A	NM_001922.3	NP_001913.2	P40126	TYRP2_HUMAN	dopachrome tautomerase	463					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)		AGTTTCTTCAACTGAAACTAA	0.428																																					p.V496A		Atlas-SNP	.											DCT_ENST00000446125,colon,carcinoma,0,2	DCT	186	2	0			c.T1487C						scavenged	.	A	ALA/VAL,ALA/VAL	0,4406		0,0,2203	56	56	56		1487,1388	-0.7	0.8	13	dbSNP_134	56	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	DCT	NM_001129889.1,NM_001922.3	64,64	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign,benign	496/553,463/520	95092324	1,13005	2203	4300	6503	SO:0001583	missense	1638	exon10			TCTTCAACTGAAA	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.1388T>C	13.37:g.95092324A>G	ENSP00000366227:p.Val463Ala	121	1	0.00826446		92	12	0.130435	NM_001129889	Q09GT4	Missense_Mutation	SNP	ENST00000377028.5	37	CCDS9470.1	.	.	.	.	.	.	.	.	.	.	A	0.006	-2.082364	0.00371	0.0	1.16E-4	ENSG00000080166	ENST00000377028;ENST00000446125	D;D	0.99023	-5.32;-5.34	4.7	-0.737	0.11129	.	0.914482	0.09445	N	0.801161	D	0.95262	0.8463	L	0.29908	0.895	0.19300	N	0.999973	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	D	0.89694	0.3900	10	0.09590	T	0.72	-2.0498	4.6745	0.12705	0.6146:0.0:0.2503:0.1351	.	496;463	Q09GT4;P40126	.;TYRP2_HUMAN	A	463;496	ENSP00000366227:V463A;ENSP00000392762:V496A	ENSP00000366227:V463A	V	-	2	0	DCT	93890325	0.000000	0.05858	0.758000	0.31321	0.085000	0.17905	-0.583000	0.05807	-0.035000	0.13691	0.460000	0.39030	GTT	A|1.000;G|0.000	0.000	weak		0.428	DCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045461.3			G	95092324	A	G	95092324	3	3	5	1	0	0	0	0	1	0	0	0	4306	43	2	3	175	3	DCT	13	95092324	Missense_Mutation	SNP	A	TCGA-FA-A6HO-01A-11D-A31X-10	51617835	95092324	20077554	32	573											
RASA3	22821	hgsc.bcm.edu	37	chr13	114783725	114783725	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgggccgcagacgctgacaCgggctgcggggaggggtgag	6	4	22	9	4	0	3	0	2	0	1	0	4	0	4	1	6	1	3	1	6	0	0			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr13:114783725C>T	ENST00000334062.7	-	11	1067	c.946G>A	c.(946-948)Gtg>Atg	p.V316M	RASA3_ENST00000542651.1_3'UTR|RASA3_ENST00000389544.4_Missense_Mutation_p.V284M	NM_007368.2	NP_031394.2	Q14644	RASA3_HUMAN	RAS p21 protein activator 3	316					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)			GACGCTGACACGGGCTGCGGG	0.682																																					p.V316M		Atlas-SNP	.											.	RASA3	83	.	0			c.G946A						PASS	.						9	8	8					13																	114783725		2091	4147	6238	SO:0001583	missense	22821	exon11			CTGACACGGGCTG		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.946G>A	13.37:g.114783725C>T	ENSP00000335029:p.Val316Met	132	0	0		84	18	0.214286	NM_007368	A6NL15|F8W6X8|Q8IUY2	Missense_Mutation	SNP	ENST00000334062.7	37	CCDS32016.1	.	.	.	.	.	.	.	.	.	.	C	18.02	3.529328	0.64860	.	.	ENSG00000185989	ENST00000334062;ENST00000389544	T;T	0.17691	2.26;2.26	4.49	4.49	0.54785	Rho GTPase activation protein (1);Ras GTPase-activating protein (1);	0.062063	0.64402	D	0.000006	T	0.36220	0.0959	M	0.62723	1.935	0.80722	D	1	D	0.69078	0.997	P	0.62649	0.905	T	0.09058	-1.0692	9	.	.	.	.	15.9295	0.79648	0.0:1.0:0.0:0.0	.	316	Q14644	RASA3_HUMAN	M	316;284	ENSP00000335029:V316M;ENSP00000374195:V284M	.	V	-	1	0	RASA3	113801827	1.000000	0.71417	0.760000	0.31359	0.031000	0.12232	4.899000	0.63245	2.004000	0.58718	0.491000	0.48974	GTG	.	.	none		0.682	RASA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045957.2	NM_007368		T	114783725	C	T	114783725	3	4	5	1	0	0	0	0	1	0	0	0	13077	536	19	1	1614	1	RASA3	13	114783725	Missense_Mutation	SNP	C	TCGA-FA-A6HO-01A-11D-A31X-10	19691401	114783725	386153	33	574											
NEDD4	4734	hgsc.bcm.edu	37	chr15	56208006	56208006	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcccttcctgtgaagcggccGtatgtctcttacttctccgg	4	13	10	14	3	2	1	0	1	2	0	5	1	3	1	4	2	2	1	4	2	3	4	rs370853036|rs370701101		TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr15:56208006G>A	ENST00000508342.1	-	1	1323	c.1024C>T	c.(1024-1026)Cgg>Tgg	p.R342W	NEDD4_ENST00000338963.2_Missense_Mutation_p.R342W|NEDD4_ENST00000506154.1_Missense_Mutation_p.R342W|NEDD4_ENST00000435532.3_Intron	NM_001284338.1	NP_001271267.1	P46934	NEDD4_HUMAN	neural precursor cell expressed, developmentally down-regulated 4, E3 ubiquitin protein ligase	342					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)		TGAAGCGGCCGTATGTCTCTT	0.418																																					p.R342W		Atlas-SNP	.											.	NEDD4	167	.	0			c.C1024T						PASS	.	G	,TRP/ARG	0,4376		0,0,2188	65	68	67		,1024	-0.7	0.8	15		67	1,8575		0,1,4287	no	intron,missense	NEDD4	NM_006154.2,NM_198400.2	,101	0,1,6475	AA,AG,GG		0.0117,0.0,0.0077	,probably-damaging	,342/1248	56208006	1,12951	2188	4288	6476	SO:0001583	missense	4734	exon1			GCGGCCGTATGTC	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.1024C>T	15.37:g.56208006G>A	ENSP00000424827:p.Arg342Trp	71	0	0		64	13	0.203125	NM_198400	A1KY35|A6ND72|A7MD29|B4E2R7|B7ZM59|B7ZM60|B9EGN5|D6RF89	Missense_Mutation	SNP	ENST00000508342.1	37		.	.	.	.	.	.	.	.	.	.	G	12.03	1.816573	0.32145	0.0	1.17E-4	ENSG00000069869	ENST00000508342;ENST00000338963;ENST00000506154	T;T;T	0.45668	0.89;0.89;0.89	5.46	-0.682	0.11339	.	215.666000	0.00166	N	0.000000	T	0.48874	0.1524	M	0.63843	1.955	0.09310	N	0.999998	B;B;B	0.18968	0.032;0.019;0.032	B;B;B	0.16722	0.016;0.012;0.016	T	0.57717	-0.7763	10	0.87932	D	0	.	17.0411	0.86489	0.0:0.0:0.5238:0.4762	.	342;342;342	P46934-2;P46934;P46934-3	.;NEDD4_HUMAN;.	W	342	ENSP00000424827:R342W;ENSP00000345530:R342W;ENSP00000422705:R342W	ENSP00000345530:R342W	R	-	1	2	NEDD4	53995298	0.277000	0.24220	0.787000	0.31911	0.260000	0.26232	1.086000	0.30853	-0.015000	0.14150	-0.488000	0.04728	CGG	.	.	weak		0.418	NEDD4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000359817.1	NM_198400		A	56208006	G	A	56208006	3	1	5	1	0	0	0	0	1	0	0	0	10319	1144	40	1	3035	1	NEDD4	15	56208006	Missense_Mutation	SNP	G	TCGA-FA-A6HO-01A-11D-A31X-10		56208006	46323386	34	575											
AAGAB	79719	hgsc.bcm.edu	37	chr15	67524188	67524188	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attggaccacacattggcatTcagggcttggacaattcgct	10	11	10	10	1	1	0	1	0	0	0	2	2	1	2	1	4	0	3	1	4	1	5			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr15:67524188T>C	ENST00000261880.5	-	5	603	c.499A>G	c.(499-501)Aat>Gat	p.N167D	AAGAB_ENST00000561452.1_Missense_Mutation_p.N58D|AAGAB_ENST00000542650.1_Missense_Mutation_p.N58D	NM_001271885.1|NM_001271886.1|NM_024666.3	NP_001258814.1|NP_001258815.1|NP_078942.3	Q6PD74	AAGAB_HUMAN	alpha- and gamma-adaptin binding protein	167					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	9						ACATTGGCATTCAGGGCTTGG	0.368																																					p.N167D		Atlas-SNP	.											.	AAGAB	24	.	0			c.A499G						PASS	.						258	249	252					15																	67524188		1926	4146	6072	SO:0001583	missense	79719	exon5			TGGCATTCAGGGC	AL136715	CCDS42050.1, CCDS61679.1	15q22.33-q23	2014-02-12	2009-07-20		ENSG00000103591	ENSG00000103591			25662	protein-coding gene	gene with protein product		614888				11230166, 10477754	Standard	NM_024666		Approved	FLJ11506, p34	uc002aqk.5	Q6PD74	OTTHUMG00000172246	ENST00000261880.5:c.499A>G	15.37:g.67524188T>C	ENSP00000261880:p.Asn167Asp	76	0	0		69	5	0.0724638	NM_024666	B4DG44|Q6FI86|Q7Z5X9|Q9H0P1|Q9HAK0	Missense_Mutation	SNP	ENST00000261880.5	37	CCDS42050.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.830795	0.91036	.	.	ENSG00000103591	ENST00000261880;ENST00000542650	T;T	0.46451	0.89;0.87	5.21	5.21	0.72293	.	0.094714	0.85682	D	0.000000	T	0.55609	0.1931	M	0.68952	2.095	0.80722	D	1	D	0.52996	0.957	P	0.55667	0.781	T	0.53760	-0.8393	10	0.32370	T	0.25	-28.4102	15.2497	0.73536	0.0:0.0:0.0:1.0	.	167	Q6PD74	AAGAB_HUMAN	D	167;58	ENSP00000261880:N167D;ENSP00000440735:N58D	ENSP00000261880:N167D	N	-	1	0	AAGAB	65311242	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	7.428000	0.80296	2.180000	0.69256	0.528000	0.53228	AAT	.	.	none		0.368	AAGAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417472.1	NM_024666		C	67524188	T	C	67524188	3	2	5	1	0	0	0	0	1	0	0	0	15	1783	62	3	472	3	AAGAB	15	67524188	Missense_Mutation	SNP	T	TCGA-FA-A6HO-01A-11D-A31X-10	11316182	67524188	35007204	35	576											
CD79B	974	hgsc.bcm.edu	37	chr17	62006798	62006798	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgcccctctccttacctcgTaggtgtgatcttcctccatg	4	14	7	16	1	2	1	0	1	2	0	6	1	4	1	6	1	2	1	6	1	2	3			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr17:62006798T>A	ENST00000006750.3	-	5	679	c.587A>T	c.(586-588)tAc>tTc	p.Y196F	CD79B_ENST00000392795.3_Missense_Mutation_p.Y197F|CD79B_ENST00000349817.2_Missense_Mutation_p.Y92F	NM_000626.2|NM_021602.2	NP_000617.1|NP_067613.1	P40259	CD79B_HUMAN	CD79b molecule, immunoglobulin-associated beta	196	ITAM. {ECO:0000255|PROSITE- ProRule:PRU00379}.				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)	p.Y196C(1)|p.Y196F(1)|p.Y196S(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	15						CCTTACCTCGTAGGTGTGATC	0.632			"Mis, O"		DLBCL																																p.Y197F		Atlas-SNP	.		Dom	yes		17	17q23	974	"CD79b molecule, immunoglobulin-associated beta"		L	CD79B,NS,lymphoid_neoplasm,-1,13	CD79B	38	13	3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	c.A590T						PASS	.						93	74	81					17																	62006798		2203	4300	6503	SO:0001583	missense	974	exon5			ACCTCGTAGGTGT	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.587A>T	17.37:g.62006798T>A	ENSP00000006750:p.Tyr196Phe	71	0	0		50	21	0.42	NM_001039933	Q53FS2|Q9BU06	Missense_Mutation	SNP	ENST00000006750.3	37	CCDS11655.1	.	.	.	.	.	.	.	.	.	.	T	15.77	2.930227	0.52866	.	.	ENSG00000007312	ENST00000349817;ENST00000392795;ENST00000006750	D;D;D	0.96587	-4.06;-4.06;-4.06	4.2	4.2	0.49525	.	0.000000	0.64402	D	0.000002	D	0.95601	0.8570	N	0.24115	0.695	0.43426	D	0.995588	D;D	0.76494	0.996;0.999	D;D	0.85130	0.986;0.997	D	0.95387	0.8478	10	0.87932	D	0	-12.4743	9.5968	0.39578	0.0:0.0:0.0:1.0	.	92;196	P40259-2;P40259	.;CD79B_HUMAN	F	92;197;196	ENSP00000245862:Y92F;ENSP00000376544:Y197F;ENSP00000006750:Y196F	ENSP00000006750:Y196F	Y	-	2	0	CD79B	59360530	0.997000	0.39634	0.977000	0.42913	0.245000	0.25701	3.902000	0.56310	1.782000	0.52362	0.358000	0.22013	TAC	.	.	none		0.632	CD79B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417711.1			A	62006798	T	A	62006798	3	1	5	1	0	0	0	0	1	0	0	0	3039	1638	57	5	110	5	CD79B	17	62006798	Missense_Mutation	SNP	T	TCGA-FA-A6HO-01A-11D-A31X-10		62006798	19188412	36	577											
NOTUM	147111	hgsc.bcm.edu	37	chr17	79912130	79912130	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcccggagcagggacactgAcctccggatgatgatctcat	9	8	12	12	2	1	3	1	3	1	0	3	6	2	6	3	3	2	1	3	3	0	0			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr17:79912130A>G	ENST00000409678.3	-	10	1568		c.e10+1			NM_178493.5	NP_848588.3	Q6P988	NOTUM_HUMAN	notum pectinacetylesterase homolog (Drosophila)							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)			AGGGACACTGACCTCCGGATG	0.607																																					.		Atlas-SNP	.											.	NOTUM	50	.	0			c.1184+2T>C						PASS	.						80	70	73					17																	79912130		2203	4300	6503	SO:0001630	splice_region_variant	147111	exon11			ACACTGACCTCCG	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.1184+1T>C	17.37:g.79912130A>G		93	0	0		84	5	0.0595238	NM_178493	Q8N410|Q8NI82	Splice_Site	SNP	ENST00000409678.3	37	CCDS32771.2	.	.	.	.	.	.	.	.	.	.	A	22.5	4.302227	0.81136	.	.	ENSG00000185269	ENST00000409678	.	.	.	4.73	4.73	0.59995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3587	0.66754	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NOTUM	77505420	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.222000	0.89777	1.985000	0.57927	0.533000	0.62120	.	.	.	none		0.607	NOTUM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335123.2	NM_178493	Intron	G	79912130	A	G	79912130	5	3	5	1	0	0	0	0	0	0	1	0	10561	289	10	3	312	3	NOTUM	17	79912130	Splice_Site	SNP	A	TCGA-FA-A6HO-01A-11D-A31X-10	17905332	79912130	1283080	37	578											
STK11	6794	hgsc.bcm.edu	37	chr19	1220490	1220490	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaccctcaaaatctccgacCtgggcgtggccgaggtaggc	8	6	13	14	3	2	0	1	0	1	0	3	2	2	0	4	4	0	2	4	4	3	1			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr19:1220490C>T	ENST00000326873.7	+	4	1756	c.583C>T	c.(583-585)Ctg>Ttg	p.L195L		NM_000455.4	NP_000446.1	Q15831	STK11_HUMAN	serine/threonine kinase 11	195	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.Y156fs*87(4)|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)		AATCTCCGACCTGGGCGTGGC	0.687		14	"D, Mis, N, F, S"		"NSCLC, pancreatic"	"jejunal harmartoma, ovarian, testicular, pancreatic"			Peutz-Jeghers syndrome	TSP Lung(3;<1E-08)																											p.L195L		Atlas-SNP	.	yes	Rec	yes	Peutz-Jeghers syndrome	19	19p13.3	6794	serine/threonine kinase 11 gene (LKB1)		"E, M, O"	STK11,NS,carcinoma,0,1	STK11	410	1	27	Whole gene deletion(20)|Deletion - Frameshift(4)|Unknown(3)	cervix(14)|lung(9)|oesophagus(1)|ovary(1)|kidney(1)|pancreas(1)	c.C583T						PASS	.						35	40	38					19																	1220490		2011	4156	6167	SO:0001819	synonymous_variant	6794	exon4	Familial Cancer Database	PJS, Hamartous Intestinal Polyposis	TCCGACCTGGGCG	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.583C>T	19.37:g.1220490C>T		66	0	0		68	10	0.147059	NM_000455	B2RBX7|E7EW76	Silent	SNP	ENST00000326873.7	37	CCDS45896.1																																																																																			.	.	none		0.687	STK11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449839.3	NM_000455		T	1220490	C	T	1220490	2	4	5	1	0	0	0	0	0	0	0	1	15302	680	24	2		2	STK11	19	1220490	Silent	SNP	C	TCGA-FA-A6HO-01A-11D-A31X-10		1220490	57908493	38	579											
DAZAP1	26528	hgsc.bcm.edu	37	chr19	1434903	1434903	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcaagggttccacccctacCgacgctagcccgcggcgccg	6	5	12	18	6	0	0	0	0	0	0	1	1	1	0	6	2	3	3	6	2	3	3			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr19:1434903C>T	ENST00000233078.4	+	12	1377	c.1216C>T	c.(1216-1218)Cga>Tga	p.R406*	DAZAP1_ENST00000336761.6_3'UTR	NM_018959.2	NP_061832.2	Q96EP5	DAZP1_HUMAN	DAZ associated protein 1	406					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)		CCACCCCTACCGACGCTAGCC	0.672																																					p.R406X		Atlas-SNP	.											.	DAZAP1	52	.	0			c.C1216T						PASS	.						9	10	10					19																	1434903		2140	4189	6329	SO:0001587	stop_gained	26528	exon12			CCCTACCGACGCT		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.1216C>T	19.37:g.1434903C>T	ENSP00000233078:p.Arg406*	49	0	0		47	19	0.404255	NM_018959	Q96MJ3|Q9NRR9	Nonsense_Mutation	SNP	ENST00000233078.4	37	CCDS12065.1	.	.	.	.	.	.	.	.	.	.	C	38	6.709031	0.97780	.	.	ENSG00000071626	ENST00000233078	.	.	.	5.26	3.02	0.34903	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.8945	0.58091	0.4422:0.5578:0.0:0.0	.	.	.	.	X	406	.	ENSP00000233078:R406X	R	+	1	2	DAZAP1	1385903	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.926000	0.40084	1.186000	0.42985	0.561000	0.74099	CGA	.	.	none		0.672	DAZAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449522.3	NM_170711		T	1434903	C	T	1434903	4	4	5	1	0	0	0	0	0	1	0	0	4246	644	23	1	1355	1	DAZAP1	19	1434903	Nonsense_Mutation	SNP	C	TCGA-FA-A6HO-01A-11D-A31X-10	214413	1434903	57694080	39	580											
PSG8	440533	hgsc.bcm.edu	37	chr19	43268286	43268286	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatggtagaggtccctgattTgccctttgtaccagatgtag	9	13	11	8	0	0	3	0	1	0	2	1	3	1	3	3	2	2	3	3	2	4	5			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chr19:43268286T>C	ENST00000306511.4	-	2	309	c.212A>G	c.(211-213)cAa>cGa	p.Q71R	PSG8_ENST00000404209.4_Missense_Mutation_p.Q71R|PSG8_ENST00000401467.2_Missense_Mutation_p.Q71R|PSG8_ENST00000406636.3_Intron	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	71	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)				GTCCCTGATTTGCCCTTTGTA	0.413																																					p.Q71R		Atlas-SNP	.											.	PSG8	101	.	0			c.A212G						PASS	.						174	186	182					19																	43268286		2203	4292	6495	SO:0001583	missense	440533	exon2			CTGATTTGCCCTT	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.212A>G	19.37:g.43268286T>C	ENSP00000305005:p.Gln71Arg	194	0	0		155	18	0.116129	NM_001130167	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Missense_Mutation	SNP	ENST00000306511.4	37	CCDS33037.1	.	.	.	.	.	.	.	.	.	.	t	5.359	0.251452	0.10130	.	.	ENSG00000124467	ENST00000404209;ENST00000401467;ENST00000407488;ENST00000306511	T;T;T	0.01484	4.84;4.84;4.84	1.35	0.162	0.14981	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.03434	0.0099	M	0.80422	2.495	0.09310	N	1	B;B;P;B;B	0.39044	0.003;0.001;0.656;0.002;0.003	B;B;B;B;B	0.40982	0.008;0.01;0.345;0.005;0.008	T	0.29610	-1.0006	9	0.52906	T	0.07	.	4.2604	0.10739	0.0:0.0:0.3569:0.6431	.	71;71;71;71;71	B5MCQ0;Q9UQ74;E7ENH0;Q9UQ74-3;A5PKV3	.;PSG8_HUMAN;.;.;.	R	71	ENSP00000385869:Q71R;ENSP00000386090:Q71R;ENSP00000305005:Q71R	ENSP00000305005:Q71R	Q	-	2	0	PSG8	47960126	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	-0.899000	0.04101	-0.017000	0.14103	0.155000	0.16302	CAA	.	.	none		0.413	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1			C	43268286	T	C	43268286	3	2	5	1	0	0	0	0	1	0	0	0	12673	1812	63	3	1105	3	PSG8	19	43268286	Missense_Mutation	SNP	T	TCGA-FA-A6HO-01A-11D-A31X-10	41833383	43268286	15860697	40	581											
NR0B1	190	hgsc.bcm.edu	37	chrX	30327153	30327153	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccaccccgggatcagagcCgcacgaacagccccagcacg	10	1	11	19	4	1	1	1	0	0	1	1	3	1	2	6	1	4	2	6	1	1	0			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chrX:30327153C>T	ENST00000378970.4	-	1	562	c.328G>A	c.(328-330)Ggc>Agc	p.G110S	NR0B1_ENST00000378963.1_5'Flank|NR0B1_ENST00000453287.1_Missense_Mutation_p.G110S	NM_000475.4	NP_000466.2	P51843	NR0B1_HUMAN	nuclear receptor subfamily 0, group B, member 1	110	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)	GGATCAGAGCCGCACGAACAG	0.692											OREG0019719	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G110S		Atlas-SNP	.											.	NR0B1	61	.	0			c.G328A						PASS	.						22	25	24					X																	30327153		2197	4287	6484	SO:0001583	missense	190	exon1			CAGAGCCGCACGA	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.328G>A	X.37:g.30327153C>T	ENSP00000368253:p.Gly110Ser	134	0	0	816	141	10	0.070922	NM_000475	Q96F69	Missense_Mutation	SNP	ENST00000378970.4	37	CCDS14223.1	.	.	.	.	.	.	.	.	.	.	C	11.35	1.612239	0.28712	.	.	ENSG00000169297	ENST00000378970;ENST00000453287	D;D	0.97404	-3.49;-4.37	4.42	3.54	0.40534	.	0.173259	0.28109	N	0.016578	D	0.94660	0.8278	L	0.55743	1.74	0.31729	N	0.637317	P	0.46621	0.881	B	0.41860	0.368	D	0.93333	0.6703	10	0.46703	T	0.11	-9.6228	9.3873	0.38352	0.0:0.8933:0.0:0.1067	.	110	P51843	NR0B1_HUMAN	S	110	ENSP00000368253:G110S;ENSP00000396403:G110S	ENSP00000368253:G110S	G	-	1	0	NR0B1	30237074	0.999000	0.42202	0.832000	0.32986	0.238000	0.25445	1.241000	0.32743	0.957000	0.37930	0.513000	0.50165	GGC	.	.	none		0.692	NR0B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056161.1	NM_000475		T	30327153	C	T	30327153	3	4	5	1	0	0	0	0	1	0	0	0	10622	652	23	1	1092	1	NR0B1	23	30327153	Missense_Mutation	SNP	C	TCGA-FA-A6HO-01A-11D-A31X-10		30327153	124943407	41	582											
SYTL5	94122	hgsc.bcm.edu	37	chrX	37965974	37965974	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggctgtacatttttgtcaaGaattgcagaaatctggccat	11	13	10	7	0	2	2	1	0	1	2	2	2	2	2	1	2	2	3	1	2	4	4			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chrX:37965974G>T	ENST00000357972.5	+	11	1830	c.1284G>T	c.(1282-1284)aaG>aaT	p.K428N	SYTL5_ENST00000297875.2_Missense_Mutation_p.K428N|TM4SF2_ENST00000465127.1_Intron|SYTL5_ENST00000456733.2_Missense_Mutation_p.K450N			Q8TDW5	SYTL5_HUMAN	synaptotagmin-like 5	428	C2 1. {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						TTTTTGTCAAGAATTGCAGAA	0.428																																					p.K450N		Atlas-SNP	.											.	SYTL5	72	.	0			c.G1350T						PASS	.						138	111	120					X																	37965974		2202	4300	6502	SO:0001583	missense	94122	exon11			TGTCAAGAATTGC		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.1284G>T	X.37:g.37965974G>T	ENSP00000350657:p.Lys428Asn	178	0	0		194	33	0.170103	NM_001163334	A2RRF2	Missense_Mutation	SNP	ENST00000357972.5	37	CCDS14244.1	.	.	.	.	.	.	.	.	.	.	G	18.79	3.699815	0.68501	.	.	ENSG00000147041	ENST00000297875;ENST00000357972;ENST00000456733	T;T;T	0.70045	-0.45;-0.45;-0.45	5.71	5.71	0.89125	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.050650	0.85682	D	0.000000	T	0.80502	0.4635	M	0.81497	2.545	0.41478	D	0.988146	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.961	T	0.78453	-0.2198	10	0.21014	T	0.42	-19.1341	13.0607	0.59005	0.0784:0.0:0.9216:0.0	.	450;428	A2RRF2;Q8TDW5	.;SYTL5_HUMAN	N	428;428;450	ENSP00000297875:K428N;ENSP00000350657:K428N;ENSP00000395220:K450N	ENSP00000297875:K428N	K	+	3	2	SYTL5	37850918	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.373000	0.44266	2.394000	0.81467	0.594000	0.82650	AAG	.	.	none		0.428	SYTL5-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080883.1	NM_138780		T	37965974	G	T	37965974	3	4	5	1	0	0	0	0	1	0	0	0	15501	933	33	4	1392	4	SYTL5	23	37965974	Missense_Mutation	SNP	G	TCGA-FA-A6HO-01A-11D-A31X-10	7638821	37965974	117304586	42	583											
RNF128	79589	hgsc.bcm.edu	37	chrX	105970554	105970554	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aagatccatctggcttatgaGagaggggcgtctggagccgt	9	9	15	8	2	2	3	0	1	2	2	3	5	3	4	2	4	1	1	2	4	2	1	rs148223909		TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chrX:105970554G>C	ENST00000255499.2	+	1	661	c.411G>C	c.(409-411)gaG>gaC	p.E137D	RNF128_ENST00000324342.3_Intron	NM_194463.1	NP_919445.1	Q8TEB7	RN128_HUMAN	ring finger protein 128, E3 ubiquitin protein ligase	137	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						TGGCTTATGAGAGAGGGGCGT	0.602																																					p.E137D		Atlas-SNP	.											.	RNF128	74	.	0			c.G411C						PASS	.	G	,ASP/GLU	0,3835		0,0,1632,571	53	49	50		,411	2.4	1	X	dbSNP_134	50	1,6727		0,1,2427,1872	no	intron,missense	RNF128	NM_024539.3,NM_194463.1	,45	0,1,4059,2443	CC,CG,GG,G		0.0149,0.0,0.0095	,benign	,137/429	105970554	1,10562	2203	4300	6503	SO:0001583	missense	79589	exon1			TTATGAGAGAGGG	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.411G>C	X.37:g.105970554G>C	ENSP00000255499:p.Glu137Asp	197	0	0		176	50	0.284091	NM_194463	A0PJI4|Q6PH80|Q6ZTJ8|Q96RF3|Q9H5E4	Missense_Mutation	SNP	ENST00000255499.2	37	CCDS14521.1	.	.	.	.	.	.	.	.	.	.	G	11.43	1.636379	0.29068	0.0	1.49E-4	ENSG00000133135	ENST00000255499	T	0.07444	3.19	4.29	2.37	0.29283	Protease-associated domain, PA (1);	0.762462	0.12450	N	0.467829	T	0.04770	0.0129	N	0.16368	0.405	0.32627	N	0.522588	B	0.02656	0.0	B	0.08055	0.003	T	0.28522	-1.0041	10	0.22706	T	0.39	.	5.6553	0.17639	0.123:0.1989:0.6781:0.0	.	137	Q8TEB7	RN128_HUMAN	D	137	ENSP00000255499:E137D	ENSP00000255499:E137D	E	+	3	2	RNF128	105857210	1.000000	0.71417	0.999000	0.59377	0.855000	0.48748	0.891000	0.28309	0.771000	0.33359	0.600000	0.82982	GAG	G|1.000;C|0.000	0.000	weak		0.602	RNF128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057804.1	NM_024539		C	105970554	G	C	105970554	3	2	5	1	0	0	0	0	1	0	0	0	13451	933	33	4	823	4	RNF128	23	105970554	Missense_Mutation	SNP	G	TCGA-FA-A6HO-01A-11D-A31X-10	68004580	105970554	49300006	43	584											
PLXNB3	5365	hgsc.bcm.edu	37	chrX	153039489	153039489	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gcccaacccccgcctggcacCcctcagccgcgaggggcctg	5	3	12	21	3	1	0	1	0	0	0	1	1	1	0	8	3	2	1	8	3	1	0			TCGA-FA-A6HO-01A-11D-A31X-10	TCGA-FA-A6HO-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4663fa5a-53e7-40be-a662-6aaa4e456475	16d8b5be-a00c-43cf-8121-f0c8b5dcc5c2	g.chrX:153039489C>T	ENST00000361971.5	+	20	3569	c.3455C>T	c.(3454-3456)cCc>cTc	p.P1152L	SRPK3_ENST00000489426.1_5'Flank|PLXNB3_ENST00000538966.1_Missense_Mutation_p.P1175L|PLXNB3_ENST00000538282.1_Missense_Mutation_p.P762L|PLXNB3_ENST00000538776.1_Missense_Mutation_p.P805L	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	1152					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)					CGCCTGGCACCCCTCAGCCGC	0.692																																					p.P1175L		Atlas-SNP	.											.	PLXNB3	208	.	0			c.C3524T						PASS	.						16	17	17					X																	153039489		2174	4240	6414	SO:0001583	missense	5365	exon21			TGGCACCCCTCAG	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.3455C>T	X.37:g.153039489C>T	ENSP00000355378:p.Pro1152Leu	58	0	0		50	10	0.2	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	37	CCDS14729.1	.	.	.	.	.	.	.	.	.	.	C	14.45	2.539525	0.45176	.	.	ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776;ENST00000538282	T;T;T;T	0.69435	5.19;5.16;4.57;-0.4	5.14	5.14	0.70334	.	0.117279	0.56097	D	0.000021	T	0.67581	0.2908	M	0.71036	2.16	0.36580	D	0.873501	B;P;P	0.45768	0.409;0.866;0.668	B;P;B	0.44811	0.168;0.461;0.318	T	0.75755	-0.3206	10	0.46703	T	0.11	.	10.9628	0.47395	0.0:0.8153:0.1847:0.0	.	805;1175;1152	B7Z3H9;F5H773;Q9ULL4	.;.;PLXB3_HUMAN	L	1175;1152;805;762	ENSP00000442736:P1175L;ENSP00000355378:P1152L;ENSP00000445569:P805L;ENSP00000441919:P762L	ENSP00000355378:P1152L	P	+	2	0	PLXNB3	152692683	0.722000	0.28017	0.054000	0.19295	0.555000	0.35460	1.617000	0.36943	2.125000	0.65367	0.529000	0.55759	CCC	.	.	none		0.692	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1			T	153039489	C	T	153039489	3	4	5	1	0	0	0	0	1	0	0	0	12134	623	22	2	3647	2	PLXNB3	23	153039489	Missense_Mutation	SNP	C	TCGA-FA-A6HO-01A-11D-A31X-10	47068935	153039489	2231071	44	585											
KLHL17	339451	hgsc.bcm.edu	37	chr1	898557	898557	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcgcaccgaccgctggcacGtggtggcctccatgtccacg	5	6	13	17	6	0	0	0	0	0	0	2	1	2	0	5	3	0	3	5	3	0	0	rs201246933		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr1:898557G>A	ENST00000338591.3	+	7	1218	c.1111G>A	c.(1111-1113)Gtg>Atg	p.V371M		NM_198317.2	NP_938073.1	Q6TDP4	KLH17_HUMAN	kelch-like family member 17	371	Interaction with F-actin. {ECO:0000250}.				actin cytoskeleton organization (GO:0030036)|brain development (GO:0007420)|protein ubiquitination (GO:0016567)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|dendrite cytoplasm (GO:0032839)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	protein complex scaffold (GO:0032947)			central_nervous_system(1)|kidney(2)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)|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)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.52e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.59e-23)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000469)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		CCGCTGGCACGTGGTGGCCTC	0.701																																					p.V371M		Atlas-SNP	.											.	KLHL17	31	.	0			c.G1111A						PASS	.						35	38	37					1																	898557		2195	4292	6487	SO:0001583	missense	339451	exon7			TGGCACGTGGTGG	AY423763	CCDS30550.1	1p36	2013-01-30	2013-01-30		ENSG00000187961	ENSG00000187961		"Kelch-like", "BTB/POZ domain containing"	24023	protein-coding gene	gene with protein product	"actinfilin"		"kelch-like 17 (Drosophila)"			12063253	Standard	NM_198317		Approved		uc001aca.2	Q6TDP4	OTTHUMG00000040721	ENST00000338591.3:c.1111G>A	1.37:g.898557G>A	ENSP00000343930:p.Val371Met	57	0	0		48	23	0.479167	NM_198317	Q5SV94	Missense_Mutation	SNP	ENST00000338591.3	37	CCDS30550.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	13.33	2.204611	0.38905	.	.	ENSG00000187961	ENST00000338591;ENST00000455747;ENST00000540863	T	0.73789	-0.78	5.52	2.27	0.28462	Galactose oxidase, beta-propeller (1);	0.158567	0.53938	D	0.000052	T	0.49813	0.1579	N	0.11870	0.19	0.39807	D	0.972655	B	0.06786	0.001	B	0.04013	0.001	T	0.29458	-1.0011	10	0.25106	T	0.35	.	5.4008	0.16295	0.5559:0.0:0.4441:0.0	.	371	Q6TDP4	KLH17_HUMAN	M	371;247;94	ENSP00000343930:V371M	ENSP00000343930:V371M	V	+	1	0	KLHL17	888420	1.000000	0.71417	0.995000	0.50966	0.986000	0.74619	4.929000	0.63455	0.711000	0.32018	-0.480000	0.04831	GTG	G|0.999;A|0.001	0.001	strong		0.701	KLHL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097875.3	NM_198317		A	898557	G	A	898557	3	1	6	1	0	0	0	0	1	0	0	0	8381	1145	40	1	1137	1	KLHL17	1	898557	Missense_Mutation	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10		898557	248352064	1	586											
PAQR7	164091	hgsc.bcm.edu	37	chr1	26189430	26189430	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaggctcatagatgggccGtcgggcctcatagtccagtg	8	8	14	11	2	2	2	2	0	0	2	4	2	3	2	3	3	0	1	3	3	2	2			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr1:26189430G>A	ENST00000374296.3	-	2	1567	c.901C>T	c.(901-903)Cgg>Tgg	p.R301W	RP1-125I3.2_ENST00000455431.1_RNA	NM_178422.5	NP_848509.1	Q86WK9	MPRA_HUMAN	progestin and adipoQ receptor family member VII	301					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)		TAGATGGGCCGTCGGGCCTCA	0.597																																					p.R301W	Esophageal Squamous(111;1206 1556 18433 19151 38418)	Atlas-SNP	.											.	PAQR7	23	.	0			c.C901T						PASS	.						60	60	60					1																	26189430		2203	4300	6503	SO:0001583	missense	164091	exon2			TGGGCCGTCGGGC		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.901C>T	1.37:g.26189430G>A	ENSP00000363414:p.Arg301Trp	143	0	0		110	47	0.427273	NM_178422	A2A2D3|Q5XKF9|Q86VE4	Missense_Mutation	SNP	ENST00000374296.3	37	CCDS267.1	.	.	.	.	.	.	.	.	.	.	G	17.86	3.491875	0.64074	.	.	ENSG00000182749	ENST00000374296	T	0.26810	1.71	5.07	3.16	0.36331	.	0.070365	0.56097	D	0.000026	T	0.39200	0.1069	M	0.62723	1.935	0.49687	D	0.999819	D	0.76494	0.999	P	0.57846	0.828	T	0.19745	-1.0296	10	0.87932	D	0	-16.9133	9.4892	0.38948	0.0:0.1248:0.5385:0.3366	.	301	Q86WK9	MPRA_HUMAN	W	301	ENSP00000363414:R301W	ENSP00000363414:R301W	R	-	1	2	PAQR7	26062017	0.767000	0.28508	0.997000	0.53966	0.992000	0.81027	1.262000	0.32992	0.687000	0.31509	0.563000	0.77884	CGG	.	.	none		0.597	PAQR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019312.1	NM_178422		A	26189430	G	A	26189430	3	1	6	1	0	0	0	0	1	0	0	0	11449	1144	40	1	143	1	PAQR7	1	26189430	Missense_Mutation	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	25290873	26189430	223061191	2	587											
YTHDF2	51441	hgsc.bcm.edu	37	chr1	29070284	29070284	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttgatgtcaggtggatttTtgtgaaggacgttcccaata	9	16	11	5	1	1	2	1	2	0	0	2	4	2	4	1	3	0	1	1	3	3	6			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr1:29070284T>C	ENST00000373812.3	+	4	1864	c.1502T>C	c.(1501-1503)tTt>tCt	p.F501S	YTHDF2_ENST00000478283.1_3'UTR|YTHDF2_ENST00000542507.1_Missense_Mutation_p.F501S|YTHDF2_ENST00000541996.1_Missense_Mutation_p.F451S	NM_016258.2	NP_057342.2	Q9Y5A9	YTHD2_HUMAN	YTH domain family, member 2	501	Interaction with m6A-containing mRNAs.|YTH. {ECO:0000255|PROSITE- ProRule:PRU00225}.				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)		AGGTGGATTTTTGTGAAGGAC	0.493																																					p.F501S		Atlas-SNP	.											.	YTHDF2	47	.	0			c.T1502C						PASS	.						84	83	84					1																	29070284		1925	4136	6061	SO:0001583	missense	51441	exon4			GGATTTTTGTGAA	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.1502T>C	1.37:g.29070284T>C	ENSP00000362918:p.Phe501Ser	129	0	0		155	64	0.412903	NM_016258	A6NKG4|A8K966|B4E1G7|D3DPM8|Q5VSZ9|Q8TDH0|Q9BUJ5	Missense_Mutation	SNP	ENST00000373812.3	37	CCDS41296.1	.	.	.	.	.	.	.	.	.	.	T	13.12	2.140965	0.37825	.	.	ENSG00000198492	ENST00000542507;ENST00000373812;ENST00000541996;ENST00000396232	T;T;T	0.26660	1.72;1.72;1.72	5.93	4.79	0.61399	YTH domain (2);	0.097053	0.64402	D	0.000001	T	0.40694	0.1127	L	0.45352	1.415	0.58432	D	0.999999	D;D	0.67145	0.996;0.996	D;D	0.75020	0.985;0.985	T	0.09015	-1.0694	9	.	.	.	-12.236	12.402	0.55418	0.0:0.0:0.1409:0.8591	.	501;501	B5BU99;Q9Y5A9	.;YTHD2_HUMAN	S	501;501;451;501	ENSP00000444660:F501S;ENSP00000362918:F501S;ENSP00000439394:F451S	.	F	+	2	0	YTHDF2	28942871	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.062000	0.71155	1.048000	0.40298	0.523000	0.50628	TTT	.	.	none		0.493	YTHDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010335.1	NM_016258		C	29070284	T	C	29070284	3	2	6	1	0	0	0	0	1	0	0	0	17514	1841	64	3	1516	3	YTHDF2	1	29070284	Missense_Mutation	SNP	T	TCGA-FA-A7DS-01A-11D-A382-10	2880854	29070284	220180337	3	588											
DLGAP3	58512	hgsc.bcm.edu	37	chr1	35369943	35369943	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caggagccccttgcctggccCggcccccgggtatccatccc	4	6	11	20	2	0	0	0	0	0	0	2	1	2	1	8	4	2	1	8	4	1	2			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr1:35369943C>T	ENST00000373347.1	-	3	1310	c.1042G>A	c.(1042-1044)Ggg>Agg	p.G348R	DLGAP3_ENST00000495979.1_5'Flank|DLGAP3_ENST00000235180.4_Missense_Mutation_p.G348R			O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated protein 3	348					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)				TTGCCTGGCCCGGCCCCCGGG	0.602																																					p.G348R		Atlas-SNP	.											.	DLGAP3	107	.	0			c.G1042A						PASS	.						40	42	41					1																	35369943		2200	4293	6493	SO:0001583	missense	58512	exon1			CTGGCCCGGCCCC	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.1042G>A	1.37:g.35369943C>T	ENSP00000362444:p.Gly348Arg	15	0	0		28	14	0.5	NM_001080418	Q5TDD5|Q9H3X7	Missense_Mutation	SNP	ENST00000373347.1	37	CCDS30670.1	.	.	.	.	.	.	.	.	.	.	C	18.76	3.692621	0.68271	.	.	ENSG00000116544	ENST00000373347;ENST00000235180;ENST00000542913	T;T	0.26373	1.74;1.74	4.49	4.49	0.54785	.	0.164823	0.53938	D	0.000053	T	0.42854	0.1221	L	0.36672	1.1	0.53005	D	0.999961	D	0.89917	1.0	D	0.83275	0.996	T	0.40175	-0.9577	10	0.72032	D	0.01	-16.0127	17.7338	0.88387	0.0:1.0:0.0:0.0	.	348	O95886	DLGP3_HUMAN	R	348;348;31	ENSP00000362444:G348R;ENSP00000235180:G348R	ENSP00000235180:G348R	G	-	1	0	DLGAP3	35142530	0.997000	0.39634	0.961000	0.40146	0.937000	0.57800	3.622000	0.54217	2.492000	0.84095	0.655000	0.94253	GGG	.	.	none		0.602	DLGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011554.1	NM_021234		T	35369943	C	T	35369943	3	4	6	1	0	0	0	0	1	0	0	0	4563	652	23	1	1937	1	DLGAP3	1	35369943	Missense_Mutation	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10	6299659	35369943	213880678	4	589											
FCRL5	83416	hgsc.bcm.edu	37	chr1	157516959	157516959	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	actgtggtccatggaggctgGaggaaaataatgggcctggg	10	8	17	6	0	0	0	0	0	0	0	1	3	1	3	2	7	0	1	2	7	3	1			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr1:157516959G>A	ENST00000361835.3	-	3	238	c.81C>T	c.(79-81)ctC>ctT	p.L27L	FCRL5_ENST00000356953.4_Silent_p.L27L|FCRL5_ENST00000368188.2_Silent_p.L27L|FCRL5_ENST00000368190.3_Silent_p.L27L|FCRL5_ENST00000368191.3_Intron|FCRL5_ENST00000368189.3_Silent_p.L27L	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	27	Ig-like C2-type 1.				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)				ATGGAGGCTGGAGGAAAATAA	0.537																																					p.L27L		Atlas-SNP	.											FCRL5,mouth,carcinoma,-1,1	FCRL5	177	1	0			c.C81T						PASS	.						119	113	115					1																	157516959		2203	4300	6503	SO:0001819	synonymous_variant	83416	exon3			AGGCTGGAGGAAA	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.81C>T	1.37:g.157516959G>A		113	0	0		121	48	0.396694	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Silent	SNP	ENST00000361835.3	37	CCDS1165.1																																																																																			.	.	none		0.537	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281		A	157516959	G	A	157516959	2	1	6	1	0	0	0	0	0	0	0	1	5806	1161	41	2		2	FCRL5	1	157516959	Silent	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	122147016	157516959	91733662	5	590											
ALLC	55821	hgsc.bcm.edu	37	chr2	3745027	3745027	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaataactcgaattgaaatTgacacaaaatattttgaagg	18	12	7	4	1	0	3	0	3	0	0	1	4	0	3	0	1	1	1	0	1	8	7			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr2:3745027T>G	ENST00000252505.3	+	10	993	c.831T>G	c.(829-831)atT>atG	p.I277M	ALLC_ENST00000471711.1_3'UTR	NM_018436.3	NP_060906.3	Q8N6M5	ALLC_HUMAN	allantoicase	296					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)		GAATTGAAATTGACACAAAAT	0.388										HNSCC(21;0.051)																											p.I277M		Atlas-SNP	.											ALLC,rectum,carcinoma,0,1	ALLC	61	1	0			c.T831G						PASS	.						127	122	124					2																	3745027		1836	4088	5924	SO:0001583	missense	55821	exon10			TGAAATTGACACA	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.831T>G	2.37:g.3745027T>G	ENSP00000252505:p.Ile277Met	102	0	0		100	42	0.42	NM_018436	Q53T95|Q5RL81|Q96RE6|Q9NZA7	Missense_Mutation	SNP	ENST00000252505.3	37	CCDS46223.1	.	.	.	.	.	.	.	.	.	.	T	5.479	0.273460	0.10403	.	.	ENSG00000151360	ENST00000252505	.	.	.	5.47	-10.9	0.00192	Allantoicase domain (1);Galactose-binding domain-like (1);	0.502623	0.22475	N	0.059570	T	0.35128	0.0921	M	0.82323	2.585	0.24126	N	0.995782	P	0.37548	0.599	B	0.39503	0.301	T	0.41270	-0.9518	9	0.87932	D	0	-5.9914	5.0435	0.14471	0.2651:0.4858:0.1398:0.1093	.	296	Q8N6M5	ALLC_HUMAN	M	277	.	ENSP00000252505:I277M	I	+	3	3	ALLC	3722902	0.000000	0.05858	0.001000	0.08648	0.014000	0.08584	-3.876000	0.00344	-3.622000	0.00131	-1.381000	0.01174	ATT	.	.	none		0.388	ALLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322855.1			G	3745027	T	G	3745027	3	3	6	1	0	0	0	0	1	0	0	0	534	1800	63	5	865	5	ALLC	2	3745027	Missense_Mutation	SNP	T	TCGA-FA-A7DS-01A-11D-A382-10		3745027	239454346	6	591											
NEB	4703	hgsc.bcm.edu	37	chr2	152432838	152432838	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggcatccagccaatgccacGcaaccactccaagtcagcct	11	5	8	17	1	1	0	1	0	0	0	3	0	3	0	6	1	4	2	6	1	3	0			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr2:152432838G>A	ENST00000172853.10	-	78	11779	c.11632C>T	c.(11632-11634)Cgt>Tgt	p.R3878C	NEB_ENST00000603639.1_Missense_Mutation_p.R5579C|NEB_ENST00000604864.1_Missense_Mutation_p.R5579C|NEB_ENST00000409198.1_Missense_Mutation_p.R3878C|NEB_ENST00000397345.3_Missense_Mutation_p.R5579C|NEB_ENST00000427231.2_Missense_Mutation_p.R5579C			P20929	NEBU_HUMAN	nebulin	3878					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)		CCAATGCCACGCAACCACTCC	0.473																																					p.R5579C		Atlas-SNP	.											NEB_ENST00000427231,NS,carcinoma,+1,3	NEB	1697	3	0			c.C16735T						PASS	.						97	101	100					2																	152432838		1918	4134	6052	SO:0001583	missense	4703	exon106			TGCCACGCAACCA	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.11632C>T	2.37:g.152432838G>A	ENSP00000172853:p.Arg3878Cys	169	0	0		163	63	0.386503	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	G	24.6	4.553342	0.86127	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000413693;ENST00000172853	T;T;T;T;T	0.51325	0.71;0.71;0.71;0.71;0.71	6.03	6.03	0.97812	.	0.048446	0.85682	D	0.000000	T	0.70894	0.3276	M	0.71920	2.185	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.71213	-0.4659	10	0.87932	D	0	.	20.5666	0.99351	0.0:0.0:1.0:0.0	.	3878;309	P20929;Q14215	NEBU_HUMAN;.	C	3878;5579;5579;309;3878	ENSP00000386259:R3878C;ENSP00000380505:R5579C;ENSP00000416578:R5579C;ENSP00000410961:R309C;ENSP00000172853:R3878C	ENSP00000172853:R3878C	R	-	1	0	NEB	152141084	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.030000	0.57260	2.854000	0.98071	0.655000	0.94253	CGT	.	.	none		0.473	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		A	152432838	G	A	152432838	3	1	6	1	0	0	0	0	1	0	0	0	10311	1087	38	1	9259	1	NEB	2	152432838	Missense_Mutation	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	148687811	152432838	90766535	7	592											
ITGA6	3655	hgsc.bcm.edu	37	chr2	173368882	173368882	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gataccatgctgtaaggatcCggaaagaagagcgagagatc	15	6	13	7	2	0	3	0	0	0	3	2	8	1	5	2	2	3	2	2	2	4	2	rs370676535		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr2:173368882C>T	ENST00000264106.6	+	26	3498	c.3295C>T	c.(3295-3297)Cgg>Tgg	p.R1099W	ITGA6_ENST00000264107.7_3'UTR|ITGA6_ENST00000375221.2_3'UTR|AC093818.1_ENST00000450443.1_RNA|ITGA6_ENST00000409080.1_Missense_Mutation_p.R1060W|ITGA6_ENST00000409532.1_3'UTR|ITGA6_ENST00000343713.4_3'UTR|AC093818.1_ENST00000442417.1_RNA			P23229	ITA6_HUMAN	integrin, alpha 6	1099					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)			TGTAAGGATCCGGAAAGAAGA	0.388																																					p.R1060W		Atlas-SNP	.											.	ITGA6	171	.	0			c.C3178T						PASS	.	C	,TRP/ARG	0,3728		0,0,1864	57	53	54		,3178	5.9	1	2		54	1,8205		0,1,4102	no	utr-3,missense	ITGA6	NM_000210.2,NM_001079818.1	,101	0,1,5966	TT,TC,CC		0.0122,0.0,0.0084	,probably-damaging	,1060/1092	173368882	1,11933	1864	4103	5967	SO:0001583	missense	3655	exon25			AGGATCCGGAAAG		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.3295C>T	2.37:g.173368882C>T	ENSP00000264106:p.Arg1099Trp	217	0	0		181	76	0.41989	NM_001079818	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Missense_Mutation	SNP	ENST00000264106.6	37		.	.	.	.	.	.	.	.	.	.	C	23.1	4.372286	0.82573	0.0	1.22E-4	ENSG00000091409	ENST00000264106;ENST00000409080;ENST00000442250;ENST00000458358;ENST00000416789	T;T;T;T;T	0.24151	1.87;1.87;1.87;1.87;1.87	5.87	5.87	0.94306	.	0.456524	0.24256	N	0.040127	T	0.36771	0.0979	L	0.43152	1.355	0.80722	D	1	D	0.64830	0.994	P	0.55965	0.788	T	0.03394	-1.1041	10	0.66056	D	0.02	.	13.4186	0.60982	0.0:0.9286:0.0:0.0714	.	1060	G5E9H1	.	W	1099;1060;1099;1055;227	ENSP00000264106:R1099W;ENSP00000386896:R1060W;ENSP00000406694:R1099W;ENSP00000394169:R1055W;ENSP00000388435:R227W	ENSP00000264106:R1099W	R	+	1	2	ITGA6	173077128	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.754000	0.62191	2.785000	0.95823	0.655000	0.94253	CGG	.	.	weak		0.388	ITGA6-201	KNOWN	basic	protein_coding	protein_coding				T	173368882	C	T	173368882	3	4	6	1	0	0	0	0	1	0	0	0	7889	643	23	1	3388	1	ITGA6	2	173368882	Missense_Mutation	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10	20936044	173368882	69830491	8	593											
ERBB4	2066	hgsc.bcm.edu	37	chr2	212522545	212522545	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgcagtcatgactagtgggaCcgttacacctgcaggcaatt	10	10	11	10	1	1	1	1	1	0	0	1	2	1	2	2	2	3	4	2	2	3	3			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr2:212522545C>G	ENST00000342788.4	-	16	2190	c.1880G>C	c.(1879-1881)gGt>gCt	p.G627A	ERBB4_ENST00000436443.1_Missense_Mutation_p.G627A|ERBB4_ENST00000402597.1_Intron	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	627	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)	ACTAGTGGGACCGTTACACCT	0.473										TSP Lung(8;0.080)																											p.G627A		Atlas-SNP	.											ERBB4,NS,malignant_melanoma,0,1	ERBB4	480	1	0			c.G1880C						PASS	.						284	216	239					2																	212522545		2203	4300	6503	SO:0001583	missense	2066	exon16			GTGGGACCGTTAC	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.1880G>C	2.37:g.212522545C>G	ENSP00000342235:p.Gly627Ala	78	0	0		73	39	0.534247	NM_001042599	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	37	CCDS2394.1	.	.	.	.	.	.	.	.	.	.	C	15.51	2.856348	0.51376	.	.	ENSG00000178568	ENST00000342788;ENST00000436443	D;D	0.87412	-2.25;-2.25	5.14	5.14	0.70334	Growth factor, receptor (1);	0.099233	0.64402	D	0.000001	D	0.87661	0.6233	M	0.77486	2.375	0.80722	D	1	B;P;P	0.51057	0.167;0.941;0.902	B;P;B	0.44447	0.076;0.45;0.263	D	0.88473	0.3063	10	0.52906	T	0.07	.	12.3529	0.55159	0.0:0.9224:0.0:0.0776	.	486;627;627	Q53QS8;Q15303-3;Q15303	.;.;ERBB4_HUMAN	A	627	ENSP00000342235:G627A;ENSP00000403204:G627A	ENSP00000342235:G627A	G	-	2	0	ERBB4	212230790	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.010000	0.49559	2.557000	0.86248	0.650000	0.86243	GGT	.	.	none		0.473	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		G	212522545	C	G	212522545	3	3	6	1	0	0	0	0	1	0	0	0	5211	507	18	4	2098	4	ERBB4	2	212522545	Missense_Mutation	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10	39153663	212522545	30676828	9	594											
MYD88	4615	hgsc.bcm.edu	37	chr3	38182641	38182641	+	Nonstop_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtgcccatcagaagcgacTgatccccatcaagtacaagg	13	6	10	12	1	2	2	2	1	0	1	3	3	3	2	3	2	3	1	3	2	4	1	rs387907272		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr3:38182641T>C	ENST00000495303.1	+	3	483	c.478T>C	c.(478-480)Tga>Cga	p.*160R	MYD88_ENST00000424893.1_Missense_Mutation_p.L220P|MYD88_ENST00000481122.1_3'UTR|MYD88_ENST00000443433.2_Nonstop_Mutation_p.*205R|MYD88_ENST00000396334.3_Missense_Mutation_p.L265P|MYD88_ENST00000417037.2_Missense_Mutation_p.L273P	NM_001172566.1	NP_001166037.1	Q99836	MYD88_HUMAN	myeloid differentiation primary response 88	0	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|cell surface receptor signaling pathway (GO:0007166)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-positive bacterium (GO:0050830)|establishment of endothelial intestinal barrier (GO:0090557)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of apoptotic process (GO:0043066)|negative regulation of growth of symbiont in host (GO:0044130)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-23 production (GO:0032747)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of lymphocyte proliferation (GO:0050671)|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 tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)|response to molecule of fungal origin (GO:0002238)|response to peptidoglycan (GO:0032494)|response to virus (GO:0009615)|signal transduction (GO:0007165)|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)|type I interferon biosynthetic process (GO:0045351)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)	death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|TIR domain binding (GO:0070976)	p.L265P(188)		breast(1)|haematopoietic_and_lymphoid_tissue(226)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	237				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		CAGAAGCGACTGATCCCCATC	0.552			Mis		ABC-DLBCL								T|||	1	0.000199681	0.0	0.0	5008	,	,		22034	0.0		0.001	False		,,,				2504	0.0				p.X205R		Atlas-SNP	.		Dom	yes		3	3p22	4615	myeloid differentiation primary response gene (88)		L	MYD88,NS,lymphoid_neoplasm,0,828	MYD88	900	828	188	Substitution - Missense(188)	haematopoietic_and_lymphoid_tissue(188)	c.T613C						PASS	.						148	119	129					3																	38182641		2203	4300	6503	SO:0001578	stop_lost	4615	exon4			AGCGACTGATCCC	U84408	CCDS2674.2, CCDS54565.1, CCDS54566.1, CCDS54567.1, CCDS54568.1	3p22	2014-09-17	2012-11-15		ENSG00000172936	ENSG00000172936			7562	protein-coding gene	gene with protein product		602170	"myeloid differentiation primary response gene (88)"			9013863	Standard	NM_002468		Approved		uc003chx.3	Q99836	OTTHUMG00000131083	ENST00000495303.1:c.478T>C	3.37:g.38182641T>C	ENSP00000417848:p.*160Argext*8	47	0	0		37	29	0.783784	NM_001172569	B4DKH8|B4DKU4|B4DQ60|B4DQ72|J3KPU4|J3KQ87|J3KQJ6|P78397|Q53XS7	Missense_Mutation	SNP	ENST00000495303.1	37	CCDS54568.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.85|18.85	3.710754|3.710754	0.68730|0.68730	.|.	.|.	ENSG00000172936|ENSG00000172936	ENST00000417037;ENST00000396334;ENST00000424893;ENST00000421516;ENST00000415158|ENST00000495303;ENST00000443433	T;T;T;T|.	0.15487|.	2.42;2.42;2.42;2.42|.	5.74|5.74	5.74|5.74	0.90152|0.90152	Toll/interleukin-1 receptor homology (TIR) domain (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.71676|.	0.3368|.	.|.	.|.	.|.	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;0.999;0.999|.	T|.	0.70626|.	-0.4820|.	9|.	0.87932|.	D|.	0|.	-17.9268|-17.9268	15.535|15.535	0.75996|0.75996	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	207;252;241|.	Q99836-2;Q99836;B4E3D6|.	.;MYD88_HUMAN;.|.	P|R	273;265;220;272;241|160;205	ENSP00000401399:L273P;ENSP00000379625:L265P;ENSP00000389979:L220P;ENSP00000391753:L272P|.	ENSP00000379625:L265P|.	L|X	+|+	2|1	0|0	MYD88|MYD88	38157645|38157645	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.639000|7.639000	0.83342|0.83342	2.326000|2.326000	0.78906|0.78906	0.533000|0.533000	0.62120|0.62120	CTG|TGA	.	.	none		0.552	MYD88-008	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000342700.1	NM_002468		C	38182641	T	C	38182641	4	2	6	1	0	0	0	0	0	0	0	0	10032	1593	55	3	836	3	MYD88	3	38182641	Nonstop_Mutation	SNP	T	TCGA-FA-A7DS-01A-11D-A382-10		38182641	159839789	10	595											
FAT4	79633	hgsc.bcm.edu	37	chr4	126370300	126370300	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agattatgaaattgttaatgGcaacatggaaaatagtttca	17	13	8	3	0	1	2	1	1	0	1	1	3	1	3	0	2	1	3	0	2	7	5			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr4:126370300G>A	ENST00000394329.3	+	9	8142	c.8129G>A	c.(8128-8130)gGc>gAc	p.G2710D	FAT4_ENST00000335110.5_Missense_Mutation_p.G1008D	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2710	Cadherin 26. {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						ATTGTTAATGGCAACATGGAA	0.373																																					p.G2710D		Atlas-SNP	.											.	FAT4	1752	.	0			c.G8129A						PASS	.						103	102	103					4																	126370300		2203	4299	6502	SO:0001583	missense	79633	exon9			TTAATGGCAACAT	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.8129G>A	4.37:g.126370300G>A	ENSP00000377862:p.Gly2710Asp	97	0	0		81	25	0.308642	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	18.26	3.584637	0.65992	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.01767	4.65;4.65	5.9	5.9	0.94986	Cadherin (4);Cadherin-like (1);	0.000000	0.35067	U	0.003472	T	0.08268	0.0206	L	0.49513	1.565	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.97110	1.0;0.998;1.0	T	0.49331	-0.8951	10	0.22706	T	0.39	.	20.2789	0.98501	0.0:0.0:1.0:0.0	.	1008;2710;2710	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	D	2710;1008	ENSP00000377862:G2710D;ENSP00000335169:G1008D	ENSP00000335169:G1008D	G	+	2	0	FAT4	126589750	1.000000	0.71417	0.960000	0.40013	0.495000	0.33615	9.666000	0.98612	2.788000	0.95919	0.650000	0.86243	GGC	.	.	none		0.373	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126370300	G	A	126370300	3	1	6	1	0	0	0	0	1	0	0	0	5700	1203	42	2	8163	2	FAT4	4	126370300	Missense_Mutation	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10		126370300	64783976	11	596											
NKD2	85409	hgsc.bcm.edu	37	chr5	1036421	1036421	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggagcgggggccctactgcGtggacgagaacacggagcgc	8	3	18	12	6	0	1	0	0	0	1	0	5	0	4	1	5	5	0	1	5	2	1	rs376557535		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr5:1036421G>A	ENST00000296849.5	+	9	938	c.709G>A	c.(709-711)Gtg>Atg	p.V237M	NKD2_ENST00000382730.2_5'Flank|NKD2_ENST00000274150.4_Missense_Mutation_p.V237M|NKD2_ENST00000537972.1_Missense_Mutation_p.V237M	NM_033120.3	NP_149111.1	Q969F2	NKD2_HUMAN	naked cuticle homolog 2 (Drosophila)	237					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)			GCCCTACTGCGTGGACGAGAA	0.657																																					p.V237M		Atlas-SNP	.											.	NKD2	39	.	0			c.G709A						PASS	.						87	70	76					5																	1036421		2203	4299	6502	SO:0001583	missense	85409	exon9			TACTGCGTGGACG	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.709G>A	5.37:g.1036421G>A	ENSP00000296849:p.Val237Met	50	0	0		37	15	0.405405	NM_001271082	Q96EK8|Q9BSN0	Missense_Mutation	SNP	ENST00000296849.5	37	CCDS3859.1	.	.	.	.	.	.	.	.	.	.	G	17.73	3.461936	0.63513	.	.	ENSG00000145506	ENST00000296849;ENST00000274150;ENST00000537972	T;T;T	0.76060	0.11;-0.99;-0.99	4.39	4.39	0.52855	.	0.000000	0.64402	D	0.000004	D	0.84884	0.5571	M	0.79123	2.44	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77004	0.975;0.989	D	0.86862	0.2030	10	0.87932	D	0	-14.8057	12.4572	0.55710	0.0:0.0:1.0:0.0	.	237;237	Q969F2-2;Q969F2	.;NKD2_HUMAN	M	237	ENSP00000296849:V237M;ENSP00000274150:V237M;ENSP00000440925:V237M	ENSP00000274150:V237M	V	+	1	0	NKD2	1089421	1.000000	0.71417	0.977000	0.42913	0.845000	0.48019	5.412000	0.66392	1.979000	0.57680	0.491000	0.48974	GTG	.	.	weak		0.657	NKD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206720.2	NM_033120		A	1036421	G	A	1036421	3	1	6	1	0	0	0	0	1	0	0	0	10451	1145	40	1	743	1	NKD2	5	1036421	Missense_Mutation	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10		1036421	179878839	12	597											
EGR1	1958	hgsc.bcm.edu	37	chr5	137801553	137801553	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccatggacaactaccctaagCtggaggagatgatgctgctg	11	8	12	10	0	0	2	0	1	0	1	0	5	0	4	2	3	5	3	2	3	3	2	rs558452520		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr5:137801553C>T	ENST00000239938.4	+	1	375	c.103C>T	c.(103-105)Ctg>Ttg	p.L35L		NM_001964.2	NP_001955.1	P18146	EGR1_HUMAN	early growth response 1	35					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)			CTACCCTAAGCTGGAGGAGAT	0.667																																					p.L35L		Atlas-SNP	.											.	EGR1	52	.	0			c.C103T						PASS	.						83	74	77					5																	137801553		2203	4300	6503	SO:0001819	synonymous_variant	1958	exon1			CCTAAGCTGGAGG	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.103C>T	5.37:g.137801553C>T		140	0	0		113	48	0.424779	NM_001964		Silent	SNP	ENST00000239938.4	37	CCDS4206.1																																																																																			.	.	none		0.667	EGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251274.1	NM_001964		T	137801553	C	T	137801553	2	4	6	1	0	0	0	0	0	0	0	1	4973	796	28	2		2	EGR1	5	137801553	Silent	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10	136765132	137801553	43113707	13	598											
GABRP	2568	hgsc.bcm.edu	37	chr5	170222292	170222292	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcaacaagagcttcactctGgatgcccgcctcgtggagtt	8	9	12	12	2	2	1	1	0	1	1	3	3	2	3	2	3	3	3	2	3	2	2	rs41315922		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr5:170222292G>T	ENST00000518525.1	+	6	785	c.321G>T	c.(319-321)ctG>ctT	p.L107L	GABRP_ENST00000519598.1_Silent_p.L107L|GABRP_ENST00000519385.1_Silent_p.L107L|GABRP_ENST00000265294.4_Silent_p.L107L			O00591	GBRP_HUMAN	gamma-aminobutyric acid (GABA) A receptor, pi	107					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)	GCTTCACTCTGGATGCCCGCC	0.567																																					p.L107L		Atlas-SNP	.											.	GABRP	65	.	0			c.G321T						PASS	.						124	128	127					5																	170222292		2203	4300	6503	SO:0001819	synonymous_variant	2568	exon5			CACTCTGGATGCC	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.321G>T	5.37:g.170222292G>T		89	0	0		67	23	0.343284	NM_014211	A8KA36|D3DQL2|Q32MJ1	Silent	SNP	ENST00000518525.1	37	CCDS4375.1																																																																																			G|1.000;C|0.000	.	alt		0.567	GABRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252834.3	NM_014211		T	170222292	G	T	170222292	2	4	6	1	0	0	0	0	0	0	0	1	6182	1335	47	4		4	GABRP	5	170222292	Silent	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	32420739	170222292	10692968	14	599											
HIST1H4H	8365	hgsc.bcm.edu	37	chr6	26285531	26285531	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtgacagcgtcacgaatcAcgttctccaggaacaccttc	12	8	8	13	3	3	1	2	1	1	0	5	3	3	2	2	1	2	1	2	1	3	2			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:26285531A>T	ENST00000377727.1	-	1	206	c.197T>A	c.(196-198)gTg>gAg	p.V66E	HIST1H4H_ENST00000289352.1_Missense_Mutation_p.V66E	NM_003543.3	NP_003534.1	P62805	H4_HUMAN	histone cluster 1, H4h	66					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						GTCACGAATCACGTTCTCCAG	0.557										HNSCC(76;0.23)																											p.V66E		Atlas-SNP	.											.	HIST1H4H	16	.	0			c.T197A						PASS	.						182	149	160					6																	26285531		2203	4300	6503	SO:0001583	missense	8365	exon1			CGAATCACGTTCT	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.197T>A	6.37:g.26285531A>T	ENSP00000366956:p.Val66Glu	102	0	0		72	29	0.402778	NM_003543	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000377727.1	37	CCDS4604.1	.	.	.	.	.	.	.	.	.	.	.	17.24	3.340399	0.60963	.	.	ENSG00000158406	ENST00000289352;ENST00000377727	T;T	0.70631	-0.5;-0.5	4.4	4.4	0.53042	.	0.000000	0.45606	U	0.000344	T	0.72326	0.3446	.	.	.	0.44194	D	0.997011	.	.	.	.	.	.	T	0.77389	-0.2606	7	0.87932	D	0	.	11.8938	0.52646	1.0:0.0:0.0:0.0	.	.	.	.	E	66	ENSP00000289352:V66E;ENSP00000366956:V66E	ENSP00000289352:V66E	V	-	2	0	HIST1H4H	26393510	1.000000	0.71417	1.000000	0.80357	0.156000	0.22039	9.196000	0.94978	1.770000	0.52166	0.402000	0.26972	GTG	.	.	none		0.557	HIST1H4H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040119.1	NM_003543		T	26285531	A	T	26285531	3	4	6	1	0	0	0	0	1	0	0	0	7181	159	6	5	118	5	HIST1H4H	6	26285531	Missense_Mutation	SNP	A	TCGA-FA-A7DS-01A-11D-A382-10		26285531	144829536	15	600											
HLA-C	3107	hgsc.bcm.edu	37	chr6	31239047	31239047	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgtaatccttgccgtcgtagGcggactggtcatacccgcgg	6	10	13	12	5	1	0	1	0	0	0	3	1	2	1	3	4	2	2	3	4	3	4	rs281860470		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:31239047G>A	ENST00000376228.5	-	3	436	c.422C>T	c.(421-423)gCc>gTc	p.A141V	HLA-C_ENST00000383329.3_Missense_Mutation_p.A141V	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	141	Alpha-2.				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)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GCCGTCGTAGGCGGACTGGTC	0.706													g|||	1	0.000199681	0.0	0.0	5008	,	,		12845	0.0		0.0	False		,,,				2504	0.001				p.A141V		Atlas-SNP	.											.	HLA-C	92	.	0			c.C422T						PASS	.						35	27	30					6																	31239047		2182	4253	6435	SO:0001583	missense	3107	exon3			TCGTAGGCGGACT	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4933	protein-coding gene	gene with protein product		142840	"psoriasis susceptibility 1"	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.422C>T	6.37:g.31239047G>A	ENSP00000365402:p.Ala141Val	114	0	0		56	22	0.392857	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.	.	.	.	.	.	.	.	.	.	.	13.97	2.394451	0.42410	.	.	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307	T;T	0.00018	9.08;9.08	2.59	2.59	0.31030	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);	0.229535	0.21218	U	0.078193	T	0.00328	0.0010	H	0.99914	4.94	0.20196	N	0.999921	D;P;P;P	0.58970	0.984;0.878;0.878;0.939	P;P;P;P	0.58391	0.838;0.482;0.61;0.662	T	0.46830	-0.9163	10	0.87932	D	0	.	7.4947	0.27481	0.0:0.2697:0.7303:0.0	.	141;141;141;141	A2AEA4;A6H578;A2AEA2;P10321	.;.;.;1C07_HUMAN	V	141;141;141;178	ENSP00000365402:A141V;ENSP00000372819:A141V	ENSP00000365402:A141V	A	-	2	0	HLA-C	31347026	0.028000	0.19301	0.011000	0.14972	0.023000	0.10783	0.934000	0.28910	1.768000	0.52137	0.305000	0.20034	GCC	.	.	weak		0.706	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117		A	31239047	G	A	31239047	3	1	6	1	0	0	0	0	1	0	0	0	7206	1203	42	2	702	2	HLA-C	6	31239047	Missense_Mutation	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	4953516	31239047	139876020	16	601											
HLA-C	3107	hgsc.bcm.edu	37	chr6	31239416	31239416	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tagccgcgcaggttccgcagGctcactcggtcagcctgtgc	5	8	13	15	4	2	0	2	0	0	0	4	0	3	0	3	3	3	4	3	3	1	2	rs281860412		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:31239416G>A	ENST00000376228.5	-	2	317	c.303C>T	c.(301-303)agC>agT	p.S101S	HLA-C_ENST00000383329.3_Silent_p.S101S	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	101	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)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						GGTTCCGCAGGCTCACTCGGT	0.711																																					p.S101S		Atlas-SNP	.											.	HLA-C	92	.	0			c.C303T						PASS	.						42	43	42					6																	31239416		1511	2709	4220	SO:0001819	synonymous_variant	3107	exon2			CCGCAGGCTCACT	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4933	protein-coding gene	gene with protein product		142840	"psoriasis susceptibility 1"	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.303C>T	6.37:g.31239416G>A		88	0	0		74	50	0.675676	NM_002117	O02864|O02958|Q29643|Q9MY30	Silent	SNP	ENST00000376228.5	37	CCDS34393.1	.	.	.	.	.	.	.	.	.	.	N	6.547	0.469265	0.12461	.	.	ENSG00000204525	ENST00000415537	.	.	.	2.81	1.92	0.25849	.	.	.	.	.	T	0.15435	0.0372	.	.	.	0.19945	N	0.999941	.	.	.	.	.	.	T	0.21381	-1.0247	4	.	.	.	.	7.0143	0.24879	0.0:0.0:0.7285:0.2715	.	.	.	.	S	101	.	.	P	-	1	0	HLA-C	31347395	0.986000	0.35501	0.023000	0.16930	0.010000	0.07245	2.812000	0.47994	0.735000	0.32537	0.305000	0.20034	CCT	.	.	weak		0.711	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117		A	31239416	G	A	31239416	2	1	6	1	0	0	0	0	0	0	0	1	7206	1194	42	2		2	HLA-C	6	31239416	Silent	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	369	31239416	139875651	17	602											
HLA-B	3106	hgsc.bcm.edu	37	chr6	31323097	31323098	+	Frame_Shift_Ins	INS	-	-	T																															tcatccccctccttaccccaINStctcagggtgaggggcttcg																								rs281864645		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:31323097_31323098insT	ENST00000412585.2	-	4	919_920	c.891_892insA	c.(889-894)agatggfs	p.W298fs		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	298	Alpha-3.				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						TCCTTACCCCATCTCAGGGTGA	0.594									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.W298fs		Atlas-Indel	.											.	HLA-B	54	.	0			c.892_893insA						PASS	.																																			SO:0001589	frameshift_variant	3106	exon4	Familial Cancer Database	;Lichen Sclerosis, Familial	.	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.892dupA	6.37:g.31323098_31323098dupT	ENSP00000399168:p.Trp298fs	65	0	0		56	20	0.357143	NM_005514	Q29764	Frame_Shift_Ins	INS	ENST00000412585.2	37	CCDS34394.1																																																																																			.	.	none		0.594	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514		T	31323098	-	T	31323097	7	5	6	1	0	1	1	0	0	0	0	0	7205	217	8	0	212	0	HLA-B	6	31323097	Frame_Shift_Ins	INS	-	TCGA-FA-A7DS-01A-11D-A382-10	83681	31323097	139791970	18	603											
PIM1	5292	hgsc.bcm.edu	37	chr6	37138372	37138372	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atgctcttgtccaaaatcaaCtcgcttgcccacctgcgcgc	8	10	7	16	3	2	0	1	0	1	0	4	0	3	0	3	0	4	2	3	0	3	2			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:37138372C>T	ENST00000373509.5	+	1	394	c.21C>T	c.(19-21)aaC>aaT	p.N7N		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	98					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)	CCAAAATCAACTCGCTTGCCC	0.721			T	BCL6	NHL																																p.N98N		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C294T						PASS	.						31	31	31					6																	37138372		2202	4298	6500	SO:0001819	synonymous_variant	5292	exon1			AATCAACTCGCTT		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.21C>T	6.37:g.37138372C>T		70	0	0		54	20	0.37037	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.721	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37138372	C	T	37138372	2	4	6	1	0	0	0	0	0	0	0	1	11936	564	20	2		2	PIM1	6	37138372	Silent	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10	5815275	37138372	133976695	19	604			1	7		10	9	2523	N	G_C	2.035573e-22
PIM1	5292	hgsc.bcm.edu	37	chr6	37138549	37138549	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cgtgcttccccctttcctagGcaaggagaaggagcccctgg	7	8	12	14	1	0	1	0	0	0	1	2	3	2	2	5	4	2	2	5	4	3	3	rs377274719		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:37138549G>A	ENST00000373509.5	+	2	456	c.83G>A	c.(82-84)gGc>gAc	p.G28D		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	119					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)	CCTTTCCTAGGCAAGGAGAAG	0.721			T	BCL6	NHL																																p.G119D		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,0,3	PIM1	71	3	0			c.G356A						PASS	.	G	ASP/GLY	1,4257		0,1,2128	18	26	23		83	3.8	1	6		23	0,8506		0,0,4253	no	missense-near-splice	PIM1	NM_002648.3	94	0,1,6381	AA,AG,GG		0.0,0.0235,0.0078	probably-damaging	28/314	37138549	1,12763	2129	4253	6382	SO:0001630	splice_region_variant	5292	exon2			TCCTAGGCAAGGA		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.83-1G>A	6.37:g.37138549G>A		65	0	0		47	24	0.510638	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	G	13.37	2.215565	0.39102	2.35E-4	0.0	ENSG00000137193	ENST00000373509	T	0.69306	-0.39	3.83	3.83	0.44106	Protein kinase-like domain (1);	0.187844	0.33772	N	0.004562	T	0.23330	0.0564	N	0.08118	0	0.30455	N	0.774827	P	0.42827	0.791	B	0.36719	0.231	T	0.07083	-1.0791	9	.	.	.	.	9.7286	0.40348	0.0983:0.0:0.9017:0.0	.	119	P11309	PIM1_HUMAN	D	28	ENSP00000362608:G28D	.	G	+	2	0	PIM1	37246527	0.119000	0.22226	0.998000	0.56505	0.963000	0.63663	-0.036000	0.12185	2.138000	0.66242	0.549000	0.68633	GGC	.	.	weak		0.721	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		Missense_Mutation	A	37138549	G	A	37138549	5	1	6	1	0	0	0	0	0	0	1	0	11936	1217	42	2	89	2	PIM1	6	37138549	Splice_Site	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	177	37138549	133976518	20	605			1	7		10	9	2523	N	G_C	2.035573e-22
PIM1	5292	hgsc.bcm.edu	37	chr6	37138577	37138577	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaggagcccctggagtcgcaGtaccaggtgggcccgctact	8	6	14	13	2	0	0	0	0	0	0	1	2	0	2	4	4	3	3	4	4	3	2			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:37138577G>A	ENST00000373509.5	+	2	484	c.111G>A	c.(109-111)caG>caA	p.Q37Q		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	128					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)	p.Q37H(2)		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)	TGGAGTCGCAGTACCAGGTGG	0.706			T	BCL6	NHL																																p.Q128Q		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,0,2	PIM1	71	2	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.G384A						PASS	.						22	32	28					6																	37138577		2167	4268	6435	SO:0001819	synonymous_variant	5292	exon2			GTCGCAGTACCAG		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.111G>A	6.37:g.37138577G>A		79	0	0		52	28	0.538462	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.706	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			A	37138577	G	A	37138577	2	1	6	1	0	0	0	0	0	0	0	1	11936	1020	36	2		2	PIM1	6	37138577	Silent	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	28	37138577	133976490	21	606			1	7		10	9	2523	N	G_C	2.035573e-22
PIM1	5292	hgsc.bcm.edu	37	chr6	37138765	37138765	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgggcttccaggtggccatCaaacacgtggagaaggaccg	10	6	14	11	2	1	1	1	0	0	1	2	3	2	2	3	5	1	1	3	5	2	1			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:37138765C>T	ENST00000373509.5	+	3	571	c.198C>T	c.(196-198)atC>atT	p.I66I		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	157					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)	AGGTGGCCATCAAACACGTGG	0.721			T	BCL6	NHL																																p.I157I		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C471T						PASS	.						53	56	55					6																	37138765		2203	4300	6503	SO:0001819	synonymous_variant	5292	exon3			GGCCATCAAACAC		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.198C>T	6.37:g.37138765C>T		70	0	0		86	21	0.244186	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.721	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37138765	C	T	37138765	2	4	6	1	0	0	0	0	0	0	0	1	11936	816	29	2		2	PIM1	6	37138765	Silent	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10	188	37138765	133976302	22	607			1	7		10	9	2523	N	G_C	2.035573e-22
PIM1	5292	hgsc.bcm.edu	37	chr6	37138901	37138901	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cggccccctcgcccctgcagCctaatggcactcgagtgccc	5	6	10	20	3	0	0	0	0	0	0	2	1	0	0	6	2	3	2	6	2	1	1			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:37138901C>T	ENST00000373509.5	+	4	614	c.241C>T	c.(241-243)Cct>Tct	p.P81S		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	172					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)	GCCCCTGCAGCCTAATGGCAC	0.667			T	BCL6	NHL																																p.P172S		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C514T						PASS	.						45	52	50					6																	37138901		2203	4299	6502	SO:0001630	splice_region_variant	5292	exon4			CTGCAGCCTAATG		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.241-1C>T	6.37:g.37138901C>T		33	0	0		48	12	0.25	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	8.304	0.820601	0.16678	.	.	ENSG00000137193	ENST00000373509	T	0.63096	-0.02	4.28	4.28	0.50868	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.230218	0.35525	N	0.003156	T	0.29882	0.0747	N	0.20610	0.595	0.41234	D	0.98659	B	0.06786	0.001	B	0.09377	0.004	T	0.10823	-1.0613	9	.	.	.	.	15.0358	0.71744	0.0:1.0:0.0:0.0	.	172	P11309	PIM1_HUMAN	S	81	ENSP00000362608:P81S	.	P	+	1	0	PIM1	37246879	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	4.378000	0.59568	2.371000	0.80710	0.549000	0.68633	CCT	.	.	none		0.667	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		Missense_Mutation	T	37138901	C	T	37138901	5	4	6	1	0	0	0	0	0	0	1	0	11936	753	26	2	255	2	PIM1	6	37138901	Splice_Site	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10	136	37138901	133976166	23	608			1	7		10	9	2523	N	G_C	2.035573e-22
PIM1	5292	hgsc.bcm.edu	37	chr6	37138951	37138951	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtcctgctgaagaaggtgagCtcgggtttctccggcgtcat	6	11	14	10	3	2	3	1	2	1	1	5	3	3	3	2	3	2	3	2	3	2	1			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:37138951C>T	ENST00000373509.5	+	4	664	c.291C>T	c.(289-291)agC>agT	p.S97S		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	188					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)	AGAAGGTGAGCTCGGGTTTCT	0.647			T	BCL6	NHL																																p.S188S		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,+1,5	PIM1	71	5	0			c.C564T						PASS	.						82	92	89					6																	37138951		2203	4300	6503	SO:0001819	synonymous_variant	5292	exon4			GGTGAGCTCGGGT		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.291C>T	6.37:g.37138951C>T		48	0	0		50	28	0.56	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.647	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37138951	C	T	37138951	2	4	6	1	0	0	0	0	0	0	0	1	11936	796	28	2		2	PIM1	6	37138951	Silent	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10	50	37138951	133976116	24	609			1	7		10	9	2523	N	G_C	2.035573e-22
PIM1	5292	hgsc.bcm.edu	37	chr6	37139042	37139042	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agaggcccgagccggtgcaaGatctcttcgacttcatcacg	9	8	11	13	4	3	2	2	0	1	2	5	4	3	2	2	2	2	1	2	2	1	2			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:37139042G>A	ENST00000373509.5	+	4	755	c.382G>A	c.(382-384)Gat>Aat	p.D128N		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	219					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)	GCCGGTGCAAGATCTCTTCGA	0.622			T	BCL6	NHL																																p.D219N		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.G655A						PASS	.						81	95	91					6																	37139042		2203	4300	6503	SO:0001583	missense	5292	exon4			GTGCAAGATCTCT		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.382G>A	6.37:g.37139042G>A	ENSP00000362608:p.Asp128Asn	78	0	0		86	38	0.44186	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.857582	0.91433	.	.	ENSG00000137193	ENST00000373509	T	0.15603	2.41	4.28	4.28	0.50868	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	0.24005	0.0581	L	0.42008	1.315	0.80722	D	1	D	0.53745	0.962	P	0.62885	0.908	T	0.02081	-1.1217	10	0.87932	D	0	.	16.8746	0.86048	0.0:0.0:1.0:0.0	.	219	P11309	PIM1_HUMAN	N	128	ENSP00000362608:D128N	ENSP00000362608:D128N	D	+	1	0	PIM1	37247020	1.000000	0.71417	1.000000	0.80357	0.773000	0.43773	9.149000	0.94659	2.371000	0.80710	0.549000	0.68633	GAT	.	.	none		0.622	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			A	37139042	G	A	37139042	3	1	6	1	0	0	0	0	1	0	0	0	11936	942	33	2	396	2	PIM1	6	37139042	Missense_Mutation	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	91	37139042	133976025	25	610			1	7		10	9	2523	N	G_C	2.035573e-22
PIM1	5292	hgsc.bcm.edu	37	chr6	37139203	37139203	+	Missense_Mutation	SNP	G	G	C																															atcgacctcaatcgcggcgaGctcaagctcatcgacttcgg																										TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:37139203G>C	ENST00000373509.5	+	4	916	c.543G>C	c.(541-543)gaG>gaC	p.E181D		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	272	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)	p.E181D(1)		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)	ATCGCGGCGAGCTCAAGCTCA	0.637			T	BCL6	NHL																																p.E272D		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,0,1	PIM1	71	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G816C						scavenged	.						32	33	32					6																	37139203		2203	4300	6503	SO:0001583	missense	5292	exon4			CGGCGAGCTCAAG		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.543G>C	6.37:g.37139203G>C	ENSP00000362608:p.Glu181Asp	75	1	0.0133333		67	31	0.462687	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	G	10.45	1.354972	0.24512	.	.	ENSG00000137193	ENST00000373509	T	0.66099	-0.19	4.36	3.47	0.39725	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.207237	0.40554	N	0.001073	T	0.26412	0.0645	L	0.45698	1.435	0.33559	D	0.597158	B	0.13594	0.008	B	0.19946	0.027	T	0.07558	-1.0766	10	0.08837	T	0.75	.	5.5129	0.16890	0.3296:0.0:0.6704:0.0	.	272	P11309	PIM1_HUMAN	D	181	ENSP00000362608:E181D	ENSP00000362608:E181D	E	+	3	2	PIM1	37247181	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.006000	0.40874	1.020000	0.39573	0.448000	0.29417	GAG	.	.	none		0.637	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			C	37139203	G	C	37139203	3	2	6	1	0	0	0	0	1	0	0	0	11936	962	34	4	557	4	PIM1	6	37139203	Missense_Mutation	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	161	37139203	133975864	26	611	12	2	1	7		10	9	2523	N	G_C	2.035573e-22
PIM1	5292	hgsc.bcm.edu	37	chr6	37139210	37139210	+	Missense_Mutation	SNP	C	C	T																															tcaatcgcggcgagctcaagCtcatcgacttcgggtcgggg																								rs200495767	byFrequency	TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:37139210C>T	ENST00000373509.5	+	4	923	c.550C>T	c.(550-552)Ctc>Ttc	p.L184F		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	275	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)	CGAGCTCAAGCTCATCGACTT	0.652			T	BCL6	NHL																																p.L275F		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,NS,0,1	PIM1	71	1	0			c.C823T						PASS	.						31	32	31					6																	37139210		2203	4300	6503	SO:0001583	missense	5292	exon4			CTCAAGCTCATCG		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.550C>T	6.37:g.37139210C>T	ENSP00000362608:p.Leu184Phe	73	0	0		70	31	0.442857	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.926320	0.92319	.	.	ENSG00000137193	ENST00000373509	T	0.26067	1.76	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	0.64402	D	0.000002	T	0.58509	0.2127	H	0.96142	3.775	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.74166	-0.3753	10	0.87932	D	0	.	15.8069	0.78520	0.0:1.0:0.0:0.0	.	275	P11309	PIM1_HUMAN	F	184	ENSP00000362608:L184F	ENSP00000362608:L184F	L	+	1	0	PIM1	37247188	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.611000	0.82962	2.254000	0.74563	0.448000	0.29417	CTC	C|1.000;G|0.000	.	alt		0.652	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37139210	C	T	37139210	3	4	6	1	0	0	0	0	1	0	0	0	11936	797	28	2	564	2	PIM1	6	37139210	Missense_Mutation	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10	7	37139210	133975857	27	612	12	2	1	7		10	9	2523	N	G_C	2.035573e-22
PIM1	5292	hgsc.bcm.edu	37	chr6	37140894	37140894	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtggagatattcctttcgagCatgacgaagagatcatcagg	12	10	12	7	2	2	3	2	1	0	2	4	7	3	3	1	2	1	1	1	2	2	3			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:37140894C>T	ENST00000373509.5	+	5	1103	c.730C>T	c.(730-732)Cat>Tat	p.H244Y	PIM1_ENST00000468243.1_3'UTR	NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	335	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)	TCCTTTCGAGCATGACGAAGA	0.537			T	BCL6	NHL																																p.H335Y		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C1003T						PASS	.						131	123	126					6																	37140894		2203	4300	6503	SO:0001583	missense	5292	exon5			TTCGAGCATGACG		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.730C>T	6.37:g.37140894C>T	ENSP00000362608:p.His244Tyr	112	0	0		133	44	0.330827	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.475129	0.84640	.	.	ENSG00000137193	ENST00000373509	T	0.65916	-0.18	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);	0.182235	0.48767	D	0.000170	T	0.45155	0.1328	L	0.45422	1.42	0.54753	D	0.999983	P	0.45957	0.869	B	0.37731	0.257	T	0.55036	-0.8203	10	0.56958	D	0.05	.	18.1853	0.89791	0.0:1.0:0.0:0.0	.	335	P11309	PIM1_HUMAN	Y	244	ENSP00000362608:H244Y	ENSP00000362608:H244Y	H	+	1	0	PIM1	37248872	1.000000	0.71417	0.998000	0.56505	0.484000	0.33280	5.755000	0.68750	2.660000	0.90430	0.591000	0.81541	CAT	.	.	none		0.537	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37140894	C	T	37140894	3	4	6	1	0	0	0	0	1	0	0	0	11936	710	25	2	748	2	PIM1	6	37140894	Missense_Mutation	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10	1684	37140894	133974173	28	613			1	7		10	9	2523	N	G_C	2.035573e-22
MRPL14	64928	hgsc.bcm.edu	37	chr6	44081581	44081584	+	Stop_Codon_Del	DEL	CACA	CACA	-																															ccagaggcctgggctcaactCacacaaagttctgagcaatg																										TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	CACA	CACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:44081581_44081584delCACA	ENST00000372014.3	-	0	565_568					NM_032111.2	NP_115487.2	Q6P1L8	RM14_HUMAN	mitochondrial ribosomal protein L14						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)			GGGCTCAACTCACACAAAGTTCTG	0.574																																					p.145_146del		Pindel,Atlas-Indel	.											.	MRPL14	15	.	0			c.435_438del						PASS	.																																			SO:0001567	stop_retained_variant	64928	exon3			.	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	Exception_encountered	6.37:g.44081581_44081584delCACA	Exception_encountered	48	0	.		62	20	0.323	NM_032111	B2R575|Q96Q72	Frame_Shift_Del	DEL	ENST00000372014.3	37	CCDS34460.1																																																																																			.	.	none		0.574	MRPL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040707.1	NM_032111		-	44081584	CACA	-	44081581	7	5	6	1	0	1	0	1	0	0	0	0	9788	837	29	0	4	0	MRPL14	6	44081581	Stop_Codon_Del	DEL	CACA	TCGA-FA-A7DS-01A-11D-A382-10	6940687	44081581	127033486	29	614											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152763351	152763351	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctgctgctgcacatctctCttctttgctgagatccgctt	5	16	7	13	1	4	1	0	1	4	1	6	2	5	1	1	0	4	5	1	0	0	3	rs371765451		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:152763351C>A	ENST00000367255.5	-	31	4468	c.3867G>T	c.(3865-3867)aaG>aaT	p.K1289N	SYNE1_ENST00000341594.5_Missense_Mutation_p.K1355N|SYNE1_ENST00000413186.2_Missense_Mutation_p.K1289N|SYNE1_ENST00000265368.4_Missense_Mutation_p.K1289N|SYNE1_ENST00000423061.1_Missense_Mutation_p.K1296N|SYNE1_ENST00000367253.4_Missense_Mutation_p.K1289N|SYNE1_ENST00000448038.1_Missense_Mutation_p.K1296N|SYNE1_ENST00000367248.3_Missense_Mutation_p.K1279N	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1289					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)		GCACATCTCTCTTCTTTGCTG	0.527										HNSCC(10;0.0054)																											p.K1296N		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G3888T						PASS	.						80	70	73					6																	152763351		2203	4300	6503	SO:0001583	missense	23345	exon31			ATCTCTCTTCTTT	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.3867G>T	6.37:g.152763351C>A	ENSP00000356224:p.Lys1289Asn	108	0	0		90	29	0.322222	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	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	14.12	2.441045	0.43326	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000367253;ENST00000367248;ENST00000413186	T;T;T;T;T;D;D;D	0.88818	0.54;0.54;0.45;0.54;0.63;-2.39;-2.43;-2.43	5.41	2.67	0.31697	.	0.096661	0.44902	D	0.000408	D	0.85678	0.5752	L	0.56769	1.78	0.80722	D	1	P;P;P;D;P;P	0.56287	0.932;0.745;0.835;0.975;0.745;0.835	B;B;B;P;B;P	0.53185	0.341;0.276;0.39;0.72;0.276;0.466	D	0.84040	0.0364	10	0.48119	T	0.1	.	10.4617	0.44583	0.0:0.7281:0.0:0.2719	.	1272;1289;1279;1289;1289;1296	B3W695;Q8NF91;F5GXQ8;Q8NF91-6;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.;.;.	N	1289;1296;1289;1296;1355;1289;1279;1289	ENSP00000356224:K1289N;ENSP00000396024:K1296N;ENSP00000265368:K1289N;ENSP00000390975:K1296N;ENSP00000341887:K1355N;ENSP00000356222:K1289N;ENSP00000356217:K1279N;ENSP00000414510:K1289N	ENSP00000265368:K1289N	K	-	3	2	SYNE1	152805044	1.000000	0.71417	0.550000	0.28217	0.423000	0.31445	1.782000	0.38654	0.350000	0.24002	-0.142000	0.14014	AAG	.	.	none		0.527	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		A	152763351	C	A	152763351	3	1	6	1	0	0	0	0	1	0	0	0	15460	912	32	4	23063	4	SYNE1	6	152763351	Missense_Mutation	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10	108681770	152763351	18351716	30	615											
ZDHHC14	79683	hgsc.bcm.edu	37	chr6	158074641	158074641	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcaccatgtacggggccacGcagtcacagagtgacatggt	11	7	12	11	2	2	2	2	1	0	1	2	2	2	2	2	3	1	2	2	3	1	1	rs35358008	byFrequency	TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr6:158074641G>A	ENST00000359775.5	+	8	1939	c.1050G>A	c.(1048-1050)acG>acA	p.T350T	ZDHHC14_ENST00000341375.8_3'UTR|ZDHHC14_ENST00000414563.2_Silent_p.T350T			Q8IZN3	ZDH14_HUMAN	zinc finger, DHHC-type containing 14	350					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)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(1)|skin(1)	17		Breast(66;0.00586)|Ovarian(120;0.123)		OV - Ovarian serous cystadenocarcinoma(65;2.9e-17)|BRCA - Breast invasive adenocarcinoma(81;5.8e-05)		ACGGGGCCACGCAGTCACAGA	0.592																																					p.T350T		Atlas-SNP	.											.	ZDHHC14	39	.	0			c.G1050A						PASS	.						69	58	62					6																	158074641		2203	4300	6503	SO:0001819	synonymous_variant	79683	exon8			GGCCACGCAGTCA	AF542388	CCDS5252.1, CCDS47510.1	6q25.3	2008-05-02			ENSG00000175048	ENSG00000175048		"Zinc fingers, DHHC-type"	20341	protein-coding gene	gene with protein product							Standard	NM_024630		Approved	FLJ20984, NEW1CP	uc003qqt.3	Q8IZN3	OTTHUMG00000015896	ENST00000359775.5:c.1050G>A	6.37:g.158074641G>A		22	0	0		33	13	0.393939	NM_024630	A6NDB7|Q5JS07|Q5JS08|Q6PHS4|Q8IZN2|Q9H7F1	Silent	SNP	ENST00000359775.5	37	CCDS5252.1																																																																																			G|0.959;T|0.041	.	alt		0.592	ZDHHC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042841.2	NM_153746		A	158074641	G	A	158074641	2	1	6	1	0	0	0	0	0	0	0	1	17619	1074	38	1		1	ZDHHC14	6	158074641	Silent	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	5311290	158074641	13040426	31	616											
SNX8	29886	hgsc.bcm.edu	37	chr7	2304007	2304007	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgatccgctcggccctgtcGcgaagcttgtgaaagctatt	7	10	12	12	5	0	1	0	1	0	0	3	3	1	1	2	1	2	3	2	1	3	3			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr7:2304007G>A	ENST00000222990.3	-	6	750	c.708C>T	c.(706-708)cgC>cgT	p.R236R		NM_013321.2	NP_037453.1	Q9Y5X2	SNX8_HUMAN	sorting nexin 8	236					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)	p.R236R(1)		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)		CGGCCCTGTCGCGAAGCTTGT	0.552																																					p.R236R		Atlas-SNP	.											SNX8,NS,carcinoma,0,2	SNX8	46	2	1	Substitution - coding silent(1)	ovary(1)	c.C708T						PASS	.						81	72	75					7																	2304007		2203	4300	6503	SO:0001819	synonymous_variant	29886	exon6			CCTGTCGCGAAGC	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.708C>T	7.37:g.2304007G>A		29	0	0		31	11	0.354839	NM_013321	A4D207|Q96I67	Silent	SNP	ENST00000222990.3	37	CCDS5331.1																																																																																			.	.	none		0.552	SNX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322949.2			A	2304007	G	A	2304007	2	1	6	1	0	0	0	0	0	0	0	1	14923	1074	38	1		1	SNX8	7	2304007	Silent	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10		2304007	156834656	32	617											
ABCA13	154664	hgsc.bcm.edu	37	chr7	48318518	48318518	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtgaaagaaatagctacttTaaaaaaaatagatcatttca	20	12	5	4	0	2	3	2	1	0	2	2	3	2	3	0	0	2	1	0	0	9	6	rs544493291	byFrequency	TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	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	0.0014	5008	,	,		18836	0.0		0.0	False		,,,				2504	0.002				p.L2576X		Atlas-SNP	.											ABCA13_ENST00000435803,NS,carcinoma,-1,4	ABCA13	1192	4	0			c.T7727A						scavenged	.						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	7.37:g.48318518T>A	ENSP00000411096:p.Leu2576*	120	1	0.00833333		97	32	0.329897	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Nonsense_Mutation	SNP	ENST00000435803.1	37	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	.	.	none		0.318	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48318518	T	A	48318518	4	1	6	1	0	0	0	0	0	1	0	0	31	1764	61	5	7626	5	ABCA13	7	48318518	Nonsense_Mutation	SNP	T	TCGA-FA-A7DS-01A-11D-A382-10	46014511	48318518	110820145	33	618											
PCLO	27445	hgsc.bcm.edu	37	chr7	82583413	82583413	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtcagtagaaacagtgtcagCaactggcccttcaggtttag	11	10	11	9	0	3	1	3	0	0	1	3	1	3	1	1	2	3	3	1	2	4	4			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr7:82583413C>A	ENST00000333891.9	-	5	7193	c.6856G>T	c.(6856-6858)Gct>Tct	p.A2286S	PCLO_ENST00000423517.2_Missense_Mutation_p.A2286S	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						ACAGTGTCAGCAACTGGCCCT	0.403																																					p.A2286S		Atlas-SNP	.											.	PCLO	1506	.	0			c.G6856T						PASS	.						107	106	106					7																	82583413		1880	4119	5999	SO:0001583	missense	27445	exon5			TGTCAGCAACTGG	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.6856G>T	7.37:g.82583413C>A	ENSP00000334319:p.Ala2286Ser	189	0	0		166	52	0.313253	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	3.075	-0.190260	0.06299	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.16457	2.35;2.34	5.48	2.37	0.29283	.	.	.	.	.	T	0.09069	0.0224	N	0.12182	0.205	0.22066	N	0.999384	B;B	0.16396	0.017;0.017	B;B	0.12156	0.007;0.007	T	0.27706	-1.0066	9	0.87932	D	0	.	4.8141	0.13358	0.2214:0.5849:0.1068:0.0869	.	2286;2286	Q9Y6V0-5;Q9Y6V0-6	.;.	S	2217;2286;2286	ENSP00000334319:A2286S;ENSP00000388393:A2286S	ENSP00000334319:A2286S	A	-	1	0	PCLO	82421349	0.003000	0.15002	0.589000	0.28718	0.072000	0.16883	-0.115000	0.10741	0.667000	0.31107	-0.230000	0.12252	GCT	.	.	none		0.403	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82583413	C	A	82583413	3	1	6	1	0	0	0	0	1	0	0	0	11592	710	25	4	8673	4	PCLO	7	82583413	Missense_Mutation	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10	34264895	82583413	76555250	34	619											
KRIT1	889	hgsc.bcm.edu	37	chr7	91855062	91855062	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taattgcttccttcaacaatTttgcagcttcttcccagttg	8	17	5	11	0	2	0	1	0	1	0	4	0	4	0	2	0	4	4	2	0	3	9			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr7:91855062T>G	ENST00000340022.2	-	12	2244	c.1226A>C	c.(1225-1227)aAa>aCa	p.K409T	KRIT1_ENST00000394505.2_Missense_Mutation_p.K409T|KRIT1_ENST00000394507.1_Missense_Mutation_p.K409T|KRIT1_ENST00000394503.2_Missense_Mutation_p.K361T|KRIT1_ENST00000412043.2_Missense_Mutation_p.K409T	NM_004912.3|NM_194455.1	NP_004903.2|NP_919437.1	O00522	KRIT1_HUMAN	KRIT1, ankyrin repeat containing	409					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)			CTTCAACAATTTTGCAGCTTC	0.338																																					p.K409T		Atlas-SNP	.											KRIT1,NS,carcinoma,-1,1	KRIT1	66	1	0			c.A1226C						PASS	.						134	133	133					7																	91855062		2202	4300	6502	SO:0001583	missense	889	exon13			AACAATTTTGCAG	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.1226A>C	7.37:g.91855062T>G	ENSP00000344668:p.Lys409Thr	262	0	0		252	85	0.337302	NM_194456	A6NNU0|O43894|Q506L6|Q6U276|Q75N19|Q9H180|Q9H264|Q9HAX5	Missense_Mutation	SNP	ENST00000340022.2	37	CCDS5624.1	.	.	.	.	.	.	.	.	.	.	T	13.90	2.374446	0.42105	.	.	ENSG00000001631	ENST00000394507;ENST00000340022;ENST00000412043;ENST00000394505;ENST00000394503;ENST00000415227	T;T;T;T;T	0.70986	-0.53;-0.53;-0.53;-0.53;1.21	5.74	5.74	0.90152	Ankyrin repeat-containing domain (2);	0.097704	0.64402	D	0.000001	T	0.45418	0.1341	N	0.02539	-0.55	0.48571	D	0.999675	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.43540	-0.9385	10	0.33940	T	0.23	-3.9337	11.9614	0.53011	0.0:0.0:0.1447:0.8553	.	361;409	A6NNU0;O00522	.;KRIT1_HUMAN	T	409;409;409;409;361;409	ENSP00000378015:K409T;ENSP00000344668:K409T;ENSP00000410909:K409T;ENSP00000378013:K409T;ENSP00000378011:K361T	ENSP00000344668:K409T	K	-	2	0	KRIT1	91692998	1.000000	0.71417	0.999000	0.59377	0.973000	0.67179	4.715000	0.61909	2.168000	0.68352	0.533000	0.62120	AAA	.	.	none		0.338	KRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253910.1			G	91855062	T	G	91855062	3	3	6	1	0	0	0	0	1	0	0	0	8454	1841	64	5	1016	5	KRIT1	7	91855062	Missense_Mutation	SNP	T	TCGA-FA-A7DS-01A-11D-A382-10	9271649	91855062	67283601	35	620											
C7orf61	402573	hgsc.bcm.edu	37	chr7	100061611	100061611	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaataatcctttgccaagccCgtctaacccatcggaagaac	14	8	6	13	2	1	1	0	0	1	1	3	2	2	2	4	1	4	0	4	1	6	3			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr7:100061611C>T	ENST00000332375.3	-	1	283	c.38G>A	c.(37-39)cGg>cAg	p.R13Q	RN7SL161P_ENST00000582642.1_RNA|TSC22D4_ENST00000496728.1_5'UTR	NM_001004323.1	NP_001004323.1	Q8IZ16	CG061_HUMAN	chromosome 7 open reading frame 61	13						nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|prostate(1)|skin(1)	4						TTGCCAAGCCCGTCTAACCCA	0.532																																					p.R13Q		Atlas-SNP	.											.	C7orf61	12	.	0			c.G38A						PASS	.						60	56	57					7																	100061611		1940	4153	6093	SO:0001583	missense	402573	exon1			CAAGCCCGTCTAA		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.38G>A	7.37:g.100061611C>T	ENSP00000327732:p.Arg13Gln	77	0	0		82	27	0.329268	NM_001004323		Missense_Mutation	SNP	ENST00000332375.3	37	CCDS47661.1	.	.	.	.	.	.	.	.	.	.	C	4.827	0.153693	0.09185	.	.	ENSG00000185955	ENST00000332375	.	.	.	2.64	-0.9	0.10544	.	.	.	.	.	T	0.12305	0.0299	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30268	-0.9984	8	0.07030	T	0.85	-2.9938	4.6723	0.12694	0.0:0.5405:0.1821:0.2774	.	13	Q8IZ16	CG061_HUMAN	Q	13	.	ENSP00000327732:R13Q	R	-	2	0	C7orf61	99899547	0.000000	0.05858	0.000000	0.03702	0.379000	0.30106	-0.051000	0.11885	-0.822000	0.04306	-1.401000	0.01141	CGG	.	.	none		0.532	C7orf61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316976.2	NM_001004323		T	100061611	C	T	100061611	3	4	6	1	0	0	0	0	1	0	0	0	2410	652	23	1	594	1	C7orf61	7	100061611	Missense_Mutation	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10	8206549	100061611	59077052	36	621											
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121684560	121684560	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggacagtcatattcatgccTatgttaatgcactcctcatt	10	15	6	10	0	3	0	3	0	0	0	4	1	4	1	2	1	2	2	2	1	3	5			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr7:121684560T>C	ENST00000393386.2	+	23	6433	c.6022T>C	c.(6022-6024)Tat>Cat	p.Y2008H	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.Y1141H	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	2008					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						TATTCATGCCTATGTTAATGC	0.438																																					p.Y2008H		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.T6022C						PASS	.						156	142	147					7																	121684560		2203	4300	6503	SO:0001583	missense	5803	exon23			CATGCCTATGTTA	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.6022T>C	7.37:g.121684560T>C	ENSP00000377047:p.Tyr2008His	123	0	0		107	34	0.317757	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	T	18.34	3.602779	0.66445	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	T;T	0.11169	2.8;2.8	5.5	5.5	0.81552	.	0.000000	0.64402	D	0.000016	T	0.32041	0.0816	M	0.69823	2.125	0.80722	D	1	D;P;D	0.89917	1.0;0.614;1.0	D;P;D	0.91635	0.999;0.517;0.999	T	0.01988	-1.1234	10	0.33141	T	0.24	.	15.6052	0.76664	0.0:0.0:0.0:1.0	.	1147;1141;2008	P23471-2;C9JFM0;P23471	.;.;PTPRZ_HUMAN	H	2008;1141	ENSP00000377047:Y2008H;ENSP00000410000:Y1141H	ENSP00000377047:Y2008H	Y	+	1	0	PTPRZ1	121471796	1.000000	0.71417	0.999000	0.59377	0.512000	0.34134	8.040000	0.89188	2.091000	0.63221	0.533000	0.62120	TAT	.	.	none		0.438	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		C	121684560	T	C	121684560	3	2	6	1	0	0	0	0	1	0	0	0	12829	1522	53	3	6112	3	PTPRZ1	7	121684560	Missense_Mutation	SNP	T	TCGA-FA-A7DS-01A-11D-A382-10	21622949	121684560	37454103	37	622											
RP1L1	94137	hgsc.bcm.edu	37	chr8	10467580	10467580	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgtccttctccttctgttTctttagtttcctctaactgc	3	20	5	13	0	4	0	0	0	4	0	7	0	6	0	3	0	2	3	3	0	2	7	rs143686100		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr8:10467580T>G	ENST00000382483.3	-	4	4251	c.4028A>C	c.(4027-4029)gAa>gCa	p.E1343A		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1359	8 X 16 AA approximate tandem repeats of T-E-E-G-L-Q-E-E-G-V-Q-L-E-E-T-K.		Missing (in allele RP1L1-1).|Missing (in allele RP1L1-2).		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)		tccttctgtttctttagtttc	0.488																																					p.E1343A		Atlas-SNP	.											.	RP1L1	453	.	0			c.A4028C						PASS	.						88	79	82					8																	10467580		1936	4125	6061	SO:0001583	missense	94137	exon4			TCTGTTTCTTTAG	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.4028A>C	8.37:g.10467580T>G	ENSP00000371923:p.Glu1343Ala	207	0	0		206	21	0.101942	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	T	0.992	-0.693556	0.03303	.	.	ENSG00000183638	ENST00000382483	T	0.04862	3.54	1.84	-3.69	0.04450	.	.	.	.	.	T	0.02929	0.0087	N	0.08118	0	0.09310	N	1	B	0.21225	0.053	B	0.13407	0.009	T	0.44982	-0.9292	9	0.25751	T	0.34	.	8.9452	0.35753	0.0:0.1894:0.0:0.8106	.	1343	A6NKC6	.	A	1343	ENSP00000371923:E1343A	ENSP00000371923:E1343A	E	-	2	0	RP1L1	10504990	0.002000	0.14202	0.001000	0.08648	0.157000	0.22087	-0.507000	0.06352	-1.515000	0.01784	-1.216000	0.01612	GAA	.	.	none		0.488	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			G	10467580	T	G	10467580	3	3	6	1	0	0	0	0	1	0	0	0	13548	1783	62	5	3178	5	RP1L1	8	10467580	Missense_Mutation	SNP	T	TCGA-FA-A7DS-01A-11D-A382-10		10467580	135896442	38	623											
ZFPM2	23414	hgsc.bcm.edu	37	chr8	106815063	106815063	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagcataataaaatgtgagaAaaatgggaatttgaagcagc	20	8	10	3	0	0	2	0	2	0	1	0	4	0	3	0	1	3	2	0	1	8	3			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr8:106815063A>C	ENST00000407775.2	+	8	3003	c.2753A>C	c.(2752-2754)aAa>aCa	p.K918T	RP11-152P17.2_ENST00000520433.1_RNA|RP11-152P17.2_ENST00000518932.1_RNA|RP11-152P17.2_ENST00000524045.2_RNA|RP11-152P17.2_ENST00000509144.2_RNA|RP11-152P17.2_ENST00000520594.1_RNA|ZFPM2_ENST00000517361.1_Missense_Mutation_p.K786T|ZFPM2_ENST00000378472.4_Missense_Mutation_p.K649T|ZFPM2_ENST00000522296.1_3'UTR|RP11-152P17.2_ENST00000521622.1_RNA|ZFPM2_ENST00000520492.1_Missense_Mutation_p.K786T	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	918					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.K918I(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)			AAATGTGAGAAAAATGGGAAT	0.458																																					p.K918T		Atlas-SNP	.											ZFPM2,colon,carcinoma,0,1	ZFPM2	219	1	1	Substitution - Missense(1)	large_intestine(1)	c.A2753C						PASS	.						40	39	39					8																	106815063		1886	4115	6001	SO:0001583	missense	23414	exon8			GTGAGAAAAATGG	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.2753A>C	8.37:g.106815063A>C	ENSP00000384179:p.Lys918Thr	61	0	0		62	21	0.33871	NM_012082	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Missense_Mutation	SNP	ENST00000407775.2	37	CCDS47908.1	.	.	.	.	.	.	.	.	.	.	A	16.53	3.150059	0.57151	.	.	ENSG00000169946	ENST00000407775;ENST00000520492;ENST00000517361;ENST00000378472	T;T;T;T	0.24723	1.84;2.34;2.34;3.54	5.76	5.76	0.90799	.	0.042154	0.85682	D	0.000000	T	0.34221	0.0890	L	0.29908	0.895	0.80722	D	1	D	0.60575	0.988	P	0.57204	0.815	T	0.03555	-1.1025	10	0.42905	T	0.14	.	16.0709	0.80928	1.0:0.0:0.0:0.0	.	918	Q8WW38	FOG2_HUMAN	T	918;786;786;649	ENSP00000384179:K918T;ENSP00000430757:K786T;ENSP00000428720:K786T;ENSP00000367733:K649T	ENSP00000367733:K649T	K	+	2	0	ZFPM2	106884239	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.339000	0.96797	2.198000	0.70561	0.528000	0.53228	AAA	.	.	none		0.458	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1			C	106815063	A	C	106815063	3	2	6	1	0	0	0	0	1	0	0	0	17673	14	1	5	2783	5	ZFPM2	8	106815063	Missense_Mutation	SNP	A	TCGA-FA-A7DS-01A-11D-A382-10	96347483	106815063	39548959	39	624											
ELAVL2	1993	hgsc.bcm.edu	37	chr9	23762079	23762079	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagactctttagttcctcctGtgtcatgttctgaggaaggt	7	15	11	8	0	3	2	1	1	2	1	5	4	5	3	2	2	0	2	2	2	2	4			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr9:23762079G>A	ENST00000397312.2	-	2	428	c.154C>T	c.(154-156)Cag>Tag	p.Q52*	ELAVL2_ENST00000380110.4_Nonsense_Mutation_p.Q81*|ELAVL2_ENST00000462649.1_5'Flank|ELAVL2_ENST00000223951.6_Nonsense_Mutation_p.Q52*|ELAVL2_ENST00000380117.1_Nonsense_Mutation_p.Q52*|ELAVL2_ENST00000544538.1_Nonsense_Mutation_p.Q52*	NM_004432.3	NP_004423.2	Q12926	ELAV2_HUMAN	ELAV like neuron-specific RNA binding protein 2	52	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)		AGTTCCTCCTGTGTCATGTTC	0.403																																					p.Q52X		Atlas-SNP	.											ELAVL2,colon,carcinoma,+1,1	ELAVL2	80	1	0			c.C154T						PASS	.						253	231	238					9																	23762079		2203	4300	6503	SO:0001587	stop_gained	1993	exon2			CCTCCTGTGTCAT	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.154C>T	9.37:g.23762079G>A	ENSP00000380479:p.Gln52*	227	0	0		233	63	0.270386	NM_001171195	D3DRK3|Q13235|Q59G15|Q8NEM4|Q9H1Q8	Nonsense_Mutation	SNP	ENST00000397312.2	37	CCDS6515.1	.	.	.	.	.	.	.	.	.	.	G	39	7.566914	0.98361	.	.	ENSG00000107105	ENST00000223951;ENST00000397312;ENST00000544538;ENST00000380110;ENST00000380117;ENST00000359598;ENST00000440102	.	.	.	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	20.33	0.98713	0.0:0.0:1.0:0.0	.	.	.	.	X	52;52;52;52;52;80;52	.	ENSP00000223951:Q52X	Q	-	1	0	ELAVL2	23752079	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.993000	0.88291	2.810000	0.96702	0.585000	0.79938	CAG	.	.	none		0.403	ELAVL2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051943.2	NM_004432		A	23762079	G	A	23762079	4	1	6	1	0	0	0	0	0	1	0	0	5052	1386	48	2	949	2	ELAVL2	9	23762079	Nonsense_Mutation	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10		23762079	117451352	40	625											
ALDH1B1	219	hgsc.bcm.edu	37	chr9	38397089	38397089	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tatggcctggctgcggctgtGttcacccgggatctggacaa	6	10	14	11	2	2	0	1	0	1	0	2	2	2	2	2	5	1	3	2	5	2	2			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr9:38397089G>A	ENST00000377698.3	+	2	1497	c.1344G>A	c.(1342-1344)gtG>gtA	p.V448V		NM_000692.4	NP_000683.3	P30837	AL1B1_HUMAN	aldehyde dehydrogenase 1 family, member B1	448					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)		CTGCGGCTGTGTTCACCCGGG	0.577																																					p.V448V		Atlas-SNP	.											.	ALDH1B1	50	.	0			c.G1344A						PASS	.						65	63	64					9																	38397089		2203	4300	6503	SO:0001819	synonymous_variant	219	exon2			GGCTGTGTTCACC	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.1344G>A	9.37:g.38397089G>A		68	0	0		65	22	0.338462	NM_000692	B2R8F0|Q8WX76|Q9BV45	Silent	SNP	ENST00000377698.3	37	CCDS6615.1																																																																																			.	.	none		0.577	ALDH1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052492.1			A	38397089	G	A	38397089	2	1	6	1	0	0	0	0	0	0	0	1	493	1364	48	2		2	ALDH1B1	9	38397089	Silent	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	14635010	38397089	102816342	41	626											
DAPK1	1612	hgsc.bcm.edu	37	chr9	90219907	90219907	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaagaaatgccgtgagaaaaGcaccggcctccagtatgccg	13	5	12	11	3	0	2	0	1	0	2	1	4	1	2	5	1	3	2	5	1	5	1			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr9:90219907G>T	ENST00000408954.3	+	3	436	c.101G>T	c.(100-102)aGc>aTc	p.S34I	DAPK1_ENST00000469640.2_Missense_Mutation_p.S34I|DAPK1_ENST00000358077.5_Missense_Mutation_p.S34I|DAPK1_ENST00000491893.1_Missense_Mutation_p.S34I|DAPK1_ENST00000472284.1_Missense_Mutation_p.S34I	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	34	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						CGTGAGAAAAGCACCGGCCTC	0.498									Chronic Lymphocytic Leukemia, Familial Clustering of																												p.S34I		Atlas-SNP	.											DAPK1_ENST00000408954,NS,carcinoma,-1,1	DAPK1	329	1	0			c.G101T						PASS	.						35	36	36					9																	90219907		2039	4222	6261	SO:0001583	missense	1612	exon3	Familial Cancer Database	Familial CLL	AGAAAAGCACCGG	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.101G>T	9.37:g.90219907G>T	ENSP00000386135:p.Ser34Ile	78	0	0		80	24	0.3	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	37	CCDS43842.1	.	.	.	.	.	.	.	.	.	.	G	16.67	3.187348	0.57909	.	.	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	T;T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26;-0.26	5.04	5.04	0.67666	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	0.000022	T	0.69993	0.3173	L	0.37507	1.11	0.58432	D	0.999999	D;P;D	0.58620	0.983;0.598;0.977	P;B;P	0.54431	0.744;0.248;0.752	T	0.73522	-0.3956	10	0.72032	D	0.01	.	17.55	0.87873	0.0:0.0:1.0:0.0	.	34;34;34	B7ZLE7;B7Z454;P53355	.;.;DAPK1_HUMAN	I	34	ENSP00000350785:S34I;ENSP00000417076:S34I;ENSP00000418885:S34I;ENSP00000386135:S34I;ENSP00000419026:S34I	ENSP00000350785:S34I	S	+	2	0	DAPK1	89409727	1.000000	0.71417	0.993000	0.49108	0.814000	0.46013	3.649000	0.54417	2.628000	0.89032	0.511000	0.50034	AGC	.	.	none		0.498	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938		T	90219907	G	T	90219907	3	4	6	1	0	0	0	0	1	0	0	0	4237	971	34	4	107	4	DAPK1	9	90219907	Missense_Mutation	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	51822818	90219907	50993524	42	627											
ZFP37	7539	hgsc.bcm.edu	37	chr9	115818843	115818843	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcacagctctcaccgcggcGctggcctcgggctcggacac	6	6	12	17	5	2	0	2	0	1	0	5	1	2	1	2	4	1	3	2	4	0	0			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr9:115818843G>A	ENST00000374227.3	-	1	153	c.126C>T	c.(124-126)agC>agT	p.S42S	ZFP37_ENST00000555206.1_Silent_p.S42S|ZFP37_ENST00000553380.1_Silent_p.S42S	NM_001282515.1|NM_001282518.1	NP_001269444.1|NP_001269447.1	Q9Y6Q3	ZFP37_HUMAN	ZFP37 zinc finger protein	42	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						TCACCGCGGCGCTGGCCTCGG	0.592																																					p.S42S		Atlas-SNP	.											.	ZFP37	93	.	0			c.C126T						PASS	.						169	180	176					9																	115818843		2203	4300	6503	SO:0001819	synonymous_variant	7539	exon1			CGCGGCGCTGGCC	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.126C>T	9.37:g.115818843G>A		65	0	0		69	24	0.347826	NM_003408	A0AVJ9|B4DVX4|G3V3L7|Q5T7Q4	Silent	SNP	ENST00000374227.3	37	CCDS6787.1																																																																																			.	.	none		0.592	ZFP37-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055439.1	NM_003408		A	115818843	G	A	115818843	2	1	6	1	0	0	0	0	0	0	0	1	17663	1078	38	1		1	ZFP37	9	115818843	Silent	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	25598936	115818843	25394588	43	628											
LCN8	389812	hgsc.bcm.edu	37	chr9	139651501	139651501	+	IGR	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctcttacctgttatatgcAaccttcacggtcaggttact	8	14	7	12	1	3	0	2	0	1	0	3	0	3	0	3	2	4	3	3	2	5	5			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr9:139651501A>C	ENST00000316144.5	-	0	762				LCN8_ENST00000482893.1_5'UTR|LCN15_ENST00000482511.1_5'Flank|LCN8_ENST00000371688.3_Silent_p.V48V	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						TGTTATATGCAACCTTCACGG	0.632																																					p.V48V		Atlas-SNP	.											.	LCN8	14	.	0			c.T144G						PASS	.						45	40	42					9																	139651501		2203	4300	6503	SO:0001628	intergenic_variant	138307	exon2			ATATGCAACCTTC		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		9.37:g.139651501A>C		53	0	0		50	19	0.38	NM_178469		Silent	SNP	ENST00000316144.5	37	CCDS7006.1																																																																																			.	.	none		0.632	LCN15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055114.2	NM_203347		C	139651501	A	C	139651501	1	2	6	0	1	0	0	0	0	0	0	0	8695	117	5	5		5	LCN8	9	139651501	IGR	SNP	A	TCGA-FA-A7DS-01A-11D-A382-10	23832658	139651501	1561930	44	629											
ITIH5	80760	hgsc.bcm.edu	37	chr10	7679231	7679231	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctctgcctgctgttgtgaagCggcagcacctccagggatgc	6	9	13	13	1	1	1	0	1	1	0	2	2	2	2	3	2	5	4	3	2	1	1			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr10:7679231C>T	ENST00000256861.6	-	5	690	c.612G>A	c.(610-612)ccG>ccA	p.P204P	ITIH5_ENST00000434980.1_5'UTR|ITIH5_ENST00000446830.2_5'UTR|ITIH5_ENST00000397146.2_Silent_p.P204P|ITIH5_ENST00000397145.2_Silent_p.P204P	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	204					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						TGTTGTGAAGCGGCAGCACCT	0.647																																					p.P204P		Atlas-SNP	.											.	ITIH5	343	.	0			c.G612A						PASS	.						83	87	86					10																	7679231		2203	4300	6503	SO:0001819	synonymous_variant	80760	exon5			GTGAAGCGGCAGC			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.612G>A	10.37:g.7679231C>T		36	0	0		33	16	0.484848	NM_001001851	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Silent	SNP	ENST00000256861.6	37																																																																																				.	.	none		0.647	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569		T	7679231	C	T	7679231	2	4	6	1	0	0	0	0	0	0	0	1	7916	755	27	1		1	ITIH5	10	7679231	Silent	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10		7679231	127855516	45	630											
AGAP6	414189	hgsc.bcm.edu	37	chr10	51769455	51769455	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatctctggagctggatgacTggccagttgagctcaggaag	9	9	15	8	0	2	2	1	2	1	0	3	6	2	5	1	4	2	3	1	4	1	1			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr10:51769455T>C	ENST00000374056.4	+	7	1899	c.1501T>C	c.(1501-1503)Tgg>Cgg	p.W501R	AGAP6_ENST00000412531.3_Missense_Mutation_p.W524R			Q5VW22	AGAP6_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 6	501	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(1)|lung(8)|prostate(3)|skin(1)|stomach(2)	29						GCTGGATGACTGGCCAGTTGA	0.522																																					p.W524R		Atlas-SNP	.											.	AGAP6	53	.	0			c.T1570C						PASS	.																																			SO:0001583	missense	414189	exon8			GATGACTGGCCAG		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.1501T>C	10.37:g.51769455T>C	ENSP00000363168:p.Trp501Arg	38	0	0		39	11	0.282051	NM_001077665		Missense_Mutation	SNP	ENST00000374056.4	37		.	.	.	.	.	.	.	.	.	.	.	13.13	2.145491	0.37825	.	.	ENSG00000204149	ENST00000374056;ENST00000412531	.	.	.	0.0465	0.0465	0.14256	.	0.000000	0.85682	D	0.000000	D	0.86439	0.5933	H	0.99746	4.745	0.53005	D	0.999966	D	0.89917	1.0	D	0.79108	0.992	T	0.81400	-0.0950	9	0.87932	D	0	.	4.565	0.12180	0.0:6.0E-4:0.0:0.9994	.	524	C9IYN2	.	R	524;501	.	ENSP00000363168:W524R	W	+	1	0	AGAP6	51439461	1.000000	0.71417	0.073000	0.20177	0.073000	0.16967	5.349000	0.66010	0.115000	0.18071	0.113000	0.15668	TGG	.	.	none		0.522	AGAP6-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_001077665		C	51769455	T	C	51769455	3	2	6	1	0	0	0	0	1	0	0	0	372	1580	55	3	1600	3	AGAP6	10	51769455	Missense_Mutation	SNP	T	TCGA-FA-A7DS-01A-11D-A382-10	44090224	51769455	83765292	46	631											
NEURL	9148	hgsc.bcm.edu	37	chr10	105331517	105331517	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcttcagcggggtccgcaCggccgacccgctctgggccc	3	7	14	17	5	3	0	1	0	2	0	4	1	4	0	4	4	1	3	4	4	0	2			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr10:105331517C>T	ENST00000369780.4	+	3	996	c.587C>T	c.(586-588)aCg>aTg	p.T196M	NEURL_ENST00000369777.2_Missense_Mutation_p.T179M|NEURL_ENST00000465048.1_3'UTR	NM_004210.4	NP_004201.3	O76050	NEUL1_HUMAN		196	NHR 1. {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)	p.T196M(1)		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)		GGGGTCCGCACGGCCGACCCG	0.652																																					p.T196M		Atlas-SNP	.											NEURL,NS,lymphoid_neoplasm,0,1	NEURL	38	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C587T						PASS	.						119	83	95					10																	105331517		2203	4300	6503	SO:0001583	missense	9148	exon3			TCCGCACGGCCGA																												ENST00000369780.4:c.587C>T	10.37:g.105331517C>T	ENSP00000358795:p.Thr196Met	83	0	0		80	30	0.375	NM_004210	Q5TDR2|Q5TDR3|Q8TAN0|Q9H463	Missense_Mutation	SNP	ENST00000369780.4	37	CCDS7551.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.034705	0.75617	.	.	ENSG00000107954	ENST00000369780;ENST00000437579;ENST00000369777	T;T	0.30981	1.51;1.51	5.64	5.64	0.86602	NEUZ (1);	0.047098	0.85682	D	0.000000	T	0.35970	0.0950	L	0.38838	1.175	0.53688	D	0.999976	D	0.65815	0.995	P	0.53185	0.72	T	0.07309	-1.0779	10	0.66056	D	0.02	-25.4468	12.0702	0.53611	0.0:0.9218:0.0:0.0782	.	196	O76050	NEU1A_HUMAN	M	196;179;179	ENSP00000358795:T196M;ENSP00000358792:T179M	ENSP00000358792:T179M	T	+	2	0	NEURL	105321507	0.002000	0.14202	0.971000	0.41717	0.856000	0.48823	0.869000	0.27996	2.648000	0.89879	0.561000	0.74099	ACG	.	.	none		0.652	NEURL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050170.1			T	105331517	C	T	105331517	3	4	6	1	0	0	0	0	1	0	0	0	10354	536	19	1	597	1	NEURL	10	105331517	Missense_Mutation	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10	53562062	105331517	30203230	47	632											
TACC2	10579	hgsc.bcm.edu	37	chr10	123843062	123843062	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacgcagagctgccctggggCttgccaagtcctgccctggt	5	8	13	15	1	0	1	0	0	0	1	1	1	1	1	4	3	4	3	4	3	1	1			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr10:123843062C>T	ENST00000369005.1	+	4	1387	c.1047C>T	c.(1045-1047)ggC>ggT	p.G349G	TACC2_ENST00000513429.1_Intron|TACC2_ENST00000515603.1_Silent_p.G349G|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515273.1_Silent_p.G349G|TACC2_ENST00000453444.2_Silent_p.G349G|TACC2_ENST00000334433.3_Silent_p.G349G	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	349					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)				TGCCCTGGGGCTTGCCAAGTC	0.627																																					p.G349G		Atlas-SNP	.											.	TACC2	271	.	0			c.C1047T						PASS	.						31	36	34					10																	123843062		2203	4298	6501	SO:0001819	synonymous_variant	10579	exon4			CTGGGGCTTGCCA	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.1047C>T	10.37:g.123843062C>T		48	0	0		52	14	0.269231	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	37	CCDS7626.1																																																																																			.	.	none		0.627	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			T	123843062	C	T	123843062	2	4	6	1	0	0	0	0	0	0	0	1	15517	784	28	2		2	TACC2	10	123843062	Silent	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10	18511545	123843062	11691685	48	633											
TACC2	10579	hgsc.bcm.edu	37	chr10	123987498	123987498	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gctggaggccatgggcttggGcaccccttcagaagcgattg	7	8	15	11	1	1	1	1	0	0	1	1	3	1	2	3	4	1	3	3	4	1	3	rs114249776	byFrequency	TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr10:123987498G>A	ENST00000369005.1	+	14	8211	c.7871G>A	c.(7870-7872)gGc>gAc	p.G2624D	TACC2_ENST00000513429.1_Missense_Mutation_p.G770D|TACC2_ENST00000515603.1_Missense_Mutation_p.G2579D|TACC2_ENST00000369000.1_Missense_Mutation_p.G324D|TACC2_ENST00000358010.1_Missense_Mutation_p.G770D|TACC2_ENST00000369001.1_Missense_Mutation_p.G328D|TACC2_ENST00000360561.3_Missense_Mutation_p.G702D|TACC2_ENST00000515273.1_Missense_Mutation_p.G2628D|TACC2_ENST00000368999.1_Missense_Mutation_p.G714D|TACC2_ENST00000369004.3_Missense_Mutation_p.G714D|TACC2_ENST00000260733.3_Missense_Mutation_p.G702D|TACC2_ENST00000453444.2_Missense_Mutation_p.G2628D|TACC2_ENST00000334433.3_Missense_Mutation_p.G2624D	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	2624					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)				ATGGGCTTGGGCACCCCTTCA	0.572													G|||	3	0.000599042	0.0023	0.0	5008	,	,		18322	0.0		0.0	False		,,,				2504	0.0				p.G2624D		Atlas-SNP	.											.	TACC2	271	.	0			c.G7871A						PASS	.	G	ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY	6,4400	11.4+/-27.6	0,6,2197	77	81	80		2105,2105,2309,7871	5.2	1	10	dbSNP_132	80	0,8600		0,0,4300	yes	missense,missense,missense,missense	TACC2	NM_006997.2,NM_206860.1,NM_206861.1,NM_206862.2	94,94,94,94	0,6,6497	AA,AG,GG		0.0,0.1362,0.0461	probably-damaging,probably-damaging,probably-damaging,probably-damaging	702/1027,702/997,770/1095,2624/2949	123987498	6,13000	2203	4300	6503	SO:0001583	missense	10579	exon14			GCTTGGGCACCCC	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.7871G>A	10.37:g.123987498G>A	ENSP00000358001:p.Gly2624Asp	48	0	0		52	20	0.384615	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	15.95	2.983285	0.53827	0.001362	0.0	ENSG00000138162	ENST00000369005;ENST00000513429;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000358010;ENST00000453444;ENST00000340076;ENST00000369001;ENST00000369000;ENST00000360561;ENST00000368999;ENST00000369004;ENST00000260733;ENST00000496913	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.18657	3.71;3.4;4.04;4.01;3.71;3.4;4.04;2.2;2.2;3.23;3.27;3.22;3.27;2.4	5.25	5.25	0.73442	.	0.000000	0.37623	N	0.002017	T	0.33235	0.0856	L	0.29908	0.895	0.53688	D	0.999977	D;D;D;D;D;D;D;D;D	0.89917	0.999;1.0;0.999;0.999;0.998;0.999;0.982;0.999;1.0	D;D;D;D;D;D;P;D;D	0.97110	0.986;1.0;0.986;0.986;0.966;0.973;0.881;0.973;0.995	T	0.02553	-1.1142	10	0.15066	T	0.55	-21.8403	17.3979	0.87451	0.0:0.0:1.0:0.0	.	2628;714;2579;2628;702;702;324;770;2624	E9PBC6;D6RAA5;E7EMZ9;B7ZMJ9;O95359-6;O95359-1;O95359-2;O95359-5;O95359	.;.;.;.;.;.;.;.;TACC2_HUMAN	D	2624;770;2628;2579;2624;770;2628;2614;328;324;702;714;714;702;359	ENSP00000358001:G2624D;ENSP00000425062:G770D;ENSP00000424467:G2628D;ENSP00000427618:G2579D;ENSP00000334280:G2624D;ENSP00000350701:G770D;ENSP00000395048:G2628D;ENSP00000357997:G328D;ENSP00000357996:G324D;ENSP00000353763:G702D;ENSP00000357995:G714D;ENSP00000422815:G714D;ENSP00000260733:G702D;ENSP00000422725:G359D	ENSP00000260733:G702D	G	+	2	0	TACC2	123977488	1.000000	0.71417	0.974000	0.42286	0.024000	0.10985	4.505000	0.60421	2.618000	0.88619	0.655000	0.94253	GGC	G|0.999;A|0.001	0.001	strong		0.572	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			A	123987498	G	A	123987498	3	1	6	1	0	0	0	0	1	0	0	0	15517	1203	42	2	7993	2	TACC2	10	123987498	Missense_Mutation	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	144436	123987498	11547249	49	634											
MUC2	4583	hgsc.bcm.edu	37	chr11	1092688	1092689	+	In_Frame_Ins	INS	-	-	CAA																															aaccaccactcccagccctcINScaacgactacgcccatcact																										TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr11:1092688_1092689insCAA	ENST00000441003.2	+	30	4534_4535	c.4507_4508insCAA	c.(4507-4509)cca>cCAAca	p.1506_1507insT	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_In_Frame_Ins_p.1507_1508insT|MUC2_ENST00000333592.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4241	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)	tcccagccctccaacgactacg	0.634																																					p.P1503delinsPT		Atlas-Indel	.											.	MUC2	614	.	0			c.4507_4508insCAA						PASS	.																																			SO:0001652	inframe_insertion	4583	exon30			.	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.4508_4510dupCAA	11.37:g.1092689_1092691dupCAA	ENSP00000415183:p.Thr1506_Thr1506dup	122	0	0		119	13	0.109244	NM_002457	Q14878	In_Frame_Ins	INS	ENST00000441003.2	37																																																																																				.	.	none		0.634	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		CAA	1092689	-	CAA	1092688	7	5	6	1	0	1	1	0	0	0	0	0	9984	855	30	0	4625	0	MUC2	11	1092688	In_Frame_Ins	INS	-	TCGA-FA-A7DS-01A-11D-A382-10		1092688	133913828	50	635											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1260239	1260239	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggcctgtgtgtgtcctggCggactccggacacctgccgt	3	9	15	14	4	0	0	0	0	0	0	2	2	2	2	5	4	1	0	5	4	0	0	rs374136981	byFrequency	TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr11:1260239C>A	ENST00000529681.1	+	26	3494	c.3436C>A	c.(3436-3438)Cgg>Agg	p.R1146R	MUC5B_ENST00000447027.1_Silent_p.R1149R	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1146	Cys-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)		TGTGTCCTGGCGGACTCCGGA	0.687													C|||	3	0.000599042	0.0	0.0014	5008	,	,		14063	0.0		0.001	False		,,,				2504	0.001				p.R1146R		Atlas-SNP	.											.	MUC5B	473	.	0			c.C3436A						PASS	.	C		0,4268		0,0,2134	11	16	14		3436	-7.6	0.6	11		14	1,8413		0,1,4206	no	coding-synonymous	MUC5B	NM_002458.2		0,1,6340	AA,AC,CC		0.0119,0.0,0.0079		1146/5763	1260239	1,12681	2134	4207	6341	SO:0001819	synonymous_variant	727897	exon26			TCCTGGCGGACTC	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.3436C>A	11.37:g.1260239C>A		94	0	0		77	26	0.337662	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			.	.	weak		0.687	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1260239	C	A	1260239	2	1	6	1	0	0	0	0	0	0	0	1	9988	759	27	4		4	MUC5B	11	1260239	Silent	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10	167551	1260239	133746277	51	636											
FGF3	2248	hgsc.bcm.edu	37	chr11	69625283	69625283	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agggaggacttctgtgtgcgGcgggtcttgaagcccctgcg	5	9	17	10	3	2	1	0	1	2	0	2	3	2	3	2	4	3	0	2	4	1	2			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr11:69625283G>A	ENST00000334134.2	-	3	600	c.510C>T	c.(508-510)cgC>cgT	p.R170R		NM_005247.2	NP_005238.1	P11487	FGF3_HUMAN	fibroblast growth factor 3	170					anatomical structure morphogenesis (GO:0009653)|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)|negative regulation of cardiac muscle tissue development (GO:0055026)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ induction (GO:0001759)|otic vesicle formation (GO:0030916)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|post-anal tail morphogenesis (GO:0036342)|semicircular canal morphogenesis (GO:0048752)|signal transduction (GO:0007165)|thymus development (GO:0048538)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)	growth factor activity (GO:0008083)	p.R170R(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|urinary_tract(1)	13			LUSC - Lung squamous cell carcinoma(11;5.05e-15)|STAD - Stomach adenocarcinoma(18;0.0278)			TCTGTGTGCGGCGGGTCTTGA	0.682																																					p.R170R		Atlas-SNP	.											FGF3,NS,carcinoma,0,1	FGF3	27	1	1	Substitution - coding silent(1)	ovary(1)	c.C510T						PASS	.						21	24	23					11																	69625283		2193	4270	6463	SO:0001819	synonymous_variant	2248	exon3			TGTGCGGCGGGTC		CCDS8195.1	11q13	2010-06-25	2010-06-25		ENSG00000186895	ENSG00000186895			3681	protein-coding gene	gene with protein product	"INT-2 proto-oncogene protein", "oncogene INT2", "V-INT2 murine mammary tumor virus integration site oncogene homolog", "murine mammary tumor virus integration site 2, mouse"	164950	"fibroblast growth factor 3 (murine mammary tumor virus integration site (v-int-2) oncogene homolog)"	INT2			Standard	NM_005247		Approved	HBGF-3	uc001oph.3	P11487	OTTHUMG00000167888	ENST00000334134.2:c.510C>T	11.37:g.69625283G>A		144	0	0		99	7	0.0707071	NM_005247	Q0VG69	Silent	SNP	ENST00000334134.2	37	CCDS8195.1																																																																																			.	.	none		0.682	FGF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396835.1	NM_005247		A	69625283	G	A	69625283	2	1	6	1	0	0	0	0	0	0	0	1	5861	1190	42	2		2	FGF3	11	69625283	Silent	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	68365044	69625283	65381233	52	637											
SERPINH1	871	hgsc.bcm.edu	37	chr11	75277917	75277917	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcgcgctgcagtccatcaacGagtgggccgcgcagaccacc	8	4	13	16	5	1	1	1	0	0	1	2	2	2	1	4	1	2	3	4	1	1	0			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr11:75277917G>A	ENST00000524558.1	+	2	1958	c.523G>A	c.(523-525)Gag>Aag	p.E175K	SERPINH1_ENST00000530284.1_Missense_Mutation_p.E175K|SERPINH1_ENST00000358171.3_Missense_Mutation_p.E175K|SERPINH1_ENST00000525876.1_5'Flank|SERPINH1_ENST00000533603.1_Missense_Mutation_p.E175K			P50454	SERPH_HUMAN	serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	175					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)					GTCCATCAACGAGTGGGCCGC	0.627																																					p.E175K		Atlas-SNP	.											.	SERPINH1	33	.	0			c.G523A						PASS	.						42	43	43					11																	75277917		2200	4293	6493	SO:0001583	missense	871	exon2			ATCAACGAGTGGG	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.523G>A	11.37:g.75277917G>A	ENSP00000434412:p.Glu175Lys	39	0	0		58	22	0.37931	NM_001235	B3KVJ3|P29043|Q5XPB4|Q6NSJ6|Q8IY96|Q9NP88	Missense_Mutation	SNP	ENST00000524558.1	37	CCDS8239.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.694570	0.88830	.	.	ENSG00000149257	ENST00000533603;ENST00000358171;ENST00000526397;ENST00000421448;ENST00000525492;ENST00000530284;ENST00000532356;ENST00000524558;ENST00000525611;ENST00000528760	D;D;D;T;D;D;D;D;D	0.87491	-2.26;-2.26;-2.26;-0.84;-2.26;-2.26;-2.26;-2.26;-2.26	4.66	4.66	0.58398	Serpin domain (3);	0.000000	0.85682	D	0.000000	D	0.86981	0.6064	L	0.32530	0.975	0.80722	D	1	D;D	0.63880	0.988;0.993	P;P	0.56216	0.752;0.794	D	0.86178	0.1604	10	0.34782	T	0.22	.	15.0624	0.71964	0.0:0.0:1.0:0.0	.	175;175	E9PPV6;P50454	.;SERPH_HUMAN	K	175;175;175;154;128;175;175;175;175;175	ENSP00000434657:E175K;ENSP00000350894:E175K;ENSP00000434964:E175K;ENSP00000434482:E128K;ENSP00000436305:E175K;ENSP00000436040:E175K;ENSP00000434412:E175K;ENSP00000435452:E175K;ENSP00000437108:E175K	ENSP00000350894:E175K	E	+	1	0	SERPINH1	74955565	1.000000	0.71417	0.999000	0.59377	0.927000	0.56198	7.850000	0.86915	2.140000	0.66376	0.563000	0.77884	GAG	.	.	none		0.627	SERPINH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383610.1	NM_004353		A	75277917	G	A	75277917	3	1	6	1	0	0	0	0	1	0	0	0	14132	1059	37	1	525	1	SERPINH1	11	75277917	Missense_Mutation	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	5652634	75277917	59728599	53	638											
ODZ4	26011	hgsc.bcm.edu	37	chr11	78516504	78516504	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	attcgcctctcacgcagacaCcccggcctgaacatgtgggg	8	7	11	15	3	1	2	1	1	1	1	3	2	1	2	4	3	1	1	4	3	1	1			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr11:78516504C>A	ENST00000278550.7	-	15	2474	c.2012G>T	c.(2011-2013)gGt>gTt	p.G671V		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	671	EGF-like 4. {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)										CACGCAGACACCCCGGCCTGA	0.572																																					p.G671V		Atlas-SNP	.											.	.	.	.	0			c.G2012T						PASS	.						34	39	37					11																	78516504		2136	4245	6381	SO:0001583	missense	26011	exon15			CAGACACCCCGGC	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.2012G>T	11.37:g.78516504C>A	ENSP00000278550:p.Gly671Val	23	0	0		24	11	0.458333	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	37	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.929751	0.92389	.	.	ENSG00000149256	ENST00000278550	T	0.14516	2.5	5.1	5.1	0.69264	Epidermal growth factor-like (1);	0.000000	0.85682	D	0.000000	T	0.56455	0.1986	H	0.98111	4.15	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.74654	-0.3593	9	.	.	.	.	18.7262	0.91714	0.0:1.0:0.0:0.0	.	671	Q6N022	TEN4_HUMAN	V	671	ENSP00000278550:G671V	.	G	-	2	0	ODZ4	78194152	1.000000	0.71417	0.980000	0.43619	0.958000	0.62258	7.651000	0.83577	2.644000	0.89710	0.563000	0.77884	GGT	.	.	none		0.572	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			A	78516504	C	A	78516504	3	1	6	1	0	0	0	0	1	0	0	0	10846	507	18	4	6377	4	ODZ4	11	78516504	Missense_Mutation	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10	3238587	78516504	56490012	54	639											
ANKK1	255239	hgsc.bcm.edu	37	chr11	113264381	113264381	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgctggaagctcaggttcCgcatcatccatgagaccagc	9	9	10	13	1	3	1	2	1	1	1	5	3	5	2	3	2	3	4	3	2	1	1	rs370146394		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr11:113264381C>T	ENST00000303941.3	+	2	458	c.364C>T	c.(364-366)Cgc>Tgc	p.R122C		NM_178510.1	NP_848605.1	Q8NFD2	ANKK1_HUMAN	ankyrin repeat and kinase domain containing 1	122	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> H (in dbSNP:rs35877321). {ECO:0000269|PubMed:17344846}.				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)		GCTCAGGTTCCGCATCATCCA	0.582													C|||	1	0.000199681	0.0	0.0	5008	,	,		18780	0.0		0.0	False		,,,				2504	0.001				p.R122C		Atlas-SNP	.											ANKK1,NS,carcinoma,0,1	ANKK1	83	1	0			c.C364T						PASS	.	C	CYS/ARG	1,4287		0,1,2143	56	59	58		364	0.9	0.2	11		58	1,8545		0,1,4272	no	missense	ANKK1	NM_178510.1	180	0,2,6415	TT,TC,CC		0.0117,0.0233,0.0156	probably-damaging	122/766	113264381	2,12832	2144	4273	6417	SO:0001583	missense	255239	exon2			AGGTTCCGCATCA	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.364C>T	11.37:g.113264381C>T	ENSP00000306678:p.Arg122Cys	76	0	0		81	27	0.333333	NM_178510		Missense_Mutation	SNP	ENST00000303941.3	37	CCDS44734.1	.	.	.	.	.	.	.	.	.	.	C	9.604	1.129502	0.21041	2.33E-4	1.17E-4	ENSG00000170209	ENST00000303941	D	0.83075	-1.68	4.84	0.896	0.19253	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.234553	0.29172	N	0.012939	T	0.80939	0.4720	M	0.84511	2.7	0.49299	D	0.999779	B	0.15930	0.015	B	0.19148	0.024	T	0.72567	-0.4254	10	0.54805	T	0.06	-4.813	5.6091	0.17396	0.1376:0.6401:0.0:0.2223	.	122	Q8NFD2	ANKK1_HUMAN	C	122	ENSP00000306678:R122C	ENSP00000306678:R122C	R	+	1	0	ANKK1	112769591	0.939000	0.31865	0.191000	0.23289	0.100000	0.18952	0.838000	0.27572	0.006000	0.14734	-0.379000	0.06801	CGC	.	.	weak		0.582	ANKK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395830.1	NM_178510		T	113264381	C	T	113264381	3	4	6	1	0	0	0	0	1	0	0	0	631	652	23	1	370	1	ANKK1	11	113264381	Missense_Mutation	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10	34747877	113264381	21742135	55	640											
TRIM29	23650	hgsc.bcm.edu	37	chr11	120008144	120008144	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccctccaggtggggcttgAgatgcagctcgcagaaggag	8	6	16	11	2	0	2	0	1	0	2	2	4	1	3	2	4	2	4	2	4	1	1			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr11:120008144A>G	ENST00000341846.5	-	1	1017	c.596T>C	c.(595-597)cTc>cCc	p.L199P		NM_012101.3	NP_036233.2	Q14134	TRI29_HUMAN	tripartite motif containing 29	199					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)		GTGGGGCTTGAGATGCAGCTC	0.652																																					p.L199P		Atlas-SNP	.											.	TRIM29	78	.	0			c.T596C						PASS	.						33	34	34					11																	120008144		2203	4300	6503	SO:0001583	missense	23650	exon1			GGCTTGAGATGCA	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.596T>C	11.37:g.120008144A>G	ENSP00000343129:p.Leu199Pro	23	0	0		26	14	0.538462	NM_012101	Q96AA9|Q9BZY7	Missense_Mutation	SNP	ENST00000341846.5	37	CCDS8428.1	.	.	.	.	.	.	.	.	.	.	A	26.8	4.773588	0.90108	.	.	ENSG00000137699	ENST00000341846	T	0.55760	0.5	5.91	5.91	0.95273	.	0.000000	0.64402	D	0.000007	T	0.79522	0.4460	M	0.92317	3.295	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.84585	0.0663	9	.	.	.	.	16.3483	0.83171	1.0:0.0:0.0:0.0	.	199	Q14134	TRI29_HUMAN	P	199	ENSP00000343129:L199P	.	L	-	2	0	TRIM29	119513354	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.326000	0.96389	2.254000	0.74563	0.533000	0.62120	CTC	.	.	none		0.652	TRIM29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277108.2	NM_012101		G	120008144	A	G	120008144	3	3	6	1	0	0	0	0	1	0	0	0	16518	304	11	3	1206	3	TRIM29	11	120008144	Missense_Mutation	SNP	A	TCGA-FA-A7DS-01A-11D-A382-10	6743763	120008144	14998372	56	641											
VWF	7450	hgsc.bcm.edu	37	chr12	6076733	6076733	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acctgcaccatgcagcggcaGgtcgtgcacacatcgatcat	10	7	10	14	3	1	0	1	0	0	0	3	1	1	0	2	2	4	4	2	2	0	0			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr12:6076733G>T	ENST00000261405.5	-	47	8060	c.7806C>A	c.(7804-7806)acC>acA	p.T2602T		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	2602	VWFC 3. {ECO:0000255|PROSITE- ProRule:PRU00220}.				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)	TGCAGCGGCAGGTCGTGCACA	0.627																																					p.T2602T		Atlas-SNP	.											.	VWF	338	.	0			c.C7806A						PASS	.						147	136	139					12																	6076733		2203	4300	6503	SO:0001819	synonymous_variant	7450	exon47			GCGGCAGGTCGTG		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.7806C>A	12.37:g.6076733G>T		44	0	0		31	18	0.580645	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																			.	.	none		0.627	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		T	6076733	G	T	6076733	2	4	6	1	0	0	0	0	0	0	0	1	17261	987	35	4		4	VWF	12	6076733	Silent	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10		6076733	127775162	57	642											
NOP2	4839	hgsc.bcm.edu	37	chr12	6672843	6672843	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	atccacattgatctgcaggcCcccatctgcctcttccacct	7	11	5	18	0	3	1	0	1	3	0	5	1	5	1	6	1	2	1	6	1	0	2			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr12:6672843C>T	ENST00000322166.5	-	7	746	c.625G>A	c.(625-627)Ggc>Agc	p.G209S	NOP2_ENST00000541778.1_Missense_Mutation_p.G205S|NOP2_ENST00000545200.1_Missense_Mutation_p.G205S|NOP2_ENST00000542015.1_Intron|NOP2_ENST00000537442.1_Missense_Mutation_p.G209S|NOP2_ENST00000399466.2_Missense_Mutation_p.G205S|NOP2_ENST00000382421.3_Missense_Mutation_p.G242S	NM_001258308.1|NM_006170.3	NP_001245237.1|NP_006161.2	P46087	NOP2_HUMAN	NOP2 nucleolar protein	209					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						ATCTGCAGGCCCCCATCTGCC	0.562											OREG0021630	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G242S		Atlas-SNP	.											.	NOP2	44	.	0			c.G724A						PASS	.						46	49	48					12																	6672843		1952	4122	6074	SO:0001583	missense	4839	exon8			GCAGGCCCCCATC		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.625G>A	12.37:g.6672843C>T	ENSP00000313272:p.Gly209Ser	71	0	0	635	68	27	0.397059	NM_001258309	A1A4Z3|B3KPD6|Q05BA7|Q0P5S5|Q3KQS4|Q58F30	Missense_Mutation	SNP	ENST00000322166.5	37	CCDS58203.1	.	.	.	.	.	.	.	.	.	.	C	11.37	1.619302	0.28801	.	.	ENSG00000111641	ENST00000537442;ENST00000382421;ENST00000545200;ENST00000399466;ENST00000322166;ENST00000541778;ENST00000542944;ENST00000542867	T;T;T;T;T;T;T;T	0.41400	2.53;2.56;2.57;2.53;2.53;2.53;1.0;1.0	5.71	3.86	0.44501	.	0.749013	0.13235	N	0.403359	T	0.27866	0.0686	L	0.33485	1.01	0.22354	N	0.999173	B;B	0.16603	0.01;0.018	B;B	0.12837	0.005;0.008	T	0.20538	-1.0272	10	0.14252	T	0.57	-1.761	6.8458	0.23987	0.0:0.6965:0.1459:0.1576	.	242;205	Q3KQS4;P46087-2	.;.	S	209;242;205;205;209;205;85;205	ENSP00000444437:G209S;ENSP00000371858:G242S;ENSP00000439422:G205S;ENSP00000382392:G205S;ENSP00000313272:G209S;ENSP00000443150:G205S;ENSP00000440754:G85S;ENSP00000443035:G205S	ENSP00000313272:G209S	G	-	1	0	NOP2	6543104	0.000000	0.05858	0.073000	0.20177	0.978000	0.69477	0.508000	0.22692	1.395000	0.46643	0.462000	0.41574	GGC	.	.	none		0.562	NOP2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402614.1	NM_006170		T	6672843	C	T	6672843	3	4	6	1	0	0	0	0	1	0	0	0	10547	623	22	2	1853	2	NOP2	12	6672843	Missense_Mutation	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10	596110	6672843	127179052	58	643											
ETV6	2120	hgsc.bcm.edu	37	chr12	11803094	11803094	+	Splice_Site	SNP	G	G	C																															cctgctcagtgtagcattaaGgtaaaaatcttctcccctcc																								rs547638904		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr12:11803094G>C	ENST00000396373.4	+	1	307	c.33G>C	c.(31-33)aaG>aaC	p.K11N	ETV6_ENST00000544715.1_3'UTR	NM_001987.4	NP_001978.1	P41212	ETV6_HUMAN	ets variant 6	11		Breakpoint for translocation to form CHIC2-ETV6 in AML.			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)				GTAGCATTAAGGTAAAAATCT	0.537			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.K11N		Atlas-SNP	.		Dom	yes		12	12p13	2120	ets variant gene 6 (TEL oncogene)		"L, E, M"	.	ETV6	91	.	0			c.G33C						PASS	.						136	133	134					12																	11803094		2203	4300	6503	SO:0001630	splice_region_variant	2120	exon1			CATTAAGGTAAAA	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.33+1G>C	12.37:g.11803094G>C		47	0	0		25	16	0.64	NM_001987	A3QVP6|A8K076|Q9UMF6|Q9UMF7|Q9UMG0	Missense_Mutation	SNP	ENST00000396373.4	37	CCDS8643.1	.	.	.	.	.	.	.	.	.	.	G	12.63	1.995060	0.35226	.	.	ENSG00000139083	ENST00000396373	T	0.09255	3.0	4.11	3.2	0.36748	.	0.964265	0.08491	N	0.937964	T	0.07954	0.0199	L	0.27053	0.805	0.80722	D	1	B	0.23650	0.089	B	0.22152	0.038	T	0.24154	-1.0168	10	0.22706	T	0.39	.	6.7932	0.23711	0.1278:0.0:0.8722:0.0	.	11	P41212	ETV6_HUMAN	N	11	ENSP00000379658:K11N	ENSP00000379658:K11N	K	+	3	2	ETV6	11694361	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	3.784000	0.55416	1.832000	0.53329	0.491000	0.48974	AAG	.	.	none		0.537	ETV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400130.2	NM_001987	Missense_Mutation	C	11803094	G	C	11803094	5	2	6	1	0	0	0	0	0	0	1	0	5285	1014	35	4	35	4	ETV6	12	11803094	Splice_Site	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	5130251	11803094	122048801	59	644	13	2									
ETV6	2120	hgsc.bcm.edu	37	chr12	11803095	11803095	+	Splice_Site	SNP	G	G	A																															ctgctcagtgtagcattaagGtaaaaatcttctcccctcct																										TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr12:11803095G>A	ENST00000396373.4	+	1	307		c.e1+1		ETV6_ENST00000544715.1_Splice_Site	NM_001987.4	NP_001978.1	P41212	ETV6_HUMAN	ets variant 6						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)				TAGCATTAAGGTAAAAATCTT	0.532			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"																																.		Atlas-SNP	.		Dom	yes		12	12p13	2120	ets variant gene 6 (TEL oncogene)		"L, E, M"	.	ETV6	91	.	0			c.33+1G>A						PASS	.						137	133	134					12																	11803095		2203	4300	6503	SO:0001630	splice_region_variant	2120	exon1			ATTAAGGTAAAAA	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.33+1G>A	12.37:g.11803095G>A		47	0	0		26	16	0.615385	NM_001987	A3QVP6|A8K076|Q9UMF6|Q9UMF7|Q9UMG0	Splice_Site	SNP	ENST00000396373.4	37	CCDS8643.1	.	.	.	.	.	.	.	.	.	.	G	14.53	2.561598	0.45590	.	.	ENSG00000139083	ENST00000396373	.	.	.	4.11	3.2	0.36748	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.7932	0.23711	0.1278:0.0:0.8722:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ETV6	11694362	1.000000	0.71417	0.995000	0.50966	0.931000	0.56810	3.784000	0.55416	1.832000	0.53329	0.491000	0.48974	.	.	.	none		0.532	ETV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400130.2	NM_001987	Intron	A	11803095	G	A	11803095	5	1	6	1	0	0	0	0	0	0	1	0	5285	1275	44	2	36	2	ETV6	12	11803095	Splice_Site	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	1	11803095	122048800	60	645	13	2									
PDE3A	5139	hgsc.bcm.edu	37	chr12	20522715	20522715	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggctgtcgcgctgctggccgCctgctgcgggggggaagcgc	2	6	20	13	5	0	0	0	0	0	0	1	1	0	1	2	5	4	4	2	5	1	0	rs532703635		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr12:20522715C>T	ENST00000359062.3	+	1	537	c.497C>T	c.(496-498)gCc>gTc	p.A166V	RP11-284H19.1_ENST00000535755.1_RNA	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	166					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)	CTGCTGGCCGCCTGCTGCGGG	0.692													C|||	1	0.000199681	0.0008	0.0	5008	,	,		12966	0.0		0.0	False		,,,				2504	0.0				p.A166V		Atlas-SNP	.											.	PDE3A	184	.	0			c.C497T						PASS	.						14	18	17					12																	20522715		2086	4148	6234	SO:0001583	missense	5139	exon1			TGGCCGCCTGCTG		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.497C>T	12.37:g.20522715C>T	ENSP00000351957:p.Ala166Val	102	0	0		104	35	0.336538	NM_000921	O60865|Q13348|Q17RD1	Missense_Mutation	SNP	ENST00000359062.3	37	CCDS31754.1	.	.	.	.	.	.	.	.	.	.	C	12.90	2.076391	0.36662	.	.	ENSG00000172572	ENST00000359062	T	0.62941	-0.01	5.21	3.38	0.38709	.	1.056470	0.07230	N	0.862436	T	0.43612	0.1255	N	0.12182	0.205	0.32681	N	0.515452	B	0.06786	0.001	B	0.06405	0.002	T	0.47522	-0.9111	10	0.41790	T	0.15	.	6.6969	0.23203	0.0:0.6939:0.1471:0.159	.	166	Q14432	PDE3A_HUMAN	V	166	ENSP00000351957:A166V	ENSP00000351957:A166V	A	+	2	0	PDE3A	20413982	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.008000	0.40893	1.196000	0.43129	0.555000	0.69702	GCC	.	.	none		0.692	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2			T	20522715	C	T	20522715	3	4	6	1	0	0	0	0	1	0	0	0	11646	739	26	2	499	2	PDE3A	12	20522715	Missense_Mutation	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10	8719620	20522715	113329180	61	646											
PDE3A	5139	hgsc.bcm.edu	37	chr12	20787928	20787928	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagatgaaacagagtgcctgAgagagcctctgaggaaagca	16	5	13	7	0	1	6	0	3	1	3	1	8	1	7	2	1	4	1	2	1	3	0			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr12:20787928A>T	ENST00000359062.3	+	8	1979	c.1939A>T	c.(1939-1941)Aga>Tga	p.R647*	PDE3A_ENST00000544307.1_3'UTR	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	647					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)	AGAGTGCCTGAGAGAGCCTCT	0.428																																					p.R647X		Atlas-SNP	.											.	PDE3A	184	.	0			c.A1939T						PASS	.						141	120	127					12																	20787928		2203	4300	6503	SO:0001587	stop_gained	5139	exon8			TGCCTGAGAGAGC		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.1939A>T	12.37:g.20787928A>T	ENSP00000351957:p.Arg647*	71	0	0		63	21	0.333333	NM_000921	O60865|Q13348|Q17RD1	Nonsense_Mutation	SNP	ENST00000359062.3	37	CCDS31754.1	.	.	.	.	.	.	.	.	.	.	A	35	5.494917	0.96339	.	.	ENSG00000172572	ENST00000359062	.	.	.	5.64	3.24	0.37175	.	1.494490	0.03493	N	0.216863	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08837	T	0.75	.	8.1704	0.31252	0.7944:0.1351:0.0705:0.0	.	.	.	.	X	647	.	ENSP00000351957:R647X	R	+	1	2	PDE3A	20679195	0.968000	0.33430	0.004000	0.12327	0.015000	0.08874	2.527000	0.45615	0.405000	0.25532	0.528000	0.53228	AGA	.	.	none		0.428	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2			T	20787928	A	T	20787928	4	4	6	1	0	0	0	0	0	1	0	0	11646	296	11	5	1969	5	PDE3A	12	20787928	Nonsense_Mutation	SNP	A	TCGA-FA-A7DS-01A-11D-A382-10	265213	20787928	113063967	62	647											
LRRK2	120892	hgsc.bcm.edu	37	chr12	40704416	40704416	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgatgctttggcaaaacttCggaaaaccatcataaacgag	15	9	8	9	2	1	1	1	1	0	0	2	3	1	2	1	2	4	2	1	2	6	3			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr12:40704416C>T	ENST00000298910.7	+	31	4559	c.4501C>T	c.(4501-4503)Cgg>Tgg	p.R1501W		NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2	1501	Roc. {ECO:0000255|PROSITE- ProRule:PRU00758}.				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)				GGCAAAACTTCGGAAAACCAT	0.408																																					p.R1501W		Atlas-SNP	.											LRRK2_ENST00000298910,NS,carcinoma,0,3	LRRK2	763	3	0			c.C4501T						PASS	.						167	164	165					12																	40704416		2203	4300	6503	SO:0001583	missense	120892	exon31			AAACTTCGGAAAA	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.4501C>T	12.37:g.40704416C>T	ENSP00000298910:p.Arg1501Trp	90	0	0		101	5	0.049505	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Missense_Mutation	SNP	ENST00000298910.7	37	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.623937	0.87460	.	.	ENSG00000188906	ENST00000298910	T	0.75367	-0.93	5.53	4.63	0.57726	ROC GTPase (1);	0.000000	0.85682	D	0.000000	D	0.84705	0.5531	M	0.70595	2.14	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.86135	0.1577	10	0.72032	D	0.01	.	14.7522	0.69533	0.0:0.9292:0.0:0.0708	.	1501;1501	Q17RV3;Q5S007	.;LRRK2_HUMAN	W	1501	ENSP00000298910:R1501W	ENSP00000298910:R1501W	R	+	1	2	LRRK2	38990683	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.294000	0.59043	2.597000	0.87782	0.650000	0.86243	CGG	.	.	none		0.408	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513		T	40704416	C	T	40704416	3	4	6	1	0	0	0	0	1	0	0	0	9042	875	31	1	4623	1	LRRK2	12	40704416	Missense_Mutation	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10	19916488	40704416	93147479	63	648											
MLL2	8085	hgsc.bcm.edu	37	chr12	49426385	49426388	+	Frame_Shift_Del	DEL	AAGA	AAGA	-																															gggcccctcagtggcctctgAagaaacggctgggtctacgg																										TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	AAGA	AAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr12:49426385_49426388delAAGA	ENST00000301067.7	-	39	12099_12102	c.12100_12103delTCTT	c.(12100-12105)tcttcafs	p.SS4034fs	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	4034	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)										GTGGCCTCTGAAGAAACGGCTGGG	0.569																																					p.4034_4035del		Pindel,Atlas-Indel	.											.	MLL2	1173	.	0			c.12101_12104del						PASS	.																																			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.12100_12103delTCTT	12.37:g.49426385_49426388delAAGA	ENSP00000301067:p.Ser4034fs	153	0	.		71	34	0.479	NM_003482	O14687	Frame_Shift_Del	DEL	ENST00000301067.7	37	CCDS44873.1																																																																																			.	.	none		0.569	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			-	49426388	AAGA	-	49426385	7	5	6	1	0	1	0	1	0	0	0	0	9630	246	9	0	4574	0	MLL2	12	49426385	Frame_Shift_Del	DEL	AAGA	TCGA-FA-A7DS-01A-11D-A382-10	8721969	49426385	84425510	64	649											
KRT6A	3853	hgsc.bcm.edu	37	chr12	52886934	52886934	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcactgaaaccccggcggctGctgctgtggctcctgatggt	5	9	14	13	2	0	2	0	2	0	0	1	2	1	2	3	4	3	5	3	4	1	0			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr12:52886934G>T	ENST00000330722.6	-	1	107	c.39C>A	c.(37-39)agC>agA	p.S13R		NM_005554.3	NP_005545.1	P02538	K2C6A_HUMAN	keratin 6A	13	Head.				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)		CCCGGCGGCTGCTGCTGTGGC	0.642																																					p.S13R		Atlas-SNP	.											.	KRT6A	89	.	0			c.C39A						PASS	.						17	21	20					12																	52886934		2153	4212	6365	SO:0001583	missense	3853	exon1			GCGGCTGCTGCTG	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.39C>A	12.37:g.52886934G>T	ENSP00000369317:p.Ser13Arg	102	0	0		136	31	0.227941	NM_005554	A4QPC1|P48667|Q08AR4|Q6NT67|Q96CL4	Missense_Mutation	SNP	ENST00000330722.6	37	CCDS41786.1	.	.	.	.	.	.	.	.	.	.	G	12.92	2.081166	0.36758	.	.	ENSG00000205420	ENST00000330722	T	0.58940	0.3	4.68	2.81	0.32909	.	0.556998	0.17430	N	0.174498	T	0.39572	0.1083	N	0.25380	0.74	0.09310	N	0.999998	B	0.02656	0.0	B	0.01281	0.0	T	0.25187	-1.0139	10	0.49607	T	0.09	.	5.6256	0.17480	0.2612:0.1981:0.5407:0.0	.	13	P02538	K2C6A_HUMAN	R	13	ENSP00000369317:S13R	ENSP00000369317:S13R	S	-	3	2	KRT6A	51173201	0.000000	0.05858	0.903000	0.35520	0.870000	0.49936	-0.124000	0.10595	1.140000	0.42260	0.549000	0.68633	AGC	.	.	none		0.642	KRT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404978.2	NM_005554		T	52886934	G	T	52886934	3	4	6	1	0	0	0	0	1	0	0	0	8489	1310	46	4	1691	4	KRT6A	12	52886934	Missense_Mutation	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	3460549	52886934	80964961	65	650											
KRT3	3850	hgsc.bcm.edu	37	chr12	53185490	53185490	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccacctgcttcttgacaccCtcgatctctgcccgcagcct	5	10	6	20	2	2	1	0	1	2	0	4	2	2	1	5	0	3	2	5	0	0	2	rs369576134		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr12:53185490C>T	ENST00000417996.2	-	6	1373	c.1299G>A	c.(1297-1299)gaG>gaA	p.E433E	KRT3_ENST00000309505.3_Silent_p.E433E	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	433	Coil 2.|Rod.				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						TCTTGACACCCTCGATCTCTG	0.567																																					p.E433E		Atlas-SNP	.											.	KRT3	65	.	0			c.G1299A						PASS	.	C		0,4404		0,0,2202	107	108	108		1299	4	0.5	12		108	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KRT3	NM_057088.2		0,1,6501	TT,TC,CC		0.0116,0.0,0.0077		433/629	53185490	1,13003	2202	4300	6502	SO:0001819	synonymous_variant	3850	exon6			GACACCCTCGATC		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.1299G>A	12.37:g.53185490C>T		154	0	0		178	99	0.55618	NM_057088	A6NIS2|Q701L8	Silent	SNP	ENST00000417996.2	37	CCDS44895.1																																																																																			.	.	weak		0.567	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1	NM_057088		T	53185490	C	T	53185490	2	4	6	1	0	0	0	0	0	0	0	1	8475	680	24	2		2	KRT3	12	53185490	Silent	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10	298556	53185490	80666405	66	651											
FAM124A	220108	hgsc.bcm.edu	37	chr13	51855115	51855115	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagatgcagcagccactgggCagctcacaaggattccaggg	12	5	13	11	0	1	1	1	0	0	1	2	2	2	2	2	3	4	4	2	3	2	1			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr13:51855115C>A	ENST00000322475.8	+	4	1499	c.1364C>A	c.(1363-1365)gCa>gAa	p.A455E	FAM124A_ENST00000280057.6_Missense_Mutation_p.A491E	NM_001242312.1	NP_001229241.1	Q86V42	F124A_HUMAN	family with sequence similarity 124A	455										breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|skin(1)	26		Acute lymphoblastic leukemia(7;0.000334)|Breast(56;0.00156)|Prostate(109;0.00538)|Lung NSC(96;0.0216)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;4.25e-07)		AGCCACTGGGCAGCTCACAAG	0.587																																					p.A491E		Atlas-SNP	.											.	FAM124A	61	.	0			c.C1472A						PASS	.						56	54	54					13																	51855115		2203	4300	6503	SO:0001583	missense	220108	exon5			ACTGGGCAGCTCA	AK096364	CCDS9427.1, CCDS55900.1	13q14.3	2006-08-11			ENSG00000150510	ENSG00000150510			26413	protein-coding gene	gene with protein product						12975309	Standard	NM_145019		Approved	FLJ30707	uc001vff.2	Q86V42	OTTHUMG00000016942	ENST00000322475.8:c.1364C>A	13.37:g.51855115C>A	ENSP00000324625:p.Ala455Glu	48	0	0		55	22	0.4	NM_145019	A2A324|Q8N8P9|Q8NE66|Q96NJ9	Missense_Mutation	SNP	ENST00000322475.8	37	CCDS55900.1	.	.	.	.	.	.	.	.	.	.	C	10.99	1.507667	0.27036	.	.	ENSG00000150510	ENST00000322475;ENST00000280057	T;T	0.47528	0.86;0.84	5.07	1.23	0.21249	.	2.466230	0.01371	N	0.012590	T	0.23370	0.0565	N	0.08118	0	0.09310	N	1	B;B	0.27732	0.0;0.187	B;B	0.25140	0.002;0.058	T	0.23511	-1.0186	10	0.02654	T	1	-11.5191	3.6365	0.08151	0.2691:0.3909:0.2621:0.078	.	455;491	Q86V42;Q86V42-2	F124A_HUMAN;.	E	455;491	ENSP00000324625:A455E;ENSP00000280057:A491E	ENSP00000280057:A491E	A	+	2	0	FAM124A	50753116	0.002000	0.14202	0.000000	0.03702	0.007000	0.05969	1.530000	0.36007	-0.100000	0.12241	-0.188000	0.12872	GCA	.	.	none		0.587	FAM124A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045019.3	NM_145019		A	51855115	C	A	51855115	3	1	6	1	0	0	0	0	1	0	0	0	5430	710	25	4	1490	4	FAM124A	13	51855115	Missense_Mutation	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10		51855115	63314763	67	652											
OR4K5	79317	hgsc.bcm.edu	37	chr14	20388876	20388876	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctctgtgttgtatacagtCattgtgctgggaaatcttct	7	18	9	7	0	4	0	1	0	3	0	5	1	4	1	0	1	2	3	0	1	3	6			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr14:20388876C>A	ENST00000315915.4	+	1	136	c.111C>A	c.(109-111)gtC>gtA	p.V37V		NM_001005483.1	NP_001005483.1	Q8NGD3	OR4K5_HUMAN	olfactory receptor, family 4, subfamily K, member 5	37						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V37V(1)		central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|liver(1)|lung(27)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TGTATACAGTCATTGTGCTGG	0.408																																					p.V37V		Atlas-SNP	.											OR4K5,NS,carcinoma,0,1	OR4K5	111	1	1	Substitution - coding silent(1)	lung(1)	c.C111A						PASS	.						202	210	207					14																	20388876		2203	4300	6503	SO:0001819	synonymous_variant	79317	exon1			TACAGTCATTGTG	BK004355	CCDS32024.1	14q11.22	2012-08-09				ENSG00000176281		"GPCR / Class A : Olfactory receptors"	14745	protein-coding gene	gene with protein product						14983052	Standard	NM_001005483		Approved		uc010tkw.2	Q8NGD3		ENST00000315915.4:c.111C>A	14.37:g.20388876C>A		182	0	0		177	56	0.316384	NM_001005483	Q6IFA7	Silent	SNP	ENST00000315915.4	37	CCDS32024.1																																																																																			.	.	none		0.408	OR4K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409867.1	NM_001005483		A	20388876	C	A	20388876	2	1	6	1	0	0	0	0	0	0	0	1	11082	813	29	4		4	OR4K5	14	20388876	Silent	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10		20388876	86960664	68	653											
TMEM90A	646658	hgsc.bcm.edu	37	chr14	74874557	74874557	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccaggtgctcttaccccctGggagaagtagaaggcagcaa	11	6	12	12	0	1	2	0	0	1	2	1	3	1	2	3	3	3	4	3	3	5	2			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr14:74874557G>T	ENST00000554823.1	-	2	614	c.553C>A	c.(553-555)Cag>Aag	p.Q185K	SYNDIG1L_ENST00000331628.3_Missense_Mutation_p.Q185K			A6NDD5	SYN1L_HUMAN	synapse differentiation inducing 1-like	185					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						CTTACCCCCTGGGAGAAGTAG	0.627																																					p.Q185K		Atlas-SNP	.											.	SYNDIG1L	24	.	0			c.C553A						PASS	.						69	77	74					14																	74874557		2203	4300	6503	SO:0001583	missense	646658	exon3			CCCCCTGGGAGAA		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.553C>A	14.37:g.74874557G>T	ENSP00000450439:p.Gln185Lys	78	0	0		82	28	0.341463	NM_001105579		Missense_Mutation	SNP	ENST00000554823.1	37	CCDS41970.1	.	.	.	.	.	.	.	.	.	.	G	19.09	3.759026	0.69763	.	.	ENSG00000183379	ENST00000331628;ENST00000554823	D;D	0.85556	-2.0;-2.0	4.85	4.85	0.62838	.	0.077405	0.56097	D	0.000040	D	0.88385	0.6422	L	0.35854	1.095	0.58432	D	0.999999	D	0.64830	0.994	D	0.64506	0.926	D	0.88933	0.3374	10	0.52906	T	0.07	-13.4894	18.1623	0.89712	0.0:0.0:1.0:0.0	.	185	A6NDD5	SYN1L_HUMAN	K	185	ENSP00000331474:Q185K;ENSP00000450439:Q185K	ENSP00000331474:Q185K	Q	-	1	0	SYNDIG1L	73944310	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	9.657000	0.98554	2.498000	0.84270	0.561000	0.74099	CAG	.	.	none		0.627	SYNDIG1L-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412341.1	XM_938515		T	74874557	G	T	74874557	3	4	6	1	0	0	0	0	1	0	0	0	16233	1357	47	4	171	4	TMEM90A	14	74874557	Missense_Mutation	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	54485681	74874557	32474983	69	654											
SECISBP2L	9728	hgsc.bcm.edu	37	chr15	49338480	49338480	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaacccgcgtacctgctccGtgggggctcggtccatggtg	5	8	14	14	4	0	0	0	0	0	0	3	0	2	0	4	4	3	3	4	4	2	1			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr15:49338480G>A	ENST00000559471.1	-	1	280	c.17C>T	c.(16-18)aCg>aTg	p.T6M	SECISBP2L_ENST00000261847.3_Missense_Mutation_p.T6M	NM_001193489.1	NP_001180418.1	Q93073	SBP2L_HUMAN	SECIS binding protein 2-like	6							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						TACCTGCTCCGTGGGGGCTCG	0.731																																					p.T6M		Atlas-SNP	.											.	SECISBP2L	118	.	0			c.C17T						PASS	.						6	9	8					15																	49338480		2064	4063	6127	SO:0001583	missense	9728	exon1			TGCTCCGTGGGGG	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.17C>T	15.37:g.49338480G>A	ENSP00000453854:p.Thr6Met	146	0	0		134	42	0.313433	NM_001193489	Q8N767	Missense_Mutation	SNP	ENST00000559471.1	37	CCDS53942.1	.	.	.	.	.	.	.	.	.	.	G	10.28	1.305656	0.23736	.	.	ENSG00000138593	ENST00000261847;ENST00000380927	T	0.72725	-0.68	4.77	2.78	0.32641	.	1.298010	0.04854	N	0.442829	T	0.54581	0.1867	N	0.08118	0	0.09310	N	1	B;B	0.30914	0.199;0.3	B;B	0.28011	0.039;0.085	T	0.51903	-0.8646	10	0.72032	D	0.01	.	11.1726	0.48579	0.0:0.3605:0.6395:0.0	.	6;6	Q93073;Q93073-2	SBP2L_HUMAN;.	M	6	ENSP00000261847:T6M	ENSP00000261847:T6M	T	-	2	0	SECISBP2L	47125772	0.492000	0.26027	0.023000	0.16930	0.141000	0.21300	2.234000	0.43035	0.660000	0.30964	0.655000	0.94253	ACG	.	.	none		0.731	SECISBP2L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417277.1	NM_014701		A	49338480	G	A	49338480	3	1	6	1	0	0	0	0	1	0	0	0	14022	1145	40	1	3221	1	SECISBP2L	15	49338480	Missense_Mutation	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10		49338480	53192912	70	655											
AAGAB	79719	hgsc.bcm.edu	37	chr15	67528329	67528329	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	acacttaccatcctcctcagGcaactcctctggactaagtt	10	11	5	15	0	2	0	1	0	1	0	5	1	5	1	4	2	2	2	4	2	3	3			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr15:67528329G>A	ENST00000261880.5	-	4	543	c.439C>T	c.(439-441)Cct>Tct	p.P147S	AAGAB_ENST00000542650.1_Missense_Mutation_p.P38S|AAGAB_ENST00000561452.1_Missense_Mutation_p.P38S	NM_001271885.1|NM_001271886.1|NM_024666.3	NP_001258814.1|NP_001258815.1|NP_078942.3	Q6PD74	AAGAB_HUMAN	alpha- and gamma-adaptin binding protein	147					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	9						TCCTCCTCAGGCAACTCCTCT	0.353																																					p.P147S		Atlas-SNP	.											.	AAGAB	24	.	0			c.C439T						PASS	.						173	151	158					15																	67528329		1865	4113	5978	SO:0001583	missense	79719	exon4			CCTCAGGCAACTC	AL136715	CCDS42050.1, CCDS61679.1	15q22.33-q23	2014-02-12	2009-07-20		ENSG00000103591	ENSG00000103591			25662	protein-coding gene	gene with protein product		614888				11230166, 10477754	Standard	NM_024666		Approved	FLJ11506, p34	uc002aqk.5	Q6PD74	OTTHUMG00000172246	ENST00000261880.5:c.439C>T	15.37:g.67528329G>A	ENSP00000261880:p.Pro147Ser	138	0	0		143	42	0.293706	NM_024666	B4DG44|Q6FI86|Q7Z5X9|Q9H0P1|Q9HAK0	Missense_Mutation	SNP	ENST00000261880.5	37	CCDS42050.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.425846	0.83667	.	.	ENSG00000103591	ENST00000261880;ENST00000542650	T;T	0.42900	0.96;0.98	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.42607	0.1210	L	0.52573	1.65	0.80722	D	1	P	0.49862	0.929	P	0.46389	0.515	T	0.30090	-0.9990	10	0.05525	T	0.97	-18.439	19.702	0.96059	0.0:0.0:1.0:0.0	.	147	Q6PD74	AAGAB_HUMAN	S	147;38	ENSP00000261880:P147S;ENSP00000440735:P38S	ENSP00000261880:P147S	P	-	1	0	AAGAB	65315383	1.000000	0.71417	0.995000	0.50966	0.996000	0.88848	9.055000	0.93873	2.738000	0.93877	0.591000	0.81541	CCT	.	.	none		0.353	AAGAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417472.1	NM_024666		A	67528329	G	A	67528329	3	1	6	1	0	0	0	0	1	0	0	0	15	1203	42	2	536	2	AAGAB	15	67528329	Missense_Mutation	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	18189849	67528329	35003063	71	656											
HCN4	10021	hgsc.bcm.edu	37	chr15	73617312	73617312	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacctccaaagtaggagccGtcggccagcttggtctcctt	7	10	10	14	2	2	0	1	0	1	0	5	1	3	1	5	3	2	2	5	3	2	3			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr15:73617312G>A	ENST00000261917.3	-	6	2955	c.1962C>T	c.(1960-1962)gaC>gaT	p.D654D		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	654					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)		AGTAGGAGCCGTCGGCCAGCT	0.617																																					p.D654D		Atlas-SNP	.											.	HCN4	150	.	0			c.C1962T						PASS	.						66	57	60					15																	73617312		2198	4297	6495	SO:0001819	synonymous_variant	10021	exon6			GGAGCCGTCGGCC	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.1962C>T	15.37:g.73617312G>A		43	0	0		46	17	0.369565	NM_005477	Q9UMQ7	Silent	SNP	ENST00000261917.3	37	CCDS10248.1																																																																																			.	.	none		0.617	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477		A	73617312	G	A	73617312	2	1	6	1	0	0	0	0	0	0	0	1	7008	1136	40	1		1	HCN4	15	73617312	Silent	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	6088983	73617312	28914080	72	657											
BFAR	51283	hgsc.bcm.edu	37	chr16	14738262	14738262	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttgagagagatgaacctcTcaaaagcaccggccctcaga	13	6	9	13	1	2	4	2	2	1	3	3	6	2	4	4	1	2	1	4	1	3	1			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr16:14738262T>C	ENST00000261658.2	+	2	336	c.59T>C	c.(58-60)cTc>cCc	p.L20P	BFAR_ENST00000426842.2_5'UTR|BFAR_ENST00000563971.1_Missense_Mutation_p.L20P|RNU7-125P_ENST00000458760.1_RNA	NM_016561.2	NP_057645.1	Q9NZS9	BFAR_HUMAN	bifunctional apoptosis regulator	20					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	structural molecule activity (GO:0005198)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|skin(1)	11						GATGAACCTCTCAAAAGCACC	0.458																																					p.L20P		Atlas-SNP	.											.	BFAR	38	.	0			c.T59C						PASS	.						119	120	120					16																	14738262		2197	4300	6497	SO:0001583	missense	51283	exon2			AACCTCTCAAAAG	AF173003	CCDS10554.1	16p13.2	2013-01-10			ENSG00000103429	ENSG00000103429		"RING-type (C3HC4) zinc fingers", "Sterile alpha motif (SAM) domain containing"	17613	protein-coding gene	gene with protein product						10716992	Standard	NM_016561		Approved	BAR, RNF47	uc002dco.3	Q9NZS9	OTTHUMG00000129848	ENST00000261658.2:c.59T>C	16.37:g.14738262T>C	ENSP00000261658:p.Leu20Pro	106	0	0		107	33	0.308411	NM_016561	A8K4Z9|B4DUT0|D3DUG8	Missense_Mutation	SNP	ENST00000261658.2	37	CCDS10554.1	.	.	.	.	.	.	.	.	.	.	T	16.84	3.233880	0.58886	.	.	ENSG00000103429	ENST00000261658	T	0.07688	3.17	5.91	2.28	0.28536	.	1.291620	0.04794	N	0.432159	T	0.07638	0.0192	L	0.29908	0.895	0.09310	N	0.999997	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.06405	0.002;0.001;0.001	T	0.38090	-0.9677	10	0.87932	D	0	.	4.258	0.10726	0.1421:0.2437:0.0:0.6142	.	20;20;20	B2R9R6;Q9NZS9;B4DLM6	.;BFAR_HUMAN;.	P	20	ENSP00000261658:L20P	ENSP00000261658:L20P	L	+	2	0	BFAR	14645763	0.000000	0.05858	0.000000	0.03702	0.207000	0.24258	0.786000	0.26844	0.498000	0.27948	0.533000	0.62120	CTC	.	.	none		0.458	BFAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252088.1	NM_016561		C	14738262	T	C	14738262	3	2	6	1	0	0	0	0	1	0	0	0	1414	1551	54	3	61	3	BFAR	16	14738262	Missense_Mutation	SNP	T	TCGA-FA-A7DS-01A-11D-A382-10		14738262	75616491	73	658											
DHX38	9785	hgsc.bcm.edu	37	chr16	72137944	72137944	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gagagtccctccgggaagccGacctggatcactacagtgcc	9	6	12	14	2	1	1	1	0	0	1	3	5	3	3	5	2	3	0	5	2	2	1			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr16:72137944G>A	ENST00000268482.3	+	14	2433	c.1924G>A	c.(1924-1926)Gac>Aac	p.D642N	DHX38_ENST00000536867.1_Intron	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	642	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				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)				CCGGGAAGCCGACCTGGATCA	0.582																																					p.D642N	Melanoma(97;711 1442 7855 13832 28836)	Atlas-SNP	.											DHX38,NS,carcinoma,0,1	DHX38	91	1	0			c.G1924A						PASS	.						117	104	108					16																	72137944		2198	4300	6498	SO:0001583	missense	9785	exon14			GAAGCCGACCTGG	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.1924G>A	16.37:g.72137944G>A	ENSP00000268482:p.Asp642Asn	96	0	0		66	23	0.348485	NM_014003	B4DVG8|D3DWS7|O75212|Q96HN7	Missense_Mutation	SNP	ENST00000268482.3	37	CCDS10907.1	.	.	.	.	.	.	.	.	.	.	G	36	5.786051	0.96937	.	.	ENSG00000140829	ENST00000268482	T	0.07688	3.17	5.49	5.49	0.81192	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.114937	0.64402	D	0.000020	T	0.20700	0.0498	L	0.42529	1.33	0.80722	D	1	D	0.58620	0.983	P	0.58820	0.846	T	0.00063	-1.2154	10	0.51188	T	0.08	.	19.7433	0.96241	0.0:0.0:1.0:0.0	.	642	Q92620	PRP16_HUMAN	N	642	ENSP00000268482:D642N	ENSP00000268482:D642N	D	+	1	0	DHX38	70695445	1.000000	0.71417	0.967000	0.41034	0.915000	0.54546	7.954000	0.87848	2.733000	0.93635	0.655000	0.94253	GAC	.	.	none		0.582	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003		A	72137944	G	A	72137944	3	1	6	1	0	0	0	0	1	0	0	0	4513	1058	37	1	1974	1	DHX38	16	72137944	Missense_Mutation	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	57399682	72137944	18216809	74	659											
TMEM93	83460	hgsc.bcm.edu	37	chr17	3572623	3572623	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tacctgctcgcctccgtcctGctctccctgctcctcattct	2	14	5	20	2	3	0	1	0	2	0	8	0	6	0	6	0	4	3	6	0	1	2			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr17:3572623G>A	ENST00000397133.2	+	2	423	c.183G>A	c.(181-183)ctG>ctA	p.L61L	EMC6_ENST00000248378.5_Silent_p.L61L|P2RX5-TAX1BP3_ENST00000550383.1_3'UTR|TAX1BP3_ENST00000225525.3_5'Flank	NM_001014764.1	NP_001014764.1	Q9BV81	EMC6_HUMAN	ER membrane protein complex subunit 6	61						ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)											CCTCCGTCCTGCTCTCCCTGC	0.607																																					p.L61L		Atlas-SNP	.											.	.	.	.	0			c.G183A						PASS	.						38	39	38					17																	3572623		2202	4300	6502	SO:0001819	synonymous_variant	83460	exon2			CGTCCTGCTCTCC		CCDS11033.1	17p13.2	2012-05-23	2012-05-23	2012-05-23		ENSG00000127774			28430	protein-coding gene	gene with protein product			"transmembrane protein 93"	TMEM93		22119785	Standard	NM_001014764		Approved	MGC2963	uc002fwg.1	Q9BV81		ENST00000397133.2:c.183G>A	17.37:g.3572623G>A		120	0	0		116	39	0.336207	NM_001014764		Silent	SNP	ENST00000397133.2	37	CCDS11033.1																																																																																			.	.	none		0.607	EMC6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450159.1	NM_031298		A	3572623	G	A	3572623	2	1	6	1	0	0	0	0	0	0	0	1	16237	1306	46	2		2	TMEM93	17	3572623	Silent	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10		3572623	77622587	75	660											
TNS4	84951	hgsc.bcm.edu	37	chr17	38645133	38645133	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccaccactgcgaagggagccGaagggcggggtgacagaggg	10	2	19	10	3	0	2	0	1	0	1	0	5	0	3	3	5	2	0	3	5	2	0			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr17:38645133G>A	ENST00000254051.6	-	3	686	c.528C>T	c.(526-528)ttC>ttT	p.F176F		NM_032865.5	NP_116254.4	Q8IZW8	TENS4_HUMAN	tensin 4	176	Ser-rich.				apoptotic process (GO:0006915)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	30		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)			GAAGGGAGCCGAAGGGCGGGG	0.622																																					p.F176F		Atlas-SNP	.											.	TNS4	72	.	0			c.C528T						PASS	.						51	63	59					17																	38645133		2200	4299	6499	SO:0001819	synonymous_variant	84951	exon3			GGAGCCGAAGGGC	AF417488	CCDS11368.1	17q21.2	2013-02-14			ENSG00000131746	ENSG00000131746		"SH2 domain containing"	24352	protein-coding gene	gene with protein product	"C terminal tensin like"	608385				12154022, 12711115	Standard	NM_032865		Approved	CTEN	uc010cxb.3	Q8IZW8	OTTHUMG00000133330	ENST00000254051.6:c.528C>T	17.37:g.38645133G>A		70	0	0		77	34	0.441558	NM_032865	A6NMJ7|Q71RB7|Q8WV64|Q96JV4	Silent	SNP	ENST00000254051.6	37	CCDS11368.1																																																																																			.	.	none		0.622	TNS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257154.3	NM_032865		A	38645133	G	A	38645133	2	1	6	1	0	0	0	0	0	0	0	1	16360	1049	37	1		1	TNS4	17	38645133	Silent	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	35072510	38645133	42550077	76	661											
ANKFN1	162282	hgsc.bcm.edu	37	chr17	54403699	54403699	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acaacttgttcctctgctgcCtcgaacagcataaactggta	11	11	7	12	1	1	0	0	0	1	0	3	1	2	0	2	1	6	4	2	1	5	4			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr17:54403699C>T	ENST00000318698.2	+	3	215	c.180C>T	c.(178-180)gcC>gcT	p.A60A	ANKFN1_ENST00000566473.2_Silent_p.A60A	NM_153228.2	NP_694960.2	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain containing 1	60										NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(11)|lung(27)|ovary(1)|prostate(1)|skin(1)	53						CCTCTGCTGCCTCGAACAGCA	0.373																																					p.A60A		Atlas-SNP	.											.	ANKFN1	115	.	0			c.C180T						PASS	.						132	119	123					17																	54403699		2203	4300	6503	SO:0001819	synonymous_variant	162282	exon3			TGCTGCCTCGAAC	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.180C>T	17.37:g.54403699C>T		145	0	0		118	35	0.29661	NM_153228		Silent	SNP	ENST00000318698.2	37	CCDS32686.1																																																																																			.	.	none		0.373	ANKFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338043.1	NM_153228		T	54403699	C	T	54403699	2	4	6	1	0	0	0	0	0	0	0	1	625	668	24	2		2	ANKFN1	17	54403699	Silent	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10	15758566	54403699	26791511	77	662											
ASXL3	80816	hgsc.bcm.edu	37	chr18	31324989	31324989	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tatttccttggctaccgatgCcctgaagagagtccctggtg	7	12	11	11	1	0	2	0	1	0	1	2	4	2	2	4	2	2	1	4	2	3	4	rs369543627		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr18:31324989C>A	ENST00000269197.5	+	12	5177	c.5177C>A	c.(5176-5178)gCc>gAc	p.A1726D		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	1726					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						GCTACCGATGCCCTGAAGAGA	0.557																																					p.A1726D		Atlas-SNP	.											.	ASXL3	405	.	0			c.C5177A						PASS	.						73	76	75					18																	31324989		2031	4190	6221	SO:0001583	missense	80816	exon12			CCGATGCCCTGAA	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.5177C>A	18.37:g.31324989C>A	ENSP00000269197:p.Ala1726Asp	57	0	0		61	15	0.245902	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	37	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	C	3.427	-0.116888	0.06838	.	.	ENSG00000141431	ENST00000269197	T	0.14022	2.54	5.86	2.87	0.33458	.	.	.	.	.	T	0.08044	0.0201	N	0.08118	0	0.09310	N	1	B	0.15141	0.012	B	0.14023	0.01	T	0.33240	-0.9876	9	0.56958	D	0.05	.	10.7813	0.46379	0.431:0.4524:0.1166:0.0	.	1726	Q9C0F0	ASXL3_HUMAN	D	1726	ENSP00000269197:A1726D	ENSP00000269197:A1726D	A	+	2	0	ASXL3	29578987	0.378000	0.25114	0.916000	0.36221	0.018000	0.09664	1.299000	0.33424	0.249000	0.21456	0.655000	0.94253	GCC	.	.	alt		0.557	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			A	31324989	C	A	31324989	3	1	6	1	0	0	0	0	1	0	0	0	1068	739	26	4	5223	4	ASXL3	18	31324989	Missense_Mutation	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10		31324989	46752259	78	663											
MUC16	94025	hgsc.bcm.edu	37	chr19	8962366	8962366	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agacttaccagaattcccagTtaagggctcatttctgttgg	10	13	9	9	0	2	2	1	0	1	2	3	2	3	2	2	2	1	3	2	2	3	5			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr19:8962366T>G	ENST00000397910.4	-	82	43536	c.43333A>C	c.(43333-43335)Act>Cct	p.T14445P	MUC16_ENST00000380951.5_Missense_Mutation_p.T1086P	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	22090	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						GAATTCCCAGTTAAGGGCTCA	0.473																																					p.T14445P		Atlas-SNP	.											.	MUC16	4315	.	0			c.A43333C						PASS	.						26	26	26					19																	8962366		1790	3970	5760	SO:0001583	missense	94025	exon82			TCCCAGTTAAGGG	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.43333A>C	19.37:g.8962366T>G	ENSP00000381008:p.Thr14445Pro	103	0	0		133	41	0.308271	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.69|11.69	1.715233|1.715233	0.30413|0.30413	.|.	.|.	ENSG00000181143|ENSG00000181143	ENST00000397910;ENST00000380951|ENST00000542240	T|.	0.02103|.	4.45|.	3.79|3.79	1.64|1.64	0.23874|0.23874	.|.	.|.	.|.	.|.	.|.	T|.	0.47173|.	0.1431|.	M|M	0.66939|0.66939	2.045|2.045	.|.	.|.	.|.	P;D|.	0.69078|.	0.838;0.997|.	B;P|.	0.62184|.	0.367;0.899|.	T|.	0.52358|.	-0.8586|.	8|.	0.62326|.	D|.	0.03|.	.|.	3.1914|3.1914	0.06618|0.06618	0.2051:0.1125:0.0:0.6824|0.2051:0.1125:0.0:0.6824	.|.	22090;14445|.	Q8WXI7;B5ME49|.	MUC16_HUMAN;.|.	P|Y	14445;1086|1267	ENSP00000381008:T14445P|.	ENSP00000370338:T1086P|.	T|X	-|-	1|3	0|2	MUC16|MUC16	8823366|8823366	0.001000|0.001000	0.12720|0.12720	0.004000|0.004000	0.12327|0.12327	0.011000|0.011000	0.07611|0.07611	0.642000|0.642000	0.24735|0.24735	0.284000|0.284000	0.22305|0.22305	0.454000|0.454000	0.30748|0.30748	ACT|TAA	.	.	none		0.473	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	8962366	T	G	8962366	3	3	6	1	0	0	0	0	1	0	0	0	9982	1725	60	5	202	5	MUC16	19	8962366	Missense_Mutation	SNP	T	TCGA-FA-A7DS-01A-11D-A382-10		8962366	50166617	79	664											
SLC44A2	57153	hgsc.bcm.edu	37	chr19	10738451	10738451	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctcctggccattgtgggctAcgtggctgtaggcatcatag	6	11	14	10	1	1	0	1	0	0	0	2	0	2	0	2	4	1	5	2	4	3	4			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr19:10738451A>C	ENST00000335757.5	+	3	516	c.140A>C	c.(139-141)tAc>tCc	p.Y47S	SLC44A2_ENST00000407327.4_Missense_Mutation_p.Y45S|SLC44A2_ENST00000586078.1_Missense_Mutation_p.Y47S			Q8IWA5	CTL2_HUMAN	solute carrier family 44 (choline transporter), member 2	47					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)	ATTGTGGGCTACGTGGCTGTA	0.592																																					p.Y47S		Atlas-SNP	.											.	SLC44A2	56	.	0			c.A140C						PASS	.						191	148	163					19																	10738451		2203	4300	6503	SO:0001583	missense	57153	exon3			TGGGCTACGTGGC	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.140A>C	19.37:g.10738451A>C	ENSP00000336888:p.Tyr47Ser	73	0	0		86	26	0.302326	NM_020428	B2RBB1|B3KNH3|B4DFJ0|F2Q9D7|Q658V1|Q658Z2|Q6PJV7|Q8N2F0|Q9NY68	Missense_Mutation	SNP	ENST00000335757.5	37	CCDS12245.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.321334	0.81580	.	.	ENSG00000129353	ENST00000407327;ENST00000335757;ENST00000380614	T;T	0.42900	0.96;0.96	4.68	4.68	0.58851	.	0.136380	0.50627	D	0.000101	T	0.65544	0.2701	M	0.82923	2.615	0.58432	D	0.999995	D;D	0.62365	0.967;0.991	P;D	0.71184	0.852;0.972	T	0.71702	-0.4513	10	0.87932	D	0	.	13.2377	0.59979	1.0:0.0:0.0:0.0	.	47;45	Q8IWA5;Q8IWA5-3	CTL2_HUMAN;.	S	45;47;47	ENSP00000385135:Y45S;ENSP00000336888:Y47S	ENSP00000336888:Y47S	Y	+	2	0	SLC44A2	10599451	1.000000	0.71417	0.967000	0.41034	0.911000	0.54048	8.419000	0.90253	1.957000	0.56846	0.379000	0.24179	TAC	.	.	none		0.592	SLC44A2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452045.1			C	10738451	A	C	10738451	3	2	6	1	0	0	0	0	1	0	0	0	14651	391	14	5	185	5	SLC44A2	19	10738451	Missense_Mutation	SNP	A	TCGA-FA-A7DS-01A-11D-A382-10	1776085	10738451	48390532	80	665											
ZFP112	7771	hgsc.bcm.edu	37	chr19	44832834	44832834	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccattcccatgctccttacgTggtttctctccaatgtgaat	7	15	6	13	1	1	1	0	1	1	0	5	1	4	1	4	1	2	2	4	1	3	3			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr19:44832834T>A	ENST00000337401.4	-	5	1582	c.1494A>T	c.(1492-1494)ccA>ccT	p.P498P	ZNF112_ENST00000536500.1_Silent_p.P515P|ZNF112_ENST00000354340.4_Silent_p.P492P	NM_001083335.1	NP_001076804.1	Q9UJU3	ZN112_HUMAN	zinc finger protein 112	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)										GCTCCTTACGTGGTTTCTCTC	0.403																																					p.P498P		Atlas-SNP	.											.	ZFP112	219	.	0			c.A1494T						PASS	.						134	130	132					19																	44832834		2203	4300	6503	SO:0001819	synonymous_variant	7771	exon5			CTTACGTGGTTTC	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.1494A>T	19.37:g.44832834T>A		142	0	0		138	46	0.333333	NM_001083335	A4FU53|Q9HCA7	Silent	SNP	ENST00000337401.4	37	CCDS54276.1																																																																																			.	.	none		0.403	ZNF112-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460744.1	NM_013380		A	44832834	T	A	44832834	2	1	6	1	0	0	0	0	0	0	0	1	17653	1683	59	5		5	ZFP112	19	44832834	Silent	SNP	T	TCGA-FA-A7DS-01A-11D-A382-10	34094383	44832834	14296149	81	666											
CACNG7	59284	hgsc.bcm.edu	37	chr19	54445378	54445378	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccggccttctaccgcccgcGtctcagcgactgctccgact	4	8	9	20	6	2	0	1	0	2	0	4	2	3	0	5	1	3	1	5	1	1	2			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr19:54445378G>A	ENST00000391767.1	+	6	871	c.659G>A	c.(658-660)cGt>cAt	p.R220H	CACNG7_ENST00000222212.2_Missense_Mutation_p.R220H			P62955	CCG7_HUMAN	calcium channel, voltage-dependent, gamma subunit 7	220				GAGVMSVYLFTKRYAEEEMYRPHPAFYRPRLSDCSDYSGQF LQPEAWRRGRSPSDISSDVSIQMTQNYPPAIKYPDHLHIST SPC -> VTSVGPRL (in Ref. 1; AAK20030). {ECO:0000305}.	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)		TACCGCCCGCGTCTCAGCGAC	0.687																																					p.R220H		Atlas-SNP	.											.	CACNG7	58	.	0			c.G659A						PASS	.						67	60	62					19																	54445378		2203	4300	6503	SO:0001583	missense	59284	exon5			GCCCGCGTCTCAG	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.659G>A	19.37:g.54445378G>A	ENSP00000375647:p.Arg220His	103	0	0		153	41	0.267974	NM_031896	Q52LL8|Q8VBX3|Q8WXS6|Q9BXT1	Missense_Mutation	SNP	ENST00000391767.1	37	CCDS12868.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.682057	0.88542	.	.	ENSG00000105605	ENST00000391767;ENST00000222212	T;T	0.66995	-0.24;-0.24	4.18	1.96	0.26148	.	0.000000	0.85682	D	0.000000	T	0.67401	0.2889	L	0.29908	0.895	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.62751	-0.6788	10	0.40728	T	0.16	-5.531	7.6938	0.28583	0.0953:0.1645:0.7402:0.0	.	220	P62955	CCG7_HUMAN	H	220	ENSP00000375647:R220H;ENSP00000222212:R220H	ENSP00000222212:R220H	R	+	2	0	CACNG7	59137190	1.000000	0.71417	0.738000	0.30950	0.997000	0.91878	9.011000	0.93618	0.343000	0.23821	0.491000	0.48974	CGT	.	.	none		0.687	CACNG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139240.2			A	54445378	G	A	54445378	3	1	6	1	0	0	0	0	1	0	0	0	2564	1145	40	1	677	1	CACNG7	19	54445378	Missense_Mutation	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	9612544	54445378	4683605	82	667											
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385790	58385790	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacattctccacattcataaGgtcttttcccagtgtgaact	10	14	5	12	0	3	1	1	1	2	0	5	1	4	1	2	1	1	0	2	1	2	5	rs111727691		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr19:58385790G>T	ENST00000435989.2	-	3	1202	c.968C>A	c.(967-969)cCt>cAt	p.P323H	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000600634.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	323					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						ACATTCATAAGGTCTTTTCCC	0.358																																					p.P323H		Atlas-SNP	.											.	ZNF814	93	.	0			c.C968A						PASS	.						15	12	13					19																	58385790		688	1563	2251	SO:0001583	missense	730051	exon3			TCATAAGGTCTTT		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.968C>A	19.37:g.58385790G>T	ENSP00000410545:p.Pro323His	168	0	0		253	23	0.0909091	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	8.139	0.784825	0.16189	.	.	ENSG00000204514	ENST00000435989	T	0.29397	1.57	2.27	1.18	0.20946	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.57080	0.2029	M	0.90019	3.08	0.20764	N	0.999853	D	0.89917	1.0	D	0.67231	0.95	T	0.46247	-0.9205	9	0.66056	D	0.02	.	9.258	0.37595	0.0:0.0:0.7811:0.2189	.	323	B7Z6K7	ZN814_HUMAN	H	323	ENSP00000410545:P323H	ENSP00000410545:P323H	P	-	2	0	ZNF814	63077602	0.000000	0.05858	0.028000	0.17463	0.016000	0.09150	-0.439000	0.06897	0.330000	0.23485	-1.407000	0.01130	CCT	G|0.500;T|0.500	0.500	weak		0.358	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		T	58385790	G	T	58385790	3	4	6	1	0	0	0	0	1	0	0	0	18191	1000	35	4	1603	4	ZNF814	19	58385790	Missense_Mutation	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	3940412	58385790	743193	83	668											
UBASH3A	53347	hgsc.bcm.edu	37	chr21	43826425	43826436	+	In_Frame_Del	DEL	CGTTGGCAGCCA	CGTTGGCAGCCA	-																															gctcttctgcaggctgaaagCgttggcagccacggggagga																										TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	CGTTGGCAGCCA	CGTTGGCAGCCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chr21:43826425_43826436delCGTTGGCAGCCA	ENST00000319294.6	+	2	153_164	c.122_133delCGTTGGCAGCCA	c.(121-135)gcgttggcagccacg>gcg	p.LAAT42del	UBASH3A_ENST00000398367.1_In_Frame_Del_p.LAAT42del|UBASH3A_ENST00000450356.1_In_Frame_Del_p.LAAT42del|UBASH3A_ENST00000291535.6_In_Frame_Del_p.LAAT42del	NM_018961.3	NP_061834.1	P57075	UBS3A_HUMAN	ubiquitin associated and SH3 domain containing A	42	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				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.A44V(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(9)|lung(12)|ovary(3)	28						AGGCTGAAAGCGTTGGCAGCCACGGGGAGGAA	0.604																																					p.41_44del		Pindel,Atlas-Indel	.											.	UBASH3A	72	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.121_132del						PASS	.																																			SO:0001651	inframe_deletion	53347	exon2			.	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.122_133delCGTTGGCAGCCA	21.37:g.43826425_43826436delCGTTGGCAGCCA	ENSP00000317327:p.Leu42_Thr45del	77	0	.		66	14	0.212	NM_018961	G5E9E4|Q6HA34|Q6HA35|Q6ISI6|Q6ISK3|Q6ISS9	In_Frame_Del	DEL	ENST00000319294.6	37	CCDS13687.1																																																																																			.	.	none		0.604	UBASH3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195382.1	NM_001001895		-	43826436	CGTTGGCAGCCA	-	43826425	7	5	6	1	0	1	0	1	0	0	0	0	16854	768	27	0	128	0	UBASH3A	21	43826425	In_Frame_Del	DEL	CGTTGGCAGCCA	TCGA-FA-A7DS-01A-11D-A382-10		43826425	4303470	84	669											
PPEF1	5475	hgsc.bcm.edu	37	chrX	18824536	18824536	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accaggtggtgactatatttTctgcttctaattattatgaa	11	17	7	6	0	2	2	0	2	2	0	2	2	2	2	1	2	1	1	1	2	6	8			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chrX:18824536T>C	ENST00000361511.4	+	15	1761	c.1267T>C	c.(1267-1269)Tct>Cct	p.S423P	PPEF1_ENST00000544635.1_Missense_Mutation_p.S358P|PPEF1_ENST00000359763.6_Missense_Mutation_p.S370P|PPEF1_ENST00000349874.5_Missense_Mutation_p.S361P|PPEF1_ENST00000543630.1_Intron	NM_006240.2|NM_152224.1	NP_006231.2|NP_689410.1	O14829	PPE1_HUMAN	protein phosphatase, EF-hand calcium binding domain 1	423	Catalytic.				detection of stimulus involved in sensory perception (GO:0050906)|phototransduction, visible light (GO:0007603)|protein dephosphorylation (GO:0006470)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)	cytosol (GO:0005829)	calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|manganese ion binding (GO:0030145)|protein serine/threonine phosphatase activity (GO:0004722)			breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(19)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	43	Hepatocellular(33;0.183)					GACTATATTTTCTGCTTCTAA	0.368																																					p.S423P		Atlas-SNP	.											.	PPEF1	89	.	0			c.T1267C						PASS	.						130	129	129					X																	18824536		2203	4300	6503	SO:0001583	missense	5475	exon15			ATATTTTCTGCTT	BC036026	CCDS14188.1, CCDS43920.1	Xp22	2013-01-10			ENSG00000086717	ENSG00000086717		"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits", "EF-hand domain containing"	9243	protein-coding gene	gene with protein product	"protein phosphatase 7, catalytic subunit, alpha isozyme"	300109		PPEF		9215685, 9326663	Standard	NM_152224		Approved	PPP7CA	uc004cyq.3	O14829	OTTHUMG00000021219	ENST00000361511.4:c.1267T>C	X.37:g.18824536T>C	ENSP00000354871:p.Ser423Pro	185	0	0		152	54	0.355263	NM_006240	A6NHP4|A8K348|O15253|Q9NU21|Q9UJH0	Missense_Mutation	SNP	ENST00000361511.4	37	CCDS14188.1	.	.	.	.	.	.	.	.	.	.	t	16.53	3.150243	0.57151	.	.	ENSG00000086717	ENST00000361511;ENST00000359763;ENST00000349874;ENST00000544635	T;T;T;T	0.28895	1.59;1.59;1.59;1.59	5.57	5.57	0.84162	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (2);	0.397724	0.23189	N	0.050933	T	0.65281	0.2676	M	0.92122	3.275	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.74386	-0.3682	10	0.72032	D	0.01	-7.5314	14.7291	0.69368	0.0:0.0:0.0:1.0	.	361;423;395	O14829-5;O14829;O14829-3	.;PPE1_HUMAN;.	P	423;370;361;358	ENSP00000354871:S423P;ENSP00000352806:S370P;ENSP00000341892:S361P;ENSP00000441289:S358P	ENSP00000341892:S361P	S	+	1	0	PPEF1	18734457	1.000000	0.71417	0.999000	0.59377	0.181000	0.23173	7.563000	0.82314	1.859000	0.53934	0.414000	0.27820	TCT	.	.	none		0.368	PPEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055953.3	NM_006240		C	18824536	T	C	18824536	3	2	6	1	0	0	0	0	1	0	0	0	12316	1783	62	3	1313	3	PPEF1	23	18824536	Missense_Mutation	SNP	T	TCGA-FA-A7DS-01A-11D-A382-10		18824536	136446024	85	670											
DMD	1756	hgsc.bcm.edu	37	chrX	32407663	32407664	+	Frame_Shift_Ins	INS	-	-	T																															ctacttcctgttccacactcINStttgtttccaatgcaggcaa																								rs398123957		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chrX:32407663_32407664insT	ENST00000357033.4	-	32	4678_4679	c.4472_4473insA	c.(4471-4473)aagfs	p.K1491fs	DMD_ENST00000378677.2_Frame_Shift_Ins_p.K1487fs	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	1491	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)				GTTCCACACTCTTTGTTTCCAA	0.401																																					p.K1491fs		Pindel,Atlas-Indel	.											.	DMD	2127	.	0			c.4473_4474insA						PASS	.																																			SO:0001589	frameshift_variant	1756	exon32			.	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.4473dupA	X.37:g.32407666_32407666dupT	ENSP00000354923:p.Lys1491fs	251	0	.		204	44	0.216	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Frame_Shift_Ins	INS	ENST00000357033.4	37	CCDS14233.1																																																																																			.	.	none		0.401	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		T	32407664	-	T	32407663	7	5	6	1	0	1	1	0	0	0	0	0	4582	912	32	0	6924	0	DMD	23	32407663	Frame_Shift_Ins	INS	-	TCGA-FA-A7DS-01A-11D-A382-10	13583127	32407663	122862897	86	671											
BCOR	54880	hgsc.bcm.edu	37	chrX	39933243	39933243	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcatgtggtcagctttggaAgcatctacatccaccacttt	9	14	7	11	0	3	0	2	0	1	0	4	1	4	1	2	2	3	2	2	2	2	4			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chrX:39933243A>G	ENST00000378444.4	-	4	1584	c.1356T>C	c.(1354-1356)gcT>gcC	p.A452A	BCOR_ENST00000378455.4_Silent_p.A452A|BCOR_ENST00000397354.3_Silent_p.A452A|BCOR_ENST00000342274.4_Silent_p.A452A	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	452					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						CAGCTTTGGAAGCATCTACAT	0.498			"F, N, S, T"	RARA	"retinoblastoma, AML, APL(translocation)"		oculo-facio-cardio-dental genetic																														p.A452A		Atlas-SNP	.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	.	0			c.T1356C						PASS	.						82	68	73					X																	39933243		2202	4300	6502	SO:0001819	synonymous_variant	54880	exon4			TTTGGAAGCATCT	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.1356T>C	X.37:g.39933243A>G		86	0	0		97	39	0.402062	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Silent	SNP	ENST00000378444.4	37	CCDS48093.1																																																																																			.	.	none		0.498	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745		G	39933243	A	G	39933243	2	3	6	1	0	0	0	0	0	0	0	1	1386	59	3	3		3	BCOR	23	39933243	Silent	SNP	A	TCGA-FA-A7DS-01A-11D-A382-10	7525580	39933243	115337317	87	672											
ZNF630	57232	hgsc.bcm.edu	37	chrX	47919314	47919314	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcaaacttatggaatttttGacttaaaggagcaaggtctg	14	13	9	5	0	2	1	1	1	1	0	2	3	2	3	0	3	2	1	0	3	6	4			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chrX:47919314G>T	ENST00000409324.3	-	5	743	c.517C>A	c.(517-519)Caa>Aaa	p.Q173K	ZNF630_ENST00000442455.3_Missense_Mutation_p.Q159K|ZNF630_ENST00000276054.4_Missense_Mutation_p.Q49K|ZNF630-AS1_ENST00000436124.1_RNA	NM_001037735.2	NP_001032824.2	Q2M218	ZN630_HUMAN	zinc finger protein 630	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(6)|lung(11)|ovary(1)	19						TGGAATTTTTGACTTAAAGGA	0.383																																					p.Q173K		Atlas-SNP	.											.	ZNF630	71	.	0			c.C517A						PASS	.						66	56	59					X																	47919314		2194	4286	6480	SO:0001583	missense	57232	exon5			ATTTTTGACTTAA	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.517C>A	X.37:g.47919314G>T	ENSP00000386393:p.Gln173Lys	145	0	0		140	46	0.328571	NM_001037735	F8WAG4|Q5H8Z5	Missense_Mutation	SNP	ENST00000409324.3	37	CCDS35237.2	.	.	.	.	.	.	.	.	.	.	.	0	-2.628014	0.00115	.	.	ENSG00000221994	ENST00000442455;ENST00000276054;ENST00000409324;ENST00000428686	T;T;T;T	0.07216	3.4;3.21;3.46;5.37	1.47	-1.99	0.07457	.	.	.	.	.	T	0.04543	0.0124	N	0.11724	0.165	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39187	-0.9626	9	0.49607	T	0.09	.	7.9755	0.30153	0.0:0.0:0.712:0.288	.	173	Q2M218	ZN630_HUMAN	K	159;49;173;173	ENSP00000393163:Q159K;ENSP00000354683:Q49K;ENSP00000386393:Q173K;ENSP00000407278:Q173K	ENSP00000354683:Q49K	Q	-	1	0	ZNF630	47804258	0.003000	0.15002	0.001000	0.08648	0.006000	0.05464	-0.458000	0.06737	-0.541000	0.06257	-0.760000	0.03462	CAA	.	.	none		0.383	ZNF630-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327254.1	NM_001037735		T	47919314	G	T	47919314	3	4	6	1	0	0	0	0	1	0	0	0	18069	1299	45	4	1460	4	ZNF630	23	47919314	Missense_Mutation	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	7986071	47919314	107351246	88	673											
MTMR8	55613	hgsc.bcm.edu	37	chrX	63568661	63568661	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagagagaggctggctacagCggcaaatggcagcctgtaag	12	5	15	9	1	0	2	0	0	0	2	0	3	0	2	1	4	3	5	1	4	3	2	rs201816063		TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chrX:63568661C>T	ENST00000374852.3	-	6	678	c.611G>A	c.(610-612)cGc>cAc	p.R204H	MTMR8_ENST00000453546.1_Missense_Mutation_p.R204H	NM_017677.3	NP_060147.2	Q96EF0	MTMR8_HUMAN	myotubularin related protein 8	204	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.					nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.0?(1)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|skin(3)	37						CTGGCTACAGCGGCAAATGGC	0.453													C|||	1	0.000264901	0.0	0.0	3775	,	,		12545	0.001		0.0	False		,,,				2504	0.0				p.R204H		Atlas-SNP	.											.	MTMR8	178	.	1	Whole gene deletion(1)	ovary(1)	c.G611A						PASS	.	C	HIS/ARG	1,3834		0,0,1,1632,570	80	64	69		611	-0.4	1	X		69	0,6728		0,0,0,2428,1872	yes	missense	MTMR8	NM_017677.3	29	0,0,1,4060,2442	TT,TC,T,CC,C		0.0,0.0261,0.0095	probably-damaging	204/705	63568661	1,10562	2203	4300	6503	SO:0001583	missense	55613	exon6			CTACAGCGGCAAA	AK000133	CCDS14379.1	Xq11.2-q12	2013-01-11			ENSG00000102043	ENSG00000102043		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	16825	protein-coding gene	gene with protein product						11275328	Standard	NM_017677		Approved	FLJ20126	uc004dvs.3	Q96EF0	OTTHUMG00000021707	ENST00000374852.3:c.611G>A	X.37:g.63568661C>T	ENSP00000363985:p.Arg204His	77	0	0		90	31	0.344444	NM_017677	Q5JT99|Q9NXP6	Missense_Mutation	SNP	ENST00000374852.3	37	CCDS14379.1	.	.	.	.	.	.	.	.	.	.	C	13.15	2.150406	0.37923	2.61E-4	0.0	ENSG00000102043	ENST00000453546;ENST00000374852	D;D	0.98164	-4.76;-4.76	2.68	-0.425	0.12317	Myotubularin phosphatase domain (1);Myotubularin-related (1);	0.000000	0.49305	U	0.000148	D	0.99208	0.9725	H	0.99312	4.51	0.49798	D	0.99982	B;D	0.89917	0.086;1.0	B;D	0.91635	0.022;0.999	D	0.97436	1.0018	10	0.87932	D	0	.	7.0652	0.25147	0.0:0.6388:0.0:0.3612	.	204;204	B4DQL0;Q96EF0	.;MTMR8_HUMAN	H	204	ENSP00000394003:R204H;ENSP00000363985:R204H	ENSP00000363985:R204H	R	-	2	0	MTMR8	63485386	0.995000	0.38212	0.991000	0.47740	0.994000	0.84299	1.318000	0.33643	-0.414000	0.07495	0.506000	0.49869	CGC	.	.	weak		0.453	MTMR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056949.2	NM_017677		T	63568661	C	T	63568661	3	4	6	1	0	0	0	0	1	0	0	0	9958	768	27	1	1539	1	MTMR8	23	63568661	Missense_Mutation	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10	15649347	63568661	91701899	89	674											
NXF3	56000	hgsc.bcm.edu	37	chrX	102338561	102338561	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	actgggacgaagggtacactGcattcattctgaatcaaatt	13	11	9	8	1	3	1	2	1	1	0	3	3	3	2	0	2	2	2	0	2	4	4			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chrX:102338561G>A	ENST00000395065.3	-	4	512	c.411C>T	c.(409-411)tgC>tgT	p.C137C	NXF3_ENST00000425644.1_5'UTR|NXF3_ENST00000425463.2_Silent_p.C48C	NM_022052.1	NP_071335.1	Q9H4D5	NXF3_HUMAN	nuclear RNA export factor 3	137	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						AGGGTACACTGCATTCATTCT	0.473																																					p.C137C		Atlas-SNP	.											.	NXF3	81	.	0			c.C411T						PASS	.						148	135	139					X																	102338561		2203	4300	6503	SO:0001819	synonymous_variant	56000	exon4			TACACTGCATTCA	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.411C>T	X.37:g.102338561G>A		235	0	0		226	75	0.331858	NM_022052	B4DYS7|Q5H9I1|Q9H1A9	Silent	SNP	ENST00000395065.3	37	CCDS14503.1	.	.	.	.	.	.	.	.	.	.	G	0.023	-1.405290	0.01155	.	.	ENSG00000147206	ENST00000427570	.	.	.	3.78	2.03	0.26663	.	.	.	.	.	.	.	.	.	.	.	0.31288	N	0.689788	.	.	.	.	.	.	.	.	.	.	.	.	.	-2.3248	5.4863	0.16751	0.2605:0.0:0.7395:0.0	.	.	.	.	X	14	.	.	Q	-	1	0	NXF3	102225217	0.513000	0.26194	0.027000	0.17364	0.003000	0.03518	0.488000	0.22371	0.428000	0.26173	-0.176000	0.13171	CAG	.	.	none		0.473	NXF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057684.1	NM_022052		A	102338561	G	A	102338561	2	1	6	1	0	0	0	0	0	0	0	1	10794	1311	46	2		2	NXF3	23	102338561	Silent	SNP	G	TCGA-FA-A7DS-01A-11D-A382-10	38769900	102338561	52931999	90	675											
ZIC3	7547	hgsc.bcm.edu	37	chrX	136649636	136649636	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	atcgacgaggctcagctgagCcggcccaagaagagctgcga	11	4	14	12	4	1	3	1	1	0	2	2	6	1	3	2	2	4	3	2	2	2	0			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chrX:136649636C>G	ENST00000287538.5	+	1	1336	c.786C>G	c.(784-786)agC>agG	p.S262R	ZIC3_ENST00000370606.3_Missense_Mutation_p.S262R	NM_003413.3	NP_003404.1	O60481	ZIC3_HUMAN	Zic family member 3	262					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)					CTCAGCTGAGCCGGCCCAAGA	0.632																																					p.S262R		Atlas-SNP	.											.	ZIC3	93	.	0			c.C786G						PASS	.						49	47	47					X																	136649636		2203	4300	6503	SO:0001583	missense	7547	exon1			GCTGAGCCGGCCC	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.786C>G	X.37:g.136649636C>G	ENSP00000287538:p.Ser262Arg	72	0	0		73	23	0.315068	NM_003413	B2CNW4|Q14DE5|Q5JY75	Missense_Mutation	SNP	ENST00000287538.5	37	CCDS14663.1	.	.	.	.	.	.	.	.	.	.	c	13.20	2.165805	0.38217	.	.	ENSG00000156925	ENST00000287538;ENST00000370606	T;T	0.12255	2.7;2.75	4.58	3.65	0.41850	Zinc finger, C2H2-like (1);	0.143603	0.64402	D	0.000008	T	0.10165	0.0249	L	0.27053	0.805	0.39225	D	0.963566	B	0.12630	0.006	B	0.14578	0.011	T	0.09122	-1.0689	10	0.62326	D	0.03	.	9.6292	0.39770	0.0:0.8829:0.0:0.1171	.	262	O60481	ZIC3_HUMAN	R	262	ENSP00000287538:S262R;ENSP00000359638:S262R	ENSP00000287538:S262R	S	+	3	2	ZIC3	136477302	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.318000	0.43779	0.807000	0.34208	0.597000	0.82753	AGC	.	.	none		0.632	ZIC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058526.1			G	136649636	C	G	136649636	3	3	6	1	0	0	0	0	1	0	0	0	17695	738	26	4	788	4	ZIC3	23	136649636	Missense_Mutation	SNP	C	TCGA-FA-A7DS-01A-11D-A382-10	34311075	136649636	18620924	91	676											
GPR50	9248	hgsc.bcm.edu	37	chrX	150348670	150348670	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctccctctcctcatcgtgggTttctgctacgtgaggatctg	4	14	10	13	2	4	1	1	1	3	0	7	2	5	2	2	2	2	2	2	2	1	2			TCGA-FA-A7DS-01A-11D-A382-10	TCGA-FA-A7DS-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	d742814c-f5f3-4231-a2e0-6014e315d672	8e110330-8f35-4680-b920-cca0e6156105	g.chrX:150348670T>A	ENST00000218316.3	+	2	684	c.615T>A	c.(613-615)ggT>ggA	p.G205G	GPR50-AS1_ENST00000454196.1_RNA|AF003625.3_ENST00000602313.1_lincRNA	NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	205					cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|identical protein binding (GO:0042802)|melatonin receptor activity (GO:0008502)			breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	38	Acute lymphoblastic leukemia(192;6.56e-05)					TCATCGTGGGTTTCTGCTACG	0.527																																					p.G205G		Atlas-SNP	.											.	GPR50	195	.	0			c.T615A						PASS	.						235	207	216					X																	150348670		2123	4223	6346	SO:0001819	synonymous_variant	9248	exon2			CGTGGGTTTCTGC	U52219	CCDS44012.1	Xq28	2012-08-21			ENSG00000102195	ENSG00000102195		"GPCR / Class A : Orphans"	4506	protein-coding gene	gene with protein product		300207				9933574, 18400093	Standard	NM_004224		Approved	H9, Mel1c	uc010ntg.2	Q13585	OTTHUMG00000024166	ENST00000218316.3:c.615T>A	X.37:g.150348670T>A		27	0	0		25	10	0.4	NM_004224	Q0VGG3|Q3ZAR0	Silent	SNP	ENST00000218316.3	37	CCDS44012.1																																																																																			.	.	none		0.527	GPR50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060874.1	NM_004224		A	150348670	T	A	150348670	2	1	6	1	0	0	0	0	0	0	0	1	6705	1712	60	5		5	GPR50	23	150348670	Silent	SNP	T	TCGA-FA-A7DS-01A-11D-A382-10	13699034	150348670	4921890	92	677											
KLHL17	339451	hgsc.bcm.edu	37	chr1	900388	900388	+	Frame_Shift_Del	DEL	G	G	-																															gacggatggttgtacgccgtGgggggtaacgacggtagctc																										TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr1:900388delG	ENST00000338591.3	+	12	1853	c.1746delG	c.(1744-1746)gtgfs	p.V582fs	PLEKHN1_ENST00000379407.3_5'Flank|PLEKHN1_ENST00000379409.2_5'Flank|PLEKHN1_ENST00000379410.3_5'Flank	NM_198317.2	NP_938073.1	Q6TDP4	KLH17_HUMAN	kelch-like family member 17	582	Interaction with F-actin. {ECO:0000250}.				actin cytoskeleton organization (GO:0030036)|brain development (GO:0007420)|protein ubiquitination (GO:0016567)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|dendrite cytoplasm (GO:0032839)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	protein complex scaffold (GO:0032947)			central_nervous_system(1)|kidney(2)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)|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)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.52e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.59e-23)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000469)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		TGTACGCCGTGGGGGGTAACG	0.657																																					p.V582fs		Pindel,Atlas-Indel	.											.	KLHL17	31	.	0			c.1745delT						PASS	.						96	71	80					1																	900388		2203	4298	6501	SO:0001589	frameshift_variant	339451	exon12			.	AY423763	CCDS30550.1	1p36	2013-01-30	2013-01-30		ENSG00000187961	ENSG00000187961		"Kelch-like", "BTB/POZ domain containing"	24023	protein-coding gene	gene with protein product	"actinfilin"		"kelch-like 17 (Drosophila)"			12063253	Standard	NM_198317		Approved		uc001aca.2	Q6TDP4	OTTHUMG00000040721	ENST00000338591.3:c.1746delG	1.37:g.900388delG	ENSP00000343930:p.Val582fs	39	0	.		38	13	0.342	NM_198317	Q5SV94	Frame_Shift_Del	DEL	ENST00000338591.3	37	CCDS30550.1																																																																																			.	.	none		0.657	KLHL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097875.3	NM_198317		-	900388	G	-	900388	7	5	7	1	0	1	0	1	0	0	0	0	8381	1335	47	0	1792	0	KLHL17	1	900388	Frame_Shift_Del	DEL	G	TCGA-FA-A7Q1-01A-11D-A382-10		900388	248350233	1	678											
PGD	5226	hgsc.bcm.edu	37	chr1	10479771	10479771	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acaccaactggacaggccatGgtggcaccgtgtcatcctcg	9	7	11	14	2	1	0	1	0	0	0	3	1	2	1	4	4	1	1	4	4	1	0			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr1:10479771G>A	ENST00000270776.8	+	13	1455	c.1417G>A	c.(1417-1419)Ggt>Agt	p.G473S	PGD_ENST00000538557.1_Missense_Mutation_p.G460S|PGD_ENST00000498356.1_3'UTR|PGD_ENST00000541529.1_Missense_Mutation_p.G451S	NM_002631.2	NP_002622.2	P52209	6PGD_HUMAN	phosphogluconate dehydrogenase	473					carbohydrate metabolic process (GO:0005975)|D-gluconate metabolic process (GO:0019521)|oxidation-reduction process (GO:0055114)|pentose biosynthetic process (GO:0019322)|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)|nucleus (GO:0005634)	NADP binding (GO:0050661)|phosphogluconate dehydrogenase (decarboxylating) activity (GO:0004616)			NS(1)|breast(1)|cervix(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	14	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;3.14e-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)|STAD - Stomach adenocarcinoma(132;0.00832)|READ - Rectum adenocarcinoma(331;0.0487)	Dacarbazine(DB00851)|Furosemide(DB00695)|Gadopentetate dimeglumine(DB00789)|Ketotifen(DB00920)|Meloxicam(DB00814)|Methotrexate(DB00563)|Ritodrine(DB00867)	GACAGGCCATGGTGGCACCGT	0.547																																					p.G473S		Atlas-SNP	.											.	PGD	39	.	0			c.G1417A						PASS	.						197	165	176					1																	10479771		2203	4300	6503	SO:0001583	missense	5226	exon13			GGCCATGGTGGCA	BC000368	CCDS113.1	1p36.22	2012-10-02			ENSG00000142657	ENSG00000142657	1.1.1.43		8891	protein-coding gene	gene with protein product		172200					Standard	NM_002631		Approved		uc001arc.3	P52209	OTTHUMG00000001905	ENST00000270776.8:c.1417G>A	1.37:g.10479771G>A	ENSP00000270776:p.Gly473Ser	62	0	0		66	37	0.560606	NM_002631	A8K2Y9|B4DQJ8|Q9BWD8	Missense_Mutation	SNP	ENST00000270776.8	37	CCDS113.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.792914	0.90453	.	.	ENSG00000142657	ENST00000541529;ENST00000543846;ENST00000270776;ENST00000538557	T;T;T	0.42900	0.96;0.96;0.96	5.08	5.08	0.68730	Fibritin/6-phosphogluconate dehydrogenase, C-terminal extension (1);6-phosphogluconate dehydrogenase, C-terminal-like (1);	0.000000	0.85682	D	0.000000	T	0.63177	0.2489	L	0.59967	1.855	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.66031	-0.6024	10	0.87932	D	0	-18.254	18.8577	0.92259	0.0:0.0:1.0:0.0	.	451;473;473	F5H7U0;A8K2Y9;P52209	.;.;6PGD_HUMAN	S	451;419;473;460	ENSP00000442285:G451S;ENSP00000270776:G473S;ENSP00000437822:G460S	ENSP00000270776:G473S	G	+	1	0	PGD	10402358	1.000000	0.71417	0.751000	0.31187	0.446000	0.32137	9.279000	0.95777	2.521000	0.84997	0.555000	0.69702	GGT	.	.	none		0.547	PGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005398.1	NM_002631		A	10479771	G	A	10479771	3	1	7	1	0	0	0	0	1	0	0	0	11796	1348	47	2	1467	2	PGD	1	10479771	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	9579383	10479771	238770850	2	679											
CTRC	11330	hgsc.bcm.edu	37	chr1	15769988	15769990	+	In_Frame_Del	DEL	AGA	AGA	-																															ccaggtggcctgcctgccagAgaaggactccctgctcccca																										TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr1:15769988_15769990delAGA	ENST00000375949.4	+	5	457_459	c.431_433delAGA	c.(430-435)gagaag>gag	p.K145del	CTRC_ENST00000483406.1_3'UTR|CTRC_ENST00000375943.2_3'UTR	NM_007272.2	NP_009203.2	Q99895	CTRC_HUMAN	chymotrypsin C (caldecrin)	145	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)		peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)	13		Breast(348;0.000207)|all_lung(284;0.00021)|Colorectal(325;0.000257)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)|Hepatocellular(190;0.0634)		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)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TGCCTGCCAGAGAAGGACTCCCT	0.576																																					p.144_144del		Pindel,Atlas-Indel	.											.	CTRC	28	.	0			c.430_432del						PASS	.																																			SO:0001651	inframe_deletion	11330	exon5			.	BC015118	CCDS156.1	1p36.21	2009-02-18			ENSG00000162438	ENSG00000162438	3.4.21.2		2523	protein-coding gene	gene with protein product	"elastase 4"	601405				8635596	Standard	NM_007272		Approved	CLCR, ELA4	uc001awi.1	Q99895	OTTHUMG00000002255	ENST00000375949.4:c.431_433delAGA	1.37:g.15769988_15769990delAGA	ENSP00000365116:p.Lys145del	56	0	.		56	19	0.339	NM_007272	A8K082|O00765|Q9NUH5	In_Frame_Del	DEL	ENST00000375949.4	37	CCDS156.1																																																																																			.	.	none		0.576	CTRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006435.1	NM_007272		-	15769990	AGA	-	15769988	7	5	7	1	0	1	0	1	0	0	0	0	4029	304	11	0	449	0	CTRC	1	15769988	In_Frame_Del	DEL	AGA	TCGA-FA-A7Q1-01A-11D-A382-10	5290217	15769988	233480633	3	680											
HSPG2	3339	hgsc.bcm.edu	37	chr1	22207014	22207014	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcacctgcagcagctccgcGcgctgcaccggccggccaga	7	3	13	18	5	0	1	0	0	0	1	1	1	1	1	5	2	5	6	5	2	0	0	rs377560753		TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr1:22207014G>A	ENST00000374695.3	-	16	2116	c.2037C>T	c.(2035-2037)cgC>cgT	p.R679R		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	679	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)	GCAGCTCCGCGCGCTGCACCG	0.632													G|||	1	0.000199681	0.0	0.0	5008	,	,		19729	0.001		0.0	False		,,,				2504	0.0				p.R679R		Atlas-SNP	.											.	HSPG2	311	.	0			c.C2037T						PASS	.	G		0,4398		0,0,2199	35	32	33		2037	-5.2	0.2	1		33	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	HSPG2	NM_005529.5		0,1,6497	AA,AG,GG		0.0116,0.0,0.0077		679/4392	22207014	1,12995	2199	4299	6498	SO:0001819	synonymous_variant	3339	exon16			CTCCGCGCGCTGC	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.2037C>T	1.37:g.22207014G>A		57	0	0		72	32	0.444444	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																			.	.	none		0.632	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		A	22207014	G	A	22207014	2	1	7	1	0	0	0	0	0	0	0	1	7439	1074	38	1		1	HSPG2	1	22207014	Silent	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	6437026	22207014	227043607	4	681											
ZBTB40	9923	hgsc.bcm.edu	37	chr1	22838451	22838451	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaagcgctgccgggtggctaAgagcaaacaggtgcagtgta	11	6	16	8	2	0	1	0	0	0	1	0	2	0	1	1	3	5	5	1	3	4	2			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr1:22838451A>C	ENST00000375647.4	+	11	2492	c.2285A>C	c.(2284-2286)aAg>aCg	p.K762T	ZBTB40_ENST00000404138.1_Missense_Mutation_p.K762T|ZBTB40_ENST00000374651.4_Missense_Mutation_p.K650T	NM_014870.3	NP_055685.3	Q9NUA8	ZBT40_HUMAN	zinc finger and BTB domain containing 40	762					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)		CGGGTGGCTAAGAGCAAACAG	0.542																																					p.K762T		Atlas-SNP	.											.	ZBTB40	87	.	0			c.A2285C						PASS	.						73	71	72					1																	22838451		2203	4300	6503	SO:0001583	missense	9923	exon12			TGGCTAAGAGCAA	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.2285A>C	1.37:g.22838451A>C	ENSP00000364798:p.Lys762Thr	80	0	0		72	30	0.416667	NM_001083621	O75066|Q5TFU5|Q8N1R1	Missense_Mutation	SNP	ENST00000375647.4	37	CCDS224.1	.	.	.	.	.	.	.	.	.	.	A	15.93	2.979425	0.53827	.	.	ENSG00000184677	ENST00000404138;ENST00000375647;ENST00000374651	T;T;T	0.28666	1.6;1.6;1.6	5.73	2.11	0.27256	.	0.333683	0.25500	N	0.030257	T	0.22936	0.0554	L	0.39085	1.19	0.30131	N	0.804809	P;B	0.35272	0.493;0.361	B;B	0.35971	0.215;0.107	T	0.10451	-1.0629	10	0.48119	T	0.1	-13.5347	8.9499	0.35783	0.705:0.0:0.295:0.0	.	650;762	F8WAI8;Q9NUA8	.;ZBT40_HUMAN	T	762;762;650	ENSP00000384527:K762T;ENSP00000364798:K762T;ENSP00000363782:K650T	ENSP00000363782:K650T	K	+	2	0	ZBTB40	22711038	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.785000	0.38684	0.101000	0.17610	0.533000	0.62120	AAG	.	.	none		0.542	ZBTB40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008094.1	NM_014870		C	22838451	A	C	22838451	3	2	7	1	0	0	0	0	1	0	0	0	17557	72	3	5	2323	5	ZBTB40	1	22838451	Missense_Mutation	SNP	A	TCGA-FA-A7Q1-01A-11D-A382-10	631437	22838451	226412170	5	682											
COL16A1	1307	hgsc.bcm.edu	37	chr1	32124550	32124550	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	agctggtcctggctggcctgGaggccctggtggcccctaaa	5	8	15	13	0	0	0	0	0	0	0	1	1	1	1	5	7	1	2	5	7	2	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr1:32124550G>A	ENST00000373672.3	-	63	4411	c.3895C>T	c.(3895-3897)Cca>Tca	p.P1299S	RP11-73M7.6_ENST00000591929.1_RNA|RP11-73M7.6_ENST00000591592.1_RNA|RP11-73M7.6_ENST00000608888.1_RNA|RP11-73M7.6_ENST00000609033.1_RNA|RP11-73M7.6_ENST00000587445.1_RNA|RP11-73M7.6_ENST00000593188.1_RNA|RP11-73M7.6_ENST00000609549.1_RNA|RP11-73M7.6_ENST00000589462.1_RNA|RP11-73M7.6_ENST00000610216.1_RNA|RP11-73M7.6_ENST00000585413.1_RNA|RP11-73M7.6_ENST00000610043.1_RNA|RP11-73M7.6_ENST00000607926.1_RNA|RP11-73M7.6_ENST00000609373.1_RNA|RP11-73M7.6_ENST00000609625.1_RNA|RP11-73M7.6_ENST00000585660.1_RNA|RP11-73M7.6_ENST00000445166.1_RNA|RP11-73M7.6_ENST00000588288.1_RNA|COL16A1_ENST00000271069.6_Missense_Mutation_p.P1299S|RP11-73M7.6_ENST00000608246.1_RNA|RP11-73M7.6_ENST00000609338.1_RNA|RP11-73M7.6_ENST00000608332.1_RNA	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	1299	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)		GGCTGGCCTGGAGGCCCTGGT	0.572																																					p.P1299S	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.C3895T						PASS	.						29	36	34					1																	32124550		1968	4118	6086	SO:0001583	missense	1307	exon63			GGCCTGGAGGCCC	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.3895C>T	1.37:g.32124550G>A	ENSP00000362776:p.Pro1299Ser	44	0	0		34	13	0.382353	NM_001856	Q16593|Q59F89|Q71RG9	Missense_Mutation	SNP	ENST00000373672.3	37	CCDS41297.1	.	.	.	.	.	.	.	.	.	.	G	13.71	2.319289	0.41096	.	.	ENSG00000084636	ENST00000373672;ENST00000271069;ENST00000440437	D;D;D	0.93859	-3.3;-3.3;-2.81	4.43	4.43	0.53597	.	0.154041	0.44097	D	0.000481	D	0.94883	0.8346	M	0.74258	2.255	0.27094	N	0.96278	D;D	0.61697	0.99;0.969	P;P	0.56278	0.757;0.795	D	0.89856	0.4013	10	0.30854	T	0.27	.	14.3521	0.66711	0.0:0.0:1.0:0.0	.	1299;1297	Q07092;Q07092-2	COGA1_HUMAN;.	S	1299;1299;156	ENSP00000362776:P1299S;ENSP00000271069:P1299S;ENSP00000390281:P156S	ENSP00000271069:P1299S	P	-	1	0	COL16A1	31897137	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.229000	0.58625	2.179000	0.69175	0.563000	0.77884	CCA	.	.	none		0.572	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856		A	32124550	G	A	32124550	3	1	7	1	0	0	0	0	1	0	0	0	3675	1174	41	2	955	2	COL16A1	1	32124550	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	9286099	32124550	217126071	6	683											
NFYC	4802	hgsc.bcm.edu	37	chr1	41213216	41213216	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttcatttcagaaagacttccGagtgcaggaactcccactgg	11	10	9	11	1	2	2	2	0	0	2	4	4	4	3	2	2	2	1	2	2	2	3			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr1:41213216G>A	ENST00000308733.5	+	2	122	c.116G>A	c.(115-117)cGa>cAa	p.R39Q	NFYC_ENST00000372653.1_Missense_Mutation_p.R39Q|NFYC_ENST00000425457.2_Missense_Mutation_p.R39Q|NFYC_ENST00000427410.2_Missense_Mutation_p.R39Q|NFYC_ENST00000372652.1_Missense_Mutation_p.R39Q|NFYC_ENST00000372651.1_Missense_Mutation_p.R39Q|NFYC_ENST00000372654.1_Missense_Mutation_p.R39Q|NFYC_ENST00000447388.3_Missense_Mutation_p.R39Q|NFYC_ENST00000456393.2_Missense_Mutation_p.R39Q|NFYC_ENST00000440226.3_Missense_Mutation_p.R39Q			Q13952	NFYC_HUMAN	nuclear transcription factor Y, gamma	39					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)			AAAGACTTCCGAGTGCAGGAA	0.403																																					p.R39Q		Atlas-SNP	.											.	NFYC	39	.	0			c.G116A						PASS	.						110	96	101					1																	41213216		2203	4300	6503	SO:0001583	missense	4802	exon3			ACTTCCGAGTGCA	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.116G>A	1.37:g.41213216G>A	ENSP00000312617:p.Arg39Gln	79	0	0		96	42	0.4375	NM_001142587	B4DUS6|B4DW63|D3DPV9|F8VWM3|Q59GY4|Q5T6K8|Q5T6K9|Q5T6L1|Q5TZR6|Q92869|Q9HBX1|Q9NXB5|Q9UM67|Q9UML0|Q9UMT7	Missense_Mutation	SNP	ENST00000308733.5	37		.	.	.	.	.	.	.	.	.	.	G	36	5.955404	0.97145	.	.	ENSG00000066136	ENST00000427410;ENST00000447388;ENST00000425457;ENST00000453631;ENST00000456393;ENST00000372654;ENST00000534399;ENST00000372653;ENST00000372669;ENST00000372652;ENST00000372651;ENST00000531464;ENST00000440226;ENST00000525290;ENST00000416859;ENST00000308733	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.50548	0.74;1.45;1.44;0.88;1.45;1.45;1.44;2.44;1.46;1.45;1.45;0.89;0.86;1.43	6.17	6.17	0.99709	Histone-fold (1);	0.000000	0.85682	D	0.000000	T	0.63628	0.2527	L	0.44542	1.39	0.80722	D	1	D;D;D;D;D;D;D	0.76494	0.997;0.999;0.994;0.999;0.997;0.997;0.986	D;D;P;D;D;D;P	0.77557	0.947;0.978;0.885;0.99;0.947;0.947;0.658	T	0.62320	-0.6879	10	0.72032	D	0.01	.	18.3732	0.90420	0.0:0.0:1.0:0.0	.	39;39;39;39;39;39;39	B4DW63;Q13952;Q5T6K9;Q13952-3;F8VWM3;Q13952-2;B4DUS6	.;NFYC_HUMAN;.;.;.;.;.	Q	39	ENSP00000408315:R39Q;ENSP00000404427:R39Q;ENSP00000396620:R39Q;ENSP00000397647:R39Q;ENSP00000408867:R39Q;ENSP00000361738:R39Q;ENSP00000361737:R39Q;ENSP00000361754:R39Q;ENSP00000361736:R39Q;ENSP00000361734:R39Q;ENSP00000414299:R39Q;ENSP00000436710:R39Q;ENSP00000409219:R39Q;ENSP00000312617:R39Q	ENSP00000312617:R39Q	R	+	2	0	NFYC	40985803	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.356000	0.97091	2.941000	0.99782	0.655000	0.94253	CGA	.	.	none		0.403	NFYC-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000020802.1	NM_014223		A	41213216	G	A	41213216	3	1	7	1	0	0	0	0	1	0	0	0	10400	1058	37	1	122	1	NFYC	1	41213216	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	9088666	41213216	208037405	7	684											
CLCA2	9635	hgsc.bcm.edu	37	chr1	86905898	86905898	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtgaccagcggagatgataAgcttcttggcaattgcttac	11	11	11	8	1	1	3	0	2	1	1	1	4	1	3	1	2	4	3	1	2	3	5			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr1:86905898A>C	ENST00000370565.4	+	8	1433	c.1271A>C	c.(1270-1272)aAg>aCg	p.K424T		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	424	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)		GGAGATGATAAGCTTCTTGGC	0.443																																					p.K424T	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.A1271C						PASS	.						160	154	156					1																	86905898		2203	4300	6503	SO:0001583	missense	9635	exon8			ATGATAAGCTTCT		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.1271A>C	1.37:g.86905898A>C	ENSP00000359596:p.Lys424Thr	135	0	0		112	45	0.401786	NM_006536	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	37	CCDS708.1	.	.	.	.	.	.	.	.	.	.	A	11.42	1.633645	0.29068	.	.	ENSG00000137975	ENST00000370565	T	0.11930	2.73	5.77	0.481	0.16809	von Willebrand factor, type A (3);	0.877147	0.10076	N	0.719128	T	0.02012	0.0063	N	0.08118	0	0.09310	N	1	B	0.21309	0.054	B	0.19148	0.024	T	0.46162	-0.9211	10	0.56958	D	0.05	-1.0854	6.223	0.20691	0.5663:0.2085:0.2252:0.0	.	424	Q9UQC9	CLCA2_HUMAN	T	424	ENSP00000359596:K424T	ENSP00000359596:K424T	K	+	2	0	CLCA2	86678486	0.000000	0.05858	0.001000	0.08648	0.133000	0.20885	0.646000	0.24797	0.440000	0.26502	0.533000	0.62120	AAG	.	.	none		0.443	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536		C	86905898	A	C	86905898	3	2	7	1	0	0	0	0	1	0	0	0	3460	72	3	5	1301	5	CLCA2	1	86905898	Missense_Mutation	SNP	A	TCGA-FA-A7Q1-01A-11D-A382-10	45692682	86905898	162344723	8	685											
AGL	178	hgsc.bcm.edu	37	chr1	100327164	100327164	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atttaatagagaaaaattccGttctctggattgggaaaatc	15	13	8	5	1	1	1	0	0	1	1	4	4	2	3	1	2	0	1	1	2	6	6	rs199958942		TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr1:100327164G>A	ENST00000294724.4	+	3	666	c.188G>A	c.(187-189)cGt>cAt	p.R63H	AGL_ENST00000370161.2_Missense_Mutation_p.R47H|AGL_ENST00000370165.3_Missense_Mutation_p.R63H|AGL_ENST00000361915.3_Missense_Mutation_p.R63H|AGL_ENST00000361522.4_Missense_Mutation_p.R46H|AGL_ENST00000361302.3_Missense_Mutation_p.R47H|AGL_ENST00000370163.3_Missense_Mutation_p.R63H	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	63					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)		GAAAAATTCCGTTCTCTGGAT	0.358													G|||	1	0.000199681	0.0	0.0	5008	,	,		16881	0.001		0.0	False		,,,				2504	0.0				p.R63H		Atlas-SNP	.											AGL,caecum,carcinoma,+1,2	AGL	137	2	0			c.G188A						PASS	.						67	70	69					1																	100327164		2203	4300	6503	SO:0001583	missense	178	exon3			AATTCCGTTCTCT	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.188G>A	1.37:g.100327164G>A	ENSP00000294724:p.Arg63His	187	0	0		177	73	0.412429	NM_000644	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Missense_Mutation	SNP	ENST00000294724.4	37	CCDS759.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	12.80	2.045875	0.36085	.	.	ENSG00000162688	ENST00000361915;ENST00000370165;ENST00000370163;ENST00000294724;ENST00000361302;ENST00000370161;ENST00000361522	T;T;T;T;T;T;T	0.49432	0.78;0.78;0.78;0.78;0.78;0.78;0.78	4.97	1.01	0.19927	.	0.387349	0.28989	N	0.013491	T	0.17152	0.0412	L	0.38175	1.15	0.36408	D	0.863555	B;B;B	0.12630	0.006;0.006;0.003	B;B;B	0.14578	0.011;0.008;0.005	T	0.04307	-1.0961	10	0.40728	T	0.16	.	8.5905	0.33684	0.4697:0.0:0.5303:0.0	.	46;47;63	P35573-2;P35573-3;P35573	.;.;GDE_HUMAN	H	63;63;63;63;47;47;46	ENSP00000355106:R63H;ENSP00000359184:R63H;ENSP00000359182:R63H;ENSP00000294724:R63H;ENSP00000354971:R47H;ENSP00000359180:R47H;ENSP00000354635:R46H	ENSP00000294724:R63H	R	+	2	0	AGL	100099752	0.382000	0.25148	0.945000	0.38365	0.993000	0.82548	0.745000	0.26259	-0.066000	0.12998	0.563000	0.77884	CGT	G|1.000;A|0.000	0.000	strong		0.358	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028		A	100327164	G	A	100327164	3	1	7	1	0	0	0	0	1	0	0	0	384	1145	40	1	263	1	AGL	1	100327164	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	13421266	100327164	148923457	9	686											
IGSF3	3321	hgsc.bcm.edu	37	chr1	117122394	117122394	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aataccaggccacagcgaagCgggagtcctggctggagcgg	10	4	16	11	3	0	0	0	0	0	0	1	3	1	2	3	5	4	1	3	5	3	1	rs374600687		TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr1:117122394C>T	ENST00000369486.3	-	10	3719	c.2954G>A	c.(2953-2955)cGc>cAc	p.R985H	IGSF3_ENST00000318837.6_Missense_Mutation_p.R1005H|IGSF3_ENST00000369483.1_Missense_Mutation_p.R1005H	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	985	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)		CACAGCGAAGCGGGAGTCCTG	0.607																																					p.R1005H		Atlas-SNP	.											.	IGSF3	294	.	0			c.G3014A						PASS	.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	35	35	35		2954,3014	3.8	1	1		35	1,8599		0,1,4299	no	missense,missense	IGSF3	NM_001007237.1,NM_001542.2	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	985/1195,1005/1215	117122394	1,13005	2203	4300	6503	SO:0001583	missense	3321	exon11			GCGAAGCGGGAGT	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.2954G>A	1.37:g.117122394C>T	ENSP00000358498:p.Arg985His	51	0	0		76	32	0.421053	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	C	15.04	2.714450	0.48622	0.0	1.16E-4	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.04551	3.75;3.6;3.6	4.67	3.76	0.43208	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.486707	0.22464	N	0.059711	T	0.01387	0.0045	N	0.16478	0.41	0.45914	D	0.998751	B;B	0.09022	0.002;0.002	B;B	0.06405	0.001;0.002	T	0.45425	-0.9262	10	0.45353	T	0.12	-27.7348	10.8654	0.46851	0.0:0.9072:0.0:0.0928	.	985;1005	O75054;A6NJZ6	IGSF3_HUMAN;.	H	985;1005;1005	ENSP00000358498:R985H;ENSP00000358495:R1005H;ENSP00000321184:R1005H	ENSP00000321184:R1005H	R	-	2	0	IGSF3	116923917	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.311000	0.43717	1.185000	0.42971	0.462000	0.41574	CGC	.	.	none		0.607	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542		T	117122394	C	T	117122394	3	4	7	1	0	0	0	0	1	0	0	0	7610	768	27	1	638	1	IGSF3	1	117122394	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	16795230	117122394	132128227	10	687											
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	145075777	145075777	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtccccggaccggtaaggcGtgtagtgagcccggcgggac	6	5	17	13	6	0	1	0	1	0	0	1	3	1	3	4	5	1	2	4	5	2	2			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr1:145075777G>A	ENST00000530740.1	-	1	124	c.86C>T	c.(85-87)aCg>aTg	p.T29M	PDE4DIP_ENST00000369359.4_Missense_Mutation_p.T29M|PDE4DIP_ENST00000369345.4_Missense_Mutation_p.T29M|PDE4DIP_ENST00000369348.3_Missense_Mutation_p.T29M			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)		CCGGTAAGGCGTGTAGTGAGC	0.711			T	PDGFRB	MPD																																p.T29M		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	PDE4DIP_ENST00000369348,NS,carcinoma,-1,2	PDE4DIP	817	2	0			c.C86T						PASS	.						46	59	54					1																	145075777		2203	4298	6501	SO:0001583	missense	9659	exon1			TAAGGCGTGTAGT	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.86C>T	1.37:g.145075777G>A	ENSP00000435654:p.Thr29Met	219	0	0		180	27	0.15	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	37		.	.	.	.	.	.	.	.	.	.	G	11.01	1.513553	0.27123	.	.	ENSG00000178104	ENST00000530740;ENST00000369359;ENST00000369348;ENST00000369345	T;T;T	0.08984	4.82;4.82;3.03	3.25	3.25	0.37280	.	.	.	.	.	T	0.01156	0.0038	N	0.08118	0	0.09310	N	0.999998	B;P	0.49358	0.079;0.923	B;B	0.25884	0.005;0.064	T	0.44711	-0.9310	9	0.72032	D	0.01	.	10.1438	0.42751	0.0:0.0:1.0:0.0	.	29;29	Q5TB27;E9PJ64	.;.	M	29	ENSP00000435654:T29M;ENSP00000358366:T29M;ENSP00000358354:T29M	ENSP00000358351:T29M	T	-	2	0	PDE4DIP	143787134	0.007000	0.16637	0.524000	0.27887	0.036000	0.12997	1.660000	0.37397	1.798000	0.52647	0.511000	0.50034	ACG	.	.	none		0.711	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000384663.2	NM_022359		A	145075777	G	A	145075777	3	1	7	1	0	0	0	0	1	0	0	0	11652	1145	40	1	8726	1	PDE4DIP	1	145075777	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	27953383	145075777	104174844	11	688											
FLG2	388698	hgsc.bcm.edu	37	chr1	152326298	152326298	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accagaatggccatgtctagTggtatctcctctctgtccat	8	13	8	12	0	3	1	0	0	3	1	6	1	4	1	4	2	0	1	4	2	3	2			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr1:152326298T>A	ENST00000388718.5	-	3	4036	c.3964A>T	c.(3964-3966)Act>Tct	p.T1322S	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1322					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)			CCATGTCTAGTGGTATCTCCT	0.473																																					p.T1322S		Atlas-SNP	.											.	FLG2	431	.	0			c.A3964T						PASS	.						369	313	332					1																	152326298		2203	4300	6503	SO:0001583	missense	388698	exon3			GTCTAGTGGTATC	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.3964A>T	1.37:g.152326298T>A	ENSP00000373370:p.Thr1322Ser	227	0	0		247	98	0.396761	NM_001014342	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	T	0.971	-0.700293	0.03279	.	.	ENSG00000143520	ENST00000388718	T	0.35236	1.32	2.89	-5.77	0.02369	.	.	.	.	.	T	0.03305	0.0096	N	0.13235	0.315	0.09310	N	1	B	0.19073	0.033	B	0.14023	0.01	T	0.30534	-0.9975	9	0.02654	T	1	-4.0209	3.9618	0.09413	0.6078:0.166:0.0:0.2263	.	1322	Q5D862	FILA2_HUMAN	S	1322	ENSP00000373370:T1322S	ENSP00000373370:T1322S	T	-	1	0	FLG2	150592922	.	.	0.000000	0.03702	0.007000	0.05969	.	.	-1.185000	0.02716	0.254000	0.18369	ACT	.	.	none		0.473	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		A	152326298	T	A	152326298	3	1	7	1	0	0	0	0	1	0	0	0	5931	1696	59	5	3215	5	FLG2	1	152326298	Missense_Mutation	SNP	T	TCGA-FA-A7Q1-01A-11D-A382-10	7250521	152326298	96924323	12	689											
ARHGEF2	9181	hgsc.bcm.edu	37	chr1	155917765	155917765	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggctacagcctccccgtcgcGgctctccgtctcctccggga	3	8	11	19	5	2	0	0	0	2	0	7	1	4	1	6	3	2	2	6	3	1	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr1:155917765G>A	ENST00000361247.4	-	22	3028	c.2929C>T	c.(2929-2931)Cgc>Tgc	p.R977C	ARHGEF2_ENST00000313667.4_Missense_Mutation_p.R976C|ARHGEF2_ENST00000368316.1_Missense_Mutation_p.R949C|ARHGEF2_ENST00000313695.7_Missense_Mutation_p.R949C|ARHGEF2_ENST00000477754.2_Intron|ARHGEF2_ENST00000368315.4_Missense_Mutation_p.R978C|ARHGEF2_ENST00000462460.2_Missense_Mutation_p.R1022C	NM_001162383.1|NM_001162384.1	NP_001155855.1|NP_001155856.1	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 2	977					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)					TCCCCGTCGCGGCTCTCCGTC	0.612																																					p.R977C	Melanoma(178;35 2768 6610 28839)	Atlas-SNP	.											.	ARHGEF2	81	.	0			c.C2929T						PASS	.						12	10	11					1																	155917765		1898	3573	5471	SO:0001583	missense	9181	exon22			CGTCGCGGCTCTC	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.2929C>T	1.37:g.155917765G>A	ENSP00000354837:p.Arg977Cys	99	0	0		102	43	0.421569	NM_001162383	D3DVA6|O75142|Q15079|Q5VY92|Q8TDA3|Q8WUG4|Q9H023	Missense_Mutation	SNP	ENST00000361247.4	37	CCDS53376.1	.	.	.	.	.	.	.	.	.	.	G	19.92	3.916847	0.73098	.	.	ENSG00000116584	ENST00000313695;ENST00000361247;ENST00000368315;ENST00000368316;ENST00000313667	T;T;T;T;T	0.70516	-0.49;-0.37;-0.38;-0.49;-0.49	5.22	5.22	0.72569	.	0.000000	0.45867	D	0.000323	T	0.65015	0.2651	N	0.19112	0.55	0.44771	D	0.997772	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;P;D;D	0.69654	0.948;0.893;0.95;0.965	T	0.71457	-0.4587	10	0.87932	D	0	-18.6811	11.2356	0.48938	0.0:0.0:0.8176:0.1824	.	1021;977;976;978	D3DVA5;Q92974;Q92974-2;Q5VY93	.;ARHG2_HUMAN;.;.	C	949;977;978;949;976	ENSP00000315325:R949C;ENSP00000354837:R977C;ENSP00000357298:R978C;ENSP00000357299:R949C;ENSP00000314787:R976C	ENSP00000314787:R976C	R	-	1	0	ARHGEF2	154184389	1.000000	0.71417	0.986000	0.45419	0.987000	0.75469	2.542000	0.45744	2.713000	0.92767	0.655000	0.94253	CGC	.	.	none		0.612	ARHGEF2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046204.2	NM_004723		A	155917765	G	A	155917765	3	1	7	1	0	0	0	0	1	0	0	0	903	1116	39	1	35	1	ARHGEF2	1	155917765	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	3591467	155917765	93332856	13	690											
C1orf61	10485	hgsc.bcm.edu	37	chr1	156386596	156386596	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tggaaaaggaggaagttcctCaagttaaatgttatgagatc	15	11	11	4	0	1	1	1	1	0	1	3	5	2	4	1	3	0	3	1	3	7	3			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr1:156386596C>G	ENST00000368243.1	-	3	152	c.36G>C	c.(34-36)ttG>ttC	p.L12F		NM_006365.1	NP_006356.1	Q13536	CROC4_HUMAN	chromosome 1 open reading frame 61	12						nucleus (GO:0005634)				large_intestine(2)|lung(2)|skin(1)	5	Hepatocellular(266;0.158)					GGAAGTTCCTCAAGTTAAATG	0.458																																					p.L12F		Atlas-SNP	.											.	C1orf61	15	.	0			c.G36C						PASS	.						131	130	130					1																	156386596		2203	4300	6503	SO:0001583	missense	10485	exon3			GTTCCTCAAGTTA		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.36G>C	1.37:g.156386596C>G	ENSP00000357226:p.Leu12Phe	152	0	0		177	39	0.220339	NM_006365	B1ALL5|B1ALL8	Missense_Mutation	SNP	ENST00000368243.1	37	CCDS1142.1	.	.	.	.	.	.	.	.	.	.	C	19.23	3.788423	0.70337	.	.	ENSG00000125462	ENST00000368243	.	.	.	2.64	2.64	0.31445	.	.	.	.	.	T	0.24353	0.0590	N	0.14661	0.345	0.23030	N	0.998407	D	0.71674	0.998	D	0.66979	0.948	T	0.07673	-1.0760	8	0.87932	D	0	.	8.9465	0.35762	0.0:1.0:0.0:0.0	.	12	Q13536	CROC4_HUMAN	F	12	.	ENSP00000357226:L12F	L	-	3	2	C1orf61	154653220	0.044000	0.20184	0.869000	0.34112	0.596000	0.36781	0.036000	0.13819	1.776000	0.52262	0.491000	0.48974	TTG	.	.	none		0.458	C1orf61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075988.1	NM_006365		G	156386596	C	G	156386596	3	3	7	1	0	0	0	0	1	0	0	0	2054	825	29	4	454	4	C1orf61	1	156386596	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	468831	156386596	92864025	14	691											
ARHGAP30	257106	hgsc.bcm.edu	37	chr1	161026256	161026256	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccttgcacagggaggagacGcagtgaatgtcttggaggta	10	8	16	7	1	1	2	0	1	1	1	1	5	1	4	1	4	1	3	1	4	2	3			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr1:161026256G>A	ENST00000368013.3	-	3	587	c.267C>T	c.(265-267)tgC>tgT	p.C89C	ARHGAP30_ENST00000368015.1_Intron|ARHGAP30_ENST00000368016.3_Silent_p.C89C	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	89	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)			GGGAGGAGACGCAGTGAATGT	0.577																																					p.C89C		Atlas-SNP	.											.	ARHGAP30	105	.	0			c.C267T						PASS	.						85	76	79					1																	161026256		2203	4300	6503	SO:0001819	synonymous_variant	257106	exon3			GGAGACGCAGTGA	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.267C>T	1.37:g.161026256G>A		35	0	0		49	14	0.285714	NM_001025598	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Silent	SNP	ENST00000368013.3	37	CCDS30918.1																																																																																			.	.	none		0.577	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720		A	161026256	G	A	161026256	2	1	7	1	0	0	0	0	0	0	0	1	879	1079	38	1		1	ARHGAP30	1	161026256	Silent	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	4639660	161026256	88224365	15	692											
DCAF6	55827	hgsc.bcm.edu	37	chr1	168014147	168014147	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttctgacagcacaatcagAtaagttcacagccaagccat	14	10	6	11	0	3	2	2	1	1	1	3	2	3	2	2	0	3	2	2	0	3	4			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr1:168014147A>G	ENST00000312263.6	+	14	1913	c.1709A>G	c.(1708-1710)gAt>gGt	p.D570G	DCAF6_ENST00000367843.3_Missense_Mutation_p.D590G|DCAF6_ENST00000367840.3_Missense_Mutation_p.D647G|DCAF6_ENST00000432587.2_Missense_Mutation_p.D616G	NM_001017977.2	NP_001017977.1	Q58WW2	DCAF6_HUMAN	DDB1 and CUL4 associated factor 6	570					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						GCACAATCAGATAAGTTCACA	0.388																																					p.D647G		Atlas-SNP	.											.	DCAF6	99	.	0			c.A1940G						PASS	.						111	123	119					1																	168014147		2203	4300	6503	SO:0001583	missense	55827	exon16			AATCAGATAAGTT	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.1709A>G	1.37:g.168014147A>G	ENSP00000311949:p.Asp570Gly	271	1	0.00369004		445	269	0.604494	NM_001198956	A2A295|B4DNB8|Q7L8I0|Q8IXH3|Q8TB19	Missense_Mutation	SNP	ENST00000312263.6	37	CCDS30933.1	.	.	.	.	.	.	.	.	.	.	A	13.26	2.185240	0.38609	.	.	ENSG00000143164	ENST00000367843;ENST00000432587;ENST00000312263;ENST00000367840	T;T;T;T	0.29655	1.56;1.56;1.56;1.56	5.29	4.16	0.48862	WD40 repeat-like-containing domain (1);	0.534254	0.18907	N	0.127876	T	0.13841	0.0335	N	0.24115	0.695	0.29487	N	0.85592	P;P;B;P	0.52170	0.951;0.814;0.002;0.702	P;B;B;B	0.48552	0.581;0.402;0.004;0.294	T	0.04203	-1.0969	9	0.51188	T	0.08	.	9.6019	0.39609	0.9203:0.0:0.0797:0.0	.	616;647;570;590	B4DNB8;Q58WW2-3;Q58WW2;Q58WW2-2	.;.;DCAF6_HUMAN;.	G	590;616;570;647	ENSP00000356817:D590G;ENSP00000396238:D616G;ENSP00000311949:D570G;ENSP00000356814:D647G	ENSP00000311949:D570G	D	+	2	0	DCAF6	166280771	1.000000	0.71417	0.670000	0.29842	0.817000	0.46193	2.828000	0.48120	0.848000	0.35191	0.460000	0.39030	GAT	.	.	none		0.388	DCAF6-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083661.2	NM_018442		G	168014147	A	G	168014147	3	3	7	1	0	0	0	0	1	0	0	0	4276	333	12	3	1827	3	DCAF6	1	168014147	Missense_Mutation	SNP	A	TCGA-FA-A7Q1-01A-11D-A382-10	6987891	168014147	81236474	16	693											
RC3H1	149041	hgsc.bcm.edu	37	chr1	173916598	173916598	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atagttttggaagttcgtgaGatggcaccaaaccgagacac	13	9	11	8	2	0	2	0	1	0	2	1	5	0	3	2	2	1	3	2	2	3	4			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr1:173916598G>A	ENST00000367696.2	-	15	2997	c.2646C>T	c.(2644-2646)atC>atT	p.I882I	RC3H1_ENST00000367694.2_Silent_p.I882I|RC3H1_ENST00000258349.4_Silent_p.I882I			Q5TC82	RC3H1_HUMAN	ring finger and CCCH-type domains 1	882					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						AAGTTCGTGAGATGGCACCAA	0.473																																					p.I882I		Atlas-SNP	.											.	RC3H1	110	.	0			c.C2646T						PASS	.						142	141	142					1																	173916598		2203	4300	6503	SO:0001819	synonymous_variant	149041	exon14			TCGTGAGATGGCA	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.2646C>T	1.37:g.173916598G>A		105	0	0		174	60	0.344828	NM_172071	B3KVK1|Q5W180|Q5W181|Q8IVE6|Q8N9V1	Silent	SNP	ENST00000367696.2	37	CCDS30940.1																																																																																			.	.	none		0.473	RC3H1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090733.2	NM_172071		A	173916598	G	A	173916598	2	1	7	1	0	0	0	0	0	0	0	1	13181	932	33	2		2	RC3H1	1	173916598	Silent	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	5902451	173916598	75334023	17	694											
BTG2	7832	hgsc.bcm.edu	37	chr1	203274815	203274823	+	In_Frame_Del	DEL	GGGCTGCGT	GGGCTGCGT	-																															tccagcctcctgaggacccgGggctgcgtgagcgagcagag																								rs55906353		TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	GGGCTGCGT	GGGCTGCGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr1:203274815_203274823delGGGCTGCGT	ENST00000290551.4	+	1	152_160	c.81_89delGGGCTGCGT	c.(79-90)cggggctgcgtg>cgg	p.GCV28del	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	28					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.R27R(1)		haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			TGAGGACCCGGGGCTGCGTGAGCGAGCAG	0.718																																					p.27_30del		Pindel,Atlas-Indel	.											BTG2,rectum,carcinoma,-1,3	BTG2	16	3	1	Substitution - coding silent(1)	skin(1)	c.80_88del						PASS	.																																			SO:0001651	inframe_deletion	7832	exon1			.		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.81_89delGGGCTGCGT	1.37:g.203274815_203274823delGGGCTGCGT	ENSP00000290551:p.Gly28_Val30del	63	0	.		114	25	0.219	NM_006763	A0A024R986|Q3KR25|Q5VUT0	In_Frame_Del	DEL	ENST00000290551.4	37	CCDS1437.1																																																																																			.	.	none		0.718	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		-	203274823	GGGCTGCGT	-	203274815	7	5	7	1	0	1	0	1	0	0	0	0	1556	1219	43	0	83	0	BTG2	1	203274815	In_Frame_Del	DEL	GGGCTGCGT	TCGA-FA-A7Q1-01A-11D-A382-10	29358217	203274815	45975806	18	695											
H3F3A	3020	hgsc.bcm.edu	37	chr1	226252097	226252097	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgcaaatcgaccggtggtaaAgcacccaggaagcaactggc	13	4	12	12	3	0	0	0	0	0	0	1	2	0	1	2	4	3	4	2	4	5	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr1:226252097A>C	ENST00000366813.1	+	1	420	c.45A>C	c.(43-45)aaA>aaC	p.K15N	H3F3A_ENST00000366816.1_Missense_Mutation_p.K15N|H3F3A_ENST00000366815.3_Missense_Mutation_p.K15N|RP11-396C23.4_ENST00000609423.1_RNA|H3F3A_ENST00000366814.3_Missense_Mutation_p.K15N			P84243	H33_HUMAN	H3 histone, family 3A	15					blood coagulation (GO:0007596)|brain development (GO:0007420)|DNA replication-independent nucleosome assembly (GO:0006336)|positive regulation of cell growth (GO:0030307)|response to hormone (GO:0009725)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nuclear nucleosome (GO:0000788)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	nucleosomal DNA binding (GO:0031492)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)			central_nervous_system(116)|endometrium(2)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	123	Breast(184;0.179)			GBM - Glioblastoma multiforme(131;0.203)		CCGGTGGTAAAGCACCCAGGA	0.478			Mis		glioma						OREG0014293	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K15N		Atlas-SNP	.		Dom	yes		1	1q42.12	3020	"H3 histone, family 3A"		O	.	H3F3A	245	.	0			c.A45C						PASS	.						29	30	30					1																	226252097		2203	4296	6499	SO:0001583	missense	3020	exon2			TGGTAAAGCACCC	BC029405	CCDS1550.1	1q42.12	2011-01-27			ENSG00000163041	ENSG00000163041		"Histones / Replication-independent"	4764	protein-coding gene	gene with protein product		601128		H3F3		3031613	Standard	NM_002107		Approved	H3.3A	uc001hpw.3	P84243	OTTHUMG00000037507	ENST00000366813.1:c.45A>C	1.37:g.226252097A>C	ENSP00000355778:p.Lys15Asn	151	0	0	2311	239	148	0.619247	NM_002107	P06351|P33155|Q5VV55|Q5VV56|Q66I33|Q9V3W4	Missense_Mutation	SNP	ENST00000366813.1	37	CCDS1550.1	.	.	.	.	.	.	.	.	.	.	A	9.163	1.019187	0.19355	.	.	ENSG00000163041	ENST00000366816;ENST00000366815;ENST00000366814;ENST00000366813	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	4.32	3.18	0.36537	Histone-fold (2);	0.000000	0.85682	D	0.000000	T	0.59266	0.2181	.	.	.	0.47276	D	0.999371	D;B	0.76494	0.999;0.001	D;B	0.78314	0.991;0.002	T	0.58618	-0.7605	9	0.72032	D	0.01	.	6.0363	0.19710	0.6485:0.0:0.3515:0.0	.	15;15	B4DEB1;P84243	.;H33_HUMAN	N	15	ENSP00000355781:K15N;ENSP00000355780:K15N;ENSP00000355779:K15N;ENSP00000355778:K15N	ENSP00000355778:K15N	K	+	3	2	H3F3A	224318720	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.096000	0.41738	0.626000	0.30322	0.533000	0.62120	AAA	.	.	none		0.478	H3F3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091324.1	NM_002107		C	226252097	A	C	226252097	3	2	7	1	0	0	0	0	1	0	0	0	6942	69	3	5	47	5	H3F3A	1	226252097	Missense_Mutation	SNP	A	TCGA-FA-A7Q1-01A-11D-A382-10	22977282	226252097	22998524	19	696											
CHRM3	1131	hgsc.bcm.edu	37	chr1	240071868	240071868	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ccatcgtgctcaagcttccgGgtcacagcaccatcctcaac	9	8	7	17	2	3	0	3	0	0	0	6	0	5	0	4	1	4	3	4	1	2	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr1:240071868G>C	ENST00000255380.4	+	5	1896	c.1117G>C	c.(1117-1119)Ggt>Cgt	p.G373R		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	373					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)	CAAGCTTCCGGGTCACAGCAC	0.592																																					p.G373R		Atlas-SNP	.											.	CHRM3	118	.	0			c.G1117C						PASS	.						33	26	28					1																	240071868		2203	4300	6503	SO:0001583	missense	1131	exon5			CTTCCGGGTCACA	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.1117G>C	1.37:g.240071868G>C	ENSP00000255380:p.Gly373Arg	89	0	0		90	18	0.2	NM_000740	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Missense_Mutation	SNP	ENST00000255380.4	37	CCDS1616.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.285109	0.80803	.	.	ENSG00000133019	ENST00000255380	T	0.60672	0.17	5.97	5.97	0.96955	GPCR, rhodopsin-like superfamily (1);	0.174679	0.49305	D	0.000152	T	0.72716	0.3495	L	0.58101	1.795	0.80722	D	1	D	0.55605	0.972	P	0.61275	0.886	T	0.70594	-0.4829	10	0.51188	T	0.08	-13.9681	20.4238	0.99064	0.0:0.0:1.0:0.0	.	373	P20309	ACM3_HUMAN	R	373	ENSP00000255380:G373R	ENSP00000255380:G373R	G	+	1	0	CHRM3	238138491	1.000000	0.71417	0.479000	0.27329	0.884000	0.51177	9.869000	0.99810	2.828000	0.97474	0.655000	0.94253	GGT	.	.	none		0.592	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740		C	240071868	G	C	240071868	3	2	7	1	0	0	0	0	1	0	0	0	3380	1232	43	4	1119	4	CHRM3	1	240071868	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	13819771	240071868	9178753	20	697											
SDCCAG8	10806	hgsc.bcm.edu	37	chr1	243437859	243437859	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatagaggtcattagaacaTgaggaaaccaatatgcctac	16	9	8	8	0	2	3	2	1	0	2	2	4	2	4	2	2	4	0	2	2	7	4			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr1:243437859T>C	ENST00000366541.3	+	4	439	c.321T>C	c.(319-321)caT>caC	p.H107H	SDCCAG8_ENST00000391846.1_Silent_p.H107H|SDCCAG8_ENST00000355875.4_Silent_p.H107H|SDCCAG8_ENST00000343783.6_Intron	NM_006642.3	NP_006633.1	Q86SQ7	SDCG8_HUMAN	serologically defined colon cancer antigen 8	107					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)		CATTAGAACATGAGGAAACCA	0.299																																					p.H107H		Atlas-SNP	.											.	SDCCAG8	73	.	0			c.T321C						PASS	.						80	78	79					1																	243437859		2203	4294	6497	SO:0001819	synonymous_variant	10806	exon4			AGAACATGAGGAA	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.321T>C	1.37:g.243437859T>C		300	0	0		454	117	0.257709	NM_006642	O60527|Q3ZCR6|Q8N5F2|Q9P0F1	Silent	SNP	ENST00000366541.3	37	CCDS31075.1																																																																																			.	.	none		0.299	SDCCAG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096485.1	NM_006642		C	243437859	T	C	243437859	2	2	7	1	0	0	0	0	0	0	0	1	13974	1461	51	3		3	SDCCAG8	1	243437859	Silent	SNP	T	TCGA-FA-A7Q1-01A-11D-A382-10	3365991	243437859	5812762	21	698											
OR2L2	26246	hgsc.bcm.edu	37	chr1	248202362	248202362	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atgtacgtccaagatccctgCgatctccaacagaggacaag	13	7	9	12	2	1	2	0	0	1	2	4	4	3	3	3	1	3	1	3	1	4	1	rs546778867		TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr1:248202362C>T	ENST00000366479.2	+	1	889	c.793C>T	c.(793-795)Cga>Tga	p.R265*	OR2L13_ENST00000366478.2_Intron	NM_001004686.2	NP_001004686.1	Q8NH16	OR2L2_HUMAN	olfactory receptor, family 2, subfamily L, member 2	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)|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)			AAGATCCCTGCGATCTCCAAC	0.498													c|||	1	0.000199681	0.0	0.0014	5008	,	,		19946	0.0		0.0	False		,,,				2504	0.0				p.R265X		Atlas-SNP	.											OR2L2,face,carcinoma,-1,4	OR2L2	115	4	0			c.C793T						scavenged	.						138	125	130					1																	248202362		2203	4300	6503	SO:0001587	stop_gained	26246	exon1			TCCCTGCGATCTC	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.793C>T	1.37:g.248202362C>T	ENSP00000355435:p.Arg265*	102	1	0.00980392		152	89	0.585526	NM_001004686	Q2M3T5	Nonsense_Mutation	SNP	ENST00000366479.2	37	CCDS31103.1	.	.	.	.	.	.	.	.	.	.	.	16.24	3.067941	0.55539	.	.	ENSG00000203663	ENST00000366479	.	.	.	1.9	0.911	0.19343	.	0.000000	0.27636	U	0.018492	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	0.05525	T	0.97	.	3.04	0.06135	0.243:0.5305:0.0:0.2264	.	.	.	.	X	265	.	ENSP00000355435:R265X	R	+	1	2	OR2L2	246268985	0.000000	0.05858	0.000000	0.03702	0.207000	0.24258	-2.234000	0.01203	0.005000	0.14708	0.194000	0.17425	CGA	.	.	none		0.498	OR2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096871.1	NM_001004686		T	248202362	C	T	248202362	4	4	7	1	0	0	0	0	0	1	0	0	11016	760	27	1	795	1	OR2L2	1	248202362	Nonsense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	4764503	248202362	1048259	22	699											
MBOAT2	129642	hgsc.bcm.edu	37	chr2	9002786	9002786	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taatatcctgggtataccccGtgccaaatggcagagagaat	13	9	10	9	1	0	2	0	0	0	2	1	3	1	2	4	2	2	2	4	2	6	4	rs142879518		TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr2:9002786G>A	ENST00000305997.3	-	11	1317	c.1119C>T	c.(1117-1119)caC>caT	p.H373H	MBOAT2_ENST00000486484.1_5'UTR	NM_138799.2	NP_620154.2	Q6ZWT7	MBOA2_HUMAN	membrane bound O-acyltransferase domain containing 2	373					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)					GGTATACCCCGTGCCAAATGG	0.408													G|||	1	0.000199681	0.0	0.0	5008	,	,		19011	0.0		0.001	False		,,,				2504	0.0				p.H373H	Ovarian(194;1699 3813 22401)	Atlas-SNP	.											.	MBOAT2	36	.	0			c.C1119T						PASS	.	G		0,4406		0,0,2203	96	92	94		1119	-2	1	2	dbSNP_134	94	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MBOAT2	NM_138799.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		373/521	9002786	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	129642	exon11			TACCCCGTGCCAA	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.1119C>T	2.37:g.9002786G>A		74	0	0		30	21	0.7	NM_138799	A9EDR2|Q8NCE7|Q96KY4	Silent	SNP	ENST00000305997.3	37	CCDS1660.1																																																																																			G|1.000;A|0.000	0.000	strong		0.408	MBOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206735.1	NM_138799		A	9002786	G	A	9002786	2	1	7	1	0	0	0	0	0	0	0	1	9366	1136	40	1		1	MBOAT2	2	9002786	Silent	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10		9002786	234196587	23	700											
CAD	790	hgsc.bcm.edu	37	chr2	27456274	27456274	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	catggccatggcgttgcatcGgcagcagtgccgggtgctgg	5	8	17	11	3	0	0	0	0	0	0	1	0	0	0	2	5	4	5	2	5	0	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr2:27456274G>A	ENST00000403525.1	+	19	3041	c.2897G>A	c.(2896-2898)cGg>cAg	p.R966Q	CAD_ENST00000264705.4_Missense_Mutation_p.R1029Q			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)					GCGTTGCATCGGCAGCAGTGC	0.567																																					p.R1029Q		Atlas-SNP	.											CAD,NS,malignant_melanoma,+1,1	CAD	199	1	0			c.G3086A						PASS	.						57	55	56					2																	27456274		2203	4300	6503	SO:0001583	missense	790	exon20			TGCATCGGCAGCA	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.2897G>A	2.37:g.27456274G>A	ENSP00000384510:p.Arg966Gln	58	0	0		76	33	0.434211	NM_004341	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Missense_Mutation	SNP	ENST00000403525.1	37		.	.	.	.	.	.	.	.	.	.	G	36	5.904524	0.97087	.	.	ENSG00000084774	ENST00000264705;ENST00000403525	D;D	0.97328	-4.34;-4.34	5.62	5.62	0.85841	Pre-ATP-grasp fold (1);PreATP-grasp-like fold (1);Carbamoyl-phosphate synthase, large subunit, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98043	0.9355	L	0.61218	1.895	0.80722	D	1	D;D	0.89917	0.987;1.0	P;D	0.78314	0.782;0.991	D	0.98147	1.0439	10	0.51188	T	0.08	-9.735	18.5877	0.91196	0.0:0.0:1.0:0.0	.	966;1029	F8VPD4;P27708	.;PYR1_HUMAN	Q	1029;966	ENSP00000264705:R1029Q;ENSP00000384510:R966Q	ENSP00000264705:R1029Q	R	+	2	0	CAD	27309778	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.064000	0.71169	2.804000	0.96469	0.655000	0.94253	CGG	.	.	none		0.567	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1			A	27456274	G	A	27456274	3	1	7	1	0	0	0	0	1	0	0	0	2567	1116	39	1	3164	1	CAD	2	27456274	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	18453488	27456274	215743099	24	701											
ALMS1	7840	hgsc.bcm.edu	37	chr2	73677595	73677595	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagaggctaagaatgtttCagcggttcctggaccagctg	10	10	13	8	1	1	3	1	1	0	2	2	4	2	4	2	3	2	4	2	3	3	3			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr2:73677595C>A	ENST00000264448.6	+	8	4049	c.3938C>A	c.(3937-3939)tCa>tAa	p.S1313*	ALMS1_ENST00000377715.1_Nonsense_Mutation_p.S1313*|ALMS1_ENST00000409009.1_Nonsense_Mutation_p.S1271*	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	1313	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						AAGAATGTTTCAGCGGTTCCT	0.448																																					p.S1313X		Atlas-SNP	.											.	ALMS1	384	.	0			c.C3938A						PASS	.						135	134	134					2																	73677595		1855	4100	5955	SO:0001587	stop_gained	7840	exon8			ATGTTTCAGCGGT	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.3938C>A	2.37:g.73677595C>A	ENSP00000264448:p.Ser1313*	72	0	0		90	34	0.377778	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Nonsense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	C	38	7.255527	0.98168	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	.	.	.	4.44	-1.82	0.07857	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.8702	0.35311	0.0:0.3542:0.0:0.6458	.	.	.	.	X	1271;1313;1313	.	ENSP00000264448:S1313X	S	+	2	0	ALMS1	73531103	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.394000	0.07296	-0.386000	0.07821	0.655000	0.94253	TCA	.	.	none		0.448	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		A	73677595	C	A	73677595	4	1	7	1	0	0	0	0	0	1	0	0	535	838	29	4	3968	4	ALMS1	2	73677595	Nonsense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	46221321	73677595	169521778	25	702											
NEB	4703	hgsc.bcm.edu	37	chr2	152486101	152486101	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagccacgatggggatggcGtcacttcgcaagtcgtagcc	8	7	14	12	4	1	0	1	0	0	0	3	2	1	1	2	3	2	3	2	3	2	2			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr2:152486101G>A	ENST00000172853.10	-	64	9201	c.9054C>T	c.(9052-9054)gaC>gaT	p.D3018D	NEB_ENST00000604864.1_Silent_p.D3261D|NEB_ENST00000409198.1_Silent_p.D3018D|NEB_ENST00000397345.3_Silent_p.D3261D|NEB_ENST00000603639.1_Silent_p.D3261D|NEB_ENST00000427231.2_Silent_p.D3261D			P20929	NEBU_HUMAN	nebulin	3018					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)		TGGGGATGGCGTCACTTCGCA	0.458																																					p.D3261D		Atlas-SNP	.											.	NEB	1697	.	0			c.C9783T						PASS	.						158	160	159					2																	152486101		1947	4142	6089	SO:0001819	synonymous_variant	4703	exon68			GATGGCGTCACTT	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.9054C>T	2.37:g.152486101G>A		147	0	0		120	52	0.433333	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				.	.	none		0.458	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		A	152486101	G	A	152486101	2	1	7	1	0	0	0	0	0	0	0	1	10311	1136	40	1		1	NEB	2	152486101	Silent	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	78808506	152486101	90713272	26	703											
LRP2	4036	hgsc.bcm.edu	37	chr2	170134323	170134323	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcaacccagtaaacacgcttCgatatcatatccagagttac	14	10	5	12	2	2	1	2	0	0	1	4	2	3	1	2	0	3	3	2	0	6	5			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr2:170134323C>T	ENST00000263816.3	-	13	1989	c.1704G>A	c.(1702-1704)tcG>tcA	p.S568S	LRP2_ENST00000443831.1_Intron	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	568					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)"	AAACACGCTTCGATATCATAT	0.413																																					p.S568S		Atlas-SNP	.											.	LRP2	751	.	0			c.G1704A						PASS	.						143	139	140					2																	170134323		2203	4300	6503	SO:0001819	synonymous_variant	4036	exon13			ACGCTTCGATATC		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.1704G>A	2.37:g.170134323C>T		209	0	0		219	107	0.488584	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			.	.	none		0.413	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		T	170134323	C	T	170134323	2	4	7	1	0	0	0	0	0	0	0	1	8965	871	31	1		1	LRP2	2	170134323	Silent	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	17648222	170134323	73065050	27	704											
TTN	7273	hgsc.bcm.edu	37	chr2	179593297	179593297	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	accttgaaagtgtactgaccGctgtcctgcttcattactga	9	13	8	11	1	1	3	1	3	0	0	2	3	2	3	3	0	3	3	3	0	3	4	rs369275615		TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr2:179593297G>A	ENST00000591111.1	-	64	18629	c.18405C>T	c.(18403-18405)agC>agT	p.S6135S	TTN_ENST00000589042.1_Silent_p.S6452S|TTN_ENST00000359218.5_Intron|RP11-171I2.1_ENST00000590024.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Silent_p.S5208S|TTN_ENST00000460472.2_Intron			Q8WZ42	TITIN_HUMAN	titin	12922	Ig-like 42.				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)			TGTACTGACCGCTGTCCTGCT	0.418																																					p.S6452S		Atlas-SNP	.											TTN_ENST00000356127,NS,carcinoma,0,3	TTN	18412	3	0			c.C19356T						PASS	.	G	,,,	1,3785		0,1,1892	69	61	64		,15624,,	-4.4	0.8	2		64	0,8244		0,0,4122	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	0,1,6014	AA,AG,GG		0.0,0.0264,0.0083	,,,	,5208/33424,,	179593297	1,12029	1893	4122	6015	SO:0001819	synonymous_variant	7273	exon66			CTGACCGCTGTCC	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.18405C>T	2.37:g.179593297G>A		120	0	0		125	60	0.48	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	37																																																																																				.	.	weak		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179593297	G	A	179593297	2	1	7	1	0	0	0	0	0	0	0	1	16750	1078	38	1		1	TTN	2	179593297	Silent	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	9458974	179593297	63606076	28	705											
ALS2CR4	65062	hgsc.bcm.edu	37	chr2	202501530	202501530	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcctctgggtgctctttgAgttctttagttgatggctca	5	16	12	8	0	4	2	1	2	3	0	4	3	4	2	1	2	2	4	1	2	1	5			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr2:202501530A>C	ENST00000409883.2	-	5	331	c.215T>G	c.(214-216)cTc>cGc	p.L72R	TMEM237_ENST00000409444.2_Missense_Mutation_p.L64R	NM_001044385.2	NP_001037850.1	Q96Q45	TM237_HUMAN	transmembrane protein 237	72					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						GTGCTCTTTGAGTTCTTTAGT	0.453																																					p.L72R		Atlas-SNP	.											.	TMEM237	21	.	0			c.T215G						PASS	.						64	60	61					2																	202501530		1835	4093	5928	SO:0001583	missense	65062	exon4			TCTTTGAGTTCTT	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.215T>G	2.37:g.202501530A>C	ENSP00000386264:p.Leu72Arg	40	0	0		35	19	0.542857	NM_001044385	B4E1R8|B4E2R8|E9PAR8|E9PBF8|E9PG24|E9PGX0|Q53TS9|Q53TT2|Q7Z3B6|Q8IZ18|Q8NBF8|Q96CY1	Missense_Mutation	SNP	ENST00000409883.2	37	CCDS46489.1	.	.	.	.	.	.	.	.	.	.	A	9.136	1.012703	0.19277	.	.	ENSG00000155755	ENST00000409444;ENST00000409883;ENST00000435876;ENST00000426684	T;T	0.51325	0.71;0.71	5.27	2.22	0.28083	.	0.509712	0.19376	N	0.115789	T	0.29321	0.0730	L	0.36672	1.1	0.09310	N	1	P;B	0.36837	0.571;0.343	B;B	0.33254	0.16;0.16	T	0.12630	-1.0540	10	0.15952	T	0.53	0.2704	6.1798	0.20465	0.3638:0.0:0.6362:0.0	.	72;96	E9PAR8;Q96Q45	.;TM237_HUMAN	R	64;72;72;94	ENSP00000387203:L64R;ENSP00000386264:L72R	ENSP00000387203:L64R	L	-	2	0	TMEM237	202209775	0.000000	0.05858	0.001000	0.08648	0.513000	0.34164	0.381000	0.20619	0.244000	0.21351	0.528000	0.53228	CTC	.	.	none		0.453	TMEM237-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335753.1	NM_152388		C	202501530	A	C	202501530	3	2	7	1	0	0	0	0	1	0	0	0	554	304	11	5	1047	5	ALS2CR4	2	202501530	Missense_Mutation	SNP	A	TCGA-FA-A7Q1-01A-11D-A382-10	22908233	202501530	40697843	29	706											
RHOA	387	hgsc.bcm.edu	37	chr3	49413010	49413010	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aacaatcaccagtttcttccGgatggcagccattgctgaaa	12	10	8	11	1	2	1	1	1	1	0	3	2	3	2	3	2	3	3	3	2	3	3			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr3:49413010G>A	ENST00000418115.1	-	2	397	c.13C>T	c.(13-15)Cgg>Tgg	p.R5W	RHOA_ENST00000422781.1_Missense_Mutation_p.R5W|RHOA_ENST00000454011.2_Missense_Mutation_p.R5W	NM_001664.2	NP_001655.1	P61586	RHOA_HUMAN	ras homolog family member A	5					actin cytoskeleton organization (GO:0030036)|androgen receptor signaling pathway (GO:0030521)|apical junction assembly (GO:0043297)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cerebral cortex cell migration (GO:0021795)|cleavage furrow formation (GO:0036089)|forebrain radial glial cell differentiation (GO:0021861)|negative chemotaxis (GO:0050919)|negative regulation of axonogenesis (GO:0050771)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron differentiation (GO:0045665)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification involved in bone maturation (GO:0043931)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of axonogenesis (GO:0050772)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytokinesis (GO:0032467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of podosome assembly (GO:0071803)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of translation (GO:0045727)|positive regulation of vasoconstriction (GO:0045907)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion transport (GO:0051924)|regulation of cell migration (GO:0030334)|regulation of dendrite development (GO:0050773)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of osteoblast proliferation (GO:0033688)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|Rho protein signal transduction (GO:0007266)|skeletal muscle tissue development (GO:0007519)|small GTPase mediated signal transduction (GO:0007264)|spindle assembly involved in mitosis (GO:0090307)|stress fiber assembly (GO:0043149)|stress-activated protein kinase signaling cascade (GO:0031098)|substantia nigra development (GO:0021762)|trabecula morphogenesis (GO:0061383)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	apical junction complex (GO:0043296)|axon (GO:0030424)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin binding (GO:0017022)			cervix(1)|kidney(1)|large_intestine(5)|lung(1)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	12				BRCA - Breast invasive adenocarcinoma(193;8.58e-05)|Kidney(197;0.0023)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		AGTTTCTTCCGGATGGCAGCC	0.473																																					p.R5W		Atlas-SNP	.											RHOA,NS,lymphoid_neoplasm,+1,7	RHOA	46	7	0			c.C13T						PASS	.						103	95	98					3																	49413010		2203	4300	6503	SO:0001583	missense	387	exon2			TCTTCCGGATGGC	BC001360	CCDS2795.1	3p21.3	2012-02-27	2012-02-27	2004-03-23	ENSG00000067560	ENSG00000067560			667	protein-coding gene	gene with protein product		165390	"ras homolog gene family, member A"	ARH12, ARHA		9605859	Standard	NM_001664		Approved	RhoA, Rho12, RHOH12	uc003cwu.3	P61586	OTTHUMG00000156838	ENST00000418115.1:c.13C>T	3.37:g.49413010G>A	ENSP00000400175:p.Arg5Trp	107	0	0		93	43	0.462366	NM_001664	P06749|Q53HM4|Q5U024|Q9UDJ0|Q9UEJ4	Missense_Mutation	SNP	ENST00000418115.1	37	CCDS2795.1	.	.	.	.	.	.	.	.	.	.	G	15.87	2.961576	0.53400	.	.	ENSG00000067560	ENST00000418115;ENST00000454011;ENST00000422781;ENST00000445425;ENST00000431929	T;T;T;T;T	0.72051	-0.45;1.68;-0.48;-0.62;2.04	5.89	-0.78	0.10969	Small GTP-binding protein domain (1);	0.000000	0.64402	D	0.000001	T	0.69904	0.3163	M	0.78344	2.41	0.80722	D	1	B	0.24920	0.114	B	0.17098	0.017	T	0.67130	-0.5748	10	0.59425	D	0.04	.	17.5915	0.87998	0.0:0.0:0.2927:0.7073	.	5	P61586	RHOA_HUMAN	W	5	ENSP00000400175:R5W;ENSP00000394483:R5W;ENSP00000413587:R5W;ENSP00000408402:R5W;ENSP00000400747:R5W	ENSP00000400175:R5W	R	-	1	2	RHOA	49388014	1.000000	0.71417	0.981000	0.43875	0.887000	0.51463	0.905000	0.28504	-0.467000	0.06932	-0.318000	0.08688	CGG	.	.	none		0.473	RHOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346157.3	NM_001664		A	49413010	G	A	49413010	3	1	7	1	0	0	0	0	1	0	0	0	13346	1115	39	1	584	1	RHOA	3	49413010	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10		49413010	148609420	30	707											
RNF123	63891	hgsc.bcm.edu	37	chr3	49751413	49751413	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcccagaccaactggatcCtggtgcggctctggagggta	7	7	16	11	1	1	1	0	0	1	1	2	3	2	3	3	6	2	2	3	6	2	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr3:49751413C>T	ENST00000327697.6	+	30	3052	c.2908C>T	c.(2908-2910)Ctg>Ttg	p.L970L	RNF123_ENST00000433785.1_Silent_p.L82L	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	970					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)		CAACTGGATCCTGGTGCGGCT	0.662																																					p.L970L		Atlas-SNP	.											.	RNF123	100	.	0			c.C2908T						PASS	.						57	62	60					3																	49751413		2203	4300	6503	SO:0001819	synonymous_variant	63891	exon30			TGGATCCTGGTGC	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.2908C>T	3.37:g.49751413C>T		60	0	0		28	13	0.464286	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Silent	SNP	ENST00000327697.6	37	CCDS33758.1																																																																																			.	.	none		0.662	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064		T	49751413	C	T	49751413	2	4	7	1	0	0	0	0	0	0	0	1	13448	680	24	2		2	RNF123	3	49751413	Silent	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	338403	49751413	148271017	31	708											
ZBTB20	26137	hgsc.bcm.edu	37	chr3	114070301	114070301	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gtgccccgcggcgtgtcctgGcccgagtcctggatccccgg	2	7	15	17	5	0	0	0	0	0	0	3	2	3	1	7	4	1	0	7	4	0	0			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr3:114070301G>C	ENST00000474710.1	-	4	802	c.624C>G	c.(622-624)ggC>ggG	p.G208G	ZBTB20_ENST00000462705.1_Silent_p.G135G|ZBTB20_ENST00000393785.2_Silent_p.G135G|ZBTB20_ENST00000471418.1_Silent_p.G135G|ZBTB20_ENST00000464560.1_Silent_p.G135G|ZBTB20_ENST00000481632.1_Silent_p.G135G|ZBTB20_ENST00000357258.3_Silent_p.G135G|ZBTB20-AS1_ENST00000496219.1_RNA|ZBTB20-AS1_ENST00000475939.1_RNA|ZBTB20-AS1_ENST00000467304.1_RNA	NM_001164342.1	NP_001157814.1	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20	208						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(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)		GCGTGTCCTGGCCCGAGTCCT	0.657																																					p.G208G	NSCLC(69;748 1344 9802 11203 30933)	Atlas-SNP	.											.	ZBTB20	157	.	0			c.C624G						PASS	.						68	61	63					3																	114070301		2203	4300	6503	SO:0001819	synonymous_variant	26137	exon4			GTCCTGGCCCGAG	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.624C>G	3.37:g.114070301G>C		51	0	0		33	12	0.363636	NM_001164342	Q63HP6|Q8N6R5|Q9Y410	Silent	SNP	ENST00000474710.1	37	CCDS54626.1																																																																																			.	.	none		0.657	ZBTB20-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354951.1	NM_015642		C	114070301	G	C	114070301	2	2	7	1	0	0	0	0	0	0	0	1	17544	1190	42	4		4	ZBTB20	3	114070301	Silent	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	64318888	114070301	83952129	32	709											
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121414039	121414039	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgtttctcggtggcctctagGttagcttgtttagatacatt	6	18	10	7	1	2	1	0	0	2	1	3	1	2	1	1	3	2	4	1	3	4	8			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr3:121414039G>A	ENST00000340645.5	-	13	5441	c.5316C>T	c.(5314-5316)aaC>aaT	p.N1772N	GOLGB1_ENST00000393667.3_Silent_p.N1777N	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	1772					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)		TGGCCTCTAGGTTAGCTTGTT	0.398																																					p.N1777N		Atlas-SNP	.											.	GOLGB1	319	.	0			c.C5331T						PASS	.						301	281	287					3																	121414039		2203	4300	6503	SO:0001819	synonymous_variant	2804	exon13			CTCTAGGTTAGCT	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.5316C>T	3.37:g.121414039G>A		342	1	0.00292398		361	141	0.390582	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Silent	SNP	ENST00000340645.5	37	CCDS3004.1																																																																																			.	.	none		0.398	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		A	121414039	G	A	121414039	2	1	7	1	0	0	0	0	0	0	0	1	6573	1252	44	2		2	GOLGB1	3	121414039	Silent	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	7343738	121414039	76608391	33	710											
XRN1	54464	hgsc.bcm.edu	37	chr3	142090122	142090122	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caaatgtcatcttcatagaaCacatcctcttggctattttt	11	16	4	10	0	4	1	2	0	2	1	5	1	5	1	1	1	1	1	1	1	4	6			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr3:142090122C>T	ENST00000264951.4	-	26	3144	c.3027G>A	c.(3025-3027)gtG>gtA	p.V1009V	XRN1_ENST00000392981.2_Silent_p.V1009V	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	1009					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						CTTCATAGAACACATCCTCTT	0.313																																					p.V1009V		Atlas-SNP	.											.	XRN1	138	.	0			c.G3027A						PASS	.						93	92	92					3																	142090122		2202	4300	6502	SO:0001819	synonymous_variant	54464	exon26			ATAGAACACATCC	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.3027G>A	3.37:g.142090122C>T		93	0	0		105	50	0.47619	NM_001042604	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Silent	SNP	ENST00000264951.4	37	CCDS3123.1																																																																																			.	.	none		0.313	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001		T	142090122	C	T	142090122	2	4	7	1	0	0	0	0	0	0	0	1	17474	465	17	2		2	XRN1	3	142090122	Silent	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	20676083	142090122	55932308	34	711											
PEX5L	51555	hgsc.bcm.edu	37	chr3	179537727	179537727	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctccgagccatttcttccCattctgcttgcatcttatcc	5	16	4	16	1	3	0	0	0	3	0	7	1	7	0	5	0	3	2	5	0	1	5			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr3:179537727C>T	ENST00000467460.1	-	9	1190	c.860G>A	c.(859-861)tGg>tAg	p.W287*	PEX5L_ENST00000464614.1_Nonsense_Mutation_p.W179*|PEX5L_ENST00000263962.8_Nonsense_Mutation_p.W285*|PEX5L_ENST00000465751.1_Nonsense_Mutation_p.W263*|PEX5L_ENST00000472994.1_Nonsense_Mutation_p.W228*|PEX5L_ENST00000467440.2_5'UTR|PEX5L_ENST00000468741.1_Nonsense_Mutation_p.W95*|PEX5L_ENST00000392649.3_Nonsense_Mutation_p.W179*|PEX5L_ENST00000485199.1_Nonsense_Mutation_p.W252*|PEX5L_ENST00000476138.1_Nonsense_Mutation_p.W244*	NM_001256751.1|NM_016559.2	NP_001243680.1|NP_057643.1	Q8IYB4	PEX5R_HUMAN	peroxisomal biogenesis factor 5-like	287					maintenance of protein location (GO:0045185)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, docking (GO:0016560)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of membrane potential (GO:0042391)	cytosol (GO:0005829)|dendrite (GO:0030425)|peroxisomal membrane (GO:0005778)|receptor complex (GO:0043235)	peroxisome matrix targeting signal-1 binding (GO:0005052)|peroxisome targeting sequence binding (GO:0000268)|small GTPase binding (GO:0031267)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	all_cancers(143;3.94e-14)|Ovarian(172;0.0338)|Breast(254;0.183)		OV - Ovarian serous cystadenocarcinoma(80;1.75e-26)|GBM - Glioblastoma multiforme(14;0.000518)			CATTTCTTCCCATTCTGCTTG	0.428																																					p.W287X		Atlas-SNP	.											.	PEX5L	104	.	0			c.G860A						PASS	.						208	185	193					3																	179537727		2203	4300	6503	SO:0001587	stop_gained	51555	exon9			TCTTCCCATTCTG	AJ245503	CCDS3236.1, CCDS58861.1, CCDS58862.1, CCDS58863.1, CCDS58864.1, CCDS58865.1, CCDS58866.1, CCDS58867.1	3q27.1	2013-01-10			ENSG00000114757	ENSG00000114757		"Tetratricopeptide (TTC) repeat domain containing"	30024	protein-coding gene	gene with protein product		611058				11463335	Standard	NM_016559		Approved	PEX5R, PXR2	uc003fki.2	Q8IYB4	OTTHUMG00000157363	ENST00000467460.1:c.860G>A	3.37:g.179537727C>T	ENSP00000419975:p.Trp287*	244	0	0		250	98	0.392	NM_016559	B7Z2A5|B7Z305|B7Z318|B7Z5Z5|B7Z8P2|E7EUV8|E7EUZ0|E9PEC1|E9PH97|Q9NQD1|Q9P2U3|Q9P2U4	Nonsense_Mutation	SNP	ENST00000467460.1	37	CCDS3236.1	.	.	.	.	.	.	.	.	.	.	C	38	6.700758	0.97772	.	.	ENSG00000114757	ENST00000467460;ENST00000263962;ENST00000485199;ENST00000382596;ENST00000392649;ENST00000468741;ENST00000476138;ENST00000467440;ENST00000472994;ENST00000464614;ENST00000465751	.	.	.	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.2226	18.9841	0.92763	0.0:1.0:0.0:0.0	.	.	.	.	X	287;285;252;285;179;95;244;175;228;179;263	.	ENSP00000263962:W285X	W	-	2	0	PEX5L	181020421	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.185000	0.77714	2.593000	0.87608	0.655000	0.94253	TGG	.	.	none		0.428	PEX5L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348577.1	NM_016559		T	179537727	C	T	179537727	4	4	7	1	0	0	0	0	0	1	0	0	11758	595	21	2	1048	2	PEX5L	3	179537727	Nonsense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	37447605	179537727	18484703	35	712											
TECRL	253017	hgsc.bcm.edu	37	chr4	65165691	65165691	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aaatatatatatgatacataCcagaaaattgatagcagata	21	11	5	4	0	0	4	0	2	0	2	0	4	0	4	1	0	3	1	1	0	11	9			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr4:65165691C>A	ENST00000381210.3	-	8	885		c.e8+1		TECRL_ENST00000513125.1_Splice_Site|TECRL_ENST00000507440.1_Splice_Site	NM_001010874.4	NP_001010874.2	Q5HYJ1	TECRL_HUMAN	trans-2,3-enoyl-CoA reductase-like						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						ATGATACATACCAGAAAATTG	0.299																																					.		Atlas-SNP	.											.	TECRL	106	.	0			c.774+1G>T						PASS	.						115	127	123					4																	65165691		2203	4294	6497	SO:0001630	splice_region_variant	253017	exon9			TACATACCAGAAA	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.774+1G>T	4.37:g.65165691C>A		361	1	0.00277008		398	159	0.399497	NM_001010874		Splice_Site	SNP	ENST00000381210.3	37	CCDS33990.1	.	.	.	.	.	.	.	.	.	.	C	17.39	3.376796	0.61735	.	.	ENSG00000205678	ENST00000507440;ENST00000381210	.	.	.	5.21	5.21	0.72293	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8349	0.78791	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TECRL	64848286	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	4.791000	0.62460	2.592000	0.87571	0.460000	0.39030	.	.	.	none		0.299	TECRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361705.4	NM_001010874	Intron	A	65165691	C	A	65165691	5	1	7	1	0	0	0	0	0	0	1	0	15761	521	18	4	336	4	TECRL	4	65165691	Splice_Site	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10		65165691	125988585	36	713											
SHROOM3	57619	hgsc.bcm.edu	37	chr4	77661110	77661110	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaagagcacccacagtaacaAaccatcttctcatccccaca	16	6	3	16	0	2	1	1	0	2	1	4	1	3	1	4	0	3	2	4	0	3	2			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr4:77661110A>T	ENST00000296043.6	+	5	2737	c.1784A>T	c.(1783-1785)aAa>aTa	p.K595I		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	595					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)			CACAGTAACAAACCATCTTCT	0.557																																					p.K595I		Atlas-SNP	.											.	SHROOM3	134	.	0			c.A1784T						PASS	.						211	199	203					4																	77661110		2203	4300	6503	SO:0001583	missense	57619	exon5			GTAACAAACCATC	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.1784A>T	4.37:g.77661110A>T	ENSP00000296043:p.Lys595Ile	36	0	0		59	23	0.38983	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Missense_Mutation	SNP	ENST00000296043.6	37	CCDS3579.2	.	.	.	.	.	.	.	.	.	.	A	7.364	0.625411	0.14257	.	.	ENSG00000138771	ENST00000296043	T	0.21191	2.02	5.46	-5.81	0.02340	.	2.025370	0.02041	N	0.049271	T	0.15392	0.0371	L	0.44542	1.39	0.09310	N	1	B;B;B	0.30763	0.294;0.139;0.139	B;B;B	0.30251	0.113;0.037;0.037	T	0.32322	-0.9911	10	0.72032	D	0.01	-1.1685	1.9131	0.03291	0.2337:0.2642:0.3582:0.144	.	419;595;373	B4E244;Q8TF72;B3KY47	.;SHRM3_HUMAN;.	I	595	ENSP00000296043:K595I	ENSP00000296043:K595I	K	+	2	0	SHROOM3	77880134	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.720000	0.04969	-0.486000	0.06744	0.379000	0.24179	AAA	.	.	none		0.557	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859		T	77661110	A	T	77661110	3	4	7	1	0	0	0	0	1	0	0	0	14310	14	1	5	1802	5	SHROOM3	4	77661110	Missense_Mutation	SNP	A	TCGA-FA-A7Q1-01A-11D-A382-10	12495419	77661110	113493166	37	714											
FAM190A	401145	hgsc.bcm.edu	37	chr4	92519732	92519732	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcttaccataggctacatatCgaaatcgaattgtgagccaa	14	11	7	9	2	1	1	0	1	1	0	3	3	1	1	2	1	3	1	2	1	7	5			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr4:92519732C>T	ENST00000509176.1	+	11	2515	c.2227C>T	c.(2227-2229)Cga>Tga	p.R743*	CCSER1_ENST00000333691.8_Nonsense_Mutation_p.R743*	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	743																	GGCTACATATCGAAATCGAAT	0.388																																					p.R743X		Atlas-SNP	.											.	.	.	.	0			c.C2227T						PASS	.						39	34	36					4																	92519732		692	1591	2283	SO:0001587	stop_gained	401145	exon11			ACATATCGAAATC		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.2227C>T	4.37:g.92519732C>T	ENSP00000425040:p.Arg743*	62	0	0		67	29	0.432836	NM_001145065	Q4W5M0|Q86V57	Nonsense_Mutation	SNP	ENST00000509176.1	37	CCDS47099.1	.	.	.	.	.	.	.	.	.	.	C	39	7.852994	0.98525	.	.	ENSG00000184305	ENST00000509176;ENST00000333691	.	.	.	5.77	4.91	0.64330	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	-3.0095	14.0425	0.64684	0.0:0.9266:0.0:0.0734	.	.	.	.	X	743	.	ENSP00000329482:R743X	R	+	1	2	FAM190A	92738755	1.000000	0.71417	0.995000	0.50966	0.900000	0.52787	3.685000	0.54678	2.890000	0.99128	0.650000	0.86243	CGA	.	.	none		0.388	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065		T	92519732	C	T	92519732	4	4	7	1	0	0	0	0	0	1	0	0	5526	876	31	1	2293	1	FAM190A	4	92519732	Nonsense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	14858622	92519732	98634544	38	715											
PRDM9	56979	hgsc.bcm.edu	37	chr5	23527595	23527595	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtcaccagaggacacacacaGgggagaagccctatgtctgc	12	5	12	12	0	2	2	1	0	1	2	2	4	2	3	2	3	2	0	2	3	2	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr5:23527595G>T	ENST00000296682.3	+	11	2580	c.2398G>T	c.(2398-2400)Ggg>Tgg	p.G800W		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	800					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						GACACACACAGGGGAGAAGCC	0.567										HNSCC(3;0.000094)																											p.G800W		Atlas-SNP	.											PRDM9,NS,carcinoma,-1,1	PRDM9	344	1	0			c.G2398T						scavenged	.						76	76	76					5																	23527595		2191	4296	6487	SO:0001583	missense	56979	exon11			CACACAGGGGAGA	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.2398G>T	5.37:g.23527595G>T	ENSP00000296682:p.Gly800Trp	118	1	0.00847458		172	102	0.593023	NM_020227	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	G	16.73	3.203927	0.58234	.	.	ENSG00000164256	ENST00000296682	T	0.26810	1.71	3.07	3.07	0.35406	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.62575	0.2439	H	0.96691	3.865	0.53005	D	0.999964	D	0.89917	1.0	D	0.97110	1.0	T	0.75425	-0.3322	9	0.87932	D	0	.	12.3824	0.55313	0.0:0.0:1.0:0.0	.	800	Q9NQV7	PRDM9_HUMAN	W	800	ENSP00000296682:G800W	ENSP00000296682:G800W	G	+	1	0	PRDM9	23563352	1.000000	0.71417	1.000000	0.80357	0.613000	0.37349	4.641000	0.61375	2.033000	0.60031	0.465000	0.42564	GGG	.	.	none		0.567	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		T	23527595	G	T	23527595	3	4	7	1	0	0	0	0	1	0	0	0	12475	1000	35	4	2436	4	PRDM9	5	23527595	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10		23527595	157387665	39	716											
C7	730	hgsc.bcm.edu	37	chr5	40958155	40958155	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgacacctttatatgagctGgtaaaggaagtaccttgtgc	11	12	10	8	0	0	2	0	2	0	0	0	3	0	3	2	2	3	3	2	2	6	6			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr5:40958155G>A	ENST00000313164.9	+	11	1640	c.1281G>A	c.(1279-1281)ctG>ctA	p.L427L		NM_000587.2	NP_000578.2	P10643	CO7_HUMAN	complement component 7	427	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				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)				TATATGAGCTGGTAAAGGAAG	0.403																																					p.L427L		Atlas-SNP	.											.	C7	136	.	0			c.G1281A						PASS	.						84	76	79					5																	40958155		1854	4084	5938	SO:0001819	synonymous_variant	730	exon11			TGAGCTGGTAAAG	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.1281G>A	5.37:g.40958155G>A		94	0	0		122	44	0.360656	NM_000587	Q6P3T5|Q92489	Silent	SNP	ENST00000313164.9	37	CCDS47201.1																																																																																			.	.	none		0.403	C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317680.1			A	40958155	G	A	40958155	2	1	7	1	0	0	0	0	0	0	0	1	2377	1335	47	2		2	C7	5	40958155	Silent	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	17430560	40958155	139957105	40	717											
HEATR7B2	133558	hgsc.bcm.edu	37	chr5	41038932	41038932	+	Missense_Mutation	SNP	G	G	T																															tgggagcatggagggccactGctccatagatgaccatgaca																										TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr5:41038932G>T	ENST00000399564.4	-	21	2570	c.2120C>A	c.(2119-2121)gCa>gAa	p.A707E	MROH2B_ENST00000506092.2_Missense_Mutation_p.A262E	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	707																	GAGGGCCACTGCTCCATAGAT	0.468																																					p.A707E		Atlas-SNP	.											.	.	.	.	0			c.C2120A						PASS	.						76	74	75					5																	41038932		1891	4108	5999	SO:0001583	missense	133558	exon21			GCCACTGCTCCAT		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.2120C>A	5.37:g.41038932G>T	ENSP00000382476:p.Ala707Glu	25	0	0		65	18	0.276923	NM_173489	Q68DM1|Q7Z4U4|Q8N7X3	Missense_Mutation	SNP	ENST00000399564.4	37	CCDS47202.1	.	.	.	.	.	.	.	.	.	.	G	6.769	0.510869	0.12883	.	.	ENSG00000171495	ENST00000506092;ENST00000296803;ENST00000399564	T;T	0.66280	5.01;-0.2	5.93	2.03	0.26663	Armadillo-type fold (1);	0.920724	0.09128	N	0.844815	T	0.45617	0.1351	L	0.44542	1.39	0.09310	N	1	P	0.35272	0.493	B	0.27380	0.079	T	0.32561	-0.9902	10	0.32370	T	0.25	.	3.4263	0.07412	0.1609:0.1346:0.5664:0.138	.	707	Q7Z745	HTRB2_HUMAN	E	262;412;707	ENSP00000441504:A262E;ENSP00000382476:A707E	ENSP00000296803:A412E	A	-	2	0	HEATR7B2	41074689	0.002000	0.14202	0.055000	0.19348	0.200000	0.23975	1.065000	0.30592	0.857000	0.35407	0.655000	0.94253	GCA	.	.	none		0.468	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489		T	41038932	G	T	41038932	3	4	7	1	0	0	0	0	1	0	0	0	7044	1319	46	4	2725	4	HEATR7B2	5	41038932	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	80777	41038932	139876328	41	718	14	2									
HEATR7B2	133558	hgsc.bcm.edu	37	chr5	41038933	41038933	+	Missense_Mutation	SNP	C	C	T																															gggagcatggagggccactgCtccatagatgaccatgacat																										TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr5:41038933C>T	ENST00000399564.4	-	21	2569	c.2119G>A	c.(2119-2121)Gca>Aca	p.A707T	MROH2B_ENST00000506092.2_Missense_Mutation_p.A262T	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	707																	AGGGCCACTGCTCCATAGATG	0.463																																					p.A707T		Atlas-SNP	.											.	.	.	.	0			c.G2119A						PASS	.						77	74	75					5																	41038933		1891	4107	5998	SO:0001583	missense	133558	exon21			CCACTGCTCCATA		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.2119G>A	5.37:g.41038933C>T	ENSP00000382476:p.Ala707Thr	24	0	0		66	18	0.272727	NM_173489	Q68DM1|Q7Z4U4|Q8N7X3	Missense_Mutation	SNP	ENST00000399564.4	37	CCDS47202.1	.	.	.	.	.	.	.	.	.	.	C	7.393	0.631255	0.14322	.	.	ENSG00000171495	ENST00000506092;ENST00000296803;ENST00000399564	T;T	0.67523	4.99;-0.27	5.93	0.268	0.15626	Armadillo-type fold (1);	0.920724	0.09128	N	0.844815	T	0.49355	0.1552	L	0.44542	1.39	0.09310	N	1	B	0.31548	0.328	B	0.24394	0.053	T	0.29488	-1.0010	10	0.24483	T	0.36	.	3.8653	0.09013	0.4933:0.2968:0.1285:0.0814	.	707	Q7Z745	HTRB2_HUMAN	T	262;412;707	ENSP00000441504:A262T;ENSP00000382476:A707T	ENSP00000296803:A412T	A	-	1	0	HEATR7B2	41074690	0.000000	0.05858	0.074000	0.20217	0.205000	0.24178	-0.383000	0.07398	0.367000	0.24454	0.655000	0.94253	GCA	.	.	none		0.463	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489		T	41038933	C	T	41038933	3	4	7	1	0	0	0	0	1	0	0	0	7044	797	28	2	2726	2	HEATR7B2	5	41038933	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	1	41038933	139876327	42	719	14	2									
FTMT	94033	hgsc.bcm.edu	37	chr5	121188183	121188183	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aacgtgaaccagtcgttgctGgaattgcacgctctagcctc	9	10	10	12	3	1	1	0	1	1	0	3	2	1	2	2	1	5	4	2	1	4	3			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr5:121188183G>A	ENST00000321339.1	+	1	534	c.525G>A	c.(523-525)ctG>ctA	p.L175L		NM_177478.1	NP_803431.1	Q8N4E7	FTMT_HUMAN	ferritin mitochondrial	175	Ferritin-like diiron. {ECO:0000255|PROSITE-ProRule:PRU00085}.				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)		AGTCGTTGCTGGAATTGCACG	0.502																																					p.L175L		Atlas-SNP	.											.	FTMT	71	.	0			c.G525A						PASS	.						133	123	126					5																	121188183		2203	4300	6503	SO:0001819	synonymous_variant	94033	exon1			GTTGCTGGAATTG	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.525G>A	5.37:g.121188183G>A		57	0	0		67	39	0.58209	NM_177478		Silent	SNP	ENST00000321339.1	37	CCDS4128.1																																																																																			.	.	none		0.502	FTMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250884.1	NM_177478		A	121188183	G	A	121188183	2	1	7	1	0	0	0	0	0	0	0	1	6093	1335	47	2		2	FTMT	5	121188183	Silent	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	80149250	121188183	59727077	43	720											
IRF1	3659	hgsc.bcm.edu	37	chr5	131825149	131825149	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catctctagccagggtctcaTgcgcatccgagtgatgggca	8	9	12	12	2	2	1	1	1	2	0	5	2	3	1	2	2	2	2	2	2	1	1	rs121912469		TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr5:131825149T>C	ENST00000245414.4	-	2	280	c.22A>G	c.(22-24)Atg>Gtg	p.M8V	IRF1_ENST00000463784.1_Intron|IRF1_ENST00000405885.2_Missense_Mutation_p.M8V	NM_002198.2	NP_002189.1	P10914	IRF1_HUMAN	interferon regulatory factor 1	8			M -> L (in GASC; somatic mutation; produces a protein with markedly reduced transcriptional activity but unaltered DNA-binding activity). {ECO:0000269|PubMed:9679752}.		apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell cycle arrest (GO:0007050)|cellular response to interferon-beta (GO:0035458)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cell proliferation (GO:0008285)|negative regulation of regulatory T cell differentiation (GO:0045590)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|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 adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta T cell proliferation (GO:2000564)|regulation of cell cycle (GO:0051726)|regulation of innate immune response (GO:0045088)|regulation of MyD88-dependent toll-like receptor signaling pathway (GO:0034124)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(2)|prostate(2)|skin(1)|urinary_tract(1)	11		all_cancers(142;0.026)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	LUAD - Lung adenocarcinoma(142;0.247)		CAGGGTCTCATGCGCATCCGA	0.507																																					p.M8V		Atlas-SNP	.											.	IRF1	26	.	0			c.A22G						PASS	.						93	92	93					5																	131825149		2203	4300	6503	SO:0001583	missense	3659	exon2			GTCTCATGCGCAT		CCDS4155.1	5q23-q31	2008-07-18			ENSG00000125347	ENSG00000125347			6116	protein-coding gene	gene with protein product	"interferon regulatory factor-1"	147575				2726461, 1680796	Standard	NM_002198		Approved	MAR	uc003kxa.2	P10914	OTTHUMG00000059497	ENST00000245414.4:c.22A>G	5.37:g.131825149T>C	ENSP00000245414:p.Met8Val	61	0	0		101	71	0.70297	NM_002198	Q96GG7	Missense_Mutation	SNP	ENST00000245414.4	37	CCDS4155.1	.	.	.	.	.	.	.	.	.	.	T	16.73	3.203638	0.58234	.	.	ENSG00000125347	ENST00000245414;ENST00000405885;ENST00000437654;ENST00000458069	D;D;D;D	0.97850	-4.57;-4.57;-4.57;-4.57	5.59	5.59	0.84812	Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (4);	0.000000	0.85682	D	0.000000	D	0.98476	0.9492	M	0.87827	2.91	0.80722	D	1	P;P	0.43352	0.744;0.804	P;B	0.53490	0.727;0.402	D	0.99568	1.0970	10	0.87932	D	0	-29.6414	16.0664	0.80878	0.0:0.0:0.0:1.0	.	8;8	Q5FBX3;P10914	.;IRF1_HUMAN	V	8	ENSP00000245414:M8V;ENSP00000384406:M8V;ENSP00000405655:M8V;ENSP00000396318:M8V	ENSP00000245414:M8V	M	-	1	0	IRF1	131853048	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.112000	0.71547	2.254000	0.74563	0.459000	0.35465	ATG	.	.	alt		0.507	IRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132340.1	NM_002198		C	131825149	T	C	131825149	3	2	7	1	0	0	0	0	1	0	0	0	7836	1464	51	3	991	3	IRF1	5	131825149	Missense_Mutation	SNP	T	TCGA-FA-A7Q1-01A-11D-A382-10	10636966	131825149	49090111	44	721											
ANKHD1	54882	hgsc.bcm.edu	37	chr5	139887371	139887371	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcacatttccccctttaggActgggagtaaactaggtatt	11	12	9	9	0	0	0	0	0	0	0	1	2	1	2	2	3	2	3	2	3	5	7			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr5:139887371A>G	ENST00000360839.2	+	20	3707	c.3553A>G	c.(3553-3555)Act>Gct	p.T1185A	ANKHD1-EIF4EBP3_ENST00000532219.1_Splice_Site_p.T1185A|ANKHD1_ENST00000297183.6_Splice_Site_p.T1185A	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	1185						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)			CCCCTTTAGGACTGGGAGTAA	0.363																																					p.T1185A		Atlas-SNP	.											.	ANKHD1	233	.	0			c.A3553G						PASS	.						63	61	61					5																	139887371		2203	4300	6503	SO:0001630	splice_region_variant	54882	exon20			TTTAGGACTGGGA	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.3552-1A>G	5.37:g.139887371A>G		97	0	0		135	81	0.6	NM_017747	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Missense_Mutation	SNP	ENST00000360839.2	37	CCDS4225.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.564615	0.86439	.	.	ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996	ENST00000360839;ENST00000422011;ENST00000297183;ENST00000253810;ENST00000310356;ENST00000235510;ENST00000421134;ENST00000412116;ENST00000532219	T;T;T;T;T	0.68624	-0.29;-0.33;-0.25;-0.34;-0.33	5.72	5.72	0.89469	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	D	0.82591	0.5070	M	0.80508	2.5	0.80722	D	1	P;P;P;D;D	0.69078	0.88;0.945;0.587;0.997;0.992	P;P;B;D;D	0.79108	0.771;0.619;0.444;0.992;0.989	D	0.84613	0.0679	10	0.62326	D	0.03	.	16.3625	0.83273	1.0:0.0:0.0:0.0	.	396;1185;1204;1185;1185	E7ET58;Q8IWZ3-4;E9PDP5;Q8IWZ2;Q8IWZ3	.;.;.;.;ANKH1_HUMAN	A	1185;1218;1185;1185;719;396;1204;338;1185	ENSP00000354085:T1185A;ENSP00000297183:T1185A;ENSP00000394489:T1204A;ENSP00000405602:T338A;ENSP00000432016:T1185A	ENSP00000432016:T1185A	T	+	1	0	ANKHD1-EIF4EBP3;ANKHD1	139867555	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.306000	0.96204	2.319000	0.78375	0.524000	0.50904	ACT	.	.	none		0.363	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747	Missense_Mutation	G	139887371	A	G	139887371	5	3	7	1	0	0	0	0	0	0	1	0	628	289	10	3	3737	3	ANKHD1	5	139887371	Splice_Site	SNP	A	TCGA-FA-A7Q1-01A-11D-A382-10	8062222	139887371	41027889	45	722											
CD14	929	hgsc.bcm.edu	37	chr5	140011945	140011945	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgccatcagtccgcgttcGcccagtccaggattgtcaga	7	8	11	15	4	2	1	2	0	0	1	5	2	4	2	5	1	0	1	5	1	0	2			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr5:140011945G>A	ENST00000302014.6	-	2	1253	c.624C>T	c.(622-624)ggC>ggT	p.G208G	CD14_ENST00000401743.2_Silent_p.G208G	NM_000591.3	NP_000582.1	P08571	CD14_HUMAN	CD14 molecule	208					apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|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)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|phagocytosis (GO:0006909)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of endocytosis (GO:0045807)|positive regulation of tumor necrosis factor production (GO:0032760)|response to ethanol (GO:0045471)|response to heat (GO:0009408)|response to magnesium ion (GO:0032026)|response to tumor necrosis factor (GO:0034612)|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)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|lipoteichoic acid binding (GO:0070891)|opsonin receptor activity (GO:0001847)|peptidoglycan receptor activity (GO:0016019)			endometrium(1)|large_intestine(1)|lung(3)|pancreas(1)	6			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTCCGCGTTCGCCCAGTCCAG	0.617																																					p.G208G		Atlas-SNP	.											.	CD14	20	.	0			c.C624T						PASS	.						56	61	59					5																	140011945		2203	4300	6503	SO:0001819	synonymous_variant	929	exon3			GCGTTCGCCCAGT		CCDS4232.1	5q31.3	2012-09-20	2006-03-28		ENSG00000170458	ENSG00000170458		"CD molecules"	1628	protein-coding gene	gene with protein product		158120	"CD14 antigen"			2472171, 2462937	Standard	NM_000591		Approved		uc003lgi.2	P08571	OTTHUMG00000129507	ENST00000302014.6:c.624C>T	5.37:g.140011945G>A		37	0	0		57	29	0.508772	NM_001174105	Q53XT5|Q96FR6|Q96L99|Q9UNS3	Silent	SNP	ENST00000302014.6	37	CCDS4232.1																																																																																			.	.	none		0.617	CD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251681.2	NM_000591		A	140011945	G	A	140011945	2	1	7	1	0	0	0	0	0	0	0	1	2966	1074	38	1		1	CD14	5	140011945	Silent	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	124574	140011945	40903315	46	723											
KIF4B	285643	hgsc.bcm.edu	37	chr5	154395805	154395805	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agaatccacctcctaaactcCggaagtgtacattctccctt	11	11	5	14	1	1	1	0	0	1	1	5	2	4	2	5	1	2	1	5	1	5	4	rs193075545		TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr5:154395805C>T	ENST00000435029.4	+	1	2546	c.2386C>T	c.(2386-2388)Cgg>Tgg	p.R796W		NM_001099293.1	NP_001092763.1	Q2VIQ3	KIF4B_HUMAN	kinesin family member 4B	796	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)			TCCTAAACTCCGGAAGTGTAC	0.428													C|||	1	0.000199681	0.0	0.0	5008	,	,		21789	0.0		0.001	False		,,,				2504	0.0				p.R796W		Atlas-SNP	.											.	KIF4B	307	.	0			c.C2386T						PASS	.						45	48	47					5																	154395805		2197	4299	6496	SO:0001583	missense	285643	exon1			AAACTCCGGAAGT	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.2386C>T	5.37:g.154395805C>T	ENSP00000387875:p.Arg796Trp	100	0	0		149	80	0.536913	NM_001099293		Missense_Mutation	SNP	ENST00000435029.4	37	CCDS47324.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	c	8.273	0.813896	0.16537	.	.	ENSG00000226650	ENST00000435029	T	0.69926	-0.44	1.48	0.588	0.17445	.	.	.	.	.	T	0.71230	0.3315	L	0.61218	1.895	0.58432	D	0.999994	D	0.76494	0.999	P	0.60886	0.88	T	0.68213	-0.5468	9	0.56958	D	0.05	.	6.1007	0.20045	0.0:0.8141:0.0:0.1858	.	796	Q2VIQ3	KIF4B_HUMAN	W	796	ENSP00000387875:R796W	ENSP00000387875:R796W	R	+	1	2	KIF4B	154375998	0.985000	0.35326	0.652000	0.29579	0.146000	0.21551	0.570000	0.23653	0.200000	0.20447	-0.222000	0.12452	CGG	C|1.000;T|0.000	0.000	strong		0.428	KIF4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377478.1			T	154395805	C	T	154395805	3	4	7	1	0	0	0	0	1	0	0	0	8313	643	23	1	2388	1	KIF4B	5	154395805	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	14383860	154395805	26519455	47	724											
HMMR	3161	hgsc.bcm.edu	37	chr5	162894753	162894753	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgaagatattagagaaagAggtaagcagtgctttaaact	16	12	10	3	0	0	4	0	1	0	3	0	5	0	4	0	1	3	3	0	1	7	6			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr5:162894753A>C	ENST00000358715.3	+	4	305	c.269A>C	c.(268-270)gAg>gCg	p.E90A	HMMR_ENST00000353866.3_Intron|HMMR_ENST00000393915.4_Splice_Site_p.E91A|HMMR_ENST00000432118.2_Intron			O75330	HMMR_HUMAN	hyaluronan-mediated motility receptor (RHAMM)	90					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)	TTAGAGAAAGAGGTAAGCAGT	0.328																																					p.E91A		Atlas-SNP	.											.	HMMR	64	.	0			c.A272C						PASS	.						40	40	40					5																	162894753		2203	4295	6498	SO:0001630	splice_region_variant	3161	exon4			AGAAAGAGGTAAG	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.270+1A>C	5.37:g.162894753A>C		272	0	0		415	95	0.228916	NM_001142556	A8K3G2|B4E114|D3DQK9|D3DQL0|E9PCS0|Q32N02|Q92767	Missense_Mutation	SNP	ENST00000358715.3	37	CCDS4362.1	.	.	.	.	.	.	.	.	.	.	A	18.00	3.526392	0.64860	.	.	ENSG00000072571	ENST00000393915;ENST00000426586;ENST00000358715	T;T	0.78364	-1.17;-1.17	5.98	4.8	0.61643	.	0.092606	0.64402	D	0.000001	D	0.86209	0.5878	M	0.74258	2.255	0.42286	D	0.992116	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.86671	0.1910	10	0.72032	D	0.01	-19.9829	10.1931	0.43039	0.833:0.167:0.0:0.0	.	91;90	O75330-3;O75330	.;HMMR_HUMAN	A	91;91;90	ENSP00000377492:E91A;ENSP00000351554:E90A	ENSP00000351554:E90A	E	+	2	0	HMMR	162827331	1.000000	0.71417	1.000000	0.80357	0.710000	0.40934	4.080000	0.57620	1.047000	0.40274	0.482000	0.46254	GAG	.	.	none		0.328	HMMR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252752.1	NM_012484	Missense_Mutation	C	162894753	A	C	162894753	5	2	7	1	0	0	0	0	0	0	1	0	7251	318	11	5	286	5	HMMR	5	162894753	Splice_Site	SNP	A	TCGA-FA-A7Q1-01A-11D-A382-10	8498948	162894753	18020507	48	725											
FBXW11	23291	hgsc.bcm.edu	37	chr5	171305089	171305089	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaggacagagcctgtgtgTcctgttaacactttcaaaca	12	10	9	10	0	1	2	1	0	0	2	2	3	2	3	2	1	3	1	2	1	2	2			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr5:171305089T>A	ENST00000265094.5	-	7	971	c.834A>T	c.(832-834)ggA>ggT	p.G278G	FBXW11_ENST00000425623.2_Silent_p.G246G|FBXW11_ENST00000393802.2_Silent_p.G244G|FBXW11_ENST00000522891.1_5'UTR|FBXW11_ENST00000296933.6_Silent_p.G265G	NM_012300.2	NP_036432.2	Q9UKB1	FBW1B_HUMAN	F-box and WD repeat domain containing 11	278					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|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)|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)|rhythmic process (GO:0048511)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|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(4)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(2)|urinary_tract(2)	21	Renal(175;0.000159)|Lung NSC(126;0.00384)|all_lung(126;0.00659)	Medulloblastoma(196;0.00853)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			AGCCTGTGTGTCCTGTTAACA	0.398																																					p.G278G		Atlas-SNP	.											.	FBXW11	72	.	0			c.A834T						PASS	.						109	95	100					5																	171305089		2203	4300	6503	SO:0001819	synonymous_variant	23291	exon7			TGTGTGTCCTGTT	AB014596	CCDS34289.1, CCDS47340.1, CCDS47341.1	5q35.1	2013-01-09	2007-02-08	2004-06-16	ENSG00000072803	ENSG00000072803		"F-boxes / WD-40 domains", "WD repeat domain containing"	13607	protein-coding gene	gene with protein product		605651	"F-box and WD-40 domain protein 1B", "F-box and WD-40 domain protein 11"	FBXW1B		10531035, 10694485	Standard	NM_033644		Approved	KIAA0696, Fbw1b, BTRCP2, BTRC2, Hos, Fbw11	uc003mbm.1	Q9UKB1	OTTHUMG00000163267	ENST00000265094.5:c.834A>T	5.37:g.171305089T>A		106	0	0		171	36	0.210526	NM_012300	B2RC98|Q9P2S8|Q9P2S9|Q9Y4C6	Silent	SNP	ENST00000265094.5	37	CCDS34289.1																																																																																			.	.	none		0.398	FBXW11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000372382.1	NM_012300		A	171305089	T	A	171305089	2	1	7	1	0	0	0	0	0	0	0	1	5772	1654	58	5		5	FBXW11	5	171305089	Silent	SNP	T	TCGA-FA-A7Q1-01A-11D-A382-10	8410336	171305089	9610171	49	726											
SERPINB9	5272	hgsc.bcm.edu	37	chr6	2890535	2890535	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actacaaagcagctcgacgcTgccgctgcctcggtgccttc	7	8	10	16	4	0	0	0	0	0	0	3	1	0	0	3	1	6	4	3	1	2	2			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr6:2890535T>C	ENST00000380698.4	-	7	1082	c.993A>G	c.(991-993)gcA>gcG	p.A331A		NM_004155.5	NP_004146.1	P50453	SPB9_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 9	331					cellular response to estrogen stimulus (GO:0071391)|immune response (GO:0006955)|mast cell mediated immunity (GO:0002448)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(4)|large_intestine(3)|lung(5)|pancreas(1)|prostate(1)	15	Ovarian(93;0.0412)	all_hematologic(90;0.108)				AGCTCGACGCTGCCGCTGCCT	0.542																																					p.A331A		Atlas-SNP	.											.	SERPINB9	37	.	0			c.A993G						PASS	.						104	91	95					6																	2890535		2203	4300	6503	SO:0001819	synonymous_variant	5272	exon7			CGACGCTGCCGCT	L40378	CCDS4478.1	6p25.2	2014-02-18	2005-08-18		ENSG00000170542	ENSG00000170542		"Serine (or cysteine) peptidase inhibitors"	8955	protein-coding gene	gene with protein product		601799	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 9"	PI9		8530382, 9858835, 24172014	Standard	NM_004155		Approved	CAP3	uc003mug.4	P50453	OTTHUMG00000014131	ENST00000380698.4:c.993A>G	6.37:g.2890535T>C		84	0	0		92	72	0.782609	NM_004155	B2RBW3|Q5TD03	Silent	SNP	ENST00000380698.4	37	CCDS4478.1																																																																																			.	.	none		0.542	SERPINB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039656.1			C	2890535	T	C	2890535	2	2	7	1	0	0	0	0	0	0	0	1	14123	1567	55	3		3	SERPINB9	6	2890535	Silent	SNP	T	TCGA-FA-A7Q1-01A-11D-A382-10		2890535	168224532	50	727											
KIF13A	63971	hgsc.bcm.edu	37	chr6	17788042	17788042	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttttttatctgttcatccAggtattctcgtcgtttaatg	6	21	6	8	2	3	0	1	0	2	0	6	0	4	0	1	1	0	3	1	1	3	9			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr6:17788042A>C	ENST00000259711.6	-	27	3431	c.3326T>G	c.(3325-3327)cTg>cGg	p.L1109R	KIF13A_ENST00000378843.2_Missense_Mutation_p.L1096R|KIF13A_ENST00000378826.2_Missense_Mutation_p.L1109R|KIF13A_ENST00000378816.5_Missense_Mutation_p.L1109R|KIF13A_ENST00000378814.5_Missense_Mutation_p.L1096R	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	1109					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)			CTGTTCATCCAGGTATTCTCG	0.398																																					p.L1109R		Atlas-SNP	.											.	KIF13A	276	.	0			c.T3326G						PASS	.						321	294	302					6																	17788042		1889	4121	6010	SO:0001583	missense	63971	exon27			TCATCCAGGTATT	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.3326T>G	6.37:g.17788042A>C	ENSP00000259711:p.Leu1109Arg	169	0	0		177	71	0.40113	NM_001105566	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Missense_Mutation	SNP	ENST00000259711.6	37	CCDS47381.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	26.2|26.2	4.710033|4.710033	0.89018|0.89018	.|.	.|.	ENSG00000137177|ENSG00000137177	ENST00000378814;ENST00000502297;ENST00000259711;ENST00000378826;ENST00000378843;ENST00000378816;ENST00000506044|ENST00000358380	D;T;D;D;D;D|.	0.82255|.	-1.57;0.67;-1.59;-1.56;-1.57;-1.55|.	5.9|5.9	5.9|5.9	0.94986|0.94986	.|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.70649|0.70649	0.3248|0.3248	M|M	0.77616|0.77616	2.38|2.38	0.58432|0.58432	D|D	0.999999|0.999999	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|T	0.72418|0.72418	-0.4300|-0.4300	10|5	0.87932|.	D|.	0|.	.|.	16.3245|16.3245	0.82970|0.82970	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1096;1109;1109;1096|.	Q9H1H9-4;Q9H1H9-2;Q9H1H9;Q9H1H9-3|.	.;.;KI13A_HUMAN;.|.	R|G	1096;113;1109;1109;1096;1109;107|503	ENSP00000368091:L1096R;ENSP00000425616:L113R;ENSP00000259711:L1109R;ENSP00000368103:L1109R;ENSP00000368120:L1096R;ENSP00000368093:L1109R|.	ENSP00000259711:L1109R|.	L|W	-|-	2|1	0|0	KIF13A|KIF13A	17896021|17896021	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.956000|0.956000	0.61745|0.61745	9.287000|9.287000	0.95975|0.95975	2.254000|2.254000	0.74563|0.74563	0.460000|0.460000	0.39030|0.39030	CTG|TGG	.	.	none		0.398	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4			C	17788042	A	C	17788042	3	2	7	1	0	0	0	0	1	0	0	0	8283	188	7	5	2168	5	KIF13A	6	17788042	Missense_Mutation	SNP	A	TCGA-FA-A7Q1-01A-11D-A382-10	14897507	17788042	153327025	51	728											
SCGN	10590	hgsc.bcm.edu	37	chr6	25701447	25701447	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccctcagcccagcatcagcGgggtggaccttgataagttc	8	8	12	13	1	2	1	2	1	0	0	3	2	2	2	3	3	3	2	3	3	1	3			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr6:25701447G>A	ENST00000377961.2	+	11	883	c.715G>A	c.(715-717)Ggg>Agg	p.G239R	SCGN_ENST00000334979.6_3'UTR	NM_006998.3	NP_008929.2	O76038	SEGN_HUMAN	secretagogin, EF-hand calcium binding protein	239						cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	24						CAGCATCAGCGGGGTGGACCT	0.512																																					p.G239R		Atlas-SNP	.											SCGN,NS,carcinoma,0,1	SCGN	57	1	0			c.G715A						PASS	.						100	87	91					6																	25701447		2203	4300	6503	SO:0001583	missense	10590	exon11			ATCAGCGGGGTGG	BC000336	CCDS4561.1	6p22.3-p22.1	2013-01-10			ENSG00000079689	ENSG00000079689		"EF-hand domain containing"	16941	protein-coding gene	gene with protein product	"calbindin-like"	609202				10811645	Standard	NM_006998		Approved	SECRET, DJ501N12.8, SEGN, CALBL	uc003nfb.3	O76038	OTTHUMG00000014409	ENST00000377961.2:c.715G>A	6.37:g.25701447G>A	ENSP00000367197:p.Gly239Arg	65	0	0		76	68	0.894737	NM_006998	A8K0B2|Q5VV44|Q96QV7|Q9UJF6	Missense_Mutation	SNP	ENST00000377961.2	37	CCDS4561.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.377577	0.82682	.	.	ENSG00000079689	ENST00000377961	D	0.85773	-2.03	5.43	5.43	0.79202	EF-hand-like domain (1);	0.048878	0.85682	D	0.000000	T	0.76471	0.3992	L	0.36672	1.1	0.80722	D	1	D	0.76494	0.999	P	0.47981	0.563	T	0.74589	-0.3615	10	0.16896	T	0.51	.	17.9971	0.89187	0.0:0.0:1.0:0.0	.	239	O76038	SEGN_HUMAN	R	239	ENSP00000367197:G239R	ENSP00000367197:G239R	G	+	1	0	SCGN	25809426	1.000000	0.71417	0.948000	0.38648	0.989000	0.77384	7.758000	0.85224	2.518000	0.84900	0.655000	0.94253	GGG	.	.	none		0.512	SCGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040067.1			A	25701447	G	A	25701447	3	1	7	1	0	0	0	0	1	0	0	0	13918	1116	39	1	757	1	SCGN	6	25701447	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	7913405	25701447	145413620	52	729											
HIST1H3B	8358	hgsc.bcm.edu	37	chr6	26031889	26031889	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	actttacatttacgctctttCtccgcgaatgcggcgagcga	8	12	9	12	6	2	0	0	0	2	0	3	3	2	0	1	1	4	1	1	1	3	5			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr6:26031889C>G	ENST00000244661.2	-	1	399	c.400G>C	c.(400-402)Gaa>Caa	p.E134Q		NM_003537.3	NP_003528.1	P68431	H31_HUMAN	histone cluster 1, H3b	134					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						TACGCTCTTTCTCCGCGAATG	0.458																																					p.E134Q		Atlas-SNP	.											.	HIST1H3B	59	.	0			c.G400C						PASS	.						58	61	60					6																	26031889		2203	4300	6503	SO:0001583	missense	8358	exon1			CTCTTTCTCCGCG	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.400G>C	6.37:g.26031889C>G	ENSP00000244661:p.Glu134Gln	66	0	0		60	51	0.85	NM_003537	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Missense_Mutation	SNP	ENST00000244661.2	37	CCDS4573.1	.	.	.	.	.	.	.	.	.	.	c	14.81	2.646170	0.47258	.	.	ENSG00000124693	ENST00000244661	T	0.48201	0.82	5.17	5.17	0.71159	.	.	.	.	.	T	0.60676	0.2287	.	.	.	0.41871	D	0.990276	.	.	.	.	.	.	T	0.65647	-0.6117	6	0.87932	D	0	.	18.0207	0.89253	0.0:1.0:0.0:0.0	.	.	.	.	Q	134	ENSP00000244661:E134Q	ENSP00000244661:E134Q	E	-	1	0	HIST1H3B	26139868	1.000000	0.71417	0.976000	0.42696	0.130000	0.20726	7.492000	0.81482	2.545000	0.85829	0.561000	0.74099	GAA	.	.	none		0.458	HIST1H3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040077.1	NM_003537		G	26031889	C	G	26031889	3	3	7	1	0	0	0	0	1	0	0	0	7165	922	32	4	14	4	HIST1H3B	6	26031889	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	330442	26031889	145083178	53	730											
HIST1H2AM	8336	hgsc.bcm.edu	37	chr6	27860757	27860757	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggatctcggcagttaggtaCtccagcaccgccgccaggta	9	7	12	13	3	1	0	0	0	1	0	3	1	2	1	4	4	2	5	4	4	3	3	rs140056231		TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr6:27860757C>T	ENST00000359611.2	-	1	206	c.171G>A	c.(169-171)gaG>gaA	p.E57E	HIST1H3J_ENST00000359303.2_5'Flank|HIST1H2BO_ENST00000303806.4_5'Flank|HIST1H3J_ENST00000479986.1_5'UTR	NM_003514.2	NP_003505.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2am	57						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						CAGTTAGGTACTCCAGCACCG	0.657																																					p.E57E		Atlas-SNP	.											.	HIST1H2AM	27	.	0			c.G171A						PASS	.						58	65	63					6																	27860757		2202	4300	6502	SO:0001819	synonymous_variant	8336	exon1			TAGGTACTCCAGC	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.171G>A	6.37:g.27860757C>T		122	1	0.00819672		125	111	0.888	NM_003514	P02261|Q2M1R2|Q76PA6	Silent	SNP	ENST00000359611.2	37	CCDS4639.1																																																																																			C|1.000;G|0.000	.	alt		0.657	HIST1H2AM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040162.1	NM_003514		T	27860757	C	T	27860757	2	4	7	1	0	0	0	0	0	0	0	1	7148	564	20	2		2	HIST1H2AM	6	27860757	Silent	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	1828868	27860757	143254310	54	731											
PGBD1	84547	hgsc.bcm.edu	37	chr6	28253469	28253469	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cacagcgtcctcaagggaacCcccaagaagtgagtggtgag	12	5	13	11	1	1	3	1	2	0	1	2	4	2	4	3	2	2	0	3	2	4	0			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr6:28253469C>T	ENST00000405948.2	+	3	958	c.538C>T	c.(538-540)Ccc>Tcc	p.P180S	PGBD1_ENST00000259883.3_Missense_Mutation_p.P180S	NM_001184743.1|NM_032507.3	NP_001171672.1|NP_115896.1	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	180						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						TCAAGGGAACCCCCAAGAAGT	0.537																																					p.P180S		Atlas-SNP	.											.	PGBD1	106	.	0			c.C538T						PASS	.						83	79	80					6																	28253469		2203	4300	6503	SO:0001583	missense	84547	exon3			GGGAACCCCCAAG	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.538C>T	6.37:g.28253469C>T	ENSP00000385213:p.Pro180Ser	70	0	0		57	48	0.842105	NM_001184743	Q53F43|Q6NTF5|Q8WWS4	Missense_Mutation	SNP	ENST00000405948.2	37	CCDS4648.1	.	.	.	.	.	.	.	.	.	.	C	0.005	-2.229706	0.00280	.	.	ENSG00000137338	ENST00000405948;ENST00000259883	T;T	0.01446	4.88;4.88	2.37	-1.27	0.09347	.	.	.	.	.	T	0.00384	0.0012	N	0.24115	0.695	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.41197	-0.9522	9	0.16896	T	0.51	.	3.7067	0.08404	0.0:0.4512:0.2324:0.3164	.	180	Q96JS3	PGBD1_HUMAN	S	180	ENSP00000385213:P180S;ENSP00000259883:P180S	ENSP00000259883:P180S	P	+	1	0	PGBD1	28361448	0.000000	0.05858	0.000000	0.03702	0.109000	0.19521	-0.800000	0.04555	-0.341000	0.08376	0.557000	0.71058	CCC	.	.	none		0.537	PGBD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040188.2			T	28253469	C	T	28253469	3	4	7	1	0	0	0	0	1	0	0	0	11789	623	22	2	544	2	PGBD1	6	28253469	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	392712	28253469	142861598	55	732											
C6orf154	221424	hgsc.bcm.edu	37	chr6	43477491	43477491	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctcggcgccggacagcggCtcccccgaaatctggatgga	8	5	13	15	5	1	0	0	0	1	0	3	4	2	3	4	5	1	1	4	5	1	0			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr6:43477491C>G	ENST00000372441.1	-	1	933	c.33G>C	c.(31-33)gaG>gaC	p.E11D		NM_001012974.1	NP_001012992.1	Q5JTD7	LRC73_HUMAN	leucine rich repeat containing 73	11																	CGGACAGCGGCTCCCCCGAAA	0.751																																					p.E11D		Atlas-SNP	.											.	.	.	.	0			c.G33C						PASS	.						7	8	8					6																	43477491		1868	3757	5625	SO:0001583	missense	221424	exon1			CAGCGGCTCCCCC		CCDS34456.1	6p21.1	2011-11-25	2011-11-25	2011-11-25	ENSG00000204052	ENSG00000204052			21375	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 154"	C6orf154			Standard	NM_001012974		Approved	dJ337H4.2	uc003ovk.2	Q5JTD7	OTTHUMG00000014737	ENST00000372441.1:c.33G>C	6.37:g.43477491C>G	ENSP00000361518:p.Glu11Asp	13	0	0		18	17	0.944444	NM_001012974		Missense_Mutation	SNP	ENST00000372441.1	37	CCDS34456.1	.	.	.	.	.	.	.	.	.	.	C	16.33	3.094211	0.56075	.	.	ENSG00000204052	ENST00000372441	T	0.52526	0.66	3.92	2.11	0.27256	.	0.220438	0.37304	U	0.002148	T	0.27900	0.0687	M	0.72118	2.19	0.80722	D	1	B	0.24768	0.111	B	0.28305	0.088	T	0.07520	-1.0768	10	0.30854	T	0.27	-2.5639	9.6261	0.39752	0.0:0.8277:0.0:0.1723	.	11	Q5JTD7	CF154_HUMAN	D	11	ENSP00000361518:E11D	ENSP00000361518:E11D	E	-	3	2	C6orf154	43585469	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	1.350000	0.34010	0.259000	0.21709	-0.379000	0.06801	GAG	.	.	none		0.751	LRRC73-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040635.1	NM_001012974		G	43477491	C	G	43477491	3	3	7	1	0	0	0	0	1	0	0	0	2341	796	28	4	941	4	C6orf154	6	43477491	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	15224022	43477491	127637576	56	733											
COL21A1	81578	hgsc.bcm.edu	37	chr6	55988901	55988901	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taatccatcctttccatgtcTtcctggttctccctaaaaaa	10	15	3	13	0	2	0	0	0	2	0	7	0	6	0	5	1	0	1	5	1	4	5			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr6:55988901T>A	ENST00000244728.5	-	16	2114	c.1717A>T	c.(1717-1719)Aga>Tga	p.R573*	COL21A1_ENST00000535941.1_Nonsense_Mutation_p.R573*|COL21A1_ENST00000370819.1_Nonsense_Mutation_p.R570*	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	573	Collagen-like 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(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)			TTTCCATGTCTTCCTGGTTCT	0.264																																					p.R573X		Atlas-SNP	.											.	COL21A1	201	.	0			c.A1717T						PASS	.						32	27	29					6																	55988901		1666	3836	5502	SO:0001587	stop_gained	81578	exon16			CATGTCTTCCTGG	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.1717A>T	6.37:g.55988901T>A	ENSP00000244728:p.Arg573*	311	0	0		247	202	0.817814	NM_030820	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Nonsense_Mutation	SNP	ENST00000244728.5	37	CCDS55025.1	.	.	.	.	.	.	.	.	.	.	T	41	8.904774	0.98998	.	.	ENSG00000124749	ENST00000244728;ENST00000370819;ENST00000535941;ENST00000370811	.	.	.	4.36	4.36	0.52297	.	0.227351	0.30584	N	0.009318	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	.	10.2225	0.43205	0.0:0.0:0.0:1.0	.	.	.	.	X	573;570;573;570	.	ENSP00000244728:R573X	R	-	1	2	COL21A1	56096860	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.795000	0.38784	1.711000	0.51337	0.402000	0.26972	AGA	.	.	none		0.264	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2			A	55988901	T	A	55988901	4	1	7	1	0	0	0	0	0	1	0	0	3682	1617	56	5	1216	5	COL21A1	6	55988901	Nonsense_Mutation	SNP	T	TCGA-FA-A7Q1-01A-11D-A382-10	12511410	55988901	115126166	57	734											
BAI3	577	hgsc.bcm.edu	37	chr6	69772924	69772924	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatagaactagctcatttggCtaatgtaagtaccatccact	13	12	7	9	0	1	1	1	0	0	1	2	2	2	1	2	1	3	4	2	1	6	6			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr6:69772924C>A	ENST00000370598.1	+	16	3253	c.2432C>A	c.(2431-2433)gCt>gAt	p.A811D		NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	811					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)				GCTCATTTGGCTAATGTAAGT	0.373																																					p.A811D		Atlas-SNP	.											.	BAI3	451	.	0			c.C2432A						PASS	.						134	111	119					6																	69772924		2203	4300	6503	SO:0001583	missense	577	exon16			ATTTGGCTAATGT	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.2432C>A	6.37:g.69772924C>A	ENSP00000359630:p.Ala811Asp	95	0	0		76	59	0.776316	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	37	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	C	14.26	2.483456	0.44147	.	.	ENSG00000135298	ENST00000370598	T	0.20881	2.04	5.07	5.07	0.68467	.	0.267579	0.36740	N	0.002430	T	0.06142	0.0159	N	0.22421	0.69	0.80722	D	1	B	0.15473	0.013	B	0.16289	0.015	T	0.18085	-1.0348	10	0.14252	T	0.57	.	13.7386	0.62833	0.154:0.846:0.0:0.0	.	811	O60242	BAI3_HUMAN	D	811	ENSP00000359630:A811D	ENSP00000359630:A811D	A	+	2	0	BAI3	69829645	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	4.695000	0.61767	2.484000	0.83849	0.484000	0.47621	GCT	.	.	none		0.373	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			A	69772924	C	A	69772924	3	1	7	1	0	0	0	0	1	0	0	0	1300	797	28	4	2486	4	BAI3	6	69772924	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	13784023	69772924	101342143	58	735											
WASF1	8936	hgsc.bcm.edu	37	chr6	110429812	110429812	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atggaataggcaaagtcttgCgatcgaaaagctgctggtct	12	10	12	7	2	2	0	0	0	2	0	3	3	2	1	0	3	3	3	0	3	5	2			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr6:110429812C>T	ENST00000392589.1	-	6	1177	c.341G>A	c.(340-342)cGc>cAc	p.R114H	WASF1_ENST00000392588.1_Missense_Mutation_p.R114H|WASF1_ENST00000392586.1_Missense_Mutation_p.R114H|WASF1_ENST00000359451.2_Missense_Mutation_p.R114H|WASF1_ENST00000392587.2_Missense_Mutation_p.R114H	NM_003931.2	NP_003922.1	Q92558	WASF1_HUMAN	WAS protein family, member 1	114					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)		CAAAGTCTTGCGATCGAAAAG	0.368																																					p.R114H		Atlas-SNP	.											.	WASF1	35	.	0			c.G341A						PASS	.						100	93	95					6																	110429812		2203	4300	6503	SO:0001583	missense	8936	exon5			GTCTTGCGATCGA	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.341G>A	6.37:g.110429812C>T	ENSP00000376368:p.Arg114His	65	0	0		88	5	0.0568182	NM_001024935	E1P5F2|Q5SZK7	Missense_Mutation	SNP	ENST00000392589.1	37	CCDS5080.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.494252	0.85069	.	.	ENSG00000112290	ENST00000392586;ENST00000392587;ENST00000392589;ENST00000392588;ENST00000359451;ENST00000444391;ENST00000265601;ENST00000368938	T;T;T;T;T;T;T;T	0.48201	1.21;1.21;1.21;1.21;1.21;1.21;0.82;0.82	6.06	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.32823	0.0842	M	0.67953	2.075	0.58432	D	0.999998	B	0.10296	0.003	B	0.04013	0.001	T	0.21143	-1.0254	10	0.34782	T	0.22	.	15.5809	0.76439	0.0:0.934:0.0:0.066	.	114	Q92558	WASF1_HUMAN	H	114	ENSP00000376365:R114H;ENSP00000376366:R114H;ENSP00000376368:R114H;ENSP00000376367:R114H;ENSP00000352425:R114H;ENSP00000407041:R114H;ENSP00000265601:R114H;ENSP00000357934:R114H	ENSP00000265601:R114H	R	-	2	0	WASF1	110536505	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.653000	0.61462	1.574000	0.49760	0.650000	0.86243	CGC	.	.	none		0.368	WASF1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041784.3	NM_003931		T	110429812	C	T	110429812	3	4	7	1	0	0	0	0	1	0	0	0	17267	768	27	1	1362	1	WASF1	6	110429812	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	40656888	110429812	60685255	59	736											
HECW1	23072	hgsc.bcm.edu	37	chr7	43360271	43360271	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aactttctggactataaaaaCcgtggagtcaatggttctca	13	12	8	8	1	3	0	2	0	2	0	4	2	3	2	1	3	2	1	1	3	6	4			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr7:43360271C>A	ENST00000395891.2	+	5	995	c.390C>A	c.(388-390)aaC>aaA	p.N130K	HECW1_ENST00000453890.1_Missense_Mutation_p.N130K	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	130					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						ACTATAAAAACCGTGGAGTCA	0.453																																					p.N130K		Atlas-SNP	.											.	HECW1	540	.	0			c.C390A						PASS	.						121	117	119					7																	43360271		1880	4111	5991	SO:0001583	missense	23072	exon5			TAAAAACCGTGGA	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.390C>A	7.37:g.43360271C>A	ENSP00000379228:p.Asn130Lys	198	0	0		178	77	0.432584	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Missense_Mutation	SNP	ENST00000395891.2	37	CCDS5469.2	.	.	.	.	.	.	.	.	.	.	C	22.2	4.253889	0.80135	.	.	ENSG00000002746	ENST00000395891;ENST00000453890;ENST00000265522	T;T	0.37235	1.21;1.21	5.94	4.13	0.48395	.	0.000000	0.85682	D	0.000000	T	0.54334	0.1852	M	0.68593	2.085	0.54753	D	0.999984	D;P;D	0.76494	0.999;0.918;0.999	D;P;D	0.80764	0.994;0.542;0.994	T	0.57394	-0.7819	10	0.87932	D	0	.	9.4899	0.38953	0.0:0.7338:0.0:0.2662	.	130;162;130	B4DH42;B3KR18;Q76N89	.;.;HECW1_HUMAN	K	130;130;129	ENSP00000379228:N130K;ENSP00000407774:N130K	ENSP00000265522:N129K	N	+	3	2	HECW1	43326796	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.241000	0.51376	1.526000	0.49068	0.650000	0.86243	AAC	.	.	none		0.453	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		A	43360271	C	A	43360271	3	1	7	1	0	0	0	0	1	0	0	0	7051	506	18	4	400	4	HECW1	7	43360271	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10		43360271	115778392	60	737											
COBL	23242	hgsc.bcm.edu	37	chr7	51203882	51203882	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgccttgtcttgcacaggTggccctgaacctggaggagg	7	9	15	10	0	1	1	0	1	1	0	1	4	1	3	3	5	3	1	3	5	1	2			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr7:51203882T>C	ENST00000265136.7	-	6	1095	c.930A>G	c.(928-930)ccA>ccG	p.P310P	COBL_ENST00000395542.2_Silent_p.P335P|COBL_ENST00000395540.2_Silent_p.P310P|COBL_ENST00000441453.1_Silent_p.P310P	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	310	Pro-rich.				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)					CTTGCACAGGTGGCCCTGAAC	0.567																																					p.P310P	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											.	COBL	167	.	0			c.A930G						PASS	.						81	62	69					7																	51203882		2203	4300	6503	SO:0001819	synonymous_variant	23242	exon6			CACAGGTGGCCCT	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.930A>G	7.37:g.51203882T>C		158	0	0		136	42	0.308824	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Silent	SNP	ENST00000265136.7	37	CCDS34637.1	.	.	.	.	.	.	.	.	.	.	T	9.074	0.997562	0.19043	.	.	ENSG00000106078	ENST00000452534	.	.	.	5.55	0.604	0.17547	.	.	.	.	.	T	0.25044	0.0608	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.26018	-1.0115	4	.	.	.	.	5.2781	0.15661	0.1214:0.2779:0.0:0.6007	.	.	.	.	A	229	.	.	T	-	1	0	COBL	51171376	0.000000	0.05858	0.000000	0.03702	0.354000	0.29330	-1.119000	0.03276	-0.112000	0.11979	0.460000	0.39030	ACC	.	.	none		0.567	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198		C	51203882	T	C	51203882	2	2	7	1	0	0	0	0	0	0	0	1	3655	1683	59	3		3	COBL	7	51203882	Silent	SNP	T	TCGA-FA-A7Q1-01A-11D-A382-10	7843611	51203882	107934781	61	738											
SEMA3C	10512	hgsc.bcm.edu	37	chr7	80418691	80418691	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atccacagctatctttgtatActtgtagtcagtgccaatac	11	14	6	10	0	2	0	1	0	1	0	3	0	3	0	2	0	4	3	2	0	6	7			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr7:80418691A>T	ENST00000265361.3	-	12	1846	c.1285T>A	c.(1285-1287)Tat>Aat	p.Y429N	SEMA3C_ENST00000544525.1_Missense_Mutation_p.Y447N|SEMA3C_ENST00000419255.2_Missense_Mutation_p.Y429N	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	429	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						ATCTTTGTATACTTGTAGTCA	0.413																																					p.Y429N		Atlas-SNP	.											.	SEMA3C	106	.	0			c.T1285A						PASS	.						200	184	189					7																	80418691		2203	4300	6503	SO:0001583	missense	10512	exon12			TTGTATACTTGTA	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.1285T>A	7.37:g.80418691A>T	ENSP00000265361:p.Tyr429Asn	221	0	0		240	100	0.416667	NM_006379	B4DRL8	Missense_Mutation	SNP	ENST00000265361.3	37	CCDS5596.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.710534	0.89018	.	.	ENSG00000075223	ENST00000265361;ENST00000419255;ENST00000544525	T;T;T	0.11385	2.78;2.78;2.78	5.94	5.94	0.96194	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.112982	0.64402	D	0.000006	T	0.30448	0.0765	M	0.71206	2.165	0.80722	D	1	P;P	0.51240	0.93;0.943	P;P	0.59171	0.771;0.853	T	0.01096	-1.1453	10	0.87932	D	0	.	16.3908	0.83537	1.0:0.0:0.0:0.0	.	447;429	F5H1Z7;Q99985	.;SEM3C_HUMAN	N	429;429;447	ENSP00000265361:Y429N;ENSP00000411193:Y429N;ENSP00000445649:Y447N	ENSP00000265361:Y429N	Y	-	1	0	SEMA3C	80256627	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.327000	0.79147	2.269000	0.75478	0.455000	0.32223	TAT	.	.	none		0.413	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379		T	80418691	A	T	80418691	3	4	7	1	0	0	0	0	1	0	0	0	14041	391	14	5	998	5	SEMA3C	7	80418691	Missense_Mutation	SNP	A	TCGA-FA-A7Q1-01A-11D-A382-10	29214809	80418691	78719972	62	739											
ORC5L	5001	hgsc.bcm.edu	37	chr7	103835607	103835607	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ttacctatgctgtaatcaggGaaatataagacaaacggctc	15	10	8	8	1	1	1	1	0	0	1	2	2	1	2	1	2	3	3	1	2	7	5			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr7:103835607G>T	ENST00000297431.4	-	5	679	c.537C>A	c.(535-537)ttC>ttA	p.F179L	ORC5_ENST00000485726.1_5'UTR|ORC5_ENST00000545943.1_Missense_Mutation_p.F47L|ORC5_ENST00000447452.2_Missense_Mutation_p.F179L	NM_002553.3	NP_002544.1	O43913	ORC5_HUMAN	origin recognition complex, subunit 5	179					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						TGTAATCAGGGAAATATAAGA	0.343																																					p.F179L		Atlas-SNP	.											.	ORC5	48	.	0			c.C537A						PASS	.						96	93	94					7																	103835607		2203	4300	6503	SO:0001583	missense	5001	exon5			ATCAGGGAAATAT		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.537C>A	7.37:g.103835607G>T	ENSP00000297431:p.Phe179Leu	74	0	0		90	45	0.5	NM_002553	A4D0P8|O60590|O95268	Missense_Mutation	SNP	ENST00000297431.4	37	CCDS5734.1	.	.	.	.	.	.	.	.	.	.	G	11.38	1.621348	0.28889	.	.	ENSG00000164815	ENST00000297431;ENST00000545943;ENST00000447452	T;T;T	0.59083	0.29;0.64;0.29	5.72	-2.03	0.07365	.	0.000000	0.85682	D	0.000000	T	0.60869	0.2302	L	0.37466	1.105	0.54753	D	0.999989	D;P;B	0.69078	0.997;0.886;0.125	D;P;B	0.70716	0.97;0.517;0.056	T	0.56902	-0.7902	10	0.40728	T	0.16	.	13.0489	0.58944	0.768:0.0:0.232:0.0	.	179;179;179	A4D0P7;O43913-2;O43913	.;.;ORC5_HUMAN	L	179;47;179	ENSP00000297431:F179L;ENSP00000438018:F47L;ENSP00000395747:F179L	ENSP00000297431:F179L	F	-	3	2	ORC5	103622843	0.999000	0.42202	0.978000	0.43139	0.964000	0.63967	0.560000	0.23500	-0.489000	0.06716	-0.137000	0.14449	TTC	.	.	none		0.343	ORC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348286.1	NM_002553		T	103835607	G	T	103835607	3	4	7	1	0	0	0	0	1	0	0	0	11274	1165	41	4	908	4	ORC5L	7	103835607	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	23416916	103835607	55303056	63	740											
FLNC	2318	hgsc.bcm.edu	37	chr7	128492881	128492881	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctaacacccactttccacaGggatctccttcacccccaag	10	8	4	19	0	2	0	1	0	1	0	4	1	3	1	6	1	1	0	6	1	2	3			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr7:128492881G>A	ENST00000325888.8	+	37	6265		c.e37-1		RP11-309L24.2_ENST00000469965.1_RNA|FLNC_ENST00000346177.6_Splice_Site	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma						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						ACTTTCCACAGGGATCTCCTT	0.647																																					.		Atlas-SNP	.											.	FLNC	339	.	0			c.6005-1G>A						PASS	.						58	65	63					7																	128492881		2033	4187	6220	SO:0001630	splice_region_variant	2318	exon37			TCCACAGGGATCT	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.6005-1G>A	7.37:g.128492881G>A		95	0	0		77	29	0.376623	NM_001458	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Splice_Site	SNP	ENST00000325888.8	37	CCDS43644.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.552313	0.86127	.	.	ENSG00000128591	ENST00000325888;ENST00000346177	.	.	.	5.73	5.73	0.89815	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.9025	0.96993	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FLNC	128280117	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	9.806000	0.99153	2.722000	0.93159	0.655000	0.94253	.	.	.	none		0.647	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		Intron	A	128492881	G	A	128492881	5	1	7	1	0	0	0	0	0	0	1	0	5943	1014	35	2	6150	2	FLNC	7	128492881	Splice_Site	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	24657274	128492881	30645782	64	741											
ZNF703	80139	hgsc.bcm.edu	37	chr8	37555934	37555934	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggggcctcgggcctgggcagCgccgccgccgccgccgccgc	1	2	18	20	8	0	0	0	0	0	0	1	0	0	0	8	4	1	1	8	4	0	0	rs568050040	byFrequency	TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr8:37555934C>T	ENST00000331569.4	+	2	1744	c.1515C>T	c.(1513-1515)agC>agT	p.S505S		NM_025069.1	NP_079345.1	Q9H7S9	ZN703_HUMAN	zinc finger protein 703	505					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)			GCCTGGGCAGcgccgccgccg	0.771																																					p.S505S		Atlas-SNP	.											.	ZNF703	16	.	0			c.C1515T						PASS	.						1	2	2					8																	37555934		1094	2312	3406	SO:0001819	synonymous_variant	80139	exon2			GGGCAGCGCCGCC	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.1515C>T	8.37:g.37555934C>T		37	0	0		12	10	0.833333	NM_025069	Q5XG76	Silent	SNP	ENST00000331569.4	37	CCDS6094.1																																																																																			.	.	none		0.771	ZNF703-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376683.2	NM_025069		T	37555934	C	T	37555934	2	4	7	1	0	0	0	0	0	0	0	1	18121	767	27	1		1	ZNF703	8	37555934	Silent	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10		37555934	108808088	65	742											
FAM135B	51059	hgsc.bcm.edu	37	chr8	139164971	139164971	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctgtctaatccatacttatCtctagagctcctactctcat	9	15	3	14	0	3	1	1	0	3	1	7	1	5	1	3	0	3	1	3	0	5	5			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr8:139164971C>T	ENST00000395297.1	-	13	1917	c.1747G>A	c.(1747-1749)Gat>Aat	p.D583N		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	583										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)			CCATACTTATCTCTAGAGCTC	0.458										HNSCC(54;0.14)																											p.D583N		Atlas-SNP	.											LOC51059,rectum,carcinoma,0,2	FAM135B	423	2	0			c.G1747A						PASS	.						153	145	148					8																	139164971		1900	4119	6019	SO:0001583	missense	51059	exon13			ACTTATCTCTAGA	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.1747G>A	8.37:g.139164971C>T	ENSP00000378710:p.Asp583Asn	90	0	0		129	77	0.596899	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	C	13.06	2.125028	0.37533	.	.	ENSG00000147724	ENST00000395297	T	0.15952	2.38	5.45	3.61	0.41365	.	1.013200	0.07872	N	0.968042	T	0.13798	0.0334	L	0.44542	1.39	0.09310	N	1	P;B;B	0.37207	0.587;0.091;0.03	B;B;B	0.32465	0.146;0.07;0.005	T	0.19095	-1.0316	10	0.25106	T	0.35	-1.7504	7.0725	0.25187	0.0:0.6997:0.1672:0.1331	.	583;583;583	Q49AJ0-3;Q49AJ0-4;Q49AJ0	.;.;F135B_HUMAN	N	583	ENSP00000378710:D583N	ENSP00000276737:D583N	D	-	1	0	FAM135B	139234153	0.000000	0.05858	0.005000	0.12908	0.005000	0.04900	0.393000	0.20817	1.423000	0.47198	-0.176000	0.13171	GAT	.	.	none		0.458	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		T	139164971	C	T	139164971	3	4	7	1	0	0	0	0	1	0	0	0	5454	913	32	2	2505	2	FAM135B	8	139164971	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	101609037	139164971	7199051	66	743											
DENND3	22898	hgsc.bcm.edu	37	chr8	142202753	142202754	+	Frame_Shift_Ins	INS	-	-	AA																															tcaactgcatgatccgggtgINSaagaagcaggtagggtggag																										TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr8:142202753_142202754insAA	ENST00000262585.2	+	22	3665_3666	c.3387_3388insAA	c.(3388-3390)aagfs	p.K1130fs	DENND3_ENST00000523308.1_Frame_Shift_Ins_p.K180fs|DENND3_ENST00000424248.1_Frame_Shift_Ins_p.K1078fs|DENND3_ENST00000519811.1_Frame_Shift_Ins_p.K1210fs	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	1130					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)			TGATCCGGGTGAAGAAGCAGGT	0.673																																					p.V1129fs		Pindel,Atlas-Indel	.											.	DENND3	127	.	0			c.3387_3388insAA						PASS	.																																			SO:0001589	frameshift_variant	22898	exon22			.	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.3388_3389dupAA	8.37:g.142202754_142202755dupAA	ENSP00000262585:p.Lys1130fs	64	0	.		74	17	0.23	NM_014957	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Frame_Shift_Ins	INS	ENST00000262585.2	37	CCDS34947.1																																																																																			.	.	none		0.673	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957		AA	142202754	-	AA	142202753	7	5	7	1	0	1	1	0	0	0	0	0	4434	1277	45	0	3469	0	DENND3	8	142202753	Frame_Shift_Ins	INS	-	TCGA-FA-A7Q1-01A-11D-A382-10	3037782	142202753	4161269	67	744											
FOXD4	2298	hgsc.bcm.edu	37	chr9	118097	118097	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcggtgtggagcgaaggCgctcagctcttggcaagttc	6	9	16	10	3	2	0	1	0	1	0	3	2	2	1	0	4	3	5	0	4	2	2			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr9:118097C>T	ENST00000382500.2	-	1	320	c.23G>A	c.(22-24)cGc>cAc	p.R8H		NM_207305.4	NP_997188.2	Q12950	FOXD4_HUMAN	forkhead box D4	8					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)			endometrium(5)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	14	all_lung(41;0.218)	all_cancers(5;0.0395)|Acute lymphoblastic leukemia(5;1.91e-07)|all_hematologic(5;1.95e-06)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		GGAGCGAAGGCGCTCAGCTCT	0.657																																					p.R8H		Atlas-SNP	.											FOXD4,colon,carcinoma,-1,1	FOXD4	75	1	0			c.G23A						PASS	.						67	77	74					9																	118097		2199	4295	6494	SO:0001583	missense	2298	exon1			CGAAGGCGCTCAG	U13223	CCDS34975.1	9p24.3	2014-09-17			ENSG00000170122	ENSG00000170122		"Forkhead boxes"	3805	protein-coding gene	gene with protein product		601092		FKHL9		7957066, 8825632, 12234674	Standard	NM_207305		Approved	FREAC5, FOXD4a	uc003zfz.4	Q12950	OTTHUMG00000021015	ENST00000382500.2:c.23G>A	9.37:g.118097C>T	ENSP00000371940:p.Arg8His	204	0	0		247	32	0.129555	NM_207305	B2RN05|B9EGL7|Q5VVK1|Q8WXT6	Missense_Mutation	SNP	ENST00000382500.2	37	CCDS34975.1	.	.	.	.	.	.	.	.	.	.	.	10.90	1.482692	0.26598	.	.	ENSG00000170122	ENST00000382500	D	0.95518	-3.73	2.31	1.34	0.21922	.	0.918410	0.08832	N	0.887090	D	0.87873	0.6287	N	0.14661	0.345	0.21762	N	0.999551	B	0.19935	0.04	B	0.08055	0.003	T	0.76000	-0.3119	10	0.19147	T	0.46	.	6.1292	0.20195	0.0:0.8198:0.0:0.1802	.	8	Q12950	FOXD4_HUMAN	H	8	ENSP00000371940:R8H	ENSP00000371940:R8H	R	-	2	0	FOXD4	108097	0.000000	0.05858	0.158000	0.22627	0.111000	0.19643	-0.054000	0.11826	0.271000	0.22005	0.291000	0.19559	CGC	.	.	none		0.657	FOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055433.1	NM_207305		T	118097	C	T	118097	3	4	7	1	0	0	0	0	1	0	0	0	6007	768	27	1	1300	1	FOXD4	9	118097	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10		118097	141095334	68	745											
C9orf47	286223	hgsc.bcm.edu	37	chr9	91606581	91606581	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcgccacccgctaggatgcCggtggccccagcgccctcag	5	4	13	19	5	1	0	1	0	0	0	1	1	1	1	6	3	2	1	6	3	1	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr9:91606581C>T	ENST00000334490.5	+	2	511	c.443C>T	c.(442-444)cCg>cTg	p.P148L	C9orf47_ENST00000375850.3_Missense_Mutation_p.P129L|S1PR3_ENST00000358157.2_5'UTR|C9orf47_ENST00000375851.2_Missense_Mutation_p.P129L			Q6ZRZ4	CI047_HUMAN	chromosome 9 open reading frame 47	148						extracellular region (GO:0005576)				endometrium(1)|large_intestine(1)|liver(1)|lung(1)	4						GCTAGGATGCCGGTGGCCCCA	0.766																																					p.P148L		Atlas-SNP	.											.	C9orf47	9	.	0			c.C443T						PASS	.						2	2	2					9																	91606581		1230	2747	3977	SO:0001583	missense	286223	exon2			GGATGCCGGTGGC	AK094842	CCDS35062.1, CCDS47989.1	9q22.1	2008-02-05	2004-11-04		ENSG00000186354	ENSG00000186354			23669	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 108"	C9orf108			Standard	NM_001001938		Approved	FLJ37523, bA791O21.3	uc004aqc.2	Q6ZRZ4	OTTHUMG00000020172	ENST00000334490.5:c.443C>T	9.37:g.91606581C>T	ENSP00000335616:p.Pro148Leu	30	0	0		39	12	0.307692	NM_001001938	B7ZMC7|Q5SQD7|Q7Z568|Q8N1V4	Missense_Mutation	SNP	ENST00000334490.5	37	CCDS35062.1	.	.	.	.	.	.	.	.	.	.	C	12.66	2.004462	0.35320	.	.	ENSG00000186354	ENST00000375851;ENST00000375850;ENST00000334490	.	.	.	2.64	-0.648	0.11464	.	.	.	.	.	T	0.10165	0.0249	N	0.08118	0	0.26189	N	0.979614	D;D	0.56287	0.975;0.975	B;B	0.40477	0.33;0.33	T	0.16482	-1.0401	8	0.87932	D	0	.	2.1044	0.03688	0.2681:0.3827:0.0:0.3492	.	148;129	Q6ZRZ4;Q6ZRZ4-2	CI047_HUMAN;.	L	129;129;148	.	ENSP00000335616:P148L	P	+	2	0	C9orf47	90796401	0.000000	0.05858	0.057000	0.19452	0.022000	0.10575	-1.050000	0.03510	-0.143000	0.11334	0.555000	0.69702	CCG	.	.	none		0.766	C9orf47-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355972.1	NM_182599		T	91606581	C	T	91606581	3	4	7	1	0	0	0	0	1	0	0	0	2487	652	23	1	449	1	C9orf47	9	91606581	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	91488484	91606581	49606850	69	746											
IARS	3376	hgsc.bcm.edu	37	chr9	95021262	95021262	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ttttctgctctcaccacaggGgagttaatcagatataatct	11	14	7	9	0	4	1	2	0	3	1	5	2	4	2	1	2	1	2	1	2	3	5			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr9:95021262G>A	ENST00000375643.3	-	19	2156	c.1890C>T	c.(1888-1890)tcC>tcT	p.S630S	IARS_ENST00000447699.2_Silent_p.S520S|IARS_ENST00000375629.3_5'UTR|IARS_ENST00000443024.2_Silent_p.S630S	NM_013417.2	NP_038203.2	P41252	SYIC_HUMAN	isoleucyl-tRNA synthetase	630					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)	TCACCACAGGGGAGTTAATCA	0.423																																					p.S630S		Atlas-SNP	.											IARS,NS,carcinoma,-2,1	IARS	74	1	0			c.C1890T						scavenged	.						63	60	61					9																	95021262		2203	4300	6503	SO:0001819	synonymous_variant	3376	exon19			CACAGGGGAGTTA	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.1890C>T	9.37:g.95021262G>A		61	1	0.0163934		44	10	0.227273	NM_013417	A8KAE9|Q5TCD0|Q7Z3T4|Q9H588	Silent	SNP	ENST00000375643.3	37	CCDS6694.1																																																																																			.	.	none		0.423	IARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053059.2	NM_002161		A	95021262	G	A	95021262	2	1	7	1	0	0	0	0	0	0	0	1	7482	1219	43	2		2	IARS	9	95021262	Silent	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	3414681	95021262	46192169	70	747											
HIATL1	84641	hgsc.bcm.edu	37	chr9	97203305	97203305	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttctgtgtctggagtcttctCggtcacgttttctgttatat	4	20	9	8	2	6	0	1	0	5	0	7	1	6	1	0	2	0	2	0	2	2	6			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr9:97203305C>T	ENST00000375344.3	+	5	703	c.434C>T	c.(433-435)tCg>tTg	p.S145L	HIATL1_ENST00000428393.2_Missense_Mutation_p.S80L	NM_032558.2	NP_115947.2	Q5SR56	HIAL1_HUMAN	hippocampus abundant transcript-like 1	145					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|pancreas(1)	11		Acute lymphoblastic leukemia(62;0.136)				GGAGTCTTCTCGGTCACGTTT	0.383																																					p.S145L	Pancreas(77;1260 1915 1973 10423)	Atlas-SNP	.											.	HIATL1	31	.	0			c.C434T						PASS	.						132	125	127					9																	97203305		2203	4300	6503	SO:0001583	missense	84641	exon5			TCTTCTCGGTCAC	AK027659	CCDS6710.2	9q22.32	2009-12-04			ENSG00000148110	ENSG00000148110			23376	protein-coding gene	gene with protein product							Standard	XM_005252277		Approved	FLJ14753	uc004aur.3	Q5SR56	OTTHUMG00000020265	ENST00000375344.3:c.434C>T	9.37:g.97203305C>T	ENSP00000364493:p.Ser145Leu	361	0	0		354	130	0.367232	NM_032558	B4DUE6|E9PD58|Q3KQT4|Q53GU5|Q8WU95|Q96SM4	Missense_Mutation	SNP	ENST00000375344.3	37	CCDS6710.2	.	.	.	.	.	.	.	.	.	.	C	32	5.118255	0.94385	.	.	ENSG00000148110	ENST00000375344;ENST00000428393	T;T	0.60920	0.15;0.15	4.16	4.16	0.48862	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.41294	D	0.000920	T	0.67822	0.2934	M	0.76002	2.32	0.80722	D	1	P;D	0.55800	0.948;0.973	P;P	0.52481	0.7;0.7	T	0.73914	-0.3832	10	0.87932	D	0	-7.144	14.7696	0.69665	0.0:1.0:0.0:0.0	.	80;145	B4DUE6;Q5SR56	.;HIAL1_HUMAN	L	145;80	ENSP00000364493:S145L;ENSP00000405909:S80L	ENSP00000364493:S145L	S	+	2	0	HIATL1	96243126	1.000000	0.71417	0.972000	0.41901	0.982000	0.71751	7.357000	0.79456	2.610000	0.88304	0.557000	0.71058	TCG	.	.	none		0.383	HIATL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053184.1	NM_032558		T	97203305	C	T	97203305	3	4	7	1	0	0	0	0	1	0	0	0	7107	893	31	1	452	1	HIATL1	9	97203305	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	2182043	97203305	44010126	71	748											
ADAMTSL2	9719	hgsc.bcm.edu	37	chr9	136404949	136404949	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cagtgcgtctccttcaactcCcacgtgtacaacgggcggac	8	8	10	15	4	2	0	1	0	1	0	4	1	3	1	2	2	4	1	2	2	3	2			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr9:136404949C>T	ENST00000354484.4	+	5	923	c.366C>T	c.(364-366)tcC>tcT	p.S122S	ADAMTSL2_ENST00000393060.1_Silent_p.S122S|ADAMTSL2_ENST00000393061.3_Silent_p.S231S	NM_001145320.1	NP_001138792.1	Q86TH1	ATL2_HUMAN	ADAMTS-like 2	122					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)		CCTTCAACTCCCACGTGTACA	0.672																																					p.S122S		Atlas-SNP	.											.	ADAMTSL2	40	.	0			c.C366T						PASS	.						45	37	40					9																	136404949		1939	3747	5686	SO:0001819	synonymous_variant	9719	exon5			CAACTCCCACGTG	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.366C>T	9.37:g.136404949C>T		24	0	0		34	11	0.323529	NM_014694	B1B0D5|O60345	Silent	SNP	ENST00000354484.4	37	CCDS6976.1																																																																																			.	.	none		0.672	ADAMTSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254619.1	NM_014694		T	136404949	C	T	136404949	2	4	7	1	0	0	0	0	0	0	0	1	275	610	22	2		2	ADAMTSL2	9	136404949	Silent	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	39201644	136404949	4808482	72	749											
COL5A1	1289	hgsc.bcm.edu	37	chr9	137726979	137726979	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acgacaaggccctccgcttcCtgggctccaacgacgaggag	9	5	12	15	4	0	0	0	0	0	0	3	4	3	1	4	3	1	2	4	3	2	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr9:137726979C>T	ENST00000371817.3	+	65	5713	c.5299C>T	c.(5299-5301)Ctg>Ttg	p.L1767L		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1767	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)		CCTCCGCTTCCTGGGCTCCAA	0.657																																					p.L1767L		Atlas-SNP	.											.	COL5A1	323	.	0			c.C5299T						PASS	.						90	72	78					9																	137726979		2203	4300	6503	SO:0001819	synonymous_variant	1289	exon65			CGCTTCCTGGGCT	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.5299C>T	9.37:g.137726979C>T		30	0	0		28	13	0.464286	NM_000093	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	37	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	C	10.64	1.406309	0.25378	.	.	ENSG00000130635	ENST00000371820	.	.	.	5.03	2.78	0.32641	.	.	.	.	.	T	0.61776	0.2374	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59789	-0.7388	4	.	.	.	.	11.6076	0.51041	0.0:0.8236:0.0:0.1764	.	.	.	.	L	186	.	.	P	+	2	0	COL5A1	136866800	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.500000	0.45381	1.090000	0.41315	0.561000	0.74099	CCT	.	.	none		0.657	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		T	137726979	C	T	137726979	2	4	7	1	0	0	0	0	0	0	0	1	3698	680	24	2		2	COL5A1	9	137726979	Silent	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	1322030	137726979	3486452	73	750											
KCNT1	57582	hgsc.bcm.edu	37	chr9	138664597	138664597	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctgcagggcacagagcaccGgcctacgcagagcggcggtg	8	3	16	14	4	0	2	0	0	0	2	0	2	0	2	3	4	4	4	3	4	1	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr9:138664597G>A	ENST00000263604.3	+	19	1988	c.1988G>A	c.(1987-1989)cGg>cAg	p.R663Q	KCNT1_ENST00000491806.2_Missense_Mutation_p.R649Q|KCNT1_ENST00000487664.1_Missense_Mutation_p.R637Q|KCNT1_ENST00000490355.2_Missense_Mutation_p.R661Q|KCNT1_ENST00000298480.5_Missense_Mutation_p.R682Q|KCNT1_ENST00000371757.2_Missense_Mutation_p.R682Q|KCNT1_ENST00000488444.2_Missense_Mutation_p.R663Q|KCNT1_ENST00000486577.2_Missense_Mutation_p.R641Q			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	663					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)		ACAGAGCACCGGCCTACGCAG	0.716																																					p.R682Q		Atlas-SNP	.											.	KCNT1	139	.	0			c.G2045A						PASS	.						4	6	5					9																	138664597		2007	4003	6010	SO:0001583	missense	57582	exon19			AGCACCGGCCTAC	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.1988G>A	9.37:g.138664597G>A	ENSP00000263604:p.Arg663Gln	86	0	0		59	33	0.559322	NM_020822	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Missense_Mutation	SNP	ENST00000263604.3	37		.	.	.	.	.	.	.	.	.	.	G	10.46	1.355993	0.24598	.	.	ENSG00000107147	ENST00000487664;ENST00000298480;ENST00000371757;ENST00000486577;ENST00000491806;ENST00000488444;ENST00000490355;ENST00000263604	T;T;T;T	0.23552	1.92;1.91;1.91;1.9	4.02	2.14	0.27477	.	0.225763	0.38492	N	0.001664	T	0.23886	0.0578	M	0.77820	2.39	0.37757	D	0.926174	P;P;P;B	0.39920	0.47;0.569;0.695;0.342	B;B;B;B	0.28916	0.044;0.044;0.096;0.044	T	0.13495	-1.0507	10	0.39692	T	0.17	-43.5149	10.0494	0.42205	0.1661:0.0:0.8339:0.0	.	649;682;637;663	C9JYL2;B9EGP2;G5E9V0;Q5JUK3	.;.;.;KCNT1_HUMAN	Q	637;682;682;641;649;663;661;663	ENSP00000417851:R637Q;ENSP00000298480:R682Q;ENSP00000360822:R682Q;ENSP00000263604:R663Q	ENSP00000263604:R663Q	R	+	2	0	KCNT1	137804418	1.000000	0.71417	0.742000	0.31022	0.011000	0.07611	2.767000	0.47637	0.197000	0.20387	0.579000	0.79373	CGG	.	.	none		0.716	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822		A	138664597	G	A	138664597	3	1	7	1	0	0	0	0	1	0	0	0	8100	1116	39	1	2119	1	KCNT1	9	138664597	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	937618	138664597	2548834	74	751											
NACC2	138151	hgsc.bcm.edu	37	chr9	138903792	138903792	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagcgcttgcgaacgcggCgggcgttggtgcacatgtcc	5	7	16	13	6	0	0	0	0	0	0	1	1	1	0	2	3	4	3	2	3	1	2			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr9:138903792C>T	ENST00000371753.1	-	5	1392	c.1334G>A	c.(1333-1335)cGc>cAc	p.R445H	NACC2_ENST00000277554.2_Missense_Mutation_p.R445H			Q96BF6	NACC2_HUMAN	NACC family member 2, BEN and BTB (POZ) domain containing	445	BEN. {ECO:0000255|PROSITE- ProRule:PRU00784}.				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						GCGAACGCGGCGGGCGTTGGT	0.662																																					p.R445H		Atlas-SNP	.											.	NACC2	16	.	0			c.G1334A						PASS	.						33	28	30					9																	138903792		2198	4296	6494	SO:0001583	missense	138151	exon6			ACGCGGCGGGCGT	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.1334G>A	9.37:g.138903792C>T	ENSP00000360818:p.Arg445His	71	0	0		83	39	0.46988	NM_144653		Missense_Mutation	SNP	ENST00000371753.1	37	CCDS6993.1	.	.	.	.	.	.	.	.	.	.	C	29.6	5.023864	0.93462	.	.	ENSG00000148411	ENST00000371753;ENST00000277554	T;T	0.52295	0.67;0.67	5.23	4.33	0.51752	BEN domain (2);	0.000000	0.85682	D	0.000000	T	0.54078	0.1836	N	0.24115	0.695	0.47123	D	0.999329	D	0.89917	1.0	D	0.85130	0.997	T	0.59069	-0.7523	10	0.87932	D	0	.	13.0677	0.59043	0.0:0.9215:0.0:0.0785	.	445	Q96BF6	NACC2_HUMAN	H	445	ENSP00000360818:R445H;ENSP00000277554:R445H	ENSP00000277554:R445H	R	-	2	0	NACC2	138043613	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.626000	0.83164	1.193000	0.43086	0.313000	0.20887	CGC	.	.	none		0.662	NACC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055040.1	NM_144653		T	138903792	C	T	138903792	3	4	7	1	0	0	0	0	1	0	0	0	10145	768	27	1	433	1	NACC2	9	138903792	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	239195	138903792	2309639	75	752											
DIP2C	22982	hgsc.bcm.edu	37	chr10	332259	332259	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gtccttttgtttctgggttgGcaattataatccgaacccct	7	16	8	10	1	1	0	0	0	1	0	3	1	3	0	4	2	1	3	4	2	4	6			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr10:332259G>A	ENST00000280886.6	-	34	4160	c.4073C>T	c.(4072-4074)gCc>gTc	p.A1358V		NM_014974.2	NP_055789.1	Q9Y2E4	DIP2C_HUMAN	DIP2 disco-interacting protein 2 homolog C (Drosophila)	1358						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)		TTCTGGGTTGGCAATTATAAT	0.478																																					p.A1358V		Atlas-SNP	.											.	DIP2C	195	.	0			c.C4073T						PASS	.						175	184	181					10																	332259		2203	4300	6503	SO:0001583	missense	22982	exon34			GGGTTGGCAATTA	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.4073C>T	10.37:g.332259G>A	ENSP00000280886:p.Ala1358Val	89	0	0		76	35	0.460526	NM_014974	B4DPI5|Q5SS78	Missense_Mutation	SNP	ENST00000280886.6	37	CCDS7054.1	.	.	.	.	.	.	.	.	.	.	G	19.49	3.836606	0.71373	.	.	ENSG00000151240	ENST00000280886;ENST00000535541	T	0.33865	1.39	5.92	5.92	0.95590	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.26484	0.0647	N	0.04320	-0.23	0.80722	D	1	B	0.23854	0.092	B	0.39971	0.315	T	0.08973	-1.0696	10	0.02654	T	1	-36.6422	20.3214	0.98679	0.0:0.0:1.0:0.0	.	1358	Q9Y2E4	DIP2C_HUMAN	V	1358;283	ENSP00000280886:A1358V	ENSP00000280886:A1358V	A	-	2	0	DIP2C	322259	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	4.974000	0.63771	2.804000	0.96469	0.655000	0.94253	GCC	.	.	none		0.478	DIP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046389.1	NM_014974		A	332259	G	A	332259	3	1	7	1	0	0	0	0	1	0	0	0	4531	1203	42	2	613	2	DIP2C	10	332259	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10		332259	135202488	76	753											
GPR158	57512	hgsc.bcm.edu	37	chr10	25887600	25887600	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgggaggtttatgacctgacCcctggtcctgtgccttcaga	6	12	12	11	0	1	3	1	2	0	1	2	4	2	4	5	3	1	1	5	3	1	3			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr10:25887600C>A	ENST00000376351.3	+	11	3404	c.3045C>A	c.(3043-3045)acC>acA	p.T1015T	GPR158_ENST00000490549.1_3'UTR	NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	1015					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						ATGACCTGACCCCTGGTCCTG	0.478																																					p.T1015T		Atlas-SNP	.											.	GPR158	255	.	0			c.C3045A						PASS	.						56	57	57					10																	25887600		2203	4300	6503	SO:0001819	synonymous_variant	57512	exon11			CCTGACCCCTGGT	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.3045C>A	10.37:g.25887600C>A		72	0	0		77	27	0.350649	NM_020752	Q6QR81|Q9ULT3	Silent	SNP	ENST00000376351.3	37	CCDS31166.1																																																																																			.	.	none		0.478	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110		A	25887600	C	A	25887600	2	1	7	1	0	0	0	0	0	0	0	1	6671	610	22	4		4	GPR158	10	25887600	Silent	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	25555341	25887600	109647147	77	754											
FAS	355	hgsc.bcm.edu	37	chr10	90773125	90773125	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agtggcaataaatttatctgGtaaggcttttatcattttat	12	18	7	4	0	2	0	1	0	1	0	2	0	2	0	0	3	0	3	0	3	7	8			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr10:90773125G>C	ENST00000355740.2	+	8	896		c.e8+1		FAS_ENST00000355279.2_Intron|FAS_ENST00000352159.4_Splice_Site|FAS_ENST00000357339.2_Splice_Site|FAS_ENST00000313771.5_Splice_Site|RP11-399O19.9_ENST00000562983.1_RNA	NM_000043.4|NM_152871.2|NM_152872.2	NP_000034.1|NP_690610.1|NP_690611.1	P49327	FAS_HUMAN	Fas cell surface death receptor						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)	AATTTATCTGGTAAGGCTTTT	0.284																																					.		Atlas-SNP	.											.	FAS	47	.	0			c.613+1G>C	GRCh37	CS994526	FAS	S		PASS	.						70	78	75					10																	90773125		2201	4279	6480	SO:0001630	splice_region_variant	355	exon7			TATCTGGTAAGGC	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	ENST00000355740.2:c.676+1G>C	10.37:g.90773125G>C		156	1	0.00641026		100	66	0.66	NM_152871	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Splice_Site	SNP	ENST00000355740.2	37	CCDS7393.1	.	.	.	.	.	.	.	.	.	.	G	10.35	1.325140	0.24080	.	.	ENSG00000026103	ENST00000355740;ENST00000352159;ENST00000357339;ENST00000371875	.	.	.	3.54	3.54	0.40534	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.9442	0.47292	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FAS	90763105	1.000000	0.71417	0.996000	0.52242	0.376000	0.30014	3.482000	0.53186	2.283000	0.76528	0.563000	0.77884	.	.	.	none		0.284	FAS-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049274.3		Intron	C	90773125	G	C	90773125	5	2	7	1	0	0	0	0	0	0	1	0	5689	1275	44	4	707	4	FAS	10	90773125	Splice_Site	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	64885525	90773125	44761622	78	755											
PLCE1	51196	hgsc.bcm.edu	37	chr10	96084266	96084266	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tcaggagtgtgtgtttcaagCccaaagcaagtggaaaggtg	12	9	14	6	0	2	0	2	0	0	0	2	2	2	2	1	3	2	2	1	3	4	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr10:96084266C>T	ENST00000371380.3	+	30	6897	c.6662C>T	c.(6661-6663)gCc>gTc	p.A2221V	PLCE1_ENST00000371385.3_Missense_Mutation_p.A1913V|PLCE1_ENST00000260766.3_Missense_Mutation_p.A2221V|NOC3L_ENST00000543788.1_Intron|PLCE1_ENST00000371375.1_Missense_Mutation_p.A1913V			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	2221	Ras-associating 2. {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)				GTGTTTCAAGCCCAAAGCAAG	0.438																																					p.A2221V		Atlas-SNP	.											.	PLCE1	543	.	0			c.C6662T						PASS	.						158	156	157					10																	96084266		1886	4112	5998	SO:0001583	missense	51196	exon31			TTCAAGCCCAAAG		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.6662C>T	10.37:g.96084266C>T	ENSP00000360431:p.Ala2221Val	72	0	0		83	30	0.361446	NM_016341	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Missense_Mutation	SNP	ENST00000371380.3	37	CCDS41552.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.585086	0.86748	.	.	ENSG00000138193	ENST00000260766;ENST00000371380;ENST00000371385;ENST00000371375	T;T;T;T	0.17691	2.26;2.26;2.26;2.26	5.59	4.69	0.59074	Ras-association (3);	0.062832	0.64402	N	0.000006	T	0.42108	0.1188	M	0.75777	2.31	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	T	0.40232	-0.9574	10	0.72032	D	0.01	.	13.8887	0.63724	0.0:0.9261:0.0:0.0739	.	2205;1913;2221	B7ZM61;Q9P212-2;Q9P212	.;.;PLCE1_HUMAN	V	2221;2221;1913;1913	ENSP00000260766:A2221V;ENSP00000360431:A2221V;ENSP00000360438:A1913V;ENSP00000360426:A1913V	ENSP00000260766:A2221V	A	+	2	0	PLCE1	96074256	1.000000	0.71417	1.000000	0.80357	0.705000	0.40729	3.805000	0.55575	1.362000	0.46000	0.655000	0.94253	GCC	.	.	none		0.438	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341		T	96084266	C	T	96084266	3	4	7	1	0	0	0	0	1	0	0	0	12043	739	26	2	7066	2	PLCE1	10	96084266	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	5311141	96084266	39450481	79	756											
CHID1	66005	hgsc.bcm.edu	37	chr11	902268	902268	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcttcagctgcagccagacGggtgagatctgtgtgaactt	8	11	12	10	1	3	3	1	2	2	2	3	4	3	3	1	1	4	2	1	1	1	2			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr11:902268G>A	ENST00000449825.1	-	4	680	c.324C>T	c.(322-324)ccC>ccT	p.P108P	CHID1_ENST00000336845.5_Silent_p.P133P|CHID1_ENST00000429789.2_Silent_p.P108P|CHID1_ENST00000323541.7_Silent_p.P138P|CHID1_ENST00000323578.8_Silent_p.P108P|CHID1_ENST00000528581.1_Silent_p.P133P|CHID1_ENST00000526714.1_5'UTR|CHID1_ENST00000436108.2_Silent_p.P108P|CHID1_ENST00000454838.2_Silent_p.P133P	NM_001142675.1	NP_001136147.1	Q9BWS9	CHID1_HUMAN	chitinase domain containing 1	108					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)		GCAGCCAGACGGGTGAGATCT	0.552																																					p.P133P	Pancreas(117;992 2327 5172 41921)	Atlas-SNP	.											.	CHID1	29	.	0			c.C399T						PASS	.						187	143	158					11																	902268		2203	4299	6502	SO:0001819	synonymous_variant	66005	exon5			CCAGACGGGTGAG	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.324C>T	11.37:g.902268G>A		69	0	0		65	26	0.4	NM_001142676	B3KWB0|Q8NBM9|Q96CZ3|Q96S93|Q96SK0|Q9BY52	Silent	SNP	ENST00000449825.1	37	CCDS7722.1																																																																																			.	.	none		0.552	CHID1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257112.1	NM_023947		A	902268	G	A	902268	2	1	7	1	0	0	0	0	0	0	0	1	3347	1103	39	1		1	CHID1	11	902268	Silent	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10		902268	134104248	80	757											
MUC6	4588	hgsc.bcm.edu	37	chr11	1016749	1016749	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gactgtgtgagtacttggagTcaccaaggaggtggagaaag	12	8	16	5	0	1	2	1	1	0	1	1	6	1	4	1	4	1	1	1	4	3	2			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr11:1016749T>C	ENST00000421673.2	-	31	6102	c.6052A>G	c.(6052-6054)Act>Gct	p.T2018A		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	2018	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)		GTACTTGGAGTCACCAAGGAG	0.542																																					p.T2018A		Atlas-SNP	.											.	MUC6	408	.	0			c.A6052G						PASS	.						795	734	755					11																	1016749		2203	4295	6498	SO:0001583	missense	4588	exon31			TTGGAGTCACCAA	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.6052A>G	11.37:g.1016749T>C	ENSP00000406861:p.Thr2018Ala	454	0	0		425	20	0.0470588	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	T	11.21	1.571617	0.28003	.	.	ENSG00000184956	ENST00000421673	T	0.26660	1.72	2.8	1.55	0.23275	.	.	.	.	.	T	0.25382	0.0617	L	0.44542	1.39	0.09310	N	1	D	0.52996	0.957	P	0.51355	0.667	T	0.13282	-1.0515	9	0.14252	T	0.57	.	6.5144	0.22240	0.2164:0.0:0.0:0.7835	.	2018	Q6W4X9	MUC6_HUMAN	A	2018	ENSP00000406861:T2018A	ENSP00000406861:T2018A	T	-	1	0	MUC6	1006749	0.175000	0.23083	0.002000	0.10522	0.030000	0.12068	1.083000	0.30815	0.243000	0.21327	0.260000	0.18958	ACT	.	.	none		0.542	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		C	1016749	T	C	1016749	3	2	7	1	0	0	0	0	1	0	0	0	9989	1667	58	3	1279	3	MUC6	11	1016749	Missense_Mutation	SNP	T	TCGA-FA-A7Q1-01A-11D-A382-10	114481	1016749	133989767	81	758											
NAV2	89797	hgsc.bcm.edu	37	chr11	20066704	20066704	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcagagtggttccgccgcCggcctggccatgatcacagc	8	6	13	14	3	1	2	1	1	0	1	2	2	2	2	5	3	2	2	5	3	1	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr11:20066704C>T	ENST00000396087.3	+	15	3558	c.3459C>T	c.(3457-3459)gcC>gcT	p.A1153A	NAV2-AS2_ENST00000533767.1_RNA|NAV2_ENST00000396085.1_Silent_p.A1130A|NAV2_ENST00000311043.8_Silent_p.A216A|NAV2_ENST00000533917.1_Silent_p.A216A|NAV2_ENST00000360655.4_Silent_p.A1066A|NAV2_ENST00000527559.2_Silent_p.A1082A|NAV2_ENST00000349880.4_Silent_p.A1130A|NAV2_ENST00000540292.1_Silent_p.A1084A	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	1153					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						GTTCCGCCGCCGGCCTGGCCA	0.587																																					p.A1153A		Atlas-SNP	.											NAV2,NS,carcinoma,+2,1	NAV2	255	1	0			c.C3459T						PASS	.						71	69	70					11																	20066704		2203	4300	6503	SO:0001819	synonymous_variant	89797	exon15			CGCCGCCGGCCTG	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.3459C>T	11.37:g.20066704C>T		48	0	0		42	15	0.357143	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	37	CCDS58126.1																																																																																			.	.	none		0.587	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		T	20066704	C	T	20066704	2	4	7	1	0	0	0	0	0	0	0	1	10193	639	23	1		1	NAV2	11	20066704	Silent	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	19049955	20066704	114939812	82	759											
OR5M11	219487	hgsc.bcm.edu	37	chr11	56310329	56310329	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagatgcaaactctcctggaCgttttcacactgtagcgcag	10	10	9	12	2	2	1	1	0	1	1	3	2	2	2	1	1	3	4	1	1	2	3			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr11:56310329C>T	ENST00000528616.2	-	1	428	c.405G>A	c.(403-405)acG>acA	p.T135T		NM_001005245.1	NP_001005245.1	Q96RB7	OR5MB_HUMAN	olfactory receptor, family 5, subfamily M, member 11	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)|large_intestine(1)|lung(14)	18						CTCTCCTGGACGTTTTCACAC	0.498																																					p.T135T		Atlas-SNP	.											OR5M11,NS,carcinoma,0,2	OR5M11	60	2	0			c.G405A						PASS	.						51	54	53					11																	56310329		2179	4283	6462	SO:0001819	synonymous_variant	219487	exon1			CCTGGACGTTTTC	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.405G>A	11.37:g.56310329C>T		41	0	0		48	26	0.541667	NM_001005245	B2RNL5|B2RNL7	Silent	SNP	ENST00000528616.2	37	CCDS53629.1																																																																																			.	.	none		0.498	OR5M11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391608.1	NM_001005245		T	56310329	C	T	56310329	2	4	7	1	0	0	0	0	0	0	0	1	11183	523	19	1		1	OR5M11	11	56310329	Silent	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	36243625	56310329	78696187	83	760											
NXF1	10482	hgsc.bcm.edu	37	chr11	62564806	62564806	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctaccttgcagggcggtaacGtcgtgggggcttcaacatca	8	9	13	11	3	2	0	2	0	0	0	3	0	2	0	1	4	4	3	1	4	3	4			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr11:62564806G>A	ENST00000532297.1	-	13	1735	c.1106C>T	c.(1105-1107)aCg>aTg	p.T369M	NXF1_ENST00000294172.2_Missense_Mutation_p.T369M|NXF1_ENST00000533048.1_5'Flank|NXF1_ENST00000531709.2_3'UTR			Q9UBU9	NXF1_HUMAN	nuclear RNA export factor 1	369					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						GGGCGGTAACGTCGTGGGGGC	0.498																																					p.T369M		Atlas-SNP	.											.	NXF1	67	.	0			c.C1106T						PASS	.						116	101	106					11																	62564806		2201	4299	6500	SO:0001583	missense	10482	exon12			GGTAACGTCGTGG	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.1106C>T	11.37:g.62564806G>A	ENSP00000436679:p.Thr369Met	143	0	0		112	54	0.482143	NM_006362	B4E269|Q99799|Q9UQL2	Missense_Mutation	SNP	ENST00000532297.1	37	CCDS8037.1	.	.	.	.	.	.	.	.	.	.	G	8.858	0.946327	0.18356	.	.	ENSG00000162231	ENST00000294172;ENST00000532297;ENST00000530875	T;T;T	0.63744	-0.06;-0.06;-0.06	5.42	-7.16	0.01516	.	0.924293	0.09295	N	0.821746	T	0.57917	0.2086	M	0.62016	1.91	0.09310	N	0.999999	B;B	0.18461	0.028;0.005	B;B	0.16289	0.015;0.001	T	0.37549	-0.9701	10	0.29301	T	0.29	0.0011	20.7843	0.99721	0.1545:0.0:0.8455:0.0	.	412;369	E9PIN3;Q9UBU9	.;NXF1_HUMAN	M	369;369;412	ENSP00000294172:T369M;ENSP00000436679:T369M;ENSP00000435742:T412M	ENSP00000294172:T369M	T	-	2	0	NXF1	62321382	0.008000	0.16893	0.001000	0.08648	0.512000	0.34134	0.602000	0.24134	-1.382000	0.02109	-0.300000	0.09419	ACG	.	.	none		0.498	NXF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395365.2	NM_006362		A	62564806	G	A	62564806	3	1	7	1	0	0	0	0	1	0	0	0	10791	1145	40	1	793	1	NXF1	11	62564806	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	6254477	62564806	72441710	84	761											
PCF11	51585	hgsc.bcm.edu	37	chr11	82872427	82872427	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggattctattgtgaaaaacgTtggaagagagtatctcactg	13	12	11	5	1	2	2	1	1	2	1	3	5	2	4	0	2	1	2	0	2	5	5			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr11:82872427T>G	ENST00000298281.4	+	2	703	c.251T>G	c.(250-252)gTt>gGt	p.V84G		NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	84	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						GTGAAAAACGTTGGAAGAGAG	0.328																																					p.V84G		Atlas-SNP	.											.	PCF11	220	.	0			c.T251G						PASS	.						87	82	84					11																	82872427		1811	4075	5886	SO:0001583	missense	51585	exon2			AAAACGTTGGAAG	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.251T>G	11.37:g.82872427T>G	ENSP00000298281:p.Val84Gly	191	0	0		151	60	0.397351	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	37	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	T	21.8	4.206596	0.79127	.	.	ENSG00000165494	ENST00000298281;ENST00000530660;ENST00000530304	T;T;T	0.48522	0.81;0.81;0.81	5.66	5.66	0.87406	ENTH/VHS (2);RNA polymerase II, large subunit, CTD (2);Domain of unknown function DUF618 (1);	0.000000	0.52532	D	0.000075	T	0.72930	0.3522	M	0.86953	2.85	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.80764	0.993;0.994	T	0.77387	-0.2607	9	.	.	.	.	16.2026	0.82095	0.0:0.0:0.0:1.0	.	84;84	E9PQ01;O94913	.;PCF11_HUMAN	G	84	ENSP00000298281:V84G;ENSP00000434540:V84G;ENSP00000431567:V84G	.	V	+	2	0	PCF11	82550075	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.965000	0.87945	2.285000	0.76669	0.533000	0.62120	GTT	.	.	none		0.328	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885		G	82872427	T	G	82872427	3	3	7	1	0	0	0	0	1	0	0	0	11582	1725	60	5	257	5	PCF11	11	82872427	Missense_Mutation	SNP	T	TCGA-FA-A7Q1-01A-11D-A382-10	20307621	82872427	52134089	85	762											
CCDC81	60494	hgsc.bcm.edu	37	chr11	86133616	86133616	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atttgctctcctctcctcagGgcttcagacaagctgtttct	6	15	7	13	0	5	1	2	0	3	1	7	1	5	1	2	1	2	4	2	1	1	3			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr11:86133616G>T	ENST00000445632.2	+	15	2090	c.1818G>T	c.(1816-1818)cgG>cgT	p.R606R	CCDC81_ENST00000278487.3_Splice_Site_p.R341R|CCDC81_ENST00000354755.1_Splice_Site_p.R516R|CCDC81_ENST00000528728.1_Splice_Site_p.R341R	NM_001156474.1	NP_001149946.1	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81	606										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)				CTCTCCTCAGGGCTTCAGACA	0.557																																					p.R606R		Atlas-SNP	.											.	CCDC81	89	.	0			c.G1818T						PASS	.						67	64	65					11																	86133616		2202	4299	6501	SO:0001630	splice_region_variant	60494	exon15			CCTCAGGGCTTCA	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.1818-1G>T	11.37:g.86133616G>T		42	0	0		42	20	0.47619	NM_001156474	A0AVL7|Q53FW3|Q9H5E5	Silent	SNP	ENST00000445632.2	37	CCDS53691.1																																																																																			.	.	none		0.557	CCDC81-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393756.1	NM_021827	Silent	T	86133616	G	T	86133616	5	4	7	1	0	0	0	0	0	0	1	0	2857	1246	43	4	1876	4	CCDC81	11	86133616	Splice_Site	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	3261189	86133616	48872900	86	763											
FAT3	120114	hgsc.bcm.edu	37	chr11	92495108	92495108	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gatgaaaatgacaacaagccCcagttcccagagaaggtcta	16	6	9	10	0	1	3	0	2	1	1	2	5	2	3	3	1	2	1	3	1	6	2			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr11:92495108C>G	ENST00000298047.6	+	4	3773	c.3756C>G	c.(3754-3756)ccC>ccG	p.P1252P	RP11-203F8.1_ENST00000529884.1_RNA|FAT3_ENST00000409404.2_Silent_p.P1252P|FAT3_ENST00000525166.1_Silent_p.P1102P			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	1252	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)				ACAACAAGCCCCAGTTCCCAG	0.473										TCGA Ovarian(4;0.039)																											p.P1252P		Atlas-SNP	.											.	FAT3	1822	.	0			c.C3756G						PASS	.						182	178	179					11																	92495108		1912	4122	6034	SO:0001819	synonymous_variant	120114	exon4			CAAGCCCCAGTTC	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.3756C>G	11.37:g.92495108C>G		88	0	0		104	42	0.403846	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				.	.	none		0.473	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		G	92495108	C	G	92495108	2	3	7	1	0	0	0	0	0	0	0	1	5699	610	22	4		4	FAT3	11	92495108	Silent	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	6361492	92495108	42511408	87	764											
TECTA	7007	hgsc.bcm.edu	37	chr11	120989139	120989139	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgtagcccctacgaggtgtgCgaacccaaaggcaaattctt	11	9	10	11	2	1	0	0	0	1	0	1	2	1	0	3	2	4	2	3	2	5	4	rs367974065		TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr11:120989139C>T	ENST00000392793.1	+	7	1186	c.915C>T	c.(913-915)tgC>tgT	p.C305C	TECTA_ENST00000264037.2_Silent_p.C305C			O75443	TECTA_HUMAN	tectorin alpha	305	VWFC.				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)		ACGAGGTGTGCGAACCCAAAG	0.532																																					p.C305C		Atlas-SNP	.											.	TECTA	329	.	0			c.C915T						PASS	.	C		0,4406		0,0,2203	102	98	99		915	0.6	1	11		99	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	TECTA	NM_005422.2		0,1,6501	TT,TC,CC		0.0116,0.0,0.0077		305/2156	120989139	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	7007	exon6			GGTGTGCGAACCC	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.915C>T	11.37:g.120989139C>T		119	0	0		127	60	0.472441	NM_005422		Silent	SNP	ENST00000392793.1	37	CCDS8434.1																																																																																			.	.	weak		0.532	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		T	120989139	C	T	120989139	2	4	7	1	0	0	0	0	0	0	0	1	15762	776	27	1		1	TECTA	11	120989139	Silent	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	28494031	120989139	14017377	88	765											
CD163L1	283316	hgsc.bcm.edu	37	chr12	7556213	7556213	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcagtcccagagagctgaCtcattcccagtgcaagatat	11	9	10	11	0	1	3	1	1	0	2	3	4	3	3	2	0	3	3	2	0	2	2			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr12:7556213C>A	ENST00000313599.3	-	6	1383	c.1326G>T	c.(1324-1326)gaG>gaT	p.E442D	CD163L1_ENST00000396630.1_Missense_Mutation_p.E442D|CD163L1_ENST00000416109.2_Missense_Mutation_p.E452D			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	442	SRCR 4. {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						AGAGAGCTGACTCATTCCCAG	0.443																																					p.E442D		Atlas-SNP	.											.	CD163L1	238	.	0			c.G1326T						PASS	.						137	128	131					12																	7556213		2203	4300	6503	SO:0001583	missense	283316	exon6			AGCTGACTCATTC	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.1326G>T	12.37:g.7556213C>A	ENSP00000315945:p.Glu442Asp	108	0	0		118	64	0.542373	NM_174941	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Missense_Mutation	SNP	ENST00000313599.3	37	CCDS8577.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.956153	0.73902	.	.	ENSG00000177675	ENST00000313599;ENST00000416109;ENST00000396630;ENST00000545926	T;T;T;T	0.45276	0.9;0.9;0.9;0.9	2.22	-1.83	0.07833	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	.	.	.	.	T	0.65811	0.2727	M	0.93062	3.375	0.24263	N	0.995277	D;D	0.89917	1.0;0.999	D;D	0.85130	0.99;0.997	T	0.54951	-0.8216	9	0.56958	D	0.05	.	6.6862	0.23146	0.0:0.42:0.0:0.58	.	452;442	E7EVK4;Q9NR16	.;C163B_HUMAN	D	442;452;442;88	ENSP00000315945:E442D;ENSP00000393474:E452D;ENSP00000379871:E442D;ENSP00000439921:E88D	ENSP00000315945:E442D	E	-	3	2	CD163L1	7447480	0.000000	0.05858	0.081000	0.20488	0.925000	0.55904	-1.439000	0.02414	-0.460000	0.07003	0.563000	0.77884	GAG	.	.	none		0.443	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941		A	7556213	C	A	7556213	3	1	7	1	0	0	0	0	1	0	0	0	2970	564	20	4	3091	4	CD163L1	12	7556213	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10		7556213	126295682	89	766											
KRAS	3845	hgsc.bcm.edu	37	chr12	25398255	25398255	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaaatgattctgaattagctGtatcgtcaaggcactcttgc	12	13	8	8	1	3	2	1	2	2	0	4	2	3	2	0	1	2	3	0	1	6	4	rs121913236		TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr12:25398255G>T	ENST00000256078.4	-	2	127	c.64C>A	c.(64-66)Cag>Aag	p.Q22K	KRAS_ENST00000556131.1_Missense_Mutation_p.Q22K|KRAS_ENST00000557334.1_Missense_Mutation_p.Q22K|KRAS_ENST00000311936.3_Missense_Mutation_p.Q22K	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	22			Q -> E (in CFC2; exhibits an increase in intrinsic and guanine nucleotide exchange factor catalyzed nucleotide exchange in combination with an impaired GTPase- activating protein-stimulated GTP hydrolysis but functional in interaction with effectors). {ECO:0000269|PubMed:17056636}.|Q -> R (in NS3; impairs GTPase-activating protein stimulated GTP hydrolysis with unaffected intrinsic functions and a virtually functional effector interaction).		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.Q22K(8)|p.Q22*(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)			TGAATTAGCTGTATCGTCAAG	0.363		119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.Q22K	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,colon,carcinoma,0,18	KRAS	30930	18	9	Substitution - Missense(8)|Substitution - Nonsense(1)	large_intestine(7)|haematopoietic_and_lymphoid_tissue(1)|small_intestine(1)	c.C64A	GRCh37	CM070964	KRAS	M	rs121913236	PASS	.						88	76	80					12																	25398255		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	TTAGCTGTATCGT	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.64C>A	12.37:g.25398255G>T	ENSP00000256078:p.Gln22Lys	209	1	0.00478469		279	167	0.598566	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	G	32	5.113031	0.94339	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.79749	-1.3;-0.43;-0.43;-0.43	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90013	0.6882	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.976	D	0.90739	0.4648	10	0.87932	D	0	.	18.3719	0.90409	0.0:0.0:1.0:0.0	.	22;22	P01116-2;P01116	.;RASK_HUMAN	K	22	ENSP00000308495:Q22K;ENSP00000452512:Q22K;ENSP00000256078:Q22K;ENSP00000451856:Q22K	ENSP00000256078:Q22K	Q	-	1	0	KRAS	25289522	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.770000	0.98971	2.668000	0.90789	0.563000	0.77884	CAG	.	.	weak		0.363	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		T	25398255	G	T	25398255	3	4	7	1	0	0	0	0	1	0	0	0	8447	1386	48	4	642	4	KRAS	12	25398255	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	17842042	25398255	108453640	90	767											
KRT79	338785	hgsc.bcm.edu	37	chr12	53216988	53216988	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagctccccacgctgctcCgcttccgcaatggccgtctg	4	8	10	19	4	1	0	0	0	1	0	4	0	4	0	6	1	2	5	6	1	1	1	rs573197551		TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr12:53216988C>T	ENST00000330553.5	-	7	1213	c.1179G>A	c.(1177-1179)gcG>gcA	p.A393A		NM_175834.2	NP_787028.1	Q5XKE5	K2C79_HUMAN	keratin 79	393	Coil 2.|Rod.		A -> V (in dbSNP:rs17688627).			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						CACGCTGCTCCGCTTCCGCAA	0.622																																					p.A393A		Atlas-SNP	.											.	KRT79	78	.	0			c.G1179A						PASS	.						67	62	64					12																	53216988		2203	4300	6503	SO:0001819	synonymous_variant	338785	exon7			CTGCTCCGCTTCC	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.1179G>A	12.37:g.53216988C>T		90	0	0		101	68	0.673267	NM_175834	Q6P465|Q7Z793	Silent	SNP	ENST00000330553.5	37	CCDS8839.1																																																																																			.	.	none		0.622	KRT79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406376.1	NM_175834		T	53216988	C	T	53216988	2	4	7	1	0	0	0	0	0	0	0	1	8501	639	23	1		1	KRT79	12	53216988	Silent	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	27818733	53216988	80634907	91	768											
AVIL	10677	hgsc.bcm.edu	37	chr12	58197059	58197059	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggtatctaggagcatcacgtCagtagggttcaggtcatcct	9	11	12	9	1	5	0	4	0	1	0	6	1	6	1	1	4	1	4	1	4	3	4			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr12:58197059C>T	ENST00000257861.3	-	15	2363	c.1933G>A	c.(1933-1935)Gac>Aac	p.D645N	RNU6-1083P_ENST00000384022.1_RNA|AVIL_ENST00000550083.1_5'Flank|TSFM_ENST00000548851.1_Intron|AVIL_ENST00000537081.1_Missense_Mutation_p.D638N|RP11-571M6.17_ENST00000602802.1_lincRNA	NM_006576.3	NP_006567.3	O75366	AVIL_HUMAN	advillin	645	Core. {ECO:0000250}.				actin filament capping (GO:0051693)|cilium morphogenesis (GO:0060271)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|positive regulation of neuron projection development (GO:0010976)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)	actin binding (GO:0003779)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(9)|ovary(1)|prostate(6)	32	Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)					AGCATCACGTCAGTAGGGTTC	0.478											OREG0021955	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D645N		Atlas-SNP	.											.	AVIL	60	.	0			c.G1933A						PASS	.						225	197	206					12																	58197059		2203	4300	6503	SO:0001583	missense	10677	exon15			TCACGTCAGTAGG	AF041449	CCDS8959.1	12q13.11	2006-03-30				ENSG00000135407			14188	protein-coding gene	gene with protein product		613397				9664034, 12034507	Standard	NM_006576		Approved	p92, FLJ12386, ADVIL, DOC6	uc001sqj.2	O75366	OTTHUMG00000170461	ENST00000257861.3:c.1933G>A	12.37:g.58197059C>T	ENSP00000257861:p.Asp645Asn	125	0	0	1029	199	58	0.291457	NM_006576	B2RAU7|Q2NKM9	Missense_Mutation	SNP	ENST00000257861.3	37	CCDS8959.1	.	.	.	.	.	.	.	.	.	.	C	19.16	3.773527	0.69992	.	.	ENSG00000135407	ENST00000537081;ENST00000257861	T;T	0.22134	1.97;1.97	4.74	4.74	0.60224	Gelsolin domain (1);	0.000000	0.85682	D	0.000000	T	0.55561	0.1928	M	0.91663	3.23	0.80722	D	1	D;D	0.69078	0.996;0.997	D;D	0.75484	0.986;0.971	T	0.67260	-0.5715	10	0.87932	D	0	-11.8772	16.6465	0.85178	0.0:1.0:0.0:0.0	.	638;645	O75366-2;O75366	.;AVIL_HUMAN	N	638;645	ENSP00000443207:D638N;ENSP00000257861:D645N	ENSP00000257861:D645N	D	-	1	0	AVIL	56483326	1.000000	0.71417	0.627000	0.29227	0.033000	0.12548	7.605000	0.82844	2.458000	0.83093	0.561000	0.74099	GAC	.	.	none		0.478	AVIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409276.1	NM_006576		T	58197059	C	T	58197059	3	4	7	1	0	0	0	0	1	0	0	0	1227	826	29	2	546	2	AVIL	12	58197059	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	4980071	58197059	75654836	92	769											
NTN4	59277	hgsc.bcm.edu	37	chr12	96076600	96076600	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccagtctatgtctgtgtggcTaacaaaatagaacatgataa	15	11	8	7	0	2	2	0	1	2	1	2	2	2	2	1	1	2	1	1	1	7	4			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr12:96076600T>C	ENST00000343702.4	-	7	1843		c.e7-2		NTN4_ENST00000538383.1_Splice_Site|NTN4_ENST00000553059.1_Splice_Site|NTN4_ENST00000344911.4_Splice_Site	NM_021229.3	NP_067052.2	Q9HB63	NET4_HUMAN	netrin 4						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						TCTGTGTGGCTAACAAAATAG	0.413																																					.		Atlas-SNP	.											.	NTN4	67	.	0			c.1395-2A>G						PASS	.						100	89	93					12																	96076600		2203	4300	6503	SO:0001630	splice_region_variant	59277	exon8			TGTGGCTAACAAA	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.1395-2A>G	12.37:g.96076600T>C		53	0	0		78	4	0.0512821	NM_021229	B2RNC2|Q658K9|Q7L3F1|Q7L9D6|Q7Z5B6|Q9BZP1|Q9NT44|Q9P133	Splice_Site	SNP	ENST00000343702.4	37	CCDS9054.1	.	.	.	.	.	.	.	.	.	.	T	13.87	2.364696	0.41902	.	.	ENSG00000074527	ENST00000343702;ENST00000344911;ENST00000538383;ENST00000553059	.	.	.	5.26	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1749	0.72903	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	NTN4	94600731	1.000000	0.71417	0.395000	0.26283	0.405000	0.30901	5.424000	0.66464	1.996000	0.58369	0.260000	0.18958	.	.	.	none		0.413	NTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408372.1	NM_021229	Intron	C	96076600	T	C	96076600	5	2	7	1	0	0	0	0	0	0	1	0	10711	1536	53	3	509	3	NTN4	12	96076600	Splice_Site	SNP	T	TCGA-FA-A7Q1-01A-11D-A382-10	37879541	96076600	37775295	93	770											
BCL7A	605	hgsc.bcm.edu	37	chr12	122460020	122460020	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gtcgggcaggtcggttcgagCcgagacgaggagccgggcca	7	4	19	11	6	0	1	0	0	0	1	3	5	0	2	3	5	2	2	3	5	0	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr12:122460020C>T	ENST00000261822.4	+	1	229	c.23C>T	c.(22-24)gCc>gTc	p.A8V	RP11-87C12.5_ENST00000538710.1_lincRNA|BCL7A_ENST00000538010.1_Missense_Mutation_p.A8V	NM_001024808.1	NP_001019979.1	Q4VC05	BCL7A_HUMAN	B-cell CLL/lymphoma 7A	8					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)		TCGGTTCGAGCCGAGACGAGG	0.711			T	MYC	BNHL																																p.A8V	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.C23T						PASS	.						20	21	20					12																	122460020		2194	4293	6487	SO:0001583	missense	605	exon1			TTCGAGCCGAGAC	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.23C>T	12.37:g.122460020C>T	ENSP00000261822:p.Ala8Val	50	0	0		59	26	0.440678	NM_020993	B4DJN6|B7ZB21|Q13843|Q14CT7	Missense_Mutation	SNP	ENST00000261822.4	37	CCDS53841.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.029586	0.75504	.	.	ENSG00000110987	ENST00000538010;ENST00000261822	T;T	0.63096	-0.02;0.04	4.24	3.35	0.38373	.	0.000000	0.85682	U	0.000000	T	0.76054	0.3934	M	0.77820	2.39	0.80722	D	1	B;D	0.71674	0.006;0.998	B;D	0.73380	0.014;0.98	T	0.76974	-0.2760	10	0.87932	D	0	.	9.7713	0.40591	0.0:0.8948:0.0:0.1052	.	8;8	Q4VC05;Q4VC05-2	BCL7A_HUMAN;.	V	8	ENSP00000445868:A8V;ENSP00000261822:A8V	ENSP00000261822:A8V	A	+	2	0	BCL7A	120944403	1.000000	0.71417	0.997000	0.53966	0.418000	0.31294	5.746000	0.68681	0.781000	0.33589	0.460000	0.39030	GCC	.	.	none		0.711	BCL7A-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000401712.1			T	122460020	C	T	122460020	3	4	7	1	0	0	0	0	1	0	0	0	1378	739	26	2	25	2	BCL7A	12	122460020	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	26383420	122460020	11391875	94	771											
GALNT9	50614	hgsc.bcm.edu	37	chr12	132837584	132837584	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagaagccgacgactggggcGgtggccgccttccagccctg	7	5	15	14	4	0	1	0	0	0	1	1	3	1	1	5	4	2	0	5	4	2	1	rs530313026		TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr12:132837584G>A	ENST00000328957.8	-	4	710	c.711C>T	c.(709-711)acC>acT	p.T237T	GALNT9_ENST00000535208.1_5'UTR	NM_001122636.1	NP_001116108.1	Q9HCQ5	GALT9_HUMAN	polypeptide N-acetylgalactosaminyltransferase 9	237	Catalytic subdomain A.				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)		CGACTGGGGCGGTGGCCGCCT	0.657													G|||	1	0.000199681	0.0	0.0	5008	,	,		15137	0.0		0.001	False		,,,				2504	0.0				p.T237T	Colon(186;2147 2752 13553 41466)	Atlas-SNP	.											.	GALNT9	74	.	0			c.C711T						PASS	.						29	34	32					12																	132837584		692	1591	2283	SO:0001819	synonymous_variant	50614	exon4			TGGGGCGGTGGCC	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.711C>T	12.37:g.132837584G>A		51	0	0		53	31	0.584906	NM_001122636	Q52LR8|Q6NT54|Q8NFR1	Silent	SNP	ENST00000328957.8	37																																																																																				.	.	none		0.657	GALNT9-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000402967.1	NM_001122636		A	132837584	G	A	132837584	2	1	7	1	0	0	0	0	0	0	0	1	6228	1103	39	1		1	GALNT9	12	132837584	Silent	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	10377564	132837584	1014311	95	772											
POLE	5426	hgsc.bcm.edu	37	chr12	133240614	133240614	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accatgatgttcaacatggcGcctgggtaggagatggtcac	10	9	13	9	1	2	2	2	1	0	1	2	3	2	2	2	4	1	2	2	4	2	2			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr12:133240614G>A	ENST00000320574.5	-	23	2725	c.2682C>T	c.(2680-2682)ggC>ggT	p.G894G	POLE_ENST00000535270.1_Silent_p.G867G	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	894					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)	TCAACATGGCGCCTGGGTAGG	0.547								DNA polymerases (catalytic subunits)																													p.G894G		Atlas-SNP	.											.	POLE	416	.	0			c.C2682T						PASS	.						196	179	185					12																	133240614		2203	4300	6503	SO:0001819	synonymous_variant	5426	exon23			CATGGCGCCTGGG		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.2682C>T	12.37:g.133240614G>A		98	0	0		145	28	0.193103	NM_006231	Q13533|Q86VH9	Silent	SNP	ENST00000320574.5	37	CCDS9278.1																																																																																			.	.	none		0.547	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231		A	133240614	G	A	133240614	2	1	7	1	0	0	0	0	0	0	0	1	12205	1074	38	1		1	POLE	12	133240614	Silent	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	403030	133240614	611281	96	773											
TPP2	7174	hgsc.bcm.edu	37	chr13	103316014	103316017	+	Frame_Shift_Del	DEL	ATTT	ATTT	-																															ataggctggattctagtgacAtttataacgaattgaaagaa																								rs370265663		TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	ATTT	ATTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr13:103316014_103316017delATTT	ENST00000376065.4	+	25	3157_3160	c.3121_3124delATTT	c.(3121-3126)atttatfs	p.IY1041fs	TPP2_ENST00000466153.1_3'UTR|TPP2_ENST00000376052.3_Frame_Shift_Del_p.IY1054fs	NM_003291.2	NP_003282.2	P29144	TPP2_HUMAN	tripeptidyl peptidase II	1041					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)					TTCTAGTGACATTTATAACGAATT	0.304																																					p.1040_1041del		Pindel,Atlas-Indel	.											.	TPP2	124	.	0			c.3120_3123del						PASS	.																																			SO:0001589	frameshift_variant	7174	exon25			.	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.3121_3124delATTT	13.37:g.103316014_103316017delATTT	ENSP00000365233:p.Ile1041fs	81	0	.		63	37	0.587	NM_003291	Q5VZU8	Frame_Shift_Del	DEL	ENST00000376065.4	37	CCDS9502.1																																																																																			.	.	none		0.304	TPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045683.2			-	103316017	ATTT	-	103316014	7	5	7	1	0	1	0	1	0	0	0	0	16427	217	8	0	3219	0	TPP2	13	103316014	Frame_Shift_Del	DEL	ATTT	TCGA-FA-A7Q1-01A-11D-A382-10		103316014	11853864	97	774											
ERCC5	2073	hgsc.bcm.edu	37	chr13	103528055	103528055	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagaacagctgcgaaagaGccaaaaaccagtgcttcaga	17	4	11	9	1	1	3	1	0	0	3	1	5	1	3	2	1	6	2	2	1	4	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr13:103528055G>T	ENST00000355739.4	+	15	4786	c.3363G>T	c.(3361-3363)gaG>gaT	p.E1121D	ERCC5_ENST00000375954.1_Missense_Mutation_p.E354D|ERCC5_ENST00000472247.1_3'UTR	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	1121					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)					CTGCGAAAGAGCCAAAAACCA	0.473			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.E1575D		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.G4725T						PASS	.						45	44	45					13																	103528055		2203	4300	6503	SO:0001583	missense	0	exon23	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	GAAAGAGCCAAAA	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.3363G>T	13.37:g.103528055G>T	ENSP00000347978:p.Glu1121Asp	81	0	0		64	59	0.921875	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Missense_Mutation	SNP	ENST00000355739.4	37	CCDS32004.1	.	.	.	.	.	.	.	.	.	.	G	9.150	1.015967	0.19355	.	.	ENSG00000134899	ENST00000418659;ENST00000355739;ENST00000375955;ENST00000375954	T;T	0.06933	3.57;3.24	4.68	0.389	0.16269	.	1.270480	0.05133	N	0.492840	T	0.07188	0.0182	L	0.41236	1.265	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.43589	-0.9382	10	0.15952	T	0.53	0.7098	4.9663	0.14093	0.074:0.1278:0.5347:0.2634	.	1121	P28715	ERCC5_HUMAN	D	1546;1121;953;354	ENSP00000347978:E1121D;ENSP00000365121:E354D	ENSP00000347978:E1121D	E	+	3	2	ERCC5	102326056	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.024000	0.12435	0.108000	0.17862	0.650000	0.86243	GAG	.	.	none		0.473	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1			T	103528055	G	T	103528055	3	4	7	1	0	0	0	0	1	0	0	0	5218	962	34	4	3421	4	ERCC5	13	103528055	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	212041	103528055	11641823	98	775											
DHRS2	10202	hgsc.bcm.edu	37	chr14	24108080	24108080	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agacaccaaccactatgctgTcagcagttgcccggggctac	10	7	10	14	1	1	1	1	0	0	1	1	1	1	1	3	2	5	4	3	2	3	3			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr14:24108080T>A	ENST00000250383.6	+	2	483	c.7T>A	c.(7-9)Tca>Aca	p.S3T	DHRS2_ENST00000344777.7_Missense_Mutation_p.S3T|DHRS2_ENST00000553896.1_3'UTR	NM_005794.3	NP_005785.1	Q13268	DHRS2_HUMAN	dehydrogenase/reductase (SDR family) member 2	3					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)		CACTATGCTGTCAGCAGTTGC	0.532																																					p.S3T		Atlas-SNP	.											.	DHRS2	78	.	0			c.T7A						PASS	.						116	114	115					14																	24108080		2203	4300	6503	SO:0001583	missense	10202	exon2			ATGCTGTCAGCAG		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.7T>A	14.37:g.24108080T>A	ENSP00000250383:p.Ser3Thr	66	0	0		55	22	0.4	NM_182908	D3DS54|Q53GS4|Q7Z789|Q9H2R2	Missense_Mutation	SNP	ENST00000250383.6	37	CCDS9604.1	.	.	.	.	.	.	.	.	.	.	.	12.39	1.923926	0.34002	.	.	ENSG00000100867	ENST00000432832;ENST00000250383;ENST00000344777	D;T;D	0.81996	-1.53;-1.49;-1.56	5.34	-4.87	0.03123	.	2.990420	0.01149	N	0.006375	T	0.62588	0.2440	N	0.08118	0	0.09310	N	1	B;B	0.17667	0.023;0.007	B;B	0.15870	0.014;0.008	T	0.50783	-0.8787	10	0.54805	T	0.06	.	0.6026	0.00747	0.3661:0.2175:0.1113:0.305	.	3;3	C9JZP6;D3DS54	.;.	T	3	ENSP00000401213:S3T;ENSP00000250383:S3T;ENSP00000344674:S3T	ENSP00000250383:S3T	S	+	1	0	DHRS2	23177920	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-0.808000	0.04515	-0.712000	0.04988	-0.251000	0.11542	TCA	.	.	none		0.532	DHRS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000071842.2	NM_182908		A	24108080	T	A	24108080	3	1	7	1	0	0	0	0	1	0	0	0	4492	1667	58	5	9	5	DHRS2	14	24108080	Missense_Mutation	SNP	T	TCGA-FA-A7Q1-01A-11D-A382-10		24108080	83241460	99	776											
ADCY4	196883	hgsc.bcm.edu	37	chr14	24802153	24802153	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agcgagaagccgcccagcgcGcacagcacagtggtcaggaa	12	2	14	13	4	1	1	1	0	0	1	1	3	1	2	2	2	4	2	2	2	2	0			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr14:24802153G>A	ENST00000310677.4	-	3	314	c.201C>T	c.(199-201)tgC>tgT	p.C67C	RP11-934B9.3_ENST00000555591.1_Missense_Mutation_p.R134C|ADCY4_ENST00000558563.1_5'UTR|ADCY4_ENST00000396747.3_5'UTR|ADCY4_ENST00000418030.2_Silent_p.C67C|ADCY4_ENST00000554068.2_Silent_p.C67C	NM_001198568.1|NM_001198592.1|NM_139247.3	NP_001185497.1|NP_001185521.1|NP_640340.2	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4	67					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)		CGCCCAGCGCGCACAGCACAG	0.647											OREG0022624	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C67C		Atlas-SNP	.											.	ADCY4	86	.	0			c.C201T						PASS	.						27	36	33					14																	24802153		2202	4299	6501	SO:0001819	synonymous_variant	196883	exon3			CAGCGCGCACAGC	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.201C>T	14.37:g.24802153G>A		67	0	0	774	47	22	0.468085	NM_001198592	B3KV74|D3DS75|Q17R40|Q6ZTM6|Q96ML7	Silent	SNP	ENST00000310677.4	37	CCDS9627.1	.	.	.	.	.	.	.	.	.	.	G	16.72	3.202543	0.58234	.	.	ENSG00000258973	ENST00000555591	.	.	.	5.66	-0.729	0.11158	.	.	.	.	.	T	0.50565	0.1623	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38178	-0.9673	4	.	.	.	.	5.6811	0.17776	0.5148:0.1478:0.3374:0.0	.	.	.	.	C	134	.	.	R	-	1	0	RP11-934B9.3	23871993	0.000000	0.05858	0.911000	0.35937	0.919000	0.55068	-0.592000	0.05747	-0.129000	0.11620	-0.266000	0.10368	CGC	.	.	none		0.647	ADCY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073200.4			A	24802153	G	A	24802153	2	1	7	1	0	0	0	0	0	0	0	1	296	1079	38	1		1	ADCY4	14	24802153	Silent	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	694073	24802153	82547387	100	777											
PSEN1	5663	hgsc.bcm.edu	37	chr14	73640277	73640277	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgtttgttttattgtagaatCtataccccattcacagaaga	12	16	6	7	0	2	3	1	0	1	3	2	3	2	3	2	0	1	3	2	0	6	8			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr14:73640277C>T	ENST00000324501.5	+	5	614	c.342C>T	c.(340-342)atC>atT	p.I114I	PSEN1_ENST00000394157.3_Silent_p.I114I|PSEN1_ENST00000394164.1_Silent_p.I110I|PSEN1_ENST00000261970.3_Silent_p.I114I|PSEN1_ENST00000344094.3_Silent_p.I114I|PSEN1_ENST00000406768.1_Silent_p.I22I|PSEN1_ENST00000557511.1_Silent_p.I114I|PSEN1_ENST00000357710.4_Silent_p.I110I	NM_000021.3|NM_007318.2	NP_000012.1|NP_015557.2	P49768	PSN1_HUMAN	presenilin 1	114					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)		ATTGTAGAATCTATACCCCAT	0.413																																					p.I114I		Atlas-SNP	.											.	PSEN1	38	.	0			c.C342T						PASS	.						137	133	134					14																	73640277		2203	4300	6503	SO:0001819	synonymous_variant	5663	exon5			TAGAATCTATACC	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.342C>T	14.37:g.73640277C>T		181	0	0		198	73	0.368687	NM_000021	B2R6D3|O95465|Q14762|Q15719|Q15720|Q96P33|Q9UIF0	Silent	SNP	ENST00000324501.5	37	CCDS9812.1																																																																																			.	.	none		0.413	PSEN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280500.2			T	73640277	C	T	73640277	2	4	7	1	0	0	0	0	0	0	0	1	12662	903	32	2		2	PSEN1	14	73640277	Silent	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	48838124	73640277	33709263	101	778											
C14orf4	64207	hgsc.bcm.edu	37	chr14	77493809	77493809	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgctgttgctgctgctgctgCtgctgttgctgttgctgttg	0	18	14	9	0	0	0	0	0	0	0	0	0	0	0	0	0	9	13	0	0	0	4	rs61991638		TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr14:77493809C>T	ENST00000238647.3	-	1	1225	c.327G>A	c.(325-327)caG>caA	p.Q109Q		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	109	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						gctgctgctgctgctgttgct	0.687																																					p.Q109Q		Atlas-SNP	.											.	IRF2BPL	40	.	0			c.G327A						PASS	.						2	2	2					14																	77493809		1179	2145	3324	SO:0001819	synonymous_variant	64207	exon1			CTGCTGCTGCTGT	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.327G>A	14.37:g.77493809C>T		22	0	0		36	7	0.194444	NM_024496	Q8NDQ2|Q96JG2|Q9H3I7	Silent	SNP	ENST00000238647.3	37	CCDS9854.1																																																																																			C|0.978;T|0.022	0.022	strong		0.687	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1	NM_024496		T	77493809	C	T	77493809	2	4	7	1	0	0	0	0	0	0	0	1	1775	796	28	2		2	C14orf4	14	77493809	Silent	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	3853532	77493809	29855731	102	779											
GABRG3	2567	hgsc.bcm.edu	37	chr15	27772698	27772698	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgcttcctgtttgtcttcGccgcgctgatggagtatgcc	3	15	12	11	3	1	1	0	1	1	0	3	2	2	2	3	1	2	4	3	1	1	4			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr15:27772698G>A	ENST00000333743.6	+	8	1239	c.985G>A	c.(985-987)Gcc>Acc	p.A329T	RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	329					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)	GTTTGTCTTCGCCGCGCTGAT	0.542																																					p.A329T	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											.	GABRG3	115	.	0			c.G985A						PASS	.						119	108	112					15																	27772698		2157	4267	6424	SO:0001583	missense	2567	exon8			GTCTTCGCCGCGC		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.985G>A	15.37:g.27772698G>A	ENSP00000331912:p.Ala329Thr	102	0	0		90	12	0.133333	NM_033223	G3V594|Q9HD46|Q9NYT2	Missense_Mutation	SNP	ENST00000333743.6	37	CCDS45195.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.422249	0.83559	.	.	ENSG00000182256	ENST00000333743	D	0.84660	-1.88	5.48	5.48	0.80851	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.90998	0.7169	M	0.67700	2.07	0.80722	D	1	D	0.69078	0.997	D	0.62955	0.909	D	0.91538	0.5247	10	0.66056	D	0.02	.	18.3414	0.90307	0.0:0.0:1.0:0.0	.	329	Q99928	GBRG3_HUMAN	T	329	ENSP00000331912:A329T	ENSP00000331912:A329T	A	+	1	0	GABRG3	25446293	1.000000	0.71417	0.987000	0.45799	0.552000	0.35366	6.201000	0.72124	2.562000	0.86427	0.563000	0.77884	GCC	.	.	none		0.542	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2			A	27772698	G	A	27772698	3	1	7	1	0	0	0	0	1	0	0	0	6181	1087	38	1	1015	1	GABRG3	15	27772698	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10		27772698	74758694	103	780											
FMN1	342184	hgsc.bcm.edu	37	chr15	33359827	33359827	+	Intron	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	atttccgaggtcaggtgaaaCccgagaccctgcttcctgtg	8	10	11	12	2	1	2	1	1	0	1	3	4	3	2	4	2	2	1	4	2	1	2	rs570854143		TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr15:33359827C>A	ENST00000559047.1	-	3	2043				FMN1_ENST00000334528.9_Missense_Mutation_p.V87F|FMN1_ENST00000559150.1_Intron|FMN1_ENST00000558197.1_Missense_Mutation_p.V87F|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)		TCAGGTGAAACCCGAGACCCT	0.483																																					p.V87F		Atlas-SNP	.											.	FMN1	174	.	0			c.G259T						PASS	.						73	72	72					15																	33359827		1927	4150	6077	SO:0001627	intron_variant	342184	exon1			GTGAAACCCGAGA	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.2044-2552G>T	15.37:g.33359827C>A		167	0	0		161	67	0.416149	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	37		.	.	.	.	.	.	.	.	.	.	C	1.806	-0.475955	0.04414	.	.	ENSG00000248905	ENST00000334528	T	0.39787	1.06	4.92	1.71	0.24356	.	.	.	.	.	T	0.28532	0.0706	.	.	.	.	.	.	B;B	0.06786	0.001;0.0	B;B	0.12156	0.007;0.003	T	0.28554	-1.0040	7	0.66056	D	0.02	.	4.1619	0.10287	0.1924:0.6092:0.0:0.1984	.	87;87	Q68DA7-3;Q68DA7-5	.;.	F	87	ENSP00000333950:V87F	ENSP00000333950:V87F	V	-	1	0	FMN1	31147119	0.000000	0.05858	0.009000	0.14445	0.019000	0.09904	-0.153000	0.10144	0.651000	0.30788	-0.137000	0.14449	GTT	.	.	none		0.483	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184		A	33359827	C	A	33359827	1	1	7	0	1	0	0	0	0	0	0	0	5957	507	18	4		4	FMN1	15	33359827	Intron	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	5587129	33359827	69171565	104	781											
MYO1E	4643	hgsc.bcm.edu	37	chr15	59506886	59506886	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taggacgccaatgttgtattCttcatggtctttctccatgg	7	16	9	9	1	4	0	1	0	3	0	5	1	4	1	2	3	0	2	2	3	3	6			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr15:59506886C>A	ENST00000288235.4	-	11	1540	c.1141G>T	c.(1141-1143)Gaa>Taa	p.E381*	AC092756.1_ENST00000401164.1_RNA|RNU4-80P_ENST00000363200.1_RNA	NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	381	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)		ATGTTGTATTCTTCATGGTCT	0.428																																					p.E381X		Atlas-SNP	.											.	MYO1E	99	.	0			c.G1141T						PASS	.						202	191	195					15																	59506886		2190	4290	6480	SO:0001587	stop_gained	4643	exon11			TGTATTCTTCATG	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.1141G>T	15.37:g.59506886C>A	ENSP00000288235:p.Glu381*	179	0	0		173	70	0.404624	NM_004998	Q14778	Nonsense_Mutation	SNP	ENST00000288235.4	37	CCDS32254.1	.	.	.	.	.	.	.	.	.	.	C	35	5.546839	0.96488	.	.	ENSG00000157483	ENST00000288235	.	.	.	5.14	5.14	0.70334	.	0.043917	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.17832	T	0.49	.	19.1568	0.93514	0.0:1.0:0.0:0.0	.	.	.	.	X	381	.	ENSP00000288235:E381X	E	-	1	0	MYO1E	57294178	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.651000	0.83577	2.832000	0.97577	0.655000	0.94253	GAA	.	.	none		0.428	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416024.1	NM_004998		A	59506886	C	A	59506886	4	1	7	1	0	0	0	0	0	1	0	0	10081	922	32	4	2257	4	MYO1E	15	59506886	Nonsense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	26147059	59506886	43024506	105	782											
TLN2	83660	hgsc.bcm.edu	37	chr15	63128104	63128104	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccccaggcccggatggtggcGgctgcgaccagcagtctctg	5	6	15	15	3	1	0	0	0	1	0	2	2	1	1	4	5	2	2	4	5	0	0	rs74020685		TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr15:63128104G>A	ENST00000561311.1	+	56	7436	c.7206G>A	c.(7204-7206)gcG>gcA	p.A2402A	TLN2_ENST00000306829.6_Silent_p.A2402A|RP11-1069G10.1_ENST00000558888.1_RNA|RP11-1069G10.1_ENST00000558404.1_RNA			Q9Y4G6	TLN2_HUMAN	talin 2	2402	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.				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						GGATGGTGGCGGCTGCGACCA	0.622																																					p.A2402A		Atlas-SNP	.											.	TLN2	253	.	0			c.G7206A						PASS	.						59	64	62					15																	63128104		2203	4300	6503	SO:0001819	synonymous_variant	83660	exon54			GGTGGCGGCTGCG	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.7206G>A	15.37:g.63128104G>A		86	0	0		91	35	0.384615	NM_015059	A6NLB8	Silent	SNP	ENST00000561311.1	37	CCDS32261.1																																																																																			G|0.999;C|0.001	.	alt		0.622	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			A	63128104	G	A	63128104	2	1	7	1	0	0	0	0	0	0	0	1	15963	1103	39	1		1	TLN2	15	63128104	Silent	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	3621218	63128104	39403288	106	783											
UACA	55075	hgsc.bcm.edu	37	chr15	71055671	71055671	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggaccgcgggactcaccgCgctggcggcggcggcgccag	4	2	18	17	9	1	0	1	0	0	0	1	2	1	2	4	6	0	1	4	6	0	0			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr15:71055671C>T	ENST00000322954.6	-	1	261	c.76G>A	c.(76-78)Gcg>Acg	p.A26T	UACA_ENST00000539319.1_Missense_Mutation_p.A26T	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	26	Poly-Ala.				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						GGACTCACCGCGCTGGCGGCG	0.731																																					p.A26T		Atlas-SNP	.											.	UACA	235	.	0			c.G76A						PASS	.						2	4	3					15																	71055671		1383	2742	4125	SO:0001583	missense	55075	exon1			TCACCGCGCTGGC	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.76G>A	15.37:g.71055671C>T	ENSP00000314556:p.Ala26Thr	114	0	0		111	52	0.468468	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Missense_Mutation	SNP	ENST00000322954.6	37	CCDS10235.1	.	.	.	.	.	.	.	.	.	.	C	10.96	1.497322	0.26861	.	.	ENSG00000137831	ENST00000322954;ENST00000539319	T;T	0.34472	1.36;1.77	4.82	1.71	0.24356	.	1.180030	0.06665	N	0.765191	T	0.12689	0.0308	N	0.02539	-0.55	0.23665	N	0.997162	B;B	0.24132	0.098;0.027	B;B	0.16289	0.015;0.003	T	0.28106	-1.0054	10	0.12103	T	0.63	-0.4557	3.4056	0.07340	0.1748:0.5599:0.1692:0.0961	.	26;26	F5H2B9;Q9BZF9	.;UACA_HUMAN	T	26	ENSP00000314556:A26T;ENSP00000438667:A26T	ENSP00000314556:A26T	A	-	1	0	UACA	68842725	0.910000	0.30920	1.000000	0.80357	0.946000	0.59487	-0.164000	0.09983	0.436000	0.26393	0.484000	0.47621	GCG	.	.	none		0.731	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			T	71055671	C	T	71055671	3	4	7	1	0	0	0	0	1	0	0	0	16839	768	27	1	4293	1	UACA	15	71055671	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	7927567	71055671	31475721	107	784											
CSK	1445	hgsc.bcm.edu	37	chr15	75094222	75094223	+	Frame_Shift_Del	DEL	GA	GA	-																															tggacagcccctgaggccctGagagagaaggtggggctggc																										TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr15:75094222_75094223delGA	ENST00000220003.9	+	11	1803_1804	c.1074_1075delGA	c.(1072-1077)ctgagafs	p.R359fs	CSK_ENST00000567571.1_Frame_Shift_Del_p.R359fs|CSK_ENST00000439220.2_Frame_Shift_Del_p.R359fs|CSK_ENST00000309470.9_Frame_Shift_Del_p.R359fs	NM_004383.2	NP_004374.1	P41240	CSK_HUMAN	c-src tyrosine kinase	359	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adherens junction organization (GO:0034332)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cellular response to peptide hormone stimulus (GO:0071375)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of bone resorption (GO:0045779)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of kinase activity (GO:0033673)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of phagocytosis (GO:0050765)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|positive regulation of MAP kinase activity (GO:0043406)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060368)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein C-terminus binding (GO:0008022)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|lung(2)	3						CTGAGGCCCTGAGAGAGAAGGT	0.644																																					p.358_358del		Pindel,Atlas-Indel	.											.	CSK	43	.	0			c.1073_1074del						PASS	.																																			SO:0001589	frameshift_variant	1445	exon12			.		CCDS10269.1	15q24.1	2013-02-14			ENSG00000103653	ENSG00000103653	2.7.10.1	"SH2 domain containing"	2444	protein-coding gene	gene with protein product		124095				1377109	Standard	NM_004383		Approved		uc010bka.3	P41240	OTTHUMG00000142814	ENST00000220003.9:c.1074_1075delGA	15.37:g.75094228_75094229delGA	ENSP00000220003:p.Arg359fs	65	0	.		61	17	0.279	NM_001127190	Q2M3N2|Q6FGZ6	Frame_Shift_Del	DEL	ENST00000220003.9	37	CCDS10269.1																																																																																			.	.	none		0.644	CSK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286398.2	NM_004383		-	75094223	GA	-	75094222	7	5	7	1	0	1	0	1	0	0	0	0	3945	1277	45	0	1112	0	CSK	15	75094222	Frame_Shift_Del	DEL	GA	TCGA-FA-A7Q1-01A-11D-A382-10	4038551	75094222	27437170	108	785											
CSPG4	1464	hgsc.bcm.edu	37	chr15	75980082	75980082	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtggcctggtgttgcccgtcGgacacctgcagctggatcca	5	9	14	13	2	0	0	0	0	0	0	2	2	1	2	4	4	3	3	4	4	0	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr15:75980082G>A	ENST00000308508.5	-	3	3416	c.3324C>T	c.(3322-3324)tcC>tcT	p.S1108S		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	1108	Gly/Ser-rich (glycosaminoglycan attachment domain).|Interaction with COL5A1. {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						GTTGCCCGTCGGACACCTGCA	0.662																																					p.S1108S		Atlas-SNP	.											.	CSPG4	175	.	0			c.C3324T						PASS	.						54	53	54					15																	75980082		2196	4290	6486	SO:0001819	synonymous_variant	1464	exon3			CCCGTCGGACACC	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.3324C>T	15.37:g.75980082G>A		55	0	0		48	21	0.4375	NM_001897	D3DW77|Q92675	Silent	SNP	ENST00000308508.5	37	CCDS10284.1																																																																																			.	.	none		0.662	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		A	75980082	G	A	75980082	2	1	7	1	0	0	0	0	0	0	0	1	3962	1103	39	1		1	CSPG4	15	75980082	Silent	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	885860	75980082	26551310	109	786											
TRAF7	84231	hgsc.bcm.edu	37	chr16	2226351	2226351	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctggctgtgtcccggggccGactcttctcaggggctgtgg	2	10	17	12	2	2	0	1	0	2	0	4	1	3	0	2	6	0	3	2	6	0	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr16:2226351G>A	ENST00000326181.6	+	20	2096	c.1964G>A	c.(1963-1965)cGa>cAa	p.R655Q		NM_032271.2	NP_115647.2	Q6Q0C0	TRAF7_HUMAN	TNF receptor-associated factor 7, E3 ubiquitin protein ligase	655					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						TCCCGGGGCCGACTCTTCTCA	0.642																																					p.R655Q		Atlas-SNP	.											.	TRAF7	158	.	0			c.G1964A						PASS	.						22	21	21					16																	2226351		2186	4297	6483	SO:0001583	missense	84231	exon20			GGGGCCGACTCTT	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.1964G>A	16.37:g.2226351G>A	ENSP00000318944:p.Arg655Gln	40	0	0		44	21	0.477273	NM_032271	Q9H073	Missense_Mutation	SNP	ENST00000326181.6	37	CCDS10461.1	.	.	.	.	.	.	.	.	.	.	G	18.65	3.670240	0.67814	.	.	ENSG00000131653	ENST00000326181	T	0.60299	0.2	5.45	4.43	0.53597	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	0.57858	0.2082	L	0.31476	0.935	0.80722	D	1	D	0.69078	0.997	P	0.55011	0.766	T	0.58103	-0.7695	10	0.42905	T	0.14	-32.9563	14.7786	0.69749	0.0:0.1449:0.8551:0.0	.	655	Q6Q0C0	TRAF7_HUMAN	Q	655	ENSP00000318944:R655Q	ENSP00000318944:R655Q	R	+	2	0	TRAF7	2166352	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	7.039000	0.76544	2.564000	0.86499	0.514000	0.50259	CGA	.	.	none		0.642	TRAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250762.1	NM_032271		A	2226351	G	A	2226351	3	1	7	1	0	0	0	0	1	0	0	0	16461	1058	37	1	2038	1	TRAF7	16	2226351	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10		2226351	88128402	110	787											
CREBBP	1387	hgsc.bcm.edu	37	chr16	3828721	3828721	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctgctgttggcagactcgtAcatgtccccttccactttct	5	14	7	15	1	1	1	0	0	1	1	4	1	3	1	4	1	2	4	4	1	1	4			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr16:3828721A>G	ENST00000262367.5	-	9	2730	c.1921T>C	c.(1921-1923)Tac>Cac	p.Y641H	CREBBP_ENST00000382070.3_Missense_Mutation_p.Y603H	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	641	KIX. {ECO:0000255|PROSITE- ProRule:PRU00311}.				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)		GCAGACTCGTACATGTCCCCT	0.512			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.Y641H		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.T1921C						PASS	.						214	185	195					16																	3828721		2197	4300	6497	SO:0001583	missense	1387	exon9			ACTCGTACATGTC	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.1921T>C	16.37:g.3828721A>G	ENSP00000262367:p.Tyr641His	116	0	0		120	49	0.408333	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	A	19.70	3.875661	0.72180	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	D;D	0.91843	-2.92;-2.87	5.01	5.01	0.66863	Coactivator CBP, KIX (4);	0.000000	0.64402	D	0.000003	D	0.96216	0.8766	M	0.85373	2.75	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96923	0.9675	10	0.87932	D	0	-11.1709	15.0035	0.71492	1.0:0.0:0.0:0.0	.	671;641	Q4LE28;Q92793	.;CBP_HUMAN	H	641;671;603	ENSP00000262367:Y641H;ENSP00000371502:Y603H	ENSP00000262367:Y641H	Y	-	1	0	CREBBP	3768722	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.206000	0.95056	1.999000	0.58509	0.460000	0.39030	TAC	.	.	none		0.512	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		G	3828721	A	G	3828721	3	3	7	1	0	0	0	0	1	0	0	0	3863	391	14	3	5499	3	CREBBP	16	3828721	Missense_Mutation	SNP	A	TCGA-FA-A7Q1-01A-11D-A382-10	1602370	3828721	86526032	111	788											
CIITA	4261	hgsc.bcm.edu	37	chr16	11001721	11001721	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaagcagaaggtgcttgcgaGgtacctgaagcggctgcagc	10	6	16	9	2	0	2	0	1	0	1	0	4	0	2	1	3	7	5	1	3	4	2			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr16:11001721G>A	ENST00000324288.8	+	11	2505	c.2372G>A	c.(2371-2373)aGg>aAg	p.R791K	CIITA_ENST00000537380.1_Intron|CIITA_ENST00000381835.5_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	791					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						GTGCTTGCGAGGTACCTGAAG	0.697			T	"FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"	"PMBL, Hodgkin Lymphona, "																																p.R791K		Atlas-SNP	.		Dom	yes		16	16p13	4261	"class II, major histocompatibility complex, transactivator"		L	.	CIITA	92	.	0			c.G2372A						PASS	.						23	30	28					16																	11001721		2182	4284	6466	SO:0001583	missense	4261	exon11			TTGCGAGGTACCT	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.2372G>A	16.37:g.11001721G>A	ENSP00000316328:p.Arg791Lys	24	0	0		42	22	0.52381	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Missense_Mutation	SNP	ENST00000324288.8	37	CCDS10544.1	.	.	.	.	.	.	.	.	.	.	G	0.138	-1.105447	0.01828	.	.	ENSG00000179583	ENST00000324288;ENST00000388910	T	0.72394	-0.65	5.0	-0.459	0.12179	.	0.293212	0.25613	N	0.029465	T	0.52948	0.1766	L	0.35723	1.085	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.001;0.0;0.002;0.002	T	0.34428	-0.9829	10	0.14656	T	0.56	.	9.8101	0.40817	0.5445:0.0:0.4555:0.0	.	791;791;743;791	A0N0N9;P33076;F2Z2G8;Q96KL4	.;C2TA_HUMAN;.;.	K	791;743	ENSP00000316328:R791K	ENSP00000316328:R791K	R	+	2	0	CIITA	10909222	0.087000	0.21565	0.029000	0.17559	0.002000	0.02628	0.791000	0.26915	-0.059000	0.13154	-0.812000	0.03155	AGG	.	.	none		0.697	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246		A	11001721	G	A	11001721	3	1	7	1	0	0	0	0	1	0	0	0	3430	1000	35	2	2414	2	CIITA	16	11001721	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	7173000	11001721	79353032	112	789											
SOCS1	8651	hgsc.bcm.edu	37	chr16	11348972	11348972	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cacgcggatgctcgtgggtcCcgaggccatcttcacgctaa	7	8	12	14	5	2	0	1	0	1	0	4	2	3	1	2	3	1	2	2	3	1	2			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr16:11348972C>A	ENST00000332029.2	-	2	514	c.364G>T	c.(364-366)Gga>Tga	p.G122*	RMI2_ENST00000572173.1_Intron	NM_003745.1	NP_003736.1	O15524	SOCS1_HUMAN	suppressor of cytokine signaling 1	122	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cellular response to amino acid stimulus (GO:0071230)|cytokine-mediated signaling pathway (GO:0019221)|fat cell differentiation (GO:0045444)|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 insulin receptor signaling pathway (GO:0046627)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of protein phosphorylation (GO:0001932)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)	insulin-like growth factor receptor binding (GO:0005159)|kinase inhibitor activity (GO:0019210)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)	p.R107_I126del(1)|p.Y64fs*1(1)|p.K118_P123>T(1)|p.0?(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(66)|lung(3)	71						CTCGTGGGTCCCGAGGCCATC	0.672			"F, O"		"Hodgkin Lymphoma, PMBL"																																p.G122X	Colon(177;456 3548 27231)	Atlas-SNP	.		Rec	yes		16	16p13.13	8651	suppressor of cytokine signaling 1		L	.	SOCS1	84	.	4	Whole gene deletion(1)|Complex - deletion inframe(1)|Deletion - In frame(1)|Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(4)	c.G364T						PASS	.						17	19	19					16																	11348972		2191	4297	6488	SO:0001587	stop_gained	8651	exon2			TGGGTCCCGAGGC	U88326	CCDS10546.1	16p13.13	2013-02-14			ENSG00000185338	ENSG00000185338		"Suppressors of cytokine signaling", "SH2 domain containing"	19383	protein-coding gene	gene with protein product		603597				7796808, 9266833	Standard	NM_003745		Approved	SOCS-1, SSI-1, JAB, TIP3, Cish1	uc002dar.1	O15524	OTTHUMG00000129792	ENST00000332029.2:c.364G>T	16.37:g.11348972C>A	ENSP00000329418:p.Gly122*	36	0	0		37	16	0.432432	NM_003745	O15097|Q9NSA7	Nonsense_Mutation	SNP	ENST00000332029.2	37	CCDS10546.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.989914	0.93106	.	.	ENSG00000185338	ENST00000332029	.	.	.	4.19	4.19	0.49359	.	0.172438	0.50627	D	0.000106	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	-21.9138	15.6933	0.77473	0.0:1.0:0.0:0.0	.	.	.	.	X	122	.	ENSP00000329418:G122X	G	-	1	0	SOCS1	11256473	0.999000	0.42202	1.000000	0.80357	0.485000	0.33311	2.783000	0.47766	2.176000	0.68965	0.561000	0.74099	GGA	.	.	none		0.672	SOCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252018.1			A	11348972	C	A	11348972	4	1	7	1	0	0	0	0	0	1	0	0	14928	632	22	4	275	4	SOCS1	16	11348972	Nonsense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	347251	11348972	79005781	113	790											
SOCS1	8651	hgsc.bcm.edu	37	chr16	11349096	11349096	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgcacgctcaggggcccccaGtagaatccgcaggcgtccag	8	5	13	15	3	1	1	1	0	0	1	3	1	3	1	4	3	1	4	4	3	2	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr16:11349096G>A	ENST00000332029.2	-	2	390	c.240C>T	c.(238-240)taC>taT	p.Y80Y	RMI2_ENST00000572173.1_Intron	NM_003745.1	NP_003736.1	O15524	SOCS1_HUMAN	suppressor of cytokine signaling 1	80	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cellular response to amino acid stimulus (GO:0071230)|cytokine-mediated signaling pathway (GO:0019221)|fat cell differentiation (GO:0045444)|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 insulin receptor signaling pathway (GO:0046627)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of protein phosphorylation (GO:0001932)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)	insulin-like growth factor receptor binding (GO:0005159)|kinase inhibitor activity (GO:0019210)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)	p.Y64fs*1(1)|p.Y80*(1)|p.0?(1)|p.D63_Q108del(1)|p.S71fs*29(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(66)|lung(3)	71						GGGGCCCCCAGTAGAATCCGC	0.726			"F, O"		"Hodgkin Lymphoma, PMBL"																																p.Y80Y	Colon(177;456 3548 27231)	Atlas-SNP	.		Rec	yes		16	16p13.13	8651	suppressor of cytokine signaling 1		L	SOCS1,lymph_node,lymphoid_neoplasm,0,1	SOCS1	84	1	5	Deletion - Frameshift(2)|Substitution - Nonsense(1)|Whole gene deletion(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(5)	c.C240T						PASS	.						3	4	4					16																	11349096		1833	3774	5607	SO:0001819	synonymous_variant	8651	exon2			CCCCCAGTAGAAT	U88326	CCDS10546.1	16p13.13	2013-02-14			ENSG00000185338	ENSG00000185338		"Suppressors of cytokine signaling", "SH2 domain containing"	19383	protein-coding gene	gene with protein product		603597				7796808, 9266833	Standard	NM_003745		Approved	SOCS-1, SSI-1, JAB, TIP3, Cish1	uc002dar.1	O15524	OTTHUMG00000129792	ENST00000332029.2:c.240C>T	16.37:g.11349096G>A		23	0	0		25	8	0.32	NM_003745	O15097|Q9NSA7	Silent	SNP	ENST00000332029.2	37	CCDS10546.1																																																																																			.	.	none		0.726	SOCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252018.1			A	11349096	G	A	11349096	2	1	7	1	0	0	0	0	0	0	0	1	14928	1024	36	2		2	SOCS1	16	11349096	Silent	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	124	11349096	79005657	114	791											
GP2	2813	hgsc.bcm.edu	37	chr16	20322559	20322559	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gagctctcagaacagccaagCcaggaggacagtcaggagga	14	3	14	10	0	2	1	2	0	1	1	3	6	2	5	2	4	4	1	2	4	2	0			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr16:20322559C>G	ENST00000381362.4	-	12	1676	c.1600G>C	c.(1600-1602)Gct>Cct	p.A534P	GP2_ENST00000302555.5_Missense_Mutation_p.A531P|GP2_ENST00000381360.5_Missense_Mutation_p.A387P|GP2_ENST00000341642.5_Missense_Mutation_p.A384P	NM_001007240.1|NM_001502.2	NP_001007241.2|NP_001493.2	P55259	GP2_HUMAN	glycoprotein 2 (zymogen granule membrane)	534					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						AACAGCCAAGCCAGGAGGACA	0.522																																					p.A534P		Atlas-SNP	.											GP2,colon,carcinoma,+1,1	GP2	122	1	0			c.G1600C						PASS	.						130	125	127					16																	20322559		2203	4300	6503	SO:0001583	missense	2813	exon12			GCCAAGCCAGGAG	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.1600G>C	16.37:g.20322559C>G	ENSP00000370767:p.Ala534Pro	109	0	0		126	69	0.547619	NM_001007240	A6NFM9|A6NJA8|Q13338|Q9UIF1	Missense_Mutation	SNP	ENST00000381362.4	37	CCDS42128.1	.	.	.	.	.	.	.	.	.	.	C	16.26	3.071751	0.55646	.	.	ENSG00000169347	ENST00000302555;ENST00000381362;ENST00000381360;ENST00000341642;ENST00000537520	D;D;D;D	0.91577	-2.87;-2.87;-1.65;-1.65	5.1	4.13	0.48395	.	.	.	.	.	D	0.92731	0.7689	L	0.59436	1.845	0.38652	D	0.951875	D;D;D;D	0.76494	0.996;0.999;0.999;0.998	D;D;D;P	0.66196	0.931;0.942;0.931;0.852	D	0.93047	0.6462	9	0.72032	D	0.01	-3.3065	10.0547	0.42237	0.0:0.9013:0.0:0.0987	.	384;512;531;534	P55259-4;B7Z1G2;P55259-3;P55259	.;.;.;GP2_HUMAN	P	531;534;387;384;512	ENSP00000304044:A531P;ENSP00000370767:A534P;ENSP00000370765:A387P;ENSP00000343861:A384P	ENSP00000304044:A531P	A	-	1	0	GP2	20230060	0.404000	0.25328	1.000000	0.80357	0.423000	0.31445	0.381000	0.20619	2.506000	0.84524	0.650000	0.86243	GCT	.	.	none		0.522	GP2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436920.1	NM_016295		G	20322559	C	G	20322559	3	3	7	1	0	0	0	0	1	0	0	0	6590	739	26	4	17	4	GP2	16	20322559	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	8973463	20322559	70032194	115	792											
TBC1D10B	26000	hgsc.bcm.edu	37	chr16	30380609	30380609	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtccgtcttgcgcagggccAgcccgtttatctctgaatct	5	13	10	13	3	3	1	0	1	3	0	5	1	4	1	3	1	2	2	3	1	2	3			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr16:30380609A>T	ENST00000409939.3	-	1	976	c.896T>A	c.(895-897)cTg>cAg	p.L299Q		NM_015527.3	NP_056342.3	Q4KMP7	TB10B_HUMAN	TBC1 domain family, member 10B	299					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)			GCGCAGGGCCAGCCCGTTTAT	0.607																																					p.L299Q		Atlas-SNP	.											.	TBC1D10B	32	.	0			c.T896A						PASS	.						42	29	33					16																	30380609		2196	4298	6494	SO:0001583	missense	26000	exon1			AGGGCCAGCCCGT	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.896T>A	16.37:g.30380609A>T	ENSP00000386538:p.Leu299Gln	51	0	0		58	18	0.310345	NM_015527	B9A6L0|Q6IN54|Q6P530|Q71RG7|Q86VC5|Q9H8Z2|Q9NUN6|Q9UFP2	Missense_Mutation	SNP	ENST00000409939.3	37	CCDS10676.2	.	.	.	.	.	.	.	.	.	.	A	16.03	3.007124	0.54361	.	.	ENSG00000169221	ENST00000409939	T	0.18960	2.18	4.1	4.1	0.47936	.	0.336532	0.23552	N	0.046944	T	0.17959	0.0431	L	0.43152	1.355	0.33877	D	0.635636	P	0.37731	0.607	B	0.34180	0.177	T	0.30937	-0.9961	10	0.46703	T	0.11	.	12.2043	0.54342	1.0:0.0:0.0:0.0	.	299	Q4KMP7	TB10B_HUMAN	Q	299	ENSP00000386538:L299Q	ENSP00000386538:L299Q	L	-	2	0	TBC1D10B	30288110	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.205000	0.51090	1.730000	0.51580	0.459000	0.35465	CTG	.	.	none		0.607	TBC1D10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255527.3	NM_015527		T	30380609	A	T	30380609	3	4	7	1	0	0	0	0	1	0	0	0	15614	188	7	5	1566	5	TBC1D10B	16	30380609	Missense_Mutation	SNP	A	TCGA-FA-A7Q1-01A-11D-A382-10	10058050	30380609	59974144	116	793											
ZNF688	146542	hgsc.bcm.edu	37	chr16	30583567	30583567	+	5'UTR	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtcctgaagcctctgttgaCagactggagcgcagcggaga	9	7	15	10	2	1	4	0	2	1	2	2	6	2	5	2	3	3	2	2	3	1	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr16:30583567C>A	ENST00000223459.6	-	0	488				ZNF688_ENST00000563707.1_5'Flank|ZNF688_ENST00000395219.1_Silent_p.L10L|AC002310.7_ENST00000486926.1_RNA|ZNF688_ENST00000567855.1_5'Flank|AC002310.7_ENST00000492040.1_RNA	NM_145271.3	NP_660314.1	P0C7X2	ZN688_HUMAN	zinc finger protein 688						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(2)|lung(2)|ovary(1)	8						CCTCTGTTGACAGACTGGAGC	0.637																																					p.L10L		Atlas-SNP	.											.	ZNF688	37	.	0			c.G30T						PASS	.						34	39	37					16																	30583567		1926	4119	6045	SO:0001623	5_prime_UTR_variant	146542	exon1			TGTTGACAGACTG	AK122680	CCDS10684.1	16p11.2	2013-01-08			ENSG00000229809	ENSG00000229809		"Zinc fingers, C2H2-type", "-"	30489	protein-coding gene	gene with protein product						10493829	Standard	XM_005255139		Approved		uc002dys.2	P0C7X2	OTTHUMG00000132408	ENST00000223459.6:c.-617G>T	16.37:g.30583567C>A		40	0	0		45	29	0.644444	NM_001024683	A8MV39|B3KV51|O75701|Q8IW91|Q8WV14|Q96MN0	Silent	SNP	ENST00000223459.6	37	CCDS10684.1																																																																																			.	.	none		0.637	ZNF688-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255544.2	NM_145271		A	30583567	C	A	30583567	1	1	7	0	1	0	0	0	0	0	0	0	18108	465	17	4		4	ZNF688	16	30583567	5'UTR	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	202958	30583567	59771186	117	794											
SALL1	6299	hgsc.bcm.edu	37	chr16	51175886	51175886	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggggctgggggagaaggtttCgggtggggaggctggatttt	5	10	23	3	1	0	1	0	0	0	1	1	4	0	3	0	10	0	3	0	10	1	3	rs376234367		TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr16:51175886C>T	ENST00000251020.4	-	2	280	c.247G>A	c.(247-249)Gaa>Aaa	p.E83K	SALL1_ENST00000440970.1_5'UTR|SALL1_ENST00000566102.1_Intron|SALL1_ENST00000562674.1_5'Flank|SALL1_ENST00000541611.1_Intron	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	83					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)	p.E83K(1)		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)			GAGAAGGTTTCGGGTGGGGAG	0.423																																					p.E83K	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											SALL1,face,carcinoma,0,2	SALL1	301	2	1	Substitution - Missense(1)	skin(1)	c.G247A						scavenged	.						78	87	84					16																	51175886		2198	4300	6498	SO:0001583	missense	6299	exon2			AGGTTTCGGGTGG	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.247G>A	16.37:g.51175886C>T	ENSP00000251020:p.Glu83Lys	101	1	0.00990099		170	95	0.558824	NM_002968	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	37	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	C	13.16	2.153321	0.38021	.	.	ENSG00000103449	ENST00000251020;ENST00000457559	T	0.08807	3.05	5.26	4.06	0.47325	.	0.301502	0.41396	N	0.000890	T	0.10637	0.0260	M	0.62723	1.935	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.05037	-1.0910	10	0.33940	T	0.23	.	11.2473	0.49004	0.0:0.8862:0.0:0.1138	.	83	Q9NSC2	SALL1_HUMAN	K	83	ENSP00000251020:E83K	ENSP00000251020:E83K	E	-	1	0	SALL1	49733387	1.000000	0.71417	0.253000	0.24343	0.946000	0.59487	6.065000	0.71176	0.867000	0.35654	0.555000	0.69702	GAA	.	.	weak		0.423	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		T	51175886	C	T	51175886	3	4	7	1	0	0	0	0	1	0	0	0	13825	893	31	1	3735	1	SALL1	16	51175886	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	20592319	51175886	39178867	118	795											
CHD9	80205	hgsc.bcm.edu	37	chr16	53256588	53256591	+	Frame_Shift_Del	DEL	AAAG	AAAG	-																															tacattgggtaagaaacaaaAaagaaagaatgagtcttcag																								rs538376255	byFrequency	TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	AAAG	AAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr16:53256588_53256591delAAAG	ENST00000398510.3	+	3	1904_1907	c.1817_1820delAAAG	c.(1816-1821)aaaagafs	p.KR606fs	CHD9_ENST00000447540.1_Frame_Shift_Del_p.KR606fs|CHD9_ENST00000564845.1_Frame_Shift_Del_p.KR606fs|CHD9_ENST00000566029.1_Frame_Shift_Del_p.KR606fs			Q3L8U1	CHD9_HUMAN	chromodomain helicase DNA binding protein 9	606	Lys-rich.				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)				AAGAAACAAAAAAGAAAGAATGAG	0.284																																					p.606_607del		Atlas-Indel	.											.	CHD9	203	.	0			c.1816_1819del						PASS	.																																			SO:0001589	frameshift_variant	80205	exon4			.	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.1817_1820delAAAG	16.37:g.53256592_53256595delAAAG	ENSP00000381522:p.Lys606fs	366	0	0		587	166	0.282794	NM_025134	B2RTU2|B9ZVQ0|O15025|Q1WF12|Q6DTK9|Q9H9V7|Q9UHM2	Frame_Shift_Del	DEL	ENST00000398510.3	37																																																																																				.	.	none		0.284	CHD9-020	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000422345.1	NM_025134		-	53256591	AAAG	-	53256588	7	5	7	1	0	1	0	1	0	0	0	0	3334	14	1	0	1827	0	CHD9	16	53256588	Frame_Shift_Del	DEL	AAAG	TCGA-FA-A7Q1-01A-11D-A382-10	2080702	53256588	37098165	119	796											
CDH11	1009	hgsc.bcm.edu	37	chr16	65016083	65016083	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggggctcatcagcatcttctActgagatcttgacggtcaca	9	11	10	11	1	6	2	3	2	3	1	6	3	6	2	0	3	2	2	0	3	1	3			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr16:65016083A>G	ENST00000268603.4	-	8	1736	c.1121T>C	c.(1120-1122)gTa>gCa	p.V374A	CDH11_ENST00000566827.1_Missense_Mutation_p.V248A|CDH11_ENST00000394156.3_Missense_Mutation_p.V374A	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	374	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)|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)		AGCATCTTCTACTGAGATCTT	0.522			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																											p.V374A		Atlas-SNP	.		Dom	yes		16	16q22.1	1009	"cadherin 11, type 2, OB-cadherin (osteoblast)"		M	CDH11,colon,carcinoma,0,1	CDH11	260	1	0			c.T1121C						scavenged	.						168	138	148					16																	65016083		2203	4300	6503	SO:0001583	missense	1009	exon8			TCTTCTACTGAGA	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.1121T>C	16.37:g.65016083A>G	ENSP00000268603:p.Val374Ala	179	1	0.00558659		240	82	0.341667	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Missense_Mutation	SNP	ENST00000268603.4	37	CCDS10803.1	.	.	.	.	.	.	.	.	.	.	A	19.17	3.775754	0.70107	.	.	ENSG00000140937	ENST00000268603;ENST00000394156;ENST00000538390	T;T	0.68181	-0.31;-0.31	5.76	5.76	0.90799	Cadherin (4);Cadherin-like (1);	0.053752	0.85682	D	0.000000	D	0.88217	0.6377	H	0.97564	4.03	0.58432	D	0.999999	D;D	0.61080	0.989;0.988	P;D	0.76071	0.826;0.987	D	0.92067	0.5661	10	0.72032	D	0.01	.	15.544	0.76081	1.0:0.0:0.0:0.0	.	374;374	P55287-2;P55287	.;CAD11_HUMAN	A	374;374;357	ENSP00000268603:V374A;ENSP00000377711:V374A	ENSP00000268603:V374A	V	-	2	0	CDH11	63573584	1.000000	0.71417	0.141000	0.22245	0.251000	0.25915	8.818000	0.91991	2.324000	0.78689	0.533000	0.62120	GTA	.	.	none		0.522	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664		G	65016083	A	G	65016083	3	3	7	1	0	0	0	0	1	0	0	0	3099	391	14	3	1293	3	CDH11	16	65016083	Missense_Mutation	SNP	A	TCGA-FA-A7Q1-01A-11D-A382-10	11759495	65016083	25338670	120	797											
COG4	197258	hgsc.bcm.edu	37	chr16	70515315	70515315	+	IGR	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagccgggcaaacttgtctcGgatggtccaggtggtcaccg	7	8	15	11	3	2	0	1	0	1	0	4	2	3	1	3	5	2	1	3	5	1	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr16:70515315G>A	ENST00000288078.6	+	0	4081				COG4_ENST00000323786.5_Nonsense_Mutation_p.R728*	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)				AACTTGTCTCGGATGGTCCAG	0.607																																					p.R728X		Atlas-SNP	.											.	COG4	64	.	0			c.C2182T						PASS	.						100	97	98					16																	70515315		2198	4300	6498	SO:0001628	intergenic_variant	25839	exon18			TGTCTCGGATGGT		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		16.37:g.70515315G>A		25	0	0		61	16	0.262295	NM_015386	Q5PSM3|Q5XKL6|Q6ZRA0|Q96MT9	Nonsense_Mutation	SNP	ENST00000288078.6	37	CCDS10891.2	.	.	.	.	.	.	.	.	.	.	G	22.1	4.237469	0.79800	.	.	ENSG00000103051	ENST00000323786;ENST00000338984;ENST00000526700;ENST00000539961	.	.	.	5.97	3.98	0.46160	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.3333	14.2419	0.65963	0.0:0.0:0.6083:0.3917	.	.	.	.	X	728;703;184;386	.	ENSP00000315775:R728X	R	-	1	2	COG4	69072816	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.403000	0.52615	0.827000	0.34685	0.655000	0.94253	CGA	.	.	none		0.607	FUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157291.2	NM_145059		A	70515315	G	A	70515315	1	1	7	0	1	0	0	0	0	0	0	0	3662	1124	39	1		1	COG4	16	70515315	IGR	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	5499232	70515315	19839438	121	798											
BANP	54971	hgsc.bcm.edu	37	chr16	88039849	88039849	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agcatcgggagcaacgtcacGctcatcaccctgaactcgga	11	6	10	14	4	3	1	3	1	0	0	5	3	3	3	1	2	4	3	1	2	2	0	rs372273341		TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr16:88039849G>A	ENST00000393207.1	+	6	830	c.609G>A	c.(607-609)acG>acA	p.T203T	BANP_ENST00000355163.5_Silent_p.T178T|BANP_ENST00000479780.2_Silent_p.T172T|BANP_ENST00000538234.1_Silent_p.T211T|BANP_ENST00000393208.2_Silent_p.T172T|BANP_ENST00000355022.4_Silent_p.T172T|BANP_ENST00000286122.7_Silent_p.T203T	NM_001173543.1	NP_001167014.1	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein	203	Interaction with CUX1 and HDAC1. {ECO:0000250}.				cell cycle (GO:0007049)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of protein catabolic process (GO:0042177)|protein localization to nucleus (GO:0034504)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.00551)		GCAACGTCACGCTCATCACCC	0.582																																					p.T211T		Atlas-SNP	.											.	BANP	67	.	0			c.G633A						PASS	.	G	,,,,,,	1,4395	2.1+/-5.4	0,1,2197	74	75	75		633,534,516,633,609,516,516	-4	1	16		75	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BANP	NM_001173539.1,NM_001173540.1,NM_001173541.1,NM_001173542.1,NM_001173543.1,NM_017869.3,NM_079837.2	,,,,,,	0,1,6497	AA,AG,GG		0.0,0.0227,0.0077	,,,,,,	211/506,178/498,172/467,211/509,203/520,172/470,172/492	88039849	1,12995	2198	4300	6498	SO:0001819	synonymous_variant	54971	exon6			CGTCACGCTCATC	AK094158	CCDS10966.2, CCDS42215.1, CCDS54052.1, CCDS54053.1, CCDS54054.1	16q24	2012-11-22			ENSG00000172530	ENSG00000172530		"BEN domain containing"	13450	protein-coding gene	gene with protein product	"BEN domain containing 1"	611564				10940556, 10950932	Standard	NM_017869		Approved	SMARBP1, SMAR1, FLJ20538, DKFZp761H172, FLJ10177, BEND1	uc010vow.2	Q8N9N5	OTTHUMG00000137678	ENST00000393207.1:c.609G>A	16.37:g.88039849G>A		70	0	0		78	48	0.615385	NM_001173542	A8MU25|A8MX25|B2RCF7|B4DNJ9|F5GZM0|Q96GJ7|Q9NWY1	Silent	SNP	ENST00000393207.1	37	CCDS54054.1																																																																																			.	.	weak		0.582	BANP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269166.1	NM_017869		A	88039849	G	A	88039849	2	1	7	1	0	0	0	0	0	0	0	1	1310	1074	38	1		1	BANP	16	88039849	Silent	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	17524534	88039849	2314904	122	799											
RTN4RL1	146760	hgsc.bcm.edu	37	chr17	1840012	1840012	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggcctgtttcccggcgccCgccttagagatctgattgcg	4	10	14	13	4	1	2	0	1	1	1	2	3	2	2	4	3	1	1	4	3	1	3			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr17:1840012C>T	ENST00000331238.6	-	2	1583	c.1104G>A	c.(1102-1104)gcG>gcA	p.A368A		NM_178568.2	NP_848663.1			reticulon 4 receptor-like 1											breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|prostate(2)|skin(1)	11						TCCCGGCGCCCGCCTTAGAGA	0.652																																					p.A368A	GBM(68;949 1139 14865 32798 38342)	Atlas-SNP	.											.	RTN4RL1	21	.	0			c.G1104A						PASS	.						27	32	30					17																	1840012		1892	4096	5988	SO:0001819	synonymous_variant	146760	exon2			GGCGCCCGCCTTA	AF532859	CCDS45569.1	17p13.3	2008-02-05				ENSG00000185924			21329	protein-coding gene	gene with protein product	"nogo-66 receptor homolog 2"	610461					Standard	NM_178568		Approved	NGRH2, NgR3, DKFZp547J144	uc002ftp.3	Q86UN2		ENST00000331238.6:c.1104G>A	17.37:g.1840012C>T		165	0	0		226	66	0.292035	NM_178568		Silent	SNP	ENST00000331238.6	37	CCDS45569.1																																																																																			.	.	none		0.652	RTN4RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450155.2	NM_178568		T	1840012	C	T	1840012	2	4	7	1	0	0	0	0	0	0	0	1	13746	639	23	1		1	RTN4RL1	17	1840012	Silent	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10		1840012	79355198	123	800											
DNAH9	1770	hgsc.bcm.edu	37	chr17	11520880	11520880	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggccacatgcaagtcctacCgctccccgggaaggctgact	8	6	12	15	2	0	1	0	1	0	0	2	2	2	2	5	3	2	3	5	3	3	1	rs377415601		TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr17:11520880C>T	ENST00000262442.4	+	5	1125	c.1057C>T	c.(1057-1059)Cgc>Tgc	p.R353C	DNAH9_ENST00000454412.2_Missense_Mutation_p.R353C	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	353	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)		CAAGTCCTACCGCTCCCCGGG	0.622																																					p.R353C		Atlas-SNP	.											.	DNAH9	695	.	0			c.C1057T						PASS	.						67	65	65					17																	11520880		2203	4300	6503	SO:0001583	missense	1770	exon5			TCCTACCGCTCCC	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.1057C>T	17.37:g.11520880C>T	ENSP00000262442:p.Arg353Cys	74	0	0		92	54	0.586957	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	C	12.57	1.978052	0.34942	.	.	ENSG00000007174	ENST00000262442;ENST00000454412	T;T	0.55413	0.52;0.52	5.91	2.42	0.29668	Dynein heavy chain, domain-1 (1);	0.416033	0.26010	N	0.026889	T	0.24699	0.0599	N	0.04018	-0.295	0.80722	D	1	B	0.11235	0.004	B	0.09377	0.004	T	0.03524	-1.1028	10	0.34782	T	0.22	.	5.084	0.14673	0.2294:0.5222:0.0:0.2484	.	353	Q9NYC9	DYH9_HUMAN	C	353	ENSP00000262442:R353C;ENSP00000414874:R353C	ENSP00000262442:R353C	R	+	1	0	DNAH9	11461605	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	1.847000	0.39299	0.839000	0.34971	0.655000	0.94253	CGC	.	.	alt		0.622	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11520880	C	T	11520880	3	4	7	1	0	0	0	0	1	0	0	0	4610	652	23	1	1075	1	DNAH9	17	11520880	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	9680868	11520880	69674330	124	801											
RHOT1	55288	hgsc.bcm.edu	37	chr17	30551748	30551748	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caaagcattattgaaacagcGatgatataaaaagaaatact	21	9	6	5	1	0	3	0	2	0	1	0	4	0	3	0	0	4	1	0	0	9	5			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr17:30551748G>A	ENST00000333942.6	+	19	2092	c.1853G>A	c.(1852-1854)cGa>cAa	p.R618Q	RHOT1_ENST00000394692.2_Missense_Mutation_p.R650Q|RHOT1_ENST00000583994.1_Missense_Mutation_p.R523Q|RHOT1_ENST00000354266.3_Missense_Mutation_p.R597Q|RHOT1_ENST00000545287.2_Missense_Mutation_p.R659Q|RHOT1_ENST00000358365.3_Missense_Mutation_p.R691Q	NM_018307.3	NP_060777.3	Q8IXI2	MIRO1_HUMAN	ras homolog family member T1	618					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)				TTGAAACAGCGATGATATAAA	0.353																																					p.R691Q		Atlas-SNP	.											RHOT1,NS,lymphoid_neoplasm,+1,1	RHOT1	69	1	0			c.G2072A						PASS	.						129	118	122					17																	30551748		2203	4300	6503	SO:0001583	missense	55288	exon21			AACAGCGATGATA	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.1853G>A	17.37:g.30551748G>A	ENSP00000334724:p.Arg618Gln	66	0	0		96	50	0.520833	NM_001033568	A4FVB6|A6NFV0|B4DG48|J9JIH9|Q6NUR3|Q6P9F8|Q6PJG1|Q6YMW8|Q86UB0|Q8IW28|Q8IXJ7|Q9H067|Q9H9N8|Q9NUZ2	Missense_Mutation	SNP	ENST00000333942.6	37	CCDS32612.1	.	.	.	.	.	.	.	.	.	.	G	14.69	2.610185	0.46527	.	.	ENSG00000126858	ENST00000358365;ENST00000354266;ENST00000394692;ENST00000333942	T;T;T	0.78126	-1.15;-1.1;-0.92	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	D	0.85133	0.5627	L	0.44542	1.39	0.80722	D	1	P;P;D	0.76494	0.895;0.809;0.999	B;B;D	0.77557	0.358;0.082;0.99	T	0.83297	-0.0030	10	0.44086	T	0.13	.	20.4387	0.99107	0.0:0.0:1.0:0.0	.	650;618;691	Q8IXI2-2;Q8IXI2;Q8IXI2-3	.;MIRO1_HUMAN;.	Q	691;659;650;618	ENSP00000351132:R691Q;ENSP00000378184:R650Q;ENSP00000334724:R618Q	ENSP00000334724:R618Q	R	+	2	0	RHOT1	27575861	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	9.476000	0.97823	2.836000	0.97738	0.655000	0.94253	CGA	.	.	none		0.353	RHOT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000447097.1	NM_018307		A	30551748	G	A	30551748	3	1	7	1	0	0	0	0	1	0	0	0	13358	1058	37	1	2154	1	RHOT1	17	30551748	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	19030868	30551748	50643462	125	802											
MLLT6	4302	hgsc.bcm.edu	37	chr17	36865739	36865739	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccttctctggttagtgccCaaatggcaggcttgctgtgt	5	14	12	10	0	1	0	0	0	1	0	2	0	1	0	2	3	3	4	2	3	2	3			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr17:36865739C>T	ENST00000325718.7	+	6	554	c.463C>T	c.(463-465)Caa>Taa	p.Q155*	MLLT6_ENST00000378137.5_Nonsense_Mutation_p.Q155*	NM_005937.3	NP_005928	P55198	AF17_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6	155					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)					GGTTAGTGCCCAAATGGCAGG	0.572			T	MLL	AL																																p.Q155X		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.C463T						PASS	.						110	85	94					17																	36865739		2203	4300	6503	SO:0001587	stop_gained	4302	exon6			AGTGCCCAAATGG		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.463C>T	17.37:g.36865739C>T	ENSP00000316426:p.Gln155*	48	0	0		78	22	0.282051	NM_005937	Q59F28|Q96IU3|Q9H5F6|Q9UF49	Nonsense_Mutation	SNP	ENST00000325718.7	37	CCDS11327.1	.	.	.	.	.	.	.	.	.	.	C	37	6.433454	0.97564	.	.	ENSG00000108292	ENST00000325718;ENST00000378137	.	.	.	4.35	4.35	0.52113	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	15.9677	0.79987	0.0:1.0:0.0:0.0	.	.	.	.	X	155	.	ENSP00000316426:Q155X	Q	+	1	0	MLLT6	34119265	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	7.347000	0.79356	2.404000	0.81709	0.591000	0.81541	CAA	.	.	none		0.572	MLLT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256799.1	NM_005937		T	36865739	C	T	36865739	4	4	7	1	0	0	0	0	0	1	0	0	9639	595	21	2	485	2	MLLT6	17	36865739	Nonsense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	6313991	36865739	44329471	126	803											
IKZF3	22806	hgsc.bcm.edu	37	chr17	37944556	37944556	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	aagaaatgtacggcagcgctCcttgtgctcctcaagggaac	11	8	11	11	2	1	1	1	0	0	1	3	2	3	2	2	2	4	4	2	2	5	2			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr17:37944556C>T	ENST00000346872.3	-	6	725	c.664G>A	c.(664-666)Gag>Aag	p.E222K	IKZF3_ENST00000439016.2_Intron|IKZF3_ENST00000535189.1_Missense_Mutation_p.E188K|IKZF3_ENST00000439167.2_Intron|IKZF3_ENST00000377952.2_Intron|IKZF3_ENST00000394189.2_Intron|IKZF3_ENST00000350532.3_Missense_Mutation_p.E222K|IKZF3_ENST00000346243.3_Intron|IKZF3_ENST00000467757.1_Missense_Mutation_p.E166K|IKZF3_ENST00000351680.3_Intron|IKZF3_ENST00000377945.3_Intron|IKZF3_ENST00000377944.3_Missense_Mutation_p.E79K|IKZF3_ENST00000377958.2_Missense_Mutation_p.E135K	NM_012481.4	NP_036613.2	Q9UKT9	IKZF3_HUMAN	IKAROS family zinc finger 3 (Aiolos)	222					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)			CGGCAGCGCTCCTTGTGCTCC	0.498																																					p.E222K		Atlas-SNP	.											.	IKZF3	79	.	0			c.G664A						PASS	.						146	114	125					17																	37944556		2203	4300	6503	SO:0001583	missense	22806	exon6			AGCGCTCCTTGTG	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.664G>A	17.37:g.37944556C>T	ENSP00000344544:p.Glu222Lys	88	0	0		145	88	0.606897	NM_012481	B4DVV5|Q69BL6|Q69BL7|Q69BL8|Q69BL9|Q69BM0|Q69BM1|Q69BM2|Q69BM3|Q69BM5|Q8N574|Q8WWQ9|Q8WWR0|Q8WWR1|Q8WWR2|Q8WWR3	Missense_Mutation	SNP	ENST00000346872.3	37	CCDS11346.1	.	.	.	.	.	.	.	.	.	.	C	37	6.027248	0.97216	.	.	ENSG00000161405	ENST00000488188;ENST00000377944;ENST00000377958;ENST00000535189;ENST00000350532;ENST00000467757	T;T;T;T;T	0.44482	0.92;3.65;3.65;3.43;4.18	6.04	6.04	0.98038	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.56097	D	0.000039	T	0.67933	0.2946	M	0.83012	2.62	0.80722	D	1	D;P;D;D;D;D	0.76494	0.972;0.669;0.998;0.979;0.999;0.997	P;B;D;P;D;D	0.76071	0.737;0.205;0.967;0.907;0.987;0.938	T	0.61667	-0.7016	10	0.20046	T	0.44	-17.2071	20.1899	0.98228	0.0:1.0:0.0:0.0	.	135;79;188;222;166;222	Q9UKT9-9;Q9UKT9-10;Q9UKT9-7;Q9UKT9-4;Q9UKT9-2;Q9UKT9	.;.;.;.;.;IKZF3_HUMAN	K	222;79;135;188;222;166	ENSP00000367179:E79K;ENSP00000367194:E135K;ENSP00000438972:E188K;ENSP00000344471:E222K;ENSP00000420463:E166K	ENSP00000344471:E222K	E	-	1	0	IKZF3	35198082	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.818000	0.86416	2.873000	0.98535	0.563000	0.77884	GAG	.	.	none		0.498	IKZF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257004.2	NM_012481		T	37944556	C	T	37944556	3	4	7	1	0	0	0	0	1	0	0	0	7625	864	30	2	877	2	IKZF3	17	37944556	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	1078817	37944556	43250654	127	804											
TBX4	9496	hgsc.bcm.edu	37	chr17	59560607	59560607	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accatgatgccgcggctgccCaccctctccgctcagagctc	6	7	9	19	3	2	2	1	1	1	1	4	2	2	2	5	1	3	3	5	1	0	0			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr17:59560607C>T	ENST00000240335.1	+	8	1413	c.1368C>T	c.(1366-1368)ccC>ccT	p.P456P	TBX4_ENST00000393853.4_Silent_p.P457P|TBX4_ENST00000589449.1_3'UTR	NM_018488.2	NP_060958.2	P57082	TBX4_HUMAN	T-box 4	456					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						CGCGGCTGCCCACCCTCTCCG	0.632																																					p.P456P		Atlas-SNP	.											.	TBX4	69	.	0			c.C1368T						PASS	.						81	76	78					17																	59560607		2203	4300	6503	SO:0001819	synonymous_variant	9496	exon8			GCTGCCCACCCTC	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.1368C>T	17.37:g.59560607C>T		57	0	0		75	25	0.333333	NM_018488	A5PKU7|B2RMT1|B7ZLV3	Silent	SNP	ENST00000240335.1	37	CCDS11629.1																																																																																			.	.	none		0.632	TBX4-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449649.1	NM_018488		T	59560607	C	T	59560607	2	4	7	1	0	0	0	0	0	0	0	1	15675	581	21	2		2	TBX4	17	59560607	Silent	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	21616051	59560607	21634603	128	805											
SGSH	6448	hgsc.bcm.edu	37	chr17	78184539	78184539	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggttcaggaggtcctggaaGgtgggtgagacgtagaagtc	9	8	18	6	2	1	2	1	1	0	2	3	5	2	4	1	6	0	2	1	6	3	2			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr17:78184539G>A	ENST00000326317.6	-	8	1307	c.1221C>T	c.(1219-1221)acC>acT	p.T407T	SGSH_ENST00000534910.1_Silent_p.T204T	NM_000199.3	NP_000190.1	P51688	SPHM_HUMAN	N-sulfoglucosamine sulfohydrolase	407					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)			GGTCCTGGAAGGTGGGTGAGA	0.617																																					p.T407T		Atlas-SNP	.											.	SGSH	27	.	0			c.C1221T						PASS	.						181	164	170					17																	78184539		2203	4300	6503	SO:0001819	synonymous_variant	6448	exon8			CTGGAAGGTGGGT	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.1221C>T	17.37:g.78184539G>A		139	0	0		147	85	0.578231	NM_000199	A8K5E2	Silent	SNP	ENST00000326317.6	37	CCDS11770.1																																																																																			.	.	none		0.617	SGSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437695.1	NM_000199		A	78184539	G	A	78184539	2	1	7	1	0	0	0	0	0	0	0	1	14236	987	35	2		2	SGSH	17	78184539	Silent	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	18623932	78184539	3010671	129	806											
KLHL14	57565	hgsc.bcm.edu	37	chr18	30350456	30350456	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgggccgtcagggtcacgtcGcaaaacagctgcttcctcca	8	8	11	14	3	2	0	2	0	0	0	5	0	4	0	3	2	3	3	3	2	2	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr18:30350456G>C	ENST00000359358.4	-	2	537	c.99C>G	c.(97-99)tgC>tgG	p.C33W	AC012123.1_ENST00000426194.1_Intron|KLHL14_ENST00000358095.4_Missense_Mutation_p.C33W	NM_020805.1	NP_065856.1	Q9P2G3	KLH14_HUMAN	kelch-like family member 14	33	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						GGGTCACGTCGCAAAACAGCT	0.642																																					p.C33W		Atlas-SNP	.											.	KLHL14	92	.	0			c.C99G						PASS	.						73	52	59					18																	30350456		2203	4300	6503	SO:0001583	missense	57565	exon2			CACGTCGCAAAAC	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.99C>G	18.37:g.30350456G>C	ENSP00000352314:p.Cys33Trp	32	0	0		53	18	0.339623	NM_020805	A6NNW1|B4DHA0|Q8WU41	Missense_Mutation	SNP	ENST00000359358.4	37	CCDS32813.1	.	.	.	.	.	.	.	.	.	.	G	5.357	0.251139	0.10130	.	.	ENSG00000197705	ENST00000359358;ENST00000358095	T;T	0.72167	-0.63;-0.63	4.29	4.29	0.51040	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.233665	0.46442	D	0.000298	T	0.81851	0.4910	M	0.78285	2.405	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	D	0.83402	0.0023	10	0.87932	D	0	.	9.3029	0.37856	0.1005:0.0:0.8995:0.0	.	33	Q9P2G3	KLH14_HUMAN	W	33	ENSP00000352314:C33W;ENSP00000350808:C33W	ENSP00000350808:C33W	C	-	3	2	KLHL14	28604454	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.623000	0.54224	2.223000	0.72356	0.460000	0.39030	TGC	.	.	none		0.642	KLHL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448376.1			C	30350456	G	C	30350456	3	2	7	1	0	0	0	0	1	0	0	0	8379	1079	38	4	1819	4	KLHL14	18	30350456	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10		30350456	47726792	130	807											
C19orf6	91304	hgsc.bcm.edu	37	chr19	1014261	1014261	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	catcttccatgtccaggttgCtgcctggttccacggccagg	5	11	11	14	1	1	0	0	0	1	0	4	0	4	0	5	4	2	3	5	4	0	3			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr19:1014261C>T	ENST00000356663.3	-	2	558	c.437G>A	c.(436-438)aGc>aAc	p.S146N	TMEM259_ENST00000333175.5_Missense_Mutation_p.S146N	NM_001033026.1	NP_001028198.1	Q4ZIN3	MBRL_HUMAN	transmembrane protein 259	146						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)											GTCCAGGTTGCTGCCTGGTTC	0.637																																					p.S146N		Atlas-SNP	.											C19orf6,NS,carcinoma,+1,1	.	.	1	0			c.G437A						scavenged	.						66	61	63					19																	1014261		2202	4300	6502	SO:0001583	missense	91304	exon2			AGGTTGCTGCCTG	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.437G>A	19.37:g.1014261C>T	ENSP00000349087:p.Ser146Asn	142	1	0.00704225		79	10	0.126582	NM_033420	O60392|Q8NF79|Q96H30	Missense_Mutation	SNP	ENST00000356663.3	37	CCDS32862.1	.	.	.	.	.	.	.	.	.	.	C	6.114	0.389285	0.11581	.	.	ENSG00000182087	ENST00000356663;ENST00000333175	.	.	.	4.06	1.86	0.25419	.	0.774128	0.11482	N	0.559656	T	0.28732	0.0712	L	0.38175	1.15	0.09310	N	1	B;B	0.25105	0.118;0.002	B;B	0.26517	0.07;0.001	T	0.19943	-1.0290	9	0.29301	T	0.29	-5.843	4.2325	0.10610	0.0:0.5855:0.1928:0.2218	.	146;146	Q4ZIN3-2;Q4ZIN3	.;MBRL_HUMAN	N	146	.	ENSP00000331423:S146N	S	-	2	0	C19orf6	965261	0.002000	0.14202	0.006000	0.13384	0.060000	0.15804	0.209000	0.17435	0.930000	0.37217	0.462000	0.41574	AGC	.	.	none		0.637	TMEM259-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458236.1	NM_033420		T	1014261	C	T	1014261	3	4	7	1	0	0	0	0	1	0	0	0	1943	797	28	2	1465	2	C19orf6	19	1014261	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10		1014261	58114722	131	808											
S1PR2	9294	hgsc.bcm.edu	37	chr19	10335123	10335123	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	agcgagatgagccacgaggcCccgatgagcagaagcatgcg	12	3	15	11	4	0	4	0	2	0	2	0	7	0	4	3	1	5	2	3	1	1	0			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr19:10335123C>T	ENST00000590320.1	-	2	569	c.459G>A	c.(457-459)ggG>ggA	p.G153G	CTD-2369P2.2_ENST00000317726.4_lincRNA	NM_004230.3	NP_004221.3	O95136	S1PR2_HUMAN	sphingosine-1-phosphate receptor 2	153					activation of MAPK activity (GO:0000187)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|positive regulation of cell proliferation (GO:0008284)|positive regulation of establishment of endothelial barrier (GO:1903142)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|G-protein coupled receptor binding (GO:0001664)|integrin binding (GO:0005178)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15						GCCACGAGGCCCCGATGAGCA	0.637																																					p.G153G	Pancreas(194;229 3020 15179 45747)	Atlas-SNP	.											.	S1PR2	36	.	0			c.G459A						PASS	.						61	57	58					19																	10335123		2203	4300	6503	SO:0001819	synonymous_variant	9294	exon2			CGAGGCCCCGATG	AF034780	CCDS12229.1	19q13	2013-03-13	2008-04-30	2008-04-30	ENSG00000267534	ENSG00000267534		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"	3169	protein-coding gene	gene with protein product		605111	"endothelial differentiation, sphingolipid G-protein-coupled receptor, 5"	EDG5		8087418, 8878560	Standard	NM_004230		Approved	Gpcr13, H218, AGR16	uc002mnl.2	O95136	OTTHUMG00000180399	ENST00000590320.1:c.459G>A	19.37:g.10335123C>T		35	0	0		33	26	0.787879	NM_004230	Q86UN8	Silent	SNP	ENST00000590320.1	37	CCDS12229.1																																																																																			.	.	none		0.637	S1PR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451194.1	NM_004230		T	10335123	C	T	10335123	2	4	7	1	0	0	0	0	0	0	0	1	13809	610	22	2		2	S1PR2	19	10335123	Silent	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	9320862	10335123	48793860	132	809											
DOCK6	57572	hgsc.bcm.edu	37	chr19	11363469	11363469	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctgaacccactcatccttggGgatcccgggctccgtggtcc	5	9	11	16	2	1	1	1	1	0	0	5	2	5	2	5	4	1	1	5	4	1	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr19:11363469G>A	ENST00000294618.7	-	3	309	c.298C>T	c.(298-300)Ccc>Tcc	p.P100S		NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	100					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						TCATCCTTGGGGATCCCGGGC	0.642																																					p.P100S		Atlas-SNP	.											.	DOCK6	104	.	0			c.C298T						PASS	.						23	26	25					19																	11363469		1960	4143	6103	SO:0001583	missense	57572	exon3			CCTTGGGGATCCC		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.298C>T	19.37:g.11363469G>A	ENSP00000294618:p.Pro100Ser	84	0	0		57	6	0.105263	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Missense_Mutation	SNP	ENST00000294618.7	37	CCDS45975.1	.	.	.	.	.	.	.	.	.	.	G	18.97	3.735441	0.69189	.	.	ENSG00000130158	ENST00000294618	T	0.79454	-1.27	4.59	4.59	0.56863	.	0.074083	0.56097	D	0.000034	D	0.88470	0.6445	M	0.85630	2.765	0.80722	D	1	D	0.67145	0.996	D	0.68039	0.955	D	0.90811	0.4701	10	0.87932	D	0	-22.0449	16.174	0.81840	0.0:0.0:1.0:0.0	.	100	Q96HP0	DOCK6_HUMAN	S	100	ENSP00000294618:P100S	ENSP00000294618:P100S	P	-	1	0	DOCK6	11224469	1.000000	0.71417	0.743000	0.31040	0.394000	0.30568	8.562000	0.90719	2.100000	0.63781	0.561000	0.74099	CCC	.	.	none		0.642	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812		A	11363469	G	A	11363469	3	1	7	1	0	0	0	0	1	0	0	0	4693	1232	43	2	6029	2	DOCK6	19	11363469	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	1028346	11363469	47765514	133	810											
CYP4F3	4051	hgsc.bcm.edu	37	chr19	15760884	15760884	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacgacttcacagatgccgTcatccaggagcggcgccgca	9	5	12	15	5	2	1	2	0	0	1	3	3	3	2	3	2	2	2	3	2	0	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr19:15760884T>C	ENST00000221307.8	+	7	856	c.809T>C	c.(808-810)gTc>gCc	p.V270A	CYP4F3_ENST00000585846.1_Missense_Mutation_p.V270A|CYP4F3_ENST00000591058.1_Missense_Mutation_p.V270A|CYP4F3_ENST00000586182.2_Missense_Mutation_p.V270A	NM_000896.2	NP_000887.2	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 3	270			V -> I (in dbSNP:rs28371536). {ECO:0000269|Ref.5}.		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						ACAGATGCCGTCATCCAGGAG	0.567																																					p.V270A		Atlas-SNP	.											.	CYP4F3	69	.	0			c.T809C						PASS	.						110	101	104					19																	15760884		2203	4300	6503	SO:0001583	missense	4051	exon7			ATGCCGTCATCCA	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.809T>C	19.37:g.15760884T>C	ENSP00000221307:p.Val270Ala	125	0	0		100	34	0.34	NM_001199209	B7Z8Z3|O60634|Q5U740	Missense_Mutation	SNP	ENST00000221307.8	37	CCDS12332.1	.	.	.	.	.	.	.	.	.	.	.	12.84	2.059024	0.36373	.	.	ENSG00000186529	ENST00000538865;ENST00000221307	T	0.69561	-0.41	3.99	2.93	0.34026	.	0.182612	0.34802	N	0.003680	T	0.73297	0.3569	M	0.83603	2.65	0.42809	D	0.993958	B;B	0.20780	0.027;0.048	B;B	0.41202	0.35;0.35	T	0.71076	-0.4697	10	0.87932	D	0	.	6.846	0.23988	0.0:0.1253:0.0:0.8747	.	270;270	B7Z8Z3;Q08477	.;CP4F3_HUMAN	A	197;270	ENSP00000221307:V270A	ENSP00000221307:V270A	V	+	2	0	CYP4F3	15621884	1.000000	0.71417	0.697000	0.30258	0.576000	0.36127	3.349000	0.52217	0.432000	0.26286	0.260000	0.18958	GTC	.	.	none		0.567	CYP4F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460819.3	NM_000896		C	15760884	T	C	15760884	3	2	7	1	0	0	0	0	1	0	0	0	4192	1667	58	3	831	3	CYP4F3	19	15760884	Missense_Mutation	SNP	T	TCGA-FA-A7Q1-01A-11D-A382-10	4397415	15760884	43368099	134	811											
OR10H3	26532	hgsc.bcm.edu	37	chr19	15852443	15852443	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcactgttgccatcacccctCgcatgctggctgatctgctc	5	12	8	16	1	3	1	2	1	1	0	5	1	3	1	3	1	3	5	3	1	0	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr19:15852443C>T	ENST00000305892.1	+	1	241	c.241C>T	c.(241-243)Cgc>Tgc	p.R81C		NM_013938.1	NP_039226.1	O60404	O10H3_HUMAN	olfactory receptor, family 10, subfamily H, member 3	81						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)|kidney(2)|large_intestine(1)|liver(1)|lung(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	17						CATCACCCCTCGCATGCTGGC	0.507																																					p.R81C		Atlas-SNP	.											OR10H3,colon,carcinoma,0,2	OR10H3	53	2	0			c.C241T						scavenged	.						537	454	482					19																	15852443		2203	4300	6503	SO:0001583	missense	26532	exon1			ACCCCTCGCATGC		CCDS12334.1	19p13.1	2012-08-09				ENSG00000171936		"GPCR / Class A : Olfactory receptors"	8174	protein-coding gene	gene with protein product							Standard	NM_013938		Approved		uc010xoq.2	O60404		ENST00000305892.1:c.241C>T	19.37:g.15852443C>T	ENSP00000307130:p.Arg81Cys	226	2	0.00884956		231	99	0.428571	NM_013938	Q2HIZ3|Q6IFQ0	Missense_Mutation	SNP	ENST00000305892.1	37	CCDS12334.1	.	.	.	.	.	.	.	.	.	.	.	2.565	-0.301047	0.05495	.	.	ENSG00000171936	ENST00000305892	T	0.80033	-1.33	2.35	1.1	0.20463	GPCR, rhodopsin-like superfamily (1);	0.823482	0.09938	U	0.736331	T	0.79358	0.4432	M	0.83603	2.65	0.09310	N	1	B	0.18968	0.032	B	0.18263	0.021	T	0.72207	-0.4360	10	0.72032	D	0.01	.	6.0982	0.20033	0.4683:0.5317:0.0:0.0	.	81	O60404	O10H3_HUMAN	C	81	ENSP00000307130:R81C	ENSP00000307130:R81C	R	+	1	0	OR10H3	15713443	0.000000	0.05858	0.416000	0.26546	0.147000	0.21601	-0.100000	0.10990	1.320000	0.45209	0.185000	0.17295	CGC	.	.	none		0.507	OR10H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460918.1			T	15852443	C	T	15852443	3	4	7	1	0	0	0	0	1	0	0	0	10916	884	31	1	243	1	OR10H3	19	15852443	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	91559	15852443	43276540	135	812											
KLF2	10365	hgsc.bcm.edu	37	chr19	16437842	16437842	+	Nonstop_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacatgaaacggcacatgtaGccgggacgcccccgcccacc	10	3	10	18	4	0	1	0	1	0	0	0	2	0	2	5	2	2	2	5	2	2	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr19:16437842G>C	ENST00000248071.5	+	3	1175	c.1068G>C	c.(1066-1068)taG>taC	p.*356Y	KLF2_ENST00000592003.1_3'UTR|CTD-2562J15.6_ENST00000588799.1_RNA	NM_016270.2	NP_057354.1	Q9Y5W3	KLF2_HUMAN	Kruppel-like factor 2	0					cell morphogenesis (GO:0000902)|cellular response to cycloheximide (GO:0071409)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to peptide (GO:1901653)|cellular response to tumor necrosis factor (GO:0071356)|erythrocyte maturation (GO:0043249)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of interleukin-6 production (GO:0032715)|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 gene expression, epigenetic (GO:0040029)|transcription, DNA-templated (GO:0006351)|Type I pneumocyte differentiation (GO:0060509)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			haematopoietic_and_lymphoid_tissue(3)|lung(1)|skin(1)	5						GGCACATGTAGCCGGGAcgcc	0.672																																					p.X356Y		Atlas-SNP	.											.	KLF2	10	.	0			c.G1068C						PASS	.						25	18	20					19																	16437842		2198	4292	6490	SO:0001578	stop_lost	10365	exon3			CATGTAGCCGGGA	AF123344	CCDS12343.1	19p13.11	2013-10-15	2013-10-15		ENSG00000127528	ENSG00000127528		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	6347	protein-coding gene	gene with protein product		602016	"Kruppel-like factor 2 (lung)"			10217429, 10458913	Standard	NM_016270		Approved	LKLF	uc002ndw.3	Q9Y5W3	OTTHUMG00000182330	ENST00000248071.5:c.1068G>C	19.37:g.16437842G>C	ENSP00000248071:p.*356Tyrext*62	52	0	0		38	17	0.447368	NM_016270	Q6IPC4|Q9UJS5|Q9UKR6	Missense_Mutation	SNP	ENST00000248071.5	37	CCDS12343.1	.	.	.	.	.	.	.	.	.	.	G	3.162	-0.171913	0.06421	.	.	ENSG00000127528	ENST00000248071	.	.	.	4.44	-0.542	0.11854	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.6784	0.05086	0.1736:0.1445:0.5337:0.1483	.	.	.	.	Y	356	.	.	X	+	3	2	KLF2	16298842	1.000000	0.71417	0.980000	0.43619	0.096000	0.18686	4.184000	0.58323	0.068000	0.16574	0.313000	0.20887	TAG	.	.	none		0.672	KLF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460562.1			C	16437842	G	C	16437842	4	2	7	1	0	0	0	0	0	0	0	0	8355	966	34	4	1078	4	KLF2	19	16437842	Nonstop_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	585399	16437842	42691141	136	813											
HAUS8	93323	hgsc.bcm.edu	37	chr19	17166719	17166719	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtggatggacctcacgggcaGctcgtgcctggtagtgtcca	6	9	15	11	2	1	0	1	0	0	0	3	2	2	2	3	4	2	3	3	4	1	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr19:17166719G>A	ENST00000253669.5	-	9	929	c.739C>T	c.(739-741)Ctg>Ttg	p.L247L	HAUS8_ENST00000448593.2_Silent_p.L246L|CTD-2528A14.3_ENST00000598893.1_RNA|HAUS8_ENST00000593360.1_Silent_p.L186L			Q9BT25	HAUS8_HUMAN	HAUS augmin-like complex, subunit 8	247					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						CTCACGGGCAGCTCGTGCCTG	0.632																																					p.L247L		Atlas-SNP	.											.	HAUS8	31	.	0			c.C739T						PASS	.						137	108	118					19																	17166719		2203	4300	6503	SO:0001819	synonymous_variant	93323	exon9			CGGGCAGCTCGTG	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.739C>T	19.37:g.17166719G>A		40	0	0		46	21	0.456522	NM_033417	B4DJA7|C9JBZ4|Q49AC4|Q86WF0|Q96FX3	Silent	SNP	ENST00000253669.5	37	CCDS32948.1																																																																																			.	.	none		0.632	HAUS8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463015.1	NM_001011699		A	17166719	G	A	17166719	2	1	7	1	0	0	0	0	0	0	0	1	6981	962	34	2		2	HAUS8	19	17166719	Silent	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	728877	17166719	41962264	137	814											
MAP1S	55201	hgsc.bcm.edu	37	chr19	17837421	17837421	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccggcgccgagcgcacgctgGcctctgtgtgcgccctgctg	2	7	15	17	6	1	0	0	0	1	0	1	1	1	0	4	2	3	3	4	2	0	0			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr19:17837421G>A	ENST00000324096.4	+	5	1379	c.1228G>A	c.(1228-1230)Gcc>Acc	p.A410T	CTD-3149D2.4_ENST00000595363.1_RNA|MAP1S_ENST00000597681.1_Intron|MAP1S_ENST00000544059.2_Missense_Mutation_p.A384T	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	410	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						GCGCACGCTGGCCTCTGTGTG	0.726																																					p.A410T		Atlas-SNP	.											MAP1S,bladder,carcinoma,-2,1	MAP1S	74	1	0			c.G1228A						PASS	.																																			SO:0001583	missense	55201	exon5			ACGCTGGCCTCTG	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.1228G>A	19.37:g.17837421G>A	ENSP00000325313:p.Ala410Thr	66	0	0		67	31	0.462687	NM_018174	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Missense_Mutation	SNP	ENST00000324096.4	37	CCDS32954.1	.	.	.	.	.	.	.	.	.	.	G	0.125	-1.121058	0.01785	.	.	ENSG00000130479	ENST00000324096;ENST00000544059	T;T	0.03635	3.86;3.86	3.39	3.39	0.38822	.	0.300651	0.23828	N	0.044172	T	0.01870	0.0059	N	0.16037	0.36	0.21064	N	0.999797	B;B;B	0.20671	0.047;0.047;0.026	B;B;B	0.17722	0.019;0.019;0.013	T	0.47341	-0.9125	10	0.02654	T	1	-11.0899	6.6284	0.22843	0.1361:0.0:0.8639:0.0	.	384;410;410	B4DH53;A8K940;Q66K74	.;.;MAP1S_HUMAN	T	410;384	ENSP00000325313:A410T;ENSP00000439243:A384T	ENSP00000325313:A410T	A	+	1	0	MAP1S	17698421	0.001000	0.12720	0.085000	0.20634	0.155000	0.21991	0.751000	0.26348	1.437000	0.47472	0.561000	0.74099	GCC	.	.	none		0.726	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174		A	17837421	G	A	17837421	3	1	7	1	0	0	0	0	1	0	0	0	9243	1203	42	2	1246	2	MAP1S	19	17837421	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	670702	17837421	41291562	138	815											
ZNF492	57615	hgsc.bcm.edu	37	chr19	22848027	22848027	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgcttgtgacaacattgcaaAgatttccaaatataaaagaa	18	11	6	6	0	0	3	0	1	0	2	1	3	1	3	1	0	3	2	1	0	7	5			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr19:22848027A>G	ENST00000456783.2	+	4	1800	c.1556A>G	c.(1555-1557)aAg>aGg	p.K519R	CTC-457E21.9_ENST00000601860.1_RNA	NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492	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)			endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				AACATTGCAAAGATTTCCAAA	0.323																																					p.K519R		Atlas-SNP	.											ZNF492_ENST00000456783,NS,carcinoma,-1,1	ZNF492	129	1	0			c.A1556G						scavenged	.						18	17	17					19																	22848027		1781	4030	5811	SO:0001583	missense	57615	exon4			TTGCAAAGATTTC	AB040906	CCDS46032.1	19p13.11	2013-01-08				ENSG00000229676		"Zinc fingers, C2H2-type"	23707	protein-coding gene	gene with protein product			"zinc finger protein 115 (Y20)"	ZNF115		10819331	Standard	NM_020855		Approved	KIAA1473	uc002nqw.3	Q9P255		ENST00000456783.2:c.1556A>G	19.37:g.22848027A>G	ENSP00000413660:p.Lys519Arg	829	1	0.00120627		761	235	0.308804	NM_020855	Q08EI7|Q08EI8	Missense_Mutation	SNP	ENST00000456783.2	37	CCDS46032.1	.	.	.	.	.	.	.	.	.	.	.	0.458	-0.890660	0.02491	.	.	ENSG00000229676	ENST00000456783	T	0.07567	3.18	1.03	1.03	0.20045	.	.	.	.	.	T	0.05181	0.0138	N	0.25380	0.74	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45600	-0.9250	9	0.16420	T	0.52	.	5.9322	0.19144	1.0:0.0:0.0:0.0	.	519	Q9P255	ZN492_HUMAN	R	519	ENSP00000413660:K519R	ENSP00000413660:K519R	K	+	2	0	ZNF492	22639867	0.000000	0.05858	0.005000	0.12908	0.029000	0.11900	-0.388000	0.07352	0.432000	0.26286	0.128000	0.15822	AAG	.	.	none		0.323	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464581.1	NM_020855		G	22848027	A	G	22848027	3	3	7	1	0	0	0	0	1	0	0	0	17958	72	3	3	1566	3	ZNF492	19	22848027	Missense_Mutation	SNP	A	TCGA-FA-A7Q1-01A-11D-A382-10	5010606	22848027	36280956	139	816											
ZNF569	148266	hgsc.bcm.edu	37	chr19	37904751	37904751	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctcacattccttacatgcaTagggcttctctccagtatga	9	14	6	12	0	2	1	1	1	2	0	6	1	4	1	2	1	2	3	2	1	3	5			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr19:37904751T>C	ENST00000316950.6	-	6	1366	c.809A>G	c.(808-810)tAt>tGt	p.Y270C	ZNF569_ENST00000392150.2_Missense_Mutation_p.Y111C|ZNF569_ENST00000392149.2_Missense_Mutation_p.Y270C	NM_152484.2	NP_689697.2	Q5MCW4	ZN569_HUMAN	zinc finger protein 569	270					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)			CTTACATGCATAGGGCTTCTC	0.343																																					p.Y270C		Atlas-SNP	.											.	ZNF569	101	.	0			c.A809G						PASS	.						79	84	82					19																	37904751		2203	4299	6502	SO:0001583	missense	148266	exon6			CATGCATAGGGCT	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.809A>G	19.37:g.37904751T>C	ENSP00000325018:p.Tyr270Cys	66	0	0		89	36	0.404494	NM_152484	A8K1S2|Q15925|Q17RR6|Q96MQ2	Missense_Mutation	SNP	ENST00000316950.6	37	CCDS12503.1	.	.	.	.	.	.	.	.	.	.	T	11.12	1.546214	0.27652	.	.	ENSG00000196437	ENST00000316950;ENST00000392150	T;T	0.25414	1.8;1.8	3.89	3.89	0.44902	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.34268	N	0.004102	T	0.45196	0.1330	M	0.71036	2.16	0.38461	D	0.947224	B;D	0.76494	0.411;0.999	B;D	0.81914	0.169;0.995	T	0.50215	-0.8854	10	0.72032	D	0.01	.	7.815	0.29254	0.1862:0.0:0.0:0.8138	.	111;270	Q17RR6;Q5MCW4	.;ZN569_HUMAN	C	270;111	ENSP00000325018:Y270C;ENSP00000375993:Y111C	ENSP00000325018:Y270C	Y	-	2	0	ZNF569	42596591	0.000000	0.05858	0.974000	0.42286	0.615000	0.37417	-0.981000	0.03766	1.745000	0.51790	0.533000	0.62120	TAT	.	.	none		0.343	ZNF569-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109594.2	NM_152484		C	37904751	T	C	37904751	3	2	7	1	0	0	0	0	1	0	0	0	18015	1406	49	3	1255	3	ZNF569	19	37904751	Missense_Mutation	SNP	T	TCGA-FA-A7Q1-01A-11D-A382-10	15056724	37904751	21224232	140	817											
AKT2	208	hgsc.bcm.edu	37	chr19	40741861	40741861	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcctcggggctgagcgtgcGcgggaagcggatctcttcca	5	7	17	12	5	1	1	0	1	1	0	4	3	2	3	2	5	3	1	2	5	1	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr19:40741861G>A	ENST00000392038.2	-	11	1409	c.1111C>T	c.(1111-1113)Cgc>Tgc	p.R371C	AKT2_ENST00000579047.1_Missense_Mutation_p.R309C|AKT2_ENST00000424901.1_Missense_Mutation_p.R371C|AKT2_ENST00000311278.6_Missense_Mutation_p.R328C	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	371	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)			breast(1)|cervix(1)|kidney(3)|large_intestine(9)|lung(10)|prostate(2)|skin(1)	27			Lung(22;0.000499)			CTGAGCGTGCGCGGGAAGCGG	0.647			A		"ovarian, pancreatic "																																p.R371C		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	0			c.C1111T						PASS	.						57	54	55					19																	40741861		2203	4300	6503	SO:0001583	missense	208	exon11			GCGTGCGCGGGAA	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.1111C>T	19.37:g.40741861G>A	ENSP00000375892:p.Arg371Cys	28	0	0		21	6	0.285714	NM_001626	B2RBD8|Q05BV0|Q0VAN0|Q0VAN1|Q68GC0	Missense_Mutation	SNP	ENST00000392038.2	37	CCDS12552.1	.	.	.	.	.	.	.	.	.	.	G	13.15	2.151570	0.38021	.	.	ENSG00000105221	ENST00000392038;ENST00000391844;ENST00000424901;ENST00000311278;ENST00000391845	T;T;T	0.59083	0.29;0.29;0.29	5.77	4.73	0.59995	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.094359	0.64402	D	0.000001	T	0.52108	0.1714	L	0.52206	1.635	0.80722	D	1	B;B;B	0.27791	0.022;0.02;0.189	B;B;B	0.25506	0.026;0.013;0.061	T	0.52815	-0.8525	10	0.51188	T	0.08	.	13.9471	0.64091	0.0744:0.0:0.9256:0.0	.	309;328;371	B4DG79;Q0VAN0;P31751	.;.;AKT2_HUMAN	C	371;272;371;328;191	ENSP00000375892:R371C;ENSP00000399532:R371C;ENSP00000309428:R328C	ENSP00000309428:R328C	R	-	1	0	AKT2	45433701	1.000000	0.71417	0.900000	0.35374	0.907000	0.53573	3.635000	0.54309	1.449000	0.47699	0.555000	0.69702	CGC	.	.	none		0.647	AKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268029.1	NM_001626		A	40741861	G	A	40741861	3	1	7	1	0	0	0	0	1	0	0	0	480	1087	38	1	350	1	AKT2	19	40741861	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	2837110	40741861	18387122	141	818											
SPTBN4	57731	hgsc.bcm.edu	37	chr19	41073666	41073666	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaactggcggccaaggcggCgcccctgctgcggccagggg	5	3	19	14	4	0	0	0	0	0	0	0	1	0	1	4	8	3	1	4	8	2	0			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr19:41073666C>T	ENST00000352632.3	+	31	6520	c.6434C>T	c.(6433-6435)gCg>gTg	p.A2145V	SPTBN4_ENST00000392025.1_Missense_Mutation_p.A888V|SPTBN4_ENST00000598249.1_Missense_Mutation_p.A2145V			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4	2145					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)			GCCAAGGCGGCGCCCCTGCTG	0.677																																					p.A2145V		Atlas-SNP	.											.	SPTBN4	213	.	0			c.C6434T						PASS	.						5	5	5					19																	41073666		2073	4105	6178	SO:0001583	missense	57731	exon31			AGGCGGCGCCCCT	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.6434C>T	19.37:g.41073666C>T	ENSP00000263373:p.Ala2145Val	33	0	0		35	13	0.371429	NM_020971	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Missense_Mutation	SNP	ENST00000352632.3	37	CCDS12559.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.481397	0.84747	.	.	ENSG00000160460	ENST00000428507;ENST00000352632;ENST00000392025	T;T	0.77750	-1.12;0.11	4.91	4.91	0.64330	.	0.161948	0.28671	U	0.014532	T	0.66287	0.2774	N	0.08118	0	0.80722	D	1	D;D	0.61080	0.989;0.989	P;P	0.47626	0.552;0.552	T	0.69573	-0.5109	10	0.32370	T	0.25	.	16.874	0.86046	0.0:1.0:0.0:0.0	.	888;2145	C9JY79;Q9H254	.;SPTN4_HUMAN	V	2145;2145;888	ENSP00000263373:A2145V;ENSP00000375879:A888V	ENSP00000263373:A2145V	A	+	2	0	SPTBN4	45765506	0.281000	0.24258	0.995000	0.50966	0.952000	0.60782	2.449000	0.44935	2.252000	0.74401	0.561000	0.74099	GCG	.	.	none		0.677	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2			T	41073666	C	T	41073666	3	4	7	1	0	0	0	0	1	0	0	0	15136	768	27	1	6646	1	SPTBN4	19	41073666	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	331805	41073666	18055317	142	819											
SYMPK	8189	hgsc.bcm.edu	37	chr19	46347378	46347378	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggagcccagcgctgtggtcaGgttgatggaggagatggcag	8	7	19	7	1	1	2	1	1	0	1	1	5	1	4	1	6	2	3	1	6	0	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr19:46347378G>C	ENST00000245934.7	-	8	1001	c.757C>G	c.(757-759)Ctg>Gtg	p.L253V		NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	253					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)		GCTGTGGTCAGGTTGATGGAG	0.547																																					p.L253V		Atlas-SNP	.											.	SYMPK	104	.	0			c.C757G						PASS	.						173	133	147					19																	46347378		2203	4300	6503	SO:0001583	missense	8189	exon8			TGGTCAGGTTGAT	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.757C>G	19.37:g.46347378G>C	ENSP00000245934:p.Leu253Val	69	0	0		88	28	0.318182	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Missense_Mutation	SNP	ENST00000245934.7	37	CCDS12676.2	.	.	.	.	.	.	.	.	.	.	G	27.9	4.876042	0.91664	.	.	ENSG00000125755	ENST00000245934	T	0.33216	1.42	5.98	5.98	0.97165	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.56426	0.1984	M	0.68593	2.085	0.80722	D	1	D;D	0.89917	1.0;0.996	D;D	0.91635	0.999;0.984	T	0.55679	-0.8103	10	0.87932	D	0	.	17.952	0.89056	0.0:0.0:1.0:0.0	.	268;253	Q4LE61;Q92797	.;SYMPK_HUMAN	V	253	ENSP00000245934:L253V	ENSP00000245934:L253V	L	-	1	2	SYMPK	51039218	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	8.941000	0.92964	2.835000	0.97688	0.650000	0.86243	CTG	.	.	none		0.547	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819		C	46347378	G	C	46347378	3	2	7	1	0	0	0	0	1	0	0	0	15454	991	35	4	3147	4	SYMPK	19	46347378	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	5273712	46347378	12781605	143	820											
IL4I1	259307	hgsc.bcm.edu	37	chr19	50397663	50397663	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgcacctccgtccacgtgttCttgtcgtactgggtgaactt	5	14	10	12	3	1	1	0	1	1	0	4	1	3	1	3	1	3	3	3	1	2	4			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr19:50397663C>G	ENST00000391826.2	-	5	571	c.429G>C	c.(427-429)aaG>aaC	p.K143N	IL4I1_ENST00000341114.3_Missense_Mutation_p.K165N|IL4I1_ENST00000595948.1_Missense_Mutation_p.K165N	NM_152899.1	NP_690863.1	Q96RQ9	OXLA_HUMAN	interleukin 4 induced 1	143						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)	TCCACGTGTTCTTGTCGTACT	0.617																																					p.K165N		Atlas-SNP	.											.	IL4I1	50	.	0			c.G495C						PASS	.						116	113	114					19																	50397663		2203	4300	6503	SO:0001583	missense	259307	exon7			CGTGTTCTTGTCG	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.429G>C	19.37:g.50397663C>G	ENSP00000375702:p.Lys143Asn	110	0	0		101	41	0.405941	NM_172374	Q1WMJ3|Q4GZN1|Q4GZN2|Q6P2Q3|Q8TEM5|Q96RQ8	Missense_Mutation	SNP	ENST00000391826.2	37	CCDS12787.1	.	.	.	.	.	.	.	.	.	.	C	2.739	-0.262761	0.05754	.	.	ENSG00000104951	ENST00000341114;ENST00000391826	D;D	0.92299	-3.01;-3.01	5.24	2.95	0.34219	Amine oxidase (1);	0.996710	0.08139	N	0.991977	T	0.79656	0.4483	N	0.02247	-0.625	0.19775	N	0.999956	P;P;B	0.38677	0.589;0.642;0.006	B;B;B	0.33121	0.098;0.158;0.01	T	0.67484	-0.5659	10	0.22109	T	0.4	-29.9311	13.0756	0.59085	0.0:0.6914:0.3086:0.0	.	165;165;143	Q96RQ9-2;Q1WMJ3;Q96RQ9	.;.;OXLA_HUMAN	N	165;143	ENSP00000342557:K165N;ENSP00000375702:K143N	ENSP00000342557:K165N	K	-	3	2	IL4I1	55089475	0.998000	0.40836	0.995000	0.50966	0.056000	0.15407	1.642000	0.37207	1.206000	0.43276	0.491000	0.48974	AAG	.	.	none		0.617	IL4I1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466413.1			G	50397663	C	G	50397663	3	3	7	1	0	0	0	0	1	0	0	0	7706	912	32	4	1290	4	IL4I1	19	50397663	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	4050285	50397663	8731320	144	821											
MYH14	79784	hgsc.bcm.edu	37	chr19	50779294	50779294	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cccagctgctgaaatccctgCgggaggctcaagcagccctg	8	6	12	15	1	1	1	1	1	0	0	2	2	2	2	3	2	5	4	3	2	2	0	rs373919106		TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr19:50779294C>T	ENST00000596571.1	+	25	3391	c.3391C>T	c.(3391-3393)Cgg>Tgg	p.R1131W	MYH14_ENST00000440075.2_Missense_Mutation_p.R1172W|MYH14_ENST00000262269.8_Missense_Mutation_p.R1172W|MYH14_ENST00000425460.1_Missense_Mutation_p.R1139W|MYH14_ENST00000376970.2_Missense_Mutation_p.R1164W|MYH14_ENST00000601313.1_Missense_Mutation_p.R1172W|MYH14_ENST00000598205.1_Missense_Mutation_p.R1139W			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1131					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)	p.R1172W(1)|p.R1131W(1)		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)		GAAATCCCTGCGGGAGGCTCA	0.677																																					p.R1172W		Atlas-SNP	.											MYH14_ENST00000262269,colon,carcinoma,0,4	MYH14	261	4	2	Substitution - Missense(2)	large_intestine(2)	c.C3514T						PASS	.						13	17	16					19																	50779294		1978	4162	6140	SO:0001583	missense	79784	exon28			TCCCTGCGGGAGG	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.3391C>T	19.37:g.50779294C>T	ENSP00000472819:p.Arg1131Trp	112	0	0		88	39	0.443182	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	37	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	C	15.58	2.874422	0.51695	.	.	ENSG00000105357	ENST00000301415;ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	T;T;T;T	0.79653	-1.29;-1.29;-1.29;-1.29	4.0	1.63	0.23807	Myosin tail (1);	.	.	.	.	D	0.86916	0.6048	M	0.71581	2.175	0.54753	D	0.999986	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.86838	0.2015	9	0.87932	D	0	.	10.4099	0.44287	0.3458:0.6542:0.0:0.0	.	1172;1131;1139	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	W	1131;1172;1164;1139;1131;1172	ENSP00000406273:R1172W;ENSP00000366169:R1164W;ENSP00000407879:R1139W;ENSP00000262269:R1172W	ENSP00000262269:R1172W	R	+	1	2	MYH14	55471106	0.996000	0.38824	0.988000	0.46212	0.268000	0.26511	1.177000	0.31969	1.031000	0.39867	0.455000	0.32223	CGG	.	.	alt		0.677	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		T	50779294	C	T	50779294	3	4	7	1	0	0	0	0	1	0	0	0	10042	759	27	1	3620	1	MYH14	19	50779294	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	381631	50779294	8349689	145	822											
RBM12	10137	hgsc.bcm.edu	37	chr20	34242575	34242575	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aggaactgggggaatcggggGcacaggaggcacaggaggca	12	2	20	7	1	0	0	0	0	0	0	1	4	0	4	0	9	1	3	0	9	2	0			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr20:34242575G>T	ENST00000374114.3	-	3	933	c.670C>A	c.(670-672)Ccc>Acc	p.P224T	RBM12_ENST00000374104.3_Missense_Mutation_p.P224T|CPNE1_ENST00000397443.1_Intron|CPNE1_ENST00000317619.3_Intron|RP1-309K20.6_ENST00000541176.2_Intron|CPNE1_ENST00000352393.4_Intron|CPNE1_ENST00000397442.1_Intron|CPNE1_ENST00000317677.5_5'Flank|RBM12_ENST00000359646.1_Missense_Mutation_p.P224T|CPNE1_ENST00000397446.1_Intron|CPNE1_ENST00000397445.1_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	224	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)			GGAATCGGGGGCACAGGAGGC	0.602																																					p.P224T		Atlas-SNP	.											.	RBM12	93	.	0			c.C670A						PASS	.						103	82	89					20																	34242575		2203	4300	6503	SO:0001583	missense	10137	exon2			TCGGGGGCACAGG	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.670C>A	20.37:g.34242575G>T	ENSP00000363228:p.Pro224Thr	49	0	0		67	32	0.477612	NM_001198840	B3KRU2|E1P5R6|O94865|Q8N3B1|Q9H196	Missense_Mutation	SNP	ENST00000374114.3	37	CCDS13261.1	.	.	.	.	.	.	.	.	.	.	G	11.58	1.681847	0.29872	.	.	ENSG00000244462	ENST00000374114;ENST00000359646;ENST00000374104;ENST00000349942;ENST00000424458	T;T;T;T	0.27402	2.53;2.53;2.53;1.67	5.23	5.23	0.72850	.	0.074210	0.56097	D	0.000030	T	0.16769	0.0403	N	0.19112	0.55	0.80722	D	1	P	0.39480	0.675	B	0.26094	0.066	T	0.09228	-1.0684	10	0.08179	T	0.78	-2.6574	19.0135	0.92884	0.0:0.0:1.0:0.0	.	224	Q9NTZ6	RBM12_HUMAN	T	224;224;224;23;224	ENSP00000363228:P224T;ENSP00000352668:P224T;ENSP00000363217:P224T;ENSP00000411036:P224T	ENSP00000339879:P23T	P	-	1	0	RBM12	33705989	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.344000	0.59354	2.719000	0.93026	0.555000	0.69702	CCC	.	.	none		0.602	RBM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078894.1	NM_006047		T	34242575	G	T	34242575	3	4	7	1	0	0	0	0	1	0	0	0	13128	1203	42	4	2132	4	RBM12	20	34242575	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10		34242575	28782945	146	823											
RIMS4	140730	hgsc.bcm.edu	37	chr20	43385538	43385538	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gagcgcgtcaatgcccctcaCctggaggactttgccctggg	6	8	13	14	2	2	0	2	0	0	0	2	3	2	2	4	3	3	0	4	3	1	1			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr20:43385538C>A	ENST00000372851.3	-	5	658		c.e5+1		RIMS4_ENST00000541604.2_Splice_Site	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)				ATGCCCCTCACCTGGAGGACT	0.587																																					.		Atlas-SNP	.											.	RIMS4	47	.	0			c.594+1G>T						PASS	.						242	211	221					20																	43385538		2203	4300	6503	SO:0001630	splice_region_variant	140730	exon6			CCCTCACCTGGAG		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	ENST00000372851.3:c.591+1G>T	20.37:g.43385538C>A		111	0	0		113	52	0.460177	NM_001205317	A4FU94|E1P613|Q3MI44|Q5JWT7	Splice_Site	SNP	ENST00000372851.3	37	CCDS13338.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.143738	0.77888	.	.	ENSG00000101098	ENST00000372851;ENST00000541604	.	.	.	5.18	5.18	0.71444	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.6881	0.91573	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RIMS4	42818952	1.000000	0.71417	1.000000	0.80357	0.740000	0.42216	7.818000	0.86416	2.404000	0.81709	0.462000	0.41574	.	.	.	none		0.587	RIMS4-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000101027.2	NM_182970	Intron	A	43385538	C	A	43385538	5	1	7	1	0	0	0	0	0	0	1	0	13385	521	18	4	225	4	RIMS4	20	43385538	Splice_Site	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	9142963	43385538	19639982	147	824											
ZBP1	81030	hgsc.bcm.edu	37	chr20	56195323	56195323	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaagaagtactgtaccttctCtgcccgggtcagcaggagcc	9	8	12	12	1	2	1	1	0	1	1	3	3	2	2	3	2	5	3	3	2	4	3			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr20:56195323C>T	ENST00000371173.3	-	1	206	c.29G>A	c.(28-30)aGa>aAa	p.R10K	ZBP1_ENST00000395822.3_Missense_Mutation_p.R10K|ZBP1_ENST00000343535.4_Missense_Mutation_p.R10K|ZBP1_ENST00000340462.4_Missense_Mutation_p.R10K|ZBP1_ENST00000541799.1_Missense_Mutation_p.R10K|ZBP1_ENST00000538947.1_5'UTR	NM_001160417.1|NM_030776.2	NP_001153889.1|NP_110403.2	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1	10					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)			TGTACCTTCTCTGCCCGGGTC	0.577																																					p.R10K		Atlas-SNP	.											.	ZBP1	65	.	0			c.G29A						PASS	.						39	34	35					20																	56195323		2198	4298	6496	SO:0001583	missense	81030	exon1			CCTTCTCTGCCCG	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.29G>A	20.37:g.56195323C>T	ENSP00000360215:p.Arg10Lys	65	0	0		69	29	0.42029	NM_001160419	A2A2F7|B3KVA1|F5GYT1|Q5JY39|Q9BYW4	Missense_Mutation	SNP	ENST00000371173.3	37	CCDS13461.1	.	.	.	.	.	.	.	.	.	.	C	3.457	-0.110823	0.06924	.	.	ENSG00000124256	ENST00000371173;ENST00000395822;ENST00000340462;ENST00000357677;ENST00000343535;ENST00000541799	T;T;T;T;T	0.13778	3.17;2.56;3.17;3.14;2.81	3.23	-4.69	0.03299	Winged helix-turn-helix transcription repressor DNA-binding (1);	1.821130	0.03512	N	0.219696	T	0.04634	0.0126	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	0.01281	0.0;0.0;0.0;0.0	T	0.39482	-0.9612	10	0.02654	T	1	4.3898	7.5004	0.27513	0.0:0.1146:0.632:0.2534	.	10;10;10;10	F5GYT1;A2RRL9;A2A2F7;Q9H171	.;.;.;ZBP1_HUMAN	K	10	ENSP00000360215:R10K;ENSP00000379167:R10K;ENSP00000344954:R10K;ENSP00000340584:R10K;ENSP00000440552:R10K	ENSP00000344954:R10K	R	-	2	0	ZBP1	55628729	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.844000	0.04345	-0.756000	0.04703	-0.658000	0.03865	AGA	.	.	none		0.577	ZBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079849.1	NM_030776		T	56195323	C	T	56195323	3	4	7	1	0	0	0	0	1	0	0	0	17536	913	32	2	1369	2	ZBP1	20	56195323	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	12809785	56195323	6830197	148	825											
HSF2BP	11077	hgsc.bcm.edu	37	chr21	45064273	45064273	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgctctttcctttccaggTctaggagaaagacataaaat	12	13	7	9	0	2	2	0	0	2	2	4	3	4	2	2	2	1	1	2	2	4	5			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr21:45064273T>C	ENST00000291560.2	-	4	519	c.188A>G	c.(187-189)aAc>aGc	p.N63S	HSF2BP_ENST00000542962.1_5'UTR	NM_007031.1	NP_008962.1	O75031	HSF2B_HUMAN	heat shock transcription factor 2 binding protein	63					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)		CCTTTCCAGGTCTAGGAGAAA	0.408																																					p.N63S		Atlas-SNP	.											.	HSF2BP	28	.	0			c.A188G						PASS	.						106	103	104					21																	45064273		2203	4300	6503	SO:0001630	splice_region_variant	11077	exon4			TCCAGGTCTAGGA	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.188-1A>G	21.37:g.45064273T>C		93	0	0		101	38	0.376238	NM_007031	B4DX36	Missense_Mutation	SNP	ENST00000291560.2	37	CCDS13697.1	.	.	.	.	.	.	.	.	.	.	T	3.845	-0.033093	0.07543	.	.	ENSG00000160207	ENST00000291560;ENST00000443485	.	.	.	5.2	4.07	0.47477	.	0.456651	0.24534	N	0.037681	T	0.23054	0.0557	N	0.04880	-0.145	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.14035	-1.0487	9	0.13108	T	0.6	.	2.7045	0.05158	0.0:0.1771:0.2775:0.5454	.	63	O75031	HSF2B_HUMAN	S	63	.	ENSP00000291560:N63S	N	-	2	0	HSF2BP	43888701	0.994000	0.37717	1.000000	0.80357	0.954000	0.61252	0.367000	0.20382	1.966000	0.57179	0.460000	0.39030	AAC	.	.	none		0.408	HSF2BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195620.1	NM_007031	Missense_Mutation	C	45064273	T	C	45064273	5	2	7	1	0	0	0	0	0	0	1	0	7406	1681	58	3	840	3	HSF2BP	21	45064273	Splice_Site	SNP	T	TCGA-FA-A7Q1-01A-11D-A382-10		45064273	3065622	149	826											
MICAL3	57553	hgsc.bcm.edu	37	chr22	18314712	18314712	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cctcctcttcattcccaggcCcaaagctctttgaggcctct	6	12	6	17	0	4	1	1	1	3	0	6	1	6	1	5	2	1	1	5	2	1	3			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr22:18314712C>T	ENST00000441493.2	-	21	3315	c.2963G>A	c.(2962-2964)gGg>gAg	p.G988E		NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	988	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)		ATTCCCAGGCCCAAAGCTCTT	0.552																																					p.G988E		Atlas-SNP	.											.	MICAL3	53	.	0			c.G2963A						PASS	.						66	58	61					22																	18314712		1564	3575	5139	SO:0001583	missense	57553	exon21			CCAGGCCCAAAGC	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.2963G>A	22.37:g.18314712C>T	ENSP00000416015:p.Gly988Glu	99	0	0		80	38	0.475	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Missense_Mutation	SNP	ENST00000441493.2	37	CCDS46659.1	.	.	.	.	.	.	.	.	.	.	C	2.016	-0.426009	0.04701	.	.	ENSG00000093100	ENST00000441493	T	0.59364	0.27	5.27	-7.39	0.01402	.	.	.	.	.	T	0.23133	0.0559	N	0.08118	0	0.40554	D	0.981146	B	0.02656	0.0	B	0.01281	0.0	T	0.37934	-0.9684	9	0.02654	T	1	.	5.9692	0.19342	0.1768:0.5039:0.0902:0.2291	.	988	Q7RTP6	MICA3_HUMAN	E	988	ENSP00000416015:G988E	ENSP00000416015:G988E	G	-	2	0	XXbac-B461K10.4	16694712	0.004000	0.15560	0.000000	0.03702	0.258000	0.26162	-0.169000	0.09911	-2.929000	0.00301	-1.183000	0.01708	GGG	.	.	none		0.552	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1			T	18314712	C	T	18314712	3	4	7	1	0	0	0	0	1	0	0	0	9580	623	22	2	3093	2	MICAL3	22	18314712	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10		18314712	32989854	150	827											
CSNK1E	1454	hgsc.bcm.edu	37	chr22	38690161	38690163	+	In_Frame_Del	DEL	GAG	GAG	-																															cttgccgcccagtgaggtctGaggaggagacgttggcgggc																										TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr22:38690161_38690163delGAG	ENST00000396832.1	-	9	1430_1432	c.1170_1172delCTC	c.(1168-1173)tcctca>tca	p.390_391SS>S	CSNK1E_ENST00000498529.1_5'Flank|CSNK1E_ENST00000403904.1_In_Frame_Del_p.390_391SS>S|CSNK1E_ENST00000400206.2_In_Frame_Del_p.390_391SS>S|CSNK1E_ENST00000359867.3_In_Frame_Del_p.390_391SS>S	NM_152221.2	NP_689407.1	P49674	KC1E_HUMAN	casein kinase 1, epsilon	390					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)					AGTGAGGTCTGAGGAGGAGACGT	0.645																																					p.391_391del	Esophageal Squamous(119;108 755 9651 12170 13692 17603 24932 28315 37982 41601)	Pindel,Atlas-Indel	.											.	CSNK1E	143	.	0			c.1171_1173del						PASS	.																																			SO:0001651	inframe_deletion	1454	exon9			.		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.1170_1172delCTC	22.37:g.38690167_38690169delGAG	ENSP00000380044:p.Ser391del	31	0	.		42	13	0.31	NM_001894		In_Frame_Del	DEL	ENST00000396832.1	37	CCDS13970.1																																																																																			.	.	none		0.645	CSNK1E-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321462.1	NM_001894		-	38690163	GAG	-	38690161	7	5	7	1	0	1	0	1	0	0	0	0	3955	1294	45	0	86	0	CSNK1E	22	38690161	In_Frame_Del	DEL	GAG	TCGA-FA-A7Q1-01A-11D-A382-10	20375449	38690161	12614405	151	828											
PLXNB2	23654	hgsc.bcm.edu	37	chr22	50727961	50727961	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cataccggcgcgtggccgccGcactggatatcgccgtggaa	7	6	14	14	7	0	0	0	0	0	0	1	2	0	2	4	4	1	1	4	4	3	2	rs541323204	byFrequency	TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chr22:50727961G>A	ENST00000449103.1	-	3	1193	c.1053C>T	c.(1051-1053)tgC>tgT	p.C351C	PLXNB2_ENST00000359337.4_Silent_p.C351C			O15031	PLXB2_HUMAN	plexin B2	351	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)		CGTGGCCGCCGCACTGGATAT	0.662													G|||	4	0.000798722	0.0	0.0	5008	,	,		15347	0.004		0.0	False		,,,				2504	0.0				p.C351C		Atlas-SNP	.											.	PLXNB2	172	.	0			c.C1053T						PASS	.						24	29	28					22																	50727961		1987	4152	6139	SO:0001819	synonymous_variant	23654	exon3			GCCGCCGCACTGG		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.1053C>T	22.37:g.50727961G>A		54	0	0		21	13	0.619048	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Silent	SNP	ENST00000449103.1	37	CCDS43035.1																																																																																			.	.	none		0.662	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401		A	50727961	G	A	50727961	2	1	7	1	0	0	0	0	0	0	0	1	12133	1079	38	1		1	PLXNB2	22	50727961	Silent	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	12037800	50727961	576605	152	829											
ARHGAP6	395	hgsc.bcm.edu	37	chrX	11160430	11160430	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatcgaaaggctcctctgacAgatctagggaaaaagtgtat	14	10	10	7	1	2	2	0	1	2	1	4	4	3	3	1	2	0	2	1	2	6	3			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chrX:11160430A>C	ENST00000337414.4	-	12	3052	c.2180T>G	c.(2179-2181)cTg>cGg	p.L727R	ARHGAP6_ENST00000534860.1_Missense_Mutation_p.L552R|ARHGAP6_ENST00000303025.6_Missense_Mutation_p.L524R|ARHGAP6_ENST00000380736.1_Missense_Mutation_p.L524R	NM_013427.2	NP_038286.2	O43182	RHG06_HUMAN	Rho GTPase activating protein 6	727					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						CTCCTCTGACAGATCTAGGGA	0.323																																					p.L727R		Atlas-SNP	.											.	ARHGAP6	130	.	0			c.T2180G						PASS	.						80	78	79					X																	11160430		2203	4300	6503	SO:0001583	missense	395	exon12			TCTGACAGATCTA	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.2180T>G	X.37:g.11160430A>C	ENSP00000338967:p.Leu727Arg	400	1	0.0025		491	151	0.307536	NM_013427	B2RWQ0|O43437|Q9P1B3|Q9UK81|Q9UK82	Missense_Mutation	SNP	ENST00000337414.4	37	CCDS14140.1	.	.	.	.	.	.	.	.	.	.	A	13.73	2.323162	0.41096	.	.	ENSG00000047648	ENST00000534860;ENST00000380736;ENST00000303025;ENST00000337414	T;T;T;T	0.24723	1.84;1.91;1.91;1.91	5.24	4.07	0.47477	.	0.213907	0.32106	N	0.006562	T	0.11879	0.0289	N	0.08118	0	0.80722	D	1	B;P	0.34780	0.138;0.468	B;B	0.29267	0.021;0.1	T	0.13602	-1.0503	10	0.36615	T	0.2	.	10.2557	0.43397	0.921:0.0:0.079:0.0	.	727;727	O43182;A8KAL3	RHG06_HUMAN;.	R	552;524;524;727	ENSP00000438135:L552R;ENSP00000370112:L524R;ENSP00000302312:L524R;ENSP00000338967:L727R	ENSP00000302312:L524R	L	-	2	0	ARHGAP6	11070351	1.000000	0.71417	0.985000	0.45067	0.872000	0.50106	6.002000	0.70693	0.656000	0.30886	0.481000	0.45027	CTG	.	.	none		0.323	ARHGAP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055760.2	NM_013427		C	11160430	A	C	11160430	3	2	7	1	0	0	0	0	1	0	0	0	887	188	7	5	752	5	ARHGAP6	23	11160430	Missense_Mutation	SNP	A	TCGA-FA-A7Q1-01A-11D-A382-10		11160430	144110130	153	830											
CTPS2	56474	hgsc.bcm.edu	37	chrX	16707682	16707682	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctttgttcctctaaaagcaCaggaactcggtatgtggaag	11	11	11	8	1	1	0	0	0	1	0	3	2	2	2	1	3	2	4	1	3	5	4			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chrX:16707682C>T	ENST00000443824.1	-	8	1506	c.763G>A	c.(763-765)Gtg>Atg	p.V255M	CTPS2_ENST00000380241.3_Missense_Mutation_p.V255M|CTPS2_ENST00000359276.4_Missense_Mutation_p.V255M	NM_001144002.1	NP_001137474.1	Q9NRF8	PYRG2_HUMAN	CTP synthase 2	255					'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)					TCTAAAAGCACAGGAACTCGG	0.383																																					p.V255M		Atlas-SNP	.											.	CTPS2	49	.	0			c.G763A						PASS	.						127	112	117					X																	16707682		2203	4300	6503	SO:0001583	missense	56474	exon8			AAAGCACAGGAAC	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.763G>A	X.37:g.16707682C>T	ENSP00000401264:p.Val255Met	483	1	0.00207039		668	169	0.252994	NM_001144002	B3KWM2|Q9BRI0|Q9H809|Q9H8K9	Missense_Mutation	SNP	ENST00000443824.1	37	CCDS14175.1	.	.	.	.	.	.	.	.	.	.	c	12.35	1.911512	0.33721	.	.	ENSG00000047230	ENST00000443824;ENST00000380241;ENST00000359276	T;T;T	0.43688	0.94;0.94;0.94	5.81	0.87	0.19102	CTP synthase, N-terminal (1);	0.440911	0.20974	N	0.082328	T	0.14527	0.0351	N	0.02412	-0.56	0.23920	N	0.996468	B	0.18741	0.03	B	0.19946	0.027	T	0.16217	-1.0410	10	0.66056	D	0.02	-4.8399	1.1054	0.01693	0.1316:0.2687:0.2635:0.3362	.	255	Q9NRF8	PYRG2_HUMAN	M	255	ENSP00000401264:V255M;ENSP00000369590:V255M;ENSP00000352222:V255M	ENSP00000352222:V255M	V	-	1	0	CTPS2	16617603	0.666000	0.27475	0.693000	0.30195	0.920000	0.55202	0.573000	0.23699	-0.261000	0.09405	0.591000	0.81541	GTG	.	.	none		0.383	CTPS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055906.1	NM_019857		T	16707682	C	T	16707682	3	4	7	1	0	0	0	0	1	0	0	0	4025	478	17	2	1041	2	CTPS2	23	16707682	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	5547252	16707682	138562878	154	831											
MAGEB10	139422	hgsc.bcm.edu	37	chrX	27839462	27839462	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtaaactccgtgccagggaAaaacgccgtcaggcccgagg	12	4	13	12	4	1	0	1	0	0	0	2	2	2	1	4	3	3	1	4	3	4	1	rs147336706	byFrequency	TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chrX:27839462A>C	ENST00000356790.2	+	3	284	c.39A>C	c.(37-39)gaA>gaC	p.E13D		NM_182506.3	NP_872312.2	Q96LZ2	MAGBA_HUMAN	melanoma antigen family B, 10	13										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						GTGCCAGGGAAAAACGCCGTC	0.527																																					p.E13D		Atlas-SNP	.											.	MAGEB10	107	.	0			c.A39C						PASS	.						54	54	54					X																	27839462		2202	4300	6502	SO:0001583	missense	139422	exon3			CAGGGAAAAACGC		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.39A>C	X.37:g.27839462A>C	ENSP00000368304:p.Glu13Asp	111	0	0		250	49	0.196	NM_182506	Q494Y6|Q494Y7|Q9BZ78	Missense_Mutation	SNP	ENST00000356790.2	37	CCDS35221.1	.	.	.	.	.	.	.	.	.	.	A	13.72	2.320930	0.41096	.	.	ENSG00000177689	ENST00000356790	T	0.08896	3.04	2.51	-1.62	0.08372	Melanoma associated antigen, MAGE, N-terminal (1);	1.247610	0.06246	U	0.691280	T	0.20007	0.0481	M	0.83223	2.63	0.09310	N	1	D	0.53462	0.96	P	0.53006	0.715	T	0.21449	-1.0245	10	0.54805	T	0.06	.	5.7982	0.18399	0.5237:0.0:0.4763:0.0	.	13	Q96LZ2	MAGBA_HUMAN	D	13	ENSP00000368304:E13D	ENSP00000368304:E13D	E	+	3	2	MAGEB10	27749383	0.044000	0.20184	0.001000	0.08648	0.012000	0.07955	-0.122000	0.10627	-0.468000	0.06922	0.339000	0.21740	GAA	A|0.993;G|0.007	.	alt		0.527	MAGEB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106216.1	NM_182506		C	27839462	A	C	27839462	3	2	7	1	0	0	0	0	1	0	0	0	9182	11	1	5	41	5	MAGEB10	23	27839462	Missense_Mutation	SNP	A	TCGA-FA-A7Q1-01A-11D-A382-10	11131780	27839462	127431098	155	832											
GRIPAP1	56850	hgsc.bcm.edu	37	chrX	48837643	48837643	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcacctgagcggctcttgctGttagtgaggatgtcctgcag	6	12	13	10	1	2	2	1	2	1	0	3	3	3	3	2	2	3	4	2	2	1	2			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chrX:48837643G>A	ENST00000376441.1	-	21	1948	c.1914C>T	c.(1912-1914)aaC>aaT	p.N638N	GRIPAP1_ENST00000376425.3_Silent_p.N607N|GRIPAP1_ENST00000376423.4_Silent_p.N559N|GRIPAP1_ENST00000376444.3_Silent_p.N593N|GRIPAP1_ENST00000473581.1_5'UTR	NM_020137.3	NP_064522.3	Q4V328	GRAP1_HUMAN	GRIP1 associated protein 1	638						blood microparticle (GO:0072562)|endosome (GO:0005768)				breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(2)	10						GGCTCTTGCTGTTAGTGAGGA	0.622																																					p.N638N		Atlas-SNP	.											.	GRIPAP1	128	.	0			c.C1914T						PASS	.						75	51	59					X																	48837643		2203	4300	6503	SO:0001819	synonymous_variant	56850	exon21			CTTGCTGTTAGTG	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.1914C>T	X.37:g.48837643G>A		97	0	0		199	124	0.623116	NM_020137	A6NL78|Q3MJ75|Q4V327|Q4V330|Q5HYG1|Q6N046|Q96DH8|Q9NQ43|Q9ULQ3	Silent	SNP	ENST00000376441.1	37	CCDS35248.1																																																																																			.	.	none		0.622	GRIPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080970.2	NM_207672		A	48837643	G	A	48837643	2	1	7	1	0	0	0	0	0	0	0	1	6798	1368	48	2		2	GRIPAP1	23	48837643	Silent	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	20998181	48837643	106432917	156	833											
NHSL2	340527	hgsc.bcm.edu	37	chrX	71358413	71358413	+	5'UTR	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtcaggatgctcggttcccaAgtctcacctcgccagtactg	7	10	10	14	2	2	0	2	0	1	0	6	1	3	1	3	2	2	3	3	2	2	2			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chrX:71358413A>G	ENST00000373677.1	+	0	1179				NHSL2_ENST00000510661.1_Missense_Mutation_p.S108G|NHSL2_ENST00000535692.1_5'UTR|NHSL2_ENST00000540800.1_Missense_Mutation_p.S339G			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)					TCGGTTCCCAAGTCTCACCTC	0.582																																					p.S339G		Atlas-SNP	.											.	NHSL2	148	.	0			c.A1015G						PASS	.						107	91	96					X																	71358413		692	1591	2283	SO:0001623	5_prime_UTR_variant	340527	exon6			TTCCCAAGTCTCA			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.-84A>G	X.37:g.71358413A>G		120	0	0		181	108	0.596685	NM_001013627	B2RN94	Missense_Mutation	SNP	ENST00000373677.1	37		.	.	.	.	.	.	.	.	.	.	A	10.15	1.271688	0.23221	.	.	ENSG00000204131	ENST00000540800;ENST00000510661	T;T	0.47177	1.45;0.85	5.79	4.63	0.57726	.	.	.	.	.	T	0.33527	0.0866	L	0.29908	0.895	0.58432	D	0.999999	B;B	0.15473	0.013;0.013	B;B	0.19391	0.025;0.025	T	0.07790	-1.0754	8	.	.	.	.	9.1966	0.37231	0.9136:0.0:0.0864:0.0	.	339;108	F5H593;D6RBM4	.;.	G	339;108	ENSP00000444617:S339G;ENSP00000424079:S108G	.	S	+	1	0	NHSL2	71275138	0.343000	0.24818	0.981000	0.43875	0.226000	0.24999	1.445000	0.35079	0.806000	0.34183	-0.334000	0.08254	AGT	.	.	none		0.582	NHSL2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057170.1	NM_001013627		G	71358413	A	G	71358413	1	3	7	0	1	0	0	0	0	0	0	0	10421	72	3	3		3	NHSL2	23	71358413	5'UTR	SNP	A	TCGA-FA-A7Q1-01A-11D-A382-10	22520770	71358413	83912147	157	834											
ATRX	546	hgsc.bcm.edu	37	chrX	76845412	76845413	+	Splice_Site	INS	-	-	A																															gactggctgaaaacaaggctINSaaaaaaacagattagtgttt																										TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chrX:76845412_76845413insA	ENST00000373344.5	-	27	6325		c.e27-2		ATRX_ENST00000480283.1_Splice_Site|ATRX_ENST00000395603.3_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						AAAACAAGGCTAAAAAAACAGA	0.332			"Mis, F, N"		"Pancreatic neuroendocrine tumors, paediatric GBM"		ATR-X (alpha thalassemia/mental retardation) syndrome																														.		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.6111-2->T						PASS	.																																			SO:0001630	splice_region_variant	546	exon28			.	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.6111-2->T	X.37:g.76845419_76845419dupA		274	0	0		386	66	0.170984	NM_000489	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Splice_Site	INS	ENST00000373344.5	37	CCDS14434.1																																																																																			.	.	none		0.332	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489	Intron	A	76845413	-	A	76845412	8	5	7	1	0	1	1	0	0	0	1	0	1208	1536	53	0	1405	0	ATRX	23	76845412	Splice_Site	INS	-	TCGA-FA-A7Q1-01A-11D-A382-10	5486999	76845412	78425148	158	835											
TRPC5	7224	hgsc.bcm.edu	37	chrX	111090430	111090430	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggtttcataatagaagtaaaGctggttcagtccattggcaa	13	12	10	6	0	2	1	2	0	0	1	3	1	3	1	1	3	1	5	1	3	6	6			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chrX:111090430G>T	ENST00000262839.2	-	6	2530	c.1612C>A	c.(1612-1614)Ctt>Att	p.L538I		NM_012471.2	NP_036603.1	Q9UL62	TRPC5_HUMAN	transient receptor potential cation channel, subfamily C, member 5	538					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						TAGAAGTAAAGCTGGTTCAGT	0.453																																					p.L538I		Atlas-SNP	.											.	TRPC5	142	.	0			c.C1612A						PASS	.						153	132	139					X																	111090430		2203	4300	6503	SO:0001583	missense	7224	exon6			AGTAAAGCTGGTT	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.1612C>A	X.37:g.111090430G>T	ENSP00000262839:p.Leu538Ile	177	0	0		216	56	0.259259	NM_012471	B2RP53|O75233|Q5JXY8|Q9Y514	Missense_Mutation	SNP	ENST00000262839.2	37	CCDS14561.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.843698	0.91197	.	.	ENSG00000072315	ENST00000262839	D	0.99080	-5.4	5.16	5.16	0.70880	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99140	0.9703	M	0.73217	2.22	0.80722	D	1	D;D	0.89917	0.993;1.0	D;D	0.79784	0.971;0.993	D	0.99818	1.1045	10	0.49607	T	0.09	-5.426	17.8405	0.88714	0.0:0.0:1.0:0.0	.	539;538	Q59G51;Q9UL62	.;TRPC5_HUMAN	I	538	ENSP00000262839:L538I	ENSP00000262839:L538I	L	-	1	0	TRPC5	110977086	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.814000	0.99346	2.145000	0.66743	0.436000	0.28706	CTT	.	.	none		0.453	TRPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057945.1	NM_012471		T	111090430	G	T	111090430	3	4	7	1	0	0	0	0	1	0	0	0	16597	971	34	4	1333	4	TRPC5	23	111090430	Missense_Mutation	SNP	G	TCGA-FA-A7Q1-01A-11D-A382-10	34245018	111090430	44180130	159	836											
MAP7D3	79649	hgsc.bcm.edu	37	chrX	135301796	135301796	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcatccgcctttctggtttTcgttgtgtgactggtcattc	3	19	9	10	2	3	1	2	1	1	0	6	1	4	1	2	2	0	2	2	2	0	6			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chrX:135301796T>C	ENST00000316077.9	-	17	2741	c.2521A>G	c.(2521-2523)Aaa>Gaa	p.K841E	MAP7D3_ENST00000370663.5_Missense_Mutation_p.K823E|MAP7D3_ENST00000370661.1_Missense_Mutation_p.K806E|MAP7D3_ENST00000495432.1_5'Flank	NM_024597.3	NP_078873.2	Q8IWC1	MA7D3_HUMAN	MAP7 domain containing 3	841					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)					TTTCTGGTTTTCGTTGTGTGA	0.433																																					p.K841E		Atlas-SNP	.											.	MAP7D3	102	.	0			c.A2521G						PASS	.						241	220	227					X																	135301796		1964	4134	6098	SO:0001583	missense	79649	exon17			TGGTTTTCGTTGT	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.2521A>G	X.37:g.135301796T>C	ENSP00000318086:p.Lys841Glu	460	0	0		636	191	0.300314	NM_024597	A2A2J0|A6NCZ7|A6NHR4|B4DWD2|H7BY77|Q5JXI5|Q5JXI6|Q6P2S1|Q9H9M8	Missense_Mutation	SNP	ENST00000316077.9	37	CCDS44004.1	.	.	.	.	.	.	.	.	.	.	T	16.25	3.071604	0.55646	.	.	ENSG00000129680	ENST00000370661;ENST00000316077;ENST00000370663;ENST00000370660	T;T;T;T	0.23147	1.92;3.75;3.75;1.95	4.0	4.0	0.46444	.	.	.	.	.	T	0.33294	0.0858	L	0.27053	0.805	0.09310	N	1	D;D;D;D	0.64830	0.989;0.994;0.989;0.994	P;D;P;D	0.65773	0.868;0.938;0.868;0.938	T	0.07065	-1.0792	9	0.72032	D	0.01	-19.2007	8.4163	0.32672	0.0:0.0:0.0:1.0	.	823;800;841;806	B4DWD2;Q8IWC1-2;Q8IWC1;Q8IWC1-3	.;.;MA7D3_HUMAN;.	E	806;841;823;800	ENSP00000359695:K806E;ENSP00000318086:K841E;ENSP00000359697:K823E;ENSP00000359694:K800E	ENSP00000318086:K841E	K	-	1	0	MAP7D3	135129462	0.045000	0.20229	0.003000	0.11579	0.012000	0.07955	1.746000	0.38288	1.805000	0.52779	0.430000	0.28490	AAA	.	.	none		0.433	MAP7D3-001	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058487.2			C	135301796	T	C	135301796	3	2	7	1	0	0	0	0	1	0	0	0	9278	1792	62	3	117	3	MAP7D3	23	135301796	Missense_Mutation	SNP	T	TCGA-FA-A7Q1-01A-11D-A382-10	24211366	135301796	19968764	160	837											
FLNA	2316	hgsc.bcm.edu	37	chrX	153578209	153578209	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accagctcccgcattgctcgTgttcacgacgaactcagctg	8	9	9	15	4	2	0	2	0	0	0	4	2	3	0	2	0	4	5	2	0	1	2			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chrX:153578209T>A	ENST00000369850.3	-	46	7596	c.7360A>T	c.(7360-7362)Acg>Tcg	p.T2454S	FLNA_ENST00000422373.1_Missense_Mutation_p.T2446S|FLNA_ENST00000344736.4_Missense_Mutation_p.T2414S|FLNA_ENST00000369856.3_Missense_Mutation_p.T587S|FLNA_ENST00000498491.1_5'UTR|FLNA_ENST00000360319.4_Missense_Mutation_p.T2446S	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	2454					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)					GCATTGCTCGTGTTCACGACG	0.637											OREG0003592	type=REGULATORY REGION|Gene=FLNA|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.T2454S		Atlas-SNP	.											.	FLNA	373	.	0			c.A7360T						PASS	.						36	36	36					X																	153578209		2070	4180	6250	SO:0001583	missense	2316	exon46			TGCTCGTGTTCAC	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.7360A>T	X.37:g.153578209T>A	ENSP00000358866:p.Thr2454Ser	56	0	0	1756	72	15	0.208333	NM_001110556	E9KL45|Q5HY53|Q5HY55|Q8NF52	Missense_Mutation	SNP	ENST00000369850.3	37	CCDS48194.1	.	.	.	.	.	.	.	.	.	.	T	16.01	3.002443	0.54254	.	.	ENSG00000196924	ENST00000360319;ENST00000369852;ENST00000422373;ENST00000369850;ENST00000369856;ENST00000344736	D;D;D;D;D	0.85258	-1.96;-1.96;-1.96;-1.96;-1.96	5.32	5.32	0.75619	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.92440	0.7600	M	0.83483	2.645	0.45161	D	0.99817	D;D;D;D	0.89917	0.968;0.965;1.0;1.0	D;P;D;D	0.85130	0.96;0.607;0.997;0.997	D	0.93165	0.6561	10	0.59425	D	0.04	.	14.335	0.66584	0.0:0.0:0.0:1.0	.	587;2446;2454;2454	E9PHF0;P21333-2;P21333;E9KL45	.;.;FLNA_HUMAN;.	S	2446;2122;2446;2454;587;2414	ENSP00000353467:T2446S;ENSP00000416926:T2446S;ENSP00000358866:T2454S;ENSP00000358872:T587S;ENSP00000358863:T2414S	ENSP00000358863:T2414S	T	-	1	0	FLNA	153231403	1.000000	0.71417	0.987000	0.45799	0.272000	0.26649	7.996000	0.88334	1.764000	0.52075	0.350000	0.21858	ACG	.	.	none		0.637	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3			A	153578209	T	A	153578209	3	1	7	1	0	0	0	0	1	0	0	0	5941	1696	59	5	595	5	FLNA	23	153578209	Missense_Mutation	SNP	T	TCGA-FA-A7Q1-01A-11D-A382-10	18276413	153578209	1692351	161	838											
SPRY3	10251	hgsc.bcm.edu	37	chrX	155004002	155004002	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gtgggcgctgcaagtgcgtcCcctgcacagcagctcgccct	5	7	13	16	3	0	0	0	0	0	0	2	0	1	0	3	1	5	5	3	1	1	0			TCGA-FA-A7Q1-01A-11D-A382-10	TCGA-FA-A7Q1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9c377b8a-f2c6-4113-8515-8eb29e95690c	722874f7-34b9-4f67-8cf3-700ec8f4c50e	g.chrX:155004002C>A	ENST00000302805.2	+	2	900	c.469C>A	c.(469-471)Ccc>Acc	p.P157T		NM_005840.1	NP_005831.1	O43610	SPY3_HUMAN	sprouty homolog 3 (Drosophila)	157	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)					CAAGTGCGTCCCCTGCACAGC	0.592																																					p.P157T		Atlas-SNP	.											.	SPRY3	52	.	0			c.C469A						PASS	.						140	140	140					X																	155004002		2203	4296	6499	SO:0001583	missense	10251	exon2			TGCGTCCCCTGCA	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.469C>A	X.37:g.155004002C>A	ENSP00000302978:p.Pro157Thr	132	0	0		157	53	0.33758	NM_005840	A8K0H8	Missense_Mutation	SNP	ENST00000302805.2	37	CCDS14769.4	.	.	.	.	.	.	.	.	.	.	C	8.853	0.945004	0.18356	.	.	ENSG00000168939	ENST00000302805	T	0.62232	0.04	2.71	2.71	0.32032	.	0.323378	0.29034	N	0.013349	T	0.44993	0.1320	.	.	.	0.09310	N	1	B	0.26975	0.165	B	0.16722	0.016	T	0.38693	-0.9649	9	0.51188	T	0.08	-30.9202	7.1284	0.25486	0.0:0.7231:0.2769:0.0	.	157	O43610	SPY3_HUMAN	T	157	ENSP00000302978:P157T	ENSP00000302978:P157T	P	+	1	0	SPRY3	154657196	0.997000	0.39634	0.995000	0.50966	0.748000	0.42578	3.822000	0.55708	1.366000	0.46076	0.279000	0.19357	CCC	.	.	none		0.592	SPRY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058823.2	NM_005840		A	155004002	C	A	155004002	3	1	7	1	0	0	0	0	1	0	0	0	15122	623	22	4	471	4	SPRY3	23	155004002	Missense_Mutation	SNP	C	TCGA-FA-A7Q1-01A-11D-A382-10	1425793	155004002	266558	162	839											
ENO1	2023	hgsc.bcm.edu	37	chr1	8927286	8927286	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gacggcaagggacacccccaGaatggcgttcgcaccaaact	12	4	11	14	3	0	1	0	0	0	1	1	3	0	2	3	3	1	3	3	3	3	1			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr1:8927286G>C	ENST00000234590.4	-	6	453	c.334C>G	c.(334-336)Ctg>Gtg	p.L112V		NM_001428.3	NP_001419.1	P06733	ENOA_HUMAN	enolase 1, (alpha)	112	Required for repression of c-myc promoter activity.				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)		GACACCCCCAGAATGGCGTTC	0.547																																					p.L112V	Esophageal Squamous(21;302 608 19946 22210 33560)	Atlas-SNP	.											.	ENO1	38	.	0			c.C334G						PASS	.						84	88	87					1																	8927286		2203	4300	6503	SO:0001583	missense	2023	exon6			CCCCCAGAATGGC	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.334C>G	1.37:g.8927286G>C	ENSP00000234590:p.Leu112Val	72	0	0		69	12	0.173913	NM_001428	B2RD59|P22712|Q16704|Q4TUS4|Q53FT9|Q53HR3|Q658M5|Q6GMP2|Q71V37|Q7Z3V6|Q8WU71|Q96GV1|Q9BT62|Q9UCH6|Q9UM55	Missense_Mutation	SNP	ENST00000234590.4	37	CCDS97.1	.	.	.	.	.	.	.	.	.	.	G	18.72	3.685277	0.68157	.	.	ENSG00000074800	ENST00000234590	T	0.36157	1.27	5.5	1.51	0.23008	Enolase, N-terminal (1);	0.000000	0.64402	D	0.000001	T	0.57607	0.2065	M	0.85859	2.78	0.39404	D	0.966647	D;D;D	0.64830	0.994;0.974;0.989	D;P;P	0.68353	0.957;0.842;0.902	T	0.63056	-0.6722	10	0.87932	D	0	-10.1455	9.0472	0.36354	0.4206:0.0:0.5794:0.0	.	79;19;112	A4UCS8;P06733-2;P06733	.;.;ENOA_HUMAN	V	112	ENSP00000234590:L112V	ENSP00000234590:L112V	L	-	1	2	ENO1	8849873	1.000000	0.71417	0.995000	0.50966	0.731000	0.41821	2.308000	0.43690	0.687000	0.31509	0.655000	0.94253	CTG	.	.	none		0.547	ENO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004945.1	NM_001428		C	8927286	G	C	8927286	3	2	8	1	0	0	0	0	1	0	0	0	5123	933	33	4	998	4	ENO1	1	8927286	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10		8927286	240323335	1	840											
HSPG2	3339	hgsc.bcm.edu	37	chr1	22181135	22181135	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggcaggctaccccctcgcCtgtaccaggtgacctgggca	7	6	13	15	1	0	1	0	1	0	0	1	2	0	1	5	4	2	4	5	4	2	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr1:22181135C>G	ENST00000374695.3	-	49	6336	c.6257G>C	c.(6256-6258)aGg>aCg	p.R2086T	HSPG2_ENST00000430507.1_Missense_Mutation_p.R36T	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2086	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)	ACCCCCTCGCCTGTACCAGGT	0.642																																					p.R2086T		Atlas-SNP	.											.	HSPG2	311	.	0			c.G6257C						PASS	.						33	33	33					1																	22181135		2199	4293	6492	SO:0001583	missense	3339	exon49			CCTCGCCTGTACC	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.6257G>C	1.37:g.22181135C>G	ENSP00000363827:p.Arg2086Thr	64	0	0		58	24	0.413793	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	C	13.93	2.383625	0.42207	.	.	ENSG00000142798	ENST00000374695;ENST00000430507	T;T	0.17854	2.25;2.25	5.54	-0.126	0.13515	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.398345	0.17595	N	0.168617	T	0.32734	0.0839	M	0.87900	2.915	0.23215	N	0.998107	P;B	0.45044	0.849;0.324	P;B	0.54174	0.744;0.174	T	0.11324	-1.0592	10	0.66056	D	0.02	.	5.4421	0.16515	0.1437:0.44:0.0:0.4163	.	26;2086	Q59EG0;P98160	.;PGBM_HUMAN	T	2086;36	ENSP00000363827:R2086T;ENSP00000416385:R36T	ENSP00000363827:R2086T	R	-	2	0	HSPG2	22053722	0.848000	0.29623	0.999000	0.59377	0.821000	0.46438	-0.049000	0.11924	0.050000	0.15949	0.561000	0.74099	AGG	.	.	none		0.642	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		G	22181135	C	G	22181135	3	3	8	1	0	0	0	0	1	0	0	0	7439	681	24	4	7114	4	HSPG2	1	22181135	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	13253849	22181135	227069486	2	841											
HSPG2	3339	hgsc.bcm.edu	37	chr1	22181246	22181246	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caatcttgaccggcggtgggCtggcatctgaggctggggcc	5	8	17	11	2	2	2	0	2	2	0	2	2	2	2	2	7	0	3	2	7	1	1			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr1:22181246C>T	ENST00000374695.3	-	49	6225	c.6146G>A	c.(6145-6147)aGc>aAc	p.S2049N	HSPG2_ENST00000430507.1_5'UTR	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2049	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)	CGGCGGTGGGCTGGCATCTGA	0.632																																					p.S2049N		Atlas-SNP	.											.	HSPG2	311	.	0			c.G6146A						PASS	.						41	45	43					1																	22181246		2202	4299	6501	SO:0001583	missense	3339	exon49			GGTGGGCTGGCAT	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.6146G>A	1.37:g.22181246C>T	ENSP00000363827:p.Ser2049Asn	112	0	0		80	33	0.4125	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	C	0.254	-1.004055	0.02112	.	.	ENSG00000142798	ENST00000374695	T	0.76448	-1.02	5.24	-0.118	0.13547	Immunoglobulin-like fold (1);	3.019920	0.01284	N	0.009819	T	0.65790	0.2725	L	0.41492	1.28	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.30822	-0.9965	10	0.19590	T	0.45	.	1.3651	0.02200	0.1379:0.3557:0.2686:0.2378	.	2049	P98160	PGBM_HUMAN	N	2049	ENSP00000363827:S2049N	ENSP00000363827:S2049N	S	-	2	0	HSPG2	22053833	0.620000	0.27068	0.004000	0.12327	0.010000	0.07245	0.119000	0.15626	0.023000	0.15187	0.561000	0.74099	AGC	.	.	none		0.632	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		T	22181246	C	T	22181246	3	4	8	1	0	0	0	0	1	0	0	0	7439	797	28	2	7225	2	HSPG2	1	22181246	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	111	22181246	227069375	3	842											
ZMYM4	9202	hgsc.bcm.edu	37	chr1	35885121	35885121	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gttttaccttcaacctgagcGctcctgtgtcccgaatagcc	7	12	8	14	2	1	1	1	1	0	0	3	2	3	1	5	0	4	2	5	0	4	4	rs142484548		TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr1:35885121G>A	ENST00000314607.6	+	30	4570	c.4490G>A	c.(4489-4491)cGc>cAc	p.R1497H	ZMYM4_ENST00000373297.2_Missense_Mutation_p.R1408H	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	1497					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)				CAACCTGAGCGCTCCTGTGTC	0.438													G|||	1	0.000199681	0.0	0.0	5008	,	,		18645	0.0		0.001	False		,,,				2504	0.0				p.R1497H		Atlas-SNP	.											.	ZMYM4	143	.	0			c.G4490A						PASS	.	G	HIS/ARG	0,4406		0,0,2203	116	114	115		4490	4.8	1	1	dbSNP_134	115	3,8597	3.0+/-9.4	0,3,4297	no	missense	ZMYM4	NM_005095.2	29	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging	1497/1549	35885121	3,13003	2203	4300	6503	SO:0001583	missense	9202	exon30			CTGAGCGCTCCTG	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.4490G>A	1.37:g.35885121G>A	ENSP00000322915:p.Arg1497His	102	0	0		89	28	0.314607	NM_005095	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Missense_Mutation	SNP	ENST00000314607.6	37	CCDS389.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	19.99	3.928681	0.73327	0.0	3.49E-4	ENSG00000146463	ENST00000314607;ENST00000373297	T;T	0.25749	1.78;1.8	5.82	4.85	0.62838	.	0.046961	0.85682	D	0.000000	T	0.48150	0.1484	M	0.68317	2.08	0.58432	D	0.999998	D	0.71674	0.998	D	0.75020	0.985	T	0.31223	-0.9951	10	0.39692	T	0.17	-7.0451	15.7205	0.77705	0.0:0.0:0.8628:0.1372	.	1497	Q5VZL5	ZMYM4_HUMAN	H	1497;1408	ENSP00000322915:R1497H;ENSP00000362394:R1408H	ENSP00000322915:R1497H	R	+	2	0	ZMYM4	35657708	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.988000	0.70579	2.752000	0.94435	0.655000	0.94253	CGC	G|1.000;A|0.000	0.000	strong		0.438	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095		A	35885121	G	A	35885121	3	1	8	1	0	0	0	0	1	0	0	0	17717	1087	38	1	4608	1	ZMYM4	1	35885121	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	13703875	35885121	213365500	4	843											
CCDC17	149483	hgsc.bcm.edu	37	chr1	46088711	46088711	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cggcctcagcttgtagttctCgaatctcctgctccaggccg	5	11	10	15	3	3	0	1	0	2	0	6	1	4	0	4	2	2	4	4	2	2	3			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr1:46088711C>T	ENST00000528266.1	-	4	719	c.572G>A	c.(571-573)cGa>cAa	p.R191Q	CCDC17_ENST00000445048.2_Intron|CCDC17_ENST00000464739.1_5'Flank|CCDC17_ENST00000343901.2_Missense_Mutation_p.R159Q|CCDC17_ENST00000421127.2_Missense_Mutation_p.R182Q			Q96LX7	CCD17_HUMAN	coiled-coil domain containing 17	191										kidney(1)|large_intestine(1)|lung(1)|ovary(2)	5	Acute lymphoblastic leukemia(166;0.155)					TTGTAGTTCTCGAATCTCCTG	0.657																																					p.R191Q		Atlas-SNP	.											.	CCDC17	54	.	0			c.G572A						PASS	.						25	29	28					1																	46088711		2203	4300	6503	SO:0001583	missense	149483	exon4			AGTTCTCGAATCT		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.572G>A	1.37:g.46088711C>T	ENSP00000432172:p.Arg191Gln	66	0	0		71	15	0.211268	NM_001114938	A1A4Y7|B4DNX7|B4E1Q5|C9J8L2|Q0P683|Q5T629	Missense_Mutation	SNP	ENST00000528266.1	37	CCDS44131.2	.	.	.	.	.	.	.	.	.	.	C	21.2	4.112474	0.77210	.	.	ENSG00000159588	ENST00000421127;ENST00000343901;ENST00000528266	T;T;T	0.18174	2.25;2.23;2.25	5.84	-1.26	0.09376	.	0.548550	0.16334	N	0.219002	T	0.15739	0.0379	L	0.29908	0.895	0.09310	N	1	D;B;B	0.76494	0.999;0.086;0.086	P;B;B	0.58660	0.843;0.014;0.014	T	0.21075	-1.0256	10	0.19147	T	0.46	-0.7778	3.7827	0.08687	0.4497:0.2992:0.0:0.2512	.	191;182;159	Q96LX7;Q96LX7-5;F2Z395	CCD17_HUMAN;.;.	Q	182;159;191	ENSP00000389415:R182Q;ENSP00000341451:R159Q;ENSP00000432172:R191Q	ENSP00000341451:R159Q	R	-	2	0	CCDC17	45861298	0.000000	0.05858	0.244000	0.24202	0.135000	0.20990	-0.186000	0.09670	0.080000	0.16959	0.561000	0.74099	CGA	.	.	none		0.657	CCDC17-008	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386833.1	NM_152500		T	46088711	C	T	46088711	3	4	8	1	0	0	0	0	1	0	0	0	2795	884	31	1	1336	1	CCDC17	1	46088711	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	10203590	46088711	203161910	5	844											
TTC24	164118	hgsc.bcm.edu	37	chr1	156551615	156551625	+	Frame_Shift_Del	DEL	GGGAGAAGCCT	GGGAGAAGCCT	-																															taccagccacagggtgaccaGggagaagcctgggcaaaaat																								rs576203714	byFrequency	TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	GGGAGAAGCCT	GGGAGAAGCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr1:156551615_156551625delGGGAGAAGCCT	ENST00000368237.3	+	1	459_469	c.459_469delGGGAGAAGCCT	c.(457-471)cagggagaagcctggfs	p.GEAW154fs	TTC24_ENST00000368236.3_Frame_Shift_Del_p.GEAW154fs			A2A3L6	TTC24_HUMAN	tetratricopeptide repeat domain 24	154										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)					AGGGTGACCAGGGAGAAGCCTGGGCAAAAAT	0.611																																					p.153_156del		Pindel,Atlas-Indel	.											.	TTC24	46	.	0			c.458_468del						PASS	.																																			SO:0001589	frameshift_variant	164118	exon2			.		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.459_469delGGGAGAAGCCT	1.37:g.156551615_156551625delGGGAGAAGCCT	ENSP00000357220:p.Gly154fs	87	0	.		69	13	0.188	NM_001105669	Q5T3H7	Frame_Shift_Del	DEL	ENST00000368237.3	37	CCDS53379.1																																																																																			.	.	none		0.611	TTC24-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158547.1	XM_089384		-	156551625	GGGAGAAGCCT	-	156551615	7	5	8	1	0	1	0	1	0	0	0	0	16707	991	35	0	461	0	TTC24	1	156551615	Frame_Shift_Del	DEL	GGGAGAAGCCT	TCGA-FA-A82F-01A-11D-A382-10	110462904	156551615	92699006	6	845											
FAM5C	339479	hgsc.bcm.edu	37	chr1	190423955	190423955	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccagcaatgaagactcagTgctatccactcccatagagc	13	7	7	14	0	1	3	1	1	0	2	3	3	3	3	3	0	3	2	3	0	4	2	rs190123682		TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr1:190423955T>C	ENST00000367462.3	-	2	297	c.66A>G	c.(64-66)gcA>gcG	p.A22A	BRINP3_ENST00000534846.1_5'UTR	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	22					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)											GAAGACTCAGTGCTATCCACT	0.512																																					p.A22A		Atlas-SNP	.											.	FAM5C	343	.	0			c.A66G						PASS	.						82	80	81					1																	190423955		2203	4300	6503	SO:0001819	synonymous_variant	339479	exon2			ACTCAGTGCTATC	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.66A>G	1.37:g.190423955T>C		100	0	0		94	29	0.308511	NM_199051	B3KVP1|B7Z260|O95726|Q2M330	Silent	SNP	ENST00000367462.3	37	CCDS1373.1																																																																																			T|0.999;G|0.001	.	alt		0.512	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		C	190423955	T	C	190423955	2	2	8	1	0	0	0	0	0	0	0	1	5602	1683	59	3		3	FAM5C	1	190423955	Silent	SNP	T	TCGA-FA-A82F-01A-11D-A382-10	33872340	190423955	58826666	7	846											
BTG2	7832	hgsc.bcm.edu	37	chr1	203274810	203274810	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctctccagcctcctgaggAcccggggctgcgtgagcgag	5	7	14	15	3	1	2	0	2	1	0	4	4	3	3	5	3	3	1	5	3	0	0			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr1:203274810A>C	ENST00000290551.4	+	1	147	c.76A>C	c.(76-78)Acc>Ccc	p.T26P	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	26					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			CCTCCTGAGGACCCGGGGCTG	0.706																																					p.T26P		Atlas-SNP	.											.	BTG2	16	.	0			c.A76C						PASS	.						16	16	16					1																	203274810		2168	4266	6434	SO:0001583	missense	7832	exon1			CTGAGGACCCGGG		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.76A>C	1.37:g.203274810A>C	ENSP00000290551:p.Thr26Pro	105	0	0		89	24	0.269663	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	A	16.48	3.135399	0.56828	.	.	ENSG00000159388	ENST00000290551	T	0.23950	1.88	4.66	4.66	0.58398	Anti-proliferative protein (3);	0.279124	0.30085	N	0.010460	T	0.34193	0.0889	M	0.79805	2.47	0.42075	D	0.991229	B	0.30193	0.272	B	0.32724	0.151	T	0.26744	-1.0094	10	0.48119	T	0.1	-24.6279	13.0384	0.58885	1.0:0.0:0.0:0.0	.	26	P78543	BTG2_HUMAN	P	26	ENSP00000290551:T26P	ENSP00000290551:T26P	T	+	1	0	BTG2	201541433	1.000000	0.71417	0.988000	0.46212	0.822000	0.46500	5.957000	0.70323	1.962000	0.57031	0.391000	0.25812	ACC	.	.	none		0.706	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		C	203274810	A	C	203274810	3	2	8	1	0	0	0	0	1	0	0	0	1556	275	10	5	78	5	BTG2	1	203274810	Missense_Mutation	SNP	A	TCGA-FA-A82F-01A-11D-A382-10	12850855	203274810	45975811	8	847			1	8		4	3	1431	N	G_AA_A	2.648692e-05
BTG2	7832	hgsc.bcm.edu	37	chr1	203274836	203274836	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggctgcgtgagcgagcagagGcttaaggtcttcagcggggc	7	7	18	9	3	2	2	1	1	1	1	2	3	2	2	0	5	4	3	0	5	1	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr1:203274836G>C	ENST00000290551.4	+	1	173	c.102G>C	c.(100-102)agG>agC	p.R34S	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	34					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			GCGAGCAGAGGCTTAAGGTCT	0.716																																					p.R34S		Atlas-SNP	.											.	BTG2	16	.	0			c.G102C						PASS	.						15	16	15					1																	203274836		2144	4202	6346	SO:0001583	missense	7832	exon1			GCAGAGGCTTAAG		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.102G>C	1.37:g.203274836G>C	ENSP00000290551:p.Arg34Ser	103	0	0		72	17	0.236111	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	G	17.51	3.406597	0.62399	.	.	ENSG00000159388	ENST00000290551	T	0.22743	1.94	4.66	-6.66	0.01789	Anti-proliferative protein (3);	0.165673	0.37761	N	0.001941	T	0.18551	0.0445	L	0.48362	1.52	0.38784	D	0.954828	P	0.38922	0.651	B	0.40329	0.326	T	0.03852	-1.0998	10	0.66056	D	0.02	-8.3253	16.012	0.80409	0.156:0.0:0.844:0.0	.	34	P78543	BTG2_HUMAN	S	34	ENSP00000290551:R34S	ENSP00000290551:R34S	R	+	3	2	BTG2	201541459	0.998000	0.40836	0.005000	0.12908	0.842000	0.47809	0.428000	0.21395	-1.534000	0.01743	-0.362000	0.07510	AGG	.	.	none		0.716	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		C	203274836	G	C	203274836	3	2	8	1	0	0	0	0	1	0	0	0	1556	1194	42	4	104	4	BTG2	1	203274836	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	26	203274836	45975785	9	848			1	8		4	3	1431	N	G_AA_A	2.648692e-05
BTG2	7832	hgsc.bcm.edu	37	chr1	203276238	203276238	+	Missense_Mutation	SNP	A	A	G																															tcctgtctccacagagcactAcaaacaccactggtttcccg																										TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr1:203276238A>G	ENST00000290551.4	+	2	220	c.149A>G	c.(148-150)tAc>tGc	p.Y50C	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	50					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			ACAGAGCACTACAAACACCAC	0.597																																					p.Y50C		Atlas-SNP	.											.	BTG2	16	.	0			c.A149G						PASS	.						39	41	40					1																	203276238		2203	4300	6503	SO:0001583	missense	7832	exon2			AGCACTACAAACA		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.149A>G	1.37:g.203276238A>G	ENSP00000290551:p.Tyr50Cys	75	0	0		51	9	0.176471	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.953961	0.73902	.	.	ENSG00000159388	ENST00000290551	T	0.34275	1.37	4.53	4.53	0.55603	Anti-proliferative protein (4);	0.000000	0.64402	D	0.000003	T	0.63733	0.2536	M	0.87269	2.87	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	T	0.71062	-0.4701	10	0.87932	D	0	-11.3369	12.8211	0.57694	1.0:0.0:0.0:0.0	.	50	P78543	BTG2_HUMAN	C	50	ENSP00000290551:Y50C	ENSP00000290551:Y50C	Y	+	2	0	BTG2	201542861	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	8.727000	0.91480	1.911000	0.55334	0.260000	0.18958	TAC	.	.	none		0.597	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		G	203276238	A	G	203276238	3	3	8	1	0	0	0	0	1	0	0	0	1556	391	14	3	155	3	BTG2	1	203276238	Missense_Mutation	SNP	A	TCGA-FA-A82F-01A-11D-A382-10	1402	203276238	45974383	10	849	15	2	1	8		4	3	1431	N	G_AA_A	2.648692e-05
BTG2	7832	hgsc.bcm.edu	37	chr1	203276240	203276241	+	Frame_Shift_Del	DEL	AA	AA	-																															ctgtctccacagagcactacAaacaccactggtttcccgaa																										TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr1:203276240_203276241delAA	ENST00000290551.4	+	2	222_223	c.151_152delAA	c.(151-153)aaafs	p.K51fs	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	51					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			AGAGCACTACAAACACCACTGG	0.594																																					p.50_51del		Atlas-Indel	.											.	BTG2	16	.	0			c.150_151del						PASS	.																																			SO:0001589	frameshift_variant	7832	exon2			.		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.151_152delAA	1.37:g.203276240_203276241delAA	ENSP00000290551:p.Lys51fs	76	0	0		52	10	0.192308	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Frame_Shift_Del	DEL	ENST00000290551.4	37	CCDS1437.1																																																																																			.	.	none		0.594	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		-	203276241	AA	-	203276240	7	5	8	1	0	1	0	1	0	0	0	0	1556	131	5	0	157	0	BTG2	1	203276240	Frame_Shift_Del	DEL	AA	TCGA-FA-A82F-01A-11D-A382-10	2	203276240	45974381	11	850	15	2	1	8		4	3	1431	N	G_AA_A	2.648692e-05
TMEM206	55248	hgsc.bcm.edu	37	chr1	212558714	212558714	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgtcagaggaggaatgacctCgtaatggtgcttacagctga	11	10	13	7	1	1	3	1	2	0	1	2	5	1	5	1	3	3	3	1	3	3	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr1:212558714C>T	ENST00000261455.4	-	4	534	c.397G>A	c.(397-399)Gag>Aag	p.E133K	TMEM206_ENST00000471937.1_5'UTR|TMEM206_ENST00000535273.1_Missense_Mutation_p.E194K	NM_018252.2	NP_060722.2	Q9H813	TM206_HUMAN	transmembrane protein 206	133						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)		GGAATGACCTCGTAATGGTGC	0.542																																					p.E194K		Atlas-SNP	.											.	TMEM206	41	.	0			c.G580A						PASS	.						123	114	117					1																	212558714		2203	4300	6503	SO:0001583	missense	55248	exon5			TGACCTCGTAATG	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.397G>A	1.37:g.212558714C>T	ENSP00000261455:p.Glu133Lys	130	0	0		97	29	0.298969	NM_001198862	B7Z4D6|Q6IA87|Q9NV85	Missense_Mutation	SNP	ENST00000261455.4	37	CCDS1504.1	.	.	.	.	.	.	.	.	.	.	C	18.99	3.739315	0.69304	.	.	ENSG00000065600	ENST00000261455;ENST00000535273	.	.	.	5.43	4.52	0.55395	.	0.094468	0.64402	D	0.000001	T	0.25975	0.0633	N	0.14661	0.345	0.37847	D	0.929241	B;P	0.49253	0.017;0.921	B;B	0.30251	0.004;0.113	T	0.30679	-0.9970	9	0.62326	D	0.03	-12.0706	14.0882	0.64973	0.0:0.9274:0.0:0.0725	.	194;133	B7Z4D6;Q9H813	.;TM206_HUMAN	K	133;194	.	ENSP00000261455:E133K	E	-	1	0	TMEM206	210625337	1.000000	0.71417	0.906000	0.35671	0.978000	0.69477	3.406000	0.52637	1.284000	0.44531	0.655000	0.94253	GAG	.	.	none		0.542	TMEM206-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089306.1	NM_018252		T	212558714	C	T	212558714	3	4	8	1	0	0	0	0	1	0	0	0	16146	893	31	1	675	1	TMEM206	1	212558714	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	9282474	212558714	36691907	12	851											
ESRRG	2104	hgsc.bcm.edu	37	chr1	216680465	216680465	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagcttcataatcctgcagcGcttcatgtaagacatcctga	11	11	7	12	1	2	2	2	1	0	1	4	2	4	2	2	0	3	4	2	0	2	4			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr1:216680465G>T	ENST00000408911.3	-	7	1346	c.1193C>A	c.(1192-1194)gCg>gAg	p.A398E	ESRRG_ENST00000360012.3_Missense_Mutation_p.A375E|ESRRG_ENST00000366938.2_Missense_Mutation_p.A375E|ESRRG_ENST00000361395.2_Missense_Mutation_p.A375E|ESRRG_ENST00000366940.2_Missense_Mutation_p.A375E|ESRRG_ENST00000359162.2_Missense_Mutation_p.A375E|ESRRG_ENST00000487276.1_Missense_Mutation_p.A375E|ESRRG_ENST00000361525.3_Missense_Mutation_p.A375E|ESRRG_ENST00000366937.1_Missense_Mutation_p.A410E|ESRRG_ENST00000391890.3_Missense_Mutation_p.A382E|ESRRG_ENST00000463665.1_Missense_Mutation_p.A336E|ESRRG_ENST00000493603.1_Missense_Mutation_p.A375E|ESRRG_ENST00000493748.1_Missense_Mutation_p.A375E	NM_001438.3	NP_001429.2	P62508	ERR3_HUMAN	estrogen-related receptor gamma	398					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)	ATCCTGCAGCGCTTCATGTAA	0.473																																					p.A410E		Atlas-SNP	.											.	ESRRG	111	.	0			c.C1229A						PASS	.						108	97	100					1																	216680465		2203	4300	6503	SO:0001583	missense	2104	exon8			TGCAGCGCTTCAT	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.1193C>A	1.37:g.216680465G>T	ENSP00000386171:p.Ala398Glu	226	0	0		171	52	0.304094	NM_001243518	A8K4I0|A8K6I2|B3KY84|E9PGB7|F8W8J3|O75454|O96021|Q68DA0|Q6P274|Q6PK28|Q6TS38|Q9R1F3|Q9UNJ4	Missense_Mutation	SNP	ENST00000408911.3	37	CCDS41468.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.493119	0.84962	.	.	ENSG00000196482	ENST00000361525;ENST00000366940;ENST00000366937;ENST00000408911;ENST00000359162;ENST00000361395;ENST00000366938;ENST00000360012;ENST00000493603;ENST00000391890;ENST00000463665;ENST00000487276;ENST00000354407;ENST00000493748	D;D;D;D;D;D;D;D;D;D;D;D;D	0.96554	-4.05;-4.05;-4.05;-4.05;-4.05;-4.05;-4.05;-4.05;-4.05;-4.05;-4.05;-4.05;-4.05	5.61	5.61	0.85477	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	H	0.96015	3.755	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	0.99391	1.0925	10	0.87932	D	0	.	19.652	0.95819	0.0:0.0:1.0:0.0	.	336;410;398	E9PGB7;F8W8J3;P62508	.;.;ERR3_HUMAN	E	375;375;410;398;375;375;375;375;375;382;336;375;375;375	ENSP00000355225:A375E;ENSP00000355907:A375E;ENSP00000355904:A410E;ENSP00000386171:A398E;ENSP00000352077:A375E;ENSP00000354584:A375E;ENSP00000355905:A375E;ENSP00000353108:A375E;ENSP00000419594:A375E;ENSP00000375761:A382E;ENSP00000418629:A336E;ENSP00000419155:A375E;ENSP00000417374:A375E	ENSP00000346386:A375E	A	-	2	0	ESRRG	214747088	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.869000	0.99810	2.656000	0.90262	0.561000	0.74099	GCG	.	.	none		0.473	ESRRG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089882.2	NM_206595		T	216680465	G	T	216680465	3	4	8	1	0	0	0	0	1	0	0	0	5264	1087	38	4	187	4	ESRRG	1	216680465	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	4121751	216680465	32570156	13	852											
EPHX1	2052	hgsc.bcm.edu	37	chr1	226016540	226016540	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agatgggtggtgggggccagGcacgaggtccgcagccaggg	7	4	21	9	2	0	1	0	0	0	1	1	2	1	1	3	7	1	2	3	7	0	0			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr1:226016540G>T	ENST00000366837.4	+	2	306	c.110G>T	c.(109-111)gGc>gTc	p.G37V	EPHX1_ENST00000272167.5_Missense_Mutation_p.G37V	NM_000120.3	NP_000111.1	P07099	HYEP_HUMAN	epoxide hydrolase 1, microsomal (xenobiotic)	37					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)					TGGGGGCCAGGCACGAGGTCC	0.592																																					p.G37V		Atlas-SNP	.											.	EPHX1	57	.	0			c.G110T						PASS	.						45	41	43					1																	226016540		2203	4300	6503	SO:0001583	missense	2052	exon2			GGCCAGGCACGAG	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.110G>T	1.37:g.226016540G>T	ENSP00000355802:p.Gly37Val	116	0	0		109	29	0.266055	NM_001136018	B2R8N0|Q5VTJ6|Q9NP75|Q9NPE7|Q9NQU6|Q9NQU7|Q9NQU8|Q9NQU9|Q9NQV0|Q9NQV1|Q9NQV2	Missense_Mutation	SNP	ENST00000366837.4	37	CCDS1547.1	.	.	.	.	.	.	.	.	.	.	G	16.03	3.006109	0.54361	.	.	ENSG00000143819	ENST00000445856;ENST00000272167;ENST00000448202;ENST00000366837	T;T;T;T	0.19250	2.47;3.52;2.16;3.52	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.50051	0.1593	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.55623	-0.8112	10	0.72032	D	0.01	-4.5382	18.2926	0.90135	0.0:0.0:1.0:0.0	.	37	P07099	HYEP_HUMAN	V	37	ENSP00000398491:G37V;ENSP00000272167:G37V;ENSP00000408469:G37V;ENSP00000355802:G37V	ENSP00000272167:G37V	G	+	2	0	EPHX1	224083163	1.000000	0.71417	0.058000	0.19502	0.009000	0.06853	9.481000	0.97933	2.316000	0.78162	0.462000	0.41574	GGC	.	.	none		0.592	EPHX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092064.1	NM_000120		T	226016540	G	T	226016540	3	4	8	1	0	0	0	0	1	0	0	0	5181	1203	42	4	112	4	EPHX1	1	226016540	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	9336075	226016540	23234081	14	853											
TRIM11	81559	hgsc.bcm.edu	37	chr1	228594049	228594049	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgccatctcggccatcttagCaagcgggcggttgggccgca	6	7	14	14	5	2	0	0	0	2	0	3	0	2	0	3	4	2	3	3	4	2	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr1:228594049C>T	ENST00000284551.6	-	1	492	c.214G>A	c.(214-216)Gct>Act	p.A72T	RP11-245P10.4_ENST00000436779.1_RNA|TRIM11_ENST00000493030.2_5'Flank|TRIM11_ENST00000366699.3_Missense_Mutation_p.A72T	NM_145214.2	NP_660215.1	Q96F44	TRI11_HUMAN	tripartite motif containing 11	72					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)				GCCATCTTAGCAAGCGGGCGG	0.761																																					p.A72T		Atlas-SNP	.											.	TRIM11	38	.	0			c.G214A						PASS	.						4	5	5					1																	228594049		1955	3850	5805	SO:0001583	missense	81559	exon1			TCTTAGCAAGCGG	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.214G>A	1.37:g.228594049C>T	ENSP00000284551:p.Ala72Thr	39	0	0		29	10	0.344828	NM_145214	A6NKE2|B2RB82|B3KUS3|B4DX88|Q5VSU1|Q8NCA6|Q9C022	Missense_Mutation	SNP	ENST00000284551.6	37	CCDS31048.1	.	.	.	.	.	.	.	.	.	.	C	15.47	2.843037	0.51057	.	.	ENSG00000154370	ENST00000284551;ENST00000366699	T;T	0.17528	2.27;2.27	4.73	2.76	0.32466	Zinc finger, RING/FYVE/PHD-type (1);	0.000000	0.39475	N	0.001359	T	0.16685	0.0401	L	0.52206	1.635	0.24507	N	0.994226	B;B;B	0.34313	0.01;0.448;0.002	B;B;B	0.41374	0.04;0.355;0.005	T	0.13019	-1.0525	10	0.40728	T	0.16	.	3.8353	0.08891	0.1669:0.5793:0.1621:0.0917	.	72;72;72	Q96F44-3;Q96F44-2;Q96F44	.;.;TRI11_HUMAN	T	72	ENSP00000284551:A72T;ENSP00000355660:A72T	ENSP00000284551:A72T	A	-	1	0	TRIM11	226660672	0.000000	0.05858	0.962000	0.40283	0.979000	0.70002	-0.146000	0.10250	0.476000	0.27440	0.491000	0.48974	GCT	.	.	none		0.761	TRIM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095995.3	NM_145214		T	228594049	C	T	228594049	3	4	8	1	0	0	0	0	1	0	0	0	16502	710	25	2	1216	2	TRIM11	1	228594049	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	2577509	228594049	20656572	15	854											
NID1	4811	hgsc.bcm.edu	37	chr1	236156994	236156994	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgccctccacctcgcggccGtcgcgatccacgcaccagca	6	5	10	20	6	0	0	0	0	0	0	4	1	2	0	6	1	2	2	6	1	0	0			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr1:236156994G>A	ENST00000264187.6	-	13	2788	c.2706C>T	c.(2704-2706)gaC>gaT	p.D902D	NID1_ENST00000366595.3_Silent_p.D769D	NM_002508.2	NP_002499.2	P14543	NID1_HUMAN	nidogen 1	902	Thyroglobulin type-1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				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)	CCTCGCGGCCGTCGCGATCCA	0.701																																					p.D902D		Atlas-SNP	.											.	NID1	196	.	0			c.C2706T						PASS	.						20	20	20					1																	236156994		2199	4295	6494	SO:0001819	synonymous_variant	4811	exon13			GCGGCCGTCGCGA	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.2706C>T	1.37:g.236156994G>A		94	0	0		89	34	0.382022	NM_002508	Q14942|Q59FL2|Q5TAF2|Q5TAF3|Q86XD7	Silent	SNP	ENST00000264187.6	37	CCDS1608.1																																																																																			.	.	none		0.701	NID1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096647.2	NM_002508		A	236156994	G	A	236156994	2	1	8	1	0	0	0	0	0	0	0	1	10423	1136	40	1		1	NID1	1	236156994	Silent	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	7562945	236156994	13093627	16	855											
GFPT1	2673	hgsc.bcm.edu	37	chr2	69565092	69565092	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aactccacaatctgtctcccGtgatatggaactgccaactg	11	10	7	13	1	2	1	0	1	2	0	4	2	3	2	3	1	4	0	3	1	5	1			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr2:69565092G>A	ENST00000357308.4	-	15	1598	c.1420C>T	c.(1420-1422)Cgg>Tgg	p.R474W	GFPT1_ENST00000361060.5_Missense_Mutation_p.R456W	NM_001244710.1	NP_001231639.1	Q06210	GFPT1_HUMAN	glutamine--fructose-6-phosphate transaminase 1	474	Isomerase.|SIS 1. {ECO:0000255|PROSITE- ProRule:PRU00797}.				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						TCTGTCTCCCGTGATATGGAA	0.428																																					p.R474W		Atlas-SNP	.											.	GFPT1	38	.	0			c.C1420T						PASS	.						258	219	232					2																	69565092		2203	4300	6503	SO:0001583	missense	2673	exon15			TCTCCCGTGATAT		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.1420C>T	2.37:g.69565092G>A	ENSP00000349860:p.Arg474Trp	144	0	0		100	32	0.32	NM_001244710	Q53QE6|Q9BXF8	Missense_Mutation	SNP	ENST00000357308.4	37	CCDS58713.1	.	.	.	.	.	.	.	.	.	.	G	15.38	2.816702	0.50633	.	.	ENSG00000198380	ENST00000357308;ENST00000361060	T;T	0.68624	-0.34;-0.34	5.43	-4.24	0.03777	.	0.000000	0.85682	D	0.000000	T	0.77391	0.4123	H	0.99011	4.4	0.80722	D	1	B	0.24768	0.111	B	0.24155	0.051	T	0.73905	-0.3835	10	0.87932	D	0	-16.2206	15.5538	0.76173	0.0937:0.0:0.7207:0.1856	.	456	Q06210-2	.	W	474;456	ENSP00000349860:R474W;ENSP00000354347:R456W	ENSP00000349860:R474W	R	-	1	2	GFPT1	69418596	0.827000	0.29292	0.471000	0.27229	0.985000	0.73830	0.479000	0.22228	-0.841000	0.04200	-0.266000	0.10368	CGG	.	.	none		0.428	GFPT1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				A	69565092	G	A	69565092	3	1	8	1	0	0	0	0	1	0	0	0	6353	1144	40	1	703	1	GFPT1	2	69565092	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10		69565092	173634281	17	856											
LRRTM1	347730	hgsc.bcm.edu	37	chr2	80529497	80529497	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtagtattcctgggcagacAtggcagccatctgatgcatg	9	10	12	10	1	1	2	0	1	1	1	2	2	2	2	2	2	2	5	2	2	2	3			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr2:80529497A>G	ENST00000295057.3	-	2	2104	c.1448T>C	c.(1447-1449)aTg>aCg	p.M483T	CTNNA2_ENST00000540488.1_Intron|CTNNA2_ENST00000361291.4_Intron|LRRTM1_ENST00000409148.1_Missense_Mutation_p.M483T|CTNNA2_ENST00000541047.1_Intron|CTNNA2_ENST00000402739.4_Intron|CTNNA2_ENST00000466387.1_Intron|CTNNA2_ENST00000496558.1_Intron	NM_178839.4	NP_849161.2	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	483					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						CTGGGCAGACATGGCAGCCAT	0.542										HNSCC(69;0.2)																											p.M483T		Atlas-SNP	.											.	LRRTM1	251	.	0			c.T1448C						PASS	.						146	119	128					2																	80529497		2203	4300	6503	SO:0001583	missense	347730	exon2			GCAGACATGGCAG	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.1448T>C	2.37:g.80529497A>G	ENSP00000295057:p.Met483Thr	123	0	0		103	23	0.223301	NM_178839	A8K397|D6W5K1|Q96DN1	Missense_Mutation	SNP	ENST00000295057.3	37	CCDS1966.1	.	.	.	.	.	.	.	.	.	.	A	5.771	0.326657	0.10900	.	.	ENSG00000162951	ENST00000295057;ENST00000409148	T;T	0.38722	1.12;1.12	5.18	5.18	0.71444	.	0.055879	0.64402	U	0.000001	T	0.21062	0.0507	N	0.03608	-0.345	0.46279	D	0.998961	B	0.12013	0.005	B	0.08055	0.003	T	0.09250	-1.0683	9	.	.	.	.	15.031	0.71708	1.0:0.0:0.0:0.0	.	483	Q86UE6	LRRT1_HUMAN	T	483	ENSP00000295057:M483T;ENSP00000386646:M483T	.	M	-	2	0	LRRTM1	80383008	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.349000	0.73013	1.930000	0.55929	0.459000	0.35465	ATG	.	.	none		0.542	LRRTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313614.1	NM_178839		G	80529497	A	G	80529497	3	3	8	1	0	0	0	0	1	0	0	0	9048	217	8	3	124	3	LRRTM1	2	80529497	Missense_Mutation	SNP	A	TCGA-FA-A82F-01A-11D-A382-10	10964405	80529497	162669876	18	857											
LONRF2	164832	hgsc.bcm.edu	37	chr2	100916227	100916227	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggtcaggtgcatcctccaCgtcatccggaaactgtctct	8	10	9	14	2	3	0	2	0	1	0	7	1	6	1	3	3	2	1	3	3	1	0	rs562655594		TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr2:100916227C>T	ENST00000393437.3	-	5	1858	c.1219G>A	c.(1219-1221)Gtg>Atg	p.V407M	LONRF2_ENST00000409647.1_Missense_Mutation_p.V164M	NM_198461.3	NP_940863.3	Q1L5Z9	LONF2_HUMAN	LON peptidase N-terminal domain and ring finger 2	407							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						GCATCCTCCACGTCATCCGGA	0.463													C|||	1	0.000199681	0.0	0.0	5008	,	,		12846	0.0		0.0	False		,,,				2504	0.001				p.V407M		Atlas-SNP	.											.	LONRF2	62	.	0			c.G1219A						PASS	.						93	91	92					2																	100916227		2203	4300	6503	SO:0001583	missense	164832	exon5			CCTCCACGTCATC	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.1219G>A	2.37:g.100916227C>T	ENSP00000377086:p.Val407Met	149	0	0		126	40	0.31746	NM_198461	B9A006|Q6ZSR4	Missense_Mutation	SNP	ENST00000393437.3	37	CCDS2046.2	.	.	.	.	.	.	.	.	.	.	C	8.636	0.894790	0.17613	.	.	ENSG00000170500	ENST00000393437;ENST00000409647	D;D	0.85171	-1.79;-1.95	4.49	0.225	0.15325	.	1.629190	0.04000	N	0.296277	T	0.70046	0.3179	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.55761	-0.8090	10	0.31617	T	0.26	0.8737	5.3436	0.15996	0.2827:0.3821:0.0:0.3351	.	407	Q1L5Z9	LONF2_HUMAN	M	407;164	ENSP00000377086:V407M;ENSP00000386823:V164M	ENSP00000377086:V407M	V	-	1	0	LONRF2	100282659	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.351000	0.07711	-0.152000	0.11156	-0.474000	0.04947	GTG	.	.	none		0.463	LONRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253161.2	NM_198461		T	100916227	C	T	100916227	3	4	8	1	0	0	0	0	1	0	0	0	8904	536	19	1	1077	1	LONRF2	2	100916227	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	20386730	100916227	142283146	19	858											
LRP1B	53353	hgsc.bcm.edu	37	chr2	141571231	141571231	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aataatttcacttacccatgAtggttagggctgtagctttt	10	16	8	7	0	1	1	1	1	0	0	1	1	1	1	1	2	2	4	1	2	5	7			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr2:141571231A>G	ENST00000389484.3	-	32	6325	c.5354T>C	c.(5353-5355)aTc>aCc	p.I1785T		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1785					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)		CTTACCCATGATGGTTAGGGC	0.368										TSP Lung(27;0.18)																											p.I1785T	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.T5354C						PASS	.						165	147	153					2																	141571231		2203	4300	6503	SO:0001583	missense	53353	exon32			CCCATGATGGTTA	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.5354T>C	2.37:g.141571231A>G	ENSP00000374135:p.Ile1785Thr	239	0	0		211	26	0.123223	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	A	17.98	3.520516	0.64747	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.91792	-2.91	5.83	5.83	0.93111	Six-bladed beta-propeller, TolB-like (1);	0.072198	0.56097	D	0.000037	D	0.90611	0.7056	M	0.72894	2.215	0.58432	D	0.999994	P	0.43094	0.799	B	0.35931	0.214	D	0.91189	0.4982	10	0.52906	T	0.07	.	16.1982	0.82046	1.0:0.0:0.0:0.0	.	1785	Q9NZR2	LRP1B_HUMAN	T	1785;1723	ENSP00000374135:I1785T	ENSP00000374135:I1785T	I	-	2	0	LRP1B	141287701	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.282000	0.95840	2.226000	0.72624	0.533000	0.62120	ATC	.	.	none		0.368	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		G	141571231	A	G	141571231	3	3	8	1	0	0	0	0	1	0	0	0	8964	333	12	3	8685	3	LRP1B	2	141571231	Missense_Mutation	SNP	A	TCGA-FA-A82F-01A-11D-A382-10	40655004	141571231	101628142	20	859											
ITGA4	3676	hgsc.bcm.edu	37	chr2	182346352	182346352	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agtcggagctggtcattttcGgagccagcatactaccgaag	10	9	12	10	3	1	0	1	0	0	0	3	3	1	2	2	3	5	2	2	3	3	4	rs148901650	byFrequency	TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr2:182346352G>A	ENST00000397033.2	+	7	1212	c.782G>A	c.(781-783)cGg>cAg	p.R261Q		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	261					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)	GGTCATTTTCGGAGCCAGCAT	0.383													g|||	4	0.000798722	0.0	0.0	5008	,	,		17178	0.003		0.0	False		,,,				2504	0.001				p.R261Q		Atlas-SNP	.											ITGA4,NS,carcinoma,+1,1	ITGA4	142	1	0			c.G782A						PASS	.						62	57	59					2																	182346352		1814	4083	5897	SO:0001583	missense	3676	exon7			ATTTTCGGAGCCA		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.782G>A	2.37:g.182346352G>A	ENSP00000380227:p.Arg261Gln	82	0	0		62	24	0.387097	NM_000885	D3DPG4|Q7Z4L6	Missense_Mutation	SNP	ENST00000397033.2	37	CCDS42788.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	g	10.52	1.373857	0.24857	.	.	ENSG00000115232	ENST00000425522;ENST00000397033;ENST00000233573	T;T	0.71341	-0.56;-0.56	5.54	2.49	0.30216	.	0.717535	0.13491	N	0.383966	T	0.51261	0.1664	N	0.21373	0.66	0.23972	N	0.996309	B;B	0.17852	0.007;0.024	B;B	0.06405	0.002;0.002	T	0.32745	-0.9895	10	0.28530	T	0.3	.	5.8849	0.18876	0.1841:0.0:0.5918:0.2241	.	261;261	E7EP60;P13612	.;ITA4_HUMAN	Q	261	ENSP00000380227:R261Q;ENSP00000233573:R261Q	ENSP00000233573:R261Q	R	+	2	0	ITGA4	182054597	0.655000	0.27376	0.213000	0.23690	0.293000	0.27360	1.099000	0.31013	0.630000	0.30394	-0.185000	0.12909	CGG	G|1.000;A|0.000	0.000	strong		0.383	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1			A	182346352	G	A	182346352	3	1	8	1	0	0	0	0	1	0	0	0	7887	1116	39	1	808	1	ITGA4	2	182346352	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	40775121	182346352	60853021	21	860											
STK36	64320	hgsc.bcm.edu	37	chr2	219538411	219538411	+	5'Flank	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggagctgaggaatttgcaaCgagagattgaaataatgcgg	15	8	14	4	2	0	3	0	2	0	1	0	7	0	5	0	3	4	2	0	3	4	3			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr2:219538411C>T	ENST00000295704.2	-	0	0				STK36_ENST00000392106.2_Nonsense_Mutation_p.R50*|STK36_ENST00000295709.3_Nonsense_Mutation_p.R50*|STK36_ENST00000440309.1_Nonsense_Mutation_p.R50*|STK36_ENST00000392105.3_Nonsense_Mutation_p.R50*	NM_022453.2	NP_071898.2	Q96BH1	RNF25_HUMAN	ring finger protein 25						positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|NF-kappaB binding (GO:0051059)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24		Renal(207;0.0474)		Epithelial(149;6.99e-07)|all cancers(144;0.000129)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GAATTTGCAACGAGAGATTGA	0.478																																					p.R50X		Atlas-SNP	.											.	STK36	111	.	0			c.C148T						PASS	.						81	78	79					2																	219538411		2203	4300	6503	SO:0001631	upstream_gene_variant	27148	exon3			TTGCAACGAGAGA		CCDS2420.1	2q35	2008-02-05			ENSG00000163481	ENSG00000163481		"RING-type (C3HC4) zinc fingers"	14662	protein-coding gene	gene with protein product						12748188	Standard	NM_022453		Approved	AO7, FLJ13906	uc002vit.3	Q96BH1	OTTHUMG00000133077		2.37:g.219538411C>T	Exception_encountered	111	0	0		97	41	0.42268	NM_015690	A8K0D6|Q53HQ5|Q9H874	Nonsense_Mutation	SNP	ENST00000295704.2	37	CCDS2420.1	.	.	.	.	.	.	.	.	.	.	C	37	6.227986	0.97394	.	.	ENSG00000163482	ENST00000295709;ENST00000392106;ENST00000392105;ENST00000440309;ENST00000424080	.	.	.	5.72	5.72	0.89469	.	0.000000	0.36444	N	0.002587	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.345	14.7034	0.69171	0.1448:0.8552:0.0:0.0	.	.	.	.	X	50	.	ENSP00000295709:R50X	R	+	1	2	STK36	219246655	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.931000	0.56529	2.717000	0.92951	0.655000	0.94253	CGA	.	.	none		0.478	RNF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256721.1	NM_022453		T	219538411	C	T	219538411	1	4	8	0	1	0	0	0	0	0	0	0	15317	528	19	1		1	STK36	2	219538411	5'Flank	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	37192059	219538411	23660962	22	861											
DES	1674	hgsc.bcm.edu	37	chr2	220283213	220283213	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcctactcgtccagccagcGcgtgtcctcctaccgccgca	5	7	10	19	5	0	0	0	0	0	0	4	0	3	0	7	1	4	1	7	1	2	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr2:220283213G>A	ENST00000373960.3	+	1	115	c.29G>A	c.(28-30)cGc>cAc	p.R10H		NM_001927.3	NP_001918.3	P17661	DESM_HUMAN	desmin	10	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)		TCCAGCCAGCGCGTGTCCTCC	0.751																																					p.R10H		Atlas-SNP	.											.	DES	53	.	0			c.G29A						PASS	.						9	11	11					2																	220283213		1907	3736	5643	SO:0001583	missense	1674	exon1			GCCAGCGCGTGTC	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.29G>A	2.37:g.220283213G>A	ENSP00000363071:p.Arg10His	82	0	0		85	18	0.211765	NM_001927	Q15787|Q549R7|Q549R8|Q549R9|Q8IZR1|Q8IZR6|Q8NES2|Q8NEU6|Q8TAC4|Q8TCX2|Q8TD99|Q9UHN5|Q9UJ80	Missense_Mutation	SNP	ENST00000373960.3	37	CCDS33383.1	.	.	.	.	.	.	.	.	.	.	G	19.19	3.780499	0.70222	.	.	ENSG00000175084	ENST00000373960	D	0.83506	-1.73	5.12	4.24	0.50183	Intermediate filament head, DNA-binding domain (1);	0.124060	0.34603	N	0.003830	T	0.81103	0.4753	L	0.57536	1.79	0.41720	D	0.989502	D	0.53885	0.963	B	0.42593	0.392	D	0.83492	0.0070	10	0.62326	D	0.03	.	14.9895	0.71374	0.0:0.0:0.8562:0.1438	.	10	P17661	DESM_HUMAN	H	10	ENSP00000363071:R10H	ENSP00000363071:R10H	R	+	2	0	DES	219991457	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.656000	0.46716	1.283000	0.44513	0.555000	0.69702	CGC	.	.	none		0.751	DES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130240.1	NM_001927		A	220283213	G	A	220283213	3	1	8	1	0	0	0	0	1	0	0	0	4451	1087	38	1	31	1	DES	2	220283213	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	744802	220283213	22916160	23	862											
SH3BP4	23677	hgsc.bcm.edu	37	chr2	235951281	235951281	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	catcaagccttccgggcaaaGgaggtttctcaagaagaacg	13	7	11	10	2	2	2	2	0	1	2	4	3	3	3	2	3	2	2	2	3	5	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr2:235951281G>A	ENST00000409212.1	+	4	2375	c.1868G>A	c.(1867-1869)aGg>aAg	p.R623K	SH3BP4_ENST00000344528.4_Missense_Mutation_p.R623K|SH3BP4_ENST00000392011.2_Missense_Mutation_p.R623K			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	623					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)		TCCGGGCAAAGGAGGTTTCTC	0.567																																					p.R623K		Atlas-SNP	.											SH3BP4,right_upper_lobe,carcinoma,+1,2	SH3BP4	109	2	0			c.G1868A						scavenged	.						58	56	57					2																	235951281		2203	4300	6503	SO:0001583	missense	23677	exon4			GGCAAAGGAGGTT	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.1868G>A	2.37:g.235951281G>A	ENSP00000386862:p.Arg623Lys	83	1	0.0120482		76	29	0.381579	NM_014521	O95082|Q309A3|Q53QD0|Q53TD1	Missense_Mutation	SNP	ENST00000409212.1	37	CCDS2513.1	.	.	.	.	.	.	.	.	.	.	G	18.43	3.621960	0.66787	.	.	ENSG00000130147	ENST00000392011;ENST00000409212;ENST00000344528	T;T;T	0.10005	2.92;2.92;2.92	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	T	0.23649	0.0572	L	0.36672	1.1	0.80722	D	1	D;D	0.64830	0.994;0.994	D;D	0.70716	0.97;0.97	T	0.00839	-1.1545	10	0.37606	T	0.19	-42.3967	17.0389	0.86483	0.0:0.0:1.0:0.0	.	623;623	A8K594;Q9P0V3	.;SH3B4_HUMAN	K	623	ENSP00000375867:R623K;ENSP00000386862:R623K;ENSP00000340237:R623K	ENSP00000340237:R623K	R	+	2	0	SH3BP4	235616020	1.000000	0.71417	0.989000	0.46669	0.922000	0.55478	9.458000	0.97634	2.354000	0.79902	0.655000	0.94253	AGG	.	.	none		0.567	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1			A	235951281	G	A	235951281	3	1	8	1	0	0	0	0	1	0	0	0	14261	1000	35	2	1874	2	SH3BP4	2	235951281	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	15668068	235951281	7248092	24	863											
HRH1	3269	hgsc.bcm.edu	37	chr3	11302022	11302022	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctggatcccttatttcatCttcttcatggtcattgcctt	5	19	6	11	0	5	0	3	0	2	0	6	1	6	1	2	2	2	1	2	2	1	6			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr3:11302022C>A	ENST00000397056.1	+	3	1490	c.1299C>A	c.(1297-1299)atC>atA	p.I433I	HRH1_ENST00000438284.2_Silent_p.I433I|HRH1_ENST00000431010.2_Silent_p.I433I	NM_000861.3|NM_001098211.1	NP_000852.1|NP_001091681.1	P35367	HRH1_HUMAN	histamine receptor H1	433					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)	CTTATTTCATCTTCTTCATGG	0.478																																					p.I433I		Atlas-SNP	.											HRH1,NS,lymphoid_neoplasm,+1,1	HRH1	58	1	0			c.C1299A						PASS	.						242	248	246					3																	11302022		2203	4300	6503	SO:0001819	synonymous_variant	3269	exon3			TTTCATCTTCTTC		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.1299C>A	3.37:g.11302022C>A		84	0	0		97	26	0.268041	NM_000861	A8K047|Q6P9E5	Silent	SNP	ENST00000397056.1	37	CCDS2604.1																																																																																			.	.	none		0.478	HRH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251928.2			A	11302022	C	A	11302022	2	1	8	1	0	0	0	0	0	0	0	1	7364	903	32	4		4	HRH1	3	11302022	Silent	SNP	C	TCGA-FA-A82F-01A-11D-A382-10		11302022	186720408	25	864											
TUSC2	11334	hgsc.bcm.edu	37	chr3	50365502	50365502	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccgaggcgaagggccacaggCcccgagctttggacccgctg	7	4	15	15	4	0	0	0	0	0	0	0	4	0	1	5	4	1	2	5	4	1	1			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr3:50365502C>T	ENST00000232496.4	-	1	172	c.29G>A	c.(28-30)gGc>gAc	p.G10D	TUSC2_ENST00000462137.1_5'UTR	NM_007275.1	NP_009206.1	O75896	TUSC2_HUMAN	tumor suppressor candidate 2	10					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)		GGGCCACAGGCCCCGAGCTTT	0.731																																					p.G10D		Atlas-SNP	.											.	TUSC2	4	.	0			c.G29A						PASS	.						2	3	2					3																	50365502		1520	3225	4745	SO:0001583	missense	11334	exon1			CACAGGCCCCGAG	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	ENST00000232496.4:c.29G>A	3.37:g.50365502C>T	ENSP00000232496:p.Gly10Asp	15	0	0		24	12	0.5	NM_007275	B2R4Y9	Missense_Mutation	SNP	ENST00000232496.4	37	CCDS2819.1	.	.	.	.	.	.	.	.	.	.	C	36	5.870022	0.97049	.	.	ENSG00000114383	ENST00000232496	.	.	.	5.55	5.55	0.83447	.	0.286088	0.37906	N	0.001889	T	0.76463	0.3991	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.76099	-0.3083	9	0.49607	T	0.09	-8.9261	17.0031	0.86385	0.0:1.0:0.0:0.0	.	10	O75896	TUSC2_HUMAN	D	10	.	ENSP00000232496:G10D	G	-	2	0	TUSC2	50340506	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.725000	0.61979	2.609000	0.88269	0.563000	0.77884	GGC	.	.	none		0.731	TUSC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346399.1	NM_007275		T	50365502	C	T	50365502	3	4	8	1	0	0	0	0	1	0	0	0	16792	739	26	2	315	2	TUSC2	3	50365502	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	39063480	50365502	147656928	26	865											
PRKCD	5580	hgsc.bcm.edu	37	chr3	53221396	53221396	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgtgtggactgcagtttctaCacagcaagggcatcatttac	10	12	10	9	0	2	0	1	0	1	0	2	1	2	1	0	2	4	4	0	2	3	4			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr3:53221396C>T	ENST00000394729.2	+	14	1721	c.1393C>T	c.(1393-1395)Cac>Tac	p.H465Y	PRKCD_ENST00000330452.3_Missense_Mutation_p.H465Y	NM_212539.1	NP_997704.1	Q05655	KPCD_HUMAN	protein kinase C, delta	465	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular senescence (GO:0090398)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|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)|gene expression (GO:0010467)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-10 production (GO:0032613)|interleukin-12 production (GO:0032615)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|mRNA metabolic process (GO:0016071)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of filopodium assembly (GO:0051490)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of inflammatory response (GO:0050728)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein binding (GO:0032091)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil activation (GO:0042119)|peptidyl-threonine phosphorylation (GO:0018107)|platelet activation (GO:0030168)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of ceramide biosynthetic process (GO:2000304)|positive regulation of glucosylceramide catabolic process (GO:2000753)|positive regulation of phospholipid scramblase activity (GO:1900163)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of response to DNA damage stimulus (GO:2001022)|positive regulation of sphingomyelin catabolic process (GO:2000755)|positive regulation of superoxide anion generation (GO:0032930)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of receptor activity (GO:0010469)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|termination of signal transduction (GO:0023021)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|insulin receptor substrate binding (GO:0043560)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26		Ovarian(412;0.0728)		OV - Ovarian serous cystadenocarcinoma(275;3.58e-08)|BRCA - Breast invasive adenocarcinoma(193;0.000142)|Kidney(197;0.00153)|KIRC - Kidney renal clear cell carcinoma(197;0.00173)	Ingenol Mebutate(DB05013)|Tamoxifen(DB00675)	GCAGTTTCTACACAGCAAGGG	0.562																																					p.H465Y		Atlas-SNP	.											.	PRKCD	124	.	0			c.C1393T						PASS	.						122	119	120					3																	53221396		2203	4300	6503	SO:0001583	missense	5580	exon14			TTTCTACACAGCA		CCDS2870.1	3p21.31	2009-07-10			ENSG00000163932	ENSG00000163932	2.7.11.1		9399	protein-coding gene	gene with protein product		176977				8188219	Standard	NM_006254		Approved		uc003dgm.3	Q05655	OTTHUMG00000133659	ENST00000394729.2:c.1393C>T	3.37:g.53221396C>T	ENSP00000378217:p.His465Tyr	119	0	0		113	42	0.371681	NM_212539	B0KZ81|B2R834|Q15144|Q86XJ6	Missense_Mutation	SNP	ENST00000394729.2	37	CCDS2870.1	.	.	.	.	.	.	.	.	.	.	C	31	5.100681	0.94245	.	.	ENSG00000163932	ENST00000394729;ENST00000330452	D;D	0.83755	-1.76;-1.76	5.47	5.47	0.80525	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	0.93825	0.8025	H	0.94658	3.565	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95242	0.8352	10	0.87932	D	0	.	18.1017	0.89508	0.0:1.0:0.0:0.0	.	465	Q05655	KPCD_HUMAN	Y	465	ENSP00000378217:H465Y;ENSP00000331602:H465Y	ENSP00000331602:H465Y	H	+	1	0	PRKCD	53196436	1.000000	0.71417	0.998000	0.56505	0.973000	0.67179	7.818000	0.86416	2.572000	0.86782	0.591000	0.81541	CAC	.	.	none		0.562	PRKCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257818.1			T	53221396	C	T	53221396	3	4	8	1	0	0	0	0	1	0	0	0	12521	478	17	2	1443	2	PRKCD	3	53221396	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	2855894	53221396	144801034	27	866											
PRICKLE2	166336	hgsc.bcm.edu	37	chr3	64148736	64148736	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgtagtagctgcttgattcGcagtttctctccaggactgt	6	15	11	9	1	1	1	0	1	1	0	4	2	2	2	1	1	2	6	1	1	2	5			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr3:64148736G>A	ENST00000295902.6	-	3	799	c.214C>T	c.(214-216)Cga>Tga	p.R72*	PRICKLE2_ENST00000564377.1_Nonsense_Mutation_p.R128*	NM_198859.3	NP_942559.1	Q7Z3G6	PRIC2_HUMAN	prickle homolog 2 (Drosophila)	72	PET. {ECO:0000255|PROSITE- ProRule:PRU00636}.				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.R72*(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)		TGCTTGATTCGCAGTTTCTCT	0.463																																					p.R72X		Atlas-SNP	.											PRICKLE2,NS,carcinoma,0,1	PRICKLE2	88	1	1	Substitution - Nonsense(1)	stomach(1)	c.C214T						PASS	.						248	232	237					3																	64148736		2203	4300	6503	SO:0001587	stop_gained	166336	exon3			TGATTCGCAGTTT	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.214C>T	3.37:g.64148736G>A	ENSP00000295902:p.Arg72*	146	0	0		134	47	0.350746	NM_198859	Q0VF44	Nonsense_Mutation	SNP	ENST00000295902.6	37	CCDS2902.1	.	.	.	.	.	.	.	.	.	.	G	41	8.954524	0.99016	.	.	ENSG00000163637	ENST00000295902;ENST00000498162	.	.	.	5.77	2.64	0.31445	.	0.000000	0.64402	D	0.000018	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.3932	15.4473	0.75240	0.0:0.0:0.5029:0.4971	.	.	.	.	X	72	.	ENSP00000295902:R72X	R	-	1	2	PRICKLE2	64123776	0.988000	0.35896	0.988000	0.46212	0.973000	0.67179	1.613000	0.36900	0.743000	0.32719	-0.284000	0.09977	CGA	.	.	none		0.463	PRICKLE2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352219.1	NM_198859		A	64148736	G	A	64148736	4	1	8	1	0	0	0	0	0	1	0	0	12499	1095	38	1	2344	1	PRICKLE2	3	64148736	Nonsense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	10927340	64148736	133873694	28	867											
FAM19A1	407738	hgsc.bcm.edu	37	chr3	68055837	68055837	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcttgtgcaatgctactctGccatggatcccttcagcaca	8	12	8	13	0	2	0	1	0	1	0	3	1	3	1	2	1	6	4	2	1	2	3			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr3:68055837G>T	ENST00000478136.1	+	2	558	c.68G>T	c.(67-69)tGc>tTc	p.C23F	FAM19A1_ENST00000496687.1_Missense_Mutation_p.C23F	NM_213609.3	NP_998774.2	Q7Z5A9	F19A1_HUMAN	family with sequence similarity 19 (chemokine (C-C motif)-like), member A1	23						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)		ATGCTACTCTGCCATGGATCC	0.502																																					p.C23F		Atlas-SNP	.											.	FAM19A1	58	.	0			c.G68T						PASS	.						229	223	225					3																	68055837		2106	4240	6346	SO:0001583	missense	407738	exon2			TACTCTGCCATGG	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.68G>T	3.37:g.68055837G>T	ENSP00000418575:p.Cys23Phe	154	0	0		196	64	0.326531	NM_213609	A8K0V3|Q8TCL8	Missense_Mutation	SNP	ENST00000478136.1	37	CCDS54606.1	.	.	.	.	.	.	.	.	.	.	.	14.30	2.493413	0.44352	.	.	ENSG00000183662	ENST00000478136;ENST00000496687	.	.	.	6.17	6.17	0.99709	.	0.181406	0.37178	N	0.002215	T	0.63165	0.2488	L	0.29908	0.895	0.51482	D	0.999929	P	0.51240	0.943	P	0.58013	0.831	T	0.51942	-0.8641	9	0.18276	T	0.48	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	23	Q7Z5A9	F19A1_HUMAN	F	23	.	ENSP00000418575:C23F	C	+	2	0	FAM19A1	68138527	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	8.074000	0.89500	2.941000	0.99782	0.655000	0.94253	TGC	.	.	none		0.502	FAM19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352004.1	NM_213609		T	68055837	G	T	68055837	3	4	8	1	0	0	0	0	1	0	0	0	5536	1319	46	4	70	4	FAM19A1	3	68055837	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	3907101	68055837	129966593	29	868											
MITF	4286	hgsc.bcm.edu	37	chr3	69988253	69988253	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcttgtgtttttgcagggatTttataagtttgaagagcaaa	11	16	11	3	0	0	2	0	1	0	1	0	3	0	3	0	1	2	5	0	1	4	7			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr3:69988253T>G	ENST00000448226.2	+	4	714	c.587T>G	c.(586-588)tTt>tGt	p.F196C	MITF_ENST00000314557.6_Missense_Mutation_p.F89C|MITF_ENST00000472437.1_Missense_Mutation_p.F144C|MITF_ENST00000394355.2_Missense_Mutation_p.F171C|MITF_ENST00000352241.4_Missense_Mutation_p.F196C|MITF_ENST00000314589.5_Missense_Mutation_p.F180C|MITF_ENST00000394351.3_Missense_Mutation_p.F89C|MITF_ENST00000531774.1_Missense_Mutation_p.F33C|MITF_ENST00000328528.6_Missense_Mutation_p.F195C			O75030	MITF_HUMAN	microphthalmia-associated transcription factor	196					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)		TTGCAGGGATTTTATAAGTTT	0.438			A		melanoma		"Waardenburg syndrome type 2, Tietz syndrome"																														p.F196C	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.T587G						PASS	.						96	92	93					3																	69988253		2203	4300	6503	SO:0001583	missense	4286	exon4			AGGGATTTTATAA		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.587T>G	3.37:g.69988253T>G	ENSP00000391803:p.Phe196Cys	225	0	0		201	54	0.268657	NM_198159	B4DJL2|D3K197|E9PFN0|Q14841|Q9P2V0|Q9P2V1|Q9P2V2|Q9P2Y8	Missense_Mutation	SNP	ENST00000448226.2	37		.	.	.	.	.	.	.	.	.	.	T	15.35	2.806498	0.50421	.	.	ENSG00000187098	ENST00000352241;ENST00000448226;ENST00000433517;ENST00000472437;ENST00000328528;ENST00000451708;ENST00000314589;ENST00000394355;ENST00000314557;ENST00000394351;ENST00000531774	T;T;T;T;T;T;T;T;T;T	0.24723	2.66;2.18;2.43;2.63;1.84;2.63;2.64;2.42;1.84;2.44	5.99	5.99	0.97316	.	0.595462	0.16404	N	0.215904	T	0.23492	0.0568	N	0.08118	0	0.46798	D	0.999201	P;P;P;D;D;P;P	0.61697	0.679;0.547;0.911;0.99;0.969;0.924;0.948	B;B;P;P;P;P;P	0.53146	0.338;0.416;0.518;0.639;0.719;0.634;0.54	T	0.10800	-1.0614	9	.	.	.	.	15.0653	0.71989	0.0:0.0:0.0:1.0	.	144;89;89;171;180;195;196	E9PFN0;O75030-9;O75030-10;O75030-4;O75030-8;O75030-6;O75030-2	.;.;.;.;.;.;.	C	196;196;88;144;195;180;180;171;89;89;33	ENSP00000295600:F196C;ENSP00000391803:F196C;ENSP00000418845:F144C;ENSP00000327867:F195C;ENSP00000398639:F180C;ENSP00000324443:F180C;ENSP00000377884:F171C;ENSP00000324246:F89C;ENSP00000377880:F89C;ENSP00000435909:F33C	.	F	+	2	0	MITF	70070943	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.848000	0.62874	2.291000	0.77112	0.533000	0.62120	TTT	.	.	none		0.438	MITF-007	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000313947.1	NM_198159		G	69988253	T	G	69988253	3	3	8	1	0	0	0	0	1	0	0	0	9605	1841	64	5	822	5	MITF	3	69988253	Missense_Mutation	SNP	T	TCGA-FA-A82F-01A-11D-A382-10	1932416	69988253	128034177	30	869											
PDZRN3	23024	hgsc.bcm.edu	37	chr3	73433731	73433731	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccgctagggtagtacaggccGtaaggggtggcgctcttcac	7	8	15	11	3	2	0	1	0	1	0	2	0	2	0	2	5	1	5	2	5	4	5	rs142044798		TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr3:73433731G>A	ENST00000263666.4	-	10	2100	c.1986C>T	c.(1984-1986)taC>taT	p.Y662Y	PDZRN3_ENST00000466780.1_Silent_p.Y319Y|PDZRN3_ENST00000462146.2_Silent_p.Y319Y|PDZRN3_ENST00000466348.1_5'Flank|PDZRN3_ENST00000535920.1_Silent_p.Y384Y|PDZRN3_ENST00000479530.1_Silent_p.Y379Y	NM_015009.1	NP_055824.1	Q9UPQ7	PZRN3_HUMAN	PDZ domain containing ring finger 3	662					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)		AGTACAGGCCGTAAGGGGTGG	0.657																																					p.Y662Y		Atlas-SNP	.											.	PDZRN3	196	.	0			c.C1986T						PASS	.	G		0,4406		0,0,2203	43	47	45		1986	3	0.4	3	dbSNP_134	45	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PDZRN3	NM_015009.1		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		662/1067	73433731	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23024	exon10			CAGGCCGTAAGGG	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.1986C>T	3.37:g.73433731G>A		83	0	0		71	28	0.394366	NM_015009	A7MCZ6|Q8N2N7|Q96CC2|Q9NSQ2	Silent	SNP	ENST00000263666.4	37	CCDS33789.1																																																																																			G|1.000;A|0.000	0.000	weak		0.657	PDZRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352460.1	XM_041363		A	73433731	G	A	73433731	2	1	8	1	0	0	0	0	0	0	0	1	11718	1140	40	1		1	PDZRN3	3	73433731	Silent	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	3445478	73433731	124588699	31	870											
ROBO1	6091	hgsc.bcm.edu	37	chr3	78711223	78711223	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcatttcccagctctctctGgacctgcttgtggtccaccc	5	12	8	16	0	2	0	0	0	2	0	5	1	4	1	4	2	3	3	4	2	0	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr3:78711223G>T	ENST00000464233.1	-	15	2121	c.2008C>A	c.(2008-2010)Cag>Aag	p.Q670K	ROBO1_ENST00000436010.2_Missense_Mutation_p.Q631K|ROBO1_ENST00000495273.1_Missense_Mutation_p.Q634K|ROBO1_ENST00000467549.1_Missense_Mutation_p.Q634K	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	670					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)		AGCTCTCTCTGGACCTGCTTG	0.488																																					p.Q670K		Atlas-SNP	.											.	ROBO1	833	.	0			c.C2008A						PASS	.						71	79	76					3																	78711223		1964	4147	6111	SO:0001583	missense	6091	exon15			CTCTCTGGACCTG	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.2008C>A	3.37:g.78711223G>T	ENSP00000420321:p.Gln670Lys	110	0	0		125	19	0.152	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	37	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.767033	0.90020	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414	T;T;T;T	0.61510	0.13;0.1;0.1;0.17	5.48	4.61	0.57282	Fibronectin, type III (1);	0.000000	0.85682	D	0.000000	T	0.74891	0.3776	M	0.77616	2.38	0.58432	D	0.999996	P;D;D;D;P;P	0.69078	0.811;0.969;0.989;0.997;0.773;0.934	P;P;D;D;B;P	0.72338	0.879;0.869;0.915;0.977;0.441;0.748	T	0.76854	-0.2805	9	.	.	.	.	14.1298	0.65245	0.0724:0.0:0.9276:0.0	.	634;634;670;634;634;631	Q9Y6N7-3;Q1RMC7;Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4	.;.;ROBO1_HUMAN;.;.;.	K	631;634;670;634;634;674	ENSP00000406043:Q631K;ENSP00000420321:Q670K;ENSP00000420637:Q634K;ENSP00000417992:Q634K	.	Q	-	1	0	ROBO1	78793913	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.850000	0.99511	1.310000	0.45006	0.555000	0.69702	CAG	.	.	none		0.488	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		T	78711223	G	T	78711223	3	4	8	1	0	0	0	0	1	0	0	0	13528	1357	47	4	3015	4	ROBO1	3	78711223	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	5277492	78711223	119311207	32	871											
LSAMP	4045	hgsc.bcm.edu	37	chr3	115805359	115805359	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagcaaaaatgatgccagaaCggttcaaccaggccaccttt	14	7	8	12	1	1	2	1	1	0	1	1	2	1	2	4	2	4	2	4	2	4	2	rs577289191		TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr3:115805359C>T	ENST00000490035.2	-	2	699	c.200G>A	c.(199-201)cGt>cAt	p.R67H	LSAMP_ENST00000539563.1_Missense_Mutation_p.R64H	NM_002338.3	NP_002329.2	Q13449	LSAMP_HUMAN	limbic system-associated membrane protein	67	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)		GATGCCAGAACGGTTCAACCA	0.473													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20144	0.0		0.0	False		,,,				2504	0.0				p.R67H		Atlas-SNP	.											.	LSAMP	62	.	0			c.G200A						PASS	.						118	106	110					3																	115805359		2203	4300	6503	SO:0001583	missense	4045	exon2			CCAGAACGGTTCA	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.200G>A	3.37:g.115805359C>T	ENSP00000419000:p.Arg67His	145	0	0		115	44	0.382609	NM_002338	Q8IV49	Missense_Mutation	SNP	ENST00000490035.2	37	CCDS2982.1	.	.	.	.	.	.	.	.	.	.	C	35	5.494944	0.96339	.	.	ENSG00000185565	ENST00000333617;ENST00000490035;ENST00000539563;ENST00000474851	T;T;T;T	0.27557	1.66;1.66;1.66;1.66	5.78	5.78	0.91487	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.70168	0.3193	H	0.95043	3.615	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.79063	-0.1957	10	0.87932	D	0	-8.0017	20.005	0.97433	0.0:1.0:0.0:0.0	.	67;67	B2RCU8;Q13449	.;LSAMP_HUMAN	H	51;67;64;101	ENSP00000328455:R51H;ENSP00000419000:R67H;ENSP00000443429:R64H;ENSP00000418506:R101H	ENSP00000328455:R51H	R	-	2	0	LSAMP	117288049	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.058000	0.71126	2.745000	0.94114	0.555000	0.69702	CGT	.	.	none		0.473	LSAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354495.4	NM_002338		T	115805359	C	T	115805359	3	4	8	1	0	0	0	0	1	0	0	0	9057	536	19	1	840	1	LSAMP	3	115805359	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	37094136	115805359	82217071	33	872											
KIAA0226	9711	hgsc.bcm.edu	37	chr3	197409444	197409444	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagatgtcagcgtgctgccCgtcatccggtgagatgggca	7	9	15	10	3	2	2	2	1	0	2	3	3	3	2	2	2	3	3	2	2	1	1			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr3:197409444C>T	ENST00000296343.5	-	14	2022	c.2023G>A	c.(2023-2025)Ggg>Agg	p.G675R	KIAA0226_ENST00000389665.5_Missense_Mutation_p.G700R|KIAA0226_ENST00000273582.5_Missense_Mutation_p.G630R	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	675					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)		GCGTGCTGCCCGTCATCCGGT	0.582																																					p.G675R	Esophageal Squamous(3;167 355 3763 15924)	Atlas-SNP	.											KIAA0226_ENST00000273582,NS,carcinoma,0,2	KIAA0226	136	2	0			c.G2023A						PASS	.						60	64	62					3																	197409444		2164	4264	6428	SO:0001583	missense	9711	exon14			GCTGCCCGTCATC	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.2023G>A	3.37:g.197409444C>T	ENSP00000296343:p.Gly675Arg	129	0	0		101	31	0.306931	NM_014687	Q96CK5	Missense_Mutation	SNP	ENST00000296343.5	37	CCDS43195.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.78|19.78	3.890439|3.890439	0.72524|0.72524	.|.	.|.	ENSG00000145016|ENSG00000145016	ENST00000273582;ENST00000296343;ENST00000389665|ENST00000413360	T;T;T|.	0.42900|.	0.96;0.96;0.96|.	5.71|5.71	5.71|5.71	0.89125|0.89125	.|.	0.057192|.	0.64402|.	D|.	0.000001|.	T|T	0.60650|0.60650	0.2285|0.2285	L|L	0.31926|0.31926	0.97|0.97	0.80722|0.80722	D|D	1|1	D;D;D|.	0.71674|.	0.998;0.961;0.986|.	P;B;P|.	0.58013|.	0.831;0.411;0.479|.	T|T	0.53258|0.53258	-0.8464|-0.8464	10|5	0.25751|.	T|.	0.34|.	.|.	19.8677|19.8677	0.96824|0.96824	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	700;630;675|.	Q92622-3;Q92622-2;Q92622|.	.;.;RUBIC_HUMAN|.	R|Q	630;675;700|636	ENSP00000273582:G630R;ENSP00000296343:G675R;ENSP00000374316:G700R|.	ENSP00000273582:G630R|.	G|R	-|-	1|2	0|0	KIAA0226|KIAA0226	198893841|198893841	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.930000|0.930000	0.56654|0.56654	7.818000|7.818000	0.86416|0.86416	2.709000|2.709000	0.92574|0.92574	0.655000|0.655000	0.94253|0.94253	GGG|CGG	.	.	none		0.582	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901		T	197409444	C	T	197409444	3	4	8	1	0	0	0	0	1	0	0	0	8171	652	23	1	923	1	KIAA0226	3	197409444	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	81604085	197409444	612986	34	873											
ARAP2	116984	hgsc.bcm.edu	37	chr4	36069898	36069898	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttcaagttctgctcttgcActctaaaaataaaattaaat	15	15	3	8	0	4	0	1	0	3	0	4	0	4	0	0	0	2	3	0	0	8	6			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr4:36069898A>G	ENST00000303965.4	-	33	5235	c.4746T>C	c.(4744-4746)agT>agC	p.S1582S		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	1582					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						CTGCTCTTGCACTCTAAAAAT	0.418																																					p.S1582S		Atlas-SNP	.											.	ARAP2	210	.	0			c.T4746C						PASS	.						41	45	44					4																	36069898		2200	4297	6497	SO:0001819	synonymous_variant	116984	exon33			TCTTGCACTCTAA	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.4746T>C	4.37:g.36069898A>G		67	0	0		57	8	0.140351	NM_015230	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Silent	SNP	ENST00000303965.4	37	CCDS3441.1																																																																																			.	.	none		0.418	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230		G	36069898	A	G	36069898	2	3	8	1	0	0	0	0	0	0	0	1	839	156	6	3		3	ARAP2	4	36069898	Silent	SNP	A	TCGA-FA-A82F-01A-11D-A382-10		36069898	155084378	35	874											
SLC4A4	8671	hgsc.bcm.edu	37	chr4	72338528	72338528	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttggttcaatacttcacaCgtttcacggaggagggcttt	8	14	10	9	2	4	0	3	0	1	0	4	2	4	2	0	4	1	3	0	4	2	6			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr4:72338528C>T	ENST00000264485.5	+	14	1861	c.1744C>T	c.(1744-1746)Cgt>Tgt	p.R582C	SLC4A4_ENST00000512686.1_Missense_Mutation_p.R538C|SLC4A4_ENST00000351898.6_Missense_Mutation_p.R582C|SLC4A4_ENST00000340595.3_Missense_Mutation_p.R538C|SLC4A4_ENST00000514331.1_3'UTR|SLC4A4_ENST00000425175.1_Missense_Mutation_p.R582C	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	582					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)	ATACTTCACACGTTTCACGGA	0.448																																					p.R582C		Atlas-SNP	.											.	SLC4A4	269	.	0			c.C1744T						PASS	.						178	170	173					4																	72338528		2203	4300	6503	SO:0001583	missense	8671	exon14			TTCACACGTTTCA	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.1744C>T	4.37:g.72338528C>T	ENSP00000264485:p.Arg582Cys	173	0	0		161	44	0.273292	NM_001098484	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	ENST00000264485.5	37	CCDS43236.1	.	.	.	.	.	.	.	.	.	.	C	32	5.150747	0.94645	.	.	ENSG00000080493	ENST00000264485;ENST00000425175;ENST00000351898;ENST00000512686;ENST00000340595	D;D;D;D;D	0.83755	-1.76;-1.76;-1.76;-1.76;-1.76	5.44	5.44	0.79542	Bicarbonate transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.94407	0.8201	H	0.96142	3.775	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;0.999;1.0;1.0	D	0.95867	0.8888	10	0.87932	D	0	.	19.2755	0.94030	0.0:1.0:0.0:0.0	.	582;582;538;538;562;582	A5JJ20;Q9Y6R1-4;Q9Y6R1-2;Q9Y6R1-3;Q9Y6R3;Q9Y6R1	.;.;.;.;.;S4A4_HUMAN	C	582;582;582;538;538	ENSP00000264485:R582C;ENSP00000393557:R582C;ENSP00000307349:R582C;ENSP00000422400:R538C;ENSP00000344272:R538C	ENSP00000264485:R582C	R	+	1	0	SLC4A4	72557392	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	7.818000	0.86416	2.553000	0.86117	0.655000	0.94253	CGT	.	.	none		0.448	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759		T	72338528	C	T	72338528	3	4	8	1	0	0	0	0	1	0	0	0	14671	536	19	1	1915	1	SLC4A4	4	72338528	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	36268630	72338528	118815748	36	875											
ANKRD17	26057	hgsc.bcm.edu	37	chr4	74005713	74005713	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agttttcagttgtaactctcGttctactttctgtagttcct	6	20	6	9	1	4	0	1	0	3	0	6	0	5	0	1	0	2	6	1	0	3	9	rs148961166		TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr4:74005713G>A	ENST00000358602.4	-	15	2736	c.2620C>T	c.(2620-2622)Cga>Tga	p.R874*	ANKRD17_ENST00000514252.1_5'UTR|ANKRD17_ENST00000509867.2_Nonsense_Mutation_p.R761*|ANKRD17_ENST00000330838.6_Intron	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	874	Gln-rich.				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)			TGTAACTCTCGTTCTACTTTC	0.403																																					p.R874X		Atlas-SNP	.											.	ANKRD17	214	.	0			c.C2620T						PASS	.						229	224	226					4																	74005713		2203	4300	6503	SO:0001587	stop_gained	26057	exon15			ACTCTCGTTCTAC	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.2620C>T	4.37:g.74005713G>A	ENSP00000351416:p.Arg874*	536	0	0		464	131	0.282328	NM_032217	E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Nonsense_Mutation	SNP	ENST00000358602.4	37	CCDS34004.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.753525	0.89753	.	.	ENSG00000132466	ENST00000358602;ENST00000426990;ENST00000509867;ENST00000411811	.	.	.	5.65	3.86	0.44501	.	0.000000	0.52532	D	0.000076	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.8091	0.63252	0.0:0.0:0.5576:0.4424	.	.	.	.	X	874;874;761;874	.	ENSP00000351416:R874X	R	-	1	2	ANKRD17	74224577	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.761000	0.55242	0.790000	0.33803	-0.182000	0.12963	CGA	G|1.000;T|0.000	.	alt		0.403	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1	NM_032217		A	74005713	G	A	74005713	4	1	8	1	0	0	0	0	0	1	0	0	646	1153	40	1	5271	1	ANKRD17	4	74005713	Nonsense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	1667185	74005713	117148563	37	876											
HNRNPD	3184	hgsc.bcm.edu	37	chr4	83294683	83294683	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cggtgcctccagacgcggttCcgcccccggtcccggctccg	2	6	13	20	7	0	1	0	0	0	1	4	1	4	1	7	4	1	2	7	4	0	1			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr4:83294683C>T	ENST00000313899.7	-	1	426	c.149G>A	c.(148-150)gGa>gAa	p.G50E	RP11-127B20.3_ENST00000609575.1_RNA|HNRNPD_ENST00000541060.1_5'UTR|HNRNPD_ENST00000352301.4_Missense_Mutation_p.G50E|RP11-127B20.3_ENST00000609552.1_RNA|HNRNPD_ENST00000543098.1_Intron|HNRNPD_ENST00000353341.4_Missense_Mutation_p.G50E	NM_031370.2	NP_112738.1	Q14103	HNRPD_HUMAN	heterogeneous nuclear ribonucleoprotein D (AU-rich element RNA binding protein 1, 37kDa)	50					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						agacgcggttccgcccccggt	0.726																																					p.G50E		Atlas-SNP	.											.	HNRNPD	23	.	0			c.G149A						PASS	.						31	22	25					4																	83294683		2046	3968	6014	SO:0001583	missense	3184	exon1			GCGGTTCCGCCCC	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.149G>A	4.37:g.83294683C>T	ENSP00000313199:p.Gly50Glu	67	0	0		60	18	0.3	NM_031370	A8K9J2|P07029|Q01858|Q14100|Q14101|Q14102|Q4W5A1|Q9UCE8|Q9UCE9	Missense_Mutation	SNP	ENST00000313899.7	37	CCDS3592.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.92|12.92	2.081828|2.081828	0.36758|0.36758	.|.	.|.	ENSG00000138668|ENSG00000138668	ENST00000307213|ENST00000313899;ENST00000353341;ENST00000352301;ENST00000507010;ENST00000503822	.|T;T;T;T;T	.|0.70749	.|-0.38;-0.13;-0.51;2.07;1.63	3.73|3.73	3.73|3.73	0.42828|0.42828	.|CARG-binding factor, N-terminal (1);	.|0.784110	.|0.11609	.|N	.|0.546925	T|T	0.64338|0.64338	0.2589|0.2589	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.69078	.|0.997;0.997;0.997;0.997	.|D;D;D;D	.|0.74023	.|0.969;0.969;0.969;0.982	T|T	0.54879|0.54879	-0.8227|-0.8227	6|10	0.10902|0.06365	T|T	0.67|0.9	.|.	11.2766|11.2766	0.49170|0.49170	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|50;50;50;50	.|Q14103-4;Q14103-3;Q14103-2;Q14103	.|.;.;.;HNRPD_HUMAN	K|E	46|50	.|ENSP00000313199:G50E;ENSP00000313327:G50E;ENSP00000305860:G50E;ENSP00000421952:G50E;ENSP00000422615:G50E	ENSP00000307544:E46K|ENSP00000313199:G50E	E|G	-|-	1|2	0|0	HNRNPD|HNRNPD	83513707|83513707	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.839000|0.839000	0.47603|0.47603	2.895000|2.895000	0.48648|0.48648	2.108000|2.108000	0.64289|0.64289	0.479000|0.479000	0.44913|0.44913	GAA|GGA	.	.	none		0.726	HNRNPD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252630.2	NM_031370		T	83294683	C	T	83294683	3	4	8	1	0	0	0	0	1	0	0	0	7273	855	30	2	950	2	HNRNPD	4	83294683	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	9288970	83294683	107859593	38	877											
MMRN1	22915	hgsc.bcm.edu	37	chr4	90856769	90856769	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aatgatttgacttatgatatGgagatccttcaacccttgct	11	15	7	8	0	1	4	1	3	0	1	2	5	2	4	2	1	2	1	2	1	4	5			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr4:90856769G>C	ENST00000394980.1	+	7	2257	c.1938G>C	c.(1936-1938)atG>atC	p.M646I	MMRN1_ENST00000394981.1_Intron|MMRN1_ENST00000264790.2_Missense_Mutation_p.M646I|MMRN1_ENST00000508372.1_Missense_Mutation_p.M388I			Q13201	MMRN1_HUMAN	multimerin 1	646					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)		CTTATGATATGGAGATCCTTC	0.363																																					p.M646I		Atlas-SNP	.											.	MMRN1	174	.	0			c.G1938C						PASS	.						76	73	74					4																	90856769		2203	4300	6503	SO:0001583	missense	22915	exon6			TGATATGGAGATC	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.1938G>C	4.37:g.90856769G>C	ENSP00000378431:p.Met646Ile	106	0	0		106	20	0.188679	NM_007351	Q4W5L1|Q6P3T8|Q6ZUL9	Missense_Mutation	SNP	ENST00000394980.1	37	CCDS3635.1	.	.	.	.	.	.	.	.	.	.	G	17.52	3.410361	0.62399	.	.	ENSG00000138722	ENST00000394980;ENST00000264790;ENST00000508372	T;T;T	0.73363	-0.48;-0.48;-0.74	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	D	0.85435	0.5696	M	0.68952	2.095	0.80722	D	1	D	0.69078	0.997	D	0.75484	0.986	D	0.85759	0.1348	10	0.56958	D	0.05	.	19.3191	0.94231	0.0:0.0:1.0:0.0	.	646	Q13201	MMRN1_HUMAN	I	646;646;388	ENSP00000378431:M646I;ENSP00000264790:M646I;ENSP00000426461:M388I	ENSP00000264790:M646I	M	+	3	0	MMRN1	91075792	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.326000	0.72905	2.718000	0.92993	0.655000	0.94253	ATG	.	.	none		0.363	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351		C	90856769	G	C	90856769	3	2	8	1	0	0	0	0	1	0	0	0	9679	1348	47	4	1960	4	MMRN1	4	90856769	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	7562086	90856769	100297507	39	878											
TET2	54790	hgsc.bcm.edu	37	chr4	106155165	106155165	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccattcctgataccatcaccTcccatttgccagacagaacc	11	9	4	17	0	1	3	1	1	0	2	3	3	3	3	7	0	3	0	7	0	2	3			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr4:106155165T>G	ENST00000540549.1	+	3	926	c.66T>G	c.(64-66)ccT>ccG	p.P22P	TET2_ENST00000545826.1_Silent_p.P22P|TET2_ENST00000380013.4_Silent_p.P22P|TET2_ENST00000513237.1_Silent_p.P43P|TET2_ENST00000413648.2_Silent_p.P22P|TET2_ENST00000305737.2_Silent_p.P22P|TET2_ENST00000394764.1_Silent_p.P22P			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	22					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)		TACCATCACCTCCCATTTGCC	0.522			"Mis N, F"		MDS																																p.P22P		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	TET2,NS,haematopoietic_neoplasm,+1,1	TET2	1762	1	0			c.T66G						PASS	.						76	65	68					4																	106155165		2203	4300	6503	SO:0001819	synonymous_variant	54790	exon3			ATCACCTCCCATT	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.66T>G	4.37:g.106155165T>G		53	0	0		54	14	0.259259	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Silent	SNP	ENST00000540549.1	37	CCDS47120.1																																																																																			.	.	none		0.522	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		G	106155165	T	G	106155165	2	3	8	1	0	0	0	0	0	0	0	1	15785	1538	54	5		5	TET2	4	106155165	Silent	SNP	T	TCGA-FA-A82F-01A-11D-A382-10	15298396	106155165	84999111	40	879											
ANKRD50	57182	hgsc.bcm.edu	37	chr4	125631534	125631534	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtgcattgacagcactatTgcagcagttacttttctcct	8	15	8	10	0	1	1	0	1	1	0	2	1	1	1	1	1	5	5	1	1	2	6			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr4:125631534T>G	ENST00000504087.1	-	2	1170	c.133A>C	c.(133-135)Aat>Cat	p.N45H	ANKRD50_ENST00000515641.1_Intron	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	45				N -> D (in Ref. 1; BAF83757). {ECO:0000305}.						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						ACAGCACTATTGCAGCAGTTA	0.473																																					p.N45H		Atlas-SNP	.											.	ANKRD50	136	.	0			c.A133C						PASS	.						98	96	97					4																	125631534		2203	4300	6503	SO:0001583	missense	57182	exon2			CACTATTGCAGCA	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.133A>C	4.37:g.125631534T>G	ENSP00000425658:p.Asn45His	95	0	0		93	32	0.344086	NM_020337	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Missense_Mutation	SNP	ENST00000504087.1	37	CCDS34060.1	.	.	.	.	.	.	.	.	.	.	T	10.93	1.490934	0.26774	.	.	ENSG00000151458	ENST00000504087	T	0.18810	2.19	5.23	2.64	0.31445	.	0.603815	0.16483	N	0.212469	T	0.09247	0.0228	N	0.08118	0	0.48511	D	0.99966	B	0.02656	0.0	B	0.01281	0.0	T	0.15093	-1.0449	10	0.59425	D	0.04	.	3.1162	0.06375	0.1441:0.0817:0.1406:0.6336	.	45	Q9ULJ7	ANR50_HUMAN	H	45	ENSP00000425658:N45H	ENSP00000425658:N45H	N	-	1	0	ANKRD50	125850984	0.969000	0.33509	0.683000	0.30040	0.990000	0.78478	1.272000	0.33109	0.382000	0.24878	0.459000	0.35465	AAT	.	.	none		0.473	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337		G	125631534	T	G	125631534	3	3	8	1	0	0	0	0	1	0	0	0	677	1812	63	5	4168	5	ANKRD50	4	125631534	Missense_Mutation	SNP	T	TCGA-FA-A82F-01A-11D-A382-10	19476369	125631534	65522742	41	880											
FAT4	79633	hgsc.bcm.edu	37	chr4	126328261	126328261	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccaaattttccagacccgTgtactcttttgacattcctg	9	14	5	13	1	1	2	0	1	1	1	3	2	3	2	4	0	1	1	4	0	2	6			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr4:126328261T>C	ENST00000394329.3	+	3	5547	c.5534T>C	c.(5533-5535)gTg>gCg	p.V1845A	FAT4_ENST00000335110.5_Missense_Mutation_p.V143A	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1845	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)			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						TCCAGACCCGTGTACTCTTTT	0.413																																					p.V1845A		Atlas-SNP	.											FAT4_ENST00000394329,NS,carcinoma,-1,4	FAT4	1752	4	0			c.T5534C						scavenged	.						133	130	131					4																	126328261		2203	4300	6503	SO:0001583	missense	79633	exon3			GACCCGTGTACTC	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.5534T>C	4.37:g.126328261T>C	ENSP00000377862:p.Val1845Ala	124	1	0.00806452		126	31	0.246032	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	T	2.201	-0.382986	0.04966	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.01228	5.14;5.14	5.41	5.41	0.78517	Cadherin (2);Cadherin-like (1);	0.000000	0.31233	U	0.008019	T	0.01421	0.0046	N	0.21324	0.655	0.28172	N	0.928529	B;B	0.22480	0.07;0.004	B;B	0.29942	0.109;0.009	T	0.45818	-0.9235	10	0.10111	T	0.7	.	12.2953	0.54842	0.0:0.0:0.1413:0.8587	.	143;1845	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	A	1845;143	ENSP00000377862:V1845A;ENSP00000335169:V143A	ENSP00000335169:V143A	V	+	2	0	FAT4	126547711	1.000000	0.71417	0.996000	0.52242	0.229000	0.25112	3.796000	0.55507	2.168000	0.68352	0.528000	0.53228	GTG	.	.	none		0.413	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		C	126328261	T	C	126328261	3	2	8	1	0	0	0	0	1	0	0	0	5700	1696	59	3	5544	3	FAT4	4	126328261	Missense_Mutation	SNP	T	TCGA-FA-A82F-01A-11D-A382-10	696727	126328261	64826015	42	881											
MAML3	55534	hgsc.bcm.edu	37	chr4	140811088	140811088	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgctgctgctgctgctgcTgctgctgctgctgctgctgc	0	13	14	14	0	0	0	0	0	0	0	0	0	0	0	0	0	13	13	0	0	0	0	rs544518608|rs58287721	byFrequency	TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr4:140811088T>C	ENST00000509479.2	-	2	2358	c.1502A>G	c.(1501-1503)cAg>cGg	p.Q501R	MAML3_ENST00000327122.5_Missense_Mutation_p.Q345R|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)					ctgctgctgctgctgctgctg	0.532																																					p.Q501R		Atlas-SNP	.											.	MAML3	192	.	0			c.A1502G						PASS	.						18	26	23					4																	140811088		2141	4284	6425	SO:0001583	missense	55534	exon2			TGCTGCTGCTGCT	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.1502A>G	4.37:g.140811088T>C	ENSP00000421180:p.Gln501Arg	82	0	0		96	15	0.15625	NM_018717		Missense_Mutation	SNP	ENST00000509479.2	37	CCDS54805.1	.	.	.	.	.	.	.	.	.	.	T	7.066	0.567353	0.13560	.	.	ENSG00000196782	ENST00000509479;ENST00000327122	T;T	0.47869	0.83;0.83	3.5	0.541	0.17168	.	0.000000	0.51477	D	0.000093	T	0.26484	0.0647	N	0.19112	0.55	0.80722	D	1	B	0.31655	0.334	B	0.26202	0.067	T	0.04946	-1.0916	10	0.48119	T	0.1	.	7.8092	0.29221	0.0:0.0:0.4022:0.5978	.	501	Q96JK9	MAML3_HUMAN	R	501;345	ENSP00000421180:Q501R;ENSP00000313316:Q345R	ENSP00000313316:Q345R	Q	-	2	0	MAML3	141030538	1.000000	0.71417	0.998000	0.56505	0.845000	0.48019	2.071000	0.41500	0.332000	0.23536	0.329000	0.21502	CAG	.	.	none		0.532	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			C	140811088	T	C	140811088	3	2	8	1	0	0	0	0	1	0	0	0	9216	1580	55	3	1922	3	MAML3	4	140811088	Missense_Mutation	SNP	T	TCGA-FA-A82F-01A-11D-A382-10	14482827	140811088	50343188	43	882			2	9		2	2	13	T		6.124497e-05
MAML3	55534	hgsc.bcm.edu	37	chr4	140811100	140811100	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgctgctgctgctgctgcTgctgctgctgctgctgctgc	0	13	14	14	0	0	0	0	0	0	0	0	0	0	0	0	0	13	13	0	0	0	0			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr4:140811100T>C	ENST00000509479.2	-	2	2346	c.1490A>G	c.(1489-1491)cAg>cGg	p.Q497R	MAML3_ENST00000327122.5_Missense_Mutation_p.Q341R|MAML3_ENST00000398940.1_Splice_Site_p.Q36R	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)					ctgctgctgctgctgctgctg	0.542																																					p.Q497R		Atlas-SNP	.											MAML3_ENST00000509479,caecum,carcinoma,+1,12	MAML3	192	12	0			c.A1490G						PASS	.						13	19	17					4																	140811100		2113	4228	6341	SO:0001583	missense	55534	exon2			TGCTGCTGCTGCT	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.1490A>G	4.37:g.140811100T>C	ENSP00000421180:p.Gln497Arg	94	0	0		90	14	0.155556	NM_018717		Missense_Mutation	SNP	ENST00000509479.2	37	CCDS54805.1	.	.	.	.	.	.	.	.	.	.	t	10.16	1.273989	0.23221	.	.	ENSG00000196782	ENST00000509479;ENST00000327122;ENST00000398940	T;T	0.55052	0.54;0.54	4.53	4.53	0.55603	.	0.270437	0.26275	N	0.025317	T	0.45577	0.1349	N	0.08118	0	0.34541	D	0.710295	P	0.45126	0.851	P	0.55391	0.775	T	0.60571	-0.7237	10	0.51188	T	0.08	.	10.2567	0.43401	0.0:0.0:0.0:1.0	.	497	Q96JK9	MAML3_HUMAN	R	497;341;36	ENSP00000421180:Q497R;ENSP00000313316:Q341R	ENSP00000313316:Q341R	Q	-	2	0	MAML3	141030550	0.992000	0.36948	0.937000	0.37676	0.553000	0.35397	-0.323000	0.07997	1.657000	0.50732	0.374000	0.22700	CAG	.	.	none		0.542	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			C	140811100	T	C	140811100	3	2	8	1	0	0	0	0	1	0	0	0	9216	1580	55	3	1934	3	MAML3	4	140811100	Missense_Mutation	SNP	T	TCGA-FA-A82F-01A-11D-A382-10	12	140811100	50343176	44	883			2	9		2	2	13	T		6.124497e-05
INPP4B	8821	hgsc.bcm.edu	37	chr4	143129658	143129658	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctaatgttttctctcctttgCtgctgcttgatttgaaagag	7	18	8	8	0	1	3	0	2	1	1	3	3	2	3	1	0	3	4	1	0	2	6			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr4:143129658C>T	ENST00000513000.1	-	15	1425	c.992G>A	c.(991-993)aGc>aAc	p.S331N	INPP4B_ENST00000262992.4_Missense_Mutation_p.S331N|INPP4B_ENST00000508116.1_Missense_Mutation_p.S331N|INPP4B_ENST00000308502.4_Missense_Mutation_p.S331N|INPP4B_ENST00000509777.1_Missense_Mutation_p.S331N	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	331					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)					CTCTCCTTTGCTGCTGCTTGA	0.303																																					p.S331N		Atlas-SNP	.											INPP4B,NS,carcinoma,-1,1	INPP4B	132	1	0			c.G992A						PASS	.						101	100	100					4																	143129658		2203	4300	6503	SO:0001583	missense	8821	exon15			CCTTTGCTGCTGC	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.992G>A	4.37:g.143129658C>T	ENSP00000425487:p.Ser331Asn	220	0	0		206	30	0.145631	NM_003866	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Missense_Mutation	SNP	ENST00000513000.1	37	CCDS3757.1	.	.	.	.	.	.	.	.	.	.	C	3.515	-0.098886	0.07010	.	.	ENSG00000109452	ENST00000513000;ENST00000262992;ENST00000308502;ENST00000543161;ENST00000508116;ENST00000509777;ENST00000511838;ENST00000542702;ENST00000510812;ENST00000514525	T;T;T;T;T;T;T;T	0.32272	1.46;1.46;1.46;1.46;1.46;1.46;1.46;1.46	5.71	3.07	0.35406	.	0.135929	0.64402	D	0.000002	T	0.23410	0.0566	L	0.44542	1.39	0.41670	D	0.989239	B;B	0.13145	0.003;0.007	B;B	0.17722	0.007;0.019	T	0.05632	-1.0873	10	0.18276	T	0.48	.	10.0078	0.41968	0.0:0.7762:0.0:0.2238	.	202;331	B7Z6T2;O15327	.;INP4B_HUMAN	N	331;331;331;202;331;331;146;146;331;202	ENSP00000425487:S331N;ENSP00000262992:S331N;ENSP00000308441:S331N;ENSP00000423954:S331N;ENSP00000422793:S331N;ENSP00000426207:S146N;ENSP00000427250:S331N;ENSP00000421065:S202N	ENSP00000262992:S331N	S	-	2	0	INPP4B	143349108	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.877000	0.39598	0.777000	0.33496	-0.300000	0.09419	AGC	.	.	none		0.303	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866		T	143129658	C	T	143129658	3	4	8	1	0	0	0	0	1	0	0	0	7762	797	28	2	1834	2	INPP4B	4	143129658	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	2318558	143129658	48024618	45	884											
INPP4B	8821	hgsc.bcm.edu	37	chr4	143235864	143235864	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggaaacgttagaaacacttaCcccaacttctggcgggggat	12	8	11	10	2	1	1	0	0	1	1	1	3	1	3	2	4	4	1	2	4	5	3			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr4:143235864C>T	ENST00000513000.1	-	9	857		c.e9+1		INPP4B_ENST00000262992.4_Splice_Site|INPP4B_ENST00000508116.1_Splice_Site|INPP4B_ENST00000308502.4_Splice_Site|INPP4B_ENST00000509777.1_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)					GAAACACTTACCCCAACTTCT	0.413																																					.		Atlas-SNP	.											.	INPP4B	132	.	0			c.423+1G>A						PASS	.						125	128	127					4																	143235864		2203	4300	6503	SO:0001630	splice_region_variant	8821	exon10			CACTTACCCCAAC	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.423+1G>A	4.37:g.143235864C>T		121	0	0		116	44	0.37931	NM_003866	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Splice_Site	SNP	ENST00000513000.1	37	CCDS3757.1	.	.	.	.	.	.	.	.	.	.	C	14.49	2.550239	0.45383	.	.	ENSG00000109452	ENST00000513000;ENST00000262992;ENST00000308502;ENST00000508116;ENST00000509777;ENST00000510812	.	.	.	6.04	6.04	0.98038	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0793	0.80989	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	INPP4B	143455314	1.000000	0.71417	1.000000	0.80357	0.310000	0.27922	4.418000	0.59828	2.873000	0.98535	0.561000	0.74099	.	.	.	none		0.413	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866	Intron	T	143235864	C	T	143235864	5	4	8	1	0	0	0	0	0	0	1	0	7762	521	18	2	2426	2	INPP4B	4	143235864	Splice_Site	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	106206	143235864	47918412	46	885											
MAB21L2	10586	hgsc.bcm.edu	37	chr4	151504768	151504768	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gccccacatcccttggcccgGccccaatcgggtggccgagg	5	5	13	18	3	0	0	0	0	0	0	2	1	1	0	7	5	0	0	7	5	1	1			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr4:151504768G>A	ENST00000317605.4	+	1	1692	c.587G>A	c.(586-588)gGc>gAc	p.G196D	RP11-1336O20.2_ENST00000507934.1_RNA|LRBA_ENST00000510413.1_Intron|LRBA_ENST00000357115.3_Intron|LRBA_ENST00000535741.1_Intron|LRBA_ENST00000507224.1_Intron|LRBA_ENST00000503716.1_5'Flank	NM_006439.4	NP_006430.1	Q9Y586	MB212_HUMAN	mab-21-like 2 (C. elegans)	196					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)		CCTTGGCCCGGCCCCAATCGG	0.647																																					p.G196D		Atlas-SNP	.											.	MAB21L2	53	.	0			c.G587A						PASS	.						34	37	36					4																	151504768		2202	4297	6499	SO:0001583	missense	10586	exon1			GGCCCGGCCCCAA	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.587G>A	4.37:g.151504768G>A	ENSP00000324701:p.Gly196Asp	45	0	0		34	10	0.294118	NM_006439	B3KP37|Q9HBA7	Missense_Mutation	SNP	ENST00000317605.4	37	CCDS3774.1	.	.	.	.	.	.	.	.	.	.	G	13.00	2.105797	0.37145	.	.	ENSG00000181541	ENST00000317605	T	0.07800	3.16	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.09247	0.0228	N	0.22421	0.69	0.80722	D	1	B	0.29232	0.238	B	0.34590	0.186	T	0.38735	-0.9647	10	0.24483	T	0.36	-20.9107	19.4978	0.95081	0.0:0.0:1.0:0.0	.	196	Q9Y586	MB212_HUMAN	D	196	ENSP00000324701:G196D	ENSP00000324701:G196D	G	+	2	0	MAB21L2	151724218	1.000000	0.71417	0.998000	0.56505	0.926000	0.56050	9.869000	0.99810	2.608000	0.88229	0.462000	0.41574	GGC	.	.	none		0.647	MAB21L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364937.1	NM_006439		A	151504768	G	A	151504768	3	1	8	1	0	0	0	0	1	0	0	0	9151	1203	42	2	589	2	MAB21L2	4	151504768	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	8268904	151504768	39649508	47	886											
C5orf42	65250	hgsc.bcm.edu	37	chr5	37169527	37169527	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaacaacagaaggtgtggacAaaaggtagaggtgagtattt	16	8	14	3	0	0	3	0	1	0	2	0	5	0	4	0	4	2	2	0	4	7	3			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr5:37169527A>G	ENST00000508244.1	-	33	6692	c.6599T>C	c.(6598-6600)tTg>tCg	p.L2200S	C5orf42_ENST00000425232.2_Missense_Mutation_p.L2200S|C5orf42_ENST00000274258.7_Missense_Mutation_p.L1080S			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2200						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)			AGGTGTGGACAAAAGGTAGAG	0.428																																					p.L2200S		Atlas-SNP	.											.	C5orf42	422	.	0			c.T6599C						PASS	.						74	76	75					5																	37169527		2203	4300	6503	SO:0001583	missense	65250	exon34			GTGGACAAAAGGT		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.6599T>C	5.37:g.37169527A>G	ENSP00000421690:p.Leu2200Ser	129	0	0		151	31	0.205298	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	A	19.34	3.809357	0.70797	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.44482	0.99;0.99;0.92;0.95	5.53	5.53	0.82687	.	0.264081	0.24523	N	0.037796	T	0.60958	0.2309	L	0.57536	1.79	0.36777	D	0.88412	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.69117	-0.5230	10	0.66056	D	0.02	.	14.2343	0.65916	1.0:0.0:0.0:0.0	.	2200;1080	E9PH94;Q9H799	.;CE042_HUMAN	S	2200;2200;1080;1248;1080	ENSP00000421690:L2200S;ENSP00000389014:L2200S;ENSP00000274258:L1080S;ENSP00000424223:L1248S	ENSP00000274258:L1080S	L	-	2	0	C5orf42	37205284	1.000000	0.71417	0.996000	0.52242	0.390000	0.30446	5.994000	0.70623	2.092000	0.63282	0.533000	0.62120	TTG	.	.	none		0.428	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		G	37169527	A	G	37169527	3	3	8	1	0	0	0	0	1	0	0	0	2303	131	5	3	3070	3	C5orf42	5	37169527	Missense_Mutation	SNP	A	TCGA-FA-A82F-01A-11D-A382-10		37169527	143745733	48	887											
TNPO1	3842	hgsc.bcm.edu	37	chr5	72173116	72173116	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttagaagcctgtgaattttGgctaactttagctgaacagc	11	14	9	7	0	0	3	0	2	0	1	0	3	0	3	1	1	5	2	1	1	6	7			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr5:72173116G>A	ENST00000337273.5	+	9	1289	c.863G>A	c.(862-864)tGg>tAg	p.W288*	TNPO1_ENST00000506351.2_Nonsense_Mutation_p.W280*|TNPO1_ENST00000454282.1_Nonsense_Mutation_p.W238*|TNPO1_ENST00000523768.1_Nonsense_Mutation_p.W238*|TNPO1_ENST00000447967.2_3'UTR|MIR4804_ENST00000581683.1_RNA	NM_002270.3	NP_002261.3	Q92973	TNPO1_HUMAN	transportin 1	288					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)		TGTGAATTTTGGCTAACTTTA	0.358																																					p.W288X		Atlas-SNP	.											.	TNPO1	90	.	0			c.G863A						PASS	.						106	103	104					5																	72173116		2203	4300	6503	SO:0001587	stop_gained	3842	exon9			AATTTTGGCTAAC	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.863G>A	5.37:g.72173116G>A	ENSP00000336712:p.Trp288*	107	0	0		116	37	0.318966	NM_002270	B4DVC6|Q92957|Q92975	Nonsense_Mutation	SNP	ENST00000337273.5	37	CCDS43329.1	.	.	.	.	.	.	.	.	.	.	G	37	6.330344	0.97480	.	.	ENSG00000083312	ENST00000337273;ENST00000454282;ENST00000523768;ENST00000506351	.	.	.	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.7328	19.7884	0.96447	0.0:0.0:1.0:0.0	.	.	.	.	X	288;238;238;280	.	ENSP00000336712:W288X	W	+	2	0	TNPO1	72208872	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.318000	0.96334	2.758000	0.94735	0.650000	0.86243	TGG	.	.	none		0.358	TNPO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000218577.3	NM_002270		A	72173116	G	A	72173116	4	1	8	1	0	0	0	0	0	1	0	0	16350	1357	47	2	897	2	TNPO1	5	72173116	Nonsense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	35003589	72173116	108742144	49	888											
PCDHA1	56147	hgsc.bcm.edu	37	chr5	140167650	140167650	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtgcgggtcatgtggtggCgaaggtgcgcgcagtggacg	5	7	22	7	5	1	0	1	0	0	0	1	2	1	1	0	6	2	1	0	6	1	0	rs190769137		TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr5:140167650C>T	ENST00000504120.2	+	1	1775	c.1775C>T	c.(1774-1776)gCg>gTg	p.A592V	PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000378133.3_Missense_Mutation_p.A592V	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	592	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)			CATGTGGTGGCGAAGGTGCGC	0.687																																					p.A592V		Atlas-SNP	.											PCDHA1_ENST00000504120,NS,carcinoma,+1,2	PCDHA1	387	2	0			c.C1775T						PASS	.						105	98	101					5																	140167650		2203	4299	6502	SO:0001583	missense	56147	exon1			TGGTGGCGAAGGT	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.1775C>T	5.37:g.140167650C>T	ENSP00000420840:p.Ala592Val	130	0	0		139	46	0.330935	NM_031410	O75288|Q9NRT7	Missense_Mutation	SNP	ENST00000504120.2	37	CCDS54913.1	.	.	.	.	.	.	.	.	.	.	c	13.07	2.127280	0.37533	.	.	ENSG00000204970	ENST00000504120;ENST00000378133	T;T	0.51574	0.7;0.7	3.36	3.36	0.38483	Cadherin (3);Cadherin-like (1);	0.410677	0.17341	U	0.177745	T	0.39860	0.1094	L	0.52011	1.625	0.26452	N	0.975595	B;B	0.34372	0.451;0.191	B;B	0.29598	0.104;0.063	T	0.40117	-0.9580	10	0.59425	D	0.04	.	11.6879	0.51497	0.0:0.7539:0.2461:0.0	.	592;592	Q9Y5I3;Q9Y5I3-3	PCDA1_HUMAN;.	V	592	ENSP00000420840:A592V;ENSP00000367373:A592V	ENSP00000367373:A592V	A	+	2	0	PCDHA1	140147834	0.000000	0.05858	0.977000	0.42913	0.384000	0.30261	0.552000	0.23376	1.572000	0.49736	0.484000	0.47621	GCG	C|1.000;G|0.000	.	alt		0.687	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900		T	140167650	C	T	140167650	3	4	8	1	0	0	0	0	1	0	0	0	11528	768	27	1	1777	1	PCDHA1	5	140167650	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	67994534	140167650	40747610	50	889											
PCDHA4	56144	hgsc.bcm.edu	37	chr5	140188702	140188702	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggacgaaacggacgctccgCgccaccgcctactggtactg	8	6	12	15	6	0	0	0	0	0	0	1	3	1	2	4	3	3	2	4	3	3	2	rs142688560		TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr5:140188702C>T	ENST00000530339.1	+	1	1930	c.1930C>T	c.(1930-1932)Cgc>Tgc	p.R644C	PCDHA4_ENST00000512229.2_Missense_Mutation_p.R644C|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000356878.4_Missense_Mutation_p.R644C|PCDHA3_ENST00000522353.2_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	644	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)			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)			GGACGCTCCGCGCCACCGCCT	0.682																																					p.R644C		Atlas-SNP	.											PCDHA4_ENST00000530339,NS,carcinoma,-1,2	PCDHA4	419	2	0			c.C1930T						PASS	.	C	,,,CYS/ARG,,CYS/ARG	4,4402	9.9+/-24.2	0,4,2199	76	79	78		,,,1930,,1930	4.1	0	5	dbSNP_134	78	13,8587	9.8+/-36.6	0,13,4287	yes	intron,intron,intron,missense,intron,missense	PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_031411.1,NM_031500.1	,,,180,,180	0,17,6486	TT,TC,CC		0.1512,0.0908,0.1307	,,,,,	,,,644/948,,644/799	140188702	17,12989	2203	4300	6503	SO:0001583	missense	56144	exon1			GCTCCGCGCCACC	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.1930C>T	5.37:g.140188702C>T	ENSP00000435300:p.Arg644Cys	93	0	0		82	6	0.0731707	NM_031500	O75285|Q2M253	Missense_Mutation	SNP	ENST00000530339.1	37	CCDS54916.1	.	.	.	.	.	.	.	.	.	.	c	8.422	0.846641	0.16963	9.08E-4	0.001512	ENSG00000204967	ENST00000512229;ENST00000356878;ENST00000530339	T;T;T	0.53206	0.63;0.63;0.63	4.08	4.08	0.47627	Cadherin (4);Cadherin-like (1);	0.194269	0.23758	U	0.044856	T	0.70833	0.3269	M	0.91663	3.23	0.09310	N	1	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.73380	0.924;0.932;0.98	T	0.64214	-0.6460	10	0.87932	D	0	.	8.772	0.34737	0.1688:0.6675:0.1636:0.0	.	644;644;644	Q9UN74-2;Q9UN74;D6RA20	.;PCDA4_HUMAN;.	C	644	ENSP00000423470:R644C;ENSP00000349344:R644C;ENSP00000435300:R644C	ENSP00000349344:R644C	R	+	1	0	PCDHA4	140168886	0.000000	0.05858	0.047000	0.18901	0.020000	0.10135	-1.228000	0.02948	2.006000	0.58801	0.484000	0.47621	CGC	C|0.998;T|0.002	0.002	strong		0.682	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		T	140188702	C	T	140188702	3	4	8	1	0	0	0	0	1	0	0	0	11535	768	27	1	1932	1	PCDHA4	5	140188702	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	21052	140188702	40726558	51	890											
PCDHA8	56140	hgsc.bcm.edu	37	chr5	140222523	140222523	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccaggtgagcgcgcgcgaCgcgggcgtgccgcctctggg	3	6	18	14	8	1	1	0	1	1	0	2	2	2	1	3	3	2	0	3	3	0	1			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr5:140222523C>T	ENST00000531613.1	+	1	1617	c.1617C>T	c.(1615-1617)gaC>gaT	p.D539D	PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA8_ENST00000378123.3_Silent_p.D539D|PCDHA3_ENST00000522353.2_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	539	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(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)			GCGCGCGCGACGCGGGCGTGC	0.672																																					p.D539D		Atlas-SNP	.											.	PCDHA8	366	.	0			c.C1617T						PASS	.						52	62	59					5																	140222523		2193	4266	6459	SO:0001819	synonymous_variant	56140	exon1			GCGCGACGCGGGC	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.1617C>T	5.37:g.140222523C>T		71	0	0		67	24	0.358209	NM_031856	B9EGT7|O75281	Silent	SNP	ENST00000531613.1	37	CCDS54919.1																																																																																			.	.	none		0.672	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911		T	140222523	C	T	140222523	2	4	8	1	0	0	0	0	0	0	0	1	11539	535	19	1		1	PCDHA8	5	140222523	Silent	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	33821	140222523	40692737	52	891											
RMND5B	64777	hgsc.bcm.edu	37	chr5	177565199	177565199	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctacgggcagcactgtgagCggagcctggaggagctgctg	7	6	17	11	2	0	1	0	1	0	0	0	4	0	4	2	4	6	4	2	4	1	1			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr5:177565199C>T	ENST00000515098.1	+	4	430	c.79C>T	c.(79-81)Cgg>Tgg	p.R27W	RMND5B_ENST00000542098.1_Intron|RMND5B_ENST00000313386.4_Missense_Mutation_p.R27W			Q96G75	RMD5B_HUMAN	required for meiotic nuclear division 5 homolog B (S. cerevisiae)	27										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)			GCACTGTGAGCGGAGCCTGGA	0.672																																					p.R27W		Atlas-SNP	.											.	RMND5B	37	.	0			c.C79T						PASS	.						58	47	50					5																	177565199		2203	4300	6503	SO:0001583	missense	64777	exon3			TGTGAGCGGAGCC	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.79C>T	5.37:g.177565199C>T	ENSP00000420875:p.Arg27Trp	136	0	0		142	44	0.309859	NM_022762	Q1HE27|Q6UVY7|Q9H6F6	Missense_Mutation	SNP	ENST00000515098.1	37	CCDS4431.1	.	.	.	.	.	.	.	.	.	.	C	16.45	3.127598	0.56721	.	.	ENSG00000145916	ENST00000313386;ENST00000515098;ENST00000502814;ENST00000507457;ENST00000508647	.	.	.	5.44	4.49	0.54785	.	0.139173	0.48286	D	0.000200	T	0.27278	0.0669	N	0.08118	0	0.80722	D	1	D	0.56521	0.976	B	0.38712	0.28	T	0.33369	-0.9871	9	0.87932	D	0	-11.477	14.4961	0.67688	0.157:0.843:0.0:0.0	.	27	Q96G75	RMD5B_HUMAN	W	27	.	ENSP00000320623:R27W	R	+	1	2	RMND5B	177497805	1.000000	0.71417	0.999000	0.59377	0.977000	0.68977	3.103000	0.50298	2.533000	0.85409	0.563000	0.77884	CGG	.	.	none		0.672	RMND5B-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373542.1	NM_022762		T	177565199	C	T	177565199	3	4	8	1	0	0	0	0	1	0	0	0	13413	759	27	1	81	1	RMND5B	5	177565199	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	37342676	177565199	3350061	53	892											
HIST1H2BO	8348	hgsc.bcm.edu	37	chr6	27861456	27861456	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcgtcaatgacatctttgaGcgcatcgctggcgaggcttc	7	12	11	11	4	2	2	1	2	1	0	5	3	2	2	0	2	1	3	0	2	1	3			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr6:27861456G>A	ENST00000303806.4	+	1	254	c.216G>A	c.(214-216)gaG>gaA	p.E72E	HIST1H3J_ENST00000359303.2_5'Flank|HIST1H2AM_ENST00000359611.2_5'Flank|HIST1H3J_ENST00000479986.1_5'Flank	NM_003527.4	NP_003518.2	P23527	H2B1O_HUMAN	histone cluster 1, H2bo	72					chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)										ACATCTTTGAGCGCATCGCTG	0.602																																					p.E72E		Atlas-SNP	.											.	HIST1H2BO	30	.	0			c.G216A						PASS	.						131	120	123					6																	27861456		2203	4300	6503	SO:0001819	synonymous_variant	8348	exon1			CTTTGAGCGCATC	X57138	CCDS4640.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000196331			"Histones / Replication-dependent"	4758	protein-coding gene	gene with protein product		602808	"H2B histone family, member N", "histone 1, H2bo"	H2BFN		1768865, 12408966	Standard	NM_003527		Approved	H2B/n, H2B.2	uc003nkc.1	P23527	OTTHUMG00000014493	ENST00000303806.4:c.216G>A	6.37:g.27861456G>A		106	0	0		144	40	0.277778	NM_003527	Q3KPI7|Q8TCV6	Silent	SNP	ENST00000303806.4	37	CCDS4640.1																																																																																			.	.	none		0.602	HIST1H2BO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040161.1	NM_003527		A	27861456	G	A	27861456	2	1	8	1	0	0	0	0	0	0	0	1	7163	962	34	2		2	HIST1H2BO	6	27861456	Silent	SNP	G	TCGA-FA-A82F-01A-11D-A382-10		27861456	143253611	54	893											
ABCF1	23	hgsc.bcm.edu	37	chr6	30553422	30553422	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgcactgatatcatccacctCgatgcccagcggctccacta	9	9	7	16	2	1	1	1	1	0	0	4	2	3	1	4	1	3	2	4	1	2	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr6:30553422C>T	ENST00000326195.8	+	16	1675	c.1563C>T	c.(1561-1563)ctC>ctT	p.L521L	MIR877_ENST00000401282.1_RNA|ABCF1_ENST00000376545.3_Silent_p.L483L|ABCF1_ENST00000396515.4_Intron	NM_001025091.1	NP_001020262.1	Q8NE71	ABCF1_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 1	521	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						TCATCCACCTCGATGCCCAGC	0.532																																					p.L521L		Atlas-SNP	.											.	ABCF1	61	.	0			c.C1563T						PASS	.						118	109	113					6																	30553422		1511	2709	4220	SO:0001819	synonymous_variant	23	exon16			CCACCTCGATGCC	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.1563C>T	6.37:g.30553422C>T		42	0	0		57	20	0.350877	NM_001025091	A2BF75|O14897|Q69YP6	Silent	SNP	ENST00000326195.8	37	CCDS34380.1																																																																																			.	.	none		0.532	ABCF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076137.3			T	30553422	C	T	30553422	2	4	8	1	0	0	0	0	0	0	0	1	65	871	31	1		1	ABCF1	6	30553422	Silent	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	2691966	30553422	140561645	55	894											
PIM1	5292	hgsc.bcm.edu	37	chr6	37138423	37138423	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aacgacctgcacgccaccaaGctggcgcccggtgagagcac	10	3	12	16	4	0	1	0	1	0	1	0	3	0	1	4	2	4	3	4	2	2	0			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr6:37138423G>A	ENST00000373509.5	+	1	445	c.72G>A	c.(70-72)aaG>aaA	p.K24K		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	115					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)	p.K24N(1)		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)	ACGCCACCAAGCTGGCGCCCG	0.726			T	BCL6	NHL																																p.K115K		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,0,1	PIM1	71	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G345A						PASS	.						22	25	24					6																	37138423		2197	4289	6486	SO:0001819	synonymous_variant	5292	exon1			CACCAAGCTGGCG		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.72G>A	6.37:g.37138423G>A		61	0	0		92	26	0.282609	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.726	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			A	37138423	G	A	37138423	2	1	8	1	0	0	0	0	0	0	0	1	11936	962	34	2		2	PIM1	6	37138423	Silent	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	6585001	37138423	133976644	56	895			3	10		5	5	665	N	G_C	5.432066e-12
PIM1	5292	hgsc.bcm.edu	37	chr6	37138804	37138804	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cggatttccgactggggagaGctggtgagtgccctgcagga	7	8	17	9	2	0	2	0	1	0	1	1	6	1	4	2	5	3	2	2	5	0	1			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr6:37138804G>T	ENST00000373509.5	+	3	610	c.237G>T	c.(235-237)gaG>gaT	p.E79D		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	170					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)	p.E79D(1)		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)	ACTGGGGAGAGCTGGTGAGTG	0.687			T	BCL6	NHL																																p.E170D		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,0,4	PIM1	71	4	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G510T						PASS	.						51	53	52					6																	37138804		2203	4300	6503	SO:0001583	missense	5292	exon3			GGGAGAGCTGGTG		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.237G>T	6.37:g.37138804G>T	ENSP00000362608:p.Glu79Asp	83	0	0		82	22	0.268293	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	G	12.64	1.999653	0.35320	.	.	ENSG00000137193	ENST00000373509	T	0.66280	-0.2	4.44	0.389	0.16269	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.068351	0.56097	D	0.000034	T	0.16938	0.0407	N	0.11023	0.085	0.34210	D	0.674133	B	0.15473	0.013	B	0.14578	0.011	T	0.02345	-1.1173	10	0.37606	T	0.19	.	4.6029	0.12363	0.4591:0.0:0.3935:0.1474	.	170	P11309	PIM1_HUMAN	D	79	ENSP00000362608:E79D	ENSP00000362608:E79D	E	+	3	2	PIM1	37246782	0.728000	0.28080	0.985000	0.45067	0.975000	0.68041	0.054000	0.14205	-0.042000	0.13535	0.549000	0.68633	GAG	.	.	none		0.687	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37138804	G	T	37138804	3	4	8	1	0	0	0	0	1	0	0	0	11936	962	34	4	247	4	PIM1	6	37138804	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	381	37138804	133976263	57	896			3	10		5	5	665	N	G_C	5.432066e-12
PIM1	5292	hgsc.bcm.edu	37	chr6	37138937	37138937	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgcccatggaagtggtcctgCtgaagaaggtgagctcgggt	8	9	16	8	1	0	3	0	2	0	1	2	4	1	4	2	4	3	2	2	4	3	0	rs548710452	byFrequency	TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr6:37138937C>T	ENST00000373509.5	+	4	650	c.277C>T	c.(277-279)Ctg>Ttg	p.L93L		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	184					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)	AGTGGTCCTGCTGAAGAAGGT	0.657			T	BCL6	NHL								C|||	2	0.000399361	0.0	0.0	5008	,	,		14843	0.002		0.0	False		,,,				2504	0.0				p.L184L		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C550T						PASS	.						73	81	79					6																	37138937		2203	4300	6503	SO:0001819	synonymous_variant	5292	exon4			GTCCTGCTGAAGA		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.277C>T	6.37:g.37138937C>T		54	0	0		73	15	0.205479	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.657	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37138937	C	T	37138937	2	4	8	1	0	0	0	0	0	0	0	1	11936	796	28	2		2	PIM1	6	37138937	Silent	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	133	37138937	133976130	58	897			3	10		5	5	665	N	G_C	5.432066e-12
PIM1	5292	hgsc.bcm.edu	37	chr6	37138950	37138950	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggtcctgctgaagaaggtgaGctcgggtttctccggcgtca	6	10	15	10	3	2	3	1	2	1	1	5	3	3	3	2	4	2	3	2	4	2	1	rs562319987		TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr6:37138950G>C	ENST00000373509.5	+	4	663	c.290G>C	c.(289-291)aGc>aCc	p.S97T		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	188					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)	p.S97N(2)		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)	AAGAAGGTGAGCTCGGGTTTC	0.647			T	BCL6	NHL																																p.S188T		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,0,5	PIM1	71	5	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.G563C						scavenged	.						82	91	88					6																	37138950		2203	4300	6503	SO:0001583	missense	5292	exon4			AGGTGAGCTCGGG		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.290G>C	6.37:g.37138950G>C	ENSP00000362608:p.Ser97Thr	67	1	0.0149254		77	6	0.0779221	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	G	11.68	1.709883	0.30322	.	.	ENSG00000137193	ENST00000373509	T	0.14640	2.49	4.14	4.14	0.48551	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.123358	0.56097	D	0.000035	T	0.06462	0.0166	L	0.48935	1.535	0.47037	D	0.99929	B	0.13145	0.007	B	0.18263	0.021	T	0.12811	-1.0533	10	0.16896	T	0.51	.	16.5618	0.84568	0.0:0.0:1.0:0.0	.	188	P11309	PIM1_HUMAN	T	97	ENSP00000362608:S97T	ENSP00000362608:S97T	S	+	2	0	PIM1	37246928	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.570000	0.82390	2.283000	0.76528	0.549000	0.68633	AGC	.	.	none		0.647	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			C	37138950	G	C	37138950	3	2	8	1	0	0	0	0	1	0	0	0	11936	971	34	4	304	4	PIM1	6	37138950	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	13	37138950	133976117	59	898			3	10		5	5	665	N	G_C	5.432066e-12
PIM1	5292	hgsc.bcm.edu	37	chr6	37139087	37139087	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggggagccctgcaagaggagCtggcccgcagcttcttctgg	6	7	16	12	1	2	1	0	0	2	1	2	3	2	3	2	5	4	4	2	5	1	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr6:37139087C>G	ENST00000373509.5	+	4	800	c.427C>G	c.(427-429)Ctg>Gtg	p.L143V		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	234	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)	GCAAGAGGAGCTGGCCCGCAG	0.612			T	BCL6	NHL																																p.L234V		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,0,1	PIM1	71	1	0			c.C700G						scavenged	.						58	69	66					6																	37139087		2203	4300	6503	SO:0001583	missense	5292	exon4			GAGGAGCTGGCCC		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.427C>G	6.37:g.37139087C>G	ENSP00000362608:p.Leu143Val	112	2	0.0178571		104	41	0.394231	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	8.238	0.806101	0.16467	.	.	ENSG00000137193	ENST00000373509	T	0.65732	-0.17	4.19	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);	0.414587	0.22060	N	0.065197	T	0.22781	0.0550	N	0.12471	0.22	0.44123	D	0.996902	B	0.22146	0.065	B	0.31751	0.135	T	0.08289	-1.0729	10	0.31617	T	0.26	.	3.7592	0.08598	0.3065:0.5026:0.0:0.1909	.	234	P11309	PIM1_HUMAN	V	143	ENSP00000362608:L143V	ENSP00000362608:L143V	L	+	1	2	PIM1	37247065	1.000000	0.71417	1.000000	0.80357	0.432000	0.31715	2.493000	0.45320	0.981000	0.38548	-0.480000	0.04831	CTG	.	.	none		0.612	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			G	37139087	C	G	37139087	3	3	8	1	0	0	0	0	1	0	0	0	11936	796	28	4	441	4	PIM1	6	37139087	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	137	37139087	133975980	60	899			3	10		5	5	665	N	G_C	5.432066e-12
KIF6	221458	hgsc.bcm.edu	37	chr6	39563864	39563864	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtagtgacaagttgatatacTtggcctctgttagaagatgg	11	13	12	5	0	1	4	0	2	1	2	1	4	1	4	1	2	1	3	1	2	6	6	rs150066437		TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr6:39563864T>G	ENST00000287152.7	-	7	906	c.812A>C	c.(811-813)aAg>aCg	p.K271T	KIF6_ENST00000373215.3_Missense_Mutation_p.K271T|KIF6_ENST00000373213.4_Missense_Mutation_p.K110T|KIF6_ENST00000538893.1_Missense_Mutation_p.K271T|KIF6_ENST00000373216.3_Missense_Mutation_p.K271T	NM_145027.4	NP_659464.3	Q6ZMV9	KIF6_HUMAN	kinesin family member 6	271	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						GTTGATATACTTGGCCTCTGT	0.438																																					p.K271T		Atlas-SNP	.											.	KIF6	233	.	0			c.A812C						PASS	.						109	100	103					6																	39563864		2203	4300	6503	SO:0001583	missense	221458	exon7			ATATACTTGGCCT	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.812A>C	6.37:g.39563864T>G	ENSP00000287152:p.Lys271Thr	138	0	0		207	71	0.342995	NM_145027	Q2MDE3|Q2MDE4|Q5T8J6|Q6ZWE3|Q86T87|Q8WTV4	Missense_Mutation	SNP	ENST00000287152.7	37	CCDS4844.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.15|16.15	3.041241|3.041241	0.55003|0.55003	.|.	.|.	ENSG00000164627|ENSG00000164627	ENST00000287152;ENST00000373216;ENST00000373213;ENST00000373215;ENST00000538893;ENST00000441975;ENST00000373211|ENST00000458470	T;T;T;T;T;T|.	0.75260|.	-0.92;-0.92;-0.92;-0.92;-0.92;-0.92|.	5.98|5.98	5.98|5.98	0.97165|0.97165	Kinesin, motor domain (4);|.	.|.	.|.	.|.	.|.	T|T	0.46795|0.46795	0.1411|0.1411	L|L	0.38692|0.38692	1.165|1.165	0.80722|0.80722	D|D	1|1	D;P;D;D|.	0.89917|.	1.0;0.929;0.959;1.0|.	D;P;P;D|.	0.85130|.	0.995;0.614;0.749;0.997|.	T|T	0.45116|0.45116	-0.9283|-0.9283	9|5	0.02654|.	T|.	1|.	.|.	14.7079|14.7079	0.69206|0.69206	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	271;271;271;271|.	E7EUN7;F6VGH2;Q6ZMV9-3;Q6ZMV9|.	.;.;.;KIF6_HUMAN|.	T|R	271;271;110;271;271;58;62|163	ENSP00000287152:K271T;ENSP00000362312:K271T;ENSP00000362309:K110T;ENSP00000362311:K271T;ENSP00000441435:K271T;ENSP00000404856:K58T|.	ENSP00000287152:K271T|.	K|S	-|-	2|1	0|0	KIF6|KIF6	39671842|39671842	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.968000|0.968000	0.65278|0.65278	8.040000|8.040000	0.89188|0.89188	2.288000|2.288000	0.76882|0.76882	0.528000|0.528000	0.53228|0.53228	AAG|AGT	T|1.000;C|0.000	.	alt		0.438	KIF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040455.2	NM_145027		G	39563864	T	G	39563864	3	3	8	1	0	0	0	0	1	0	0	0	8317	1609	56	5	1700	5	KIF6	6	39563864	Missense_Mutation	SNP	T	TCGA-FA-A82F-01A-11D-A382-10	2424777	39563864	131551203	61	900											
IMPG1	3617	hgsc.bcm.edu	37	chr6	76713610	76713610	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctctgttataacagcaaaaGatgtgggcagctctgattgg	11	11	11	8	0	2	2	0	1	2	1	2	2	2	2	1	2	3	4	1	2	4	3			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr6:76713610G>T	ENST00000369950.3	-	11	1382	c.1193C>A	c.(1192-1194)tCt>tAt	p.S398Y	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)				AACAGCAAAAGATGTGGGCAG	0.378																																					p.S398Y	Pancreas(37;839 1141 2599 26037)	Atlas-SNP	.											.	IMPG1	143	.	0			c.C1193A						PASS	.						86	77	80					6																	76713610		2203	4300	6503	SO:0001583	missense	3617	exon11			GCAAAAGATGTGG	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.1193C>A	6.37:g.76713610G>T	ENSP00000358966:p.Ser398Tyr	51	0	0		60	15	0.25	NM_001563		Missense_Mutation	SNP	ENST00000369950.3	37	CCDS4985.1	.	.	.	.	.	.	.	.	.	.	G	8.289	0.817231	0.16607	.	.	ENSG00000112706	ENST00000369950	T	0.21734	1.99	4.32	1.36	0.22044	.	0.570121	0.16822	N	0.198108	T	0.02012	0.0063	N	0.08118	0	0.09310	N	1	P	0.46706	0.883	B	0.34722	0.188	T	0.34502	-0.9826	10	0.35671	T	0.21	.	2.3028	0.04166	0.2982:0.0:0.4574:0.2445	.	398	Q17R60	IMPG1_HUMAN	Y	398	ENSP00000358966:S398Y	ENSP00000358966:S398Y	S	-	2	0	IMPG1	76770330	0.002000	0.14202	0.000000	0.03702	0.002000	0.02628	1.090000	0.30902	0.138000	0.18790	0.563000	0.77884	TCT	.	.	none		0.378	IMPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041288.1	NM_001563		T	76713610	G	T	76713610	3	4	8	1	0	0	0	0	1	0	0	0	7737	942	33	4	1228	4	IMPG1	6	76713610	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	37149746	76713610	94401457	62	901											
KIF25	3834	hgsc.bcm.edu	37	chr6	168440827	168440827	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaccccaccctggtgcacGcggattcctccaggtctcac	7	7	9	18	2	1	0	1	0	1	0	4	1	3	1	5	3	2	2	5	3	0	1	rs148907230	byFrequency	TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr6:168440827G>A	ENST00000443060.2	+	7	968	c.577G>A	c.(577-579)Gcg>Acg	p.A193T	KIF25_ENST00000354419.2_Missense_Mutation_p.A193T|KIF25_ENST00000351261.3_Missense_Mutation_p.A193T			Q9UIL4	KIF25_HUMAN	kinesin family member 25	193	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)		CCTGGTGCACGCGGATTCCTC	0.572													G|||	2	0.000399361	0.0008	0.0	5008	,	,		19153	0.0		0.0	False		,,,				2504	0.001				p.A193T		Atlas-SNP	.											.	KIF25	75	.	0			c.G577A						PASS	.	G	THR/ALA,THR/ALA	0,4406		0,0,2203	85	74	78		577,577	3.6	0	6	dbSNP_134	78	3,8597	3.0+/-9.4	0,3,4297	no	missense,missense	KIF25	NM_005355.3,NM_030615.2	58,58	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging,probably-damaging	193/333,193/385	168440827	3,13003	2203	4300	6503	SO:0001583	missense	3834	exon6			GTGCACGCGGATT	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.577G>A	6.37:g.168440827G>A	ENSP00000388878:p.Ala193Thr	41	0	0		49	14	0.285714	NM_030615	O94775|Q5SZU9	Missense_Mutation	SNP	ENST00000443060.2	37	CCDS5305.1	.	.	.	.	.	.	.	.	.	.	G	14.25	2.479459	0.44044	0.0	3.49E-4	ENSG00000125337	ENST00000443060;ENST00000354419;ENST00000351261	T;T;T	0.75477	-0.94;-0.94;-0.94	3.56	3.56	0.40772	Kinesin, motor domain (5);	0.256528	0.30879	N	0.008681	T	0.56381	0.1981	L	0.55743	1.74	0.26415	N	0.976198	P;B	0.42357	0.777;0.169	B;B	0.41691	0.364;0.046	T	0.53136	-0.8481	10	0.52906	T	0.07	-14.4088	10.5163	0.44892	0.0:0.0:1.0:0.0	.	193;193	Q9UIL4-2;Q9UIL4	.;KIF25_HUMAN	T	193	ENSP00000388878:A193T;ENSP00000346401:A193T;ENSP00000252688:A193T	ENSP00000252688:A193T	A	+	1	0	KIF25	168183676	0.242000	0.23868	0.012000	0.15200	0.007000	0.05969	1.256000	0.32921	1.821000	0.53095	0.411000	0.27672	GCG	G|1.000;A|0.000	0.000	weak		0.572	KIF25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362509.1			A	168440827	G	A	168440827	3	1	8	1	0	0	0	0	1	0	0	0	8302	1087	38	1	595	1	KIF25	6	168440827	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	91727217	168440827	2674240	63	902											
THSD7A	221981	hgsc.bcm.edu	37	chr7	11418733	11418733	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagaaaccaggtccttccccGtcctgctgggttactggagg	7	10	12	12	1	0	1	0	0	0	1	3	2	3	2	5	4	3	2	5	4	3	3			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr7:11418733G>A	ENST00000423059.4	-	26	5016	c.4765C>T	c.(4765-4767)Cgg>Tgg	p.R1589W	AC004538.3_ENST00000421121.1_RNA|AC004538.3_ENST00000595972.1_RNA|AC004538.3_ENST00000599875.1_RNA|AC004538.3_ENST00000428967.1_RNA|AC004538.3_ENST00000445839.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	1589					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)		GTCCTTCCCCGTCCTGCTGGG	0.493										HNSCC(18;0.044)																											p.R1589W		Atlas-SNP	.											THSD7A,NS,carcinoma,+2,1	THSD7A	219	1	0			c.C4765T						PASS	.						101	100	100					7																	11418733		1895	4112	6007	SO:0001583	missense	221981	exon25			TTCCCCGTCCTGC		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.4765C>T	7.37:g.11418733G>A	ENSP00000406482:p.Arg1589Trp	244	0	0		288	110	0.381944	NM_015204		Missense_Mutation	SNP	ENST00000423059.4	37	CCDS47543.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.066037	0.76187	.	.	ENSG00000005108	ENST00000262042;ENST00000423059	T	0.59502	0.26	5.87	3.08	0.35506	.	0.226724	0.46145	N	0.000304	T	0.56124	0.1964	L	0.38175	1.15	0.37238	D	0.906008	D;D	0.69078	0.997;0.997	P;P	0.57468	0.821;0.821	T	0.58973	-0.7541	10	0.54805	T	0.06	.	5.9024	0.18974	0.2052:0.0:0.6592:0.1356	.	1589;1589	Q9UPZ6;C9JL67	THS7A_HUMAN;.	W	1589	ENSP00000406482:R1589W	ENSP00000262042:R1589W	R	-	1	2	THSD7A	11385258	0.960000	0.32886	0.994000	0.49952	0.996000	0.88848	0.464000	0.21988	0.382000	0.24878	0.650000	0.86243	CGG	.	.	none		0.493	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		A	11418733	G	A	11418733	3	1	8	1	0	0	0	0	1	0	0	0	15894	1144	40	1	220	1	THSD7A	7	11418733	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10		11418733	147719930	64	903											
C7orf65	401335	hgsc.bcm.edu	37	chr7	47694914	47694914	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agagtcaacagaaggaagacGgctctggccgggccccaggg	11	3	16	11	2	2	3	1	0	1	3	2	4	2	4	3	5	1	1	3	5	3	0			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr7:47694914G>A	ENST00000408988.2	+	1	73	c.38G>A	c.(37-39)cGg>cAg	p.R13Q		NM_001123065.1	NP_001116537.1	Q6ZTY9	CG065_HUMAN	chromosome 7 open reading frame 65	13										endometrium(1)|lung(2)	3						GAAGGAAGACGGCTCTGGCCG	0.622																																					p.R13Q		Atlas-SNP	.											.	C7orf65	18	.	0			c.G38A						PASS	.						47	52	51					7																	47694914		1568	3582	5150	SO:0001583	missense	401335	exon1			GAAGACGGCTCTG		CCDS43580.1	7p12.3	2009-02-11			ENSG00000221845	ENSG00000221845			34432	protein-coding gene	gene with protein product							Standard	NM_001123065		Approved	FLJ44108	uc010kyp.1	Q6ZTY9	OTTHUMG00000155550	ENST00000408988.2:c.38G>A	7.37:g.47694914G>A	ENSP00000386198:p.Arg13Gln	196	0	0		197	18	0.0913706	NM_001123065	A4D2F8	Missense_Mutation	SNP	ENST00000408988.2	37	CCDS43580.1	.	.	.	.	.	.	.	.	.	.	G	9.775	1.173730	0.21704	.	.	ENSG00000221845	ENST00000408988	.	.	.	2.48	-0.944	0.10392	.	.	.	.	.	T	0.16854	0.0405	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.04013	0.001	T	0.20009	-1.0288	8	0.87932	D	0	.	5.4423	0.16515	0.6062:0.0:0.3938:0.0	.	13	Q6ZTY9	CG065_HUMAN	Q	13	.	ENSP00000386198:R13Q	R	+	2	0	C7orf65	47661439	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.321000	0.08018	-0.248000	0.09583	-0.123000	0.14984	CGG	.	.	none		0.622	C7orf65-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340616.1	NM_001123065		A	47694914	G	A	47694914	3	1	8	1	0	0	0	0	1	0	0	0	2413	1116	39	1	40	1	C7orf65	7	47694914	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	36276181	47694914	111443749	65	904											
FKBP6	8468	hgsc.bcm.edu	37	chr7	72743416	72743416	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gacccttcgattctaattacTttaggaaaactcctcggcta	11	13	6	11	2	1	0	0	0	1	0	4	3	2	1	2	2	2	1	2	2	6	7			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr7:72743416T>G	ENST00000252037.4	+	3	298	c.229T>G	c.(229-231)Ttt>Gtt	p.F77V	TRIM50_ENST00000333149.2_5'Flank|FKBP6_ENST00000413573.2_Intron|TRIM50_ENST00000493498.1_5'Flank|FKBP6_ENST00000431982.2_Missense_Mutation_p.F72V	NM_003602.3	NP_003593.3	O75344	FKBP6_HUMAN	FK506 binding protein 6, 36kDa	77	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)				TTCTAATTACTTTAGGAAAAC	0.448																																					p.F77V		Atlas-SNP	.											.	FKBP6	35	.	0			c.T229G						PASS	.						179	178	178					7																	72743416		2203	4300	6503	SO:0001583	missense	8468	exon3			AATTACTTTAGGA	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.229T>G	7.37:g.72743416T>G	ENSP00000252037:p.Phe77Val	118	0	0		96	32	0.333333	NM_003602	B4DXT7|G3V0I2|Q7Z4T4|Q9UDS0	Missense_Mutation	SNP	ENST00000252037.4	37	CCDS43595.1	.	.	.	.	.	.	.	.	.	.	T	10.91	1.484818	0.26598	.	.	ENSG00000077800	ENST00000431982;ENST00000442793;ENST00000252037	D;D;D	0.85411	-1.98;-1.98;-1.98	4.76	2.36	0.29203	Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain (2);	0.301814	0.36101	N	0.002792	T	0.64283	0.2584	N	0.08118	0	0.30677	N	0.752777	B;B	0.20988	0.05;0.005	B;B	0.21360	0.034;0.03	T	0.52939	-0.8508	10	0.15499	T	0.54	-9.3851	4.5343	0.12020	0.1432:0.1673:0.0:0.6895	.	72;77	O75344-2;O75344	.;FKBP6_HUMAN	V	72;72;77	ENSP00000416277:F72V;ENSP00000402360:F72V;ENSP00000252037:F77V	ENSP00000252037:F77V	F	+	1	0	FKBP6	72381352	0.006000	0.16342	0.983000	0.44433	0.769000	0.43574	1.100000	0.31025	0.208000	0.20626	-0.611000	0.04053	TTT	.	.	none		0.448	FKBP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318723.1	NM_003602		G	72743416	T	G	72743416	3	3	8	1	0	0	0	0	1	0	0	0	5920	1609	56	5	285	5	FKBP6	7	72743416	Missense_Mutation	SNP	T	TCGA-FA-A82F-01A-11D-A382-10	25048502	72743416	86395247	66	905											
PCLO	27445	hgsc.bcm.edu	37	chr7	82583245	82583245	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tattacagaagaaggtgggtGatcaaacacggtttcggata	14	10	12	5	2	1	3	1	1	0	2	2	4	1	4	0	4	2	1	0	4	6	4			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr7:82583245G>T	ENST00000333891.9	-	5	7361	c.7024C>A	c.(7024-7026)Cac>Aac	p.H2342N	PCLO_ENST00000423517.2_Missense_Mutation_p.H2342N	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						GAAGGTGGGTGATCAAACACG	0.423																																					p.H2342N		Atlas-SNP	.											.	PCLO	1506	.	0			c.C7024A						PASS	.						90	92	91					7																	82583245		1870	4105	5975	SO:0001583	missense	27445	exon5			GTGGGTGATCAAA	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.7024C>A	7.37:g.82583245G>T	ENSP00000334319:p.His2342Asn	195	0	0		195	23	0.117949	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	G	8.129	0.782662	0.16189	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.15487	2.42;2.42	4.75	4.75	0.60458	.	.	.	.	.	T	0.10465	0.0256	N	0.08118	0	0.58432	D	0.999995	B;B	0.16396	0.017;0.017	B;B	0.13407	0.009;0.009	T	0.10823	-1.0613	9	0.87932	D	0	.	13.4843	0.61355	0.0:0.1571:0.8429:0.0	.	2342;2342	Q9Y6V0-5;Q9Y6V0-6	.;.	N	2273;2342;2342	ENSP00000334319:H2342N;ENSP00000388393:H2342N	ENSP00000334319:H2342N	H	-	1	0	PCLO	82421181	0.840000	0.29493	0.029000	0.17559	0.660000	0.38997	3.412000	0.52679	2.169000	0.68431	0.505000	0.49811	CAC	.	.	none		0.423	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82583245	G	T	82583245	3	4	8	1	0	0	0	0	1	0	0	0	11592	1290	45	4	8505	4	PCLO	7	82583245	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	9839829	82583245	76555418	67	906											
SEMA3D	223117	hgsc.bcm.edu	37	chr7	84685039	84685039	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taaatatatcttgccttacaAactcttccaactcgagaaag	15	12	4	10	1	2	1	0	0	2	1	4	2	3	1	2	0	4	0	2	0	8	6			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr7:84685039A>G	ENST00000284136.6	-	7	898	c.855T>C	c.(853-855)gtT>gtC	p.V285V	SEMA3D_ENST00000444867.1_Silent_p.V285V	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	285	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						TTGCCTTACAAACTCTTCCAA	0.259																																					p.V285V	Ovarian(63;442 1191 17318 29975 31528)	Atlas-SNP	.											.	SEMA3D	177	.	0			c.T855C						PASS	.																																			SO:0001819	synonymous_variant	223117	exon7			CTTACAAACTCTT	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.855T>C	7.37:g.84685039A>G		46	0	0		49	19	0.387755	NM_152754	A6NK46|Q6UW77|Q8NCQ1	Silent	SNP	ENST00000284136.6	37	CCDS34676.1																																																																																			.	.	none		0.259	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754		G	84685039	A	G	84685039	2	3	8	1	0	0	0	0	0	0	0	1	14042	1	1	3		3	SEMA3D	7	84685039	Silent	SNP	A	TCGA-FA-A82F-01A-11D-A382-10	2101794	84685039	74453624	68	907											
EPHB4	2050	hgsc.bcm.edu	37	chr7	100420197	100420197	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tagaagccagccttgctgagCggtcccagacgcagcgtctt	8	8	12	13	3	1	3	0	1	1	2	2	3	2	3	3	1	5	2	3	1	2	3	rs532613401		TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr7:100420197C>T	ENST00000358173.3	-	4	972	c.504G>A	c.(502-504)ccG>ccA	p.P168P	RN7SL750P_ENST00000582814.1_RNA|EPHB4_ENST00000477446.1_5'UTR|EPHB4_ENST00000360620.3_Silent_p.P168P	NM_004444.4	NP_004435.3	P54760	EPHB4_HUMAN	EPH receptor B4	168	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				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)					CCTTGCTGAGCGGTCCCAGAC	0.657													C|||	1	0.000199681	0.0008	0.0	5008	,	,		15631	0.0		0.0	False		,,,				2504	0.0				p.P168P	GBM(200;2113 3072 25865 52728)	Atlas-SNP	.											.	EPHB4	106	.	0			c.G504A						PASS	.						44	44	44					7																	100420197		2203	4300	6503	SO:0001819	synonymous_variant	2050	exon4			GCTGAGCGGTCCC	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.504G>A	7.37:g.100420197C>T		110	0	0		86	18	0.209302	NM_004444	B5A970|B5A971|B5A972|Q7Z635|Q9BTA5|Q9BXP0	Silent	SNP	ENST00000358173.3	37	CCDS5706.1																																																																																			.	.	none		0.657	EPHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347222.1	NM_004444		T	100420197	C	T	100420197	2	4	8	1	0	0	0	0	0	0	0	1	5179	755	27	1		1	EPHB4	7	100420197	Silent	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	15735158	100420197	58718466	69	908											
SLC26A3	1811	hgsc.bcm.edu	37	chr7	107408040	107408040	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttacctcatatacccgattaCgtaatcctccatttgtattt	10	17	3	11	2	1	0	1	0	0	0	3	1	3	0	4	0	3	2	4	0	6	8			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr7:107408040C>T	ENST00000340010.5	-	20	2439	c.2255G>A	c.(2254-2256)cGt>cAt	p.R752H	SLC26A3_ENST00000422236.2_Missense_Mutation_p.R639H	NM_000111.2	NP_000102.1	P40879	S26A3_HUMAN	solute carrier family 26 (anion exchanger), member 3	752					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						TACCCGATTACGTAATCCTCC	0.343																																					p.R752H		Atlas-SNP	.											SLC26A3,NS,carcinoma,0,4	SLC26A3	120	4	0			c.G2255A						PASS	.						101	105	103					7																	107408040		2203	4299	6502	SO:0001583	missense	1811	exon20			CGATTACGTAATC	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.2255G>A	7.37:g.107408040C>T	ENSP00000345873:p.Arg752His	176	0	0		156	40	0.25641	NM_000111		Missense_Mutation	SNP	ENST00000340010.5	37	CCDS5748.1	.	.	.	.	.	.	.	.	.	.	C	14.03	2.415080	0.42817	.	.	ENSG00000091138	ENST00000422236;ENST00000340010	D;D	0.94613	-3.47;-3.31	4.64	3.77	0.43336	.	0.392271	0.27961	N	0.017141	D	0.90013	0.6882	L	0.46885	1.475	0.25690	N	0.985706	B;B	0.29955	0.163;0.263	B;B	0.20767	0.029;0.031	T	0.81976	-0.0686	10	0.38643	T	0.18	.	10.1245	0.42641	0.0:0.9054:0.0:0.0946	.	639;752	G5E9U3;P40879	.;S26A3_HUMAN	H	639;752	ENSP00000415817:R639H;ENSP00000345873:R752H	ENSP00000345873:R752H	R	-	2	0	SLC26A3	107195276	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	1.672000	0.37523	1.185000	0.42971	0.644000	0.83932	CGT	.	.	none		0.343	SLC26A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337190.1	NM_000111		T	107408040	C	T	107408040	3	4	8	1	0	0	0	0	1	0	0	0	14533	536	19	1	47	1	SLC26A3	7	107408040	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	6987843	107408040	51730623	70	909											
TNKS	8658	hgsc.bcm.edu	37	chr8	9567708	9567708	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccataatgatgtcatggaagTtctgcataagcatggcgcca	12	10	10	9	1	2	1	1	1	1	0	2	2	2	2	2	2	2	3	2	2	3	3			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr8:9567708T>G	ENST00000310430.6	+	11	1753	c.1727T>G	c.(1726-1728)gTt>gGt	p.V576G	TNKS_ENST00000518281.1_Missense_Mutation_p.V339G|TNKS_ENST00000520408.1_Missense_Mutation_p.V576G	NM_003747.2	NP_003738.2	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	576					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)		GTCATGGAAGTTCTGCATAAG	0.488																																					p.V576G		Atlas-SNP	.											.	TNKS	198	.	0			c.T1727G						PASS	.						67	62	63					8																	9567708		2203	4300	6503	SO:0001583	missense	8658	exon11			TGGAAGTTCTGCA	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.1727T>G	8.37:g.9567708T>G	ENSP00000311579:p.Val576Gly	163	0	0		122	29	0.237705	NM_003747	O95272|Q4G0F2	Missense_Mutation	SNP	ENST00000310430.6	37	CCDS5974.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.720979	0.89205	.	.	ENSG00000173273	ENST00000520408;ENST00000310430;ENST00000518281	T;T;T	0.65916	-0.18;-0.18;-0.18	5.53	5.53	0.82687	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.77445	0.4131	M	0.70787	2.145	0.80722	D	1	D;P	0.71674	0.998;0.607	D;P	0.72982	0.979;0.589	T	0.77558	-0.2543	10	0.41790	T	0.15	.	15.6624	0.77197	0.0:0.0:0.0:1.0	.	576;576	E7EWY6;O95271	.;TNKS1_HUMAN	G	576;576;339	ENSP00000428299:V576G;ENSP00000311579:V576G;ENSP00000429890:V339G	ENSP00000311579:V576G	V	+	2	0	TNKS	9605118	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.022000	0.88759	2.095000	0.63458	0.533000	0.62120	GTT	.	.	none		0.488	TNKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206935.1	NM_003747		G	9567708	T	G	9567708	3	3	8	1	0	0	0	0	1	0	0	0	16334	1725	60	5	1769	5	TNKS	8	9567708	Missense_Mutation	SNP	T	TCGA-FA-A82F-01A-11D-A382-10		9567708	136796314	71	910											
MTUS1	57509	hgsc.bcm.edu	37	chr8	17611707	17611707	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	atgagggtgatgaggcactgGtctgctgaggtctgggcgtg	6	10	19	6	1	2	4	0	4	2	0	2	4	2	4	0	5	1	2	0	5	0	0			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr8:17611707G>T	ENST00000262102.6	-	2	1834	c.1610C>A	c.(1609-1611)aCc>aAc	p.T537N	MTUS1_ENST00000519263.1_Missense_Mutation_p.T537N|MTUS1_ENST00000381862.3_Missense_Mutation_p.T537N|MTUS1_ENST00000381869.3_Missense_Mutation_p.T537N	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	537					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)		TGAGGCACTGGTCTGCTGAGG	0.438																																					p.T537N		Atlas-SNP	.											MTUS1,colon,carcinoma,0,3	MTUS1	144	3	0			c.C1610A						PASS	.						214	206	209					8																	17611707		2077	4205	6282	SO:0001583	missense	57509	exon2			GCACTGGTCTGCT	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.1610C>A	8.37:g.17611707G>T	ENSP00000262102:p.Thr537Asn	210	0	0		196	59	0.30102	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	.	.	.	.	.	.	.	.	.	.	G	12.86	2.063884	0.36373	.	.	ENSG00000129422	ENST00000381869;ENST00000262102;ENST00000519263;ENST00000381862	T;T;T;T	0.37752	3.02;1.18;3.02;2.04	5.1	3.23	0.37069	.	0.444177	0.20589	N	0.089392	T	0.25195	0.0612	L	0.29908	0.895	0.09310	N	1	P;B;B	0.43287	0.802;0.091;0.091	B;B;B	0.36719	0.231;0.018;0.018	T	0.08764	-1.0706	10	0.72032	D	0.01	-0.6686	11.7274	0.51716	0.0:0.1343:0.726:0.1397	.	537;537;537	Q9ULD2-5;Q9ULD2-2;Q9ULD2	.;.;MTUS1_HUMAN	N	537	ENSP00000371293:T537N;ENSP00000262102:T537N;ENSP00000430167:T537N;ENSP00000371286:T537N	ENSP00000262102:T537N	T	-	2	0	MTUS1	17655987	0.002000	0.14202	0.001000	0.08648	0.541000	0.35023	1.088000	0.30877	0.803000	0.34113	0.650000	0.86243	ACC	.	.	none		0.438	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		T	17611707	G	T	17611707	3	4	8	1	0	0	0	0	1	0	0	0	9974	1261	44	4	2577	4	MTUS1	8	17611707	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	8043999	17611707	128752315	72	911											
UNC5D	137970	hgsc.bcm.edu	37	chr8	35624423	35624423	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccgtctcccctgcaggaaGtcccgttctcccgcgtgtgg	3	10	11	17	4	2	0	0	0	2	0	6	1	4	1	5	2	1	2	5	2	1	1			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr8:35624423G>A	ENST00000404895.2	+	15	2645	c.2317G>A	c.(2317-2319)Gtc>Atc	p.V773I	UNC5D_ENST00000453357.2_Missense_Mutation_p.V768I|UNC5D_ENST00000287272.2_Missense_Mutation_p.V704I|UNC5D_ENST00000449677.1_Missense_Mutation_p.V349I|UNC5D_ENST00000416672.1_Missense_Mutation_p.V778I|UNC5D_ENST00000420357.1_Missense_Mutation_p.V706I	NM_080872.2	NP_543148.2	Q6UXZ4	UNC5D_HUMAN	unc-5 homolog D (C. elegans)	773					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)		CCTGCAGGAAGTCCCGTTCTC	0.552																																					p.V773I		Atlas-SNP	.											.	UNC5D	393	.	0			c.G2317A						PASS	.						83	71	75					8																	35624423		2203	4300	6503	SO:0001583	missense	137970	exon15			CAGGAAGTCCCGT	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.2317G>A	8.37:g.35624423G>A	ENSP00000385143:p.Val773Ile	63	0	0		63	14	0.222222	NM_080872	Q8WYP7	Missense_Mutation	SNP	ENST00000404895.2	37	CCDS6093.2	.	.	.	.	.	.	.	.	.	.	G	8.206	0.799214	0.16397	.	.	ENSG00000156687	ENST00000404895;ENST00000420357;ENST00000287272;ENST00000416672;ENST00000453357;ENST00000449677	T;T;T;T;T;T	0.39997	1.08;1.55;1.58;1.09;1.05;3.01	5.79	5.79	0.91817	.	0.055301	0.64402	D	0.000001	T	0.21801	0.0525	N	0.04018	-0.295	0.47737	D	0.999503	B;B;B	0.26445	0.149;0.095;0.149	B;B;B	0.20955	0.025;0.032;0.014	T	0.18777	-1.0326	10	0.02654	T	1	-26.7072	20.0411	0.97590	0.0:0.0:1.0:0.0	.	349;768;773	E9PDS8;Q6UXZ4-2;Q6UXZ4	.;.;UNC5D_HUMAN	I	773;706;704;778;768;349	ENSP00000385143:V773I;ENSP00000392739:V706I;ENSP00000287272:V704I;ENSP00000412652:V778I;ENSP00000394303:V768I;ENSP00000397211:V349I	ENSP00000287272:V704I	V	+	1	0	UNC5D	35743965	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.193000	0.65120	2.739000	0.93911	0.655000	0.94253	GTC	.	.	none		0.552	UNC5D-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347586.2			A	35624423	G	A	35624423	3	1	8	1	0	0	0	0	1	0	0	0	17010	1029	36	2	2375	2	UNC5D	8	35624423	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	18012716	35624423	110739599	73	912											
RAB11FIP1	80223	hgsc.bcm.edu	37	chr8	37729420	37729420	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gatctattctttcatcatccGatgcgacttcaggaatggaa	11	13	8	9	2	5	0	3	0	2	0	6	5	6	2	1	2	1	0	1	2	3	4	rs560008452		TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr8:37729420G>A	ENST00000330843.4	-	4	2912	c.2900C>T	c.(2899-2901)tCg>tTg	p.S967L	RAB11FIP1_ENST00000524118.1_Intron|RAB11FIP1_ENST00000522727.1_Intron|RAB11FIP1_ENST00000287263.4_Intron|RAB11FIP1_ENST00000523182.1_5'UTR	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	967					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)			TTCATCATCCGATGCGACTTC	0.453													G|||	1	0.000199681	0.0008	0.0	5008	,	,		23664	0.0		0.0	False		,,,				2504	0.0				p.S967L		Atlas-SNP	.											.	RAB11FIP1	105	.	0			c.C2900T						PASS	.						157	130	139					8																	37729420		2203	4300	6503	SO:0001583	missense	80223	exon4			TCATCCGATGCGA	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.2900C>T	8.37:g.37729420G>A	ENSP00000331342:p.Ser967Leu	113	0	0		103	7	0.0679612	NM_001002814	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Missense_Mutation	SNP	ENST00000330843.4	37	CCDS34882.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.342297	0.81911	.	.	ENSG00000156675	ENST00000330843	T	0.26660	1.72	5.33	5.33	0.75918	.	0.000000	0.45867	D	0.000321	T	0.41511	0.1162	L	0.34521	1.04	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.14952	-1.0454	10	0.45353	T	0.12	-12.8301	17.2186	0.86951	0.0:0.0:1.0:0.0	.	296;967	Q67C35;Q6WKZ4	.;RFIP1_HUMAN	L	967	ENSP00000331342:S967L	ENSP00000331342:S967L	S	-	2	0	RAB11FIP1	37848578	0.999000	0.42202	0.119000	0.21687	0.783000	0.44284	5.604000	0.67626	2.491000	0.84063	0.655000	0.94253	TCG	.	.	none		0.453	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151		A	37729420	G	A	37729420	3	1	8	1	0	0	0	0	1	0	0	0	12908	1059	37	1	963	1	RAB11FIP1	8	37729420	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	2104997	37729420	108634602	74	913											
IDO2	169355	hgsc.bcm.edu	37	chr8	39872937	39872937	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagagctgcggagctatcAcatcaccatggtcaccaaat	12	7	10	12	1	3	1	3	0	0	1	3	2	3	2	2	3	3	3	2	3	2	1			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr8:39872937A>T	ENST00000389060.4	+	10	1040	c.1040A>T	c.(1039-1041)cAc>cTc	p.H347L	IDO2_ENST00000343295.4_3'UTR|IDO2_ENST00000502986.2_Missense_Mutation_p.H360L			Q6ZQW0	I23O2_HUMAN	indoleamine 2,3-dioxygenase 2	347					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						CGGAGCTATCACATCACCATG	0.547																																					p.H360L		Atlas-SNP	.											.	IDO2	78	.	0			c.A1079T						PASS	.						80	79	80					8																	39872937		2080	4202	6282	SO:0001583	missense	169355	exon11			GCTATCACATCAC	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.1040A>T	8.37:g.39872937A>T	ENSP00000426447:p.His347Leu	94	0	0		87	32	0.367816	NM_194294	A4UD41	Missense_Mutation	SNP	ENST00000389060.4	37		.	.	.	.	.	.	.	.	.	.	A	23.8	4.459110	0.84317	.	.	ENSG00000188676	ENST00000502986;ENST00000389060	D;D	0.93712	-3.27;-3.27	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	D	0.97742	0.9259	H	0.95504	3.68	0.58432	D	0.999992	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.98886	1.0771	9	.	.	.	.	15.5325	0.75974	1.0:0.0:0.0:0.0	.	360;347	F5H5G0;Q6ZQW0	.;I23O2_HUMAN	L	360;347	ENSP00000443432:H360L;ENSP00000426447:H347L	.	H	+	2	0	IDO2	39992094	1.000000	0.71417	0.999000	0.59377	0.717000	0.41224	6.577000	0.74027	2.252000	0.74401	0.533000	0.62120	CAC	.	.	none		0.547	IDO2-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372742.1	NM_194294		T	39872937	A	T	39872937	3	4	8	1	0	0	0	0	1	0	0	0	7511	159	6	5	1121	5	IDO2	8	39872937	Missense_Mutation	SNP	A	TCGA-FA-A82F-01A-11D-A382-10	2143517	39872937	106491085	75	914											
HNF4G	3174	hgsc.bcm.edu	37	chr8	76463645	76463645	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtacaaaatgaacgtgacagAataagcaccagaagaagcac	20	4	9	8	1	0	5	0	2	0	3	0	5	0	5	1	0	4	3	1	0	8	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr8:76463645A>C	ENST00000354370.1	+	5	534	c.264A>C	c.(262-264)agA>agC	p.R88S	HNF4G_ENST00000396423.2_Missense_Mutation_p.R125S			Q14541	HNF4G_HUMAN	hepatocyte nuclear factor 4, gamma	88					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)			AACGTGACAGAATAAGCACCA	0.423																																					p.R125S		Atlas-SNP	.											.	HNF4G	111	.	0			c.A375C						PASS	.						134	105	115					8																	76463645		2203	4300	6503	SO:0001583	missense	3174	exon4			TGACAGAATAAGC		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.264A>C	8.37:g.76463645A>C	ENSP00000346339:p.Arg88Ser	70	0	0		49	9	0.183673	NM_004133	Q7Z2V9|Q9UH81|Q9UIS6	Missense_Mutation	SNP	ENST00000354370.1	37		.	.	.	.	.	.	.	.	.	.	A	18.28	3.589200	0.66105	.	.	ENSG00000164749	ENST00000354370;ENST00000396423	D;D	0.94687	-3.49;-3.49	5.07	3.74	0.42951	Nuclear hormone receptor, ligand-binding (2);	0.000000	0.85682	D	0.000000	D	0.93090	0.7800	M	0.81942	2.565	0.58432	D	0.999992	B;P	0.41784	0.269;0.762	B;B	0.43194	0.141;0.411	D	0.92226	0.5788	10	0.72032	D	0.01	.	3.366	0.07203	0.6409:0.0:0.3591:0.0	.	125;88	F1D8Q4;Q14541	.;HNF4G_HUMAN	S	88;125	ENSP00000346339:R88S;ENSP00000379701:R125S	ENSP00000346339:R88S	R	+	3	2	HNF4G	76626200	1.000000	0.71417	0.996000	0.52242	0.873000	0.50193	2.625000	0.46452	2.026000	0.59711	0.528000	0.53228	AGA	.	.	none		0.423	HNF4G-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000313914.2	NM_004133		C	76463645	A	C	76463645	3	2	8	1	0	0	0	0	1	0	0	0	7263	243	9	5	389	5	HNF4G	8	76463645	Missense_Mutation	SNP	A	TCGA-FA-A82F-01A-11D-A382-10	36590708	76463645	69900377	76	915											
EIF3E	3646	hgsc.bcm.edu	37	chr8	109215229	109215229	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tacctctgacctgctattctGattaagtttcttctcaatat	9	18	4	10	0	4	2	1	2	4	0	5	2	4	2	2	0	2	2	2	0	5	7			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr8:109215229G>A	ENST00000220849.5	-	12	1344	c.1282C>T	c.(1282-1284)Cag>Tag	p.Q428*	EIF3E_ENST00000519030.1_Nonsense_Mutation_p.Q335*|EIF3E_ENST00000519517.1_5'Flank	NM_001568.2	NP_001559.1			eukaryotic translation initiation factor 3, subunit E									p.Q428*(3)	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)			CTGCTATTCTGATTAAGTTTC	0.383																																					p.Q428X	GBM(15;360 410 8460 34179 52246)	Atlas-SNP	.											EIF3E,NS,carcinoma,0,3	EIF3E	73	3	3	Substitution - Nonsense(3)	endometrium(3)	c.C1282T						PASS	.						160	144	150					8																	109215229		2203	4300	6503	SO:0001587	stop_gained	3646	exon12			TATTCTGATTAAG	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.1282C>T	8.37:g.109215229G>A	ENSP00000220849:p.Gln428*	131	0	0		115	41	0.356522	NM_001568		Nonsense_Mutation	SNP	ENST00000220849.5	37	CCDS6308.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.5|26.5	4.746950|4.746950	0.89663|0.89663	.|.	.|.	ENSG00000104408|ENSG00000104408	ENST00000220849;ENST00000519030|ENST00000522352	.|.	.|.	.|.	5.7|5.7	5.7|5.7	0.88788|0.88788	.|.	0.213853|.	0.50627|.	D|.	0.000113|.	.|T	.|0.71728	.|0.3374	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.69587	.|-0.5105	.|4	0.06625|.	T|.	0.88|.	-9.9569|-9.9569	15.4346|15.4346	0.75137|0.75137	0.0:0.0:0.8605:0.1395|0.0:0.0:0.8605:0.1395	.|.	.|.	.|.	.|.	X|L	428;335|138	.|.	ENSP00000220849:Q428X|.	Q|S	-|-	1|2	0|0	EIF3E|EIF3E	109284405|109284405	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	4.670000|4.670000	0.61583|0.61583	2.697000|2.697000	0.92050|0.92050	0.585000|0.585000	0.79938|0.79938	CAG|TCA	.	.	none		0.383	EIF3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380612.2	NM_001568		A	109215229	G	A	109215229	4	1	8	1	0	0	0	0	0	1	0	0	5017	1299	45	2	63	2	EIF3E	8	109215229	Nonsense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	32751584	109215229	37148793	77	916											
TRAPPC9	83696	hgsc.bcm.edu	37	chr8	141468446	141468448	+	5'Flank	DEL	GAA	GAA	-																															tcaggggtggaggccccgcgGaagcccactgtggatccctg																										TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr8:141468446_141468448delGAA	ENST00000438773.2	-	0	0				TRAPPC9_ENST00000389328.4_In_Frame_Del_p.S73del|TRAPPC9_ENST00000389327.3_5'Flank	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9						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						AGGCCCCGCGGAAGCCCACTGTG	0.68																																					p.73_73del		Pindel,Atlas-Indel	.											.	TRAPPC9	114	.	0			c.217_219del						PASS	.																																			SO:0001631	upstream_gene_variant	83696	exon1			.	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		8.37:g.141468446_141468448delGAA	Exception_encountered	137	0	.		120	24	0.2	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	In_Frame_Del	DEL	ENST00000438773.2	37	CCDS55278.1																																																																																			.	.	none		0.68	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466		-	141468448	GAA	-	141468446	6	5	8	0	1	1	0	1	0	0	0	0	16480	1174	41	0		0	TRAPPC9	8	141468446	5'Flank	DEL	GAA	TCGA-FA-A82F-01A-11D-A382-10	32253217	141468446	4895576	78	917											
TLN1	7094	hgsc.bcm.edu	37	chr9	35720844	35720844	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcgatgtagccggcaatgaGctgtgcaatctgctcccctt	8	11	10	12	2	1	1	0	1	1	0	3	2	2	1	3	1	4	5	3	1	3	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr9:35720844G>A	ENST00000314888.9	-	11	1524	c.1171C>T	c.(1171-1173)Ctc>Ttc	p.L391F	TLN1_ENST00000540444.1_Missense_Mutation_p.L391F	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	391	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.|Interaction with LAYN. {ECO:0000250}.				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)			CCGGCAATGAGCTGTGCAATC	0.512																																					p.L391F		Atlas-SNP	.											.	TLN1	185	.	0			c.C1171T						PASS	.						163	137	146					9																	35720844		2203	4300	6503	SO:0001583	missense	7094	exon11			CAATGAGCTGTGC	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.1171C>T	9.37:g.35720844G>A	ENSP00000316029:p.Leu391Phe	59	0	0		59	9	0.152542	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	37	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	G	35	5.425854	0.96131	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.73897	-0.79;-0.79	5.71	5.71	0.89125	FERM domain (1);Pleckstrin homology-type (1);Insulin receptor substrate-1, PTB (1);	0.000000	0.85682	D	0.000000	D	0.89054	0.6606	M	0.88979	2.995	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.90327	0.4349	10	0.87932	D	0	-10.4026	19.8677	0.96824	0.0:0.0:1.0:0.0	.	391	Q9Y490	TLN1_HUMAN	F	391	ENSP00000316029:L391F;ENSP00000442981:L391F	ENSP00000316029:L391F	L	-	1	0	TLN1	35710844	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.753000	0.68736	2.709000	0.92574	0.655000	0.94253	CTC	.	.	none		0.512	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		A	35720844	G	A	35720844	3	1	8	1	0	0	0	0	1	0	0	0	15962	971	34	2	6642	2	TLN1	9	35720844	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10		35720844	105492587	79	918											
GRHPR	9380	hgsc.bcm.edu	37	chr9	37424891	37424891	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcccatccctgccaaggagCtagagcgaggtgtggcgggg	8	5	17	11	2	0	1	0	0	0	1	1	3	1	2	3	5	4	1	3	5	2	1			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr9:37424891C>G	ENST00000318158.6	+	2	218	c.133C>G	c.(133-135)Cta>Gta	p.L45V	GRHPR_ENST00000607784.1_Missense_Mutation_p.L45V|GRHPR_ENST00000493368.1_3'UTR	NM_012203.1	NP_036335.1	Q9UBQ7	GRHPR_HUMAN	glyoxylate reductase/hydroxypyruvate reductase	45					cellular nitrogen compound metabolic process (GO:0034641)|dicarboxylic acid metabolic process (GO:0043648)|excretion (GO:0007588)|glyoxylate metabolic process (GO:0046487)|metabolic process (GO:0008152)|oxidation-reduction process (GO:0055114)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisomal matrix (GO:0005782)	carboxylic acid binding (GO:0031406)|glycerate dehydrogenase activity (GO:0008465)|glyoxylate reductase (NADP) activity (GO:0030267)|hydroxypyruvate reductase activity (GO:0016618)|NAD binding (GO:0051287)|NADPH binding (GO:0070402)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12				GBM - Glioblastoma multiforme(29;0.00687)		TGCCAAGGAGCTAGAGCGAGG	0.667																																					p.L45V		Atlas-SNP	.											.	GRHPR	35	.	0			c.C133G						PASS	.						51	48	49					9																	37424891		2203	4300	6503	SO:0001583	missense	9380	exon2			AAGGAGCTAGAGC	AF134895	CCDS6609.1	9q12	2012-07-13			ENSG00000137106	ENSG00000137106	1.1.1.79, 1.1.1.81		4570	protein-coding gene	gene with protein product	"primary hyperoxaluria type 2"	604296		GLXR		10524214, 10484776	Standard	XM_005251631		Approved	PH2	uc003zzu.1	Q9UBQ7	OTTHUMG00000019914	ENST00000318158.6:c.133C>G	9.37:g.37424891C>G	ENSP00000313432:p.Leu45Val	59	0	0		45	9	0.2	NM_012203	Q5T945|Q9H3E9|Q9H636|Q9UKX1	Missense_Mutation	SNP	ENST00000318158.6	37	CCDS6609.1	.	.	.	.	.	.	.	.	.	.	C	15.84	2.950791	0.53186	.	.	ENSG00000137106	ENST00000377824;ENST00000318158	D;D	0.86497	-2.13;-2.13	5.98	4.14	0.48551	D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.91123	0.7205	M	0.71206	2.165	0.80722	D	1	P	0.52577	0.954	P	0.61800	0.894	D	0.91620	0.5310	10	0.72032	D	0.01	-4.6267	11.2546	0.49045	0.0:0.8007:0.0:0.1993	.	45	Q9UBQ7	GRHPR_HUMAN	V	45	ENSP00000367055:L45V;ENSP00000313432:L45V	ENSP00000313432:L45V	L	+	1	2	GRHPR	37414891	1.000000	0.71417	1.000000	0.80357	0.084000	0.17831	2.842000	0.48230	1.558000	0.49541	0.650000	0.86243	CTA	.	.	none		0.667	GRHPR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052442.1	NM_012203		G	37424891	C	G	37424891	3	3	8	1	0	0	0	0	1	0	0	0	6775	796	28	4	139	4	GRHPR	9	37424891	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	1704047	37424891	103788540	80	919											
RASEF	158158	hgsc.bcm.edu	37	chr9	85597645	85597645	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctttttggaattggtcccggTtagattggtaatggatctgc	7	16	12	6	1	1	1	0	0	1	1	2	3	2	3	1	5	1	2	1	5	3	6			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr9:85597645T>A	ENST00000376447.3	-	17	2430	c.2170A>T	c.(2170-2172)Acc>Tcc	p.T724S		NM_152573.2	NP_689786.2	Q8IZ41	RASEF_HUMAN	RAS and EF-hand domain containing	724					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						TTGGTCCCGGTTAGATTGGTA	0.428																																					p.T724S		Atlas-SNP	.											.	RASEF	69	.	0			c.A2170T						PASS	.						390	359	369					9																	85597645		2203	4300	6503	SO:0001583	missense	158158	exon17			TCCCGGTTAGATT	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.2170A>T	9.37:g.85597645T>A	ENSP00000365630:p.Thr724Ser	303	0	0		216	54	0.25	NM_152573	A6NC29|Q96N04	Missense_Mutation	SNP	ENST00000376447.3	37	CCDS6662.1	.	.	.	.	.	.	.	.	.	.	T	1.831	-0.469844	0.04445	.	.	ENSG00000165105	ENST00000376447	T	0.60299	0.2	5.05	2.74	0.32292	.	0.565295	0.19132	N	0.121917	T	0.23806	0.0576	N	0.03608	-0.345	0.09310	N	0.999993	B	0.02656	0.0	B	0.04013	0.001	T	0.18272	-1.0342	10	0.07482	T	0.82	.	2.812	0.05444	0.1889:0.2494:0.0:0.5616	.	724	Q8IZ41	RASEF_HUMAN	S	724	ENSP00000365630:T724S	ENSP00000365630:T724S	T	-	1	0	RASEF	84787465	0.035000	0.19736	0.053000	0.19242	0.783000	0.44284	0.275000	0.18698	0.795000	0.33922	0.482000	0.46254	ACC	.	.	none		0.428	RASEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052825.1	NM_152573		A	85597645	T	A	85597645	3	1	8	1	0	0	0	0	1	0	0	0	13083	1725	60	5	56	5	RASEF	9	85597645	Missense_Mutation	SNP	T	TCGA-FA-A82F-01A-11D-A382-10	48172754	85597645	55615786	81	920											
C9orf79	286234	hgsc.bcm.edu	37	chr9	90502053	90502053	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgggcctcctgggtatctcGggttgaatctgtacccaagg	6	11	13	11	1	2	1	0	1	2	0	4	1	3	1	3	4	1	3	3	4	4	3			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr9:90502053G>T	ENST00000325643.5	+	4	2717	c.2651G>T	c.(2650-2652)cGg>cTg	p.R884L		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	884					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.R884L(1)									TGGGTATCTCGGGTTGAATCT	0.562																																					p.R884L		Atlas-SNP	.											C9orf79,NS,carcinoma,-1,1	.	.	1	1	Substitution - Missense(1)	lung(1)	c.G2651T						PASS	.						43	41	42					9																	90502053		2203	4300	6503	SO:0001583	missense	286234	exon4			TATCTCGGGTTGA	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.2651G>T	9.37:g.90502053G>T	ENSP00000322640:p.Arg884Leu	49	0	0		37	11	0.297297	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Missense_Mutation	SNP	ENST00000325643.5	37	CCDS6676.1	.	.	.	.	.	.	.	.	.	.	g	5.225	0.227059	0.09916	.	.	ENSG00000177992	ENST00000325643;ENST00000539327	T	0.03951	3.75	2.41	-3.47	0.04753	.	1.897450	0.02755	N	0.117952	T	0.04182	0.0116	L	0.29908	0.895	0.09310	N	1	B;B	0.10296	0.003;0.001	B;B	0.10450	0.005;0.002	T	0.41215	-0.9521	10	0.40728	T	0.16	.	4.3943	0.11355	0.5512:0.1897:0.259:0.0	.	884;536	Q6ZUB1;Q8NA33	CI079_HUMAN;.	L	884;536	ENSP00000322640:R884L	ENSP00000322640:R884L	R	+	2	0	C9orf79	89691873	0.002000	0.14202	0.000000	0.03702	0.001000	0.01503	1.059000	0.30517	-0.998000	0.03446	-0.259000	0.10710	CGG	.	.	none		0.562	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828		T	90502053	G	T	90502053	3	4	8	1	0	0	0	0	1	0	0	0	2499	1116	39	4	2665	4	C9orf79	9	90502053	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	4904408	90502053	50711378	82	921											
ASTN2	23245	hgsc.bcm.edu	37	chr9	120053673	120053673	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggctcctggagagtgggggCggtggcttgggccagctgcc	3	7	21	10	1	0	1	0	0	0	1	1	2	1	1	3	7	2	3	3	7	0	1			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr9:120053673C>T	ENST00000313400.4	-	2	662	c.562G>A	c.(562-564)Gcc>Acc	p.A188T	ASTN2_ENST00000373996.3_Missense_Mutation_p.A188T|ASTN2_ENST00000361477.3_5'UTR|ASTN2_ENST00000361209.2_Missense_Mutation_p.A188T			O75129	ASTN2_HUMAN	astrotactin 2	188					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						AGAGTGGGGGCGGTGGCTTGG	0.612																																					p.A188T		Atlas-SNP	.											.	ASTN2	307	.	0			c.G562A						PASS	.						58	59	59					9																	120053673		2203	4300	6503	SO:0001583	missense	23245	exon2			TGGGGGCGGTGGC	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.562G>A	9.37:g.120053673C>T	ENSP00000314038:p.Ala188Thr	108	0	0		102	30	0.294118	NM_014010	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Missense_Mutation	SNP	ENST00000313400.4	37		.	.	.	.	.	.	.	.	.	.	C	19.69	3.874260	0.72180	.	.	ENSG00000148219	ENST00000313400;ENST00000373996;ENST00000361209	T;T;T	0.09911	2.94;2.94;2.93	5.06	2.05	0.26809	.	0.244788	0.32548	N	0.005950	T	0.06917	0.0176	N	0.24115	0.695	0.32617	N	0.523907	P;B;P	0.44627	0.769;0.003;0.839	B;B;B	0.42188	0.113;0.001;0.379	T	0.25222	-1.0138	9	.	.	.	-22.1157	6.4925	0.22123	0.0:0.5158:0.3027:0.1815	.	188;188;188	O75129-2;O75129;O75129-3	.;ASTN2_HUMAN;.	T	188	ENSP00000314038:A188T;ENSP00000363108:A188T;ENSP00000354504:A188T	.	A	-	1	0	ASTN2	119093494	0.958000	0.32768	0.990000	0.47175	0.990000	0.78478	1.685000	0.37659	0.840000	0.34995	-0.119000	0.15052	GCC	.	.	none		0.612	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010		T	120053673	C	T	120053673	3	4	8	1	0	0	0	0	1	0	0	0	1065	768	27	1	3620	1	ASTN2	9	120053673	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	29551620	120053673	21159758	83	922											
ADAMTS13	11093	hgsc.bcm.edu	37	chr9	136310909	136310909	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcacacgtgtggacccctgcGgcagggtcgtgctccgtctc	4	8	14	15	4	1	0	0	0	1	0	4	1	2	1	3	3	2	3	3	3	0	0			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr9:136310909G>A	ENST00000371929.3	+	21	3144	c.2700G>A	c.(2698-2700)gcG>gcA	p.A900A	ADAMTS13_ENST00000485925.1_3'UTR|ADAMTS13_ENST00000371916.1_3'UTR|ADAMTS13_ENST00000356589.2_Silent_p.A869A|ADAMTS13_ENST00000355699.2_Silent_p.A900A|ADAMTS13_ENST00000536611.1_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	900	TSP type-1 5. {ECO:0000255|PROSITE- ProRule:PRU00210}.		A -> V (in dbSNP:rs685523). {ECO:0000269|PubMed:11557746, ECO:0000269|PubMed:11586351, ECO:0000269|Ref.6}.		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)		GGACCCCTGCGGCAGGGTCGT	0.662																																					p.A900A		Atlas-SNP	.											.	ADAMTS13	113	.	0			c.G2700A						PASS	.						49	48	48					9																	136310909		2203	4300	6503	SO:0001819	synonymous_variant	11093	exon21			CCCTGCGGCAGGG	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.2700G>A	9.37:g.136310909G>A		88	0	0		51	7	0.137255	NM_139027	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Silent	SNP	ENST00000371929.3	37	CCDS6970.1																																																																																			.	.	none		0.662	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025		A	136310909	G	A	136310909	2	1	8	1	0	0	0	0	0	0	0	1	258	1103	39	1		1	ADAMTS13	9	136310909	Silent	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	16257236	136310909	4902522	84	923											
NACC2	138151	hgsc.bcm.edu	37	chr9	138903497	138903497	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcgggcagcggctcgggggcGgccacctcctggatgaccga	5	4	18	14	5	0	1	0	1	0	0	2	3	1	2	4	6	1	2	4	6	0	0			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr9:138903497G>A	ENST00000371753.1	-	5	1687	c.1629C>T	c.(1627-1629)gcC>gcT	p.A543A	NACC2_ENST00000277554.2_Silent_p.A543A			Q96BF6	NACC2_HUMAN	NACC family member 2, BEN and BTB (POZ) domain containing	543					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						GCTCGGGGGCGGCCACCTCCT	0.761																																					p.A543A		Atlas-SNP	.											.	NACC2	16	.	0			c.C1629T						PASS	.						2	3	2					9																	138903497		1676	3402	5078	SO:0001819	synonymous_variant	138151	exon6			GGGGGCGGCCACC	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.1629C>T	9.37:g.138903497G>A		27	0	0		34	12	0.352941	NM_144653		Silent	SNP	ENST00000371753.1	37	CCDS6993.1																																																																																			.	.	none		0.761	NACC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055040.1	NM_144653		A	138903497	G	A	138903497	2	1	8	1	0	0	0	0	0	0	0	1	10145	1103	39	1		1	NACC2	9	138903497	Silent	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	2592588	138903497	2309934	85	924											
EGFL7	51162	hgsc.bcm.edu	37	chr9	139566493	139566493	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagcagctcggccgcatcgActccctgagcgagcagattt	8	7	11	15	4	0	2	0	1	0	1	3	4	1	2	3	1	4	4	3	1	0	1			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr9:139566493A>C	ENST00000371699.1	+	9	1663	c.752A>C	c.(751-753)gAc>gCc	p.D251A	EGFL7_ENST00000371698.3_Missense_Mutation_p.D251A|MIR126_ENST00000362291.1_RNA|EGFL7_ENST00000308874.7_Missense_Mutation_p.D251A|EGFL7_ENST00000406555.3_Missense_Mutation_p.D251A			Q9UHF1	EGFL7_HUMAN	EGF-like-domain, multiple 7	251					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)		GGCCGCATCGACTCCCTGAGC	0.701											OREG0019619	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D251A		Atlas-SNP	.											.	EGFL7	11	.	0			c.A752C						PASS	.						9	10	9					9																	139566493		2094	4090	6184	SO:0001583	missense	51162	exon10			GCATCGACTCCCT	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.752A>C	9.37:g.139566493A>C	ENSP00000360764:p.Asp251Ala	48	0	0	1649	37	10	0.27027	NM_016215	B3KRP0|M9VTX9|Q5M7Y5|Q5VUD5|Q96EG0	Missense_Mutation	SNP	ENST00000371699.1	37	CCDS7002.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.150127	0.78001	.	.	ENSG00000172889	ENST00000371699;ENST00000308874;ENST00000406555;ENST00000371698	D;D;D;D	0.86769	-2.17;-2.17;-2.17;-2.17	4.15	4.15	0.48705	.	0.063724	0.64402	D	0.000013	D	0.91710	0.7379	M	0.66939	2.045	0.58432	D	0.999999	D	0.89917	1.0	D	0.83275	0.996	D	0.91909	0.5538	10	0.59425	D	0.04	-25.9573	12.025	0.53365	1.0:0.0:0.0:0.0	.	251	Q9UHF1	EGFL7_HUMAN	A	251	ENSP00000360764:D251A;ENSP00000307843:D251A;ENSP00000385639:D251A;ENSP00000360763:D251A	ENSP00000307843:D251A	D	+	2	0	EGFL7	138686314	1.000000	0.71417	0.984000	0.44739	0.768000	0.43524	6.528000	0.73807	1.518000	0.48934	0.459000	0.35465	GAC	.	.	none		0.701	EGFL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055094.1	NM_016215		C	139566493	A	C	139566493	3	2	8	1	0	0	0	0	1	0	0	0	4966	275	10	5	778	5	EGFL7	9	139566493	Missense_Mutation	SNP	A	TCGA-FA-A82F-01A-11D-A382-10	662996	139566493	1646938	86	925											
ANKRD30A	91074	hgsc.bcm.edu	37	chr10	37490169	37490169	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	attacttttaacagagtctcCgtgagactgtttcacagaag	12	13	8	8	1	2	3	1	1	1	3	3	4	2	3	1	0	2	1	1	0	3	4			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr10:37490169C>T	ENST00000602533.1	+	31	2716	c.2617C>T	c.(2617-2619)Cgt>Tgt	p.R873C	ANKRD30A_ENST00000361713.1_Missense_Mutation_p.R873C|ANKRD30A_ENST00000374660.1_Missense_Mutation_p.R992C			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	929					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						ACAGAGTCTCCGTGAGACTGT	0.274																																					p.R873C		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.C2617T						PASS	.						75	69	71					10																	37490169		1789	4054	5843	SO:0001583	missense	91074	exon31			AGTCTCCGTGAGA	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.2617C>T	10.37:g.37490169C>T	ENSP00000473551:p.Arg873Cys	644	0	0		620	79	0.127419	NM_052997	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	37		.	.	.	.	.	.	.	.	.	.	c	7.328	0.618303	0.14129	.	.	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.07021	3.23;3.23	1.38	-2.76	0.05896	.	.	.	.	.	T	0.02156	0.0067	N	0.03608	-0.345	0.09310	N	1	P	0.35793	0.521	B	0.08055	0.003	T	0.39210	-0.9625	9	0.59425	D	0.04	.	1.5295	0.02532	0.3039:0.2234:0.0:0.4727	.	929	Q9BXX3	AN30A_HUMAN	C	873;992	ENSP00000354432:R873C;ENSP00000363792:R992C	ENSP00000354432:R873C	R	+	1	0	ANKRD30A	37530175	0.004000	0.15560	0.000000	0.03702	0.001000	0.01503	0.369000	0.20416	-0.455000	0.07054	-0.760000	0.03462	CGT	.	.	none		0.274	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		T	37490169	C	T	37490169	3	4	8	1	0	0	0	0	1	0	0	0	658	652	23	1	2739	1	ANKRD30A	10	37490169	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10		37490169	98044578	87	926											
C10orf10	11067	hgsc.bcm.edu	37	chr10	45473249	45473249	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcgcagggacacagcagggCggcccttccggcaggcctgg	6	4	16	15	3	0	0	0	0	0	0	2	1	1	1	3	6	1	3	3	6	0	1	rs143373089	byFrequency	TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr10:45473249C>T	ENST00000298295.3	-	2	447	c.230G>A	c.(229-231)cGc>cAc	p.R77H	RASSF4_ENST00000472561.1_Intron|C10orf10_ENST00000496638.1_Intron|RASSF4_ENST00000340258.5_Intron|RASSF4_ENST00000374417.2_Intron|RASSF4_ENST00000334940.6_Intron	NM_007021.3	NP_008952.1	Q9NTK1	DEPP_HUMAN	chromosome 10 open reading frame 10	77						mitochondrion (GO:0005739)				lung(1)	1						CACAGCAGGGCGGCCCTTCCG	0.662													C|||	9	0.00179712	0.0	0.0	5008	,	,		16959	0.0		0.0089	False		,,,				2504	0.0				p.R77H		Atlas-SNP	.											.	C10orf10	6	.	0			c.G230A						PASS	.	C	HIS/ARG,	3,4401		0,3,2199	37	38	38		230,	-4.3	0	10	dbSNP_134	38	26,8568		0,26,4271	yes	missense,intron	C10orf10,RASSF4	NM_007021.3,NM_032023.3	29,	0,29,6470	TT,TC,CC		0.3025,0.0681,0.2231	benign,	77/213,	45473249	29,12969	2202	4297	6499	SO:0001583	missense	11067	exon2			GCAGGGCGGCCCT	AB022718	CCDS7210.1	10q11.21	2014-07-31			ENSG00000165507	ENSG00000165507			23355	protein-coding gene	gene with protein product	"decidual protein induced by progesterone", "fasting induced", "fat-specific expressed gene"	611309				24530860, 19937567, 16123073	Standard	NM_007021		Approved	DEPP, FIG, Fseg	uc001jbr.4	Q9NTK1	OTTHUMG00000018063	ENST00000298295.3:c.230G>A	10.37:g.45473249C>T	ENSP00000298295:p.Arg77His	60	0	0		47	11	0.234043	NM_007021	B2R6A1|O94997|Q5T735|Q76MX8	Missense_Mutation	SNP	ENST00000298295.3	37	CCDS7210.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	6.078	0.382727	0.11524	6.81E-4	0.003025	ENSG00000165507	ENST00000298295;ENST00000432283;ENST00000448778	T;T	0.41400	1.0;1.0	5.6	-4.3	0.03710	.	1.632960	0.03404	N	0.203779	T	0.12603	0.0306	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.07328	-1.0778	10	0.13853	T	0.58	0.1242	2.0776	0.03628	0.1107:0.292:0.3247:0.2726	.	77	Q9NTK1	DEPP_HUMAN	H	77	ENSP00000298295:R77H;ENSP00000414494:R77H	ENSP00000298295:R77H	R	-	2	0	C10orf10	44793255	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.941000	0.03925	-1.319000	0.02286	-1.332000	0.01269	CGC	C|0.998;T|0.002	0.002	strong		0.662	C10orf10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047758.1	NM_007021		T	45473249	C	T	45473249	3	4	8	1	0	0	0	0	1	0	0	0	1582	768	27	1	412	1	C10orf10	10	45473249	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	7983080	45473249	90061498	88	927											
MBL2	4153	hgsc.bcm.edu	37	chr10	54527908	54527908	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tatgacccttcagatagggaActcacagacggccagatggg	12	7	12	10	1	2	4	2	1	0	3	2	5	2	5	2	3	1	0	2	3	3	3			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr10:54527908A>C	ENST00000373968.3	-	4	800	c.736T>G	c.(736-738)Ttc>Gtc	p.F246V		NM_000242.2	NP_000233.1	P11226	MBL2_HUMAN	mannose-binding lectin (protein C) 2, soluble	246					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						CAGATAGGGAACTCACAGACG	0.463																																					p.F246V		Atlas-SNP	.											.	MBL2	55	.	0			c.T736G						PASS	.						211	195	201					10																	54527908		2202	4300	6502	SO:0001583	missense	4153	exon4			TAGGGAACTCACA	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.736T>G	10.37:g.54527908A>C	ENSP00000363079:p.Phe246Val	117	0	0		101	21	0.207921	NM_000242	Q4VB12|Q4VB13|Q4VB14|Q5SQS3|Q86SI4|Q96KE4|Q96TF7|Q96TF8|Q96TF9	Missense_Mutation	SNP	ENST00000373968.3	37	CCDS7247.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.575473	0.86645	.	.	ENSG00000165471	ENST00000373968	T	0.18810	2.19	5.03	5.03	0.67393	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (1);	0.092185	0.48286	D	0.000196	T	0.40067	0.1102	L	0.58354	1.805	0.45995	D	0.998802	D	0.62365	0.991	D	0.64877	0.93	T	0.25328	-1.0135	10	0.87932	D	0	-16.6059	13.0118	0.58735	1.0:0.0:0.0:0.0	.	246	P11226	MBL2_HUMAN	V	246	ENSP00000363079:F246V	ENSP00000363079:F246V	F	-	1	0	MBL2	54197914	1.000000	0.71417	0.626000	0.29213	0.320000	0.28249	4.676000	0.61627	2.010000	0.58986	0.482000	0.46254	TTC	.	.	none		0.463	MBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048115.1	NM_000242		C	54527908	A	C	54527908	3	2	8	1	0	0	0	0	1	0	0	0	9359	43	2	5	14	5	MBL2	10	54527908	Missense_Mutation	SNP	A	TCGA-FA-A82F-01A-11D-A382-10	9054659	54527908	81006839	89	928											
PLCE1	51196	hgsc.bcm.edu	37	chr10	95791436	95791436	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagaaaacttaattttagaCgattgtggaaattgtgtacc	14	14	8	5	1	1	2	1	0	0	2	1	4	1	3	1	1	2	1	1	1	6	6	rs201117145		TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr10:95791436C>T	ENST00000371380.3	+	1	868	c.633C>T	c.(631-633)gaC>gaT	p.D211D	PLCE1_ENST00000260766.3_Silent_p.D211D			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	211					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)				TAATTTTAGACGATTGTGGAA	0.393													C|||	1	0.000199681	0.0008	0.0	5008	,	,		22116	0.0		0.0	False		,,,				2504	0.0				p.D211D		Atlas-SNP	.											.	PLCE1	543	.	0			c.C633T						PASS	.	C		9,3749		0,9,1870	84	80	81		633	-0.5	1	10		81	0,8202		0,0,4101	no	coding-synonymous	PLCE1	NM_016341.3		0,9,5971	TT,TC,CC		0.0,0.2395,0.0753		211/2303	95791436	9,11951	1879	4101	5980	SO:0001819	synonymous_variant	51196	exon2			TTTAGACGATTGT		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.633C>T	10.37:g.95791436C>T		98	0	0		100	33	0.33	NM_016341	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Silent	SNP	ENST00000371380.3	37	CCDS41552.1																																																																																			C|1.000;T|0.000	0.000	strong		0.393	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341		T	95791436	C	T	95791436	2	4	8	1	0	0	0	0	0	0	0	1	12043	535	19	1		1	PLCE1	10	95791436	Silent	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	41263528	95791436	39743311	90	929											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1268741	1268741	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggaccacagccacagccaCacccagcaagacccgcacct	13	1	7	20	1	0	1	0	0	0	1	0	2	0	2	6	1	3	2	6	1	1	0			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr11:1268741C>T	ENST00000529681.1	+	31	10689	c.10631C>T	c.(10630-10632)aCa>aTa	p.T3544I	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.T3547I	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3544	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)		GCCACAGCCACACCCAGCAAG	0.692																																					p.T3544I		Atlas-SNP	.											.	MUC5B	473	.	0			c.C10631T						PASS	.						65	100	88					11																	1268741		2085	4208	6293	SO:0001583	missense	727897	exon31			CAGCCACACCCAG	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.10631C>T	11.37:g.1268741C>T	ENSP00000436812:p.Thr3544Ile	195	0	0		181	46	0.254144	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	C	6.567	0.472919	0.12461	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.19806	2.12;2.35	2.4	-2.44	0.06502	.	.	.	.	.	T	0.31827	0.0809	L	0.47716	1.5	0.09310	N	1	D;D	0.69078	0.967;0.997	P;P	0.60789	0.835;0.879	T	0.31194	-0.9952	9	0.87932	D	0	.	11.534	0.50626	0.0:0.5071:0.4929:0.0	.	4072;3547	A7Y9J9;E9PBJ0	.;.	I	3544;3547;3516;3449	ENSP00000436812:T3544I;ENSP00000415793:T3547I	ENSP00000343037:T3516I	T	+	2	0	MUC5B	1225317	0.000000	0.05858	0.002000	0.10522	0.095000	0.18619	-0.017000	0.12590	-0.588000	0.05882	0.297000	0.19635	ACA	.	.	none		0.692	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		T	1268741	C	T	1268741	3	4	8	1	0	0	0	0	1	0	0	0	9988	478	17	2	10762	2	MUC5B	11	1268741	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10		1268741	133737775	91	930											
KRTAP5-5	439915	hgsc.bcm.edu	37	chr11	1651379	1651379	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	agaggctgtgtctcctgtggGgtgtccaagggggcctgtgg	4	10	19	8	0	1	1	0	0	1	1	3	1	2	1	3	6	0	1	3	6	1	0			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr11:1651379G>A	ENST00000399676.2	+	1	347	c.309G>A	c.(307-309)ggG>ggA	p.G103G		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	103	8 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		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)		TCTCCTGTGGGGTGTCCAAGG	0.677																																					p.G103G		Atlas-SNP	.											.	KRTAP5-5	86	.	0			c.G309A						PASS	.						53	69	63					11																	1651379		2199	4296	6495	SO:0001819	synonymous_variant	439915	exon1			CTGTGGGGTGTCC	AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"Keratin associated proteins"	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.309G>A	11.37:g.1651379G>A		69	0	0		73	20	0.273973	NM_001001480	A8MWN2	Silent	SNP	ENST00000399676.2	37	CCDS41592.1																																																																																			.	.	none		0.677	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1			A	1651379	G	A	1651379	2	1	8	1	0	0	0	0	0	0	0	1	8573	1219	43	2		2	KRTAP5-5	11	1651379	Silent	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	382638	1651379	133355137	92	931											
OR52M1	119772	hgsc.bcm.edu	37	chr11	4566782	4566782	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcatcttccttgccatggCttttgatcgctacgtggcca	6	13	10	12	2	1	1	0	1	1	0	3	1	2	1	3	3	2	3	3	3	1	5			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr11:4566782C>G	ENST00000360213.1	+	1	362	c.362C>G	c.(361-363)gCt>gGt	p.A121G		NM_001004137.1	NP_001004137.1	Q8NGK5	O52M1_HUMAN	olfactory receptor, family 52, subfamily M, member 1	121						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)		CTTGCCATGGCTTTTGATCGC	0.537																																					p.A121G		Atlas-SNP	.											OR52M1,NS,haematopoietic_neoplasm,+1,3	OR52M1	53	3	0			c.C362G						PASS	.						149	130	136					11																	4566782		2201	4298	6499	SO:0001583	missense	119772	exon1			CCATGGCTTTTGA	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.362C>G	11.37:g.4566782C>G	ENSP00000353343:p.Ala121Gly	252	0	0		257	69	0.268482	NM_001004137		Missense_Mutation	SNP	ENST00000360213.1	37	CCDS31353.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.669144	0.88348	.	.	ENSG00000197790	ENST00000360213	T	0.55052	0.54	4.98	4.98	0.66077	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47093	D	0.000248	T	0.75642	0.3877	M	0.89658	3.05	0.47441	D	0.999421	D	0.71674	0.998	P	0.61397	0.888	T	0.80959	-0.1149	10	0.66056	D	0.02	.	17.3425	0.87301	0.0:1.0:0.0:0.0	.	121	Q8NGK5	O52M1_HUMAN	G	121	ENSP00000353343:A121G	ENSP00000353343:A121G	A	+	2	0	OR52M1	4523358	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.560000	0.82277	2.756000	0.94617	0.650000	0.86243	GCT	.	.	none		0.537	OR52M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385847.1	NM_001004137		G	4566782	C	G	4566782	3	3	8	1	0	0	0	0	1	0	0	0	11135	797	28	4	364	4	OR52M1	11	4566782	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	2915403	4566782	130439734	93	932											
OR51B6	390058	hgsc.bcm.edu	37	chr11	5372968	5372968	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgacattgaccacaatgccCacagtgctaggtgttctgtg	9	11	11	10	0	1	2	0	2	1	0	1	2	1	2	2	1	2	2	2	1	2	3			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr11:5372968C>A	ENST00000380219.1	+	1	231	c.231C>A	c.(229-231)ccC>ccA	p.P77P	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001004750.1	NP_001004750.1	Q9H340	O51B6_HUMAN	olfactory receptor, family 51, subfamily B, member 6	77					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)		CCACAATGCCCACAGTGCTAG	0.468																																					p.P77P		Atlas-SNP	.											.	OR51B6	53	.	0			c.C231A						PASS	.						134	122	126					11																	5372968		2201	4297	6498	SO:0001819	synonymous_variant	390058	exon1			AATGCCCACAGTG		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.231C>A	11.37:g.5372968C>A		122	0	0		127	56	0.440945	NM_001004750		Silent	SNP	ENST00000380219.1	37	CCDS31379.1																																																																																			.	.	none		0.468	OR51B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142960.1	NM_001004750		A	5372968	C	A	5372968	2	1	8	1	0	0	0	0	0	0	0	1	11101	581	21	4		4	OR51B6	11	5372968	Silent	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	806186	5372968	129633548	94	933											
DNHD1	144132	hgsc.bcm.edu	37	chr11	6561152	6561152	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcatgcccaagagactatacGgcggttgcagcggtactggg	9	8	14	10	3	1	1	1	0	0	1	1	2	1	1	1	4	5	3	1	4	4	4			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr11:6561152G>A	ENST00000527990.2	+	16	3467	c.3467G>A	c.(3466-3468)cGg>cAg	p.R1156Q	DNHD1_ENST00000254579.6_Missense_Mutation_p.R1156Q			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	1156					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)		GAGACTATACGGCGGTTGCAG	0.587																																					p.R1156Q		Atlas-SNP	.											.	DNHD1	198	.	0			c.G3467A						PASS	.						44	49	47					11																	6561152		692	1591	2283	SO:0001583	missense	144132	exon18			CTATACGGCGGTT	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.3467G>A	11.37:g.6561152G>A	ENSP00000436180:p.Arg1156Gln	83	0	0		84	25	0.297619	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	G	5.646	0.303779	0.10678	.	.	ENSG00000179532	ENST00000254579;ENST00000527990	T;T	0.61040	0.14;0.14	5.57	-3.68	0.04463	Dynein heavy chain, domain-2 (1);	.	.	.	.	T	0.27241	0.0668	N	0.08118	0	0.09310	N	1	B	0.18741	0.03	B	0.09377	0.004	T	0.22695	-1.0209	9	0.12766	T	0.61	.	5.6098	0.17398	0.5358:0.0:0.235:0.2292	.	1156	Q96M86	DNHD1_HUMAN	Q	1156	ENSP00000254579:R1156Q;ENSP00000436180:R1156Q	ENSP00000254579:R1156Q	R	+	2	0	DNHD1	6517728	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.491000	0.06474	-0.308000	0.08792	-0.221000	0.12465	CGG	.	.	none		0.587	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		A	6561152	G	A	6561152	3	1	8	1	0	0	0	0	1	0	0	0	4670	1116	39	1	3538	1	DNHD1	11	6561152	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	1188184	6561152	128445364	95	934											
SBF2	81846	hgsc.bcm.edu	37	chr11	10051375	10051375	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcaattagactttccaaggaGacattcaggctgtccacata	13	10	8	10	0	1	2	1	0	0	2	3	3	3	2	2	2	0	2	2	2	4	4			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr11:10051375G>A	ENST00000256190.8	-	5	587	c.450C>T	c.(448-450)gtC>gtT	p.V150V	SBF2_ENST00000527019.1_5'UTR	NM_030962.3	NP_112224.1	Q86WG5	MTMRD_HUMAN	SET binding factor 2	150	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				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)		TTTCCAAGGAGACATTCAGGC	0.408																																					p.V150V		Atlas-SNP	.											SBF2,NS,carcinoma,-2,1	SBF2	146	1	0			c.C450T						PASS	.						205	205	205					11																	10051375		2201	4294	6495	SO:0001819	synonymous_variant	81846	exon5			CAAGGAGACATTC	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.450C>T	11.37:g.10051375G>A		69	0	0		57	19	0.333333	NM_030962	Q3MJF0|Q68DQ3|Q6P459|Q6PJD1|Q7Z325|Q7Z621|Q86VE2|Q96FE2|Q9C097	Silent	SNP	ENST00000256190.8	37	CCDS31427.1																																																																																			.	.	none		0.408	SBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386911.2	NM_030962		A	10051375	G	A	10051375	2	1	8	1	0	0	0	0	0	0	0	1	13874	929	33	2		2	SBF2	11	10051375	Silent	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	3490223	10051375	124955141	96	935											
AMPD3	272	hgsc.bcm.edu	37	chr11	10523046	10523046	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctgagcacgttcctgttccGgccgcactgtggggaagccg	5	8	14	14	4	0	1	0	1	0	0	2	2	2	2	5	3	2	4	5	3	1	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr11:10523046G>A	ENST00000396554.3	+	12	2119	c.1778G>A	c.(1777-1779)cGg>cAg	p.R593Q	AMPD3_ENST00000530864.1_3'UTR|AMPD3_ENST00000444303.2_Missense_Mutation_p.R425Q	NM_000480.2	NP_000471.1	Q01432	AMPD3_HUMAN	adenosine monophosphate deaminase 3	584					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)		TTCCTGTTCCGGCCGCACTGT	0.632																																					p.R593Q		Atlas-SNP	.											.	AMPD3	68	.	0			c.G1778A						PASS	.						48	40	43					11																	10523046		2201	4294	6495	SO:0001583	missense	272	exon12			TGTTCCGGCCGCA	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.1778G>A	11.37:g.10523046G>A	ENSP00000379802:p.Arg593Gln	44	0	0		61	23	0.377049	NM_000480	A0AUX0|B7Z2S2|B7Z763|B7Z877	Missense_Mutation	SNP	ENST00000396554.3	37	CCDS7802.1	.	.	.	.	.	.	.	.	.	.	G	37	6.087583	0.97271	.	.	ENSG00000133805	ENST00000444303;ENST00000396554;ENST00000396553;ENST00000528723;ENST00000529507	D;D;D;D;D	0.82711	-1.64;-1.64;-1.64;-1.64;-1.64	5.75	5.75	0.90469	Adenosine/AMP deaminase (1);	0.000000	0.85682	D	0.000000	D	0.94324	0.8176	H	0.95679	3.705	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	0.95346	0.8442	10	0.87932	D	0	-21.5258	19.9577	0.97228	0.0:0.0:1.0:0.0	.	591;584;593	B7Z763;Q01432;A0AUX0	.;AMPD3_HUMAN;.	Q	425;593;584;591;584	ENSP00000396000:R425Q;ENSP00000379802:R593Q;ENSP00000379801:R584Q;ENSP00000436987:R591Q;ENSP00000431648:R584Q	ENSP00000379801:R584Q	R	+	2	0	AMPD3	10479622	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.869000	0.99810	2.714000	0.92807	0.563000	0.77884	CGG	.	.	none		0.632	AMPD3-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385783.2	NM_000480		A	10523046	G	A	10523046	3	1	8	1	0	0	0	0	1	0	0	0	587	1116	39	1	1844	1	AMPD3	11	10523046	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	471671	10523046	124483470	97	936											
VEGFB	7423	hgsc.bcm.edu	37	chr11	64004667	64004667	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttacttttcagacctaaaaAaaaggacagtgctgtgaagc	15	10	8	8	0	1	2	1	1	0	1	1	3	1	3	1	1	3	1	1	1	6	4			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr11:64004667A>G	ENST00000309422.2	+	5	679	c.383A>G	c.(382-384)aAa>aGa	p.K128R	RP11-783K16.14_ENST00000539963.1_RNA|VEGFB_ENST00000426086.2_Missense_Mutation_p.K128R|RP11-783K16.14_ENST00000534988.1_RNA	NM_001243733.1|NM_003377.4	NP_001230662.1|NP_003368.1	P49765	VEGFB_HUMAN	vascular endothelial growth factor B	128					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|coronary vasculature development (GO:0060976)|induction of positive chemotaxis (GO:0050930)|negative regulation of apoptotic process (GO:0043066)|negative regulation of gene expression (GO:0010629)|negative regulation of neuron apoptotic process (GO:0043524)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell division (GO:0051781)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of vascular wound healing (GO:0035470)|protein O-linked glycosylation (GO:0006493)|response to drug (GO:0042493)|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)|heparin binding (GO:0008201)|vascular endothelial growth factor receptor 1 binding (GO:0043183)			endometrium(2)|large_intestine(2)|prostate(1)|stomach(1)	6					Aflibercept(DB08885)	AGACCTAAAAAAAAGGACAGT	0.468																																					p.K128R		Atlas-SNP	.											VEGFB,NS,carcinoma,+1,2	VEGFB	18	2	0			c.A383G						PASS	.						138	122	128					11																	64004667		2201	4297	6498	SO:0001583	missense	7423	exon5			CTAAAAAAAAGGA	BC008818	CCDS8062.1, CCDS58144.1	11q13	2005-09-29				ENSG00000173511			12681	protein-coding gene	gene with protein product		601398		VRF		8637916, 8919691	Standard	NM_001243733		Approved	VEGFL	uc001nyw.3	P49765		ENST00000309422.2:c.383A>G	11.37:g.64004667A>G	ENSP00000311127:p.Lys128Arg	93	0	0		72	23	0.319444	NM_003377	Q16528	Missense_Mutation	SNP	ENST00000309422.2	37	CCDS8062.1	.	.	.	.	.	.	.	.	.	.	A	6.839	0.523936	0.13066	.	.	ENSG00000173511	ENST00000309422;ENST00000426086	.	.	.	4.49	2.07	0.26955	Platelet-derived growth factor (PDGF) (1);	0.627685	0.14547	N	0.312918	T	0.23846	0.0577	N	0.16656	0.425	0.20821	N	0.999844	B;B	0.12630	0.005;0.006	B;B	0.11329	0.006;0.005	T	0.17198	-1.0377	9	0.33141	T	0.24	-0.6901	6.5128	0.22232	0.7986:0.0:0.2014:0.0	.	128;128	P49765-2;P49765	.;VEGFB_HUMAN	R	128	.	ENSP00000311127:K128R	K	+	2	0	VEGFB	63761243	0.305000	0.24481	0.257000	0.24404	0.294000	0.27393	0.587000	0.23909	0.303000	0.22785	-0.421000	0.06004	AAA	.	.	none		0.468	VEGFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396393.2	NM_003377		G	64004667	A	G	64004667	3	3	8	1	0	0	0	0	1	0	0	0	17166	14	1	3	401	3	VEGFB	11	64004667	Missense_Mutation	SNP	A	TCGA-FA-A82F-01A-11D-A382-10	53481621	64004667	71001849	98	937											
HEPHL1	341208	hgsc.bcm.edu	37	chr11	93819329	93819329	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtttccccacatggccacaaCagcattcatgcagccagacc	11	7	7	16	0	1	1	1	0	0	1	2	1	2	1	5	1	4	3	5	1	1	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr11:93819329C>G	ENST00000315765.9	+	11	2062	c.2054C>G	c.(2053-2055)aCa>aGa	p.T685R		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	685	Plastocyanin-like 4.				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)	p.A687fs*12(1)		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)				ATGGCCACAACAGCATTCATG	0.517																																					p.T685R		Atlas-SNP	.											.	HEPHL1	144	.	1	Deletion - Frameshift(1)	ovary(1)	c.C2054G						PASS	.						72	69	70					11																	93819329		2013	4186	6199	SO:0001583	missense	341208	exon11			CCACAACAGCATT	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.2054C>G	11.37:g.93819329C>G	ENSP00000313699:p.Thr685Arg	68	0	0		71	7	0.0985916	NM_001098672	Q3C1W7	Missense_Mutation	SNP	ENST00000315765.9	37	CCDS44710.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.269221	0.80469	.	.	ENSG00000181333	ENST00000315765	D	0.99834	-7.04	5.94	5.94	0.96194	Cupredoxin (2);	0.099149	0.64402	D	0.000001	D	0.99680	0.9880	M	0.81239	2.535	0.51012	D	0.999906	D	0.54772	0.968	P	0.50231	0.635	D	0.98400	1.0567	10	0.72032	D	0.01	.	20.3736	0.98901	0.0:1.0:0.0:0.0	.	685	Q6MZM0	HPHL1_HUMAN	R	685	ENSP00000313699:T685R	ENSP00000313699:T685R	T	+	2	0	HEPHL1	93458977	1.000000	0.71417	0.100000	0.21137	0.672000	0.39443	7.332000	0.79203	2.820000	0.97059	0.650000	0.86243	ACA	.	.	none		0.517	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947		G	93819329	C	G	93819329	3	3	8	1	0	0	0	0	1	0	0	0	7064	478	17	4	2096	4	HEPHL1	11	93819329	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	29814662	93819329	41187187	99	938											
ARHGAP20	57569	hgsc.bcm.edu	37	chr11	110582853	110582853	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ccgctcagcgtcctcaccttCttggtgcagctgcctcccgc	3	10	9	19	3	3	0	2	0	1	0	5	0	5	0	5	1	4	3	5	1	0	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr11:110582853C>G	ENST00000260283.4	-	2	386	c.102G>C	c.(100-102)aaG>aaC	p.K34N	ARHGAP20_ENST00000528829.1_Intron|ARHGAP20_ENST00000533353.1_Intron|ARHGAP20_ENST00000524756.1_5'Flank|ARHGAP20_ENST00000527598.1_Intron	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	34					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)		TCCTCACCTTCTTGGTGCAGC	0.741																																					p.K34N		Atlas-SNP	.											ARHGAP20,brain,primitive_neuroectodermal_tumour-medulloblastoma,-1,1	ARHGAP20	150	1	0			c.G102C						scavenged	.						6	7	7					11																	110582853		2157	4251	6408	SO:0001583	missense	57569	exon2			CACCTTCTTGGTG	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.102G>C	11.37:g.110582853C>G	ENSP00000260283:p.Lys34Asn	35	1	0.0285714		33	12	0.363636	NM_020809	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Missense_Mutation	SNP	ENST00000260283.4	37	CCDS31673.1	.	.	.	.	.	.	.	.	.	.	C	11.51	1.661627	0.29515	.	.	ENSG00000137727	ENST00000260283	T	0.12569	2.67	3.91	2.98	0.34508	.	0.290587	0.25186	N	0.032496	T	0.07954	0.0199	N	0.22421	0.69	0.80722	D	1	P	0.41313	0.745	B	0.35413	0.202	T	0.16867	-1.0388	10	0.59425	D	0.04	.	7.9066	0.29765	0.0:0.8768:0.0:0.1232	.	34	Q9P2F6	RHG20_HUMAN	N	34	ENSP00000260283:K34N	ENSP00000260283:K34N	K	-	3	2	ARHGAP20	110088063	1.000000	0.71417	0.995000	0.50966	0.042000	0.13812	1.072000	0.30678	1.728000	0.51552	0.555000	0.69702	AAG	.	.	none		0.741	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809		G	110582853	C	G	110582853	3	3	8	1	0	0	0	0	1	0	0	0	870	912	32	4	3533	4	ARHGAP20	11	110582853	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	16763524	110582853	24423663	100	939											
MLL	4297	hgsc.bcm.edu	37	chr11	118372519	118372519	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggtccccaggattcgaacacCcagttattctccaacacaga	12	8	7	14	1	1	1	0	0	1	1	4	3	2	2	4	2	2	1	4	2	3	3			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr11:118372519C>T	ENST00000389506.5	+	26	6443	c.6443C>T	c.(6442-6444)cCc>cTc	p.P2148L	KMT2A_ENST00000534358.1_Missense_Mutation_p.P2151L|KMT2A_ENST00000354520.4_Missense_Mutation_p.P2110L			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	2148					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)										ATTCGAACACCCAGTTATTCT	0.468																																					p.P2151L		Atlas-SNP	.											.	MLL	548	.	0			c.C6452T						PASS	.						125	123	124					11																	118372519		2200	4296	6496	SO:0001583	missense	4297	exon26			GAACACCCAGTTA	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.6443C>T	11.37:g.118372519C>T	ENSP00000374157:p.Pro2148Leu	103	0	0		86	29	0.337209	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	37	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	C	19.52	3.843826	0.71488	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	D;D;D	0.85411	-1.97;-1.98;-1.84	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.91560	0.7334	M	0.68317	2.08	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.991;0.996	D	0.91992	0.5604	10	0.87932	D	0	.	16.9819	0.86329	0.0:1.0:0.0:0.0	.	2151;2148	E9PQG7;Q03164	.;MLL1_HUMAN	L	2151;2148;2110;1058	ENSP00000436786:P2151L;ENSP00000374157:P2148L;ENSP00000346516:P2110L	ENSP00000346516:P2110L	P	+	2	0	MLL	117877729	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.419000	0.66435	2.750000	0.94351	0.591000	0.81541	CCC	.	.	none		0.468	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		T	118372519	C	T	118372519	3	4	8	1	0	0	0	0	1	0	0	0	9629	623	22	2	6545	2	MLL	11	118372519	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	7789666	118372519	16633997	101	940											
SORL1	6653	hgsc.bcm.edu	37	chr11	121414264	121414264	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgcatttgggcagatacagtAccaatgaaggggagacctgg	12	8	14	7	0	0	3	0	1	0	2	0	4	0	3	2	4	3	3	2	4	4	3			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr11:121414264A>C	ENST00000260197.7	+	13	1822	c.1693A>C	c.(1693-1695)Acc>Ccc	p.T565P	SORL1_ENST00000532451.1_3'UTR	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	565					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)		CAGATACAGTACCAATGAAGG	0.468																																					p.T565P		Atlas-SNP	.											.	SORL1	218	.	0			c.A1693C						PASS	.						127	127	127					11																	121414264		2203	4299	6502	SO:0001583	missense	6653	exon13			TACAGTACCAATG	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.1693A>C	11.37:g.121414264A>C	ENSP00000260197:p.Thr565Pro	93	0	0		103	30	0.291262	NM_003105	B2RNX7|Q92856	Missense_Mutation	SNP	ENST00000260197.7	37	CCDS8436.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.654993	0.88056	.	.	ENSG00000137642	ENST00000260197	T	0.43294	0.95	5.8	5.8	0.92144	VPS10 (1);	0.000000	0.85682	D	0.000000	T	0.66665	0.2812	M	0.78456	2.415	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.70741	-0.4789	10	0.72032	D	0.01	.	16.1549	0.81657	1.0:0.0:0.0:0.0	.	565	Q92673	SORL_HUMAN	P	565	ENSP00000260197:T565P	ENSP00000260197:T565P	T	+	1	0	SORL1	120919474	1.000000	0.71417	0.995000	0.50966	0.993000	0.82548	9.056000	0.93881	2.209000	0.71365	0.533000	0.62120	ACC	.	.	none		0.468	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105		C	121414264	A	C	121414264	3	2	8	1	0	0	0	0	1	0	0	0	14949	391	14	5	1743	5	SORL1	11	121414264	Missense_Mutation	SNP	A	TCGA-FA-A82F-01A-11D-A382-10	3041745	121414264	13592252	102	941											
OR10G8	219869	hgsc.bcm.edu	37	chr11	123900714	123900714	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctggccatcagttacccgCtcaggtacaccagcatgatg	10	8	9	14	1	2	1	2	1	0	0	2	1	2	1	4	2	3	4	4	2	2	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr11:123900714C>A	ENST00000431524.1	+	1	418	c.385C>A	c.(385-387)Ctc>Atc	p.L129I		NM_001004464.1	NP_001004464.1	Q8NGN5	O10G8_HUMAN	olfactory receptor, family 10, subfamily G, member 8	129						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)		CAGTTACCCGCTCAGGTACAC	0.557																																					p.L129I		Atlas-SNP	.											.	OR10G8	132	.	0			c.C385A						PASS	.						152	142	146					11																	123900714		2201	4299	6500	SO:0001583	missense	219869	exon1			TACCCGCTCAGGT	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.385C>A	11.37:g.123900714C>A	ENSP00000389072:p.Leu129Ile	263	0	0		315	81	0.257143	NM_001004464	B2RNJ3|Q6IEV2	Missense_Mutation	SNP	ENST00000431524.1	37	CCDS31704.1	.	.	.	.	.	.	.	.	.	.	C	16.60	3.167711	0.57476	.	.	ENSG00000234560	ENST00000431524	T	0.32753	1.44	3.04	2.11	0.27256	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38605	N	0.001629	T	0.61912	0.2385	H	0.97491	4.015	0.31448	N	0.671088	D	0.76494	0.999	D	0.85130	0.997	T	0.65825	-0.6074	10	0.87932	D	0	.	3.7997	0.08753	0.0:0.6176:0.0:0.3824	.	129	Q8NGN5	O10G8_HUMAN	I	129	ENSP00000389072:L129I	ENSP00000389072:L129I	L	+	1	0	OR10G8	123405924	0.486000	0.25980	0.977000	0.42913	0.770000	0.43624	1.056000	0.30480	1.684000	0.51022	0.650000	0.86243	CTC	.	.	none		0.557	OR10G8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387270.1	NM_001004464		A	123900714	C	A	123900714	3	1	8	1	0	0	0	0	1	0	0	0	10912	797	28	4	387	4	OR10G8	11	123900714	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	2486450	123900714	11105802	103	942											
CNTN1	1272	hgsc.bcm.edu	37	chr12	41316167	41316167	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaaagatgctggaatatacTactgtttagcatctaataac	16	12	7	6	0	1	2	0	0	1	2	1	3	1	3	0	1	5	3	0	1	8	7			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr12:41316167T>A	ENST00000551295.2	+	5	454	c.337T>A	c.(337-339)Tac>Aac	p.Y113N	CNTN1_ENST00000547849.1_Missense_Mutation_p.Y113N|CNTN1_ENST00000360099.3_Missense_Mutation_p.Y113N|CNTN1_ENST00000547702.1_Missense_Mutation_p.Y113N|CNTN1_ENST00000347616.1_Missense_Mutation_p.Y113N|CNTN1_ENST00000348761.2_Missense_Mutation_p.Y102N	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	113	Ig-like C2-type 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)				TGGAATATACTACTGTTTAGC	0.408																																					p.Y113N		Atlas-SNP	.											.	CNTN1	207	.	0			c.T337A						PASS	.						126	113	117					12																	41316167		2203	4300	6503	SO:0001583	missense	1272	exon5			ATATACTACTGTT	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.337T>A	12.37:g.41316167T>A	ENSP00000447006:p.Tyr113Asn	110	0	0		121	17	0.140496	NM_001256063	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Missense_Mutation	SNP	ENST00000551295.2	37	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	T	16.11	3.031394	0.54790	.	.	ENSG00000018236	ENST00000547702;ENST00000551295;ENST00000547849;ENST00000347616;ENST00000360099;ENST00000348761	T;T;T;T;T;T	0.11930	2.73;2.73;2.73;2.73;2.73;2.73	5.65	4.43	0.53597	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.389023	0.28560	N	0.014920	T	0.12518	0.0304	N	0.16833	0.445	0.32815	D	0.501984	B;B;B	0.25206	0.12;0.072;0.089	B;B;B	0.38156	0.137;0.173;0.266	T	0.12192	-1.0557	10	0.72032	D	0.01	.	11.327	0.49454	0.0:0.0:0.3207:0.6793	.	113;102;113	Q12860-3;Q12860-2;Q12860	.;.;CNTN1_HUMAN	N	113;113;113;113;113;102	ENSP00000448004:Y113N;ENSP00000447006:Y113N;ENSP00000448653:Y113N;ENSP00000325660:Y113N;ENSP00000353213:Y113N;ENSP00000261160:Y102N	ENSP00000325660:Y113N	Y	+	1	0	CNTN1	39602434	1.000000	0.71417	0.998000	0.56505	0.951000	0.60555	2.599000	0.46231	2.285000	0.76669	0.477000	0.44152	TAC	.	.	none		0.408	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		A	41316167	T	A	41316167	3	1	8	1	0	0	0	0	1	0	0	0	3642	1522	53	5	351	5	CNTN1	12	41316167	Missense_Mutation	SNP	T	TCGA-FA-A82F-01A-11D-A382-10		41316167	92535728	104	943											
MLL2	8085	hgsc.bcm.edu	37	chr12	49426852	49426853	+	Frame_Shift_Del	DEL	CT	CT	-																															gcccactgtgtgacatcagaCtctgctgaagatgggacagc																										TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr12:49426852_49426853delCT	ENST00000301067.7	-	39	11634_11635	c.11635_11636delAG	c.(11635-11637)agtfs	p.S3879fs	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3879	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)										TGACATCAGACTCTGCTGAAGA	0.584																																					p.3879_3879del		Pindel,Atlas-Indel	.											.	MLL2	1173	.	0			c.11636_11637del						PASS	.																																			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.11635_11636delAG	12.37:g.49426854_49426855delCT	ENSP00000301067:p.Ser3879fs	66	0	.		69	14	0.203	NM_003482	O14687	Frame_Shift_Del	DEL	ENST00000301067.7	37	CCDS44873.1																																																																																			.	.	none		0.584	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			-	49426853	CT	-	49426852	7	5	8	1	0	1	0	1	0	0	0	0	9630	565	20	0	5041	0	MLL2	12	49426852	Frame_Shift_Del	DEL	CT	TCGA-FA-A82F-01A-11D-A382-10	8110685	49426852	84425043	105	944											
HOXC11	3227	hgsc.bcm.edu	37	chr12	54367692	54367692	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtggccaaggagccggccAaaggagccgcccccagtagg	9	2	15	15	3	0	0	0	0	0	0	0	2	0	2	7	5	2	1	7	5	3	1			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr12:54367692A>T	ENST00000546378.1	+	1	783	c.667A>T	c.(667-669)Aaa>Taa	p.K223*	HOTAIR_ENST00000455246.1_RNA|HOTAIR_ENST00000424518.1_RNA|HOXC11_ENST00000243082.4_Nonsense_Mutation_p.K223*			O43248	HXC11_HUMAN	homeobox C11	223					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						GGAGCCGGCCAAAGGAGCCGC	0.716			T	NUP98	AML																																p.K223X		Atlas-SNP	.		Dom	yes		12	12q13.3	3227	homeo box C11		L	.	HOXC11	32	.	0			c.A667T						PASS	.						2	3	2					12																	54367692		1539	2840	4379	SO:0001587	stop_gained	3227	exon1			CCGGCCAAAGGAG		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.667A>T	12.37:g.54367692A>T	ENSP00000446680:p.Lys223*	31	0	0		22	7	0.318182	NM_014212	A8K7D1|Q96DH2	Nonsense_Mutation	SNP	ENST00000546378.1	37	CCDS8867.1	.	.	.	.	.	.	.	.	.	.	A	36	5.906095	0.97087	.	.	ENSG00000123388	ENST00000546378;ENST00000243082	.	.	.	4.22	4.22	0.49857	.	0.150308	0.64402	D	0.000014	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.7199	0.57136	1.0:0.0:0.0:0.0	.	.	.	.	X	223	.	ENSP00000243082:K223X	K	+	1	0	HOXC11	52653959	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.596000	0.61055	1.898000	0.54952	0.459000	0.35465	AAA	.	.	none		0.716	HOXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358869.2			T	54367692	A	T	54367692	4	4	8	1	0	0	0	0	0	1	0	0	7319	131	5	5	669	5	HOXC11	12	54367692	Nonsense_Mutation	SNP	A	TCGA-FA-A82F-01A-11D-A382-10	4940840	54367692	79484203	106	945											
OR6C75	390323	hgsc.bcm.edu	37	chr12	55759668	55759668	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agctgtatcttcatgtacatTaagacttctgccagagaaag	13	12	8	8	0	3	2	1	0	2	2	3	3	3	2	1	0	3	3	1	0	4	5			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr12:55759668T>G	ENST00000343399.3	+	1	774	c.774T>G	c.(772-774)atT>atG	p.I258M		NM_001005497.1	NP_001005497.1	A6NL08	O6C75_HUMAN	olfactory receptor, family 6, subfamily C, member 75	258						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						TCATGTACATTAAGACTTCTG	0.413																																					p.I258M		Atlas-SNP	.											.	OR6C75	67	.	0			c.T774G						PASS	.						94	83	87					12																	55759668		2203	4300	6503	SO:0001583	missense	390323	exon1			GTACATTAAGACT		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.774T>G	12.37:g.55759668T>G	ENSP00000368987:p.Ile258Met	79	0	0		88	27	0.306818	NM_001005497		Missense_Mutation	SNP	ENST00000343399.3	37	CCDS31820.1	.	.	.	.	.	.	.	.	.	.	t	10.13	1.265821	0.23136	.	.	ENSG00000187857	ENST00000343399	T	0.38722	1.12	5.22	-2.86	0.05717	GPCR, rhodopsin-like superfamily (1);	0.145223	0.31199	N	0.008068	T	0.21387	0.0515	N	0.20986	0.625	0.24027	N	0.99612	B	0.28128	0.201	B	0.33799	0.17	T	0.08848	-1.0702	10	0.44086	T	0.13	.	1.1064	0.01694	0.2021:0.2798:0.2947:0.2233	.	258	A6NL08	O6C75_HUMAN	M	258	ENSP00000368987:I258M	ENSP00000368987:I258M	I	+	3	3	OR6C75	54045935	0.000000	0.05858	0.991000	0.47740	0.983000	0.72400	-3.438000	0.00471	-0.367000	0.08052	-0.362000	0.07510	ATT	.	.	none		0.413	OR6C75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406418.1			G	55759668	T	G	55759668	3	3	8	1	0	0	0	0	1	0	0	0	11208	1742	61	5	776	5	OR6C75	12	55759668	Missense_Mutation	SNP	T	TCGA-FA-A82F-01A-11D-A382-10	1391976	55759668	78092227	107	946											
MON2	23041	hgsc.bcm.edu	37	chr12	62936884	62936884	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	attttctccctaggaaccatCtctttttgctgttgccaaat	8	17	5	11	0	2	0	0	0	2	0	4	1	2	1	3	1	3	2	3	1	3	6			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr12:62936884C>G	ENST00000393632.2	+	20	2763	c.2372C>G	c.(2371-2373)tCt>tGt	p.S791C	RNU6-399P_ENST00000365164.1_RNA|MON2_ENST00000393629.2_Missense_Mutation_p.S791C|MON2_ENST00000552115.1_Missense_Mutation_p.S791C|MON2_ENST00000393630.3_Missense_Mutation_p.S791C|MON2_ENST00000546600.1_Missense_Mutation_p.S791C|MON2_ENST00000552738.1_Missense_Mutation_p.S768C|MON2_ENST00000280379.6_Missense_Mutation_p.S791C	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	791					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)		TAGGAACCATCTCTTTTTGCT	0.353																																					p.S791C		Atlas-SNP	.											.	MON2	160	.	0			c.C2372G						PASS	.						93	94	94					12																	62936884		2203	4299	6502	SO:0001583	missense	23041	exon20			AACCATCTCTTTT		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.2372C>G	12.37:g.62936884C>G	ENSP00000377252:p.Ser791Cys	129	0	0		122	42	0.344262	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Missense_Mutation	SNP	ENST00000393632.2	37	CCDS31849.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.553734	0.86231	.	.	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000552738;ENST00000393629;ENST00000552115	T;T;T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;1.42	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.73241	0.3562	L	0.49350	1.555	0.80722	D	1	P;P;P;P	0.49559	0.877;0.709;0.709;0.925	B;P;P;P	0.53313	0.431;0.518;0.723;0.634	T	0.70059	-0.4976	9	.	.	.	-18.2064	19.7314	0.96182	0.0:1.0:0.0:0.0	.	791;768;791;791	B9EGP5;F8VWA6;F8W1Z6;Q7Z3U7-4	.;.;.;.	C	791;791;791;791;768;791;791	ENSP00000377252:S791C;ENSP00000377250:S791C;ENSP00000280379:S791C;ENSP00000447407:S791C;ENSP00000449215:S768C;ENSP00000377249:S791C;ENSP00000446635:S791C	.	S	+	2	0	MON2	61223151	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.776000	0.85560	2.727000	0.93392	0.655000	0.94253	TCT	.	.	none		0.353	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026		G	62936884	C	G	62936884	3	3	8	1	0	0	0	0	1	0	0	0	9709	913	32	4	2450	4	MON2	12	62936884	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	7177216	62936884	70915011	108	947											
PPM1H	57460	hgsc.bcm.edu	37	chr12	63328431	63328431	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcaggtccgagcctccgcagCtgccgccgccgtgctcggag	4	5	15	17	6	0	0	0	0	0	0	3	2	2	1	6	2	4	4	6	2	0	0			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr12:63328431C>T	ENST00000228705.6	-	1	386	c.86G>A	c.(85-87)aGc>aAc	p.S29N	Y_RNA_ENST00000516851.1_RNA	NM_020700.1	NP_065751.1	Q9ULR3	PPM1H_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1H	29							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)		GCCTCCGCAGCTGCCGCCGCC	0.667																																					p.S29N		Atlas-SNP	.											.	PPM1H	42	.	0			c.G86A						PASS	.						6	9	8					12																	63328431		1801	3941	5742	SO:0001583	missense	57460	exon1			CCGCAGCTGCCGC	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.86G>A	12.37:g.63328431C>T	ENSP00000228705:p.Ser29Asn	76	0	0		77	27	0.350649	NM_020700	B1Q2A9|B2RXG4|Q6PI86	Missense_Mutation	SNP	ENST00000228705.6	37	CCDS44934.1	.	.	.	.	.	.	.	.	.	.	C	13.79	2.341429	0.41498	.	.	ENSG00000111110	ENST00000228705	T	0.23147	1.92	3.82	3.82	0.43975	.	0.240619	0.25247	N	0.032057	T	0.18215	0.0437	L	0.33485	1.01	0.22666	N	0.99887	B	0.02656	0.0	B	0.01281	0.0	T	0.12066	-1.0562	9	.	.	.	-2.3967	11.0859	0.48086	0.0:1.0:0.0:0.0	.	29	Q9ULR3	PPM1H_HUMAN	N	29	ENSP00000228705:S29N	.	S	-	2	0	PPM1H	61614698	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	2.755000	0.47540	1.964000	0.57103	0.561000	0.74099	AGC	.	.	none		0.667	PPM1H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406760.2	NM_020700		T	63328431	C	T	63328431	3	4	8	1	0	0	0	0	1	0	0	0	12353	797	28	2	1498	2	PPM1H	12	63328431	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	391547	63328431	70523464	109	948											
BTG1	694	hgsc.bcm.edu	37	chr12	92539203	92539203	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctctggctgaaggtctgcaGctgtcgctcgctcgtgagcc	4	10	14	13	3	2	2	0	2	2	0	5	2	2	2	1	2	3	6	1	2	1	0	rs369374957		TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr12:92539203G>A	ENST00000256015.3	-	1	470	c.109C>T	c.(109-111)Ctg>Ttg	p.L37L	C12orf79_ENST00000549802.1_5'Flank|C12orf79_ENST00000546975.1_5'Flank|RP11-796E2.4_ENST00000501008.2_RNA|RP11-796E2.4_ENST00000499685.2_RNA|C12orf79_ENST00000551563.2_5'Flank	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	37					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)	p.L37L(1)		haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				AAGGTCTGCAGCTGTCGCTCG	0.677			T	MYC	BCLL																																p.L37L		Atlas-SNP	.		Dom	yes		12	12q22	694	"B-cell translocation gene 1, anti-proliferative"		L	BTG1,NS,lymphoid_neoplasm,0,3	BTG1	30	3	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C109T						PASS	.						38	41	40					12																	92539203		2203	4300	6503	SO:0001819	synonymous_variant	694	exon1			TCTGCAGCTGTCG		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.109C>T	12.37:g.92539203G>A		150	0	0		123	37	0.300813	NM_001731	P31607	Silent	SNP	ENST00000256015.3	37	CCDS9043.1																																																																																			.	.	alt		0.677	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1			A	92539203	G	A	92539203	2	1	8	1	0	0	0	0	0	0	0	1	1555	962	34	2		2	BTG1	12	92539203	Silent	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	29210772	92539203	41312692	110	949											
SLC5A8	160728	hgsc.bcm.edu	37	chr12	101603483	101603483	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgcggtcattctgcggccGcccatcaggaagtccttgga	7	9	12	13	3	3	0	2	0	1	0	4	2	4	2	3	4	2	0	3	4	1	2	rs147835898	byFrequency	TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr12:101603483G>A	ENST00000536262.2	-	1	702	c.144C>T	c.(142-144)ggC>ggT	p.G48G		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						TTCTGCGGCCGCCCATCAGGA	0.652																																					p.G48G	GBM(60;420 1056 13605 22380 47675)	Atlas-SNP	.											.	SLC5A8	102	.	0			c.C144T						PASS	.						45	42	43					12																	101603483		2203	4300	6503	SO:0001819	synonymous_variant	160728	exon1			GCGGCCGCCCATC	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.144C>T	12.37:g.101603483G>A		22	0	0		24	10	0.416667	NM_145913		Silent	SNP	ENST00000536262.2	37	CCDS9080.1																																																																																			G|0.999;T|0.001	.	alt		0.652	SLC5A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409401.1	NM_145913		A	101603483	G	A	101603483	2	1	8	1	0	0	0	0	0	0	0	1	14686	1074	38	1		1	SLC5A8	12	101603483	Silent	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	9064280	101603483	32248412	111	950											
DTX1	1840	hgsc.bcm.edu	37	chr12	113496147	113496147	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgtgccaccacattgagaaCgtgctgaaggaggacgctcg	10	7	14	10	3	0	2	0	2	0	1	1	5	0	4	2	2	3	2	2	2	2	1			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr12:113496147C>T	ENST00000257600.3	+	1	653	c.150C>T	c.(148-150)aaC>aaT	p.N50N		NM_004416.2	NP_004407.2	Q86Y01	DTX1_HUMAN	deltex 1, E3 ubiquitin ligase	50	WWE 1. {ECO:0000255|PROSITE- ProRule:PRU00248}.				cell surface receptor signaling pathway (GO:0007166)|glial cell differentiation (GO:0010001)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of T cell differentiation (GO:0045581)|Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)|regulation of Notch signaling pathway (GO:0008593)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Notch binding (GO:0005112)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	32						ACATTGAGAACGTGCTGAAGG	0.652																																					p.N50N		Atlas-SNP	.											.	DTX1	83	.	0			c.C150T						PASS	.						118	102	108					12																	113496147		2203	4300	6503	SO:0001819	synonymous_variant	1840	exon1			TGAGAACGTGCTG	AF053700	CCDS9164.1	12q24	2014-01-28	2014-01-28			ENSG00000135144			3060	protein-coding gene	gene with protein product		602582	"deltex homolog 1 (Drosophila)"			9590294, 12670957	Standard	NM_004416		Approved	hDx-1	uc001tuk.1	Q86Y01	OTTHUMG00000169610	ENST00000257600.3:c.150C>T	12.37:g.113496147C>T		66	0	0		59	9	0.152542	NM_004416	O60630|Q9BS04	Silent	SNP	ENST00000257600.3	37	CCDS9164.1																																																																																			.	.	none		0.652	DTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405045.2			T	113496147	C	T	113496147	2	4	8	1	0	0	0	0	0	0	0	1	4795	535	19	1		1	DTX1	12	113496147	Silent	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	11892664	113496147	20355748	112	951											
RAN	5901	hgsc.bcm.edu	37	chr12	131359242	131359242	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aaggacaggaaagtgaaggcGaaatccattgtcttccaccg	14	7	11	9	2	1	1	0	1	1	0	3	4	3	3	3	3	0	0	3	3	4	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr12:131359242G>A	ENST00000543796.1	+	5	657	c.399G>A	c.(397-399)gcG>gcA	p.A133A	RAN_ENST00000392367.3_Silent_p.A150A|RAN_ENST00000392369.2_Silent_p.A133A|RAN_ENST00000254675.3_Silent_p.A45A|RAN_ENST00000541630.1_Silent_p.A45A			P62826	RAN_HUMAN	RAN, member RAS oncogene family	133					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)		AAGTGAAGGCGAAATCCATTG	0.398																																					p.A133A		Atlas-SNP	.											.	RAN	18	.	0			c.G399A						PASS	.						100	88	92					12																	131359242		2203	4300	6503	SO:0001819	synonymous_variant	5901	exon5			GAAGGCGAAATCC	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.399G>A	12.37:g.131359242G>A		107	0	0		81	18	0.222222	NM_006325	A8K3Z8|P17080|P28746|P28747|Q6IPB2|Q86V08|Q8NI90|Q9CSP3|Q9CWI7|Q9CZA2|Q9UDJ5|Q9UEU9	Silent	SNP	ENST00000543796.1	37	CCDS9271.1																																																																																			.	.	none		0.398	RAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259441.2	NM_006325		A	131359242	G	A	131359242	2	1	8	1	0	0	0	0	0	0	0	1	13039	1045	37	1		1	RAN	12	131359242	Silent	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	17863095	131359242	2492653	113	952											
LATS2	26524	hgsc.bcm.edu	37	chr13	21562181	21562181	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctctgctgtttttgcggaCgggaacgggagaggtctgaa	7	11	16	7	3	2	2	0	1	2	1	3	5	2	4	0	4	3	2	0	4	2	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr13:21562181C>T	ENST00000382592.4	-	4	2143	c.1738G>A	c.(1738-1740)Gtc>Atc	p.V580I	LATS2_ENST00000542899.1_Missense_Mutation_p.V580I|LATS2_ENST00000472754.1_5'Flank	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)		TTTTTGCGGACGGGAACGGGA	0.557																																					p.V580I		Atlas-SNP	.											.	LATS2	176	.	0			c.G1738A						PASS	.						240	243	242					13																	21562181		2203	4300	6503	SO:0001583	missense	26524	exon4			TGCGGACGGGAAC	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.1738G>A	13.37:g.21562181C>T	ENSP00000372035:p.Val580Ile	450	1	0.00222222		385	96	0.249351	NM_014572		Missense_Mutation	SNP	ENST00000382592.4	37	CCDS9294.1	.	.	.	.	.	.	.	.	.	.	C	18.14	3.558695	0.65538	.	.	ENSG00000150457	ENST00000382592;ENST00000542899	T;T	0.41758	0.99;0.99	5.12	5.12	0.69794	.	0.000000	0.64402	D	0.000018	T	0.42854	0.1221	L	0.52905	1.665	0.58432	D	0.999998	P	0.47106	0.89	B	0.40741	0.339	T	0.41787	-0.9489	10	0.44086	T	0.13	.	18.8138	0.92070	0.0:1.0:0.0:0.0	.	580	Q9NRM7	LATS2_HUMAN	I	580	ENSP00000372035:V580I;ENSP00000441817:V580I	ENSP00000372035:V580I	V	-	1	0	LATS2	20460181	1.000000	0.71417	0.029000	0.17559	0.542000	0.35054	7.273000	0.78527	2.691000	0.91804	0.549000	0.68633	GTC	.	.	none		0.557	LATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044102.1			T	21562181	C	T	21562181	3	4	8	1	0	0	0	0	1	0	0	0	8656	536	19	1	1548	1	LATS2	13	21562181	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10		21562181	93607697	114	953											
NFKBIA	4792	hgsc.bcm.edu	37	chr14	35873697	35873697	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcctgcggctcgaggcggaTctcctgcagctccttgacca	5	9	11	16	3	1	1	0	1	1	0	5	3	3	2	4	3	3	3	4	3	0	1			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr14:35873697T>A	ENST00000216797.5	-	1	255	c.154A>T	c.(154-156)Atc>Ttc	p.I52F	NFKBIA_ENST00000557100.1_5'UTR|NFKBIA_ENST00000557140.1_Missense_Mutation_p.I52F|NFKBIA_ENST00000557389.1_5'Flank	NM_020529.2	NP_065390.1	P25963	IKBA_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha	52					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)	TCGAGGCGGATCTCCTGCAGC	0.682																																					p.I52F		Atlas-SNP	.											.	NFKBIA	28	.	0			c.A154T						PASS	.						17	18	18					14																	35873697		2200	4296	6496	SO:0001583	missense	4792	exon1			GGCGGATCTCCTG		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.154A>T	14.37:g.35873697T>A	ENSP00000216797:p.Ile52Phe	74	0	0		55	18	0.327273	NM_020529	B2R8L6	Missense_Mutation	SNP	ENST00000216797.5	37	CCDS9656.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.057033	0.76074	.	.	ENSG00000100906	ENST00000216797;ENST00000557140	T;T	0.49720	0.87;0.77	3.87	3.87	0.44632	.	.	.	.	.	T	0.41994	0.1183	L	0.51422	1.61	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.32134	-0.9918	9	0.36615	T	0.2	-37.6328	12.9569	0.58432	0.0:0.0:0.0:1.0	.	52;52	G3V3I4;P25963	.;IKBA_HUMAN	F	52	ENSP00000216797:I52F;ENSP00000451257:I52F	ENSP00000216797:I52F	I	-	1	0	NFKBIA	34943448	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	5.352000	0.66028	1.510000	0.48803	0.260000	0.18958	ATC	.	.	none		0.682	NFKBIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276683.1	NM_020529		A	35873697	T	A	35873697	3	1	8	1	0	0	0	0	1	0	0	0	10386	1435	50	5	823	5	NFKBIA	14	35873697	Missense_Mutation	SNP	T	TCGA-FA-A82F-01A-11D-A382-10		35873697	71475843	115	954											
SMEK1	55671	hgsc.bcm.edu	37	chr14	91937274	91937274	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gttctttatgtggtaggtatGgtgctccacacaaaatgtta	10	15	10	6	0	1	0	0	0	1	0	2	0	2	0	1	3	1	5	1	3	6	6			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr14:91937274G>A	ENST00000554943.1	-	10	1682	c.1567C>T	c.(1567-1569)Cat>Tat	p.H523Y	SMEK1_ENST00000555462.1_Missense_Mutation_p.H284Y|SMEK1_ENST00000554684.1_Missense_Mutation_p.H510Y|SMEK1_ENST00000337238.4_Missense_Mutation_p.H510Y|SMEK1_ENST00000428424.2_Missense_Mutation_p.H284Y			Q6IN85	P4R3A_HUMAN	SMEK homolog 1, suppressor of mek1 (Dictyostelium)	523					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)		TGGTAGGTATGGTGCTCCACA	0.353																																					p.H510Y		Atlas-SNP	.											.	SMEK1	94	.	0			c.C1528T						PASS	.						108	110	110					14																	91937274		2203	4300	6503	SO:0001583	missense	55671	exon11			AGGTATGGTGCTC	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.1567C>T	14.37:g.91937274G>A	ENSP00000450883:p.His523Tyr	117	0	0		132	46	0.348485	NM_032560	Q69YK6|Q86U23|Q86YI7|Q8IVG1|Q9H3F1|Q9H7U8|Q9NV01|Q9NWP1	Missense_Mutation	SNP	ENST00000554943.1	37		.	.	.	.	.	.	.	.	.	.	G	15.55	2.866703	0.51588	.	.	ENSG00000100796	ENST00000554684;ENST00000337238;ENST00000428424;ENST00000554943;ENST00000555462;ENST00000554390	D;D;D;D;D;D	0.95035	-3.59;-3.59;-3.59;-3.59;-3.59;-3.59	5.6	4.71	0.59529	Armadillo-like helical (1);Armadillo-type fold (1);	0.045903	0.85682	D	0.000000	D	0.97698	0.9245	M	0.90198	3.095	0.80722	D	1	P;D;D	0.89917	0.701;1.0;1.0	B;D;D	0.97110	0.201;0.999;1.0	D	0.98583	1.0651	10	0.87932	D	0	-16.6192	16.5223	0.84320	0.0:0.131:0.869:0.0	.	284;523;510	Q6IN85-4;Q6IN85;Q6IN85-2	.;P4R3A_HUMAN;.	Y	510;510;284;523;284;510	ENSP00000450864:H510Y;ENSP00000337125:H510Y;ENSP00000392704:H284Y;ENSP00000450883:H523Y;ENSP00000450891:H284Y;ENSP00000452596:H510Y	ENSP00000337125:H510Y	H	-	1	0	SMEK1	91007027	1.000000	0.71417	1.000000	0.80357	0.048000	0.14542	9.869000	0.99810	1.346000	0.45694	-0.182000	0.12963	CAT	.	.	none		0.353	SMEK1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000411665.1	NM_032560		A	91937274	G	A	91937274	3	1	8	1	0	0	0	0	1	0	0	0	14808	1348	47	2	958	2	SMEK1	14	91937274	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	56063577	91937274	15412266	116	955											
BEGAIN	57596	hgsc.bcm.edu	37	chr14	101004957	101004957	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccgggaagcggaaggtctcGgccgggtacggtgacatggt	7	6	19	9	5	1	1	0	1	1	0	2	3	1	3	2	7	2	1	2	7	3	1	rs542292676		TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr14:101004957G>A	ENST00000355173.2	-	7	1202	c.1131C>T	c.(1129-1131)gcC>gcT	p.A377A	BEGAIN_ENST00000443071.2_Silent_p.A377A|BEGAIN_ENST00000556751.1_Silent_p.A313A|CTD-2062F14.3_ENST00000553301.1_lincRNA	NM_020836.3	NP_065887.1	Q9BUH8	BEGIN_HUMAN	brain-enriched guanylate kinase-associated	377						cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				cervix(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|skin(2)|stomach(1)	14		Melanoma(154;0.212)				GGAAGGTCTCGGCCGGGTACG	0.751																																					p.A377A	NSCLC(159;1889 2010 9965 27479 40101)	Atlas-SNP	.											.	BEGAIN	32	.	0			c.C1131T						PASS	.						7	9	9					14																	101004957		2048	4022	6070	SO:0001819	synonymous_variant	57596	exon7			GGTCTCGGCCGGG	BC002607	CCDS9962.1	14q32.2	2012-12-07	2012-12-07			ENSG00000183092			24163	protein-coding gene	gene with protein product			"brain-enriched guanylate kinase-associated homolog (rat)"			10819331	Standard	NM_020836		Approved	KIAA1446	uc010txa.2	Q9BUH8		ENST00000355173.2:c.1131C>T	14.37:g.101004957G>A		86	0	0		334	28	0.0838323	NM_020836	Q9NPU3|Q9P282	Silent	SNP	ENST00000355173.2	37	CCDS9962.1																																																																																			.	.	none		0.751	BEGAIN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414329.1	NM_020836		A	101004957	G	A	101004957	2	1	8	1	0	0	0	0	0	0	0	1	1397	1103	39	1		1	BEGAIN	14	101004957	Silent	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	9067683	101004957	6344583	117	956											
BEGAIN	57596	hgsc.bcm.edu	37	chr14	101005056	101005056	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggcaaagcgagggctgccCtcgtaggtggtggcgggtgg	5	8	20	8	3	0	0	0	0	0	0	1	1	0	0	1	7	2	3	1	7	2	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr14:101005056C>G	ENST00000355173.2	-	7	1103	c.1032G>C	c.(1030-1032)gaG>gaC	p.E344D	BEGAIN_ENST00000443071.2_Missense_Mutation_p.E344D|BEGAIN_ENST00000556751.1_Missense_Mutation_p.E280D|CTD-2062F14.3_ENST00000553301.1_lincRNA	NM_020836.3	NP_065887.1	Q9BUH8	BEGIN_HUMAN	brain-enriched guanylate kinase-associated	344						cytoplasm (GO:0005737)|dendrite (GO:0030425)|membrane (GO:0016020)|neuronal cell body (GO:0043025)				cervix(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|skin(2)|stomach(1)	14		Melanoma(154;0.212)				GAGGGCTGCCCTCGTAGGTGG	0.721																																					p.E344D	NSCLC(159;1889 2010 9965 27479 40101)	Atlas-SNP	.											.	BEGAIN	32	.	0			c.G1032C						PASS	.						26	21	23					14																	101005056		2155	4244	6399	SO:0001583	missense	57596	exon7			GCTGCCCTCGTAG	BC002607	CCDS9962.1	14q32.2	2012-12-07	2012-12-07			ENSG00000183092			24163	protein-coding gene	gene with protein product			"brain-enriched guanylate kinase-associated homolog (rat)"			10819331	Standard	NM_020836		Approved	KIAA1446	uc010txa.2	Q9BUH8		ENST00000355173.2:c.1032G>C	14.37:g.101005056C>G	ENSP00000347301:p.Glu344Asp	147	0	0		625	37	0.0592	NM_020836	Q9NPU3|Q9P282	Missense_Mutation	SNP	ENST00000355173.2	37	CCDS9962.1	.	.	.	.	.	.	.	.	.	.	C	7.497	0.651923	0.14516	.	.	ENSG00000183092	ENST00000355173;ENST00000556751;ENST00000443071	.	.	.	4.17	2.26	0.28386	.	0.267762	0.26282	N	0.025278	T	0.15522	0.0374	N	0.04880	-0.145	0.22796	N	0.998728	B	0.22211	0.066	B	0.24006	0.05	T	0.29427	-1.0012	9	0.14252	T	0.57	.	8.346	0.32272	0.0:0.719:0.1908:0.0902	.	344	Q9BUH8	BEGIN_HUMAN	D	344;280;344	.	ENSP00000347301:E344D	E	-	3	2	BEGAIN	100074809	0.958000	0.32768	0.475000	0.27278	0.055000	0.15305	0.567000	0.23608	0.201000	0.20466	0.462000	0.41574	GAG	.	.	none		0.721	BEGAIN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000414329.1	NM_020836		G	101005056	C	G	101005056	3	3	8	1	0	0	0	0	1	0	0	0	1397	680	24	4	753	4	BEGAIN	14	101005056	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	99	101005056	6344484	118	957											
C14orf73	91828	hgsc.bcm.edu	37	chr14	103570659	103570659	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctggagcagagtcactgggCggccgccgaggtccccgagg	6	4	18	13	4	1	1	1	0	0	1	2	4	2	2	4	5	1	2	4	5	0	0			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr14:103570659C>T	ENST00000380069.3	+	4	1293	c.1217C>T	c.(1216-1218)gCg>gTg	p.A406V		NM_001077594.1	NP_001071062.1	Q17RC7	EX3L4_HUMAN	exocyst complex component 3-like 4	406					exocytosis (GO:0006887)	exocyst (GO:0000145)				cervix(2)|endometrium(2)|lung(4)|ovary(1)|skin(1)	10						AGTCACTGGGCGGCCGCCGAG	0.687																																					p.A406V		Atlas-SNP	.											.	EXOC3L4	35	.	0			c.C1217T						PASS	.						10	12	11					14																	103570659		2188	4293	6481	SO:0001583	missense	91828	exon4			ACTGGGCGGCCGC	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.1217C>T	14.37:g.103570659C>T	ENSP00000369409:p.Ala406Val	97	0	0		54	30	0.555556	NM_001077594	Q14CR2	Missense_Mutation	SNP	ENST00000380069.3	37	CCDS32163.1	.	.	.	.	.	.	.	.	.	.	C	2.404	-0.336881	0.05278	.	.	ENSG00000205436	ENST00000380069	T	0.05925	3.37	4.18	-2.7	0.06004	.	0.665977	0.14024	N	0.346640	T	0.05135	0.0137	L	0.57536	1.79	0.09310	N	1	B	0.32543	0.375	B	0.28139	0.086	T	0.28202	-1.0051	10	0.33141	T	0.24	-4.2103	3.2771	0.06902	0.3063:0.3183:0.0:0.3754	.	406	Q17RC7	EX3L4_HUMAN	V	406	ENSP00000369409:A406V	ENSP00000369409:A406V	A	+	2	0	EXOC3L4	102640412	0.005000	0.15991	0.001000	0.08648	0.081000	0.17604	-0.056000	0.11787	-0.925000	0.03775	-0.284000	0.09977	GCG	.	.	none		0.687	EXOC3L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415663.1	XM_941093		T	103570659	C	T	103570659	3	4	8	1	0	0	0	0	1	0	0	0	1781	768	27	1	1231	1	C14orf73	14	103570659	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	2565603	103570659	3778881	119	958											
NDN	4692	hgsc.bcm.edu	37	chr15	23931597	23931597	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccccaaaagaactcgtattcGggcggctccacgtatgggac	10	7	11	13	4	0	1	0	0	0	1	3	2	1	2	3	3	1	3	3	3	5	3	rs142210120	byFrequency	TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr15:23931597G>A	ENST00000331837.4	-	1	853	c.768C>T	c.(766-768)ccC>ccT	p.P256P		NM_002487.2	NP_002478.1	Q99608	NECD_HUMAN	necdin, melanoma antigen (MAGE) family member	256	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)		ACTCGTATTCGGGCGGCTCCA	0.562									Prader-Willi syndrome				G|||	9	0.00179712	0.0053	0.0029	5008	,	,		19044	0.0		0.0	False		,,,				2504	0.0				p.P256P		Atlas-SNP	.											NDN,right_upper_lobe,carcinoma,0,1	NDN	79	1	0			c.C768T						PASS	.	G		17,4389		0,17,2186	35	35	35		768	-7	0	15	dbSNP_134	35	3,8595		0,3,4296	no	coding-synonymous	NDN	NM_002487.2		0,20,6482	AA,AG,GG		0.0349,0.3858,0.1538		256/322	23931597	20,12984	2203	4299	6502	SO:0001819	synonymous_variant	4692	exon1	Familial Cancer Database	Prader-Labhart-Willi syndrome	GTATTCGGGCGGC	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.768C>T	15.37:g.23931597G>A		86	0	0		84	30	0.357143	NM_002487	B2R6Z5	Silent	SNP	ENST00000331837.4	37	CCDS10014.1																																																																																			G|0.998;A|0.002	0.002	strong		0.562	NDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251226.2	NM_002487		A	23931597	G	A	23931597	2	1	8	1	0	0	0	0	0	0	0	1	10256	1103	39	1		1	NDN	15	23931597	Silent	SNP	G	TCGA-FA-A82F-01A-11D-A382-10		23931597	78599795	120	959											
NMRAL1	57407	hgsc.bcm.edu	37	chr16	4516347	4516347	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttcttgatgttctccaggccGctgtagaccacatagtggag	8	12	11	10	1	2	2	0	1	2	1	3	3	2	3	3	2	0	3	3	2	2	5			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr16:4516347G>A	ENST00000574733.1	-	4	1065	c.336C>T	c.(334-336)agC>agT	p.S112S	NMRAL1_ENST00000572391.1_5'UTR|NMRAL1_ENST00000404295.3_Silent_p.S112S|NMRAL1_ENST00000283429.6_Silent_p.S112S|NMRAL1_ENST00000574425.1_Silent_p.S112S			Q9HBL8	NMRL1_HUMAN	NmrA-like family domain containing 1	112						cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|prostate(2)|stomach(1)	15						TCTCCAGGCCGCTGTAGACCA	0.597																																					p.S112S		Atlas-SNP	.											.	NMRAL1	31	.	0			c.C336T						PASS	.						45	44	44					16																	4516347		2197	4300	6497	SO:0001819	synonymous_variant	57407	exon4			CAGGCCGCTGTAG	AF225419	CCDS10516.1	16p13.3	2013-10-11			ENSG00000153406	ENSG00000153406		"Short chain dehydrogenase/reductase superfamily / Atypical members"	24987	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 48A, member 1"					19027726	Standard	NM_020677		Approved	FLJ25918, HSCARG, SDR48A1	uc002cwo.3	Q9HBL8	OTTHUMG00000129468	ENST00000574733.1:c.336C>T	16.37:g.4516347G>A		40	0	0		42	19	0.452381	NM_020677		Silent	SNP	ENST00000574733.1	37	CCDS10516.1																																																																																			.	.	none		0.597	NMRAL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438579.1	NM_020677		A	4516347	G	A	4516347	2	1	8	1	0	0	0	0	0	0	0	1	10510	1078	38	1		1	NMRAL1	16	4516347	Silent	SNP	G	TCGA-FA-A82F-01A-11D-A382-10		4516347	85838406	121	960											
MMP2	4313	hgsc.bcm.edu	37	chr16	55518022	55518022	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcgatgtgaccccactgcggTtttctcgaatccatgatgga	8	11	11	11	3	1	2	0	2	1	0	3	5	2	3	3	2	1	1	3	2	1	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr16:55518022T>G	ENST00000219070.4	+	3	984	c.475T>G	c.(475-477)Ttt>Gtt	p.F159V	MMP2_ENST00000437642.2_Missense_Mutation_p.F109V|MMP2_ENST00000570308.1_Missense_Mutation_p.F83V|MMP2_ENST00000543485.1_Missense_Mutation_p.F83V	NM_004530.4	NP_004521.1	P08253	MMP2_HUMAN	matrix metallopeptidase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)	159	Collagenase-like 1.				angiogenesis (GO:0001525)|blood vessel maturation (GO:0001955)|bone trabecula formation (GO:0060346)|cellular protein metabolic process (GO:0044267)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|positive regulation of innate immune response (GO:0045089)|proteolysis (GO:0006508)|response to hypoxia (GO:0001666)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|sarcomere (GO:0030017)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(12)|liver(2)|lung(23)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	58		Renal(780;0.00183)|Breast(268;0.00354)|Hepatocellular(780;0.00826)|all_neural(199;0.0189)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0185)|all cancers(182;7.16e-45)|Epithelial(162;5.26e-37)|GBM - Glioblastoma multiforme(240;9e-08)|Kidney(780;0.00227)|BRCA - Breast invasive adenocarcinoma(181;0.00786)	Captopril(DB01197)|Marimastat(DB00786)	CCCACTGCGGTTTTCTCGAAT	0.552																																					p.F159V		Atlas-SNP	.											MMP2,NS,carcinoma,-1,1	MMP2	119	1	0			c.T475G						PASS	.						150	121	131					16																	55518022		2198	4300	6498	SO:0001583	missense	4313	exon3			CTGCGGTTTTCTC		CCDS10752.1, CCDS45487.1	16q13-q21	2008-02-05	2005-08-08		ENSG00000087245	ENSG00000087245	3.4.24.24		7166	protein-coding gene	gene with protein product		120360	"matrix metalloproteinase 2 (gelatinase A, 72kD gelatinase, 72kD type IV collagenase)", "matrix metalloproteinase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase)"	CLG4, CLG4A			Standard	NM_004530		Approved	TBE-1	uc002ehz.4	P08253	OTTHUMG00000133202	ENST00000219070.4:c.475T>G	16.37:g.55518022T>G	ENSP00000219070:p.Phe159Val	117	0	0		123	56	0.455285	NM_004530	B2R6U1|B4DWH3|E9PE45|Q9UCJ8	Missense_Mutation	SNP	ENST00000219070.4	37	CCDS10752.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.162604	0.78226	.	.	ENSG00000087245	ENST00000219070;ENST00000543485;ENST00000437642	T;T;T	0.54279	0.58;0.58;0.58	4.72	4.72	0.59763	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.047110	0.85682	D	0.000000	T	0.67449	0.2894	M	0.90198	3.095	0.80722	D	1	P;P	0.50369	0.75;0.934	P;P	0.48227	0.571;0.538	T	0.77005	-0.2748	10	0.72032	D	0.01	.	14.5064	0.67755	0.0:0.0:0.0:1.0	.	109;159	E9PE45;P08253	.;MMP2_HUMAN	V	159;83;109	ENSP00000219070:F159V;ENSP00000444143:F83V;ENSP00000394237:F109V	ENSP00000219070:F159V	F	+	1	0	MMP2	54075523	1.000000	0.71417	0.975000	0.42487	0.982000	0.71751	5.073000	0.64395	1.902000	0.55061	0.374000	0.22700	TTT	.	.	none		0.552	MMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256913.3			G	55518022	T	G	55518022	3	3	8	1	0	0	0	0	1	0	0	0	9667	1725	60	5	492	5	MMP2	16	55518022	Missense_Mutation	SNP	T	TCGA-FA-A82F-01A-11D-A382-10	51001675	55518022	34836731	122	961											
ADAT1	23536	hgsc.bcm.edu	37	chr16	75646759	75646759	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gaatgatggaggcatccccaCctgcagagaatgaacccact	13	6	10	12	0	0	3	0	2	0	1	1	6	1	4	4	2	2	2	4	2	3	0			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr16:75646759C>T	ENST00000307921.3	-	7	570	c.425G>A	c.(424-426)tGt>tAt	p.C142Y		NM_012091.3	NP_036223.2	Q9BUB4	ADAT1_HUMAN	adenosine deaminase, tRNA-specific 1	142	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						GGCATCCCCACCTGCAGAGAA	0.473																																					p.C142Y		Atlas-SNP	.											.	ADAT1	45	.	0			c.G425A						PASS	.						41	44	43					16																	75646759		2197	4299	6496	SO:0001630	splice_region_variant	23536	exon7			TCCCCACCTGCAG	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.425-1G>A	16.37:g.75646759C>T		119	0	0		121	15	0.123967	NM_012091	Q9NVB7|Q9UNG3	Missense_Mutation	SNP	ENST00000307921.3	37	CCDS10922.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.971912	0.92919	.	.	ENSG00000065457	ENST00000307921;ENST00000542252	D	0.98221	-4.8	5.75	5.75	0.90469	Adenosine deaminase/editase (3);	0.085290	0.85682	D	0.000000	D	0.99318	0.9761	H	0.95187	3.635	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.98931	1.0787	10	0.87932	D	0	.	18.5379	0.91017	0.0:1.0:0.0:0.0	.	142	Q9BUB4	ADAT1_HUMAN	Y	142;113	ENSP00000310015:C142Y	ENSP00000310015:C142Y	C	-	2	0	ADAT1	74204260	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.747000	0.85070	2.716000	0.92895	0.655000	0.94253	TGT	.	.	none		0.473	ADAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269027.1	NM_012091	Missense_Mutation	T	75646759	C	T	75646759	5	4	8	1	0	0	0	0	0	0	1	0	284	521	18	2	1103	2	ADAT1	16	75646759	Splice_Site	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	20128737	75646759	14707994	123	962											
KLHL36	79786	hgsc.bcm.edu	37	chr16	84691156	84691156	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagaacgacctgctgcaccGcgtcaagccggccgtgtgct	8	6	12	15	5	1	1	1	0	0	1	1	2	1	1	4	1	5	3	4	1	3	0			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr16:84691156G>A	ENST00000564996.1	+	3	884	c.743G>A	c.(742-744)cGc>cAc	p.R248H	KLHL36_ENST00000258157.5_Missense_Mutation_p.R248H	NM_024731.2	NP_079007.2	Q8N4N3	KLH36_HUMAN	kelch-like family member 36	248	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						CTGCTGCACCGCGTCAAGCCG	0.687																																					p.R248H		Atlas-SNP	.											.	KLHL36	51	.	0			c.G743A						PASS	.						36	30	32					16																	84691156		2197	4290	6487	SO:0001583	missense	79786	exon3			TGCACCGCGTCAA	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.743G>A	16.37:g.84691156G>A	ENSP00000456743:p.Arg248His	39	0	0		43	4	0.0930233	NM_024731	Q8N5G6|Q9H9U6	Missense_Mutation	SNP	ENST00000564996.1	37	CCDS10948.1	.	.	.	.	.	.	.	.	.	.	G	14.29	2.491508	0.44249	.	.	ENSG00000135686	ENST00000325279;ENST00000258157	T	0.68903	-0.36	5.51	5.51	0.81932	BTB/Kelch-associated (2);	0.115666	0.64402	D	0.000018	T	0.66848	0.2831	L	0.27053	0.805	0.58432	D	0.99999	P;D	0.61080	0.72;0.989	B;P	0.56514	0.053;0.8	T	0.60826	-0.7186	10	0.15499	T	0.54	.	18.4088	0.90543	0.0:0.0:1.0:0.0	.	248;248	Q8N4N3-2;Q8N4N3	.;KLH36_HUMAN	H	248	ENSP00000258157:R248H	ENSP00000258157:R248H	R	+	2	0	KLHL36	83248657	0.998000	0.40836	1.000000	0.80357	0.983000	0.72400	4.951000	0.63610	2.582000	0.87167	0.563000	0.77884	CGC	.	.	none		0.687	KLHL36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269084.2			A	84691156	G	A	84691156	3	1	8	1	0	0	0	0	1	0	0	0	8398	1087	38	1	749	1	KLHL36	16	84691156	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	9044397	84691156	5663597	124	963											
ZNF276	92822	hgsc.bcm.edu	37	chr16	89790056	89790056	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcctccttcggacagcgaCgcggtggggcccaggtcggg	5	5	17	14	5	0	0	0	0	0	0	3	2	1	1	3	6	2	0	3	6	0	1			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr16:89790056C>T	ENST00000443381.2	+	4	1042	c.945C>T	c.(943-945)gaC>gaT	p.D315D	ZNF276_ENST00000446326.2_Missense_Mutation_p.T112M|ZNF276_ENST00000568064.1_Missense_Mutation_p.T234M|ZNF276_ENST00000289816.5_Silent_p.D240D|VPS9D1_ENST00000389386.3_5'Flank	NM_001113525.1	NP_001106997.1	Q8N554	ZN276_HUMAN	zinc finger protein 276	315					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)		CGGACAGCGACGCGGTGGGGC	0.672																																					p.D315D		Atlas-SNP	.											ZNF276_ENST00000443381,NS,carcinoma,0,2	ZNF276	70	2	0			c.C945T						PASS	.						25	31	29					16																	89790056		2190	4277	6467	SO:0001819	synonymous_variant	92822	exon4			CAGCGACGCGGTG	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.945C>T	16.37:g.89790056C>T		58	0	0		80	23	0.2875	NM_001113525	Q0VGA1|Q2TBE8|Q3B7H7	Silent	SNP	ENST00000443381.2	37	CCDS45554.1	.	.	.	.	.	.	.	.	.	.	C	0.556	-0.847515	0.02651	.	.	ENSG00000158805	ENST00000446326	T	0.06528	3.29	5.55	-0.243	0.13035	.	.	.	.	.	T	0.05044	0.0135	.	.	.	0.09310	N	1	B	0.24258	0.1	B	0.11329	0.006	T	0.36237	-0.9756	8	0.48119	T	0.1	-5.262	8.8218	0.35030	0.0:0.5882:0.0:0.4118	.	112	A8K186	.	M	112	ENSP00000415999:T112M	ENSP00000415999:T112M	T	+	2	0	ZNF276	88317557	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.878000	0.28126	-0.243000	0.09653	-2.262000	0.00279	ACG	.	.	none		0.672	ZNF276-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422517.1	NM_152287		T	89790056	C	T	89790056	2	4	8	1	0	0	0	0	0	0	0	1	17826	535	19	1		1	ZNF276	16	89790056	Silent	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	5098900	89790056	564697	125	964											
P2RX5	5026	hgsc.bcm.edu	37	chr17	3599171	3599171	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cggagaacttacacgaccagGtacgccaggatggaggcctg	11	5	14	11	3	0	1	0	0	0	1	0	5	0	3	3	5	3	1	3	5	3	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr17:3599171G>T	ENST00000225328.5	-	1	527	c.129C>A	c.(127-129)taC>taA	p.Y43*	P2RX5_ENST00000345901.3_Nonsense_Mutation_p.Y43*|P2RX5-TAX1BP3_ENST00000550383.1_Nonsense_Mutation_p.Y43*|P2RX5_ENST00000551178.1_Nonsense_Mutation_p.Y43*|P2RX5_ENST00000547178.1_Nonsense_Mutation_p.Y43*|P2RX5_ENST00000435558.1_Nonsense_Mutation_p.Y43*|P2RX5_ENST00000552276.1_Nonsense_Mutation_p.Y43*	NM_001204519.1|NM_002561.3	NP_001191448.1|NP_002552.2	Q93086	P2RX5_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 5	43					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|nervous system development (GO:0007399)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|purinergic nucleotide receptor signaling pathway (GO:0035590)|signal transduction (GO:0007165)|transport (GO:0006810)	integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|ion channel activity (GO:0005216)|purinergic nucleotide receptor activity (GO:0001614)|transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(2)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	11						ACACGACCAGGTACGCCAGGA	0.632																																					p.Y43X		Atlas-SNP	.											.	P2RX5	36	.	0			c.C129A						PASS	.						62	55	57					17																	3599171		2203	4300	6503	SO:0001587	stop_gained	5026	exon1			GACCAGGTACGCC	AF016709	CCDS11034.1, CCDS11035.1, CCDS56014.1, CCDS56015.1	17p13.3	2012-01-17			ENSG00000083454	ENSG00000083454		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	8536	protein-coding gene	gene with protein product		602836				9414125	Standard	NM_002561		Approved	P2X5	uc002fwi.3	Q93086	OTTHUMG00000090700	ENST00000225328.5:c.129C>A	17.37:g.3599171G>T	ENSP00000225328:p.Tyr43*	97	0	0		60	33	0.55	NM_001204519	G5E981|O43450|O75540|Q308M5|Q59F38|Q8IXW4|Q93087|Q9NZV0	Nonsense_Mutation	SNP	ENST00000225328.5	37	CCDS11034.1	.	.	.	.	.	.	.	.	.	.	G	37	5.998360	0.97184	.	.	ENSG00000083454	ENST00000435558;ENST00000551178;ENST00000547178;ENST00000225328;ENST00000345901;ENST00000440619	.	.	.	3.86	2.78	0.32641	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.4541	6.3266	0.21246	0.1038:0.1894:0.7068:0.0	.	.	.	.	X	43	.	ENSP00000225328:Y43X	Y	-	3	2	P2RX5	3545920	1.000000	0.71417	0.990000	0.47175	0.652000	0.38707	5.955000	0.70306	1.877000	0.54381	0.313000	0.20887	TAC	.	.	none		0.632	P2RX5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207388.3	NM_002561, NM_175080, NM_175081		T	3599171	G	T	3599171	4	4	8	1	0	0	0	0	0	1	0	0	11352	1256	44	4	1191	4	P2RX5	17	3599171	Nonsense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10		3599171	77596039	126	965											
ATP2A3	489	hgsc.bcm.edu	37	chr17	3844337	3844338	+	Frame_Shift_Del	DEL	GA	GA	-																															tgtgcgggctccacgcgggcGaagcagcgggcggtgcggca																										TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr17:3844337_3844338delGA	ENST00000352011.3	-	14	2081_2082	c.2027_2028delTC	c.(2026-2028)ttcfs	p.F676fs	ATP2A3_ENST00000359983.3_Frame_Shift_Del_p.F676fs|ATP2A3_ENST00000397035.3_Frame_Shift_Del_p.F676fs|ATP2A3_ENST00000397039.1_5'UTR|ATP2A3_ENST00000309890.7_Frame_Shift_Del_p.F676fs|ATP2A3_ENST00000397041.3_Frame_Shift_Del_p.F676fs|ATP2A3_ENST00000397043.3_Frame_Shift_Del_p.F676fs			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	676					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)		CCACGCGGGCGAAGCAGCGGGC	0.673																																					p.676_677del	GBM(32;29 774 15719 37967)	Atlas-Indel	.											.	ATP2A3	148	.	0			c.2028_2029del						PASS	.																																			SO:0001589	frameshift_variant	489	exon14			.		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.2027_2028delTC	17.37:g.3844337_3844338delGA	ENSP00000301387:p.Phe676fs	78	0	0		46	25	0.543478	NM_174958	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Frame_Shift_Del	DEL	ENST00000352011.3	37	CCDS11041.1																																																																																			.	.	none		0.673	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953		-	3844338	GA	-	3844337	7	5	8	1	0	1	0	1	0	0	0	0	1138	1049	37	0	1214	0	ATP2A3	17	3844337	Frame_Shift_Del	DEL	GA	TCGA-FA-A82F-01A-11D-A382-10	245166	3844337	77350873	127	966	16	3									
ATP2A3	489	hgsc.bcm.edu	37	chr17	3844340	3844340	+	Missense_Mutation	SNP	G	G	C																															gcgggctccacgcgggcgaaGcagcgggcggtgcggcaggc																										TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr17:3844340G>C	ENST00000352011.3	-	14	2079	c.2025C>G	c.(2023-2025)tgC>tgG	p.C675W	ATP2A3_ENST00000359983.3_Missense_Mutation_p.C675W|ATP2A3_ENST00000397035.3_Missense_Mutation_p.C675W|ATP2A3_ENST00000397039.1_5'UTR|ATP2A3_ENST00000309890.7_Missense_Mutation_p.C675W|ATP2A3_ENST00000397041.3_Missense_Mutation_p.C675W|ATP2A3_ENST00000397043.3_Missense_Mutation_p.C675W			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	675					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)		CGCGGGCGAAGCAGCGGGCGG	0.667																																					p.C675W	GBM(32;29 774 15719 37967)	Atlas-SNP	.											.	ATP2A3	148	.	0			c.C2025G						PASS	.						58	63	61					17																	3844340		2203	4296	6499	SO:0001583	missense	489	exon14			GGCGAAGCAGCGG		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.2025C>G	17.37:g.3844340G>C	ENSP00000301387:p.Cys675Trp	82	0	0		44	25	0.568182	NM_174956	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Missense_Mutation	SNP	ENST00000352011.3	37	CCDS11041.1	.	.	.	.	.	.	.	.	.	.	G	18.20	3.570816	0.65765	.	.	ENSG00000074370	ENST00000397043;ENST00000352011;ENST00000359983;ENST00000397041;ENST00000397045;ENST00000309890;ENST00000397035	D;D;D;D;D;D	0.95918	-3.85;-3.85;-3.85;-3.85;-3.85;-3.85	4.16	2.19	0.27852	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.95204	0.8445	L	0.34521	1.04	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;0.974;0.985;0.974;0.974;0.974	D	0.94182	0.7433	10	0.87932	D	0	.	10.0362	0.42131	0.1683:0.0:0.8317:0.0	.	675;675;675;675;675;675	Q93084-4;Q93084-2;Q93084;Q93084-6;G3XAE1;Q93084-3	.;.;AT2A3_HUMAN;.;.;.	W	675	ENSP00000380236:C675W;ENSP00000301387:C675W;ENSP00000353072:C675W;ENSP00000380234:C675W;ENSP00000312577:C675W;ENSP00000380229:C675W	ENSP00000312577:C675W	C	-	3	2	ATP2A3	3791089	1.000000	0.71417	0.997000	0.53966	0.890000	0.51754	6.421000	0.73353	0.714000	0.32081	0.561000	0.74099	TGC	.	.	none		0.667	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953		C	3844340	G	C	3844340	3	2	8	1	0	0	0	0	1	0	0	0	1138	963	34	4	1217	4	ATP2A3	17	3844340	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	3	3844340	77350870	128	967	16	3									
ATP2A3	489	hgsc.bcm.edu	37	chr17	3844342	3844343	+	Frame_Shift_Ins	INS	-	-	C																															ggctccacgcgggcgaagcaINSgcgggcggtgcggcaggcct																										TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr17:3844342_3844343insC	ENST00000352011.3	-	14	2076_2077	c.2022_2023insG	c.(2020-2025)cgctgcfs	p.C675fs	ATP2A3_ENST00000359983.3_Frame_Shift_Ins_p.C675fs|ATP2A3_ENST00000397035.3_Frame_Shift_Ins_p.C675fs|ATP2A3_ENST00000397039.1_5'UTR|ATP2A3_ENST00000309890.7_Frame_Shift_Ins_p.C675fs|ATP2A3_ENST00000397041.3_Frame_Shift_Ins_p.C675fs|ATP2A3_ENST00000397043.3_Frame_Shift_Ins_p.C675fs			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	675					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)		CGGGCGAAGCAGCGGGCGGTGC	0.663																																					p.C675fs	GBM(32;29 774 15719 37967)	Atlas-Indel	.											.	ATP2A3	148	.	0			c.2023_2024insG						PASS	.																																			SO:0001589	frameshift_variant	489	exon14			.		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.2022_2023insG	17.37:g.3844342_3844343insC	ENSP00000301387:p.Cys675fs	81	0	0		46	25	0.543478	NM_174958	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Frame_Shift_Ins	INS	ENST00000352011.3	37	CCDS11041.1																																																																																			.	.	none		0.663	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953		C	3844343	-	C	3844342	7	5	8	1	0	1	1	0	0	0	0	0	1138	188	7	0	1219	0	ATP2A3	17	3844342	Frame_Shift_Ins	INS	-	TCGA-FA-A82F-01A-11D-A382-10	2	3844342	77350868	129	968	16	3									
TP53	7157	hgsc.bcm.edu	37	chr17	7577121	7577121	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccaggacaggcacaaacacGcacctcaaagctgttccgtc	12	5	8	16	2	1	0	1	0	0	0	3	1	2	1	3	2	2	4	3	2	2	1	rs121913343		TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr17:7577121G>A	ENST00000269305.4	-	8	1006	c.817C>T	c.(817-819)Cgt>Tgt	p.R273C	TP53_ENST00000445888.2_Missense_Mutation_p.R273C|TP53_ENST00000359597.4_Missense_Mutation_p.R273C|TP53_ENST00000455263.2_Missense_Mutation_p.R273C|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000413465.2_Intron|TP53_ENST00000420246.2_Missense_Mutation_p.R273C	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.R273C	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,+1,1300	TP53	33396	1300	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.C817T	GRCh37	CM010471|CM010473|CM951233	TP53	M	rs121913343	PASS	.						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>T	17.37:g.7577121G>A	ENSP00000269305:p.Arg273Cys	71	0	0		56	28	0.5	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	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.400216	0.62177	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D	0.99869	-7.34;-7.34;-7.34;-7.34;-7.34;-7.34	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	0.80722	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;0.996	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;.	C	273;273;273;273;273;262;141	ENSP00000352610:R273C;ENSP00000269305:R273C;ENSP00000398846:R273C;ENSP00000391127:R273C;ENSP00000391478:R273C;ENSP00000425104:R141C	ENSP00000269305:R273C	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	.	.	weak		0.542	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577121	G	A	7577121	3	1	8	1	0	0	0	0	1	0	0	0	16396	1087	38	1	469	1	TP53	17	7577121	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	3732779	7577121	73618089	130	969											
RCVRN	5957	hgsc.bcm.edu	37	chr17	9804381	9804381	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gttttcatcgtctggaaggaGcttcacgtcctcgggagtga	7	12	13	9	3	3	1	2	1	1	0	6	4	4	4	1	3	1	2	1	3	1	3			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr17:9804381G>T	ENST00000226193.5	-	2	858	c.418C>A	c.(418-420)Ctc>Atc	p.L140I	RCVRN_ENST00000570909.3_5'UTR	NM_002903.2	NP_002894.1	P35243	RECO_HUMAN	recoverin	140					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						TCTGGAAGGAGCTTCACGTCC	0.453																																					p.L140I		Atlas-SNP	.											.	RCVRN	34	.	0			c.C418A						PASS	.						105	98	100					17																	9804381		2203	4300	6503	SO:0001583	missense	5957	exon2			GAAGGAGCTTCAC	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.418C>A	17.37:g.9804381G>T	ENSP00000226193:p.Leu140Ile	96	0	0		70	33	0.471429	NM_002903	Q53XL0	Missense_Mutation	SNP	ENST00000226193.5	37	CCDS11151.1	.	.	.	.	.	.	.	.	.	.	G	7.190	0.591431	0.13812	.	.	ENSG00000109047	ENST00000226193	T	0.67345	-0.26	5.89	-1.12	0.09808	EF-hand-like domain (1);	0.735456	0.13380	N	0.392228	T	0.41305	0.1153	N	0.11023	0.085	0.20489	N	0.999893	B	0.09022	0.002	B	0.18561	0.022	T	0.22243	-1.0222	10	0.51188	T	0.08	.	5.0991	0.14749	0.1996:0.0:0.4512:0.3493	.	140	P35243	RECO_HUMAN	I	140	ENSP00000226193:L140I	ENSP00000226193:L140I	L	-	1	0	RCVRN	9745106	0.005000	0.15991	0.002000	0.10522	0.266000	0.26442	0.055000	0.14229	-0.375000	0.07955	-0.136000	0.14681	CTC	.	.	none		0.453	RCVRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252600.2	NM_002903		T	9804381	G	T	9804381	3	4	8	1	0	0	0	0	1	0	0	0	13201	971	34	4	192	4	RCVRN	17	9804381	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	2227260	9804381	71390829	131	970											
C17orf76	388341	hgsc.bcm.edu	37	chr17	16351219	16351219	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccactgggagtgggggctgAggtggtatgtcagctgccgg	5	9	19	8	1	1	1	1	1	0	0	2	2	2	2	2	6	2	3	2	6	1	1			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr17:16351219A>C	ENST00000470794.1	-	3	458	c.431T>G	c.(430-432)cTc>cGc	p.L144R	C17orf76-AS1_ENST00000580770.1_RNA|FAM211A_ENST00000409083.3_Intron|C17orf76-AS1_ENST00000579473.1_RNA|C17orf76-AS1_ENST00000584177.1_RNA|C17orf76-AS1_ENST00000581718.1_RNA|C17orf76-AS1_ENST00000583400.2_RNA|C17orf76-AS1_ENST00000472367.1_RNA|C17orf76-AS1_ENST00000478103.2_RNA	NM_001113567.2	NP_001107039.1														lung(1)	1						GTGGGGGCTGAGGTGGTATGT	0.657																																					p.L144R		Atlas-SNP	.											.	FAM211A	21	.	0			c.T431G						PASS	.						31	40	37					17																	16351219		692	1591	2283	SO:0001583	missense	388341	exon3			GGGCTGAGGTGGT																												ENST00000470794.1:c.431T>G	17.37:g.16351219A>C	ENSP00000419502:p.Leu144Arg	69	0	0		52	27	0.519231	NM_001113567		Missense_Mutation	SNP	ENST00000470794.1	37	CCDS45620.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.522899	0.85600	.	.	ENSG00000181350	ENST00000470794	T	0.63744	-0.06	5.12	5.12	0.69794	.	.	.	.	.	T	0.75759	0.3893	M	0.62723	1.935	0.51482	D	0.999924	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.78494	-0.2182	9	0.87932	D	0	.	13.1626	0.59552	1.0:0.0:0.0:0.0	.	144;117	Q8NAA5;B7ZMA3	CQ076_HUMAN;.	R	144	ENSP00000419502:L144R	ENSP00000419502:L144R	L	-	2	0	C17orf76	16291944	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.285000	0.89914	2.068000	0.61886	0.402000	0.26972	CTC	.	.	none		0.657	FAM211A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130463.3			C	16351219	A	C	16351219	3	2	8	1	0	0	0	0	1	0	0	0	1883	304	11	5	611	5	C17orf76	17	16351219	Missense_Mutation	SNP	A	TCGA-FA-A82F-01A-11D-A382-10	6546838	16351219	64843991	132	971											
ALDOC	230	hgsc.bcm.edu	37	chr17	26901736	26901736	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctggcagatactggcataaCgggccagcacgttggcgttc	8	8	14	11	3	0	1	0	0	0	1	1	1	0	1	1	4	3	6	1	4	2	4	rs148239543		TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr17:26901736C>T	ENST00000226253.4	-	5	993	c.518G>A	c.(517-519)cGt>cAt	p.R173H	ALDOC_ENST00000395321.2_Missense_Mutation_p.R173H|RP11-192H23.5_ENST00000585189.1_RNA|ALDOC_ENST00000395319.3_Missense_Mutation_p.R173H|PIGS_ENST00000308360.7_5'Flank	NM_005165.2	NP_005156.1	P09972	ALDOC_HUMAN	aldolase C, fructose-bisphosphate	173					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)					ACTGGCATAACGGGCCAGCAC	0.557											OREG0024278	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R173H		Atlas-SNP	.											ALDOC,colon,carcinoma,-1,1	ALDOC	22	1	0			c.G518A						PASS	.	C	HIS/ARG	0,4406		0,0,2203	96	79	84		518	5.5	1	17	dbSNP_134	84	1,8599	1.2+/-3.3	0,1,4299	no	missense	ALDOC	NM_005165.2	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	173/365	26901736	1,13005	2203	4300	6503	SO:0001583	missense	230	exon5			GCATAACGGGCCA	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.518G>A	17.37:g.26901736C>T	ENSP00000226253:p.Arg173His	49	0	0	790	59	4	0.0677966	NM_005165	B2R5R3|Q3SYL3|Q6FH94|Q6P0L5	Missense_Mutation	SNP	ENST00000226253.4	37	CCDS11236.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.907215	0.92107	0.0	1.16E-4	ENSG00000109107	ENST00000395319;ENST00000226253;ENST00000395321	D;D;D	0.88818	-2.43;-2.43;-2.43	5.5	5.5	0.81552	Aldolase-type TIM barrel (1);	0.000000	0.85682	D	0.000000	D	0.95683	0.8596	M	0.91459	3.21	0.80722	D	1	P;D	0.76494	0.562;0.999	B;D	0.71656	0.192;0.974	D	0.96213	0.9154	10	0.87932	D	0	.	18.5367	0.91013	0.0:1.0:0.0:0.0	.	173;173	A8MVZ9;P09972	.;ALDOC_HUMAN	H	173	ENSP00000378729:R173H;ENSP00000226253:R173H;ENSP00000378731:R173H	ENSP00000226253:R173H	R	-	2	0	ALDOC	23925863	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.810000	0.86072	2.741000	0.93983	0.650000	0.86243	CGT	C|1.000;T|0.000	0.000	weak		0.557	ALDOC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255839.4			T	26901736	C	T	26901736	3	4	8	1	0	0	0	0	1	0	0	0	509	536	19	1	596	1	ALDOC	17	26901736	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	10550517	26901736	54293474	133	972											
CCL2	6347	hgsc.bcm.edu	37	chr17	32583751	32583751	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccccacagcttcaagaccAttgtggccaaggagatctgt	10	9	9	13	0	2	2	1	0	1	2	3	3	3	2	4	2	1	1	4	2	2	2	rs148285031	byFrequency	TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr17:32583751A>T	ENST00000225831.4	+	3	270	c.205A>T	c.(205-207)Att>Ttt	p.I69F	CCL2_ENST00000580907.1_3'UTR|AC005549.3_ENST00000601918.1_5'Flank	NM_002982.3	NP_002973.1	P13500	CCL2_HUMAN	chemokine (C-C motif) ligand 2	69					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|aging (GO:0007568)|angiogenesis (GO:0001525)|astrocyte cell migration (GO:0043615)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cellular calcium ion homeostasis (GO:0006874)|cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|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 lipopolysaccharide (GO:0071222)|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)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeleton organization (GO:0007010)|endoplasmic reticulum unfolded protein response (GO:0030968)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|helper T cell extravasation (GO:0035684)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|JAK-STAT cascade (GO:0007259)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lymphocyte chemotaxis (GO:0048247)|macrophage chemotaxis (GO:0048246)|MAPK cascade (GO:0000165)|maternal process involved in parturition (GO:0060137)|monocyte chemotaxis (GO:0002548)|negative regulation of angiogenesis (GO:0016525)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of natural killer cell chemotaxis (GO:2000502)|negative regulation of neuron apoptotic process (GO:0043524)|neutrophil chemotaxis (GO:0030593)|organ morphogenesis (GO:0009887)|organ regeneration (GO:0031100)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of calcium ion import (GO:0090280)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of immune complex clearance by monocytes and macrophages (GO:0090265)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of synaptic transmission (GO:0050806)|positive regulation of T cell activation (GO:0050870)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|regulation of cell shape (GO:0008360)|regulation of vascular endothelial growth factor production (GO:0010574)|response to activity (GO:0014823)|response to amino acid (GO:0043200)|response to antibiotic (GO:0046677)|response to bacterium (GO:0009617)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to glucocorticoid (GO:0051384)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to vitamin B3 (GO:0033552)|response to wounding (GO:0009611)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|viral genome replication (GO:0019079)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)	CCR2 chemokine receptor binding (GO:0031727)|chemokine activity (GO:0008009)|heparin binding (GO:0008201)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)			kidney(1)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	6	Breast(3;0.00224)	Ovarian(249;0.0694)|Breast(31;0.151)|Lung NSC(157;0.153)		UCEC - Uterine corpus endometrioid carcinoma (308;0.000241)|BRCA - Breast invasive adenocarcinoma(366;0.0103)	Danazol(DB01406)|Mimosine(DB01055)	CTTCAAGACCATTGTGGCCAA	0.522																																					p.I69F		Atlas-SNP	.											.	CCL2	10	.	0			c.A205T						PASS	.						102	86	92					17																	32583751		2203	4300	6503	SO:0001583	missense	6347	exon3			AAGACCATTGTGG	BC009716	CCDS11277.1	17q11.2-q21.1	2013-02-25	2002-08-22	2002-08-23	ENSG00000108691	ENSG00000108691		"Chemokine ligands", "Endogenous ligands"	10618	protein-coding gene	gene with protein product	"monocyte chemotactic protein 1, homologous to mouse Sig-je", "monocyte chemoattractant protein-1", "monocyte chemotactic and activating factor", "monocyte secretory protein JE", "small inducible cytokine subfamily A (Cys-Cys), member 2"	158105	"small inducible cytokine A2 (monocyte chemotactic protein 1, homologous to mouse Sig-je)"	SCYA2		2004761	Standard	NM_002982		Approved	MCP1, MCP-1, MCAF, SMC-CF, GDCF-2, HC11, MGC9434	uc002hhy.3	P13500	OTTHUMG00000132887	ENST00000225831.4:c.205A>T	17.37:g.32583751A>T	ENSP00000225831:p.Ile69Phe	90	0	0		91	12	0.131868	NM_002982	B2R4V3|Q9UDF3	Missense_Mutation	SNP	ENST00000225831.4	37	CCDS11277.1	.	.	.	.	.	.	.	.	.	.	A	12.69	2.012994	0.35511	.	.	ENSG00000108691	ENST00000225831	T	0.04603	3.59	4.97	2.68	0.31781	CC chemokine, conserved site (1);Chemokine interleukin-8-like domain (3);	1.619000	0.03674	N	0.244424	T	0.04998	0.0134	.	.	.	0.09310	N	1	B	0.12013	0.005	B	0.15052	0.012	T	0.40136	-0.9579	9	0.66056	D	0.02	.	4.3276	0.11048	0.7323:0.0:0.0939:0.1739	.	69	P13500	CCL2_HUMAN	F	69	ENSP00000225831:I69F	ENSP00000225831:I69F	I	+	1	0	CCL2	29607864	0.000000	0.05858	0.000000	0.03702	0.862000	0.49288	-0.199000	0.09491	0.430000	0.26230	0.402000	0.26972	ATT	A|0.999;G|0.001	.	alt		0.522	CCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256384.2	NM_002982		T	32583751	A	T	32583751	3	4	8	1	0	0	0	0	1	0	0	0	2893	217	8	5	215	5	CCL2	17	32583751	Missense_Mutation	SNP	A	TCGA-FA-A82F-01A-11D-A382-10	5682015	32583751	48611459	134	973											
XYLT2	64132	hgsc.bcm.edu	37	chr17	48431146	48431146	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cccgtggccaaggtggtacgGgcagtaaccagccggcagag	9	4	16	12	3	0	1	0	0	0	1	0	1	0	1	4	5	3	4	4	5	3	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr17:48431146G>A	ENST00000017003.2	+	2	340	c.291G>A	c.(289-291)cgG>cgA	p.R97R	XYLT2_ENST00000507602.1_Silent_p.R97R	NM_022167.2	NP_071450.2	Q9H1B5	XYLT2_HUMAN	xylosyltransferase II	97					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)					AGGTGGTACGGGCAGTAACCA	0.721																																					p.R97R		Atlas-SNP	.											.	XYLT2	51	.	0			c.G291A						PASS	.						7	8	7					17																	48431146		2124	4155	6279	SO:0001819	synonymous_variant	64132	exon2			GGTACGGGCAGTA	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.291G>A	17.37:g.48431146G>A		44	0	0		40	16	0.4	NM_022167	Q6UY41|Q86V00	Silent	SNP	ENST00000017003.2	37	CCDS11563.1																																																																																			.	.	none		0.721	XYLT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367046.1	NM_022167		A	48431146	G	A	48431146	2	1	8	1	0	0	0	0	0	0	0	1	17479	1219	43	2		2	XYLT2	17	48431146	Silent	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	15847395	48431146	32764064	135	974											
WIPI1	55062	hgsc.bcm.edu	37	chr17	66423340	66423340	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgcataagactgaggtaaGgaaggtctgaggtcattttc	11	11	13	6	0	2	3	1	2	1	1	3	4	2	4	0	4	1	3	0	4	3	4			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr17:66423340G>T	ENST00000262139.5	-	11	1127	c.1128C>A	c.(1126-1128)tcC>tcA	p.S376S	RP11-120M18.2_ENST00000592030.1_RNA|MIR635_ENST00000384830.1_RNA|WIPI1_ENST00000546360.1_Silent_p.S294S|WIPI1_ENST00000589459.1_5'UTR	NM_017983.5	NP_060453.3	Q5MNZ9	WIPI1_HUMAN	WD repeat domain, phosphoinositide interacting 1	376					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|autophagy (GO:0006914)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|vesicle targeting, trans-Golgi to endosome (GO:0048203)	autophagic vacuole membrane (GO:0000421)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|pre-autophagosomal structure (GO:0000407)|pre-autophagosomal structure membrane (GO:0034045)|trans-Golgi network (GO:0005802)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	18						ACTGAGGTAAGGAAGGTCTGA	0.498																																					p.S376S		Atlas-SNP	.											.	WIPI1	46	.	0			c.C1128A						PASS	.						356	280	306					17																	66423340		2203	4300	6503	SO:0001819	synonymous_variant	55062	exon11			AGGTAAGGAAGGT		CCDS11677.1	17q24.2	2014-02-12				ENSG00000070540		"WD repeat domain containing"	25471	protein-coding gene	gene with protein product		609224				15020712, 15602573	Standard	NM_017983		Approved	FLJ10055, WIPI49, Atg18, ATG18A	uc010dey.3	Q5MNZ9		ENST00000262139.5:c.1128C>A	17.37:g.66423340G>T		121	0	0		108	5	0.0462963	NM_017983	Q8IXM5|Q9NWF8	Silent	SNP	ENST00000262139.5	37	CCDS11677.1																																																																																			.	.	none		0.498	WIPI1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448739.1	NM_017983		T	66423340	G	T	66423340	2	4	8	1	0	0	0	0	0	0	0	1	17385	987	35	4		4	WIPI1	17	66423340	Silent	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	17992194	66423340	14771870	136	975											
MGAT5B	146664	hgsc.bcm.edu	37	chr17	74922752	74922752	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggagtacgccacgctgcacGgctaccggaccaactggggc	9	4	14	14	4	0	0	0	0	0	0	0	2	0	2	3	5	4	4	3	5	3	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr17:74922752G>A	ENST00000569840.2	+	10	1805	c.1231G>A	c.(1231-1233)Ggc>Agc	p.G411S	MGAT5B_ENST00000428789.2_Missense_Mutation_p.G422S|MGAT5B_ENST00000301618.4_Missense_Mutation_p.G411S	NM_001199172.1	NP_001186101.1	Q3V5L5	MGT5B_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase, isozyme B	411					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						CACGCTGCACGGCTACCGGAC	0.637																																					p.G422S		Atlas-SNP	.											.	MGAT5B	98	.	0			c.G1264A						PASS	.						119	103	108					17																	74922752		2203	4295	6498	SO:0001583	missense	146664	exon9			CTGCACGGCTACC	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.1231G>A	17.37:g.74922752G>A	ENSP00000456037:p.Gly411Ser	28	0	0		25	9	0.36	NM_198955	Q6P3S8|Q6P6B3|Q766X5|Q76D04|Q96LS2	Missense_Mutation	SNP	ENST00000569840.2	37	CCDS59299.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.886158	0.91814	.	.	ENSG00000167889	ENST00000301618;ENST00000428789	T;T	0.48522	0.81;0.81	5.14	4.13	0.48395	.	0.000000	0.85682	D	0.000000	T	0.63815	0.2543	L	0.58302	1.8	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.73380	0.98;0.98	T	0.66252	-0.5970	10	0.59425	D	0.04	-39.314	14.4167	0.67155	0.0:0.1487:0.8513:0.0	.	422;411	Q3V5L5-2;Q3V5L5-5	.;.	S	411;422	ENSP00000301618:G411S;ENSP00000391227:G422S	ENSP00000301618:G411S	G	+	1	0	MGAT5B	72434347	1.000000	0.71417	0.992000	0.48379	0.969000	0.65631	9.627000	0.98412	1.082000	0.41137	0.561000	0.74099	GGC	.	.	none		0.637	MGAT5B-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460624.2	NM_144677		A	74922752	G	A	74922752	3	1	8	1	0	0	0	0	1	0	0	0	9558	1116	39	1	1370	1	MGAT5B	17	74922752	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	8499412	74922752	6272458	137	976											
KLHL14	57565	hgsc.bcm.edu	37	chr18	30350108	30350108	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctccaccgtgtccagggaCagggtcacgttggccgtgta	6	9	13	13	3	1	0	1	0	0	0	4	1	4	1	5	3	0	2	5	3	1	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr18:30350108C>T	ENST00000359358.4	-	2	885	c.447G>A	c.(445-447)ctG>ctA	p.L149L	KLHL14_ENST00000358095.4_Silent_p.L149L|AC012123.1_ENST00000426194.1_Intron	NM_020805.1	NP_065856.1	Q9P2G3	KLH14_HUMAN	kelch-like family member 14	149	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						TGTCCAGGGACAGGGTCACGT	0.637																																					p.L149L		Atlas-SNP	.											.	KLHL14	92	.	0			c.G447A						PASS	.						99	94	95					18																	30350108		2203	4300	6503	SO:0001819	synonymous_variant	57565	exon2			CAGGGACAGGGTC	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.447G>A	18.37:g.30350108C>T		112	0	0		159	82	0.515723	NM_020805	A6NNW1|B4DHA0|Q8WU41	Silent	SNP	ENST00000359358.4	37	CCDS32813.1																																																																																			.	.	none		0.637	KLHL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448376.1			T	30350108	C	T	30350108	2	4	8	1	0	0	0	0	0	0	0	1	8379	465	17	2		2	KLHL14	18	30350108	Silent	SNP	C	TCGA-FA-A82F-01A-11D-A382-10		30350108	47727140	138	977											
ASXL3	80816	hgsc.bcm.edu	37	chr18	31250736	31250736	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cattaaaggtgtctgatgagCagtcggattcgccttcaggt	9	12	12	8	2	2	2	1	2	1	0	4	3	2	3	1	3	1	1	1	3	2	3			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr18:31250736C>A	ENST00000269197.5	+	6	577	c.577C>A	c.(577-579)Cag>Aag	p.Q193K		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	193					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						GTCTGATGAGCAGTCGGATTC	0.428																																					p.Q193K		Atlas-SNP	.											.	ASXL3	405	.	0			c.C577A						PASS	.						57	58	58					18																	31250736		1881	4091	5972	SO:0001583	missense	80816	exon6			GATGAGCAGTCGG	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.577C>A	18.37:g.31250736C>A	ENSP00000269197:p.Gln193Lys	110	0	0		154	31	0.201299	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	37	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	C	17.29	3.353018	0.61293	.	.	ENSG00000141431	ENST00000269197	T	0.15487	2.42	5.48	5.48	0.80851	.	.	.	.	.	T	0.35307	0.0927	L	0.43152	1.355	0.41121	D	0.985811	D	0.63880	0.993	D	0.67548	0.952	T	0.01480	-1.1344	9	0.44086	T	0.13	.	19.3689	0.94477	0.0:1.0:0.0:0.0	.	193	Q9C0F0	ASXL3_HUMAN	K	193	ENSP00000269197:Q193K	ENSP00000269197:Q193K	Q	+	1	0	ASXL3	29504734	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.677000	0.68142	2.595000	0.87683	0.655000	0.94253	CAG	.	.	none		0.428	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			A	31250736	C	A	31250736	3	1	8	1	0	0	0	0	1	0	0	0	1068	711	25	4	599	4	ASXL3	18	31250736	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	900628	31250736	46826512	139	978											
ALPK2	115701	hgsc.bcm.edu	37	chr18	56246643	56246643	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	taatcattttcagcagcctcGggagcagtggggagtttata	10	12	12	7	1	2	0	2	0	0	0	3	2	2	2	1	3	3	3	1	3	3	6	rs373786602		TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr18:56246643G>T	ENST00000361673.3	-	4	1578	c.1365C>A	c.(1363-1365)ccC>ccA	p.P455P	ALPK2_ENST00000587399.1_5'Flank	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	455						nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.P455P(1)		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						CAGCAGCCTCGGGAGCAGTGG	0.493											OREG0025011	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P455P		Atlas-SNP	.											ALPK2_ENST00000361673,medulla,primitive_neuroectodermal_tumour-medulloblastoma,0,1	ALPK2	487	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C1365A						PASS	.						138	139	138					18																	56246643		2203	4300	6503	SO:0001819	synonymous_variant	115701	exon4			AGCCTCGGGAGCA	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.1365C>A	18.37:g.56246643G>T		201	0	0	1014	270	59	0.218519	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	37	CCDS11966.2																																																																																			.	.	alt		0.493	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		T	56246643	G	T	56246643	2	4	8	1	0	0	0	0	0	0	0	1	545	1103	39	4		4	ALPK2	18	56246643	Silent	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	24995907	56246643	21830605	140	979											
TSHZ1	10194	hgsc.bcm.edu	37	chr18	72998479	72998479	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agccagcaggaatggccgcaGaggtggccctgagtgagtca	10	5	16	10	1	1	3	1	2	0	1	1	4	1	4	3	4	2	2	3	4	1	0			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr18:72998479G>C	ENST00000580243.1	+	2	1465	c.1117G>C	c.(1117-1119)Gag>Cag	p.E373Q	TSHZ1_ENST00000322038.5_Missense_Mutation_p.E328Q			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	373					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)		AATGGCCGCAGAGGTGGCCCT	0.627																																					p.E328Q		Atlas-SNP	.											.	TSHZ1	104	.	0			c.G982C						PASS	.						77	84	82					18																	72998479		2203	4300	6503	SO:0001583	missense	10194	exon2			GCCGCAGAGGTGG	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.1117G>C	18.37:g.72998479G>C	ENSP00000464391:p.Glu373Gln	73	0	0		99	12	0.121212	NM_005786	O60534|Q4LE29|Q53EU4	Missense_Mutation	SNP	ENST00000580243.1	37		.	.	.	.	.	.	.	.	.	.	G	2.206	-0.381839	0.04966	.	.	ENSG00000179981	ENST00000322038	T	0.11821	2.74	5.27	5.27	0.74061	.	0.632498	0.16025	N	0.233147	T	0.12178	0.0296	L	0.36672	1.1	0.25438	N	0.988122	B	0.23058	0.079	B	0.20384	0.029	T	0.17379	-1.0371	10	0.25751	T	0.34	-12.3326	12.2676	0.54686	0.0775:0.0:0.9225:0.0	.	373	Q6ZSZ6	TSH1_HUMAN	Q	328	ENSP00000323584:E328Q	ENSP00000323584:E328Q	E	+	1	0	TSHZ1	71127467	0.988000	0.35896	0.040000	0.18447	0.018000	0.09664	4.584000	0.60971	1.986000	0.57962	0.459000	0.35465	GAG	.	.	none		0.627	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786		C	72998479	G	C	72998479	3	2	8	1	0	0	0	0	1	0	0	0	16638	943	33	4	984	4	TSHZ1	18	72998479	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	16751836	72998479	5078769	141	980											
ZNF236	7776	hgsc.bcm.edu	37	chr18	74606988	74606988	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggctccatccgcgaggagaaCggcgtgcgctggcatgtgtg	6	7	17	11	5	0	1	0	0	0	1	2	3	2	1	2	4	2	3	2	4	1	0			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr18:74606988C>T	ENST00000253159.8	+	10	1629	c.1431C>T	c.(1429-1431)aaC>aaT	p.N477N	ZNF236_ENST00000320610.9_Silent_p.N479N	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	477					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)		GCGAGGAGAACGGCGTGCGCT	0.662																																					p.N477N		Atlas-SNP	.											.	ZNF236	325	.	0			c.C1431T						PASS	.						81	94	90					18																	74606988		2184	4274	6458	SO:0001819	synonymous_variant	7776	exon10			GGAGAACGGCGTG	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.1431C>T	18.37:g.74606988C>T		40	0	0		53	23	0.433962	NM_007345	B2RTX9|Q9UL37	Silent	SNP	ENST00000253159.8	37	CCDS42447.1																																																																																			.	.	none		0.662	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1			T	74606988	C	T	74606988	2	4	8	1	0	0	0	0	0	0	0	1	17804	535	19	1		1	ZNF236	18	74606988	Silent	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	1608509	74606988	3470260	142	981											
AP1M1	8907	hgsc.bcm.edu	37	chr19	16319908	16319908	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccagccaccgtcaccaacGcggtgtcctggcggtccgaa	8	5	11	17	5	1	0	1	0	0	0	3	1	3	0	6	3	2	0	6	3	2	0			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr19:16319908G>A	ENST00000291439.3	+	5	915	c.466G>A	c.(466-468)Gcg>Acg	p.A156T	AP1M1_ENST00000590756.1_Missense_Mutation_p.A84T|AP1M1_ENST00000444449.2_Missense_Mutation_p.A156T|AP1M1_ENST00000429941.2_Missense_Mutation_p.A156T|AP1M1_ENST00000541844.1_Missense_Mutation_p.A84T	NM_032493.3	NP_115882.1	Q9BXS5	AP1M1_HUMAN	adaptor-related protein complex 1, mu 1 subunit	156					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						CGTCACCAACGCGGTGTCCTG	0.582																																					p.A156T		Atlas-SNP	.											.	AP1M1	48	.	0			c.G466A						PASS	.						132	119	124					19																	16319908		2203	4300	6503	SO:0001583	missense	8907	exon5			ACCAACGCGGTGT		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.466G>A	19.37:g.16319908G>A	ENSP00000291439:p.Ala156Thr	109	0	0		98	26	0.265306	NM_001130524	Q4TTY5	Missense_Mutation	SNP	ENST00000291439.3	37	CCDS12342.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.027439	0.75390	.	.	ENSG00000072958	ENST00000444449;ENST00000291439;ENST00000541844;ENST00000429941	T;T;T;T	0.66460	0.4;0.37;0.38;-0.21	4.35	4.35	0.52113	.	0.000000	0.85682	D	0.000000	T	0.79981	0.4540	M	0.68728	2.09	0.80722	D	1	P;D;D	0.89917	0.539;1.0;1.0	B;D;D	0.97110	0.14;1.0;0.999	T	0.81936	-0.0705	10	0.56958	D	0.05	-20.3738	16.0736	0.80951	0.0:0.0:1.0:0.0	.	156;156;156	E7ENJ6;Q4TTY5;Q9BXS5	.;.;AP1M1_HUMAN	T	156;156;84;156	ENSP00000388996:A156T;ENSP00000291439:A156T;ENSP00000445682:A84T;ENSP00000411498:A156T	ENSP00000291439:A156T	A	+	1	0	AP1M1	16180908	1.000000	0.71417	0.668000	0.29813	0.779000	0.44077	9.400000	0.97290	2.249000	0.74217	0.563000	0.77884	GCG	.	.	none		0.582	AP1M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460492.1	NM_032493		A	16319908	G	A	16319908	3	1	8	1	0	0	0	0	1	0	0	0	734	1087	38	1	484	1	AP1M1	19	16319908	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10		16319908	42809075	143	982											
C19orf40	91442	hgsc.bcm.edu	37	chr19	33465059	33465059	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agtttactgtgctggaccttGgaatggtgctgcttccagtg	6	14	13	8	0	0	0	0	0	0	0	1	2	1	2	2	3	4	4	2	3	2	4			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr19:33465059G>A	ENST00000588258.1	+	4	447	c.337G>A	c.(337-339)Gga>Aga	p.G113R	CEP89_ENST00000305768.5_5'Flank|C19orf40_ENST00000590281.1_Missense_Mutation_p.G113R|CEP89_ENST00000591863.1_5'Flank|C19orf40_ENST00000589646.1_Missense_Mutation_p.G18R|C19orf40_ENST00000590179.1_Missense_Mutation_p.G18R|CEP89_ENST00000590597.2_5'Flank	NM_152266.3	NP_689479.1	Q9BTP7	FAP24_HUMAN	chromosome 19 open reading frame 40	113					DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|large_intestine(2)|lung(2)|prostate(2)	7	Esophageal squamous(110;0.137)					GCTGGACCTTGGAATGGTGCT	0.483								Direct reversal of damage																													p.G113R		Atlas-SNP	.											.	C19orf40	21	.	0			c.G337A						PASS	.						99	84	89					19																	33465059		2203	4300	6503	SO:0001583	missense	91442	exon4			GACCTTGGAATGG	AK128668	CCDS12426.1, CCDS74327.1	19q13.11	2011-11-24			ENSG00000131944	ENSG00000131944			28467	protein-coding gene	gene with protein product	"Fanconi anemia-associated protein, 24kDa"	610884				17289582	Standard	XM_005259393		Approved	FLJ46828, MGC32020, FAAP24	uc002nud.4	Q9BTP7		ENST00000588258.1:c.337G>A	19.37:g.33465059G>A	ENSP00000466121:p.Gly113Arg	99	0	0		179	27	0.150838	NM_152266	B3KY46|Q8WUJ7|Q96FX6	Missense_Mutation	SNP	ENST00000588258.1	37	CCDS12426.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.759304	0.89932	.	.	ENSG00000131944	ENST00000254262	.	.	.	4.53	4.53	0.55603	.	0.000000	0.85682	D	0.000000	T	0.78272	0.4257	M	0.72894	2.215	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	T	0.80291	-0.1444	9	0.52906	T	0.07	-16.8937	17.2132	0.86936	0.0:0.0:1.0:0.0	.	113	Q9BTP7	FAP24_HUMAN	R	113	.	ENSP00000254262:G113R	G	+	1	0	C19orf40	38156899	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	9.004000	0.93583	2.229000	0.72834	0.467000	0.42956	GGA	.	.	none		0.483	C19orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450823.2	NM_152266		A	33465059	G	A	33465059	3	1	8	1	0	0	0	0	1	0	0	0	1925	1349	47	2	347	2	C19orf40	19	33465059	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	17145151	33465059	25663924	144	983											
MED29	55588	hgsc.bcm.edu	37	chr19	39884260	39884260	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agttctatgcactctgtgacCagctggagctgtgcctggta	7	12	12	10	0	2	1	0	1	2	0	2	2	2	2	2	2	4	5	2	2	2	3			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr19:39884260C>T	ENST00000599213.2	+	3	370	c.343C>T	c.(343-345)Cag>Tag	p.Q115*	PAF1_ENST00000595564.1_5'Flank|PAF1_ENST00000221266.7_5'Flank|MED29_ENST00000315588.5_Nonsense_Mutation_p.Q136*|PAF1_ENST00000221265.3_5'Flank|MED29_ENST00000594368.1_Nonsense_Mutation_p.Q115*			Q9NX70	MED29_HUMAN	mediator complex subunit 29	115					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)			ACTCTGTGACCAGCTGGAGCT	0.502																																					p.Q136X		Atlas-SNP	.											.	MED29	13	.	0			c.C406T						PASS	.						160	158	159					19																	39884260		2203	4300	6503	SO:0001587	stop_gained	55588	exon3			TGTGACCAGCTGG	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		ENST00000599213.2:c.343C>T	19.37:g.39884260C>T	ENSP00000471802:p.Gln115*	55	0	0		54	11	0.203704	NM_017592	B4DNQ6|M0R2E4|Q5XX09|Q9NTF4	Nonsense_Mutation	SNP	ENST00000599213.2	37		.	.	.	.	.	.	.	.	.	.	c	34	5.321841	0.95682	.	.	ENSG00000063322	ENST00000315588;ENST00000435462	.	.	.	4.39	4.39	0.52855	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-0.4415	14.4916	0.67654	0.0:1.0:0.0:0.0	.	.	.	.	X	136;54	.	ENSP00000314343:Q136X	Q	+	1	0	MED29	44576100	1.000000	0.71417	1.000000	0.80357	0.782000	0.44232	7.286000	0.78671	2.261000	0.74972	0.558000	0.71614	CAG	.	.	none		0.502	MED29-011	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000470870.1	XM_290829		T	39884260	C	T	39884260	4	4	8	1	0	0	0	0	0	1	0	0	9456	595	21	2	416	2	MED29	19	39884260	Nonsense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	6419201	39884260	19244723	145	984											
POU2F2	5452	hgsc.bcm.edu	37	chr19	42603967	42603967	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctggagctggaggagctgctGtatgtcctggcagggagtgg	6	9	19	7	0	0	0	0	0	0	0	1	4	1	4	1	6	3	5	1	6	1	1			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr19:42603967G>A	ENST00000526816.2	-	6	325	c.310C>T	c.(310-312)Cag>Tag	p.Q104*	POU2F2_ENST00000529952.1_Nonsense_Mutation_p.Q104*|POU2F2_ENST00000342301.4_Nonsense_Mutation_p.Q104*|POU2F2_ENST00000529067.1_Nonsense_Mutation_p.Q104*|POU2F2_ENST00000560558.1_Nonsense_Mutation_p.Q65*|POU2F2_ENST00000389341.5_Nonsense_Mutation_p.Q104*|POU2F2_ENST00000560398.1_Nonsense_Mutation_p.Q126*|POU2F2_ENST00000533720.1_Nonsense_Mutation_p.Q104*			P09086	PO2F2_HUMAN	POU class 2 homeobox 2	104					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)	AGGAGCTGCTGTATGTCCTGG	0.617																																					p.Q104X		Atlas-SNP	.											.	POU2F2	106	.	0			c.C310T						PASS	.						37	37	37					19																	42603967		2191	4286	6477	SO:0001587	stop_gained	5452	exon6			GCTGCTGTATGTC		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.310C>T	19.37:g.42603967G>A	ENSP00000431603:p.Gln104*	75	0	0		77	25	0.324675	NM_002698	Q16648|Q7M4M8|Q9BRS4	Nonsense_Mutation	SNP	ENST00000526816.2	37	CCDS56095.1	.	.	.	.	.	.	.	.	.	.	G	19.97	3.924697	0.73213	.	.	ENSG00000028277	ENST00000389341;ENST00000342301;ENST00000292077;ENST00000533720;ENST00000526816;ENST00000529067;ENST00000529952;ENST00000531773	.	.	.	4.93	4.93	0.64822	.	0.968583	0.08425	N	0.947819	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	17.4661	0.87633	0.0:0.0:1.0:0.0	.	.	.	.	X	104;104;104;104;103;104;104;92	.	ENSP00000292077:Q104X	Q	-	1	0	POU2F2	47295807	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.174000	0.89682	2.746000	0.94184	0.655000	0.94253	CAG	.	.	none		0.617	POU2F2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387329.3			A	42603967	G	A	42603967	4	1	8	1	0	0	0	0	0	1	0	0	12281	1386	48	2	1117	2	POU2F2	19	42603967	Nonsense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	2719707	42603967	16525016	146	985											
PANK2	80025	hgsc.bcm.edu	37	chr20	3891366	3891367	+	Frame_Shift_Ins	INS	-	-	A																															tctgaaaagtgtcagaagttINSaccatttgatttgaaaaatc																										TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr20:3891366_3891367insA	ENST00000316562.4	+	3	1130_1131	c.1124_1125insA	c.(1123-1128)ttaccafs	p.P376fs	PANK2_ENST00000497424.1_Frame_Shift_Ins_p.P85fs|PANK2_ENST00000610179.1_Frame_Shift_Ins_p.P253fs|PANK2_ENST00000464452.1_3'UTR	NM_153638.2	NP_705902.2	Q9BZ23	PANK2_HUMAN	pantothenate kinase 2	376					aerobic respiration (GO:0009060)|cell death (GO:0008219)|coenzyme A biosynthetic process (GO:0015937)|coenzyme biosynthetic process (GO:0009108)|mitochondrion morphogenesis (GO:0070584)|pantothenate metabolic process (GO:0015939)|regulation of mitochondrial membrane potential (GO:0051881)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)	ATP binding (GO:0005524)|pantothenate kinase activity (GO:0004594)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						TGTCAGAAGTTACCATTTGATT	0.386																																					p.L375fs		Pindel,Atlas-Indel	.											.	PANK2	37	.	0			c.1124_1125insA						PASS	.																																			SO:0001589	frameshift_variant	80025	exon3			.	AK021791	CCDS13071.2, CCDS13072.1	20p13	2008-07-31	2008-07-31	2002-09-06	ENSG00000125779	ENSG00000125779	2.7.1.33		15894	protein-coding gene	gene with protein product	"Hallervorden-Spatz syndrome"	606157	"neurodegeneration with brain iron accumulation 1 (Hallervorden-Spatz syndrome)"	C20orf48, NBIA1		8944032, 11479594	Standard	XM_005260835		Approved	HSS, FLJ11729, PKAN, HARP	uc002wkc.3	Q9BZ23	OTTHUMG00000031768	ENST00000316562.4:c.1125dupA	20.37:g.3891367_3891367dupA	ENSP00000313377:p.Pro376fs	131	0	.		148	39	0.264	NM_153638	B1AK33|B2Z3X0|D3DVZ0|Q5T7I2|Q5T7I4|Q7RTX5|Q8N7Q4|Q8TCR5|Q9BYW5|Q9HAF2	Frame_Shift_Ins	INS	ENST00000316562.4	37	CCDS13071.2																																																																																			.	.	none		0.386	PANK2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077793.2	NM_024960		A	3891367	-	A	3891366	7	5	8	1	0	1	1	0	0	0	0	0	11426	1764	61	0	1134	0	PANK2	20	3891366	Frame_Shift_Ins	INS	-	TCGA-FA-A82F-01A-11D-A382-10		3891366	59134154	147	986											
NINL	22981	hgsc.bcm.edu	37	chr20	25462663	25462663	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgggctccatgaggggctgTgccggttcttgggcagccgc	3	8	17	13	3	1	1	0	1	1	0	2	1	2	1	4	5	2	4	4	5	0	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr20:25462663T>A	ENST00000278886.6	-	14	1824	c.1751A>T	c.(1750-1752)cAc>cTc	p.H584L	NINL_ENST00000422516.1_Missense_Mutation_p.H584L	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	584					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						TGAGGGGCTGTGCCGGTTCTT	0.697																																					p.H584L		Atlas-SNP	.											.	NINL	148	.	0			c.A1751T						PASS	.						42	49	47					20																	25462663		2202	4300	6502	SO:0001583	missense	22981	exon14			GGGCTGTGCCGGT		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.1751A>T	20.37:g.25462663T>A	ENSP00000278886:p.His584Leu	18	0	0		24	9	0.375	NM_025176	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Missense_Mutation	SNP	ENST00000278886.6	37	CCDS33452.1	.	.	.	.	.	.	.	.	.	.	T	6.869	0.529744	0.13127	.	.	ENSG00000101004	ENST00000278886;ENST00000422516	T;T	0.29917	1.8;1.55	4.52	-4.41	0.03590	.	1.487320	0.04044	N	0.303550	T	0.16896	0.0406	L	0.29908	0.895	0.09310	N	1	P;B	0.38370	0.628;0.276	B;B	0.33254	0.16;0.037	T	0.17137	-1.0379	10	0.11182	T	0.66	-0.0542	7.4738	0.27363	0.0:0.1375:0.235:0.6276	.	584;584	Q9Y2I6-2;Q9Y2I6	.;NINL_HUMAN	L	584	ENSP00000278886:H584L;ENSP00000410431:H584L	ENSP00000278886:H584L	H	-	2	0	NINL	25410663	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.352000	0.07701	-0.660000	0.05352	0.454000	0.30748	CAC	.	.	none		0.697	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176		A	25462663	T	A	25462663	3	1	8	1	0	0	0	0	1	0	0	0	10429	1696	59	5	2441	5	NINL	20	25462663	Missense_Mutation	SNP	T	TCGA-FA-A82F-01A-11D-A382-10	21571297	25462663	37562857	148	987											
CDH4	1002	hgsc.bcm.edu	37	chr20	60427861	60427861	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acaaggtggagaaccccatcGacctgtacatctacgtcatc	12	8	8	13	2	2	1	1	0	1	1	4	3	2	1	3	2	3	1	3	2	4	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr20:60427861G>A	ENST00000360469.5	+	6	872	c.784G>A	c.(784-786)Gac>Aac	p.D262N	CDH4_ENST00000543233.1_Missense_Mutation_p.D188N	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	262	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)	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)			GAACCCCATCGACCTGTACAT	0.597																																					p.D262N		Atlas-SNP	.											.	CDH4	172	.	0			c.G784A						PASS	.						174	131	146					20																	60427861		2203	4300	6503	SO:0001583	missense	1002	exon6			CCCATCGACCTGT	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.784G>A	20.37:g.60427861G>A	ENSP00000353656:p.Asp262Asn	44	0	0		59	19	0.322034	NM_001794	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Missense_Mutation	SNP	ENST00000360469.5	37	CCDS13488.1	.	.	.	.	.	.	.	.	.	.	G	18.09	3.546059	0.65198	.	.	ENSG00000179242	ENST00000360469;ENST00000536643;ENST00000543233	T;T	0.50548	0.74;0.74	4.76	4.76	0.60689	Cadherin (4);Cadherin-like (1);	0.050803	0.85682	D	0.000000	T	0.35307	0.0927	L	0.37630	1.12	0.80722	D	1	P	0.40431	0.717	B	0.29716	0.106	T	0.21042	-1.0257	9	.	.	.	.	17.758	0.88455	0.0:0.0:1.0:0.0	.	262	P55283	CADH4_HUMAN	N	262;170;188	ENSP00000353656:D262N;ENSP00000443301:D188N	.	D	+	1	0	CDH4	59861256	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	9.517000	0.98020	2.202000	0.70862	0.561000	0.74099	GAC	.	.	none		0.597	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794		A	60427861	G	A	60427861	3	1	8	1	0	0	0	0	1	0	0	0	3114	1058	37	1	806	1	CDH4	20	60427861	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	34965198	60427861	2597659	149	988											
NTSR1	4923	hgsc.bcm.edu	37	chr20	61386045	61386045	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctctcctgcaggtcaacacCttcatgtccttcatattccc	7	13	4	17	0	4	0	3	0	1	0	7	0	6	0	5	1	2	1	5	1	2	4			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr20:61386045C>T	ENST00000370501.3	+	2	1094	c.723C>T	c.(721-723)acC>acT	p.T241T		NM_002531.2	NP_002522.2	P30989	NTR1_HUMAN	neurotensin receptor 1 (high affinity)	241					adult locomotory behavior (GO:0008344)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of apoptotic process (GO:0043066)|neuropeptide signaling pathway (GO:0007218)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	G-protein coupled neurotensin receptor activity (GO:0016492)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(16)|prostate(1)|skin(3)	27	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;3.63e-06)			AGGTCAACACCTTCATGTCCT	0.612																																					p.T241T	GBM(37;400 780 6403 19663 35669)	Atlas-SNP	.											.	NTSR1	59	.	0			c.C723T						PASS	.						129	115	120					20																	61386045		2202	4300	6502	SO:0001819	synonymous_variant	4923	exon2			CAACACCTTCATG		CCDS13502.1	20q13	2012-08-08			ENSG00000101188	ENSG00000101188		"GPCR / Class A : Neurotensin receptors"	8039	protein-coding gene	gene with protein product		162651				8075503	Standard	NM_002531		Approved	NTR	uc002ydf.3	P30989	OTTHUMG00000032932	ENST00000370501.3:c.723C>T	20.37:g.61386045C>T		42	0	0		40	4	0.1	NM_002531	Q9H4H1|Q9H4T5	Silent	SNP	ENST00000370501.3	37	CCDS13502.1																																																																																			.	.	none		0.612	NTSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080061.1			T	61386045	C	T	61386045	2	4	8	1	0	0	0	0	0	0	0	1	10719	668	24	2		2	NTSR1	20	61386045	Silent	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	958184	61386045	1639475	150	989											
HUNK	30811	hgsc.bcm.edu	37	chr21	33371069	33371069	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcgcgacgaccacgtagaaGtgctgtctccctctcatcac	9	9	8	15	4	3	1	2	0	2	1	6	3	3	1	2	0	1	2	2	0	2	1			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr21:33371069G>A	ENST00000270112.2	+	11	2077	c.1717G>A	c.(1717-1719)Gtg>Atg	p.V573M		NM_014586.1	NP_055401.1	P57058	HUNK_HUMAN	hormonally up-regulated Neu-associated kinase	573					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						CCACGTAGAAGTGCTGTCTCC	0.617																																					p.V573M		Atlas-SNP	.											.	HUNK	74	.	0			c.G1717A						PASS	.						84	62	69					21																	33371069		2203	4300	6503	SO:0001583	missense	30811	exon11			GTAGAAGTGCTGT	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.1717G>A	21.37:g.33371069G>A	ENSP00000270112:p.Val573Met	85	0	0		88	33	0.375	NM_014586		Missense_Mutation	SNP	ENST00000270112.2	37	CCDS13610.1	.	.	.	.	.	.	.	.	.	.	G	3.553	-0.091199	0.07053	.	.	ENSG00000142149	ENST00000270112	T	0.67865	-0.29	4.39	-2.03	0.07365	.	0.724836	0.12754	N	0.441957	T	0.36799	0.0980	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.04013	0.001	T	0.12167	-1.0558	10	0.40728	T	0.16	-0.7464	2.5976	0.04858	0.2287:0.2923:0.3446:0.1344	.	573	P57058	HUNK_HUMAN	M	573	ENSP00000270112:V573M	ENSP00000270112:V573M	V	+	1	0	HUNK	32292940	0.704000	0.27836	0.030000	0.17652	0.184000	0.23303	0.554000	0.23407	-0.353000	0.08224	-1.434000	0.01081	GTG	.	.	none		0.617	HUNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192782.1	NM_014586		A	33371069	G	A	33371069	3	1	8	1	0	0	0	0	1	0	0	0	7467	1029	36	2	1759	2	HUNK	21	33371069	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10		33371069	14758826	151	990											
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230295	23230295	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggagctgggccctggtcccaGgcagcgctggcccctgctgc	3	6	16	16	1	0	0	0	0	0	0	1	1	1	1	4	5	4	4	4	5	0	0			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr22:23230295G>C	ENST00000526893.1	+	1	336	c.62G>C	c.(61-63)aGg>aCg	p.R21T	IGLL5_ENST00000532223.2_Missense_Mutation_p.R21T|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000531372.1_Missense_Mutation_p.R21T	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	21						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CCTGGTCCCAGGCAGCGCTGG	0.672																																					p.R21T		Atlas-SNP	.											.	IGLL5	26	.	0			c.G62C						PASS	.																																			SO:0001583	missense	100423062	exon1			GTCCCAGGCAGCG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.62G>C	22.37:g.23230295G>C	ENSP00000431254:p.Arg21Thr	146	0	0		111	33	0.297297	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	9.712	1.157214	0.21454	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00609	6.24;6.25	3.25	-1.58	0.08479	.	.	.	.	.	T	0.00468	0.0015	L	0.29908	0.895	0.09310	N	1	D	0.61697	0.99	P	0.44647	0.456	T	0.49532	-0.8930	9	0.20519	T	0.43	.	3.5094	0.07703	0.3613:0.1968:0.4419:0.0	.	21	B9A064	IGLL5_HUMAN	T	21	ENSP00000436353:R21T;ENSP00000431254:R21T	ENSP00000431254:R21T	R	+	2	0	IGLL5	21560295	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.328000	0.07945	-0.196000	0.10366	0.643000	0.83706	AGG	.	.	none		0.672	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		C	23230295	G	C	23230295	3	2	8	1	0	0	0	0	1	0	0	0	7603	1000	35	4	64	4	IGLL5	22	23230295	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10		23230295	28074271	152	991			4	11		3	3	106	N	T_G_C	1.421815e-07
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230348	23230348	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccatggtcgcccatggcctgCtgcgcccaatggttgcaccg	5	8	12	16	3	0	0	0	0	0	0	1	0	0	0	5	3	3	3	5	3	1	1			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr22:23230348C>T	ENST00000526893.1	+	1	389	c.115C>T	c.(115-117)Ctg>Ttg	p.L39L	IGLL5_ENST00000532223.2_Silent_p.L39L|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000531372.1_Silent_p.L39L	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	39						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CCATGGCCTGCTGCGCCCAAT	0.687																																					p.L39L		Atlas-SNP	.											.	IGLL5	26	.	0			c.C115T						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			GGCCTGCTGCGCC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.115C>T	22.37:g.23230348C>T		128	0	0		95	32	0.336842	NM_001178126		Silent	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.687	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		T	23230348	C	T	23230348	2	4	8	1	0	0	0	0	0	0	0	1	7603	796	28	2		2	IGLL5	22	23230348	Silent	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	53	23230348	28074218	153	992			4	11		3	3	106	N	T_G_C	1.421815e-07
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230400	23230400	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cccagaccctggagcctcagTtggaagcagccgatccagcc	9	5	11	16	1	1	1	1	0	0	1	2	4	2	3	6	2	4	2	6	2	1	1	rs189360394		TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr22:23230400T>C	ENST00000526893.1	+	1	441	c.167T>C	c.(166-168)gTt>gCt	p.V56A	IGLL5_ENST00000532223.2_Missense_Mutation_p.V56A|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000531372.1_Missense_Mutation_p.V56A	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	56						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GGAGCCTCAGTTGGAAGCAGC	0.667													T|||	1	0.000199681	0.0	0.0014	5008	,	,		10673	0.0		0.0	False		,,,				2504	0.0				p.V56A		Atlas-SNP	.											.	IGLL5	26	.	0			c.T167C						PASS	.																																			SO:0001583	missense	100423062	exon1			CCTCAGTTGGAAG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.167T>C	22.37:g.23230400T>C	ENSP00000431254:p.Val56Ala	105	0	0		97	29	0.298969	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	T	0.035	-1.312432	0.01331	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00571	6.5;6.5	3.92	-3.93	0.04143	.	.	.	.	.	T	0.00356	0.0011	L	0.27053	0.805	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.45071	-0.9286	9	0.54805	T	0.06	.	0.8497	0.01169	0.1514:0.2511:0.2977:0.2998	.	56	B9A064	IGLL5_HUMAN	A	56	ENSP00000436353:V56A;ENSP00000431254:V56A	ENSP00000431254:V56A	V	+	2	0	IGLL5	21560400	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.389000	0.02530	-0.629000	0.05575	-1.272000	0.01410	GTT	T|1.000;C|0.000	0.000	strong		0.667	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		C	23230400	T	C	23230400	3	2	8	1	0	0	0	0	1	0	0	0	7603	1725	60	3	169	3	IGLL5	22	23230400	Missense_Mutation	SNP	T	TCGA-FA-A82F-01A-11D-A382-10	52	23230400	28074166	154	993			4	11		3	3	106	N	T_G_C	1.421815e-07
APOL5	80831	hgsc.bcm.edu	37	chr22	36122574	36122574	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gtttctggggtcatgaacatCctgggtttggccctagcacc	6	12	12	11	0	2	1	1	1	1	0	3	1	3	1	3	4	2	3	3	4	2	3			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr22:36122574C>T	ENST00000249044.2	+	3	459	c.459C>T	c.(457-459)atC>atT	p.I153I		NM_030642.1	NP_085145.1	Q9BWW9	APOL5_HUMAN	apolipoprotein L, 5	153					lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|skin(2)|urinary_tract(1)	19						TCATGAACATCCTGGGTTTGG	0.567																																					p.I153I		Atlas-SNP	.											.	APOL5	45	.	0			c.C459T						PASS	.						66	67	67					22																	36122574		2203	4300	6503	SO:0001819	synonymous_variant	80831	exon3			GAACATCCTGGGT	AY014878	CCDS13920.1	22q12.3	2013-01-24			ENSG00000128313	ENSG00000128313		"Apolipoproteins"	14869	protein-coding gene	gene with protein product		607255				11374903	Standard	NM_030642		Approved	APOLV	uc003aof.3	Q9BWW9	OTTHUMG00000150588	ENST00000249044.2:c.459C>T	22.37:g.36122574C>T		113	0	0		109	27	0.247706	NM_030642	Q5TFL9|Q9UGW5	Silent	SNP	ENST00000249044.2	37	CCDS13920.1																																																																																			.	.	none		0.567	APOL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318979.1	NM_030642		T	36122574	C	T	36122574	2	4	8	1	0	0	0	0	0	0	0	1	809	845	30	2		2	APOL5	22	36122574	Silent	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	12892174	36122574	15181992	155	994											
MPPED1	758	hgsc.bcm.edu	37	chr22	43870785	43870785	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgctgctgaccaactgcatCtaccttcaggactcggaggt	8	10	10	13	2	2	1	1	1	1	0	4	3	2	3	2	3	4	3	2	3	2	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr22:43870785C>A	ENST00000417669.2	+	4	1020	c.576C>A	c.(574-576)atC>atA	p.I192I	MPPED1_ENST00000443721.1_Silent_p.I192I|MPPED1_ENST00000538182.1_Silent_p.I225I|MPPED1_ENST00000414469.2_Silent_p.I86I|MPPED1_ENST00000542779.1_Silent_p.I192I|MPPED1_ENST00000439548.1_Silent_p.I34I			O15442	MPPD1_HUMAN	metallophosphoesterase domain containing 1	192							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)				CCAACTGCATCTACCTTCAGG	0.577																																					p.I192I		Atlas-SNP	.											.	MPPED1	59	.	0			c.C576A						PASS	.						108	112	111					22																	43870785		2047	4195	6242	SO:0001819	synonymous_variant	758	exon4			CTGCATCTACCTT	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.576C>A	22.37:g.43870785C>A		105	0	0		85	24	0.282353	NM_001044370	A8K159|B7Z2S9|Q8N361	Silent	SNP	ENST00000417669.2	37	CCDS46723.1																																																																																			.	.	none		0.577	MPPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318938.2	NM_001044370		A	43870785	C	A	43870785	2	1	8	1	0	0	0	0	0	0	0	1	9750	903	32	4		4	MPPED1	22	43870785	Silent	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	7748211	43870785	7433781	156	995											
MLC1	23209	hgsc.bcm.edu	37	chr22	50521550	50521550	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcaagtaatccatctcagccGggaacacgttccccaggtac	11	7	9	14	2	1	0	1	0	1	0	4	1	3	1	4	2	3	4	4	2	4	3	rs145484765		TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chr22:50521550G>A	ENST00000311597.5	-	3	836	c.230C>T	c.(229-231)cCg>cTg	p.P77L	MLC1_ENST00000450140.2_Missense_Mutation_p.P77L|MLC1_ENST00000395876.2_Missense_Mutation_p.P77L|MLC1_ENST00000431262.2_Intron|MLC1_ENST00000538737.1_Missense_Mutation_p.P77L|MLC1_ENST00000535444.1_5'UTR	NM_015166.3	NP_055981.1	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with subcortical cysts 1	77					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)		CATCTCAGCCGGGAACACGTT	0.612																																					p.P77L		Atlas-SNP	.											.	MLC1	48	.	0			c.C230T						PASS	.	G	LEU/PRO,LEU/PRO	0,4406		0,0,2203	173	137	149		230,230	5.1	0.9	22	dbSNP_134	149	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	MLC1	NM_015166.3,NM_139202.2	98,98	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging,probably-damaging	77/378,77/378	50521550	3,13003	2203	4300	6503	SO:0001583	missense	23209	exon3			TCAGCCGGGAACA	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.230C>T	22.37:g.50521550G>A	ENSP00000310375:p.Pro77Leu	37	0	0		50	15	0.3	NM_015166	B3KW61|B7Z659|Q5JZ83|Q8TAG4|Q96RP5|Q9UGY8	Missense_Mutation	SNP	ENST00000311597.5	37	CCDS14083.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.226551	0.79576	0.0	3.49E-4	ENSG00000100427	ENST00000395876;ENST00000311597;ENST00000538737;ENST00000450140	D;D;D;D	0.93906	-3.31;-3.31;-3.31;-3.31	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	D	0.96331	0.8803	M	0.70275	2.135	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	D	0.96877	0.9643	10	0.87932	D	0	-1.3356	17.2773	0.87119	0.0:0.0:1.0:0.0	.	77;77;77	F5H1B9;B7Z1X1;Q15049	.;.;MLC1_HUMAN	L	77	ENSP00000379216:P77L;ENSP00000310375:P77L;ENSP00000445805:P77L;ENSP00000412448:P77L	ENSP00000310375:P77L	P	-	2	0	MLC1	48863677	1.000000	0.71417	0.902000	0.35471	0.418000	0.31294	8.814000	0.91968	2.360000	0.80028	0.655000	0.94253	CCG	G|1.000;A|0.000	0.000	weak		0.612	MLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316979.2	NM_015166		A	50521550	G	A	50521550	3	1	8	1	0	0	0	0	1	0	0	0	9621	1116	39	1	943	1	MLC1	22	50521550	Missense_Mutation	SNP	G	TCGA-FA-A82F-01A-11D-A382-10	6650765	50521550	783016	157	996											
ARSE	415	hgsc.bcm.edu	37	chrX	2873470	2873470	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gactgacctgatcgcacaggGtatctgcccgtgaggaaggc	9	7	14	11	2	1	3	0	3	1	0	2	5	1	4	2	3	1	2	2	3	2	1			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chrX:2873470G>A	ENST00000381134.3	-	4	360	c.294C>T	c.(292-294)taC>taT	p.Y98Y	ARSE_ENST00000545496.1_Silent_p.Y123Y|ARSE_ENST00000496095.1_5'Flank|ARSE_ENST00000540563.1_Silent_p.Y53Y	NM_000047.2	NP_000038.2	P51690	ARSE_HUMAN	arylsulfatase E (chondrodysplasia punctata 1)	98					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)				ATCGCACAGGGTATCTGCCCG	0.498																																					p.Y98Y		Atlas-SNP	.											.	ARSE	43	.	0			c.C294T						PASS	.						106	69	82					X																	2873470		2203	4300	6503	SO:0001819	synonymous_variant	415	exon4			CACAGGGTATCTG	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.294C>T	X.37:g.2873470G>A		159	0	0		117	55	0.470085	NM_000047	Q53FT2|Q53FU8	Silent	SNP	ENST00000381134.3	37	CCDS14122.1																																																																																			.	.	none		0.498	ARSE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055643.1	NM_000047		A	2873470	G	A	2873470	2	1	8	1	0	0	0	0	0	0	0	1	990	1256	44	2		2	ARSE	23	2873470	Silent	SNP	G	TCGA-FA-A82F-01A-11D-A382-10		2873470	152397090	158	997											
KDM6A	7403	hgsc.bcm.edu	37	chrX	44942730	44942730	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttgcagctacatgagctgActaaacttcctgcttttgtg	9	14	9	9	0	0	2	0	2	0	0	1	2	1	2	1	0	6	5	1	0	3	6			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chrX:44942730A>C	ENST00000377967.4	+	23	3351	c.3310A>C	c.(3310-3312)Act>Cct	p.T1104P	KDM6A_ENST00000543216.1_Missense_Mutation_p.T1025P|KDM6A_ENST00000382899.4_Missense_Mutation_p.T1111P|KDM6A_ENST00000536777.1_Missense_Mutation_p.T1059P	NM_021140.2	NP_066963.2	O15550	KDM6A_HUMAN	lysine (K)-specific demethylase 6A	1104	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				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						ACATGAGCTGACTAAACTTCC	0.398			"D, N, F, S"		"renal, oesophageal SCC, MM"																																p.T1104P	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.A3310C						PASS	.						142	106	118					X																	44942730		2203	4300	6503	SO:0001583	missense	7403	exon23			GAGCTGACTAAAC	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.3310A>C	X.37:g.44942730A>C	ENSP00000367203:p.Thr1104Pro	356	0	0		200	113	0.565	NM_021140	Q52LL9|Q5JVQ7	Missense_Mutation	SNP	ENST00000377967.4	37	CCDS14265.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.42|18.42	3.619989|3.619989	0.66787|0.66787	.|.	.|.	ENSG00000147050|ENSG00000147050	ENST00000414389;ENST00000433797|ENST00000334516;ENST00000377967;ENST00000536777;ENST00000382899;ENST00000543216	.|T;T;T;T	.|0.79247	.|-1.25;-1.25;-1.25;-1.25	5.24|5.24	5.24|5.24	0.73138|0.73138	.|Transcription factor jumonji/aspartyl beta-hydroxylase (2);	.|0.149876	.|0.64402	.|D	.|0.000018	D|D	0.82944|0.82944	0.5147|0.5147	L|L	0.60455|0.60455	1.87|1.87	0.53688|0.53688	D|D	0.999971|0.999971	.|P;P;P;P;P	.|0.51147	.|0.838;0.852;0.942;0.592;0.88	.|B;P;P;B;P	.|0.55871	.|0.202;0.474;0.786;0.239;0.623	D|D	0.84984|0.84984	0.0890|0.0890	5|10	.|0.87932	.|D	.|0	-7.075|-7.075	14.2463|14.2463	0.65990|0.65990	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|743;1111;1059;1156;1104	.|B4E0L8;F8W8R6;F5H6S1;B7ZKN5;O15550	.|.;.;.;.;KDM6A_HUMAN	A|P	701;746|801;1104;1059;1111;1025	.|ENSP00000367203:T1104P;ENSP00000437405:T1059P;ENSP00000372355:T1111P;ENSP00000443078:T1025P	.|ENSP00000334340:T801P	D|T	+|+	2|1	0|0	KDM6A|KDM6A	44827674|44827674	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.818000|5.818000	0.69236|0.69236	1.742000|1.742000	0.51746|0.51746	0.472000|0.472000	0.43445|0.43445	GAC|ACT	.	.	none		0.398	KDM6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056324.1	NM_021140		C	44942730	A	C	44942730	3	2	8	1	0	0	0	0	1	0	0	0	8146	275	10	5	3400	5	KDM6A	23	44942730	Missense_Mutation	SNP	A	TCGA-FA-A82F-01A-11D-A382-10	42069260	44942730	110327830	159	998											
AMOT	154796	hgsc.bcm.edu	37	chrX	112065819	112065819	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtggccagtgacatctgcAttagtcgttcactcaaggaa	10	11	11	9	1	3	1	2	1	1	0	4	2	3	2	1	3	1	2	1	3	3	2			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chrX:112065819A>G	ENST00000524145.1	-	2	610	c.536T>C	c.(535-537)aTg>aCg	p.M179T	AMOT_ENST00000304758.1_Intron|AMOT_ENST00000371959.3_Missense_Mutation_p.M179T|AMOT_ENST00000371958.1_5'Flank|AMOT_ENST00000462114.1_5'Flank|AMOT_ENST00000371962.1_5'Flank			Q4VCS5	AMOT_HUMAN	angiomotin	179					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						TGACATCTGCATTAGTCGTTC	0.537																																					p.M179T		Atlas-SNP	.											.	AMOT	204	.	0			c.T536C						PASS	.						264	194	215					X																	112065819		692	1591	2283	SO:0001583	missense	154796	exon1			ATCTGCATTAGTC	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.536T>C	X.37:g.112065819A>G	ENSP00000429013:p.Met179Thr	105	0	0		83	40	0.481928	NM_001113490	Q504X5|Q9HD27|Q9UPT1	Missense_Mutation	SNP	ENST00000524145.1	37	CCDS48154.1	.	.	.	.	.	.	.	.	.	.	A	17.07	3.296211	0.60086	.	.	ENSG00000126016	ENST00000371959;ENST00000524145	T;T	0.16196	2.36;2.36	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.42314	0.1197	M	0.77103	2.36	0.58432	D	0.999999	D	0.62365	0.991	D	0.68192	0.956	T	0.32295	-0.9912	9	.	.	.	-14.4782	14.2221	0.65833	1.0:0.0:0.0:0.0	.	179	Q4VCS5	AMOT_HUMAN	T	179	ENSP00000361027:M179T;ENSP00000429013:M179T	.	M	-	2	0	AMOT	111952475	1.000000	0.71417	0.995000	0.50966	0.987000	0.75469	9.339000	0.96797	1.956000	0.56807	0.486000	0.48141	ATG	.	.	none		0.537	AMOT-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378570.1	NM_133265		G	112065819	A	G	112065819	3	3	8	1	0	0	0	0	1	0	0	0	582	217	8	3	2762	3	AMOT	23	112065819	Missense_Mutation	SNP	A	TCGA-FA-A82F-01A-11D-A382-10	67123089	112065819	43204741	160	999											
PLXNB3	5365	hgsc.bcm.edu	37	chrX	153039097	153039097	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cccagccccaggacccacagCcaaggaggagctgtggagcc	10	2	13	16	0	0	0	0	0	0	0	0	4	0	4	6	4	4	1	6	4	1	0			TCGA-FA-A82F-01A-11D-A382-10	TCGA-FA-A82F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5ebd77cf-f8b7-4164-9d3c-dac8c78331ef	089c6a18-5963-41a2-8224-5793318db837	g.chrX:153039097C>A	ENST00000361971.5	+	19	3322	c.3208C>A	c.(3208-3210)Cca>Aca	p.P1070T	PLXNB3_ENST00000538776.1_Missense_Mutation_p.P723T|SRPK3_ENST00000489426.1_5'Flank|PLXNB3_ENST00000538966.1_Missense_Mutation_p.P1093T|PLXNB3_ENST00000538282.1_Missense_Mutation_p.P680T	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	1070	IPT/TIG 3.				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)					GGACCCACAGCCAAGGAGGAG	0.697																																					p.P1093T		Atlas-SNP	.											.	PLXNB3	208	.	0			c.C3277A						PASS	.						10	10	10					X																	153039097		2157	4225	6382	SO:0001583	missense	5365	exon20			CCACAGCCAAGGA	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.3208C>A	X.37:g.153039097C>A	ENSP00000355378:p.Pro1070Thr	61	0	0		46	29	0.630435	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	37	CCDS14729.1	.	.	.	.	.	.	.	.	.	.	C	12.09	1.835091	0.32421	.	.	ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776;ENST00000538282	T;T;T;T	0.66460	5.36;5.32;4.73;-0.21	4.62	3.75	0.43078	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.818716	0.10553	N	0.661165	T	0.57548	0.2061	M	0.68593	2.085	0.09310	N	1	P;B;P	0.38922	0.651;0.375;0.514	B;B;B	0.36922	0.198;0.236;0.079	T	0.46925	-0.9156	10	0.06891	T	0.86	.	5.9284	0.19124	0.0:0.6995:0.19:0.1105	.	723;1093;1070	B7Z3H9;F5H773;Q9ULL4	.;.;PLXB3_HUMAN	T	1093;1070;723;680	ENSP00000442736:P1093T;ENSP00000355378:P1070T;ENSP00000445569:P723T;ENSP00000441919:P680T	ENSP00000355378:P1070T	P	+	1	0	PLXNB3	152692291	0.000000	0.05858	0.001000	0.08648	0.013000	0.08279	0.402000	0.20965	0.740000	0.32651	0.436000	0.28706	CCA	.	.	none		0.697	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1			A	153039097	C	A	153039097	3	1	8	1	0	0	0	0	1	0	0	0	12134	739	26	4	3396	4	PLXNB3	23	153039097	Missense_Mutation	SNP	C	TCGA-FA-A82F-01A-11D-A382-10	40973278	153039097	2231463	161	1000											
SPEN	23013	hgsc.bcm.edu	37	chr1	16255388	16255388	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggttttgactcgagtgaaaGagaaagagggaaaggtcatt	14	10	14	3	1	1	4	1	2	0	2	2	7	1	5	0	3	0	1	0	3	3	3			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr1:16255388G>T	ENST00000375759.3	+	11	2857	c.2653G>T	c.(2653-2655)Gag>Tag	p.E885*		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	885					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)		TCGAGTGAAAGAGAAAGAGGG	0.453																																					p.E885X		Atlas-SNP	.											.	SPEN	374	.	0			c.G2653T						PASS	.						104	110	108					1																	16255388		2203	4300	6503	SO:0001587	stop_gained	23013	exon11			GTGAAAGAGAAAG		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.2653G>T	1.37:g.16255388G>T	ENSP00000364912:p.Glu885*	92	0	0		66	6	0.0909091	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Nonsense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	.	.	.	.	.	.	.	.	.	.	G	40	8.364123	0.98779	.	.	ENSG00000065526	ENST00000375759	.	.	.	4.92	4.92	0.64577	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	-13.6494	18.3094	0.90194	0.0:0.0:1.0:0.0	.	.	.	.	X	885	.	ENSP00000364912:E885X	E	+	1	0	SPEN	16127975	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.792000	0.91856	2.548000	0.85928	0.591000	0.81541	GAG	.	.	none		0.453	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		T	16255388	G	T	16255388	4	4	9	1	0	0	0	0	0	1	0	0	15053	943	33	4	2695	4	SPEN	1	16255388	Nonsense_Mutation	SNP	G	TCGA-FA-A86F-01A-11D-A382-10		16255388	232995233	1	1001											
PADI1	29943	hgsc.bcm.edu	37	chr1	17566209	17566209	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cttcttgcagggttaaaacaCcaggcaaaaagaagcattaa	17	8	8	8	0	1	1	0	0	1	1	1	1	1	1	1	2	3	4	1	2	6	4			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr1:17566209C>G	ENST00000375471.4	+	14	1655	c.1563C>G	c.(1561-1563)caC>caG	p.H521Q	PADI1_ENST00000460293.1_3'UTR|PADI1_ENST00000413717.2_Missense_Mutation_p.H78Q|PADI1_ENST00000536552.1_5'UTR|PADI1_ENST00000537499.1_Missense_Mutation_p.H78Q	NM_013358.2	NP_037490.2	Q9ULC6	PADI1_HUMAN	peptidyl arginine deiminase, type I	521					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)	GGTTAAAACACCAGGCAAAAA	0.517																																					p.H521Q	Esophageal Squamous(80;414 1257 4580 27746 50832)	Atlas-SNP	.											.	PADI1	77	.	0			c.C1563G						PASS	.						63	61	62					1																	17566209		2203	4300	6503	SO:0001583	missense	29943	exon14			AAAACACCAGGCA	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.1563C>G	1.37:g.17566209C>G	ENSP00000364620:p.His521Gln	203	0	0		128	14	0.109375	NM_013358	A1L4K6|Q70SX6	Missense_Mutation	SNP	ENST00000375471.4	37	CCDS178.1	.	.	.	.	.	.	.	.	.	.	C	3.748	-0.052131	0.07362	.	.	ENSG00000142623	ENST00000375471;ENST00000537499;ENST00000413717	T;T;T	0.21361	2.01;2.01;2.01	5.0	-3.5	0.04710	Protein-arginine deiminase, C-terminal (1);	1.843040	0.02096	N	0.053523	T	0.14141	0.0342	L	0.39898	1.24	0.18873	N	0.999982	B;B	0.13594	0.008;0.002	B;B	0.14578	0.011;0.005	T	0.15549	-1.0433	10	0.23302	T	0.38	-5.7269	0.9834	0.01441	0.1784:0.3415:0.1289:0.3512	.	78;521	B4DPX6;Q9ULC6	.;PADI1_HUMAN	Q	521;78;78	ENSP00000364620:H521Q;ENSP00000444032:H78Q;ENSP00000396697:H78Q	ENSP00000364620:H521Q	H	+	3	2	PADI1	17438796	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-1.834000	0.01693	-0.305000	0.08831	0.563000	0.77884	CAC	.	.	none		0.517	PADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006621.1	NM_013358		G	17566209	C	G	17566209	3	3	9	1	0	0	0	0	1	0	0	0	11386	506	18	4	1617	4	PADI1	1	17566209	Missense_Mutation	SNP	C	TCGA-FA-A86F-01A-11D-A382-10	1310821	17566209	231684412	2	1002											
ARID1A	8289	hgsc.bcm.edu	37	chr1	27101417	27101417	+	Frame_Shift_Del	DEL	C	C	-																															ctgtgccccccatgacaaggCcccctccatctaactaccag																										TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr1:27101417delC	ENST00000324856.7	+	18	5070	c.4699delC	c.(4699-4701)cccfs	p.P1569fs	ARID1A_ENST00000540690.1_Intron|ARID1A_ENST00000457599.2_Intron|ARID1A_ENST00000374152.2_Frame_Shift_Del_p.P1186fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1569					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)		CATGACAAGGCCCCCTCCATC	0.632			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.R1566fs		Atlas-Indel	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.4698delG						PASS	.						51	50	51					1																	27101417		2203	4300	6503	SO:0001589	frameshift_variant	8289	exon18			.	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.4699delC	1.37:g.27101417delC	ENSP00000320485:p.Pro1569fs	124	0	0		119	28	0.235294	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Del	DEL	ENST00000324856.7	37	CCDS285.1																																																																																			.	.	none		0.632	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		-	27101417	C	-	27101417	7	5	9	1	0	1	0	1	0	0	0	0	913	739	26	0	4769	0	ARID1A	1	27101417	Frame_Shift_Del	DEL	C	TCGA-FA-A86F-01A-11D-A382-10	9535208	27101417	222149204	3	1003											
INPP5B	3633	hgsc.bcm.edu	37	chr1	38355355	38355355	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ccgacactgtgatagtggagGagcgaaccatgtcagtaatt	12	9	12	8	2	1	1	1	1	0	0	1	5	1	3	2	2	2	1	2	2	3	3			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr1:38355355G>A	ENST00000373026.1	-	8	911	c.911C>T	c.(910-912)tCc>tTc	p.S304F	INPP5B_ENST00000373024.3_Missense_Mutation_p.S224F|INPP5B_ENST00000373023.2_Missense_Mutation_p.S304F|INPP5B_ENST00000467066.1_5'Flank|INPP5B_ENST00000373027.1_Missense_Mutation_p.S60F|INPP5B_ENST00000458109.2_5'Flank			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	304					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)				GATAGTGGAGGAGCGAACCAT	0.393																																					p.S224F		Atlas-SNP	.											.	INPP5B	76	.	0			c.C671T						PASS	.						157	146	149					1																	38355355		1845	4092	5937	SO:0001583	missense	3633	exon9			GTGGAGGAGCGAA	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.911C>T	1.37:g.38355355G>A	ENSP00000362117:p.Ser304Phe	177	0	0		122	6	0.0491803	NM_005540	C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	Missense_Mutation	SNP	ENST00000373026.1	37		.	.	.	.	.	.	.	.	.	.	G	18.95	3.732267	0.69189	.	.	ENSG00000204084	ENST00000373027;ENST00000373023;ENST00000373029;ENST00000373026;ENST00000373024	D;D;D;D	0.93488	-3.23;-3.11;-3.11;-3.07	5.85	5.85	0.93711	.	0.446945	0.25549	N	0.029904	D	0.96722	0.8930	M	0.73962	2.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76071	0.987;0.983	D	0.96665	0.9492	10	0.87932	D	0	.	20.1731	0.98165	0.0:0.0:1.0:0.0	.	304;224	P32019;P32019-2	I5P2_HUMAN;.	F	60;304;304;304;224	ENSP00000362118:S60F;ENSP00000362114:S304F;ENSP00000362117:S304F;ENSP00000362115:S224F	ENSP00000362114:S304F	S	-	2	0	INPP5B	38127942	1.000000	0.71417	0.998000	0.56505	0.482000	0.33219	4.276000	0.58933	2.768000	0.95171	0.655000	0.94253	TCC	.	.	none		0.393	INPP5B-003	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000012968.1	NM_005540		A	38355355	G	A	38355355	3	1	9	1	0	0	0	0	1	0	0	0	7764	1174	41	2	2134	2	INPP5B	1	38355355	Missense_Mutation	SNP	G	TCGA-FA-A86F-01A-11D-A382-10	11253938	38355355	210895266	4	1004											
SLC5A9	200010	hgsc.bcm.edu	37	chr1	48688529	48688529	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	acgcctacgacatcagcgtgGtggtcatctactttgtcttc	7	13	9	12	3	4	0	2	0	2	0	5	1	4	0	1	2	3	0	1	2	2	4			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr1:48688529G>C	ENST00000438567.2	+	1	173	c.121G>C	c.(121-123)Gtg>Ctg	p.V41L	SLC5A9_ENST00000420136.2_Missense_Mutation_p.V34L|SLC5A9_ENST00000533824.1_Missense_Mutation_p.V41L|SLC5A9_ENST00000236495.5_Missense_Mutation_p.V41L	NM_001011547.2	NP_001011547.2	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 9	41					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						CATCAGCGTGGTGGTCATCTA	0.587																																					p.V41L		Atlas-SNP	.											.	SLC5A9	82	.	0			c.G121C						PASS	.						147	100	116					1																	48688529		2203	4300	6503	SO:0001583	missense	200010	exon1			AGCGTGGTGGTCA	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.121G>C	1.37:g.48688529G>C	ENSP00000401730:p.Val41Leu	163	0	0		135	9	0.0666667	NM_001135181	B3KY87|B7ZL45|B7ZL47|E9PAK4|E9PJ08|Q5TET3	Missense_Mutation	SNP	ENST00000438567.2	37	CCDS30709.2	.	.	.	.	.	.	.	.	.	.	G	11.22	1.575087	0.28092	.	.	ENSG00000117834	ENST00000533824;ENST00000438567;ENST00000236495;ENST00000420136	D;D;D;D	0.87412	-2.14;-2.15;-2.25;-1.56	4.83	3.92	0.45320	.	0.132348	0.49916	N	0.000137	T	0.76205	0.3955	N	0.16656	0.425	0.48830	D	0.999719	B;B;B	0.09022	0.002;0.001;0.002	B;B;B	0.08055	0.001;0.003;0.001	T	0.69034	-0.5252	10	0.19590	T	0.45	.	13.2689	0.60150	0.0:0.2305:0.7695:0.0	.	41;41;41	E9PJ08;Q2M3M2;E9PAK4	.;SC5A9_HUMAN;.	L	41;41;41;34	ENSP00000431900:V41L;ENSP00000401730:V41L;ENSP00000236495:V41L;ENSP00000408881:V34L	ENSP00000236495:V41L	V	+	1	0	SLC5A9	48461116	0.971000	0.33674	0.977000	0.42913	0.648000	0.38561	1.581000	0.36558	1.365000	0.46057	0.557000	0.71058	GTG	.	.	none		0.587	SLC5A9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022061.3	XM_117174		C	48688529	G	C	48688529	3	2	9	1	0	0	0	0	1	0	0	0	14687	1261	44	4	123	4	SLC5A9	1	48688529	Missense_Mutation	SNP	G	TCGA-FA-A86F-01A-11D-A382-10	10333174	48688529	200562092	5	1005											
HIST2H2BE	8349	hgsc.bcm.edu	37	chr1	149857825	149857825	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggactcacttggagctggtGtacttggtgaccgccttggt	5	12	15	9	1	1	1	1	1	0	0	1	3	1	3	2	5	2	2	2	5	1	4			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr1:149857825G>A	ENST00000369155.2	-	1	407	c.366C>T	c.(364-366)taC>taT	p.Y122Y	HIST2H2AC_ENST00000331380.2_5'Flank|BOLA1_ENST00000369153.2_5'Flank	NM_003528.2	NP_003519.1	Q16778	H2B2E_HUMAN	histone cluster 2, H2be	122					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)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	14	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			TGGAGCTGGTGTACTTGGTGA	0.657																																					p.Y122Y		Atlas-SNP	.											.	HIST2H2BE	33	.	0			c.C366T						PASS	.						30	35	33					1																	149857825		2202	4299	6501	SO:0001819	synonymous_variant	8349	exon1			GCTGGTGTACTTG	AY131979	CCDS936.1	1q21.2	2011-01-27	2006-10-11	2003-03-07	ENSG00000184678	ENSG00000184678		"Histones / Replication-dependent"	4760	protein-coding gene	gene with protein product		601831	"H2B histone family, member Q", "histone 2, H2be"	H2B, H2BFQ		1469070, 12408966	Standard	NM_003528		Approved	H2B/q, H2B.1	uc001etc.3	Q16778	OTTHUMG00000012095	ENST00000369155.2:c.366C>T	1.37:g.149857825G>A		160	0	0		166	9	0.0542169	NM_003528	A3KMC7|A8K110|Q4KMY1|Q5QNX0|Q9UE88	Silent	SNP	ENST00000369155.2	37	CCDS936.1																																																																																			.	.	none		0.657	HIST2H2BE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033455.1	NM_003528		A	149857825	G	A	149857825	2	1	9	1	0	0	0	0	0	0	0	1	7188	1372	48	2		2	HIST2H2BE	1	149857825	Silent	SNP	G	TCGA-FA-A86F-01A-11D-A382-10	101169296	149857825	99392796	6	1006											
ITLN1	55600	hgsc.bcm.edu	37	chr1	160850422	160850422	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	atgctgttttctgggcgtcgCcaaaatcatagaccacaggg	10	10	11	10	2	2	1	1	0	1	1	3	1	2	1	2	2	1	2	2	2	3	3			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr1:160850422C>T	ENST00000326245.3	-	6	756	c.641G>A	c.(640-642)gGc>gAc	p.G214D	ITLN1_ENST00000487531.1_5'UTR	NM_017625.2	NP_060095.2	Q8WWA0	ITLN1_HUMAN	intelectin 1 (galactofuranose binding)	214	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)			CTGGGCGTCGCCAAAATCATA	0.438																																					p.G214D		Atlas-SNP	.											ITLN1,caecum,carcinoma,+1,1	ITLN1	45	1	0			c.G641A						PASS	.						181	181	181					1																	160850422		2203	4300	6503	SO:0001583	missense	55600	exon6			GCGTCGCCAAAAT	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.641G>A	1.37:g.160850422C>T	ENSP00000323587:p.Gly214Asp	132	0	0		91	22	0.241758	NM_017625	Q5IWS4|Q5VYI4|Q6YDJ3|Q9NP67	Missense_Mutation	SNP	ENST00000326245.3	37	CCDS1211.1	.	.	.	.	.	.	.	.	.	.	C	14.31	2.496243	0.44352	.	.	ENSG00000179914	ENST00000326245	T	0.20200	2.09	4.17	3.25	0.37280	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (1);	0.000000	0.64402	D	0.000005	T	0.41282	0.1152	M	0.91510	3.215	0.45194	D	0.998203	D	0.89917	1.0	D	0.97110	1.0	T	0.50866	-0.8777	10	0.87932	D	0	-11.3367	9.6915	0.40131	0.0:0.8959:0.0:0.1041	.	214	Q8WWA0	ITLN1_HUMAN	D	214	ENSP00000323587:G214D	ENSP00000323587:G214D	G	-	2	0	ITLN1	159117046	0.856000	0.29760	0.825000	0.32803	0.184000	0.23303	4.577000	0.60922	0.942000	0.37525	0.655000	0.94253	GGC	.	.	none		0.438	ITLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071462.1	NM_017625		T	160850422	C	T	160850422	3	4	9	1	0	0	0	0	1	0	0	0	7919	739	26	2	312	2	ITLN1	1	160850422	Missense_Mutation	SNP	C	TCGA-FA-A86F-01A-11D-A382-10	10992597	160850422	88400199	7	1007											
KCNH1	3756	hgsc.bcm.edu	37	chr1	210856924	210856924	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcacccacgttgtccaggCgcaagtcgctcttggtgatg	6	10	11	14	3	2	1	1	1	1	0	4	1	3	1	3	2	0	3	3	2	1	2			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr1:210856924C>T	ENST00000271751.4	-	11	2696	c.2669G>A	c.(2668-2670)cGc>cAc	p.R890H	KCNH1_ENST00000367007.4_Missense_Mutation_p.R863H			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	890					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)		GTTGTCCAGGCGCAAGTCGCT	0.592																																					p.R890H		Atlas-SNP	.											.	KCNH1	199	.	0			c.G2669A						PASS	.						73	67	69					1																	210856924		2203	4300	6503	SO:0001583	missense	3756	exon11			TCCAGGCGCAAGT	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.2669G>A	1.37:g.210856924C>T	ENSP00000271751:p.Arg890His	166	0	0		136	6	0.0441176	NM_172362	B1AQ26|O76035|Q14CL3	Missense_Mutation	SNP	ENST00000271751.4	37	CCDS1496.1	.	.	.	.	.	.	.	.	.	.	C	19.67	3.870929	0.72065	.	.	ENSG00000143473	ENST00000271751;ENST00000367007	D;D	0.99537	-6.03;-6.11	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	D	0.99444	0.9803	L	0.58101	1.795	0.80722	D	1	D;D	0.89917	0.998;1.0	P;D	0.71184	0.858;0.972	D	0.98847	1.0757	10	0.56958	D	0.05	.	18.1618	0.89710	0.0:1.0:0.0:0.0	.	863;890	Q14CL3;O95259	.;KCNH1_HUMAN	H	890;863	ENSP00000271751:R890H;ENSP00000355974:R863H	ENSP00000271751:R890H	R	-	2	0	KCNH1	208923547	1.000000	0.71417	0.907000	0.35723	0.337000	0.28794	7.538000	0.82048	2.290000	0.77057	0.561000	0.74099	CGC	.	.	none		0.592	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238		T	210856924	C	T	210856924	3	4	9	1	0	0	0	0	1	0	0	0	8040	768	27	1	304	1	KCNH1	1	210856924	Missense_Mutation	SNP	C	TCGA-FA-A86F-01A-11D-A382-10	50006502	210856924	38393697	8	1008											
KCTD3	51133	hgsc.bcm.edu	37	chr1	215751396	215751396	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cgttcctcttgtggcagtgtCctttttcatggttacttgcc	3	18	9	11	1	2	0	1	0	1	0	4	0	4	0	3	2	2	3	3	2	1	6			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr1:215751396C>T	ENST00000259154.4	+	6	663	c.369C>T	c.(367-369)gtC>gtT	p.V123V		NM_016121.3	NP_057205.2	Q9Y597	KCTD3_HUMAN	potassium channel tetramerization domain containing 3	123					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)		GTGGCAGTGTCCTTTTTCATG	0.348																																					p.V123V		Atlas-SNP	.											.	KCTD3	101	.	0			c.C369T						PASS	.						187	180	182					1																	215751396		2203	4300	6503	SO:0001819	synonymous_variant	51133	exon6			CAGTGTCCTTTTT	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.369C>T	1.37:g.215751396C>T		297	0	0		184	23	0.125	NM_016121	A0AV15|D3DTA6|Q49AG7|Q504Q9|Q6PJN6|Q8ND58|Q8NDJ0|Q8WX16	Silent	SNP	ENST00000259154.4	37	CCDS1515.1	.	.	.	.	.	.	.	.	.	.	C	9.424	1.083728	0.20309	.	.	ENSG00000136636	ENST00000448333	.	.	.	5.8	0.154	0.14901	.	.	.	.	.	T	0.60818	0.2298	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57596	-0.7784	4	.	.	.	-26.6937	12.4313	0.55575	0.0:0.4808:0.4559:0.0632	.	.	.	.	S	96	.	.	P	+	1	0	KCTD3	213818019	0.883000	0.30277	0.984000	0.44739	0.988000	0.76386	-0.075000	0.11431	0.050000	0.15949	-0.479000	0.04858	CCT	.	.	none		0.348	KCTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089871.2	NM_016121		T	215751396	C	T	215751396	2	4	9	1	0	0	0	0	0	0	0	1	8119	842	30	2		2	KCTD3	1	215751396	Silent	SNP	C	TCGA-FA-A86F-01A-11D-A382-10	4894472	215751396	33499225	9	1009											
ZNF496	84838	hgsc.bcm.edu	37	chr1	247492064	247492064	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gttatgggctgggcatcctgGttctttgcaaggtcgctgtg	4	14	15	8	1	1	0	0	0	1	0	3	0	2	0	1	4	1	6	1	4	2	3	rs146066456		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr1:247492064G>A	ENST00000294753.4	-	4	959	c.495C>T	c.(493-495)aaC>aaT	p.N165N	ZNF496_ENST00000366498.2_Silent_p.N165N	NM_032752.1	NP_116141.1	Q96IT1	ZN496_HUMAN	zinc finger protein 496	165					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)			GGGCATCCTGGTTCTTTGCAA	0.627																																					p.N165N		Atlas-SNP	.											.	ZNF496	80	.	0			c.C495T						PASS	.						131	133	133					1																	247492064		2203	4300	6503	SO:0001819	synonymous_variant	84838	exon4			ATCCTGGTTCTTT	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.495C>T	1.37:g.247492064G>A		102	0	0		93	5	0.0537634	NM_032752	Q8TBS2	Silent	SNP	ENST00000294753.4	37	CCDS1631.1																																																																																			G|1.000;T|0.000	.	alt		0.627	ZNF496-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098655.2	NM_032752		A	247492064	G	A	247492064	2	1	9	1	0	0	0	0	0	0	0	1	17960	1252	44	2		2	ZNF496	1	247492064	Silent	SNP	G	TCGA-FA-A86F-01A-11D-A382-10	31740668	247492064	1758557	10	1010											
OR2T34	127068	hgsc.bcm.edu	37	chr1	248737510	248737511	+	Frame_Shift_Ins	INS	-	-	A																															gcagggcaggagtctcacagINSaaaaaactcaggattttcct																								rs150608839	byFrequency	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr1:248737510_248737511insA	ENST00000328782.2	-	1	569_570	c.548_549insT	c.(547-549)ttcfs	p.F183fs		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	183						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F183S(1)		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)			GAGTCTCACAGAAAAAACTCAG	0.515																																					p.F183fs		Atlas-Indel	.											OR2T34,NS,haematopoietic_neoplasm,-1,2	OR2T34	72	2	1	Substitution - Missense(1)	stomach(1)	c.549_550insT						PASS	.																																			SO:0001589	frameshift_variant	127068	exon1			.	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.549dupT	1.37:g.248737516_248737516dupA	ENSP00000330904:p.Phe183fs	333	0	0		230	39	0.169565	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Frame_Shift_Ins	INS	ENST00000328782.2	37	CCDS31120.1																																																																																			.	.	none		0.515	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821		A	248737511	-	A	248737510	7	5	9	1	0	1	1	0	0	0	0	0	11034	933	33	0	411	0	OR2T34	1	248737510	Frame_Shift_Ins	INS	-	TCGA-FA-A86F-01A-11D-A382-10	1245446	248737510	513111	11	1011											
SCN9A	6335	hgsc.bcm.edu	37	chr2	167055184	167055185	+	Stop_Codon_Ins	INS	-	-	T																															atatcaaaaatgaagctctaINSttttttgctttccttgctgt																										TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr2:167055184_167055185insT	ENST00000409435.1	-	0	5963_5964				SCN9A_ENST00000409672.1_Stop_Codon_Ins|SCN9A_ENST00000375387.4_Stop_Codon_Ins|AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Stop_Codon_Ins			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit						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)	ATGAAGCTCTATTTTTTGCTTT	0.327																																					p.X1978delinsI		Atlas-Indel	.											.	SCN9A	296	.	0			c.5932_5933insA						PASS	.																																			SO:0001567	stop_retained_variant	6335	exon27			.	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.5965dupA	2.37:g.167055190_167055190dupT	ENSP00000386330:p.*1989Ileext*?	372	0	0		243	22	0.090535	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Frame_Shift_Ins	INS	ENST00000409435.1	37	CCDS46441.1																																																																																			.	.	none		0.327	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		T	167055185	-	T	167055184	7	5	9	1	0	1	1	0	0	0	0	0	13940	462	16	0	5	0	SCN9A	2	167055184	Stop_Codon_Ins	INS	-	TCGA-FA-A86F-01A-11D-A382-10		167055184	76144189	12	1012											
GPC1	2817	hgsc.bcm.edu	37	chr2	241401695	241401695	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagctgtacacgcagaacgCgagggccttccgggacctgt	9	6	14	12	4	0	2	0	0	0	2	1	4	1	3	3	2	3	3	3	2	2	2			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr2:241401695C>T	ENST00000264039.2	+	3	661	c.413C>T	c.(412-414)gCg>gTg	p.A138V		NM_002081.2	NP_002072.2	P35052	GPC1_HUMAN	glypican 1	138					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)		ACGCAGAACGCGAGGGCCTTC	0.672																																					p.A138V		Atlas-SNP	.											.	GPC1	32	.	0			c.C413T						PASS	.						21	23	22					2																	241401695		2190	4296	6486	SO:0001583	missense	2817	exon3			AGAACGCGAGGGC	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.413C>T	2.37:g.241401695C>T	ENSP00000264039:p.Ala138Val	147	0	0		111	11	0.0990991	NM_002081	B3KTD1|Q53QM4	Missense_Mutation	SNP	ENST00000264039.2	37	CCDS2534.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	12.09|12.09	1.832212|1.832212	0.32421|0.32421	.|.	.|.	ENSG00000063660|ENSG00000063660	ENST00000264039;ENST00000426280|ENST00000427506;ENST00000425056	T;T|.	0.52057|.	0.68;0.68|.	3.1|3.1	1.2|1.2	0.21068|0.21068	.|.	1.004560|.	0.08007|.	N|.	0.989674|.	T|.	0.36331|.	0.0963|.	L|L	0.53617|0.53617	1.68|1.68	0.09310|0.09310	N|N	1|1	B|.	0.30193|.	0.272|.	B|.	0.39617|.	0.305|.	T|.	0.31641|.	-0.9936|.	10|.	0.52906|.	T|.	0.07|.	-13.7881|-13.7881	1.889|1.889	0.03243|0.03243	0.2067:0.4686:0.2019:0.1227|0.2067:0.4686:0.2019:0.1227	.|.	138|.	P35052|.	GPC1_HUMAN|.	V|X	138;88|95;134	ENSP00000264039:A138V;ENSP00000410251:A88V|.	ENSP00000264039:A138V|.	A|R	+|+	2|1	0|2	GPC1|GPC1	241050368|241050368	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.583000|0.583000	0.36354|0.36354	-0.002000|-0.002000	0.12924|0.12924	0.161000|0.161000	0.19458|0.19458	0.586000|0.586000	0.80456|0.80456	GCG|CGA	.	.	none		0.672	GPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257179.3	NM_002081		T	241401695	C	T	241401695	3	4	9	1	0	0	0	0	1	0	0	0	6605	768	27	1	423	1	GPC1	2	241401695	Missense_Mutation	SNP	C	TCGA-FA-A86F-01A-11D-A382-10	74346511	241401695	1797678	13	1013											
NKTR	4820	hgsc.bcm.edu	37	chr3	42674280	42674280	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaggaagcaagcagttcagaAgagccaaggaataaacatgc	19	4	11	7	0	1	2	1	0	0	2	1	4	1	4	1	2	5	3	1	2	8	2			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr3:42674280A>C	ENST00000232978.8	+	9	926	c.738A>C	c.(736-738)gaA>gaC	p.E246D	RP4-613B23.1_ENST00000434363.1_RNA|RP4-613B23.1_ENST00000445452.1_RNA|RP4-613B23.1_ENST00000438017.1_RNA	NM_005385.3	NP_005376.2	P30414	NKTR_HUMAN	natural killer cell triggering receptor	246					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)		GCAGTTCAGAAGAGCCAAGGA	0.393																																					p.E246D		Atlas-SNP	.											.	NKTR	116	.	0			c.A738C						PASS	.						91	96	94					3																	42674280		2203	4300	6503	SO:0001583	missense	4820	exon9			TTCAGAAGAGCCA		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.738A>C	3.37:g.42674280A>C	ENSP00000232978:p.Glu246Asp	214	0	0		127	18	0.141732	NM_005385		Missense_Mutation	SNP	ENST00000232978.8	37	CCDS2702.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.317054	0.81469	.	.	ENSG00000114857	ENST00000232978	T	0.13196	2.61	5.83	-1.96	0.07525	.	0.387908	0.30142	N	0.010302	T	0.22166	0.0534	M	0.63428	1.95	0.80722	D	1	P;D	0.62365	0.935;0.991	B;P	0.53689	0.315;0.732	T	0.03818	-1.1001	10	0.62326	D	0.03	-10.0199	12.9061	0.58154	0.3415:0.0:0.6585:0.0	.	126;246	Q59EC3;P30414	.;NKTR_HUMAN	D	246	ENSP00000232978:E246D	ENSP00000232978:E246D	E	+	3	2	NKTR	42649284	1.000000	0.71417	0.990000	0.47175	0.899000	0.52679	0.525000	0.22956	-0.326000	0.08564	0.533000	0.62120	GAA	.	.	none		0.393	NKTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256642.2	NM_005385		C	42674280	A	C	42674280	3	2	9	1	0	0	0	0	1	0	0	0	10457	69	3	5	768	5	NKTR	3	42674280	Missense_Mutation	SNP	A	TCGA-FA-A86F-01A-11D-A382-10		42674280	155348150	14	1014											
FRAS1	80144	hgsc.bcm.edu	37	chr4	79328899	79328899	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cctgatgggaggacagctacCcccaccagcaccttcaccca	10	5	8	18	0	1	1	1	1	0	0	1	3	1	3	6	2	3	2	6	2	1	2			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr4:79328899C>G	ENST00000325942.6	+	31	4652	c.4212C>G	c.(4210-4212)acC>acG	p.T1404T	FRAS1_ENST00000264895.6_Silent_p.T1404T	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	1404					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						GGACAGCTACCCCCACCAGCA	0.597																																					p.T1404T		Atlas-SNP	.											.	FRAS1	779	.	0			c.C4212G						PASS	.						80	87	85					4																	79328899		2124	4233	6357	SO:0001819	synonymous_variant	80144	exon31			AGCTACCCCCACC	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.4212C>G	4.37:g.79328899C>G		121	0	0		98	8	0.0816327	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000325942.6	37	CCDS54772.1																																																																																			.	.	none		0.597	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			G	79328899	C	G	79328899	2	3	9	1	0	0	0	0	0	0	0	1	6050	610	22	4		4	FRAS1	4	79328899	Silent	SNP	C	TCGA-FA-A86F-01A-11D-A382-10		79328899	111825377	15	1015											
ELOVL6	79071	hgsc.bcm.edu	37	chr4	111119485	111119485	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtaaagtcaacactgacaTgttcattggggctgatcttc	10	14	9	8	0	3	2	2	2	1	0	4	2	3	2	0	2	1	3	0	2	3	5			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr4:111119485T>G	ENST00000394607.3	-	2	170	c.7A>C	c.(7-9)Atg>Ctg	p.M3L	ELOVL6_ENST00000506461.1_5'UTR|ELOVL6_ENST00000302274.3_Missense_Mutation_p.M3L			Q9H5J4	ELOV6_HUMAN	ELOVL fatty acid elongase 6	3					cellular lipid metabolic process (GO:0044255)|fatty acid elongation, saturated fatty acid (GO:0019367)|long-chain fatty acid biosynthetic process (GO:0042759)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|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)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	8				OV - Ovarian serous cystadenocarcinoma(123;0.00462)		AACACTGACATGTTCATTGGG	0.428																																					p.M3L		Atlas-SNP	.											.	ELOVL6	27	.	0			c.A7C						PASS	.						200	174	183					4																	111119485		2203	4300	6503	SO:0001583	missense	79071	exon2			CTGACATGTTCAT	AK027031	CCDS3690.1	4q25	2011-05-25	2011-05-25		ENSG00000170522	ENSG00000170522			15829	protein-coding gene	gene with protein product		611546	"ELOVL family member 6, elongation of long chain fatty acids (FEN1/Elo2, SUR4/Elo3-like, yeast)"			11567032	Standard	NM_024090		Approved	FLJ23378, MGC5487, LCE	uc003hzz.3	Q9H5J4	OTTHUMG00000132547	ENST00000394607.3:c.7A>C	4.37:g.111119485T>G	ENSP00000378105:p.Met3Leu	126	0	0		102	7	0.0686275	NM_001130721	Q4W5L0|Q8NCD1	Missense_Mutation	SNP	ENST00000394607.3	37	CCDS3690.1	.	.	.	.	.	.	.	.	.	.	T	16.99	3.274309	0.59649	.	.	ENSG00000170522	ENST00000394607;ENST00000302274;ENST00000506625;ENST00000503885	T;T	0.20200	2.09;2.09	5.68	5.68	0.88126	.	0.150731	0.64402	D	0.000016	T	0.14399	0.0348	N	0.19112	0.55	0.47511	D	0.999443	B	0.02656	0.0	B	0.01281	0.0	T	0.11131	-1.0600	10	0.16420	T	0.52	-11.0653	14.9246	0.70866	0.0:0.0:0.0:1.0	.	3	Q9H5J4	ELOV6_HUMAN	L	3	ENSP00000378105:M3L;ENSP00000304736:M3L	ENSP00000304736:M3L	M	-	1	0	ELOVL6	111338934	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.985000	0.76193	2.168000	0.68352	0.533000	0.62120	ATG	.	.	none		0.428	ELOVL6-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255748.1	NM_024090		G	111119485	T	G	111119485	3	3	9	1	0	0	0	0	1	0	0	0	5080	1464	51	5	806	5	ELOVL6	4	111119485	Missense_Mutation	SNP	T	TCGA-FA-A86F-01A-11D-A382-10	31790586	111119485	80034791	16	1016											
TRAM1L1	133022	hgsc.bcm.edu	37	chr4	118005633	118005633	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgttacgtaggcttggatcGtgcaactggacgacagaaca	12	9	12	8	3	0	1	0	0	0	1	1	4	0	3	0	3	4	4	0	3	4	3			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr4:118005633G>A	ENST00000310754.4	-	1	1103	c.917C>T	c.(916-918)aCg>aTg	p.T306M		NM_152402.2	NP_689615.2	Q8N609	TR1L1_HUMAN	translocation associated membrane protein 1-like 1	306	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				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						GGCTTGGATCGTGCAACTGGA	0.453																																					p.T306M		Atlas-SNP	.											.	TRAM1L1	55	.	0			c.C917T						PASS	.						129	120	123					4																	118005633		2203	4300	6503	SO:0001583	missense	133022	exon1			TGGATCGTGCAAC	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.917C>T	4.37:g.118005633G>A	ENSP00000309402:p.Thr306Met	225	0	0		179	18	0.100559	NM_152402	Q8N2L7	Missense_Mutation	SNP	ENST00000310754.4	37	CCDS3707.1	.	.	.	.	.	.	.	.	.	.	G	7.466	0.645766	0.14451	.	.	ENSG00000174599	ENST00000310754	D	0.85258	-1.96	3.74	2.87	0.33458	TRAM/LAG1/CLN8 homology domain (3);	0.890367	0.09839	N	0.749176	T	0.79936	0.4532	L	0.29908	0.895	0.09310	N	1	P	0.48089	0.905	P	0.45946	0.498	T	0.67837	-0.5567	10	0.45353	T	0.12	-6.284	9.0284	0.36243	0.0:0.2389:0.7611:0.0	.	306	Q8N609	TR1L1_HUMAN	M	306	ENSP00000309402:T306M	ENSP00000309402:T306M	T	-	2	0	TRAM1L1	118225081	0.009000	0.17119	0.428000	0.26697	0.038000	0.13279	1.409000	0.34680	1.113000	0.41760	0.650000	0.86243	ACG	.	.	none		0.453	TRAM1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256513.1	NM_152402		A	118005633	G	A	118005633	3	1	9	1	0	0	0	0	1	0	0	0	16467	1145	40	1	196	1	TRAM1L1	4	118005633	Missense_Mutation	SNP	G	TCGA-FA-A86F-01A-11D-A382-10	6886148	118005633	73148643	17	1017											
FAT1	2195	hgsc.bcm.edu	37	chr4	187539303	187539303	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aacaatgaatgcctcatatgGactagattcaaagaccgggc	15	8	9	9	1	2	3	2	1	0	2	2	4	2	4	2	2	2	0	2	2	6	3			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr4:187539303G>T	ENST00000441802.2	-	10	8646	c.8437C>A	c.(8437-8439)Cca>Aca	p.P2813T		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2813	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						GCCTCATATGGACTAGATTCA	0.463										HNSCC(5;0.00058)																											p.P2813T	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C8437A						PASS	.						125	120	122					4																	187539303		1879	4121	6000	SO:0001583	missense	2195	exon10			CATATGGACTAGA	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.8437C>A	4.37:g.187539303G>T	ENSP00000406229:p.Pro2813Thr	151	0	0		103	14	0.135922	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	G	12.30	1.897051	0.33535	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.37411	1.2	5.0	5.0	0.66597	Cadherin (2);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.42653	0.1212	N	0.16862	0.45	0.80722	D	1	D	0.76494	0.999	D	0.69142	0.962	T	0.16512	-1.0400	10	0.17832	T	0.49	.	18.8402	0.92180	0.0:0.0:1.0:0.0	.	2813	Q14517	FAT1_HUMAN	T	2813;2815	ENSP00000406229:P2813T	ENSP00000260147:P2815T	P	-	1	0	FAT1	187776297	1.000000	0.71417	0.268000	0.24571	0.914000	0.54420	7.674000	0.83992	2.757000	0.94681	0.655000	0.94253	CCA	.	.	none		0.463	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		T	187539303	G	T	187539303	3	4	9	1	0	0	0	0	1	0	0	0	5697	1174	41	4	5401	4	FAT1	4	187539303	Missense_Mutation	SNP	G	TCGA-FA-A86F-01A-11D-A382-10	69533670	187539303	3614973	18	1018											
IRF4	3662	hgsc.bcm.edu	37	chr6	394899	394899	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggaagacgcgcctgcggTgcgctttgaacaagagcaat	10	7	13	11	4	0	3	0	1	0	2	0	4	0	4	2	2	4	2	2	2	4	1			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr6:394899T>C	ENST00000380956.4	+	3	421	c.295T>C	c.(295-297)Tgc>Cgc	p.C99R	IRF4_ENST00000495137.1_3'UTR	NM_001195286.1|NM_002460.3	NP_001182215.1|NP_002451.2	Q15306	IRF4_HUMAN	interferon regulatory factor 4	99					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)		GCGCCTGCGGTGCGCTTTGAA	0.542			T	IGH@	MM																																p.C99R		Atlas-SNP	.		Dom	yes		6	6p25-p23	3662	interferon regulatory factor 4		L	IRF4_ENST00000380956,NS,carcinoma,-1,1	IRF4	65	1	0			c.T295C						PASS	.						89	94	92					6																	394899		2203	4300	6503	SO:0001583	missense	3662	exon3			CTGCGGTGCGCTT	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.295T>C	6.37:g.394899T>C	ENSP00000370343:p.Cys99Arg	55	0	0		46	8	0.173913	NM_001195286	Q5VUI7|Q99660	Missense_Mutation	SNP	ENST00000380956.4	37	CCDS4469.1	.	.	.	.	.	.	.	.	.	.	T	16.04	3.011366	0.54468	.	.	ENSG00000137265	ENST00000380956;ENST00000412334	D	0.99418	-5.87	5.81	5.81	0.92471	Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (4);	0.000000	0.85682	D	0.000000	D	0.99664	0.9875	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	0.999;1.0;1.0	D	0.97583	1.0112	10	0.87932	D	0	-17.4096	16.1535	0.81640	0.0:0.0:0.0:1.0	.	99;99;99	F2Z3D5;Q15306-2;Q15306	.;.;IRF4_HUMAN	R	99;129	ENSP00000370343:C99R	ENSP00000370343:C99R	C	+	1	0	IRF4	339899	1.000000	0.71417	0.108000	0.21378	0.035000	0.12851	7.586000	0.82596	2.217000	0.71921	0.528000	0.53228	TGC	.	.	none		0.542	IRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043638.1			C	394899	T	C	394899	3	2	9	1	0	0	0	0	1	0	0	0	7841	1696	59	3	301	3	IRF4	6	394899	Missense_Mutation	SNP	T	TCGA-FA-A86F-01A-11D-A382-10		394899	170720168	19	1019											
HIST1H2BD	3017	hgsc.bcm.edu	37	chr6	26158776	26158776	+	Nonstop_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccaagtacaccagttccaagTaactttgccaagtaagcatc	14	9	6	12	0	0	0	0	0	0	0	2	0	1	0	4	0	4	5	4	0	6	5			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr6:26158776T>C	ENST00000289316.2	+	1	403	c.379T>C	c.(379-381)Taa>Caa	p.*127Q	HIST1H2BD_ENST00000377777.4_Nonstop_Mutation_p.*127Q	NM_138720.2	NP_619790.1	P58876	H2B1D_HUMAN	histone cluster 1, H2bd	0					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						CAGTTCCAAGTAACTTTGCCA	0.512																																					p.X127Q		Atlas-SNP	.											.	HIST1H2BD	45	.	0			c.T379C						PASS	.						61	66	64					6																	26158776		2203	4300	6503	SO:0001578	stop_lost	3017	exon1			TCCAAGTAACTTT	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.379T>C	6.37:g.26158776T>C	ENSP00000289316:p.*127Glnext*13	163	0	0		105	14	0.133333	NM_021063		Missense_Mutation	SNP	ENST00000289316.2	37	CCDS4587.1	.	.	.	.	.	.	.	.	.	.	.	8.266	0.812203	0.16537	.	.	ENSG00000158373	ENST00000377777;ENST00000289316	.	.	.	5.1	3.89	0.44902	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.6541	0.17633	0.155:0.0888:0.0:0.7563	.	.	.	.	Q	127	.	.	X	+	1	0	HIST1H2BD	26266755	1.000000	0.71417	0.599000	0.28851	0.305000	0.27757	4.678000	0.61641	0.988000	0.38734	0.529000	0.55759	TAA	.	.	none		0.512	HIST1H2BD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040088.1	NM_021063		C	26158776	T	C	26158776	4	2	9	1	0	0	0	0	0	0	0	0	7152	1651	57	3	381	3	HIST1H2BD	6	26158776	Nonstop_Mutation	SNP	T	TCGA-FA-A86F-01A-11D-A382-10	25763877	26158776	144956291	20	1020											
UHRF1BP1	54887	hgsc.bcm.edu	37	chr6	34825160	34825160	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctacactcctttcctgcagtCggaaacttcacaacctccct	9	11	4	17	1	1	0	1	0	0	0	5	1	4	1	4	1	4	1	4	1	3	3	rs201864059		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr6:34825160C>T	ENST00000192788.5	+	12	1657	c.1486C>T	c.(1486-1488)Cgg>Tgg	p.R496W	UHRF1BP1_ENST00000452449.2_Missense_Mutation_p.R496W	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	496							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						TTCCTGCAGTCGGAAACTTCA	0.433																																					p.R496W		Atlas-SNP	.											.	UHRF1BP1	102	.	0			c.C1486T						PASS	.						124	118	120					6																	34825160		1875	4119	5994	SO:0001583	missense	54887	exon12			TGCAGTCGGAAAC	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.1486C>T	6.37:g.34825160C>T	ENSP00000192788:p.Arg496Trp	152	0	0		105	9	0.0857143	NM_017754	Q9NXE0	Missense_Mutation	SNP	ENST00000192788.5	37	CCDS43455.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.014324	0.75161	.	.	ENSG00000065060	ENST00000192788;ENST00000452449	T;T	0.12879	2.64;2.64	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.21718	0.0523	L	0.50333	1.59	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.00196	-1.1931	10	0.87932	D	0	-22.6533	11.8255	0.52265	0.2922:0.7078:0.0:0.0	.	496	Q6BDS2	URFB1_HUMAN	W	496	ENSP00000192788:R496W;ENSP00000400628:R496W	ENSP00000192788:R496W	R	+	1	2	UHRF1BP1	34933138	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	2.939000	0.48995	2.758000	0.94735	0.563000	0.77884	CGG	.	.	weak		0.433	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754		T	34825160	C	T	34825160	3	4	9	1	0	0	0	0	1	0	0	0	16983	875	31	1	1532	1	UHRF1BP1	6	34825160	Missense_Mutation	SNP	C	TCGA-FA-A86F-01A-11D-A382-10	8666384	34825160	136289907	21	1021											
RIMS1	22999	hgsc.bcm.edu	37	chr6	73023228	73023228	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtataacatacataaagatcAgtacagaagctgtgataacg	18	9	8	6	1	1	3	1	1	0	2	1	3	1	3	0	0	5	3	0	0	8	6			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr6:73023228A>G	ENST00000521978.1	+	28	3983	c.3983A>G	c.(3982-3984)cAg>cGg	p.Q1328R	RIMS1_ENST00000491071.2_Missense_Mutation_p.Q1151R|RIMS1_ENST00000538414.1_Missense_Mutation_p.Q134R|RIMS1_ENST00000348717.5_Missense_Mutation_p.Q1120R|RIMS1_ENST00000517960.1_Missense_Mutation_p.Q1120R|RIMS1_ENST00000264839.7_Missense_Mutation_p.Q1177R|RIMS1_ENST00000518273.1_Intron|RIMS1_ENST00000425662.2_Intron|RIMS1_ENST00000520567.1_Intron|RIMS1_ENST00000517827.1_Intron|RIMS1_ENST00000401910.3_Missense_Mutation_p.Q648R|RIMS1_ENST00000522291.1_Intron|RIMS1_ENST00000523963.1_Intron	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	1328					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)				CATAAAGATCAGTACAGAAGC	0.403																																					p.Q1328R		Atlas-SNP	.											.	RIMS1	278	.	0			c.A3983G						PASS	.						57	60	59					6																	73023228		1962	4152	6114	SO:0001583	missense	22999	exon28			AAGATCAGTACAG	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.3983A>G	6.37:g.73023228A>G	ENSP00000428417:p.Gln1328Arg	93	0	0		78	19	0.24359	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	37	CCDS47449.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.95|11.95	1.792225|1.792225	0.31685|0.31685	.|.	.|.	ENSG00000079841|ENSG00000079841	ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000264839;ENST00000517960;ENST00000521978;ENST00000401910;ENST00000453976;ENST00000370420;ENST00000538414|ENST00000522211	T;T;T;T;T;T;T;T;T|.	0.18338|.	2.55;2.68;2.6;2.68;2.58;2.67;2.55;2.28;2.22|.	5.74|5.74	5.74|5.74	0.90152|0.90152	.|.	0.000000|.	0.64402|.	D|.	0.000007|.	T|T	0.59266|0.59266	0.2181|0.2181	L|L	0.50333|0.50333	1.59|1.59	0.47308|0.47308	D|D	0.999389|0.999389	B;P;P;B;D;B;P|.	0.56035|.	0.017;0.949;0.885;0.003;0.974;0.016;0.936|.	B;D;P;B;P;B;P|.	0.64042|.	0.016;0.921;0.549;0.003;0.521;0.01;0.885|.	T|T	0.58869|0.58869	-0.7560|-0.7560	10|5	0.07990|.	T|.	0.79|.	-18.4387|-18.4387	16.0343|16.0343	0.80612|0.80612	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	134;1177;648;1120;404;1151;1328|.	B7Z7W2;E9PHR1;E9PF48;E7ENC2;Q5JY21;C9JNW6;Q86UR5|.	.;.;.;.;.;.;RIMS1_HUMAN|.	R|G	1151;1177;1151;1120;1177;1120;1328;648;493;376;134|246	ENSP00000430101:Q1151R;ENSP00000275037:Q1120R;ENSP00000264839:Q1177R;ENSP00000429959:Q1120R;ENSP00000428417:Q1328R;ENSP00000385649:Q648R;ENSP00000389503:Q493R;ENSP00000359448:Q376R;ENSP00000439730:Q134R|.	ENSP00000264839:Q1177R|.	Q|S	+|+	2|1	0|0	RIMS1|RIMS1	73079949|73079949	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	6.914000|6.914000	0.75764|0.75764	2.198000|2.198000	0.70561|0.70561	0.533000|0.533000	0.62120|0.62120	CAG|AGT	.	.	none		0.403	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			G	73023228	A	G	73023228	3	3	9	1	0	0	0	0	1	0	0	0	13382	188	7	3	4256	3	RIMS1	6	73023228	Missense_Mutation	SNP	A	TCGA-FA-A86F-01A-11D-A382-10	38198068	73023228	98091839	22	1022											
TNFAIP3	7128	hgsc.bcm.edu	37	chr6	138198239	138198240	+	Frame_Shift_Del	DEL	AG	AG	-																															gagctgttccacttgttaacAgagaccggggaagatttgaa																										TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr6:138198239_138198240delAG	ENST00000237289.4	+	6	898_899	c.832_833delAG	c.(832-834)agafs	p.R278fs	TNFAIP3_ENST00000485192.1_3'UTR	NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	278	TRAF-binding.				apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|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 interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|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 protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		ACTTGTTAACAGAGACCGGGGA	0.342			"D, N, F"		"marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"																																p.277_278del	GBM(130;153 1739 22295 28918 47987)	Atlas-Indel	.		Rec	yes		6	6q23	7128	"tumor necrosis factor, alpha-induced protein 3"		L	.	TNFAIP3	340	.	25	Whole gene deletion(25)	haematopoietic_and_lymphoid_tissue(25)	c.831_832del						PASS	.																																			SO:0001589	frameshift_variant	7128	exon6			.	M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"OTU domain containing"	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.832_833delAG	6.37:g.138198241_138198242delAG	ENSP00000237289:p.Arg278fs	286	0	0		165	12	0.0727273	NM_001270508	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Frame_Shift_Del	DEL	ENST00000237289.4	37	CCDS5187.1																																																																																			.	.	none		0.342	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1			-	138198240	AG	-	138198239	7	5	9	1	0	1	0	1	0	0	0	0	16289	180	7	0	850	0	TNFAIP3	6	138198239	Frame_Shift_Del	DEL	AG	TCGA-FA-A86F-01A-11D-A382-10	65175011	138198239	32916828	23	1023											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152768599	152768599	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtaaatgctgtacctctgaCagcagcgtcacaagagcctt	12	9	9	11	1	2	2	1	1	1	1	2	2	2	2	2	0	5	4	2	0	4	3			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr6:152768599C>G	ENST00000367255.5	-	29	4264	c.3663G>C	c.(3661-3663)ctG>ctC	p.L1221L	SYNE1_ENST00000413186.2_Silent_p.L1221L|SYNE1_ENST00000341594.5_Silent_p.L1287L|SYNE1_ENST00000448038.1_Silent_p.L1228L|SYNE1_ENST00000367248.3_Silent_p.L1211L|SYNE1_ENST00000265368.4_Silent_p.L1221L|SYNE1_ENST00000367253.4_Silent_p.L1221L|SYNE1_ENST00000423061.1_Silent_p.L1228L	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1221					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)		GTACCTCTGACAGCAGCGTCA	0.413										HNSCC(10;0.0054)																											p.L1228L		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G3684C						PASS	.						55	55	55					6																	152768599		2203	4300	6503	SO:0001819	synonymous_variant	23345	exon29			CTCTGACAGCAGC	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.3663G>C	6.37:g.152768599C>G		105	0	0		69	7	0.101449	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																			.	.	none		0.413	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		G	152768599	C	G	152768599	2	3	9	1	0	0	0	0	0	0	0	1	15460	465	17	4		4	SYNE1	6	152768599	Silent	SNP	C	TCGA-FA-A86F-01A-11D-A382-10	14570360	152768599	18346468	24	1024											
KIF25	3834	hgsc.bcm.edu	37	chr6	168443315	168443315	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccttgcggccctggcaggcGtcctgggggctttgttggag	2	10	18	11	2	0	0	0	0	0	0	1	1	1	1	3	6	1	3	3	6	0	3	rs146787013	byFrequency	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr6:168443315G>A	ENST00000443060.2	+	9	1295	c.904G>A	c.(904-906)Gtc>Atc	p.V302I	KIF25_ENST00000351261.3_Intron|KIF25_ENST00000354419.2_Missense_Mutation_p.V302I			Q9UIL4	KIF25_HUMAN	kinesin family member 25	302	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)		CCTGGCAGGCGTCCTGGGGGC	0.647													G|||	46	0.0091853	0.0318	0.0058	5008	,	,		16877	0.0		0.0	False		,,,				2504	0.0				p.V302I		Atlas-SNP	.											KIF25,NS,carcinoma,-2,1	KIF25	75	1	0			c.G904A						PASS	.	G	,ILE/VAL	88,4318	73.6+/-111.7	0,88,2115	98	95	96		,904	3.2	0.3	6	dbSNP_134	96	0,8600		0,0,4300	yes	intron,missense	KIF25	NM_005355.3,NM_030615.2	,29	0,88,6415	AA,AG,GG		0.0,1.9973,0.6766	,probably-damaging	,302/385	168443315	88,12918	2203	4300	6503	SO:0001583	missense	3834	exon8			GCAGGCGTCCTGG	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.904G>A	6.37:g.168443315G>A	ENSP00000388878:p.Val302Ile	91	0	0		62	12	0.193548	NM_030615	O94775|Q5SZU9	Missense_Mutation	SNP	ENST00000443060.2	37	CCDS5305.1	14	0.00641025641025641	11	0.022357723577235773	3	0.008287292817679558	0	0.0	0	0.0	G	14.81	2.647615	0.47258	0.019973	0.0	ENSG00000125337	ENST00000443060;ENST00000354419	T;T	0.79454	-1.27;-1.27	4.13	3.24	0.37175	Kinesin, motor domain (3);	0.000000	0.64402	D	0.000002	D	0.84433	0.5471	M	0.87900	2.915	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.86005	0.1497	10	0.87932	D	0	-20.8353	9.7087	0.40231	0.1042:0.0:0.8958:0.0	.	302	Q9UIL4	KIF25_HUMAN	I	302	ENSP00000388878:V302I;ENSP00000346401:V302I	ENSP00000346401:V302I	V	+	1	0	KIF25	168186164	1.000000	0.71417	0.297000	0.24988	0.082000	0.17680	4.083000	0.57643	0.839000	0.34971	0.543000	0.68304	GTC	G|0.993;A|0.007	0.007	strong		0.647	KIF25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362509.1			A	168443315	G	A	168443315	3	1	9	1	0	0	0	0	1	0	0	0	8302	1145	40	1	930	1	KIF25	6	168443315	Missense_Mutation	SNP	G	TCGA-FA-A86F-01A-11D-A382-10	15674716	168443315	2671752	25	1025											
ABCB5	340273	hgsc.bcm.edu	37	chr7	20683092	20683092	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcttgtttcagtgacattgAcaaaatcagtgatggtattg	11	15	10	5	0	2	3	2	3	0	0	2	3	2	3	0	1	1	3	0	1	3	5			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr7:20683092A>G	ENST00000404938.2	+	7	1167	c.515A>G	c.(514-516)gAc>gGc	p.D172G		NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	172	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						AGTGACATTGACAAAATCAGT	0.368																																					p.D172G		Atlas-SNP	.											.	ABCB5	357	.	0			c.A515G						PASS	.						224	197	205					7																	20683092		1568	3582	5150	SO:0001583	missense	340273	exon7			ACATTGACAAAAT	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.515A>G	7.37:g.20683092A>G	ENSP00000384881:p.Asp172Gly	214	0	0		149	17	0.114094	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	37	CCDS55090.1	.	.	.	.	.	.	.	.	.	.	A	9.693	1.152310	0.21371	.	.	ENSG00000004846	ENST00000404938	D	0.90261	-2.64	3.85	-0.101	0.13618	.	.	.	.	.	D	0.82472	0.5044	L	0.41492	1.28	0.80722	D	1	B	0.18013	0.025	B	0.23275	0.045	T	0.67480	-0.5660	9	0.25106	T	0.35	.	4.5733	0.12221	0.6388:0.1667:0.1946:0.0	.	172	A7BKA4	.	G	172	ENSP00000384881:D172G	ENSP00000384881:D172G	D	+	2	0	ABCB5	20649617	1.000000	0.71417	0.999000	0.59377	0.371000	0.29859	2.424000	0.44714	-0.012000	0.14223	0.460000	0.39030	GAC	.	.	none		0.368	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559		G	20683092	A	G	20683092	3	3	9	1	0	0	0	0	1	0	0	0	44	275	10	3	537	3	ABCB5	7	20683092	Missense_Mutation	SNP	A	TCGA-FA-A86F-01A-11D-A382-10		20683092	138455571	26	1026											
DDC	1644	hgsc.bcm.edu	37	chr7	50531011	50531011	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacatgggcagattccaccGtgcgagaacagatggcaaag	13	5	13	10	2	0	3	0	0	0	3	1	4	1	3	2	2	2	3	2	2	2	1	rs147562019		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr7:50531011G>A	ENST00000444124.2	-	14	1561	c.1361C>T	c.(1360-1362)aCg>aTg	p.T454M	DDC_ENST00000426377.1_Missense_Mutation_p.T376M|DDC_ENST00000431062.1_Missense_Mutation_p.T361M|DDC_ENST00000357936.5_Missense_Mutation_p.T454M	NM_001082971.1	NP_001076440	P20711	DDC_HUMAN	dopa decarboxylase (aromatic L-amino acid decarboxylase)	454					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)			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)	AGATTCCACCGTGCGAGAACA	0.547																																					p.T454M		Atlas-SNP	.											.	DDC	100	.	0			c.C1361T						PASS	.	G	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	1,4405		0,1,2202	120	104	110		1361,1361,1247,1217,1127,1082	2.6	0	7	dbSNP_134	110	0,8600		0,0,4300	no	missense,missense,missense,missense,missense,missense	DDC	NM_000790.3,NM_001082971.1,NM_001242886.1,NM_001242887.1,NM_001242888.1,NM_001242889.1	81,81,81,81,81,81	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	454/481,454/481,416/443,406/433,376/403,361/388	50531011	1,13005	2203	4300	6503	SO:0001583	missense	1644	exon14			TCCACCGTGCGAG		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.1361C>T	7.37:g.50531011G>A	ENSP00000403644:p.Thr454Met	218	0	0		165	14	0.0848485	NM_001082971	C9IYA0|E7ER62|E7EU95|Q16723|Q5W5T9|Q75MJ6	Missense_Mutation	SNP	ENST00000444124.2	37	CCDS5511.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.557|7.557	0.663813|0.663813	0.14710|0.14710	2.27E-4|2.27E-4	0.0|0.0	ENSG00000132437|ENSG00000132437	ENST00000430300|ENST00000357936;ENST00000431062;ENST00000426377;ENST00000444124	.|T;T;T;T	.|0.38077	.|1.16;1.16;1.16;1.16	5.44|5.44	2.61|2.61	0.31194|0.31194	.|Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	.|0.388045	.|0.31102	.|N	.|0.008259	T|T	0.35451|0.35451	0.0932|0.0932	M|M	0.73962|0.73962	2.25|2.25	0.27720|0.27720	N|N	0.945142|0.945142	.|B;B	.|0.21147	.|0.052;0.052	.|B;B	.|0.12156	.|0.007;0.007	T|T	0.33548|0.33548	-0.9864|-0.9864	5|10	.|0.59425	.|D	.|0.04	-7.455|-7.455	7.8343|7.8343	0.29362|0.29362	0.1397:0.0:0.728:0.1323|0.1397:0.0:0.728:0.1323	.|.	.|454;454	.|Q53Y41;P20711	.|.;DDC_HUMAN	W|M	335|454;361;376;454	.|ENSP00000350616:T454M;ENSP00000399184:T361M;ENSP00000395069:T376M;ENSP00000403644:T454M	.|ENSP00000350616:T454M	R|T	-|-	1|2	2|0	DDC|DDC	50498505|50498505	0.021000|0.021000	0.18746|0.18746	0.002000|0.002000	0.10522|0.10522	0.066000|0.066000	0.16364|0.16364	0.704000|0.704000	0.25661|0.25661	0.245000|0.245000	0.21373|0.21373	0.655000|0.655000	0.94253|0.94253	CGG|ACG	G|1.000;A|0.000	0.000	weak		0.547	DDC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342593.1			A	50531011	G	A	50531011	3	1	9	1	0	0	0	0	1	0	0	0	4327	1145	40	1	85	1	DDC	7	50531011	Missense_Mutation	SNP	G	TCGA-FA-A86F-01A-11D-A382-10	29847919	50531011	108607652	27	1027											
CD36	948	hgsc.bcm.edu	37	chr7	80285936	80285936	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttacagacagttttggatCtttgatgtgcaaaatccaca	12	14	8	7	0	1	2	0	1	1	1	2	3	2	3	1	1	2	3	1	1	3	5			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr7:80285936C>A	ENST00000435819.1	+	7	885	c.201C>A	c.(199-201)atC>atA	p.I67I	CD36_ENST00000309881.7_Silent_p.I67I|CD36_ENST00000432207.1_Silent_p.I67I|CD36_ENST00000394788.3_Silent_p.I67I|CD36_ENST00000441109.2_3'UTR|CD36_ENST00000538969.1_Silent_p.I67I|CD36_ENST00000447544.2_Silent_p.I67I|CD36_ENST00000534394.1_5'UTR|CD36_ENST00000433696.2_Silent_p.I67I|CD36_ENST00000544133.1_Silent_p.I67I			P16671	CD36_HUMAN	CD36 molecule (thrombospondin receptor)	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)|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						AGTTTTGGATCTTTGATGTGC	0.378																																					p.I67I		Atlas-SNP	.											.	CD36	185	.	0			c.C201A						PASS	.						92	88	90					7																	80285936		2203	4300	6503	SO:0001819	synonymous_variant	948	exon2			TTGGATCTTTGAT	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.201C>A	7.37:g.80285936C>A		156	0	0		126	22	0.174603	NM_001127444	D9IX66|D9IX67|D9IX68|D9IX69|Q13966|Q16093|Q8TCV7|Q9BPZ8|Q9BQC2|Q9BZM8|Q9BZN3|Q9BZN4|Q9BZN5	Silent	SNP	ENST00000435819.1	37	CCDS34673.1																																																																																			.	.	none		0.378	CD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339767.6	NM_001001547		A	80285936	C	A	80285936	2	1	9	1	0	0	0	0	0	0	0	1	3009	903	32	4		4	CD36	7	80285936	Silent	SNP	C	TCGA-FA-A86F-01A-11D-A382-10	29754925	80285936	78852727	28	1028											
LRRC4	64101	hgsc.bcm.edu	37	chr7	127669744	127669744	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggaattggtgggtatatacTctcgaagccaccaggctagc	10	10	12	9	1	1	0	0	0	1	0	2	2	1	1	2	4	3	2	2	4	6	5			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr7:127669744T>C	ENST00000249363.3	-	2	1207	c.950A>G	c.(949-951)gAg>gGg	p.E317G	SND1_ENST00000354725.3_Intron	NM_022143.4	NP_071426.1	Q9HBW1	LRRC4_HUMAN	leucine rich repeat containing 4	317	LRRCT.				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)		GGGTATATACTCTCGAAGCCA	0.572																																					p.E317G		Atlas-SNP	.											.	LRRC4	72	.	0			c.A950G						PASS	.						44	38	40					7																	127669744		2203	4300	6503	SO:0001583	missense	64101	exon2			ATATACTCTCGAA	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.950A>G	7.37:g.127669744T>C	ENSP00000249363:p.Glu317Gly	135	0	0		110	17	0.154545	NM_022143	A4D0Y9|Q14DU9|Q6ZMI8|Q96A85	Missense_Mutation	SNP	ENST00000249363.3	37	CCDS5799.1	.	.	.	.	.	.	.	.	.	.	T	12.70	2.016570	0.35606	.	.	ENSG00000128594	ENST00000249363	T	0.02656	4.21	4.46	4.46	0.54185	Cysteine-rich flanking region, C-terminal (1);	0.000000	0.64402	D	0.000001	T	0.02767	0.0083	L	0.45137	1.4	0.80722	D	1	P	0.40515	0.719	B	0.29524	0.103	T	0.58567	-0.7614	10	0.39692	T	0.17	.	11.7482	0.51832	0.0:0.0:0.0:1.0	.	317	Q9HBW1	LRRC4_HUMAN	G	317	ENSP00000249363:E317G	ENSP00000249363:E317G	E	-	2	0	LRRC4	127456980	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.854000	0.86942	1.858000	0.53909	0.533000	0.62120	GAG	.	.	none		0.572	LRRC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349170.1	NM_022143		C	127669744	T	C	127669744	3	2	9	1	0	0	0	0	1	0	0	0	9006	1551	54	3	1015	3	LRRC4	7	127669744	Missense_Mutation	SNP	T	TCGA-FA-A86F-01A-11D-A382-10	47383808	127669744	31468919	29	1029											
XRCC2	7516	hgsc.bcm.edu	37	chr7	152346254	152346254	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggcagtatttgattatttCttcagagctttgggatagtc	9	16	10	6	0	2	2	1	1	1	1	3	3	2	3	0	2	1	3	0	2	3	7			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr7:152346254C>A	ENST00000359321.1	-	3	401	c.316G>T	c.(316-318)Gaa>Taa	p.E106*	XRCC2_ENST00000495707.1_5'UTR	NM_005431.1	NP_005422.1	O43543	XRCC2_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 2	106					centrosome organization (GO:0051297)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|in utero embryonic development (GO:0001701)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of neurogenesis (GO:0050769)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|strand invasion (GO:0042148)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|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)			NS(1)|breast(1)|large_intestine(5)|liver(1)|lung(1)|prostate(2)	11		all_hematologic(28;0.0592)|Prostate(32;0.081)	OV - Ovarian serous cystadenocarcinoma(82;0.0423)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0429)		TTGATTATTTCTTCAGAGCTT	0.378								Homologous recombination																													p.E106X		Atlas-SNP	.											.	XRCC2	30	.	0			c.G316T						PASS	.						81	83	82					7																	152346254		2203	4300	6503	SO:0001587	stop_gained	7516	exon3			TTATTTCTTCAGA	Y08837	CCDS5933.1	7q36	2006-05-04			ENSG00000196584	ENSG00000196584			12829	protein-coding gene	gene with protein product	"RAD51-like"	600375				7607692, 10422536	Standard	NM_005431		Approved		uc003wld.3	O43543	OTTHUMG00000151470	ENST00000359321.1:c.316G>T	7.37:g.152346254C>A	ENSP00000352271:p.Glu106*	59	0	0		35	5	0.142857	NM_005431	B2R925	Nonsense_Mutation	SNP	ENST00000359321.1	37	CCDS5933.1	.	.	.	.	.	.	.	.	.	.	C	15.70	2.911472	0.52439	.	.	ENSG00000196584	ENST00000359321	.	.	.	5.11	5.11	0.69529	.	0.363029	0.29522	N	0.011904	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-13.1414	17.5401	0.87845	0.0:1.0:0.0:0.0	.	.	.	.	X	106	.	ENSP00000352271:E106X	E	-	1	0	XRCC2	151977187	1.000000	0.71417	0.763000	0.31416	0.118000	0.20060	4.693000	0.61753	2.367000	0.80283	0.591000	0.81541	GAA	.	.	none		0.378	XRCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322783.1	NM_005431		A	152346254	C	A	152346254	4	1	9	1	0	0	0	0	0	1	0	0	17468	922	32	4	530	4	XRCC2	7	152346254	Nonsense_Mutation	SNP	C	TCGA-FA-A86F-01A-11D-A382-10	24676510	152346254	6792409	30	1030											
VIPR2	7434	hgsc.bcm.edu	37	chr7	158935181	158935181	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcagaagctctgcacatttTgtttcttcctcctgtatttc	6	18	5	12	0	3	1	1	0	2	1	6	1	5	1	2	0	2	4	2	0	2	6			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr7:158935181T>C	ENST00000262178.2	-	2	293	c.108A>G	c.(106-108)acA>acG	p.T36T	VIPR2_ENST00000402066.1_Silent_p.T177T|VIPR2_ENST00000421760.2_Silent_p.T36T	NM_003382.4	NP_003373.2	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2	36					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)		CTGCACATTTTGTTTCTTCCT	0.423																																					p.T36T	Pancreas(154;1876 1931 2329 17914 20079)	Atlas-SNP	.											.	VIPR2	53	.	0			c.A108G						PASS	.						217	202	207					7																	158935181		2203	4298	6501	SO:0001819	synonymous_variant	7434	exon2			ACATTTTGTTTCT	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.108A>G	7.37:g.158935181T>C		264	0	0		190	21	0.110526	NM_003382	Q13053|Q15870|Q53Y09|Q6ZN22|Q9UCW0	Silent	SNP	ENST00000262178.2	37	CCDS5950.1	.	.	.	.	.	.	.	.	.	.	T	14.89	2.671893	0.47781	.	.	ENSG00000106018	ENST00000418475	.	.	.	5.09	-3.04	0.05412	.	.	.	.	.	T	0.49012	0.1532	.	.	.	0.53688	D	0.999975	.	.	.	.	.	.	T	0.45234	-0.9275	4	.	.	.	.	6.3447	0.21343	0.0:0.1642:0.4153:0.4205	.	.	.	.	R	31	.	.	Q	-	2	0	VIPR2	158627942	0.850000	0.29656	0.923000	0.36655	0.980000	0.70556	-0.238000	0.08977	-0.256000	0.09473	0.482000	0.46254	CAA	.	.	none		0.423	VIPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322675.1	NM_003382		C	158935181	T	C	158935181	2	2	9	1	0	0	0	0	0	0	0	1	17185	1799	63	3		3	VIPR2	7	158935181	Silent	SNP	T	TCGA-FA-A86F-01A-11D-A382-10	6588927	158935181	203482	31	1031											
BMP1	649	hgsc.bcm.edu	37	chr8	22052356	22052356	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgatgacatcaagagcacGtccagccgcctctggctcaa	10	7	9	15	2	3	3	2	2	1	1	4	3	4	3	4	1	2	2	4	1	2	0	rs11552824		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr8:22052356G>A	ENST00000306385.5	+	12	2233	c.1563G>A	c.(1561-1563)acG>acA	p.T521T	BMP1_ENST00000354870.5_3'UTR|BMP1_ENST00000306349.8_Silent_p.T521T|BMP1_ENST00000397816.3_Silent_p.T521T|BMP1_ENST00000397814.3_Silent_p.T521T	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1	521	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of cartilage development (GO:0061036)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(3)	30				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)		TCAAGAGCACGTCCAGCCGCC	0.567																																					p.T521T		Atlas-SNP	.											.	BMP1	131	.	0			c.G1563A						PASS	.						84	83	83					8																	22052356		2203	4300	6503	SO:0001819	synonymous_variant	649	exon12			GAGCACGTCCAGC		CCDS6026.1, CCDS34856.1	8p21	2013-02-06	2004-08-09		ENSG00000168487	ENSG00000168487	3.4.24.19	"Bone morphogenetic proteins"	1067	protein-coding gene	gene with protein product	"procollagen C-endopeptidase"	112264	"procollagen C-endopeptidase"	PCOLC		2004778	Standard	NM_006129		Approved		uc003xbg.3	P13497	OTTHUMG00000097761	ENST00000306385.5:c.1563G>A	8.37:g.22052356G>A		84	0	0		70	10	0.142857	NM_001199	A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Silent	SNP	ENST00000306385.5	37	CCDS6026.1																																																																																			.	.	alt		0.567	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132		A	22052356	G	A	22052356	2	1	9	1	0	0	0	0	0	0	0	1	1456	1132	40	1		1	BMP1	8	22052356	Silent	SNP	G	TCGA-FA-A86F-01A-11D-A382-10		22052356	124311666	32	1032											
MYBL1	4603	hgsc.bcm.edu	37	chr8	67492515	67492515	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccatactgtaaaactcactAgtgtgctcgtcaaggctatt	11	13	7	10	1	2	0	2	0	0	0	4	0	3	0	1	1	3	3	1	1	6	5			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr8:67492515A>G	ENST00000522677.3	-	9	1364	c.954T>C	c.(952-954)acT>acC	p.T318T	MYBL1_ENST00000517885.1_Intron|MYBL1_ENST00000524176.2_Silent_p.T318T	NM_001080416.2|NM_001144755.1	NP_001073885.1|NP_001138227.1	P10243	MYBA_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 1	318	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)			AAAACTCACTAGTGTGCTCGT	0.438																																					p.T318T		Atlas-SNP	.											.	MYBL1	73	.	0			c.T954C						PASS	.						72	71	71					8																	67492515		1917	4134	6051	SO:0001819	synonymous_variant	4603	exon9			CTCACTAGTGTGC	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.954T>C	8.37:g.67492515A>G		116	0	0		87	6	0.0689655	NM_001080416	E7EW29|Q495F9	Silent	SNP	ENST00000522677.3	37	CCDS47867.1																																																																																			.	.	none		0.438	MYBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379221.3	XM_034274		G	67492515	A	G	67492515	2	3	9	1	0	0	0	0	0	0	0	1	10018	407	15	3		3	MYBL1	8	67492515	Silent	SNP	A	TCGA-FA-A86F-01A-11D-A382-10	45440159	67492515	78871507	33	1033											
HNF4G	3174	hgsc.bcm.edu	37	chr8	76471075	76471075	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagtaaaaattaagaacaTgaggttccaagtgcagatcg	16	9	9	7	1	0	3	0	1	0	2	3	3	2	3	2	1	2	3	2	1	6	3			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr8:76471075T>C	ENST00000354370.1	+	9	1055	c.785T>C	c.(784-786)aTg>aCg	p.M262T	HNF4G_ENST00000396423.2_Missense_Mutation_p.M299T			Q14541	HNF4G_HUMAN	hepatocyte nuclear factor 4, gamma	262					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)			ATTAAGAACATGAGGTTCCAA	0.448																																					p.M299T		Atlas-SNP	.											.	HNF4G	111	.	0			c.T896C						PASS	.						81	75	77					8																	76471075		2203	4300	6503	SO:0001583	missense	3174	exon8			AGAACATGAGGTT		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.785T>C	8.37:g.76471075T>C	ENSP00000346339:p.Met262Thr	117	0	0		89	9	0.101124	NM_004133	Q7Z2V9|Q9UH81|Q9UIS6	Missense_Mutation	SNP	ENST00000354370.1	37		.	.	.	.	.	.	.	.	.	.	T	21.4	4.150652	0.78001	.	.	ENSG00000164749	ENST00000354370;ENST00000396423	D;D	0.96427	-4.01;-4.01	5.62	5.62	0.85841	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.033448	0.85682	D	0.000000	D	0.96728	0.8932	L	0.42245	1.32	0.80722	D	1	B;P	0.42409	0.121;0.779	B;P	0.57620	0.234;0.824	D	0.97499	1.0059	10	0.87932	D	0	.	15.8221	0.78662	0.0:0.0:0.0:1.0	.	299;262	F1D8Q4;Q14541	.;HNF4G_HUMAN	T	262;299	ENSP00000346339:M262T;ENSP00000379701:M299T	ENSP00000346339:M262T	M	+	2	0	HNF4G	76633630	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	7.991000	0.88244	2.139000	0.66308	0.533000	0.62120	ATG	.	.	none		0.448	HNF4G-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000313914.2	NM_004133		C	76471075	T	C	76471075	3	2	9	1	0	0	0	0	1	0	0	0	7263	1464	51	3	926	3	HNF4G	8	76471075	Missense_Mutation	SNP	T	TCGA-FA-A86F-01A-11D-A382-10	8978560	76471075	69892947	34	1034											
ANKRD30A	91074	hgsc.bcm.edu	37	chr10	37508026	37508026	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaccaataccaggaaaaggAaaataaatactttgaggaca	21	6	7	7	0	0	1	0	1	0	0	0	4	0	4	2	3	2	0	2	3	9	4			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr10:37508026A>T	ENST00000602533.1	+	34	3317	c.3218A>T	c.(3217-3219)gAa>gTa	p.E1073V	ANKRD30A_ENST00000374660.1_Missense_Mutation_p.E1192V|ANKRD30A_ENST00000361713.1_Missense_Mutation_p.E1073V			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1129					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						CAGGAAAAGGAAAATAAATAC	0.318																																					p.E1073V		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.A3218T						PASS	.						77	77	77					10																	37508026		1813	4064	5877	SO:0001583	missense	91074	exon34			AAAAGGAAAATAA	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.3218A>T	10.37:g.37508026A>T	ENSP00000473551:p.Glu1073Val	216	0	0		160	12	0.075	NM_052997	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	37		.	.	.	.	.	.	.	.	.	.	a	9.278	1.047446	0.19827	.	.	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.28454	1.61;1.61	2.81	2.81	0.32909	.	.	.	.	.	T	0.52533	0.1740	M	0.81112	2.525	0.32056	N	0.596317	D	0.69078	0.997	D	0.68483	0.958	T	0.61481	-0.7054	9	0.87932	D	0	.	8.8066	0.34941	1.0:0.0:0.0:0.0	.	1129	Q9BXX3	AN30A_HUMAN	V	1073;1192	ENSP00000354432:E1073V;ENSP00000363792:E1192V	ENSP00000354432:E1073V	E	+	2	0	ANKRD30A	37548032	1.000000	0.71417	0.063000	0.19743	0.004000	0.04260	3.826000	0.55738	1.151000	0.42436	0.381000	0.24937	GAA	.	.	none		0.318	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		T	37508026	A	T	37508026	3	4	9	1	0	0	0	0	1	0	0	0	658	246	9	5	3352	5	ANKRD30A	10	37508026	Missense_Mutation	SNP	A	TCGA-FA-A86F-01A-11D-A382-10		37508026	98026721	35	1035											
PCDH15	65217	hgsc.bcm.edu	37	chr10	55626476	55626476	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgaaacttgaagtaggatcTcctcatattatggaagagca	14	12	9	6	0	2	3	1	2	1	1	3	5	2	5	1	2	2	2	1	2	6	5			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr10:55626476T>G	ENST00000320301.6	-	27	4037	c.3643A>C	c.(3643-3645)Aga>Cga	p.R1215R	PCDH15_ENST00000414778.1_Silent_p.R1220R|PCDH15_ENST00000395433.1_Silent_p.R1193R|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000437009.1_Silent_p.R1144R|PCDH15_ENST00000395432.2_Silent_p.R1178R|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000409834.1_Silent_p.R826R|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395445.1_Silent_p.R1222R|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000373965.2_Silent_p.R1222R|PCDH15_ENST00000395438.1_Silent_p.R1215R|PCDH15_ENST00000361849.3_Silent_p.R1215R|PCDH15_ENST00000395430.1_Silent_p.R1215R	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1215	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)				AAGTAGGATCTCCTCATATTA	0.403										HNSCC(58;0.16)																											p.R1220R		Atlas-SNP	.											.	PCDH15	1715	.	0			c.A3658C						PASS	.						145	127	133					10																	55626476		2203	4300	6503	SO:0001819	synonymous_variant	65217	exon28			AGGATCTCCTCAT	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.3643A>C	10.37:g.55626476T>G		214	0	0		145	6	0.0413793	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	ENST00000320301.6	37	CCDS7248.1																																																																																			.	.	none		0.403	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		G	55626476	T	G	55626476	2	3	9	1	0	0	0	0	0	0	0	1	11520	1559	54	5		5	PCDH15	10	55626476	Silent	SNP	T	TCGA-FA-A86F-01A-11D-A382-10	18118450	55626476	79908271	36	1036											
BICC1	80114	hgsc.bcm.edu	37	chr10	60549152	60549152	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttcagtatcatttaaacagcGttcccgaatgtatggtgcta	11	14	8	8	2	2	0	2	0	0	0	3	1	3	0	1	1	3	4	1	1	6	7	rs192860241	byFrequency	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr10:60549152G>A	ENST00000373886.3	+	7	735	c.731G>A	c.(730-732)cGt>cAt	p.R244H		NM_001080512.1	NP_001073981.1	Q9H694	BICC1_HUMAN	BicC family RNA binding protein 1	244					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						TTTAAACAGCGTTCCCGAATG	0.388													G|||	2	0.000399361	0.0	0.0014	5008	,	,		18107	0.0		0.0	False		,,,				2504	0.001				p.R244H		Atlas-SNP	.											BICC1,colon,carcinoma,+1,1	BICC1	121	1	0			c.G731A						PASS	.						138	132	134					10																	60549152		2203	4300	6503	SO:0001583	missense	80114	exon7			AACAGCGTTCCCG	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.731G>A	10.37:g.60549152G>A	ENSP00000362993:p.Arg244His	221	0	0		155	10	0.0645161	NM_001080512		Missense_Mutation	SNP	ENST00000373886.3	37	CCDS31206.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	26.2	4.712381	0.89112	.	.	ENSG00000122870	ENST00000373886	T	0.32023	1.47	5.66	5.66	0.87406	.	0.048305	0.85682	D	0.000000	T	0.51075	0.1653	L	0.60455	1.87	0.80722	D	1	D	0.76494	0.999	P	0.60117	0.869	T	0.46871	-0.9160	10	0.56958	D	0.05	-7.8917	19.756	0.96291	0.0:0.0:1.0:0.0	.	244	Q9H694	BICC1_HUMAN	H	244	ENSP00000362993:R244H	ENSP00000362993:R244H	R	+	2	0	BICC1	60219158	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.939000	0.70179	2.665000	0.90641	0.655000	0.94253	CGT	G|1.000;A|0.000	0.000	strong		0.388	BICC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048150.2	NM_025044		A	60549152	G	A	60549152	3	1	9	1	0	0	0	0	1	0	0	0	1427	1145	40	1	757	1	BICC1	10	60549152	Missense_Mutation	SNP	G	TCGA-FA-A86F-01A-11D-A382-10	4922676	60549152	74985595	37	1037											
CTNNA3	29119	hgsc.bcm.edu	37	chr10	67829199	67829199	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tttcttgaaatcagcaacttGctcagcaatcttttcttttt	9	19	4	9	0	5	1	2	1	3	0	5	1	5	1	0	0	4	3	0	0	3	7			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr10:67829199G>T	ENST00000433211.2	-	15	2200	c.2026C>A	c.(2026-2028)Caa>Aaa	p.Q676K	CTNNA3_ENST00000373744.4_Missense_Mutation_p.Q676K|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						TCAGCAACTTGCTCAGCAATC	0.378																																					p.Q676K		Atlas-SNP	.											.	CTNNA3	401	.	0			c.C2026A						PASS	.						207	178	188					10																	67829199		2203	4300	6503	SO:0001583	missense	29119	exon15			CAACTTGCTCAGC	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.2026C>A	10.37:g.67829199G>T	ENSP00000389714:p.Gln676Lys	260	0	0		150	16	0.106667	NM_013266		Missense_Mutation	SNP	ENST00000433211.2	37	CCDS7269.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.815033	0.90790	.	.	ENSG00000183230	ENST00000433211;ENST00000373744;ENST00000373735	T;T;T	0.39787	1.06;1.06;1.06	5.29	5.29	0.74685	.	0.000000	0.49916	D	0.000129	T	0.69223	0.3087	M	0.88105	2.93	0.80722	D	1	D	0.53885	0.963	D	0.71414	0.973	T	0.71494	-0.4576	10	0.37606	T	0.19	-13.4866	16.4194	0.83753	0.0:0.0:1.0:0.0	.	676	Q9UI47	CTNA3_HUMAN	K	676;676;15	ENSP00000389714:Q676K;ENSP00000362849:Q676K;ENSP00000362840:Q15K	ENSP00000362840:Q15K	Q	-	1	0	CTNNA3	67499205	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.492000	0.97957	2.483000	0.83821	0.591000	0.81541	CAA	.	.	none		0.378	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048282.2	NM_013266		T	67829199	G	T	67829199	3	4	9	1	0	0	0	0	1	0	0	0	4016	1328	46	4	677	4	CTNNA3	10	67829199	Missense_Mutation	SNP	G	TCGA-FA-A86F-01A-11D-A382-10	7280047	67829199	67705548	38	1038											
TLX1	3195	hgsc.bcm.edu	37	chr10	102896618	102896618	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatctgcagccgtggtctgAcgactcgaccaaaatcacta	12	8	9	12	3	3	1	1	1	2	0	4	4	3	1	2	1	2	1	2	1	4	1	rs567197994	byFrequency	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr10:102896618A>G	ENST00000370196.6	+	3	2983	c.941A>G	c.(940-942)gAc>gGc	p.D314G	RP11-31L23.3_ENST00000411459.1_RNA|TLX1_ENST00000467928.2_3'UTR			P31314	TLX1_HUMAN	T-cell leukemia homeobox 1	314					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)		CCGTGGTCTGACGACTCGACC	0.647			T	"TRB@, TRD@"	T-ALL																																p.D314G		Atlas-SNP	.		Dom	yes		10	10q24	3195	" T-cell leukemia, homeobox 1 (HOX11)"		L	TLX1,NS,carcinoma,-1,1	TLX1	20	1	0			c.A941G						PASS	.						87	71	76					10																	102896618		2203	4300	6503	SO:0001583	missense	3195	exon3			GGTCTGACGACTC	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.941A>G	10.37:g.102896618A>G	ENSP00000359215:p.Asp314Gly	144	0	0		124	18	0.145161	NM_005521	A1L4G3|O75699|Q5VXP2|Q9HCA0|Q9UD59	Missense_Mutation	SNP	ENST00000370196.6	37	CCDS7510.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.333134	0.81801	.	.	ENSG00000107807	ENST00000370196	D	0.90069	-2.61	4.39	4.39	0.52855	.	0.048467	0.85682	D	0.000000	D	0.82458	0.5041	L	0.31664	0.95	0.80722	D	1	P	0.37864	0.61	B	0.34873	0.191	D	0.84604	0.0674	10	0.72032	D	0.01	.	13.8955	0.63768	1.0:0.0:0.0:0.0	.	314	P31314	TLX1_HUMAN	G	314	ENSP00000359215:D314G	ENSP00000359215:D314G	D	+	2	0	TLX1	102886608	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.774000	0.91767	1.750000	0.51863	0.379000	0.24179	GAC	.	.	none		0.647	TLX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051193.3	NM_005521		G	102896618	A	G	102896618	3	3	9	1	0	0	0	0	1	0	0	0	15974	275	10	3	951	3	TLX1	10	102896618	Missense_Mutation	SNP	A	TCGA-FA-A86F-01A-11D-A382-10	35067419	102896618	32638129	39	1039											
C10orf78	119392	hgsc.bcm.edu	37	chr10	105883796	105883796	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttcctaaacaaagattaaacGctgaaaaagccaaattggtg	18	9	7	7	1	0	2	0	1	0	1	1	2	1	2	2	1	3	1	2	1	8	4			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr10:105883796G>A	ENST00000369727.3	+	3	479	c.460G>A	c.(460-462)Gct>Act	p.A154T	SFR1_ENST00000336358.5_Missense_Mutation_p.A216T|SFR1_ENST00000369729.3_Missense_Mutation_p.A141T	NM_001002759.1	NP_001002759.1	Q86XK3	SFR1_HUMAN	SWI5-dependent recombination repair 1	154					double-strand break repair via homologous recombination (GO:0000724)	nucleus (GO:0005634)|Swi5-Sfr1 complex (GO:0032798)											AAGATTAAACGCTGAAAAAGC	0.393																																					p.A154T		Atlas-SNP	.											MEIR5,NS,carcinoma,-2,1	.	.	1	0			c.G460A						PASS	.						44	46	45					10																	105883796		2203	4300	6503	SO:0001583	missense	119392	exon3			TTAAACGCTGAAA	BC020892	CCDS31279.1, CCDS31280.1	10q25.1	2013-10-11	2011-08-01	2011-08-01	ENSG00000156384	ENSG00000156384			29574	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 78", "MEI5 recombination repair protein homolog (S. cerevisiae)"	C10orf78, MEIR5		21252223, 21779174, 20976249	Standard	NM_145247		Approved	MEI5, bA373N18.1, FLJ41960	uc001kxu.3	Q86XK3	OTTHUMG00000019000	ENST00000369727.3:c.460G>A	10.37:g.105883796G>A	ENSP00000358742:p.Ala154Thr	297	0	0		203	24	0.118227	NM_001002759	A8K569|B2RTV8|Q5JT39|Q5JT40|Q8WW47	Missense_Mutation	SNP	ENST00000369727.3	37	CCDS31279.1	.	.	.	.	.	.	.	.	.	.	G	14.40	2.524280	0.44866	.	.	ENSG00000156384	ENST00000369729;ENST00000369727;ENST00000336358	T;T;T	0.45276	0.95;0.94;0.9	5.72	2.67	0.31697	.	0.329743	0.32190	N	0.006447	T	0.18759	0.0450	N	0.08118	0	0.09310	N	0.999995	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.20739	-1.0266	10	0.17369	T	0.5	-5.8542	7.0584	0.25111	0.1524:0.2566:0.591:0.0	.	216;154	Q86XK3-2;Q86XK3	.;SFR1_HUMAN	T	141;154;216	ENSP00000358744:A141T;ENSP00000358742:A154T;ENSP00000338089:A216T	ENSP00000338089:A216T	A	+	1	0	SFR1	105873786	1.000000	0.71417	0.879000	0.34478	0.681000	0.39784	2.676000	0.46883	0.350000	0.24002	0.655000	0.94253	GCT	.	.	none		0.393	SFR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050191.1	NM_145247		A	105883796	G	A	105883796	3	1	9	1	0	0	0	0	1	0	0	0	1619	1087	38	1	470	1	C10orf78	10	105883796	Missense_Mutation	SNP	G	TCGA-FA-A86F-01A-11D-A382-10	2987178	105883796	29650951	40	1040											
SORCS3	22986	hgsc.bcm.edu	37	chr10	106959775	106959775	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agagtttttggccacttcagCctccgctccgaatggcaatt	8	12	9	12	2	1	1	1	0	0	1	3	2	3	1	4	2	1	3	4	2	2	4			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr10:106959775C>T	ENST00000369701.3	+	15	2255	c.2028C>T	c.(2026-2028)agC>agT	p.S676S	SORCS3_ENST00000369699.4_5'UTR	NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	676					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)		GCCACTTCAGCCTCCGCTCCG	0.502																																					p.S676S	NSCLC(116;1497 1690 7108 13108 14106)	Atlas-SNP	.											.	SORCS3	282	.	0			c.C2028T						PASS	.						112	100	104					10																	106959775		2203	4300	6503	SO:0001819	synonymous_variant	22986	exon15			CTTCAGCCTCCGC	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.2028C>T	10.37:g.106959775C>T		91	0	0		81	9	0.111111	NM_014978	Q5VXF9|Q9NQJ2	Silent	SNP	ENST00000369701.3	37	CCDS7558.1																																																																																			.	.	none		0.502	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		T	106959775	C	T	106959775	2	4	9	1	0	0	0	0	0	0	0	1	14947	738	26	2		2	SORCS3	10	106959775	Silent	SNP	C	TCGA-FA-A86F-01A-11D-A382-10	1075979	106959775	28574972	41	1041											
AMBRA1	55626	hgsc.bcm.edu	37	chr11	46419037	46419037	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcccctagggcctgcagcgTcccccctgctgctgccacca	4	7	9	21	1	0	0	0	0	0	0	2	0	2	0	8	1	5	3	8	1	1	1			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr11:46419037T>C	ENST00000458649.2	-	18	4278	c.3860A>G	c.(3859-3861)gAc>gGc	p.D1287G	AMBRA1_ENST00000528950.1_Missense_Mutation_p.D1258G|AMBRA1_ENST00000298834.3_Missense_Mutation_p.D1227G|AMBRA1_ENST00000534300.1_Missense_Mutation_p.D1227G|AMBRA1_ENST00000533727.1_Missense_Mutation_p.D1168G|AMBRA1_ENST00000314845.3_Missense_Mutation_p.D1197G|AMBRA1_ENST00000426438.1_Missense_Mutation_p.D1258G			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	1287					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)		GCCTGCAGCGTCCCCCCTGCT	0.602																																					p.D1290G		Atlas-SNP	.											AMBRA1_ENST00000458649,bladder,carcinoma,0,2	AMBRA1	201	2	0			c.A3869G						scavenged	.						99	92	94					11																	46419037		2202	4299	6501	SO:0001583	missense	55626	exon20			GCAGCGTCCCCCC	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.3860A>G	11.37:g.46419037T>C	ENSP00000415327:p.Asp1287Gly	64	1	0.015625		50	6	0.12	NM_001267782	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Missense_Mutation	SNP	ENST00000458649.2	37		.	.	.	.	.	.	.	.	.	.	T	3.583	-0.085189	0.07097	.	.	ENSG00000110497	ENST00000314845;ENST00000533727;ENST00000534300;ENST00000426438;ENST00000298834;ENST00000458649;ENST00000526545;ENST00000528950	T;T;T;T;T;T;T	0.71103	-0.39;-0.54;-0.13;-0.25;-0.13;-0.25;-0.25	4.22	4.22	0.49857	.	0.672381	0.14331	N	0.326324	T	0.49304	0.1549	N	0.08118	0	0.20196	N	0.999929	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	0.41680	-0.9495	10	0.66056	D	0.02	.	8.3457	0.32272	0.0:0.0907:0.0:0.9093	.	1287;1258;1227;1168;1290;1197	Q9C0C7;Q9C0C7-3;Q9C0C7-2;G3V193;Q9C0C7-5;Q9C0C7-4	AMRA1_HUMAN;.;.;.;.;.	G	1197;1168;1227;1258;1227;1287;245;1258	ENSP00000318313:D1197G;ENSP00000433372:D1168G;ENSP00000431926:D1227G;ENSP00000410899:D1258G;ENSP00000298834:D1227G;ENSP00000415327:D1287G;ENSP00000433945:D1258G	ENSP00000298834:D1227G	D	-	2	0	AMBRA1	46375613	0.641000	0.27251	0.867000	0.34043	0.009000	0.06853	1.775000	0.38584	2.135000	0.66039	0.459000	0.35465	GAC	.	.	none		0.602	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749		C	46419037	T	C	46419037	3	2	9	1	0	0	0	0	1	0	0	0	565	1667	58	3	40	3	AMBRA1	11	46419037	Missense_Mutation	SNP	T	TCGA-FA-A86F-01A-11D-A382-10		46419037	88587479	42	1042											
OR4S1	256148	hgsc.bcm.edu	37	chr11	48328231	48328231	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctggttagctggcttcctgCattccatcctgcagaccctc	5	12	8	16	0	0	1	0	0	0	1	4	1	3	1	5	2	3	5	5	2	1	3			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr11:48328231C>T	ENST00000319988.1	+	1	457	c.457C>T	c.(457-459)Cat>Tat	p.H153Y		NM_001004725.1	NP_001004725.1	Q8NGB4	OR4S1_HUMAN	olfactory receptor, family 4, subfamily S, 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)			endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|skin(3)	21						TGGCTTCCTGCATTCCATCCT	0.567																																					p.H153Y		Atlas-SNP	.											.	OR4S1	52	.	0			c.C457T						PASS	.						119	102	108					11																	48328231		2201	4298	6499	SO:0001583	missense	256148	exon1			TTCCTGCATTCCA	AB065908	CCDS31488.1	11p11.2	2012-08-09			ENSG00000176555	ENSG00000176555		"GPCR / Class A : Olfactory receptors"	14705	protein-coding gene	gene with protein product							Standard	NM_001004725		Approved		uc010rhu.2	Q8NGB4	OTTHUMG00000166578	ENST00000319988.1:c.457C>T	11.37:g.48328231C>T	ENSP00000321447:p.His153Tyr	191	0	0		113	10	0.0884956	NM_001004725	Q6IFB4	Missense_Mutation	SNP	ENST00000319988.1	37	CCDS31488.1	.	.	.	.	.	.	.	.	.	.	C	18.14	3.558614	0.65538	.	.	ENSG00000176555	ENST00000319988	T	0.36699	1.24	5.02	5.02	0.67125	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.60090	0.2242	M	0.66506	2.035	0.09310	N	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.53781	-0.8390	9	0.87932	D	0	.	16.186	0.81950	0.0:1.0:0.0:0.0	.	153	Q8NGB4	OR4S1_HUMAN	Y	153	ENSP00000321447:H153Y	ENSP00000321447:H153Y	H	+	1	0	OR4S1	48284807	0.000000	0.05858	0.759000	0.31340	0.986000	0.74619	-0.017000	0.12590	2.497000	0.84241	0.655000	0.94253	CAT	.	.	none		0.567	OR4S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390556.1	NM_001004725		T	48328231	C	T	48328231	3	4	9	1	0	0	0	0	1	0	0	0	11091	710	25	2	459	2	OR4S1	11	48328231	Missense_Mutation	SNP	C	TCGA-FA-A86F-01A-11D-A382-10	1909194	48328231	86678285	43	1043											
MPEG1	219972	hgsc.bcm.edu	37	chr11	58978519	58978519	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tggtcactatgacagtattgGtggcagcctgactcatgagg	9	11	13	8	0	2	3	2	3	0	0	2	3	2	3	1	4	1	2	1	4	2	3	rs376216311		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr11:58978519G>A	ENST00000361050.3	-	1	1905	c.1820C>T	c.(1819-1821)aCc>aTc	p.T607I		NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	607						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)				GACAGTATTGGTGGCAGCCTG	0.582																																					p.T607I		Atlas-SNP	.											.	MPEG1	72	.	0			c.C1820T						PASS	.						108	114	112					11																	58978519		1948	4124	6072	SO:0001583	missense	219972	exon1			GTATTGGTGGCAG	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.1820C>T	11.37:g.58978519G>A	ENSP00000354335:p.Thr607Ile	119	0	0		126	15	0.119048	NM_001039396	Q2M1T6|Q8TEF8	Missense_Mutation	SNP	ENST00000361050.3	37	CCDS41650.1	.	.	.	.	.	.	.	.	.	.	G	11.17	1.559489	0.27827	.	.	ENSG00000197629	ENST00000361050	T	0.25085	1.82	5.69	5.69	0.88448	.	0.113776	0.64402	D	0.000019	T	0.47619	0.1455	M	0.72894	2.215	0.43300	D	0.995291	D	0.65815	0.995	P	0.59424	0.857	T	0.40608	-0.9554	10	0.54805	T	0.06	-19.9386	16.7224	0.85413	0.0:0.0:1.0:0.0	.	607	Q2M385	MPEG1_HUMAN	I	607	ENSP00000354335:T607I	ENSP00000354335:T607I	T	-	2	0	MPEG1	58735095	1.000000	0.71417	1.000000	0.80357	0.398000	0.30690	3.083000	0.50136	2.682000	0.91365	0.655000	0.94253	ACC	.	.	alt		0.582	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396		A	58978519	G	A	58978519	3	1	9	1	0	0	0	0	1	0	0	0	9732	1261	44	2	334	2	MPEG1	11	58978519	Missense_Mutation	SNP	G	TCGA-FA-A86F-01A-11D-A382-10	10650288	58978519	76027997	44	1044			1	12		3	3	1026	N	G_C	3.675578e-06
MPEG1	219972	hgsc.bcm.edu	37	chr11	58979509	58979509	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaaaaggaacccctccaatgCtctgcaccctggagttggtt	11	9	9	12	0	1	0	0	0	1	0	2	2	2	2	4	3	3	4	4	3	4	2			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr11:58979509C>T	ENST00000361050.3	-	1	915	c.830G>A	c.(829-831)aGc>aAc	p.S277N	RN7SL42P_ENST00000579786.1_RNA	NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	277	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)				CCCTCCAATGCTCTGCACCCT	0.542																																					p.S277N		Atlas-SNP	.											.	MPEG1	72	.	0			c.G830A						PASS	.						29	26	27					11																	58979509		1851	4082	5933	SO:0001583	missense	219972	exon1			CCAATGCTCTGCA	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.830G>A	11.37:g.58979509C>T	ENSP00000354335:p.Ser277Asn	119	0	0		117	11	0.0940171	NM_001039396	Q2M1T6|Q8TEF8	Missense_Mutation	SNP	ENST00000361050.3	37	CCDS41650.1	.	.	.	.	.	.	.	.	.	.	C	20.0	3.930767	0.73327	.	.	ENSG00000197629	ENST00000361050	D	0.84589	-1.87	5.38	5.38	0.77491	Membrane attack complex component/perforin (MACPF) domain (3);	0.000000	0.85682	D	0.000000	D	0.91297	0.7256	M	0.67953	2.075	0.50313	D	0.999864	D	0.89917	1.0	D	0.91635	0.999	D	0.91418	0.5156	10	0.54805	T	0.06	-33.9117	16.1079	0.81237	0.0:1.0:0.0:0.0	.	277	Q2M385	MPEG1_HUMAN	N	277	ENSP00000354335:S277N	ENSP00000354335:S277N	S	-	2	0	MPEG1	58736085	1.000000	0.71417	0.677000	0.29947	0.973000	0.67179	7.032000	0.76498	2.541000	0.85698	0.650000	0.86243	AGC	.	.	none		0.542	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396		T	58979509	C	T	58979509	3	4	9	1	0	0	0	0	1	0	0	0	9732	797	28	2	1324	2	MPEG1	11	58979509	Missense_Mutation	SNP	C	TCGA-FA-A86F-01A-11D-A382-10	990	58979509	76027007	45	1045			1	12		3	3	1026	N	G_C	3.675578e-06
MPEG1	219972	hgsc.bcm.edu	37	chr11	58979544	58979544	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttggttcggtttgagaggtaGctcttggtgaggacattctg	6	15	15	5	1	2	2	0	2	2	1	3	4	2	3	0	5	1	4	0	5	1	6			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr11:58979544G>A	ENST00000361050.3	-	1	880	c.795C>T	c.(793-795)agC>agT	p.S265S	RN7SL42P_ENST00000579786.1_RNA	NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	265	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)				TTGAGAGGTAGCTCTTGGTGA	0.532																																					p.S265S		Atlas-SNP	.											.	MPEG1	72	.	0			c.C795T						PASS	.						38	36	37					11																	58979544		1901	4108	6009	SO:0001819	synonymous_variant	219972	exon1			GAGGTAGCTCTTG	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.795C>T	11.37:g.58979544G>A		128	0	0		133	12	0.0902256	NM_001039396	Q2M1T6|Q8TEF8	Silent	SNP	ENST00000361050.3	37	CCDS41650.1																																																																																			.	.	none		0.532	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396		A	58979544	G	A	58979544	2	1	9	1	0	0	0	0	0	0	0	1	9732	962	34	2		2	MPEG1	11	58979544	Silent	SNP	G	TCGA-FA-A86F-01A-11D-A382-10	35	58979544	76026972	46	1046			1	12		3	3	1026	N	G_C	3.675578e-06
NPAT	4863	hgsc.bcm.edu	37	chr11	108044437	108044437	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagctgttttaaaggcctttTtctgtatgctggtacttatt	7	19	8	7	0	1	0	0	0	1	0	1	0	1	0	1	2	3	5	1	2	5	8			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr11:108044437T>A	ENST00000278612.8	-	13	1379	c.1274A>T	c.(1273-1275)aAa>aTa	p.K425I	NPAT_ENST00000610253.1_5'UTR	NM_002519.2	NP_002510.2	Q14207	NPAT_HUMAN	nuclear protein, ataxia-telangiectasia locus	425					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)		AAAGGCCTTTTTCTGTATGCT	0.378																																					p.K425I		Atlas-SNP	.											.	NPAT	124	.	0			c.A1274T						PASS	.						151	141	144					11																	108044437		1861	4089	5950	SO:0001583	missense	4863	exon13			GCCTTTTTCTGTA	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.1274A>T	11.37:g.108044437T>A	ENSP00000278612:p.Lys425Ile	543	0	0		391	34	0.0869565	NM_002519	A8K1V5|A8K6M2|Q13632|Q14967|Q16580|Q86W55|Q8IWE9	Missense_Mutation	SNP	ENST00000278612.8	37	CCDS41710.1	.	.	.	.	.	.	.	.	.	.	T	14.14	2.447588	0.43429	.	.	ENSG00000149308	ENST00000278612	T	0.05925	3.37	5.54	5.54	0.83059	.	0.119077	0.56097	D	0.000025	T	0.23688	0.0573	M	0.69823	2.125	0.42227	D	0.991876	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.00386	-1.1772	10	0.56958	D	0.05	-24.8189	13.7058	0.62639	0.0:0.0:0.0:1.0	.	425;425	B9EG70;Q14207	.;NPAT_HUMAN	I	425	ENSP00000278612:K425I	ENSP00000278612:K425I	K	-	2	0	NPAT	107549647	1.000000	0.71417	1.000000	0.80357	0.089000	0.18198	2.613000	0.46351	2.231000	0.72958	0.455000	0.32223	AAA	.	.	none		0.378	NPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389506.2	NM_002519		A	108044437	T	A	108044437	3	1	9	1	0	0	0	0	1	0	0	0	10575	1841	64	5	3033	5	NPAT	11	108044437	Missense_Mutation	SNP	T	TCGA-FA-A86F-01A-11D-A382-10	49064893	108044437	26962079	47	1047											
ATN1	1822	hgsc.bcm.edu	37	chr12	7045906	7045906	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagcaacagcagcagcagcaGcagcagcagcagcagcagca	15	0	12	14	0	0	0	0	0	0	0	0	0	0	0	0	0	13	12	0	0	1	0	rs377147612		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr12:7045906G>A	ENST00000356654.4	+	5	1713	c.1476G>A	c.(1474-1476)caG>caA	p.Q492Q	ATN1_ENST00000396684.2_Silent_p.Q492Q	NM_001007026.1	NP_001007027.1	P54259	ATN1_HUMAN	atrophin 1	492	Poly-Gln.				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						agcagcagcagcagcagcagc	0.647																																					p.Q492Q		Atlas-SNP	.											.	ATN1	95	.	0			c.G1476A						PASS	.						43	53	49					12																	7045906		2188	4263	6451	SO:0001819	synonymous_variant	1822	exon5			GCAGCAGCAGCAG	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.1476G>A	12.37:g.7045906G>A		58	0	0		46	5	0.108696	NM_001007026	Q99495|Q99621|Q9UEK7	Silent	SNP	ENST00000356654.4	37	CCDS31734.1																																																																																			.	.	none		0.647	ATN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401948.2	NM_001940		A	7045906	G	A	7045906	2	1	9	1	0	0	0	0	0	0	0	1	1111	962	34	2		2	ATN1	12	7045906	Silent	SNP	G	TCGA-FA-A86F-01A-11D-A382-10		7045906	126805989	48	1048											
PIK3C2G	5288	hgsc.bcm.edu	37	chr12	18491371	18491371	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatctacaggaaaacgtgtaTaatattattgaagaagttaa	18	13	7	3	1	1	2	0	1	1	1	1	3	1	3	0	1	2	2	0	1	11	8			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr12:18491371T>C	ENST00000266497.5	+	8	1322	c.1284T>C	c.(1282-1284)taT>taC	p.Y428Y	PIK3C2G_ENST00000433979.1_Silent_p.Y428Y|PIK3C2G_ENST00000538779.1_Silent_p.Y428Y|PIK3C2G_ENST00000535651.1_Silent_p.Y428Y			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	428					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)				AAAACGTGTATAATATTATTG	0.308																																					p.Y428Y		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.T1284C						PASS	.						81	83	82					12																	18491371		1824	4063	5887	SO:0001819	synonymous_variant	5288	exon9			CGTGTATAATATT	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.1284T>C	12.37:g.18491371T>C		171	0	0		124	7	0.0564516	NM_004570	A1L3U0	Silent	SNP	ENST00000266497.5	37	CCDS44839.1																																																																																			.	.	none		0.308	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570		C	18491371	T	C	18491371	2	2	9	1	0	0	0	0	0	0	0	1	11920	1413	49	3		3	PIK3C2G	12	18491371	Silent	SNP	T	TCGA-FA-A86F-01A-11D-A382-10	11445465	18491371	115360524	49	1049											
LYRM5	144363	hgsc.bcm.edu	37	chr12	25357062	25357062	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agactatccaaaaggagcagActattttaaaaagcgtttga	17	10	8	6	1	0	3	0	1	0	2	1	4	1	4	1	1	2	2	1	1	7	5	rs534127550	byFrequency	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr12:25357062A>C	ENST00000381356.4	+	3	248	c.89A>C	c.(88-90)gAc>gCc	p.D30A	LYRM5_ENST00000556402.1_3'UTR|LYRM5_ENST00000556351.1_Missense_Mutation_p.D28A|LYRM5_ENST00000555711.1_Missense_Mutation_p.R36S|LYRM5_ENST00000557540.2_Missense_Mutation_p.D28A|LYRM5_ENST00000556885.1_Missense_Mutation_p.D28A|LYRM5_ENST00000554266.1_3'UTR|LYRM5_ENST00000553788.1_Intron|LYRM5_ENST00000556927.1_Missense_Mutation_p.D28A	NM_001001660.2	NP_001001660.2	Q6IPR1	LYRM5_HUMAN	LYR motif containing 5	30						mitochondrion (GO:0005739)				large_intestine(3)	3	all_cancers(2;4.75e-35)|all_epithelial(2;1.91e-37)|all_lung(3;1.07e-23)|Lung NSC(3;5.49e-23)|Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.0016)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;2.21e-21)|Epithelial(3;8.04e-19)|all cancers(3;2.26e-16)|STAD - Stomach adenocarcinoma(2;0.00138)			AAAGGAGCAGACTATTTTAAA	0.303																																					p.D30A		Atlas-SNP	.											.	LYRM5	10	.	0			c.A89C						PASS	.						28	25	26					12																	25357062		1786	4064	5850	SO:0001583	missense	144363	exon3			GAGCAGACTATTT	AK057730	CCDS53764.1	12p12.1	2006-09-19				ENSG00000205707		"LYR motif containing"	27052	protein-coding gene	gene with protein product							Standard	NM_001001660		Approved		uc001rgn.3	Q6IPR1		ENST00000381356.4:c.89A>C	12.37:g.25357062A>C	ENSP00000370761:p.Asp30Ala	260	0	0		194	26	0.134021	NM_001001660	J3KPI7	Missense_Mutation	SNP	ENST00000381356.4	37	CCDS53764.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	8.182|8.182	0.794003|0.794003	0.16327|0.16327	.|.	.|.	ENSG00000205707|ENSG00000205707	ENST00000557540;ENST00000381356;ENST00000556885;ENST00000556351;ENST00000556927;ENST00000556198|ENST00000555711	T;T;T;T;T|.	0.68331|.	-0.32;-0.32;-0.32;-0.32;-0.32|.	5.88|5.88	5.88|5.88	0.94601|0.94601	.|.	0.179966|.	0.64402|.	D|.	0.000015|.	T|T	0.61451|0.61451	0.2348|0.2348	.|.	.|.	.|.	0.48135|0.48135	D|D	0.999595|0.999595	B;B|.	0.17268|.	0.001;0.021|.	B;B|.	0.18561|.	0.009;0.022|.	T|T	0.60954|0.60954	-0.7160|-0.7160	9|4	0.19590|.	T|.	0.45|.	.|.	9.8919|9.8919	0.41296|0.41296	0.9246:0.0:0.0753:0.0|0.9246:0.0:0.0753:0.0	.|.	28;28|.	Q6IPR1;G3V521|.	LYRM5_HUMAN;.|.	A|S	28;30;28;28;28;28|36	ENSP00000450584:D28A;ENSP00000370761:D30A;ENSP00000451494:D28A;ENSP00000452146:D28A;ENSP00000450443:D28A|.	ENSP00000370761:D30A|.	D|R	+|+	2|3	0|2	LYRM5|LYRM5	25248329|25248329	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	4.399000|4.399000	0.59703|0.59703	2.239000|2.239000	0.73571|0.73571	0.533000|0.533000	0.62120|0.62120	GAC|AGA	.	.	none		0.303	LYRM5-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001001660		C	25357062	A	C	25357062	3	2	9	1	0	0	0	0	1	0	0	0	9131	275	10	5	95	5	LYRM5	12	25357062	Missense_Mutation	SNP	A	TCGA-FA-A86F-01A-11D-A382-10	6865691	25357062	108494833	50	1050											
MLL2	8085	hgsc.bcm.edu	37	chr12	49436376	49436377	+	Frame_Shift_Ins	INS	-	-	G																															acggggactggcagaggcctINSgggtaggagtccattgggct																										TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr12:49436376_49436377insG	ENST00000301067.7	-	27	5833_5834	c.5834_5835insC	c.(5833-5835)ccafs	p.P1945fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1945					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)										GGCAGAGGCCTGGGTAGGAGTC	0.559																																					p.P1945fs		Atlas-Indel	.											.	MLL2	1173	.	0			c.5835_5836insC						PASS	.																																			SO:0001589	frameshift_variant	8085	exon27			.	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.5835dupC	12.37:g.49436379_49436379dupG	ENSP00000301067:p.Pro1945fs	87	0	0		66	11	0.166667	NM_003482	O14687	Frame_Shift_Ins	INS	ENST00000301067.7	37	CCDS44873.1																																																																																			.	.	none		0.559	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			G	49436377	-	G	49436376	7	5	9	1	0	1	1	0	0	0	0	0	9630	1567	55	0	10890	0	MLL2	12	49436376	Frame_Shift_Ins	INS	-	TCGA-FA-A86F-01A-11D-A382-10	24079314	49436376	84415519	51	1051											
BTG1	694	hgsc.bcm.edu	37	chr12	92539203	92539203	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctctggctgaaggtctgcaGctgtcgctcgctcgtgagcc	4	10	14	13	3	2	2	0	2	2	0	5	2	2	2	1	2	3	6	1	2	1	0	rs369374957		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr12:92539203G>A	ENST00000256015.3	-	1	470	c.109C>T	c.(109-111)Ctg>Ttg	p.L37L	C12orf79_ENST00000551563.2_5'Flank|RP11-796E2.4_ENST00000501008.2_RNA|C12orf79_ENST00000546975.1_5'Flank|C12orf79_ENST00000549802.1_5'Flank|RP11-796E2.4_ENST00000499685.2_RNA	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	37					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)	p.L37L(1)		haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				AAGGTCTGCAGCTGTCGCTCG	0.677			T	MYC	BCLL																																p.L37L		Atlas-SNP	.		Dom	yes		12	12q22	694	"B-cell translocation gene 1, anti-proliferative"		L	BTG1,NS,lymphoid_neoplasm,0,3	BTG1	30	3	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C109T						PASS	.						38	41	40					12																	92539203		2203	4300	6503	SO:0001819	synonymous_variant	694	exon1			TCTGCAGCTGTCG		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.109C>T	12.37:g.92539203G>A		187	0	0		181	8	0.0441989	NM_001731	P31607	Silent	SNP	ENST00000256015.3	37	CCDS9043.1																																																																																			.	.	alt		0.677	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1			A	92539203	G	A	92539203	2	1	9	1	0	0	0	0	0	0	0	1	1555	962	34	2		2	BTG1	12	92539203	Silent	SNP	G	TCGA-FA-A86F-01A-11D-A382-10	43102827	92539203	41312692	52	1052											
NAA25	80018	hgsc.bcm.edu	37	chr12	112516526	112516526	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acattgtttttgagaggtttTcatcctgtgccgatatagac	9	16	9	7	1	1	2	1	1	0	2	2	4	2	2	2	1	1	2	2	1	2	7			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr12:112516526T>C	ENST00000261745.4	-	6	745	c.497A>G	c.(496-498)gAa>gGa	p.E166G		NM_024953.3	NP_079229.2	Q14CX7	NAA25_HUMAN	N(alpha)-acetyltransferase 25, NatB auxiliary subunit	166						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						TGAGAGGTTTTCATCCTGTGC	0.373																																					p.E166G		Atlas-SNP	.											.	NAA25	105	.	0			c.A497G						PASS	.						150	136	141					12																	112516526		2203	4300	6503	SO:0001583	missense	80018	exon6			AGGTTTTCATCCT	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.497A>G	12.37:g.112516526T>C	ENSP00000261745:p.Glu166Gly	219	0	0		153	10	0.0653595	NM_024953	A0JLU7|Q6MZH1|Q7Z4N6|Q9H911	Missense_Mutation	SNP	ENST00000261745.4	37	CCDS9159.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.7|25.7	4.661054|4.661054	0.88154|0.88154	.|.	.|.	ENSG00000111300|ENSG00000111300	ENST00000261745|ENST00000547133	T|.	0.26223|.	1.75|.	6.05|6.05	6.05|6.05	0.98169|0.98169	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.55609|.	0.1931|.	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.69307|.	0.963;0.963|.	T|.	0.51694|.	-0.8673|.	10|.	0.44086|.	T|.	0.13|.	-17.6823|-17.6823	16.5932|16.5932	0.84781|0.84781	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	166;166|.	A8K8X0;Q14CX7|.	.;NAA25_HUMAN|.	G|W	166|127	ENSP00000261745:E166G|.	ENSP00000261745:E166G|.	E|X	-|-	2|3	0|0	NAA25|NAA25	111000909|111000909	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.454000|7.454000	0.80714|0.80714	2.320000|2.320000	0.78422|0.78422	0.528000|0.528000	0.53228|0.53228	GAA|TGA	.	.	none		0.373	NAA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405205.1	NM_024953		C	112516526	T	C	112516526	3	2	9	1	0	0	0	0	1	0	0	0	10130	1783	62	3	2497	3	NAA25	12	112516526	Missense_Mutation	SNP	T	TCGA-FA-A86F-01A-11D-A382-10	19977323	112516526	21335369	53	1053											
NBEA	26960	hgsc.bcm.edu	37	chr13	35729913	35729913	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaattcttcatttttcagatCttgacagaacaagtatgtac	14	15	5	7	0	4	3	2	1	2	2	4	3	4	3	0	0	2	2	0	0	5	7			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr13:35729913C>A	ENST00000400445.3	+	19	2982	c.2448C>A	c.(2446-2448)atC>atA	p.I816I	NBEA_ENST00000379939.2_Silent_p.I816I|NBEA_ENST00000310336.4_Silent_p.I816I|NBEA_ENST00000540320.1_Silent_p.I816I	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	816					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)		TTTTTCAGATCTTGACAGAAC	0.323																																					p.I816I		Atlas-SNP	.											.	NBEA	340	.	0			c.C2448A						PASS	.						92	86	88					13																	35729913		1846	4092	5938	SO:0001819	synonymous_variant	26960	exon19			TCAGATCTTGACA	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.2448C>A	13.37:g.35729913C>A		118	0	0		64	9	0.140625	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Silent	SNP	ENST00000400445.3	37	CCDS45026.1																																																																																			.	.	none		0.323	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		A	35729913	C	A	35729913	2	1	9	1	0	0	0	0	0	0	0	1	10196	903	32	4		4	NBEA	13	35729913	Silent	SNP	C	TCGA-FA-A86F-01A-11D-A382-10		35729913	79439965	54	1054											
SMAD9	4093	hgsc.bcm.edu	37	chr13	37453460	37453460	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtaagggttaatgcacacttCtttctgcttggagccaaatg	10	13	10	8	0	2	0	0	0	2	0	2	1	2	1	1	2	3	4	1	2	3	5			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr13:37453460C>T	ENST00000399275.2	-	1	506	c.367G>A	c.(367-369)Gaa>Aaa	p.E123K	SMAD9_ENST00000350148.5_Missense_Mutation_p.E123K|SMAD9_ENST00000483941.1_5'Flank|SMAD9_ENST00000379826.4_Missense_Mutation_p.E123K			O15198	SMAD9_HUMAN	SMAD family member 9	123	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.				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)		ATGCACACTTCTTTCTGCTTG	0.557																																					p.E123K		Atlas-SNP	.											.	SMAD9	91	.	0			c.G367A						PASS	.						38	41	40					13																	37453460		2202	4300	6502	SO:0001583	missense	4093	exon2			ACACTTCTTTCTG		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.367G>A	13.37:g.37453460C>T	ENSP00000382216:p.Glu123Lys	81	0	0		52	6	0.115385	NM_005905	A2A2Y6|O14989|Q5TBA1	Missense_Mutation	SNP	ENST00000399275.2	37	CCDS45032.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.715825	0.89112	.	.	ENSG00000120693	ENST00000399275;ENST00000350148;ENST00000379826	T;T;T	0.77098	-1.07;-1.07;-1.07	5.47	5.47	0.80525	MAD homology, MH1 (3);MAD homology 1, Dwarfin-type (2);	0.092522	0.64402	D	0.000001	D	0.87481	0.6188	M	0.85859	2.78	0.80722	D	1	B;D	0.53745	0.408;0.962	B;P	0.56216	0.138;0.794	D	0.89288	0.3617	10	0.72032	D	0.01	.	18.3033	0.90171	0.0:1.0:0.0:0.0	.	123;123	O15198-2;O15198	.;SMAD9_HUMAN	K	123	ENSP00000382216:E123K;ENSP00000239885:E123K;ENSP00000369154:E123K	ENSP00000239885:E123K	E	-	1	0	SMAD9	36351460	1.000000	0.71417	0.999000	0.59377	0.979000	0.70002	7.762000	0.85270	2.565000	0.86533	0.514000	0.50259	GAA	.	.	none		0.557	SMAD9-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044525.2	NM_005905		T	37453460	C	T	37453460	3	4	9	1	0	0	0	0	1	0	0	0	14779	922	32	2	1060	2	SMAD9	13	37453460	Missense_Mutation	SNP	C	TCGA-FA-A86F-01A-11D-A382-10	1723547	37453460	77716418	55	1055											
PCDH17	27253	hgsc.bcm.edu	37	chr13	58209024	58209024	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagaggaacgccatgaacGtcatgaacgtggtgagcagc	13	5	15	8	3	1	4	1	3	0	1	1	6	1	5	1	3	5	1	1	3	3	0			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr13:58209024G>A	ENST00000377918.3	+	1	2370	c.2344G>A	c.(2344-2346)Gtc>Atc	p.V782I		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	782					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)		CGCCATGAACGTCATGAACGT	0.597																																					p.V782I	Melanoma(72;952 1291 1619 12849 33676)	Atlas-SNP	.											.	PCDH17	304	.	0			c.G2344A						PASS	.						106	99	102					13																	58209024		2203	4300	6503	SO:0001583	missense	27253	exon1			ATGAACGTCATGA	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.2344G>A	13.37:g.58209024G>A	ENSP00000367151:p.Val782Ile	58	0	0		41	5	0.121951	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Missense_Mutation	SNP	ENST00000377918.3	37	CCDS31986.1	.	.	.	.	.	.	.	.	.	.	G	12.57	1.976644	0.34848	.	.	ENSG00000118946	ENST00000377918	T	0.53640	0.61	5.21	5.21	0.72293	.	0.055010	0.64402	D	0.000001	T	0.40272	0.1110	L	0.36672	1.1	0.46131	D	0.998881	B;B	0.23442	0.085;0.051	B;B	0.18263	0.021;0.011	T	0.15292	-1.0442	9	.	.	.	.	18.9482	0.92630	0.0:0.0:1.0:0.0	.	782;782	O14917-2;O14917	.;PCD17_HUMAN	I	782	ENSP00000367151:V782I	.	V	+	1	0	PCDH17	57107025	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.375000	0.79646	2.708000	0.92522	0.467000	0.42956	GTC	.	.	none		0.597	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		A	58209024	G	A	58209024	3	1	9	1	0	0	0	0	1	0	0	0	11521	1145	40	1	2346	1	PCDH17	13	58209024	Missense_Mutation	SNP	G	TCGA-FA-A86F-01A-11D-A382-10	20755564	58209024	56960854	56	1056											
F7	2155	hgsc.bcm.edu	37	chr13	113773002	113773002	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctggagctcatggtcctcAacgtgccccggctgatgacc	6	8	11	16	2	2	2	2	2	0	0	3	3	3	3	5	3	3	2	5	3	1	0			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr13:113773002A>G	ENST00000375581.3	+	9	1116	c.1081A>G	c.(1081-1083)Aac>Gac	p.N361D	F7_ENST00000346342.3_Missense_Mutation_p.N339D|F7_ENST00000541084.1_Missense_Mutation_p.N292D	NM_000131.4	NP_000122.1	P08709	FA7_HUMAN	coagulation factor VII (serum prothrombin conversion accelerator)	361	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|cellular protein metabolic process (GO:0044267)|circadian rhythm (GO:0007623)|organ regeneration (GO:0031100)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of blood coagulation (GO:0030194)|positive regulation of cell migration (GO:0030335)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of platelet-derived growth factor receptor signaling pathway (GO:0010641)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein kinase B signaling (GO:0051897)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|response to estrogen (GO:0043627)|response to growth hormone (GO:0060416)|response to vitamin K (GO:0032571)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			large_intestine(4)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16	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;0.0364)|all_epithelial(44;0.0393)|Lung NSC(25;0.128)|Breast(118;0.188)	all cancers(43;0.0737)|Epithelial(84;0.213)|BRCA - Breast invasive adenocarcinoma(86;0.218)		Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Menadione(DB00170)	CATGGTCCTCAACGTGCCCCG	0.632																																					p.N361D		Atlas-SNP	.											.	F7	49	.	0			c.A1081G						PASS	.						33	32	32					13																	113773002		2202	4298	6500	SO:0001583	missense	2155	exon9			GTCCTCAACGTGC		CCDS9528.1, CCDS9529.1, CCDS73602.1	13q34	2014-02-03			ENSG00000057593	ENSG00000057593	3.4.21.21		3544	protein-coding gene	gene with protein product	"eptacog alfa", "FVII coagulation protein", "factor VII"	613878				3264725, 2511201	Standard	NM_000131		Approved		uc001vsv.4	P08709	OTTHUMG00000017373	ENST00000375581.3:c.1081A>G	13.37:g.113773002A>G	ENSP00000364731:p.Asn361Asp	122	0	0		100	22	0.22	NM_000131	B0YJC8|Q14339|Q5JVF1|Q5JVF2|Q9UD52|Q9UD53|Q9UD54	Missense_Mutation	SNP	ENST00000375581.3	37	CCDS9528.1	.	.	.	.	.	.	.	.	.	.	A	0.753	-0.772186	0.02951	.	.	ENSG00000057593	ENST00000346342;ENST00000541084;ENST00000375581	D;D;D	0.88741	-2.42;-2.42;-2.42	4.17	-1.31	0.09230	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.595590	0.03454	N	0.211073	T	0.76521	0.3999	N	0.04820	-0.15	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	0.63305	-0.6667	10	0.24483	T	0.36	.	8.5642	0.33530	0.2473:0.4789:0.2738:0.0	.	292;339;361	F5H8B0;P08709-2;P08709	.;.;FA7_HUMAN	D	339;292;361	ENSP00000329546:N339D;ENSP00000442051:N292D;ENSP00000364731:N361D	ENSP00000329546:N339D	N	+	1	0	F7	112821003	0.003000	0.15002	0.001000	0.08648	0.008000	0.06430	0.407000	0.21049	-0.234000	0.09782	0.383000	0.25322	AAC	.	.	none		0.632	F7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045838.4	NM_000131		G	113773002	A	G	113773002	3	3	9	1	0	0	0	0	1	0	0	0	5351	130	5	3	1115	3	F7	13	113773002	Missense_Mutation	SNP	A	TCGA-FA-A86F-01A-11D-A382-10	55563978	113773002	1396876	57	1057											
NPAS3	64067	hgsc.bcm.edu	37	chr14	34270175	34270175	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtcaggaccgttcggcggcGcagtgagcgcagctagcctg	6	7	16	12	5	1	1	1	1	0	0	2	2	1	2	2	3	3	4	2	3	1	2			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr14:34270175G>A	ENST00000356141.4	+	12	2662	c.2662G>A	c.(2662-2664)Gca>Aca	p.A888T	NPAS3_ENST00000551492.1_Missense_Mutation_p.A893T|NPAS3_ENST00000357798.5_Missense_Mutation_p.A875T|NPAS3_ENST00000548645.1_Missense_Mutation_p.A858T|NPAS3_ENST00000346562.2_Missense_Mutation_p.A856T			Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3	888					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)		GTTCGGCGGCGCAGTGAGCGC	0.652																																					p.A888T		Atlas-SNP	.											.	NPAS3	266	.	0			c.G2662A						PASS	.						31	20	24					14																	34270175		2201	4289	6490	SO:0001583	missense	64067	exon12			GGCGGCGCAGTGA	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.2662G>A	14.37:g.34270175G>A	ENSP00000348460:p.Ala888Thr	65	0	0		55	7	0.127273	NM_001164749	Q86US6|Q86US7|Q8IXF2|Q9BY81|Q9H323|Q9Y4L8	Missense_Mutation	SNP	ENST00000356141.4	37	CCDS53891.1	.	.	.	.	.	.	.	.	.	.	G	6.253	0.414758	0.11870	.	.	ENSG00000151322	ENST00000551634;ENST00000551492;ENST00000346562;ENST00000548645;ENST00000356141;ENST00000357798	T;T;T;T;T;T	0.08458	3.35;3.22;3.23;3.23;3.22;3.09	5.68	3.85	0.44370	.	0.169134	0.52532	N	0.000071	T	0.06508	0.0167	N	0.19112	0.55	0.80722	D	1	B;B;B;B	0.15719	0.014;0.008;0.014;0.014	B;B;B;B	0.11329	0.006;0.003;0.006;0.006	T	0.23119	-1.0197	10	0.59425	D	0.04	.	11.8985	0.52669	0.1404:0.0:0.8595:0.0	.	858;888;856;875	Q8IXF0-2;Q8IXF0;Q8IXF0-4;Q8IXF0-3	.;NPAS3_HUMAN;.;.	T	862;893;856;858;888;875	ENSP00000448373:A862T;ENSP00000450392:A893T;ENSP00000319610:A856T;ENSP00000448916:A858T;ENSP00000348460:A888T;ENSP00000350446:A875T	ENSP00000319610:A856T	A	+	1	0	NPAS3	33339926	1.000000	0.71417	0.869000	0.34112	0.006000	0.05464	5.397000	0.66302	1.398000	0.46701	-0.300000	0.09419	GCA	.	.	none		0.652	NPAS3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276645.1			A	34270175	G	A	34270175	3	1	9	1	0	0	0	0	1	0	0	0	10573	1087	38	1	2763	1	NPAS3	14	34270175	Missense_Mutation	SNP	G	TCGA-FA-A86F-01A-11D-A382-10		34270175	73079365	58	1058											
CTSH	1512	hgsc.bcm.edu	37	chr15	79221796	79221797	+	Frame_Shift_Ins	INS	-	-	T																															cttcacccatgatccccttgINSttgtacaggatatactcgaa																										TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr15:79221796_79221797insT	ENST00000220166.5	-	8	696_697	c.587_588insA	c.(586-588)aacfs	p.N196fs	CTSH_ENST00000534533.1_5'UTR	NM_004390.3	NP_004381.2	P09668	CATH_HUMAN	cathepsin H	196					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						TGATCCCCTTGTTGTACAGGAT	0.579																																					p.N196fs		Atlas-Indel	.											.	CTSH	23	.	0			c.588_589insA						PASS	.																																			SO:0001589	frameshift_variant	1512	exon8			.	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.588dupA	15.37:g.79221798_79221798dupT	ENSP00000220166:p.Asn196fs	226	0	0		129	12	0.0930233	NM_004390	B2RBK0|Q96NY6|Q9BUM7	Frame_Shift_Ins	INS	ENST00000220166.5	37	CCDS10308.1																																																																																			.	.	none		0.579	CTSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291370.1	NM_004390		T	79221797	-	T	79221796	7	5	9	1	0	1	1	0	0	0	0	0	4038	1368	48	0	439	0	CTSH	15	79221796	Frame_Shift_Ins	INS	-	TCGA-FA-A86F-01A-11D-A382-10		79221796	23309596	59	1059											
ITPRIPL2	162073	hgsc.bcm.edu	37	chr16	19126812	19126812	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctccctgagggcctgcgtgcGgaggcactgtggggtgtgaa	5	8	18	10	2	0	2	0	2	0	0	1	3	1	3	2	5	2	1	2	5	1	0			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr16:19126812G>A	ENST00000381440.3	+	1	1559	c.1029G>A	c.(1027-1029)gcG>gcA	p.A343A	CTD-2349B8.1_ENST00000564808.2_Intron	NM_001034841.3	NP_001030013.1	Q3MIP1	IPIL2_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein-like 2	343						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						GCCTGCGTGCGGAGGCACTGT	0.667																																					p.A343A		Atlas-SNP	.											.	ITPRIPL2	40	.	0			c.G1029A						PASS	.						32	36	35					16																	19126812		2197	4300	6497	SO:0001819	synonymous_variant	162073	exon1			GCGTGCGGAGGCA		CCDS32395.1	16p12.3	2011-04-28	2011-04-28		ENSG00000205730	ENSG00000205730			27257	protein-coding gene	gene with protein product			"inositol 1,4,5-triphosphate receptor interacting protein-like 2"				Standard	NM_001034841		Approved	FLJ22994, MGC126798, MGC126800, LOC162073	uc002dfu.4	Q3MIP1		ENST00000381440.3:c.1029G>A	16.37:g.19126812G>A		54	0	0		44	4	0.0909091	NM_001034841		Silent	SNP	ENST00000381440.3	37	CCDS32395.1																																																																																			.	.	none		0.667	ITPRIPL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435827.3	NM_001034841		A	19126812	G	A	19126812	2	1	9	1	0	0	0	0	0	0	0	1	7934	1103	39	1		1	ITPRIPL2	16	19126812	Silent	SNP	G	TCGA-FA-A86F-01A-11D-A382-10		19126812	71227941	60	1060											
CDH11	1009	hgsc.bcm.edu	37	chr16	64981740	64981740	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtattctcgtgttgatgaaGtcatcgacatccacgctgtt	8	15	9	9	3	2	2	1	2	1	0	5	3	3	2	1	0	0	4	1	0	2	4			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr16:64981740G>T	ENST00000268603.4	-	13	2772	c.2157C>A	c.(2155-2157)gaC>gaA	p.D719E	CDH11_ENST00000394156.3_3'UTR|CDH11_ENST00000566827.1_Missense_Mutation_p.D593E	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	719					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)		TGTTGATGAAGTCATCGACAT	0.527			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																											p.D719E		Atlas-SNP	.		Dom	yes		16	16q22.1	1009	"cadherin 11, type 2, OB-cadherin (osteoblast)"		M	.	CDH11	260	.	0			c.C2157A						PASS	.						120	110	114					16																	64981740		2203	4300	6503	SO:0001583	missense	1009	exon13			GATGAAGTCATCG	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.2157C>A	16.37:g.64981740G>T	ENSP00000268603:p.Asp719Glu	190	0	0		162	15	0.0925926	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Missense_Mutation	SNP	ENST00000268603.4	37	CCDS10803.1	.	.	.	.	.	.	.	.	.	.	G	7.665	0.685808	0.14973	.	.	ENSG00000140937	ENST00000268603;ENST00000538390	T	0.76709	-1.04	6.02	2.6	0.31112	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	T	0.54679	0.1873	N	0.05012	-0.13	0.48135	D	0.999594	B	0.13594	0.008	B	0.24006	0.05	T	0.39961	-0.9588	10	0.18276	T	0.48	.	9.6097	0.39654	0.3055:0.0:0.6945:0.0	.	719	P55287	CAD11_HUMAN	E	719;702	ENSP00000268603:D719E	ENSP00000268603:D719E	D	-	3	2	CDH11	63539241	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.451000	0.52964	0.890000	0.36211	0.655000	0.94253	GAC	.	.	none		0.527	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664		T	64981740	G	T	64981740	3	4	9	1	0	0	0	0	1	0	0	0	3099	1020	36	4	237	4	CDH11	16	64981740	Missense_Mutation	SNP	G	TCGA-FA-A86F-01A-11D-A382-10	45854928	64981740	25373013	61	1061											
CDH3	1001	hgsc.bcm.edu	37	chr16	68716273	68716273	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgacggtcactgatctggaCgcccccaactcaccagcgtg	8	7	10	16	3	3	2	2	2	1	0	3	3	3	3	3	2	2	0	3	2	1	0			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr16:68716273C>T	ENST00000264012.4	+	9	1609	c.1065C>T	c.(1063-1065)gaC>gaT	p.D355D	CDH3_ENST00000581171.1_Silent_p.D300D|CDH3_ENST00000429102.2_Silent_p.D355D	NM_001793.4	NP_001784.2	P22223	CADH3_HUMAN	cadherin 3, type 1, P-cadherin (placental)	355	Cadherin 3. {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)		CTGATCTGGACGCCCCCAACT	0.592																																					p.D355D		Atlas-SNP	.											.	CDH3	68	.	2	Unknown(2)	breast(2)	c.C1065T						PASS	.						102	73	83					16																	68716273		2198	4300	6498	SO:0001819	synonymous_variant	1001	exon9			TCTGGACGCCCCC	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.1065C>T	16.37:g.68716273C>T		76	0	0		63	8	0.126984	NM_001793	B2R6F4|Q05DI6	Silent	SNP	ENST00000264012.4	37	CCDS10868.1																																																																																			.	.	none		0.592	CDH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268896.2	NM_001793		T	68716273	C	T	68716273	2	4	9	1	0	0	0	0	0	0	0	1	3113	535	19	1		1	CDH3	16	68716273	Silent	SNP	C	TCGA-FA-A86F-01A-11D-A382-10	3734533	68716273	21638480	62	1062											
KLHDC4	54758	hgsc.bcm.edu	37	chr16	87748161	87748161	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tgagtgccgtgtgcccttgtCcacgtctttcttaactctct	4	16	8	13	2	3	1	0	1	3	0	5	1	4	1	3	0	3	0	3	0	1	3			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr16:87748161C>T	ENST00000270583.5	-	8	836	c.778G>A	c.(778-780)Gac>Aac	p.D260N	KLHDC4_ENST00000566349.1_5'UTR|KLHDC4_ENST00000353170.5_Missense_Mutation_p.D203N|KLHDC4_ENST00000347925.5_Missense_Mutation_p.D229N	NM_017566.3	NP_060036.2	Q8TBB5	KLDC4_HUMAN	kelch domain containing 4	260										breast(2)|endometrium(3)|lung(10)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(2)	21				BRCA - Breast invasive adenocarcinoma(80;0.0283)		GTGCCCTTGTCCACGTCTTTC	0.567																																					p.D260N		Atlas-SNP	.											.	KLHDC4	45	.	0			c.G778A						PASS	.						231	191	204					16																	87748161		2198	4300	6498	SO:0001583	missense	54758	exon8			CCTTGTCCACGTC	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.778G>A	16.37:g.87748161C>T	ENSP00000270583:p.Asp260Asn	169	0	0		138	7	0.0507246	NM_017566	D3DUN3|D3DUN4|D3DUN5|Q96F29|Q9BVN3	Missense_Mutation	SNP	ENST00000270583.5	37	CCDS10963.1	.	.	.	.	.	.	.	.	.	.	C	19.36	3.812535	0.70912	.	.	ENSG00000104731	ENST00000270583;ENST00000316853;ENST00000347925;ENST00000353170	T;T;T	0.67698	-0.28;-0.28;-0.28	5.21	5.21	0.72293	Kelch-type beta propeller (1);	0.093608	0.64402	D	0.000001	D	0.84293	0.5440	M	0.89095	3.005	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.999;0.992	D;D;D;D	0.78314	0.991;0.991;0.971;0.925	D	0.85106	0.0960	10	0.38643	T	0.18	-18.2028	17.7521	0.88438	0.0:1.0:0.0:0.0	.	79;203;229;260	Q9UF94;Q8TBB5-2;Q8TBB5-3;Q8TBB5	.;.;.;KLDC4_HUMAN	N	260;79;229;203	ENSP00000270583:D260N;ENSP00000325717:D229N;ENSP00000262530:D203N	ENSP00000270583:D260N	D	-	1	0	KLHDC4	86305662	1.000000	0.71417	1.000000	0.80357	0.066000	0.16364	7.012000	0.76366	2.427000	0.82271	0.561000	0.74099	GAC	.	.	none		0.567	KLHDC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269109.2	NM_017566		T	87748161	C	T	87748161	3	4	9	1	0	0	0	0	1	0	0	0	8367	855	30	2	800	2	KLHDC4	16	87748161	Missense_Mutation	SNP	C	TCGA-FA-A86F-01A-11D-A382-10	19031888	87748161	2606592	63	1063											
PYY	5697	hgsc.bcm.edu	37	chr17	42030694	42030694	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaccaggttgaggtagtggCgcagggaggcgtagtagcgg	8	7	20	6	3	0	2	0	2	0	0	0	3	0	3	1	6	1	5	1	6	3	4			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr17:42030694C>T	ENST00000360085.2	-	5	698	c.158G>A	c.(157-159)cGc>cAc	p.R53H	PYY_ENST00000592796.1_Missense_Mutation_p.R53H	NM_004160.4	NP_004151	P10082	PYY_HUMAN	peptide YY	53					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|digestion (GO:0007586)|eating behavior (GO:0042755)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)			endometrium(1)|ovary(1)	2		Breast(137;0.00314)|Prostate(33;0.0724)		BRCA - Breast invasive adenocarcinoma(366;0.12)		GAGGTAGTGGCGCAGGGAGGC	0.726																																					p.R53H		Atlas-SNP	.											.	PYY	11	.	0			c.G158A						PASS	.						17	19	19					17																	42030694		2200	4297	6497	SO:0001583	missense	5697	exon5			TAGTGGCGCAGGG		CCDS32662.1	17q21.1	2013-02-28				ENSG00000131096		"Endogenous ligands"	9748	protein-coding gene	gene with protein product	"prepro-PYY"	600781				7782089	Standard	NM_004160		Approved	PYY1	uc002ieq.3	P10082		ENST00000360085.2:c.158G>A	17.37:g.42030694C>T	ENSP00000353198:p.Arg53His	188	0	0		178	13	0.0730337	NM_004160	Q5U5Q6|Q6FGH8	Missense_Mutation	SNP	ENST00000360085.2	37	CCDS32662.1	.	.	.	.	.	.	.	.	.	.	.	35	5.542943	0.96474	.	.	ENSG00000131096	ENST00000360085	T	0.52983	0.64	4.64	4.64	0.57946	Pancreatic hormone-like, conserved site (1);	.	.	.	.	T	0.67804	0.2932	.	.	.	0.58432	D	0.999999	D	0.89917	1.0	D	0.81914	0.995	T	0.72673	-0.4222	8	0.87932	D	0	-1.6458	12.9887	0.58606	0.0:1.0:0.0:0.0	.	53	P10082	PYY_HUMAN	H	53	ENSP00000353198:R53H	ENSP00000353198:R53H	R	-	2	0	PYY	39386220	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.097000	0.64542	2.109000	0.64355	0.549000	0.68633	CGC	.	.	none		0.726	PYY-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000457658.1	NM_004160		T	42030694	C	T	42030694	3	4	9	1	0	0	0	0	1	0	0	0	12883	768	27	1	147	1	PYY	17	42030694	Missense_Mutation	SNP	C	TCGA-FA-A86F-01A-11D-A382-10		42030694	39164516	64	1064											
DLX4	1748	hgsc.bcm.edu	37	chr17	48051195	48051195	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccccacccctcccctcccTctgggatctacccaaggcag	6	7	6	22	0	2	0	0	0	2	0	5	1	5	1	8	2	1	1	8	2	2	1			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr17:48051195T>C	ENST00000240306.3	+	3	906	c.611T>C	c.(610-612)cTc>cCc	p.L204P	DLX4_ENST00000411890.2_Missense_Mutation_p.L132P	NM_138281.2	NP_612138.1	Q92988	DLX4_HUMAN	distal-less homeobox 4	204					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						CTCCCCTCCCTCTGGGATCTA	0.592																																					p.L204P		Atlas-SNP	.											.	DLX4	25	.	0			c.T611C						PASS	.						57	61	60					17																	48051195		2203	4300	6503	SO:0001583	missense	1748	exon3			CCTCCCTCTGGGA		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.611T>C	17.37:g.48051195T>C	ENSP00000240306:p.Leu204Pro	92	0	0		70	11	0.157143	NM_138281	D3DTX2|D3DTX3|O60480|Q13265|Q6PJK0|Q9HBE0	Missense_Mutation	SNP	ENST00000240306.3	37	CCDS11555.1	.	.	.	.	.	.	.	.	.	.	T	11.42	1.633462	0.29068	.	.	ENSG00000108813	ENST00000240306;ENST00000411890	D;D	0.93189	-2.97;-3.18	5.14	2.91	0.33838	.	.	.	.	.	D	0.94318	0.8174	L	0.60455	1.87	0.32491	N	0.540234	D;B	0.60160	0.987;0.001	P;B	0.62649	0.905;0.0	D	0.92773	0.6234	9	0.54805	T	0.06	-12.0893	8.3009	0.32014	0.0:0.1652:0.0:0.8348	.	132;204	Q92988-2;Q92988	.;DLX4_HUMAN	P	204;132	ENSP00000240306:L204P;ENSP00000410622:L132P	ENSP00000240306:L204P	L	+	2	0	DLX4	45406194	0.443000	0.25641	0.650000	0.29550	0.931000	0.56810	3.111000	0.50360	0.406000	0.25560	-0.411000	0.06167	CTC	.	.	none		0.592	DLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366214.1			C	48051195	T	C	48051195	3	2	9	1	0	0	0	0	1	0	0	0	4575	1551	54	3	688	3	DLX4	17	48051195	Missense_Mutation	SNP	T	TCGA-FA-A86F-01A-11D-A382-10	6020501	48051195	33144015	65	1065											
MYOM1	8736	hgsc.bcm.edu	37	chr18	3089200	3089200	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcaatagtacattacattcaCcagtcacttcccagctcaaa	14	11	3	13	0	4	0	4	0	0	0	5	0	5	0	2	0	3	2	2	0	5	5			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr18:3089200C>A	ENST00000356443.4	-	29	4442	c.4109G>T	c.(4108-4110)gGt>gTt	p.G1370V	MYOM1_ENST00000261606.7_Missense_Mutation_p.G1274V|MYOM1_ENST00000400569.3_Missense_Mutation_p.G1370V	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1370	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						ATTACATTCACCAGTCACTTC	0.308																																					p.G1370V		Atlas-SNP	.											.	MYOM1	192	.	0			c.G4109T						PASS	.						80	74	76					18																	3089200		1820	4083	5903	SO:0001583	missense	8736	exon29			CATTCACCAGTCA	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.4109G>T	18.37:g.3089200C>A	ENSP00000348821:p.Gly1370Val	492	0	0		316	52	0.164557	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	C	12.58	1.980320	0.34942	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.70399	-0.48;-0.48;-0.48	5.98	4.19	0.49359	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.528555	0.22207	N	0.063145	T	0.48187	0.1486	N	0.08118	0	0.53688	D	0.999972	B;B	0.25235	0.099;0.121	B;B	0.31191	0.076;0.125	T	0.33777	-0.9855	10	0.33141	T	0.24	.	5.6992	0.17873	0.0:0.5235:0.2513:0.2252	.	1274;1370	P52179-2;P52179	.;MYOM1_HUMAN	V	1370;1370;1274	ENSP00000348821:G1370V;ENSP00000383413:G1370V;ENSP00000261606:G1274V	ENSP00000261606:G1274V	G	-	2	0	MYOM1	3079200	0.943000	0.32029	0.999000	0.59377	0.996000	0.88848	1.552000	0.36244	0.851000	0.35264	0.591000	0.81541	GGT	.	.	none		0.308	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		A	3089200	C	A	3089200	3	1	9	1	0	0	0	0	1	0	0	0	10100	507	18	4	988	4	MYOM1	18	3089200	Missense_Mutation	SNP	C	TCGA-FA-A86F-01A-11D-A382-10		3089200	74988048	66	1066											
PTBP1	5725	hgsc.bcm.edu	37	chr19	804886	804886	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccttcaccaagaacaaccagTtccaggccctgctgcagtat	11	8	7	15	0	1	1	1	0	0	1	2	1	2	1	5	1	4	4	5	1	4	3			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr19:804886T>C	ENST00000349038.4	+	7	737	c.664T>C	c.(664-666)Ttc>Ctc	p.F222L	PTBP1_ENST00000350092.4_Intron|PTBP1_ENST00000394601.4_Missense_Mutation_p.F222L|PTBP1_ENST00000356948.6_Missense_Mutation_p.F222L|MIR4745_ENST00000577608.1_RNA	NM_031991.3	NP_114368.1	P26599	PTBP1_HUMAN	polypyrimidine tract binding protein 1	222	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)		GAACAACCAGTTCCAGGCCCT	0.662																																					p.F222L		Atlas-SNP	.											PTBP1,larynx,carcinoma,-2,1	PTBP1	43	1	0			c.T664C						scavenged	.						100	90	94					19																	804886		2203	4300	6503	SO:0001583	missense	5725	exon7			AACCAGTTCCAGG	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.664T>C	19.37:g.804886T>C	ENSP00000014112:p.Phe222Leu	60	0	0		63	3	0.047619	NM_031990	Q9BUQ0	Missense_Mutation	SNP	ENST00000349038.4	37	CCDS32859.1	.	.	.	.	.	.	.	.	.	.	T	27.7	4.851512	0.91355	.	.	ENSG00000011304	ENST00000356948;ENST00000394601;ENST00000349038	T;T;T	0.50548	0.74;0.77;1.06	5.09	5.09	0.68999	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.207707	0.51477	D	0.000096	T	0.63838	0.2545	L	0.53561	1.675	0.80722	D	1	D;D;P	0.89917	1.0;0.964;0.923	D;P;P	0.83275	0.996;0.884;0.856	T	0.67241	-0.5720	10	0.87932	D	0	-30.2985	14.045	0.64700	0.0:0.0:0.0:1.0	.	222;222;222	P26599;P26599-2;Q9BUQ0	PTBP1_HUMAN;.;.	L	222	ENSP00000349428:F222L;ENSP00000408096:F222L;ENSP00000014112:F222L	ENSP00000014112:F222L	F	+	1	0	PTBP1	755886	1.000000	0.71417	1.000000	0.80357	0.790000	0.44656	7.904000	0.87408	1.915000	0.55452	0.460000	0.39030	TTC	.	.	none		0.662	PTBP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457605.1			C	804886	T	C	804886	3	2	9	1	0	0	0	0	1	0	0	0	12737	1725	60	3	690	3	PTBP1	19	804886	Missense_Mutation	SNP	T	TCGA-FA-A86F-01A-11D-A382-10		804886	58324097	67	1067											
TSHZ3	57616	hgsc.bcm.edu	37	chr19	31768074	31768074	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctcctccagagtggccccGtcaatgtcagacttctcgga	7	9	10	15	2	3	2	2	0	1	2	6	3	5	3	5	2	0	0	5	2	1	1			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr19:31768074G>A	ENST00000240587.4	-	2	2952	c.2625C>T	c.(2623-2625)gaC>gaT	p.D875D		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	875					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)					GAGTGGCCCCGTCAATGTCAG	0.572																																					p.D875D		Atlas-SNP	.											.	TSHZ3	549	.	0			c.C2625T						PASS	.						70	65	66					19																	31768074		2203	4300	6503	SO:0001819	synonymous_variant	57616	exon2			GGCCCCGTCAATG	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.2625C>T	19.37:g.31768074G>A		125	0	0		90	19	0.211111	NM_020856	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																			.	.	none		0.572	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		A	31768074	G	A	31768074	2	1	9	1	0	0	0	0	0	0	0	1	16640	1136	40	1		1	TSHZ3	19	31768074	Silent	SNP	G	TCGA-FA-A86F-01A-11D-A382-10	30963188	31768074	27360909	68	1068											
KCNN4	3783	hgsc.bcm.edu	37	chr19	44278489	44278489	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	attgagagcgccgatgctgcGgtaggaagcgttgagcagga	10	7	17	7	4	0	2	0	2	0	1	0	6	0	4	1	3	5	4	1	3	2	3			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr19:44278489G>C	ENST00000262888.3	-	3	933	c.538C>G	c.(538-540)Cgc>Ggc	p.R180G		NM_002250.2	NP_002241.1	O15554	KCNN4_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4	180					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)	CCGATGCTGCGGTAGGAAGCG	0.662											OREG0025535	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R180G		Atlas-SNP	.											.	KCNN4	37	.	0			c.C538G						PASS	.						27	25	26					19																	44278489		2196	4300	6496	SO:0001583	missense	3783	exon3			TGCTGCGGTAGGA	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.538C>G	19.37:g.44278489G>C	ENSP00000262888:p.Arg180Gly	119	0	0	922	98	11	0.112245	NM_002250	Q53XR4	Missense_Mutation	SNP	ENST00000262888.3	37	CCDS12630.1	.	.	.	.	.	.	.	.	.	.	G	18.46	3.628785	0.67015	.	.	ENSG00000104783	ENST00000262888;ENST00000407385	D	0.99896	-7.6	4.38	3.33	0.38152	.	0.053759	0.64402	D	0.000002	D	0.99789	0.9911	M	0.74467	2.265	0.50039	D	0.999843	D;D	0.89917	0.98;1.0	P;D	0.87578	0.67;0.998	D	0.98041	1.0382	10	0.87932	D	0	-21.927	5.9886	0.19448	0.1001:0.0:0.7138:0.1861	.	74;180	D1MQ10;O15554	.;KCNN4_HUMAN	G	180;48	ENSP00000262888:R180G	ENSP00000262888:R180G	R	-	1	0	KCNN4	48970329	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	2.516000	0.45520	0.972000	0.38314	-0.300000	0.09419	CGC	.	.	none		0.662	KCNN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463598.1	NM_002250		C	44278489	G	C	44278489	3	2	9	1	0	0	0	0	1	0	0	0	8090	1116	39	4	769	4	KCNN4	19	44278489	Missense_Mutation	SNP	G	TCGA-FA-A86F-01A-11D-A382-10	12510415	44278489	14850494	69	1069											
ZNF880	400713	hgsc.bcm.edu	37	chr19	52877609	52877609	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggagcaaaggagagatccccGgaatctgcagagtgaagtga	14	5	15	7	1	1	4	0	2	1	2	2	8	2	7	2	3	2	2	2	3	3	0			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr19:52877609G>A	ENST00000422689.2	+	3	212	c.197G>A	c.(196-198)cGg>cAg	p.R66Q	ZNF880_ENST00000597976.1_Missense_Mutation_p.R66Q|ZNF880_ENST00000344085.5_Missense_Mutation_p.R66Q|ZNF880_ENST00000424032.2_Missense_Mutation_p.R66Q|ZNF880_ENST00000600321.1_Missense_Mutation_p.R66Q	NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	66	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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						AGAGATCCCCGGAATCTGCAG	0.458																																					p.R66Q		Atlas-SNP	.											.	ZNF880	45	.	0			c.G197A						PASS	.						79	71	73					19																	52877609		692	1591	2283	SO:0001583	missense	400713	exon3			ATCCCCGGAATCT	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.197G>A	19.37:g.52877609G>A	ENSP00000406318:p.Arg66Gln	118	0	0		138	13	0.0942029	NM_001145434	B4DNA6	Missense_Mutation	SNP	ENST00000422689.2	37	CCDS46164.1	.	.	.	.	.	.	.	.	.	.	G	4.337	0.061871	0.08339	.	.	ENSG00000221923	ENST00000424032;ENST00000344085;ENST00000422689	T;T;T	0.06294	5.42;5.46;3.32	1.13	0.00405	0.14057	Krueppel-associated box (2);	.	.	.	.	T	0.03305	0.0096	N	0.12527	0.23	0.09310	N	1	B	0.16603	0.018	B	0.01281	0.0	T	0.42015	-0.9476	9	0.54805	T	0.06	.	3.5828	0.07959	0.2752:0.0:0.7248:0.0	.	66	Q6PDB4	ZN880_HUMAN	Q	66	ENSP00000414470:R66Q;ENSP00000343625:R66Q;ENSP00000406318:R66Q	ENSP00000343625:R66Q	R	+	2	0	ZNF880	57569421	0.002000	0.14202	0.002000	0.10522	0.006000	0.05464	0.073000	0.14640	0.044000	0.15775	0.448000	0.29417	CGG	.	.	none		0.458	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434		A	52877609	G	A	52877609	3	1	9	1	0	0	0	0	1	0	0	0	18212	1116	39	1	207	1	ZNF880	19	52877609	Missense_Mutation	SNP	G	TCGA-FA-A86F-01A-11D-A382-10	8599120	52877609	6251374	70	1070											
PRPF31	26121	hgsc.bcm.edu	37	chr19	54632434	54632434	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctcctcttccccctagatCgaggaggacgcctaccagga	8	7	10	16	2	1	1	0	0	1	1	4	5	3	4	6	3	1	0	6	3	2	3			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr19:54632434C>A	ENST00000321030.4	+	12	1498	c.1149C>A	c.(1147-1149)atC>atA	p.I383I	PRPF31_ENST00000391755.1_Silent_p.I377I|PRPF31_ENST00000419967.1_Silent_p.I383I	NM_015629.3	NP_056444.3	Q8WWY3	PRP31_HUMAN	pre-mRNA processing factor 31	383					mRNA splicing, via spliceosome (GO:0000398)|spliceosomal tri-snRNP complex assembly (GO:0000244)	Cajal body (GO:0015030)|MLL1 complex (GO:0071339)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|U2-type spliceosomal complex (GO:0005684)|U4 snRNP (GO:0005687)|U4/U6 x U5 tri-snRNP complex (GO:0046540)|U4atac snRNP (GO:0005690)	poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)|snRNP binding (GO:0070990)			breast(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(2)|urinary_tract(3)	12	all_cancers(19;0.00681)|all_epithelial(19;0.00362)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					CCCCCTAGATCGAGGAGGACG	0.682																																					p.I383I		Atlas-SNP	.											.	PRPF31	48	.	0			c.C1149A						PASS	.						21	20	21					19																	54632434		2176	4259	6435	SO:0001819	synonymous_variant	26121	exon12			CTAGATCGAGGAG	AL050369	CCDS12879.1	19q13.4	2013-07-16	2013-06-10		ENSG00000105618	ENSG00000105618			15446	protein-coding gene	gene with protein product		606419	"PRP31 pre-mRNA processing factor 31 homolog (yeast)", "PRP31 pre-mRNA processing factor 31 homolog (S. cerevisiae)"	RP11		11545739	Standard	NM_015629		Approved	NY-BR-99, PRP31, hPrp31, SNRNP61	uc002qdh.2	Q8WWY3	OTTHUMG00000066040	ENST00000321030.4:c.1149C>A	19.37:g.54632434C>A		53	0	0		51	8	0.156863	NM_015629	Q17RB4|Q8N7F9|Q9H271|Q9Y439	Silent	SNP	ENST00000321030.4	37	CCDS12879.1																																																																																			.	.	none		0.682	PRPF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141417.2			A	54632434	C	A	54632434	2	1	9	1	0	0	0	0	0	0	0	1	12578	874	31	4		4	PRPF31	19	54632434	Silent	SNP	C	TCGA-FA-A86F-01A-11D-A382-10	1754825	54632434	4496549	71	1071											
E2F1	1869	hgsc.bcm.edu	37	chr20	32267687	32267690	+	Frame_Shift_Del	DEL	CCGT	CCGT	-																															cccagttcaggtcgacgacaCcgtcagccgagtggctcagc																										TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	CCGT	CCGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr20:32267687_32267690delCCGT	ENST00000343380.5	-	3	582_585	c.443_446delACGG	c.(442-447)gacggtfs	p.DG148fs		NM_005225.2	NP_005216.1	Q01094	E2F1_HUMAN	E2F transcription factor 1	148	Interaction with BIRC2/c-IAP1.				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						GTCGACGACACCGTCAGCCGAGTG	0.593																																					p.148_149del		Atlas-Indel	.											.	E2F1	41	.	0			c.444_447del						PASS	.																																			SO:0001589	frameshift_variant	1869	exon3			.		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.443_446delACGG	20.37:g.32267687_32267690delCCGT	ENSP00000345571:p.Asp148fs	125	0	0		91	12	0.131868	NM_005225	Q13143|Q92768	Frame_Shift_Del	DEL	ENST00000343380.5	37	CCDS13224.1																																																																																			.	.	none		0.593	E2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078731.2			-	32267690	CCGT	-	32267687	7	5	9	1	0	1	0	1	0	0	0	0	4868	507	18	0	887	0	E2F1	20	32267687	Frame_Shift_Del	DEL	CCGT	TCGA-FA-A86F-01A-11D-A382-10		32267687	30757833	72	1072											
ITCH	83737	hgsc.bcm.edu	37	chr20	32996580	32996580	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caacacaaacagtcccaagtGgaagcaaccccttacagtgt	15	6	7	13	0	0	0	0	0	0	0	1	1	1	1	3	1	5	1	3	1	6	1			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr20:32996580G>A	ENST00000262650.6	+	4	330	c.194G>A	c.(193-195)tGg>tAg	p.W65*	ITCH_ENST00000535650.1_Intron|ITCH_ENST00000374864.4_Nonsense_Mutation_p.W65*			Q96J02	ITCH_HUMAN	itchy E3 ubiquitin protein ligase	65	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				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						AGTCCCAAGTGGAAGCAACCC	0.353																																					p.W65X		Atlas-SNP	.											.	ITCH	73	.	0			c.G194A						PASS	.						127	117	120					20																	32996580		2203	4300	6503	SO:0001587	stop_gained	83737	exon4			CCAAGTGGAAGCA	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.194G>A	20.37:g.32996580G>A	ENSP00000262650:p.Trp65*	151	0	0		105	10	0.0952381	NM_001257137	A6NEW4|B4E234|E1P5P3|F5H217|O43584|Q5QP37|Q5TEL0|Q96F66|Q9BY75|Q9H451|Q9H4U5	Nonsense_Mutation	SNP	ENST00000262650.6	37	CCDS58768.1	.	.	.	.	.	.	.	.	.	.	G	36	5.743412	0.96873	.	.	ENSG00000078747	ENST00000374864;ENST00000262650	.	.	.	5.24	5.24	0.73138	.	0.177655	0.53938	D	0.000057	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.4283	0.90617	0.0:0.0:1.0:0.0	.	.	.	.	X	65	.	ENSP00000262650:W65X	W	+	2	0	ITCH	32460241	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.385000	0.97223	2.464000	0.83262	0.655000	0.94253	TGG	.	.	none		0.353	ITCH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078783.2			A	32996580	G	A	32996580	4	1	9	1	0	0	0	0	0	1	0	0	7877	1357	47	2	200	2	ITCH	20	32996580	Nonsense_Mutation	SNP	G	TCGA-FA-A86F-01A-11D-A382-10	728893	32996580	30028940	73	1073											
KRTAP10-12	386685	hgsc.bcm.edu	37	chr21	46117576	46117576	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gtcaacagtcctgctgtgtgCccgtctgctgcaagcccatc	6	10	10	15	1	2	0	1	0	1	0	4	0	3	0	3	0	6	3	3	0	2	0			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr21:46117576C>T	ENST00000400365.3	+	1	490	c.460C>T	c.(460-462)Ccc>Tcc	p.P154S	TSPEAR_ENST00000323084.4_Intron	NM_198699.1	NP_941972.1	P60413	KR10C_HUMAN	keratin associated protein 10-12	154	19 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(8)	9						CTGCTGTGTGCCCGTCTGCTG	0.617																																					p.P154S		Atlas-SNP	.											KRTAP10-12,rectum,carcinoma,0,2	KRTAP10-12	21	2	0			c.C460T						scavenged	.						177	182	180					21																	46117576		2203	4300	6503	SO:0001583	missense	386685	exon1			TGTGTGCCCGTCT	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.460C>T	21.37:g.46117576C>T	ENSP00000383216:p.Pro154Ser	88	0	0		64	4	0.0625	NM_198699	B2RPA3	Missense_Mutation	SNP	ENST00000400365.3	37	CCDS42967.1	.	.	.	.	.	.	.	.	.	.	c	2.310	-0.358108	0.05138	.	.	ENSG00000189169	ENST00000400365;ENST00000452870	T	0.00648	5.99	3.7	1.73	0.24493	.	.	.	.	.	T	0.00815	0.0027	L	0.49778	1.585	0.09310	N	1	B	0.24963	0.115	B	0.25884	0.064	T	0.44360	-0.9333	9	0.15952	T	0.53	.	10.0177	0.42024	0.3626:0.6374:0.0:0.0	.	154	P60413	KR10C_HUMAN	S	154;62	ENSP00000383216:P154S	ENSP00000383216:P154S	P	+	1	0	KRTAP10-12	44942004	0.001000	0.12720	0.001000	0.08648	0.016000	0.09150	0.087000	0.14958	0.117000	0.18138	0.305000	0.20034	CCC	.	.	none		0.617	KRTAP10-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128032.1	NM_198699		T	46117576	C	T	46117576	3	4	9	1	0	0	0	0	1	0	0	0	8517	739	26	2	462	2	KRTAP10-12	21	46117576	Missense_Mutation	SNP	C	TCGA-FA-A86F-01A-11D-A382-10		46117576	2012319	74	1074											
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230409	23230409	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggagcctcagttggaagcaGccgatccagcctgcggagcc	8	6	14	13	2	1	0	1	0	0	0	2	4	2	3	5	3	6	2	5	3	1	1			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr22:23230409G>A	ENST00000526893.1	+	1	450	c.176G>A	c.(175-177)aGc>aAc	p.S59N	IGLL5_ENST00000531372.1_Missense_Mutation_p.S59N|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Missense_Mutation_p.S59N	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	59						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GTTGGAAGCAGCCGATCCAGC	0.657																																					p.S59N		Atlas-SNP	.											.	IGLL5	26	.	0			c.G176A						PASS	.																																			SO:0001583	missense	100423062	exon1			GAAGCAGCCGATC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.176G>A	22.37:g.23230409G>A	ENSP00000431254:p.Ser59Asn	117	0	0		102	14	0.137255	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	10.14	1.267343	0.23136	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00583	6.41;6.41	3.92	-0.797	0.10909	.	.	.	.	.	T	0.00440	0.0014	N	0.19112	0.55	0.09310	N	1	B	0.21821	0.061	B	0.17098	0.017	T	0.45056	-0.9287	9	0.59425	D	0.04	.	3.0635	0.06207	0.2132:0.0:0.4153:0.3715	.	59	B9A064	IGLL5_HUMAN	N	59	ENSP00000436353:S59N;ENSP00000431254:S59N	ENSP00000431254:S59N	S	+	2	0	IGLL5	21560409	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.100000	0.10990	-0.036000	0.13669	-0.196000	0.12772	AGC	.	.	none		0.657	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		A	23230409	G	A	23230409	3	1	9	1	0	0	0	0	1	0	0	0	7603	971	34	2	178	2	IGLL5	22	23230409	Missense_Mutation	SNP	G	TCGA-FA-A86F-01A-11D-A382-10		23230409	28074157	75	1075											
TAB3	257397	hgsc.bcm.edu	37	chrX	30873153	30873153	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaagaatttgtaaagctcttGgtacagtctgtccagaaggg	12	11	12	6	0	2	2	0	0	2	2	3	3	3	2	1	2	2	3	1	2	6	4			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chrX:30873153G>T	ENST00000378933.1	-	3	806	c.629C>A	c.(628-630)cCa>cAa	p.P210Q	TAB3_ENST00000378928.1_5'Flank|TAB3-AS2_ENST00000445240.1_RNA|TAB3_ENST00000378932.2_Missense_Mutation_p.P210Q|TAB3_ENST00000288422.2_Missense_Mutation_p.P210Q|TAB3_ENST00000378930.3_Missense_Mutation_p.P210Q	NM_152787.3	NP_690000.2	Q8N5C8	TAB3_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 3	210	Pro-rich.				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						TAAAGCTCTTGGTACAGTCTG	0.428																																					p.P210Q	Pancreas(164;1598 1985 29022 43301 49529)	Atlas-SNP	.											.	TAB3	82	.	0			c.C629A						PASS	.						74	67	69					X																	30873153		2202	4300	6502	SO:0001583	missense	257397	exon6			GCTCTTGGTACAG	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.629C>A	X.37:g.30873153G>T	ENSP00000368215:p.Pro210Gln	243	0	0		170	22	0.129412	NM_152787	A6NDD9|Q6VQR0	Missense_Mutation	SNP	ENST00000378933.1	37	CCDS14226.1	.	.	.	.	.	.	.	.	.	.	G	15.34	2.805702	0.50315	.	.	ENSG00000157625	ENST00000378933;ENST00000378930;ENST00000288422;ENST00000378932	D;D;D;D	0.91464	-2.85;-2.85;-2.85;-2.84	5.31	4.42	0.53409	.	0.000000	0.85682	D	0.000000	D	0.87625	0.6224	L	0.54323	1.7	0.58432	D	0.999996	B;B	0.33318	0.408;0.286	B;B	0.31101	0.124;0.058	D	0.87804	0.2627	10	0.51188	T	0.08	-3.3679	14.5534	0.68084	0.0:0.0:0.8535:0.1465	.	210;210	Q8N5C8-2;Q8N5C8	.;TAB3_HUMAN	Q	210	ENSP00000368215:P210Q;ENSP00000368212:P210Q;ENSP00000288422:P210Q;ENSP00000368214:P210Q	ENSP00000288422:P210Q	P	-	2	0	TAB3	30783074	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.915000	0.69973	2.219000	0.72066	0.600000	0.82982	CCA	.	.	none		0.428	TAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056173.1	NM_152787		T	30873153	G	T	30873153	3	4	9	1	0	0	0	0	1	0	0	0	15512	1348	47	4	1533	4	TAB3	23	30873153	Missense_Mutation	SNP	G	TCGA-FA-A86F-01A-11D-A382-10		30873153	124397407	76	1076											
CYBB	1536	hgsc.bcm.edu	37	chrX	37663373	37663373	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagtttcaagatgcgtggAaactacctaagtgagtaaaa	16	9	11	5	1	1	2	1	1	0	1	1	4	1	4	1	2	3	2	1	2	6	4			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chrX:37663373A>T	ENST00000378588.4	+	9	1208	c.1141A>T	c.(1141-1143)Aaa>Taa	p.K381*	CYBB_ENST00000536160.1_Nonsense_Mutation_p.K114*|CYBB_ENST00000545017.1_Nonsense_Mutation_p.K349*|TM4SF2_ENST00000465127.1_Intron	NM_000397.3	NP_000388.2	P04839	CY24B_HUMAN	cytochrome b-245, beta polypeptide	381	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				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)	AGATGCGTGGAAACTACCTAA	0.428																																					p.K381X		Atlas-SNP	.											.	CYBB	62	.	0			c.A1141T						PASS	.						66	61	63					X																	37663373		2202	4300	6502	SO:0001587	stop_gained	1536	exon9			GCGTGGAAACTAC	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.1141A>T	X.37:g.37663373A>T	ENSP00000367851:p.Lys381*	324	0	0		196	24	0.122449	NM_000397	A8K138|Q2PP16	Nonsense_Mutation	SNP	ENST00000378588.4	37	CCDS14242.1	.	.	.	.	.	.	.	.	.	.	A	39	7.610350	0.98387	.	.	ENSG00000165168	ENST00000378588;ENST00000545017;ENST00000536160	.	.	.	5.77	5.77	0.91146	.	0.042364	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.0692	0.72021	1.0:0.0:0.0:0.0	.	.	.	.	X	381;349;114	.	ENSP00000367851:K381X	K	+	1	0	CYBB	37548317	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	5.161000	0.64935	1.941000	0.56285	0.441000	0.28932	AAA	.	.	none		0.428	CYBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080881.1			T	37663373	A	T	37663373	4	4	9	1	0	0	0	0	0	1	0	0	4135	247	9	5	1175	5	CYBB	23	37663373	Nonsense_Mutation	SNP	A	TCGA-FA-A86F-01A-11D-A382-10	6790220	37663373	117607187	77	1077											
EFNB1	1947	hgsc.bcm.edu	37	chrX	68058642	68058642	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gttggtcacctgcaataggcCagagcaggaaatacgcttta	12	9	11	9	1	1	1	1	0	0	1	1	2	1	2	2	3	3	4	2	3	5	5			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chrX:68058642C>A	ENST00000204961.4	+	2	1091	c.311C>A	c.(310-312)cCa>cAa	p.P104Q		NM_004429.4	NP_004420.1	P98172	EFNB1_HUMAN	ephrin-B1	104	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|embryonic pattern specification (GO:0009880)|ephrin receptor signaling pathway (GO:0048013)|neural crest cell migration (GO:0001755)|positive regulation of T cell proliferation (GO:0042102)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ephrin receptor binding (GO:0046875)			breast(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)	22						TGCAATAGGCCAGAGCAGGAA	0.532																																					p.P104Q		Atlas-SNP	.											.	EFNB1	37	.	0			c.C311A						PASS	.						110	62	78					X																	68058642		2203	4300	6503	SO:0001583	missense	1947	exon2			ATAGGCCAGAGCA	U09303	CCDS14391.1	Xq12	2011-03-09			ENSG00000090776	ENSG00000090776		"Ephrins"	3226	protein-coding gene	gene with protein product		300035	"craniofrontonasal syndrome (craniofrontonasal dysplasia)"	EPLG2, CFNS		7774950, 16526919	Standard	NM_004429		Approved	LERK2, Elk-L	uc004dxd.4	P98172	OTTHUMG00000021751	ENST00000204961.4:c.311C>A	X.37:g.68058642C>A	ENSP00000204961:p.Pro104Gln	389	0	0		195	9	0.0461538	NM_004429	D3DVU0	Missense_Mutation	SNP	ENST00000204961.4	37	CCDS14391.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.519345	0.85495	.	.	ENSG00000090776	ENST00000204961	D	0.97303	-4.33	5.13	5.13	0.70059	Cupredoxin (2);	0.000000	0.85682	D	0.000000	D	0.98419	0.9474	M	0.86268	2.805	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99218	1.0878	10	0.66056	D	0.02	-10.4548	14.8667	0.70422	0.0:1.0:0.0:0.0	.	104	P98172	EFNB1_HUMAN	Q	104	ENSP00000204961:P104Q	ENSP00000204961:P104Q	P	+	2	0	EFNB1	67975367	1.000000	0.71417	0.996000	0.52242	0.871000	0.50021	7.320000	0.79064	2.390000	0.81377	0.436000	0.28706	CCA	.	.	none		0.532	EFNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057029.1	NM_004429		A	68058642	C	A	68058642	3	1	9	1	0	0	0	0	1	0	0	0	4957	594	21	4	317	4	EFNB1	23	68058642	Missense_Mutation	SNP	C	TCGA-FA-A86F-01A-11D-A382-10	30395269	68058642	87211918	78	1078											
IRS4	8471	hgsc.bcm.edu	37	chrX	107977810	107977810	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctgagcctttgcccccccCagagttcttgccaccacctg	5	10	7	19	0	1	2	0	1	1	1	2	2	2	2	9	0	3	1	9	0	0	3			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chrX:107977810C>A	ENST00000372129.2	-	1	1841	c.1765G>T	c.(1765-1767)Ggg>Tgg	p.G589W	RP6-24A23.3_ENST00000608811.1_RNA|RP6-24A23.3_ENST00000436013.1_RNA|RP6-24A23.6_ENST00000563887.1_5'Flank	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	589					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						TTGCCCCCCCCAGAGTTCTTG	0.552																																					p.G589W		Atlas-SNP	.											.	IRS4	253	.	0			c.G1765T						PASS	.						165	171	169					X																	107977810		2203	4300	6503	SO:0001583	missense	8471	exon1			CCCCCCCAGAGTT	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.1765G>T	X.37:g.107977810C>A	ENSP00000361202:p.Gly589Trp	103	0	0		76	7	0.0921053	NM_003604		Missense_Mutation	SNP	ENST00000372129.2	37	CCDS14544.1	.	.	.	.	.	.	.	.	.	.	C	4.030	0.003029	0.07866	.	.	ENSG00000133124	ENST00000372129	T	0.36340	1.26	4.9	4.02	0.46733	.	0.343723	0.21762	N	0.069500	T	0.48677	0.1513	M	0.66939	2.045	0.09310	N	1	D	0.69078	0.997	P	0.58577	0.841	T	0.38286	-0.9668	10	0.62326	D	0.03	-4.4135	8.2031	0.31436	0.0:0.8871:0.0:0.1129	.	589	O14654	IRS4_HUMAN	W	589	ENSP00000361202:G589W	ENSP00000361202:G589W	G	-	1	0	IRS4	107864466	0.147000	0.22687	0.968000	0.41197	0.287000	0.27160	1.500000	0.35682	2.257000	0.74773	0.600000	0.82982	GGG	.	.	none		0.552	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604		A	107977810	C	A	107977810	3	1	9	1	0	0	0	0	1	0	0	0	7851	594	21	4	2012	4	IRS4	23	107977810	Missense_Mutation	SNP	C	TCGA-FA-A86F-01A-11D-A382-10	39919168	107977810	47292750	79	1079											
AGTR2	186	hgsc.bcm.edu	37	chrX	115304549	115304549	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtttagggttccaattacttGgctccaagggaaaagagaga	13	10	12	6	0	0	2	0	0	0	2	2	4	2	3	2	3	1	3	2	3	6	5			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chrX:115304549G>T	ENST00000371906.4	+	3	1206	c.1016G>T	c.(1015-1017)tGg>tTg	p.W339L		NM_000686.4	NP_000677.2	P50052	AGTR2_HUMAN	angiotensin II receptor, type 2	339					aldosterone secretion (GO:0035932)|angiotensin-activated signaling pathway (GO:0038166)|blood vessel remodeling (GO:0001974)|brain development (GO:0007420)|brain renin-angiotensin system (GO:0002035)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell surface receptor signaling pathway (GO:0007166)|cellular response to dexamethasone stimulus (GO:0071549)|cellular sodium ion homeostasis (GO:0006883)|cerebellar cortex development (GO:0021695)|dopamine biosynthetic process (GO:0042416)|exploration behavior (GO:0035640)|extracellular negative regulation of signal transduction (GO:1900116)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell growth (GO:0030308)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of heart rate (GO:0010459)|negative regulation of icosanoid secretion (GO:0032304)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of norepinephrine secretion (GO:0010700)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasodilation (GO:0045909)|regulation of blood pressure (GO:0008217)|regulation of metanephros size (GO:0035566)|regulation of systemic arterial blood pressure by circulatory renin-angiotensin (GO:0001991)|regulation of transcription factor import into nucleus (GO:0042990)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to organonitrogen compound (GO:0010243)|vasodilation by angiotensin involved in regulation of systemic arterial blood pressure (GO:0002033)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	angiotensin type II receptor activity (GO:0004945)|peptide hormone binding (GO:0017046)|receptor antagonist activity (GO:0048019)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|skin(1)	24					Tasosartan(DB01349)	CCAATTACTTGGCTCCAAGGG	0.433																																					p.W339L		Atlas-SNP	.											.	AGTR2	62	.	0			c.G1016T						PASS	.						121	112	115					X																	115304549		2203	4300	6503	SO:0001583	missense	186	exon3			TTACTTGGCTCCA	AY324607	CCDS14569.1	Xq22-q23	2012-08-08			ENSG00000180772	ENSG00000180772		"GPCR / Class A : Angiotensin receptors"	338	protein-coding gene	gene with protein product		300034	"angiotensin receptor 2"			1550596	Standard	NM_000686		Approved	AT2, MRX88	uc004eqh.4	P50052	OTTHUMG00000022243	ENST00000371906.4:c.1016G>T	X.37:g.115304549G>T	ENSP00000360973:p.Trp339Leu	334	0	0		215	12	0.055814	NM_000686	B2R9V1|Q13016|Q6FGY7	Missense_Mutation	SNP	ENST00000371906.4	37	CCDS14569.1	.	.	.	.	.	.	.	.	.	.	G	3.385	-0.125487	0.06795	.	.	ENSG00000180772	ENST00000371906	T	0.35421	1.31	4.63	3.68	0.42216	.	0.416542	0.24431	N	0.038588	T	0.13841	0.0335	N	0.08118	0	0.27245	N	0.959054	B	0.09022	0.002	B	0.01281	0.0	T	0.22138	-1.0225	10	0.09843	T	0.71	-0.0597	4.2132	0.10521	0.1367:0.237:0.6263:0.0	.	339	P50052	AGTR2_HUMAN	L	339	ENSP00000360973:W339L	ENSP00000360973:W339L	W	+	2	0	AGTR2	115218577	0.999000	0.42202	1.000000	0.80357	0.917000	0.54804	2.382000	0.44345	2.129000	0.65627	0.506000	0.49869	TGG	.	.	none		0.433	AGTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057984.1	NM_000686		T	115304549	G	T	115304549	3	4	9	1	0	0	0	0	1	0	0	0	402	1357	47	4	1018	4	AGTR2	23	115304549	Missense_Mutation	SNP	G	TCGA-FA-A86F-01A-11D-A382-10	7326739	115304549	39966011	80	1080											
SLC6A14	11254	hgsc.bcm.edu	37	chrX	115588850	115588850	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cataccctgactggggagttGctttaggctggtgtatgatt	7	14	13	7	0	0	2	0	2	0	0	0	3	0	3	1	4	2	4	1	4	3	6			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chrX:115588850G>A	ENST00000371900.4	+	13	1778	c.1690G>A	c.(1690-1692)Gct>Act	p.A564T	SLC6A14_ENST00000463626.1_Intron	NM_007231.3	NP_009162.1	Q9UN76	S6A14_HUMAN	solute carrier family 6 (amino acid transporter), member 14	564					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)	CTGGGGAGTTGCTTTAGGCTG	0.368																																					p.A564T		Atlas-SNP	.											.	SLC6A14	56	.	0			c.G1690A						PASS	.						205	184	191					X																	115588850		2203	4300	6503	SO:0001583	missense	11254	exon13			GGAGTTGCTTTAG	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.1690G>A	X.37:g.115588850G>A	ENSP00000360967:p.Ala564Thr	252	0	0		136	8	0.0588235	NM_007231	Q5H942	Missense_Mutation	SNP	ENST00000371900.4	37	CCDS14570.1	.	.	.	.	.	.	.	.	.	.	G	14.37	2.516113	0.44763	.	.	ENSG00000087916	ENST00000371900	T	0.74947	-0.89	5.17	4.31	0.51392	.	0.169081	0.51477	D	0.000091	T	0.69477	0.3115	L	0.51914	1.62	0.39830	D	0.972966	B	0.32604	0.377	B	0.37047	0.24	T	0.68243	-0.5460	10	0.44086	T	0.13	.	10.5295	0.44969	0.0965:0.0:0.9035:0.0	.	564	Q9UN76	S6A14_HUMAN	T	564	ENSP00000360967:A564T	ENSP00000360967:A564T	A	+	1	0	SLC6A14	115502878	0.998000	0.40836	0.991000	0.47740	0.970000	0.65996	3.357000	0.52277	0.974000	0.38366	0.538000	0.68166	GCT	.	.	none		0.368	SLC6A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057986.1			A	115588850	G	A	115588850	3	1	9	1	0	0	0	0	1	0	0	0	14692	1319	46	2	1740	2	SLC6A14	23	115588850	Missense_Mutation	SNP	G	TCGA-FA-A86F-01A-11D-A382-10	284301	115588850	39681710	81	1081											
HS6ST2	90161	hgsc.bcm.edu	37	chrX	132091067	132091067	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agtggcggccgaaagtggtgCccccggtcttctggatgtgc	5	9	16	11	3	2	0	0	0	2	0	2	2	2	1	3	5	2	0	3	5	1	1			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chrX:132091067C>A	ENST00000370836.2	-	3	1131	c.716G>T	c.(715-717)gGc>gTc	p.G239V	HS6ST2_ENST00000370833.2_Missense_Mutation_p.G93V|HS6ST2_ENST00000521489.1_Missense_Mutation_p.G239V	NM_147175.3	NP_671704.3	Q96MM7	H6ST2_HUMAN	heparan sulfate 6-O-sulfotransferase 2	239	5'-phosphosulfate-binding. {ECO:0000255}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(2)	9	Acute lymphoblastic leukemia(192;0.000127)					GAAAGTGGTGCCCCCGGTCTT	0.617																																					p.G239V		Atlas-SNP	.											.	HS6ST2	89	.	0			c.G716T						PASS	.						28	34	32					X																	132091067		2186	4279	6465	SO:0001583	missense	90161	exon3			GTGGTGCCCCCGG	AB067776	CCDS48169.1, CCDS48170.1	Xq26.2	2008-02-05			ENSG00000171004	ENSG00000171004		"Sulfotransferases, membrane-bound"	19133	protein-coding gene	gene with protein product		300545				10644753	Standard	NM_147175		Approved		uc011mvd.1	Q96MM7	OTTHUMG00000022430	ENST00000370836.2:c.716G>T	X.37:g.132091067C>A	ENSP00000359873:p.Gly239Val	134	0	0		100	8	0.08	NM_001077188	B9WRT4|B9WRT5|E9PDY5|Q2TB13|Q4VC07|Q6PIC4|Q86SM9|Q8N3T4|Q8NBN4|Q96SJ4	Missense_Mutation	SNP	ENST00000370836.2	37	CCDS48169.1	.	.	.	.	.	.	.	.	.	.	C	19.88	3.909561	0.72868	.	.	ENSG00000171004	ENST00000370837;ENST00000370836;ENST00000521489;ENST00000370833;ENST00000319809	T;T;T;T	0.45276	0.9;0.9;0.9;0.9	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.70613	0.3244	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	0.78375	-0.2228	10	0.87932	D	0	-18.7584	15.4915	0.75607	0.0:1.0:0.0:0.0	.	239;239	Q96MM7;E9PDY5	H6ST2_HUMAN;.	V	93;239;239;93;80	ENSP00000359874:G93V;ENSP00000359873:G239V;ENSP00000429473:G239V;ENSP00000359870:G93V	ENSP00000324617:G80V	G	-	2	0	HS6ST2	131918749	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.244000	0.78228	2.212000	0.71576	0.529000	0.55759	GGC	.	.	none		0.617	HS6ST2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058332.3	NM_147174		A	132091067	C	A	132091067	3	1	9	1	0	0	0	0	1	0	0	0	7380	739	26	4	1237	4	HS6ST2	23	132091067	Missense_Mutation	SNP	C	TCGA-FA-A86F-01A-11D-A382-10	16502217	132091067	23179493	82	1082											
AURKAIP1	54998	hgsc.bcm.edu	37	chr1	1309461	1309461	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agcttccggtacttgtggtgGttcatcttccgccggcggat	4	13	13	11	4	2	0	1	0	1	0	4	1	4	1	3	5	2	3	3	5	1	5			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:1309461G>A	ENST00000338370.3	-	2	817	c.417C>T	c.(415-417)aaC>aaT	p.N139N	AURKAIP1_ENST00000378853.3_Silent_p.N139N|AURKAIP1_ENST00000338338.5_Silent_p.N139N|AURKAIP1_ENST00000321751.5_Silent_p.N139N|AURKAIP1_ENST00000489799.1_5'Flank			Q9NWT8	AKIP_HUMAN	aurora kinase A interacting protein 1	139					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)		ACTTGTGGTGGTTCATCTTCC	0.617																																					p.N139N		Atlas-SNP	.											.	AURKAIP1	12	.	0			c.C417T						PASS	.						101	100	100					1																	1309461		2203	4296	6499	SO:0001819	synonymous_variant	54998	exon3			GTGGTGGTTCATC		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.417C>T	1.37:g.1309461G>A		63	0	0		73	29	0.39726	NM_001127230	Q5TA36|Q8TBD3	Silent	SNP	ENST00000338370.3	37	CCDS25.1																																																																																			.	.	none		0.617	AURKAIP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008273.1	NM_017900		A	1309461	G	A	1309461	2	1	10	1	0	0	0	0	0	0	0	1	1222	1252	44	2		2	AURKAIP1	1	1309461	Silent	SNP	G	TCGA-FF-8041-01A-11D-2210-10		1309461	247941160	1	1083											
SLC45A1	50651	hgsc.bcm.edu	37	chr1	8390740	8390740	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggccatccctggcagcgtccCcaggccgcccatcagcgtca	6	5	11	19	3	2	0	2	0	0	0	4	0	4	0	6	3	2	1	6	3	0	0			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:8390740C>T	ENST00000471889.1	+	5	1572	c.1187C>T	c.(1186-1188)cCc>cTc	p.P396L	SLC45A1_ENST00000377479.2_Missense_Mutation_p.P430L|SLC45A1_ENST00000289877.8_Missense_Mutation_p.P396L|Y_RNA_ENST00000516445.1_RNA|SLC45A1_ENST00000481265.1_3'UTR			Q9Y2W3	S45A1_HUMAN	solute carrier family 45, member 1	396					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)		GGCAGCGTCCCCAGGCCGCCC	0.672																																					p.P396L		Atlas-SNP	.											.	SLC45A1	85	.	0			c.C1187T						PASS	.						32	33	33					1																	8390740		2203	4300	6503	SO:0001583	missense	50651	exon4			GCGTCCCCAGGCC	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.1187C>T	1.37:g.8390740C>T	ENSP00000418096:p.Pro396Leu	125	0	0		59	17	0.288136	NM_001080397	Q5VY46|Q5VY49	Missense_Mutation	SNP	ENST00000471889.1	37	CCDS30577.1	.	.	.	.	.	.	.	.	.	.	C	8.089	0.774143	0.16051	.	.	ENSG00000162426	ENST00000471889;ENST00000377479;ENST00000289877	T;T;T	0.22134	2.01;1.97;2.01	4.66	4.66	0.58398	.	0.349376	0.30260	N	0.010030	T	0.22085	0.0532	M	0.64997	1.995	0.80722	D	1	P	0.40144	0.704	B	0.30495	0.116	T	0.10132	-1.0643	10	0.51188	T	0.08	-30.6706	16.5386	0.84378	0.0:1.0:0.0:0.0	.	396	Q9Y2W3	S45A1_HUMAN	L	396;430;396	ENSP00000418096:P396L;ENSP00000366699:P430L;ENSP00000289877:P396L	ENSP00000289877:P396L	P	+	2	0	SLC45A1	8313327	1.000000	0.71417	0.068000	0.19968	0.014000	0.08584	7.095000	0.76952	2.121000	0.65114	0.561000	0.74099	CCC	.	.	none		0.672	SLC45A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001245.5			T	8390740	C	T	8390740	3	4	10	1	0	0	0	0	1	0	0	0	14655	623	22	2	1201	2	SLC45A1	1	8390740	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	7081279	8390740	240859881	2	1084											
CELA3B	23436	hgsc.bcm.edu	37	chr1	22304901	22304901	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcctctcgcccttccagccGcgttgtcaatggtgaggatg	5	12	11	13	3	2	1	1	1	1	0	5	2	4	2	4	2	1	1	4	2	1	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:22304901G>A	ENST00000337107.6	+	2	102	c.83G>A	c.(82-84)cGc>cAc	p.R28H	RN7SL421P_ENST00000582599.1_RNA	NM_007352.2	NP_031378.1	P08861	CEL3B_HUMAN	chymotrypsin-like elastase family, member 3B	28					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						CCTTCCAGCCGCGTTGTCAAT	0.612																																					p.R28H		Atlas-SNP	.											.	CELA3B	24	.	0			c.G83A						PASS	.						166	103	124					1																	22304901		2203	4300	6503	SO:0001583	missense	23436	exon2			CCAGCCGCGTTGT	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.83G>A	1.37:g.22304901G>A	ENSP00000338369:p.Arg28His	232	0	0		239	45	0.188285	NM_007352	B2RE44|P11423|Q5VU28|Q5VU29|Q5VU30	Missense_Mutation	SNP	ENST00000337107.6	37	CCDS219.1	.	.	.	.	.	.	.	.	.	.	G	37	6.058413	0.97246	.	.	ENSG00000219073	ENST00000337107;ENST00000374666	T;T	0.23552	1.9;1.9	5.1	5.1	0.69264	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1);	0.000000	0.85682	D	0.000000	T	0.53158	0.1779	M	0.78049	2.395	0.36974	D	0.893974	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.984	T	0.64588	-0.6372	10	0.87932	D	0	-47.2794	16.0019	0.80301	0.0:0.0:1.0:0.0	.	28;28	B1AQ52;P08861	.;CEL3B_HUMAN	H	28;44	ENSP00000338369:R28H;ENSP00000363798:R44H	ENSP00000338369:R28H	R	+	2	0	CELA3B	22177488	0.998000	0.40836	0.262000	0.24481	0.821000	0.46438	8.940000	0.92958	2.375000	0.81037	0.650000	0.86243	CGC	.	.	none		0.612	CELA3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007797.1	NM_007352		A	22304901	G	A	22304901	3	1	10	1	0	0	0	0	1	0	0	0	3216	1087	38	1	89	1	CELA3B	1	22304901	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	13914161	22304901	226945720	3	1085											
GLIS1	148979	hgsc.bcm.edu	37	chr1	53980302	53980302	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ggcctggtgtacatacccatCccgggtgctctcagccatgg	6	9	12	14	1	1	0	1	0	1	0	3	0	2	0	4	4	4	2	4	4	2	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:53980302C>T	ENST00000312233.2	-	7	1920	c.1354G>A	c.(1354-1356)Gat>Aat	p.D452N		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						ACATACCCATCCCGGGTGCTC	0.647																																					p.D452N		Atlas-SNP	.											.	GLIS1	52	.	0			c.G1354A						PASS	.						76	78	77					1																	53980302		2203	4300	6503	SO:0001583	missense	148979	exon7			ACCCATCCCGGGT	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.1354G>A	1.37:g.53980302C>T	ENSP00000309653:p.Asp452Asn	143	0	0		161	29	0.180124	NM_147193		Missense_Mutation	SNP	ENST00000312233.2	37	CCDS582.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.237047	0.79800	.	.	ENSG00000174332	ENST00000312233	T	0.10573	2.86	4.97	4.97	0.65823	.	0.106321	0.41097	D	0.000949	T	0.13798	0.0334	L	0.29908	0.895	0.38952	D	0.958378	P	0.52842	0.956	P	0.50082	0.63	T	0.10132	-1.0643	10	0.23891	T	0.37	.	16.8949	0.86097	0.0:1.0:0.0:0.0	.	452	Q8NBF1	GLIS1_HUMAN	N	452	ENSP00000309653:D452N	ENSP00000309653:D452N	D	-	1	0	GLIS1	53752890	1.000000	0.71417	1.000000	0.80357	0.646000	0.38490	3.887000	0.56197	2.688000	0.91661	0.563000	0.77884	GAT	.	.	none		0.647	GLIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022109.1	NM_147193		T	53980302	C	T	53980302	3	4	10	1	0	0	0	0	1	0	0	0	6453	855	30	2	524	2	GLIS1	1	53980302	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	31675401	53980302	195270319	4	1086											
FLG2	388698	hgsc.bcm.edu	37	chr1	152325925	152325925	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagatccggcttggccatgaGtttgttcttgtgattgtggt	5	16	14	6	1	1	3	0	2	1	1	2	4	2	3	2	3	0	3	2	3	0	5			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:152325925G>A	ENST00000388718.5	-	3	4409	c.4337C>T	c.(4336-4338)aCt>aTt	p.T1446I	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1446					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)			TTGGCCATGAGTTTGTTCTTG	0.527																																					p.T1446I		Atlas-SNP	.											.	FLG2	431	.	0			c.C4337T						PASS	.						366	329	341					1																	152325925		2203	4300	6503	SO:0001583	missense	388698	exon3			CCATGAGTTTGTT	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.4337C>T	1.37:g.152325925G>A	ENSP00000373370:p.Thr1446Ile	307	0	0		314	149	0.474522	NM_001014342	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	G	4.655	0.121725	0.08931	.	.	ENSG00000143520	ENST00000388718	T	0.40476	1.03	3.22	-6.43	0.01926	.	.	.	.	.	T	0.11965	0.0291	M	0.68593	2.085	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13229	-1.0517	9	0.52906	T	0.07	3.444	0.1468	0.00089	0.2725:0.2261:0.1625:0.3389	.	1446	Q5D862	FILA2_HUMAN	I	1446	ENSP00000373370:T1446I	ENSP00000373370:T1446I	T	-	2	0	FLG2	150592549	0.029000	0.19370	0.000000	0.03702	0.001000	0.01503	-0.043000	0.12043	-2.658000	0.00420	-0.913000	0.02753	ACT	.	.	none		0.527	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		A	152325925	G	A	152325925	3	1	10	1	0	0	0	0	1	0	0	0	5931	1029	36	2	2842	2	FLG2	1	152325925	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	98345623	152325925	96924696	5	1087											
ITPKB	3707	hgsc.bcm.edu	37	chr1	226924388	226924388	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	actggcagggatacccttctCcatccttacaaaagcggatg	11	9	9	12	1	1	0	0	0	1	0	3	2	2	2	3	3	3	1	3	3	4	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:226924388C>G	ENST00000272117.3	-	1	771	c.772G>C	c.(772-774)Gag>Cag	p.E258Q	ITPKB_ENST00000429204.1_Missense_Mutation_p.E258Q|ITPKB_ENST00000366784.1_Missense_Mutation_p.E258Q			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	258					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)				ATACCCTTCTCCATCCTTACA	0.597																																					p.E258Q	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											.	ITPKB	158	.	0			c.G772C						PASS	.						49	48	49					1																	226924388		2203	4300	6503	SO:0001583	missense	3707	exon2			CCTTCTCCATCCT	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.772G>C	1.37:g.226924388C>G	ENSP00000272117:p.Glu258Gln	110	0	0		134	62	0.462687	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Missense_Mutation	SNP	ENST00000272117.3	37	CCDS1555.1	.	.	.	.	.	.	.	.	.	.	C	16.57	3.159960	0.57368	.	.	ENSG00000143772	ENST00000272117;ENST00000429204;ENST00000366784	T;T;T	0.35973	1.32;1.32;1.28	4.6	3.68	0.42216	.	0.263808	0.27064	N	0.021114	T	0.23014	0.0556	N	0.24115	0.695	0.27144	N	0.961579	P	0.50443	0.935	B	0.42245	0.381	T	0.06588	-1.0818	10	0.21014	T	0.42	-16.2733	10.3145	0.43729	0.0:0.905:0.0:0.095	.	258	P27987	IP3KB_HUMAN	Q	258	ENSP00000272117:E258Q;ENSP00000411152:E258Q;ENSP00000355748:E258Q	ENSP00000272117:E258Q	E	-	1	0	ITPKB	224991011	0.888000	0.30383	0.751000	0.31187	0.218000	0.24690	1.098000	0.31000	1.137000	0.42214	0.561000	0.74099	GAG	.	.	none		0.597	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221		G	226924388	C	G	226924388	3	3	10	1	0	0	0	0	1	0	0	0	7927	864	30	4	2096	4	ITPKB	1	226924388	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	74598463	226924388	22326233	6	1088											
ITPKB	3707	hgsc.bcm.edu	37	chr1	226925148	226925148	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggctattgagcgcatagcaGtacacagccatagtactggg	12	8	12	9	1	0	1	0	1	0	0	0	1	0	1	1	2	5	5	1	2	5	6			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:226925148G>A	ENST00000272117.3	-	1	11	c.12C>T	c.(10-12)taC>taT	p.Y4Y	ITPKB_ENST00000429204.1_Silent_p.Y4Y|ITPKB_ENST00000366784.1_Silent_p.Y4Y			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	4					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)				GCGCATAGCAGTACACAGCCA	0.726																																					p.Y4Y	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											.	ITPKB	158	.	0			c.C12T						PASS	.						17	20	19					1																	226925148		2139	4199	6338	SO:0001819	synonymous_variant	3707	exon2			ATAGCAGTACACA	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.12C>T	1.37:g.226925148G>A		32	0	0		33	7	0.212121	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Silent	SNP	ENST00000272117.3	37	CCDS1555.1																																																																																			.	.	none		0.726	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221		A	226925148	G	A	226925148	2	1	10	1	0	0	0	0	0	0	0	1	7927	1024	36	2		2	ITPKB	1	226925148	Silent	SNP	G	TCGA-FF-8041-01A-11D-2210-10	760	226925148	22325473	7	1089											
KCNK1	3775	hgsc.bcm.edu	37	chr1	233802348	233802348	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gttctccttgcaggttatggCcacaccgtgcccttgtcaga	6	12	10	13	1	2	1	1	0	1	1	3	1	2	1	4	2	2	3	4	2	1	4			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:233802348C>G	ENST00000366621.3	+	2	531	c.363C>G	c.(361-363)ggC>ggG	p.G121G	KCNK1_ENST00000472190.1_3'UTR|KCNK1_ENST00000366620.1_Silent_p.G5G	NM_002245.3	NP_002236.1	O00180	KCNK1_HUMAN	potassium channel, subfamily K, member 1	121					potassium ion transport (GO:0006813)|response to nicotine (GO:0035094)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endosome (GO:0005768)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)|skin(1)	11		all_cancers(173;0.00217)|all_epithelial(177;0.121)|Prostate(94;0.122)|Acute lymphoblastic leukemia(190;0.175)			Ibutilide(DB00308)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)	CAGGTTATGGCCACACCGTGC	0.502																																					p.G121G		Atlas-SNP	.											KCNK1,colon,carcinoma,+1,1	KCNK1	36	1	0			c.C363G						PASS	.						166	119	135					1																	233802348		2203	4300	6503	SO:0001819	synonymous_variant	3775	exon2			TTATGGCCACACC	U33632	CCDS1599.1	1q42-q43	2012-03-07			ENSG00000135750	ENSG00000135750		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6272	protein-coding gene	gene with protein product		601745				8661042, 16382106	Standard	NM_002245		Approved	K2p1.1, DPK, TWIK-1	uc010pxo.1	O00180	OTTHUMG00000037923	ENST00000366621.3:c.363C>G	1.37:g.233802348C>G		239	0	0		230	108	0.469565	NM_002245	Q13307|Q5T5E8	Silent	SNP	ENST00000366621.3	37	CCDS1599.1																																																																																			.	.	none		0.502	KCNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092565.1	NM_002245		G	233802348	C	G	233802348	2	3	10	1	0	0	0	0	0	0	0	1	8067	726	26	4		4	KCNK1	1	233802348	Silent	SNP	C	TCGA-FF-8041-01A-11D-2210-10	6877200	233802348	15448273	8	1090											
OR2W3	343171	hgsc.bcm.edu	37	chr1	248059470	248059470	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctgcgtcagcactgtggcCatcgaaggcaccgtctttgt	6	10	12	13	3	2	0	1	0	1	0	3	1	2	0	3	2	2	2	3	2	1	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr1:248059470C>T	ENST00000360358.3	+	1	582	c.582C>T	c.(580-582)gcC>gcT	p.A194A	OR2W3_ENST00000537741.1_Silent_p.A194A	NM_001001957.2	NP_001001957.2	Q7Z3T1	OR2W3_HUMAN	olfactory receptor, family 2, subfamily W, member 3	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)|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)			GCACTGTGGCCATCGAAGGCA	0.597																																					p.A194A		Atlas-SNP	.											OR2W3,right_lower_lobe,carcinoma,+2,1	OR2W3	113	1	0			c.C582T						PASS	.						143	122	130					1																	248059470		2203	4300	6503	SO:0001819	synonymous_variant	343171	exon1			TGTGGCCATCGAA	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.582C>T	1.37:g.248059470C>T		248	0	0		298	64	0.214765	NM_001001957	Q6IF06|Q8NG86	Silent	SNP	ENST00000360358.3	37	CCDS31099.1																																																																																			.	.	none		0.597	OR2W3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096861.1	NM_001001957		T	248059470	C	T	248059470	2	4	10	1	0	0	0	0	0	0	0	1	11042	581	21	2		2	OR2W3	1	248059470	Silent	SNP	C	TCGA-FF-8041-01A-11D-2210-10	14257122	248059470	1191151	9	1091											
DPYSL5	56896	hgsc.bcm.edu	37	chr2	27147877	27147877	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cccaaggtctgctgtgattaCgccctccacgtggggatcac	7	9	11	14	2	2	1	1	1	1	0	3	2	3	2	3	3	2	1	3	3	2	1	rs147434661		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:27147877C>T	ENST00000288699.6	+	3	542	c.384C>T	c.(382-384)taC>taT	p.Y128Y	DPYSL5_ENST00000401478.1_Silent_p.Y128Y	NM_001253724.1|NM_020134.3	NP_001240653.1|NP_064519.2	Q9BPU6	DPYL5_HUMAN	dihydropyrimidinase-like 5	128					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)					GCTGTGATTACGCCCTCCACG	0.602																																					p.Y128Y		Atlas-SNP	.											.	DPYSL5	69	.	0			c.C384T						PASS	.	C		0,4406		0,0,2203	100	87	91		384	-3.6	1	2	dbSNP_134	91	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DPYSL5	NM_020134.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		128/565	27147877	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	56896	exon3			TGATTACGCCCTC	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.384C>T	2.37:g.27147877C>T		71	0	0		105	34	0.32381	NM_001253724	Q8TCL6|Q9NQC4|Q9NRY9	Silent	SNP	ENST00000288699.6	37	CCDS1730.1																																																																																			C|1.000;T|0.000	0.000	weak		0.602	DPYSL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214187.2	NM_020134		T	27147877	C	T	27147877	2	4	10	1	0	0	0	0	0	0	0	1	4752	547	19	1		1	DPYSL5	2	27147877	Silent	SNP	C	TCGA-FF-8041-01A-11D-2210-10		27147877	216051496	10	1092											
REL	5966	hgsc.bcm.edu	37	chr2	61147230	61147230	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aactctgcttttccagaaacTgtgccaggatcacggtaaga	12	10	9	10	1	2	2	1	0	1	2	3	3	3	3	2	2	4	2	2	2	3	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:61147230T>A	ENST00000295025.8	+	8	1228	c.908T>A	c.(907-909)cTg>cAg	p.L303Q	REL_ENST00000394479.3_Missense_Mutation_p.L303Q	NM_002908.2	NP_002899.1	Q04864	REL_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog	303					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)			TTCCAGAAACTGTGCCAGGAT	0.289			A		Hodgkin Lymphoma																																p.L303Q		Atlas-SNP	.		Dom	yes		2	2p13-p12	5966	v-rel reticuloendotheliosis viral oncogene homolog (avian)		L	.	REL	48	.	0			c.T908A						PASS	.						79	80	80					2																	61147230		2203	4300	6503	SO:0001583	missense	5966	exon8			AGAAACTGTGCCA	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.908T>A	2.37:g.61147230T>A	ENSP00000295025:p.Leu303Gln	403	0	0		444	163	0.367117	NM_002908	Q17RU2|Q2PNZ7|Q6LDY0	Missense_Mutation	SNP	ENST00000295025.8	37	CCDS1864.1	.	.	.	.	.	.	.	.	.	.	T	16.67	3.188258	0.57909	.	.	ENSG00000162924	ENST00000295025;ENST00000394479	T;T	0.48522	0.81;0.81	5.49	5.49	0.81192	Immunoglobulin E-set (1);	0.423339	0.21659	N	0.071053	T	0.63319	0.2501	L	0.59436	1.845	0.42356	D	0.992391	D;D	0.89917	0.999;1.0	D;D	0.71184	0.956;0.972	T	0.63427	-0.6640	10	0.46703	T	0.11	-42.4869	13.2498	0.60045	0.0:0.0:0.0:1.0	.	303;303	Q17RU2;Q04864	.;REL_HUMAN	Q	303	ENSP00000295025:L303Q;ENSP00000377989:L303Q	ENSP00000295025:L303Q	L	+	2	0	REL	61000734	0.935000	0.31712	0.991000	0.47740	0.502000	0.33828	4.438000	0.59961	2.213000	0.71641	0.397000	0.26171	CTG	.	.	none		0.289	REL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251576.3	NM_002908		A	61147230	T	A	61147230	3	1	10	1	0	0	0	0	1	0	0	0	13230	1580	55	5	938	5	REL	2	61147230	Missense_Mutation	SNP	T	TCGA-FF-8041-01A-11D-2210-10	33999353	61147230	182052143	11	1093											
ANKRD53	79998	hgsc.bcm.edu	37	chr2	71212171	71212171	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtggacggccactgggtggCgcccgtgccgcggctgcctt	3	7	17	14	5	0	0	0	0	0	0	0	1	0	1	4	5	2	1	4	5	0	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:71212171C>T	ENST00000360589.3	+	6	1368	c.1334C>T	c.(1333-1335)gCg>gTg	p.A445V	AC007040.11_ENST00000606025.1_Intron|ANKRD53_ENST00000441349.1_3'UTR|ANKRD53_ENST00000272421.6_3'UTR|ANKRD53_ENST00000457410.1_Missense_Mutation_p.A411V	NM_001115116.1	NP_001108588.1	Q8N9V6	ANR53_HUMAN	ankyrin repeat domain 53	445										endometrium(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	11						CACTGGGTGGCGCCCGTGCCG	0.652											OREG0014687	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A445V		Atlas-SNP	.											.	ANKRD53	55	.	0			c.C1334T						PASS	.						7	10	9					2																	71212171		683	1580	2263	SO:0001583	missense	79998	exon6			GGGTGGCGCCCGT	BC035234	CCDS1913.1, CCDS46321.1	2p13.3	2013-01-10			ENSG00000144031	ENSG00000144031		"Ankyrin repeat domain containing"	25691	protein-coding gene	gene with protein product							Standard	NM_024933		Approved	FLJ12056, FLJ36160	uc002shl.4	Q8N9V6	OTTHUMG00000129712	ENST00000360589.3:c.1334C>T	2.37:g.71212171C>T	ENSP00000353796:p.Ala445Val	39	0	0	1128	22	5	0.227273	NM_001115116	Q8IYP8	Missense_Mutation	SNP	ENST00000360589.3	37	CCDS46321.1	.	.	.	.	.	.	.	.	.	.	C	14.89	2.669230	0.47677	.	.	ENSG00000144031	ENST00000457410;ENST00000360589	T;T	0.64085	0.01;-0.08	5.16	-0.376	0.12505	.	1.236970	0.05473	N	0.553515	T	0.40791	0.1131	L	0.29908	0.895	0.09310	N	1	P	0.49961	0.93	B	0.34873	0.191	T	0.38090	-0.9677	10	0.40728	T	0.16	-1.5817	2.8344	0.05509	0.2989:0.3228:0.2918:0.0865	.	445	Q8N9V6	ANR53_HUMAN	V	411;445	ENSP00000407004:A411V;ENSP00000353796:A445V	ENSP00000353796:A445V	A	+	2	0	ANKRD53	71065679	0.000000	0.05858	0.006000	0.13384	0.054000	0.15201	-0.783000	0.04638	0.076000	0.16826	0.561000	0.74099	GCG	.	.	none		0.652	ANKRD53-004	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330275.2	NM_024933		T	71212171	C	T	71212171	3	4	10	1	0	0	0	0	1	0	0	0	679	768	27	1	1487	1	ANKRD53	2	71212171	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	10064941	71212171	171987202	12	1094											
DYSF	8291	hgsc.bcm.edu	37	chr2	71748030	71748030	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctggggcctggggacgaagCgcctgtgagtacatttccct	6	9	15	11	2	0	1	0	1	0	0	1	3	1	2	3	4	2	2	3	4	2	2	rs115279465	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:71748030C>T	ENST00000258104.3	+	11	1326	c.1049C>T	c.(1048-1050)gCg>gTg	p.A350V	DYSF_ENST00000409744.1_Missense_Mutation_p.A351V|DYSF_ENST00000409582.3_Missense_Mutation_p.A381V|DYSF_ENST00000394120.2_Missense_Mutation_p.A351V|DYSF_ENST00000410020.3_Missense_Mutation_p.A382V|DYSF_ENST00000429174.2_Missense_Mutation_p.A350V|DYSF_ENST00000409762.1_Missense_Mutation_p.A381V|DYSF_ENST00000409651.1_Missense_Mutation_p.A382V|DYSF_ENST00000410041.1_Missense_Mutation_p.A382V|DYSF_ENST00000413539.2_Missense_Mutation_p.A381V|DYSF_ENST00000409366.1_Missense_Mutation_p.A351V	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	350					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						GGGGACGAAGCGCCTGTGAGT	0.547													C|||	34	0.00678914	0.0242	0.0	5008	,	,		16178	0.002		0.0	False		,,,				2504	0.0				p.A382V		Atlas-SNP	.											DYSF_ENST00000410020,bladder,carcinoma,-1,2	DYSF	536	2	0			c.C1145T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	39,4367	43.1+/-76.7	0,39,2164	86	73	77		1052,1049,1049,1049,1142,1142,1142,1145,1052,1052,1145,1052,1145,1049	5.2	1	2	dbSNP_132	77	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	DYSF	NM_001130455.1,NM_001130976.1,NM_001130977.1,NM_001130978.1,NM_001130979.1,NM_001130980.1,NM_001130981.1,NM_001130982.1,NM_001130983.1,NM_001130984.1,NM_001130985.1,NM_001130986.1,NM_001130987.1,NM_003494.3	64,64,64,64,64,64,64,64,64,64,64,64,64,64	0,39,6464	TT,TC,CC		0.0,0.8852,0.2999	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	351/2082,350/2067,350/2088,350/2102,381/2112,381/2098,381/2119,382/2113,351/2103,351/2089,382/2099,351/2068,382/2120,350/2081	71748030	39,12967	2203	4300	6503	SO:0001583	missense	8291	exon12			ACGAAGCGCCTGT	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.1049C>T	2.37:g.71748030C>T	ENSP00000258104:p.Ala350Val	207	0	0		213	74	0.347418	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	37	CCDS1918.1	16	0.007326007326007326	14	0.028455284552845527	0	0.0	1	0.0017482517482517483	1	0.0013192612137203166	C	18.71	3.681825	0.68042	0.008852	0.0	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	T;T;T;T;T;T;T;T;T;T;T	0.80566	-1.39;-1.39;-1.39;-1.39;-1.39;-1.39;-1.39;-1.39;-1.39;-1.39;-1.39	5.23	5.23	0.72850	C2 calcium/lipid-binding domain, CaLB (1);FerIin domain (1);	0.234979	0.43919	D	0.000501	T	0.51449	0.1675	N	0.25245	0.725	0.31618	N	0.65062	P;P;P;P;B;P;B;P;P;P;P;P;P;P	0.49559	0.775;0.775;0.775;0.648;0.423;0.622;0.423;0.925;0.775;0.633;0.797;0.648;0.775;0.812	B;B;B;B;B;B;B;P;B;B;P;B;B;P	0.49528	0.231;0.335;0.435;0.315;0.135;0.207;0.135;0.614;0.231;0.207;0.598;0.315;0.435;0.571	T	0.66015	-0.6028	10	0.20046	T	0.44	-3.0016	12.5642	0.56300	0.0:0.8325:0.1675:0.0	.	382;382;351;351;382;351;381;350;381;381;350;350;351;350	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	V	381;381;381;350;350;382;351;351;351;382;382	ENSP00000407046:A381V;ENSP00000387137:A381V;ENSP00000386547:A381V;ENSP00000398305:A350V;ENSP00000258104:A350V;ENSP00000386683:A382V;ENSP00000377678:A351V;ENSP00000386285:A351V;ENSP00000386512:A351V;ENSP00000386881:A382V;ENSP00000386617:A382V	ENSP00000258104:A350V	A	+	2	0	DYSF	71601538	1.000000	0.71417	0.962000	0.40283	0.318000	0.28184	4.576000	0.60915	2.663000	0.90544	0.536000	0.68110	GCG	C|0.995;T|0.005	0.005	strong		0.547	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		T	71748030	C	T	71748030	3	4	10	1	0	0	0	0	1	0	0	0	4861	768	27	1	1283	1	DYSF	2	71748030	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	535859	71748030	171451343	13	1095											
DUSP2	1844	hgsc.bcm.edu	37	chr2	96810595	96810595	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcagagcacagatcgggacAgcagccctggaagccgtcga	11	4	13	13	3	1	2	1	0	0	2	3	5	1	4	2	2	4	2	2	2	1	0			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:96810595A>C	ENST00000288943.4	-	2	500	c.415T>G	c.(415-417)Tgt>Ggt	p.C139G	AC012307.2_ENST00000449242.1_lincRNA	NM_004418.3	NP_004409.1	Q05923	DUS2_HUMAN	dual specificity phosphatase 2	139	Rhodanese. {ECO:0000255|PROSITE- ProRule:PRU00173}.				endoderm formation (GO:0001706)|inactivation of MAPK activity (GO:0000188)|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)|protein tyrosine/threonine phosphatase activity (GO:0008330)			NS(1)|breast(1)|lung(2)|skin(1)	5		Ovarian(717;0.0228)				AGATCGGGACAGCAGCCCTGG	0.692																																					p.C139G		Atlas-SNP	.											.	DUSP2	20	.	0			c.T415G						PASS	.						15	21	19					2																	96810595		2119	4214	6333	SO:0001583	missense	1844	exon2			CGGGACAGCAGCC	L11329	CCDS2016.1	2q11	2011-06-09			ENSG00000158050	ENSG00000158050		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3068	protein-coding gene	gene with protein product		603068				7806236, 7590752, 12673251	Standard	NM_004418		Approved	PAC-1	uc002svk.4	Q05923	OTTHUMG00000130456	ENST00000288943.4:c.415T>G	2.37:g.96810595A>C	ENSP00000288943:p.Cys139Gly	84	0	0		98	37	0.377551	NM_004418	Q53T45	Missense_Mutation	SNP	ENST00000288943.4	37	CCDS2016.1	.	.	.	.	.	.	.	.	.	.	A	11.95	1.791720	0.31685	.	.	ENSG00000158050	ENST00000288943	T	0.35421	1.31	4.31	4.31	0.51392	Rhodanese-like (4);	0.305675	0.32258	N	0.006346	T	0.27933	0.0688	L	0.49778	1.585	0.35359	D	0.788057	P	0.38335	0.627	B	0.28916	0.096	T	0.47947	-0.9077	10	0.66056	D	0.02	.	9.8111	0.40824	1.0:0.0:0.0:0.0	.	139	Q05923	DUS2_HUMAN	G	139	ENSP00000288943:C139G	ENSP00000288943:C139G	C	-	1	0	DUSP2	96174322	0.132000	0.22450	0.778000	0.31720	0.171000	0.22731	3.037000	0.49775	1.812000	0.52913	0.374000	0.22700	TGT	.	.	none		0.692	DUSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252847.1	NM_004418		C	96810595	A	C	96810595	3	2	10	1	0	0	0	0	1	0	0	0	4821	188	7	5	541	5	DUSP2	2	96810595	Missense_Mutation	SNP	A	TCGA-FF-8041-01A-11D-2210-10	25062565	96810595	146388778	14	1096											
PAX8	7849	hgsc.bcm.edu	37	chr2	114004442	114004442	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgcgctggcggaccacttccGgcagaggtctgccattcaca	7	8	12	14	3	2	1	1	0	1	1	3	2	3	2	3	4	2	2	3	4	0	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:114004442G>A	ENST00000429538.3	-	3	274	c.80C>T	c.(79-81)cCg>cTg	p.P27L	AC016683.6_ENST00000436293.2_RNA|AC016683.6_ENST00000445745.1_RNA|AC016683.6_ENST00000422956.2_RNA|AC016683.6_ENST00000553869.2_RNA|AC016683.6_ENST00000451179.1_RNA|AC016683.6_ENST00000333145.5_RNA|PAX8_ENST00000263335.7_Missense_Mutation_p.P27L|PAX8_ENST00000397647.3_Missense_Mutation_p.P27L|PAX8_ENST00000263334.5_Missense_Mutation_p.P27L|PAX8_ENST00000348715.5_Missense_Mutation_p.P27L|AC016683.6_ENST00000556070.1_RNA	NM_003466.3	NP_003457.1	Q06710	PAX8_HUMAN	paired box 8	27	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						GACCACTTCCGGCAGAGGTCT	0.622			T	PPARG	follicular thyroid		Thyroid dysgenesis																														p.P27L	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.C80T						PASS	.						33	38	37					2																	114004442		2100	4256	6356	SO:0001583	missense	7849	exon3			ACTTCCGGCAGAG	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.80C>T	2.37:g.114004442G>A	ENSP00000395498:p.Pro27Leu	122	0	0		168	71	0.422619	NM_013952	Q09155|Q16337|Q16338|Q16339|Q4ZG35|Q96J49	Missense_Mutation	SNP	ENST00000429538.3	37	CCDS46398.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.504596	0.85176	.	.	ENSG00000125618	ENST00000263335;ENST00000397647;ENST00000348715;ENST00000429538;ENST00000263334	D;D;D;D;D	0.99709	-6.48;-6.48;-6.48;-6.48;-6.48	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	0.99792	0.9912	H	0.94698	3.57	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;0.994;1.0;0.998;0.995	D	0.96959	0.9700	10	0.87932	D	0	.	16.0313	0.80579	0.0:0.0:1.0:0.0	.	27;27;27;27;27	Q06710-2;Q06710-3;Q06710;Q06710-5;Q06710-4	.;.;PAX8_HUMAN;.;.	L	27	ENSP00000263335:P27L;ENSP00000380768:P27L;ENSP00000314750:P27L;ENSP00000395498:P27L;ENSP00000263334:P27L	ENSP00000263334:P27L	P	-	2	0	PAX8	113720912	1.000000	0.71417	0.940000	0.37924	0.600000	0.36913	9.796000	0.99103	2.382000	0.81193	0.655000	0.94253	CCG	.	.	none		0.622	PAX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250353.5			A	114004442	G	A	114004442	3	1	10	1	0	0	0	0	1	0	0	0	11494	1116	39	1	1187	1	PAX8	2	114004442	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	17193847	114004442	129194931	15	1097											
SAP130	79595	hgsc.bcm.edu	37	chr2	128758026	128758026	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctggatagacaaggttggcCtactgaaaagataacaaaga	17	7	11	6	0	0	4	0	1	0	3	0	5	0	5	1	3	2	2	1	3	7	4			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:128758026C>T	ENST00000259235.3	-	8	1079	c.950G>A	c.(949-951)aGg>aAg	p.R317K	SAP130_ENST00000259234.6_Missense_Mutation_p.R291K|SAP130_ENST00000357702.5_Missense_Mutation_p.R317K	NM_024545.3	NP_078821.2	Q9H0E3	SP130_HUMAN	Sin3A-associated protein, 130kDa	317					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)		CAAGGTTGGCCTACTGAAAAG	0.428																																					p.R317K		Atlas-SNP	.											.	SAP130	169	.	0			c.G950A						PASS	.						155	135	141					2																	128758026		2203	4300	6503	SO:0001583	missense	79595	exon8			GTTGGCCTACTGA	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.950G>A	2.37:g.128758026C>T	ENSP00000259235:p.Arg317Lys	77	0	0		86	20	0.232558	NM_001145928	B7ZLM3|C9K0X9|Q4ZFV4|Q53T46|Q8WVW4|Q9H9G8	Missense_Mutation	SNP	ENST00000259235.3	37	CCDS2153.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.543573	0.86022	.	.	ENSG00000136715	ENST00000357702;ENST00000259235;ENST00000259234	.	.	.	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.65523	0.2699	L	0.29908	0.895	0.80722	D	1	D;D	0.67145	0.996;0.99	D;D	0.76071	0.987;0.979	T	0.57911	-0.7729	9	0.16896	T	0.51	-20.9485	19.5036	0.95105	0.0:1.0:0.0:0.0	.	317;317	B7ZLM3;Q9H0E3	.;SP130_HUMAN	K	317;317;291	.	ENSP00000259234:R291K	R	-	2	0	SAP130	128474496	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.105000	0.77031	2.672000	0.90937	0.650000	0.86243	AGG	.	.	none		0.428	SAP130-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254436.3	NM_024545		T	128758026	C	T	128758026	3	4	10	1	0	0	0	0	1	0	0	0	13846	681	24	2	2357	2	SAP130	2	128758026	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	14753584	128758026	114441347	16	1098											
LRP1B	53353	hgsc.bcm.edu	37	chr2	141259273	141259273	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	taccttataactgaccggaaGgtcttgacagtcttgagaac	12	11	9	9	1	2	3	0	3	2	1	2	5	2	4	2	2	3	0	2	2	5	5			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:141259273G>A	ENST00000389484.3	-	55	9804	c.8833C>T	c.(8833-8835)Ctt>Ttt	p.L2945F		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2945	EGF-like 11. {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)		CTGACCGGAAGGTCTTGACAG	0.363										TSP Lung(27;0.18)																											p.L2945F	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.C8833T						PASS	.						112	115	114					2																	141259273		2203	4300	6503	SO:0001583	missense	53353	exon55			CCGGAAGGTCTTG	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.8833C>T	2.37:g.141259273G>A	ENSP00000374135:p.Leu2945Phe	83	0	0		63	31	0.492063	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	G	19.73	3.881949	0.72294	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.87887	-2.31	5.41	4.29	0.51040	Growth factor, receptor (1);EGF-like calcium-binding (1);	0.086330	0.45361	U	0.000370	D	0.83179	0.5198	M	0.73372	2.23	0.43347	D	0.995408	B	0.30664	0.289	B	0.26517	0.07	T	0.77130	-0.2701	10	0.10902	T	0.67	.	11.8149	0.52204	0.1088:0.0:0.8912:0.0	.	2945	Q9NZR2	LRP1B_HUMAN	F	2945;2883	ENSP00000374135:L2945F	ENSP00000374135:L2945F	L	-	1	0	LRP1B	140975743	1.000000	0.71417	0.996000	0.52242	0.937000	0.57800	5.559000	0.67326	1.080000	0.41073	0.585000	0.79938	CTT	.	.	none		0.363	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141259273	G	A	141259273	3	1	10	1	0	0	0	0	1	0	0	0	8964	1000	35	2	5114	2	LRP1B	2	141259273	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	12501247	141259273	101940100	17	1099											
RIF1	55183	hgsc.bcm.edu	37	chr2	152300225	152300225	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aactgaattgattaatcaggTatgaaataaatctgctacgt	16	13	7	5	1	2	3	1	3	1	0	2	3	2	3	0	1	3	2	0	1	8	5			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:152300225T>G	ENST00000243326.5	+	17	2469		c.e17+2		RIF1_ENST00000430328.2_Splice_Site|RIF1_ENST00000444746.2_Splice_Site|RIF1_ENST00000453091.2_Splice_Site|RIF1_ENST00000428287.2_Splice_Site			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1						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)		ATTAATCAGGTATGAAATAAA	0.313																																					.		Atlas-SNP	.											.	RIF1	244	.	0			c.1986+2T>G						PASS	.						63	67	65					2																	152300225		2202	4300	6502	SO:0001630	splice_region_variant	55183	exon18			ATCAGGTATGAAA	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.1986+2T>G	2.37:g.152300225T>G		64	0	0		74	28	0.378378	NM_018151	A0AVS0|Q9NS16	Splice_Site	SNP	ENST00000243326.5	37	CCDS2194.1	.	.	.	.	.	.	.	.	.	.	T	19.10	3.762703	0.69763	.	.	ENSG00000080345	ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000414861;ENST00000430328	.	.	.	5.34	5.34	0.76211	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.5395	0.61666	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	RIF1	152008471	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	6.811000	0.75221	2.027000	0.59764	0.377000	0.23210	.	.	.	none		0.313	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3		Intron	G	152300225	T	G	152300225	5	3	10	1	0	0	0	0	0	0	1	0	13374	1652	57	5	2054	5	RIF1	2	152300225	Splice_Site	SNP	T	TCGA-FF-8041-01A-11D-2210-10	11040952	152300225	90899148	18	1100											
XIRP2	129446	hgsc.bcm.edu	37	chr2	168107691	168107691	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gacgctcaagaggaaatcagGaaagtggagaagagagctac	17	4	14	6	1	2	3	2	0	0	3	2	8	2	5	0	3	2	2	0	3	5	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:168107691G>T	ENST00000409195.1	+	9	9878	c.9789G>T	c.(9787-9789)agG>agT	p.R3263S	XIRP2_ENST00000295237.9_Missense_Mutation_p.R3263S|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.R3041S|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000420519.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	3088					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						AGGAAATCAGGAAAGTGGAGA	0.423																																					p.R3263S		Atlas-SNP	.											.	XIRP2	914	.	0			c.G9789T						PASS	.						70	66	67					2																	168107691		1908	4138	6046	SO:0001583	missense	129446	exon9			AATCAGGAAAGTG	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.9789G>T	2.37:g.168107691G>T	ENSP00000386840:p.Arg3263Ser	76	0	0		108	10	0.0925926	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	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	G	8.433	0.849012	0.17034	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.02656	4.21;4.21;4.21	5.61	4.73	0.59995	.	0.251797	0.42053	D	0.000767	T	0.04003	0.0112	L	0.56769	1.78	0.34058	D	0.656942	P;P;P	0.46142	0.651;0.763;0.873	B;B;B	0.39660	0.084;0.173;0.306	T	0.40961	-0.9535	10	0.39692	T	0.17	-11.0608	8.8487	0.35186	0.17:0.0:0.83:0.0	.	3088;3088;3041	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	S	3263;3263;3041;677	ENSP00000386840:R3263S;ENSP00000295237:R3263S;ENSP00000387255:R3041S	ENSP00000295237:R3263S	R	+	3	2	XIRP2	167815937	0.962000	0.33011	0.852000	0.33557	0.171000	0.22731	1.442000	0.35046	1.504000	0.48704	0.460000	0.39030	AGG	.	.	none		0.423	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		T	168107691	G	T	168107691	3	4	10	1	0	0	0	0	1	0	0	0	17445	1165	41	4	9819	4	XIRP2	2	168107691	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	15807466	168107691	75091682	19	1101											
NEUROD1	4760	hgsc.bcm.edu	37	chr2	182543437	182543437	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcccccgttcctcagtgagtCctcctctgcgttcatggttt	3	15	8	15	2	3	1	2	1	1	0	7	1	7	1	5	1	1	3	5	1	0	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:182543437C>A	ENST00000295108.3	-	2	608	c.151G>T	c.(151-153)Gac>Tac	p.D51Y	CERKL_ENST00000479558.1_Intron|NEUROD1_ENST00000496876.1_Intron	NM_002500.4	NP_002491.2	Q13562	NDF1_HUMAN	neuronal differentiation 1	51					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.D51Y(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)			CTCAGTGAGTCCTCCTCTGCG	0.562																																					p.D51Y		Atlas-SNP	.											NEUROD1,NS,carcinoma,0,1	NEUROD1	67	1	1	Substitution - Missense(1)	lung(1)	c.G151T						PASS	.						133	103	113					2																	182543437		2203	4300	6503	SO:0001583	missense	4760	exon2			GTGAGTCCTCCTC	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.151G>T	2.37:g.182543437C>A	ENSP00000295108:p.Asp51Tyr	133	0	0		187	70	0.374332	NM_002500	B2R9I8|F1T0E1|O00343|Q13340|Q5U095|Q96TH0|Q99455|Q9UEC8	Missense_Mutation	SNP	ENST00000295108.3	37	CCDS2283.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.070590	0.76301	.	.	ENSG00000162992	ENST00000295108	D	0.95588	-3.75	5.9	5.9	0.94986	.	0.281498	0.32503	N	0.006008	D	0.91885	0.7431	L	0.40543	1.245	0.58432	D	0.999998	P	0.49090	0.919	B	0.34779	0.189	D	0.92806	0.6260	10	0.62326	D	0.03	-0.0043	17.7728	0.88497	0.0:1.0:0.0:0.0	.	51	Q13562	NDF1_HUMAN	Y	51	ENSP00000295108:D51Y	ENSP00000295108:D51Y	D	-	1	0	NEUROD1	182251682	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	2.332000	0.43903	2.788000	0.95919	0.650000	0.86243	GAC	.	.	none		0.562	NEUROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255792.2	NM_002500		A	182543437	C	A	182543437	3	1	10	1	0	0	0	0	1	0	0	0	10357	855	30	4	923	4	NEUROD1	2	182543437	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	14435746	182543437	60655936	20	1102											
HECW2	57520	hgsc.bcm.edu	37	chr2	197298113	197298113	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctggggatttcgacgcctcAcaaaaagcaggtgctcccgg	9	8	12	12	3	2	0	1	0	1	0	4	2	3	1	2	4	2	2	2	4	2	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:197298113A>G	ENST00000260983.3	-	2	217	c.35T>C	c.(34-36)gTg>gCg	p.V12A		NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	12					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						TCGACGCCTCACAAAAAGCAG	0.547																																					p.V12A		Atlas-SNP	.											.	HECW2	239	.	0			c.T35C						PASS	.						63	58	60					2																	197298113		2203	4300	6503	SO:0001583	missense	57520	exon2			CGCCTCACAAAAA	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.35T>C	2.37:g.197298113A>G	ENSP00000260983:p.Val12Ala	167	0	0		225	84	0.373333	NM_020760	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Missense_Mutation	SNP	ENST00000260983.3	37	CCDS33354.1	.	.	.	.	.	.	.	.	.	.	A	7.043	0.563022	0.13498	.	.	ENSG00000138411	ENST00000260983;ENST00000452031;ENST00000427457	T	0.30714	1.52	5.27	5.27	0.74061	.	0.214433	0.39759	N	0.001275	T	0.26484	0.0647	L	0.51422	1.61	0.41396	D	0.987641	P	0.38767	0.646	B	0.35770	0.21	T	0.05435	-1.0885	10	0.13853	T	0.58	.	13.9092	0.63855	1.0:0.0:0.0:0.0	.	12	Q9P2P5	HECW2_HUMAN	A	12	ENSP00000260983:V12A	ENSP00000260983:V12A	V	-	2	0	HECW2	197006358	0.999000	0.42202	1.000000	0.80357	0.878000	0.50629	2.801000	0.47908	2.209000	0.71365	0.459000	0.35465	GTG	.	.	none		0.547	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760		G	197298113	A	G	197298113	3	3	10	1	0	0	0	0	1	0	0	0	7052	159	6	3	4795	3	HECW2	2	197298113	Missense_Mutation	SNP	A	TCGA-FF-8041-01A-11D-2210-10	14754676	197298113	45901260	21	1103											
PTH2R	5746	hgsc.bcm.edu	37	chr2	209358138	209358138	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacaggtggcggccagcacAcgcatggtgcttatctctgg	7	9	13	12	2	2	0	1	0	1	0	3	0	2	0	1	5	2	3	1	5	1	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:209358138A>C	ENST00000272847.2	+	13	1620	c.1407A>C	c.(1405-1407)acA>acC	p.T469T	AC019185.4_ENST00000424628.1_RNA|PTH2R_ENST00000413482.1_3'UTR	NM_005048.2	NP_005039.1	P49190	PTH2R_HUMAN	parathyroid hormone 2 receptor	469					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)	CGGCCAGCACACGCATGGTGC	0.592																																					p.T469T		Atlas-SNP	.											.	PTH2R	92	.	0			c.A1407C						PASS	.						44	36	39					2																	209358138		2203	4300	6503	SO:0001819	synonymous_variant	5746	exon13			CAGCACACGCATG	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.1407A>C	2.37:g.209358138A>C		154	0	0		165	26	0.157576	NM_005048	Q8N429	Silent	SNP	ENST00000272847.2	37	CCDS2383.1																																																																																			.	.	none		0.592	PTH2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256519.2	NM_005048		C	209358138	A	C	209358138	2	2	10	1	0	0	0	0	0	0	0	1	12773	146	6	5		5	PTH2R	2	209358138	Silent	SNP	A	TCGA-FF-8041-01A-11D-2210-10	12060025	209358138	33841235	22	1104											
IQCA1	79781	hgsc.bcm.edu	37	chr2	237374287	237374287	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctttatctgcacctcattccGcaggcggtccaccttttcag	6	13	7	15	2	3	0	2	0	1	0	5	0	5	0	4	2	1	2	4	2	1	5	rs35814876	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr2:237374287G>A	ENST00000409907.3	-	6	1061	c.787C>T	c.(787-789)Cgg>Tgg	p.R263W	IQCA1_ENST00000431676.2_Missense_Mutation_p.R263W|IQCA1_ENST00000309507.5_Missense_Mutation_p.R259W	NM_024726.4	NP_079002.3	Q86XH1	IQCA1_HUMAN	IQ motif containing with AAA domain 1	263							ATP binding (GO:0005524)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(1)	26						ACCTCATTCCGCAGGCGGTCC	0.448													G|||	4	0.000798722	0.0	0.0014	5008	,	,		19395	0.0		0.002	False		,,,				2504	0.001				p.R270W		Atlas-SNP	.											IQCA1_ENST00000409907,NS,carcinoma,+1,4	IQCA1	170	4	0			c.C808T						scavenged	.	G	TRP/ARG	4,3850		0,4,1923	131	119	123		787	1.3	0	2	dbSNP_126	123	21,8257		0,21,4118	yes	missense	IQCA1	NM_024726.3	101	0,25,6041	AA,AG,GG		0.2537,0.1038,0.2061	probably-damaging	263/823	237374287	25,12107	1927	4139	6066	SO:0001583	missense	79781	exon6			CATTCCGCAGGCG	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.787C>T	2.37:g.237374287G>A	ENSP00000387347:p.Arg263Trp	202	1	0.00495049		255	40	0.156863	NM_001270585	B4DFH9|E7EWQ0|Q4G164|Q53R37|Q53RV3|Q96NS7|Q9H680	Missense_Mutation	SNP	ENST00000409907.3	37	CCDS46549.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.73|15.73	2.918853|2.918853	0.52546|0.52546	0.001038|0.001038	0.002537|0.002537	ENSG00000132321|ENSG00000132321	ENST00000418802|ENST00000409907;ENST00000457693;ENST00000309507;ENST00000431676;ENST00000412437	.|D;D;D	.|0.96041	.|-3.86;-3.89;-3.89	5.37|5.37	1.31|1.31	0.21738|0.21738	.|.	.|0.120895	.|0.37393	.|N	.|0.002106	D|D	0.97770|0.97770	0.9268|0.9268	M|M	0.88906|0.88906	2.99|2.99	0.09310|0.09310	N|N	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.91635	.|0.999;0.995;0.998	D|D	0.94404|0.94404	0.7625|0.7625	5|10	.|0.87932	.|D	.|0	.|.	15.7632|15.7632	0.78103|0.78103	0.0:0.0:0.3887:0.6113|0.0:0.0:0.3887:0.6113	rs35814876|rs35814876	.|263;270;263	.|E7EWQ0;E9PH78;Q86XH1	.|.;.;IQCA1_HUMAN	V|W	281|263;270;259;263;259	.|ENSP00000387347:R263W;ENSP00000311951:R259W;ENSP00000407213:R263W	.|ENSP00000254653:R263W	A|R	-|-	2|1	0|2	IQCA1|IQCA1	237039026|237039026	0.017000|0.017000	0.18338|0.18338	0.022000|0.022000	0.16811|0.16811	0.026000|0.026000	0.11368|0.11368	0.527000|0.527000	0.22987|0.22987	-0.043000|-0.043000	0.13513|0.13513	0.563000|0.563000	0.77884|0.77884	GCG|CGG	G|0.986;A|0.014	0.014	weak		0.448	IQCA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000329266.1	NM_024726		A	237374287	G	A	237374287	3	1	10	1	0	0	0	0	1	0	0	0	7811	1086	38	1	1737	1	IQCA1	2	237374287	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	28016149	237374287	5825086	23	1105											
SEC22C	9117	hgsc.bcm.edu	37	chr3	42610481	42610481	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggtaaaaatcagtagaggCtgagaggggcagtccatccc	12	7	14	8	0	1	2	1	1	0	2	3	3	3	2	2	4	0	4	2	4	4	2	rs141431943		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:42610481C>G	ENST00000264454.3	-	2	201	c.58G>C	c.(58-60)Gcc>Ccc	p.A20P	SEC22C_ENST00000273156.7_Missense_Mutation_p.A20P|SEC22C_ENST00000493107.1_5'UTR|SEC22C_ENST00000423701.2_Missense_Mutation_p.A20P|SEC22C_ENST00000536332.1_5'UTR|SEC22C_ENST00000417572.1_Missense_Mutation_p.A20P			Q9BRL7	SC22C_HUMAN	SEC22 vesicle trafficking protein homolog C (S. cerevisiae)	20	Longin. {ECO:0000255|PROSITE- ProRule:PRU00231}.				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)		TCAGTAGAGGCTGAGAGGGGC	0.517																																					p.A20P		Atlas-SNP	.											.	SEC22C	27	.	0			c.G58C						PASS	.						74	72	72					3																	42610481		2203	4300	6503	SO:0001583	missense	9117	exon2			TAGAGGCTGAGAG	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.58G>C	3.37:g.42610481C>G	ENSP00000264454:p.Ala20Pro	178	0	0		168	30	0.178571	NM_001201584	O95152|Q68CX3|Q6UW18	Missense_Mutation	SNP	ENST00000264454.3	37	CCDS2700.1	.	.	.	.	.	.	.	.	.	.	C	32	5.146526	0.94603	.	.	ENSG00000093183	ENST00000423701;ENST00000273156;ENST00000417572;ENST00000264454;ENST00000456515;ENST00000450981;ENST00000416880;ENST00000420163	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	5.41	5.41	0.78517	Longin (2);Longin-like (1);	0.000000	0.85682	D	0.000000	T	0.59418	0.2192	M	0.86740	2.835	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	0.66670	-0.5865	10	0.87932	D	0	-10.4295	19.1881	0.93653	0.0:1.0:0.0:0.0	.	20;20;20	Q9BRL7-3;Q9BRL7;Q9BRL7-2	.;SC22C_HUMAN;.	P	20	ENSP00000414576:A20P;ENSP00000273156:A20P;ENSP00000407564:A20P;ENSP00000264454:A20P;ENSP00000391170:A20P;ENSP00000397170:A20P;ENSP00000391957:A20P;ENSP00000408242:A20P	ENSP00000264454:A20P	A	-	1	0	SEC22C	42585485	1.000000	0.71417	0.946000	0.38457	0.871000	0.50021	7.246000	0.78247	2.522000	0.85027	0.655000	0.94253	GCC	C|1.000;T|0.000	.	alt		0.517	SEC22C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254734.1	NM_004206		G	42610481	C	G	42610481	3	3	10	1	0	0	0	0	1	0	0	0	14005	797	28	4	923	4	SEC22C	3	42610481	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10		42610481	155411949	24	1106											
ZNF502	91392	hgsc.bcm.edu	37	chr3	44762425	44762425	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctgtaaaattgactcatcagGgatagtagtaaagaggttcc	14	11	10	6	0	2	2	2	1	0	1	3	3	3	3	1	2	0	4	1	2	6	6			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:44762425G>C	ENST00000296091.4	+	4	372	c.116G>C	c.(115-117)gGg>gCg	p.G39A	ZNF502_ENST00000436624.2_Missense_Mutation_p.G39A|ZNF502_ENST00000449836.1_Missense_Mutation_p.G39A	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	39					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)		GACTCATCAGGGATAGTAGTA	0.418																																					p.G39A		Atlas-SNP	.											.	ZNF502	58	.	0			c.G116C						PASS	.						73	75	74					3																	44762425		2203	4300	6503	SO:0001583	missense	91392	exon4			CATCAGGGATAGT	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.116G>C	3.37:g.44762425G>C	ENSP00000296091:p.Gly39Ala	87	0	0		96	21	0.21875	NM_001134440		Missense_Mutation	SNP	ENST00000296091.4	37	CCDS2719.1	.	.	.	.	.	.	.	.	.	.	G	10.61	1.398645	0.25205	.	.	ENSG00000196653	ENST00000449836;ENST00000296091;ENST00000436624;ENST00000427783;ENST00000411443	T;T;T;T	0.54675	3.42;3.42;3.42;0.56	4.92	0.917	0.19380	.	.	.	.	.	T	0.22513	0.0543	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.28073	-1.0055	9	0.05620	T	0.96	-3.7166	3.6154	0.08075	0.4034:0.1908:0.4058:0.0	.	39	Q8TBZ5	ZN502_HUMAN	A	39	ENSP00000397390:G39A;ENSP00000296091:G39A;ENSP00000406469:G39A;ENSP00000401717:G39A	ENSP00000296091:G39A	G	+	2	0	ZNF502	44737429	0.002000	0.14202	0.053000	0.19242	0.051000	0.14879	0.321000	0.19558	0.668000	0.31126	0.655000	0.94253	GGG	.	.	none		0.418	ZNF502-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256744.4	NM_033210		C	44762425	G	C	44762425	3	2	10	1	0	0	0	0	1	0	0	0	17965	1232	43	4	122	4	ZNF502	3	44762425	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	2151944	44762425	153260005	25	1107											
HYAL3	8372	hgsc.bcm.edu	37	chr3	50332345	50332345	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcccagagccaatgcagtTgagtgttgcgggcaagggtg	8	7	17	9	2	0	2	0	1	0	1	0	2	0	2	2	3	3	4	2	3	2	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:50332345T>G	ENST00000336307.1	-	2	961	c.689A>C	c.(688-690)cAa>cCa	p.Q230P	HYAL3_ENST00000415204.1_Intron|IFRD2_ENST00000484043.1_5'Flank|IFRD2_ENST00000336089.4_5'Flank|IFRD2_ENST00000417626.2_5'Flank|HYAL3_ENST00000450982.1_Missense_Mutation_p.Q230P|HYAL3_ENST00000513170.1_Intron|IFRD2_ENST00000429673.2_5'Flank|IFRD2_ENST00000436390.1_5'Flank|HYAL3_ENST00000359051.3_Missense_Mutation_p.Q230P	NM_001200029.1|NM_003549.3	NP_001186958.1|NP_003540.2	O43820	HYAL3_HUMAN	hyaluronoglucosaminidase 3	230					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)		CCAATGCAGTTGAGTGTTGCG	0.622																																					p.Q230P		Atlas-SNP	.											.	HYAL3	34	.	0			c.A689C						PASS	.						64	64	64					3																	50332345		2203	4300	6503	SO:0001583	missense	8372	exon2			TGCAGTTGAGTGT	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.689A>C	3.37:g.50332345T>G	ENSP00000337425:p.Gln230Pro	208	0	0		211	88	0.417062	NM_001200030	O60540|Q8NFK2|Q8NFK3|Q8NFK4|Q96E56|Q9BRW9	Missense_Mutation	SNP	ENST00000336307.1	37	CCDS2815.1	.	.	.	.	.	.	.	.	.	.	T	16.70	3.196026	0.58126	.	.	ENSG00000186792	ENST00000359051;ENST00000336307;ENST00000450982	T;T;T	0.24908	1.83;1.83;1.83	5.26	1.71	0.24356	Aldolase-type TIM barrel (1);Glycoside hydrolase, superfamily (1);	0.428784	0.22758	U	0.055998	T	0.42675	0.1213	M	0.88979	2.995	0.27105	N	0.962515	P;D	0.53151	0.939;0.958	P;P	0.52386	0.697;0.571	T	0.35992	-0.9766	10	0.72032	D	0.01	-2.7947	7.8275	0.29324	0.0:0.2392:0.0:0.7608	.	230;230	O43820;O43820-2	HYAL3_HUMAN;.	P	230	ENSP00000351946:Q230P;ENSP00000337425:Q230P;ENSP00000391922:Q230P	ENSP00000337425:Q230P	Q	-	2	0	HYAL3	50307349	0.000000	0.05858	0.992000	0.48379	0.932000	0.56968	-0.339000	0.07832	0.850000	0.35239	0.460000	0.39030	CAA	.	.	none		0.622	HYAL3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000346664.1	NM_003549		G	50332345	T	G	50332345	3	3	10	1	0	0	0	0	1	0	0	0	7474	1812	63	5	576	5	HYAL3	3	50332345	Missense_Mutation	SNP	T	TCGA-FF-8041-01A-11D-2210-10	5569920	50332345	147690085	26	1108											
CD200	4345	hgsc.bcm.edu	37	chr3	112059764	112059764	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcaggtgatcaggatgcccTtctctcatctgtctacctac	7	14	7	13	0	6	1	3	1	3	0	7	2	6	2	2	2	3	0	2	2	2	4			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:112059764T>G	ENST00000315711.8	+	2	85	c.28T>G	c.(28-30)Ttc>Gtc	p.F10V	CD200_ENST00000473539.1_Missense_Mutation_p.F35V|CD200_ENST00000383681.3_Intron	NM_005944.5	NP_005935.4	P41217	OX2G_HUMAN	CD200 molecule	10					regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16		Acute lymphoblastic leukemia(4;1.7e-08)|all_hematologic(4;8.82e-05)				CAGGATGCCCTTCTCTCATCT	0.483																																					p.F35V		Atlas-SNP	.											.	CD200	33	.	0			c.T103G						PASS	.						153	126	135					3																	112059764		2203	4300	6503	SO:0001583	missense	4345	exon3			ATGCCCTTCTCTC		CCDS2965.1, CCDS33818.1	3q13.2	2013-09-20	2006-03-28	2004-09-01	ENSG00000091972	ENSG00000091972		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	7203	protein-coding gene	gene with protein product		155970	"antigen identified by monoclonal antibody MRC OX-2", "CD200 antigen"	MOX1, MOX2			Standard	XM_005247482		Approved	MRC, OX-2	uc003dyw.3	P41217	OTTHUMG00000159248	ENST00000315711.8:c.28T>G	3.37:g.112059764T>G	ENSP00000312766:p.Phe10Val	127	0	0		94	24	0.255319	NM_001004196	B3KQI1|B4DLW9|D3DN65|Q6J2Q6|Q6PIQ4|Q8TB85|Q9H3J3	Missense_Mutation	SNP	ENST00000315711.8	37	CCDS2965.1	.	.	.	.	.	.	.	.	.	.	T	11.59	1.685253	0.29872	.	.	ENSG00000091972	ENST00000315711;ENST00000473539	T;T	0.72505	1.05;-0.66	5.18	4.01	0.46588	.	0.230049	0.31102	N	0.008250	T	0.54351	0.1853	N	0.24115	0.695	0.47183	D	0.999341	B;B	0.23249	0.082;0.01	B;B	0.19946	0.027;0.011	T	0.51076	-0.8751	10	0.49607	T	0.09	-6.9091	9.0178	0.36182	0.0:0.0:0.1864:0.8136	.	10;35	P41217-2;P41217-3	.;.	V	10;35	ENSP00000312766:F10V;ENSP00000420298:F35V	ENSP00000312766:F10V	F	+	1	0	CD200	113542454	0.584000	0.26766	0.303000	0.25071	0.960000	0.62799	0.805000	0.27112	0.971000	0.38288	0.533000	0.62120	TTC	.	.	none		0.483	CD200-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354078.1			G	112059764	T	G	112059764	3	3	10	1	0	0	0	0	1	0	0	0	2982	1609	56	5	113	5	CD200	3	112059764	Missense_Mutation	SNP	T	TCGA-FF-8041-01A-11D-2210-10	61727419	112059764	85962666	27	1109											
C3orf15	89876	hgsc.bcm.edu	37	chr3	119466110	119466110	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgcttatgaaatggaaagccGgtgtgtatcaagagaacaga	15	9	12	5	1	1	3	1	1	0	2	1	5	1	4	1	2	3	2	1	2	6	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:119466110G>A	ENST00000273390.5	+	15	2128	c.2051G>A	c.(2050-2052)cGc>cAc	p.R684H	RP11-169N13.4_ENST00000489428.2_RNA	NM_033364.3	NP_203528	Q7Z4T9	MAAT1_HUMAN	MYCBP-associated, testis expressed 1	520						mitochondrion (GO:0005739)											ATGGAAAGCCGGTGTGTATCA	0.388																																					p.R684H		Atlas-SNP	.											C3orf15,NS,carcinoma,+1,2	.	.	2	0			c.G2051A						scavenged	.						76	68	71					3																	119466110		2203	4300	6503	SO:0001630	splice_region_variant	89876	exon15			AAAGCCGGTGTGT	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.2051+1G>A	3.37:g.119466110G>A		95	0	0		56	3	0.0535714	NM_033364	A0AVK2|A8K1J9|B3KP23|B4DG52|B4DZ14|C9JUG4|Q68DX2|Q8TD41|Q96A45|Q96JE8	Missense_Mutation	SNP	ENST00000273390.5	37	CCDS2994.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.389491	0.82902	.	.	ENSG00000183833	ENST00000273390	T	0.24350	1.86	5.68	4.8	0.61643	.	0.241129	0.40222	N	0.001147	T	0.50171	0.1600	M	0.77103	2.36	0.80722	D	1	B;D;P	0.76494	0.391;0.999;0.647	B;D;B	0.65874	0.067;0.939;0.111	T	0.54589	-0.8271	10	0.54805	T	0.06	-13.3469	14.3754	0.66869	0.0707:0.0:0.9293:0.0	.	520;622;684	Q7Z4T9;Q7Z4T9-3;Q7Z4T9-7	AAT1_HUMAN;.;.	H	684	ENSP00000273390:R684H	ENSP00000273390:R684H	R	+	2	0	C3orf15	120948800	1.000000	0.71417	0.994000	0.49952	0.918000	0.54935	4.272000	0.58908	1.403000	0.46800	0.591000	0.81541	CGC	.	.	none		0.388	MAATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355222.1	NM_033364	Missense_Mutation	A	119466110	G	A	119466110	5	1	10	1	0	0	0	0	0	0	1	0	2211	1130	39	1	2109	1	C3orf15	3	119466110	Splice_Site	SNP	G	TCGA-FF-8041-01A-11D-2210-10	7406346	119466110	78556320	28	1110											
SEMA5B	54437	hgsc.bcm.edu	37	chr3	122632728	122632728	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcctcccggctcttgcccacGcagatgcggcccccgtggcg	3	7	12	19	5	1	1	0	0	1	1	3	1	3	1	5	3	2	2	5	3	0	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:122632728G>A	ENST00000357599.3	-	15	2495	c.2109C>T	c.(2107-2109)tgC>tgT	p.C703C	SEMA5B_ENST00000451055.2_Silent_p.C757C|SEMA5B_ENST00000195173.4_Silent_p.C703C	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	703	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.			C -> F (in Ref. 2; AAQ88491). {ECO:0000305}.	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)		TCTTGCCCACGCAGATGCGGC	0.657																																					p.C757C		Atlas-SNP	.											.	SEMA5B	303	.	0			c.C2271T						PASS	.						49	53	51					3																	122632728		2203	4299	6502	SO:0001819	synonymous_variant	54437	exon15			GCCCACGCAGATG	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.2109C>T	3.37:g.122632728G>A		143	0	0		80	38	0.475	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Silent	SNP	ENST00000357599.3	37	CCDS35491.1																																																																																			.	.	none		0.657	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702		A	122632728	G	A	122632728	2	1	10	1	0	0	0	0	0	0	0	1	14053	1079	38	1		1	SEMA5B	3	122632728	Silent	SNP	G	TCGA-FF-8041-01A-11D-2210-10	3166618	122632728	75389702	29	1111											
DNAJC13	23317	hgsc.bcm.edu	37	chr3	132245067	132245067	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcgagcagatactgttggtcTagcctgtgaagcaattaatc	11	11	11	8	1	1	2	0	1	1	1	2	3	1	2	1	1	4	3	1	1	5	4			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:132245067T>C	ENST00000260818.6	+	53	6571	c.6323T>C	c.(6322-6324)cTa>cCa	p.L2108P		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	2108					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						ACTGTTGGTCTAGCCTGTGAA	0.413																																					p.L2108P		Atlas-SNP	.											.	DNAJC13	253	.	0			c.T6323C						PASS	.						118	112	114					3																	132245067		2203	4300	6503	SO:0001583	missense	23317	exon53			TTGGTCTAGCCTG	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.6323T>C	3.37:g.132245067T>C	ENSP00000260818:p.Leu2108Pro	98	0	0		94	5	0.0531915	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	37	CCDS33857.1	.	.	.	.	.	.	.	.	.	.	T	15.62	2.886801	0.51908	.	.	ENSG00000138246	ENST00000260818;ENST00000538066	T	0.50548	0.74	5.58	5.58	0.84498	Armadillo-like helical (1);Armadillo-type fold (1);	0.233516	0.36482	N	0.002575	T	0.49847	0.1581	M	0.76838	2.35	0.80722	D	1	P	0.39131	0.661	B	0.33521	0.165	T	0.57487	-0.7803	10	0.52906	T	0.07	.	16.0439	0.80704	0.0:0.0:0.0:1.0	.	2108	O75165	DJC13_HUMAN	P	2108;755	ENSP00000260818:L2108P	ENSP00000260818:L2108P	L	+	2	0	DNAJC13	133727757	1.000000	0.71417	0.979000	0.43373	0.989000	0.77384	7.864000	0.87037	2.250000	0.74265	0.482000	0.46254	CTA	.	.	none		0.413	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268		C	132245067	T	C	132245067	3	2	10	1	0	0	0	0	1	0	0	0	4634	1522	53	3	6529	3	DNAJC13	3	132245067	Missense_Mutation	SNP	T	TCGA-FF-8041-01A-11D-2210-10	9612339	132245067	65777363	30	1112											
LRRC15	131578	hgsc.bcm.edu	37	chr3	194080325	194080325	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accatggtgtttctgggtaaCtaggcacctcggggacatgg	8	10	14	9	1	1	0	0	0	1	0	2	1	1	1	2	6	1	3	2	6	2	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr3:194080325C>G	ENST00000347624.3	-	2	1533	c.1448G>C	c.(1447-1449)aGt>aCt	p.S483T	LRRC15_ENST00000428839.1_Missense_Mutation_p.S489T|LRRC15_ENST00000439944.2_Missense_Mutation_p.S489T	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	483					negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of cell migration (GO:0030335)|receptor-mediated virion attachment to host cell (GO:0046813)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	collagen binding (GO:0005518)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)			biliary_tract(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(20)|ovary(4)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		TTCTGGGTAACTAGGCACCTC	0.532																																					p.S489T		Atlas-SNP	.											.	LRRC15	137	.	0			c.G1466C						PASS	.						162	151	155					3																	194080325		2203	4300	6503	SO:0001583	missense	131578	exon3			GGGTAACTAGGCA	AB071037	CCDS3306.1, CCDS46984.1	3q29	2008-02-05			ENSG00000172061	ENSG00000172061			20818	protein-coding gene	gene with protein product						12923058	Standard	NM_001135057		Approved	LIB	uc003ftu.3	Q8TF66	OTTHUMG00000156048	ENST00000347624.3:c.1448G>C	3.37:g.194080325C>G	ENSP00000306276:p.Ser483Thr	291	0	0		242	55	0.227273	NM_001135057	Q495Q6|Q7RTN7	Missense_Mutation	SNP	ENST00000347624.3	37	CCDS3306.1	.	.	.	.	.	.	.	.	.	.	C	0.557	-0.846990	0.02651	.	.	ENSG00000172061	ENST00000347624;ENST00000439944;ENST00000428839	T;T;T	0.56941	0.43;0.45;0.45	5.24	-0.0103	0.13997	.	1.652070	0.03016	N	0.150004	T	0.37544	0.1007	N	0.19112	0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.17592	-1.0364	10	0.13470	T	0.59	.	10.0974	0.42484	0.253:0.3793:0.3677:0.0	.	483;489	Q8TF66;Q8TF66-2	LRC15_HUMAN;.	T	483;489;489	ENSP00000306276:S483T;ENSP00000389128:S489T;ENSP00000413707:S489T	ENSP00000306276:S483T	S	-	2	0	LRRC15	195561620	0.000000	0.05858	0.003000	0.11579	0.006000	0.05464	-0.283000	0.08433	-0.217000	0.10033	-0.309000	0.09137	AGT	.	.	none		0.532	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2			G	194080325	C	G	194080325	3	3	10	1	0	0	0	0	1	0	0	0	8979	565	20	4	301	4	LRRC15	3	194080325	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	61835258	194080325	3942105	31	1113											
LAP3	51056	hgsc.bcm.edu	37	chr4	17606285	17606285	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctggctctggaacaaactcTtcgaggtaggaataatattt	12	12	9	8	1	2	0	0	0	2	0	3	3	2	2	1	4	2	2	1	4	6	5			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr4:17606285T>C	ENST00000226299.4	+	11	1529	c.1255T>C	c.(1255-1257)Ttc>Ctc	p.F419L	LAP3_ENST00000606142.1_Missense_Mutation_p.F388L|AC006160.5_ENST00000511010.1_RNA|LAP3_ENST00000503467.1_3'UTR	NM_015907.2	NP_056991.2	P28838	AMPL_HUMAN	leucine aminopeptidase 3	419					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						GAACAAACTCTTCGAGGTAGG	0.418																																					p.F419L		Atlas-SNP	.											.	LAP3	50	.	0			c.T1255C						PASS	.						107	101	103					4																	17606285		2203	4300	6503	SO:0001583	missense	51056	exon11			AAACTCTTCGAGG	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.1255T>C	4.37:g.17606285T>C	ENSP00000226299:p.Phe419Leu	114	0	0		107	39	0.364486	NM_015907	B3KMQ3|Q6IAM6|Q6P0L6|Q9UQE3	Missense_Mutation	SNP	ENST00000226299.4	37	CCDS3422.1	.	.	.	.	.	.	.	.	.	.	T	9.660	1.143920	0.21205	.	.	ENSG00000002549	ENST00000226299;ENST00000513105	T;T	0.39229	1.09;1.14	5.84	3.41	0.39046	Peptidase M17, leucyl aminopeptidase, C-terminal (1);	0.261443	0.44097	N	0.000492	T	0.12689	0.0308	N	0.00707	-1.245	0.29001	N	0.887486	B	0.27416	0.178	B	0.30495	0.116	T	0.31052	-0.9957	10	0.09338	T	0.73	-2.9227	8.5381	0.33375	0.0:0.2084:0.0:0.7916	.	419	P28838	AMPL_HUMAN	L	419;189	ENSP00000226299:F419L;ENSP00000424724:F189L	ENSP00000226299:F419L	F	+	1	0	LAP3	17215383	1.000000	0.71417	0.216000	0.23742	0.270000	0.26580	5.560000	0.67332	0.473000	0.27368	-0.290000	0.09829	TTC	.	.	none		0.418	LAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250365.1			C	17606285	T	C	17606285	3	2	10	1	0	0	0	0	1	0	0	0	8632	1609	56	3	1297	3	LAP3	4	17606285	Missense_Mutation	SNP	T	TCGA-FF-8041-01A-11D-2210-10		17606285	173547991	32	1114											
AIMP1	9255	hgsc.bcm.edu	37	chr4	107246152	107246152	+	5'UTR	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcctataggattttctgcCgtctcttggcaaaaatggca	9	15	8	9	1	2	0	0	0	2	0	4	1	3	1	2	3	1	2	2	3	4	6			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr4:107246152C>T	ENST00000442366.1	+	0	38				AIMP1_ENST00000358008.3_5'UTR|AIMP1_ENST00000394701.4_Missense_Mutation_p.R20C	NM_001142415.1	NP_001135887.1	Q12904	AIMP1_HUMAN	aminoacyl tRNA synthetase complex-interacting multifunctional protein 1						angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|inflammatory response (GO:0006954)|leukocyte migration (GO:0050900)|negative regulation of endothelial cell proliferation (GO:0001937)|response to wounding (GO:0009611)|signal transduction (GO:0007165)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|protein homodimerization activity (GO:0042803)|tRNA binding (GO:0000049)			breast(1)|endometrium(2)|kidney(1)|lung(5)|skin(1)|urinary_tract(1)	11						GATTTTCTGCCGTCTCTTGGC	0.358																																					p.R20C		Atlas-SNP	.											.	AIMP1	20	.	0			c.C58T						PASS	.						42	41	41					4																	107246152		2202	4300	6502	SO:0001623	5_prime_UTR_variant	9255	exon2			TTCTGCCGTCTCT	U10117	CCDS3674.1, CCDS47121.1	4q24	2009-05-20	2009-05-20	2009-05-20	ENSG00000164022	ENSG00000164022			10648	protein-coding gene	gene with protein product	"EMAP II", "ARS-interacting multifunctional protein 1"	603605	"small inducible cytokine subfamily E, member 1 (endothelial monocyte-activating)"	SCYE1		7929199, 7545917	Standard	NM_004757		Approved	EMAPII, EMAP-2, p43	uc011cfg.2	Q12904	OTTHUMG00000131217	ENST00000442366.1:c.-15C>T	4.37:g.107246152C>T		349	0	0		295	69	0.233898	NM_001142416	B3KTR2|B4E1S7|Q6FG28|Q96CQ9	Missense_Mutation	SNP	ENST00000442366.1	37	CCDS3674.1	.	.	.	.	.	.	.	.	.	.	C	7.740	0.701160	0.15172	.	.	ENSG00000164022	ENST00000394701	T	0.26223	1.75	5.06	2.42	0.29668	.	0.253283	0.34268	U	0.004120	T	0.38401	0.1039	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.11324	-1.0592	7	0.59425	D	0.04	-8.449	10.7435	0.46166	0.0:0.7985:0.0:0.2015	.	.	.	.	C	20	ENSP00000378191:R20C	ENSP00000378191:R20C	R	+	1	0	AIMP1	107465601	1.000000	0.71417	0.985000	0.45067	0.115000	0.19883	2.116000	0.41930	0.195000	0.20347	-0.964000	0.02622	CGT	.	.	none		0.358	AIMP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253961.1	NM_004757		T	107246152	C	T	107246152	1	4	10	0	1	0	0	0	0	0	0	0	433	652	23	1		1	AIMP1	4	107246152	5'UTR	SNP	C	TCGA-FF-8041-01A-11D-2210-10	89639867	107246152	83908124	33	1115											
PITX2	5308	hgsc.bcm.edu	37	chr4	111539469	111539469	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaggcaggcgtcggcaccgCggaattcagcgacgggctac	9	4	15	13	6	1	0	1	0	0	0	2	2	1	1	1	5	2	3	1	5	2	2	rs149181425		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr4:111539469C>T	ENST00000354925.2	-	7	2471	c.766G>A	c.(766-768)Gcg>Acg	p.A256T	PITX2_ENST00000556049.1_5'Flank|RP11-380D23.2_ENST00000503456.1_lincRNA|PITX2_ENST00000306732.3_Missense_Mutation_p.A263T|PITX2_ENST00000355080.5_Missense_Mutation_p.A210T|PITX2_ENST00000394598.2_Missense_Mutation_p.A256T|PITX2_ENST00000394595.3_3'UTR	NM_001204397.1	NP_001191326.1	Q99697	PITX2_HUMAN	paired-like homeodomain 2	256					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)		GTCGGCACCGCGGAATTCAGC	0.592																																					p.A263T		Atlas-SNP	.											.	PITX2	73	.	0			c.G787A						PASS	.						45	49	48					4																	111539469		2203	4300	6503	SO:0001583	missense	5308	exon3			GCACCGCGGAATT	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.766G>A	4.37:g.111539469C>T	ENSP00000347004:p.Ala256Thr	146	0	0		162	40	0.246914	NM_000325	A8K6C6|B2RA02|B3KXS0|O60578|O60579|O60580|Q3KQX9|Q9BY17	Missense_Mutation	SNP	ENST00000354925.2	37	CCDS3692.1	.	.	.	.	.	.	.	.	.	.	C	17.15	3.315299	0.60524	.	.	ENSG00000164093	ENST00000306732;ENST00000394598;ENST00000355080;ENST00000354925;ENST00000511837	D;D;D;D;D	0.93366	-2.86;-2.99;-3.13;-2.99;-3.21	5.68	4.84	0.62591	.	0.267779	0.42548	D	0.000699	D	0.91334	0.7267	L	0.54908	1.71	0.80722	D	1	P;B;P;P	0.48162	0.802;0.104;0.906;0.701	B;B;B;B	0.42738	0.355;0.016;0.283;0.396	D	0.89846	0.4006	10	0.33141	T	0.24	.	14.5613	0.68140	0.0:0.9297:0.0:0.0703	.	210;210;256;263	A8K6C6;Q99697-3;Q99697;Q99697-2	.;.;PITX2_HUMAN;.	T	263;256;210;256;256	ENSP00000304169:A263T;ENSP00000378097:A256T;ENSP00000347192:A210T;ENSP00000347004:A256T;ENSP00000421454:A256T	ENSP00000304169:A263T	A	-	1	0	PITX2	111758918	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	7.818000	0.86416	1.405000	0.46838	0.655000	0.94253	GCG	C|1.000;A|0.000	.	alt		0.592	PITX2-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256308.2			T	111539469	C	T	111539469	3	4	10	1	0	0	0	0	1	0	0	0	11964	768	27	1	191	1	PITX2	4	111539469	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	4293317	111539469	79614807	34	1116											
FAT1	2195	hgsc.bcm.edu	37	chr4	187629904	187629904	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttgactggcccggctttgaActgtggagaagtcacgtgaa	9	10	13	9	2	1	4	1	3	0	1	1	5	1	4	1	3	1	1	1	3	3	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr4:187629904A>C	ENST00000441802.2	-	2	1287	c.1078T>G	c.(1078-1080)Ttc>Gtc	p.F360V		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	360					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						CCGGCTTTGAACTGTGGAGAA	0.458										HNSCC(5;0.00058)																											p.F360V	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T1078G						PASS	.						121	114	116					4																	187629904		1864	4103	5967	SO:0001583	missense	2195	exon2			CTTTGAACTGTGG	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.1078T>G	4.37:g.187629904A>C	ENSP00000406229:p.Phe360Val	89	0	0		88	19	0.215909	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	A	9.719	1.159141	0.21454	.	.	ENSG00000083857	ENST00000441802;ENST00000260147;ENST00000509647	T;T	0.69306	-0.39;0.54	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.50034	0.1592	N	0.17278	0.47	0.80722	D	1	P	0.43431	0.807	B	0.40940	0.344	T	0.49051	-0.8979	10	0.11485	T	0.65	.	15.4097	0.74908	1.0:0.0:0.0:0.0	.	360	Q14517	FAT1_HUMAN	V	360	ENSP00000406229:F360V;ENSP00000423736:F360V	ENSP00000260147:F360V	F	-	1	0	FAT1	187866898	1.000000	0.71417	0.997000	0.53966	0.958000	0.62258	5.956000	0.70315	2.229000	0.72834	0.482000	0.46254	TTC	.	.	none		0.458	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		C	187629904	A	C	187629904	3	2	10	1	0	0	0	0	1	0	0	0	5697	43	2	5	12792	5	FAT1	4	187629904	Missense_Mutation	SNP	A	TCGA-FF-8041-01A-11D-2210-10	76090435	187629904	3524372	35	1117											
C5orf38	153571	hgsc.bcm.edu	37	chr5	2752510	2752510	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctggtcgcctacccctcgcGgtccactccgcccagcatgg	4	8	10	19	4	1	0	0	0	1	0	5	0	3	0	6	3	2	1	6	3	1	1	rs181498861	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:2752510G>A	ENST00000334000.3	+	1	249	c.132G>A	c.(130-132)gcG>gcA	p.A44A	C5orf38_ENST00000505778.1_Silent_p.A44A|IRX2_ENST00000502957.1_Intron|C5orf38_ENST00000397835.4_Silent_p.A44A|IRX2_ENST00000382611.6_5'Flank|C5orf38_ENST00000457752.2_Silent_p.A44A|C5orf38_ENST00000515640.1_Silent_p.A44A|IRX2_ENST00000302057.5_5'Flank	NM_178569.2	NP_848664.1	Q86SI9	CEI_HUMAN	chromosome 5 open reading frame 38	44						extracellular region (GO:0005576)				endometrium(2)|large_intestine(1)|lung(1)	4				GBM - Glioblastoma multiforme(108;0.205)		TACCCCTCGCGGTCCACTCCG	0.701																																					p.A44A		Atlas-SNP	.											.	C5orf38	20	.	0			c.G132A						PASS	.						14	16	15					5																	2752510		2199	4294	6493	SO:0001819	synonymous_variant	153571	exon1			CCTCGCGGTCCAC	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.132G>A	5.37:g.2752510G>A		58	0	0		51	17	0.333333	NM_178569		Silent	SNP	ENST00000334000.3	37	CCDS34131.1																																																																																			G|0.999;C|0.001	.	alt		0.701	C5orf38-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365956.2	NM_178569		A	2752510	G	A	2752510	2	1	10	1	0	0	0	0	0	0	0	1	2298	1103	39	1		1	C5orf38	5	2752510	Silent	SNP	G	TCGA-FF-8041-01A-11D-2210-10		2752510	178162750	36	1118											
ERAP1	51752	hgsc.bcm.edu	37	chr5	96116871	96116871	+	Frame_Shift_Del	DEL	T	T	-																															tggaaactcctgagtttttaTtttatctcccttaaagcttt																										TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:96116871delT	ENST00000443439.2	-	17	2545	c.2479delA	c.(2479-2481)atafs	p.I827fs	ERAP1_ENST00000296754.3_Frame_Shift_Del_p.I827fs|ERAP1_ENST00000514604.1_5'Flank	NM_001040458.1|NM_001198541.1	NP_001035548.1|NP_001185470.1	Q9NZ08	ERAP1_HUMAN	endoplasmic reticulum aminopeptidase 1	827					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)		TGAGTTTTTATTTTATCTCCC	0.373																																					p.I827fs		Pindel,Atlas-Indel	.											.	ERAP1	59	.	0			c.2480delT						PASS	.						84	89	87					5																	96116871		2203	4300	6503	SO:0001589	frameshift_variant	51752	exon17			.	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.2479delA	5.37:g.96116871delT	ENSP00000406304:p.Ile827fs	87	0	.		128	31	0.242	NM_001198541	O60278|Q6UWY6|Q8NEL4|Q8TAD0|Q9UHF8|Q9UKY2	Frame_Shift_Del	DEL	ENST00000443439.2	37	CCDS47250.1																																																																																			.	.	none		0.373	ERAP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370699.1	NM_016442		-	96116871	T	-	96116871	7	5	10	1	0	1	0	1	0	0	0	0	5205	1493	52	0	391	0	ERAP1	5	96116871	Frame_Shift_Del	DEL	T	TCGA-FF-8041-01A-11D-2210-10	93364361	96116871	84798389	37	1119											
TNFAIP8	25816	hgsc.bcm.edu	37	chr5	118728686	118728686	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	caaaacaagaaggaggcagaGaagatcatcaagaacctcat	20	4	9	8	0	3	4	3	0	0	4	3	6	3	5	1	2	2	1	1	2	7	0			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:118728686G>A	ENST00000503646.1	+	3	895	c.207G>A	c.(205-207)gaG>gaA	p.E69E	TNFAIP8_ENST00000274456.6_Silent_p.E59E|TNFAIP8_ENST00000415806.2_3'UTR|TNFAIP8_ENST00000513374.1_Silent_p.E81E|TNFAIP8_ENST00000504642.1_Silent_p.E71E|TNFAIP8_ENST00000504771.2_Silent_p.E69E			O95379	TFIP8_HUMAN	tumor necrosis factor, alpha-induced protein 8	69					defense response to Gram-positive bacterium (GO:0050830)|interleukin-1 beta production (GO:0032611)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)	cytoplasm (GO:0005737)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)			ovary(1)	1		all_cancers(142;0.0317)|Prostate(80;0.111)|Breast(839;0.231)		Epithelial(69;4.63e-83)|OV - Ovarian serous cystadenocarcinoma(64;1.39e-82)|all cancers(49;4.88e-75)|GBM - Glioblastoma multiforme(465;0.00338)|BRCA - Breast invasive adenocarcinoma(61;0.0148)|COAD - Colon adenocarcinoma(49;0.0829)		AGGAGGCAGAGAAGATCATCA	0.428																																					p.E69E		Atlas-SNP	.											.	TNFAIP8	12	.	0			c.G207A						PASS	.						70	67	68					5																	118728686		2021	4191	6212	SO:0001819	synonymous_variant	25816	exon2			GGCAGAGAAGATC	AF070671	CCDS47257.1, CCDS47258.1, CCDS68933.1	5q23.1	2008-02-05			ENSG00000145779	ENSG00000145779			17260	protein-coding gene	gene with protein product		612111				10233894, 10644768	Standard	NM_001286813		Approved	GG2-1, MDC-3.13, SCC-S2	uc003ksi.3	O95379	OTTHUMG00000162949	ENST00000503646.1:c.207G>A	5.37:g.118728686G>A		149	0	0		170	54	0.317647	NM_014350	B3KMH1|B3KMI2|B7Z713|Q9P1Q1|Q9UER5|Q9UP47	Silent	SNP	ENST00000503646.1	37	CCDS47258.1																																																																																			.	.	none		0.428	TNFAIP8-002	PUTATIVE	alternative_5_UTR|basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000371134.2	NM_014350		A	118728686	G	A	118728686	2	1	10	1	0	0	0	0	0	0	0	1	16291	933	33	2		2	TNFAIP8	5	118728686	Silent	SNP	G	TCGA-FF-8041-01A-11D-2210-10	22611815	118728686	62186574	38	1120											
GRAMD3	65983	hgsc.bcm.edu	37	chr5	125813449	125813449	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	actgctcttctagtgccaaaCgccctgatcatagcaacagt	11	10	7	13	1	3	1	1	1	2	0	3	1	3	1	2	0	5	2	2	0	4	3	rs375006587		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:125813449C>T	ENST00000285689.3	+	6	1013	c.552C>T	c.(550-552)aaC>aaT	p.N184N	RP11-517I3.1_ENST00000512500.1_RNA|RP11-517I3.1_ENST00000515808.1_RNA|GRAMD3_ENST00000542322.1_Silent_p.N192N|GRAMD3_ENST00000543198.1_Silent_p.N161N|GRAMD3_ENST00000515200.1_Silent_p.N161N|GRAMD3_ENST00000513040.1_Silent_p.N199N|GRAMD3_ENST00000511134.1_Silent_p.N168N|GRAMD3_ENST00000502348.1_Silent_p.N75N|GRAMD3_ENST00000544396.1_Silent_p.N80N	NM_023927.2	NP_076416.2	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3	184						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)		TAGTGCCAAACGCCCTGATCA	0.488																																					p.N199N		Atlas-SNP	.											.	GRAMD3	30	.	0			c.C597T						PASS	.	C	,,,,	1,4405	2.1+/-5.4	0,1,2202	114	116	115		597,240,576,504,552	-0.1	1	5		115	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GRAMD3	NM_001146319.1,NM_001146320.1,NM_001146321.1,NM_001146322.1,NM_023927.2	,,,,	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	,,,,	199/448,80/329,192/441,168/417,184/433	125813449	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	65983	exon6			GCCAAACGCCCTG	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.552C>T	5.37:g.125813449C>T		107	0	0		146	35	0.239726	NM_001146319	B7Z1F2|B7Z3R1|B7Z6D8|B7Z8T2|D3DSZ3|Q9H753	Silent	SNP	ENST00000285689.3	37	CCDS4136.1																																																																																			.	.	weak		0.488	GRAMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250922.2	NM_023927		T	125813449	C	T	125813449	2	4	10	1	0	0	0	0	0	0	0	1	6760	535	19	1		1	GRAMD3	5	125813449	Silent	SNP	C	TCGA-FF-8041-01A-11D-2210-10	7084763	125813449	55101811	39	1121											
FNIP1	96459	hgsc.bcm.edu	37	chr5	131013444	131013444	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	atgagtctttgccaacatgtCcacactctgagaggaatgct	11	11	9	10	0	2	2	0	2	2	1	3	4	3	3	2	1	3	1	2	1	2	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:131013444C>G	ENST00000510461.1	-	13	1566	c.1471G>C	c.(1471-1473)Gac>Cac	p.D491H	FNIP1_ENST00000511848.1_Missense_Mutation_p.D491H|FNIP1_ENST00000307954.8_Missense_Mutation_p.D446H|FNIP1_ENST00000307968.7_Missense_Mutation_p.D463H|CTC-432M15.3_ENST00000514667.1_Intron	NM_133372.2	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1	491					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)		GCCAACATGTCCACACTCTGA	0.398																																					p.D491H		Atlas-SNP	.											.	FNIP1	104	.	0			c.G1471C						PASS	.						128	124	125					5																	131013444		2203	4300	6503	SO:0001583	missense	96459	exon13			ACATGTCCACACT	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.1471G>C	5.37:g.131013444C>G	ENSP00000421985:p.Asp491His	96	0	0		126	37	0.293651	NM_133372	D6RJH5|Q86T47|Q9BUT0	Missense_Mutation	SNP	ENST00000510461.1	37	CCDS34227.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.756687	0.89843	.	.	ENSG00000217128	ENST00000307968;ENST00000307954;ENST00000544351;ENST00000510461;ENST00000511848	T;T;T;T	0.31769	1.48;1.48;1.48;1.48	5.45	5.45	0.79879	.	.	.	.	.	T	0.53981	0.1830	L	0.55481	1.735	0.80722	D	1	D;D;D;P	0.89917	0.997;1.0;0.997;0.855	P;D;D;P	0.91635	0.858;0.999;0.91;0.667	T	0.53251	-0.8465	9	0.72032	D	0.01	-1.7286	19.6467	0.95778	0.0:1.0:0.0:0.0	.	491;491;463;491	A8K8V8;Q8TF40-2;Q8TF40-3;Q8TF40	.;.;.;FNIP1_HUMAN	H	463;446;251;491;491	ENSP00000309266:D463H;ENSP00000310453:D446H;ENSP00000421985:D491H;ENSP00000425619:D491H	ENSP00000310453:D446H	D	-	1	0	FNIP1	131041343	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.445000	0.80570	2.716000	0.92895	0.655000	0.94253	GAC	.	.	none		0.398	FNIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370077.1	NM_133372		G	131013444	C	G	131013444	3	3	10	1	0	0	0	0	1	0	0	0	5983	855	30	4	2053	4	FNIP1	5	131013444	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	5199995	131013444	49901816	40	1122											
SHROOM1	134549	hgsc.bcm.edu	37	chr5	132159799	132159799	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctagggcagtattgtgagaGggacctggagtatcattgcc	9	10	15	7	0	1	1	1	1	0	1	1	4	1	3	2	3	1	4	2	3	3	5			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:132159799G>A	ENST00000378679.3	-	7	2358	c.1554C>T	c.(1552-1554)ccC>ccT	p.P518P	SHROOM1_ENST00000378676.1_Silent_p.P449P|SHROOM1_ENST00000488072.1_5'Flank|SHROOM1_ENST00000319854.3_Silent_p.P518P	NM_001172700.1	NP_001166171.1	Q2M3G4	SHRM1_HUMAN	shroom family member 1	518					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)			TATTGTGAGAGGGACCTGGAG	0.597																																					p.P518P		Atlas-SNP	.											.	SHROOM1	35	.	0			c.C1554T						PASS	.						71	70	70					5																	132159799		2203	4300	6503	SO:0001819	synonymous_variant	134549	exon4			GTGAGAGGGACCT	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.1554C>T	5.37:g.132159799G>A		156	0	0		221	39	0.176471	NM_133456	B7WP40|B7ZL01|Q8TDP0|Q8TF41	Silent	SNP	ENST00000378679.3	37	CCDS54902.1																																																																																			.	.	none		0.597	SHROOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133033.1	NM_133456		A	132159799	G	A	132159799	2	1	10	1	0	0	0	0	0	0	0	1	14308	987	35	2		2	SHROOM1	5	132159799	Silent	SNP	G	TCGA-FF-8041-01A-11D-2210-10	1146355	132159799	48755461	41	1123											
SKP1	6500	hgsc.bcm.edu	37	chr5	133494195	133494195	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttttgatattgaaggtcttgCgaatctcctcaggagttttc	8	17	9	7	1	3	2	1	2	2	0	5	4	3	3	1	2	1	1	1	2	3	7			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:133494195C>T	ENST00000353411.6	-	5	590	c.407G>A	c.(406-408)cGc>cAc	p.R136H	SKP1_ENST00000517625.1_Missense_Mutation_p.R136H|SKP1_ENST00000521216.1_Missense_Mutation_p.R136H|SKP1_ENST00000522855.1_Missense_Mutation_p.R136H|SKP1_ENST00000522552.1_Missense_Mutation_p.R136H	NM_170679.2	NP_733779.1	P63208	SKP1_HUMAN	S-phase kinase-associated protein 1	136	Interaction with the F-box domain of F- box proteins. {ECO:0000250}.				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)			GAAGGTCTTGCGAATCTCCTC	0.408																																					p.R136H		Atlas-SNP	.											SKP1,colon,carcinoma,-1,1	SKP1	10	1	0			c.G407A						scavenged	.						156	152	153					5																	133494195		2203	4300	6503	SO:0001583	missense	6500	exon5			GTCTTGCGAATCT	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	ENST00000353411.6:c.407G>A	5.37:g.133494195C>T	ENSP00000231487:p.Arg136His	145	1	0.00689655		132	45	0.340909	NM_170679	D3DQ97|D3DQ98|P34991|Q8TAY2	Missense_Mutation	SNP	ENST00000353411.6	37	CCDS4171.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.405507	0.83230	.	.	ENSG00000113558	ENST00000353411;ENST00000522552;ENST00000521216;ENST00000517625;ENST00000522855;ENST00000328392;ENST00000519321	T;T;T;T;T;T;T	0.59364	0.34;0.29;0.27;0.34;0.34;0.29;0.27	5.06	5.06	0.68205	SKP1 component, dimerisation (2);BTB/POZ fold (1);	0.000000	0.85682	U	0.000000	T	0.75968	0.3922	H	0.95151	3.63	0.80722	D	1	B;B;D	0.59357	0.072;0.048;0.985	B;B;P	0.47528	0.038;0.005;0.549	D	0.85050	0.0928	10	0.66056	D	0.02	-0.7947	18.7998	0.92011	0.0:1.0:0.0:0.0	.	136;136;136	E5RJR5;P63208-2;P63208	.;.;SKP1_HUMAN	H	136	ENSP00000231487:R136H;ENSP00000429472:R136H;ENSP00000431067:R136H;ENSP00000429961:R136H;ENSP00000429686:R136H;ENSP00000331708:R136H;ENSP00000429415:R136H	ENSP00000331708:R136H	R	-	2	0	SKP1	133522094	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	7.214000	0.77958	2.522000	0.85027	0.563000	0.77884	CGC	.	.	none		0.408	SKP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251162.2	NM_170679		T	133494195	C	T	133494195	3	4	10	1	0	0	0	0	1	0	0	0	14376	768	27	1	119	1	SKP1	5	133494195	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	1334396	133494195	47421065	42	1124											
ANKHD1	54882	hgsc.bcm.edu	37	chr5	139917069	139917069	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggaacagagagactggccCgaattcggcaaggagggtct	11	7	15	8	2	1	2	0	0	1	2	2	6	1	4	1	5	1	1	1	5	3	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:139917069C>T	ENST00000360839.2	+	31	7277	c.7123C>T	c.(7123-7125)Cga>Tga	p.R2375*	ANKHD1-EIF4EBP3_ENST00000532219.1_Nonsense_Mutation_p.R2375*|ANKHD1_ENST00000544120.1_Nonsense_Mutation_p.R699*|ANKHD1_ENST00000297183.6_Nonsense_Mutation_p.R2375*	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	2375						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)			GAGACTGGCCCGAATTCGGCA	0.552																																					p.R2375X		Atlas-SNP	.											.	ANKHD1	233	.	0			c.C7123T						PASS	.						98	92	94					5																	139917069		2203	4300	6503	SO:0001587	stop_gained	54882	exon31			CTGGCCCGAATTC	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.7123C>T	5.37:g.139917069C>T	ENSP00000354085:p.Arg2375*	153	0	0		162	65	0.401235	NM_017747	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Nonsense_Mutation	SNP	ENST00000360839.2	37	CCDS4225.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	39|39	7.365931|7.365931	0.98238|0.98238	.|.	.|.	ENSG00000131503|ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996;ENSG00000254996	ENST00000435794;ENST00000432301|ENST00000360839;ENST00000297183;ENST00000253810;ENST00000431508;ENST00000433049;ENST00000544120;ENST00000532219;ENST00000437495	.|.	.|.	.|.	6.08|6.08	5.19|5.19	0.71726|0.71726	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.36991|.	0.0987|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.35748|.	-0.9776|.	3|.	.|0.02654	.|T	.|1	.|.	14.9548|14.9548	0.71104|0.71104	0.2808:0.7192:0.0:0.0|0.2808:0.7192:0.0:0.0	.|.	.|.	.|.	.|.	L|X	865;766|2375;2375;2392;1048;914;699;2375;403	.|.	.|ENSP00000396882:R403X	P|R	+|+	2|1	0|2	ANKHD1|ANKHD1-EIF4EBP3;ANKHD1	139897253|139897253	0.993000|0.993000	0.37304|0.37304	0.999000|0.999000	0.59377|0.59377	0.992000|0.992000	0.81027|0.81027	3.195000|3.195000	0.51013|0.51013	1.523000|1.523000	0.49018|0.49018	0.591000|0.591000	0.81541|0.81541	CCG|CGA	.	.	none		0.552	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		T	139917069	C	T	139917069	4	4	10	1	0	0	0	0	0	1	0	0	628	644	23	1	7351	1	ANKHD1	5	139917069	Nonsense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	6422874	139917069	40998191	43	1125											
PCDHB1	29930	hgsc.bcm.edu	37	chr5	140432615	140432615	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctctacgcgctgagaaccatGgattatgaggccattcaaga	12	9	10	10	2	2	3	1	2	1	2	2	5	2	4	2	2	2	1	2	2	4	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:140432615G>A	ENST00000306549.3	+	1	1637	c.1560G>A	c.(1558-1560)atG>atA	p.M520I		NM_013340.2	NP_037472.2	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1	520	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)			TGAGAACCATGGATTATGAGG	0.433																																					p.M520I		Atlas-SNP	.											.	PCDHB1	148	.	0			c.G1560A						PASS	.						76	77	77					5																	140432615		2203	4300	6503	SO:0001583	missense	29930	exon1			AACCATGGATTAT	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.1560G>A	5.37:g.140432615G>A	ENSP00000307234:p.Met520Ile	94	0	0		143	62	0.433566	NM_013340	Q2M257	Missense_Mutation	SNP	ENST00000306549.3	37	CCDS4243.1	.	.	.	.	.	.	.	.	.	.	G	11.31	1.601493	0.28534	.	.	ENSG00000171815	ENST00000306549	T	0.47177	0.85	6.11	5.24	0.73138	Cadherin (5);Cadherin-like (1);	0.000000	0.53938	D	0.000046	T	0.32704	0.0838	N	0.17674	0.51	0.35001	D	0.755995	B	0.02656	0.0	B	0.06405	0.002	T	0.38585	-0.9654	10	0.62326	D	0.03	.	10.0729	0.42343	0.0:0.1218:0.5105:0.3678	.	520	Q9Y5F3	PCDB1_HUMAN	I	520	ENSP00000307234:M520I	ENSP00000307234:M520I	M	+	3	0	PCDHB1	140412799	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.839000	0.48207	1.579000	0.49836	0.655000	0.94253	ATG	.	.	none		0.433	PCDHB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251822.2	NM_013340		A	140432615	G	A	140432615	3	1	10	1	0	0	0	0	1	0	0	0	11543	1348	47	2	1562	2	PCDHB1	5	140432615	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	515546	140432615	40482645	44	1126											
PCDHB4	56131	hgsc.bcm.edu	37	chr5	140503797	140503797	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggcatctggtggacgtaagCggcaccgggaccctgtccca	7	6	15	13	3	1	0	0	0	1	0	2	2	2	2	3	5	1	3	3	5	1	1	rs561916518		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:140503797C>T	ENST00000194152.1	+	1	2217	c.2217C>T	c.(2215-2217)agC>agT	p.S739S		NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	739					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)			TGGACGTAAGCGGCACCGGGA	0.622													C|||	1	0.000199681	0.0	0.0	5008	,	,		14549	0.0		0.001	False		,,,				2504	0.0				p.S739S		Atlas-SNP	.											.	PCDHB4	177	.	0			c.C2217T						PASS	.						84	96	92					5																	140503797		2203	4300	6503	SO:0001819	synonymous_variant	56131	exon1			CGTAAGCGGCACC	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.2217C>T	5.37:g.140503797C>T		100	0	0		81	4	0.0493827	NM_018938	Q4V761	Silent	SNP	ENST00000194152.1	37	CCDS4246.1																																																																																			.	.	none		0.622	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938		T	140503797	C	T	140503797	2	4	10	1	0	0	0	0	0	0	0	1	11553	767	27	1		1	PCDHB4	5	140503797	Silent	SNP	C	TCGA-FF-8041-01A-11D-2210-10	71182	140503797	40411463	45	1127											
PCDHB7	56129	hgsc.bcm.edu	37	chr5	140554429	140554429	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcttctcccagccctacctGcggctcccggaggcggcccc	3	6	12	20	3	1	0	0	0	1	0	3	1	2	1	6	5	3	2	6	5	1	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:140554429G>A	ENST00000231137.3	+	1	2187	c.2013G>A	c.(2011-2013)ctG>ctA	p.L671L	PCDHB8_ENST00000239444.2_5'Flank	NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	671	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(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)			AGCCCTACCTGCGGCTCCCGG	0.692																																					p.L671L		Atlas-SNP	.											.	PCDHB7	231	.	0			c.G2013A						PASS	.						49	78	69					5																	140554429		2170	4274	6444	SO:0001819	synonymous_variant	56129	exon1			CTACCTGCGGCTC	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.2013G>A	5.37:g.140554429G>A		73	0	0		37	19	0.513514	NM_018940	A1L3Y8	Silent	SNP	ENST00000231137.3	37	CCDS4249.1																																																																																			.	.	none		0.692	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940		A	140554429	G	A	140554429	2	1	10	1	0	0	0	0	0	0	0	1	11556	1306	46	2		2	PCDHB7	5	140554429	Silent	SNP	G	TCGA-FF-8041-01A-11D-2210-10	50632	140554429	40360831	46	1128											
PCDHB16	57717	hgsc.bcm.edu	37	chr5	140564228	140564228	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggcgttggcctcggtgtcGtcgctcttcctcttttcggt	0	16	13	12	5	2	0	0	0	2	0	7	0	3	0	2	4	0	2	2	4	0	4	rs540563709		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:140564228G>A	ENST00000361016.2	+	1	3249	c.2094G>A	c.(2092-2094)tcG>tcA	p.S698S		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	698					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)			CCTCGGTGTCGTCGCTCTTCC	0.697																																					p.S698S		Atlas-SNP	.											PCDHB16,colon,carcinoma,0,2	PCDHB16	159	2	0			c.G2094A						PASS	.						71	75	74					5																	140564228		2201	4297	6498	SO:0001819	synonymous_variant	57717	exon1			GGTGTCGTCGCTC	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.2094G>A	5.37:g.140564228G>A		86	0	0		55	19	0.345455	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Silent	SNP	ENST00000361016.2	37	CCDS4251.1																																																																																			.	.	none		0.697	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957		A	140564228	G	A	140564228	2	1	10	1	0	0	0	0	0	0	0	1	11550	1132	40	1		1	PCDHB16	5	140564228	Silent	SNP	G	TCGA-FF-8041-01A-11D-2210-10	9799	140564228	40351032	47	1129											
PPP2R2B	5521	hgsc.bcm.edu	37	chr5	145969730	145969730	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcctcaagggtcacatcaCgcttggtgtttctgtcgaac	9	11	10	11	2	4	0	3	0	1	0	5	1	4	0	1	2	2	2	1	2	3	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:145969730C>T	ENST00000394413.3	-	9	1682	c.1112G>A	c.(1111-1113)cGt>cAt	p.R371H	PPP2R2B_ENST00000453001.1_Missense_Mutation_p.R371H|PPP2R2B_ENST00000504198.1_Missense_Mutation_p.R377H|PPP2R2B_ENST00000394409.3_Missense_Mutation_p.R429H|PPP2R2B_ENST00000394410.2_Missense_Mutation_p.R360H|CTB-99A3.1_ENST00000512730.1_RNA|PPP2R2B_ENST00000508545.2_Missense_Mutation_p.R360H|PPP2R2B_ENST00000394414.1_Missense_Mutation_p.R437H|PPP2R2B_ENST00000336640.6_Missense_Mutation_p.R374H|PPP2R2B_ENST00000530902.1_5'UTR|PPP2R2B_ENST00000356826.3_Missense_Mutation_p.R371H|PPP2R2B_ENST00000394411.4_Missense_Mutation_p.R371H			Q00005	2ABB_HUMAN	protein phosphatase 2, regulatory subunit B, beta	371					apoptotic process (GO:0006915)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(9)|ovary(1)|prostate(4)|skin(3)	32			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGTCACATCACGCTTGGTGTT	0.512																																					p.R477H		Atlas-SNP	.											PPP2R2B_ENST00000508545,NS,haematopoietic_neoplasm,-1,4	PPP2R2B	271	4	0			c.G1430A						PASS	.						85	79	81					5																	145969730		2203	4300	6503	SO:0001583	missense	5521	exon10			ACATCACGCTTGG	M64930	CCDS4283.1, CCDS4284.1, CCDS43380.1, CCDS4284.2, CCDS64282.1	5q32	2013-01-10	2010-04-14		ENSG00000156475	ENSG00000156475	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "WD repeat domain containing"	9305	protein-coding gene	gene with protein product	"PP2A subunit B isoform beta"	604325	"spinocerebellar ataxia 12", "protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), beta isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B, beta isoform"	SCA12		1849734, 10581021	Standard	NM_181674		Approved	PR55-BETA, PR52B	uc003log.5	Q00005	OTTHUMG00000163381	ENST00000394413.3:c.1112G>A	5.37:g.145969730C>T	ENSP00000377935:p.Arg371His	117	0	0		142	47	0.330986	NM_181675	A6NEJ2|A8K102|B3KPD0|B7Z2F2|B7Z304|D3DQF7|D3DQF8|G3V149	Missense_Mutation	SNP	ENST00000394413.3	37	CCDS4284.1	.	.	.	.	.	.	.	.	.	.	C	18.36	3.607021	0.66558	.	.	ENSG00000156475	ENST00000394413;ENST00000508545;ENST00000394414;ENST00000394411;ENST00000356826;ENST00000453001;ENST00000394410;ENST00000336640;ENST00000504198;ENST00000394409	T;T;T;T;T;T;T;T;T;T	0.74315	-0.83;-0.83;1.47;-0.83;-0.83;-0.83;-0.83;-0.83;-0.83;1.47	5.29	5.29	0.74685	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.115539	0.64402	D	0.000011	T	0.73249	0.3563	L	0.58669	1.825	0.80722	D	1	B;B;B;B;B;B	0.19445	0.036;0.011;0.011;0.022;0.024;0.02	B;B;B;B;B;B	0.15870	0.008;0.005;0.005;0.014;0.005;0.009	T	0.69803	-0.5046	10	0.54805	T	0.06	-2.5928	19.1301	0.93402	0.0:1.0:0.0:0.0	.	429;377;360;437;374;371	Q00005-4;Q00005-3;G3V149;Q00005-5;Q00005-2;Q00005	.;.;.;.;.;2ABB_HUMAN	H	371;360;437;371;371;371;360;374;377;429	ENSP00000377935:R371H;ENSP00000431320:R360H;ENSP00000377936:R437H;ENSP00000377933:R371H;ENSP00000349283:R371H;ENSP00000398779:R371H;ENSP00000377932:R360H;ENSP00000336591:R374H;ENSP00000421396:R377H;ENSP00000377931:R429H	ENSP00000336591:R374H	R	-	2	0	AC011357.1	145949923	1.000000	0.71417	0.973000	0.42090	0.973000	0.67179	4.465000	0.60141	2.767000	0.95098	0.655000	0.94253	CGT	.	.	none		0.512	PPP2R2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251893.2	NM_181678		T	145969730	C	T	145969730	3	4	10	1	0	0	0	0	1	0	0	0	12397	536	19	1	223	1	PPP2R2B	5	145969730	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	5405502	145969730	34945530	48	1130											
THG1L	54974	hgsc.bcm.edu	37	chr5	157161623	157161623	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcctcccagtttgcctccagCtatgtgttttattggcggga	5	14	11	11	1	0	0	0	0	0	0	2	1	2	1	4	2	2	3	4	2	2	5			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr5:157161623C>G	ENST00000231198.7	+	3	652	c.408C>G	c.(406-408)agC>agG	p.S136R	AC026407.1_ENST00000599823.1_Missense_Mutation_p.A35P	NM_017872.3	NP_060342.2	Q9NWX6	THG1_HUMAN	tRNA-histidine guanylyltransferase 1-like (S. cerevisiae)	136					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)			TTGCCTCCAGCTATGTGTTTT	0.458																																					p.S136R		Atlas-SNP	.											.	THG1L	31	.	0			c.C408G						PASS	.						160	158	158					5																	157161623		2203	4300	6503	SO:0001583	missense	54974	exon3			CTCCAGCTATGTG	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.408C>G	5.37:g.157161623C>G	ENSP00000231198:p.Ser136Arg	203	0	0		209	82	0.392345	NM_017872	D3DQJ5|Q53G12|Q7L5R3|Q9H0S2	Missense_Mutation	SNP	ENST00000231198.7	37	CCDS4341.1	.	.	.	.	.	.	.	.	.	.	C	15.80	2.940943	0.52972	.	.	ENSG00000113272	ENST00000231198;ENST00000448153	T	0.46063	0.88	5.95	3.8	0.43715	.	0.203335	0.64402	N	0.000017	T	0.54549	0.1865	M	0.83483	2.645	0.58432	D	0.999995	D	0.60160	0.987	P	0.57468	0.821	T	0.53851	-0.8380	10	0.21540	T	0.41	-19.4724	6.4975	0.22150	0.1369:0.669:0.0:0.1941	.	136	Q9NWX6	THG1_HUMAN	R	136;11	ENSP00000231198:S136R	ENSP00000231198:S136R	S	+	3	2	THG1L	157094201	0.992000	0.36948	1.000000	0.80357	0.997000	0.91878	0.323000	0.19593	0.583000	0.29574	0.650000	0.86243	AGC	.	.	none		0.458	THG1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252579.2	NM_017872		G	157161623	C	G	157161623	3	3	10	1	0	0	0	0	1	0	0	0	15876	796	28	4	418	4	THG1L	5	157161623	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	11191893	157161623	23753637	49	1131											
HIST1H1C	3006	hgsc.bcm.edu	37	chr6	26056385	26056385	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctttcgtttgcaccagagtgCccttgctcaccaggctcttg	5	13	9	14	1	2	1	1	0	1	1	3	1	2	1	3	1	3	4	3	1	0	4			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:26056385C>T	ENST00000343677.2	-	1	314	c.272G>A	c.(271-273)gGc>gAc	p.G91D		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	91	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				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						CACCAGAGTGCCCTTGCTCAC	0.542																																					p.G91D		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.G272A						PASS	.						111	115	114					6																	26056385		2203	4300	6503	SO:0001583	missense	3006	exon1			AGAGTGCCCTTGC	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.272G>A	6.37:g.26056385C>T	ENSP00000339566:p.Gly91Asp	171	0	0		188	87	0.462766	NM_005319	A8K4I2	Missense_Mutation	SNP	ENST00000343677.2	37	CCDS4577.1	.	.	.	.	.	.	.	.	.	.	C	18.78	3.696243	0.68386	.	.	ENSG00000187837	ENST00000343677	T	0.59083	0.29	5.63	5.63	0.86233	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.107097	0.64402	D	0.000006	T	0.79902	0.4526	M	0.92026	3.265	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.83425	0.0035	10	0.87932	D	0	-22.419	19.032	0.92961	0.0:1.0:0.0:0.0	.	91	P16403	H12_HUMAN	D	91	ENSP00000339566:G91D	ENSP00000339566:G91D	G	-	2	0	HIST1H1C	26164364	1.000000	0.71417	1.000000	0.80357	0.311000	0.27955	5.879000	0.69690	2.814000	0.96858	0.655000	0.94253	GGC	.	.	none		0.542	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319		T	26056385	C	T	26056385	3	4	10	1	0	0	0	0	1	0	0	0	7133	739	26	2	373	2	HIST1H1C	6	26056385	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10		26056385	145058682	50	1132											
HIST1H1C	3006	hgsc.bcm.edu	37	chr6	26056488	26056488	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttcagagcagccagagaaaCtccgctacgctctttagagg	11	9	10	11	2	2	3	1	0	1	3	3	4	3	3	2	1	4	3	2	1	3	4			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:26056488C>T	ENST00000343677.2	-	1	211	c.169G>A	c.(169-171)Gtt>Att	p.V57I		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	57	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				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						GCCAGAGAAACTCCGCTACGC	0.572																																					p.V57I		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.G169A						PASS	.						74	83	80					6																	26056488		2203	4300	6503	SO:0001583	missense	3006	exon1			GAGAAACTCCGCT	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.169G>A	6.37:g.26056488C>T	ENSP00000339566:p.Val57Ile	136	0	0		144	61	0.423611	NM_005319	A8K4I2	Missense_Mutation	SNP	ENST00000343677.2	37	CCDS4577.1	.	.	.	.	.	.	.	.	.	.	C	14.93	2.681630	0.47991	.	.	ENSG00000187837	ENST00000343677	T	0.21932	1.98	5.73	5.73	0.89815	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.135447	0.48286	D	0.000194	T	0.25195	0.0612	M	0.87682	2.9	0.58432	D	0.999992	B	0.32968	0.392	B	0.37989	0.262	T	0.02477	-1.1153	10	0.42905	T	0.14	-28.79	15.5188	0.75846	0.0:0.8523:0.1477:0.0	.	57	P16403	H12_HUMAN	I	57	ENSP00000339566:V57I	ENSP00000339566:V57I	V	-	1	0	HIST1H1C	26164467	0.879000	0.30193	0.960000	0.40013	0.011000	0.07611	1.731000	0.38135	2.861000	0.98227	0.655000	0.94253	GTT	.	.	none		0.572	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319		T	26056488	C	T	26056488	3	4	10	1	0	0	0	0	1	0	0	0	7133	565	20	2	476	2	HIST1H1C	6	26056488	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	103	26056488	145058579	51	1133											
UHRF1BP1	54887	hgsc.bcm.edu	37	chr6	34803143	34803144	+	Frame_Shift_Ins	INS	-	-	CACA																															gctctgggtgctgactgactINScacagctcaaggctatgatg																										TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:34803143_34803144insCACA	ENST00000192788.5	+	7	913_914	c.742_743insCACA	c.(742-744)tcafs	p.-248fs	UHRF1BP1_ENST00000452449.2_Frame_Shift_Ins_p.-248fs	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1								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						GCTGACTGACTCACAGCTCAAG	0.505																																					p.S248fs		Atlas-Indel	.											.	UHRF1BP1	102	.	0			c.742_743insCACA						PASS	.																																			SO:0001589	frameshift_variant	54887	exon7			.	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.743_746dupCACA	6.37:g.34803144_34803147dupCACA	ENSP00000192788:p.Ser248fs	114	0	0		120	18	0.15	NM_017754	Q9NXE0	Frame_Shift_Ins	INS	ENST00000192788.5	37	CCDS43455.1																																																																																			.	.	none		0.505	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754		CACA	34803144	-	CACA	34803143	7	5	10	1	0	1	1	0	0	0	0	0	16983	1551	54	0	768	0	UHRF1BP1	6	34803143	Frame_Shift_Ins	INS	-	TCGA-FF-8041-01A-11D-2210-10	8746655	34803143	136311924	52	1134											
KIAA0240	23506	hgsc.bcm.edu	37	chr6	42797411	42797411	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcatgtcatgttgaacagaaActcttccaacatgctcagga	13	10	8	10	0	3	2	2	1	1	1	4	3	4	3	1	1	4	3	1	1	3	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:42797411A>T	ENST00000314073.5	+	6	1516	c.1340A>T	c.(1339-1341)aAc>aTc	p.N447I	GLTSCR1L_ENST00000394168.1_Missense_Mutation_p.N447I			Q6AI39	GSC1L_HUMAN	GLTSCR1-like	447																	TTGAACAGAAACTCTTCCAAC	0.478																																					p.N447I		Atlas-SNP	.											KIAA0240,NS,carcinoma,-1,1	.	.	1	0			c.A1340T						PASS	.						179	175	177					6																	42797411		2203	4300	6503	SO:0001583	missense	23506	exon5			ACAGAAACTCTTC	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.1340A>T	6.37:g.42797411A>T	ENSP00000313933:p.Asn447Ile	73	0	0		89	46	0.516854	NM_015349	A1L3W2|Q5TFZ3|Q92514	Missense_Mutation	SNP	ENST00000314073.5	37	CCDS34451.1	.	.	.	.	.	.	.	.	.	.	A	14.07	2.424540	0.43020	.	.	ENSG00000112624	ENST00000394167;ENST00000536004;ENST00000314073;ENST00000394168	T;T	0.48836	0.8;0.8	5.87	0.737	0.18314	.	0.368457	0.28730	N	0.014329	T	0.18635	0.0447	L	0.44542	1.39	0.40580	D	0.981383	B;P;P	0.40834	0.226;0.631;0.73	B;B;B	0.37304	0.176;0.165;0.246	T	0.02391	-1.1166	10	0.41790	T	0.15	-5.3689	6.926	0.24416	0.6928:0.1162:0.191:0.0	.	447;447;447	F5H616;Q6AI39;B7Z2G7	.;K0240_HUMAN;.	I	447	ENSP00000313933:N447I;ENSP00000377723:N447I	ENSP00000313933:N447I	N	+	2	0	KIAA0240	42905389	0.975000	0.34042	0.824000	0.32777	0.974000	0.67602	1.117000	0.31234	0.190000	0.20209	0.533000	0.62120	AAC	.	.	none		0.478	GLTSCR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040562.3	NM_015349		T	42797411	A	T	42797411	3	4	10	1	0	0	0	0	1	0	0	0	8173	43	2	5	1354	5	KIAA0240	6	42797411	Missense_Mutation	SNP	A	TCGA-FF-8041-01A-11D-2210-10	7994268	42797411	128317656	53	1135											
BMP5	653	hgsc.bcm.edu	37	chr6	55659189	55659189	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	caacccacatctaaagcttgGgcctttcttgtgtctaacaa	11	12	6	12	0	3	0	0	0	3	0	3	0	3	0	2	1	3	1	2	1	5	5			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:55659189G>T	ENST00000370830.3	-	3	1418	c.720C>A	c.(718-720)gcC>gcA	p.A240A	BMP5_ENST00000446683.2_Silent_p.A240A	NM_021073.2	NP_066551.1	P22003	BMP5_HUMAN	bone morphogenetic protein 5	240					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)			CTAAAGCTTGGGCCTTTCTTG	0.383																																					p.A240A		Atlas-SNP	.											.	BMP5	94	.	0			c.C720A						PASS	.						100	101	101					6																	55659189		2203	4300	6503	SO:0001819	synonymous_variant	653	exon3			AGCTTGGGCCTTT		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.720C>A	6.37:g.55659189G>T		75	0	0		52	9	0.173077	NM_021073	B4E0Y4|Q9H547|Q9NTM5	Silent	SNP	ENST00000370830.3	37	CCDS4958.1																																																																																			.	.	none		0.383	BMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041000.1			T	55659189	G	T	55659189	2	4	10	1	0	0	0	0	0	0	0	1	1463	1219	43	4		4	BMP5	6	55659189	Silent	SNP	G	TCGA-FF-8041-01A-11D-2210-10	12861778	55659189	115455878	54	1136											
EYS	346007	hgsc.bcm.edu	37	chr6	65300359	65300359	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agacgtctgtattgaaagtgCtggagttgctgaaactgtat	11	13	12	5	1	1	3	0	2	1	1	1	4	1	4	0	1	3	5	0	1	4	4			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:65300359C>G	ENST00000370621.3	-	26	5927	c.5401G>C	c.(5401-5403)Gca>Cca	p.A1801P	EYS_ENST00000503581.1_Missense_Mutation_p.A1801P|EYS_ENST00000370616.2_Missense_Mutation_p.A1801P			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	1801					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						ATTGAAAGTGCTGGAGTTGCT	0.388																																					p.A1801P		Atlas-SNP	.											.	EYS	527	.	0			c.G5401C						PASS	.						136	126	129					6																	65300359		692	1590	2282	SO:0001583	missense	346007	exon26			AAAGTGCTGGAGT		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.5401G>C	6.37:g.65300359C>G	ENSP00000359655:p.Ala1801Pro	163	0	0		168	46	0.27381	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	37		.	.	.	.	.	.	.	.	.	.	C	7.913	0.736998	0.15574	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	D;D;D	0.84730	-1.89;-1.87;-1.87	5.87	2.14	0.27477	.	.	.	.	.	T	0.46405	0.1391	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.41466	-0.9507	9	0.66056	D	0.02	.	1.4311	0.02334	0.4143:0.259:0.21:0.1168	.	1801;1801	Q5T1H1-1;Q5T1H1	.;EYS_HUMAN	P	1801	ENSP00000424243:A1801P;ENSP00000359655:A1801P;ENSP00000359650:A1801P	ENSP00000359650:A1801P	A	-	1	0	EYS	65357080	0.000000	0.05858	0.005000	0.12908	0.036000	0.12997	-0.187000	0.09656	0.132000	0.18615	-0.467000	0.05162	GCA	.	.	none		0.388	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		G	65300359	C	G	65300359	3	3	10	1	0	0	0	0	1	0	0	0	5334	797	28	4	3950	4	EYS	6	65300359	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	9641170	65300359	105814708	55	1137											
QRSL1	55278	hgsc.bcm.edu	37	chr6	107100238	107100238	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gaatcttaaccagatgtgtgGatgatgcagcaattgtgttg	11	13	12	5	0	1	2	0	1	1	1	1	4	1	3	1	1	3	3	1	1	3	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:107100238G>A	ENST00000369046.4	+	6	816	c.712G>A	c.(712-714)Gat>Aat	p.D238N	QRSL1_ENST00000369044.1_Missense_Mutation_p.D238N	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)		CAGATGTGTGGATGATGCAGC	0.383																																					p.D238N	NSCLC(192;2127 2142 11668 26277 49545)	Atlas-SNP	.											.	QRSL1	30	.	0			c.G712A						PASS	.						103	95	98					6																	107100238		2203	4300	6503	SO:0001583	missense	55278	exon6			TGTGTGGATGATG	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.712G>A	6.37:g.107100238G>A	ENSP00000358042:p.Asp238Asn	203	0	0		212	44	0.207547	NM_018292		Missense_Mutation	SNP	ENST00000369046.4	37	CCDS5057.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.399837	0.62177	.	.	ENSG00000130348	ENST00000369046;ENST00000369044	T;T	0.64260	0.56;-0.09	5.93	5.93	0.95920	.	0.262307	0.42548	D	0.000688	T	0.57227	0.2039	M	0.71581	2.175	0.45172	D	0.998186	B;B	0.21821	0.02;0.061	B;B	0.27608	0.071;0.081	T	0.55068	-0.8198	10	0.46703	T	0.11	-19.3649	20.3495	0.98807	0.0:0.0:1.0:0.0	.	238;238	Q9H0R6;Q9H0R6-2	GATA_HUMAN;.	N	238	ENSP00000358042:D238N;ENSP00000358040:D238N	ENSP00000358040:D238N	D	+	1	0	QRSL1	107206931	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	2.726000	0.47302	2.814000	0.96858	0.591000	0.81541	GAT	.	.	none		0.383	QRSL1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041667.1	NM_018292		A	107100238	G	A	107100238	3	1	10	1	0	0	0	0	1	0	0	0	12896	1174	41	2	734	2	QRSL1	6	107100238	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	41799879	107100238	64014829	56	1138											
SCML4	256380	hgsc.bcm.edu	37	chr6	108070921	108070921	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tggggccgccaagctggggaCcgtggctgcgtcctgaggga	5	6	19	11	3	0	1	0	1	0	0	1	3	1	3	4	6	2	2	4	6	1	0			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:108070921C>T	ENST00000369020.3	-	3	498	c.253G>A	c.(253-255)Gtc>Atc	p.V85I	SCML4_ENST00000369021.3_Missense_Mutation_p.V56I|SCML4_ENST00000369022.2_Missense_Mutation_p.V27I	NM_198081.3	NP_932347.2	Q8N228	SCML4_HUMAN	sex comb on midleg-like 4 (Drosophila)	85					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(1)	25		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)		AAGCTGGGGACCGTGGCTGCG	0.592																																					p.V85I		Atlas-SNP	.											.	SCML4	65	.	0			c.G253A						PASS	.						73	77	76					6																	108070921		2203	4300	6503	SO:0001583	missense	256380	exon3			TGGGGACCGTGGC		CCDS5060.2, CCDS69163.1, CCDS75500.1	6q21	2013-01-10			ENSG00000146285	ENSG00000146285		"Sterile alpha motif (SAM) domain containing"	21397	protein-coding gene	gene with protein product							Standard	NM_001286409		Approved	dJ47M23.1	uc010kdf.3	Q8N228	OTTHUMG00000015313	ENST00000369020.3:c.253G>A	6.37:g.108070921C>T	ENSP00000358016:p.Val85Ile	101	0	0		106	42	0.396226	NM_198081	B0QZ10|B0QZ11|B7ZBX3|Q5JXD0|Q5T0T6|Q8IYY6	Missense_Mutation	SNP	ENST00000369020.3	37	CCDS5060.2	.	.	.	.	.	.	.	.	.	.	C	1.726	-0.495425	0.04291	.	.	ENSG00000146285	ENST00000369022;ENST00000369020;ENST00000369021;ENST00000440927	T;T;T;T	0.42513	0.98;0.99;0.98;0.97	5.15	-4.99	0.03010	.	0.692695	0.12891	N	0.430560	T	0.07954	0.0199	N	0.17872	0.535	0.09310	N	1	B;B;B	0.12630	0.001;0.0;0.006	B;B;B	0.11329	0.002;0.001;0.006	T	0.48896	-0.8994	10	0.02654	T	1	.	17.2554	0.87055	0.0:0.7296:0.0:0.2704	.	85;85;56	B4E0X3;Q8N228;Q8N228-3	.;SCML4_HUMAN;.	I	27;85;56;56	ENSP00000358018:V27I;ENSP00000358016:V85I;ENSP00000358017:V56I;ENSP00000404688:V56I	ENSP00000358016:V85I	V	-	1	0	SCML4	108177614	0.000000	0.05858	0.000000	0.03702	0.684000	0.39900	-1.014000	0.03641	-0.689000	0.05149	0.655000	0.94253	GTC	.	.	none		0.592	SCML4-005	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000041700.3	XM_171128		T	108070921	C	T	108070921	3	4	10	1	0	0	0	0	1	0	0	0	13926	507	18	2	1015	2	SCML4	6	108070921	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	970683	108070921	63044146	57	1139											
NKAIN2	154215	hgsc.bcm.edu	37	chr6	124676480	124676480	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctgcttctatttggaggctgGggacctctcaaaggtaattt	8	14	11	8	0	2	0	1	0	2	0	3	2	2	2	1	5	1	3	1	5	3	5			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:124676480G>C	ENST00000368417.1	+	3	320	c.260G>C	c.(259-261)gGg>gCg	p.G87A	NKAIN2_ENST00000545433.1_Missense_Mutation_p.G72A|NKAIN2_ENST00000368416.1_Missense_Mutation_p.G87A|NKAIN2_ENST00000476571.1_3'UTR|NKAIN2_ENST00000546092.1_Missense_Mutation_p.G87A	NM_001040214.1	NP_001035304.1	Q5VXU1	NKAI2_HUMAN	Na+/K+ transporting ATPase interacting 2	87						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|large_intestine(3)|lung(12)|skin(2)	19				GBM - Glioblastoma multiforme(226;0.104)		TTGGAGGCTGGGGACCTCTCA	0.423																																					p.G87A		Atlas-SNP	.											.	NKAIN2	34	.	0			c.G260C						PASS	.						246	223	231					6																	124676480		2203	4300	6503	SO:0001583	missense	154215	exon3			AGGCTGGGGACCT	AB070452	CCDS34526.1	6q21	2008-02-05	2007-10-04	2007-10-04	ENSG00000188580	ENSG00000188580		"Na+/K+ transporting ATPase interacting"	16443	protein-coding gene	gene with protein product		609758	"T-cell lymphoma breakpoint associated target 1"	TCBA1		17606467	Standard	XM_005266833		Approved	FAM77B	uc003pzo.3	Q5VXU1	OTTHUMG00000015500	ENST00000368417.1:c.260G>C	6.37:g.124676480G>C	ENSP00000357402:p.Gly87Ala	283	0	0		234	116	0.495726	NM_153355	Q8IYR4|Q8TF67	Missense_Mutation	SNP	ENST00000368417.1	37	CCDS34526.1	.	.	.	.	.	.	.	.	.	.	G	16.34	3.094672	0.56075	.	.	ENSG00000188580	ENST00000368416;ENST00000368417;ENST00000546092;ENST00000539866;ENST00000545433	T;T;T;T	0.38077	1.16;1.16;1.16;1.16	5.74	4.86	0.63082	.	0.382836	0.29100	N	0.013152	T	0.30727	0.0774	M	0.80746	2.51	0.54753	D	0.999985	B;B;B;P	0.38473	0.082;0.452;0.294;0.633	B;B;B;B	0.36289	0.088;0.211;0.132;0.221	T	0.35276	-0.9795	10	0.59425	D	0.04	0.1499	16.0861	0.81049	0.0:0.0:0.8649:0.1351	.	87;86;87;87	F5GY48;Q5VXU1-3;Q5VXU1;Q5VXU1-2	.;.;NKAI2_HUMAN;.	A	87;87;87;86;72	ENSP00000357401:G87A;ENSP00000357402:G87A;ENSP00000440287:G87A;ENSP00000437798:G72A	ENSP00000357401:G87A	G	+	2	0	NKAIN2	124718179	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.421000	0.90259	1.410000	0.46936	0.650000	0.86243	GGG	.	.	none		0.423	NKAIN2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042057.1	NM_001040214		C	124676480	G	C	124676480	3	2	10	1	0	0	0	0	1	0	0	0	10445	1232	43	4	270	4	NKAIN2	6	124676480	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	16605559	124676480	46438587	58	1140											
ALDH8A1	64577	hgsc.bcm.edu	37	chr6	135271176	135271176	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gttttccagcatcaaaagtgCgtttgttccagccatagcaa	11	12	8	10	1	1	0	1	0	0	0	3	0	3	0	3	0	4	5	3	0	4	5	rs150345681	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:135271176C>T	ENST00000265605.2	-	1	84	c.16G>A	c.(16-18)Gca>Aca	p.A6T	ALDH8A1_ENST00000367845.2_Missense_Mutation_p.A6T|ALDH8A1_ENST00000367847.2_Missense_Mutation_p.A6T	NM_022568.3	NP_072090.1	Q9H2A2	AL8A1_HUMAN	aldehyde dehydrogenase 8 family, member A1	6					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)	p.A6T(1)		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)		ATCAAAAGTGCGTTTGTTCCA	0.448													C|||	3	0.000599042	0.0	0.0	5008	,	,		19818	0.0		0.003	False		,,,				2504	0.0				p.A6T		Atlas-SNP	.											ALDH8A1,colon,carcinoma,0,1	ALDH8A1	68	1	1	Substitution - Missense(1)	large_intestine(1)	c.G16A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	2,4404	4.2+/-10.8	0,2,2201	103	103	103		16,16,16	0.7	0	6	dbSNP_134	103	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense,missense	ALDH8A1	NM_001193480.1,NM_022568.3,NM_170771.2	58,58,58	0,8,6495	TT,TC,CC		0.0698,0.0454,0.0615	benign,benign,benign	6/438,6/488,6/434	135271176	8,12998	2203	4300	6503	SO:0001583	missense	64577	exon1			AAAGTGCGTTTGT	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.16G>A	6.37:g.135271176C>T	ENSP00000265605:p.Ala6Thr	111	0	0		109	5	0.0458716	NM_022568	B7Z521|O60793|Q24JS9|Q53GT3|Q5TI80	Missense_Mutation	SNP	ENST00000265605.2	37	CCDS5171.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	15.19	2.758936	0.49468	4.54E-4	6.98E-4	ENSG00000118514	ENST00000265605;ENST00000367845;ENST00000367847	T;T;T	0.76186	-1.0;-0.99;-1.0	6.14	0.675	0.17952	.	0.376195	0.27294	N	0.020038	T	0.30293	0.0760	N	0.17082	0.46	0.09310	N	1	B;B;B	0.12013	0.003;0.005;0.003	B;B;B	0.11329	0.004;0.006;0.003	T	0.31558	-0.9939	10	0.19147	T	0.46	.	7.8484	0.29440	0.0:0.5556:0.1117:0.3328	.	6;6;6	B7Z521;Q9H2A2-2;Q9H2A2	.;.;AL8A1_HUMAN	T	6	ENSP00000265605:A6T;ENSP00000356819:A6T;ENSP00000356821:A6T	ENSP00000265605:A6T	A	-	1	0	ALDH8A1	135312869	0.000000	0.05858	0.000000	0.03702	0.934000	0.57294	-0.277000	0.08502	0.128000	0.18479	0.650000	0.86243	GCA	C|0.999;T|0.001	0.001	strong		0.448	ALDH8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042334.2			T	135271176	C	T	135271176	3	4	10	1	0	0	0	0	1	0	0	0	505	768	27	1	1475	1	ALDH8A1	6	135271176	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	10594696	135271176	35843891	59	1141											
HBS1L	10767	hgsc.bcm.edu	37	chr6	135358694	135358694	+	Intron	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atcagacagtgaattattttGaatatataaagaattattcg	17	15	6	3	1	1	4	1	2	0	2	2	4	1	4	0	0	0	0	0	0	9	8			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:135358694G>C	ENST00000367837.5	-	4	637				HBS1L_ENST00000415177.2_Intron|HBS1L_ENST00000314674.3_Intron|HBS1L_ENST00000367820.2_Intron|HBS1L_ENST00000367822.5_Missense_Mutation_p.Q301E|HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000367824.4_Intron|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)		GAATTATTTTGAATATATAAA	0.313																																					p.Q301E		Atlas-SNP	.											.	HBS1L	75	.	0			c.C901G						PASS	.						36	32	33					6																	135358694		692	1590	2282	SO:0001627	intron_variant	10767	exon5			TATTTTGAATATA	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+2016C>G	6.37:g.135358694G>C		117	0	0		92	38	0.413043	NM_001145207	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Missense_Mutation	SNP	ENST00000367837.5	37	CCDS5173.1	.	.	.	.	.	.	.	.	.	.	G	0.406	-0.915705	0.02415	.	.	ENSG00000112339	ENST00000367822	.	.	.	4.82	2.91	0.33838	.	.	.	.	.	T	0.10723	0.0262	.	.	.	0.25267	N	0.989545	B	0.28636	0.218	B	0.25291	0.059	T	0.10613	-1.0622	7	0.62326	D	0.03	.	4.5597	0.12154	0.0899:0.1409:0.6046:0.1646	.	301	Q9Y450-2	.	E	301	.	ENSP00000356796:Q301E	Q	-	1	0	HBS1L	135400387	0.001000	0.12720	0.257000	0.24404	0.077000	0.17291	0.204000	0.17335	2.382000	0.81193	0.655000	0.94253	CAA	.	.	none		0.313	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2			C	135358694	G	C	135358694	1	2	10	0	1	0	0	0	0	0	0	0	6996	1299	45	4		4	HBS1L	6	135358694	Intron	SNP	G	TCGA-FF-8041-01A-11D-2210-10	87518	135358694	35756373	60	1142											
TNFAIP3	7128	hgsc.bcm.edu	37	chr6	138198372	138198376	+	Frame_Shift_Del	DEL	CTCAT	CTCAT	-																															aggctgggaccatggcacaaCtcatctcatcaatgccgcaa																								rs543150550		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	CTCAT	CTCAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:138198372_138198376delCTCAT	ENST00000237289.4	+	6	1031_1035	c.965_969delCTCAT	c.(964-969)actcatfs	p.TH322fs	TNFAIP3_ENST00000485192.1_3'UTR	NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	322	2 X approximate repeats.				apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|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 interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|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 protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		CATGGCACAACTCATCTCATCAATG	0.454			"D, N, F"		"marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"																																p.322_323del	GBM(130;153 1739 22295 28918 47987)	Pindel,Atlas-Indel	.		Rec	yes		6	6q23	7128	"tumor necrosis factor, alpha-induced protein 3"		L	.	TNFAIP3	340	.	25	Whole gene deletion(25)	haematopoietic_and_lymphoid_tissue(25)	c.964_968del						PASS	.																																			SO:0001589	frameshift_variant	7128	exon6			.	M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"OTU domain containing"	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.965_969delCTCAT	6.37:g.138198377_138198381delCTCAT	ENSP00000237289:p.Thr322fs	91	0	.		70	33	0.471	NM_001270508	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Frame_Shift_Del	DEL	ENST00000237289.4	37	CCDS5187.1																																																																																			.	.	none		0.454	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1			-	138198376	CTCAT	-	138198372	7	5	10	1	0	1	0	1	0	0	0	0	16289	565	20	0	983	0	TNFAIP3	6	138198372	Frame_Shift_Del	DEL	CTCAT	TCGA-FF-8041-01A-11D-2210-10	2839678	138198372	32916695	61	1143											
TIAM2	26230	hgsc.bcm.edu	37	chr6	155577707	155577707	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaaccttgctggactctgacGagggcagcttgagcagcggc	8	7	15	11	2	1	2	0	2	1	0	1	5	1	3	1	3	5	4	1	3	1	2	rs116807909	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:155577707G>A	ENST00000461783.3	+	29	5831	c.4558G>A	c.(4558-4560)Gag>Aag	p.E1520K	TIAM2_ENST00000528391.2_Missense_Mutation_p.E864K|TIAM2_ENST00000275246.7_Missense_Mutation_p.E445K|TIAM2_ENST00000367174.2_Missense_Mutation_p.E896K|TIAM2_ENST00000456877.2_Missense_Mutation_p.E832K|TIAM2_ENST00000318981.5_Missense_Mutation_p.E1520K|TIAM2_ENST00000360366.4_Missense_Mutation_p.E1544K|RP11-477D19.2_ENST00000435295.1_RNA|TIAM2_ENST00000456144.1_Missense_Mutation_p.E1549K|TIAM2_ENST00000529824.2_Missense_Mutation_p.E1549K			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1520					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)		GGACTCTGACGAGGGCAGCTT	0.597													G|||	3	0.000599042	0.0023	0.0	5008	,	,		17970	0.0		0.0	False		,,,				2504	0.0				p.E1520K		Atlas-SNP	.											.	TIAM2	161	.	0			c.G4558A						PASS	.	G	LYS/GLU,LYS/GLU,	11,4395	17.9+/-39.9	0,11,2192	35	38	37		1333,4558,	5.9	1	6	dbSNP_132	37	0,8598		0,0,4299	yes	missense,missense,utr-3	TIAM2,TFB1M	NM_001010927.2,NM_012454.3,NM_016020.3	56,56,	0,11,6491	AA,AG,GG		0.0,0.2497,0.0846	benign,benign,	445/627,1520/1702,	155577707	11,12993	2203	4299	6502	SO:0001583	missense	26230	exon26			TCTGACGAGGGCA		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.4558G>A	6.37:g.155577707G>A	ENSP00000437188:p.Glu1520Lys	175	0	0		183	85	0.464481	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Missense_Mutation	SNP	ENST00000461783.3	37	CCDS34558.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	18.40	3.615581	0.66672	0.002497	0.0	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000456144;ENST00000318981;ENST00000367174;ENST00000360366;ENST00000529824;ENST00000456877;ENST00000528391;ENST00000275246	T;T;T;T;T;T;T;T;T	0.08546	3.56;3.5;3.56;3.39;3.56;3.5;3.38;3.38;3.08	5.86	5.86	0.93980	.	0.351137	0.32357	N	0.006205	T	0.04497	0.0123	L	0.59436	1.845	0.37039	D	0.897031	P;P;P;P	0.52061	0.95;0.937;0.854;0.896	B;B;B;B	0.38296	0.154;0.27;0.27;0.139	T	0.43147	-0.9409	10	0.10377	T	0.69	.	18.3756	0.90435	0.0:0.0:1.0:0.0	.	864;1549;1544;1520	E9PKT1;Q8IVF5-2;Q8IVF5-5;Q8IVF5	.;.;.;TIAM2_HUMAN	K	1520;1766;1549;1520;896;1544;1549;832;864;445	ENSP00000437188:E1520K;ENSP00000407746:E1549K;ENSP00000327315:E1520K;ENSP00000356142:E896K;ENSP00000353528:E1544K;ENSP00000433348:E1549K;ENSP00000407183:E832K;ENSP00000435335:E864K;ENSP00000275246:E445K	ENSP00000275246:E445K	E	+	1	0	TIAM2	155619399	1.000000	0.71417	0.994000	0.49952	0.865000	0.49528	6.868000	0.75516	2.780000	0.95670	0.585000	0.79938	GAG	G|0.998;A|0.002	0.002	strong		0.597	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454		A	155577707	G	A	155577707	3	1	10	1	0	0	0	0	1	0	0	0	15906	1059	37	1	4652	1	TIAM2	6	155577707	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	17379335	155577707	15537360	62	1144											
GTF2H5	404672	hgsc.bcm.edu	37	chr6	158613139	158613139	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggttaatgtcctccaggagCgagtgggtgaattaatggac	10	11	14	6	1	0	1	0	1	0	0	2	4	2	3	2	4	1	1	2	4	3	2	rs121434364		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr6:158613139C>T	ENST00000607778.1	+	3	244	c.166C>T	c.(166-168)Cga>Tga	p.R56*		NM_207118.2	NP_997001.1	Q6ZYL4	TF2H5_HUMAN	general transcription factor IIH, polypeptide 5	56					cellular response to gamma radiation (GO:0071480)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, preincision complex assembly (GO:0006294)|regulation of transcription, DNA-templated (GO:0006355)|rRNA processing (GO:0006364)|transcription elongation from RNA polymerase I promoter (GO:0006362)	core TFIIH complex (GO:0000439)|nucleolus (GO:0005730)	rDNA binding (GO:0000182)						Breast(66;0.00519)|Ovarian(120;0.123)|Prostate(117;0.178)		OV - Ovarian serous cystadenocarcinoma(65;5.98e-18)|BRCA - Breast invasive adenocarcinoma(81;2.83e-05)		CCTCCAGGAGCGAGTGGGTGA	0.403								Nucleotide excision repair (NER)																													p.R56X		Atlas-SNP	.											.	GTF2H5	1	.	0			c.C166T	GRCh37	CM041784	GTF2H5	M	rs121434364	PASS	.						104	97	99					6																	158613139		2203	4300	6503	SO:0001587	stop_gained	404672	exon3			CAGGAGCGAGTGG	AK055106	CCDS5256.1	6q25.3	2014-09-17	2004-07-15	2004-07-16		ENSG00000272047		"General transcription factors", "General transcription factor IIH complex subunits"	21157	protein-coding gene	gene with protein product	"DNA repair syndrome trichothiodystrophy group A"	608780	"chromosome 6 open reading frame 175", "trichothiodystrophy"	C6orf175, TTD		15220921	Standard	NM_207118		Approved	FLJ30544, bA120J8.2, TTD-A, TFB5, TFIIH, TTDA	uc003qrd.3	Q6ZYL4		ENST00000607778.1:c.166C>T	6.37:g.158613139C>T	ENSP00000476100:p.Arg56*	201	0	0		173	87	0.50289	NM_207118	Q0P5V8	Nonsense_Mutation	SNP	ENST00000607778.1	37	CCDS5256.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.150837	0.78001	.	.	ENSG00000185068	ENST00000438073	.	.	.	6.06	5.15	0.70609	.	0.056997	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	-1.3438	7.5749	0.27931	0.1988:0.7139:0.0:0.0873	.	.	.	.	X	56	.	ENSP00000415032:R56X	R	+	1	2	GTF2H5	158533127	1.000000	0.71417	1.000000	0.80357	0.696000	0.40369	3.192000	0.50989	1.482000	0.48325	-0.355000	0.07637	CGA	.	.	weak		0.403	GTF2H5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042865.2	NM_207118		T	158613139	C	T	158613139	4	4	10	1	0	0	0	0	0	1	0	0	6875	760	27	1	172	1	GTF2H5	6	158613139	Nonsense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	3035432	158613139	12501928	63	1145											
CARD11	84433	hgsc.bcm.edu	37	chr7	2976756	2976756	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcccgccgcaccatctcgAtcctcatctcgtcgttcttc	4	12	5	20	5	4	0	1	0	3	0	10	1	6	0	5	0	0	2	5	0	0	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:2976756A>C	ENST00000396946.4	-	9	1659	c.1256T>G	c.(1255-1257)aTc>aGc	p.I419S		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	419					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)		CACCATCTCGATCCTCATCTC	0.592			Mis		DLBCL																																p.I419S		Atlas-SNP	.		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	.	CARD11	339	.	0			c.T1256G						PASS	.						165	133	144					7																	2976756		2203	4300	6503	SO:0001583	missense	84433	exon9			ATCTCGATCCTCA	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.1256T>G	7.37:g.2976756A>C	ENSP00000380150:p.Ile419Ser	175	0	0		148	63	0.425676	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	A	9.722	1.159872	0.21454	.	.	ENSG00000198286	ENST00000396946	T	0.31510	1.49	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.22244	0.0536	N	0.19112	0.55	0.80722	D	1	B	0.19331	0.035	B	0.20384	0.029	T	0.03608	-1.1020	10	0.38643	T	0.18	-22.9658	14.2746	0.66173	1.0:0.0:0.0:0.0	.	419	Q9BXL7	CAR11_HUMAN	S	419	ENSP00000380150:I419S	ENSP00000380150:I419S	I	-	2	0	CARD11	2943282	1.000000	0.71417	0.252000	0.24328	0.976000	0.68499	7.318000	0.79029	1.981000	0.57761	0.459000	0.35465	ATC	.	.	none		0.592	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		C	2976756	A	C	2976756	3	2	10	1	0	0	0	0	1	0	0	0	2647	333	12	5	2276	5	CARD11	7	2976756	Missense_Mutation	SNP	A	TCGA-FF-8041-01A-11D-2210-10		2976756	156161907	64	1146											
ACTB	60	hgsc.bcm.edu	37	chr7	5568917	5568917	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ccagattttctccatgtcgtCccagttggtgacgatgccgt	6	13	10	12	3	1	2	0	1	1	1	4	3	2	2	4	1	1	1	4	1	0	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:5568917C>T	ENST00000331789.5	-	3	429	c.238G>A	c.(238-240)Gac>Aac	p.D80N	ACTB_ENST00000464611.1_5'Flank|AC006483.1_ENST00000579427.1_RNA	NM_001101.3	NP_001092.1	P63261	ACTG_HUMAN	actin, beta	80					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)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(2)	8		Ovarian(82;0.0606)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)|OV - Ovarian serous cystadenocarcinoma(56;4.24e-37)		TCCATGTCGTCCCAGTTGGTG	0.602																																					p.D80N		Atlas-SNP	.											.	ACTB	45	.	0			c.G238A						PASS	.						70	70	70					7																	5568917		2203	4300	6503	SO:0001583	missense	60	exon3			TGTCGTCCCAGTT	M28424	CCDS5341.1	7p22	2014-09-17			ENSG00000075624	ENSG00000075624			132	protein-coding gene	gene with protein product		102630				1505215	Standard	NM_001101		Approved		uc003sot.4	P60709	OTTHUMG00000023268	ENST00000331789.5:c.238G>A	7.37:g.5568917C>T	ENSP00000349960:p.Asp80Asn	119	0	0		108	24	0.222222	NM_001101	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000331789.5	37	CCDS5341.1	.	.	.	.	.	.	.	.	.	.	C	19.24	3.788988	0.70337	.	.	ENSG00000075624	ENST00000331789;ENST00000445914;ENST00000400179;ENST00000432588;ENST00000443528;ENST00000417101;ENST00000414620	D;D;D;D;D	0.95853	-3.83;-3.83;-3.83;-3.83;-3.83	5.01	5.01	0.66863	.	0.000000	0.64402	D	0.000005	D	0.95306	0.8477	M	0.81112	2.525	0.52501	D	0.99995	B	0.02656	0.0	B	0.21917	0.037	D	0.93780	0.7083	10	0.87932	D	0	.	15.8267	0.78711	0.0:1.0:0.0:0.0	.	80	P60709	ACTB_HUMAN	N	80;80;52;80;80;83;80	ENSP00000349960:D80N;ENSP00000407473:D80N;ENSP00000393951:D80N;ENSP00000399487:D83N;ENSP00000401032:D80N	ENSP00000349960:D80N	D	-	1	0	ACTB	5535443	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.600000	0.82769	2.312000	0.78011	0.563000	0.77884	GAC	.	.	none		0.602	ACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059589.4	NM_001101		T	5568917	C	T	5568917	3	4	10	1	0	0	0	0	1	0	0	0	193	855	30	2	905	2	ACTB	7	5568917	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	2592161	5568917	153569746	65	1147											
ABCA13	154664	hgsc.bcm.edu	37	chr7	48314897	48314897	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccatgttcaaatgaaagctcCcgaatggaaataactaggaa	17	8	8	8	1	1	1	1	1	0	0	2	4	2	3	2	2	2	2	2	2	7	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:48314897C>T	ENST00000435803.1	+	17	5658	c.5634C>T	c.(5632-5634)tcC>tcT	p.S1878S		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1878					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						ATGAAAGCTCCCGAATGGAAA	0.408																																					p.S1878S		Atlas-SNP	.											.	ABCA13	1192	.	0			c.C5634T						PASS	.						60	61	61					7																	48314897		1824	4073	5897	SO:0001819	synonymous_variant	154664	exon17			AAGCTCCCGAATG	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.5634C>T	7.37:g.48314897C>T		144	0	0		138	26	0.188406	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1																																																																																			.	.	none		0.408	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48314897	C	T	48314897	2	4	10	1	0	0	0	0	0	0	0	1	31	610	22	2		2	ABCA13	7	48314897	Silent	SNP	C	TCGA-FF-8041-01A-11D-2210-10	42745980	48314897	110823766	66	1148											
SGCE	8910	hgsc.bcm.edu	37	chr7	94218023	94218023	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtagtctgctgttggggaatCtgagtctgatgtggcaagtt	7	14	15	5	0	3	2	0	2	3	0	3	3	3	3	0	3	1	5	0	3	3	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:94218023C>T	ENST00000265735.7	-	10	1385	c.1275G>A	c.(1273-1275)caG>caA	p.Q425Q	SGCE_ENST00000428696.2_Silent_p.Q416Q|SGCE_ENST00000415788.2_Silent_p.Q461Q|SGCE_ENST00000437425.2_Silent_p.Q384Q|SGCE_ENST00000447873.1_Silent_p.Q416Q|SGCE_ENST00000445866.2_Silent_p.Q450Q	NM_003919.2	NP_003910.1	O43556	SGCE_HUMAN	sarcoglycan, epsilon	425					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)			GTTGGGGAATCTGAGTCTGAT	0.308																																					p.Q450Q		Atlas-SNP	.											.	SGCE	68	.	0			c.G1350A						PASS	.						130	129	130					7																	94218023		2203	4300	6503	SO:0001819	synonymous_variant	8910	exon11			GGGAATCTGAGTC	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.1275G>A	7.37:g.94218023C>T		68	0	0		94	4	0.0425532	NM_001099401	B2R8N2|D6W5Q8|E9PF60|G5E9K6|Q6L8P0|Q75MH8|Q8NFG8|Q8WW28	Silent	SNP	ENST00000265735.7	37	CCDS5637.1																																																																																			.	.	none		0.308	SGCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255251.2			T	94218023	C	T	94218023	2	4	10	1	0	0	0	0	0	0	0	1	14217	912	32	2		2	SGCE	7	94218023	Silent	SNP	C	TCGA-FF-8041-01A-11D-2210-10	45903126	94218023	64920640	67	1149											
PON3	5446	hgsc.bcm.edu	37	chr7	95025645	95025645	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccgacccccagcaggaccagCgccacgagcttccccatggt	8	4	10	19	3	0	0	0	0	0	0	1	3	1	1	7	2	3	2	7	2	0	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:95025645C>T	ENST00000265627.5	-	1	28	c.18G>A	c.(16-18)gcG>gcA	p.A6A	PON3_ENST00000427422.1_Silent_p.A6A|PON3_ENST00000475439.1_5'Flank|PON1_ENST00000542556.1_Silent_p.A6A|PON3_ENST00000451904.1_Silent_p.A6A	NM_000940.2	NP_000931.1	Q15166	PON3_HUMAN	paraoxonase 3	6					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)	GCAGGACCAGCGCCACGAGCT	0.672																																					p.A6A		Atlas-SNP	.											PON3,NS,carcinoma,-1,1	PON3	59	1	0			c.G18A						PASS	.						97	87	91					7																	95025645		2203	4300	6503	SO:0001819	synonymous_variant	5446	exon1			GACCAGCGCCACG	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.18G>A	7.37:g.95025645C>T		72	0	0		47	9	0.191489	NM_000940	A4D1H8|O75855|O76060|Q6IRU9|Q8IX97|Q9BZH9	Silent	SNP	ENST00000265627.5	37	CCDS5639.1																																																																																			.	.	none		0.672	PON3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333007.1	NM_000940		T	95025645	C	T	95025645	2	4	10	1	0	0	0	0	0	0	0	1	12259	755	27	1		1	PON3	7	95025645	Silent	SNP	C	TCGA-FF-8041-01A-11D-2210-10	807622	95025645	64113018	68	1150											
CUX1	1523	hgsc.bcm.edu	37	chr7	101845432	101845432	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catcgagctcacccggcaggTtaaggaaaagctggccaaga	13	5	12	11	2	1	1	1	0	0	1	2	3	1	2	2	4	2	4	2	4	4	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:101845432T>C	ENST00000292535.7	+	18	2893	c.2855T>C	c.(2854-2856)gTt>gCt	p.V952A	CUX1_ENST00000556210.1_Missense_Mutation_p.V794A|CUX1_ENST00000560541.1_Intron|CUX1_ENST00000393824.3_Intron|CUX1_ENST00000546411.2_Missense_Mutation_p.V850A|CUX1_ENST00000425244.2_Intron|CUX1_ENST00000292538.4_Intron|CUX1_ENST00000550008.2_Missense_Mutation_p.V896A|CUX1_ENST00000547394.2_Intron|CUX1_ENST00000549414.2_Missense_Mutation_p.V930A|CUX1_ENST00000437600.4_Intron|CUX1_ENST00000360264.3_Missense_Mutation_p.V963A	NM_181552.3	NP_853530.2	P39880	CUX1_HUMAN	cut-like homeobox 1	952					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						ACCCGGCAGGTTAAGGAAAAG	0.587																																					p.V963A		Atlas-SNP	.											.	CUX1	253	.	0			c.T2888C						PASS	.						93	99	97					7																	101845432		2203	4300	6503	SO:0001583	missense	1523	exon18			GGCAGGTTAAGGA	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.2855T>C	7.37:g.101845432T>C	ENSP00000292535:p.Val952Ala	125	0	0		96	4	0.0416667	NM_001202543	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000292535.7	37	CCDS5721.1	.	.	.	.	.	.	.	.	.	.	T	18.82	3.704680	0.68615	.	.	ENSG00000257923	ENST00000360264;ENST00000292535;ENST00000549414;ENST00000550008;ENST00000546411;ENST00000556210	T;T;T;T;T;T	0.71461	-0.55;-0.52;-0.55;-0.57;-0.52;-0.53	5.29	5.29	0.74685	Homeodomain protein CUT (2);Lambda repressor-like, DNA-binding (2);	0.162599	0.40554	N	0.001077	T	0.77955	0.4208	M	0.75615	2.305	0.80722	D	1	P;D	0.55385	0.78;0.971	P;P	0.50934	0.471;0.654	T	0.81908	-0.0717	10	0.87932	D	0	-24.5424	15.2336	0.73411	0.0:0.0:0.0:1.0	.	952;963	P39880;P39880-3	CUX1_HUMAN;.	A	963;952;930;896;850;794	ENSP00000353401:V963A;ENSP00000292535:V952A;ENSP00000446630:V930A;ENSP00000447373:V896A;ENSP00000450125:V850A;ENSP00000451558:V794A	ENSP00000292535:V952A	V	+	2	0	CUX1	101632152	1.000000	0.71417	0.955000	0.39395	0.969000	0.65631	7.698000	0.84413	2.010000	0.58986	0.533000	0.62120	GTT	.	.	none		0.587	CUX1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347535.1	NM_001913		C	101845432	T	C	101845432	3	2	10	1	0	0	0	0	1	0	0	0	4066	1725	60	3	2992	3	CUX1	7	101845432	Missense_Mutation	SNP	T	TCGA-FF-8041-01A-11D-2210-10	6819787	101845432	57293231	69	1151											
KIAA1549	57670	hgsc.bcm.edu	37	chr7	138602479	138602479	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atggagccgctgagttccagCgggggtgttgagaaaaagct	10	8	16	7	2	0	2	0	2	0	1	1	4	1	3	2	3	3	4	2	3	2	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr7:138602479C>T	ENST00000422774.1	-	2	1941	c.1893G>A	c.(1891-1893)ccG>ccA	p.P631P	KIAA1549_ENST00000242365.4_Silent_p.P581P|KIAA1549_ENST00000440172.1_Silent_p.P631P			Q9HCM3	K1549_HUMAN	KIAA1549	631	Ser-rich.					integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						TGAGTTCCAGCGGGGGTGTTG	0.502			O	BRAF	pilocytic astrocytoma																																p.P631P	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549	314	.	0			c.G1893A						PASS	.						29	33	32					7																	138602479		1899	4122	6021	SO:0001819	synonymous_variant	57670	exon2			TTCCAGCGGGGGT		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.1893G>A	7.37:g.138602479C>T		69	0	0		71	11	0.15493	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Silent	SNP	ENST00000422774.1	37	CCDS56513.1																																																																																			.	.	none		0.502	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			T	138602479	C	T	138602479	2	4	10	1	0	0	0	0	0	0	0	1	8253	755	27	1		1	KIAA1549	7	138602479	Silent	SNP	C	TCGA-FF-8041-01A-11D-2210-10	36757047	138602479	20536184	70	1152											
USP17L2	377630	hgsc.bcm.edu	37	chr8	11994795	11994795	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcctgatctgtccgggtcGtcgaagagaggtttagcagg	8	10	14	9	3	1	2	0	1	1	1	5	4	3	2	2	3	1	2	2	3	2	2	rs201012791	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:11994795G>A	ENST00000333796.3	-	1	1791	c.1475C>T	c.(1474-1476)aCg>aTg	p.T492M	FAM66D_ENST00000434078.2_RNA	NM_001256869.1|NM_001256871.1|NM_001256872.1|NM_001256873.1|NM_001256874.1|NM_201402.2	NP_001243798.1|NP_001243800.1|NP_001243801.1|NP_001243802.1|NP_001243803.1|NP_958804.2	Q6R6M4	U17L2_HUMAN	ubiquitin specific peptidase 17-like family member 2	492	Mediates interaction with SUDS3.				apoptotic process (GO:0006915)|CAAX-box protein processing (GO:0071586)|cell cycle checkpoint (GO:0000075)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of histone deacetylation (GO:0031064)|negative regulation of protein processing (GO:0010955)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of Ras GTPase activity (GO:0034261)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of RIG-I signaling pathway (GO:1900246)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of apoptotic process (GO:0042981)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of defense response to virus by host (GO:0050691)|regulation of ruffle assembly (GO:1900027)|ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(1)|kidney(1)|large_intestine(11)|liver(1)|lung(8)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	29						TGTCCGGGTCGTCGAAGAGAG	0.512													G|||	2	0.000399361	0.0008	0.0	5008	,	,		21462	0.0		0.001	False		,,,				2504	0.0				p.T492M		Atlas-SNP	.											.	USP17L2	47	.	0			c.C1475T						PASS	.	A	MET/THR	3,2647		1,1,1323	62	67	65		1475	-0.7	0	8		65	2,5746		0,2,2872	no	missense	USP17L2	NM_201402.2	81	1,3,4195	AA,AG,GG		0.0348,0.1132,0.0595	benign	492/531	11994795	5,8393	1325	2874	4199	SO:0001583	missense	377630	exon1			CGGGTCGTCGAAG	BC156290	CCDS43713.1	8p23.1	2012-10-09	2012-10-09		ENSG00000223443	ENSG00000223443			34434	protein-coding gene	gene with protein product	"deubiquitinating enzyme 3"	610186	"ubiquitin specific peptidase 17-like 2"				Standard	NM_201402		Approved	DUB3	uc003wvc.1	Q6R6M4	OTTHUMG00000165295	ENST00000333796.3:c.1475C>T	8.37:g.11994795G>A	ENSP00000333329:p.Thr492Met	293	0	0		362	96	0.265193	NM_201402		Missense_Mutation	SNP	ENST00000333796.3	37	CCDS43713.1	.	.	.	.	.	.	.	.	.	.	G	7.058	0.565875	0.13560	0.001132	3.48E-4	ENSG00000223443	ENST00000333796	T	0.11821	2.74	0.36	-0.721	0.11189	.	1.611680	0.04297	U	0.346582	T	0.12390	0.0301	.	.	.	0.09310	N	1	D	0.57571	0.98	B	0.44044	0.439	T	0.19063	-1.0317	8	0.51188	T	0.08	.	.	.	.	.	492	Q6R6M4	U17L2_HUMAN	M	492	ENSP00000333329:T492M	ENSP00000333329:T492M	T	-	2	0	USP17L2	12032204	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.296000	0.01142	-0.412000	0.07519	-0.410000	0.06199	ACG	.	.	weak		0.512	USP17L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383303.2	NM_201402		A	11994795	G	A	11994795	3	1	10	1	0	0	0	0	1	0	0	0	17063	1145	40	1	121	1	USP17L2	8	11994795	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10		11994795	134369227	71	1153											
PCM1	5108	hgsc.bcm.edu	37	chr8	17843569	17843569	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcaaactcagaacttactccTagtgagagccttgctactac	12	11	6	12	0	2	2	2	1	0	2	3	3	3	2	2	0	7	1	2	0	6	5			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:17843569T>C	ENST00000519253.1	+	26	4634	c.4383T>C	c.(4381-4383)ccT>ccC	p.P1461P	PCM1_ENST00000524226.1_Silent_p.P1407P|PCM1_ENST00000327578.8_Silent_p.P160P|PCM1_ENST00000325083.8_Silent_p.P1461P			Q15154	PCM1_HUMAN	pericentriolar material 1	1461	Interaction with HAP1.				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)		AACTTACTCCTAGTGAGAGCC	0.323			T	"RET, JAK2"	"papillary thyroid, CML, MPD"																																p.P1461P		Atlas-SNP	.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"E, L"	.	PCM1	120	.	0			c.T4383C						PASS	.						85	82	83					8																	17843569		1842	4078	5920	SO:0001819	synonymous_variant	5108	exon26			TACTCCTAGTGAG		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.4383T>C	8.37:g.17843569T>C		100	0	0		97	4	0.0412371	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Silent	SNP	ENST00000519253.1	37		.	.	.	.	.	.	.	.	.	.	T	9.433	1.086118	0.20390	.	.	ENSG00000078674	ENST00000522275	.	.	.	5.05	0.866	0.19079	.	.	.	.	.	T	0.42921	0.1224	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.20773	-1.0265	4	.	.	.	-5.5681	2.3121	0.04189	0.2364:0.3965:0.2305:0.1365	.	.	.	.	P	201	.	.	L	+	2	0	PCM1	17887849	0.921000	0.31238	0.999000	0.59377	0.981000	0.71138	0.014000	0.13333	0.071000	0.16664	-0.182000	0.12963	CTA	.	.	none		0.323	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197		C	17843569	T	C	17843569	2	2	10	1	0	0	0	0	0	0	0	1	11593	1509	53	3		3	PCM1	8	17843569	Silent	SNP	T	TCGA-FF-8041-01A-11D-2210-10	5848774	17843569	128520453	72	1154											
SLC25A37	51312	hgsc.bcm.edu	37	chr8	23429088	23429088	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctcaggcgggctggccggggCcctcgccgcggccgccacga	3	3	17	18	7	1	0	1	0	0	0	2	1	1	0	5	6	0	1	5	6	0	0			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:23429088C>A	ENST00000519973.1	+	4	935	c.737C>A	c.(736-738)gCc>gAc	p.A246D	FP15737_ENST00000399967.3_5'Flank	NM_016612.2	NP_057696.2	Q9NYZ2	MFRN1_HUMAN	solute carrier family 25 (mitochondrial iron transporter), member 37	246					iron ion homeostasis (GO:0055072)|mitochondrial iron ion transport (GO:0048250)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	iron ion transmembrane transporter activity (GO:0005381)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|urinary_tract(1)	15		Prostate(55;0.114)		Colorectal(74;0.0198)|COAD - Colon adenocarcinoma(73;0.0751)		CTGGCCGGGGCCCTCGCCGCG	0.652																																					p.A246D		Atlas-SNP	.											.	SLC25A37	27	.	0			c.C737A						PASS	.						25	29	28					8																	23429088		1913	4111	6024	SO:0001583	missense	51312	exon4			CCGGGGCCCTCGC	AF495725	CCDS47828.1	8p21.2	2013-05-22	2012-03-29		ENSG00000147454	ENSG00000147454		"Solute carriers"	29786	protein-coding gene	gene with protein product	"mitoferrin"	610387	"solute carrier family 25, member 37"			16511496	Standard	XM_006716352		Approved	MSCP, MFRN, MFRN1	uc003xdo.3	Q9NYZ2	OTTHUMG00000163865	ENST00000519973.1:c.737C>A	8.37:g.23429088C>A	ENSP00000429200:p.Ala246Asp	56	0	0		57	32	0.561404	NM_016612	A2RU93|Q53FT7|Q69YJ8|Q969S1|Q9P0J2	Missense_Mutation	SNP	ENST00000519973.1	37	CCDS47828.1	.	.	.	.	.	.	.	.	.	.	C	30	5.055259	0.93793	.	.	ENSG00000147454	ENST00000519973	D	0.81821	-1.54	5.8	5.8	0.92144	Mitochondrial carrier domain (2);	0.046862	0.85682	D	0.000000	D	0.93973	0.8070	H	0.97829	4.085	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.95648	0.8704	10	0.72032	D	0.01	1.0198	18.6148	0.91299	0.0:1.0:0.0:0.0	.	246	Q9NYZ2	MFRN1_HUMAN	D	246	ENSP00000429200:A246D	ENSP00000429200:A246D	A	+	2	0	SLC25A37	23485033	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.473000	0.81007	2.740000	0.93945	0.650000	0.86243	GCC	.	.	none		0.652	SLC25A37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376039.1	NM_016612		A	23429088	C	A	23429088	3	1	10	1	0	0	0	0	1	0	0	0	14516	739	26	4	751	4	SLC25A37	8	23429088	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	5585519	23429088	122934934	73	1155											
LRRC67	286187	hgsc.bcm.edu	37	chr8	67922976	67922976	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atgcagaagttggttgtcaaCggctatgagctgattaagat	12	12	12	5	1	1	4	1	2	0	2	1	4	1	4	0	2	3	5	0	2	4	4	rs200466525	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:67922976C>T	ENST00000324682.5	-	5	670	c.526G>A	c.(526-528)Gtt>Att	p.V176I	PPP1R42_ENST00000517834.1_5'Flank|PPP1R42_ENST00000522909.1_Missense_Mutation_p.V176I	NM_001013626.2	NP_001013648.1	Q7Z4L9	PPR42_HUMAN	protein phosphatase 1, regulatory subunit 42	176					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)										TGGTTGTCAACGGCTATGAGC	0.284													C|||	2	0.000399361	0.0008	0.0014	5008	,	,		16546	0.0		0.0	False		,,,				2504	0.0				p.V176I		Atlas-SNP	.											.	PPP1R42	2	.	0			c.G526A						PASS	.						75	74	75					8																	67922976		2203	4297	6500	SO:0001583	missense	286187	exon5			TGTCAACGGCTAT	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.526G>A	8.37:g.67922976C>T	ENSP00000315035:p.Val176Ile	83	0	0		63	20	0.31746	NM_001013626		Missense_Mutation	SNP	ENST00000324682.5	37	CCDS34902.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	14.75	2.629273	0.46944	.	.	ENSG00000178125	ENST00000522909;ENST00000421742;ENST00000324682	T;T	0.37058	2.25;1.22	5.83	4.06	0.47325	.	0.157823	0.56097	N	0.000040	T	0.20170	0.0485	N	0.04746	-0.17	0.27969	N	0.936469	B	0.23442	0.085	B	0.25987	0.065	T	0.13764	-1.0497	10	0.37606	T	0.19	-4.3848	12.6376	0.56692	0.0:0.8663:0.0:0.1337	.	176	Q7Z4L9-2	.	I	176	ENSP00000429721:V176I;ENSP00000315035:V176I	ENSP00000315035:V176I	V	-	1	0	LRRC67	68085530	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	3.529000	0.53532	0.838000	0.34948	-0.194000	0.12790	GTT	C|1.000;T|0.000	0.000	strong		0.284	PPP1R42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380034.2	NM_001013626		T	67922976	C	T	67922976	3	4	10	1	0	0	0	0	1	0	0	0	9028	536	19	1	168	1	LRRC67	8	67922976	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	44493888	67922976	78441046	74	1156											
CRISPLD1	83690	hgsc.bcm.edu	37	chr8	75898242	75898242	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatgaagtgtaccgcgcgggAgtggctcagagtaaccacag	11	7	14	9	3	1	2	1	1	0	1	1	3	1	3	2	2	2	3	2	2	4	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:75898242A>T	ENST00000262207.4	+	2	488	c.20A>T	c.(19-21)gAg>gTg	p.E7V	CRISPLD1_ENST00000519798.1_3'UTR	NM_031461.5	NP_113649.1	Q9H336	CRLD1_HUMAN	cysteine-rich secretory protein LCCL domain containing 1	7					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)			ACCGCGCGGGAGTGGCTCAGA	0.463																																					p.E7V		Atlas-SNP	.											.	CRISPLD1	94	.	0			c.A20T						PASS	.						139	150	146					8																	75898242		2203	4300	6503	SO:0001583	missense	83690	exon2			CGCGGGAGTGGCT	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.20A>T	8.37:g.75898242A>T	ENSP00000262207:p.Glu7Val	58	0	0		79	19	0.240506	NM_031461	B2RA60|B7Z929	Missense_Mutation	SNP	ENST00000262207.4	37	CCDS6219.1	.	.	.	.	.	.	.	.	.	.	A	14.60	2.583707	0.46006	.	.	ENSG00000121005	ENST00000262207;ENST00000520277	T;T	0.60299	0.2;1.85	5.37	5.37	0.77165	.	0.261213	0.39985	N	0.001208	T	0.48519	0.1504	L	0.47716	1.5	0.80722	D	1	B	0.20671	0.047	B	0.19946	0.027	T	0.41787	-0.9489	10	0.25751	T	0.34	.	10.6874	0.45852	0.9261:0.0:0.0738:0.0	.	7	Q9H336	CRLD1_HUMAN	V	7	ENSP00000262207:E7V;ENSP00000430504:E7V	ENSP00000262207:E7V	E	+	2	0	CRISPLD1	76060797	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.642000	0.54367	2.254000	0.74563	0.460000	0.39030	GAG	.	.	none		0.463	CRISPLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379117.1	NM_031461		T	75898242	A	T	75898242	3	4	10	1	0	0	0	0	1	0	0	0	3884	304	11	5	22	5	CRISPLD1	8	75898242	Missense_Mutation	SNP	A	TCGA-FF-8041-01A-11D-2210-10	7975266	75898242	70465780	75	1157											
PABPC1	26986	hgsc.bcm.edu	37	chr8	101721960	101721960	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaccaccctccatcataacCtattaaaaaaaagaaaaaaa	22	6	2	11	1	1	1	1	0	0	1	2	2	2	1	4	0	1	0	4	0	9	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:101721960C>A	ENST00000318607.5	-	8	2101		c.e8-1		PABPC1_ENST00000519596.1_Splice_Site|PABPC1_ENST00000519004.1_Splice_Site|AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000522387.1_Splice_Site	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1						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)			CCATCATAACCTATTAAAAAA	0.348																																					.		Atlas-SNP	.											.	PABPC1	76	.	0			c.973-1G>T						PASS	.						35	34	35					8																	101721960		2203	4300	6503	SO:0001630	splice_region_variant	26986	exon9			CATAACCTATTAA	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.973-1G>T	8.37:g.101721960C>A		116	0	0		126	42	0.333333	NM_002568	Q15097|Q93004	Splice_Site	SNP	ENST00000318607.5	37	CCDS6289.1	.	.	.	.	.	.	.	.	.	.	C	14.47	2.545658	0.45280	.	.	ENSG00000070756	ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387;ENST00000519596;ENST00000519100	.	.	.	5.06	4.17	0.49024	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.6976	0.57014	0.0:0.9191:0.0:0.0809	.	.	.	.	.	-1	.	.	.	-	.	.	PABPC1	101791136	1.000000	0.71417	0.998000	0.56505	0.877000	0.50540	7.706000	0.84615	2.514000	0.84764	0.655000	0.94253	.	.	.	none		0.348	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	Intron	A	101721960	C	A	101721960	5	1	10	1	0	0	0	0	0	0	1	0	11372	695	24	4	966	4	PABPC1	8	101721960	Splice_Site	SNP	C	TCGA-FF-8041-01A-11D-2210-10	25823718	101721960	44642062	76	1158											
RIMS2	9699	hgsc.bcm.edu	37	chr8	104513283	104513283	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaggagaaggagcagtccGtgctcaagtaaggacctggc	13	5	15	8	1	1	2	1	0	0	2	2	5	2	4	2	4	2	3	2	4	4	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:104513283G>C	ENST00000406091.3	+	1	169	c.169G>C	c.(169-171)Gtg>Ctg	p.V57L	RP11-1C8.4_ENST00000523422.1_RNA|RP11-1C8.4_ENST00000517376.1_RNA	NM_001100117.2	NP_001093587.1	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	75	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)			GGAGCAGTCCGTGCTCAAGTA	0.647										HNSCC(12;0.0054)																											p.V57L		Atlas-SNP	.											.	RIMS2	1357	.	0			c.G169C						PASS	.						34	39	38					8																	104513283		1986	4141	6127	SO:0001583	missense	9699	exon1			CAGTCCGTGCTCA	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.169G>C	8.37:g.104513283G>C	ENSP00000384892:p.Val57Leu	198	0	0		197	68	0.345178	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Missense_Mutation	SNP	ENST00000406091.3	37	CCDS55269.1	.	.	.	.	.	.	.	.	.	.	G	14.58	2.577298	0.45902	.	.	ENSG00000176406	ENST00000504942;ENST00000406091	T;T	0.76060	-0.99;-0.99	3.76	3.76	0.43208	.	.	.	.	.	T	0.67192	0.2867	L	0.47716	1.5	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.63782	-0.6559	9	0.29301	T	0.29	.	14.5166	0.67824	0.0:0.0:1.0:0.0	.	57	F8WD47	.	L	57	ENSP00000427018:V57L;ENSP00000384892:V57L	ENSP00000384892:V57L	V	+	1	0	RIMS2	104582459	0.985000	0.35326	1.000000	0.80357	0.988000	0.76386	2.166000	0.42406	1.791000	0.52520	0.462000	0.41574	GTG	.	.	none		0.647	RIMS2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001100117		C	104513283	G	C	104513283	3	2	10	1	0	0	0	0	1	0	0	0	13383	1145	40	4	171	4	RIMS2	8	104513283	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	2791323	104513283	41850739	77	1159											
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110495331	110495331	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctgatggatgctgtggattgGcaggtagacaaaataattat	13	12	12	4	0	0	2	0	1	0	1	0	4	0	4	0	4	1	3	0	4	5	4			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:110495331G>T	ENST00000378402.5	+	57	9677	c.9573G>T	c.(9571-9573)tgG>tgT	p.W3191C		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3191					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)			CTGTGGATTGGCAGGTAGACA	0.368										HNSCC(38;0.096)																											p.W3191C		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.G9573T						PASS	.						75	71	72					8																	110495331		1863	4096	5959	SO:0001583	missense	93035	exon57			GGATTGGCAGGTA	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.9573G>T	8.37:g.110495331G>T	ENSP00000367655:p.Trp3191Cys	83	0	0		103	32	0.31068	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.129890	0.77549	.	.	ENSG00000205038	ENST00000378402;ENST00000526472	D;D	0.85339	-1.97;-1.97	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.94660	0.8278	H	0.94847	3.59	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95742	0.8784	10	0.87932	D	0	.	17.1705	0.86828	0.0:0.0:1.0:0.0	.	3191	Q86WI1	PKHL1_HUMAN	C	3191;119	ENSP00000367655:W3191C;ENSP00000437376:W119C	ENSP00000367655:W3191C	W	+	3	0	PKHD1L1	110564507	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.552000	0.82192	2.654000	0.90174	0.585000	0.79938	TGG	.	.	none		0.368	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		T	110495331	G	T	110495331	3	4	10	1	0	0	0	0	1	0	0	0	11981	1212	42	4	9799	4	PKHD1L1	8	110495331	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	5982048	110495331	35868691	78	1160											
PLEC	5339	hgsc.bcm.edu	37	chr8	144993567	144993567	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggctgtgcacggggtcgatGatgccgcccgtggcgatctg	4	9	17	11	5	1	1	0	1	1	0	2	3	1	1	2	4	2	2	2	4	0	0			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr8:144993567G>T	ENST00000322810.4	-	32	11002	c.10833C>A	c.(10831-10833)atC>atA	p.I3611I	PLEC_ENST00000527096.1_Silent_p.I3497I|PLEC_ENST00000398774.2_Silent_p.I3442I|PLEC_ENST00000354589.3_Silent_p.I3474I|PLEC_ENST00000354958.2_Silent_p.I3452I|PLEC_ENST00000356346.3_Silent_p.I3460I|PLEC_ENST00000357649.2_Silent_p.I3478I|PLEC_ENST00000345136.3_Silent_p.I3474I|PLEC_ENST00000436759.2_Silent_p.I3501I	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3611	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						CGGGGTCGATGATGCCGCCCG	0.687																																					p.I3611I		Atlas-SNP	.											PLEC_ENST00000436759,bladder,carcinoma,-2,6	PLEC	1144	6	0			c.C10833A						scavenged	.						47	52	50					8																	144993567		2042	4183	6225	SO:0001819	synonymous_variant	5339	exon32			GTCGATGATGCCG	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.10833C>A	8.37:g.144993567G>T		52	0	0		37	2	0.0540541	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			.	.	none		0.687	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		T	144993567	G	T	144993567	2	4	10	1	0	0	0	0	0	0	0	1	12061	1280	45	4		4	PLEC	8	144993567	Silent	SNP	G	TCGA-FF-8041-01A-11D-2210-10	34498236	144993567	1370455	79	1161											
TLE4	7091	hgsc.bcm.edu	37	chr9	82337469	82337469	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caagccagacaaataccaacTacatcttcatgagagctgtg	15	8	7	11	0	2	2	1	1	1	2	2	3	2	2	2	0	5	1	2	0	5	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr9:82337469T>G	ENST00000376552.2	+	18	3108	c.2090T>G	c.(2089-2091)cTa>cGa	p.L697R	TLE4_ENST00000265284.6_Missense_Mutation_p.L672R|TLE4_ENST00000376537.4_Missense_Mutation_p.L729R|TLE4_ENST00000376520.4_Missense_Mutation_p.L729R|TLE4_ENST00000376544.3_Missense_Mutation_p.L628R|TLE4_ENST00000376534.4_Missense_Mutation_p.L334R	NM_007005.3	NP_008936.2	Q04727	TLE4_HUMAN	transducin-like enhancer of split 4	697					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						AAATACCAACTACATCTTCAT	0.488																																					p.L697R		Atlas-SNP	.											.	TLE4	187	.	0			c.T2090G						PASS	.						142	139	140					9																	82337469		2032	4228	6260	SO:0001583	missense	7091	exon18			ACCAACTACATCT	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.2090T>G	9.37:g.82337469T>G	ENSP00000365735:p.Leu697Arg	127	0	0		129	46	0.356589	NM_007005	F8W6T6|Q3ZCS1|Q5T1Y2|Q6PCB3|Q9BZ07|Q9BZ08|Q9BZ09|Q9NSL3|Q9ULF9	Missense_Mutation	SNP	ENST00000376552.2	37	CCDS43837.1	.	.	.	.	.	.	.	.	.	.	T	30	5.049799	0.93740	.	.	ENSG00000106829	ENST00000376552;ENST00000376544;ENST00000376520;ENST00000376537;ENST00000376534;ENST00000265284	T;T;T;T;T;T	0.68331	-0.32;-0.32;-0.32;-0.32;-0.32;-0.32	6.17	6.17	0.99709	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	0.83119	0.5185	M	0.81682	2.555	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	0.85181	0.1004	10	0.87932	D	0	-13.1859	16.8222	0.85835	0.0:0.0:0.0:1.0	.	672;628;729;697	F8W6T6;Q04727-2;Q04727-3;Q04727	.;.;.;TLE4_HUMAN	R	697;628;729;729;334;672	ENSP00000365735:L697R;ENSP00000365727:L628R;ENSP00000365703:L729R;ENSP00000365720:L729R;ENSP00000365717:L334R;ENSP00000265284:L672R	ENSP00000265284:L672R	L	+	2	0	TLE4	81527289	1.000000	0.71417	0.980000	0.43619	0.992000	0.81027	8.040000	0.89188	2.371000	0.80710	0.533000	0.62120	CTA	.	.	none		0.488	TLE4-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052792.4	XM_212237		G	82337469	T	G	82337469	3	3	10	1	0	0	0	0	1	0	0	0	15956	1522	53	5	2160	5	TLE4	9	82337469	Missense_Mutation	SNP	T	TCGA-FF-8041-01A-11D-2210-10		82337469	58875962	80	1162											
C9orf103	414328	hgsc.bcm.edu	37	chr9	86258428	86258428	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atattaacacaaggaaaagaTggtgtagctctgaagtgtga	16	10	11	4	0	1	3	0	2	1	1	1	4	1	4	0	2	2	2	0	2	7	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr9:86258428T>C	ENST00000376419.4	+	5	301	c.297T>C	c.(295-297)gaT>gaC	p.D99D	IDNK_ENST00000405990.3_3'UTR|IDNK_ENST00000454393.1_Silent_p.D142D|IDNK_ENST00000376417.4_Missense_Mutation_p.W85R|IDNK_ENST00000277124.8_Silent_p.D53D	NM_001001551.3	NP_001001551.2	Q5T6J7	GNTK_HUMAN	idnK, gluconokinase homolog (E. coli)	99					D-gluconate catabolic process (GO:0046177)		ATP binding (GO:0005524)|gluconokinase activity (GO:0046316)										AAGGAAAAGATGGTGTAGCTC	0.493																																					p.D99D		Atlas-SNP	.											C9orf103,colon,carcinoma,+2,1	.	.	1	0			c.T297C						PASS	.						80	80	80					9																	86258428		2203	4300	6503	SO:0001819	synonymous_variant	414328	exon5			AAAAGATGGTGTA	BC036421	CCDS35048.1, CCDS35048.2, CCDS59134.1	9q21.32	2012-03-30	2012-03-30	2012-03-30	ENSG00000148057	ENSG00000148057			31367	protein-coding gene	gene with protein product		611343	"chromosome 9 open reading frame 103"	C9orf103			Standard	NM_001001551		Approved	bA522I20.2	uc004amu.3	Q5T6J7	OTTHUMG00000020105	ENST00000376419.4:c.297T>C	9.37:g.86258428T>C		116	0	0		152	31	0.203947	NM_001001551	A5PLN6|Q5T6J6	Silent	SNP	ENST00000376419.4	37	CCDS35048.2	.	.	.	.	.	.	.	.	.	.	T	6.660	0.490211	0.12702	.	.	ENSG00000148057	ENST00000376417	.	.	.	5.53	-7.14	0.01527	.	.	.	.	.	T	0.24547	0.0595	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.39354	-0.9618	5	0.87932	D	0	-7.5855	1.0152	0.01505	0.2267:0.2169:0.3482:0.2082	.	.	.	.	R	85	.	ENSP00000365599:W85R	W	+	1	0	C9orf103	85448248	0.000000	0.05858	0.000000	0.03702	0.121000	0.20230	-0.065000	0.11617	-1.401000	0.02058	-1.262000	0.01453	TGG	.	.	none		0.493	IDNK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052837.2	NM_001001551		C	86258428	T	C	86258428	2	2	10	1	0	0	0	0	0	0	0	1	2448	1461	51	3		3	C9orf103	9	86258428	Silent	SNP	T	TCGA-FF-8041-01A-11D-2210-10	3920959	86258428	54955003	81	1163											
ZNF189	7743	hgsc.bcm.edu	37	chr9	104170651	104170651	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	atcagagaattcacactgggGaaaggccctatgagtgtaat	14	9	11	7	0	2	2	2	1	0	1	2	4	2	3	1	3	0	1	1	3	4	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr9:104170651G>A	ENST00000339664.2	+	3	730	c.601G>A	c.(601-603)Gaa>Aaa	p.E201K	ZNF189_ENST00000374861.3_Missense_Mutation_p.E187K|ZNF189_ENST00000259395.4_Missense_Mutation_p.E159K	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	201					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)				TCACACTGGGGAAAGGCCCTA	0.413																																					p.E201K		Atlas-SNP	.											.	ZNF189	79	.	0			c.G601A						PASS	.						77	81	80					9																	104170651		2203	4300	6503	SO:0001583	missense	7743	exon3			ACTGGGGAAAGGC	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.601G>A	9.37:g.104170651G>A	ENSP00000342019:p.Glu201Lys	106	0	0		132	55	0.416667	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Missense_Mutation	SNP	ENST00000339664.2	37	CCDS6754.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.306653	0.81247	.	.	ENSG00000136870	ENST00000374861;ENST00000339664;ENST00000259395	T;T;T	0.24350	1.86;1.86;1.86	4.79	4.79	0.61399	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.50627	D	0.000113	T	0.48150	0.1484	M	0.64080	1.96	0.54753	D	0.999982	D;D;D	0.71674	0.985;0.995;0.998	P;D;D	0.74023	0.807;0.931;0.982	T	0.40156	-0.9578	10	0.62326	D	0.03	.	16.1533	0.81636	0.0:0.0:1.0:0.0	.	186;187;201	B7ZLK9;Q5T7D8;O75820	.;.;ZN189_HUMAN	K	187;201;159	ENSP00000363995:E187K;ENSP00000342019:E201K;ENSP00000259395:E159K	ENSP00000259395:E159K	E	+	1	0	ZNF189	103210472	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.478000	0.73596	2.941000	0.99782	0.655000	0.94253	GAA	.	.	none		0.413	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452		A	104170651	G	A	104170651	3	1	10	1	0	0	0	0	1	0	0	0	17769	1175	41	2	611	2	ZNF189	9	104170651	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	17912223	104170651	37042780	82	1164											
ZNF462	58499	hgsc.bcm.edu	37	chr9	109691621	109691621	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggggctacttcacggccGtctatgcagatgagcatgag	8	9	15	9	2	2	3	1	2	1	1	2	3	2	3	1	4	3	3	1	4	2	3	rs376844260		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr9:109691621G>A	ENST00000277225.5	+	3	5717	c.5428G>A	c.(5428-5430)Gtc>Atc	p.V1810I	ZNF462_ENST00000457913.1_Missense_Mutation_p.V1810I|ZNF462_ENST00000441147.2_Missense_Mutation_p.V655I			Q96JM2	ZN462_HUMAN	zinc finger protein 462	1810					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)	p.V1810I(1)		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						CTTCACGGCCGTCTATGCAGA	0.547																																					p.V1810I		Atlas-SNP	.											ZNF462,NS,carcinoma,0,1	ZNF462	322	1	1	Substitution - Missense(1)	breast(1)	c.G5428A						PASS	.	G	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	92	94	93		5428	5.1	1	9		93	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZNF462	NM_021224.4	29	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	benign	1810/2507	109691621	2,13004	2203	4300	6503	SO:0001583	missense	58499	exon3			ACGGCCGTCTATG	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.5428G>A	9.37:g.109691621G>A	ENSP00000277225:p.Val1810Ile	80	0	0		100	20	0.2	NM_021224	Q5T0T4|Q8N408	Missense_Mutation	SNP	ENST00000277225.5	37	CCDS35096.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.166219	0.38217	2.27E-4	1.16E-4	ENSG00000148143	ENST00000277225;ENST00000457913;ENST00000374686;ENST00000441147	T;T;T;T	0.05319	3.46;3.89;4.01;4.01	5.97	5.07	0.68467	.	0.110994	0.64402	N	0.000008	T	0.02727	0.0082	N	0.04508	-0.205	0.80722	D	1	P;B	0.39748	0.686;0.016	B;B	0.26094	0.066;0.008	T	0.60016	-0.7345	10	0.19590	T	0.45	.	15.0554	0.71910	0.068:0.0:0.932:0.0	.	1810;1810	Q96JM2-3;Q96JM2	.;ZN462_HUMAN	I	1810;1810;693;655	ENSP00000277225:V1810I;ENSP00000414570:V1810I;ENSP00000363818:V693I;ENSP00000397306:V655I	ENSP00000277225:V1810I	V	+	1	0	ZNF462	108731442	1.000000	0.71417	0.998000	0.56505	0.968000	0.65278	5.989000	0.70587	1.524000	0.49035	0.591000	0.81541	GTC	.	.	weak		0.547	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224		A	109691621	G	A	109691621	3	1	10	1	0	0	0	0	1	0	0	0	17941	1145	40	1	5434	1	ZNF462	9	109691621	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	5520970	109691621	31521810	83	1165											
DBC1	1620	hgsc.bcm.edu	37	chr9	121929513	121929513	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agtccagctggggtttccccGgggccacaggaggggccagg	6	5	18	12	1	0	0	0	0	0	0	2	1	2	1	5	8	1	2	5	8	0	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr9:121929513G>A	ENST00000265922.3	-	8	2596	c.2135C>T	c.(2134-2136)cCg>cTg	p.P712L	BRINP1_ENST00000482797.1_Intron	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	712			P -> T (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		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)		p.P712L(1)									GGGTTTCCCCGGGGCCACAGG	0.557																																					p.P712L		Atlas-SNP	.											DBC1,rectum,carcinoma,0,4	DBC1	194	4	1	Substitution - Missense(1)	kidney(1)	c.C2135T						PASS	.						86	94	91					9																	121929513		2203	4300	6503	SO:0001583	missense	1620	exon8			TTCCCCGGGGCCA	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.2135C>T	9.37:g.121929513G>A	ENSP00000265922:p.Pro712Leu	189	0	0		226	79	0.349558	NM_014618	Q6IPV6|Q6P1A0|Q8WU22	Missense_Mutation	SNP	ENST00000265922.3	37	CCDS6822.1	.	.	.	.	.	.	.	.	.	.	G	18.02	3.531209	0.64972	.	.	ENSG00000078725	ENST00000373969;ENST00000265922	T	0.19250	2.16	5.64	4.73	0.59995	.	0.100848	0.64402	D	0.000001	T	0.23727	0.0574	M	0.61703	1.905	0.80722	D	1	P	0.35433	0.501	B	0.28011	0.085	T	0.07121	-1.0789	10	0.87932	D	0	-22.0002	16.2315	0.82344	0.0:0.0:0.8659:0.1341	.	712	O60477	DBC1_HUMAN	L	712	ENSP00000265922:P712L	ENSP00000265922:P712L	P	-	2	0	DBC1	120969334	1.000000	0.71417	0.961000	0.40146	0.998000	0.95712	7.234000	0.78134	1.508000	0.48769	0.585000	0.79938	CCG	.	.	none		0.557	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618		A	121929513	G	A	121929513	3	1	10	1	0	0	0	0	1	0	0	0	4249	1116	39	1	154	1	DBC1	9	121929513	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	12237892	121929513	19283918	84	1166											
CEP110	11064	hgsc.bcm.edu	37	chr9	123931934	123931934	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gcaattggtggagaaatcagGtgagctgttggccctccaga	10	9	14	8	0	1	3	1	1	0	2	2	4	2	3	2	4	1	3	2	4	2	2	rs376768102		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr9:123931934G>T	ENST00000373855.1	+	39	6376	c.6116G>T	c.(6115-6117)gGt>gTt	p.G2039V	CNTRL_ENST00000373850.1_Missense_Mutation_p.G1487V|CNTRL_ENST00000238341.5_Missense_Mutation_p.G2039V|CNTRL_ENST00000373845.2_3'UTR			Q7Z7A1	CNTRL_HUMAN	centriolin	2039	Required for centrosome localization.|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						GAGAAATCAGGTGAGCTGTTG	0.502																																					p.G2039V		Atlas-SNP	.											.	CNTRL	161	.	0			c.G6116T						PASS	.						94	96	95					9																	123931934		2203	4300	6503	SO:0001583	missense	11064	exon37			AATCAGGTGAGCT	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.6116G>T	9.37:g.123931934G>T	ENSP00000362962:p.Gly2039Val	76	0	0		96	41	0.427083	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	37	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	G	2.693	-0.272727	0.05716	.	.	ENSG00000119397	ENST00000373855;ENST00000238341;ENST00000454238;ENST00000439778;ENST00000394368;ENST00000373850;ENST00000373845	T;T;T	0.30182	1.84;1.84;1.54	6.02	-1.54	0.08584	.	.	.	.	.	T	0.17916	0.0430	L	0.29908	0.895	0.19300	N	0.99998	B	0.24823	0.112	B	0.16722	0.016	T	0.19516	-1.0303	9	0.33141	T	0.24	.	5.9625	0.19307	0.4083:0.223:0.3687:0.0	.	2039	Q7Z7A1	CNTRL_HUMAN	V	2039;2039;2039;795;196;1487;721	ENSP00000362962:G2039V;ENSP00000238341:G2039V;ENSP00000362956:G1487V	ENSP00000238341:G2039V	G	+	2	0	CNTRL	122971755	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.236000	0.09003	-0.605000	0.05753	-0.150000	0.13652	GGT	.	.	alt		0.502	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018		T	123931934	G	T	123931934	3	4	10	1	0	0	0	0	1	0	0	0	3247	1261	44	4	6262	4	CEP110	9	123931934	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	2002421	123931934	17281497	85	1167											
PMPCA	23203	hgsc.bcm.edu	37	chr9	139306549	139306549	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tacccaagcctgtttttgctAcagttgatggacaggaaaag	12	11	10	8	0	0	1	0	1	0	0	0	3	0	3	2	2	4	3	2	2	5	5	rs367845329		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr9:139306549A>G	ENST00000371717.3	+	2	181	c.172A>G	c.(172-174)Aca>Gca	p.T58A	SDCCAG3_ENST00000357365.3_5'Flank|PMPCA_ENST00000371720.1_Missense_Mutation_p.T58A|SDCCAG3_ENST00000371725.3_5'Flank|PMPCA_ENST00000399219.3_5'UTR|SDCCAG3_ENST00000298537.7_5'Flank	NM_001282946.1|NM_015160.1	NP_001269875.1|NP_055975.1	Q10713	MPPA_HUMAN	peptidase (mitochondrial processing) alpha	58					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)		TGTTTTTGCTACAGTTGATGG	0.473																																					p.T58A		Atlas-SNP	.											.	PMPCA	29	.	0			c.A172G						PASS	.	A	ALA/THR	0,4406		0,0,2203	177	163	167		172	3.3	0.8	9		167	1,8599	1.2+/-3.3	0,1,4299	no	missense	PMPCA	NM_015160.1	58	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign	58/526	139306549	1,13005	2203	4300	6503	SO:0001583	missense	23203	exon2			TTTGCTACAGTTG	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.172A>G	9.37:g.139306549A>G	ENSP00000360782:p.Thr58Ala	268	0	0		288	72	0.25	NM_015160	B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Missense_Mutation	SNP	ENST00000371717.3	37	CCDS35180.1	.	.	.	.	.	.	.	.	.	.	A	8.346	0.829805	0.16749	0.0	1.16E-4	ENSG00000165688	ENST00000371720;ENST00000371717	T	0.11821	2.74	4.46	3.31	0.37934	.	0.246395	0.41396	D	0.000886	T	0.09158	0.0226	L	0.28556	0.865	0.80722	D	1	B;B	0.13145	0.007;0.001	B;B	0.09377	0.004;0.002	T	0.21245	-1.0251	10	0.20046	T	0.44	.	8.9219	0.35617	0.8332:0.0:0.0:0.1668	.	58;58	B4DRK5;Q10713	.;MPPA_HUMAN	A	58	ENSP00000360782:T58A	ENSP00000360782:T58A	T	+	1	0	PMPCA	138426370	0.602000	0.26916	0.813000	0.32504	0.911000	0.54048	1.358000	0.34102	0.670000	0.31165	-0.368000	0.07277	ACA	.	.	weak		0.473	PMPCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055054.1	NM_015160		G	139306549	A	G	139306549	3	3	10	1	0	0	0	0	1	0	0	0	12149	391	14	3	178	3	PMPCA	9	139306549	Missense_Mutation	SNP	A	TCGA-FF-8041-01A-11D-2210-10	15374615	139306549	1906882	86	1168											
FAM107B	83641	hgsc.bcm.edu	37	chr10	14816655	14816655	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtgagtcttgctttccacGtggacatgacttgcagtgaa	8	13	12	8	1	1	3	0	3	1	0	2	4	2	4	1	2	2	2	1	2	1	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:14816655G>A	ENST00000181796.2	-	1	241	c.8C>T	c.(7-9)aCg>aTg	p.T3M		NM_031453.2	NP_113641.2	Q9H098	F107B_HUMAN	family with sequence similarity 107, member B	0					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						TGCTTTCCACGTGGACATGAC	0.483																																					p.T3M		Atlas-SNP	.											.	FAM107B	43	.	0			c.C8T						PASS	.						82	65	71					10																	14816655		2203	4300	6503	SO:0001583	missense	83641	exon1			TTCCACGTGGACA	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	ENST00000181796.2:c.8C>T	10.37:g.14816655G>A	ENSP00000181796:p.Thr3Met	103	0	0		152	44	0.289474	NM_031453	A8K1P4|D3DRT2|Q5T9K7|Q5T9K8|Q6ZSI4	Missense_Mutation	SNP	ENST00000181796.2	37	CCDS7102.1	.	.	.	.	.	.	.	.	.	.	G	11.55	1.672163	0.29693	.	.	ENSG00000065809	ENST00000181796	T	0.39229	1.09	5.84	1.91	0.25777	.	0.778029	0.11243	N	0.584448	T	0.20577	0.0495	N	0.14661	0.345	0.80722	D	1	B	0.31054	0.306	B	0.22152	0.038	T	0.12656	-1.0539	10	0.87932	D	0	-0.0064	2.2074	0.03939	0.2697:0.1203:0.4863:0.1237	.	3	Q9H098-2	.	M	3	ENSP00000181796:T3M	ENSP00000181796:T3M	T	-	2	0	FAM107B	14856661	0.013000	0.17824	1.000000	0.80357	0.694000	0.40290	0.028000	0.13644	0.389000	0.25086	0.650000	0.86243	ACG	.	.	none		0.483	FAM107B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356966.1	NM_031453		A	14816655	G	A	14816655	3	1	10	1	0	0	0	0	1	0	0	0	5395	1145	40	1	932	1	FAM107B	10	14816655	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10		14816655	120718092	87	1169											
LGI1	9211	hgsc.bcm.edu	37	chr10	95552602	95552602	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gaagacatctactgcgaaggCcccccagaatacaagaagcg	15	4	10	12	2	1	3	0	0	1	3	1	5	1	3	3	1	4	0	3	1	7	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:95552602C>A	ENST00000371418.4	+	6	866	c.606C>A	c.(604-606)ggC>ggA	p.G202G	LGI1_ENST00000542308.1_Silent_p.G154G|LGI1_ENST00000371413.3_Silent_p.G202G	NM_005097.2	NP_005088.1	O95970	LGI1_HUMAN	leucine-rich, glioma inactivated 1	202	LRRCT.				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)	p.E205fs*9(1)		central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(18)|ovary(2)|skin(1)	29		Colorectal(252;0.124)				ACTGCGAAGGCCCCCCAGAAT	0.418																																					p.G202G		Atlas-SNP	.											.	LGI1	69	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.C606A						PASS	.						133	135	134					10																	95552602		2203	4300	6503	SO:0001819	synonymous_variant	9211	exon6			CGAAGGCCCCCCA	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.606C>A	10.37:g.95552602C>A		100	0	0		134	61	0.455224	NM_005097	A8K0Z1|B4E1S0|Q5W001|Q5W002|Q8NI23|Q96LF5	Silent	SNP	ENST00000371418.4	37	CCDS7431.1																																																																																			.	.	none		0.418	LGI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049445.1	NM_005097		A	95552602	C	A	95552602	2	1	10	1	0	0	0	0	0	0	0	1	8760	726	26	4		4	LGI1	10	95552602	Silent	SNP	C	TCGA-FF-8041-01A-11D-2210-10	80735947	95552602	39982145	88	1170											
TBC1D12	23232	hgsc.bcm.edu	37	chr10	96259982	96259982	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctcctttaattctaggcgtAgtacaagaagagttcgagaa	13	11	9	8	2	1	3	0	0	1	3	3	4	2	3	2	1	1	3	2	1	7	7			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:96259982A>G	ENST00000225235.4	+	6	1527	c.1417A>G	c.(1417-1419)Agt>Ggt	p.S473G		NM_015188.1	NP_056003.1	O60347	TBC12_HUMAN	TBC1 domain family, member 12	473							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)				TTCTAGGCGTAGTACAAGAAG	0.403																																					p.S473G		Atlas-SNP	.											TBC1D12,NS,carcinoma,-1,1	TBC1D12	51	1	0			c.A1417G						scavenged	.						128	115	119					10																	96259982		1839	4096	5935	SO:0001583	missense	23232	exon6			AGGCGTAGTACAA	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.1417A>G	10.37:g.96259982A>G	ENSP00000225235:p.Ser473Gly	99	0	0		75	3	0.04	NM_015188	Q5VYA6|Q8WX26|Q8WX59|Q9UG83	Missense_Mutation	SNP	ENST00000225235.4	37	CCDS41553.1	.	.	.	.	.	.	.	.	.	.	A	14.98	2.697073	0.48202	.	.	ENSG00000108239	ENST00000225235	T	0.57595	0.39	4.8	4.8	0.61643	Rab-GAP/TBC domain (1);	0.287488	0.39759	N	0.001273	T	0.31734	0.0806	N	0.10874	0.06	0.50039	D	0.999843	B	0.10296	0.003	B	0.06405	0.002	T	0.12400	-1.0549	10	0.19590	T	0.45	-15.3937	12.5865	0.56421	1.0:0.0:0.0:0.0	.	473	O60347	TBC12_HUMAN	G	473	ENSP00000225235:S473G	ENSP00000225235:S473G	S	+	1	0	TBC1D12	96249972	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.084000	0.57650	2.124000	0.65301	0.533000	0.62120	AGT	.	.	none		0.403	TBC1D12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049482.2			G	96259982	A	G	96259982	3	3	10	1	0	0	0	0	1	0	0	0	15616	420	15	3	1439	3	TBC1D12	10	96259982	Missense_Mutation	SNP	A	TCGA-FF-8041-01A-11D-2210-10	707380	96259982	39274765	89	1171											
CYP2C19	1557	hgsc.bcm.edu	37	chr10	96580331	96580331	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acttacttggagctgggacaGagacaacaagcacaaccctg	14	6	10	11	0	0	1	0	0	0	1	0	4	0	3	1	2	5	2	1	2	4	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:96580331G>A	ENST00000371321.3	+	6	980	c.898G>A	c.(898-900)Gag>Aag	p.E300K	CYP2C19_ENST00000464755.1_3'UTR	NM_000769.1	NP_000760	P33261	CP2CJ_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 19	300					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|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)|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)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)|steroid hydroxylase activity (GO:0008395)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	43		Colorectal(252;0.09)		all cancers(201;6.02e-07)|KIRC - Kidney renal clear cell carcinoma(50;0.0672)|Kidney(138;0.0838)	Acenocoumarol(DB01418)|Acetylsalicylic acid(DB00945)|Adinazolam(DB00546)|Almotriptan(DB00918)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amoxicillin(DB01060)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atomoxetine(DB00289)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Benzatropine(DB00245)|Bicalutamide(DB01128)|Bifonazole(DB04794)|Bortezomib(DB00188)|Bromazepam(DB01558)|Brompheniramine(DB00835)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carisoprodol(DB00395)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clevidipine(DB04920)|Clobazam(DB00349)|Clomipramine(DB01242)|Clopidogrel(DB00758)|Clotiazepam(DB01559)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diltiazem(DB00343)|Dimethyl sulfoxide(DB01093)|Diphenhydramine(DB01075)|Dopamine(DB00988)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enfuvirtide(DB00109)|Enzalutamide(DB08899)|Escitalopram(DB01175)|Esomeprazole(DB00736)|Estradiol(DB00783)|Ethanol(DB00898)|Ethotoin(DB00754)|Etoricoxib(DB01628)|Etravirine(DB06414)|Famotidine(DB00927)|Felbamate(DB00949)|Fluconazole(DB00196)|Flunitrazepam(DB01544)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Gliclazide(DB01120)|Glucosamine(DB01296)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Hexobarbital(DB01355)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Indomethacin(DB00328)|Isoniazid(DB00951)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Lopinavir(DB01601)|Loratadine(DB00455)|Lorcaserin(DB04871)|Losartan(DB00678)|Lovastatin(DB00227)|LULICONAZOLE(DB08933)|Lumiracoxib(DB01283)|MACITENTAN(DB08932)|Melatonin(DB01065)|Memantine(DB01043)|Meprobamate(DB00371)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methsuximide(DB05246)|Methylphenobarbital(DB00849)|Metoprolol(DB00264)|Miconazole(DB01110)|Moclobemide(DB01171)|Modafinil(DB00745)|Nelfinavir(DB00220)|Nicardipine(DB00622)|Nicotine(DB00184)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Norethindrone(DB00717)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ospemifene(DB04938)|Oxcarbazepine(DB00776)|Oxiconazole(DB00239)|Pantoprazole(DB00213)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Pentobarbital(DB00312)|Perphenazine(DB00850)|Pethidine(DB00454)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phensuximide(DB00832)|Phenytoin(DB00252)|Pimozide(DB01100)|Pioglitazone(DB01132)|Pipotiazine(DB01621)|Podofilox(DB01179)|Prasugrel(DB06209)|Praziquantel(DB01058)|Prednisone(DB00635)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propofol(DB00818)|Propranolol(DB00571)|Quazepam(DB01589)|Quetiapine(DB01224)|Quinine(DB00468)|Rabeprazole(DB01129)|Ramelteon(DB00980)|Ranitidine(DB00863)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfanilamide(DB00259)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Telmisartan(DB00966)|Temazepam(DB00231)|Teniposide(DB00444)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Timolol(DB00373)|Tioconazole(DB01007)|Tipranavir(DB00932)|Tofacitinib(DB08895)|Tolbutamide(DB01124)|Tolterodine(DB01036)|Topiramate(DB00273)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Trimethadione(DB00347)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zolpidem(DB00425)|Zonisamide(DB00909)	AGCTGGGACAGAGACAACAAG	0.428																																					p.E300K		Atlas-SNP	.											.	CYP2C19	88	.	0			c.G898A						PASS	.						193	174	181					10																	96580331		2203	4300	6503	SO:0001583	missense	1557	exon6			GGGACAGAGACAA	M61854	CCDS7436.1	10q24	2007-12-14	2003-01-14		ENSG00000165841	ENSG00000165841		"Cytochrome P450s"	2621	protein-coding gene	gene with protein product		124020	"cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 19"	CYP2C		2009263, 8530044	Standard	NM_000769		Approved	P450IIC19, CPCJ	uc010qnz.2	P33261	OTTHUMG00000018799	ENST00000371321.3:c.898G>A	10.37:g.96580331G>A	ENSP00000360372:p.Glu300Lys	103	0	0		102	30	0.294118	NM_000769	P33259|Q8WZB1|Q8WZB2|Q9UCD4	Missense_Mutation	SNP	ENST00000371321.3	37	CCDS7436.1	.	.	.	.	.	.	.	.	.	.	G	15.31	2.796723	0.50208	.	.	ENSG00000165841	ENST00000371321	T	0.17213	2.29	3.95	3.95	0.45737	.	0.074405	0.51477	U	0.000091	T	0.47488	0.1448	M	0.92604	3.325	0.29808	N	0.831907	D	0.89917	1.0	D	0.69654	0.965	T	0.56768	-0.7924	10	0.87932	D	0	.	11.4092	0.49915	0.0:0.0:1.0:0.0	.	300	P33261	CP2CJ_HUMAN	K	300	ENSP00000360372:E300K	ENSP00000360372:E300K	E	+	1	0	CYP2C19	96570321	1.000000	0.71417	0.996000	0.52242	0.192000	0.23643	5.180000	0.65048	2.016000	0.59253	0.400000	0.26472	GAG	.	.	none		0.428	CYP2C19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049490.1	NM_000769		A	96580331	G	A	96580331	3	1	10	1	0	0	0	0	1	0	0	0	4168	943	33	2	920	2	CYP2C19	10	96580331	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	320349	96580331	38954416	90	1172											
PIK3AP1	118788	hgsc.bcm.edu	37	chr10	98369476	98369476	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccagctgctcacttgctgtGctggaggtgctgtctgtttt	3	15	12	11	0	2	0	1	0	1	0	2	1	2	1	1	2	5	6	1	2	0	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:98369476G>A	ENST00000339364.5	-	14	2282	c.2163C>T	c.(2161-2163)agC>agT	p.S721S	PIK3AP1_ENST00000371110.2_Silent_p.S543S|PIK3AP1_ENST00000371109.3_Silent_p.S320S	NM_152309.2	NP_689522.2	Q6ZUJ8	BCAP_HUMAN	phosphoinositide-3-kinase adaptor protein 1	721					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)		CACTTGCTGTGCTGGAGGTGC	0.572																																					p.S721S		Atlas-SNP	.											.	PIK3AP1	111	.	0			c.C2163T						PASS	.						99	106	104					10																	98369476		2203	4300	6503	SO:0001819	synonymous_variant	118788	exon14			TGCTGTGCTGGAG	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.2163C>T	10.37:g.98369476G>A		101	0	0		111	48	0.432432	NM_152309	Q5TB56|Q5VXJ9|Q8N6J6|Q8NAC8	Silent	SNP	ENST00000339364.5	37	CCDS31259.1																																																																																			.	.	none		0.572	PIK3AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049619.2	NM_152309		A	98369476	G	A	98369476	2	1	10	1	0	0	0	0	0	0	0	1	11917	1310	46	2		2	PIK3AP1	10	98369476	Silent	SNP	G	TCGA-FF-8041-01A-11D-2210-10	1789145	98369476	37165271	91	1173											
PDZD7	79955	hgsc.bcm.edu	37	chr10	102778029	102778029	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccaggggaccccgacttcTccttcttccgctgctgcttc	3	11	8	19	2	2	0	0	0	2	0	5	2	3	1	6	2	2	3	6	2	0	4	rs555444131	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:102778029T>G	ENST00000370215.3	-	9	1574	c.1349A>C	c.(1348-1350)gAg>gCg	p.E450A		NM_024895.4	NP_079171.1	Q9H5P4	PDZD7_HUMAN	PDZ domain containing 7	450						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)		CCCCGACTTCTCCTTCTTCCG	0.667																																					p.E450A		Atlas-SNP	.											.	PDZD7	101	.	0			c.A1349C						PASS	.						42	42	42					10																	102778029		2203	4300	6503	SO:0001583	missense	79955	exon9			GACTTCTCCTTCT	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.1349A>C	10.37:g.102778029T>G	ENSP00000359234:p.Glu450Ala	122	0	0		110	45	0.409091	NM_001195263	D5FJ77|Q8N321	Missense_Mutation	SNP	ENST00000370215.3	37	CCDS31269.1	.	.	.	.	.	.	.	.	.	.	T	15.48	2.844861	0.51164	.	.	ENSG00000186862	ENST00000393462;ENST00000370215	T	0.14266	2.52	3.98	2.75	0.32379	.	1.878030	0.03231	N	0.179010	T	0.14184	0.0343	L	0.34521	1.04	0.33421	D	0.579826	B;B	0.30406	0.278;0.122	B;B	0.30572	0.057;0.117	T	0.23547	-1.0185	10	0.62326	D	0.03	.	8.9983	0.36066	0.0:0.0:0.1856:0.8144	.	450;450	Q9H5P4;Q9H5P4-2	PDZD7_HUMAN;.	A	450	ENSP00000359234:E450A	ENSP00000359234:E450A	E	-	2	0	PDZD7	102768019	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	3.560000	0.53763	1.661000	0.50771	0.418000	0.28097	GAG	.	.	none		0.667	PDZD7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049883.1	NM_024895		G	102778029	T	G	102778029	3	3	10	1	0	0	0	0	1	0	0	0	11713	1551	54	5	212	5	PDZD7	10	102778029	Missense_Mutation	SNP	T	TCGA-FF-8041-01A-11D-2210-10	4408553	102778029	32756718	92	1174											
NFKB2	4791	hgsc.bcm.edu	37	chr10	104160764	104160764	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacccctgcacctggcagctGgactggggtacccgaccctc	6	6	11	18	1	0	0	0	0	0	0	1	2	0	1	5	4	3	4	5	4	1	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:104160764G>A	ENST00000369966.3	+	18	2279	c.2029G>A	c.(2029-2031)Gga>Aga	p.G677R	NFKB2_ENST00000189444.6_Missense_Mutation_p.G677R|NFKB2_ENST00000428099.1_Missense_Mutation_p.G677R	NM_001077494.2	NP_001070962.1	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)	677			Missing (in truncated form EB308).|Missing (in truncated form p80HT).		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)	CCTGGCAGCTGGACTGGGGTA	0.647			T	IGH@	B-NHL																																p.G677R		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.G2029A						PASS	.						33	41	39					10																	104160764		2063	4206	6269	SO:0001583	missense	4791	exon18			GCAGCTGGACTGG	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.2029G>A	10.37:g.104160764G>A	ENSP00000358983:p.Gly677Arg	96	0	0		112	54	0.482143	NM_001077494	A8K9D9|D3DR83|Q04860|Q9BU75|Q9H471|Q9H472	Missense_Mutation	SNP	ENST00000369966.3	37	CCDS41564.1	.	.	.	.	.	.	.	.	.	.	g	20.4	3.990200	0.74589	.	.	ENSG00000077150	ENST00000428099;ENST00000369966;ENST00000336486;ENST00000189444	T;T;T	0.61742	0.08;0.08;0.08	4.48	4.48	0.54585	Ankyrin repeat-containing domain (4);	0.109105	0.64402	D	0.000009	T	0.53562	0.1804	N	0.04724	-0.175	0.32550	N	0.532449	D;D	0.76494	0.999;0.999	D;D	0.75484	0.986;0.986	T	0.63377	-0.6651	10	0.52906	T	0.07	.	11.0484	0.47872	0.0869:0.0:0.9131:0.0	.	677;677	Q00653;A8K9D9	NFKB2_HUMAN;.	R	677	ENSP00000410256:G677R;ENSP00000358983:G677R;ENSP00000189444:G677R	ENSP00000189444:G677R	G	+	1	0	NFKB2	104150754	1.000000	0.71417	1.000000	0.80357	0.721000	0.41392	4.183000	0.58317	2.526000	0.85167	0.531000	0.56144	GGA	.	.	none		0.647	NFKB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050080.2			A	104160764	G	A	104160764	3	1	10	1	0	0	0	0	1	0	0	0	10385	1349	47	2	2095	2	NFKB2	10	104160764	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	1382735	104160764	31373983	93	1175											
JAKMIP3	282973	hgsc.bcm.edu	37	chr10	133962951	133962951	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcacccgccatcagcttccaCcacacgcccttcgtggacgg	7	7	8	19	4	2	0	2	0	0	0	4	1	3	1	5	2	1	1	5	2	0	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr10:133962951C>T	ENST00000298622.4	+	14	2022	c.1884C>T	c.(1882-1884)caC>caT	p.H628H	JAKMIP3_ENST00000477275.1_3'UTR	NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	628						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)		TCAGCTTCCACCACACGCCCT	0.657																																					p.H628H		Atlas-SNP	.											.	JAKMIP3	69	.	0			c.C1884T						PASS	.						71	51	58					10																	133962951		2184	4286	6470	SO:0001819	synonymous_variant	282973	exon14			CTTCCACCACACG	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.1884C>T	10.37:g.133962951C>T		80	0	0		64	29	0.453125	NM_001105521	A6PW00|Q69YM6|Q6ZT29	Silent	SNP	ENST00000298622.4	37	CCDS44494.1																																																																																			.	.	none		0.657	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303		T	133962951	C	T	133962951	2	4	10	1	0	0	0	0	0	0	0	1	7951	506	18	2		2	JAKMIP3	10	133962951	Silent	SNP	C	TCGA-FF-8041-01A-11D-2210-10	29802187	133962951	1571796	94	1176											
MUC2	4583	hgsc.bcm.edu	37	chr11	1092929	1092929	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cggcacacagaccccaacatCgacacccatcaccaccacca	14	2	4	21	2	1	1	1	0	0	1	2	2	1	1	6	1	1	1	6	1	1	0			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:1092929C>T	ENST00000441003.2	+	30	4775	c.4748C>T	c.(4747-4749)tCg>tTg	p.S1583L	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Missense_Mutation_p.S1584L|MUC2_ENST00000361558.6_Intron	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)	accccaacatcgacacccatc	0.632																																					p.S1583L		Atlas-SNP	.											MUC2_ENST00000441003,rectum,carcinoma,+1,4	MUC2	614	4	0			c.C4748T						scavenged	.						78	115	102					11																	1092929		1918	3556	5474	SO:0001583	missense	4583	exon30			CAACATCGACACC	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.4748C>T	11.37:g.1092929C>T	ENSP00000415183:p.Ser1583Leu	111	1	0.00900901		105	9	0.0857143	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	4.659	0.122508	0.08931	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.13538	2.58;3.12	1.75	-1.21	0.09524	.	3.022220	0.02729	U	0.114829	T	0.09202	0.0227	.	.	.	0.09310	N	1	B	0.22541	0.071	B	0.10450	0.005	T	0.31336	-0.9947	9	0.29301	T	0.29	.	6.8082	0.23788	0.6899:0.3101:0.0:0.0	.	1583	E7EUV1	.	L	1583;1584	ENSP00000415183:S1583L;ENSP00000351956:S1584L	ENSP00000351956:S1584L	S	+	2	0	MUC2	1082929	0.156000	0.22821	0.002000	0.10522	0.037000	0.13140	2.746000	0.47467	0.075000	0.16796	0.121000	0.15741	TCG	.	.	none		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1092929	C	T	1092929	3	4	10	1	0	0	0	0	1	0	0	0	9984	893	31	1	4866	1	MUC2	11	1092929	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10		1092929	133913587	95	1177											
CTR9	9646	hgsc.bcm.edu	37	chr11	10777233	10777233	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	attacttcatagaaccatttGttgggaagagcctgcttctg	10	14	9	8	0	2	2	1	0	1	2	2	3	2	3	2	1	4	2	2	1	4	6			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:10777233G>T	ENST00000361367.2	+	4	819	c.393G>T	c.(391-393)ttG>ttT	p.L131F		NM_014633.3	NP_055448.1	Q6PD62	CTR9_HUMAN	CTR9, Paf1/RNA polymerase II complex component	131					cellular response to lipopolysaccharide (GO:0071222)|endodermal cell fate commitment (GO:0001711)|histone H2B ubiquitination (GO:0033523)|histone H3-K4 trimethylation (GO:0080182)|histone monoubiquitination (GO:0010390)|interleukin-6-mediated signaling pathway (GO:0070102)|JAK-STAT cascade (GO:0007259)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|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)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	Cdc73/Paf1 complex (GO:0016593)|transcriptionally active chromatin (GO:0035327)				breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|pancreas(1)|stomach(1)	40				all cancers(16;1.64e-07)|Epithelial(150;2.47e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		AGAACCATTTGTTGGGAAGAG	0.383																																					p.L131F		Atlas-SNP	.											.	CTR9	94	.	0			c.G393T						PASS	.						139	136	137					11																	10777233		2201	4294	6495	SO:0001583	missense	9646	exon4			CCATTTGTTGGGA	D63875	CCDS7805.1	11p15.3	2013-07-03	2013-07-03	2006-05-22	ENSG00000198730	ENSG00000198730		"Tetratricopeptide (TTC) repeat domain containing"	16850	protein-coding gene	gene with protein product		609366	"SH2 domain binding protein 1 (tetratricopeptide repeat containing)", "Ctr9, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)"	SH2BP1		8590280, 8636124	Standard	NM_014633		Approved	KIAA0155, TSBP, p150TSP	uc001mja.3	Q6PD62	OTTHUMG00000165789	ENST00000361367.2:c.393G>T	11.37:g.10777233G>T	ENSP00000355013:p.Leu131Phe	139	0	0		116	48	0.413793	NM_014633	D3DQV8|Q15015	Missense_Mutation	SNP	ENST00000361367.2	37	CCDS7805.1	.	.	.	.	.	.	.	.	.	.	G	14.44	2.536972	0.45176	.	.	ENSG00000198730	ENST00000361367;ENST00000524523	T;T	0.78707	-1.2;1.12	5.97	2.57	0.30868	Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.69088	0.3072	M	0.77820	2.39	0.80722	D	1	P	0.40834	0.73	B	0.31547	0.132	T	0.64474	-0.6399	10	0.19590	T	0.45	-8.2928	8.3402	0.32239	0.1941:0.0:0.6841:0.1217	.	131	Q6PD62	CTR9_HUMAN	F	131;118	ENSP00000355013:L131F;ENSP00000431458:L118F	ENSP00000355013:L131F	L	+	3	2	CTR9	10733809	1.000000	0.71417	1.000000	0.80357	0.420000	0.31355	1.477000	0.35431	0.814000	0.34374	0.591000	0.81541	TTG	.	.	none		0.383	CTR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386215.1	NM_014633		T	10777233	G	T	10777233	3	4	10	1	0	0	0	0	1	0	0	0	4026	1368	48	4	407	4	CTR9	11	10777233	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	9684304	10777233	124229283	96	1178											
AMBRA1	55626	hgsc.bcm.edu	37	chr11	46564251	46564251	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcaccgaagaggcactggttCtgggcgggggcatggattcc	7	8	16	10	2	2	1	1	0	1	1	3	3	3	2	2	6	0	3	2	6	1	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:46564251C>T	ENST00000458649.2	-	7	1734	c.1316G>A	c.(1315-1317)aGa>aAa	p.R439K	AMBRA1_ENST00000314845.3_Missense_Mutation_p.R349K|AMBRA1_ENST00000533727.1_Missense_Mutation_p.R349K|AMBRA1_ENST00000534300.1_Missense_Mutation_p.R439K|AMBRA1_ENST00000426438.1_Missense_Mutation_p.R439K|AMBRA1_ENST00000528950.1_Missense_Mutation_p.R439K|AMBRA1_ENST00000298834.3_Missense_Mutation_p.R439K			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	439					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)		GGCACTGGTTCTGGGCGGGGG	0.562																																					p.R349K		Atlas-SNP	.											.	AMBRA1	201	.	0			c.G1046A						PASS	.						67	67	67					11																	46564251		2201	4299	6500	SO:0001583	missense	55626	exon8			CTGGTTCTGGGCG	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.1316G>A	11.37:g.46564251C>T	ENSP00000415327:p.Arg439Lys	162	0	0		172	38	0.22093	NM_001267783	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Missense_Mutation	SNP	ENST00000458649.2	37		.	.	.	.	.	.	.	.	.	.	C	18.52	3.642548	0.67244	.	.	ENSG00000110497	ENST00000314845;ENST00000533727;ENST00000534300;ENST00000426438;ENST00000298834;ENST00000314823;ENST00000458649;ENST00000528950	T;D;T;T;T;T;T	0.84146	-1.24;-1.81;-1.08;-1.21;-1.08;-1.05;-1.21	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	D	0.89339	0.6687	L	0.32530	0.975	0.58432	D	0.999992	D;D;D;D;D;D	0.64830	0.994;0.99;0.99;0.974;0.99;0.974	D;D;D;D;D;D	0.72982	0.97;0.979;0.979;0.969;0.979;0.969	D	0.89784	0.3963	10	0.72032	D	0.01	.	20.1542	0.98100	0.0:1.0:0.0:0.0	.	439;439;439;349;349;349	Q9C0C7;Q9C0C7-3;Q9C0C7-2;G3V193;Q9C0C7-5;Q9C0C7-4	AMRA1_HUMAN;.;.;.;.;.	K	349;349;439;439;439;349;439;439	ENSP00000318313:R349K;ENSP00000433372:R349K;ENSP00000431926:R439K;ENSP00000410899:R439K;ENSP00000298834:R439K;ENSP00000415327:R439K;ENSP00000433945:R439K	ENSP00000298834:R439K	R	-	2	0	AMBRA1	46520827	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.172000	0.77604	2.767000	0.95098	0.563000	0.77884	AGA	.	.	none		0.562	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749		T	46564251	C	T	46564251	3	4	10	1	0	0	0	0	1	0	0	0	565	913	32	2	2628	2	AMBRA1	11	46564251	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	35787018	46564251	88442265	97	1179											
FNBP4	23360	hgsc.bcm.edu	37	chr11	47744591	47744591	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgggagctggtggtggtggAggaggaggaggaggaggtgg	7	7	26	1	0	0	0	0	0	0	0	0	7	0	7	0	12	1	1	0	12	0	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	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	1	Substitution - coding silent(1)	endometrium(1)	c.T2742A						PASS	.						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	11.37:g.47744591A>T		48	0	0		53	4	0.0754717	NM_015308	Q9H985|Q9NT81|Q9Y2L7	Silent	SNP	ENST00000263773.5	37	CCDS41644.1																																																																																			.	.	none		0.463	FNBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390237.3			T	47744591	A	T	47744591	2	4	10	1	0	0	0	0	0	0	0	1	5975	291	11	5		5	FNBP4	11	47744591	Silent	SNP	A	TCGA-FF-8041-01A-11D-2210-10	1180340	47744591	87261925	98	1180											
OR8K5	219453	hgsc.bcm.edu	37	chr11	55927379	55927379	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caccagtacatgacacagtcGctgagacataataacataat	17	8	6	10	1	0	2	0	2	0	1	1	3	0	2	1	0	2	2	1	0	4	4	rs199580379		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:55927379G>A	ENST00000313447.1	-	1	414	c.415C>T	c.(415-417)Cga>Tga	p.R139*		NM_001004058.2	NP_001004058.2	Q8NH50	OR8K5_HUMAN	olfactory receptor, family 8, subfamily K, 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)			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)				TGACACAGTCGCTGAGACATA	0.403																																					p.R139X		Atlas-SNP	.											.	OR8K5	82	.	0			c.C415T						PASS	.	G	stop/ARG	0,4402		0,0,2201	84	86	85		415	-0.1	0	11		85	5,8585	4.3+/-15.6	0,5,4290	yes	stop-gained	OR8K5	NM_001004058.2		0,5,6491	AA,AG,GG		0.0582,0.0,0.0385		139/308	55927379	5,12987	2201	4295	6496	SO:0001587	stop_gained	219453	exon1			ACAGTCGCTGAGA	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.415C>T	11.37:g.55927379G>A	ENSP00000323853:p.Arg139*	103	0	0		80	4	0.05	NM_001004058	Q6IFB5	Nonsense_Mutation	SNP	ENST00000313447.1	37	CCDS31521.1	.	.	.	.	.	.	.	.	.	.	G	4.734	0.136431	0.09032	0.0	5.82E-4	ENSG00000181752	ENST00000313447	.	.	.	4.18	-0.0501	0.13832	.	0.217057	0.32952	N	0.005447	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.1815	0.48631	0.0:0.0:0.4694:0.5306	.	.	.	.	X	139	.	ENSP00000323853:R139X	R	-	1	2	OR8K5	55683955	0.000000	0.05858	0.004000	0.12327	0.008000	0.06430	-1.402000	0.02499	0.222000	0.20900	-0.612000	0.04053	CGA	.	.	weak		0.403	OR8K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391543.1	NM_001004058		A	55927379	G	A	55927379	4	1	10	1	0	0	0	0	0	1	0	0	11254	1095	38	1	511	1	OR8K5	11	55927379	Nonsense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	8182788	55927379	79079137	99	1181											
SYT7	9066	hgsc.bcm.edu	37	chr11	61291310	61291310	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gccccgtacctgatgtgcccCcgatgtccatggctttgagg	5	10	12	14	2	0	2	0	2	0	0	1	3	1	2	6	2	2	2	6	2	1	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:61291310C>T	ENST00000263846.4	-	7	1223	c.896G>A	c.(895-897)gGg>gAg	p.G299E	SYT7_ENST00000540677.1_Missense_Mutation_p.G374E|SYT7_ENST00000540831.1_5'Flank|SYT7_ENST00000542670.1_Missense_Mutation_p.G507E|SYT7_ENST00000542836.1_Missense_Mutation_p.G343E|SYT7_ENST00000535826.1_Missense_Mutation_p.G418E|SYT7_ENST00000539008.1_Missense_Mutation_p.G582E	NM_004200.3	NP_004191.2	O43581	SYT7_HUMAN	synaptotagmin VII	299	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				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						TGATGTGCCCCCGATGTCCAT	0.597																																					p.G374E		Atlas-SNP	.											.	SYT7	39	.	0			c.G1121A						PASS	.						289	275	280					11																	61291310		2202	4299	6501	SO:0001583	missense	9066	exon8			GTGCCCCCGATGT	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.896G>A	11.37:g.61291310C>T	ENSP00000263846:p.Gly299Glu	224	0	0		192	41	0.213542	NM_001252065	F5GZU9|Q08AH6	Missense_Mutation	SNP	ENST00000263846.4	37	CCDS31577.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.233456	0.79688	.	.	ENSG00000011347	ENST00000263846;ENST00000540677;ENST00000539008;ENST00000542836;ENST00000542670;ENST00000535826	T;T;T;T;T;T	0.69040	-0.37;-0.37;-0.37;-0.37;-0.37;-0.37	4.48	4.48	0.54585	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	0.73892	0.3645	L	0.43701	1.375	0.80722	D	1	P;D	0.53151	0.948;0.958	P;P	0.59171	0.689;0.853	T	0.77702	-0.2489	10	0.72032	D	0.01	.	17.5306	0.87813	0.0:1.0:0.0:0.0	.	374;299	F5GZU9;O43581	.;SYT7_HUMAN	E	299;374;582;343;507;418	ENSP00000263846:G299E;ENSP00000444201:G374E;ENSP00000439694:G582E;ENSP00000444568:G343E;ENSP00000444019:G507E;ENSP00000437720:G418E	ENSP00000263846:G299E	G	-	2	0	SYT7	61047886	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.190000	0.50973	2.192000	0.70111	0.462000	0.41574	GGG	.	.	none		0.597	SYT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398733.1	NM_004200		T	61291310	C	T	61291310	3	4	10	1	0	0	0	0	1	0	0	0	15494	623	22	2	327	2	SYT7	11	61291310	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	5363931	61291310	73715206	100	1182											
CDC42BPG	55561	hgsc.bcm.edu	37	chr11	64594201	64594201	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggctgggcgccgcaacgcCtcggagaagctgtggggccg	6	4	19	12	5	0	1	0	0	0	1	1	3	0	1	3	5	2	3	3	5	2	0			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:64594201C>T	ENST00000342711.5	-	35	4454	c.4455G>A	c.(4453-4455)gaG>gaA	p.E1485E		NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)											central_nervous_system(1)|lung(3)	4						GCCGCAACGCCTCGGAGAAGC	0.711																																					p.E1485E		Atlas-SNP	.											.	CDC42BPG	101	.	0			c.G4455A						PASS	.						11	15	14					11																	64594201		2184	4250	6434	SO:0001819	synonymous_variant	55561	exon35			CAACGCCTCGGAG	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.4455G>A	11.37:g.64594201C>T		49	0	0		16	10	0.625	NM_017525		Silent	SNP	ENST00000342711.5	37	CCDS31601.1																																																																																			.	.	none		0.711	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516		T	64594201	C	T	64594201	2	4	10	1	0	0	0	0	0	0	0	1	3076	680	24	2		2	CDC42BPG	11	64594201	Silent	SNP	C	TCGA-FF-8041-01A-11D-2210-10	3302891	64594201	70412315	101	1183											
PPP2R5B	5526	hgsc.bcm.edu	37	chr11	64699058	64699058	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gggggctgctcaaatactggCcaaaaacctgcacccagaag	13	5	11	12	0	1	1	1	0	0	1	1	1	1	1	3	3	4	3	3	3	5	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:64699058C>T	ENST00000164133.2	+	10	1595	c.973C>T	c.(973-975)Cca>Tca	p.P325S		NM_006244.3	NP_006235.1	Q15173	2A5B_HUMAN	protein phosphatase 2, regulatory subunit B', beta	325					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						CAAATACTGGCCAAAAACCTG	0.597																																					p.P325S		Atlas-SNP	.											.	PPP2R5B	47	.	0			c.C973T						PASS	.						41	38	39					11																	64699058		2201	4297	6498	SO:0001583	missense	5526	exon10			TACTGGCCAAAAA	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.973C>T	11.37:g.64699058C>T	ENSP00000164133:p.Pro325Ser	40	0	0		47	25	0.531915	NM_006244	Q13853	Missense_Mutation	SNP	ENST00000164133.2	37	CCDS8085.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.4|26.4	4.729428|4.729428	0.89390|0.89390	.|.	.|.	ENSG00000068971|ENSG00000068971	ENST00000359279|ENST00000164133;ENST00000527441	.|.	.|.	.|.	4.53|4.53	4.53|4.53	0.55603|0.55603	.|Armadillo-type fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.83367|0.83367	0.5239|0.5239	M|M	0.90595|0.90595	3.13|3.13	0.80722|0.80722	D|D	1|1	.|D	.|0.67145	.|0.996	.|D	.|0.64410	.|0.925	D|D	0.87185|0.87185	0.2230|0.2230	6|9	0.09338|0.87932	T|D	0.73|0	-8.6715|-8.6715	15.1517|15.1517	0.72706|0.72706	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|325	.|Q15173	.|2A5B_HUMAN	V|S	350|325	.|.	ENSP00000352225:A350V|ENSP00000164133:P325S	A|P	+|+	2|1	0|0	PPP2R5B|PPP2R5B	64455634|64455634	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	5.549000|5.549000	0.67261|0.67261	2.509000|2.509000	0.84616|0.84616	0.462000|0.462000	0.41574|0.41574	GCC|CCA	.	.	none		0.597	PPP2R5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385465.1	NM_006244		T	64699058	C	T	64699058	3	4	10	1	0	0	0	0	1	0	0	0	12405	739	26	2	1007	2	PPP2R5B	11	64699058	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	104857	64699058	70307458	102	1184											
CCDC87	55231	hgsc.bcm.edu	37	chr11	66359191	66359191	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acctcatttctaagcttcaaAgtaatggtcactggctgtgg	10	13	9	9	0	4	0	3	0	1	0	4	0	4	0	1	3	1	3	1	3	3	4			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:66359191A>T	ENST00000333861.3	-	1	1363	c.1296T>A	c.(1294-1296)acT>acA	p.T432T	CCS_ENST00000533244.1_5'Flank|CCS_ENST00000310190.4_5'Flank	NM_018219.2	NP_060689.2	Q9NVE4	CCD87_HUMAN	coiled-coil domain containing 87	432					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						TAAGCTTCAAAGTAATGGTCA	0.552																																					p.T432T		Atlas-SNP	.											.	CCDC87	83	.	0			c.T1296A						PASS	.						38	43	41					11																	66359191		2200	4295	6495	SO:0001819	synonymous_variant	55231	exon1			CTTCAAAGTAATG	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.1296T>A	11.37:g.66359191A>T		54	0	0		75	25	0.333333	NM_018219	Q8NE76	Silent	SNP	ENST00000333861.3	37	CCDS8145.1																																																																																			.	.	none		0.552	CCDC87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393825.1	NM_018219		T	66359191	A	T	66359191	2	4	10	1	0	0	0	0	0	0	0	1	2864	59	3	5		5	CCDC87	11	66359191	Silent	SNP	A	TCGA-FF-8041-01A-11D-2210-10	1660133	66359191	68647325	103	1185											
ODZ4	26011	hgsc.bcm.edu	37	chr11	78437206	78437208	+	In_Frame_Del	DEL	TGT	TGT	-																															atttcatagccctgcagcacTgttgttcttttttcccacag																										TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:78437206_78437208delTGT	ENST00000278550.7	-	23	3928_3930	c.3466_3468delACA	c.(3466-3468)acadel	p.T1156del		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1156					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)										CCTGCAGCACTGTTGTTCTTTTT	0.433																																					p.1156_1157del		Pindel,Atlas-Indel	.											.	.	.	.	0			c.3467_3469del						PASS	.																																			SO:0001651	inframe_deletion	26011	exon23			.	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.3466_3468delACA	11.37:g.78437209_78437211delTGT	ENSP00000278550:p.Thr1156del	237	0	.		255	39	0.153	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	In_Frame_Del	DEL	ENST00000278550.7	37	CCDS44688.1																																																																																			.	.	none		0.433	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			-	78437208	TGT	-	78437206	7	5	10	1	0	1	0	1	0	0	0	0	10846	1567	55	0	4889	0	ODZ4	11	78437206	In_Frame_Del	DEL	TGT	TCGA-FF-8041-01A-11D-2210-10	12078015	78437206	56569310	104	1186											
KDM4DL	390245	hgsc.bcm.edu	37	chr11	94759726	94759726	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttatgagctctggaaacaCaggcaagacttggccattgt	12	10	11	8	0	1	2	0	1	1	1	1	3	1	3	1	3	2	3	1	3	3	3	rs76354273	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:94759726C>T	ENST00000450979.2	+	1	1305	c.1005C>T	c.(1003-1005)caC>caT	p.H335H		NM_001161630.1	NP_001155102.1	B2RXH2	KDM4E_HUMAN	lysine (K)-specific demethylase 4E	335					histone H3-K9 demethylation (GO:0033169)|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(1)|endometrium(7)|kidney(1)|lung(3)	12						TCTGGAAACACAGGCAAGACT	0.512													C|||	220	0.0439297	0.0174	0.0014	5008	,	,		21472	0.1637		0.001	False		,,,				2504	0.0307				p.H335H		Atlas-SNP	.											.	KDM4E	60	.	0			c.C1005T						PASS	.	C		34,1350		0,34,658	64	59	61		1005	1.4	0.2	11	dbSNP_132	61	6,3176		0,6,1585	no	coding-synonymous	KDM4DL	NM_001161630.1		0,40,2243	TT,TC,CC		0.1886,2.4566,0.876		335/507	94759726	40,4526	692	1591	2283	SO:0001819	synonymous_variant	390245	exon1			GAAACACAGGCAA	BC157851	CCDS44713.1	11q21	2012-03-30	2012-03-28	2012-03-28		ENSG00000235268		"Chromatin-modifying enzymes / K-demethylases"	37098	protein-coding gene	gene with protein product			"lysine (K)-specific demethylase 4D-like"	KDM4DL		21076780	Standard	NM_001161630		Approved	JMJD2E	uc010ruf.1	B2RXH2		ENST00000450979.2:c.1005C>T	11.37:g.94759726C>T		6	0	0		12	6	0.5	NM_001161630		Silent	SNP	ENST00000450979.2	37	CCDS44713.1																																																																																			C|0.947;T|0.053	0.053	strong		0.512	KDM4E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396649.1	NM_001161630		T	94759726	C	T	94759726	2	4	10	1	0	0	0	0	0	0	0	1	8141	477	17	2		2	KDM4DL	11	94759726	Silent	SNP	C	TCGA-FF-8041-01A-11D-2210-10	16322520	94759726	40246790	105	1187											
PGR	5241	hgsc.bcm.edu	37	chr11	100922186	100922186	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tagatcaggtgcaaaatacaGcatctgcccactgacgtgtt	12	10	9	10	1	2	2	1	1	1	1	2	2	2	2	1	1	4	3	1	1	4	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:100922186G>T	ENST00000325455.5	-	5	3779	c.2326C>A	c.(2326-2328)Ctg>Atg	p.L776M	PGR_ENST00000263463.5_Missense_Mutation_p.L674M|PGR_ENST00000534013.1_Missense_Mutation_p.L182M	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	776	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)	GCAAAATACAGCATCTGCCCA	0.333																																					p.L776M	Pancreas(124;2271 2354 21954 22882)	Atlas-SNP	.											.	PGR	115	.	0			c.C2326A						PASS	.						125	120	122					11																	100922186		2203	4300	6503	SO:0001583	missense	5241	exon5			AATACAGCATCTG	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.2326C>A	11.37:g.100922186G>T	ENSP00000325120:p.Leu776Met	195	0	0		199	71	0.356784	NM_000926	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Missense_Mutation	SNP	ENST00000325455.5	37	CCDS8310.1	.	.	.	.	.	.	.	.	.	.	G	15.63	2.891764	0.52014	.	.	ENSG00000082175	ENST00000325455;ENST00000534013;ENST00000263463;ENST00000537623	D;D;D	0.97620	-4.46;-4.46;-4.46	5.24	2.36	0.29203	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.64402	D	0.000002	D	0.98526	0.9508	M	0.93808	3.46	0.33891	D	0.637314	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.99898	1.1153	10	0.87932	D	0	.	9.8858	0.41260	0.2843:0.0:0.7157:0.0	.	674;776;157	Q8TDS3;P06401;A7LQ08	.;PRGR_HUMAN;.	M	776;182;674;674	ENSP00000325120:L776M;ENSP00000436561:L182M;ENSP00000263463:L674M	ENSP00000263463:L674M	L	-	1	2	PGR	100427396	1.000000	0.71417	0.972000	0.41901	0.980000	0.70556	0.819000	0.27308	0.220000	0.20860	-0.157000	0.13467	CTG	.	.	none		0.333	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1			T	100922186	G	T	100922186	3	4	10	1	0	0	0	0	1	0	0	0	11814	962	34	4	491	4	PGR	11	100922186	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	6162460	100922186	34084330	106	1188											
NPAT	4863	hgsc.bcm.edu	37	chr11	108044441	108044441	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgttttaaaggcctttttctGtatgctggtacttatttggg	6	20	10	5	0	1	0	0	0	1	0	1	0	1	0	1	3	2	4	1	3	5	8			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:108044441G>A	ENST00000278612.8	-	13	1375	c.1270C>T	c.(1270-1272)Cag>Tag	p.Q424*	NPAT_ENST00000610253.1_5'UTR	NM_002519.2	NP_002510.2	Q14207	NPAT_HUMAN	nuclear protein, ataxia-telangiectasia locus	424					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)		GCCTTTTTCTGTATGCTGGTA	0.383																																					p.Q424X		Atlas-SNP	.											.	NPAT	124	.	0			c.C1270T						PASS	.						147	138	141					11																	108044441		1860	4091	5951	SO:0001587	stop_gained	4863	exon13			TTTTCTGTATGCT	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.1270C>T	11.37:g.108044441G>A	ENSP00000278612:p.Gln424*	331	0	0		381	54	0.141732	NM_002519	A8K1V5|A8K6M2|Q13632|Q14967|Q16580|Q86W55|Q8IWE9	Nonsense_Mutation	SNP	ENST00000278612.8	37	CCDS41710.1	.	.	.	.	.	.	.	.	.	.	G	14.02	2.409649	0.42715	.	.	ENSG00000149308	ENST00000278612	.	.	.	5.54	5.54	0.83059	.	0.297500	0.30989	N	0.008468	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12430	T	0.62	-1.0278	12.4896	0.55893	0.0:0.0:0.8223:0.1777	.	.	.	.	X	424	.	ENSP00000278612:Q424X	Q	-	1	0	NPAT	107549651	1.000000	0.71417	0.998000	0.56505	0.034000	0.12701	3.320000	0.51991	2.765000	0.95021	0.557000	0.71058	CAG	.	.	none		0.383	NPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389506.2	NM_002519		A	108044441	G	A	108044441	4	1	10	1	0	0	0	0	0	1	0	0	10575	1386	48	2	3037	2	NPAT	11	108044441	Nonsense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	7122255	108044441	26962075	107	1189											
FAM55B	120406	hgsc.bcm.edu	37	chr11	114576570	114576571	+	Frame_Shift_Ins	INS	-	-	A																															tccccagtggttatactttgINSaaaaaaatgtggattacagc																										TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:114576570_114576571insA	ENST00000389586.4	+	5	1186_1187	c.996_997insA	c.(997-999)aaafs	p.K333fs	NXPE2_ENST00000375475.5_Intron	NM_182495.5	NP_872301.2	Q96DL1	NXPE2_HUMAN	neurexophilin and PC-esterase domain family, member 2	333						integral component of membrane (GO:0016021)											GTTATACTTTGAAAAAAATGTG	0.322																																					p.L332fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.996_997insA						PASS	.																																			SO:0001589	frameshift_variant	120406	exon5			.	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.1003dupA	11.37:g.114576577_114576577dupA	ENSP00000374237:p.Lys333fs	222	0	.		256	60	0.234	NM_182495	Q2NKI8	Frame_Shift_Ins	INS	ENST00000389586.4	37	CCDS44738.1																																																																																			.	.	none		0.322	NXPE2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399181.1	NM_182495		A	114576571	-	A	114576570	7	5	10	1	0	1	1	0	0	0	0	0	5593	1281	45	0	1014	0	FAM55B	11	114576570	Frame_Shift_Ins	INS	-	TCGA-FF-8041-01A-11D-2210-10	6532129	114576570	20429946	108	1190											
NLRX1	79671	hgsc.bcm.edu	37	chr11	119045894	119045894	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtggctgagctcgtgggcCgtgttggggaggacgtcagc	6	8	19	8	3	1	1	1	1	0	0	2	3	1	3	1	5	2	3	1	5	1	1	rs574477974		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr11:119045894C>T	ENST00000409109.1	+	6	2169	c.1582C>T	c.(1582-1584)Cgt>Tgt	p.R528C	NLRX1_ENST00000525863.1_Missense_Mutation_p.R528C|NLRX1_ENST00000292199.2_Missense_Mutation_p.R528C|NLRX1_ENST00000409991.1_Missense_Mutation_p.R528C|NLRX1_ENST00000409265.4_Missense_Mutation_p.R528C	NM_001282144.1	NP_001269073.1	Q86UT6	NLRX1_HUMAN	NLR family member X1	528	Required for interaction with MAVS.				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)		GCTCGTGGGCCGTGTTGGGGA	0.607													C|||	1	0.000199681	0.0	0.0	5008	,	,		18271	0.0		0.0	False		,,,				2504	0.001				p.R528C		Atlas-SNP	.											.	NLRX1	128	.	0			c.C1582T						PASS	.						145	132	136					11																	119045894		2200	4295	6495	SO:0001583	missense	79671	exon6			GTGGGCCGTGTTG	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.1582C>T	11.37:g.119045894C>T	ENSP00000387334:p.Arg528Cys	130	0	0		125	5	0.04	NM_024618	A8K6Q1|B3KPK2|B3KTA2|Q7RTR3|Q96D51|Q9H724	Missense_Mutation	SNP	ENST00000409109.1	37	CCDS8416.1	.	.	.	.	.	.	.	.	.	.	C	11.65	1.703299	0.30232	.	.	ENSG00000160703	ENST00000409991;ENST00000292199;ENST00000409265;ENST00000409109;ENST00000525863	T;T;T;T;T	0.73047	-0.6;-0.6;-0.71;-0.6;-0.71	5.62	4.7	0.59300	.	0.188113	0.38217	N	0.001762	T	0.53610	0.1807	N	0.19112	0.55	0.42859	D	0.994101	B;B	0.19706	0.038;0.005	B;B	0.12156	0.007;0.002	T	0.53851	-0.8380	10	0.87932	D	0	.	8.1864	0.31341	0.2513:0.6692:0.0:0.0795	.	528;528	Q86UT6-2;Q86UT6	.;NLRX1_HUMAN	C	528	ENSP00000386851:R528C;ENSP00000292199:R528C;ENSP00000386858:R528C;ENSP00000387334:R528C;ENSP00000433442:R528C	ENSP00000292199:R528C	R	+	1	0	NLRX1	118551104	1.000000	0.71417	0.993000	0.49108	0.759000	0.43091	4.547000	0.60712	1.346000	0.45694	0.561000	0.74099	CGT	.	.	none		0.607	NLRX1-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335403.1	NM_170722		T	119045894	C	T	119045894	3	4	10	1	0	0	0	0	1	0	0	0	10494	652	23	1	1600	1	NLRX1	11	119045894	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	4469324	119045894	15960622	109	1191											
PRMT8	56341	hgsc.bcm.edu	37	chr12	3692249	3692249	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacatttacacagtgaagaCggaagagctatcgttcacat	14	9	10	8	2	1	3	1	1	0	2	2	5	1	5	0	2	2	2	0	2	4	4			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:3692249C>T	ENST00000382622.3	+	8	1244	c.854C>T	c.(853-855)aCg>aTg	p.T285M	PRMT8_ENST00000261252.4_Intron|PRMT8_ENST00000452611.2_Missense_Mutation_p.T276M	NM_019854.4	NP_062828.3	Q9NR22	ANM8_HUMAN	protein arginine methyltransferase 8	285	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)			ACAGTGAAGACGGAAGAGCTA	0.517																																					p.T285M		Atlas-SNP	.											PRMT8,NS,carcinoma,-1,3	PRMT8	97	3	0			c.C854T						PASS	.						128	104	112					12																	3692249		2203	4300	6503	SO:0001583	missense	56341	exon8			TGAAGACGGAAGA	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.854C>T	12.37:g.3692249C>T	ENSP00000372067:p.Thr285Met	85	0	0		102	22	0.215686	NM_019854	B2RDP0|Q8TBJ8	Missense_Mutation	SNP	ENST00000382622.3	37	CCDS8521.2	.	.	.	.	.	.	.	.	.	.	C	11.07	1.530304	0.27387	.	.	ENSG00000111218	ENST00000452611;ENST00000382622	T;T	0.78707	-1.2;-1.2	5.4	3.57	0.40892	.	0.202156	0.52532	D	0.000070	T	0.70193	0.3196	L	0.54323	1.7	0.37506	D	0.91696	P;P	0.42649	0.786;0.68	B;B	0.39027	0.288;0.15	T	0.73588	-0.3935	10	0.46703	T	0.11	.	9.2713	0.37673	0.0:0.8267:0.0:0.1733	.	276;285	Q9NR22-2;Q9NR22	.;ANM8_HUMAN	M	276;285	ENSP00000414507:T276M;ENSP00000372067:T285M	ENSP00000372067:T285M	T	+	2	0	PRMT8	3562510	0.988000	0.35896	1.000000	0.80357	0.093000	0.18481	2.678000	0.46900	1.298000	0.44778	-0.142000	0.14014	ACG	.	.	none		0.517	PRMT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250297.2	NM_019854		T	3692249	C	T	3692249	3	4	10	1	0	0	0	0	1	0	0	0	12554	536	19	1	884	1	PRMT8	12	3692249	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10		3692249	130159646	110	1192											
CHD4	1108	hgsc.bcm.edu	37	chr12	6710854	6710854	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cttgtagttggtgagggttcGataatcctcctctgagaaca	9	13	11	8	1	1	2	0	2	1	1	4	4	3	2	2	2	1	3	2	2	3	5			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:6710854G>A	ENST00000357008.2	-	5	680	c.517C>T	c.(517-519)Cga>Tga	p.R173*	CHD4_ENST00000309577.6_Nonsense_Mutation_p.R173*|CHD4_ENST00000544484.1_Nonsense_Mutation_p.R170*|CHD4_ENST00000544040.1_Nonsense_Mutation_p.R166*	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	173					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						GTGAGGGTTCGATAATCCTCC	0.488																																					p.R173X	Colon(32;586 792 4568 16848 45314)	Atlas-SNP	.											CHD4_ENST00000357008,NS,malignant_melanoma,0,3	CHD4	539	3	0			c.C517T						scavenged	.						274	278	277					12																	6710854		2203	4300	6503	SO:0001587	stop_gained	1108	exon5			GGGTTCGATAATC	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.517C>T	12.37:g.6710854G>A	ENSP00000349508:p.Arg173*	174	1	0.00574713		221	75	0.339367	NM_001273	Q8IXZ5	Nonsense_Mutation	SNP	ENST00000357008.2	37	CCDS8552.1	.	.	.	.	.	.	.	.	.	.	G	37	6.145184	0.97324	.	.	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464;ENST00000545942	.	.	.	5.87	5.87	0.94306	.	0.228496	0.32081	N	0.006603	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10377	T	0.69	-0.807	16.49	0.84198	0.0:0.0:0.8686:0.1314	.	.	.	.	X	170;166;173;173;147;173	.	ENSP00000312419:R173X	R	-	1	2	CHD4	6581115	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.382000	0.79729	2.774000	0.95407	0.650000	0.86243	CGA	.	.	none		0.488	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273		A	6710854	G	A	6710854	4	1	10	1	0	0	0	0	0	1	0	0	3329	1066	37	1	5365	1	CHD4	12	6710854	Nonsense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	3018605	6710854	127141041	111	1193											
SYT10	341359	hgsc.bcm.edu	37	chr12	33579301	33579301	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaatgctctgtggaagcgtaGtgatgttggaagtcacaggt	11	11	14	5	1	2	1	1	1	1	0	2	3	2	3	0	3	2	3	0	3	4	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:33579301G>T	ENST00000228567.3	-	2	577	c.281C>A	c.(280-282)aCt>aAt	p.T94N	SYT10_ENST00000535526.1_5'UTR|SYT10_ENST00000567656.1_5'Flank	NM_198992.3	NP_945343.1	Q6XYQ8	SYT10_HUMAN	synaptotagmin X	94					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)					TGGAAGCGTAGTGATGTTGGA	0.423																																					p.T94N		Atlas-SNP	.											.	SYT10	109	.	0			c.C281A						PASS	.						91	90	90					12																	33579301		2203	4300	6503	SO:0001583	missense	341359	exon2			AGCGTAGTGATGT	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.281C>A	12.37:g.33579301G>T	ENSP00000228567:p.Thr94Asn	113	0	0		135	21	0.155556	NM_198992	Q495U2	Missense_Mutation	SNP	ENST00000228567.3	37	CCDS8732.1	.	.	.	.	.	.	.	.	.	.	G	0.496	-0.873133	0.02570	.	.	ENSG00000110975	ENST00000228567	T	0.46451	0.87	4.1	-2.4	0.06583	.	0.459403	0.18019	N	0.154304	T	0.21468	0.0517	N	0.19112	0.55	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.09378	-1.0677	10	0.36615	T	0.2	.	6.502	0.22174	0.0:0.3531:0.4103:0.2366	.	94	Q6XYQ8	SYT10_HUMAN	N	94	ENSP00000228567:T94N	ENSP00000228567:T94N	T	-	2	0	SYT10	33470568	0.000000	0.05858	0.000000	0.03702	0.174000	0.22865	-0.030000	0.12308	-0.492000	0.06687	-0.147000	0.13772	ACT	.	.	none		0.423	SYT10-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403222.1	NM_198992		T	33579301	G	T	33579301	3	4	10	1	0	0	0	0	1	0	0	0	15481	1029	36	4	1314	4	SYT10	12	33579301	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	26868447	33579301	100272594	112	1194											
NELL2	4753	hgsc.bcm.edu	37	chr12	44915940	44915940	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cacagtcacagaccatccgtCgacacataacgaatccattc	14	7	5	15	3	1	1	1	0	0	1	5	3	3	1	3	0	1	0	3	0	2	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:44915940C>T	ENST00000429094.2	-	18	2522	c.2018G>A	c.(2017-2019)cGa>cAa	p.R673Q	NELL2_ENST00000452445.2_Missense_Mutation_p.R673Q|NELL2_ENST00000395487.2_Missense_Mutation_p.R672Q|NELL2_ENST00000437801.2_Missense_Mutation_p.R723Q|NELL2_ENST00000333837.4_Missense_Mutation_p.R696Q|NELL2_ENST00000549027.1_Missense_Mutation_p.R672Q|NELL2_ENST00000551601.1_Missense_Mutation_p.R625Q	NM_001145108.1	NP_001138580.1	Q99435	NELL2_HUMAN	NEL-like 2 (chicken)	673	VWFC 2. {ECO:0000255|PROSITE- ProRule:PRU00220}.					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)		GACCATCCGTCGACACATAAC	0.438																																					p.R723Q		Atlas-SNP	.											NELL2_ENST00000437801,colon,carcinoma,-1,2	NELL2	286	2	0			c.G2168A						scavenged	.						95	87	90					12																	44915940		2203	4300	6503	SO:0001583	missense	4753	exon19			ATCCGTCGACACA	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.2018G>A	12.37:g.44915940C>T	ENSP00000390680:p.Arg673Gln	52	0	0		64	3	0.046875	NM_001145107	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Missense_Mutation	SNP	ENST00000429094.2	37	CCDS8746.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.940970	0.73557	.	.	ENSG00000184613	ENST00000395487;ENST00000429094;ENST00000551601;ENST00000452445;ENST00000549027;ENST00000333837;ENST00000437801	D;T;T;T;D;T;D	0.81821	-1.5;-1.47;-1.18;-1.47;-1.5;-1.43;-1.54	5.7	4.81	0.61882	von Willebrand factor, type C (2);EGF-like region, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.70937	0.3281	L	0.53617	1.68	0.58432	D	0.999997	P;P;B;B;B	0.42827	0.539;0.791;0.056;0.009;0.258	B;B;B;B;B	0.28232	0.024;0.087;0.018;0.005;0.053	T	0.69978	-0.4998	10	0.21014	T	0.42	-9.7144	14.8365	0.70187	0.0:0.931:0.0:0.069	.	696;723;625;673;672	B7Z2U7;B7Z9U3;F8VVB6;Q99435;Q96JS2	.;.;.;NELL2_HUMAN;.	Q	672;673;625;673;672;696;723	ENSP00000378866:R672Q;ENSP00000390680:R673Q;ENSP00000449332:R625Q;ENSP00000394612:R673Q;ENSP00000447927:R672Q;ENSP00000327988:R696Q;ENSP00000416341:R723Q	ENSP00000327988:R696Q	R	-	2	0	NELL2	43202207	1.000000	0.71417	0.973000	0.42090	0.938000	0.57974	7.814000	0.86154	1.405000	0.46838	0.650000	0.86243	CGA	.	.	none		0.438	NELL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404180.1	NM_006159		T	44915940	C	T	44915940	3	4	10	1	0	0	0	0	1	0	0	0	10343	884	31	1	444	1	NELL2	12	44915940	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	11336639	44915940	88935955	113	1195											
STAT6	6778	hgsc.bcm.edu	37	chr12	57493818	57493818	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagacagcgtttggtgaggTccaggacaccatcaaaccac	12	6	12	11	1	1	2	1	1	0	1	2	4	2	3	3	4	2	1	3	4	1	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:57493818T>C	ENST00000300134.3	-	14	1893	c.1568A>G	c.(1567-1569)gAc>gGc	p.D523G	STAT6_ENST00000543873.2_Missense_Mutation_p.D523G|STAT6_ENST00000537215.2_Missense_Mutation_p.D413G|STAT6_ENST00000538913.2_Missense_Mutation_p.D413G|STAT6_ENST00000556155.1_Missense_Mutation_p.D523G|STAT6_ENST00000454075.3_Missense_Mutation_p.D523G	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	523	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						TTTGGTGAGGTCCAGGACACC	0.612																																					p.D523G		Atlas-SNP	.											.	STAT6	69	.	0			c.A1568G						PASS	.						93	73	80					12																	57493818		2203	4300	6503	SO:0001583	missense	6778	exon14			GTGAGGTCCAGGA	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.1568A>G	12.37:g.57493818T>C	ENSP00000300134:p.Asp523Gly	137	0	0		152	56	0.368421	NM_001178079	A8K316|B7ZA27|F5GXI9|Q5FBW5|Q71UP4	Missense_Mutation	SNP	ENST00000300134.3	37	CCDS8931.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.527568	0.85706	.	.	ENSG00000166888	ENST00000300134;ENST00000535201;ENST00000538913;ENST00000543873;ENST00000556155;ENST00000537215;ENST00000454075;ENST00000542721;ENST00000542516;ENST00000555375	D;D;D;D;D;D;D	0.89875	-2.58;-2.58;-2.58;-2.58;-2.58;-2.58;-2.58	4.92	4.92	0.64577	STAT transcription factor, DNA-binding (1);p53-like transcription factor, DNA-binding (1);SH2 motif (1);EF-hand-like domain (1);	0.055888	0.64402	D	0.000001	D	0.92766	0.7700	M	0.64997	1.995	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.79784	0.984;0.993	D	0.93346	0.6714	10	0.87932	D	0	-25.2637	12.5465	0.56203	0.0:0.0:0.0:1.0	.	523;523	A8K4S9;P42226	.;STAT6_HUMAN	G	523;413;413;523;523;413;523;413;523;89	ENSP00000300134:D523G;ENSP00000445409:D413G;ENSP00000438451:D523G;ENSP00000451742:D523G;ENSP00000444530:D413G;ENSP00000401486:D523G;ENSP00000450921:D89G	ENSP00000300134:D523G	D	-	2	0	STAT6	55780085	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.810000	0.86072	2.062000	0.61559	0.533000	0.62120	GAC	.	.	none		0.612	STAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412248.3	NM_003153		C	57493818	T	C	57493818	3	2	10	1	0	0	0	0	1	0	0	0	15285	1667	58	3	1011	3	STAT6	12	57493818	Missense_Mutation	SNP	T	TCGA-FF-8041-01A-11D-2210-10	12577878	57493818	76358077	114	1196											
BEST3	144453	hgsc.bcm.edu	37	chr12	70087575	70087575	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccttctaagcaggcgcccGtgctcgtcgcttccgtgaac	5	10	11	15	5	1	1	0	1	1	0	5	1	3	1	3	1	3	3	3	1	2	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:70087575G>A	ENST00000330891.5	-	4	586	c.360C>T	c.(358-360)caC>caT	p.H120H	BEST3_ENST00000553096.1_Silent_p.H14H|BEST3_ENST00000476098.1_De_novo_Start_OutOfFrame|BEST3_ENST00000551160.1_Silent_p.H14H|BEST3_ENST00000393365.1_Silent_p.H14H|BEST3_ENST00000266661.4_Silent_p.H14H|BEST3_ENST00000331471.4_Silent_p.H120H|BEST3_ENST00000533674.1_5'UTR	NM_001282613.1|NM_032735.2	NP_001269542.1|NP_116124.2	Q8N1M1	BEST3_HUMAN	bestrophin 3	120					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)			GCAGGCGCCCGTGCTCGTCGC	0.532																																					p.H120H		Atlas-SNP	.											.	BEST3	129	.	0			c.C360T						PASS	.						103	89	93					12																	70087575		2203	4300	6503	SO:0001819	synonymous_variant	144453	exon4			GCGCCCGTGCTCG	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.360C>T	12.37:g.70087575G>A		138	0	0		162	60	0.37037	NM_032735	B5MDI8|F8VVZ2|Q53YQ7|Q8N356|Q8NFT9|Q9BR80	Silent	SNP	ENST00000330891.5	37	CCDS8992.2																																																																																			.	.	none		0.532	BEST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313908.2	NM_152439		A	70087575	G	A	70087575	2	1	10	1	0	0	0	0	0	0	0	1	1406	1136	40	1		1	BEST3	12	70087575	Silent	SNP	G	TCGA-FF-8041-01A-11D-2210-10	12593757	70087575	63764320	115	1197											
ACSS3	79611	hgsc.bcm.edu	37	chr12	81472143	81472143	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggttctggggcaaagctgccGagcagatcagctggtacaag	10	7	15	9	1	2	1	1	0	1	1	2	2	2	1	1	4	5	6	1	4	3	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:81472143G>A	ENST00000548058.1	+	1	1154	c.244G>A	c.(244-246)Gag>Aag	p.E82K	ACSS3_ENST00000261206.3_Missense_Mutation_p.E82K			Q9H6R3	ACSS3_HUMAN	acyl-CoA synthetase short-chain family member 3	82						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						CAAAGCTGCCGAGCAGATCAG	0.617																																					p.E82K		Atlas-SNP	.											.	ACSS3	118	.	0			c.G244A						PASS	.						46	43	44					12																	81472143		1984	4018	6002	SO:0001583	missense	79611	exon1			GCTGCCGAGCAGA		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.244G>A	12.37:g.81472143G>A	ENSP00000449535:p.Glu82Lys	49	0	0		56	20	0.357143	NM_024560	Q8NC66	Missense_Mutation	SNP	ENST00000548058.1	37	CCDS9022.1	.	.	.	.	.	.	.	.	.	.	G	8.471	0.857542	0.17106	.	.	ENSG00000111058	ENST00000548058;ENST00000261206	T;T	0.10960	2.82;2.82	5.03	4.11	0.48088	Acyl-CoA synthase, domain of unknown function DUF3448 (1);	0.506389	0.20979	N	0.082246	T	0.04407	0.0121	N	0.04636	-0.2	0.80722	D	1	P	0.39520	0.676	B	0.35413	0.202	T	0.49093	-0.8975	10	0.11182	T	0.66	-23.7543	11.5895	0.50938	0.0:0.3487:0.6513:0.0	.	82	Q9H6R3	ACSS3_HUMAN	K	82	ENSP00000449535:E82K;ENSP00000261206:E82K	ENSP00000261206:E82K	E	+	1	0	ACSS3	79996274	0.962000	0.33011	0.863000	0.33907	0.385000	0.30292	1.612000	0.36889	1.292000	0.44672	0.655000	0.94253	GAG	.	.	none		0.617	ACSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407794.1	NM_024560		A	81472143	G	A	81472143	3	1	10	1	0	0	0	0	1	0	0	0	190	1059	37	1	246	1	ACSS3	12	81472143	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	11384568	81472143	52379752	116	1198											
PLXNC1	10154	hgsc.bcm.edu	37	chr12	94543629	94543629	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cccgacggccgccgcctgctCctctcctccagcctagtgga	4	7	10	20	4	1	0	0	0	1	0	4	2	3	1	8	2	2	1	8	2	1	1	rs560001465	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:94543629C>T	ENST00000258526.4	+	1	1131	c.882C>T	c.(880-882)ctC>ctT	p.L294L		NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	294	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						GCCGCCTGCTCCTCTCCTCCA	0.746													C|||	4	0.000798722	0.0	0.0	5008	,	,		13674	0.0		0.0	False		,,,				2504	0.0041				p.L294L		Atlas-SNP	.											.	PLXNC1	135	.	0			c.C882T						PASS	.						5	7	6					12																	94543629		2040	4096	6136	SO:0001819	synonymous_variant	10154	exon1			CCTGCTCCTCTCC	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.882C>T	12.37:g.94543629C>T		9	0	0		9	6	0.666667	NM_005761	Q59H25	Silent	SNP	ENST00000258526.4	37	CCDS9049.1																																																																																			.	.	none		0.746	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2			T	94543629	C	T	94543629	2	4	10	1	0	0	0	0	0	0	0	1	12135	842	30	2		2	PLXNC1	12	94543629	Silent	SNP	C	TCGA-FF-8041-01A-11D-2210-10	13071486	94543629	39308266	117	1199											
CCDC64	92558	hgsc.bcm.edu	37	chr12	120518805	120518805	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agaaggccatcagggaccgcGacgaggccattgcaaagtga	13	4	14	10	3	1	2	1	1	0	1	1	5	1	3	3	3	1	1	3	3	2	1	rs373363052		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr12:120518805G>A	ENST00000397558.2	+	7	1423	c.1423G>A	c.(1423-1425)Gac>Aac	p.D475N	CCDC64_ENST00000257583.4_Missense_Mutation_p.D172N|CCDC64_ENST00000446727.2_Missense_Mutation_p.D146N	NM_207311.2	NP_997194.2	Q6ZP65	BICR1_HUMAN	coiled-coil domain containing 64	475					Golgi to secretory granule transport (GO:0055107)|neuron projection development (GO:0031175)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	dynactin binding (GO:0034452)|Rab GTPase binding (GO:0017137)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(2)|lung(4)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	22	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CAGGGACCGCGACGAGGCCAT	0.438																																					p.D475N		Atlas-SNP	.											.	CCDC64	40	.	0			c.G1423A						PASS	.	G	ASN/ASP	0,4044		0,0,2022	70	79	76		1423	5.3	1	12		76	1,8361		0,1,4180	no	missense	CCDC64	NM_207311.2	23	0,1,6202	AA,AG,GG		0.012,0.0,0.0081	probably-damaging	475/574	120518805	1,12405	2022	4181	6203	SO:0001583	missense	92558	exon7			GACCGCGACGAGG	U88834, AK129960	CCDS41845.1	12q24.23	2006-01-24				ENSG00000135127			28095	protein-coding gene	gene with protein product							Standard	NM_207311		Approved	FLJ26450	uc001txl.1	Q6ZP65	OTTHUMG00000169311	ENST00000397558.2:c.1423G>A	12.37:g.120518805G>A	ENSP00000380690:p.Asp475Asn	33	0	0		29	9	0.310345	NM_207311	A8MUC8|B4DWL0|B5MDJ0|O95000	Missense_Mutation	SNP	ENST00000397558.2	37	CCDS41845.1	.	.	.	.	.	.	.	.	.	.	G	35	5.417810	0.96092	0.0	1.2E-4	ENSG00000135127	ENST00000397558;ENST00000446727;ENST00000548673;ENST00000257583	T;T;T	0.04862	3.56;3.6;3.54	5.32	5.32	0.75619	.	529.136000	0.00166	N	0.000000	T	0.35038	0.0918	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	0.999;0.998;0.998	T	0.00699	-1.1604	10	0.87932	D	0	-12.8386	18.9942	0.92806	0.0:0.0:1.0:0.0	.	172;146;475	B4DWL0;B4DNE7;Q6ZP65	.;.;BICR1_HUMAN	N	475;146;193;172	ENSP00000380690:D475N;ENSP00000399658:D146N;ENSP00000447477:D193N	ENSP00000257583:D172N	D	+	1	0	CCDC64	119003188	1.000000	0.71417	0.955000	0.39395	0.944000	0.59088	9.731000	0.98807	2.492000	0.84095	0.561000	0.74099	GAC	.	.	weak		0.438	CCDC64-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403390.2	NM_207311		A	120518805	G	A	120518805	3	1	10	1	0	0	0	0	1	0	0	0	2837	1058	37	1	1449	1	CCDC64	12	120518805	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	25975176	120518805	13333090	118	1200											
NBEA	26960	hgsc.bcm.edu	37	chr13	35691562	35691562	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ttgttctagatggtccccggCcatcacaaaaagaaattata	14	11	7	9	1	2	2	1	0	1	2	3	2	3	2	3	2	0	1	3	2	6	5			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr13:35691562C>T	ENST00000400445.3	+	14	2548	c.2014C>T	c.(2014-2016)Cca>Tca	p.P672S	NBEA_ENST00000379939.2_Missense_Mutation_p.P672S|NBEA_ENST00000310336.4_Missense_Mutation_p.P672S|NBEA_ENST00000540320.1_Missense_Mutation_p.P672S	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	672					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)		TGGTCCCCGGCCATCACAAAA	0.269																																					p.P672S		Atlas-SNP	.											.	NBEA	340	.	0			c.C2014T						PASS	.						4	4	4					13																	35691562		1566	3452	5018	SO:0001583	missense	26960	exon14			CCCCGGCCATCAC	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.2014C>T	13.37:g.35691562C>T	ENSP00000383295:p.Pro672Ser	109	0	0		120	22	0.183333	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	37	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.106573	0.77096	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	T;T;T;T	0.39229	1.09;1.09;1.09;1.09	4.29	4.29	0.51040	.	0.000000	0.85682	D	0.000000	T	0.66548	0.2800	M	0.82056	2.57	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.73062	-0.4101	10	0.62326	D	0.03	.	16.7133	0.85391	0.0:1.0:0.0:0.0	.	672	Q5T321	.	S	672	ENSP00000440951:P672S;ENSP00000383295:P672S;ENSP00000369271:P672S;ENSP00000308534:P672S	ENSP00000308534:P672S	P	+	1	0	NBEA	34589562	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.265000	0.78442	1.929000	0.55896	0.460000	0.39030	CCA	.	.	none		0.269	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		T	35691562	C	T	35691562	3	4	10	1	0	0	0	0	1	0	0	0	10196	739	26	2	2068	2	NBEA	13	35691562	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10		35691562	79478316	119	1201											
ELF1	1997	hgsc.bcm.edu	37	chr13	41507882	41507882	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acggttccattgcaaatggtCtgaacattgctagtaaggac	12	11	10	8	1	1	1	0	1	1	0	2	2	2	2	1	3	3	4	1	3	4	5			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr13:41507882C>T	ENST00000239882.3	-	9	1853	c.1539G>A	c.(1537-1539)caG>caA	p.Q513Q	ELF1_ENST00000498824.1_5'UTR|ELF1_ENST00000442101.1_Silent_p.Q489Q	NM_172373.3	NP_758961.1	P32519	ELF1_HUMAN	E74-like factor 1 (ets domain transcription factor)	513					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)		TGCAAATGGTCTGAACATTGC	0.517																																					p.Q513Q		Atlas-SNP	.											ELF1,NS,carcinoma,-2,1	ELF1	65	1	0			c.G1539A						PASS	.						108	104	106					13																	41507882		2203	4300	6503	SO:0001819	synonymous_variant	1997	exon9			AATGGTCTGAACA	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.1539G>A	13.37:g.41507882C>T		118	0	0		137	62	0.452555	NM_172373	B4E2I5|E9PDQ9|Q8N6F6|Q9UDE1	Silent	SNP	ENST00000239882.3	37	CCDS9374.1																																																																																			.	.	none		0.517	ELF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044654.3	NM_172373		T	41507882	C	T	41507882	2	4	10	1	0	0	0	0	0	0	0	1	5055	912	32	2		2	ELF1	13	41507882	Silent	SNP	C	TCGA-FF-8041-01A-11D-2210-10	5816320	41507882	73661996	120	1202											
DACH1	1602	hgsc.bcm.edu	37	chr13	72440219	72440219	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcttcagcttggtgtagaccGtatgcaagccccccaccaag	9	8	10	14	1	1	1	1	0	0	1	1	1	1	1	5	1	3	5	5	1	4	4			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr13:72440219G>C	ENST00000359684.2	-	1	688	c.689C>G	c.(688-690)aCg>aGg	p.T230R	DACH1_ENST00000354591.4_Missense_Mutation_p.T230R|DACH1_ENST00000313174.7_Missense_Mutation_p.T230R|DACH1_ENST00000305425.4_Missense_Mutation_p.T230R			Q9UI36	DACH1_HUMAN	dachshund family transcription factor 1	230	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)	p.T230fs*6(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)		GGTGTAGACCGTATGCAAGCC	0.617																																					p.T230R		Atlas-SNP	.											.	DACH1	123	.	1	Deletion - Frameshift(1)	lung(1)	c.C689G						PASS	.						79	85	83					13																	72440219		2070	4222	6292	SO:0001583	missense	1602	exon1			TAGACCGTATGCA	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.689C>G	13.37:g.72440219G>C	ENSP00000352712:p.Thr230Arg	149	0	0		133	66	0.496241	NM_080759	D0FY35|D0FY36|O75523|O75687|Q5VYY3|Q5VYY4|Q96SG3|Q96SG4|Q9H524|Q9UMH4	Missense_Mutation	SNP	ENST00000359684.2	37		.	.	.	.	.	.	.	.	.	.	G	18.36	3.606479	0.66445	.	.	ENSG00000165659	ENST00000305425;ENST00000313174;ENST00000354591;ENST00000359684;ENST00000377826	D;D;D;D	0.83506	-1.73;-1.73;-1.73;-1.73	4.08	4.08	0.47627	.	0.000000	0.85682	D	0.000000	D	0.91012	0.7173	M	0.80982	2.52	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.997;0.999	D	0.92697	0.6171	10	0.87932	D	0	-6.469	15.8733	0.79141	0.0:0.0:1.0:0.0	.	228;228;228	Q9UI36-4;Q9UI36-3;Q9UI36-2	.;.;.	R	230	ENSP00000304994:T230R;ENSP00000318506:T230R;ENSP00000346604:T230R;ENSP00000352712:T230R	ENSP00000304994:T230R	T	-	2	0	DACH1	71338220	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	9.144000	0.94629	1.803000	0.52742	0.313000	0.20887	ACG	.	.	none		0.617	DACH1-002	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000045240.1	NM_004392		C	72440219	G	C	72440219	3	2	10	1	0	0	0	0	1	0	0	0	4222	1145	40	4	1481	4	DACH1	13	72440219	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	30932337	72440219	42729659	121	1203											
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77657173	77657173	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gataccaaaattacctcaggGccatttgctgtaatgaactg	13	11	8	9	0	1	1	1	1	0	0	1	2	1	1	3	1	4	2	3	1	6	4			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr13:77657173G>A	ENST00000544440.2	-	63	10933	c.10916C>T	c.(10915-10917)gCc>gTc	p.A3639V	MYCBP2_ENST00000407578.2_Missense_Mutation_p.A3677V|MYCBP2-AS1_ENST00000593933.1_RNA|MYCBP2-AS2_ENST00000428716.2_RNA|MYCBP2-AS1_ENST00000450627.2_RNA|MYCBP2-AS1_ENST00000448470.2_RNA|MYCBP2-AS1_ENST00000422231.2_RNA|MYCBP2_ENST00000357337.6_Missense_Mutation_p.A3639V					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)		TTACCTCAGGGCCATTTGCTG	0.423																																					p.A3677V		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.C11030T						PASS	.						130	126	127					13																	77657173		2203	4300	6503	SO:0001583	missense	23077	exon63			CTCAGGGCCATTT	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.10916C>T	13.37:g.77657173G>A	ENSP00000444596:p.Ala3639Val	150	0	0		141	56	0.397163	NM_015057		Missense_Mutation	SNP	ENST00000544440.2	37		.	.	.	.	.	.	.	.	.	.	G	27.0	4.795732	0.90453	.	.	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	T;T;T	0.69806	-0.43;-0.43;-0.43	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.79281	0.4419	L	0.55213	1.73	0.80722	D	1	D	0.63880	0.993	D	0.68192	0.956	T	0.80879	-0.1185	10	0.87932	D	0	.	19.165	0.93553	0.0:0.0:1.0:0.0	.	3639	O75592	MYCB2_HUMAN	V	3639;3677;3639	ENSP00000349892:A3639V;ENSP00000384288:A3677V;ENSP00000444596:A3639V	ENSP00000349892:A3639V	A	-	2	0	MYCBP2	76555174	1.000000	0.71417	1.000000	0.80357	0.537000	0.34900	9.869000	0.99810	2.504000	0.84457	0.650000	0.86243	GCC	.	.	none		0.423	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		A	77657173	G	A	77657173	3	1	10	1	0	0	0	0	1	0	0	0	10027	1203	42	2	3090	2	MYCBP2	13	77657173	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	5216954	77657173	37512705	122	1204											
CUL4A	8451	hgsc.bcm.edu	37	chr13	113909104	113909104	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaggagataaaaatggccaCggggataggtacgaaaactg	16	6	14	5	2	0	2	0	1	0	1	0	5	0	3	1	5	2	1	1	5	7	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr13:113909104C>T	ENST00000375440.4	+	17	1934	c.1850C>T	c.(1849-1851)aCg>aTg	p.T617M	CUL4A_ENST00000451881.1_Missense_Mutation_p.T517M|CUL4A_ENST00000326335.4_Missense_Mutation_p.T517M|CUL4A_ENST00000375441.3_Missense_Mutation_p.T517M	NM_001008895.1	NP_001008895.1	Q13619	CUL4A_HUMAN	cullin 4A	617					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)			AAAATGGCCACGGGGATAGGT	0.453																																					p.T617M		Atlas-SNP	.											CUL4A,NS,carcinoma,0,1	CUL4A	50	1	0			c.C1850T						scavenged	.						98	95	96					13																	113909104		2203	4300	6503	SO:0001583	missense	8451	exon17			TGGCCACGGGGAT	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.1850C>T	13.37:g.113909104C>T	ENSP00000364589:p.Thr617Met	91	1	0.010989		70	17	0.242857	NM_001008895	A2A2W2|O75834|Q589T6|Q5TC62|Q6UP08|Q9UP17	Missense_Mutation	SNP	ENST00000375440.4	37	CCDS41908.1	.	.	.	.	.	.	.	.	.	.	C	18.35	3.605273	0.66445	.	.	ENSG00000139842	ENST00000375441;ENST00000451881;ENST00000326335;ENST00000375440	T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07	5.3	5.3	0.74995	Cullin, N-terminal (1);Winged helix-turn-helix transcription repressor DNA-binding (1);Cullin homology (2);	0.000000	0.85682	D	0.000000	D	0.91730	0.7385	H	0.95004	3.61	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.993	D	0.93689	0.7005	10	0.87932	D	0	-30.3978	19.3097	0.94182	0.0:1.0:0.0:0.0	.	617;617	Q13619;A8MSH7	CUL4A_HUMAN;.	M	517;517;517;617	ENSP00000364590:T517M;ENSP00000389118:T517M;ENSP00000322132:T517M;ENSP00000364589:T617M	ENSP00000322132:T517M	T	+	2	0	CUL4A	112957105	1.000000	0.71417	0.952000	0.39060	0.144000	0.21451	5.880000	0.69698	2.627000	0.88993	0.561000	0.74099	ACG	.	.	none		0.453	CUL4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045888.3	NM_003589		T	113909104	C	T	113909104	3	4	10	1	0	0	0	0	1	0	0	0	4059	536	19	1	1916	1	CUL4A	13	113909104	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	36251931	113909104	1260774	123	1205											
MYH6	4624	hgsc.bcm.edu	37	chr14	23865523	23865523	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctatcttcttgaactcaatgCgcatgagctggccccgggct	7	11	10	13	2	3	2	1	2	2	0	3	2	3	2	2	2	3	3	2	2	3	3	rs535438755		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr14:23865523C>T	ENST00000356287.3	-	19	2428	c.2399G>A	c.(2398-2400)cGc>cAc	p.R800H	MYH6_ENST00000405093.3_Missense_Mutation_p.R800H			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	800	IQ. {ECO:0000255|PROSITE- ProRule:PRU00116}.				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)		GAACTCAATGCGCATGAGCTG	0.577													C|||	1	0.000199681	0.0	0.0	5008	,	,		18438	0.0		0.0	False		,,,				2504	0.001				p.R800H		Atlas-SNP	.											MYH6,NS,carcinoma,-1,1	MYH6	274	1	0			c.G2399A						PASS	.						101	89	93					14																	23865523		2203	4300	6503	SO:0001583	missense	4624	exon20			TCAATGCGCATGA	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.2399G>A	14.37:g.23865523C>T	ENSP00000348634:p.Arg800His	121	0	0		136	63	0.463235	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Missense_Mutation	SNP	ENST00000356287.3	37	CCDS9600.1	.	.	.	.	.	.	.	.	.	.	c	20.4	3.991779	0.74703	.	.	ENSG00000197616	ENST00000405093;ENST00000356287	T;T	0.77098	-1.07;-1.07	4.78	4.78	0.61160	.	.	.	.	.	D	0.91915	0.7440	H	0.96365	3.81	0.58432	D	0.999999	D	0.89917	1.0	D	0.72075	0.976	D	0.94612	0.7805	9	0.87932	D	0	.	18.1704	0.89743	0.0:1.0:0.0:0.0	.	800	P13533	MYH6_HUMAN	H	800	ENSP00000386041:R800H;ENSP00000348634:R800H	ENSP00000348634:R800H	R	-	2	0	MYH6	22935363	1.000000	0.71417	1.000000	0.80357	0.200000	0.23975	7.522000	0.81844	2.382000	0.81193	0.650000	0.86243	CGC	.	.	none		0.577	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			T	23865523	C	T	23865523	3	4	10	1	0	0	0	0	1	0	0	0	10047	768	27	1	3500	1	MYH6	14	23865523	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10		23865523	83484017	124	1206											
PRKD1	5587	hgsc.bcm.edu	37	chr14	30046446	30046446	+	Nonstop_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gattataggagatggaactcAgaggatgctgacacgctcac	13	8	12	8	1	2	3	2	1	0	2	2	7	2	5	0	3	2	2	0	3	3	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr14:30046446A>T	ENST00000331968.5	-	18	2966	c.2737T>A	c.(2737-2739)Tga>Aga	p.*913R	PRKD1_ENST00000415220.2_Nonstop_Mutation_p.*921R	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	0					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)		GATGGAACTCAGAGGATGCTG	0.443																																					p.X913R		Atlas-SNP	.											.	PRKD1	316	.	0			c.T2737A						PASS	.						99	87	91					14																	30046446		2203	4300	6503	SO:0001578	stop_lost	5587	exon18			GAACTCAGAGGAT		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.2737T>A	14.37:g.30046446A>T		212	0	0		205	49	0.239024	NM_002742	A6NL64|B2RAF6	Missense_Mutation	SNP	ENST00000331968.5	37	CCDS9637.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.076302	0.76415	.	.	ENSG00000184304	ENST00000331968;ENST00000415220	.	.	.	6.03	6.03	0.97812	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5582	0.84512	1.0:0.0:0.0:0.0	.	.	.	.	R	913;921	.	.	X	-	1	0	PRKD1	29116197	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.300000	0.96151	2.308000	0.77769	0.533000	0.62120	TGA	.	.	none		0.443	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742		T	30046446	A	T	30046446	4	4	10	1	0	0	0	0	0	0	0	0	12530	201	7	5	5	5	PRKD1	14	30046446	Nonstop_Mutation	SNP	A	TCGA-FF-8041-01A-11D-2210-10	6180923	30046446	77303094	125	1207											
PRKD1	5587	hgsc.bcm.edu	37	chr14	30046591	30046591	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctcccacctcaggtcatcActttcatgggtgatgtagcg	7	13	9	12	1	5	1	4	1	1	0	6	1	5	1	2	2	1	1	2	2	1	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr14:30046591A>G	ENST00000331968.5	-	18	2821	c.2592T>C	c.(2590-2592)agT>agC	p.S864S	PRKD1_ENST00000415220.2_Silent_p.S872S	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	864					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)		TCAGGTCATCACTTTCATGGG	0.498																																					p.S864S		Atlas-SNP	.											.	PRKD1	316	.	0			c.T2592C						PASS	.						145	128	134					14																	30046591		2203	4300	6503	SO:0001819	synonymous_variant	5587	exon18			GTCATCACTTTCA		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.2592T>C	14.37:g.30046591A>G		199	0	0		189	37	0.195767	NM_002742	A6NL64|B2RAF6	Silent	SNP	ENST00000331968.5	37	CCDS9637.1																																																																																			.	.	none		0.498	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742		G	30046591	A	G	30046591	2	3	10	1	0	0	0	0	0	0	0	1	12530	156	6	3		3	PRKD1	14	30046591	Silent	SNP	A	TCGA-FF-8041-01A-11D-2210-10	145	30046591	77302949	126	1208											
C14orf37	145407	hgsc.bcm.edu	37	chr14	58598352	58598352	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcaggggaaatgctgggtTcccccaccattattccagga	9	9	12	11	0	0	0	0	0	0	0	2	2	2	2	4	4	2	3	4	4	2	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr14:58598352T>C	ENST00000267485.7	-	4	1903	c.1709A>G	c.(1708-1710)gAa>gGa	p.E570G	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	570						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						AATGCTGGGTTCCCCCACCAT	0.493																																					p.E570G		Atlas-SNP	.											C14orf37,NS,carcinoma,-1,1	C14orf37	87	1	0			c.A1709G						PASS	.						114	107	109					14																	58598352		2203	4300	6503	SO:0001583	missense	145407	exon4			CTGGGTTCCCCCA		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.1709A>G	14.37:g.58598352T>C	ENSP00000267485:p.Glu570Gly	111	0	0		110	40	0.363636	NM_001001872	A8K8Z8|Q6P5Q1|Q86TY1	Missense_Mutation	SNP	ENST00000267485.7	37	CCDS32089.1	.	.	.	.	.	.	.	.	.	.	T	5.939	0.357220	0.11239	.	.	ENSG00000139971	ENST00000267485;ENST00000438670	T	0.18338	2.22	5.78	-2.62	0.06152	.	1.333660	0.04700	N	0.415699	T	0.10252	0.0251	N	0.22421	0.69	0.09310	N	1	B;B;B;B	0.26400	0.039;0.148;0.039;0.039	B;B;B;B	0.24394	0.023;0.053;0.023;0.023	T	0.28038	-1.0056	10	0.32370	T	0.25	0.0768	4.1407	0.10191	0.2759:0.0:0.3626:0.3615	.	608;570;570;570	B4DMS4;Q86TY3-2;A8K990;Q86TY3	.;.;.;CN037_HUMAN	G	570;608	ENSP00000267485:E570G	ENSP00000267485:E570G	E	-	2	0	C14orf37	57668105	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	0.036000	0.13819	-0.865000	0.04073	-0.219000	0.12488	GAA	.	.	none		0.493	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872		C	58598352	T	C	58598352	3	2	10	1	0	0	0	0	1	0	0	0	1773	1783	62	3	635	3	C14orf37	14	58598352	Missense_Mutation	SNP	T	TCGA-FF-8041-01A-11D-2210-10	28551761	58598352	48751188	127	1209											
HSPA2	3306	hgsc.bcm.edu	37	chr14	65008064	65008064	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaggacgcaggcaccatcaCggggctcaatgtgctgcgca	10	5	13	13	3	2	0	2	0	0	0	2	1	2	1	1	4	2	5	1	4	2	0			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr14:65008064C>T	ENST00000394709.1	+	2	573	c.497C>T	c.(496-498)aCg>aTg	p.T166M	HSPA2_ENST00000554883.1_3'UTR|RP11-973N13.4_ENST00000554918.1_RNA|HSPA2_ENST00000247207.6_Missense_Mutation_p.T166M			P54652	HSP72_HUMAN	heat shock 70kDa protein 2	166					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)	p.T166M(1)		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)		GGCACCATCACGGGGCTCAAT	0.662																																					p.T166M	Pancreas(136;1211 1835 24894 31984 38227)	Atlas-SNP	.											HSPA2,NS,carcinoma,0,2	HSPA2	83	2	1	Substitution - Missense(1)	endometrium(1)	c.C497T						PASS	.						51	52	52					14																	65008064		2203	4300	6503	SO:0001583	missense	3306	exon1			CCATCACGGGGCT	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.497C>T	14.37:g.65008064C>T	ENSP00000378199:p.Thr166Met	87	0	0		81	39	0.481481	NM_021979	Q15508|Q53XM3|Q9UE78	Missense_Mutation	SNP	ENST00000394709.1	37	CCDS9766.1	.	.	.	.	.	.	.	.	.	.	C	19.15	3.772333	0.69992	.	.	ENSG00000126803	ENST00000394709;ENST00000247207	T;T	0.01015	5.44;5.44	5.18	5.18	0.71444	.	0.112431	0.38605	U	0.001623	T	0.01905	0.0060	N	0.08118	0	0.39563	D	0.969168	D	0.71674	0.998	P	0.62014	0.897	T	0.75505	-0.3294	10	0.87932	D	0	-7.4702	18.6851	0.91560	0.0:1.0:0.0:0.0	.	166	P54652	HSP72_HUMAN	M	166	ENSP00000378199:T166M;ENSP00000247207:T166M	ENSP00000247207:T166M	T	+	2	0	HSPA2	64077817	1.000000	0.71417	0.993000	0.49108	0.983000	0.72400	7.818000	0.86416	2.407000	0.81776	0.563000	0.77884	ACG	.	.	none		0.662	HSPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280651.1			T	65008064	C	T	65008064	3	4	10	1	0	0	0	0	1	0	0	0	7420	536	19	1	499	1	HSPA2	14	65008064	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	6409712	65008064	42341476	128	1210											
ALKBH1	8846	hgsc.bcm.edu	37	chr14	78174250	78174250	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtctgcggtcccgggccggCtctgacggtagaagcggaaa	7	6	17	11	5	2	2	0	1	2	1	3	3	3	3	2	6	2	2	2	6	3	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr14:78174250C>T	ENST00000216489.3	-	1	113	c.98G>A	c.(97-99)aGc>aAc	p.S33N	SLIRP_ENST00000557623.1_5'Flank|SLIRP_ENST00000557342.1_5'Flank|SLIRP_ENST00000557431.1_5'Flank|SLIRP_ENST00000238688.5_5'Flank	NM_006020.2	NP_006011.2	Q13686	ALKB1_HUMAN	alkB, alkylation repair homolog 1 (E. coli)	33					developmental growth (GO:0048589)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|in utero embryonic development (GO:0001701)|negative regulation of neuron apoptotic process (GO:0043524)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|oxidative demethylation (GO:0070989)|placenta development (GO:0001890)|RNA repair (GO:0042245)	mitochondrion (GO:0005739)|nuclear euchromatin (GO:0005719)	chemoattractant activity (GO:0042056)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)			endometrium(2)|lung(4)|ovary(1)|prostate(1)|skin(1)	9			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0291)		CCCGGGCCGGCTCTGACGGTA	0.657																																					p.S33N		Atlas-SNP	.											.	ALKBH1	30	.	0			c.G98A						PASS	.						37	41	39					14																	78174250		2201	4298	6499	SO:0001583	missense	8846	exon1			GGCCGGCTCTGAC	X91992	CCDS32127.1	14q24	2014-07-23	2006-02-09	2006-02-09	ENSG00000100601	ENSG00000100601		"Alkylation repair homologs"	17911	protein-coding gene	gene with protein product		605345	"alkB, alkylation repair homolog (E. coli)"	ALKBH		8600462	Standard	XM_005268165		Approved	hABH, alkB, ABH	uc001xuc.1	Q13686	OTTHUMG00000171542	ENST00000216489.3:c.98G>A	14.37:g.78174250C>T	ENSP00000216489:p.Ser33Asn	81	0	0		93	4	0.0430108	NM_006020	Q8TAU1|Q9ULA7	Missense_Mutation	SNP	ENST00000216489.3	37	CCDS32127.1	.	.	.	.	.	.	.	.	.	.	C	17.16	3.318509	0.60524	.	.	ENSG00000100601	ENST00000216489	T	0.29655	1.56	5.96	5.05	0.67936	.	0.328069	0.36972	N	0.002319	T	0.26484	0.0647	L	0.44542	1.39	0.28458	N	0.916036	B	0.28128	0.201	B	0.23419	0.046	T	0.10405	-1.0631	10	0.24483	T	0.36	-11.9065	14.3693	0.66828	0.1594:0.8406:0.0:0.0	.	33	Q13686	ALKB1_HUMAN	N	33	ENSP00000216489:S33N	ENSP00000216489:S33N	S	-	2	0	ALKBH1	77244003	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.926000	0.48892	1.456000	0.47831	0.655000	0.94253	AGC	.	.	none		0.657	ALKBH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414037.1	NM_006020		T	78174250	C	T	78174250	3	4	10	1	0	0	0	0	1	0	0	0	526	797	28	2	1095	2	ALKBH1	14	78174250	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	13166186	78174250	29175290	129	1211											
BUB1B	701	hgsc.bcm.edu	37	chr15	40453452	40453452	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgaagaaggaagggggtgctCtgaggtaggtacgggagaaa	13	6	19	3	1	1	4	0	2	1	2	1	6	1	5	0	6	2	3	0	6	6	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr15:40453452C>T	ENST00000287598.6	+	1	226	c.31C>T	c.(31-33)Ctg>Ttg	p.L11L	BUB1B_ENST00000412359.3_Silent_p.L11L|BUB1B_ENST00000560120.1_3'UTR	NM_001211.5	NP_001202	O60566	BUB1B_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase B	11					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)		AGGGGGTGCTCTGAGGTAGGT	0.637			"Mis, N, F, S"			rhabdomyosarcoma			Mosaic Variegated Aneuploidy Syndrome																												p.L11L		Atlas-SNP	.	yes	Rec		Mosaic variegated aneuploidy	15	15q15	701	BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)		M	.	BUB1B	71	.	0			c.C31T						PASS	.						66	54	58					15																	40453452		2202	4298	6500	SO:0001819	synonymous_variant	701	exon1	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	GGTGCTCTGAGGT	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.31C>T	15.37:g.40453452C>T		91	0	0		78	17	0.217949	NM_001211	B2R6U0|B4DL09|B4DLG3|O60501|O60627|O60758|O75389|Q59HH6|Q8WV50|Q96KM4	Silent	SNP	ENST00000287598.6	37	CCDS10053.1																																																																																			.	.	none		0.637	BUB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252122.4			T	40453452	C	T	40453452	2	4	10	1	0	0	0	0	0	0	0	1	1573	912	32	2		2	BUB1B	15	40453452	Silent	SNP	C	TCGA-FF-8041-01A-11D-2210-10		40453452	62077940	130	1212											
B2M	567	hgsc.bcm.edu	37	chr15	45003766	45003781	+	Frame_Shift_Del	DEL	GCTGTGCTCGCGCTAC	GCTGTGCTCGCGCTAC	-																															tgtctcgctccgtggccttaGctgtgctcgcgctactctct																								rs11553033|rs104894481|rs11553044|rs369474839|rs552741313		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	GCTGTGCTCGCGCTAC	GCTGTGCTCGCGCTAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr15:45003766_45003781delGCTGTGCTCGCGCTAC	ENST00000558401.1	+	1	92_107	c.22_37delGCTGTGCTCGCGCTAC	c.(22-39)gctgtgctcgcgctactcfs	p.AVLALL8fs	PATL2_ENST00000558573.1_5'Flank|B2M_ENST00000559916.1_Frame_Shift_Del_p.AVLALL8fs|B2M_ENST00000544417.1_Frame_Shift_Del_p.AVLALL8fs	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	8					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 exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|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 T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|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)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)	p.L15fs*41(4)|p.L13F(1)|p.A8T(1)|p.A11fs*42(1)|p.L12Q(1)		breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		CGTGGCCTTAGCTGTGCTCGCGCTACTCTCTCTTTC	0.616																																					p.7_12del		Pindel,Atlas-Indel	.											B2M,NS,lymphoid_neoplasm,+1,1	B2M	99	1	8	Deletion - Frameshift(5)|Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(4)|large_intestine(2)|kidney(1)|skin(1)	c.21_36del	GRCh37	CM060840	B2M	M	rs104894481	PASS	.																																			SO:0001589	frameshift_variant	567	exon1			.	AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"Immunoglobulin superfamily / C1-set domain containing"	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.22_37delGCTGTGCTCGCGCTAC	15.37:g.45003766_45003781delGCTGTGCTCGCGCTAC	ENSP00000452780:p.Ala8fs	93	0	.		68	25	0.368	NM_004048	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Frame_Shift_Del	DEL	ENST00000558401.1	37	CCDS10113.1																																																																																			.	.	none		0.616	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048		-	45003781	GCTGTGCTCGCGCTAC	-	45003766	7	5	10	1	0	1	0	1	0	0	0	0	1244	971	34	0	24	0	B2M	15	45003766	Frame_Shift_Del	DEL	GCTGTGCTCGCGCTAC	TCGA-FF-8041-01A-11D-2210-10	4550314	45003766	57527626	131	1213											
DUOX2	50506	hgsc.bcm.edu	37	chr15	45403769	45403769	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgctgccgtccagccagccCgtcacctggttggcctgcgg	3	7	14	17	4	1	0	1	0	0	0	2	0	2	0	6	3	4	2	6	3	0	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr15:45403769C>T	ENST00000603300.1	-	6	730	c.528G>A	c.(526-528)acG>acA	p.T176T	DUOXA2_ENST00000323030.5_5'Flank|DUOX2_ENST00000389039.6_Silent_p.T176T	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	176	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)		CCAGCCAGCCCGTCACCTGGT	0.781																																					p.T176T		Atlas-SNP	.											.	DUOX2	137	.	0			c.G528A						PASS	.						4	4	4					15																	45403769		1903	3798	5701	SO:0001819	synonymous_variant	50506	exon6			CCAGCCCGTCACC	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.528G>A	15.37:g.45403769C>T		6	0	0		7	6	0.857143	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Silent	SNP	ENST00000603300.1	37	CCDS10117.1																																																																																			.	.	none		0.781	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080		T	45403769	C	T	45403769	2	4	10	1	0	0	0	0	0	0	0	1	4803	639	23	1		1	DUOX2	15	45403769	Silent	SNP	C	TCGA-FF-8041-01A-11D-2210-10	400003	45403769	57127623	132	1214											
SEMA6D	80031	hgsc.bcm.edu	37	chr15	48063877	48063877	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	agtaatggcactcttcctagGacgggactaaagaggacgcc	12	7	12	10	2	1	1	0	0	1	1	2	4	2	4	2	4	0	2	2	4	4	4			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr15:48063877G>A	ENST00000316364.5	+	19	3556	c.3117G>A	c.(3115-3117)agG>agA	p.R1039R	SEMA6D_ENST00000389433.2_Silent_p.R1020R|SEMA6D_ENST00000389432.2_Silent_p.R996R|SEMA6D_ENST00000536845.2_Silent_p.R1039R|SEMA6D_ENST00000558014.1_Silent_p.R977R|SEMA6D_ENST00000355997.3_3'UTR|SEMA6D_ENST00000354744.4_Silent_p.R983R|SEMA6D_ENST00000358066.4_Silent_p.R977R|SEMA6D_ENST00000389428.3_Silent_p.R964R|SEMA6D_ENST00000558816.1_3'UTR|SEMA6D_ENST00000537942.1_Silent_p.R977R	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	1039					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)		CTCTTCCTAGGACGGGACTAA	0.512																																					p.R1039R		Atlas-SNP	.											.	SEMA6D	322	.	0			c.G3117A						PASS	.						167	165	165					15																	48063877		2198	4297	6495	SO:0001819	synonymous_variant	80031	exon19			TCCTAGGACGGGA	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.3117G>A	15.37:g.48063877G>A		146	0	0		146	8	0.0547945	NM_153618	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Silent	SNP	ENST00000316364.5	37	CCDS32225.1																																																																																			.	.	none		0.512	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		A	48063877	G	A	48063877	2	1	10	1	0	0	0	0	0	0	0	1	14057	1165	41	2		2	SEMA6D	15	48063877	Silent	SNP	G	TCGA-FF-8041-01A-11D-2210-10	2660108	48063877	54467515	133	1215											
PPIB	5479	hgsc.bcm.edu	37	chr15	64455114	64455114	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gaaggtcccggcagcagcagGaagaagacggaccccgcgat	12	2	15	12	4	0	2	0	0	0	2	1	6	1	4	3	4	2	3	3	4	3	0			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr15:64455114G>A	ENST00000300026.3	-	1	290	c.72C>T	c.(70-72)ttC>ttT	p.F24F	PPIB_ENST00000558492.1_5'UTR	NM_000942.4	NP_000933.1	P23284	PPIB_HUMAN	peptidylprolyl isomerase B (cyclophilin B)	24					bone development (GO:0060348)|chaperone-mediated protein folding (GO:0061077)|extracellular matrix organization (GO:0030198)|positive regulation of multicellular organism growth (GO:0040018)|protein peptidyl-prolyl isomerization (GO:0000413)|protein stabilization (GO:0050821)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|macromolecular complex (GO:0032991)|membrane (GO:0016020)|nucleus (GO:0005634)	peptide binding (GO:0042277)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|unfolded protein binding (GO:0051082)			kidney(2)|large_intestine(2)|lung(6)	10					L-Proline(DB00172)	GCAGCAGCAGGAAGAAGACGG	0.652																																					p.F24F	GBM(105;399 1481 32889 33051 36637)	Atlas-SNP	.											.	PPIB	20	.	0			c.C72T						PASS	.						24	28	27					15																	64455114		2203	4300	6503	SO:0001819	synonymous_variant	5479	exon1			CAGCAGGAAGAAG		CCDS10191.1	15q21-q22	2014-09-17			ENSG00000166794	ENSG00000166794	5.2.1.8		9255	protein-coding gene	gene with protein product		123841				2000394, 20089953	Standard	NM_000942		Approved	CYPB, OI9	uc002and.3	P23284	OTTHUMG00000133018	ENST00000300026.3:c.72C>T	15.37:g.64455114G>A		172	0	0		162	27	0.166667	NM_000942	A8K534|Q6IBH5|Q9BVK5	Silent	SNP	ENST00000300026.3	37	CCDS10191.1																																																																																			.	.	none		0.652	PPIB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256604.1			A	64455114	G	A	64455114	2	1	10	1	0	0	0	0	0	0	0	1	12331	1165	41	2		2	PPIB	15	64455114	Silent	SNP	G	TCGA-FF-8041-01A-11D-2210-10	16391237	64455114	38076278	134	1216											
DIS3L	115752	hgsc.bcm.edu	37	chr15	66621332	66621332	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aataaaacactggctgattcTctggataatgcgaacgaccc	14	9	8	10	2	1	1	0	1	1	0	2	4	1	2	1	2	3	1	1	2	5	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr15:66621332T>C	ENST00000319212.4	+	13	2276	c.2226T>C	c.(2224-2226)tcT>tcC	p.S742S	DIS3L_ENST00000319194.5_Silent_p.S659S|RP11-352G18.2_ENST00000565993.1_RNA	NM_001143688.1	NP_001137160.1	Q8TF46	DI3L1_HUMAN	DIS3 like exosome 3'-5' exoribonuclease	742					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						TGGCTGATTCTCTGGATAATG	0.493																																					p.S742S		Atlas-SNP	.											.	DIS3L	175	.	0			c.T2226C						PASS	.						131	135	134					15																	66621332		2201	4299	6500	SO:0001819	synonymous_variant	115752	exon13			TGATTCTCTGGAT		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.2226T>C	15.37:g.66621332T>C		91	0	0		94	4	0.0425532	NM_001143688	Q8N1N8|Q8WTU9|Q96CM7	Silent	SNP	ENST00000319212.4	37	CCDS45286.1																																																																																			.	.	none		0.493	DIS3L-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382792.2	NM_133375		C	66621332	T	C	66621332	2	2	10	1	0	0	0	0	0	0	0	1	4538	1538	54	3		3	DIS3L	15	66621332	Silent	SNP	T	TCGA-FF-8041-01A-11D-2210-10	2166218	66621332	35910060	135	1217											
SH3GL3	6457	hgsc.bcm.edu	37	chr15	84287010	84287010	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gattcttccccattaattacGtggaagtgatcgtgccttta	9	15	8	9	2	1	1	0	1	1	0	3	3	2	2	3	1	2	0	3	1	4	6	rs376114446		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr15:84287010G>A	ENST00000427482.2	+	9	1321	c.1015G>A	c.(1015-1017)Gtg>Atg	p.V339M	SH3GL3_ENST00000535412.1_3'UTR|SH3GL3_ENST00000324537.5_Missense_Mutation_p.V347M|SH3GL3_ENST00000434347.1_Missense_Mutation_p.V347M|SH3GL3_ENST00000564054.1_3'UTR|AC087738.1_ENST00000411248.1_RNA	NM_003027.3	NP_003018.3	Q99963	SH3G3_HUMAN	SH3-domain GRB2-like 3	339	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				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						CATTAATTACGTGGAAGTGAT	0.393																																					p.V339M		Atlas-SNP	.											SH3GL3_ENST00000427482,NS,carcinoma,0,2	SH3GL3	91	2	0			c.G1015A						PASS	.	G	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	106	94	98		1015	5.6	1	15		98	0,8600		0,0,4300	no	missense	SH3GL3	NM_003027.3	21	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	339/348	84287010	1,13005	2203	4300	6503	SO:0001583	missense	6457	exon9			AATTACGTGGAAG	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.1015G>A	15.37:g.84287010G>A	ENSP00000391372:p.Val339Met	79	0	0		80	14	0.175	NM_003027	O43553|O43554	Missense_Mutation	SNP	ENST00000427482.2	37	CCDS10325.2	.	.	.	.	.	.	.	.	.	.	G	28.8	4.950836	0.92660	2.27E-4	0.0	ENSG00000140600	ENST00000427482;ENST00000324537;ENST00000434347	T;T;T	0.55234	0.53;0.53;0.53	5.57	5.57	0.84162	Src homology-3 domain (4);	0.264468	0.37483	N	0.002070	D	0.82697	0.5093	H	0.96805	3.885	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.992	D	0.88419	0.3027	10	0.87932	D	0	-31.8197	18.5386	0.91019	0.0:0.0:1.0:0.0	.	339;347	Q99963;Q99963-3	SH3G3_HUMAN;.	M	339;347;347	ENSP00000391372:V339M;ENSP00000320092:V347M;ENSP00000397871:V347M	ENSP00000320092:V347M	V	+	1	0	SH3GL3	82078014	1.000000	0.71417	0.979000	0.43373	0.986000	0.74619	9.300000	0.96151	2.612000	0.88384	0.655000	0.94253	GTG	.	.	weak		0.393	SH3GL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347797.1	NM_003027		A	84287010	G	A	84287010	3	1	10	1	0	0	0	0	1	0	0	0	14267	1145	40	1	1049	1	SH3GL3	15	84287010	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	17665678	84287010	18244382	136	1218											
CHTF18	63922	hgsc.bcm.edu	37	chr16	840179	840179	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcctcccttccccacagggCtctctcctccacgtcccatg	4	10	6	21	1	1	0	0	0	1	0	8	0	7	0	7	1	0	1	7	1	0	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:840179C>T	ENST00000262315.9	+	5	672	c.609C>T	c.(607-609)ggC>ggT	p.G203G	CHTF18_ENST00000455171.2_Silent_p.G231G|RPUSD1_ENST00000561734.1_5'Flank|RPUSD1_ENST00000007264.2_5'Flank|RPUSD1_ENST00000565809.1_5'Flank|CHTF18_ENST00000317063.6_Silent_p.G400G|RPUSD1_ENST00000567114.1_5'Flank|CHTF18_ENST00000491530.1_3'UTR	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	203					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)				CCCCACAGGGCTCTCTCCTCC	0.657																																					p.G203G		Atlas-SNP	.											.	CHTF18	52	.	0			c.C609T						PASS	.						32	36	35					16																	840179		2048	4196	6244	SO:0001819	synonymous_variant	63922	exon5			ACAGGGCTCTCTC	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.609C>T	16.37:g.840179C>T		108	0	0		91	23	0.252747	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Silent	SNP	ENST00000262315.9	37	CCDS45371.1	.	.	.	.	.	.	.	.	.	.	C	6.013	0.370712	0.11409	.	.	ENSG00000127586	ENST00000426047	.	.	.	4.9	-2.96	0.05547	.	.	.	.	.	T	0.20210	0.0486	.	.	.	0.19945	N	0.999945	.	.	.	.	.	.	T	0.28522	-1.0041	4	.	.	.	-9.3545	3.1824	0.06589	0.3147:0.2606:0.0:0.4247	.	.	.	.	F	99	.	.	L	+	1	0	CHTF18	780180	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.736000	0.04882	-0.299000	0.08909	-0.455000	0.05494	CTC	.	.	none		0.657	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092		T	840179	C	T	840179	2	4	10	1	0	0	0	0	0	0	0	1	3416	784	28	2		2	CHTF18	16	840179	Silent	SNP	C	TCGA-FF-8041-01A-11D-2210-10		840179	89514574	137	1219											
ABCA3	21	hgsc.bcm.edu	37	chr16	2338028	2338028	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cccccgggatgccccttaccGagcacctcgcggggctcctg	4	6	12	19	4	0	0	0	0	0	0	2	2	1	1	7	3	3	2	7	3	1	1	rs76519389	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:2338028G>A	ENST00000301732.5	-	21	3703	c.3003C>T	c.(3001-3003)ctC>ctT	p.L1001L	ABCA3_ENST00000382381.3_Splice_Site_p.L943L	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	1001					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)	GCCCCTTACCGAGCACCTCGC	0.667													G|||	4	0.000798722	0.0023	0.0	5008	,	,		14175	0.0		0.0	False		,,,				2504	0.001				p.L1001L		Atlas-SNP	.											.	ABCA3	176	.	0			c.C3003T						PASS	.	G		2,4394		0,2,2196	22	23	23		3003	-1.2	1	16	dbSNP_131	23	0,8598		0,0,4299	yes	coding-synonymous-near-splice	ABCA3	NM_001089.2		0,2,6495	AA,AG,GG		0.0,0.0455,0.0154		1001/1705	2338028	2,12992	2198	4299	6497	SO:0001630	splice_region_variant	21	exon21			CTTACCGAGCACC	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.3004+1C>T	16.37:g.2338028G>A		27	0	0		20	8	0.4	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Silent	SNP	ENST00000301732.5	37	CCDS10466.1																																																																																			G|1.000;A|0.000	0.000	strong		0.667	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089	Silent	A	2338028	G	A	2338028	5	1	10	1	0	0	0	0	0	0	1	0	33	1072	37	1	2163	1	ABCA3	16	2338028	Splice_Site	SNP	G	TCGA-FF-8041-01A-11D-2210-10	1497849	2338028	88016725	138	1220											
ZNF434	54925	hgsc.bcm.edu	37	chr16	3434848	3434848	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctgtagatctggctgttcTgctgacaggtctggagtttt	5	15	12	9	0	3	2	0	1	3	1	3	3	3	3	1	3	1	5	1	3	1	4			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:3434848T>C	ENST00000396852.4	-	6	1152	c.845A>G	c.(844-846)cAg>cGg	p.Q282R	ZSCAN32_ENST00000439568.2_5'UTR|ZSCAN32_ENST00000422427.2_Missense_Mutation_p.Q70R|ZSCAN32_ENST00000304926.3_Missense_Mutation_p.Q70R|ZSCAN32_ENST00000574940.1_Missense_Mutation_p.Q282R|ZSCAN32_ENST00000396846.3_Missense_Mutation_p.Q282R|ZSCAN32_ENST00000573830.1_5'UTR	NM_001284527.1|NM_001284529.1	NP_001271456.1|NP_001271458.1	Q9NX65	ZSC32_HUMAN	zinc finger and SCAN domain containing 32	282	KRAB.				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)										CTGGCTGTTCTGCTGACAGGT	0.532																																					p.Q70R		Atlas-SNP	.											.	.	.	.	0			c.A209G						PASS	.						104	110	108					16																	3434848		2197	4300	6497	SO:0001583	missense	54925	exon5			CTGTTCTGCTGAC	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.845A>G	16.37:g.3434848T>C	ENSP00000380061:p.Gln282Arg	160	0	0		128	31	0.242188	NM_017810	B4DWL5|C9JB03|Q6WMU8|Q7Z6G2|Q8NFX8|Q9BU74	Missense_Mutation	SNP	ENST00000396852.4	37		.	.	.	.	.	.	.	.	.	.	T	0.032	-1.329858	0.01298	.	.	ENSG00000140987	ENST00000304926;ENST00000396852;ENST00000396846;ENST00000422427	T;T;T;T	0.36699	1.24;1.24;1.24;1.24	3.68	-0.497	0.12023	.	1.118750	0.07237	U	0.863657	T	0.09379	0.0231	N	0.00517	-1.405	0.09310	N	1	B;B;B	0.21606	0.002;0.058;0.058	B;B;B	0.22880	0.005;0.042;0.025	T	0.30119	-0.9989	10	0.02654	T	1	.	7.606	0.28103	0.0:0.1686:0.0:0.8314	.	70;70;282	B4DR24;Q9NX65;Q6WMU8	.;ZN434_HUMAN;.	R	70;282;282;70	ENSP00000302502:Q70R;ENSP00000380061:Q282R;ENSP00000380057:Q282R;ENSP00000407312:Q70R	ENSP00000302502:Q70R	Q	-	2	0	ZNF434	3374849	0.000000	0.05858	0.000000	0.03702	0.073000	0.16967	-0.014000	0.12656	-0.454000	0.07066	-0.912000	0.02778	CAG	.	.	none		0.532	ZSCAN32-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000251509.2	NM_017810		C	3434848	T	C	3434848	3	2	10	1	0	0	0	0	1	0	0	0	17923	1580	55	3	1256	3	ZNF434	16	3434848	Missense_Mutation	SNP	T	TCGA-FF-8041-01A-11D-2210-10	1096820	3434848	86919905	139	1221											
ZNF597	146434	hgsc.bcm.edu	37	chr16	3490834	3490834	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agccgcatcctccaaagactCttttgtaccatctttgctga	9	13	6	13	1	2	2	0	1	2	1	4	2	4	2	4	0	3	3	4	0	2	4			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:3490834C>T	ENST00000301744.4	-	3	368	c.133G>A	c.(133-135)Gag>Aag	p.E45K	NAA60_ENST00000424546.2_5'Flank|NAA60_ENST00000608722.1_5'Flank|NAA60_ENST00000573580.1_5'Flank|NAA60_ENST00000407558.4_5'Flank	NM_152457.1	NP_689670.1	Q96LX8	ZN597_HUMAN	zinc finger protein 597	45	KRAB.				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						TCCAAAGACTCTTTTGTACCA	0.463																																					p.E45K		Atlas-SNP	.											ZNF597,NS,carcinoma,0,1	ZNF597	41	1	0			c.G133A						scavenged	.						107	90	96					16																	3490834		2197	4300	6497	SO:0001583	missense	146434	exon3			AAGACTCTTTTGT	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.133G>A	16.37:g.3490834C>T	ENSP00000301744:p.Glu45Lys	65	0	0		70	3	0.0428571	NM_152457		Missense_Mutation	SNP	ENST00000301744.4	37	CCDS10505.1	.	.	.	.	.	.	.	.	.	.	C	5.452	0.268558	0.10349	.	.	ENSG00000167981	ENST00000301744	T	0.04234	3.67	4.07	3.12	0.35913	Krueppel-associated box (3);	0.418161	0.17752	N	0.163194	T	0.10337	0.0253	M	0.89095	3.005	0.09310	N	1	B	0.23937	0.094	B	0.24269	0.052	T	0.12426	-1.0548	10	0.87932	D	0	-5.0167	7.5987	0.28063	0.0:0.8832:0.0:0.1168	.	45	Q96LX8	ZN597_HUMAN	K	45	ENSP00000301744:E45K	ENSP00000301744:E45K	E	-	1	0	ZNF597	3430835	0.067000	0.21026	0.031000	0.17742	0.023000	0.10783	2.230000	0.42999	1.058000	0.40530	0.563000	0.77884	GAG	.	.	none		0.463	ZNF597-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251511.2	NM_152457		T	3490834	C	T	3490834	3	4	10	1	0	0	0	0	1	0	0	0	18042	922	32	2	1149	2	ZNF597	16	3490834	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	55986	3490834	86863919	140	1222											
CIITA	4261	hgsc.bcm.edu	37	chr16	11010310	11010310	+	Frame_Shift_Del	DEL	C	C	-																															ccagctgaagtccttggaaaCcctcaagtgagtgagctggg																										TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:11010310delC	ENST00000324288.8	+	15	3189	c.3056delC	c.(3055-3057)accfs	p.T1019fs	CIITA_ENST00000381835.5_Frame_Shift_Del_p.T435fs	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	1019					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						TCCTTGGAAACCCTCAAGTGA	0.522			T	"FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"	"PMBL, Hodgkin Lymphona, "																																p.T1019fs		Pindel,Atlas-Indel	.		Dom	yes		16	16p13	4261	"class II, major histocompatibility complex, transactivator"		L	.	CIITA	92	.	0			c.3055delA						PASS	.						47	38	41					16																	11010310		2197	4300	6497	SO:0001589	frameshift_variant	4261	exon15			.	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.3056delC	16.37:g.11010310delC	ENSP00000316328:p.Thr1019fs	76	0	.		46	11	0.239	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Frame_Shift_Del	DEL	ENST00000324288.8	37	CCDS10544.1																																																																																			.	.	none		0.522	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246		-	11010310	C	-	11010310	7	5	10	1	0	1	0	1	0	0	0	0	3430	507	18	0	3114	0	CIITA	16	11010310	Frame_Shift_Del	DEL	C	TCGA-FF-8041-01A-11D-2210-10	7519476	11010310	79344443	141	1223											
SOCS1	8651	hgsc.bcm.edu	37	chr16	11348808	11348808	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acgatgcgctggcggcacagCtcctgcagcggccgcacgcg	6	4	15	16	7	0	0	0	0	0	0	1	1	1	0	2	3	4	5	2	3	0	0			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:11348808C>T	ENST00000332029.2	-	2	678	c.528G>A	c.(526-528)gaG>gaA	p.E176E	RMI2_ENST00000572173.1_Intron	NM_003745.1	NP_003736.1	O15524	SOCS1_HUMAN	suppressor of cytokine signaling 1	176	Interaction with Elongin BC complex. {ECO:0000250}.|SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				cellular response to amino acid stimulus (GO:0071230)|cytokine-mediated signaling pathway (GO:0019221)|fat cell differentiation (GO:0045444)|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 insulin receptor signaling pathway (GO:0046627)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of protein phosphorylation (GO:0001932)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)	insulin-like growth factor receptor binding (GO:0005159)|kinase inhibitor activity (GO:0019210)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)	p.E176fs*35(3)|p.0?(1)|p.Y64fs*1(1)|p.V171_R179del(1)|p.E176E(1)|p.R127_*212del(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(66)|lung(3)	71						GGCGGCACAGCTCCTGCAGCG	0.731			"F, O"		"Hodgkin Lymphoma, PMBL"																																p.E176E	Colon(177;456 3548 27231)	Atlas-SNP	.		Rec	yes		16	16p13.13	8651	suppressor of cytokine signaling 1		L	SOCS1,lymph_node,lymphoid_neoplasm,0,1	SOCS1	84	1	8	Deletion - Frameshift(4)|Deletion - In frame(2)|Whole gene deletion(1)|Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(8)	c.G528A						PASS	.						7	7	7					16																	11348808		2131	4193	6324	SO:0001819	synonymous_variant	8651	exon2			GCACAGCTCCTGC	U88326	CCDS10546.1	16p13.13	2013-02-14			ENSG00000185338	ENSG00000185338		"Suppressors of cytokine signaling", "SH2 domain containing"	19383	protein-coding gene	gene with protein product		603597				7796808, 9266833	Standard	NM_003745		Approved	SOCS-1, SSI-1, JAB, TIP3, Cish1	uc002dar.1	O15524	OTTHUMG00000129792	ENST00000332029.2:c.528G>A	16.37:g.11348808C>T		18	0	0		11	6	0.545455	NM_003745	O15097|Q9NSA7	Silent	SNP	ENST00000332029.2	37	CCDS10546.1																																																																																			.	.	none		0.731	SOCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252018.1			T	11348808	C	T	11348808	2	4	10	1	0	0	0	0	0	0	0	1	14928	796	28	2		2	SOCS1	16	11348808	Silent	SNP	C	TCGA-FF-8041-01A-11D-2210-10	338498	11348808	79005945	142	1224											
SOCS1	8651	hgsc.bcm.edu	37	chr16	11349329	11349329	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggctgccacctggttgtgtgCtaccatcctacagaaggggc	7	9	13	12	0	0	1	0	0	0	1	1	1	1	1	4	4	4	3	4	4	3	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:11349329C>T	ENST00000332029.2	-	2	157	c.7G>A	c.(7-9)Gca>Aca	p.A3T	RMI2_ENST00000572173.1_Intron	NM_003745.1	NP_003736.1	O15524	SOCS1_HUMAN	suppressor of cytokine signaling 1	3					cellular response to amino acid stimulus (GO:0071230)|cytokine-mediated signaling pathway (GO:0019221)|fat cell differentiation (GO:0045444)|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 insulin receptor signaling pathway (GO:0046627)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of protein phosphorylation (GO:0001932)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)	insulin-like growth factor receptor binding (GO:0005159)|kinase inhibitor activity (GO:0019210)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)	p.0?(1)|p.A3T(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(66)|lung(3)	71						TGGTTGTGTGCTACCATCCTA	0.697			"F, O"		"Hodgkin Lymphoma, PMBL"																																p.A3T	Colon(177;456 3548 27231)	Atlas-SNP	.		Rec	yes		16	16p13.13	8651	suppressor of cytokine signaling 1		L	SOCS1,NS,lymphoid_neoplasm,0,2	SOCS1	84	2	2	Substitution - Missense(1)|Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(2)	c.G7A						scavenged	.						6	7	6					16																	11349329		1898	3954	5852	SO:0001583	missense	8651	exon2			TGTGTGCTACCAT	U88326	CCDS10546.1	16p13.13	2013-02-14			ENSG00000185338	ENSG00000185338		"Suppressors of cytokine signaling", "SH2 domain containing"	19383	protein-coding gene	gene with protein product		603597				7796808, 9266833	Standard	NM_003745		Approved	SOCS-1, SSI-1, JAB, TIP3, Cish1	uc002dar.1	O15524	OTTHUMG00000129792	ENST00000332029.2:c.7G>A	16.37:g.11349329C>T	ENSP00000329418:p.Ala3Thr	16	2	0.125		12	8	0.666667	NM_003745	O15097|Q9NSA7	Missense_Mutation	SNP	ENST00000332029.2	37	CCDS10546.1	.	.	.	.	.	.	.	.	.	.	C	19.78	3.891903	0.72524	.	.	ENSG00000185338	ENST00000332029	T	0.27104	1.69	3.27	3.27	0.37495	.	0.182614	0.47455	D	0.000237	T	0.15825	0.0381	N	0.08118	0	0.44871	D	0.997889	D	0.55385	0.971	P	0.44772	0.46	T	0.09530	-1.0670	10	0.46703	T	0.11	-4.6538	13.6611	0.62368	0.0:1.0:0.0:0.0	.	3	O15524	SOCS1_HUMAN	T	3	ENSP00000329418:A3T	ENSP00000329418:A3T	A	-	1	0	SOCS1	11256830	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.316000	0.65815	1.668000	0.50843	0.491000	0.48974	GCA	.	.	none		0.697	SOCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252018.1			T	11349329	C	T	11349329	3	4	10	1	0	0	0	0	1	0	0	0	14928	797	28	2	632	2	SOCS1	16	11349329	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	521	11349329	79005424	143	1225											
RSL1D1	26156	hgsc.bcm.edu	37	chr16	11944196	11944196	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaccattaaaaataaacttTcattctcattcaaaagcaac	18	11	1	11	0	3	0	3	0	1	0	4	0	3	0	2	0	3	1	2	0	8	5			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:11944196T>C	ENST00000571133.1	-	2	257	c.185A>G	c.(184-186)gAa>gGa	p.E62G	RP11-166B2.8_ENST00000574364.1_RNA|RSL1D1_ENST00000542106.1_Intron	NM_015659.2	NP_056474.2	O76021	RL1D1_HUMAN	ribosomal L1 domain containing 1	62					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						AAATAAACTTTCATTCTCATT	0.363																																					p.E62G		Atlas-SNP	.											.	RSL1D1	40	.	0			c.A185G						PASS	.						80	76	78					16																	11944196		2197	4300	6497	SO:0001583	missense	26156	exon2			AAACTTTCATTCT	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.185A>G	16.37:g.11944196T>C	ENSP00000460871:p.Glu62Gly	89	0	0		101	5	0.049505	NM_015659	B4DJ58|D3DUG7|Q2M1T7|Q6PL22|Q8IWS7|Q8WUZ1|Q9HDA9|Q9Y3Z9	Missense_Mutation	SNP	ENST00000571133.1	37	CCDS10551.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.947427	0.73672	.	.	ENSG00000171490	ENST00000355674;ENST00000396503	T	0.52295	0.67	5.91	5.91	0.95273	Ribosomal protein L1, superfamily (1);	0.240132	0.42420	D	0.000719	T	0.69033	0.3066	M	0.80616	2.505	0.80722	D	1	P;D	0.63880	0.947;0.993	P;D	0.64687	0.849;0.928	T	0.73509	-0.3960	10	0.72032	D	0.01	-13.9832	15.1713	0.72875	0.0:0.0:0.0:1.0	.	62;62	Q32Q62;O76021	.;RL1D1_HUMAN	G	62	ENSP00000347897:E62G	ENSP00000347897:E62G	E	-	2	0	RSL1D1	11851697	0.997000	0.39634	0.850000	0.33497	0.298000	0.27526	5.671000	0.68095	2.266000	0.75297	0.454000	0.30748	GAA	.	.	none		0.363	RSL1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252059.2	NM_015659		C	11944196	T	C	11944196	3	2	10	1	0	0	0	0	1	0	0	0	13715	1783	62	3	1319	3	RSL1D1	16	11944196	Missense_Mutation	SNP	T	TCGA-FF-8041-01A-11D-2210-10	594867	11944196	78410557	144	1226											
ABCC6	368	hgsc.bcm.edu	37	chr16	16244433	16244438	+	Splice_Site	DEL	ACCGGG	ACCGGG	-																															caggccggggcgggagccttAccgggcacagtccatcacgg																										TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	ACCGGG	ACCGGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:16244433_16244438delACCGGG	ENST00000205557.7	-	30	4429_4433	c.4400_4404delCCCGGT	c.(4399-4404)gcccgg>g	p.AR1467del		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1467	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)	CGGGAGCCTTACCGGGCACAGTCCAT	0.675																																					p.1467_1468del		Atlas-Indel	.											.	ABCC6	110	.	0			c.4401_4403del						PASS	.																																			SO:0001630	splice_region_variant	368	exon30			.	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.4403+1CCCGGT>-	16.37:g.16244433_16244438delACCGGG		192	0	0		155	12	0.0774194	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	In_Frame_Del	DEL	ENST00000205557.7	37	CCDS10568.1																																																																																			.	.	none		0.675	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		In_Frame_Del	-	16244438	ACCGGG	-	16244433	8	5	10	1	0	1	0	1	0	0	1	0	57	405	14	0	114	0	ABCC6	16	16244433	Splice_Site	DEL	ACCGGG	TCGA-FF-8041-01A-11D-2210-10	4300237	16244433	74110320	145	1227											
LCMT1	51451	hgsc.bcm.edu	37	chr16	25186263	25186263	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taattctttccacaggatagAatcacttgaattcctggatg	12	14	7	8	0	2	2	1	1	1	1	4	4	4	4	2	2	0	0	2	2	4	6			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:25186263A>G	ENST00000399069.3	+	10	1045	c.890A>G	c.(889-891)gAa>gGa	p.E297G	LCMT1_ENST00000572869.1_3'UTR|LCMT1_ENST00000380966.4_Missense_Mutation_p.E242G	NM_016309.2	NP_057393.2	Q9UIC8	LCMT1_HUMAN	leucine carboxyl methyltransferase 1	297					C-terminal protein methylation (GO:0006481)|cellular protein modification process (GO:0006464)|negative regulation of protein complex assembly (GO:0031333)|protein methylation (GO:0006479)|regulation of apoptotic process (GO:0042981)|regulation of glucose metabolic process (GO:0010906)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)	cytosol (GO:0005829)	protein C-terminal carboxyl O-methyltransferase activity (GO:0003880)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)								GBM - Glioblastoma multiforme(48;0.0336)	L-Leucine(DB00149)	CACAGGATAGAATCACTTGAA	0.428																																					p.E297G	Colon(200;565 2072 24396 47922 50898)	Atlas-SNP	.											.	LCMT1	22	.	0			c.A890G						PASS	.						57	55	56					16																	25186263		1850	4091	5941	SO:0001583	missense	51451	exon10			GGATAGAATCACT	AF037601	CCDS45445.1, CCDS45446.1	16p12.1	2014-08-01			ENSG00000205629	ENSG00000205629			17557	protein-coding gene	gene with protein product	"protein phosphatase methyltransferase 1"	610286				10810093	Standard	XM_005255354		Approved	CGI-68, PPMT1	uc002dnx.1	Q9UIC8	OTTHUMG00000177182	ENST00000399069.3:c.890A>G	16.37:g.25186263A>G	ENSP00000382021:p.Glu297Gly	90	0	0		85	18	0.211765	NM_016309	A6NL89|A8K770|Q53FC5|Q96CI5|Q9H6I9|Q9NTG4|Q9Y378	Missense_Mutation	SNP	ENST00000399069.3	37	CCDS45445.1	.	.	.	.	.	.	.	.	.	.	A	16.74	3.207519	0.58343	.	.	ENSG00000205629	ENST00000399069;ENST00000380966;ENST00000380962	T;T	0.24350	1.86;1.86	5.15	4.04	0.47022	.	0.000000	0.85682	D	0.000000	T	0.50803	0.1637	M	0.84156	2.68	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.99	T	0.53337	-0.8453	10	0.87932	D	0	-25.0191	9.3407	0.38079	0.8194:0.1806:0.0:0.0	.	242;297	Q9UIC8-3;Q9UIC8	.;LCMT1_HUMAN	G	297;242;314	ENSP00000382021:E297G;ENSP00000370353:E242G	ENSP00000370349:E314G	E	+	2	0	LCMT1	25093764	1.000000	0.71417	0.875000	0.34327	0.525000	0.34531	7.428000	0.80296	0.900000	0.36469	0.533000	0.62120	GAA	.	.	none		0.428	LCMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435747.4	NM_016309		G	25186263	A	G	25186263	3	3	10	1	0	0	0	0	1	0	0	0	8687	246	9	3	928	3	LCMT1	16	25186263	Missense_Mutation	SNP	A	TCGA-FF-8041-01A-11D-2210-10	8941830	25186263	65168490	146	1228											
IL4R	3566	hgsc.bcm.edu	37	chr16	27373599	27373599	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagaattgtcttaccaagcTcttgccctgttttctggagc	8	14	9	10	0	3	1	0	0	3	1	3	3	3	2	2	1	4	2	2	1	4	5			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:27373599T>C	ENST00000395762.2	+	11	1185	c.926T>C	c.(925-927)cTc>cCc	p.L309P	IL4R_ENST00000170630.2_Missense_Mutation_p.L309P|IL4R_ENST00000543915.2_Missense_Mutation_p.L309P|IL4R_ENST00000565915.1_3'UTR|IL4R_ENST00000380922.3_Missense_Mutation_p.L294P	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	309					defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|ovulation (GO:0030728)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|production of molecular mediator involved in inflammatory response (GO:0002532)|regulation of cell proliferation (GO:0042127)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	interleukin-4 receptor activity (GO:0004913)|receptor signaling protein activity (GO:0005057)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	33						CTTACCAAGCTCTTGCCCTGT	0.468																																					p.L309P		Atlas-SNP	.											.	IL4R	70	.	0			c.T926C						PASS	.						84	93	90					16																	27373599		2197	4300	6497	SO:0001583	missense	3566	exon11			CCAAGCTCTTGCC	X52425	CCDS10629.1, CCDS58441.1	16p12.1-p11.2	2008-05-14			ENSG00000077238	ENSG00000077238		"Interleukins and interleukin receptors", "CD molecules"	6015	protein-coding gene	gene with protein product		147781				1679753	Standard	NM_000418		Approved	CD124	uc010bxy.4	P24394	OTTHUMG00000097015	ENST00000395762.2:c.926T>C	16.37:g.27373599T>C	ENSP00000379111:p.Leu309Pro	128	0	0		129	21	0.162791	NM_000418	B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Missense_Mutation	SNP	ENST00000395762.2	37	CCDS10629.1	.	.	.	.	.	.	.	.	.	.	T	18.59	3.657837	0.67586	.	.	ENSG00000077238	ENST00000395762;ENST00000543915;ENST00000380922;ENST00000170630	T;T;T;T	0.16196	2.36;2.36;2.36;2.36	4.8	4.8	0.61643	.	0.430475	0.18627	N	0.135694	T	0.37019	0.0988	M	0.62723	1.935	0.48087	D	0.999589	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.78314	0.991;0.991;0.991	T	0.08289	-1.0729	10	0.62326	D	0.03	-23.6721	10.7721	0.46330	0.0:0.0:0.0:1.0	.	294;309;309	B4E076;B9EGC0;P24394	.;.;IL4RA_HUMAN	P	309;309;294;309	ENSP00000379111:L309P;ENSP00000441667:L309P;ENSP00000370309:L294P;ENSP00000170630:L309P	ENSP00000170630:L309P	L	+	2	0	IL4R	27281100	1.000000	0.71417	0.980000	0.43619	0.957000	0.61999	3.498000	0.53302	1.801000	0.52704	0.533000	0.62120	CTC	.	.	none		0.468	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4			C	27373599	T	C	27373599	3	2	10	1	0	0	0	0	1	0	0	0	7707	1551	54	3	978	3	IL4R	16	27373599	Missense_Mutation	SNP	T	TCGA-FF-8041-01A-11D-2210-10	2187336	27373599	62981154	147	1229											
ATXN2L	11273	hgsc.bcm.edu	37	chr16	28845868	28845884	+	Frame_Shift_Del	DEL	TCAGCCCCGCCGATGAT	TCAGCCCCGCCGATGAT	-																															cggaccaacaccagccagccTcagccccgccgatgatgcag																								rs147688158|rs367754572		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	TCAGCCCCGCCGATGAT	TCAGCCCCGCCGATGAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr16:28845868_28845884delTCAGCCCCGCCGATGAT	ENST00000336783.4	+	18	2454_2470	c.2287_2303delTCAGCCCCGCCGATGAT	c.(2287-2304)tcagccccgccgatgatgfs	p.SAPPMM763fs	RP11-24N18.1_ENST00000563565.1_RNA|ATXN2L_ENST00000395547.2_Frame_Shift_Del_p.SAPPMM763fs|ATXN2L_ENST00000564304.1_Frame_Shift_Del_p.SAPPMM769fs|ATXN2L_ENST00000340394.8_Frame_Shift_Del_p.SAPPMM763fs|ATXN2L_ENST00000570200.1_Frame_Shift_Del_p.SAPPMM763fs|ATXN2L_ENST00000325215.6_Frame_Shift_Del_p.SAPPMM763fs|ATXN2L_ENST00000382686.4_Frame_Shift_Del_p.SAPPMM763fs|ATXN2L_ENST00000565845.1_3'UTR	NM_007245.3	NP_009176.2	Q8WWM7	ATX2L_HUMAN	ataxin 2-like	763					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						CCAGCCAGCCTCAGCCCCGCCGATGATGCAGGCCGCC	0.668																																					p.762_768del		Atlas-Indel	.											.	ATXN2L	159	.	0			c.2286_2302del						PASS	.																																			SO:0001589	frameshift_variant	11273	exon18			.		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.2287_2303delTCAGCCCCGCCGATGAT	16.37:g.28845868_28845884delTCAGCCCCGCCGATGAT	ENSP00000338718:p.Ser763fs	34	0	0		24	11	0.458333	NM_148416	A8K1R6|B9EGM2|E9PAR9|O95135|Q63ZY4|Q6NVJ8|Q6PJW6|Q8IU61|Q8IU95|Q8WWM3|Q8WWM4|Q8WWM5|Q8WWM6|Q99703	Frame_Shift_Del	DEL	ENST00000336783.4	37	CCDS10641.1																																																																																			.	.	none		0.668	ATXN2L-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214139.1	NM_007245		-	28845884	TCAGCCCCGCCGATGAT	-	28845868	7	5	10	1	0	1	0	1	0	0	0	0	1212	1551	54	0	2357	0	ATXN2L	16	28845868	Frame_Shift_Del	DEL	TCAGCCCCGCCGATGAT	TCGA-FF-8041-01A-11D-2210-10	1472269	28845868	61508885	148	1230											
RNMTL1	51031	hgsc.bcm.edu	37	chr17	685705	685705	+	5'Flank	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gaccttgacgcgaggcgctgGgtccgggcgctgcggcggag	4	5	20	12	7	0	1	0	1	0	0	1	4	1	2	2	5	1	2	2	5	0	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:685705G>A	ENST00000301328.5	-	0	0				GLOD4_ENST00000536578.1_5'Flank|RNMTL1_ENST00000304478.4_Nonsense_Mutation_p.W29*|GLOD4_ENST00000301329.6_5'Flank			Q9HC38	GLOD4_HUMAN	glyoxalase domain containing 4							extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|prostate(1)	3				UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		CGAGGCGCTGGGTCCGGGCGC	0.667																																					p.W29X		Atlas-SNP	.											.	RNMTL1	25	.	0			c.G87A						PASS	.						31	35	34					17																	685705		2203	4299	6502	SO:0001631	upstream_gene_variant	55178	exon1			GCGCTGGGTCCGG	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			17.37:g.685705G>A	Exception_encountered	40	0	0		35	21	0.6	NM_018146	D3DTG9|D3DTH1|Q96B89|Q9H3J8|Q9HC37|Q9NVN1	Nonsense_Mutation	SNP	ENST00000301328.5	37		.	.	.	.	.	.	.	.	.	.	G	36	5.630251	0.96671	.	.	ENSG00000171861	ENST00000304478	.	.	.	5.5	4.51	0.55191	.	0.465011	0.25355	N	0.031276	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.268	0.43466	0.0:0.1477:0.6992:0.1531	.	.	.	.	X	29	.	.	W	+	3	0	RNMTL1	632455	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	1.774000	0.38573	1.410000	0.46936	0.563000	0.77884	TGG	.	.	none		0.667	GLOD4-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000437190.1	NM_016080		A	685705	G	A	685705	1	1	10	0	1	0	0	0	0	0	0	0	13522	1241	43	2		2	RNMTL1	17	685705	5'Flank	SNP	G	TCGA-FF-8041-01A-11D-2210-10		685705	80509505	149	1231											
DHRS7B	25979	hgsc.bcm.edu	37	chr17	21092024	21092024	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctccgtccacatgtgtagAtgcagcctccaagcacgcaa	10	8	8	15	2	1	1	0	0	1	1	4	1	3	1	4	0	3	4	4	0	3	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:21092024A>G	ENST00000395511.3	+	6	940	c.620A>G	c.(619-621)tAt>tGt	p.Y207C	DHRS7B_ENST00000581463.1_Splice_Site_p.Y27C|DHRS7B_ENST00000579303.1_Splice_Site_p.Y192C	NM_015510.4	NP_056325.2	Q6IAN0	DRS7B_HUMAN	dehydrogenase/reductase (SDR family) member 7B	207						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						ACATGTGTAGATGCAGCCTCC	0.547																																					p.Y207C		Atlas-SNP	.											.	DHRS7B	27	.	0			c.A620G						PASS	.						225	183	197					17																	21092024		2203	4300	6503	SO:0001630	splice_region_variant	25979	exon6			GTGTAGATGCAGC	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.620-1A>G	17.37:g.21092024A>G		85	0	0		94	41	0.43617	NM_015510	B5MEF4|Q6UX59|Q9BTF9|Q9UFM6|Q9Y3A1	Missense_Mutation	SNP	ENST00000395511.3	37	CCDS11215.1	.	.	.	.	.	.	.	.	.	.	A	9.784	1.176052	0.21704	.	.	ENSG00000109016	ENST00000395511;ENST00000346603	D	0.97352	-4.35	5.28	5.28	0.74379	Short-chain dehydrogenase/reductase, conserved site (1);NAD(P)-binding domain (1);	0.055538	0.85682	N	0.000000	D	0.98940	0.9640	H	0.97186	3.955	0.80722	D	1	D	0.76494	0.999	D	0.68943	0.961	D	0.99482	1.0948	9	.	.	.	.	15.2134	0.73244	1.0:0.0:0.0:0.0	.	207	Q6IAN0	DRS7B_HUMAN	C	207	ENSP00000378887:Y207C	.	Y	+	2	0	DHRS7B	21032616	1.000000	0.71417	0.897000	0.35233	0.109000	0.19521	9.179000	0.94861	2.001000	0.58596	0.383000	0.25322	TAT	.	.	none		0.547	DHRS7B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000444066.3	NM_015510	Missense_Mutation	G	21092024	A	G	21092024	5	3	10	1	0	0	0	0	0	0	1	0	4498	347	12	3	642	3	DHRS7B	17	21092024	Splice_Site	SNP	A	TCGA-FF-8041-01A-11D-2210-10	20406319	21092024	60103186	150	1232											
SARM1	23098	hgsc.bcm.edu	37	chr17	26708753	26708753	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cagcgcctcgtgccgttgctCgactctaaccgcttggaggc	5	9	12	15	5	1	0	0	0	1	0	3	2	1	1	3	2	4	3	3	2	1	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:26708753C>T	ENST00000457710.3	+	2	1371	c.900C>T	c.(898-900)ctC>ctT	p.L300L	CTB-96E2.3_ENST00000591482.1_RNA|SARM1_ENST00000379061.4_3'UTR	NM_015077.2	NP_055892.2	Q6SZW1	SARM1_HUMAN	sterile alpha and TIR motif containing 1	334					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)		TGCCGTTGCTCGACTCTAACC	0.677																																					p.L333L		Atlas-SNP	.											.	SARM1	40	.	0			c.C999T						PASS	.						11	13	12					17																	26708753		2134	4199	6333	SO:0001819	synonymous_variant	23098	exon3			GTTGCTCGACTCT	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.900C>T	17.37:g.26708753C>T		40	0	0		38	4	0.105263	NM_015077	O60277|Q7LGG3|Q9NXY5	Silent	SNP	ENST00000457710.3	37																																																																																				.	.	none		0.677	SARM1-001	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000255679.3	NM_015077		T	26708753	C	T	26708753	2	4	10	1	0	0	0	0	0	0	0	1	13857	871	31	1		1	SARM1	17	26708753	Silent	SNP	C	TCGA-FF-8041-01A-11D-2210-10	5616729	26708753	54486457	151	1233											
UNC45B	146862	hgsc.bcm.edu	37	chr17	33504529	33504529	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aacaggtgtatgaggtggtgCggccccttgtaagactcttg	8	11	14	8	1	1	2	0	1	1	1	1	2	1	2	2	4	2	2	2	4	3	4			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:33504529C>T	ENST00000268876.5	+	17	2258	c.2161C>T	c.(2161-2163)Cgg>Tgg	p.R721W	UNC45B_ENST00000433649.1_Missense_Mutation_p.R719W|UNC45B_ENST00000591048.1_Missense_Mutation_p.R640W|UNC45B_ENST00000394570.2_Missense_Mutation_p.R719W|UNC45B_ENST00000378449.1_Missense_Mutation_p.R640W	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	721					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)				TGAGGTGGTGCGGCCCCTTGT	0.542																																					p.R721W		Atlas-SNP	.											UNC45B,NS,carcinoma,-1,2	UNC45B	133	2	0			c.C2161T						PASS	.						44	30	35					17																	33504529		2201	4293	6494	SO:0001583	missense	146862	exon17			GTGGTGCGGCCCC	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.2161C>T	17.37:g.33504529C>T	ENSP00000268876:p.Arg721Trp	83	0	0		101	41	0.405941	NM_173167	Q495Q8|Q495Q9	Missense_Mutation	SNP	ENST00000268876.5	37	CCDS11292.1	.	.	.	.	.	.	.	.	.	.	C	17.90	3.502276	0.64298	.	.	ENSG00000141161	ENST00000394570;ENST00000268876;ENST00000433649;ENST00000378449	T;T;T	0.51325	3.54;1.52;0.71	5.3	3.21	0.36854	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.73877	0.3643	M	0.92923	3.36	0.51482	D	0.999929	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.998	T	0.79729	-0.1681	10	0.87932	D	0	-29.8644	12.8752	0.57986	0.4433:0.5567:0.0:0.0	.	640;719;721	Q8IWX7-2;Q8IWX7-3;Q8IWX7	.;.;UN45B_HUMAN	W	721;721;719;640	ENSP00000268876:R721W;ENSP00000412840:R719W;ENSP00000367710:R640W	ENSP00000268876:R721W	R	+	1	2	UNC45B	30528642	0.984000	0.35163	1.000000	0.80357	0.787000	0.44495	1.138000	0.31491	0.725000	0.32318	0.563000	0.77884	CGG	.	.	none		0.542	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2	NM_173167		T	33504529	C	T	33504529	3	4	10	1	0	0	0	0	1	0	0	0	17004	759	27	1	2223	1	UNC45B	17	33504529	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	6795776	33504529	47690681	152	1234											
PIGW	284098	hgsc.bcm.edu	37	chr17	34894125	34894125	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagtagtttattactgggtgAtataattttgagttttgcca	10	19	9	3	0	0	2	0	2	0	0	0	2	0	2	1	1	2	3	1	1	6	11			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:34894125A>G	ENST00000592983.1	+	2	1755	c.1175A>G	c.(1174-1176)gAt>gGt	p.D392G	PIGW_ENST00000328396.2_Missense_Mutation_p.D392G|MYO19_ENST00000590081.1_Intron			Q7Z7B1	PIGW_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class W	392					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)		TTACTGGGTGATATAATTTTG	0.338																																					p.D392G		Atlas-SNP	.											.	PIGW	50	.	0			c.A1175G						PASS	.						61	65	64					17																	34894125		2192	4296	6488	SO:0001583	missense	284098	exon2			TGGGTGATATAAT	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.1175A>G	17.37:g.34894125A>G	ENSP00000468778:p.Asp392Gly	51	0	0		57	25	0.438596	NM_178517	Q8N9G3	Missense_Mutation	SNP	ENST00000592983.1	37	CCDS11313.1	.	.	.	.	.	.	.	.	.	.	A	13.25	2.181962	0.38511	.	.	ENSG00000184886	ENST00000328396	.	.	.	5.79	4.72	0.59763	.	0.105198	0.64402	N	0.000006	T	0.41581	0.1165	N	0.16833	0.445	0.52501	D	0.999957	B	0.29162	0.235	B	0.34824	0.19	T	0.19877	-1.0292	8	.	.	.	-4.2695	10.3149	0.43732	0.922:0.0:0.078:0.0	.	392	Q7Z7B1	PIGW_HUMAN	G	392	.	.	D	+	2	0	PIGW	31968238	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.836000	0.75349	1.039000	0.40074	0.459000	0.35465	GAT	.	.	none		0.338	PIGW-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451318.1	NM_178517		G	34894125	A	G	34894125	3	3	10	1	0	0	0	0	1	0	0	0	11911	333	12	3	1177	3	PIGW	17	34894125	Missense_Mutation	SNP	A	TCGA-FF-8041-01A-11D-2210-10	1389596	34894125	46301085	153	1235											
IGFBP4	3487	hgsc.bcm.edu	37	chr17	38612729	38612729	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agctctggatgggcagcgtgGcaagtgctggtgtgtggacc	6	9	18	8	1	1	0	0	0	1	0	1	2	1	2	1	5	3	4	1	5	1	0			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:38612729G>A	ENST00000269593.4	+	4	946	c.671G>A	c.(670-672)gGc>gAc	p.G224D	IGFBP4_ENST00000542955.1_Missense_Mutation_p.G124D	NM_001552.2	NP_001543.2	P22692	IBP4_HUMAN	insulin-like growth factor binding protein 4	224	Thyroglobulin type-1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				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)			GGGCAGCGTGGCAAGTGCTGG	0.627																																					p.G224D	GBM(160;940 3581 26177)	Atlas-SNP	.											.	IGFBP4	17	.	0			c.G671A						PASS	.						54	57	56					17																	38612729		2203	4300	6503	SO:0001583	missense	3487	exon4			AGCGTGGCAAGTG	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.671G>A	17.37:g.38612729G>A	ENSP00000269593:p.Gly224Asp	162	0	0		193	24	0.124352	NM_001552	A0N9W2|B4E351|Q5U012|Q9UCL6	Missense_Mutation	SNP	ENST00000269593.4	37	CCDS11367.1	.	.	.	.	.	.	.	.	.	.	G	32	5.110443	0.94292	.	.	ENSG00000141753	ENST00000542955;ENST00000269593	T;T	0.70282	-0.47;-0.47	5.43	5.43	0.79202	Thyroglobulin type-1 (5);	0.000000	0.85682	D	0.000000	D	0.85017	0.5601	M	0.80332	2.49	0.58432	D	0.999992	D	0.89917	1.0	D	0.97110	1.0	D	0.86889	0.2047	10	0.87932	D	0	-2.4357	17.0572	0.86537	0.0:0.0:1.0:0.0	.	224	P22692	IBP4_HUMAN	D	124;224	ENSP00000437734:G124D;ENSP00000269593:G224D	ENSP00000269593:G224D	G	+	2	0	IGFBP4	35866255	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	8.449000	0.90337	2.546000	0.85860	0.655000	0.94253	GGC	.	.	none		0.627	IGFBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257134.1	NM_001552		A	38612729	G	A	38612729	3	1	10	1	0	0	0	0	1	0	0	0	7590	1203	42	2	685	2	IGFBP4	17	38612729	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	3718604	38612729	42582481	154	1236											
KRT12	3859	hgsc.bcm.edu	37	chr17	39021152	39021152	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagggtcagctcgtccagcAcccggcgcaggccattgatg	7	7	13	14	3	2	1	2	1	0	0	4	1	3	1	3	3	2	3	3	3	0	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:39021152A>T	ENST00000251643.4	-	3	736	c.713T>A	c.(712-714)gTg>gAg	p.V238E	RP5-1110E20.1_ENST00000579136.1_RNA	NM_000223.3	NP_000214.1	Q99456	K1C12_HUMAN	keratin 12	238	Coil 1B.|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)	CTCGTCCAGCACCCGGCGCAG	0.572																																					p.V238E		Atlas-SNP	.											.	KRT12	53	.	0			c.T713A						PASS	.						102	98	100					17																	39021152		2203	4300	6503	SO:0001583	missense	3859	exon3			TCCAGCACCCGGC		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.713T>A	17.37:g.39021152A>T	ENSP00000251643:p.Val238Glu	125	0	0		148	26	0.175676	NM_000223	B2R9E0	Missense_Mutation	SNP	ENST00000251643.4	37	CCDS11378.1	.	.	.	.	.	.	.	.	.	.	A	34	5.341017	0.95783	.	.	ENSG00000187242	ENST00000251643	D	0.88431	-2.38	5.96	5.96	0.96718	Filament (1);	0.000000	0.44688	D	0.000422	D	0.94961	0.8370	M	0.84585	2.705	0.58432	D	0.999999	D	0.89917	1.0	D	0.79784	0.993	D	0.95526	0.8599	10	0.87932	D	0	.	16.4484	0.83959	1.0:0.0:0.0:0.0	.	238	Q99456	K1C12_HUMAN	E	238	ENSP00000251643:V238E	ENSP00000251643:V238E	V	-	2	0	KRT12	36274678	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.193000	0.94954	2.285000	0.76669	0.533000	0.62120	GTG	.	.	none		0.572	KRT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257214.2	NM_000223		T	39021152	A	T	39021152	3	4	10	1	0	0	0	0	1	0	0	0	8458	159	6	5	795	5	KRT12	17	39021152	Missense_Mutation	SNP	A	TCGA-FF-8041-01A-11D-2210-10	408423	39021152	42174058	155	1237											
GRN	2896	hgsc.bcm.edu	37	chr17	42430050	42430050	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgtctgttgtgctgatcggCgccactgctgtcctgctggc	2	12	14	13	3	1	1	0	1	1	0	3	1	2	1	2	2	3	4	2	2	0	1	rs63750116		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:42430050C>T	ENST00000053867.3	+	13	1728	c.1666C>T	c.(1666-1668)Cgc>Tgc	p.R556C	GRN_ENST00000589265.1_Missense_Mutation_p.R399C	NM_002087.2	NP_002078.1	P28799	GRN_HUMAN	granulin	556					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)		TGCTGATCGGCGCCACTGCTG	0.682																																					p.R556C		Atlas-SNP	.											.	GRN	51	.	0			c.C1666T						PASS	.						62	65	64					17																	42430050		2203	4300	6503	SO:0001583	missense	2896	exon13			GATCGGCGCCACT	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.1666C>T	17.37:g.42430050C>T	ENSP00000053867:p.Arg556Cys	51	0	0		62	30	0.483871	NM_002087	D3DX55|P23781|P23782|P23783|P23784|Q53HQ8|Q53Y88|Q540U8|Q9BWE7|Q9H8S1|Q9UCH0	Missense_Mutation	SNP	ENST00000053867.3	37	CCDS11483.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.388125	0.82902	.	.	ENSG00000030582	ENST00000053867;ENST00000357351;ENST00000393566	T	0.72725	-0.68	5.53	4.52	0.55395	Granulin (3);	0.909924	0.09476	N	0.797014	T	0.82148	0.4974	M	0.78801	2.425	0.09310	N	0.999999	D	0.76494	0.999	D	0.67725	0.953	T	0.68765	-0.5322	10	0.39692	T	0.17	-19.1959	9.4761	0.38873	0.1587:0.6877:0.1536:0.0	rs63750116	556	P28799	GRN_HUMAN	C	556;401;376	ENSP00000053867:R556C	ENSP00000053867:R556C	R	+	1	0	GRN	39785576	0.000000	0.05858	0.021000	0.16686	0.641000	0.38312	0.559000	0.23485	2.599000	0.87857	0.561000	0.74099	CGC	.	.	weak		0.682	GRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457766.1	NM_002087		T	42430050	C	T	42430050	3	4	10	1	0	0	0	0	1	0	0	0	6813	768	27	1	1712	1	GRN	17	42430050	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	3408898	42430050	38765160	156	1238											
PRAC	84366	hgsc.bcm.edu	37	chr17	46799191	46799191	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcttcctgcctcggcctcccGaaattccagaattacaggct	8	11	7	15	2	1	1	0	0	1	1	5	2	4	1	5	2	2	1	5	2	3	3	rs554311327	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:46799191G>A	ENST00000290294.3	-	2	275	c.146C>T	c.(145-147)tCg>tTg	p.S49L	PRAC2_ENST00000422730.2_RNA|PRAC2_ENST00000432056.1_RNA|MIR3185_ENST00000583892.1_RNA	NM_032391.2	NP_115767.1	Q96KF2	PRAC1_HUMAN	prostate cancer susceptibility candidate 1	49						nucleus (GO:0005634)											tcggcctcccgaaattccaga	0.398													G|||	4	0.000798722	0.0	0.0043	5008	,	,		13775	0.0		0.001	False		,,,				2504	0.0				p.S49L		Atlas-SNP	.											.	PRAC	6	.	0			c.C146T						PASS	.						33	41	38					17																	46799191		1327	2309	3636	SO:0001583	missense	84366	exon2			CCTCCCGAAATTC	AF331165	CCDS11535.1	17q21	2013-08-29	2013-08-29	2013-08-29	ENSG00000159182	ENSG00000159182			30591	protein-coding gene	gene with protein product	"prostate, rectum and colon"	609819	"chromosome 17 open reading frame 92", "prostate cancer susceptibility candidate"	C17orf92, PRAC		11340635	Standard	NM_032391		Approved		uc002iny.3	Q96KF2	OTTHUMG00000159899	ENST00000290294.3:c.146C>T	17.37:g.46799191G>A	ENSP00000290294:p.Ser49Leu	171	0	0		181	60	0.331492	NM_032391		Missense_Mutation	SNP	ENST00000290294.3	37	CCDS11535.1	.	.	.	.	.	.	.	.	.	.	G	5.599	0.295270	0.10622	.	.	ENSG00000159182	ENST00000290294	T	0.58652	0.32	0.664	-1.33	0.09172	.	.	.	.	.	T	0.40815	0.1132	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33548	-0.9864	7	0.87932	D	0	.	.	.	.	.	49	Q96KF2	PRAC_HUMAN	L	49	ENSP00000290294:S49L	ENSP00000290294:S49L	S	-	2	0	PRAC	44154190	0.001000	0.12720	0.002000	0.10522	0.001000	0.01503	-0.678000	0.05209	-0.355000	0.08199	-0.752000	0.03492	TCG	.	.	none		0.398	PRAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358086.1	NM_032391		A	46799191	G	A	46799191	3	1	10	1	0	0	0	0	1	0	0	0	12433	1059	37	1	31	1	PRAC	17	46799191	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	4369141	46799191	34396019	157	1239											
CA10	56934	hgsc.bcm.edu	37	chr17	49713329	49713329	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaaactagaggtctctggatAtagttcctctatattaagcc	12	13	8	8	0	2	1	0	0	2	1	4	3	3	2	2	2	2	1	2	2	7	7			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr17:49713329A>G	ENST00000285273.4	-	8	1787	c.676T>C	c.(676-678)Tat>Cat	p.Y226H	CA10_ENST00000340813.6_Missense_Mutation_p.Y232H|CA10_ENST00000570565.1_Missense_Mutation_p.Y151H|CA10_ENST00000442502.2_Missense_Mutation_p.Y226H|CA10_ENST00000571918.1_5'UTR|CA10_ENST00000451037.2_Missense_Mutation_p.Y226H	NM_001082533.1	NP_001076002.1	Q9NS85	CAH10_HUMAN	carbonic anhydrase X	226					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)	GTCTCTGGATATAGTTCCTCT	0.388																																					p.Y226H		Atlas-SNP	.											.	CA10	84	.	0			c.T676C						PASS	.						114	109	110					17																	49713329		2203	4300	6503	SO:0001583	missense	56934	exon8			CTGGATATAGTTC	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.676T>C	17.37:g.49713329A>G	ENSP00000285273:p.Tyr226His	97	0	0		93	4	0.0430108	NM_001082534	B2R7J0|B4DGL6	Missense_Mutation	SNP	ENST00000285273.4	37	CCDS32684.1	.	.	.	.	.	.	.	.	.	.	A	29.6	5.021686	0.93462	.	.	ENSG00000154975	ENST00000442502;ENST00000285273;ENST00000451037;ENST00000340813	T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23	6.16	6.16	0.99307	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.000000	0.85682	D	0.000000	T	0.79569	0.4468	L	0.59436	1.845	0.58432	D	0.999999	D;D;D	0.89917	1.0;0.999;0.994	D;D;P	0.76071	0.987;0.987;0.873	T	0.81070	-0.1099	10	0.87932	D	0	.	15.9872	0.80168	1.0:0.0:0.0:0.0	.	226;232;151	Q9NS85;Q68D28;B4DGL6	CAH10_HUMAN;.;.	H	226;226;226;232	ENSP00000390666:Y226H;ENSP00000285273:Y226H;ENSP00000405388:Y226H;ENSP00000340363:Y232H	ENSP00000285273:Y226H	Y	-	1	0	CA10	47068328	1.000000	0.71417	0.985000	0.45067	0.985000	0.73830	9.157000	0.94714	2.367000	0.80283	0.528000	0.53228	TAT	.	.	none		0.388	CA10-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000437480.1	NM_020178		G	49713329	A	G	49713329	3	3	10	1	0	0	0	0	1	0	0	0	2513	449	16	3	322	3	CA10	17	49713329	Missense_Mutation	SNP	A	TCGA-FF-8041-01A-11D-2210-10	2914138	49713329	31481881	158	1240											
AFG3L2	10939	hgsc.bcm.edu	37	chr18	12356754	12356754	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atccactaacggtgatgaagGggacattggcttctccggct	9	10	12	10	2	1	2	0	2	1	0	3	3	2	3	2	5	1	2	2	5	2	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr18:12356754G>A	ENST00000269143.3	-	9	1334	c.1103C>T	c.(1102-1104)cCc>cTc	p.P368L		NM_006796.2	NP_006787.2	Q9Y4W6	AFG32_HUMAN	AFG3-like AAA ATPase 2	368					axonogenesis (GO:0007409)|cell death (GO:0008219)|cristae formation (GO:0042407)|mitochondrial fusion (GO:0008053)|mitochondrial protein processing (GO:0034982)|muscle fiber development (GO:0048747)|myelination (GO:0042552)|nerve development (GO:0021675)|neuromuscular junction development (GO:0007528)|regulation of multicellular organism growth (GO:0040014)|righting reflex (GO:0060013)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(12)|prostate(3)|skin(1)|stomach(3)|urinary_tract(1)	27					Adenosine triphosphate(DB00171)	GGTGATGAAGGGGACATTGGC	0.502																																					p.P368L		Atlas-SNP	.											.	AFG3L2	60	.	0			c.C1103T						PASS	.						166	124	138					18																	12356754		2203	4300	6503	SO:0001583	missense	10939	exon9			ATGAAGGGGACAT	Y18314	CCDS11859.1	18p11.21	2014-09-17	2013-10-17		ENSG00000141385	ENSG00000141385		"ATPases / AAA-type"	315	protein-coding gene	gene with protein product		604581	"AFG3 (ATPase family gene 3, yeast)-like 2", "spinocerebellar ataxia 28", "AFG3 ATPase family gene 3-like 2 (yeast)", "AFG3 ATPase family gene 3-like 2 (S. cerevisiae)", "AFG3 ATPase family member 3-like 2 (S. cerevisiae)"	SCA28		10395799, 18769991	Standard	NM_006796		Approved	SPAX5	uc002kqz.2	Q9Y4W6	OTTHUMG00000131695	ENST00000269143.3:c.1103C>T	18.37:g.12356754G>A	ENSP00000269143:p.Pro368Leu	92	0	0		97	4	0.0412371	NM_006796	Q6P1L0	Missense_Mutation	SNP	ENST00000269143.3	37	CCDS11859.1	.	.	.	.	.	.	.	.	.	.	G	33	5.231900	0.95207	.	.	ENSG00000141385	ENST00000269143;ENST00000537174	T	0.80824	-1.42	5.28	5.28	0.74379	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);Peptidase M41, FtsH (2);	0.000000	0.85682	D	0.000000	D	0.90191	0.6934	M	0.78344	2.41	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91042	0.4872	10	0.87932	D	0	-24.2564	19.282	0.94055	0.0:0.0:1.0:0.0	.	368	Q9Y4W6	AFG32_HUMAN	L	368;383	ENSP00000269143:P368L	ENSP00000269143:P368L	P	-	2	0	AFG3L2	12346754	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.813000	0.99286	2.631000	0.89168	0.563000	0.77884	CCC	.	.	none		0.502	AFG3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254603.2	NM_006796		A	12356754	G	A	12356754	3	1	10	1	0	0	0	0	1	0	0	0	360	1232	43	2	1326	2	AFG3L2	18	12356754	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10		12356754	65720494	159	1241											
MBD1	4152	hgsc.bcm.edu	37	chr18	47799097	47799097	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgggttccacccaggctgaaAatctccgtgatctagagaag	11	8	11	11	2	2	3	0	2	2	1	4	4	3	3	3	2	0	2	3	2	4	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr18:47799097A>G	ENST00000591416.1	-	15	2159	c.1728T>C	c.(1726-1728)atT>atC	p.I576I	MBD1_ENST00000590208.1_Silent_p.I576I|MBD1_ENST00000585672.1_Silent_p.I526I|MBD1_ENST00000588937.1_Silent_p.I507I|MBD1_ENST00000398495.2_Silent_p.I537I|MBD1_ENST00000436910.1_Silent_p.I507I|MBD1_ENST00000585595.1_Silent_p.I601I|MBD1_ENST00000347968.3_Silent_p.I520I|MBD1_ENST00000398488.1_Silent_p.I474I|MBD1_ENST00000587605.1_Silent_p.I474I|MBD1_ENST00000591535.1_Silent_p.I507I|MBD1_ENST00000424334.2_Silent_p.I627I|MBD1_ENST00000269471.5_Silent_p.I507I|MBD1_ENST00000457839.2_Silent_p.I601I|MBD1_ENST00000382948.5_Silent_p.I576I|MBD1_ENST00000353909.3_Silent_p.I527I|MBD1_ENST00000349085.2_Silent_p.I474I|MBD1_ENST00000269468.5_Silent_p.I576I|MBD1_ENST00000339998.6_Intron|MBD1_ENST00000398493.1_Silent_p.I520I			Q9UIS9	MBD1_HUMAN	methyl-CpG binding domain protein 1	576	TRD.				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						CCAGGCTGAAAATCTCCGTGA	0.577																																					p.I601I		Atlas-SNP	.											.	MBD1	228	.	0			c.T1803C						PASS	.						141	146	144					18																	47799097		2203	4300	6503	SO:0001819	synonymous_variant	4152	exon16			GCTGAAAATCTCC	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.1728T>C	18.37:g.47799097A>G		114	0	0		105	27	0.257143	NM_001204137	A4UTZ0|B4DXJ5|E9PEC5|K7ELI2|K7EQZ4|K7ESN0|O15248|O95241|Q7Z7B5|Q8N4W4|Q9UNZ6|Q9UNZ7|Q9UNZ8|Q9UNZ9	Silent	SNP	ENST00000591416.1	37	CCDS11943.1																																																																																			.	.	none		0.577	MBD1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255926.3	NM_015846		G	47799097	A	G	47799097	2	3	10	1	0	0	0	0	0	0	0	1	9351	10	1	3		3	MBD1	18	47799097	Silent	SNP	A	TCGA-FF-8041-01A-11D-2210-10	35442343	47799097	30278151	160	1242											
RAX	30062	hgsc.bcm.edu	37	chr18	56940307	56940307	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggtgccgaggatcccgtcGtccttggtaaaccccaggat	9	8	12	12	3	0	0	0	0	0	0	3	3	2	2	5	4	2	1	5	4	3	2	rs2271733	byFrequency	TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr18:56940307G>T	ENST00000334889.3	-	1	318	c.132C>A	c.(130-132)gaC>gaA	p.D44E	RAX_ENST00000256852.7_Missense_Mutation_p.D44E	NM_013435.2	NP_038463.2	Q9Y2V3	RX_HUMAN	retina and anterior neural fold homeobox	44			D -> E (in dbSNP:rs2271733). {ECO:0000269|PubMed:14662654}.		camera-type eye development (GO:0043010)|hypothalamus development (GO:0021854)|limb development (GO:0060173)|pattern specification process (GO:0007389)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|visual perception (GO:0007601)	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)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|prostate(1)	6		Lung NSC(161;0.0804)|Colorectal(73;0.0946)		STAD - Stomach adenocarcinoma(84;0.18)		GGATCCCGTCGTCCTTGGTAA	0.746													G|||	980	0.195687	0.1452	0.1571	5008	,	,		10556	0.128		0.3002	False		,,,				2504	0.2536				p.D44E	GBM(150;770 1898 17679 24325 37807)	Atlas-SNP	.											RAX,NS,carcinoma,0,1	RAX	19	1	0			c.C132A						scavenged	.	G	GLU/ASP	490,2640		39,412,1114	11	9	10		132	0.1	1	18	dbSNP_100	10	1484,4096		212,1060,1518	yes	missense	RAX	NM_013435.2	45	251,1472,2632	TT,TG,GG		26.595,15.655,22.6636	benign	44/347	56940307	1974,6736	1565	2790	4355	SO:0001583	missense	30062	exon1			CCCGTCGTCCTTG	AF115392	CCDS11972.1	18q21.31	2011-06-20			ENSG00000134438	ENSG00000134438		"Homeoboxes / PRD class"	18662	protein-coding gene	gene with protein product		601881				10625658, 10766016, 14662654	Standard	NM_013435		Approved	RX	uc002lhx.3	Q9Y2V3	OTTHUMG00000132757	ENST00000334889.3:c.132C>A	18.37:g.56940307G>T	ENSP00000334813:p.Asp44Glu	1	1	1		5	3	0.6	NM_013435	Q86V11	Missense_Mutation	SNP	ENST00000334889.3	37	CCDS11972.1	453	0.20741758241758243	75	0.1524390243902439	69	0.19060773480662985	76	0.13286713286713286	233	0.3073878627968338	G	12.43	1.936984	0.34189	0.15655	0.26595	ENSG00000134438	ENST00000256852;ENST00000334889;ENST00000555288	T;D;T	0.87966	0.09;-2.32;0.09	5.56	0.117	0.14652	.	0.213892	0.50627	N	0.000107	T	0.00012	0.0000	N	0.12182	0.205	0.42455	P	0.0072349999999999914	B;B	0.22800	0.075;0.004	B;B	0.23574	0.047;0.009	T	0.06481	-1.0824	9	0.06365	T	0.9	.	0.4639	0.00520	0.2353:0.2064:0.3162:0.2421	rs2271733;rs58469971;rs2271733	44;44	Q86V11;Q9Y2V3	.;RX_HUMAN	E	44	ENSP00000256852:D44E;ENSP00000334813:D44E;ENSP00000450583:D44E	ENSP00000256852:D44E	D	-	3	2	RAX	55091287	0.002000	0.14202	0.999000	0.59377	0.992000	0.81027	-0.819000	0.04462	0.271000	0.22005	0.561000	0.74099	GAC	G|0.801;T|0.199	0.199	strong		0.746	RAX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256128.2			T	56940307	G	T	56940307	3	4	10	1	0	0	0	0	1	0	0	0	13111	1136	40	4	920	4	RAX	18	56940307	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	9141210	56940307	21136941	161	1243											
ZNF846	162993	hgsc.bcm.edu	37	chr19	9873975	9873975	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tacctagtataatgagattcTtgtagttctccaacatcaca	13	14	5	9	0	3	1	1	1	2	1	4	2	3	1	2	0	2	3	2	0	6	8			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:9873975T>C	ENST00000397902.2	-	3	538	c.125A>G	c.(124-126)aAg>aGg	p.K42R	ZNF846_ENST00000588267.1_5'UTR|ZNF846_ENST00000586293.1_Missense_Mutation_p.K42R|ZNF846_ENST00000592859.1_Intron	NM_001077624.1	NP_001071092.1	Q147U1	ZN846_HUMAN	zinc finger protein 846	42	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)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22						AATGAGATTCTTGTAGTTCTC	0.413																																					p.K42R		Atlas-SNP	.											ZNF846,NS,carcinoma,0,1	ZNF846	61	1	0			c.A125G						PASS	.						109	114	113					19																	9873975		2202	4300	6502	SO:0001583	missense	162993	exon3			AGATTCTTGTAGT	AK097652	CCDS42496.1	19p13.2	2013-01-08			ENSG00000196605	ENSG00000196605		"Zinc fingers, C2H2-type", "-"	27260	protein-coding gene	gene with protein product							Standard	NM_001077624		Approved		uc002mmb.1	Q147U1		ENST00000397902.2:c.125A>G	19.37:g.9873975T>C	ENSP00000380999:p.Lys42Arg	54	0	0		95	4	0.0421053	NM_001077624	A8K0H1|B3KUP1	Missense_Mutation	SNP	ENST00000397902.2	37	CCDS42496.1	.	.	.	.	.	.	.	.	.	.	.	0.313	-0.966567	0.02232	.	.	ENSG00000196605	ENST00000397902	T	0.01516	4.81	2.17	-1.17	0.09648	Krueppel-associated box (4);	.	.	.	.	T	0.01156	0.0038	N	0.13168	0.305	0.09310	N	1	B	0.06786	0.001	B	0.12156	0.007	T	0.48547	-0.9026	8	.	.	.	.	5.7018	0.17887	0.0:0.5061:0.0:0.4938	.	42	Q147U1	ZN846_HUMAN	R	42	ENSP00000380999:K42R	.	K	-	2	0	ZNF846	9734975	0.001000	0.12720	0.313000	0.25210	0.740000	0.42216	0.078000	0.14761	-0.400000	0.07656	0.421000	0.28195	AAG	.	.	none		0.413	ZNF846-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450253.1	NM_001077624		C	9873975	T	C	9873975	3	2	10	1	0	0	0	0	1	0	0	0	18207	1609	56	3	1492	3	ZNF846	19	9873975	Missense_Mutation	SNP	T	TCGA-FF-8041-01A-11D-2210-10		9873975	49255008	162	1244											
RAVER1	112812	hgsc.bcm.edu	37	chr19	10428229	10428229	+	5'Flank	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttctgggctgggctcgggCgagggcagcaggtgggcaaa	6	6	19	10	2	1	0	0	0	1	0	2	1	1	0	1	6	1	5	1	6	1	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:10428229C>T	ENST00000393708.3	-	0	0				CTD-2369P2.10_ENST00000452032.2_5'Flank|RAVER1_ENST00000293677.6_Silent_p.S724S|FDX1L_ENST00000494368.1_5'Flank|FDX1L_ENST00000541276.1_5'Flank|CTD-2369P2.12_ENST00000586529.1_Silent_p.S125S|FDX1L_ENST00000492239.1_5'Flank	NM_001031734.2	NP_001026904.1	Q6P4F2	ADXL_HUMAN	ferredoxin 1-like						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)			TGGGCTCGGGCGAGGGCAGCA	0.701																																					p.S724S		Atlas-SNP	.											.	RAVER1	67	.	0			c.G2172A						PASS	.						31	33	33					19																	10428229		2002	4163	6165	SO:0001631	upstream_gene_variant	125950	exon13			CTCGGGCGAGGGC	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		19.37:g.10428229C>T	Exception_encountered	89	0	0		67	4	0.0597015	NM_133452	Q8N8B8	Silent	SNP	ENST00000393708.3	37	CCDS32905.1	.	.	.	.	.	.	.	.	.	.	C	6.949	0.544861	0.13312	.	.	ENSG00000161847	ENST00000331131	.	.	.	5.15	-10.3	0.00346	.	.	.	.	.	T	0.37183	0.0994	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13361	-1.0512	7	0.54805	T	0.06	-0.625	5.394	0.16259	0.0732:0.1836:0.2306:0.5125	.	581	Q8IY67	RAVR1_HUMAN	H	581	.	ENSP00000327543:R581H	R	-	2	0	RAVER1	10289229	0.000000	0.05858	0.057000	0.19452	0.729000	0.41735	-5.027000	0.00158	-2.789000	0.00357	-2.358000	0.00240	CGC	.	.	none		0.701	FDX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280567.2			T	10428229	C	T	10428229	1	4	10	0	1	0	0	0	0	0	0	0	13109	755	27	1		1	RAVER1	19	10428229	5'Flank	SNP	C	TCGA-FF-8041-01A-11D-2210-10	554254	10428229	48700754	163	1245											
MED26	9441	hgsc.bcm.edu	37	chr19	16687805	16687805	+	Missense_Mutation	SNP	C	C	A																															gggcaaaggagccctcatgcCgtgagttccgaggactgaaa																										TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:16687805C>A	ENST00000263390.3	-	3	1098	c.836G>T	c.(835-837)cGg>cTg	p.R279L	CTD-3222D19.2_ENST00000409035.1_Missense_Mutation_p.R287L|CTC-429P9.4_ENST00000593962.1_5'Flank	NM_004831.3	NP_004822.2	O95402	MED26_HUMAN	mediator complex subunit 26	279	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						GCCCTCATGCCGTGAGTTCCG	0.667																																					p.R279L		Atlas-SNP	.											MED26,colon,carcinoma,0,1	MED26	25	1	0			c.G836T						PASS	.						30	32	32					19																	16687805		2203	4299	6502	SO:0001583	missense	9441	exon3			TCATGCCGTGAGT	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.836G>T	19.37:g.16687805C>A	ENSP00000263390:p.Arg279Leu	129	0	0		102	17	0.166667	NM_004831	A1A4S3|Q0VGB6	Missense_Mutation	SNP	ENST00000263390.3	37	CCDS12347.1	.	.	.	.	.	.	.	.	.	.	C	13.81	2.349489	0.41599	.	.	ENSG00000105085	ENST00000263390	.	.	.	4.74	3.69	0.42338	.	0.198170	0.41294	D	0.000907	T	0.61652	0.2364	L	0.57536	1.79	0.30471	N	0.773314	D	0.76494	0.999	D	0.79784	0.993	T	0.61797	-0.6989	9	0.28530	T	0.3	-30.7651	13.3549	0.60623	0.1589:0.8411:0.0:0.0	.	279	O95402	MED26_HUMAN	L	279	.	ENSP00000263390:R279L	R	-	2	0	MED26	16548805	1.000000	0.71417	0.997000	0.53966	0.076000	0.17211	4.328000	0.59253	0.977000	0.38444	-0.324000	0.08512	CGG	.	.	none		0.667	MED26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461178.1	NM_004831		A	16687805	C	A	16687805	3	1	10	1	0	0	0	0	1	0	0	0	9453	652	23	4	970	4	MED26	19	16687805	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	6259576	16687805	42441178	164	1246	17	2									
MED26	9441	hgsc.bcm.edu	37	chr19	16687806	16687806	+	Missense_Mutation	SNP	G	G	A																															ggcaaaggagccctcatgccGtgagttccgaggactgaaag																								rs201182566		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:16687806G>A	ENST00000263390.3	-	3	1097	c.835C>T	c.(835-837)Cgg>Tgg	p.R279W	CTD-3222D19.2_ENST00000409035.1_Missense_Mutation_p.R287W|CTC-429P9.4_ENST00000593962.1_5'Flank	NM_004831.3	NP_004822.2	O95402	MED26_HUMAN	mediator complex subunit 26	279	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						CCCTCATGCCGTGAGTTCCGA	0.662																																					p.R279W		Atlas-SNP	.											MED26,colon,carcinoma,+1,1	MED26	25	1	0			c.C835T						PASS	.						31	33	32					19																	16687806		2203	4300	6503	SO:0001583	missense	9441	exon3			CATGCCGTGAGTT	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.835C>T	19.37:g.16687806G>A	ENSP00000263390:p.Arg279Trp	131	0	0		103	18	0.174757	NM_004831	A1A4S3|Q0VGB6	Missense_Mutation	SNP	ENST00000263390.3	37	CCDS12347.1	.	.	.	.	.	.	.	.	.	.	G	14.24	2.475948	0.44044	.	.	ENSG00000105085	ENST00000263390	.	.	.	4.74	3.61	0.41365	.	0.198170	0.41294	D	0.000907	T	0.63331	0.2502	L	0.57536	1.79	0.29237	N	0.87285	D	0.89917	1.0	D	0.87578	0.998	T	0.60801	-0.7191	9	0.72032	D	0.01	-30.7651	13.7896	0.63131	0.0:0.0:0.803:0.197	.	279	O95402	MED26_HUMAN	W	279	.	ENSP00000263390:R279W	R	-	1	2	MED26	16548806	1.000000	0.71417	1.000000	0.80357	0.129000	0.20672	2.921000	0.48852	2.194000	0.70268	0.555000	0.69702	CGG	G|0.999;A|0.001	0.001	weak		0.662	MED26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461178.1	NM_004831		A	16687806	G	A	16687806	3	1	10	1	0	0	0	0	1	0	0	0	9453	1144	40	1	971	1	MED26	19	16687806	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	1	16687806	42441177	165	1247	17	2									
JAK3	3718	hgsc.bcm.edu	37	chr19	17948006	17948006	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acacttggctcatcaagctcGctgcttccaggaatgactgg	9	10	10	12	1	2	1	2	1	0	0	4	2	3	2	1	3	2	4	1	3	2	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:17948006G>A	ENST00000527670.1	-	12	1747	c.1718C>T	c.(1717-1719)gCg>gTg	p.A573V	JAK3_ENST00000458235.1_Missense_Mutation_p.A573V|JAK3_ENST00000526008.1_5'Flank|JAK3_ENST00000534444.1_Missense_Mutation_p.A573V			P52333	JAK3_HUMAN	Janus kinase 3	573	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)	p.A573V(5)		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)	CATCAAGCTCGCTGCTTCCAG	0.577		2	Mis		"acute megakaryocytic leukemia, ETP ALL"																																p.A573V		Atlas-SNP	.		Dom	yes		19	19p13.1	3718	Janus kinase 3		L	JAK3,NS,lymphoid_neoplasm,0,5	JAK3	341	5	5	Substitution - Missense(5)	haematopoietic_and_lymphoid_tissue(5)	c.C1718T						PASS	.						45	34	38					19																	17948006		2201	4291	6492	SO:0001583	missense	3718	exon13			AAGCTCGCTGCTT	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.1718C>T	19.37:g.17948006G>A	ENSP00000432511:p.Ala573Val	114	0	0		133	68	0.511278	NM_000215	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Missense_Mutation	SNP	ENST00000527670.1	37	CCDS12366.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.669605	0.88348	.	.	ENSG00000105639	ENST00000458235;ENST00000428406;ENST00000527670;ENST00000534444	T;T;T	0.60920	0.15;0.15;0.15	4.17	4.17	0.49024	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	0.000010	T	0.68467	0.3004	L	0.52206	1.635	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.65987	0.916;0.94	T	0.72312	-0.4331	10	0.87932	D	0	-22.3785	14.3465	0.66668	0.0:0.0:1.0:0.0	.	573;573	P52333-2;P52333	.;JAK3_HUMAN	V	573	ENSP00000391676:A573V;ENSP00000432511:A573V;ENSP00000436421:A573V	ENSP00000413248:A573V	A	-	2	0	JAK3	17809006	1.000000	0.71417	0.854000	0.33618	0.985000	0.73830	8.985000	0.93487	2.316000	0.78162	0.484000	0.47621	GCG	.	.	none		0.577	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215		A	17948006	G	A	17948006	3	1	10	1	0	0	0	0	1	0	0	0	7948	1087	38	1	1704	1	JAK3	19	17948006	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	1260200	17948006	41180977	166	1248											
ZNF101	94039	hgsc.bcm.edu	37	chr19	19790525	19790525	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atcccagtttatttcaaattCatgttagaactcacactgga	13	14	5	9	0	3	1	3	0	0	1	4	2	4	2	1	1	1	2	1	1	4	5			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:19790525C>T	ENST00000592502.1	+	4	837	c.727C>T	c.(727-729)Cat>Tat	p.H243Y	ZNF101_ENST00000444249.2_3'UTR|ZNF101_ENST00000415784.2_Missense_Mutation_p.H123Y			Q8IZC7	ZN101_HUMAN	zinc finger protein 101	243					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						ATTTCAAATTCATGTTAGAAC	0.358																																					p.H243Y		Atlas-SNP	.											.	ZNF101	43	.	0			c.C727T						PASS	.						31	32	32					19																	19790525		2203	4300	6503	SO:0001583	missense	94039	exon4			CAAATTCATGTTA	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.727C>T	19.37:g.19790525C>T	ENSP00000468049:p.His243Tyr	50	0	0		54	13	0.240741	NM_033204	C9JU83|Q0VDG9	Missense_Mutation	SNP	ENST00000592502.1	37	CCDS32971.1	.	.	.	.	.	.	.	.	.	.	C	19.96	3.923897	0.73213	.	.	ENSG00000181896	ENST00000318110;ENST00000415440;ENST00000415784	D;D	0.86769	-2.17;-2.17	0.235	0.235	0.15431	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.93569	0.7947	M	0.93763	3.455	0.30664	N	0.754114	D	0.89917	1.0	D	0.91635	0.999	D	0.87769	0.2604	8	.	.	.	.	6.2532	0.20859	0.0:0.9997:0.0:3.0E-4	.	243	Q8IZC7	ZN101_HUMAN	Y	243;243;123	ENSP00000319716:H243Y;ENSP00000400952:H123Y	.	H	+	1	0	ZNF101	19651525	0.996000	0.38824	0.884000	0.34674	0.883000	0.51084	5.267000	0.65530	0.308000	0.22923	0.313000	0.20887	CAT	.	.	none		0.358	ZNF101-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460559.1	NM_033204		T	19790525	C	T	19790525	3	4	10	1	0	0	0	0	1	0	0	0	17729	826	29	2	741	2	ZNF101	19	19790525	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	1842519	19790525	39338458	167	1249											
BLVRB	645	hgsc.bcm.edu	37	chr19	40964385	40964385	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaacatctcccactaccacGtgggccggccggggcccctc	7	5	11	18	3	1	1	0	0	1	1	3	1	1	1	6	4	2	0	6	4	2	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:40964385G>A	ENST00000263368.4	-	2	298	c.147C>T	c.(145-147)caC>caT	p.H49H	BLVRB_ENST00000595483.1_Silent_p.H49H	NM_000713.2	NP_000704.1	P30043	BLVRB_HUMAN	biliverdin reductase B (flavin reductase (NADPH))	49					heme catabolic process (GO:0042167)|porphyrin-containing compound metabolic process (GO:0006778)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	biliverdin reductase activity (GO:0004074)|riboflavin reductase (NADPH) activity (GO:0042602)			large_intestine(3)|lung(3)	6			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)		Riboflavin(DB00140)	CCACTACCACGTGGGCCGGCC	0.637																																					p.H49H		Atlas-SNP	.											.	BLVRB	12	.	0			c.C147T						PASS	.																																			SO:0001819	synonymous_variant	645	exon2			TACCACGTGGGCC	D26308	CCDS33029.1	19q13.1-q13.2	2011-09-14				ENSG00000090013	1.3.1.24, 1.5.1.30	"Short chain dehydrogenase/reductase superfamily / Atypical members"	1063	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 43U, member 1"	600941	"Flavin reductase"	FLR		7656592, 19027726	Standard	NM_000713		Approved	SDR43U1	uc002onw.2	P30043		ENST00000263368.4:c.147C>T	19.37:g.40964385G>A		84	0	0		92	51	0.554348	NM_000713	A6NKD8|B2R5C6|P32078|P53005|Q32LZ2	Silent	SNP	ENST00000263368.4	37	CCDS33029.1																																																																																			.	.	none		0.637	BLVRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462563.1			A	40964385	G	A	40964385	2	1	10	1	0	0	0	0	0	0	0	1	1452	1136	40	1		1	BLVRB	19	40964385	Silent	SNP	G	TCGA-FF-8041-01A-11D-2210-10	21173860	40964385	18164598	168	1250											
EML2	24139	hgsc.bcm.edu	37	chr19	46116911	46116911	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgttgatatcagtgccgtccGccccctcagaccagatccct	7	9	8	17	3	2	3	2	1	0	2	4	3	4	3	6	0	1	1	6	0	1	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:46116911G>A	ENST00000245925.3	-	18	1762	c.1712C>T	c.(1711-1713)gCg>gTg	p.A571V	EML2_ENST00000587152.1_Missense_Mutation_p.A772V|EML2_ENST00000589876.1_Missense_Mutation_p.A571V|EML2_ENST00000536630.1_Missense_Mutation_p.A718V	NM_012155.2	NP_036287.1	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like 2	571	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.A571V(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)		AGTGCCGTCCGCCCCCTCAGA	0.572																																					p.A772V		Atlas-SNP	.											EML2,caecum,carcinoma,0,1	EML2	64	1	1	Substitution - Missense(1)	large_intestine(1)	c.C2315T						PASS	.						113	94	100					19																	46116911		2203	4300	6503	SO:0001583	missense	24139	exon21			CCGTCCGCCCCCT	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.1712C>T	19.37:g.46116911G>A	ENSP00000245925:p.Ala571Val	107	0	0		113	18	0.159292	NM_001193268	B7Z3I2|B7Z3Q9|K7ERL7|Q59EN8|Q8N5A2|Q9UG50	Missense_Mutation	SNP	ENST00000245925.3	37	CCDS12670.1	.	.	.	.	.	.	.	.	.	.	G	10.25	1.299646	0.23650	.	.	ENSG00000125746	ENST00000536630;ENST00000245925;ENST00000448055	T;T	0.29397	1.57;2.74	4.75	2.65	0.31530	WD40/YVTN repeat-like-containing domain (1);Soluble quinoprotein glucose/sorbosone dehydrogenase (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.26231	0.0640	M	0.66439	2.03	0.52501	D	0.999954	B;B;B	0.34255	0.206;0.445;0.03	B;B;B	0.24155	0.051;0.03;0.022	T	0.15694	-1.0428	10	0.54805	T	0.06	-19.9707	8.8426	0.35151	0.1883:0.0:0.8117:0.0	.	737;718;571	B7Z3Q9;B7Z3I2;O95834	.;.;EMAL2_HUMAN	V	718;571;729	ENSP00000442365:A718V;ENSP00000245925:A571V	ENSP00000245925:A571V	A	-	2	0	EML2	50808751	0.860000	0.29831	0.756000	0.31282	0.028000	0.11728	4.029000	0.57253	1.385000	0.46445	0.563000	0.77884	GCG	.	.	none		0.572	EML2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459608.1	NM_012155		A	46116911	G	A	46116911	3	1	10	1	0	0	0	0	1	0	0	0	5099	1087	38	1	245	1	EML2	19	46116911	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	5152526	46116911	13012072	169	1251											
SYMPK	8189	hgsc.bcm.edu	37	chr19	46352062	46352062	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggatagccttcttcaccacGttcacattctcgtccctcaa	9	12	5	15	2	5	0	3	0	2	0	7	1	6	1	3	1	1	1	3	1	2	5			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:46352062G>A	ENST00000245934.7	-	6	616	c.372C>T	c.(370-372)aaC>aaT	p.N124N		NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	124	Interaction with HSF1.				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)		TCTTCACCACGTTCACATTCT	0.552																																					p.N124N		Atlas-SNP	.											.	SYMPK	104	.	0			c.C372T						PASS	.						190	147	161					19																	46352062		2203	4300	6503	SO:0001819	synonymous_variant	8189	exon6			CACCACGTTCACA	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.372C>T	19.37:g.46352062G>A		218	0	0		260	135	0.519231	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Silent	SNP	ENST00000245934.7	37	CCDS12676.2																																																																																			.	.	none		0.552	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819		A	46352062	G	A	46352062	2	1	10	1	0	0	0	0	0	0	0	1	15454	1136	40	1		1	SYMPK	19	46352062	Silent	SNP	G	TCGA-FF-8041-01A-11D-2210-10	235151	46352062	12776921	170	1252											
PLA2G4C	8605	hgsc.bcm.edu	37	chr19	48558246	48558246	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccacaaatccagctcagcctCttctacttggggaaagggga	11	8	10	12	0	3	0	1	0	2	0	4	2	4	2	3	4	3	1	3	4	3	3	rs370150895		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:48558246C>T	ENST00000599921.1	-	15	1675	c.1318G>A	c.(1318-1320)Gag>Aag	p.E440K	PLA2G4C_ENST00000413144.2_Missense_Mutation_p.E440K|PLA2G4C_ENST00000596510.1_5'UTR|PLA2G4C_ENST00000599111.1_Missense_Mutation_p.E450K|PLA2G4C_ENST00000354276.3_Missense_Mutation_p.E440K			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	440	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)		AGCTCAGCCTCTTCTACTTGG	0.537																																					p.E450K		Atlas-SNP	.											.	PLA2G4C	76	.	0			c.G1348A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU	2,4404	4.2+/-10.8	0,2,2201	93	94	94		1348,1318,1318	-0.4	0	19		94	0,8600		0,0,4300	no	missense,missense,missense	PLA2G4C	NM_001159322.1,NM_001159323.1,NM_003706.2	56,56,56	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign,benign,benign	450/552,440/528,440/542	48558246	2,13004	2203	4300	6503	SO:0001583	missense	8605	exon15			CAGCCTCTTCTAC	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.1318G>A	19.37:g.48558246C>T	ENSP00000469473:p.Glu440Lys	138	0	0		145	77	0.531034	NM_001159322	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Missense_Mutation	SNP	ENST00000599921.1	37	CCDS12710.1	.	.	.	.	.	.	.	.	.	.	C	2.940	-0.219120	0.06101	4.54E-4	0.0	ENSG00000105499	ENST00000354276;ENST00000413144	T;T	0.04317	3.65;3.65	3.19	-0.385	0.12470	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	0.170328	0.37809	U	0.001933	T	0.03783	0.0107	L	0.41236	1.265	0.09310	N	1	B;B	0.10296	0.003;0.002	B;B	0.08055	0.003;0.003	T	0.35400	-0.9790	10	0.41790	T	0.15	-12.1445	5.3436	0.15996	0.0:0.5724:0.0:0.4276	.	450;440	B4DI40;Q9UP65	.;PA24C_HUMAN	K	440	ENSP00000346228:E440K;ENSP00000400036:E440K	ENSP00000346228:E440K	E	-	1	0	PLA2G4C	53250058	0.011000	0.17503	0.002000	0.10522	0.020000	0.10135	0.887000	0.28254	0.033000	0.15463	-0.474000	0.04947	GAG	.	.	weak		0.537	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1			T	48558246	C	T	48558246	3	4	10	1	0	0	0	0	1	0	0	0	12012	922	32	2	323	2	PLA2G4C	19	48558246	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	2206184	48558246	10570737	171	1253											
ZNF816A	125893	hgsc.bcm.edu	37	chr19	53456125	53456125	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccacatccctgaaagtcaaGcgtccctaaaataaaaaaca	18	6	5	12	1	1	1	1	1	0	0	3	1	3	1	3	0	2	0	3	0	7	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr19:53456125G>C	ENST00000357666.4	-	4	369	c.69C>G	c.(67-69)cgC>cgG	p.R23R	ZNF816_ENST00000535506.1_Silent_p.R23R|ZNF321P_ENST00000391777.3_Silent_p.R23R|ZNF816_ENST00000434371.2_Silent_p.R23R|ZNF816_ENST00000444460.2_Silent_p.R23R|ZNF816_ENST00000270457.4_Silent_p.R23R|ZNF816_ENST00000438970.2_Silent_p.R23R|ZNF816_ENST00000391786.2_Intron	NM_001031665.2	NP_001026835.1	Q0VGE8	ZN816_HUMAN	zinc finger protein 816	23					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						TGAAAGTCAAGCGTCCCTAAA	0.408																																					p.R23R		Atlas-SNP	.											.	ZNF816	73	.	0			c.C69G						PASS	.						85	93	90					19																	53456125		2203	4300	6503	SO:0001819	synonymous_variant	125893	exon3			AGTCAAGCGTCCC	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.69C>G	19.37:g.53456125G>C		43	0	0		49	14	0.285714	NM_001202457	A8K7H5|Q3KR39|Q659B3	Silent	SNP	ENST00000357666.4	37	CCDS33096.1	.	.	.	.	.	.	.	.	.	.	g	1.272	-0.612855	0.03690	.	.	ENSG00000180257	ENST00000332302	T	0.42513	0.97	1.84	0.498	0.16908	.	.	.	.	.	T	0.42245	0.1194	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.39482	-0.9612	6	0.72032	D	0.01	.	8.3219	0.32134	0.0:0.3546:0.6454:0.0	.	.	.	.	V	59	ENSP00000333199:L59V	ENSP00000333199:L59V	L	-	1	0	ZNF816	58147937	0.000000	0.05858	0.011000	0.14972	0.541000	0.35023	-0.031000	0.12287	0.003000	0.14656	0.305000	0.20034	CTT	.	.	none		0.408	ZNF816-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396132.1	NM_001031665		C	53456125	G	C	53456125	2	2	10	1	0	0	0	0	0	0	0	1	18192	958	34	4		4	ZNF816A	19	53456125	Silent	SNP	G	TCGA-FF-8041-01A-11D-2210-10	4897879	53456125	5672858	172	1254											
ZNF845	91664	hgsc.bcm.edu	37	chr19	53855284	53855284	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaagctttcagtttcaaatcGaaccttgaaagacataggag	15	10	9	7	1	2	2	2	1	0	1	3	5	2	3	1	1	2	2	1	1	5	4			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	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	1	2	Substitution - coding silent(2)	prostate(1)|kidney(1)	c.G1356A						scavenged	.						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	19.37:g.53855284G>A		48	0	0		77	4	0.0519481	NM_138374		Silent	SNP	ENST00000595091.1	37	CCDS46170.1																																																																																			.	.	none		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	10	1	0	0	0	0	0	0	0	1	18206	1045	37	1		1	ZNF845	19	53855284	Silent	SNP	G	TCGA-FF-8041-01A-11D-2210-10	399159	53855284	5273699	173	1255											
PLCB4	5332	hgsc.bcm.edu	37	chr20	9374297	9374297	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agaaaaatactcataaaaaaCaagcggctgaaacctgaagt	21	6	7	7	1	1	3	1	2	0	1	1	3	1	3	1	1	4	1	1	1	9	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr20:9374297C>T	ENST00000378493.1	+	15	1401	c.1386C>T	c.(1384-1386)aaC>aaT	p.N462N	PLCB4_ENST00000278655.4_Silent_p.N462N|PLCB4_ENST00000334005.3_Silent_p.N462N|PLCB4_ENST00000414679.2_Silent_p.N462N|PLCB4_ENST00000378473.3_Silent_p.N462N|PLCB4_ENST00000492632.1_3'UTR|PLCB4_ENST00000378501.2_Silent_p.N462N			Q15147	PLCB4_HUMAN	phospholipase C, beta 4	462	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				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						TCATAAAAAACAAGCGGCTGA	0.393											OREG0025771	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N462N		Atlas-SNP	.											.	PLCB4	204	.	0			c.C1386T						PASS	.						60	62	61					20																	9374297		2203	4300	6503	SO:0001819	synonymous_variant	5332	exon16			AAAAAACAAGCGG		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.1386C>T	20.37:g.9374297C>T		32	0	0	656	58	10	0.172414	NM_182797	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	Silent	SNP	ENST00000378493.1	37	CCDS13105.1																																																																																			.	.	none		0.393	PLCB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077948.2			T	9374297	C	T	9374297	2	4	10	1	0	0	0	0	0	0	0	1	12039	477	17	2		2	PLCB4	20	9374297	Silent	SNP	C	TCGA-FF-8041-01A-11D-2210-10		9374297	53651223	174	1256											
KIF16B	55614	hgsc.bcm.edu	37	chr20	16360313	16360313	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgtacctccccacgccgcagGagctggatcatctcctgctt	6	10	9	16	2	2	0	1	0	1	0	4	2	3	2	5	2	3	4	5	2	1	2	rs374151470		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr20:16360313G>A	ENST00000354981.2	-	19	2491	c.2334C>T	c.(2332-2334)ctC>ctT	p.L778L	KIF16B_ENST00000378003.2_Silent_p.L4L|KIF16B_ENST00000355755.3_Silent_p.L778L|KIF16B_ENST00000408042.1_Silent_p.L778L	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	778	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						CACGCCGCAGGAGCTGGATCA	0.597																																					p.L778L		Atlas-SNP	.											.	KIF16B	305	.	0			c.C2334T						PASS	.						97	95	96					20																	16360313		2203	4300	6503	SO:0001819	synonymous_variant	55614	exon19			CCGCAGGAGCTGG	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.2334C>T	20.37:g.16360313G>A		147	0	0		202	73	0.361386	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	37	CCDS13122.1																																																																																			.	.	alt		0.597	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683		A	16360313	G	A	16360313	2	1	10	1	0	0	0	0	0	0	0	1	8287	1161	41	2		2	KIF16B	20	16360313	Silent	SNP	G	TCGA-FF-8041-01A-11D-2210-10	6986016	16360313	46665207	175	1257											
SERINC3	10955	hgsc.bcm.edu	37	chr20	43129937	43129937	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttggctattagtggaagtgcGgatgctggaaagtgatccca	10	11	14	6	1	0	1	0	1	0	0	1	4	1	4	1	4	2	2	1	4	4	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr20:43129937G>A	ENST00000342374.4	-	9	1217	c.1060C>T	c.(1060-1062)Cgc>Tgc	p.R354C	SERINC3_ENST00000255175.1_Missense_Mutation_p.R354C|SERINC3_ENST00000541235.1_Missense_Mutation_p.R299C	NM_006811.2	NP_006802.1	Q13530	SERC3_HUMAN	serine incorporator 3	354					phosphatidylserine metabolic process (GO:0006658)|positive regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902237)|sphingolipid metabolic process (GO:0006665)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-serine transmembrane transporter activity (GO:0015194)			endometrium(4)|large_intestine(2)|lung(8)|skin(3)|urinary_tract(1)	18		Myeloproliferative disorder(115;0.0122)	Colorectal(3;0.000291)|COAD - Colon adenocarcinoma(18;0.00189)			GTGGAAGTGCGGATGCTGGAA	0.493																																					p.R354C		Atlas-SNP	.											.	SERINC3	42	.	0			c.C1060T						PASS	.						95	78	84					20																	43129937		2203	4300	6503	SO:0001583	missense	10955	exon9			AAGTGCGGATGCT	U49188	CCDS13333.1	20q13.12	2008-05-14	2005-11-15	2005-11-15	ENSG00000132824	ENSG00000132824			11699	protein-coding gene	gene with protein product		607165	"tumor differentially expressed 1"	TDE1		10559794	Standard	NM_006811		Approved	DIFF33, TDE, SBBI99, TMS-1, AIGP1	uc002xme.3	Q13530	OTTHUMG00000033087	ENST00000342374.4:c.1060C>T	20.37:g.43129937G>A	ENSP00000340243:p.Arg354Cys	78	0	0		103	50	0.485437	NM_006811	B4DUE9|O43717|Q9BR33	Missense_Mutation	SNP	ENST00000342374.4	37	CCDS13333.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.618830	0.87460	.	.	ENSG00000132824	ENST00000411544;ENST00000255175;ENST00000342374;ENST00000538937;ENST00000541235	T;T;T;T	0.18174	2.23;2.23;2.23;2.23	5.4	4.45	0.53987	.	0.143233	0.64402	N	0.000004	T	0.50871	0.1641	M	0.92970	3.365	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.993;0.996	T	0.64330	-0.6433	10	0.72032	D	0.01	.	14.1243	0.65210	0.0719:0.0:0.9281:0.0	.	354;354	Q53GK8;Q13530	.;SERC3_HUMAN	C	93;354;354;321;299	ENSP00000414197:R93C;ENSP00000255175:R354C;ENSP00000340243:R354C;ENSP00000440966:R299C	ENSP00000255175:R354C	R	-	1	0	SERINC3	42563351	1.000000	0.71417	0.991000	0.47740	0.968000	0.65278	9.480000	0.97931	1.506000	0.48736	0.563000	0.77884	CGC	.	.	none		0.493	SERINC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080544.3	NM_006811		A	43129937	G	A	43129937	3	1	10	1	0	0	0	0	1	0	0	0	14096	1116	39	1	369	1	SERINC3	20	43129937	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	26769624	43129937	19895583	176	1258											
NCOA3	8202	hgsc.bcm.edu	37	chr20	46265035	46265035	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgatgaccggggtcattcCtccttgaccaactcccccct	6	11	7	17	1	2	3	1	3	1	0	5	3	5	3	7	2	1	0	7	2	1	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr20:46265035C>T	ENST00000371998.3	+	12	2096	c.1905C>T	c.(1903-1905)tcC>tcT	p.S635S	NCOA3_ENST00000372004.3_Silent_p.S635S|NCOA3_ENST00000341724.6_Silent_p.S645S|NCOA3_ENST00000371997.3_Silent_p.S645S			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	635	Ser-rich.				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						GGGGTCATTCCTCCTTGACCA	0.473																																					p.S645S		Atlas-SNP	.											.	NCOA3	156	.	0			c.C1935T						PASS	.						79	71	74					20																	46265035		2203	4300	6503	SO:0001819	synonymous_variant	8202	exon12			TCATTCCTCCTTG	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.1905C>T	20.37:g.46265035C>T		104	0	0		123	22	0.178862	NM_001174088	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Silent	SNP	ENST00000371998.3	37	CCDS13407.1																																																																																			.	.	none		0.473	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		T	46265035	C	T	46265035	2	4	10	1	0	0	0	0	0	0	0	1	10239	668	24	2		2	NCOA3	20	46265035	Silent	SNP	C	TCGA-FF-8041-01A-11D-2210-10	3135098	46265035	16760485	177	1259											
CDH4	1002	hgsc.bcm.edu	37	chr20	60427856	60427856	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tggcaacaaggtggagaaccCcatcgacctgtacatctacg	12	7	10	12	2	1	1	0	0	1	1	2	3	1	1	3	3	4	2	3	3	5	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr20:60427856C>T	ENST00000360469.5	+	6	867	c.779C>T	c.(778-780)cCc>cTc	p.P260L	CDH4_ENST00000543233.1_Missense_Mutation_p.P186L	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	260	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)	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)			GTGGAGAACCCCATCGACCTG	0.592																																					p.P260L		Atlas-SNP	.											.	CDH4	172	.	0			c.C779T						PASS	.						163	123	136					20																	60427856		2203	4300	6503	SO:0001583	missense	1002	exon6			AGAACCCCATCGA	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.779C>T	20.37:g.60427856C>T	ENSP00000353656:p.Pro260Leu	114	0	0		133	45	0.338346	NM_001794	B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Missense_Mutation	SNP	ENST00000360469.5	37	CCDS13488.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.927112	0.92389	.	.	ENSG00000179242	ENST00000360469;ENST00000536643;ENST00000543233	T;T	0.51817	0.69;0.69	4.76	4.76	0.60689	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.69771	0.3148	M	0.78801	2.425	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.72802	-0.4183	9	.	.	.	.	17.758	0.88455	0.0:1.0:0.0:0.0	.	260	P55283	CADH4_HUMAN	L	260;168;186	ENSP00000353656:P260L;ENSP00000443301:P186L	.	P	+	2	0	CDH4	59861251	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.549000	0.82163	2.202000	0.70862	0.561000	0.74099	CCC	.	.	none		0.592	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794		T	60427856	C	T	60427856	3	4	10	1	0	0	0	0	1	0	0	0	3114	623	22	2	801	2	CDH4	20	60427856	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	14162821	60427856	2597664	178	1260											
LAMA5	3911	hgsc.bcm.edu	37	chr20	60892438	60892438	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagctggcccagctgctgtgCgtgggcctcggcggcctcca	3	7	15	16	3	0	0	0	0	0	0	2	0	1	0	4	4	4	3	4	4	0	0	rs373181217		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr20:60892438C>T	ENST00000252999.3	-	55	7540	c.7474G>A	c.(7474-7476)Gca>Aca	p.A2492T		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2492	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)			AGCTGCTGTGCGTGGGCCTCG	0.701																																					p.A2492T		Atlas-SNP	.											.	LAMA5	268	.	0			c.G7474A						PASS	.		THR/ALA	1,4311		0,1,2155	13	16	15		7474	3.5	0.8	20		15	1,8509		0,1,4254	no	missense	LAMA5	NM_005560.3	58	0,2,6409	TT,TC,CC		0.0118,0.0232,0.0156	probably-damaging	2492/3696	60892438	2,12820	2156	4255	6411	SO:0001583	missense	3911	exon55			GCTGTGCGTGGGC	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.7474G>A	20.37:g.60892438C>T	ENSP00000252999:p.Ala2492Thr	39	0	0		25	9	0.36	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	c	25.3	4.629064	0.87560	2.32E-4	1.18E-4	ENSG00000130702	ENST00000252999	T	0.39592	1.07	3.54	3.54	0.40534	.	0.000000	0.85682	U	0.000000	T	0.64349	0.2590	M	0.77486	2.375	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.71227	-0.4655	10	0.72032	D	0.01	.	14.7386	0.69437	0.0:1.0:0.0:0.0	.	2492	O15230	LAMA5_HUMAN	T	2492	ENSP00000252999:A2492T	ENSP00000252999:A2492T	A	-	1	0	LAMA5	60325833	1.000000	0.71417	0.833000	0.33012	0.717000	0.41224	7.039000	0.76544	1.522000	0.49001	0.436000	0.28706	GCA	.	.	weak		0.701	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		T	60892438	C	T	60892438	3	4	10	1	0	0	0	0	1	0	0	0	8618	768	27	1	3717	1	LAMA5	20	60892438	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	464582	60892438	2133082	179	1261											
PIGP	51227	hgsc.bcm.edu	37	chr21	38437947	38437947	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtttacttcactaatagaaaTatctcttaaggctggaatgg	13	14	8	6	0	2	1	1	0	1	1	3	2	2	2	0	3	1	2	0	3	7	7			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr21:38437947T>A	ENST00000464265.1	-	4	635	c.412A>T	c.(412-414)Att>Ttt	p.I138F	PIGP_ENST00000399098.1_Missense_Mutation_p.I88F|PIGP_ENST00000329667.3_5'UTR|PIGP_ENST00000399103.1_Missense_Mutation_p.I114F|PIGP_ENST00000360525.4_Missense_Mutation_p.I114F|PIGP_ENST00000399102.1_Missense_Mutation_p.I114F	NM_153681.2	NP_710148.1	P57054	PIGP_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class P	138					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)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			kidney(1)|urinary_tract(1)	2		Myeloproliferative disorder(46;0.0412)				CTAATAGAAATATCTCTTAAG	0.358																																					p.I138F		Atlas-SNP	.											.	PIGP	9	.	0			c.A412T						PASS	.						143	139	140					21																	38437947		2203	4300	6503	SO:0001583	missense	51227	exon4			TAGAAATATCTCT	AB037162	CCDS13649.1, CCDS13650.1	21q22.2	2013-02-26	2006-06-28	2005-11-10	ENSG00000185808	ENSG00000185808	2.4.1.198	"Phosphatidylinositol glycan anchor biosynthesis"	3046	protein-coding gene	gene with protein product	"phosphatidylinositol-n-acetylglucosaminyltranferase subunit"	605938	"Down syndrome critical region gene 5", "phosphatidylinositol glycan, class P"	DSCR5		10814524, 15221505	Standard	NR_028352		Approved	DCRC, DSRC	uc002yvw.1	P57054	OTTHUMG00000086653	ENST00000464265.1:c.412A>T	21.37:g.38437947T>A	ENSP00000420037:p.Ile138Phe	143	0	0		191	45	0.235602	NM_153681	B2RB18|B2RE99|B5BU92|D3DSG7|J3KR75|Q53Y28|Q96KI1|Q9NZA6	Missense_Mutation	SNP	ENST00000464265.1	37	CCDS13649.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.000227	0.74818	.	.	ENSG00000185808	ENST00000464265;ENST00000360525;ENST00000399102;ENST00000399103;ENST00000399098	T;T;T;T;T	0.36340	1.26;1.26;1.26;1.26;1.26	5.52	3.01	0.34805	PIG-P (1);	0.107627	0.64402	D	0.000007	T	0.53578	0.1805	M	0.84683	2.71	0.39299	D	0.964862	P	0.49253	0.921	P	0.54210	0.745	T	0.59337	-0.7473	10	0.72032	D	0.01	-8.0575	10.1016	0.42509	0.0:0.1415:0.0:0.8585	.	138	P57054	PIGP_HUMAN	F	138;114;114;114;88	ENSP00000420037:I138F;ENSP00000353719:I114F;ENSP00000382053:I114F;ENSP00000382054:I114F;ENSP00000382049:I88F	ENSP00000353719:I114F	I	-	1	0	PIGP	37359817	0.997000	0.39634	0.999000	0.59377	0.996000	0.88848	1.091000	0.30915	0.323000	0.23307	0.533000	0.62120	ATT	.	.	none		0.358	PIGP-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000194769.2	NM_153681		A	38437947	T	A	38437947	3	1	10	1	0	0	0	0	1	0	0	0	11904	1406	49	5	68	5	PIGP	21	38437947	Missense_Mutation	SNP	T	TCGA-FF-8041-01A-11D-2210-10		38437947	9691948	180	1262											
MYO18B	84700	hgsc.bcm.edu	37	chr22	26164606	26164606	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggagggtcaaagcatagtGgggaaggggcttgggacccc	10	5	19	7	0	1	0	1	0	0	0	1	4	1	3	2	7	1	2	2	7	3	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:26164606G>A	ENST00000407587.2	+	4	892	c.723G>A	c.(721-723)gtG>gtA	p.V241V	MYO18B_ENST00000335473.7_Silent_p.V241V|MYO18B_ENST00000536101.1_Silent_p.V241V			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	241						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						AAAGCATAGTGGGGAAGGGGC	0.637																																					p.V241V		Atlas-SNP	.											.	MYO18B	322	.	0			c.G723A						PASS	.						27	33	31					22																	26164606		1893	4105	5998	SO:0001819	synonymous_variant	84700	exon4			CATAGTGGGGAAG	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.723G>A	22.37:g.26164606G>A		30	0	0		32	7	0.21875	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37																																																																																				.	.	none		0.637	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		A	26164606	G	A	26164606	2	1	10	1	0	0	0	0	0	0	0	1	10075	1335	47	2		2	MYO18B	22	26164606	Silent	SNP	G	TCGA-FF-8041-01A-11D-2210-10		26164606	25139960	181	1263											
EIF3D	8664	hgsc.bcm.edu	37	chr22	36907798	36907798	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtgcctaggatgacgtggCgtgaggagtctttcacgtgg	6	10	18	7	3	2	2	1	2	1	0	2	4	2	4	1	5	1	0	1	5	1	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:36907798C>T	ENST00000216190.8	-	14	1755	c.1385G>A	c.(1384-1386)cGc>cAc	p.R462H	EIF3D_ENST00000541106.1_Missense_Mutation_p.R413H|EIF3D_ENST00000478547.1_5'Flank|EIF3D_ENST00000405442.1_Missense_Mutation_p.R462H	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						GATGACGTGGCGTGAGGAGTC	0.532											OREG0026522	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R462H		Atlas-SNP	.											.	EIF3D	37	.	0			c.G1385A						PASS	.						98	72	81					22																	36907798		2203	4300	6503	SO:0001583	missense	8664	exon14			ACGTGGCGTGAGG	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.1385G>A	22.37:g.36907798C>T	ENSP00000216190:p.Arg462His	180	0	0	866	194	90	0.463918	NM_003753		Missense_Mutation	SNP	ENST00000216190.8	37	CCDS13930.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.166071	0.78339	.	.	ENSG00000100353	ENST00000216190;ENST00000397177;ENST00000541106;ENST00000405442;ENST00000426531;ENST00000458572	.	.	.	6.07	5.04	0.67666	.	0.044401	0.85682	D	0.000000	T	0.47673	0.1458	L	0.39326	1.205	0.80722	D	1	B;P	0.38565	0.162;0.637	B;B	0.31547	0.017;0.132	T	0.45323	-0.9269	9	0.34782	T	0.22	-13.3282	17.384	0.87411	0.0:0.8752:0.1248:0.0	.	413;462	B4DVY1;O15371	.;EIF3D_HUMAN	H	462;447;413;462;115;149	.	ENSP00000216190:R462H	R	-	2	0	EIF3D	35237744	1.000000	0.71417	0.986000	0.45419	0.995000	0.86356	7.129000	0.77225	1.554000	0.49487	0.655000	0.94253	CGC	.	.	none		0.532	EIF3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319026.1			T	36907798	C	T	36907798	3	4	10	1	0	0	0	0	1	0	0	0	5016	768	27	1	269	1	EIF3D	22	36907798	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	10743192	36907798	14396768	182	1264											
CARD10	29775	hgsc.bcm.edu	37	chr22	37912258	37912258	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcgagcttcccgcagccgtcGcacctctgtcatcaagaatt	8	9	9	15	4	3	1	2	0	1	1	5	2	4	1	3	0	2	3	3	0	2	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:37912258G>A	ENST00000403299.1	-	4	637	c.421C>T	c.(421-423)Cga>Tga	p.R141*	CARD10_ENST00000494166.1_5'Flank|CARD10_ENST00000251973.5_Nonsense_Mutation_p.R141*			Q9BWT7	CAR10_HUMAN	caspase recruitment domain family, member 10	141					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)					CGCAGCCGTCGCACCTCTGTC	0.647																																					p.R141X		Atlas-SNP	.											CARD10,NS,carcinoma,+1,1	CARD10	55	1	0			c.C421T						scavenged	.						14	15	14					22																	37912258		2191	4291	6482	SO:0001587	stop_gained	29775	exon3			GCCGTCGCACCTC	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.421C>T	22.37:g.37912258G>A	ENSP00000384570:p.Arg141*	36	0	0		33	2	0.0606061	NM_014550	Q14CQ8|Q5TFG6|Q8NC81|Q9UGR5|Q9UGR6|Q9Y3H0	Nonsense_Mutation	SNP	ENST00000403299.1	37	CCDS13948.1	.	.	.	.	.	.	.	.	.	.	G	37	6.491763	0.97612	.	.	ENSG00000100065	ENST00000403299;ENST00000251973	.	.	.	5.27	4.16	0.48862	.	0.143577	0.44483	D	0.000451	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	-28.1082	11.0124	0.47669	0.0:0.0:0.5985:0.4015	.	.	.	.	X	141	.	ENSP00000251973:R141X	R	-	1	2	CARD10	36242204	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.304000	0.59104	2.610000	0.88304	0.563000	0.77884	CGA	.	.	none		0.647	CARD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318997.1	NM_014550		A	37912258	G	A	37912258	4	1	10	1	0	0	0	0	0	1	0	0	2646	1095	38	1	2749	1	CARD10	22	37912258	Nonsense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	1004460	37912258	13392308	183	1265											
SH3BP1	23616	hgsc.bcm.edu	37	chr22	38035817	38035817	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gatgaagaggcagctgcaccGcatgcggcagctggcccaga	10	4	15	12	2	0	3	0	1	0	2	0	4	0	3	2	3	4	6	2	3	1	0			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:38035817G>A	ENST00000357436.4	+	1	336	c.23G>A	c.(22-24)cGc>cAc	p.R8H	SH3BP1_ENST00000336738.5_Missense_Mutation_p.R8H|Z83844.1_ENST00000456099.1_RNA|SH3BP1_ENST00000442465.2_Missense_Mutation_p.R8H|SH3BP1_ENST00000599616.1_5'Flank	NM_018957.3	NP_061830.3	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	8					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)					CAGCTGCACCGCATGCGGCAG	0.706																																					p.R8H		Atlas-SNP	.											.	SH3BP1	41	.	0			c.G23A						PASS	.						5	7	6					22																	38035817		1930	3890	5820	SO:0001583	missense	23616	exon1			TGCACCGCATGCG		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.23G>A	22.37:g.38035817G>A	ENSP00000350018:p.Arg8His	75	0	0		61	7	0.114754	NM_018957	Q5R3N0|Q6IBZ2|Q6ZVL9|Q96HQ5|Q9NSQ9	Missense_Mutation	SNP	ENST00000357436.4	37	CCDS13952.2	.	.	.	.	.	.	.	.	.	.	G	29.5	5.015241	0.93404	.	.	ENSG00000100092	ENST00000357436;ENST00000336738;ENST00000442465	T;T;T	0.80653	-1.4;-1.4;-1.4	3.95	3.95	0.45737	BAR (1);	0.000000	0.47455	D	0.000234	D	0.86493	0.5946	L	0.54323	1.7	0.47621	D	0.999478	D;D	0.89917	1.0;0.999	D;D	0.76575	0.988;0.959	D	0.88038	0.2779	10	0.87932	D	0	.	14.2854	0.66243	0.0:0.0:1.0:0.0	.	8;8	F5GZA8;Q9Y3L3	.;3BP1_HUMAN	H	8	ENSP00000350018:R8H;ENSP00000337213:R8H;ENSP00000395126:R8H	ENSP00000337213:R8H	R	+	2	0	SH3BP1	36365763	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.636000	0.61339	2.187000	0.69744	0.609000	0.83330	CGC	.	.	none		0.706	SH3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075884.4	NM_018957		A	38035817	G	A	38035817	3	1	10	1	0	0	0	0	1	0	0	0	14259	1087	38	1	25	1	SH3BP1	22	38035817	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	123559	38035817	13268749	184	1266											
PDGFB	5155	hgsc.bcm.edu	37	chr22	39627798	39627798	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcggtgcgcgtcttgcactcGgcgatcatggccggctcagc	4	9	14	14	6	3	0	2	0	1	0	5	1	3	0	1	4	3	2	1	4	0	1	rs147036196		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:39627798G>A	ENST00000331163.6	-	4	1072	c.285C>T	c.(283-285)gcC>gcT	p.A95A	PDGFB_ENST00000381551.4_Silent_p.A80A	NM_002608.2	NP_002599.1	P01127	PDGFB_HUMAN	platelet-derived growth factor beta polypeptide	95					actin cytoskeleton organization (GO:0030036)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|blood vessel morphogenesis (GO:0048514)|branching involved in salivary gland morphogenesis (GO:0060445)|cell chemotaxis (GO:0060326)|cell growth (GO:0016049)|cell projection assembly (GO:0030031)|cellular response to growth factor stimulus (GO:0071363)|cellular response to mycophenolic acid (GO:0071506)|DNA replication (GO:0006260)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|extracellular matrix organization (GO:0030198)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|metanephric glomerular endothelium development (GO:0072264)|metanephric glomerular mesangial cell development (GO:0072255)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|monocyte chemotaxis (GO:0002548)|negative regulation of cell migration (GO:0030336)|negative regulation of phosphatidylinositol biosynthetic process (GO:0010512)|negative regulation of platelet activation (GO:0010544)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|paracrine signaling (GO:0038001)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemotaxis (GO:0050921)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of DNA replication (GO:0045740)|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 fibroblast proliferation (GO:0048146)|positive regulation of glomerular filtration (GO:0003104)|positive regulation of glomerular mesangial cell proliferation (GO:0072126)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of metanephric mesenchymal cell migration (GO:2000591)|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 peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein tyrosine kinase activity (GO:0061098)|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)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|reactive oxygen species metabolic process (GO:0072593)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to wounding (GO:0009611)|substrate-dependent cell migration (GO:0006929)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)|platelet alpha granule lumen (GO:0031093)	chemoattractant activity (GO:0042056)|collagen binding (GO:0005518)|growth factor activity (GO:0008083)|identical protein binding (GO:0042802)|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)|superoxide-generating NADPH oxidase activator activity (GO:0016176)		COL1A1/PDGFB(429)	central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(2)	7	Melanoma(58;0.04)					TCTTGCACTCGGCGATCATGG	0.647			T	COL1A1	DFSP								G|||	1	0.000199681	0.0008	0.0	5008	,	,		14561	0.0		0.0	False		,,,				2504	0.0				p.A95A		Atlas-SNP	.		Dom	yes		22	22q12.3-q13.1	5155	platelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog)		M	.	PDGFB	91	.	0			c.C285T						PASS	.	G	,	5,4401	11.4+/-27.6	0,5,2198	46	39	41		285,240	-4	1	22	dbSNP_134	41	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PDGFB	NM_002608.2,NM_033016.2	,	0,5,6498	AA,AG,GG		0.0,0.1135,0.0384	,	95/242,80/227	39627798	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	5155	exon4			GCACTCGGCGATC		CCDS13987.1, CCDS33650.1	22q13.1	2012-10-02	2011-05-19		ENSG00000100311	ENSG00000100311			8800	protein-coding gene	gene with protein product	"oncogene SIS", "becaplermin"	190040	"platelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog)"	SIS		2991848, 1661670	Standard	NM_002608		Approved	SSV	uc003axf.3	P01127	OTTHUMG00000151029	ENST00000331163.6:c.285C>T	22.37:g.39627798G>A		79	0	0		61	31	0.508197	NM_002608	G3XAG8|P78431|Q15354|Q6FHE7|Q9UF23	Silent	SNP	ENST00000331163.6	37	CCDS13987.1																																																																																			G|1.000;A|0.000	0.000	weak		0.647	PDGFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321043.1	NM_002608		A	39627798	G	A	39627798	2	1	10	1	0	0	0	0	0	0	0	1	11667	1103	39	1		1	PDGFB	22	39627798	Silent	SNP	G	TCGA-FF-8041-01A-11D-2210-10	1591981	39627798	11676768	185	1267											
RPL3	6122	hgsc.bcm.edu	37	chr22	39714450	39714450	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cacgatgtgagtcatgccagCcttgtatcccaggaaggctg	9	9	12	11	1	1	1	1	1	0	0	2	3	2	2	3	2	2	2	3	2	2	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:39714450C>T	ENST00000216146.4	-	2	324	c.151G>A	c.(151-153)Gct>Act	p.A51T	SNORD43_ENST00000583861.1_RNA|RPL3_ENST00000465618.1_5'UTR|RPL3_ENST00000401609.1_5'UTR	NM_000967.3|NM_001033853.1	NP_000958.1|NP_001029025.1	P39023	RL3_HUMAN	ribosomal protein L3	51					cellular protein metabolic process (GO:0044267)|cellular response to interleukin-4 (GO:0071353)|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)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|kidney(4)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	Melanoma(58;0.04)				Homoharringtonine(DB04865)	GTCATGCCAGCCTTGTATCCC	0.577																																					p.A51T		Atlas-SNP	.											.	RPL3	29	.	0			c.G151A						PASS	.						77	72	74					22																	39714450		2203	4300	6503	SO:0001583	missense	6122	exon2			TGCCAGCCTTGTA	AB007166	CCDS13988.1	22q13	2011-04-06			ENSG00000100316	ENSG00000100316		"L ribosomal proteins"	10332	protein-coding gene	gene with protein product		604163				2891103, 9582194	Standard	NM_000967		Approved	L3	uc003axi.3	P39023	OTTHUMG00000151079	ENST00000216146.4:c.151G>A	22.37:g.39714450C>T	ENSP00000346001:p.Ala51Thr	70	0	0		90	21	0.233333	NM_001033853	B2RDV9|Q15548|Q5I0G0	Missense_Mutation	SNP	ENST00000216146.4	37	CCDS13988.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.552848|5.552848	0.96501|0.96501	.|.	.|.	ENSG00000100316|ENSG00000100316	ENST00000216146;ENST00000453303|ENST00000427905	T;T|.	0.25749|.	1.78;1.78|.	4.68|4.68	4.68|4.68	0.58851|0.58851	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);|.	0.051981|.	0.85682|.	D|.	0.000000|.	D|D	0.90280|0.90280	0.6960|0.6960	H|H	0.98111|0.98111	4.15|4.15	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	0.94293|0.94293	0.7530|0.7530	10|5	0.87932|.	D|.	0|.	.|.	17.6103|17.6103	0.88050|0.88050	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	51;51|.	P39023;B3KS36|.	RL3_HUMAN;.|.	T|D	51;78|82	ENSP00000346001:A51T;ENSP00000415198:A78T|.	ENSP00000346001:A51T|.	A|G	-|-	1|2	0|0	RPL3|RPL3	38044396|38044396	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	4.464000|4.464000	0.60134|0.60134	2.150000|2.150000	0.67090|0.67090	0.455000|0.455000	0.32223|0.32223	GCT|GGC	.	.	none		0.577	RPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321196.1	NM_000967		T	39714450	C	T	39714450	3	4	10	1	0	0	0	0	1	0	0	0	13594	739	26	2	1096	2	RPL3	22	39714450	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	86652	39714450	11590116	186	1268											
TNRC6B	23112	hgsc.bcm.edu	37	chr22	40661027	40661027	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tctggaaatctgaccctaagGctaaatctgttcaatcttcc	11	13	6	11	0	5	1	1	1	4	0	6	2	6	2	2	2	0	2	2	2	5	4			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:40661027G>T	ENST00000454349.2	+	5	1004	c.793G>T	c.(793-795)Gct>Tct	p.A265S	TNRC6B_ENST00000402203.1_Intron|TNRC6B_ENST00000301923.9_Intron|TNRC6B_ENST00000335727.9_Missense_Mutation_p.A265S	NM_001162501.1	NP_001155973.1	Q9UPQ9	TNR6B_HUMAN	trinucleotide repeat containing 6B	265	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						TGACCCTAAGGCTAAATCTGT	0.468																																					p.A265S		Atlas-SNP	.											.	TNRC6B	195	.	0			c.G793T						PASS	.						109	105	107					22																	40661027		1899	4123	6022	SO:0001583	missense	23112	exon5			CCTAAGGCTAAAT	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.793G>T	22.37:g.40661027G>T	ENSP00000401946:p.Ala265Ser	65	0	0		71	37	0.521127	NM_001162501	B0QY73|B0QY78|B4DGC0|Q5TH52|Q8TBX2	Missense_Mutation	SNP	ENST00000454349.2	37	CCDS54533.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.104|8.104	0.777317|0.777317	0.16120|0.16120	.|.	.|.	ENSG00000100354|ENSG00000100354	ENST00000454349;ENST00000400140;ENST00000335727|ENST00000446273	T;T|.	0.51574|.	0.7;0.7|.	4.93|4.93	3.77|3.77	0.43336|0.43336	.|.	0.324254|.	0.32769|.	N|.	0.005673|.	T|T	0.30008|0.30008	0.0751|0.0751	N|N	0.16903|0.16903	0.455|0.455	0.31485|0.31485	N|N	0.666686|0.666686	B;B;B|.	0.22683|.	0.044;0.005;0.073|.	B;B;B|.	0.21917|.	0.036;0.01;0.037|.	T|T	0.30822|0.30822	-0.9965|-0.9965	10|5	0.08179|.	T|.	0.78|.	-0.1419|-0.1419	10.9081|10.9081	0.47092|0.47092	0.1037:0.0:0.8963:0.0|0.1037:0.0:0.8963:0.0	.|.	265;265;265|.	Q9UPQ9;A8MYY3;Q9UPQ9-1|.	TNR6B_HUMAN;.;.|.	S|S	265|7	ENSP00000401946:A265S;ENSP00000338371:A265S|.	ENSP00000338371:A265S|.	A|R	+|+	1|3	0|2	TNRC6B|TNRC6B	38990973|38990973	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.482000|1.482000	0.35486|0.35486	0.801000|0.801000	0.34066|0.34066	0.650000|0.650000	0.86243|0.86243	GCT|AGG	.	.	none		0.468	TNRC6B-202	KNOWN	basic|CCDS	protein_coding	protein_coding				T	40661027	G	T	40661027	3	4	10	1	0	0	0	0	1	0	0	0	16356	1203	42	4	932	4	TNRC6B	22	40661027	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	946577	40661027	10643539	187	1269											
SLC25A17	10478	hgsc.bcm.edu	37	chr22	41188619	41188619	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctattaaaagtgtagaaatAgacaaaattggagcagcaga	19	8	10	4	0	0	3	0	0	0	3	0	4	0	4	0	1	2	4	0	1	8	5			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chr22:41188619A>C	ENST00000435456.2	-	4	377	c.244T>G	c.(244-246)Tat>Gat	p.Y82D	SLC25A17_ENST00000491545.1_5'UTR|SLC25A17_ENST00000544408.1_Missense_Mutation_p.Y45D|SLC25A17_ENST00000542412.1_Intron	NM_006358.2	NP_006349.1	O43808	PM34_HUMAN	solute carrier family 25 (mitochondrial carrier; peroxisomal membrane protein, 34kDa), member 17	82	Necessary for targeting to peroxisomes and interaction with PEX19.				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						gtgtagaaatagacaaaattg	0.433																																					p.Y82D		Atlas-SNP	.											.	SLC25A17	25	.	0			c.T244G						PASS	.						75	73	74					22																	41188619		2203	4300	6503	SO:0001583	missense	10478	exon4			AGAAATAGACAAA	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.244T>G	22.37:g.41188619A>C	ENSP00000390722:p.Tyr82Asp	150	0	0		161	38	0.236025	NM_006358	A8KA59|Q5TFL0|Q9UGW8|Q9UGY7	Missense_Mutation	SNP	ENST00000435456.2	37	CCDS14005.1	.	.	.	.	.	.	.	.	.	.	A	8.423	0.846912	0.17034	.	.	ENSG00000100372	ENST00000435456;ENST00000544408;ENST00000434185	T;T;T	0.80123	-1.34;-1.34;-1.34	1.83	1.83	0.25207	Mitochondrial carrier domain (2);	0.065605	0.64402	D	0.000006	D	0.89705	0.6792	M	0.93241	3.395	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.83275	0.995;0.996	D	0.88155	0.2853	10	0.72032	D	0.01	-27.4517	5.7627	0.18209	1.0:0.0:0.0:0.0	.	45;82	B4DU97;O43808	.;PM34_HUMAN	D	82;45;65	ENSP00000390722:Y82D;ENSP00000438355:Y45D;ENSP00000404200:Y65D	ENSP00000394539:Y82D	Y	-	1	0	SLC25A17	39518565	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.290000	0.43531	1.108000	0.41662	0.327000	0.21459	TAT	.	.	none		0.433	SLC25A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321487.1	NM_006358		C	41188619	A	C	41188619	3	2	10	1	0	0	0	0	1	0	0	0	14494	420	15	5	703	5	SLC25A17	22	41188619	Missense_Mutation	SNP	A	TCGA-FF-8041-01A-11D-2210-10	527592	41188619	10115947	188	1270											
P2RY8	286530	hgsc.bcm.edu	37	chrX	1584574	1584574	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attcccgggacgcaaagtaaTaaacaaacgggtccagacag	16	5	10	10	3	0	1	0	0	0	1	2	2	2	2	2	2	2	2	2	2	5	3			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:1584574T>A	ENST00000381297.4	-	2	1088	c.878A>T	c.(877-879)tAt>tTt	p.Y293F	P2RY8_ENST00000460672.1_5'Flank	NM_178129.4	NP_835230.1	Q86VZ1	P2RY8_HUMAN	purinergic receptor P2Y, G-protein coupled, 8	293						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(13)|prostate(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)				CGCAAAGTAATAAACAAACGG	0.592			T	CRLF2	"B-ALL, Downs associated ALL"																																p.Y293F		Atlas-SNP	.		Dom	yes		"X,Y"	Xp22.3; Yp11.3	286530	"purinergic receptor P2Y, G-protein coupled, 8"		L	.	P2RY8	53	.	0			c.A878T						PASS	.						110	110	110					X																	1584574		2203	4296	6499	SO:0001583	missense	286530	exon2			AAGTAATAAACAA	AA804531	CCDS14115.1	Xp22.33 and Yp11.3	2012-08-08			ENSG00000182162	ENSG00000182162		"Pseudoautosomal regions / PAR1", "Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	15524	protein-coding gene	gene with protein product		300525				11004484	Standard	NM_178129		Approved	P2Y8	uc004cpz.2	Q86VZ1	OTTHUMG00000021060	ENST00000381297.4:c.878A>T	X.37:g.1584574T>A	ENSP00000370697:p.Tyr293Phe	180	0	0		120	74	0.616667	NM_178129		Missense_Mutation	SNP	ENST00000381297.4	37	CCDS14115.1	.	.	.	.	.	.	.	.	.	.	t	14.85	2.658567	0.47467	.	.	ENSG00000182162	ENST00000381297	D	0.92911	-3.13	2.73	2.73	0.32206	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	U	0.000003	D	0.94288	0.8165	M	0.64260	1.97	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	D	0.87643	0.2523	10	0.87932	D	0	.	10.6579	0.45686	0.0:0.0:0.0:1.0	.	293	Q86VZ1	P2RY8_HUMAN	F	293	ENSP00000370697:Y293F	ENSP00000370697:Y293F	Y	-	2	0	P2RY8	1544574	1.000000	0.71417	0.971000	0.41717	0.141000	0.21300	6.181000	0.71988	0.823000	0.34589	0.230000	0.17803	TAT	.	.	none		0.592	P2RY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055602.1	NM_178129		A	1584574	T	A	1584574	3	1	10	1	0	0	0	0	1	0	0	0	11364	1406	49	5	205	5	P2RY8	23	1584574	Missense_Mutation	SNP	T	TCGA-FF-8041-01A-11D-2210-10		1584574	153685986	189	1271											
CTPS2	56474	hgsc.bcm.edu	37	chrX	16711587	16711587	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccacaaacggcattccttcGatgtctccaatggtgcctcc	8	11	7	15	2	1	0	0	0	1	0	6	1	4	0	5	2	2	1	5	2	2	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:16711587G>T	ENST00000443824.1	-	5	1205	c.462C>A	c.(460-462)atC>atA	p.I154I	CTPS2_ENST00000359276.4_Silent_p.I154I|CTPS2_ENST00000380241.3_Silent_p.I154I	NM_001144002.1	NP_001137474.1	Q9NRF8	PYRG2_HUMAN	CTP synthase 2	154					'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)					GCATTCCTTCGATGTCTCCAA	0.438																																					p.I154I		Atlas-SNP	.											.	CTPS2	49	.	0			c.C462A						PASS	.						104	96	99					X																	16711587		2203	4300	6503	SO:0001819	synonymous_variant	56474	exon5			TCCTTCGATGTCT	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.462C>A	X.37:g.16711587G>T		188	0	0		156	44	0.282051	NM_001144002	B3KWM2|Q9BRI0|Q9H809|Q9H8K9	Silent	SNP	ENST00000443824.1	37	CCDS14175.1																																																																																			.	.	none		0.438	CTPS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055906.1	NM_019857		T	16711587	G	T	16711587	2	4	10	1	0	0	0	0	0	0	0	1	4025	1048	37	4		4	CTPS2	23	16711587	Silent	SNP	G	TCGA-FF-8041-01A-11D-2210-10	15127013	16711587	138558973	190	1272											
USP11	8237	hgsc.bcm.edu	37	chrX	47092477	47092477	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcaaatccagctgctgctgCggcggctgtggcggcggcag	6	6	17	12	4	0	0	0	0	0	0	1	0	1	0	1	5	5	6	1	5	1	0			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:47092477C>T	ENST00000218348.3	+	1	164	c.164C>T	c.(163-165)gCg>gTg	p.A55V	USP11_ENST00000377107.2_Missense_Mutation_p.A12V	NM_004651.3	NP_004642.2	P51784	UBP11_HUMAN	ubiquitin specific peptidase 11	55					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|ovary(3)|pancreas(1)|stomach(1)	40						gctgctgctgcggcggctgtg	0.647																																					p.A55V		Atlas-SNP	.											.	USP11	93	.	0			c.C164T						PASS	.						11	11	11					X																	47092477		2170	4226	6396	SO:0001583	missense	8237	exon1			CTGCTGCGGCGGC	U44839	CCDS14277.1	Xp11.23	2008-02-05	2005-08-08		ENSG00000102226	ENSG00000102226		"Ubiquitin-specific peptidases"	12609	protein-coding gene	gene with protein product		300050	"ubiquitin specific protease 11"			12838346	Standard	XM_005272674		Approved	UHX1	uc004dhp.3	P51784	OTTHUMG00000021437	ENST00000218348.3:c.164C>T	X.37:g.47092477C>T	ENSP00000218348:p.Ala55Val	120	0	0		83	24	0.289157	NM_004651	B2RTX1|Q8IUG6|Q9BWE1	Missense_Mutation	SNP	ENST00000218348.3	37	CCDS14277.1	.	.	.	.	.	.	.	.	.	.	C	16.54	3.151779	0.57151	.	.	ENSG00000102226	ENST00000377107;ENST00000218348	T;T	0.22134	1.97;1.99	1.61	1.61	0.23674	.	0.542706	0.13946	N	0.351850	T	0.19406	0.0466	N	0.19112	0.55	0.09310	N	1	D	0.67145	0.996	P	0.54372	0.75	T	0.06679	-1.0813	10	0.66056	D	0.02	.	6.0062	0.19547	0.0:1.0:0.0:0.0	.	55	P51784	UBP11_HUMAN	V	12;55	ENSP00000366311:A12V;ENSP00000218348:A55V	ENSP00000218348:A55V	A	+	2	0	USP11	46977421	0.069000	0.21087	0.003000	0.11579	0.006000	0.05464	0.406000	0.21032	1.066000	0.40716	0.513000	0.50165	GCG	.	.	none		0.647	USP11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_004651		T	47092477	C	T	47092477	3	4	10	1	0	0	0	0	1	0	0	0	17057	768	27	1	166	1	USP11	23	47092477	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	30380890	47092477	108178083	191	1273											
SSX3	10214	hgsc.bcm.edu	37	chrX	48209473	48209473	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggttttcccggggggcacaGctgtttcccatcgttttgtg	3	15	13	10	2	0	0	0	0	0	0	3	0	2	0	2	4	1	5	2	4	0	5			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:48209473G>A	ENST00000298396.2	-	6	467	c.415C>T	c.(415-417)Ctg>Ttg	p.L139L	SSX3_ENST00000376893.3_Silent_p.L139L|SSX3_ENST00000376895.1_Silent_p.L51L	NM_021014.2	NP_066294.1	Q99909	SSX3_HUMAN	synovial sarcoma, X breakpoint 3	139					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			endometrium(3)|large_intestine(1)|lung(9)	13						GGGGGGCACAGCTGTTTCCCA	0.488																																					p.L139L	Colon(37;227 826 19399 40970 48007)	Atlas-SNP	.											.	SSX3	64	.	0			c.C415T						PASS	.						251	230	237					X																	48209473		2203	4300	6503	SO:0001819	synonymous_variant	10214	exon6			GGCACAGCTGTTT	U90840	CCDS14291.1	Xp11.23	2009-06-17			ENSG00000165584	ENSG00000165584			11337	protein-coding gene	gene with protein product		300325				8697803, 9378559	Standard	NM_021014		Approved	CT5.3	uc004djd.1	Q99909	OTTHUMG00000021489	ENST00000298396.2:c.415C>T	X.37:g.48209473G>A		858	1	0.0011655		825	350	0.424242	NM_021014	O60223|Q5JQZ3|Q9BRW7	Silent	SNP	ENST00000298396.2	37	CCDS14291.1																																																																																			.	.	none		0.488	SSX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056486.1	NM_021014		A	48209473	G	A	48209473	2	1	10	1	0	0	0	0	0	0	0	1	15220	962	34	2		2	SSX3	23	48209473	Silent	SNP	G	TCGA-FF-8041-01A-11D-2210-10	1116996	48209473	107061087	192	1274											
CACNA1F	778	hgsc.bcm.edu	37	chrX	49061779	49061779	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcctgcttggccagggccaCgaaacgtgggtctcgagcaa	8	7	13	13	3	1	0	0	0	1	0	3	2	2	0	3	3	3	2	3	3	2	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:49061779C>T	ENST00000376265.2	-	48	5813	c.5752G>A	c.(5752-5754)Gtg>Atg	p.V1918M	SYP-AS1_ENST00000433499.1_RNA|CACNA1F_ENST00000376251.1_Missense_Mutation_p.V1853M|CACNA1F_ENST00000323022.5_Missense_Mutation_p.V1907M|AF196779.1_ENST00000583131.1_RNA	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	1918					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)	GCCAGGGCCACGAAACGTGGG	0.597																																					p.V1918M		Atlas-SNP	.											.	CACNA1F	218	.	0			c.G5752A						PASS	.						65	39	47					X																	49061779		2203	4300	6503	SO:0001583	missense	778	exon48			GGGCCACGAAACG	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.5752G>A	X.37:g.49061779C>T	ENSP00000365441:p.Val1918Met	137	0	0		137	65	0.474453	NM_005183	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Missense_Mutation	SNP	ENST00000376265.2	37	CCDS35253.1	.	.	.	.	.	.	.	.	.	.	C	17.08	3.297889	0.60086	.	.	ENSG00000102001	ENST00000376251;ENST00000323022;ENST00000376265	T;T;T	0.60548	0.18;0.18;0.18	4.95	4.02	0.46733	.	0.000000	0.64402	D	0.000001	T	0.69052	0.3068	M	0.74467	2.265	0.48452	D	0.999656	D;D	0.76494	0.999;0.997	P;P	0.57057	0.812;0.654	T	0.74349	-0.3694	10	0.87932	D	0	.	12.3113	0.54929	0.1697:0.8303:0.0:0.0	.	1907;1918	F5CIQ9;O60840	.;CAC1F_HUMAN	M	1853;1907;1918	ENSP00000365427:V1853M;ENSP00000321618:V1907M;ENSP00000365441:V1918M	ENSP00000321618:V1907M	V	-	1	0	CACNA1F	48948723	0.999000	0.42202	0.915000	0.36163	0.519000	0.34347	3.722000	0.54948	2.178000	0.69098	0.529000	0.55759	GTG	.	.	none		0.597	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183		T	49061779	C	T	49061779	3	4	10	1	0	0	0	0	1	0	0	0	2545	536	19	1	185	1	CACNA1F	23	49061779	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	852306	49061779	106208781	193	1275											
UBQLN2	29978	hgsc.bcm.edu	37	chrX	56591532	56591532	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagatttggctgcacagaTgatgctgaatagcccgctgt	9	11	11	10	1	0	4	0	2	0	2	1	4	1	4	2	1	3	4	2	1	2	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:56591532T>C	ENST00000338222.5	+	1	1507	c.1226T>C	c.(1225-1227)aTg>aCg	p.M409T		NM_013444.3	NP_038472.2	Q9UHD9	UBQL2_HUMAN	ubiquilin 2	409					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						GCTGCACAGATGATGCTGAAT	0.527																																					p.M409T	Esophageal Squamous(104;218 1492 6022 10838 28884)	Atlas-SNP	.											.	UBQLN2	55	.	0			c.T1226C						PASS	.						39	33	35					X																	56591532		2203	4300	6503	SO:0001583	missense	29978	exon1			CACAGATGATGCT	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.1226T>C	X.37:g.56591532T>C	ENSP00000345195:p.Met409Thr	117	0	0		131	57	0.435115	NM_013444	O94798|Q5D027|Q9H3W6|Q9HAZ4	Missense_Mutation	SNP	ENST00000338222.5	37	CCDS14374.1	.	.	.	.	.	.	.	.	.	.	T	12.66	2.004951	0.35415	.	.	ENSG00000188021	ENST00000338222;ENST00000535171	D	0.85088	-1.94	4.73	4.73	0.59995	Heat shock chaperonin-binding (1);	0.145633	0.49916	D	0.000140	D	0.84028	0.5382	M	0.80616	2.505	0.47245	D	0.999362	P;P	0.42649	0.786;0.61	B;B	0.37451	0.25;0.191	D	0.85805	0.1376	10	0.59425	D	0.04	-10.2918	11.3192	0.49410	0.0:0.0:0.0:1.0	.	409;409	B4DZF1;Q9UHD9	.;UBQL2_HUMAN	T	409	ENSP00000345195:M409T	ENSP00000345195:M409T	M	+	2	0	UBQLN2	56608257	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.816000	0.86201	1.874000	0.54306	0.481000	0.45027	ATG	.	.	none		0.527	UBQLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056891.1	NM_013444		C	56591532	T	C	56591532	3	2	10	1	0	0	0	0	1	0	0	0	16912	1464	51	3	1228	3	UBQLN2	23	56591532	Missense_Mutation	SNP	T	TCGA-FF-8041-01A-11D-2210-10	7529753	56591532	98679028	194	1276											
AR	367	hgsc.bcm.edu	37	chrX	66905872	66905872	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaaacagaagtacctgtgcGccagcagaaatgattgcact	14	7	11	9	1	0	3	0	1	0	2	0	4	0	4	2	1	5	3	2	1	4	2	rs137852569		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:66905872G>A	ENST00000374690.3	+	3	2313	c.1789G>A	c.(1789-1791)Gcc>Acc	p.A597T	AR_ENST00000396044.3_Missense_Mutation_p.A597T|AR_ENST00000504326.1_Missense_Mutation_p.A597T|AR_ENST00000396043.2_Missense_Mutation_p.A65T|AR_ENST00000513847.1_3'UTR	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	596	Interaction with HIPK3. {ECO:0000250}.|Interaction with LPXN.		S -> G (in PAIS; high dissociation rate; associated with P-617 in a PAIS patient; partially restores DNA-binding activity of P-617 mutant receptors). {ECO:0000269|PubMed:1316540}.|S -> T (in a patient with severe hypospadias). {ECO:0000269|PubMed:10092153}.		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)	GTACCTGTGCGCCAGCAGAAA	0.413									Androgen Insensitivity Syndrome																												p.A597T		Atlas-SNP	.											.	AR	249	.	0			c.G1789A	GRCh37	CM920071	AR	M	rs137852569	PASS	.						106	93	97					X																	66905872		2203	4300	6503	SO:0001583	missense	367	exon3	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	CTGTGCGCCAGCA	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.1789G>A	X.37:g.66905872G>A	ENSP00000363822:p.Ala597Thr	60	0	0		59	4	0.0677966	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	37	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	G	16.77	3.214457	0.58452	.	.	ENSG00000169083	ENST00000544984;ENST00000374690;ENST00000504326;ENST00000396044;ENST00000396043	D;D;D;D	0.97209	-4.29;-4.29;-4.29;-4.29	5.32	4.47	0.54385	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (3);	0.000000	0.85682	D	0.000000	D	0.97155	0.9070	L	0.45352	1.415	0.80722	D	1	P;P;D;B	0.89917	0.881;0.881;1.0;0.343	B;B;D;B	0.97110	0.175;0.175;1.0;0.076	D	0.97171	0.9844	10	0.87932	D	0	.	10.6719	0.45764	0.0936:0.0:0.9064:0.0	.	597;597;65;596	E7EVX6;D3YPQ2;F1D8N5;P10275	.;.;.;ANDR_HUMAN	T	407;597;597;597;65	ENSP00000363822:A597T;ENSP00000421155:A597T;ENSP00000379359:A597T;ENSP00000379358:A65T	ENSP00000363822:A597T	A	+	1	0	AR	66822597	1.000000	0.71417	0.987000	0.45799	0.102000	0.19082	9.050000	0.93843	1.228000	0.43614	-0.306000	0.09157	GCC	.	.	weak		0.413	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		A	66905872	G	A	66905872	3	1	10	1	0	0	0	0	1	0	0	0	836	1087	38	1	1823	1	AR	23	66905872	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	10314340	66905872	88364688	195	1277											
DGAT2L6	347516	hgsc.bcm.edu	37	chrX	69424867	69424867	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agacagtagacaagtatcacGcactctacatcagtgccctg	13	8	8	12	1	3	2	2	0	1	2	3	2	3	2	1	0	2	3	1	0	4	3	rs35142503		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:69424867G>A	ENST00000333026.3	+	7	1025	c.925G>A	c.(925-927)Gca>Aca	p.A309T		NM_198512.1	NP_940914.1	Q6ZPD8	DG2L6_HUMAN	diacylglycerol O-acyltransferase 2-like 6	309					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						CAAGTATCACGCACTCTACAT	0.458																																					p.A309T		Atlas-SNP	.											.	DGAT2L6	40	.	0			c.G925A						PASS	.	G	THR/ALA	4,3831		0,4,1628,571	95	75	82		925	1.6	0.2	X	dbSNP_126	82	0,6728		0,0,2428,1872	yes	missense	DGAT2L6	NM_198512.1	58	0,4,4056,2443	AA,AG,GG,G		0.0,0.1043,0.0379	benign	309/338	69424867	4,10559	2203	4300	6503	SO:0001583	missense	347516	exon7			TATCACGCACTCT	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.925G>A	X.37:g.69424867G>A	ENSP00000328036:p.Ala309Thr	260	0	0		297	49	0.164983	NM_198512	Q6IEE2	Missense_Mutation	SNP	ENST00000333026.3	37	CCDS14397.1	.	.	.	.	.	.	.	.	.	.	G	8.546	0.874318	0.17395	0.001043	0.0	ENSG00000184210	ENST00000333026	D	0.93547	-3.24	4.74	1.62	0.23740	.	0.774326	0.12002	N	0.508712	D	0.88640	0.6491	L	0.49455	1.56	0.21822	N	0.999526	B	0.16603	0.018	B	0.16289	0.015	T	0.73404	-0.3993	10	0.19147	T	0.46	-22.9304	7.1522	0.25616	0.3674:0.0:0.6325:0.0	rs35142503	309	Q6ZPD8	DG2L6_HUMAN	T	309	ENSP00000328036:A309T	ENSP00000328036:A309T	A	+	1	0	DGAT2L6	69341592	0.000000	0.05858	0.172000	0.22920	0.534000	0.34807	0.658000	0.24979	0.002000	0.14630	-0.192000	0.12808	GCA	G|0.987;A|0.013	0.013	weak		0.458	DGAT2L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057067.1	NM_198512		A	69424867	G	A	69424867	3	1	10	1	0	0	0	0	1	0	0	0	4461	1087	38	1	951	1	DGAT2L6	23	69424867	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	2518995	69424867	85845693	196	1278											
CXorf26	51260	hgsc.bcm.edu	37	chrX	75395309	75395309	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtcttactgtttcgcagcTgatttcatcagttgacccac	7	16	7	11	1	3	2	2	2	1	0	4	2	3	2	1	0	2	4	1	0	1	5			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:75395309T>C	ENST00000373358.3	+	4	361	c.158T>C	c.(157-159)cTg>cCg	p.L53P	PBDC1_ENST00000373357.3_Splice_Site_p.L53P	NM_016500.3	NP_057584.2	Q9BVG4	PBDC1_HUMAN	polysaccharide biosynthesis domain containing 1	53																	GTTTCGCAGCTGATTTCATCA	0.413																																					p.L53P		Atlas-SNP	.											.	.	.	.	0			c.T158C						PASS	.						86	75	79					X																	75395309		2203	4300	6503	SO:0001630	splice_region_variant	51260	exon4			CGCAGCTGATTTC	BC001220	CCDS14432.1, CCDS75995.1	Xq13.2	2012-11-28	2012-11-28	2012-11-28	ENSG00000102390	ENSG00000102390			28790	protein-coding gene	gene with protein product			"chromosome X open reading frame 26"	CXorf26		11042152	Standard	NM_016500		Approved	MGC874	uc004ecl.1	Q9BVG4	OTTHUMG00000021876	ENST00000373358.3:c.157-1T>C	X.37:g.75395309T>C		100	0	0		99	28	0.282828	NM_016500		Missense_Mutation	SNP	ENST00000373358.3	37	CCDS14432.1	.	.	.	.	.	.	.	.	.	.	T	19.75	3.885632	0.72410	.	.	ENSG00000102390	ENST00000373358;ENST00000373357	.	.	.	4.77	4.77	0.60923	Yst0336-like domain (1);	0.000000	0.85682	D	0.000000	T	0.81767	0.4892	M	0.91561	3.22	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85370	0.1113	9	0.87932	D	0	-8.4595	11.3241	0.49438	0.0:0.0:0.0:1.0	.	53	Q9BVG4	CX026_HUMAN	P	53	.	ENSP00000362455:L53P	L	+	2	0	CXorf26	75311711	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	5.748000	0.68697	1.875000	0.54330	0.486000	0.48141	CTG	.	.	none		0.413	PBDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057294.1	NM_016500	Missense_Mutation	C	75395309	T	C	75395309	5	2	10	1	0	0	0	0	0	0	1	0	4106	1594	55	3	172	3	CXorf26	23	75395309	Splice_Site	SNP	T	TCGA-FF-8041-01A-11D-2210-10	5970442	75395309	79875251	197	1279											
MAGEE1	57692	hgsc.bcm.edu	37	chrX	75648638	75648638	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacctggcacctccgtgctGcccacccccagtgagggcct	5	6	12	18	1	0	1	0	1	0	0	1	2	1	2	7	3	2	2	7	3	0	0			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:75648638G>A	ENST00000361470.2	+	1	593	c.315G>A	c.(313-315)ctG>ctA	p.L105L		NM_020932.2	NP_065983.1	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	105						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						CCTCCGTGCTGCCCACCCCCA	0.677																																					p.L105L		Atlas-SNP	.											.	MAGEE1	236	.	0			c.G315A						PASS	.						21	22	22					X																	75648638		2203	4299	6502	SO:0001819	synonymous_variant	57692	exon1			CGTGCTGCCCACC	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.315G>A	X.37:g.75648638G>A		166	0	0		152	21	0.138158	NM_020932	Q5JXC7|Q86TG0|Q8TD92|Q9H216	Silent	SNP	ENST00000361470.2	37	CCDS14433.1																																																																																			.	.	none		0.677	MAGEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057298.1	NM_020932		A	75648638	G	A	75648638	2	1	10	1	0	0	0	0	0	0	0	1	9194	1306	46	2		2	MAGEE1	23	75648638	Silent	SNP	G	TCGA-FF-8041-01A-11D-2210-10	253329	75648638	79621922	198	1280											
NAP1L3	4675	hgsc.bcm.edu	37	chrX	92928107	92928107	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggctgcggctgctagtgctgCcgctgctgctgctgctgctg	1	11	16	13	2	0	0	0	0	0	0	0	0	0	0	1	2	9	10	1	2	1	1	rs62635803		TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:92928107C>A	ENST00000373079.3	-	1	460	c.197G>T	c.(196-198)gGc>gTc	p.G66V	FAM133A_ENST00000332647.4_5'Flank|FAM133A_ENST00000355813.5_5'Flank|NAP1L3_ENST00000475430.2_Missense_Mutation_p.G59V|FAM133A_ENST00000538690.1_5'Flank|FAM133A_ENST00000322139.4_5'Flank	NM_004538.5	NP_004529.2	Q99457	NP1L3_HUMAN	nucleosome assembly protein 1-like 3	66	Ser-rich.				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						gctagtgctgccgctgctgct	0.612													C|||	27	0.00715232	0.0204	0.0	3775	,	,		7467	0.0		0.0	False		,,,				2504	0.0				p.G66V		Atlas-SNP	.											.	NAP1L3	81	.	0			c.G197T						PASS	.	C	VAL/GLY	81,3313		1,68,11,1394,457	8	9	9		197	0.9	0.1	X	dbSNP_129	9	0,5910		0,0,0,2185,1540	yes	missense	NAP1L3	NM_004538.5	109	1,68,11,3579,1997	AA,AC,A,CC,C		0.0,2.3866,0.8706	probably-damaging	66/507	92928107	81,9223	1931	3725	5656	SO:0001583	missense	4675	exon1			GTGCTGCCGCTGC		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.197G>T	X.37:g.92928107C>A	ENSP00000362171:p.Gly66Val	59	0	0		68	14	0.205882	NM_004538	B2RCM0|O60788	Missense_Mutation	SNP	ENST00000373079.3	37	CCDS14465.1	12	0.007233273056057866	9	0.01859504132231405	0	0.0	0	0.0	0	0.0	C	3.961	-0.010248	0.07727	0.023866	0.0	ENSG00000186310	ENST00000373079;ENST00000543136	T	0.29142	1.58	0.913	0.913	0.19354	.	0.385153	0.26231	N	0.025574	T	0.06234	0.0161	N	0.14661	0.345	0.32519	N	0.536487	B	0.30482	0.281	B	0.22753	0.041	T	0.26155	-1.0111	9	0.12766	T	0.61	.	.	.	.	.	66	Q99457	NP1L3_HUMAN	V	66;59	ENSP00000362171:G66V	ENSP00000362171:G66V	G	-	2	0	NAP1L3	92814763	0.001000	0.12720	0.051000	0.19133	0.018000	0.09664	0.098000	0.15189	0.718000	0.32166	0.292000	0.19580	GGC	C|0.992;A|0.008	0.008	strong		0.612	NAP1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057449.1	NM_004538		A	92928107	C	A	92928107	3	1	10	1	0	0	0	0	1	0	0	0	10167	739	26	4	1327	4	NAP1L3	23	92928107	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	17279469	92928107	62342453	199	1281											
NAP1L3	4675	hgsc.bcm.edu	37	chrX	92928124	92928124	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgccgctgctgctgctgctGctgccgctgccgctgctgct	0	11	13	17	3	0	0	0	0	0	0	0	0	0	0	3	0	10	10	3	0	0	0			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:92928124G>T	ENST00000373079.3	-	1	443	c.180C>A	c.(178-180)agC>agA	p.S60R	FAM133A_ENST00000332647.4_5'Flank|FAM133A_ENST00000355813.5_5'Flank|NAP1L3_ENST00000475430.2_Missense_Mutation_p.S53R|FAM133A_ENST00000538690.1_5'Flank|FAM133A_ENST00000322139.4_5'Flank	NM_004538.5	NP_004529.2	Q99457	NP1L3_HUMAN	nucleosome assembly protein 1-like 3	60	Ser-rich.				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						tgctgctgctgctgccgctgc	0.617																																					p.S60R		Atlas-SNP	.											.	NAP1L3	81	.	0			c.C180A						PASS	.						8	9	9					X																	92928124		1938	3702	5640	SO:0001583	missense	4675	exon1			GCTGCTGCTGCCG		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.180C>A	X.37:g.92928124G>T	ENSP00000362171:p.Ser60Arg	56	0	0		63	10	0.15873	NM_004538	B2RCM0|O60788	Missense_Mutation	SNP	ENST00000373079.3	37	CCDS14465.1	.	.	.	.	.	.	.	.	.	.	G	3.522	-0.097600	0.07010	.	.	ENSG00000186310	ENST00000373079;ENST00000543136	T	0.35048	1.33	1.57	1.57	0.23409	.	.	.	.	.	T	0.18045	0.0433	N	0.14661	0.345	0.09310	N	1	B	0.21225	0.053	B	0.13407	0.009	T	0.17137	-1.0379	9	0.28530	T	0.3	.	4.6764	0.12713	0.0:0.0:0.6303:0.3697	.	60	Q99457	NP1L3_HUMAN	R	60;53	ENSP00000362171:S60R	ENSP00000362171:S60R	S	-	3	2	NAP1L3	92814780	0.521000	0.26258	0.014000	0.15608	0.005000	0.04900	0.666000	0.25097	1.056000	0.40484	0.292000	0.19580	AGC	.	.	none		0.617	NAP1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057449.1	NM_004538		T	92928124	G	T	92928124	3	4	10	1	0	0	0	0	1	0	0	0	10167	1310	46	4	1344	4	NAP1L3	23	92928124	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	17	92928124	62342436	200	1282											
DRP2	1821	hgsc.bcm.edu	37	chrX	100509422	100509422	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcctcctcagaccacatcCagtgagaacatgagggactt	11	9	8	13	0	2	3	1	2	1	2	5	5	4	4	4	1	1	0	4	1	1	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:100509422C>T	ENST00000395209.3	+	18	2513	c.1986C>T	c.(1984-1986)tcC>tcT	p.S662S	DRP2_ENST00000402866.1_Silent_p.S662S|DRP2_ENST00000538510.1_Silent_p.S662S|DRP2_ENST00000541709.1_Silent_p.S584S	NM_001939.2	NP_001930.2	Q13474	DRP2_HUMAN	dystrophin related protein 2	662					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						AGACCACATCCAGTGAGAACA	0.507																																					p.S662S		Atlas-SNP	.											.	DRP2	98	.	0			c.C1986T						PASS	.						110	81	90					X																	100509422		2203	4300	6503	SO:0001819	synonymous_variant	1821	exon18			CACATCCAGTGAG	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.1986C>T	X.37:g.100509422C>T		314	0	0		351	67	0.190883	NM_001939	A6ZKI5|A8K1B0|B1B1F3|B4DIZ0	Silent	SNP	ENST00000395209.3	37	CCDS14480.2																																																																																			.	.	none		0.507	DRP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057522.3	NM_001939		T	100509422	C	T	100509422	2	4	10	1	0	0	0	0	0	0	0	1	4766	581	21	2		2	DRP2	23	100509422	Silent	SNP	C	TCGA-FF-8041-01A-11D-2210-10	7581298	100509422	54761138	201	1283											
MUM1L1	139221	hgsc.bcm.edu	37	chrX	105449437	105449437	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	taaaccataatggagtctgaGtatgtcctatgcaactggaa	14	11	9	7	0	1	1	0	1	1	0	2	3	2	3	2	2	3	2	2	2	7	4			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:105449437G>A	ENST00000357175.2	+	4	661	c.12G>A	c.(10-12)gaG>gaA	p.E4E	MUM1L1_ENST00000372552.1_Silent_p.E4E|MUM1L1_ENST00000337685.2_Silent_p.E4E	NM_001171020.1	NP_001164491.1	Q5H9M0	MUML1_HUMAN	melanoma associated antigen (mutated) 1-like 1	4						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						TGGAGTCTGAGTATGTCCTAT	0.398																																					p.E4E		Atlas-SNP	.											.	MUM1L1	166	.	0			c.G12A						PASS	.						20	20	20					X																	105449437		1900	4117	6017	SO:0001819	synonymous_variant	139221	exon5			GTCTGAGTATGTC	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.12G>A	X.37:g.105449437G>A		256	0	0		261	136	0.521073	NM_152423	D3DUX2|Q49AS5|Q8N2C0|Q96MT6	Silent	SNP	ENST00000357175.2	37	CCDS55469.1																																																																																			.	.	none		0.398	MUM1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057795.1	NM_152423		A	105449437	G	A	105449437	2	1	10	1	0	0	0	0	0	0	0	1	9995	1020	36	2		2	MUM1L1	23	105449437	Silent	SNP	G	TCGA-FF-8041-01A-11D-2210-10	4940015	105449437	49821123	202	1284											
LONRF3	79836	hgsc.bcm.edu	37	chrX	118109491	118109491	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cgtcgcaactccggcacgagGgcaaccgactgtaccgcgag	9	4	13	15	7	0	0	0	0	0	0	2	3	1	0	3	2	3	4	3	2	3	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:118109491G>A	ENST00000371628.3	+	1	779	c.748G>A	c.(748-750)Ggc>Agc	p.G250S	LONRF3_ENST00000304778.7_Missense_Mutation_p.G250S|LONRF3_ENST00000422289.2_5'Flank	NM_001031855.1	NP_001027026.1	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger 3	250							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						CCGGCACGAGGGCAACCGACT	0.687																																					p.G250S		Atlas-SNP	.											.	LONRF3	138	.	0			c.G748A						PASS	.						16	11	13					X																	118109491		2177	4244	6421	SO:0001583	missense	79836	exon1			CACGAGGGCAACC	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.748G>A	X.37:g.118109491G>A	ENSP00000360690:p.Gly250Ser	165	0	0		147	24	0.163265	NM_001031855	Q5JPN6|Q8NB00|Q9H647	Missense_Mutation	SNP	ENST00000371628.3	37	CCDS35374.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.78|17.78	3.473780|3.473780	0.63737|0.63737	.|.	.|.	ENSG00000175556|ENSG00000175556	ENST00000439603|ENST00000365713;ENST00000304778;ENST00000371628	.|T;T;T	.|0.80566	.|-1.39;-1.39;-1.39	4.26|4.26	4.26|4.26	0.50523|0.50523	.|Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	D|D	0.87245|0.87245	0.6129|0.6129	M|M	0.86343|0.86343	2.81|2.81	0.80722|0.80722	D|D	1|1	.|P;P	.|0.47762	.|0.9;0.866	.|B;P	.|0.51701	.|0.397;0.677	D|D	0.88596|0.88596	0.3146|0.3146	6|10	.|0.44086	.|T	.|0.13	-0.604|-0.604	15.2074|15.2074	0.73190|0.73190	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|250;250	.|Q496Y0-2;Q496Y0	.|.;LONF3_HUMAN	E|S	56|250	.|ENSP00000360691:G250S;ENSP00000307732:G250S;ENSP00000360690:G250S	.|ENSP00000307732:G250S	G|G	+|+	2|1	0|0	LONRF3|LONRF3	117993519|117993519	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	5.909000|5.909000	0.69923|0.69923	2.122000|2.122000	0.65172|0.65172	0.529000|0.529000	0.55759|0.55759	GGG|GGC	.	.	none		0.687	LONRF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355124.2	NM_024778		A	118109491	G	A	118109491	3	1	10	1	0	0	0	0	1	0	0	0	8905	1232	43	2	750	2	LONRF3	23	118109491	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	12660054	118109491	37161069	203	1285											
UBE2A	7319	hgsc.bcm.edu	37	chrX	118715490	118715490	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaacatttaaacttacaataGaattcactgaagaatatcca	19	11	4	7	0	1	3	1	1	0	2	2	4	2	3	1	0	3	0	1	0	10	6			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:118715490G>T	ENST00000371558.2	+	4	346	c.172G>T	c.(172-174)Gaa>Taa	p.E58*	UBE2A_ENST00000346330.3_Intron|UBE2A_ENST00000371569.5_5'UTR	NM_001282161.1|NM_003336.2|NM_181762.1	NP_001269090.1|NP_003327.2|NP_861427.1	P49459	UBE2A_HUMAN	ubiquitin-conjugating enzyme E2A	58					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|DNA repair (GO:0006281)|histone H2A ubiquitination (GO:0033522)|in utero embryonic development (GO:0001701)|maternal process involved in female pregnancy (GO:0060135)|positive regulation of cell proliferation (GO:0008284)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein polyubiquitination (GO:0000209)|response to UV (GO:0009411)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|cytosol (GO:0005829)|HULC complex (GO:0033503)|nuclear chromatin (GO:0000790)|XY body (GO:0001741)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)	p.E58*(1)		haematopoietic_and_lymphoid_tissue(1)|lung(7)	8						ACTTACAATAGAATTCACTGA	0.299								Rad6 pathway																													p.E58X		Atlas-SNP	.											.	UBE2A	43	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.G172T						PASS	.						81	79	80					X																	118715490		2202	4298	6500	SO:0001587	stop_gained	7319	exon4			ACAATAGAATTCA	AK223045	CCDS14580.1, CCDS14581.1	Xq24	2011-05-19	2011-05-19		ENSG00000077721	ENSG00000077721		"Ubiquitin-conjugating enzymes E2"	12472	protein-coding gene	gene with protein product		312180	"ubiquitin-conjugating enzyme E2A (RAD6 homolog)"			1559696	Standard	NM_003336		Approved	UBC2, HHR6A, RAD6A	uc004erl.3	P49459	OTTHUMG00000022275	ENST00000371558.2:c.172G>T	X.37:g.118715490G>T	ENSP00000360613:p.Glu58*	383	1	0.00261097		508	203	0.399606	NM_003336	A6NFE9|A6NGR2|A6NMF5|B2R7R9|D3DWI1|Q4TTG1|Q96FX4	Nonsense_Mutation	SNP	ENST00000371558.2	37	CCDS14580.1	.	.	.	.	.	.	.	.	.	.	G	38	7.024582	0.98010	.	.	ENSG00000077721	ENST00000371558	.	.	.	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	-0.6356	17.9034	0.88911	0.0:0.0:1.0:0.0	.	.	.	.	X	58	.	ENSP00000360613:E58X	E	+	1	0	UBE2A	118599518	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.858000	0.99539	2.448000	0.82819	0.600000	0.82982	GAA	.	.	none		0.299	UBE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058036.1	NM_003336		T	118715490	G	T	118715490	4	4	10	1	0	0	0	0	0	1	0	0	16859	943	33	4	186	4	UBE2A	23	118715490	Nonsense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	605999	118715490	36555070	204	1286											
SLITRK2	84631	hgsc.bcm.edu	37	chrX	144904787	144904787	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagccatgctgacacccacGtccaaaggctgtcacctaca	11	6	8	16	1	1	1	1	1	0	0	2	1	2	1	4	1	3	3	4	1	2	1			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:144904787G>A	ENST00000370490.1	+	1	5099	c.844G>A	c.(844-846)Gtc>Atc	p.V282I	SLITRK2_ENST00000428560.2_Missense_Mutation_p.V282I|SLITRK2_ENST00000413937.2_Missense_Mutation_p.V282I|SLITRK2_ENST00000434188.2_Missense_Mutation_p.V282I|SLITRK2_ENST00000447897.2_Missense_Mutation_p.V282I			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	282					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)					TGACACCCACGTCCAAAGGCT	0.562																																					p.V282I		Atlas-SNP	.											.	SLITRK2	221	.	0			c.G844A						PASS	.						79	72	74					X																	144904787		2203	4300	6503	SO:0001583	missense	84631	exon5			ACCCACGTCCAAA	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.844G>A	X.37:g.144904787G>A	ENSP00000359521:p.Val282Ile	68	0	0		78	13	0.166667	NM_001144005	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Missense_Mutation	SNP	ENST00000370490.1	37	CCDS14680.1	.	.	.	.	.	.	.	.	.	.	G	4.111	0.018746	0.07959	.	.	ENSG00000185985	ENST00000335565;ENST00000447897;ENST00000370490;ENST00000434188;ENST00000413937;ENST00000428560	T;T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98;0.98	5.67	-4.09	0.03951	.	0.813170	0.11203	N	0.588607	T	0.22322	0.0538	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21143	-1.0254	10	0.18710	T	0.47	-1.0238	14.6093	0.68504	0.7205:0.0:0.2795:0.0	.	282	Q9H156	SLIK2_HUMAN	I	282	ENSP00000334374:V282I;ENSP00000411681:V282I;ENSP00000359521:V282I;ENSP00000397015:V282I;ENSP00000407347:V282I;ENSP00000412010:V282I	ENSP00000334374:V282I	V	+	1	0	SLITRK2	144712479	0.000000	0.05858	0.001000	0.08648	0.837000	0.47467	-0.586000	0.05787	-1.074000	0.03132	-0.914000	0.02751	GTC	.	.	none		0.562	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		A	144904787	G	A	144904787	3	1	10	1	0	0	0	0	1	0	0	0	14758	1145	40	1	846	1	SLITRK2	23	144904787	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	26189297	144904787	10365773	205	1287											
GABRQ	55879	hgsc.bcm.edu	37	chrX	151820129	151820129	+	Missense_Mutation	SNP	T	T	C																															tgtccttgctggagtatgtcTacatcaactatcttttctac																										TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:151820129T>C	ENST00000370306.2	+	8	1062	c.1042T>C	c.(1042-1044)Tac>Cac	p.Y348H		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	348					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)	GGAGTATGTCTACATCAACTA	0.512																																					p.Y348H		Atlas-SNP	.											.	GABRQ	131	.	0			c.T1042C						PASS	.						320	251	274					X																	151820129		2203	4300	6503	SO:0001583	missense	55879	exon8			TATGTCTACATCA	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.1042T>C	X.37:g.151820129T>C	ENSP00000359329:p.Tyr348His	251	0	0		305	47	0.154098	NM_018558	A6NFN1|Q32MB4|Q9NZK8	Missense_Mutation	SNP	ENST00000370306.2	37	CCDS14707.1	.	.	.	.	.	.	.	.	.	.	T	15.54	2.862737	0.51482	.	.	ENSG00000147402	ENST00000370306	D	0.85411	-1.98	5.88	4.72	0.59763	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.153676	0.30969	N	0.008512	T	0.78685	0.4322	L	0.45137	1.4	0.36846	D	0.887645	B	0.28208	0.203	B	0.32583	0.148	T	0.72174	-0.4370	10	0.16420	T	0.52	.	9.1238	0.36803	0.0:0.0866:0.0:0.9133	.	348	Q9UN88	GBRT_HUMAN	H	348	ENSP00000359329:Y348H	ENSP00000359329:Y348H	Y	+	1	0	GABRQ	151570785	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.032000	0.64140	0.837000	0.34925	0.486000	0.48141	TAC	.	.	none		0.512	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558		C	151820129	T	C	151820129	3	2	10	1	0	0	0	0	1	0	0	0	6183	1522	53	3	1072	3	GABRQ	23	151820129	Missense_Mutation	SNP	T	TCGA-FF-8041-01A-11D-2210-10	6915342	151820129	3450431	206	1288	18	2									
GABRQ	55879	hgsc.bcm.edu	37	chrX	151820139	151820139	+	Missense_Mutation	SNP	A	A	C																															ggagtatgtctacatcaactAtcttttctacagtcgaggac																										TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:151820139A>C	ENST00000370306.2	+	8	1072	c.1052A>C	c.(1051-1053)tAt>tCt	p.Y351S		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	351					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)	TACATCAACTATCTTTTCTAC	0.507																																					p.Y351S		Atlas-SNP	.											.	GABRQ	131	.	0			c.A1052C						PASS	.						282	225	244					X																	151820139		2203	4300	6503	SO:0001583	missense	55879	exon8			TCAACTATCTTTT	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.1052A>C	X.37:g.151820139A>C	ENSP00000359329:p.Tyr351Ser	222	0	0		289	47	0.16263	NM_018558	A6NFN1|Q32MB4|Q9NZK8	Missense_Mutation	SNP	ENST00000370306.2	37	CCDS14707.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.256619	0.80246	.	.	ENSG00000147402	ENST00000370306	D	0.87809	-2.3	5.88	4.68	0.58851	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.156200	0.30565	N	0.009347	D	0.91253	0.7243	M	0.62723	1.935	0.44337	D	0.997227	D	0.89917	1.0	D	0.83275	0.996	D	0.90553	0.4510	10	0.87932	D	0	.	9.5	0.39011	0.8398:0.0:0.0:0.1602	.	351	Q9UN88	GBRT_HUMAN	S	351	ENSP00000359329:Y351S	ENSP00000359329:Y351S	Y	+	2	0	GABRQ	151570795	1.000000	0.71417	0.740000	0.30986	0.936000	0.57629	7.438000	0.80431	0.786000	0.33708	0.486000	0.48141	TAT	.	.	none		0.507	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558		C	151820139	A	C	151820139	3	2	10	1	0	0	0	0	1	0	0	0	6183	449	16	5	1082	5	GABRQ	23	151820139	Missense_Mutation	SNP	A	TCGA-FF-8041-01A-11D-2210-10	10	151820139	3450421	207	1289	18	2									
PLXNB3	5365	hgsc.bcm.edu	37	chrX	153037066	153037066	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gctatgggcccttgtgcccgCcgggggctgtggagctgctg	2	9	18	12	2	0	0	0	0	0	0	0	1	0	1	3	4	3	4	3	4	1	2			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:153037066C>T	ENST00000361971.5	+	14	2587	c.2473C>T	c.(2473-2475)Ccg>Tcg	p.P825S	PLXNB3_ENST00000538543.1_Intron|PLXNB3_ENST00000538776.1_Missense_Mutation_p.P478S|PLXNB3_ENST00000538966.1_Missense_Mutation_p.P848S|PLXNB3_ENST00000538282.1_Missense_Mutation_p.P435S	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	825	PSI 3.				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)					CTTGTGCCCGCCGGGGGCTGT	0.697																																					p.P848S		Atlas-SNP	.											.	PLXNB3	208	.	0			c.C2542T						PASS	.						19	20	20					X																	153037066		2183	4289	6472	SO:0001583	missense	5365	exon15			TGCCCGCCGGGGG	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.2473C>T	X.37:g.153037066C>T	ENSP00000355378:p.Pro825Ser	151	0	0		79	17	0.21519	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	37	CCDS14729.1	.	.	.	.	.	.	.	.	.	.	C	9.903	1.207288	0.22205	.	.	ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776;ENST00000538282	T;T;T;T	0.67698	5.3;5.27;4.68;-0.28	5.11	5.11	0.69529	.	0.369273	0.25900	N	0.027580	T	0.55705	0.1937	L	0.37630	1.12	0.09310	N	0.99999	B;B;B;B	0.24132	0.004;0.098;0.071;0.001	B;B;B;B	0.28916	0.004;0.031;0.096;0.007	T	0.38457	-0.9660	10	0.07990	T	0.79	.	14.9334	0.70935	0.0:1.0:0.0:0.0	.	478;507;848;825	B7Z3H9;B7Z9A5;F5H773;Q9ULL4	.;.;.;PLXB3_HUMAN	S	848;825;478;435	ENSP00000442736:P848S;ENSP00000355378:P825S;ENSP00000445569:P478S;ENSP00000441919:P435S	ENSP00000355378:P825S	P	+	1	0	PLXNB3	152690260	0.026000	0.19158	0.068000	0.19968	0.010000	0.07245	2.416000	0.44644	2.111000	0.64477	0.529000	0.55759	CCG	.	.	none		0.697	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1			T	153037066	C	T	153037066	3	4	10	1	0	0	0	0	1	0	0	0	12134	739	26	2	2641	2	PLXNB3	23	153037066	Missense_Mutation	SNP	C	TCGA-FF-8041-01A-11D-2210-10	1216927	153037066	2233494	208	1290											
OPN1LW	5956	hgsc.bcm.edu	37	chrX	153421999	153421999	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cccgttatctatgtctttatGaaccggcaggtaagcaacac	11	11	8	11	2	2	1	0	1	2	0	2	1	2	1	2	2	3	4	2	2	6	5			TCGA-FF-8041-01A-11D-2210-10	TCGA-FF-8041-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fa676301-902f-473f-8313-5bff34ae549a	d3ef8780-62a6-4dbb-ab8f-3e7122632efc	g.chrX:153421999G>A	ENST00000369951.4	+	5	1035	c.975G>A	c.(973-975)atG>atA	p.M325I		NM_020061.4	NP_064445.2	P04000	OPSR_HUMAN	opsin 1 (cone pigments), long-wave-sensitive	325					phototransduction, visible light (GO:0007603)|positive regulation of cytokinesis (GO:0032467)|protein-chromophore linkage (GO:0018298)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	G-protein coupled receptor activity (GO:0004930)|photoreceptor activity (GO:0009881)			endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	15	all_cancers(53;1.83e-16)|all_epithelial(53;2.73e-10)|all_lung(58;6.39e-07)|Lung NSC(58;8.37e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					ATGTCTTTATGAACCGGCAGG	0.522																																					p.M325I		Atlas-SNP	.											.	OPN1LW	87	.	0			c.G975A						PASS	.						160	162	161					X																	153421999		2193	4268	6461	SO:0001583	missense	5956	exon5			CTTTATGAACCGG	Z68193	CCDS14742.1	Xq28	2013-01-08	2008-04-16		ENSG00000102076	ENSG00000102076		"GPCR / Class A : Opsin receptors"	9936	protein-coding gene	gene with protein product	"cone dystrophy 5 (X-linked)"	300822	"color blindness, protan", "red cone photoreceptor pigment"	CBBM, RCP, CBP			Standard	NM_020061		Approved	COD5	uc004fjz.4	P04000	OTTHUMG00000034295	ENST00000369951.4:c.975G>A	X.37:g.153421999G>A	ENSP00000358967:p.Met325Ile	409	0	0		464	71	0.153017	NM_020061		Missense_Mutation	SNP	ENST00000369951.4	37	CCDS14742.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.940464	0.73557	.	.	ENSG00000102076	ENST00000369951	T	0.37752	1.18	4.57	4.57	0.56435	.	0.000000	0.85682	D	0.000000	T	0.66781	0.2824	M	0.89601	3.045	0.58432	D	0.999999	D	0.65815	0.995	D	0.77004	0.989	T	0.75909	-0.3151	10	0.87932	D	0	.	15.5112	0.75782	0.0:0.0:1.0:0.0	.	325	P04000	OPSR_HUMAN	I	325	ENSP00000358967:M325I	ENSP00000358967:M325I	M	+	3	0	OPN1LW	153075193	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	5.384000	0.66225	1.989000	0.58080	0.436000	0.28706	ATG	.	.	none		0.522	OPN1LW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082839.2	NM_020061		A	153421999	G	A	153421999	3	1	10	1	0	0	0	0	1	0	0	0	10886	1290	45	2	993	2	OPN1LW	23	153421999	Missense_Mutation	SNP	G	TCGA-FF-8041-01A-11D-2210-10	384933	153421999	1848561	209	1291											
TMEM201	199953	hgsc.bcm.edu	37	chr1	9670573	9670573	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctccctccagattacttctCtcttctgtcggggagctgcc	4	13	8	16	1	3	1	0	0	3	1	7	2	5	2	4	2	3	1	4	2	1	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr1:9670573C>T	ENST00000340381.6	+	9	1484	c.1475C>T	c.(1474-1476)tCt>tTt	p.S492F	TMEM201_ENST00000377376.4_Missense_Mutation_p.S468F	NM_001130924.2	NP_001124396.2	Q5SNT2	TM201_HUMAN	transmembrane protein 201	492	Ser-rich.				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)		GATTACTTCTCTCTTCTGTCG	0.607																																					p.S492F		Atlas-SNP	.											.	TMEM201	63	.	0			c.C1475T						PASS	.						17	16	16					1																	9670573		692	1590	2282	SO:0001583	missense	199953	exon9			ACTTCTCTCTTCT		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.1475C>T	1.37:g.9670573C>T	ENSP00000344503:p.Ser492Phe	53	0	0		39	14	0.358974	NM_001130924	B9EH90|Q5SNT3	Missense_Mutation	SNP	ENST00000340381.6	37	CCDS44055.2	.	.	.	.	.	.	.	.	.	.	C	18.53	3.644780	0.67358	.	.	ENSG00000188807	ENST00000377376;ENST00000340381	.	.	.	4.98	4.98	0.66077	.	0.141592	0.49305	D	0.000154	T	0.51143	0.1657	L	0.32530	0.975	0.38522	D	0.948745	P	0.48834	0.916	P	0.49953	0.627	T	0.56165	-0.8024	9	0.48119	T	0.1	-6.3899	13.771	0.63023	0.0:0.847:0.153:0.0	.	468	E9PBR6	.	F	468;492	.	ENSP00000344503:S492F	S	+	2	0	TMEM201	9593160	1.000000	0.71417	0.996000	0.52242	0.737000	0.42083	5.405000	0.66351	2.312000	0.78011	0.561000	0.74099	TCT	.	.	none		0.607	TMEM201-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127672.1	NM_001010866		T	9670573	C	T	9670573	3	4	11	1	0	0	0	0	1	0	0	0	16141	913	32	2	1528	2	TMEM201	1	9670573	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10		9670573	239580048	1	1292											
KIF1B	23095	hgsc.bcm.edu	37	chr1	10363223	10363223	+	Intron	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gattttgtttttccaaaggaCgcggattctgatagcgggga	9	13	13	6	3	1	1	0	1	1	0	2	5	2	4	1	4	1	1	1	4	2	6	rs151053483		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr1:10363223C>T	ENST00000377086.1	+	22	2317				KIF1B_ENST00000377081.1_Intron|KIF1B_ENST00000263934.6_Intron|KIF1B_ENST00000377093.4_Silent_p.D660D|KIF1B_ENST00000377083.1_Silent_p.D660D			O60333	KIF1B_HUMAN	kinesin family member 1B						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)		ttCCAAAGGACGCGGATTCTG	0.388													C|||	1	0.000199681	0.0	0.0	5008	,	,		16904	0.0		0.001	False		,,,				2504	0.0				p.D660D		Atlas-SNP	.											.	KIF1B	242	.	0			c.C1980T						PASS	.	C	,	0,4402		0,0,2201	48	50	49		,1980	2.4	1	1	dbSNP_134	49	13,8587	9.1+/-34.3	0,13,4287	no	intron,coding-synonymous	KIF1B	NM_015074.3,NM_183416.3	,	0,13,6488	TT,TC,CC		0.1512,0.0,0.1	,	,660/1154	10363223	13,12989	2201	4300	6501	SO:0001627	intron_variant	23095	exon21			AAAGGACGCGGAT	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.2115+5919C>T	1.37:g.10363223C>T		286	0	0		242	12	0.0495868	NM_183416	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Silent	SNP	ENST00000377086.1	37																																																																																				C|0.999;T|0.001	0.001	strong		0.388	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1			T	10363223	C	T	10363223	1	4	11	0	1	0	0	0	0	0	0	0	8293	535	19	1		1	KIF1B	1	10363223	Intron	SNP	C	TCGA-FF-8042-01A-11D-2210-10	692650	10363223	238887398	2	1293											
AADACL3	126767	hgsc.bcm.edu	37	chr1	12785877	12785877	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggatggtttccatggagtgCtcaggaccattgacatgagc	10	10	13	8	0	1	2	1	2	0	0	2	5	2	5	2	4	2	2	2	4	0	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr1:12785877C>T	ENST00000359318.5	+	4	1172	c.967C>T	c.(967-969)Ctc>Ttc	p.L323F	AADACL3_ENST00000332530.3_Missense_Mutation_p.L253F	NM_001103170.1	NP_001096640.1	Q5VUY0	ADCL3_HUMAN	arylacetamide deacetylase-like 3	323							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)		CCATGGAGTGCTCAGGACCAT	0.483																																					p.L323F		Atlas-SNP	.											.	AADACL3	84	.	0			c.C967T						PASS	.						75	72	73					1																	12785877		1972	4161	6133	SO:0001583	missense	126767	exon4			GGAGTGCTCAGGA		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.967C>T	1.37:g.12785877C>T	ENSP00000352268:p.Leu323Phe	154	0	0		137	52	0.379562	NM_001103170	B3KXR9|Q5VUY1	Missense_Mutation	SNP	ENST00000359318.5	37	CCDS41253.1	.	.	.	.	.	.	.	.	.	.	C	6.539	0.467660	0.12402	.	.	ENSG00000188984	ENST00000332530;ENST00000359318	T;T	0.12039	2.72;2.72	5.54	-1.38	0.09027	Alpha/beta hydrolase fold-3 (1);	0.292854	0.28533	N	0.015012	T	0.07324	0.0185	N	0.21448	0.665	0.19300	N	0.99998	B;B	0.24675	0.109;0.079	B;B	0.35312	0.2;0.099	T	0.28839	-1.0031	10	0.25751	T	0.34	-9.5847	0.808	0.01088	0.1831:0.207:0.3041:0.3058	.	323;253	Q5VUY0;Q5VUY0-2	ADCL3_HUMAN;.	F	253;323	ENSP00000333352:L253F;ENSP00000352268:L323F	ENSP00000333352:L253F	L	+	1	0	AADACL3	12708464	0.639000	0.27234	0.006000	0.13384	0.044000	0.14063	0.255000	0.18333	-0.211000	0.10124	-0.339000	0.08088	CTC	.	.	none		0.483	AADACL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005324.2	NM_001103170		T	12785877	C	T	12785877	3	4	11	1	0	0	0	0	1	0	0	0	12	797	28	2	985	2	AADACL3	1	12785877	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	2422654	12785877	236464744	3	1294											
PADI6	353238	hgsc.bcm.edu	37	chr1	17701957	17701957	+	RNA	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tatgggcccaacgaggatgcCcccgtgggcacagctgtgct	7	7	14	13	2	0	0	0	0	0	0	0	2	0	1	3	3	4	3	3	3	2	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr1:17701957C>T	ENST00000434762.2	+	0	380							Q6TGC4	PADI6_HUMAN	peptidyl arginine deiminase, type VI						cytoplasm organization (GO:0007028)|cytoskeleton organization (GO:0007010)|protein citrullination (GO:0018101)|regulation of translation by machinery localization (GO:0043143)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(2)	29		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;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	ACGAGGATGCCCCCGTGGGCA	0.622																																					p.A110A		Atlas-SNP	.											.	PADI6	51	.	0			c.C330T						PASS	.						49	50	50					1																	17701957		2064	4204	6268			353238	exon3			GGATGCCCCCGTG	AY422079	CCDS72715.1	1p36.13	2014-07-10			ENSG00000256049	ENSG00000276747	3.5.3.15	"Peptidyl arginine deiminases"	20449	protein-coding gene	gene with protein product		610363				15087120	Standard	NM_207421		Approved		uc001bak.1	Q6TGC4	OTTHUMG00000002372		1.37:g.17701957C>T		32	0	0		60	4	0.0666667	NM_207421	Q330K5|Q70SX3	Silent	SNP	ENST00000434762.2	37																																																																																				.	.	none		0.622	PADI6-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000006804.4	NM_207421		T	17701957	C	T	17701957	1	4	11	0	1	0	0	0	0	0	0	0	11390	610	22	2		2	PADI6	1	17701957	RNA	SNP	C	TCGA-FF-8042-01A-11D-2210-10	4916080	17701957	231548664	4	1295											
ZNF436	80818	hgsc.bcm.edu	37	chr1	23689381	23689381	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cacattcataacatttatagGgtctgtctccagtgtgggtc	9	14	9	9	0	3	0	1	0	2	0	5	0	3	0	1	2	1	0	1	2	3	5			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr1:23689381G>T	ENST00000314011.4	-	4	630	c.494C>A	c.(493-495)cCc>cAc	p.P165H	ZNF436_ENST00000374608.3_Missense_Mutation_p.P165H	NM_001077195.1	NP_001070663.1	Q9C0F3	ZN436_HUMAN	zinc finger protein 436	165					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)		ACATTTATAGGGTCTGTCTCC	0.453																																					p.P165H		Atlas-SNP	.											.	ZNF436	49	.	0			c.C494A						PASS	.						94	88	90					1																	23689381		2203	4300	6503	SO:0001583	missense	80818	exon4			TTATAGGGTCTGT	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.494C>A	1.37:g.23689381G>T	ENSP00000313582:p.Pro165His	249	1	0.00401606		222	91	0.40991	NM_001077195	Q658I9	Missense_Mutation	SNP	ENST00000314011.4	37	CCDS233.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.103046	0.76983	.	.	ENSG00000125945	ENST00000314011;ENST00000374609;ENST00000374608	T;T;T	0.29397	1.57;1.57;1.57	6.03	6.03	0.97812	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000018	T	0.61464	0.2349	M	0.82716	2.605	0.58432	D	0.999998	D	0.89917	1.0	D	0.87578	0.998	T	0.64262	-0.6449	10	0.87932	D	0	-22.7732	18.0604	0.89375	0.0:0.0:1.0:0.0	.	165	Q9C0F3	ZN436_HUMAN	H	165	ENSP00000313582:P165H;ENSP00000363737:P165H;ENSP00000363736:P165H	ENSP00000313582:P165H	P	-	2	0	ZNF436	23561968	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.871000	0.87180	2.854000	0.98071	0.655000	0.94253	CCC	.	.	none		0.453	ZNF436-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008908.1	NM_030634		T	23689381	G	T	23689381	3	4	11	1	0	0	0	0	1	0	0	0	17924	1232	43	4	922	4	ZNF436	1	23689381	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	5987424	23689381	225561240	5	1296											
ZMYM4	9202	hgsc.bcm.edu	37	chr1	35847205	35847205	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actttgcagtgatgcctgctTctctaagtttcgttctgcta	6	17	8	10	1	2	1	0	1	2	0	4	1	2	1	1	0	4	5	1	0	2	6			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr1:35847205T>G	ENST00000314607.6	+	9	1495	c.1415T>G	c.(1414-1416)tTc>tGc	p.F472C	ZMYM4_ENST00000373297.2_Missense_Mutation_p.F472C	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	472					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)				GATGCCTGCTTCTCTAAGTTT	0.418																																					p.F472C		Atlas-SNP	.											ZMYM4,NS,carcinoma,-1,1	ZMYM4	143	1	0			c.T1415G						scavenged	.						199	185	190					1																	35847205		2203	4300	6503	SO:0001583	missense	9202	exon9			CCTGCTTCTCTAA	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.1415T>G	1.37:g.35847205T>G	ENSP00000322915:p.Phe472Cys	122	1	0.00819672		128	33	0.257812	NM_005095	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Missense_Mutation	SNP	ENST00000314607.6	37	CCDS389.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.090933	0.76756	.	.	ENSG00000146463	ENST00000314607;ENST00000373297	T;T	0.49720	0.77;1.11	5.01	5.01	0.66863	TRASH (1);	0.000000	0.85682	D	0.000000	T	0.69214	0.3086	M	0.77313	2.365	0.24658	N	0.993483	D	0.89917	1.0	D	0.91635	0.999	T	0.65051	-0.6262	10	0.72032	D	0.01	-2.4899	15.0118	0.71555	0.0:0.0:0.0:1.0	.	472	Q5VZL5	ZMYM4_HUMAN	C	472	ENSP00000322915:F472C;ENSP00000362394:F472C	ENSP00000322915:F472C	F	+	2	0	ZMYM4	35619792	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.608000	0.82898	2.012000	0.59069	0.482000	0.46254	TTC	.	.	none		0.418	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095		G	35847205	T	G	35847205	3	3	11	1	0	0	0	0	1	0	0	0	17717	1783	62	5	1449	5	ZMYM4	1	35847205	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	12157824	35847205	213403416	6	1297											
ZMYM4	9202	hgsc.bcm.edu	37	chr1	35847247	35847247	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacctcaccatgaactgttGtgagaactgtgggggttact	10	11	11	9	0	1	2	1	2	0	1	1	3	1	2	2	2	4	2	2	2	4	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr1:35847247G>T	ENST00000314607.6	+	9	1537	c.1457G>T	c.(1456-1458)tGt>tTt	p.C486F	ZMYM4_ENST00000373297.2_Missense_Mutation_p.C486F	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	486					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)				ATGAACTGTTGTGAGAACTGT	0.438																																					p.C486F		Atlas-SNP	.											.	ZMYM4	143	.	0			c.G1457T						PASS	.						205	187	193					1																	35847247		2203	4300	6503	SO:0001583	missense	9202	exon9			ACTGTTGTGAGAA	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.1457G>T	1.37:g.35847247G>T	ENSP00000322915:p.Cys486Phe	166	0	0		163	33	0.202454	NM_005095	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Missense_Mutation	SNP	ENST00000314607.6	37	CCDS389.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.5|21.5	4.156265|4.156265	0.78114|0.78114	.|.	.|.	ENSG00000146463|ENSG00000146463	ENST00000314607;ENST00000373297|ENST00000457946	T;T|.	0.80653|.	-1.4;1.15|.	5.01|5.01	5.01|5.01	0.66863|0.66863	TRASH (1);Zinc finger, MYM-type (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.75273|0.75273	0.3827|0.3827	M|M	0.72894|0.72894	2.215|2.215	0.36207|0.36207	D|D	0.851107|0.851107	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	T|T	0.79725|0.79725	-0.1683|-0.1683	10|5	0.87932|.	D|.	0|.	-1.461|-1.461	18.6737|18.6737	0.91521|0.91521	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	486|.	Q5VZL5|.	ZMYM4_HUMAN|.	F|F	486|234	ENSP00000322915:C486F;ENSP00000362394:C486F|.	ENSP00000322915:C486F|.	C|L	+|+	2|3	0|2	ZMYM4|ZMYM4	35619834|35619834	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	9.361000|9.361000	0.97122|0.97122	2.487000|2.487000	0.83934|0.83934	0.591000|0.591000	0.81541|0.81541	TGT|TTG	.	.	none		0.438	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095		T	35847247	G	T	35847247	3	4	11	1	0	0	0	0	1	0	0	0	17717	1377	48	4	1491	4	ZMYM4	1	35847247	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	42	35847247	213403374	7	1298											
ZNF691	51058	hgsc.bcm.edu	37	chr1	43317125	43317125	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcaagatcacctaggcaagCggccataccgctgtgacatc	12	6	10	13	2	1	2	1	1	0	1	2	2	1	2	3	2	3	3	3	2	4	2	rs201360083		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr1:43317125C>T	ENST00000372506.1	+	4	836	c.496C>T	c.(496-498)Cgg>Tgg	p.R166W	ZNF691_ENST00000372502.1_Missense_Mutation_p.R188W|ZNF691_ENST00000372507.1_Missense_Mutation_p.R166W|ZNF691_ENST00000372508.3_Missense_Mutation_p.R166W|ZNF691_ENST00000397044.3_Missense_Mutation_p.R197W|ZNF691_ENST00000372504.1_Missense_Mutation_p.R188W	NM_001242739.1	NP_001229668.1	Q5VV52	ZN691_HUMAN	zinc finger protein 691	197						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)				CCTAGGCAAGCGGCCATACCG	0.592													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18616	0.0		0.0	False		,,,				2504	0.0				p.R197W		Atlas-SNP	.											.	ZNF691	30	.	0			c.C589T						PASS	.						65	58	60					1																	43317125		2203	4300	6503	SO:0001583	missense	51058	exon4			GGCAAGCGGCCAT		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.496C>T	1.37:g.43317125C>T	ENSP00000361584:p.Arg166Trp	68	0	0		66	4	0.0606061	NM_001242739	A8MXP6|B4DJR7|O95878|Q9NWE8	Missense_Mutation	SNP	ENST00000372506.1	37	CCDS476.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	18.52	3.641667	0.67244	.	.	ENSG00000164011	ENST00000372508;ENST00000372507;ENST00000372506;ENST00000397044;ENST00000372504;ENST00000372503;ENST00000372502	T;T;T;T;T;T	0.20332	2.08;2.08;2.08;2.08;2.08;2.08	5.31	2.19	0.27852	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.50627	D	0.000110	T	0.26955	0.0660	M	0.90252	3.1	0.35155	D	0.770112	B;B	0.30973	0.195;0.302	B;B	0.25759	0.039;0.063	T	0.37361	-0.9709	10	0.87932	D	0	-11.7827	6.4447	0.21869	0.423:0.4921:0.0:0.0849	.	197;197	B4DJR7;Q5VV52	.;ZN691_HUMAN	W	166;166;166;197;188;197;188	ENSP00000361586:R166W;ENSP00000361585:R166W;ENSP00000361584:R166W;ENSP00000380237:R197W;ENSP00000361582:R188W;ENSP00000361580:R188W	ENSP00000361580:R188W	R	+	1	2	ZNF691	43089712	0.991000	0.36638	1.000000	0.80357	0.976000	0.68499	2.198000	0.42705	0.887000	0.36136	0.561000	0.74099	CGG	C|1.000;T|0.000	0.000	strong		0.592	ZNF691-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020192.1	NM_015911		T	43317125	C	T	43317125	3	4	11	1	0	0	0	0	1	0	0	0	18111	759	27	1	498	1	ZNF691	1	43317125	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	7469878	43317125	205933496	8	1299											
HPDL	84842	hgsc.bcm.edu	37	chr1	45793485	45793485	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agccctgcaggcccagccggGcagcattgtccccactcttg	6	7	11	17	1	1	0	0	0	1	0	2	0	2	0	5	2	4	3	5	2	0	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr1:45793485G>A	ENST00000334815.3	+	1	941	c.665G>A	c.(664-666)gGc>gAc	p.G222D		NM_032756.2	NP_116145.1	Q96IR7	HPDL_HUMAN	4-hydroxyphenylpyruvate dioxygenase-like	222					aromatic amino acid family metabolic process (GO:0009072)		4-hydroxyphenylpyruvate dioxygenase activity (GO:0003868)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4	Acute lymphoblastic leukemia(166;0.155)					GCCCAGCCGGGCAGCATTGTC	0.662																																					p.G222D		Atlas-SNP	.											.	HPDL	14	.	0			c.G665A						PASS	.						49	53	52					1																	45793485		2203	4300	6503	SO:0001583	missense	84842	exon1			AGCCGGGCAGCAT	BC007293	CCDS519.1	1p34.1	2008-02-05	2007-03-14	2007-03-14	ENSG00000186603	ENSG00000186603			28242	protein-coding gene	gene with protein product			"glyoxalase domain containing 1"	GLOXD1		12477932	Standard	NM_032756		Approved	MGC15668, 4-HPPD-L	uc001cne.3	Q96IR7	OTTHUMG00000007681	ENST00000334815.3:c.665G>A	1.37:g.45793485G>A	ENSP00000335060:p.Gly222Asp	90	0	0		79	31	0.392405	NM_032756	B2R9B0	Missense_Mutation	SNP	ENST00000334815.3	37	CCDS519.1	.	.	.	.	.	.	.	.	.	.	G	0.012	-1.651635	0.00785	.	.	ENSG00000186603	ENST00000334815	T	0.66099	-0.19	5.31	2.43	0.29744	.	0.671557	0.15482	N	0.260037	T	0.57227	0.2039	M	0.76938	2.355	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.52117	-0.8618	10	0.41790	T	0.15	-1.1847	4.4552	0.11640	0.3094:0.0:0.5451:0.1454	.	222	Q96IR7	HPDL_HUMAN	D	222	ENSP00000335060:G222D	ENSP00000335060:G222D	G	+	2	0	HPDL	45566072	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.435000	0.21510	0.378000	0.24764	-0.258000	0.10820	GGC	.	.	none		0.662	HPDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020527.1	NM_032756		A	45793485	G	A	45793485	3	1	11	1	0	0	0	0	1	0	0	0	7342	1203	42	2	667	2	HPDL	1	45793485	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	2476360	45793485	203457136	9	1300											
SLC1A7	6512	hgsc.bcm.edu	37	chr1	53569135	53569135	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagggcgaagttctgcacatGggagccattctcctcctgga	8	9	12	12	1	2	0	0	0	2	0	4	3	3	2	3	3	2	2	3	3	1	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr1:53569135G>T	ENST00000371494.4	-	5	707	c.580C>A	c.(580-582)Cat>Aat	p.H194N		NM_006671.4	NP_006662.3	O00341	EAA5_HUMAN	solute carrier family 1 (glutamate transporter), member 7	194					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)		TTCTGCACATGGGAGCCATTC	0.627																																					p.H194N	NSCLC(128;80 1811 21245 38490 51715)	Atlas-SNP	.											.	SLC1A7	65	.	0			c.C580A						PASS	.						41	46	44					1																	53569135		2203	4300	6503	SO:0001583	missense	6512	exon5			GCACATGGGAGCC	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.580C>A	1.37:g.53569135G>T	ENSP00000360549:p.His194Asn	96	0	0		90	34	0.377778	NM_006671	Q5VVZ0|Q969Z8|Q9BW45	Missense_Mutation	SNP	ENST00000371494.4	37	CCDS574.1	.	.	.	.	.	.	.	.	.	.	G	1.852	-0.464809	0.04476	.	.	ENSG00000162383	ENST00000371494	T	0.47528	0.84	4.82	3.84	0.44239	.	0.682012	0.15341	N	0.267509	T	0.21186	0.0510	N	0.01874	-0.695	0.22511	N	0.999034	B	0.02656	0.0	B	0.01281	0.0	T	0.07366	-1.0776	10	0.16896	T	0.51	-16.8183	12.8002	0.57582	0.0:0.0:0.7557:0.2443	.	194	O00341	EAA5_HUMAN	N	194	ENSP00000360549:H194N	ENSP00000360549:H194N	H	-	1	0	SLC1A7	53341723	0.170000	0.23016	0.077000	0.20336	0.232000	0.25224	3.331000	0.52075	2.346000	0.79739	0.563000	0.77884	CAT	.	.	none		0.627	SLC1A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024746.1	NM_006671		T	53569135	G	T	53569135	3	4	11	1	0	0	0	0	1	0	0	0	14452	1348	47	4	1130	4	SLC1A7	1	53569135	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	7775650	53569135	195681486	10	1301											
BARHL2	343472	hgsc.bcm.edu	37	chr1	91180266	91180266	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	cttcttggctctcacaggggGactctcacggctactcgtaa	7	11	10	13	2	3	0	2	0	3	0	6	1	3	1	0	4	1	3	0	4	2	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr1:91180266G>C	ENST00000370445.4	-	2	714	c.673C>G	c.(673-675)Ccc>Gcc	p.P225A		NM_020063.1	NP_064447.1	Q9NY43	BARH2_HUMAN	BarH-like homeobox 2	225					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)		CTCACAGGGGGACTCTCACGG	0.542																																					p.P225A	GBM(199;3561 4100 22440)	Atlas-SNP	.											BARHL2,NS,carcinoma,+1,1	BARHL2	62	1	0			c.C673G						PASS	.						155	154	154					1																	91180266		2203	4300	6503	SO:0001583	missense	343472	exon2			CAGGGGGACTCTC	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.673C>G	1.37:g.91180266G>C	ENSP00000359474:p.Pro225Ala	159	0	0		133	48	0.360902	NM_020063	A0AVP2|Q7Z4N7	Missense_Mutation	SNP	ENST00000370445.4	37	CCDS730.1	.	.	.	.	.	.	.	.	.	.	G	18.30	3.592727	0.66219	.	.	ENSG00000143032	ENST00000370445	D	0.95656	-3.77	5.1	5.1	0.69264	Homeodomain-related (1);Homeodomain-like (1);	0.059845	0.64402	D	0.000002	D	0.94604	0.8261	L	0.32530	0.975	0.80722	D	1	D	0.76494	0.999	D	0.75484	0.986	D	0.92857	0.6302	10	0.18276	T	0.48	.	17.1014	0.86651	0.0:0.0:1.0:0.0	.	225	Q9NY43	BARH2_HUMAN	A	225	ENSP00000359474:P225A	ENSP00000359474:P225A	P	-	1	0	BARHL2	90952854	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.561000	0.98142	2.348000	0.79779	0.655000	0.94253	CCC	.	.	none		0.542	BARHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027728.2			C	91180266	G	C	91180266	3	2	11	1	0	0	0	0	1	0	0	0	1314	1174	41	4	498	4	BARHL2	1	91180266	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	37611131	91180266	158070355	11	1302											
COL11A1	1301	hgsc.bcm.edu	37	chr1	103449740	103449740	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctggtaatcctggaactccaAgttttccctacagttaaaat	12	13	6	10	0	0	0	0	0	0	0	3	1	3	1	3	2	2	3	3	2	6	5			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr1:103449740A>G	ENST00000370096.3	-	31	2822	c.2510T>C	c.(2509-2511)cTt>cCt	p.L837P	COL11A1_ENST00000353414.4_Missense_Mutation_p.L798P|COL11A1_ENST00000512756.1_Missense_Mutation_p.L721P|COL11A1_ENST00000358392.2_Missense_Mutation_p.L849P	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	837	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)		TGGAACTCCAAGTTTTCCCTA	0.249																																					p.L849P		Atlas-SNP	.											COL11A1_ENST00000370096,right_lower_lobe,carcinoma,+1,4	COL11A1	972	4	0			c.T2546C						PASS	.						62	62	62					1																	103449740		2203	4297	6500	SO:0001583	missense	1301	exon31			ACTCCAAGTTTTC	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.2510T>C	1.37:g.103449740A>G	ENSP00000359114:p.Leu837Pro	24	0	0		12	6	0.5	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	37	CCDS778.1	.	.	.	.	.	.	.	.	.	.	A	18.39	3.613637	0.66672	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000512756	D;D;D;D	0.93604	-3.25;-3.25;-3.25;-3.25	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	D	0.84133	0.5405	N	0.00303	-1.675	0.80722	D	1	P;D;D;D	0.89917	0.575;0.999;1.0;0.998	P;D;D;D	0.91635	0.563;0.998;0.999;0.995	D	0.91528	0.5240	10	0.41790	T	0.15	.	15.224	0.73336	1.0:0.0:0.0:0.0	.	721;798;849;837	E9PCU0;P12107-3;P12107-2;P12107	.;.;.;COBA1_HUMAN	P	837;849;798;721	ENSP00000359114:L837P;ENSP00000351163:L849P;ENSP00000302551:L798P;ENSP00000426533:L721P	ENSP00000302551:L798P	L	-	2	0	COL11A1	103222328	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.417000	0.90247	2.171000	0.68590	0.528000	0.53228	CTT	.	.	none		0.249	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		G	103449740	A	G	103449740	3	3	11	1	0	0	0	0	1	0	0	0	3669	72	3	3	3058	3	COL11A1	1	103449740	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	12269474	103449740	145800881	12	1303											
AMY2B	280	hgsc.bcm.edu	37	chr1	104116508	104116508	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aattttggacaaactgcataAtctaaacagtaactggttcc	15	12	6	8	0	1	0	0	0	1	0	2	1	2	1	1	2	4	3	1	2	6	6			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr1:104116508A>T	ENST00000361355.4	+	6	1308	c.692A>T	c.(691-693)aAt>aTt	p.N231I	AMY2B_ENST00000491397.1_3'UTR	NM_020978.3	NP_066188.1	P19961	AMY2B_HUMAN	amylase, alpha 2B (pancreatic)	231					carbohydrate metabolic process (GO:0005975)|digestion (GO:0007586)	extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|metal ion binding (GO:0046872)	p.N231T(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)		AAACTGCATAATCTAAACAGT	0.373																																					p.N231I		Atlas-SNP	.											AMY2B,rectum,carcinoma,0,1	AMY2B	80	1	1	Substitution - Missense(1)	large_intestine(1)	c.A692T						PASS	.						173	172	172					1																	104116508		2203	4297	6500	SO:0001583	missense	280	exon6			TGCATAATCTAAA	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.692A>T	1.37:g.104116508A>T	ENSP00000354610:p.Asn231Ile	380	0	0		321	115	0.358255	NM_020978	B3KTI1|B3KXB7|D3DT76|Q9UBH3	Missense_Mutation	SNP	ENST00000361355.4	37	CCDS782.1	.	.	.	.	.	.	.	.	.	.	A	17.88	3.497641	0.64186	.	.	ENSG00000240038	ENST00000361355	D	0.98400	-4.91	4.47	4.47	0.54385	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);	0.109676	0.64402	D	0.000011	D	0.98548	0.9515	H	0.96604	3.85	0.80722	D	1	P	0.41131	0.739	P	0.45577	0.486	D	0.99891	1.1134	10	0.87932	D	0	.	13.7962	0.63173	1.0:0.0:0.0:0.0	.	231	P19961	AMY2B_HUMAN	I	231	ENSP00000354610:N231I	ENSP00000354610:N231I	N	+	2	0	AMY2B	103918031	1.000000	0.71417	0.996000	0.52242	0.337000	0.28794	6.148000	0.71788	1.662000	0.50781	0.451000	0.29950	AAT	.	.	none		0.373	AMY2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030318.1	NM_020978		T	104116508	A	T	104116508	3	4	11	1	0	0	0	0	1	0	0	0	595	101	4	5	706	5	AMY2B	1	104116508	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	666768	104116508	145134113	13	1304											
CSDE1	7812	hgsc.bcm.edu	37	chr1	115276720	115276720	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttacaacatcacctctttCaataaagccaaatgcctcct	13	13	2	13	0	3	0	2	0	1	0	4	0	4	0	4	0	4	0	4	0	6	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr1:115276720C>A	ENST00000358528.4	-	8	1027	c.601G>T	c.(601-603)Gaa>Taa	p.E201*	CSDE1_ENST00000534699.1_Nonsense_Mutation_p.E201*|CSDE1_ENST00000438362.2_Nonsense_Mutation_p.E247*|CSDE1_ENST00000339438.6_Nonsense_Mutation_p.E170*|CSDE1_ENST00000369530.1_Nonsense_Mutation_p.E216*|CSDE1_ENST00000261443.5_Nonsense_Mutation_p.E170*|CSDE1_ENST00000530886.1_Nonsense_Mutation_p.E71*	NM_001007553.2	NP_001007554.1	O75534	CSDE1_HUMAN	cold shock domain containing E1, RNA-binding	201	CSD 3.				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)		TCACCTCTTTCAATAAAGCCA	0.323																																					p.E247X		Atlas-SNP	.											.	CSDE1	145	.	0			c.G739T						PASS	.						44	44	44					1																	115276720		2203	4300	6503	SO:0001587	stop_gained	7812	exon9			CTCTTTCAATAAA		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.601G>T	1.37:g.115276720C>A	ENSP00000351329:p.Glu201*	44	0	0		34	16	0.470588	NM_001242891	A8K281|E9PGZ0|G5E9Q2|O94961|Q5TF04|Q5TF05|Q68DF1|Q68DI9|Q9Y2S4	Nonsense_Mutation	SNP	ENST00000358528.4	37	CCDS30812.1	.	.	.	.	.	.	.	.	.	.	C	40	8.400554	0.98794	.	.	ENSG00000009307	ENST00000339438;ENST00000438362;ENST00000358528;ENST00000261443;ENST00000530886;ENST00000369530;ENST00000534699;ENST00000529046	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-7.445	20.6593	0.99626	0.0:1.0:0.0:0.0	.	.	.	.	X	170;247;201;170;71;216;201;71	.	ENSP00000261443:E170X	E	-	1	0	CSDE1	115078243	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.885000	0.99019	0.655000	0.94253	GAA	.	.	none		0.323	CSDE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033397.1	NM_007158		A	115276720	C	A	115276720	4	1	11	1	0	0	0	0	0	1	0	0	3931	835	29	4	1847	4	CSDE1	1	115276720	Nonsense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	11160212	115276720	133973901	14	1305											
SYCP1	6847	hgsc.bcm.edu	37	chr1	115487569	115487569	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taagcgatgtcaacataaaaTagctgaaatggtagcactta	17	10	8	6	1	1	1	1	1	0	0	1	2	1	1	0	1	4	3	0	1	8	5			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr1:115487569T>G	ENST00000369522.3	+	25	2360	c.2120T>G	c.(2119-2121)aTa>aGa	p.I707R	SYCP1_ENST00000369518.1_Missense_Mutation_p.I707R	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	707					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)		CAACATAAAATAGCTGAAATG	0.264																																					p.I707R		Atlas-SNP	.											.	SYCP1	149	.	0			c.T2120G						PASS	.						39	40	40					1																	115487569		2200	4280	6480	SO:0001583	missense	6847	exon25			ATAAAATAGCTGA	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.2120T>G	1.37:g.115487569T>G	ENSP00000358535:p.Ile707Arg	137	0	0		120	42	0.35	NM_003176	O14963|Q5VXJ6	Missense_Mutation	SNP	ENST00000369522.3	37	CCDS879.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.043678	0.75732	.	.	ENSG00000198765	ENST00000369522;ENST00000536734;ENST00000455987;ENST00000369518	T;T;T	0.56611	0.45;0.45;0.45	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	T	0.65439	0.2691	M	0.74258	2.255	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.998	T	0.71477	-0.4581	10	0.72032	D	0.01	-13.3514	14.2117	0.65769	0.0:0.0:0.0:1.0	.	707;707	B7ZLS9;Q15431	.;SYCP1_HUMAN	R	707	ENSP00000358535:I707R;ENSP00000410011:I707R;ENSP00000358531:I707R	ENSP00000358531:I707R	I	+	2	0	SYCP1	115289092	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.517000	0.67061	1.840000	0.53500	0.528000	0.53228	ATA	.	.	none		0.264	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176		G	115487569	T	G	115487569	3	3	11	1	0	0	0	0	1	0	0	0	15446	1406	49	5	2214	5	SYCP1	1	115487569	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	210849	115487569	133763052	15	1306											
FLG	2312	hgsc.bcm.edu	37	chr1	152284337	152284337	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	accagaggaagtctctgcgtGaggagttcctgattgtctgg	8	11	14	8	1	2	3	0	2	2	1	4	5	3	5	2	3	1	1	2	3	1	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr1:152284337G>C	ENST00000368799.1	-	3	3060	c.3025C>G	c.(3025-3027)Cac>Gac	p.H1009D	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	1009	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)			GTCTCTGCGTGAGGAGTTCCT	0.582									Ichthyosis																												p.H1009D		Atlas-SNP	.											.	FLG	900	.	0			c.C3025G						PASS	.						304	306	305					1																	152284337		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTGCGTGAGGAGT	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.3025C>G	1.37:g.152284337G>C	ENSP00000357789:p.His1009Asp	440	1	0.00227273		342	121	0.353801	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	g	3.802	-0.041479	0.07452	.	.	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.00801	5.68	1.92	1.92	0.25849	.	.	.	.	.	T	0.00384	0.0012	M	0.76574	2.34	0.09310	N	1	P	0.41232	0.743	B	0.26094	0.066	T	0.38845	-0.9642	9	0.12430	T	0.62	.	7.4495	0.27229	0.0:0.0:1.0:0.0	.	1009	P20930	FILA_HUMAN	D	1009;216	ENSP00000357789:H1009D	ENSP00000357789:H1009D	H	-	1	0	FLG	150550961	0.023000	0.18921	0.002000	0.10522	0.005000	0.04900	0.112000	0.15479	1.409000	0.46915	0.291000	0.19559	CAC	.	.	none		0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		C	152284337	G	C	152284337	3	2	11	1	0	0	0	0	1	0	0	0	5930	1290	45	4	9164	4	FLG	1	152284337	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	36796768	152284337	96966284	16	1307											
MEX3A	92312	hgsc.bcm.edu	37	chr1	156047300	156047300	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacaccaaaggcggcgcctgActtgttgcgggaggcacgga	9	5	15	12	4	0	1	0	1	0	0	0	3	0	3	2	5	1	2	2	5	1	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr1:156047300A>G	ENST00000532414.2	-	2	627	c.628T>C	c.(628-630)Tca>Cca	p.S210P	MEX3A_ENST00000442784.1_5'UTR|AL355388.1_ENST00000410679.1_RNA	NM_001093725.1	NP_001087194.1	A1L020	MEX3A_HUMAN	mex-3 RNA binding family member A	210						cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)	9	Hepatocellular(266;0.158)|all_neural(408;0.195)					GCGGCGCCTGACTTGTTGCGG	0.672																																					p.S210P		Atlas-SNP	.											.	MEX3A	33	.	0			c.T628C						PASS	.						40	48	45					1																	156047300		2159	4272	6431	SO:0001583	missense	92312	exon2			CGCCTGACTTGTT	AK024097	CCDS53377.1	1q22	2013-09-24	2013-08-21	2007-07-18	ENSG00000254726	ENSG00000254726		"RING-type (C3HC4) zinc fingers", "Mex-3 homologs"	33482	protein-coding gene	gene with protein product		611007	"ring finger and KH domain containing 4", "mex-3 homolog A (C. elegans)"	RKHD4		17267406	Standard	NM_001093725		Approved		uc001fnd.4	A1L020	OTTHUMG00000017465	ENST00000532414.2:c.628T>C	1.37:g.156047300A>G	ENSP00000432845:p.Ser210Pro	140	0	0		108	7	0.0648148	NM_001093725		Missense_Mutation	SNP	ENST00000532414.2	37	CCDS53377.1	.	.	.	.	.	.	.	.	.	.	A	12.75	2.032059	0.35893	.	.	ENSG00000254726	ENST00000532414	T	0.47869	0.83	5.15	3.95	0.45737	.	0.280783	0.30293	N	0.009946	T	0.14270	0.0345	N	0.19112	0.55	0.31477	N	0.667688	P	0.44195	0.828	B	0.36289	0.221	T	0.05273	-1.0895	10	0.38643	T	0.18	.	9.7334	0.40374	0.6547:0.3453:0.0:0.0	.	210	A1L020	MEX3A_HUMAN	P	210	ENSP00000432845:S210P	ENSP00000432845:S210P	S	-	1	0	MEX3A	154313924	0.999000	0.42202	0.995000	0.50966	0.944000	0.59088	2.028000	0.41088	1.950000	0.56595	0.379000	0.24179	TCA	.	.	none		0.672	MEX3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046218.3	NM_001093725		G	156047300	A	G	156047300	3	3	11	1	0	0	0	0	1	0	0	0	9518	275	10	3	938	3	MEX3A	1	156047300	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	3762963	156047300	93203321	17	1308											
PEAR1	375033	hgsc.bcm.edu	37	chr1	156883019	156883019	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctacagtcactactactccaAccccagctaccacaccctgt	11	8	3	19	0	1	0	1	0	0	0	2	0	2	0	5	0	6	1	5	0	5	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr1:156883019A>T	ENST00000338302.3	+	20	2681	c.2456A>T	c.(2455-2457)aAc>aTc	p.N819I	PEAR1_ENST00000292357.7_Missense_Mutation_p.N819I			Q5VY43	PEAR1_HUMAN	platelet endothelial aggregation receptor 1	819	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)					TACTACTCCAACCCCAGCTAC	0.602																																					p.N819I		Atlas-SNP	.											.	PEAR1	118	.	0			c.A2456T						PASS	.						134	127	130					1																	156883019		2203	4300	6503	SO:0001583	missense	375033	exon19			ACTCCAACCCCAG	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.2456A>T	1.37:g.156883019A>T	ENSP00000344465:p.Asn819Ile	133	0	0		108	50	0.462963	NM_001080471	Q8TEK2	Missense_Mutation	SNP	ENST00000338302.3	37	CCDS30892.1	.	.	.	.	.	.	.	.	.	.	A	30	5.050917	0.93740	.	.	ENSG00000187800	ENST00000338302;ENST00000292357	D;D	0.92446	-3.04;-3.04	5.41	5.41	0.78517	.	0.000000	0.52532	D	0.000068	D	0.94568	0.8250	M	0.71036	2.16	0.54753	D	0.999983	D	0.89917	1.0	D	0.87578	0.998	D	0.95172	0.8291	10	0.72032	D	0.01	.	13.4467	0.61144	1.0:0.0:0.0:0.0	.	819	Q5VY43	PEAR1_HUMAN	I	819	ENSP00000344465:N819I;ENSP00000292357:N819I	ENSP00000292357:N819I	N	+	2	0	PEAR1	155149643	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.227000	0.89787	2.272000	0.75746	0.460000	0.39030	AAC	.	.	none		0.602	PEAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098937.2	NM_001080471		T	156883019	A	T	156883019	3	4	11	1	0	0	0	0	1	0	0	0	11721	43	2	5	2526	5	PEAR1	1	156883019	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	835719	156883019	92367602	18	1309											
SLAMF6	114836	hgsc.bcm.edu	37	chr1	160461146	160461146	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catattctgaaatagctgacTgtgattggtaacttgtatgt	11	16	9	5	0	1	3	0	3	1	0	1	3	1	3	0	1	2	3	0	1	5	7			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr1:160461146T>C	ENST00000368057.3	-	3	475	c.415A>G	c.(415-417)Agt>Ggt	p.S139G	SLAMF6_ENST00000368055.1_Missense_Mutation_p.S28G|SLAMF6_ENST00000368059.3_Missense_Mutation_p.S139G			Q96DU3	SLAF6_HUMAN	SLAM family member 6	139	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)			AATAGCTGACTGTGATTGGTA	0.428																																					p.S139G		Atlas-SNP	.											.	SLAMF6	46	.	0			c.A415G						PASS	.						109	104	106					1																	160461146		2203	4300	6503	SO:0001583	missense	114836	exon3			GCTGACTGTGATT	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.415A>G	1.37:g.160461146T>C	ENSP00000357036:p.Ser139Gly	84	0	0		95	36	0.378947	NM_052931	A6NMW2|B2R8X8|Q14CF0|Q5TAS4|Q5TAS6|Q5TAT3|Q96DV0	Missense_Mutation	SNP	ENST00000368057.3	37	CCDS53394.1	.	.	.	.	.	.	.	.	.	.	T	13.47	2.247160	0.39697	.	.	ENSG00000162739	ENST00000368059;ENST00000368057;ENST00000368055	T;T;T	0.38887	1.11;1.11;1.11	4.37	-3.72	0.04411	Immunoglobulin-like fold (1);	1.726580	0.02671	N	0.108596	T	0.18718	0.0449	M	0.65975	2.015	0.09310	N	1	P;P;D;D;D;D	0.61080	0.897;0.897;0.986;0.986;0.989;0.989	P;P;P;B;P;P	0.46299	0.459;0.459;0.494;0.376;0.511;0.511	T	0.20405	-1.0276	10	0.23891	T	0.37	-0.0012	0.4572	0.00511	0.3174:0.2848:0.1478:0.25	.	28;28;90;139;139;139	B7Z6A7;Q5TAS6;B4E1U5;Q96DU3-2;Q96DU3;B2R8X8	.;.;.;.;SLAF6_HUMAN;.	G	139;139;28	ENSP00000357038:S139G;ENSP00000357036:S139G;ENSP00000357034:S28G	ENSP00000357034:S28G	S	-	1	0	SLAMF6	158727770	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.900000	0.04097	-0.582000	0.05929	0.533000	0.62120	AGT	.	.	none		0.428	SLAMF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059010.1	NM_052931		C	160461146	T	C	160461146	3	2	11	1	0	0	0	0	1	0	0	0	14383	1580	55	3	607	3	SLAMF6	1	160461146	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	3578127	160461146	88789475	19	1310											
DUSP27	92235	hgsc.bcm.edu	37	chr1	167097477	167097477	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	caagttcccgagaggagagcCcagagccctacttcttccgc	9	7	10	15	2	1	3	0	0	1	3	3	5	3	3	4	1	3	1	4	1	2	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr1:167097477C>T	ENST00000361200.2	+	6	3275	c.3109C>T	c.(3109-3111)Cca>Tca	p.P1037S	DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000443333.1_Missense_Mutation_p.P1037S|DUSP27_ENST00000271385.5_Missense_Mutation_p.P1037S			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	1037					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						AGAGGAGAGCCCAGAGCCCTA	0.587																																					p.P1037S		Atlas-SNP	.											.	DUSP27	235	.	0			c.C3109T						PASS	.						36	40	39					1																	167097477		2203	4300	6503	SO:0001583	missense	92235	exon5			GAGAGCCCAGAGC	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.3109C>T	1.37:g.167097477C>T	ENSP00000354483:p.Pro1037Ser	99	0	0		88	41	0.465909	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	37	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	C	19.12	3.766633	0.69878	.	.	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.03663	3.85;3.85;3.85	5.42	5.42	0.78866	.	0.000000	0.50627	D	0.000120	T	0.12433	0.0302	M	0.65975	2.015	0.44956	D	0.997975	D	0.89917	1.0	D	0.83275	0.996	T	0.01152	-1.1435	10	0.87932	D	0	-14.3953	19.2273	0.93822	0.0:1.0:0.0:0.0	.	1037	Q5VZP5	DUS27_HUMAN	S	1037	ENSP00000354483:P1037S;ENSP00000271385:P1037S;ENSP00000404874:P1037S	ENSP00000271385:P1037S	P	+	1	0	DUSP27	165364101	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	3.548000	0.53670	2.530000	0.85305	0.643000	0.83706	CCA	.	.	none		0.587	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		T	167097477	C	T	167097477	3	4	11	1	0	0	0	0	1	0	0	0	4826	623	22	2	3127	2	DUSP27	1	167097477	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	6636331	167097477	82153144	20	1311											
ADORA1	134	hgsc.bcm.edu	37	chr1	203134499	203134499	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggctggaacaatctgagtgCggtggagcgggcctgggcag	7	7	19	8	2	1	1	0	1	1	0	1	3	1	3	1	6	3	2	1	6	2	0	rs145647777	byFrequency	TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr1:203134499C>T	ENST00000367236.4	+	3	1373	c.452C>T	c.(451-453)gCg>gTg	p.A151V	ADORA1_ENST00000472535.1_3'UTR|ADORA1_ENST00000309502.3_Missense_Mutation_p.A151V|ADORA1_ENST00000367235.1_3'UTR|ADORA1_ENST00000337894.4_Missense_Mutation_p.A151V	NM_001048230.1	NP_001041695.1	P30542	AA1R_HUMAN	adenosine A1 receptor	151					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)	AATCTGAGTGCGGTGGAGCGG	0.622																																					p.A151V		Atlas-SNP	.											.	ADORA1	62	.	0			c.C452T						PASS	.	C	VAL/ALA,VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	96	98	97		452,452	-2.5	0	1	dbSNP_134	97	3,8597	3.0+/-9.4	0,3,4297	no	missense,missense	ADORA1	NM_000674.2,NM_001048230.1	64,64	0,4,6499	TT,TC,CC		0.0349,0.0227,0.0308	benign,benign	151/327,151/327	203134499	4,13002	2203	4300	6503	SO:0001583	missense	134	exon3			TGAGTGCGGTGGA	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.452C>T	1.37:g.203134499C>T	ENSP00000356205:p.Ala151Val	157	0	0		128	60	0.46875	NM_001048230	A6NFY5|A6NGP4|A8K1L3|B3KXQ4|D2CGD0|Q6FHK3|Q8TAM8	Missense_Mutation	SNP	ENST00000367236.4	37	CCDS1434.1	.	.	.	.	.	.	.	.	.	.	C	9.043	0.990226	0.18966	2.27E-4	3.49E-4	ENSG00000163485	ENST00000309502;ENST00000367236;ENST00000337894	T;T;T	0.36699	1.24;1.24;1.24	5.04	-2.45	0.06481	GPCR, rhodopsin-like superfamily (1);	1.079960	0.06915	N	0.808370	T	0.19005	0.0456	N	0.12471	0.22	0.09310	N	1	B;B;B	0.14438	0.007;0.01;0.0	B;B;B	0.12156	0.005;0.007;0.002	T	0.27400	-1.0075	10	0.30854	T	0.27	-2.041	7.6008	0.28075	0.4019:0.3808:0.0:0.2173	.	184;83;151	B7Z379;B7Z1L9;P30542	.;.;AA1R_HUMAN	V	151	ENSP00000308549:A151V;ENSP00000356205:A151V;ENSP00000338435:A151V	ENSP00000308549:A151V	A	+	2	0	ADORA1	201401122	0.001000	0.12720	0.029000	0.17559	0.521000	0.34408	0.081000	0.14823	-0.240000	0.09696	-0.538000	0.04264	GCG	C|1.000;T|0.000	0.000	strong		0.622	ADORA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100273.1	NM_000674		T	203134499	C	T	203134499	3	4	11	1	0	0	0	0	1	0	0	0	326	768	27	1	458	1	ADORA1	1	203134499	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	36037022	203134499	46116122	21	1312											
PROX1	5629	hgsc.bcm.edu	37	chr1	214178516	214178516	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attgcatcctacatgcaggaAggattgtcacccaatcactt	12	11	7	11	0	2	0	2	0	0	0	3	2	3	2	2	2	3	2	2	2	3	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr1:214178516A>C	ENST00000366958.4	+	3	2342	c.1734A>C	c.(1732-1734)gaA>gaC	p.E578D	PROX1_ENST00000261454.4_Missense_Mutation_p.E578D|PROX1_ENST00000435016.1_Missense_Mutation_p.E578D|PROX1_ENST00000498508.2_Missense_Mutation_p.E578D	NM_001270616.1	NP_001257545.1	Q92786	PROX1_HUMAN	prospero homeobox 1	578					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)		ACATGCAGGAAGGATTGTCAC	0.473																																					p.E578D		Atlas-SNP	.											.	PROX1	124	.	0			c.A1734C						PASS	.						107	106	106					1																	214178516		2203	4300	6503	SO:0001583	missense	5629	exon3			GCAGGAAGGATTG	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.1734A>C	1.37:g.214178516A>C	ENSP00000355925:p.Glu578Asp	122	0	0		98	31	0.316327	NM_001270616	A6NK29|A8K2B1|Q5SW76|Q8TB91	Missense_Mutation	SNP	ENST00000366958.4	37	CCDS31021.1	.	.	.	.	.	.	.	.	.	.	A	16.78	3.219080	0.58560	.	.	ENSG00000117707	ENST00000541470;ENST00000498508;ENST00000366958;ENST00000435016;ENST00000261454	T;T;T;T	0.47528	0.84;0.84;0.84;0.84	5.78	5.78	0.91487	Homeo-prospero domain (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	T	0.58906	0.2155	M	0.81942	2.565	0.80722	D	1	P	0.38455	0.632	P	0.46389	0.515	T	0.64390	-0.6419	10	0.72032	D	0.01	-4.296	10.4496	0.44513	0.9278:0.0:0.0722:0.0	.	578	Q92786	PROX1_HUMAN	D	150;578;578;578;578	ENSP00000420283:E578D;ENSP00000355925:E578D;ENSP00000400694:E578D;ENSP00000261454:E578D	ENSP00000261454:E578D	E	+	3	2	PROX1	212245139	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.179000	0.50887	2.200000	0.70718	0.460000	0.39030	GAA	.	.	none		0.473	PROX1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089727.6	NM_002763		C	214178516	A	C	214178516	3	2	11	1	0	0	0	0	1	0	0	0	12572	69	3	5	1740	5	PROX1	1	214178516	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	11044017	214178516	35072105	22	1313											
RYR2	6262	hgsc.bcm.edu	37	chr1	237580416	237580416	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttggagactagagacgctaAgagttgcgtaagtagaactt	13	11	12	5	2	0	4	0	0	0	4	0	6	0	4	0	1	2	4	0	1	5	7			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr1:237580416A>C	ENST00000366574.2	+	11	1158	c.841A>C	c.(841-843)Aga>Cga	p.R281R	RYR2_ENST00000360064.6_Silent_p.R279R|RYR2_ENST00000542537.1_Silent_p.R265R	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	281					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)			AGAGACGCTAAGAGTTGCGTA	0.443																																					p.R281R		Atlas-SNP	.											RYR2,NS,carcinoma,-1,2	RYR2	1273	2	0			c.A841C						PASS	.						120	117	118					1																	237580416		2050	4217	6267	SO:0001819	synonymous_variant	6262	exon11			ACGCTAAGAGTTG	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.841A>C	1.37:g.237580416A>C		65	0	0		63	22	0.349206	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	37	CCDS55691.1																																																																																			.	.	none		0.443	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		C	237580416	A	C	237580416	2	2	11	1	0	0	0	0	0	0	0	1	13784	64	3	5		5	RYR2	1	237580416	Silent	SNP	A	TCGA-FF-8042-01A-11D-2210-10	23401900	237580416	11670205	23	1314											
OR2M2	391194	hgsc.bcm.edu	37	chr1	248344182	248344182	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccgcaacaaggaggtgactAgagcattcatgaagatctta	14	9	10	8	1	2	4	1	2	1	2	3	5	3	5	1	2	2	2	1	2	5	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr1:248344182A>G	ENST00000359682.2	+	1	895	c.895A>G	c.(895-897)Aga>Gga	p.R299G		NM_001004688.1	NP_001004688.1	Q96R28	OR2M2_HUMAN	olfactory receptor, family 2, subfamily M, member 2	299						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)			GGAGGTGACTAGAGCATTCAT	0.438																																					p.R299G		Atlas-SNP	.											.	OR2M2	149	.	0			c.A895G						PASS	.						206	199	201					1																	248344182		2203	4300	6503	SO:0001583	missense	391194	exon1			GTGACTAGAGCAT	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.895A>G	1.37:g.248344182A>G	ENSP00000352710:p.Arg299Gly	295	0	0		137	93	0.678832	NM_001004688	A3KFT4	Missense_Mutation	SNP	ENST00000359682.2	37	CCDS31106.1	.	.	.	.	.	.	.	.	.	.	a	0.003	-2.433136	0.00182	.	.	ENSG00000198601	ENST00000359682	T	0.39056	1.1	2.03	-4.06	0.03986	.	.	.	.	.	T	0.15392	0.0371	N	0.12471	0.22	0.09310	N	1	B	0.17268	0.021	B	0.15484	0.013	T	0.28870	-1.0030	9	0.02654	T	1	.	3.493	0.07645	0.1485:0.1352:0.5811:0.1351	.	299	Q96R28	OR2M2_HUMAN	G	299	ENSP00000352710:R299G	ENSP00000352710:R299G	R	+	1	2	OR2M2	246410805	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.567000	0.05916	-1.524000	0.01764	-0.478000	0.04885	AGA	.	.	none		0.438	OR2M2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097356.2	NM_001004688		G	248344182	A	G	248344182	3	3	11	1	0	0	0	0	1	0	0	0	11019	412	15	3	897	3	OR2M2	1	248344182	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	10763766	248344182	906439	24	1315											
OR2M3	127062	hgsc.bcm.edu	37	chr1	248366819	248366819	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	atgactgccttttcctggatCctgggctctacggatggaat	7	13	11	10	1	1	1	0	1	1	0	3	4	3	4	3	4	2	1	3	4	2	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr1:248366819C>T	ENST00000456743.1	+	1	488	c.450C>T	c.(448-450)atC>atT	p.I150I		NM_001004689.1	NP_001004689.1	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M, 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)			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)			TTTCCTGGATCCTGGGCTCTA	0.468																																					p.I150I		Atlas-SNP	.											.	OR2M3	116	.	0			c.C450T						PASS	.						202	196	198					1																	248366819		2203	4300	6503	SO:0001819	synonymous_variant	127062	exon1			CTGGATCCTGGGC		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.450C>T	1.37:g.248366819C>T		384	1	0.00260417		180	116	0.644444	NM_001004689	B9EH06|Q6IEY0	Silent	SNP	ENST00000456743.1	37	CCDS31107.1																																																																																			.	.	none		0.468	OR2M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097355.1	NM_001004689		T	248366819	C	T	248366819	2	4	11	1	0	0	0	0	0	0	0	1	11020	845	30	2		2	OR2M3	1	248366819	Silent	SNP	C	TCGA-FF-8042-01A-11D-2210-10	22637	248366819	883802	25	1316											
DPYSL5	56896	hgsc.bcm.edu	37	chr2	27163001	27163001	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcccacatggagtgagtggCgtgcaggaccgcatgagcgt	9	7	15	10	3	0	2	0	2	0	0	1	4	1	4	2	3	2	2	2	3	0	0			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr2:27163001C>T	ENST00000288699.6	+	9	1208	c.1050C>T	c.(1048-1050)ggC>ggT	p.G350G	DPYSL5_ENST00000401478.1_Silent_p.G350G	NM_001253724.1|NM_020134.3	NP_001240653.1|NP_064519.2	Q9BPU6	DPYL5_HUMAN	dihydropyrimidinase-like 5	350					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)					GAGTGAGTGGCGTGCAGGACC	0.552																																					p.G350G		Atlas-SNP	.											.	DPYSL5	69	.	0			c.C1050T						PASS	.						165	140	148					2																	27163001		2203	4300	6503	SO:0001819	synonymous_variant	56896	exon9			GAGTGGCGTGCAG	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.1050C>T	2.37:g.27163001C>T		58	0	0		65	20	0.307692	NM_001253724	Q8TCL6|Q9NQC4|Q9NRY9	Silent	SNP	ENST00000288699.6	37	CCDS1730.1																																																																																			.	.	none		0.552	DPYSL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214187.2	NM_020134		T	27163001	C	T	27163001	2	4	11	1	0	0	0	0	0	0	0	1	4752	755	27	1		1	DPYSL5	2	27163001	Silent	SNP	C	TCGA-FF-8042-01A-11D-2210-10		27163001	216036372	26	1317											
FAM179A	165186	hgsc.bcm.edu	37	chr2	29225519	29225519	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctctcatccagagcatccCtaccacccctgaggccagcg	8	6	8	19	1	1	2	1	1	1	1	4	2	3	2	7	1	3	1	7	1	1	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr2:29225519C>T	ENST00000379558.4	+	5	896	c.545C>T	c.(544-546)cCt>cTt	p.P182L	FAM179A_ENST00000403861.2_Missense_Mutation_p.P182L	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	182										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						CAGAGCATCCCTACCACCCCT	0.652																																					p.P182L		Atlas-SNP	.											.	FAM179A	106	.	0			c.C545T						PASS	.						31	38	36					2																	29225519		1994	4161	6155	SO:0001583	missense	165186	exon5			GCATCCCTACCAC	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.545C>T	2.37:g.29225519C>T	ENSP00000368876:p.Pro182Leu	156	0	0		95	35	0.368421	NM_199280	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	37	CCDS1769.2	.	.	.	.	.	.	.	.	.	.	C	17.06	3.291836	0.59976	.	.	ENSG00000189350	ENST00000379558;ENST00000403861	T;T	0.52526	1.47;0.66	5.03	5.03	0.67393	.	.	.	.	.	T	0.57740	0.2074	L	0.32530	0.975	0.43632	D	0.996029	D;P	0.89917	1.0;0.779	D;B	0.91635	0.999;0.251	T	0.61357	-0.7079	9	0.87932	D	0	.	13.87	0.63612	0.0:1.0:0.0:0.0	.	182;182	F8W8E4;Q6ZUX3	.;F179A_HUMAN	L	182	ENSP00000368876:P182L;ENSP00000384699:P182L	ENSP00000368876:P182L	P	+	2	0	FAM179A	29079023	0.966000	0.33281	1.000000	0.80357	0.304000	0.27724	2.654000	0.46699	2.319000	0.78375	0.555000	0.69702	CCT	.	.	none		0.652	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280		T	29225519	C	T	29225519	3	4	11	1	0	0	0	0	1	0	0	0	5510	681	24	2	559	2	FAM179A	2	29225519	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	2062518	29225519	213973854	27	1318											
TTC7A	57217	hgsc.bcm.edu	37	chr2	47249048	47249048	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atggtgatcagcctcggagaGgaagccggggagttcctccc	8	7	15	11	2	1	2	1	1	0	1	4	5	3	4	4	5	2	1	4	5	1	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr2:47249048G>A	ENST00000319190.5	+	12	1808	c.1440G>A	c.(1438-1440)gaG>gaA	p.E480E	TTC7A_ENST00000263737.6_Silent_p.E126E|TTC7A_ENST00000409245.1_Silent_p.E446E|TTC7A_ENST00000461601.1_3'UTR|TTC7A_ENST00000394850.2_Silent_p.E480E	NM_020458.2	NP_065191.2	Q9ULT0	TTC7A_HUMAN	tetratricopeptide repeat domain 7A	480					cellular iron ion homeostasis (GO:0006879)|hemopoiesis (GO:0030097)					breast(4)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.18)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			GCCTCGGAGAGGAAGCCGGGG	0.602																																					p.E480E		Atlas-SNP	.											.	TTC7A	80	.	0			c.G1440A						PASS	.						107	104	105					2																	47249048		2203	4300	6503	SO:0001819	synonymous_variant	57217	exon12			CGGAGAGGAAGCC	AB032966	CCDS33193.1, CCDS74510.1, CCDS74511.1	2p16.3	2013-01-10	2004-06-02	2004-06-02	ENSG00000068724	ENSG00000068724		"Tetratricopeptide (TTC) repeat domain containing"	19750	protein-coding gene	gene with protein product		609332	"tetratricopeptide repeat domain 7"	TTC7		10574461	Standard	XM_005264439		Approved	KIAA1140	uc002rvo.3	Q9ULT0	OTTHUMG00000153121	ENST00000319190.5:c.1440G>A	2.37:g.47249048G>A		78	0	0		81	4	0.0493827	NM_020458	Q6PIX4|Q8ND67|Q9BUS3	Silent	SNP	ENST00000319190.5	37	CCDS33193.1																																																																																			.	.	none		0.602	TTC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329667.2	XM_372927		A	47249048	G	A	47249048	2	1	11	1	0	0	0	0	0	0	0	1	16727	991	35	2		2	TTC7A	2	47249048	Silent	SNP	G	TCGA-FF-8042-01A-11D-2210-10	18023529	47249048	195950325	28	1319											
RETSAT	54884	hgsc.bcm.edu	37	chr2	85577909	85577909	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	catgtccatgttaccttaacCagctttatatacttgtcaat	11	16	4	10	0	1	0	1	0	0	0	2	0	2	0	3	0	4	2	3	0	6	7			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr2:85577909C>A	ENST00000295802.4	-	3	703	c.591G>T	c.(589-591)ctG>ctT	p.L197L	RETSAT_ENST00000263854.6_Silent_p.L197L|RETSAT_ENST00000457495.2_Silent_p.L136L	NM_017750.3	NP_060220.3	Q6NUM9	RETST_HUMAN	retinol saturase (all-trans-retinol 13,14-reductase)	197					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)	TTACCTTAACCAGCTTTATAT	0.473																																					p.L197L		Atlas-SNP	.											.	RETSAT	56	.	0			c.G591T						PASS	.						161	158	159					2																	85577909		2203	4300	6503	SO:0001819	synonymous_variant	54884	exon3			CTTAACCAGCTTT	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.591G>T	2.37:g.85577909C>A		140	0	0		124	46	0.370968	NM_017750	A6NIK3|Q53R95|Q53SA9|Q6UX05|Q8N2H5|Q96FA4|Q9NXE5	Silent	SNP	ENST00000295802.4	37	CCDS1972.1	.	.	.	.	.	.	.	.	.	.	C	8.785	0.929119	0.18131	.	.	ENSG00000042445	ENST00000409984	.	.	.	5.92	5.03	0.67393	.	.	.	.	.	T	0.70675	0.3251	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.70029	-0.4984	4	.	.	.	-9.9361	14.7022	0.69164	0.0:0.854:0.146:0.0	.	.	.	.	L	136	.	.	W	-	2	0	RETSAT	85431420	0.089000	0.21612	0.998000	0.56505	0.939000	0.58152	0.046000	0.14035	1.478000	0.48253	0.655000	0.94253	TGG	.	.	none		0.473	RETSAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252489.1	NM_017750		A	85577909	C	A	85577909	2	1	11	1	0	0	0	0	0	0	0	1	13253	581	21	4		4	RETSAT	2	85577909	Silent	SNP	C	TCGA-FF-8042-01A-11D-2210-10	38328861	85577909	157621464	29	1320											
PROM2	150696	hgsc.bcm.edu	37	chr2	95953995	95953995	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccacctgccagcccctctccGgagccctggacaacagccgt	7	5	9	20	2	1	0	0	0	1	0	2	2	1	2	8	2	5	0	8	2	1	0			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr2:95953995G>A	ENST00000317620.9	+	21	2414	c.2281G>A	c.(2281-2283)Gga>Aga	p.G761R	PROM2_ENST00000542147.1_Missense_Mutation_p.G712R|PROM2_ENST00000317668.4_Missense_Mutation_p.G761R|PROM2_ENST00000403131.2_Missense_Mutation_p.G761R	NM_001165978.1	NP_001159450.1	Q8N271	PROM2_HUMAN	prominin 2	761					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						GCCCCTCTCCGGAGCCCTGGA	0.622																																					p.G761R		Atlas-SNP	.											PROM2,NS,carcinoma,-1,1	PROM2	78	1	0			c.G2281A						scavenged	.						110	109	109					2																	95953995		2203	4300	6503	SO:0001583	missense	150696	exon21			CTCTCCGGAGCCC	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.2281G>A	2.37:g.95953995G>A	ENSP00000318270:p.Gly761Arg	79	0	0		68	3	0.0441176	NM_001165977	A8K2V1|Q2HIX6|Q8NB84|Q8TAE2	Missense_Mutation	SNP	ENST00000317620.9	37	CCDS2012.1	.	.	.	.	.	.	.	.	.	.	G	0.091	-1.167753	0.01660	.	.	ENSG00000155066	ENST00000403131;ENST00000317668;ENST00000317620;ENST00000542147	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	5.58	0.453	0.16639	.	1.356780	0.04605	N	0.399145	T	0.27765	0.0683	L	0.38175	1.15	0.09310	N	1	B	0.16396	0.017	B	0.14023	0.01	T	0.11060	-1.0603	10	0.13853	T	0.58	3.5562	1.1033	0.01688	0.2652:0.1535:0.4234:0.1579	.	761	Q8N271	PROM2_HUMAN	R	761;761;761;712	ENSP00000385716:G761R;ENSP00000318520:G761R;ENSP00000318270:G761R;ENSP00000442542:G712R	ENSP00000318270:G761R	G	+	1	0	PROM2	95317722	0.000000	0.05858	0.000000	0.03702	0.093000	0.18481	0.021000	0.13489	0.014000	0.14944	0.655000	0.94253	GGA	.	.	none		0.622	PROM2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252771.1	NM_144707		A	95953995	G	A	95953995	3	1	11	1	0	0	0	0	1	0	0	0	12568	1117	39	1	2363	1	PROM2	2	95953995	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	10376086	95953995	147245378	30	1321											
DPP10	57628	hgsc.bcm.edu	37	chr2	116257116	116257116	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggtgtataaaagcgagaatgGacatgtcattaaactgaata	17	10	10	4	1	1	2	1	1	0	1	1	4	1	3	0	2	2	1	0	2	8	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr2:116257116G>T	ENST00000410059.1	+	4	782	c.302G>T	c.(301-303)gGa>gTa	p.G101V	DPP10_ENST00000409163.1_Missense_Mutation_p.G51V|DPP10_ENST00000393147.2_Missense_Mutation_p.G105V|DPP10_ENST00000488208.1_3'UTR|DPP10_ENST00000310323.8_Missense_Mutation_p.G94V	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	101						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						AGCGAGAATGGACATGTCATT	0.294																																					p.G105V		Atlas-SNP	.											.	DPP10	415	.	0			c.G314T						PASS	.						148	143	145					2																	116257116		2203	4300	6503	SO:0001583	missense	57628	exon4			AGAATGGACATGT	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.302G>T	2.37:g.116257116G>T	ENSP00000386565:p.Gly101Val	204	0	0		134	51	0.380597	NM_001178034	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	37	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.940675	0.73557	.	.	ENSG00000175497	ENST00000436732;ENST00000410059;ENST00000409163;ENST00000393146;ENST00000393147;ENST00000310323;ENST00000419287;ENST00000476155	T;T;T;T;T;T;T	0.69685	-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	D	0.82939	0.5146	M	0.84082	2.675	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	0.85227	0.1030	10	0.87932	D	0	-32.1676	16.0293	0.80567	0.0:0.0:1.0:0.0	.	94;105;97;101	Q8N608-2;Q0GLB8;Q0GLB9;Q8N608	.;.;.;DPP10_HUMAN	V	51;101;51;97;105;94;51;51	ENSP00000391092:G51V;ENSP00000386565:G101V;ENSP00000387038:G51V;ENSP00000376854:G97V;ENSP00000376855:G105V;ENSP00000309066:G94V;ENSP00000402499:G51V	ENSP00000309066:G94V	G	+	2	0	DPP10	115973586	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.323000	0.72891	2.705000	0.92388	0.561000	0.74099	GGA	.	.	none		0.294	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		T	116257116	G	T	116257116	3	4	11	1	0	0	0	0	1	0	0	0	4729	1174	41	4	487	4	DPP10	2	116257116	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	20303121	116257116	126942257	31	1322											
PTPN4	5775	hgsc.bcm.edu	37	chr2	120725435	120725435	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctggaatcggaagaactgggGttcttattactatggaaaca	13	11	11	6	1	1	1	0	0	1	1	2	4	1	4	0	5	3	1	0	5	7	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr2:120725435G>A	ENST00000263708.2	+	26	3352	c.2581G>A	c.(2581-2583)Gtt>Att	p.V861I	PTPN4_ENST00000544261.1_Missense_Mutation_p.V494I	NM_002830.3	NP_002821.1	P29074	PTN4_HUMAN	protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)	861	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)			endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|urinary_tract(1)	30					Alendronate(DB00630)	AAGAACTGGGGTTCTTATTAC	0.378																																					p.V861I		Atlas-SNP	.											.	PTPN4	89	.	0			c.G2581A						PASS	.						160	160	160					2																	120725435		2203	4300	6503	SO:0001583	missense	5775	exon26			ACTGGGGTTCTTA		CCDS2129.1	2q14.2	2011-06-09			ENSG00000088179	ENSG00000088179		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9656	protein-coding gene	gene with protein product		176878				1648233	Standard	NM_002830		Approved	PTPMEG	uc002tmf.2	P29074	OTTHUMG00000131436	ENST00000263708.2:c.2581G>A	2.37:g.120725435G>A	ENSP00000263708:p.Val861Ile	59	0	0		52	19	0.365385	NM_002830	B2RBV8|Q9UDA7	Missense_Mutation	SNP	ENST00000263708.2	37	CCDS2129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	35|35	5.437199|5.437199	0.96168|0.96168	.|.	.|.	ENSG00000088179|ENSG00000088179	ENST00000441089|ENST00000263708;ENST00000544261	T|T;T	0.29142|0.15256	1.58|2.44;2.44	5.2|5.2	5.2|5.2	0.72013|0.72013	.|Protein-tyrosine phosphatase, receptor/non-receptor type (4);Protein-tyrosine/Dual-specificity phosphatase (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.34542|0.34542	0.0901|0.0901	M|M	0.88906|0.88906	2.99|2.99	0.80722|0.80722	D|D	1|1	.|B	.|0.26876	.|0.162	.|B	.|0.32342	.|0.144	T|T	0.37407|0.37407	-0.9707|-0.9707	7|10	0.87932|0.87932	D|D	0|0	.|.	18.7366|18.7366	0.91757|0.91757	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|861	.|P29074	.|PTN4_HUMAN	D|I	144|861;494	ENSP00000394706:G144D|ENSP00000263708:V861I;ENSP00000445841:V494I	ENSP00000394706:G144D|ENSP00000263708:V861I	G|V	+|+	2|1	0|0	PTPN4|PTPN4	120441905|120441905	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	9.756000|9.756000	0.98918|0.98918	2.426000|2.426000	0.82243|0.82243	0.585000|0.585000	0.79938|0.79938	GGT|GTT	.	.	none		0.378	PTPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254233.2			A	120725435	G	A	120725435	3	1	11	1	0	0	0	0	1	0	0	0	12805	1261	44	2	2679	2	PTPN4	2	120725435	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	4468319	120725435	122473938	32	1323											
LRP1B	53353	hgsc.bcm.edu	37	chr2	141079638	141079638	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaagaaattcgcatgctaaAtccaagcatggattgggtac	15	9	9	8	1	0	1	0	0	0	1	2	2	1	2	1	2	3	4	1	2	6	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr2:141079638A>G	ENST00000389484.3	-	82	13505	c.12534T>C	c.(12532-12534)gaT>gaC	p.D4178D		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	4178	EGF-like 16. {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)		CGCATGCTAAATCCAAGCATG	0.373										TSP Lung(27;0.18)																											p.D4178D	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.T12534C						PASS	.						50	53	52					2																	141079638		2203	4300	6503	SO:0001819	synonymous_variant	53353	exon82			TGCTAAATCCAAG	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.12534T>C	2.37:g.141079638A>G		166	0	0		127	54	0.425197	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	a	9.034	0.988116	0.18966	.	.	ENSG00000168702	ENST00000437977	.	.	.	5.19	1.6	0.23607	.	.	.	.	.	T	0.51517	0.1679	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38628	-0.9652	4	.	.	.	.	5.0496	0.14501	0.5306:0.1535:0.3159:0.0	.	.	.	.	T	410	.	.	I	-	2	0	LRP1B	140796108	0.112000	0.22096	1.000000	0.80357	0.989000	0.77384	-0.485000	0.06520	0.401000	0.25424	0.528000	0.53228	ATT	.	.	none		0.373	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		G	141079638	A	G	141079638	2	3	11	1	0	0	0	0	0	0	0	1	8964	98	4	3		3	LRP1B	2	141079638	Silent	SNP	A	TCGA-FF-8042-01A-11D-2210-10	20354203	141079638	102119735	33	1324											
FMNL2	114793	hgsc.bcm.edu	37	chr2	153463872	153463872	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggtttgtggagaaaaacagcGctttgagaagttgatggaac	13	10	14	4	1	0	3	0	2	0	2	0	6	0	4	0	3	3	3	0	3	4	3	rs377497365		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr2:153463872G>A	ENST00000288670.9	+	10	1263	c.896G>A	c.(895-897)cGc>cAc	p.R299H		NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	299	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						GAAAAACAGCGCTTTGAGAAG	0.313													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18174	0.0		0.0	False		,,,				2504	0.0				p.R299H		Atlas-SNP	.											.	FMNL2	75	.	0			c.G896A						PASS	.	G	HIS/ARG	1,3705		0,1,1852	92	88	89		896	5.9	1	2		89	0,8204		0,0,4102	no	missense	FMNL2	NM_052905.3	29	0,1,5954	AA,AG,GG		0.0,0.027,0.0084	probably-damaging	299/1093	153463872	1,11909	1853	4102	5955	SO:0001583	missense	114793	exon10			AACAGCGCTTTGA	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.896G>A	2.37:g.153463872G>A	ENSP00000288670:p.Arg299His	369	0	0		278	81	0.291367	NM_052905	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Missense_Mutation	SNP	ENST00000288670.9	37	CCDS46429.1	.	.	.	.	.	.	.	.	.	.	G	35	5.436354	0.96168	2.7E-4	0.0	ENSG00000157827	ENST00000288670	D	0.89875	-2.58	5.92	5.92	0.95590	.	0.092942	0.85682	D	0.000000	D	0.96386	0.8821	H	0.94771	3.58	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.96788	0.9580	10	0.87932	D	0	.	19.9118	0.97027	0.0:0.0:1.0:0.0	.	299	Q96PY5-3	.	H	299	ENSP00000288670:R299H	ENSP00000288670:R299H	R	+	2	0	FMNL2	153172118	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.809000	0.96659	0.557000	0.71058	CGC	.	.	weak		0.313	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905		A	153463872	G	A	153463872	3	1	11	1	0	0	0	0	1	0	0	0	5960	1087	38	1	934	1	FMNL2	2	153463872	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	12384234	153463872	89735501	34	1325											
PRPF40A	55660	hgsc.bcm.edu	37	chr2	153547487	153547487	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtacttactgcaccagatgCtgtacctaaaaaataaaaaa	19	9	5	8	0	0	1	0	0	0	1	0	1	0	1	2	0	5	4	2	0	9	5			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr2:153547487C>T	ENST00000410080.1	-	5	875	c.334G>A	c.(334-336)Gca>Aca	p.A112T		NM_017892.3	NP_060362.3	O75400	PR40A_HUMAN	PRP40 pre-mRNA processing factor 40 homolog A (S. cerevisiae)	139					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						GCACCAGATGCTGTACCTAAA	0.254																																					p.A112T		Atlas-SNP	.											.	PRPF40A	149	.	0			c.G334A						PASS	.						15	15	15					2																	153547487		1762	4001	5763	SO:0001583	missense	55660	exon5			CAGATGCTGTACC	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.334G>A	2.37:g.153547487C>T	ENSP00000386458:p.Ala112Thr	100	0	0		85	5	0.0588235	NM_017892	O43856|O75404|Q8TBQ1|Q9H782|Q9NWU9|Q9P0Q2|Q9Y5A8	Missense_Mutation	SNP	ENST00000410080.1	37	CCDS46430.1	.	.	.	.	.	.	.	.	.	.	C	4.111	0.018714	0.07959	.	.	ENSG00000196504	ENST00000410080;ENST00000440252;ENST00000545856;ENST00000493468	T	0.35236	1.32	4.59	-2.47	0.06442	.	.	.	.	.	T	0.13415	0.0325	N	0.08118	0	0.24969	N	0.991671	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.0	T	0.33033	-0.9884	9	0.10111	T	0.7	16.2594	4.8208	0.13390	0.1543:0.3167:0.0:0.5289	.	139;112	O75400-3;E9PFS0	.;.	T	112;8;139;132	ENSP00000386458:A112T	ENSP00000386458:A112T	A	-	1	0	PRPF40A	153255733	0.088000	0.21588	0.976000	0.42696	0.886000	0.51366	-1.734000	0.01848	-0.351000	0.08249	-0.237000	0.12165	GCA	.	.	none		0.254	PRPF40A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333559.2	XM_371575		T	153547487	C	T	153547487	3	4	11	1	0	0	0	0	1	0	0	0	12583	797	28	2	2546	2	PRPF40A	2	153547487	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	83615	153547487	89651886	35	1326											
MARCH7	64844	hgsc.bcm.edu	37	chr2	160599591	160599591	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtctacatcagcatcagcatCtgcgtcaccatttcaatctg	10	12	6	13	1	7	0	4	0	3	0	7	0	7	0	1	0	4	2	1	0	2	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr2:160599591C>G	ENST00000259050.4	+	3	295	c.173C>G	c.(172-174)tCt>tGt	p.S58C	MARCH7_ENST00000409175.1_Missense_Mutation_p.S58C|MARCH7_ENST00000409591.1_Missense_Mutation_p.S20C|MARCH7_ENST00000539065.1_Missense_Mutation_p.S58C|MARCH7_ENST00000473749.1_3'UTR	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	58	Ser-rich.				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						GCATCAGCATCTGCGTCACCA	0.393																																					p.S58C		Atlas-SNP	.											.	MARCH7	48	.	0			c.C173G						PASS	.						99	97	98					2																	160599591		2203	4300	6503	SO:0001583	missense	64844	exon3			CAGCATCTGCGTC	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.173C>G	2.37:g.160599591C>G	ENSP00000259050:p.Ser58Cys	147	0	0		143	62	0.433566	NM_022826	A8K9X1|B7Z7P5|D3DPB0|Q53GQ1|Q9BTR9	Missense_Mutation	SNP	ENST00000259050.4	37	CCDS2210.1	.	.	.	.	.	.	.	.	.	.	C	7.695	0.691842	0.15039	.	.	ENSG00000136536	ENST00000409175;ENST00000539065;ENST00000259050;ENST00000421037;ENST00000409591	T;T;T;T;T	0.50813	2.57;2.52;2.57;0.73;2.44	5.54	2.29	0.28610	.	0.329624	0.29964	N	0.010759	T	0.29749	0.0743	N	0.19112	0.55	0.23589	N	0.99735	B;B;B	0.10296	0.003;0.002;0.002	B;B;B	0.08055	0.003;0.001;0.002	T	0.20907	-1.0261	10	0.49607	T	0.09	-37.7217	8.7404	0.34554	0.0:0.7161:0.1278:0.1561	.	58;20;58	F5H6W4;B7Z7P5;Q9H992	.;.;MARH7_HUMAN	C	58;58;58;58;20	ENSP00000386830:S58C;ENSP00000442992:S58C;ENSP00000259050:S58C;ENSP00000392862:S58C;ENSP00000387238:S20C	ENSP00000259050:S58C	S	+	2	0	MARCH7	160307837	1.000000	0.71417	0.998000	0.56505	0.826000	0.46750	2.550000	0.45811	0.693000	0.31634	-0.142000	0.14014	TCT	.	.	none		0.393	MARCH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255040.3	NM_022826		G	160599591	C	G	160599591	3	3	11	1	0	0	0	0	1	0	0	0	9315	913	32	4	179	4	MARCH7	2	160599591	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	7052104	160599591	82599782	36	1327											
TTN	7273	hgsc.bcm.edu	37	chr2	179428230	179428233	+	Frame_Shift_Del	DEL	TCTG	TCTG	-																															gctgcattttcagcagcaacTctgaattcataggaatggcc																										TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	TCTG	TCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr2:179428230_179428233delTCTG	ENST00000591111.1	-	276	77927_77930	c.77703_77706delCAGA	c.(77701-77706)ttcagafs	p.FR25901fs	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Frame_Shift_Del_p.FR27542fs|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Frame_Shift_Del_p.FR24974fs|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Frame_Shift_Del_p.FR18602fs|TTN_ENST00000342175.6_Frame_Shift_Del_p.FR18669fs|TTN_ENST00000460472.2_Frame_Shift_Del_p.FR18477fs|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592630.1_RNA			Q8WZ42	TITIN_HUMAN	titin	25901	Fibronectin type-III 88. {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)			CAGCAGCAACTCTGAATTCATAGG	0.495																																					p.27543_27544del		Pindel,Atlas-Indel	.											.	TTN	18412	.	0			c.82627_82630del						PASS	.																																			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.77703_77706delCAGA	2.37:g.179428230_179428233delTCTG	ENSP00000465570:p.Phe25901fs	157	0	.		108	31	0.287	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	37																																																																																				.	.	none		0.495	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		-	179428233	TCTG	-	179428230	7	5	11	1	0	1	0	1	0	0	0	0	16750	1548	54	0	25498	0	TTN	2	179428230	Frame_Shift_Del	DEL	TCTG	TCGA-FF-8042-01A-11D-2210-10	18828639	179428230	63771143	37	1328											
GULP1	51454	hgsc.bcm.edu	37	chr2	189405948	189405948	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttcatagaatatctttttGtgcagatgataaaactgaca	14	14	7	6	0	2	4	1	2	1	2	2	4	2	4	0	0	2	2	0	0	5	6			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr2:189405948G>A	ENST00000409580.1	+	8	1016	c.302G>A	c.(301-303)tGt>tAt	p.C101Y	GULP1_ENST00000409609.1_Missense_Mutation_p.C101Y|GULP1_ENST00000409830.1_Missense_Mutation_p.C101Y|GULP1_ENST00000409637.3_Missense_Mutation_p.C101Y|GULP1_ENST00000479019.1_3'UTR|GULP1_ENST00000409805.1_Intron|GULP1_ENST00000409843.1_Missense_Mutation_p.C101Y|GULP1_ENST00000410051.1_Missense_Mutation_p.C101Y|GULP1_ENST00000359135.3_Missense_Mutation_p.C101Y			Q9UBP9	GULP1_HUMAN	GULP, engulfment adaptor PTB domain containing 1	101	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				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)			ATATCTTTTTGTGCAGATGAT	0.323																																					p.C101Y	Pancreas(178;563 2065 20199 42378 52815)	Atlas-SNP	.											.	GULP1	35	.	0			c.G302A						PASS	.						110	109	109					2																	189405948		2203	4300	6503	SO:0001583	missense	51454	exon7			CTTTTTGTGCAGA	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.302G>A	2.37:g.189405948G>A	ENSP00000386289:p.Cys101Tyr	135	0	0		96	39	0.40625	NM_016315	B2RB51|B4DQ40|B8ZZ72|D3DPH1|E9PB86|Q53PC1|Q53RF3|Q9BVL3	Missense_Mutation	SNP	ENST00000409580.1	37	CCDS2295.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.482106	0.84747	.	.	ENSG00000144366	ENST00000409843;ENST00000409830;ENST00000410051;ENST00000359135;ENST00000409580;ENST00000409637;ENST00000409609	T;T;T;T;T;T;T	0.20463	2.07;2.07;2.07;2.07;2.07;2.07;2.07	5.36	5.36	0.76844	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	T	0.56396	0.1982	M	0.90705	3.14	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	0.999;1.0;0.996	T	0.65274	-0.6208	10	0.87932	D	0	-5.6024	18.4419	0.90669	0.0:0.0:1.0:0.0	.	101;101;101	Q9UBP9;B8ZZ72;Q9UBP9-2	GULP1_HUMAN;.;.	Y	101	ENSP00000387144:C101Y;ENSP00000386732:C101Y;ENSP00000387013:C101Y;ENSP00000352047:C101Y;ENSP00000386289:C101Y;ENSP00000386402:C101Y;ENSP00000386867:C101Y	ENSP00000352047:C101Y	C	+	2	0	GULP1	189114193	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	9.813000	0.99286	2.671000	0.90904	0.555000	0.69702	TGT	.	.	none		0.323	GULP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335722.1	NM_016315		A	189405948	G	A	189405948	3	1	11	1	0	0	0	0	1	0	0	0	6910	1377	48	2	320	2	GULP1	2	189405948	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	9977718	189405948	53793425	38	1329											
COL5A2	1290	hgsc.bcm.edu	37	chr2	189927788	189927788	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctccaggtttcccagggtcaCcctaaagaataaatgaaact	14	9	7	11	0	1	2	1	1	0	1	3	2	3	2	3	2	1	1	3	2	6	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr2:189927788C>T	ENST00000374866.3	-	28	2145	c.1871G>A	c.(1870-1872)gGt>gAt	p.G624D		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	624					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)			CCCAGGGTCACCCTAAAGAAT	0.368																																					p.G624D		Atlas-SNP	.											.	COL5A2	230	.	0			c.G1871A						PASS	.						97	114	108					2																	189927788		2202	4300	6502	SO:0001630	splice_region_variant	1290	exon28			GGGTCACCCTAAA	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.1870-1G>A	2.37:g.189927788C>T		81	0	0		68	8	0.117647	NM_000393	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Missense_Mutation	SNP	ENST00000374866.3	37	CCDS33350.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.342360	0.81911	.	.	ENSG00000204262	ENST00000374866;ENST00000452536	D	0.99619	-6.28	4.74	4.74	0.60224	.	0.000000	0.49305	D	0.000156	D	0.99746	0.9899	H	0.94808	3.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.97117	0.9808	9	.	.	.	.	18.1082	0.89527	0.0:1.0:0.0:0.0	.	264;624	Q5PR22;P05997	.;CO5A2_HUMAN	D	624;264	ENSP00000364000:G624D	.	G	-	2	0	COL5A2	189636033	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	7.445000	0.80570	2.339000	0.79563	0.467000	0.42956	GGT	.	.	none		0.368	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393	Missense_Mutation	T	189927788	C	T	189927788	5	4	11	1	0	0	0	0	0	0	1	0	3699	521	18	2	2736	2	COL5A2	2	189927788	Splice_Site	SNP	C	TCGA-FF-8042-01A-11D-2210-10	521840	189927788	53271585	39	1330											
SDPR	8436	hgsc.bcm.edu	37	chr2	192700876	192700876	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcagcagcctcctctgcaaTttccccttccaccagagcgc	7	9	6	19	1	2	1	1	0	1	1	5	1	5	1	6	0	4	2	6	0	1	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr2:192700876T>G	ENST00000304141.4	-	2	1380	c.1051A>C	c.(1051-1053)Att>Ctt	p.I351L		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)			TCCTCTGCAATTTCCCCTTCC	0.567																																					p.I351L		Atlas-SNP	.											.	SDPR	67	.	0			c.A1051C						PASS	.						116	113	114					2																	192700876		2203	4300	6503	SO:0001583	missense	8436	exon2			CTGCAATTTCCCC	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.1051A>C	2.37:g.192700876T>G	ENSP00000305675:p.Ile351Leu	137	0	0		128	51	0.398438	NM_004657		Missense_Mutation	SNP	ENST00000304141.4	37	CCDS2313.1	.	.	.	.	.	.	.	.	.	.	T	11.27	1.588786	0.28357	.	.	ENSG00000168497	ENST00000304141	T	0.62639	0.01	4.66	-2.51	0.06365	.	2.341900	0.01171	N	0.006876	T	0.40886	0.1135	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.30387	-0.9980	10	0.49607	T	0.09	0.7853	5.9015	0.18970	0.0:0.3185:0.1309:0.5506	.	351	O95810	SDPR_HUMAN	L	351	ENSP00000305675:I351L	ENSP00000305675:I351L	I	-	1	0	SDPR	192409121	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.388000	0.20735	-0.632000	0.05553	-0.371000	0.07208	ATT	.	.	none		0.567	SDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334791.2	NM_004657		G	192700876	T	G	192700876	3	3	11	1	0	0	0	0	1	0	0	0	13985	1493	52	5	230	5	SDPR	2	192700876	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	2773088	192700876	50498497	40	1331											
PARD3B	117583	hgsc.bcm.edu	37	chr2	206110509	206110509	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcttctcctcagtgccagaTgaaagcaaggttcactcatt	10	13	7	11	0	5	2	3	1	2	1	6	2	5	2	2	1	2	2	2	1	2	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr2:206110509T>C	ENST00000406610.2	+	16	2355	c.2148T>C	c.(2146-2148)gaT>gaC	p.D716D	PARD3B_ENST00000349953.3_Silent_p.D716D|PARD3B_ENST00000351153.1_Silent_p.D716D|PARD3B_ENST00000462231.1_Silent_p.D716D|PARD3B_ENST00000358768.2_Silent_p.D654D	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	716					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)		CAGTGCCAGATGAAAGCAAGG	0.363																																					p.D716D		Atlas-SNP	.											.	PARD3B	314	.	0			c.T2148C						PASS	.						152	142	145					2																	206110509		1828	4090	5918	SO:0001819	synonymous_variant	117583	exon16			GCCAGATGAAAGC	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.2148T>C	2.37:g.206110509T>C		234	0	0		169	61	0.360947	NM_205863	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	Silent	SNP	ENST00000406610.2	37																																																																																				.	.	none		0.363	PARD3B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000335992.1	NM_057177		C	206110509	T	C	206110509	2	2	11	1	0	0	0	0	0	0	0	1	11453	1461	51	3		3	PARD3B	2	206110509	Silent	SNP	T	TCGA-FF-8042-01A-11D-2210-10	13409633	206110509	37088864	41	1332											
EEF1B2	1933	hgsc.bcm.edu	37	chr2	207024768	207024768	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caacgattacctggcggacaAgagctacatcgaggggtgag	12	6	14	9	3	0	2	0	1	0	1	1	5	0	3	1	4	4	1	1	4	4	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr2:207024768A>G	ENST00000392222.2	+	1	440	c.65A>G	c.(64-66)aAg>aGg	p.K22R	NDUFS1_ENST00000432169.1_5'Flank|EEF1B2_ENST00000236957.5_Missense_Mutation_p.K22R|NDUFS1_ENST00000423725.1_5'Flank|SNORA41_ENST00000384675.1_RNA|NDUFS1_ENST00000455934.2_5'Flank|NDUFS1_ENST00000457011.1_5'Flank|NDUFS1_ENST00000440274.1_5'Flank|SNORD51_ENST00000384320.2_RNA|NDUFS1_ENST00000449699.1_5'Flank|EEF1B2_ENST00000392221.1_Missense_Mutation_p.K22R|NDUFS1_ENST00000233190.6_5'Flank	NM_001959.3	NP_001950.1	P24534	EF1B_HUMAN	eukaryotic translation elongation factor 1 beta 2	22	GST C-terminal.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)	translation elongation factor activity (GO:0003746)			breast(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(6)	16						CTGGCGGACAAGAGCTACATC	0.682																																					p.K22R		Atlas-SNP	.											EEF1B2,colon,carcinoma,-1,1	EEF1B2	58	1	0			c.A65G						scavenged	.						40	46	44					2																	207024768		2203	4299	6502	SO:0001583	missense	1933	exon2			CGGACAAGAGCTA	X60489	CCDS2367.1	2q33.3	2011-04-28			ENSG00000114942	ENSG00000114942			3208	protein-coding gene	gene with protein product		600655				8250921	Standard	NM_001959		Approved		uc002vbf.1	P24534	OTTHUMG00000132891	ENST00000392222.2:c.65A>G	2.37:g.207024768A>G	ENSP00000376056:p.Lys22Arg	163	2	0.0122699		110	5	0.0454545	NM_021121	A8K795|Q6IBH9	Missense_Mutation	SNP	ENST00000392222.2	37	CCDS2367.1	.	.	.	.	.	.	.	.	.	.	A	6.084	0.383763	0.11524	.	.	ENSG00000114942	ENST00000236957;ENST00000392221;ENST00000392222;ENST00000445505	T;T;T;T	0.37752	1.18;1.18;1.18;1.18	4.8	1.01	0.19927	Glutathione S-transferase, C-terminal-like (2);	0.258042	0.38548	N	0.001652	T	0.12135	0.0295	N	0.05306	-0.075	0.39419	D	0.966889	B	0.06786	0.001	B	0.10450	0.005	T	0.31916	-0.9926	10	0.02654	T	1	-6.5504	5.1665	0.15088	0.7193:0.0:0.148:0.1327	.	22	P24534	EF1B_HUMAN	R	22	ENSP00000236957:K22R;ENSP00000376055:K22R;ENSP00000376056:K22R;ENSP00000407730:K22R	ENSP00000236957:K22R	K	+	2	0	EEF1B2	206733013	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	2.389000	0.44407	0.024000	0.15214	-0.290000	0.09829	AAG	.	.	weak		0.682	EEF1B2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336436.1	NM_001037663		G	207024768	A	G	207024768	3	3	11	1	0	0	0	0	1	0	0	0	4927	72	3	3	67	3	EEF1B2	2	207024768	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	914259	207024768	36174605	42	1333											
PLEKHM3	389072	hgsc.bcm.edu	37	chr2	208795754	208795754	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acggcggccagcggctctgcGtggtggtacagcatggcgtt	5	8	17	11	5	1	0	0	0	1	0	1	0	1	0	1	6	4	4	1	6	1	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr2:208795754G>T	ENST00000427836.2	-	5	2271	c.1782C>A	c.(1780-1782)caC>caA	p.H594Q	PLEKHM3_ENST00000457206.1_Missense_Mutation_p.H594Q|PLEKHM3_ENST00000389247.4_Missense_Mutation_p.H594Q	NM_001080475.2	NP_001073944.1	Q6ZWE6	PKHM3_HUMAN	pleckstrin homology domain containing, family M, member 3	594					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						GCGGCTCTGCGTGGTGGTACA	0.622																																					p.H594Q		Atlas-SNP	.											.	PLEKHM3	101	.	0			c.C1782A						PASS	.						69	75	73					2																	208795754		2024	4186	6210	SO:0001583	missense	389072	exon5			CTCTGCGTGGTGG	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.1782C>A	2.37:g.208795754G>T	ENSP00000417003:p.His594Gln	177	0	0		150	66	0.44	NM_001080475	B9EKV2|Q8WW68	Missense_Mutation	SNP	ENST00000427836.2	37	CCDS42808.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.33|14.33	2.504060|2.504060	0.44558|0.44558	.|.	.|.	ENSG00000178385|ENSG00000178385	ENST00000427836;ENST00000389247;ENST00000457206|ENST00000447645	D;D;D|.	0.84146|.	-1.74;-1.74;-1.81|.	5.79|5.79	-0.289|-0.289	0.12851|0.12851	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.55081|0.55081	0.1898|0.1898	L|L	0.46670|0.46670	1.46|1.46	0.58432|0.58432	D|D	0.999999|0.999999	D;D|.	0.76494|.	0.999;0.984|.	D;D|.	0.79108|.	0.992;0.921|.	T|T	0.49263|0.49263	-0.8958|-0.8958	10|5	0.87932|.	D|.	0|.	0.1349|0.1349	10.7072|10.7072	0.45962|0.45962	0.5176:0.0:0.4824:0.0|0.5176:0.0:0.4824:0.0	.|.	594;594|.	C9J119;Q6ZWE6|.	.;PKHM3_HUMAN|.	Q|S	594|346	ENSP00000417003:H594Q;ENSP00000373899:H594Q;ENSP00000400150:H594Q|.	ENSP00000373899:H594Q|.	H|R	-|-	3|1	2|0	PLEKHM3|PLEKHM3	208503999|208503999	0.897000|0.897000	0.30589|0.30589	0.964000|0.964000	0.40570|0.40570	0.034000|0.034000	0.12701|0.12701	0.063000|0.063000	0.14410|0.14410	0.036000|0.036000	0.15547|0.15547	0.460000|0.460000	0.39030|0.39030	CAC|CGC	.	.	none		0.622	PLEKHM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337036.1	NM_001080475		T	208795754	G	T	208795754	3	4	11	1	0	0	0	0	1	0	0	0	12091	1136	40	4	519	4	PLEKHM3	2	208795754	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	1770986	208795754	34403619	43	1334											
IKZF2	22807	hgsc.bcm.edu	37	chr2	213872764	213872764	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttctcatatgttaagttcaTatcaaagtgaatatctgggt	12	16	7	6	0	4	1	3	1	2	0	5	1	4	1	0	1	0	2	0	1	6	6			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr2:213872764T>C	ENST00000434687.1	-	9	1210	c.901A>G	c.(901-903)Atg>Gtg	p.M301V	IKZF2_ENST00000374319.4_Missense_Mutation_p.M275V|AC079610.1_ENST00000415387.1_RNA|IKZF2_ENST00000451136.2_Missense_Mutation_p.M229V|IKZF2_ENST00000374327.4_Missense_Mutation_p.M156V|IKZF2_ENST00000413091.3_3'UTR|IKZF2_ENST00000457361.1_Missense_Mutation_p.M301V|IKZF2_ENST00000421754.2_Missense_Mutation_p.M227V|IKZF2_ENST00000342002.2_Missense_Mutation_p.M307V			Q9UKS7	IKZF2_HUMAN	IKAROS family zinc finger 2 (Helios)	301					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)		GTTAAGTTCATATCAAAGTGA	0.418																																					p.M301V		Atlas-SNP	.											IKZF2,NS,carcinoma,+2,1	IKZF2	71	1	0			c.A901G						PASS	.						63	60	61					2																	213872764		2203	4300	6503	SO:0001583	missense	22807	exon8			AGTTCATATCAAA	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.901A>G	2.37:g.213872764T>C	ENSP00000412869:p.Met301Val	116	0	0		110	41	0.372727	NM_016260	Q53YJ5|Q6PQC5|Q6PQC6|Q6PQC7|Q6PQC8|Q6PQD0|Q6PQD1|Q8N6S1	Missense_Mutation	SNP	ENST00000434687.1	37	CCDS2395.1	.	.	.	.	.	.	.	.	.	.	T	6.998	0.554240	0.13374	.	.	ENSG00000030419	ENST00000457361;ENST00000342002;ENST00000434687;ENST00000374319;ENST00000451136;ENST00000421754;ENST00000374327	T;T;T;T;T;T;T	0.13538	3.33;3.3;3.33;3.36;3.31;3.35;2.58	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	T	0.10680	0.0261	L	0.41027	1.25	0.80722	D	1	B;B;B;B;B;B	0.14438	0.0;0.0;0.01;0.0;0.0;0.0	B;B;B;B;B;B	0.10450	0.001;0.0;0.005;0.003;0.0;0.001	T	0.21759	-1.0236	10	0.19147	T	0.46	-8.1552	7.3309	0.26582	0.0:0.0723:0.1458:0.7819	.	229;227;156;275;301;79	C9JCG7;C9JTM9;F5H8M1;Q9UKS7-2;Q9UKS7;Q96LD7	.;.;.;.;IKZF2_HUMAN;.	V	301;307;301;275;229;227;156	ENSP00000410447:M301V;ENSP00000342876:M307V;ENSP00000412869:M301V;ENSP00000363439:M275V;ENSP00000395203:M229V;ENSP00000399574:M227V;ENSP00000363447:M156V	ENSP00000342876:M307V	M	-	1	0	IKZF2	213581009	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.783000	0.55409	2.220000	0.72140	0.533000	0.62120	ATG	.	.	none		0.418	IKZF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256593.3	NM_016260		C	213872764	T	C	213872764	3	2	11	1	0	0	0	0	1	0	0	0	7624	1406	49	3	683	3	IKZF2	2	213872764	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	5077010	213872764	29326609	44	1335											
SPHKAP	80309	hgsc.bcm.edu	37	chr2	228882763	228882763	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagttgccatggagacgaccGtgtctgctaattcttccgca	8	11	10	12	3	2	1	0	0	2	1	3	3	3	1	3	1	2	3	3	1	1	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr2:228882763G>A	ENST00000392056.3	-	7	2853	c.2807C>T	c.(2806-2808)aCg>aTg	p.T936M	SPHKAP_ENST00000344657.5_Missense_Mutation_p.T936M	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	936	PKA-RII subunit binding domain. {ECO:0000250}.					extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)	p.T936R(2)		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)		GGAGACGACCGTGTCTGCTAA	0.473																																					p.T936M		Atlas-SNP	.											SPHKAP_ENST00000392056,NS,carcinoma,0,2	SPHKAP	750	2	2	Substitution - Missense(2)	lung(2)	c.C2807T						scavenged	.						177	159	165					2																	228882763		2203	4300	6503	SO:0001583	missense	80309	exon7			ACGACCGTGTCTG		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.2807C>T	2.37:g.228882763G>A	ENSP00000375909:p.Thr936Met	201	1	0.00497512		159	68	0.427673	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	.	.	.	.	.	.	.	.	.	.	G	14.42	2.530106	0.45073	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.26067	1.78;1.76	6.08	5.18	0.71444	.	0.044191	0.85682	N	0.000000	T	0.30916	0.0780	L	0.32530	0.975	0.58432	D	0.999993	D;D	0.67145	0.996;0.996	P;P	0.52881	0.462;0.712	T	0.03453	-1.1035	10	0.52906	T	0.07	.	13.6707	0.62422	0.0763:0.0:0.9237:0.0	.	936;936	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	M	936	ENSP00000375909:T936M;ENSP00000339886:T936M	ENSP00000339886:T936M	T	-	2	0	SPHKAP	228591007	1.000000	0.71417	0.897000	0.35233	0.273000	0.26683	7.275000	0.78548	1.520000	0.48965	0.655000	0.94253	ACG	.	.	none		0.473	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		A	228882763	G	A	228882763	3	1	11	1	0	0	0	0	1	0	0	0	15063	1145	40	1	2319	1	SPHKAP	2	228882763	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	15009999	228882763	14316610	45	1336											
UGT1A3	54659	hgsc.bcm.edu	37	chr2	234638243	234638243	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acagaccccgttaacctctgCgcggcagtgctggctaagta	9	8	11	13	3	1	1	0	0	1	1	1	1	1	1	3	2	3	5	3	2	3	3	rs375083511		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr2:234638243C>T	ENST00000482026.1	+	1	490	c.471C>T	c.(469-471)tgC>tgT	p.C157C	UGT1A4_ENST00000373409.3_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A1_ENST00000609767.1_Silent_p.C157C|UGT1A6_ENST00000373424.1_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A6_ENST00000406651.1_Intron			P35503	UD13_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A3	157					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)	TTAACCTCTGCGCGGCAGTGC	0.458																																					p.C157C		Atlas-SNP	.											.	UGT1A3	91	.	0			c.C471T						PASS	.						187	194	191					2																	234638243		2203	4300	6503	SO:0001819	synonymous_variant	54659	exon1			CCTCTGCGCGGCA	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.471C>T	2.37:g.234638243C>T		277	1	0.00361011		258	105	0.406977	NM_019093	B8K287	Silent	SNP	ENST00000482026.1	37	CCDS2509.1																																																																																			.	.	weak		0.458	UGT1A3-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130983.1	NM_019093		T	234638243	C	T	234638243	2	4	11	1	0	0	0	0	0	0	0	1	16961	776	27	1		1	UGT1A3	2	234638243	Silent	SNP	C	TCGA-FF-8042-01A-11D-2210-10	5755480	234638243	8561130	46	1337											
LRRFIP1	9208	hgsc.bcm.edu	37	chr2	238688143	238688143	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agcgtctggaaaaaatgaaaGcaaatcggagtgcactcttg	15	8	11	7	2	2	1	0	1	2	0	3	3	2	3	0	2	3	2	0	2	5	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr2:238688143G>A	ENST00000308482.9	+	24	1960	c.1891G>A	c.(1891-1893)Gca>Aca	p.A631T		NM_001137550.1	NP_001131022.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1	477					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)		AAAAATGAAAGCAAATCGGAG	0.493																																					p.A631T		Atlas-SNP	.											.	LRRFIP1	171	.	0			c.G1891A						PASS	.						76	71	72					2																	238688143		1568	3582	5150	SO:0001583	missense	9208	exon24			ATGAAAGCAAATC	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.1891G>A	2.37:g.238688143G>A	ENSP00000310109:p.Ala631Thr	60	0	0		55	24	0.436364	NM_001137550	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Missense_Mutation	SNP	ENST00000308482.9	37	CCDS46551.1	.	.	.	.	.	.	.	.	.	.	G	16.11	3.031177	0.54790	.	.	ENSG00000124831	ENST00000308482;ENST00000391999	T	0.48201	0.82	4.85	4.85	0.62838	.	.	.	.	.	T	0.41696	0.1170	L	0.42245	1.32	0.80722	D	1	B;P	0.48503	0.298;0.911	B;B	0.39027	0.178;0.288	T	0.44205	-0.9343	9	0.45353	T	0.12	.	17.3552	0.87334	0.0:0.0:1.0:0.0	.	385;631	B4DPC0;E9PGZ2	.;.	T	631;621	ENSP00000310109:A631T	ENSP00000310109:A631T	A	+	1	0	LRRFIP1	238352882	1.000000	0.71417	0.987000	0.45799	0.618000	0.37518	4.253000	0.58791	2.409000	0.81822	0.563000	0.77884	GCA	.	.	none		0.493	LRRFIP1-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000257169.3	NM_004735		A	238688143	G	A	238688143	3	1	11	1	0	0	0	0	1	0	0	0	9036	971	34	2	3597	2	LRRFIP1	2	238688143	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	4049900	238688143	4511230	47	1338											
IRAK2	3656	hgsc.bcm.edu	37	chr3	10251272	10251272	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccatagtccctcctttccaGggtcctctccagccagagcc	6	9	7	19	0	1	1	0	0	1	1	6	1	5	1	8	1	2	0	8	1	1	2	rs140330791		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:10251272G>A	ENST00000256458.4	+	4	514		c.e4-1			NM_001570.3	NP_001561.3	O43187	IRAK2_HUMAN	interleukin-1 receptor-associated kinase 2						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						CTCCTTTCCAGGGTCCTCTCC	0.592																																					.		Atlas-SNP	.											IRAK2_ENST00000256458,caecum,carcinoma,-1,2	IRAK2	113	2	0			c.425-1G>A						PASS	.						125	134	131					3																	10251272		2203	4300	6503	SO:0001630	splice_region_variant	3656	exon4			TTTCCAGGGTCCT	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.425-1G>A	3.37:g.10251272G>A		54	0	0		68	14	0.205882	NM_001570	B4DQZ6|Q08AG6|Q5K546	Splice_Site	SNP	ENST00000256458.4	37	CCDS33697.1	.	.	.	.	.	.	.	.	.	.	G	9.512	1.106048	0.20632	.	.	ENSG00000134070	ENST00000256458	.	.	.	4.44	4.44	0.53790	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.9411	0.58345	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	IRAK2	10226272	0.977000	0.34250	0.969000	0.41365	0.014000	0.08584	3.911000	0.56378	2.181000	0.69327	0.563000	0.77884	.	G|1.000;C|0.000	.	alt		0.592	IRAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339623.1		Intron	A	10251272	G	A	10251272	5	1	11	1	0	0	0	0	0	0	1	0	7832	1014	35	2	438	2	IRAK2	3	10251272	Splice_Site	SNP	G	TCGA-FF-8042-01A-11D-2210-10		10251272	187771158	48	1339											
PPARG	5468	hgsc.bcm.edu	37	chr3	12475443	12475443	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccattgaagacattcaagaCaacctgctacaagccctgga	14	7	7	13	0	1	3	1	1	0	2	1	4	1	4	3	1	4	1	3	1	5	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:12475443C>A	ENST00000287820.6	+	7	1438	c.1317C>A	c.(1315-1317)gaC>gaA	p.D439E	PPARG_ENST00000397015.2_Missense_Mutation_p.D411E|PPARG_ENST00000309576.6_Missense_Mutation_p.D411E|PPARG_ENST00000397010.2_Missense_Mutation_p.D411E|PPARG_ENST00000397000.1_3'UTR|PPARG_ENST00000539812.1_3'UTR|PPARG_ENST00000397026.2_Missense_Mutation_p.D417E|PPARG_ENST00000397012.2_Missense_Mutation_p.D411E	NM_015869.4	NP_056953.2	P37231	PPARG_HUMAN	peroxisome proliferator-activated receptor gamma	439	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)	ACATTCAAGACAACCTGCTAC	0.507			T	PAX8	follicular thyroid		"Insulin resistance ; lipodystrophy, familial partial L;diabetes mellitus, insulin-resistantI, with acanthosis nigricans and hypertension"																														p.D439E		Atlas-SNP	.		Dom	yes		3	3p25	5468	"peroxisome proliferative activated receptor, gamma"	yes	E	.	PPARG	49	.	0			c.C1317A						PASS	.						104	100	102					3																	12475443		2203	4300	6503	SO:0001583	missense	5468	exon7			TCAAGACAACCTG	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.1317C>A	3.37:g.12475443C>A	ENSP00000287820:p.Asp439Glu	217	0	0		287	61	0.212544	NM_015869	A8K3G6|B5BUA1|O00684|O00710|O14515|Q0QJH8|Q15178|Q15179|Q15180|Q15832|Q86U60|Q96J12	Missense_Mutation	SNP	ENST00000287820.6	37	CCDS2609.1	.	.	.	.	.	.	.	.	.	.	C	2.364	-0.345921	0.05208	.	.	ENSG00000132170	ENST00000397010;ENST00000309576;ENST00000397015;ENST00000397012;ENST00000397026;ENST00000287820	D;D;D;D;D;D	0.96168	-3.93;-3.93;-3.93;-3.93;-3.93;-3.93	5.61	2.41	0.29592	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.154798	0.56097	D	0.000021	T	0.79747	0.4499	N	0.01188	-0.97	0.80722	D	1	B	0.06786	0.001	B	0.12156	0.007	T	0.72513	-0.4270	10	0.02654	T	1	.	4.3276	0.11048	0.1297:0.4992:0.2553:0.1158	.	439	P37231	PPARG_HUMAN	E	411;411;411;411;417;439	ENSP00000380205:D411E;ENSP00000312472:D411E;ENSP00000380210:D411E;ENSP00000380207:D411E;ENSP00000380221:D417E;ENSP00000287820:D439E	ENSP00000287820:D439E	D	+	3	2	PPARG	12450443	0.988000	0.35896	1.000000	0.80357	0.933000	0.57130	0.263000	0.18478	0.724000	0.32296	0.650000	0.86243	GAC	.	.	none		0.507	PPARG-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251979.2	NM_005037		A	12475443	C	A	12475443	3	1	11	1	0	0	0	0	1	0	0	0	12308	477	17	4	1343	4	PPARG	3	12475443	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	2224171	12475443	185546987	49	1340											
MKRN2	23609	hgsc.bcm.edu	37	chr3	12610409	12610409	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgtgtcgggaaggaagtcAgtgcctattctcacatgact	9	12	12	8	1	2	1	2	1	1	0	4	3	2	3	1	2	1	0	1	2	3	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:12610409A>G	ENST00000170447.7	+	2	199	c.62A>G	c.(61-63)cAg>cGg	p.Q21R	MKRN2_ENST00000411987.1_Intron|MKRN2_ENST00000448482.1_Missense_Mutation_p.Q21R	NM_001271707.1|NM_014160.3	NP_001258636.1|NP_054879.3	Q9H000	MKRN2_HUMAN	makorin ring finger protein 2	21					protein ubiquitination (GO:0016567)	intracellular (GO:0005622)	ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|prostate(3)	16						GAAGGAAGTCAGTGCCTATTC	0.453																																					p.Q21R		Atlas-SNP	.											.	MKRN2	32	.	0			c.A62G						PASS	.						203	170	181					3																	12610409		2203	4300	6503	SO:0001583	missense	23609	exon2			GAAGTCAGTGCCT		CCDS33702.1, CCDS63545.1	3p25	2008-08-13	2008-08-13		ENSG00000075975	ENSG00000075975		"RING-type (C3HC4) zinc fingers"	7113	protein-coding gene	gene with protein product		608426				11597136	Standard	NM_014160		Approved	RNF62, HSPC070	uc003bxd.4	Q9H000	OTTHUMG00000155371	ENST00000170447.7:c.62A>G	3.37:g.12610409A>G	ENSP00000170447:p.Gln21Arg	128	0	0		172	42	0.244186	NM_014160	A6NIA2|B3KRC5|B4DPR4|Q8N391|Q96BD4|Q9BUY2|Q9NRY1	Missense_Mutation	SNP	ENST00000170447.7	37	CCDS33702.1	.	.	.	.	.	.	.	.	.	.	A	12.41	1.928178	0.34002	.	.	ENSG00000075975	ENST00000170447;ENST00000448482	T;T	0.41758	0.99;0.99	5.78	5.78	0.91487	Zinc finger, CCCH-type (2);	0.276343	0.31859	N	0.006945	T	0.14570	0.0352	N	0.01352	-0.895	0.28154	N	0.929267	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18840	-1.0324	10	0.12430	T	0.62	.	8.7215	0.34443	0.8586:0.0:0.1414:0.0	.	21;21	C9J494;Q9H000	.;MKRN2_HUMAN	R	21	ENSP00000170447:Q21R;ENSP00000397983:Q21R	ENSP00000170447:Q21R	Q	+	2	0	MKRN2	12585409	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	2.757000	0.47557	2.333000	0.79357	0.482000	0.46254	CAG	.	.	none		0.453	MKRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339679.1	NM_014160		G	12610409	A	G	12610409	3	3	11	1	0	0	0	0	1	0	0	0	9616	188	7	3	68	3	MKRN2	3	12610409	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	134966	12610409	185412021	50	1341											
RAF1	5894	hgsc.bcm.edu	37	chr3	12627284	12627284	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aattttcactgttaagccttCatggagaaatatatctcaat	14	15	5	7	0	3	1	3	0	1	1	4	2	3	1	1	1	1	1	1	1	6	6			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:12627284C>T	ENST00000251849.4	-	14	1871	c.1432G>A	c.(1432-1434)Gaa>Aaa	p.E478K	RAF1_ENST00000442415.2_Missense_Mutation_p.E498K|RAF1_ENST00000542177.1_Missense_Mutation_p.E397K|RAF1_ENST00000534997.1_Missense_Mutation_p.E263K	NM_002880.3	NP_002871.1	P04049	RAF1_HUMAN	Raf-1 proto-oncogene, serine/threonine kinase	478	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		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)	GTTAAGCCTTCATGGAGAAAT	0.388			T	SRGAP3	pilocytic astrocytoma				Noonan syndrome																												p.E478K		Atlas-SNP	.		Dom	yes		3	3p25	5894	v-raf-1 murine leukemia viral oncogene homolog 1		M	RAF1,NS,lymphoid_neoplasm,0,2	RAF1	66	2	0			c.G1432A						PASS	.						99	98	98					3																	12627284		2203	4300	6503	SO:0001583	missense	5894	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	AGCCTTCATGGAG	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.1432G>A	3.37:g.12627284C>T	ENSP00000251849:p.Glu478Lys	54	0	0		81	16	0.197531	NM_002880	B0LPH8|B2R5N3|Q15278|Q9UC20	Missense_Mutation	SNP	ENST00000251849.4	37	CCDS2612.1	.	.	.	.	.	.	.	.	.	.	C	36	5.763115	0.96906	.	.	ENSG00000132155	ENST00000251849;ENST00000442415;ENST00000432427;ENST00000534997;ENST00000542177	D;D;D;D;D	0.82984	-1.67;-1.67;-1.67;-1.67;-1.67	5.26	5.26	0.73747	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.85401	0.5688	N	0.17872	0.535	0.80722	D	1	D;P;D	0.53619	0.96;0.762;0.961	D;P;D	0.68039	0.91;0.893;0.955	D	0.87465	0.2410	10	0.87932	D	0	.	19.0661	0.93110	0.0:1.0:0.0:0.0	.	397;263;478	B4E0X2;B4E1N6;P04049	.;.;RAF1_HUMAN	K	478;498;357;263;397	ENSP00000251849:E478K;ENSP00000401888:E498K;ENSP00000398591:E357K;ENSP00000441186:E263K;ENSP00000443567:E397K	ENSP00000251849:E478K	E	-	1	0	RAF1	12602284	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.646000	0.83445	2.746000	0.94184	0.655000	0.94253	GAA	.	.	none		0.388	RAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252015.2	NM_002880		T	12627284	C	T	12627284	3	4	11	1	0	0	0	0	1	0	0	0	13017	835	29	2	530	2	RAF1	3	12627284	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	16875	12627284	185395146	51	1342											
THRB	7068	hgsc.bcm.edu	37	chr3	24231565	24231565	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctaataaaaatctggttacCtttacatttcttctcctccg	10	16	4	11	1	3	0	0	0	3	0	5	0	4	0	3	1	2	2	3	1	6	7			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:24231565C>T	ENST00000356447.4	-	4	567	c.283G>A	c.(283-285)Ggg>Agg	p.G95R	THRB_ENST00000416420.1_Splice_Site_p.G95R|THRB_ENST00000396671.2_Splice_Site_p.G95R	NM_000461.4|NM_001128177.1	NP_000452.2|NP_001121649.1	P10828	THB_HUMAN	thyroid hormone receptor, beta	95	Modulating.				female courtship behavior (GO:0008050)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of female receptivity (GO:0007621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart contraction (GO:0008016)|sensory perception of sound (GO:0007605)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|Type I pneumocyte differentiation (GO:0060509)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone binding (GO:0070324)|thyroid hormone receptor activity (GO:0004887)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(6)|pancreas(2)|prostate(1)|skin(3)	19					Dextrothyroxine(DB00509)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	ATCTGGTTACCTTTACATTTC	0.393																																					p.G95R	Melanoma(21;896 1043 15021 37958)	Atlas-SNP	.											.	THRB	52	.	0			c.G283A						PASS	.						159	151	154					3																	24231565		2203	4300	6503	SO:0001630	splice_region_variant	7068	exon4			GGTTACCTTTACA		CCDS2641.1	3p24.2	2013-01-16	2011-05-19		ENSG00000151090	ENSG00000151090		"Nuclear hormone receptors"	11799	protein-coding gene	gene with protein product	"avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 2", "oncogene ERBA2", "generalized resistance to thyroid hormone", "thyroid hormone receptor beta 1"	190160	"thyroid hormone receptor, beta (avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 2)", "pituitary resistance to thyroid hormone", "thyroid hormone receptor, beta (erythroblastic leukemia viral (v-erb-a) oncogene homolog 2, avian)"	ERBA2, PRTH		1973914, 8040303	Standard	NM_000461		Approved	THRB1, THRB2, NR1A2, THR1, ERBA-BETA, GRTH	uc003ccy.4	P10828	OTTHUMG00000130478	ENST00000356447.4:c.283+1G>A	3.37:g.24231565C>T		88	0	0		103	26	0.252427	NM_000461	B3KU79|P37243|Q13986|Q3KP35|Q6WGL2|Q9UD41	Missense_Mutation	SNP	ENST00000356447.4	37	CCDS2641.1	.	.	.	.	.	.	.	.	.	.	C	18.39	3.612710	0.66672	.	.	ENSG00000151090	ENST00000396671;ENST00000356447;ENST00000416420;ENST00000413780;ENST00000415021;ENST00000447875;ENST00000453729;ENST00000431815;ENST00000447414	D;D;D;D	0.96745	-3.3;-3.3;-3.3;-4.11	6.07	6.07	0.98685	.	.	.	.	.	D	0.96765	0.8944	L	0.32530	0.975	0.80722	D	1	D	0.71674	0.998	D	0.66847	0.947	D	0.97177	0.9848	9	0.72032	D	0.01	.	18.8399	0.92180	0.0:1.0:0.0:0.0	.	95	P10828	THB_HUMAN	R	95;95;95;64;95;95;95;95;95	ENSP00000379904:G95R;ENSP00000348827:G95R;ENSP00000414444:G95R;ENSP00000414100:G64R	ENSP00000348827:G95R	G	-	1	0	THRB	24206569	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	4.956000	0.63645	2.885000	0.99019	0.655000	0.94253	GGG	.	.	none		0.393	THRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252877.3	NM_000461	Missense_Mutation	T	24231565	C	T	24231565	5	4	11	1	0	0	0	0	0	0	1	0	15890	695	24	2	1130	2	THRB	3	24231565	Splice_Site	SNP	C	TCGA-FF-8042-01A-11D-2210-10	11604281	24231565	173790865	52	1343											
SLC4A7	9497	hgsc.bcm.edu	37	chr3	27424644	27424644	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcataaagtcatatctcacCtatattttagggccttgact	12	14	6	9	0	2	1	2	1	1	0	3	1	2	1	2	1	1	1	2	1	6	7			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:27424644C>A	ENST00000295736.5	-	24	3633	c.3563G>T	c.(3562-3564)aGt>aTt	p.S1188I	SLC4A7_ENST00000428386.1_Splice_Site_p.S1064I|SLC4A7_ENST00000440156.1_Splice_Site_p.S1184I|SLC4A7_ENST00000437179.1_Splice_Site_p.S1069I|SLC4A7_ENST00000454389.1_Splice_Site_p.S1197I|SLC4A7_ENST00000435667.2_Splice_Site_p.S1073I|SLC4A7_ENST00000425128.2_3'UTR|SLC4A7_ENST00000445684.1_Splice_Site_p.S1184I|SLC4A7_ENST00000388777.4_Splice_Site_p.S738I|SLC4A7_ENST00000446700.1_Splice_Site_p.S1180I|SLC4A7_ENST00000455077.1_Splice_Site_p.S1069I	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	1188					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)	CATATCTCACCTATATTTTAG	0.333																																					p.S1188I		Atlas-SNP	.											.	SLC4A7	119	.	0			c.G3563T						PASS	.						100	97	98					3																	27424644		2203	4300	6503	SO:0001630	splice_region_variant	9497	exon24			TCTCACCTATATT	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.3563+1G>T	3.37:g.27424644C>A		104	0	0		109	22	0.201835	NM_003615	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Missense_Mutation	SNP	ENST00000295736.5	37	CCDS33721.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.446651	0.63178	.	.	ENSG00000033867	ENST00000419036;ENST00000295736;ENST00000428386;ENST00000454389;ENST00000440156;ENST00000437179;ENST00000446700;ENST00000455077;ENST00000445684;ENST00000435667;ENST00000388777	T;T;T;T;T;T;T;T;T;T;T	0.80994	-1.44;-1.24;-1.25;-1.13;-1.21;-1.25;-1.32;-1.16;-1.32;-1.16;-1.44	5.41	5.41	0.78517	.	0.254953	0.42964	D	0.000621	D	0.85737	0.5766	L	0.39898	1.24	0.80722	D	1	D;D;D;P;B;B;D;D;B	0.67145	0.996;0.99;0.996;0.543;0.048;0.001;0.994;0.996;0.002	D;D;D;B;B;B;D;D;B	0.74348	0.974;0.962;0.974;0.059;0.017;0.009;0.983;0.974;0.006	D	0.84259	0.0482	9	.	.	.	.	18.784	0.91946	0.0:1.0:0.0:0.0	.	1184;1069;1180;1184;1197;738;1064;1188;1069	E9PFN4;B5M452;E9PGC1;B5M453;E9PDL9;F8W7E6;Q9Y6M7-2;Q9Y6M7;B2CI53	.;.;.;.;.;.;.;S4A7_HUMAN;.	I	739;1188;1064;1197;1184;1069;1180;1069;1184;1073;738	ENSP00000411031:S739I;ENSP00000295736:S1188I;ENSP00000416368:S1064I;ENSP00000390394:S1197I;ENSP00000414797:S1184I;ENSP00000394252:S1069I;ENSP00000406605:S1180I;ENSP00000407382:S1069I;ENSP00000406804:S1184I;ENSP00000395336:S1073I;ENSP00000373429:S738I	.	S	-	2	0	SLC4A7	27399648	1.000000	0.71417	1.000000	0.80357	0.440000	0.31957	5.587000	0.67510	2.509000	0.84616	0.650000	0.86243	AGT	.	.	none		0.333	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615	Missense_Mutation	A	27424644	C	A	27424644	5	1	11	1	0	0	0	0	0	0	1	0	14673	695	24	4	89	4	SLC4A7	3	27424644	Splice_Site	SNP	C	TCGA-FF-8042-01A-11D-2210-10	3193079	27424644	170597786	53	1344											
ARPP21	10777	hgsc.bcm.edu	37	chr3	35758809	35758809	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtaggctcttggaagacagtAacatatgcaatgagacctat	14	10	10	7	0	1	2	0	1	1	2	1	4	1	3	1	2	2	4	1	2	6	5			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:35758809A>T	ENST00000187397.4	+	13	1411	c.955A>T	c.(955-957)Aac>Tac	p.N319Y	ARPP21_ENST00000337271.5_Intron|ARPP21_ENST00000417925.1_Missense_Mutation_p.N285Y|ARPP21_ENST00000458225.1_Missense_Mutation_p.N285Y|ARPP21_ENST00000444190.1_Intron	NM_016300.4	NP_057384.2	Q9UBL0	ARP21_HUMAN	cAMP-regulated phosphoprotein, 21kDa	319					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						GGAAGACAGTAACATATGCAA	0.333																																					p.N319Y		Atlas-SNP	.											.	ARPP21	153	.	0			c.A955T						PASS	.						170	172	171					3																	35758809		2203	4299	6502	SO:0001583	missense	10777	exon13			GACAGTAACATAT	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.955A>T	3.37:g.35758809A>T	ENSP00000187397:p.Asn319Tyr	130	0	0		120	37	0.308333	NM_016300	B4DG96|Q49AK3|Q49AS6|Q4G0V4|Q6NYC3|Q86V31|Q9UF93	Missense_Mutation	SNP	ENST00000187397.4	37	CCDS2661.1	.	.	.	.	.	.	.	.	.	.	A	14.89	2.670639	0.47781	.	.	ENSG00000172995	ENST00000458225;ENST00000187397;ENST00000417925;ENST00000425289	T;T;T	0.24723	1.89;1.84;1.89	5.45	4.27	0.50696	.	0.343723	0.33110	N	0.005261	T	0.15262	0.0368	N	0.08118	0	0.80722	D	1	P;P	0.44090	0.826;0.558	B;B	0.42653	0.394;0.107	T	0.06041	-1.0849	10	0.72032	D	0.01	-10.8417	10.3625	0.44003	0.8283:0.1717:0.0:0.0	.	285;319	Q9UBL0-3;Q9UBL0	.;ARP21_HUMAN	Y	285;319;285;90	ENSP00000414351:N285Y;ENSP00000187397:N319Y;ENSP00000412326:N285Y	ENSP00000187397:N319Y	N	+	1	0	ARPP21	35733813	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.073000	0.50057	0.882000	0.36016	0.528000	0.53228	AAC	.	.	none		0.333	ARPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253334.2	NM_198399		T	35758809	A	T	35758809	3	4	11	1	0	0	0	0	1	0	0	0	978	362	13	5	1010	5	ARPP21	3	35758809	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	8334165	35758809	162263621	54	1345											
TTC21A	199223	hgsc.bcm.edu	37	chr3	39174704	39174704	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtacagtcttataaggatgtCttctcctacttgccaactga	10	14	7	10	0	3	1	0	1	3	0	4	2	3	2	2	1	4	1	2	1	5	6			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:39174704C>A	ENST00000431162.2	+	20	2879	c.2745C>A	c.(2743-2745)gtC>gtA	p.V915V	TTC21A_ENST00000301819.6_Silent_p.V916V|TTC21A_ENST00000440121.1_Silent_p.V867V|TTC21A_ENST00000493856.1_3'UTR			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	915										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)		ATAAGGATGTCTTCTCCTACT	0.507																																					p.V915V		Atlas-SNP	.											.	TTC21A	96	.	0			c.C2745A						PASS	.						86	88	87					3																	39174704		2044	4192	6236	SO:0001819	synonymous_variant	199223	exon20			GGATGTCTTCTCC	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.2745C>A	3.37:g.39174704C>A		112	0	0		108	34	0.314815	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Silent	SNP	ENST00000431162.2	37	CCDS46800.1																																																																																			.	.	none		0.507	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755		A	39174704	C	A	39174704	2	1	11	1	0	0	0	0	0	0	0	1	16702	900	32	4		4	TTC21A	3	39174704	Silent	SNP	C	TCGA-FF-8042-01A-11D-2210-10	3415895	39174704	158847726	55	1346											
TRAK1	22906	hgsc.bcm.edu	37	chr3	42264607	42264607	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgtgtggctgttgaaggagcGgggcatttctgctgccgtgt	4	12	17	8	3	1	1	0	1	1	0	1	2	1	2	1	4	3	4	1	4	1	2	rs537037086		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:42264607G>A	ENST00000327628.5	+	16	2640	c.2240G>A	c.(2239-2241)cGg>cAg	p.R747Q	TRAK1_ENST00000487159.1_3'UTR|TRAK1_ENST00000396175.1_Missense_Mutation_p.R689Q|RNU4-78P_ENST00000410940.1_RNA	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	747					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						TTGAAGGAGCGGGGCATTTCT	0.637													G|||	1	0.000199681	0.0	0.0	5008	,	,		15086	0.001		0.0	False		,,,				2504	0.0				p.R747Q	GBM(44;195 884 22595 31865 41850)	Atlas-SNP	.											.	TRAK1	188	.	0			c.G2240A						PASS	.						46	56	53					3																	42264607		2038	4177	6215	SO:0001583	missense	22906	exon16			AGGAGCGGGGCAT		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.2240G>A	3.37:g.42264607G>A	ENSP00000328998:p.Arg747Gln	106	0	0		118	28	0.237288	NM_001042646	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Missense_Mutation	SNP	ENST00000327628.5	37	CCDS43072.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.125799	0.77436	.	.	ENSG00000182606	ENST00000327628;ENST00000543338;ENST00000396175	T;T	0.53206	0.63;0.63	5.32	4.45	0.53987	Trafficking kinesin-binding protein domain (1);	0.067564	0.56097	D	0.000026	T	0.44117	0.1278	L	0.41492	1.28	0.80722	D	1	D;P	0.53462	0.96;0.904	P;P	0.46629	0.522;0.522	T	0.34004	-0.9846	10	0.40728	T	0.16	.	12.8284	0.57733	0.0787:0.0:0.9213:0.0	.	689;747	C9JC32;Q9UPV9	.;TRAK1_HUMAN	Q	747;726;689	ENSP00000328998:R747Q;ENSP00000379478:R689Q	ENSP00000328998:R747Q	R	+	2	0	TRAK1	42239611	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.267000	0.51577	1.267000	0.44247	0.591000	0.81541	CGG	.	.	none		0.637	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965		A	42264607	G	A	42264607	3	1	11	1	0	0	0	0	1	0	0	0	16464	1116	39	1	2690	1	TRAK1	3	42264607	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	3089903	42264607	155757823	56	1347											
SNRK	54861	hgsc.bcm.edu	37	chr3	43345043	43345043	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtcttaatgaagacttggcCaagaagtattttgctcagat	12	13	10	6	0	2	4	1	1	1	3	2	4	2	4	1	2	1	2	1	2	5	5			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:43345043C>T	ENST00000296088.7	+	3	652	c.348C>T	c.(346-348)gcC>gcT	p.A116A	SNRK_ENST00000454177.1_Silent_p.A116A|SNRK_ENST00000429705.2_Silent_p.A116A|SNRK_ENST00000462810.1_3'UTR|SNRK_ENST00000437827.1_Intron	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)		AAGACTTGGCCAAGAAGTATT	0.363																																					p.A116A		Atlas-SNP	.											.	SNRK	118	.	0			c.C348T						PASS	.						76	73	73					3																	43345043		1849	4090	5939	SO:0001819	synonymous_variant	54861	exon3			CTTGGCCAAGAAG	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.348C>T	3.37:g.43345043C>T		67	0	0		58	22	0.37931	NM_017719		Silent	SNP	ENST00000296088.7	37	CCDS43075.1																																																																																			.	.	none		0.363	SNRK-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344325.1	NM_017719		T	43345043	C	T	43345043	2	4	11	1	0	0	0	0	0	0	0	1	14866	581	21	2		2	SNRK	3	43345043	Silent	SNP	C	TCGA-FF-8042-01A-11D-2210-10	1080436	43345043	154677387	57	1348											
CCR3	1232	hgsc.bcm.edu	37	chr3	46307515	46307515	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgctggtgacagaggtgaTcgcctactcccactgctgca	8	9	11	13	1	0	3	0	2	0	1	2	3	1	3	2	2	4	3	2	2	1	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:46307515T>G	ENST00000357422.2	+	4	1409	c.866T>G	c.(865-867)aTc>aGc	p.I289S	CCR3_ENST00000395940.2_Missense_Mutation_p.I289S|CCR3_ENST00000545097.1_Missense_Mutation_p.I310S|CCR3_ENST00000395942.2_Missense_Mutation_p.I289S|CCR3_ENST00000541018.1_Missense_Mutation_p.I289S			P51677	CCR3_HUMAN	chemokine (C-C motif) receptor 3	289					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)		ACAGAGGTGATCGCCTACTCC	0.517																																					p.I310S		Atlas-SNP	.											.	CCR3	52	.	0			c.T929G						PASS	.						125	105	112					3																	46307515		2203	4300	6503	SO:0001583	missense	1232	exon3			AGGTGATCGCCTA	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.866T>G	3.37:g.46307515T>G	ENSP00000350003:p.Ile289Ser	122	0	0		142	45	0.316901	NM_178328	B3KVQ1|F5GWL6|Q15748|Q2YDB9|Q86WD2|Q8TDP6|Q9ULY8	Missense_Mutation	SNP	ENST00000357422.2	37	CCDS2738.1	.	.	.	.	.	.	.	.	.	.	T	19.72	3.881031	0.72294	.	.	ENSG00000183625	ENST00000357422;ENST00000545097;ENST00000541018;ENST00000395940;ENST00000395942	T;T;T;T;T	0.38240	1.15;1.15;1.15;1.15;1.15	5.73	5.73	0.89815	GPCR, rhodopsin-like superfamily (1);	0.272597	0.28236	N	0.016084	T	0.73032	0.3535	H	0.97103	3.94	0.58432	D	0.999995	D;D	0.67145	0.987;0.996	D;D	0.72625	0.956;0.978	T	0.83140	-0.0109	10	0.87932	D	0	.	16.0235	0.80516	0.0:0.0:0.0:1.0	.	310;289	F5GWL6;P51677	.;CCR3_HUMAN	S	289;310;289;289;289	ENSP00000350003:I289S;ENSP00000441600:I310S;ENSP00000440097:I289S;ENSP00000379271:I289S;ENSP00000379273:I289S	ENSP00000350003:I289S	I	+	2	0	CCR3	46282519	1.000000	0.71417	0.954000	0.39281	0.493000	0.33554	8.036000	0.88901	2.177000	0.69029	0.533000	0.62120	ATC	.	.	none		0.517	CCR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257380.2			G	46307515	T	G	46307515	3	3	11	1	0	0	0	0	1	0	0	0	2944	1435	50	5	935	5	CCR3	3	46307515	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	2962472	46307515	151714915	58	1349											
BSN	8927	hgsc.bcm.edu	37	chr3	49692749	49692749	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	actggcaccttccacccggcCcccagtgtgcctgagaagag	8	6	11	16	1	0	2	0	1	0	2	1	3	1	2	6	2	1	1	6	2	1	1	rs185582385	byFrequency	TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:49692749C>T	ENST00000296452.4	+	5	5874	c.5760C>T	c.(5758-5760)gcC>gcT	p.A1920A		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	1920					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)		TCCACCCGGCCCCCAGTGTGC	0.637													C|||	2	0.000399361	0.0	0.0014	5008	,	,		19178	0.0		0.001	False		,,,				2504	0.0				p.A1920A		Atlas-SNP	.											.	BSN	272	.	0			c.C5760T						PASS	.						40	40	40					3																	49692749		2203	4299	6502	SO:0001819	synonymous_variant	8927	exon5			CCCGGCCCCCAGT	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.5760C>T	3.37:g.49692749C>T		192	0	0		254	68	0.267717	NM_003458	O43161|Q7LGH3	Silent	SNP	ENST00000296452.4	37	CCDS2800.1																																																																																			C|0.999;T|0.001	0.001	strong		0.637	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		T	49692749	C	T	49692749	2	4	11	1	0	0	0	0	0	0	0	1	1532	610	22	2		2	BSN	3	49692749	Silent	SNP	C	TCGA-FF-8042-01A-11D-2210-10	3385234	49692749	148329681	59	1350											
DNAH1	25981	hgsc.bcm.edu	37	chr3	52398997	52398997	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcctggatgaggccatccGcgaggcctgcaggaacagca	10	5	13	13	2	0	1	0	1	0	0	2	4	2	3	4	4	3	2	4	4	1	0	rs377201322		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:52398997G>A	ENST00000420323.2	+	34	5741	c.5480G>A	c.(5479-5481)cGc>cAc	p.R1827H		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1827	AAA 2. {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)		GAGGCCATCCGCGAGGCCTGC	0.622																																					p.R1827H		Atlas-SNP	.											DNAH1_ENST00000420323,NS,carcinoma,0,4	DNAH1	534	4	0			c.G5480A						PASS	.	G	HIS/ARG	0,4214		0,0,2107	67	71	70		5480	4.6	1	3		70	1,8439		0,1,4219	no	missense	DNAH1	NM_015512.4	29	0,1,6326	AA,AG,GG		0.0118,0.0,0.0079	possibly-damaging	1827/4266	52398997	1,12653	2107	4220	6327	SO:0001583	missense	25981	exon34			CCATCCGCGAGGC	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.5480G>A	3.37:g.52398997G>A	ENSP00000401514:p.Arg1827His	94	0	0		103	35	0.339806	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	G	12.40	1.926969	0.34002	0.0	1.18E-4	ENSG00000114841	ENST00000420323	T	0.44881	0.91	4.6	4.6	0.57074	.	0.000000	0.46758	D	0.000261	T	0.38134	0.1029	L	0.59912	1.85	0.50467	D	0.999871	B	0.29037	0.231	B	0.23852	0.049	T	0.31081	-0.9956	10	0.45353	T	0.12	.	11.9735	0.53078	0.0841:0.0:0.9159:0.0	.	1827	C9JXH6	.	H	1827	ENSP00000401514:R1827H	ENSP00000401514:R1827H	R	+	2	0	DNAH1	52374037	0.855000	0.29742	0.988000	0.46212	0.252000	0.25951	2.447000	0.44917	2.128000	0.65567	0.467000	0.42956	CGC	.	.	weak		0.622	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		A	52398997	G	A	52398997	3	1	11	1	0	0	0	0	1	0	0	0	4599	1087	38	1	5610	1	DNAH1	3	52398997	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	2706248	52398997	145623433	60	1351											
THOC7	80145	hgsc.bcm.edu	37	chr3	63824125	63824125	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctagtaaagttttgcccattGaaaattcacattgagacagc	14	12	7	8	0	1	2	1	2	0	1	1	3	1	2	1	0	2	2	1	0	5	7			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:63824125G>A	ENST00000295899.5	-	3	300	c.188C>T	c.(187-189)tCa>tTa	p.S63L	THOC7_ENST00000498422.1_5'UTR|C3orf49_ENST00000295896.8_Intron	NM_025075.2	NP_079351.2	Q6I9Y2	THOC7_HUMAN	THO complex 7 homolog (Drosophila)	63	Interaction with THOC5.				mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|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)	RNA binding (GO:0003723)			central_nervous_system(1)|large_intestine(1)|ovary(1)|pancreas(1)	4				BRCA - Breast invasive adenocarcinoma(55;0.000439)|Kidney(15;0.00194)|KIRC - Kidney renal clear cell carcinoma(15;0.00218)		TTTGCCCATTGAAAATTCACA	0.299																																					p.S63L	Colon(48;665 1127 6720 18651)	Atlas-SNP	.											.	THOC7	24	.	0			c.C188T						PASS	.						62	64	63					3																	63824125		2202	4299	6501	SO:0001583	missense	80145	exon3			CCCATTGAAAATT	BC020599	CCDS2900.1, CCDS74957.1	3p14.1	2013-02-11			ENSG00000163634	ENSG00000163634		"THO complex subunits"	29874	protein-coding gene	gene with protein product	"Ngg1 interacting factor 3 like 1 binding protein 1", "functional spliceosome-associated protein 24"	611965				12951069	Standard	NM_001285404		Approved	NIF3L1BP1, FLJ23445, fSAP24	uc003dlt.4	Q6I9Y2	OTTHUMG00000158767	ENST00000295899.5:c.188C>T	3.37:g.63824125G>A	ENSP00000295899:p.Ser63Leu	264	0	0		263	74	0.281369	NM_025075	Q6P1L3|Q8WUF2|Q9H5H0	Missense_Mutation	SNP	ENST00000295899.5	37	CCDS2900.1	.	.	.	.	.	.	.	.	.	.	G	36	5.795790	0.96952	.	.	ENSG00000163634	ENST00000295899	.	.	.	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.74772	0.3760	L	0.59436	1.845	0.80722	D	1	D	0.57571	0.98	P	0.57846	0.828	T	0.74054	-0.3788	9	0.56958	D	0.05	-34.2799	20.4324	0.99085	0.0:0.0:1.0:0.0	.	63	Q6I9Y2	THOC7_HUMAN	L	63	.	ENSP00000295899:S63L	S	-	2	0	THOC7	63799165	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.823000	0.99369	2.833000	0.97629	0.585000	0.79938	TCA	.	.	none		0.299	THOC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352096.1	NM_025075		A	63824125	G	A	63824125	3	1	11	1	0	0	0	0	1	0	0	0	15885	1294	45	2	450	2	THOC7	3	63824125	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	11425128	63824125	134198305	61	1352											
ADAMTS9	56999	hgsc.bcm.edu	37	chr3	64536662	64536662	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgctcacgtcacagcgtgccCcatgcacctcgtttttgttg	5	13	9	14	3	2	0	2	0	0	0	3	0	2	0	3	0	4	4	3	0	0	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:64536662C>A	ENST00000498707.1	-	31	5117	c.4775G>T	c.(4774-4776)gGg>gTg	p.G1592V	ADAMTS9_ENST00000295903.4_Missense_Mutation_p.G1564V	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	1592	TSP type-1 13. {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)		ACAGCGTGCCCCATGCACCTC	0.542																																					p.G1592V		Atlas-SNP	.											.	ADAMTS9	206	.	0			c.G4775T						PASS	.						209	173	185					3																	64536662		2203	4300	6503	SO:0001583	missense	56999	exon31			CGTGCCCCATGCA	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.4775G>T	3.37:g.64536662C>A	ENSP00000418735:p.Gly1592Val	184	0	0		208	52	0.25	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Missense_Mutation	SNP	ENST00000498707.1	37	CCDS2903.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.705|7.705	0.693825|0.693825	0.15039|0.15039	.|.	.|.	ENSG00000163638|ENSG00000163638	ENST00000295903;ENST00000498707|ENST00000481060	T;T|T	0.65178|0.65549	-0.14;-0.14|-0.16	5.83|5.83	3.0|3.0	0.34707|0.34707	.|.	0.407807|0.407807	0.28203|0.28203	N|N	0.016217|0.016217	T|T	0.55737|0.55737	0.1939|0.1939	L|L	0.41415|0.41415	1.275|1.275	0.09310|0.09310	N|N	0.999994|0.999994	B;B;B|.	0.26258|.	0.003;0.145;0.001|.	B;B;B|.	0.27380|.	0.016;0.079;0.016|.	T|T	0.51236|0.51236	-0.8731|-0.8731	10|8	0.62326|0.72032	D|D	0.03|0.01	.|.	7.4549|7.4549	0.27261|0.27261	0.0:0.6035:0.2603:0.1362|0.0:0.6035:0.2603:0.1362	.|.	1564;1592;1592|.	B7ZVX9;Q9P2N4-1;Q9P2N4|.	.;.;ATS9_HUMAN|.	V|W	1564;1592|648	ENSP00000295903:G1564V;ENSP00000418735:G1592V|ENSP00000417521:G648W	ENSP00000295903:G1564V|ENSP00000417521:G648W	G|G	-|-	2|1	0|0	ADAMTS9|ADAMTS9	64511702|64511702	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.011000|0.011000	0.07611|0.07611	1.480000|1.480000	0.35464|0.35464	0.345000|0.345000	0.23873|0.23873	0.585000|0.585000	0.79938|0.79938	GGG|GGG	.	.	none		0.542	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1			A	64536662	C	A	64536662	3	1	11	1	0	0	0	0	1	0	0	0	273	623	22	4	1068	4	ADAMTS9	3	64536662	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	712537	64536662	133485768	62	1353											
ROBO1	6091	hgsc.bcm.edu	37	chr3	78667095	78667095	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttcctcttctggcgcatcCgtatccatatctgagaccag	7	13	7	14	2	4	1	0	1	4	1	7	2	7	1	4	1	0	2	4	1	2	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:78667095C>T	ENST00000464233.1	-	27	4085	c.3972G>A	c.(3970-3972)acG>acA	p.T1324T	ROBO1_ENST00000495273.1_Silent_p.T1279T|ROBO1_ENST00000467549.1_Silent_p.T1224T|ROBO1_ENST00000436010.2_Silent_p.T1285T	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	1324					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)		CTGGCGCATCCGTATCCATAT	0.557																																					p.T1324T		Atlas-SNP	.											ROBO1_ENST00000495273,NS,carcinoma,-1,4	ROBO1	833	4	0			c.G3972A						scavenged	.						58	65	63					3																	78667095		2002	4165	6167	SO:0001819	synonymous_variant	6091	exon27			CGCATCCGTATCC	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.3972G>A	3.37:g.78667095C>T		178	1	0.00561798		192	55	0.286458	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Silent	SNP	ENST00000464233.1	37	CCDS54611.1																																																																																			.	.	none		0.557	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		T	78667095	C	T	78667095	2	4	11	1	0	0	0	0	0	0	0	1	13528	639	23	1		1	ROBO1	3	78667095	Silent	SNP	C	TCGA-FF-8042-01A-11D-2210-10	14130433	78667095	119355335	63	1354											
OR5H1	26341	hgsc.bcm.edu	37	chr3	97852211	97852211	+	Missense_Mutation	SNP	G	G	A																															cttatacatttgttctcttcGcaatcttaaaaaagaaatct																								rs72926074	byFrequency	TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:97852211G>A	ENST00000354565.2	+	1	670	c.670G>A	c.(670-672)Gca>Aca	p.A224T	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005338.1	NP_001005338.1	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H, member 1	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(7)|kidney(8)|large_intestine(3)|lung(13)|ovary(1)|skin(1)	34						TGTTCTCTTCGCAATCTTAAA	0.343													A|||	126	0.0251597	0.0908	0.0043	5008	,	,		19300	0.0		0.003	False		,,,				2504	0.0				p.A224T		Atlas-SNP	.											.	OR5H1	71	.	0			c.G670A						PASS	.	A	THR/ALA	262,4142	791.4+/-415.1	10,242,1950	71	78	76		670	-0.4	0	3	dbSNP_130	76	9,8589	815.9+/-406.9	0,9,4290	yes	missense	OR5H1	NM_001005338.1	58	10,251,6240	AA,AG,GG		0.1047,5.9491,2.0843	benign	224/314	97852211	271,12731	2202	4299	6501	SO:0001583	missense	26341	exon1			CTCTTCGCAATCT	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.670G>A	3.37:g.97852211G>A	ENSP00000346575:p.Ala224Thr	268	0	0		204	11	0.0539216	NM_001005338		Missense_Mutation	SNP	ENST00000354565.2	37	CCDS33797.1	43	0.019688644688644688	40	0.08130081300813008	0	0.0	0	0.0	3	0.00395778364116095	A	0	-2.610351	0.00121	0.059491	0.001047	ENSG00000231192	ENST00000354565	T	0.00188	8.59	3.57	-0.435	0.12279	GPCR, rhodopsin-like superfamily (1);	0.627824	0.14082	N	0.342661	T	0.00012	0.0000	N	0.03930	-0.32	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08722	-1.0708	10	0.07325	T	0.83	.	3.9726	0.09460	0.3411:0.0:0.4652:0.1937	.	224	A6NKK0	OR5H1_HUMAN	T	224	ENSP00000346575:A224T	ENSP00000346575:A224T	A	+	1	0	OR5H1	99334901	0.000000	0.05858	0.003000	0.11579	0.002000	0.02628	-0.171000	0.09883	-0.302000	0.08869	-1.298000	0.01336	GCA	G|0.981;A|0.019	0.019	strong		0.343	OR5H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359100.2	NM_001005338		A	97852211	G	A	97852211	3	1	11	1	0	0	0	0	1	0	0	0	11168	1087	38	1	672	1	OR5H1	3	97852211	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	19185116	97852211	100170219	64	1355	19	2									
OR5H1	26341	hgsc.bcm.edu	37	chr3	97852220	97852220	+	Missense_Mutation	SNP	A	A	G																															ttgttctcttcgcaatcttaAaaaagaaatctgataaaggt																										TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:97852220A>G	ENST00000354565.2	+	1	679	c.679A>G	c.(679-681)Aaa>Gaa	p.K227E	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005338.1	NP_001005338.1	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H, 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)			breast(1)|endometrium(7)|kidney(8)|large_intestine(3)|lung(13)|ovary(1)|skin(1)	34						CGCAATCTTAAAAAAGAAATC	0.338																																					p.K227E		Atlas-SNP	.											.	OR5H1	71	.	0			c.A679G						PASS	.						73	81	78					3																	97852220		2202	4299	6501	SO:0001583	missense	26341	exon1			ATCTTAAAAAAGA	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.679A>G	3.37:g.97852220A>G	ENSP00000346575:p.Lys227Glu	255	0	0		211	19	0.0900474	NM_001005338		Missense_Mutation	SNP	ENST00000354565.2	37	CCDS33797.1	.	.	.	.	.	.	.	.	.	.	A	3.686	-0.064561	0.07273	.	.	ENSG00000231192	ENST00000354565	T	0.00169	8.63	3.57	3.57	0.40892	GPCR, rhodopsin-like superfamily (1);	0.264153	0.26915	N	0.021841	T	0.00356	0.0011	M	0.92784	3.345	0.09310	N	1	B	0.10296	0.003	B	0.23574	0.047	T	0.28870	-1.0030	10	0.87932	D	0	.	10.1009	0.42504	1.0:0.0:0.0:0.0	.	227	A6NKK0	OR5H1_HUMAN	E	227	ENSP00000346575:K227E	ENSP00000346575:K227E	K	+	1	0	OR5H1	99334910	0.000000	0.05858	0.030000	0.17652	0.006000	0.05464	0.423000	0.21313	1.481000	0.48307	0.164000	0.16699	AAA	.	.	none		0.338	OR5H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359100.2	NM_001005338		G	97852220	A	G	97852220	3	3	11	1	0	0	0	0	1	0	0	0	11168	15	1	3	681	3	OR5H1	3	97852220	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	9	97852220	100170210	65	1356	19	2									
OR5H1	26341	hgsc.bcm.edu	37	chr3	97852237	97852237	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttaaaaaagaaatctgataaAggtgtaaggaaagccttttc	18	11	8	4	0	1	2	0	1	1	1	2	3	1	3	1	2	1	1	1	2	8	5	rs150614363		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:97852237A>G	ENST00000354565.2	+	1	696	c.696A>G	c.(694-696)aaA>aaG	p.K232K	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005338.1	NP_001005338.1	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H, 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)|endometrium(7)|kidney(8)|large_intestine(3)|lung(13)|ovary(1)|skin(1)	34						AATCTGATAAAGGTGTAAGGA	0.388																																					p.K232K		Atlas-SNP	.											.	OR5H1	71	.	0			c.A696G						PASS	.	A		3,4403	4.2+/-10.8	0,3,2200	90	98	95		696	-1.9	0	3	dbSNP_134	95	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	OR5H1	NM_001005338.1		0,4,6498	GG,GA,AA		0.0116,0.0681,0.0308		232/314	97852237	4,13000	2203	4299	6502	SO:0001819	synonymous_variant	26341	exon1			TGATAAAGGTGTA	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.696A>G	3.37:g.97852237A>G		257	0	0		237	35	0.147679	NM_001005338		Silent	SNP	ENST00000354565.2	37	CCDS33797.1																																																																																			A|1.000;G|0.000	0.000	weak		0.388	OR5H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359100.2	NM_001005338		G	97852237	A	G	97852237	2	3	11	1	0	0	0	0	0	0	0	1	11168	69	3	3		3	OR5H1	3	97852237	Silent	SNP	A	TCGA-FF-8042-01A-11D-2210-10	17	97852237	100170193	66	1357											
OR5H15	403274	hgsc.bcm.edu	37	chr3	97888289	97888289	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agcccatctcttctctgtctGtttatactatggcccccttc	5	16	5	15	0	3	0	0	0	3	0	6	0	3	0	3	1	2	1	3	1	3	6	rs140807945		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:97888289G>C	ENST00000356526.2	+	1	746	c.746G>C	c.(745-747)tGt>tCt	p.C249S		NM_001005515.1	NP_001005515.1	A6NDH6	O5H15_HUMAN	olfactory receptor, family 5, subfamily H, member 15	249						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(2)|lung(20)|ovary(1)|prostate(1)|skin(2)|stomach(1)	35						TTCTCTGTCTGTTTATACTAT	0.428													g|||	1	0.000199681	0.0	0.0	5008	,	,		16343	0.001		0.0	False		,,,				2504	0.0				p.C249S		Atlas-SNP	.											OR5H15,colon,carcinoma,0,2	OR5H15	70	2	0			c.G746C						PASS	.						101	103	102					3																	97888289		2203	4300	6503	SO:0001583	missense	403274	exon1			CTGTCTGTTTATA		CCDS33799.1	3q11.2	2013-09-23			ENSG00000233412	ENSG00000233412		"GPCR / Class A : Olfactory receptors"	31287	protein-coding gene	gene with protein product							Standard	NM_001005515		Approved		uc011bgu.2	A6NDH6	OTTHUMG00000160076	ENST00000356526.2:c.746G>C	3.37:g.97888289G>C	ENSP00000373195:p.Cys249Ser	209	0	0		292	23	0.0787671	NM_001005515		Missense_Mutation	SNP	ENST00000356526.2	37	CCDS33799.1	.	.	.	.	.	.	.	.	.	.	-	0	-2.618780	0.00118	.	.	ENSG00000233412	ENST00000356526;ENST00000454529	T	0.35789	1.29	2.48	0.465	0.16711	GPCR, rhodopsin-like superfamily (1);	0.476318	0.17871	N	0.159188	T	0.07638	0.0192	N	0.00630	-1.315	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.36089	-0.9762	10	0.02654	T	1	.	4.8111	0.13344	0.0:0.4161:0.4463:0.1376	.	249	A6NDH6	O5H15_HUMAN	S	249	ENSP00000373195:C249S	ENSP00000373195:C249S	C	+	2	0	OR5H15	99370979	0.000000	0.05858	0.136000	0.22124	0.013000	0.08279	-0.279000	0.08479	-0.036000	0.13669	-1.406000	0.01132	TGT	G|0.999;C|0.001	0.001	weak		0.428	OR5H15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359109.1			C	97888289	G	C	97888289	3	2	11	1	0	0	0	0	1	0	0	0	11170	1377	48	4	748	4	OR5H15	3	97888289	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	36052	97888289	100134141	67	1358											
COL8A1	1295	hgsc.bcm.edu	37	chr3	99514003	99514003	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaggagaaggtgggattgtaGggccacaggggccaccaggt	11	5	18	7	0	0	1	0	0	0	1	0	3	0	2	3	7	0	1	3	7	3	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:99514003G>A	ENST00000261037.3	+	5	1638	c.1258G>A	c.(1258-1260)Ggg>Agg	p.G420R	COL8A1_ENST00000273342.4_Missense_Mutation_p.G420R	NM_001850.4	NP_001841.2	P27658	CO8A1_HUMAN	collagen, type VIII, alpha 1	420	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						TGGGATTGTAGGGCCACAGGG	0.617																																					p.G420R		Atlas-SNP	.											.	COL8A1	68	.	0			c.G1258A						PASS	.						38	38	38					3																	99514003		2203	4299	6502	SO:0001583	missense	1295	exon5			ATTGTAGGGCCAC	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.1258G>A	3.37:g.99514003G>A	ENSP00000261037:p.Gly420Arg	43	0	0		77	31	0.402597	NM_001850	D3DN42|Q53XI6|Q96D07	Missense_Mutation	SNP	ENST00000261037.3	37	CCDS2934.1	.	.	.	.	.	.	.	.	.	.	G	16.57	3.159714	0.57368	.	.	ENSG00000144810	ENST00000261037;ENST00000273342	D;D	0.99353	-5.77;-5.77	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	D	0.99582	0.9849	M	0.93638	3.44	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.98206	1.0470	10	0.87932	D	0	.	17.6174	0.88071	0.0:0.0:1.0:0.0	.	421;420	E7EPK9;P27658	.;CO8A1_HUMAN	R	420	ENSP00000261037:G420R;ENSP00000273342:G420R	ENSP00000261037:G420R	G	+	1	0	COL8A1	100996693	1.000000	0.71417	0.972000	0.41901	0.930000	0.56654	9.819000	0.99357	2.746000	0.94184	0.563000	0.77884	GGG	.	.	none		0.617	COL8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309001.1	NM_001850		A	99514003	G	A	99514003	3	1	11	1	0	0	0	0	1	0	0	0	3707	1000	35	2	1264	2	COL8A1	3	99514003	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	1625714	99514003	98508427	68	1359											
TBC1D23	55773	hgsc.bcm.edu	37	chr3	100039768	100039768	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctgaactcattaccttcaaGtatggaaatagcagtgcttc	12	12	7	10	0	2	1	2	1	0	0	3	2	2	2	2	1	4	3	2	1	6	5			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:100039768G>C	ENST00000394144.4	+	18	1978	c.1971G>C	c.(1969-1971)aaG>aaC	p.K657N	TBC1D23_ENST00000486274.1_3'UTR|TBC1D23_ENST00000344949.5_Missense_Mutation_p.K642N|TBC1D23_ENST00000475134.1_Missense_Mutation_p.K520N	NM_001199198.2	NP_001186127.1	Q9NUY8	TBC23_HUMAN	TBC1 domain family, member 23	657					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						TTACCTTCAAGTATGGAAATA	0.328																																					p.K657N		Atlas-SNP	.											.	TBC1D23	133	.	0			c.G1971C						PASS	.						64	65	64					3																	100039768		2203	4300	6503	SO:0001583	missense	55773	exon18			CTTCAAGTATGGA	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.1971G>C	3.37:g.100039768G>C	ENSP00000377700:p.Lys657Asn	76	0	0		85	28	0.329412	NM_001199198	B9A6M5|Q8TCN8|Q8WUB7|Q96D90|Q9NV75	Missense_Mutation	SNP	ENST00000394144.4	37	CCDS56265.1	.	.	.	.	.	.	.	.	.	.	G	17.87	3.495039	0.64186	.	.	ENSG00000036054	ENST00000344949;ENST00000394144;ENST00000475134	T;T;T	0.43294	0.95;0.96;1.02	5.55	3.76	0.43208	.	0.000000	0.85682	D	0.000000	T	0.58764	0.2145	M	0.73962	2.25	0.80722	D	1	D;D	0.76494	0.994;0.999	P;D	0.69479	0.829;0.964	T	0.57177	-0.7856	9	.	.	.	.	8.4773	0.33021	0.3074:0.0:0.6926:0.0	.	657;642	Q9NUY8;Q9NUY8-2	TBC23_HUMAN;.	N	642;657;520	ENSP00000340693:K642N;ENSP00000377700:K657N;ENSP00000418059:K520N	.	K	+	3	2	TBC1D23	101522458	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.160000	0.31761	0.694000	0.31654	0.655000	0.94253	AAG	.	.	none		0.328	TBC1D23-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353150.1	NM_018309		C	100039768	G	C	100039768	3	2	11	1	0	0	0	0	1	0	0	0	15628	1020	36	4	1992	4	TBC1D23	3	100039768	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	525765	100039768	97982662	69	1360											
ZBTB20	26137	hgsc.bcm.edu	37	chr3	114069130	114069130	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgacactcacctgtgtgtaCgaacatgtgcttgacgtagt	9	12	11	9	2	1	2	1	2	0	0	1	3	1	2	1	0	3	3	1	0	3	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:114069130C>T	ENST00000474710.1	-	4	1973	c.1795G>A	c.(1795-1797)Gta>Ata	p.V599I	ZBTB20-AS1_ENST00000467304.1_RNA|ZBTB20_ENST00000481632.1_Missense_Mutation_p.V526I|ZBTB20_ENST00000464560.1_Missense_Mutation_p.V526I|ZBTB20-AS1_ENST00000475939.1_RNA|ZBTB20_ENST00000471418.1_Missense_Mutation_p.V526I|ZBTB20_ENST00000357258.3_Missense_Mutation_p.V526I|ZBTB20_ENST00000393785.2_Missense_Mutation_p.V526I|ZBTB20-AS1_ENST00000496219.1_RNA|ZBTB20_ENST00000462705.1_Missense_Mutation_p.V526I	NM_001164342.1	NP_001157814.1	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20	599						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(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)		CCTGTGTGTACGAACATGTGC	0.557																																					p.V599I	NSCLC(69;748 1344 9802 11203 30933)	Atlas-SNP	.											.	ZBTB20	157	.	0			c.G1795A						PASS	.						156	154	155					3																	114069130		2203	4300	6503	SO:0001583	missense	26137	exon4			TGTGTACGAACAT	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.1795G>A	3.37:g.114069130C>T	ENSP00000419153:p.Val599Ile	252	0	0		323	87	0.26935	NM_001164342	Q63HP6|Q8N6R5|Q9Y410	Missense_Mutation	SNP	ENST00000474710.1	37	CCDS54626.1	.	.	.	.	.	.	.	.	.	.	C	13.05	2.121532	0.37436	.	.	ENSG00000181722	ENST00000462705;ENST00000393785;ENST00000481632;ENST00000471418;ENST00000474710;ENST00000357258;ENST00000464560	T;T;T;T;T;T;T	0.19105	3.17;3.17;3.17;3.17;2.17;3.17;3.17	6.03	6.03	0.97812	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	0.26955	0.0660	N	0.11000	0.08	0.80722	D	1	D	0.76494	0.999	D	0.74674	0.984	T	0.06356	-1.0831	10	0.07644	T	0.81	.	20.5753	0.99366	0.0:1.0:0.0:0.0	.	599	Q9HC78	ZBT20_HUMAN	I	526;526;526;526;599;526;526	ENSP00000420324:V526I;ENSP00000377375:V526I;ENSP00000418092:V526I;ENSP00000419902:V526I;ENSP00000419153:V599I;ENSP00000349803:V526I;ENSP00000417307:V526I	ENSP00000349803:V526I	V	-	1	0	ZBTB20	115551820	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	7.482000	0.81143	2.868000	0.98415	0.557000	0.71058	GTA	.	.	none		0.557	ZBTB20-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354951.1	NM_015642		T	114069130	C	T	114069130	3	4	11	1	0	0	0	0	1	0	0	0	17544	536	19	1	438	1	ZBTB20	3	114069130	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	14029362	114069130	83953300	70	1361											
KALRN	8997	hgsc.bcm.edu	37	chr3	124385389	124385389	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtcccggaccaaagagaggCgcgtgttcctcttcgagcag	9	7	13	12	4	1	1	0	0	1	1	4	4	3	2	3	2	1	2	3	2	1	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:124385389C>T	ENST00000291478.5	+	13	1508	c.1345C>T	c.(1345-1347)Cgc>Tgc	p.R449C	KALRN_ENST00000360013.3_Missense_Mutation_p.R2146C|KALRN_ENST00000459915.1_Missense_Mutation_p.R238C|KALRN_ENST00000393496.1_Missense_Mutation_p.R487C|KALRN_ENST00000428018.2_Missense_Mutation_p.R417C	NM_007064.3	NP_008995.2	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	2145					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						CAAAGAGAGGCGCGTGTTCCT	0.547																																					p.R2146C		Atlas-SNP	.											.	KALRN	556	.	0			c.C6436T						PASS	.						96	85	89					3																	124385389		2203	4300	6503	SO:0001583	missense	8997	exon46			GAGAGGCGCGTGT	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.1345C>T	3.37:g.124385389C>T	ENSP00000291478:p.Arg449Cys	171	0	0		184	50	0.271739	NM_001024660	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Missense_Mutation	SNP	ENST00000291478.5	37	CCDS3028.1	.	.	.	.	.	.	.	.	.	.	C	19.96	3.923372	0.73213	.	.	ENSG00000160145	ENST00000360013;ENST00000393496;ENST00000291478;ENST00000428018;ENST00000459915	T;T;T;T;T	0.12984	2.63;2.63;2.63;2.63;2.63	5.15	5.15	0.70609	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	T	0.44393	0.1291	M	0.90650	3.135	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	0.997;0.999;1.0;0.996	T	0.51084	-0.8750	10	0.87932	D	0	.	13.566	0.61819	0.193:0.807:0.0:0.0	.	238;449;487;2145	E7EUZ8;C9JQ37;O60229-5;O60229	.;.;.;KALRN_HUMAN	C	2146;487;449;417;238	ENSP00000353109:R2146C;ENSP00000377134:R487C;ENSP00000291478:R449C;ENSP00000402419:R417C;ENSP00000420318:R238C	ENSP00000291478:R449C	R	+	1	0	KALRN	125868079	0.883000	0.30277	0.999000	0.59377	0.993000	0.82548	1.698000	0.37794	2.687000	0.91594	0.563000	0.77884	CGC	.	.	none		0.547	KALRN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000246891.5	NM_003947		T	124385389	C	T	124385389	3	4	11	1	0	0	0	0	1	0	0	0	7984	768	27	1	6774	1	KALRN	3	124385389	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	10316259	124385389	73637041	71	1362											
KLF15	28999	hgsc.bcm.edu	37	chr3	126070934	126070934	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacaggggcaatgcgcacaaActtggagggcaggttcaagt	12	6	14	9	1	1	0	1	0	0	0	1	1	1	1	0	5	2	4	0	5	3	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:126070934A>C	ENST00000296233.3	-	2	1062	c.832T>G	c.(832-834)Ttt>Gtt	p.F278V	KLF15_ENST00000509675.1_5'Flank	NM_014079.3	NP_054798.1	Q9UIH9	KLF15_HUMAN	Kruppel-like factor 15	278					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)		ATGCGCACAAACTTGGAGGGC	0.627																																					p.F278V		Atlas-SNP	.											.	KLF15	40	.	0			c.T832G						PASS	.						33	24	27					3																	126070934		2173	4274	6447	SO:0001583	missense	28999	exon2			GCACAAACTTGGA	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.832T>G	3.37:g.126070934A>C	ENSP00000296233:p.Phe278Val	331	0	0		389	96	0.246787	NM_014079		Missense_Mutation	SNP	ENST00000296233.3	37	CCDS3036.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.060597	0.76074	.	.	ENSG00000163884	ENST00000296233	T	0.08896	3.04	4.98	4.98	0.66077	.	0.046500	0.85682	D	0.000000	T	0.21761	0.0524	L	0.57536	1.79	0.80722	D	1	D	0.89917	1.0	D	0.69307	0.963	T	0.01448	-1.1352	10	0.26408	T	0.33	.	12.9208	0.58230	1.0:0.0:0.0:0.0	.	278	Q9UIH9	KLF15_HUMAN	V	278	ENSP00000296233:F278V	ENSP00000296233:F278V	F	-	1	0	KLF15	127553624	1.000000	0.71417	0.999000	0.59377	0.869000	0.49853	9.264000	0.95635	2.003000	0.58678	0.398000	0.26397	TTT	.	.	none		0.627	KLF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370096.1	NM_014079		C	126070934	A	C	126070934	3	2	11	1	0	0	0	0	1	0	0	0	8352	43	2	5	426	5	KLF15	3	126070934	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	1685545	126070934	71951496	72	1363											
CCDC37	348807	hgsc.bcm.edu	37	chr3	126142198	126142198	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccatcccccccacgcaggaGgacaccgacagcgatgggga	10	2	12	17	3	0	0	0	0	0	0	1	5	1	3	5	4	1	1	5	4	0	0			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:126142198G>A	ENST00000352312.1	+	12	1212	c.1113G>A	c.(1111-1113)gaG>gaA	p.E371E	CCDC37_ENST00000505024.1_Silent_p.E372E|CCDC37_ENST00000393425.1_Silent_p.E372E	NM_182628.2	NP_872434.2	Q494V2	CCD37_HUMAN	coiled-coil domain containing 37	371										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)		CCACGCAGGAGGACACCGACA	0.667																																					p.E371E		Atlas-SNP	.											.	CCDC37	69	.	0			c.G1113A						PASS	.						41	37	38					3																	126142198		2203	4300	6503	SO:0001819	synonymous_variant	348807	exon12			GCAGGAGGACACC	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.1113G>A	3.37:g.126142198G>A		154	0	0		145	42	0.289655	NM_182628	D3DNA8|Q494V1|Q494V4|Q8N838	Silent	SNP	ENST00000352312.1	37	CCDS3037.1																																																																																			.	.	none		0.667	CCDC37-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000370099.4	NM_182628		A	126142198	G	A	126142198	2	1	11	1	0	0	0	0	0	0	0	1	2811	991	35	2		2	CCDC37	3	126142198	Silent	SNP	G	TCGA-FF-8042-01A-11D-2210-10	71264	126142198	71880232	73	1364											
EPHB3	2049	hgsc.bcm.edu	37	chr3	184290807	184290807	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	actggggcggagcccacctcGctggtcattgctcctggcac	5	8	13	15	2	1	0	1	0	0	0	3	1	2	1	3	5	2	3	3	5	0	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:184290807G>A	ENST00000330394.2	+	3	1151	c.699G>A	c.(697-699)tcG>tcA	p.S233S	EIF2B5_ENST00000444495.1_Intron	NM_004443.3	NP_004434.2	P54753	EPHB3_HUMAN	EPH receptor B3	233	Cys-rich.				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)			AGCCCACCTCGCTGGTCATTG	0.632																																					p.S233S		Atlas-SNP	.											.	EPHB3	114	.	0			c.G699A						PASS	.						53	59	57					3																	184290807		2203	4299	6502	SO:0001819	synonymous_variant	2049	exon3			CACCTCGCTGGTC	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.699G>A	3.37:g.184290807G>A		99	0	0		139	45	0.323741	NM_004443	Q7Z740	Silent	SNP	ENST00000330394.2	37	CCDS3268.1																																																																																			.	.	none		0.632	EPHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345413.1	NM_004443		A	184290807	G	A	184290807	2	1	11	1	0	0	0	0	0	0	0	1	5178	1074	38	1		1	EPHB3	3	184290807	Silent	SNP	G	TCGA-FF-8042-01A-11D-2210-10	58148609	184290807	13731623	74	1365											
VPS8	23355	hgsc.bcm.edu	37	chr3	184616396	184616396	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgtttatatgatgctatgaTctatgtctacaacagaggca	12	14	8	7	1	2	3	0	2	2	1	3	3	2	3	0	1	3	3	0	1	6	6			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:184616396T>C	ENST00000437079.3	+	24	2219	c.2048T>C	c.(2047-2049)aTc>aCc	p.I683T	VPS8_ENST00000436792.2_Missense_Mutation_p.I681T|VPS8_ENST00000446204.2_Missense_Mutation_p.I591T|VPS8_ENST00000287546.4_Missense_Mutation_p.I683T	NM_001009921.2	NP_001009921.1	Q8N3P4	VPS8_HUMAN	vacuolar protein sorting 8 homolog (S. cerevisiae)	683							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)			GATGCTATGATCTATGTCTAC	0.338																																					p.I683T		Atlas-SNP	.											.	VPS8	109	.	0			c.T2048C						PASS	.						119	118	118					3																	184616396		1838	4084	5922	SO:0001583	missense	23355	exon23			CTATGATCTATGT	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.2048T>C	3.37:g.184616396T>C	ENSP00000397879:p.Ile683Thr	222	0	0		241	64	0.26556	NM_001009921	A8K8Q8|B9EIQ1|C9JB61|O94896|Q63HP2|Q9BVP9|Q9H9B0	Missense_Mutation	SNP	ENST00000437079.3	37	CCDS46971.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.589816	0.86851	.	.	ENSG00000156931	ENST00000287546;ENST00000437079;ENST00000436792;ENST00000446204	T;T;T;T	0.33865	1.47;1.47;1.47;1.39	5.75	5.75	0.90469	Quinonprotein alcohol dehydrogenase-like (1);	0.042417	0.85682	D	0.000000	T	0.62551	0.2437	M	0.80028	2.48	0.80722	D	1	P;D;P	0.65815	0.756;0.995;0.661	P;D;B	0.69307	0.644;0.963;0.43	T	0.67837	-0.5567	10	0.87932	D	0	-21.0896	16.0544	0.80788	0.0:0.0:0.0:1.0	.	683;591;681	Q8N3P4;Q8N3P4-2;Q8N3P4-3	VPS8_HUMAN;.;.	T	683;683;681;591	ENSP00000287546:I683T;ENSP00000397879:I683T;ENSP00000404704:I681T;ENSP00000405483:I591T	ENSP00000287546:I683T	I	+	2	0	VPS8	186099090	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.495000	0.81514	2.188000	0.69820	0.477000	0.44152	ATC	.	.	none		0.338	VPS8-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015303		C	184616396	T	C	184616396	3	2	11	1	0	0	0	0	1	0	0	0	17233	1435	50	3	2134	3	VPS8	3	184616396	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	325589	184616396	13406034	75	1366											
ATP13A5	344905	hgsc.bcm.edu	37	chr3	193051546	193051546	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccccagtacttactccatggTacatatatacccctagggca	11	10	6	14	0	0	0	0	0	0	0	1	0	1	0	5	2	4	3	5	2	7	7			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:193051546T>C	ENST00000342358.4	-	11	1382	c.1265A>G	c.(1264-1266)tAc>tGc	p.Y422C		NM_198505.2	NP_940907.2	Q4VNC0	AT135_HUMAN	ATPase type 13A5	422						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)		TACTCCATGGTACATATATAC	0.438																																					p.Y422C		Atlas-SNP	.											.	ATP13A5	171	.	0			c.A1265G						PASS	.						73	74	74					3																	193051546		2203	4300	6503	SO:0001583	missense	344905	exon11			CCATGGTACATAT	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.1265A>G	3.37:g.193051546T>C	ENSP00000341942:p.Tyr422Cys	80	0	0		112	29	0.258929	NM_198505	Q6UWS4|Q6ZWL0	Missense_Mutation	SNP	ENST00000342358.4	37	CCDS33914.1	.	.	.	.	.	.	.	.	.	.	T	12.33	1.904221	0.33628	.	.	ENSG00000187527	ENST00000342358	D	0.90620	-2.7	5.53	5.53	0.82687	ATPase, P-type, ATPase-associated domain (1);	0.000000	0.64402	D	0.000010	D	0.92557	0.7636	L	0.55743	1.74	0.27566	N	0.950029	D	0.76494	0.999	D	0.68353	0.957	D	0.86778	0.1977	10	0.38643	T	0.18	-5.2622	9.8364	0.40971	0.153:0.0:0.0:0.847	.	422	Q4VNC0	AT135_HUMAN	C	422	ENSP00000341942:Y422C	ENSP00000341942:Y422C	Y	-	2	0	ATP13A5	194534240	0.000000	0.05858	0.943000	0.38184	0.061000	0.15899	0.525000	0.22956	2.111000	0.64477	0.528000	0.53228	TAC	.	.	none		0.438	ATP13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343012.1	NM_198505		C	193051546	T	C	193051546	3	2	11	1	0	0	0	0	1	0	0	0	1127	1638	57	3	2469	3	ATP13A5	3	193051546	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	8435150	193051546	4970884	76	1367											
TNK2	10188	hgsc.bcm.edu	37	chr3	195605200	195605200	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcaaagtcctgaagggcccGcatgtctgtgggctgggcct	6	9	14	12	1	2	1	1	1	1	0	3	1	3	1	3	3	0	2	3	3	2	0			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr3:195605200G>A	ENST00000333602.6	-	9	1797	c.1180C>T	c.(1180-1182)Cgg>Tgg	p.R394W	TNK2_ENST00000316664.3_Missense_Mutation_p.R394W|TNK2_ENST00000428187.1_Missense_Mutation_p.R426W|TNK2_ENST00000381916.2_Missense_Mutation_p.R457W|TNK2_ENST00000392400.1_Missense_Mutation_p.R394W|TNK2_ENST00000468819.1_5'Flank	NM_005781.4	NP_005772.3	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2	394	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.			Missing (in Ref. 4; AAH08884). {ECO:0000305}.	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)	TGAAGGGCCCGCATGTCTGTG	0.617																																					p.R457W		Atlas-SNP	.											.	TNK2	246	.	0			c.C1369T						PASS	.						117	112	114					3																	195605200		2203	4300	6503	SO:0001583	missense	10188	exon9			GGGCCCGCATGTC	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.1180C>T	3.37:g.195605200G>A	ENSP00000329425:p.Arg394Trp	160	0	0		212	47	0.221698	NM_001010938	Q6ZMQ0|Q8N6U7|Q96H59	Missense_Mutation	SNP	ENST00000333602.6	37	CCDS33928.1	.	.	.	.	.	.	.	.	.	.	G	18.58	3.655314	0.67586	.	.	ENSG00000061938	ENST00000333602;ENST00000381916;ENST00000428187;ENST00000392400;ENST00000316664	T;T;T;T;T	0.62639	0.01;0.01;0.01;0.01;0.01	4.47	1.45	0.22620	Src homology-3 domain (3);Protein kinase-like domain (1);	0.181464	0.44097	D	0.000500	T	0.79941	0.4533	M	0.93507	3.425	0.45867	D	0.998722	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.70935	0.918;0.958;0.971;0.952	T	0.79374	-0.1830	10	0.72032	D	0.01	.	7.4437	0.27198	0.0839:0.0:0.3517:0.5644	.	270;394;457;426	Q59FX1;Q07912;Q07912-3;C9J1X3	.;ACK1_HUMAN;.;.	W	394;457;426;394;394	ENSP00000329425:R394W;ENSP00000371341:R457W;ENSP00000392546:R426W;ENSP00000376201:R394W;ENSP00000323216:R394W	ENSP00000323216:R394W	R	-	1	2	TNK2	197089597	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	0.601000	0.24119	0.491000	0.27793	0.655000	0.94253	CGG	.	.	none		0.617	TNK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341437.3	NM_005781		A	195605200	G	A	195605200	3	1	11	1	0	0	0	0	1	0	0	0	16333	1086	38	1	2013	1	TNK2	3	195605200	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	2553654	195605200	2417230	77	1368											
HTT	3064	hgsc.bcm.edu	37	chr4	3129287	3129287	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acagctcccagaccaccaccGaagggcctgattcagctgtt	10	7	9	15	1	1	2	1	1	0	1	2	3	2	2	5	1	2	3	5	1	1	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr4:3129287G>A	ENST00000355072.5	+	12	1844	c.1699G>A	c.(1699-1701)Gaa>Aaa	p.E567K		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	567					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)		GACCACCACCGAAGGGCCTGA	0.537																																					p.E567K		Atlas-SNP	.											.	HTT	221	.	0			c.G1699A						PASS	.						50	54	53					4																	3129287		1997	4158	6155	SO:0001583	missense	3064	exon12			ACCACCGAAGGGC	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.1699G>A	4.37:g.3129287G>A	ENSP00000347184:p.Glu567Lys	238	0	0		226	92	0.40708	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	37	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	G	32	5.190556	0.94923	.	.	ENSG00000197386	ENST00000355072	T	0.06768	3.26	4.84	4.84	0.62591	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.20414	0.0491	L	0.38175	1.15	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.01084	-1.1457	10	0.36615	T	0.2	.	17.722	0.88355	0.0:0.0:1.0:0.0	.	567	P42858	HD_HUMAN	K	567	ENSP00000347184:E567K	ENSP00000347184:E567K	E	+	1	0	HTT	3099085	1.000000	0.71417	0.958000	0.39756	0.941000	0.58515	9.017000	0.93651	2.533000	0.85409	0.655000	0.94253	GAA	.	.	none		0.537	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		A	3129287	G	A	3129287	3	1	11	1	0	0	0	0	1	0	0	0	7466	1059	37	1	1745	1	HTT	4	3129287	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10		3129287	188024989	78	1369											
OTOP1	133060	hgsc.bcm.edu	37	chr4	4199791	4199791	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agatggcagtgcacagagttGggggcgtgcagttacactgc	9	8	16	8	1	0	2	0	0	0	2	0	2	0	2	0	3	4	5	0	3	1	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr4:4199791G>A	ENST00000296358.4	-	5	794	c.770C>T	c.(769-771)cCa>cTa	p.P257L		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	257					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)		GCACAGAGTTGGGGGCGTGCA	0.532																																					p.P257L		Atlas-SNP	.											.	OTOP1	118	.	0			c.C770T						PASS	.						64	52	56					4																	4199791		2203	4300	6503	SO:0001583	missense	133060	exon5			AGAGTTGGGGGCG	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.770C>T	4.37:g.4199791G>A	ENSP00000296358:p.Pro257Leu	144	0	0		150	64	0.426667	NM_177998	A1L476	Missense_Mutation	SNP	ENST00000296358.4	37	CCDS3372.1	.	.	.	.	.	.	.	.	.	.	G	5.616	0.298361	0.10622	.	.	ENSG00000163982	ENST00000296358	T	0.08807	3.05	4.56	2.75	0.32379	.	0.653632	0.15845	N	0.241839	T	0.08088	0.0202	L	0.44542	1.39	0.09310	N	1	B	0.31351	0.32	B	0.30716	0.119	T	0.24905	-1.0147	10	0.59425	D	0.04	.	7.7448	0.28862	0.0786:0.0:0.6134:0.3079	.	257	Q7RTM1	OTOP1_HUMAN	L	257	ENSP00000296358:P257L	ENSP00000296358:P257L	P	-	2	0	OTOP1	4250692	0.283000	0.24277	0.001000	0.08648	0.003000	0.03518	1.794000	0.38774	0.426000	0.26116	0.404000	0.27445	CCA	.	.	none		0.532	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206661.2	NM_177998		A	4199791	G	A	4199791	3	1	11	1	0	0	0	0	1	0	0	0	11314	1348	47	2	1076	2	OTOP1	4	4199791	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	1070504	4199791	186954485	79	1370											
SH3TC1	54436	hgsc.bcm.edu	37	chr4	8224646	8224646	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctgaggaggatgccaggCagttgctgaggcggatgtcg	7	10	17	7	2	1	2	0	2	1	0	2	5	1	5	1	5	2	3	1	5	0	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr4:8224646C>T	ENST00000245105.3	+	10	1259	c.1192C>T	c.(1192-1194)Cag>Tag	p.Q398*	SH3TC1_ENST00000539824.1_Nonsense_Mutation_p.Q322*	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	398										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						GGATGCCAGGCAGTTGCTGAG	0.547																																					p.Q398X	NSCLC(145;2298 2623 35616 37297)	Atlas-SNP	.											.	SH3TC1	105	.	0			c.C1192T						PASS	.						87	79	81					4																	8224646		2203	4300	6503	SO:0001587	stop_gained	54436	exon10			GCCAGGCAGTTGC	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.1192C>T	4.37:g.8224646C>T	ENSP00000245105:p.Gln398*	125	0	0		95	45	0.473684	NM_018986	Q4W5G5	Nonsense_Mutation	SNP	ENST00000245105.3	37	CCDS3399.1	.	.	.	.	.	.	.	.	.	.	C	13.87	2.366069	0.41902	.	.	ENSG00000125089	ENST00000382516;ENST00000245105;ENST00000539824;ENST00000535265;ENST00000508641	.	.	.	4.31	1.4	0.22301	.	1.151220	0.06322	N	0.704583	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06757	T	0.87	-11.1481	8.0625	0.30642	0.2675:0.4488:0.2837:0.0	.	.	.	.	X	136;398;322;227;180	.	ENSP00000245105:Q398X	Q	+	1	0	SH3TC1	8275546	0.425000	0.25498	0.001000	0.08648	0.170000	0.22686	0.931000	0.28871	-0.047000	0.13423	0.561000	0.74099	CAG	.	.	none		0.547	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986		T	8224646	C	T	8224646	4	4	11	1	0	0	0	0	0	1	0	0	14276	711	25	2	1226	2	SH3TC1	4	8224646	Nonsense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	4024855	8224646	182929630	80	1371											
PCDH7	5099	hgsc.bcm.edu	37	chr4	30725116	30725116	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttttctattgaaaatgacaCggggaccatttactccacaa	13	13	6	9	1	1	2	0	2	1	0	2	3	2	3	2	2	1	0	2	2	5	6			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr4:30725116C>T	ENST00000361762.2	+	1	3080	c.2072C>T	c.(2071-2073)aCg>aTg	p.T691M	PCDH7_ENST00000543491.1_Missense_Mutation_p.T691M	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	691	Cadherin 6. {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						GAAAATGACACGGGGACCATT	0.488																																					p.T691M		Atlas-SNP	.											.	PCDH7	215	.	0			c.C2072T						PASS	.						118	118	118					4																	30725116		2203	4300	6503	SO:0001583	missense	5099	exon1			ATGACACGGGGAC	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.2072C>T	4.37:g.30725116C>T	ENSP00000355243:p.Thr691Met	94	0	0		66	4	0.0606061	NM_032457	O60246|O60247|Q4W5C4	Missense_Mutation	SNP	ENST00000361762.2	37	CCDS33971.1	.	.	.	.	.	.	.	.	.	.	C	17.60	3.431137	0.62844	.	.	ENSG00000169851	ENST00000361762;ENST00000543491;ENST00000333135	T;T	0.58060	0.36;0.36	5.25	5.25	0.73442	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.80706	0.4674	M	0.93808	3.46	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	0.85549	0.1220	9	0.87932	D	0	.	19.0454	0.93018	0.0:1.0:0.0:0.0	.	691;644;691	F5GWJ1;O60245-3;O60245	.;.;PCDH7_HUMAN	M	691;691;644	ENSP00000355243:T691M;ENSP00000441802:T691M	ENSP00000330302:T644M	T	+	2	0	PCDH7	30334214	1.000000	0.71417	0.969000	0.41365	0.982000	0.71751	7.647000	0.83462	2.722000	0.93159	0.655000	0.94253	ACG	.	.	none		0.488	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589		T	30725116	C	T	30725116	3	4	11	1	0	0	0	0	1	0	0	0	11525	536	19	1	2074	1	PCDH7	4	30725116	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	22500470	30725116	160429160	81	1372											
YIPF7	285525	hgsc.bcm.edu	37	chr4	44652108	44652108	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atcagagtcaaattgtgccaAgtttgacatcctgaaaaata	16	11	7	7	0	2	3	2	2	0	1	3	3	3	3	2	0	1	1	2	0	5	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr4:44652108A>C	ENST00000332990.5	-	2	98	c.82T>G	c.(82-84)Ttg>Gtg	p.L28V	YIPF7_ENST00000415895.4_Missense_Mutation_p.L4V	NM_182592.2	NP_872398.2	Q8N8F6	YIPF7_HUMAN	Yip1 domain family, member 7	28						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(1)|large_intestine(1)|lung(9)|upper_aerodigestive_tract(1)	12						AATTGTGCCAAGTTTGACATC	0.299																																					p.L28V		Atlas-SNP	.											.	YIPF7	33	.	0			c.T82G						PASS	.						39	36	37					4																	44652108		1809	4068	5877	SO:0001583	missense	285525	exon2			GTGCCAAGTTTGA	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.82T>G	4.37:g.44652108A>C	ENSP00000332772:p.Leu28Val	118	0	0		101	45	0.445545	NM_182592	Q3SY21|Q3SY22	Missense_Mutation	SNP	ENST00000332990.5	37	CCDS54766.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.39|12.39	1.923362|1.923362	0.33908|0.33908	.|.	.|.	ENSG00000177752|ENSG00000177752	ENST00000415895|ENST00000332990	.|T	.|0.43294	.|0.95	5.45|5.45	0.453|0.453	0.16639|0.16639	.|.	.|.	.|.	.|.	.|.	T|T	0.19846|0.19846	0.0477|0.0477	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	0.999998|0.999998	.|B;B	.|0.23806	.|0.091;0.002	.|B;B	.|0.19946	.|0.027;0.009	T|T	0.19516|0.19516	-1.0303|-1.0303	5|9	.|0.16896	.|T	.|0.51	-0.5497|-0.5497	0.8365|0.8365	0.01141|0.01141	0.5011:0.1696:0.1654:0.1639|0.5011:0.1696:0.1654:0.1639	.|.	.|28;28	.|Q8N8F6-4;Q8N8F6	.|.;YIPF7_HUMAN	R|V	4|28	.|ENSP00000332772:L28V	.|ENSP00000332772:L28V	L|L	-|-	2|1	0|2	YIPF7|YIPF7	44346865|44346865	0.980000|0.980000	0.34600|0.34600	0.977000|0.977000	0.42913|0.42913	0.976000|0.976000	0.68499|0.68499	0.167000|0.167000	0.16602|0.16602	0.549000|0.549000	0.28973|0.28973	0.524000|0.524000	0.50904|0.50904	CTT|TTG	.	.	none		0.299	YIPF7-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_182592		C	44652108	A	C	44652108	3	2	11	1	0	0	0	0	1	0	0	0	17498	69	3	5	780	5	YIPF7	4	44652108	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	13926992	44652108	146502168	82	1373											
GABRB1	2560	hgsc.bcm.edu	37	chr4	47427752	47427752	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccggaatgagacgagtggctCggaagtgctcacgagcgtga	10	6	16	9	5	1	2	1	2	0	1	2	7	1	4	1	3	2	2	1	3	2	0	rs539587921		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr4:47427752C>T	ENST00000295454.3	+	9	1434	c.1142C>T	c.(1141-1143)tCg>tTg	p.S381L	GABRB1_ENST00000538619.1_Missense_Mutation_p.S311L	NM_000812.3	NP_000803.2	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 1	381					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)	ACGAGTGGCTCGGAAGTGCTC	0.597													C|||	1	0.000199681	0.0	0.0	5008	,	,		16678	0.0		0.0	False		,,,				2504	0.001				p.S381L		Atlas-SNP	.											GABRB1,NS,carcinoma,-1,1	GABRB1	107	1	0			c.C1142T						PASS	.						64	66	66					4																	47427752		2203	4300	6503	SO:0001583	missense	2560	exon9			GTGGCTCGGAAGT		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.1142C>T	4.37:g.47427752C>T	ENSP00000295454:p.Ser381Leu	73	0	0		74	30	0.405405	NM_000812	B2R6U7|D6REL3|Q16166|Q8TBK3	Missense_Mutation	SNP	ENST00000295454.3	37	CCDS3474.1	.	.	.	.	.	.	.	.	.	.	C	12.57	1.976578	0.34848	.	.	ENSG00000163288	ENST00000295454;ENST00000538619	D;D	0.84370	-1.84;-1.84	5.48	4.64	0.57946	Neurotransmitter-gated ion-channel transmembrane domain (2);	1.455620	0.05312	U	0.524982	T	0.80199	0.4579	N	0.21097	0.63	0.47441	D	0.999423	B;B	0.18013	0.025;0.004	B;B	0.13407	0.009;0.003	T	0.56105	-0.8034	10	0.40728	T	0.16	-5.7084	14.2643	0.66107	0.0:0.9292:0.0:0.0708	.	311;381	F5GXV5;P18505	.;GBRB1_HUMAN	L	381;311	ENSP00000295454:S381L;ENSP00000440330:S311L	ENSP00000295454:S381L	S	+	2	0	GABRB1	47122509	0.997000	0.39634	0.890000	0.34922	0.042000	0.13812	3.301000	0.51842	1.558000	0.49541	0.650000	0.86243	TCG	.	.	none		0.597	GABRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216896.1			T	47427752	C	T	47427752	3	4	11	1	0	0	0	0	1	0	0	0	6174	893	31	1	1176	1	GABRB1	4	47427752	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	2775644	47427752	143726524	83	1374											
ATP10D	57205	hgsc.bcm.edu	37	chr4	47593309	47593309	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgctattgagcaaggaaacTtatctctgtgtgaaactgct	11	13	10	7	0	1	2	0	2	1	0	2	3	1	3	0	1	5	3	0	1	5	3	rs536235043	byFrequency	TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr4:47593309T>G	ENST00000273859.3	+	23	4461	c.4192T>G	c.(4192-4194)Tta>Gta	p.L1398V		NM_020453.3	NP_065186.3	Q9P241	AT10D_HUMAN	ATPase, class V, type 10D	1398					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						GCAAGGAAACTTATCTCTGTG	0.458																																					p.L1398V		Atlas-SNP	.											.	ATP10D	168	.	0			c.T4192G						PASS	.						144	143	143					4																	47593309		2203	4299	6502	SO:0001583	missense	57205	exon23			GGAAACTTATCTC	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.4192T>G	4.37:g.47593309T>G	ENSP00000273859:p.Leu1398Val	106	0	0		71	28	0.394366	NM_020453	A2RRC8|D6REN2|Q8NC70|Q96SR3	Missense_Mutation	SNP	ENST00000273859.3	37	CCDS3476.1	.	.	.	.	.	.	.	.	.	.	T	10.03	1.239183	0.22711	.	.	ENSG00000145246	ENST00000273859	T	0.38722	1.12	4.33	-8.66	0.00866	.	4.506970	0.00166	N	0.000015	T	0.31040	0.0784	L	0.46157	1.445	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30736	-0.9968	10	0.10636	T	0.68	11.4644	9.5229	0.39147	0.4141:0.0:0.4591:0.1268	.	1398	Q9P241	AT10D_HUMAN	V	1398	ENSP00000273859:L1398V	ENSP00000273859:L1398V	L	+	1	2	ATP10D	47288066	0.000000	0.05858	0.000000	0.03702	0.435000	0.31806	-2.282000	0.01156	-3.824000	0.00102	-0.898000	0.02899	TTA	.	.	none		0.458	ATP10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216900.1	NM_020453		G	47593309	T	G	47593309	3	3	11	1	0	0	0	0	1	0	0	0	1118	1606	56	5	4278	5	ATP10D	4	47593309	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	165557	47593309	143560967	84	1375											
CDKL2	8999	hgsc.bcm.edu	37	chr4	76507055	76507055	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatggttctcagtgctggtgTtccatttgaggcaaatcagc	9	13	11	8	0	2	1	2	1	1	0	4	1	3	1	1	3	2	4	1	3	2	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr4:76507055T>G	ENST00000429927.2	-	11	2173	c.1470A>C	c.(1468-1470)gaA>gaC	p.E490D	CDKL2_ENST00000307465.4_Missense_Mutation_p.E567D	NM_003948.3	NP_003939.1	Q92772	CDKL2_HUMAN	cyclin-dependent kinase-like 2 (CDC2-related kinase)	490					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)			AGTGCTGGTGTTCCATTTGAG	0.428																																					p.E490D		Atlas-SNP	.											.	CDKL2	58	.	0			c.A1470C						PASS	.						88	81	83					4																	76507055		2203	4300	6503	SO:0001583	missense	8999	exon11			CTGGTGTTCCATT	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.1470A>C	4.37:g.76507055T>G	ENSP00000412365:p.Glu490Asp	94	0	0		91	40	0.43956	NM_003948	B2R695	Missense_Mutation	SNP	ENST00000429927.2	37	CCDS3570.1	.	.	.	.	.	.	.	.	.	.	T	11.06	1.528127	0.27299	.	.	ENSG00000138769	ENST00000429927;ENST00000307465	T;T	0.72725	-0.55;-0.68	4.75	-5.16	0.02857	.	.	.	.	.	T	0.65647	0.2711	N	0.08118	0	0.21627	N	0.999612	D;D	0.58970	0.984;0.984	D;D	0.68192	0.956;0.956	T	0.65117	-0.6246	9	0.87932	D	0	-14.3407	13.6115	0.62080	0.0:0.6766:0.0:0.3234	.	567;490	B4DH08;Q92772	.;CDKL2_HUMAN	D	490;567	ENSP00000412365:E490D;ENSP00000306340:E567D	ENSP00000306340:E567D	E	-	3	2	CDKL2	76726079	0.746000	0.28272	0.961000	0.40146	0.689000	0.40095	-0.848000	0.04326	-0.800000	0.04433	-0.424000	0.05967	GAA	.	.	none		0.428	CDKL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252409.2	NM_003948		G	76507055	T	G	76507055	3	3	11	1	0	0	0	0	1	0	0	0	3156	1722	60	5	15	5	CDKL2	4	76507055	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	28913746	76507055	114647221	85	1376											
ANTXR2	118429	hgsc.bcm.edu	37	chr4	80899206	80899206	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgaggaggctggtgtgtgggTttgggtcgaggtggtctagg	4	12	22	3	1	1	1	0	1	1	0	2	3	1	2	0	8	0	2	0	8	1	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr4:80899206T>C	ENST00000307333.7	-	15	1304	c.1302A>G	c.(1300-1302)aaA>aaG	p.K434K	ANTXR2_ENST00000404191.1_Silent_p.K357K|ANTXR2_ENST00000346652.6_Silent_p.K331K|ANTXR2_ENST00000403729.2_Silent_p.K434K	NM_001145794.1	NP_001139266.1	P58335	ANTR2_HUMAN	anthrax toxin receptor 2	434					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						GGTGTGTGGGTTTGGGTCGAG	0.453									Juvenile Hyaline Fibromatosis																												p.K434K		Atlas-SNP	.											.	ANTXR2	97	.	0			c.A1302G						PASS	.						275	269	271					4																	80899206		1922	4130	6052	SO:0001819	synonymous_variant	118429	exon15	Familial Cancer Database	incl. Infantile Systemic Hyalinosis	TGTGGGTTTGGGT	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.1302A>G	4.37:g.80899206T>C		331	1	0.00302115		296	105	0.35473	NM_001145794	Q4W5H6|Q59E98|Q5JPE9|Q86UI1|Q8N4J8|Q8NB13|Q96NC7	Silent	SNP	ENST00000307333.7	37	CCDS47086.1																																																																																			.	.	none		0.453	ANTXR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324663.1	NM_058172		C	80899206	T	C	80899206	2	2	11	1	0	0	0	0	0	0	0	1	712	1722	60	3		3	ANTXR2	4	80899206	Silent	SNP	T	TCGA-FF-8042-01A-11D-2210-10	4392151	80899206	110255070	86	1377											
DMP1	1758	hgsc.bcm.edu	37	chr4	88580612	88580612	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagtcatcagaaggcagtaaAgttagctcagaggaacaggt	15	7	13	6	0	3	2	3	0	0	2	3	4	3	3	0	3	2	4	0	3	5	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr4:88580612A>C	ENST00000339673.6	+	5	264	c.165A>C	c.(163-165)aaA>aaC	p.K55N	RP11-742B18.1_ENST00000506480.1_RNA|RP11-742B18.1_ENST00000506814.1_RNA|RP11-742B18.1_ENST00000507894.1_RNA|DMP1_ENST00000282479.7_Intron	NM_004407.3	NP_004398.1	Q13316	DMP1_HUMAN	dentin matrix acidic phosphoprotein 1	55					biomineral tissue development (GO:0031214)|extracellular matrix organization (GO:0030198)|ossification (GO:0001503)|positive regulation of cell-substrate adhesion (GO:0010811)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(1)|stomach(1)	32		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.227)		OV - Ovarian serous cystadenocarcinoma(123;0.000516)		AAGGCAGTAAAGTTAGCTCAG	0.358																																					p.K55N		Atlas-SNP	.											.	DMP1	72	.	0			c.A165C						PASS	.						102	109	107					4																	88580612		2203	4300	6503	SO:0001583	missense	1758	exon5			CAGTAAAGTTAGC	U34037	CCDS3623.1, CCDS43249.1	4q21	2008-08-29	2008-08-29		ENSG00000152592	ENSG00000152592			2932	protein-coding gene	gene with protein product		600980	"dentin matrix acidic phosphoprotein"			8586437, 9177774	Standard	NM_001079911		Approved		uc003hqv.3	Q13316	OTTHUMG00000130598	ENST00000339673.6:c.165A>C	4.37:g.88580612A>C	ENSP00000340935:p.Lys55Asn	217	0	0		175	61	0.348571	NM_004407	A1L4L3|O43265	Missense_Mutation	SNP	ENST00000339673.6	37	CCDS3623.1	.	.	.	.	.	.	.	.	.	.	A	10.51	1.371693	0.24771	.	.	ENSG00000152592	ENST00000339673	T	0.52754	0.65	6.07	4.86	0.63082	.	0.309128	0.27787	N	0.017854	T	0.53045	0.1772	L	0.32530	0.975	0.80722	D	1	D	0.64830	0.994	D	0.63793	0.918	T	0.52313	-0.8592	10	0.51188	T	0.08	-8.5836	10.2286	0.43241	0.8335:0.1665:0.0:0.0	.	55	Q13316	DMP1_HUMAN	N	55	ENSP00000340935:K55N	ENSP00000340935:K55N	K	+	3	2	DMP1	88799636	1.000000	0.71417	0.987000	0.45799	0.071000	0.16799	1.915000	0.39976	1.066000	0.40716	0.533000	0.62120	AAA	.	.	none		0.358	DMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253047.1			C	88580612	A	C	88580612	3	2	11	1	0	0	0	0	1	0	0	0	4585	69	3	5	179	5	DMP1	4	88580612	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	7681406	88580612	102573664	87	1378											
HERC5	51191	hgsc.bcm.edu	37	chr4	89427002	89427002	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagaagcgcttcaagaagcCatcaacaacaacagaggatt	18	5	9	9	1	2	3	2	0	0	3	2	5	2	4	1	1	5	1	1	1	7	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr4:89427002C>T	ENST00000264350.3	+	23	3201	c.3048C>T	c.(3046-3048)gcC>gcT	p.A1016A	HERC5_ENST00000508159.1_Silent_p.A654A	NM_016323.3	NP_057407.2	Q9UII4	HERC5_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 5	1016	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				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)		TTCAAGAAGCCATCAACAACA	0.408																																					p.A1016A	Esophageal Squamous(39;887 1012 34045 50514)	Atlas-SNP	.											.	HERC5	114	.	0			c.C3048T						PASS	.						59	59	59					4																	89427002		2203	4300	6503	SO:0001819	synonymous_variant	51191	exon23			AGAAGCCATCAAC	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.3048C>T	4.37:g.89427002C>T		207	0	0		173	68	0.393064	NM_016323	B2RTQ1|Q69G20	Silent	SNP	ENST00000264350.3	37	CCDS3630.1																																																																																			.	.	none		0.408	HERC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253554.2	NM_016323		T	89427002	C	T	89427002	2	4	11	1	0	0	0	0	0	0	0	1	7070	581	21	2		2	HERC5	4	89427002	Silent	SNP	C	TCGA-FF-8042-01A-11D-2210-10	846390	89427002	101727274	88	1379											
FAT4	79633	hgsc.bcm.edu	37	chr4	126239318	126239318	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaaagccagtatttagccaGccagaagggtatgatgtgtc	13	9	12	7	0	0	2	0	1	0	1	1	3	0	2	3	1	3	2	3	1	6	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr4:126239318G>A	ENST00000394329.3	+	1	1765	c.1752G>A	c.(1750-1752)caG>caA	p.Q584Q		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	584	Cadherin 6. {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						TATTTAGCCAGCCAGAAGGGT	0.517																																					p.Q584Q		Atlas-SNP	.											.	FAT4	1752	.	0			c.G1752A						PASS	.						68	71	70					4																	126239318		2007	4176	6183	SO:0001819	synonymous_variant	79633	exon1			TAGCCAGCCAGAA	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.1752G>A	4.37:g.126239318G>A		98	0	0		78	33	0.423077	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																			.	.	none		0.517	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126239318	G	A	126239318	2	1	11	1	0	0	0	0	0	0	0	1	5700	962	34	2		2	FAT4	4	126239318	Silent	SNP	G	TCGA-FF-8042-01A-11D-2210-10	36812316	126239318	64914958	89	1380											
FAT4	79633	hgsc.bcm.edu	37	chr4	126408517	126408517	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagattaagaatggcaaagtAtattttacatccgatgcagg	15	11	9	6	1	0	2	0	0	0	2	1	3	1	2	1	2	2	3	1	2	6	5			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr4:126408517A>G	ENST00000394329.3	+	16	12847	c.12834A>G	c.(12832-12834)gtA>gtG	p.V4278V	FAT4_ENST00000335110.5_Silent_p.V2519V	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4278	Laminin G-like 2. {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						ATGGCAAAGTATATTTTACAT	0.299																																					p.V4278V		Atlas-SNP	.											.	FAT4	1752	.	0			c.A12834G						PASS	.						48	51	50					4																	126408517		2203	4298	6501	SO:0001819	synonymous_variant	79633	exon16			CAAAGTATATTTT	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.12834A>G	4.37:g.126408517A>G		69	0	0		36	10	0.277778	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																			.	.	none		0.299	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		G	126408517	A	G	126408517	2	3	11	1	0	0	0	0	0	0	0	1	5700	436	16	3		3	FAT4	4	126408517	Silent	SNP	A	TCGA-FF-8042-01A-11D-2210-10	169199	126408517	64745759	90	1381											
INPP4B	8821	hgsc.bcm.edu	37	chr4	143003328	143003328	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgaaacgaataccattcagtTtgcggcaaatctgtaacata	15	11	7	8	2	2	1	1	1	1	0	2	2	2	1	1	1	4	3	1	1	6	5			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr4:143003328T>G	ENST00000513000.1	-	26	2931	c.2498A>C	c.(2497-2499)aAa>aCa	p.K833T	INPP4B_ENST00000262992.4_Missense_Mutation_p.K833T|INPP4B_ENST00000508116.1_Missense_Mutation_p.K833T|INPP4B_ENST00000509777.1_Missense_Mutation_p.K833T|INPP4B_ENST00000308502.4_Missense_Mutation_p.K833T	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	833					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)					ACCATTCAGTTTGCGGCAAAT	0.413																																					p.K833T		Atlas-SNP	.											.	INPP4B	132	.	0			c.A2498C						PASS	.						141	125	130					4																	143003328		2203	4300	6503	SO:0001583	missense	8821	exon26			TTCAGTTTGCGGC	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.2498A>C	4.37:g.143003328T>G	ENSP00000425487:p.Lys833Thr	219	0	0		227	97	0.427313	NM_003866	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Missense_Mutation	SNP	ENST00000513000.1	37	CCDS3757.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.99|19.99	3.928315|3.928315	0.73327|0.73327	.|.	.|.	ENSG00000109452|ENSG00000109452	ENST00000513000;ENST00000262992;ENST00000308502;ENST00000508116;ENST00000509777;ENST00000511838|ENST00000542702	T;T;T;T;T;T|.	0.23754|.	1.89;1.89;1.89;1.89;1.89;1.89|.	5.7|5.7	4.52|4.52	0.55395|0.55395	.|.	0.050528|.	0.85682|.	D|.	0.000000|.	T|T	0.65739|0.65739	0.2720|0.2720	M|M	0.61703|0.61703	1.905|1.905	0.47037|0.47037	D|D	0.999293|0.999293	D|.	0.62365|.	0.991|.	P|.	0.59703|.	0.862|.	T|T	0.67745|0.67745	-0.5591|-0.5591	10|6	0.56958|0.87932	D|D	0.05|0	.|.	11.4577|11.4577	0.50191|0.50191	0.0:0.0702:0.0:0.9298|0.0:0.0702:0.0:0.9298	.|.	833|.	O15327|.	INP4B_HUMAN|.	T|H	833;833;833;833;833;648|647	ENSP00000425487:K833T;ENSP00000262992:K833T;ENSP00000308441:K833T;ENSP00000423954:K833T;ENSP00000422793:K833T;ENSP00000426207:K648T|.	ENSP00000262992:K833T|ENSP00000446046:Q647H	K|Q	-|-	2|3	0|2	INPP4B|INPP4B	143222778|143222778	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	4.389000|4.389000	0.59639|0.59639	1.001000|1.001000	0.39076|0.39076	0.455000|0.455000	0.32223|0.32223	AAA|CAA	.	.	none		0.413	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866		G	143003328	T	G	143003328	3	3	11	1	0	0	0	0	1	0	0	0	7762	1841	64	5	284	5	INPP4B	4	143003328	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	16594811	143003328	48150948	91	1382											
ADCY2	108	hgsc.bcm.edu	37	chr5	7709382	7709382	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccacacccttgatggagccaAaatgagggcctcggtccgca	10	6	11	14	2	0	2	0	2	0	0	2	3	1	3	5	3	1	1	5	3	2	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr5:7709382A>C	ENST00000338316.4	+	10	1549	c.1460A>C	c.(1459-1461)aAa>aCa	p.K487T	RP11-711G10.1_ENST00000514105.2_RNA|ADCY2_ENST00000537121.1_Missense_Mutation_p.K307T	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	487					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						GATGGAGCCAAAATGAGGGCC	0.592																																					p.K487T		Atlas-SNP	.											.	ADCY2	337	.	0			c.A1460C						PASS	.						73	65	68					5																	7709382		2203	4300	6503	SO:0001583	missense	108	exon10			GAGCCAAAATGAG	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.1460A>C	5.37:g.7709382A>C	ENSP00000342952:p.Lys487Thr	87	0	0		72	32	0.444444	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	37	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	a	19.22	3.785732	0.70337	.	.	ENSG00000078295	ENST00000338316;ENST00000537121	T;D	0.82526	-1.15;-1.62	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	D	0.84853	0.5564	M	0.81497	2.545	0.50313	D	0.999862	B;B	0.18461	0.015;0.028	B;B	0.25759	0.041;0.063	T	0.82548	-0.0402	10	0.52906	T	0.07	.	15.8247	0.78690	1.0:0.0:0.0:0.0	.	307;487	B7Z2C1;Q08462	.;ADCY2_HUMAN	T	487;307	ENSP00000342952:K487T;ENSP00000444803:K307T	ENSP00000342952:K487T	K	+	2	0	ADCY2	7762382	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	5.844000	0.69430	2.137000	0.66172	0.456000	0.33151	AAA	.	.	none		0.592	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		C	7709382	A	C	7709382	3	2	11	1	0	0	0	0	1	0	0	0	294	14	1	5	1498	5	ADCY2	5	7709382	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10		7709382	173205878	92	1383											
SEMA5A	9037	hgsc.bcm.edu	37	chr5	9066712	9066712	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tccagggtgtccagggcgtgGtcttcttcagctcaggacac	6	10	13	12	1	4	0	2	0	2	0	6	1	6	1	2	4	1	1	2	4	0	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr5:9066712G>T	ENST00000382496.5	-	17	2785	c.2120C>A	c.(2119-2121)aCc>aAc	p.T707N		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	707	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						CCAGGGCGTGGTCTTCTTCAG	0.557																																					p.T707N		Atlas-SNP	.											.	SEMA5A	236	.	0			c.C2120A						PASS	.						167	154	158					5																	9066712		2203	4300	6503	SO:0001583	missense	9037	exon17			GGCGTGGTCTTCT	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.2120C>A	5.37:g.9066712G>T	ENSP00000371936:p.Thr707Asn	172	0	0		129	51	0.395349	NM_003966	D3DTC6|O60408|Q1RLL9	Missense_Mutation	SNP	ENST00000382496.5	37	CCDS3875.1	.	.	.	.	.	.	.	.	.	.	G	8.800	0.932750	0.18131	.	.	ENSG00000112902	ENST00000382496	T	0.36520	1.25	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	T	0.19644	0.0472	N	0.14661	0.345	0.54753	D	0.999989	B	0.20550	0.046	B	0.16722	0.016	T	0.07849	-1.0751	10	0.07325	T	0.83	.	12.2699	0.54700	0.0:0.0:0.8304:0.1696	.	707	Q13591	SEM5A_HUMAN	N	707	ENSP00000371936:T707N	ENSP00000371936:T707N	T	-	2	0	SEMA5A	9119712	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	6.149000	0.71795	2.761000	0.94854	0.591000	0.81541	ACC	.	.	none		0.557	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2			T	9066712	G	T	9066712	3	4	11	1	0	0	0	0	1	0	0	0	14052	1261	44	4	1132	4	SEMA5A	5	9066712	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	1357330	9066712	171848548	93	1384											
TRIO	7204	hgsc.bcm.edu	37	chr5	14359502	14359502	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtaacaagaccccccacaaCagctccatcaaccacattga	16	5	4	16	0	1	2	1	1	0	1	2	2	2	2	5	0	4	2	5	0	4	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr5:14359502C>G	ENST00000344204.4	+	13	2277	c.2253C>G	c.(2251-2253)aaC>aaG	p.N751K	TRIO_ENST00000537187.1_Missense_Mutation_p.N751K|TRIO_ENST00000509967.2_Missense_Mutation_p.N702K	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	751					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)					CCCCCCACAACAGCTCCATCA	0.542																																					p.N751K		Atlas-SNP	.											.	TRIO	305	.	0			c.C2253G						PASS	.						89	86	87					5																	14359502		2203	4300	6503	SO:0001583	missense	7204	exon13			CCACAACAGCTCC	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.2253C>G	5.37:g.14359502C>G	ENSP00000339299:p.Asn751Lys	456	0	0		376	155	0.412234	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Missense_Mutation	SNP	ENST00000344204.4	37	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	C	15.80	2.940315	0.52972	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000509967;ENST00000513206	T;T;T	0.56444	1.01;1.01;0.46	5.31	3.53	0.40419	.	0.000000	0.85682	D	0.000000	T	0.45296	0.1335	N	0.08118	0	0.53688	D	0.999978	P;D;B	0.58970	0.486;0.984;0.295	B;P;B	0.58454	0.205;0.839;0.091	T	0.38200	-0.9672	10	0.33141	T	0.24	.	11.5233	0.50565	0.0:0.855:0.0:0.145	.	702;751;751	F5H228;O75962-5;O75962	.;.;TRIO_HUMAN	K	751;751;702;438	ENSP00000339299:N751K;ENSP00000446348:N751K;ENSP00000445592:N702K	ENSP00000339299:N751K	N	+	3	2	TRIO	14412502	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.089000	0.71384	0.631000	0.30412	0.650000	0.86243	AAC	.	.	none		0.542	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		G	14359502	C	G	14359502	3	3	11	1	0	0	0	0	1	0	0	0	16567	477	17	4	2303	4	TRIO	5	14359502	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	5292790	14359502	166555758	94	1385											
PLCXD3	345557	hgsc.bcm.edu	37	chr5	41381956	41381956	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gattgtttctctgaggccacTtgccacccctttgaccacag	7	12	8	14	0	1	2	0	2	1	0	2	3	1	2	5	1	1	1	5	1	0	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr5:41381956T>G	ENST00000377801.3	-	2	858	c.784A>C	c.(784-786)Agt>Cgt	p.S262R	PLCXD3_ENST00000328457.3_Missense_Mutation_p.S262R			Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 3	262					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						CTGAGGCCACTTGCCACCCCT	0.418																																					p.S262R		Atlas-SNP	.											.	PLCXD3	86	.	0			c.A784C						PASS	.						80	84	83					5																	41381956		2203	4300	6503	SO:0001583	missense	345557	exon2			GGCCACTTGCCAC		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.784A>C	5.37:g.41381956T>G	ENSP00000367032:p.Ser262Arg	208	0	0		144	54	0.375	NM_001005473	A6NL04	Missense_Mutation	SNP	ENST00000377801.3	37	CCDS34150.1	.	.	.	.	.	.	.	.	.	.	T	15.94	2.980845	0.53827	.	.	ENSG00000182836	ENST00000377801;ENST00000328457	.	.	.	6.07	4.9	0.64082	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	0.036051	0.85682	D	0.000000	T	0.65059	0.2655	L	0.48642	1.525	0.80722	D	1	D	0.61697	0.99	D	0.66497	0.944	T	0.59841	-0.7378	9	0.15499	T	0.54	-11.2139	12.7602	0.57359	0.1231:0.0:0.0:0.8769	.	262	Q63HM9	PLCX3_HUMAN	R	262	.	ENSP00000333751:S262R	S	-	1	0	PLCXD3	41417713	1.000000	0.71417	0.997000	0.53966	0.983000	0.72400	3.912000	0.56386	1.097000	0.41459	0.533000	0.62120	AGT	.	.	none		0.418	PLCXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367109.1	XM_293875		G	41381956	T	G	41381956	3	3	11	1	0	0	0	0	1	0	0	0	12052	1609	56	5	189	5	PLCXD3	5	41381956	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	27022454	41381956	139533304	95	1386											
HMGCR	3156	hgsc.bcm.edu	37	chr5	74655105	74655105	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacgcccatgcagcaaacatTgtcaccgccatctacattgc	12	8	6	15	2	2	0	1	0	1	0	2	0	2	0	3	0	6	2	3	0	3	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr5:74655105T>G	ENST00000287936.4	+	17	2424	c.2268T>G	c.(2266-2268)atT>atG	p.I756M	HMGCR_ENST00000511206.1_Missense_Mutation_p.I756M|HMGCR_ENST00000343975.5_Missense_Mutation_p.I703M	NM_000859.2	NP_000850.1	P04035	HMDH_HUMAN	3-hydroxy-3-methylglutaryl-CoA reductase	756	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)	CAGCAAACATTGTCACCGCCA	0.458																																					p.I756M		Atlas-SNP	.											.	HMGCR	53	.	0			c.T2268G						PASS	.						102	95	97					5																	74655105		2203	4300	6503	SO:0001583	missense	3156	exon17			AAACATTGTCACC		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.2268T>G	5.37:g.74655105T>G	ENSP00000287936:p.Ile756Met	84	0	0		64	30	0.46875	NM_000859	B7Z3Y9|Q8N190	Missense_Mutation	SNP	ENST00000287936.4	37	CCDS4027.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.10|13.10	2.136618|2.136618	0.37728|0.37728	.|.	.|.	ENSG00000113161|ENSG00000113161	ENST00000511206;ENST00000544469;ENST00000287936;ENST00000343975;ENST00000429286|ENST00000509085	T;T;T|.	0.48836|.	0.8;0.8;0.8|.	5.11|5.11	-5.61|-5.61	0.02489|0.02489	Hydroxymethylglutaryl-CoA reductase, class I/II, catalytic domain (1);Hydroxymethylglutaryl-CoA reductase, class I/II, substrate-binding (1);|.	0.054543|.	0.64402|.	D|.	0.000001|.	T|T	0.64681|0.64681	0.2620|0.2620	L|L	0.61218|0.61218	1.895|1.895	0.51482|0.51482	D|D	0.999929|0.999929	P;B;P;P|.	0.48089|.	0.642;0.261;0.905;0.793|.	B;B;P;P|.	0.48552|.	0.405;0.183;0.581;0.486|.	T|T	0.67162|0.67162	-0.5740|-0.5740	10|5	0.38643|.	T|.	0.18|.	-9.0541|-9.0541	14.1509|14.1509	0.65384|0.65384	0.0:0.5119:0.0:0.4881|0.0:0.5119:0.0:0.4881	.|.	756;133;703;756|.	B2R649;B4DSB1;P04035-2;P04035|.	.;.;.;HMDH_HUMAN|.	M|W	756;687;756;703;133|86	ENSP00000426745:I756M;ENSP00000287936:I756M;ENSP00000340816:I703M|.	ENSP00000287936:I756M|.	I|L	+|+	3|2	3|0	HMGCR|HMGCR	74690861|74690861	0.000000|0.000000	0.05858|0.05858	0.675000|0.675000	0.29917|0.29917	0.895000|0.895000	0.52256|0.52256	-3.976000|-3.976000	0.00321|0.00321	-0.947000|-0.947000	0.03673|0.03673	-0.250000|-0.250000	0.11733|0.11733	ATT|TTG	.	.	none		0.458	HMGCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219877.2			G	74655105	T	G	74655105	3	3	11	1	0	0	0	0	1	0	0	0	7240	1800	63	5	2330	5	HMGCR	5	74655105	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	33273149	74655105	106260155	96	1387											
VCAN	1462	hgsc.bcm.edu	37	chr5	82834917	82834917	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcttcccagtgctgtgcaaaAgttttctggtacagcttcct	7	14	9	11	0	1	0	0	0	1	0	3	0	3	0	2	1	4	6	2	1	3	5			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr5:82834917A>C	ENST00000265077.3	+	8	6660	c.6095A>C	c.(6094-6096)aAg>aCg	p.K2032T	VCAN_ENST00000512590.2_Intron|VCAN_ENST00000343200.5_Missense_Mutation_p.K1045T|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Intron|VCAN-AS1_ENST00000513899.1_RNA|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000513016.1_3'UTR	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2032	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)	GCTGTGCAAAAGTTTTCTGGT	0.478																																					p.K2032T		Atlas-SNP	.											.	VCAN	498	.	0			c.A6095C						PASS	.						65	70	68					5																	82834917		2203	4300	6503	SO:0001583	missense	1462	exon8			TGCAAAAGTTTTC	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.6095A>C	5.37:g.82834917A>C	ENSP00000265077:p.Lys2032Thr	112	0	0		103	44	0.427184	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	A	10.83	1.460599	0.26248	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000513960	D;D;T	0.86865	-2.16;-2.18;3.01	5.39	-2.02	0.07388	.	1.361960	0.04546	N	0.389071	T	0.76723	0.4027	L	0.38175	1.15	0.09310	N	0.999999	B;B	0.30361	0.277;0.1	B;B	0.24394	0.053;0.024	T	0.58595	-0.7609	10	0.15499	T	0.54	.	4.4646	0.11682	0.5024:0.0:0.1504:0.3472	.	1045;2032	P13611-2;P13611	.;CSPG2_HUMAN	T	2032;1045;1045	ENSP00000265077:K2032T;ENSP00000340062:K1045T;ENSP00000426251:K1045T	ENSP00000265077:K2032T	K	+	2	0	VCAN	82870673	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	0.107000	0.15375	-0.896000	0.03915	-2.845000	0.00104	AAG	.	.	none		0.478	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		C	82834917	A	C	82834917	3	2	11	1	0	0	0	0	1	0	0	0	17153	72	3	5	6121	5	VCAN	5	82834917	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	8179812	82834917	98080343	97	1388											
PPIP5K2	23262	hgsc.bcm.edu	37	chr5	102465357	102465357	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aaataaatcctggaaattatCgacatttcttccaccatgca	15	12	4	10	1	1	0	0	0	1	0	4	2	3	1	3	1	1	1	3	1	5	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr5:102465357C>T	ENST00000358359.3	+	2	573	c.64C>T	c.(64-66)Cga>Tga	p.R22*	PPIP5K2_ENST00000414217.1_Nonsense_Mutation_p.R22*|PPIP5K2_ENST00000321521.9_Nonsense_Mutation_p.R22*|PPIP5K2_ENST00000513500.1_3'UTR	NM_001276277.1	NP_001263206.1	O43314	VIP2_HUMAN	diphosphoinositol pentakisphosphate kinase 2	22					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						TGGAAATTATCGACATTTCTT	0.363																																					p.R22X		Atlas-SNP	.											.	PPIP5K2	98	.	0			c.C64T						PASS	.						110	105	106					5																	102465357		2203	4300	6503	SO:0001587	stop_gained	23262	exon1			AATTATCGACATT	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.64C>T	5.37:g.102465357C>T	ENSP00000351126:p.Arg22*	39	0	0		40	4	0.1	NM_015216	A1NI53|A6NGS8|Q8TB50	Nonsense_Mutation	SNP	ENST00000358359.3	37		.	.	.	.	.	.	.	.	.	.	C	29.5	5.011757	0.93346	.	.	ENSG00000145725	ENST00000515845;ENST00000321521;ENST00000358359;ENST00000451606;ENST00000414217	.	.	.	5.75	2.74	0.32292	.	0.167313	0.39615	N	0.001314	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.0712	0.06231	0.2478:0.4349:0.2312:0.0861	.	.	.	.	X	22	.	ENSP00000313070:R22X	R	+	1	2	PPIP5K2	102493256	0.615000	0.27026	0.907000	0.35723	0.977000	0.68977	0.906000	0.28517	0.880000	0.35969	0.650000	0.86243	CGA	.	.	none		0.363	PPIP5K2-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000370487.1	NM_015216		T	102465357	C	T	102465357	4	4	11	1	0	0	0	0	0	1	0	0	12345	876	31	1	66	1	PPIP5K2	5	102465357	Nonsense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	19630440	102465357	78449903	98	1389											
APC	324	hgsc.bcm.edu	37	chr5	112173494	112173494	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctcatggcaaataggcctGcgaagtacaaggatgccaat	14	8	10	9	1	1	0	1	0	1	0	2	2	1	1	2	3	3	2	2	3	6	2	rs559313229	byFrequency	TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr5:112173494G>A	ENST00000457016.1	+	16	2583	c.2203G>A	c.(2203-2205)Gcg>Acg	p.A735T	APC_ENST00000508376.2_Missense_Mutation_p.A735T|APC_ENST00000257430.4_Missense_Mutation_p.A735T|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	735	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)		AAATAGGCCTGCGAAGTACAA	0.443		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.A735T	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,-2,1	APC	4158	1	1	Unknown(1)	skin(1)	c.G2203A						PASS	.						77	67	71					5																	112173494		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,	AGGCCTGCGAAGT	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.2203G>A	5.37:g.112173494G>A	ENSP00000413133:p.Ala735Thr	91	0	0		76	23	0.302632	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	G	15.44	2.833345	0.50951	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	T;T;T;T;T	0.64618	-0.11;0.97;-0.11;-0.11;0.97	6.17	5.29	0.74685	Armadillo-like helical (1);Armadillo-type fold (1);	0.046835	0.85682	D	0.000000	T	0.64538	0.2607	M	0.71581	2.175	0.80722	D	1	B;B	0.19935	0.04;0.04	B;B	0.21546	0.023;0.035	T	0.61535	-0.7043	10	0.39692	T	0.17	-18.6539	17.5212	0.87787	0.0:0.1239:0.8761:0.0	.	737;735	Q4LE70;P25054	.;APC_HUMAN	T	735;717;735;735;735	ENSP00000413133:A735T;ENSP00000423224:A717T;ENSP00000257430:A735T;ENSP00000427089:A735T;ENSP00000423828:A735T	ENSP00000257430:A735T	A	+	1	0	APC	112201393	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.663000	0.83820	1.593000	0.50029	0.655000	0.94253	GCG	.	.	none		0.443	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112173494	G	A	112173494	3	1	11	1	0	0	0	0	1	0	0	0	763	1319	46	2	2261	2	APC	5	112173494	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	9708137	112173494	68741766	99	1390											
PCDHA13	56136	hgsc.bcm.edu	37	chr5	140264046	140264046	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaccgcccaccgagggcgcGtgcgcgccgggcaagcccac	6	1	15	19	7	0	0	0	0	0	0	0	1	0	0	5	2	2	2	5	2	1	0			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr5:140264046G>A	ENST00000289272.2	+	1	2193	c.2193G>A	c.(2191-2193)gcG>gcA	p.A731A	PCDHA11_ENST00000398640.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA13_ENST00000409494.1_Silent_p.A731A|PCDHA12_ENST00000398631.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	731					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)			CCGAGGGCGCGTGCGCGCCGG	0.672																																					p.A731A	Melanoma(147;1739 1852 5500 27947 37288)	Atlas-SNP	.											.	PCDHA13	213	.	0			c.G2193A						PASS	.						61	66	64					5																	140264046		2203	4297	6500	SO:0001819	synonymous_variant	56136	exon1			GGGCGCGTGCGCG	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.2193G>A	5.37:g.140264046G>A		73	0	0		103	79	0.76699	NM_031865	O75277	Silent	SNP	ENST00000289272.2	37	CCDS4240.1																																																																																			.	.	none		0.672	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		A	140264046	G	A	140264046	2	1	11	1	0	0	0	0	0	0	0	1	11532	1132	40	1		1	PCDHA13	5	140264046	Silent	SNP	G	TCGA-FF-8042-01A-11D-2210-10	28090552	140264046	40651214	100	1391											
PCDHB10	56126	hgsc.bcm.edu	37	chr5	140574381	140574381	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	accctgtcccagagctaccaGtatgaggtgtgtctgacggg	8	9	13	11	1	1	3	0	2	1	1	2	3	2	3	3	2	2	2	3	2	2	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr5:140574381G>T	ENST00000239446.4	+	1	2440	c.2256G>T	c.(2254-2256)caG>caT	p.Q752H		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	752					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)			AGAGCTACCAGTATGAGGTGT	0.622																																					p.Q752H		Atlas-SNP	.											.	PCDHB10	177	.	0			c.G2256T						PASS	.						78	86	83					5																	140574381		2203	4300	6503	SO:0001583	missense	56126	exon1			CTACCAGTATGAG	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.2256G>T	5.37:g.140574381G>T	ENSP00000239446:p.Gln752His	84	0	0		128	64	0.5	NM_018930	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	37	CCDS4252.1	.	.	.	.	.	.	.	.	.	.	G	7.623	0.677262	0.14841	.	.	ENSG00000120324	ENST00000239446	T	0.49432	0.78	3.28	1.41	0.22369	.	.	.	.	.	T	0.59676	0.2211	M	0.75615	2.305	0.31114	N	0.709598	D	0.76494	0.999	D	0.67900	0.954	T	0.58702	-0.7590	9	0.56958	D	0.05	.	3.3998	0.07319	0.3694:0.203:0.4276:0.0	.	752	Q9UN67	PCDBA_HUMAN	H	752	ENSP00000239446:Q752H	ENSP00000239446:Q752H	Q	+	3	2	PCDHB10	140554565	0.000000	0.05858	0.996000	0.52242	0.394000	0.30568	-1.938000	0.01546	0.213000	0.20722	0.298000	0.19748	CAG	.	.	none		0.622	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		T	140574381	G	T	140574381	3	4	11	1	0	0	0	0	1	0	0	0	11544	1020	36	4	2258	4	PCDHB10	5	140574381	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	310335	140574381	40340879	101	1392											
PCDHGB2	56103	hgsc.bcm.edu	37	chr5	140741034	140741034	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcaccctgcacatctccgaCgtcaacgataatgccccagt	10	8	7	16	3	3	0	2	0	1	0	4	2	3	0	4	0	3	1	4	0	2	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr5:140741034C>T	ENST00000522605.1	+	1	1332	c.1332C>T	c.(1330-1332)gaC>gaT	p.D444D	PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA5_ENST00000518069.1_5'Flank|PCDHGA2_ENST00000394576.2_Intron	NM_018923.2|NM_032096.1	NP_061746.1|NP_115267.1	Q9Y5G2	PCDGE_HUMAN	protocadherin gamma subfamily B, 2	444	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(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)			ACATCTCCGACGTCAACGATA	0.552																																					p.D444D		Atlas-SNP	.											.	PCDHGB2	196	.	0			c.C1332T						PASS	.						105	109	108					5																	140741034		2069	4208	6277	SO:0001819	synonymous_variant	56103	exon1			CTCCGACGTCAAC	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.1332C>T	5.37:g.140741034C>T		158	0	0		145	92	0.634483	NM_018923	Q3MIJ3|Q9UN65	Silent	SNP	ENST00000522605.1	37	CCDS54924.1																																																																																			.	.	none		0.552	PCDHGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374741.1	NM_018923		T	140741034	C	T	140741034	2	4	11	1	0	0	0	0	0	0	0	1	11572	535	19	1		1	PCDHGB2	5	140741034	Silent	SNP	C	TCGA-FF-8042-01A-11D-2210-10	166653	140741034	40174226	102	1393											
LARP1	23367	hgsc.bcm.edu	37	chr5	154179585	154179585	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagaagaggcctcggccaTccccagcacggcccaaggtg	10	4	13	14	2	0	3	0	1	0	2	2	3	1	3	5	4	1	1	5	4	3	0			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr5:154179585T>C	ENST00000336314.4	+	10	1492	c.1468T>C	c.(1468-1470)Tcc>Ccc	p.S490P		NM_015315.3	NP_056130.2	Q6PKG0	LARP1_HUMAN	La ribonucleoprotein domain family, member 1	567					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)			GCCTCGGCCATCCCCAGCACG	0.577																																					p.S490P		Atlas-SNP	.											.	LARP1	187	.	0			c.T1468C						PASS	.						50	49	49					5																	154179585		2203	4300	6503	SO:0001583	missense	23367	exon10			CGGCCATCCCCAG	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.1468T>C	5.37:g.154179585T>C	ENSP00000336721:p.Ser490Pro	59	0	0		56	46	0.821429	NM_015315	O94836|Q8N4M2|Q8NB73|Q9UFD7	Missense_Mutation	SNP	ENST00000336314.4	37	CCDS4328.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.300724	0.81136	.	.	ENSG00000155506	ENST00000336314;ENST00000518297;ENST00000524248;ENST00000523163;ENST00000518742	T;T;T;T;T	0.52983	1.83;1.39;1.42;0.73;0.64	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.51483	0.1677	M	0.76574	2.34	0.80722	D	1	B;B	0.27068	0.167;0.084	B;B	0.25614	0.048;0.062	T	0.50767	-0.8789	10	0.48119	T	0.1	-22.2417	16.4484	0.83959	0.0:0.0:0.0:1.0	.	567;490	Q6PKG0;Q6PKG0-3	LARP1_HUMAN;.	P	490;567;362;275;165	ENSP00000336721:S490P;ENSP00000428589:S567P;ENSP00000429904:S362P;ENSP00000430438:S275P;ENSP00000431072:S165P	ENSP00000336721:S490P	S	+	1	0	LARP1	154159778	1.000000	0.71417	0.999000	0.59377	0.618000	0.37518	5.893000	0.69798	2.285000	0.76669	0.533000	0.62120	TCC	.	.	none		0.577	LARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252509.1	NM_033551		C	154179585	T	C	154179585	3	2	11	1	0	0	0	0	1	0	0	0	8637	1435	50	3	1506	3	LARP1	5	154179585	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	13438551	154179585	26735675	103	1394											
SLC22A23	63027	hgsc.bcm.edu	37	chr6	3273638	3273638	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tggccagcaccagccccagcCcgccacacctgcagggggag	8	2	13	18	1	0	0	0	0	0	0	0	1	0	1	7	3	4	2	7	3	0	0			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr6:3273638C>T	ENST00000406686.3	-	10	1711	c.1712G>A	c.(1711-1713)gGg>gAg	p.G571E	SLC22A23_ENST00000380302.4_Missense_Mutation_p.G290E|SLC22A23_ENST00000490273.1_Missense_Mutation_p.G290E|SLC22A23_ENST00000436008.2_Missense_Mutation_p.G579E|PSMG4_ENST00000451246.2_Intron	NM_015482.1	NP_056297.1	A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23	571					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)				CAGCCCCAGCCCGCCACACCT	0.642																																					p.G571E		Atlas-SNP	.											SLC22A23_ENST00000406686,colon,carcinoma,-1,2	SLC22A23	89	2	0			c.G1712A						PASS	.						44	38	40					6																	3273638		2177	4257	6434	SO:0001583	missense	63027	exon10			CCCAGCCCGCCAC	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.1712G>A	6.37:g.3273638C>T	ENSP00000385028:p.Gly571Glu	48	0	0		92	27	0.293478	NM_015482	A1A5C8|Q5T8B8|Q6ZMH3|Q8IW73	Missense_Mutation	SNP	ENST00000406686.3	37	CCDS47363.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.708450	0.89018	.	.	ENSG00000137266	ENST00000436008;ENST00000406686;ENST00000380302;ENST00000490273	T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18	5.41	5.41	0.78517	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.85164	0.5634	M	0.62723	1.935	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86066	0.1535	10	0.87932	D	0	-29.3275	18.5442	0.91040	0.0:1.0:0.0:0.0	.	571	A1A5C7	S22AN_HUMAN	E	579;571;290;290	ENSP00000410245:G579E;ENSP00000385028:G571E;ENSP00000369657:G290E;ENSP00000419463:G290E	ENSP00000369657:G290E	G	-	2	0	SLC22A23	3218637	1.000000	0.71417	1.000000	0.80357	0.767000	0.43475	5.521000	0.67086	2.689000	0.91719	0.561000	0.74099	GGG	.	.	none		0.642	SLC22A23-006	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353059.1	NM_021945		T	3273638	C	T	3273638	3	4	11	1	0	0	0	0	1	0	0	0	14467	623	22	2	352	2	SLC22A23	6	3273638	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10		3273638	167841429	104	1395											
HIST1H2AC	8334	hgsc.bcm.edu	37	chr6	26124573	26124585	+	Frame_Shift_Del	DEL	GCAACTACGCAGA	GCAACTACGCAGA	-																															gcaccgcctgctccgtaaagGcaactacgcagagcgggttg																										TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	GCAACTACGCAGA	GCAACTACGCAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr6:26124573_26124585delGCAACTACGCAGA	ENST00000602637.1	+	1	143_155	c.113_125delGCAACTACGCAGA	c.(112-126)ggcaactacgcagagfs	p.GNYAE38fs	HIST1H2BC_ENST00000396984.1_5'Flank|HIST1H2BC_ENST00000314332.5_5'Flank|HIST1H2AC_ENST00000377791.2_Frame_Shift_Del_p.GNYAE38fs			Q93077	H2A1C_HUMAN	histone cluster 1, H2ac	38						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E42Q(1)		NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(5)	12						CTCCGTAAAGGCAACTACGCAGAGCGGGTTGGG	0.657																																					p.38_42del		Atlas-Indel	.											.	HIST1H2AC	29	.	1	Substitution - Missense(1)	NS(1)	c.112_124del						PASS	.																																			SO:0001589	frameshift_variant	8334	exon1			.	Z80778	CCDS4585.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000180573	ENSG00000180573		"Histones / Replication-dependent"	4733	protein-coding gene	gene with protein product		602794	"H2A histone family, member L", "histone 1, H2ac"	H2AFL		9119399, 12408966	Standard	NM_003512		Approved		uc003ngm.3	Q93077	OTTHUMG00000014428	ENST00000602637.1:c.113_125delGCAACTACGCAGA	6.37:g.26124573_26124585delGCAACTACGCAGA	ENSP00000473534:p.Gly38fs	168	0	0		196	35	0.178571	NM_003512	B2R4F7|O00775|O00776|O00777|O00778|Q540R1	Frame_Shift_Del	DEL	ENST00000602637.1	37	CCDS4585.1																																																																																			.	.	none		0.657	HIST1H2AC-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468023.1	NM_003512		-	26124585	GCAACTACGCAGA	-	26124573	7	5	11	1	0	1	0	1	0	0	0	0	7139	1203	42	0	115	0	HIST1H2AC	6	26124573	Frame_Shift_Del	DEL	GCAACTACGCAGA	TCGA-FF-8042-01A-11D-2210-10	22850935	26124573	144990494	105	1396											
HIST1H1E	3008	hgsc.bcm.edu	37	chr6	26156929	26156929	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	gggcaccggcgcgtcgggttCcttcaaactcaacaagaagg	10	6	13	12	4	2	1	2	0	0	1	4	1	3	1	2	4	2	2	2	4	4	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr6:26156929C>G	ENST00000304218.3	+	1	371	c.311C>G	c.(310-312)tCc>tGc	p.S104C	HIST1H2BD_ENST00000377777.4_5'Flank|HIST1H2BD_ENST00000289316.2_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	104	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						GCGTCGGGTTCCTTCAAACTC	0.602																																					p.S104C		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.C311G						PASS	.						39	45	43					6																	26156929		2203	4300	6503	SO:0001583	missense	3008	exon1			CGGGTTCCTTCAA	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.311C>G	6.37:g.26156929C>G	ENSP00000307705:p.Ser104Cys	194	0	0		222	50	0.225225	NM_005321	Q4VB25	Missense_Mutation	SNP	ENST00000304218.3	37	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	19.18	3.777704	0.70107	.	.	ENSG00000168298	ENST00000304218	T	0.10960	2.82	5.35	5.35	0.76521	Histone H1/H5 (2);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.40522	0.1120	H	0.95850	3.73	0.80722	D	1	D	0.56287	0.975	D	0.64410	0.925	T	0.58725	-0.7586	10	0.87932	D	0	-5.7108	18.4042	0.90528	0.0:1.0:0.0:0.0	.	104	P10412	H14_HUMAN	C	104	ENSP00000307705:S104C	ENSP00000307705:S104C	S	+	2	0	HIST1H1E	26264908	1.000000	0.71417	0.711000	0.30485	0.551000	0.35334	7.751000	0.85126	2.658000	0.90341	0.561000	0.74099	TCC	.	.	none		0.602	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321		G	26156929	C	G	26156929	3	3	11	1	0	0	0	0	1	0	0	0	7135	855	30	4	313	4	HIST1H1E	6	26156929	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	32356	26156929	144958138	106	1397											
HIST1H2BJ	8970	hgsc.bcm.edu	37	chr6	27100241	27100241	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcagcaggcgcacggccgTctggatctccctggaggtga	7	6	15	13	3	2	1	0	1	2	0	3	3	2	3	2	5	2	3	2	5	0	0			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr6:27100241T>C	ENST00000607124.1	-	1	288	c.289A>G	c.(289-291)Acg>Gcg	p.T97A	HIST1H2AG_ENST00000359193.2_5'Flank|HIST1H2BJ_ENST00000541790.1_Missense_Mutation_p.T97A|HIST1H2BJ_ENST00000339812.2_Missense_Mutation_p.T97A			P06899	H2B1J_HUMAN	histone cluster 1, H2bj	97					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						CGCACGGCCGTCTGGATCTCC	0.592																																					p.T97A		Atlas-SNP	.											.	HIST1H2BJ	21	.	0			c.A289G						PASS	.						82	85	84					6																	27100241		2203	4300	6503	SO:0001583	missense	8970	exon1			CGGCCGTCTGGAT	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.289A>G	6.37:g.27100241T>C	ENSP00000476136:p.Thr97Ala	98	0	0		99	4	0.040404	NM_021058	B2R4J4|O60816	Missense_Mutation	SNP	ENST00000607124.1	37	CCDS4618.1	.	.	.	.	.	.	.	.	.	.	T	19.82	3.897676	0.72639	.	.	ENSG00000124635	ENST00000541790;ENST00000339812	T;T	0.41758	0.99;0.99	4.16	4.16	0.48862	Histone-fold (2);Histone core (1);	0.000000	0.44097	U	0.000498	T	0.53786	0.1818	M	0.81802	2.56	0.58432	D	0.999996	D	0.57899	0.981	D	0.64042	0.921	T	0.61973	-0.6952	10	0.87932	D	0	.	11.8112	0.52183	0.0:0.0:0.0:1.0	.	97	P06899	H2B1J_HUMAN	A	97	ENSP00000445633:T97A;ENSP00000342886:T97A	ENSP00000342886:T97A	T	-	1	0	HIST1H2BJ	27208220	1.000000	0.71417	1.000000	0.80357	0.362000	0.29581	3.651000	0.54431	1.841000	0.53522	0.477000	0.44152	ACG	.	.	none		0.592	HIST1H2BJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040138.2	NM_021058		C	27100241	T	C	27100241	3	2	11	1	0	0	0	0	1	0	0	0	7158	1667	58	3	95	3	HIST1H2BJ	6	27100241	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	943312	27100241	144014826	107	1398											
NKAPL	222698	hgsc.bcm.edu	37	chr6	28227333	28227333	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggagtgagttggacgtgggcGctctttacccctttagtcgc	5	12	14	10	3	1	1	0	1	1	0	2	3	1	3	2	3	1	2	2	3	2	5			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr6:28227333G>A	ENST00000343684.3	+	1	236	c.184G>A	c.(184-186)Gct>Act	p.A62T	ZKSCAN4_ENST00000423974.2_5'Flank	NM_001007531.1	NP_001007532.1	Q5M9Q1	NKAPL_HUMAN	NFKB activating protein-like	62										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						GGACGTGGGCGCTCTTTACCC	0.622																																					p.A62T		Atlas-SNP	.											.	NKAPL	72	.	0			c.G184A						PASS	.						54	59	57					6																	28227333		2203	4300	6503	SO:0001583	missense	222698	exon1			GTGGGCGCTCTTT	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.184G>A	6.37:g.28227333G>A	ENSP00000345716:p.Ala62Thr	88	0	0		80	44	0.55	NM_001007531	Q3MIV1|Q9H4Q7	Missense_Mutation	SNP	ENST00000343684.3	37	CCDS34353.1	.	.	.	.	.	.	.	.	.	.	G	12.46	1.944889	0.34283	.	.	ENSG00000189134	ENST00000343684	T	0.13778	2.56	4.21	-0.871	0.10642	.	1.031910	0.07675	N	0.936094	T	0.02342	0.0072	L	0.42245	1.32	0.09310	N	1	B	0.21147	0.052	B	0.08055	0.003	T	0.45862	-0.9232	10	0.08179	T	0.78	-0.4142	5.0106	0.14310	0.3089:0.3156:0.3754:0.0	.	62	Q5M9Q1	NKAPL_HUMAN	T	62	ENSP00000345716:A62T	ENSP00000345716:A62T	A	+	1	0	NKAPL	28335312	0.001000	0.12720	0.000000	0.03702	0.004000	0.04260	0.408000	0.21065	-0.318000	0.08665	-0.136000	0.14681	GCT	.	.	none		0.622	NKAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040185.1			A	28227333	G	A	28227333	3	1	11	1	0	0	0	0	1	0	0	0	10449	1087	38	1	186	1	NKAPL	6	28227333	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	1127092	28227333	142887734	108	1399											
RUNX2	860	hgsc.bcm.edu	37	chr6	45390482	45390482	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcaacagcagcagcagcagCaggaggcggcggcggcggct	10	1	18	12	4	0	0	0	0	0	0	0	1	0	1	0	6	7	7	0	6	1	0			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr6:45390482C>G	ENST00000371438.1	+	2	569	c.211C>G	c.(211-213)Cag>Gag	p.Q71E	RUNX2_ENST00000352853.5_Missense_Mutation_p.Q139E|RUNX2_ENST00000371436.6_Missense_Mutation_p.Q71E|RUNX2_ENST00000576263.1_Missense_Mutation_p.Q71E|RUNX2_ENST00000371432.3_Missense_Mutation_p.Q57E|RP1-244F24.1_ENST00000606796.1_RNA|RUNX2_ENST00000465038.2_Missense_Mutation_p.Q71E|RUNX2_ENST00000541979.1_Missense_Mutation_p.Q139E|RUNX2_ENST00000359524.5_Missense_Mutation_p.Q57E	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	71	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						gcagcagcagcaggaggcggc	0.716																																					p.Q71E		Atlas-SNP	.											RUNX2_ENST00000352853,NS,carcinoma,0,2	RUNX2	128	2	0			c.C211G						scavenged	.						6	10	9					6																	45390482		1279	2789	4068	SO:0001583	missense	860	exon3			CAGCAGCAGGAGG	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.211C>G	6.37:g.45390482C>G	ENSP00000360493:p.Gln71Glu	13	0	0		25	2	0.08	NM_001024630	O14614|O14615|O95181	Missense_Mutation	SNP	ENST00000371438.1	37	CCDS43467.2	.	.	.	.	.	.	.	.	.	.	C	12.60	1.985548	0.35036	.	.	ENSG00000124813	ENST00000465038;ENST00000352853;ENST00000541979;ENST00000371438;ENST00000371436;ENST00000359524;ENST00000371432	T;T;T;T;T;T;T	0.61742	0.08;0.08;0.08;0.08;0.08;0.08;0.08	3.45	3.45	0.39498	.	1.972660	0.03402	N	0.203449	T	0.19248	0.0462	N	0.14661	0.345	0.27094	N	0.962779	B;B;B	0.23806	0.033;0.055;0.091	B;B;B	0.20384	0.029;0.013;0.029	T	0.13818	-1.0495	10	0.02654	T	1	.	14.8379	0.70197	0.0:1.0:0.0:0.0	.	139;71;57	F6RGB9;Q13950;Q13950-2	.;RUNX2_HUMAN;.	E	71;139;139;71;71;57;57	ENSP00000420707:Q71E;ENSP00000319087:Q139E;ENSP00000446290:Q139E;ENSP00000360493:Q71E;ENSP00000360491:Q71E;ENSP00000352514:Q57E;ENSP00000360486:Q57E	ENSP00000319087:Q139E	Q	+	1	0	RUNX2	45498460	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	1.268000	0.33062	1.622000	0.50330	0.407000	0.27541	CAG	.	.	none		0.716	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348		G	45390482	C	G	45390482	3	3	11	1	0	0	0	0	1	0	0	0	13763	711	25	4	233	4	RUNX2	6	45390482	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	17163149	45390482	125724585	109	1400											
ENPP4	22875	hgsc.bcm.edu	37	chr6	46111076	46111076	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atttctagctgcccacggacCtgcatttcacaaaggctaca	11	10	7	13	1	2	0	1	0	1	0	2	1	2	1	2	2	4	3	2	2	3	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr6:46111076C>T	ENST00000321037.4	+	4	1291	c.1061C>T	c.(1060-1062)cCt>cTt	p.P354L		NM_014936.4	NP_055751.1	Q9Y6X5	ENPP4_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 4 (putative)	354					blood coagulation (GO:0007596)|positive regulation of blood coagulation (GO:0030194)|purine ribonucleoside catabolic process (GO:0046130)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	bis(5'-adenosyl)-triphosphatase activity (GO:0047710)|metal ion binding (GO:0046872)			central_nervous_system(1)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	18						GCCCACGGACCTGCATTTCAC	0.393																																					p.P354L		Atlas-SNP	.											.	ENPP4	44	.	0			c.C1061T						PASS	.						146	136	139					6																	46111076		2203	4300	6503	SO:0001583	missense	22875	exon4			ACGGACCTGCATT	AB020686	CCDS34468.1	6p12.3	2010-06-24	2010-06-24		ENSG00000001561	ENSG00000001561			3359	protein-coding gene	gene with protein product						11027689	Standard	NM_014936		Approved	NPP4, KIAA0879	uc003oxy.3	Q9Y6X5	OTTHUMG00000014779	ENST00000321037.4:c.1061C>T	6.37:g.46111076C>T	ENSP00000318066:p.Pro354Leu	97	0	0		100	4	0.04	NM_014936	A8K5G1|Q7L2N1	Missense_Mutation	SNP	ENST00000321037.4	37	CCDS34468.1	.	.	.	.	.	.	.	.	.	.	C	32	5.171481	0.94807	.	.	ENSG00000001561	ENST00000321037;ENST00000371401	D	0.81579	-1.51	5.9	5.9	0.94986	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.93481	0.7920	H	0.96777	3.88	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94748	0.7925	10	0.87932	D	0	-18.2243	20.2789	0.98501	0.0:1.0:0.0:0.0	.	354	Q9Y6X5	ENPP4_HUMAN	L	354	ENSP00000318066:P354L	ENSP00000318066:P354L	P	+	2	0	ENPP4	46219035	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	7.487000	0.81328	2.788000	0.95919	0.650000	0.86243	CCT	.	.	none		0.393	ENPP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040777.2			T	46111076	C	T	46111076	3	4	11	1	0	0	0	0	1	0	0	0	5134	681	24	2	1071	2	ENPP4	6	46111076	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	720594	46111076	125003991	110	1401											
TDRD6	221400	hgsc.bcm.edu	37	chr6	46658993	46658993	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggaaccttgtgccttgccaAgtatactgatggaaactggt	10	12	11	8	0	0	1	0	1	0	0	0	3	0	3	3	3	5	1	3	3	5	4	rs138212613		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr6:46658993A>C	ENST00000316081.6	+	1	3128	c.3128A>C	c.(3127-3129)aAg>aCg	p.K1043T	TDRD6_ENST00000544460.1_Missense_Mutation_p.K1043T	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	1043	Tudor 5. {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)			TGCCTTGCCAAGTATACTGAT	0.338																																					p.K1043T		Atlas-SNP	.											TDRD6,NS,carcinoma,0,1	TDRD6	205	1	0			c.A3128C						scavenged	.						71	76	74					6																	46658993		2203	4300	6503	SO:0001583	missense	221400	exon1			TTGCCAAGTATAC	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.3128A>C	6.37:g.46658993A>C	ENSP00000346065:p.Lys1043Thr	95	1	0.0105263		127	38	0.299213	NM_001168359	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Missense_Mutation	SNP	ENST00000316081.6	37	CCDS34470.1	.	.	.	.	.	.	.	.	.	.	A	10.72	1.428736	0.25726	.	.	ENSG00000180113	ENST00000544460;ENST00000316081	T;T	0.09723	2.95;2.95	5.45	-1.74	0.08056	Tudor subgroup (1);Maternal tudor protein (1);Tudor domain (1);	0.515089	0.21750	N	0.069696	T	0.17619	0.0423	M	0.86420	2.815	0.25095	N	0.99083	D;D	0.67145	0.995;0.996	D;D	0.70935	0.951;0.971	T	0.04579	-1.0941	10	0.39692	T	0.17	-3.58	11.919	0.52781	0.5826:0.0:0.4174:0.0	.	1043;1043	F5H5M3;O60522	.;TDRD6_HUMAN	T	1043	ENSP00000443299:K1043T;ENSP00000346065:K1043T	ENSP00000346065:K1043T	K	+	2	0	TDRD6	46766952	0.041000	0.20044	0.545000	0.28153	0.307000	0.27823	-0.057000	0.11768	-0.545000	0.06224	-0.977000	0.02584	AAG	A|1.000;G|0.000	.	alt		0.338	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443		C	46658993	A	C	46658993	3	2	11	1	0	0	0	0	1	0	0	0	15749	72	3	5	3130	5	TDRD6	6	46658993	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	547917	46658993	124456074	111	1402											
MUT	4594	hgsc.bcm.edu	37	chr6	49423828	49423828	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tcaattgtcaggccagcctgGagtccagttctagagtactc	9	11	10	11	0	3	1	2	0	1	1	5	2	4	2	3	2	2	2	3	2	3	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr6:49423828G>A	ENST00000274813.3	-	4	1003	c.876C>T	c.(874-876)ctC>ctT	p.L292L		NM_000255.3	NP_000246.2	P22033	MUTA_HUMAN	methylmalonyl CoA mutase	292					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)	GGCCAGCCTGGAGTCCAGTTC	0.403																																					p.L292L		Atlas-SNP	.											.	MUT	70	.	0			c.C876T						PASS	.						80	74	76					6																	49423828		2203	4300	6503	SO:0001819	synonymous_variant	4594	exon4			AGCCTGGAGTCCA		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.876C>T	6.37:g.49423828G>A		193	0	0		208	10	0.0480769	NM_000255	A8K953|Q5SYZ3|Q96B11|Q9UD64	Silent	SNP	ENST00000274813.3	37	CCDS4924.1																																																																																			.	.	none		0.403	MUT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040854.1			A	49423828	G	A	49423828	2	1	11	1	0	0	0	0	0	0	0	1	10000	1161	41	2		2	MUT	6	49423828	Silent	SNP	G	TCGA-FF-8042-01A-11D-2210-10	2764835	49423828	121691239	112	1403											
BMP5	653	hgsc.bcm.edu	37	chr6	55739470	55739470	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ttccaggtgaaaatggtctgGgtctgtgaggcaaacccaag	11	9	13	8	0	2	2	0	2	2	0	3	2	3	2	2	4	1	1	2	4	4	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr6:55739470G>T	ENST00000370830.3	-	1	892	c.194C>A	c.(193-195)cCc>cAc	p.P65H	BMP5_ENST00000446683.2_Missense_Mutation_p.P65H	NM_021073.2	NP_066551.1	P22003	BMP5_HUMAN	bone morphogenetic protein 5	65					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)			AAATGGTCTGGGTCTGTGAGG	0.433																																					p.P65H		Atlas-SNP	.											.	BMP5	94	.	0			c.C194A						PASS	.						197	177	184					6																	55739470		2203	4300	6503	SO:0001583	missense	653	exon1			GGTCTGGGTCTGT		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.194C>A	6.37:g.55739470G>T	ENSP00000359866:p.Pro65His	116	0	0		146	31	0.212329	NM_021073	B4E0Y4|Q9H547|Q9NTM5	Missense_Mutation	SNP	ENST00000370830.3	37	CCDS4958.1	.	.	.	.	.	.	.	.	.	.	G	19.69	3.874739	0.72180	.	.	ENSG00000112175	ENST00000370830;ENST00000446683	D;D	0.91068	-2.78;-2.78	5.71	5.71	0.89125	Transforming growth factor-beta, N-terminal (1);	0.157746	0.64402	D	0.000019	D	0.95937	0.8677	M	0.87381	2.88	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	D	0.95966	0.8966	10	0.87932	D	0	.	19.8478	0.96722	0.0:0.0:1.0:0.0	.	65;65	B4E0Y4;P22003	.;BMP5_HUMAN	H	65	ENSP00000359866:P65H;ENSP00000391818:P65H	ENSP00000359866:P65H	P	-	2	0	BMP5	55847429	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.685000	0.91497	0.650000	0.86243	CCC	.	.	none		0.433	BMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041000.1			T	55739470	G	T	55739470	3	4	11	1	0	0	0	0	1	0	0	0	1463	1232	43	4	1198	4	BMP5	6	55739470	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	6315642	55739470	115375597	113	1404											
FILIP1	27145	hgsc.bcm.edu	37	chr6	76018589	76018589	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aatgcgggtgggtgtaggccGctgggatgacccgtcttgtc	5	10	17	9	3	1	1	0	1	1	0	2	2	1	2	2	4	1	2	2	4	2	2	rs369386052		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr6:76018589G>A	ENST00000237172.7	-	6	3790	c.3460C>T	c.(3460-3462)Cgg>Tgg	p.R1154W	FILIP1_ENST00000393004.2_Missense_Mutation_p.R1154W|FILIP1_ENST00000370020.1_Missense_Mutation_p.R1055W|FILIP1_ENST00000498523.1_5'UTR	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	1154										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						GGTGTAGGCCGCTGGGATGAC	0.493																																					p.R1154W		Atlas-SNP	.											FILIP1,right_upper_lobe,carcinoma,0,1	FILIP1	173	1	0			c.C3460T						PASS	.	G	TRP/ARG	0,4406		0,0,2203	93	90	91		3460	5.9	1	6		91	1,8599	1.2+/-3.3	0,1,4299	no	missense	FILIP1	NM_015687.2	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	1154/1214	76018589	1,13005	2203	4300	6503	SO:0001583	missense	27145	exon6			TAGGCCGCTGGGA	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.3460C>T	6.37:g.76018589G>A	ENSP00000237172:p.Arg1154Trp	149	0	0		174	57	0.327586	NM_015687	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Missense_Mutation	SNP	ENST00000237172.7	37	CCDS4984.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.958904	0.74016	0.0	1.16E-4	ENSG00000118407	ENST00000393004;ENST00000237172;ENST00000370020	T;T;T	0.27720	1.66;1.65;1.67	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.45994	0.1370	M	0.61703	1.905	0.58432	D	0.999995	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.992;0.997	T	0.40869	-0.9540	10	0.87932	D	0	-16.9412	14.9358	0.70954	0.0:0.0:0.8235:0.1765	.	1154;1154;1154	A8K2G7;Q7Z7B0;Q7Z7B0-2	.;FLIP1_HUMAN;.	W	1154;1154;1055	ENSP00000376728:R1154W;ENSP00000237172:R1154W;ENSP00000359037:R1055W	ENSP00000237172:R1154W	R	-	1	2	FILIP1	76075309	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.609000	0.54117	2.794000	0.96219	0.655000	0.94253	CGG	.	.	weak		0.493	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		A	76018589	G	A	76018589	3	1	11	1	0	0	0	0	1	0	0	0	5902	1086	38	1	185	1	FILIP1	6	76018589	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	20279119	76018589	95096478	114	1405											
TRDN	10345	hgsc.bcm.edu	37	chr6	123759264	123759264	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttctttttgatatcttctTtttctgctggtaaaataaga	9	22	5	5	0	4	2	0	1	4	1	4	2	4	2	0	1	1	2	0	1	4	10			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr6:123759264T>C	ENST00000398178.3	-	12	1016	c.995A>G	c.(994-996)aAa>aGa	p.K332R	RP11-532N4.2_ENST00000589182.1_RNA|RP11-532N4.2_ENST00000587106.2_RNA|RP11-532N4.2_ENST00000587049.1_RNA|RP11-532N4.2_ENST00000434768.1_RNA|RP11-532N4.2_ENST00000418467.2_RNA|TRDN_ENST00000334268.4_Missense_Mutation_p.K332R|RP11-532N4.2_ENST00000427828.1_RNA	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin	332					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)		GATATCTTCTTTTTCTGCTGG	0.343																																					p.K333R		Atlas-SNP	.											.	TRDN	88	.	0			c.A998G						PASS	.						108	100	102					6																	123759264		1815	4058	5873	SO:0001583	missense	10345	exon12			TCTTCTTTTTCTG	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.995A>G	6.37:g.123759264T>C	ENSP00000381240:p.Lys332Arg	52	0	0		79	26	0.329114	NM_001251987	A5D6W5|F5H2W7|Q6NSB8	Missense_Mutation	SNP	ENST00000398178.3	37	CCDS55053.1	.	.	.	.	.	.	.	.	.	.	T	18.29	3.592330	0.66219	.	.	ENSG00000186439	ENST00000398178;ENST00000398161;ENST00000334268;ENST00000542014	T;T	0.64260	-0.09;-0.09	5.64	5.64	0.86602	.	0.152578	0.41938	D	0.000781	T	0.56834	0.2012	N	0.24115	0.695	0.80722	D	1	D;D;D	0.76494	0.993;0.993;0.999	D;D;D	0.78314	0.978;0.978;0.991	T	0.61043	-0.7142	10	0.38643	T	0.18	-6.8293	12.5428	0.56182	0.0:0.0:0.0:1.0	.	332;333;332	Q5SWK9;Q8IVK2;Q13061	.;.;TRDN_HUMAN	R	332	ENSP00000381240:K332R;ENSP00000333984:K332R	ENSP00000333984:K332R	K	-	2	0	TRDN	123800963	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	2.046000	0.41260	2.275000	0.75901	0.528000	0.53228	AAA	.	.	none		0.343	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				C	123759264	T	C	123759264	3	2	11	1	0	0	0	0	1	0	0	0	16483	1841	64	3	1314	3	TRDN	6	123759264	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	47740675	123759264	47355803	115	1406											
TAAR2	9287	hgsc.bcm.edu	37	chr6	132938981	132938981	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tatgctaagcatcaggtcaaAactataataaatcttgcaaa	18	11	5	7	0	3	0	2	0	1	0	3	0	3	0	0	1	4	3	0	1	9	6			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr6:132938981A>C	ENST00000367931.1	-	2	363	c.364T>G	c.(364-366)Ttt>Gtt	p.F122V	TAAR2_ENST00000275191.2_Missense_Mutation_p.F77V|TAAR2_ENST00000537809.1_Missense_Mutation_p.F77V			Q9P1P5	TAAR2_HUMAN	trace amine associated receptor 2	122					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)		ATCAGGTCAAAACTATAATAA	0.363																																					p.F122V		Atlas-SNP	.											.	TAAR2	45	.	0			c.T364G						PASS	.						77	74	75					6																	132938981		2203	4300	6503	SO:0001583	missense	9287	exon2			GGTCAAAACTATA	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.364T>G	6.37:g.132938981A>C	ENSP00000356908:p.Phe122Val	88	0	0		98	25	0.255102	NM_001033080	Q5QD02|Q6NWS1|Q6NWS2|Q6NWS3	Missense_Mutation	SNP	ENST00000367931.1	37	CCDS34541.1	.	.	.	.	.	.	.	.	.	.	A	14.25	2.480293	0.44044	.	.	ENSG00000146378	ENST00000275191;ENST00000367931;ENST00000537809	T;T;T	0.39056	1.1;1.1;1.1	6.0	6.0	0.97389	GPCR, rhodopsin-like superfamily (1);	0.060936	0.64402	D	0.000003	T	0.44767	0.1309	L	0.40543	1.245	0.40300	D	0.978594	D	0.89917	1.0	D	0.91635	0.999	T	0.43750	-0.9372	10	0.42905	T	0.14	-34.3902	12.6876	0.56956	0.8767:0.0:0.0:0.1233	.	122	Q9P1P5	TAAR2_HUMAN	V	77;122;77	ENSP00000275191:F77V;ENSP00000356908:F122V;ENSP00000441263:F77V	ENSP00000275191:F77V	F	-	1	0	TAAR2	132980674	0.998000	0.40836	1.000000	0.80357	0.746000	0.42486	2.252000	0.43196	2.295000	0.77249	0.528000	0.53228	TTT	.	.	none		0.363	TAAR2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390735.1	NM_014626		C	132938981	A	C	132938981	3	2	11	1	0	0	0	0	1	0	0	0	15505	14	1	5	695	5	TAAR2	6	132938981	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	9179717	132938981	38176086	116	1407											
EYA4	2070	hgsc.bcm.edu	37	chr6	133836535	133836535	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtctgacagattcctggctAacaaatgcacttaagtcttt	11	13	8	9	0	2	2	0	1	2	1	3	2	3	2	1	2	2	2	1	2	3	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr6:133836535A>G	ENST00000367895.5	+	17	2042	c.1578A>G	c.(1576-1578)ctA>ctG	p.L526L	EYA4_ENST00000452339.2_Silent_p.L472L|EYA4_ENST00000355167.3_Silent_p.L526L|EYA4_ENST00000431403.2_Silent_p.L526L|EYA4_ENST00000525849.1_Silent_p.L503L|EYA4_ENST00000430974.2_Silent_p.L478L|RP3-323P13.2_ENST00000607033.1_RNA|EYA4_ENST00000355286.6_Silent_p.L503L|EYA4_ENST00000531901.1_Silent_p.L532L	NM_004100.4	NP_004091.3	O95677	EYA4_HUMAN	EYA transcriptional coactivator and phosphatase 4	526					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)		ATTCCTGGCTAACAAATGCAC	0.413																																					p.L526L	Melanoma(57;398 1237 3528 4702 7415)	Atlas-SNP	.											EYA4_ENST00000355167,NS,carcinoma,+2,2	EYA4	196	2	0			c.A1578G						PASS	.						192	183	186					6																	133836535		2203	4300	6503	SO:0001819	synonymous_variant	2070	exon17			CTGGCTAACAAAT	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.1578A>G	6.37:g.133836535A>G		82	0	0		94	20	0.212766	NM_172105	B7Z7F7|O95464|O95679|Q8IW39|Q9NTR7	Silent	SNP	ENST00000367895.5	37	CCDS5165.1																																																																																			.	.	none		0.413	EYA4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042282.2	NM_004100		G	133836535	A	G	133836535	2	3	11	1	0	0	0	0	0	0	0	1	5333	349	13	3		3	EYA4	6	133836535	Silent	SNP	A	TCGA-FF-8042-01A-11D-2210-10	897554	133836535	37278532	117	1408											
SYNJ2	8871	hgsc.bcm.edu	37	chr6	158504550	158504550	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	attcggaaacgagacagcatGgcccccgtgtctcccactgc	9	7	10	15	3	1	1	0	0	1	1	3	3	1	2	3	2	3	1	3	2	1	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr6:158504550G>A	ENST00000355585.4	+	21	3030	c.2955G>A	c.(2953-2955)atG>atA	p.M985I	SYNJ2_ENST00000367121.3_Missense_Mutation_p.M985I|SYNJ2_ENST00000367122.2_Missense_Mutation_p.M985I|SYNJ2_ENST00000367112.1_Missense_Mutation_p.M70I	NM_001178088.1|NM_003898.3	NP_001171559.1|NP_003889.1	O15056	SYNJ2_HUMAN	synaptojanin 2	985					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)		GAGACAGCATGGCCCCCGTGT	0.527																																					p.M985I		Atlas-SNP	.											.	SYNJ2	111	.	0			c.G2955A						PASS	.						106	99	102					6																	158504550		2203	4300	6503	SO:0001583	missense	8871	exon21			CAGCATGGCCCCC	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.2955G>A	6.37:g.158504550G>A	ENSP00000347792:p.Met985Ile	77	0	0		92	29	0.315217	NM_003898	Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226	Missense_Mutation	SNP	ENST00000355585.4	37	CCDS5254.1	.	.	.	.	.	.	.	.	.	.	G	1.051	-0.675929	0.03378	.	.	ENSG00000078269	ENST00000367122;ENST00000367121;ENST00000355585;ENST00000367112	D;D;D;T	0.92699	-2.84;-3.09;-2.83;1.21	5.43	3.59	0.41128	Domain of unknown function DUF1866 (1);	0.963904	0.08620	N	0.918599	T	0.52273	0.1724	N	0.01109	-1.01	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.002	T	0.59815	-0.7383	10	0.05525	T	0.97	.	3.6538	0.08213	0.1642:0.151:0.5613:0.1235	.	985;985	O15056;O15056-3	SYNJ2_HUMAN;.	I	985;985;985;70	ENSP00000356089:M985I;ENSP00000356088:M985I;ENSP00000347792:M985I;ENSP00000356079:M70I	ENSP00000347792:M985I	M	+	3	0	SYNJ2	158424538	0.989000	0.36119	0.069000	0.20011	0.935000	0.57460	0.611000	0.24268	1.271000	0.44313	0.591000	0.81541	ATG	.	.	none		0.527	SYNJ2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042858.2			A	158504550	G	A	158504550	3	1	11	1	0	0	0	0	1	0	0	0	15468	1348	47	2	3037	2	SYNJ2	6	158504550	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	24668015	158504550	12610517	118	1409											
TCP1	6950	hgsc.bcm.edu	37	chr6	160208813	160208813	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tccaacttctttgtcttgcaGatcagccagctcacaaagaa	12	11	6	12	0	4	2	2	0	2	2	5	2	5	2	2	0	4	2	2	0	3	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr6:160208813G>A	ENST00000321394.7	-	3	521	c.241C>T	c.(241-243)Ctg>Ttg	p.L81L	TCP1_ENST00000546023.1_5'Flank|MRPL18_ENST00000367034.4_5'Flank|TCP1_ENST00000392168.2_5'UTR|TCP1_ENST00000420894.2_Silent_p.L81L|TCP1_ENST00000544255.1_5'UTR|SNORA29_ENST00000384183.1_RNA	NM_030752.2	NP_110379.2	P17987	TCPA_HUMAN	t-complex 1	81					'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)		TTGTCTTGCAGATCAGCCAGC	0.403																																					p.L81L		Atlas-SNP	.											.	TCP1	37	.	0			c.C241T						PASS	.						100	99	99					6																	160208813		2203	4300	6503	SO:0001819	synonymous_variant	6950	exon3			CTTGCAGATCAGC	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.241C>T	6.37:g.160208813G>A		380	0	0		455	124	0.272527	NM_030752	E1P5B2|Q15556|Q5TCM3	Silent	SNP	ENST00000321394.7	37	CCDS5269.1																																																																																			.	.	none		0.403	TCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042917.2	NM_030752		A	160208813	G	A	160208813	2	1	11	1	0	0	0	0	0	0	0	1	15724	933	33	2		2	TCP1	6	160208813	Silent	SNP	G	TCGA-FF-8042-01A-11D-2210-10	1704263	160208813	10906254	119	1410											
PDE10A	10846	hgsc.bcm.edu	37	chr6	165848819	165848819	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggcccagcagggatgaggCggggttttccttcctttatc	5	12	14	10	1	0	1	0	1	0	0	3	2	2	2	3	5	1	2	3	5	1	5			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr6:165848819C>T	ENST00000366882.1	-	7	567	c.413G>A	c.(412-414)cGc>cAc	p.R138H	PDE10A_ENST00000354448.4_Missense_Mutation_p.R138H|PDE10A_ENST00000539869.2_Missense_Mutation_p.R148H			Q9Y233	PDE10_HUMAN	phosphodiesterase 10A	138	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)	p.R138H(1)		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)	AGGGATGAGGCGGGGTTTTCC	0.488																																					p.R148H	Esophageal Squamous(22;308 615 5753 12038 40624)	Atlas-SNP	.											PDE10A,NS,carcinoma,-1,3	PDE10A	154	3	1	Substitution - Missense(1)	large_intestine(1)	c.G443A						PASS	.						146	125	132					6																	165848819		2203	4300	6503	SO:0001583	missense	10846	exon6			ATGAGGCGGGGTT	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.413G>A	6.37:g.165848819C>T	ENSP00000355847:p.Arg138His	133	0	0		139	40	0.28777	NM_001130690	Q6FHX1|Q9HCP9|Q9NTV4|Q9ULW9|Q9Y5T1	Missense_Mutation	SNP	ENST00000366882.1	37		.	.	.	.	.	.	.	.	.	.	C	16.42	3.118205	0.56505	.	.	ENSG00000112541	ENST00000366882;ENST00000539869;ENST00000343842;ENST00000354448;ENST00000392126	T;T	0.69306	-0.39;-0.39	5.32	2.57	0.30868	GAF (1);	0.473990	0.25535	N	0.030018	T	0.36441	0.0967	L	0.38175	1.15	0.21527	N	0.999651	P;P	0.52842	0.66;0.956	B;P	0.47102	0.149;0.537	T	0.28713	-1.0035	10	0.45353	T	0.12	.	2.4185	0.04442	0.1336:0.5251:0.1293:0.212	.	148;138	Q9ULW9;Q9Y233	.;PDE10_HUMAN	H	138;166;148;138;137	ENSP00000355847:R138H;ENSP00000346435:R138H	ENSP00000341187:R148H	R	-	2	0	PDE10A	165768809	0.001000	0.12720	0.070000	0.20053	0.702000	0.40608	0.827000	0.27421	0.321000	0.23259	0.460000	0.39030	CGC	.	.	none		0.488	PDE10A-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000043031.1			T	165848819	C	T	165848819	3	4	11	1	0	0	0	0	1	0	0	0	11639	768	27	1	1994	1	PDE10A	6	165848819	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	5640006	165848819	5266248	120	1411											
MLLT4	4301	hgsc.bcm.edu	37	chr6	168369872	168369872	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggatgcaaaagagaagcgctCtaaaaggtatggacggttgc	14	7	14	6	2	1	1	0	0	1	1	1	4	1	3	0	4	3	4	0	4	6	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr6:168369872C>T	ENST00000447894.2	+	32	5315	c.5315C>T	c.(5314-5316)tCt>tTt	p.S1772F	MLLT4_ENST00000351017.4_Missense_Mutation_p.S1779F|MLLT4_ENST00000400822.3_Missense_Mutation_p.S1782F|MLLT4_ENST00000366806.2_Missense_Mutation_p.S1772F|MLLT4_ENST00000392112.1_Missense_Mutation_p.S1691F			P55196	AFAD_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 4	1772					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)		GAGAAGCGCTCTAAAAGGTAT	0.468			T	MLL	AL																																p.S1691F		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.C5072T						PASS	.						107	113	111					6																	168369872		1981	4159	6140	SO:0001583	missense	4301	exon31			AGCGCTCTAAAAG	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.5315C>T	6.37:g.168369872C>T	ENSP00000404595:p.Ser1772Phe	84	0	0		84	28	0.333333	NM_001207008	O75087|O75088|O75089|Q59FP0|Q5TIG6|Q5TIG7|Q9NSN7|Q9NU92	Missense_Mutation	SNP	ENST00000447894.2	37		.	.	.	.	.	.	.	.	.	.	C	14.91	2.676349	0.47886	.	.	ENSG00000130396	ENST00000351017;ENST00000366806;ENST00000392112;ENST00000400822;ENST00000447894	T;T;T;T;T	0.04862	3.69;3.79;3.54;3.69;3.69	4.81	2.97	0.34412	.	0.783620	0.11677	N	0.540149	T	0.03564	0.0102	M	0.72479	2.2	0.09310	N	1	B	0.31227	0.314	B	0.32342	0.144	T	0.34875	-0.9811	10	0.59425	D	0.04	-2.7937	8.6982	0.34310	0.0:0.6327:0.2889:0.0784	.	1782	P55196-5	.	F	1779;1772;1691;1782;1772	ENSP00000252692:S1779F;ENSP00000355771:S1772F;ENSP00000375960:S1691F;ENSP00000383623:S1782F;ENSP00000404595:S1772F	ENSP00000252692:S1779F	S	+	2	0	MLLT4	168112721	0.001000	0.12720	0.001000	0.08648	0.721000	0.41392	1.210000	0.32370	0.418000	0.25898	0.655000	0.94253	TCT	.	.	none		0.468	MLLT4-013	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000372077.1	NM_005936		T	168369872	C	T	168369872	3	4	11	1	0	0	0	0	1	0	0	0	9638	913	32	2	5568	2	MLLT4	6	168369872	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	2521053	168369872	2745195	121	1412											
THBS2	7058	hgsc.bcm.edu	37	chr6	169632988	169632988	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggcggggtcacccacctcGtccaggtcctcacagtgggt	6	7	14	14	2	2	0	2	0	0	0	5	0	4	0	4	5	0	0	4	5	0	0	rs148676859		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr6:169632988G>A	ENST00000366787.3	-	12	2025	c.1776C>T	c.(1774-1776)gaC>gaT	p.D592D	XXyac-YX65C7_A.2_ENST00000444188.1_RNA	NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	592					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)		CACCCACCTCGTCCAGGTCCT	0.687													G|||	1	0.000199681	0.0008	0.0	5008	,	,		15698	0.0		0.0	False		,,,				2504	0.0				p.D592D	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-SNP	.											.	THBS2	230	.	0			c.C1776T						PASS	.	G		1,4399		0,1,2199	39	41	41		1776	-6.7	0.8	6	dbSNP_134	41	0,8600		0,0,4300	no	coding-synonymous	THBS2	NM_003247.2		0,1,6499	AA,AG,GG		0.0,0.0227,0.0077		592/1173	169632988	1,12999	2200	4300	6500	SO:0001819	synonymous_variant	7058	exon12			CACCTCGTCCAGG		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.1776C>T	6.37:g.169632988G>A		65	0	0		82	20	0.243902	NM_003247	A6H8N1|A7E232|Q5RI52	Silent	SNP	ENST00000366787.3	37	CCDS34574.1																																																																																			G|1.000;A|0.000	0.000	weak		0.687	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247		A	169632988	G	A	169632988	2	1	11	1	0	0	0	0	0	0	0	1	15869	1136	40	1		1	THBS2	6	169632988	Silent	SNP	G	TCGA-FF-8042-01A-11D-2210-10	1263116	169632988	1482079	122	1413											
CARD11	84433	hgsc.bcm.edu	37	chr7	2983885	2983885	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctcctcatgaccgccatgttCttctcctcactgagctgtgc	5	13	7	16	1	4	2	2	2	2	0	6	2	5	2	4	0	2	2	4	0	0	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr7:2983885C>G	ENST00000396946.4	-	5	1048	c.645G>C	c.(643-645)aaG>aaC	p.K215N	AC004906.3_ENST00000423194.1_RNA	NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	215					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.K208N(1)|p.K208del(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)		CCGCCATGTTCTTCTCCTCAC	0.577			Mis		DLBCL																																p.K215N		Atlas-SNP	.		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	CARD11,colon,carcinoma,-2,6	CARD11	339	6	2	Substitution - Missense(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(2)	c.G645C						PASS	.						186	114	138					7																	2983885		2203	4300	6503	SO:0001583	missense	84433	exon5			CATGTTCTTCTCC	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.645G>C	7.37:g.2983885C>G	ENSP00000380150:p.Lys215Asn	239	0	0		292	160	0.547945	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	C	16.06	3.015955	0.54468	.	.	ENSG00000198286	ENST00000396946	T	0.37915	1.17	4.16	-3.11	0.05299	.	0.000000	0.85682	D	0.000000	T	0.49012	0.1532	L	0.57536	1.79	0.46336	D	0.998996	D	0.65815	0.995	D	0.69479	0.964	T	0.40979	-0.9534	10	0.52906	T	0.07	-28.1579	13.3536	0.60615	0.0:0.8991:0.0:0.1009	.	215	Q9BXL7	CAR11_HUMAN	N	215	ENSP00000380150:K215N	ENSP00000380150:K215N	K	-	3	2	CARD11	2950411	1.000000	0.71417	0.961000	0.40146	0.982000	0.71751	1.434000	0.34958	-1.079000	0.03113	-0.367000	0.07326	AAG	.	.	none		0.577	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		G	2983885	C	G	2983885	3	3	11	1	0	0	0	0	1	0	0	0	2647	912	32	4	2903	4	CARD11	7	2983885	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10		2983885	156154778	123	1414											
THSD7A	221981	hgsc.bcm.edu	37	chr7	11509616	11509616	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttcaggtcgaaggctttcaGgacatctagaaaggcaaagg	13	9	12	7	1	3	1	2	0	1	1	4	3	3	2	0	5	0	2	0	5	4	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr7:11509616G>T	ENST00000423059.4	-	9	2509	c.2258C>A	c.(2257-2259)cCt>cAt	p.P753H	AC004538.3_ENST00000445839.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	753	TSP type-1 7. {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)		AAGGCTTTCAGGACATCTAGA	0.393										HNSCC(18;0.044)																											p.P753H		Atlas-SNP	.											THSD7A,mouth,carcinoma,+1,1	THSD7A	219	1	0			c.C2258A						PASS	.						47	40	43					7																	11509616		1858	4094	5952	SO:0001583	missense	221981	exon9			CTTTCAGGACATC		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.2258C>A	7.37:g.11509616G>T	ENSP00000406482:p.Pro753His	79	0	0		85	28	0.329412	NM_015204		Missense_Mutation	SNP	ENST00000423059.4	37	CCDS47543.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.716373	0.89205	.	.	ENSG00000005108	ENST00000262042;ENST00000423059	T	0.61742	0.08	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.76407	0.3983	M	0.73372	2.23	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.77008	-0.2747	10	0.56958	D	0.05	.	19.5548	0.95338	0.0:0.0:1.0:0.0	.	753	Q9UPZ6	THS7A_HUMAN	H	753	ENSP00000406482:P753H	ENSP00000262042:P753H	P	-	2	0	THSD7A	11476141	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	9.813000	0.99286	2.686000	0.91538	0.650000	0.86243	CCT	.	.	none		0.393	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2		T	11509616	G	T	11509616	3	4	11	1	0	0	0	0	1	0	0	0	15894	1000	35	4	2791	4	THSD7A	7	11509616	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	8525731	11509616	147629047	124	1415											
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47876625	47876625	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gcaggtagcggctggaggagGgcctgctgtacaccgacagc	8	5	17	11	2	0	0	0	0	0	0	0	3	0	2	2	5	4	5	2	5	2	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	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						PASS	.						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	7.37:g.47876625G>A	ENSP00000289672:p.Pro1946Leu	129	0	0		169	42	0.248521	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	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	.	.	none		0.582	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		A	47876625	G	A	47876625	3	1	11	1	0	0	0	0	1	0	0	0	11973	1232	43	2	2796	2	PKD1L1	7	47876625	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	36367009	47876625	111262038	125	1416											
CCT6A	908	hgsc.bcm.edu	37	chr7	56129454	56129454	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctttaggttcttgctcagaaCtctggttttgaccttcagga	7	16	9	9	0	4	2	2	1	2	1	4	3	4	3	1	3	2	3	1	3	2	7			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr7:56129454C>G	ENST00000275603.4	+	12	1581	c.1362C>G	c.(1360-1362)aaC>aaG	p.N454K	SUMF2_ENST00000434526.2_5'Flank|SUMF2_ENST00000275607.9_5'Flank|CCT6A_ENST00000335503.3_Missense_Mutation_p.N409K|SUMF2_ENST00000395436.2_5'Flank|SUMF2_ENST00000437307.2_5'Flank|SUMF2_ENST00000342190.6_5'Flank|SNORA15_ENST00000384439.1_RNA|SUMF2_ENST00000413756.1_5'Flank|CCT6A_ENST00000462133.1_3'UTR|SUMF2_ENST00000395435.2_5'Flank|CCT6A_ENST00000540286.1_Missense_Mutation_p.N423K	NM_001762.3	NP_001753.1	P40227	TCPZ_HUMAN	chaperonin containing TCP1, subunit 6A (zeta 1)	454					'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)			TTGCTCAGAACTCTGGTTTTG	0.318																																					p.N454K		Atlas-SNP	.											.	CCT6A	44	.	0			c.C1362G						PASS	.						41	42	41					7																	56129454		2203	4300	6503	SO:0001583	missense	908	exon12			TCAGAACTCTGGT	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.1362C>G	7.37:g.56129454C>G	ENSP00000275603:p.Asn454Lys	303	0	0		295	66	0.223729	NM_001762	A6NCD2|Q3KP28|Q75LP4|Q96S46	Missense_Mutation	SNP	ENST00000275603.4	37	CCDS5523.1	.	.	.	.	.	.	.	.	.	.	C	16.53	3.148303	0.57151	.	.	ENSG00000146731	ENST00000275603;ENST00000335503;ENST00000540286;ENST00000539340	D;D;D	0.86366	-2.11;-2.11;-2.11	4.96	2.18	0.27775	.	0.044542	0.85682	N	0.000000	D	0.94703	0.8291	H	0.97587	4.035	0.80722	D	1	P;P;P	0.37663	0.566;0.604;0.559	P;P;P	0.56278	0.598;0.795;0.711	D	0.93087	0.6496	10	0.87932	D	0	-14.3993	9.0157	0.36168	0.0:0.7582:0.0:0.2418	.	423;409;454	B4DPJ8;A6NCD2;P40227	.;.;TCPZ_HUMAN	K	454;409;423;312	ENSP00000275603:N454K;ENSP00000352019:N409K;ENSP00000438488:N423K	ENSP00000275603:N454K	N	+	3	2	CCT6A	56096948	0.746000	0.28272	1.000000	0.80357	0.988000	0.76386	-0.053000	0.11846	0.157000	0.19338	0.456000	0.33151	AAC	.	.	none		0.318	CCT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251526.2	NM_001762		G	56129454	C	G	56129454	3	3	11	1	0	0	0	0	1	0	0	0	2959	564	20	4	1408	4	CCT6A	7	56129454	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	8252829	56129454	103009209	126	1417											
SEMA3E	9723	hgsc.bcm.edu	37	chr7	82997329	82997329	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agagtaaaccaaggtccatcTtaaccactctgtcatctgtc	12	11	6	12	0	4	1	1	0	3	1	6	1	5	1	3	1	2	1	3	1	4	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr7:82997329T>G	ENST00000307792.3	-	17	2368	c.1901A>C	c.(1900-1902)aAg>aCg	p.K634T	SEMA3E_ENST00000427262.1_Missense_Mutation_p.K574T	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	634	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)				AAGGTCCATCTTAACCACTCT	0.418																																					p.K634T		Atlas-SNP	.											.	SEMA3E	125	.	0			c.A1901C						PASS	.						118	114	115					7																	82997329		2203	4300	6503	SO:0001583	missense	9723	exon17			TCCATCTTAACCA	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.1901A>C	7.37:g.82997329T>G	ENSP00000303212:p.Lys634Thr	123	0	0		143	30	0.20979	NM_012431	B4E1P1|Q75M94|Q75M97	Missense_Mutation	SNP	ENST00000307792.3	37	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	T	17.43	3.386952	0.61956	.	.	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514	T;T	0.01495	4.83;4.83	5.77	5.77	0.91146	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.173767	0.49916	D	0.000122	T	0.03959	0.0111	M	0.68593	2.085	0.39645	D	0.970385	P	0.37688	0.605	B	0.39771	0.309	T	0.56372	-0.7990	10	0.22109	T	0.4	.	16.0802	0.81001	0.0:0.0:0.0:1.0	.	634	O15041	SEM3E_HUMAN	T	634;574;634	ENSP00000303212:K634T;ENSP00000405052:K574T	ENSP00000303212:K634T	K	-	2	0	SEMA3E	82835265	1.000000	0.71417	0.999000	0.59377	0.976000	0.68499	3.679000	0.54634	2.201000	0.70794	0.477000	0.44152	AAG	.	.	none		0.418	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431		G	82997329	T	G	82997329	3	3	11	1	0	0	0	0	1	0	0	0	14043	1609	56	5	430	5	SEMA3E	7	82997329	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	26867875	82997329	76141334	127	1418											
TFPI2	7980	hgsc.bcm.edu	37	chr7	93519470	93519470	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttctatcctccagcaagcatCgtcgcaagcctcccaggtgt	8	10	8	15	2	1	0	0	0	1	0	6	0	4	0	4	1	3	3	4	1	3	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr7:93519470C>T	ENST00000222543.5	-	2	562	c.250G>A	c.(250-252)Gat>Aat	p.D84N	GNGT1_ENST00000455502.1_Intron|AC002076.10_ENST00000435257.1_RNA|TFPI2_ENST00000545378.1_Missense_Mutation_p.D84N	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	84	BPTI/Kunitz inhibitor 1. {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)			CAGCAAGCATCGTCGCAAGCC	0.617																																					p.D84N		Atlas-SNP	.											.	TFPI2	37	.	0			c.G250A						PASS	.						33	35	34					7																	93519470		2203	4300	6503	SO:0001583	missense	7980	exon2			AAGCATCGTCGCA	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.250G>A	7.37:g.93519470C>T	ENSP00000222543:p.Asp84Asn	66	0	0		83	4	0.0481928	NM_006528	Q66ME8|Q8NAK6|Q9UC86	Missense_Mutation	SNP	ENST00000222543.5	37	CCDS5632.1	.	.	.	.	.	.	.	.	.	.	C	12.03	1.815932	0.32145	.	.	ENSG00000105825	ENST00000222543;ENST00000545378;ENST00000451238	T;T;T	0.56275	0.47;0.47;0.55	5.09	-1.78	0.07957	Proteinase inhibitor I2, Kunitz metazoa (5);	0.446267	0.26542	N	0.023783	T	0.18087	0.0434	N	0.02539	-0.55	0.09310	N	1	B;B;B;B	0.23540	0.087;0.0;0.011;0.0	B;B;B;B	0.11329	0.006;0.0;0.005;0.0	T	0.26224	-1.0109	10	0.13853	T	0.58	.	6.3313	0.21272	0.0:0.2858:0.2387:0.4755	.	55;73;84;84	A4ZVU7;Q8NAK6;F5H3J8;P48307	.;.;.;TFPI2_HUMAN	N	84;84;5	ENSP00000222543:D84N;ENSP00000438861:D84N;ENSP00000416370:D5N	ENSP00000222543:D84N	D	-	1	0	TFPI2	93357406	0.018000	0.18449	0.000000	0.03702	0.014000	0.08584	0.525000	0.22956	-0.223000	0.09943	-0.657000	0.03884	GAT	.	.	none		0.617	TFPI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254720.2	NM_006528		T	93519470	C	T	93519470	3	4	11	1	0	0	0	0	1	0	0	0	15824	884	31	1	473	1	TFPI2	7	93519470	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	10522141	93519470	65619193	128	1419											
DLX6	1750	hgsc.bcm.edu	37	chr7	96639340	96639340	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccacaccaggacacgatgcAgagaccacagatgatgtgag	14	5	11	11	1	0	4	0	2	0	2	1	7	1	5	3	1	1	1	3	1	0	0			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr7:96639340A>C	ENST00000518156.2	+	3	1293	c.863A>C	c.(862-864)cAg>cCg	p.Q288P	DLX6_ENST00000007660.5_Missense_Mutation_p.Q260P|DLX6-AS1_ENST00000437541.1_RNA|DLX6-AS1_ENST00000430027.3_RNA|DLX6_ENST00000493273.2_3'UTR|DLX6-AS1_ENST00000430404.2_RNA|DLX6-AS1_ENST00000458352.2_RNA|DLX6-AS1_ENST00000452769.2_RNA|DLX6-AS2_ENST00000606174.1_RNA|DLX6-AS1_ENST00000437331.2_RNA|DLX6-AS1_ENST00000605417.1_RNA|DLX6_ENST00000555308.1_Missense_Mutation_p.Q160P			P56179	DLX6_HUMAN	distal-less homeobox 6	170					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)					GACACGATGCAGAGACCACAG	0.547																																					p.Q288P		Atlas-SNP	.											.	DLX6	37	.	0			c.A863C						PASS	.						23	24	23					7																	96639340		2121	4253	6374	SO:0001583	missense	1750	exon3			CGATGCAGAGACC		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.863A>C	7.37:g.96639340A>C	ENSP00000428480:p.Gln288Pro	123	0	0		190	39	0.205263	NM_005222	A4D1I2|B3KSQ0|J3KR92|Q3ZAR6|Q9UPL2	Missense_Mutation	SNP	ENST00000518156.2	37	CCDS47647.2	.	.	.	.	.	.	.	.	.	.	A	19.33	3.807640	0.70797	.	.	ENSG00000006377	ENST00000518156;ENST00000007660;ENST00000555308	D;D;D	0.91686	-2.89;-2.83;-2.89	5.76	5.76	0.90799	.	1.660890	0.02777	N	0.120406	D	0.91061	0.7187	L	0.42245	1.32	0.80722	D	1	B	0.17852	0.024	B	0.20577	0.03	T	0.60999	-0.7151	10	0.20519	T	0.43	-15.5545	16.0796	0.80995	1.0:0.0:0.0:0.0	.	260	P56179-2	.	P	288;260;160	ENSP00000428480:Q288P;ENSP00000007660:Q260P;ENSP00000451635:Q160P	ENSP00000007660:Q260P	Q	+	2	0	DLX6	96477276	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.085000	0.76875	2.206000	0.71126	0.533000	0.62120	CAG	.	.	none		0.547	DLX6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334373.4	NM_005222		C	96639340	A	C	96639340	3	2	11	1	0	0	0	0	1	0	0	0	4577	188	7	5	873	5	DLX6	7	96639340	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	3119870	96639340	62499323	129	1420											
RNF133	168433	hgsc.bcm.edu	37	chr7	122338257	122338257	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccccctcttttactactcgaAgttggagttgtccaaatgtg	8	14	8	11	1	1	0	0	0	1	0	3	2	2	1	3	1	2	2	3	1	4	5			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr7:122338257A>C	ENST00000340112.2	-	1	953	c.716T>G	c.(715-717)cTt>cGt	p.L239R	CADPS2_ENST00000412584.2_Intron|CADPS2_ENST00000334010.7_Intron|CADPS2_ENST00000449022.2_Intron|CADPS2_ENST00000313070.7_Intron	NM_139175.1	NP_631914.1	Q8WVZ7	RN133_HUMAN	ring finger protein 133	239					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						TACTACTCGAAGTTGGAGTTG	0.388																																					p.L239R	Colon(198;1778 2057 7449 19869 45985)	Atlas-SNP	.											.	RNF133	41	.	0			c.T716G						PASS	.						157	151	153					7																	122338257		2203	4300	6503	SO:0001583	missense	168433	exon1			ACTCGAAGTTGGA	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.716T>G	7.37:g.122338257A>C	ENSP00000344489:p.Leu239Arg	326	0	0		455	87	0.191209	NM_139175	A4D0W2|Q8N7G7	Missense_Mutation	SNP	ENST00000340112.2	37	CCDS5784.1	.	.	.	.	.	.	.	.	.	.	A	12.76	2.035419	0.35893	.	.	ENSG00000188050	ENST00000340112	T	0.16597	2.33	5.53	5.53	0.82687	.	0.435749	0.19868	U	0.104271	T	0.38348	0.1037	M	0.62723	1.935	0.80722	D	1	D	0.71674	0.998	D	0.69824	0.966	T	0.06516	-1.0822	10	0.49607	T	0.09	.	13.8971	0.63778	1.0:0.0:0.0:0.0	.	239	Q8WVZ7	RN133_HUMAN	R	239	ENSP00000344489:L239R	ENSP00000344489:L239R	L	-	2	0	RNF133	122125493	0.933000	0.31639	0.140000	0.22221	0.021000	0.10359	5.341000	0.65964	2.099000	0.63709	0.402000	0.26972	CTT	.	.	none		0.388	RNF133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347413.1	NM_139175		C	122338257	A	C	122338257	3	2	11	1	0	0	0	0	1	0	0	0	13454	72	3	5	418	5	RNF133	7	122338257	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	25698917	122338257	36800406	130	1421											
PAX4	5078	hgsc.bcm.edu	37	chr7	127253851	127253851	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcttggggagaagatagtcCgattccggtggccggtccct	6	9	16	10	3	0	2	0	0	0	2	3	4	3	2	4	6	0	1	4	6	2	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr7:127253851C>T	ENST00000341640.2	-	4	702	c.497G>A	c.(496-498)cGg>cAg	p.R166Q	PAX4_ENST00000378740.2_Missense_Mutation_p.R166Q|PAX4_ENST00000463946.1_Missense_Mutation_p.R164Q|PAX4_ENST00000338516.3_Missense_Mutation_p.R174Q	NM_006193.2	NP_006184.2	O43316	PAX4_HUMAN	paired box 4	174					cell differentiation (GO:0030154)|circadian rhythm (GO:0007623)|endocrine pancreas development (GO:0031018)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|positive regulation of cell differentiation (GO:0045597)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|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)			cervix(1)|kidney(2)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35						GAAGATAGTCCGATTCCGGTG	0.587																																					p.R166Q	Ovarian(113;737 1605 7858 27720 34092)	Atlas-SNP	.											PAX4,NS,carcinoma,0,1	PAX4	66	1	0			c.G497A						scavenged	.						85	83	84					7																	127253851		2203	4300	6503	SO:0001583	missense	5078	exon4			ATAGTCCGATTCC		CCDS5797.1	7q32.1	2011-06-20	2007-07-12		ENSG00000106331	ENSG00000106331		"Paired boxes", "Homeoboxes / PRD class"	8618	protein-coding gene	gene with protein product		167413	"paired box gene 4"				Standard	NM_006193		Approved	MODY9	uc010lld.1	O43316	OTTHUMG00000157562	ENST00000341640.2:c.497G>A	7.37:g.127253851C>T	ENSP00000339906:p.Arg166Gln	133	1	0.0075188		147	36	0.244898	NM_006193	O95161|Q6B0H0	Missense_Mutation	SNP	ENST00000341640.2	37	CCDS5797.1	.	.	.	.	.	.	.	.	.	.	C	36	5.598306	0.96614	.	.	ENSG00000106331	ENST00000341640;ENST00000338516;ENST00000378740;ENST00000463946	D;D;D	0.99150	-5.49;-5.49;-5.49	5.32	5.32	0.75619	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.070525	0.64402	D	0.000019	D	0.99423	0.9796	M	0.91249	3.19	0.53688	D	0.999971	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;0.994	D	0.98683	1.0693	10	0.87932	D	0	.	16.8665	0.86030	0.0:1.0:0.0:0.0	.	166;164;174;164	O43316-4;Q1W386;O43316;G3V4Q1	.;.;PAX4_HUMAN;.	Q	166;174;174;164	ENSP00000339906:R166Q;ENSP00000344297:R174Q;ENSP00000451923:R164Q	ENSP00000344297:R174Q	R	-	2	0	PAX4	127041087	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.543000	0.73874	2.661000	0.90470	0.650000	0.86243	CGG	.	.	none		0.587	PAX4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349165.1			T	127253851	C	T	127253851	3	4	11	1	0	0	0	0	1	0	0	0	11490	652	23	1	558	1	PAX4	7	127253851	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	4915594	127253851	31884812	131	1422											
FLNC	2318	hgsc.bcm.edu	37	chr7	128489252	128489252	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagtgtccattggaggccatGgcctgggtgagtgccctttc	5	11	14	11	0	0	1	0	1	0	0	2	2	1	2	4	4	1	0	4	4	0	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr7:128489252G>A	ENST00000325888.8	+	29	5206	c.4945G>A	c.(4945-4947)Ggc>Agc	p.G1649S	FLNC_ENST00000346177.6_Missense_Mutation_p.G1649S|RP11-309L24.2_ENST00000469965.1_RNA	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	1649					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						TGGAGGCCATGGCCTGGGTGA	0.667																																					p.G1649S		Atlas-SNP	.											FLNC,NS,carcinoma,0,1	FLNC	339	1	0			c.G4945A						scavenged	.						64	65	65					7																	128489252		1930	4115	6045	SO:0001583	missense	2318	exon29			GGCCATGGCCTGG	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.4945G>A	7.37:g.128489252G>A	ENSP00000327145:p.Gly1649Ser	181	1	0.00552486		254	70	0.275591	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Missense_Mutation	SNP	ENST00000325888.8	37	CCDS43644.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.991672	0.93106	.	.	ENSG00000128591	ENST00000325888;ENST00000346177	D;D	0.92048	-2.96;-2.96	5.76	5.76	0.90799	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.94981	0.8376	M	0.61703	1.905	0.58432	D	0.99999	P;D	0.56035	0.465;0.974	B;D	0.63381	0.411;0.914	D	0.95051	0.8187	10	0.72032	D	0.01	.	17.4698	0.87642	0.0:0.0:1.0:0.0	.	1649;1649	Q14315-2;Q14315	.;FLNC_HUMAN	S	1649	ENSP00000327145:G1649S;ENSP00000344002:G1649S	ENSP00000327145:G1649S	G	+	1	0	FLNC	128276488	1.000000	0.71417	0.978000	0.43139	0.951000	0.60555	5.950000	0.70265	2.713000	0.92767	0.655000	0.94253	GGC	.	.	none		0.667	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			A	128489252	G	A	128489252	3	1	11	1	0	0	0	0	1	0	0	0	5943	1348	47	2	5059	2	FLNC	7	128489252	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	1235401	128489252	30649411	132	1423											
NEFL	4747	hgsc.bcm.edu	37	chr8	24813297	24813297	+	RNA	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttggtcacgtccatctccaCggagatctgcgcgtactgga	7	10	11	13	4	3	1	1	0	2	1	5	3	4	2	2	3	2	1	2	3	1	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr8:24813297C>T	ENST00000221169.5	-	0	1327				CTD-2168K21.2_ENST00000607735.1_RNA			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)		TCCATCTCCACGGAGATCTGC	0.582																																					p.V245M		Atlas-SNP	.											.	NEFL	47	.	0			c.G733A						PASS	.						47	52	50					8																	24813297		2139	4250	6389			4747	exon1			TCTCCACGGAGAT		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		8.37:g.24813297C>T		94	0	0		80	30	0.375	NM_006158	B9ZVN2|Q16154|Q8IU72	Missense_Mutation	SNP	ENST00000221169.5	37																																																																																				.	.	none		0.582	NEFL-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000258943.4	NM_006158		T	24813297	C	T	24813297	1	4	11	0	1	0	0	0	0	0	0	0	10324	536	19	1		1	NEFL	8	24813297	RNA	SNP	C	TCGA-FF-8042-01A-11D-2210-10		24813297	121550725	133	1424											
DPYS	1807	hgsc.bcm.edu	37	chr8	105405212	105405212	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgatgatgagtttttgctgAgatagtcctatatttgtgaa	10	17	10	4	0	0	5	0	5	0	1	1	6	1	5	1	0	1	2	1	0	4	6			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr8:105405212A>C	ENST00000351513.2	-	8	1375	c.1243T>G	c.(1243-1245)Tca>Gca	p.S415A	DPYS_ENST00000521601.1_Intron	NM_001385.2	NP_001376.1	Q14117	DPYS_HUMAN	dihydropyrimidinase	415					beta-alanine metabolic process (GO:0019482)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein homotetramerization (GO:0051289)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymine catabolic process (GO:0006210)|uracil catabolic process (GO:0006212)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|dihydropyrimidinase activity (GO:0004157)|thymine binding (GO:0002059)|uracil binding (GO:0002058)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(57;1.61e-06)|STAD - Stomach adenocarcinoma(118;0.229)			GTTTTTGCTGAGATAGTCCTA	0.368																																					p.S415A		Atlas-SNP	.											.	DPYS	107	.	0			c.T1243G						PASS	.						67	71	70					8																	105405212		2203	4300	6503	SO:0001583	missense	1807	exon8			TTGCTGAGATAGT	D78011	CCDS6302.1	8q22	2004-01-22			ENSG00000147647	ENSG00000147647			3013	protein-coding gene	gene with protein product		613326				8973361	Standard	NM_001385		Approved	DHPase	uc003yly.4	Q14117	OTTHUMG00000164891	ENST00000351513.2:c.1243T>G	8.37:g.105405212A>C	ENSP00000276651:p.Ser415Ala	36	0	0		42	20	0.47619	NM_001385		Missense_Mutation	SNP	ENST00000351513.2	37	CCDS6302.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.670756	0.88348	.	.	ENSG00000147647	ENST00000351513	T	0.76578	-1.03	6.02	6.02	0.97574	Metal-dependent hydrolase, composite domain (1);	0.000000	0.85682	D	0.000000	D	0.88005	0.6321	M	0.75884	2.315	0.80722	D	1	D	0.69078	0.997	D	0.85130	0.997	D	0.89012	0.3429	10	0.72032	D	0.01	-14.0938	16.5494	0.84464	1.0:0.0:0.0:0.0	.	415	Q14117	DPYS_HUMAN	A	415	ENSP00000276651:S415A	ENSP00000276651:S415A	S	-	1	0	DPYS	105474388	1.000000	0.71417	0.996000	0.52242	0.936000	0.57629	8.962000	0.93254	2.299000	0.77371	0.528000	0.53228	TCA	.	.	none		0.368	DPYS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380814.1	NM_001385		C	105405212	A	C	105405212	3	2	11	1	0	0	0	0	1	0	0	0	4748	304	11	5	324	5	DPYS	8	105405212	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	80591915	105405212	40958810	134	1425											
EXT1	2131	hgsc.bcm.edu	37	chr8	118812014	118812014	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acctggtctttaaagaggacGgggtcgagcctcatctgaga	10	9	13	9	2	3	2	1	1	2	2	4	5	3	3	2	4	1	0	2	4	2	2	rs557560039	byFrequency	TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr8:118812014G>A	ENST00000378204.2	-	11	2984	c.2178C>T	c.(2176-2178)ccC>ccT	p.P726P		NM_000127.2	NP_000118.2	Q16394	EXT1_HUMAN	exostosin glycosyltransferase 1	726					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)			TAAAGAGGACGGGGTCGAGCC	0.537			"Mis, N, F, S"			"exostoses, osteosarcoma"			Langer-Giedion syndrome;Hereditary Multiple Exostoses				G|||	2	0.000399361	0.0	0.0	5008	,	,		17425	0.0		0.0	False		,,,				2504	0.002				p.P726P		Atlas-SNP	.	yes	Rec		Multiple Exostoses Type 1	8	8q24.11-q24.13	2131	multiple exostoses type 1 gene		M	.	EXT1	98	.	0			c.C2178T						PASS	.						88	84	85					8																	118812014		2203	4300	6503	SO:0001819	synonymous_variant	2131	exon11	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II;HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	GAGGACGGGGTCG	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.2178C>T	8.37:g.118812014G>A		102	0	0		188	26	0.138298	NM_000127	B2R7V2|Q9BVI9	Silent	SNP	ENST00000378204.2	37	CCDS6324.1																																																																																			.	.	none		0.537	EXT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132768.3	NM_000127		A	118812014	G	A	118812014	2	1	11	1	0	0	0	0	0	0	0	1	5325	1103	39	1		1	EXT1	8	118812014	Silent	SNP	G	TCGA-FF-8042-01A-11D-2210-10	13406802	118812014	27552008	135	1426											
SCRIB	23513	hgsc.bcm.edu	37	chr8	144887138	144887138	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccaacctgcagtgtgcccGcgcggtgagcagcaccgccc	6	4	13	18	5	0	1	0	1	0	0	0	1	0	1	5	1	5	3	5	1	1	0			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr8:144887138G>A	ENST00000320476.3	-	20	2723	c.2717C>T	c.(2716-2718)gCg>gTg	p.A906V	SCRIB_ENST00000356994.2_Missense_Mutation_p.A906V|SCRIB_ENST00000377533.3_Missense_Mutation_p.A825V	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	906	Interaction with ARHGEF7.|PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)			CAGTGTGCCCGCGCGGTGAGC	0.736																																					p.A906V	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											SCRIB_ENST00000356994,lower_third,carcinoma,+1,2	SCRIB	192	2	0			c.C2717T						PASS	.						8	9	9					8																	144887138		2159	4250	6409	SO:0001583	missense	23513	exon20			GTGCCCGCGCGGT	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.2717C>T	8.37:g.144887138G>A	ENSP00000322938:p.Ala906Val	14	0	0		32	6	0.1875	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Missense_Mutation	SNP	ENST00000320476.3	37	CCDS6411.1	.	.	.	.	.	.	.	.	.	.	G	15.35	2.806868	0.50421	.	.	ENSG00000180900	ENST00000356994;ENST00000320476;ENST00000377533;ENST00000377539	T;T;T	0.29655	1.56;1.56;1.56	4.58	4.58	0.56647	PDZ/DHR/GLGF (4);	.	.	.	.	T	0.43964	0.1271	L	0.46670	1.46	0.29848	N	0.828673	D;D	0.89917	1.0;1.0	P;D	0.64506	0.891;0.926	T	0.36163	-0.9759	9	0.59425	D	0.04	.	9.2305	0.37434	0.0:0.1566:0.6819:0.1615	.	906;906	Q14160;Q14160-3	SCRIB_HUMAN;.	V	906;906;825;275	ENSP00000349486:A906V;ENSP00000322938:A906V;ENSP00000366756:A825V	ENSP00000322938:A906V	A	-	2	0	SCRIB	144959126	0.111000	0.22076	0.841000	0.33234	0.040000	0.13550	0.937000	0.28951	2.090000	0.63153	0.442000	0.29010	GCG	.	.	none		0.736	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356		A	144887138	G	A	144887138	3	1	11	1	0	0	0	0	1	0	0	0	13952	1087	38	1	2322	1	SCRIB	8	144887138	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	26075124	144887138	1476884	136	1427											
NFIB	4781	hgsc.bcm.edu	37	chr9	14307015	14307015	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgcacgtagtatgccaaaaAcaaatcaagctccttaactg	15	9	6	11	1	1	0	1	0	0	0	2	0	2	0	2	0	5	4	2	0	7	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr9:14307015A>C	ENST00000380959.3	-	2	1008	c.535T>G	c.(535-537)Ttt>Gtt	p.F179V	NFIB_ENST00000397575.3_Missense_Mutation_p.F179V|NFIB_ENST00000380934.4_Missense_Mutation_p.F205V|NFIB_ENST00000380921.3_Missense_Mutation_p.F179V|NFIB_ENST00000397579.2_Missense_Mutation_p.F179V|NFIB_ENST00000397581.2_Missense_Mutation_p.F179V|NFIB_ENST00000380953.1_Missense_Mutation_p.F179V	NM_005596.3	NP_005587.2	O00712	NFIB_HUMAN	nuclear factor I/B	179					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)		TATGCCAAAAACAAATCAAGC	0.468			T	"MYB, HGMA2"	"adenoid cystic carcinoma, lipoma"																																p.F205V	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.T613G						PASS	.						144	131	135					9																	14307015		2203	4300	6503	SO:0001583	missense	4781	exon2			CCAAAAACAAATC	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.535T>G	9.37:g.14307015A>C	ENSP00000370346:p.Phe179Val	172	0	0		140	44	0.314286	NM_001190738	G3V1P1|H7BYE8|O00166|Q12858|Q5VW29|Q63HM5|Q6ZNF9|Q96J45	Missense_Mutation	SNP	ENST00000380959.3	37	CCDS6474.1	.	.	.	.	.	.	.	.	.	.	A	16.39	3.108877	0.56398	.	.	ENSG00000147862	ENST00000380934;ENST00000380959;ENST00000380953;ENST00000397575;ENST00000397581;ENST00000397579;ENST00000380921	T;T;T;T;T;T	0.51325	0.71;0.74;0.76;0.72;0.71;0.74	5.53	5.53	0.82687	CTF transcription factor/nuclear factor 1, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.34454	0.0898	N	0.22421	0.69	0.80722	D	1	P;P;P	0.42409	0.779;0.779;0.779	B;B;B	0.35510	0.191;0.204;0.191	T	0.35475	-0.9787	10	0.87932	D	0	.	15.6677	0.77242	1.0:0.0:0.0:0.0	.	179;179;179	Q5VW27;Q5VW29;O00712	.;.;NFIB_HUMAN	V	205;179;179;179;179;179;179	ENSP00000370321:F205V;ENSP00000370346:F179V;ENSP00000370340:F179V;ENSP00000380705:F179V;ENSP00000380711:F179V;ENSP00000380709:F179V	ENSP00000370308:F179V	F	-	1	0	NFIB	14297015	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.092000	0.63282	0.482000	0.46254	TTT	.	.	none		0.468	NFIB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055468.1	NM_005596		C	14307015	A	C	14307015	3	2	11	1	0	0	0	0	1	0	0	0	10380	43	2	5	759	5	NFIB	9	14307015	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10		14307015	126906416	137	1428											
OR2S2	56656	hgsc.bcm.edu	37	chr9	35957229	35957229	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atgatggggttgagcatcggGgtcaccaccccatagaaaag	12	7	13	9	1	1	3	1	2	0	1	2	3	1	3	3	4	1	2	3	4	3	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr9:35957229G>T	ENST00000341959.2	-	1	922	c.867C>A	c.(865-867)acC>acA	p.T289T		NM_019897.2	NP_063950.2	Q9NQN1	OR2S1_HUMAN	olfactory receptor, family 2, subfamily S, member 2	289					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(2)|large_intestine(2)|lung(8)|ovary(1)|skin(1)|stomach(1)	17			LUSC - Lung squamous cell carcinoma(32;0.00613)|STAD - Stomach adenocarcinoma(86;0.194)			TGAGCATCGGGGTCACCACCC	0.493																																					p.T289T	Pancreas(172;293 2036 17878 24427 30946)	Atlas-SNP	.											.	OR2S2	46	.	0			c.C867A						PASS	.						98	95	96					9																	35957229		2203	4300	6503	SO:0001819	synonymous_variant	56656	exon1			CATCGGGGTCACC	AL135841	CCDS6596.2	9p13.3	2012-08-09			ENSG00000122718	ENSG00000122718		"GPCR / Class A : Olfactory receptors"	8276	protein-coding gene	gene with protein product							Standard	NM_019897		Approved		uc011lpi.2	Q9NQN1	OTTHUMG00000019891	ENST00000341959.2:c.867C>A	9.37:g.35957229G>T		88	0	0		87	37	0.425287	NM_019897	Q2M3L0|Q6IF19|Q96R42	Silent	SNP	ENST00000341959.2	37	CCDS6596.2																																																																																			.	.	none		0.493	OR2S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052400.2	NM_019897		T	35957229	G	T	35957229	2	4	11	1	0	0	0	0	0	0	0	1	11024	1219	43	4		4	OR2S2	9	35957229	Silent	SNP	G	TCGA-FF-8042-01A-11D-2210-10	21650214	35957229	105256202	138	1429											
PAX5	5079	hgsc.bcm.edu	37	chr9	36923482	36923482	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atggctgaatactctgtggtCtgaaagaagaaacagagacg	15	8	12	6	1	2	5	0	2	2	3	2	6	2	5	0	2	2	1	0	2	5	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr9:36923482C>T	ENST00000358127.4	-	7	855		c.e7-1		PAX5_ENST00000377852.2_Splice_Site|PAX5_ENST00000523241.1_Intron|PAX5_ENST00000414447.1_Splice_Site|PAX5_ENST00000446742.1_Splice_Site|PAX5_ENST00000523145.1_Splice_Site|PAX5_ENST00000377853.2_Splice_Site|PAX5_ENST00000520281.1_Splice_Site|PAX5_ENST00000522003.1_Splice_Site|PAX5_ENST00000377847.2_Splice_Site|PAX5_ENST00000520154.1_Intron	NM_001280554.1|NM_001280556.1|NM_016734.1	NP_001267483.1|NP_001267485.1|NP_057953.1	Q02548	PAX5_HUMAN	paired box 5						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.?(19)	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)		ACTCTGTGGTCTGAAAGAAGA	0.562			"T, Mis, D, F, S"	"IGH@, ETV6, PML, FOXP1, ZNF521, ELN"	"NHL, ALL, B-ALL"																																.		Atlas-SNP	.		Dom	yes		9	9p13	5079	paired box gene 5 (B-cell lineage specific activator protein)		L	.	PAX5	250	.	19	Unknown(19)	haematopoietic_and_lymphoid_tissue(19)	c.781-1G>A						PASS	.						51	55	53					9																	36923482		2203	4300	6503	SO:0001630	splice_region_variant	5079	exon8			TGTGGTCTGAAAG		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.781-1G>A	9.37:g.36923482C>T		27	0	0		29	15	0.517241	NM_016734	A3QVP6|A3QVP7|A3QVP8|C0KTF6|C0KTF7|C0KTF8|C0KTF9|C0KTG0|O75933|Q5SFM2|Q6S728|Q6S729|Q6S730|Q6S731|Q6S732	Splice_Site	SNP	ENST00000358127.4	37	CCDS6607.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.003406	0.74932	.	.	ENSG00000196092	ENST00000358127;ENST00000377849;ENST00000377853;ENST00000377852;ENST00000520281;ENST00000446742;ENST00000522003;ENST00000523145;ENST00000414447;ENST00000377847;ENST00000524340	.	.	.	6.03	5.12	0.69794	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.1148	0.36750	0.1484:0.7782:0.0:0.0734	.	.	.	.	.	-1	.	.	.	-	.	.	PAX5	36913482	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	6.657000	0.74402	1.544000	0.49359	0.655000	0.94253	.	.	.	none		0.562	PAX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052433.1		Intron	T	36923482	C	T	36923482	5	4	11	1	0	0	0	0	0	0	1	0	11491	927	32	2	411	2	PAX5	9	36923482	Splice_Site	SNP	C	TCGA-FF-8042-01A-11D-2210-10	966253	36923482	104289949	139	1430											
TRPM3	80036	hgsc.bcm.edu	37	chr9	73477843	73477843	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccatggctttgttggaatggCcacctccttggaactcaatg	8	12	10	11	0	1	0	1	0	0	0	2	2	2	2	4	4	1	2	4	4	3	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr9:73477843C>T	ENST00000377111.2	-	3	686	c.443G>A	c.(442-444)gGc>gAc	p.G148D	TRPM3_ENST00000377110.3_Missense_Mutation_p.G148D|TRPM3_ENST00000396283.1_5'UTR|TRPM3_ENST00000357533.2_Missense_Mutation_p.G150D|TRPM3_ENST00000437699.3_5'UTR|TRPM3_ENST00000396285.1_5'Flank|TRPM3_ENST00000360823.2_5'UTR|TRPM3_ENST00000423814.3_Missense_Mutation_p.G150D|TRPM3_ENST00000377097.3_5'UTR|TRPM3_ENST00000396292.4_5'Flank|TRPM3_ENST00000377105.1_5'UTR|TRPM3_ENST00000396280.5_5'Flank|TRPM3_ENST00000377101.1_5'UTR|TRPM3_ENST00000358082.3_5'Flank|TRPM3_ENST00000408909.2_5'Flank|TRPM3_ENST00000377106.1_5'UTR|TRPM3_ENST00000361823.5_5'UTR	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	148					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						GTTGGAATGGCCACCTCCTTG	0.473																																					p.G148D		Atlas-SNP	.											.	TRPM3	700	.	0			c.G443A						PASS	.						217	202	207					9																	73477843		2203	4300	6503	SO:0001583	missense	80036	exon3			GAATGGCCACCTC	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.443G>A	9.37:g.73477843C>T	ENSP00000366315:p.Gly148Asp	299	0	0		212	82	0.386792	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	ENST00000377111.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.82|14.82	2.649070|2.649070	0.47362|0.47362	.|.	.|.	ENSG00000083067|ENSG00000083067	ENST00000377097|ENST00000377111;ENST00000377110;ENST00000357533;ENST00000423814	.|T;T;T;T	.|0.04360	.|3.64;3.64;3.64;3.64	5.95|5.95	5.95|5.95	0.96441|0.96441	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.24470|0.24470	0.0593|0.0593	M|M	0.75615|0.75615	2.305|2.305	0.80722|0.80722	D|D	1|1	.|D;D;B;B	.|0.89917	.|0.991;1.0;0.078;0.065	.|P;D;B;B	.|0.97110	.|0.874;1.0;0.108;0.071	T|T	0.00025|0.00025	-1.2321|-1.2321	5|10	.|0.59425	.|D	.|0.04	-15.6026|-15.6026	20.3854|20.3854	0.98941|0.98941	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|148;150;148;148	.|Q9HCF6;Q4VXD2;Q9HCF6-2;Q9HCF6-10	.|TRPM3_HUMAN;.;.;.	T|D	38|148;148;150;150	.|ENSP00000366315:G148D;ENSP00000366314:G148D;ENSP00000350140:G150D;ENSP00000389542:G150D	.|ENSP00000350140:G150D	A|G	-|-	1|2	0|0	TRPM3|TRPM3	72667663|72667663	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.986000|0.986000	0.74619|0.74619	4.564000|4.564000	0.60830|0.60830	2.825000|2.825000	0.97269|0.97269	0.655000|0.655000	0.94253|0.94253	GCC|GGC	.	.	none		0.473	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945		T	73477843	C	T	73477843	3	4	11	1	0	0	0	0	1	0	0	0	16602	739	26	2	4895	2	TRPM3	9	73477843	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	36554361	73477843	67735588	140	1431											
TMC1	117531	hgsc.bcm.edu	37	chr9	75355045	75355045	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attttctcagggaggcaaaaAaatttgtgagtgaaaatgaa	17	11	10	3	0	1	3	1	3	1	0	2	4	1	4	0	2	0	1	0	2	6	3	rs377607548		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr9:75355045A>C	ENST00000297784.5	+	9	913	c.373A>C	c.(373-375)Aaa>Caa	p.K125Q	TMC1_ENST00000340019.3_Missense_Mutation_p.K125Q|TMC1_ENST00000396237.3_Missense_Mutation_p.K125Q	NM_138691.2	NP_619636.2	Q8TDI8	TMC1_HUMAN	transmembrane channel-like 1	125	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						GGAGGCAAAAAAATTTGTGAG	0.368																																					p.K125Q	Pancreas(75;173 1345 14232 34245 43413)	Atlas-SNP	.											.	TMC1	87	.	0			c.A373C						PASS	.						72	74	73					9																	75355045		2203	4300	6503	SO:0001583	missense	117531	exon9			GCAAAAAAATTTG	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.373A>C	9.37:g.75355045A>C	ENSP00000297784:p.Lys125Gln	80	0	0		60	20	0.333333	NM_138691	A8MVZ2|B1AM91	Missense_Mutation	SNP	ENST00000297784.5	37	CCDS6643.1	.	.	.	.	.	.	.	.	.	.	A	13.37	2.218045	0.39201	.	.	ENSG00000165091	ENST00000297784;ENST00000340019;ENST00000396235;ENST00000537917;ENST00000538054;ENST00000542143;ENST00000396237	T;T;T	0.17528	2.27;2.27;2.27	5.62	4.5	0.54988	.	0.378995	0.26079	N	0.026471	T	0.07908	0.0198	N	0.11560	0.145	0.28108	N	0.931139	B;B	0.15930	0.001;0.015	B;B	0.12156	0.001;0.007	T	0.13335	-1.0513	10	0.31617	T	0.26	-29.0715	5.1393	0.14950	0.8494:0.0:0.1506:0.0	.	92;125	A4FUA6;Q8TDI8	.;TMC1_HUMAN	Q	125;125;92;92;92;119;125	ENSP00000297784:K125Q;ENSP00000341433:K125Q;ENSP00000379538:K125Q	ENSP00000297784:K125Q	K	+	1	0	TMC1	74544865	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.709000	0.25734	2.133000	0.65898	0.533000	0.62120	AAA	.	.	weak		0.368	TMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052655.1			C	75355045	A	C	75355045	3	2	11	1	0	0	0	0	1	0	0	0	15999	15	1	5	391	5	TMC1	9	75355045	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	1877202	75355045	65858386	141	1432											
TRPM6	140803	hgsc.bcm.edu	37	chr9	77473596	77473596	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaattttacctgtgaggattTtttgagctgggtatgattgt	9	18	11	3	0	0	3	0	3	0	0	0	4	0	4	1	2	2	2	1	2	3	7			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr9:77473596T>G	ENST00000360774.1	-	2	339	c.102A>C	c.(100-102)aaA>aaC	p.K34N	TRPM6_ENST00000449912.2_Missense_Mutation_p.K29N|RNU6-445P_ENST00000516949.1_RNA|TRPM6_ENST00000376872.3_Missense_Mutation_p.K34N|TRPM6_ENST00000361255.3_Missense_Mutation_p.K29N|TRPM6_ENST00000376864.4_Missense_Mutation_p.K34N|TRPM6_ENST00000451710.3_Missense_Mutation_p.K34N|TRPM6_ENST00000359047.2_Missense_Mutation_p.K34N|TRPM6_ENST00000376871.3_Missense_Mutation_p.K34N	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	34					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						TGTGAGGATTTTTTGAGCTGG	0.313																																					p.K34N		Atlas-SNP	.											.	TRPM6	377	.	0			c.A102C						PASS	.						96	95	95					9																	77473596		2201	4299	6500	SO:0001583	missense	140803	exon2			AGGATTTTTTGAG	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.102A>C	9.37:g.77473596T>G	ENSP00000354006:p.Lys34Asn	199	0	0		73	46	0.630137	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	37	CCDS6647.1	.	.	.	.	.	.	.	.	.	.	T	18.87	3.714639	0.68730	.	.	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000376872;ENST00000376871;ENST00000449912;ENST00000361255;ENST00000376870;ENST00000376864;ENST00000359047	T;T;T;T;T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02;-0.02	5.29	-0.0403	0.13872	.	0.107996	0.64402	D	0.000007	T	0.73442	0.3587	M	0.74546	2.27	0.40657	D	0.982093	D;D;D;P;D;P	0.76494	0.999;0.999;0.999;0.599;0.978;0.809	D;D;D;P;P;P	0.83275	0.994;0.994;0.996;0.802;0.71;0.535	T	0.71919	-0.4447	10	0.87932	D	0	.	8.3884	0.32514	0.0:0.3417:0.0:0.6583	.	34;34;34;34;34;29	Q9BX84-7;Q9BX84-6;Q9BX84-5;Q96LV9;Q9BX84;Q9BX84-3	.;.;.;.;TRPM6_HUMAN;.	N	34;34;34;34;29;29;33;34;34	ENSP00000354006:K34N;ENSP00000407341:K34N;ENSP00000366068:K34N;ENSP00000366067:K34N;ENSP00000396672:K29N;ENSP00000354962:K29N;ENSP00000366060:K34N;ENSP00000351942:K34N	ENSP00000351942:K34N	K	-	3	2	TRPM6	76663416	1.000000	0.71417	0.992000	0.48379	0.853000	0.48598	1.298000	0.33412	-0.168000	0.10853	0.454000	0.30748	AAA	.	.	none		0.313	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662		G	77473596	T	G	77473596	3	3	11	1	0	0	0	0	1	0	0	0	16605	1838	64	5	6118	5	TRPM6	9	77473596	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	2118551	77473596	63739835	142	1433											
TEX10	54881	hgsc.bcm.edu	37	chr9	103090132	103090132	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttatttgctcgtgctgcagCggtatgaatgatatcgataa	10	15	10	6	3	0	2	0	2	0	0	2	3	0	2	0	1	4	4	0	1	5	6			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr9:103090132C>T	ENST00000374902.4	-	8	1914	c.1738G>A	c.(1738-1740)Gct>Act	p.A580T	TEX10_ENST00000535814.1_Missense_Mutation_p.A583T	NM_017746.3	NP_060216.2	Q9NXF1	TEX10_HUMAN	testis expressed 10	580						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)		CGTGCTGCAGCGGTATGAATG	0.423																																					p.A583T		Atlas-SNP	.											.	TEX10	99	.	0			c.G1747A						PASS	.						113	102	106					9																	103090132		2203	4300	6503	SO:0001583	missense	54881	exon8			CTGCAGCGGTATG	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.1738G>A	9.37:g.103090132C>T	ENSP00000364037:p.Ala580Thr	162	0	0		125	51	0.408	NM_001161584	B4DYV2|Q5T722|Q5T723|Q8NCN8|Q8TDY0	Missense_Mutation	SNP	ENST00000374902.4	37	CCDS6748.1	.	.	.	.	.	.	.	.	.	.	C	35	5.531474	0.96446	.	.	ENSG00000136891	ENST00000535814;ENST00000374902;ENST00000444730	.	.	.	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.72391	0.3454	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	0.996;0.998;0.985	T	0.71922	-0.4446	9	0.46703	T	0.11	-10.4144	19.6241	0.95671	0.0:1.0:0.0:0.0	.	583;448;580	B4DYV2;E7ERG2;Q9NXF1	.;.;TEX10_HUMAN	T	583;580;448	.	ENSP00000364037:A580T	A	-	1	0	TEX10	102129953	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.064000	0.76721	2.640000	0.89533	0.655000	0.94253	GCT	.	.	none		0.423	TEX10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053416.1	NM_017746		T	103090132	C	T	103090132	3	4	11	1	0	0	0	0	1	0	0	0	15787	768	27	1	1083	1	TEX10	9	103090132	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	25616536	103090132	38123299	143	1434											
ZNF462	58499	hgsc.bcm.edu	37	chr9	109689973	109689973	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatctggagcgggacaaaacGaaactccgagcactcaaatg	16	5	10	10	3	2	0	1	0	1	0	3	4	3	2	1	2	4	1	1	2	5	0			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr9:109689973G>T	ENST00000277225.5	+	3	4069	c.3780G>T	c.(3778-3780)acG>acT	p.T1260T	ZNF462_ENST00000457913.1_Silent_p.T1260T|ZNF462_ENST00000441147.2_Silent_p.T105T			Q96JM2	ZN462_HUMAN	zinc finger protein 462	1260					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)	p.T1260T(1)		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						GGGACAAAACGAAACTCCGAG	0.542																																					p.T1260T		Atlas-SNP	.											ZNF462,rectum,carcinoma,0,1	ZNF462	322	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G3780T						PASS	.						154	162	159					9																	109689973		2203	4300	6503	SO:0001819	synonymous_variant	58499	exon3			CAAAACGAAACTC	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.3780G>T	9.37:g.109689973G>T		103	0	0		71	28	0.394366	NM_021224	Q5T0T4|Q8N408	Silent	SNP	ENST00000277225.5	37	CCDS35096.1																																																																																			.	.	none		0.542	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224		T	109689973	G	T	109689973	2	4	11	1	0	0	0	0	0	0	0	1	17941	1045	37	4		4	ZNF462	9	109689973	Silent	SNP	G	TCGA-FF-8042-01A-11D-2210-10	6599841	109689973	31523458	144	1435											
MPP7	143098	hgsc.bcm.edu	37	chr10	28412969	28412969	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttacagcttaccaaaatctgTattatttcctcaggcctttt	10	17	4	10	0	2	0	1	0	1	0	3	0	3	0	3	1	3	2	3	1	6	7			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr10:28412969T>C	ENST00000375732.1	-	8	865	c.606A>G	c.(604-606)atA>atG	p.I202M	MPP7_ENST00000375719.3_Missense_Mutation_p.I202M|MPP7_ENST00000540098.1_Missense_Mutation_p.I202M|MPP7_ENST00000445954.2_Missense_Mutation_p.I77M|MPP7_ENST00000481244.1_5'Flank|MPP7_ENST00000337532.5_Missense_Mutation_p.I202M			Q5T2T1	MPP7_HUMAN	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	202	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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						CCAAAATCTGTATTATTTCCT	0.343																																					p.I202M		Atlas-SNP	.											.	MPP7	60	.	0			c.A606G						PASS	.						85	88	87					10																	28412969		2203	4300	6503	SO:0001583	missense	143098	exon10			AATCTGTATTATT	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.606A>G	10.37:g.28412969T>C	ENSP00000364884:p.Ile202Met	62	0	0		51	19	0.372549	NM_173496	B2RCC9|B4DWL9|B5MDZ3|D3DRW3|Q5T2T0|Q8IY28	Missense_Mutation	SNP	ENST00000375732.1	37	CCDS7158.1	.	.	.	.	.	.	.	.	.	.	T	17.80	3.477566	0.63849	.	.	ENSG00000150054	ENST00000375732;ENST00000337532;ENST00000540098;ENST00000375719;ENST00000445954	T;T;T;T;T	0.27890	1.64;1.64;1.64;1.64;1.64	5.58	1.86	0.25419	PDZ/DHR/GLGF (4);	0.039978	0.85682	D	0.000000	T	0.44746	0.1308	M	0.69358	2.11	0.58432	D	0.999999	D	0.58620	0.983	D	0.64321	0.924	T	0.17228	-1.0376	10	0.32370	T	0.25	.	8.3462	0.32275	0.1678:0.0:0.1068:0.7254	.	202	Q5T2T1	MPP7_HUMAN	M	202;202;202;202;77	ENSP00000364884:I202M;ENSP00000337907:I202M;ENSP00000438693:I202M;ENSP00000364871:I202M;ENSP00000405397:I77M	ENSP00000337907:I202M	I	-	3	3	MPP7	28452975	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	1.284000	0.33249	0.117000	0.18138	0.454000	0.30748	ATA	.	.	none		0.343	MPP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047345.1	NM_173496		C	28412969	T	C	28412969	3	2	11	1	0	0	0	0	1	0	0	0	9748	1628	57	3	1164	3	MPP7	10	28412969	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10		28412969	107121778	145	1436											
ANK3	288	hgsc.bcm.edu	37	chr10	61845008	61845008	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cccactgagcaggcgaagtgCcccctgagagaacaacagca	13	3	11	14	1	0	3	0	2	0	1	0	5	0	3	3	1	5	2	3	1	3	0			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr10:61845008C>T	ENST00000280772.2	-	31	3943	c.3752G>A	c.(3751-3753)gGc>gAc	p.G1251D	ANK3_ENST00000503366.1_Missense_Mutation_p.G1252D|ANK3_ENST00000373827.2_Missense_Mutation_p.G1245D|ANK3_ENST00000355288.2_Missense_Mutation_p.G385D	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	1251	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						AGGCGAAGTGCCCCCTGAGAG	0.428																																					p.G1252D		Atlas-SNP	.											.	ANK3	703	.	0			c.G3755A						PASS	.						64	61	62					10																	61845008		2203	4300	6503	SO:0001583	missense	288	exon32			GAAGTGCCCCCTG	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.3752G>A	10.37:g.61845008C>T	ENSP00000280772:p.Gly1251Asp	99	0	0		90	4	0.0444444	NM_001204404	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	37	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	C	34	5.383214	0.95967	.	.	ENSG00000151150	ENST00000280772;ENST00000373827;ENST00000355288;ENST00000423532;ENST00000503366;ENST00000395299;ENST00000373817;ENST00000395293;ENST00000395304;ENST00000544789;ENST00000536348	T;T;T;T	0.28666	1.6;1.6;1.6;1.6	6.17	6.17	0.99709	.	0.000000	0.42821	D	0.000647	T	0.66733	0.2819	M	0.89904	3.07	0.80722	D	1	D;D;D;D;D;D;D	0.89917	0.998;1.0;1.0;1.0;1.0;0.996;1.0	D;D;D;D;D;D;D	0.97110	0.98;1.0;0.999;1.0;0.999;0.982;0.999	T	0.70949	-0.4733	10	0.87932	D	0	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	1252;385;784;1245;1251;486;385	E9PE32;A8KA62;Q59G01;Q5CZH9;Q12955;F5GXK0;B1AQT2	.;.;.;.;ANK3_HUMAN;.;.	D	1251;1245;385;385;1252;1231;486;886;886;384;784	ENSP00000280772:G1251D;ENSP00000362933:G1245D;ENSP00000347436:G385D;ENSP00000425236:G1252D	ENSP00000280772:G1251D	G	-	2	0	ANK3	61515014	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.797000	0.85911	2.941000	0.99782	0.655000	0.94253	GGC	.	.	none		0.428	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		T	61845008	C	T	61845008	3	4	11	1	0	0	0	0	1	0	0	0	622	739	26	2	9746	2	ANK3	10	61845008	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	33432039	61845008	73689739	146	1437											
UNC5B	219699	hgsc.bcm.edu	37	chr10	73053316	73053316	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agctcaagacccaggcccacCagggccactgggaggtgagg	10	3	15	13	0	1	2	1	1	0	1	1	3	1	3	4	5	1	1	4	5	1	0			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr10:73053316C>T	ENST00000335350.6	+	12	2343	c.1927C>T	c.(1927-1929)Cag>Tag	p.Q643*	UNC5B_ENST00000373192.4_Nonsense_Mutation_p.Q632*	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	643	ZU5. {ECO:0000255|PROSITE- ProRule:PRU00485}.				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						CCAGGCCCACCAGGGCCACTG	0.642																																					p.Q643X		Atlas-SNP	.											.	UNC5B	123	.	0			c.C1927T						PASS	.						58	59	59					10																	73053316		2203	4300	6503	SO:0001587	stop_gained	219699	exon12			GCCCACCAGGGCC	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.1927C>T	10.37:g.73053316C>T	ENSP00000334329:p.Gln643*	49	0	0		45	23	0.511111	NM_170744	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Nonsense_Mutation	SNP	ENST00000335350.6	37	CCDS7309.1	.	.	.	.	.	.	.	.	.	.	C	42	9.790481	0.99264	.	.	ENSG00000107731	ENST00000335350;ENST00000373192	.	.	.	4.76	3.84	0.44239	.	0.168672	0.43416	D	0.000573	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.35671	T	0.21	-19.7677	12.3129	0.54938	0.0:0.9181:0.0:0.0819	.	.	.	.	X	643;632	.	ENSP00000334329:Q643X	Q	+	1	0	UNC5B	72723322	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.041000	0.57339	2.208000	0.71279	0.462000	0.41574	CAG	.	.	none		0.642	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744		T	73053316	C	T	73053316	4	4	11	1	0	0	0	0	0	1	0	0	17007	595	21	2	1973	2	UNC5B	10	73053316	Nonsense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	11208308	73053316	62481431	147	1438											
GRID1	2894	hgsc.bcm.edu	37	chr10	87615870	87615870	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttgaggctcgccatgctatgCcacttccggtcctccagctt	5	12	9	15	2	0	1	0	1	0	0	4	1	3	1	5	2	3	3	5	2	1	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr10:87615870C>T	ENST00000327946.7	-	7	1114	c.1029G>A	c.(1027-1029)tgG>tgA	p.W343*		NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	343					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						CCATGCTATGCCACTTCCGGT	0.522										Multiple Myeloma(13;0.14)																											p.W343X		Atlas-SNP	.											.	GRID1	204	.	0			c.G1029A						PASS	.						137	112	120					10																	87615870		2203	4300	6503	SO:0001587	stop_gained	2894	exon7			GCTATGCCACTTC	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.1029G>A	10.37:g.87615870C>T	ENSP00000330148:p.Trp343*	159	0	0		138	57	0.413043	NM_017551	B3KXD5|B7Z7L0|Q8IXT3	Nonsense_Mutation	SNP	ENST00000327946.7	37	CCDS31236.1	.	.	.	.	.	.	.	.	.	.	C	38	7.285199	0.98186	.	.	ENSG00000182771	ENST00000327946	.	.	.	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	.	18.0162	0.89241	0.0:1.0:0.0:0.0	.	.	.	.	X	343	.	ENSP00000330148:W343X	W	-	3	0	GRID1	87605850	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.811000	0.86092	2.501000	0.84356	0.655000	0.94253	TGG	.	.	none		0.522	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613		T	87615870	C	T	87615870	4	4	11	1	0	0	0	0	0	1	0	0	6780	740	26	2	2040	2	GRID1	10	87615870	Nonsense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	14562554	87615870	47918877	148	1439											
TBC1D12	23232	hgsc.bcm.edu	37	chr10	96163177	96163177	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcctgggcttttctgacatTcacttcaactctcgcaacac	8	12	6	15	2	4	1	2	1	2	0	5	1	4	1	1	1	2	2	1	1	2	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr10:96163177T>C	ENST00000225235.4	+	1	917	c.807T>C	c.(805-807)atT>atC	p.I269I		NM_015188.1	NP_056003.1	O60347	TBC12_HUMAN	TBC1 domain family, member 12	269							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)				TTTCTGACATTCACTTCAACT	0.736																																					p.I269I		Atlas-SNP	.											.	TBC1D12	51	.	0			c.T807C						PASS	.						8	11	10					10																	96163177		1757	3890	5647	SO:0001819	synonymous_variant	23232	exon1			TGACATTCACTTC	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.807T>C	10.37:g.96163177T>C		134	0	0		119	6	0.0504202	NM_015188	Q5VYA6|Q8WX26|Q8WX59|Q9UG83	Silent	SNP	ENST00000225235.4	37	CCDS41553.1																																																																																			.	.	none		0.736	TBC1D12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049482.2			C	96163177	T	C	96163177	2	2	11	1	0	0	0	0	0	0	0	1	15616	1771	62	3		3	TBC1D12	10	96163177	Silent	SNP	T	TCGA-FF-8042-01A-11D-2210-10	8547307	96163177	39371570	149	1440											
SORCS3	22986	hgsc.bcm.edu	37	chr10	106907486	106907486	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acacgcgtgggatttacttcActctggccatggagaacatc	10	10	10	11	2	2	1	1	0	1	1	3	3	2	2	1	3	2	0	1	3	2	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr10:106907486A>C	ENST00000369701.3	+	9	1641	c.1414A>C	c.(1414-1416)Act>Cct	p.T472P		NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	472					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)		GATTTACTTCACTCTGGCCAT	0.463																																					p.T472P	NSCLC(116;1497 1690 7108 13108 14106)	Atlas-SNP	.											.	SORCS3	282	.	0			c.A1414C						PASS	.						235	188	204					10																	106907486		2203	4299	6502	SO:0001583	missense	22986	exon9			TACTTCACTCTGG	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.1414A>C	10.37:g.106907486A>C	ENSP00000358715:p.Thr472Pro	232	0	0		196	86	0.438776	NM_014978	Q5VXF9|Q9NQJ2	Missense_Mutation	SNP	ENST00000369701.3	37	CCDS7558.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.698172	0.88830	.	.	ENSG00000156395	ENST00000369701	T	0.26067	1.76	5.42	5.42	0.78866	VPS10 (1);	0.051975	0.85682	D	0.000000	T	0.52741	0.1753	M	0.77616	2.38	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	T	0.58205	-0.7677	10	0.87932	D	0	.	15.7709	0.78167	1.0:0.0:0.0:0.0	.	472	Q9UPU3	SORC3_HUMAN	P	472	ENSP00000358715:T472P	ENSP00000358715:T472P	T	+	1	0	SORCS3	106897476	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	9.287000	0.95975	2.194000	0.70268	0.528000	0.53228	ACT	.	.	none		0.463	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		C	106907486	A	C	106907486	3	2	11	1	0	0	0	0	1	0	0	0	14947	159	6	5	1448	5	SORCS3	10	106907486	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	10744309	106907486	28627261	150	1441											
KCNK18	338567	hgsc.bcm.edu	37	chr10	118969290	118969290	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgctgaagagcttccaggccCcaaacttggcacatgtcctt	9	10	9	13	0	0	2	0	1	0	1	2	2	2	2	4	2	3	3	4	2	2	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr10:118969290C>T	ENST00000334549.1	+	3	635	c.635C>T	c.(634-636)cCc>cTc	p.P212L		NM_181840.1	NP_862823.1	Q7Z418	KCNKI_HUMAN	potassium channel, subfamily K, member 18	212					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)		CTTCCAGGCCCCAAACTTGGC	0.527																																					p.P212L		Atlas-SNP	.											.	KCNK18	70	.	0			c.C635T						PASS	.						74	75	75					10																	118969290		2203	4300	6503	SO:0001583	missense	338567	exon3			CAGGCCCCAAACT	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.635C>T	10.37:g.118969290C>T	ENSP00000334650:p.Pro212Leu	86	0	0		75	31	0.413333	NM_181840	Q5SQQ8	Missense_Mutation	SNP	ENST00000334549.1	37	CCDS7598.1	.	.	.	.	.	.	.	.	.	.	C	7.395	0.631626	0.14322	.	.	ENSG00000186795	ENST00000334549	T	0.14022	2.54	4.72	1.75	0.24633	.	0.572860	0.19090	N	0.122981	T	0.06781	0.0173	L	0.27053	0.805	0.09310	N	0.999999	B	0.26318	0.146	B	0.18871	0.023	T	0.31447	-0.9943	10	0.27082	T	0.32	.	1.6533	0.02776	0.2389:0.4293:0.1165:0.2153	.	212	Q7Z418	KCNKI_HUMAN	L	212	ENSP00000334650:P212L	ENSP00000334650:P212L	P	+	2	0	KCNK18	118959280	0.000000	0.05858	0.002000	0.10522	0.027000	0.11550	0.311000	0.19380	0.258000	0.21686	0.655000	0.94253	CCC	.	.	none		0.527	KCNK18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050562.2	NM_181840		T	118969290	C	T	118969290	3	4	11	1	0	0	0	0	1	0	0	0	8074	623	22	2	645	2	KCNK18	10	118969290	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	12061804	118969290	16565457	151	1442											
PHRF1	57661	hgsc.bcm.edu	37	chr11	608546	608546	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaatccagggacaggagctcGaggtcagcgtcaccatcagt	11	6	13	11	2	3	0	3	0	0	0	5	4	4	2	2	3	2	1	2	3	1	0			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr11:608546G>A	ENST00000264555.5	+	14	3218	c.3090G>A	c.(3088-3090)tcG>tcA	p.S1030S	PHRF1_ENST00000416188.2_Silent_p.S1029S|PHRF1_ENST00000533464.1_Silent_p.S1026S|PHRF1_ENST00000413872.2_Silent_p.S1028S	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	1030	Arg-rich.				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						ACAGGAGCTCGAGGTCAGCGT	0.677																																					p.S1029S		Atlas-SNP	.											PHRF1_ENST00000264555,NS,lymphoid_neoplasm,+1,2	PHRF1	188	2	0			c.G3087A						PASS	.						26	31	29					11																	608546		2189	4293	6482	SO:0001819	synonymous_variant	57661	exon14			GAGCTCGAGGTCA	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.3090G>A	11.37:g.608546G>A		98	0	0		97	39	0.402062	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Silent	SNP	ENST00000264555.5	37																																																																																				.	.	none		0.677	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901		A	608546	G	A	608546	2	1	11	1	0	0	0	0	0	0	0	1	11870	1045	37	1		1	PHRF1	11	608546	Silent	SNP	G	TCGA-FF-8042-01A-11D-2210-10		608546	134397970	152	1443											
EPS8L2	64787	hgsc.bcm.edu	37	chr11	726366	726366	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggaaaatcagcaacatcaggGcgcagccacagaggcacttc	14	4	11	12	1	2	1	2	0	0	1	3	2	2	2	1	3	3	3	1	3	3	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr11:726366G>A	ENST00000533256.1	+	20	2191	c.1816G>A	c.(1816-1818)Gcg>Acg	p.A606T	AP006621.9_ENST00000527021.2_RNA|EPS8L2_ENST00000530636.1_Missense_Mutation_p.A606T|EPS8L2_ENST00000526198.1_Missense_Mutation_p.A622T|EPS8L2_ENST00000318562.8_Missense_Mutation_p.A606T			Q9H6S3	ES8L2_HUMAN	EPS8-like 2	606					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)		CAACATCAGGGCGCAGCCACA	0.677																																					p.A606T		Atlas-SNP	.											.	EPS8L2	42	.	0			c.G1816A						PASS	.						22	24	23					11																	726366		2191	4288	6479	SO:0001583	missense	64787	exon19			ATCAGGGCGCAGC	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.1816G>A	11.37:g.726366G>A	ENSP00000435585:p.Ala606Thr	125	0	0		154	67	0.435065	NM_022772	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Missense_Mutation	SNP	ENST00000533256.1	37	CCDS31328.1	.	.	.	.	.	.	.	.	.	.	G	8.791	0.930546	0.18131	.	.	ENSG00000177106	ENST00000318562;ENST00000533256;ENST00000530636;ENST00000526198	T;T;T;T	0.15834	2.39;2.39;2.39;2.39	3.11	-1.15	0.09709	.	0.791425	0.10418	N	0.677052	T	0.05456	0.0144	N	0.04746	-0.17	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.40887	-0.9539	10	0.12766	T	0.61	-3.7233	1.0949	0.01671	0.267:0.1586:0.4134:0.161	.	622;606	B7ZKL3;Q9H6S3	.;ES8L2_HUMAN	T	606;606;606;622	ENSP00000320828:A606T;ENSP00000435585:A606T;ENSP00000436035:A606T;ENSP00000436230:A622T	ENSP00000320828:A606T	A	+	1	0	EPS8L2	716366	0.001000	0.12720	0.003000	0.11579	0.497000	0.33675	0.551000	0.23361	-0.375000	0.07955	0.298000	0.19748	GCG	.	.	none		0.677	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772		A	726366	G	A	726366	3	1	11	1	0	0	0	0	1	0	0	0	5198	1203	42	2	1886	2	EPS8L2	11	726366	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	117820	726366	134280150	153	1444											
MUC2	4583	hgsc.bcm.edu	37	chr11	1093448	1093448	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	caccaccacggtgaccccaaCcccgacacccaccggcacac	11	1	6	23	3	0	1	0	1	0	0	0	2	0	1	8	2	1	1	8	2	1	0			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr11:1093448C>A	ENST00000441003.2	+	30	5294	c.5267C>A	c.(5266-5268)aCc>aAc	p.T1756N	MUC2_ENST00000333592.6_Missense_Mutation_p.T44N|MUC2_ENST00000359061.5_Missense_Mutation_p.T1723N|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0					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)		p.T1756N(3)|p.T1723N(3)		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)	gtgaccccaaccccgacaccc	0.622																																					p.T1756N		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,8	MUC2	614	8	6	Substitution - Missense(6)	kidney(6)	c.C5267A						scavenged	.						133	160	151					11																	1093448		2049	4049	6098	SO:0001583	missense	4583	exon30			CCCCAACCCCGAC	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.5267C>A	11.37:g.1093448C>A	ENSP00000415183:p.Thr1756Asn	89	2	0.0224719		62	4	0.0645161	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	7.928	0.739947	0.15642	.	.	ENSG00000198788	ENST00000441003;ENST00000359061;ENST00000333592	T;T;T	0.12465	2.73;2.68;2.81	1.81	0.625	0.17665	.	1.255720	0.06522	U	0.739910	T	0.10852	0.0265	.	.	.	0.09310	N	1	B	0.16802	0.019	B	0.15052	0.012	T	0.35176	-0.9799	9	0.62326	D	0.03	.	6.7886	0.23687	0.2734:0.7266:0.0:0.0	.	1756	E7EUV1	.	N	1756;1723;44	ENSP00000415183:T1756N;ENSP00000351956:T1723N;ENSP00000331373:T44N	ENSP00000331373:T44N	T	+	2	0	MUC2	1083448	0.012000	0.17670	0.001000	0.08648	0.007000	0.05969	0.908000	0.28545	1.004000	0.39156	0.195000	0.17529	ACC	.	.	none		0.622	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1093448	C	A	1093448	3	1	11	1	0	0	0	0	1	0	0	0	9984	507	18	4	5385	4	MUC2	11	1093448	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	367082	1093448	133913068	154	1445											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1253691	1253691	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccccacagagaactacgccCggcactggtgctcgcgcctg	7	6	11	17	4	0	1	0	0	0	1	2	2	1	1	4	2	3	2	4	2	2	1	rs56411917	byFrequency	TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr11:1253691C>T	ENST00000529681.1	+	16	1913	c.1855C>T	c.(1855-1857)Cgg>Tgg	p.R619W	MUC5B_ENST00000447027.1_Missense_Mutation_p.R622W	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	619	VWFD 2. {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)		GAACTACGCCCGGCACTGGTG	0.662													c|||	4	0.000798722	0.0	0.0	5008	,	,		16017	0.001		0.002	False		,,,				2504	0.001				p.R619W		Atlas-SNP	.											.	MUC5B	473	.	0			c.C1855T						PASS	.	C	TRP/ARG	3,4183		0,3,2090	38	43	42		1855	4.3	0.9	11	dbSNP_129	42	32,8388		0,32,4178	yes	missense	MUC5B	NM_002458.2	101	0,35,6268	TT,TC,CC		0.38,0.0717,0.2776	probably-damaging	619/5763	1253691	35,12571	2093	4210	6303	SO:0001583	missense	727897	exon16			TACGCCCGGCACT	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.1855C>T	11.37:g.1253691C>T	ENSP00000436812:p.Arg619Trp	101	0	0		96	42	0.4375	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	6.454	0.451926	0.12283	7.17E-4	0.0038	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.77229	-1.08;-1.08	4.32	4.32	0.51571	von Willebrand factor, type D domain (1);Uncharacterised domain, cysteine-rich (2);	.	.	.	.	D	0.85557	0.5724	M	0.79475	2.455	0.09310	N	1	D;D;D	0.89917	0.999;1.0;1.0	P;D;D	0.70935	0.761;0.971;0.971	T	0.75451	-0.3313	9	0.87932	D	0	.	6.7306	0.23381	0.1774:0.732:0.0:0.0907	rs56411917	619;1278;622	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	W	619;622;620;655	ENSP00000436812:R619W;ENSP00000415793:R622W	ENSP00000343037:R620W	R	+	1	2	MUC5B	1210267	0.000000	0.05858	0.905000	0.35620	0.385000	0.30292	-0.600000	0.05693	1.946000	0.56461	0.462000	0.41574	CGG	C|0.997;T|0.003	0.003	strong		0.662	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		T	1253691	C	T	1253691	3	4	11	1	0	0	0	0	1	0	0	0	9988	643	23	1	1926	1	MUC5B	11	1253691	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	160243	1253691	133752825	155	1446											
OR51A4	401666	hgsc.bcm.edu	37	chr11	4967768	4967768	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgttgtcagaacaggccaacTtcatgacatcctggtggaga	11	10	11	9	0	2	3	2	1	0	2	3	4	3	3	2	3	2	1	2	3	2	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr11:4967768T>G	ENST00000380373.2	-	1	588	c.563A>C	c.(562-564)aAg>aCg	p.K188T	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	188						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)		ACAGGCCAACTTCATGACATC	0.413																																					p.K188T		Atlas-SNP	.											.	OR51A4	73	.	0			c.A563C						PASS	.						72	70	70					11																	4967768		2196	4284	6480	SO:0001583	missense	401666	exon1			GCCAACTTCATGA	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.563A>C	11.37:g.4967768T>G	ENSP00000369731:p.Lys188Thr	905	0	0		805	200	0.248447	NM_001005329		Missense_Mutation	SNP	ENST00000380373.2	37	CCDS31367.1	.	.	.	.	.	.	.	.	.	.	T	11.76	1.734892	0.30774	.	.	ENSG00000205497	ENST00000380373	T	0.39997	1.05	3.44	1.13	0.20643	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.64583	0.2611	M	0.89163	3.01	0.09310	N	1	D	0.67145	0.996	D	0.72625	0.978	T	0.51356	-0.8716	9	0.87932	D	0	.	7.4109	0.27017	0.0:0.2083:0.0:0.7917	.	188	Q8NGJ6	O51A4_HUMAN	T	188	ENSP00000369731:K188T	ENSP00000369731:K188T	K	-	2	0	OR51A4	4924344	0.000000	0.05858	0.695000	0.30226	0.651000	0.38670	0.338000	0.19858	0.509000	0.28195	-0.627000	0.03993	AAG	.	.	none		0.413	OR51A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142821.1	NM_001005329		G	4967768	T	G	4967768	3	3	11	1	0	0	0	0	1	0	0	0	11096	1609	56	5	380	5	OR51A4	11	4967768	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	3714077	4967768	130038748	156	1447											
TRIM34	53840	hgsc.bcm.edu	37	chr11	5664047	5664047	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaatcttttattatttcagAactgacagctgtccggtgct	9	16	8	8	1	2	3	1	2	1	1	3	3	3	3	1	1	3	2	1	1	4	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr11:5664047A>G	ENST00000514226.1	+	7	1212	c.875A>G	c.(874-876)gAa>gGa	p.E292G	TRIM34_ENST00000429814.2_Splice_Site_p.E292G|HBG2_ENST00000380259.2_Intron|TRIM6-TRIM34_ENST00000354852.5_Splice_Site_p.E646G|TRIM34_ENST00000495668.1_3'UTR|TRIM6-TRIM34_ENST00000457787.2_Splice_Site_p.E292G	NM_001003827.1	NP_001003827.1	Q9BYJ4	TRI34_HUMAN	tripartite motif containing 34	292	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein trimerization (GO:0070206)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			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)		ATTATTTCAGAACTGACAGCT	0.358																																					p.E646G		Atlas-SNP	.											.	TRIM6-TRIM34	68	.	0			c.A1937G						PASS	.						68	66	67					11																	5664047		2201	4297	6498	SO:0001630	splice_region_variant	445372	exon13			TTTCAGAACTGAC	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.875-1A>G	11.37:g.5664047A>G		85	0	0		97	4	0.0412371	NM_001003819	D3DQS7|Q9C016|Q9HCR0|Q9HCR1|Q9HCR2	Missense_Mutation	SNP	ENST00000514226.1	37	CCDS31391.1	.	.	.	.	.	.	.	.	.	.	A	10.03	1.237849	0.22711	.	.	ENSG00000258659;ENSG00000258659;ENSG00000258659;ENSG00000258659;ENSG00000258588	ENST00000337072;ENST00000514226;ENST00000429814;ENST00000457787;ENST00000354852	T;T;T;T	0.70164	-0.46;-0.46;-0.46;-0.45	3.02	3.02	0.34903	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.61362	0.2341	L	0.54908	1.71	0.26629	N	0.972503	B;B	0.32939	0.009;0.391	B;B	0.37780	0.008;0.258	T	0.53781	-0.8390	8	.	.	.	.	7.8167	0.29263	1.0:0.0:0.0:0.0	.	292;646	Q9BYJ4;B2RNG4	TRI34_HUMAN;.	G	646;292;292;292;646	ENSP00000422947:E292G;ENSP00000402595:E292G;ENSP00000395982:E292G;ENSP00000346916:E646G	.	E	+	2	0	TRIM34;TRIM6-TRIM34	5620623	0.733000	0.28132	0.972000	0.41901	0.555000	0.35460	1.063000	0.30567	1.617000	0.50277	0.377000	0.23210	GAA	.	.	none		0.358	TRIM34-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143357.2	NM_001003827	Missense_Mutation	G	5664047	A	G	5664047	5	3	11	1	0	0	0	0	0	0	1	0	16523	260	9	3	870	3	TRIM34	11	5664047	Splice_Site	SNP	A	TCGA-FF-8042-01A-11D-2210-10	696279	5664047	129342469	157	1448											
DCHS1	8642	hgsc.bcm.edu	37	chr11	6643761	6643761	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactggccacacgggggaacTcattgatcatgcggatctca	10	8	11	12	2	3	1	3	1	1	0	4	3	3	3	1	4	2	0	1	4	1	1	rs368872716		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr11:6643761T>A	ENST00000299441.3	-	21	9557	c.9146A>T	c.(9145-9147)gAg>gTg	p.E3049V	RP11-732A19.5_ENST00000526456.1_RNA|RP11-732A19.9_ENST00000545572.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	3049					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)		ACGGGGGAACTCATTGATCAT	0.602																																					p.E3049V		Atlas-SNP	.											.	DCHS1	277	.	0			c.A9146T						PASS	.	T	VAL/GLU	0,4386		0,0,2193	31	23	26		9146	4.6	1	11		26	1,8573		0,1,4286	no	missense	DCHS1	NM_003737.2	121	0,1,6479	AA,AT,TT		0.0117,0.0,0.0077	probably-damaging	3049/3299	6643761	1,12959	2193	4287	6480	SO:0001583	missense	8642	exon21			GGGAACTCATTGA	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.9146A>T	11.37:g.6643761T>A	ENSP00000299441:p.Glu3049Val	77	0	0		60	25	0.416667	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	37	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	T	18.05	3.535958	0.64972	0.0	1.17E-4	ENSG00000166341	ENST00000299441	T	0.64991	-0.13	4.62	4.62	0.57501	.	0.000000	0.37857	N	0.001901	T	0.78323	0.4265	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.81252	-0.1017	10	0.66056	D	0.02	.	13.346	0.60573	0.0:0.0:0.0:1.0	.	3049	Q96JQ0	PCD16_HUMAN	V	3049	ENSP00000299441:E3049V	ENSP00000299441:E3049V	E	-	2	0	DCHS1	6600337	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	7.811000	0.86092	1.939000	0.56221	0.379000	0.24179	GAG	.	.	weak		0.602	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		A	6643761	T	A	6643761	3	1	11	1	0	0	0	0	1	0	0	0	4289	1551	54	5	754	5	DCHS1	11	6643761	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	979714	6643761	128362755	158	1449											
DCHS1	8642	hgsc.bcm.edu	37	chr11	6646497	6646497	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacaagcactgtgaggttggCacggccctcatgaggcccat	9	7	12	13	1	1	2	1	2	0	0	1	2	1	2	2	4	1	3	2	4	1	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr11:6646497C>T	ENST00000299441.3	-	19	7489	c.7078G>A	c.(7078-7080)Gcc>Acc	p.A2360T	RP11-732A19.5_ENST00000526456.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	2360	Cadherin 22. {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)		GTGAGGTTGGCACGGCCCTCA	0.587																																					p.A2360T		Atlas-SNP	.											.	DCHS1	277	.	0			c.G7078A						PASS	.						89	82	85					11																	6646497		2201	4296	6497	SO:0001583	missense	8642	exon19			GGTTGGCACGGCC	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.7078G>A	11.37:g.6646497C>T	ENSP00000299441:p.Ala2360Thr	77	0	0		52	25	0.480769	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	37	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	C	18.97	3.735641	0.69189	.	.	ENSG00000166341	ENST00000299441	T	0.50548	0.74	4.95	4.95	0.65309	Cadherin (4);Cadherin-like (1);	0.000000	0.42548	D	0.000684	T	0.53834	0.1821	L	0.35414	1.06	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.40850	-0.9541	10	0.05959	T	0.93	.	16.9484	0.86236	0.0:1.0:0.0:0.0	.	2360	Q96JQ0	PCD16_HUMAN	T	2360	ENSP00000299441:A2360T	ENSP00000299441:A2360T	A	-	1	0	DCHS1	6603073	1.000000	0.71417	0.963000	0.40424	0.860000	0.49131	5.826000	0.69293	2.563000	0.86464	0.655000	0.94253	GCC	.	.	none		0.587	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		T	6646497	C	T	6646497	3	4	11	1	0	0	0	0	1	0	0	0	4289	710	25	2	2830	2	DCHS1	11	6646497	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	2736	6646497	128360019	159	1450											
OR4C46	119749	hgsc.bcm.edu	37	chr11	51516008	51516008	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacctgtgtctcccacatcAcggttgtcatcttattcttt	6	16	5	14	1	5	0	2	0	3	0	6	0	5	0	3	1	0	1	3	1	1	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr11:51516008A>G	ENST00000328188.1	+	1	727	c.727A>G	c.(727-729)Acg>Gcg	p.T243A		NM_001004703.1	NP_001004703.1	A6NHA9	O4C46_HUMAN	olfactory receptor, family 4, subfamily C, member 46	243						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						CTCCCACATCACGGTTGTCAT	0.468																																					p.T243A		Atlas-SNP	.											.	OR4C46	96	.	0			c.A727G						PASS	.						134	113	120					11																	51516008		2201	4296	6497	SO:0001583	missense	119749	exon1			CACATCACGGTTG		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.727A>G	11.37:g.51516008A>G	ENSP00000329056:p.Thr243Ala	238	0	0		199	77	0.386935	NM_001004703		Missense_Mutation	SNP	ENST00000328188.1	37	CCDS31498.1	.	.	.	.	.	.	.	.	.	.	.	4.480	0.089001	0.08583	.	.	ENSG00000185926	ENST00000328188	T	0.37235	1.21	2.33	1.08	0.20341	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47093	D	0.000249	T	0.26919	0.0659	L	0.41824	1.3	0.09310	N	1	B	0.33826	0.427	B	0.40940	0.344	T	0.12319	-1.0552	10	0.39692	T	0.17	.	1.9961	0.03457	0.5748:0.0:0.1596:0.2656	.	243	A6NHA9	O4C46_HUMAN	A	243	ENSP00000329056:T243A	ENSP00000329056:T243A	T	+	1	0	OR4C46	51372584	0.000000	0.05858	0.375000	0.26029	0.060000	0.15804	0.118000	0.15605	0.145000	0.18977	0.102000	0.15555	ACG	.	.	none		0.468	OR4C46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391155.1	NM_001004703		G	51516008	A	G	51516008	3	3	11	1	0	0	0	0	1	0	0	0	11060	159	6	3	729	3	OR4C46	11	51516008	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	44869511	51516008	83490508	160	1451											
OR5T1	390155	hgsc.bcm.edu	37	chr11	56043714	56043714	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctcctctgcttgctatttcTtgttctgacactcacgtaat	6	17	5	13	1	4	1	1	1	3	0	5	1	5	1	2	0	2	4	2	0	2	6			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr11:56043714T>G	ENST00000313033.2	+	1	686	c.600T>G	c.(598-600)tcT>tcG	p.S200S		NM_001004745.1	NP_001004745.1	Q8NG75	OR5T1_HUMAN	olfactory receptor, family 5, subfamily T, 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)	p.S200S(1)		NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(27)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	43	Esophageal squamous(21;0.00448)					TTGCTATTTCTTGTTCTGACA	0.398																																					p.S200S		Atlas-SNP	.											OR5T1,NS,carcinoma,0,1	OR5T1	95	1	1	Substitution - coding silent(1)	lung(1)	c.T600G						PASS	.						236	224	228					11																	56043714		2201	4296	6497	SO:0001819	synonymous_variant	390155	exon1			TATTTCTTGTTCT	AB065962	CCDS31525.1	11q11	2012-08-09		2004-03-10	ENSG00000181698	ENSG00000181698		"GPCR / Class A : Olfactory receptors"	14821	protein-coding gene	gene with protein product				OR5T1P			Standard	NM_001004745		Approved		uc001nio.1	Q8NG75	OTTHUMG00000166853	ENST00000313033.2:c.600T>G	11.37:g.56043714T>G		402	0	0		315	115	0.365079	NM_001004745	B2RNM9	Silent	SNP	ENST00000313033.2	37	CCDS31525.1																																																																																			.	.	none		0.398	OR5T1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391600.1	NM_001004745		G	56043714	T	G	56043714	2	3	11	1	0	0	0	0	0	0	0	1	11190	1596	56	5		5	OR5T1	11	56043714	Silent	SNP	T	TCGA-FF-8042-01A-11D-2210-10	4527706	56043714	78962802	161	1452											
SDHAF2	54949	hgsc.bcm.edu	37	chr11	61205178	61205178	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gcttctacagaggtgacagcCcaacagattcccaaaaggac	14	6	9	12	0	1	3	0	1	1	2	2	4	2	4	2	2	3	1	2	2	4	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr11:61205178C>T	ENST00000543265.1	+	2	121	c.118C>T	c.(118-120)Cca>Tca	p.P40S	SDHAF2_ENST00000534878.1_Missense_Mutation_p.P40S|SDHAF2_ENST00000537782.1_Missense_Mutation_p.P40S|RP11-286N22.8_ENST00000543044.1_Missense_Mutation_p.P28S|SDHAF2_ENST00000301761.2_Missense_Mutation_p.P40S|SDHAF2_ENST00000542074.1_Intron|RP11-286N22.8_ENST00000544880.1_3'UTR					succinate dehydrogenase complex assembly factor 2											large_intestine(3)|lung(4)|ovary(2)	9						AGGTGACAGCCCAACAGATTC	0.468																																					p.P40S		Atlas-SNP	.											.	SDHAF2	26	.	0			c.C118T						PASS	.						179	177	177					11																	61205178		2202	4299	6501	SO:0001583	missense	54949	exon2			GACAGCCCAACAG	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.118C>T	11.37:g.61205178C>T	ENSP00000443660:p.Pro40Ser	180	0	0		171	78	0.45614	NM_017841		Missense_Mutation	SNP	ENST00000543265.1	37		.	.	.	.	.	.	.	.	.	.	C	16.56	3.156855	0.57259	.	.	ENSG00000256591;ENSG00000167985;ENSG00000167985	ENST00000541135;ENST00000301761;ENST00000543265	T;T;T	0.78126	-1.14;-1.1;-1.15	5.87	2.88	0.33553	.	0.155706	0.64402	D	0.000017	T	0.70798	0.3265	M	0.76002	2.32	0.42212	D	0.991818	P	0.35077	0.483	B	0.30943	0.122	T	0.64605	-0.6368	10	0.37606	T	0.19	-2.9957	6.0537	0.19799	0.2891:0.5695:0.0:0.1414	.	40	Q9NX18	SDHF2_HUMAN	S	40	ENSP00000443130:P40S;ENSP00000301761:P40S;ENSP00000443660:P40S	ENSP00000440939:P40S	P	+	1	0	SDHAF2;RP11-286N22.8	60961754	0.999000	0.42202	0.990000	0.47175	0.952000	0.60782	2.180000	0.42537	0.415000	0.25817	0.655000	0.94253	CCA	.	.	none		0.468	SDHAF2-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000398484.1	NM_017841		T	61205178	C	T	61205178	3	4	11	1	0	0	0	0	1	0	0	0	13979	623	22	2	124	2	SDHAF2	11	61205178	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	5161464	61205178	73801338	162	1453											
DAGLA	747	hgsc.bcm.edu	37	chr11	61495668	61495668	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctctttgcggagttcttccGggaccttgacattgtgccat	5	14	10	12	2	2	1	0	1	2	0	3	3	3	3	4	2	2	1	4	2	0	5			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr11:61495668G>A	ENST00000257215.5	+	7	796	c.680G>A	c.(679-681)cGg>cAg	p.R227Q		NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	227					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)		GAGTTCTTCCGGGACCTTGAC	0.627																																					p.R227Q		Atlas-SNP	.											.	DAGLA	109	.	0			c.G680A						PASS	.						203	182	189					11																	61495668		2202	4299	6501	SO:0001583	missense	747	exon7			TCTTCCGGGACCT	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.680G>A	11.37:g.61495668G>A	ENSP00000257215:p.Arg227Gln	126	0	0		94	37	0.393617	NM_006133	A7E233|Q6WQJ0	Missense_Mutation	SNP	ENST00000257215.5	37	CCDS31578.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.225249	0.79576	.	.	ENSG00000134780	ENST00000257215	T	0.25414	1.8	4.78	4.78	0.61160	.	0.133125	0.49916	D	0.000137	T	0.43809	0.1264	L	0.42245	1.32	0.80722	D	1	D	0.69078	0.997	D	0.70227	0.968	T	0.25467	-1.0131	10	0.44086	T	0.13	-22.5485	18.2062	0.89855	0.0:0.0:1.0:0.0	.	227	Q9Y4D2	DGLA_HUMAN	Q	227	ENSP00000257215:R227Q	ENSP00000257215:R227Q	R	+	2	0	DAGLA	61252244	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	7.753000	0.85153	2.373000	0.80994	0.555000	0.69702	CGG	.	.	none		0.627	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133		A	61495668	G	A	61495668	3	1	11	1	0	0	0	0	1	0	0	0	4228	1116	39	1	702	1	DAGLA	11	61495668	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	290490	61495668	73510848	163	1454											
NXF1	10482	hgsc.bcm.edu	37	chr11	62564687	62564687	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgcaagaccagactcttcaaGttttctgttccaaaatagct	12	13	6	10	0	3	2	1	0	2	2	4	2	4	2	2	0	2	4	2	0	5	5			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr11:62564687G>C	ENST00000532297.1	-	14	1775	c.1146C>G	c.(1144-1146)aaC>aaG	p.N382K	NXF1_ENST00000533048.1_5'Flank|NXF1_ENST00000531709.2_3'UTR|NXF1_ENST00000294172.2_Missense_Mutation_p.N382K			Q9UBU9	NXF1_HUMAN	nuclear RNA export factor 1	382					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						GACTCTTCAAGTTTTCTGTTC	0.502																																					p.N382K		Atlas-SNP	.											.	NXF1	67	.	0			c.C1146G						PASS	.						66	60	62					11																	62564687		2201	4299	6500	SO:0001583	missense	10482	exon13			CTTCAAGTTTTCT	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.1146C>G	11.37:g.62564687G>C	ENSP00000436679:p.Asn382Lys	157	0	0		168	53	0.315476	NM_006362	B4E269|Q99799|Q9UQL2	Missense_Mutation	SNP	ENST00000532297.1	37	CCDS8037.1	.	.	.	.	.	.	.	.	.	.	G	11.56	1.674708	0.29693	.	.	ENSG00000162231	ENST00000294172;ENST00000532297;ENST00000530875	T;T;T	0.62788	-0.0;-0.0;-0.0	5.42	2.51	0.30379	.	0.279688	0.40818	N	0.001013	T	0.34048	0.0884	N	0.05280	-0.08	0.80722	D	1	B;B	0.13145	0.007;0.005	B;B	0.09377	0.002;0.004	T	0.06075	-1.0847	10	0.11485	T	0.65	-12.4081	9.1261	0.36816	0.2447:0.0:0.7553:0.0	.	425;382	E9PIN3;Q9UBU9	.;NXF1_HUMAN	K	382;382;425	ENSP00000294172:N382K;ENSP00000436679:N382K;ENSP00000435742:N425K	ENSP00000294172:N382K	N	-	3	2	NXF1	62321263	1.000000	0.71417	0.998000	0.56505	0.970000	0.65996	1.659000	0.37387	0.267000	0.21916	0.555000	0.69702	AAC	.	.	none		0.502	NXF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395365.2	NM_006362		C	62564687	G	C	62564687	3	2	11	1	0	0	0	0	1	0	0	0	10791	1020	36	4	749	4	NXF1	11	62564687	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	1069019	62564687	72441829	164	1455											
CHKA	1119	hgsc.bcm.edu	37	chr11	67833918	67833918	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtaattgtaactgctgtattCgaaatcaatgagcatcagtt	13	14	8	6	1	2	1	2	1	0	0	3	2	2	1	0	0	3	6	0	0	5	6			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr11:67833918C>T	ENST00000265689.4	-	8	1020	c.994G>A	c.(994-996)Gaa>Aaa	p.E332K	CHKA_ENST00000356135.5_Missense_Mutation_p.E314K	NM_001277.2	NP_001268.2	P35790	CHKA_HUMAN	choline kinase alpha	332					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)	CTGCTGTATTCGAAATCAATG	0.338																																					p.E332K		Atlas-SNP	.											.	CHKA	41	.	0			c.G994A						PASS	.						200	186	191					11																	67833918		2200	4294	6494	SO:0001583	missense	1119	exon8			TGTATTCGAAATC	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.994G>A	11.37:g.67833918C>T	ENSP00000265689:p.Glu332Lys	133	0	0		164	57	0.347561	NM_001277	Q8NE29	Missense_Mutation	SNP	ENST00000265689.4	37	CCDS8178.1	.	.	.	.	.	.	.	.	.	.	C	36	5.789905	0.96945	.	.	ENSG00000110721	ENST00000265689;ENST00000356135	D;D	0.86366	-2.11;-2.11	5.63	5.63	0.86233	Protein kinase-like domain (1);Choline/ethanolamine kinase (1);	0.106946	0.64402	D	0.000008	D	0.96134	0.8740	H	0.96633	3.855	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.97;0.993	D	0.97172	0.9845	10	0.87932	D	0	-21.1536	19.6499	0.95796	0.0:1.0:0.0:0.0	.	314;332	P35790-2;P35790	.;CHKA_HUMAN	K	332;314	ENSP00000265689:E332K;ENSP00000348454:E314K	ENSP00000265689:E332K	E	-	1	0	CHKA	67590494	1.000000	0.71417	0.891000	0.34965	0.990000	0.78478	7.730000	0.84881	2.647000	0.89833	0.491000	0.48974	GAA	.	.	none		0.338	CHKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394570.1	NM_001277		T	67833918	C	T	67833918	3	4	11	1	0	0	0	0	1	0	0	0	3349	893	31	1	399	1	CHKA	11	67833918	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	5269231	67833918	67172598	165	1456											
SERPINH1	871	hgsc.bcm.edu	37	chr11	75277624	75277624	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acccgtggtggtggcctcgtCgctagggctcgtgtcgctgg	2	10	17	12	5	0	0	0	0	0	0	4	0	0	0	2	5	0	3	2	5	1	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr11:75277624C>T	ENST00000524558.1	+	2	1665	c.230C>T	c.(229-231)tCg>tTg	p.S77L	SERPINH1_ENST00000530284.1_Missense_Mutation_p.S77L|SERPINH1_ENST00000525876.1_5'Flank|SERPINH1_ENST00000533603.1_Missense_Mutation_p.S77L|SERPINH1_ENST00000358171.3_Missense_Mutation_p.S77L			P50454	SERPH_HUMAN	serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, (collagen binding protein 1)	77					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)					GTGGCCTCGTCGCTAGGGCTC	0.706																																					p.S77L		Atlas-SNP	.											.	SERPINH1	33	.	0			c.C230T						PASS	.						45	32	36					11																	75277624		2197	4292	6489	SO:0001583	missense	871	exon2			CCTCGTCGCTAGG	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.230C>T	11.37:g.75277624C>T	ENSP00000434412:p.Ser77Leu	14	0	0		12	5	0.416667	NM_001235	B3KVJ3|P29043|Q5XPB4|Q6NSJ6|Q8IY96|Q9NP88	Missense_Mutation	SNP	ENST00000524558.1	37	CCDS8239.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.598021	0.87055	.	.	ENSG00000149257	ENST00000533603;ENST00000358171;ENST00000526242;ENST00000526397;ENST00000421448;ENST00000529643;ENST00000530284;ENST00000532356;ENST00000524558;ENST00000528990;ENST00000533449;ENST00000525611;ENST00000528760	D;D;D;D;D;D;D;D;D;D;D	0.84146	-1.81;-1.81;-1.81;-1.81;-1.81;-1.81;-1.81;-1.81;-1.81;-1.81;-1.81	5.28	5.28	0.74379	Serpin domain (3);	0.055957	0.64402	D	0.000001	D	0.91405	0.7288	M	0.73598	2.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.65010	0.931;0.931	D	0.92387	0.5918	10	0.87932	D	0	.	16.4242	0.83809	0.0:1.0:0.0:0.0	.	77;77	E9PPV6;P50454	.;SERPH_HUMAN	L	77;77;52;77;77;77;77;77;77;77;77;77;77	ENSP00000434657:S77L;ENSP00000350894:S77L;ENSP00000431384:S52L;ENSP00000434964:S77L;ENSP00000435936:S77L;ENSP00000436305:S77L;ENSP00000436040:S77L;ENSP00000434412:S77L;ENSP00000431827:S77L;ENSP00000435452:S77L;ENSP00000437108:S77L	ENSP00000350894:S77L	S	+	2	0	SERPINH1	74955272	1.000000	0.71417	0.874000	0.34290	0.562000	0.35680	7.731000	0.84895	2.470000	0.83445	0.563000	0.77884	TCG	.	.	none		0.706	SERPINH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383610.1	NM_004353		T	75277624	C	T	75277624	3	4	11	1	0	0	0	0	1	0	0	0	14132	893	31	1	232	1	SERPINH1	11	75277624	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	7443706	75277624	59728892	166	1457											
BIRC2	329	hgsc.bcm.edu	37	chr11	102248352	102248352	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggaacatgatattattaaaCaaaaaacacagataccttta	21	10	4	6	0	0	2	0	1	0	1	0	3	0	3	1	1	4	0	1	1	10	6			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr11:102248352C>G	ENST00000227758.2	+	7	2891	c.1492C>G	c.(1492-1494)Caa>Gaa	p.Q498E	BIRC2_ENST00000532672.1_Missense_Mutation_p.Q477E|BIRC2_ENST00000530675.1_Missense_Mutation_p.Q449E|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	498	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				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)		TATTATTAAACAAAAAACACA	0.338																																					p.Q498E		Atlas-SNP	.											.	BIRC2	51	.	0			c.C1492G						PASS	.						67	76	73					11																	102248352		2203	4296	6499	SO:0001583	missense	329	exon7			ATTAAACAAAAAA	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.1492C>G	11.37:g.102248352C>G	ENSP00000227758:p.Gln498Glu	77	0	0		75	25	0.333333	NM_001256163	B4E026|Q16516|Q4TTG0	Missense_Mutation	SNP	ENST00000227758.2	37	CCDS8316.1	.	.	.	.	.	.	.	.	.	.	C	17.33	3.361246	0.61403	.	.	ENSG00000110330	ENST00000530675;ENST00000533742;ENST00000227758;ENST00000541741;ENST00000532672;ENST00000531259	T;T;T;T;T	0.25414	1.8;1.8;1.8;1.8;1.8	5.83	5.83	0.93111	DEATH-like (2);Caspase Recruitment (3);	0.259553	0.46145	D	0.000306	T	0.33933	0.0880	L	0.46819	1.47	0.42351	D	0.992372	B	0.31931	0.347	B	0.40864	0.342	T	0.02829	-1.1105	10	0.30854	T	0.27	-21.752	20.1316	0.98000	0.0:1.0:0.0:0.0	.	498	Q13490	BIRC2_HUMAN	E	449;160;498;498;477;33	ENSP00000431723:Q449E;ENSP00000433851:Q160E;ENSP00000227758:Q498E;ENSP00000434979:Q477E;ENSP00000436741:Q33E	ENSP00000227758:Q498E	Q	+	1	0	BIRC2	101753562	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.898000	0.56281	2.766000	0.95052	0.650000	0.86243	CAA	.	.	none		0.338	BIRC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394170.1	NM_001166		G	102248352	C	G	102248352	3	3	11	1	0	0	0	0	1	0	0	0	1435	479	17	4	1514	4	BIRC2	11	102248352	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	26970728	102248352	32758164	167	1458											
ROBO3	64221	hgsc.bcm.edu	37	chr11	124740064	124740064	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcactaccactccatagagcGtccctcattcctgcgcagac	9	9	6	17	2	2	2	2	0	0	2	5	2	5	2	4	0	3	1	4	0	2	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr11:124740064G>T	ENST00000397801.1	+	5	962	c.770G>T	c.(769-771)cGt>cTt	p.R257L	ROBO3_ENST00000538940.1_Missense_Mutation_p.R235L	NM_022370.3	NP_071765.2	Q96MS0	ROBO3_HUMAN	roundabout, axon guidance receptor, homolog 3 (Drosophila)	257					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)		TCCATAGAGCGTCCCTCATTC	0.552																																					p.R257L		Atlas-SNP	.											ROBO3_ENST00000397801,NS,carcinoma,0,6	ROBO3	199	6	0			c.G770T						PASS	.						132	139	137					11																	124740064		2074	4209	6283	SO:0001583	missense	64221	exon5			TAGAGCGTCCCTC	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.770G>T	11.37:g.124740064G>T	ENSP00000380903:p.Arg257Leu	130	0	0		138	67	0.485507	NM_022370		Missense_Mutation	SNP	ENST00000397801.1	37	CCDS44755.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.323040	0.81580	.	.	ENSG00000154134	ENST00000397801;ENST00000538940	T;T	0.29655	1.56;1.56	4.96	4.02	0.46733	Immunoglobulin-like fold (1);	0.000000	0.33753	U	0.004590	T	0.49474	0.1559	L	0.49699	1.58	0.58432	D	0.999992	D	0.89917	1.0	D	0.91635	0.999	T	0.51076	-0.8751	10	0.59425	D	0.04	.	15.0	0.71464	0.0:0.1438:0.8562:0.0	.	257	Q96MS0	ROBO3_HUMAN	L	257;235	ENSP00000380903:R257L;ENSP00000441797:R235L	ENSP00000380903:R257L	R	+	2	0	ROBO3	124245274	1.000000	0.71417	0.990000	0.47175	0.935000	0.57460	9.608000	0.98331	1.173000	0.42796	0.462000	0.41574	CGT	.	.	none		0.552	ROBO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387091.1	XM_370663		T	124740064	G	T	124740064	3	4	11	1	0	0	0	0	1	0	0	0	13530	1145	40	4	788	4	ROBO3	11	124740064	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	22491712	124740064	10266452	168	1459											
PRDM10	56980	hgsc.bcm.edu	37	chr11	129801147	129801147	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcctttgtgggaaaatgtaGcaagtcctgaaatttgcaat	12	13	9	7	0	0	1	0	1	0	0	2	2	2	2	2	1	2	3	2	1	6	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr11:129801147G>A	ENST00000360871.3	-	11	1525	c.1294C>T	c.(1294-1296)Cta>Tta	p.L432L	PRDM10_ENST00000528746.1_Silent_p.L406L|PRDM10_ENST00000358825.5_Silent_p.L432L|PRDM10_ENST00000304538.6_Silent_p.L346L|PRDM10_ENST00000423662.2_Silent_p.L346L|PRDM10_ENST00000526082.1_Silent_p.L346L	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	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)|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)		GGAAAATGTAGCAAGTCCTGA	0.458																																					p.L432L		Atlas-SNP	.											.	PRDM10	120	.	0			c.C1294T						PASS	.						92	95	94					11																	129801147		2201	4297	6498	SO:0001819	synonymous_variant	56980	exon11			AATGTAGCAAGTC	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.1294C>T	11.37:g.129801147G>A		99	0	0		140	43	0.307143	NM_020228	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Silent	SNP	ENST00000360871.3	37	CCDS8484.1																																																																																			.	.	none		0.458	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437		A	129801147	G	A	129801147	2	1	11	1	0	0	0	0	0	0	0	1	12463	962	34	2		2	PRDM10	11	129801147	Silent	SNP	G	TCGA-FF-8042-01A-11D-2210-10	5061083	129801147	5205369	169	1460											
KCNA6	3742	hgsc.bcm.edu	37	chr12	4919954	4919957	+	Frame_Shift_Del	DEL	CTCA	CTCA	-																															atggggaccgggggctcctcCtcactcagtactcttggggg																										TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	CTCA	CTCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr12:4919954_4919957delCTCA	ENST00000280684.3	+	1	1613_1616	c.747_750delCTCA	c.(745-750)tcctcafs	p.SS249fs	RP11-234B24.4_ENST00000542988.1_lincRNA|KCNA6_ENST00000433855.1_Frame_Shift_Del_p.SS249fs			P17658	KCNA6_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 6	249					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)	GGGGCTCCTCCTCACTCAGTACTC	0.554										HNSCC(72;0.22)																											p.249_250del		Pindel,Atlas-Indel	.											.	KCNA6	122	.	0			c.746_749del						PASS	.																																			SO:0001589	frameshift_variant	3742	exon1			.	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.747_750delCTCA	12.37:g.4919958_4919961delCTCA	ENSP00000280684:p.Ser249fs	149	0	.		121	36	0.298	NM_002235		Frame_Shift_Del	DEL	ENST00000280684.3	37	CCDS8534.1																																																																																			.	.	none		0.554	KCNA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398909.1	NM_002235		-	4919957	CTCA	-	4919954	7	5	11	1	0	1	0	1	0	0	0	0	8016	668	24	0	749	0	KCNA6	12	4919954	Frame_Shift_Del	DEL	CTCA	TCGA-FF-8042-01A-11D-2210-10		4919954	128931941	170	1461											
CHD4	1108	hgsc.bcm.edu	37	chr12	6702746	6702746	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ccagttgatgatggtagaaaGaggggcgctcactaggaagg	12	7	16	6	1	1	4	1	2	0	2	1	5	1	5	1	5	0	3	1	5	4	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr12:6702746G>C	ENST00000357008.2	-	16	2513	c.2350C>G	c.(2350-2352)Ctt>Gtt	p.L784V	CHD4_ENST00000544484.1_Missense_Mutation_p.L781V|CHD4_ENST00000544040.1_Missense_Mutation_p.L777V|CHD4_ENST00000309577.6_Missense_Mutation_p.L784V	NM_001273.2	NP_001264.2	Q14839	CHD4_HUMAN	chromodomain helicase DNA binding protein 4	784	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				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						ATGGTAGAAAGAGGGGCGCTC	0.547																																					p.L784V	Colon(32;586 792 4568 16848 45314)	Atlas-SNP	.											.	CHD4	539	.	0			c.C2350G						PASS	.						83	82	82					12																	6702746		2203	4300	6503	SO:0001583	missense	1108	exon16			TAGAAAGAGGGGC	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.2350C>G	12.37:g.6702746G>C	ENSP00000349508:p.Leu784Val	88	0	0		77	25	0.324675	NM_001273	Q8IXZ5	Missense_Mutation	SNP	ENST00000357008.2	37	CCDS8552.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.938881	0.73557	.	.	ENSG00000111642	ENST00000544484;ENST00000544040;ENST00000309577;ENST00000357008;ENST00000537464	D;D;D;D	0.93906	-3.31;-3.31;-3.31;-3.31	4.8	4.8	0.61643	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.64402	D	0.000001	D	0.95645	0.8584	M	0.69248	2.105	0.80722	D	1	D;D;D	0.76494	0.999;0.995;0.996	D;D;D	0.79784	0.993;0.955;0.986	D	0.95649	0.8705	10	0.87932	D	0	-0.7394	12.4824	0.55852	0.0801:0.0:0.9199:0.0	.	784;784;777	Q14839-2;Q14839;F5GWX5	.;CHD4_HUMAN;.	V	781;777;784;784;758	ENSP00000440392:L781V;ENSP00000440542:L777V;ENSP00000312419:L784V;ENSP00000349508:L784V	ENSP00000312419:L784V	L	-	1	0	CHD4	6573007	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.793000	0.85851	2.493000	0.84123	0.591000	0.81541	CTT	.	.	none		0.547	CHD4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001273		C	6702746	G	C	6702746	3	2	11	1	0	0	0	0	1	0	0	0	3329	942	33	4	3488	4	CHD4	12	6702746	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	1782792	6702746	127149149	171	1462											
A2ML1	144568	hgsc.bcm.edu	37	chr12	9006740	9006740	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcaggtcacattaactttacTattagtacaaagattctgga	14	14	6	7	0	3	1	2	0	1	1	3	2	3	2	0	2	3	1	0	2	6	7			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr12:9006740T>C	ENST00000299698.7	+	21	2787	c.2607T>C	c.(2605-2607)acT>acC	p.T869T	A2ML1_ENST00000539547.1_Silent_p.T378T	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						TTAACTTTACTATTAGTACAA	0.478																																					p.T869T		Atlas-SNP	.											.	A2ML1	199	.	0			c.T2607C						PASS	.						56	57	57					12																	9006740		1862	4096	5958	SO:0001819	synonymous_variant	144568	exon21			CTTTACTATTAGT	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.2607T>C	12.37:g.9006740T>C		83	0	0		61	21	0.344262	NM_144670		Silent	SNP	ENST00000299698.7	37	CCDS8596.2																																																																																			.	.	none		0.478	A2ML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250304.3	NM_144670		C	9006740	T	C	9006740	2	2	11	1	0	0	0	0	0	0	0	1	5	1509	53	3		3	A2ML1	12	9006740	Silent	SNP	T	TCGA-FF-8042-01A-11D-2210-10	2303994	9006740	124845155	172	1463											
GRIN2B	2904	hgsc.bcm.edu	37	chr12	13716441	13716441	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttgcctgctttcttgcaaGcctcacaccggatgcacgcc	6	10	10	15	2	2	0	1	0	1	0	2	1	2	1	4	2	5	4	4	2	1	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr12:13716441G>A	ENST00000609686.1	-	13	3940	c.3731C>T	c.(3730-3732)gCt>gTt	p.A1244V		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	1244					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)	TTTCTTGCAAGCCTCACACCG	0.622																																					p.A1244V		Atlas-SNP	.											.	GRIN2B	303	.	0			c.C3731T						PASS	.						81	83	82					12																	13716441		2203	4300	6503	SO:0001583	missense	2904	exon13			TTGCAAGCCTCAC		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.3731C>T	12.37:g.13716441G>A	ENSP00000477455:p.Ala1244Val	75	0	0		64	20	0.3125	NM_000834	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Missense_Mutation	SNP	ENST00000609686.1	37	CCDS8662.1	.	.	.	.	.	.	.	.	.	.	G	11.80	1.746037	0.30955	.	.	ENSG00000150086	ENST00000279593	T	0.15952	2.38	4.97	4.97	0.65823	Glutamate [NMDA] receptor, epsilon subunit, C-terminal (1);	0.116103	0.56097	D	0.000021	T	0.14270	0.0345	L	0.27053	0.805	0.44168	D	0.996978	B	0.18461	0.028	B	0.27076	0.076	T	0.04178	-1.0971	10	0.51188	T	0.08	.	12.1704	0.54155	0.078:0.0:0.922:0.0	.	1244	Q13224	NMDE2_HUMAN	V	1244	ENSP00000279593:A1244V	ENSP00000279593:A1244V	A	-	2	0	GRIN2B	13607708	1.000000	0.71417	0.969000	0.41365	0.903000	0.53119	4.723000	0.61965	2.735000	0.93741	0.655000	0.94253	GCT	.	.	none		0.622	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2			A	13716441	G	A	13716441	3	1	11	1	0	0	0	0	1	0	0	0	6789	971	34	2	727	2	GRIN2B	12	13716441	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	4709701	13716441	120135454	173	1464											
OVCH1	341350	hgsc.bcm.edu	37	chr12	29604411	29604411	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctgaaactctgagcacccaAgaacattccagtcttcctct	11	10	6	14	0	3	3	0	2	3	1	5	3	5	3	3	0	3	2	3	0	3	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr12:29604411A>G	ENST00000318184.5	-	22	2621	c.2622T>C	c.(2620-2622)tcT>tcC	p.S874S	OVCH1-AS1_ENST00000551108.1_Intron|OVCH1-AS1_ENST00000549411.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	874	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)					TGAGCACCCAAGAACATTCCA	0.438																																					p.S874S		Atlas-SNP	.											.	OVCH1	195	.	0			c.T2622C						PASS	.						85	80	81					12																	29604411		1880	4105	5985	SO:0001819	synonymous_variant	341350	exon22			CACCCAAGAACAT	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.2622T>C	12.37:g.29604411A>G		154	0	0		121	33	0.272727	NM_183378		Silent	SNP	ENST00000318184.5	37																																																																																				.	.	none		0.438	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378		G	29604411	A	G	29604411	2	3	11	1	0	0	0	0	0	0	0	1	11332	59	3	3		3	OVCH1	12	29604411	Silent	SNP	A	TCGA-FF-8042-01A-11D-2210-10	15887970	29604411	104247484	174	1465											
ALG10	84920	hgsc.bcm.edu	37	chr12	34179242	34179242	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgcttttgtagtagttaatGgtggaattgttattggcgat	8	18	13	2	1	0	0	0	0	0	0	0	2	0	1	0	3	1	5	0	3	5	8			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr12:34179242G>A	ENST00000266483.2	+	3	1133	c.814G>A	c.(814-816)Ggt>Agt	p.G272S	ALG10_ENST00000538927.1_Intron|AC046130.1_ENST00000401300.2_RNA|RP11-847H18.2_ENST00000501954.2_RNA	NM_032834.3	NP_116223.3	Q5BKT4	AG10A_HUMAN	ALG10, alpha-1,2-glucosyltransferase	272					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)	transferase activity, transferring hexosyl groups (GO:0016758)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	26	Lung NSC(5;3.82e-05)|Acute lymphoblastic leukemia(23;0.0142)|all_hematologic(23;0.0429)	Lung NSC(34;0.204)|all_lung(34;0.235)				AGTAGTTAATGGTGGAATTGT	0.373																																					p.G272S		Atlas-SNP	.											.	ALG10	53	.	0			c.G814A						PASS	.						174	180	178					12																	34179242		2203	4297	6500	SO:0001583	missense	84920	exon3			GTTAATGGTGGAA	AJ312278	CCDS41769.1	12p11.21	2013-03-04	2013-03-04		ENSG00000139133	ENSG00000139133	2.4.1.256		23162	protein-coding gene	gene with protein product	"derepression of ITR1 expression 2 homolog (S. cerevisiae)", "dolichyl-P-Glc:Glc(2)Man(9)GlcNAc(2)-PP-dolichol alpha-1,2- glucosyltransferase"	603313	"asparagine-linked glycosylation 10, alpha-1,2-glucosyltransferase homolog (yeast)", "asparagine-linked glycosylation 10, alpha-1,2-glucosyltransferase homolog (S. pombe)"				Standard	NM_032834		Approved	FLJ14751, DIE2, ALG10A	uc001rlm.3	Q5BKT4	OTTHUMG00000169285	ENST00000266483.2:c.814G>A	12.37:g.34179242G>A	ENSP00000266483:p.Gly272Ser	343	0	0		292	111	0.380137	NM_032834	Q6NS98|Q96DU0|Q96SM6	Missense_Mutation	SNP	ENST00000266483.2	37	CCDS41769.1	.	.	.	.	.	.	.	.	.	.	G	17.05	3.288670	0.59976	.	.	ENSG00000139133	ENST00000266483	T	0.56611	0.45	3.37	2.46	0.29980	.	0.194989	0.53938	N	0.000042	T	0.66218	0.2767	M	0.91038	3.17	0.80722	D	1	D	0.54964	0.969	P	0.51487	0.671	T	0.69647	-0.5089	10	0.66056	D	0.02	.	8.4466	0.32845	0.1241:0.0:0.8759:0.0	.	272	Q5BKT4	AG10A_HUMAN	S	272	ENSP00000266483:G272S	ENSP00000266483:G272S	G	+	1	0	ALG10	34070509	1.000000	0.71417	0.030000	0.17652	0.829000	0.46940	4.077000	0.57598	0.537000	0.28751	0.184000	0.17185	GGT	.	.	none		0.373	ALG10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403309.1	NM_032834		A	34179242	G	A	34179242	3	1	11	1	0	0	0	0	1	0	0	0	511	1348	47	2	824	2	ALG10	12	34179242	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	4574831	34179242	99672653	175	1466											
MLL2	8085	hgsc.bcm.edu	37	chr12	49415920	49415920	+	Missense_Mutation	SNP	G	G	T																															ccacacagttaggggcacagGaatggttaatgtacctgggc																										TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr12:49415920G>T	ENST00000301067.7	-	53	16426	c.16427C>A	c.(16426-16428)tCc>tAc	p.S5476Y	RP11-386G11.5_ENST00000552933.1_RNA|PRKAG1_ENST00000548065.1_5'Flank|RP11-386G11.5_ENST00000547866.1_RNA	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	5476	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				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)										AGGGGCACAGGAATGGTTAAT	0.507																																					p.S5476Y		Atlas-SNP	.											.	MLL2	1173	.	0			c.C16427A						PASS	.						159	154	156					12																	49415920		2066	4208	6274	SO:0001583	missense	8085	exon53			GCACAGGAATGGT	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.16427C>A	12.37:g.49415920G>T	ENSP00000301067:p.Ser5476Tyr	81	0	0		49	16	0.326531	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	g	15.78	2.935624	0.52972	.	.	ENSG00000167548	ENST00000301067;ENST00000526209	D;D	0.94184	-3.37;-3.37	4.97	4.97	0.65823	SET domain (3);	0.000000	0.35207	N	0.003365	D	0.98400	0.9468	H	0.99535	4.615	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99782	1.1028	10	0.87932	D	0	.	17.4382	0.87558	0.0:0.0:1.0:0.0	.	5476	O14686	MLL2_HUMAN	Y	5476;157	ENSP00000301067:S5476Y;ENSP00000435714:S157Y	ENSP00000301067:S5476Y	S	-	2	0	MLL2	47702187	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.753000	0.98904	2.492000	0.84095	0.550000	0.68814	TCC	.	.	none		0.507	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			T	49415920	G	T	49415920	3	4	11	1	0	0	0	0	1	0	0	0	9630	1174	41	4	194	4	MLL2	12	49415920	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	15236678	49415920	84435975	176	1467	20	2									
MLL2	8085	hgsc.bcm.edu	37	chr12	49415922	49415922	+	Missense_Mutation	SNP	A	A	T																															acacagttaggggcacaggaAtggttaatgtacctgggcag																										TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr12:49415922A>T	ENST00000301067.7	-	53	16424	c.16425T>A	c.(16423-16425)caT>caA	p.H5475Q	RP11-386G11.5_ENST00000552933.1_RNA|PRKAG1_ENST00000548065.1_5'Flank|RP11-386G11.5_ENST00000547866.1_RNA	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	5475	S-adenosyl-L-methionine binding. {ECO:0000250}.|SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				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)										GGGCACAGGAATGGTTAATGT	0.507																																					p.H5475Q		Atlas-SNP	.											.	MLL2	1173	.	0			c.T16425A						PASS	.						159	154	156					12																	49415922		2065	4208	6273	SO:0001583	missense	8085	exon53			ACAGGAATGGTTA	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.16425T>A	12.37:g.49415922A>T	ENSP00000301067:p.His5475Gln	76	0	0		47	16	0.340426	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	a	12.42	1.932692	0.34096	.	.	ENSG00000167548	ENST00000301067;ENST00000526209	D;D	0.99503	-6.03;-6.03	4.97	2.62	0.31277	SET domain (3);	0.000000	0.36740	N	0.002439	D	0.99704	0.9887	H	0.99732	4.735	0.47476	D	0.999434	D	0.89917	1.0	D	0.91635	0.999	D	0.97764	1.0222	10	0.87932	D	0	.	6.8531	0.24026	0.7287:0.0:0.2713:0.0	.	5475	O14686	MLL2_HUMAN	Q	5475;156	ENSP00000301067:H5475Q;ENSP00000435714:H156Q	ENSP00000301067:H5475Q	H	-	3	2	MLL2	47702189	0.942000	0.31987	1.000000	0.80357	0.995000	0.86356	0.105000	0.15333	0.877000	0.35895	0.450000	0.29827	CAT	.	.	none		0.507	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			T	49415922	A	T	49415922	3	4	11	1	0	0	0	0	1	0	0	0	9630	98	4	5	196	5	MLL2	12	49415922	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	2	49415922	84435973	177	1468	20	2									
MLL2	8085	hgsc.bcm.edu	37	chr12	49441815	49441816	+	Frame_Shift_Ins	INS	-	-	C																															ggcaaggaggtggccctctgINSccccccggccaaagctgcca																										TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr12:49441815_49441816insC	ENST00000301067.7	-	14	4167_4168	c.4168_4169insG	c.(4168-4170)gcafs	p.A1390fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1390					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)										GTGGCCCTCTGCCCCCCGGCCA	0.564																																					p.A1390fs		Pindel,Atlas-Indel	.											.	MLL2	1173	.	0			c.4169_4170insG						PASS	.																																			SO:0001589	frameshift_variant	8085	exon14			.	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.4169dupG	12.37:g.49441821_49441821dupC	ENSP00000301067:p.Ala1390fs	67	0	.		55	17	0.309	NM_003482	O14687	Frame_Shift_Ins	INS	ENST00000301067.7	37	CCDS44873.1																																																																																			.	.	none		0.564	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			C	49441816	-	C	49441815	7	5	11	1	0	1	1	0	0	0	0	0	9630	1319	46	0	12608	0	MLL2	12	49441815	Frame_Shift_Ins	INS	-	TCGA-FF-8042-01A-11D-2210-10	25893	49441815	84410080	178	1469											
TMPRSS12	283471	hgsc.bcm.edu	37	chr12	51237782	51237782	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggaaccctagtgagagagagGtgggtcctcacagctgccca	10	6	14	11	0	1	2	1	1	0	2	2	5	2	3	3	3	3	1	3	3	2	1	rs374807523		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr12:51237782G>A	ENST00000398458.3	+	2	377	c.345G>A	c.(343-345)agG>agA	p.R115R	TMPRSS12_ENST00000551456.1_Silent_p.R115R|RN7SL519P_ENST00000497925.2_RNA	NM_182559.2	NP_872365	Q86WS5	TMPSC_HUMAN	transmembrane (C-terminal) protease, serine 12	115	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					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						TGAGAGAGAGGTGGGTCCTCA	0.498																																					p.R115R		Atlas-SNP	.											.	TMPRSS12	33	.	0			c.G345A						PASS	.	G		0,4136		0,0,2068	49	51	51		345	-2	0.2	12		51	2,8434		0,2,4216	no	coding-synonymous	TMPRSS12	NM_182559.2		0,2,6284	AA,AG,GG		0.0237,0.0,0.0159		115/349	51237782	2,12570	2068	4218	6286	SO:0001819	synonymous_variant	283471	exon2			AGAGAGGTGGGTC	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.345G>A	12.37:g.51237782G>A		111	0	0		90	40	0.444444	NM_182559	B9ZVX2	Silent	SNP	ENST00000398458.3	37	CCDS44881.1																																																																																			.	.	weak		0.498	TMPRSS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404289.1	NM_182559		A	51237782	G	A	51237782	2	1	11	1	0	0	0	0	0	0	0	1	16259	1252	44	2		2	TMPRSS12	12	51237782	Silent	SNP	G	TCGA-FF-8042-01A-11D-2210-10	1795967	51237782	82614113	179	1470											
ANKRD33	341405	hgsc.bcm.edu	37	chr12	52284881	52284881	+	Intron	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggcatattgagcaagtgccTtcagtggctacaacccaggg	10	8	13	10	0	1	1	1	1	0	0	1	1	1	1	2	3	4	3	2	3	4	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr12:52284881T>C	ENST00000340970.4	+	6	1035				ANKRD33_ENST00000547119.1_3'UTR|ANKRD33_ENST00000538991.1_Intron|ANKRD33_ENST00000301190.6_Missense_Mutation_p.L384P			Q7Z3H0	ANR33_HUMAN	ankyrin repeat domain 33						negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|skeletal muscle cell differentiation (GO:0035914)	cytosol (GO:0005829)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	22				BRCA - Breast invasive adenocarcinoma(357;0.0969)		AGCAAGTGCCTTCAGTGGCTA	0.647																																					p.L384P		Atlas-SNP	.											.	ANKRD33	33	.	0			c.T1151C						PASS	.						62	54	57					12																	52284881		2203	4300	6503	SO:0001627	intron_variant	341405	exon5			AGTGCCTTCAGTG		CCDS8815.1, CCDS44892.1	12q13.13	2013-01-10	2005-01-07	2005-01-07		ENSG00000167612		"Ankyrin repeat domain containing"	13788	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 7"	C12orf7		20026326	Standard	NM_182608		Approved	DKFZp686O1689, PANKY	uc001rzd.3	Q7Z3H0	OTTHUMG00000169506	ENST00000340970.4:c.665-89T>C	12.37:g.52284881T>C		100	0	0		118	6	0.0508475	NM_182608	Q0VAA7|Q5K619|Q5K621|Q5K622|Q5K623|Q5K624|Q6ZUN0	Missense_Mutation	SNP	ENST00000340970.4	37	CCDS44892.1	.	.	.	.	.	.	.	.	.	.	T	2.706	-0.269834	0.05716	.	.	ENSG00000167612	ENST00000301190	T	0.24908	1.83	4.48	2.53	0.30540	.	0.645195	0.15887	N	0.239728	T	0.13756	0.0333	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22521	-1.0214	9	0.26408	T	0.33	.	4.1627	0.10291	0.184:0.6209:0.0:0.1951	.	384	Q7Z3H0-2	.	P	384	ENSP00000301190:L384P	ENSP00000301190:L384P	L	+	2	0	ANKRD33	50571148	0.246000	0.23909	0.912000	0.35992	0.589000	0.36550	1.831000	0.39141	0.606000	0.29965	-0.337000	0.08149	CTT	.	.	none		0.647	ANKRD33-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404515.1	NM_182608		C	52284881	T	C	52284881	1	2	11	0	1	0	0	0	0	0	0	0	661	1609	56	3		3	ANKRD33	12	52284881	Intron	SNP	T	TCGA-FF-8042-01A-11D-2210-10	1047099	52284881	81567014	180	1471											
SLC35E3	55508	hgsc.bcm.edu	37	chr12	69140524	69140524	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatccagaccttctgctacCagaaaaccttctccaccaga	12	8	4	17	0	2	3	0	0	2	3	4	3	3	3	7	0	3	1	7	0	3	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr12:69140524C>T	ENST00000398004.2	+	1	639	c.367C>T	c.(367-369)Cag>Tag	p.Q123*		NM_018656.2	NP_061126.2	Q7Z769	S35E3_HUMAN	solute carrier family 35, member E3	123						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)			CTTCTGCTACCAGAAAACCTT	0.572																																					p.Q123X		Atlas-SNP	.											.	SLC35E3	23	.	0			c.C367T						PASS	.						109	115	114					12																	69140524		1955	4154	6109	SO:0001587	stop_gained	55508	exon1			TGCTACCAGAAAA	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.367C>T	12.37:g.69140524C>T	ENSP00000381089:p.Gln123*	92	0	0		86	4	0.0465116	NM_018656	A8K0T0|Q0P5Y5|Q9P0V1	Nonsense_Mutation	SNP	ENST00000398004.2	37	CCDS41808.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.615301	0.87359	.	.	ENSG00000175782	ENST00000398004	.	.	.	4.84	-4.92	0.03075	.	0.978663	0.08427	N	0.947515	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-19.4926	11.8581	0.52451	0.1162:0.3976:0.4862:0.0	.	.	.	.	X	123	.	.	Q	+	1	0	SLC35E3	67426791	1.000000	0.71417	0.374000	0.26016	0.191000	0.23601	1.223000	0.32527	-0.906000	0.03866	-0.274000	0.10170	CAG	.	.	none		0.572	SLC35E3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403241.1	NM_018656		T	69140524	C	T	69140524	4	4	11	1	0	0	0	0	0	1	0	0	14601	595	21	2	369	2	SLC35E3	12	69140524	Nonsense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	16855643	69140524	64711371	181	1472											
MYF6	4618	hgsc.bcm.edu	37	chr12	81101689	81101689	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggagaggaacatgtcctggCgcccccgggcctgcagcctc	6	5	14	16	3	0	1	0	0	0	1	2	3	1	2	5	4	3	1	5	4	1	0			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr12:81101689C>T	ENST00000228641.3	+	1	413	c.191C>T	c.(190-192)gCg>gTg	p.A64V		NM_002469.2	NP_002460.1	P23409	MYF6_HUMAN	myogenic factor 6 (herculin)	64					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)	p.A64V(1)		central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(12)|skin(1)	26						CATGTCCTGGCGCCCCCGGGC	0.632																																					p.A64V		Atlas-SNP	.											MYF6,NS,carcinoma,0,1	MYF6	74	1	1	Substitution - Missense(1)	endometrium(1)	c.C191T						PASS	.						36	42	40					12																	81101689		2203	4300	6503	SO:0001583	missense	4618	exon1			TCCTGGCGCCCCC		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.191C>T	12.37:g.81101689C>T	ENSP00000228641:p.Ala64Val	67	0	0		58	25	0.431034	NM_002469	B2R898|Q53X80|Q6FHI9	Missense_Mutation	SNP	ENST00000228641.3	37	CCDS9019.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.653792	0.88056	.	.	ENSG00000111046	ENST00000228641	T	0.80909	-1.43	5.62	5.62	0.85841	Myogenic basic muscle-specific protein (2);	0.000000	0.85682	D	0.000000	D	0.87904	0.6295	L	0.53671	1.685	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	D	0.86881	0.2042	10	0.46703	T	0.11	.	19.6517	0.95819	0.0:1.0:0.0:0.0	.	64	P23409	MYF6_HUMAN	V	64	ENSP00000228641:A64V	ENSP00000228641:A64V	A	+	2	0	MYF6	79625820	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.487000	0.81328	2.662000	0.90505	0.655000	0.94253	GCG	.	.	none		0.632	MYF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407756.1	NM_002469		T	81101689	C	T	81101689	3	4	11	1	0	0	0	0	1	0	0	0	10037	768	27	1	193	1	MYF6	12	81101689	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	11961165	81101689	52750206	182	1473											
SYCP3	50511	hgsc.bcm.edu	37	chr12	102131710	102131710	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	atacttttttccggaggacaCcatatttagatgcttcctga	10	15	7	9	1	0	2	0	1	0	1	2	4	2	4	3	2	2	1	3	2	3	8			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr12:102131710C>T	ENST00000392927.3	-	2	135	c.4G>A	c.(4-6)Gtg>Atg	p.V2M	SYCP3_ENST00000392924.1_Missense_Mutation_p.V2M|SYCP3_ENST00000266743.2_Missense_Mutation_p.V2M	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	2					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						CCGGAGGACACCATATTTAGA	0.353																																					p.V2M		Atlas-SNP	.											.	SYCP3	19	.	0			c.G4A						PASS	.						142	143	143					12																	102131710		2203	4300	6503	SO:0001583	missense	50511	exon2			AGGACACCATATT	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.4G>A	12.37:g.102131710C>T	ENSP00000376658:p.Val2Met	99	0	0		70	4	0.0571429	NM_001177949		Missense_Mutation	SNP	ENST00000392927.3	37	CCDS9087.1	.	.	.	.	.	.	.	.	.	.	C	14.62	2.589299	0.46214	.	.	ENSG00000139351	ENST00000266743;ENST00000392927;ENST00000392924	.	.	.	5.23	3.36	0.38483	.	0.992267	0.08182	N	0.985316	T	0.36054	0.0953	L	0.46157	1.445	0.29107	N	0.881125	B	0.32653	0.379	B	0.28305	0.088	T	0.25293	-1.0136	9	0.36615	T	0.2	-46.7494	10.1367	0.42710	0.0:0.7867:0.1387:0.0746	.	2	Q8IZU3	SYCP3_HUMAN	M	2	.	ENSP00000266743:V2M	V	-	1	0	SYCP3	100655841	1.000000	0.71417	0.175000	0.22980	0.193000	0.23685	1.638000	0.37165	1.170000	0.42753	0.655000	0.94253	GTG	.	.	none		0.353	SYCP3-001	KNOWN	alternative_5_UTR|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316478.2	NM_153694		T	102131710	C	T	102131710	3	4	11	1	0	0	0	0	1	0	0	0	15449	507	18	2	738	2	SYCP3	12	102131710	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	21030021	102131710	31720185	183	1474											
CHST11	50515	hgsc.bcm.edu	37	chr12	105150950	105150950	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtcctgaccgggcgggggaAgtacagcgaccccatggaga	9	4	17	11	3	0	2	0	1	0	1	1	5	1	3	4	5	2	1	4	5	2	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr12:105150950A>C	ENST00000303694.5	+	3	867	c.428A>C	c.(427-429)aAg>aCg	p.K143T	CHST11_ENST00000549260.1_Missense_Mutation_p.K138T	NM_018413.5	NP_060883.1	Q9NPF2	CHSTB_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 11	143					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						GGGCGGGGGAAGTACAGCGAC	0.602																																					p.K143T		Atlas-SNP	.											.	CHST11	54	.	0			c.A428C						PASS	.						69	69	69					12																	105150950		2203	4300	6503	SO:0001583	missense	50515	exon3			GGGGGAAGTACAG	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.428A>C	12.37:g.105150950A>C	ENSP00000305725:p.Lys143Thr	135	0	0		154	64	0.415584	NM_018413	A8K4F8|Q9NXY6|Q9NY36	Missense_Mutation	SNP	ENST00000303694.5	37	CCDS9099.1	.	.	.	.	.	.	.	.	.	.	A	14.73	2.623524	0.46840	.	.	ENSG00000171310	ENST00000549260;ENST00000303694;ENST00000549016	T;T;T	0.73363	-0.74;-0.74;-0.74	5.42	5.42	0.78866	.	0.089513	0.85682	D	0.000000	T	0.66645	0.2810	L	0.33485	1.01	0.80722	D	1	P;P	0.43169	0.762;0.8	B;B	0.41988	0.255;0.372	T	0.65529	-0.6146	10	0.27785	T	0.31	-8.0608	15.4614	0.75359	1.0:0.0:0.0:0.0	.	138;143	Q9NPF2-2;Q9NPF2	.;CHSTB_HUMAN	T	138;143;103	ENSP00000450004:K138T;ENSP00000305725:K143T;ENSP00000449095:K103T	ENSP00000305725:K143T	K	+	2	0	CHST11	103675080	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.355000	0.79434	2.065000	0.61736	0.533000	0.62120	AAG	.	.	none		0.602	CHST11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000405960.2	NM_018413		C	105150950	A	C	105150950	3	2	11	1	0	0	0	0	1	0	0	0	3401	72	3	5	438	5	CHST11	12	105150950	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	3019240	105150950	28700945	184	1475											
C12orf52	84934	hgsc.bcm.edu	37	chr12	113629195	113629195	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgccagcttcggggccccgcGgatggcgaagggggatgccg	5	4	19	13	6	0	0	0	0	0	0	1	3	0	2	4	6	2	1	4	6	1	1	rs368110690	byFrequency	TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr12:113629195G>A	ENST00000548278.1	+	4	1075	c.383G>A	c.(382-384)cGg>cAg	p.R128Q	RP11-545P7.4_ENST00000552525.1_RNA|C12orf52_ENST00000552495.1_Missense_Mutation_p.R152Q|C12orf52_ENST00000549621.1_Missense_Mutation_p.R128Q	NM_032848.1	NP_116237.1	Q96K30	RITA1_HUMAN		128	Interaction with RBPJ/RBPSUH.				negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurogenesis (GO:0022008)|Notch signaling pathway (GO:0007219)|nuclear export (GO:0051168)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	tubulin binding (GO:0015631)	p.R128Q(1)		large_intestine(2)|lung(1)|prostate(1)|urinary_tract(1)	5						GGGGCCCCGCGGATGGCGAAG	0.642													G|||	4	0.000798722	0.0	0.0	5008	,	,		14839	0.0		0.0	False		,,,				2504	0.0041				p.R128Q		Atlas-SNP	.											C12orf52,colon,carcinoma,0,1	C12orf52	19	1	1	Substitution - Missense(1)	large_intestine(1)	c.G383A						PASS	.	G	GLN/ARG	0,4406		0,0,2203	27	30	29		383	3.7	0	12		29	1,8599	1.2+/-3.3	0,1,4299	no	missense	C12orf52	NM_032848.1	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	128/270	113629195	1,13005	2203	4300	6503	SO:0001583	missense	84934	exon4			CCCCGCGGATGGC																												ENST00000548278.1:c.383G>A	12.37:g.113629195G>A	ENSP00000449841:p.Arg128Gln	50	0	0		51	16	0.313726	NM_032848	B3KVZ4|C9JIN1|F8VRG5|Q53GM3|Q96K25	Missense_Mutation	SNP	ENST00000548278.1	37	CCDS9166.1	.	.	.	.	.	.	.	.	.	.	G	5.660	0.306471	0.10733	0.0	1.16E-4	ENSG00000139405	ENST00000549621;ENST00000548278;ENST00000552495;ENST00000436053;ENST00000299731;ENST00000266813	T;T;T	0.32988	1.45;1.45;1.43	4.6	3.71	0.42584	.	0.364168	0.23708	N	0.045345	T	0.12603	0.0306	N	0.12182	0.205	0.09310	N	1	D;P;D	0.55800	0.973;0.951;0.973	B;B;B	0.35278	0.199;0.199;0.199	T	0.10776	-1.0615	10	0.26408	T	0.33	-2.164	8.434	0.32775	0.1057:0.0:0.8943:0.0	.	128;152;128	Q96K30-2;F8VRG5;Q96K30	.;.;RITA_HUMAN	Q	128;128;152;128;128;125	ENSP00000448289:R128Q;ENSP00000449841:R128Q;ENSP00000448680:R152Q	ENSP00000266813:R125Q	R	+	2	0	C12orf52	112113578	0.993000	0.37304	0.023000	0.16930	0.004000	0.04260	2.374000	0.44274	1.151000	0.42436	-0.136000	0.14681	CGG	.	.	weak		0.642	C12orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405239.1			A	113629195	G	A	113629195	3	1	11	1	0	0	0	0	1	0	0	0	1699	1116	39	1	389	1	C12orf52	12	113629195	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	8478245	113629195	20222700	185	1476											
ARL6IP4	23457	hgsc.bcm.edu	37	chr12	123465786	123465786	+	5'UTR	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagcaggaaagacacctcgAggaactgctcggcctccaca	13	4	11	13	2	0	2	0	0	0	2	3	5	1	4	3	3	3	2	3	3	2	0			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr12:123465786A>G	ENST00000542678.1	-	0	410				ARL6IP4_ENST00000426960.2_Missense_Mutation_p.R34G|ARL6IP4_ENST00000412505.2_Missense_Mutation_p.R34G|ARL6IP4_ENST00000439686.2_Missense_Mutation_p.R34G|RP11-197N18.2_ENST00000540866.2_RNA|ARL6IP4_ENST00000454885.2_Missense_Mutation_p.R34G|ARL6IP4_ENST00000453766.2_Missense_Mutation_p.R157G|ARL6IP4_ENST00000357866.4_Missense_Mutation_p.R34G|ARL6IP4_ENST00000392435.2_Missense_Mutation_p.R157G|ARL6IP4_ENST00000315580.5_Missense_Mutation_p.R157G|ARL6IP4_ENST00000543566.1_Missense_Mutation_p.R157G			Q9NP78	ABCB9_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 9						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)		AGACACCTCGAGGAACTGCTC	0.657																																					p.R157G	Ovarian(49;786 1333 9175 38236)	Atlas-SNP	.											ARL6IP4,NS,carcinoma,-2,1	ARL6IP4	14	1	0			c.A469G						PASS	.						48	42	44					12																	123465786		1879	3582	5461	SO:0001623	5_prime_UTR_variant	51329	exon2			ACCTCGAGGAACT	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.-2429T>C	12.37:g.123465786A>G		165	0	0		139	45	0.323741	NM_018694	B4E2J0|Q5W9G7|Q769F3|Q769F4|Q96AB1|Q9P208	Missense_Mutation	SNP	ENST00000542678.1	37	CCDS9241.1	.	.	.	.	.	.	.	.	.	.	A	13.98	2.397855	0.42512	.	.	ENSG00000182196	ENST00000544323;ENST00000543566;ENST00000315580;ENST00000542099;ENST00000392435;ENST00000413381;ENST00000426960;ENST00000453766;ENST00000454885;ENST00000412505;ENST00000439686;ENST00000456762;ENST00000357866	T;T;T;T;T;T;T;T;T;T;T;T;T	0.55052	1.13;0.54;0.54;0.54;0.54;0.54;0.54;0.54;0.54;0.73;0.54;0.54;0.76	4.73	-2.5	0.06384	.	1.340920	0.05558	N	0.568681	T	0.47820	0.1466	M	0.66939	2.045	0.09310	N	1	B;B;B;B;B;B	0.09022	0.0;0.0;0.002;0.002;0.002;0.002	B;B;B;B;B;B	0.12156	0.001;0.001;0.006;0.007;0.007;0.004	T	0.47749	-0.9093	10	0.56958	D	0.05	.	5.3709	0.16138	0.3465:0.3857:0.2678:0.0	.	34;157;157;157;157;157	B3V0L1;Q66PJ3-5;Q66PJ3-4;B3V0L0;Q66PJ3;Q66PJ3-2	.;.;.;.;AR6P4_HUMAN;.	G	157;157;157;157;157;34;34;157;34;34;34;35;34	ENSP00000445309:R157G;ENSP00000442718:R157G;ENSP00000313422:R157G;ENSP00000442200:R157G;ENSP00000376230:R157G;ENSP00000441406:R34G;ENSP00000406036:R34G;ENSP00000414847:R157G;ENSP00000396723:R34G;ENSP00000413132:R34G;ENSP00000396365:R34G;ENSP00000391598:R35G;ENSP00000350532:R34G	ENSP00000313422:R157G	R	+	1	2	ARL6IP4	122031739	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	0.197000	0.17197	-0.238000	0.09724	0.444000	0.29173	AGG	.	.	none		0.657	ABCB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400956.1	NM_019624		G	123465786	A	G	123465786	1	3	11	0	1	0	0	0	0	0	0	0	943	295	11	3		3	ARL6IP4	12	123465786	5'UTR	SNP	A	TCGA-FF-8042-01A-11D-2210-10	9836591	123465786	10386109	186	1477											
RIMBP2	23504	hgsc.bcm.edu	37	chr12	130926675	130926675	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	caggtgggagggggccaccaCcacgtccttgcccaccagca	8	4	13	16	1	0	0	0	0	0	0	1	1	1	1	6	4	2	1	6	4	0	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr12:130926675C>T	ENST00000261655.4	-	8	1334	c.1171G>A	c.(1171-1173)Gtg>Atg	p.V391M	RIMBP2_ENST00000536002.1_Missense_Mutation_p.V299M|RIMBP2_ENST00000535703.1_Missense_Mutation_p.V299M	NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	391					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)		GGGGCCACCACCACGTCCTTG	0.637																																					p.V391M		Atlas-SNP	.											RIMBP2,colon,carcinoma,+2,1	RIMBP2	220	1	0			c.G1171A						PASS	.						106	89	94					12																	130926675		2203	4300	6503	SO:0001583	missense	23504	exon8			CCACCACCACGTC	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.1171G>A	12.37:g.130926675C>T	ENSP00000261655:p.Val391Met	157	0	0		127	52	0.409449	NM_015347	Q96ID2	Missense_Mutation	SNP	ENST00000261655.4	37	CCDS31925.1	.	.	.	.	.	.	.	.	.	.	c	15.13	2.743213	0.49151	.	.	ENSG00000060709	ENST00000261655;ENST00000392375;ENST00000535703;ENST00000536002	T;T;T	0.54071	0.59;0.59;0.59	4.23	3.18	0.36537	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.305389	0.30483	N	0.009533	T	0.53174	0.1780	L	0.57536	1.79	0.33880	D	0.636045	P;P;P	0.43477	0.664;0.745;0.808	B;P;B	0.51516	0.388;0.672;0.391	T	0.61118	-0.7127	10	0.30078	T	0.28	-23.0745	5.5813	0.17250	0.0:0.6862:0.0:0.3138	.	299;299;391	C9JWN3;O15034-2;O15034	.;.;RIMB2_HUMAN	M	391;299;299;299	ENSP00000261655:V391M;ENSP00000440347:V299M;ENSP00000439159:V299M	ENSP00000261655:V391M	V	-	1	0	RIMBP2	129492628	0.998000	0.40836	1.000000	0.80357	0.991000	0.79684	3.020000	0.49643	1.867000	0.54127	0.537000	0.68136	GTG	.	.	none		0.637	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347		T	130926675	C	T	130926675	3	4	11	1	0	0	0	0	1	0	0	0	13378	507	18	2	2035	2	RIMBP2	12	130926675	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	7460889	130926675	2925220	187	1478											
SACS	26278	hgsc.bcm.edu	37	chr13	23908805	23908805	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcagtttcatcacagttataAaccaagttgaaaccaatttc	15	12	5	9	0	2	1	2	1	0	0	3	1	2	1	2	0	2	4	2	0	6	5			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr13:23908805A>G	ENST00000382292.3	-	9	9483	c.9210T>C	c.(9208-9210)gtT>gtC	p.V3070V	SACS_ENST00000402364.1_Silent_p.V2320V|SACS_ENST00000382298.3_Silent_p.V3070V			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3070					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)		CACAGTTATAAACCAAGTTGA	0.343																																					p.V3070V		Atlas-SNP	.											.	SACS	871	.	0			c.T9210C						PASS	.						97	91	93					13																	23908805		2203	4300	6503	SO:0001819	synonymous_variant	26278	exon10			GTTATAAACCAAG	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.9210T>C	13.37:g.23908805A>G		125	0	0		117	46	0.393162	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2																																																																																			.	.	none		0.343	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		G	23908805	A	G	23908805	2	3	11	1	0	0	0	0	0	0	0	1	13819	1	1	3		3	SACS	13	23908805	Silent	SNP	A	TCGA-FF-8042-01A-11D-2210-10		23908805	91261073	188	1479											
MIPEP	4285	hgsc.bcm.edu	37	chr13	24436455	24436455	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acttacggaattttgaggatTcagtttcattttcatccctc	9	17	6	9	1	3	1	3	1	0	0	5	3	4	3	1	2	1	1	1	2	2	7			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr13:24436455T>C	ENST00000382172.3	-	9	1137	c.1039A>G	c.(1039-1041)Aat>Gat	p.N347D		NM_005932.3	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase	347					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)		TTTTGAGGATTCAGTTTCATT	0.279																																					p.N347D		Atlas-SNP	.											.	MIPEP	53	.	0			c.A1039G						PASS	.						47	43	44					13																	24436455		2196	4289	6485	SO:0001583	missense	4285	exon9			GAGGATTCAGTTT		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.1039A>G	13.37:g.24436455T>C	ENSP00000371607:p.Asn347Asp	212	0	0		133	48	0.360902	NM_005932	Q5JV15|Q5T9Q9|Q96G65	Missense_Mutation	SNP	ENST00000382172.3	37	CCDS9303.1	.	.	.	.	.	.	.	.	.	.	T	19.34	3.808264	0.70797	.	.	ENSG00000027001	ENST00000382172	T	0.07908	3.15	4.79	4.79	0.61399	Neurolysin/Thimet oligopeptidase, domain 2 (1);	0.000000	0.85682	D	0.000000	T	0.18002	0.0432	M	0.67953	2.075	0.45747	D	0.998648	P	0.42296	0.775	P	0.48873	0.593	T	0.00670	-1.1617	10	0.42905	T	0.14	.	14.4368	0.67287	0.0:0.0:0.0:1.0	.	347	Q99797	MIPEP_HUMAN	D	347	ENSP00000371607:N347D	ENSP00000371607:N347D	N	-	1	0	MIPEP	23334455	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	6.106000	0.71511	2.132000	0.65825	0.533000	0.62120	AAT	.	.	none		0.279	MIPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044169.1			C	24436455	T	C	24436455	3	2	11	1	0	0	0	0	1	0	0	0	9601	1783	62	3	1146	3	MIPEP	13	24436455	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	527650	24436455	90733423	189	1480											
ENOX1	55068	hgsc.bcm.edu	37	chr13	43987001	43987001	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgcagccatcatctgaggaAgctcctggggaagctgggtg	8	8	15	10	0	2	1	1	1	1	0	3	3	3	3	2	4	4	3	2	4	2	0			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr13:43987001A>G	ENST00000261488.6	-	4	627	c.50T>C	c.(49-51)cTt>cCt	p.L17P	ENOX1_ENST00000412891.1_Missense_Mutation_p.L17P	NM_001242863.1|NM_017993.3	NP_001229792.1|NP_060463.2	Q8TC92	ENOX1_HUMAN	ecto-NOX disulfide-thiol exchanger 1	17					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)		CATCTGAGGAAGCTCCTGGGG	0.493																																					p.L17P		Atlas-SNP	.											.	ENOX1	158	.	0			c.T50C						PASS	.						126	112	116					13																	43987001		2203	4300	6503	SO:0001583	missense	55068	exon4			TGAGGAAGCTCCT	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.50T>C	13.37:g.43987001A>G	ENSP00000261488:p.Leu17Pro	89	0	0		64	22	0.34375	NM_017993	A4GU15|A6NMH9|B7Z5K1|Q2TU81|Q5VT11|Q9NWE0	Missense_Mutation	SNP	ENST00000261488.6	37	CCDS9389.1	.	.	.	.	.	.	.	.	.	.	A	14.16	2.452066	0.43531	.	.	ENSG00000120658	ENST00000261488;ENST00000412891	T;T	0.48201	0.82;0.82	5.91	5.91	0.95273	.	0.312364	0.26594	N	0.023508	T	0.27098	0.0664	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.11348	-1.0591	10	0.32370	T	0.25	-3.7208	10.059	0.42263	0.9229:0.0:0.0771:0.0	.	17	Q8TC92	ENOX1_HUMAN	P	17	ENSP00000261488:L17P;ENSP00000415054:L17P	ENSP00000261488:L17P	L	-	2	0	ENOX1	42885001	0.998000	0.40836	0.997000	0.53966	0.989000	0.77384	2.011000	0.40922	2.254000	0.74563	0.533000	0.62120	CTT	.	.	none		0.493	ENOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044717.2	NM_017993		G	43987001	A	G	43987001	3	3	11	1	0	0	0	0	1	0	0	0	5128	72	3	3	1937	3	ENOX1	13	43987001	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	19550546	43987001	71182877	190	1481											
GPC6	10082	hgsc.bcm.edu	37	chr13	93879792	93879792	+	Missense_Mutation	SNP	G	G	T																															cggggcggatgtgaaggctcGgagctgcggagaggtccgcc																										TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr13:93879792G>T	ENST00000377047.4	+	1	698	c.83G>T	c.(82-84)cGg>cTg	p.R28L		NM_005708.3	NP_005699.1	Q9Y625	GPC6_HUMAN	glypican 6	28					carbohydrate metabolic process (GO:0005975)|cell migration (GO:0016477)|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)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	38	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				GTGAAGGCTCGGAGCTGCGGA	0.652											OREG0022460	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R28L		Atlas-SNP	.											.	GPC6	102	.	0			c.G83T						PASS	.						76	75	75					13																	93879792		2203	4300	6503	SO:0001583	missense	10082	exon1			AGGCTCGGAGCTG	AF111178	CCDS9469.1	13q32	2008-02-05			ENSG00000183098	ENSG00000183098		"Proteoglycans / Cell Surface : Glypicans"	4454	protein-coding gene	gene with protein product	"glypican proteoglycan 6"	604404				10329016	Standard	NM_005708		Approved		uc001vlt.3	Q9Y625	OTTHUMG00000017205	ENST00000377047.4:c.83G>T	13.37:g.93879792G>T	ENSP00000366246:p.Arg28Leu	87	0	0	1301	66	26	0.393939	NM_005708	A8K279|Q96SG5|Q96SG8|Q9H1P4	Missense_Mutation	SNP	ENST00000377047.4	37	CCDS9469.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.074921	0.76415	.	.	ENSG00000183098	ENST00000377047	T	0.53206	0.63	5.52	5.52	0.82312	.	0.000000	0.51477	D	0.000084	T	0.54581	0.1867	M	0.74467	2.265	0.42422	D	0.992645	B;B	0.22080	0.021;0.064	B;B	0.31686	0.019;0.134	T	0.51733	-0.8668	10	0.25751	T	0.34	.	19.0471	0.93025	0.0:0.0:1.0:0.0	.	28;28	B4E2M1;Q9Y625	.;GPC6_HUMAN	L	28	ENSP00000366246:R28L	ENSP00000366246:R28L	R	+	2	0	GPC6	92677793	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.124000	0.77185	2.604000	0.88044	0.655000	0.94253	CGG	.	.	none		0.652	GPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045460.4	NM_005708		T	93879792	G	T	93879792	3	4	11	1	0	0	0	0	1	0	0	0	6610	1116	39	4	85	4	GPC6	13	93879792	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	49892791	93879792	21290086	191	1482	21	2									
GPC6	10082	hgsc.bcm.edu	37	chr13	93879793	93879793	+	Silent	SNP	G	G	T																															ggggcggatgtgaaggctcgGagctgcggagaggtccgcca																										TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr13:93879793G>T	ENST00000377047.4	+	1	699	c.84G>T	c.(82-84)cgG>cgT	p.R28R		NM_005708.3	NP_005699.1	Q9Y625	GPC6_HUMAN	glypican 6	28					carbohydrate metabolic process (GO:0005975)|cell migration (GO:0016477)|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)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	38	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				TGAAGGCTCGGAGCTGCGGAG	0.652											OREG0022460	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R28R		Atlas-SNP	.											.	GPC6	102	.	0			c.G84T						PASS	.						75	74	74					13																	93879793		2203	4300	6503	SO:0001819	synonymous_variant	10082	exon1			GGCTCGGAGCTGC	AF111178	CCDS9469.1	13q32	2008-02-05			ENSG00000183098	ENSG00000183098		"Proteoglycans / Cell Surface : Glypicans"	4454	protein-coding gene	gene with protein product	"glypican proteoglycan 6"	604404				10329016	Standard	NM_005708		Approved		uc001vlt.3	Q9Y625	OTTHUMG00000017205	ENST00000377047.4:c.84G>T	13.37:g.93879793G>T		86	0	0	1301	66	26	0.393939	NM_005708	A8K279|Q96SG5|Q96SG8|Q9H1P4	Silent	SNP	ENST00000377047.4	37	CCDS9469.1																																																																																			.	.	none		0.652	GPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045460.4	NM_005708		T	93879793	G	T	93879793	2	4	11	1	0	0	0	0	0	0	0	1	6610	1161	41	4		4	GPC6	13	93879793	Silent	SNP	G	TCGA-FF-8042-01A-11D-2210-10	1	93879793	21290085	192	1483	21	2									
G2E3	55632	hgsc.bcm.edu	37	chr14	31066658	31066658	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatgcgggagtgtttttcttTaggtgtacaatatgcaataa	12	15	10	4	1	1	0	0	0	1	0	1	1	1	1	0	2	3	3	0	2	7	7			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr14:31066658T>G	ENST00000206595.6	+	7	715	c.561T>G	c.(559-561)ttT>ttG	p.F187L	G2E3_ENST00000553504.1_Missense_Mutation_p.F217L|G2E3_ENST00000438909.2_Missense_Mutation_p.F141L|G2E3_ENST00000544007.1_3'UTR	NM_017769.3	NP_060239.2	Q7L622	G2E3_HUMAN	G2/M-phase specific E3 ubiquitin protein ligase	187					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						TGTTTTTCTTTAGGTGTACAA	0.308																																					p.F187L		Atlas-SNP	.											.	G2E3	82	.	0			c.T561G						PASS	.						150	167	161					14																	31066658		2203	4299	6502	SO:0001583	missense	55632	exon7			TTTCTTTAGGTGT	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.561T>G	14.37:g.31066658T>G	ENSP00000206595:p.Phe187Leu	183	0	0		206	59	0.286408	NM_017769	Q9BVR2|Q9H9E9|Q9NXC0|Q9P2L3	Missense_Mutation	SNP	ENST00000206595.6	37	CCDS9638.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.396616	0.83011	.	.	ENSG00000092140	ENST00000206595;ENST00000438909;ENST00000553504	T;T;T	0.69040	-0.37;-0.37;-0.37	5.67	0.657	0.17850	Zinc finger, RING-type (1);Zinc finger, PHD-type (1);	0.000000	0.85682	D	0.000000	T	0.73345	0.3575	L	0.55834	1.745	0.48341	D	0.999638	D;D	0.69078	0.973;0.997	P;D	0.75020	0.786;0.985	T	0.70513	-0.4851	10	0.48119	T	0.1	-22.4009	10.3259	0.43793	0.0:0.2489:0.0:0.7511	.	141;187	B4DIF9;Q7L622	.;G2E3_HUMAN	L	187;141;217	ENSP00000206595:F187L;ENSP00000391068:F141L;ENSP00000451653:F217L	ENSP00000206595:F187L	F	+	3	2	G2E3	30136409	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.630000	0.24553	0.170000	0.19704	0.482000	0.46254	TTT	.	.	none		0.308	G2E3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276613.2	NM_017769		G	31066658	T	G	31066658	3	3	11	1	0	0	0	0	1	0	0	0	6148	1751	61	5	583	5	G2E3	14	31066658	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10		31066658	76282882	193	1484											
LRFN5	145581	hgsc.bcm.edu	37	chr14	42356853	42356853	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtgtatgataacggaacacTtgacattcttatcacaactg	13	12	8	8	1	2	2	1	2	1	0	2	3	2	3	0	2	3	1	0	2	5	5			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr14:42356853T>G	ENST00000298119.4	+	3	2214	c.1025T>G	c.(1024-1026)cTt>cGt	p.L342R	LRFN5_ENST00000554120.1_Missense_Mutation_p.L342R|LRFN5_ENST00000554171.1_Missense_Mutation_p.L342R	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	342	Ig-like.					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)		AACGGAACACTTGACATTCTT	0.423										HNSCC(30;0.082)																											p.L342R		Atlas-SNP	.											LRFN5,NS,carcinoma,-1,2	LRFN5	269	2	0			c.T1025G						PASS	.						120	118	119					14																	42356853		2203	4300	6503	SO:0001583	missense	145581	exon3			GAACACTTGACAT	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.1025T>G	14.37:g.42356853T>G	ENSP00000298119:p.Leu342Arg	121	0	0		135	39	0.288889	NM_152447	B3KU78|Q86XL2	Missense_Mutation	SNP	ENST00000298119.4	37	CCDS9678.1	.	.	.	.	.	.	.	.	.	.	T	16.41	3.116036	0.56505	.	.	ENSG00000165379	ENST00000298119;ENST00000554120;ENST00000554171	D;D;D	0.90004	-2.6;-2.6;-2.6	5.4	5.4	0.78164	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.50627	D	0.000117	D	0.96552	0.8875	H	0.97918	4.105	0.80722	D	1	D;D	0.89917	1.0;0.994	D;D	0.97110	1.0;0.982	D	0.97779	1.0231	10	0.87932	D	0	.	13.6708	0.62424	0.0:0.0:0.0:1.0	.	342;342	G3V364;Q96NI6	.;LRFN5_HUMAN	R	342	ENSP00000298119:L342R;ENSP00000451897:L342R;ENSP00000451067:L342R	ENSP00000298119:L342R	L	+	2	0	LRFN5	41426603	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	7.997000	0.88414	2.165000	0.68154	0.460000	0.39030	CTT	.	.	none		0.423	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1	NM_152447		G	42356853	T	G	42356853	3	3	11	1	0	0	0	0	1	0	0	0	8950	1609	56	5	1027	5	LRFN5	14	42356853	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	11290195	42356853	64992687	194	1485											
MDGA2	161357	hgsc.bcm.edu	37	chr14	47530650	47530650	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taatggacgaccatttttaaAccaactaaatgttagctcct	14	13	5	9	1	0	0	0	0	0	0	1	2	1	1	3	1	3	2	3	1	7	6			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr14:47530650A>C	ENST00000399232.2	-	7	1484	c.1120T>G	c.(1120-1122)Ttt>Gtt	p.F374V	MDGA2_ENST00000357362.3_Missense_Mutation_p.F145V|MDGA2_ENST00000439988.3_Missense_Mutation_p.F443V|MDGA2_ENST00000426342.1_Missense_Mutation_p.F145V	NM_001113498.2	NP_001106970.3	Q7Z553	MDGA2_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 2	374	Ig-like 4.				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						CCATTTTTAAACCAACTAAAT	0.413																																					p.F443V		Atlas-SNP	.											.	MDGA2	470	.	0			c.T1327G						PASS	.						128	115	119					14																	47530650		1882	4103	5985	SO:0001583	missense	161357	exon7			TTTTAAACCAACT	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.1120T>G	14.37:g.47530650A>C	ENSP00000382178:p.Phe374Val	203	0	0		228	53	0.232456	NM_001113498	F6W3S7|J3KPX6	Missense_Mutation	SNP	ENST00000399232.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.91|13.91	2.376692|2.376692	0.42105|0.42105	.|.	.|.	ENSG00000139915|ENSG00000139915	ENST00000439988;ENST00000426342;ENST00000399232;ENST00000357362|ENST00000554762	T;T;T;T|.	0.46063|.	0.88;0.88;0.88;0.88|.	5.96|5.96	4.81|4.81	0.61882|0.61882	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);|.	0.000000|.	0.53938|.	U|.	0.000054|.	T|T	0.59662|0.59662	0.2210|0.2210	L|L	0.46670|0.46670	1.46|1.46	0.80722|0.80722	D|D	1|1	P|.	0.41848|.	0.763|.	P|.	0.49421|.	0.61|.	T|T	0.55490|0.55490	-0.8133|-0.8133	10|5	0.42905|.	T|.	0.14|.	.|.	12.4319|12.4319	0.55578|0.55578	0.8597:0.1403:0.0:0.0|0.8597:0.1403:0.0:0.0	.|.	374|.	Q7Z553|.	MDGA2_HUMAN|.	V|G	374;145;443;145|148	ENSP00000400011:F374V;ENSP00000405456:F145V;ENSP00000382178:F443V;ENSP00000349925:F145V|.	ENSP00000349925:F145V|.	F|V	-|-	1|2	0|0	MDGA2|MDGA2	46600400|46600400	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.511000|5.511000	0.67024|0.67024	1.061000|1.061000	0.40601|0.40601	0.533000|0.533000	0.62120|0.62120	TTT|GTT	.	.	none		0.413	MDGA2-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000073352.5	NM_182830		C	47530650	A	C	47530650	3	2	11	1	0	0	0	0	1	0	0	0	9416	43	2	5	1794	5	MDGA2	14	47530650	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	5173797	47530650	59818890	195	1486											
PYGL	5836	hgsc.bcm.edu	37	chr14	51378473	51378473	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcagcaagagatactctgtaGttctccaagaagatgacttt	13	12	8	8	0	3	4	1	1	2	3	4	5	3	4	1	0	2	3	1	0	5	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr14:51378473G>A	ENST00000216392.7	-	16	2276	c.1944C>T	c.(1942-1944)aaC>aaT	p.N648N	PYGL_ENST00000532462.1_Silent_p.N648N|PYGL_ENST00000544180.2_Silent_p.N614N|RP11-218E20.5_ENST00000557343.1_RNA	NM_002863.4	NP_002854.3	P06737	PYGL_HUMAN	phosphorylase, glycogen, liver	648					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)	ATACTCTGTAGTTCTCCAAGA	0.438																																					p.N648N		Atlas-SNP	.											.	PYGL	77	.	0			c.C1944T						PASS	.						86	78	81					14																	51378473		2203	4300	6503	SO:0001819	synonymous_variant	5836	exon16			TCTGTAGTTCTCC		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.1944C>T	14.37:g.51378473G>A		149	0	0		212	56	0.264151	NM_002863	A6NDQ4|B4DUB7|F5H816|O60567|O60752|O60913|Q501V9|Q641R5|Q96G82	Silent	SNP	ENST00000216392.7	37	CCDS32080.1																																																																																			.	.	none		0.438	PYGL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390654.3	NM_002863		A	51378473	G	A	51378473	2	1	11	1	0	0	0	0	0	0	0	1	12876	1020	36	2		2	PYGL	14	51378473	Silent	SNP	G	TCGA-FF-8042-01A-11D-2210-10	3847823	51378473	55971067	196	1487											
RGS6	9628	hgsc.bcm.edu	37	chr14	72976974	72976974	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctggagtccgaattcagtTcagaaaacctcaggtaaatc	13	10	8	10	1	3	1	3	0	0	1	6	3	5	2	3	2	1	2	3	2	5	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr14:72976974T>C	ENST00000553530.1	+	14	1285	c.1078T>C	c.(1078-1080)Tca>Cca	p.S360P	RGS6_ENST00000553525.1_Missense_Mutation_p.S360P|RGS6_ENST00000406236.4_Missense_Mutation_p.S360P|RGS6_ENST00000404301.2_Missense_Mutation_p.S360P|RGS6_ENST00000343854.6_Missense_Mutation_p.S323P|RGS6_ENST00000402788.2_Missense_Mutation_p.S360P|RGS6_ENST00000555571.1_Missense_Mutation_p.S360P|RGS6_ENST00000407322.4_Missense_Mutation_p.S360P|RGS6_ENST00000556437.1_Missense_Mutation_p.S360P|RGS6_ENST00000554782.1_Missense_Mutation_p.S221P|RGS6_ENST00000355512.6_Missense_Mutation_p.S360P|RGS6_ENST00000434263.2_Missense_Mutation_p.S291P	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	360	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)		CGAATTCAGTTCAGAAAACCT	0.458																																					p.S360P	Ovarian(143;1926 2468 21071 48641)	Atlas-SNP	.											.	RGS6	92	.	0			c.T1078C						PASS	.						89	100	96					14																	72976974		2203	4300	6503	SO:0001583	missense	9628	exon14			TTCAGTTCAGAAA	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.1078T>C	14.37:g.72976974T>C	ENSP00000452331:p.Ser360Pro	78	0	0		90	31	0.344444	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	37	CCDS9808.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.188405	0.78789	.	.	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	0.02121	4.44;4.44;4.44;4.44;4.44;4.44;4.44;4.44;4.44;4.44;4.44;4.44	5.72	5.72	0.89469	Regulator of G protein signalling (4);Regulator of G protein signalling superfamily (1);	0.000000	0.85682	D	0.000000	T	0.13457	0.0326	M	0.78049	2.395	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;0.999	D;D;D;D	0.97110	0.999;0.973;1.0;0.971	T	0.00110	-1.2048	10	0.62326	D	0.03	-9.758	16.2988	0.82793	0.0:0.0:0.0:1.0	.	291;360;365;360	B7Z7N5;P49758-2;Q59FJ8;P49758	.;.;.;RGS6_HUMAN	P	360;360;360;360;360;360;360;360;360;323;332;291;221;221	ENSP00000451030:S360P;ENSP00000450936:S360P;ENSP00000452331:S360P;ENSP00000451855:S360P;ENSP00000347699:S360P;ENSP00000385243:S360P;ENSP00000384218:S360P;ENSP00000384612:S360P;ENSP00000383953:S360P;ENSP00000341199:S323P;ENSP00000412144:S291P;ENSP00000451912:S221P	ENSP00000341199:S323P	S	+	1	0	RGS6	72046727	1.000000	0.71417	0.980000	0.43619	0.978000	0.69477	7.997000	0.88414	2.311000	0.77944	0.533000	0.62120	TCA	.	.	none		0.458	RGS6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413033.2			C	72976974	T	C	72976974	3	2	11	1	0	0	0	0	1	0	0	0	13324	1783	62	3	1128	3	RGS6	14	72976974	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	21598501	72976974	34372566	197	1488											
NRXN3	9369	hgsc.bcm.edu	37	chr14	79175759	79175759	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatgggctccatctcctttgActtccgcaccacagagccca	8	10	7	16	1	1	2	0	1	1	1	4	2	3	2	5	1	1	2	5	1	1	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr14:79175759A>G	ENST00000554719.1	+	4	793	c.302A>G	c.(301-303)gAc>gGc	p.D101G	RP11-232C2.2_ENST00000555680.1_RNA|NRXN3_ENST00000335750.5_Missense_Mutation_p.D101G	NM_004796.4	NP_004787.2	Q9HDB5	NRX3B_HUMAN	neurexin 3	0	Laminin G-like. {ECO:0000255|PROSITE- ProRule:PRU00122}.				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)		ATCTCCTTTGACTTCCGCACC	0.517																																					p.D101G		Atlas-SNP	.											.	NRXN3	342	.	0			c.A302G						PASS	.						131	116	121					14																	79175759		2203	4300	6503	SO:0001583	missense	9369	exon4			CCTTTGACTTCCG	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.302A>G	14.37:g.79175759A>G	ENSP00000451648:p.Asp101Gly	118	0	0		163	46	0.282209	NM_004796	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Missense_Mutation	SNP	ENST00000554719.1	37	CCDS9870.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.269142	0.80469	.	.	ENSG00000021645	ENST00000330071;ENST00000332068;ENST00000553631;ENST00000554719;ENST00000335750;ENST00000557081	T;T;T;T	0.79141	-1.22;-1.24;-1.24;-1.22	5.38	5.38	0.77491	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);	0.000000	0.85682	D	0.000000	D	0.88119	0.6351	M	0.87547	2.89	0.80722	D	1	D;P	0.67145	0.996;0.782	P;P	0.61477	0.889;0.569	D	0.89852	0.4010	9	.	.	.	.	15.3852	0.74691	1.0:0.0:0.0:0.0	.	474;101	Q9Y4C0;Q9Y4C0-3	NRX3A_HUMAN;.	G	474;472;45;101;101;45	ENSP00000451947:D45G;ENSP00000451648:D101G;ENSP00000338349:D101G;ENSP00000450462:D45G	.	D	+	2	0	NRXN3	78245512	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.339000	0.96797	2.037000	0.60232	0.460000	0.39030	GAC	.	.	none		0.517	NRXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413787.1	NM_001105250		G	79175759	A	G	79175759	3	3	11	1	0	0	0	0	1	0	0	0	10676	275	10	3	308	3	NRXN3	14	79175759	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	6198785	79175759	28173781	198	1489											
PTPN21	11099	hgsc.bcm.edu	37	chr14	88951488	88951488	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcggtgggggaggcatcacgTagggctggggtttaggctaa	7	8	20	6	2	1	0	1	0	0	0	1	1	1	1	0	8	0	5	0	8	3	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr14:88951488T>C	ENST00000556564.1	-	12	1294	c.1010A>G	c.(1009-1011)tAc>tGc	p.Y337C	PTPN21_ENST00000328736.3_Missense_Mutation_p.Y337C	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	337					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						AGGCATCACGTAGGGCTGGGG	0.428																																					p.Y337C		Atlas-SNP	.											.	PTPN21	113	.	0			c.A1010G						PASS	.						125	117	120					14																	88951488		2203	4300	6503	SO:0001583	missense	11099	exon12			ATCACGTAGGGCT	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.1010A>G	14.37:g.88951488T>C	ENSP00000452414:p.Tyr337Cys	138	0	0		89	34	0.382022	NM_007039		Missense_Mutation	SNP	ENST00000556564.1	37	CCDS9884.1	.	.	.	.	.	.	.	.	.	.	T	17.34	3.365736	0.61513	.	.	ENSG00000070778	ENST00000328736;ENST00000556564	D;D	0.82255	-1.59;-1.59	5.49	4.27	0.50696	.	0.073893	0.56097	D	0.000025	D	0.88994	0.6589	M	0.71581	2.175	0.43724	D	0.996202	D	0.89917	1.0	D	0.80764	0.994	D	0.88828	0.3303	10	0.49607	T	0.09	.	11.6649	0.51368	0.1326:0.0:0.0:0.8674	.	337	Q16825	PTN21_HUMAN	C	337	ENSP00000330276:Y337C;ENSP00000452414:Y337C	ENSP00000330276:Y337C	Y	-	2	0	PTPN21	88021241	1.000000	0.71417	0.996000	0.52242	0.925000	0.55904	3.230000	0.51286	2.212000	0.71576	0.533000	0.62120	TAC	.	.	none		0.428	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1			C	88951488	T	C	88951488	3	2	11	1	0	0	0	0	1	0	0	0	12801	1638	57	3	2546	3	PTPN21	14	88951488	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	9775729	88951488	18398052	199	1490											
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105418968	105418968	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cctttcaggtccagcttgggGcccttaacatctatctgggg	6	12	11	12	0	3	0	1	0	2	0	4	0	4	0	3	5	2	1	3	5	2	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr14:105418968G>C	ENST00000333244.5	-	7	2939	c.2820C>G	c.(2818-2820)ggC>ggG	p.G940G	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	940						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)			CCAGCTTGGGGCCCTTAACAT	0.622																																					p.G940G		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C2820G						PASS	.						138	159	152					14																	105418968		1861	4088	5949	SO:0001819	synonymous_variant	113146	exon7			CTTGGGGCCCTTA	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.2820C>G	14.37:g.105418968G>C		236	0	0		183	67	0.36612	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			.	.	none		0.622	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		C	105418968	G	C	105418968	2	2	11	1	0	0	0	0	0	0	0	1	415	1190	42	4		4	AHNAK2	14	105418968	Silent	SNP	G	TCGA-FF-8042-01A-11D-2210-10	16467480	105418968	1930572	200	1491											
GABRG3	2567	hgsc.bcm.edu	37	chr15	27777873	27777873	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcaaagactgtcagagctTcttctgctgctatgaagaat	11	12	10	8	0	3	4	1	1	2	3	3	4	3	4	0	1	3	4	0	1	4	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr15:27777873T>G	ENST00000333743.6	+	10	1504	c.1250T>G	c.(1249-1251)tTc>tGc	p.F417C	RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	417					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)	TGTCAGAGCTTCTTCTGCTGC	0.463																																					p.F417C	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											.	GABRG3	115	.	0			c.T1250G						PASS	.						105	107	106					15																	27777873		1973	4142	6115	SO:0001583	missense	2567	exon10			AGAGCTTCTTCTG		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.1250T>G	15.37:g.27777873T>G	ENSP00000331912:p.Phe417Cys	184	0	0		151	56	0.370861	NM_033223	G3V594|Q9HD46|Q9NYT2	Missense_Mutation	SNP	ENST00000333743.6	37	CCDS45195.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.043813	0.75732	.	.	ENSG00000182256	ENST00000333743	D	0.84298	-1.83	5.85	4.7	0.59300	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.055639	0.64402	D	0.000001	D	0.87861	0.6284	L	0.39514	1.22	0.80722	D	1	D	0.71674	0.998	D	0.72075	0.976	D	0.86989	0.2109	10	0.49607	T	0.09	.	11.4819	0.50331	0.1347:0.0:0.0:0.8653	.	417	Q99928	GBRG3_HUMAN	C	417	ENSP00000331912:F417C	ENSP00000331912:F417C	F	+	2	0	GABRG3	25451468	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.941000	0.70195	1.003000	0.39130	0.528000	0.53228	TTC	.	.	none		0.463	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2			G	27777873	T	G	27777873	3	3	11	1	0	0	0	0	1	0	0	0	6181	1783	62	5	1288	5	GABRG3	15	27777873	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10		27777873	74753519	201	1492											
PGBD4	161779	hgsc.bcm.edu	37	chr15	34396115	34396115	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctttcaccatcttctacaCattacagtgctgaactccta	10	15	3	13	0	4	1	1	1	3	0	5	1	5	1	2	0	4	1	2	0	4	6			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr15:34396115C>A	ENST00000397766.2	+	1	1842	c.1383C>A	c.(1381-1383)caC>caA	p.H461Q	EMC7_ENST00000532113.1_5'Flank|EMC7_ENST00000256545.4_5'Flank	NM_152595.4	NP_689808.2	Q96DM1	PGBD4_HUMAN	piggyBac transposable element derived 4	461										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)		ATCTTCTACACATTACAGTGC	0.423																																					p.H461Q		Atlas-SNP	.											.	PGBD4	58	.	0			c.C1383A						PASS	.						75	70	71					15																	34396115		2201	4298	6499	SO:0001583	missense	161779	exon1			TCTACACATTACA	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.1383C>A	15.37:g.34396115C>A	ENSP00000380872:p.His461Gln	24	0	0		45	14	0.311111	NM_152595	A1L487|A8K0C6|Q8N9E8	Missense_Mutation	SNP	ENST00000397766.2	37	CCDS10033.1	.	.	.	.	.	.	.	.	.	.	c	5.706	0.314803	0.10789	.	.	ENSG00000182405	ENST00000397766	T	0.15718	2.4	0.7	-0.4	0.12411	.	0.778304	0.10025	U	0.725529	T	0.04452	0.0122	N	0.01352	-0.895	0.20926	N	0.999826	B	0.15473	0.013	B	0.04013	0.001	T	0.37337	-0.9710	10	0.31617	T	0.26	.	1.6567	0.02783	0.3278:0.4027:0.0:0.2695	.	461	Q96DM1	PGBD4_HUMAN	Q	461	ENSP00000380872:H461Q	ENSP00000380872:H461Q	H	+	3	2	PGBD4	32183407	1.000000	0.71417	0.542000	0.28115	0.953000	0.61014	2.024000	0.41049	-0.152000	0.11156	0.306000	0.20318	CAC	.	.	none		0.423	PGBD4-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251522.1			A	34396115	C	A	34396115	3	1	11	1	0	0	0	0	1	0	0	0	11792	477	17	4	1385	4	PGBD4	15	34396115	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	6618242	34396115	68135277	202	1493											
FBN1	2200	hgsc.bcm.edu	37	chr15	48703210	48703210	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgaagcaaaacctggatttTcatcttcagattatcaccca	14	12	5	10	0	4	2	3	1	1	1	4	3	4	3	2	1	2	1	2	1	4	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr15:48703210T>G	ENST00000316623.5	-	66	9048	c.8593A>C	c.(8593-8595)Aaa>Caa	p.K2865Q	FBN1_ENST00000561429.1_5'Flank	NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	2865					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)		ACCTGGATTTTCATCTTCAGA	0.328																																					p.K2865Q		Atlas-SNP	.											.	FBN1	310	.	0			c.A8593C						PASS	.						87	85	85					15																	48703210		2198	4297	6495	SO:0001583	missense	2200	exon66			GGATTTTCATCTT	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.8593A>C	15.37:g.48703210T>G	ENSP00000325527:p.Lys2865Gln	243	0	0		155	65	0.419355	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	37	CCDS32232.1	.	.	.	.	.	.	.	.	.	.	T	13.93	2.384485	0.42308	.	.	ENSG00000166147	ENST00000316623	D	0.82711	-1.64	5.87	5.87	0.94306	.	0.088256	0.85682	D	0.000000	T	0.80071	0.4556	M	0.68317	2.08	0.80722	D	1	P	0.41313	0.745	B	0.31686	0.134	T	0.82808	-0.0274	10	0.62326	D	0.03	.	15.9277	0.79632	0.0:0.0:0.0:1.0	.	2865	P35555	FBN1_HUMAN	Q	2865	ENSP00000325527:K2865Q	ENSP00000325527:K2865Q	K	-	1	0	FBN1	46490502	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.087000	0.64480	2.247000	0.74100	0.528000	0.53228	AAA	.	.	none		0.328	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			G	48703210	T	G	48703210	3	3	11	1	0	0	0	0	1	0	0	0	5710	1792	62	5	26	5	FBN1	15	48703210	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	14307095	48703210	53828182	203	1494											
UNC13C	440279	hgsc.bcm.edu	37	chr15	54792317	54792317	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	tgcaatggctagatgaaaacGaagatgtgtcaatggaattc	15	10	11	5	1	1	3	1	1	0	2	2	5	1	4	0	2	2	2	0	2	7	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr15:54792317G>C	ENST00000260323.11	+	20	5101	c.5101G>C	c.(5101-5103)Gaa>Caa	p.E1701Q	UNC13C_ENST00000537900.1_Missense_Mutation_p.E1699Q|UNC13C_ENST00000545554.1_Missense_Mutation_p.E1701Q	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1701	MHD1. {ECO:0000255|PROSITE- ProRule:PRU00587}.				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)		AGATGAAAACGAAGATGTGTC	0.348																																					p.E1701Q		Atlas-SNP	.											.	UNC13C	674	.	0			c.G5101C						PASS	.						131	122	125					15																	54792317		1847	4102	5949	SO:0001583	missense	440279	exon19			GAAAACGAAGATG	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.5101G>C	15.37:g.54792317G>C	ENSP00000260323:p.Glu1701Gln	225	0	0		207	73	0.352657	NM_001080534	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	37	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.664366	0.88251	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	T;T;T	0.80123	-1.33;-1.34;-1.33	5.5	5.5	0.81552	Munc13 homology 1 (1);	0.105919	0.64402	D	0.000007	D	0.90000	0.6878	M	0.77820	2.39	0.58432	D	0.999999	D	0.89917	1.0	D	0.85130	0.997	D	0.89805	0.3978	10	0.52906	T	0.07	.	18.7617	0.91855	0.0:0.0:1.0:0.0	.	1701	Q8NB66	UN13C_HUMAN	Q	1701;1701;1699	ENSP00000260323:E1701Q;ENSP00000438156:E1701Q;ENSP00000442569:E1699Q	ENSP00000260323:E1701Q	E	+	1	0	UNC13C	52579609	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.683000	0.98657	2.744000	0.94065	0.655000	0.94253	GAA	.	.	none		0.348	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		C	54792317	G	C	54792317	3	2	11	1	0	0	0	0	1	0	0	0	17001	1059	37	4	5175	4	UNC13C	15	54792317	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	6089107	54792317	47739075	204	1495											
NR2E3	10002	hgsc.bcm.edu	37	chr15	72103180	72103180	+	RNA	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aggagtctccaggcagatggGgcctgggggaggatcccaca	9	5	17	10	0	1	1	0	0	1	1	3	4	2	4	3	7	0	1	3	7	0	0			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr15:72103180G>T	ENST00000398840.2	+	0	287							Q9Y5X4	NR2E3_HUMAN	nuclear receptor subfamily 2, group E, member 3						eye photoreceptor cell development (GO:0042462)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phototransduction (GO:0007602)|positive regulation of rhodopsin gene expression (GO:0045872)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|lung(1)	3						AGGCAGATGGGGCCTGGGGGA	0.642																																					p.G33C		Atlas-SNP	.											.	NR2E3	53	.	0			c.G97T						PASS	.						10	12	11					15																	72103180		1868	4092	5960			10002	exon1			AGATGGGGCCTGG		CCDS73750.1, CCDS73751.1	15q23	2013-01-16			ENSG00000031544	ENSG00000278570		"Nuclear hormone receptors"	7974	protein-coding gene	gene with protein product		604485				10220376	Standard	NM_016346		Approved	PNR, rd7, RP37	uc002ath.1	Q9Y5X4	OTTHUMG00000172841		15.37:g.72103180G>T		260	0	0		283	64	0.226148	NM_016346	B6ZGU0|Q9UHM4	Missense_Mutation	SNP	ENST00000398840.2	37		.	.	.	.	.	.	.	.	.	.	G	12.04	1.817162	0.32145	.	.	ENSG00000031544	ENST00000398840	.	.	.	3.15	3.15	0.36227	.	0.163797	0.37393	N	0.002104	T	0.42787	0.1218	N	0.08118	0	0.43540	D	0.995838	D	0.76494	0.999	P	0.61201	0.885	T	0.59495	-0.7444	8	0.56958	D	0.05	.	12.1851	0.54234	0.0:0.0:1.0:0.0	.	33	Q9Y5X4	NR2E3_HUMAN	C	33	.	ENSP00000381820:G33C	G	+	1	0	NR2E3	69890234	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.240000	0.43088	2.037000	0.60232	0.655000	0.94253	GGC	.	.	none		0.642	NR2E3-202	KNOWN	basic	processed_transcript	processed_transcript		NM_014249		T	72103180	G	T	72103180	1	4	11	0	1	0	0	0	0	0	0	0	10635	1232	43	4		4	NR2E3	15	72103180	RNA	SNP	G	TCGA-FF-8042-01A-11D-2210-10	17310863	72103180	30428212	205	1496											
HCN4	10021	hgsc.bcm.edu	37	chr15	73616204	73616204	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccggtcatgctgcacaatctGctggatgatctcattctcct	7	13	8	13	1	4	1	2	1	3	0	6	2	4	2	2	2	3	3	2	2	1	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr15:73616204G>T	ENST00000261917.3	-	8	3223	c.2230C>A	c.(2230-2232)Cag>Aag	p.Q744K		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	744					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)		TGCACAATCTGCTGGATGATC	0.617																																					p.Q744K		Atlas-SNP	.											.	HCN4	150	.	0			c.C2230A						PASS	.						65	71	69					15																	73616204		2198	4297	6495	SO:0001583	missense	10021	exon8			CAATCTGCTGGAT	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.2230C>A	15.37:g.73616204G>T	ENSP00000261917:p.Gln744Lys	67	0	0		77	6	0.0779221	NM_005477	Q9UMQ7	Missense_Mutation	SNP	ENST00000261917.3	37	CCDS10248.1	.	.	.	.	.	.	.	.	.	.	G	13.11	2.138747	0.37728	.	.	ENSG00000138622	ENST00000261917	T	0.42900	0.96	3.46	3.46	0.39613	.	.	.	.	.	T	0.39091	0.1065	M	0.63843	1.955	0.37183	D	0.903603	B	0.25667	0.131	B	0.22386	0.039	T	0.41980	-0.9478	9	0.15499	T	0.54	.	15.125	0.72475	0.0:0.0:1.0:0.0	.	744	Q9Y3Q4	HCN4_HUMAN	K	744	ENSP00000261917:Q744K	ENSP00000261917:Q744K	Q	-	1	0	HCN4	71403257	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	3.267000	0.51577	1.761000	0.52028	0.313000	0.20887	CAG	.	.	none		0.617	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477		T	73616204	G	T	73616204	3	4	11	1	0	0	0	0	1	0	0	0	7008	1328	46	4	1385	4	HCN4	15	73616204	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	1513024	73616204	28915188	206	1497											
LINGO1	84894	hgsc.bcm.edu	37	chr15	77906709	77906709	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcgggcgagtagctgcgcaCatgcaggtgggcgggcatgg	6	6	20	9	4	0	0	0	0	0	0	1	1	0	0	0	5	3	5	0	5	1	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr15:77906709C>G	ENST00000355300.6	-	2	1714	c.1540G>C	c.(1540-1542)Gtg>Ctg	p.V514L	LINGO1_ENST00000561030.1_Missense_Mutation_p.V508L	NM_032808.5	NP_116197.4	Q96FE5	LIGO1_HUMAN	leucine rich repeat and Ig domain containing 1	514					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						TAGCTGCGCACATGCAGGTGG	0.672																																					p.V514L		Atlas-SNP	.											.	LINGO1	76	.	0			c.G1540C						PASS	.						55	60	58					15																	77906709		2130	4227	6357	SO:0001583	missense	84894	exon2			TGCGCACATGCAG	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.1540G>C	15.37:g.77906709C>G	ENSP00000347451:p.Val514Leu	92	0	0		84	24	0.285714	NM_032808	D3DW80|Q6NUK3|Q6UXM3|Q6VVG0|Q6VVG1|Q6VVG2|Q8N3K5|Q96K52	Missense_Mutation	SNP	ENST00000355300.6	37	CCDS45313.1	.	.	.	.	.	.	.	.	.	.	C	15.20	2.762626	0.49574	.	.	ENSG00000169783	ENST00000355300	T	0.60299	0.2	5.08	5.08	0.68730	Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.055741	0.64402	D	0.000001	T	0.70219	0.3199	M	0.93283	3.4	0.80722	D	1	P	0.49253	0.921	B	0.41135	0.348	T	0.81540	-0.0886	10	0.66056	D	0.02	.	18.482	0.90815	0.0:1.0:0.0:0.0	.	514	Q96FE5	LIGO1_HUMAN	L	514	ENSP00000347451:V514L	ENSP00000347451:V514L	V	-	1	0	LINGO1	75693764	1.000000	0.71417	0.990000	0.47175	0.965000	0.64279	5.938000	0.70170	2.359000	0.80004	0.462000	0.41574	GTG	.	.	none		0.672	LINGO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419546.1	NM_032808		G	77906709	C	G	77906709	3	3	11	1	0	0	0	0	1	0	0	0	8823	478	17	4	326	4	LINGO1	15	77906709	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	4290505	77906709	24624683	207	1498											
AGBL1	123624	hgsc.bcm.edu	37	chr15	87089240	87089240	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggctattgtaggttttctGtgacttccatggccactccc	5	15	10	11	0	1	1	0	1	1	0	3	1	3	1	3	3	0	3	3	3	2	6			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr15:87089240G>T	ENST00000441037.2	+	19	2650	c.2555G>T	c.(2554-2556)tGt>tTt	p.C852F	AGBL1_ENST00000389298.3_Missense_Mutation_p.C583F|AGBL1_ENST00000421325.2_Missense_Mutation_p.C852F	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	852					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						TAGGTTTTCTGTGACTTCCAT	0.433																																					p.C852F		Atlas-SNP	.											AGBL1,NS,carcinoma,+1,1	AGBL1	151	1	0			c.G2555T						PASS	.						130	120	123					15																	87089240		1902	4120	6022	SO:0001583	missense	123624	exon19			TTTTCTGTGACTT	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.2555G>T	15.37:g.87089240G>T	ENSP00000413001:p.Cys852Phe	244	0	0		201	55	0.273632	NM_152336	A1A4X5|A6NJH6|C9JHL5	Missense_Mutation	SNP	ENST00000441037.2	37	CCDS58398.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.155644	0.78114	.	.	ENSG00000166748	ENST00000441037;ENST00000421325;ENST00000389298	T;T	0.10477	2.87;2.87	5.53	5.53	0.82687	Peptidase M14, carboxypeptidase A (1);	0.965353	0.08432	U	0.946782	T	0.38772	0.1053	M	0.69823	2.125	0.50467	D	0.999876	D	0.89917	1.0	D	0.97110	1.0	T	0.01848	-1.1261	10	0.87932	D	0	-3.2391	18.6325	0.91364	0.0:0.0:1.0:0.0	.	852	Q96MI9	CBPC4_HUMAN	F	887;852;583	ENSP00000397173:C852F;ENSP00000373949:C583F	ENSP00000373949:C583F	C	+	2	0	AGBL1	84890244	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.072000	0.93986	2.882000	0.98803	0.655000	0.94253	TGT	.	.	none		0.433	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336		T	87089240	G	T	87089240	3	4	11	1	0	0	0	0	1	0	0	0	375	1377	48	4	2625	4	AGBL1	15	87089240	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	9182531	87089240	15442152	208	1499											
NTRK3	4916	hgsc.bcm.edu	37	chr15	88727487	88727487	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tccggtgtagagctccatgtCcacggcgttgagcgtgtgaa	7	10	14	10	4	0	3	0	2	0	1	3	3	3	3	3	2	2	3	3	2	2	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr15:88727487C>T	ENST00000360948.2	-	3	453	c.292G>A	c.(292-294)Gac>Aac	p.D98N	NTRK3_ENST00000394480.2_Missense_Mutation_p.D98N|NTRK3_ENST00000355254.2_Missense_Mutation_p.D98N|NTRK3_ENST00000557856.1_Missense_Mutation_p.D98N|NTRK3_ENST00000540489.2_Missense_Mutation_p.D98N|NTRK3_ENST00000542733.2_5'UTR|NTRK3_ENST00000558676.1_Missense_Mutation_p.D98N|NTRK3_ENST00000357724.2_Missense_Mutation_p.D98N|NTRK3_ENST00000317501.3_Missense_Mutation_p.D98N	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	98					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)			AGCTCCATGTCCACGGCGTTG	0.577			T	ETV6	"congenital fibrosarcoma, Secretory breast "					TSP Lung(13;0.10)																											p.D98N		Atlas-SNP	.		Dom	yes		15	15q25	4916	"neurotrophic tyrosine kinase, receptor, type 3"		"E, M"	.	NTRK3	587	.	0			c.G292A						PASS	.						110	81	91					15																	88727487		2201	4299	6500	SO:0001583	missense	4916	exon4			CCATGTCCACGGC	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.292G>A	15.37:g.88727487C>T	ENSP00000354207:p.Asp98Asn	52	0	0		99	21	0.212121	NM_001243101	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Missense_Mutation	SNP	ENST00000360948.2	37	CCDS32322.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.601130	0.87055	.	.	ENSG00000140538	ENST00000394480;ENST00000360948;ENST00000357724;ENST00000355254;ENST00000540489;ENST00000317501	D;D;D;D;D;D	0.90004	-2.6;-2.6;-2.6;-2.6;-2.6;-2.6	4.42	4.42	0.53409	.	0.000000	0.85682	D	0.000000	D	0.87422	0.6173	N	0.08118	0	0.40417	D	0.979807	D;D;D;D;D	0.89917	0.993;0.997;1.0;0.996;0.982	D;D;D;D;P	0.83275	0.977;0.971;0.996;0.993;0.855	D	0.89666	0.3880	10	0.72032	D	0.01	.	12.4109	0.55466	0.0:1.0:0.0:0.0	.	98;98;98;98;98	E9PG56;B7Z4C5;Q96CY4;Q16288-3;Q16288	.;.;.;.;NTRK3_HUMAN	N	98	ENSP00000377990:D98N;ENSP00000354207:D98N;ENSP00000350356:D98N;ENSP00000347397:D98N;ENSP00000444673:D98N;ENSP00000318328:D98N	ENSP00000318328:D98N	D	-	1	0	NTRK3	86528491	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	5.258000	0.65479	2.299000	0.77371	0.655000	0.94253	GAC	.	.	none		0.577	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				T	88727487	C	T	88727487	3	4	11	1	0	0	0	0	1	0	0	0	10717	855	30	2	2557	2	NTRK3	15	88727487	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	1638247	88727487	13803905	209	1500											
SEMA4B	10519	hgsc.bcm.edu	37	chr15	90770838	90770838	+	IGR	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgccaaggacctttgcagcGcgtcttcggttgtgtccccg	4	10	13	14	5	1	0	0	0	1	0	3	1	2	1	4	2	2	2	4	2	1	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr15:90770838G>A	ENST00000328649.6	-	0	1247				SEMA4B_ENST00000411539.2_Missense_Mutation_p.A580T|SEMA4B_ENST00000332496.6_Missense_Mutation_p.A580T|SEMA4B_ENST00000379122.3_Missense_Mutation_p.A575T	NM_006384.3	NP_006375.2	Q99828	CIB1_HUMAN	calcium and integrin binding 1 (calmyrin)						angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell division (GO:0051301)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to growth factor stimulus (GO:0071363)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to tumor necrosis factor (GO:0071356)|cytoplasmic microtubule organization (GO:0031122)|double-strand break repair (GO:0006302)|endomitotic cell cycle (GO:0007113)|extrinsic apoptotic signaling pathway (GO:0097191)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of megakaryocyte differentiation (GO:0045653)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|platelet formation (GO:0030220)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell growth (GO:0030307)|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-matrix adhesion (GO:0001954)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of male germ cell proliferation (GO:2000256)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of cell division (GO:0051302)|regulation of cell proliferation (GO:0042127)|response to ischemia (GO:0002931)|spermatid development (GO:0007286)|thrombopoietin-mediated signaling pathway (GO:0038163)	cell periphery (GO:0071944)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|protein anchor (GO:0043495)|Ras GTPase binding (GO:0017016)			lung(1)|prostate(1)	2	Melanoma(11;0.00551)|Lung NSC(78;0.0141)|all_lung(78;0.0303)		BRCA - Breast invasive adenocarcinoma(143;0.00269)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217)			CCTTTGCAGCGCGTCTTCGGT	0.607																																					p.A580T		Atlas-SNP	.											.	SEMA4B	51	.	0			c.G1738A						PASS	.						68	73	71					15																	90770838		2021	4190	6211	SO:0001628	intergenic_variant	10509	exon14			TGCAGCGCGTCTT	U82226	CCDS10360.1, CCDS73781.1	15q25.3-q26	2013-01-10			ENSG00000185043	ENSG00000185043		"EF-hand domain containing"	16920	protein-coding gene	gene with protein product		602293				9030514, 10826701	Standard	NM_006384		Approved	SIP2-28, CALMYRIN, CIB, KIP	uc031qtq.1	Q99828	OTTHUMG00000149808		15.37:g.90770838G>A		74	0	0		77	17	0.220779	NM_020210	B5BU40|H6WJF3|O00693|O00735|Q6IB49|Q96J54|Q99971	Missense_Mutation	SNP	ENST00000328649.6	37	CCDS10360.1	.	.	.	.	.	.	.	.	.	.	G	14.93	2.682933	0.47991	.	.	ENSG00000185033	ENST00000332496;ENST00000379122;ENST00000411539	T;T;T	0.21361	2.01;2.21;2.01	5.38	-1.92	0.07618	.	1.464410	0.03864	N	0.274414	T	0.06280	0.0162	N	0.00538	-1.39	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.29731	-1.0002	10	0.29301	T	0.29	.	7.3344	0.26601	0.4842:0.1203:0.3956:0.0	.	575;580;575	Q9NPR2-2;Q2NL81;Q9NPR2	.;.;SEM4B_HUMAN	T	580;575;580	ENSP00000332204:A580T;ENSP00000368417:A575T;ENSP00000394720:A580T	ENSP00000332204:A580T	A	+	1	0	SEMA4B	88571842	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.873000	0.04214	-0.596000	0.05821	-0.416000	0.06073	GCG	.	.	none		0.607	CIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313419.1			A	90770838	G	A	90770838	1	1	11	0	1	0	0	0	0	0	0	0	14047	1087	38	1		1	SEMA4B	15	90770838	IGR	SNP	G	TCGA-FF-8042-01A-11D-2210-10	2043351	90770838	11760554	210	1501											
CRTC3	64784	hgsc.bcm.edu	37	chr15	91172567	91172567	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacagacatctgttcccaacGcatctgctcttcacccttcg	8	11	5	17	2	4	1	1	0	3	1	6	1	5	1	2	0	2	3	2	0	1	3	rs140158187	byFrequency	TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr15:91172567G>A	ENST00000268184.6	+	11	1073	c.1069G>A	c.(1069-1071)Gca>Aca	p.A357T	RP11-387D10.2_ENST00000559531.1_RNA|CRTC3_ENST00000420329.2_Missense_Mutation_p.A357T			Q6UUV7	CRTC3_HUMAN	CREB regulated transcription coactivator 3	357					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)			TGTTCCCAACGCATCTGCTCT	0.547			T	MAML2	salivary gland mucoepidermoid								G|||	11	0.00219649	0.0076	0.0	5008	,	,		20116	0.001		0.0	False		,,,				2504	0.0				p.A357T		Atlas-SNP	.		Dom	yes		15	15q26.1	64784	CREB regulated transcription coactivator 3		E	.	CRTC3	47	.	0			c.G1069A						PASS	.	G	THR/ALA,THR/ALA	45,4351	47.5+/-82.1	0,45,2153	261	253	255		1069,1069	3.3	0	15	dbSNP_134	255	0,8596		0,0,4298	yes	missense,missense	CRTC3	NM_001042574.1,NM_022769.3	58,58	0,45,6451	AA,AG,GG		0.0,1.0237,0.3464	possibly-damaging,possibly-damaging	357/619,357/620	91172567	45,12947	2198	4298	6496	SO:0001583	missense	64784	exon11			CCCAACGCATCTG		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.1069G>A	15.37:g.91172567G>A	ENSP00000268184:p.Ala357Thr	169	0	0		250	70	0.28	NM_022769	Q6DK61|Q6DK62|Q8NF38|Q9H6U2	Missense_Mutation	SNP	ENST00000268184.6	37	CCDS32331.1	5	0.0022893772893772895	4	0.008130081300813009	0	0.0	1	0.0017482517482517483	0	0.0	G	0.759	-0.770132	0.02974	0.010237	0.0	ENSG00000140577	ENST00000437186;ENST00000268184;ENST00000420329	T;T	0.11495	2.77;2.77	5.18	3.32	0.38043	.	0.686881	0.14923	N	0.290567	T	0.05960	0.0155	L	0.54323	1.7	0.09310	N	1	B;B	0.16396	0.01;0.017	B;B	0.10450	0.002;0.005	T	0.45220	-0.9276	10	0.02654	T	1	-6.7224	6.7728	0.23602	0.2749:0.0:0.7251:0.0	.	357;357	Q6UUV7;Q6UUV7-3	CRTC3_HUMAN;.	T	321;357;357	ENSP00000268184:A357T;ENSP00000416573:A357T	ENSP00000268184:A357T	A	+	1	0	CRTC3	88973571	0.479000	0.25925	0.002000	0.10522	0.001000	0.01503	0.892000	0.28322	0.771000	0.33359	0.655000	0.94253	GCA	G|0.996;A|0.004	0.004	strong		0.547	CRTC3-001	KNOWN	NAGNAG_splice_site|non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417716.2	NM_022769		A	91172567	G	A	91172567	3	1	11	1	0	0	0	0	1	0	0	0	3903	1087	38	1	1111	1	CRTC3	15	91172567	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	401729	91172567	11358825	211	1502											
PGPEP1L	145814	hgsc.bcm.edu	37	chr15	99511839	99511839	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cccagcaggctggccgggagCccgcgcgatagtggagggac	7	3	18	13	4	0	0	0	0	0	0	0	4	0	3	3	5	2	2	3	5	1	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr15:99511839C>T	ENST00000378919.6	-	5	664	c.459G>A	c.(457-459)ggG>ggA	p.G153G	RP11-654A16.3_ENST00000559468.1_RNA|PGPEP1L_ENST00000535714.1_Silent_p.G99G	NM_001102612.2	NP_001096082.2	A6NFU8	PGPIL_HUMAN	pyroglutamyl-peptidase I-like	153							cysteine-type peptidase activity (GO:0008234)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(2)|skin(1)|stomach(1)	14						TGGCCGGGAGCCCGCGCGATA	0.552																																					p.G153G		Atlas-SNP	.											PGPEP1L,NS,carcinoma,-1,1	PGPEP1L	26	1	0			c.G459A						PASS	.						32	32	32					15																	99511839		1964	4147	6111	SO:0001819	synonymous_variant	145814	exon5			CGGGAGCCCGCGC		CCDS53977.1, CCDS58400.1	15q26.3	2010-02-16			ENSG00000183571	ENSG00000183571			27080	protein-coding gene	gene with protein product							Standard	NM_001102612		Approved		uc002bum.3	A6NFU8		ENST00000378919.6:c.459G>A	15.37:g.99511839C>T		137	0	0		178	47	0.264045	NM_001102612	H0YF86	Silent	SNP	ENST00000378919.6	37	CCDS53977.1																																																																																			.	.	none		0.552	PGPEP1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415703.1	NM_001102612.2		T	99511839	C	T	99511839	2	4	11	1	0	0	0	0	0	0	0	1	11813	726	26	2		2	PGPEP1L	15	99511839	Silent	SNP	C	TCGA-FF-8042-01A-11D-2210-10	8339272	99511839	3019553	212	1503											
GRIN2A	2903	hgsc.bcm.edu	37	chr16	10274133	10274133	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgaagttcgcgctctgtcaCgtcgtggctgtgacccagca	6	10	12	13	5	2	1	1	1	1	0	5	2	2	1	1	1	1	4	1	1	1	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr16:10274133C>T	ENST00000396573.2	-	3	445	c.136G>A	c.(136-138)Gtg>Atg	p.V46M	GRIN2A_ENST00000562109.1_Missense_Mutation_p.V46M|GRIN2A_ENST00000404927.2_Missense_Mutation_p.V46M|GRIN2A_ENST00000396575.2_Missense_Mutation_p.V46M|GRIN2A_ENST00000330684.3_Missense_Mutation_p.V46M	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	46					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.V46L(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)	CGCTCTGTCACGTCGTGGCTG	0.697																																					p.V46M		Atlas-SNP	.											GRIN2A,NS,carcinoma,0,1	GRIN2A	366	1	1	Substitution - Missense(1)	lung(1)	c.G136A						PASS	.						50	55	53					16																	10274133		2197	4300	6497	SO:0001583	missense	2903	exon3			CTGTCACGTCGTG		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.136G>A	16.37:g.10274133C>T	ENSP00000379818:p.Val46Met	49	0	0		40	16	0.4	NM_000833	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	37	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	C	13.76	2.334675	0.41297	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000330684;ENST00000396575	D;D;D;D	0.86497	-2.13;-2.13;-2.13;-2.13	4.54	3.58	0.41010	.	0.264378	0.28977	N	0.013526	T	0.72700	0.3493	N	0.22421	0.69	0.80722	D	1	B;P;P	0.41041	0.002;0.736;0.609	B;B;B	0.30782	0.0;0.12;0.041	T	0.65561	-0.6138	9	.	.	.	.	8.8007	0.34907	0.0:0.7269:0.0:0.2731	.	46;46;46	Q547U9;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	M	46	ENSP00000379818:V46M;ENSP00000385872:V46M;ENSP00000332549:V46M;ENSP00000379820:V46M	.	V	-	1	0	GRIN2A	10181634	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	1.062000	0.30555	0.378000	0.24764	-1.134000	0.01955	GTG	.	.	none		0.697	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			T	10274133	C	T	10274133	3	4	11	1	0	0	0	0	1	0	0	0	6788	536	19	1	4306	1	GRIN2A	16	10274133	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10		10274133	80080620	213	1504											
CNTNAP4	85445	hgsc.bcm.edu	37	chr16	76350339	76350339	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgatcctcttgtgtctgccTtgcctcaggcatccttcagc	5	14	8	14	0	4	1	2	1	2	0	6	1	6	1	4	1	3	1	4	1	0	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr16:76350339T>G	ENST00000476707.1	+	1	263	c.124T>G	c.(124-126)Ttg>Gtg	p.L42V	CNTNAP4_ENST00000377504.4_Missense_Mutation_p.L38V|CNTNAP4_ENST00000307431.8_Missense_Mutation_p.L38V|CNTNAP4_ENST00000478060.1_Missense_Mutation_p.L14V|CNTNAP4_ENST00000469589.1_3'UTR			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	39	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				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						TGTGTCTGCCTTGCCTCAGGC	0.483																																					p.L14V		Atlas-SNP	.											.	CNTNAP4	600	.	0			c.T40G						PASS	.						128	92	104					16																	76350339		2198	4300	6498	SO:0001583	missense	85445	exon2			TCTGCCTTGCCTC	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.124T>G	16.37:g.76350339T>G	ENSP00000417628:p.Leu42Val	150	0	0		126	54	0.428571	NM_138994	E9PFZ6|Q86YZ7	Missense_Mutation	SNP	ENST00000476707.1	37		.	.	.	.	.	.	.	.	.	.	T	17.04	3.287086	0.59867	.	.	ENSG00000152910	ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707	D;D;D;D	0.97328	-4.34;-4.34;-4.34;-4.34	4.39	0.937	0.19494	Coagulation factor 5/8 C-terminal type domain (2);Galactose-binding domain-like (1);	0.000000	0.31554	N	0.007446	D	0.97704	0.9247	.	.	.	0.34919	D	0.748277	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.83275	0.983;0.983;0.982;0.996	D	0.97326	0.9947	9	0.87932	D	0	.	7.0566	0.25104	0.0:0.402:0.0:0.598	.	14;42;14;39	E9PFZ6;E9PDN6;Q96M80;Q9C0A0	.;.;.;CNTP4_HUMAN	V	38;38;14;42	ENSP00000306893:L38V;ENSP00000439733:L38V;ENSP00000418741:L14V;ENSP00000417628:L42V	ENSP00000306893:L38V	L	+	1	2	CNTNAP4	74907840	0.986000	0.35501	0.932000	0.37286	0.951000	0.60555	2.133000	0.42093	0.040000	0.15660	0.533000	0.62120	TTG	.	.	none		0.483	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401		G	76350339	T	G	76350339	3	3	11	1	0	0	0	0	1	0	0	0	3651	1606	56	5	134	5	CNTNAP4	16	76350339	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	66076206	76350339	14004414	214	1505											
PITPNM3	83394	hgsc.bcm.edu	37	chr17	6367558	6367558	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcggcacattgtatgtgatGcgaccactgctgttggtgat	7	12	13	9	3	0	2	0	2	0	0	0	3	0	2	1	2	2	4	1	2	1	3	rs561217506		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr17:6367558G>C	ENST00000262483.8	-	16	2175	c.2088C>G	c.(2086-2088)cgC>cgG	p.R696R	PITPNM3_ENST00000421306.3_Silent_p.R660R|PITPNM3_ENST00000576664.1_5'UTR	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	696					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)		TGTATGTGATGCGACCACTGC	0.597																																					p.R696R		Atlas-SNP	.											PITPNM3,colon,carcinoma,-1,1	PITPNM3	91	1	0			c.C2088G						PASS	.						83	81	81					17																	6367558		2203	4300	6503	SO:0001819	synonymous_variant	83394	exon16			TGTGATGCGACCA	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.2088C>G	17.37:g.6367558G>C		140	0	0		77	25	0.324675	NM_031220	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	Silent	SNP	ENST00000262483.8	37	CCDS11076.1																																																																																			.	.	none		0.597	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219824.2	NM_031220		C	6367558	G	C	6367558	2	2	11	1	0	0	0	0	0	0	0	1	11961	1306	46	4		4	PITPNM3	17	6367558	Silent	SNP	G	TCGA-FF-8042-01A-11D-2210-10		6367558	74827652	215	1506											
AMAC1L3	643664	hgsc.bcm.edu	37	chr17	7386300	7386300	+	Missense_Mutation	SNP	G	G	A																															ggaacctcagctgtgagaggGaagggaaggtggaggagtga																										TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr17:7386300G>A	ENST00000412468.2	+	2	1112	c.997G>A	c.(997-999)Gaa>Aaa	p.E333K	POLR2A_ENST00000322644.6_5'Flank|ZBTB4_ENST00000311403.4_Intron|POLR2A_ENST00000572844.1_5'Flank	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	333						integral component of membrane (GO:0016021)											CTGTGAGAGGGAAGGGAAGGT	0.557																																					p.E333K		Atlas-SNP	.											POLR2A_ENST00000412468,NS,carcinoma,-1,1	.	.	1	0			c.G997A						scavenged	.						60	59	59					17																	7386300		2203	4300	6503	SO:0001583	missense	643664	exon2			GAGAGGGAAGGGA		CCDS45603.1	17p13.1	2013-05-22	2011-08-03	2011-08-03		ENSG00000259224		"Solute carriers"	31351	protein-coding gene	gene with protein product			"transmembrane protein 21B", "acyl-malonyl condensing enzyme 1-like 3"	TMEM21B, AMAC1L3			Standard	NM_001102614		Approved		uc010cmj.1	P0C7Q6		ENST00000412468.2:c.997G>A	17.37:g.7386300G>A	ENSP00000396523:p.Glu333Lys	142	2	0.0140845		134	12	0.0895522	NM_001102614		Missense_Mutation	SNP	ENST00000412468.2	37	CCDS45603.1	.	.	.	.	.	.	.	.	.	.	G	0.033	-1.322479	0.01320	.	.	ENSG00000181222	ENST00000412468	T	0.26518	1.73	4.69	1.44	0.22558	.	.	.	.	.	T	0.14056	0.0340	L	0.36672	1.1	0.09310	N	1	B	0.18013	0.025	B	0.15870	0.014	T	0.37526	-0.9702	9	0.02654	T	1	-0.2286	4.7772	0.13185	0.2637:0.1728:0.5636:0.0	.	333	P0C7Q6	S35G6_HUMAN	K	333	ENSP00000396523:E333K	ENSP00000396523:E333K	E	+	1	0	SLC35G6	7327024	1.000000	0.71417	0.321000	0.25320	0.451000	0.32288	4.403000	0.59729	0.499000	0.27970	-0.225000	0.12378	GAA	.	.	none		0.557	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614		A	7386300	G	A	7386300	3	1	11	1	0	0	0	0	1	0	0	0	561	1175	41	2	1003	2	AMAC1L3	17	7386300	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	1018742	7386300	73808910	216	1507	22	2									
AMAC1L3	643664	hgsc.bcm.edu	37	chr17	7386301	7386301	+	Missense_Mutation	SNP	A	A	C																															gaacctcagctgtgagagggAagggaaggtggaggagtgag																										TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr17:7386301A>C	ENST00000412468.2	+	2	1113	c.998A>C	c.(997-999)gAa>gCa	p.E333A	POLR2A_ENST00000322644.6_5'Flank|ZBTB4_ENST00000311403.4_Intron|POLR2A_ENST00000572844.1_5'Flank	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	333						integral component of membrane (GO:0016021)		p.E333A(1)									TGTGAGAGGGAAGGGAAGGTG	0.557																																					p.E333A		Atlas-SNP	.											POLR2A_ENST00000412468,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	prostate(1)	c.A998C						scavenged	.						60	58	59					17																	7386301		2203	4300	6503	SO:0001583	missense	643664	exon2			AGAGGGAAGGGAA		CCDS45603.1	17p13.1	2013-05-22	2011-08-03	2011-08-03		ENSG00000259224		"Solute carriers"	31351	protein-coding gene	gene with protein product			"transmembrane protein 21B", "acyl-malonyl condensing enzyme 1-like 3"	TMEM21B, AMAC1L3			Standard	NM_001102614		Approved		uc010cmj.1	P0C7Q6		ENST00000412468.2:c.998A>C	17.37:g.7386301A>C	ENSP00000396523:p.Glu333Ala	141	2	0.0141844		132	11	0.0833333	NM_001102614		Missense_Mutation	SNP	ENST00000412468.2	37	CCDS45603.1	.	.	.	.	.	.	.	.	.	.	A	2.913	-0.225018	0.06022	.	.	ENSG00000181222	ENST00000412468	T	0.26067	1.76	4.69	1.0	0.19881	.	.	.	.	.	T	0.15609	0.0376	N	0.25647	0.755	0.09310	N	1	B	0.12013	0.005	B	0.13407	0.009	T	0.22626	-1.0211	9	0.36615	T	0.2	-0.2286	5.7938	0.18375	0.4278:0.471:0.1012:0.0	.	333	P0C7Q6	S35G6_HUMAN	A	333	ENSP00000396523:E333A	ENSP00000396523:E333A	E	+	2	0	SLC35G6	7327025	0.886000	0.30341	0.428000	0.26697	0.484000	0.33280	1.649000	0.37281	0.732000	0.32470	0.477000	0.44152	GAA	.	.	none		0.557	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614		C	7386301	A	C	7386301	3	2	11	1	0	0	0	0	1	0	0	0	561	246	9	5	1004	5	AMAC1L3	17	7386301	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	1	7386301	73808909	217	1508	22	2									
RAI1	10743	hgsc.bcm.edu	37	chr17	17699094	17699095	+	Frame_Shift_Del	DEL	CT	CT	-																															gtccagagctggtttgagtcCtctctgtcacacatgaagcc																										TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr17:17699094_17699095delCT	ENST00000353383.1	+	3	3301_3302	c.2832_2833delCT	c.(2830-2835)tcctctfs	p.SS944fs	RAI1_ENST00000261641.6_Frame_Shift_Del_p.SS944fs	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	944					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)		GGTTTGAGTCCTCTCTGTCACA	0.634																																					p.944_944del		Pindel,Atlas-Indel	.											.	RAI1	121	.	0			c.2831_2832del						PASS	.																																			SO:0001589	frameshift_variant	10743	exon3			.	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.2832_2833delCT	17.37:g.17699098_17699099delCT	ENSP00000323074:p.Ser944fs	125	0	.		126	41	0.325	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Frame_Shift_Del	DEL	ENST00000353383.1	37	CCDS11188.1																																																																																			.	.	none		0.634	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665		-	17699095	CT	-	17699094	7	5	11	1	0	1	0	1	0	0	0	0	13022	668	24	0	2834	0	RAI1	17	17699094	Frame_Shift_Del	DEL	CT	TCGA-FF-8042-01A-11D-2210-10	10312793	17699094	63496116	218	1509											
RAI1	10743	hgsc.bcm.edu	37	chr17	17701758	17701758	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggcctgtgccgtgtggacCggcggcgtctacctggtggc	3	8	18	12	4	1	0	0	0	1	0	1	2	1	1	4	6	2	0	4	6	1	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr17:17701758C>T	ENST00000353383.1	+	3	5965	c.5496C>T	c.(5494-5496)acC>acT	p.T1832T	RAI1_ENST00000261641.6_Intron	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	1832					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)		CCGTGTGGACCGGCGGCGTCT	0.677																																					p.T1832T		Atlas-SNP	.											.	RAI1	121	.	0			c.C5496T						PASS	.						21	21	21					17																	17701758		2200	4298	6498	SO:0001819	synonymous_variant	10743	exon3			GTGGACCGGCGGC	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.5496C>T	17.37:g.17701758C>T		37	0	0		24	11	0.458333	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Silent	SNP	ENST00000353383.1	37	CCDS11188.1																																																																																			.	.	none		0.677	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665		T	17701758	C	T	17701758	2	4	11	1	0	0	0	0	0	0	0	1	13022	639	23	1		1	RAI1	17	17701758	Silent	SNP	C	TCGA-FF-8042-01A-11D-2210-10	2664	17701758	63493452	219	1510											
SLC47A1	55244	hgsc.bcm.edu	37	chr17	19470152	19470152	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccaatttatgctgtttccCacctctttgaagctcttgct	6	18	5	12	0	2	1	0	1	2	0	4	1	4	1	3	0	3	4	3	0	3	6	rs547527862		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr17:19470152C>T	ENST00000270570.4	+	13	1242	c.1156C>T	c.(1156-1158)Cac>Tac	p.H386Y	SLC47A1_ENST00000436810.2_Missense_Mutation_p.H363Y|SLC47A1_ENST00000575023.1_Intron|SLC47A1_ENST00000571335.1_Missense_Mutation_p.H191Y|RP11-1113L8.1_ENST00000574267.1_RNA|SLC47A1_ENST00000457293.1_Missense_Mutation_p.H386Y|SLC47A1_ENST00000395585.1_Missense_Mutation_p.H386Y	NM_018242.2	NP_060712.2	Q96FL8	S47A1_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 1	386					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)	TGCTGTTTCCCACCTCTTTGA	0.433																																					p.H386Y		Atlas-SNP	.											.	SLC47A1	55	.	0			c.C1156T						PASS	.						229	200	210					17																	19470152		2203	4300	6503	SO:0001583	missense	55244	exon13			GTTTCCCACCTCT		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.1156C>T	17.37:g.19470152C>T	ENSP00000270570:p.His386Tyr	291	0	0		194	76	0.391753	NM_018242	Q53HF5|Q6PD77|Q86VL4|Q9NVA3	Missense_Mutation	SNP	ENST00000270570.4	37	CCDS11209.1	.	.	.	.	.	.	.	.	.	.	C	16.18	3.051596	0.55218	.	.	ENSG00000142494	ENST00000436810;ENST00000270570;ENST00000457293;ENST00000395585;ENST00000455670;ENST00000424755	T;T;T;T	0.26957	1.7;1.7;1.7;1.7	5.37	4.41	0.53225	.	0.213703	0.47852	D	0.000204	T	0.52517	0.1739	M	0.92026	3.265	0.80722	D	1	P;D;B;D;D	0.76494	0.951;0.999;0.295;0.994;0.978	P;D;B;D;P	0.72982	0.837;0.968;0.356;0.979;0.888	T	0.63967	-0.6517	10	0.07482	T	0.82	-3.635	12.7652	0.57388	0.0:0.9198:0.0:0.0802	.	120;363;120;386;386	E7ENC3;E7EX57;B4DDH5;Q96FL8;Q96FL8-3	.;.;.;S47A1_HUMAN;.	Y	363;386;386;386;120;98	ENSP00000407155:H363Y;ENSP00000270570:H386Y;ENSP00000415586:H386Y;ENSP00000378951:H386Y	ENSP00000270570:H386Y	H	+	1	0	SLC47A1	19410744	0.998000	0.40836	0.995000	0.50966	0.563000	0.35712	4.492000	0.60334	1.277000	0.44412	-0.136000	0.14681	CAC	.	.	none		0.433	SLC47A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132250.1	NM_018242		T	19470152	C	T	19470152	3	4	11	1	0	0	0	0	1	0	0	0	14662	594	21	2	1206	2	SLC47A1	17	19470152	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	1768394	19470152	61725058	220	1511											
GGNBP2	79893	hgsc.bcm.edu	37	chr17	34912947	34912947	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	atggtatgcttaagcaacagGatctaagtattgccatggtg	12	12	11	6	0	1	0	0	0	1	0	1	1	1	1	1	3	4	4	1	3	5	5			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr17:34912947G>T	ENST00000304718.4	+	4	515	c.199G>T	c.(199-201)Gat>Tat	p.D67Y		NM_024835.3	NP_079111.1	Q9H3C7	GGNB2_HUMAN	gametogenetin binding protein 2	67					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)		TAAGCAACAGGATCTAAGTAT	0.443																																					p.D67Y		Atlas-SNP	.											.	GGNBP2	72	.	0			c.G199T						PASS	.						193	178	183					17																	34912947		2203	4300	6503	SO:0001583	missense	79893	exon4			CAACAGGATCTAA	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.199G>T	17.37:g.34912947G>T	ENSP00000307617:p.Asp67Tyr	100	0	0		90	30	0.333333	NM_024835	B2RPK7|Q96T90|Q9GZR8|Q9H767	Missense_Mutation	SNP	ENST00000304718.4	37	CCDS11314.1	.	.	.	.	.	.	.	.	.	.	G	22.3	4.274508	0.80580	.	.	ENSG00000005955	ENST00000304718	.	.	.	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	T	0.58119	0.2100	L	0.36672	1.1	0.80722	D	1	P;P	0.52692	0.955;0.891	P;P	0.48141	0.549;0.568	T	0.64166	-0.6471	9	0.87932	D	0	-6.3477	18.5109	0.90916	0.0:0.0:1.0:0.0	.	67;67	Q9H3C7;Q9H3C7-3	GGNB2_HUMAN;.	Y	67	.	ENSP00000307617:D67Y	D	+	1	0	GGNBP2	31987060	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	8.991000	0.93514	2.376000	0.81061	0.579000	0.79373	GAT	.	.	none		0.443	GGNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256684.2	NM_024835		T	34912947	G	T	34912947	3	4	11	1	0	0	0	0	1	0	0	0	6367	1174	41	4	209	4	GGNBP2	17	34912947	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	15442795	34912947	46282263	221	1512											
AATF	26574	hgsc.bcm.edu	37	chr17	35307529	35307529	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacagccactgctgccagggTgattgacaggtttgatgaag	10	9	14	8	0	0	4	0	4	0	0	0	5	0	4	2	2	3	2	2	2	1	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr17:35307529T>C	ENST00000225402.5	+	2	358	c.107T>C	c.(106-108)gTg>gCg	p.V36A		NM_012138.3	NP_036270.1	Q9NY61	AATF_HUMAN	apoptosis antagonizing transcription factor	36					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)				GCTGCCAGGGTGATTGACAGG	0.493																																					p.V36A	NSCLC(49;901 1159 19183 41572 46244)	Atlas-SNP	.											.	AATF	36	.	0			c.T107C						PASS	.						128	131	130					17																	35307529		2203	4300	6503	SO:0001583	missense	26574	exon2			CCAGGGTGATTGA	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.107T>C	17.37:g.35307529T>C	ENSP00000225402:p.Val36Ala	116	0	0		127	50	0.393701	NM_012138	A6NCJ6|B3KQ26|Q9P0A4|Q9UNX5	Missense_Mutation	SNP	ENST00000225402.5	37	CCDS32632.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.607702	0.87157	.	.	ENSG00000108270	ENST00000225402	T	0.38887	1.11	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.61337	0.2339	M	0.76574	2.34	0.58432	D	0.999997	D	0.76494	0.999	D	0.78314	0.991	T	0.59440	-0.7454	10	0.10902	T	0.67	-15.8584	15.3994	0.74827	0.0:0.0:0.0:1.0	.	36	Q9NY61	AATF_HUMAN	A	36	ENSP00000225402:V36A	ENSP00000225402:V36A	V	+	2	0	AATF	32381642	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.762000	0.74950	2.117000	0.64856	0.402000	0.26972	GTG	.	.	none		0.493	AATF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451543.1	NM_012138		C	35307529	T	C	35307529	3	2	11	1	0	0	0	0	1	0	0	0	25	1696	59	3	113	3	AATF	17	35307529	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	394582	35307529	45887681	222	1513											
CASC3	22794	hgsc.bcm.edu	37	chr17	38325589	38325589	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggtcccaggccccatcacagGtatatggaggagtgacctac	10	7	12	12	0	1	1	1	1	0	0	2	3	2	3	4	5	1	1	4	5	3	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr17:38325589G>A	ENST00000264645.7	+	12	2204	c.1978G>A	c.(1978-1980)Gta>Ata	p.V660I		NM_007359.4	NP_031385.2	O15234	CASC3_HUMAN	cancer susceptibility candidate 3	660	Necessary for localization in cytoplasmic stress granules.				gene expression (GO:0010467)|intracellular mRNA localization (GO:0008298)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translation (GO:0006417)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)	cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|ribonucleoprotein complex (GO:0030529)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|kidney(2)|large_intestine(3)|lung(4)|ovary(1)|urinary_tract(2)	16						CCCATCACAGGTATATGGAGG	0.537																																					p.V660I		Atlas-SNP	.											.	CASC3	39	.	0			c.G1978A						PASS	.						80	90	87					17																	38325589		2203	4300	6503	SO:0001583	missense	22794	exon12			TCACAGGTATATG	X80199	CCDS11362.1	17q21.1	2012-09-20			ENSG00000108349	ENSG00000108349			17040	protein-coding gene	gene with protein product		606504				7490069, 18332872	Standard	NM_007359		Approved	MLN51, BTZ	uc002hue.3	O15234	OTTHUMG00000133323	ENST00000264645.7:c.1978G>A	17.37:g.38325589G>A	ENSP00000264645:p.Val660Ile	222	0	0		206	68	0.330097	NM_007359	A8K8R0	Missense_Mutation	SNP	ENST00000264645.7	37	CCDS11362.1	.	.	.	.	.	.	.	.	.	.	G	32	5.120484	0.94385	.	.	ENSG00000108349	ENST00000264645;ENST00000394114	.	.	.	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.65883	0.2734	L	0.27053	0.805	0.80722	D	1	D	0.64830	0.994	D	0.72625	0.978	T	0.66748	-0.5845	9	0.49607	T	0.09	-11.1308	18.5194	0.90947	0.0:0.0:1.0:0.0	.	660	O15234	CASC3_HUMAN	I	660	.	ENSP00000264645:V660I	V	+	1	0	CASC3	35579115	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.121000	0.94375	2.778000	0.95560	0.655000	0.94253	GTA	.	.	none		0.537	CASC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257127.3	NM_007359		A	38325589	G	A	38325589	3	1	11	1	0	0	0	0	1	0	0	0	2663	1261	44	2	2024	2	CASC3	17	38325589	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	3018060	38325589	42869621	223	1514											
KRT12	3859	hgsc.bcm.edu	37	chr17	39019783	39019783	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctccaggttctgaaaggcgCgacgcaggtcggtgacctcg	7	8	14	12	5	2	2	0	2	2	0	5	3	2	2	2	4	0	2	2	4	1	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr17:39019783C>T	ENST00000251643.4	-	5	1072	c.1049G>A	c.(1048-1050)cGc>cAc	p.R350H	RP5-1110E20.1_ENST00000579136.1_RNA	NM_000223.3	NP_000214.1	Q99456	K1C12_HUMAN	keratin 12	350	Coil 2.|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)	CTGAAAGGCGCGACGCAGGTC	0.562																																					p.R350H		Atlas-SNP	.											.	KRT12	53	.	0			c.G1049A						PASS	.						80	66	71					17																	39019783		2203	4300	6503	SO:0001583	missense	3859	exon5			AAGGCGCGACGCA		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.1049G>A	17.37:g.39019783C>T	ENSP00000251643:p.Arg350His	139	0	0		99	36	0.363636	NM_000223	B2R9E0	Missense_Mutation	SNP	ENST00000251643.4	37	CCDS11378.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.178992	0.78564	.	.	ENSG00000187242	ENST00000251643	D	0.90504	-2.68	5.44	5.44	0.79542	Filament (1);	0.000000	0.49305	D	0.000145	D	0.93167	0.7824	M	0.84156	2.68	0.53688	D	0.999972	D	0.69078	0.997	P	0.51101	0.659	D	0.93791	0.7092	10	0.62326	D	0.03	.	14.4797	0.67573	0.0:0.9274:0.0:0.0726	.	350	Q99456	K1C12_HUMAN	H	350	ENSP00000251643:R350H	ENSP00000251643:R350H	R	-	2	0	KRT12	36273309	1.000000	0.71417	0.959000	0.39883	0.443000	0.32047	3.335000	0.52105	2.542000	0.85734	0.491000	0.48974	CGC	.	.	none		0.562	KRT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257214.2	NM_000223		T	39019783	C	T	39019783	3	4	11	1	0	0	0	0	1	0	0	0	8458	768	27	1	451	1	KRT12	17	39019783	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	694194	39019783	42175427	224	1515											
HELZ	9931	hgsc.bcm.edu	37	chr17	65186460	65186460	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccatacctacagattcctTgttctaaaaatctaagtaga	15	12	4	10	0	2	2	0	0	2	2	3	2	3	2	3	0	2	2	3	0	7	8			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr17:65186460T>C	ENST00000358691.5	-	10	735	c.569A>G	c.(568-570)cAa>cGa	p.Q190R	HELZ_ENST00000580168.1_Missense_Mutation_p.Q190R|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)					ACAGATTCCTTGTTCTAAAAA	0.363																																					p.Q190R		Atlas-SNP	.											.	HELZ	160	.	0			c.A569G						PASS	.						108	98	101					17																	65186460		1841	4088	5929	SO:0001583	missense	9931	exon10			ATTCCTTGTTCTA	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.569A>G	17.37:g.65186460T>C	ENSP00000351524:p.Gln190Arg	179	0	0		144	57	0.395833	NM_014877	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	37	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	T	11.57	1.678552	0.29783	.	.	ENSG00000198265	ENST00000358691;ENST00000417253	T;T	0.40476	1.03;1.03	5.38	4.3	0.51218	Zinc finger, CCCH-type (3);	0.000000	0.85682	D	0.000000	T	0.49218	0.1544	L	0.56769	1.78	0.58432	D	0.999997	P;P	0.49961	0.93;0.529	P;B	0.52189	0.692;0.198	T	0.44097	-0.9350	10	0.44086	T	0.13	-11.9044	11.1502	0.48453	0.0:0.0722:0.0:0.9278	.	190;190	B7ZLW2;P42694	.;HELZ_HUMAN	R	190	ENSP00000351524:Q190R;ENSP00000411144:Q190R	ENSP00000351524:Q190R	Q	-	2	0	HELZ	62616922	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.003000	0.57061	0.894000	0.36317	0.533000	0.62120	CAA	.	.	none		0.363	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		C	65186460	T	C	65186460	3	2	11	1	0	0	0	0	1	0	0	0	7058	1812	63	3	5355	3	HELZ	17	65186460	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	26166677	65186460	16008750	225	1516											
DNAI2	64446	hgsc.bcm.edu	37	chr17	72287205	72287205	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgaagccatcgtctccactCgtgacgttggagttcaaccc	8	10	9	14	3	2	2	1	2	1	0	5	3	2	3	3	1	2	2	3	1	2	2	rs539461253		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr17:72287205C>T	ENST00000311014.6	+	6	724	c.657C>T	c.(655-657)ctC>ctT	p.L219L	DNAI2_ENST00000582036.1_Silent_p.L219L|DNAI2_ENST00000307504.5_Silent_p.L76L|DNAI2_ENST00000446837.2_Silent_p.L219L|DNAI2_ENST00000579490.1_Silent_p.L276L			Q9GZS0	DNAI2_HUMAN	dynein, axonemal, intermediate chain 2	219					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						CGTCTCCACTCGTGACGTTGG	0.463									Kartagener syndrome																												p.L219L		Atlas-SNP	.											.	DNAI2	102	.	0			c.C657T						PASS	.						183	189	187					17																	72287205		2203	4300	6503	SO:0001819	synonymous_variant	64446	exon6	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	TCCACTCGTGACG	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.657C>T	17.37:g.72287205C>T		123	0	0		111	53	0.477477	NM_001172810	C9J0S6|Q8IUW4|Q9H179|Q9NT53	Silent	SNP	ENST00000311014.6	37	CCDS11697.1																																																																																			.	.	none		0.463	DNAI2-001	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442537.1	NM_023036		T	72287205	C	T	72287205	2	4	11	1	0	0	0	0	0	0	0	1	4612	871	31	1		1	DNAI2	17	72287205	Silent	SNP	C	TCGA-FF-8042-01A-11D-2210-10	7100745	72287205	8908005	226	1517											
HN1	51155	hgsc.bcm.edu	37	chr17	73132201	73132201	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttcaggacagtcagagctaaCccaagacgaggctggacttg	12	7	12	10	1	2	2	2	0	0	2	2	5	2	4	1	3	2	2	1	3	2	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr17:73132201C>T	ENST00000409753.3	-	5	746	c.461G>A	c.(460-462)gGt>gAt	p.G154D	RP11-649A18.5_ENST00000584339.1_RNA|HN1_ENST00000482348.1_Missense_Mutation_p.G108D|HN1_ENST00000392566.2_Missense_Mutation_p.G108D|HN1_ENST00000476258.1_Missense_Mutation_p.G108D|HN1_ENST00000481647.1_Missense_Mutation_p.G108D|HN1_ENST00000470924.1_Missense_Mutation_p.G108D|HN1_ENST00000356033.4_Missense_Mutation_p.V148I|HN1_ENST00000405458.3_Missense_Mutation_p.G108D	NM_016185.2	NP_057269.1	Q9UK76	HN1_HUMAN	hematological and neurological expressed 1	154					developmental process (GO:0032502)	nucleus (GO:0005634)			HN1/USH1G(2)	breast(1)	1	all_lung(278;0.14)|Lung NSC(278;0.168)					TCAGAGCTAACCCAAGACGAG	0.582																																					p.G154D		Atlas-SNP	.											.	HN1	17	.	0			c.G461A						PASS	.						81	78	79					17																	73132201		2203	4300	6503	SO:0001583	missense	51155	exon5			AGCTAACCCAAGA	AF086910	CCDS32729.1, CCDS45771.1, CCDS45772.1	17q25.1	2013-09-20			ENSG00000189159	ENSG00000189159			14569	protein-coding gene	gene with protein product	"androgen-regulated protein 2"					15094197	Standard	NM_001002032		Approved	ARM2, HN1A	uc002jnb.1	Q9UK76	OTTHUMG00000154521	ENST00000409753.3:c.461G>A	17.37:g.73132201C>T	ENSP00000387059:p.Gly154Asp	172	0	0		128	49	0.382812	NM_016185	B2R6K3|Q53FG7|Q7Z2D2|Q7Z2F0	Missense_Mutation	SNP	ENST00000409753.3	37	CCDS45771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.6|25.6	4.658406|4.658406	0.88154|0.88154	.|.	.|.	ENSG00000189159|ENSG00000189159	ENST00000405458;ENST00000409753;ENST00000392566|ENST00000356033	.|.	.|.	.|.	5.87|5.87	5.87|5.87	0.94306|0.94306	.|.	.|0.921149	.|0.09115	.|N	.|0.846595	T|T	0.57227|0.57227	0.2039|0.2039	.|.	.|.	.|.	0.48040|0.48040	D|D	0.999573|0.999573	D|P	0.89917|0.39480	1.0|0.675	D|B	0.91635|0.36134	0.999|0.218	T|T	0.59915|0.59915	-0.7364|-0.7364	7|8	0.87932|0.87932	D|D	0|0	-20.073|-20.073	18.3821|18.3821	0.90454|0.90454	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	154|148	Q9UK76|Q9UK76-2	HN1_HUMAN|.	D|I	108;154;108|148	.|.	ENSP00000440912:G108D|ENSP00000348316:V148I	G|V	-|-	2|1	0|0	HN1|HN1	70643796|70643796	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.822000|0.822000	0.46500|0.46500	4.949000|4.949000	0.63596|0.63596	2.773000|2.773000	0.95371|0.95371	0.643000|0.643000	0.83706|0.83706	GGT|GTT	.	.	none		0.582	HN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335692.1	NM_001002032		T	73132201	C	T	73132201	3	4	11	1	0	0	0	0	1	0	0	0	7258	507	18	2	107	2	HN1	17	73132201	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	844996	73132201	8063009	227	1518											
ACOX1	51	hgsc.bcm.edu	37	chr17	73944495	73944495	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtgagtaactcctttacaCgctggtttacttgtgtaatc	9	15	9	8	1	0	1	0	1	0	0	2	2	1	1	1	1	3	4	1	1	4	7	rs369561903		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr17:73944495C>T	ENST00000301608.4	-	13	1832	c.1772G>A	c.(1771-1773)cGt>cAt	p.R591H	ACOX1_ENST00000293217.5_Missense_Mutation_p.R591H|ACOX1_ENST00000537812.1_Missense_Mutation_p.R553H	NM_007292.5	NP_009223.2	Q15067	ACOX1_HUMAN	acyl-CoA oxidase 1, palmitoyl	591					alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid oxidation (GO:0019395)|generation of precursor metabolites and energy (GO:0006091)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|peroxisome fission (GO:0016559)|positive regulation of cholesterol homeostasis (GO:2000189)|prostaglandin metabolic process (GO:0006693)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|FAD binding (GO:0071949)|fatty acid binding (GO:0005504)|flavin adenine dinucleotide binding (GO:0050660)|palmitoyl-CoA oxidase activity (GO:0016401)|PDZ domain binding (GO:0030165)|protein N-terminus binding (GO:0047485)|receptor binding (GO:0005102)			large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(1)	14					Flavin adenine dinucleotide(DB03147)	CTCCTTTACACGCTGGTTTAC	0.388																																					p.R591H		Atlas-SNP	.											ACOX1_ENST00000301608,caecum,carcinoma,-1,2	ACOX1	85	2	0			c.G1772A						scavenged	.	T	HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	157	135	143		1658,1772,1772	2.2	0.1	17		143	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	ACOX1	NM_001185039.1,NM_004035.6,NM_007292.5	29,29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	553/623,591/661,591/661	73944495	1,13005	2203	4300	6503	SO:0001583	missense	51	exon13			TTTACACGCTGGT	U03254	CCDS11734.1, CCDS11735.1	17q25.1	2012-10-04	2010-04-30		ENSG00000161533	ENSG00000161533	1.3.3.6		119	protein-coding gene	gene with protein product		609751	"acyl-Coenzyme A oxidase 1, palmitoyl"			8159712	Standard	NM_007292		Approved	PALMCOX	uc002jqe.3	Q15067	OTTHUMG00000180027	ENST00000301608.4:c.1772G>A	17.37:g.73944495C>T	ENSP00000301608:p.Arg591His	74	0	0		58	3	0.0517241	NM_007292	A8K6X8|A8KAA0|B4DK61|F5GYQ8|Q12863|Q15068|Q15101|Q16131|Q7Z3W5|Q9UD31	Missense_Mutation	SNP	ENST00000301608.4	37	CCDS11735.1	.	.	.	.	.	.	.	.	.	.	c	10.48	1.360962	0.24684	0.0	1.16E-4	ENSG00000161533	ENST00000301608;ENST00000293217;ENST00000537812;ENST00000539791;ENST00000538781	T;T;T	0.44881	0.91;0.91;0.91	5.25	2.23	0.28157	Acyl-CoA oxidase, C-terminal (1);Acyl-CoA dehydrogenase/oxidase C-terminal (2);	0.099482	0.64402	N	0.000003	T	0.36413	0.0966	L	0.58669	1.825	0.27295	N	0.957734	B;B;B;B	0.16166	0.006;0.003;0.016;0.007	B;B;B;B	0.12156	0.005;0.005;0.007;0.003	T	0.27938	-1.0059	10	0.33940	T	0.23	-11.4201	10.7402	0.46149	0.0:0.7301:0.0:0.2699	.	523;553;591;591	F5H0M0;F5GYQ8;Q15067;Q15067-2	.;.;ACOX1_HUMAN;.	H	591;591;553;591;523	ENSP00000301608:R591H;ENSP00000293217:R591H;ENSP00000441257:R553H	ENSP00000293217:R591H	R	-	2	0	ACOX1	71456090	0.882000	0.30256	0.075000	0.20258	0.408000	0.30992	1.744000	0.38268	0.891000	0.36235	-0.726000	0.03593	CGT	.	.	weak		0.388	ACOX1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439503.1			T	73944495	C	T	73944495	3	4	11	1	0	0	0	0	1	0	0	0	158	536	19	1	218	1	ACOX1	17	73944495	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	812294	73944495	7250715	228	1519											
ACOX1	51	hgsc.bcm.edu	37	chr17	73945827	73945827	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acggagtttatatgcttcggTtaggctttcggggctgttga	6	15	14	6	3	0	1	0	1	0	0	2	2	0	2	0	5	1	6	0	5	3	7			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr17:73945827T>G	ENST00000301608.4	-	10	1510	c.1450A>C	c.(1450-1452)Acc>Ccc	p.T484P	ACOX1_ENST00000293217.5_Missense_Mutation_p.T484P|ACOX1_ENST00000537812.1_Missense_Mutation_p.T446P	NM_007292.5	NP_009223.2	Q15067	ACOX1_HUMAN	acyl-CoA oxidase 1, palmitoyl	484					alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid oxidation (GO:0019395)|generation of precursor metabolites and energy (GO:0006091)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|peroxisome fission (GO:0016559)|positive regulation of cholesterol homeostasis (GO:2000189)|prostaglandin metabolic process (GO:0006693)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|FAD binding (GO:0071949)|fatty acid binding (GO:0005504)|flavin adenine dinucleotide binding (GO:0050660)|palmitoyl-CoA oxidase activity (GO:0016401)|PDZ domain binding (GO:0030165)|protein N-terminus binding (GO:0047485)|receptor binding (GO:0005102)			large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(1)	14					Flavin adenine dinucleotide(DB03147)	TATGCTTCGGTTAGGCTTTCG	0.562																																					p.T484P		Atlas-SNP	.											.	ACOX1	85	.	0			c.A1450C						PASS	.						117	93	101					17																	73945827		2203	4300	6503	SO:0001583	missense	51	exon10			CTTCGGTTAGGCT	U03254	CCDS11734.1, CCDS11735.1	17q25.1	2012-10-04	2010-04-30		ENSG00000161533	ENSG00000161533	1.3.3.6		119	protein-coding gene	gene with protein product		609751	"acyl-Coenzyme A oxidase 1, palmitoyl"			8159712	Standard	NM_007292		Approved	PALMCOX	uc002jqe.3	Q15067	OTTHUMG00000180027	ENST00000301608.4:c.1450A>C	17.37:g.73945827T>G	ENSP00000301608:p.Thr484Pro	151	0	0		147	58	0.394558	NM_007292	A8K6X8|A8KAA0|B4DK61|F5GYQ8|Q12863|Q15068|Q15101|Q16131|Q7Z3W5|Q9UD31	Missense_Mutation	SNP	ENST00000301608.4	37	CCDS11735.1	.	.	.	.	.	.	.	.	.	.	T	12.87	2.066538	0.36470	.	.	ENSG00000161533	ENST00000301608;ENST00000293217;ENST00000537812;ENST00000539791;ENST00000538781	T;T;T	0.46819	0.86;0.86;0.86	5.62	1.07	0.20283	Acyl-CoA oxidase, C-terminal (1);Acyl-CoA dehydrogenase/oxidase C-terminal (2);	0.418244	0.27060	N	0.021135	T	0.51770	0.1694	M	0.73962	2.25	0.09310	N	0.999999	P;P;P;P	0.50369	0.688;0.838;0.536;0.934	B;P;P;P	0.50082	0.43;0.63;0.566;0.513	T	0.45323	-0.9269	10	0.56958	D	0.05	-4.3019	7.6917	0.28571	0.0:0.5105:0.0:0.4895	.	416;446;484;484	F5H0M0;F5GYQ8;Q15067;Q15067-2	.;.;ACOX1_HUMAN;.	P	484;484;446;484;416	ENSP00000301608:T484P;ENSP00000293217:T484P;ENSP00000441257:T446P	ENSP00000293217:T484P	T	-	1	0	ACOX1	71457422	0.350000	0.24878	0.002000	0.10522	0.230000	0.25150	1.643000	0.37217	0.428000	0.26173	0.528000	0.53228	ACC	.	.	none		0.562	ACOX1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439503.1			G	73945827	T	G	73945827	3	3	11	1	0	0	0	0	1	0	0	0	158	1725	60	5	552	5	ACOX1	17	73945827	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	1332	73945827	7249383	229	1520											
ZNF519	162655	hgsc.bcm.edu	37	chr18	14105585	14105585	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattccttacacttgaaaggCttctctccagtatggattct	9	15	6	11	0	2	1	0	1	2	0	5	2	4	2	2	2	1	2	2	2	3	6			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr18:14105585C>T	ENST00000590202.1	-	3	1106	c.954G>A	c.(952-954)aaG>aaA	p.K318K	ZNF519_ENST00000589203.1_Intron|ZNF519_ENST00000589498.1_Intron|RP11-411B10.3_ENST00000592926.1_RNA	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	1	0			c.G954A						PASS	.						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	18.37:g.14105585C>T		49	0	0		86	4	0.0465116	NM_145287		Silent	SNP	ENST00000590202.1	37	CCDS32797.1																																																																																			.	.	none		0.393	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287		T	14105585	C	T	14105585	2	4	11	1	0	0	0	0	0	0	0	1	17979	796	28	2		2	ZNF519	18	14105585	Silent	SNP	C	TCGA-FF-8042-01A-11D-2210-10		14105585	63971663	230	1521											
ANKRD30B	374860	hgsc.bcm.edu	37	chr18	14787093	14787093	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatgaagaaaattcttgggaTtctgaggtactatgtgttat	12	15	11	3	0	2	3	0	2	2	1	2	5	2	4	0	2	1	2	0	2	6	6			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr18:14787093T>A	ENST00000358984.4	+	15	1908	c.1728T>A	c.(1726-1728)gaT>gaA	p.D576E	ANKRD30B_ENST00000579292.1_Intron|ANKRD30B_ENST00000447268.2_Missense_Mutation_p.D576E	NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	576										breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						ATTCTTGGGATTCTGAGGTAC	0.313																																					p.D576E		Atlas-SNP	.											.	ANKRD30B	237	.	0			c.T1728A						PASS	.						163	140	147					18																	14787093		692	1585	2277	SO:0001583	missense	374860	exon15			TTGGGATTCTGAG	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.1728T>A	18.37:g.14787093T>A	ENSP00000351875:p.Asp576Glu	367	0	0		478	74	0.154812	NM_001145029	B4DGP1|F8WAG3|Q4G175	Missense_Mutation	SNP	ENST00000358984.4	37	CCDS54182.1	.	.	.	.	.	.	.	.	.	.	N	14.45	2.540315	0.45176	.	.	ENSG00000180777	ENST00000358984;ENST00000447268	T;T	0.58210	0.37;0.35	1.15	1.15	0.20763	.	.	.	.	.	T	0.60560	0.2278	L	0.61218	1.895	0.20975	N	0.999819	D	0.55605	0.972	P	0.62184	0.899	T	0.46331	-0.9199	9	0.51188	T	0.08	.	4.5356	0.12026	0.0:0.0:0.0:1.0	.	576	F8WAG3	.	E	576	ENSP00000351875:D576E;ENSP00000399031:D576E	ENSP00000351875:D576E	D	+	3	2	ANKRD30B	14777093	0.996000	0.38824	0.911000	0.35937	0.011000	0.07611	1.029000	0.30140	0.788000	0.33755	0.241000	0.17934	GAT	.	.	none		0.313	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029		A	14787093	T	A	14787093	3	1	11	1	0	0	0	0	1	0	0	0	659	1490	52	5	1786	5	ANKRD30B	18	14787093	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	681508	14787093	63290155	231	1522											
ANKRD29	147463	hgsc.bcm.edu	37	chr18	21197729	21197729	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agagtgggtgagaatttaagCaactcttttatgacatcatt	13	14	9	5	0	2	3	1	2	1	2	2	4	2	3	0	1	2	1	0	1	4	5			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr18:21197729C>T	ENST00000592179.1	-	8	844	c.690G>A	c.(688-690)ttG>ttA	p.L230L	ANKRD29_ENST00000586511.1_5'Flank|ANKRD29_ENST00000322980.9_Silent_p.L230L|ANKRD29_ENST00000284207.7_Silent_p.L230L	NM_173505.2	NP_775776.2	Q8N6D5	ANR29_HUMAN	ankyrin repeat domain 29	230										breast(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|skin(1)	13	all_cancers(21;5.07e-05)|all_epithelial(16;2.49e-07)|Lung NSC(20;0.00211)|all_lung(20;0.00676)|Colorectal(14;0.0202)|Ovarian(20;0.127)					AGAATTTAAGCAACTCTTTTA	0.343																																					p.L230L		Atlas-SNP	.											.	ANKRD29	24	.	0			c.G690A						PASS	.						145	133	137					18																	21197729		2202	4300	6502	SO:0001819	synonymous_variant	147463	exon8			TTTAAGCAACTCT	AK057782	CCDS11879.1	18q11.2	2013-01-10			ENSG00000154065	ENSG00000154065		"Ankyrin repeat domain containing"	27110	protein-coding gene	gene with protein product							Standard	NM_173505		Approved	FLJ25053	uc002kun.3	Q8N6D5	OTTHUMG00000131875	ENST00000592179.1:c.690G>A	18.37:g.21197729C>T		85	0	0		177	28	0.158192	NM_173505	B2R972|Q6ZWE8|Q96LU9	Silent	SNP	ENST00000592179.1	37	CCDS11879.1																																																																																			.	.	none		0.343	ANKRD29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254825.1	NM_173505		T	21197729	C	T	21197729	2	4	11	1	0	0	0	0	0	0	0	1	657	709	25	2		2	ANKRD29	18	21197729	Silent	SNP	C	TCGA-FF-8042-01A-11D-2210-10	6410636	21197729	56879519	232	1523											
ZNF521	25925	hgsc.bcm.edu	37	chr18	22669489	22669489	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtacagtcatagatcttgtcTtcttgtccatgggcagagaa	10	13	10	8	0	4	2	1	0	3	2	5	3	5	2	1	1	1	2	1	1	3	5			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr18:22669489T>G	ENST00000361524.3	-	7	3994	c.3846A>C	c.(3844-3846)gaA>gaC	p.E1282D	ZNF521_ENST00000584787.1_Missense_Mutation_p.E1062D|ZNF521_ENST00000538137.2_Missense_Mutation_p.E1282D	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	1282					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)					AGATCTTGTCTTCTTGTCCAT	0.403			T	PAX5	ALL																																p.E1282D		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	.	ZNF521	269	.	0			c.A3846C						PASS	.						190	173	179					18																	22669489		2203	4300	6503	SO:0001583	missense	25925	exon7			CTTGTCTTCTTGT	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.3846A>C	18.37:g.22669489T>G	ENSP00000354794:p.Glu1282Asp	235	0	0		472	70	0.148305	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	37	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	T	11.99	1.804717	0.31961	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	T	0.09445	2.98	5.79	4.62	0.57501	Zinc finger, C2H2 (1);	0.000000	0.64402	D	0.000001	T	0.17746	0.0426	N	0.24115	0.695	0.38064	D	0.93617	D	0.63046	0.992	D	0.77004	0.989	T	0.06144	-1.0843	10	0.48119	T	0.1	-20.6004	9.4859	0.38928	0.0:0.1539:0.0:0.8461	.	1282	Q96K83	ZN521_HUMAN	D	1282;1316;1282	ENSP00000354794:E1282D	ENSP00000354794:E1282D	E	-	3	2	ZNF521	20923487	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.711000	0.47177	0.998000	0.38996	0.528000	0.53228	GAA	.	.	none		0.403	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		G	22669489	T	G	22669489	3	3	11	1	0	0	0	0	1	0	0	0	17980	1606	56	5	97	5	ZNF521	18	22669489	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	1471760	22669489	55407759	233	1524											
ZNF521	25925	hgsc.bcm.edu	37	chr18	22804688	22804688	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgaggcaagatgcgcacttaTacagtttttggacgtgctgg	9	12	13	7	2	0	2	0	1	0	1	0	3	0	3	0	3	3	4	0	3	3	4	rs576191621		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr18:22804688T>G	ENST00000361524.3	-	4	3342	c.3194A>C	c.(3193-3195)tAt>tCt	p.Y1065S	ZNF521_ENST00000584787.1_Missense_Mutation_p.Y845S|ZNF521_ENST00000538137.2_Missense_Mutation_p.Y1065S|ZNF521_ENST00000579111.1_5'Flank	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	1065					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)	p.Y1065F(1)		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)					TGCGCACTTATACAGTTTTTG	0.502			T	PAX5	ALL																																p.Y1065S		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	ZNF521,lymph_node,lymphoid_neoplasm,0,1	ZNF521	269	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.A3194C						PASS	.						73	62	66					18																	22804688		2203	4300	6503	SO:0001583	missense	25925	exon4			CACTTATACAGTT	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.3194A>C	18.37:g.22804688T>G	ENSP00000354794:p.Tyr1065Ser	62	0	0		162	28	0.17284	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Missense_Mutation	SNP	ENST00000361524.3	37	CCDS32806.1	.	.	.	.	.	.	.	.	.	.	T	9.873	1.199473	0.22121	.	.	ENSG00000198795	ENST00000361524;ENST00000538137;ENST00000399425	T;T	0.10005	3.0;2.92	5.86	5.86	0.93980	.	0.120227	0.64402	D	0.000019	T	0.18635	0.0447	L	0.27053	0.805	0.34858	D	0.742331	P	0.49862	0.929	P	0.56398	0.797	T	0.10086	-1.0645	10	0.87932	D	0	-45.4225	16.2652	0.82574	0.0:0.0:0.0:1.0	.	1065	Q96K83	ZN521_HUMAN	S	1065;1099;1065	ENSP00000354794:Y1065S;ENSP00000382352:Y1065S	ENSP00000354794:Y1065S	Y	-	2	0	ZNF521	21058686	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.773000	0.55333	2.241000	0.73720	0.528000	0.53228	TAT	.	.	none		0.502	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		G	22804688	T	G	22804688	3	3	11	1	0	0	0	0	1	0	0	0	17980	1406	49	5	761	5	ZNF521	18	22804688	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	135199	22804688	55272560	234	1525											
KLHL14	57565	hgsc.bcm.edu	37	chr18	30257201	30257201	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cactgcacagccagggccacTtcgaccctccaaaatgggag	11	5	10	15	1	0	0	0	0	0	0	2	2	1	1	4	2	2	1	4	2	2	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr18:30257201T>G	ENST00000359358.4	-	8	2119	c.1681A>C	c.(1681-1683)Agt>Cgt	p.S561R		NM_020805.1	NP_065856.1	Q9P2G3	KLH14_HUMAN	kelch-like family member 14	561						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						CCAGGGCCACTTCGACCCTCC	0.468																																					p.S561R		Atlas-SNP	.											.	KLHL14	92	.	0			c.A1681C						PASS	.						168	140	150					18																	30257201		2203	4300	6503	SO:0001583	missense	57565	exon8			GGCCACTTCGACC	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.1681A>C	18.37:g.30257201T>G	ENSP00000352314:p.Ser561Arg	188	0	0		273	56	0.205128	NM_020805	A6NNW1|B4DHA0|Q8WU41	Missense_Mutation	SNP	ENST00000359358.4	37	CCDS32813.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.720055	0.89205	.	.	ENSG00000197705	ENST00000359358	T	0.80994	-1.44	5.73	5.73	0.89815	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	D	0.84379	0.5459	L	0.35288	1.05	0.80722	D	1	D	0.67145	0.996	D	0.77557	0.99	D	0.83414	0.0029	10	0.34782	T	0.22	.	16.3197	0.82945	0.0:0.0:0.0:1.0	.	561	Q9P2G3	KLH14_HUMAN	R	561	ENSP00000352314:S561R	ENSP00000352314:S561R	S	-	1	0	KLHL14	28511199	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.648000	0.83479	2.302000	0.77476	0.533000	0.62120	AGT	.	.	none		0.468	KLHL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448376.1			G	30257201	T	G	30257201	3	3	11	1	0	0	0	0	1	0	0	0	8379	1609	56	5	213	5	KLHL14	18	30257201	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	7452513	30257201	47820047	235	1526											
GALNT1	2589	hgsc.bcm.edu	37	chr18	33283603	33283603	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaactctgggagtatgaccCagtggtaagttatgcagttg	10	11	12	8	0	1	1	0	1	1	0	1	2	1	2	2	2	2	5	2	2	4	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr18:33283603C>T	ENST00000269195.5	+	10	1632	c.1529C>T	c.(1528-1530)cCa>cTa	p.P510L	GALNT1_ENST00000537549.1_Missense_Mutation_p.P450L	NM_020474.3	NP_065207.2	Q10472	GALT1_HUMAN	polypeptide N-acetylgalactosaminyltransferase 1	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)|protein O-linked glycosylation (GO:0006493)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(4)|stomach(1)	21						GAGTATGACCCAGTGGTAAGT	0.388																																					p.P510L		Atlas-SNP	.											.	GALNT1	53	.	0			c.C1529T						PASS	.						72	71	71					18																	33283603		2203	4300	6503	SO:0001583	missense	2589	exon10			ATGACCCAGTGGT		CCDS11915.1	18q12.1	2014-03-13	2014-03-13		ENSG00000141429	ENSG00000141429	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4123	protein-coding gene	gene with protein product	"protein-UDP acetylgalactosaminyltransferase 1", "polypeptide GalNAc transferase 1"	602273	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 1 (GalNAc-T1)"			7592619, 12199709	Standard	NM_020474		Approved	GalNAc-T1	uc002kzb.3	Q10472	OTTHUMG00000132567	ENST00000269195.5:c.1529C>T	18.37:g.33283603C>T	ENSP00000269195:p.Pro510Leu	49	0	0		100	14	0.14	NM_020474	Q86TJ7|Q9UM86	Missense_Mutation	SNP	ENST00000269195.5	37	CCDS11915.1	.	.	.	.	.	.	.	.	.	.	C	15.59	2.879507	0.51801	.	.	ENSG00000141429	ENST00000537748;ENST00000269195;ENST00000537549	T;T	0.77877	-1.13;-1.13	5.72	4.83	0.62350	Ricin B-related lectin (1);Ricin B lectin (3);	0.045423	0.85682	D	0.000000	T	0.68183	0.2973	L	0.29908	0.895	0.80722	D	1	B	0.14438	0.01	B	0.17722	0.019	T	0.63950	-0.6521	10	0.46703	T	0.11	.	13.7188	0.62714	0.1552:0.8448:0.0:0.0	.	510	Q10472	GALT1_HUMAN	L	510;510;450	ENSP00000269195:P510L;ENSP00000440910:P450L	ENSP00000269195:P510L	P	+	2	0	GALNT1	31537601	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.777000	0.62361	1.373000	0.46208	0.585000	0.79938	CCA	.	.	none		0.388	GALNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255771.2	NM_020474		T	33283603	C	T	33283603	3	4	11	1	0	0	0	0	1	0	0	0	6215	594	21	2	1567	2	GALNT1	18	33283603	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	3026402	33283603	44793645	236	1527											
DCC	1630	hgsc.bcm.edu	37	chr18	50432601	50432601	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tctggagcattgcagatcagCcgactccaaccgggggacat	10	7	12	12	2	2	1	1	0	1	1	3	4	3	3	3	3	4	2	3	3	1	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr18:50432601C>T	ENST00000442544.2	+	3	1216	c.600C>T	c.(598-600)agC>agT	p.S200S	DCC_ENST00000412726.1_Silent_p.S48S	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	200	Ig-like C2-type 2.				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)		TGCAGATCAGCCGACTCCAAC	0.512																																					p.S200S		Atlas-SNP	.											DCC,NS,carcinoma,+1,1	DCC	360	1	0			c.C600T						PASS	.						81	75	77					18																	50432601		2203	4300	6503	SO:0001819	synonymous_variant	1630	exon3			GATCAGCCGACTC	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.600C>T	18.37:g.50432601C>T		113	0	0		203	34	0.167488	NM_005215		Silent	SNP	ENST00000442544.2	37	CCDS11952.1																																																																																			.	.	none		0.512	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		T	50432601	C	T	50432601	2	4	11	1	0	0	0	0	0	0	0	1	4284	738	26	2		2	DCC	18	50432601	Silent	SNP	C	TCGA-FF-8042-01A-11D-2210-10	17148998	50432601	27644647	237	1528											
NEDD4L	23327	hgsc.bcm.edu	37	chr18	56057939	56057939	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcagtttgtcacagggacatCgcgagtacctatgaatggat	11	10	12	8	2	1	1	1	1	0	0	2	4	1	3	1	2	1	3	1	2	3	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr18:56057939C>T	ENST00000400345.3	+	29	3000	c.2717C>T	c.(2716-2718)tCg>tTg	p.S906L	NEDD4L_ENST00000586263.1_Missense_Mutation_p.S878L|NEDD4L_ENST00000431212.2_Missense_Mutation_p.S785L|NEDD4L_ENST00000382850.4_Missense_Mutation_p.S886L|NEDD4L_ENST00000456173.2_Missense_Mutation_p.S765L|NEDD4L_ENST00000256830.9_Missense_Mutation_p.S802L|NEDD4L_ENST00000256832.7_Missense_Mutation_p.S766L|NEDD4L_ENST00000589054.1_Missense_Mutation_p.S37L|NEDD4L_ENST00000357895.5_Missense_Mutation_p.S898L|NEDD4L_ENST00000456986.1_Missense_Mutation_p.S785L|NEDD4L_ENST00000356462.6_Missense_Mutation_p.S842L|NEDD4L_ENST00000435432.2_Missense_Mutation_p.S765L	NM_001144967.2	NP_001138439.1	Q96PU5	NED4L_HUMAN	neural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligase	906	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						ACAGGGACATCGCGAGTACCT	0.507																																					p.S906L		Atlas-SNP	.											.	NEDD4L	126	.	0			c.C2717T						PASS	.						116	111	113					18																	56057939		2036	4184	6220	SO:0001583	missense	23327	exon29			GGACATCGCGAGT	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.2717C>T	18.37:g.56057939C>T	ENSP00000383199:p.Ser906Leu	168	0	0		211	44	0.208531	NM_001144967	O43165|Q3LSM7|Q7Z5F1|Q7Z5F2|Q7Z5N3|Q8N5A7|Q8WUU9|Q9BW58|Q9H2W4|Q9NT88	Missense_Mutation	SNP	ENST00000400345.3	37	CCDS45872.1	.	.	.	.	.	.	.	.	.	.	C	36	5.713196	0.96830	.	.	ENSG00000049759	ENST00000400345;ENST00000382850;ENST00000356462;ENST00000256830;ENST00000256832;ENST00000456986;ENST00000357895;ENST00000435432;ENST00000456173;ENST00000431212	T;T;T;T;T;T;T;T;T;T	0.61040	0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14	5.66	5.66	0.87406	HECT (4);	0.106741	0.64402	D	0.000003	D	0.87103	0.6094	H	0.99211	4.47	0.80722	D	1	D;D;P;D;D;D	0.89917	1.0;1.0;0.931;0.978;1.0;1.0	D;D;B;B;D;D	0.75020	0.974;0.974;0.279;0.305;0.977;0.985	D	0.92318	0.5863	10	0.87932	D	0	.	19.7559	0.96291	0.0:1.0:0.0:0.0	.	878;898;765;842;906;886	Q96PU5-6;Q96PU5-7;Q3LSM7;Q96PU5-2;Q96PU5;Q96PU5-5	.;.;.;.;NED4L_HUMAN;.	L	906;886;842;802;766;785;898;765;765;785	ENSP00000383199:S906L;ENSP00000372301:S886L;ENSP00000348847:S842L;ENSP00000256830:S802L;ENSP00000256832:S766L;ENSP00000411947:S785L;ENSP00000350569:S898L;ENSP00000393395:S765L;ENSP00000405440:S765L;ENSP00000389406:S785L	ENSP00000256830:S802L	S	+	2	0	NEDD4L	54208919	1.000000	0.71417	0.971000	0.41717	0.938000	0.57974	7.773000	0.85462	2.656000	0.90262	0.655000	0.94253	TCG	.	.	none		0.507	NEDD4L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000448749.1			T	56057939	C	T	56057939	3	4	11	1	0	0	0	0	1	0	0	0	10320	893	31	1	2859	1	NEDD4L	18	56057939	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	5625338	56057939	22019309	238	1529											
CDH20	28316	hgsc.bcm.edu	37	chr18	59166652	59166652	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaattcaagacatcaatgaCaatgagcccaagttcctgga	17	8	7	9	0	2	3	2	2	0	1	3	4	3	4	2	1	1	1	2	1	6	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr18:59166652C>A	ENST00000262717.4	+	3	878	c.480C>A	c.(478-480)gaC>gaA	p.D160E	CDH20_ENST00000536675.2_Missense_Mutation_p.D160E|CDH20_ENST00000538374.1_Missense_Mutation_p.D160E			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	160	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)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				ACATCAATGACAATGAGCCCA	0.522																																					p.D160E		Atlas-SNP	.											.	CDH20	117	.	0			c.C480A						PASS	.						73	74	73					18																	59166652		2203	4300	6503	SO:0001583	missense	28316	exon2			CAATGACAATGAG	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.480C>A	18.37:g.59166652C>A	ENSP00000262717:p.Asp160Glu	113	0	0		211	23	0.109005	NM_031891	Q495S3	Missense_Mutation	SNP	ENST00000262717.4	37	CCDS11977.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.141010	0.77775	.	.	ENSG00000101542	ENST00000536675;ENST00000538374;ENST00000262717	T;T;T	0.74526	-0.85;-0.85;-0.85	6.06	2.93	0.34026	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.094194	0.64402	D	0.000001	D	0.91314	0.7261	H	0.99261	4.49	0.51233	D	0.999916	D	0.65815	0.995	D	0.81914	0.995	D	0.93533	0.6871	10	0.87932	D	0	.	12.9137	0.58195	0.0:0.7957:0.0:0.2043	.	160	Q9HBT6	CAD20_HUMAN	E	160	ENSP00000444767:D160E;ENSP00000442226:D160E;ENSP00000262717:D160E	ENSP00000262717:D160E	D	+	3	2	CDH20	57317632	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.309000	0.51903	0.903000	0.36546	-0.145000	0.13849	GAC	.	.	none		0.522	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891		A	59166652	C	A	59166652	3	1	11	1	0	0	0	0	1	0	0	0	3108	477	17	4	486	4	CDH20	18	59166652	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	3108713	59166652	18910596	239	1530											
SERPINB2	5055	hgsc.bcm.edu	37	chr18	61562516	61562516	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtgcttcagtttaatgaaGtgggagccaatgcagttacc	11	11	12	7	0	1	1	1	1	0	0	1	2	1	2	2	2	4	4	2	2	4	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr18:61562516G>T	ENST00000299502.4	+	3	267	c.187G>T	c.(187-189)Gtg>Ttg	p.V63L	SERPINB2_ENST00000457692.1_Missense_Mutation_p.V63L|SERPINB2_ENST00000482254.1_3'UTR	NM_002575.2	NP_002566.1	P05120	PAI2_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 2	63					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)	GTTTAATGAAGTGGGAGCCAA	0.453																																					p.V63L		Atlas-SNP	.											.	SERPINB2	63	.	0			c.G187T						PASS	.						149	150	150					18																	61562516		2203	4300	6503	SO:0001583	missense	5055	exon3			AATGAAGTGGGAG	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.187G>T	18.37:g.61562516G>T	ENSP00000299502:p.Val63Leu	125	0	0		182	35	0.192308	NM_002575	Q96E96	Missense_Mutation	SNP	ENST00000299502.4	37	CCDS11989.1	.	.	.	.	.	.	.	.	.	.	G	11.90	1.778022	0.31502	.	.	ENSG00000197632	ENST00000404622;ENST00000299502;ENST00000457692;ENST00000413956;ENST00000443281	D;T;T;D;T	0.82711	-1.64;2.83;2.83;-1.55;-1.17	5.93	0.531	0.17108	Serpin domain (3);	4.311900	0.00508	N	0.000179	T	0.75925	0.3916	L	0.33668	1.02	0.09310	N	1	B	0.21520	0.057	B	0.21360	0.034	T	0.56727	-0.7931	10	0.25751	T	0.34	.	8.6478	0.34016	0.4471:0.0:0.5529:0.0	.	63	P05120	PAI2_HUMAN	L	63	ENSP00000385397:V63L;ENSP00000299502:V63L;ENSP00000401645:V63L;ENSP00000402386:V63L;ENSP00000397096:V63L	ENSP00000299502:V63L	V	+	1	0	SERPINB2	59713496	0.001000	0.12720	0.001000	0.08648	0.013000	0.08279	-0.105000	0.10907	0.019000	0.15079	0.655000	0.94253	GTG	.	.	none		0.453	SERPINB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134009.1	NM_002575		T	61562516	G	T	61562516	3	4	11	1	0	0	0	0	1	0	0	0	14116	1029	36	4	193	4	SERPINB2	18	61562516	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	2395864	61562516	16514732	240	1531											
DSEL	92126	hgsc.bcm.edu	37	chr18	65180354	65180354	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcaaacaccaatacattgtTaaggtggctcaacttgggtc	13	10	9	9	0	1	0	1	0	0	0	2	0	1	0	1	3	4	3	1	3	5	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr18:65180354T>G	ENST00000310045.7	-	2	2995	c.1522A>C	c.(1522-1524)Aac>Cac	p.N508H	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	498					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)				AATACATTGTTAAGGTGGCTC	0.483																																					p.N508H		Atlas-SNP	.											.	DSEL	196	.	0			c.A1522C						PASS	.						92	83	86					18																	65180354		2203	4300	6503	SO:0001583	missense	92126	exon2			CATTGTTAAGGTG	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.1522A>C	18.37:g.65180354T>G	ENSP00000310565:p.Asn508His	97	0	0		206	29	0.140777	NM_032160	Q17RH1|Q6P5Z3	Missense_Mutation	SNP	ENST00000310045.7	37	CCDS11995.1	.	.	.	.	.	.	.	.	.	.	T	17.58	3.425856	0.62733	.	.	ENSG00000171451	ENST00000310045;ENST00000397964	T	0.29917	1.55	5.46	5.46	0.80206	.	0.000000	0.85682	U	0.000000	T	0.57519	0.2059	M	0.80746	2.51	0.53688	D	0.999975	D	0.89917	1.0	D	0.87578	0.998	T	0.59064	-0.7524	10	0.38643	T	0.18	-16.4224	15.2042	0.73165	0.0:0.0:0.0:1.0	.	498	Q8IZU8	DSEL_HUMAN	H	508;498	ENSP00000310565:N508H	ENSP00000310565:N508H	N	-	1	0	DSEL	63331334	1.000000	0.71417	0.988000	0.46212	0.958000	0.62258	7.849000	0.86908	2.083000	0.62718	0.460000	0.39030	AAC	.	.	none		0.483	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160		G	65180354	T	G	65180354	3	3	11	1	0	0	0	0	1	0	0	0	4777	1754	61	5	2150	5	DSEL	18	65180354	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	3617838	65180354	12896894	241	1532											
CCDC102B	79839	hgsc.bcm.edu	37	chr18	66721311	66721311	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgtaagctccagaggtctctGgatgaagagaaagaaagaaa	17	6	12	6	1	1	5	0	1	1	4	3	7	2	6	1	2	1	2	1	2	5	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr18:66721311G>A	ENST00000360242.5	+	8	1596	c.1479G>A	c.(1477-1479)ctG>ctA	p.L493L	CCDC102B_ENST00000319445.6_Silent_p.L493L	NM_024781.2	NP_079057	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B	493										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)				AGAGGTCTCTGGATGAAGAGA	0.373																																					p.L493L		Atlas-SNP	.											CCDC102B,NS,carcinoma,0,1	CCDC102B	92	1	0			c.G1479A						PASS	.						81	79	80					18																	66721311		2203	4300	6503	SO:0001819	synonymous_variant	79839	exon10			GTCTCTGGATGAA	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.1479G>A	18.37:g.66721311G>A		28	0	0		39	15	0.384615	NM_001093729	Q7Z467|Q8NDK7|Q9H5C1	Silent	SNP	ENST00000360242.5	37	CCDS11996.2																																																																																			.	.	none		0.373	CCDC102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256225.2	NM_024781		A	66721311	G	A	66721311	2	1	11	1	0	0	0	0	0	0	0	1	2739	1335	47	2		2	CCDC102B	18	66721311	Silent	SNP	G	TCGA-FF-8042-01A-11D-2210-10	1540957	66721311	11355937	242	1533											
FBXO15	201456	hgsc.bcm.edu	37	chr18	71749236	71749236	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagaggtaggtgttctctgtTattttttaaatgtataacaa	13	17	8	3	0	1	1	0	0	1	1	2	1	1	1	0	2	1	4	0	2	8	8			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr18:71749236T>A	ENST00000419743.2	-	9	1268	c.1189A>T	c.(1189-1191)Aac>Tac	p.N397Y	FBXO15_ENST00000580806.1_5'UTR|FBXO15_ENST00000269500.5_Missense_Mutation_p.N321Y	NM_001142958.1	NP_001136430.1	Q8NCQ5	FBX15_HUMAN	F-box protein 15	397						SCF ubiquitin ligase complex (GO:0019005)				autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)	27		Esophageal squamous(42;0.103)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.143)		TGTTCTCTGTTATTTTTTAAA	0.333																																					p.N397Y		Atlas-SNP	.											.	FBXO15	97	.	0			c.A1189T						PASS	.						103	97	99					18																	71749236		2203	4300	6503	SO:0001583	missense	201456	exon9			CTCTGTTATTTTT	AK094215	CCDS45884.1	18q22.3	2006-03-09	2004-06-15		ENSG00000141665	ENSG00000141665		"F-boxes /  "other""	13617	protein-coding gene	gene with protein product		609093	"F-box only protein 15"			12665572	Standard	NM_152676		Approved	MGC39671, FBX15	uc002llf.2	Q8NCQ5	OTTHUMG00000132842	ENST00000419743.2:c.1189A>T	18.37:g.71749236T>A	ENSP00000393154:p.Asn397Tyr	106	0	0		187	30	0.160428	NM_001142958	B3KST3	Missense_Mutation	SNP	ENST00000419743.2	37	CCDS45884.1	.	.	.	.	.	.	.	.	.	.	T	8.465	0.856251	0.17106	.	.	ENSG00000141665	ENST00000269500;ENST00000419743	T;T	0.47528	0.84;0.84	4.93	2.54	0.30619	.	0.737265	0.13656	N	0.371884	T	0.48995	0.1531	M	0.68317	2.08	0.09310	N	1	D;P	0.54397	0.966;0.883	P;P	0.48030	0.564;0.467	T	0.41680	-0.9495	10	0.72032	D	0.01	-25.5126	5.933	0.19150	0.0:0.1488:0.1391:0.7121	.	397;321	B3KST3;Q8NCQ5	.;FBX15_HUMAN	Y	321;397	ENSP00000269500:N321Y;ENSP00000393154:N397Y	ENSP00000269500:N321Y	N	-	1	0	FBXO15	69900216	0.987000	0.35691	0.111000	0.21465	0.029000	0.11900	1.114000	0.31196	0.329000	0.23460	-0.256000	0.11100	AAC	.	.	none		0.333	FBXO15-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000444223.1	NM_152676		A	71749236	T	A	71749236	3	1	11	1	0	0	0	0	1	0	0	0	5736	1754	61	5	351	5	FBXO15	18	71749236	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	5027925	71749236	6328012	243	1534											
SALL3	27164	hgsc.bcm.edu	37	chr18	76755256	76755256	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgggcgtccaggtccccgccGggcctcagacagtgatgggc	5	5	16	15	4	1	2	1	1	0	1	3	2	3	2	5	4	0	0	5	4	0	0	rs200983101	byFrequency	TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr18:76755256G>A	ENST00000537592.2	+	2	3265	c.3265G>A	c.(3265-3267)Ggg>Agg	p.G1089R	SALL3_ENST00000575389.2_Missense_Mutation_p.G1017R|SALL3_ENST00000536229.3_Missense_Mutation_p.G884R	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	1089					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)		GGTCCCCGCCGGGCCTCAGAC	0.716													G|||	16	0.00319489	0.0	0.0	5008	,	,		11981	0.0149		0.0	False		,,,				2504	0.001				p.G1089R		Atlas-SNP	.											.	SALL3	162	.	0			c.G3265A						PASS	.						9	12	11					18																	76755256		2171	4226	6397	SO:0001583	missense	27164	exon2			CCCGCCGGGCCTC	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.3265G>A	18.37:g.76755256G>A	ENSP00000441823:p.Gly1089Arg	0	0	.		8	8	1	NM_171999	Q9UGH1	Missense_Mutation	SNP	ENST00000537592.2	37	CCDS12013.1	9	0.004120879120879121	0	0.0	0	0.0	9	0.015734265734265736	0	0.0	G	15.42	2.829352	0.50845	.	.	ENSG00000256463	ENST00000537592;ENST00000536229;ENST00000543056	T;T	0.67171	2.81;-0.25	5.23	4.34	0.51931	.	0.104089	0.40064	N	0.001187	T	0.36193	0.0958	N	0.19112	0.55	0.33084	D	0.53701	B;D	0.60575	0.044;0.988	B;P	0.45506	0.02;0.483	T	0.54463	-0.8290	10	0.12430	T	0.62	-33.686	14.6441	0.68748	0.0:0.0:0.8532:0.1468	.	749;1089	F5GXY4;Q9BXA9	.;SALL3_HUMAN	R	1089;1017;749	ENSP00000441823:G1089R;ENSP00000439975:G1017R	ENSP00000299466:G1089R	G	+	1	0	SALL3	74856244	1.000000	0.71417	0.433000	0.26760	0.042000	0.13812	6.028000	0.70889	1.154000	0.42482	0.655000	0.94253	GGG	G|0.996;A|0.004	0.004	strong		0.716	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999		A	76755256	G	A	76755256	3	1	11	1	0	0	0	0	1	0	0	0	13827	1116	39	1	3271	1	SALL3	18	76755256	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	5006020	76755256	1321992	244	1535											
MED16	10025	hgsc.bcm.edu	37	chr19	879943	879943	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccagcagctcaccttcccGtggctgtcaatccccaccag	7	7	7	20	1	2	0	2	0	0	0	4	0	4	0	7	1	2	3	7	1	1	1	rs201392672|rs76403059	byFrequency	TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr19:879943G>C	ENST00000589119.1	-	7	1346	c.1347C>G	c.(1345-1347)caC>caG	p.H449Q	MED16_ENST00000312090.6_Missense_Mutation_p.H449Q|MED16_ENST00000325464.1_Missense_Mutation_p.H449Q|MED16_ENST00000395808.3_Missense_Mutation_p.H449Q|MED16_ENST00000269814.4_Missense_Mutation_p.H449Q|MED16_ENST00000606828.1_Intron			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	449					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)		TCACCTTCCCGTGGCTGTCAA	0.672																																					p.H449Q		Atlas-SNP	.											MED16,colon,carcinoma,0,1	MED16	61	1	0			c.C1347G						scavenged	.						13	11	12					19																	879943		2152	4247	6399	SO:0001583	missense	10025	exon8			CTTCCCGTGGCTG	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.1347C>G	19.37:g.879943G>C	ENSP00000464810:p.His449Gln	99	0	0		100	4	0.04	NM_005481	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Missense_Mutation	SNP	ENST00000589119.1	37	CCDS12047.1	.	.	.	.	.	.	.	.	.	.	C	3.376	-0.127462	0.06753	.	.	ENSG00000175221	ENST00000325464;ENST00000312090;ENST00000395808;ENST00000269814;ENST00000534906;ENST00000537596;ENST00000540679;ENST00000538572;ENST00000424039	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	4.21	-7.89	0.01174	WD40 repeat-like-containing domain (1);	0.323237	0.32357	N	0.006220	T	0.21307	0.0513	L	0.37850	1.14	0.37741	D	0.925623	B;B;B;B;B	0.13145	0.006;0.007;0.002;0.001;0.001	B;B;B;B;B	0.14023	0.006;0.006;0.003;0.006;0.01	T	0.20009	-1.0288	10	0.15066	T	0.55	-14.2411	8.1092	0.30905	0.4704:0.1904:0.3392:0.0	.	449;449;449;449;449	Q9Y2X0-2;E7ETV0;Q9Y2X0-4;Q9Y2X0-3;Q9Y2X0	.;.;.;.;MED16_HUMAN	Q	449;449;449;449;449;305;210;208;449	ENSP00000325612:H449Q;ENSP00000308528:H449Q;ENSP00000379153:H449Q;ENSP00000269814:H449Q	ENSP00000269814:H449Q	H	-	3	2	MED16	830943	0.000000	0.05858	0.886000	0.34754	0.057000	0.15508	-3.404000	0.00482	-1.779000	0.01280	-2.326000	0.00250	CAC	.	.	weak		0.672	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481		C	879943	G	C	879943	3	2	11	1	0	0	0	0	1	0	0	0	9443	1136	40	4	1322	4	MED16	19	879943	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10		879943	58249040	245	1536											
MYO1F	4542	hgsc.bcm.edu	37	chr19	8601222	8601222	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcccgaagcaggtgctggaCgccctggcgttcgtccccac	5	6	13	17	5	0	0	0	0	0	0	2	2	1	1	4	3	2	3	4	3	1	1	rs199663368		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr19:8601222C>T	ENST00000338257.8	-	19	2224	c.1957G>A	c.(1957-1959)Gtc>Atc	p.V653I		NM_012335.3	NP_036467.2	O00160	MYO1F_HUMAN	myosin IF	653	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						AGGTGCTGGACGCCCTGGCGT	0.632													C|||	1	0.000199681	0.0	0.0	5008	,	,		12969	0.001		0.0	False		,,,				2504	0.0				p.V653I		Atlas-SNP	.											.	MYO1F	128	.	0			c.G1957A						PASS	.						60	62	62					19																	8601222		2039	4212	6251	SO:0001583	missense	4542	exon19			GCTGGACGCCCTG	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.1957G>A	19.37:g.8601222C>T	ENSP00000344871:p.Val653Ile	34	0	0		24	11	0.458333	NM_012335	Q8WWN7	Missense_Mutation	SNP	ENST00000338257.8	37	CCDS42494.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	13.83	2.353346	0.41700	.	.	ENSG00000142347	ENST00000305795;ENST00000338257	D	0.87491	-2.26	4.51	3.44	0.39384	Myosin head, motor domain (2);	0.154695	0.42420	N	0.000713	T	0.79907	0.4527	L	0.35593	1.075	0.51012	D	0.9999	B	0.27823	0.19	B	0.26864	0.074	T	0.74850	-0.3524	10	0.39692	T	0.17	.	11.8667	0.52496	0.0:0.9123:0.0:0.0877	.	653	O00160	MYO1F_HUMAN	I	698;653	ENSP00000344871:V653I	ENSP00000304899:V698I	V	-	1	0	MYO1F	8507222	0.999000	0.42202	0.873000	0.34254	0.921000	0.55340	4.018000	0.57174	0.876000	0.35872	0.454000	0.30748	GTC	C|1.000;T|0.000	0.000	strong		0.632	MYO1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342716.2			T	8601222	C	T	8601222	3	4	11	1	0	0	0	0	1	0	0	0	10082	536	19	1	1379	1	MYO1F	19	8601222	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	7721279	8601222	50527761	246	1537											
SLC44A2	57153	hgsc.bcm.edu	37	chr19	10748564	10748564	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcaccaatttctgcacctcGgccaggaatgccttcttcct	7	11	8	15	1	2	0	0	0	2	0	4	1	3	1	5	3	2	2	5	3	2	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr19:10748564G>A	ENST00000335757.5	+	18	2104	c.1728G>A	c.(1726-1728)tcG>tcA	p.S576S	SLC44A2_ENST00000586078.1_Silent_p.S576S|SLC44A2_ENST00000407327.4_Silent_p.S574S|SLC44A2_ENST00000588214.1_3'UTR			Q8IWA5	CTL2_HUMAN	solute carrier family 44 (choline transporter), member 2	576					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)	TCTGCACCTCGGCCAGGAATG	0.577																																					p.S576S		Atlas-SNP	.											.	SLC44A2	56	.	0			c.G1728A						PASS	.						152	139	144					19																	10748564		2203	4300	6503	SO:0001819	synonymous_variant	57153	exon18			CACCTCGGCCAGG	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.1728G>A	19.37:g.10748564G>A		274	0	0		237	114	0.481013	NM_020428	B2RBB1|B3KNH3|B4DFJ0|F2Q9D7|Q658V1|Q658Z2|Q6PJV7|Q8N2F0|Q9NY68	Silent	SNP	ENST00000335757.5	37	CCDS12245.1																																																																																			.	.	none		0.577	SLC44A2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452045.1			A	10748564	G	A	10748564	2	1	11	1	0	0	0	0	0	0	0	1	14651	1103	39	1		1	SLC44A2	19	10748564	Silent	SNP	G	TCGA-FF-8042-01A-11D-2210-10	2147342	10748564	48380419	247	1538											
ZNF443	10224	hgsc.bcm.edu	37	chr19	12542646	12542646	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	acaattaagggatgaatgacCcatgactttttctcctctca	12	13	6	10	0	2	3	1	3	2	0	4	4	2	4	2	1	0	0	2	1	3	3	rs199587788		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr19:12542646C>T	ENST00000301547.5	-	4	537	c.340G>A	c.(340-342)Ggt>Agt	p.G114S	CTD-3105H18.16_ENST00000595562.1_Intron	NM_005815.4	NP_005806	Q9Y2A4	ZN443_HUMAN	zinc finger protein 443	114					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						GATGAATGACCCATGACTTTT	0.433																																					p.G114S		Atlas-SNP	.											ZNF443,caecum,carcinoma,0,1	ZNF443	63	1	0			c.G340A						PASS	.						137	117	124					19																	12542646		2203	4300	6503	SO:0001583	missense	10224	exon4			AATGACCCATGAC	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.340G>A	19.37:g.12542646C>T	ENSP00000301547:p.Gly114Ser	244	0	0		200	90	0.45	NM_005815		Missense_Mutation	SNP	ENST00000301547.5	37	CCDS32918.1	.	.	.	.	.	.	.	.	.	.	C	6.531	0.466301	0.12402	.	.	ENSG00000180855	ENST00000301547;ENST00000411622	T	0.06849	3.25	1.37	-2.74	0.05932	.	.	.	.	.	T	0.09862	0.0242	L	0.28400	0.85	0.09310	N	1	D	0.62365	0.991	P	0.60949	0.881	T	0.19943	-1.0290	9	0.16896	T	0.51	.	4.7986	0.13284	0.0:0.3592:0.3668:0.274	.	114	Q9Y2A4	ZN443_HUMAN	S	114	ENSP00000301547:G114S	ENSP00000301547:G114S	G	-	1	0	ZNF443	12403646	0.000000	0.05858	0.002000	0.10522	0.049000	0.14656	-1.109000	0.03309	-0.783000	0.04534	-0.384000	0.06662	GGT	.	.	alt		0.433	ZNF443-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344084.1	NM_005815		T	12542646	C	T	12542646	3	4	11	1	0	0	0	0	1	0	0	0	17931	623	22	2	1679	2	ZNF443	19	12542646	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	1794082	12542646	46586337	248	1539											
IER2	9592	hgsc.bcm.edu	37	chr19	13264330	13264330	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gccgaggagacctccgcctgCtgtgccccgcgccccgccaa	5	4	12	20	5	0	1	0	0	0	1	1	3	1	1	9	1	2	1	9	1	1	0			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr19:13264330C>T	ENST00000588173.1	+	1	1542	c.330C>T	c.(328-330)tgC>tgT	p.C110C	CTC-250I14.6_ENST00000592882.1_RNA|IER2_ENST00000292433.3_Silent_p.C110C|IER2_ENST00000587885.1_Silent_p.C110C|CTC-250I14.6_ENST00000586483.1_RNA			Q9BTL4	IER2_HUMAN	immediate early response 2	110						cytoplasm (GO:0005737)				kidney(1)|lung(1)|ovary(1)|skin(1)	4			OV - Ovarian serous cystadenocarcinoma(19;3.41e-21)			CCTCCGCCTGCTGTGCCCCGC	0.706											OREG0025291	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C110C		Atlas-SNP	.											.	IER2	14	.	0			c.C330T						PASS	.						8	9	9					19																	13264330		2152	4205	6357	SO:0001819	synonymous_variant	9592	exon2			CGCCTGCTGTGCC	M62831	CCDS12295.1	19p13.13	2008-02-05				ENSG00000160888			28871	protein-coding gene	gene with protein product						2061303	Standard	NM_004907		Approved	ETR101	uc002mwr.3	Q9BTL4		ENST00000588173.1:c.330C>T	19.37:g.13264330C>T		17	0	0	686	12	7	0.583333	NM_004907	Q03827|Q2TAZ2	Silent	SNP	ENST00000588173.1	37	CCDS12295.1																																																																																			.	.	none		0.706	IER2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453033.1	NM_004907		T	13264330	C	T	13264330	2	4	11	1	0	0	0	0	0	0	0	1	7514	805	28	2		2	IER2	19	13264330	Silent	SNP	C	TCGA-FF-8042-01A-11D-2210-10	721684	13264330	45864653	249	1540											
ZSWIM4	65249	hgsc.bcm.edu	37	chr19	13915887	13915887	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctcatcagcgcccatcacActgaggtgctgcccactgct	8	8	8	17	1	3	1	3	1	0	0	3	1	3	1	3	1	4	2	3	1	0	0	rs199644245		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr19:13915887A>C	ENST00000254323.2	+	3	826	c.637A>C	c.(637-639)Act>Cct	p.T213P	ZSWIM4_ENST00000440752.2_5'UTR	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	213							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)			CGCCCATCACACTGAGGTGCT	0.627											OREG0025298	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	a|||	1	0.000199681	0.0	0.0014	5008	,	,		19520	0.0		0.0	False		,,,				2504	0.0				p.T213P		Atlas-SNP	.											.	ZSWIM4	69	.	0			c.A637C						PASS	.						47	41	43					19																	13915887		2203	4300	6503	SO:0001583	missense	65249	exon3			CATCACACTGAGG	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.637A>C	19.37:g.13915887A>C	ENSP00000254323:p.Thr213Pro	24	0	0	691	39	16	0.410256	NM_023072		Missense_Mutation	SNP	ENST00000254323.2	37	CCDS32924.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	A	18.12	3.552511	0.65425	.	.	ENSG00000132003	ENST00000254323	T	0.43294	0.95	4.58	4.58	0.56647	.	0.000000	0.64402	D	0.000015	T	0.64103	0.2568	M	0.84082	2.675	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.65475	-0.6159	10	0.34782	T	0.22	-10.3035	11.9253	0.52817	1.0:0.0:0.0:0.0	.	213	Q9H7M6	ZSWM4_HUMAN	P	213	ENSP00000254323:T213P	ENSP00000254323:T213P	T	+	1	0	ZSWIM4	13776887	1.000000	0.71417	0.995000	0.50966	0.436000	0.31835	8.974000	0.93433	1.714000	0.51371	0.459000	0.35465	ACT	A|1.000;C|0.000	0.000	strong		0.627	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457457.1	XM_031342		C	13915887	A	C	13915887	3	2	11	1	0	0	0	0	1	0	0	0	18258	159	6	5	647	5	ZSWIM4	19	13915887	Missense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10	651557	13915887	45213096	250	1541											
CPAMD8	27151	hgsc.bcm.edu	37	chr19	17039035	17039035	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcattggatggctctggacCatggccaacctggaaaaaga	12	8	11	10	0	2	1	1	0	1	1	2	4	2	4	3	5	1	1	3	5	3	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr19:17039035C>T	ENST00000443236.1	-	25	3326	c.3295G>A	c.(3295-3297)Ggt>Agt	p.G1099S		NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	1052						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						GGCTCTGGACCATGGCCAACC	0.597																																					p.G1099S		Atlas-SNP	.											.	CPAMD8	192	.	0			c.G3295A						PASS	.						28	31	30					19																	17039035		2007	4168	6175	SO:0001583	missense	27151	exon25			CTGGACCATGGCC	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.3295G>A	19.37:g.17039035C>T	ENSP00000402505:p.Gly1099Ser	54	0	0		62	27	0.435484	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.70|16.70	3.195939|3.195939	0.58126|0.58126	.|.	.|.	ENSG00000160111|ENSG00000160111	ENST00000291440|ENST00000443236	.|.	.|.	.|.	3.13|3.13	3.13|3.13	0.36017|0.36017	Farnesoic acid O-methyl transferase (1);|.	0.205858|.	0.29631|.	U|.	0.011619|.	T|T	0.76126|0.76126	0.3944|0.3944	M|M	0.83774|0.83774	2.66|2.66	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	T|T	0.79369|0.79369	-0.1832|-0.1832	9|5	0.62326|.	D|.	0.03|.	.|.	14.2237|14.2237	0.65845|0.65845	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1052|.	Q8IZJ3|.	CPMD8_HUMAN|.	S|I	1099|1109	.|.	ENSP00000291440:G1099S|.	G|M	-|-	1|3	0|0	CPAMD8|CPAMD8	16900035|16900035	0.999000|0.999000	0.42202|0.42202	0.969000|0.969000	0.41365|0.41365	0.129000|0.129000	0.20672|0.20672	4.687000|4.687000	0.61708|0.61708	1.300000|1.300000	0.44818|0.44818	0.655000|0.655000	0.94253|0.94253	GGT|ATG	.	.	none		0.597	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692		T	17039035	C	T	17039035	3	4	11	1	0	0	0	0	1	0	0	0	3797	594	21	2	2575	2	CPAMD8	19	17039035	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	3123148	17039035	42089948	251	1542											
DMKN	93099	hgsc.bcm.edu	37	chr19	36002369	36002369	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accactgttgccactgctgcCaccactgctgccgccactgc	6	8	8	19	1	0	0	0	0	0	0	0	0	0	0	6	0	6	3	6	0	0	1	rs56743379		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr19:36002369C>T	ENST00000339686.3	-	5	1038	c.862G>A	c.(862-864)Ggc>Agc	p.G288S	DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000418261.1_Missense_Mutation_p.G288S|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000424570.2_Missense_Mutation_p.G288S|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000451297.2_Missense_Mutation_p.G288S|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000440396.1_Missense_Mutation_p.G288S|DMKN_ENST00000447113.2_Missense_Mutation_p.G288S|DMKN_ENST00000488892.1_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	288	Gly-rich.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.S274_S290del(1)		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)			ccactgctgccaccactgctg	0.632																																					p.G288S		Atlas-SNP	.											DMKN_ENST00000424570,NS,carcinoma,0,3	DMKN	116	3	1	Deletion - In frame(1)	ovary(1)	c.G862A						scavenged	.						29	23	25					19																	36002369		2194	4290	6484	SO:0001583	missense	93099	exon5			TGCTGCCACCACT	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.862G>A	19.37:g.36002369C>T	ENSP00000342012:p.Gly288Ser	55	2	0.0363636		55	5	0.0909091	NM_001126058	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Missense_Mutation	SNP	ENST00000339686.3	37	CCDS12463.1	.	.	.	.	.	.	.	.	.	.	C	0.218	-1.030758	0.02045	.	.	ENSG00000161249	ENST00000339686;ENST00000392207;ENST00000447113;ENST00000440396;ENST00000418261;ENST00000424570;ENST00000451297	T;T;T;T;T;T	0.49432	0.78;0.78;0.78;0.78;0.78;0.78	2.68	-4.69	0.03299	.	1.453220	0.04292	N	0.345661	T	0.23210	0.0561	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.17465	0.0;0.0;0.0;0.0;0.022	B;B;B;B;B	0.15484	0.001;0.001;0.001;0.001;0.013	T	0.24799	-1.0150	10	0.09590	T	0.72	-0.9644	8.7065	0.34358	0.0:0.4947:0.0:0.5053	.	288;288;288;288;288	E7EUS0;Q6E0U4-7;Q6E0U4-3;Q6E0U4-5;Q6E0U4	.;.;.;.;DMKN_HUMAN	S	288	ENSP00000342012:G288S;ENSP00000394908:G288S;ENSP00000415277:G288S;ENSP00000414743:G288S;ENSP00000388404:G288S;ENSP00000409513:G288S	ENSP00000342012:G288S	G	-	1	0	DMKN	40694209	.	.	0.000000	0.03702	0.022000	0.10575	.	.	-1.118000	0.02961	-0.959000	0.02639	GGC	.	.	none		0.632	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317		T	36002369	C	T	36002369	3	4	11	1	0	0	0	0	1	0	0	0	4584	594	21	2	933	2	DMKN	19	36002369	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	18963334	36002369	23126614	252	1543											
ZNF461	92283	hgsc.bcm.edu	37	chr19	37129817	37129817	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggtgtgaatgaagtctaaagGccttaccacatatcatgcat	13	11	9	8	0	2	2	1	2	1	0	2	2	2	2	2	2	2	1	2	2	6	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr19:37129817G>A	ENST00000588268.1	-	6	1657	c.1430C>T	c.(1429-1431)gCc>gTc	p.A477V	ZNF461_ENST00000540605.2_5'UTR|ZNF461_ENST00000360357.4_Missense_Mutation_p.A454V	NM_153257.2	NP_694989.2	Q8TAF7	ZN461_HUMAN	zinc finger protein 461	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)|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)			AAGTCTAAAGGCCTTACCACA	0.388																																					p.A477V		Atlas-SNP	.											.	ZNF461	73	.	0			c.C1430T						PASS	.						62	66	65					19																	37129817		2201	4297	6498	SO:0001583	missense	92283	exon6			CTAAAGGCCTTAC	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.1430C>T	19.37:g.37129817G>A	ENSP00000467931:p.Ala477Val	105	0	0		94	34	0.361702	NM_153257	A8K9W9|Q6VSF7|Q9ULZ8	Missense_Mutation	SNP	ENST00000588268.1	37	CCDS54257.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.776220	0.49786	.	.	ENSG00000197808	ENST00000396893;ENST00000396896;ENST00000360357;ENST00000540605;ENST00000396892	T	0.19105	2.17	3.48	3.48	0.39840	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.29389	0.0732	N	0.25031	0.7	0.09310	N	1	P;D;P	0.76494	0.901;0.999;0.901	P;D;P	0.70487	0.707;0.969;0.767	T	0.06041	-1.0849	9	0.72032	D	0.01	.	9.8006	0.40761	0.0:0.358:0.6419:0.0	.	454;399;477	B4DRP8;Q59G30;Q8TAF7	.;.;ZN461_HUMAN	V	477;208;454;350;171	ENSP00000353515:A454V	ENSP00000353515:A454V	A	-	2	0	ZNF461	41821657	0.000000	0.05858	1.000000	0.80357	0.919000	0.55068	0.018000	0.13422	1.941000	0.56285	0.491000	0.48974	GCC	.	.	none		0.388	ZNF461-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453202.1	NM_153257		A	37129817	G	A	37129817	3	1	11	1	0	0	0	0	1	0	0	0	17940	1203	42	2	265	2	ZNF461	19	37129817	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	1127448	37129817	21999166	253	1544											
SUPT5H	6829	hgsc.bcm.edu	37	chr19	39948337	39948337	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgacgatgagtatgaggaCgaggaccagtgggaggatgg	11	7	19	4	2	0	3	0	3	0	0	0	9	0	7	1	5	0	2	1	5	1	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr19:39948337C>T	ENST00000599117.1	+	5	631	c.264C>T	c.(262-264)gaC>gaT	p.D88D	SUPT5H_ENST00000598725.1_Silent_p.D88D|SUPT5H_ENST00000402194.2_Silent_p.D88D|SUPT5H_ENST00000359191.6_Silent_p.D88D|SUPT5H_ENST00000432763.2_Silent_p.D88D			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	88	Glu-rich.				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)			AGTATGAGGACGAGGACCAGT	0.537																																					p.D88D		Atlas-SNP	.											.	SUPT5H	119	.	0			c.C264T						PASS	.						242	197	212					19																	39948337		2203	4300	6503	SO:0001819	synonymous_variant	6829	exon4			TGAGGACGAGGAC	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.264C>T	19.37:g.39948337C>T		160	0	0		179	72	0.402235	NM_001130825	O43279|Q59G52|Q99639	Silent	SNP	ENST00000599117.1	37	CCDS12536.1																																																																																			.	.	none		0.537	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464918.1	NM_003169		T	39948337	C	T	39948337	2	4	11	1	0	0	0	0	0	0	0	1	15414	535	19	1		1	SUPT5H	19	39948337	Silent	SNP	C	TCGA-FF-8042-01A-11D-2210-10	2818520	39948337	19180646	254	1545											
SPTBN4	57731	hgsc.bcm.edu	37	chr19	41066402	41066402	+	Intron	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agcccccttctcaatggaatGacaacagccaatatctgtgt	12	10	7	12	0	2	1	1	1	2	0	3	2	2	2	3	1	3	0	3	1	5	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr19:41066402G>A	ENST00000352632.3	+	27	6001				SPTBN4_ENST00000598249.1_Intron|SPTBN4_ENST00000338932.3_Intron|SPTBN4_ENST00000595535.1_Silent_p.*2003*|SPTBN4_ENST00000392025.1_Intron|SPTBN4_ENST00000392023.1_Silent_p.*679*			Q9H254	SPTN4_HUMAN	spectrin, beta, non-erythrocytic 4						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)			TCAATGGAATGacaacagcca	0.582																																					p.X679X		Atlas-SNP	.											.	SPTBN4	213	.	0			c.G2036A						PASS	.						11	14	13					19																	41066402		2126	4185	6311	SO:0001627	intron_variant	57731	exon10			TGGAATGACAACA	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.5915+93G>A	19.37:g.41066402G>A		123	0	0		94	40	0.425532	NM_025213	E9PGQ5|Q9H1K7|Q9H1K8|Q9H1K9|Q9H253|Q9H3G8|Q9HCD0	Silent	SNP	ENST00000352632.3	37	CCDS12559.1																																																																																			.	.	none		0.582	SPTBN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462559.2			A	41066402	G	A	41066402	1	1	11	0	1	0	0	0	0	0	0	0	15136	1285	45	2		2	SPTBN4	19	41066402	Intron	SNP	G	TCGA-FF-8042-01A-11D-2210-10	1118065	41066402	18062581	255	1546											
SLC17A7	57030	hgsc.bcm.edu	37	chr19	49937049	49937049	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtacttgcgctcctcctcCgagatgctggggtgcagcgc	5	10	13	13	3	0	1	0	0	0	1	3	2	3	1	3	2	5	4	3	2	1	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr19:49937049C>T	ENST00000221485.3	-	7	972	c.801G>A	c.(799-801)tcG>tcA	p.S267S	SLC17A7_ENST00000600601.1_Silent_p.S200S|SLC17A7_ENST00000543531.1_Silent_p.S255S	NM_020309.3	NP_064705.1	Q9P2U7	VGLU1_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 7	267					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)		GCTCCTCCTCCGAGATGCTGG	0.647																																					p.S267S		Atlas-SNP	.											SLC17A7,caecum,carcinoma,-1,1	SLC17A7	57	1	0			c.G801A						scavenged	.						63	54	57					19																	49937049		2203	4300	6503	SO:0001819	synonymous_variant	57030	exon7			CTCCTCCGAGATG	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.801G>A	19.37:g.49937049C>T		62	0	0		58	3	0.0517241	NM_020309	B4DFR9|B4DG46|Q6PCD0	Silent	SNP	ENST00000221485.3	37	CCDS12764.1																																																																																			.	.	none		0.647	SLC17A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465367.2			T	49937049	C	T	49937049	2	4	11	1	0	0	0	0	0	0	0	1	14437	639	23	1		1	SLC17A7	19	49937049	Silent	SNP	C	TCGA-FF-8042-01A-11D-2210-10	8870647	49937049	9191934	256	1547											
MYADM	91663	hgsc.bcm.edu	37	chr19	54377236	54377236	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgcatcgcgtgtgtggcttaCgccaccgaagtggcctggac	6	9	14	12	4	0	0	0	0	0	0	1	2	0	1	3	3	2	2	3	3	2	1	rs376434685		TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr19:54377236C>T	ENST00000391769.2	+	3	733	c.453C>T	c.(451-453)taC>taT	p.Y151Y	MYADM_ENST00000391770.4_Silent_p.Y151Y|MYADM_ENST00000336967.3_Silent_p.Y151Y|MYADM_ENST00000391771.1_Silent_p.Y151Y|MYADM_ENST00000391768.2_Silent_p.Y151Y|AC008440.5_ENST00000413496.2_RNA	NM_001020821.1	NP_001018657.1	Q96S97	MYADM_HUMAN	myeloid-associated differentiation marker	151	MARVEL 1. {ECO:0000255|PROSITE- ProRule:PRU00581}.				establishment of endothelial barrier (GO:0061028)|membrane raft organization (GO:0031579)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of gene expression (GO:0010629)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of protein kinase C signaling (GO:0090038)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of cell migration (GO:0030335)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|protein targeting to plasma membrane (GO:0072661)	cell-cell junction (GO:0005911)|cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|ruffle (GO:0001726)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.0488)		GTGTGGCTTACGCCACCGAAG	0.652																																					p.Y151Y		Atlas-SNP	.											.	MYADM	39	.	0			c.C453T						PASS	.	C	,,,,	0,4406		0,0,2203	54	55	54		453,453,453,453,453	-5.3	0.1	19		54	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MYADM	NM_001020818.1,NM_001020819.1,NM_001020820.1,NM_001020821.1,NM_138373.3	,,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,,	151/323,151/323,151/323,151/323,151/323	54377236	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	91663	exon3			GGCTTACGCCACC	AF087882	CCDS12866.1	19q13.33-q13.4	2004-07-23			ENSG00000179820	ENSG00000179820			7544	protein-coding gene	gene with protein product		609959				10733104, 12075932	Standard	NM_001020818		Approved		uc002qcl.3	Q96S97	OTTHUMG00000060775	ENST00000391769.2:c.453C>T	19.37:g.54377236C>T		72	0	0		84	36	0.428571	NM_138373	B2RE58|Q542Z1|Q7Z507|Q8N9R4|Q96CS6|Q96SK9	Silent	SNP	ENST00000391769.2	37	CCDS12866.1																																																																																			.	.	weak		0.652	MYADM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134337.1	NM_138373		T	54377236	C	T	54377236	2	4	11	1	0	0	0	0	0	0	0	1	10015	547	19	1		1	MYADM	19	54377236	Silent	SNP	C	TCGA-FF-8042-01A-11D-2210-10	4440187	54377236	4751747	257	1548											
CNOT3	4849	hgsc.bcm.edu	37	chr19	54646891	54646891	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cctcaagaaggtgtccgaggGcgtggagcagtttgaagata	11	8	15	7	2	1	3	1	1	0	2	2	5	2	4	2	3	1	2	2	3	4	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr19:54646891G>T	ENST00000406403.1	+	2	1665	c.62G>T	c.(61-63)gGc>gTc	p.G21V	CNOT3_ENST00000358389.3_5'UTR|CNOT3_ENST00000221232.5_Missense_Mutation_p.G21V			O75175	CNOT3_HUMAN	CCR4-NOT transcription complex, subunit 3	21					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)					GTGTCCGAGGGCGTGGAGCAG	0.557																																					p.G21V		Atlas-SNP	.											.	CNOT3	133	.	0			c.G62T						PASS	.						171	171	171					19																	54646891		2203	4300	6503	SO:0001583	missense	4849	exon3			CCGAGGGCGTGGA	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.62G>T	19.37:g.54646891G>T	ENSP00000383954:p.Gly21Val	75	0	0		65	23	0.353846	NM_014516	Q9NZN7|Q9UF76	Missense_Mutation	SNP	ENST00000406403.1	37	CCDS12880.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.738074	0.89573	.	.	ENSG00000088038	ENST00000221232;ENST00000406403	T;T	0.74632	-0.86;-0.86	5.04	5.04	0.67666	Not CCR4-Not complex component, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.88855	0.6550	M	0.90425	3.115	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.91135	0.4941	10	0.87932	D	0	-25.3415	17.5375	0.87837	0.0:0.0:1.0:0.0	.	21;21	B7Z6J7;O75175	.;CNOT3_HUMAN	V	21	ENSP00000221232:G21V;ENSP00000383954:G21V	ENSP00000221232:G21V	G	+	2	0	CNOT3	59338703	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	8.832000	0.92079	2.512000	0.84698	0.655000	0.94253	GGC	.	.	none		0.557	CNOT3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142130.3	NM_014516		T	54646891	G	T	54646891	3	4	11	1	0	0	0	0	1	0	0	0	3622	1203	42	4	68	4	CNOT3	19	54646891	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	269655	54646891	4482092	258	1549											
GPCPD1	56261	hgsc.bcm.edu	37	chr20	5559162	5559162	+	Nonsense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgaactcattgtcgcttattAaggatatctccaagctattg	11	15	7	8	1	2	1	1	1	1	0	4	2	2	2	1	1	2	2	1	1	6	6			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr20:5559162A>C	ENST00000379019.4	-	8	781	c.569T>G	c.(568-570)tTa>tGa	p.L190*	GPCPD1_ENST00000481038.1_5'UTR	NM_019593.3	NP_062539.1	Q9NPB8	GPCP1_HUMAN	glycerophosphocholine phosphodiesterase GDE1 homolog (S. cerevisiae)	190					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						GTCGCTTATTAAGGATATCTC	0.483																																					p.L190X		Atlas-SNP	.											.	GPCPD1	52	.	0			c.T569G						PASS	.						126	103	111					20																	5559162		2203	4300	6503	SO:0001587	stop_gained	56261	exon8			CTTATTAAGGATA		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.569T>G	20.37:g.5559162A>C	ENSP00000368305:p.Leu190*	130	0	0		154	71	0.461039	NM_019593	D3DW06|Q9BQL8|Q9NUX0	Nonsense_Mutation	SNP	ENST00000379019.4	37	CCDS13090.1	.	.	.	.	.	.	.	.	.	.	A	38	6.968935	0.97971	.	.	ENSG00000125772	ENST00000379019	.	.	.	5.35	5.35	0.76521	.	0.128536	0.50627	D	0.000106	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07813	T	0.8	-2.9154	15.6389	0.76981	1.0:0.0:0.0:0.0	.	.	.	.	X	190	.	ENSP00000368305:L190X	L	-	2	0	GPCPD1	5507162	1.000000	0.71417	0.992000	0.48379	0.994000	0.84299	7.334000	0.79224	2.156000	0.67533	0.533000	0.62120	TTA	.	.	none		0.483	GPCPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077869.1	NM_019593		C	5559162	A	C	5559162	4	2	11	1	0	0	0	0	0	1	0	0	6611	372	13	5	1501	5	GPCPD1	20	5559162	Nonsense_Mutation	SNP	A	TCGA-FF-8042-01A-11D-2210-10		5559162	57466358	259	1550											
ASXL1	171023	hgsc.bcm.edu	37	chr20	31023636	31023636	+	Frame_Shift_Del	DEL	G	G	-																															aacccaattggaaccaatctGccccactgtccaaggtgaat																										TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr20:31023636delG	ENST00000375687.4	+	13	3545	c.3121delG	c.(3121-3123)gccfs	p.A1041fs	ASXL1_ENST00000306058.5_Frame_Shift_Del_p.A1036fs	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	1041					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						GAACCAATCTGCCCCACTGTC	0.542			"F, N, Mis"		"MDS, CMML"																																p.S1040fs		Pindel,Atlas-Indel	.		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	.	ASXL1	1114	.	0			c.3120delT						PASS	.						226	187	200					20																	31023636		2203	4300	6503	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.3121delG	20.37:g.31023636delG	ENSP00000364839:p.Ala1041fs	121	0	.		136	32	0.235	NM_015338	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Frame_Shift_Del	DEL	ENST00000375687.4	37	CCDS13201.1																																																																																			.	.	none		0.542	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338		-	31023636	G	-	31023636	7	5	11	1	0	1	0	1	0	0	0	0	1066	1319	46	0	3177	0	ASXL1	20	31023636	Frame_Shift_Del	DEL	G	TCGA-FF-8042-01A-11D-2210-10	25464474	31023636	32001884	260	1551											
SAMHD1	25939	hgsc.bcm.edu	37	chr20	35559188	35559188	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatgacaaagtccagcaatCtgaacacagagaacatctcg	16	7	7	11	1	3	3	1	2	2	1	5	4	4	3	1	0	3	1	1	0	4	0			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr20:35559188C>A	ENST00000262878.4	-	5	799	c.600G>T	c.(598-600)caG>caT	p.Q200H	SAMHD1_ENST00000373694.5_5'UTR	NM_015474.3	NP_056289.2	Q9Y3Z3	SAMH1_HUMAN	SAM domain and HD domain 1	200	HD.				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)				GTCCAGCAATCTGAACACAGA	0.413																																					p.Q200H		Atlas-SNP	.											.	SAMHD1	62	.	0			c.G600T						PASS	.						194	177	183					20																	35559188		2203	4300	6503	SO:0001583	missense	25939	exon5			AGCAATCTGAACA	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.600G>T	20.37:g.35559188C>A	ENSP00000262878:p.Gln200His	114	0	0		91	44	0.483516	NM_015474	B4E2A5|E1P5V2|Q5JXG8|Q8N491|Q9H004|Q9H005|Q9H3U9	Missense_Mutation	SNP	ENST00000262878.4	37	CCDS13288.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.529296	0.85706	.	.	ENSG00000101347	ENST00000262878	D	0.90385	-2.66	6.02	6.02	0.97574	Metal-dependent phosphohydrolase, HD domain (1);Metal-dependent phosphohydrolase, HD subdomain (1);HD domain (1);	0.106561	0.64402	D	0.000003	D	0.94042	0.8091	M	0.75150	2.29	0.80722	D	1	D	0.60160	0.987	P	0.62014	0.897	D	0.93147	0.6546	10	0.44086	T	0.13	-16.5248	14.1219	0.65192	0.0:0.9234:0.0:0.0766	.	200	Q9Y3Z3	SAMH1_HUMAN	H	200	ENSP00000262878:Q200H	ENSP00000262878:Q200H	Q	-	3	2	SAMHD1	34992602	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.216000	0.51176	2.850000	0.98022	0.650000	0.86243	CAG	.	.	none		0.413	SAMHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079062.2	NM_015474		A	35559188	C	A	35559188	3	1	11	1	0	0	0	0	1	0	0	0	13843	912	32	4	1328	4	SAMHD1	20	35559188	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	4535552	35559188	27466332	261	1552											
LAMA5	3911	hgsc.bcm.edu	37	chr20	60885315	60885315	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atcagtccggtgactgccagGggccgcacctccagttccag	7	7	12	15	2	1	1	1	1	0	0	4	1	4	1	6	3	1	2	6	3	0	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr20:60885315G>A	ENST00000252999.3	-	77	10719	c.10653C>T	c.(10651-10653)ccC>ccT	p.P3551P	LAMA5_ENST00000492698.1_5'Flank	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	3551	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)			TGACTGCCAGGGGCCGCACCT	0.652																																					p.P3551P		Atlas-SNP	.											.	LAMA5	268	.	0			c.C10653T						PASS	.						33	39	37					20																	60885315		2201	4294	6495	SO:0001819	synonymous_variant	3911	exon77			TGCCAGGGGCCGC	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.10653C>T	20.37:g.60885315G>A		44	0	0		47	18	0.382979	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			.	.	none		0.652	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		A	60885315	G	A	60885315	2	1	11	1	0	0	0	0	0	0	0	1	8618	1219	43	2		2	LAMA5	20	60885315	Silent	SNP	G	TCGA-FF-8042-01A-11D-2210-10	25326127	60885315	2140205	262	1553											
HUNK	30811	hgsc.bcm.edu	37	chr21	33371236	33371236	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttgctcacgaagataagaaCagccccccaaaagaggaggg	15	5	11	10	1	1	3	1	0	0	3	1	5	1	4	3	2	3	1	3	2	5	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr21:33371236C>T	ENST00000270112.2	+	11	2244	c.1884C>T	c.(1882-1884)aaC>aaT	p.N628N		NM_014586.1	NP_055401.1	P57058	HUNK_HUMAN	hormonally up-regulated Neu-associated kinase	628					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						AAGATAAGAACAGCCCCCCAA	0.597																																					p.N628N		Atlas-SNP	.											.	HUNK	74	.	0			c.C1884T						PASS	.						48	48	48					21																	33371236		2203	4300	6503	SO:0001819	synonymous_variant	30811	exon11			TAAGAACAGCCCC	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.1884C>T	21.37:g.33371236C>T		121	0	0		100	33	0.33	NM_014586		Silent	SNP	ENST00000270112.2	37	CCDS13610.1																																																																																			.	.	none		0.597	HUNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192782.1	NM_014586		T	33371236	C	T	33371236	2	4	11	1	0	0	0	0	0	0	0	1	7467	477	17	2		2	HUNK	21	33371236	Silent	SNP	C	TCGA-FF-8042-01A-11D-2210-10		33371236	14758659	263	1554											
ETS2	2114	hgsc.bcm.edu	37	chr21	40194761	40194761	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagaacttgctggggttcaCgcccgaggaactgcacgcca	9	6	12	14	3	1	1	1	0	0	1	1	3	1	2	3	3	4	3	3	3	2	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr21:40194761C>T	ENST00000360214.3	+	11	1818	c.1358C>T	c.(1357-1359)aCg>aTg	p.T453M	ETS2_ENST00000360938.3_Missense_Mutation_p.T453M	NM_001256295.1	NP_001243224.1	P15036	ETS2_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 2	453					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)				CTGGGGTTCACGCCCGAGGAA	0.632																																					p.T593M		Atlas-SNP	.											ETS2_ENST00000360214,caecum,carcinoma,-1,2	ETS2	87	2	0			c.C1778T						PASS	.						77	60	66					21																	40194761		2203	4300	6503	SO:0001583	missense	2114	exon11			GGTTCACGCCCGA		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.1358C>T	21.37:g.40194761C>T	ENSP00000353344:p.Thr453Met	53	0	0		40	23	0.575	NM_001256295	A6NM68|D3DSH6|Q53Y89	Missense_Mutation	SNP	ENST00000360214.3	37	CCDS13659.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.414164	0.83449	.	.	ENSG00000157557	ENST00000360214;ENST00000360938	T;T	0.14640	2.49;2.49	5.62	5.62	0.85841	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.155857	0.56097	D	0.000028	T	0.33585	0.0868	M	0.68952	2.095	0.58432	D	0.999998	D	0.89917	1.0	P	0.57620	0.824	T	0.02498	-1.1150	10	0.87932	D	0	.	19.2718	0.94013	0.0:1.0:0.0:0.0	.	453	P15036	ETS2_HUMAN	M	453	ENSP00000353344:T453M;ENSP00000354194:T453M	ENSP00000353344:T453M	T	+	2	0	ETS2	39116631	1.000000	0.71417	0.979000	0.43373	0.927000	0.56198	5.598000	0.67585	2.634000	0.89283	0.655000	0.94253	ACG	.	.	none		0.632	ETS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207544.1			T	40194761	C	T	40194761	3	4	11	1	0	0	0	0	1	0	0	0	5278	536	19	1	1392	1	ETS2	21	40194761	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	6823525	40194761	7935134	264	1555											
DSCAM	1826	hgsc.bcm.edu	37	chr21	41446993	41446993	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctttagcctctgctcccgcCgcctcctccgcacaaccagc	5	9	6	21	3	2	0	0	0	2	0	5	0	5	0	7	0	4	2	7	0	2	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr21:41446993C>T	ENST00000400454.1	-	27	5336	c.4859G>A	c.(4858-4860)cGg>cAg	p.R1620Q		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	1620					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)				CTGCTCCCGCCGCCTCCTCCG	0.627																																					p.R1620Q	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											DSCAM,NS,carcinoma,-1,1	DSCAM	347	1	0			c.G4859A						PASS	.						63	79	73					21																	41446993		2109	4217	6326	SO:0001583	missense	1826	exon27			TCCCGCCGCCTCC	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.4859G>A	21.37:g.41446993C>T	ENSP00000383303:p.Arg1620Gln	114	0	0		128	52	0.40625	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	37	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	C	34	5.302381	0.95601	.	.	ENSG00000171587	ENST00000400454;ENST00000404019	T;T	0.59638	0.25;0.37	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.64227	0.2579	L	0.36672	1.1	0.44388	D	0.99729	D	0.89917	1.0	P	0.55965	0.788	T	0.61879	-0.6972	10	0.41790	T	0.15	.	19.812	0.96551	0.0:1.0:0.0:0.0	.	1620	O60469	DSCAM_HUMAN	Q	1620;1372	ENSP00000383303:R1620Q;ENSP00000385342:R1372Q	ENSP00000383303:R1620Q	R	-	2	0	DSCAM	40368863	1.000000	0.71417	0.509000	0.27700	0.879000	0.50718	7.395000	0.79876	2.685000	0.91497	0.655000	0.94253	CGG	.	.	none		0.627	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		T	41446993	C	T	41446993	3	4	11	1	0	0	0	0	1	0	0	0	4770	652	23	1	1207	1	DSCAM	21	41446993	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	1252232	41446993	6682902	265	1556											
MX1	4599	hgsc.bcm.edu	37	chr21	42817373	42817373	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attttctctccattttcctcAgaaatctctgcccctgttag	7	17	4	13	0	3	1	1	0	2	1	7	1	5	1	4	0	1	1	4	0	2	5			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr21:42817373A>G	ENST00000398600.2	+	14	2033		c.e14-1		MX1_ENST00000288383.6_Splice_Site|AP001610.5_ENST00000411427.1_RNA|MX1_ENST00000398598.3_Splice_Site|MX1_ENST00000455164.2_Splice_Site	NM_001144925.1	NP_001138397.1	P20591	MX1_HUMAN	MX dynamin-like GTPase 1						apoptotic process (GO:0006915)|cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|response to type I interferon (GO:0034340)|response to virus (GO:0009615)|signal transduction (GO:0007165)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	27		Prostate(19;3.18e-07)|all_epithelial(19;0.0277)				CATTTTCCTCAGAAATCTCTG	0.438																																					.		Atlas-SNP	.											.	MX1	58	.	0			c.1009-2A>G						PASS	.						79	85	83					21																	42817373		2203	4300	6503	SO:0001630	splice_region_variant	4599	exon14			TTCCTCAGAAATC		CCDS13673.1, CCDS74796.1	21q22.3	2014-07-15	2014-07-15		ENSG00000157601	ENSG00000157601			7532	protein-coding gene	gene with protein product	"interferon-inducible protein p78"	147150	"myxovirus (influenza) resistance 1, homolog of murine (interferon-inducible protein p78)", "myxovirus (influenza virus) resistance 1, interferon-inducible protein p78 (mouse)"			17570575	Standard	XM_005260979		Approved	IFI-78K, MxA	uc010goq.3	P20591	OTTHUMG00000086755	ENST00000398600.2:c.1009-1A>G	21.37:g.42817373A>G		74	0	0		60	21	0.35	NM_001144925	B2RDA5|B3KU10|C9IYV7|C9J8D6|C9JN19|C9JN88|C9JUL1|C9JZS6|D3DSI8|Q86YP5|Q96CI3	Splice_Site	SNP	ENST00000398600.2	37	CCDS13673.1	.	.	.	.	.	.	.	.	.	.	A	12.18	1.859458	0.32884	.	.	ENSG00000157601	ENST00000398600;ENST00000398598;ENST00000455164;ENST00000288383	.	.	.	4.89	3.72	0.42706	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.317	0.49399	0.8471:0.1529:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MX1	41739243	1.000000	0.71417	0.943000	0.38184	0.530000	0.34684	7.482000	0.81143	0.937000	0.37394	0.528000	0.53228	.	.	.	none		0.438	MX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195161.2		Intron	G	42817373	A	G	42817373	5	3	11	1	0	0	0	0	0	0	1	0	10006	202	7	3	1037	3	MX1	21	42817373	Splice_Site	SNP	A	TCGA-FF-8042-01A-11D-2210-10	1370380	42817373	5312522	266	1557											
MCM3AP	8888	hgsc.bcm.edu	37	chr21	47704722	47704723	+	Frame_Shift_Ins	INS	-	-	C																															tttctctggctcagattcagINScccccagtattggtttgaac																										TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr21:47704722_47704723insC	ENST00000397708.1	-	2	732_733	c.478_479insG	c.(478-480)gctfs	p.A160fs	YBEY_ENST00000397701.4_5'Flank|MCM3AP_ENST00000291688.1_Frame_Shift_Ins_p.A160fs|YBEY_ENST00000397692.1_5'Flank|YBEY_ENST00000339195.6_5'Flank|YBEY_ENST00000329319.3_5'Flank|YBEY_ENST00000397691.1_5'Flank|YBEY_ENST00000397694.1_5'Flank			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	160	FG-repeats.				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)					CTCAGATTCAGCCCCCAGTATT	0.446																																					p.A160fs		Pindel,Atlas-Indel	.											.	MCM3AP	146	.	0			c.479_480insG						PASS	.																																			SO:0001589	frameshift_variant	8888	exon1			.	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.479dupG	21.37:g.47704727_47704727dupC	ENSP00000380820:p.Ala160fs	49	0	.		39	15	0.385	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Frame_Shift_Ins	INS	ENST00000397708.1	37	CCDS13734.1																																																																																			.	.	none		0.446	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906		C	47704723	-	C	47704722	7	5	11	1	0	1	1	0	0	0	0	0	9397	971	34	0	5575	0	MCM3AP	21	47704722	Frame_Shift_Ins	INS	-	TCGA-FF-8042-01A-11D-2210-10	4887349	47704722	425173	267	1558											
CBX6	23466	hgsc.bcm.edu	37	chr22	39263079	39263079	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggcgggacatacggtggcagCggcggatgtccttcttgagc	6	8	17	10	4	1	1	0	1	1	0	2	3	2	3	1	6	3	1	1	6	1	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr22:39263079C>T	ENST00000407418.3	-	5	497	c.374G>A	c.(373-375)cGc>cAc	p.R125H	CBX6_ENST00000216083.6_Missense_Mutation_p.R107H			O95503	CBX6_HUMAN	chromobox homolog 6	125					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)					ACGGTGGCAGCGGCGGATGTC	0.697																																					p.R125H		Atlas-SNP	.											.	CBX6	26	.	0			c.G374A						PASS	.						10	9	9					22																	39263079		1978	3955	5933	SO:0001583	missense	23466	exon5			TGGCAGCGGCGGA		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.374G>A	22.37:g.39263079C>T	ENSP00000384490:p.Arg125His	26	0	0		30	10	0.333333	NM_014292	A8KAH0|Q96EM5	Missense_Mutation	SNP	ENST00000407418.3	37	CCDS13980.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.044789	0.93685	.	.	ENSG00000183741	ENST00000407418;ENST00000216083	.	.	.	4.13	4.13	0.48395	.	0.317552	0.20986	U	0.082124	T	0.67249	0.2873	L	0.34521	1.04	0.58432	D	0.999992	D	0.89917	1.0	D	0.83275	0.996	T	0.71820	-0.4477	9	0.72032	D	0.01	.	16.5945	0.84792	0.0:1.0:0.0:0.0	.	125	O95503	CBX6_HUMAN	H	125;107	.	ENSP00000216083:R107H	R	-	2	0	CBX6	37593025	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.822000	0.75277	2.138000	0.66242	0.407000	0.27541	CGC	.	.	none		0.697	CBX6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318190.1	NM_014292		T	39263079	C	T	39263079	3	4	11	1	0	0	0	0	1	0	0	0	2724	768	27	1	868	1	CBX6	22	39263079	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10		39263079	12041487	268	1559											
FBLN1	2192	hgsc.bcm.edu	37	chr22	45970519	45970519	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcctaccttccgcgagtTcacccgccctgaaggtgagt	6	9	11	15	3	1	2	1	2	0	0	2	3	2	2	5	1	2	2	5	1	2	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chr22:45970519T>C	ENST00000327858.6	+	15	1921	c.1826T>C	c.(1825-1827)tTc>tCc	p.F609S	FBLN1_ENST00000348697.2_Splice_Site_p.F609S	NM_006486.2	NP_006477	P23142	FBLN1_HUMAN	fibulin 1	609					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)		TTCCGCGAGTTCACCCGCCCT	0.642																																					p.F609S		Atlas-SNP	.											.	FBLN1	143	.	0			c.T1826C						PASS	.						131	77	96					22																	45970519		2203	4300	6503	SO:0001583	missense	2192	exon15			GCGAGTTCACCCG		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.1826T>C	22.37:g.45970519T>C	ENSP00000331544:p.Phe609Ser	76	0	0		46	4	0.0869565	NM_006486	B0QY42|B1AHL4|P23143|P23144|P37888|Q5TIC4|Q8TBH8|Q9HBQ5|Q9UC21|Q9UGR4|Q9UH41	Missense_Mutation	SNP	ENST00000327858.6	37	CCDS14067.1	.	.	.	.	.	.	.	.	.	.	T	18.77	3.695144	0.68386	.	.	ENSG00000077942	ENST00000348697;ENST00000327858	D;D	0.83250	-1.59;-1.7	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	D	0.85626	0.5740	L	0.32530	0.975	0.52501	D	0.999959	D	0.76494	0.999	D	0.80764	0.994	D	0.85636	0.1273	10	0.44086	T	0.13	.	13.1527	0.59498	0.0:0.0:0.0:1.0	.	609	P23142	FBLN1_HUMAN	S	609	ENSP00000262723:F609S;ENSP00000331544:F609S	ENSP00000331544:F609S	F	+	2	0	FBLN1	44349183	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.632000	0.74281	1.921000	0.55644	0.460000	0.39030	TTC	.	.	none		0.642	FBLN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322287.1	NM_006486		C	45970519	T	C	45970519	3	2	11	1	0	0	0	0	1	0	0	0	5706	1783	62	3	2364	3	FBLN1	22	45970519	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	6707440	45970519	5334047	269	1560											
P2RY8	286530	hgsc.bcm.edu	37	chrX	1584851	1584851	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacgaacgggatgaggaacaGcaggatgaagatggtgaaga	16	4	16	5	2	0	5	0	3	0	2	0	9	0	8	0	4	3	1	0	4	4	0			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chrX:1584851G>C	ENST00000381297.4	-	2	811	c.601C>G	c.(601-603)Ctg>Gtg	p.L201V	P2RY8_ENST00000460672.1_5'Flank	NM_178129.4	NP_835230.1	Q86VZ1	P2RY8_HUMAN	purinergic receptor P2Y, G-protein coupled, 8	201						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(13)|prostate(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)				ATGAGGAACAGCAGGATGAAG	0.632			T	CRLF2	"B-ALL, Downs associated ALL"																																p.L201V		Atlas-SNP	.		Dom	yes		"X,Y"	Xp22.3; Yp11.3	286530	"purinergic receptor P2Y, G-protein coupled, 8"		L	.	P2RY8	53	.	0			c.C601G						PASS	.						134	71	93					X																	1584851		2203	4296	6499	SO:0001583	missense	286530	exon2			GGAACAGCAGGAT	AA804531	CCDS14115.1	Xp22.33 and Yp11.3	2012-08-08			ENSG00000182162	ENSG00000182162		"Pseudoautosomal regions / PAR1", "Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	15524	protein-coding gene	gene with protein product		300525				11004484	Standard	NM_178129		Approved	P2Y8	uc004cpz.2	Q86VZ1	OTTHUMG00000021060	ENST00000381297.4:c.601C>G	X.37:g.1584851G>C	ENSP00000370697:p.Leu201Val	87	0	0		48	35	0.729167	NM_178129		Missense_Mutation	SNP	ENST00000381297.4	37	CCDS14115.1	.	.	.	.	.	.	.	.	.	.	g	3.766	-0.048645	0.07407	.	.	ENSG00000182162	ENST00000381297	T	0.71461	-0.57	2.41	2.41	0.29592	GPCR, rhodopsin-like superfamily (1);	0.085770	0.48286	U	0.000193	T	0.68531	0.3011	L	0.41632	1.29	0.09310	N	1	D	0.61080	0.989	P	0.62298	0.9	T	0.56523	-0.7965	10	0.17369	T	0.5	.	5.7904	0.18357	0.269:0.0:0.731:0.0	.	201	Q86VZ1	P2RY8_HUMAN	V	201	ENSP00000370697:L201V	ENSP00000370697:L201V	L	-	1	2	P2RY8	1544851	0.994000	0.37717	0.486000	0.27416	0.409000	0.31022	2.274000	0.43390	0.838000	0.34948	0.279000	0.19357	CTG	.	.	none		0.632	P2RY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055602.1	NM_178129		C	1584851	G	C	1584851	3	2	11	1	0	0	0	0	1	0	0	0	11364	962	34	4	482	4	P2RY8	23	1584851	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10		1584851	153685709	270	1561											
ARSF	416	hgsc.bcm.edu	37	chrX	3021805	3021805	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aattgcattgtcttataggtGgaaaaggcatggggggctgg	10	11	16	4	0	1	0	0	0	1	0	1	1	1	1	0	7	1	3	0	7	5	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chrX:3021805G>A	ENST00000381127.1	+	9	1326	c.1105G>A	c.(1105-1107)Gga>Aga	p.G369R	ARSF_ENST00000359361.2_Missense_Mutation_p.G369R|ARSF_ENST00000537104.1_Missense_Mutation_p.G369R	NM_001201538.1|NM_001201539.1	NP_001188467.1|NP_001188468.1	P54793	ARSF_HUMAN	arylsulfatase F	369					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)				TCTTATAGGTGGAAAAGGCAT	0.428																																					p.G369R		Atlas-SNP	.											.	ARSF	97	.	0			c.G1105A						PASS	.						70	65	67					X																	3021805		2203	4300	6503	SO:0001583	missense	416	exon9			ATAGGTGGAAAAG	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.1105G>A	X.37:g.3021805G>A	ENSP00000370519:p.Gly369Arg	226	1	0.00442478		109	72	0.66055	NM_004042	Q8TCC5	Missense_Mutation	SNP	ENST00000381127.1	37	CCDS14123.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.471316	0.43942	.	.	ENSG00000062096	ENST00000381127;ENST00000537104;ENST00000359361	D;D;D	0.94576	-3.46;-3.46;-3.46	3.43	3.43	0.39272	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	U	0.000000	D	0.97028	0.9029	M	0.82323	2.585	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	D	0.97468	1.0039	10	0.66056	D	0.02	.	14.2451	0.65983	0.0:0.0:1.0:0.0	.	369	P54793	ARSF_HUMAN	R	369	ENSP00000370519:G369R;ENSP00000445594:G369R;ENSP00000352319:G369R	ENSP00000352319:G369R	G	+	1	0	ARSF	3031805	1.000000	0.71417	0.066000	0.19879	0.007000	0.05969	6.109000	0.71528	1.316000	0.45131	0.411000	0.27672	GGA	.	.	none		0.428	ARSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055652.1			A	3021805	G	A	3021805	3	1	11	1	0	0	0	0	1	0	0	0	991	1349	47	2	1135	2	ARSF	23	3021805	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	1436954	3021805	152248755	271	1562											
TMSB4X	7114	hgsc.bcm.edu	37	chrX	12994407	12994407	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gacaaacccgatatggctgaGatcgagaaattcgataagtc	15	8	10	8	3	0	2	0	1	0	2	3	7	0	2	1	1	1	1	1	1	4	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chrX:12994407G>C	ENST00000380635.1	+	2	243	c.27G>C	c.(25-27)gaG>gaC	p.E9D	TMSB4X_ENST00000380636.1_Missense_Mutation_p.E9D|TMSB4X_ENST00000380633.1_Missense_Mutation_p.E9D|TMSB4X_ENST00000451311.2_Missense_Mutation_p.E9D			P62328	TYB4_HUMAN	thymosin beta 4, X-linked	9					actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|sequestering of actin monomers (GO:0042989)	cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	poly(A) RNA binding (GO:0044822)			upper_aerodigestive_tract(1)	1						ATATGGCTGAGATCGAGAAAT	0.527																																					p.E9D		Atlas-SNP	.											.	TMSB4X	3	.	0			c.G27C						PASS	.						65	63	64					X																	12994407		2203	4298	6501	SO:0001583	missense	7114	exon2			GGCTGAGATCGAG		CCDS35202.1	Xp22.2	2013-05-14	2008-02-25		ENSG00000205542	ENSG00000205542			11881	protein-coding gene	gene with protein product		300159	"thymosin, beta 4, X chromosome"	TMSB4		2677145, 9381176	Standard	NM_021109		Approved	TB4X	uc004cvf.3	P62328	OTTHUMG00000021144	ENST00000380635.1:c.27G>C	X.37:g.12994407G>C	ENSP00000370009:p.Glu9Asp	366	0	0		212	141	0.665094	NM_021109	P01253|P01254|Q546P5|Q63576|Q9UE55	Missense_Mutation	SNP	ENST00000380635.1	37	CCDS35202.1	.	.	.	.	.	.	.	.	.	.	G	18.08	3.544587	0.65198	.	.	ENSG00000205542	ENST00000451311;ENST00000380636;ENST00000380635;ENST00000380633	T;T;T;T	0.59906	0.23;0.23;0.23;0.23	4.66	4.66	0.58398	.	0.000000	0.64402	U	0.000010	T	0.69396	0.3106	.	.	.	0.36331	D	0.858899	D	0.62365	0.991	P	0.59595	0.86	T	0.78041	-0.2359	9	0.66056	D	0.02	-11.1719	11.3215	0.49424	0.0926:0.0:0.9074:0.0	.	9	P62328	TYB4_HUMAN	D	9	ENSP00000414376:E9D;ENSP00000370010:E9D;ENSP00000370009:E9D;ENSP00000370007:E9D	ENSP00000370007:E9D	E	+	3	2	TMSB4X	12904328	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.324000	0.43831	2.064000	0.61679	0.600000	0.82982	GAG	.	.	none		0.527	TMSB4X-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000055779.1	NM_021109		C	12994407	G	C	12994407	3	2	11	1	0	0	0	0	1	0	0	0	16272	933	33	4	29	4	TMSB4X	23	12994407	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	9972602	12994407	142276153	272	1563											
ZFX	7543	hgsc.bcm.edu	37	chrX	24229464	24229464	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaaagaaccagcacataatgCgacatcataaagaagttggc	19	6	8	8	1	1	2	1	0	0	2	1	3	1	2	1	1	3	2	1	1	7	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chrX:24229464C>T	ENST00000379177.1	+	11	2816	c.2389C>T	c.(2389-2391)Cga>Tga	p.R797*	ZFX_ENST00000304543.5_Nonsense_Mutation_p.R797*|ZFX_ENST00000539115.1_Nonsense_Mutation_p.R568*|ZFX_ENST00000338565.3_Nonsense_Mutation_p.R747*|ZFX_ENST00000540034.1_Nonsense_Mutation_p.R836*|ZFX_ENST00000379188.3_Nonsense_Mutation_p.R797*	NM_001178085.1|NM_003410.3	NP_001171556.1|NP_003401.2	P17010	ZFX_HUMAN	zinc finger protein, X-linked	797					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						GCACATAATGCGACATCATAA	0.423																																					p.R797X	Esophageal Squamous(20;306 562 7346 32868 37983)	Atlas-SNP	.											.	ZFX	61	.	0			c.C2389T						PASS	.						57	47	51					X																	24229464		2202	4300	6502	SO:0001587	stop_gained	7543	exon10			ATAATGCGACATC		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.2389C>T	X.37:g.24229464C>T	ENSP00000368475:p.Arg797*	292	0	0		147	100	0.680272	NM_003410	B9EG97|O43668|Q8WYJ8	Nonsense_Mutation	SNP	ENST00000379177.1	37	CCDS14211.1	.	.	.	.	.	.	.	.	.	.	C	37	6.393586	0.97533	.	.	ENSG00000005889	ENST00000539115;ENST00000379188;ENST00000535562;ENST00000379177;ENST00000304543;ENST00000540034;ENST00000338565	.	.	.	5.41	3.63	0.41609	.	0.120124	0.36519	N	0.002558	.	.	.	.	.	.	0.41696	D	0.989374	.	.	.	.	.	.	.	.	.	.	0.05351	T	0.99	-7.1264	15.3833	0.74676	0.3533:0.6467:0.0:0.0	.	.	.	.	X	568;797;519;797;797;836;747	.	ENSP00000304985:R797X	R	+	1	2	ZFX	24139385	0.999000	0.42202	0.992000	0.48379	0.962000	0.63368	0.752000	0.26362	0.203000	0.20529	-0.936000	0.02699	CGA	.	.	none		0.423	ZFX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056084.1	NM_003410		T	24229464	C	T	24229464	4	4	11	1	0	0	0	0	0	1	0	0	17676	760	27	1	2474	1	ZFX	23	24229464	Nonsense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	11235057	24229464	131041096	273	1564											
MAGEB16	139604	hgsc.bcm.edu	37	chrX	35821008	35821008	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggaagtgctgaatttgaCgggagtatattctgggaaga	11	11	15	4	1	1	3	0	2	1	1	1	6	1	6	0	3	1	2	0	3	5	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chrX:35821008C>T	ENST00000399989.1	+	2	974	c.695C>T	c.(694-696)aCg>aTg	p.T232M	MAGEB16_ENST00000399987.1_Missense_Mutation_p.T232M|MAGEB16_ENST00000399992.1_Missense_Mutation_p.T264M|MAGEB16_ENST00000399988.1_Missense_Mutation_p.T232M|MAGEB16_ENST00000399985.1_Missense_Mutation_p.T232M	NM_001099921.1	NP_001093391.1	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	232	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31						CTGAATTTGACGGGAGTATAT	0.498																																					p.T232M		Atlas-SNP	.											.	MAGEB16	64	.	0			c.C695T						PASS	.						66	63	64					X																	35821008		2174	4283	6457	SO:0001583	missense	139604	exon2			ATTTGACGGGAGT		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.695C>T	X.37:g.35821008C>T	ENSP00000382871:p.Thr232Met	173	0	0		83	52	0.626506	NM_001099921	A8MU30	Missense_Mutation	SNP	ENST00000399989.1	37	CCDS43927.1	.	.	.	.	.	.	.	.	.	.	C	0.006	-2.023161	0.00414	.	.	ENSG00000189023	ENST00000399988;ENST00000399992;ENST00000399987;ENST00000399989;ENST00000399985	T;T;T;T;T	0.04156	3.69;3.69;3.69;3.69;3.69	3.13	-2.0	0.07433	.	0.556178	0.18983	N	0.125826	T	0.00875	0.0029	N	0.00275	-1.725	0.09310	N	1	B	0.25441	0.126	B	0.15484	0.013	T	0.41928	-0.9481	10	0.02654	T	1	.	7.8393	0.29389	0.0:0.3154:0.0:0.6846	.	232	A2A368	MAGBG_HUMAN	M	232;264;232;232;232	ENSP00000382870:T232M;ENSP00000382874:T264M;ENSP00000382869:T232M;ENSP00000382871:T232M;ENSP00000382867:T232M	ENSP00000382867:T232M	T	+	2	0	MAGEB16	35730929	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.451000	0.00466	-0.690000	0.05142	0.521000	0.50471	ACG	.	.	none		0.498	MAGEB16-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251034.1			T	35821008	C	T	35821008	3	4	11	1	0	0	0	0	1	0	0	0	9183	536	19	1	697	1	MAGEB16	23	35821008	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	11591544	35821008	119449552	274	1565											
MSN	4478	hgsc.bcm.edu	37	chrX	64955264	64955264	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agatgaaggcacaggcccggGaggagaagcaccagaagcag	15	1	16	9	1	0	4	0	1	0	3	0	6	0	5	2	4	2	3	2	4	3	0			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chrX:64955264G>T	ENST00000360270.5	+	8	1103	c.931G>T	c.(931-933)Gag>Tag	p.E311*		NM_002444.2	NP_002435.1	P26038	MOES_HUMAN	moesin	311					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						ACAGGCCCGGGAGGAGAAGCA	0.587			T	ALK	ALCL																																p.E311X		Atlas-SNP	.		Dom	yes		X	Xq11.2-q12	4478	moesin		L	.	MSN	89	.	0			c.G931T						PASS	.						51	33	39					X																	64955264		2203	4300	6503	SO:0001587	stop_gained	4478	exon8			GCCCGGGAGGAGA	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.931G>T	X.37:g.64955264G>T	ENSP00000353408:p.Glu311*	151	0	0		77	55	0.714286	NM_002444		Nonsense_Mutation	SNP	ENST00000360270.5	37	CCDS14382.1	.	.	.	.	.	.	.	.	.	.	G	39	7.666558	0.98422	.	.	ENSG00000147065	ENST00000360270	.	.	.	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	16.7763	0.85551	0.0:0.0:1.0:0.0	.	.	.	.	X	311	.	ENSP00000353408:E311X	E	+	1	0	MSN	64871989	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.756000	0.98918	2.278000	0.76064	0.594000	0.82650	GAG	.	.	none		0.587	MSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056981.1	NM_002444		T	64955264	G	T	64955264	4	4	11	1	0	0	0	0	0	1	0	0	9894	1175	41	4	961	4	MSN	23	64955264	Nonsense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	29134256	64955264	90315296	275	1566											
ZMYM3	9203	hgsc.bcm.edu	37	chrX	70462020	70462020	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggagggggcagcctcgtacCtcgccctttcctctggcgga	4	8	15	14	3	1	0	0	0	1	0	4	2	2	2	4	5	2	2	4	5	1	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chrX:70462020C>T	ENST00000353904.2	-	23	3989	c.3802G>A	c.(3802-3804)Gac>Aac	p.D1268N	ZMYM3_ENST00000314425.5_Splice_Site_p.D1268N|ZMYM3_ENST00000373988.1_Splice_Site_p.D1270N|ZMYM3_ENST00000373998.1_Splice_Site_p.D1256N|ZMYM3_ENST00000489332.1_5'UTR|ZMYM3_ENST00000373984.3_Intron	NM_005096.3	NP_005087.1	Q14202	ZMYM3_HUMAN	zinc finger, MYM-type 3	1268					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)					AGCCTCGTACCTCGCCCTTTC	0.637																																					p.D1268N		Atlas-SNP	.											.	ZMYM3	137	.	0			c.G3802A						PASS	.						38	26	30					X																	70462020		2188	4286	6474	SO:0001630	splice_region_variant	9203	exon23			TCGTACCTCGCCC	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.3802+1G>A	X.37:g.70462020C>T		84	0	0		35	27	0.771429	NM_005096	D3DVV3|O15089|Q96E26	Missense_Mutation	SNP	ENST00000353904.2	37	CCDS14409.1	.	.	.	.	.	.	.	.	.	.	c	17.31	3.356776	0.61293	.	.	ENSG00000147130	ENST00000314425;ENST00000373998;ENST00000353904;ENST00000373988	T;T;T;T	0.45668	1.48;0.89;1.48;1.48	4.66	4.66	0.58398	.	0.175419	0.39544	N	0.001325	T	0.27697	0.0681	N	0.14661	0.345	0.50313	D	0.999865	B;B	0.09022	0.002;0.002	B;B	0.10450	0.003;0.005	T	0.06463	-1.0825	9	.	.	.	-13.7907	16.8803	0.86061	0.0:1.0:0.0:0.0	.	1256;1268	Q14202-2;Q14202	.;ZMYM3_HUMAN	N	1268;1256;1268;1270	ENSP00000322845:D1268N;ENSP00000363110:D1256N;ENSP00000343909:D1268N;ENSP00000363100:D1270N	.	D	-	1	0	ZMYM3	70378745	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	6.625000	0.74248	2.161000	0.67846	0.519000	0.50382	GAC	.	.	none		0.637	ZMYM3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057154.1	NM_201599	Missense_Mutation	T	70462020	C	T	70462020	5	4	11	1	0	0	0	0	0	0	1	0	17716	695	24	2	322	2	ZMYM3	23	70462020	Splice_Site	SNP	C	TCGA-FF-8042-01A-11D-2210-10	5506756	70462020	84808540	276	1567											
BRWD3	254065	hgsc.bcm.edu	37	chrX	80064532	80064532	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgatgctcctcgagctcctGcactagcacctgagcaaaag	10	8	9	14	1	0	2	0	2	0	0	3	3	2	2	3	0	5	5	3	0	3	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chrX:80064532G>A	ENST00000373275.4	-	3	316	c.100C>T	c.(100-102)Cag>Tag	p.Q34*		NM_153252.4	NP_694984	Q6RI45	BRWD3_HUMAN	bromodomain and WD repeat domain containing 3	34					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						TCGAGCTCCTGCACTAGCACC	0.602																																					p.Q34X		Atlas-SNP	.											.	BRWD3	251	.	0			c.C100T						PASS	.						52	49	50					X																	80064532		2199	4298	6497	SO:0001587	stop_gained	254065	exon3			GCTCCTGCACTAG		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.100C>T	X.37:g.80064532G>A	ENSP00000362372:p.Gln34*	253	1	0.00395257		123	83	0.674797	NM_153252	C9IZ39|C9J3F3|Q2T9J6|Q5JRN1|Q6RI37|Q6RI42|Q6RI44|Q8N916	Nonsense_Mutation	SNP	ENST00000373275.4	37	CCDS14447.1	.	.	.	.	.	.	.	.	.	.	G	37	6.619038	0.97709	.	.	ENSG00000165288	ENST00000373275	.	.	.	4.6	3.66	0.41972	.	0.081539	0.47455	D	0.000229	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-11.9026	8.9154	0.35579	0.0:0.2224:0.7776:0.0	.	.	.	.	X	34	.	.	Q	-	1	0	BRWD3	79951188	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.261000	0.51530	2.273000	0.75805	0.529000	0.55759	CAG	.	.	none		0.602	BRWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057344.1	NM_153252		A	80064532	G	A	80064532	4	1	11	1	0	0	0	0	0	1	0	0	1528	1328	46	2	5464	2	BRWD3	23	80064532	Nonsense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	9602512	80064532	75206028	277	1568											
DRP2	1821	hgsc.bcm.edu	37	chrX	100497418	100497418	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cacttgtcaatggagaattcCcaggccctggaacagatcaa	13	8	9	11	0	2	2	2	0	0	2	3	4	3	3	2	3	1	0	2	3	4	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chrX:100497418C>T	ENST00000395209.3	+	8	1460	c.933C>T	c.(931-933)tcC>tcT	p.S311S	DRP2_ENST00000541709.1_Silent_p.S233S|DRP2_ENST00000402866.1_Silent_p.S311S|DRP2_ENST00000538510.1_Silent_p.S311S	NM_001939.2	NP_001930.2	Q13474	DRP2_HUMAN	dystrophin related protein 2	311					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						TGGAGAATTCCCAGGCCCTGG	0.488																																					p.S311S		Atlas-SNP	.											.	DRP2	98	.	0			c.C933T						PASS	.						141	128	132					X																	100497418		2203	4300	6503	SO:0001819	synonymous_variant	1821	exon8			GAATTCCCAGGCC	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.933C>T	X.37:g.100497418C>T		190	0	0		70	53	0.757143	NM_001939	A6ZKI5|A8K1B0|B1B1F3|B4DIZ0	Silent	SNP	ENST00000395209.3	37	CCDS14480.2																																																																																			.	.	none		0.488	DRP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057522.3	NM_001939		T	100497418	C	T	100497418	2	4	11	1	0	0	0	0	0	0	0	1	4766	610	22	2		2	DRP2	23	100497418	Silent	SNP	C	TCGA-FF-8042-01A-11D-2210-10	20432886	100497418	54773142	278	1569											
ARMCX5	64860	hgsc.bcm.edu	37	chrX	101858511	101858511	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	actgtcatcattggttgcacCctttaacaagaatgagtcaa	13	12	7	9	0	3	2	3	1	0	1	3	2	3	2	1	1	2	2	1	1	4	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chrX:101858511C>T	ENST00000604957.1	+	1	4064	c.1442C>T	c.(1441-1443)cCc>cTc	p.P481L	RP4-769N13.7_ENST00000602441.1_RNA|ARMCX5_ENST00000537008.1_Missense_Mutation_p.P481L|ARMCX5_ENST00000246174.2_Missense_Mutation_p.P481L|RP4-769N13.6_ENST00000476910.2_RNA|ARMCX5_ENST00000372742.1_Missense_Mutation_p.P481L|ARMCX5_ENST00000536530.1_Missense_Mutation_p.P481L|ARMCX5_ENST00000541409.1_Missense_Mutation_p.P481L	NM_001168478.1	NP_001161950.1	Q6P1M9	ARMX5_HUMAN	armadillo repeat containing, X-linked 5	481										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	22						TTGGTTGCACCCTTTAACAAG	0.308																																					p.P481L		Atlas-SNP	.											.	ARMCX5	55	.	0			c.C1442T						PASS	.						55	52	53					X																	101858511		2203	4298	6501	SO:0001583	missense	64860	exon3			TTGCACCCTTTAA		CCDS14500.1	Xq22.1-q22.3	2014-03-21			ENSG00000125962	ENSG00000125962		"Armadillo repeat containing"	25772	protein-coding gene	gene with protein product						16221301, 22569362	Standard	NM_022838		Approved	FLJ12969, GASP5	uc004ejh.3	Q6P1M9	OTTHUMG00000022062	ENST00000604957.1:c.1442C>T	X.37:g.101858511C>T	ENSP00000474720:p.Pro481Leu	166	0	0		78	4	0.0512821	NM_022838	B3KU88|D3DX99|Q68DB4|Q9BVZ3|Q9H969	Missense_Mutation	SNP	ENST00000604957.1	37	CCDS14500.1	.	.	.	.	.	.	.	.	.	.	C	0.003	-2.497123	0.00159	.	.	ENSG00000125962	ENST00000246174;ENST00000537008;ENST00000541409;ENST00000536530;ENST00000372742	T;T;T;T;T	0.18810	2.19;2.19;2.19;2.19;2.19	4.1	-1.49	0.08718	Armadillo-like helical (1);Armadillo-type fold (1);	0.671371	0.12373	N	0.474583	T	0.04634	0.0126	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.37009	-0.9724	10	0.02654	T	1	1.1091	3.7361	0.08511	0.1792:0.3098:0.0:0.511	.	481	Q6P1M9	ARMX5_HUMAN	L	481	ENSP00000246174:P481L;ENSP00000439001:P481L;ENSP00000446385:P481L;ENSP00000445851:P481L;ENSP00000361827:P481L	ENSP00000246174:P481L	P	+	2	0	ARMCX5	101745167	0.000000	0.05858	0.000000	0.03702	0.173000	0.22820	-0.653000	0.05360	-0.442000	0.07190	-0.192000	0.12808	CCC	.	.	none		0.308	ARMCX5-013	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469659.1	NM_022838		T	101858511	C	T	101858511	3	4	11	1	0	0	0	0	1	0	0	0	962	623	22	2	1444	2	ARMCX5	23	101858511	Missense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	1361093	101858511	53412049	279	1570											
AMOT	154796	hgsc.bcm.edu	37	chrX	112033851	112033851	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cacagttgcagcagcatccaGagcaaaatgtctcatcacat	14	8	7	12	0	2	1	2	0	1	1	4	1	3	1	1	0	4	5	1	0	2	1			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chrX:112033851G>C	ENST00000524145.1	-	8	2160	c.2086C>G	c.(2086-2088)Ctg>Gtg	p.L696V	AMOT_ENST00000371959.3_Missense_Mutation_p.L696V|AMOT_ENST00000371962.1_Missense_Mutation_p.L464V|AMOT_ENST00000371958.1_Missense_Mutation_p.L464V|AMOT_ENST00000304758.1_Missense_Mutation_p.L287V			Q4VCS5	AMOT_HUMAN	angiomotin	696					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						GCAGCATCCAGAGCAAAATGT	0.473																																					p.L696V		Atlas-SNP	.											.	AMOT	204	.	0			c.C2086G						PASS	.						245	226	233					X																	112033851		2203	4300	6503	SO:0001583	missense	154796	exon7			CATCCAGAGCAAA	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.2086C>G	X.37:g.112033851G>C	ENSP00000429013:p.Leu696Val	424	0	0		191	116	0.60733	NM_001113490	Q504X5|Q9HD27|Q9UPT1	Missense_Mutation	SNP	ENST00000524145.1	37	CCDS48154.1	.	.	.	.	.	.	.	.	.	.	G	17.39	3.377766	0.61735	.	.	ENSG00000126016	ENST00000304758;ENST00000371959;ENST00000371962;ENST00000524145;ENST00000371958	T;T;T;T;T	0.22945	1.99;2.2;2.46;2.2;1.93	5.86	4.08	0.47627	Angiomotin, C-terminal (1);	0.000000	0.64402	D	0.000001	T	0.34571	0.0902	L	0.39898	1.24	0.46749	D	0.999188	D	0.67145	0.996	D	0.65573	0.936	T	0.04216	-1.0968	10	0.25751	T	0.34	-11.8944	9.0425	0.36327	0.2535:0.0:0.7465:0.0	.	696	Q4VCS5	AMOT_HUMAN	V	287;696;464;696;464	ENSP00000305557:L287V;ENSP00000361027:L696V;ENSP00000361030:L464V;ENSP00000429013:L696V;ENSP00000361026:L464V	ENSP00000305557:L287V	L	-	1	2	AMOT	111920507	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	2.017000	0.40981	1.211000	0.43351	0.600000	0.82982	CTG	.	.	none		0.473	AMOT-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378570.1	NM_133265		C	112033851	G	C	112033851	3	2	11	1	0	0	0	0	1	0	0	0	582	933	33	4	1188	4	AMOT	23	112033851	Missense_Mutation	SNP	G	TCGA-FF-8042-01A-11D-2210-10	10175340	112033851	43236709	280	1571											
SEPT6	23157	hgsc.bcm.edu	37	chrX	118797638	118797638	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacttgcccaaacctgtctCtcctgaaaagcaaaaggata	14	8	8	11	0	1	1	0	1	1	0	3	3	2	3	3	2	3	1	3	2	6	2			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chrX:118797638C>A	ENST00000343984.5	-	3	412	c.148G>T	c.(148-150)Gag>Tag	p.E50*	SEPT6_ENST00000394616.4_5'UTR|SEPT6_ENST00000394610.1_Nonsense_Mutation_p.E50*|SEPT6_ENST00000354228.4_Nonsense_Mutation_p.E50*|SEPT6_ENST00000489216.1_Nonsense_Mutation_p.E50*|SEPT6_ENST00000394617.2_Nonsense_Mutation_p.E80*|SEPT6_ENST00000360156.7_Nonsense_Mutation_p.E50*|SEPT6_ENST00000354416.3_Nonsense_Mutation_p.E50*	NM_015129.5	NP_055944.2	Q14141	SEPT6_HUMAN	septin 6	50	Septin-type G.				cytokinesis (GO:0000910)|viral process (GO:0016032)	axon terminus (GO:0043679)|kinetochore (GO:0000776)|septin complex (GO:0031105)|synaptic vesicle (GO:0008021)	GTP binding (GO:0005525)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(3)	17						AAACCTGTCTCTCCTGAAAAG	0.478			T	MLL	AML																																p.E50X		Atlas-SNP	.		Dom	yes		X	Xq24	23157	septin 6		L	.	SEPT6	53	.	0			c.G148T						PASS	.						140	131	134					X																	118797638		2203	4300	6503	SO:0001587	stop_gained	23157	exon3			CTGTCTCTCCTGA	D50918	CCDS14583.1, CCDS14584.1, CCDS14585.1	Xq24	2013-01-21			ENSG00000125354	ENSG00000125354		"Septins"	15848	protein-coding gene	gene with protein product		300683				8590280, 10744683	Standard	NM_015129		Approved	KIAA0128, SEP2, SEPT2, MGC16619, MGC20339	uc004erv.3	Q14141	OTTHUMG00000022280	ENST00000343984.5:c.148G>T	X.37:g.118797638C>A	ENSP00000341524:p.Glu50*	107	0	0		50	32	0.64	NM_145802	Q5JTK0|Q969W5|Q96A13|Q96GR1|Q96P86|Q96P87	Nonsense_Mutation	SNP	ENST00000343984.5	37	CCDS14584.1	.	.	.	.	.	.	.	.	.	.	c	38	7.016911	0.98006	.	.	ENSG00000125354	ENST00000360156;ENST00000354228;ENST00000489216;ENST00000354416;ENST00000394610;ENST00000343984;ENST00000394617;ENST00000520510	.	.	.	4.27	4.27	0.50696	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	15.6198	0.76796	0.0:1.0:0.0:0.0	.	.	.	.	X	50;50;50;50;50;50;80;50	.	ENSP00000341524:E50X	E	-	1	0	SEPT6	118681666	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.439000	0.80444	2.073000	0.62155	0.597000	0.82753	GAG	.	.	none		0.478	SEPT6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058059.1	NM_145802		A	118797638	C	A	118797638	4	1	11	1	0	0	0	0	0	1	0	0	14083	922	32	4	1210	4	SEPT6	23	118797638	Nonsense_Mutation	SNP	C	TCGA-FF-8042-01A-11D-2210-10	6763787	118797638	36472922	281	1572											
OCRL	4952	hgsc.bcm.edu	37	chrX	128709154	128709154	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acgaaggtaccggaaagtctTtgaagatagtgtacgcatca	14	9	11	7	3	2	2	1	1	1	1	2	4	2	3	1	2	2	3	1	2	6	4			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chrX:128709154T>G	ENST00000371113.4	+	16	1805	c.1640T>G	c.(1639-1641)tTt>tGt	p.F547C	OCRL_ENST00000357121.5_Missense_Mutation_p.F547C	NM_000276.3	NP_000267.2	Q01968	OCRL_HUMAN	oculocerebrorenal syndrome of Lowe	547	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						CGGAAAGTCTTTGAAGATAGT	0.423																																					p.F547C		Atlas-SNP	.											.	OCRL	117	.	0			c.T1640G						PASS	.						217	176	190					X																	128709154		2203	4300	6503	SO:0001583	missense	4952	exon16			AAGTCTTTGAAGA	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.1640T>G	X.37:g.128709154T>G	ENSP00000360154:p.Phe547Cys	136	1	0.00735294		105	86	0.819048	NM_000276	A6NKI1|A8KAP2|B7ZLX2|O60800|Q15684|Q15774|Q4VY09|Q4VY10|Q5JQF1|Q5JQF2|Q9UJG5|Q9UMA5	Missense_Mutation	SNP	ENST00000371113.4	37	CCDS35393.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.059371	0.76074	.	.	ENSG00000122126	ENST00000371113;ENST00000357121	D;D	0.95412	-3.7;-3.7	5.68	5.68	0.88126	Endonuclease/exonuclease/phosphatase (1);	0.047623	0.85682	D	0.000000	D	0.97084	0.9047	M	0.71581	2.175	0.80722	D	1	D;D	0.89917	1.0;0.997	D;P	0.69824	0.966;0.9	D	0.97274	0.9913	10	0.56958	D	0.05	.	13.6193	0.62128	0.0:0.0:0.0:1.0	.	547;547	Q01968-2;Q01968	.;OCRL_HUMAN	C	547	ENSP00000360154:F547C;ENSP00000349635:F547C	ENSP00000349635:F547C	F	+	2	0	OCRL	128536835	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	7.698000	0.84413	1.896000	0.54893	0.441000	0.28932	TTT	.	.	none		0.423	OCRL-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058917.1	NM_000276		G	128709154	T	G	128709154	3	3	11	1	0	0	0	0	1	0	0	0	10832	1841	64	5	1702	5	OCRL	23	128709154	Missense_Mutation	SNP	T	TCGA-FF-8042-01A-11D-2210-10	9911516	128709154	26561406	282	1573											
MAGEC3	139081	hgsc.bcm.edu	37	chrX	140985325	140985325	+	Intron	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatcccagaaagctgctcaCtatacattgggtgcagagaa	13	8	11	9	0	1	2	1	0	0	2	2	4	2	3	1	2	4	3	1	2	4	3			TCGA-FF-8042-01A-11D-2210-10	TCGA-FF-8042-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	897a4500-6fb8-4e81-aa07-021a26d632fb	92bd05d0-5cb1-4e14-9c66-c3b020b1d9c2	g.chrX:140985325C>A	ENST00000298296.1	+	7	1728				MAGEC3_ENST00000443323.2_Missense_Mutation_p.T216N|MAGEC3_ENST00000536088.1_Missense_Mutation_p.T296N|MAGEC3_ENST00000544766.1_Missense_Mutation_p.T296N|MAGEC3_ENST00000409007.1_Missense_Mutation_p.T296N	NM_138702.1	NP_619647.1	Q8TD91	MAGC3_HUMAN	melanoma antigen family C, 3											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)					AAGCTGCTCACTATACATTGG	0.527																																					p.T296N		Atlas-SNP	.											.	MAGEC3	228	.	0			c.C887A						PASS	.						73	73	73					X																	140985325		2203	4300	6503	SO:0001627	intron_variant	139081	exon5			TGCTCACTATACA	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.1728+53C>A	X.37:g.140985325C>A		211	0	0		169	141	0.83432	NM_177456	Q3SYA7|Q5JZ43|Q9BZ80	Missense_Mutation	SNP	ENST00000298296.1	37	CCDS14676.1	.	.	.	.	.	.	.	.	.	.	c	8.239	0.806342	0.16467	.	.	ENSG00000165509	ENST00000536088;ENST00000443323;ENST00000544766;ENST00000409007	T;T;T;T	0.05996	3.36;3.36;3.36;3.36	1.25	0.292	0.15737	.	.	.	.	.	T	0.30916	0.0780	H	0.96048	3.76	0.09310	N	1	D	0.89917	1.0	D	0.81914	0.995	T	0.08249	-1.0731	8	.	.	.	.	6.1961	0.20550	0.0:0.7821:0.0:0.2179	.	296	Q3SYA7	.	N	296;216;296;296	ENSP00000441107:T296N;ENSP00000438254:T216N;ENSP00000440444:T296N;ENSP00000386566:T296N	.	T	+	2	0	MAGEC3	140812991	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.207000	0.09384	-0.423000	0.07394	-1.954000	0.00483	ACT	.	.	none		0.527	MAGEC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058606.1	NM_138702		A	140985325	C	A	140985325	1	1	11	0	1	0	0	0	0	0	0	0	9191	565	20	4		4	MAGEC3	23	140985325	Intron	SNP	C	TCGA-FF-8042-01A-11D-2210-10	12276171	140985325	14285235	283	1574											
PRAMEF11	440560	hgsc.bcm.edu	37	chr1	12887686	12887686	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagcacttgaagtttccaTctcctgtgggaaaatagagg	11	11	10	9	0	1	2	0	1	1	1	4	3	3	3	3	2	1	2	3	2	4	3	rs59802947	byFrequency	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr1:12887686T>C	ENST00000535591.1	-	3	366	c.171A>G	c.(169-171)agA>agG	p.R57R		NM_001146344.1	NP_001139816.1	O60813	PRA11_HUMAN	PRAME family member 11	57					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)			p.R57R(1)		NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|lung(7)|pancreas(2)|skin(4)|urinary_tract(1)	27						GAAGTTTCCATCTCCTGTGGG	0.468													.|||	5	0.000998403	0.0008	0.0	5008	,	,		21622	0.001		0.0	False		,,,				2504	0.0031				p.R57R		Atlas-SNP	.											PRAMEF11,NS,carcinoma,0,1	PRAMEF11	72	1	1	Substitution - coding silent(1)	endometrium(1)	c.A171G						scavenged	.																																			SO:0001819	synonymous_variant	440560	exon3			TTTCCATCTCCTG	AL049680	CCDS53268.1	1p36.21	2013-01-17			ENSG00000204513	ENSG00000239810		"-"	14086	protein-coding gene	gene with protein product							Standard	XM_006710645		Approved		uc001auk.2	O60813	OTTHUMG00000001929	ENST00000535591.1:c.171A>G	1.37:g.12887686T>C		41	0	0		53	5	0.0943396	NM_001146344		Silent	SNP	ENST00000535591.1	37	CCDS53268.1																																																																																			T|0.986;C|0.014	0.014	strong		0.468	PRAMEF11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_496341		C	12887686	T	C	12887686	2	2	12	1	0	0	0	0	0	0	0	1	12439	1432	50	3		3	PRAMEF11	1	12887686	Silent	SNP	T	TCGA-FF-8043-01A-11D-2210-10		12887686	236362935	1	1575											
UBXN11	91544	hgsc.bcm.edu	37	chr1	26608867	26608867	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actggggccgggaccgggacCgggactggggccgggaccgg	5	2	22	12	5	0	0	0	0	0	0	0	4	0	4	5	9	0	0	5	9	0	0	rs193142354		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr1:26608867C>A	ENST00000374222.1	-	16	1950	c.1486G>T	c.(1486-1488)Ggt>Tgt	p.G496C	UBXN11_ENST00000374221.3_Missense_Mutation_p.G496C|UBXN11_ENST00000357089.4_Missense_Mutation_p.G463C|UBXN11_ENST00000374223.1_Missense_Mutation_p.G253C|UBXN11_ENST00000314675.7_Missense_Mutation_p.G376C|UBXN11_ENST00000374217.2_Missense_Mutation_p.G463C			Q5T124	UBX11_HUMAN	UBX domain protein 11	496	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						ggaccgggaccgggactgggg	0.721																																					p.G496C		Atlas-SNP	.											UBXN11,colon,carcinoma,0,2	UBXN11	54	2	1	Deletion - In frame(1)	ovary(1)	c.G1486T						scavenged	.						25	29	28					1																	26608867		1765	4016	5781	SO:0001583	missense	91544	exon16			CGGGACCGGGACT	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.1486G>T	1.37:g.26608867C>A	ENSP00000363339:p.Gly496Cys	26	2	0.0769231		26	7	0.269231	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Missense_Mutation	SNP	ENST00000374222.1	37	CCDS41288.1	261	0.11950549450549451	72	0.14634146341463414	35	0.09668508287292818	16	0.027972027972027972	138	0.1820580474934037	A	8.132	0.783217	0.16189	.	.	ENSG00000158062	ENST00000314675;ENST00000374223;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217	T;T;T;T;T;T	0.23950	1.88;1.96;2.3;2.24;2.24;2.3	.	.	.	.	.	.	.	.	T	0.00073	0.0002	N	0.22421	0.69	0.58432	P	2.9999999999752447E-6	D;D;D;D	0.76494	0.999;0.999;0.999;0.998	D;D;D;P	0.65323	0.934;0.934;0.934;0.861	T	0.12578	-1.0542	7	0.66056	D	0.02	.	6.1326	0.20213	0.0:0.6805:0.3194:0.0	.	463;458;376;496	Q5T124-2;Q5T124-4;Q5T124-3;Q5T124	.;.;.;UBX11_HUMAN	C	376;253;463;496;496;463	ENSP00000324721:G376C;ENSP00000363340:G253C;ENSP00000349601:G463C;ENSP00000363338:G496C;ENSP00000363339:G496C;ENSP00000363334:G463C	ENSP00000324721:G376C	G	-	1	0	UBXN11	26481454	0.000000	0.05858	0.121000	0.21740	0.128000	0.20619	-1.193000	0.03049	0.392000	0.25172	0.391000	0.25812	GGT	C|0.880;A|0.120	0.120	strong		0.721	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345		A	26608867	C	A	26608867	3	1	12	1	0	0	0	0	1	0	0	0	16928	652	23	4	80	4	UBXN11	1	26608867	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10	13721181	26608867	222641754	2	1576											
ORC1L	4998	hgsc.bcm.edu	37	chr1	52838903	52838903	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcctggctgacgttgagccGcacccgaaggagcagatcgt	9	7	13	12	4	0	3	0	2	0	1	2	5	1	4	3	2	2	4	3	2	1	1			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr1:52838903G>A	ENST00000371568.3	-	17	2754	c.2536C>T	c.(2536-2538)Cgg>Tgg	p.R846W	ORC1_ENST00000371566.1_Missense_Mutation_p.R846W	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	846	Necessary and sufficient for ORC complex assembly.				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						ACGTTGAGCCGCACCCGAAGG	0.552																																					p.R846W		Atlas-SNP	.											.	ORC1	79	.	0			c.C2536T						PASS	.						102	107	105					1																	52838903		2203	4300	6503	SO:0001583	missense	4998	exon17			TGAGCCGCACCCG		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.2536C>T	1.37:g.52838903G>A	ENSP00000360623:p.Arg846Trp	146	0	0		148	61	0.412162	NM_004153	D3DQ34|Q13471|Q5T0F5	Missense_Mutation	SNP	ENST00000371568.3	37	CCDS566.1	.	.	.	.	.	.	.	.	.	.	G	14.41	2.527904	0.44969	.	.	ENSG00000085840	ENST00000371568;ENST00000371566	T;T	0.46819	0.86;0.86	5.25	2.27	0.28462	CDC6, C-terminal (1);	0.115966	0.56097	D	0.000023	T	0.64505	0.2604	M	0.78637	2.42	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.63537	-0.6615	10	0.87932	D	0	-16.4175	8.0772	0.30722	0.0714:0.0:0.5136:0.415	.	841;846	B7Z8H0;Q13415	.;ORC1_HUMAN	W	846	ENSP00000360623:R846W;ENSP00000360621:R846W	ENSP00000360621:R846W	R	-	1	2	ORC1	52611491	1.000000	0.71417	0.994000	0.49952	0.007000	0.05969	4.294000	0.59043	0.318000	0.23185	-0.142000	0.14014	CGG	.	.	none		0.552	ORC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022202.1	NM_004153		A	52838903	G	A	52838903	3	1	12	1	0	0	0	0	1	0	0	0	11270	1086	38	1	53	1	ORC1L	1	52838903	Missense_Mutation	SNP	G	TCGA-FF-8043-01A-11D-2210-10	26230036	52838903	196411718	3	1577											
CYP2J2	1573	hgsc.bcm.edu	37	chr1	60381646	60381646	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgttctcgcataggggtcaCggggcggttcccaaagtttt	7	12	13	9	3	2	0	1	0	1	0	4	0	3	0	1	5	0	4	1	5	2	5	rs11572242	byFrequency	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr1:60381646C>T	ENST00000371204.3	-	2	380	c.337G>A	c.(337-339)Gtg>Atg	p.V113M	CYP2J2_ENST00000492633.1_5'Flank	NM_000775.2	NP_000766.2	P51589	CP2J2_HUMAN	cytochrome P450, family 2, subfamily J, polypeptide 2	113			V -> M (in dbSNP:rs11572242).		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)	p.V113M(1)		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)	ATAGGGGTCACGGGGCGGTTC	0.428													C|||	3	0.000599042	0.0008	0.0029	5008	,	,		19082	0.0		0.0	False		,,,				2504	0.0				p.V113M		Atlas-SNP	.											CYP2J2,colon,carcinoma,0,1	CYP2J2	34	1	1	Substitution - Missense(1)	large_intestine(1)	c.G337A						PASS	.						108	110	110					1																	60381646		2203	4300	6503	SO:0001583	missense	1573	exon2			GGGTCACGGGGCG	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.337G>A	1.37:g.60381646C>T	ENSP00000360247:p.Val113Met	88	0	0		128	44	0.34375	NM_000775	B2RD33|Q8TF13	Missense_Mutation	SNP	ENST00000371204.3	37	CCDS613.1	3	0.0013736263736263737	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	0	0.0	C	7.417	0.635998	0.14386	.	.	ENSG00000134716	ENST00000371204	T	0.69040	-0.37	5.8	-11.6	0.00059	.	3.755470	0.00166	N	0.000010	T	0.40372	0.1114	N	0.25789	0.76	0.09310	N	1	P	0.38020	0.615	B	0.36186	0.219	T	0.56275	-0.8006	10	0.44086	T	0.13	.	10.2805	0.43537	0.0643:0.5248:0.2124:0.1986	rs11572242;rs52814181;rs11572242	113	P51589	CP2J2_HUMAN	M	113	ENSP00000360247:V113M	ENSP00000360247:V113M	V	-	1	0	CYP2J2	60154234	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.110000	0.00150	-3.492000	0.00153	-2.084000	0.00378	GTG	C|0.998;T|0.002	0.002	strong		0.428	CYP2J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024940.1	NM_000775		T	60381646	C	T	60381646	3	4	12	1	0	0	0	0	1	0	0	0	4174	536	19	1	1203	1	CYP2J2	1	60381646	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10	7542743	60381646	188868975	4	1578											
PTGER3	5733	hgsc.bcm.edu	37	chr1	71318536	71318536	+	3'UTR	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caggttttaatttccccaaaAttcctcctggaaaacaaaca	15	11	4	11	0	0	0	0	0	0	0	3	1	3	1	4	2	2	1	4	2	6	4			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr1:71318536A>C	ENST00000370931.3	-	0	1413				PTGER3_ENST00000370932.2_Missense_Mutation_p.F362V|PTGER3_ENST00000460330.1_Missense_Mutation_p.F371V|PTGER3_ENST00000351052.5_3'UTR	NM_198714.1	NP_942007.1	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)	TTTCCCCAAAATTCCTCCTGG	0.328																																					p.F371V		Atlas-SNP	.											PTGER3_ENST00000460330,NS,carcinoma,0,1	PTGER3	246	1	0			c.T1111G						PASS	.						131	146	141					1																	71318536		2203	4300	6503	SO:0001624	3_prime_UTR_variant	5733	exon4			CCCAAAATTCCTC	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	ENST00000370931.3:c.*30T>G	1.37:g.71318536A>C		118	0	0		122	45	0.368852	NM_198716	B0AZN4|B1AK19|B5BUP5|O00326|Q12943|Q12944|Q12945|Q16546|Q5CZ59|Q5CZ61|Q5CZ62|Q5CZ63|Q5CZ64	Missense_Mutation	SNP	ENST00000370931.3	37	CCDS656.1	.	.	.	.	.	.	.	.	.	.	A	3.509	-0.100135	0.07010	.	.	ENSG00000050628	ENST00000370932;ENST00000460330	T;T	0.17370	2.28;2.5	2.92	1.79	0.24919	.	.	.	.	.	T	0.02494	0.0076	.	.	.	0.30139	N	0.804125	B;B	0.15141	0.012;0.012	B;B	0.19946	0.017;0.027	T	0.47156	-0.9139	8	0.17369	T	0.5	.	4.5446	0.12074	0.8453:0.0:0.1547:0.0	.	362;371	P43115-3;P43115-4	.;.	V	362;371	ENSP00000359970:F362V;ENSP00000418073:F371V	ENSP00000359970:F362V	F	-	1	0	PTGER3	71091124	0.128000	0.22383	0.482000	0.27366	0.272000	0.26649	0.026000	0.13599	0.528000	0.28580	0.377000	0.23210	TTT	.	.	none		0.328	PTGER3-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026077.1	NM_000957		C	71318536	A	C	71318536	1	2	12	0	1	0	0	0	0	0	0	0	12757	101	4	5		5	PTGER3	1	71318536	3'UTR	SNP	A	TCGA-FF-8043-01A-11D-2210-10	10936890	71318536	177932085	5	1579											
HIAT1	64645	hgsc.bcm.edu	37	chr1	100547630	100547630	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctggctctgcttgttgccttGtttattccggaacataccaa	7	15	8	11	1	1	0	0	0	1	0	2	1	2	1	3	2	4	4	3	2	4	7			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr1:100547630G>A	ENST00000370152.3	+	12	1474	c.1338G>A	c.(1336-1338)ttG>ttA	p.L446L	SASS6_ENST00000462159.1_5'Flank|RP4-714D9.2_ENST00000432294.1_RNA	NM_033055.2	NP_149044.2	Q96MC6	HIAT1_HUMAN	hippocampus abundant transcript 1	446					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)		TTGTTGCCTTGTTTATTCCGG	0.463																																					p.L446L		Atlas-SNP	.											.	HIAT1	46	.	0			c.G1338A						PASS	.						109	100	103					1																	100547630		2203	4300	6503	SO:0001819	synonymous_variant	64645	exon12			TGCCTTGTTTATT	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.1338G>A	1.37:g.100547630G>A		214	0	0		257	112	0.435798	NM_033055	Q6P2N7|Q8N8K2|Q8NBV3|Q96NY0|Q9NT25	Silent	SNP	ENST00000370152.3	37	CCDS763.1																																																																																			.	.	none		0.463	HIAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029657.1	NM_033055		A	100547630	G	A	100547630	2	1	12	1	0	0	0	0	0	0	0	1	7106	1368	48	2		2	HIAT1	1	100547630	Silent	SNP	G	TCGA-FF-8043-01A-11D-2210-10	29229094	100547630	148702991	6	1580											
COL11A1	1301	hgsc.bcm.edu	37	chr1	103484376	103484376	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttaaaacatttacatactgCaggtcctgctggtcctggtg	9	13	9	10	0	0	0	0	0	0	0	2	0	2	0	2	3	5	2	2	3	4	4			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr1:103484376C>T	ENST00000370096.3	-	10	1660	c.1348G>A	c.(1348-1350)Gca>Aca	p.A450T	COL11A1_ENST00000358392.2_Missense_Mutation_p.A462T|COL11A1_ENST00000512756.1_Missense_Mutation_p.A334T|COL11A1_ENST00000353414.4_Missense_Mutation_p.A411T	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	450	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)		TTACATACTGCAGGTCCTGCT	0.328																																					p.A462T		Atlas-SNP	.											.	COL11A1	972	.	0			c.G1384A						PASS	.						54	55	55					1																	103484376		2203	4300	6503	SO:0001583	missense	1301	exon10			ATACTGCAGGTCC	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.1348G>A	1.37:g.103484376C>T	ENSP00000359114:p.Ala450Thr	94	0	0		130	53	0.407692	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	37	CCDS778.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.845119	0.51164	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000512756;ENST00000427239	D;D;D;D;D	0.93604	-3.25;-3.25;-3.25;-3.25;-3.25	5.68	4.72	0.59763	.	0.172573	0.50627	D	0.000108	T	0.81192	0.4771	N	0.17082	0.46	0.45867	D	0.998729	B;B;B;B	0.23650	0.089;0.073;0.073;0.089	B;B;B;B	0.29077	0.098;0.059;0.059;0.098	T	0.76798	-0.2826	10	0.25106	T	0.35	.	11.916	0.52765	0.1356:0.7333:0.131:0.0	.	334;411;462;450	E9PCU0;P12107-3;P12107-2;P12107	.;.;.;COBA1_HUMAN	T	450;462;411;334;462	ENSP00000359114:A450T;ENSP00000351163:A462T;ENSP00000302551:A411T;ENSP00000426533:A334T;ENSP00000408640:A462T	ENSP00000302551:A411T	A	-	1	0	COL11A1	103256964	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.673000	0.37534	2.676000	0.91093	0.637000	0.83480	GCA	.	.	none		0.328	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		T	103484376	C	T	103484376	3	4	12	1	0	0	0	0	1	0	0	0	3669	710	25	2	4304	2	COL11A1	1	103484376	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10	2936746	103484376	145766245	7	1581											
IGSF3	3321	hgsc.bcm.edu	37	chr1	117158983	117158983	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctgctcagaaggtccctggTagccactcacattgcaccag	9	9	9	14	0	3	1	2	0	1	1	4	1	4	1	3	2	3	3	3	2	2	2			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr1:117158983T>G	ENST00000369486.3	-	3	905	c.140A>C	c.(139-141)tAc>tCc	p.Y47S	IGSF3_ENST00000369483.1_Missense_Mutation_p.Y47S|IGSF3_ENST00000318837.6_Missense_Mutation_p.Y47S	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	47	Ig-like C2-type 1.				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)		AGGTCCCTGGTAGCCACTCAC	0.577																																					p.Y47S		Atlas-SNP	.											IGSF3_ENST00000369483,NS,carcinoma,+1,2	IGSF3	294	2	0			c.A140C						scavenged	.						28	28	28					1																	117158983		2203	4292	6495	SO:0001583	missense	3321	exon3			CCCTGGTAGCCAC	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.140A>C	1.37:g.117158983T>G	ENSP00000358498:p.Tyr47Ser	88	2	0.0227273		139	6	0.0431655	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	T	18.18	3.567123	0.65651	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.02323	4.34;4.34;4.34	4.65	-3.71	0.04424	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.463445	0.23369	N	0.048939	T	0.03915	0.0110	M	0.69823	2.125	0.52099	D	0.999948	P;P	0.49783	0.928;0.919	P;P	0.56823	0.784;0.807	T	0.16394	-1.0404	10	0.72032	D	0.01	-17.8621	10.721	0.46040	0.6328:0.0:0.0:0.3672	.	47;47	O75054;A6NJZ6	IGSF3_HUMAN;.	S	47	ENSP00000358498:Y47S;ENSP00000358495:Y47S;ENSP00000321184:Y47S	ENSP00000321184:Y47S	Y	-	2	0	IGSF3	116960506	1.000000	0.71417	0.995000	0.50966	0.983000	0.72400	1.704000	0.37857	-0.387000	0.07809	0.454000	0.30748	TAC	T|0.500;G|0.500	0.500	weak		0.577	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542		G	117158983	T	G	117158983	3	3	12	1	0	0	0	0	1	0	0	0	7610	1638	57	5	3544	5	IGSF3	1	117158983	Missense_Mutation	SNP	T	TCGA-FF-8043-01A-11D-2210-10	13674607	117158983	132091638	8	1582											
ALDH9A1	223	hgsc.bcm.edu	37	chr1	165652258	165652258	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgcataatactccaggcaCtgccaggaaatgtcaatgtc	12	8	8	13	1	1	0	1	0	0	0	3	1	2	1	3	2	2	2	3	2	4	2			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr1:165652258C>T	ENST00000354775.4	-	3	721	c.417G>A	c.(415-417)caG>caA	p.Q139Q	ALDH9A1_ENST00000538148.1_Silent_p.Q45Q|ALDH9A1_ENST00000461664.1_5'UTR	NM_000696.3	NP_000687.3	P49189	AL9A1_HUMAN	aldehyde dehydrogenase 9 family, member A1	115					carnitine biosynthetic process (GO:0045329)|cellular aldehyde metabolic process (GO:0006081)|cellular nitrogen compound metabolic process (GO:0034641)|hormone metabolic process (GO:0042445)|kidney development (GO:0001822)|liver development (GO:0001889)|neurotransmitter biosynthetic process (GO:0042136)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	1-pyrroline dehydrogenase activity (GO:0033737)|3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|4-trimethylammoniobutyraldehyde dehydrogenase activity (GO:0047105)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|amine binding (GO:0043176)|aminobutyraldehyde dehydrogenase activity (GO:0019145)|NAD binding (GO:0051287)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	21	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)					ACTCCAGGCACTGCCAGGAAA	0.512																																					p.Q139Q	Ovarian(179;1583 2014 18106 33801 42447)	Atlas-SNP	.											.	ALDH9A1	75	.	0			c.G417A						PASS	.						113	98	103					1																	165652258		2203	4300	6503	SO:0001819	synonymous_variant	223	exon3			CAGGCACTGCCAG	U34252	CCDS1250.2	1q22-q23	2008-02-05			ENSG00000143149	ENSG00000143149		"Aldehyde dehydrogenases"	412	protein-coding gene	gene with protein product		602733		ALDH7, ALDH4, ALDH9		8112751, 8786138	Standard	NM_000696		Approved	E3	uc001gdh.1	P49189	OTTHUMG00000034677	ENST00000354775.4:c.417G>A	1.37:g.165652258C>T		64	0	0		92	4	0.0434783	NM_000696	B2R6X1|B4DXY7|Q5VV90|Q6LCL1|Q9NZT7	Silent	SNP	ENST00000354775.4	37	CCDS1250.2																																																																																			.	.	none		0.512	ALDH9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083899.1			T	165652258	C	T	165652258	2	4	12	1	0	0	0	0	0	0	0	1	506	564	20	2		2	ALDH9A1	1	165652258	Silent	SNP	C	TCGA-FF-8043-01A-11D-2210-10	48493275	165652258	83598363	9	1583											
DUSP27	92235	hgsc.bcm.edu	37	chr1	167095865	167095865	+	Frame_Shift_Del	DEL	C	C	-																															cggaggtaccacgccaagagCaagagagaggaggcggcaga																										TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr1:167095865delC	ENST00000361200.2	+	6	1663	c.1497delC	c.(1495-1497)agcfs	p.S499fs	DUSP27_ENST00000271385.5_Frame_Shift_Del_p.S499fs|DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000443333.1_Frame_Shift_Del_p.S499fs			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	499					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						ACGCCAAGAGCAAGAGAGAGG	0.617																																					p.S499fs		Pindel,Atlas-Indel	.											.	DUSP27	235	.	0			c.1496delG						PASS	.						48	46	47					1																	167095865		2203	4300	6503	SO:0001589	frameshift_variant	92235	exon5			.	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.1497delC	1.37:g.167095865delC	ENSP00000354483:p.Ser499fs	155	0	.		186	48	0.258	NM_001080426	A0AUM4|Q9C074	Frame_Shift_Del	DEL	ENST00000361200.2	37	CCDS30932.1																																																																																			.	.	none		0.617	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		-	167095865	C	-	167095865	7	5	12	1	0	1	0	1	0	0	0	0	4826	709	25	0	1515	0	DUSP27	1	167095865	Frame_Shift_Del	DEL	C	TCGA-FF-8043-01A-11D-2210-10	1443607	167095865	82154756	10	1584											
NAV1	89796	hgsc.bcm.edu	37	chr1	201779198	201779198	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccgagatgcctccttgccGtcgaggtgtcaataacatat	9	10	9	13	3	1	1	1	0	0	1	3	3	2	1	5	1	3	0	5	1	3	3	rs201416032		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr1:201779198G>A	ENST00000367296.4	+	23	4946	c.4526G>A	c.(4525-4527)cGt>cAt	p.R1509H	NAV1_ENST00000367300.3_Missense_Mutation_p.R1449H|NAV1_ENST00000367295.1_Missense_Mutation_p.R1115H|NAV1_ENST00000367297.4_Missense_Mutation_p.R1501H|MIR1231_ENST00000408101.1_RNA|NAV1_ENST00000295624.6_Missense_Mutation_p.R1506H|NAV1_ENST00000367302.1_Missense_Mutation_p.R1462H|IPO9-AS1_ENST00000413035.1_RNA	NM_020443.4	NP_065176.3	Q8NEY1	NAV1_HUMAN	neuron navigator 1	1509					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						CCTCCTTGCCGTCGAGGTGTC	0.532																																					p.R1509H		Atlas-SNP	.											NAV1,right_upper_lobe,carcinoma,0,2	NAV1	143	2	0			c.G4526A						PASS	.	G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	150	114	126		3344,4526	5.4	1	1		126	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	NAV1	NM_001167738.1,NM_020443.4	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	1115/1484,1509/1878	201779198	1,13005	2203	4300	6503	SO:0001583	missense	89796	exon23			CTTGCCGTCGAGG	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.4526G>A	1.37:g.201779198G>A	ENSP00000356265:p.Arg1509His	122	0	0		164	10	0.0609756	NM_020443	A8MS88|Q5SVH1|Q5SVH2|Q5SVH3|Q5SVH7|Q5VUY9|Q8IVL2|Q96II1|Q9H7V9|Q9H9S9|Q9H9T5|Q9UGI1|Q9ULK7|Q9ULR9	Missense_Mutation	SNP	ENST00000367296.4	37	CCDS1414.2	.	.	.	.	.	.	.	.	.	.	G	20.1	3.940056	0.73557	0.0	1.16E-4	ENSG00000134369	ENST00000367302;ENST00000367296;ENST00000295624;ENST00000367297;ENST00000367300;ENST00000367295	T;T;T;T;T;T	0.07444	3.2;3.19;3.19;3.19;3.2;3.19	5.38	5.38	0.77491	.	0.252855	0.38897	N	0.001527	T	0.09291	0.0229	L	0.43152	1.355	0.40705	D	0.982517	P;P	0.42248	0.774;0.774	B;B	0.33454	0.096;0.164	T	0.09037	-1.0693	10	0.52906	T	0.07	-14.844	18.7379	0.91763	0.0:0.0:1.0:0.0	.	1115;1506	Q8NEY1-5;Q8NEY1-3	.;.	H	1462;1509;1506;1501;1449;1115	ENSP00000356271:R1462H;ENSP00000356265:R1509H;ENSP00000295624:R1506H;ENSP00000356266:R1501H;ENSP00000356269:R1449H;ENSP00000356264:R1115H	ENSP00000295624:R1506H	R	+	2	0	NAV1	200045821	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	4.197000	0.58413	2.498000	0.84270	0.561000	0.74099	CGT	G|0.999;A|0.001	0.001	weak		0.532	NAV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000087013.1	NM_020443		A	201779198	G	A	201779198	3	1	12	1	0	0	0	0	1	0	0	0	10192	1145	40	1	4673	1	NAV1	1	201779198	Missense_Mutation	SNP	G	TCGA-FF-8043-01A-11D-2210-10	34683333	201779198	47471423	11	1585											
LEFTY2	7044	hgsc.bcm.edu	37	chr1	226127479	226127479	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gagtcgatgagggaggtgcgGttggagccgtcgtcgcggac	6	7	20	8	6	0	1	0	1	0	0	3	6	0	4	1	5	2	1	1	5	0	1	rs188858500	byFrequency	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr1:226127479G>A	ENST00000366820.5	-	2	822	c.474C>T	c.(472-474)aaC>aaT	p.N158N	LEFTY2_ENST00000420304.2_Silent_p.N124N|RP4-559A3.6_ENST00000513672.1_RNA|LEFTY2_ENST00000474493.1_5'UTR	NM_003240.3	NP_003231.2	O00292	LFTY2_HUMAN	left-right determination factor 2	158					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)					GGGAGGTGCGGTTGGAGCCGT	0.776													G|||	32	0.00638978	0.0	0.0014	5008	,	,		12140	0.0298		0.0	False		,,,				2504	0.001				p.N158N	Colon(172;116 2643 9098 43333)	Atlas-SNP	.											.	LEFTY2	25	.	0			c.C474T						PASS	.						3	5	4					1																	226127479		1604	3499	5103	SO:0001819	synonymous_variant	7044	exon2			GGTGCGGTTGGAG	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.474C>T	1.37:g.226127479G>A		1	0	0		14	12	0.857143	NM_003240	B3KNH4|B4E332|E9PDM4|O75611|Q5TE89|Q8NBQ9	Silent	SNP	ENST00000366820.5	37	CCDS1549.1																																																																																			G|0.990;A|0.010	0.010	strong		0.776	LEFTY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091152.1	NM_003240		A	226127479	G	A	226127479	2	1	12	1	0	0	0	0	0	0	0	1	8725	1252	44	2		2	LEFTY2	1	226127479	Silent	SNP	G	TCGA-FF-8043-01A-11D-2210-10	24348281	226127479	23123142	12	1586											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228522538	228522538	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcatgagcagctggtgccGccccgaatgctggagaggtt	7	8	16	10	2	0	2	0	1	0	1	0	4	0	2	3	3	5	5	3	3	1	1	rs373968488		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr1:228522538G>A	ENST00000422127.1	+	61	16154	c.16110G>A	c.(16108-16110)ccG>ccA	p.P5370P	OBSCN_ENST00000570156.2_Silent_p.P6327P|OBSCN_ENST00000284548.11_Silent_p.P5370P|OBSCN_ENST00000366707.4_Silent_p.P3004P|OBSCN_ENST00000366709.4_Silent_p.P2489P	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5370					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)				AGCTGGTGCCGCCCCGAATGC	0.617																																					p.P6327P		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G18981A						PASS	.	G	,	0,4092		0,0,2046	25	31	29		16110,16110	-6.5	1	1		29	1,8309		0,1,4154	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	0,1,6200	AA,AG,GG		0.012,0.0,0.0081	,	5370/7969,5370/6621	228522538	1,12401	2046	4155	6201	SO:0001819	synonymous_variant	84033	exon72			GGTGCCGCCCCGA	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.16110G>A	1.37:g.228522538G>A		62	0	0		42	32	0.761905	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			.	.	none		0.617	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228522538	G	A	228522538	2	1	12	1	0	0	0	0	0	0	0	1	10821	1074	38	1		1	OBSCN	1	228522538	Silent	SNP	G	TCGA-FF-8043-01A-11D-2210-10	2395059	228522538	20728083	13	1587											
PSME4	23198	hgsc.bcm.edu	37	chr2	54135501	54135501	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	taagttgaagcttttccatcGggagtcaaattcatgcttgt	10	15	9	7	1	2	1	2	1	0	0	4	2	3	2	1	1	2	3	1	1	3	6			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr2:54135501G>A	ENST00000404125.1	-	24	2795	c.2740C>T	c.(2740-2742)Cga>Tga	p.R914*	PSME4_ENST00000421748.2_Nonsense_Mutation_p.R58*	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	914					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)			CTTTTCCATCGGGAGTCAAAT	0.338																																					p.R914X		Atlas-SNP	.											PSME4,rectum,carcinoma,+1,1	PSME4	247	1	0			c.C2740T						PASS	.						55	55	55					2																	54135501		2203	4298	6501	SO:0001587	stop_gained	23198	exon24			TCCATCGGGAGTC	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.2740C>T	2.37:g.54135501G>A	ENSP00000384211:p.Arg914*	64	0	0		57	43	0.754386	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Nonsense_Mutation	SNP	ENST00000404125.1	37	CCDS33197.2	.	.	.	.	.	.	.	.	.	.	G	25.1	4.600660	0.87055	.	.	ENSG00000068878	ENST00000421748;ENST00000404125	.	.	.	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	.	13.9841	0.64324	0.0:0.0:0.8484:0.1515	.	.	.	.	X	58;914	.	ENSP00000384211:R914X	R	-	1	2	PSME4	53989005	1.000000	0.71417	0.990000	0.47175	0.983000	0.72400	3.927000	0.56499	2.486000	0.83907	0.655000	0.94253	CGA	.	.	none		0.338	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		A	54135501	G	A	54135501	4	1	12	1	0	0	0	0	0	1	0	0	12721	1124	39	1	2883	1	PSME4	2	54135501	Nonsense_Mutation	SNP	G	TCGA-FF-8043-01A-11D-2210-10		54135501	189063872	14	1588											
SFXN5	94097	hgsc.bcm.edu	37	chr2	73215387	73215387	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtggtgtgcaggtcttacCtacagcagggaacggcacaa	11	8	13	9	1	1	0	0	0	1	0	1	1	1	1	1	4	5	3	1	4	4	2			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr2:73215387C>T	ENST00000272433.2	-	10	755	c.625G>A	c.(625-627)Gcc>Acc	p.A209T	SFXN5_ENST00000474528.1_5'UTR|SFXN5_ENST00000410065.1_Splice_Site_p.G209R	NM_144579.2	NP_653180.1	Q8TD22	SFXN5_HUMAN	sideroflexin 5	209					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						CAGGTCTTACCTACAGCAGGG	0.572																																					p.A209T		Atlas-SNP	.											.	SFXN5	31	.	0			c.G625A						PASS	.						107	92	97					2																	73215387		2203	4300	6503	SO:0001630	splice_region_variant	94097	exon10			TCTTACCTACAGC	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.625+1G>A	2.37:g.73215387C>T		61	0	0		91	4	0.043956	NM_144579	A8K116|Q494Y3|Q53T29	Missense_Mutation	SNP	ENST00000272433.2	37	CCDS1922.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	27.7|27.7|27.7	4.856674|4.856674|4.856674	0.91433|0.91433|0.91433	.|.|.	.|.|.	ENSG00000144040|ENSG00000144040|ENSG00000144040	ENST00000272433|ENST00000410065|ENST00000411783	T|T|.	0.36157|0.30714|.	1.27|1.52|.	5.39|5.39|5.39	4.5|4.5|4.5	0.54988|0.54988|0.54988	.|.|.	0.000000|.|.	0.85682|.|.	D|.|.	0.000000|.|.	T|T|T	0.66973|0.66973|0.66973	0.2844|0.2844|0.2844	M|M|M	0.82193|0.82193|0.82193	2.58|2.58|2.58	0.30785|0.30785|0.30785	N|N|N	0.741602|0.741602|0.741602	D|P|.	0.55605|0.42584|.	0.972|0.784|.	P|B|.	0.55303|0.42522|.	0.773|0.39|.	T|T|T	0.69262|0.69262|0.69262	-0.5191|-0.5191|-0.5191	9|8|5	.|.|.	.|.|.	.|.|.	-17.7252|-17.7252|-17.7252	11.478|11.478|11.478	0.50310|0.50310|0.50310	0.0:0.9128:0.0:0.0872|0.0:0.9128:0.0:0.0872|0.0:0.9128:0.0:0.0872	.|.|.	209|209|.	Q8TD22|B8ZZJ6|.	SFXN5_HUMAN|.|.	T|R|K	209|209|198	ENSP00000272433:A209T|ENSP00000387076:G209R|.	.|.|.	A|G|R	-|-|-	1|1|2	0|0|0	SFXN5|SFXN5|SFXN5	73068895|73068895|73068895	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.994000|0.994000|0.994000	0.84299|0.84299|0.84299	4.673000|4.673000|4.673000	0.61604|0.61604|0.61604	2.699000|2.699000|2.699000	0.92147|0.92147|0.92147	0.591000|0.591000|0.591000	0.81541|0.81541|0.81541	GCC|GGA|AGG	.	.	none		0.572	SFXN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251991.1	NM_144579	Missense_Mutation	T	73215387	C	T	73215387	5	4	12	1	0	0	0	0	0	0	1	0	14213	695	24	2	417	2	SFXN5	2	73215387	Splice_Site	SNP	C	TCGA-FF-8043-01A-11D-2210-10	19079886	73215387	169983986	15	1589											
RAPH1	65059	hgsc.bcm.edu	37	chr2	204304225	204304225	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agcaggagggggtcctctccGcaacgttgcatagcctgata	9	8	13	11	2	1	1	0	1	1	0	3	2	2	2	3	3	4	4	3	3	3	3			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr2:204304225G>T	ENST00000319170.5	-	14	3987	c.3688C>A	c.(3688-3690)Cgg>Agg	p.R1230R	ABI2_ENST00000295851.5_3'UTR|RAPH1_ENST00000457812.1_Intron|RAPH1_ENST00000374493.3_Silent_p.R1282R	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	1230					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						GGTCCTCTCCGCAACGTTGCA	0.507																																					p.R1230R		Atlas-SNP	.											.	RAPH1	118	.	0			c.C3688A						PASS	.						85	81	83					2																	204304225		2203	4300	6503	SO:0001819	synonymous_variant	65059	exon14			CTCTCCGCAACGT	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.3688C>A	2.37:g.204304225G>T		62	0	0		87	4	0.045977	NM_213589	Q96Q37|Q9C0I2	Silent	SNP	ENST00000319170.5	37	CCDS2359.1																																																																																			.	.	none		0.507	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2	NM_025252		T	204304225	G	T	204304225	2	4	12	1	0	0	0	0	0	0	0	1	13065	1086	38	4		4	RAPH1	2	204304225	Silent	SNP	G	TCGA-FF-8043-01A-11D-2210-10	131088838	204304225	38895148	16	1590											
EXOG	9941	hgsc.bcm.edu	37	chr3	38537954	38537954	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gtgggcgctgcgggagctggGctcgcggccctgcagttctt	2	9	18	12	4	1	0	0	0	1	0	2	1	1	1	1	4	3	5	1	4	0	2			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr3:38537954G>A	ENST00000287675.5	+	1	192	c.96G>A	c.(94-96)ggG>ggA	p.G32G	EXOG_ENST00000422077.2_Silent_p.G32G|EXOG_ENST00000358249.2_5'UTR	NM_005107.3	NP_005098.2	Q9Y2C4	EXOG_HUMAN	endo/exonuclease (5'-3'), endonuclease G-like	32					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						CGGGAGCTGGGCTCGCGGCCC	0.657											OREG0015479	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G32G		Atlas-SNP	.											.	EXOG	29	.	0			c.G96A						PASS	.						45	46	45					3																	38537954		2203	4300	6503	SO:0001819	synonymous_variant	9941	exon1			AGCTGGGCTCGCG	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	ENST00000287675.5:c.96G>A	3.37:g.38537954G>A		61	0	0	879	98	50	0.510204	NM_005107	A8K242|B4DVG2|Q3SXM9|Q9Y2C8	Silent	SNP	ENST00000287675.5	37	CCDS2680.1																																																																																			.	.	none		0.657	EXOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254063.2	NM_005107		A	38537954	G	A	38537954	2	1	12	1	0	0	0	0	0	0	0	1	5314	1190	42	2		2	EXOG	3	38537954	Silent	SNP	G	TCGA-FF-8043-01A-11D-2210-10		38537954	159484476	17	1591											
WNT5A	7474	hgsc.bcm.edu	37	chr3	55508445	55508445	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttggcgtggatgcgctcccGctcgcgggcgtccacgaact	4	8	14	15	7	0	0	0	0	0	0	3	2	2	1	2	3	2	2	2	3	1	1			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr3:55508445G>A	ENST00000474267.1	-	5	1125	c.604C>T	c.(604-606)Cgg>Tgg	p.R202W	WNT5A_ENST00000264634.4_Missense_Mutation_p.R202W|WNT5A_ENST00000497027.1_Missense_Mutation_p.R187W			P41221	WNT5A_HUMAN	wingless-type MMTV integration site family, member 5A	202					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)		ATGCGCTCCCGCTCGCGGGCG	0.682																																					p.R202W		Atlas-SNP	.											WNT5A,NS,carcinoma,+1,1	WNT5A	43	1	0			c.C604T						scavenged	.						16	22	20					3																	55508445		2142	4269	6411	SO:0001583	missense	7474	exon4			GCTCCCGCTCGCG	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.604C>T	3.37:g.55508445G>A	ENSP00000417310:p.Arg202Trp	149	2	0.0134228		172	86	0.5	NM_003392	A8K4A4|Q6P278	Missense_Mutation	SNP	ENST00000474267.1	37	CCDS46850.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.171647	0.78452	.	.	ENSG00000114251	ENST00000474267;ENST00000264634;ENST00000536765;ENST00000497027;ENST00000482079	T;T;T;D	0.85861	-1.12;-1.12;-1.12;-2.04	4.84	1.2	0.21068	.	0.113021	0.56097	D	0.000031	D	0.92831	0.7720	M	0.93854	3.465	0.58432	D	0.999994	D	0.76494	0.999	D	0.63192	0.912	D	0.94072	0.7336	10	0.87932	D	0	.	13.9657	0.64207	0.0:0.0:0.4521:0.5478	.	202	P41221	WNT5A_HUMAN	W	202;202;113;187;187	ENSP00000417310:R202W;ENSP00000264634:R202W;ENSP00000420104:R187W;ENSP00000418184:R187W	ENSP00000264634:R202W	R	-	1	2	WNT5A	55483485	0.992000	0.36948	1.000000	0.80357	0.971000	0.66376	0.423000	0.21313	0.479000	0.27511	0.557000	0.71058	CGG	.	.	none		0.682	WNT5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350793.3	NM_003392		A	55508445	G	A	55508445	3	1	12	1	0	0	0	0	1	0	0	0	17406	1086	38	1	546	1	WNT5A	3	55508445	Missense_Mutation	SNP	G	TCGA-FF-8043-01A-11D-2210-10	16970491	55508445	142513985	18	1592											
TFG	10342	hgsc.bcm.edu	37	chr3	100467168	100467168	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcacaaacttacactgcccaAacttctcagcctactaatta	14	10	3	14	0	1	0	1	0	1	0	2	0	1	0	2	0	6	1	2	0	6	5			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr3:100467168A>T	ENST00000240851.4	+	8	1336	c.996A>T	c.(994-996)caA>caT	p.Q332H	TFG_ENST00000418917.2_Missense_Mutation_p.Q328H|TFG_ENST00000481203.1_3'UTR|TFG_ENST00000490574.1_Missense_Mutation_p.Q332H|TFG_ENST00000476228.1_Missense_Mutation_p.Q328H	NM_001195478.1|NM_001195479.1|NM_006070.5	NP_001182407.1|NP_001182408.1|NP_006061.2	Q92734	TFG_HUMAN	TRK-fused gene	332					cell death (GO:0008219)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	signal transducer activity (GO:0004871)		TFG/NR4A3(2)|TFG/NTRK1_ENST00000392302(5)|TFG/ALK(9)	large_intestine(4)|lung(2)|prostate(1)|stomach(1)	8						ACACTGCCCAAACTTCTCAGC	0.527			T	"NTRK1, ALK"	"papillary thyroid, ALCL, NSCLC"																																p.Q332H		Atlas-SNP	.		Dom	yes		3	3q11-q12	10342	TRK-fused gene		"E, L"	.	TFG	42	.	0			c.A996T						PASS	.						84	86	85					3																	100467168		2203	4300	6503	SO:0001583	missense	10342	exon8			TGCCCAAACTTCT	BC009241	CCDS2939.1, CCDS56266.1	3q12.2	2013-03-13	2001-12-04		ENSG00000114354	ENSG00000114354			11758	protein-coding gene	gene with protein product		602498				9169129, 23479643	Standard	NM_001007565		Approved	TF6, FLJ36137, SPG57	uc003dui.3	Q92734	OTTHUMG00000159085	ENST00000240851.4:c.996A>T	3.37:g.100467168A>T	ENSP00000240851:p.Gln332His	143	0	0		165	62	0.375758	NM_006070	D3DN49|G5E9V1|Q15656|Q969I2	Missense_Mutation	SNP	ENST00000240851.4	37	CCDS2939.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.92|15.92	2.976031|2.976031	0.53720|0.53720	.|.	.|.	ENSG00000114354|ENSG00000114354	ENST00000443578|ENST00000418917;ENST00000490574;ENST00000240851;ENST00000476228	.|T;T;T;T	.|0.54479	.|0.62;0.57;0.57;0.62	6.16|6.16	-2.35|-2.35	0.06684|0.06684	.|.	.|0.117044	.|0.64402	.|D	.|0.000009	T|T	0.55657|0.55657	0.1934|0.1934	L|L	0.29908|0.29908	0.895|0.895	0.53688|0.53688	D|D	0.999979|0.999979	.|D;D	.|0.64830	.|0.994;0.99	.|D;D	.|0.78314	.|0.991;0.979	T|T	0.55075|0.55075	-0.8197|-0.8197	6|10	0.87932|0.56958	D|D	0|0.05	-3.1538|-3.1538	13.2698|13.2698	0.60153|0.60153	0.5279:0.0:0.4721:0.0|0.5279:0.0:0.4721:0.0	.|.	.|328;332	.|G5E9V1;Q92734	.|.;TFG_HUMAN	I|H	328|328;332;332;328	.|ENSP00000397182:Q328H;ENSP00000419960:Q332H;ENSP00000240851:Q332H;ENSP00000417952:Q328H	ENSP00000409727:K328I|ENSP00000240851:Q332H	K|Q	+|+	2|3	0|2	TFG|TFG	101949858|101949858	0.992000|0.992000	0.36948|0.36948	0.582000|0.582000	0.28627|0.28627	0.885000|0.885000	0.51271|0.51271	0.363000|0.363000	0.20301|0.20301	-0.351000|-0.351000	0.08249|0.08249	-0.297000|-0.297000	0.09499|0.09499	AAA|CAA	.	.	none		0.527	TFG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353242.1	NM_006070		T	100467168	A	T	100467168	3	4	12	1	0	0	0	0	1	0	0	0	15821	11	1	5	1022	5	TFG	3	100467168	Missense_Mutation	SNP	A	TCGA-FF-8043-01A-11D-2210-10	44958723	100467168	97555262	19	1593											
RABL3	285282	hgsc.bcm.edu	37	chr3	120409318	120409318	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gattaccttctcttaaaaagTatctcttctctatgacctgt	10	17	4	10	0	3	1	0	1	3	0	6	2	3	1	2	0	1	1	2	0	6	6			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr3:120409318T>C	ENST00000273375.3	-	7	652	c.623A>G	c.(622-624)tAc>tGc	p.Y208C	RABL3_ENST00000491398.1_5'UTR|RABL3_ENST00000483733.1_Missense_Mutation_p.Y184C	NM_173825.3	NP_776186.2	Q5HYI8	RABL3_HUMAN	RAB, member of RAS oncogene family-like 3	208	Small GTPase-like.				small GTPase mediated signal transduction (GO:0007264)		GTP binding (GO:0005525)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)	17				GBM - Glioblastoma multiforme(114;0.151)		TCTTAAAAAGTATCTCTTCTC	0.323																																					p.Y208C		Atlas-SNP	.											.	RABL3	23	.	0			c.A623G						PASS	.						40	43	42					3																	120409318		2199	4290	6489	SO:0001583	missense	285282	exon7			AAAAAGTATCTCT	BC020832	CCDS3001.1	3q13.33	2008-02-05			ENSG00000144840	ENSG00000144840			18072	protein-coding gene	gene with protein product						12477932	Standard	NM_173825		Approved	MGC23920	uc003edx.3	Q5HYI8	OTTHUMG00000159668	ENST00000273375.3:c.623A>G	3.37:g.120409318T>C	ENSP00000273375:p.Tyr208Cys	199	0	0		237	102	0.43038	NM_173825	Q8WUD3	Missense_Mutation	SNP	ENST00000273375.3	37	CCDS3001.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.338274	0.81911	.	.	ENSG00000144840	ENST00000273375;ENST00000483733	T;T	0.74737	-0.58;-0.87	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	T	0.69459	0.3113	N	0.08118	0	0.80722	D	1	D	0.64830	0.994	P	0.57371	0.819	T	0.75184	-0.3407	10	0.52906	T	0.07	-7.5345	14.2018	0.65710	0.0:0.0:0.0:1.0	.	208	Q5HYI8	RABL3_HUMAN	C	208;184	ENSP00000273375:Y208C;ENSP00000419986:Y184C	ENSP00000273375:Y208C	Y	-	2	0	RABL3	121892008	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.258000	0.78371	2.288000	0.76882	0.533000	0.62120	TAC	.	.	none		0.323	RABL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356776.1	NM_173825		C	120409318	T	C	120409318	3	2	12	1	0	0	0	0	1	0	0	0	12987	1638	57	3	95	3	RABL3	3	120409318	Missense_Mutation	SNP	T	TCGA-FF-8043-01A-11D-2210-10	19942150	120409318	77613112	20	1594											
AADAC	13	hgsc.bcm.edu	37	chr3	151542519	151542519	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atataatgccttaaggtggtTcttacgtaaaaaagttcttg	13	15	8	5	1	2	0	0	0	2	0	2	0	2	0	1	2	2	3	1	2	7	8			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr3:151542519T>C	ENST00000232892.7	+	4	626	c.500T>C	c.(499-501)tTc>tCc	p.F167S	RP11-454C18.2_ENST00000483843.2_RNA|AADAC_ENST00000488869.1_Missense_Mutation_p.F167S|RP11-454C18.2_ENST00000475855.1_RNA	NM_001086.2	NP_001077.2	P22760	AAAD_HUMAN	arylacetamide deacetylase	167					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)			TTAAGGTGGTTCTTACGTAAA	0.368																																					p.F167S	Ovarian(30;839 841 2699 32801 46334)	Atlas-SNP	.											.	AADAC	49	.	0			c.T500C						PASS	.						100	100	100					3																	151542519		2203	4300	6503	SO:0001583	missense	13	exon4			GGTGGTTCTTACG	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.500T>C	3.37:g.151542519T>C	ENSP00000232892:p.Phe167Ser	103	0	0		123	5	0.0406504	NM_001086	A8K3L3|D3DNJ6|Q8N1A9	Missense_Mutation	SNP	ENST00000232892.7	37	CCDS33877.1	.	.	.	.	.	.	.	.	.	.	T	15.90	2.970163	0.53614	.	.	ENSG00000114771	ENST00000232892;ENST00000488869	T;T	0.58940	0.3;2.79	4.73	4.73	0.59995	Alpha/beta hydrolase fold-3 (1);	0.000000	0.85682	D	0.000000	T	0.76278	0.3965	M	0.81682	2.555	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	T	0.80535	-0.1339	10	0.87932	D	0	-49.2631	14.2071	0.65741	0.0:0.0:0.0:1.0	.	167	P22760	AAAD_HUMAN	S	167	ENSP00000232892:F167S;ENSP00000419620:F167S	ENSP00000232892:F167S	F	+	2	0	AADAC	153025209	1.000000	0.71417	0.780000	0.31762	0.078000	0.17371	7.000000	0.76290	1.739000	0.51704	0.472000	0.43445	TTC	.	.	none		0.368	AADAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357883.2	NM_001086		C	151542519	T	C	151542519	3	2	12	1	0	0	0	0	1	0	0	0	10	1783	62	3	514	3	AADAC	3	151542519	Missense_Mutation	SNP	T	TCGA-FF-8043-01A-11D-2210-10	31133201	151542519	46479911	21	1595											
MLF1	4291	hgsc.bcm.edu	37	chr3	158289125	158289125	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aacagcagttttgaggatgaCcccttcttctcgtgagttac	9	13	9	10	1	2	3	0	3	2	0	3	4	2	4	2	1	3	3	2	1	2	5			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr3:158289125C>T	ENST00000355893.5	+	1	174	c.36C>T	c.(34-36)gaC>gaT	p.D12D	MLF1_ENST00000469452.1_5'UTR|MLF1_ENST00000497004.1_3'UTR|MLF1_ENST00000392822.3_5'UTR|MLF1_ENST00000471745.1_5'UTR|MLF1_ENST00000484955.1_5'UTR|MLF1_ENST00000359117.5_5'UTR|RP11-538P18.2_ENST00000475981.1_RNA|MLF1_ENST00000478894.2_5'UTR|RP11-538P18.2_ENST00000479233.1_RNA|MLF1_ENST00000482628.1_5'UTR	NM_022443.4	NP_071888.1	P58340	MLF1_HUMAN	myeloid leukemia factor 1	12					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)			TTGAGGATGACCCCTTCTTCT	0.542			T	NPM1	AML																																p.D12D		Atlas-SNP	.		Dom	yes		3	3q25.1	4291	myeloid leukemia factor 1		L	.	MLF1	62	.	0			c.C36T						PASS	.						58	59	58					3																	158289125		2203	4300	6503	SO:0001819	synonymous_variant	4291	exon1			GGATGACCCCTTC	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.36C>T	3.37:g.158289125C>T		223	0	0		276	120	0.434783	NM_022443	E9PEU9|Q2TLE3|Q2TLE5|Q8N8F8|Q96MH1	Silent	SNP	ENST00000355893.5	37	CCDS3182.1	.	.	.	.	.	.	.	.	.	.	C	3.726	-0.056610	0.07362	.	.	ENSG00000178053	ENST00000498592	T	0.44083	0.93	4.0	-2.07	0.07276	.	.	.	.	.	T	0.47060	0.1425	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51942	-0.8641	6	0.87932	D	0	.	8.357	0.32335	0.0:0.3789:0.0:0.6211	.	.	.	.	I	2	ENSP00000419636:T2I	ENSP00000419636:T2I	T	+	2	0	MLF1	159771819	0.450000	0.25697	0.841000	0.33234	0.072000	0.16883	-1.082000	0.03400	-0.346000	0.08312	-0.379000	0.06801	ACC	.	.	none		0.542	MLF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352164.3	NM_022443		T	158289125	C	T	158289125	2	4	12	1	0	0	0	0	0	0	0	1	9623	506	18	2		2	MLF1	3	158289125	Silent	SNP	C	TCGA-FF-8043-01A-11D-2210-10	6746606	158289125	39733305	22	1596											
CLCN2	1181	hgsc.bcm.edu	37	chr3	184071474	184071474	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggactccactagggccagcaTtcggcccttggtcctgtgca	6	9	12	14	1	0	0	0	0	0	0	3	1	2	1	4	4	2	2	4	4	1	3			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr3:184071474T>G	ENST00000265593.4	-	16	2002	c.1831A>C	c.(1831-1833)Atg>Ctg	p.M611L	CLCN2_ENST00000475279.1_5'Flank|CLCN2_ENST00000344937.7_Missense_Mutation_p.M594L|CLCN2_ENST00000434054.2_Missense_Mutation_p.M567L|EIF2B5_ENST00000444495.1_Intron|CLCN2_ENST00000457512.1_Missense_Mutation_p.M611L|CLCN2_ENST00000423355.2_3'UTR	NM_004366.5	NP_004357.3	P51788	CLCN2_HUMAN	chloride channel, voltage-sensitive 2	611	CBS 1. {ECO:0000255|PROSITE- ProRule:PRU00703}.				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)	AGGGCCAGCATTCGGCCCTTG	0.657																																					p.M611L		Atlas-SNP	.											.	CLCN2	74	.	0			c.A1831C						PASS	.						38	37	37					3																	184071474		2202	4300	6502	SO:0001583	missense	1181	exon16			CCAGCATTCGGCC	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.1831A>C	3.37:g.184071474T>G	ENSP00000265593:p.Met611Leu	76	0	0		74	30	0.405405	NM_004366	B4DQT9|B4DZ58|E9PBD9|E9PCD2|O14864|Q6IPA9|Q8WU13	Missense_Mutation	SNP	ENST00000265593.4	37	CCDS3263.1	.	.	.	.	.	.	.	.	.	.	t	16.00	2.998041	0.54147	.	.	ENSG00000114859	ENST00000265593;ENST00000344937;ENST00000434054;ENST00000457512	D;D;D;D	0.87334	-2.24;-2.24;-2.24;-2.24	5.0	3.81	0.43845	Cystathionine beta-synthase, core (1);	0.387182	0.31709	N	0.007192	T	0.76364	0.3977	N	0.22421	0.69	0.80722	D	1	B;B;B;B;B	0.16166	0.016;0.009;0.015;0.004;0.009	B;B;B;B;B	0.15052	0.005;0.005;0.012;0.005;0.005	T	0.69172	-0.5215	10	0.62326	D	0.03	-12.1521	5.9788	0.19395	0.1445:0.0793:0.0:0.7762	.	567;611;594;611;567	E9PBD9;E9PCD2;P51788-3;P51788;B4DZ58	.;.;.;CLCN2_HUMAN;.	L	611;594;567;611	ENSP00000265593:M611L;ENSP00000345056:M594L;ENSP00000400425:M567L;ENSP00000391928:M611L	ENSP00000265593:M611L	M	-	1	0	CLCN2	185554168	1.000000	0.71417	0.997000	0.53966	0.988000	0.76386	3.305000	0.51873	0.734000	0.32515	0.460000	0.39030	ATG	.	.	none		0.657	CLCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345571.1			G	184071474	T	G	184071474	3	3	12	1	0	0	0	0	1	0	0	0	3465	1493	52	5	901	5	CLCN2	3	184071474	Missense_Mutation	SNP	T	TCGA-FF-8043-01A-11D-2210-10	25782349	184071474	13950956	23	1597											
FAM43A	131583	hgsc.bcm.edu	37	chr3	194408350	194408350	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcgaacagctggagcaggaGctgcaggaggaagaggaaga	14	2	19	6	1	0	2	0	0	0	2	0	8	0	7	0	6	5	4	0	6	3	0			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr3:194408350G>A	ENST00000329759.4	+	1	1729	c.795G>A	c.(793-795)gaG>gaA	p.E265E		NM_153690.4	NP_710157.2	Q8N2R8	FA43A_HUMAN	family with sequence similarity 43, member A	265										breast(2)|central_nervous_system(1)|lung(6)|skin(1)	10	all_cancers(143;2.04e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.147)	OV - Ovarian serous cystadenocarcinoma(49;8.37e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;1.78e-05)		TGGAGCAGGAGCTGCAGGAGG	0.677																																					p.E265E		Atlas-SNP	.											.	FAM43A	24	.	0			c.G795A						PASS	.						15	18	17					3																	194408350		2194	4293	6487	SO:0001819	synonymous_variant	131583	exon1			GCAGGAGCTGCAG	AK074503	CCDS33923.1	3q29	2004-07-28			ENSG00000185112	ENSG00000185112			26888	protein-coding gene	gene with protein product						12477932	Standard	NM_153690		Approved	FLJ90022	uc003fuj.3	Q8N2R8	OTTHUMG00000156016	ENST00000329759.4:c.795G>A	3.37:g.194408350G>A		121	0	0		183	88	0.480874	NM_153690	A3KME2|Q8IXP4|Q8WZ07	Silent	SNP	ENST00000329759.4	37	CCDS33923.1																																																																																			.	.	none		0.677	FAM43A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342734.1	NM_153690		A	194408350	G	A	194408350	2	1	12	1	0	0	0	0	0	0	0	1	5570	962	34	2		2	FAM43A	3	194408350	Silent	SNP	G	TCGA-FF-8043-01A-11D-2210-10	10336876	194408350	3614080	24	1598											
DSPP	1834	hgsc.bcm.edu	37	chr4	88537205	88537213	+	In_Frame_Del	DEL	GACAGCAGT	GACAGCAGT	-																															gtgacagcagtgacagcagcGacagcagtgatagcagtgac																								rs143067236|rs151217478|rs551655835	byFrequency	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	GACAGCAGT	GACAGCAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr4:88537205_88537213delGACAGCAGT	ENST00000282478.7	+	4	3424_3432	c.3391_3399delGACAGCAGT	c.(3391-3399)gacagcagtdel	p.DSS1137del	DSPP_ENST00000399271.1_In_Frame_Del_p.DSS1137del|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1137	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)		tgacagcagcgacagcagtgatagcagtg	0.569																																					p.1130_1133del		Atlas-Indel	.											.	DSPP	174	.	0			c.3390_3398del						PASS	.			357,1999		74,209,895						-1.1	0			19	1005,3537		137,731,1403	no	coding	DSPP	NM_014208.3		211,940,2298	A1A1,A1R,RR		22.1268,15.1528,19.7449				1362,5536				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.3391_3399delGACAGCAGT	4.37:g.88537205_88537213delGACAGCAGT	ENSP00000282478:p.Asp1137_Ser1139del	107	0	0		57	30	0.526316	NM_014208	A8MUI0|O95815	In_Frame_Del	DEL	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	none		0.569	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		-	88537213	GACAGCAGT	-	88537205	7	5	12	1	0	1	0	1	0	0	0	0	4784	1058	37	0	3405	0	DSPP	4	88537205	In_Frame_Del	DEL	GACAGCAGT	TCGA-FF-8043-01A-11D-2210-10		88537205	102617071	25	1599											
GPRIN3	285513	hgsc.bcm.edu	37	chr4	90170368	90170368	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcttggttggtcatcgtactGgcttctttgaaccttgacat	6	16	10	9	1	2	2	1	2	1	0	3	2	2	2	1	3	2	4	1	3	2	6			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr4:90170368G>A	ENST00000609438.1	-	2	1412	c.894C>T	c.(892-894)gcC>gcT	p.A298A	GPRIN3_ENST00000333209.4_Silent_p.A298A	NM_198281.2	NP_938022.2	Q6ZVF9	GRIN3_HUMAN	GPRIN family member 3	298										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)		TCATCGTACTGGCTTCTTTGA	0.567																																					p.A298A		Atlas-SNP	.											.	GPRIN3	90	.	0			c.C894T						PASS	.						117	116	116					4																	90170368		2203	4300	6503	SO:0001819	synonymous_variant	285513	exon2			CGTACTGGCTTCT	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.894C>T	4.37:g.90170368G>A		141	0	0		115	5	0.0434783	NM_198281	Q8IVE4	Silent	SNP	ENST00000609438.1	37	CCDS34030.1																																																																																			.	.	none		0.567	GPRIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363540.2	NM_198281		A	90170368	G	A	90170368	2	1	12	1	0	0	0	0	0	0	0	1	6740	1335	47	2		2	GPRIN3	4	90170368	Silent	SNP	G	TCGA-FF-8043-01A-11D-2210-10	1633163	90170368	100983908	26	1600											
C6	729	hgsc.bcm.edu	37	chr5	41199992	41199992	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcccccaaactgactgggaCgcaagacagatctaacttta	13	8	8	12	1	1	3	0	1	1	2	2	4	2	4	2	1	2	1	2	1	4	3	rs200213547		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr5:41199992C>T	ENST00000263413.3	-	4	587	c.323G>A	c.(322-324)cGt>cAt	p.R108H	C6_ENST00000337836.5_Missense_Mutation_p.R108H	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	108	TSP type-1 2. {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)				CTGACTGGGACGCAAGACAGA	0.468													C|||	1	0.000199681	0.0008	0.0	5008	,	,		16584	0.0		0.0	False		,,,				2504	0.0				p.R108H		Atlas-SNP	.											.	C6	197	.	0			c.G323A						PASS	.	C	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	77	72	74		323,323	3.3	1	5		74	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	C6	NM_000065.2,NM_001115131.1	29,29	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging,probably-damaging	108/935,108/935	41199992	2,13004	2203	4300	6503	SO:0001583	missense	729	exon4			CTGGGACGCAAGA	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.323G>A	5.37:g.41199992C>T	ENSP00000263413:p.Arg108His	95	0	0		144	64	0.444444	NM_001115131		Missense_Mutation	SNP	ENST00000263413.3	37	CCDS3936.1	.	.	.	.	.	.	.	.	.	.	C	16.87	3.240753	0.58995	2.27E-4	1.16E-4	ENSG00000039537	ENST00000337836;ENST00000263413;ENST00000417809	T;T;T	0.54279	0.58;0.58;0.58	6.02	3.34	0.38264	.	0.153716	0.56097	D	0.000026	T	0.54615	0.1869	M	0.83312	2.635	0.46849	D	0.99922	B	0.30281	0.275	B	0.31245	0.126	T	0.54964	-0.8214	10	0.66056	D	0.02	-6.8361	9.4574	0.38762	0.0:0.7151:0.0:0.2849	.	108	P13671	CO6_HUMAN	H	108	ENSP00000338861:R108H;ENSP00000263413:R108H;ENSP00000396565:R108H	ENSP00000263413:R108H	R	-	2	0	C6	41235749	0.445000	0.25657	0.999000	0.59377	0.907000	0.53573	0.370000	0.20433	0.460000	0.27045	0.650000	0.86243	CGT	.	.	weak		0.468	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1			T	41199992	C	T	41199992	3	4	12	1	0	0	0	0	1	0	0	0	2317	536	19	1	2541	1	C6	5	41199992	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10		41199992	139715268	27	1601											
NRG2	9542	hgsc.bcm.edu	37	chr5	139260442	139260442	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tctgtctgggcccacctaccGctgttgacgtaaagccggcc	6	9	11	15	3	2	1	0	1	2	0	2	1	2	1	5	2	2	3	5	2	3	3			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr5:139260442G>A	ENST00000361474.1	-	3	1214	c.990C>T	c.(988-990)agC>agT	p.S330S	NRG2_ENST00000541337.1_Splice_Site_p.S330S|NRG2_ENST00000394770.1_Splice_Site_p.S330S|NRG2_ENST00000340391.3_Splice_Site_p.S127S|NRG2_ENST00000518130.1_5'UTR|NRG2_ENST00000358522.3_Splice_Site_p.S330S|NRG2_ENST00000289422.7_Splice_Site_p.S330S|NRG2_ENST00000289409.4_Splice_Site_p.S330S|NRG2_ENST00000545385.1_Splice_Site_p.S330S	NM_004883.2	NP_004874.1	O14511	NRG2_HUMAN	neuregulin 2	330	Ig-like C2-type.|Ser/Thr-rich.				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)	p.S330S(1)		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)			CCCACCTACCGCTGTTGACGT	0.642																																					p.S330S		Atlas-SNP	.											NRG2,NS,carcinoma,0,1	NRG2	69	1	1	Substitution - coding silent(1)	stomach(1)	c.C990T						PASS	.						75	78	77					5																	139260442		2203	4300	6503	SO:0001630	splice_region_variant	9542	exon3			CCTACCGCTGTTG		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.991+1C>T	5.37:g.139260442G>A		67	0	0		86	26	0.302326	NM_013982		Silent	SNP	ENST00000361474.1	37	CCDS4217.1																																																																																			.	.	none		0.642	NRG2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251340.1	NM_013982	Silent	A	139260442	G	A	139260442	5	1	12	1	0	0	0	0	0	0	1	0	10657	1101	38	1	1685	1	NRG2	5	139260442	Splice_Site	SNP	G	TCGA-FF-8043-01A-11D-2210-10	98060450	139260442	41654818	28	1602											
ARAP3	64411	hgsc.bcm.edu	37	chr5	141033945	141033945	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcatacactggctcctcgtAcacaggctcctccagctcct	7	10	6	18	1	1	0	1	0	0	0	6	0	5	0	4	2	3	4	4	2	2	2			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr5:141033945A>G	ENST00000239440.4	-	33	4272	c.4207T>C	c.(4207-4209)Tac>Cac	p.Y1403H	ARAP3_ENST00000508305.1_Missense_Mutation_p.Y1234H|ARAP3_ENST00000512390.1_5'UTR|FCHSD1_ENST00000519800.1_5'Flank|FCHSD1_ENST00000435817.2_5'Flank|ARAP3_ENST00000513878.1_Missense_Mutation_p.Y1052H	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	1403					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						GGCTCCTCGTACACAGGCTCC	0.552																																					p.Y1403H		Atlas-SNP	.											.	ARAP3	139	.	0			c.T4207C						PASS	.						96	97	97					5																	141033945		2203	4300	6503	SO:0001583	missense	64411	exon33			CCTCGTACACAGG	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.4207T>C	5.37:g.141033945A>G	ENSP00000239440:p.Tyr1403His	69	0	0		78	36	0.461538	NM_022481	B4DIT1|D3DQE3	Missense_Mutation	SNP	ENST00000239440.4	37	CCDS4266.1	.	.	.	.	.	.	.	.	.	.	A	13.65	2.300151	0.40694	.	.	ENSG00000120318	ENST00000508305;ENST00000239440;ENST00000513878	T;T;T	0.14516	2.5;3.2;3.05	3.92	3.92	0.45320	.	0.405610	0.23234	N	0.050433	T	0.18882	0.0453	N	0.24115	0.695	0.34030	D	0.65374	D;D;D	0.69078	0.995;0.997;0.995	D;D;D	0.75484	0.969;0.986;0.969	T	0.13629	-1.0502	10	0.20046	T	0.44	.	9.4487	0.38712	1.0:0.0:0.0:0.0	.	1052;1234;1403	B4DIT1;G5E9Y3;Q8WWN8	.;.;ARAP3_HUMAN	H	1234;1403;1052	ENSP00000421826:Y1234H;ENSP00000239440:Y1403H;ENSP00000421468:Y1052H	ENSP00000239440:Y1403H	Y	-	1	0	ARAP3	141014129	0.997000	0.39634	0.998000	0.56505	0.502000	0.33828	2.505000	0.45424	1.983000	0.57843	0.482000	0.46254	TAC	.	.	none		0.552	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481		G	141033945	A	G	141033945	3	3	12	1	0	0	0	0	1	0	0	0	840	391	14	3	431	3	ARAP3	5	141033945	Missense_Mutation	SNP	A	TCGA-FF-8043-01A-11D-2210-10	1773503	141033945	39881315	29	1603											
IRF4	3662	hgsc.bcm.edu	37	chr6	393224	393224	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	agctgcggcaacgggaagctCcgccagtggctgatcgacca	9	5	14	13	4	0	1	0	1	0	0	2	3	1	2	3	3	4	4	3	3	2	0			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr6:393224C>T	ENST00000380956.4	+	2	198	c.72C>T	c.(70-72)ctC>ctT	p.L24L	IRF4_ENST00000495137.1_Intron	NM_001195286.1|NM_002460.3	NP_001182215.1|NP_002451.2	Q15306	IRF4_HUMAN	interferon regulatory factor 4	24					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)		ACGGGAAGCTCCGCCAGTGGC	0.701			T	IGH@	MM																																p.L24L		Atlas-SNP	.		Dom	yes		6	6p25-p23	3662	interferon regulatory factor 4		L	.	IRF4	65	.	0			c.C72T						PASS	.						31	32	32					6																	393224		2192	4288	6480	SO:0001819	synonymous_variant	3662	exon2			GAAGCTCCGCCAG	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.72C>T	6.37:g.393224C>T		84	0	0		124	46	0.370968	NM_001195286	Q5VUI7|Q99660	Silent	SNP	ENST00000380956.4	37	CCDS4469.1																																																																																			.	.	none		0.701	IRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043638.1			T	393224	C	T	393224	2	4	12	1	0	0	0	0	0	0	0	1	7841	842	30	2		2	IRF4	6	393224	Silent	SNP	C	TCGA-FF-8043-01A-11D-2210-10		393224	170721843	30	1604											
SSR1	6745	hgsc.bcm.edu	37	chr6	7313275	7313275	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacactcccccagcctcacCtctggggccgcctcggaaca	7	5	9	20	2	2	0	1	0	1	0	4	1	3	1	6	3	2	1	6	3	1	0			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr6:7313275C>T	ENST00000244763.4	-	1	165	c.79G>A	c.(79-81)Ggc>Agc	p.G27S	SSR1_ENST00000474597.1_Splice_Site_p.G27S|SSR1_ENST00000489567.1_Splice_Site_p.G27S|SSR1_ENST00000397511.2_Splice_Site_p.G27S|SSR1_ENST00000488834.1_Intron|SSR1_ENST00000479365.1_Splice_Site_p.G27S|SSR1_ENST00000462112.1_Splice_Site_p.G27S|SSR1_ENST00000534851.1_Splice_Site_p.G27S	NM_003144.3	NP_003135.2	P43307	SSRA_HUMAN	signal sequence receptor, alpha	27					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)					CCAGCCTCACCTCTGGGGCCG	0.647																																					p.G27S		Atlas-SNP	.											.	SSR1	21	.	0			c.G79A						PASS	.						43	41	42					6																	7313275		2193	4282	6475	SO:0001630	splice_region_variant	6745	exon1			CCTCACCTCTGGG		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.79+1G>A	6.37:g.7313275C>T		69	0	0		80	42	0.525	NM_003144	A8K685|Q53GX2|Q53H19|Q5TAM3|Q6IB43|Q8NBH9|Q96IA2|Q9TNQ8|Q9UN49	Missense_Mutation	SNP	ENST00000244763.4	37	CCDS4499.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.040668	0.75732	.	.	ENSG00000124783	ENST00000474597;ENST00000244763;ENST00000397511;ENST00000534851;ENST00000489567;ENST00000479365;ENST00000462112	T;T;T;T;T;T;T	0.41400	1.0;1.0;1.0;1.0;1.0;1.0;1.0	4.32	4.32	0.51571	.	0.133138	0.49305	D	0.000157	T	0.32556	0.0833	N	0.12569	0.235	0.49915	D	0.99983	P;D;P	0.62365	0.928;0.991;0.833	P;D;P	0.68621	0.756;0.959;0.677	T	0.21895	-1.0232	9	.	.	.	.	15.7303	0.77794	0.0:1.0:0.0:0.0	.	27;27;27	C9J5W0;C9JBX5;P43307	.;.;SSRA_HUMAN	S	27	ENSP00000418617:G27S;ENSP00000244763:G27S;ENSP00000380647:G27S;ENSP00000443020:G27S;ENSP00000420730:G27S;ENSP00000417911:G27S;ENSP00000417290:G27S	.	G	-	1	0	SSR1	7258274	1.000000	0.71417	0.997000	0.53966	0.595000	0.36748	2.096000	0.41738	2.089000	0.63090	0.462000	0.41574	GGC	.	.	none		0.647	SSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039775.2		Missense_Mutation	T	7313275	C	T	7313275	5	4	12	1	0	0	0	0	0	0	1	0	15205	695	24	2	813	2	SSR1	6	7313275	Splice_Site	SNP	C	TCGA-FF-8043-01A-11D-2210-10	6920051	7313275	163801792	31	1605											
VARS2	57176	hgsc.bcm.edu	37	chr6	30893890	30893890	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttttctcctcgtccagctttCttccctccagctggaattgt	4	17	6	14	1	2	0	0	0	2	0	7	1	5	1	4	1	2	2	4	1	1	5			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr6:30893890C>T	ENST00000321897.5	+	29	3727	c.3095C>T	c.(3094-3096)tCt>tTt	p.S1032F	VARS2_ENST00000476162.1_3'UTR|VARS2_ENST00000541562.1_Missense_Mutation_p.S1062F|VARS2_ENST00000416670.2_Missense_Mutation_p.S1032F|VARS2_ENST00000542001.1_Missense_Mutation_p.S892F			Q5ST30	SYVM_HUMAN	valyl-tRNA synthetase 2, mitochondrial	1032					gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(15)|ovary(3)|prostate(3)|skin(4)|urinary_tract(1)	46						GTCCAGCTTTCTTCCCTCCAG	0.617																																					p.S1062F		Atlas-SNP	.											.	VARS2	60	.	0			c.C3185T						PASS	.						63	65	64					6																	30893890		1510	2709	4219	SO:0001583	missense	57176	exon30			AGCTTTCTTCCCT	AB067472	CCDS34387.1, CCDS54980.1	6p21.33	2012-10-26	2012-10-26	2007-02-23	ENSG00000137411	ENSG00000137411	6.1.1.9	"Aminoacyl tRNA synthetases / Class I"	21642	protein-coding gene	gene with protein product	"valine tRNA ligase 2, mitochondrial"	612802	"valyl-tRNA synthetase 2-like", "valyl-tRNA synthetase like", "valyl-tRNA synthetase 2, mitochondrial (putative)"	VARS2L, VARSL		1898367, 11572484, 18400783	Standard	NM_001167734		Approved	DKFZP434L1435, KIAA1885, G7a	uc011dmz.2	Q5ST30	OTTHUMG00000031263	ENST00000321897.5:c.3095C>T	6.37:g.30893890C>T	ENSP00000316092:p.Ser1032Phe	263	0	0		307	128	0.416938	NM_001167734	A2ABL7|B4DET4|B4E3P5|F5GXJ0|F5H323|Q2M2A0|Q59FI1|Q5SQ96|Q5SS98|Q6DKJ5|Q6ZV24|Q96GN2|Q96H77|Q96Q02|Q9H6R2|Q9UFH7	Missense_Mutation	SNP	ENST00000321897.5	37	CCDS34387.1	.	.	.	.	.	.	.	.	.	.	C	17.73	3.461584	0.63513	.	.	ENSG00000137411	ENST00000321897;ENST00000416670;ENST00000542001;ENST00000541562	T;T;T;T	0.32753	1.44;1.44;1.44;1.44	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.48241	0.1489	M	0.70595	2.14	0.37604	D	0.920671	D;D;D;D	0.76494	0.983;0.998;0.999;0.998	P;D;D;D	0.85130	0.837;0.994;0.997;0.994	T	0.50448	-0.8827	10	0.72032	D	0.01	-21.6103	15.561	0.76244	0.0:1.0:0.0:0.0	.	470;1030;1062;1032	Q5ST30-2;B7ZL25;F5GXJ0;Q5ST30	.;.;.;SYVM_HUMAN	F	1032;1032;892;1062	ENSP00000316092:S1032F;ENSP00000394802:S1032F;ENSP00000438200:S892F;ENSP00000441000:S1062F	ENSP00000316092:S1032F	S	+	2	0	VARS2	31001869	1.000000	0.71417	1.000000	0.80357	0.398000	0.30690	3.549000	0.53681	2.755000	0.94549	0.655000	0.94253	TCT	.	.	none		0.617	VARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076566.2	NM_020442		T	30893890	C	T	30893890	3	4	12	1	0	0	0	0	1	0	0	0	17139	913	32	2	3303	2	VARS2	6	30893890	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10	23580615	30893890	140221177	32	1606											
ZBTB22	9278	hgsc.bcm.edu	37	chr6	33283277	33283277	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	actgccagtccctccagggaCcccaccaacgctacccggca	9	4	8	20	2	0	0	0	0	0	0	2	1	2	1	7	2	3	2	7	2	2	1			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr6:33283277C>G	ENST00000431845.2	-	2	1568	c.1417G>C	c.(1417-1419)Gtc>Ctc	p.V473L	TAPBP_ENST00000456592.2_5'Flank|TAPBP_ENST00000426633.2_5'Flank|TAPBP_ENST00000489157.1_5'Flank|ZBTB22_ENST00000418724.1_Missense_Mutation_p.V473L|TAPBP_ENST00000475304.1_5'Flank|TAPBP_ENST00000434618.2_5'Flank	NM_005453.4	NP_005444.4	O15209	ZBT22_HUMAN	zinc finger and BTB domain containing 22	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)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(3)	21						CCTCCAGGGACCCCACCAACG	0.642																																					p.V473L		Atlas-SNP	.											.	ZBTB22	48	.	0			c.G1417C						PASS	.						131	145	141					6																	33283277		2203	4300	6503	SO:0001583	missense	9278	exon2			CAGGGACCCCACC	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.1417G>C	6.37:g.33283277C>G	ENSP00000407545:p.Val473Leu	69	0	0		78	35	0.448718	NM_001145338	B0V007|Q5HYV4|Q5STL0|Q5STR7|Q8WV82	Missense_Mutation	SNP	ENST00000431845.2	37	CCDS4775.1	.	.	.	.	.	.	.	.	.	.	C	0.004	-2.332545	0.00227	.	.	ENSG00000236104	ENST00000418724;ENST00000431845	T;T	0.04970	3.52;3.52	4.11	-1.01	0.10169	.	1.112010	0.07113	N	0.842560	T	0.00998	0.0033	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48246	-0.9052	10	0.27082	T	0.32	.	8.6065	0.33775	0.0:0.3929:0.0:0.6071	.	473	O15209	ZBT22_HUMAN	L	473	ENSP00000404403:V473L;ENSP00000407545:V473L	ENSP00000404403:V473L	V	-	1	0	ZBTB22	33391255	0.000000	0.05858	0.011000	0.14972	0.025000	0.11179	-0.980000	0.03770	-0.115000	0.11915	0.448000	0.29417	GTC	.	.	none		0.642	ZBTB22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076183.2			G	33283277	C	G	33283277	3	3	12	1	0	0	0	0	1	0	0	0	17545	507	18	4	491	4	ZBTB22	6	33283277	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10	2389387	33283277	137831790	33	1607											
DST	667	hgsc.bcm.edu	37	chr6	56374517	56374517	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgtttaagagtttcatacAacggctgtagcttttccatg	9	16	8	8	1	2	1	1	0	1	1	3	1	3	1	1	1	3	5	1	1	4	7			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr6:56374517A>G	ENST00000361203.3	-	69	17982	c.17975T>C	c.(17974-17976)tTg>tCg	p.L5992S	DST_ENST00000244364.6_Missense_Mutation_p.L3689S|DST_ENST00000312431.6_3'UTR|DST_ENST00000421834.2_Missense_Mutation_p.L4015S|DST_ENST00000370754.5_Missense_Mutation_p.L6281S|DST_ENST00000340834.4_5'UTR|DST_ENST00000370769.4_Missense_Mutation_p.L6103S|DST_ENST00000370788.2_Missense_Mutation_p.L3906S|DST_ENST00000446842.2_Missense_Mutation_p.L5777S			Q03001	DYST_HUMAN	dystonin	5993					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)			AGTTTCATACAACGGCTGTAG	0.428																																					p.L3689S		Atlas-SNP	.											.	DST	1427	.	0			c.T11066C						PASS	.						118	109	112					6																	56374517		1872	4115	5987	SO:0001583	missense	667	exon55			TCATACAACGGCT	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.17975T>C	6.37:g.56374517A>G	ENSP00000354508:p.Leu5992Ser	219	0	0		239	94	0.393305	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	37		.	.	.	.	.	.	.	.	.	.	A	11.64	1.698379	0.30142	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203;ENST00000537444	T;T;T;T;T;T;T	0.47528	0.84;0.84;0.84;0.84;0.84;0.84;0.84	5.76	5.76	0.90799	.	0.185737	0.24242	N	0.040256	T	0.25827	0.0629	N	0.04880	-0.145	0.28311	N	0.922675	D;B;B;B;B	0.53745	0.962;0.201;0.104;0.016;0.007	P;B;B;B;B	0.58077	0.832;0.2;0.059;0.034;0.01	T	0.14200	-1.0481	9	0.08179	T	0.78	.	16.0663	0.80878	1.0:0.0:0.0:0.0	.	4015;6103;6281;6101;3689	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	S	3689;6281;6103;4015;5777;3906;5992;105	ENSP00000244364:L3689S;ENSP00000359790:L6281S;ENSP00000359805:L6103S;ENSP00000400883:L4015S;ENSP00000393645:L5777S;ENSP00000359824:L3906S;ENSP00000354508:L5992S	ENSP00000244364:L3689S	L	-	2	0	DST	56482476	0.160000	0.22878	0.882000	0.34594	0.831000	0.47069	3.609000	0.54117	2.196000	0.70406	0.533000	0.62120	TTG	.	.	none		0.428	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		G	56374517	A	G	56374517	3	3	12	1	0	0	0	0	1	0	0	0	4785	131	5	3	4569	3	DST	6	56374517	Missense_Mutation	SNP	A	TCGA-FF-8043-01A-11D-2210-10	23091240	56374517	114740550	34	1608											
EYS	346007	hgsc.bcm.edu	37	chr6	65612316	65612316	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgaaattgttgaccatatCttcacagtcaccataatcct	12	13	4	12	0	3	2	2	2	1	0	4	2	4	2	4	0	0	1	4	0	3	5			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr6:65612316C>A	ENST00000370621.3	-	17	3245	c.2719G>T	c.(2719-2721)Gat>Tat	p.D907Y	EYS_ENST00000370616.2_Missense_Mutation_p.D907Y|EYS_ENST00000503581.1_Missense_Mutation_p.D907Y			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	907	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						TTGACCATATCTTCACAGTCA	0.333																																					p.D907Y		Atlas-SNP	.											EYS_ENST00000370621,NS,carcinoma,+2,1	EYS	527	1	0			c.G2719T						PASS	.						151	125	133					6																	65612316		692	1591	2283	SO:0001583	missense	346007	exon17			CCATATCTTCACA		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.2719G>T	6.37:g.65612316C>A	ENSP00000359655:p.Asp907Tyr	119	0	0		98	43	0.438776	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	37		.	.	.	.	.	.	.	.	.	.	C	5.293	0.239526	0.10023	.	.	ENSG00000188107	ENST00000503581;ENST00000370621;ENST00000370616	D;D;D	0.95656	-3.77;-3.77;-3.77	4.36	1.38	0.22167	.	.	.	.	.	D	0.93099	0.7803	M	0.94142	3.5	0.80722	D	1	B	0.18741	0.03	B	0.23419	0.046	D	0.88285	0.2939	9	0.87932	D	0	.	4.268	0.10773	0.1613:0.5952:0.156:0.0876	.	907	Q5T1H1-1	.	Y	907	ENSP00000424243:D907Y;ENSP00000359655:D907Y;ENSP00000359650:D907Y	ENSP00000359650:D907Y	D	-	1	0	EYS	65669037	1.000000	0.71417	0.010000	0.14722	0.116000	0.19942	2.134000	0.42102	0.034000	0.15491	-0.218000	0.12543	GAT	.	.	none		0.333	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		A	65612316	C	A	65612316	3	1	12	1	0	0	0	0	1	0	0	0	5334	913	32	4	6668	4	EYS	6	65612316	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10	9237799	65612316	105502751	35	1609											
DGKB	1607	hgsc.bcm.edu	37	chr7	14217692	14217692	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	agcactgagccagccgccggCcagcacttttcaggcctgtg	7	7	12	15	2	1	1	1	1	0	0	1	1	1	1	5	2	4	2	5	2	0	2			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr7:14217692C>A	ENST00000403951.2	-	24	2629	c.2210G>T	c.(2209-2211)gGc>gTc	p.G737V	DGKB_ENST00000399322.3_Missense_Mutation_p.G737V|DGKB_ENST00000402815.1_Missense_Mutation_p.G736V|DGKB_ENST00000407950.1_Missense_Mutation_p.G729V|DGKB_ENST00000444700.2_Missense_Mutation_p.G718V|DGKB_ENST00000406247.3_Missense_Mutation_p.G737V|DGKB_ENST00000258767.5_Missense_Mutation_p.G737V			Q9Y6T7	DGKB_HUMAN	diacylglycerol kinase, beta 90kDa	737					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)	p.G737V(1)		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						CAGCCGCCGGCCAGCACTTTT	0.502																																					p.G737V		Atlas-SNP	.											DGKB,NS,carcinoma,0,1	DGKB	166	1	1	Substitution - Missense(1)	lung(1)	c.G2210T						PASS	.						62	71	68					7																	14217692		2108	4277	6385	SO:0001583	missense	1607	exon23			CGCCGGCCAGCAC	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.2210G>T	7.37:g.14217692C>A	ENSP00000385780:p.Gly737Val	62	0	0		48	17	0.354167	NM_145695	A4D116|A4D117|A8MXU2|O75241|Q2M377|Q75MF9|Q75MU7|Q86UI5|Q86UM9|Q9UQ29	Missense_Mutation	SNP	ENST00000403951.2	37	CCDS47547.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.637047	0.87760	.	.	ENSG00000136267	ENST00000403951;ENST00000399322;ENST00000258767;ENST00000402815;ENST00000407950;ENST00000444700;ENST00000406247	T;T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92;0.92	5.8	5.8	0.92144	Diacylglycerol kinase, accessory domain (2);	0.000000	0.85682	D	0.000000	T	0.75133	0.3808	M	0.93241	3.395	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;0.999;1.0	D;D;D;D	0.79108	0.991;0.99;0.987;0.992	T	0.81297	-0.0996	10	0.87932	D	0	.	19.6455	0.95775	0.0:1.0:0.0:0.0	.	736;718;737;737	B7ZL83;C9JTC0;Q9Y6T7-2;Q9Y6T7	.;.;.;DGKB_HUMAN	V	737;737;737;736;729;718;737	ENSP00000385780:G737V;ENSP00000382260:G737V;ENSP00000258767:G737V;ENSP00000384909:G736V;ENSP00000385031:G729V;ENSP00000388451:G718V;ENSP00000386066:G737V	ENSP00000258767:G737V	G	-	2	0	DGKB	14184217	1.000000	0.71417	0.994000	0.49952	0.937000	0.57800	5.812000	0.69194	2.739000	0.93911	0.561000	0.74099	GGC	.	.	none		0.502	DGKB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000326356.2	NM_004080		A	14217692	C	A	14217692	3	1	12	1	0	0	0	0	1	0	0	0	4468	739	26	4	231	4	DGKB	7	14217692	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10		14217692	144920971	36	1610											
DGKB	1607	hgsc.bcm.edu	37	chr7	14378196	14378196	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cggtggtccttttgtcagacCcttttttctctattcgtcga	4	18	8	11	3	2	1	1	0	1	1	6	2	3	1	2	2	0	0	2	2	1	7			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr7:14378196C>A	ENST00000403951.2	-	23	2488	c.2069G>T	c.(2068-2070)gGg>gTg	p.G690V	DGKB_ENST00000399322.3_Missense_Mutation_p.G690V|DGKB_ENST00000403963.1_5'UTR|DGKB_ENST00000402815.1_Missense_Mutation_p.G689V|DGKB_ENST00000407950.1_Missense_Mutation_p.G682V|DGKB_ENST00000444700.2_Missense_Mutation_p.G671V|DGKB_ENST00000406247.3_Missense_Mutation_p.G690V|DGKB_ENST00000258767.5_Missense_Mutation_p.G690V			Q9Y6T7	DGKB_HUMAN	diacylglycerol kinase, beta 90kDa	690					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)	p.G690V(1)		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						TTTGTCAGACCCTTTTTTCTC	0.398																																					p.G690V		Atlas-SNP	.											DGKB,NS,carcinoma,0,1	DGKB	166	1	1	Substitution - Missense(1)	lung(1)	c.G2069T						PASS	.						192	177	182					7																	14378196		1852	4091	5943	SO:0001583	missense	1607	exon22			TCAGACCCTTTTT	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.2069G>T	7.37:g.14378196C>A	ENSP00000385780:p.Gly690Val	156	0	0		180	64	0.355556	NM_145695	A4D116|A4D117|A8MXU2|O75241|Q2M377|Q75MF9|Q75MU7|Q86UI5|Q86UM9|Q9UQ29	Missense_Mutation	SNP	ENST00000403951.2	37	CCDS47547.1	.	.	.	.	.	.	.	.	.	.	C	10.57	1.387379	0.25031	.	.	ENSG00000136267	ENST00000403951;ENST00000399322;ENST00000258767;ENST00000402815;ENST00000407950;ENST00000444700;ENST00000406247	T;T;T;T;T;T;T	0.80480	-1.3;-1.3;-1.3;-1.3;-1.3;-1.29;-1.38	5.5	4.62	0.57501	Diacylglycerol kinase, accessory domain (2);	0.442134	0.23977	N	0.042716	T	0.65439	0.2691	N	0.17082	0.46	0.48975	D	0.999736	B;B;B;B	0.06786	0.001;0.0;0.001;0.0	B;B;B;B	0.08055	0.003;0.002;0.002;0.0	T	0.58875	-0.7559	10	0.29301	T	0.29	.	10.1713	0.42911	0.0:0.8495:0.0:0.1505	.	689;671;690;690	B7ZL83;C9JTC0;Q9Y6T7-2;Q9Y6T7	.;.;.;DGKB_HUMAN	V	690;690;690;689;682;671;690	ENSP00000385780:G690V;ENSP00000382260:G690V;ENSP00000258767:G690V;ENSP00000384909:G689V;ENSP00000385031:G682V;ENSP00000388451:G671V;ENSP00000386066:G690V	ENSP00000258767:G690V	G	-	2	0	DGKB	14344721	0.684000	0.27642	0.995000	0.50966	0.989000	0.77384	1.375000	0.34295	1.313000	0.45069	0.650000	0.86243	GGG	.	.	none		0.398	DGKB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000326356.2	NM_004080		A	14378196	C	A	14378196	3	1	12	1	0	0	0	0	1	0	0	0	4468	623	22	4	376	4	DGKB	7	14378196	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10	160504	14378196	144760467	37	1611											
MAGI2	9863	hgsc.bcm.edu	37	chr7	77885700	77885700	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgtcttccattgaccatcActggaggtggcctctccatt	6	14	9	12	0	3	1	1	1	2	0	5	2	4	2	4	3	0	0	4	3	0	3			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr7:77885700A>G	ENST00000354212.4	-	10	1860	c.1607T>C	c.(1606-1608)gTg>gCg	p.V536A	MAGI2_ENST00000535697.1_Missense_Mutation_p.V373A|MAGI2_ENST00000522391.1_Missense_Mutation_p.V536A|MAGI2_ENST00000536571.1_Missense_Mutation_p.V368A|MAGI2_ENST00000419488.1_Missense_Mutation_p.V536A	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	536					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)				ATTGACCATCACTGGAGGTGG	0.493																																					p.V536A		Atlas-SNP	.											.	MAGI2	246	.	0			c.T1607C						PASS	.						101	83	89					7																	77885700		2203	4300	6503	SO:0001583	missense	9863	exon10			ACCATCACTGGAG	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.1607T>C	7.37:g.77885700A>G	ENSP00000346151:p.Val536Ala	267	0	0		278	124	0.446043	NM_012301	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Missense_Mutation	SNP	ENST00000354212.4	37	CCDS5594.1	.	.	.	.	.	.	.	.	.	.	A	15.16	2.751936	0.49362	.	.	ENSG00000187391	ENST00000419488;ENST00000354212;ENST00000536298;ENST00000522391;ENST00000536571;ENST00000535697	T;T;T;T;T	0.10573	2.96;2.96;2.86;3.81;3.82	5.93	4.75	0.60458	.	0.229068	0.20981	U	0.082212	T	0.12178	0.0296	L	0.36672	1.1	0.39497	D	0.96814	P;B;B;B;B;B	0.39601	0.68;0.312;0.038;0.038;0.059;0.08	B;B;B;B;B;B	0.41412	0.356;0.356;0.02;0.02;0.064;0.025	T	0.04268	-1.0964	10	0.56958	D	0.05	.	12.5202	0.56054	0.8606:0.1394:0.0:0.0	.	373;368;536;536;536;536	F5GWH1;F5GWK7;B7Z4H4;E7EWI0;Q86UL8-2;Q86UL8	.;.;.;.;.;MAGI2_HUMAN	A	536;536;536;536;368;373	ENSP00000405766:V536A;ENSP00000346151:V536A;ENSP00000428389:V536A;ENSP00000441584:V368A;ENSP00000441603:V373A	ENSP00000346151:V536A	V	-	2	0	MAGI2	77723636	0.995000	0.38212	0.998000	0.56505	0.992000	0.81027	5.314000	0.65804	1.031000	0.39867	0.454000	0.30748	GTG	.	.	none		0.493	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		G	77885700	A	G	77885700	3	3	12	1	0	0	0	0	1	0	0	0	9200	159	6	3	2812	3	MAGI2	7	77885700	Missense_Mutation	SNP	A	TCGA-FF-8043-01A-11D-2210-10	63507504	77885700	81252963	38	1612											
BCAP29	55973	hgsc.bcm.edu	37	chr7	107221236	107221236	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaatgacactccaatgggctGcagtggcaacctttctttat	11	12	8	10	0	1	1	0	1	1	0	2	1	2	1	2	2	2	3	2	2	4	3			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr7:107221236G>A	ENST00000005259.4	+	2	358	c.19G>A	c.(19-21)Gca>Aca	p.A7T	BCAP29_ENST00000445771.2_Missense_Mutation_p.A7T|BCAP29_ENST00000379119.2_Missense_Mutation_p.A7T|BCAP29_ENST00000494086.1_Intron|BCAP29_ENST00000379117.2_Missense_Mutation_p.A7T|BCAP29_ENST00000465919.1_Intron|RP4-593H12.1_ENST00000610269.1_RNA	NM_018844.3	NP_061332.2	Q9UHQ4	BAP29_HUMAN	B-cell receptor-associated protein 29	7					apoptotic process (GO:0006915)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|osteoblast differentiation (GO:0001649)|protein localization to endoplasmic reticulum exit site (GO:0070973)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				cervix(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	14						CCAATGGGCTGCAGTGGCAAC	0.413																																					p.A7T		Atlas-SNP	.											.	BCAP29	46	.	0			c.G19A						PASS	.						104	93	97					7																	107221236		2203	4300	6503	SO:0001583	missense	55973	exon2			TGGGCTGCAGTGG		CCDS34730.1, CCDS34731.1	7q22.3	2012-09-20			ENSG00000075790	ENSG00000075790			24131	protein-coding gene	gene with protein product						12477932	Standard	NM_018844		Approved	BAP29, DKFZp686M2086	uc011kma.1	Q9UHQ4	OTTHUMG00000154770	ENST00000005259.4:c.19G>A	7.37:g.107221236G>A	ENSP00000005259:p.Ala7Thr	113	0	0		123	42	0.341463	NM_018844	G5E9L4|O95003	Missense_Mutation	SNP	ENST00000005259.4	37	CCDS34731.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.600874	0.87055	.	.	ENSG00000075790	ENST00000005259;ENST00000445771;ENST00000479917;ENST00000421217;ENST00000457837;ENST00000379117;ENST00000473124;ENST00000379119	.	.	.	4.63	4.63	0.57726	.	0.054140	0.64402	D	0.000001	T	0.78886	0.4354	M	0.81942	2.565	0.80722	D	1	D;D;D	0.76494	0.993;0.999;0.999	D;D;D	0.68943	0.91;0.961;0.961	T	0.80379	-0.1407	9	0.48119	T	0.1	-14.1844	16.2143	0.82195	0.0:0.0:1.0:0.0	.	7;7;7	G5E9L4;C9JTE9;Q9UHQ4	.;.;BAP29_HUMAN	T	7	.	ENSP00000005259:A7T	A	+	1	0	BCAP29	107008472	1.000000	0.71417	0.932000	0.37286	0.854000	0.48673	7.886000	0.87288	2.548000	0.85928	0.655000	0.94253	GCA	.	.	none		0.413	BCAP29-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337011.2	NM_018844		A	107221236	G	A	107221236	3	1	12	1	0	0	0	0	1	0	0	0	1346	1319	46	2	21	2	BCAP29	7	107221236	Missense_Mutation	SNP	G	TCGA-FF-8043-01A-11D-2210-10	29335536	107221236	51917427	39	1613											
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121650463	121650463	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagtgctacaaaccaaatcAggaaaaaggaaccccagatt	19	5	7	10	0	1	1	1	0	0	1	1	3	1	3	3	2	4	1	3	2	6	2	rs199595173	byFrequency	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr7:121650463A>C	ENST00000393386.2	+	12	1774	c.1363A>C	c.(1363-1365)Agg>Cgg	p.R455R	PTPRZ1_ENST00000449182.1_Silent_p.R455R	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	455					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						AAACCAAATCAGGAAAAAGGA	0.423													A|||	6	0.00119808	0.0	0.0	5008	,	,		18694	0.0		0.0	False		,,,				2504	0.0061				p.R455R		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.A1363C						PASS	.						153	143	146					7																	121650463		2203	4300	6503	SO:0001819	synonymous_variant	5803	exon12			CAAATCAGGAAAA	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.1363A>C	7.37:g.121650463A>C		78	0	0		80	38	0.475	NM_001206838	A4D0W5|C9JFM0|O76043|Q9UDR6	Silent	SNP	ENST00000393386.2	37	CCDS34740.1																																																																																			A|0.999;C|0.001	0.001	weak		0.423	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		C	121650463	A	C	121650463	2	2	12	1	0	0	0	0	0	0	0	1	12829	179	7	5		5	PTPRZ1	7	121650463	Silent	SNP	A	TCGA-FF-8043-01A-11D-2210-10	14429227	121650463	37488200	40	1614											
PLXNA4	91584	hgsc.bcm.edu	37	chr7	132174144	132174144	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcatgcggtccctgtcctcCgtgaagacgggaattccacg	7	9	12	13	4	1	2	1	1	0	1	5	3	5	3	4	2	1	0	4	2	2	1			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr7:132174144C>T	ENST00000359827.3	-	3	2240	c.1278G>A	c.(1276-1278)acG>acA	p.T426T	PLXNA4_ENST00000423507.2_Silent_p.T426T|PLXNA4_ENST00000321063.4_Silent_p.T426T|PLXNA4_ENST00000378539.5_Silent_p.T426T			Q9HCM2	PLXA4_HUMAN	plexin A4	426	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						CCCTGTCCTCCGTGAAGACGG	0.512																																					p.T426T		Atlas-SNP	.											.	PLXNA4	873	.	0			c.G1278A						PASS	.						115	94	101					7																	132174144		2203	4300	6503	SO:0001819	synonymous_variant	91584	exon3			GTCCTCCGTGAAG	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.1278G>A	7.37:g.132174144C>T		109	0	0		132	57	0.431818	NM_001105543	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	37	CCDS43646.1																																																																																			.	.	none		0.512	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		T	132174144	C	T	132174144	2	4	12	1	0	0	0	0	0	0	0	1	12131	639	23	1		1	PLXNA4	7	132174144	Silent	SNP	C	TCGA-FF-8043-01A-11D-2210-10	10523681	132174144	26964519	41	1615											
CSMD1	64478	hgsc.bcm.edu	37	chr8	3141793	3141793	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccactccttcagcaggatGtcactgtccaccggcccgtc	6	9	8	18	2	2	0	2	0	0	0	6	1	5	1	5	2	1	1	5	2	0	1			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr8:3141793G>A	ENST00000520002.1	-	27	4584	c.4029C>T	c.(4027-4029)gaC>gaT	p.D1343D	CSMD1_ENST00000400186.3_Silent_p.D1343D|CSMD1_ENST00000542608.1_Silent_p.D1342D|CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000602557.1_Silent_p.D1343D|CSMD1_ENST00000602723.1_Silent_p.D1343D|CSMD1_ENST00000537824.1_Silent_p.D1342D|CSMD1_ENST00000539096.1_Silent_p.D1342D			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1343	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)		TCAGCAGGATGTCACTGTCCA	0.562											OREG0018505	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D1342D		Atlas-SNP	.											.	CSMD1	1469	.	0			c.C4026T						PASS	.						99	107	104					8																	3141793		2131	4245	6376	SO:0001819	synonymous_variant	64478	exon26			CAGGATGTCACTG			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.4029C>T	8.37:g.3141793G>A		51	0	0	608	64	22	0.34375	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	g	3.847	-0.032700	0.07543	.	.	ENSG00000183117	ENST00000335551	.	.	.	5.12	4.25	0.50352	.	.	.	.	.	T	0.59074	0.2167	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56025	-0.8047	4	.	.	.	.	8.5228	0.33287	0.2323:0.0:0.7677:0.0	.	.	.	.	Y	823	.	.	H	-	1	0	CSMD1	3129200	0.999000	0.42202	0.879000	0.34478	0.348000	0.29142	0.833000	0.27504	1.165000	0.42670	-0.213000	0.12676	CAT	.	.	none		0.562	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	3141793	G	A	3141793	2	1	12	1	0	0	0	0	0	0	0	1	3946	1368	48	2		2	CSMD1	8	3141793	Silent	SNP	G	TCGA-FF-8043-01A-11D-2210-10		3141793	143222229	42	1616											
RP1L1	94137	hgsc.bcm.edu	37	chr8	10470003	10470003	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagagccggtgctggctgaCgagtccgaagaagccccctc	8	6	14	13	3	0	3	0	2	0	2	2	6	1	3	4	2	3	2	4	2	2	0	rs200772091		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr8:10470003C>T	ENST00000382483.3	-	4	1828	c.1605G>A	c.(1603-1605)tcG>tcA	p.S535S		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	535					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)		TGCTGGCTGACGAGTCCGAAG	0.692																																					p.S535S		Atlas-SNP	.											.	RP1L1	453	.	0			c.G1605A						PASS	.	C		0,4096		0,0,2048	39	47	45		1605	-5.8	0	8		45	2,8346		0,2,4172	no	coding-synonymous	RP1L1	NM_178857.5		0,2,6220	TT,TC,CC		0.024,0.0,0.0161		535/2401	10470003	2,12442	2048	4174	6222	SO:0001819	synonymous_variant	94137	exon4			GGCTGACGAGTCC	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.1605G>A	8.37:g.10470003C>T		42	0	0		38	13	0.342105	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																			C|0.999;T|0.001	0.001	weak		0.692	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			T	10470003	C	T	10470003	2	4	12	1	0	0	0	0	0	0	0	1	13548	523	19	1		1	RP1L1	8	10470003	Silent	SNP	C	TCGA-FF-8043-01A-11D-2210-10	7328210	10470003	135894019	43	1617											
TEX15	56154	hgsc.bcm.edu	37	chr8	30701914	30701914	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	actttaatttcccccttcttCtctcttttgttaagcggatt	6	20	4	11	1	3	0	0	0	3	0	5	1	4	1	2	1	1	1	2	1	2	9			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr8:30701914C>T	ENST00000256246.2	-	1	4694	c.4620G>A	c.(4618-4620)gaG>gaA	p.E1540E		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	1540					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)		CCCCCTTCTTCTCTCTTTTGT	0.368																																					p.E1540E		Atlas-SNP	.											.	TEX15	350	.	0			c.G4620A						PASS	.						185	188	187					8																	30701914		2203	4300	6503	SO:0001819	synonymous_variant	56154	exon1			CTTCTTCTCTCTT	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.4620G>A	8.37:g.30701914C>T		172	0	0		196	75	0.382653	NM_031271		Silent	SNP	ENST00000256246.2	37	CCDS6080.1																																																																																			.	.	none		0.368	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			T	30701914	C	T	30701914	2	4	12	1	0	0	0	0	0	0	0	1	15794	912	32	2		2	TEX15	8	30701914	Silent	SNP	C	TCGA-FF-8043-01A-11D-2210-10	20231911	30701914	115662108	44	1618											
RP1	6101	hgsc.bcm.edu	37	chr8	55534023	55534023	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggaatggcgacccgaagaCgaggcgtgcggttcttctga	9	7	15	10	5	2	2	0	1	2	1	2	6	2	3	1	4	1	1	1	4	2	2			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr8:55534023C>T	ENST00000220676.1	+	2	645	c.497C>T	c.(496-498)aCg>aTg	p.T166M		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	166	Doublecortin 2. {ECO:0000255|PROSITE- ProRule:PRU00072}.				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)	p.T166M(1)		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)			GACCCGAAGACGAGGCGTGCG	0.642																																					p.T166M	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											RP1,NS,carcinoma,0,1	RP1	429	1	1	Substitution - Missense(1)	lung(1)	c.C497T						PASS	.						83	85	84					8																	55534023		2203	4300	6503	SO:0001583	missense	6101	exon2			CGAAGACGAGGCG	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.497C>T	8.37:g.55534023C>T	ENSP00000220676:p.Thr166Met	163	0	0		212	91	0.429245	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	C	11.68	1.709586	0.30322	.	.	ENSG00000104237	ENST00000220676	D	0.86562	-2.14	5.14	1.26	0.21427	Doublecortin domain (4);	0.635417	0.14570	N	0.311486	T	0.72930	0.3522	L	0.38175	1.15	0.09310	N	1	P	0.47604	0.898	B	0.30029	0.11	T	0.65496	-0.6154	10	0.62326	D	0.03	6.4508	4.3984	0.11374	0.1478:0.4103:0.0:0.4419	.	166	P56715	RP1_HUMAN	M	166	ENSP00000220676:T166M	ENSP00000220676:T166M	T	+	2	0	RP1	55696576	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.109000	0.15417	-0.050000	0.13356	0.650000	0.86243	ACG	.	.	none		0.642	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		T	55534023	C	T	55534023	3	4	12	1	0	0	0	0	1	0	0	0	13547	536	19	1	499	1	RP1	8	55534023	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10	24832109	55534023	90829999	45	1619											
KCNQ3	3786	hgsc.bcm.edu	37	chr8	133186530	133186530	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaattaaggaaaaggtggCggcaatcagacggccttccc	12	6	12	11	2	1	1	1	0	0	1	2	2	2	2	3	5	0	1	3	5	5	2			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr8:133186530C>T	ENST00000388996.4	-	6	1420	c.1000G>A	c.(1000-1002)Gcc>Acc	p.A334T	KCNQ3_ENST00000519445.1_Missense_Mutation_p.A334T|KCNQ3_ENST00000521134.1_Missense_Mutation_p.A214T	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	334					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)	GAAAAGGTGGCGGCAATCAGA	0.512																																					p.A334T		Atlas-SNP	.											.	KCNQ3	164	.	0			c.G1000A						PASS	.						125	82	96					8																	133186530		2166	4186	6352	SO:0001583	missense	3786	exon6			AGGTGGCGGCAAT	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.1000G>A	8.37:g.133186530C>T	ENSP00000373648:p.Ala334Thr	94	0	0		150	45	0.3	NM_004519	A2VCT8|B4DJY4|E7EQ89	Missense_Mutation	SNP	ENST00000388996.4	37	CCDS34943.1	.	.	.	.	.	.	.	.	.	.	C	36	5.679407	0.96774	.	.	ENSG00000184156	ENST00000388996;ENST00000521134;ENST00000519445;ENST00000542679;ENST00000423790	D;D;D	0.98329	-4.87;-4.87;-4.87	4.96	4.96	0.65561	Ion transport (1);	0.055265	0.64402	D	0.000001	D	0.98232	0.9415	L	0.43757	1.38	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.69479	0.964;0.964	D	0.99859	1.1081	10	0.87932	D	0	-23.3549	17.5496	0.87872	0.0:1.0:0.0:0.0	.	334;334	E7ET42;O43525	.;KCNQ3_HUMAN	T	334;214;334;323;213	ENSP00000373648:A334T;ENSP00000429799:A214T;ENSP00000428790:A334T	ENSP00000373648:A334T	A	-	1	0	KCNQ3	133255712	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.814000	0.86154	2.446000	0.82766	0.563000	0.77884	GCC	.	.	none		0.512	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519		T	133186530	C	T	133186530	3	4	12	1	0	0	0	0	1	0	0	0	8093	768	27	1	1658	1	KCNQ3	8	133186530	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10	77652507	133186530	13177492	46	1620											
TESK1	7016	hgsc.bcm.edu	37	chr9	35608460	35608460	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatggatcctggagcagctGcctgagccagccccactcac	9	6	11	15	0	1	1	1	1	0	0	2	4	2	3	5	2	5	2	5	2	1	0			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr9:35608460G>A	ENST00000336395.5	+	9	1204	c.954G>A	c.(952-954)ctG>ctA	p.L318L	CD72_ENST00000490239.1_5'Flank|TESK1_ENST00000498522.1_3'UTR|MIR4667_ENST00000578933.1_RNA	NM_006285.2	NP_006276.2	Q15569	TESK1_HUMAN	testis-specific kinase 1	318					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)			TGGAGCAGCTGCCTGAGCCAG	0.587																																					p.L318L		Atlas-SNP	.											TESK1,NS,neuroblastoma,0,1	TESK1	46	1	0			c.G954A						PASS	.						57	54	55					9																	35608460		2203	4300	6503	SO:0001819	synonymous_variant	7016	exon9			GCAGCTGCCTGAG	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.954G>A	9.37:g.35608460G>A		60	0	0		68	30	0.441176	NM_006285	Q8IXZ8	Silent	SNP	ENST00000336395.5	37	CCDS6580.1																																																																																			.	.	none		0.587	TESK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052314.1	NM_006285		A	35608460	G	A	35608460	2	1	12	1	0	0	0	0	0	0	0	1	15782	1306	46	2		2	TESK1	9	35608460	Silent	SNP	G	TCGA-FF-8043-01A-11D-2210-10		35608460	105604971	47	1621											
SMC5	23137	hgsc.bcm.edu	37	chr9	72897468	72897468	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagaaatggaaaacgagcGtcacaatttggaggctcgaa	16	7	12	6	3	1	2	1	1	0	1	2	6	1	4	0	3	2	1	0	3	6	1	rs115131883		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr9:72897468G>A	ENST00000361138.5	+	7	1008	c.950G>A	c.(949-951)cGt>cAt	p.R317H		NM_015110.3	NP_055925.2	Q8IY18	SMC5_HUMAN	structural maintenance of chromosomes 5	317					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						GAAAACGAGCGTCACAATTTG	0.343													G|||	1	0.000199681	0.0	0.0	5008	,	,		16784	0.0		0.001	False		,,,				2504	0.0				p.R317H		Atlas-SNP	.											.	SMC5	96	.	0			c.G950A						PASS	.						80	79	79					9																	72897468		2203	4300	6503	SO:0001583	missense	23137	exon7			ACGAGCGTCACAA	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.950G>A	9.37:g.72897468G>A	ENSP00000354957:p.Arg317His	257	0	0		247	103	0.417004	NM_015110	A6NM81|O60335|Q05D92|Q5VZ60|Q96SB9	Missense_Mutation	SNP	ENST00000361138.5	37	CCDS6632.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	8.955	0.969095	0.18659	.	.	ENSG00000198887	ENST00000361138	T	0.18016	2.24	5.61	5.61	0.85477	RecF/RecN/SMC (1);	0.276654	0.37715	N	0.001971	T	0.12689	0.0308	N	0.19112	0.55	0.09310	N	1	D	0.64830	0.994	P	0.49192	0.602	T	0.23226	-1.0194	10	0.15952	T	0.53	-11.1893	7.1841	0.25789	0.1378:0.0:0.7171:0.1451	.	317	Q8IY18	SMC5_HUMAN	H	317	ENSP00000354957:R317H	ENSP00000354957:R317H	R	+	2	0	SMC5	72087288	0.357000	0.24938	0.463000	0.27130	0.326000	0.28443	2.392000	0.44433	2.804000	0.96469	0.650000	0.86243	CGT	G|1.000;A|0.000	0.000	strong		0.343	SMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052603.1	NM_015110		A	72897468	G	A	72897468	3	1	12	1	0	0	0	0	1	0	0	0	14801	1145	40	1	976	1	SMC5	9	72897468	Missense_Mutation	SNP	G	TCGA-FF-8043-01A-11D-2210-10	37289008	72897468	68315963	48	1622											
KCNT1	57582	hgsc.bcm.edu	37	chr9	138671231	138671231	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccagcctcagcatcaccaCggagctcacccacccttcca	9	5	5	22	1	3	0	3	0	0	0	4	1	4	1	7	1	3	2	7	1	0	1			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr9:138671231C>T	ENST00000263604.3	+	24	2699	c.2699C>T	c.(2698-2700)aCg>aTg	p.T900M	KCNT1_ENST00000491806.2_Missense_Mutation_p.T886M|KCNT1_ENST00000487664.1_Missense_Mutation_p.T874M|KCNT1_ENST00000488444.2_Missense_Mutation_p.T900M|KCNT1_ENST00000298480.5_Missense_Mutation_p.T919M|KCNT1_ENST00000371757.2_Missense_Mutation_p.T919M|KCNT1_ENST00000486577.2_Missense_Mutation_p.T878M|KCNT1_ENST00000490355.2_Missense_Mutation_p.T898M			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	900					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)		AGCATCACCACGGAGCTCACC	0.622																																					p.T919M		Atlas-SNP	.											.	KCNT1	139	.	0			c.C2756T						PASS	.						149	146	147					9																	138671231		2203	4300	6503	SO:0001583	missense	57582	exon24			TCACCACGGAGCT	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.2699C>T	9.37:g.138671231C>T	ENSP00000263604:p.Thr900Met	92	0	0		101	46	0.455446	NM_020822	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Missense_Mutation	SNP	ENST00000263604.3	37		.	.	.	.	.	.	.	.	.	.	C	19.41	3.821619	0.71028	.	.	ENSG00000107147	ENST00000487664;ENST00000298480;ENST00000371757;ENST00000486577;ENST00000491806;ENST00000488444;ENST00000490355;ENST00000263604	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	3.77	3.77	0.43336	.	0.000000	0.85682	U	0.000000	D	0.86994	0.6067	M	0.81497	2.545	0.58432	D	0.999994	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.80764	0.978;0.978;0.994;0.978	D	0.88055	0.2790	10	0.54805	T	0.06	-30.3053	12.6769	0.56899	0.1657:0.8343:0.0:0.0	.	886;919;874;900	C9JYL2;B9EGP2;G5E9V0;Q5JUK3	.;.;.;KCNT1_HUMAN	M	874;919;919;878;886;900;898;900	ENSP00000417851:T874M;ENSP00000298480:T919M;ENSP00000360822:T919M;ENSP00000263604:T900M	ENSP00000263604:T900M	T	+	2	0	KCNT1	137811052	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.830000	0.69324	1.778000	0.52293	0.455000	0.32223	ACG	.	.	none		0.622	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822		T	138671231	C	T	138671231	3	4	12	1	0	0	0	0	1	0	0	0	8100	536	19	1	2850	1	KCNT1	9	138671231	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10	65773763	138671231	2542200	49	1623											
GAD2	2572	hgsc.bcm.edu	37	chr10	26508109	26508109	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tccattatcctaatgagcttCtccaagaatataattgggaa	14	13	6	8	0	1	2	0	1	1	1	4	3	3	3	3	1	1	1	3	1	7	6			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr10:26508109C>T	ENST00000376261.3	+	4	927	c.424C>T	c.(424-426)Ctc>Ttc	p.L142F	GAD2_ENST00000259271.3_Missense_Mutation_p.L142F|GAD2_ENST00000376248.1_Missense_Mutation_p.L28F	NM_001134366.1	NP_001127838.1	Q05329	DCE2_HUMAN	glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa)	142					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						TAATGAGCTTCTCCAAGAATA	0.343																																					p.L142F		Atlas-SNP	.											.	GAD2	116	.	0			c.C424T						PASS	.						100	105	103					10																	26508109		2203	4300	6503	SO:0001583	missense	2572	exon4			GAGCTTCTCCAAG	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.424C>T	10.37:g.26508109C>T	ENSP00000365437:p.Leu142Phe	81	0	0		87	4	0.045977	NM_000818	Q9UD87	Missense_Mutation	SNP	ENST00000376261.3	37	CCDS7149.1	.	.	.	.	.	.	.	.	.	.	C	17.20	3.328723	0.60743	.	.	ENSG00000136750	ENST00000376261;ENST00000259271;ENST00000428517;ENST00000376248	T;T;T;T	0.59906	0.23;0.23;0.23;1.13	5.61	5.61	0.85477	Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	T	0.70762	0.3261	L	0.53671	1.685	0.80722	D	1	D;B	0.89917	1.0;0.288	D;B	0.91635	0.999;0.12	T	0.62751	-0.6788	10	0.09843	T	0.71	-15.2362	19.6436	0.95767	0.0:1.0:0.0:0.0	.	142;142	Q4G154;Q05329	.;DCE2_HUMAN	F	142;142;142;28	ENSP00000365437:L142F;ENSP00000259271:L142F;ENSP00000390434:L142F;ENSP00000365424:L28F	ENSP00000259271:L142F	L	+	1	0	GAD2	26548115	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	5.666000	0.68059	2.621000	0.88768	0.650000	0.86243	CTC	.	.	none		0.343	GAD2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047255.1	NM_000818		T	26508109	C	T	26508109	3	4	12	1	0	0	0	0	1	0	0	0	6188	913	32	2	438	2	GAD2	10	26508109	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10		26508109	109026638	50	1624											
H2AFY2	55506	hgsc.bcm.edu	37	chr10	71835546	71835546	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtaccggatcagcgtgggCgcccctgtctacatggcggc	7	7	14	13	4	2	0	1	0	1	0	2	1	2	1	3	4	3	1	3	4	3	2	rs373125930		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr10:71835546C>T	ENST00000373255.4	+	2	396	c.132C>T	c.(130-132)ggC>ggT	p.G44G		NM_018649.2	NP_061119.1	Q9P0M6	H2AW_HUMAN	H2A histone family, member Y2	44	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						TCAGCGTGGGCGCCCCTGTCT	0.602																																					p.G44G		Atlas-SNP	.											.	H2AFY2	30	.	0			c.C132T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	120	95	103		132	-11.8	0	10		103	0,8600		0,0,4300	no	coding-synonymous	H2AFY2	NM_018649.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		44/373	71835546	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	55506	exon2			CGTGGGCGCCCCT	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.132C>T	10.37:g.71835546C>T		136	0	0		162	73	0.450617	NM_018649	Q5SQT2	Silent	SNP	ENST00000373255.4	37	CCDS7296.1																																																																																			.	.	none		0.602	H2AFY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048480.2	NM_018649		T	71835546	C	T	71835546	2	4	12	1	0	0	0	0	0	0	0	1	6939	755	27	1		1	H2AFY2	10	71835546	Silent	SNP	C	TCGA-FF-8043-01A-11D-2210-10	45327437	71835546	63699201	51	1625											
CBARA1	10367	hgsc.bcm.edu	37	chr10	74183072	74183072	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caccccactgtaggcaagtaGcatgccaccaaactgcctct	11	7	7	16	0	1	0	0	0	1	0	1	0	1	0	5	1	4	4	5	1	4	2			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr10:74183072G>A	ENST00000361114.5	-	9	1087	c.991C>T	c.(991-993)Cta>Tta	p.L331L	MICU1_ENST00000398763.4_Silent_p.L133L|MICU1_ENST00000401998.3_Silent_p.L331L|MICU1_ENST00000398761.4_Silent_p.L333L|MICU1_ENST00000418483.2_Silent_p.L133L	NM_001195518.1|NM_006077.3	NP_001182447.1|NP_006068.2	Q9BPX6	MICU1_HUMAN	mitochondrial calcium uptake 1	331					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)										TAGGCAAGTAGCATGCCACCA	0.512																																					p.L331L		Atlas-SNP	.											.	.	.	.	0			c.C991T						PASS	.						104	96	99					10																	74183072		2000	4197	6197	SO:0001819	synonymous_variant	10367	exon9			CAAGTAGCATGCC	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.991C>T	10.37:g.74183072G>A		136	0	0		149	54	0.362416	NM_001195518	A8MV96|B3KN20|B4DJH9|B4DPI1|B5MBY3|D3YTJ3|O75785|Q9H9N6|Q9UFX0	Silent	SNP	ENST00000361114.5	37	CCDS55715.1																																																																																			.	.	none		0.512	MICU1-002	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048586.1	NM_006077		A	74183072	G	A	74183072	2	1	12	1	0	0	0	0	0	0	0	1	2698	962	34	2		2	CBARA1	10	74183072	Silent	SNP	G	TCGA-FF-8043-01A-11D-2210-10	2347526	74183072	61351675	52	1626											
DMBT1	1755	hgsc.bcm.edu	37	chr10	124358568	124358568	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccccacaatggctggctcTcccacaactgtggccatagt	8	8	9	16	0	1	0	0	0	1	0	2	0	1	0	4	3	1	2	4	3	3	1	rs201802690		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr10:124358568T>A	ENST00000338354.3	+	26	3341	c.3235T>A	c.(3235-3237)Tcc>Acc	p.S1079T	DMBT1_ENST00000330163.4_Missense_Mutation_p.S580T|DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000368956.2_Missense_Mutation_p.S580T|DMBT1_ENST00000368909.3_Missense_Mutation_p.S1079T|DMBT1_ENST00000344338.3_Missense_Mutation_p.S1069T|DMBT1_ENST00000368955.3_Missense_Mutation_p.S1069T			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	1079	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)				TGGCTGGCTCTCCCACAACTG	0.572																																					p.S1079T	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											DMBT1_ENST00000368915,NS,carcinoma,0,3	DMBT1	677	3	0			c.T3235A						scavenged	.						101	96	98					10																	124358568		1929	4141	6070	SO:0001583	missense	1755	exon26			TGGCTCTCCCACA		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.3235T>A	10.37:g.124358568T>A	ENSP00000342210:p.Ser1079Thr	184	2	0.0108696		224	14	0.0625	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	37		.	.	.	.	.	.	.	.	.	.	T	8.702	0.909917	0.17833	.	.	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956	T;T;T;T;T;T	0.43688	0.94;0.94;0.94;0.94;0.94;0.94	3.57	-6.98	0.01611	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	0.838313	0.10030	N	0.724884	T	0.30541	0.0768	L	0.27944	0.81	0.09310	N	1	B;D;B;B;B	0.57257	0.167;0.979;0.107;0.0;0.0	B;P;B;B;B	0.56563	0.087;0.801;0.023;0.001;0.001	T	0.20605	-1.0270	10	0.13853	T	0.58	.	4.1715	0.10332	0.6029:0.0791:0.1583:0.1597	.	586;1079;580;1069;1079	Q9UGM3-8;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;DMBT1_HUMAN	T	1079;1079;1079;1079;1079;1079;580;1069;580;580;1079;1069;580	ENSP00000342210:S1079T;ENSP00000343175:S1069T;ENSP00000327747:S580T;ENSP00000357905:S1079T;ENSP00000357951:S1069T;ENSP00000357952:S580T	ENSP00000331522:S580T	S	+	1	0	DMBT1	124348558	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-5.877000	0.00093	-0.959000	0.03618	-0.386000	0.06593	TCC	.	.	weak		0.572	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		A	124358568	T	A	124358568	3	1	12	1	0	0	0	0	1	0	0	0	4579	1551	54	5	3337	5	DMBT1	10	124358568	Missense_Mutation	SNP	T	TCGA-FF-8043-01A-11D-2210-10	50175496	124358568	11176179	53	1627											
DOCK1	1793	hgsc.bcm.edu	37	chr10	129209114	129209114	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctctgtacagtttttacaggGtgaacgaggtccagcgattt	9	13	11	8	2	1	1	0	1	1	0	2	3	2	1	1	2	4	2	1	2	3	5			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr10:129209114G>T	ENST00000280333.6	+	43	4400	c.4291G>T	c.(4291-4293)Gtg>Ttg	p.V1431L		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	1431	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)		TTTTTACAGGGTGAACGAGGT	0.438																																					p.V1431L		Atlas-SNP	.											.	DOCK1	188	.	0			c.G4291T						PASS	.						73	69	70					10																	129209114		1875	4103	5978	SO:0001583	missense	1793	exon43			TACAGGGTGAACG	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.4291G>T	10.37:g.129209114G>T	ENSP00000280333:p.Val1431Leu	70	0	0		60	23	0.383333	NM_001380	A9Z1Z5	Missense_Mutation	SNP	ENST00000280333.6	37		.	.	.	.	.	.	.	.	.	.	G	22.4	4.288809	0.80914	.	.	ENSG00000150760	ENST00000280333	T	0.17370	2.28	4.9	4.9	0.64082	.	0.062614	0.64402	D	0.000006	T	0.40839	0.1133	M	0.69523	2.12	0.54753	D	0.999989	P;D;P	0.63046	0.898;0.992;0.772	P;D;B	0.64237	0.542;0.923;0.326	T	0.19844	-1.0293	10	0.51188	T	0.08	.	18.3037	0.90172	0.0:0.0:1.0:0.0	.	1431;1497;1431	B2RUU3;A8MU08;Q14185	.;.;DOCK1_HUMAN	L	1431	ENSP00000280333:V1431L	ENSP00000280333:V1431L	V	+	1	0	DOCK1	129099104	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.097000	0.64542	2.546000	0.85860	0.655000	0.94253	GTG	.	.	none		0.438	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380		T	129209114	G	T	129209114	3	4	12	1	0	0	0	0	1	0	0	0	4686	1261	44	4	4461	4	DOCK1	10	129209114	Missense_Mutation	SNP	G	TCGA-FF-8043-01A-11D-2210-10	4850546	129209114	6325633	54	1628											
EBF3	253738	hgsc.bcm.edu	37	chr10	131761680	131761680	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggtcctttcaatctccaccGgctgcccctgcctatcgtag	5	11	8	17	3	2	0	1	0	1	0	5	0	3	0	6	2	2	2	6	2	3	3			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr10:131761680G>A	ENST00000355311.5	-	2	314	c.242C>T	c.(241-243)cCg>cTg	p.P81L	EBF3_ENST00000368648.3_Missense_Mutation_p.P81L			Q9H4W6	COE3_HUMAN	early B-cell factor 3	81					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)		AATCTCCACCGGCTGCCCCTG	0.557																																					p.P81L		Atlas-SNP	.											EBF3_ENST00000355311,NS,carcinoma,+1,2	EBF3	193	2	0			c.C242T						scavenged	.						70	78	75					10																	131761680		2203	4300	6503	SO:0001583	missense	253738	exon2			TCCACCGGCTGCC		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.242C>T	10.37:g.131761680G>A	ENSP00000347463:p.Pro81Leu	127	1	0.00787402		142	65	0.457746	NM_001005463	A0AUY1|Q5T6H9|Q9H4W5	Missense_Mutation	SNP	ENST00000355311.5	37		.	.	.	.	.	.	.	.	.	.	G	19.06	3.754033	0.69648	.	.	ENSG00000108001	ENST00000355311;ENST00000368648	T;T	0.52754	0.65;0.66	3.45	3.45	0.39498	.	0.000000	0.85682	U	0.000000	T	0.67078	0.2855	M	0.75447	2.3	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.971	T	0.71111	-0.4687	10	0.51188	T	0.08	-6.4879	14.5175	0.67827	0.0:0.0:1.0:0.0	.	81;81	Q9H4W6;Q9H4W6-2	COE3_HUMAN;.	L	81	ENSP00000347463:P81L;ENSP00000357637:P81L	ENSP00000347463:P81L	P	-	2	0	EBF3	131651670	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	8.831000	0.92068	1.453000	0.47775	0.205000	0.17691	CCG	.	.	none		0.557	EBF3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051015.2	NM_001005463		A	131761680	G	A	131761680	3	1	12	1	0	0	0	0	1	0	0	0	4884	1116	39	1	1473	1	EBF3	10	131761680	Missense_Mutation	SNP	G	TCGA-FF-8043-01A-11D-2210-10	2552566	131761680	3773067	55	1629											
NLRP6	171389	hgsc.bcm.edu	37	chr11	279844	279844	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcccttccagggctcgggctCggctccgggacgctgctctc	2	9	13	17	4	1	0	0	0	1	0	7	1	4	1	3	4	1	5	3	4	0	1			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr11:279844C>T	ENST00000312165.5	+	3	321	c.321C>T	c.(319-321)ctC>ctT	p.L107L	NLRP6_ENST00000534750.1_Silent_p.L107L	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	107					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)		GGCTCGGGCTCGGCTCCGGGA	0.726																																					p.L107L		Atlas-SNP	.											.	NLRP6	4	.	0			c.C321T						PASS	.						13	16	15					11																	279844		2190	4294	6484	SO:0001819	synonymous_variant	171389	exon3			CGGGCTCGGCTCC	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.321C>T	11.37:g.279844C>T		38	0	0		42	7	0.166667	NM_138329	A8K9F3|E9PJZ8	Silent	SNP	ENST00000312165.5	37	CCDS7693.1																																																																																			.	.	none		0.726	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329		T	279844	C	T	279844	2	4	12	1	0	0	0	0	0	0	0	1	10490	871	31	1		1	NLRP6	11	279844	Silent	SNP	C	TCGA-FF-8043-01A-11D-2210-10		279844	134726672	56	1630											
IFITM3	10410	hgsc.bcm.edu	37	chr11	320723	320723	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgtggggcgcccccagcaCagccacctcgtgctcctcct	4	8	11	18	2	0	0	0	0	0	0	3	0	2	0	6	2	3	3	6	2	0	1	rs199582787	byFrequency	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr11:320723C>T	ENST00000399808.4	-	1	327	c.91G>A	c.(91-93)Gtg>Atg	p.V31M	RP11-326C3.11_ENST00000508004.2_RNA|RP11-326C3.11_ENST00000602429.1_RNA|RP11-326C3.10_ENST00000534271.1_RNA|IFITM3_ENST00000526811.1_Missense_Mutation_p.V10M|RP11-326C3.14_ENST00000602809.1_lincRNA|RP11-326C3.11_ENST00000602756.1_RNA|IFITM3_ENST00000602735.1_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	1	0			c.G91A						scavenged	.						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	11.37:g.320723C>T	ENSP00000382707:p.Val31Met	53	1	0.0188679		86	4	0.0465116	NM_021034	Q53Y76|Q96HK8|Q96J15	Missense_Mutation	SNP	ENST00000399808.4	37	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	.	.	weak		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	12	1	0	0	0	0	1	0	0	0	7537	478	17	2	318	2	IFITM3	11	320723	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10	40879	320723	134685793	57	1631											
BRSK2	9024	hgsc.bcm.edu	37	chr11	1467077	1467077	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catggaggtgctcagcgtgaCggacggcggctccccggtgc	5	6	17	13	5	1	1	1	1	0	0	2	3	2	3	2	6	3	2	2	6	0	0	rs368418167		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr11:1467077C>T	ENST00000528841.1	+	12	1550	c.1166C>T	c.(1165-1167)aCg>aTg	p.T389M	BRSK2_ENST00000308219.9_Missense_Mutation_p.T389M|BRSK2_ENST00000526678.1_Missense_Mutation_p.T389M|BRSK2_ENST00000528710.1_Missense_Mutation_p.T329M|BRSK2_ENST00000382179.1_Missense_Mutation_p.T435M|BRSK2_ENST00000308230.5_Missense_Mutation_p.T389M|BRSK2_ENST00000531197.1_Missense_Mutation_p.T389M|BRSK2_ENST00000544817.1_Missense_Mutation_p.T84M			Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2	389					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)		CTCAGCGTGACGGACGGCGGC	0.701																																					p.T435M		Atlas-SNP	.											.	BRSK2	97	.	0			c.C1304T						PASS	.	C	MET/THR	0,4342		0,0,2171	35	45	42		1166	3.7	0.9	11		42	1,8531		0,1,4265	no	missense	BRSK2	NM_003957.2	81	0,1,6436	TT,TC,CC		0.0117,0.0,0.0078	probably-damaging	389/669	1467077	1,12873	2171	4266	6437	SO:0001583	missense	9024	exon12			GCGTGACGGACGG	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.1166C>T	11.37:g.1467077C>T	ENSP00000432000:p.Thr389Met	43	0	0		61	32	0.52459	NM_001256630	B3KVE9|E9PLM7|O60843|O95099|Q5J5B4|Q6ZMQ4|Q8TB60	Missense_Mutation	SNP	ENST00000528841.1	37	CCDS58107.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.732292	0.89482	0.0	1.17E-4	ENSG00000174672	ENST00000308219;ENST00000531197;ENST00000308230;ENST00000528841;ENST00000526678;ENST00000528710;ENST00000382179;ENST00000544817	T;T;T;T;T;T;T;T	0.73469	-0.75;1.82;-0.7;1.82;-0.7;1.82;-0.59;0.76	4.71	3.73	0.42828	Protein kinase-like domain (1);	0.000000	0.85682	U	0.000000	D	0.83792	0.5331	M	0.65975	2.015	0.51767	D	0.999935	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;0.994;1.0;0.998;0.992	D	0.85738	0.1335	10	0.66056	D	0.02	.	14.2379	0.65938	0.0:0.8498:0.1502:0.0	.	389;435;389;389;389	Q8IWQ3-4;Q8IWQ3-5;Q8IWQ3-3;Q8IWQ3;Q8IWQ3-2	.;.;.;BRSK2_HUMAN;.	M	389;389;389;389;389;329;435;84	ENSP00000310697:T389M;ENSP00000431152:T389M;ENSP00000310805:T389M;ENSP00000432000:T389M;ENSP00000433370:T389M;ENSP00000433235:T329M;ENSP00000371614:T435M;ENSP00000445168:T84M	ENSP00000310697:T389M	T	+	2	0	BRSK2	1423653	1.000000	0.71417	0.920000	0.36463	0.942000	0.58702	5.583000	0.67484	2.182000	0.69389	0.462000	0.41574	ACG	.	.	weak		0.701	BRSK2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393033.1	NM_003957		T	1467077	C	T	1467077	3	4	12	1	0	0	0	0	1	0	0	0	1526	536	19	1	1212	1	BRSK2	11	1467077	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10	1146354	1467077	133539439	58	1632											
RRAS2	22800	hgsc.bcm.edu	37	chr11	14300971	14300971	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	attcctgctcttgaaatttcCtgtaagataaaaaattctaa	15	15	4	7	0	2	2	0	1	2	1	4	2	4	2	2	0	1	2	2	0	6	7			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr11:14300971C>T	ENST00000256196.4	-	6	841		c.e6-1		RRAS2_ENST00000414023.2_Splice_Site|RRAS2_ENST00000532814.1_Splice_Site|RRAS2_ENST00000545643.1_Splice_Site|RRAS2_ENST00000534746.1_Splice_Site|RRAS2_ENST00000529237.1_Splice_Site|RRAS2_ENST00000526063.1_Splice_Site|RRAS2_ENST00000537760.1_Splice_Site			P62070	RRAS2_HUMAN	related RAS viral (r-ras) oncogene homolog 2						osteoblast differentiation (GO:0001649)|positive regulation of cell migration (GO:0030335)|Ras protein signal transduction (GO:0007265)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(3)|endometrium(4)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	12				Epithelial(150;0.203)		TTGAAATTTCCTGTAAGATAA	0.343																																					.		Atlas-SNP	.											.	RRAS2	29	.	0			c.528-1G>A						PASS	.						121	117	118					11																	14300971		2200	4294	6494	SO:0001630	splice_region_variant	22800	exon7			AATTTCCTGTAAG	M31468	CCDS7814.1, CCDS44544.1, CCDS53603.1	11p15.2	2014-05-09			ENSG00000133818	ENSG00000133818			17271	protein-coding gene	gene with protein product		600098				2108320, 8052619	Standard	NM_012250		Approved	TC21	uc001mlf.4	P62070	OTTHUMG00000165756	ENST00000256196.4:c.528-1G>A	11.37:g.14300971C>T		124	0	0		107	5	0.046729	NM_012250	B2R9Z3|B7Z5Z2|B7Z6C4|B7Z7H6|P17082	Splice_Site	SNP	ENST00000256196.4	37	CCDS7814.1	.	.	.	.	.	.	.	.	.	.	C	15.57	2.871523	0.51695	.	.	ENSG00000133818	ENST00000537760;ENST00000545643;ENST00000414023;ENST00000529237;ENST00000256196;ENST00000534746;ENST00000526063;ENST00000532814;ENST00000531807	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.3437	0.98782	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RRAS2	14257547	1.000000	0.71417	1.000000	0.80357	0.665000	0.39181	7.760000	0.85248	2.821000	0.97095	0.555000	0.69702	.	.	.	none		0.343	RRAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386035.1	NM_012250	Intron	T	14300971	C	T	14300971	5	4	12	1	0	0	0	0	0	0	1	0	13692	695	24	2	91	2	RRAS2	11	14300971	Splice_Site	SNP	C	TCGA-FF-8043-01A-11D-2210-10	12833894	14300971	120705545	59	1633											
WT1	7490	hgsc.bcm.edu	37	chr11	32456397	32456397	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgtgccagtgaactggccGgaaaagtggacagtgaaggc	11	6	16	8	1	0	2	0	2	0	0	0	4	0	4	2	4	2	1	2	4	4	0			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr11:32456397G>A	ENST00000332351.3	-	1	779	c.495C>T	c.(493-495)tcC>tcT	p.S165S	WT1-AS_ENST00000525436.1_RNA|WT1-AS_ENST00000478367.1_RNA|WT1_ENST00000448076.3_Silent_p.S165S|WT1-AS_ENST00000395900.1_RNA|WT1-AS_ENST00000494911.1_RNA|WT1-AS_ENST00000459866.1_RNA	NM_024424.3|NM_024426.4	NP_077742.2|NP_077744	P19544	WT1_HUMAN	Wilms tumor 1	97					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)			TGAACTGGCCGGAAAAGTGGA	0.682			"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.S165S		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.C495T						PASS	.						17	19	18					11																	32456397		2198	4292	6490	SO:0001819	synonymous_variant	7490	exon1	Familial Cancer Database	WAGR syndrome; ; ;incl.: Early Onset Nephrotic Syndrome-WT1 associated	CTGGCCGGAAAAG		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.495C>T	11.37:g.32456397G>A		90	0	0		109	41	0.376147	NM_024424	A8K6S1|B3KSA5|Q15881|Q16256|Q16575|Q4VXV4|Q4VXV5|Q4VXV6|Q8IYZ5	Silent	SNP	ENST00000332351.3	37	CCDS7878.2																																																																																			.	.	none		0.682	WT1-001	KNOWN	non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000095436.2	NM_000378		A	32456397	G	A	32456397	2	1	12	1	0	0	0	0	0	0	0	1	17423	1103	39	1		1	WT1	11	32456397	Silent	SNP	G	TCGA-FF-8043-01A-11D-2210-10	18155426	32456397	102550119	60	1634											
AMOTL1	154810	hgsc.bcm.edu	37	chr11	94583290	94583290	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cccttctagacaaagaattcTtgaaggaaaaggagaaatta	18	9	8	6	0	2	4	0	1	2	3	2	6	2	5	1	2	0	0	1	2	8	5			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr11:94583290T>G	ENST00000433060.2	+	7	1801	c.1660T>G	c.(1660-1662)Ttg>Gtg	p.L554V	AMOTL1_ENST00000317837.9_Intron|AMOTL1_ENST00000317829.8_Missense_Mutation_p.L504V	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	554					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)				CAAAGAATTCTTGAAGGAAAA	0.468																																					p.L554V		Atlas-SNP	.											.	AMOTL1	95	.	0			c.T1660G						PASS	.						27	29	28					11																	94583290		1959	4155	6114	SO:0001583	missense	154810	exon7			GAATTCTTGAAGG	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.1660T>G	11.37:g.94583290T>G	ENSP00000387739:p.Leu554Val	34	0	0		89	22	0.247191	NM_130847	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Missense_Mutation	SNP	ENST00000433060.2	37	CCDS44712.1	.	.	.	.	.	.	.	.	.	.	T	7.496	0.651759	0.14516	.	.	ENSG00000166025	ENST00000317829;ENST00000542840;ENST00000433060	T;T	0.21543	2.0;2.0	5.82	-0.383	0.12477	.	0.000000	0.64402	D	0.000019	T	0.20536	0.0494	L	0.43152	1.355	0.80722	D	1	B;B	0.32302	0.363;0.024	B;B	0.42030	0.373;0.044	T	0.04737	-1.0930	10	0.23302	T	0.38	-15.6535	10.8757	0.46909	0.0:0.3874:0.0:0.6126	.	504;554	Q8IY63-2;Q8IY63	.;AMOL1_HUMAN	V	504;560;554	ENSP00000320968:L504V;ENSP00000387739:L554V	ENSP00000320968:L504V	L	+	1	2	AMOTL1	94222938	0.999000	0.42202	0.989000	0.46669	0.903000	0.53119	0.533000	0.23082	-0.318000	0.08665	-0.250000	0.11733	TTG	.	.	none		0.468	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847		G	94583290	T	G	94583290	3	3	12	1	0	0	0	0	1	0	0	0	583	1606	56	5	1686	5	AMOTL1	11	94583290	Missense_Mutation	SNP	T	TCGA-FF-8043-01A-11D-2210-10	62126893	94583290	40423226	61	1635											
OR10G7	390265	hgsc.bcm.edu	37	chr11	123909644	123909644	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agattccaaagaggggggcgTccagccctggggcatgggga	9	5	18	9	1	0	2	0	0	0	2	2	3	2	3	3	7	1	1	3	7	1	1			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr11:123909644T>C	ENST00000330487.5	-	1	73	c.65A>G	c.(64-66)gAc>gGc	p.D22G		NM_001004463.1	NP_001004463.1	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G, member 7	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(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)		GAGGGGGGCGTCCAGCCCTGG	0.562																																					p.D22G		Atlas-SNP	.											OR10G7,NS,carcinoma,+1,1	OR10G7	103	1	0			c.A65G						PASS	.						97	93	94					11																	123909644		2200	4299	6499	SO:0001583	missense	390265	exon1			GGGGCGTCCAGCC	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.65A>G	11.37:g.123909644T>C	ENSP00000329689:p.Asp22Gly	236	0	0		341	68	0.199413	NM_001004463	Q6IFE8	Missense_Mutation	SNP	ENST00000330487.5	37	CCDS31705.1	.	.	.	.	.	.	.	.	.	.	T	10.29	1.309984	0.23821	.	.	ENSG00000182634	ENST00000330487	T	0.00438	7.42	3.38	2.25	0.28309	.	0.495982	0.18008	N	0.154666	T	0.00178	0.0005	N	0.02697	-0.525	0.27635	N	0.947893	B	0.06786	0.001	B	0.12837	0.008	T	0.30238	-0.9985	10	0.46703	T	0.11	.	6.8806	0.24170	0.0:0.1112:0.0:0.8888	.	22	Q8NGN6	O10G7_HUMAN	G	22	ENSP00000329689:D22G	ENSP00000329689:D22G	D	-	2	0	OR10G7	123414854	0.000000	0.05858	0.681000	0.30009	0.009000	0.06853	-0.093000	0.11111	0.503000	0.28060	0.455000	0.32223	GAC	.	.	none		0.562	OR10G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387271.1	NM_001004463		C	123909644	T	C	123909644	3	2	12	1	0	0	0	0	1	0	0	0	10911	1667	58	3	874	3	OR10G7	11	123909644	Missense_Mutation	SNP	T	TCGA-FF-8043-01A-11D-2210-10	29326354	123909644	11096872	62	1636											
RPUSD4	84881	hgsc.bcm.edu	37	chr11	126075445	126075445	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gttacagcaacttgcgcattCcggctgcgccgcactttcac	7	10	9	15	4	1	0	1	0	0	0	2	0	2	0	2	1	5	5	2	1	2	4	rs201545291		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr11:126075445C>T	ENST00000298317.4	-	5	767	c.714G>A	c.(712-714)cgG>cgA	p.R238R	RPUSD4_ENST00000533628.1_Intron|RPUSD4_ENST00000534393.1_5'Flank	NM_032795.2	NP_116184.2	Q96CM3	RUSD4_HUMAN	RNA pseudouridylate synthase domain containing 4	238					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)		CTTGCGCATTCCGGCTGCGCC	0.537																																					p.R238R		Atlas-SNP	.											.	RPUSD4	36	.	0			c.G714A						PASS	.						137	123	128					11																	126075445		2201	4299	6500	SO:0001819	synonymous_variant	84881	exon5			CGCATTCCGGCTG	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.714G>A	11.37:g.126075445C>T		111	0	0		226	63	0.278761	NM_032795	E9PML2|Q96K56	Silent	SNP	ENST00000298317.4	37	CCDS8469.1																																																																																			C|0.999;A|0.001	.	alt		0.537	RPUSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386336.1	NM_032795		T	126075445	C	T	126075445	2	4	12	1	0	0	0	0	0	0	0	1	13684	842	30	2		2	RPUSD4	11	126075445	Silent	SNP	C	TCGA-FF-8043-01A-11D-2210-10	2165801	126075445	8931071	63	1637											
ATF7IP	55729	hgsc.bcm.edu	37	chr12	14578150	14578150	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agactctatggagacagatgAaatcattcctattttggaaa	15	12	8	6	0	2	4	1	1	1	3	3	6	3	5	1	2	0	0	1	2	4	5			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr12:14578150A>G	ENST00000540793.1	+	1	1456	c.1301A>G	c.(1300-1302)gAa>gGa	p.E434G	ATF7IP_ENST00000536444.1_Missense_Mutation_p.E434G|ATF7IP_ENST00000544627.1_Missense_Mutation_p.E442G|ATF7IP_ENST00000261168.4_Missense_Mutation_p.E434G|ATF7IP_ENST00000543189.1_Missense_Mutation_p.E434G|ATF7IP_ENST00000541654.1_3'UTR			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	434	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						GAGACAGATGAAATCATTCCT	0.338																																					p.E434G		Atlas-SNP	.											.	ATF7IP	136	.	0			c.A1301G						PASS	.						64	66	65					12																	14578150		2203	4300	6503	SO:0001583	missense	55729	exon2			CAGATGAAATCAT	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.1301A>G	12.37:g.14578150A>G	ENSP00000444589:p.Glu434Gly	118	0	0		126	49	0.388889	NM_018179	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Missense_Mutation	SNP	ENST00000540793.1	37	CCDS8663.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.204229	0.79127	.	.	ENSG00000171681	ENST00000261168;ENST00000543189;ENST00000536444;ENST00000544627;ENST00000396279;ENST00000540793	T;T;T;T;T;T	0.36699	1.64;1.64;1.64;1.64;1.24;1.64	5.36	5.36	0.76844	.	0.000000	0.64402	D	0.000019	T	0.57242	0.2040	L	0.59436	1.845	0.47441	D	0.999429	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.992;0.998;0.998;0.999;0.999	D;D;D;D;D;D;D	0.85130	0.997;0.995;0.943;0.961;0.961;0.984;0.984	T	0.60581	-0.7235	10	0.87932	D	0	-21.0202	15.639	0.76981	1.0:0.0:0.0:0.0	.	442;434;442;434;434;434;45	B4E2A2;B4DRL6;F5GX74;G3V1U0;Q6VMQ6;Q6VMQ6-2;B3KQF8	.;.;.;.;MCAF1_HUMAN;.;.	G	434;434;434;442;434;434	ENSP00000261168:E434G;ENSP00000443179:E434G;ENSP00000445955:E434G;ENSP00000440440:E442G;ENSP00000379575:E434G;ENSP00000444589:E434G	ENSP00000261168:E434G	E	+	2	0	ATF7IP	14469417	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.355000	0.73041	2.140000	0.66376	0.482000	0.46254	GAA	.	.	none		0.338	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179		G	14578150	A	G	14578150	3	3	12	1	0	0	0	0	1	0	0	0	1087	246	9	3	1303	3	ATF7IP	12	14578150	Missense_Mutation	SNP	A	TCGA-FF-8043-01A-11D-2210-10		14578150	119273745	64	1638											
RAPGEF3	10411	hgsc.bcm.edu	37	chr12	48144895	48144895	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggagagcagggccacagcttCggccaactcctcctccatct	8	7	10	16	1	1	1	0	0	1	1	5	2	4	1	5	3	3	2	5	3	1	1			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr12:48144895C>T	ENST00000449771.2	-	6	695	c.607G>A	c.(607-609)Gaa>Aaa	p.E203K	RAPGEF3_ENST00000405493.2_Missense_Mutation_p.E161K|RAPGEF3_ENST00000549151.1_Missense_Mutation_p.E161K|RAPGEF3_ENST00000171000.4_Missense_Mutation_p.E161K|RAPGEF3_ENST00000395358.3_Missense_Mutation_p.E203K|RAPGEF3_ENST00000549347.1_5'Flank|RAPGEF3_ENST00000389212.3_Missense_Mutation_p.E203K|RAPGEF3_ENST00000548919.1_Missense_Mutation_p.E161K			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	203					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)		GCCACAGCTTCGGCCAACTCC	0.657																																					p.E203K		Atlas-SNP	.											.	RAPGEF3	98	.	0			c.G607A						PASS	.						22	23	23					12																	48144895		2201	4292	6493	SO:0001583	missense	10411	exon6			CAGCTTCGGCCAA	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.607G>A	12.37:g.48144895C>T	ENSP00000395708:p.Glu203Lys	91	0	0		184	42	0.228261	NM_001098531	A8K2G5|E7EQC8|O95634|Q8WVN0	Missense_Mutation	SNP	ENST00000449771.2	37	CCDS41775.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.952233	0.73787	.	.	ENSG00000079337	ENST00000405493;ENST00000449771;ENST00000549151;ENST00000171000;ENST00000389211;ENST00000389212;ENST00000397089;ENST00000548919;ENST00000395358;ENST00000466322	T;T;T;T;T;T;T;T	0.14144	2.53;2.53;2.53;2.53;2.53;2.53;2.53;2.53	4.97	4.97	0.65823	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.28632	0.0709	L	0.41710	1.295	0.80722	D	1	D;D;D	0.89917	0.977;1.0;1.0	P;D;D	0.87578	0.611;0.998;0.996	T	0.01074	-1.1460	10	0.27082	T	0.32	.	17.1887	0.86873	0.0:1.0:0.0:0.0	.	215;203;203	B7Z5J6;O95398-2;O95398	.;.;RPGF3_HUMAN	K	161;203;161;161;161;203;215;161;203;161	ENSP00000384521:E161K;ENSP00000395708:E203K;ENSP00000448619:E161K;ENSP00000171000:E161K;ENSP00000373864:E203K;ENSP00000448480:E161K;ENSP00000378764:E203K;ENSP00000446731:E161K	ENSP00000171000:E161K	E	-	1	0	RAPGEF3	46431162	1.000000	0.71417	0.914000	0.36105	0.338000	0.28826	7.125000	0.77193	2.478000	0.83669	0.561000	0.74099	GAA	.	.	none		0.657	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257848.1	NM_006105		T	48144895	C	T	48144895	3	4	12	1	0	0	0	0	1	0	0	0	13060	893	31	1	2256	1	RAPGEF3	12	48144895	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10	33566745	48144895	85707000	65	1639											
MLL2	8085	hgsc.bcm.edu	37	chr12	49445040	49445041	+	Frame_Shift_Ins	INS	-	-	G																															caggtgcggctcctcagtctINSggggggacaggtgcaattcc																										TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr12:49445040_49445041insG	ENST00000301067.7	-	10	2424_2425	c.2425_2426insC	c.(2425-2427)cagfs	p.Q809fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	809	Pro-rich.			Missing (in Ref. 1; AAC51734). {ECO:0000305}.	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)										CTCCTCAGTCTGGGGGGACAGG	0.634																																					p.Q809fs		Pindel	.											.	MLL2	1173	.	0			c.2426_2427insC						PASS	.																																			SO:0001589	frameshift_variant	8085	exon10			.	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.2426dupC	12.37:g.49445046_49445046dupG	ENSP00000301067:p.Gln809fs	126	0	.		286	80	0.28	NM_003482	O14687	Frame_Shift_Ins	INS	ENST00000301067.7	37	CCDS44873.1																																																																																			.	.	none		0.634	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			G	49445041	-	G	49445040	7	5	12	1	0	1	1	0	0	0	0	0	9630	1580	55	0	14367	0	MLL2	12	49445040	Frame_Shift_Ins	INS	-	TCGA-FF-8043-01A-11D-2210-10	1300145	49445040	84406855	66	1640	23	2									
MLL2	8085	hgsc.bcm.edu	37	chr12	49445046	49445047	+	Frame_Shift_Ins	INS	-	-	A																															cggctcctcagtctggggggINSacaggtgcaattcctcaggc																										TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr12:49445046_49445047insA	ENST00000301067.7	-	10	2418_2419	c.2419_2420insT	c.(2419-2421)tccfs	p.S807fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	807	Pro-rich.			Missing (in Ref. 1; AAC51734). {ECO:0000305}.	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)										AGTCTGGGGGGACAGGTGCAAT	0.634																																					p.S807fs		Atlas-Indel	.											.	MLL2	1173	.	0			c.2420_2421insT						PASS	.																																			SO:0001589	frameshift_variant	8085	exon10			.	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.2420dupT	12.37:g.49445047_49445047dupA	ENSP00000301067:p.Ser807fs	125	0	0		286	172	0.601399	NM_003482	O14687	Frame_Shift_Ins	INS	ENST00000301067.7	37	CCDS44873.1																																																																																			.	.	none		0.634	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49445047	-	A	49445046	7	5	12	1	0	1	1	0	0	0	0	0	9630	1174	41	0	14373	0	MLL2	12	49445046	Frame_Shift_Ins	INS	-	TCGA-FF-8043-01A-11D-2210-10	6	49445046	84406849	67	1641	23	2									
ATF7	11016	hgsc.bcm.edu	37	chr12	53911012	53911012	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttggctggccatctgagtgAggaccgaggtggccacagct	7	9	15	10	1	1	2	0	2	1	0	1	4	1	3	3	5	1	2	3	5	0	1			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr12:53911012A>G	ENST00000548446.2	-	12	1506	c.1394T>C	c.(1393-1395)cTc>cCc	p.L465P	ATF7_ENST00000415113.1_Missense_Mutation_p.L433P|ATF7_ENST00000546661.1_5'UTR|ATF7_ENST00000328463.7_Missense_Mutation_p.L465P|ATF7_ENST00000456903.4_Missense_Mutation_p.L454P|RP11-793H13.3_ENST00000548347.1_RNA|ATF7_ENST00000420353.2_Missense_Mutation_p.L454P|RP11-793H13.10_ENST00000591834.1_Intron			P17544	ATF7_HUMAN	activating transcription factor 7	465	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)	CATCTGAGTGAGGACCGAGGT	0.577																																					p.L454P		Atlas-SNP	.											.	ATF7	51	.	0			c.T1361C						PASS	.						103	104	104					12																	53911012		2075	4205	6280	SO:0001583	missense	11016	exon12			TGAGTGAGGACCG	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.1394T>C	12.37:g.53911012A>G	ENSP00000449938:p.Leu465Pro	74	0	0		147	7	0.047619	NM_006856	A5D6Y4|B2RMP1|B4DQL4|Q13814|Q8IVR8|Q9UD83	Missense_Mutation	SNP	ENST00000548446.2	37		.	.	.	.	.	.	.	.	.	.	A	20.8	4.045077	0.75846	.	.	ENSG00000170653	ENST00000548446;ENST00000328463;ENST00000306727;ENST00000415113;ENST00000420353;ENST00000456903	T;T;T;T;T	0.57107	0.42;0.42;0.58;0.43;0.43	4.6	4.6	0.57074	.	0.000000	0.85682	D	0.000000	T	0.63522	0.2518	L	0.41710	1.295	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.97110	1.0;0.993;0.999	T	0.66999	-0.5781	10	0.87932	D	0	-16.28	13.4618	0.61231	1.0:0.0:0.0:0.0	.	433;454;465	P17544-2;B2RMP1;P17544	.;.;ATF7_HUMAN	P	465;465;278;433;454;454	ENSP00000449938:L465P;ENSP00000329212:L465P;ENSP00000404880:L433P;ENSP00000399465:L454P;ENSP00000387406:L454P	ENSP00000304187:L278P	L	-	2	0	ATF7	52197279	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.366000	0.90111	2.087000	0.62958	0.454000	0.30748	CTC	.	.	none		0.577	ATF7-007	KNOWN	NMD_exception|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000406302.2	NM_001130059		G	53911012	A	G	53911012	3	3	12	1	0	0	0	0	1	0	0	0	1086	304	11	3	94	3	ATF7	12	53911012	Missense_Mutation	SNP	A	TCGA-FF-8043-01A-11D-2210-10	4465966	53911012	79940883	68	1642											
HOXC13	3229	hgsc.bcm.edu	37	chr12	54333307	54333307	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacccggagccgcgtcacgAcgccctcatccccgtcgaag	7	4	11	19	7	2	0	2	0	0	0	4	3	3	1	5	1	1	1	5	1	1	0			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr12:54333307A>G	ENST00000243056.3	+	1	773	c.617A>G	c.(616-618)gAc>gGc	p.D206G	HOXC-AS5_ENST00000512916.2_RNA	NM_017410.2	NP_059106.2	P31276	HXC13_HUMAN	homeobox C13	206					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						CCGCGTCACGACGCCCTCATC	0.672			T	NUP98	AML																																p.D206G		Atlas-SNP	.		Dom	yes		12	12q13.3	3229	homeo box C13		L	.	HOXC13	24	.	0			c.A617G						PASS	.						18	20	19					12																	54333307		2199	4291	6490	SO:0001583	missense	3229	exon1			GTCACGACGCCCT		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.617A>G	12.37:g.54333307A>G	ENSP00000243056:p.Asp206Gly	43	0	0		57	11	0.192982	NM_017410	Q5BL02|Q96J32|Q9NR24|Q9NYD5	Missense_Mutation	SNP	ENST00000243056.3	37	CCDS8865.1	.	.	.	.	.	.	.	.	.	.	A	18.36	3.606534	0.66445	.	.	ENSG00000123364	ENST00000243056	D	0.93604	-3.25	3.16	3.16	0.36331	.	0.058843	0.64402	D	0.000003	D	0.93158	0.7821	M	0.76574	2.34	0.54753	D	0.999983	P	0.45569	0.861	P	0.46389	0.515	D	0.93361	0.6727	10	0.66056	D	0.02	.	11.3352	0.49500	1.0:0.0:0.0:0.0	.	206	P31276	HXC13_HUMAN	G	206	ENSP00000243056:D206G	ENSP00000243056:D206G	D	+	2	0	HOXC13	52619574	1.000000	0.71417	1.000000	0.80357	0.602000	0.36980	8.443000	0.90320	1.709000	0.51313	0.260000	0.18958	GAC	.	.	none		0.672	HOXC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358865.2			G	54333307	A	G	54333307	3	3	12	1	0	0	0	0	1	0	0	0	7321	275	10	3	619	3	HOXC13	12	54333307	Missense_Mutation	SNP	A	TCGA-FF-8043-01A-11D-2210-10	422295	54333307	79518588	69	1643											
MSRB3	253827	hgsc.bcm.edu	37	chr12	65857048	65857048	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggatagcagtggcaccgcCgagggaggcagtggggtcgc	7	4	20	10	4	0	0	0	0	0	0	1	3	0	2	2	6	1	3	2	6	1	1			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr12:65857048C>T	ENST00000355192.3	+	6	651	c.525C>T	c.(523-525)gcC>gcT	p.A175A	MSRB3_ENST00000308259.5_Silent_p.A168A|MSRB3_ENST00000535664.1_Silent_p.A168A	NM_198080.3	NP_932346.1	Q8IXL7	MSRB3_HUMAN	methionine sulfoxide reductase B3	175					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)		GTGGCACCGCCGAGGGAGGCA	0.527																																					p.A175A		Atlas-SNP	.											MSRB3_ENST00000355192,colon,carcinoma,+2,4	MSRB3	80	4	0			c.C525T						PASS	.						68	63	65					12																	65857048		2203	4300	6503	SO:0001819	synonymous_variant	253827	exon6			CACCGCCGAGGGA	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.525C>T	12.37:g.65857048C>T		126	0	0		190	55	0.289474	NM_198080	B4DR19|B7ZAQ0|Q6UXS2	Silent	SNP	ENST00000355192.3	37	CCDS8973.1																																																																																			.	.	none		0.527	MSRB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401421.1	NM_198080		T	65857048	C	T	65857048	2	4	12	1	0	0	0	0	0	0	0	1	9898	639	23	1		1	MSRB3	12	65857048	Silent	SNP	C	TCGA-FF-8043-01A-11D-2210-10	11523741	65857048	67994847	70	1644											
BTG1	694	hgsc.bcm.edu	37	chr12	92538187	92538187	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aacggtaacccgatcccttgCatggcttttctgggaaccag	9	10	10	12	2	1	0	0	0	1	0	2	2	2	1	3	3	4	3	3	3	3	4			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr12:92538187C>T	ENST00000256015.3	-	2	546	c.185G>A	c.(184-186)tGc>tAc	p.C62Y	C12orf79_ENST00000551843.1_5'Flank|C12orf79_ENST00000549802.1_5'Flank|RP11-796E2.4_ENST00000501008.2_RNA|RP11-796E2.4_ENST00000499685.2_RNA|C12orf79_ENST00000546975.1_5'Flank|C12orf79_ENST00000551563.2_5'Flank	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	62					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)			haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				CGATCCCTTGCATGGCTTTTC	0.463			T	MYC	BCLL						OREG0022024	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C62Y		Atlas-SNP	.		Dom	yes		12	12q22	694	"B-cell translocation gene 1, anti-proliferative"		L	.	BTG1	30	.	0			c.G185A						PASS	.						119	120	120					12																	92538187		2203	4300	6503	SO:0001583	missense	694	exon2			CCCTTGCATGGCT		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.185G>A	12.37:g.92538187C>T	ENSP00000256015:p.Cys62Tyr	118	0	0	1291	131	39	0.29771	NM_001731	P31607	Missense_Mutation	SNP	ENST00000256015.3	37	CCDS9043.1	.	.	.	.	.	.	.	.	.	.	C	12.92	2.081433	0.36758	.	.	ENSG00000133639	ENST00000256015	T	0.22336	1.96	5.81	5.81	0.92471	Anti-proliferative protein (4);	0.139437	0.64402	D	0.000002	T	0.16128	0.0388	L	0.39085	1.19	0.51482	D	0.999929	B	0.06786	0.001	B	0.13407	0.009	T	0.04565	-1.0942	10	0.02654	T	1	-4.1118	15.5494	0.76137	0.0:0.8627:0.1373:0.0	.	62	P62324	BTG1_HUMAN	Y	62	ENSP00000256015:C62Y	ENSP00000256015:C62Y	C	-	2	0	BTG1	91062318	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.537000	0.60643	2.738000	0.93877	0.655000	0.94253	TGC	.	.	none		0.463	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1			T	92538187	C	T	92538187	3	4	12	1	0	0	0	0	1	0	0	0	1555	710	25	2	334	2	BTG1	12	92538187	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10	26681139	92538187	41313708	71	1645											
BTG1	694	hgsc.bcm.edu	37	chr12	92539174	92539180	+	Frame_Shift_Del	DEL	CTCCTGC	CTCCTGC	-																															ccctgctcacctgccagcagCtcctgcaggctctggctgaa																								rs377174658|rs199587257|rs200623021|rs549978043		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	CTCCTGC	CTCCTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr12:92539174_92539180delCTCCTGC	ENST00000256015.3	-	1	493_499	c.132_138delGCAGGAG	c.(130-138)ctgcaggagfs	p.LQE44fs	C12orf79_ENST00000549802.1_5'Flank|RP11-796E2.4_ENST00000501008.2_RNA|RP11-796E2.4_ENST00000499685.2_RNA|C12orf79_ENST00000546975.1_5'Flank|C12orf79_ENST00000551563.2_5'Flank	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	44					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)	p.E46D(1)		haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				CTGCCAGCAGCTCCTGCAGGCTCTGGC	0.691			T	MYC	BCLL																																p.45_47del		Pindel,Atlas-Indel	.		Dom	yes		12	12q22	694	"B-cell translocation gene 1, anti-proliferative"		L	.	BTG1	30	.	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.133_139del						PASS	.																																			SO:0001589	frameshift_variant	694	exon1			.		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.132_138delGCAGGAG	12.37:g.92539174_92539180delCTCCTGC	ENSP00000256015:p.Leu44fs	110	0	.		110	25	0.227	NM_001731	P31607	Frame_Shift_Del	DEL	ENST00000256015.3	37	CCDS9043.1																																																																																			.	.	none		0.691	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1			-	92539180	CTCCTGC	-	92539174	7	5	12	1	0	1	0	1	0	0	0	0	1555	796	28	0	385	0	BTG1	12	92539174	Frame_Shift_Del	DEL	CTCCTGC	TCGA-FF-8043-01A-11D-2210-10	987	92539174	41312721	72	1646											
NR2C1	7181	hgsc.bcm.edu	37	chr12	95442844	95442844	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aaaaaaacatatagaaatacCctgaaagctacatgtgaatc	21	8	5	7	0	0	3	0	2	0	1	1	3	0	3	1	0	4	1	1	0	10	4			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr12:95442844C>T	ENST00000333003.5	-	9	1461	c.1131G>A	c.(1129-1131)agG>agA	p.R377R	NR2C1_ENST00000330677.7_Splice_Site_p.R377R|NR2C1_ENST00000393101.3_Splice_Site_p.R377R|NR2C1_ENST00000545833.1_5'UTR	NM_003297.3	NP_003288.2	P13056	NR2C1_HUMAN	nuclear receptor subfamily 2, group C, member 1	377					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						ATAGAAATACCCTGAAAGCTA	0.363																																					p.R377R		Atlas-SNP	.											.	NR2C1	56	.	0			c.G1131A						PASS	.						100	92	95					12																	95442844		2203	4300	6503	SO:0001630	splice_region_variant	7181	exon9			AAATACCCTGAAA	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.1131+1G>A	12.37:g.95442844C>T		93	0	0		67	24	0.358209	NM_001032287	A8K5K4|Q15625|Q15626	Silent	SNP	ENST00000333003.5	37	CCDS9051.1																																																																																			.	.	none		0.363	NR2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407565.2	NM_003297	Silent	T	95442844	C	T	95442844	5	4	12	1	0	0	0	0	0	0	1	0	10631	637	22	2	782	2	NR2C1	12	95442844	Splice_Site	SNP	C	TCGA-FF-8043-01A-11D-2210-10	2903670	95442844	38409051	73	1647											
DTX1	1840	hgsc.bcm.edu	37	chr12	113496135	113496135	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tacacggccaccgtgtgccaCcacattgagaacgtgctgaa	11	7	10	13	3	0	2	0	2	0	1	0	3	0	2	4	1	4	1	4	1	3	2			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr12:113496135C>T	ENST00000257600.3	+	1	641	c.138C>T	c.(136-138)caC>caT	p.H46H		NM_004416.2	NP_004407.2	Q86Y01	DTX1_HUMAN	deltex 1, E3 ubiquitin ligase	46	WWE 1. {ECO:0000255|PROSITE- ProRule:PRU00248}.				cell surface receptor signaling pathway (GO:0007166)|glial cell differentiation (GO:0010001)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of T cell differentiation (GO:0045581)|Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)|regulation of Notch signaling pathway (GO:0008593)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Notch binding (GO:0005112)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	32						CCGTGTGCCACCACATTGAGA	0.652																																					p.H46H		Atlas-SNP	.											.	DTX1	83	.	0			c.C138T						PASS	.						106	92	97					12																	113496135		2203	4300	6503	SO:0001819	synonymous_variant	1840	exon1			GTGCCACCACATT	AF053700	CCDS9164.1	12q24	2014-01-28	2014-01-28			ENSG00000135144			3060	protein-coding gene	gene with protein product		602582	"deltex homolog 1 (Drosophila)"			9590294, 12670957	Standard	NM_004416		Approved	hDx-1	uc001tuk.1	Q86Y01	OTTHUMG00000169610	ENST00000257600.3:c.138C>T	12.37:g.113496135C>T		111	0	0		93	38	0.408602	NM_004416	O60630|Q9BS04	Silent	SNP	ENST00000257600.3	37	CCDS9164.1																																																																																			.	.	none		0.652	DTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405045.2			T	113496135	C	T	113496135	2	4	12	1	0	0	0	0	0	0	0	1	4795	506	18	2		2	DTX1	12	113496135	Silent	SNP	C	TCGA-FF-8043-01A-11D-2210-10	18053291	113496135	20355760	74	1648											
MLXIP	22877	hgsc.bcm.edu	37	chr12	122516989	122516989	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccgcgccgccagcagatcaTccacagcggccacttcatgg	8	6	10	17	4	2	1	2	0	0	1	4	1	4	1	5	2	2	1	5	2	0	1			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr12:122516989T>C	ENST00000319080.7	+	1	362	c.230T>C	c.(229-231)aTc>aCc	p.I77T						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)		CAGCAGATCATCCACAGCGGC	0.726																																					p.I77T	Esophageal Squamous(105;787 1493 16200 18566 52466)	Atlas-SNP	.											.	MLXIP	46	.	0			c.T230C						PASS	.						35	35	35					12																	122516989		692	1591	2283	SO:0001583	missense	22877	exon1			AGATCATCCACAG	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.230T>C	12.37:g.122516989T>C	ENSP00000312834:p.Ile77Thr	32	0	0		38	17	0.447368	NM_014938		Missense_Mutation	SNP	ENST00000319080.7	37		.	.	.	.	.	.	.	.	.	.	T	27.7	4.857990	0.91433	.	.	ENSG00000175727	ENST00000319080	T	0.22539	1.95	4.1	4.1	0.47936	.	0.000000	0.85682	D	0.000000	T	0.46014	0.1371	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.50575	-0.8812	9	0.87932	D	0	-21.7018	12.1646	0.54123	0.0:0.0:0.0:1.0	.	77	Q9HAP2	MLXIP_HUMAN	T	77	ENSP00000312834:I77T	ENSP00000312834:I77T	I	+	2	0	MLXIP	121001372	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.191000	0.77763	1.611000	0.50210	0.379000	0.24179	ATC	.	.	none		0.726	MLXIP-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401718.2	NM_014938		C	122516989	T	C	122516989	3	2	12	1	0	0	0	0	1	0	0	0	9645	1435	50	3	232	3	MLXIP	12	122516989	Missense_Mutation	SNP	T	TCGA-FF-8043-01A-11D-2210-10	9020854	122516989	11334906	75	1649											
SFRS8	6433	hgsc.bcm.edu	37	chr12	132198771	132198771	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatacggacttgcttgaggAggaggcaaggcaaggtactg	11	7	16	7	1	0	1	0	1	0	0	0	4	0	4	0	6	3	5	0	6	4	4			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr12:132198771A>G	ENST00000261674.4	+	2	515	c.374A>G	c.(373-375)gAg>gGg	p.E125G	SFSWAP_ENST00000541286.1_Missense_Mutation_p.E125G	NM_004592.3	NP_004583.2	Q12872	SFSWA_HUMAN	splicing factor, suppressor of white-apricot family	125					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						TTGCTTGAGGAGGAGGCAAGG	0.393																																					p.E125G		Atlas-SNP	.											.	SFSWAP	69	.	0			c.A374G						PASS	.						98	83	88					12																	132198771		2203	4300	6503	SO:0001583	missense	6433	exon2			TTGAGGAGGAGGC	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.374A>G	12.37:g.132198771A>G	ENSP00000261674:p.Glu125Gly	59	0	0		92	4	0.0434783	NM_001261411	B2RN45|B7ZM97|F5H6B8|Q6PJF7	Missense_Mutation	SNP	ENST00000261674.4	37	CCDS9273.1	.	.	.	.	.	.	.	.	.	.	A	17.48	3.400017	0.62177	.	.	ENSG00000061936	ENST00000261674;ENST00000544623;ENST00000541286	T;T	0.24538	1.85;1.85	5.84	4.68	0.58851	Splicing factor, suppressor of white apricot (1);	0.048341	0.85682	D	0.000000	T	0.53658	0.1810	M	0.85197	2.74	0.80722	D	1	P;P	0.41673	0.699;0.759	P;P	0.60609	0.565;0.877	T	0.57329	-0.7830	10	0.66056	D	0.02	-35.4576	13.2516	0.60055	0.8674:0.1325:0.0:0.0	.	125;125	F5H6B8;Q12872	.;SFSWA_HUMAN	G	125;62;125	ENSP00000261674:E125G;ENSP00000437738:E125G	ENSP00000261674:E125G	E	+	2	0	SFSWAP	130764724	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.361000	0.79497	1.017000	0.39495	0.533000	0.62120	GAG	.	.	none		0.393	SFSWAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399276.1	NM_004592		G	132198771	A	G	132198771	3	3	12	1	0	0	0	0	1	0	0	0	14198	304	11	3	380	3	SFRS8	12	132198771	Missense_Mutation	SNP	A	TCGA-FF-8043-01A-11D-2210-10	9681782	132198771	1653124	76	1650											
ACIN1	22985	hgsc.bcm.edu	37	chr14	23548787	23548787	+	Missense_Mutation	SNP	C	C	T																															tgcttgatgctgaacgagaaCgtgaacgtgaccttgatctg																								rs55838227|rs34870944|rs61741619	byFrequency	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr14:23548787C>T	ENST00000262710.1	-	6	2258	c.1931G>A	c.(1930-1932)cGt>cAt	p.R644H	ACIN1_ENST00000605057.1_Missense_Mutation_p.R586H|ACIN1_ENST00000555352.1_5'Flank|ACIN1_ENST00000457657.1_Missense_Mutation_p.R604H|ACIN1_ENST00000555053.1_Missense_Mutation_p.R644H	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	644	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)	p.S643_R644insHS(1)		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)		TGAACGAGAACGTGAACGTGA	0.488																																					p.R644H		Atlas-SNP	.											.	ACIN1	147	.	1	Insertion - In frame(1)	upper_aerodigestive_tract(1)	c.G1931A						PASS	.						255	224	235					14																	23548787		2203	4300	6503	SO:0001583	missense	22985	exon6			CGAGAACGTGAAC	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.1931G>A	14.37:g.23548787C>T	ENSP00000262710:p.Arg644His	150	0	0		198	34	0.171717	NM_001164814	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Missense_Mutation	SNP	ENST00000262710.1	37	CCDS9587.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.061864	0.76187	.	.	ENSG00000100813	ENST00000262710;ENST00000457657;ENST00000555053	T;T;T	0.30448	2.29;1.53;2.29	5.46	5.46	0.80206	.	0.000000	0.41001	D	0.000979	T	0.42720	0.1215	L	0.27053	0.805	0.36352	D	0.86012	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.79784	0.993;0.984;0.984	T	0.50808	-0.8784	10	0.59425	D	0.04	-1.7144	14.8141	0.70017	0.0:1.0:0.0:0.0	.	644;644;604	G3V3M7;Q9UKV3;E7EQT4	.;ACINU_HUMAN;.	H	644;604;644	ENSP00000262710:R644H;ENSP00000405677:R604H;ENSP00000451328:R644H	ENSP00000262710:R644H	R	-	2	0	ACIN1	22618627	0.999000	0.42202	1.000000	0.80357	0.906000	0.53458	1.398000	0.34554	2.556000	0.86216	0.655000	0.94253	CGT	C|0.985;T|0.015	0.015	strong		0.488	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977		T	23548787	C	T	23548787	3	4	12	1	0	0	0	0	1	0	0	0	142	536	19	1	2297	1	ACIN1	14	23548787	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10		23548787	83800753	77	1651	24	2									
ACIN1	22985	hgsc.bcm.edu	37	chr14	23548793	23548793	+	Missense_Mutation	SNP	C	C	T																															atgctgaacgagaacgtgaaCgtgaccttgatctggactct																								rs80007670	byFrequency	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr14:23548793C>T	ENST00000262710.1	-	6	2252	c.1925G>A	c.(1924-1926)cGt>cAt	p.R642H	ACIN1_ENST00000605057.1_Missense_Mutation_p.R584H|ACIN1_ENST00000555352.1_5'Flank|ACIN1_ENST00000457657.1_Missense_Mutation_p.R602H|ACIN1_ENST00000555053.1_Missense_Mutation_p.R642H	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	642	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)		AGAACGTGAACGTGACCTTGA	0.478																																					p.R642H		Atlas-SNP	.											.	ACIN1	147	.	0			c.G1925A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG	6,4400	6.2+/-15.9	0,6,2197	258	226	237		1925,1805,1925	3.2	0.8	14	dbSNP_131	237	24,8576	11.9+/-42.8	0,24,4276	yes	missense,missense,missense	ACIN1	NM_001164814.1,NM_001164815.1,NM_014977.3	29,29,29	0,30,6473	TT,TC,CC		0.2791,0.1362,0.2307	probably-damaging,probably-damaging,probably-damaging	642/1329,602/1302,642/1342	23548793	30,12976	2203	4300	6503	SO:0001583	missense	22985	exon6			CGTGAACGTGACC	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.1925G>A	14.37:g.23548793C>T	ENSP00000262710:p.Arg642His	160	0	0		204	11	0.0539216	NM_001164814	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Missense_Mutation	SNP	ENST00000262710.1	37	CCDS9587.1	9	0.004120879120879121	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	4	0.005277044854881266	C	14.59	2.580077	0.46006	0.001362	0.002791	ENSG00000100813	ENST00000262710;ENST00000457657;ENST00000555053	T;T;T	0.29917	2.39;1.55;2.39	5.05	3.18	0.36537	.	0.000000	0.40144	N	0.001165	T	0.20170	0.0485	L	0.27053	0.805	0.26413	N	0.976231	D;D;D	0.67145	0.992;0.986;0.996	P;P;P	0.51582	0.674;0.475;0.572	T	0.04440	-1.0951	10	0.59425	D	0.04	-4.3727	7.238	0.26079	0.0:0.7908:0.0:0.2092	.	642;642;602	G3V3M7;Q9UKV3;E7EQT4	.;ACINU_HUMAN;.	H	642;602;642	ENSP00000262710:R642H;ENSP00000405677:R602H;ENSP00000451328:R642H	ENSP00000262710:R642H	R	-	2	0	ACIN1	22618633	0.984000	0.35163	0.847000	0.33407	0.542000	0.35054	0.703000	0.25646	0.669000	0.31146	-0.216000	0.12614	CGT	C|0.994;T|0.006	0.006	strong		0.478	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977		T	23548793	C	T	23548793	3	4	12	1	0	0	0	0	1	0	0	0	142	536	19	1	2303	1	ACIN1	14	23548793	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10	6	23548793	83800747	78	1652	24	2									
POMT2	29954	hgsc.bcm.edu	37	chr14	77746416	77746416	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgtcattgacccctgagaagCgtaggccctgtggaatagag	10	9	13	9	1	1	3	1	2	0	2	1	5	1	4	3	2	1	1	3	2	4	3	rs571330846		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr14:77746416C>T	ENST00000261534.4	-	17	1935	c.1733G>A	c.(1732-1734)cGc>cAc	p.R578H		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)		CCCTGAGAAGCGTAGGCCCTG	0.597													C|||	1	0.000199681	0.0	0.0	5008	,	,		17795	0.0		0.0	False		,,,				2504	0.001				p.R578H		Atlas-SNP	.											POMT2,colon,carcinoma,-1,2	POMT2	47	2	0			c.G1733A						PASS	.						120	99	106					14																	77746416		2203	4300	6503	SO:0001583	missense	29954	exon17			GAGAAGCGTAGGC	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.1733G>A	14.37:g.77746416C>T	ENSP00000261534:p.Arg578His	114	0	0		116	54	0.465517	NM_013382	Q9NSG6|Q9P1W0|Q9P1W2	Missense_Mutation	SNP	ENST00000261534.4	37	CCDS9857.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.3|27.3	4.815127|4.815127	0.90790|0.90790	.|.	.|.	ENSG00000009830|ENSG00000009830	ENST00000556171|ENST00000261534	.|D	.|0.92299	.|-3.01	5.67|5.67	4.79|4.79	0.61399|0.61399	.|.	.|0.051252	.|0.85682	.|N	.|0.000000	D|D	0.90113|0.90113	0.6911|0.6911	M|M	0.72894|0.72894	2.215|2.215	0.80722|0.80722	D|D	1|1	.|B	.|0.18461	.|0.028	.|B	.|0.14023	.|0.01	D|D	0.86195|0.86195	0.1615|0.1615	5|10	.|0.14656	.|T	.|0.56	-12.6745|-12.6745	14.5883|14.5883	0.68344|0.68344	0.0:0.9299:0.0:0.0701|0.0:0.9299:0.0:0.0701	.|.	.|578	.|Q9UKY4	.|POMT2_HUMAN	T|H	46|578	.|ENSP00000261534:R578H	.|ENSP00000261534:R578H	A|R	-|-	1|2	0|0	POMT2|POMT2	76816169|76816169	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.739000|0.739000	0.42172|0.42172	3.812000|3.812000	0.55628|0.55628	1.416000|1.416000	0.47057|0.47057	0.563000|0.563000	0.77884|0.77884	GCT|CGC	.	.	none		0.597	POMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414155.1	NM_013382		T	77746416	C	T	77746416	3	4	12	1	0	0	0	0	1	0	0	0	12255	768	27	1	539	1	POMT2	14	77746416	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10	54197623	77746416	29603124	79	1653											
AMN	81693	hgsc.bcm.edu	37	chr14	103394811	103394811	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggcttcaggagccggattcGgcgtctcagacgtgggctcg	5	9	16	11	5	2	1	2	0	1	1	5	3	2	3	1	5	1	2	1	5	0	2			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr14:103394811G>A	ENST00000299155.5	+	4	289	c.256G>A	c.(256-258)Ggc>Agc	p.G86S		NM_030943.3	NP_112205.2	Q9BXJ7	AMNLS_HUMAN	amnion associated transmembrane protein	86					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)	AGCCGGATTCGGCGTCTCAGA	0.716																																					p.G86S		Atlas-SNP	.											.	AMN	13	.	0			c.G256A						PASS	.						17	17	17					14																	103394811		2193	4292	6485	SO:0001583	missense	81693	exon4			GGATTCGGCGTCT	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.256G>A	14.37:g.103394811G>A	ENSP00000299155:p.Gly86Ser	84	0	0		103	43	0.417476	NM_030943	Q6UX83	Missense_Mutation	SNP	ENST00000299155.5	37	CCDS9977.1	.	.	.	.	.	.	.	.	.	.	G	6.859	0.527850	0.13127	.	.	ENSG00000166126	ENST00000299155;ENST00000541086	D	0.87887	-2.31	3.33	-3.8	0.04307	.	1.167550	0.06155	N	0.674896	T	0.67887	0.2941	N	0.11560	0.145	0.09310	N	1	B	0.22983	0.078	B	0.20384	0.029	T	0.59752	-0.7395	10	0.06099	T	0.92	-10.4145	5.7356	0.18065	0.2807:0.1937:0.5256:0.0	.	86	Q9BXJ7	AMNLS_HUMAN	S	86;32	ENSP00000299155:G86S	ENSP00000299155:G86S	G	+	1	0	AMN	102464564	0.000000	0.05858	0.063000	0.19743	0.325000	0.28411	-0.484000	0.06528	-0.663000	0.05331	-0.390000	0.06520	GGC	.	.	none		0.716	AMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415704.1			A	103394811	G	A	103394811	3	1	12	1	0	0	0	0	1	0	0	0	580	1116	39	1	270	1	AMN	14	103394811	Missense_Mutation	SNP	G	TCGA-FF-8043-01A-11D-2210-10	25648395	103394811	3954729	80	1654											
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105418008	105418008	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tccacctgggggcccttgagGtccactttgggcatcttcaa	6	11	11	13	0	2	1	1	1	1	0	4	1	4	1	4	4	0	1	4	4	1	3			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr14:105418008G>T	ENST00000333244.5	-	7	3899	c.3780C>A	c.(3778-3780)gaC>gaA	p.D1260E	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1260						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)			GGCCCTTGAGGTCCACTTTGG	0.617																																					p.D1260E		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C3780A						PASS	.						85	70	75					14																	105418008		1788	3218	5006	SO:0001583	missense	113146	exon7			CTTGAGGTCCACT	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.3780C>A	14.37:g.105418008G>T	ENSP00000353114:p.Asp1260Glu	197	0	0		209	86	0.411483	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	N	9.476	1.096873	0.20552	.	.	ENSG00000185567	ENST00000333244	T	0.01838	4.61	3.99	-2.74	0.05932	.	.	.	.	.	T	0.02342	0.0072	M	0.76328	2.33	0.09310	N	1	B	0.30146	0.27	B	0.28139	0.086	T	0.49606	-0.8922	9	0.05959	T	0.93	.	3.689	0.08339	0.0883:0.1204:0.4663:0.325	.	1260	Q8IVF2	AHNK2_HUMAN	E	1260	ENSP00000353114:D1260E	ENSP00000353114:D1260E	D	-	3	2	AHNAK2	104489053	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.304000	0.08199	-0.748000	0.04753	-1.280000	0.01385	GAC	.	.	none		0.617	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		T	105418008	G	T	105418008	3	4	12	1	0	0	0	0	1	0	0	0	415	1252	44	4	13611	4	AHNAK2	14	105418008	Missense_Mutation	SNP	G	TCGA-FF-8043-01A-11D-2210-10	2023197	105418008	1931532	81	1655											
ATPBD4	89978	hgsc.bcm.edu	37	chr15	35830516	35830516	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atagagatcttcaacctcatCaccttcacatttggtgtaca	12	13	5	11	0	5	1	4	0	1	1	5	2	5	1	2	1	2	1	2	1	3	5			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr15:35830516C>T	ENST00000256538.4	-	3	297	c.271G>A	c.(271-273)Gat>Aat	p.D91N	DPH6_ENST00000440392.2_Missense_Mutation_p.D91N	NM_080650.3	NP_542381.1	Q7L8W6	DPH6_HUMAN	diphthamine biosynthesis 6	91					peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)		ATP binding (GO:0005524)|diphthine-ammonia ligase activity (GO:0017178)										TCAACCTCATCACCTTCACAT	0.378																																					p.D91N		Atlas-SNP	.											.	ATPBD4	30	.	0			c.G271A						PASS	.						238	207	218					15																	35830516		2201	4298	6499	SO:0001583	missense	89978	exon3			CCTCATCACCTTC		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.271G>A	15.37:g.35830516C>T	ENSP00000256538:p.Asp91Asn	283	0	0		163	127	0.779141	NM_001141972	B3KWG1|Q96HJ6	Missense_Mutation	SNP	ENST00000256538.4	37	CCDS10043.1	.	.	.	.	.	.	.	.	.	.	C	32	5.175413	0.94807	.	.	ENSG00000134146	ENST00000256538;ENST00000440392	T;T	0.68181	0.91;-0.31	5.75	5.75	0.90469	Domain of unknown function DUF71, ATP-binding domain (2);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	D	0.87378	0.6162	M	0.93808	3.46	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.999	D	0.89087	0.3480	10	0.62326	D	0.03	-29.0226	20.312	0.98644	0.0:1.0:0.0:0.0	.	91;91	B3KWG1;Q7L8W6	.;ATBD4_HUMAN	N	91	ENSP00000256538:D91N;ENSP00000406976:D91N	ENSP00000256538:D91N	D	-	1	0	ATPBD4	33617808	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.887000	0.69751	2.880000	0.98712	0.655000	0.94253	GAT	.	.	none		0.378	DPH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251973.1	NM_080650		T	35830516	C	T	35830516	3	4	12	1	0	0	0	0	1	0	0	0	1202	826	29	2	750	2	ATPBD4	15	35830516	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10		35830516	66700876	82	1656											
ADAMTS7	11173	hgsc.bcm.edu	37	chr15	79066981	79066981	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctcaccgtcattgaccacggGcacccatgtgtgcagctggc	7	8	11	15	2	2	1	2	1	0	0	2	1	2	1	3	2	2	3	3	2	0	1			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr15:79066981G>C	ENST00000388820.4	-	12	2071	c.1861C>G	c.(1861-1863)Ccc>Gcc	p.P621A	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	621	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						TTGACCACGGGCACCCATGTG	0.632																																					p.P621A		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.C1861G						PASS	.						56	54	55					15																	79066981		2196	4293	6489	SO:0001583	missense	11173	exon12			CCACGGGCACCCA	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.1861C>G	15.37:g.79066981G>C	ENSP00000373472:p.Pro621Ala	75	0	0		51	25	0.490196	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	37	CCDS32303.1	.	.	.	.	.	.	.	.	.	.	G	10.98	1.505696	0.26949	.	.	ENSG00000136378	ENST00000388820	T	0.00428	7.44	3.61	3.61	0.41365	.	0.145698	0.47852	D	0.000209	T	0.00468	0.0015	M	0.64676	1.99	0.35073	D	0.762647	B;B	0.32071	0.355;0.189	B;B	0.32211	0.142;0.077	T	0.64415	-0.6413	10	0.59425	D	0.04	.	14.4931	0.67665	0.0:0.0:1.0:0.0	.	621;621	A8MQ00;Q9UKP4	.;ATS7_HUMAN	A	621	ENSP00000373472:P621A	ENSP00000373472:P621A	P	-	1	0	ADAMTS7	76854036	1.000000	0.71417	0.960000	0.40013	0.885000	0.51271	4.864000	0.62990	2.044000	0.60594	0.289000	0.19496	CCC	.	.	none		0.632	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272		C	79066981	G	C	79066981	3	2	12	1	0	0	0	0	1	0	0	0	271	1203	42	4	3251	4	ADAMTS7	15	79066981	Missense_Mutation	SNP	G	TCGA-FF-8043-01A-11D-2210-10	43236465	79066981	23464411	83	1657											
CTSH	1512	hgsc.bcm.edu	37	chr15	79220112	79220112	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcctttccaggttggaacttGcaataaccatcctgttgagg	9	12	10	10	0	0	1	0	1	0	0	2	2	2	2	4	3	3	3	4	3	3	5	rs142506062		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr15:79220112G>C	ENST00000220166.5	-	9	751	c.642C>G	c.(640-642)tgC>tgG	p.C214W	CTSH_ENST00000534533.1_5'UTR	NM_004390.3	NP_004381.2	P09668	CATH_HUMAN	cathepsin H	214					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						GTTGGAACTTGCAATAACCAT	0.483																																					p.C214W		Atlas-SNP	.											.	CTSH	23	.	0			c.C642G						PASS	.						158	119	132					15																	79220112		2196	4293	6489	SO:0001583	missense	1512	exon9			GAACTTGCAATAA	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.642C>G	15.37:g.79220112G>C	ENSP00000220166:p.Cys214Trp	58	0	0		44	28	0.636364	NM_004390	B2RBK0|Q96NY6|Q9BUM7	Missense_Mutation	SNP	ENST00000220166.5	37	CCDS10308.1	.	.	.	.	.	.	.	.	.	.	G	10.13	1.264475	0.23136	.	.	ENSG00000103811	ENST00000220166;ENST00000394758	D	0.93712	-3.27	4.94	4.02	0.46733	Peptidase C1A, papain C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.97936	0.9321	H	0.99225	4.475	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97240	0.9890	10	0.87932	D	0	.	9.4585	0.38769	0.0996:0.0:0.9004:0.0	.	214;202	P09668;E9PBP2	CATH_HUMAN;.	W	214;202	ENSP00000220166:C214W	ENSP00000220166:C214W	C	-	3	2	CTSH	77007167	1.000000	0.71417	0.996000	0.52242	0.027000	0.11550	2.681000	0.46926	1.094000	0.41399	-0.216000	0.12614	TGC	G|1.000;A|0.000	.	alt		0.483	CTSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291370.1	NM_004390		C	79220112	G	C	79220112	3	2	12	1	0	0	0	0	1	0	0	0	4038	1311	46	4	381	4	CTSH	15	79220112	Missense_Mutation	SNP	G	TCGA-FF-8043-01A-11D-2210-10	153131	79220112	23311280	84	1658											
LITAF	9516	hgsc.bcm.edu	37	chr16	11650529	11650529	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgtctcttcataggatggagGtgcggatggtgctgaggaag	8	11	17	5	1	2	1	1	1	1	0	3	5	2	5	0	6	2	1	0	6	2	2			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr16:11650529G>A	ENST00000571688.1	-	2	288	c.58C>T	c.(58-60)Cct>Tct	p.P20S	LITAF_ENST00000574703.1_Missense_Mutation_p.P20S|LITAF_ENST00000574763.1_Missense_Mutation_p.P20S|LITAF_ENST00000413364.2_Missense_Mutation_p.P20S|LITAF_ENST00000571976.1_Missense_Mutation_p.P20S|LITAF_ENST00000570904.1_Missense_Mutation_p.P20S|LITAF_ENST00000572255.1_Intron|LITAF_ENST00000571459.1_Missense_Mutation_p.P20S|LITAF_ENST00000576036.1_Missense_Mutation_p.P20S|LITAF_ENST00000381810.3_Missense_Mutation_p.P20S|LITAF_ENST00000339430.5_Missense_Mutation_p.P20S	NM_001136472.1	NP_001129944.1	Q99732	LITAF_HUMAN	lipopolysaccharide-induced TNF factor	20					aging (GO:0007568)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of cytokine production (GO:0001817)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			endometrium(1)|large_intestine(1)|liver(1)|lung(3)|skin(1)	7						TAGGATGGAGGTGCGGATGGT	0.532																																					p.P20S		Atlas-SNP	.											.	LITAF	16	.	0			c.C58T						PASS	.						95	87	90					16																	11650529		2197	4300	6497	SO:0001583	missense	9516	exon2			ATGGAGGTGCGGA	AB034747	CCDS32386.1, CCDS45411.1	16p13.3-p12	2014-09-17							16841	protein-coding gene	gene with protein product		603795				9305847, 10200294	Standard	NM_004862		Approved	PIG7, SIMPLE, FLJ38636, TP53I7	uc002dbb.3	Q99732		ENST00000571688.1:c.58C>T	16.37:g.11650529G>A	ENSP00000459533:p.Pro20Ser	177	0	0		309	40	0.12945	NM_001136473	D3DUG1|G5E9K0|Q05DW0|Q9C0L6	Missense_Mutation	SNP	ENST00000571688.1	37	CCDS32386.1	.	.	.	.	.	.	.	.	.	.	G	17.15	3.316524	0.60524	.	.	ENSG00000189067	ENST00000339430;ENST00000413364;ENST00000381810	D;D;D	0.93189	-2.45;-3.18;-2.52	5.63	5.63	0.86233	.	0.065688	0.64402	D	0.000010	D	0.95579	0.8563	L	0.52364	1.645	0.58432	D	0.999997	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;0.996	D	0.95558	0.8627	10	0.59425	D	0.04	-23.8973	17.2034	0.86912	0.0:0.0:1.0:0.0	.	20;20;20	Q99732-2;G5E9K0;Q99732	.;.;LITAF_HUMAN	S	20	ENSP00000340118:P20S;ENSP00000397958:P20S;ENSP00000371231:P20S	ENSP00000340118:P20S	P	-	1	0	LITAF	11558030	1.000000	0.71417	0.451000	0.26982	0.146000	0.21551	5.921000	0.70028	2.652000	0.90054	0.655000	0.94253	CCT	.	.	none		0.532	LITAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436794.2	NM_004862		A	11650529	G	A	11650529	3	1	12	1	0	0	0	0	1	0	0	0	8839	1261	44	2	525	2	LITAF	16	11650529	Missense_Mutation	SNP	G	TCGA-FF-8043-01A-11D-2210-10		11650529	78704224	85	1659											
ABCC1	4363	hgsc.bcm.edu	37	chr16	16162160	16162160	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tcatcagcagcatcgtgcagGtacagggggaagctggggcg	9	6	17	9	2	2	0	2	0	0	0	3	1	2	1	0	5	5	5	0	5	2	1			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr16:16162160G>A	ENST00000399410.3	+	13	1999		c.e13+1		ABCC1_ENST00000349029.5_Splice_Site|ABCC1_ENST00000399408.2_Splice_Site|ABCC1_ENST00000345148.5_Splice_Site|ABCC1_ENST00000346370.5_Splice_Site|ABCC1_ENST00000351154.5_Splice_Site	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1						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)	CATCGTGCAGGTACAGGGGGA	0.597																																					.		Atlas-SNP	.											.	ABCC1	156	.	0			c.1824+1G>A						PASS	.						142	131	134					16																	16162160		2003	4168	6171	SO:0001630	splice_region_variant	4363	exon13			GTGCAGGTACAGG	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.1824+1G>A	16.37:g.16162160G>A		108	0	0		159	102	0.641509	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Splice_Site	SNP	ENST00000399410.3	37	CCDS42122.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.967961	0.74131	.	.	ENSG00000103222	ENST00000399410;ENST00000399408;ENST00000346370;ENST00000351154;ENST00000345148;ENST00000349029;ENST00000536381	.	.	.	4.61	4.61	0.57282	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0161	0.80441	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ABCC1	16069661	1.000000	0.71417	0.998000	0.56505	0.738000	0.42128	9.413000	0.97351	2.108000	0.64289	0.462000	0.41574	.	.	.	none		0.597	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996	Intron	A	16162160	G	A	16162160	5	1	12	1	0	0	0	0	0	0	1	0	49	1275	44	2	1875	2	ABCC1	16	16162160	Splice_Site	SNP	G	TCGA-FF-8043-01A-11D-2210-10	4511631	16162160	74192593	86	1660											
TMC5	79838	hgsc.bcm.edu	37	chr16	19481009	19481009	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgccttctctagcatggcCaagtatttccggaacaactt	9	13	7	12	1	2	0	0	0	2	0	4	1	3	1	3	2	4	2	3	2	5	5	rs145726955		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr16:19481009C>T	ENST00000396229.2	+	10	2393	c.1644C>T	c.(1642-1644)gcC>gcT	p.A548A	TMC5_ENST00000564959.1_Silent_p.A231A|TMC5_ENST00000381414.4_Silent_p.A548A|TMC5_ENST00000542583.2_Silent_p.A548A|TMC5_ENST00000219821.5_Silent_p.A302A|TMC5_ENST00000561503.1_Silent_p.A189A|TMC5_ENST00000541464.1_Silent_p.A548A	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5	548					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						CTAGCATGGCCAAGTATTTCC	0.473													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17834	0.0		0.0	False		,,,				2504	0.0				p.A548A		Atlas-SNP	.											.	TMC5	169	.	0			c.C1644T						PASS	.	C	,,	8,4386	14.3+/-33.2	0,8,2189	112	103	106		1644,1644,906	2.5	1	16	dbSNP_134	106	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	TMC5	NM_001105248.1,NM_001105249.1,NM_024780.4	,,	0,8,6489	TT,TC,CC		0.0,0.1821,0.0616	,,	548/1007,548/949,302/761	19481009	8,12986	2197	4300	6497	SO:0001819	synonymous_variant	79838	exon10			CATGGCCAAGTAT	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.1644C>T	16.37:g.19481009C>T		113	0	0		304	94	0.309211	NM_001105249	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	Silent	SNP	ENST00000396229.2	37	CCDS45431.1																																																																																			C|0.999;T|0.001	0.001	strong		0.473	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	NM_024780		T	19481009	C	T	19481009	2	4	12	1	0	0	0	0	0	0	0	1	16003	581	21	2		2	TMC5	16	19481009	Silent	SNP	C	TCGA-FF-8043-01A-11D-2210-10	3318849	19481009	70873744	87	1661											
CP110	9738	hgsc.bcm.edu	37	chr16	19556216	19556216	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acttcaggaaagagtgttagCtcaggtaaatacatggatcc	14	10	10	7	0	2	1	2	0	0	1	3	3	3	3	1	3	2	3	1	3	5	4			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr16:19556216C>T	ENST00000381396.5	+	9	2829	c.2582C>T	c.(2581-2583)gCt>gTt	p.A861V	CCP110_ENST00000396208.2_Missense_Mutation_p.A861V|CCP110_ENST00000396212.2_Missense_Mutation_p.A861V	NM_001199022.1	NP_001185951	O43303	CP110_HUMAN	centriolar coiled coil protein 110kDa	861					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						AGAGTGTTAGCTCAGGTAAAT	0.338																																					p.A861V		Atlas-SNP	.											.	CCP110	57	.	0			c.C2582T						PASS	.						106	105	105					16																	19556216		2197	4300	6497	SO:0001583	missense	9738	exon9			TGTTAGCTCAGGT	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.2582C>T	16.37:g.19556216C>T	ENSP00000370803:p.Ala861Val	195	0	0		405	159	0.392593	NM_001199022	B7WP23|O43335|Q68DV9|Q8NE13	Missense_Mutation	SNP	ENST00000381396.5	37	CCDS55992.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.795586	0.90453	.	.	ENSG00000103540	ENST00000396212;ENST00000381396;ENST00000396208	T;T;T	0.17370	2.28;2.29;2.28	5.48	5.48	0.80851	.	0.057778	0.64402	D	0.000002	T	0.38161	0.1030	L	0.53249	1.67	0.58432	D	0.999999	D;D	0.59767	0.986;0.986	D;D	0.67103	0.949;0.949	T	0.01757	-1.1280	10	0.39692	T	0.17	-16.6553	19.364	0.94454	0.0:1.0:0.0:0.0	.	861;861	O43303;O43303-2	CP110_HUMAN;.	V	861	ENSP00000379515:A861V;ENSP00000370803:A861V;ENSP00000379511:A861V	ENSP00000370803:A861V	A	+	2	0	CCP110	19463717	1.000000	0.71417	0.991000	0.47740	0.992000	0.81027	4.349000	0.59385	2.547000	0.85894	0.655000	0.94253	GCT	.	.	none		0.338	CCP110-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254284.2	NM_014711		T	19556216	C	T	19556216	3	4	12	1	0	0	0	0	1	0	0	0	3790	797	28	2	2612	2	CP110	16	19556216	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10	75207	19556216	70798537	88	1662											
SULT1A1	6817	hgsc.bcm.edu	37	chr16	28618318	28618318	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagctgtcccaggtcccaggCtcagggtgcaccttggccat	7	8	12	14	0	1	0	1	0	0	0	3	0	3	0	4	4	2	3	4	4	1	1	rs1042014	byFrequency	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr16:28618318C>G	ENST00000395607.1	-	5	726	c.453G>C	c.(451-453)gaG>gaC	p.E151D	SULT1A1_ENST00000569554.1_Missense_Mutation_p.E151D|SULT1A1_ENST00000395609.1_Missense_Mutation_p.E151D|SULT1A1_ENST00000350842.4_Missense_Mutation_p.E73D|SULT1A1_ENST00000314752.7_Missense_Mutation_p.E151D	NM_177530.2|NM_177534.2	NP_803566.1|NP_803878.1	P50225	ST1A1_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 1	151			E -> D (in dbSNP:rs1042014).|E -> Q (in dbSNP:rs1042011).		3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|estrogen metabolic process (GO:0008210)|flavonoid metabolic process (GO:0009812)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|flavonol 3-sulfotransferase activity (GO:0047894)|steroid sulfotransferase activity (GO:0050294)|sulfotransferase activity (GO:0008146)			endometrium(2)|kidney(7)|large_intestine(2)|lung(2)|ovary(1)|stomach(2)	16					Acetaminophen(DB00316)|Tamoxifen(DB00675)	AGGTCCCAGGCTCAGGGTGCA	0.562																																					p.E151D		Atlas-SNP	.											.	SULT1A1	53	.	0			c.G453C						PASS	.						226	167	187					16																	28618318		2197	4300	6497	SO:0001583	missense	6817	exon4			CCCAGGCTCAGGG	U52852	CCDS10637.1, CCDS32420.1	16p12.1	2008-02-05			ENSG00000196502	ENSG00000196502	2.8.2.1	"Sulfotransferases, cytosolic"	11453	protein-coding gene	gene with protein product		171150		STP, STP1		8288252, 8912648	Standard	NM_177534		Approved	P-PST	uc002dqj.3	P50225	OTTHUMG00000131765	ENST00000395607.1:c.453G>C	16.37:g.28618318C>G	ENSP00000378971:p.Glu151Asp	239	0	0		393	248	0.631043	NM_177534	Q2NL71|Q86U58|Q92818|Q9BVU6|Q9UGG7	Missense_Mutation	SNP	ENST00000395607.1	37	CCDS32420.1	.	.	.	.	.	.	.	.	.	.	c	0.006	-2.097513	0.00360	.	.	ENSG00000196502	ENST00000314752;ENST00000350842;ENST00000395609;ENST00000395607	D;D;D;D	0.82344	-1.6;-1.6;-1.6;-1.6	2.42	-4.84	0.03151	Sulfotransferase domain (1);	0.388985	0.26345	N	0.024915	T	0.44808	0.1311	N	0.02345	-0.59	0.22034	N	0.999403	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.55354	-0.8154	10	0.02654	T	1	.	0.2745	0.00236	0.3382:0.2548:0.1587:0.2483	rs1042014;rs1042014	103;73;151	Q59GG0;P50225-2;P50225	.;.;ST1A1_HUMAN	D	151;73;151;151	ENSP00000321988:E151D;ENSP00000329399:E73D;ENSP00000378972:E151D;ENSP00000378971:E151D	ENSP00000321988:E151D	E	-	3	2	SULT1A1	28525819	0.000000	0.05858	0.817000	0.32601	0.539000	0.34962	-2.571000	0.00913	-2.066000	0.00886	-0.840000	0.03056	GAG	C|0.970;G|0.030	0.030	strong		0.562	SULT1A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254694.2	NM_001055		G	28618318	C	G	28618318	3	3	12	1	0	0	0	0	1	0	0	0	15387	796	28	4	450	4	SULT1A1	16	28618318	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10	9062102	28618318	61736435	89	1663											
TUFM	7284	hgsc.bcm.edu	37	chr16	28854369	28854369	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctagaccggtgccaatagtcCggttgccatctcgcagggtg	7	9	13	12	3	1	1	0	0	1	1	3	1	2	1	4	3	2	2	4	3	3	3			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr16:28854369C>T	ENST00000313511.3	-	10	1433	c.1295G>A	c.(1294-1296)cGg>cAg	p.R432Q	MIR4721_ENST00000577590.1_RNA	NM_003321.4	NP_003312.3	P49411	EFTU_HUMAN	Tu translation elongation factor, mitochondrial	429					translational elongation (GO:0006414)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation elongation factor activity (GO:0003746)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	13						GCCAATAGTCCGGTTGCCATC	0.542																																					p.R432Q		Atlas-SNP	.											TUFM,colon,carcinoma,-1,1	TUFM	33	1	0			c.G1295A						PASS	.						171	142	152					16																	28854369		2197	4300	6497	SO:0001583	missense	7284	exon10			ATAGTCCGGTTGC	L38995	CCDS10642.1	16p11.2	2010-10-26			ENSG00000178952	ENSG00000178952			12420	protein-coding gene	gene with protein product		602389				9332382, 9545647	Standard	NM_003321		Approved	EFTu, EF-TuMT, EFTU	uc002drh.2	P49411	OTTHUMG00000097039	ENST00000313511.3:c.1295G>A	16.37:g.28854369C>T	ENSP00000322439:p.Arg432Gln	170	0	0		98	4	0.0408163	NM_003321	O15276	Missense_Mutation	SNP	ENST00000313511.3	37	CCDS10642.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.734727	0.48939	.	.	ENSG00000178952	ENST00000313511	T	0.73258	-0.73	4.92	2.46	0.29980	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal (1);Translation elongation factor EFTu/EF1A, C-terminal (1);	0.448187	0.22595	N	0.058034	T	0.57740	0.2074	L	0.38838	1.175	0.25971	N	0.982508	B	0.12013	0.005	B	0.10450	0.005	T	0.55438	-0.8141	10	0.87932	D	0	-5.2056	8.3795	0.32463	0.0:0.6754:0.0:0.3246	.	429	P49411	EFTU_HUMAN	Q	432	ENSP00000322439:R432Q	ENSP00000322439:R432Q	R	-	2	0	TUFM	28761870	0.522000	0.26266	1.000000	0.80357	0.871000	0.50021	0.842000	0.27627	0.870000	0.35726	0.655000	0.94253	CGG	.	.	none		0.542	TUFM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214140.1	NM_003321		T	28854369	C	T	28854369	3	4	12	1	0	0	0	0	1	0	0	0	16786	652	23	1	76	1	TUFM	16	28854369	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10	236051	28854369	61500384	90	1664											
CDH5	1003	hgsc.bcm.edu	37	chr16	66423379	66423379	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcgggcacggccaccgtgctGgtcactctgcaagacatcaa	9	7	11	14	3	3	1	2	0	1	1	4	1	3	1	2	3	2	3	2	3	2	0			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr16:66423379G>A	ENST00000341529.3	+	5	883	c.735G>A	c.(733-735)ctG>ctA	p.L245L	CDH5_ENST00000563425.2_Silent_p.L245L	NM_001795.3	NP_001786.2	P33151	CADH5_HUMAN	cadherin 5, type 2 (vascular endothelium)	245	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)	CCACCGTGCTGGTCACTCTGC	0.627																																					p.L245L		Atlas-SNP	.											.	CDH5	111	.	0			c.G735A						PASS	.						64	62	63					16																	66423379		2202	4300	6502	SO:0001819	synonymous_variant	1003	exon5			CGTGCTGGTCACT	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.735G>A	16.37:g.66423379G>A		144	0	0		91	57	0.626374	NM_001795	Q4VAI5|Q4VAI6	Silent	SNP	ENST00000341529.3	37	CCDS10804.1																																																																																			.	.	none		0.627	CDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268767.1	NM_001795		A	66423379	G	A	66423379	2	1	12	1	0	0	0	0	0	0	0	1	3115	1335	47	2		2	CDH5	16	66423379	Silent	SNP	G	TCGA-FF-8043-01A-11D-2210-10	37569010	66423379	23931374	91	1665											
CDH5	1003	hgsc.bcm.edu	37	chr16	66423409	66423409	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	caagacatcaatgacaacttCcccttcttcacccagagtga	13	9	5	14	0	3	4	2	2	1	2	4	4	4	4	3	0	1	0	3	0	3	3			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr16:66423409C>T	ENST00000341529.3	+	5	913	c.765C>T	c.(763-765)ttC>ttT	p.F255F	CDH5_ENST00000563425.2_Silent_p.F255F	NM_001795.3	NP_001786.2	P33151	CADH5_HUMAN	cadherin 5, type 2 (vascular endothelium)	255	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)	ATGACAACTTCCCCTTCTTCA	0.612																																					p.F255F		Atlas-SNP	.											.	CDH5	111	.	0			c.C765T						PASS	.						59	57	58					16																	66423409		2202	4300	6502	SO:0001819	synonymous_variant	1003	exon5			CAACTTCCCCTTC	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.765C>T	16.37:g.66423409C>T		129	0	0		82	5	0.0609756	NM_001795	Q4VAI5|Q4VAI6	Silent	SNP	ENST00000341529.3	37	CCDS10804.1																																																																																			.	.	none		0.612	CDH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268767.1	NM_001795		T	66423409	C	T	66423409	2	4	12	1	0	0	0	0	0	0	0	1	3115	854	30	2		2	CDH5	16	66423409	Silent	SNP	C	TCGA-FF-8043-01A-11D-2210-10	30	66423409	23931344	92	1666											
NQO1	1728	hgsc.bcm.edu	37	chr16	69745172	69745172	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gacttggaagccacagaaatGcagaatgccactctgaggat	14	7	11	9	0	1	3	0	1	1	2	1	6	1	5	2	2	3	1	2	2	3	1	rs148539025	byFrequency	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr16:69745172G>A	ENST00000320623.5	-	6	1043	c.532C>T	c.(532-534)Cat>Tat	p.H178Y	snoU13_ENST00000459361.1_RNA|NQO1_ENST00000439109.2_Missense_Mutation_p.H106Y|NQO1_ENST00000564043.1_Missense_Mutation_p.H157Y|NQO1_ENST00000379046.2_Missense_Mutation_p.H140Y|CTD-2033A16.1_ENST00000562696.1_RNA|NQO1_ENST00000379047.3_Missense_Mutation_p.H144Y|NQO1_ENST00000561500.1_Missense_Mutation_p.H140Y	NM_000903.2	NP_000894.1	P15559	NQO1_HUMAN	NAD(P)H dehydrogenase, quinone 1	178					aging (GO:0007568)|cellular nitrogen compound metabolic process (GO:0034641)|negative regulation of catalytic activity (GO:0043086)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cellular amino acid metabolic process (GO:0006521)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|synaptic transmission, cholinergic (GO:0007271)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|NAD(P)H dehydrogenase (quinone) activity (GO:0003955)|poly(A) RNA binding (GO:0044822)|superoxide dismutase activity (GO:0004784)			autonomic_ganglia(1)|large_intestine(2)|lung(5)|prostate(1)|stomach(1)	10					Carboplatin(DB00958)|Cisplatin(DB00515)|Dicoumarol(DB00266)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|Menadione(DB00170)|Oxaliplatin(DB00526)|Vitamin E(DB00163)	CCACAGAAATGCAGAATGCCA	0.458													G|||	3	0.000599042	0.0023	0.0	5008	,	,		21546	0.0		0.0	False		,,,				2504	0.0				p.H178Y		Atlas-SNP	.											.	NQO1	21	.	0			c.C532T						PASS	.	G	TYR/HIS,TYR/HIS,TYR/HIS	4,4392	8.1+/-20.4	0,4,2194	132	135	134		532,430,418	1.3	1	16	dbSNP_134	134	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	NQO1	NM_000903.2,NM_001025433.1,NM_001025434.1	83,83,83	0,5,6493	AA,AG,GG		0.0116,0.091,0.0385	benign,benign,benign	178/275,144/241,140/237	69745172	5,12991	2198	4300	6498	SO:0001583	missense	1728	exon6			AGAAATGCAGAAT	M81600	CCDS10883.1, CCDS32471.1, CCDS32472.1, CCDS67067.1	16q12-q22	2012-10-02	2001-11-30	2001-12-07	ENSG00000181019	ENSG00000181019	1.6.5.2		2874	protein-coding gene	gene with protein product		125860	"diaphorase (NADH/NADPH) (cytochrome b-5 reductase)"	NMOR1, DIA4		2843525	Standard	NM_001286137		Approved	DHQU, QR1, DTD	uc002exp.3	P15559	OTTHUMG00000137575	ENST00000320623.5:c.532C>T	16.37:g.69745172G>A	ENSP00000319788:p.His178Tyr	76	0	0		86	4	0.0465116	NM_000903	B2R5Y9|B4DNM7|B7ZAD1|Q86UK1	Missense_Mutation	SNP	ENST00000320623.5	37	CCDS10883.1	.	.	.	.	.	.	.	.	.	.	G	13.29	2.193510	0.38707	9.1E-4	1.16E-4	ENSG00000181019	ENST00000320623;ENST00000379047;ENST00000379046;ENST00000439109	T;T;T;T	0.10099	2.91;3.15;3.15;3.15	5.41	1.26	0.21427	Flavodoxin-like fold (1);	0.392618	0.30428	N	0.009659	T	0.05823	0.0152	N	0.16478	0.41	0.32949	D	0.51943	B;B;B;B	0.18610	0.005;0.029;0.006;0.028	B;B;B;B	0.23716	0.005;0.048;0.005;0.014	T	0.36040	-0.9764	10	0.12430	T	0.62	-2.5129	9.1805	0.37138	0.3053:0.0:0.6947:0.0	.	106;140;144;178	B4DLR8;B4DNM7;B7ZAD1;P15559	.;.;.;NQO1_HUMAN	Y	178;144;140;106	ENSP00000319788:H178Y;ENSP00000368335:H144Y;ENSP00000368334:H140Y;ENSP00000398330:H106Y	ENSP00000319788:H178Y	H	-	1	0	NQO1	68302673	1.000000	0.71417	0.995000	0.50966	0.989000	0.77384	1.942000	0.40243	0.355000	0.24131	0.655000	0.94253	CAT	G|1.000;A|0.000	0.000	weak		0.458	NQO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268956.2			A	69745172	G	A	69745172	3	1	12	1	0	0	0	0	1	0	0	0	10620	1319	46	2	296	2	NQO1	16	69745172	Missense_Mutation	SNP	G	TCGA-FF-8043-01A-11D-2210-10	3321763	69745172	20609581	93	1667											
TP53	7157	hgsc.bcm.edu	37	chr17	7578419	7578419	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggggcagcgcctcacaacctCcgtcatgtgctgtgactgct	6	9	12	14	2	2	1	2	1	0	0	3	1	3	1	3	2	4	3	3	2	1	0	rs587781845		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	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_ENST00000455263.2_Nonsense_Mutation_p.E171*|TP53_ENST00000574684.1_5'UTR|TP53_ENST00000445888.2_Nonsense_Mutation_p.E171*|TP53_ENST00000359597.4_Nonsense_Mutation_p.E171*|TP53_ENST00000420246.2_Nonsense_Mutation_p.E171*	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)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"L, E, M, O"	TP53_ENST00000545858,bladder,carcinoma,0,47	TP53	33396	47	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						PASS	.						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*	137	0	0		83	72	0.86747	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	.	.	none		0.662	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7578419	C	A	7578419	4	1	12	1	0	0	0	0	0	1	0	0	16396	864	30	4	787	4	TP53	17	7578419	Nonsense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10		7578419	73616791	94	1668											
SMCR8	140775	hgsc.bcm.edu	37	chr17	18220270	18220270	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtggagaaacaagaaagcatAccctctaagcccagtcaaga	17	5	9	10	0	2	3	1	0	1	3	2	4	2	3	2	1	4	1	2	1	6	2			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr17:18220270A>G	ENST00000406438.3	+	1	1647	c.1167A>G	c.(1165-1167)atA>atG	p.I389M	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	389						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						AAGAAAGCATACCCTCTAAGC	0.423																																					p.I389M		Atlas-SNP	.											.	SMCR8	62	.	0			c.A1167G						PASS	.						117	113	114					17																	18220270		2203	4300	6503	SO:0001583	missense	140775	exon1			AAGCATACCCTCT	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.1167A>G	17.37:g.18220270A>G	ENSP00000385025:p.Ile389Met	115	0	0		137	6	0.0437956	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Missense_Mutation	SNP	ENST00000406438.3	37	CCDS11195.2	.	.	.	.	.	.	.	.	.	.	A	1.223	-0.626275	0.03610	.	.	ENSG00000176994	ENST00000406438	T	0.22134	1.97	5.9	-10.4	0.00318	.	1.175130	0.06061	N	0.658377	T	0.05640	0.0148	N	0.02011	-0.69	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.36456	-0.9747	10	0.30854	T	0.27	-20.6322	6.4044	0.21656	0.1744:0.1901:0.4992:0.1362	.	389	Q8TEV9	SMCR8_HUMAN	M	389	ENSP00000385025:I389M	ENSP00000385025:I389M	I	+	3	3	SMCR8	18160995	0.000000	0.05858	0.000000	0.03702	0.276000	0.26787	-0.920000	0.04013	-1.650000	0.01506	-0.263000	0.10527	ATA	.	.	none		0.423	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775		G	18220270	A	G	18220270	3	3	12	1	0	0	0	0	1	0	0	0	14807	381	14	3	1169	3	SMCR8	17	18220270	Missense_Mutation	SNP	A	TCGA-FF-8043-01A-11D-2210-10	10641851	18220270	62974940	95	1669											
SUPT6H	6830	hgsc.bcm.edu	37	chr17	27010108	27010108	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccccaccaagaaaggtagaAaggtgagctgggtgaagggc	13	4	15	9	0	0	4	0	2	0	2	0	4	0	4	3	4	1	2	3	4	5	1			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr17:27010108A>G	ENST00000314616.6	+	15	2159	c.1876A>G	c.(1876-1878)Aag>Gag	p.K626E	SUPT6H_ENST00000347486.4_Missense_Mutation_p.K626E	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	626	Interaction with KDM6A. {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)					GAAAGGTAGAAAGGTGAGCTG	0.512																																					p.K626E		Atlas-SNP	.											.	SUPT6H	165	.	0			c.A1876G						PASS	.						28	26	26					17																	27010108		2203	4300	6503	SO:0001583	missense	6830	exon15			GGTAGAAAGGTGA	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.1876A>G	17.37:g.27010108A>G	ENSP00000319104:p.Lys626Glu	56	0	0		70	31	0.442857	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Missense_Mutation	SNP	ENST00000314616.6	37	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	A	13.21	2.167849	0.38315	.	.	ENSG00000109111	ENST00000314616	T	0.39997	1.05	5.95	5.95	0.96441	Tex-like domain (1);	0.000000	0.85682	D	0.000000	T	0.36826	0.0981	L	0.55481	1.735	0.58432	D	0.999999	B	0.33103	0.397	B	0.28011	0.085	T	0.18053	-1.0349	10	0.33940	T	0.23	-27.6642	12.212	0.54386	0.9322:0.0:0.0678:0.0	.	626	Q7KZ85	SPT6H_HUMAN	E	626	ENSP00000319104:K626E	ENSP00000319104:K626E	K	+	1	0	SUPT6H	24034235	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.068000	0.76748	2.279000	0.76181	0.533000	0.62120	AAG	.	.	none		0.512	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		G	27010108	A	G	27010108	3	3	12	1	0	0	0	0	1	0	0	0	15415	15	1	3	1930	3	SUPT6H	17	27010108	Missense_Mutation	SNP	A	TCGA-FF-8043-01A-11D-2210-10	8789838	27010108	54185102	96	1670											
SUMO2	6613	hgsc.bcm.edu	37	chr17	73177275	73177275	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgatcgttgttctcagtcttGactccttcctgttaaaagaa	9	16	7	9	1	2	3	1	2	2	1	6	3	4	3	2	0	0	3	2	0	3	5			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr17:73177275G>A	ENST00000420826.2	-	2	178	c.30C>T	c.(28-30)gtC>gtT	p.V10V	SUMO2_ENST00000578238.1_5'UTR|SUMO2_ENST00000314523.7_Silent_p.V10V	NM_006937.3	NP_008868.3			small ubiquitin-like modifier 2											NS(1)	1	all_lung(278;0.14)|Lung NSC(278;0.168)					TCTCAGTCTTGACTCCTTCCT	0.378																																					p.V10V		Atlas-SNP	.											.	SUMO2	4	.	0			c.C30T						PASS	.						32	35	34					17																	73177275		2195	4297	6492	SO:0001819	synonymous_variant	6613	exon2			AGTCTTGACTCCT		CCDS45773.1, CCDS45774.1	17q25	2013-06-05	2013-06-05	2004-05-19	ENSG00000188612	ENSG00000188612			11125	protein-coding gene	gene with protein product		603042	"SMT3 (suppressor of mif two 3, yeast) homolog 2", "SMT3 suppressor of mif two 3 homolog 2 (yeast)", "SMT3 suppressor of mif two 3 homolog 2 (S. cerevisiae)"	SMT3H2		8630065	Standard	NM_006937		Approved	SMT3B	uc002jne.3	P61956		ENST00000420826.2:c.30C>T	17.37:g.73177275G>A		131	0	0		115	60	0.521739	NM_006937		Silent	SNP	ENST00000420826.2	37	CCDS45774.1																																																																																			.	.	none		0.378	SUMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446614.1	NM_006937		A	73177275	G	A	73177275	2	1	12	1	0	0	0	0	0	0	0	1	15403	1277	45	2		2	SUMO2	17	73177275	Silent	SNP	G	TCGA-FF-8043-01A-11D-2210-10	46167167	73177275	8017935	97	1671											
ENPP7	339221	hgsc.bcm.edu	37	chr17	77709108	77709108	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcggcaggtggaccggacCgtgggctacctccgggagag	6	5	19	11	4	0	1	0	0	0	1	1	4	1	3	4	6	2	2	4	6	1	1			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr17:77709108C>T	ENST00000328313.5	+	3	887	c.666C>T	c.(664-666)acC>acT	p.T222T		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)			TGGACCGGACCGTGGGCTACC	0.657																																					p.T222T		Atlas-SNP	.											.	ENPP7	63	.	0			c.C666T						PASS	.						53	51	51					17																	77709108		2203	4300	6503	SO:0001819	synonymous_variant	339221	exon3			CCGGACCGTGGGC	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.666C>T	17.37:g.77709108C>T		35	0	0		41	17	0.414634	NM_178543		Silent	SNP	ENST00000328313.5	37	CCDS11763.1																																																																																			.	.	none		0.657	ENPP7-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437038.1	NM_178543		T	77709108	C	T	77709108	2	4	12	1	0	0	0	0	0	0	0	1	5137	639	23	1		1	ENPP7	17	77709108	Silent	SNP	C	TCGA-FF-8043-01A-11D-2210-10	4531833	77709108	3486102	98	1672											
RNF213	57674	hgsc.bcm.edu	37	chr17	78332155	78332155	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cgagcatgatatcattcatcGacagagacggcaacctagag	14	7	10	10	3	2	3	2	1	0	2	3	6	2	3	1	1	2	2	1	1	3	3			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr17:78332155G>A	ENST00000582970.1	+	37	11073	c.10930G>A	c.(10930-10932)Gac>Aac	p.D3644N	CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000508628.2_Missense_Mutation_p.D3693N|CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000336301.6_Missense_Mutation_p.D1717N	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3644					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)			ATCATTCATCGACAGAGACGG	0.542																																					p.D3644N		Atlas-SNP	.											.	RNF213	766	.	0			c.G10930A						PASS	.						104	86	92					17																	78332155		2203	4300	6503	SO:0001583	missense	57674	exon37			TTCATCGACAGAG	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.10930G>A	17.37:g.78332155G>A	ENSP00000464087:p.Asp3644Asn	121	0	0		123	6	0.0487805	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.990624	0.74589	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301	T	0.53206	0.63	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.72977	0.3528	M	0.84511	2.7	0.39810	D	0.972696	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.78191	-0.2300	10	0.72032	D	0.01	.	17.3431	0.87303	0.0:0.0:1.0:0.0	.	3693;1717	C9JCP4;Q63HN8	.;RN213_HUMAN	N	3644;3693;1717	ENSP00000338218:D1717N	ENSP00000338218:D1717N	D	+	1	0	RNF213	75946750	1.000000	0.71417	0.312000	0.25196	0.177000	0.22998	7.921000	0.87530	2.612000	0.88384	0.637000	0.83480	GAC	.	.	none		0.542	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		A	78332155	G	A	78332155	3	1	12	1	0	0	0	0	1	0	0	0	13492	1058	37	1	11391	1	RNF213	17	78332155	Missense_Mutation	SNP	G	TCGA-FF-8043-01A-11D-2210-10	623047	78332155	2863055	99	1673											
NPLOC4	55666	hgsc.bcm.edu	37	chr17	79532602	79532602	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgagctcctcatttctggtcCgcacggcctccagcagcaag	7	8	10	16	3	2	0	1	0	1	0	5	1	5	0	4	2	3	4	4	2	1	1	rs371370139		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr17:79532602C>T	ENST00000331134.6	-	16	1813	c.1598G>A	c.(1597-1599)cGg>cAg	p.R533Q	NPLOC4_ENST00000374747.5_Missense_Mutation_p.R533Q|NPLOC4_ENST00000539314.1_Missense_Mutation_p.R372Q|NPLOC4_ENST00000572760.1_5'UTR|NPLOC4_ENST00000573876.1_5'UTR	NM_017921.2	NP_060391.2	Q8TAT6	NPL4_HUMAN	nuclear protein localization 4 homolog (S. cerevisiae)	533					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)			ATTTCTGGTCCGCACGGCCTC	0.597																																					p.R533Q		Atlas-SNP	.											.	NPLOC4	27	.	0			c.G1598A						PASS	.	C	GLN/ARG	0,4110		0,0,2055	16	20	19		1598	5	0.9	17		19	1,8323		0,1,4161	no	missense	NPLOC4	NM_017921.2	43	0,1,6216	TT,TC,CC		0.012,0.0,0.0080	possibly-damaging	533/609	79532602	1,12433	2055	4162	6217	SO:0001583	missense	55666	exon16			CTGGTCCGCACGG	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.1598G>A	17.37:g.79532602C>T	ENSP00000331487:p.Arg533Gln	34	0	0		32	4	0.125	NM_017921	Q8N3J1|Q9H8V2|Q9H964|Q9NWR5|Q9P229	Missense_Mutation	SNP	ENST00000331134.6	37	CCDS45812.1	.	.	.	.	.	.	.	.	.	.	C	13.82	2.350695	0.41599	0.0	1.2E-4	ENSG00000182446	ENST00000331134;ENST00000374747;ENST00000539314	.	.	.	5.02	5.02	0.67125	Nuclear pore localisation protein NPL4 (1);	0.095949	0.64402	D	0.000002	T	0.62258	0.2413	M	0.70787	2.145	0.53005	D	0.999964	P;D;P	0.52996	0.636;0.957;0.894	B;B;P	0.44897	0.354;0.424;0.463	T	0.64909	-0.6296	9	0.36615	T	0.2	-33.3332	18.5911	0.91212	0.0:1.0:0.0:0.0	.	372;533;533	B4DG89;Q8TAT6-2;Q8TAT6	.;.;NPL4_HUMAN	Q	533;532;372	.	ENSP00000331487:R533Q	R	-	2	0	NPLOC4	77143044	1.000000	0.71417	0.944000	0.38274	0.130000	0.20726	3.250000	0.51445	2.628000	0.89032	0.650000	0.86243	CGG	.	.	weak		0.597	NPLOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440140.1			T	79532602	C	T	79532602	3	4	12	1	0	0	0	0	1	0	0	0	10595	652	23	1	236	1	NPLOC4	17	79532602	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10	1200447	79532602	1662608	100	1674											
JSRP1	126306	hgsc.bcm.edu	37	chr19	2254194	2254194	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctgcaaacccactcgctccgGctttcagcctctccttcccc	5	10	5	21	2	2	0	1	0	1	0	6	0	4	0	6	1	3	3	6	1	1	2			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr19:2254194G>T	ENST00000300961.6	-	4	318	c.254C>A	c.(253-255)gCc>gAc	p.A85D	JSRP1_ENST00000586471.2_Missense_Mutation_p.A85D	NM_144616.3	NP_653217.1	Q96MG2	JSPR1_HUMAN	junctional sarcoplasmic reticulum protein 1	85					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)		ACTCGCTCCGGCTTTCAGCCT	0.642											OREG0025137	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A85D		Atlas-SNP	.											.	JSRP1	18	.	0			c.C254A						PASS	.						133	131	132					19																	2254194		2203	4300	6503	SO:0001583	missense	126306	exon4			GCTCCGGCTTTCA	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.254C>A	19.37:g.2254194G>T	ENSP00000300961:p.Ala85Asp	60	0	0	602	62	24	0.387097	NM_144616		Missense_Mutation	SNP	ENST00000300961.6	37	CCDS12086.1	.	.	.	.	.	.	.	.	.	.	G	13.15	2.150195	0.37923	.	.	ENSG00000167476	ENST00000300961	T	0.22336	1.96	3.24	-0.348	0.12613	.	0.669075	0.12336	N	0.477943	T	0.14657	0.0354	L	0.29908	0.895	0.09310	N	1	P	0.47677	0.899	P	0.45099	0.469	T	0.14783	-1.0460	10	0.87932	D	0	-0.0226	2.9112	0.05738	0.2903:0.245:0.4647:0.0	.	85	Q96MG2	JSPR1_HUMAN	D	85	ENSP00000300961:A85D	ENSP00000300961:A85D	A	-	2	0	JSRP1	2205194	0.000000	0.05858	0.259000	0.24435	0.174000	0.22865	-0.004000	0.12878	0.137000	0.18759	0.555000	0.69702	GCC	.	.	none		0.642	JSRP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451266.2	NM_144616		T	2254194	G	T	2254194	3	4	12	1	0	0	0	0	1	0	0	0	7975	1203	42	4	757	4	JSRP1	19	2254194	Missense_Mutation	SNP	G	TCGA-FF-8043-01A-11D-2210-10		2254194	56874789	101	1675											
TUBB4	10382	hgsc.bcm.edu	37	chr19	6495416	6495416	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctgttgccgatgaaggtcGcggccatcttcaggccgcgg	5	9	15	12	5	2	1	1	1	1	0	3	2	2	1	3	4	2	2	3	4	1	2	rs1053267		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr19:6495416G>A	ENST00000264071.2	-	4	1465	c.1094C>T	c.(1093-1095)gCg>gTg	p.A365V	TUBB4A_ENST00000540257.1_Missense_Mutation_p.A365V|CTD-2396E7.9_ENST00000599292.1_RNA|CTD-2396E7.10_ENST00000596027.1_RNA			P04350	TBB4A_HUMAN	tubulin, beta 4A class IVa	365			A -> V (in dbSNP:rs1053267). {ECO:0000269|PubMed:6462917}.		'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)										GATGAAGGTCGCGGCCATCTT	0.617																																					p.A365V		Atlas-SNP	.											TUBB4,colon,carcinoma,+1,1	.	.	1	0			c.C1094T						scavenged	.						176	154	162					19																	6495416		2203	4300	6503	SO:0001583	missense	10382	exon4			AAGGTCGCGGCCA	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.1094C>T	19.37:g.6495416G>A	ENSP00000264071:p.Ala365Val	98	1	0.0102041		108	57	0.527778	NM_006087	B3KQP4|Q969E5	Missense_Mutation	SNP	ENST00000264071.2	37	CCDS12168.1	.	.	.	.	.	.	.	.	.	.	G	11.03	1.519188	0.27211	.	.	ENSG00000104833	ENST00000264071;ENST00000540257;ENST00000412858	D;D	0.83837	-1.77;-1.77	3.43	3.43	0.39272	.	0.000000	0.64402	U	0.000003	T	0.71525	0.3350	N	0.16478	0.41	0.48452	D	0.999651	B	0.14012	0.009	B	0.12837	0.008	T	0.70594	-0.4829	10	0.87932	D	0	.	13.6752	0.62449	0.0:0.0:1.0:0.0	rs1053267	365	P04350	TBB4A_HUMAN	V	365;365;283	ENSP00000264071:A365V;ENSP00000443590:A365V	ENSP00000264071:A365V	A	-	2	0	TUBB4	6446416	1.000000	0.71417	0.965000	0.40720	0.833000	0.47200	5.606000	0.67641	1.473000	0.48159	0.306000	0.20318	GCG	G|1.000;|0.000	.	weak		0.617	TUBB4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457841.1	NM_006087		A	6495416	G	A	6495416	3	1	12	1	0	0	0	0	1	0	0	0	16773	1087	38	1	244	1	TUBB4	19	6495416	Missense_Mutation	SNP	G	TCGA-FF-8043-01A-11D-2210-10	4241222	6495416	52633567	102	1676											
ZNF20	7568	hgsc.bcm.edu	37	chr19	12243529	12243529	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttcatgatatcgaatgtaaTtggaaataaaggccttacca	15	13	7	6	1	1	1	1	1	0	0	2	3	1	2	2	2	1	1	2	2	7	6	rs557758485		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr19:12243529T>C	ENST00000334213.5	-	4	1696	c.1472A>G	c.(1471-1473)aAt>aGt	p.N491S	ZNF20_ENST00000485451.1_5'Flank|ZNF625-ZNF20_ENST00000430024.1_3'UTR|ZNF20_ENST00000600335.1_Intron	NM_001203250.1|NM_021143.3	NP_001190179.1|NP_066966.2	P17024	ZNF20_HUMAN	zinc finger protein 20	491					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						TCGAATGTAATTGGAAATAAA	0.418													T|||	1	0.000199681	0.0008	0.0	5008	,	,		22095	0.0		0.0	False		,,,				2504	0.0				p.N491S		Atlas-SNP	.											.	ZNF20	86	.	0			c.A1472G						PASS	.						172	183	179					19																	12243529		2203	4298	6501	SO:0001583	missense	7568	exon4			ATGTAATTGGAAA	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.1472A>G	19.37:g.12243529T>C	ENSP00000335437:p.Asn491Ser	85	0	0		78	38	0.487179	NM_021143	Q8N457|Q9UG41	Missense_Mutation	SNP	ENST00000334213.5	37	CCDS45986.1	.	.	.	.	.	.	.	.	.	.	T	0.165	-1.077307	0.01903	.	.	ENSG00000132010	ENST00000334213;ENST00000292241	T	0.05319	3.46	0.94	-1.88	0.07713	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00875	0.0029	N	0.00064	-2.31	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.40572	-0.9556	9	0.02654	T	1	.	2.726	0.05214	0.0:0.268:0.2608:0.4712	.	491	P17024	ZNF20_HUMAN	S	491	ENSP00000335437:N491S	ENSP00000292241:N491S	N	-	2	0	ZNF20	12104529	0.000000	0.05858	0.001000	0.08648	0.910000	0.53928	-3.261000	0.00536	-0.843000	0.04189	0.260000	0.18958	AAT	.	.	none		0.418	ZNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344101.1	NM_021143		C	12243529	T	C	12243529	3	2	12	1	0	0	0	0	1	0	0	0	17776	1493	52	3	130	3	ZNF20	19	12243529	Missense_Mutation	SNP	T	TCGA-FF-8043-01A-11D-2210-10	5748113	12243529	46885454	103	1677											
RTBDN	83546	hgsc.bcm.edu	37	chr19	12936596	12936596	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggtgcgagggctgcgggaaCgccgggagggagcttcccgg	6	4	21	10	5	0	0	0	0	0	0	1	4	1	3	2	6	4	2	2	6	1	1			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr19:12936596C>T	ENST00000458671.2	-	6	766	c.614G>A	c.(613-615)cGt>cAt	p.R205H	RTBDN_ENST00000393233.2_3'UTR|RTBDN_ENST00000322912.5_Missense_Mutation_p.R237H|RTBDN_ENST00000592204.1_Missense_Mutation_p.R215H|RTBDN_ENST00000589272.1_3'UTR|CTD-2265O21.3_ENST00000588469.1_RNA	NM_001080997.2	NP_001074466.1	Q9BSG5	RTBDN_HUMAN	retbindin	205						extracellular region (GO:0005576)				kidney(1)|large_intestine(5)|liver(1)|lung(4)|prostate(1)	12						GCTGCGGGAACGCCGGGAGGG	0.711											OREG0025275	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R237H		Atlas-SNP	.											.	RTBDN	26	.	0			c.G710A						PASS	.						17	17	17					19																	12936596		2199	4289	6488	SO:0001583	missense	83546	exon7			CGGGAACGCCGGG	AY028917	CCDS12283.1, CCDS45994.1, CCDS59355.1, CCDS59356.1	19p13	2006-03-22				ENSG00000132026			30310	protein-coding gene	gene with protein product		609553				12107411	Standard	NM_001080997		Approved	FLJ36353	uc002mvj.4	Q9BSG5		ENST00000458671.2:c.614G>A	19.37:g.12936596C>T	ENSP00000416375:p.Arg205His	123	0	0	683	131	53	0.40458	NM_031429	F1T0I8|Q9BWT5	Missense_Mutation	SNP	ENST00000458671.2	37	CCDS45994.1	.	.	.	.	.	.	.	.	.	.	C	13.98	2.399729	0.42512	.	.	ENSG00000132026	ENST00000322912;ENST00000458671	T;T	0.58358	0.34;0.44	3.32	1.17	0.20885	.	0.665039	0.12535	N	0.460449	T	0.54515	0.1863	L	0.32530	0.975	0.09310	N	0.999993	D;D	0.89917	1.0;1.0	D;D	0.71414	0.973;0.939	T	0.37709	-0.9694	10	0.87932	D	0	-27.7491	4.204	0.10480	0.0:0.621:0.2441:0.1349	.	237;205	Q9BSG5-2;Q9BSG5	.;RTBDN_HUMAN	H	237;205	ENSP00000326253:R237H;ENSP00000416375:R205H	ENSP00000326253:R237H	R	-	2	0	RTBDN	12797596	0.000000	0.05858	0.012000	0.15200	0.141000	0.21300	-0.190000	0.09615	0.760000	0.33108	-0.195000	0.12781	CGT	.	.	none		0.711	RTBDN-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000451513.1	NM_031429		T	12936596	C	T	12936596	3	4	12	1	0	0	0	0	1	0	0	0	13732	536	19	1	79	1	RTBDN	19	12936596	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10	693067	12936596	46192387	104	1678											
OR10H5	284433	hgsc.bcm.edu	37	chr19	15905664	15905664	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccaaaggtccccagtctcCggaaggagacaccttgatgg	10	6	12	13	1	1	2	0	1	1	1	3	4	2	3	5	4	0	0	5	4	2	1	rs144567857	byFrequency	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr19:15905664C>T	ENST00000308940.8	+	1	904	c.806C>T	c.(805-807)cCg>cTg	p.P269L		NM_001004466.1	NP_001004466.1	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H, member 5	269						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)|liver(1)|lung(9)|ovary(1)	20						CCCCAGTCTCCGGAAGGAGAC	0.567													.|||	5	0.000998403	0.003	0.0014	5008	,	,		17105	0.0		0.0	False		,,,				2504	0.0				p.P269L		Atlas-SNP	.											OR10H5,NS,carcinoma,-1,1	OR10H5	49	1	0			c.C806T						scavenged	.						111	90	98					19																	15905664		2203	4300	6503	SO:0001583	missense	284433	exon1			AGTCTCCGGAAGG	AC011537	CCDS32940.1	19p13.12	2013-09-24			ENSG00000172519	ENSG00000172519		"GPCR / Class A : Olfactory receptors"	15389	protein-coding gene	gene with protein product							Standard	NM_001004466		Approved		uc010xos.2	Q8NGA6	OTTHUMG00000182284	ENST00000308940.8:c.806C>T	19.37:g.15905664C>T	ENSP00000310704:p.Pro269Leu	222	1	0.0045045		173	63	0.364162	NM_001004466	Q6IFJ0|Q96R60	Missense_Mutation	SNP	ENST00000308940.8	37	CCDS32940.1	5	0.0022893772893772895	1	0.0020325203252032522	0	0.0	0	0.0	4	0.005277044854881266	.	0	-2.679788	0.00102	.	.	ENSG00000172519	ENST00000308940	T	0.00207	8.55	3.88	-4.19	0.03835	GPCR, rhodopsin-like superfamily (1);	0.571038	0.14488	N	0.316535	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	0.14200	-1.0481	10	0.26408	T	0.33	.	2.5734	0.04800	0.2427:0.418:0.1238:0.2154	.	269	Q8NGA6	O10H5_HUMAN	L	269	ENSP00000310704:P269L	ENSP00000310704:P269L	P	+	2	0	OR10H5	15766664	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.821000	0.00749	-1.726000	0.01370	-4.535000	0.00005	CCG	C|0.998;T|0.002	0.002	strong		0.567	OR10H5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460363.1			T	15905664	C	T	15905664	3	4	12	1	0	0	0	0	1	0	0	0	10918	652	23	1	808	1	OR10H5	19	15905664	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10	2969068	15905664	43223319	105	1679											
ZNF224	7767	hgsc.bcm.edu	37	chr19	44605366	44605366	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgaagacagcaatccaaaggGaagggaattcaggtaagaat	18	6	12	5	0	1	3	1	1	0	2	2	5	2	5	1	3	1	2	1	3	7	2			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr19:44605366G>T	ENST00000336976.6	+	5	477	c.223G>T	c.(223-225)Gaa>Taa	p.E75*	AC084219.3_ENST00000591772.1_RNA	NM_013398.2	NP_037530.2	Q9NZL3	ZN224_HUMAN	zinc finger protein 224	75	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)				AATCCAAAGGGAAGGGAATTC	0.438																																					p.E75X		Atlas-SNP	.											.	ZNF224	70	.	0			c.G223T						PASS	.						115	106	109					19																	44605366		2203	4300	6503	SO:0001587	stop_gained	7767	exon5			CAAAGGGAAGGGA	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.223G>T	19.37:g.44605366G>T	ENSP00000337368:p.Glu75*	87	0	0		43	21	0.488372	NM_013398	A6NFW9|P17033|Q86V10|Q8IZC8|Q9UID9|Q9Y2P6	Nonsense_Mutation	SNP	ENST00000336976.6	37	CCDS33046.1	.	.	.	.	.	.	.	.	.	.	g	19.31	3.802189	0.70682	.	.	ENSG00000186019	ENST00000336976;ENST00000269981	.	.	.	1.89	-0.0148	0.13979	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	.	4.7134	0.12884	0.2729:0.0:0.7271:0.0	.	.	.	.	X	75	.	ENSP00000269981:E75X	E	+	1	0	ZNF224	49297206	0.001000	0.12720	0.002000	0.10522	0.020000	0.10135	-0.140000	0.10342	0.040000	0.15660	0.579000	0.79373	GAA	.	.	none		0.438	ZNF224-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460477.1	NM_013398		T	44605366	G	T	44605366	4	4	12	1	0	0	0	0	0	1	0	0	17793	1175	41	4	233	4	ZNF224	19	44605366	Nonsense_Mutation	SNP	G	TCGA-FF-8043-01A-11D-2210-10	28699702	44605366	14523617	106	1680											
TPRX1	284355	hgsc.bcm.edu	37	chr19	48305613	48305624	+	In_Frame_Del	DEL	TTGGGCCTGAGA	TTGGGCCTGAGA	-																															gcctgggatcgggcctgggtTtgggcctgagattgggcctg																								rs201007421		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	TTGGGCCTGAGA	TTGGGCCTGAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr19:48305613_48305624delTTGGGCCTGAGA	ENST00000322175.3	-	2	799_810	c.644_655delTCTCAGGCCCAA	c.(643-657)atctcaggcccaaac>aac	p.ISGP215del	TPRX1_ENST00000535759.1_In_Frame_Del_p.ISGP312del|TPRX1_ENST00000543508.1_In_Frame_Del_p.ISGP205del	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)		gggcctgggtttgggcctgagattgggcctga	0.67																																					p.215_219del	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-Indel	.											TPRX1,NS,carcinoma,0,1	TPRX1	46	1	0			c.645_656del						PASS	.																																			SO:0001651	inframe_deletion	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.644_655delTCTCAGGCCCAA	19.37:g.48305613_48305624delTTGGGCCTGAGA	ENSP00000323455:p.Ile215_Pro218del	32	0	0		39	11	0.282051	NM_198479	A5D8Y3|B2RPL5	In_Frame_Del	DEL	ENST00000322175.3	37	CCDS33066.1																																																																																			.	.	none		0.67	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479		-	48305624	TTGGGCCTGAGA	-	48305613	7	5	12	1	0	1	0	1	0	0	0	0	16437	1841	64	0	584	0	TPRX1	19	48305613	In_Frame_Del	DEL	TTGGGCCTGAGA	TCGA-FF-8043-01A-11D-2210-10	3700247	48305613	10823370	107	1681											
BMP2	650	hgsc.bcm.edu	37	chr20	6750880	6750880	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgcaggaagttcgcggcggCgtcgtcgggccgcccctcat	4	6	15	16	8	1	0	1	0	0	0	4	1	1	1	4	4	0	2	4	4	1	1			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr20:6750880C>T	ENST00000378827.4	+	2	1326	c.107C>T	c.(106-108)gCg>gTg	p.A36V		NM_001200.2	NP_001191.1	P12643	BMP2_HUMAN	bone morphogenetic protein 2	36					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						TTCGCGGCGGCGTCGTCGGGC	0.697																																					p.A36V		Atlas-SNP	.											.	BMP2	45	.	0			c.C107T						PASS	.						16	18	17					20																	6750880		2198	4294	6492	SO:0001583	missense	650	exon2			CGGCGGCGTCGTC		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.107C>T	20.37:g.6750880C>T	ENSP00000368104:p.Ala36Val	27	0	0		43	14	0.325581	NM_001200		Missense_Mutation	SNP	ENST00000378827.4	37	CCDS13099.1	.	.	.	.	.	.	.	.	.	.	C	12.18	1.860846	0.32884	.	.	ENSG00000125845	ENST00000378827	T	0.72394	-0.65	5.02	5.02	0.67125	.	0.340113	0.31199	N	0.008078	T	0.50017	0.1591	N	0.08118	0	0.22446	N	0.999094	B	0.28820	0.224	B	0.18263	0.021	T	0.40905	-0.9538	10	0.31617	T	0.26	.	16.1926	0.82004	0.0:1.0:0.0:0.0	.	36	P12643	BMP2_HUMAN	V	36	ENSP00000368104:A36V	ENSP00000368104:A36V	A	+	2	0	BMP2	6698880	0.348000	0.24861	0.012000	0.15200	0.042000	0.13812	5.100000	0.64560	2.466000	0.83321	0.460000	0.39030	GCG	.	.	none		0.697	BMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077918.3			T	6750880	C	T	6750880	3	4	12	1	0	0	0	0	1	0	0	0	1459	768	27	1	109	1	BMP2	20	6750880	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10		6750880	56274640	108	1682											
PAK7	57144	hgsc.bcm.edu	37	chr20	9560944	9560944	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggacctctgccgcatggtggGctgagggcttgtctgattca	5	11	15	10	1	3	2	1	2	2	0	3	3	3	3	2	4	1	3	2	4	0	2			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr20:9560944G>A	ENST00000378429.3	-	5	1384	c.838C>T	c.(838-840)Ccc>Tcc	p.P280S	PAK7_ENST00000378423.1_Missense_Mutation_p.P280S|PAK7_ENST00000353224.5_Missense_Mutation_p.P280S|RP5-986I17.2_ENST00000428769.1_RNA	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	280	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)			CGCATGGTGGGCTGAGGGCTT	0.552																																					p.P280S		Atlas-SNP	.											.	PAK7	194	.	0			c.C838T						PASS	.						169	147	155					20																	9560944		2203	4300	6503	SO:0001583	missense	57144	exon4			TGGTGGGCTGAGG	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.838C>T	20.37:g.9560944G>A	ENSP00000367686:p.Pro280Ser	266	0	0		400	125	0.3125	NM_177990	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	SNP	ENST00000378429.3	37	CCDS13107.1	.	.	.	.	.	.	.	.	.	.	G	14.74	2.625175	0.46840	.	.	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423;ENST00000439520	T;T;T	0.29917	1.55;1.55;1.55	5.6	5.6	0.85130	.	0.047698	0.85682	D	0.000000	T	0.26122	0.0637	L	0.29908	0.895	0.80722	D	1	P;P	0.48503	0.911;0.911	B;B	0.39840	0.311;0.311	T	0.01492	-1.1341	9	.	.	.	.	19.9969	0.97387	0.0:0.0:1.0:0.0	.	280;280	B0AZM9;Q9P286	.;PAK7_HUMAN	S	280;280;280;228	ENSP00000367686:P280S;ENSP00000322957:P280S;ENSP00000367679:P280S	.	P	-	1	0	PAK7	9508944	1.000000	0.71417	0.999000	0.59377	0.016000	0.09150	9.424000	0.97464	2.813000	0.96785	0.637000	0.83480	CCC	.	.	none		0.552	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1			A	9560944	G	A	9560944	3	1	12	1	0	0	0	0	1	0	0	0	11414	1203	42	2	1349	2	PAK7	20	9560944	Missense_Mutation	SNP	G	TCGA-FF-8043-01A-11D-2210-10	2810064	9560944	53464576	109	1683											
WFDC9	259240	hgsc.bcm.edu	37	chr20	44238795	44238795	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caactccagagatgaacatgAcgagtagaagaatccagggc	16	5	11	9	1	0	5	0	2	0	3	2	7	2	5	2	1	2	1	2	1	5	1			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr20:44238795A>G	ENST00000326000.1	-	3	243	c.26T>C	c.(25-27)gTc>gCc	p.V9A		NM_147198.3	NP_671731.1	Q8NEX5	WFDC9_HUMAN	WAP four-disulfide core domain 9	9						extracellular region (GO:0005576)				breast(1)|large_intestine(1)|liver(1)|lung(1)|prostate(1)|stomach(1)	6		Myeloproliferative disorder(115;0.0122)				GATGAACATGACGAGTAGAAG	0.498																																					p.V9A		Atlas-SNP	.											.	WFDC9	10	.	0			c.T26C						PASS	.						141	123	129					20																	44238795		2203	4300	6503	SO:0001583	missense	259240	exon3			AACATGACGAGTA	AL031671	CCDS13362.1	20q13.12	2013-01-21			ENSG00000180205	ENSG00000180205		"WAP four-disulfide core domain containing"	20380	protein-coding gene	gene with protein product						12206714	Standard	NM_147198		Approved	WAP9, dJ688G8.2	uc002xoy.3	Q8NEX5	OTTHUMG00000046332	ENST00000326000.1:c.26T>C	20.37:g.44238795A>G	ENSP00000320532:p.Val9Ala	131	0	0		120	54	0.45	NM_147198	Q3MIX6|Q5TGZ8	Missense_Mutation	SNP	ENST00000326000.1	37	CCDS13362.1	.	.	.	.	.	.	.	.	.	.	A	9.066	0.995806	0.19043	.	.	ENSG00000180205	ENST00000326000	T	0.36157	1.27	3.71	-1.07	0.09968	.	0.959088	0.08545	N	0.929885	T	0.17789	0.0427	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.11329	0.006	T	0.26224	-1.0109	9	0.27785	T	0.31	.	0.372	0.00381	0.4004:0.1899:0.2258:0.184	.	9	Q8NEX5	WFDC9_HUMAN	A	9	ENSP00000320532:V9A	ENSP00000320532:V9A	V	-	2	0	WFDC9	43672209	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.580000	0.05827	-0.234000	0.09782	-0.280000	0.10049	GTC	.	.	none		0.498	WFDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106945.1			G	44238795	A	G	44238795	3	3	12	1	0	0	0	0	1	0	0	0	17372	275	10	3	255	3	WFDC9	20	44238795	Missense_Mutation	SNP	A	TCGA-FF-8043-01A-11D-2210-10	34677851	44238795	18786725	110	1684											
PMEPA1	56937	hgsc.bcm.edu	37	chr20	56227142	56227142	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctttctgtttatccttctcTttgctccagatggctgcgct	3	18	7	13	1	2	1	0	0	2	1	5	1	4	1	3	1	2	4	3	1	1	5	rs138355480		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr20:56227142T>C	ENST00000341744.3	-	4	1150	c.831A>G	c.(829-831)aaA>aaG	p.K277K	PMEPA1_ENST00000395816.3_Silent_p.K227K|PMEPA1_ENST00000265626.4_Silent_p.K227K|PMEPA1_ENST00000395814.1_Silent_p.K227K|PMEPA1_ENST00000347215.4_Silent_p.K242K	NM_020182.4	NP_064567.2	Q969W9	PMEPA_HUMAN	prostate transmembrane protein, androgen induced 1	277					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						TATCCTTCTCTTTGCTCCAGA	0.627																																					p.K277K		Atlas-SNP	.											.	PMEPA1	29	.	0			c.A831G						PASS	.	T	,,,	0,4390		0,0,2195	27	30	29		831,726,681,681	-6.6	0.5	20	dbSNP_134	29	1,8579		0,1,4289	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PMEPA1	NM_020182.3,NM_199169.1,NM_199170.1,NM_199171.1	,,,	0,1,6484	CC,CT,TT		0.0117,0.0,0.0077	,,,	277/288,242/253,227/238,227/238	56227142	1,12969	2195	4290	6485	SO:0001819	synonymous_variant	56937	exon4			CTTCTCTTTGCTC	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.831A>G	20.37:g.56227142T>C		95	0	0		115	6	0.0521739	NM_020182	Q5TDR6|Q8NER4|Q96B72|Q9UJD3	Silent	SNP	ENST00000341744.3	37	CCDS13463.1																																																																																			T|1.000;C|0.000	0.000	weak		0.627	PMEPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079858.2	NM_020182		C	56227142	T	C	56227142	2	2	12	1	0	0	0	0	0	0	0	1	12141	1606	56	3		3	PMEPA1	20	56227142	Silent	SNP	T	TCGA-FF-8043-01A-11D-2210-10	11988347	56227142	6798378	111	1685											
NCAM2	4685	hgsc.bcm.edu	37	chr21	22656612	22656612	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaaggaaggtgttaggtcaCggttaaccatctacaatgca	15	9	10	7	1	2	0	1	0	1	0	2	1	2	1	1	4	3	3	1	4	7	3	rs576610818		TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr21:22656612C>T	ENST00000400546.1	+	3	478	c.229C>T	c.(229-231)Cgg>Tgg	p.R77W	NCAM2_ENST00000486367.1_3'UTR|NCAM2_ENST00000284894.7_Intron|NCAM2_ENST00000535285.1_Missense_Mutation_p.R102W	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	77	Ig-like C2-type 1.				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)		p.R77G(1)		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)		TGTTAGGTCACGGTTAACCAT	0.398													C|||	1	0.000199681	0.0	0.0	5008	,	,		13851	0.0		0.0	False		,,,				2504	0.001				p.R77W		Atlas-SNP	.											NCAM2,colon,carcinoma,0,2	NCAM2	220	2	1	Substitution - Missense(1)	lung(1)	c.C229T						PASS	.						124	117	119					21																	22656612		1886	4109	5995	SO:0001583	missense	4685	exon3			AGGTCACGGTTAA		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.229C>T	21.37:g.22656612C>T	ENSP00000383392:p.Arg77Trp	83	0	0		130	31	0.238462	NM_004540	A8MQ06|B7Z841|Q7Z7F2	Missense_Mutation	SNP	ENST00000400546.1	37	CCDS42910.1	.	.	.	.	.	.	.	.	.	.	C	15.56	2.868687	0.51588	.	.	ENSG00000154654	ENST00000400546;ENST00000535285	T;T	0.68479	-0.33;-0.33	5.58	2.61	0.31194	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.167812	0.49916	D	0.000140	T	0.46814	0.1412	N	0.26162	0.8	0.49130	D	0.999757	P;P	0.49253	0.921;0.921	B;B	0.38458	0.274;0.274	T	0.32903	-0.9889	10	0.44086	T	0.13	-14.5846	7.7334	0.28799	0.4708:0.4548:0.0:0.0744	.	102;77	B7Z841;O15394	.;NCAM2_HUMAN	W	77;102	ENSP00000383392:R77W;ENSP00000441887:R102W	ENSP00000383392:R77W	R	+	1	2	NCAM2	21578483	0.379000	0.25123	0.999000	0.59377	0.990000	0.78478	0.230000	0.17852	0.230000	0.21059	0.591000	0.81541	CGG	.	.	none		0.398	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		T	22656612	C	T	22656612	3	4	12	1	0	0	0	0	1	0	0	0	10212	527	19	1	239	1	NCAM2	21	22656612	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10		22656612	25473283	112	1686											
KRTAP10-2	386679	hgsc.bcm.edu	37	chr21	45970774	45970774	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gatggacttgcagcagacagGcttgcagcagacggacacac	12	5	13	11	1	0	2	0	0	0	2	0	5	0	4	0	3	4	5	0	3	0	2	rs76536096|rs67692969|rs71199610	byFrequency	TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chr21:45970774G>A	ENST00000391621.1	-	1	614	c.568C>T	c.(568-570)Cct>Tct	p.P190S	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron|KRTAP10-2_ENST00000498210.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	190	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						CAGCAGACAGGCTTGCAGCAG	0.607																																					p.P190S		Atlas-SNP	.											.	KRTAP10-2	21	.	0			c.C568T						PASS	.						110	112	111					21																	45970774		2192	4279	6471	SO:0001583	missense	386679	exon1			AGACAGGCTTGCA	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"Keratin associated proteins"	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.568C>T	21.37:g.45970774G>A	ENSP00000375479:p.Pro190Ser	95	0	0		201	12	0.0597015	NM_198693	Q70LJ5	Missense_Mutation	SNP	ENST00000391621.1	37	CCDS42955.1	.	.	.	.	.	.	.	.	.	.	g	9.523	1.108901	0.20714	.	.	ENSG00000205445	ENST00000391621	T	0.01705	4.68	3.28	0.222	0.15288	.	.	.	.	.	T	0.02083	0.0065	L	0.49455	1.56	0.09310	N	1	B	0.26672	0.156	B	0.24394	0.053	T	0.42310	-0.9459	9	0.62326	D	0.03	.	4.9369	0.13944	0.2108:0.1755:0.6137:0.0	.	190	P60368	KR102_HUMAN	S	190	ENSP00000375479:P190S	ENSP00000375479:P190S	P	-	1	0	KRTAP10-2	44795202	0.105000	0.21958	0.000000	0.03702	0.002000	0.02628	1.284000	0.33249	-0.177000	0.10690	0.462000	0.41574	CCT	G|0.917;A|0.083	0.083	strong		0.607	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1			A	45970774	G	A	45970774	3	1	12	1	0	0	0	0	1	0	0	0	8518	1203	42	2	203	2	KRTAP10-2	21	45970774	Missense_Mutation	SNP	G	TCGA-FF-8043-01A-11D-2210-10	23314162	45970774	2159121	113	1687											
P2RY8	286530	hgsc.bcm.edu	37	chrX	1585400	1585400	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caccgcgatcgccgggttccGcagcatctgcagcgtcgcgt	5	7	13	16	8	1	0	0	0	1	0	4	1	2	0	3	1	3	4	3	1	0	1			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chrX:1585400G>A	ENST00000381297.4	-	2	262	c.52C>T	c.(52-54)Cgg>Tgg	p.R18W	P2RY8_ENST00000460672.1_5'UTR	NM_178129.4	NP_835230.1	Q86VZ1	P2RY8_HUMAN	purinergic receptor P2Y, G-protein coupled, 8	18						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(13)|prostate(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)				GCCGGGTTCCGCAGCATCTGC	0.697			T	CRLF2	"B-ALL, Downs associated ALL"																																p.R18W		Atlas-SNP	.		Dom	yes		"X,Y"	Xp22.3; Yp11.3	286530	"purinergic receptor P2Y, G-protein coupled, 8"		L	.	P2RY8	53	.	0			c.C52T						PASS	.						32	37	36					X																	1585400		2203	4294	6497	SO:0001583	missense	286530	exon2			GGTTCCGCAGCAT	AA804531	CCDS14115.1	Xp22.33 and Yp11.3	2012-08-08			ENSG00000182162	ENSG00000182162		"Pseudoautosomal regions / PAR1", "Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	15524	protein-coding gene	gene with protein product		300525				11004484	Standard	NM_178129		Approved	P2Y8	uc004cpz.2	Q86VZ1	OTTHUMG00000021060	ENST00000381297.4:c.52C>T	X.37:g.1585400G>A	ENSP00000370697:p.Arg18Trp	32	0	0		52	44	0.846154	NM_178129		Missense_Mutation	SNP	ENST00000381297.4	37	CCDS14115.1	.	.	.	.	.	.	.	.	.	.	g	7.771	0.707456	0.15239	.	.	ENSG00000182162	ENST00000381297	T	0.37752	1.18	1.87	-1.37	0.09056	.	1.062470	0.07489	U	0.905207	T	0.21103	0.0508	N	0.08118	0	0.09310	N	1	D	0.67145	0.996	P	0.46629	0.522	T	0.25502	-1.0130	10	0.66056	D	0.02	.	5.9234	0.19094	0.0:0.2784:0.4476:0.274	.	18	Q86VZ1	P2RY8_HUMAN	W	18	ENSP00000370697:R18W	ENSP00000370697:R18W	R	-	1	2	P2RY8	1545400	0.008000	0.16893	0.082000	0.20525	0.013000	0.08279	0.872000	0.28037	0.473000	0.27368	0.279000	0.19357	CGG	.	.	none		0.697	P2RY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055602.1	NM_178129		A	1585400	G	A	1585400	3	1	12	1	0	0	0	0	1	0	0	0	11364	1086	38	1	1031	1	P2RY8	23	1585400	Missense_Mutation	SNP	G	TCGA-FF-8043-01A-11D-2210-10		1585400	153685160	114	1688											
FAM47C	442444	hgsc.bcm.edu	37	chrX	37028314	37028314	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cccatctctgcccggagcctCcagagactcgcgtatctcat	7	9	8	17	3	2	1	1	0	2	1	6	3	3	2	4	1	2	1	4	1	1	1			TCGA-FF-8043-01A-11D-2210-10	TCGA-FF-8043-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e89e9c69-ffcd-4a4c-818d-1dee43ddc76a	dfa74511-2a52-4bd5-88f2-dad8c7450be4	g.chrX:37028314C>T	ENST00000358047.3	+	1	1883	c.1831C>T	c.(1831-1833)Cca>Tca	p.P611S		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	611										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						CCCGGAGCCTCCAGAGACTCG	0.647																																					p.P611S		Atlas-SNP	.											.	FAM47C	267	.	0			c.C1831T						PASS	.						22	25	24					X																	37028314		2186	4274	6460	SO:0001583	missense	442444	exon1			GAGCCTCCAGAGA	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.1831C>T	X.37:g.37028314C>T	ENSP00000367913:p.Pro611Ser	178	0	0		227	94	0.414097	NM_001013736	Q6ZU46	Missense_Mutation	SNP	ENST00000358047.3	37	CCDS35227.1	.	.	.	.	.	.	.	.	.	.	-	12.85	2.061132	0.36373	.	.	ENSG00000198173	ENST00000358047	T	0.22134	1.97	1.02	0.0439	0.14224	.	.	.	.	.	T	0.22898	0.0553	M	0.80183	2.485	0.09310	N	1	P	0.50710	0.938	B	0.41202	0.35	T	0.15009	-1.0452	9	0.42905	T	0.14	.	5.3242	0.15896	0.0:0.7636:0.0:0.2364	.	611	Q5HY64	FA47C_HUMAN	S	611	ENSP00000367913:P611S	ENSP00000367913:P611S	P	+	1	0	FAM47C	36938235	0.001000	0.12720	0.001000	0.08648	0.002000	0.02628	0.449000	0.21744	-0.043000	0.13513	-0.457000	0.05445	CCA	.	.	none		0.647	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736		T	37028314	C	T	37028314	3	4	12	1	0	0	0	0	1	0	0	0	5579	855	30	2	1833	2	FAM47C	23	37028314	Missense_Mutation	SNP	C	TCGA-FF-8043-01A-11D-2210-10	35442914	37028314	118242246	115	1689											
ID3	3399	hgsc.bcm.edu	37	chr1	23885690	23885690	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	actacctgcaggtcgagaatGtagtcgatgacgcgctgtag	10	9	13	9	4	0	2	0	1	0	1	2	4	0	2	1	1	2	4	1	1	4	3			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr1:23885690G>T	ENST00000374561.5	-	1	595	c.228C>A	c.(226-228)taC>taA	p.Y76*	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	76	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				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)		GGTCGAGAATGTAGTCGATGA	0.622																																					p.Y76X		Atlas-SNP	.											ID3,NS,lymphoid_neoplasm,-1,1	ID3	29	1	0			c.C228A						PASS	.						58	64	62					1																	23885690		2203	4300	6503	SO:0001587	stop_gained	3399	exon1			GAGAATGTAGTCG	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.228C>A	1.37:g.23885690G>T	ENSP00000363689:p.Tyr76*	96	0	0		111	70	0.630631	NM_002167	A8K1T8|O75641	Nonsense_Mutation	SNP	ENST00000374561.5	37	CCDS237.1	.	.	.	.	.	.	.	.	.	.	G	39	7.592021	0.98378	.	.	ENSG00000117318	ENST00000374561	.	.	.	5.6	3.74	0.42951	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.6025	10.9515	0.47332	0.1528:0.0:0.8472:0.0	.	.	.	.	X	76	.	ENSP00000363689:Y76X	Y	-	3	2	ID3	23758277	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.456000	0.53000	0.736000	0.32559	0.591000	0.81541	TAC	.	.	none		0.622	ID3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008904.1	NM_002167		T	23885690	G	T	23885690	4	4	13	1	0	0	0	0	0	1	0	0	7500	1372	48	4	139	4	ID3	1	23885690	Nonsense_Mutation	SNP	G	TCGA-FF-8046-01A-11D-2210-10		23885690	225364931	1	1690											
ALG6	29929	hgsc.bcm.edu	37	chr1	63867944	63867944	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtattttaacagcagtgatAacaatttacagtattgggga	14	13	10	4	0	0	1	0	1	0	0	0	2	0	2	0	3	4	3	0	3	6	8			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr1:63867944A>G	ENST00000371108.4	+	4	492	c.187A>G	c.(187-189)Aac>Gac	p.N63D	ALG6_ENST00000263440.4_Missense_Mutation_p.N63D	NM_013339.3	NP_037471.2	Q9Y672	ALG6_HUMAN	ALG6, alpha-1,3-glucosyltransferase	63					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						CAGCAGTGATAACAATTTACA	0.318																																					p.N63D		Atlas-SNP	.											.	ALG6	33	.	0			c.A187G						PASS	.						109	109	109					1																	63867944		2203	4299	6502	SO:0001583	missense	29929	exon4			AGTGATAACAATT	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.187A>G	1.37:g.63867944A>G	ENSP00000360149:p.Asn63Asp	89	0	0		66	4	0.0606061	NM_013339	B3KMU2|Q5SXR9|Q9H3I0	Missense_Mutation	SNP	ENST00000371108.4	37	CCDS30735.1	.	.	.	.	.	.	.	.	.	.	a	26.4	4.734192	0.89482	.	.	ENSG00000088035	ENST00000371108;ENST00000263440	D;D	0.83837	-1.77;-1.77	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	D	0.90515	0.7028	M	0.91406	3.205	0.80722	D	1	D	0.67145	0.996	D	0.72625	0.978	D	0.90800	0.4693	10	0.36615	T	0.2	-20.3602	14.4035	0.67065	1.0:0.0:0.0:0.0	.	63	A2A2G4	.	D	63	ENSP00000360149:N63D;ENSP00000263440:N63D	ENSP00000263440:N63D	N	+	1	0	ALG6	63640532	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.928000	0.92853	1.806000	0.52798	0.455000	0.32223	AAC	.	.	none		0.318	ALG6-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025330.2	NM_013339		G	63867944	A	G	63867944	3	3	13	1	0	0	0	0	1	0	0	0	522	362	13	3	197	3	ALG6	1	63867944	Missense_Mutation	SNP	A	TCGA-FF-8046-01A-11D-2210-10	39982254	63867944	185382677	2	1691											
ITGA10	8515	hgsc.bcm.edu	37	chr1	145528314	145528314	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatgcacctggggatgtctcTgttagagacagatggtgatg	9	12	14	6	0	1	3	0	1	1	2	2	5	1	4	1	3	1	2	1	3	2	2			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr1:145528314T>A	ENST00000369304.3	+	4	510	c.335T>A	c.(334-336)cTg>cAg	p.L112Q	ITGA10_ENST00000538811.1_Intron|ITGA10_ENST00000539363.1_Intron	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	112					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)					GGGATGTCTCTGTTAGAGACA	0.483																																					p.L112Q		Atlas-SNP	.											.	ITGA10	131	.	0			c.T335A						PASS	.						101	99	99					1																	145528314		2203	4300	6503	SO:0001583	missense	8515	exon4			TGTCTCTGTTAGA	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.335T>A	1.37:g.145528314T>A	ENSP00000358310:p.Leu112Gln	199	0	0		235	63	0.268085	NM_003637	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Missense_Mutation	SNP	ENST00000369304.3	37	CCDS918.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.062469	0.76187	.	.	ENSG00000143127	ENST00000369304;ENST00000543043	T	0.72835	-0.69	5.46	5.46	0.80206	.	0.000000	0.56097	D	0.000028	T	0.80396	0.4615	M	0.80183	2.485	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	D	0.83917	0.0299	10	0.87932	D	0	.	11.9274	0.52827	0.0:0.0:0.0:1.0	.	78;112;112	F5H3T9;O75578;O75578-2	.;ITA10_HUMAN;.	Q	112;78	ENSP00000358310:L112Q	ENSP00000358310:L112Q	L	+	2	0	ITGA10	144239671	0.940000	0.31905	0.900000	0.35374	0.992000	0.81027	4.296000	0.59055	2.070000	0.61991	0.459000	0.35465	CTG	.	.	none		0.483	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637		A	145528314	T	A	145528314	3	1	13	1	0	0	0	0	1	0	0	0	7882	1580	55	5	349	5	ITGA10	1	145528314	Missense_Mutation	SNP	T	TCGA-FF-8046-01A-11D-2210-10	81660370	145528314	103722307	3	1692											
ARHGEF11	9826	hgsc.bcm.edu	37	chr1	156941496	156941496	+	Intron	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctacatcactcaccactgagCcaccagtctcctgctggatc	9	9	6	17	0	3	1	2	1	1	0	5	2	3	2	4	1	3	1	4	1	1	1			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr1:156941496C>A	ENST00000361409.2	-	8	1325				ARHGEF11_ENST00000368194.3_Missense_Mutation_p.G232V	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11						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)					CACCACTGAGCCACCAGTCTC	0.557																																					p.G232V		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.G695T						PASS	.						98	91	93					1																	156941496		2203	4300	6503	SO:0001627	intron_variant	9826	exon8			ACTGAGCCACCAG	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.583-1661G>T	1.37:g.156941496C>A		68	0	0		61	17	0.278689	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Missense_Mutation	SNP	ENST00000361409.2	37	CCDS1162.1	.	.	.	.	.	.	.	.	.	.	C	15.42	2.829147	0.50845	.	.	ENSG00000132694	ENST00000368194	T	0.65732	-0.17	5.46	4.54	0.55810	.	0.203312	0.34828	N	0.003657	T	0.41351	0.1155	.	.	.	0.80722	D	1	B	0.17268	0.021	B	0.18263	0.021	T	0.42783	-0.9431	9	0.45353	T	0.12	-21.6118	15.2508	0.73545	0.0:0.8587:0.1413:0.0	.	232	O15085-2	.	V	232	ENSP00000357177:G232V	ENSP00000357177:G232V	G	-	2	0	ARHGEF11	155208120	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.332000	0.43903	1.517000	0.48917	0.655000	0.94253	GGC	.	.	none		0.557	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236		A	156941496	C	A	156941496	1	1	13	0	1	0	0	0	0	0	0	0	896	739	26	4		4	ARHGEF11	1	156941496	Intron	SNP	C	TCGA-FF-8046-01A-11D-2210-10	11413182	156941496	92309125	4	1693											
C1orf27	54953	hgsc.bcm.edu	37	chr1	186357578	186357578	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttttctctctttcagctaaTgtttgctgtggaaaagtcta	8	19	7	7	0	4	0	1	0	3	0	5	1	4	1	0	1	2	3	0	1	4	6			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr1:186357578T>A	ENST00000287859.6	+	5	460	c.335T>A	c.(334-336)aTg>aAg	p.M112K	C1orf27_ENST00000432021.3_Missense_Mutation_p.M112K|C1orf27_ENST00000367470.3_Missense_Mutation_p.M112K|C1orf27_ENST00000419367.3_Missense_Mutation_p.M80K	NM_017847.5	NP_060317.3	Q5SWX8	ODR4_HUMAN	chromosome 1 open reading frame 27	112						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						TTTCAGCTAATGTTTGCTGTG	0.333																																					p.M112K		Atlas-SNP	.											C1orf27_ENST00000287859,NS,carcinoma,-1,2	C1orf27	41	2	0			c.T335A						PASS	.						32	31	31					1																	186357578		1807	4068	5875	SO:0001583	missense	54953	exon5			AGCTAATGTTTGC	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.335T>A	1.37:g.186357578T>A	ENSP00000287859:p.Met112Lys	115	0	0		120	38	0.316667	NM_001164245	B4DNY0|E9PFR7|Q19CC6|Q8WYB6|Q9BTS2|Q9H6A6|Q9NX06	Missense_Mutation	SNP	ENST00000287859.6	37	CCDS53448.1	.	.	.	.	.	.	.	.	.	.	T	11.70	1.717373	0.30413	.	.	ENSG00000157181	ENST00000367470;ENST00000419367;ENST00000432021;ENST00000287859	T;T;T;T	0.42900	1.03;0.96;1.03;1.03	5.3	4.15	0.48705	.	0.545614	0.20190	N	0.097330	T	0.26122	0.0637	N	0.08118	0	0.28249	N	0.925366	B;B;B	0.20459	0.045;0.014;0.014	B;B;B	0.24848	0.056;0.006;0.006	T	0.22906	-1.0203	10	0.66056	D	0.02	-17.5983	12.025	0.53365	0.0:0.0:0.1449:0.8551	.	80;112;112	E9PFR7;Q5SWX8-2;Q5SWX8	.;.;ODR4_HUMAN	K	112;80;112;112	ENSP00000356440:M112K;ENSP00000395084:M80K;ENSP00000402029:M112K;ENSP00000287859:M112K	ENSP00000287859:M112K	M	+	2	0	C1orf27	184624201	0.988000	0.35896	0.998000	0.56505	0.369000	0.29798	6.000000	0.70678	0.817000	0.34445	0.460000	0.39030	ATG	.	.	none		0.333	C1orf27-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086352.2	NM_017847		A	186357578	T	A	186357578	3	1	13	1	0	0	0	0	1	0	0	0	2038	1464	51	5	349	5	C1orf27	1	186357578	Missense_Mutation	SNP	T	TCGA-FF-8046-01A-11D-2210-10	29416082	186357578	62893043	5	1694											
CHIT1	1118	hgsc.bcm.edu	37	chr1	203186088	203186088	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagctttgctggaacagccGccccgctgcacagctgtaga	8	7	12	14	2	0	1	0	0	0	1	0	2	0	2	3	1	6	7	3	1	2	2			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr1:203186088G>A	ENST00000367229.1	-	11	1364	c.1330C>T	c.(1330-1332)Cgg>Tgg	p.R444W	CHIT1_ENST00000535569.1_Missense_Mutation_p.R435W|CHIT1_ENST00000484834.1_Intron|CHIT1_ENST00000255427.3_Missense_Mutation_p.R425W	NM_001270509.1|NM_003465.2	NP_001257438.1|NP_003456.1	Q13231	CHIT1_HUMAN	chitinase 1 (chitotriosidase)	444	Chitin-binding type-2. {ECO:0000255|PROSITE-ProRule:PRU00144}.				chitin catabolic process (GO:0006032)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|response to bacterium (GO:0009617)	extracellular space (GO:0005615)|lysosome (GO:0005764)	chitin binding (GO:0008061)|chitinase activity (GO:0004568)|endochitinase activity (GO:0008843)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|stomach(2)	27						TGGAACAGCCGCCCCGCTGCA	0.597											OREG0014113	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R444W		Atlas-SNP	.											CHIT1,NS,carcinoma,+2,1	CHIT1	61	1	0			c.C1330T						PASS	.						87	92	90					1																	203186088		2203	4300	6503	SO:0001583	missense	1118	exon11			ACAGCCGCCCCGC	U29615	CCDS1436.1, CCDS58057.1	1q32.1	2013-06-06			ENSG00000133063	ENSG00000133063			1936	protein-coding gene	gene with protein product		600031				9748235, 9492324	Standard	NM_003465		Approved	CHIT, CHI3	uc001gzn.2	Q13231	OTTHUMG00000042126	ENST00000367229.1:c.1330C>T	1.37:g.203186088G>A	ENSP00000356198:p.Arg444Trp	55	0	0	2135	54	11	0.203704	NM_003465	B3KNW6|J3KN09|Q0VGG5|Q0VGG6|Q3ZAR1|Q6ISC2|Q9H3V8|Q9UDJ8	Missense_Mutation	SNP	ENST00000367229.1	37	CCDS1436.1	.	.	.	.	.	.	.	.	.	.	G	15.67	2.903086	0.52227	.	.	ENSG00000133063	ENST00000367229;ENST00000255427;ENST00000535569	T;T;T	0.32272	1.46;1.46;1.46	4.81	0.807	0.18714	Chitin binding domain (5);	0.540328	0.15465	N	0.260936	T	0.42040	0.1185	M	0.72624	2.21	0.09310	N	1	B;D;B	0.76494	0.01;0.999;0.031	B;P;B	0.61800	0.003;0.894;0.007	T	0.21861	-1.0233	10	0.37606	T	0.19	-4.997	3.3947	0.07302	0.2568:0.0:0.4399:0.3033	.	415;435;444	Q13231-3;G5EA51;Q13231	.;.;CHIT1_HUMAN	W	444;425;435	ENSP00000356198:R444W;ENSP00000255427:R425W;ENSP00000438078:R435W	ENSP00000255427:R425W	R	-	1	2	CHIT1	201452711	0.000000	0.05858	0.043000	0.18650	0.768000	0.43524	-0.593000	0.05740	-0.110000	0.12022	0.650000	0.86243	CGG	.	.	none		0.597	CHIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100275.2	NM_003465		A	203186088	G	A	203186088	3	1	13	1	0	0	0	0	1	0	0	0	3348	1086	38	1	74	1	CHIT1	1	203186088	Missense_Mutation	SNP	G	TCGA-FF-8046-01A-11D-2210-10	16828510	203186088	46064533	6	1695											
TMCC2	9911	hgsc.bcm.edu	37	chr1	205238355	205238355	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttcgagaagaagaaccagaAgtcagcccagaccatcgccc	14	4	10	13	2	1	5	1	0	0	5	3	6	1	5	4	0	2	1	4	0	4	1			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr1:205238355A>G	ENST00000358024.3	+	3	1414	c.1025A>G	c.(1024-1026)aAg>aGg	p.K342R	TMCC2_ENST00000329800.7_Missense_Mutation_p.K102R|TMCC2_ENST00000545499.1_Missense_Mutation_p.K264R|TMCC2_ENST00000495538.1_3'UTR|TMCC2_ENST00000330675.7_Missense_Mutation_p.K117R	NM_014858.3	NP_055673.2	O75069	TMCC2_HUMAN	transmembrane and coiled-coil domain family 2	342						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)			AAGAACCAGAAGTCAGCCCAG	0.592																																					p.K342R		Atlas-SNP	.											.	TMCC2	89	.	0			c.A1025G						PASS	.						57	46	50					1																	205238355		2203	4300	6503	SO:0001583	missense	9911	exon3			ACCAGAAGTCAGC	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.1025A>G	1.37:g.205238355A>G	ENSP00000350718:p.Lys342Arg	87	0	0		83	4	0.0481928	NM_014858	A2RRH3|B7Z1P7|Q6ZN09	Missense_Mutation	SNP	ENST00000358024.3	37	CCDS30984.1	.	.	.	.	.	.	.	.	.	.	A	26.5	4.746863	0.89663	.	.	ENSG00000133069	ENST00000358024;ENST00000545499;ENST00000367159;ENST00000330675;ENST00000329800	T;T;T;T;T	0.53423	0.62;0.62;0.62;0.62;0.62	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.64811	0.2632	L	0.59912	1.85	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.972	D;D;D;D	0.87578	0.998;0.997;0.998;0.946	T	0.62609	-0.6818	10	0.35671	T	0.21	.	15.5977	0.76599	1.0:0.0:0.0:0.0	.	138;102;117;342	Q8IW47;G5E963;B2RAX5;O75069	.;.;.;TMCC2_HUMAN	R	342;264;146;117;102	ENSP00000350718:K342R;ENSP00000437943:K264R;ENSP00000356127:K146R;ENSP00000331842:K117R;ENSP00000329436:K102R	ENSP00000329436:K102R	K	+	2	0	TMCC2	203504978	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.339000	0.96797	2.170000	0.68504	0.379000	0.24179	AAG	.	.	none		0.592	TMCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090383.1	NM_014858		G	205238355	A	G	205238355	3	3	13	1	0	0	0	0	1	0	0	0	16008	72	3	3	1035	3	TMCC2	1	205238355	Missense_Mutation	SNP	A	TCGA-FF-8046-01A-11D-2210-10	2052267	205238355	44012266	7	1696											
SFRS7	6432	hgsc.bcm.edu	37	chr2	38976739	38976739	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccttttcgccacactcataGcatctatcatttggatcaaa	11	13	4	13	1	4	0	3	0	1	0	5	1	4	1	2	1	1	1	2	1	3	5			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr2:38976739G>C	ENST00000313117.6	-	3	555	c.318C>G	c.(316-318)tgC>tgG	p.C106W	SRSF7_ENST00000446327.2_Missense_Mutation_p.C106W|GEMIN6_ENST00000409011.1_5'Flank|SRSF7_ENST00000409276.1_Missense_Mutation_p.C106W	NM_001031684.2|NM_001195446.1	NP_001026854.1|NP_001182375.1	Q16629	SRSF7_HUMAN	serine/arginine-rich splicing factor 7	106					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						CACACTCATAGCATCTATCAT	0.458																																					p.C106W		Atlas-SNP	.											.	SRSF7	29	.	0			c.C318G						PASS	.						147	139	141					2																	38976739		2203	4300	6503	SO:0001583	missense	6432	exon3			CTCATAGCATCTA	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.318C>G	2.37:g.38976739G>C	ENSP00000325905:p.Cys106Trp	295	0	0		280	91	0.325	NM_001195446	B4DLU6|G5E9M3|Q564D3	Missense_Mutation	SNP	ENST00000313117.6	37	CCDS33183.1	.	.	.	.	.	.	.	.	.	.	G	15.13	2.741058	0.49151	.	.	ENSG00000115875	ENST00000313117;ENST00000446327;ENST00000409276	D;D;D	0.98028	-4.67;-4.67;-4.67	5.93	1.43	0.22495	Zinc finger, CCHC retroviral-type (1);Zinc finger, CCHC-type (2);	0.000000	0.85682	D	0.000000	D	0.98582	0.9526	M	0.88105	2.93	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98776	1.0730	10	0.87932	D	0	.	11.8039	0.52143	0.3644:0.0:0.6356:0.0	.	106;106	G5E9M3;Q16629	.;SRSF7_HUMAN	W	106	ENSP00000325905:C106W;ENSP00000402264:C106W;ENSP00000386806:C106W	ENSP00000325905:C106W	C	-	3	2	SRSF7	38830243	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.830000	0.27462	0.355000	0.24131	0.655000	0.94253	TGC	.	.	none		0.458	SRSF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219889.2	NM_001031684		C	38976739	G	C	38976739	3	2	13	1	0	0	0	0	1	0	0	0	14197	963	34	4	422	4	SFRS7	2	38976739	Missense_Mutation	SNP	G	TCGA-FF-8046-01A-11D-2210-10		38976739	204222634	8	1697											
SFRS7	6432	hgsc.bcm.edu	37	chr2	38977316	38977316	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccagcgccagttcccaggtTaccaacatacaccttggttt	9	10	8	14	1	0	0	0	0	0	0	1	0	1	0	5	2	4	3	5	2	3	5			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr2:38977316T>A	ENST00000313117.6	-	2	286	c.49A>T	c.(49-51)Aac>Tac	p.N17Y	SRSF7_ENST00000446327.2_Missense_Mutation_p.N17Y|GEMIN6_ENST00000409011.1_5'Flank|SRSF7_ENST00000409276.1_Missense_Mutation_p.N17Y	NM_001031684.2|NM_001195446.1	NP_001026854.1|NP_001182375.1	Q16629	SRSF7_HUMAN	serine/arginine-rich splicing factor 7	17	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)|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						GTTCCCAGGTTACCAACATAC	0.413																																					p.N17Y		Atlas-SNP	.											.	SRSF7	29	.	0			c.A49T						PASS	.						101	100	100					2																	38977316		2203	4300	6503	SO:0001583	missense	6432	exon2			CCAGGTTACCAAC	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.49A>T	2.37:g.38977316T>A	ENSP00000325905:p.Asn17Tyr	86	0	0		87	33	0.37931	NM_001195446	B4DLU6|G5E9M3|Q564D3	Missense_Mutation	SNP	ENST00000313117.6	37	CCDS33183.1	.	.	.	.	.	.	.	.	.	.	T	19.10	3.762475	0.69763	.	.	ENSG00000115875	ENST00000313117;ENST00000446327;ENST00000409276	D;D;D	0.82803	-1.65;-1.65;-1.65	6.07	6.07	0.98685	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	D	0.92993	0.7770	M	0.91090	3.175	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.80764	0.993;0.994	D	0.94275	0.7514	10	0.87932	D	0	.	16.6407	0.85098	0.0:0.0:0.0:1.0	.	17;17	G5E9M3;Q16629	.;SRSF7_HUMAN	Y	17	ENSP00000325905:N17Y;ENSP00000402264:N17Y;ENSP00000386806:N17Y	ENSP00000325905:N17Y	N	-	1	0	SRSF7	38830820	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.233000	0.51311	2.326000	0.78906	0.533000	0.62120	AAC	.	.	none		0.413	SRSF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219889.2	NM_001031684		A	38977316	T	A	38977316	3	1	13	1	0	0	0	0	1	0	0	0	14197	1754	61	5	695	5	SFRS7	2	38977316	Missense_Mutation	SNP	T	TCGA-FF-8046-01A-11D-2210-10	577	38977316	204222057	9	1698											
LRP1B	53353	hgsc.bcm.edu	37	chr2	141294279	141294279	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gttgcaggaggaatttttagCtgcaagaaaaaaaaaaaaag	20	8	10	3	0	0	1	0	0	0	1	0	3	0	3	0	2	3	4	0	2	9	4			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr2:141294279C>A	ENST00000389484.3	-	46	8485		c.e46-1			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)		GAATTTTTAGCTGCAAGAAAA	0.328										TSP Lung(27;0.18)																											.	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.7514-1G>T						PASS	.						49	48	48					2																	141294279		2203	4300	6503	SO:0001630	splice_region_variant	53353	exon47			TTTTAGCTGCAAG	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.7514-1G>T	2.37:g.141294279C>A		84	0	0		94	27	0.287234	NM_018557	Q8WY29|Q8WY30|Q8WY31	Splice_Site	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.970286	0.74246	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	.	.	.	5.3	5.3	0.74995	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.9639	0.92687	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	LRP1B	141010749	1.000000	0.71417	1.000000	0.80357	0.696000	0.40369	7.726000	0.84824	2.490000	0.84030	0.650000	0.86243	.	.	.	none		0.328	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	Intron	A	141294279	C	A	141294279	5	1	13	1	0	0	0	0	0	0	1	0	8964	811	28	4	6470	4	LRP1B	2	141294279	Splice_Site	SNP	C	TCGA-FF-8046-01A-11D-2210-10	102316963	141294279	101905094	10	1699											
NEB	4703	hgsc.bcm.edu	37	chr2	152432215	152432215	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgtagtacttacattgctCacattaagagcatttgctct	10	16	7	8	0	2	1	1	0	1	1	2	1	2	1	0	0	5	6	0	0	4	7			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr2:152432215C>A	ENST00000172853.10	-	79	12051	c.11904G>T	c.(11902-11904)gtG>gtT	p.V3968V	NEB_ENST00000397345.3_Silent_p.V5669V|NEB_ENST00000603639.1_Silent_p.V5669V|NEB_ENST00000409198.1_Silent_p.V3968V|NEB_ENST00000604864.1_Silent_p.V5669V|NEB_ENST00000427231.2_Silent_p.V5669V			P20929	NEBU_HUMAN	nebulin	3968					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)		TTACATTGCTCACATTAAGAG	0.423																																					p.V5669V		Atlas-SNP	.											.	NEB	1697	.	0			c.G17007T						PASS	.						234	233	233					2																	152432215		1861	4099	5960	SO:0001819	synonymous_variant	4703	exon107			ATTGCTCACATTA	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.11904G>T	2.37:g.152432215C>A		135	0	0		159	52	0.327044	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				.	.	none		0.423	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		A	152432215	C	A	152432215	2	1	13	1	0	0	0	0	0	0	0	1	10311	813	29	4		4	NEB	2	152432215	Silent	SNP	C	TCGA-FF-8046-01A-11D-2210-10	11137936	152432215	90767158	11	1700											
TTN	7273	hgsc.bcm.edu	37	chr2	179600638	179600638	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaatgtgtttgttttctgcGtcggaaatcctccagttagg	9	15	10	7	2	1	0	0	0	1	0	4	1	3	1	2	2	1	3	2	2	4	4	rs184307461	byFrequency	TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr2:179600638G>A	ENST00000591111.1	-	48	13808	c.13584C>T	c.(13582-13584)gaC>gaT	p.D4528D	TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Silent_p.D3601D|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000589042.1_Silent_p.D4845D|TTN-AS1_ENST00000582847.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12284	Ig-like 25.				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)			TGTTTTCTGCGTCGGAAATCC	0.443													G|||	3	0.000599042	0.0	0.0043	5008	,	,		20196	0.0		0.0	False		,,,				2504	0.0				p.D4845D		Atlas-SNP	.											TTN_ENST00000356127,NS,carcinoma,-2,2	TTN	18412	2	0			c.C14535T						PASS	.	G	,,,	0,3874		0,0,1937	135	131	132		,10803,,	-0.5	0.5	2		132	2,8284		0,2,4141	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	0,2,6078	AA,AG,GG		0.0241,0.0,0.0164	,,,	,3601/33424,,	179600638	2,12158	1937	4143	6080	SO:0001819	synonymous_variant	7273	exon50			TTCTGCGTCGGAA	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.13584C>T	2.37:g.179600638G>A		155	0	0		205	43	0.209756	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	37																																																																																				G|1.000;A|0.000	0.000	strong		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179600638	G	A	179600638	2	1	13	1	0	0	0	0	0	0	0	1	16750	1136	40	1		1	TTN	2	179600638	Silent	SNP	G	TCGA-FF-8046-01A-11D-2210-10	27168423	179600638	63598735	12	1701											
CASP8	841	hgsc.bcm.edu	37	chr2	202141586	202141586	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	accaaatgaaaagcaaacctCggggatactgtctgatcatc	15	8	8	10	1	2	2	1	2	1	0	4	3	2	3	2	2	3	1	2	2	5	1			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr2:202141586C>T	ENST00000432109.2	+	8	886	c.697C>T	c.(697-699)Cgg>Tgg	p.R233W	CASP8_ENST00000264274.9_Intron|CASP8_ENST00000392259.2_Missense_Mutation_p.S211L|CASP8_ENST00000392266.3_Missense_Mutation_p.S196L|CASP8_ENST00000392258.3_Missense_Mutation_p.S211L|CASP8_ENST00000264275.5_Missense_Mutation_p.R250W|CASP8_ENST00000358485.4_Missense_Mutation_p.R292W|CASP8_ENST00000323492.7_Missense_Mutation_p.R218W	NM_033355.3	NP_203519.1	Q14790	CASP8_HUMAN	caspase 8, apoptosis-related cysteine peptidase	233					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						AAGCAAACCTCGGGGATACTG	0.428										HNSCC(4;0.00038)																											p.R292W	Melanoma(82;831 1348 20716 36952 40159)	Atlas-SNP	.											CASP8_ENST00000358485,NS,carcinoma,0,6	CASP8	272	6	0			c.C874T						PASS	.						79	76	77					2																	202141586		2203	4300	6503	SO:0001583	missense	841	exon7			AAACCTCGGGGAT	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.697C>T	2.37:g.202141586C>T	ENSP00000412523:p.Arg233Trp	176	0	0		230	19	0.0826087	NM_001080125	O14676|Q14791|Q14792|Q14793|Q14794|Q14795|Q14796|Q15780|Q15806|Q53TT5|Q8TDI1|Q8TDI2|Q8TDI3|Q8TDI4|Q8TDI5|Q96T22|Q9C0K4|Q9UQ81	Missense_Mutation	SNP	ENST00000432109.2	37	CCDS2342.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.43|16.43	3.120327|3.120327	0.56613|0.56613	.|.	.|.	ENSG00000064012|ENSG00000064012	ENST00000392263;ENST00000432109;ENST00000264275;ENST00000450491;ENST00000358485;ENST00000392261;ENST00000323492|ENST00000392259;ENST00000392266;ENST00000392258;ENST00000447616;ENST00000424461	D;D;D;D;D;D|.	0.84223|.	-1.53;-1.53;-1.82;-1.82;-1.53;-1.53|.	5.6|5.6	5.6|5.6	0.85130|0.85130	Peptidase C14, caspase precursor p45, core (2);DEATH-like (1);Peptidase C14, ICE, catalytic subunit p20 (1);|.	0.194920|.	0.44097|.	D|.	0.000497|.	T|T	0.29458|0.29458	0.0734|0.0734	N|N	0.24115|0.24115	0.695|0.695	0.24514|0.24514	N|N	0.994191|0.994191	D;D;D;D;D;D|D;P	0.89917|0.62365	1.0;1.0;1.0;1.0;1.0;1.0|0.991;0.931	D;D;D;D;D;D|P;B	0.91635|0.45753	0.994;0.987;0.997;0.998;0.999;0.997|0.492;0.356	T|T	0.10428|0.10428	-1.0630|-1.0630	10|8	0.66056|0.33141	D|T	0.02|0.24	.|.	12.1349|12.1349	0.53966|0.53966	0.0:0.9188:0.0:0.0812|0.0:0.9188:0.0:0.0812	.|.	233;218;292;233;218;250|196;211	Q14790-7;A8MU92;Q14790-9;Q14790;Q14790-2;Q14790-4|Q14790-6;Q14790-5	.;.;.;CASP8_HUMAN;.;.|.;.	W|L	218;233;250;115;292;218;218|211;196;211;196;59	ENSP00000376091:R218W;ENSP00000412523:R233W;ENSP00000264275:R250W;ENSP00000391709:R115W;ENSP00000351273:R292W;ENSP00000325722:R218W|.	ENSP00000264275:R250W|ENSP00000376087:S211L	R|S	+|+	1|2	2|0	CASP8|CASP8	201849831|201849831	0.984000|0.984000	0.35163|0.35163	1.000000|1.000000	0.80357|0.80357	0.328000|0.328000	0.28507|0.28507	1.051000|1.051000	0.30417|0.30417	2.624000|2.624000	0.88883|0.88883	0.561000|0.561000	0.74099|0.74099	CGG|TCG	.	.	none		0.428	CASP8-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000336853.2	NM_001228		T	202141586	C	T	202141586	3	4	13	1	0	0	0	0	1	0	0	0	2679	893	31	1	1000	1	CASP8	2	202141586	Missense_Mutation	SNP	C	TCGA-FF-8046-01A-11D-2210-10	22540948	202141586	41057787	13	1702			1	13		2	2	12	N	T_C	3.269026e-05
CASP8	841	hgsc.bcm.edu	37	chr2	202141597	202141597	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaaacctcggggatactgTctgatcatcaacaatcacaa	15	8	7	11	1	4	1	3	1	1	0	5	2	4	2	1	2	4	1	1	2	5	1			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr2:202141597T>A	ENST00000432109.2	+	8	897	c.708T>A	c.(706-708)tgT>tgA	p.C236*	CASP8_ENST00000264274.9_Intron|CASP8_ENST00000392259.2_Missense_Mutation_p.S215T|CASP8_ENST00000392266.3_Missense_Mutation_p.S200T|CASP8_ENST00000392258.3_Missense_Mutation_p.S215T|CASP8_ENST00000264275.5_Nonsense_Mutation_p.C253*|CASP8_ENST00000358485.4_Nonsense_Mutation_p.C295*|CASP8_ENST00000323492.7_Nonsense_Mutation_p.C221*	NM_033355.3	NP_203519.1	Q14790	CASP8_HUMAN	caspase 8, apoptosis-related cysteine peptidase	236					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						GGGGATACTGTCTGATCATCA	0.448										HNSCC(4;0.00038)																											p.C295X	Melanoma(82;831 1348 20716 36952 40159)	Atlas-SNP	.											CASP8_ENST00000358485,NS,carcinoma,+1,3	CASP8	272	3	0			c.T885A						PASS	.						91	84	86					2																	202141597		2203	4300	6503	SO:0001587	stop_gained	841	exon7			ATACTGTCTGATC	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.708T>A	2.37:g.202141597T>A	ENSP00000412523:p.Cys236*	173	0	0		224	16	0.0714286	NM_001080125	O14676|Q14791|Q14792|Q14793|Q14794|Q14795|Q14796|Q15780|Q15806|Q53TT5|Q8TDI1|Q8TDI2|Q8TDI3|Q8TDI4|Q8TDI5|Q96T22|Q9C0K4|Q9UQ81	Nonsense_Mutation	SNP	ENST00000432109.2	37	CCDS2342.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.28|16.28	3.078350|3.078350	0.55753|0.55753	.|.	.|.	ENSG00000064012|ENSG00000064012	ENST00000392263;ENST00000432109;ENST00000264275;ENST00000450491;ENST00000358485;ENST00000392261;ENST00000323492|ENST00000392259;ENST00000392266;ENST00000392258;ENST00000447616;ENST00000424461	.|.	.|.	.|.	5.6|5.6	3.27|3.27	0.37495|0.37495	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.19446	.|0.0467	.|.	.|.	.|.	0.21256|0.21256	N|N	0.999742|0.999742	.|P;P	.|0.36249	.|0.545;0.545	.|B;B	.|0.32677	.|0.15;0.098	.|T	.|0.09975	.|-1.0650	.|7	0.02654|0.25106	T|T	1|0.35	.|.	4.4221|4.4221	0.11486|0.11486	0.0:0.3337:0.0:0.6663|0.0:0.3337:0.0:0.6663	.|.	.|200;215	.|Q14790-6;Q14790-5	.|.;.	X|T	221;236;253;118;295;221;221|215;200;215;200;63	.|.	ENSP00000264275:C253X|ENSP00000376087:S215T	C|S	+|+	3|1	2|0	CASP8|CASP8	201849842|201849842	0.964000|0.964000	0.33143|0.33143	1.000000|1.000000	0.80357|0.80357	0.254000|0.254000	0.26022|0.26022	1.912000|1.912000	0.39946|0.39946	0.954000|0.954000	0.37851|0.37851	0.459000|0.459000	0.35465|0.35465	TGT|TCT	.	.	none		0.448	CASP8-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000336853.2	NM_001228		A	202141597	T	A	202141597	4	1	13	1	0	0	0	0	0	1	0	0	2679	1676	58	5	1011	5	CASP8	2	202141597	Nonsense_Mutation	SNP	T	TCGA-FF-8046-01A-11D-2210-10	11	202141597	41057776	14	1703			1	13		2	2	12	N	T_C	3.269026e-05
ITPR1	3708	hgsc.bcm.edu	37	chr3	4681129	4681129	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caggaaattgctggggaccgTaatccagtatggcaatgtga	12	9	13	7	1	0	1	0	1	0	0	1	3	1	3	2	4	1	4	2	4	4	3			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr3:4681129T>C	ENST00000443694.2	+	4	341	c.341T>C	c.(340-342)gTa>gCa	p.V114A	ITPR1_ENST00000357086.4_Missense_Mutation_p.V114A|ITPR1_ENST00000456211.2_Missense_Mutation_p.V114A|ITPR1_ENST00000423119.2_Missense_Mutation_p.V114A|ITPR1_ENST00000544951.1_Missense_Mutation_p.V114A|ITPR1_ENST00000354582.6_Missense_Mutation_p.V114A|ITPR1_ENST00000302640.8_Missense_Mutation_p.V114A			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	114	MIR 1. {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)	CTGGGGACCGTAATCCAGTAT	0.453																																					p.V114A		Atlas-SNP	.											.	ITPR1	659	.	0			c.T341C						PASS	.						82	85	84					3																	4681129		1986	4151	6137	SO:0001583	missense	3708	exon6			GGACCGTAATCCA	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.341T>C	3.37:g.4681129T>C	ENSP00000401671:p.Val114Ala	92	0	0		93	25	0.268817	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	37	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.610731	0.87258	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000544951;ENST00000443694	D;D;D;D;D;D;D	0.98947	-5.26;-5.26;-5.26;-5.26;-5.26;-5.26;-5.26	5.32	5.32	0.75619	Inositol 1,4,5-trisphosphate/ryanodine receptor (1);MIR motif (2);MIR (1);	0.116894	0.64402	D	0.000020	D	0.98469	0.9490	M	0.81341	2.54	0.40494	D	0.980576	B;P;P;P;P	0.43633	0.353;0.722;0.576;0.512;0.813	B;P;P;P;B	0.50162	0.17;0.633;0.45;0.45;0.432	D	0.99915	1.1220	10	0.22109	T	0.4	.	15.608	0.76689	0.0:0.0:0.0:1.0	.	114;114;114;114;114	B7ZMI3;E7EPX7;Q14643;E7EVP7;G5E9P1	.;.;ITPR1_HUMAN;.;.	A	114	ENSP00000306253:V114A;ENSP00000346595:V114A;ENSP00000405934:V114A;ENSP00000349597:V114A;ENSP00000397885:V114A;ENSP00000440564:V114A;ENSP00000401671:V114A	ENSP00000306253:V114A	V	+	2	0	ITPR1	4656129	1.000000	0.71417	0.050000	0.19076	0.964000	0.63967	7.908000	0.87438	2.141000	0.66446	0.528000	0.53228	GTA	.	.	none		0.453	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		C	4681129	T	C	4681129	3	2	13	1	0	0	0	0	1	0	0	0	7929	1638	57	3	355	3	ITPR1	3	4681129	Missense_Mutation	SNP	T	TCGA-FF-8046-01A-11D-2210-10		4681129	193341301	15	1704											
TATDN2	9797	hgsc.bcm.edu	37	chr3	10318158	10318158	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaaagtttgtgccccctgaCtacaagatccataggttaga	14	10	8	9	0	0	3	0	1	0	2	1	3	1	3	3	1	2	2	3	1	6	4			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr3:10318158C>T	ENST00000287652.4	+	5	2998	c.1947C>T	c.(1945-1947)gaC>gaT	p.D649D	RP11-438J1.1_ENST00000450534.1_3'UTR|TATDN2_ENST00000448281.2_Silent_p.D649D|TATDN2_ENST00000496355.1_3'UTR	NM_014760.3	NP_055575.3	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	649					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						TGCCCCCTGACTACAAGATCC	0.458																																					p.D649D		Atlas-SNP	.											.	TATDN2	59	.	0			c.C1947T						PASS	.						72	65	68					3																	10318158		2203	4300	6503	SO:0001819	synonymous_variant	9797	exon5			CCCTGACTACAAG	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.1947C>T	3.37:g.10318158C>T		58	0	0		52	4	0.0769231	NM_014760	Q3MIL9|Q5BKU0	Silent	SNP	ENST00000287652.4	37	CCDS33698.1																																																																																			.	.	none		0.458	TATDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339641.1	XM_376203		T	10318158	C	T	10318158	2	4	13	1	0	0	0	0	0	0	0	1	15607	564	20	2		2	TATDN2	3	10318158	Silent	SNP	C	TCGA-FF-8046-01A-11D-2210-10	5637029	10318158	187704272	16	1705											
DOCK3	1795	hgsc.bcm.edu	37	chr3	51317590	51317590	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgccagatgtgtgacacccaTttccagcacctcctggacaa	10	8	8	15	1	0	2	0	1	0	1	2	3	2	3	5	1	1	1	5	1	1	1			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr3:51317590T>C	ENST00000266037.9	+	27	2900	c.2877T>C	c.(2875-2877)caT>caC	p.H959H		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	959					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)		GTGACACCCATTTCCAGCACC	0.537																																					p.H959H		Atlas-SNP	.											.	DOCK3	397	.	0			c.T2877C						PASS	.						76	77	77					3																	51317590		2092	4220	6312	SO:0001819	synonymous_variant	1795	exon27			CACCCATTTCCAG	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.2877T>C	3.37:g.51317590T>C		175	0	0		228	64	0.280702	NM_004947	O15017	Silent	SNP	ENST00000266037.9	37	CCDS46835.1																																																																																			.	.	none		0.537	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		C	51317590	T	C	51317590	2	2	13	1	0	0	0	0	0	0	0	1	4690	1490	52	3		3	DOCK3	3	51317590	Silent	SNP	T	TCGA-FF-8046-01A-11D-2210-10	40999432	51317590	146704840	17	1706											
LRIG1	26018	hgsc.bcm.edu	37	chr3	66432748	66432748	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaccctcggtcctgaccaCggtttcttgtcggtcagaaa	7	10	10	14	3	2	2	1	1	1	1	5	2	3	2	4	3	0	1	4	3	1	2	rs147267806		TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr3:66432748C>G	ENST00000273261.3	-	16	3090	c.2566G>C	c.(2566-2568)Gtg>Ctg	p.V856L	SLC25A26_ENST00000536651.1_Intron|LRIG1_ENST00000383703.3_Missense_Mutation_p.V833L|LRIG1_ENST00000496559.2_5'UTR	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	856					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)		GTCCTGACCACGGTTTCTTGT	0.532																																					p.V856L		Atlas-SNP	.											.	LRIG1	138	.	0			c.G2566C						PASS	.						149	153	151					3																	66432748		2203	4300	6503	SO:0001583	missense	26018	exon16			TGACCACGGTTTC	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.2566G>C	3.37:g.66432748C>G	ENSP00000273261:p.Val856Leu	139	0	0		146	39	0.267123	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Missense_Mutation	SNP	ENST00000273261.3	37	CCDS33783.1	.	.	.	.	.	.	.	.	.	.	C	6.761	0.509283	0.12883	.	.	ENSG00000144749	ENST00000273261;ENST00000383703;ENST00000383702	T;T	0.63913	-0.05;-0.07	5.5	2.73	0.32206	.	0.414681	0.26991	N	0.021468	T	0.49813	0.1579	L	0.40543	1.245	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.001	T	0.35549	-0.9784	10	0.33141	T	0.24	.	10.5755	0.45225	0.0:0.7859:0.0:0.2141	.	833;856;856	Q96JA1-2;Q5XWD3;Q96JA1	.;.;LRIG1_HUMAN	L	856;833;759	ENSP00000273261:V856L;ENSP00000373208:V833L	ENSP00000273261:V856L	V	-	1	0	LRIG1	66515438	0.000000	0.05858	0.117000	0.21633	0.136000	0.21042	0.099000	0.15210	0.280000	0.22209	-0.751000	0.03497	GTG	C|1.000;T|0.000	.	alt		0.532	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541		G	66432748	C	G	66432748	3	3	13	1	0	0	0	0	1	0	0	0	8953	536	19	4	731	4	LRIG1	3	66432748	Missense_Mutation	SNP	C	TCGA-FF-8046-01A-11D-2210-10	15115158	66432748	131589682	18	1707											
MITF	4286	hgsc.bcm.edu	37	chr3	69928321	69928321	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cctggggcctccaagcctccGataagctcctccagtatgac	8	8	9	16	1	0	1	0	1	0	0	4	2	4	1	7	2	2	2	7	2	3	2	rs199697494		TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr3:69928321G>A	ENST00000448226.2	+	2	268	c.141G>A	c.(139-141)ccG>ccA	p.P47P	MITF_ENST00000394355.2_Silent_p.P22P|MITF_ENST00000328528.6_Silent_p.P46P|MITF_ENST00000472437.1_5'UTR|MITF_ENST00000314589.5_Silent_p.P31P|MITF_ENST00000352241.4_Silent_p.P47P			O75030	MITF_HUMAN	microphthalmia-associated transcription factor	47					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)		CCAAGCCTCCGATAAGCTCCT	0.537			A		melanoma		"Waardenburg syndrome type 2, Tietz syndrome"						G|||	1	0.000199681	0.0	0.0	5008	,	,		18415	0.001		0.0	False		,,,				2504	0.0				p.P47P	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.G141A						PASS	.						43	48	46					3																	69928321		2035	4202	6237	SO:0001819	synonymous_variant	4286	exon2			GCCTCCGATAAGC		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.141G>A	3.37:g.69928321G>A		107	0	0		93	30	0.322581	NM_198159	B4DJL2|D3K197|E9PFN0|Q14841|Q9P2V0|Q9P2V1|Q9P2V2|Q9P2Y8	Silent	SNP	ENST00000448226.2	37																																																																																				G|1.000;A|0.000	0.000	strong		0.537	MITF-007	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000313947.1	NM_198159		A	69928321	G	A	69928321	2	1	13	1	0	0	0	0	0	0	0	1	9605	1045	37	1		1	MITF	3	69928321	Silent	SNP	G	TCGA-FF-8046-01A-11D-2210-10	3495573	69928321	128094109	19	1708											
CWH43	80157	hgsc.bcm.edu	37	chr4	48990495	48990495	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actttttttttttttgtaggAtgtgtttcttggtctctcta	4	25	7	5	0	3	0	0	0	3	0	4	1	3	1	0	2	0	2	0	2	2	10			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr4:48990495A>G	ENST00000226432.4	+	2	228	c.45A>G	c.(43-45)ggA>ggG	p.G15G	CWH43_ENST00000513409.1_5'UTR	NM_025087.2	NP_079363.2	Q9H720	PG2IP_HUMAN	cell wall biogenesis 43 C-terminal homolog (S. cerevisiae)	15					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						TTTTTGTAGGATGTGTTTCTT	0.418																																					p.G15G		Atlas-SNP	.											.	CWH43	101	.	0			c.A45G						PASS	.						77	79	78					4																	48990495		2203	4300	6503	SO:0001630	splice_region_variant	80157	exon2			TGTAGGATGTGTT		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.44-1A>G	4.37:g.48990495A>G		40	0	0		66	4	0.0606061	NM_025087	B2RPD7	Silent	SNP	ENST00000226432.4	37	CCDS3486.1																																																																																			.	.	none		0.418	CWH43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250496.2	NM_025087	Silent	G	48990495	A	G	48990495	5	3	13	1	0	0	0	0	0	0	1	0	4075	347	12	3	51	3	CWH43	4	48990495	Splice_Site	SNP	A	TCGA-FF-8046-01A-11D-2210-10		48990495	142163781	20	1709											
PLK4	10733	hgsc.bcm.edu	37	chr4	128804641	128804641	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tatgtgtatctggtattagaAatgtgccataatggagaaat	14	14	10	3	0	1	2	0	0	1	2	1	3	1	2	1	2	1	2	1	2	7	5			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr4:128804641A>G	ENST00000270861.5	+	4	544	c.270A>G	c.(268-270)gaA>gaG	p.E90E	PLK4_ENST00000514379.1_Silent_p.E49E|PLK4_ENST00000513090.1_Silent_p.E58E|PLK4_ENST00000515069.1_Silent_p.E90E|PLK4_ENST00000511942.1_3'UTR|PLK4_ENST00000507249.1_Silent_p.E90E	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	90	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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						TGGTATTAGAAATGTGCCATA	0.299																																					p.E90E	Colon(135;508 1718 19061 31832 42879)	Atlas-SNP	.											PLK4,NS,carcinoma,+1,1	PLK4	65	1	0			c.A270G						scavenged	.						66	71	69					4																	128804641		2203	4294	6497	SO:0001819	synonymous_variant	10733	exon4			ATTAGAAATGTGC	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.270A>G	4.37:g.128804641A>G		88	0	0		71	3	0.0422535	NM_014264	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Silent	SNP	ENST00000270861.5	37	CCDS3735.1																																																																																			.	.	none		0.299	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257095.3			G	128804641	A	G	128804641	2	3	13	1	0	0	0	0	0	0	0	1	12107	11	1	3		3	PLK4	4	128804641	Silent	SNP	A	TCGA-FF-8046-01A-11D-2210-10	79814146	128804641	62349635	21	1710											
ACCN5	51802	hgsc.bcm.edu	37	chr4	156784634	156784634	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	aaatgtcacagctgggaactCcatcttttccacatattgaa	13	12	6	10	0	2	1	1	1	1	0	4	2	4	2	2	1	2	1	2	1	4	4			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr4:156784634C>T	ENST00000537611.2	-	2	359	c.313G>A	c.(313-315)Gag>Aag	p.E105K	TDO2_ENST00000506181.1_Intron	NM_017419.2	NP_059115.1	Q9NY37	ASIC5_HUMAN	acid-sensing (proton-gated) ion channel family member 5	105					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrogen ion channel activity (GO:0015252)|ligand-gated sodium channel activity (GO:0015280)										GCTGGGAACTCCATCTTTTCC	0.358																																					p.E105K		Atlas-SNP	.											.	.	.	.	0			c.G313A						PASS	.						73	64	67					4																	156784634		2203	4300	6503	SO:0001583	missense	51802	exon2			GGAACTCCATCTT	AJ252011	CCDS3793.1	4q32.1	2012-10-03	2012-03-02	2012-03-02	ENSG00000256394	ENSG00000256394			17537	protein-coding gene	gene with protein product			"amiloride-sensitive cation channel 5, intestinal"	ACCN5		10767424	Standard	NM_017419		Approved	INAC, HINAC	uc003ipe.1	Q9NY37	OTTHUMG00000161941	ENST00000537611.2:c.313G>A	4.37:g.156784634C>T	ENSP00000442477:p.Glu105Lys	86	0	0		96	4	0.0416667	NM_017419		Missense_Mutation	SNP	ENST00000537611.2	37	CCDS3793.1	.	.	.	.	.	.	.	.	.	.	C	14.43	2.533035	0.45073	.	.	ENSG00000256394	ENST00000537611	T	0.63417	-0.04	4.34	4.34	0.51931	.	0.501251	0.19042	N	0.124277	T	0.48892	0.1525	L	0.40543	1.245	0.80722	D	1	B	0.12630	0.006	B	0.15870	0.014	T	0.36383	-0.9750	10	0.09590	T	0.72	0.3777	11.8835	0.52589	0.0:0.9036:0.0:0.0964	.	105	Q9NY37	ACCN5_HUMAN	K	105	ENSP00000442477:E105K	ENSP00000264432:E105K	E	-	1	0	ACCN5	157004084	0.985000	0.35326	0.997000	0.53966	0.998000	0.95712	2.520000	0.45554	2.369000	0.80426	0.650000	0.86243	GAG	.	.	none		0.358	ASIC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366464.1			T	156784634	C	T	156784634	3	4	13	1	0	0	0	0	1	0	0	0	132	864	30	2	1240	2	ACCN5	4	156784634	Missense_Mutation	SNP	C	TCGA-FF-8046-01A-11D-2210-10	27979993	156784634	34369642	22	1711											
ADAM29	11086	hgsc.bcm.edu	37	chr4	175899130	175899130	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagtcaacctcctgtgacGccctcctagagccaacctca	10	7	7	17	1	2	3	2	1	0	2	4	3	4	3	6	0	3	0	6	0	3	1	rs376108430	byFrequency	TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr4:175899130G>A	ENST00000359240.3	+	5	3124	c.2454G>A	c.(2452-2454)acG>acA	p.T818T	RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000514159.1_Silent_p.T818T|ADAM29_ENST00000404450.4_Silent_p.T818T|ADAM29_ENST00000445694.1_Silent_p.T818T	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	818	9 X 9 AA approximate repeats.				spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.T818T(1)		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)		CTCCTGTGACGCCCTCCTAGA	0.587													G|||	9	0.00179712	0.0	0.0	5008	,	,		17825	0.0069		0.0	False		,,,				2504	0.002				p.T818T	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-SNP	.											ADAM29,NS,carcinoma,0,1	ADAM29	262	1	1	Substitution - coding silent(1)	lung(1)	c.G2454A						scavenged	.	G	,,,	2,4404	4.2+/-10.8	0,2,2201	107	105	106		2454,2454,2454,2454	-1.3	0	4		106	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ADAM29	NM_001130703.1,NM_001130704.1,NM_001130705.1,NM_014269.4	,,,	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	,,,	818/821,818/821,818/821,818/821	175899130	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	11086	exon4			TGTGACGCCCTCC	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.2454G>A	4.37:g.175899130G>A		63	2	0.031746		75	9	0.12	NM_001130703	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Silent	SNP	ENST00000359240.3	37	CCDS3823.1																																																																																			.	.	weak		0.587	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding				A	175899130	G	A	175899130	2	1	13	1	0	0	0	0	0	0	0	1	247	1074	38	1		1	ADAM29	4	175899130	Silent	SNP	G	TCGA-FF-8046-01A-11D-2210-10	19114496	175899130	15255146	23	1712											
ITGA2	3673	hgsc.bcm.edu	37	chr5	52351856	52351856	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acgcccttgatactaaaaatTtaataaaagaaataaaagca	22	9	4	6	1	0	2	0	1	0	1	0	2	0	2	1	0	2	1	1	0	10	7			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr5:52351856T>C	ENST00000296585.5	+	9	1116	c.973T>C	c.(973-975)Tta>Cta	p.L325L		NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)	325	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				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)				TACTAAAAATTTAATAAAAGA	0.358																																					p.L325L		Atlas-SNP	.											.	ITGA2	211	.	0			c.T973C						PASS	.						37	42	41					5																	52351856		2198	4297	6495	SO:0001819	synonymous_variant	3673	exon9			AAAAATTTAATAA		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.973T>C	5.37:g.52351856T>C		79	0	0		102	5	0.0490196	NM_002203	Q14595	Silent	SNP	ENST00000296585.5	37	CCDS3957.1																																																																																			.	.	none		0.358	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203		C	52351856	T	C	52351856	2	2	13	1	0	0	0	0	0	0	0	1	7884	1838	64	3		3	ITGA2	5	52351856	Silent	SNP	T	TCGA-FF-8046-01A-11D-2210-10		52351856	128563404	24	1713											
MSH3	4437	hgsc.bcm.edu	37	chr5	79950717	79950717	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcagcggctgcagcggcCgcagcggccgcagcgccccc	4	2	16	19	6	0	0	0	0	0	0	0	0	0	0	4	3	6	6	4	3	0	0	rs201874762|rs201906899	byFrequency	TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr5:79950717C>T	ENST00000265081.6	+	1	251	c.171C>T	c.(169-171)gcC>gcT	p.A57A	DHFR_ENST00000511032.1_5'Flank|DHFR_ENST00000504396.1_5'Flank|DHFR_ENST00000505337.1_5'Flank|DHFR_ENST00000513048.1_5'Flank|DHFR_ENST00000439211.2_5'UTR	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	57	Poly-Ala.		Missing. {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8942985}.		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)		ctgcagcggccgcagcggccg	0.701								Mismatch excision repair (MMR)					-|||	1025	0.204673	0.2602	0.1715	5008	,	,		6102	0.0466		0.2048	False		,,,				2504	0.316				p.A57A	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											MSH3_ENST00000265081,NS,carcinoma,+2,1	MSH3	129	1	0			c.C171T						scavenged	.						6	7	7					5																	79950717		2068	4046	6114	SO:0001819	synonymous_variant	4437	exon1			AGCGGCCGCAGCG	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.171C>T	5.37:g.79950717C>T		7	0	0		12	3	0.25	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Silent	SNP	ENST00000265081.6	37	CCDS34195.1																																																																																			C|0.979;T|0.021	0.021	strong		0.701	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		T	79950717	C	T	79950717	2	4	13	1	0	0	0	0	0	0	0	1	9880	639	23	1		1	MSH3	5	79950717	Silent	SNP	C	TCGA-FF-8046-01A-11D-2210-10	27598861	79950717	100964543	25	1714											
AQPEP	206338	hgsc.bcm.edu	37	chr5	115351066	115351066	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaaacaaagaagaaaagatTcaacttgcttatgcaatgag	20	8	7	6	0	1	4	1	1	0	3	1	4	1	4	0	0	4	2	0	0	8	3			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr5:115351066T>A	ENST00000357872.4	+	17	2692	c.2568T>A	c.(2566-2568)atT>atA	p.I856I	AQPEP_ENST00000515454.1_3'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		856						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										AAGAAAAGATTCAACTTGCTT	0.343																																					p.I856I		Atlas-SNP	.											FLJ90650,caecum,carcinoma,0,1	.	.	1	0			c.T2568A						scavenged	.						91	87	88					5																	115351066		2202	4300	6502	SO:0001819	synonymous_variant	0	exon17			AAAGATTCAACTT																												ENST00000357872.4:c.2568T>A	5.37:g.115351066T>A		46	2	0.0434783		45	3	0.0666667	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Silent	SNP	ENST00000357872.4	37	CCDS4124.1																																																																																			.	.	none		0.343	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1			A	115351066	T	A	115351066	2	1	13	1	0	0	0	0	0	0	0	1	834	1771	62	5		5	AQPEP	5	115351066	Silent	SNP	T	TCGA-FF-8046-01A-11D-2210-10	35400349	115351066	65564194	26	1715											
RBM27	54439	hgsc.bcm.edu	37	chr5	145631422	145631422	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catacctcagtctccagcccTacccctctggttccaggtaa	8	10	6	17	0	3	0	1	0	2	0	5	0	4	0	6	2	3	2	6	2	3	4			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr5:145631422T>C	ENST00000265271.5	+	9	1594	c.1428T>C	c.(1426-1428)ccT>ccC	p.P476P	RBM27_ENST00000506502.1_Intron	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	476					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)			TCTCCAGCCCTACCCCTCTGG	0.547																																					p.P476P		Atlas-SNP	.											.	RBM27	119	.	0			c.T1428C						PASS	.						246	226	232					5																	145631422		1568	3582	5150	SO:0001819	synonymous_variant	54439	exon9			CAGCCCTACCCCT	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.1428T>C	5.37:g.145631422T>C		70	0	0		82	4	0.0487805	NM_018989	Q8IYW9	Silent	SNP	ENST00000265271.5	37	CCDS43378.1																																																																																			.	.	none		0.547	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128		C	145631422	T	C	145631422	2	2	13	1	0	0	0	0	0	0	0	1	13142	1509	53	3		3	RBM27	5	145631422	Silent	SNP	T	TCGA-FF-8046-01A-11D-2210-10	30280356	145631422	35283838	27	1716											
HAVCR1	26762	hgsc.bcm.edu	37	chr5	156479571	156479571	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gttgtcgttggaacagtcgtCattggaacagtcgttgtcgt	7	14	13	7	4	1	0	1	0	0	0	5	2	1	2	0	2	2	3	0	2	2	4	rs6149307|rs386693994|rs183130208|rs141023871	byFrequency	TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	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_ENST00000522693.1_Missense_Mutation_p.M158I|HAVCR1_ENST00000425854.1_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						PASS	.						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	5.37:g.156479571C>T	ENSP00000344844:p.Met158Ile	342	0	0		437	23	0.0526316	NM_001099414	O43656	Missense_Mutation	SNP	ENST00000339252.3	37	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	.	.	weak		0.488	HAVCR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373698.1			T	156479571	C	T	156479571	3	4	13	1	0	0	0	0	1	0	0	0	6982	826	29	2	644	2	HAVCR1	5	156479571	Missense_Mutation	SNP	C	TCGA-FF-8046-01A-11D-2210-10	10848149	156479571	24435689	28	1717											
NUP153	9972	hgsc.bcm.edu	37	chr6	17706506	17706506	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccgcggcgtcggggtcccatAcctgatgctgttgtcgcccc	3	9	13	16	5	0	1	0	1	0	0	3	1	1	1	5	3	2	2	5	3	1	2			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr6:17706506A>T	ENST00000262077.2	-	1	111		c.e1+1		RP11-500C11.3_ENST00000606771.1_RNA|NUP153_ENST00000537253.1_Splice_Site	NM_005124.2	NP_005115.2	P49790	NU153_HUMAN	nucleoporin 153kDa						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)			GGGGTCCCATACCTGATGCTG	0.716																																					.		Atlas-SNP	.											.	NUP153	116	.	0			c.111+2T>A						PASS	.						59	49	52					6																	17706506		2200	4299	6499	SO:0001630	splice_region_variant	9972	exon2			TCCCATACCTGAT	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.111+1T>A	6.37:g.17706506A>T		72	0	0		37	11	0.297297	NM_005124	B4DIK2|E7EPX5|F6QR24|Q4LE47|Q5T9I7|Q7Z743	Splice_Site	SNP	ENST00000262077.2	37	CCDS4541.1	.	.	.	.	.	.	.	.	.	.	A	12.30	1.898108	0.33535	.	.	ENSG00000124789	ENST00000262077;ENST00000430136;ENST00000537253	.	.	.	3.91	3.91	0.45181	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.4521	0.38731	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NUP153	17814485	1.000000	0.71417	0.977000	0.42913	0.328000	0.28507	2.201000	0.42734	2.006000	0.58801	0.482000	0.46254	.	.	.	none		0.716	NUP153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039953.1		Intron	T	17706506	A	T	17706506	5	4	13	1	0	0	0	0	0	0	1	0	10764	405	14	5	4402	5	NUP153	6	17706506	Splice_Site	SNP	A	TCGA-FF-8046-01A-11D-2210-10		17706506	153408561	29	1718											
HIST1H2AC	8334	hgsc.bcm.edu	37	chr6	26124688	26124688	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcggctcgcgacaacaagaaGactcgcatcatcccgcgcca	11	4	10	16	6	1	2	1	0	0	2	4	3	2	2	2	1	1	2	2	1	3	0			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr6:26124688G>A	ENST00000602637.1	+	1	258	c.228G>A	c.(226-228)aaG>aaA	p.K76K	HIST1H2AC_ENST00000377791.2_Silent_p.K76K|HIST1H2BC_ENST00000396984.1_5'Flank|HIST1H2BC_ENST00000314332.5_5'Flank			Q93077	H2A1C_HUMAN	histone cluster 1, H2ac	76						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(5)	12						ACAACAAGAAGACTCGCATCA	0.657																																					p.K76K		Atlas-SNP	.											.	HIST1H2AC	29	.	0			c.G228A						PASS	.						97	94	95					6																	26124688		2203	4300	6503	SO:0001819	synonymous_variant	8334	exon1			CAAGAAGACTCGC	Z80778	CCDS4585.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000180573	ENSG00000180573		"Histones / Replication-dependent"	4733	protein-coding gene	gene with protein product		602794	"H2A histone family, member L", "histone 1, H2ac"	H2AFL		9119399, 12408966	Standard	NM_003512		Approved		uc003ngm.3	Q93077	OTTHUMG00000014428	ENST00000602637.1:c.228G>A	6.37:g.26124688G>A		276	0	0		265	59	0.222642	NM_003512	B2R4F7|O00775|O00776|O00777|O00778|Q540R1	Silent	SNP	ENST00000602637.1	37	CCDS4585.1																																																																																			.	.	none		0.657	HIST1H2AC-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468023.1	NM_003512		A	26124688	G	A	26124688	2	1	13	1	0	0	0	0	0	0	0	1	7139	933	33	2		2	HIST1H2AC	6	26124688	Silent	SNP	G	TCGA-FF-8046-01A-11D-2210-10	8418182	26124688	144990379	30	1719											
GRM4	2914	hgsc.bcm.edu	37	chr6	34004150	34004150	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ggcgagccccactcaagcttGatgatggggatgggccggca	8	6	16	11	2	1	2	1	2	0	0	1	4	1	3	3	5	2	2	3	5	1	1			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr6:34004150G>C	ENST00000538487.2	-	9	2180	c.1737C>G	c.(1735-1737)atC>atG	p.I579M	GRM4_ENST00000374181.4_Missense_Mutation_p.I579M|GRM4_ENST00000545715.1_5'UTR|GRM4_ENST00000535756.1_Missense_Mutation_p.I446M|GRM4_ENST00000609222.1_Missense_Mutation_p.I446M|GRM4_ENST00000544773.2_Missense_Mutation_p.I410M|GRM4_ENST00000455714.2_Missense_Mutation_p.I439M|GRM4_ENST00000374177.3_Missense_Mutation_p.I463M	NM_000841.2|NM_001256811.1	NP_000832.1|NP_001243740.1	Q14833	GRM4_HUMAN	glutamate receptor, metabotropic 4	579					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						ACTCAAGCTTGATGATGGGGA	0.632																																					p.I579M		Atlas-SNP	.											.	GRM4	317	.	0			c.C1737G						PASS	.						47	45	46					6																	34004150		2203	4300	6503	SO:0001583	missense	2914	exon9			AAGCTTGATGATG	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.1737C>G	6.37:g.34004150G>C	ENSP00000440556:p.Ile579Met	87	0	0		79	15	0.189873	NM_000841	B3KVL9|B7Z1T9|B7Z1U6|F5GXM5|Q5SZ84|Q6ZMQ2	Missense_Mutation	SNP	ENST00000538487.2	37	CCDS4787.1	.	.	.	.	.	.	.	.	.	.	G	10.53	1.376436	0.24857	.	.	ENSG00000124493	ENST00000374181;ENST00000374177;ENST00000545715;ENST00000535756;ENST00000544773;ENST00000538487;ENST00000455714	D;D;D;D;D;D;D	0.88201	-2.35;-2.34;-2.1;-2.14;-2.17;-2.35;-2.18	4.81	2.11	0.27256	.	0.230082	0.44483	D	0.000446	D	0.84880	0.5570	M	0.76328	2.33	0.29060	N	0.883982	B;P;P;P;P	0.44344	0.447;0.58;0.773;0.664;0.833	B;B;P;B;B	0.48840	0.326;0.39;0.592;0.216;0.438	T	0.78899	-0.2022	10	0.49607	T	0.09	.	9.8402	0.40993	0.2272:0.0:0.7728:0.0	.	532;410;439;579;446	B7ZLU9;B7Z1T9;F5GXM5;Q14833;B3KVL9	.;.;.;GRM4_HUMAN;.	M	579;463;271;446;410;579;439	ENSP00000363296:I579M;ENSP00000363292:I463M;ENSP00000445533:I271M;ENSP00000437925:I446M;ENSP00000437730:I410M;ENSP00000440556:I579M;ENSP00000398456:I439M	ENSP00000363292:I463M	I	-	3	3	GRM4	34112128	1.000000	0.71417	1.000000	0.80357	0.380000	0.30137	1.355000	0.34068	0.259000	0.21709	-0.480000	0.04831	ATC	.	.	none		0.632	GRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040213.2			C	34004150	G	C	34004150	3	2	13	1	0	0	0	0	1	0	0	0	6808	1280	45	4	1013	4	GRM4	6	34004150	Missense_Mutation	SNP	G	TCGA-FF-8046-01A-11D-2210-10	7879462	34004150	137110917	31	1720											
TMEM30A	55754	hgsc.bcm.edu	37	chr6	75969072	75969072	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	taatgttttacctttaaatcGttcttccaggttgtctcctc	7	19	5	10	1	2	0	0	0	2	0	6	0	3	0	3	1	1	3	3	1	4	8			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr6:75969072G>A	ENST00000230461.6	-	5	1005	c.676C>T	c.(676-678)Cga>Tga	p.R226*	TMEM30A_ENST00000475111.2_Nonsense_Mutation_p.R190*|TMEM30A_ENST00000370050.5_Nonsense_Mutation_p.R107*	NM_018247.3	NP_060717.1	Q9NV96	CC50A_HUMAN	transmembrane protein 30A	226					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)		p.R226*(1)		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						CCTTTAAATCGTTCTTCCAGG	0.308																																					p.R226X		Atlas-SNP	.											TMEM30A,caecum,carcinoma,0,2	TMEM30A	40	2	1	Substitution - Nonsense(1)	lung(1)	c.C676T						PASS	.						74	79	77					6																	75969072		2203	4298	6501	SO:0001587	stop_gained	55754	exon5			TAAATCGTTCTTC	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.676C>T	6.37:g.75969072G>A	ENSP00000230461:p.Arg226*	199	0	0		140	51	0.364286	NM_018247	A8K9V8|E1P539|Q658Z3|Q96H09|Q9NSL9	Nonsense_Mutation	SNP	ENST00000230461.6	37	CCDS4983.1	.	.	.	.	.	.	.	.	.	.	G	39	7.311733	0.98203	.	.	ENSG00000112697	ENST00000230461;ENST00000545449;ENST00000370050;ENST00000475111	.	.	.	5.51	2.43	0.29744	.	0.572479	0.17857	N	0.159668	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	.	10.4926	0.44760	0.0:0.1178:0.5054:0.3768	.	.	.	.	X	226;210;107;190	.	ENSP00000230461:R226X	R	-	1	2	TMEM30A	76025792	0.004000	0.15560	1.000000	0.80357	0.933000	0.57130	0.839000	0.27586	0.724000	0.32296	0.655000	0.94253	CGA	.	.	none		0.308	TMEM30A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041248.2	NM_018247		A	75969072	G	A	75969072	4	1	13	1	0	0	0	0	0	1	0	0	16168	1153	40	1	421	1	TMEM30A	6	75969072	Nonsense_Mutation	SNP	G	TCGA-FF-8046-01A-11D-2210-10	41964922	75969072	95145995	32	1721											
TMEM184A	202915	hgsc.bcm.edu	37	chr7	1590488	1590488	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcacagagtcgaagtagacgTagtactggtggtctccgagg	10	8	15	8	3	1	2	0	0	1	2	3	4	1	2	1	3	1	4	1	3	4	3			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr7:1590488T>C	ENST00000297477.5	-	3	666	c.350A>G	c.(349-351)tAc>tGc	p.Y117C		NM_001097620.1	NP_001091089.1	Q6ZMB5	T184A_HUMAN	transmembrane protein 184A	117					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)		GAAGTAGACGTAGTACTGGTG	0.647																																					p.Y117C		Atlas-SNP	.											.	TMEM184A	35	.	0			c.A350G						PASS	.						82	89	87					7																	1590488		2203	4300	6503	SO:0001583	missense	202915	exon3			TAGACGTAGTACT		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.350A>G	7.37:g.1590488T>C	ENSP00000297477:p.Tyr117Cys	62	0	0		62	4	0.0645161	NM_001097620	Q8TBQ6	Missense_Mutation	SNP	ENST00000297477.5	37	CCDS43537.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.114546	0.77210	.	.	ENSG00000164855	ENST00000297477;ENST00000319010;ENST00000414730;ENST00000441933;ENST00000431208	T;T;T;T;T	0.49139	1.42;0.84;0.79;0.81;0.81	5.03	5.03	0.67393	.	0.000000	0.85682	U	0.000000	T	0.73466	0.3590	M	0.89601	3.045	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.79240	-0.1885	10	0.54805	T	0.06	0.0726	14.7478	0.69501	0.0:0.0:0.0:1.0	.	117	Q6ZMB5	T184A_HUMAN	C	117	ENSP00000297477:Y117C;ENSP00000325945:Y117C;ENSP00000398382:Y117C;ENSP00000389092:Y117C;ENSP00000403499:Y117C	ENSP00000297477:Y117C	Y	-	2	0	TMEM184A	1557014	1.000000	0.71417	0.939000	0.37840	0.784000	0.44337	7.869000	0.87170	1.891000	0.54761	0.334000	0.21626	TAC	.	.	none		0.647	TMEM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239229.4	NM_152689		C	1590488	T	C	1590488	3	2	13	1	0	0	0	0	1	0	0	0	16119	1638	57	3	919	3	TMEM184A	7	1590488	Missense_Mutation	SNP	T	TCGA-FF-8046-01A-11D-2210-10		1590488	157548175	33	1722											
FKBP9	11328	hgsc.bcm.edu	37	chr7	33014897	33014897	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cacacctatttcaagcccccGagttgccctcggaccatcca	9	8	6	18	2	1	0	1	0	0	0	3	2	2	1	6	1	2	1	6	1	2	3			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr7:33014897G>A	ENST00000242209.4	+	3	640	c.471G>A	c.(469-471)ccG>ccA	p.P157P	FKBP9_ENST00000538443.1_Silent_p.P19P|AVL9_ENST00000404479.1_Intron|FKBP9_ENST00000538336.1_Silent_p.P210P	NM_001284343.1|NM_007270.3	NP_001271272.1|NP_009201.2	O95302	FKBP9_HUMAN	FK506 binding protein 9, 63 kDa	157					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)			TCAAGCCCCCGAGTTGCCCTC	0.483																																					p.P157P		Atlas-SNP	.											FKBP9,brain,glioma,+1,9	FKBP9	335	9	0			c.G471A						scavenged	.						100	90	93					7																	33014897		2203	4300	6503	SO:0001819	synonymous_variant	11328	exon3			GCCCCCGAGTTGC	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.471G>A	7.37:g.33014897G>A		138	1	0.00724638		135	43	0.318519	NM_007270	B3KY35|B7Z1G9|B7Z6H3|Q2M2A1|Q3MIR7|Q6IN76|Q6P2N1|Q96EX5|Q96IJ9	Silent	SNP	ENST00000242209.4	37	CCDS5439.1																																																																																			.	.	none		0.483	FKBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215137.1	NM_007270		A	33014897	G	A	33014897	2	1	13	1	0	0	0	0	0	0	0	1	5923	1045	37	1		1	FKBP9	7	33014897	Silent	SNP	G	TCGA-FF-8046-01A-11D-2210-10	31424409	33014897	126123766	34	1723											
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47873941	47873941	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ataatgattgatttaccttgCgtggctcctgtgcgtctggt	6	16	11	8	2	1	2	0	2	1	0	2	2	2	2	2	2	3	1	2	2	2	5	rs17131834	byFrequency	TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr7:47873941C>T	ENST00000289672.2	-	40	6220	c.6170G>A	c.(6169-6171)cGc>cAc	p.R2057H		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2057			R -> H (in dbSNP:rs17131834).		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						ATTTACCTTGCGTGGCTCCTG	0.428													C|||	98	0.0195687	0.0696	0.0072	5008	,	,		21422	0.001		0.0	False		,,,				2504	0.0				p.R2057H		Atlas-SNP	.											.	PKD1L1	328	.	0			c.G6170A						PASS	.	C	HIS/ARG	203,4203	125.3+/-162.5	6,191,2006	144	128	134		6170	-7.9	0	7	dbSNP_123	134	0,8600		0,0,4300	yes	missense	PKD1L1	NM_138295.3	29	6,191,6306	TT,TC,CC		0.0,4.6074,1.5608	benign	2057/2850	47873941	203,12803	2203	4300	6503	SO:0001583	missense	168507	exon40			ACCTTGCGTGGCT	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.6170G>A	7.37:g.47873941C>T	ENSP00000289672:p.Arg2057His	81	0	0		81	4	0.0493827	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	37	0.01694139194139194	32	0.06504065040650407	4	0.011049723756906077	1	0.0017482517482517483	0	0.0	C	3.158	-0.172750	0.06421	0.046074	0.0	ENSG00000158683	ENST00000289672	T	0.19669	2.13	3.93	-7.87	0.01183	.	2749.160000	0.00357	U	0.000035	T	0.00724	0.0024	N	0.22421	0.69	0.09310	N	1	B	0.31077	0.307	B	0.20384	0.029	T	0.06534	-1.0821	10	0.15499	T	0.54	.	8.1002	0.30852	0.0:0.1383:0.574:0.2877	rs17131834	2057	Q8TDX9	PK1L1_HUMAN	H	2057	ENSP00000289672:R2057H	ENSP00000289672:R2057H	R	-	2	0	PKD1L1	47840466	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.982000	0.03762	-2.060000	0.00893	-0.369000	0.07265	CGC	C|0.978;T|0.022	0.022	strong		0.428	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		T	47873941	C	T	47873941	3	4	13	1	0	0	0	0	1	0	0	0	11973	768	27	1	2451	1	PKD1L1	7	47873941	Missense_Mutation	SNP	C	TCGA-FF-8046-01A-11D-2210-10	14859044	47873941	111264722	35	1724											
TSGA14	95681	hgsc.bcm.edu	37	chr7	130067800	130067800	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctaatctttactcaccagtGtccagtcttgatttgatatg	9	17	6	9	0	4	2	1	2	3	0	5	2	5	2	2	0	1	0	2	0	3	6			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr7:130067800G>T	ENST00000223208.5	-	2	363	c.93C>A	c.(91-93)gaC>gaA	p.D31E	CEP41_ENST00000489512.1_Missense_Mutation_p.D31E|CEP41_ENST00000495702.1_5'UTR|CEP41_ENST00000343969.5_Missense_Mutation_p.D31E|CEP41_ENST00000541543.1_Missense_Mutation_p.D31E	NM_001257158.1|NM_018718.2	NP_001244087.1|NP_061188.1	Q9BYV8	CEP41_HUMAN	centrosomal protein 41kDa	31					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)											ACTCACCAGTGTCCAGTCTTG	0.303																																					p.D31E		Atlas-SNP	.											.	.	.	.	0			c.C93A						PASS	.						80	79	79					7																	130067800		2203	4300	6503	SO:0001583	missense	95681	exon2			ACCAGTGTCCAGT	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.93C>A	7.37:g.130067800G>T	ENSP00000223208:p.Asp31Glu	66	0	0		64	25	0.390625	NM_001257159	A4D1M0|B4DQ35|F5H0V6|Q7Z496|Q86TM1|Q8NFU8|Q9H6A3|Q9NPV3	Missense_Mutation	SNP	ENST00000223208.5	37	CCDS5821.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.756933	0.69648	.	.	ENSG00000106477	ENST00000223208;ENST00000541543;ENST00000343969;ENST00000477003;ENST00000469826;ENST00000489512	D;D;D;D;D	0.92965	-3.14;-2.34;-3.06;-2.83;-2.61	5.68	2.79	0.32731	.	0.000000	0.85682	D	0.000000	D	0.95085	0.8408	M	0.82630	2.6	0.46901	D	0.999244	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.83275	0.996;0.984;0.948	D	0.93213	0.6602	10	0.87932	D	0	-10.9368	6.9984	0.24795	0.3038:0.0:0.6962:0.0	.	31;31;31	F5H0V6;Q9BYV8-2;Q9BYV8	.;.;CEP41_HUMAN	E	31;31;31;28;18;31	ENSP00000223208:D31E;ENSP00000445888:D31E;ENSP00000342738:D31E;ENSP00000420670:D28E;ENSP00000418712:D18E	ENSP00000223208:D31E	D	-	3	2	TSGA14	129855036	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	0.757000	0.26433	0.282000	0.22254	0.591000	0.81541	GAC	.	.	none		0.303	CEP41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349702.2	NM_018718		T	130067800	G	T	130067800	3	4	13	1	0	0	0	0	1	0	0	0	16635	1368	48	4	1068	4	TSGA14	7	130067800	Missense_Mutation	SNP	G	TCGA-FF-8046-01A-11D-2210-10	82193859	130067800	29070863	36	1725											
MTMR7	9108	hgsc.bcm.edu	37	chr8	17206499	17206499	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agtaagaaaggacaggaaatCgccgtctactccggaatttg	14	8	11	8	3	1	1	0	0	1	1	3	4	2	4	2	3	1	1	2	3	5	3			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr8:17206499C>T	ENST00000180173.5	-	5	594	c.560G>A	c.(559-561)cGa>cAa	p.R187Q	MTMR7_ENST00000523571.1_5'UTR|MTMR7_ENST00000521857.1_Missense_Mutation_p.R187Q	NM_004686.4	NP_004677.3	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	187	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)		GACAGGAAATCGCCGTCTACT	0.433																																					p.R187Q		Atlas-SNP	.											MTMR7,NS,carcinoma,0,1	MTMR7	75	1	0			c.G560A						scavenged	.						135	129	131					8																	17206499		2203	4300	6503	SO:0001583	missense	9108	exon5			GGAAATCGCCGTC	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.560G>A	8.37:g.17206499C>T	ENSP00000180173:p.Arg187Gln	58	0	0		71	3	0.0422535	NM_004686	A1L4K9|B4DG87|Q68DX4	Missense_Mutation	SNP	ENST00000180173.5	37	CCDS34851.1	.	.	.	.	.	.	.	.	.	.	C	35	5.516652	0.96402	.	.	ENSG00000003987	ENST00000180173;ENST00000521857	D;D	0.98135	-4.74;-4.74	5.24	5.24	0.73138	Myotubularin phosphatase domain (1);Myotubularin-related (1);	0.000000	0.85682	D	0.000000	D	0.99272	0.9746	H	0.99286	4.5	0.80722	D	1	D	0.76494	0.999	P	0.59288	0.855	D	0.98623	1.0668	10	0.87932	D	0	.	19.719	0.96135	0.0:1.0:0.0:0.0	.	187	Q9Y216	MTMR7_HUMAN	Q	187	ENSP00000180173:R187Q;ENSP00000429733:R187Q	ENSP00000180173:R187Q	R	-	2	0	MTMR7	17250870	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.364000	0.79526	2.828000	0.97474	0.655000	0.94253	CGA	.	.	none		0.433	MTMR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375311.1	NM_004686		T	17206499	C	T	17206499	3	4	13	1	0	0	0	0	1	0	0	0	9957	884	31	1	1462	1	MTMR7	8	17206499	Missense_Mutation	SNP	C	TCGA-FF-8046-01A-11D-2210-10		17206499	129157523	37	1726											
LGI3	203190	hgsc.bcm.edu	37	chr8	22005779	22005779	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caggcatgtagcagaaggccCgaggagcctgcacagccagc	11	3	14	13	1	0	1	0	0	0	1	0	3	0	2	3	3	5	4	3	3	2	1			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr8:22005779C>T	ENST00000306317.2	-	8	1830	c.1541G>A	c.(1540-1542)cGg>cAg	p.R514Q	LGI3_ENST00000424267.2_Missense_Mutation_p.R490Q	NM_139278.2	NP_644807.1	Q8N145	LGI3_HUMAN	leucine-rich repeat LGI family, member 3	514					exocytosis (GO:0006887)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|extracellular region (GO:0005576)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	catalytic activity (GO:0003824)			endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	17				Colorectal(74;0.00189)|COAD - Colon adenocarcinoma(73;0.0612)|READ - Rectum adenocarcinoma(644;0.0999)		GCAGAAGGCCCGAGGAGCCTG	0.582																																					p.R514Q		Atlas-SNP	.											LGI3,mouth,carcinoma,-1,1	LGI3	44	1	0			c.G1541A						scavenged	.						70	64	66					8																	22005779		2203	4300	6503	SO:0001583	missense	203190	exon8			AAGGCCCGAGGAG	AJ487518	CCDS6025.1	8p21.2	2008-07-28			ENSG00000168481	ENSG00000168481			18711	protein-coding gene	gene with protein product		608302				12023020, 18628660	Standard	NM_139278		Approved		uc003xav.3	Q8N145	OTTHUMG00000131599	ENST00000306317.2:c.1541G>A	8.37:g.22005779C>T	ENSP00000302297:p.Arg514Gln	62	1	0.016129		47	8	0.170213	NM_139278	A5PLP2|Q86TL4|Q8N296	Missense_Mutation	SNP	ENST00000306317.2	37	CCDS6025.1	.	.	.	.	.	.	.	.	.	.	C	28.9	4.962688	0.92791	.	.	ENSG00000168481	ENST00000306317;ENST00000424267	T;T	0.80994	-1.44;-1.44	4.95	4.95	0.65309	.	0.000000	0.64402	D	0.000001	D	0.89022	0.6597	M	0.73598	2.24	0.52501	D	0.99995	D;D	0.71674	0.998;0.998	D;D	0.76575	0.988;0.988	D	0.90464	0.4448	10	0.87932	D	0	-46.0234	15.6803	0.77364	0.0:1.0:0.0:0.0	.	490;514	A5PLP2;Q8N145	.;LGI3_HUMAN	Q	514;490	ENSP00000302297:R514Q;ENSP00000399121:R490Q	ENSP00000302297:R514Q	R	-	2	0	LGI3	22061724	0.981000	0.34729	0.993000	0.49108	0.994000	0.84299	7.479000	0.81095	2.246000	0.74042	0.561000	0.74099	CGG	.	.	none		0.582	LGI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254482.1			T	22005779	C	T	22005779	3	4	13	1	0	0	0	0	1	0	0	0	8762	652	23	1	109	1	LGI3	8	22005779	Missense_Mutation	SNP	C	TCGA-FF-8046-01A-11D-2210-10	4799280	22005779	124358243	38	1727											
TACC1	6867	hgsc.bcm.edu	37	chr8	38677553	38677553	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acctctccccaaggcatcctAtcacttcagtcctgaagagt	10	10	6	15	0	3	2	2	1	1	1	6	2	5	2	5	1	0	1	5	1	3	2			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr8:38677553A>G	ENST00000317827.4	+	3	1170	c.791A>G	c.(790-792)tAt>tGt	p.Y264C	TACC1_ENST00000520611.1_5'Flank|TACC1_ENST00000520973.1_Missense_Mutation_p.Y69C|TACC1_ENST00000520615.1_Missense_Mutation_p.Y69C|TACC1_ENST00000330691.6_Intron|TACC1_ENST00000276520.8_Intron|TACC1_ENST00000379931.3_Missense_Mutation_p.Y264C|TACC1_ENST00000518415.1_Missense_Mutation_p.Y219C|TACC1_ENST00000348567.4_Intron|TACC1_ENST00000522752.1_Intron|TACC1_ENST00000520340.1_Missense_Mutation_p.Y228C|TACC1_ENST00000519416.1_Missense_Mutation_p.Y69C|TACC1_ENST00000443286.2_Missense_Mutation_p.Y280C	NM_006283.2	NP_006274.2	O75410	TACC1_HUMAN	transforming, acidic coiled-coil containing protein 1	264	Interaction with YEATS4.|SPAZ 1.				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)			AAGGCATCCTATCACTTCAGT	0.532																																					p.Y264C		Atlas-SNP	.											.	TACC1	98	.	0			c.A791G						PASS	.						40	41	40					8																	38677553		2203	4300	6503	SO:0001583	missense	6867	exon3			CATCCTATCACTT	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.791A>G	8.37:g.38677553A>G	ENSP00000321703:p.Tyr264Cys	16	0	0		22	7	0.318182	NM_006283	B2RBD9|D3DSX6|Q6Y687|Q86YG7|Q8IUJ2|Q8IUJ3|Q8IUJ4|Q8IZG2|Q8NEY7|Q9UPP9	Missense_Mutation	SNP	ENST00000317827.4	37	CCDS6109.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.514|0.514	-0.865152|-0.865152	0.02590|0.02590	.|.	.|.	ENSG00000147526|ENSG00000147526	ENST00000521866|ENST00000519416;ENST00000520615;ENST00000443388;ENST00000443286;ENST00000518415;ENST00000522904;ENST00000317827;ENST00000379931;ENST00000520973;ENST00000521935	.|T;T;T;T;T;T;T;T;T	.|0.45668	.|2.63;2.63;2.74;2.71;2.56;2.78;2.77;2.58;0.89	4.93|4.93	-1.26|-1.26	0.09376|0.09376	.|.	.|0.676508	.|0.14325	.|N	.|0.326751	T|T	0.26159|0.26159	0.0638|0.0638	L|L	0.33485|0.33485	1.01|1.01	0.09310|0.09310	N|N	1|1	.|B;B;B;B;B;B;B;B	.|0.17667	.|0.023;0.009;0.009;0.004;0.004;0.004;0.002;0.02	.|B;B;B;B;B;B;B;B	.|0.18871	.|0.015;0.007;0.005;0.005;0.006;0.003;0.001;0.023	T|T	0.13818|0.13818	-1.0495|-1.0495	5|10	.|0.42905	.|T	.|0.14	1.732|1.732	4.9397|4.9397	0.13960|0.13960	0.4702:0.2082:0.3216:0.0|0.4702:0.2082:0.3216:0.0	.|.	.|69;69;69;280;264;264;69;219	.|B7Z3G3;E7EVI4;B4DH49;B4E302;O75410-2;O75410;E7ET87;O75410-7	.|.;.;.;.;.;TACC1_HUMAN;.;.	V|C	39|69;69;69;280;219;236;264;264;69;69	.|ENSP00000428687:Y69C;ENSP00000428450:Y69C;ENSP00000393647:Y280C;ENSP00000428706:Y219C;ENSP00000430355:Y236C;ENSP00000321703:Y264C;ENSP00000369263:Y264C;ENSP00000430959:Y69C;ENSP00000428175:Y69C	.|ENSP00000321703:Y264C	I|Y	+|+	1|2	0|0	TACC1|TACC1	38796710|38796710	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.044000|0.044000	0.14063|0.14063	0.935000|0.935000	0.28924|0.28924	-0.540000|-0.540000	0.06265|0.06265	-0.376000|-0.376000	0.06991|0.06991	ATC|TAT	.	.	none		0.532	TACC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376768.1	NM_006283		G	38677553	A	G	38677553	3	3	13	1	0	0	0	0	1	0	0	0	15516	449	16	3	801	3	TACC1	8	38677553	Missense_Mutation	SNP	A	TCGA-FF-8046-01A-11D-2210-10	16671774	38677553	107686469	39	1728											
IKBKB	3551	hgsc.bcm.edu	37	chr8	42166458	42166458	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagaagtacacagtgaccGtcgactactggagcttcggc	11	7	12	11	3	0	2	0	1	0	1	2	4	0	3	1	2	4	3	1	2	3	3			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr8:42166458G>A	ENST00000520810.1	+	8	793	c.607G>A	c.(607-609)Gtc>Atc	p.V203I	IKBKB_ENST00000519735.1_Missense_Mutation_p.V203I|IKBKB_ENST00000379708.3_Intron|IKBKB_ENST00000520835.1_Missense_Mutation_p.V201I|IKBKB_ENST00000416505.2_Missense_Mutation_p.V144I|IKBKB_ENST00000522147.1_Intron	NM_001556.2	NP_001547.1	O14920	IKKB_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta	203	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)	CACAGTGACCGTCGACTACTG	0.657																																					p.V203I		Atlas-SNP	.											.	IKBKB	88	.	0			c.G607A						PASS	.						149	129	136					8																	42166458		2203	4300	6503	SO:0001583	missense	3551	exon8			GTGACCGTCGACT	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.607G>A	8.37:g.42166458G>A	ENSP00000430684:p.Val203Ile	104	0	0		91	36	0.395604	NM_001556	B4DZ30|B4E0U4|O75327	Missense_Mutation	SNP	ENST00000520810.1	37	CCDS6128.1	.	.	.	.	.	.	.	.	.	.	G	34	5.373729	0.95923	.	.	ENSG00000104365	ENST00000520810;ENST00000416505;ENST00000519735;ENST00000520835	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	4.92	4.92	0.64577	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	0.62392	0.2424	M	0.62209	1.925	0.80722	D	1	P;D;D;D;D	0.76494	0.947;0.994;0.998;0.999;0.986	B;P;D;D;P	0.68621	0.4;0.864;0.959;0.915;0.834	T	0.64630	-0.6362	10	0.56958	D	0.05	.	18.4904	0.90844	0.0:0.0:1.0:0.0	.	144;201;154;203;203	B4E0U4;O14920-2;Q59GL9;O14920;Q32ND9	.;.;.;IKKB_HUMAN;.	I	203;144;203;201	ENSP00000430684:V203I;ENSP00000404920:V144I;ENSP00000430483:V203I;ENSP00000430868:V201I	ENSP00000404920:V144I	V	+	1	0	IKBKB	42285615	1.000000	0.71417	0.833000	0.33012	0.967000	0.64934	9.743000	0.98849	2.437000	0.82529	0.563000	0.77884	GTC	.	.	none		0.657	IKBKB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377214.1			A	42166458	G	A	42166458	3	1	13	1	0	0	0	0	1	0	0	0	7620	1145	40	1	633	1	IKBKB	8	42166458	Missense_Mutation	SNP	G	TCGA-FF-8046-01A-11D-2210-10	3488905	42166458	104197564	40	1729											
CNGB3	54714	hgsc.bcm.edu	37	chr8	87641188	87641188	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtatattcataccaagtcCgaactcgcttttgcacaagt	12	13	6	10	2	1	0	1	0	0	0	3	1	2	0	2	0	3	3	2	0	6	6	rs77277189	byFrequency	TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr8:87641188C>T	ENST00000320005.5	-	12	1486	c.1439G>A	c.(1438-1440)cGg>cAg	p.R480Q		NM_019098.4	NP_061971.3	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	480					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						ATACCAAGTCCGAACTCGCTT	0.418													C|||	11	0.00219649	0.0083	0.0	5008	,	,		18826	0.0		0.0	False		,,,				2504	0.0				p.R480Q		Atlas-SNP	.											.	CNGB3	176	.	0			c.G1439A						PASS	.	C	GLN/ARG	30,4376	36.0+/-67.5	0,30,2173	221	207	212		1439	4.1	0.8	8	dbSNP_131	212	0,8600		0,0,4300	yes	missense	CNGB3	NM_019098.4	43	0,30,6473	TT,TC,CC		0.0,0.6809,0.2307	probably-damaging	480/810	87641188	30,12976	2203	4300	6503	SO:0001583	missense	54714	exon12			CAAGTCCGAACTC	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.1439G>A	8.37:g.87641188C>T	ENSP00000316605:p.Arg480Gln	190	0	0		165	41	0.248485	NM_019098	C9JA51|Q9NRE9	Missense_Mutation	SNP	ENST00000320005.5	37	CCDS6244.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	C	22.5	4.298296	0.81025	0.006809	0.0	ENSG00000170289	ENST00000320005	D	0.97186	-4.28	5.92	4.14	0.48551	Cyclic nucleotide-binding-like (1);	0.062472	0.64402	D	0.000013	D	0.94879	0.8345	M	0.68728	2.09	0.52501	D	0.999959	P;P	0.50819	0.939;0.899	P;P	0.47162	0.54;0.49	D	0.92368	0.5903	10	0.33141	T	0.24	.	12.7654	0.57388	0.0:0.8674:0.0:0.1326	.	480;480	Q9NQW8-2;Q9NQW8	.;CNGB3_HUMAN	Q	480	ENSP00000316605:R480Q	ENSP00000316605:R480Q	R	-	2	0	CNGB3	87710304	0.964000	0.33143	0.750000	0.31169	0.945000	0.59286	3.226000	0.51254	0.853000	0.35312	0.555000	0.69702	CGG	C|0.997;T|0.003	0.003	strong		0.418	CNGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375107.1	NM_019098		T	87641188	C	T	87641188	3	4	13	1	0	0	0	0	1	0	0	0	3603	652	23	1	1018	1	CNGB3	8	87641188	Missense_Mutation	SNP	C	TCGA-FF-8046-01A-11D-2210-10	45474730	87641188	58722834	41	1730											
MYC	4609	hgsc.bcm.edu	37	chr8	128750536	128750536	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaacgttagcttcaccaacAggaactatgacctcgactac	13	9	6	13	2	2	1	2	1	0	0	3	3	2	2	2	1	5	2	2	1	6	4			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr8:128750536A>G	ENST00000259523.6	+	2	1233	c.28A>G	c.(28-30)Agg>Ggg	p.R10G	MYC_ENST00000377970.2_Missense_Mutation_p.R25G|MYC_ENST00000524013.1_Missense_Mutation_p.R24G			P01106	MYC_HUMAN	v-myc avian myelocytomatosis viral oncogene homolog	10				R -> K (in Ref. 5; no nucleotide entry). {ECO:0000305}.	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)	CTTCACCAACAGGAACTATGA	0.597		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.R25G		Atlas-SNP	.		Dom	yes		8	8q24.12-q24.13	4609	v-myc myelocytomatosis viral oncogene homolog (avian)		"L, E"	.	MYC	168	.	0			c.A73G						PASS	.						74	74	74					8																	128750536		2203	4300	6503	SO:0001583	missense	4609	exon2			ACCAACAGGAACT		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.28A>G	8.37:g.128750536A>G	ENSP00000259523:p.Arg10Gly	75	0	0	1567	88	31	0.352273	NM_002467	A8WFE7|P01107|Q14026	Missense_Mutation	SNP	ENST00000259523.6	37		.	.	.	.	.	.	.	.	.	.	A	18.41	3.617613	0.66787	.	.	ENSG00000136997	ENST00000259523;ENST00000517291;ENST00000377970;ENST00000524013;ENST00000454617	T;T;T;T	0.19669	2.13;2.13;2.13;2.13	5.08	5.08	0.68730	Transcription regulator Myc, N-terminal (1);	0.194195	0.53938	D	0.000047	T	0.19565	0.0470	L	0.40543	1.245	0.30828	N	0.737012	B	0.31459	0.324	B	0.30716	0.119	T	0.11036	-1.0604	10	0.46703	T	0.11	-13.7167	14.1763	0.65544	1.0:0.0:0.0:0.0	.	10	P01106	MYC_HUMAN	G	10;24;25;24;10	ENSP00000259523:R10G;ENSP00000429441:R24G;ENSP00000367207:R25G;ENSP00000430235:R24G	ENSP00000259523:R10G	R	+	1	2	MYC	128819718	1.000000	0.71417	0.998000	0.56505	0.929000	0.56500	6.799000	0.75160	2.144000	0.66660	0.459000	0.35465	AGG	.	.	none		0.597	MYC-002	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000250278.1			G	128750536	A	G	128750536	3	3	13	1	0	0	0	0	1	0	0	0	10025	179	7	3	79	3	MYC	8	128750536	Missense_Mutation	SNP	A	TCGA-FF-8046-01A-11D-2210-10	41109348	128750536	17613486	42	1731			2	14		7	7	2372	N	G_C_A	1.679128e-16
MYC	4609	hgsc.bcm.edu	37	chr8	128750559	128750559	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aactatgacctcgactacgaCtcggtgcagccgtatttcta	10	11	8	12	4	1	1	0	1	1	0	3	3	1	1	2	1	4	2	2	1	5	5	rs146504683	byFrequency	TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr8:128750559C>G	ENST00000259523.6	+	2	1256	c.51C>G	c.(49-51)gaC>gaG	p.D17E	MYC_ENST00000377970.2_Missense_Mutation_p.D32E|MYC_ENST00000524013.1_Missense_Mutation_p.D31E			P01106	MYC_HUMAN	v-myc avian myelocytomatosis viral oncogene homolog	17					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)	TCGACTACGACTCGGTGCAGC	0.612		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.D32E		Atlas-SNP	.		Dom	yes		8	8q24.12-q24.13	4609	v-myc myelocytomatosis viral oncogene homolog (avian)		"L, E"	.	MYC	168	.	0			c.C96G						PASS	.						59	61	60					8																	128750559		2203	4300	6503	SO:0001583	missense	4609	exon2			CTACGACTCGGTG		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.51C>G	8.37:g.128750559C>G	ENSP00000259523:p.Asp17Glu	82	0	0	1567	94	31	0.329787	NM_002467	A8WFE7|P01107|Q14026	Missense_Mutation	SNP	ENST00000259523.6	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.62|12.62	1.991184|1.991184	0.35131|0.35131	.|.	.|.	ENSG00000136997|ENSG00000136997	ENST00000259523;ENST00000517291;ENST00000377970;ENST00000524013;ENST00000454617|ENST00000520751	T;T;T;T|.	0.34072|.	1.38;1.38;1.38;1.38|.	5.08|5.08	2.27|2.27	0.28462|0.28462	Transcription regulator Myc, N-terminal (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.71771|0.71771	0.3379|0.3379	M|M	0.79011|0.79011	2.435|2.435	0.53688|0.53688	D|D	0.999977|0.999977	D|.	0.69078|.	0.997|.	D|.	0.79108|.	0.992|.	T|T	0.73569|0.73569	-0.3941|-0.3941	10|6	0.56958|0.87932	D|D	0.05|0	-39.7262|-39.7262	9.824|9.824	0.40901|0.40901	0.0:0.7719:0.0:0.2281|0.0:0.7719:0.0:0.2281	.|.	17|.	P01106|.	MYC_HUMAN|.	E|S	17;31;32;31;17|6	ENSP00000259523:D17E;ENSP00000429441:D31E;ENSP00000367207:D32E;ENSP00000430235:D31E|.	ENSP00000259523:D17E|ENSP00000430226:T6S	D|T	+|+	3|2	2|0	MYC|MYC	128819741|128819741	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	1.519000|1.519000	0.35888|0.35888	0.742000|0.742000	0.32697|0.32697	0.561000|0.561000	0.74099|0.74099	GAC|ACT	C|0.999;T|0.001	.	alt		0.612	MYC-002	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000250278.1			G	128750559	C	G	128750559	3	3	13	1	0	0	0	0	1	0	0	0	10025	564	20	4	102	4	MYC	8	128750559	Missense_Mutation	SNP	C	TCGA-FF-8046-01A-11D-2210-10	23	128750559	17613463	43	1732			2	14		7	7	2372	N	G_C_A	1.679128e-16
MYC	4609	hgsc.bcm.edu	37	chr8	128750613	128750613	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagaacttctaccagcagcaGcagcagagcgagctgcagcc	12	4	12	13	1	1	2	0	0	1	2	1	4	1	2	2	0	10	6	2	0	2	2			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr8:128750613G>A	ENST00000259523.6	+	2	1310	c.105G>A	c.(103-105)caG>caA	p.Q35Q	MYC_ENST00000377970.2_Silent_p.Q50Q|MYC_ENST00000524013.1_Silent_p.Q49Q			P01106	MYC_HUMAN	v-myc avian myelocytomatosis viral oncogene homolog	35	Poly-Gln.				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)	ACCAGCAGCAGCAGCAGAGCG	0.622		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.Q50Q		Atlas-SNP	.		Dom	yes		8	8q24.12-q24.13	4609	v-myc myelocytomatosis viral oncogene homolog (avian)		"L, E"	MYC_ENST00000377970,NS,lymphoid_neoplasm,0,4	MYC	168	4	0			c.G150A						PASS	.						42	44	44					8																	128750613		2203	4300	6503	SO:0001819	synonymous_variant	4609	exon2			GCAGCAGCAGCAG		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.105G>A	8.37:g.128750613G>A		75	0	0	1567	88	29	0.329545	NM_002467	A8WFE7|P01107|Q14026	Silent	SNP	ENST00000259523.6	37		.	.	.	.	.	.	.	.	.	.	G	9.434	1.086417	0.20390	.	.	ENSG00000136997	ENST00000520751	.	.	.	5.08	2.26	0.28386	.	.	.	.	.	T	0.65964	0.2742	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.64812	-0.6319	5	0.87932	D	0	-22.7786	9.9515	0.41642	0.3084:0.0:0.6916:0.0	.	.	.	.	N	24	.	ENSP00000430226:S24N	S	+	2	0	MYC	128819795	1.000000	0.71417	0.998000	0.56505	0.774000	0.43823	1.221000	0.32503	0.054000	0.16065	-1.134000	0.01955	AGC	.	.	none		0.622	MYC-002	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000250278.1			A	128750613	G	A	128750613	2	1	13	1	0	0	0	0	0	0	0	1	10025	962	34	2		2	MYC	8	128750613	Silent	SNP	G	TCGA-FF-8046-01A-11D-2210-10	54	128750613	17613409	44	1733			2	14		7	7	2372	N	G_C_A	1.679128e-16
MYC	4609	hgsc.bcm.edu	37	chr8	128750625	128750625	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagcagcagcagcagagcgaGctgcagcccccggcgcccag	9	1	14	17	3	0	1	0	0	0	1	0	2	0	1	3	1	8	6	3	1	0	0	rs121918684		TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr8:128750625G>C	ENST00000259523.6	+	2	1322	c.117G>C	c.(115-117)gaG>gaC	p.E39D	MYC_ENST00000377970.2_Missense_Mutation_p.E54D|MYC_ENST00000524013.1_Missense_Mutation_p.E53D			P01106	MYC_HUMAN	v-myc avian myelocytomatosis viral oncogene homolog	39			E -> D (in a Burkitt lymphoma symple). {ECO:0000269|PubMed:6419122, ECO:0000269|PubMed:8220424}.		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)	AGCAGAGCGAGCTGCAGCCCC	0.632		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.E54D		Atlas-SNP	.		Dom	yes		8	8q24.12-q24.13	4609	v-myc myelocytomatosis viral oncogene homolog (avian)		"L, E"	MYC_ENST00000377970,NS,lymphoid_neoplasm,0,8	MYC	168	8	0			c.G162C						PASS	.						35	39	38					8																	128750625		2203	4300	6503	SO:0001583	missense	4609	exon2			GAGCGAGCTGCAG		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.117G>C	8.37:g.128750625G>C	ENSP00000259523:p.Glu39Asp	71	0	0	1567	74	25	0.337838	NM_002467	A8WFE7|P01107|Q14026	Missense_Mutation	SNP	ENST00000259523.6	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.32|12.32	1.903276|1.903276	0.33628|0.33628	.|.	.|.	ENSG00000136997|ENSG00000136997	ENST00000259523;ENST00000517291;ENST00000377970;ENST00000524013|ENST00000520751	T;T;T;T|.	0.18810|.	2.19;2.19;2.19;2.19|.	4.78|4.78	3.9|3.9	0.45041|0.45041	Transcription regulator Myc, N-terminal (1);|.	0.367998|.	0.32671|.	N|.	0.005795|.	T|T	0.25717|0.25717	0.0626|0.0626	N|N	0.04508|0.04508	-0.205|-0.205	0.35092|0.35092	A|A	0.764443|0.764443	B|.	0.28667|.	0.219|.	B|.	0.30251|.	0.113|.	T|T	0.39461|0.39461	-0.9613|-0.9613	9|5	0.38643|0.87932	T|D	0.18|0	-20.4721|-20.4721	8.9469|8.9469	0.35764|0.35764	0.1688:0.0:0.8312:0.0|0.1688:0.0:0.8312:0.0	.|.	39|.	P01106|.	MYC_HUMAN|.	D|T	39;53;54;53|28	ENSP00000259523:E39D;ENSP00000429441:E53D;ENSP00000367207:E54D;ENSP00000430235:E53D|.	ENSP00000259523:E39D|ENSP00000430226:S28T	E|S	+|+	3|2	2|0	MYC|MYC	128819807|128819807	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	4.447000|4.447000	0.60020|0.60020	1.389000|1.389000	0.46526|0.46526	0.561000|0.561000	0.74099|0.74099	GAG|AGC	.	.	weak		0.632	MYC-002	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000250278.1			C	128750625	G	C	128750625	3	2	13	1	0	0	0	0	1	0	0	0	10025	962	34	4	168	4	MYC	8	128750625	Missense_Mutation	SNP	G	TCGA-FF-8046-01A-11D-2210-10	12	128750625	17613397	45	1734			2	14		7	7	2372	N	G_C_A	1.679128e-16
MYC	4609	hgsc.bcm.edu	37	chr8	128751021	128751021	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcccgcggccacagcgtctgCtccacctccagcttgtacct	5	8	9	19	3	1	0	0	0	1	0	3	0	3	0	6	1	4	3	6	1	1	2			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr8:128751021C>T	ENST00000259523.6	+	2	1718	c.513C>T	c.(511-513)tgC>tgT	p.C171C	MYC_ENST00000377970.2_Silent_p.C186C|MYC_ENST00000524013.1_Silent_p.C185C			P01106	MYC_HUMAN	v-myc avian myelocytomatosis viral oncogene homolog	171				C -> S (in Ref. 5; no nucleotide entry). {ECO:0000305}.	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)	ACAGCGTCTGCTCCACCTCCA	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.C186C		Atlas-SNP	.		Dom	yes		8	8q24.12-q24.13	4609	v-myc myelocytomatosis viral oncogene homolog (avian)		"L, E"	.	MYC	168	.	0			c.C558T						PASS	.						21	23	22					8																	128751021		2203	4298	6501	SO:0001819	synonymous_variant	4609	exon2			CGTCTGCTCCACC		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.513C>T	8.37:g.128751021C>T		65	0	0	1567	59	16	0.271186	NM_002467	A8WFE7|P01107|Q14026	Silent	SNP	ENST00000259523.6	37																																																																																				.	.	none		0.677	MYC-002	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000250278.1			T	128751021	C	T	128751021	2	4	13	1	0	0	0	0	0	0	0	1	10025	805	28	2		2	MYC	8	128751021	Silent	SNP	C	TCGA-FF-8046-01A-11D-2210-10	396	128751021	17613001	46	1735			2	14		7	7	2372	N	G_C_A	1.679128e-16
MYC	4609	hgsc.bcm.edu	37	chr8	128752802	128752802	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgccacgtctccacacatcaGcacaactacgcagcgcctcc	10	6	6	19	3	2	0	1	0	1	0	4	0	3	0	4	0	5	2	4	0	2	1			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr8:128752802G>C	ENST00000377970.2	+	3	1473	c.963G>C	c.(961-963)caG>caC	p.Q321H	MYC_ENST00000524013.1_Missense_Mutation_p.Q320H	NM_002467.4	NP_002458	P01106	MYC_HUMAN	v-myc avian myelocytomatosis viral oncogene homolog	306					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)	CCACACATCAGCACAACTACG	0.567		3	"A, T"	"IGK@, BCL5, BCL7A , BTG1, TRA@, IGH@"	"Burkitt lymphoma,  amplified in other cancers, B-CLL"																																p.Q321H		Atlas-SNP	.		Dom	yes		8	8q24.12-q24.13	4609	v-myc myelocytomatosis viral oncogene homolog (avian)		"L, E"	MYC_ENST00000377970,NS,carcinoma,+2,2	MYC	168	2	0			c.G963C						scavenged	.						87	66	73					8																	128752802		2203	4300	6503	SO:0001583	missense	4609	exon3			ACATCAGCACAAC		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	ENST00000377970.2:c.963G>C	8.37:g.128752802G>C	ENSP00000367207:p.Gln321His	131	1	0.00763359		127	46	0.362205	NM_002467	A8WFE7|P01107|Q14026	Missense_Mutation	SNP	ENST00000377970.2	37	CCDS6359.2	.	.	.	.	.	.	.	.	.	.	G	17.63	3.437078	0.62955	.	.	ENSG00000136997	ENST00000377970;ENST00000524013;ENST00000454617	T;T	0.29142	1.58;1.58	5.54	3.75	0.43078	Transcription regulator Myc, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.51007	0.1649	M	0.76328	2.33	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.53136	-0.8481	10	0.87932	D	0	-23.0286	7.9696	0.30119	0.3035:0.0:0.6965:0.0	.	306	P01106	MYC_HUMAN	H	321;320;287	ENSP00000367207:Q321H;ENSP00000430235:Q320H	ENSP00000367207:Q321H	Q	+	3	2	MYC	128821984	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	0.831000	0.27476	1.338000	0.45544	0.650000	0.86243	CAG	.	.	none		0.567	MYC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250277.3			C	128752802	G	C	128752802	3	2	13	1	0	0	0	0	1	0	0	0	10025	962	34	4	973	4	MYC	8	128752802	Missense_Mutation	SNP	G	TCGA-FF-8046-01A-11D-2210-10	1781	128752802	17611220	47	1736			2	14		7	7	2372	N	G_C_A	1.679128e-16
MYC	4609	hgsc.bcm.edu	37	chr8	128752907	128752907	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagatcagcaacaaccgaaaAtgcaccagccccaggtcctc	14	4	7	16	1	1	1	1	0	0	1	3	2	2	1	5	1	5	2	5	1	4	0			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr8:128752907A>G	ENST00000377970.2	+	3	1578	c.1068A>G	c.(1066-1068)aaA>aaG	p.K356K	MYC_ENST00000524013.1_Silent_p.K355K	NM_002467.4	NP_002458	P01106	MYC_HUMAN	v-myc avian myelocytomatosis viral oncogene homolog	341	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				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)	ACAACCGAAAATGCACCAGCC	0.557		3	"A, T"	"IGK@, BCL5, BCL7A , BTG1, TRA@, IGH@"	"Burkitt lymphoma,  amplified in other cancers, B-CLL"																																p.K356K		Atlas-SNP	.		Dom	yes		8	8q24.12-q24.13	4609	v-myc myelocytomatosis viral oncogene homolog (avian)		"L, E"	.	MYC	168	.	0			c.A1068G						PASS	.						91	86	87					8																	128752907		2203	4300	6503	SO:0001819	synonymous_variant	4609	exon3			CCGAAAATGCACC		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	ENST00000377970.2:c.1068A>G	8.37:g.128752907A>G		124	0	0		144	56	0.388889	NM_002467	A8WFE7|P01107|Q14026	Silent	SNP	ENST00000377970.2	37	CCDS6359.2																																																																																			.	.	none		0.557	MYC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250277.3			G	128752907	A	G	128752907	2	3	13	1	0	0	0	0	0	0	0	1	10025	98	4	3		3	MYC	8	128752907	Silent	SNP	A	TCGA-FF-8046-01A-11D-2210-10	105	128752907	17611115	48	1737			2	14		7	7	2372	N	G_C_A	1.679128e-16
COL22A1	169044	hgsc.bcm.edu	37	chr8	139626110	139626110	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agtcgcaaagcaaaactcacCggtgggccccttggtccttg	9	8	11	13	2	1	0	1	0	0	0	3	0	2	0	4	3	2	2	4	3	3	2	rs139816222		TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr8:139626110C>T	ENST00000303045.6	-	56	4424	c.3978G>A	c.(3976-3978)ccG>ccA	p.P1326P	COL22A1_ENST00000435777.1_Splice_Site_p.P1306P|COL22A1_ENST00000341807.4_5'UTR	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1326	Collagen-like 13.|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)			CAAAACTCACCGGTGGGCCCC	0.478										HNSCC(7;0.00092)																											p.P1326P		Atlas-SNP	.											COL22A1,rectum,carcinoma,-1,1	COL22A1	390	1	0			c.G3978A						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	131	139	137		3978	3.8	1	8	dbSNP_134	137	0,8600		0,0,4300	no	coding-synonymous-near-splice	COL22A1	NM_152888.1		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		1326/1627	139626110	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	169044	exon56			ACTCACCGGTGGG	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.3978+1G>A	8.37:g.139626110C>T		126	0	0		142	35	0.246479	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Silent	SNP	ENST00000303045.6	37	CCDS6376.1																																																																																			C|1.000;T|0.000	0.000	weak		0.478	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	Silent	T	139626110	C	T	139626110	5	4	13	1	0	0	0	0	0	0	1	0	3683	666	23	1	942	1	COL22A1	8	139626110	Splice_Site	SNP	C	TCGA-FF-8046-01A-11D-2210-10	10873203	139626110	6737912	49	1738											
HRCT1	646962	hgsc.bcm.edu	37	chr9	35906607	35906607	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaccaccaccacccccaccGccaccatccccgccacgctc	8	2	3	28	3	0	0	0	0	0	0	2	0	1	0	12	0	0	1	12	0	0	0	rs201684694		TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr9:35906607G>C	ENST00000354323.2	+	1	419	c.323G>C	c.(322-324)cGc>cCc	p.R108P	LINC00961_ENST00000443779.1_lincRNA	NM_001039792.1	NP_001034881.1	Q6UXD1	HRCT1_HUMAN	histidine rich carboxyl terminus 1	108	His-rich.					integral component of membrane (GO:0016021)				NS(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(1)	4						cacccccaccgccaccatccc	0.677																																					p.R108P		Atlas-SNP	.											HRCT1,NS,carcinoma,0,1	HRCT1	14	1	0			c.G323C						scavenged	.						5	6	5					9																	35906607		1670	3248	4918	SO:0001583	missense	646962	exon1			CCCACCGCCACCA		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.323G>C	9.37:g.35906607G>C	ENSP00000346283:p.Arg108Pro	32	2	0.0625		22	11	0.5	NM_001039792	B7ZBJ1	Missense_Mutation	SNP	ENST00000354323.2	37	CCDS35012.1	.	.	.	.	.	.	.	.	.	.	G	3.247	-0.154060	0.06585	.	.	ENSG00000196196	ENST00000354323	.	.	.	0.698	-1.4	0.08968	.	0.824948	0.09848	N	0.747995	T	0.09335	0.0230	N	0.08118	0	0.09310	N	1	D	0.53312	0.959	B	0.36989	0.238	T	0.17077	-1.0381	8	0.87932	D	0	-29.2099	.	.	.	.	108	Q6UXD1	HRCT1_HUMAN	P	108	.	ENSP00000346283:R108P	R	+	2	0	HRCT1	35896607	0.000000	0.05858	0.002000	0.10522	0.343000	0.28985	-0.250000	0.08830	-0.783000	0.04534	-0.346000	0.07831	CGC	.	.	alt		0.677	HRCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334099.1	NM_001039792		C	35906607	G	C	35906607	3	2	13	1	0	0	0	0	1	0	0	0	7362	1087	38	4	325	4	HRCT1	9	35906607	Missense_Mutation	SNP	G	TCGA-FF-8046-01A-11D-2210-10		35906607	105306824	50	1739											
FRMD3	257019	hgsc.bcm.edu	37	chr9	85863362	85863362	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tagggggatcttcatactccCgggctgccttcactggggag	6	10	14	11	1	3	0	2	0	1	0	4	2	4	2	2	5	2	1	2	5	2	4			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr9:85863362C>T	ENST00000304195.3	-	14	1471	c.1265G>A	c.(1264-1266)cGg>cAg	p.R422Q	FRMD3_ENST00000376434.1_Missense_Mutation_p.R228Q|FRMD3_ENST00000328788.1_Missense_Mutation_p.R79Q|FRMD3_ENST00000376438.1_Missense_Mutation_p.R422Q|FRMD3_ENST00000465485.1_5'UTR	NM_001244960.1|NM_174938.5	NP_001231889.1|NP_777598.3	A2A2Y4	FRMD3_HUMAN	FERM domain containing 3	422						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	30						TTCATACTCCCGGGCTGCCTT	0.443																																					p.R422Q		Atlas-SNP	.											FRMD3,NS,carcinoma,+1,1	FRMD3	96	1	0			c.G1265A						PASS	.						72	72	72					9																	85863362		1847	4100	5947	SO:0001583	missense	257019	exon14			TACTCCCGGGCTG	AK094281	CCDS43840.1, CCDS59131.1, CCDS59132.1, CCDS59133.1, CCDS75852.1	9q21.33	2008-02-05			ENSG00000172159	ENSG00000172159			24125	protein-coding gene	gene with protein product		607619				12601556	Standard	NM_174938		Approved	EPB41L4O, MGC20553	uc004ams.2	A2A2Y4	OTTHUMG00000020103	ENST00000304195.3:c.1265G>A	9.37:g.85863362C>T	ENSP00000303508:p.Arg422Gln	65	0	0		68	25	0.367647	NM_174938	A8MQB0|B4DN14|Q53EP2|Q5JV59|Q5VZA1|Q86WP8|Q8IZ44|Q8N3Y5|Q8N9L2	Missense_Mutation	SNP	ENST00000304195.3	37	CCDS43840.1	.	.	.	.	.	.	.	.	.	.	C	5.988	0.366206	0.11352	.	.	ENSG00000172159	ENST00000376438;ENST00000376434;ENST00000328788;ENST00000304195	D;D;T;D	0.85411	-1.57;-1.98;0.97;-1.59	5.38	-0.87	0.10646	.	1.075110	0.07080	N	0.836929	T	0.73171	0.3553	N	0.21448	0.665	0.09310	N	1	B;B;B	0.20261	0.0;0.0;0.043	B;B;B	0.09377	0.0;0.001;0.004	T	0.52609	-0.8553	10	0.13470	T	0.59	.	10.6066	0.45398	0.0:0.5266:0.0:0.4734	.	422;422;79	A2A2Y4;A2A2Y4-2;A2A2Y4-4	FRMD3_HUMAN;.;.	Q	422;228;79;422	ENSP00000365621:R422Q;ENSP00000365617:R228Q;ENSP00000328615:R79Q;ENSP00000303508:R422Q	ENSP00000303508:R422Q	R	-	2	0	FRMD3	85053182	0.000000	0.05858	0.897000	0.35233	0.991000	0.79684	-0.925000	0.03992	-0.358000	0.08162	-0.131000	0.14894	CGG	.	.	none		0.443	FRMD3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157355.1	NM_174938		T	85863362	C	T	85863362	3	4	13	1	0	0	0	0	1	0	0	0	6058	652	23	1	532	1	FRMD3	9	85863362	Missense_Mutation	SNP	C	TCGA-FF-8046-01A-11D-2210-10	49956755	85863362	55350069	51	1740											
ALDOB	229	hgsc.bcm.edu	37	chr9	104189813	104189813	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcgttggcgttttcctggAtagcgaggctggatggacac	6	10	17	8	3	0	0	0	0	0	0	1	4	1	3	1	6	1	3	1	6	1	4			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr9:104189813A>G	ENST00000374855.4	-	5	615	c.491T>C	c.(490-492)aTc>aCc	p.I164T	ALDOB_ENST00000468981.3_Intron	NM_000035.3	NP_000026.2	P05062	ALDOB_HUMAN	aldolase B, fructose-bisphosphate	164					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)				GTTTTCCTGGATAGCGAGGCT	0.552																																					p.I164T		Atlas-SNP	.											.	ALDOB	69	.	0			c.T491C						PASS	.						110	86	94					9																	104189813		2203	4300	6503	SO:0001583	missense	229	exon5			TCCTGGATAGCGA	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.491T>C	9.37:g.104189813A>G	ENSP00000363988:p.Ile164Thr	105	0	0		125	27	0.216	NM_000035	Q13741|Q13742|Q5T7D6	Missense_Mutation	SNP	ENST00000374855.4	37	CCDS6756.1	.	.	.	.	.	.	.	.	.	.	A	26.9	4.784232	0.90282	.	.	ENSG00000136872	ENST00000374855;ENST00000374853;ENST00000430164	D	0.89196	-2.48	6.17	6.17	0.99709	Aldolase-type TIM barrel (1);	0.000000	0.85682	D	0.000000	D	0.96377	0.8818	H	0.96333	3.805	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.97485	1.0050	10	0.87932	D	0	-22.1026	16.0034	0.80327	1.0:0.0:0.0:0.0	.	164	P05062	ALDOB_HUMAN	T	164;91;164	ENSP00000363988:I164T	ENSP00000363986:I91T	I	-	2	0	ALDOB	103229634	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	9.339000	0.96797	2.371000	0.80710	0.533000	0.62120	ATC	.	.	none		0.552	ALDOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053434.2			G	104189813	A	G	104189813	3	3	13	1	0	0	0	0	1	0	0	0	508	333	12	3	623	3	ALDOB	9	104189813	Missense_Mutation	SNP	A	TCGA-FF-8046-01A-11D-2210-10	18326451	104189813	37023618	52	1741											
SVEP1	79987	hgsc.bcm.edu	37	chr9	113259095	113259095	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cataattgcacaaaccttacCttttcaccagagttgtcttt	11	15	4	11	0	2	1	1	0	1	1	2	1	2	1	3	0	3	2	3	0	3	7			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr9:113259095C>G	ENST00000401783.2	-	8	2136	c.1800G>C	c.(1798-1800)aaG>aaC	p.K600N	SVEP1_ENST00000374461.1_Splice_Site_p.K577N|SVEP1_ENST00000302728.8_Splice_Site_p.K600N|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374469.1_Splice_Site_p.K577N	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	600	HYR 1. {ECO:0000255|PROSITE- ProRule:PRU00113}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)	p.K600N(1)		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						CAAACCTTACCTTTTCACCAG	0.383																																					p.K600N		Atlas-SNP	.											SVEP1,colon,carcinoma,0,1	SVEP1	326	1	1	Substitution - Missense(1)	large_intestine(1)	c.G1800C						PASS	.						122	110	114					9																	113259095		1867	4071	5938	SO:0001630	splice_region_variant	79987	exon8			CCTTACCTTTTCA	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.1800+1G>C	9.37:g.113259095C>G		204	0	0		198	60	0.30303	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	C	16.65	3.181594	0.57800	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728;ENST00000374461	T;T;T;T	0.77750	-0.97;-0.98;-1.12;1.21	5.71	4.81	0.61882	Hyalin (2);	0.152075	0.64402	D	0.000013	T	0.70657	0.3249	N	0.16233	0.39	0.39786	D	0.972375	P;P;P	0.43231	0.801;0.801;0.557	P;B;B	0.49192	0.602;0.339;0.167	T	0.69993	-0.4994	9	.	.	.	.	13.6089	0.62063	0.0:0.9241:0.0:0.0759	.	600;600;600	E9PBN8;Q4LDE5;Q4LDE5-2	.;SVEP1_HUMAN;.	N	600;577;600;577	ENSP00000384917:K600N;ENSP00000363593:K577N;ENSP00000304118:K600N;ENSP00000363585:K577N	.	K	-	3	2	SVEP1	112298916	1.000000	0.71417	1.000000	0.80357	0.750000	0.42670	6.089000	0.71384	1.430000	0.47334	-0.237000	0.12165	AAG	.	.	none		0.383	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			Missense_Mutation	G	113259095	C	G	113259095	5	3	13	1	0	0	0	0	0	0	1	0	15435	695	24	4	9079	4	SVEP1	9	113259095	Splice_Site	SNP	C	TCGA-FF-8046-01A-11D-2210-10	9069282	113259095	27954336	53	1742											
ZNF438	220929	hgsc.bcm.edu	37	chr10	31137635	31137635	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcacaaaactcacaacacaTgagtttcttcagacggttct	13	11	6	11	1	4	2	2	1	2	1	4	2	4	2	0	1	3	3	0	1	3	3			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr10:31137635T>G	ENST00000361310.3	-	6	2028	c.1699A>C	c.(1699-1701)Atg>Ctg	p.M567L	ZNF438_ENST00000436087.2_Missense_Mutation_p.M567L|ZNF438_ENST00000442986.1_Missense_Mutation_p.M567L|ZNF438_ENST00000452305.1_Missense_Mutation_p.M557L|ZNF438_ENST00000413025.1_Missense_Mutation_p.M567L|ZNF438_ENST00000444692.2_Missense_Mutation_p.M557L|ZNF438_ENST00000331737.6_Missense_Mutation_p.M557L|ZNF438_ENST00000538351.2_Missense_Mutation_p.M518L|ZNF438_ENST00000375311.1_Missense_Mutation_p.M131L			Q7Z4V0	ZN438_HUMAN	zinc finger protein 438	567					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)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(15)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(175;0.0587)				TCACAACACATGAGTTTCTTC	0.483																																					p.M567L		Atlas-SNP	.											.	ZNF438	90	.	0			c.A1699C						PASS	.						165	157	160					10																	31137635		2203	4300	6503	SO:0001583	missense	220929	exon7			AACACATGAGTTT	AK057323	CCDS7168.1, CCDS44369.1, CCDS53504.1	10p11.23	2006-02-15			ENSG00000183621	ENSG00000183621		"Zinc fingers, C2H2-type"	21029	protein-coding gene	gene with protein product							Standard	NM_182755		Approved	bA330O11.1	uc010qeb.2	Q7Z4V0	OTTHUMG00000017904	ENST00000361310.3:c.1699A>C	10.37:g.31137635T>G	ENSP00000354663:p.Met567Leu	202	0	0		237	60	0.253165	NM_182755	A2A3J4|A8K9L5|Q5T426|Q658Q4|Q6ZN65	Missense_Mutation	SNP	ENST00000361310.3	37	CCDS7168.1	.	.	.	.	.	.	.	.	.	.	T	7.360	0.624731	0.14193	.	.	ENSG00000183621	ENST00000331737;ENST00000361310;ENST00000436087;ENST00000442986;ENST00000413025;ENST00000452305;ENST00000444692;ENST00000538351;ENST00000430896;ENST00000375311	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;3.22	5.4	-3.69	0.04450	Zinc finger, C2H2-like (1);	0.541309	0.20921	N	0.083263	T	0.04679	0.0127	N	0.08118	0	0.09310	N	0.999998	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.002	T	0.40813	-0.9543	10	0.16420	T	0.52	-2.4183	7.8113	0.29232	0.0:0.3656:0.1286:0.5057	.	567;557	Q7Z4V0;Q7Z4V0-2	ZN438_HUMAN;.	L	557;567;567;567;567;557;557;518;286;131	ENSP00000333571:M557L;ENSP00000354663:M567L;ENSP00000406934:M567L;ENSP00000412363:M567L;ENSP00000387546:M567L;ENSP00000413060:M557L;ENSP00000410898:M557L;ENSP00000445461:M518L;ENSP00000364460:M131L	ENSP00000333571:M557L	M	-	1	0	ZNF438	31177641	0.000000	0.05858	0.053000	0.19242	0.996000	0.88848	-0.371000	0.07513	-0.355000	0.08199	0.482000	0.46254	ATG	.	.	none		0.483	ZNF438-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277006.1	NM_182755		G	31137635	T	G	31137635	3	3	13	1	0	0	0	0	1	0	0	0	17925	1464	51	5	795	5	ZNF438	10	31137635	Missense_Mutation	SNP	T	TCGA-FF-8046-01A-11D-2210-10		31137635	104397112	54	1743											
ZNF33A	7581	hgsc.bcm.edu	37	chr10	38343345	38343345	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaaagagaggagccaagaaaAccaatctaaacatttgtggg	18	6	11	6	0	1	2	0	0	1	2	1	5	1	3	2	2	3	0	2	2	7	2			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr10:38343345A>C	ENST00000458705.2	+	5	448	c.290A>C	c.(289-291)aAc>aCc	p.N97T	ZNF33A_ENST00000469037.2_Missense_Mutation_p.N98T|ZNF33A_ENST00000374618.3_Missense_Mutation_p.N98T|ZNF33A_ENST00000307441.9_Missense_Mutation_p.N97T|ZNF33A_ENST00000432900.2_Missense_Mutation_p.N104T			Q06730	ZN33A_HUMAN	zinc finger protein 33A	97					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						AGCCAAGAAAACCAATCTAAA	0.348																																					p.N98T		Atlas-SNP	.											.	ZNF33A	103	.	0			c.A293C						PASS	.						90	91	90					10																	38343345		2203	4300	6503	SO:0001583	missense	7581	exon5			AAGAAAACCAATC	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.290A>C	10.37:g.38343345A>C	ENSP00000387713:p.Asn97Thr	116	0	0		122	24	0.196721	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Missense_Mutation	SNP	ENST00000458705.2	37	CCDS31182.1	.	.	.	.	.	.	.	.	.	.	A	10.12	1.263115	0.23051	.	.	ENSG00000189180	ENST00000374618;ENST00000432900;ENST00000458705;ENST00000277672;ENST00000307441	T;T;T;T	0.06218	3.34;3.34;3.33;3.33	1.46	1.46	0.22682	.	0.192021	0.25487	N	0.030322	T	0.09247	0.0228	L	0.45228	1.405	0.25885	N	0.983546	D;B;P;D	0.55385	0.971;0.031;0.952;0.971	P;B;P;P	0.52554	0.691;0.012;0.494;0.702	T	0.09552	-1.0669	10	0.51188	T	0.08	.	6.9664	0.24625	1.0:0.0:0.0:0.0	.	104;98;97;98	F6TH33;Q9H5I4;Q06730;F8WAJ5	.;.;ZN33A_HUMAN;.	T	98;104;97;98;97	ENSP00000363747:N98T;ENSP00000402467:N104T;ENSP00000387713:N97T;ENSP00000304268:N97T	ENSP00000277672:N98T	N	+	2	0	ZNF33A	38383351	0.912000	0.30974	0.296000	0.24974	0.924000	0.55760	1.642000	0.37207	0.918000	0.36919	0.377000	0.23210	AAC	.	.	none		0.348	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974		C	38343345	A	C	38343345	3	2	13	1	0	0	0	0	1	0	0	0	17869	43	2	5	307	5	ZNF33A	10	38343345	Missense_Mutation	SNP	A	TCGA-FF-8046-01A-11D-2210-10	7205710	38343345	97191402	55	1744											
MAPK8	5599	hgsc.bcm.edu	37	chr10	49618087	49618087	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataaagttacatagtcatggAgctcatggatgcaaatcttt	14	13	8	6	0	3	0	2	0	1	0	3	2	3	2	0	2	3	3	0	2	5	4			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr10:49618087A>G	ENST00000374189.1	+	5	507	c.326A>G	c.(325-327)gAg>gGg	p.E109G	MAPK8_ENST00000374182.3_Missense_Mutation_p.E109G|MAPK8_ENST00000395611.3_Missense_Mutation_p.E109G|MAPK8_ENST00000374174.1_Missense_Mutation_p.E109G|MAPK8_ENST00000360332.3_Missense_Mutation_p.E109G			P45983	MK08_HUMAN	mitogen-activated protein kinase 8	109	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)		ATAGTCATGGAGCTCATGGAT	0.358																																					p.E109G		Atlas-SNP	.											.	MAPK8	118	.	0			c.A326G						PASS	.						161	151	155					10																	49618087		2203	4300	6503	SO:0001583	missense	5599	exon4			TCATGGAGCTCAT	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.326A>G	10.37:g.49618087A>G	ENSP00000363304:p.Glu109Gly	144	0	0		154	7	0.0454545	NM_139047	B5BTZ5|B7ZLV4|D3DX88|D3DX92|Q15709|Q15712|Q15713|Q308M2	Missense_Mutation	SNP	ENST00000374189.1	37	CCDS7224.1	.	.	.	.	.	.	.	.	.	.	A	26.5	4.747324	0.89663	.	.	ENSG00000107643	ENST00000432379;ENST00000429041;ENST00000374189;ENST00000426557;ENST00000374182;ENST00000374179;ENST00000360332;ENST00000374176;ENST00000374174;ENST00000395611	D;D;D;D;D;D;D;D;D;D	0.91792	-2.91;-2.91;-2.91;-2.91;-2.91;-2.91;-2.91;-2.91;-2.91;-2.91	5.4	5.4	0.78164	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	D	0.97056	0.9038	M	0.93763	3.455	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	0.98041	1.0382	10	0.72032	D	0.01	.	15.7272	0.77770	1.0:0.0:0.0:0.0	.	109;109;109;109;109	Q308M2;P45983-2;P45983;A1L4K2;P45983-3	.;.;MK08_HUMAN;.;.	G	109;26;109;109;109;109;109;109;109;109	ENSP00000387936:E109G;ENSP00000393223:E26G;ENSP00000363304:E109G;ENSP00000397729:E109G;ENSP00000363297:E109G;ENSP00000363294:E109G;ENSP00000353483:E109G;ENSP00000363291:E109G;ENSP00000363289:E109G;ENSP00000378974:E109G	ENSP00000353483:E109G	E	+	2	0	MAPK8	49288093	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.287000	0.95975	2.176000	0.68965	0.528000	0.53228	GAG	.	.	none		0.358	MAPK8-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047931.1			G	49618087	A	G	49618087	3	3	13	1	0	0	0	0	1	0	0	0	9292	304	11	3	340	3	MAPK8	10	49618087	Missense_Mutation	SNP	A	TCGA-FF-8046-01A-11D-2210-10	11274742	49618087	85916660	56	1745											
SLC29A3	55315	hgsc.bcm.edu	37	chr10	73111474	73111474	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatcctcagcggtgcctccaCtgtcttcagcagcagcatct	7	10	9	15	1	4	0	2	0	2	0	6	1	6	0	3	1	5	3	3	1	0	1			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr10:73111474C>T	ENST00000373189.5	+	4	591	c.539C>T	c.(538-540)aCt>aTt	p.T180I	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	180					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						GGTGCCTCCACTGTCTTCAGC	0.567																																					p.T180I	Esophageal Squamous(200;1319 2142 18949 31248 39672)	Atlas-SNP	.											.	SLC29A3	51	.	0			c.C539T						PASS	.						129	97	108					10																	73111474		2203	4300	6503	SO:0001583	missense	55315	exon4			CCTCCACTGTCTT	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.539C>T	10.37:g.73111474C>T	ENSP00000362285:p.Thr180Ile	108	0	0		91	4	0.043956	NM_018344	B2RB50|B4E2Z9|B7ZA37|Q0VAM9|Q5T465|Q7RTT8|Q8IVZ0|Q9BWI2|Q9NUS9	Missense_Mutation	SNP	ENST00000373189.5	37	CCDS7310.1	.	.	.	.	.	.	.	.	.	.	C	12.53	1.964306	0.34659	.	.	ENSG00000198246	ENST00000373189	T	0.63580	-0.05	5.83	2.91	0.33838	.	0.231809	0.45606	N	0.000358	T	0.62221	0.2410	M	0.78916	2.43	0.35689	D	0.814676	B	0.18013	0.025	B	0.27076	0.076	T	0.66404	-0.5932	9	0.72032	D	0.01	-22.0043	8.8699	0.35309	0.0:0.7627:0.0:0.2373	.	180	Q9BZD2	S29A3_HUMAN	I	180	ENSP00000362285:T180I	ENSP00000362285:T180I	T	+	2	0	SLC29A3	72781480	0.977000	0.34250	0.048000	0.18961	0.667000	0.39255	2.530000	0.45641	0.345000	0.23873	0.555000	0.69702	ACT	.	.	none		0.567	SLC29A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048544.1	NM_018344		T	73111474	C	T	73111474	3	4	13	1	0	0	0	0	1	0	0	0	14551	565	20	2	553	2	SLC29A3	10	73111474	Missense_Mutation	SNP	C	TCGA-FF-8046-01A-11D-2210-10	23493387	73111474	62423273	57	1746											
IFITM3	10410	hgsc.bcm.edu	37	chr11	320723	320723	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgtggggcgcccccagcaCagccacctcgtgctcctcct	4	8	11	18	2	0	0	0	0	0	0	3	0	2	0	6	2	3	3	6	2	0	1	rs199582787	byFrequency	TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr11:320723C>T	ENST00000399808.4	-	1	327	c.91G>A	c.(91-93)Gtg>Atg	p.V31M	IFITM3_ENST00000602735.1_Missense_Mutation_p.V10M|RP11-326C3.14_ENST00000602809.1_lincRNA|RP11-326C3.11_ENST00000602756.1_RNA|RP11-326C3.10_ENST00000534271.1_RNA|RP11-326C3.11_ENST00000508004.2_RNA|IFITM3_ENST00000526811.1_Missense_Mutation_p.V10M|RP11-326C3.11_ENST00000602429.1_RNA	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	1	0			c.G91A						scavenged	.						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	11.37:g.320723C>T	ENSP00000382707:p.Val31Met	78	2	0.025641		116	12	0.103448	NM_021034	Q53Y76|Q96HK8|Q96J15	Missense_Mutation	SNP	ENST00000399808.4	37	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	.	.	weak		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	13	1	0	0	0	0	1	0	0	0	7537	478	17	2	318	2	IFITM3	11	320723	Missense_Mutation	SNP	C	TCGA-FF-8046-01A-11D-2210-10		320723	134685793	58	1747											
MICAL2	9645	hgsc.bcm.edu	37	chr11	12281376	12281376	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcaagagcaggaagcccctcGgagagacactcccaccgaaa	14	2	11	14	2	0	2	0	0	0	2	2	6	1	4	4	2	2	2	4	2	3	0	rs2270515	byFrequency	TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr11:12281376G>A	ENST00000256194.4	+	26	3554	c.3266G>A	c.(3265-3267)cGg>cAg	p.R1089Q	MICAL2_ENST00000379612.3_Missense_Mutation_p.R863Q|MICAL2_ENST00000342902.5_Missense_Mutation_p.R1068Q|MICAL2_ENST00000537344.1_Missense_Mutation_p.R899Q|MICAL2_ENST00000527546.1_Missense_Mutation_p.R899Q|RP11-265D17.2_ENST00000527288.1_RNA	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	1089			R -> Q (in dbSNP:rs2270515).		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)		GAAGCCCCTCGGAGAGACACT	0.552													G|||	8	0.00159744	0.0	0.0	5008	,	,		17690	0.0079		0.0	False		,,,				2504	0.0				p.R1089Q		Atlas-SNP	.											MICAL2,NS,carcinoma,+1,1	MICAL2	114	1	0			c.G3266A						PASS	.						54	54	54					11																	12281376		2201	4294	6495	SO:0001583	missense	9645	exon26			CCCCTCGGAGAGA	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.3266G>A	11.37:g.12281376G>A	ENSP00000256194:p.Arg1089Gln	131	0	0		161	56	0.347826	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Missense_Mutation	SNP	ENST00000256194.4	37	CCDS7809.1	7	0.003205128205128205	0	0.0	0	0.0	7	0.012237762237762238	0	0.0	G	1.895	-0.454548	0.04540	.	.	ENSG00000133816	ENST00000537344;ENST00000544073;ENST00000256194;ENST00000527546;ENST00000342902;ENST00000379612	T;T;T;T;T	0.60299	0.2;0.2;0.2;0.2;0.26	5.26	-3.4	0.04853	.	1.374950	0.04696	N	0.414963	T	0.23611	0.0571	N	0.19112	0.55	0.09310	N	1	B;B;B;B;B;B	0.32128	0.002;0.03;0.0;0.0;0.001;0.357	B;B;B;B;B;B	0.18871	0.001;0.005;0.0;0.0;0.001;0.023	T	0.06058	-1.0848	10	0.13470	T	0.59	.	3.761	0.08604	0.2276:0.3179:0.3678:0.0867	rs2270515;rs52826400;rs2270515	432;1068;899;842;863;1089	B4DYS3;G3XAC8;B7Z849;Q5KTR3;Q5KTR4;O94851	.;.;.;.;.;MICA2_HUMAN	Q	899;432;1089;899;1068;863	ENSP00000441689:R899Q;ENSP00000256194:R1089Q;ENSP00000433965:R899Q;ENSP00000344894:R1068Q;ENSP00000368932:R863Q	ENSP00000256194:R1089Q	R	+	2	0	MICAL2	12237952	0.000000	0.05858	0.016000	0.15963	0.370000	0.29829	-0.913000	0.04042	-0.723000	0.04915	-1.378000	0.01179	CGG	G|0.994;A|0.006	0.006	strong		0.552	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632		A	12281376	G	A	12281376	3	1	13	1	0	0	0	0	1	0	0	0	9579	1116	39	1	3360	1	MICAL2	11	12281376	Missense_Mutation	SNP	G	TCGA-FF-8046-01A-11D-2210-10	11960653	12281376	122725140	59	1748											
PTPRO	5800	hgsc.bcm.edu	37	chr12	15637161	15637161	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgtggtgaccaagccatccaGatcaatcactgtgttaacaa	13	10	8	10	0	2	2	2	1	0	1	3	2	3	2	3	1	2	1	3	1	4	1			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr12:15637161G>A	ENST00000281171.4	+	2	659	c.329G>A	c.(328-330)aGa>aAa	p.R110K	PTPRO_ENST00000543886.1_Missense_Mutation_p.R110K|PTPRO_ENST00000348962.2_Missense_Mutation_p.R110K	NM_030667.2	NP_109592.1	Q16827	PTPRO_HUMAN	protein tyrosine phosphatase, receptor type, O	110	Fibronectin type-III 1. {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)				AAGCCATCCAGATCAATCACT	0.413																																					p.R110K		Atlas-SNP	.											.	PTPRO	148	.	0			c.G329A						PASS	.						95	95	95					12																	15637161		2203	4300	6503	SO:0001583	missense	5800	exon2			CATCCAGATCAAT	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.329G>A	12.37:g.15637161G>A	ENSP00000281171:p.Arg110Lys	114	0	0		145	6	0.0413793	NM_002848	A0AV39|Q13101|Q8IYG3|Q9UBF0|Q9UBT5	Missense_Mutation	SNP	ENST00000281171.4	37	CCDS8675.1	.	.	.	.	.	.	.	.	.	.	G	14.68	2.606381	0.46527	.	.	ENSG00000151490	ENST00000281171;ENST00000543886;ENST00000348962	T;T	0.03889	3.78;3.77	5.58	4.69	0.59074	Fibronectin, type III (1);	0.000000	0.56097	D	0.000029	T	0.03564	0.0102	N	0.14661	0.345	0.80722	D	1	B;B;B	0.24963	0.049;0.029;0.115	B;B;B	0.24848	0.008;0.004;0.056	T	0.48843	-0.8999	10	0.48119	T	0.1	.	10.1372	0.42715	0.1479:0.0:0.8521:0.0	.	110;110;110	Q16827-2;Q16827;Q8IYG3	.;PTPRO_HUMAN;.	K	110	ENSP00000281171:R110K;ENSP00000343434:R110K	ENSP00000281171:R110K	R	+	2	0	PTPRO	15528428	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.889000	0.56212	2.630000	0.89119	0.655000	0.94253	AGA	.	.	none		0.413	PTPRO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401079.1			A	15637161	G	A	15637161	3	1	13	1	0	0	0	0	1	0	0	0	12824	942	33	2	335	2	PTPRO	12	15637161	Missense_Mutation	SNP	G	TCGA-FF-8046-01A-11D-2210-10		15637161	118214734	60	1749											
PDE3A	5139	hgsc.bcm.edu	37	chr12	20787945	20787945	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgagagagcctctgaggaaAgcatcggcttgcagcaccta	11	7	12	11	1	1	3	0	2	1	1	2	5	1	4	2	2	4	4	2	2	2	2			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr12:20787945A>T	ENST00000359062.3	+	8	1996	c.1956A>T	c.(1954-1956)aaA>aaT	p.K652N	PDE3A_ENST00000544307.1_3'UTR	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	652					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)	CTCTGAGGAAAGCATCGGCTT	0.433																																					p.K652N		Atlas-SNP	.											.	PDE3A	184	.	0			c.A1956T						PASS	.						135	114	121					12																	20787945		2203	4300	6503	SO:0001583	missense	5139	exon8			GAGGAAAGCATCG		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.1956A>T	12.37:g.20787945A>T	ENSP00000351957:p.Lys652Asn	95	0	0		111	7	0.0630631	NM_000921	O60865|Q13348|Q17RD1	Missense_Mutation	SNP	ENST00000359062.3	37	CCDS31754.1	.	.	.	.	.	.	.	.	.	.	A	7.711	0.695201	0.15039	.	.	ENSG00000172572	ENST00000359062	T	0.62105	0.05	5.64	-0.807	0.10872	.	7739.210000	0.00166	N	0.000000	T	0.50565	0.1623	L	0.36672	1.1	0.09310	N	1	B	0.16396	0.017	B	0.06405	0.002	T	0.17501	-1.0367	10	0.27785	T	0.31	.	6.338	0.21306	0.4635:0.1377:0.3988:0.0	.	652	Q14432	PDE3A_HUMAN	N	652	ENSP00000351957:K652N	ENSP00000351957:K652N	K	+	3	2	PDE3A	20679212	0.993000	0.37304	0.091000	0.20842	0.139000	0.21198	1.258000	0.32944	-0.134000	0.11516	0.528000	0.53228	AAA	.	.	none		0.433	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2			T	20787945	A	T	20787945	3	4	13	1	0	0	0	0	1	0	0	0	11646	69	3	5	1986	5	PDE3A	12	20787945	Missense_Mutation	SNP	A	TCGA-FF-8046-01A-11D-2210-10	5150784	20787945	113063950	61	1750											
TMTC4	84899	hgsc.bcm.edu	37	chr13	101287335	101287335	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aaagtcagcagcacacagtaCccaacgctggggaggtagag	14	4	13	10	1	1	1	1	0	0	1	1	2	1	2	1	3	4	5	1	3	4	2			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr13:101287335C>A	ENST00000376234.3	-	10	1449	c.1260G>T	c.(1258-1260)ggG>ggT	p.G420G	TMTC4_ENST00000342624.5_Silent_p.G439G|TMTC4_ENST00000462211.1_5'UTR|TMTC4_ENST00000328767.5_Silent_p.G309G	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	420						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)					GCACACAGTACCCAACGCTGG	0.537																																					p.G439G		Atlas-SNP	.											.	TMTC4	103	.	0			c.G1317T						PASS	.						84	77	79					13																	101287335		2203	4300	6503	SO:0001819	synonymous_variant	84899	exon11			ACAGTACCCAACG		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.1260G>T	13.37:g.101287335C>A		160	0	0		216	12	0.0555556	NM_032813	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Silent	SNP	ENST00000376234.3	37	CCDS41904.1																																																																																			.	.	none		0.537	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813		A	101287335	C	A	101287335	2	1	13	1	0	0	0	0	0	0	0	1	16278	494	18	4		4	TMTC4	13	101287335	Silent	SNP	C	TCGA-FF-8046-01A-11D-2210-10		101287335	13882543	62	1751											
ERCC5	2073	hgsc.bcm.edu	37	chr13	103504506	103504506	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accaagcacttaaaggagtcCgggatcgccatgggaactca	13	6	11	11	2	1	0	1	0	0	0	3	3	2	3	3	3	2	1	3	3	4	1			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr13:103504506C>G	ENST00000355739.4	+	2	1550	c.127C>G	c.(127-129)Cgg>Ggg	p.R43G	BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.P468R|ERCC5_ENST00000535557.1_Missense_Mutation_p.R43G	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	43	N-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)					TAAAGGAGTCCGGGATCGCCA	0.378			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.R497G		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.C1489G						PASS	.						128	131	130					13																	103504506		2203	4300	6503	SO:0001583	missense	0	exon10	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	GGAGTCCGGGATC	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.127C>G	13.37:g.103504506C>G	ENSP00000347978:p.Arg43Gly	113	0	0		180	47	0.261111	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Missense_Mutation	SNP	ENST00000355739.4	37	CCDS32004.1	.	.	.	.	.	.	.	.	.	.	C	13.10	2.136257	0.37728	.	.	ENSG00000134899	ENST00000418659;ENST00000355739;ENST00000535557	T;T	0.69435	-0.4;-0.4	5.39	3.47	0.39725	XPG N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.77025	0.4070	M	0.79258	2.445	0.53005	D	0.999964	P;P;D	0.64830	0.933;0.954;0.994	D;P;P	0.63033	0.91;0.765;0.903	T	0.77948	-0.2396	10	0.62326	D	0.03	-16.4647	8.4298	0.32750	0.2594:0.6527:0.0:0.0879	.	43;43;468	B4DSI5;P28715;Q59FZ7	.;ERCC5_HUMAN;.	G	468;43;43	ENSP00000347978:R43G;ENSP00000442117:R43G	ENSP00000347978:R43G	R	+	1	2	ERCC5	102302507	1.000000	0.71417	1.000000	0.80357	0.690000	0.40134	2.390000	0.44416	1.269000	0.44280	-0.233000	0.12211	CGG	.	.	none		0.378	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1			G	103504506	C	G	103504506	3	3	13	1	0	0	0	0	1	0	0	0	5218	643	23	4	133	4	ERCC5	13	103504506	Missense_Mutation	SNP	C	TCGA-FF-8046-01A-11D-2210-10	2217171	103504506	11665372	63	1752											
RFX7	64864	hgsc.bcm.edu	37	chr15	56387864	56387864	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttaacactgccttgtttctGcccttctatggtagctgctg	5	16	8	12	0	2	0	0	0	2	0	2	0	2	0	2	1	5	4	2	1	3	6			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr15:56387864G>A	ENST00000559447.2	-	9	2042	c.1771C>T	c.(1771-1773)Cag>Tag	p.Q591*	RFX7_ENST00000423270.1_Nonsense_Mutation_p.Q688*|RFX7_ENST00000422057.1_Nonsense_Mutation_p.Q591*|RFX7_ENST00000317318.6_Nonsense_Mutation_p.Q688*			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	591					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						CCTTGTTTCTGCCCTTCTATG	0.458																																					p.Q688X		Atlas-SNP	.											.	RFX7	170	.	0			c.C2062T						PASS	.						119	110	113					15																	56387864		1903	4122	6025	SO:0001587	stop_gained	64864	exon9			GTTTCTGCCCTTC			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.1771C>T	15.37:g.56387864G>A	ENSP00000453281:p.Gln591*	242	0	0		319	127	0.398119	NM_022841	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Nonsense_Mutation	SNP	ENST00000559447.2	37		.	.	.	.	.	.	.	.	.	.	G	35	5.487851	0.96323	.	.	ENSG00000181827	ENST00000422057;ENST00000317318;ENST00000423270	.	.	.	5.57	5.57	0.84162	.	0.272984	0.27134	N	0.020761	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	-2.2321	18.5333	0.91000	0.0:0.0:1.0:0.0	.	.	.	.	X	591;688;688	.	ENSP00000313299:Q688X	Q	-	1	0	RFX7	54175156	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	4.113000	0.57851	2.600000	0.87896	0.655000	0.94253	CAG	.	.	none		0.458	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841		A	56387864	G	A	56387864	4	1	13	1	0	0	0	0	0	1	0	0	13283	1328	46	2	2324	2	RFX7	15	56387864	Nonsense_Mutation	SNP	G	TCGA-FF-8046-01A-11D-2210-10		56387864	46143528	64	1753											
CSPG4	1464	hgsc.bcm.edu	37	chr15	75980270	75980270	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agcaaagcccgagtcagcatCgctgaaggccacgtcgtctg	10	6	12	13	4	2	1	1	1	1	0	4	2	2	1	2	1	3	3	2	1	2	0	rs552897521		TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr15:75980270C>T	ENST00000308508.5	-	3	3228	c.3136G>A	c.(3136-3138)Gat>Aat	p.D1046N		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	1046	Gly/Ser-rich (glycosaminoglycan attachment domain).|Interaction with COL5A1. {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						GAGTCAGCATCGCTGAAGGCC	0.642													C|||	1	0.000199681	0.0	0.0	5008	,	,		19833	0.001		0.0	False		,,,				2504	0.0				p.D1046N		Atlas-SNP	.											.	CSPG4	175	.	0			c.G3136A						PASS	.																																			SO:0001583	missense	1464	exon3			CAGCATCGCTGAA	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.3136G>A	15.37:g.75980270C>T	ENSP00000312506:p.Asp1046Asn	124	0	0		203	101	0.497537	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	26.0	4.692443	0.88735	.	.	ENSG00000173546	ENST00000308508	T	0.51071	0.72	4.89	4.89	0.63831	.	0.000000	0.64402	D	0.000002	T	0.69975	0.3171	M	0.78456	2.415	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.73839	-0.3856	10	0.56958	D	0.05	.	17.0533	0.86525	0.0:1.0:0.0:0.0	.	1046	Q6UVK1	CSPG4_HUMAN	N	1046	ENSP00000312506:D1046N	ENSP00000312506:D1046N	D	-	1	0	CSPG4	73767325	1.000000	0.71417	0.708000	0.30435	0.809000	0.45718	7.817000	0.86213	2.253000	0.74438	0.555000	0.69702	GAT	.	.	none		0.642	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		T	75980270	C	T	75980270	3	4	13	1	0	0	0	0	1	0	0	0	3962	884	31	1	3864	1	CSPG4	15	75980270	Missense_Mutation	SNP	C	TCGA-FF-8046-01A-11D-2210-10	19592406	75980270	26551122	65	1754											
ARRDC4	91947	hgsc.bcm.edu	37	chr15	98512603	98512603	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	attatcagagtggactattcCttagctgtaagcaaagctct	12	13	8	8	0	2	1	1	0	1	1	3	2	3	2	1	1	3	4	1	1	5	5			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr15:98512603C>G	ENST00000268042.6	+	5	1040	c.876C>G	c.(874-876)tcC>tcG	p.S292S	ARRDC4_ENST00000538249.1_Silent_p.S205S	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)			TGGACTATTCCTTAGCTGTAA	0.398																																					p.S292S		Atlas-SNP	.											.	ARRDC4	30	.	0			c.C876G						PASS	.						86	78	81					15																	98512603		2197	4298	6495	SO:0001819	synonymous_variant	91947	exon5			CTATTCCTTAGCT	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.876C>G	15.37:g.98512603C>G		75	0	0		95	36	0.378947	NM_183376	Q6NSI9	Silent	SNP	ENST00000268042.6	37	CCDS10377.1																																																																																			.	.	none		0.398	ARRDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313535.1	NM_183376		G	98512603	C	G	98512603	2	3	13	1	0	0	0	0	0	0	0	1	985	668	24	4		4	ARRDC4	15	98512603	Silent	SNP	C	TCGA-FF-8046-01A-11D-2210-10	22532333	98512603	4018789	66	1755											
SRRM2	23524	hgsc.bcm.edu	37	chr16	2816548	2816548	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtaactcgaagaaggtccCgctctcgaacctcaccagtg	11	7	9	14	3	2	1	1	0	1	1	5	3	3	1	3	1	2	2	3	1	4	1	rs555127784		TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr16:2816548C>T	ENST00000301740.8	+	11	6568	c.6019C>T	c.(6019-6021)Cgc>Tgc	p.R2007C		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	2007	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						AAGAAGGTCCCGCTCTCGAAC	0.567													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17179	0.0		0.0	False		,,,				2504	0.0				p.R2007C		Atlas-SNP	.											SRRM2,colon,carcinoma,-1,1	SRRM2	263	1	0			c.C6019T						PASS	.						73	78	76					16																	2816548		2198	4300	6498	SO:0001583	missense	23524	exon11			AGGTCCCGCTCTC	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.6019C>T	16.37:g.2816548C>T	ENSP00000301740:p.Arg2007Cys	114	0	0		114	5	0.0438596	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	37	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	C	9.797	1.179393	0.21787	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933	T	0.27890	1.64	5.46	5.46	0.80206	.	0.000000	0.64402	D	0.000020	T	0.33818	0.0876	N	0.08118	0	0.45791	D	0.998673	D	0.89917	1.0	D	0.80764	0.994	T	0.35822	-0.9773	10	0.72032	D	0.01	-6.8635	11.8353	0.52321	0.1749:0.8251:0.0:0.0	.	2007	Q9UQ35	SRRM2_HUMAN	C	2007;2007;1259	ENSP00000301740:R2007C	ENSP00000301740:R2007C	R	+	1	0	SRRM2	2756549	0.999000	0.42202	1.000000	0.80357	0.996000	0.88848	2.556000	0.45862	2.572000	0.86782	0.650000	0.86243	CGC	.	.	none		0.567	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			T	2816548	C	T	2816548	3	4	13	1	0	0	0	0	1	0	0	0	15184	652	23	1	6057	1	SRRM2	16	2816548	Missense_Mutation	SNP	C	TCGA-FF-8046-01A-11D-2210-10		2816548	87538205	67	1756											
CHST4	10164	hgsc.bcm.edu	37	chr16	71570645	71570645	+	Frame_Shift_Del	DEL	T	T	-																															ccagatggccatcttggctcTattcttccacatgtacagcc																										TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr16:71570645delT	ENST00000338482.5	+	3	408	c.65delT	c.(64-66)ctafs	p.L22fs	CHST4_ENST00000572450.1_Frame_Shift_Del_p.L22fs|CHST4_ENST00000539698.3_Frame_Shift_Del_p.L22fs|ZNF19_ENST00000568446.1_Intron			Q8NCG5	CHST4_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 4	22					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|immune response (GO:0006955)|inflammatory response (GO:0006954)|leukocyte tethering or rolling (GO:0050901)|N-acetylglucosamine metabolic process (GO:0006044)|protein sulfation (GO:0006477)|sulfur compound metabolic process (GO:0006790)	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)			cervix(1)|kidney(3)|large_intestine(9)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	21						ATCTTGGCTCTATTCTTCCAC	0.502																																					p.L22fs		Pindel,Atlas-Indel	.											.	CHST4	47	.	0			c.64delC						PASS	.						111	108	109					16																	71570645		2198	4300	6498	SO:0001589	frameshift_variant	10164	exon2			.	AF131235	CCDS10902.1	16q22.2	2008-02-05			ENSG00000140835	ENSG00000140835		"Sulfotransferases, membrane-bound"	1972	protein-coding gene	gene with protein product						10330415	Standard	NM_001166395		Approved	HEC-GLCNAC-6-ST, LSST	uc002fao.3	Q8NCG5	OTTHUMG00000137592	ENST00000338482.5:c.65delT	16.37:g.71570645delT	ENSP00000341206:p.Leu22fs	84	0	.		83	17	0.205	NM_001166395	Q8IV46|Q9Y5R3	Frame_Shift_Del	DEL	ENST00000338482.5	37	CCDS10902.1																																																																																			.	.	none		0.502	CHST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268992.4	NM_005769		-	71570645	T	-	71570645	7	5	13	1	0	1	0	1	0	0	0	0	3408	1522	53	0	67	0	CHST4	16	71570645	Frame_Shift_Del	DEL	T	TCGA-FF-8046-01A-11D-2210-10	68754097	71570645	18784108	68	1757											
ZMYND15	84225	hgsc.bcm.edu	37	chr17	4645298	4645298	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccggccaggcttcacctttGcttcccttcgtgctcgaacc	4	11	8	18	3	1	0	1	0	0	0	4	1	2	0	5	2	3	3	5	2	1	4			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr17:4645298G>A	ENST00000433935.1	+	4	973	c.916G>A	c.(916-918)Gct>Act	p.A306T	CXCL16_ENST00000574412.1_5'Flank|ZMYND15_ENST00000573751.2_Missense_Mutation_p.A306T|ZMYND15_ENST00000269289.6_Missense_Mutation_p.A306T|CXCL16_ENST00000293778.6_5'Flank|ZMYND15_ENST00000592813.1_Missense_Mutation_p.A306T	NM_001136046.2|NM_001267822.1	NP_001129518.1|NP_001254751.1	Q9H091	ZMY15_HUMAN	zinc finger, MYND-type containing 15	306					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						CTTCACCTTTGCTTCCCTTCG	0.567																																					p.A306T		Atlas-SNP	.											.	ZMYND15	87	.	0			c.G916A						PASS	.						79	83	82					17																	4645298		2203	4300	6503	SO:0001583	missense	84225	exon4			ACCTTTGCTTCCC	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.916G>A	17.37:g.4645298G>A	ENSP00000391742:p.Ala306Thr	94	0	0		118	40	0.338983	NM_001136046	B4DXY5|I3L296	Missense_Mutation	SNP	ENST00000433935.1	37	CCDS45584.1	.	.	.	.	.	.	.	.	.	.	G	19.33	3.806938	0.70797	.	.	ENSG00000141497	ENST00000433935;ENST00000269289	T;T	0.53206	0.67;0.63	5.15	5.15	0.70609	.	0.094778	0.45606	D	0.000355	T	0.53965	0.1829	L	0.29908	0.895	0.33804	D	0.627042	D;D	0.69078	0.997;0.997	D;D	0.73380	0.913;0.98	T	0.64322	-0.6435	10	0.56958	D	0.05	-19.1442	11.1144	0.48252	0.0:0.0:0.8159:0.1841	.	306;306	B4DXY5;Q9H091	.;ZMY15_HUMAN	T	306	ENSP00000391742:A306T;ENSP00000269289:A306T	ENSP00000269289:A306T	A	+	1	0	ZMYND15	4592047	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.585000	0.46111	2.677000	0.91161	0.563000	0.77884	GCT	.	.	none		0.567	ZMYND15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439580.1	NM_032265		A	4645298	G	A	4645298	3	1	13	1	0	0	0	0	1	0	0	0	17723	1319	46	2	926	2	ZMYND15	17	4645298	Missense_Mutation	SNP	G	TCGA-FF-8046-01A-11D-2210-10		4645298	76549912	69	1758											
FAM64A	54478	hgsc.bcm.edu	37	chr17	6352690	6352690	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcagcatctccagaagctgTcccaagagctagatgaagcc	12	8	9	12	0	2	4	1	1	1	3	4	4	3	4	3	0	4	3	3	0	4	2			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr17:6352690T>C	ENST00000250056.8	+	4	732	c.649T>C	c.(649-651)Tcc>Ccc	p.S217P	FAM64A_ENST00000576056.1_Missense_Mutation_p.S217P|FAM64A_ENST00000572447.1_Missense_Mutation_p.S217P|FAM64A_ENST00000570337.2_Missense_Mutation_p.S217P|FAM64A_ENST00000572595.2_Missense_Mutation_p.S248P|FAM64A_ENST00000571373.1_Missense_Mutation_p.S217P	NM_001195228.1	NP_001182157.1	Q9BSJ6	FA64A_HUMAN	family with sequence similarity 64, member A	217					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)		CCAGAAGCTGTCCCAAGAGCT	0.537																																					p.S217P		Atlas-SNP	.											.	FAM64A	20	.	0			c.T649C						PASS	.						86	82	84					17																	6352690		2203	4300	6503	SO:0001583	missense	54478	exon4			AAGCTGTCCCAAG		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.649T>C	17.37:g.6352690T>C	ENSP00000250056:p.Ser217Pro	68	0	0		78	5	0.0641026	NM_019013	Q96CT4|Q9NVV1|Q9NWB5	Missense_Mutation	SNP	ENST00000250056.8	37	CCDS56016.1	.	.	.	.	.	.	.	.	.	.	.	20.5	4.007184	0.75046	.	.	ENSG00000129195	ENST00000250056;ENST00000308855	T	0.56611	0.45	5.75	5.75	0.90469	.	0.076511	0.51477	D	0.000093	T	0.70343	0.3213	M	0.72118	2.19	0.41665	D	0.989202	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.997	T	0.73852	-0.3852	10	0.66056	D	0.02	-19.9763	12.4405	0.55621	0.0:0.0:0.0:1.0	.	217;217	Q9BSJ6;Q9BSJ6-2	FA64A_HUMAN;.	P	217	ENSP00000250056:S217P	ENSP00000250056:S217P	S	+	1	0	FAM64A	6293414	1.000000	0.71417	1.000000	0.80357	0.858000	0.48976	2.868000	0.48436	2.196000	0.70406	0.460000	0.39030	TCC	.	.	none		0.537	FAM64A-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000439156.1	NM_019013		C	6352690	T	C	6352690	3	2	13	1	0	0	0	0	1	0	0	0	5606	1667	58	3	659	3	FAM64A	17	6352690	Missense_Mutation	SNP	T	TCGA-FF-8046-01A-11D-2210-10	1707392	6352690	74842520	70	1759											
SPAG5	10615	hgsc.bcm.edu	37	chr17	26919654	26919654	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggatttggtggagactccTctaagagatgggacggagat	11	9	16	5	1	1	3	0	0	1	3	2	8	2	5	1	5	0	0	1	5	1	2			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr17:26919654T>C	ENST00000321765.5	-	3	940	c.608A>G	c.(607-609)gAg>gGg	p.E203G		NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	203					chromosome segregation (GO:0007059)|mitotic sister chromatid segregation (GO:0000070)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|microtubule plus-end (GO:0035371)|mitotic spindle (GO:0072686)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43	Lung NSC(42;0.00431)					TGGAGACTCCTCTAAGAGATG	0.493																																					p.E203G		Atlas-SNP	.											.	SPAG5	92	.	0			c.A608G						PASS	.						103	102	103					17																	26919654		2203	4300	6503	SO:0001583	missense	10615	exon3			GACTCCTCTAAGA	AF063308	CCDS32594.1	17q11.2	2008-07-18			ENSG00000076382	ENSG00000076382			13452	protein-coding gene	gene with protein product	"mitotic spindle coiled-coil related protein", "astrin", "mitotic spindle associated protein p126"	615562				11549262	Standard	NM_006461		Approved	DEEPEST, MAP126, hMAP126	uc002hbq.3	Q96R06	OTTHUMG00000166586	ENST00000321765.5:c.608A>G	17.37:g.26919654T>C	ENSP00000323300:p.Glu203Gly	126	0	0		134	48	0.358209	NM_006461	O95213|Q9BWE8|Q9NT17|Q9UFE6	Missense_Mutation	SNP	ENST00000321765.5	37	CCDS32594.1	.	.	.	.	.	.	.	.	.	.	T	1.807	-0.475729	0.04414	.	.	ENSG00000076382	ENST00000321765	T	0.43688	0.94	5.33	2.99	0.34606	.	0.841403	0.10417	N	0.677155	T	0.22437	0.0541	N	0.08118	0	0.09310	N	1	B	0.11235	0.004	B	0.12156	0.007	T	0.18335	-1.0340	10	0.87932	D	0	-0.7221	4.8055	0.13317	0.0:0.0969:0.1906:0.7125	.	203	Q96R06	SPAG5_HUMAN	G	203	ENSP00000323300:E203G	ENSP00000323300:E203G	E	-	2	0	SPAG5	23943781	0.008000	0.16893	0.003000	0.11579	0.058000	0.15608	1.333000	0.33816	0.857000	0.35407	0.533000	0.62120	GAG	.	.	none		0.493	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461		C	26919654	T	C	26919654	3	2	13	1	0	0	0	0	1	0	0	0	14996	1551	54	3	3061	3	SPAG5	17	26919654	Missense_Mutation	SNP	T	TCGA-FF-8046-01A-11D-2210-10	20566964	26919654	54275556	71	1760											
ABCA8	10351	hgsc.bcm.edu	37	chr17	66918384	66918384	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttttttttttttttttaccTttcaaggcttctattttatc	5	28	2	6	0	2	0	1	0	1	0	3	0	2	0	1	1	1	1	1	1	4	14			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr17:66918384T>C	ENST00000269080.2	-	11	1637	c.1500A>G	c.(1498-1500)aaA>aaG	p.K500K	ABCA8_ENST00000586539.1_Splice_Site_p.K500K|ABCA8_ENST00000430352.2_Splice_Site_p.K500K	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	500	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)					tttttttACCTTTCAAGGCTT	0.209																																					p.K500K		Atlas-SNP	.											.	ABCA8	213	.	0			c.A1500G						PASS	.						18	18	18					17																	66918384		2152	4259	6411	SO:0001630	splice_region_variant	10351	exon11			TTTACCTTTCAAG	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.1501+1A>G	17.37:g.66918384T>C		64	0	0		60	20	0.333333	NM_007168	A1L3U3|C9JQE6|Q86WW0	Silent	SNP	ENST00000269080.2	37	CCDS11680.1																																																																																			.	.	none		0.209	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168	Silent	C	66918384	T	C	66918384	5	2	13	1	0	0	0	0	0	0	1	0	38	1623	56	3	3357	3	ABCA8	17	66918384	Splice_Site	SNP	T	TCGA-FF-8046-01A-11D-2210-10	39998730	66918384	14276826	72	1761											
SDK2	54549	hgsc.bcm.edu	37	chr17	71431699	71431699	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctgatctgcaggcccccgTcgttgcgctgccggaagcgg	4	7	15	15	6	1	1	0	1	1	0	2	2	1	2	3	3	4	4	3	3	1	1			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr17:71431699T>C	ENST00000392650.3	-	9	1085	c.1085A>G	c.(1084-1086)gAc>gGc	p.D362G	SDK2_ENST00000388726.3_Missense_Mutation_p.D362G	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	362	Ig-like C2-type 4.				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						CAGGCCCCCGTCGTTGCGCTG	0.652																																					p.D362G		Atlas-SNP	.											SDK2,NS,carcinoma,+1,1	SDK2	219	1	0			c.A1085G						scavenged	.						48	34	39					17																	71431699		2201	4297	6498	SO:0001583	missense	54549	exon9			CCCCCGTCGTTGC	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.1085A>G	17.37:g.71431699T>C	ENSP00000376421:p.Asp362Gly	101	1	0.00990099		69	3	0.0434783	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	37	CCDS45769.1	.	.	.	.	.	.	.	.	.	.	T	12.88	2.071712	0.36566	.	.	ENSG00000069188	ENST00000392650;ENST00000388726;ENST00000316893	T;T	0.38722	1.12;1.12	4.84	4.84	0.62591	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.127433	0.53938	D	0.000057	T	0.20740	0.0499	N	0.04768	-0.165	0.33996	D	0.649673	B;B	0.11235	0.004;0.001	B;B	0.15052	0.012;0.012	T	0.25012	-1.0144	9	.	.	.	.	10.5573	0.45125	0.0:0.0:0.162:0.838	.	362;362	Q58EX2-2;Q58EX2	.;SDK2_HUMAN	G	362	ENSP00000376421:D362G;ENSP00000373378:D362G	.	D	-	2	0	SDK2	68943294	0.990000	0.36364	0.843000	0.33291	0.816000	0.46133	3.419000	0.52728	1.798000	0.52647	0.459000	0.35465	GAC	.	.	none		0.652	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064		C	71431699	T	C	71431699	3	2	13	1	0	0	0	0	1	0	0	0	13984	1667	58	3	5581	3	SDK2	17	71431699	Missense_Mutation	SNP	T	TCGA-FF-8046-01A-11D-2210-10	4513315	71431699	9763511	73	1762											
GRB2	2885	hgsc.bcm.edu	37	chr17	73321980	73321980	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagcaggaaatacttactTgacagagagggagaagtccc	14	7	12	8	0	0	3	0	1	0	2	1	6	1	4	1	2	4	2	1	2	4	3			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr17:73321980T>C	ENST00000392562.1	-	4	1080	c.298A>G	c.(298-300)Aag>Gag	p.K100E	GRB2_ENST00000316804.5_Splice_Site_p.K100E|GRB2_ENST00000392564.1_Splice_Site_p.K100E|GRB2_ENST00000462266.1_5'UTR|GRB2_ENST00000392563.1_Intron|GRB2_ENST00000316615.5_Intron|GRB2_ENST00000578961.1_Splice_Site_p.N100D			P62993	GRB2_HUMAN	growth factor receptor-bound protein 2	100	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				aging (GO:0007568)|anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|cell-cell signaling (GO:0007267)|cellular response to ionizing radiation (GO:0071479)|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)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|protein heterooligomerization (GO:0051291)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of MAPK cascade (GO:0043408)|signal transduction in response to DNA damage (GO:0042770)|T cell costimulation (GO:0031295)|viral process (GO:0016032)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Grb2-EGFR complex (GO:0070436)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	ephrin receptor binding (GO:0046875)|epidermal growth factor receptor binding (GO:0005154)|identical protein binding (GO:0042802)|insulin receptor substrate binding (GO:0043560)|neurotrophin TRKA receptor binding (GO:0005168)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(3)|skin(1)	17	all_cancers(13;5.44e-09)|all_epithelial(9;1.1e-09)|Breast(9;1.85e-09)|all_lung(278;0.222)		all cancers(21;1.09e-07)|Epithelial(20;1.23e-06)|Lung(188;0.185)		Pegademase bovine(DB00061)	AATACTTACTTGACAGAGAGG	0.522																																					p.K100E		Atlas-SNP	.											.	GRB2	33	.	0			c.A298G						PASS	.						87	91	90					17																	73321980		2203	4300	6503	SO:0001630	splice_region_variant	2885	exon4			CTTACTTGACAGA		CCDS11721.1, CCDS11722.1	17q24-q25	2013-02-14			ENSG00000177885	ENSG00000177885		"SH2 domain containing"	4566	protein-coding gene	gene with protein product		108355					Standard	NM_002086		Approved	NCKAP2	uc002jnx.4	P62993	OTTHUMG00000134332	ENST00000392562.1:c.299+1A>G	17.37:g.73321980T>C		57	0	0		41	11	0.268293	NM_002086	P29354|Q14450|Q63057|Q63059	Missense_Mutation	SNP	ENST00000392562.1	37	CCDS11721.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.396281	0.83011	.	.	ENSG00000177885	ENST00000316804;ENST00000392562;ENST00000392564	D;D;D	0.89196	-2.48;-2.48;-2.48	5.28	5.28	0.74379	SH2 motif (5);	0.083338	0.85682	D	0.000000	D	0.93239	0.7846	M	0.93420	3.415	0.80722	D	1	B	0.22211	0.066	B	0.35770	0.21	D	0.92705	0.6178	10	0.72032	D	0.01	-25.8083	15.4247	0.75041	0.0:0.0:0.0:1.0	.	100	P62993	GRB2_HUMAN	E	100	ENSP00000339007:K100E;ENSP00000376345:K100E;ENSP00000376347:K100E	ENSP00000339007:K100E	K	-	1	0	GRB2	70833575	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.838000	0.86804	2.240000	0.73641	0.477000	0.44152	AAG	.	.	none		0.522	GRB2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259476.1		Missense_Mutation	C	73321980	T	C	73321980	5	2	13	1	0	0	0	0	0	0	1	0	6767	1826	63	3	367	3	GRB2	17	73321980	Splice_Site	SNP	T	TCGA-FF-8046-01A-11D-2210-10	1890281	73321980	7873230	74	1763											
ZBTB7C	201501	hgsc.bcm.edu	37	chr18	45566798	45566798	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttctcccttagcagagattcGatggagaagtcccggatcac	10	10	10	11	2	2	2	1	0	1	2	5	6	3	3	2	2	1	1	2	2	2	3			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr18:45566798G>A	ENST00000588982.1	-	3	1182	c.681C>T	c.(679-681)atC>atT	p.I227I	ZBTB7C_ENST00000590800.1_Silent_p.I227I|ZBTB7C_ENST00000535628.2_Silent_p.I227I|ZBTB7C_ENST00000332053.2_Silent_p.I227I|ZBTB7C_ENST00000586438.1_Silent_p.I227I			A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C	227							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						GCAGAGATTCGATGGAGAAGT	0.587																																					p.I227I		Atlas-SNP	.											.	ZBTB7C	73	.	0			c.C681T						PASS	.						49	50	49					18																	45566798		2203	4300	6503	SO:0001819	synonymous_variant	201501	exon2			AGATTCGATGGAG	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.681C>T	18.37:g.45566798G>A		145	0	0		171	63	0.368421	NM_001039360	O73453	Silent	SNP	ENST00000588982.1	37	CCDS32830.1																																																																																			.	.	none		0.587	ZBTB7C-025	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450731.1	NM_001039360		A	45566798	G	A	45566798	2	1	13	1	0	0	0	0	0	0	0	1	17570	1048	37	1		1	ZBTB7C	18	45566798	Silent	SNP	G	TCGA-FF-8046-01A-11D-2210-10		45566798	32510450	75	1764											
MYO5B	4645	hgsc.bcm.edu	37	chr18	47462675	47462675	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cagcggacatagtgaggtgtCgtggcattcagggtctccat	8	10	14	9	2	2	1	1	1	1	0	4	2	2	2	1	4	1	1	1	4	1	2	rs180849030	byFrequency	TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr18:47462675C>T	ENST00000285039.7	-	16	2249	c.1950G>A	c.(1948-1950)acG>acA	p.T650T		NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	650	Actin-binding. {ECO:0000255}.|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)	p.T650T(1)		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)		AGTGAGGTGTCGTGGCATTCA	0.517													C|||	2	0.000399361	0.0	0.0	5008	,	,		20181	0.0		0.002	False		,,,				2504	0.0				p.T650T		Atlas-SNP	.											MYO5B,NS,carcinoma,0,1	MYO5B	178	1	1	Substitution - coding silent(1)	lung(1)	c.G1950A						PASS	.						97	100	99					18																	47462675		2083	4237	6320	SO:0001819	synonymous_variant	4645	exon16			AGGTGTCGTGGCA	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.1950G>A	18.37:g.47462675C>T		120	0	0		159	56	0.352201	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	Silent	SNP	ENST00000285039.7	37	CCDS42436.1																																																																																			C|0.999;T|0.001	0.001	strong		0.517	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2			T	47462675	C	T	47462675	2	4	13	1	0	0	0	0	0	0	0	1	10088	871	31	1		1	MYO5B	18	47462675	Silent	SNP	C	TCGA-FF-8046-01A-11D-2210-10	1895877	47462675	30614573	76	1765											
FZR1	51343	hgsc.bcm.edu	37	chr19	3532490	3532490	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcggccgtgaaggccatcGcctggtccccacatcagcac	7	6	12	16	3	1	1	1	1	0	0	3	1	2	1	5	4	1	1	5	4	1	0	rs371550562		TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr19:3532490G>A	ENST00000395095.3	+	10	1084	c.1084G>A	c.(1084-1086)Gcc>Acc	p.A362T	FZR1_ENST00000441788.2_Missense_Mutation_p.A362T|FZR1_ENST00000313639.8_Missense_Mutation_p.A273T	NM_001136198.1	NP_001129670.1	Q9UM11	FZR_HUMAN	fizzy/cell division cycle 20 related 1 (Drosophila)	362					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)		GAAGGCCATCGCCTGGTCCCC	0.672																																					p.A362T		Atlas-SNP	.											.	FZR1	42	.	0			c.G1084A						PASS	.		THR/ALA,THR/ALA,THR/ALA	0,4398		0,0,2199	29	31	30		817,1084,1084	5.4	1	19		30	1,8595	1.2+/-3.3	0,1,4297	no	missense,missense,missense	FZR1	NM_001136197.1,NM_001136198.1,NM_016263.3	58,58,58	0,1,6496	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign	273/405,362/497,362/494	3532490	1,12993	2199	4298	6497	SO:0001583	missense	51343	exon10			GCCATCGCCTGGT	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.1084G>A	19.37:g.3532490G>A	ENSP00000378529:p.Ala362Thr	143	0	0		83	4	0.0481928	NM_001136198	O75869|Q86U66|Q96NW8|Q9UI96|Q9ULH8|Q9UM10|Q9UNQ1|Q9Y2T8	Missense_Mutation	SNP	ENST00000395095.3	37	CCDS45916.1	.	.	.	.	.	.	.	.	.	.	g	36	5.780530	0.96929	0.0	1.16E-4	ENSG00000105325	ENST00000441788;ENST00000395095;ENST00000313639	T;T;T	0.63744	-0.06;-0.06;-0.06	5.39	5.39	0.77823	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.047137	0.85682	D	0.000000	T	0.81749	0.4888	M	0.84773	2.715	0.80722	D	1	P;D;D	0.89917	0.889;0.999;1.0	P;D;D	0.91635	0.723;0.968;0.999	D	0.84022	0.0354	10	0.59425	D	0.04	-45.9139	17.7131	0.88327	0.0:0.0:1.0:0.0	.	362;273;362	Q9UM11;Q9UM11-3;Q9UM11-2	FZR_HUMAN;.;.	T	362;362;273	ENSP00000410369:A362T;ENSP00000378529:A362T;ENSP00000321800:A273T	ENSP00000321800:A273T	A	+	1	0	FZR1	3483490	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	9.420000	0.97426	2.531000	0.85337	0.543000	0.68304	GCC	.	.	weak		0.672	FZR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452869.2	NM_016263		A	3532490	G	A	3532490	3	1	13	1	0	0	0	0	1	0	0	0	6146	1087	38	1	1122	1	FZR1	19	3532490	Missense_Mutation	SNP	G	TCGA-FF-8046-01A-11D-2210-10		3532490	55596493	77	1766											
SYDE1	85360	hgsc.bcm.edu	37	chr19	15224520	15224520	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccccccgagcaaccgctacGccggcgactggagcgtttgc	6	5	13	17	6	0	0	0	0	0	0	0	3	0	1	5	2	5	3	5	2	2	2			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr19:15224520G>A	ENST00000342784.2	+	8	1985	c.1954G>A	c.(1954-1956)Gcc>Acc	p.A652T	SYDE1_ENST00000600252.1_Missense_Mutation_p.A309T|SYDE1_ENST00000600440.1_Missense_Mutation_p.A585T	NM_033025.4	NP_149014.3	Q6ZW31	SYDE1_HUMAN	synapse defective 1, Rho GTPase, homolog 1 (C. elegans)	652					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						CAACCGCTACGCCGGCGACTG	0.692																																					p.A652T		Atlas-SNP	.											.	SYDE1	44	.	0			c.G1954A						PASS	.						43	53	50					19																	15224520		2203	4298	6501	SO:0001583	missense	85360	exon8			CGCTACGCCGGCG	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.1954G>A	19.37:g.15224520G>A	ENSP00000341489:p.Ala652Thr	80	0	0		34	8	0.235294	NM_033025	Q7L2I8|Q8N6J2|Q9H8K4	Missense_Mutation	SNP	ENST00000342784.2	37	CCDS12324.1	.	.	.	.	.	.	.	.	.	.	G	35	5.533392	0.96460	.	.	ENSG00000105137	ENST00000342784	T	0.55930	0.49	5.52	5.52	0.82312	.	0.134668	0.48767	D	0.000170	T	0.73916	0.3648	M	0.79123	2.44	0.54753	D	0.99998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	T	0.76995	-0.2752	10	0.87932	D	0	.	16.928	0.86182	0.0:0.0:1.0:0.0	.	585;585;652	B2RD93;Q6ZW31-2;Q6ZW31	.;.;SYDE1_HUMAN	T	652	ENSP00000341489:A652T	ENSP00000341489:A652T	A	+	1	0	SYDE1	15085520	1.000000	0.71417	0.979000	0.43373	0.968000	0.65278	9.146000	0.94640	2.604000	0.88044	0.491000	0.48974	GCC	.	.	none		0.692	SYDE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465666.1	NM_033025		A	15224520	G	A	15224520	3	1	13	1	0	0	0	0	1	0	0	0	15450	1087	38	1	1984	1	SYDE1	19	15224520	Missense_Mutation	SNP	G	TCGA-FF-8046-01A-11D-2210-10	11692030	15224520	43904463	78	1767											
RHPN2	85415	hgsc.bcm.edu	37	chr19	33517507	33517507	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagctcagctccagccgcaCttgctcccgcacctttgagt	7	9	9	16	2	1	1	1	1	0	0	3	2	3	1	4	0	4	5	4	0	1	2			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr19:33517507C>T	ENST00000254260.3	-	3	252	c.217G>A	c.(217-219)Gtg>Atg	p.V73M	RHPN2_ENST00000400226.4_De_novo_Start_OutOfFrame	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	73					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)		p.V73M(2)		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)					TCCAGCCGCACTTGCTCCCGC	0.552																																					p.V73M		Atlas-SNP	.											RHPN2,face,carcinoma,0,2	RHPN2	107	2	2	Substitution - Missense(2)	NS(1)|skin(1)	c.G217A						scavenged	.						84	83	83					19																	33517507		2203	4300	6503	SO:0001583	missense	85415	exon3			GCCGCACTTGCTC	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.217G>A	19.37:g.33517507C>T	ENSP00000254260:p.Val73Met	23	0	0		38	4	0.105263	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	C	18.08	3.542997	0.65198	.	.	ENSG00000131941	ENST00000254260	T	0.39787	1.06	3.88	3.88	0.44766	.	0.000000	0.85682	D	0.000000	T	0.64853	0.2636	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.71984	-0.4427	10	0.87932	D	0	11.9954	16.025	0.80536	0.0:1.0:0.0:0.0	.	73	Q8IUC4	RHPN2_HUMAN	M	73	ENSP00000254260:V73M	ENSP00000254260:V73M	V	-	1	0	RHPN2	38209347	1.000000	0.71417	1.000000	0.80357	0.343000	0.28985	7.267000	0.78462	2.167000	0.68274	0.557000	0.71058	GTG	.	.	none		0.552	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103		T	33517507	C	T	33517507	3	4	13	1	0	0	0	0	1	0	0	0	13366	565	20	2	1895	2	RHPN2	19	33517507	Missense_Mutation	SNP	C	TCGA-FF-8046-01A-11D-2210-10	18292987	33517507	25611476	79	1768											
ZNF233	353355	hgsc.bcm.edu	37	chr19	44777859	44777859	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagatgtcaggtatatgcccGgagctccaaccagaactcct	11	8	9	13	1	1	2	1	0	0	2	3	3	3	3	4	2	4	2	4	2	4	2	rs569951523		TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr19:44777859G>A	ENST00000391958.2	+	5	1173	c.1046G>A	c.(1045-1047)cGg>cAg	p.R349Q	ZNF233_ENST00000334152.1_Missense_Mutation_p.R331Q|ZNF235_ENST00000589799.1_Intron|ZNF233_ENST00000592581.1_3'UTR	NM_181756.2	NP_861421.2	A6NK53	ZN233_HUMAN	zinc finger protein 233	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(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|skin(3)|urinary_tract(1)	20		Prostate(69;0.0435)|all_neural(266;0.226)				GTATATGCCCGGAGCTCCAAC	0.527													G|||	1	0.000199681	0.0	0.0	5008	,	,		20355	0.0		0.0	False		,,,				2504	0.001				p.R349Q		Atlas-SNP	.											.	ZNF233	73	.	0			c.G1046A						PASS	.						102	97	99					19																	44777859		2203	4300	6503	SO:0001583	missense	353355	exon5			ATGCCCGGAGCTC	AY166792	CCDS33047.1	19q13.31	2013-01-08				ENSG00000159915		"Zinc fingers, C2H2-type", "-"	30946	protein-coding gene	gene with protein product						12743021	Standard	NM_001207005		Approved	FLJ38032	uc021uvi.1	A6NK53		ENST00000391958.2:c.1046G>A	19.37:g.44777859G>A	ENSP00000375820:p.Arg349Gln	125	0	0		142	44	0.309859	NM_001207005	B2RN78|B2RN79|Q86WL8	Missense_Mutation	SNP	ENST00000391958.2	37	CCDS33047.1	.	.	.	.	.	.	.	.	.	.	G	11.34	1.610015	0.28712	.	.	ENSG00000159915	ENST00000334152;ENST00000391958;ENST00000280305	T;T	0.15718	2.4;2.4	4.29	-0.708	0.11241	.	.	.	.	.	T	0.11024	0.0269	L	0.28400	0.85	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30119	-0.9989	9	0.62326	D	0.03	0.0227	5.1768	0.15139	0.6014:0.1424:0.2562:0.0	.	349	A6NK53	ZN233_HUMAN	Q	331;349;270	ENSP00000334957:R331Q;ENSP00000375820:R349Q	ENSP00000280305:R270Q	R	+	2	0	ZNF233	49469699	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.049000	0.14099	-0.106000	0.12110	-0.355000	0.07637	CGG	.	.	none		0.527	ZNF233-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000460737.1	NM_181756		A	44777859	G	A	44777859	3	1	13	1	0	0	0	0	1	0	0	0	17801	1116	39	1	1060	1	ZNF233	19	44777859	Missense_Mutation	SNP	G	TCGA-FF-8046-01A-11D-2210-10	11260352	44777859	14351124	80	1769											
MACROD2	140733	hgsc.bcm.edu	37	chr20	14665585	14665585	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	acatgcaaaaatcacatgtgGctatgaccttcctgcaaaat	15	10	6	10	0	1	1	1	1	0	0	2	1	2	1	2	1	2	3	2	1	5	2			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr20:14665585G>T	ENST00000310348.4	+	5	398	c.398G>T	c.(397-399)gGc>gTc	p.G133V	MACROD2_ENST00000464883.1_3'UTR|MACROD2_ENST00000217246.4_Missense_Mutation_p.G133V			A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2	133	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				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)				ATCACATGTGGCTATGACCTT	0.418																																					p.G133V		Atlas-SNP	.											.	MACROD2	34	.	0			c.G398T						PASS	.						133	125	127					20																	14665585		1924	4158	6082	SO:0001583	missense	140733	exon5			CATGTGGCTATGA	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.398G>T	20.37:g.14665585G>T	ENSP00000309809:p.Gly133Val	140	0	0		139	51	0.366906	NM_080676	A6NFF7|B0QZ39|B3KWV0|Q0P6D5|Q495E0|Q5W199|Q6ZN71	Missense_Mutation	SNP	ENST00000310348.4	37	CCDS13120.2	.	.	.	.	.	.	.	.	.	.	G	28.8	4.947925	0.92593	.	.	ENSG00000172264	ENST00000217246;ENST00000310348	T;T	0.26957	1.7;1.7	5.62	5.62	0.85841	Appr-1-p processing (3);	0.000000	0.64402	D	0.000006	T	0.70666	0.3250	H	0.98866	4.355	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.83547	0.0099	10	0.87932	D	0	-13.8763	18.6571	0.91458	0.0:0.0:1.0:0.0	.	133;133	A1Z1Q3;A1Z1Q3-2	MACD2_HUMAN;.	V	133	ENSP00000217246:G133V;ENSP00000309809:G133V	ENSP00000217246:G133V	G	+	2	0	MACROD2	14613585	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.476000	0.97823	2.642000	0.89623	0.655000	0.94253	GGC	.	.	none		0.418	MACROD2-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_080676		T	14665585	G	T	14665585	3	4	13	1	0	0	0	0	1	0	0	0	9155	1203	42	4	416	4	MACROD2	20	14665585	Missense_Mutation	SNP	G	TCGA-FF-8046-01A-11D-2210-10		14665585	48359935	81	1770											
MACROD2	140733	hgsc.bcm.edu	37	chr20	16021849	16021849	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctttttctcttccagctcCaggcgaggacacacctagga	8	11	9	13	1	2	0	0	0	2	0	5	3	4	2	3	3	1	1	3	3	1	4			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr20:16021849C>T	ENST00000310348.4	+	16	1157	c.1157C>T	c.(1156-1158)cCa>cTa	p.P386L	MACROD2_ENST00000402914.1_Missense_Mutation_p.P151L|MACROD2_ENST00000407045.3_Missense_Mutation_p.P37L|MACROD2_ENST00000378058.3_Missense_Mutation_p.P151L|MACROD2_ENST00000217246.4_Missense_Mutation_p.P386L			A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2	386	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)				CTTCCAGCTCCAGGCGAGGAC	0.478																																					p.P386L		Atlas-SNP	.											.	MACROD2	34	.	0			c.C1157T						PASS	.						69	68	69					20																	16021849		2203	4299	6502	SO:0001583	missense	140733	exon16			CAGCTCCAGGCGA	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.1157C>T	20.37:g.16021849C>T	ENSP00000309809:p.Pro386Leu	77	0	0		93	4	0.0430108	NM_080676	A6NFF7|B0QZ39|B3KWV0|Q0P6D5|Q495E0|Q5W199|Q6ZN71	Missense_Mutation	SNP	ENST00000310348.4	37	CCDS13120.2	.	.	.	.	.	.	.	.	.	.	C	0.003	-2.409786	0.00193	.	.	ENSG00000172264	ENST00000217246;ENST00000310348;ENST00000402914;ENST00000378058;ENST00000407045	T;T;T;T	0.43688	2.54;2.55;0.94;0.94	5.37	-1.96	0.07525	.	0.458260	0.18726	N	0.132894	T	0.13670	0.0331	N	0.02011	-0.69	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.0;0.001	T	0.20338	-1.0278	10	0.30854	T	0.27	-3.5581	6.857	0.24046	0.3256:0.4397:0.0:0.2348	.	37;386;386	A1Z1Q3-6;A1Z1Q3;A1Z1Q3-2	.;MACD2_HUMAN;.	L	386;386;151;151;37	ENSP00000217246:P386L;ENSP00000309809:P386L;ENSP00000385290:P151L;ENSP00000367297:P151L	ENSP00000217246:P386L	P	+	2	0	MACROD2	15969849	0.197000	0.23362	0.044000	0.18714	0.188000	0.23474	-0.121000	0.10643	-0.211000	0.10124	-1.268000	0.01426	CCA	.	.	none		0.478	MACROD2-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_080676		T	16021849	C	T	16021849	3	4	13	1	0	0	0	0	1	0	0	0	9155	594	21	2	1219	2	MACROD2	20	16021849	Missense_Mutation	SNP	C	TCGA-FF-8046-01A-11D-2210-10	1356264	16021849	47003671	82	1771											
LPIN3	64900	hgsc.bcm.edu	37	chr20	39977298	39977299	+	Frame_Shift_Ins	INS	-	-	G																															gtgcacctcacccatcccttINSgggggggtctgtctggcttc																								rs546459459		TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr20:39977298_39977299insG	ENST00000373257.3	+	4	419_420	c.328_329insG	c.(328-330)tggfs	p.W110fs		NM_022896.1	NP_075047.1	Q9BQK8	LPIN3_HUMAN	lipin 3	110					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)				ACCCATCCCTTGGGGGGGTCTG	0.663																																					p.W110fs		Pindel,Atlas-Indel	.											.	LPIN3	69	.	0			c.328_329insG						PASS	.																																			SO:0001589	frameshift_variant	64900	exon4			.	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.335dupG	20.37:g.39977305_39977305dupG	ENSP00000362354:p.Trp110fs	40	0	.		56	12	0.214	NM_022896	B2RTT5|Q5TDB9|Q9NPY8|Q9UJE5	Frame_Shift_Ins	INS	ENST00000373257.3	37	CCDS33469.1																																																																																			.	.	none		0.663	LPIN3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080393.1	NM_022896		G	39977299	-	G	39977298	7	5	13	1	0	1	1	0	0	0	0	0	8929	1812	63	0	338	0	LPIN3	20	39977298	Frame_Shift_Ins	INS	-	TCGA-FF-8046-01A-11D-2210-10	23955449	39977298	23048222	83	1772											
TPTE	7179	hgsc.bcm.edu	37	chr21	10971306	10971306	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	actcacctgtcattggggccGagctcaatgatgactcccgc	8	9	10	14	2	3	2	3	2	0	0	4	3	4	2	3	2	1	1	3	2	1	1			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr21:10971306G>A	ENST00000361285.4	-	5	380	c.51C>T	c.(49-51)ctC>ctT	p.L17L	TPTE_ENST00000342420.5_Silent_p.L17L|TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000298232.7_Silent_p.L17L	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	17					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)		CATTGGGGCCGAGCTCAATGA	0.468																																					p.L17L		Atlas-SNP	.											.	TPTE	513	.	0			c.C51T						PASS	.						130	100	110					21																	10971306		2203	4300	6503	SO:0001819	synonymous_variant	7179	exon5			GGGGCCGAGCTCA	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.51C>T	21.37:g.10971306G>A		105	0	0		124	15	0.120968	NM_199259	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Silent	SNP	ENST00000361285.4	37	CCDS13560.2																																																																																			.	.	none		0.468	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1			A	10971306	G	A	10971306	2	1	13	1	0	0	0	0	0	0	0	1	16445	1045	37	1		1	TPTE	21	10971306	Silent	SNP	G	TCGA-FF-8046-01A-11D-2210-10		10971306	37158589	84	1773											
KRTAP26-1	388818	hgsc.bcm.edu	37	chr21	31692282	31692282	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcagaggtcgatggaggtGagaggaatatggcgggaggt	10	6	22	3	2	0	2	0	1	0	2	1	7	0	5	0	8	0	1	0	8	2	1			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr21:31692282G>T	ENST00000360542.3	-	1	325	c.72C>A	c.(70-72)ctC>ctA	p.L24L		NM_203405.1	NP_981950.1	Q6PEX3	KR261_HUMAN	keratin associated protein 26-1	24						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						CGATGGAGGTGAGAGGAATAT	0.537																																					p.L24L		Atlas-SNP	.											KRTAP26-1,NS,carcinoma,0,1	KRTAP26-1	58	1	0			c.C72A						PASS	.						61	64	63					21																	31692282		2203	4300	6503	SO:0001819	synonymous_variant	388818	exon1			GGAGGTGAGAGGA	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.72C>A	21.37:g.31692282G>T		165	0	0		157	57	0.363057	NM_203405	B0RZD3	Silent	SNP	ENST00000360542.3	37	CCDS13588.1																																																																																			.	.	none		0.537	KRTAP26-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128218.1	NM_203405		T	31692282	G	T	31692282	2	4	13	1	0	0	0	0	0	0	0	1	8552	1277	45	4		4	KRTAP26-1	21	31692282	Silent	SNP	G	TCGA-FF-8046-01A-11D-2210-10	20720976	31692282	16437613	85	1774											
SEPT5	5413	hgsc.bcm.edu	37	chr22	19709201	19709201	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gttataggcagcaacacggtGgtggaggccaaggggcagcg	10	5	18	8	2	0	0	0	0	0	0	0	1	0	1	1	7	3	4	1	7	4	2			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr22:19709201G>T	ENST00000455784.2	+	9	881	c.756G>T	c.(754-756)gtG>gtT	p.V252V	SEPT5_ENST00000383045.3_Silent_p.V261V|GP1BB_ENST00000366425.3_5'Flank|SEPT5_ENST00000438754.2_Silent_p.V261V|SEPT5_ENST00000406395.1_Silent_p.V252V	NM_002688.5	NP_002679.2	Q99719	SEPT5_HUMAN	septin 5	252	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)					GCAACACGGTGGTGGAGGCCA	0.642																																					p.V261V		Atlas-SNP	.											.	SEPT5	32	.	0			c.G783T						PASS	.						38	48	44					22																	19709201		2203	4299	6502	SO:0001819	synonymous_variant	5413	exon8			CACGGTGGTGGAG	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.756G>T	22.37:g.19709201G>T		104	0	0		108	5	0.0462963	NM_001009939	O15251|Q96MY5	Silent	SNP	ENST00000455784.2	37	CCDS13764.1																																																																																			.	.	none		0.642	SEPT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317937.1	NM_002688		T	19709201	G	T	19709201	2	4	13	1	0	0	0	0	0	0	0	1	14082	1335	47	4		4	SEPT5	22	19709201	Silent	SNP	G	TCGA-FF-8046-01A-11D-2210-10		19709201	31595365	86	1775											
SEC14L3	266629	hgsc.bcm.edu	37	chr22	30867895	30867895	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggggaggggctctcaccttGgccagggtctctgcctgttt	3	11	16	11	0	2	0	1	0	2	0	4	1	2	1	3	6	1	2	3	6	0	2			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr22:30867895G>C	ENST00000215812.4	-	1	141	c.51C>G	c.(49-51)gcC>gcG	p.A17A	SEC14L3_ENST00000540910.1_5'Flank|SEC14L3_ENST00000402286.1_5'UTR|SEC14L3_ENST00000401751.1_5'UTR|SEC14L3_ENST00000415957.2_5'Flank|SEC14L3_ENST00000539629.1_5'UTR|SEC14L3_ENST00000403066.1_5'UTR	NM_174975.4	NP_777635.1	Q9UDX4	S14L3_HUMAN	SEC14-like 3 (S. cerevisiae)	17						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)	CTCTCACCTTGGCCAGGGTCT	0.622																																					p.A17A	Esophageal Squamous(108;290 1516 3584 23771 37333)	Atlas-SNP	.											.	SEC14L3	46	.	0			c.C51G						PASS	.						63	65	64					22																	30867895		2203	4300	6503	SO:0001819	synonymous_variant	266629	exon1			CACCTTGGCCAGG	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.51C>G	22.37:g.30867895G>C		43	0	0		44	12	0.272727	NM_174975	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Silent	SNP	ENST00000215812.4	37	CCDS13877.1																																																																																			.	.	none		0.622	SEC14L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321950.4	NM_174975		C	30867895	G	C	30867895	2	2	13	1	0	0	0	0	0	0	0	1	13998	1335	47	4		4	SEC14L3	22	30867895	Silent	SNP	G	TCGA-FF-8046-01A-11D-2210-10	11158694	30867895	20436671	87	1776											
SMC1B	27127	hgsc.bcm.edu	37	chr22	45802439	45802439	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcggctttttgtaactttcTtttcttttcttcatattctc	4	25	3	9	1	5	0	1	0	4	0	7	0	5	0	0	1	1	2	0	1	2	12			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chr22:45802439T>G	ENST00000357450.4	-	4	516	c.517A>C	c.(517-519)Aga>Cga	p.R173R	SMC1B_ENST00000404354.3_Silent_p.R173R	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	173					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)		TGTAACTTTCTTTTCTTTTCT	0.368																																					p.R173R		Atlas-SNP	.											.	SMC1B	215	.	0			c.A517C						PASS	.						85	77	80					22																	45802439		1809	4072	5881	SO:0001819	synonymous_variant	27127	exon4			ACTTTCTTTTCTT	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.517A>C	22.37:g.45802439T>G		66	0	0		70	28	0.4	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Silent	SNP	ENST00000357450.4	37	CCDS43027.1																																																																																			.	.	none		0.368	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674		G	45802439	T	G	45802439	2	3	13	1	0	0	0	0	0	0	0	1	14797	1617	56	5		5	SMC1B	22	45802439	Silent	SNP	T	TCGA-FF-8046-01A-11D-2210-10	14934544	45802439	5502127	88	1777											
DDX3X	1654	hgsc.bcm.edu	37	chrX	41204802	41204802	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgacctcctaaatgcaacagGtaacattatgaattttttat	14	15	5	7	0	0	2	0	2	0	0	1	2	1	2	2	1	3	2	2	1	7	6			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chrX:41204802G>T	ENST00000399959.2	+	12	2170		c.e12+1		DDX3X_ENST00000457138.2_Splice_Site|DDX3X_ENST00000441189.2_Intron|DDX3X_ENST00000542215.1_Splice_Site|RN7SL15P_ENST00000582825.1_RNA|DDX3X_ENST00000478993.1_Splice_Site	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						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						AATGCAACAGGTAACATTATG	0.418										HNSCC(61;0.18)																											.		Atlas-SNP	.											.	DDX3X	138	.	0			c.1267+1G>T						PASS	.						77	70	72					X																	41204802		1990	4159	6149	SO:0001630	splice_region_variant	1654	exon11			CAACAGGTAACAT	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.1315+1G>T	X.37:g.41204802G>T		80	0	0		129	68	0.527132	NM_001193417	A8K538|B4E3E8|O15536	Splice_Site	SNP	ENST00000399959.2	37	CCDS43931.1	.	.	.	.	.	.	.	.	.	.	g	19.49	3.837914	0.71373	.	.	ENSG00000215301	ENST00000399959;ENST00000457138	.	.	.	5.23	5.23	0.72850	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.0725	0.89415	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DDX3X	41089746	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	9.737000	0.98831	2.203000	0.70933	0.522000	0.50473	.	.	.	none		0.418	DDX3X-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056253.1	NM_024005	Intron	T	41204802	G	T	41204802	5	4	13	1	0	0	0	0	0	0	1	0	4360	1275	44	4	1362	4	DDX3X	23	41204802	Splice_Site	SNP	G	TCGA-FF-8046-01A-11D-2210-10		41204802	114065758	89	1778											
AR	367	hgsc.bcm.edu	37	chrX	66765158	66765159	+	In_Frame_Ins	INS	-	-	GCTGCA																															ggcgccagtttgctgctgctINSgcagcagcagcagcagcagc																								rs78686797|rs3032358|rs4045402		TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chrX:66765158_66765159insGCTGCA	ENST00000374690.3	+	1	694_695	c.170_171insGCTGCA	c.(169-174)ctgcag>ctGCTGCAgcag	p.57_58LQ>LLQQ	AR_ENST00000504326.1_In_Frame_Ins_p.57_58LQ>LLQQ|AR_ENST00000396044.3_In_Frame_Ins_p.57_58LQ>LLQQ|AR_ENST00000513847.1_3'UTR	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	57	Gln-rich.|Modulating.|Poly-Gln.|Poly-Leu.		L -> Q (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)	p.L57Q(3)		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)	TTGCTGCTGCTgcagcagcagc	0.668									Androgen Insensitivity Syndrome																												p.L57delinsLLQ		Atlas-Indel	.											.	AR	249	.	3	Substitution - Missense(3)	lung(1)|endometrium(1)|central_nervous_system(1)	c.170_171insGCTGCA						PASS	.																																			SO:0001652	inframe_insertion	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	Exception_encountered	X.37:g.66765158_66765159insGCTGCA	ENSP00000363822:p.Leu57_Gln58insLeuGln	32	0	0		20	14	0.7	NM_000044	A2RUN2|B1AKD7|Q9UD95	In_Frame_Ins	INS	ENST00000374690.3	37	CCDS14387.1																																																																																			.	.	alt		0.668	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		GCTGCA	66765159	-	GCTGCA	66765158	7	5	13	1	0	1	1	0	0	0	0	0	836	1580	55	0	172	0	AR	23	66765158	In_Frame_Ins	INS	-	TCGA-FF-8046-01A-11D-2210-10	25560356	66765158	88505402	90	1779											
NAP1L3	4675	hgsc.bcm.edu	37	chrX	92928071	92928071	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggaaggctcaggtaccctcTtctttctatacaagcggctg	8	12	10	11	1	4	0	1	0	3	0	4	1	4	1	1	4	3	3	1	4	5	5			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chrX:92928071T>G	ENST00000373079.3	-	1	496	c.233A>C	c.(232-234)aAg>aCg	p.K78T	FAM133A_ENST00000538690.1_5'Flank|FAM133A_ENST00000355813.5_5'Flank|FAM133A_ENST00000322139.4_5'Flank|NAP1L3_ENST00000475430.2_Missense_Mutation_p.K71T|FAM133A_ENST00000332647.4_5'Flank	NM_004538.5	NP_004529.2	Q99457	NP1L3_HUMAN	nucleosome assembly protein 1-like 3	78					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						AGGTACCCTCTTCTTTCTATA	0.612																																					p.K78T		Atlas-SNP	.											.	NAP1L3	81	.	0			c.A233C						PASS	.						16	17	16					X																	92928071		2201	4286	6487	SO:0001583	missense	4675	exon1			ACCCTCTTCTTTC		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.233A>C	X.37:g.92928071T>G	ENSP00000362171:p.Lys78Thr	33	0	0		40	10	0.25	NM_004538	B2RCM0|O60788	Missense_Mutation	SNP	ENST00000373079.3	37	CCDS14465.1	.	.	.	.	.	.	.	.	.	.	T	5.105	0.204991	0.09704	.	.	ENSG00000186310	ENST00000373079;ENST00000543136	T	0.32988	1.43	3.53	-3.32	0.04973	.	0.287732	0.37348	N	0.002124	T	0.12902	0.0313	N	0.24115	0.695	0.28377	N	0.919728	P	0.34522	0.455	B	0.33568	0.166	T	0.33904	-0.9850	10	0.15066	T	0.55	.	4.8148	0.13362	0.153:0.4055:0.0:0.4415	.	78	Q99457	NP1L3_HUMAN	T	78;71	ENSP00000362171:K78T	ENSP00000362171:K78T	K	-	2	0	NAP1L3	92814727	0.157000	0.22836	0.689000	0.30133	0.173000	0.22820	-0.320000	0.08028	-0.886000	0.03966	-0.509000	0.04479	AAG	.	.	none		0.612	NAP1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057449.1	NM_004538		G	92928071	T	G	92928071	3	3	13	1	0	0	0	0	1	0	0	0	10167	1609	56	5	1291	5	NAP1L3	23	92928071	Missense_Mutation	SNP	T	TCGA-FF-8046-01A-11D-2210-10	26162913	92928071	62342489	91	1780											
GPR101	83550	hgsc.bcm.edu	37	chrX	136112327	136112327	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcaaggaaaagtagcagaatCgtaggaagggacaatcttgc	16	7	12	6	1	2	1	1	0	1	1	3	4	2	4	0	3	2	3	0	3	8	3			TCGA-FF-8046-01A-11D-2210-10	TCGA-FF-8046-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	aa847c3d-d3a7-46aa-a81b-db5099a458fb	35736b32-0a2a-45c0-aef9-5e7f3d2733aa	g.chrX:136112327C>T	ENST00000298110.1	-	1	1506	c.1507G>A	c.(1507-1509)Gat>Aat	p.D503N		NM_054021.1	NP_473362.1	Q96P66	GP101_HUMAN	G protein-coupled receptor 101	503						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)					GTAGCAGAATCGTAGGAAGGG	0.463																																					p.D503N		Atlas-SNP	.											.	GPR101	96	.	0			c.G1507A						PASS	.						82	76	78					X																	136112327		2203	4300	6503	SO:0001583	missense	83550	exon1			CAGAATCGTAGGA	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.1507G>A	X.37:g.136112327C>T	ENSP00000298110:p.Asp503Asn	48	0	0		48	33	0.6875	NM_054021	Q5JSM8|Q8NG93	Missense_Mutation	SNP	ENST00000298110.1	37	CCDS14662.1	.	.	.	.	.	.	.	.	.	.	C	2.727	-0.265337	0.05754	.	.	ENSG00000165370	ENST00000298110	T	0.64618	-0.11	5.32	0.906	0.19314	.	.	.	.	.	T	0.38772	0.1053	N	0.14661	0.345	0.09310	N	1	B	0.14012	0.009	B	0.06405	0.002	T	0.21759	-1.0236	9	0.45353	T	0.12	-6.3616	3.4501	0.07495	0.2836:0.4116:0.0:0.3048	.	503	Q96P66	GP101_HUMAN	N	503	ENSP00000298110:D503N	ENSP00000298110:D503N	D	-	1	0	GPR101	135939993	0.319000	0.24607	0.010000	0.14722	0.254000	0.26022	0.603000	0.24149	0.194000	0.20326	-0.511000	0.04467	GAT	.	.	none		0.463	GPR101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058519.1			T	136112327	C	T	136112327	3	4	13	1	0	0	0	0	1	0	0	0	6630	884	31	1	22	1	GPR101	23	136112327	Missense_Mutation	SNP	C	TCGA-FF-8046-01A-11D-2210-10	43184256	136112327	19158233	92	1781											
TAS1R2	80834	hgsc.bcm.edu	37	chr1	19175988	19175988	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gccacgtccccttgcgggtcGaagaagatttggtggtccag	7	9	14	11	3	0	2	0	0	0	2	3	3	2	2	4	3	1	0	4	3	2	2	rs146531311	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:19175988G>A	ENST00000375371.3	-	4	1335	c.1314C>T	c.(1312-1314)ttC>ttT	p.F438F	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	438					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)	CTTGCGGGTCGAAGAAGATTT	0.582																																					p.F438F		Atlas-SNP	.											TAS1R2,NS,carcinoma,0,1	TAS1R2	134	1	0			c.C1314T						PASS	.	A		0,4406		0,0,2203	75	68	70		1314	-5.2	0	1	dbSNP_134	70	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TAS1R2	NM_152232.2		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		438/840	19175988	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	80834	exon4			CGGGTCGAAGAAG		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.1314C>T	1.37:g.19175988G>A		113	0	0		125	54	0.432	NM_152232	Q5TZ19	Silent	SNP	ENST00000375371.3	37	CCDS187.1																																																																																			G|1.000;A|0.000	0.000	strong		0.582	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1			A	19175988	G	A	19175988	2	1	14	1	0	0	0	0	0	0	0	1	15578	1049	37	1		1	TAS1R2	1	19175988	Silent	SNP	G	TCGA-FF-8047-01A-11D-2210-10		19175988	230074633	1	1782											
EPHB2	2048	hgsc.bcm.edu	37	chr1	23236932	23236932	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcccatggactgcccgagcGccctgcaccaactcatgctg	7	6	10	18	3	1	0	1	0	0	0	1	2	1	1	4	1	5	2	4	1	1	0	rs549199396		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:23236932G>A	ENST00000400191.3	+	14	2578	c.2560G>A	c.(2560-2562)Gcc>Acc	p.A854T	EPHB2_ENST00000374632.3_Missense_Mutation_p.A855T|EPHB2_ENST00000374630.3_Missense_Mutation_p.A854T|EPHB2_ENST00000374627.1_Missense_Mutation_p.A849T	NM_004442.6|NM_017449.3	NP_004433.2|NP_059145.2	P29323	EPHB2_HUMAN	EPH receptor B2	854	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)	p.A854T(1)		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)		CTGCCCGAGCGCCCTGCACCA	0.587																																					p.A855T		Atlas-SNP	.											EPHB2,colon,carcinoma,0,1	EPHB2	257	1	1	Substitution - Missense(1)	large_intestine(1)	c.G2563A						PASS	.						122	89	100					1																	23236932		2203	4300	6503	SO:0001583	missense	2048	exon14			CCGAGCGCCCTGC	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.2560G>A	1.37:g.23236932G>A	ENSP00000383053:p.Ala854Thr	138	0	0		78	59	0.75641	NM_004442	O43477|Q5T0U6|Q5T0U7|Q5T0U8	Missense_Mutation	SNP	ENST00000400191.3	37		.	.	.	.	.	.	.	.	.	.	G	20.9	4.070225	0.76301	.	.	ENSG00000133216	ENST00000374625;ENST00000374630;ENST00000400191;ENST00000374632;ENST00000374627	D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63	4.64	4.64	0.57946	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	T	0.73908	0.3647	L	0.28556	0.865	0.80722	D	1	B;B;B;B	0.32203	0.043;0.36;0.066;0.017	B;B;B;B	0.23150	0.006;0.044;0.018;0.019	T	0.76506	-0.2934	10	0.66056	D	0.02	.	16.6405	0.85070	0.0:0.0:1.0:0.0	.	796;854;872;855	A6NJM0;P29323;Q4LE53;P29323-3	.;EPHB2_HUMAN;.;.	T	796;854;854;855;849	ENSP00000363761:A854T;ENSP00000383053:A854T;ENSP00000363763:A855T;ENSP00000363758:A849T	ENSP00000363755:A796T	A	+	1	0	EPHB2	23109519	1.000000	0.71417	0.995000	0.50966	0.981000	0.71138	7.803000	0.85983	2.586000	0.87340	0.555000	0.69702	GCC	.	.	none		0.587	EPHB2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000008060.2	NM_017449		A	23236932	G	A	23236932	3	1	14	1	0	0	0	0	1	0	0	0	5177	1087	38	1	2617	1	EPHB2	1	23236932	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	4060944	23236932	226013689	2	1783											
MAGI3	260425	hgsc.bcm.edu	37	chr1	114191926	114191926	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggtttggcttcagggtgctAggaggagatggacctgacca	8	9	17	7	0	1	2	1	1	0	1	1	5	1	4	2	6	1	3	2	6	1	3			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:114191926A>G	ENST00000307546.9	+	13	2298	c.2223A>G	c.(2221-2223)ctA>ctG	p.L741L	MAGI3_ENST00000369611.4_Silent_p.L741L|MAGI3_ENST00000369617.4_Silent_p.L766L|MAGI3_ENST00000369615.1_Silent_p.L741L	NM_001142782.1	NP_001136254.1	Q5TCQ9	MAGI3_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 3	766					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)		TCAGGGTGCTAGGAGGAGATG	0.413																																					p.L741L		Atlas-SNP	.											.	MAGI3	181	.	0			c.A2223G						PASS	.						127	126	126					1																	114191926		2203	4300	6503	SO:0001819	synonymous_variant	260425	exon13			GGTGCTAGGAGGA	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.2223A>G	1.37:g.114191926A>G		42	0	0		85	4	0.0470588	NM_152900	Q5TCQ8|Q5TCR0|Q9H2V6|Q9H5Y8|Q9HBC4|Q9HCD8	Silent	SNP	ENST00000307546.9	37	CCDS44196.1																																																																																			.	.	none		0.413	MAGI3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000032429.1	NM_152900		G	114191926	A	G	114191926	2	3	14	1	0	0	0	0	0	0	0	1	9201	407	15	3		3	MAGI3	1	114191926	Silent	SNP	A	TCGA-FF-8047-01A-11D-2210-10	90954994	114191926	135058695	3	1784											
SPAG17	200162	hgsc.bcm.edu	37	chr1	118567949	118567949	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctctgcgggtggcatcaccGttttatagaactcatagtgc	8	12	11	10	2	3	1	2	0	1	1	3	1	3	1	1	2	3	3	1	2	4	4			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:118567949G>A	ENST00000336338.5	-	27	3886	c.3821C>T	c.(3820-3822)aCg>aTg	p.T1274M		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1274						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)		TGGCATCACCGTTTTATAGAA	0.463																																					p.T1274M		Atlas-SNP	.											.	SPAG17	263	.	0			c.C3821T						PASS	.						96	93	94					1																	118567949		2203	4300	6503	SO:0001583	missense	200162	exon27			ATCACCGTTTTAT		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.3821C>T	1.37:g.118567949G>A	ENSP00000337804:p.Thr1274Met	56	0	0		90	44	0.488889	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	.	.	.	.	.	.	.	.	.	.	G	15.63	2.889137	0.52014	.	.	ENSG00000155761	ENST00000336338	T	0.19532	2.14	5.58	4.67	0.58626	.	0.573492	0.19744	N	0.107042	T	0.20700	0.0498	L	0.51422	1.61	0.09310	N	1	D	0.71674	0.998	P	0.58130	0.833	T	0.04178	-1.0971	10	0.59425	D	0.04	.	12.3516	0.55151	0.0788:0.0:0.9212:0.0	.	1274	Q6Q759	SPG17_HUMAN	M	1274	ENSP00000337804:T1274M	ENSP00000337804:T1274M	T	-	2	0	SPAG17	118369472	0.008000	0.16893	0.013000	0.15412	0.441000	0.31987	1.697000	0.37784	1.350000	0.45770	0.655000	0.94253	ACG	.	.	none		0.463	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		A	118567949	G	A	118567949	3	1	14	1	0	0	0	0	1	0	0	0	14994	1145	40	1	2938	1	SPAG17	1	118567949	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	4376023	118567949	130682672	4	1785											
NBPF10	100132406	hgsc.bcm.edu	37	chr1	145293535	145293535	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	acctcaaagagaaatgttttCtaactcaactggccggcttc	12	11	7	11	1	3	1	2	0	1	1	4	2	3	1	2	2	2	2	2	2	4	4	rs55936365		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:145293535C>G	ENST00000369339.3	+	3	383	c.130C>G	c.(130-132)Cta>Gta	p.L44V	NBPF10_ENST00000369338.1_Intron|RP11-458D21.5_ENST00000468030.1_3'UTR|NBPF10_ENST00000342960.5_Missense_Mutation_p.L44V			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	315						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.L44V(2)		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)		GAAATGTTTTCTAACTCAACT	0.443																																					p.L44V		Atlas-SNP	.											NBPF10,NS,carcinoma,0,2	NBPF10	221	2	2	Substitution - Missense(2)	kidney(2)	c.C130G						scavenged	.																																			SO:0001583	missense	100132406	exon1			TGTTTTCTAACTC	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.130C>G	1.37:g.145293535C>G	ENSP00000358345:p.Leu44Val	98	1	0.0102041		142	7	0.0492958	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000369339.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.027|0.027	-1.360141|-1.360141	0.01245|0.01245	.|.	.|.	ENSG00000163386|ENSG00000163386	ENST00000369339;ENST00000342960|ENST00000448873	T|.	0.02837|.	4.14|.	0.687|0.687	-1.37|-1.37	0.09056|0.09056	.|.	.|.	.|.	.|.	.|.	T|T	0.01765|0.01765	0.0056|0.0056	N|N	0.01122|0.01122	-1.005|-1.005	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.33007|0.33007	-0.9885|-0.9885	9|6	0.02654|0.33141	T|T	1|0.24	.|.	3.2142|3.2142	0.06692|0.06692	0.3787:0.2355:0.3858:0.0|0.3787:0.2355:0.3858:0.0	rs55936365|rs55936365	44|.	A8MQ30|.	.|.	V|C	44|3	ENSP00000345684:L44V|.	ENSP00000345684:L44V|ENSP00000414194:S3C	L|S	+|+	1|2	2|0	NBPF10|NBPF10	144004892|144004892	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-3.451000|-3.451000	0.00466|0.00466	-3.626000|-3.626000	0.00130|0.00130	-3.729000|-3.729000	0.00022|0.00022	CTA|TCT	.	.	weak		0.443	NBPF10-001	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038550.3	NM_001039703		G	145293535	C	G	145293535	3	3	14	1	0	0	0	0	1	0	0	0	10202	912	32	4	132	4	NBPF10	1	145293535	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	26725586	145293535	103957086	5	1786											
S100A6	6277	hgsc.bcm.edu	37	chr1	153507187	153507187	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tattttcagcccttgagggcTtcattgtagatcaaagccaa	11	13	8	9	0	3	2	3	1	0	1	3	2	3	2	2	1	2	2	2	1	4	7			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:153507187T>C	ENST00000368720.2	-	4	560	c.258A>G	c.(256-258)gaA>gaG	p.E86E	S100A6_ENST00000496817.1_Silent_p.E86E|S100A6_ENST00000368719.4_Silent_p.E86E|BX470102.3_ENST00000420695.1_RNA			P06703	S10A6_HUMAN	S100 calcium binding protein A6	86					axonogenesis (GO:0007409)|positive regulation of fibroblast proliferation (GO:0048146)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|ion transmembrane transporter activity (GO:0015075)|protein homodimerization activity (GO:0042803)|S100 protein binding (GO:0044548)|tropomyosin binding (GO:0005523)|zinc ion binding (GO:0008270)			ovary(1)	1	all_lung(78;1.66e-32)|Lung NSC(65;5.71e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCTTGAGGGCTTCATTGTAGA	0.478																																					p.E86E		Atlas-SNP	.											.	S100A6	8	.	0			c.A258G						PASS	.						69	69	69					1																	153507187		2203	4300	6503	SO:0001819	synonymous_variant	6277	exon3			GAGGGCTTCATTG	BC001431	CCDS1040.1	1q21	2013-01-10	2006-09-11		ENSG00000197956	ENSG00000197956		"S100 calcium binding proteins", "EF-hand domain containing"	10496	protein-coding gene	gene with protein product		114110	"S100 calcium-binding protein A6 (calcyclin)", "S100 calcium binding protein A6 (calcyclin)"	CACY			Standard	NM_014624		Approved	2A9, PRA, CABP	uc001fbw.1	P06703	OTTHUMG00000013549	ENST00000368720.2:c.258A>G	1.37:g.153507187T>C		89	0	0		93	4	0.0430108	NM_014624	D3DV39|Q5RHS4	Silent	SNP	ENST00000368720.2	37	CCDS1040.1																																																																																			.	.	none		0.478	S100A6-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037723.2	NM_014624		C	153507187	T	C	153507187	2	2	14	1	0	0	0	0	0	0	0	1	13797	1606	56	3		3	S100A6	1	153507187	Silent	SNP	T	TCGA-FF-8047-01A-11D-2210-10	8213652	153507187	95743434	6	1787											
C2orf53	339779	hgsc.bcm.edu	37	chr2	27360666	27360666	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgtccctgtactgatgccAgcgccatgtctgcctgttag	6	12	11	12	1	1	1	0	1	1	0	2	1	2	1	4	0	4	2	4	0	2	2			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:27360666A>G	ENST00000335524.3	-	3	1057	c.532T>C	c.(532-534)Tgg>Cgg	p.W178R		NM_178553.3	NP_848648.2	Q53SZ7	PRR30_HUMAN		178										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)					TACTGATGCCAGCGCCATGTC	0.627																																					p.W178R		Atlas-SNP	.											.	C2orf53	45	.	0			c.T532C						PASS	.						53	55	54					2																	27360666		2203	4300	6503	SO:0001583	missense	339779	exon3			GATGCCAGCGCCA																												ENST00000335524.3:c.532T>C	2.37:g.27360666A>G	ENSP00000335017:p.Trp178Arg	72	0	0		96	7	0.0729167	NM_178553	Q86UE2	Missense_Mutation	SNP	ENST00000335524.3	37	CCDS1739.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.32|12.32	1.901753|1.901753	0.33535|0.33535	.|.	.|.	ENSG00000186143|ENSG00000186143	ENST00000432962|ENST00000335524	.|T	.|0.34072	.|1.38	4.56|4.56	0.778|0.778	0.18543|0.18543	.|.	.|0.231694	.|0.22575	.|N	.|0.058287	T|T	0.20700|0.20700	0.0498|0.0498	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	1|1	.|B	.|0.24368	.|0.102	.|B	.|0.23852	.|0.049	T|T	0.13548|0.13548	-1.0505|-1.0505	6|10	0.87932|0.59425	D|D	0|0.04	-2.4502|-2.4502	2.6344|2.6344	0.04954|0.04954	0.5896:0.0:0.2152:0.1952|0.5896:0.0:0.2152:0.1952	.|.	.|178	.|Q53SZ7	.|CB053_HUMAN	P|R	13|178	.|ENSP00000335017:W178R	ENSP00000393468:L13P|ENSP00000335017:W178R	L|W	-|-	2|1	0|0	C2orf53|C2orf53	27214170|27214170	0.075000|0.075000	0.21258|0.21258	0.008000|0.008000	0.14137|0.14137	0.183000|0.183000	0.23260|0.23260	1.140000|1.140000	0.31516|0.31516	0.773000|0.773000	0.33404|0.33404	0.459000|0.459000	0.35465|0.35465	CTG|TGG	.	.	none		0.627	C2orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250188.1			G	27360666	A	G	27360666	3	3	14	1	0	0	0	0	1	0	0	0	2176	188	7	3	710	3	C2orf53	2	27360666	Missense_Mutation	SNP	A	TCGA-FF-8047-01A-11D-2210-10		27360666	215838707	7	1788											
VIT	5212	hgsc.bcm.edu	37	chr2	36970315	36970315	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gttcattgtgaaatgtccagCaggatgccaagaccccaaat	13	9	9	10	0	1	2	1	1	0	1	2	3	2	3	4	1	2	2	4	1	3	2			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:36970315C>A	ENST00000389975.3	+	4	493	c.191C>A	c.(190-192)gCa>gAa	p.A64E	VIT_ENST00000379241.3_Missense_Mutation_p.A64E|VIT_ENST00000379242.3_Missense_Mutation_p.A64E|VIT_ENST00000401530.1_Missense_Mutation_p.A64E|VIT_ENST00000457137.2_Missense_Mutation_p.A64E|VIT_ENST00000497382.1_5'UTR|VIT_ENST00000404084.1_Missense_Mutation_p.A42E	NM_001177969.1|NM_001177970.1	NP_001171440.1|NP_001171441.1	Q6UXI7	VITRN_HUMAN	vitrin	64	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)				AAATGTCCAGCAGGATGCCAA	0.483																																					p.A64E		Atlas-SNP	.											.	VIT	138	.	0			c.C191A						PASS	.						173	142	152					2																	36970315		2203	4300	6503	SO:0001583	missense	5212	exon4			GTCCAGCAGGATG	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.191C>A	2.37:g.36970315C>A	ENSP00000374625:p.Ala64Glu	109	0	0		101	48	0.475248	NM_001177969	A1A526|A6NKI9|A8K7Y4|E9PF47|Q6P7T3|Q96DM8|Q96DT1|Q9UDN0	Missense_Mutation	SNP	ENST00000389975.3	37	CCDS54347.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.721566	0.89298	.	.	ENSG00000205221	ENST00000379242;ENST00000389975;ENST00000402257;ENST00000457137;ENST00000404084;ENST00000379241;ENST00000401530	D;D;D;D;D;D	0.89681	-2.55;-2.55;-2.55;-2.55;-2.55;-2.55	4.77	4.77	0.60923	LCCL (5);	0.124941	0.52532	D	0.000062	D	0.93598	0.7956	M	0.75777	2.31	0.47584	D	0.999461	D;D;D;D;D;D	0.71674	0.998;0.998;0.994;0.996;0.995;0.997	D;P;P;D;P;P	0.65773	0.932;0.903;0.897;0.938;0.888;0.888	D	0.94337	0.7567	10	0.72032	D	0.01	-8.2082	16.3687	0.83346	0.0:1.0:0.0:0.0	.	64;64;64;64;64;64	B4DRU4;E9PF47;Q6UXI7-2;Q6UXI7;Q6UXI7-4;Q6UXI7-3	.;.;.;VITRN_HUMAN;.;.	E	64;64;64;64;42;64;64	ENSP00000368544:A64E;ENSP00000374625:A64E;ENSP00000393561:A64E;ENSP00000384154:A42E;ENSP00000368543:A64E;ENSP00000385658:A64E	ENSP00000368543:A64E	A	+	2	0	VIT	36823819	1.000000	0.71417	0.995000	0.50966	0.912000	0.54170	5.496000	0.66918	2.358000	0.79984	0.650000	0.86243	GCA	.	.	none		0.483	VIT-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding				A	36970315	C	A	36970315	3	1	14	1	0	0	0	0	1	0	0	0	17186	710	25	4	201	4	VIT	2	36970315	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	9609649	36970315	206229058	8	1789											
CNNM3	26505	hgsc.bcm.edu	37	chr2	97483238	97483238	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcctggaggaattcaagcgAggtaacggcccgggcatggt	9	7	16	9	3	1	0	1	0	0	0	2	3	2	2	2	6	2	2	2	6	3	2			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:97483238A>G	ENST00000305510.3	+	1	1252	c.1224A>G	c.(1222-1224)cgA>cgG	p.R408R	CNNM3_ENST00000377060.3_Splice_Site_p.R408R	NM_017623.4	NP_060093.3	Q8NE01	CNNM3_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 3	408	CBS 2. {ECO:0000255|PROSITE- ProRule:PRU00703}.				ion transport (GO:0006811)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)	p.R408R(1)		NS(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(2)|skin(1)|urinary_tract(2)	13						AATTCAAGCGAGGTAACGGCC	0.602																																					p.R408R		Atlas-SNP	.											CNNM3,NS,carcinoma,0,1	CNNM3	33	1	1	Substitution - coding silent(1)	kidney(1)	c.A1224G						scavenged	.						103	99	100					2																	97483238		2203	4300	6503	SO:0001630	splice_region_variant	26505	exon1			CAAGCGAGGTAAC	AF216965	CCDS2025.1, CCDS2026.1	2q11.2	2014-08-08	2014-08-07		ENSG00000168763	ENSG00000168763			104	protein-coding gene	gene with protein product		607804	"cyclin M3"	ACDP3		21393841, 24632616	Standard	XM_005263917		Approved		uc002swy.3	Q8NE01	OTTHUMG00000130531	ENST00000305510.3:c.1225+1A>G	2.37:g.97483238A>G		70	1	0.0142857		66	3	0.0454545	NM_199078	B3KX67|Q8TBV4|Q96IW4|Q9NRK4|Q9NXW6	Silent	SNP	ENST00000305510.3	37	CCDS2025.1																																																																																			.	.	none		0.602	CNNM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252952.2	NM_017623	Silent	G	97483238	A	G	97483238	5	3	14	1	0	0	0	0	0	0	1	0	3616	318	11	3	1226	3	CNNM3	2	97483238	Splice_Site	SNP	A	TCGA-FF-8047-01A-11D-2210-10	60512923	97483238	145716135	9	1790											
IL1F7	27178	hgsc.bcm.edu	37	chr2	113674819	113674819	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttccagataaaaactacataCgcccaggtgactctcagttt	13	11	6	11	1	1	2	1	1	1	1	3	2	2	2	2	1	3	1	2	1	5	5	rs370690543		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:113674819C>T	ENST00000263326.3	+	3	301	c.259C>T	c.(259-261)Cgc>Tgc	p.R87C	IL37_ENST00000311328.2_Missense_Mutation_p.R61C|IL37_ENST00000353225.3_Intron|IL37_ENST00000352179.3_Missense_Mutation_p.R66C|IL37_ENST00000349806.3_Intron	NM_014439.3	NP_055254.2	Q9NZH6	IL37_HUMAN	interleukin 37	87					immune response (GO:0006955)|inflammatory response (GO:0006954)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)	interleukin-1 receptor binding (GO:0005149)			NS(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(7)|ovary(2)|skin(3)	19						AAACTACATACGCCCAGGTGA	0.493																																					p.R87C		Atlas-SNP	.											.	IL37	56	.	0			c.C259T						PASS	.		CYS/ARG,CYS/ARG,,,CYS/ARG	0,4406		0,0,2203	139	134	136		259,196,,,181	0	0	2		136	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,intron,intron,missense	IL37	NM_014439.3,NM_173202.1,NM_173203.1,NM_173204.1,NM_173205.1	180,180,,,180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,,,possibly-damaging	87/219,66/198,,,61/193	113674819	1,13005	2203	4300	6503	SO:0001583	missense	27178	exon3			TACATACGCCCAG	AF201832	CCDS2103.1, CCDS2104.1, CCDS2105.1, CCDS2106.1, CCDS2107.1	2q12-q14.1	2011-06-06	2011-06-06	2011-06-06	ENSG00000125571	ENSG00000125571		"Interleukins and interleukin receptors"	15563	protein-coding gene	gene with protein product	"interleukin 1, zeta", "interleukin-1 homolog 4", "interleukin-1-related protein"	605510	"interleukin 1 family, member 7 (zeta)"	IL1F7		10625660, 10512743, 12496389	Standard	NM_014439		Approved	FIL1, FIL1Z, FIL1(ZETA), IL-1H4, IL-1RP1, IL-1F7	uc002tij.3	Q9NZH6	OTTHUMG00000131345	ENST00000263326.3:c.259C>T	2.37:g.113674819C>T	ENSP00000263326:p.Arg87Cys	121	0	0		127	42	0.330709	NM_014439	B5BU97|Q56AP9|Q8TD04|Q8TD05|Q9HBF2|Q9HBF3|Q9UHA6	Missense_Mutation	SNP	ENST00000263326.3	37	CCDS2103.1	.	.	.	.	.	.	.	.	.	.	c	5.381	0.255487	0.10185	0.0	1.16E-4	ENSG00000125571	ENST00000263326;ENST00000352179;ENST00000311328	T;T;T	0.58358	0.34;0.34;0.34	2.85	-0.033	0.13902	.	3.274280	0.01053	N	0.004506	T	0.32675	0.0837	N	0.11064	0.09	0.09310	N	1	B;B;B	0.13145	0.007;0.003;0.007	B;B;B	0.06405	0.002;0.001;0.001	T	0.24048	-1.0171	10	0.56958	D	0.05	0.8511	2.8893	0.05671	0.2145:0.5315:0.0:0.254	.	61;66;87	Q9NZH6-2;Q9NZH6-4;Q9NZH6	.;.;IL37_HUMAN	C	87;66;61	ENSP00000263326:R87C;ENSP00000263327:R66C;ENSP00000309883:R61C	ENSP00000263326:R87C	R	+	1	0	IL37	113391290	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.073000	0.00300	-0.016000	0.14127	-0.763000	0.03452	CGC	.	.	weak		0.493	IL37-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254126.1	NM_014439		T	113674819	C	T	113674819	3	4	14	1	0	0	0	0	1	0	0	0	7664	536	19	1	340	1	IL1F7	2	113674819	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	16191581	113674819	129524554	10	1791											
CLASP1	23332	hgsc.bcm.edu	37	chr2	122135079	122135079	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctagggatacttacaataTcacactcctttttgccatct	10	14	5	12	0	2	0	1	0	1	0	3	1	3	1	3	1	3	0	3	1	5	6			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:122135079T>C	ENST00000263710.4	-	34	4027	c.3638A>G	c.(3637-3639)gAt>gGt	p.D1213G	CLASP1_ENST00000541859.1_Missense_Mutation_p.D930G|CLASP1_ENST00000545861.1_Missense_Mutation_p.D920G|CLASP1_ENST00000409078.3_Missense_Mutation_p.D1146G|CLASP1_ENST00000397587.3_Missense_Mutation_p.D1153G|CLASP1_ENST00000541377.1_Missense_Mutation_p.D1152G|CLASP1_ENST00000455322.2_Missense_Mutation_p.D1169G	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	1213					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)					ACTTACAATATCACACTCCTT	0.378																																					p.D1213G		Atlas-SNP	.											.	CLASP1	135	.	0			c.A3638G						PASS	.						165	140	148					2																	122135079		1863	4104	5967	SO:0001583	missense	23332	exon33			ACAATATCACACT	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.3638A>G	2.37:g.122135079T>C	ENSP00000263710:p.Asp1213Gly	165	0	0		157	70	0.44586	NM_015282	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Missense_Mutation	SNP	ENST00000263710.4	37		.	.	.	.	.	.	.	.	.	.	T	17.18	3.323437	0.60634	.	.	ENSG00000074054	ENST00000263710;ENST00000455322;ENST00000397587;ENST00000541377;ENST00000541859;ENST00000409078;ENST00000545861	T;T;T;T;T;T	0.47869	2.17;2.15;2.15;2.14;0.83;2.15	5.74	5.74	0.90152	Armadillo-type fold (1);	0.226336	0.44285	N	0.000463	T	0.41994	0.1183	L	0.39020	1.185	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	0.28073	-1.0055	10	0.87932	D	0	-13.4635	16.0335	0.80603	0.0:0.0:0.0:1.0	.	1146;1153;1154;1213	E7EUA5;F5GWS0;A2RU21;Q7Z460	.;.;.;CLAP1_HUMAN	G	1213;1169;1153;1152;930;1146;920	ENSP00000263710:D1213G;ENSP00000389372:D1169G;ENSP00000380717:D1153G;ENSP00000441625:D1152G;ENSP00000441770:D930G;ENSP00000386442:D1146G	ENSP00000263710:D1213G	D	-	2	0	CLASP1	121851549	1.000000	0.71417	0.986000	0.45419	0.816000	0.46133	7.578000	0.82498	2.195000	0.70347	0.533000	0.62120	GAT	.	.	none		0.378	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282		C	122135079	T	C	122135079	3	2	14	1	0	0	0	0	1	0	0	0	3456	1435	50	3	1006	3	CLASP1	2	122135079	Missense_Mutation	SNP	T	TCGA-FF-8047-01A-11D-2210-10	8460260	122135079	121064294	11	1792											
NEB	4703	hgsc.bcm.edu	37	chr2	152536281	152536281	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggcagctctgatgggaatcGcatcagttctcaggtcatat	9	12	11	9	1	4	1	3	1	2	0	6	2	4	2	0	3	1	4	0	3	2	2	rs371710158		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:152536281G>A	ENST00000172853.10	-	32	3356	c.3209C>T	c.(3208-3210)gCg>gTg	p.A1070V	NEB_ENST00000427231.2_Missense_Mutation_p.A1070V|NEB_ENST00000603639.1_Missense_Mutation_p.A1070V|NEB_ENST00000409198.1_Missense_Mutation_p.A1070V|NEB_ENST00000397345.3_Missense_Mutation_p.A1070V|NEB_ENST00000604864.1_Missense_Mutation_p.A1070V			P20929	NEBU_HUMAN	nebulin	1070					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)	p.A1070V(2)		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)		GATGGGAATCGCATCAGTTCT	0.468																																					p.A1070V		Atlas-SNP	.											NEB,NS,carcinoma,0,1	NEB	1697	1	2	Substitution - Missense(2)	endometrium(2)	c.C3209T						scavenged	.						102	100	100					2																	152536281		1954	4153	6107	SO:0001583	missense	4703	exon32			GGAATCGCATCAG	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.3209C>T	2.37:g.152536281G>A	ENSP00000172853:p.Ala1070Val	132	1	0.00757576		149	60	0.402685	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	G	35	5.526780	0.96431	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.49139	0.79;0.79;0.79;0.79	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.65554	0.2702	M	0.91406	3.205	0.80722	D	1	P	0.51147	0.942	P	0.46362	0.514	T	0.75566	-0.3273	10	0.87932	D	0	.	18.7041	0.91631	0.0:0.0:1.0:0.0	.	1070	P20929	NEBU_HUMAN	V	1070	ENSP00000386259:A1070V;ENSP00000380505:A1070V;ENSP00000416578:A1070V;ENSP00000172853:A1070V	ENSP00000172853:A1070V	A	-	2	0	NEB	152244527	1.000000	0.71417	0.687000	0.30102	0.982000	0.71751	9.705000	0.98719	2.720000	0.93068	0.650000	0.86243	GCG	.	.	alt		0.468	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		A	152536281	G	A	152536281	3	1	14	1	0	0	0	0	1	0	0	0	10311	1087	38	1	23081	1	NEB	2	152536281	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	30401202	152536281	90663092	12	1793											
COL3A1	1281	hgsc.bcm.edu	37	chr2	189864021	189864021	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tttgtcacagggtgatgctgGtgcccctggtgaacgtggac	6	11	15	9	1	1	2	1	2	0	0	1	3	1	3	2	4	3	1	2	4	1	1			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:189864021G>A	ENST00000304636.3	+	30	2203	c.2033G>A	c.(2032-2034)gGt>gAt	p.G678D	COL3A1_ENST00000317840.5_Missense_Mutation_p.G678D	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	678	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)	GGTGATGCTGGTGCCCCTGGT	0.498																																					p.G678D		Atlas-SNP	.											.	COL3A1	292	.	0			c.G2033A						PASS	.						40	40	40					2																	189864021		2202	4299	6501	SO:0001583	missense	1281	exon30			ATGCTGGTGCCCC	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.2033G>A	2.37:g.189864021G>A	ENSP00000304408:p.Gly678Asp	54	0	0		62	35	0.564516	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	37	CCDS2297.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.056475	0.76074	.	.	ENSG00000168542	ENST00000304636;ENST00000317840	D;D	0.99619	-6.28;-6.28	4.96	4.96	0.65561	.	0.000000	0.44688	D	0.000428	D	0.99792	0.9912	H	0.96720	3.87	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96883	0.9647	10	0.87932	D	0	.	18.6093	0.91277	0.0:0.0:1.0:0.0	.	678	P02461	CO3A1_HUMAN	D	678	ENSP00000304408:G678D;ENSP00000315243:G678D	ENSP00000304408:G678D	G	+	2	0	COL3A1	189572266	1.000000	0.71417	0.996000	0.52242	0.969000	0.65631	9.813000	0.99286	2.472000	0.83506	0.650000	0.86243	GGT	.	.	none		0.498	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090		A	189864021	G	A	189864021	3	1	14	1	0	0	0	0	1	0	0	0	3690	1261	44	2	2151	2	COL3A1	2	189864021	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	37327740	189864021	53335352	13	1794											
ARMC9	80210	hgsc.bcm.edu	37	chr2	232099952	232099952	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctagaaatcttgcagcagcTccaccagcagctggttgaag	11	8	10	12	0	1	2	0	1	1	1	2	2	2	2	3	1	5	6	3	1	3	3			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:232099952T>C	ENST00000349938.4	+	8	832	c.638T>C	c.(637-639)cTc>cCc	p.L213P	ARMC9_ENST00000483477.1_3'UTR	NM_001271466.1|NM_025139.4	NP_001258395.1|NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9	213						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)		TTGCAGCAGCTCCACCAGCAG	0.398																																					p.L213P		Atlas-SNP	.											.	ARMC9	129	.	0			c.T638C						PASS	.						57	57	57					2																	232099952		2203	4300	6503	SO:0001583	missense	80210	exon8			AGCAGCTCCACCA	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.638T>C	2.37:g.232099952T>C	ENSP00000258417:p.Leu213Pro	61	0	0		88	4	0.0454545	NM_025139	Q53TI3|Q6P162|Q7L594|Q86WG2|Q96JF9|Q9H9R8	Missense_Mutation	SNP	ENST00000349938.4	37	CCDS2484.1	.	.	.	.	.	.	.	.	.	.	T	19.54	3.846960	0.71603	.	.	ENSG00000135931	ENST00000349938;ENST00000359743	T	0.19669	2.13	5.61	5.61	0.85477	.	0.000000	0.64402	D	0.000001	T	0.46814	0.1412	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.46665	-0.9175	10	0.66056	D	0.02	-21.8479	15.7937	0.78388	0.0:0.0:0.0:1.0	.	213	Q7Z3E5	ARMC9_HUMAN	P	213	ENSP00000258417:L213P	ENSP00000258417:L213P	L	+	2	0	ARMC9	231808196	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	5.588000	0.67517	2.126000	0.65437	0.533000	0.62120	CTC	.	.	none		0.398	ARMC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256966.3	NM_025139		C	232099952	T	C	232099952	3	2	14	1	0	0	0	0	1	0	0	0	958	1551	54	3	664	3	ARMC9	2	232099952	Missense_Mutation	SNP	T	TCGA-FF-8047-01A-11D-2210-10	42235931	232099952	11099421	14	1795											
SNED1	25992	hgsc.bcm.edu	37	chr2	241992639	241992639	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacggcacgcggctgggcgCggtggccctgtatgcatgtg	5	7	17	12	5	0	0	0	0	0	0	0	0	0	0	1	5	2	4	1	5	2	1			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:241992639C>T	ENST00000310397.8	+	16	2153	c.2153C>T	c.(2152-2154)gCg>gTg	p.A718V	SNED1_ENST00000342631.6_Missense_Mutation_p.A718V|SNED1_ENST00000401884.1_Missense_Mutation_p.A718V|SNED1_ENST00000405547.3_Missense_Mutation_p.A718V|AC005237.4_ENST00000458377.1_RNA|SNED1_ENST00000469006.1_3'UTR	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	718	Sushi. {ECO:0000255|PROSITE- ProRule:PRU00302}.				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)		CGGCTGGGCGCGGTGGCCCTG	0.697																																					p.A718V		Atlas-SNP	.											.	SNED1	76	.	0			c.C2153T						PASS	.						19	25	23					2																	241992639		2042	4152	6194	SO:0001583	missense	25992	exon16			TGGGCGCGGTGGC	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.2153C>T	2.37:g.241992639C>T	ENSP00000308893:p.Ala718Val	63	0	0		46	29	0.630435	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Missense_Mutation	SNP	ENST00000310397.8	37	CCDS46562.1	.	.	.	.	.	.	.	.	.	.	C	9.411	1.080605	0.20309	.	.	ENSG00000162804	ENST00000401884;ENST00000405547;ENST00000310397;ENST00000342631	T;T;T;T	0.25414	1.8;1.8;1.8;1.8	4.28	4.28	0.50868	Complement control module (1);Sushi/SCR/CCP (2);	0.437637	0.19414	N	0.114867	T	0.16514	0.0397	L	0.39326	1.205	0.24368	N	0.994843	P	0.42993	0.797	B	0.27500	0.08	T	0.14643	-1.0465	10	0.33141	T	0.24	.	12.5961	0.56470	0.0:0.8327:0.1673:0.0	.	718	Q8TER0	SNED1_HUMAN	V	718	ENSP00000384871:A718V;ENSP00000386007:A718V;ENSP00000308893:A718V;ENSP00000342992:A718V	ENSP00000308893:A718V	A	+	2	0	SNED1	241641312	0.996000	0.38824	0.010000	0.14722	0.007000	0.05969	4.403000	0.59729	1.927000	0.55829	0.561000	0.74099	GCG	.	.	none		0.697	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482		T	241992639	C	T	241992639	3	4	14	1	0	0	0	0	1	0	0	0	14860	768	27	1	2215	1	SNED1	2	241992639	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	9892687	241992639	1206734	15	1796											
DNAH1	25981	hgsc.bcm.edu	37	chr3	52400534	52400534	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtacgacacggcctcatgctCgtcgggcccacaggctccgg	6	6	13	16	5	1	0	1	0	0	0	4	1	2	0	3	4	2	3	3	4	1	1			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:52400534C>T	ENST00000420323.2	+	35	5841	c.5580C>T	c.(5578-5580)ctC>ctT	p.L1860L		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1860	AAA 2. {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)		GCCTCATGCTCGTCGGGCCCA	0.622																																					p.L1860L		Atlas-SNP	.											.	DNAH1	534	.	0			c.C5580T						PASS	.						31	32	32					3																	52400534		2091	4214	6305	SO:0001819	synonymous_variant	25981	exon35			CATGCTCGTCGGG	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.5580C>T	3.37:g.52400534C>T		117	0	0		114	48	0.421053	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Silent	SNP	ENST00000420323.2	37	CCDS46842.1																																																																																			.	.	none		0.622	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		T	52400534	C	T	52400534	2	4	14	1	0	0	0	0	0	0	0	1	4599	871	31	1		1	DNAH1	3	52400534	Silent	SNP	C	TCGA-FF-8047-01A-11D-2210-10		52400534	145621896	16	1797											
STAB1	23166	hgsc.bcm.edu	37	chr3	52549477	52549477	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgtgtctaccgatctggcttCtccttctcccggggctgctc	2	14	10	15	2	4	0	0	0	4	0	7	1	4	0	3	3	2	3	3	3	1	3			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:52549477C>T	ENST00000321725.6	+	37	3979	c.3903C>T	c.(3901-3903)ttC>ttT	p.F1301F		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	1301					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)		GATCTGGCTTCTCCTTCTCCC	0.612																																					p.F1301F		Atlas-SNP	.											.	STAB1	178	.	0			c.C3903T						PASS	.						82	76	78					3																	52549477		2202	4300	6502	SO:0001819	synonymous_variant	23166	exon37			TGGCTTCTCCTTC	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.3903C>T	3.37:g.52549477C>T		108	0	0		95	4	0.0421053	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Silent	SNP	ENST00000321725.6	37	CCDS33768.1																																																																																			.	.	none		0.612	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		T	52549477	C	T	52549477	2	4	14	1	0	0	0	0	0	0	0	1	15252	912	32	2		2	STAB1	3	52549477	Silent	SNP	C	TCGA-FF-8047-01A-11D-2210-10	148943	52549477	145472953	17	1798											
ARMC8	25852	hgsc.bcm.edu	37	chr3	138009387	138009387	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aacctggctttaatcgtttaGgttcacaagaacgccaggat	12	11	9	9	2	1	1	1	0	0	1	2	2	1	2	2	3	2	3	2	3	5	5			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:138009387G>A	ENST00000469044.1	+	21	2165		c.e21-1		ARMC8_ENST00000538260.1_Splice_Site|NME9_ENST00000341790.5_Intron|NME9_ENST00000484930.1_Intron|NME9_ENST00000317876.4_Intron|NME9_ENST00000383180.2_Intron|NME9_ENST00000536478.1_Intron|ARMC8_ENST00000461822.1_Splice_Site|ARMC8_ENST00000485396.1_Splice_Site|ARMC8_ENST00000491704.1_Splice_Site|ARMC8_ENST00000481646.1_Splice_Site|ARMC8_ENST00000393058.3_Splice_Site	NM_001267041.1|NM_001267042.1	NP_001253970.1|NP_001253971.1	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8											endometrium(2)|kidney(1)|large_intestine(7)|lung(5)|upper_aerodigestive_tract(1)	16						TAATCGTTTAGGTTCACAAGA	0.428																																					.		Atlas-SNP	.											.	ARMC8	79	.	0			c.1853-1G>A						PASS	.						68	64	65					3																	138009387		1918	4126	6044	SO:0001630	splice_region_variant	25852	exon22			CGTTTAGGTTCAC		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.1895-1G>A	3.37:g.138009387G>A		83	0	0		147	44	0.29932	NM_015396	A8K0L2|B7Z441|B7Z453|D3DNE6|F5GWK4|Q6PIL2|Q96D19|Q96HZ5|Q9NV02|Q9NV94|Q9Y4R9	Splice_Site	SNP	ENST00000469044.1	37		.	.	.	.	.	.	.	.	.	.	G	17.36	3.370690	0.61624	.	.	ENSG00000114098	ENST00000481646;ENST00000469044;ENST00000491704;ENST00000461822;ENST00000485396;ENST00000538260;ENST00000393058;ENST00000539459	.	.	.	5.02	5.02	0.67125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.834	0.78782	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARMC8	139492077	1.000000	0.71417	0.966000	0.40874	0.711000	0.40976	9.281000	0.95811	2.305000	0.77605	0.442000	0.29010	.	.	.	none		0.428	ARMC8-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000357560.1	NM_015396	Intron	A	138009387	G	A	138009387	5	1	14	1	0	0	0	0	0	0	1	0	957	1014	35	2	2000	2	ARMC8	3	138009387	Splice_Site	SNP	G	TCGA-FF-8047-01A-11D-2210-10	85459910	138009387	60013043	18	1799											
ESYT3	83850	hgsc.bcm.edu	37	chr3	138181019	138181019	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctgtgaagaaggggctggatCtgaccaacctgcgcttccct	8	9	12	12	1	1	3	0	2	1	1	2	4	2	4	3	3	2	2	3	3	3	1			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:138181019C>G	ENST00000389567.4	+	8	1072	c.886C>G	c.(886-888)Ctg>Gtg	p.L296V	ESYT3_ENST00000289135.4_Missense_Mutation_p.L296V	NM_031913.3	NP_114119.2	A0FGR9	ESYT3_HUMAN	extended synaptotagmin-like protein 3	296	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						GGGGCTGGATCTGACCAACCT	0.577																																					p.L296V		Atlas-SNP	.											.	ESYT3	64	.	0			c.C886G						PASS	.						186	137	154					3																	138181019		2203	4300	6503	SO:0001583	missense	83850	exon8			CTGGATCTGACCA	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.886C>G	3.37:g.138181019C>G	ENSP00000374218:p.Leu296Val	130	0	0		254	148	0.582677	NM_031913	A8K0G5|Q6ZV21|Q8NDZ5|Q9BQR9	Missense_Mutation	SNP	ENST00000389567.4	37	CCDS3101.2	.	.	.	.	.	.	.	.	.	.	C	0.363	-0.938291	0.02340	.	.	ENSG00000158220	ENST00000389567;ENST00000289135	T;T	0.35236	1.32;1.61	4.65	1.56	0.23342	.	0.297369	0.32459	N	0.006061	T	0.08846	0.0219	N	0.01624	-0.795	0.20821	N	0.999845	B	0.02656	0.0	B	0.01281	0.0	T	0.33929	-0.9849	10	0.02654	T	1	-8.7761	3.55	0.07843	0.3091:0.2142:0.4766:0.0	.	296	A0FGR9	ESYT3_HUMAN	V	296	ENSP00000374218:L296V;ENSP00000289135:L296V	ENSP00000289135:L296V	L	+	1	2	ESYT3	139663709	0.000000	0.05858	0.970000	0.41538	0.979000	0.70002	-0.565000	0.05929	0.556000	0.29098	-0.321000	0.08615	CTG	.	.	none		0.577	ESYT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303993.1	NM_031913		G	138181019	C	G	138181019	3	3	14	1	0	0	0	0	1	0	0	0	5268	912	32	4	916	4	ESYT3	3	138181019	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	171632	138181019	59841411	19	1800											
C3orf79	152118	hgsc.bcm.edu	37	chr3	153203809	153203809	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatttctttgacagacttcCggttgtctaacccaaatgcc	9	14	6	12	1	3	2	1	1	2	1	4	2	4	2	3	1	2	1	3	1	2	5	rs57748412	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:153203809C>T	ENST00000446603.2	+	2	200	c.138C>T	c.(136-138)tcC>tcT	p.S46S	RP11-23D24.2_ENST00000493214.2_RNA	NM_001101337.1	NP_001094807.1	P0CE67	CC079_HUMAN	chromosome 3 open reading frame 79	46										endometrium(1)|large_intestine(3)	4						GACAGACTTCCGGTTGTCTAA	0.358													C|||	77	0.0153754	0.0567	0.0029	5008	,	,		16257	0.0		0.0	False		,,,				2504	0.0				p.S46S		Atlas-SNP	.											.	C3orf79	13	.	0			c.C138T						PASS	.	C		144,3480		4,136,1672	37	34	35		138	0.8	0	3	dbSNP_129	35	1,8135		0,1,4067	no	coding-synonymous	C3orf79	NM_001101337.1		4,137,5739	TT,TC,CC		0.0123,3.9735,1.233		46/101	153203809	145,11615	1812	4068	5880	SO:0001819	synonymous_variant	152118	exon2			GACTTCCGGTTGT	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.138C>T	3.37:g.153203809C>T		53	0	0		95	4	0.0421053	NM_001101337		Silent	SNP	ENST00000446603.2	37	CCDS46937.1																																																																																			C|0.985;T|0.015	0.015	strong		0.358	C3orf79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356570.1	NM_001101337		T	153203809	C	T	153203809	2	4	14	1	0	0	0	0	0	0	0	1	2248	639	23	1		1	C3orf79	3	153203809	Silent	SNP	C	TCGA-FF-8047-01A-11D-2210-10	15022790	153203809	44818621	20	1801											
KLHL6	89857	hgsc.bcm.edu	37	chr3	183273170	183273170	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgaaatagttgctggctgcgGcaagcaccacgcggtggcag	9	7	15	10	3	0	1	0	1	0	0	0	1	0	1	1	4	3	6	1	4	3	2			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:183273170G>A	ENST00000341319.3	-	1	307	c.272C>T	c.(271-273)gCc>gTc	p.A91V		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	91	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				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)			GCTGGCTGCGGCAAGCACCAC	0.512																																					p.A91V		Atlas-SNP	.											.	KLHL6	100	.	0			c.C272T						PASS	.						94	85	88					3																	183273170		2203	4300	6503	SO:0001583	missense	89857	exon1			GCTGCGGCAAGCA	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.272C>T	3.37:g.183273170G>A	ENSP00000341342:p.Ala91Val	172	0	0		282	99	0.351064	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Missense_Mutation	SNP	ENST00000341319.3	37	CCDS3245.2	.	.	.	.	.	.	.	.	.	.	G	27.7	4.851144	0.91277	.	.	ENSG00000172578	ENST00000341319	T	0.72725	-0.68	5.56	5.56	0.83823	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.83059	0.5172	M	0.88570	2.965	0.80722	D	1	P	0.37370	0.592	P	0.46885	0.53	D	0.84866	0.0822	10	0.62326	D	0.03	.	19.5245	0.95199	0.0:0.0:1.0:0.0	.	91	Q8WZ60	KLHL6_HUMAN	V	91	ENSP00000341342:A91V	ENSP00000341342:A91V	A	-	2	0	KLHL6	184755864	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	7.900000	0.87376	2.608000	0.88229	0.655000	0.94253	GCC	.	.	none		0.512	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446		A	183273170	G	A	183273170	3	1	14	1	0	0	0	0	1	0	0	0	8402	1203	42	2	1621	2	KLHL6	3	183273170	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	30069361	183273170	14749260	21	1802											
ABLIM2	84448	hgsc.bcm.edu	37	chr4	8089920	8089920	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggccctgggacaggtgcgCgctgctgcccaccgatacgg	6	5	16	14	4	0	0	0	0	0	0	0	3	0	1	3	4	4	2	3	4	1	1	rs371815593		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr4:8089920C>T	ENST00000341937.5	-	4	494	c.430G>A	c.(430-432)Gcg>Acg	p.A144T	ABLIM2_ENST00000505872.1_Missense_Mutation_p.A144T|ABLIM2_ENST00000545242.1_Missense_Mutation_p.A144T|ABLIM2_ENST00000428004.2_Missense_Mutation_p.A144T|ABLIM2_ENST00000318888.4_5'UTR|ABLIM2_ENST00000407564.3_Missense_Mutation_p.A144T|ABLIM2_ENST00000361581.5_Missense_Mutation_p.A144T|ABLIM2_ENST00000361737.5_Missense_Mutation_p.A144T|ABLIM2_ENST00000296372.8_Missense_Mutation_p.A144T|ABLIM2_ENST00000546334.1_Missense_Mutation_p.A144T|ABLIM2_ENST00000447017.2_Missense_Mutation_p.A144T	NM_001130084.1	NP_001123556.1	Q6H8Q1	ABLM2_HUMAN	actin binding LIM protein family, member 2	144					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						GACAGGTGCGCGCTGCTGCCC	0.627																																					p.A144T		Atlas-SNP	.											.	ABLIM2	59	.	0			c.G430A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	0,4108		0,0,2054	34	40	38		430,430,430,430,430,430,430	-1.5	0	4		38	2,8350		0,2,4174	no	missense,missense,missense,missense,missense,missense,missense	ABLIM2	NM_001130083.1,NM_001130084.1,NM_001130085.1,NM_001130086.1,NM_001130087.1,NM_001130088.1,NM_032432.4	58,58,58,58,58,58,58	0,2,6228	TT,TC,CC		0.0239,0.0,0.0161	benign,benign,benign,benign,benign,benign,benign	144/646,144/612,144/573,144/560,144/532,144/471,144/522	8089920	2,12458	2054	4176	6230	SO:0001583	missense	84448	exon4			GGTGCGCGCTGCT	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.430G>A	4.37:g.8089920C>T	ENSP00000342813:p.Ala144Thr	399	0	0		394	190	0.482233	NM_001130083	E9PF39|Q08E71|Q19VH0|Q6H8Q0|Q6NX73|Q8N3C5|Q8N9E9|Q8N9G2|Q96JL7	Missense_Mutation	SNP	ENST00000341937.5	37	CCDS47013.1	.	.	.	.	.	.	.	.	.	.	C	4.648	0.120390	0.08881	0.0	2.39E-4	ENSG00000163995	ENST00000361737;ENST00000400045;ENST00000296372;ENST00000545242;ENST00000546334;ENST00000447017;ENST00000341937;ENST00000361581;ENST00000407564;ENST00000505872;ENST00000428004	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	4.02	-1.51	0.08664	.	0.721192	0.12976	U	0.423720	T	0.23289	0.0563	L	0.37850	1.14	0.09310	N	0.999998	B;B;B;B;B;B;B;B	0.15141	0.012;0.001;0.007;0.0;0.001;0.0;0.001;0.0	B;B;B;B;B;B;B;B	0.09377	0.003;0.002;0.004;0.002;0.002;0.0;0.0;0.0	T	0.16689	-1.0394	10	0.30078	T	0.28	.	0.3069	0.00282	0.2364:0.3013:0.2088:0.2534	.	149;144;144;144;144;144;144;144	B7Z6W4;Q6H8Q1-6;Q08E71;Q6H8Q1-2;Q6H8Q1-3;Q6H8Q1;Q19VH0;E9PF39	.;.;.;.;.;ABLM2_HUMAN;.;.	T	144	ENSP00000354887:A144T;ENSP00000296372:A144T;ENSP00000441255:A144T;ENSP00000444365:A144T;ENSP00000393511:A144T;ENSP00000342813:A144T;ENSP00000355003:A144T;ENSP00000384658:A144T;ENSP00000421283:A144T;ENSP00000389410:A144T	ENSP00000296372:A144T	A	-	1	0	ABLIM2	8140820	0.000000	0.05858	0.000000	0.03702	0.067000	0.16453	-0.120000	0.10660	-0.226000	0.09899	-0.263000	0.10527	GCG	.	.	weak		0.627	ABLIM2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358862.2	NM_001130083		T	8089920	C	T	8089920	3	4	14	1	0	0	0	0	1	0	0	0	95	768	27	1	1633	1	ABLIM2	4	8089920	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10		8089920	183064356	22	1803											
PRKG2	5593	hgsc.bcm.edu	37	chr4	82092909	82092909	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccccaaatgtggtccacatAgggatggaggacagcaattt	12	9	11	9	0	0	0	0	0	0	0	2	3	2	3	3	4	1	1	3	4	3	2			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr4:82092909A>G	ENST00000395578.1	-	4	794	c.678T>C	c.(676-678)ccT>ccC	p.P226P	RP11-100N20.1_ENST00000505175.1_RNA|RP11-100N20.1_ENST00000512502.1_RNA|PRKG2_ENST00000418486.2_Silent_p.P226P|PRKG2_ENST00000264399.1_Silent_p.P226P			Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	226					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						TGGTCCACATAGGGATGGAGG	0.408																																					p.P226P		Atlas-SNP	.											.	PRKG2	195	.	0			c.T678C						PASS	.						97	99	98					4																	82092909		2203	4300	6503	SO:0001819	synonymous_variant	5593	exon3			CCACATAGGGATG	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.678T>C	4.37:g.82092909A>G		78	0	0		77	5	0.0649351	NM_006259	B4DMX3|E7EPE6|O00125|O60916	Silent	SNP	ENST00000395578.1	37	CCDS3589.1																																																																																			.	.	none		0.408	PRKG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252639.1	NM_006259		G	82092909	A	G	82092909	2	3	14	1	0	0	0	0	0	0	0	1	12535	407	15	3		3	PRKG2	4	82092909	Silent	SNP	A	TCGA-FF-8047-01A-11D-2210-10	74002989	82092909	109061367	23	1804											
DCHS2	54798	hgsc.bcm.edu	37	chr4	155411418	155411418	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtctccacactcgcaccaCgccgctcagctcctccaccg	7	6	7	21	4	2	0	1	0	1	0	6	0	4	0	6	1	1	3	6	1	0	0			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr4:155411418C>T	ENST00000339452.1	-	1	1450	c.1090G>A	c.(1090-1092)Gtg>Atg	p.V364M	DCHS2_ENST00000443500.1_Missense_Mutation_p.V364M|DCHS2_ENST00000456341.2_Missense_Mutation_p.V357M	NM_001142552.1	NP_001136024.1	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1533	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)		ACTCGCACCACGCCGCTCAGC	0.731																																					p.V364M		Atlas-SNP	.											.	DCHS2	594	.	0			c.G1090A						PASS	.						8	11	10					4																	155411418		688	1580	2268	SO:0001583	missense	54798	exon1			GCACCACGCCGCT	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.1090G>A	4.37:g.155411418C>T	ENSP00000345062:p.Val364Met	31	0	0		10	7	0.7	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000339452.1	37	CCDS47150.1	.	.	.	.	.	.	.	.	.	.	C	11.98	1.800606	0.31869	.	.	ENSG00000197410	ENST00000339452;ENST00000544161;ENST00000456341;ENST00000443500	T;T;T	0.53423	0.62;0.62;0.62	4.7	2.9	0.33743	.	.	.	.	.	T	0.62429	0.2427	M	0.64260	1.97	0.19300	N	0.999978	P;D	0.89917	0.955;1.0	P;D	0.73380	0.523;0.98	T	0.51164	-0.8740	9	0.48119	T	0.1	.	10.3423	0.43887	0.1419:0.5835:0.2746:0.0	.	364;364	E9PG03;E9PC11	.;.	M	364;364;357;364	ENSP00000345062:V364M;ENSP00000408543:V357M;ENSP00000395539:V364M	ENSP00000345062:V364M	V	-	1	0	DCHS2	155630868	0.091000	0.21658	0.990000	0.47175	0.214000	0.24535	0.793000	0.26944	0.468000	0.27243	0.561000	0.74099	GTG	.	.	none		0.731	DCHS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000365282.1	NM_001142552		T	155411418	C	T	155411418	3	4	14	1	0	0	0	0	1	0	0	0	4290	536	19	1	9994	1	DCHS2	4	155411418	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	73318509	155411418	35742858	24	1805											
NEK1	4750	hgsc.bcm.edu	37	chr4	170400567	170400567	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aacttaccacgccaacttctTtcaaagctgaagttacagaa	15	10	5	11	1	2	2	1	1	1	1	2	2	2	2	2	0	5	2	2	0	7	4			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr4:170400567T>A	ENST00000439128.2	-	22	2682	c.2042A>T	c.(2041-2043)aAa>aTa	p.K681I	NEK1_ENST00000507142.1_Missense_Mutation_p.K709I|NEK1_ENST00000512193.1_Missense_Mutation_p.K612I|NEK1_ENST00000510533.1_Missense_Mutation_p.K637I|NEK1_ENST00000511633.1_Missense_Mutation_p.K665I	NM_012224.2	NP_036356.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	681					cellular response to DNA damage stimulus (GO:0006974)|cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|stomach(1)	45		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		GCCAACTTCTTTCAAAGCTGA	0.353																																					p.K709I		Atlas-SNP	.											.	NEK1	203	.	0			c.A2126T						PASS	.						75	73	74					4																	170400567		1843	4074	5917	SO:0001583	missense	4750	exon24			ACTTCTTTCAAAG	AB067488	CCDS47162.1, CCDS56348.1, CCDS56349.1, CCDS56350.1, CCDS56351.1	4q32.3	2012-11-15	2012-11-15		ENSG00000137601	ENSG00000137601			7744	protein-coding gene	gene with protein product		604588	"NIMA (never in mitosis gene a)-related kinase 1"			1382974, 8274451	Standard	NM_012224		Approved	NY-REN-55, KIAA1901	uc003isd.2	Q96PY6	OTTHUMG00000160963	ENST00000439128.2:c.2042A>T	4.37:g.170400567T>A	ENSP00000408020:p.Lys681Ile	152	0	0		109	92	0.844037	NM_001199397	G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	Missense_Mutation	SNP	ENST00000439128.2	37	CCDS47162.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.970361	0.74246	.	.	ENSG00000137601	ENST00000439128;ENST00000511633;ENST00000510533;ENST00000507142;ENST00000512193	T;T;T;T;T	0.74842	-0.88;-0.81;-0.81;-0.8;-0.83	4.74	4.74	0.60224	.	0.191168	0.36482	N	0.002565	D	0.82802	0.5116	M	0.64997	1.995	0.46078	D	0.998856	D;D;D;D;D	0.63880	0.993;0.993;0.993;0.993;0.987	D;P;D;P;P	0.68353	0.957;0.898;0.957;0.898;0.907	D	0.84491	0.0611	10	0.66056	D	0.02	.	12.9491	0.58389	0.0:0.0:0.0:1.0	.	612;665;709;637;681	Q96PY6-4;G5E9Z3;Q96PY6-3;Q96PY6-2;Q96PY6	.;.;.;.;NEK1_HUMAN	I	681;665;637;709;612	ENSP00000408020:K681I;ENSP00000423332:K665I;ENSP00000427653:K637I;ENSP00000424757:K709I;ENSP00000424938:K612I	ENSP00000408020:K681I	K	-	2	0	NEK1	170637142	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	3.033000	0.49743	1.988000	0.58038	0.397000	0.26171	AAA	.	.	none		0.353	NEK1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363157.3			A	170400567	T	A	170400567	3	1	14	1	0	0	0	0	1	0	0	0	10330	1841	64	5	1786	5	NEK1	4	170400567	Missense_Mutation	SNP	T	TCGA-FF-8047-01A-11D-2210-10	14989149	170400567	20753709	25	1806											
UFSP2	55325	hgsc.bcm.edu	37	chr4	186329507	186329507	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agcagatagtctgcagagatCgataagcacagccccagcca	14	5	10	12	1	1	2	0	0	1	2	2	4	1	2	3	0	5	3	3	0	2	2			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr4:186329507C>T	ENST00000264689.6	-	8	1030	c.914G>A	c.(913-915)cGa>cAa	p.R305Q		NM_018359.3	NP_060829.2	Q9NUQ7	UFSP2_HUMAN	UFM1-specific peptidase 2	305						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)		CTGCAGAGATCGATAAGCACA	0.428																																					p.R305Q		Atlas-SNP	.											.	UFSP2	33	.	0			c.G914A						PASS	.						132	117	122					4																	186329507		2203	4300	6503	SO:0001583	missense	55325	exon8			AGAGATCGATAAG	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.914G>A	4.37:g.186329507C>T	ENSP00000264689:p.Arg305Gln	127	0	0		73	4	0.0547945	NM_018359	Q6IA77|Q96FS3	Missense_Mutation	SNP	ENST00000264689.6	37	CCDS3842.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.235189|5.235189	0.95207|0.95207	.|.	.|.	ENSG00000109775|ENSG00000109775	ENST00000509180|ENST00000264689	.|T	.|0.41400	.|1.0	6.03|6.03	6.03|6.03	0.97812|0.97812	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.79287|0.79287	0.4420|0.4420	H|H	0.97611|0.97611	4.04|4.04	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	0.85593|0.85593	0.1247|0.1247	5|10	.|0.87932	.|D	.|0	-8.9285|-8.9285	20.5568|20.5568	0.99304|0.99304	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|305;205	.|Q9NUQ7;B3KRI4	.|UFSP2_HUMAN;.	N|Q	34|305	.|ENSP00000264689:R305Q	.|ENSP00000264689:R305Q	D|R	-|-	1|2	0|0	UFSP2|UFSP2	186566501|186566501	1.000000|1.000000	0.71417|0.71417	0.041000|0.041000	0.18516|0.18516	0.712000|0.712000	0.41017|0.41017	7.478000|7.478000	0.81082|0.81082	2.861000|2.861000	0.98227|0.98227	0.655000|0.655000	0.94253|0.94253	GAT|CGA	.	.	none		0.428	UFSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360589.2	NM_018359		T	186329507	C	T	186329507	3	4	14	1	0	0	0	0	1	0	0	0	16953	884	31	1	515	1	UFSP2	4	186329507	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	15928940	186329507	4824769	26	1807											
CTNND2	1501	hgsc.bcm.edu	37	chr5	11732341	11732341	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggggctcagggaactcgtCttctctgaggctgatgaagg	7	9	15	10	2	3	3	1	3	2	0	5	4	3	4	1	5	1	2	1	5	2	1			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr5:11732341C>A	ENST00000304623.8	-	2	270	c.81G>T	c.(79-81)aaG>aaT	p.K27N	CTNND2_ENST00000458100.2_5'UTR|CTNND2_ENST00000359640.2_Missense_Mutation_p.K27N	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	27					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						GGGAACTCGTCTTCTCTGAGG	0.502																																					p.K27N		Atlas-SNP	.											.	CTNND2	289	.	0			c.G81T						PASS	.						126	127	126					5																	11732341		2203	4300	6503	SO:0001583	missense	1501	exon2			ACTCGTCTTCTCT	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.81G>T	5.37:g.11732341C>A	ENSP00000307134:p.Lys27Asn	45	0	0		58	25	0.431034	NM_001332	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Missense_Mutation	SNP	ENST00000304623.8	37	CCDS3881.1	.	.	.	.	.	.	.	.	.	.	C	7.609	0.674382	0.14841	.	.	ENSG00000169862	ENST00000304623;ENST00000359640;ENST00000502551;ENST00000508761	T;T	0.76060	-0.94;-0.99	5.8	3.08	0.35506	.	0.000000	0.46758	D	0.000274	T	0.50034	0.1592	N	0.08118	0	0.80722	D	1	B	0.09022	0.002	B	0.09377	0.004	T	0.20874	-1.0262	10	0.12430	T	0.62	-20.7622	10.2002	0.43077	0.0:0.7052:0.0:0.2948	.	27	Q9UQB3	CTND2_HUMAN	N	27;27;13;13	ENSP00000307134:K27N;ENSP00000352661:K27N	ENSP00000307134:K27N	K	-	3	2	CTNND2	11785341	1.000000	0.71417	0.999000	0.59377	0.902000	0.53008	0.865000	0.27940	0.109000	0.17891	-0.829000	0.03081	AAG	.	.	none		0.502	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332		A	11732341	C	A	11732341	3	1	14	1	0	0	0	0	1	0	0	0	4022	912	32	4	3680	4	CTNND2	5	11732341	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10		11732341	169182919	27	1808											
ERBB2IP	55914	hgsc.bcm.edu	37	chr5	65349497	65349497	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accagagatcatggaaagatCaaaaacacaggatattgtgc	18	7	9	7	0	2	2	2	0	0	2	2	5	2	4	1	2	2	0	1	2	4	2			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr5:65349497C>A	ENST00000284037.5	+	21	2740	c.2351C>A	c.(2350-2352)tCa>tAa	p.S784*	ERBB2IP_ENST00000511297.1_Nonsense_Mutation_p.S780*|ERBB2IP_ENST00000416865.2_Intron|ERBB2IP_ENST00000380936.1_Nonsense_Mutation_p.S784*|ERBB2IP_ENST00000380938.2_Nonsense_Mutation_p.S784*|ERBB2IP_ENST00000380943.2_Nonsense_Mutation_p.S784*|ERBB2IP_ENST00000508515.1_Nonsense_Mutation_p.S784*|ERBB2IP_ENST00000380935.1_Nonsense_Mutation_p.S784*|ERBB2IP_ENST00000506030.1_Nonsense_Mutation_p.S784*|ERBB2IP_ENST00000380939.2_Nonsense_Mutation_p.S784*	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	784					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)	p.S784*(1)		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)		ATGGAAAGATCAAAAACACAG	0.323																																					p.S784X		Atlas-SNP	.											ERBB2IP,medulla,primitive_neuroectodermal_tumour-medulloblastoma,0,1	ERBB2IP	120	1	1	Substitution - Nonsense(1)	central_nervous_system(1)	c.C2351A						PASS	.						48	50	49					5																	65349497		2203	4299	6502	SO:0001587	stop_gained	55914	exon21			AAAGATCAAAAAC		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.2351C>A	5.37:g.65349497C>A	ENSP00000284037:p.Ser784*	48	0	0		59	32	0.542373	NM_001253699	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Nonsense_Mutation	SNP	ENST00000284037.5	37	CCDS58953.1	.	.	.	.	.	.	.	.	.	.	C	38	6.691405	0.97768	.	.	ENSG00000112851	ENST00000284037;ENST00000380943;ENST00000380939;ENST00000380936;ENST00000380935;ENST00000380938;ENST00000511297;ENST00000506030;ENST00000508515	.	.	.	5.56	4.69	0.59074	.	0.350015	0.29653	N	0.011556	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06625	T	0.88	.	9.0238	0.36215	0.0:0.7891:0.0:0.2109	.	.	.	.	X	784;784;784;784;784;784;780;784;784	.	ENSP00000284037:S784X	S	+	2	0	ERBB2IP	65385253	1.000000	0.71417	1.000000	0.80357	0.516000	0.34256	2.844000	0.48246	1.347000	0.45714	0.467000	0.42956	TCA	.	.	none		0.323	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695		A	65349497	C	A	65349497	4	1	14	1	0	0	0	0	0	1	0	0	5209	838	29	4	2425	4	ERBB2IP	5	65349497	Nonsense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	53617156	65349497	115565763	28	1809											
JMY	133746	hgsc.bcm.edu	37	chr5	78587039	78587039	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aacggatggaaaaactccagTatgcagtttctaaggaaact	16	9	9	7	1	1	0	0	0	1	0	2	3	2	3	1	3	4	3	1	3	6	3			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr5:78587039T>C	ENST00000396137.4	+	4	1906	c.1444T>C	c.(1444-1446)Tat>Cat	p.Y482H		NM_152405.4	NP_689618.4	Q8N9B5	JMY_HUMAN	junction mediating and regulatory protein, p53 cofactor	482	Interaction with p300/EP300. {ECO:0000250}.				'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)		AAAACTCCAGTATGCAGTTTC	0.403																																					p.Y482H		Atlas-SNP	.											.	JMY	82	.	0			c.T1444C						PASS	.						76	74	75					5																	78587039		1879	4094	5973	SO:0001583	missense	133746	exon4			CTCCAGTATGCAG	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.1444T>C	5.37:g.78587039T>C	ENSP00000379441:p.Tyr482His	49	0	0		65	4	0.0615385	NM_152405	A1L4P5|B5MDS2|B5MDT0	Missense_Mutation	SNP	ENST00000396137.4	37	CCDS4047.3	.	.	.	.	.	.	.	.	.	.	T	25.6	4.659897	0.88154	.	.	ENSG00000152409	ENST00000282259;ENST00000396137	T	0.11169	2.8	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.33000	0.0848	M	0.72894	2.215	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.04855	-1.0922	10	0.66056	D	0.02	.	15.2486	0.73526	0.0:0.0:0.0:1.0	.	482	Q8N9B5	JMY_HUMAN	H	482	ENSP00000379441:Y482H	ENSP00000282259:Y482H	Y	+	1	0	JMY	78622795	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.223000	0.78033	1.999000	0.58509	0.454000	0.30748	TAT	.	.	none		0.403	JMY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254070.4	NM_152405		C	78587039	T	C	78587039	3	2	14	1	0	0	0	0	1	0	0	0	7966	1638	57	3	1458	3	JMY	5	78587039	Missense_Mutation	SNP	T	TCGA-FF-8047-01A-11D-2210-10	13237542	78587039	102328221	29	1810											
SPINK5	11005	hgsc.bcm.edu	37	chr5	147470759	147470759	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctgaaaatgccaagcgagagGgtgaaactagaattcgacga	16	6	12	7	3	0	4	0	2	0	2	1	7	0	4	1	1	3	0	1	1	6	2			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr5:147470759G>A	ENST00000256084.7	+	8	676	c.634G>A	c.(634-636)Ggt>Agt	p.G212S	SPINK5_ENST00000476608.1_3'UTR|SPINK5_ENST00000359874.3_Missense_Mutation_p.G212S|SPINK5_ENST00000398454.1_Missense_Mutation_p.G212S	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	212	Kazal-like 3. {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)			CAAGCGAGAGGGTGAAACTAG	0.363																																					p.G212S		Atlas-SNP	.											.	SPINK5	245	.	0			c.G634A						PASS	.						90	86	87					5																	147470759		1866	4104	5970	SO:0001583	missense	11005	exon8			CGAGAGGGTGAAA	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.634G>A	5.37:g.147470759G>A	ENSP00000256084:p.Gly212Ser	27	0	0		26	10	0.384615	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	37	CCDS43382.1	.	.	.	.	.	.	.	.	.	.	G	9.653	1.142058	0.21205	.	.	ENSG00000133710	ENST00000398454;ENST00000359874;ENST00000508733;ENST00000256084	T;T;T;T	0.39406	1.08;1.11;1.17;1.12	4.3	-0.561	0.11785	Proteinase inhibitor I1, Kazal (1);	1.472930	0.04149	N	0.321015	T	0.18841	0.0452	N	0.02539	-0.55	0.09310	N	1	B;B;B;B	0.22146	0.044;0.014;0.02;0.065	B;B;B;B	0.21360	0.034;0.013;0.034;0.02	T	0.16778	-1.0391	10	0.23302	T	0.38	-0.4099	7.2188	0.25975	0.5383:0.0:0.4617:0.0	.	193;212;212;212	B4DWS3;Q9NQ38-3;Q9NQ38;Q9NQ38-2	.;.;ISK5_HUMAN;.	S	212;212;193;212	ENSP00000381472:G212S;ENSP00000352936:G212S;ENSP00000421519:G193S;ENSP00000256084:G212S	ENSP00000256084:G212S	G	+	1	0	SPINK5	147450952	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.154000	0.16343	-0.127000	0.11661	0.650000	0.86243	GGT	.	.	none		0.363	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698		A	147470759	G	A	147470759	3	1	14	1	0	0	0	0	1	0	0	0	15077	1232	43	2	664	2	SPINK5	5	147470759	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	68883720	147470759	33444501	30	1811											
HIST1H4F	8361	hgsc.bcm.edu	37	chr6	26240696	26240696	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtaaaggtttaggaaagggaGgcgccaagcgccatcgcaaa	14	5	14	8	3	0	0	0	0	0	0	1	2	0	2	2	4	1	3	2	4	6	3			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:26240696G>A	ENST00000377745.2	+	1	136	c.43G>A	c.(43-45)Ggc>Agc	p.G15S		NM_003540.3	NP_003531.1	P62805	H4_HUMAN	histone cluster 1, H4f	15					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)			cervix(1)|endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				AGGAAAGGGAGGCGCCAAGCG	0.537																																					p.G15S		Atlas-SNP	.											.	HIST1H4F	9	.	0			c.G43A						PASS	.						46	47	46					6																	26240696		2203	4300	6503	SO:0001583	missense	8361	exon1			AAGGGAGGCGCCA	M60749	CCDS4598.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000198327			"Histones / Replication-dependent"	4783	protein-coding gene	gene with protein product		602824	"H4 histone family, member C", "histone 1, H4f"	H4FC		1916825, 9119399, 12408966	Standard	NM_003540		Approved	H4/c, H4	uc003nhe.1	P62805	OTTHUMG00000014443	ENST00000377745.2:c.43G>A	6.37:g.26240696G>A	ENSP00000366974:p.Gly15Ser	66	0	0		80	37	0.4625	NM_003540	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000377745.2	37	CCDS4598.1	.	.	.	.	.	.	.	.	.	.	.	15.20	2.761893	0.49468	.	.	ENSG00000198327	ENST00000377745	.	.	.	4.48	4.48	0.54585	.	0.000000	0.85682	D	0.000000	T	0.69637	0.3133	.	.	.	0.45899	D	0.998749	.	.	.	.	.	.	T	0.72861	-0.4164	6	0.59425	D	0.04	.	16.6943	0.85330	0.0:0.0:1.0:0.0	.	.	.	.	S	15	.	ENSP00000366974:G15S	G	+	1	0	HIST1H4F	26348675	1.000000	0.71417	0.813000	0.32504	0.016000	0.09150	9.222000	0.95196	2.503000	0.84419	0.655000	0.94253	GGC	.	.	none		0.537	HIST1H4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040106.1	NM_003540		A	26240696	G	A	26240696	3	1	14	1	0	0	0	0	1	0	0	0	7179	1000	35	2	45	2	HIST1H4F	6	26240696	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10		26240696	144874371	31	1812											
OR2H1	26716	hgsc.bcm.edu	37	chr6	29429915	29429915	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctttgaccgatacgtggcTgtctgccagcccctccacta	6	10	9	16	2	1	1	0	1	1	0	2	2	2	1	6	1	3	1	6	1	2	3	rs538200065	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:29429915T>C	ENST00000377136.1	+	4	834	c.369T>C	c.(367-369)gcT>gcC	p.A123A	OR2H1_ENST00000377133.1_Silent_p.A123A|OR2H1_ENST00000396792.2_Silent_p.A123A|OR2H1_ENST00000473369.1_3'UTR|OR2H1_ENST00000377132.1_Silent_p.A123A|OR2H1_ENST00000442615.1_Silent_p.A123A			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, 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)			large_intestine(5)|lung(12)	17						GATACGTGGCTGTCTGCCAGC	0.582																																					p.A123A		Atlas-SNP	.											.	OR2H1	38	.	0			c.T369C						PASS	.						163	167	165					6																	29429915		1510	2709	4219	SO:0001819	synonymous_variant	26716	exon3			CGTGGCTGTCTGC	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.369T>C	6.37:g.29429915T>C		88	0	0		111	6	0.0540541	NM_030883	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Silent	SNP	ENST00000377136.1	37	CCDS4660.1																																																																																			.	.	none		0.582	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3			C	29429915	T	C	29429915	2	2	14	1	0	0	0	0	0	0	0	1	11010	1567	55	3		3	OR2H1	6	29429915	Silent	SNP	T	TCGA-FF-8047-01A-11D-2210-10	3189219	29429915	141685152	32	1813											
TREML2	79865	hgsc.bcm.edu	37	chr6	41166123	41166123	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcacagacagagtctcccCttcaaggagcctcacttttg	9	10	8	14	0	3	2	2	0	1	2	4	3	3	3	3	1	2	1	3	1	1	3			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	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						PASS	.						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	6.37:g.41166123C>T	ENSP00000418767:p.Gly34Arg	70	0	0		100	6	0.06	NM_024807	Q08AP8|Q08AP9|Q8IWY0|Q9H8E9	Missense_Mutation	SNP	ENST00000483722.1	37	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	.	.	none		0.493	TREML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043756.3	NM_024807		T	41166123	C	T	41166123	3	4	14	1	0	0	0	0	1	0	0	0	16488	681	24	2	881	2	TREML2	6	41166123	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	11736208	41166123	129948944	33	1814											
FOXP4	116113	hgsc.bcm.edu	37	chr6	41557528	41557528	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctcgccaaggagagcgagcGgctgcaggccatgatggccc	8	4	16	13	3	0	2	0	1	0	1	1	4	0	2	3	4	3	3	3	4	1	0			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:41557528G>A	ENST00000307972.4	+	9	1097	c.1085G>A	c.(1084-1086)cGg>cAg	p.R362Q	FOXP4_ENST00000373057.3_Missense_Mutation_p.R360Q|FOXP4_ENST00000373060.1_Missense_Mutation_p.R362Q|FOXP4_ENST00000409208.1_Missense_Mutation_p.R362Q|FOXP4_ENST00000373063.3_Missense_Mutation_p.R361Q			Q8IVH2	FOXP4_HUMAN	forkhead box P4	362	Leucine-zipper.				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)					GAGAGCGAGCGGCTGCAGGCC	0.692											OREG0004066	type=REGULATORY REGION|Gene=FOXP4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.R362Q		Atlas-SNP	.											.	FOXP4	83	.	0			c.G1085A						PASS	.						34	37	36					6																	41557528		2202	4298	6500	SO:0001583	missense	116113	exon10			GCGAGCGGCTGCA	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.1085G>A	6.37:g.41557528G>A	ENSP00000309823:p.Arg362Gln	70	0	0	902	107	35	0.327103	NM_001012426	Q5W098|Q7Z7F8|Q8IW55|Q96E19	Missense_Mutation	SNP	ENST00000307972.4	37	CCDS34447.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.615982	0.87359	.	.	ENSG00000137166	ENST00000373060;ENST00000373063;ENST00000409208;ENST00000373057;ENST00000307972	T;T;T;T;T	0.19806	2.12;2.12;2.12;2.12;2.12	4.5	4.5	0.54988	.	0.000000	0.64402	D	0.000001	T	0.32734	0.0839	M	0.74258	2.255	0.80722	D	1	D;D;D	0.67145	0.996;0.993;0.987	P;P;P	0.56563	0.801;0.801;0.701	T	0.32052	-0.9921	10	0.87932	D	0	.	17.2142	0.86938	0.0:0.0:1.0:0.0	.	361;360;362	Q8IW55;Q7Z7F8;Q8IVH2	.;.;FOXP4_HUMAN	Q	362;361;362;360;362	ENSP00000362151:R362Q;ENSP00000362154:R361Q;ENSP00000386958:R362Q;ENSP00000362148:R360Q;ENSP00000309823:R362Q	ENSP00000309823:R362Q	R	+	2	0	FOXP4	41665506	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.688000	0.61715	2.072000	0.62099	0.305000	0.20034	CGG	.	.	none		0.692	FOXP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000106767.1	NM_138457		A	41557528	G	A	41557528	3	1	14	1	0	0	0	0	1	0	0	0	6037	1116	39	1	1119	1	FOXP4	6	41557528	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	391405	41557528	129557539	34	1815											
CUL7	9820	hgsc.bcm.edu	37	chr6	43007981	43007981	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcagtgtgtggcagattgAggcaacaggccaggagtgtc	9	9	16	7	0	1	2	1	1	0	1	2	3	1	3	1	4	1	3	1	4	1	2			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:43007981A>G	ENST00000265348.3	-	22	4292	c.4207T>C	c.(4207-4209)Tca>Cca	p.S1403P	CUL7_ENST00000535468.1_Missense_Mutation_p.S1487P			Q14999	CUL7_HUMAN	cullin 7	1403					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)			TGGCAGATTGAGGCAACAGGC	0.552																																					p.S1487P		Atlas-SNP	.											.	CUL7	133	.	0			c.T4459C						PASS	.						163	123	136					6																	43007981		2203	4300	6503	SO:0001583	missense	9820	exon22			AGATTGAGGCAAC	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.4207T>C	6.37:g.43007981A>G	ENSP00000265348:p.Ser1403Pro	116	0	0		123	5	0.0406504	NM_001168370	B4DYZ0|F5H0L1|Q5T654	Missense_Mutation	SNP	ENST00000265348.3	37	CCDS4881.1	.	.	.	.	.	.	.	.	.	.	A	10.75	1.438588	0.25900	.	.	ENSG00000044090	ENST00000265348;ENST00000535468	T;T	0.79653	-1.29;-1.29	5.71	4.58	0.56647	Cullin, N-terminal (1);Cullin homology (2);	0.242102	0.45126	D	0.000398	T	0.45895	0.1365	N	0.25286	0.73	0.44117	D	0.996898	B;B;B;B	0.33171	0.05;0.061;0.031;0.4	B;B;B;B	0.37833	0.019;0.032;0.017;0.259	T	0.55134	-0.8188	10	0.02654	T	1	-1.3666	5.3129	0.15841	0.8032:0.0:0.1968:0.0	.	1487;1403;1487;1403	F5H0L1;A8K9U1;B4DYZ0;Q14999	.;.;.;CUL7_HUMAN	P	1403;1487	ENSP00000265348:S1403P;ENSP00000438788:S1487P	ENSP00000265348:S1403P	S	-	1	0	CUL7	43115959	0.997000	0.39634	0.953000	0.39169	0.828000	0.46876	1.426000	0.34870	2.179000	0.69175	0.459000	0.35465	TCA	.	.	none		0.552	CUL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040575.1	NM_014780		G	43007981	A	G	43007981	3	3	14	1	0	0	0	0	1	0	0	0	4062	304	11	3	909	3	CUL7	6	43007981	Missense_Mutation	SNP	A	TCGA-FF-8047-01A-11D-2210-10	1450453	43007981	128107086	35	1816											
TDRD6	221400	hgsc.bcm.edu	37	chr6	46656149	46656149	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggcaggcacaggagagccGtgtcttcctgctggacgagg	7	6	16	12	3	1	1	0	0	1	1	2	4	2	2	3	5	2	3	3	5	0	1			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:46656149G>A	ENST00000316081.6	+	1	284	c.284G>A	c.(283-285)cGt>cAt	p.R95H	TDRD6_ENST00000544460.1_Missense_Mutation_p.R95H|RP11-446F17.3_ENST00000434329.2_RNA|RP11-446F17.3_ENST00000422284.2_RNA|RP11-446F17.3_ENST00000571590.1_RNA	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	95	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)			CAGGAGAGCCGTGTCTTCCTG	0.701																																					p.R95H		Atlas-SNP	.											.	TDRD6	205	.	0			c.G284A						PASS	.						6	8	7					6																	46656149		2017	3951	5968	SO:0001583	missense	221400	exon1			AGAGCCGTGTCTT	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.284G>A	6.37:g.46656149G>A	ENSP00000346065:p.Arg95His	18	0	0		23	12	0.521739	NM_001168359	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Missense_Mutation	SNP	ENST00000316081.6	37	CCDS34470.1	.	.	.	.	.	.	.	.	.	.	G	17.05	3.289084	0.59976	.	.	ENSG00000180113	ENST00000544460;ENST00000316081	T;T	0.09723	2.95;2.95	5.31	5.31	0.75309	Maternal tudor protein (1);Tudor domain (1);	0.869952	0.10294	N	0.692000	T	0.19366	0.0465	L	0.56769	1.78	0.29552	N	0.851296	D;D	0.89917	1.0;1.0	D;D	0.76071	0.977;0.987	T	0.02411	-1.1163	10	0.51188	T	0.08	-5.4554	13.8844	0.63699	0.0:0.0:0.8474:0.1525	.	95;95	F5H5M3;O60522	.;TDRD6_HUMAN	H	95	ENSP00000443299:R95H;ENSP00000346065:R95H	ENSP00000346065:R95H	R	+	2	0	TDRD6	46764108	0.940000	0.31905	1.000000	0.80357	0.978000	0.69477	1.391000	0.34475	2.482000	0.83794	0.563000	0.77884	CGT	.	.	none		0.701	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443		A	46656149	G	A	46656149	3	1	14	1	0	0	0	0	1	0	0	0	15749	1145	40	1	286	1	TDRD6	6	46656149	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	3648168	46656149	124458918	36	1817											
EPHA7	2045	hgsc.bcm.edu	37	chr6	94120454	94120454	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagcacttcttgtagtacacTttgacagaaaccaaagctat	14	11	6	10	0	1	2	0	1	1	1	1	2	1	2	1	0	4	4	1	0	5	6			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:94120454T>G	ENST00000369303.4	-	3	781	c.597A>C	c.(595-597)aaA>aaC	p.K199N	EPHA7_ENST00000369297.1_Missense_Mutation_p.K199N	NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	199	Cys-rich.|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)		TGTAGTACACTTTGACAGAAA	0.428																																					p.K199N		Atlas-SNP	.											.	EPHA7	251	.	0			c.A597C						PASS	.						81	85	84					6																	94120454		2203	4300	6503	SO:0001583	missense	2045	exon3			GTACACTTTGACA	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.597A>C	6.37:g.94120454T>G	ENSP00000358309:p.Lys199Asn	143	0	0		178	78	0.438202	NM_004440	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Missense_Mutation	SNP	ENST00000369303.4	37	CCDS5031.1	.	.	.	.	.	.	.	.	.	.	T	17.72	3.458621	0.63401	.	.	ENSG00000135333	ENST00000369303;ENST00000369297	T;T	0.04317	3.65;3.65	5.66	3.26	0.37387	Tyrosine-protein kinase, receptor class V, conserved site (1);Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	T	0.06005	0.0156	L	0.61036	1.89	0.52099	D	0.999943	P;D;D;D	0.63880	0.728;0.993;0.96;0.967	B;P;P;P	0.53224	0.277;0.596;0.6;0.721	T	0.10474	-1.0628	10	0.87932	D	0	.	10.4747	0.44657	0.0:0.1379:0.0:0.8621	.	199;199;199;199	Q15375-4;Q15375-3;Q15375-2;Q15375	.;.;.;EPHA7_HUMAN	N	199	ENSP00000358309:K199N;ENSP00000358303:K199N	ENSP00000358303:K199N	K	-	3	2	EPHA7	94177175	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.685000	0.37659	1.090000	0.41315	0.533000	0.62120	AAA	.	.	none		0.428	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1			G	94120454	T	G	94120454	3	3	14	1	0	0	0	0	1	0	0	0	5174	1606	56	5	2459	5	EPHA7	6	94120454	Missense_Mutation	SNP	T	TCGA-FF-8047-01A-11D-2210-10	47464305	94120454	76994613	37	1818											
MANEA	79694	hgsc.bcm.edu	37	chr6	96053987	96053987	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ggatacatagataccagcatCcgtccatggaacacgcaaaa	16	6	8	11	2	0	1	0	0	0	1	2	3	2	3	3	2	4	2	3	2	6	3			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:96053987C>T	ENST00000358812.4	+	5	1229	c.1095C>T	c.(1093-1095)atC>atT	p.I365I		NM_024641.3	NP_078917.2	Q5SRI9	MANEA_HUMAN	mannosidase, endo-alpha	365	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)		ATACCAGCATCCGTCCATGGA	0.423																																					p.I365I		Atlas-SNP	.											.	MANEA	58	.	0			c.C1095T						PASS	.						99	107	104					6																	96053987		2203	4300	6503	SO:0001819	synonymous_variant	79694	exon5			CAGCATCCGTCCA	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.1095C>T	6.37:g.96053987C>T		52	0	0		50	28	0.56	NM_024641	A6H8M6|Q5SRJ0|Q6MZV0|Q70JE9|Q7Z3V7|Q8WWX5|Q9H9D2	Silent	SNP	ENST00000358812.4	37	CCDS5032.1																																																																																			.	.	none		0.423	MANEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043644.1	NM_024641		T	96053987	C	T	96053987	2	4	14	1	0	0	0	0	0	0	0	1	9230	845	30	2		2	MANEA	6	96053987	Silent	SNP	C	TCGA-FF-8047-01A-11D-2210-10	1933533	96053987	75061080	38	1819											
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138583857	138583857	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcatcatggatggcatgaccGaagcatgcatcaagggtggc	11	7	14	9	1	2	1	2	1	0	0	2	3	2	2	1	4	2	4	1	4	2	0	rs149573553	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:138583857G>A	ENST00000251691.4	+	12	1403	c.1237G>A	c.(1237-1239)Gaa>Aaa	p.E413K		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)		TGGCATGACCGAAGCATGCAT	0.473													G|||	2	0.000399361	0.0	0.0	5008	,	,		23811	0.002		0.0	False		,,,				2504	0.0				p.E413K		Atlas-SNP	.											.	KIAA1244	236	.	0			c.G1237A						PASS	.						110	104	106					6																	138583857		2203	4300	6503	SO:0001583	missense	57221	exon12			ATGACCGAAGCAT	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.1237G>A	6.37:g.138583857G>A	ENSP00000251691:p.Glu413Lys	116	0	0		127	49	0.385827	NM_020340		Missense_Mutation	SNP	ENST00000251691.4	37	CCDS5189.2	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	G	22.9	4.348964	0.82132	.	.	ENSG00000112379	ENST00000251691	T	0.04275	3.66	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.09468	0.0233	M	0.73962	2.25	0.58432	D	0.999992	D	0.67145	0.996	P	0.50570	0.644	T	0.01178	-1.1427	10	0.72032	D	0.01	-13.0813	18.2897	0.90126	0.0:0.0:1.0:0.0	.	413	Q5TH69	BIG3_HUMAN	K	413	ENSP00000251691:E413K	ENSP00000251691:E413K	E	+	1	0	KIAA1244	138625550	1.000000	0.71417	0.709000	0.30452	0.865000	0.49528	7.342000	0.79310	2.745000	0.94114	0.655000	0.94253	GAA	G|0.999;A|0.001	0.001	strong		0.473	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		A	138583857	G	A	138583857	3	1	14	1	0	0	0	0	1	0	0	0	8226	1059	37	1	1283	1	KIAA1244	6	138583857	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	42529870	138583857	32531210	39	1820											
STXBP5	134957	hgsc.bcm.edu	37	chr6	147612247	147612247	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	taggaaaacagttaaaggatGggaagaagccagaaccatgc	18	5	12	6	0	0	2	0	0	0	2	0	5	0	5	2	3	4	1	2	3	8	2			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:147612247G>T	ENST00000321680.6	+	9	856	c.856G>T	c.(856-858)Ggg>Tgg	p.G286W	STXBP5_ENST00000367480.3_Missense_Mutation_p.G286W|STXBP5_ENST00000179882.6_5'UTR|STXBP5_ENST00000367481.3_Missense_Mutation_p.G286W|STXBP5_ENST00000546097.1_Missense_Mutation_p.G286W	NM_001127715.2	NP_001121187.1	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn)	286					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)		GTTAAAGGATGGGAAGAAGCC	0.308																																					p.G286W		Atlas-SNP	.											.	STXBP5	163	.	0			c.G856T						PASS	.						93	89	90					6																	147612247		2203	4300	6503	SO:0001583	missense	134957	exon9			AAGGATGGGAAGA	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.856G>T	6.37:g.147612247G>T	ENSP00000321826:p.Gly286Trp	114	0	0		97	45	0.463918	NM_139244	Q14DF3|Q5T5C1|Q5T5C2|Q8NBG8|Q96NG9	Missense_Mutation	SNP	ENST00000321680.6	37	CCDS47499.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.511125	0.85389	.	.	ENSG00000164506	ENST00000367481;ENST00000546097;ENST00000321680;ENST00000367480	T;D;T;T	0.86366	2.45;-2.11;2.44;2.56	5.35	5.35	0.76521	WD40 repeat-like-containing domain (1);Lethal giant larvae homologue 2 (1);	0.000000	0.85682	D	0.000000	D	0.92172	0.7518	M	0.65975	2.015	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92395	0.5924	10	0.72032	D	0.01	.	19.0338	0.92969	0.0:0.0:1.0:0.0	.	286;286	Q5T5C0-2;Q5T5C0	.;STXB5_HUMAN	W	286	ENSP00000356451:G286W;ENSP00000441479:G286W;ENSP00000321826:G286W;ENSP00000356450:G286W	ENSP00000321826:G286W	G	+	1	0	STXBP5	147653940	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.580000	0.90784	2.656000	0.90262	0.650000	0.86243	GGG	.	.	none		0.308	STXBP5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042606.1			T	147612247	G	T	147612247	3	4	14	1	0	0	0	0	1	0	0	0	15371	1348	47	4	890	4	STXBP5	6	147612247	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	9028390	147612247	23502820	40	1821											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152651974	152651974	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagcgtaagtagaagattttCatattctggagattgttcaa	13	14	9	5	1	3	3	2	0	1	3	3	4	3	3	0	1	1	3	0	1	5	8			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:152651974C>T	ENST00000367255.5	-	78	14447	c.13846G>A	c.(13846-13848)Gaa>Aaa	p.E4616K	SYNE1_ENST00000448038.1_Missense_Mutation_p.E4545K|SYNE1_ENST00000265368.4_Missense_Mutation_p.E4616K|SYNE1_ENST00000341594.5_Missense_Mutation_p.E4363K|SYNE1_ENST00000423061.1_Missense_Mutation_p.E4545K	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4616					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)		AGAAGATTTTCATATTCTGGA	0.383										HNSCC(10;0.0054)																											p.E4616K		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G13846A						PASS	.						164	166	165					6																	152651974		2203	4300	6503	SO:0001583	missense	23345	exon78			GATTTTCATATTC	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.13846G>A	6.37:g.152651974C>T	ENSP00000356224:p.Glu4616Lys	79	0	0		74	34	0.459459	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	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	19.37	3.815534	0.70912	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.53857	1.33;1.33;1.33;1.33;0.6	5.93	5.93	0.95920	.	0.000000	0.64402	D	0.000004	T	0.64832	0.2634	L	0.54323	1.7	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;0.997;0.997;0.999	T	0.59434	-0.7455	10	0.41790	T	0.15	.	20.3368	0.98748	0.0:1.0:0.0:0.0	.	4616;4616;4616;4545	Q8NF91-7;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	K	4616;4545;4616;4545;4363	ENSP00000356224:E4616K;ENSP00000396024:E4545K;ENSP00000265368:E4616K;ENSP00000390975:E4545K;ENSP00000341887:E4363K	ENSP00000265368:E4616K	E	-	1	0	SYNE1	152693667	1.000000	0.71417	0.951000	0.38953	0.909000	0.53808	7.818000	0.86416	2.805000	0.96524	0.655000	0.94253	GAA	.	.	none		0.383	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152651974	C	T	152651974	3	4	14	1	0	0	0	0	1	0	0	0	15460	835	29	2	12896	2	SYNE1	6	152651974	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	5039727	152651974	18463093	41	1822											
T	6862	hgsc.bcm.edu	37	chr6	166578142	166578142	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccgggttcctccatcatctcTttgtgatcacttctatcaaa	8	15	5	13	1	5	1	3	1	2	0	8	1	7	1	3	1	0	1	3	1	2	4			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:166578142T>C	ENST00000296946.2	-	6	1149	c.681A>G	c.(679-681)aaA>aaG	p.K227K	T_ENST00000366871.3_Silent_p.K227K	NM_003181.3	NP_003172.1	O15178	BRAC_HUMAN	T, brachyury homolog (mouse)	227					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)		CCATCATCTCTTTGTGATCAC	0.388									Chordoma, Familial Clustering of																												p.K227K		Atlas-SNP	.											.	T	77	.	0			c.A681G						PASS	.						95	97	96					6																	166578142		2203	4300	6503	SO:0001819	synonymous_variant	6862	exon6	Familial Cancer Database		CATCTCTTTGTGA	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.681A>G	6.37:g.166578142T>C		58	0	0		87	4	0.045977	NM_003181	E7ERD6|Q4KMP4	Silent	SNP	ENST00000296946.2	37	CCDS5290.1																																																																																			.	.	none		0.388	T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043037.2	NM_003181		C	166578142	T	C	166578142	2	2	14	1	0	0	0	0	0	0	0	1	15503	1606	56	3		3	T	6	166578142	Silent	SNP	T	TCGA-FF-8047-01A-11D-2210-10	13926168	166578142	4536925	42	1823											
KIAA0415	9907	hgsc.bcm.edu	37	chr7	4823361	4823361	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcggctggtcgactggctgCgctacgccagcctccagcaa	7	6	13	15	4	0	0	0	0	0	0	2	1	1	0	3	3	5	4	3	3	2	1			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr7:4823361C>T	ENST00000348624.4	+	5	647	c.553C>T	c.(553-555)Cgc>Tgc	p.R185C	AP5Z1_ENST00000401897.1_Missense_Mutation_p.R185C	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	185					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)											CGACTGGCTGCGCTACGCCAG	0.657																																					p.R185C		Atlas-SNP	.											.	.	.	.	0			c.C553T						PASS	.						5	8	7					7																	4823361		1760	3730	5490	SO:0001583	missense	9907	exon5			TGGCTGCGCTACG	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.553C>T	7.37:g.4823361C>T	ENSP00000297562:p.Arg185Cys	101	0	0		83	39	0.46988	NM_014855	Q8N3X2|Q96H80	Missense_Mutation	SNP	ENST00000348624.4	37	CCDS47528.1	.	.	.	.	.	.	.	.	.	.	C	16.11	3.029717	0.54790	.	.	ENSG00000242802	ENST00000348624;ENST00000401897	T;T	0.50277	0.76;0.75	4.37	4.37	0.52481	.	0.000000	0.85682	D	0.000000	T	0.66973	0.2844	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.71119	-0.4685	10	0.66056	D	0.02	.	11.8038	0.52143	0.1882:0.8118:0.0:0.0	.	185	O43299	K0415_HUMAN	C	185	ENSP00000297562:R185C;ENSP00000384980:R185C	ENSP00000297562:R185C	R	+	1	0	KIAA0415	4789887	0.929000	0.31497	0.969000	0.41365	0.255000	0.26057	1.781000	0.38644	1.983000	0.57843	0.462000	0.41574	CGC	.	.	none		0.657	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1			T	4823361	C	T	4823361	3	4	14	1	0	0	0	0	1	0	0	0	8184	768	27	1	571	1	KIAA0415	7	4823361	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10		4823361	154315302	43	1824											
SNX13	23161	hgsc.bcm.edu	37	chr7	17874490	17874490	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagtaactcttggagatgccTaacagagaaaaataatagta	18	9	8	6	0	1	2	0	0	1	2	1	4	1	2	1	1	3	2	1	1	7	6			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr7:17874490T>C	ENST00000409389.1	-	14	1532		c.e14-2		SNX13_ENST00000428135.3_Splice_Site			Q9Y5W8	SNX13_HUMAN	sorting nexin 13						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)					TGGAGATGCCTAACAGAGAAA	0.299																																					.		Atlas-SNP	.											.	SNX13	113	.	0			c.1360-2A>G						PASS	.						41	40	40					7																	17874490		1805	4059	5864	SO:0001630	splice_region_variant	23161	exon15			GATGCCTAACAGA	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.1360-2A>G	7.37:g.17874490T>C		95	0	0		89	4	0.0449438	NM_015132	B2RCI9|O94821|Q8WVZ2|Q8WXH8	Splice_Site	SNP	ENST00000409389.1	37		.	.	.	.	.	.	.	.	.	.	T	19.85	3.904370	0.72868	.	.	ENSG00000071189	ENST00000409389;ENST00000428135;ENST00000242044	.	.	.	4.93	4.93	0.64822	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.863	0.70394	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	SNX13	17841015	1.000000	0.71417	0.951000	0.38953	0.887000	0.51463	5.681000	0.68175	1.979000	0.57680	0.402000	0.26972	.	.	.	none		0.299	SNX13-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000327608.1	NM_015132	Intron	C	17874490	T	C	17874490	5	2	14	1	0	0	0	0	0	0	1	0	14899	1536	53	3	1567	3	SNX13	7	17874490	Splice_Site	SNP	T	TCGA-FF-8047-01A-11D-2210-10	13051129	17874490	141264173	44	1825											
TWISTNB	221830	hgsc.bcm.edu	37	chr7	19738329	19738329	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctgtaacttcttcagaaacTtcagagcgcttgaattgtaa	12	14	7	8	1	4	3	2	1	2	2	4	3	4	3	0	0	3	3	0	0	4	7			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr7:19738329T>C	ENST00000222567.5	-	4	697	c.627A>G	c.(625-627)gaA>gaG	p.E209E		NM_001002926.1	NP_001002926.1	Q3B726	RPA43_HUMAN	TWIST neighbor	209					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						CTTCAGAAACTTCAGAGCGCT	0.323																																					p.E209E		Atlas-SNP	.											.	TWISTNB	63	.	0			c.A627G						PASS	.						53	61	59					7																	19738329		2199	4289	6488	SO:0001819	synonymous_variant	221830	exon4			AGAAACTTCAGAG	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.627A>G	7.37:g.19738329T>C		48	0	0		49	24	0.489796	NM_001002926	A0PJ45|B7Z724	Silent	SNP	ENST00000222567.5	37	CCDS34606.1																																																																																			.	.	none		0.323	TWISTNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326463.1			C	19738329	T	C	19738329	2	2	14	1	0	0	0	0	0	0	0	1	16799	1606	56	3		3	TWISTNB	7	19738329	Silent	SNP	T	TCGA-FF-8047-01A-11D-2210-10	1863839	19738329	139400334	45	1826											
FKBP9	11328	hgsc.bcm.edu	37	chr7	33014908	33014908	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caagcccccgagttgccctcGgaccatccaggtgtctgatt	7	9	10	15	2	1	1	0	1	1	0	3	3	2	2	5	2	2	1	5	2	1	2			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr7:33014908G>A	ENST00000242209.4	+	3	651	c.482G>A	c.(481-483)cGg>cAg	p.R161Q	AVL9_ENST00000404479.1_Intron|FKBP9_ENST00000538443.1_Missense_Mutation_p.R23Q|FKBP9_ENST00000538336.1_Missense_Mutation_p.R214Q	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	9	0			c.G482A						scavenged	.						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	7.37:g.33014908G>A	ENSP00000242209:p.Arg161Gln	98	1	0.0102041		121	7	0.0578512	NM_007270	B3KY35|B7Z1G9|B7Z6H3|Q2M2A1|Q3MIR7|Q6IN76|Q6P2N1|Q96EX5|Q96IJ9	Missense_Mutation	SNP	ENST00000242209.4	37	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	.	.	none		0.473	FKBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215137.1	NM_007270		A	33014908	G	A	33014908	3	1	14	1	0	0	0	0	1	0	0	0	5923	1116	39	1	492	1	FKBP9	7	33014908	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	13276579	33014908	126123755	46	1827											
ZP3	7784	hgsc.bcm.edu	37	chr7	76058885	76058885	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctccatgacccccgcccCgtgggaaacctgtccatcgt	6	8	9	18	3	0	1	0	1	0	0	3	2	2	2	7	1	2	1	7	1	1	0			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr7:76058885C>T	ENST00000394857.3	+	2	424	c.366C>T	c.(364-366)ccC>ccT	p.P122P	ZP3_ENST00000416245.1_5'UTR|ZP3_ENST00000336517.4_Silent_p.P71P	NM_001110354.1	NP_001103824.1	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 (sperm receptor)	122	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						ACCCCCGCCCCGTGGGAAACC	0.612																																					p.P122P		Atlas-SNP	.											.	ZP3	32	.	0			c.C366T						PASS	.						112	83	93					7																	76058885		2203	4300	6503	SO:0001819	synonymous_variant	7784	exon2			CCGCCCCGTGGGA	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.366C>T	7.37:g.76058885C>T		136	0	0		127	54	0.425197	NM_001110354	Q06633|Q29RW0	Silent	SNP	ENST00000394857.3	37	CCDS47618.1																																																																																			.	.	none		0.612	ZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253004.1			T	76058885	C	T	76058885	2	4	14	1	0	0	0	0	0	0	0	1	18232	639	23	1		1	ZP3	7	76058885	Silent	SNP	C	TCGA-FF-8047-01A-11D-2210-10	43043977	76058885	83079778	47	1828											
LRRN3	54674	hgsc.bcm.edu	37	chr7	110764121	110764121	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgagagctttccttctaaTctaaatgtagaagctgggag	11	12	10	8	0	2	2	0	1	2	2	3	4	3	3	2	1	2	3	2	1	5	5			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr7:110764121T>C	ENST00000422987.3	+	2	2124	c.1293T>C	c.(1291-1293)aaT>aaC	p.N431N	IMMP2L_ENST00000489381.1_Intron|IMMP2L_ENST00000405709.2_Intron|LRRN3_ENST00000451085.1_Silent_p.N431N|IMMP2L_ENST00000452895.1_Intron|IMMP2L_ENST00000331762.3_Intron|IMMP2L_ENST00000437687.1_Intron|IMMP2L_ENST00000447215.1_Intron|IMMP2L_ENST00000415362.1_Intron|LRRN3_ENST00000308478.5_Silent_p.N431N|IMMP2L_ENST00000450877.1_Intron	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	431	Ig-like C2-type.				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)		TTCCTTCTAATCTAAATGTAG	0.438																																					p.N431N		Atlas-SNP	.											.	LRRN3	132	.	0			c.T1293C						PASS	.						111	117	115					7																	110764121		2203	4300	6503	SO:0001819	synonymous_variant	54674	exon2			TTCTAATCTAAAT	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.1293T>C	7.37:g.110764121T>C		58	0	0		64	34	0.53125	NM_018334	O43377|Q6I9V8|Q8IYQ6	Silent	SNP	ENST00000422987.3	37	CCDS5754.1																																																																																			.	.	none		0.438	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334		C	110764121	T	C	110764121	2	2	14	1	0	0	0	0	0	0	0	1	9045	1432	50	3		3	LRRN3	7	110764121	Silent	SNP	T	TCGA-FF-8047-01A-11D-2210-10	34705236	110764121	48374542	48	1829											
SND1	27044	hgsc.bcm.edu	37	chr7	127447592	127447592	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccttacatgtttgaggccCgggaatttcttcgaaaaaag	11	13	9	8	2	1	1	0	1	1	0	3	3	2	2	2	2	1	1	2	2	5	5			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr7:127447592C>T	ENST00000354725.3	+	11	1401	c.1207C>T	c.(1207-1209)Cgg>Tgg	p.R403W		NM_014390.2	NP_055205.2	Q7KZF4	SND1_HUMAN	staphylococcal nuclease and tudor domain containing 1	403	TNase-like 3. {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						GTTTGAGGCCCGGGAATTTCT	0.368																																					p.R403W		Atlas-SNP	.											.	SND1	104	.	0			c.C1207T						PASS	.						138	136	137					7																	127447592		2203	4300	6503	SO:0001583	missense	27044	exon11			GAGGCCCGGGAAT		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.1207C>T	7.37:g.127447592C>T	ENSP00000346762:p.Arg403Trp	101	0	0		88	4	0.0454545	NM_014390	Q13122|Q96AG0	Missense_Mutation	SNP	ENST00000354725.3	37	CCDS34747.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.740470	0.89573	.	.	ENSG00000197157	ENST00000354725;ENST00000438400	T	0.34072	1.38	5.86	5.86	0.93980	Staphylococcal nuclease (SNase-like) (4);Staphylococcal nuclease (SNase-like), OB-fold (1);	0.052414	0.85682	D	0.000000	T	0.69396	0.3106	H	0.94582	3.555	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.76664	-0.2876	10	0.87932	D	0	-19.8134	12.9338	0.58303	0.1619:0.8381:0.0:0.0	.	403	Q7KZF4	SND1_HUMAN	W	403;393	ENSP00000346762:R403W	ENSP00000346762:R403W	R	+	1	2	SND1	127234828	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.304000	0.43655	2.937000	0.99478	0.650000	0.86243	CGG	.	.	none		0.368	SND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349148.1	NM_014390		T	127447592	C	T	127447592	3	4	14	1	0	0	0	0	1	0	0	0	14859	643	23	1	1249	1	SND1	7	127447592	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	16683471	127447592	31691071	49	1830											
PTN	5764	hgsc.bcm.edu	37	chr7	136936058	136936058	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttcggcattgtgcagggctcGcttcagacttccagttctgg	5	13	12	11	2	2	1	1	0	1	1	5	1	3	1	1	3	1	5	1	3	0	5			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr7:136936058G>A	ENST00000348225.2	-	4	797	c.370C>T	c.(370-372)Cga>Tga	p.R124*	PTN_ENST00000393083.2_Nonsense_Mutation_p.R124*	NM_002825.5	NP_002816.1	P21246	PTN_HUMAN	pleiotrophin	124					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						TGCAGGGCTCGCTTCAGACTT	0.527																																					p.R124X		Atlas-SNP	.											.	PTN	38	.	0			c.C370T						PASS	.						292	266	275					7																	136936058		2203	4300	6503	SO:0001587	stop_gained	5764	exon4			GGGCTCGCTTCAG	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.370C>T	7.37:g.136936058G>A	ENSP00000341170:p.Arg124*	229	0	0		274	131	0.478102	NM_002825	Q5U0B0|Q6ICQ5|Q9UCC6	Nonsense_Mutation	SNP	ENST00000348225.2	37	CCDS5844.1	.	.	.	.	.	.	.	.	.	.	G	39	7.527019	0.98339	.	.	ENSG00000105894	ENST00000348225;ENST00000393083	.	.	.	6.02	4.05	0.47172	.	0.115288	0.64402	D	0.000017	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06625	T	0.88	-9.3356	14.1566	0.65422	0.0:0.0:0.5946:0.4054	.	.	.	.	X	124	.	ENSP00000341170:R124X	R	-	1	2	PTN	136586598	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.741000	0.47426	1.528000	0.49103	0.650000	0.86243	CGA	.	.	none		0.527	PTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341339.1	NM_002825		A	136936058	G	A	136936058	4	1	14	1	0	0	0	0	0	1	0	0	12781	1095	38	1	144	1	PTN	7	136936058	Nonsense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	9488466	136936058	22202605	50	1831											
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77766731	77766731	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctcaaaaccaattccttcActctccgttcttggaaaggc	10	12	6	13	1	4	0	2	0	2	0	6	1	5	1	3	2	2	2	3	2	4	4			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr8:77766731A>T	ENST00000521891.2	+	10	8022	c.7574A>T	c.(7573-7575)cAc>cTc	p.H2525L	ZFHX4_ENST00000518282.1_Missense_Mutation_p.H2499L|ZFHX4_ENST00000455469.2_Missense_Mutation_p.H2480L|ZFHX4_ENST00000050961.6_Missense_Mutation_p.H2480L	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2480					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)			CAATTCCTTCACTCTCCGTTC	0.498										HNSCC(33;0.089)																											p.H2525L		Atlas-SNP	.											.	ZFHX4	878	.	0			c.A7574T						PASS	.						167	167	167					8																	77766731		2038	4213	6251	SO:0001583	missense	79776	exon10			TCCTTCACTCTCC		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.7574A>T	8.37:g.77766731A>T	ENSP00000430497:p.His2525Leu	81	0	0		105	12	0.114286	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	A	16.66	3.184571	0.57909	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.53857	0.6;0.66;0.63;0.62	4.94	4.94	0.65067	.	0.000000	0.46758	U	0.000276	T	0.65554	0.2702	M	0.71581	2.175	0.80722	D	1	P;P;P	0.52316	0.92;0.896;0.952	P;P;P	0.55999	0.727;0.789;0.789	T	0.66444	-0.5922	10	0.39692	T	0.17	.	14.7648	0.69632	1.0:0.0:0.0:0.0	.	2480;2480;2525	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	L	2525;2509;2480;2480;2499	ENSP00000430497:H2525L;ENSP00000399605:H2480L;ENSP00000050961:H2480L;ENSP00000430848:H2499L	ENSP00000050961:H2480L	H	+	2	0	ZFHX4	77929286	1.000000	0.71417	0.999000	0.59377	0.960000	0.62799	9.131000	0.94446	2.077000	0.62373	0.528000	0.53228	CAC	.	.	none		0.498	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77766731	A	T	77766731	3	4	14	1	0	0	0	0	1	0	0	0	17650	159	6	5	7608	5	ZFHX4	8	77766731	Missense_Mutation	SNP	A	TCGA-FF-8047-01A-11D-2210-10		77766731	68597291	51	1832											
UBR5	51366	hgsc.bcm.edu	37	chr8	103269903	103269903	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatcttctctactattgacCagaaccaacgcttgaactgc	11	12	5	13	1	3	3	1	2	2	1	4	3	3	3	2	0	5	1	2	0	5	5			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr8:103269903C>T	ENST00000520539.1	-	58	8750	c.8144G>A	c.(8143-8145)tGg>tAg	p.W2715*	UBR5_ENST00000518205.1_Nonsense_Mutation_p.W443*|UBR5_ENST00000521922.1_Nonsense_Mutation_p.W2708*|UBR5_ENST00000220959.4_Nonsense_Mutation_p.W2714*|KB-431C1.5_ENST00000606361.1_RNA	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	2715	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				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)			TACTATTGACCAGAACCAACG	0.323																																					p.W2715X	Ovarian(131;96 1741 5634 7352 27489)	Atlas-SNP	.											.	UBR5	285	.	0			c.G8144A						PASS	.						89	84	85					8																	103269903		2202	4300	6502	SO:0001587	stop_gained	51366	exon58			ATTGACCAGAACC	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.8144G>A	8.37:g.103269903C>T	ENSP00000429084:p.Trp2715*	72	0	0		76	40	0.526316	NM_015902	B2RP24|J3KMW7|O94970|Q9NPL3	Nonsense_Mutation	SNP	ENST00000520539.1	37	CCDS34933.1	.	.	.	.	.	.	.	.	.	.	C	53	20.275754	0.99929	.	.	ENSG00000104517	ENST00000520539;ENST00000220959;ENST00000518205;ENST00000521922	.	.	.	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.3216	0.94243	0.0:1.0:0.0:0.0	.	.	.	.	X	2715;2714;443;2708	.	ENSP00000220959:W2714X	W	-	2	0	UBR5	103339079	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.578000	0.87016	0.585000	0.79938	TGG	.	.	none		0.323	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902		T	103269903	C	T	103269903	4	4	14	1	0	0	0	0	0	1	0	0	16920	595	21	2	263	2	UBR5	8	103269903	Nonsense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	25503172	103269903	43094119	52	1833											
CSMD3	114788	hgsc.bcm.edu	37	chr8	114111175	114111175	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actggatcctctcattgttcCtccacaagcatcttcagctg	8	13	6	14	0	3	0	2	0	2	0	7	1	6	1	3	1	2	3	3	1	1	3			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr8:114111175C>A	ENST00000297405.5	-	5	971	c.727G>T	c.(727-729)Gga>Tga	p.G243*	CSMD3_ENST00000343508.3_Nonsense_Mutation_p.G203*|CSMD3_ENST00000352409.3_Nonsense_Mutation_p.G243*|CSMD3_ENST00000455883.2_Nonsense_Mutation_p.G243*|CSMD3_ENST00000519485.1_5'UTR	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	243	CUB 2. {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						CTCATTGTTCCTCCACAAGCA	0.383										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.G243X		Atlas-SNP	.											CSMD3_ENST00000343508,NS,carcinoma,+1,2	CSMD3	2325	2	0			c.G727T						PASS	.						110	96	101					8																	114111175		2203	4299	6502	SO:0001587	stop_gained	114788	exon5			TTGTTCCTCCACA	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.727G>T	8.37:g.114111175C>A	ENSP00000297405:p.Gly243*	57	0	0		80	40	0.5	NM_052900	Q96PZ3	Nonsense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	37	6.448676	0.97577	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000455883;ENST00000352409	.	.	.	5.1	5.1	0.69264	.	0.000000	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	.	18.8655	0.92290	0.0:1.0:0.0:0.0	.	.	.	.	X	203;243;243;243	.	ENSP00000297405:G243X	G	-	1	0	CSMD3	114180351	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.771000	0.85420	2.542000	0.85734	0.591000	0.81541	GGA	.	.	none		0.383	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	114111175	C	A	114111175	4	1	14	1	0	0	0	0	0	1	0	0	3948	690	24	4	10664	4	CSMD3	8	114111175	Nonsense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	10841272	114111175	32252847	53	1834											
TNFRSF11B	4982	hgsc.bcm.edu	37	chr8	119938922	119938922	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgtaaactttgtaggaacagCaaacctgaagaatgcctcct	14	9	8	10	1	0	2	0	1	0	1	1	3	1	3	3	1	5	3	3	1	7	3			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr8:119938922C>A	ENST00000297350.4	-	4	1006	c.628G>T	c.(628-630)Gct>Tct	p.A210S		NM_002546.3	NP_002537.3	O00300	TR11B_HUMAN	tumor necrosis factor receptor superfamily, member 11b	210	Death 1.				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)			GTAGGAACAGCAAACCTGAAG	0.413																																					p.A210S		Atlas-SNP	.											.	TNFRSF11B	87	.	0			c.G628T						PASS	.						102	91	95					8																	119938922		2203	4300	6503	SO:0001583	missense	4982	exon4			GAACAGCAAACCT	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.628G>T	8.37:g.119938922C>A	ENSP00000297350:p.Ala210Ser	96	0	0		106	5	0.0471698	NM_002546	B2R9A8|O60236|Q53FX6|Q9UHP4	Missense_Mutation	SNP	ENST00000297350.4	37	CCDS6326.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.599564	0.87055	.	.	ENSG00000164761	ENST00000297350	T	0.62639	0.01	5.6	5.6	0.85130	DEATH-like (1);	0.151580	0.44097	D	0.000494	T	0.71517	0.3349	L	0.44542	1.39	0.40998	D	0.984908	D	0.76494	0.999	D	0.63793	0.918	T	0.69499	-0.5129	9	.	.	.	-6.7848	17.8092	0.88610	0.0:1.0:0.0:0.0	.	210	O00300	TR11B_HUMAN	S	210	ENSP00000297350:A210S	.	A	-	1	0	TNFRSF11B	120008103	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	2.309000	0.43699	2.652000	0.90054	0.563000	0.77884	GCT	.	.	none		0.413	TNFRSF11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381220.1			A	119938922	C	A	119938922	3	1	14	1	0	0	0	0	1	0	0	0	16300	710	25	4	585	4	TNFRSF11B	8	119938922	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	5827747	119938922	26425100	54	1835											
MYC	4609	hgsc.bcm.edu	37	chr8	128750820	128750820	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagctggagatggtgaccgaGctgctgggaggagacatggt	9	7	18	7	1	0	3	0	1	0	2	0	7	0	4	1	5	3	3	1	5	0	0			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr8:128750820G>A	ENST00000259523.6	+	2	1517	c.312G>A	c.(310-312)gaG>gaA	p.E104E	MYC_ENST00000524013.1_Silent_p.E118E|MYC_ENST00000377970.2_Silent_p.E119E			P01106	MYC_HUMAN	v-myc avian myelocytomatosis viral oncogene homolog	104					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)	TGGTGACCGAGCTGCTGGGAG	0.602		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.E119E		Atlas-SNP	.		Dom	yes		8	8q24.12-q24.13	4609	v-myc myelocytomatosis viral oncogene homolog (avian)		"L, E"	.	MYC	168	.	0			c.G357A						PASS	.						52	52	52					8																	128750820		2203	4300	6503	SO:0001819	synonymous_variant	4609	exon2			GACCGAGCTGCTG		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.312G>A	8.37:g.128750820G>A		94	0	0	1567	122	60	0.491803	NM_002467	A8WFE7|P01107|Q14026	Silent	SNP	ENST00000259523.6	37																																																																																				.	.	none		0.602	MYC-002	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000250278.1			A	128750820	G	A	128750820	2	1	14	1	0	0	0	0	0	0	0	1	10025	962	34	2		2	MYC	8	128750820	Silent	SNP	G	TCGA-FF-8047-01A-11D-2210-10	8811898	128750820	17613202	55	1836											
C9orf150	286343	hgsc.bcm.edu	37	chr9	12775861	12775861	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcggggggagcggtggtggTggcggcggcggcggcggctg	1	5	27	8	7	0	0	0	0	0	0	0	1	0	1	0	12	2	1	0	12	0	0	rs3833707|rs139315731		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr9:12775861T>C	ENST00000319264.3	+	1	842	c.147T>C	c.(145-147)ggT>ggC	p.G49G	RP11-3L8.3_ENST00000417638.1_RNA|LURAP1L_ENST00000489107.1_3'UTR	NM_203403.1	NP_981948.1	Q8IV03	LUR1L_HUMAN	leucine rich adaptor protein 1-like	52	Gly-rich.		Missing.					p.G49_G50insGGG(2)									gcggtggtggtggcggcggcg	0.687																																					p.G49G		Atlas-SNP	.											C9orf150,NS,carcinoma,0,1	.	.	1	2	Insertion - In frame(2)	prostate(1)|central_nervous_system(1)	c.T147C						scavenged	.						4	5	5					9																	12775861		2038	3961	5999	SO:0001819	synonymous_variant	286343	exon1			TGGTGGTGGCGGC	AK095824	CCDS6473.1	9p22.3	2012-02-01	2012-02-01	2012-02-01	ENSG00000153714	ENSG00000153714			31452	protein-coding gene	gene with protein product	"similar to DNA segment, Chr 4, Brigham & Womens Genetics 0951 expressed"		"chromosome 9 open reading frame 150"	C9orf150		12766061	Standard	NM_203403		Approved	MGC46502, FLJ38505, bA3L8.2	uc003zkw.3	Q8IV03	OTTHUMG00000019557	ENST00000319264.3:c.147T>C	9.37:g.12775861T>C		12	2	0.166667		15	5	0.333333	NM_203403	Q5VZX7|Q8N923|Q8NCG2	Silent	SNP	ENST00000319264.3	37	CCDS6473.1																																																																																			.	.	none		0.687	LURAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051730.1	NM_203403		C	12775861	T	C	12775861	2	2	14	1	0	0	0	0	0	0	0	1	2464	1683	59	3		3	C9orf150	9	12775861	Silent	SNP	T	TCGA-FF-8047-01A-11D-2210-10		12775861	128437570	56	1837											
MPDZ	8777	hgsc.bcm.edu	37	chr9	13150599	13150599	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgaaaatgcccctcatcaCttctccattgcttagccgac	10	11	6	14	1	3	1	2	1	1	0	4	3	3	1	4	0	3	1	4	0	3	3			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr9:13150599C>T	ENST00000319217.7	-	25	3788	c.3541G>A	c.(3541-3543)Gtg>Atg	p.V1181M	MPDZ_ENST00000447879.1_Missense_Mutation_p.V1181M|MPDZ_ENST00000546205.1_Missense_Mutation_p.V1195M|MPDZ_ENST00000381022.2_Missense_Mutation_p.V1181M|MPDZ_ENST00000541718.1_Missense_Mutation_p.V1181M|MPDZ_ENST00000538841.1_Missense_Mutation_p.V73M|MPDZ_ENST00000536827.1_Missense_Mutation_p.V1181M|MPDZ_ENST00000381015.4_Missense_Mutation_p.V1181M	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	1181	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)		CCCCTCATCACTTCTCCATTG	0.458																																					p.V1181M		Atlas-SNP	.											.	MPDZ	324	.	0			c.G3541A						PASS	.						140	138	138					9																	13150599		1911	4137	6048	SO:0001583	missense	8777	exon25			TCATCACTTCTCC	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.3541G>A	9.37:g.13150599C>T	ENSP00000320006:p.Val1181Met	91	0	0		109	42	0.385321	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	37		.	.	.	.	.	.	.	.	.	.	C	15.87	2.960646	0.53400	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000545857;ENST00000538841;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205;ENST00000433359;ENST00000542239	T;T;T;T;T;T;T;T;T;T;T	0.47177	2.78;2.73;2.73;2.61;2.76;2.74;2.79;2.78;2.79;0.85;0.9	5.95	5.95	0.96441	.	0.000000	0.38272	N	0.001757	T	0.64450	0.2599	L	0.45352	1.415	0.80722	D	1	D;B;D;D;D	0.89917	0.992;0.057;0.99;1.0;0.99	D;B;P;D;P	0.91635	0.94;0.069;0.901;0.999;0.901	T	0.60596	-0.7232	10	0.48119	T	0.1	.	20.3854	0.98941	0.0:1.0:0.0:0.0	.	1181;73;1181;1131;1181	B7ZMI4;B7ZB24;O75970-3;E7EPZ1;O75970-2	.;.;.;.;.	M	1181;1181;1181;187;73;1181;1181;1181;1131;1195;73;73	ENSP00000320006:V1181M;ENSP00000439807:V1181M;ENSP00000370410:V1181M;ENSP00000444230:V187M;ENSP00000444717:V73M;ENSP00000444151:V1181M;ENSP00000415208:V1181M;ENSP00000370403:V1181M;ENSP00000446358:V1195M;ENSP00000389705:V73M;ENSP00000443672:V73M	ENSP00000320006:V1181M	V	-	1	0	MPDZ	13140599	1.000000	0.71417	1.000000	0.80357	0.004000	0.04260	2.324000	0.43831	2.825000	0.97269	0.655000	0.94253	GTG	.	.	none		0.458	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829		T	13150599	C	T	13150599	3	4	14	1	0	0	0	0	1	0	0	0	9731	565	20	2	2672	2	MPDZ	9	13150599	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	374738	13150599	128062832	57	1838											
CBWD3	445571	hgsc.bcm.edu	37	chr9	70871857	70871857	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcagtggcttctatgtttTgggttgatgctgaattaggg	6	16	15	4	0	1	2	0	2	1	0	1	2	1	2	0	3	2	5	0	3	3	6			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr9:70871857T>A	ENST00000360171.6	+	5	1002	c.451T>A	c.(451-453)Tgg>Agg	p.W151R	CBWD3_ENST00000377342.5_Intron	NM_201453.2	NP_958861.2	Q5JTY5	CBWD3_HUMAN	COBW domain containing 3	151							ATP binding (GO:0005524)			kidney(1)|large_intestine(1)|lung(2)|prostate(1)	5				all cancers(8;0.00136)|Epithelial(8;0.0288)|GBM - Glioblastoma multiforme(74;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		TTCTATGTTTTGGGTTGATGC	0.269																																					p.W151R		Atlas-SNP	.											.	CBWD3	10	.	0			c.T451A						PASS	.						25	31	29					9																	70871857		2189	4258	6447	SO:0001583	missense	445571	exon5			ATGTTTTGGGTTG	BC069006	CCDS35038.1, CCDS35038.2	9q13	2014-05-06			ENSG00000196873	ENSG00000196873			18519	protein-coding gene	gene with protein product		611080				15233989, 12421752	Standard	XM_005277637		Approved	bA561O23.1	uc004aga.4	Q5JTY5	OTTHUMG00000184383	ENST00000360171.6:c.451T>A	9.37:g.70871857T>A	ENSP00000353295:p.Trp151Arg	399	0	0		484	112	0.231405	NM_201453	B4DNG9|Q6VB91	Missense_Mutation	SNP	ENST00000360171.6	37	CCDS35038.1	.	.	.	.	.	.	.	.	.	.	.	17.24	3.338396	0.60963	.	.	ENSG00000196873	ENST00000360171;ENST00000447896;ENST00000455061;ENST00000455820;ENST00000377344	T	0.41065	1.01	3.38	3.38	0.38709	Cobalamin (vitamin B12) biosynthesis CobW-like (1);	0.000000	0.85682	D	0.000000	T	0.61578	0.2358	M	0.75264	2.295	0.80722	D	1	D;P	0.89917	1.0;0.815	D;P	0.87578	0.998;0.733	T	0.65685	-0.6108	10	0.87932	D	0	-30.7068	11.0695	0.47995	0.0:0.0:0.0:1.0	.	151;151	E7ETY5;Q5JTY5	.;CBWD3_HUMAN	R	151;151;151;151;115	ENSP00000353295:W151R	ENSP00000353295:W151R	W	+	1	0	CBWD3	70061677	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.201000	0.77847	1.311000	0.45024	0.254000	0.18369	TGG	.	.	none		0.269	CBWD3-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052526.1	NM_201453		A	70871857	T	A	70871857	3	1	14	1	0	0	0	0	1	0	0	0	2716	1812	63	5	1717	5	CBWD3	9	70871857	Missense_Mutation	SNP	T	TCGA-FF-8047-01A-11D-2210-10	57721258	70871857	70341574	58	1839											
MED27	9442	hgsc.bcm.edu	37	chr9	134736013	134736013	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctgcagaaacttcccgcagCgctggcacggggcctggaac	8	5	13	15	3	0	1	0	0	0	1	1	2	1	2	3	4	4	4	3	4	2	1			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr9:134736013C>T	ENST00000292035.5	-	8	911	c.848G>A	c.(847-849)cGc>cAc	p.R283H	MED27_ENST00000357028.2_Missense_Mutation_p.R247H	NM_004269.3	NP_004260.2	Q6P2C8	MED27_HUMAN	mediator complex subunit 27	283					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)		CTTCCCGCAGCGCTGGCACGG	0.562																																					p.R283H	Colon(41;784 923 6932 42329 52483)	Atlas-SNP	.											.	MED27	37	.	0			c.G848A						PASS	.						33	32	32					9																	134736013		2203	4300	6503	SO:0001583	missense	9442	exon8			CCGCAGCGCTGGC	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.848G>A	9.37:g.134736013C>T	ENSP00000292035:p.Arg283His	141	0	0		121	9	0.0743802	NM_004269	O95401|Q4F964|Q5VTA4|Q5VTA5|Q9BU57|Q9NYR4|V9GYV9	Missense_Mutation	SNP	ENST00000292035.5	37	CCDS6945.1	.	.	.	.	.	.	.	.	.	.	C	33	5.219164	0.95104	.	.	ENSG00000160563	ENST00000292035;ENST00000357028;ENST00000372184	.	.	.	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.78572	0.4304	M	0.73598	2.24	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74674	0.984;0.96	T	0.80600	-0.1310	9	0.62326	D	0.03	0.0762	16.105	0.81213	0.0:1.0:0.0:0.0	.	247;283	Q6P2C8-2;Q6P2C8	.;MED27_HUMAN	H	283;209;247	.	ENSP00000292035:R283H	R	-	2	0	MED27	133725834	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	7.611000	0.82962	2.472000	0.83506	0.655000	0.94253	CGC	.	.	none		0.562	MED27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054770.2	NM_004269		T	134736013	C	T	134736013	3	4	14	1	0	0	0	0	1	0	0	0	9454	768	27	1	91	1	MED27	9	134736013	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	63864156	134736013	6477418	59	1840											
MPP7	143098	hgsc.bcm.edu	37	chr10	28527517	28527517	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagtgtcactcccagatcccGttgacaaagctggcatgatg	10	9	10	12	1	1	3	1	2	0	1	3	3	3	3	2	1	1	3	2	1	1	1			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr10:28527517G>A	ENST00000375732.1	-	2	276	c.17C>T	c.(16-18)aCg>aTg	p.T6M	MPP7_ENST00000375719.3_Missense_Mutation_p.T6M|MPP7_ENST00000445954.2_De_novo_Start_OutOfFrame|MPP7_ENST00000481244.1_5'UTR|MPP7_ENST00000540098.1_Missense_Mutation_p.T6M|MPP7_ENST00000337532.5_Missense_Mutation_p.T6M			Q5T2T1	MPP7_HUMAN	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	6					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						CCCAGATCCCGTTGACAAAGC	0.512																																					p.T6M		Atlas-SNP	.											MPP7,rectum,carcinoma,+1,2	MPP7	60	2	0			c.C17T						PASS	.						147	117	128					10																	28527517		2203	4300	6503	SO:0001583	missense	143098	exon4			GATCCCGTTGACA	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.17C>T	10.37:g.28527517G>A	ENSP00000364884:p.Thr6Met	49	0	0		53	24	0.45283	NM_173496	B2RCC9|B4DWL9|B5MDZ3|D3DRW3|Q5T2T0|Q8IY28	Missense_Mutation	SNP	ENST00000375732.1	37	CCDS7158.1	.	.	.	.	.	.	.	.	.	.	G	14.76	2.632038	0.46944	.	.	ENSG00000150054	ENST00000375732;ENST00000337532;ENST00000540098;ENST00000375719;ENST00000441595	T;T;T;T;T	0.33216	2.7;2.7;2.7;2.7;1.42	6.07	5.16	0.70880	.	0.115089	0.64402	N	0.000016	T	0.32496	0.0831	L	0.36672	1.1	0.80722	D	1	P	0.39535	0.677	P	0.44732	0.459	T	0.08889	-1.0700	10	0.56958	D	0.05	.	13.615	0.62103	0.0713:0.0:0.9287:0.0	.	6	Q5T2T1	MPP7_HUMAN	M	6	ENSP00000364884:T6M;ENSP00000337907:T6M;ENSP00000438693:T6M;ENSP00000364871:T6M;ENSP00000398319:T6M	ENSP00000337907:T6M	T	-	2	0	MPP7	28567523	0.998000	0.40836	0.049000	0.19019	0.259000	0.26198	6.263000	0.72521	1.571000	0.49722	0.655000	0.94253	ACG	.	.	none		0.512	MPP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047345.1	NM_173496		A	28527517	G	A	28527517	3	1	14	1	0	0	0	0	1	0	0	0	9748	1145	40	1	1777	1	MPP7	10	28527517	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10		28527517	107007230	60	1841											
ABLIM1	3983	hgsc.bcm.edu	37	chr10	116331143	116331143	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctcccattgaatgtgactcGgtctccgggtggaaacgggc	7	10	13	11	3	2	2	0	2	2	0	5	3	2	3	2	4	1	0	2	4	2	1			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr10:116331143G>A	ENST00000277895.5	-	4	683	c.586C>T	c.(586-588)Cga>Tga	p.R196*	ABLIM1_ENST00000533213.2_Nonsense_Mutation_p.R136*|ABLIM1_ENST00000369252.4_Nonsense_Mutation_p.R136*	NM_002313.5	NP_002304.3	O14639	ABLM1_HUMAN	actin binding LIM protein 1	196	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				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)		AATGTGACTCGGTCTCCGGGT	0.537																																					p.R196X		Atlas-SNP	.											.	ABLIM1	131	.	0			c.C586T						PASS	.						121	118	119					10																	116331143		2203	4300	6503	SO:0001587	stop_gained	3983	exon4			TGACTCGGTCTCC	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.586C>T	10.37:g.116331143G>A	ENSP00000277895:p.Arg196*	85	0	0		106	52	0.490566	NM_002313	A6NI16|A6NJ06|A8MXA9|B3KVH2|Q15039|Q5JVV1|Q5JVV2|Q5T6N2|Q5T6N3|Q5T6N5|Q68CQ9|Q9BUP1	Nonsense_Mutation	SNP	ENST00000277895.5	37	CCDS7590.1	.	.	.	.	.	.	.	.	.	.	G	39	7.324017	0.98210	.	.	ENSG00000099204	ENST00000336585;ENST00000369252;ENST00000369267;ENST00000533213;ENST00000369262;ENST00000369263;ENST00000369256;ENST00000369260;ENST00000277895	.	.	.	5.97	5.02	0.67125	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.8323	0.63389	0.0:0.0:0.7325:0.2675	.	.	.	.	X	196;136;136;136;196;120;120;120;196	.	ENSP00000277895:R196X	R	-	1	2	ABLIM1	116321133	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.205000	0.58466	2.836000	0.97738	0.655000	0.94253	CGA	.	.	none		0.537	ABLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050469.3			A	116331143	G	A	116331143	4	1	14	1	0	0	0	0	0	1	0	0	94	1124	39	1	1914	1	ABLIM1	10	116331143	Nonsense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	87803626	116331143	19203604	61	1842											
HSPA12A	259217	hgsc.bcm.edu	37	chr10	118464772	118464772	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aatgactgctgttctgagacGttggagtcagtgtcgttctg	7	14	13	7	2	3	2	1	2	2	1	4	4	3	3	0	1	1	4	0	1	1	3			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr10:118464772G>A	ENST00000369209.3	-	3	248	c.144C>T	c.(142-144)aaC>aaT	p.N48N		NM_025015.2	NP_079291.2	O43301	HS12A_HUMAN	heat shock 70kDa protein 12A	48						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)		GTTCTGAGACGTTGGAGTCAG	0.582																																					p.N48N		Atlas-SNP	.											.	HSPA12A	81	.	0			c.C144T						PASS	.						177	188	185					10																	118464772		2150	4269	6419	SO:0001819	synonymous_variant	259217	exon3			TGAGACGTTGGAG	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.144C>T	10.37:g.118464772G>A		103	0	0		119	45	0.378151	NM_025015		Silent	SNP	ENST00000369209.3	37	CCDS41569.1																																																																																			.	.	none		0.582	HSPA12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050530.1	NM_025015		A	118464772	G	A	118464772	2	1	14	1	0	0	0	0	0	0	0	1	7413	1136	40	1		1	HSPA12A	10	118464772	Silent	SNP	G	TCGA-FF-8047-01A-11D-2210-10	2133629	118464772	17069975	62	1843											
KRTAP5-4	387267	hgsc.bcm.edu	37	chr11	1643255	1643255	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccccacagccagagccacaGcccccacagccggagccaca	11	0	8	22	1	0	1	0	0	0	1	0	2	0	2	8	1	5	0	8	1	0	0			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:1643255G>A	ENST00000399682.1	-	1	113	c.69C>T	c.(67-69)ggC>ggT	p.G23G		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0						keratin filament (GO:0045095)		p.G23G(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)		cagagccacagcccccacagc	0.687																																					p.G23G		Atlas-SNP	.											KRTAP5-4,NS,carcinoma,0,1	KRTAP5-4	78	1	1	Substitution - coding silent(1)	kidney(1)	c.C69T						scavenged	.						4	8	7					11																	1643255		646	1526	2172	SO:0001819	synonymous_variant	387267	exon1			GCCACAGCCCCCA	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.69C>T	11.37:g.1643255G>A		124	2	0.016129		165	8	0.0484848	NM_001012709		Silent	SNP	ENST00000399682.1	37																																																																																				.	.	none		0.687	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709		A	1643255	G	A	1643255	2	1	14	1	0	0	0	0	0	0	0	1	8572	958	34	2		2	KRTAP5-4	11	1643255	Silent	SNP	G	TCGA-FF-8047-01A-11D-2210-10		1643255	133363261	63	1844											
OR52R1	119695	hgsc.bcm.edu	37	chr11	4825192	4825192	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gtttgatcacgaccgatgggGtcaggatgctagagtgtcgg	8	10	16	7	3	2	2	2	1	0	1	3	5	2	3	1	4	1	2	1	4	1	2			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:4825192G>A	ENST00000356069.2	-	1	418	c.419C>T	c.(418-420)aCc>aTc	p.T140I	MMP26_ENST00000380390.1_Intron|OR52R1_ENST00000380382.1_Missense_Mutation_p.T219I|MMP26_ENST00000477339.1_Intron	NM_001005177.3	NP_001005177.3	Q8NGF1	O52R1_HUMAN	olfactory receptor, family 52, subfamily R, 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)			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)		GACCGATGGGGTCAGGATGCT	0.567																																					p.T140I		Atlas-SNP	.											.	OR52R1	81	.	0			c.C419T						PASS	.						105	93	97					11																	4825192		2201	4298	6499	SO:0001583	missense	119695	exon1			GATGGGGTCAGGA	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.419C>T	11.37:g.4825192G>A	ENSP00000348368:p.Thr140Ile	52	0	0		56	27	0.482143	NM_001005177	Q6IFI0	Missense_Mutation	SNP	ENST00000356069.2	37	CCDS31360.2	.	.	.	.	.	.	.	.	.	.	G	14.60	2.582644	0.46006	.	.	ENSG00000176937	ENST00000356069;ENST00000380382	T;T	0.00381	7.63;7.63	5.42	5.42	0.78866	GPCR, rhodopsin-like superfamily (1);	0.133368	0.33670	N	0.004668	T	0.01661	0.0053	H	0.97611	4.04	0.32673	N	0.51654	D	0.60160	0.987	P	0.57776	0.827	T	0.01961	-1.1239	10	0.87932	D	0	.	17.9523	0.89057	0.0:0.0:1.0:0.0	.	140	Q8NGF1	O52R1_HUMAN	I	140;219	ENSP00000348368:T140I;ENSP00000369742:T219I	ENSP00000348368:T140I	T	-	2	0	OR52R1	4781768	0.021000	0.18746	0.396000	0.26296	0.137000	0.21094	1.265000	0.33027	2.826000	0.97356	0.650000	0.86243	ACC	.	.	none		0.567	OR52R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142183.1	NM_001005177		A	4825192	G	A	4825192	3	1	14	1	0	0	0	0	1	0	0	0	11140	1261	44	2	531	2	OR52R1	11	4825192	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	3181937	4825192	130181324	64	1845											
COPB1	1315	hgsc.bcm.edu	37	chr11	14504615	14504615	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcaggatgctcttttaatTctatcaagcgatccaaaact	13	12	7	9	1	3	0	1	0	2	0	4	3	4	1	1	1	4	2	1	1	5	4			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:14504615T>C	ENST00000249923.3	-	8	1220	c.920A>G	c.(919-921)gAa>gGa	p.E307G	COPB1_ENST00000439561.2_Missense_Mutation_p.E307G	NM_016451.4	NP_057535.1	P53618	COPB_HUMAN	coatomer protein complex, subunit beta 1	307					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						CTCTTTTAATTCTATCAAGCG	0.318																																					p.E307G		Atlas-SNP	.											.	COPB1	81	.	0			c.A920G						PASS	.						82	77	79					11																	14504615		2199	4293	6492	SO:0001583	missense	1315	exon8			TTTAATTCTATCA	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.920A>G	11.37:g.14504615T>C	ENSP00000249923:p.Glu307Gly	53	0	0		40	4	0.1	NM_001144062	D3DQX0|Q6GTT7|Q9NTK2|Q9UNW7	Missense_Mutation	SNP	ENST00000249923.3	37	CCDS7815.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.011321	0.75046	.	.	ENSG00000129083	ENST00000249923;ENST00000439561;ENST00000534234	T;T;T	0.26957	1.7;1.7;1.7	5.56	5.56	0.83823	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.30008	0.0751	L	0.56769	1.78	0.80722	D	1	B	0.20459	0.045	B	0.26614	0.071	T	0.04053	-1.0981	10	0.33940	T	0.23	.	15.7137	0.77652	0.0:0.0:0.0:1.0	.	307	P53618	COPB_HUMAN	G	307	ENSP00000249923:E307G;ENSP00000397873:E307G;ENSP00000436383:E307G	ENSP00000249923:E307G	E	-	2	0	COPB1	14461191	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.018000	0.88722	2.118000	0.64928	0.482000	0.46254	GAA	.	.	none		0.318	COPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386410.1	NM_016451		C	14504615	T	C	14504615	3	2	14	1	0	0	0	0	1	0	0	0	3730	1783	62	3	2001	3	COPB1	11	14504615	Missense_Mutation	SNP	T	TCGA-FF-8047-01A-11D-2210-10	9679423	14504615	120501901	65	1846											
KCNC1	3746	hgsc.bcm.edu	37	chr11	17793670	17793670	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acgctccgagccagcaccaaCgagttcctgctgctcatcat	9	8	8	16	3	2	0	2	0	0	0	4	2	4	0	4	0	5	5	4	0	1	1			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:17793670C>T	ENST00000379472.3	+	2	1059	c.1029C>T	c.(1027-1029)aaC>aaT	p.N343N	KCNC1_ENST00000265969.6_Silent_p.N343N	NM_004976.4	NP_004967.1	P48547	KCNC1_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 1	343					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)	CCAGCACCAACGAGTTCCTGC	0.617																																					p.N343N		Atlas-SNP	.											.	KCNC1	149	.	0			c.C1029T						PASS	.						37	35	36					11																	17793670		2200	4293	6493	SO:0001819	synonymous_variant	3746	exon2			CACCAACGAGTTC	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.1029C>T	11.37:g.17793670C>T		51	0	0		64	31	0.484375	NM_004976	K4DI87	Silent	SNP	ENST00000379472.3	37	CCDS7827.1																																																																																			.	.	none		0.617	KCNC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389389.1	NM_004976		T	17793670	C	T	17793670	2	4	14	1	0	0	0	0	0	0	0	1	8023	535	19	1		1	KCNC1	11	17793670	Silent	SNP	C	TCGA-FF-8047-01A-11D-2210-10	3289055	17793670	117212846	66	1847											
OR4C6	219432	hgsc.bcm.edu	37	chr11	55433333	55433333	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtcttacagctctaaagggCggcacaaagccctctctacc	11	8	8	14	1	3	0	0	0	3	0	4	0	3	0	2	2	4	2	2	2	5	3	rs140747151	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:55433333C>T	ENST00000314259.3	+	1	720	c.691C>T	c.(691-693)Cgg>Tgg	p.R231W		NM_001004704.1	NP_001004704.1	Q8NH72	OR4C6_HUMAN	olfactory receptor, family 4, subfamily C, member 6	231						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R231W(1)		breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|lung(49)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	71						CTCTAAAGGGCGGCACAAAGC	0.502													c|||	2	0.000399361	0.0	0.0	5008	,	,		18006	0.0		0.002	False		,,,				2504	0.0				p.R231W		Atlas-SNP	.											OR4C6,middle_lobe,carcinoma,0,4	OR4C6	114	4	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C691T						PASS	.	C	TRP/ARG	0,4400		0,0,2200	132	126	128		691	-8.1	0	11	dbSNP_134	128	3,8589	3.0+/-9.4	0,3,4293	yes	missense	OR4C6	NM_001004704.1	101	0,3,6493	TT,TC,CC		0.0349,0.0,0.0231	benign	231/310	55433333	3,12989	2200	4296	6496	SO:0001583	missense	219432	exon1			AAAGGGCGGCACA	CR593785	CCDS31506.1	11q11	2012-08-09			ENSG00000181903	ENSG00000181903		"GPCR / Class A : Olfactory receptors"	14743	protein-coding gene	gene with protein product							Standard	NM_001004704		Approved		uc010rik.2	Q8NH72	OTTHUMG00000166800	ENST00000314259.3:c.691C>T	11.37:g.55433333C>T	ENSP00000324769:p.Arg231Trp	109	0	0		172	68	0.395349	NM_001004704	B2RP11|Q6IFD2	Missense_Mutation	SNP	ENST00000314259.3	37	CCDS31506.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	5.384	0.256036	0.10185	0.0	3.49E-4	ENSG00000181903	ENST00000314259	T	0.00335	8.06	4.07	-8.14	0.01069	GPCR, rhodopsin-like superfamily (1);	0.754623	0.10587	N	0.657205	T	0.00328	0.0010	M	0.87971	2.92	0.09310	N	1	B	0.22146	0.065	B	0.26693	0.072	T	0.27773	-1.0064	10	0.72032	D	0.01	.	6.9124	0.24342	0.6124:0.1383:0.0:0.2493	.	231	Q8NH72	OR4C6_HUMAN	W	231	ENSP00000324769:R231W	ENSP00000324769:R231W	R	+	1	2	OR4C6	55189909	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-4.913000	0.00170	-1.249000	0.02500	0.543000	0.68304	CGG	C|0.999;T|0.001	0.001	strong		0.502	OR4C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391504.1	NM_001004704		T	55433333	C	T	55433333	3	4	14	1	0	0	0	0	1	0	0	0	11061	759	27	1	693	1	OR4C6	11	55433333	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	37639663	55433333	79573183	67	1848											
OR4C6	219432	hgsc.bcm.edu	37	chr11	55433434	55433434	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcctgtggtcactcacccCatagacaaggcaatggctgt	10	8	11	12	0	2	1	2	0	0	1	2	1	2	1	3	4	0	2	3	4	3	1			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:55433434C>A	ENST00000314259.3	+	1	821	c.792C>A	c.(790-792)ccC>ccA	p.P264P		NM_001004704.1	NP_001004704.1	Q8NH72	OR4C6_HUMAN	olfactory receptor, family 4, subfamily C, member 6	264						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P264P(1)		breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|lung(49)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	71						TCACTCACCCCATAGACAAGG	0.483																																					p.P264P		Atlas-SNP	.											OR4C6,NS,carcinoma,0,1	OR4C6	114	1	1	Substitution - coding silent(1)	lung(1)	c.C792A						PASS	.						105	103	104					11																	55433434		2200	4296	6496	SO:0001819	synonymous_variant	219432	exon1			TCACCCCATAGAC	CR593785	CCDS31506.1	11q11	2012-08-09			ENSG00000181903	ENSG00000181903		"GPCR / Class A : Olfactory receptors"	14743	protein-coding gene	gene with protein product							Standard	NM_001004704		Approved		uc010rik.2	Q8NH72	OTTHUMG00000166800	ENST00000314259.3:c.792C>A	11.37:g.55433434C>A		106	0	0		146	64	0.438356	NM_001004704	B2RP11|Q6IFD2	Silent	SNP	ENST00000314259.3	37	CCDS31506.1																																																																																			.	.	none		0.483	OR4C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391504.1	NM_001004704		A	55433434	C	A	55433434	2	1	14	1	0	0	0	0	0	0	0	1	11061	581	21	4		4	OR4C6	11	55433434	Silent	SNP	C	TCGA-FF-8047-01A-11D-2210-10	101	55433434	79573082	68	1849											
SPTBN2	6712	hgsc.bcm.edu	37	chr11	66472275	66472275	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tccagggtgggcacccggctCtgcacctcgggcgtgcggct	3	7	16	15	4	1	0	0	0	1	0	3	0	2	0	3	5	2	4	3	5	0	0			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:66472275C>T	ENST00000533211.1	-	15	2803	c.2472G>A	c.(2470-2472)caG>caA	p.Q824Q	SPTBN2_ENST00000529997.1_Silent_p.Q824Q|SPTBN2_ENST00000309996.2_Silent_p.Q824Q			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	824					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						GCACCCGGCTCTGCACCTCGG	0.716																																					p.Q824Q		Atlas-SNP	.											SPTBN2,right_lower_lobe,carcinoma,0,1	SPTBN2	188	1	0			c.G2472A						scavenged	.						13	14	14					11																	66472275		2184	4272	6456	SO:0001819	synonymous_variant	6712	exon14			CCGGCTCTGCACC	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.2472G>A	11.37:g.66472275C>T		11	0	0		20	2	0.1	NM_006946	O14872|O14873	Silent	SNP	ENST00000533211.1	37	CCDS8150.1																																																																																			.	.	none		0.716	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946		T	66472275	C	T	66472275	2	4	14	1	0	0	0	0	0	0	0	1	15135	912	32	2		2	SPTBN2	11	66472275	Silent	SNP	C	TCGA-FF-8047-01A-11D-2210-10	11038841	66472275	68534241	69	1850											
KIAA1377	57562	hgsc.bcm.edu	37	chr11	101834522	101834522	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtttgtgaagaaagttatcCgtctgtgactctaagaactg	11	14	10	6	1	2	4	0	2	2	2	3	4	3	4	1	0	1	2	1	0	5	3	rs370774279		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:101834522C>T	ENST00000263468.8	+	6	3026	c.2756C>T	c.(2755-2757)cCg>cTg	p.P919L	KIAA1377_ENST00000537689.1_Missense_Mutation_p.P720L	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	919										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)		GAAAGTTATCCGTCTGTGACT	0.403																																					p.P919L		Atlas-SNP	.											KIAA1377,NS,carcinoma,-1,2	KIAA1377	111	2	0			c.C2756T						PASS	.	C	LEU/PRO	0,4406		0,0,2203	88	94	92		2756	0.1	0	11		92	1,8597	1.2+/-3.3	0,1,4298	no	missense	KIAA1377	NM_020802.2	98	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	benign	919/1118	101834522	1,13003	2203	4299	6502	SO:0001583	missense	57562	exon6			GTTATCCGTCTGT	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.2756C>T	11.37:g.101834522C>T	ENSP00000263468:p.Pro919Leu	133	0	0		134	65	0.485075	NM_020802	Q4G0U6	Missense_Mutation	SNP	ENST00000263468.8	37	CCDS31658.1	.	.	.	.	.	.	.	.	.	.	C	4.369	0.067932	0.08436	0.0	1.16E-4	ENSG00000110318	ENST00000263468;ENST00000537689	T;T	0.06068	3.35;3.35	5.51	0.134	0.14771	.	0.796339	0.11112	N	0.598499	T	0.05868	0.0153	L	0.47716	1.5	0.09310	N	1	B	0.32425	0.371	B	0.19148	0.024	T	0.33879	-0.9851	10	0.08599	T	0.76	3.4773	16.234	0.82361	0.3611:0.6389:0.0:0.0	.	919	Q9P2H0	K1377_HUMAN	L	919;720	ENSP00000263468:P919L;ENSP00000443184:P720L	ENSP00000263468:P919L	P	+	2	0	KIAA1377	101339732	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	0.508000	0.22692	0.123000	0.18342	-0.266000	0.10368	CCG	.	.	weak		0.403	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802		T	101834522	C	T	101834522	3	4	14	1	0	0	0	0	1	0	0	0	8236	652	23	1	2778	1	KIAA1377	11	101834522	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	35362247	101834522	33171994	70	1851											
C11orf88	399949	hgsc.bcm.edu	37	chr11	111385703	111385703	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agacagcagtcagcgtctgcCggtggcgcggcccaggagga	8	4	17	12	4	2	1	1	0	1	1	2	3	2	3	2	5	3	1	2	5	0	0			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:111385703C>T	ENST00000375618.4	+	1	194	c.194C>T	c.(193-195)cCg>cTg	p.P65L	C11orf88_ENST00000332814.6_Missense_Mutation_p.P65L|MIR34B_ENST00000385076.1_RNA|BTG4_ENST00000356018.2_5'Flank|C11orf88_ENST00000529167.1_Missense_Mutation_p.P65L|MIR34C_ENST00000384831.1_RNA|RP11-794P6.6_ENST00000530283.1_RNA|BTG4_ENST00000525791.1_5'Flank	NM_001100388.1	NP_001093858.1	Q6PI97	CK088_HUMAN	chromosome 11 open reading frame 88	65										endometrium(1)|large_intestine(3)|lung(2)	6						CAGCGTCTGCCGGTGGCGCGG	0.597											OREG0021329	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P65L		Atlas-SNP	.											.	C11orf88	37	.	0			c.C194T						PASS	.						40	47	44					11																	111385703		2153	4278	6431	SO:0001583	missense	399949	exon1			GTCTGCCGGTGGC	BC039505, AK128145	CCDS41712.1, CCDS41713.1	11q23.1	2012-08-10			ENSG00000183644	ENSG00000183644			25061	protein-coding gene	gene with protein product	"hypothetical gene supported by BC039505"					12477932	Standard	NM_001100388		Approved	FLJ46266	uc009yyd.3	Q6PI97	OTTHUMG00000166720	ENST00000375618.4:c.194C>T	11.37:g.111385703C>T	ENSP00000364768:p.Pro65Leu	50	0	0	1434	59	28	0.474576	NM_001100388	E9PAN0|Q6ZRL3	Missense_Mutation	SNP	ENST00000375618.4	37	CCDS41713.1	.	.	.	.	.	.	.	.	.	.	C	13.79	2.342184	0.41498	.	.	ENSG00000183644	ENST00000375618;ENST00000529167;ENST00000332814	.	.	.	5.09	0.987	0.19790	.	0.159222	0.40144	N	0.001171	T	0.72598	0.3480	M	0.66939	2.045	0.44677	D	0.997668	D;D	0.76494	0.999;0.996	P;P	0.60886	0.88;0.866	T	0.74850	-0.3524	9	0.62326	D	0.03	-1.5825	14.7899	0.69833	0.0:0.4087:0.5913:0.0	.	65;65	E9PAN0;Q6PI97	.;CK088_HUMAN	L	65	.	ENSP00000333845:P65L	P	+	2	0	C11orf88	110890913	0.097000	0.21791	0.804000	0.32291	0.030000	0.12068	0.229000	0.17833	0.033000	0.15463	-0.282000	0.10007	CCG	.	.	none		0.597	C11orf88-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391181.1	NM_001100388		T	111385703	C	T	111385703	3	4	14	1	0	0	0	0	1	0	0	0	1672	652	23	1	196	1	C11orf88	11	111385703	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	9551181	111385703	23620813	71	1852											
DSCAML1	57453	hgsc.bcm.edu	37	chr11	117374656	117374656	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtcctcttctaggacgtggcGgatcagcagcgagctgttgg	6	10	15	10	3	3	0	1	0	2	0	4	3	4	2	1	4	3	3	1	4	1	3			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:117374656G>A	ENST00000321322.6	-	11	2444	c.2443C>T	c.(2443-2445)Cgc>Tgc	p.R815C	DSCAML1_ENST00000527706.1_Missense_Mutation_p.R545C	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	755	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)		AGGACGTGGCGGATCAGCAGC	0.607																																					p.R815C		Atlas-SNP	.											DSCAML1,NS,carcinoma,+1,1	DSCAML1	286	1	0			c.C2443T						PASS	.						110	91	97					11																	117374656		2201	4296	6497	SO:0001583	missense	57453	exon11			CGTGGCGGATCAG		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.2443C>T	11.37:g.117374656G>A	ENSP00000315465:p.Arg815Cys	112	0	0		134	65	0.485075	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	37	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.192049	0.78902	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.68479	-0.33;-0.33	4.29	4.29	0.51040	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.82944	0.5147	M	0.84433	2.695	0.80722	D	1	D	0.89917	1.0	D	0.70487	0.969	D	0.86461	0.1779	9	0.66056	D	0.02	.	16.9369	0.86205	0.0:0.0:1.0:0.0	.	755	Q8TD84	DSCL1_HUMAN	C	545;815;522	ENSP00000434335:R545C;ENSP00000315465:R815C	ENSP00000315465:R815C	R	-	1	0	DSCAML1	116879866	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.560000	0.53763	2.237000	0.73441	0.462000	0.41574	CGC	.	.	none		0.607	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		A	117374656	G	A	117374656	3	1	14	1	0	0	0	0	1	0	0	0	4771	1116	39	1	3990	1	DSCAML1	11	117374656	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	5988953	117374656	17631860	72	1853											
MLL	4297	hgsc.bcm.edu	37	chr11	118371761	118371761	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcgctgtgtatatacatgcaAgatagtggagtgccgtcctc	9	11	12	9	2	0	1	0	0	0	1	2	2	1	2	2	1	3	3	2	1	5	4			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:118371761A>G	ENST00000389506.5	+	25	6209	c.6209A>G	c.(6208-6210)aAg>aGg	p.K2070R	KMT2A_ENST00000354520.4_Missense_Mutation_p.K2032R|KMT2A_ENST00000534358.1_Missense_Mutation_p.K2073R			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	2070	FYR N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00875}.				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)										TATACATGCAAGATAGTGGAG	0.468																																					p.K2073R		Atlas-SNP	.											.	MLL	548	.	0			c.A6218G						PASS	.						150	118	129					11																	118371761		2200	4296	6496	SO:0001583	missense	4297	exon25			CATGCAAGATAGT	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.6209A>G	11.37:g.118371761A>G	ENSP00000374157:p.Lys2070Arg	112	0	0		121	25	0.206612	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	37	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	A	17.83	3.485424	0.63962	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	T;T;T	0.77358	-1.09;-1.09;-1.09	5.83	5.83	0.93111	FY-rich, N-terminal (1);FY-rich, N-terminal subgroup (1);	0.047613	0.85682	D	0.000000	T	0.56124	0.1964	N	0.02842	-0.48	0.53005	D	0.999968	B;B	0.30326	0.276;0.219	B;B	0.35278	0.199;0.138	T	0.60383	-0.7274	10	0.02654	T	1	.	16.2011	0.82078	1.0:0.0:0.0:0.0	.	2073;2070	E9PQG7;Q03164	.;MLL1_HUMAN	R	2073;2070;2032;980	ENSP00000436786:K2073R;ENSP00000374157:K2070R;ENSP00000346516:K2032R	ENSP00000346516:K2032R	K	+	2	0	MLL	117876971	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	6.135000	0.71696	2.219000	0.72066	0.482000	0.46254	AAG	.	.	none		0.468	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933		G	118371761	A	G	118371761	3	3	14	1	0	0	0	0	1	0	0	0	9629	72	3	3	6307	3	MLL	11	118371761	Missense_Mutation	SNP	A	TCGA-FF-8047-01A-11D-2210-10	997105	118371761	16634755	73	1854											
SORL1	6653	hgsc.bcm.edu	37	chr11	121429298	121429298	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttctgtccccattttcgctAgggtgatgttctggacagac	6	14	11	10	1	2	2	0	1	2	1	4	3	3	3	2	2	0	3	2	2	1	5			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:121429298A>G	ENST00000260197.7	+	20	2792		c.e20-1			NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing						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)		CATTTTCGCTAGGGTGATGTT	0.473																																					.		Atlas-SNP	.											.	SORL1	218	.	0			c.2664-2A>G						PASS	.						168	163	164					11																	121429298		2203	4299	6502	SO:0001630	splice_region_variant	6653	exon20			TTCGCTAGGGTGA	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.2664-1A>G	11.37:g.121429298A>G		90	0	0		101	37	0.366337	NM_003105	B2RNX7|Q92856	Splice_Site	SNP	ENST00000260197.7	37	CCDS8436.1	.	.	.	.	.	.	.	.	.	.	A	16.57	3.160296	0.57368	.	.	ENSG00000137642	ENST00000260197	.	.	.	5.53	5.53	0.82687	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6637	0.77209	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SORL1	120934508	1.000000	0.71417	0.337000	0.25536	0.644000	0.38419	9.087000	0.94110	2.105000	0.64084	0.533000	0.62120	.	.	.	none		0.473	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105	Intron	G	121429298	A	G	121429298	5	3	14	1	0	0	0	0	0	0	1	0	14949	434	15	3	2740	3	SORL1	11	121429298	Splice_Site	SNP	A	TCGA-FF-8047-01A-11D-2210-10	3057537	121429298	13577218	74	1855											
GLB1L3	112937	hgsc.bcm.edu	37	chr11	134188798	134188798	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtttgagaagatgatgagtGgctcagatatcaaatctaca	14	12	10	5	0	3	5	2	3	1	3	3	6	3	5	0	1	1	2	0	1	4	3			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:134188798G>A	ENST00000431683.2	+	20	1924	c.1924G>A	c.(1924-1926)Ggc>Agc	p.G642S		NM_001080407.2	NP_001073876.2	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1-like 3	642					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)		GATGATGAGTGGCTCAGATAT	0.413																																					p.G642S		Atlas-SNP	.											.	GLB1L3	102	.	0			c.G1924A						PASS	.						116	106	109					11																	134188798		1871	4118	5989	SO:0001583	missense	112937	exon20			ATGAGTGGCTCAG		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.1924G>A	11.37:g.134188798G>A	ENSP00000396615:p.Gly642Ser	100	0	0		80	30	0.375	NM_001080407	A6NEM0|A6NN15|Q6P3S3|Q96FF8	Missense_Mutation	SNP	ENST00000431683.2	37	CCDS44780.1	.	.	.	.	.	.	.	.	.	.	G	18.24	3.579506	0.65878	.	.	ENSG00000166105	ENST00000431683	D	0.95588	-3.75	5.14	5.14	0.70334	Galactose-binding domain-like (1);	0.237649	0.44097	D	0.000491	D	0.88952	0.6577	N	0.11845	0.185	0.19575	N	0.999964	P	0.37824	0.609	B	0.34590	0.186	T	0.81874	-0.0732	10	0.30854	T	0.27	.	14.3466	0.66668	0.0:0.0:1.0:0.0	.	642	Q8NCI6	GLBL3_HUMAN	S	642	ENSP00000396615:G642S	ENSP00000396615:G642S	G	+	1	0	GLB1L3	133694008	0.566000	0.26618	0.093000	0.20910	0.010000	0.07245	2.785000	0.47782	2.844000	0.97970	0.650000	0.86243	GGC	.	.	none		0.413	GLB1L3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393625.1	NM_138416		A	134188798	G	A	134188798	3	1	14	1	0	0	0	0	1	0	0	0	6438	1348	47	2	2002	2	GLB1L3	11	134188798	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	12759500	134188798	817718	75	1856											
RAD51AP1	10635	hgsc.bcm.edu	37	chr12	4668142	4668142	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagttaaacctttgcatccaAatgccactagcacctgagtg	12	10	8	11	0	0	1	0	1	0	0	1	2	1	1	4	0	4	3	4	0	4	3			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:4668142A>G	ENST00000352618.4	+	9	1041	c.991A>G	c.(991-993)Aat>Gat	p.N331D	RAD51AP1_ENST00000228843.9_Missense_Mutation_p.N348D|RAD51AP1_ENST00000543041.1_Missense_Mutation_p.N229D|RAD51AP1_ENST00000544931.1_3'UTR|RAD51AP1_ENST00000321524.7_Missense_Mutation_p.N298D	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)			TTTGCATCCAAATGCCACTAG	0.458																																					p.N348D		Atlas-SNP	.											.	RAD51AP1	30	.	0			c.A1042G						PASS	.						128	118	121					12																	4668142		2203	4300	6503	SO:0001583	missense	10635	exon10			CATCCAAATGCCA	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.991A>G	12.37:g.4668142A>G	ENSP00000309479:p.Asn331Asp	68	0	0		70	29	0.414286	NM_001130862		Missense_Mutation	SNP	ENST00000352618.4	37	CCDS8529.1	.	.	.	.	.	.	.	.	.	.	A	13.98	2.399685	0.42512	.	.	ENSG00000111247	ENST00000321524;ENST00000543041;ENST00000228843;ENST00000352618	T;T;T;T	0.48201	1.0;1.0;0.82;0.82	4.32	4.32	0.51571	.	0.680081	0.13888	N	0.355802	T	0.42449	0.1203	L	0.58101	1.795	0.30391	N	0.780976	P;B;B;P	0.41848	0.763;0.341;0.341;0.634	B;B;B;B	0.36608	0.229;0.08;0.08;0.178	T	0.52132	-0.8616	10	0.59425	D	0.04	-4.8877	9.7988	0.40751	1.0:0.0:0.0:0.0	.	229;348;348;331	B4DUS5;Q96B01;A8K313;Q96B01-2	.;R51A1_HUMAN;.;.	D	298;229;348;331	ENSP00000323750:N298D;ENSP00000439960:N229D;ENSP00000228843:N348D;ENSP00000309479:N331D	ENSP00000228843:N348D	N	+	1	0	RAD51AP1	4538403	0.581000	0.26741	0.803000	0.32268	0.451000	0.32288	1.716000	0.37981	1.809000	0.52856	0.533000	0.62120	AAT	.	.	none		0.458	RAD51AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398293.1	NM_006479		G	4668142	A	G	4668142	3	3	14	1	0	0	0	0	1	0	0	0	13001	14	1	3	1080	3	RAD51AP1	12	4668142	Missense_Mutation	SNP	A	TCGA-FF-8047-01A-11D-2210-10		4668142	129183753	76	1857											
MLL2	8085	hgsc.bcm.edu	37	chr12	49421689	49421689	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggccagtgtctgggctcttgCcttccagacccttttccttc	3	14	9	15	0	2	1	0	0	2	1	5	1	4	1	5	2	1	1	5	2	0	5			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:49421689C>A	ENST00000301067.7	-	47	14539	c.14540G>T	c.(14539-14541)gGc>gTc	p.G4847V		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	4847					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)										TGGGCTCTTGCCTTCCAGACC	0.547																																					p.G4847V		Atlas-SNP	.											.	MLL2	1173	.	0			c.G14540T						PASS	.						60	62	61					12																	49421689		1987	4141	6128	SO:0001583	missense	8085	exon47			CTCTTGCCTTCCA	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.14540G>T	12.37:g.49421689C>A	ENSP00000301067:p.Gly4847Val	145	0	0		182	65	0.357143	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	10.23	1.292727	0.23564	.	.	ENSG00000167548	ENST00000301067	T	0.79033	-1.23	5.01	2.11	0.27256	.	0.851336	0.09837	N	0.749407	T	0.66336	0.2779	L	0.38175	1.15	0.47621	D	0.999471	B	0.06786	0.001	B	0.06405	0.002	T	0.59300	-0.7480	10	0.87932	D	0	.	4.6868	0.12762	0.2706:0.5222:0.1314:0.0759	.	4847	O14686	MLL2_HUMAN	V	4847	ENSP00000301067:G4847V	ENSP00000301067:G4847V	G	-	2	0	MLL2	47707956	0.996000	0.38824	0.978000	0.43139	0.990000	0.78478	0.607000	0.24209	0.226000	0.20979	0.655000	0.94253	GGC	.	.	none		0.547	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49421689	C	A	49421689	3	1	14	1	0	0	0	0	1	0	0	0	9630	739	26	4	2105	4	MLL2	12	49421689	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	44753547	49421689	84430206	77	1858											
ZCCHC8	55596	hgsc.bcm.edu	37	chr12	122975093	122975093	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actaaatttgatacaaattcCtctatttcttgatgatattg	13	18	4	6	0	2	3	0	3	2	0	3	3	3	3	1	0	1	0	1	0	6	9			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:122975093C>T	ENST00000336229.4	-	4	469	c.339G>A	c.(337-339)gaG>gaA	p.E113E	SNORA9_ENST00000516383.1_RNA|ZCCHC8_ENST00000543897.1_5'UTR|ZCCHC8_ENST00000536306.1_5'UTR	NM_017612.3	NP_060082.2	Q6NZY4	ZCHC8_HUMAN	zinc finger, CCHC domain containing 8	113					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)		ATACAAATTCCTCTATTTCTT	0.333																																					p.E113E		Atlas-SNP	.											.	ZCCHC8	56	.	0			c.G339A						PASS	.						52	50	50					12																	122975093		1810	4068	5878	SO:0001819	synonymous_variant	55596	exon4			AAATTCCTCTATT	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.339G>A	12.37:g.122975093C>T		37	0	0		78	4	0.0512821	NM_017612	Q7L2P6|Q8N2K5|Q96SK7|Q9NSS2|Q9NSS3	Silent	SNP	ENST00000336229.4	37																																																																																				.	.	none		0.333	ZCCHC8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017612		T	122975093	C	T	122975093	2	4	14	1	0	0	0	0	0	0	0	1	17609	680	24	2		2	ZCCHC8	12	122975093	Silent	SNP	C	TCGA-FF-8047-01A-11D-2210-10	73553404	122975093	10876802	78	1859											
GPR109A	338442	hgsc.bcm.edu	37	chr12	123187023	123187023	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaacgccaggtccaccgagcGgtacacttcacaattctgcg	10	7	10	14	4	2	0	1	0	1	0	3	2	3	0	3	2	4	1	3	2	3	3	rs201423596		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:123187023G>A	ENST00000328880.5	-	1	867	c.808C>T	c.(808-810)Cgc>Tgc	p.R270C	RP11-324E6.6_ENST00000543611.1_lincRNA|HCAR1_ENST00000356987.2_Intron	NM_177551.3	NP_808219.1	Q8TDS4	HCAR2_HUMAN	hydroxycarboxylic acid receptor 2	270					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)	TCCACCGAGCGGTACACTTCA	0.552																																					p.R270C		Atlas-SNP	.											.	HCAR2	36	.	0			c.C808T						PASS	.						50	46	47					12																	123187023		2203	4294	6497	SO:0001583	missense	338442	exon1			CCGAGCGGTACAC	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.808C>T	12.37:g.123187023G>A	ENSP00000375066:p.Arg270Cys	238	0	0		285	67	0.235088	NM_177551	A0PJL5|A7LGG3	Missense_Mutation	SNP	ENST00000328880.5	37	CCDS9235.1	.	.	.	.	.	.	.	.	.	.	G	10.23	1.292018	0.23564	.	.	ENSG00000182782	ENST00000328880;ENST00000536970	T	0.37584	1.19	4.83	-1.66	0.08265	GPCR, rhodopsin-like superfamily (1);	0.524402	0.18457	N	0.140657	T	0.41465	0.1160	M	0.62088	1.915	0.09310	N	1	D	0.54207	0.965	P	0.56788	0.806	T	0.26538	-1.0100	10	0.62326	D	0.03	-6.7453	3.923	0.09251	0.3275:0.0:0.4073:0.2652	.	270	Q8TDS4	HCAR2_HUMAN	C	270	ENSP00000375066:R270C	ENSP00000375066:R270C	R	-	1	0	HCAR2	121752976	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.110000	0.10824	-0.192000	0.10432	0.563000	0.77884	CGC	.	.	weak		0.552	HCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370202.1	NM_177551		A	123187023	G	A	123187023	3	1	14	1	0	0	0	0	1	0	0	0	6633	1116	39	1	287	1	GPR109A	12	123187023	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	211930	123187023	10664872	79	1860											
GPR109B	8843	hgsc.bcm.edu	37	chr12	123200477	123200477	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaacgccaggtccaccgagcGgtacacttcacaattctgcg	10	7	10	14	4	2	0	1	0	1	0	3	2	3	0	3	2	4	1	3	2	3	3	rs562598836		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:123200477G>A	ENST00000528880.2	-	1	962	c.808C>T	c.(808-810)Cgc>Tgc	p.R270C	RP11-324E6.6_ENST00000543611.1_lincRNA|HCAR1_ENST00000356987.2_Intron	NM_006018.2	NP_006009.2	P49019	HCAR3_HUMAN	hydroxycarboxylic acid receptor 3	270					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)			endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	9					Niacin(DB00627)	TCCACCGAGCGGTACACTTCA	0.547													g|||	1	0.000199681	0.0	0.0014	5008	,	,		17943	0.0		0.0	False		,,,				2504	0.0				p.R270C		Atlas-SNP	.											.	HCAR3	49	.	0			c.C808T						PASS	.						14	17	16					12																	123200477		2072	4240	6312	SO:0001583	missense	8843	exon1			CCGAGCGGTACAC	D10923	CCDS53842.1	12q24.31	2012-08-08	2011-05-30	2011-05-30		ENSG00000255398		"GPCR / Class A : Hydroxy-carboxylic acid receptors"	16824	protein-coding gene	gene with protein product		606039	"G protein-coupled receptor 109B"	GPR109B		7505609, 9205127, 18983141, 21454438	Standard	NM_006018		Approved	HCA3, HM74	uc001ucy.4	P49019		ENST00000528880.2:c.808C>T	12.37:g.123200477G>A	ENSP00000436714:p.Arg270Cys	118	0	0		148	20	0.135135	NM_006018	A8K4G5|B2R830|E9PI97|Q8NGE4	Missense_Mutation	SNP	ENST00000528880.2	37	CCDS53842.1	.	.	.	.	.	.	.	.	.	.	g	12.25	1.881324	0.33255	.	.	ENSG00000255398	ENST00000528880	T	0.37584	1.19	3.26	2.01	0.26516	.	.	.	.	.	T	0.47097	0.1427	L	0.60067	1.865	0.09310	N	1	D	0.57899	0.981	P	0.59595	0.86	T	0.27938	-1.0059	9	0.66056	D	0.02	.	6.4754	0.22033	0.2217:0.0:0.7783:0.0	.	270	E9PI97	.	C	270	ENSP00000436714:R270C	ENSP00000436714:R270C	R	-	1	0	HCAR3	121766430	0.000000	0.05858	0.023000	0.16930	0.275000	0.26752	-0.123000	0.10611	0.206000	0.20587	0.184000	0.17185	CGC	.	.	weak		0.547	HCAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387549.2	NM_006018		A	123200477	G	A	123200477	3	1	14	1	0	0	0	0	1	0	0	0	6634	1116	39	1	359	1	GPR109B	12	123200477	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	13454	123200477	10651418	80	1861											
PIWIL1	9271	hgsc.bcm.edu	37	chr12	130847589	130847589	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatgcccagccggatcatcGtgtaccgcgatggcgtagga	9	7	13	12	5	1	0	1	0	0	0	2	3	1	2	3	3	3	2	3	3	2	2			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:130847589G>A	ENST00000245255.3	+	18	2367	c.2095G>A	c.(2095-2097)Gtg>Atg	p.V699M		NM_001190971.1|NM_004764.4	NP_001177900.1|NP_004755.2	Q96J94	PIWL1_HUMAN	piwi-like RNA-mediated gene silencing 1	699	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)		CCGGATCATCGTGTACCGCGA	0.488																																					p.V699M		Atlas-SNP	.											.	PIWIL1	157	.	0			c.G2095A						PASS	.						114	112	113					12																	130847589		2203	4300	6503	SO:0001583	missense	9271	exon18			ATCATCGTGTACC	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.2095G>A	12.37:g.130847589G>A	ENSP00000245255:p.Val699Met	139	0	0		130	43	0.330769	NM_004764	A4F266|O95404|Q8NA60|Q8TBY5|Q96JD5	Missense_Mutation	SNP	ENST00000245255.3	37	CCDS9268.1	.	.	.	.	.	.	.	.	.	.	G	18.80	3.700418	0.68501	.	.	ENSG00000125207	ENST00000245255	T	0.16597	2.33	5.66	5.66	0.87406	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.056584	0.64402	D	0.000001	T	0.37785	0.1016	M	0.79258	2.445	0.58432	D	0.999999	D;D	0.71674	0.998;0.994	P;P	0.59546	0.859;0.815	T	0.14699	-1.0463	10	0.66056	D	0.02	-15.817	12.0926	0.53736	0.0782:0.0:0.9218:0.0	.	699;699	Q96J94;Q96J94-2	PIWL1_HUMAN;.	M	699	ENSP00000245255:V699M	ENSP00000245255:V699M	V	+	1	0	PIWIL1	129413542	1.000000	0.71417	0.960000	0.40013	0.456000	0.32438	5.444000	0.66587	2.663000	0.90544	0.591000	0.81541	GTG	.	.	none		0.488	PIWIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399510.1			A	130847589	G	A	130847589	3	1	14	1	0	0	0	0	1	0	0	0	11966	1145	40	1	2161	1	PIWIL1	12	130847589	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	7647112	130847589	3004306	81	1862											
DOCK9	23348	hgsc.bcm.edu	37	chr13	99537314	99537314	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcgcttgtcaccacccttcCgtctttcaggaggggaagcc	6	10	10	15	2	3	0	2	0	1	0	5	2	4	2	4	3	1	1	4	3	1	3	rs370847473		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr13:99537314C>T	ENST00000376460.1	-	21	2373	c.2293G>A	c.(2293-2295)Gga>Aga	p.G765R	DOCK9_ENST00000448493.2_Missense_Mutation_p.G777R|DOCK9_ENST00000339416.2_Missense_Mutation_p.G766R|DOCK9_ENST00000442173.1_Missense_Mutation_p.G765R	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9	766	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)					ACCACCCTTCCGTCTTTCAGG	0.512																																					p.G766R		Atlas-SNP	.											DOCK9_ENST00000448493,left_upper_lobe,carcinoma,+1,3	DOCK9	311	3	0			c.G2296A						scavenged	.	C	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	0,3882		0,0,1941	50	50	50		2293,2296,2293,2296	6	1	13		50	1,8283		0,1,4141	no	missense,missense,missense,missense	DOCK9	NM_001130048.1,NM_001130049.1,NM_001130050.1,NM_015296.2	125,125,125,125	0,1,6082	TT,TC,CC		0.0121,0.0,0.0082	probably-damaging,probably-damaging,probably-damaging,probably-damaging	765/2069,766/1255,765/1254,766/2070	99537314	1,12165	1941	4142	6083	SO:0001583	missense	23348	exon21			CCCTTCCGTCTTT	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.2293G>A	13.37:g.99537314C>T	ENSP00000365643:p.Gly765Arg	57	0	0		60	3	0.05	NM_001130049	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Missense_Mutation	SNP	ENST00000376460.1	37	CCDS45062.1	.	.	.	.	.	.	.	.	.	.	C	34	5.398347	0.96030	0.0	1.21E-4	ENSG00000088387	ENST00000376460;ENST00000357329;ENST00000376455;ENST00000400235;ENST00000428223;ENST00000339416;ENST00000448493;ENST00000442173	T;T;T;T	0.24350	1.86;1.86;1.86;1.86	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.57301	0.2044	M	0.81239	2.535	0.80722	D	1	D;D;D;P;D	0.89917	0.995;1.0;0.995;0.921;1.0	P;D;P;P;D	0.97110	0.88;1.0;0.819;0.479;1.0	T	0.57528	-0.7796	10	0.62326	D	0.03	.	20.422	0.99049	0.0:1.0:0.0:0.0	.	766;765;765;765;766	A6H8Z6;E9PFM9;B3KX25;Q9BZ29-5;Q9BZ29	.;.;.;.;DOCK9_HUMAN	R	765;766;766;766;765;766;777;765	ENSP00000365643:G765R;ENSP00000341086:G766R;ENSP00000401958:G777R;ENSP00000406883:G765R	ENSP00000341086:G766R	G	-	1	0	DOCK9	98335315	1.000000	0.71417	0.999000	0.59377	0.942000	0.58702	7.281000	0.78621	2.832000	0.97577	0.655000	0.94253	GGA	.	.	weak		0.512	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296		T	99537314	C	T	99537314	3	4	14	1	0	0	0	0	1	0	0	0	4696	661	23	1	4118	1	DOCK9	13	99537314	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10		99537314	15632564	82	1863											
TM9SF2	9375	hgsc.bcm.edu	37	chr13	100204538	100204538	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttggttctgcatatctgtGcctctgacgtttattggtgc	4	18	10	9	1	3	1	0	1	3	0	3	1	3	1	1	2	3	3	1	2	2	6			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr13:100204538G>C	ENST00000376387.4	+	13	1636	c.1446G>C	c.(1444-1446)gtG>gtC	p.V482V		NM_004800.1	NP_004791.1	Q99805	TM9S2_HUMAN	transmembrane 9 superfamily member 2	482					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)					GCATATCTGTGCCTCTGACGT	0.388																																					p.V482V		Atlas-SNP	.											.	TM9SF2	52	.	0			c.G1446C						PASS	.						213	195	201					13																	100204538		2203	4300	6503	SO:0001819	synonymous_variant	9375	exon13			ATCTGTGCCTCTG	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.1446G>C	13.37:g.100204538G>C		177	0	0		234	25	0.106838	NM_004800	A8K399|Q2TAY5	Silent	SNP	ENST00000376387.4	37	CCDS9493.1																																																																																			.	.	none		0.388	TM9SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045602.3			C	100204538	G	C	100204538	2	2	14	1	0	0	0	0	0	0	0	1	15993	1306	46	4		4	TM9SF2	13	100204538	Silent	SNP	G	TCGA-FF-8047-01A-11D-2210-10	667224	100204538	14965340	83	1864											
UPF3A	65110	hgsc.bcm.edu	37	chr13	115057219	115057219	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaagaaagatgcaaaaaaaaAgagacagataaacagaagaa	27	2	9	3	0	0	6	0	0	0	6	0	8	0	6	0	0	2	1	0	0	10	1			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr13:115057219A>G	ENST00000375299.3	+	7	854	c.798A>G	c.(796-798)aaA>aaG	p.K266K	UPF3A_ENST00000475218.2_3'UTR|UPF3A_ENST00000351487.5_Silent_p.K233K	NM_023011.3	NP_075387.1	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A (yeast)	266					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)		gcaaaaaaaaagagacagata	0.353																																					p.K266K		Atlas-SNP	.											.	UPF3A	47	.	0			c.A798G						PASS	.						39	40	40					13																	115057219		2201	4289	6490	SO:0001819	synonymous_variant	65110	exon7			AAAAAAAGAGACA	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.798A>G	13.37:g.115057219A>G		67	0	0		103	5	0.0485437	NM_023011	A2A366|Q5T8C3|Q5T8C9|Q7Z6N3|Q86YK1|Q9BZI8	Silent	SNP	ENST00000375299.3	37	CCDS9543.1																																																																																			.	.	none		0.353	UPF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045968.2			G	115057219	A	G	115057219	2	3	14	1	0	0	0	0	0	0	0	1	17020	69	3	3		3	UPF3A	13	115057219	Silent	SNP	A	TCGA-FF-8047-01A-11D-2210-10	14852681	115057219	112659	84	1865											
FANCM	57697	hgsc.bcm.edu	37	chr14	45624650	45624650	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagttgtaattgaacacttcAagtcatggaatggtaggtca	14	12	10	5	0	3	1	3	1	0	0	3	2	3	2	0	3	1	3	0	3	6	5			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr14:45624650A>T	ENST00000267430.5	+	8	1469	c.1384A>T	c.(1384-1386)Aag>Tag	p.K462*	FANCM_ENST00000556036.1_Nonsense_Mutation_p.K462*|FANCM_ENST00000542564.2_Nonsense_Mutation_p.K436*	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	462	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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						TGAACACTTCAAGTCATGGAA	0.313								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.K462X		Atlas-SNP	.											.	FANCM	225	.	0			c.A1384T						PASS	.						69	73	72					14																	45624650		2202	4300	6502	SO:0001587	stop_gained	57697	exon8	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CACTTCAAGTCAT	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.1384A>T	14.37:g.45624650A>T	ENSP00000267430:p.Lys462*	119	0	0		128	40	0.3125	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Nonsense_Mutation	SNP	ENST00000267430.5	37	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	A	38	6.864036	0.97893	.	.	ENSG00000187790	ENST00000556036;ENST00000267430;ENST00000542564;ENST00000556250	.	.	.	5.42	5.42	0.78866	.	0.409870	0.28834	N	0.013998	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.7616	0.51908	0.853:0.147:0.0:0.0	.	.	.	.	X	462;462;436;47	.	ENSP00000267430:K462X	K	+	1	0	FANCM	44694400	0.968000	0.33430	0.984000	0.44739	0.854000	0.48673	2.342000	0.43992	2.040000	0.60383	0.460000	0.39030	AAG	.	.	none		0.313	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		T	45624650	A	T	45624650	4	4	14	1	0	0	0	0	0	1	0	0	5679	131	5	5	1414	5	FANCM	14	45624650	Nonsense_Mutation	SNP	A	TCGA-FF-8047-01A-11D-2210-10		45624650	61724890	85	1866											
GALNTL1	57452	hgsc.bcm.edu	37	chr14	69727023	69727023	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaccatgaggaagatccgcGccaatgccatcgccatcctg	10	6	9	16	3	0	2	0	1	0	1	3	3	2	3	7	1	1	0	7	1	2	0			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr14:69727023G>A	ENST00000337827.4	+	1	343	c.16G>A	c.(16-18)Gcc>Acc	p.A6T	RP11-363J20.2_ENST00000556316.1_lincRNA|GALNT16_ENST00000554858.1_3'UTR|GALNT16_ENST00000448469.3_Missense_Mutation_p.A6T|GALNT16_ENST00000553669.1_Missense_Mutation_p.A6T	NM_001168368.1|NM_020692.2	NP_001161840.1|NP_065743.2	Q8N428	GLT16_HUMAN	polypeptide N-acetylgalactosaminyltransferase 16	6					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)										GAAGATCCGCGCCAATGCCAT	0.697																																					p.A6T		Atlas-SNP	.											.	GALNT16	8	.	0			c.G16A						PASS	.						84	65	72					14																	69727023		2202	4300	6502	SO:0001583	missense	57452	exon1			ATCCGCGCCAATG	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.16G>A	14.37:g.69727023G>A	ENSP00000336729:p.Ala6Thr	76	0	0		72	4	0.0555556	NM_001168368	Q4KMG3|Q58A55|Q9ULT9	Missense_Mutation	SNP	ENST00000337827.4	37	CCDS32107.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.722824	0.89298	.	.	ENSG00000100626	ENST00000337827;ENST00000448469;ENST00000553669	T;T;T	0.56941	0.56;0.56;0.43	4.35	2.45	0.29901	.	0.240329	0.32736	N	0.005718	T	0.37919	0.1021	L	0.43152	1.355	0.51012	D	0.999904	B;B	0.18166	0.014;0.026	B;B	0.06405	0.002;0.002	T	0.10870	-1.0611	10	0.13470	T	0.59	.	8.5824	0.33637	0.0828:0.0:0.7656:0.1517	.	6;6	Q8N428;Q58A55	GLTL1_HUMAN;.	T	6	ENSP00000336729:A6T;ENSP00000402970:A6T;ENSP00000451200:A6T	ENSP00000336729:A6T	A	+	1	0	GALNTL1	68796776	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.332000	0.65911	0.360000	0.24265	0.455000	0.32223	GCC	.	.	none		0.697	GALNT16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412434.1	NM_001168368		A	69727023	G	A	69727023	3	1	14	1	0	0	0	0	1	0	0	0	6229	1087	38	1	18	1	GALNTL1	14	69727023	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	24102373	69727023	37622517	86	1867											
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102476412	102476412	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gtgcttgccaacaaaatcgtCccgttttttaagtaagtagc	11	13	8	9	2	0	0	0	0	0	0	2	0	1	0	2	0	4	4	2	0	6	6			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr14:102476412C>T	ENST00000360184.4	+	30	6374	c.6210C>T	c.(6208-6210)gtC>gtT	p.V2070V		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	2070	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						ACAAAATCGTCCCGTTTTTTA	0.418																																					p.V2070V		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.C6210T						PASS	.						61	65	64					14																	102476412		2203	4299	6502	SO:0001819	synonymous_variant	1778	exon30			AATCGTCCCGTTT	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.6210C>T	14.37:g.102476412C>T		38	0	0		53	4	0.0754717	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																			.	.	none		0.418	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		T	102476412	C	T	102476412	2	4	14	1	0	0	0	0	0	0	0	1	4843	842	30	2		2	DYNC1H1	14	102476412	Silent	SNP	C	TCGA-FF-8047-01A-11D-2210-10	32749389	102476412	4873128	87	1868											
MAGEL2	54551	hgsc.bcm.edu	37	chr15	23890645	23890645	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtggcagcaaagatcatgcGgtcttttgaaggggccctgc	8	9	15	9	1	2	2	1	1	1	1	2	2	2	2	1	5	3	2	1	5	2	2			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr15:23890645G>A	ENST00000532292.1	-	1	530	c.436C>T	c.(436-438)Cgc>Tgc	p.R146C		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2	29					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)		AAGATCATGCGGTCTTTTGAA	0.602																																					p.R749C		Atlas-SNP	.											MAGEL2_ENST00000532292,colon,carcinoma,0,2	MAGEL2	108	2	0			c.C2245T						PASS	.						33	37	35					15																	23890645		1971	4150	6121	SO:0001583	missense	54551	exon1			TCATGCGGTCTTT	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.436C>T	15.37:g.23890645G>A	ENSP00000433433:p.Arg146Cys	72	0	0		88	34	0.386364	NM_019066		Missense_Mutation	SNP	ENST00000532292.1	37																																																																																				.	.	none		0.602	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395182.2	NM_019066		A	23890645	G	A	23890645	3	1	14	1	0	0	0	0	1	0	0	0	9198	1116	39	1	1508	1	MAGEL2	15	23890645	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10		23890645	78640747	88	1869											
MTMR10	54893	hgsc.bcm.edu	37	chr15	31266590	31266590	+	Nonsense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatctttacaataaataattAactctgttggattaaatttc	16	17	3	5	0	2	0	0	0	2	0	3	1	2	1	0	1	2	1	0	1	9	8			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr15:31266590A>C	ENST00000435680.1	-	5	498	c.401T>G	c.(400-402)tTa>tGa	p.L134*	MTMR10_ENST00000425768.1_Nonsense_Mutation_p.L134*|MTMR10_ENST00000314404.8_5'UTR|MTMR10_ENST00000563714.1_Nonsense_Mutation_p.L52*	NM_017762.2	NP_060232.2	Q9NXD2	MTMRA_HUMAN	myotubularin related protein 10	134							phosphatase activity (GO:0016791)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	9		all_lung(180;2.81e-11)		all cancers(64;7.26e-15)|Epithelial(43;7.2e-11)|GBM - Glioblastoma multiforme(186;0.000158)|BRCA - Breast invasive adenocarcinoma(123;0.00426)|Lung(196;0.174)		ATAAATAATTAACTCTGTTGG	0.323																																					p.L134X		Atlas-SNP	.											.	MTMR10	74	.	0			c.T401G						PASS	.						52	52	52					15																	31266590		1797	4057	5854	SO:0001587	stop_gained	54893	exon5			ATAATTAACTCTG	AK000320	CCDS45204.1	15q13.3	2011-06-09				ENSG00000166912		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	25999	protein-coding gene	gene with protein product						12495846	Standard	NM_017762		Approved	FLJ20313	uc001zfh.1	Q9NXD2		ENST00000435680.1:c.401T>G	15.37:g.31266590A>C	ENSP00000402537:p.Leu134*	104	0	0		127	70	0.551181	NM_017762	Q6P4Q6	Nonsense_Mutation	SNP	ENST00000435680.1	37	CCDS45204.1	.	.	.	.	.	.	.	.	.	.	A	37	6.370397	0.97511	.	.	ENSG00000166912	ENST00000435680;ENST00000425768;ENST00000340566	.	.	.	5.49	3.15	0.36227	.	0.065888	0.64402	D	0.000011	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.7074	0.28659	0.8072:0.0:0.068:0.1248	.	.	.	.	X	134;134;52	.	ENSP00000340637:L52X	L	-	2	0	MTMR10	29053882	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	8.910000	0.92685	0.446000	0.26666	0.533000	0.62120	TTA	.	.	none		0.323	MTMR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430747.1	NM_017762		C	31266590	A	C	31266590	4	2	14	1	0	0	0	0	0	1	0	0	9948	372	13	5	1980	5	MTMR10	15	31266590	Nonsense_Mutation	SNP	A	TCGA-FF-8047-01A-11D-2210-10	7375945	31266590	71264802	89	1870											
FBN1	2200	hgsc.bcm.edu	37	chr15	48779516	48779516	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctttctccttaccgatacaCgcggagatgttgggggacag	8	11	12	10	3	2	1	0	0	2	1	3	4	2	2	2	3	2	1	2	3	2	4			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr15:48779516C>T	ENST00000316623.5	-	28	3911	c.3456G>A	c.(3454-3456)gcG>gcA	p.A1152A		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1152	EGF-like 17; 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)		TACCGATACACGCGGAGATGT	0.488																																					p.A1152A		Atlas-SNP	.											FBN1,colon,carcinoma,-1,1	FBN1	310	1	0			c.G3456A						scavenged	.						98	98	98					15																	48779516		2198	4296	6494	SO:0001819	synonymous_variant	2200	exon28			GATACACGCGGAG	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.3456G>A	15.37:g.48779516C>T		96	1	0.0104167		71	38	0.535211	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Silent	SNP	ENST00000316623.5	37	CCDS32232.1																																																																																			.	.	none		0.488	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			T	48779516	C	T	48779516	2	4	14	1	0	0	0	0	0	0	0	1	5710	523	19	1		1	FBN1	15	48779516	Silent	SNP	C	TCGA-FF-8047-01A-11D-2210-10	17512926	48779516	53751876	90	1871											
PLEKHO2	80301	hgsc.bcm.edu	37	chr15	65157677	65157677	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	acagtcctgagcctgccaagCcctctcaggctgagggcacc	8	6	11	16	0	1	2	1	2	1	0	3	2	2	2	5	2	3	2	5	2	1	0			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr15:65157677C>G	ENST00000323544.4	+	6	1191	c.1063C>G	c.(1063-1065)Ccc>Gcc	p.P355A	AC069368.3_ENST00000437723.1_Intron	NM_001195059.1|NM_025201.4	NP_001181988.1|NP_079477.2	Q8TD55	PKHO2_HUMAN	pleckstrin homology domain containing, family O member 2	355	Pro-rich.									NS(1)|breast(1)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	25						GCCTGCCAAGCCCTCTCAGGC	0.612																																					p.P355A		Atlas-SNP	.											.	PLEKHO2	50	.	0			c.C1063G						PASS	.						70	70	70					15																	65157677		2202	4299	6501	SO:0001583	missense	80301	exon6			GCCAAGCCCTCTC	AF318373	CCDS10196.1, CCDS73739.1	15q22.31	2013-01-10	2007-12-14	2007-12-14	ENSG00000241839	ENSG00000241839		"Pleckstrin homology (PH) domain containing"	30026	protein-coding gene	gene with protein product			"pleckstrin homology domain containing, family Q member 1"	PLEKHQ1		12477932	Standard	NM_025201		Approved	DKFZp761K2312, PP1628, pp9099	uc002anv.3	Q8TD55	OTTHUMG00000133050	ENST00000323544.4:c.1063C>G	15.37:g.65157677C>G	ENSP00000326706:p.Pro355Ala	22	0	0		29	14	0.482759	NM_025201	Q7L4H4|Q8WYS8	Missense_Mutation	SNP	ENST00000323544.4	37	CCDS10196.1	.	.	.	.	.	.	.	.	.	.	C	0.005	-2.120411	0.00346	.	.	ENSG00000241839	ENST00000323544	T	0.34275	1.37	5.05	2.03	0.26663	.	0.935404	0.09141	N	0.842938	T	0.16727	0.0402	N	0.11560	0.145	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.002	T	0.32561	-0.9902	10	0.12430	T	0.62	.	4.9907	0.14213	0.0:0.5785:0.1598:0.2617	.	305;355	Q8TD55-2;Q8TD55	.;PKHO2_HUMAN	A	355	ENSP00000326706:P355A	ENSP00000326706:P355A	P	+	1	0	PLEKHO2	62944730	0.000000	0.05858	0.007000	0.13788	0.112000	0.19704	0.094000	0.15107	0.497000	0.27926	0.655000	0.94253	CCC	.	.	none		0.612	PLEKHO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256659.1	NM_025201		G	65157677	C	G	65157677	3	3	14	1	0	0	0	0	1	0	0	0	12094	739	26	4	1085	4	PLEKHO2	15	65157677	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	16378161	65157677	37373715	91	1872											
ABCA3	21	hgsc.bcm.edu	37	chr16	2326687	2326687	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccacccctcatcgcccctcCtctgcggtgggcggctgcag	3	7	12	19	3	2	0	1	0	1	0	4	0	3	0	6	3	2	2	6	3	0	0			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr16:2326687C>A	ENST00000301732.5	-	33	5803	c.5103G>T	c.(5101-5103)gaG>gaT	p.E1701D	ABCA3_ENST00000382381.3_Missense_Mutation_p.E1643D|MIR4717_ENST00000584656.1_RNA	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	1701					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)	ATCGCCCCTCCTCTGCGGTGG	0.612																																					p.E1701D		Atlas-SNP	.											ABCA3,NS,carcinoma,-2,1	ABCA3	176	1	0			c.G5103T						PASS	.						47	45	46					16																	2326687		2198	4300	6498	SO:0001583	missense	21	exon33			CCCCTCCTCTGCG	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.5103G>T	16.37:g.2326687C>A	ENSP00000301732:p.Glu1701Asp	55	0	0		56	24	0.428571	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Missense_Mutation	SNP	ENST00000301732.5	37	CCDS10466.1	.	.	.	.	.	.	.	.	.	.	C	10.36	1.328649	0.24167	.	.	ENSG00000167972	ENST00000301732;ENST00000382381	D	0.83673	-1.75	5.44	-7.48	0.01360	.	0.438733	0.26503	N	0.024012	T	0.52773	0.1755	N	0.12422	0.21	0.26390	N	0.97659	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.50092	-0.8868	10	0.19590	T	0.45	.	0.6966	0.00900	0.3859:0.1226:0.1741:0.3175	.	1705;1701	Q4LE27;Q99758	.;ABCA3_HUMAN	D	1701;1705	ENSP00000301732:E1701D	ENSP00000301732:E1701D	E	-	3	2	ABCA3	2266688	0.000000	0.05858	0.198000	0.23420	0.008000	0.06430	-0.742000	0.04850	-1.113000	0.02981	-0.895000	0.02911	GAG	.	.	none		0.612	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089		A	2326687	C	A	2326687	3	1	14	1	0	0	0	0	1	0	0	0	33	680	24	4	15	4	ABCA3	16	2326687	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10		2326687	88028066	92	1873											
C16orf58	64755	hgsc.bcm.edu	37	chr16	31510677	31510677	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaacagattgggtatacaggAgccataatctcaaggaacat	17	8	9	7	0	1	1	1	0	1	1	2	3	1	3	1	3	4	1	1	3	6	4			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr16:31510677A>G	ENST00000327237.2	-	5	585	c.546T>C	c.(544-546)gcT>gcC	p.A182A	C16orf58_ENST00000430477.2_Silent_p.A40A|C16orf58_ENST00000567994.1_Silent_p.A137A|C16orf58_ENST00000570164.1_Silent_p.A182A			Q96GQ5	RUS1_HUMAN	chromosome 16 open reading frame 58	182						integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)	14						GGTATACAGGAGCCATAATCT	0.517																																					p.S182S		Atlas-SNP	.											.	C16orf58	28	.	0			c.T546C						PASS	.						94	87	89					16																	31510677		2197	4300	6497	SO:0001819	synonymous_variant	64755	exon5			TACAGGAGCCATA	AK023930	CCDS10715.1	16p11.2	2013-03-04			ENSG00000140688	ENSG00000140688			25848	protein-coding gene	gene with protein product							Standard	NM_022744		Approved	FLJ13868	uc002eci.3	Q96GQ5	OTTHUMG00000132466	ENST00000327237.2:c.546T>C	16.37:g.31510677A>G		156	0	0		175	9	0.0514286	NM_022744	Q53GL8|Q8NAJ4|Q9BVY3|Q9H887	Silent	SNP	ENST00000327237.2	37	CCDS10715.1																																																																																			.	.	none		0.517	C16orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255629.2	NM_022744		G	31510677	A	G	31510677	2	3	14	1	0	0	0	0	0	0	0	1	1824	291	11	3		3	C16orf58	16	31510677	Silent	SNP	A	TCGA-FF-8047-01A-11D-2210-10	29183990	31510677	58844076	93	1874											
GPR56	9289	hgsc.bcm.edu	37	chr16	57691387	57691387	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgccttgtcaccattgccGcctacctctgctccaggtga	5	11	8	17	1	2	1	1	1	1	0	3	1	3	1	7	1	4	1	7	1	1	3	rs147479620	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr16:57691387G>A	ENST00000388812.4	+	10	1710	c.1270G>A	c.(1270-1272)Gcc>Acc	p.A424T	GPR56_ENST00000562558.1_Missense_Mutation_p.A424T|GPR56_ENST00000568909.1_Missense_Mutation_p.A424T|GPR56_ENST00000567835.1_Missense_Mutation_p.A424T|GPR56_ENST00000456916.1_Missense_Mutation_p.A424T|GPR56_ENST00000568908.1_Missense_Mutation_p.A424T|GPR56_ENST00000538815.1_Missense_Mutation_p.A424T|GPR56_ENST00000562631.1_Missense_Mutation_p.A424T|GPR56_ENST00000388813.5_Missense_Mutation_p.A424T|GPR56_ENST00000540164.2_Missense_Mutation_p.A424T|GPR56_ENST00000544297.1_Missense_Mutation_p.A249T|GPR56_ENST00000379694.4_Missense_Mutation_p.A254T|GPR56_ENST00000379696.3_Missense_Mutation_p.A424T			Q9Y653	GPR56_HUMAN	G protein-coupled receptor 56	424					angiogenesis (GO:0001525)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cerebral cortex radial glia guided migration (GO:0021801)|G-protein coupled receptor signaling pathway (GO:0007186)|layer formation in cerebral cortex (GO:0021819)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron migration (GO:2001223)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cell adhesion (GO:0045785)|positive regulation of Rho protein signal transduction (GO:0035025)|protein kinase C signaling (GO:0070528)|Rho protein signal transduction (GO:0007266)|vascular endothelial growth factor production (GO:0010573)	extracellular vesicular exosome (GO:0070062)|glial limiting end-foot (GO:0097451)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|G-protein coupled receptor activity (GO:0004930)			kidney(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)	15						CACCATTGCCGCCTACCTCTG	0.647													G|||	2	0.000399361	0.0	0.0	5008	,	,		13233	0.0		0.002	False		,,,				2504	0.0				p.A429T		Atlas-SNP	.											.	GPR56	44	.	0			c.G1285A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	0,4396		0,0,2198	153	137	142		1270,1270,1270,1285,1270,1270,1270,1270	1.7	1	16	dbSNP_134	142	9,8591	7.1+/-27.0	0,9,4291	yes	missense,missense,missense,missense,missense,missense,missense,missense	GPR56	NM_001145770.1,NM_001145771.1,NM_001145772.1,NM_001145773.1,NM_001145774.1,NM_005682.5,NM_201524.2,NM_201525.2	58,58,58,58,58,58,58,58	0,9,6489	AA,AG,GG		0.1047,0.0,0.0693	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	424/688,424/694,424/688,429/693,424/688,424/694,424/688,424/688	57691387	9,12987	2198	4300	6498	SO:0001583	missense	9289	exon10			ATTGCCGCCTACC	AJ011001	CCDS32460.1, CCDS32461.1, CCDS73893.1	16q13	2014-08-08				ENSG00000205336		"-", "GPCR / Class B : Orphans"	4512	protein-coding gene	gene with protein product		604110				10049584, 10100861	Standard	XM_005256237		Approved	TM7LN4, TM7XN1	uc002emb.2	Q9Y653		ENST00000388812.4:c.1270G>A	16.37:g.57691387G>A	ENSP00000373464:p.Ala424Thr	49	0	0		24	20	0.833333	NM_001145773	A6NIT7|A6NJV9|B0M0K4|B4DR54|O95966|Q6ZMP1|Q8NGB3|Q96HB4	Missense_Mutation	SNP	ENST00000388812.4	37	CCDS32460.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	14.17	2.455466	0.43634	0.0	0.001047	ENSG00000205336	ENST00000388813;ENST00000388812;ENST00000538815;ENST00000456916;ENST00000540164;ENST00000544297;ENST00000379694;ENST00000379696	T;T;T;T;T;T;T;T	0.47177	1.13;0.85;1.13;0.85;1.13;0.85;0.85;0.85	5.11	1.66	0.24008	GPCR, family 2-like (1);	0.474781	0.19007	N	0.125183	T	0.15522	0.0374	N	0.02391	-0.57	0.29960	N	0.819489	P;P;B;P;P	0.49783	0.911;0.928;0.37;0.91;0.928	B;B;B;B;B	0.40534	0.224;0.332;0.04;0.264;0.332	T	0.07385	-1.0775	10	0.13470	T	0.59	.	3.5997	0.08020	0.2112:0.0:0.4261:0.3628	.	249;429;424;424;254	F5H144;B4DR54;Q9Y653-2;Q9Y653;E7ENB2	.;.;.;GPR56_HUMAN;.	T	424;424;424;424;424;249;254;424	ENSP00000373465:A424T;ENSP00000373464:A424T;ENSP00000444415:A424T;ENSP00000398034:A424T;ENSP00000444911:A424T;ENSP00000438006:A249T;ENSP00000369016:A254T;ENSP00000369018:A424T	ENSP00000369016:A254T	A	+	1	0	GPR56	56248888	0.879000	0.30193	0.974000	0.42286	0.663000	0.39108	1.354000	0.34056	1.142000	0.42291	0.491000	0.48974	GCC	G|0.999;A|0.001	0.001	strong		0.647	GPR56-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433436.3			A	57691387	G	A	57691387	3	1	14	1	0	0	0	0	1	0	0	0	6708	1087	38	1	1319	1	GPR56	16	57691387	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	26180710	57691387	32663366	94	1875											
MMP15	4324	hgsc.bcm.edu	37	chr16	58073912	58073912	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggacatccggctgcggcgaCagaaggaggccgacatcatg	11	4	15	11	4	1	1	1	0	0	1	2	5	2	3	2	5	1	1	2	5	1	0			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr16:58073912C>T	ENST00000219271.3	+	4	1359	c.574C>T	c.(574-576)Cag>Tag	p.Q192*		NM_002428.2	NP_002419.1	P51511	MMP15_HUMAN	matrix metallopeptidase 15 (membrane-inserted)	192					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)	GCTGCGGCGACAGAAGGAGGC	0.652																																					p.Q192X		Atlas-SNP	.											MMP15,NS,malignant_melanoma,0,1	MMP15	58	1	0			c.C574T						PASS	.						69	62	64					16																	58073912		2198	4300	6498	SO:0001587	stop_gained	4324	exon4			CGGCGACAGAAGG	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.574C>T	16.37:g.58073912C>T	ENSP00000219271:p.Gln192*	84	0	0		48	6	0.125	NM_002428	A0A2U6|Q14111	Nonsense_Mutation	SNP	ENST00000219271.3	37	CCDS10792.1	.	.	.	.	.	.	.	.	.	.	C	44	11.154668	0.99523	.	.	ENSG00000102996	ENST00000219271	.	.	.	4.68	4.68	0.58851	.	0.189298	0.47455	D	0.000222	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	.	6.2159	0.20656	0.1999:0.7043:0.0:0.0958	.	.	.	.	X	192	.	ENSP00000219271:Q192X	Q	+	1	0	MMP15	56631413	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	1.584000	0.36589	2.157000	0.67596	0.455000	0.32223	CAG	.	.	none		0.652	MMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257342.1	NM_002428		T	58073912	C	T	58073912	4	4	14	1	0	0	0	0	0	1	0	0	9663	479	17	2	588	2	MMP15	16	58073912	Nonsense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	382525	58073912	32280841	95	1876											
EXOC3L	283849	hgsc.bcm.edu	37	chr16	67220777	67220777	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtgcattctgcagccactgaGacacacttgcctggggggag	8	8	14	11	0	1	1	0	1	1	1	1	3	1	2	2	3	4	2	2	3	0	2			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr16:67220777G>A	ENST00000314586.6	-	7	1409	c.1169C>T	c.(1168-1170)tCt>tTt	p.S390F	KIAA0895L_ENST00000563902.1_5'Flank|EXOC3L1_ENST00000562887.1_5'Flank|KIAA0895L_ENST00000561621.1_5'Flank|KIAA0895L_ENST00000290881.7_5'Flank	NM_178516.3	NP_848611.2	Q86VI1	EX3L1_HUMAN	exocyst complex component 3-like 1	390					exocytosis (GO:0006887)|peptide hormone secretion (GO:0030072)	exocyst (GO:0000145)|secretory granule (GO:0030141)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	21						CAGCCACTGAGACACACTTGC	0.592																																					p.S390F		Atlas-SNP	.											.	EXOC3L1	52	.	0			c.C1169T						PASS	.						55	60	58					16																	67220777		2198	4300	6498	SO:0001583	missense	283849	exon7			CACTGAGACACAC	AK092858	CCDS10832.1	16q22.1	2011-01-31	2011-01-31	2011-01-31	ENSG00000179044	ENSG00000179044			27540	protein-coding gene	gene with protein product		614117	"exocyst complex component 3-like"	EXOC3L		12477932	Standard	NM_178516		Approved	FLJ35539, FLJ35587	uc002erx.1	Q86VI1	OTTHUMG00000137508	ENST00000314586.6:c.1169C>T	16.37:g.67220777G>A	ENSP00000325674:p.Ser390Phe	35	0	0		28	25	0.892857	NM_178516	A8K7I9|Q8NAD2|Q8TEN2	Missense_Mutation	SNP	ENST00000314586.6	37	CCDS10832.1	.	.	.	.	.	.	.	.	.	.	G	7.721	0.697108	0.15106	.	.	ENSG00000179044	ENST00000314586	T	0.07114	3.22	5.19	3.21	0.36854	.	0.413929	0.26723	N	0.022835	T	0.05318	0.0141	N	0.14661	0.345	0.22754	N	0.998779	B	0.02656	0.0	B	0.01281	0.0	T	0.33599	-0.9862	10	0.56958	D	0.05	-0.2662	9.1371	0.36881	0.2452:0.0:0.7548:0.0	.	390	Q86VI1	EX3L1_HUMAN	F	390	ENSP00000325674:S390F	ENSP00000325674:S390F	S	-	2	0	EXOC3L1	65778278	0.101000	0.21875	0.823000	0.32752	0.108000	0.19459	2.780000	0.47742	0.576000	0.29452	0.455000	0.32223	TCT	.	.	none		0.592	EXOC3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268827.2	NM_178516		A	67220777	G	A	67220777	3	1	14	1	0	0	0	0	1	0	0	0	5306	942	33	2	1103	2	EXOC3L	16	67220777	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	9146865	67220777	23133976	96	1877											
USP6	9098	hgsc.bcm.edu	37	chr17	5049419	5049419	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgagggatctctgtggaCttaattcagaacaaatccta	13	11	9	8	0	2	2	1	1	1	1	4	4	3	4	1	2	2	1	1	2	4	3			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:5049419C>G	ENST00000574788.1	+	28	4499	c.2269C>G	c.(2269-2271)Ctt>Gtt	p.L757V	USP6_ENST00000304328.5_Missense_Mutation_p.L440V|USP6_ENST00000250066.6_Missense_Mutation_p.L757V|USP6_ENST00000332776.4_Missense_Mutation_p.L757V			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	757	USP.				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						TCTCTGTGGACTTAATTCAGA	0.358			T	"COL1A1, CDH11, ZNF9, OMD"	aneurysmal bone cysts																																p.L757V		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	.	USP6	213	.	0			c.C2269G						PASS	.						149	147	148					17																	5049419		2203	4300	6503	SO:0001583	missense	9098	exon20			TGTGGACTTAATT	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.2269C>G	17.37:g.5049419C>G	ENSP00000460380:p.Leu757Val	425	0	0		457	172	0.376368	NM_004505	Q15634|Q86WP6|Q8IWT4	Missense_Mutation	SNP	ENST00000574788.1	37	CCDS11069.2	.	.	.	.	.	.	.	.	.	.	C	8.818	0.936782	0.18206	.	.	ENSG00000129204	ENST00000332776;ENST00000250066;ENST00000304328	T;T;T	0.14144	2.53;2.94;2.55	2.55	2.55	0.30701	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.14614	0.0353	N	0.16833	0.445	0.50813	D	0.999894	D;D	0.71674	0.998;0.966	D;P	0.77557	0.99;0.908	T	0.23655	-1.0182	10	0.15499	T	0.54	.	5.4016	0.16299	0.0:0.8349:0.0:0.1651	.	440;757	P35125-2;P35125	.;UBP6_HUMAN	V	757;757;440	ENSP00000328010:L757V;ENSP00000250066:L757V;ENSP00000305473:L440V	ENSP00000250066:L757V	L	+	1	0	USP6	4990143	1.000000	0.71417	0.999000	0.59377	0.133000	0.20885	3.846000	0.55888	1.433000	0.47394	0.194000	0.17425	CTT	.	.	none		0.358	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505		G	5049419	C	G	5049419	3	3	14	1	0	0	0	0	1	0	0	0	17101	565	20	4	2343	4	USP6	17	5049419	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10		5049419	76145791	97	1878											
MAP2K3	5606	hgsc.bcm.edu	37	chr17	21208440	21208440	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggagcctgggcatcaccatGgtactgtggggggccagggc	6	7	18	10	0	1	0	1	0	0	0	1	1	1	1	3	7	2	2	3	7	1	1			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:21208440G>A	ENST00000342679.4	+	9	1023	c.774G>A	c.(772-774)atG>atA	p.M258I	MAP2K3_ENST00000316920.6_Splice_Site_p.M229I|MAP2K3_ENST00000361818.5_Splice_Site_p.M229I	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	258	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		GCATCACCATGGTACTGTGGG	0.612																																					p.M258I		Atlas-SNP	.											.	MAP2K3	135	.	0			c.G774A						PASS	.						113	99	104					17																	21208440		2203	4300	6503	SO:0001630	splice_region_variant	5606	exon9			CACCATGGTACTG	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.774+1G>A	17.37:g.21208440G>A		101	0	0		124	17	0.137097	NM_145109	B3KSK7|Q99441|Q9UE71|Q9UE72	Missense_Mutation	SNP	ENST00000342679.4	37	CCDS11217.1	.	.	.	.	.	.	.	.	.	.	G	18.82	3.705218	0.68615	.	.	ENSG00000034152	ENST00000342679;ENST00000395491;ENST00000361818;ENST00000316920	T;T	0.62941	-0.01;-0.01	4.97	4.97	0.65823	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	0.37785	0.1016	N	0.01134	-0.995	0.80722	D	1	B	0.32160	0.358	B	0.34242	0.178	T	0.52185	-0.8609	10	0.51188	T	0.08	-50.5579	18.2339	0.89944	0.0:0.0:1.0:0.0	.	258	P46734	MP2K3_HUMAN	I	258;229;229;262	ENSP00000345083:M258I;ENSP00000355081:M229I	ENSP00000319139:M262I	M	+	3	0	MAP2K3	21149033	1.000000	0.71417	1.000000	0.80357	0.632000	0.37999	9.690000	0.98676	2.309000	0.77851	0.462000	0.41574	ATG	.	.	none		0.612	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259374.2	NM_145109	Missense_Mutation	A	21208440	G	A	21208440	5	1	14	1	0	0	0	0	0	0	1	0	9247	1362	47	2	808	2	MAP2K3	17	21208440	Splice_Site	SNP	G	TCGA-FF-8047-01A-11D-2210-10	16159021	21208440	59986770	98	1879											
TAOK1	57551	hgsc.bcm.edu	37	chr17	27829683	27829683	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctccaccccaagtatctcGtcacaaatcacactatcgta	13	10	3	15	2	4	0	2	0	2	0	7	0	4	0	3	0	0	2	3	0	5	3			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:27829683G>A	ENST00000261716.3	+	13	1799	c.1280G>A	c.(1279-1281)cGt>cAt	p.R427H	TAOK1_ENST00000536202.1_Missense_Mutation_p.R427H	NM_020791.2	NP_065842.1	Q7L7X3	TAOK1_HUMAN	TAO kinase 1	427					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)			CAAGTATCTCGTCACAAATCA	0.373																																					p.R427H		Atlas-SNP	.											.	TAOK1	151	.	0			c.G1280A						PASS	.						173	141	152					17																	27829683		2203	4300	6503	SO:0001583	missense	57551	exon13			TATCTCGTCACAA	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.1280G>A	17.37:g.27829683G>A	ENSP00000261716:p.Arg427His	111	0	0		146	65	0.445205	NM_025142	A2RUT8|B7ZLV6|Q96L75|Q9H2K7|Q9H7S5|Q9P2I6	Missense_Mutation	SNP	ENST00000261716.3	37	CCDS32601.1	.	.	.	.	.	.	.	.	.	.	G	35	5.539205	0.96474	.	.	ENSG00000160551	ENST00000261716;ENST00000536202	T;T	0.43294	0.95;0.95	6.03	6.03	0.97812	Protein kinase-like domain (1);	0.050877	0.85682	D	0.000000	T	0.46889	0.1416	L	0.34521	1.04	0.80722	D	1	D;P;B	0.67145	0.996;0.853;0.004	P;P;B	0.50708	0.648;0.616;0.006	T	0.30851	-0.9964	10	0.48119	T	0.1	.	20.5666	0.99351	0.0:0.0:1.0:0.0	.	427;253;427	B7ZLV6;Q7L7X3-2;Q7L7X3	.;.;TAOK1_HUMAN	H	427	ENSP00000261716:R427H;ENSP00000438819:R427H	ENSP00000261716:R427H	R	+	2	0	TAOK1	24853809	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.701000	0.74624	2.854000	0.98071	0.655000	0.94253	CGT	.	.	none		0.373	TAOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447790.1	NM_020791		A	27829683	G	A	27829683	3	1	14	1	0	0	0	0	1	0	0	0	15562	1145	40	1	1326	1	TAOK1	17	27829683	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	6621243	27829683	53365527	99	1880											
DDX52	11056	hgsc.bcm.edu	37	chr17	36003419	36003419	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcgaatttggcccccgcgcCgagccggcgaaagagatcgt	8	6	14	13	7	0	1	0	0	0	1	2	5	0	1	4	2	1	0	4	2	2	1			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:36003419C>T	ENST00000349699.2	-	1	74	c.31G>A	c.(31-33)Ggc>Agc	p.G11S	RP11-697E22.2_ENST00000586950.1_RNA|DDX52_ENST00000394367.3_5'UTR|RP11-697E22.2_ENST00000586163.1_RNA	NM_007010.3	NP_008941.2	Q9Y2R4	DDX52_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52	11						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)				GCCCCCGCGCCGAGCCGGCGA	0.632																																					p.G11S		Atlas-SNP	.											.	DDX52	40	.	0			c.G31A						PASS	.						44	45	45					17																	36003419		2203	4300	6503	SO:0001583	missense	11056	exon1			CCGCGCCGAGCCG	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.31G>A	17.37:g.36003419C>T	ENSP00000268854:p.Gly11Ser	40	0	0		53	4	0.0754717	NM_007010	Q86YG1|Q8N213|Q9NVE0|Q9Y482	Missense_Mutation	SNP	ENST00000349699.2	37	CCDS11323.1	.	.	.	.	.	.	.	.	.	.	C	12.22	1.871577	0.33069	.	.	ENSG00000141141	ENST00000349699	T	0.13778	2.56	5.5	4.53	0.55603	.	2.488010	0.00945	N	0.002898	T	0.13970	0.0338	L	0.41710	1.295	0.80722	D	1	B	0.26672	0.156	B	0.18263	0.021	T	0.43637	-0.9379	10	0.07990	T	0.79	.	11.6948	0.51538	0.1761:0.8239:0.0:0.0	.	11	Q9Y2R4	DDX52_HUMAN	S	11	ENSP00000268854:G11S	ENSP00000268854:G11S	G	-	1	0	DDX52	33077532	0.436000	0.25586	0.246000	0.24233	0.197000	0.23852	2.315000	0.43752	1.555000	0.49500	-0.152000	0.13540	GGC	.	.	none		0.632	DDX52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256795.1	NM_152300		T	36003419	C	T	36003419	3	4	14	1	0	0	0	0	1	0	0	0	4372	652	23	1	1828	1	DDX52	17	36003419	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	8173736	36003419	45191791	100	1881											
KRT24	192666	hgsc.bcm.edu	37	chr17	38859553	38859553	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagagaaaagccccccatcGccaacaccacctcccatacc	13	3	4	21	1	0	1	0	0	0	1	2	2	1	1	9	0	3	0	9	0	4	1	rs367736597		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:38859553G>T	ENST00000264651.2	-	1	449	c.393C>A	c.(391-393)ggC>ggA	p.G131G		NM_019016.2	NP_061889.2	Q2M2I5	K1C24_HUMAN	keratin 24	131	Gly-rich.|Head.					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)				GCCCCCCATCGCCAACACCAC	0.537																																					p.G131G	GBM(61;380 1051 14702 23642 31441)	Atlas-SNP	.											.	KRT24	60	.	0			c.C393A						PASS	.						176	194	188					17																	38859553		2203	4300	6503	SO:0001819	synonymous_variant	192666	exon1			CCCATCGCCAACA		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.393C>A	17.37:g.38859553G>T		77	0	0		69	34	0.492754	NM_019016	Q9NXG7	Silent	SNP	ENST00000264651.2	37	CCDS11372.1																																																																																			.	.	alt		0.537	KRT24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257217.1	NM_019016		T	38859553	G	T	38859553	2	4	14	1	0	0	0	0	0	0	0	1	8470	1074	38	4		4	KRT24	17	38859553	Silent	SNP	G	TCGA-FF-8047-01A-11D-2210-10	2856134	38859553	42335657	101	1882											
KRTAP4-11	653240	hgsc.bcm.edu	37	chr17	39274172	39274172	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagctggggtggcagcaggtGggctggcagcacacagactg	8	5	18	10	0	0	1	0	0	0	1	0	1	0	1	0	6	3	6	0	6	0	0			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:39274172G>T	ENST00000391413.2	-	1	434	c.396C>A	c.(394-396)ccC>ccA	p.P132P		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	132	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)			ggcagcaggtgggctggcagc	0.672																																					p.P132P		Atlas-SNP	.											KRTAP4-11,NS,carcinoma,-2,2	KRTAP4-11	94	2	0			c.C396A						scavenged	.						7	12	11					17																	39274172		675	1578	2253	SO:0001819	synonymous_variant	653240	exon1			GCAGGTGGGCTGG	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.396C>A	17.37:g.39274172G>T		78	0	0		93	4	0.0430108	NM_033059	A0AUY2	Silent	SNP	ENST00000391413.2	37	CCDS45675.1																																																																																			.	.	none		0.672	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1			T	39274172	G	T	39274172	2	4	14	1	0	0	0	0	0	0	0	1	8558	1335	47	4		4	KRTAP4-11	17	39274172	Silent	SNP	G	TCGA-FF-8047-01A-11D-2210-10	414619	39274172	41921038	102	1883											
PSME3	10197	hgsc.bcm.edu	37	chr17	40985663	40985663	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccggccatggcctcgttgctGaaggtggatcaggaagtgaa	9	8	15	9	2	1	2	1	2	0	0	2	4	1	4	3	5	1	2	3	5	3	1			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:40985663G>A	ENST00000590720.1	+	1	248	c.15G>A	c.(13-15)ctG>ctA	p.L5L	PSME3_ENST00000441946.2_5'UTR|PSME3_ENST00000592169.1_Silent_p.L5L|PSME3_ENST00000293362.3_Silent_p.L5L|PSME3_ENST00000592578.1_3'UTR|PSME3_ENST00000545225.1_Intron|PSME3_ENST00000541124.1_Silent_p.L5L			P61289	PSME3_HUMAN	proteasome (prosome, macropain) activator subunit 3 (PA28 gamma; Ki)	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 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)		CCTCGTTGCTGAAGGTGGATC	0.652																																					p.L5L		Atlas-SNP	.											.	PSME3	11	.	0			c.G15A						PASS	.						69	58	62					17																	40985663		2203	4300	6503	SO:0001819	synonymous_variant	10197	exon1			GTTGCTGAAGGTG	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.15G>A	17.37:g.40985663G>A		153	0	0		160	70	0.4375	NM_176863	A8K9A3|O35563|P97373|Q12920|Q13172|Q9BQD9	Silent	SNP	ENST00000590720.1	37	CCDS45689.1																																																																																			.	.	none		0.652	PSME3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452430.1	NM_176863		A	40985663	G	A	40985663	2	1	14	1	0	0	0	0	0	0	0	1	12720	1277	45	2		2	PSME3	17	40985663	Silent	SNP	G	TCGA-FF-8047-01A-11D-2210-10	1711491	40985663	40209547	103	1884											
IMP5	162540	hgsc.bcm.edu	37	chr17	43923211	43923211	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cggcaataccagaggcctccGcacagcctctgggcctctct	7	7	10	17	2	2	1	0	0	2	1	4	1	3	1	5	3	2	2	5	3	2	1	rs150961436		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:43923211G>A	ENST00000329196.5	+	1	956	c.939G>A	c.(937-939)ccG>ccA	p.P313P	MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579599.1_RNA|MAPT-AS1_ENST00000579244.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	313						endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										AGAGGCCTCCGCACAGCCTCT	0.642													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17815	0.0		0.0	False		,,,				2504	0.0				p.P313P		Atlas-SNP	.											IMP5,colon,carcinoma,+1,1	.	.	1	0			c.G939A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	47	51	50		939	1.1	0	17	dbSNP_134	50	0,8600		0,0,4300	no	coding-synonymous	IMP5	NM_175882.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		313/685	43923211	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	162540	exon1			GCCTCCGCACAGC		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"intramembrane protease 5"	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.939G>A	17.37:g.43923211G>A		33	0	0		47	19	0.404255	NM_175882	Q8TC67|Q8WVZ6	Silent	SNP	ENST00000329196.5	37	CCDS32673.1																																																																																			G|1.000;A|0.000	0.000	weak		0.642	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882		A	43923211	G	A	43923211	2	1	14	1	0	0	0	0	0	0	0	1	7730	1074	38	1		1	IMP5	17	43923211	Silent	SNP	G	TCGA-FF-8047-01A-11D-2210-10	2937548	43923211	37271999	104	1885											
CDC27	996	hgsc.bcm.edu	37	chr17	45234463	45234463	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaggagtactttgaattggAagattctaaattcaatctgt	14	14	8	5	0	3	2	1	1	2	1	3	4	3	4	0	2	1	1	0	2	7	6			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:45234463A>C	ENST00000066544.3	-	7	751	c.658T>G	c.(658-660)Tcc>Gcc	p.S220A	CDC27_ENST00000531206.1_Missense_Mutation_p.S220A|CDC27_ENST00000527547.1_Missense_Mutation_p.S220A|CDC27_ENST00000446365.2_Missense_Mutation_p.S159A|CDC27_ENST00000528748.1_5'UTR	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	220					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						TTTGAATTGGAAGATTCTAAA	0.323																																					p.S220A		Atlas-SNP	.											CDC27_ENST00000531206,NS,carcinoma,0,2	CDC27	337	2	0			c.T658G						scavenged	.						25	27	26					17																	45234463		2153	4281	6434	SO:0001583	missense	996	exon7			AATTGGAAGATTC	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.658T>G	17.37:g.45234463A>C	ENSP00000066544:p.Ser220Ala	31	0	0		45	3	0.0666667	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	A	13.62	2.291146	0.40494	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	T;T;T;T;T	0.68331	-0.32;-0.27;-0.05;-0.32;0.81	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.48150	0.1484	N	0.19112	0.55	0.58432	D	0.999998	B;B;B;B	0.21225	0.013;0.023;0.053;0.031	B;B;B;B	0.15484	0.004;0.004;0.013;0.009	T	0.45086	-0.9285	10	0.07175	T	0.84	-13.9867	13.9377	0.64034	1.0:0.0:0.0:0.0	.	159;220;220;220	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	A	220;220;159;220;220	ENSP00000066544:S220A;ENSP00000434614:S220A;ENSP00000392802:S159A;ENSP00000437339:S220A;ENSP00000432105:S220A	ENSP00000066544:S220A	S	-	1	0	CDC27	42589462	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.754000	0.91642	2.180000	0.69256	0.455000	0.32223	TCC	.	.	none		0.323	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			C	45234463	A	C	45234463	3	2	14	1	0	0	0	0	1	0	0	0	3068	246	9	5	1886	5	CDC27	17	45234463	Missense_Mutation	SNP	A	TCGA-FF-8047-01A-11D-2210-10	1311252	45234463	35960747	105	1886											
ITGB3	3690	hgsc.bcm.edu	37	chr17	45331302	45331302	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcgctggcgggcgttggcgtAggaggtgagtgaggctccgg	4	7	22	8	5	0	2	0	2	0	0	1	3	1	3	1	7	0	4	1	7	1	2			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:45331302A>G	ENST00000559488.1	+	1	91	c.75A>G	c.(73-75)gtA>gtG	p.V25V	ITGB3_ENST00000435993.2_5'UTR|ITGB3_ENST00000571680.1_Silent_p.V25V|ITGB3_ENST00000560629.1_Missense_Mutation_p.R14G	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	25					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)	GCGTTGGCGTAGGAGGTGAGT	0.756																																					p.V25V		Atlas-SNP	.											.	ITGB3	157	.	0			c.A75G						PASS	.						3	4	4					17																	45331302		1794	3699	5493	SO:0001819	synonymous_variant	3690	exon1			TGGCGTAGGAGGT		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.75A>G	17.37:g.45331302A>G		4	0	0		7	5	0.714286	NM_000212	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Silent	SNP	ENST00000559488.1	37	CCDS11511.1																																																																																			.	.	none		0.756	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212		G	45331302	A	G	45331302	2	3	14	1	0	0	0	0	0	0	0	1	7904	407	15	3		3	ITGB3	17	45331302	Silent	SNP	A	TCGA-FF-8047-01A-11D-2210-10	96839	45331302	35863908	106	1887											
CHAD	1101	hgsc.bcm.edu	37	chr17	48543124	48543124	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gggttattggtaagggcgagGgtctccaggctgtcgaaggg	7	9	19	6	2	1	0	0	0	1	0	3	2	1	0	1	6	0	3	1	6	3	3			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:48543124G>A	ENST00000508540.1	-	2	1034	c.882C>T	c.(880-882)acC>acT	p.T294T	CHAD_ENST00000258969.4_Silent_p.T294T|ACSF2_ENST00000541920.1_Intron|ACSF2_ENST00000504392.1_Intron|ACSF2_ENST00000300441.4_Intron|ACSF2_ENST00000427954.2_Intron|ACSF2_ENST00000502667.1_Intron	NM_001267.2	NP_001258.2	O15335	CHAD_HUMAN	chondroadherin	294					bone development (GO:0060348)|cartilage condensation (GO:0001502)|negative regulation of bone trabecula formation (GO:1900155)	proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(2)|ovary(2)	15	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			TAAGGGCGAGGGTCTCCAGGC	0.572																																					p.T294T		Atlas-SNP	.											.	CHAD	36	.	0			c.C882T						PASS	.						178	158	164					17																	48543124		2203	4300	6503	SO:0001819	synonymous_variant	1101	exon2			GGCGAGGGTCTCC	U96767	CCDS11568.1	17q21.33	2008-02-05			ENSG00000136457	ENSG00000136457		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	1909	protein-coding gene	gene with protein product	"chondroadherin proteoglycan"	602178				9344663	Standard	NM_001267		Approved	SLRR4A	uc010dbr.3	O15335	OTTHUMG00000162129	ENST00000508540.1:c.882C>T	17.37:g.48543124G>A		119	0	0		92	40	0.434783	NM_001267	A8K812|Q6GTU0|Q96RJ5	Silent	SNP	ENST00000508540.1	37	CCDS11568.1																																																																																			.	.	none		0.572	CHAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367447.3	NM_001267		A	48543124	G	A	48543124	2	1	14	1	0	0	0	0	0	0	0	1	3312	1219	43	2		2	CHAD	17	48543124	Silent	SNP	G	TCGA-FF-8047-01A-11D-2210-10	3211822	48543124	32652086	107	1888											
OR4D1	26689	hgsc.bcm.edu	37	chr17	56232687	56232687	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgactgccggctccacacacCcatgtattttctgctccgaa	8	11	7	15	2	1	1	0	1	1	0	3	2	3	1	4	1	2	3	4	1	2	3			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:56232687C>A	ENST00000268912.5	+	1	194	c.173C>A	c.(172-174)cCc>cAc	p.P58H		NM_012374.1	NP_036506.1	Q15615	OR4D1_HUMAN	olfactory receptor, family 4, subfamily D, member 1	58					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						CTCCACACACCCATGTATTTT	0.473																																					p.P58H		Atlas-SNP	.											.	OR4D1	48	.	0			c.C173A						PASS	.						175	172	173					17																	56232687		2114	4269	6383	SO:0001583	missense	26689	exon1			ACACACCCATGTA	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.173C>A	17.37:g.56232687C>A	ENSP00000365451:p.Pro58His	103	0	0		131	64	0.48855	NM_012374	B2RN14|Q8NGB1|Q96R76	Missense_Mutation	SNP	ENST00000268912.5	37	CCDS42365.1	.	.	.	.	.	.	.	.	.	.	c	23.1	4.369670	0.82573	.	.	ENSG00000141194	ENST00000268912	T	0.02050	4.48	5.63	5.63	0.86233	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40908	U	0.000991	T	0.22742	0.0549	H	0.97131	3.945	0.58432	D	0.99999	D	0.76494	0.999	D	0.72338	0.977	T	0.25433	-1.0132	10	0.87932	D	0	-29.8376	17.1781	0.86846	0.0:1.0:0.0:0.0	.	58	Q15615	OR4D1_HUMAN	H	58	ENSP00000365451:P58H	ENSP00000365451:P58H	P	+	2	0	OR4D1	53587686	1.000000	0.71417	0.986000	0.45419	0.980000	0.70556	5.971000	0.70440	2.652000	0.90054	0.543000	0.68304	CCC	.	.	none		0.473	OR4D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443364.1			A	56232687	C	A	56232687	3	1	14	1	0	0	0	0	1	0	0	0	11062	623	22	4	175	4	OR4D1	17	56232687	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	7689563	56232687	24962523	108	1889											
LIMD2	80774	hgsc.bcm.edu	37	chr17	61775957	61775957	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acctccttgtgggcccagagCtccttgtgctgcttgcggcc	3	11	12	15	1	0	1	0	0	0	1	2	1	2	1	5	2	4	3	5	2	0	3			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:61775957C>T	ENST00000259006.3	-	5	497	c.339G>A	c.(337-339)gaG>gaA	p.E113E	LIMD2_ENST00000578061.1_Silent_p.E113E|LIMD2_ENST00000578402.1_Silent_p.E113E|LIMD2_ENST00000578993.1_Silent_p.E73E|LIMD2_ENST00000582055.1_Silent_p.E64E|LIMD2_ENST00000583211.1_Silent_p.E64E	NM_030576.3	NP_085053.1	Q9BT23	LIMD2_HUMAN	LIM domain containing 2	113							zinc ion binding (GO:0008270)			kidney(1)|lung(2)	3						GGGCCCAGAGCTCCTTGTGCT	0.637																																					p.E113E		Atlas-SNP	.											.	LIMD2	6	.	0			c.G339A						PASS	.						67	53	58					17																	61775957		2203	4300	6503	SO:0001819	synonymous_variant	80774	exon5			CCAGAGCTCCTTG	AK092301	CCDS11641.1	17q23.3	2006-02-03				ENSG00000136490			28142	protein-coding gene	gene with protein product						12477932	Standard	NM_030576		Approved	MGC10986	uc002jbj.4	Q9BT23		ENST00000259006.3:c.339G>A	17.37:g.61775957C>T		76	0	0		55	23	0.418182	NM_030576	D3DU16|Q96S91	Silent	SNP	ENST00000259006.3	37	CCDS11641.1																																																																																			.	.	none		0.637	LIMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443877.1	NM_030576		T	61775957	C	T	61775957	2	4	14	1	0	0	0	0	0	0	0	1	8808	796	28	2		2	LIMD2	17	61775957	Silent	SNP	C	TCGA-FF-8047-01A-11D-2210-10	5543270	61775957	19419253	109	1890											
LIMD2	80774	hgsc.bcm.edu	37	chr17	61776164	61776164	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agggcaggggcgcacctgagCttggtgtgacagtgcttgca	7	8	17	9	1	0	2	0	2	0	0	0	2	0	2	1	4	3	5	1	4	0	2			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:61776164C>T	ENST00000259006.3	-	4	377	c.219G>A	c.(217-219)aaG>aaA	p.K73K	LIMD2_ENST00000578061.1_Silent_p.K73K|LIMD2_ENST00000578402.1_Silent_p.K73K|LIMD2_ENST00000578993.1_Silent_p.K33K|LIMD2_ENST00000582055.1_Silent_p.K24K|LIMD2_ENST00000583211.1_Silent_p.K24K	NM_030576.3	NP_085053.1	Q9BT23	LIMD2_HUMAN	LIM domain containing 2	73	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.						zinc ion binding (GO:0008270)			kidney(1)|lung(2)	3						CGCACCTGAGCTTGGTGTGAC	0.657																																					p.K73K		Atlas-SNP	.											.	LIMD2	6	.	0			c.G219A						PASS	.						44	44	44					17																	61776164		2203	4300	6503	SO:0001819	synonymous_variant	80774	exon4			CCTGAGCTTGGTG	AK092301	CCDS11641.1	17q23.3	2006-02-03				ENSG00000136490			28142	protein-coding gene	gene with protein product						12477932	Standard	NM_030576		Approved	MGC10986	uc002jbj.4	Q9BT23		ENST00000259006.3:c.219G>A	17.37:g.61776164C>T		93	0	0		91	39	0.428571	NM_030576	D3DU16|Q96S91	Silent	SNP	ENST00000259006.3	37	CCDS11641.1																																																																																			.	.	none		0.657	LIMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443877.1	NM_030576		T	61776164	C	T	61776164	2	4	14	1	0	0	0	0	0	0	0	1	8808	796	28	2		2	LIMD2	17	61776164	Silent	SNP	C	TCGA-FF-8047-01A-11D-2210-10	207	61776164	19419046	110	1891											
WIPI1	55062	hgsc.bcm.edu	37	chr17	66449072	66449072	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcttccgtggacttgatccaGctgctccacagaactcagag	9	9	10	13	1	1	3	1	1	0	2	4	4	4	4	3	1	3	3	3	1	1	2			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:66449072G>A	ENST00000262139.5	-	2	141	c.142C>T	c.(142-144)Ctg>Ttg	p.L48L	WIPI1_ENST00000546360.1_Intron|WIPI1_ENST00000589459.1_Intron	NM_017983.5	NP_060453.3	Q5MNZ9	WIPI1_HUMAN	WD repeat domain, phosphoinositide interacting 1	48					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|autophagy (GO:0006914)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|vesicle targeting, trans-Golgi to endosome (GO:0048203)	autophagic vacuole membrane (GO:0000421)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|pre-autophagosomal structure (GO:0000407)|pre-autophagosomal structure membrane (GO:0034045)|trans-Golgi network (GO:0005802)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	18						ACTTGATCCAGCTGCTCCACA	0.502																																					p.L48L		Atlas-SNP	.											.	WIPI1	46	.	0			c.C142T						PASS	.						121	106	111					17																	66449072		2203	4300	6503	SO:0001819	synonymous_variant	55062	exon2			GATCCAGCTGCTC		CCDS11677.1	17q24.2	2014-02-12				ENSG00000070540		"WD repeat domain containing"	25471	protein-coding gene	gene with protein product		609224				15020712, 15602573	Standard	NM_017983		Approved	FLJ10055, WIPI49, Atg18, ATG18A	uc010dey.3	Q5MNZ9		ENST00000262139.5:c.142C>T	17.37:g.66449072G>A		66	0	0		68	4	0.0588235	NM_017983	Q8IXM5|Q9NWF8	Silent	SNP	ENST00000262139.5	37	CCDS11677.1																																																																																			.	.	none		0.502	WIPI1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448739.1	NM_017983		A	66449072	G	A	66449072	2	1	14	1	0	0	0	0	0	0	0	1	17385	962	34	2		2	WIPI1	17	66449072	Silent	SNP	G	TCGA-FF-8047-01A-11D-2210-10	4672908	66449072	14746138	111	1892											
OTOP2	92736	hgsc.bcm.edu	37	chr17	72923357	72923357	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctaaagactgcgttcacGtccacctggatctgacctgg	8	10	10	13	2	2	2	1	1	1	1	3	3	3	3	3	2	2	2	3	2	2	2	rs374632139		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:72923357G>A	ENST00000580223.1	+	3	520	c.490G>A	c.(490-492)Gtc>Atc	p.V164I	OTOP2_ENST00000331427.4_Missense_Mutation_p.V164I			Q7RTS6	OTOP2_HUMAN	otopetrin 2	164						integral component of membrane (GO:0016021)		p.V164I(1)		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)					CTGCGTTCACGTCCACCTGGA	0.532																																					p.V164I		Atlas-SNP	.											OTOP2,NS,carcinoma,0,1	OTOP2	81	1	1	Substitution - Missense(1)	prostate(1)	c.G490A						PASS	.	G	ILE/VAL	0,4406		0,0,2203	169	136	147		490	-4.9	0	17		147	1,8599	1.2+/-3.3	0,1,4299	no	missense	OTOP2	NM_178160.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	164/563	72923357	1,13005	2203	4300	6503	SO:0001583	missense	92736	exon4			GTTCACGTCCACC	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.490G>A	17.37:g.72923357G>A	ENSP00000463837:p.Val164Ile	186	0	0		185	89	0.481081	NM_178160		Missense_Mutation	SNP	ENST00000580223.1	37	CCDS11708.1	.	.	.	.	.	.	.	.	.	.	G	8.144	0.785922	0.16189	0.0	1.16E-4	ENSG00000183034	ENST00000331427	T	0.21734	1.99	4.96	-4.9	0.03094	.	1.057470	0.07294	N	0.873019	T	0.15003	0.0362	L	0.33753	1.03	0.09310	N	1	B	0.10296	0.003	B	0.13407	0.009	T	0.36456	-0.9747	10	0.21540	T	0.41	-6.2717	13.0707	0.59059	0.6472:0.0:0.3528:0.0	.	164	Q7RTS6	OTOP2_HUMAN	I	164	ENSP00000332528:V164I	ENSP00000332528:V164I	V	+	1	0	OTOP2	70434952	0.000000	0.05858	0.021000	0.16686	0.635000	0.38103	-0.132000	0.10467	-0.832000	0.04251	-1.020000	0.02445	GTC	.	.	weak		0.532	OTOP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445306.1	NM_178160		A	72923357	G	A	72923357	3	1	14	1	0	0	0	0	1	0	0	0	11315	1145	40	1	500	1	OTOP2	17	72923357	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	6474285	72923357	8271853	112	1893											
ARHGAP28	79822	hgsc.bcm.edu	37	chr18	6882194	6882194	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaatttaaatgggacaaaaTgtgccatagagaagctgcag	17	9	10	5	0	0	1	0	0	0	1	0	3	0	2	1	1	3	2	1	1	8	4			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr18:6882194T>A	ENST00000383472.4	+	11	1453	c.1349T>A	c.(1348-1350)aTg>aAg	p.M450K	ARHGAP28_ENST00000262227.3_Missense_Mutation_p.M398K|ARHGAP28_ENST00000314319.3_Missense_Mutation_p.M291K|ARHGAP28_ENST00000400091.2_Missense_Mutation_p.M450K|ARHGAP28_ENST00000418986.1_Missense_Mutation_p.M291K|ARHGAP28_ENST00000419673.2_Missense_Mutation_p.M291K|ARHGAP28_ENST00000532996.1_Missense_Mutation_p.M273K|ARHGAP28_ENST00000531294.1_Missense_Mutation_p.M286K			Q9P2N2	RHG28_HUMAN	Rho GTPase activating protein 28	450	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)				TGGGACAAAATGTGCCATAGA	0.383																																					p.M291K		Atlas-SNP	.											.	ARHGAP28	181	.	0			c.T872A						PASS	.						174	167	169					18																	6882194		2203	4300	6503	SO:0001583	missense	79822	exon10			ACAAAATGTGCCA	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.1349T>A	18.37:g.6882194T>A	ENSP00000372964:p.Met450Lys	172	0	0		101	83	0.821782	NM_001010000	A8MQB7|A8MU88|Q6P160|Q8N4T3|Q9NW53	Missense_Mutation	SNP	ENST00000383472.4	37		.	.	.	.	.	.	.	.	.	.	T	25.4	4.633106	0.87660	.	.	ENSG00000088756	ENST00000400091;ENST00000262227;ENST00000419673;ENST00000531294;ENST00000314319;ENST00000418986;ENST00000532996;ENST00000383472	T;T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01;1.01	5.68	5.68	0.88126	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.048511	0.85682	D	0.000000	T	0.42063	0.1186	N	0.22421	0.69	0.44409	D	0.997329	P;P;P;B	0.49961	0.93;0.8;0.762;0.239	P;P;P;B	0.50270	0.631;0.636;0.503;0.249	T	0.42032	-0.9475	10	0.72032	D	0.01	.	15.9369	0.79717	0.0:0.0:0.0:1.0	.	450;282;291;398	Q9P2N2;E9PRP2;F6VKJ9;Q9P2N2-2	RHG28_HUMAN;.;.;.	K	450;398;291;286;291;291;282;273	ENSP00000382963:M450K;ENSP00000262227:M398K;ENSP00000392660:M291K;ENSP00000437262:M286K;ENSP00000313506:M291K;ENSP00000406907:M291K	ENSP00000262227:M398K	M	+	2	0	ARHGAP28	6872194	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.655000	0.74392	2.172000	0.68678	0.533000	0.62120	ATG	.	.	none		0.383	ARHGAP28-006	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442123.3	XM_371108		A	6882194	T	A	6882194	3	1	14	1	0	0	0	0	1	0	0	0	877	1464	51	5	906	5	ARHGAP28	18	6882194	Missense_Mutation	SNP	T	TCGA-FF-8047-01A-11D-2210-10		6882194	71195054	113	1894											
ONECUT2	9480	hgsc.bcm.edu	37	chr18	55103350	55103350	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caccacgccatgagcatgtcCtgcgactcgtctccgcctgg	6	8	10	17	4	1	1	0	1	1	0	4	2	2	1	5	1	2	1	5	1	0	0			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr18:55103350C>T	ENST00000491143.2	+	1	434	c.402C>T	c.(400-402)tcC>tcT	p.S134S	AC090340.1_ENST00000581316.1_RNA	NM_004852.2	NP_004843.2	O95948	ONEC2_HUMAN	one cut homeobox 2	134					cell fate commitment (GO:0045165)|cilium assembly (GO:0042384)|endocrine pancreas development (GO:0031018)|epithelial cell development (GO:0002064)|liver development (GO:0001889)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ morphogenesis (GO:0009887)|peripheral nervous system neuron development (GO:0048935)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)	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(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|lung(4)|ovary(2)|skin(1)	15		Colorectal(73;0.234)		READ - Rectum adenocarcinoma(59;0.227)|Colorectal(16;0.245)		TGAGCATGTCCTGCGACTCGT	0.662																																					p.S134S		Atlas-SNP	.											.	ONECUT2	42	.	0			c.C402T						PASS	.						41	46	44					18																	55103350		2203	4300	6503	SO:0001819	synonymous_variant	9480	exon1			CATGTCCTGCGAC	Y18198	CCDS42440.1	18q21.31	2012-03-09	2007-07-16		ENSG00000119547	ENSG00000119547		"Homeoboxes / CUT class"	8139	protein-coding gene	gene with protein product		604894	"one cut domain, family member 2"			9915796	Standard	NM_004852		Approved	OC-2	uc002lgo.3	O95948	OTTHUMG00000159776	ENST00000491143.2:c.402C>T	18.37:g.55103350C>T		27	0	0		25	9	0.36	NM_004852		Silent	SNP	ENST00000491143.2	37	CCDS42440.1																																																																																			.	.	none		0.662	ONECUT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357264.3			T	55103350	C	T	55103350	2	4	14	1	0	0	0	0	0	0	0	1	10878	668	24	2		2	ONECUT2	18	55103350	Silent	SNP	C	TCGA-FF-8047-01A-11D-2210-10	48221156	55103350	22973898	114	1895											
ABCA7	10347	hgsc.bcm.edu	37	chr19	1049321	1049321	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gcgtctccgttcgcagcctgGagaagcgctttcctggaagc	6	9	13	13	4	1	1	0	0	1	1	4	3	2	2	3	2	3	3	3	2	2	2			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:1049321G>A	ENST00000263094.6	+	18	2668	c.2437G>A	c.(2437-2439)Gag>Aag	p.E813K	ABCA7_ENST00000435683.2_Missense_Mutation_p.E675K|ABCA7_ENST00000433129.1_Missense_Mutation_p.E813K	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	813	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)		TCGCAGCCTGGAGAAGCGCTT	0.677																																					p.E813K		Atlas-SNP	.											.	ABCA7	174	.	0			c.G2437A						PASS	.						49	57	55					19																	1049321		2202	4296	6498	SO:0001583	missense	10347	exon18			AGCCTGGAGAAGC	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.2437G>A	19.37:g.1049321G>A	ENSP00000263094:p.Glu813Lys	132	0	0		133	6	0.0451128	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	G	9.960	1.222447	0.22457	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	T;T	0.79554	-1.28;-1.28	4.0	2.94	0.34122	ABC transporter-like (1);	.	.	.	.	T	0.56001	0.1956	N	0.03209	-0.39	0.26432	N	0.975921	B;B	0.13145	0.007;0.004	B;B	0.14578	0.011;0.003	T	0.38351	-0.9665	9	0.07813	T	0.8	.	9.7753	0.40614	0.109:0.0:0.891:0.0	.	675;813	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	K	813	ENSP00000263094:E813K;ENSP00000414062:E813K	ENSP00000263094:E813K	E	+	1	0	ABCA7	1000321	1.000000	0.71417	0.995000	0.50966	0.197000	0.23852	5.512000	0.67030	0.777000	0.33496	0.462000	0.41574	GAG	.	.	none		0.677	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		A	1049321	G	A	1049321	3	1	14	1	0	0	0	0	1	0	0	0	37	1175	41	2	2503	2	ABCA7	19	1049321	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10		1049321	58079662	115	1896											
ZNF555	148254	hgsc.bcm.edu	37	chr19	2852470	2852470	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttaatctgtacaagaaaaTtccacctggagtaaaacagt	16	11	6	8	0	2	1	0	0	2	1	3	2	3	2	2	1	2	2	2	1	7	4			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:2852470T>A	ENST00000334241.4	+	4	545	c.407T>A	c.(406-408)aTt>aAt	p.I136N	ZNF555_ENST00000591539.1_Missense_Mutation_p.I135N|AC006130.3_ENST00000589365.1_RNA	NM_001172775.1|NM_152791.4	NP_001166246.1|NP_690004.4	Q8NEP9	ZN555_HUMAN	zinc finger protein 555	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(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|skin(3)|urinary_tract(4)	23				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)		TACAAGAAAATTCCACCTGGA	0.428																																					p.I136N		Atlas-SNP	.											.	ZNF555	61	.	0			c.T407A						PASS	.						85	82	83					19																	2852470		2203	4300	6503	SO:0001583	missense	148254	exon4			AGAAAATTCCACC	AL832140	CCDS12096.1, CCDS59329.1	19p13.3	2013-09-20			ENSG00000186300	ENSG00000186300		"Zinc fingers, C2H2-type", "-"	28382	protein-coding gene	gene with protein product						12477932	Standard	NM_152791		Approved	MGC26707	uc002lwo.3	Q8NEP9	OTTHUMG00000180500	ENST00000334241.4:c.407T>A	19.37:g.2852470T>A	ENSP00000334853:p.Ile136Asn	70	0	0		74	30	0.405405	NM_152791	A8KA89|K7EQM2|Q8NA46|Q96MP1	Missense_Mutation	SNP	ENST00000334241.4	37	CCDS12096.1	.	.	.	.	.	.	.	.	.	.	T	10.26	1.302445	0.23736	.	.	ENSG00000186300	ENST00000334241;ENST00000382127	T	0.06933	3.24	3.62	-0.788	0.10939	.	.	.	.	.	T	0.08447	0.0210	M	0.64260	1.97	0.09310	N	1	B;B	0.23650	0.001;0.089	B;B	0.16289	0.001;0.015	T	0.32640	-0.9899	9	0.66056	D	0.02	.	3.7148	0.08434	0.0:0.4382:0.1968:0.3651	.	136;135	Q8NEP9;A8KA89	ZN555_HUMAN;.	N	136;135	ENSP00000334853:I136N	ENSP00000334853:I136N	I	+	2	0	ZNF555	2803470	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-0.427000	0.06999	-0.198000	0.10333	0.459000	0.35465	ATT	.	.	none		0.428	ZNF555-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451637.3	NM_152791		A	2852470	T	A	2852470	3	1	14	1	0	0	0	0	1	0	0	0	18001	1493	52	5	421	5	ZNF555	19	2852470	Missense_Mutation	SNP	T	TCGA-FF-8047-01A-11D-2210-10	1803149	2852470	56276513	116	1897											
C19orf29	58509	hgsc.bcm.edu	37	chr19	3612193	3612193	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tccctgcacgatcttgggcgGtgggttgtcaaagtcgtagt	6	12	14	9	3	2	0	1	0	1	0	4	1	3	0	1	3	1	3	1	3	2	3			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:3612193G>A	ENST00000429344.2	-	10	2057	c.2005C>T	c.(2005-2007)Ccg>Tcg	p.P669S	CACTIN_ENST00000221899.3_Missense_Mutation_p.P601S|CACTIN_ENST00000248420.5_Missense_Mutation_p.P669S|CACTIN-AS1_ENST00000592274.1_RNA	NM_001080543.1	NP_001074012.1	Q8WUQ7	CATIN_HUMAN	cactin, spliceosome C complex subunit	669					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)										ATCTTGGGCGGTGGGTTGTCA	0.587																																					p.P669S		Atlas-SNP	.											.	.	.	.	0			c.C2005T						PASS	.						139	156	150					19																	3612193		2166	4255	6421	SO:0001583	missense	58509	exon10			TGGGCGGTGGGTT	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.2005C>T	19.37:g.3612193G>A	ENSP00000415078:p.Pro669Ser	201	0	0		222	107	0.481982	NM_021231	A6NNA9|A9UL12|O75229|Q7LE08|Q9BTA6|Q9Y5A4	Missense_Mutation	SNP	ENST00000429344.2	37	CCDS45920.1	.	.	.	.	.	.	.	.	.	.	G	13.96	2.393353	0.42410	.	.	ENSG00000105298	ENST00000429344;ENST00000248420;ENST00000221899	.	.	.	4.2	2.06	0.26882	Cactin protein, cactus-binding domain, C-terminal (1);	0.120124	0.56097	D	0.000023	T	0.80226	0.4584	M	0.91300	3.195	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.80841	-0.1202	9	0.87932	D	0	.	9.1523	0.36971	0.1829:0.0:0.8171:0.0	.	669;669	Q8WUQ7-2;Q8WUQ7	.;CS029_HUMAN	S	669;669;601	.	ENSP00000221899:P601S	P	-	1	0	C19orf29	3563193	1.000000	0.71417	0.029000	0.17559	0.001000	0.01503	9.150000	0.94667	0.539000	0.28788	-0.148000	0.13756	CCG	.	.	none		0.587	CACTIN-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457370.2			A	3612193	G	A	3612193	3	1	14	1	0	0	0	0	1	0	0	0	1920	1261	44	2	275	2	C19orf29	19	3612193	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	759723	3612193	55516790	117	1898											
RGL3	57139	hgsc.bcm.edu	37	chr19	11529920	11529920	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cggggatcccttgtccccttAccagggccagctctttgcct	4	11	10	16	1	1	0	0	0	1	0	3	1	3	1	6	3	3	1	6	3	1	3			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:11529920A>G	ENST00000380456.3	-	1	97		c.e1+1		RGL3_ENST00000393423.3_Splice_Site	NM_001035223.2|NM_001161616.1	NP_001030300.2|NP_001155088.1	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation stimulator-like 3						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						TTGTCCCCTTACCAGGGCCAG	0.697																																					.	GBM(174;751 2067 17998 27979 33959)	Atlas-SNP	.											.	RGL3	100	.	0			c.33+2T>C						PASS	.						60	74	69					19																	11529920		2203	4300	6503	SO:0001630	splice_region_variant	57139	exon2			CCCCTTACCAGGG	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.33+1T>C	19.37:g.11529920A>G		76	0	0		98	5	0.0510204	NM_001161616	B5ME84|B7ZL22|Q0P6G0	Splice_Site	SNP	ENST00000380456.3	37	CCDS32910.1	.	.	.	.	.	.	.	.	.	.	A	15.87	2.961190	0.53400	.	.	ENSG00000205517	ENST00000393423;ENST00000380456;ENST00000453604	.	.	.	4.22	3.11	0.35812	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.2496	0.26142	0.7737:0.2263:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RGL3	11390920	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	1.747000	0.38298	1.694000	0.51137	0.254000	0.18369	.	.	.	none		0.697	RGL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421208.3	XM_290867	Intron	G	11529920	A	G	11529920	5	3	14	1	0	0	0	0	0	0	1	0	13293	405	14	3	2191	3	RGL3	19	11529920	Splice_Site	SNP	A	TCGA-FF-8047-01A-11D-2210-10	7917727	11529920	47599063	118	1899											
CCDC130	81576	hgsc.bcm.edu	37	chr19	13873535	13873535	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcacagagccgcagaaccGcgcttgccacctcccccatc	8	5	9	19	3	0	2	0	0	0	2	2	2	1	2	6	1	3	3	6	1	1	1			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:13873535G>A	ENST00000586600.1	+	11	1347	c.844G>A	c.(844-846)Gcg>Acg	p.A282T	CCDC130_ENST00000221554.8_Missense_Mutation_p.A282T|CCDC130_ENST00000587019.1_3'UTR|MRI1_ENST00000040663.6_5'Flank|MRI1_ENST00000319545.8_5'Flank			P13994	CC130_HUMAN	coiled-coil domain containing 130	282					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)			CCGCAGAACCGCGCTTGCCAC	0.697																																					p.A282T		Atlas-SNP	.											CCDC130,NS,carcinoma,-1,1	CCDC130	25	1	0			c.G844A						PASS	.						21	21	21					19																	13873535		2202	4300	6502	SO:0001583	missense	81576	exon10			AGAACCGCGCTTG	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.844G>A	19.37:g.13873535G>A	ENSP00000465776:p.Ala282Thr	36	0	0		38	14	0.368421	NM_030818	Q9BQ72	Missense_Mutation	SNP	ENST00000586600.1	37	CCDS12296.1	.	.	.	.	.	.	.	.	.	.	G	12.72	2.023846	0.35701	.	.	ENSG00000104957	ENST00000221554	T	0.31510	1.49	5.23	-3.93	0.04143	.	0.706623	0.13770	N	0.363927	T	0.14743	0.0356	L	0.31926	0.97	0.09310	N	1	B;B	0.15141	0.012;0.012	B;B	0.09377	0.004;0.004	T	0.18967	-1.0320	10	0.24483	T	0.36	-24.402	2.0876	0.03650	0.4101:0.1249:0.3384:0.1265	.	282;282	B3KUZ1;P13994	.;CC130_HUMAN	T	282	ENSP00000221554:A282T	ENSP00000221554:A282T	A	+	1	0	CCDC130	13734535	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.701000	0.05075	-0.174000	0.10743	0.561000	0.74099	GCG	.	.	none		0.697	CCDC130-001	KNOWN	alternative_5_UTR|upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453216.2	NM_030818		A	13873535	G	A	13873535	3	1	14	1	0	0	0	0	1	0	0	0	2768	1087	38	1	878	1	CCDC130	19	13873535	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	2343615	13873535	45255448	119	1900											
RBM42	79171	hgsc.bcm.edu	37	chr19	36124108	36124108	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgccaccaatggctcgggCtccagggcccccgctgggct	4	6	14	17	2	0	0	0	0	0	0	2	0	1	0	5	4	1	5	5	4	1	0			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:36124108C>T	ENST00000262633.4	+	6	743	c.638C>T	c.(637-639)gCt>gTt	p.A213V	RBM42_ENST00000592202.1_Missense_Mutation_p.A159V|RBM42_ENST00000588161.1_Missense_Mutation_p.A183V|RBM42_ENST00000589559.1_Missense_Mutation_p.A184V|RBM42_ENST00000589871.1_Missense_Mutation_p.A191V|RBM42_ENST00000586618.1_Intron|RBM42_ENST00000360475.4_Missense_Mutation_p.A184V	NM_024321.3	NP_077297.2	Q9BTD8	RBM42_HUMAN	RNA binding motif protein 42	213	Pro-rich.					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)			ATGGCTCGGGCTCCAGGGCCC	0.697																																					p.A213V		Atlas-SNP	.											.	RBM42	40	.	0			c.C638T						PASS	.						38	49	45					19																	36124108		2196	4291	6487	SO:0001583	missense	79171	exon6			CTCGGGCTCCAGG	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.638C>T	19.37:g.36124108C>T	ENSP00000262633:p.Ala213Val	32	0	0		32	4	0.125	NM_024321	O00320|Q8N5R7|Q9BU66	Missense_Mutation	SNP	ENST00000262633.4	37	CCDS12468.1	.	.	.	.	.	.	.	.	.	.	C	18.22	3.576124	0.65878	.	.	ENSG00000126254	ENST00000262633;ENST00000360475	T;T	0.06449	3.3;3.34	5.05	5.05	0.67936	.	0.180852	0.47455	D	0.000236	T	0.11537	0.0281	N	0.14661	0.345	0.29843	N	0.829062	D;D;D;D	0.60575	0.988;0.988;0.988;0.98	D;D;D;D	0.70935	0.971;0.971;0.971;0.935	T	0.03555	-1.1025	10	0.48119	T	0.1	-7.1616	13.7681	0.63008	0.0:1.0:0.0:0.0	.	179;184;183;213	Q9BTD8-4;Q9BTD8-3;Q9BTD8-2;Q9BTD8	.;.;.;RBM42_HUMAN	V	213;184	ENSP00000262633:A213V;ENSP00000353663:A184V	ENSP00000262633:A213V	A	+	2	0	RBM42	40815948	0.988000	0.35896	1.000000	0.80357	0.968000	0.65278	2.033000	0.41136	2.628000	0.89032	0.561000	0.74099	GCT	.	.	none		0.697	RBM42-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459057.2	NM_024321		T	36124108	C	T	36124108	3	4	14	1	0	0	0	0	1	0	0	0	13151	797	28	2	660	2	RBM42	19	36124108	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	22250573	36124108	23004875	120	1901											
BCL3	602	hgsc.bcm.edu	37	chr19	45261657	45261657	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgacacgccgctcatggtggCgcgcagccgcagggtgagcc	6	4	16	15	6	1	1	1	1	0	0	1	2	1	1	3	3	2	3	3	3	0	0			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:45261657C>T	ENST00000164227.5	+	7	1290	c.1046C>T	c.(1045-1047)gCg>gTg	p.A349V		NM_005178.4	NP_005169.2	P20749	BCL3_HUMAN	B-cell CLL/lymphoma 3	349					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)				CTCATGGTGGCGCGCAGCCGC	0.711			T	IGH@	CLL																																p.A349V		Atlas-SNP	.		Dom	yes		19	19q13	602	B-cell CLL/lymphoma 3		L	.	BCL3	28	.	0			c.C1046T						PASS	.						6	5	6					19																	45261657		1987	3872	5859	SO:0001583	missense	602	exon7			TGGTGGCGCGCAG	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.1046C>T	19.37:g.45261657C>T	ENSP00000164227:p.Ala349Val	85	0	0		82	41	0.5	NM_005178		Missense_Mutation	SNP	ENST00000164227.5	37	CCDS12642.2	.	.	.	.	.	.	.	.	.	.	C	33	5.265975	0.95399	.	.	ENSG00000069399	ENST00000403534;ENST00000164227	T	0.62364	0.03	4.88	4.88	0.63580	Ankyrin repeat-containing domain (3);	0.409242	0.20420	N	0.092683	T	0.67711	0.2922	M	0.62209	1.925	0.45648	D	0.998571	D	0.89917	1.0	P	0.49332	0.607	T	0.73065	-0.4100	10	0.72032	D	0.01	-29.5782	15.5034	0.75719	0.0:1.0:0.0:0.0	.	349	P20749	BCL3_HUMAN	V	309;349	ENSP00000164227:A349V	ENSP00000164227:A349V	A	+	2	0	BCL3	49953497	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.532000	0.53553	2.257000	0.74773	0.491000	0.48974	GCG	.	.	none		0.711	BCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322976.1	NM_005178		T	45261657	C	T	45261657	3	4	14	1	0	0	0	0	1	0	0	0	1375	768	27	1	1072	1	BCL3	19	45261657	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	9137549	45261657	13867326	121	1902											
SLC27A5	10998	hgsc.bcm.edu	37	chr19	59010920	59010920	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcgcggtccatggccagtaCgtccccggtgttgtagtaaa	7	11	12	11	4	0	0	0	0	0	0	3	0	2	0	4	3	1	4	4	3	4	5			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:59010920C>T	ENST00000263093.2	-	7	1715	c.1606G>A	c.(1606-1608)Gta>Ata	p.V536I	SLC27A5_ENST00000599700.1_5'Flank|SLC27A5_ENST00000594786.1_5'Flank|SLC27A5_ENST00000601355.1_Missense_Mutation_p.V452I	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	536					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)		ATGGCCAGTACGTCCCCGGTG	0.687																																					p.V536I		Atlas-SNP	.											.	SLC27A5	58	.	0			c.G1606A						PASS	.						85	78	81					19																	59010920		2203	4300	6503	SO:0001583	missense	10998	exon7			CCAGTACGTCCCC	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.1606G>A	19.37:g.59010920C>T	ENSP00000263093:p.Val536Ile	64	0	0		76	28	0.368421	NM_012254	B3KVP6|B4DPQ1	Missense_Mutation	SNP	ENST00000263093.2	37	CCDS12983.1	.	.	.	.	.	.	.	.	.	.	C	17.77	3.470540	0.63625	.	.	ENSG00000083807	ENST00000263093	T	0.37915	1.17	5.26	-0.904	0.10530	AMP-dependent synthetase/ligase (1);	0.216318	0.39985	N	0.001207	T	0.19886	0.0478	L	0.35414	1.06	0.26467	N	0.975346	B	0.20780	0.048	B	0.20767	0.031	T	0.10154	-1.0642	10	0.56958	D	0.05	-17.5506	1.7058	0.02881	0.1539:0.3661:0.2999:0.1802	.	536	Q9Y2P5	S27A5_HUMAN	I	536	ENSP00000263093:V536I	ENSP00000263093:V536I	V	-	1	0	SLC27A5	63702732	0.996000	0.38824	0.016000	0.15963	0.983000	0.72400	0.379000	0.20585	0.312000	0.23038	0.462000	0.41574	GTA	.	.	none		0.687	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254		T	59010920	C	T	59010920	3	4	14	1	0	0	0	0	1	0	0	0	14544	536	19	1	482	1	SLC27A5	19	59010920	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	13749263	59010920	118063	122	1903											
ARFGAP1	55738	hgsc.bcm.edu	37	chr20	61907883	61907883	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaggacattgagcttgagaaGatgaaagctggtgggaatgc	14	8	15	4	0	0	4	0	3	0	2	0	7	0	6	0	3	3	2	0	3	4	2			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr20:61907883G>A	ENST00000370283.4	+	4	362	c.222G>A	c.(220-222)aaG>aaA	p.K74K	ARFGAP1_ENST00000353546.3_Silent_p.K74K|ARFGAP1_ENST00000370275.4_Silent_p.K74K|ARFGAP1_ENST00000519273.2_De_novo_Start_OutOfFrame|ARFGAP1_ENST00000547204.1_De_novo_Start_InFrame|ARFGAP1_ENST00000519604.1_Silent_p.K21K	NM_018209.2	NP_060679.1	Q8N6T3	ARFG1_HUMAN	ADP-ribosylation factor GTPase activating protein 1	74	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				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)					AGCTTGAGAAGATGAAAGCTG	0.527																																					p.K74K		Atlas-SNP	.											.	ARFGAP1	38	.	0			c.G222A						PASS	.						135	111	119					20																	61907883		2203	4300	6503	SO:0001819	synonymous_variant	55738	exon4			TGAGAAGATGAAA	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.222G>A	20.37:g.61907883G>A		207	0	0		256	105	0.410156	NM_018209	B7Z3U0|B7Z8H8|B7ZBI3|E1P5I9|E7EV62|Q6PK71|Q96KC4|Q96T02|Q9NSU3|Q9NVF6|Q9UIL0	Silent	SNP	ENST00000370283.4	37	CCDS13515.1																																																																																			.	.	none		0.527	ARFGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080134.3	NM_018209		A	61907883	G	A	61907883	2	1	14	1	0	0	0	0	0	0	0	1	849	933	33	2		2	ARFGAP1	20	61907883	Silent	SNP	G	TCGA-FF-8047-01A-11D-2210-10		61907883	1117637	123	1904											
C21orf2	755	hgsc.bcm.edu	37	chr21	45753051	45753051	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagccccttcaggtagaagaGctcagccaggctggggatgc	9	6	14	12	0	2	2	2	0	0	2	2	3	2	3	3	4	4	3	3	4	2	2			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr21:45753051G>A	ENST00000339818.4	-	4	445	c.238C>T	c.(238-240)Ctc>Ttc	p.L80F	C21orf2_ENST00000325223.7_Missense_Mutation_p.L80F|C21orf2_ENST00000397956.3_Missense_Mutation_p.L80F|C21orf2_ENST00000496321.1_5'UTR|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	80					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)		AGGTAGAAGAGCTCAGCCAGG	0.677																																					p.L80F		Atlas-SNP	.											.	C21orf2	10	.	0			c.C238T						PASS	.						23	24	24					21																	45753051		2202	4300	6502	SO:0001583	missense	755	exon4			AGAAGAGCTCAGC	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.238C>T	21.37:g.45753051G>A	ENSP00000344566:p.Leu80Phe	100	0	0		129	56	0.434109	NM_004928	A8MPS9|O14993|Q8N5X6|Q99837|Q99838	Missense_Mutation	SNP	ENST00000339818.4	37	CCDS13709.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.041713	0.93685	.	.	ENSG00000160226	ENST00000339818;ENST00000380160;ENST00000397956;ENST00000325223	T;T;T	0.25085	1.82;1.82;1.82	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.60470	0.2271	M	0.92317	3.295	0.80722	D	1	D;D;D;D	0.89917	1.0;0.988;1.0;1.0	D;P;D;D	0.97110	0.999;0.908;1.0;0.999	T	0.69483	-0.5133	10	0.54805	T	0.06	-34.0877	15.5737	0.76359	0.0:0.0:1.0:0.0	.	80;80;80;39	G5E952;Q8N5X6;O43822;O43822-2	.;.;CU002_HUMAN;.	F	80;116;80;80	ENSP00000344566:L80F;ENSP00000381047:L80F;ENSP00000317302:L80F	ENSP00000317302:L80F	L	-	1	0	C21orf2	44577479	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.037000	0.93765	2.482000	0.83794	0.655000	0.94253	CTC	.	.	none		0.677	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195799.1	NM_004928		A	45753051	G	A	45753051	3	1	14	1	0	0	0	0	1	0	0	0	2125	971	34	2	548	2	C21orf2	21	45753051	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10		45753051	2376844	124	1905											
COL6A1	1291	hgsc.bcm.edu	37	chr21	47423737	47423737	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gcaggaagcccagcgggcagGcatcgagatcttcgtggtgg	8	6	17	10	3	1	1	0	0	1	1	3	3	1	2	1	5	2	3	1	5	1	1			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr21:47423737G>A	ENST00000361866.3	+	35	3011	c.2897G>A	c.(2896-2898)gGc>gAc	p.G966D	COL6A1_ENST00000498614.1_3'UTR	NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	966	C-terminal globular domain.|VWFA 3. {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)		CAGCGGGCAGGCATCGAGATC	0.672																																					p.G966D		Atlas-SNP	.											.	COL6A1	101	.	0			c.G2897A						PASS	.						39	40	39					21																	47423737		2200	4298	6498	SO:0001583	missense	1291	exon35			GGGCAGGCATCGA	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.2897G>A	21.37:g.47423737G>A	ENSP00000355180:p.Gly966Asp	95	0	0		88	39	0.443182	NM_001848	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Missense_Mutation	SNP	ENST00000361866.3	37	CCDS13727.1	.	.	.	.	.	.	.	.	.	.	G	14.47	2.544844	0.45280	.	.	ENSG00000142156	ENST00000361866	D	0.82803	-1.65	4.83	2.7	0.31948	von Willebrand factor, type A (3);	0.364959	0.27280	N	0.020091	T	0.81351	0.4804	M	0.78049	2.395	0.54753	D	0.999987	B	0.15473	0.013	B	0.20184	0.028	T	0.77035	-0.2737	10	0.44086	T	0.13	-12.9407	10.1343	0.42697	0.1868:0.0:0.8132:0.0	.	966	P12109	CO6A1_HUMAN	D	966	ENSP00000355180:G966D	ENSP00000355180:G966D	G	+	2	0	COL6A1	46248165	0.968000	0.33430	0.912000	0.35992	0.308000	0.27856	1.709000	0.37909	0.771000	0.33359	0.596000	0.82720	GGC	.	.	none		0.672	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848		A	47423737	G	A	47423737	3	1	14	1	0	0	0	0	1	0	0	0	3701	1203	42	2	3035	2	COL6A1	21	47423737	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	1670686	47423737	706158	125	1906											
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230278	23230278	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggttgtgagacccctgaggaGctgggccctggtcccaggca	6	7	16	12	0	0	2	0	2	0	1	1	4	1	3	4	5	1	3	4	5	0	1	rs544778929	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr22:23230278G>A	ENST00000526893.1	+	1	319	c.45G>A	c.(43-45)gaG>gaA	p.E15E	IGLL5_ENST00000531372.1_Silent_p.E15E|IGLL5_ENST00000532223.2_Silent_p.E15E|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	15						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CCCCTGAGGAGCTGGGCCCTG	0.672													G|||	6	0.00119808	0.0023	0.0029	5008	,	,		13267	0.0		0.0	False		,,,				2504	0.001				p.E15E		Atlas-SNP	.											IGLL5,NS,lymphoid_neoplasm,0,1	IGLL5	26	1	0			c.G45A						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			TGAGGAGCTGGGC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.45G>A	22.37:g.23230278G>A		159	0	0		75	65	0.866667	NM_001178126		Silent	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.672	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		A	23230278	G	A	23230278	2	1	14	1	0	0	0	0	0	0	0	1	7603	962	34	2		2	IGLL5	22	23230278	Silent	SNP	G	TCGA-FF-8047-01A-11D-2210-10		23230278	28074288	126	1907											
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230371	23230371	+	Missense_Mutation	SNP	A	A	T																															cgcccaatggttgcaccgcaAagcggggacccagaccctgg																								rs554492007	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr22:23230371A>T	ENST00000526893.1	+	1	412	c.138A>T	c.(136-138)caA>caT	p.Q46H	IGLL5_ENST00000531372.1_Missense_Mutation_p.Q46H|IGLL5_ENST00000532223.2_Missense_Mutation_p.Q46H|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	46						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						TTGCACCGCAAAGCGGGGACC	0.682																																					p.Q46H		Atlas-SNP	.											.	IGLL5	26	.	0			c.A138T						PASS	.																																			SO:0001583	missense	100423062	exon1			ACCGCAAAGCGGG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.138A>T	22.37:g.23230371A>T	ENSP00000431254:p.Gln46His	131	0	0		63	49	0.777778	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	A	13.60	2.284481	0.40394	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00597	6.31;6.41	3.55	-2.34	0.06704	.	.	.	.	.	T	0.00496	0.0016	N	0.24115	0.695	0.09310	N	1	P	0.52316	0.952	B	0.42692	0.395	T	0.53556	-0.8422	9	0.59425	D	0.04	.	7.4227	0.27081	0.5576:0.0:0.4424:0.0	.	46	B9A064	IGLL5_HUMAN	H	46	ENSP00000436353:Q46H;ENSP00000431254:Q46H	ENSP00000431254:Q46H	Q	+	3	2	IGLL5	21560371	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.209000	0.09358	-0.338000	0.08413	-1.039000	0.02377	CAA	.	.	none		0.682	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		T	23230371	A	T	23230371	3	4	14	1	0	0	0	0	1	0	0	0	7603	11	1	5	140	5	IGLL5	22	23230371	Missense_Mutation	SNP	A	TCGA-FF-8047-01A-11D-2210-10	93	23230371	28074195	127	1908	25	2									
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230380	23230380	+	Silent	SNP	C	C	T																															gttgcaccgcaaagcggggaCccagaccctggagcctcagt																										TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr22:23230380C>T	ENST00000526893.1	+	1	421	c.147C>T	c.(145-147)gaC>gaT	p.D49D	IGLL5_ENST00000531372.1_Silent_p.D49D|IGLL5_ENST00000532223.2_Silent_p.D49D|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	49						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						AAAGCGGGGACCCAGACCCTG	0.682																																					p.T14I		Atlas-SNP	.											.	IGLL5	26	.	0			c.C41T						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			CGGGGACCCAGAC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.147C>T	22.37:g.23230380C>T		123	0	0		63	50	0.793651	NM_001256296		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.682	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		T	23230380	C	T	23230380	2	4	14	1	0	0	0	0	0	0	0	1	7603	506	18	2		2	IGLL5	22	23230380	Silent	SNP	C	TCGA-FF-8047-01A-11D-2210-10	9	23230380	28074186	128	1909	25	2									
PLXNB2	23654	hgsc.bcm.edu	37	chr22	50714348	50714348	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tacttctgcgtgtattggtaGagctggtggagtgccacgag	7	12	15	7	2	1	1	0	0	1	1	1	3	1	2	1	3	4	3	1	3	3	5			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr22:50714348G>A	ENST00000449103.1	-	36	5522	c.5382C>T	c.(5380-5382)ctC>ctT	p.L1794L	PLXNB2_ENST00000359337.4_Silent_p.L1794L|AL022328.1_ENST00000595015.1_Missense_Mutation_p.E56K			O15031	PLXB2_HUMAN	plexin B2	1794					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)		TGTATTGGTAGAGCTGGTGGA	0.672											OREG0026679	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L1794L		Atlas-SNP	.											.	PLXNB2	172	.	0			c.C5382T						PASS	.						51	62	58					22																	50714348		2082	4203	6285	SO:0001819	synonymous_variant	23654	exon36			TTGGTAGAGCTGG		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.5382C>T	22.37:g.50714348G>A		138	0	0	971	126	38	0.301587	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Silent	SNP	ENST00000449103.1	37	CCDS43035.1																																																																																			.	.	none		0.672	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401		A	50714348	G	A	50714348	2	1	14	1	0	0	0	0	0	0	0	1	12133	929	33	2		2	PLXNB2	22	50714348	Silent	SNP	G	TCGA-FF-8047-01A-11D-2210-10	27483968	50714348	590218	129	1910											
PHEX	5251	hgsc.bcm.edu	37	chrX	22117216	22117216	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccgagaatgtggtggtccgCgtcccgcagtactttaaaga	9	10	12	10	4	0	2	0	0	0	2	3	3	3	2	3	2	1	2	3	2	4	3			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chrX:22117216C>T	ENST00000379374.4	+	9	1591	c.1026C>T	c.(1024-1026)cgC>cgT	p.R342R	PHEX_ENST00000418858.3_Silent_p.R45R|PHEX_ENST00000535894.1_Silent_p.R245R|PHEX_ENST00000475778.1_3'UTR|PHEX_ENST00000537599.1_Silent_p.R342R	NM_000444.4	NP_000435.3	P78562	PHEX_HUMAN	phosphate regulating endopeptidase homolog, X-linked	342					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						TGGTGGTCCGCGTCCCGCAGT	0.448																																					p.R342R		Atlas-SNP	.											.	PHEX	95	.	0			c.C1026T						PASS	.						117	106	110					X																	22117216		2203	4300	6503	SO:0001819	synonymous_variant	5251	exon9			GGTCCGCGTCCCG	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.1026C>T	X.37:g.22117216C>T		83	0	0		64	6	0.09375	NM_000444	O00678|Q13646|Q2M325|Q93032|Q99827	Silent	SNP	ENST00000379374.4	37	CCDS14204.1																																																																																			.	.	none		0.448	PHEX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056035.1	NM_000444		T	22117216	C	T	22117216	2	4	14	1	0	0	0	0	0	0	0	1	11828	755	27	1		1	PHEX	23	22117216	Silent	SNP	C	TCGA-FF-8047-01A-11D-2210-10		22117216	133153344	130	1911											
FAM48B1	100130302	hgsc.bcm.edu	37	chrX	24382373	24382374	+	IGR	INS	-	-	TGCTGC																															ttttctgctgctgctgctatINStgctgctgctgctgctgctg																								rs371342199|rs35206911|rs201827126		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chrX:24382373_24382374insTGCTGC								AC004552.1 (15350 upstream) : PDK3 (100963 downstream)																							gctgctgctattgctgctgctg	0.574																																					p.I499delinsIAA		Atlas-Indel	.											.	.	.	.	0			c.1496_1497insTGCTGC						PASS	.																																			SO:0001628	intergenic_variant	100130302	exon1			.																													X.37:g.24382374_24382379dupTGCTGC		261	0	0		206	37	0.179612	NM_001136234		In_Frame_Ins	INS		37																																																																																				.	.	alt	0	0.574									TGCTGC	24382374	-	TGCTGC	24382373	6	5	14	0	1	1	1	0	0	0	0	0	5581	1493	52	0		0	FAM48B1	23	24382373	IGR	INS	-	TCGA-FF-8047-01A-11D-2210-10	2265157	24382373	130888187	131	1912											
FAM47A	158724	hgsc.bcm.edu	37	chrX	34148961	34148961	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtcttgggatgttccgggtGgggatgggacacctgagtct	5	12	17	7	1	2	1	0	1	2	0	3	4	3	4	2	5	0	1	2	5	0	2			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chrX:34148961G>A	ENST00000346193.3	-	1	1486	c.1435C>T	c.(1435-1437)Cac>Tac	p.H479Y		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	479										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						TGTTCCGGGTGGGGATGGGAC	0.622																																					p.H479Y		Atlas-SNP	.											.	FAM47A	249	.	0			c.C1435T						PASS	.						48	54	52					X																	34148961		2170	4263	6433	SO:0001583	missense	158724	exon1			CCGGGTGGGGATG	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.1435C>T	X.37:g.34148961G>A	ENSP00000345029:p.His479Tyr	92	0	0		84	67	0.797619	NM_203408	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	37	CCDS43926.1	.	.	.	.	.	.	.	.	.	.	g	1.827	-0.470858	0.04445	.	.	ENSG00000185448	ENST00000346193	T	0.13657	2.57	0.48	-0.96	0.10340	.	.	.	.	.	T	0.06234	0.0161	N	0.03608	-0.345	0.20873	N	0.999838	D	0.54772	0.968	P	0.46758	0.526	T	0.22243	-1.0222	8	0.40728	T	0.16	.	.	.	.	.	479	Q5JRC9	FA47A_HUMAN	Y	479	ENSP00000345029:H479Y	ENSP00000345029:H479Y	H	-	1	0	FAM47A	34058882	0.002000	0.14202	0.009000	0.14445	0.040000	0.13550	-0.289000	0.08365	-0.679000	0.05217	0.183000	0.17082	CAC	.	.	none		0.622	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408		A	34148961	G	A	34148961	3	1	14	1	0	0	0	0	1	0	0	0	5577	1348	47	2	944	2	FAM47A	23	34148961	Missense_Mutation	SNP	G	TCGA-FF-8047-01A-11D-2210-10	9766588	34148961	121121599	132	1913											
WDR13	64743	hgsc.bcm.edu	37	chrX	48462764	48462765	+	Frame_Shift_Ins	INS	-	-	G																															cccctcatgtccttccgccaINSgggggcctgcgtgggtgagt																										TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chrX:48462764_48462765insG	ENST00000218056.5	+	8	1764_1765	c.1259_1260insG	c.(1258-1263)caggggfs	p.QG420fs	WDR13_ENST00000376729.5_Frame_Shift_Ins_p.QG420fs	NM_001166426.1|NM_017883.4	NP_001159898.1|NP_060353	Q9H1Z4	WDR13_HUMAN	WD repeat domain 13	420						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|large_intestine(4)|lung(4)|ovary(2)	11						TCCTTCCGCCAGGGGGCCTGCG	0.629																																					p.Q420fs		Pindel,Atlas-Indel	.											.	WDR13	96	.	0			c.1259_1260insG						PASS	.																																			SO:0001589	frameshift_variant	64743	exon8			.	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.1264dupG	X.37:g.48462769_48462769dupG	ENSP00000218056:p.Gln420fs	121	0	.		45	25	0.556	NM_017883	Q06DW8|Q06DX0|Q06DX1|Q9BUL7|Q9NWW4	Frame_Shift_Ins	INS	ENST00000218056.5	37	CCDS14302.1																																																																																			.	.	none		0.629	WDR13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060743.2			G	48462765	-	G	48462764	7	5	14	1	0	1	1	0	0	0	0	0	17290	188	7	0	1289	0	WDR13	23	48462764	Frame_Shift_Ins	INS	-	TCGA-FF-8047-01A-11D-2210-10	14313803	48462764	106807796	133	1914											
RGAG1	57529	hgsc.bcm.edu	37	chrX	109697658	109697658	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tggtctgatgccattctacgGaccaggtttctggaaggact	8	12	12	9	1	3	1	0	1	3	0	3	4	3	4	2	5	2	1	2	5	2	3			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chrX:109697658G>A	ENST00000465301.2	+	3	4059	c.3813G>A	c.(3811-3813)cgG>cgA	p.R1271R	RGAG1_ENST00000540313.1_Silent_p.R1271R	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	1271										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						CCATTCTACGGACCAGGTTTC	0.522																																					p.R1271R		Atlas-SNP	.											.	RGAG1	168	.	0			c.G3813A						PASS	.						126	122	123					X																	109697658		2203	4300	6503	SO:0001819	synonymous_variant	57529	exon3			TCTACGGACCAGG	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.3813G>A	X.37:g.109697658G>A		161	0	0		107	8	0.0747664	NM_020769	Q9P2M8	Silent	SNP	ENST00000465301.2	37	CCDS14552.1																																																																																			.	.	none		0.522	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		A	109697658	G	A	109697658	2	1	14	1	0	0	0	0	0	0	0	1	13289	1161	41	2		2	RGAG1	23	109697658	Silent	SNP	G	TCGA-FF-8047-01A-11D-2210-10	61234894	109697658	45572902	134	1915											
UBE2A	7319	hgsc.bcm.edu	37	chrX	118708868	118708868	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtctgtcttcccgaaggttgCaggaggatcctccagccgga	7	9	13	12	2	2	0	0	0	2	0	5	4	5	3	4	4	2	2	4	4	1	2			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chrX:118708868C>T	ENST00000371558.2	+	2	223	c.49C>T	c.(49-51)Cag>Tag	p.Q17*	UBE2A_ENST00000346330.3_Nonsense_Mutation_p.Q17*|UBE2A_ENST00000469205.1_3'UTR	NM_001282161.1|NM_003336.2|NM_181762.1	NP_001269090.1|NP_003327.2|NP_861427.1	P49459	UBE2A_HUMAN	ubiquitin-conjugating enzyme E2A	17					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|DNA repair (GO:0006281)|histone H2A ubiquitination (GO:0033522)|in utero embryonic development (GO:0001701)|maternal process involved in female pregnancy (GO:0060135)|positive regulation of cell proliferation (GO:0008284)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein polyubiquitination (GO:0000209)|response to UV (GO:0009411)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|cytosol (GO:0005829)|HULC complex (GO:0033503)|nuclear chromatin (GO:0000790)|XY body (GO:0001741)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)			haematopoietic_and_lymphoid_tissue(1)|lung(7)	8						CCGAAGGTTGCAGGAGGATCC	0.701								Rad6 pathway																													p.Q17X		Atlas-SNP	.											.	UBE2A	43	.	0			c.C49T						PASS	.						137	111	120					X																	118708868		2203	4300	6503	SO:0001587	stop_gained	7319	exon2			AGGTTGCAGGAGG	AK223045	CCDS14580.1, CCDS14581.1	Xq24	2011-05-19	2011-05-19		ENSG00000077721	ENSG00000077721		"Ubiquitin-conjugating enzymes E2"	12472	protein-coding gene	gene with protein product		312180	"ubiquitin-conjugating enzyme E2A (RAD6 homolog)"			1559696	Standard	NM_003336		Approved	UBC2, HHR6A, RAD6A	uc004erl.3	P49459	OTTHUMG00000022275	ENST00000371558.2:c.49C>T	X.37:g.118708868C>T	ENSP00000360613:p.Gln17*	183	0	0		106	81	0.764151	NM_003336	A6NFE9|A6NGR2|A6NMF5|B2R7R9|D3DWI1|Q4TTG1|Q96FX4	Nonsense_Mutation	SNP	ENST00000371558.2	37	CCDS14580.1	.	.	.	.	.	.	.	.	.	.	C	33	5.277119	0.95459	.	.	ENSG00000077721	ENST00000371558;ENST00000346330	.	.	.	4.6	4.6	0.57074	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-3.7589	15.601	0.76626	0.0:1.0:0.0:0.0	.	.	.	.	X	17	.	ENSP00000335027:Q17X	Q	+	1	0	UBE2A	118592896	1.000000	0.71417	0.999000	0.59377	0.572000	0.35998	7.145000	0.77365	2.131000	0.65755	0.529000	0.55759	CAG	.	.	none		0.701	UBE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058036.1	NM_003336		T	118708868	C	T	118708868	4	4	14	1	0	0	0	0	0	1	0	0	16859	711	25	2	55	2	UBE2A	23	118708868	Nonsense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	9011210	118708868	36561692	135	1916											
STAG2	10735	hgsc.bcm.edu	37	chrX	123182892	123182892	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgaaatagaaaatatgatgaAtgcaatatttaaaggagtgt	19	12	9	1	0	0	4	0	3	0	1	0	5	0	5	0	1	1	1	0	1	10	5			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chrX:123182892A>T	ENST00000371160.1	+	10	1147	c.857A>T	c.(856-858)aAt>aTt	p.N286I	STAG2_ENST00000354548.5_Missense_Mutation_p.N217I|STAG2_ENST00000371157.3_Missense_Mutation_p.N286I|STAG2_ENST00000371145.3_Missense_Mutation_p.N286I|STAG2_ENST00000371144.3_Missense_Mutation_p.N286I|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Missense_Mutation_p.N286I	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	286					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						AATATGATGAATGCAATATTT	0.294																																					p.N286I		Atlas-SNP	.											.	STAG2	309	.	0			c.A857T						PASS	.						100	93	96					X																	123182892		2203	4297	6500	SO:0001583	missense	10735	exon10			TGATGAATGCAAT	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.857A>T	X.37:g.123182892A>T	ENSP00000360202:p.Asn286Ile	341	0	0		256	21	0.0820312	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Missense_Mutation	SNP	ENST00000371160.1	37	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.419454	0.83559	.	.	ENSG00000101972	ENST00000218089;ENST00000455404;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	T;T;T;T;T;T;T	0.33438	1.41;1.41;1.41;1.41;1.41;1.41;1.41	5.47	5.47	0.80525	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.58192	0.2105	M	0.85041	2.73	0.80722	D	1	D;D	0.63046	0.987;0.992	D;D	0.65684	0.937;0.933	T	0.65059	-0.6260	10	0.62326	D	0.03	-0.079	14.1713	0.65512	1.0:0.0:0.0:0.0	.	286;286	Q8N3U4-2;Q8N3U4	.;STAG2_HUMAN	I	286;286;217;286;286;286;286	ENSP00000218089:N286I;ENSP00000397265:N286I;ENSP00000346555:N217I;ENSP00000360202:N286I;ENSP00000360199:N286I;ENSP00000360187:N286I;ENSP00000360186:N286I	ENSP00000218089:N286I	N	+	2	0	STAG2	123010573	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.228000	0.95250	1.809000	0.52856	0.486000	0.48141	AAT	.	.	none		0.294	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		T	123182892	A	T	123182892	3	4	14	1	0	0	0	0	1	0	0	0	15258	101	4	5	887	5	STAG2	23	123182892	Missense_Mutation	SNP	A	TCGA-FF-8047-01A-11D-2210-10	4474024	123182892	32087668	136	1917											
PLAC1	10761	hgsc.bcm.edu	37	chrX	133700486	133700486	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatgccacattcagtaacaCggtaggtgaactggtaggcg	11	9	13	8	2	1	2	1	2	0	0	1	2	1	2	1	4	3	3	1	4	4	4	rs200146589		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chrX:133700486C>T	ENST00000359237.4	-	3	512	c.227G>A	c.(226-228)cGt>cAt	p.R76H	PLAC1_ENST00000476971.1_5'UTR	NM_021796.3	NP_068568.1			placenta-specific 1											large_intestine(4)|lung(1)|pancreas(1)	6	Acute lymphoblastic leukemia(192;0.000127)					TTCAGTAACACGGTAGGTGAA	0.488													C|||	1	0.000264901	0.0	0.0	3775	,	,		17035	0.001		0.0	False		,,,				2504	0.0				p.R76H		Atlas-SNP	.											.	PLAC1	17	.	0			c.G227A						PASS	.						234	193	207					X																	133700486		2203	4300	6503	SO:0001583	missense	10761	exon3			GTAACACGGTAGG	AF234654	CCDS14642.1	Xq26.3	2013-10-14			ENSG00000170965	ENSG00000170965			9044	protein-coding gene	gene with protein product	"cancer/testis antigen 92"	300296				10995572	Standard	NM_021796		Approved	CT92, OOSP2L	uc004exo.1	Q9HBJ0	OTTHUMG00000022457	ENST00000359237.4:c.227G>A	X.37:g.133700486C>T	ENSP00000352173:p.Arg76His	207	0	0		116	5	0.0431034	NM_021796		Missense_Mutation	SNP	ENST00000359237.4	37	CCDS14642.1	1	6.027727546714888E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	15.39	2.818858	0.50633	.	.	ENSG00000170965	ENST00000359237	D	0.82526	-1.62	4.5	3.63	0.41609	.	0.165937	0.29159	N	0.012976	D	0.88085	0.6342	M	0.72479	2.2	0.32859	D	0.507722	D	0.89917	1.0	D	0.76575	0.988	D	0.88235	0.2906	10	0.35671	T	0.21	-20.1143	8.8436	0.35157	0.2223:0.7777:0.0:0.0	.	76	Q9HBJ0	PLAC1_HUMAN	H	76	ENSP00000352173:R76H	ENSP00000352173:R76H	R	-	2	0	PLAC1	133528152	0.907000	0.30839	0.869000	0.34112	0.580000	0.36256	1.622000	0.36997	1.226000	0.43582	0.600000	0.82982	CGT	C|0.999;T|0.001	0.001	strong		0.488	PLAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058375.1	NM_021796		T	133700486	C	T	133700486	3	4	14	1	0	0	0	0	1	0	0	0	12021	536	19	1	415	1	PLAC1	23	133700486	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	10517594	133700486	21570074	137	1918											
LDOC1	23641	hgsc.bcm.edu	37	chrX	140271025	140271025	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	taaactcggggagccgggagCtctcgccattaaacgtttcg	9	9	12	11	5	1	0	0	0	1	0	4	2	1	2	2	3	4	2	2	3	4	3			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chrX:140271025C>A	ENST00000370526.2	-	1	285	c.182G>T	c.(181-183)aGc>aTc	p.S61I	LDOC1_ENST00000460721.1_Intron	NM_012317.2	NP_036449.1	O95751	LDOC1_HUMAN	leucine zipper, down-regulated in cancer 1	61					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)					GAGCCGGGAGCTCTCGCCATT	0.617																																					p.S61I		Atlas-SNP	.											.	LDOC1	26	.	0			c.G182T						PASS	.						49	44	45					X																	140271025		2203	4300	6503	SO:0001583	missense	23641	exon1			CGGGAGCTCTCGC	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.182G>T	X.37:g.140271025C>A	ENSP00000359557:p.Ser61Ile	54	0	0		35	24	0.685714	NM_012317	Q6IAR6	Missense_Mutation	SNP	ENST00000370526.2	37	CCDS14672.1	.	.	.	.	.	.	.	.	.	.	.	12.62	1.991895	0.35131	.	.	ENSG00000182195	ENST00000370526	T	0.32023	1.47	3.61	1.75	0.24633	.	0.179052	0.36591	N	0.002511	T	0.22244	0.0536	L	0.46157	1.445	0.09310	N	0.999999	P	0.39665	0.682	B	0.33690	0.168	T	0.09885	-1.0654	10	0.51188	T	0.08	-8.3488	8.8927	0.35444	0.0:0.5574:0.4426:0.0	.	61	O95751	LDOC1_HUMAN	I	61	ENSP00000359557:S61I	ENSP00000359557:S61I	S	-	2	0	LDOC1	140098691	0.893000	0.30496	0.335000	0.25508	0.944000	0.59088	0.619000	0.24388	0.331000	0.23511	0.287000	0.19450	AGC	.	.	none		0.617	LDOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058592.1	NM_012317		A	140271025	C	A	140271025	3	1	14	1	0	0	0	0	1	0	0	0	8718	797	28	4	262	4	LDOC1	23	140271025	Missense_Mutation	SNP	C	TCGA-FF-8047-01A-11D-2210-10	6570539	140271025	14999535	138	1919											
MTMR1	8776	hgsc.bcm.edu	37	chrX	149896207	149896207	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtgatcagcagagtggagAagattggagcacagagccat	14	6	15	6	0	1	5	1	1	0	4	1	8	1	6	1	2	3	2	1	2	1	1			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chrX:149896207A>C	ENST00000370390.3	+	5	632	c.475A>C	c.(475-477)Aag>Cag	p.K159Q	MTMR1_ENST00000538506.1_Missense_Mutation_p.K46Q|MTMR1_ENST00000445323.2_Missense_Mutation_p.K167Q|MTMR1_ENST00000544228.1_Missense_Mutation_p.K159Q|MTMR1_ENST00000542156.1_Missense_Mutation_p.K159Q|MTMR1_ENST00000451863.2_Missense_Mutation_p.K159Q|MTMR1_ENST00000541925.1_Missense_Mutation_p.K65Q	NM_003828.2	NP_003819.1	Q13613	MTMR1_HUMAN	myotubularin related protein 1	159	GRAM.				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)					CAGAGTGGAGAAGATTGGAGC	0.423																																					p.K159Q		Atlas-SNP	.											.	MTMR1	82	.	0			c.A475C						PASS	.						125	108	114					X																	149896207		2203	4300	6503	SO:0001583	missense	8776	exon5			GTGGAGAAGATTG	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.475A>C	X.37:g.149896207A>C	ENSP00000359417:p.Lys159Gln	196	0	0		122	92	0.754098	NM_003828	A0A024RC07|Q9UBX6|Q9UEM0|Q9UQD5	Missense_Mutation	SNP	ENST00000370390.3	37	CCDS14695.1	.	.	.	.	.	.	.	.	.	.	a	20.2	3.953853	0.73902	.	.	ENSG00000063601	ENST00000541925;ENST00000493995;ENST00000439546;ENST00000429965;ENST00000434699;ENST00000542156;ENST00000370390;ENST00000490316;ENST00000445323;ENST00000544228;ENST00000451863;ENST00000438018;ENST00000436701;ENST00000538506	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.90732	-2.72;-2.72;-2.72;-2.72;-2.72;-2.72;-2.72;-2.72;-2.72;-2.72;-2.72;-2.72;-2.72;-2.72	5.08	5.08	0.68730	GRAM (2);	0.154112	0.56097	D	0.000028	D	0.94275	0.8161	M	0.80847	2.515	0.58432	D	0.999997	P;P;D	0.57899	0.921;0.904;0.981	P;P;P	0.58970	0.849;0.704;0.804	D	0.94951	0.8100	10	0.87932	D	0	.	14.1476	0.65360	1.0:0.0:0.0:0.0	.	159;167;159	Q13613;F8WA39;Q8NEC6	MTMR1_HUMAN;.;.	Q	65;65;65;65;65;159;159;176;167;159;159;123;140;46	ENSP00000441879:K65Q;ENSP00000431992:K65Q;ENSP00000404599:K65Q;ENSP00000390736:K65Q;ENSP00000405946:K65Q;ENSP00000445281:K159Q;ENSP00000359417:K159Q;ENSP00000436957:K176Q;ENSP00000414178:K167Q;ENSP00000440534:K159Q;ENSP00000387446:K159Q;ENSP00000389884:K123Q;ENSP00000414925:K140Q;ENSP00000443444:K46Q	ENSP00000359417:K159Q	K	+	1	0	MTMR1	149646865	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	5.001000	0.63946	1.787000	0.52448	0.441000	0.28932	AAG	.	.	none		0.423	MTMR1-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060863.2	NM_003828, NM_176789		C	149896207	A	C	149896207	3	2	14	1	0	0	0	0	1	0	0	0	9947	247	9	5	493	5	MTMR1	23	149896207	Missense_Mutation	SNP	A	TCGA-FF-8047-01A-11D-2210-10	9625182	149896207	5374353	139	1920											
MTMR1	8776	hgsc.bcm.edu	37	chrX	149896262	149896262	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggtatagagatagtgtgcaAggtataatagaaacgccaag	16	9	12	4	1	0	2	0	0	0	2	0	3	0	2	1	2	2	3	1	2	9	6			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chrX:149896262A>G	ENST00000370390.3	+	5	687	c.530A>G	c.(529-531)aAg>aGg	p.K177R	MTMR1_ENST00000538506.1_Splice_Site_p.K64R|MTMR1_ENST00000445323.2_Splice_Site_p.K185R|MTMR1_ENST00000544228.1_Splice_Site_p.K177R|MTMR1_ENST00000542156.1_Splice_Site_p.K177R|MTMR1_ENST00000451863.2_Splice_Site_p.K177R|MTMR1_ENST00000541925.1_Splice_Site_p.K83R	NM_003828.2	NP_003819.1	Q13613	MTMR1_HUMAN	myotubularin related protein 1	177					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)					ATAGTGTGCAAGGTATAATAG	0.423																																					p.K177R		Atlas-SNP	.											.	MTMR1	82	.	0			c.A530G						PASS	.						89	81	84					X																	149896262		2203	4300	6503	SO:0001630	splice_region_variant	8776	exon5			TGTGCAAGGTATA	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.531+1A>G	X.37:g.149896262A>G		110	0	0		67	50	0.746269	NM_003828	A0A024RC07|Q9UBX6|Q9UEM0|Q9UQD5	Missense_Mutation	SNP	ENST00000370390.3	37	CCDS14695.1	.	.	.	.	.	.	.	.	.	.	a	24.9	4.582513	0.86748	.	.	ENSG00000063601	ENST00000541925;ENST00000493995;ENST00000439546;ENST00000429965;ENST00000434699;ENST00000542156;ENST00000370390;ENST00000445323;ENST00000544228;ENST00000451863;ENST00000538506	D;D;D;D;D;D;D;D;D;D;D	0.88277	-2.36;-2.36;-2.36;-2.36;-2.36;-2.36;-2.36;-2.36;-2.36;-2.36;-2.36	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	D	0.94029	0.8087	M	0.78637	2.42	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.97110	1.0;0.993;0.999	D	0.94719	0.7899	10	0.87932	D	0	.	14.1476	0.65360	1.0:0.0:0.0:0.0	.	177;185;177	Q13613;F8WA39;Q8NEC6	MTMR1_HUMAN;.;.	R	83;83;83;83;83;177;177;185;177;177;64	ENSP00000441879:K83R;ENSP00000431992:K83R;ENSP00000404599:K83R;ENSP00000390736:K83R;ENSP00000405946:K83R;ENSP00000445281:K177R;ENSP00000359417:K177R;ENSP00000414178:K185R;ENSP00000440534:K177R;ENSP00000387446:K177R;ENSP00000443444:K64R	ENSP00000359417:K177R	K	+	2	0	MTMR1	149646920	1.000000	0.71417	1.000000	0.80357	0.801000	0.45260	9.026000	0.93700	1.787000	0.52448	0.441000	0.28932	AAG	.	.	none		0.423	MTMR1-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060863.2	NM_003828, NM_176789	Missense_Mutation	G	149896262	A	G	149896262	5	3	14	1	0	0	0	0	0	0	1	0	9947	86	3	3	548	3	MTMR1	23	149896262	Splice_Site	SNP	A	TCGA-FF-8047-01A-11D-2210-10	55	149896262	5374298	140	1921											
PLEKHM2	23207	hgsc.bcm.edu	37	chr1	16051840	16051840	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcacagacacggtcagtggTccccgctccacagcctccga	8	6	9	18	3	2	1	2	0	0	1	5	2	5	1	5	2	1	1	5	2	0	0			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:16051840T>C	ENST00000375799.3	+	8	968	c.741T>C	c.(739-741)ggT>ggC	p.G247G	RP11-288I21.1_ENST00000453804.1_RNA|PLEKHM2_ENST00000375793.2_Silent_p.G227G	NM_015164.2	NP_055979.2	Q8IWE5	PKHM2_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 2	247	Interaction with KIF5B.				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)		CGGTCAGTGGTCCCCGCTCCA	0.662																																					p.G247G		Atlas-SNP	.											.	PLEKHM2	94	.	0			c.T741C						PASS	.						23	31	28					1																	16051840		1874	3784	5658	SO:0001819	synonymous_variant	23207	exon8			CAGTGGTCCCCGC	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.741T>C	1.37:g.16051840T>C		85	0	0		95	4	0.0421053	NM_015164	O94928|Q5VT65|Q6NUH9|Q7L8G1|Q8IVT7|Q8N2T4|Q96AY0|Q9NTF7	Silent	SNP	ENST00000375799.3	37	CCDS44063.1																																																																																			.	.	none		0.662	PLEKHM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008463.1	NM_015164		C	16051840	T	C	16051840	2	2	15	1	0	0	0	0	0	0	0	1	12090	1654	58	3		3	PLEKHM2	1	16051840	Silent	SNP	T	TCGA-FF-8061-01A-11D-2210-10		16051840	233198781	1	1922											
KIF17	57576	hgsc.bcm.edu	37	chr1	21031010	21031010	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgatctcctcctggtactcGcgaagcagcgcatccttggg	6	11	11	13	3	1	1	0	1	1	0	5	2	3	1	3	2	3	3	3	2	2	3	rs76507805		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:21031010G>A	ENST00000247986.2	-	5	1363	c.1053C>T	c.(1051-1053)cgC>cgT	p.R351R	KIF17_ENST00000375044.1_Silent_p.R251R|KIF17_ENST00000400463.3_Silent_p.R351R			Q9P2E2	KIF17_HUMAN	kinesin family member 17	351					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)		CCTGGTACTCGCGAAGCAGCG	0.602													G|||	1	0.000199681	0.0	0.0	5008	,	,		15725	0.001		0.0	False		,,,				2504	0.0				p.R351R		Atlas-SNP	.											KIF17,colon,carcinoma,0,1	KIF17	130	1	0			c.C1053T						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	134	105	115		1053,1053	-4.3	1	1	dbSNP_131	115	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	KIF17	NM_001122819.1,NM_020816.2	,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	,	351/1029,351/1030	21031010	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	57576	exon5			GTACTCGCGAAGC	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.1053C>T	1.37:g.21031010G>A		183	0	0		168	53	0.315476	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Silent	SNP	ENST00000247986.2	37	CCDS213.1																																																																																			G|1.000;A|0.000	0.000	strong		0.602	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816		A	21031010	G	A	21031010	2	1	15	1	0	0	0	0	0	0	0	1	8288	1074	38	1		1	KIF17	1	21031010	Silent	SNP	G	TCGA-FF-8061-01A-11D-2210-10	4979170	21031010	228219611	2	1923											
COL16A1	1307	hgsc.bcm.edu	37	chr1	32149326	32149326	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	acctggggtccctggactccCcttcctggaggccctggctc	3	9	12	17	0	0	0	0	0	0	0	4	2	3	2	6	6	0	1	6	6	0	1			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:32149326C>T	ENST00000373672.3	-	34	2877	c.2361G>A	c.(2359-2361)agG>agA	p.R787R	COL16A1_ENST00000271069.6_Silent_p.R786R|COL16A1_ENST00000373668.3_Silent_p.R787R	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	787	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)		CCTGGACTCCCCTTCCTGGAG	0.602																																					p.R787R	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.G2361A						PASS	.						73	92	86					1																	32149326		1979	4151	6130	SO:0001819	synonymous_variant	1307	exon34			GACTCCCCTTCCT	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.2361G>A	1.37:g.32149326C>T		64	0	0		73	31	0.424658	NM_001856	Q16593|Q59F89|Q71RG9	Silent	SNP	ENST00000373672.3	37	CCDS41297.1																																																																																			.	.	none		0.602	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856		T	32149326	C	T	32149326	2	4	15	1	0	0	0	0	0	0	0	1	3675	622	22	2		2	COL16A1	1	32149326	Silent	SNP	C	TCGA-FF-8061-01A-11D-2210-10	11118316	32149326	217101295	3	1924											
COL16A1	1307	hgsc.bcm.edu	37	chr1	32164126	32164126	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcacttgaaacagataccaCgtcttctggtgggtgtgttt	8	14	11	8	1	3	2	1	1	2	1	3	2	3	2	1	2	2	1	1	2	2	4			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:32164126C>T	ENST00000373672.3	-	5	864	c.348G>A	c.(346-348)acG>acA	p.T116T	COL16A1_ENST00000271069.6_Silent_p.T116T|COL16A1_ENST00000373668.3_Silent_p.T116T	NM_001856.3	NP_001847.3	Q07092	COGA1_HUMAN	collagen, type XVI, alpha 1	116	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)		ACAGATACCACGTCTTCTGGT	0.557																																					p.T116T	Colon(143;498 1786 21362 25193 36625)	Atlas-SNP	.											.	COL16A1	137	.	0			c.G348A						PASS	.						122	128	126					1																	32164126		2023	4176	6199	SO:0001819	synonymous_variant	1307	exon5			ATACCACGTCTTC	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.348G>A	1.37:g.32164126C>T		58	0	0		83	7	0.0843373	NM_001856	Q16593|Q59F89|Q71RG9	Silent	SNP	ENST00000373672.3	37	CCDS41297.1																																																																																			.	.	none		0.557	COL16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011057.2	NM_001856		T	32164126	C	T	32164126	2	4	15	1	0	0	0	0	0	0	0	1	3675	523	19	1		1	COL16A1	1	32164126	Silent	SNP	C	TCGA-FF-8061-01A-11D-2210-10	14800	32164126	217086495	4	1925											
DPYD	1806	hgsc.bcm.edu	37	chr1	97548004	97548004	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccaaatgttccaaggtacTgcagtgcttttcctattaca	11	13	6	11	0	0	0	0	0	0	0	2	0	2	0	3	1	4	4	3	1	5	6	rs568169006		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:97548004T>C	ENST00000370192.3	-	22	2889	c.2789A>G	c.(2788-2790)cAg>cGg	p.Q930R		NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	930					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)	TCCAAGGTACTGCAGTGCTTT	0.343																																					p.Q930R		Atlas-SNP	.											.	DPYD	219	.	0			c.A2789G						PASS	.						206	194	198					1																	97548004		2203	4299	6502	SO:0001583	missense	1806	exon22			AGGTACTGCAGTG	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.2789A>G	1.37:g.97548004T>C	ENSP00000359211:p.Gln930Arg	116	0	0		109	44	0.40367	NM_000110	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	37	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	T	6.890	0.533671	0.13188	.	.	ENSG00000188641	ENST00000370192	D	0.89939	-2.59	5.82	3.5	0.40072	.	0.511060	0.21827	N	0.068524	T	0.70789	0.3264	L	0.39245	1.2	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.63651	-0.6589	10	0.31617	T	0.26	-0.5352	6.781	0.23646	0.0:0.1332:0.1289:0.7378	.	930	Q12882	DPYD_HUMAN	R	930	ENSP00000359211:Q930R	ENSP00000359211:Q930R	Q	-	2	0	DPYD	97320592	1.000000	0.71417	0.988000	0.46212	0.110000	0.19582	1.641000	0.37197	0.461000	0.27071	-0.291000	0.09656	CAG	.	.	none		0.343	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110		C	97548004	T	C	97548004	3	2	15	1	0	0	0	0	1	0	0	0	4747	1580	55	3	296	3	DPYD	1	97548004	Missense_Mutation	SNP	T	TCGA-FF-8061-01A-11D-2210-10	65383878	97548004	151702617	5	1926											
OVGP1	5016	hgsc.bcm.edu	37	chr1	111957523	111957523	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cacagactgatgactcacagGggtcacagactgatgaccca	13	6	10	12	0	2	6	2	4	0	2	2	6	2	6	1	2	0	0	1	2	0	0	rs3767608|rs201350653		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:111957523G>T	ENST00000369732.3	-	11	1655	c.1600C>A	c.(1600-1602)Cct>Act	p.P534T		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	534					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)	p.T597_V604delTPVSHQSV(2)|p.T533_V540delTPVSHQSV(2)		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)		TGACTCACAGGGGTCACAGAC	0.537																																					p.P534T		Atlas-SNP	.											OVGP1_ENST00000369728,NS,carcinoma,0,2	OVGP1	177	2	4	Deletion - In frame(4)	haematopoietic_and_lymphoid_tissue(2)|stomach(2)	c.C1600A						PASS	.																																			SO:0001583	missense	5016	exon11			TCACAGGGGTCAC	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.1600C>A	1.37:g.111957523G>T	ENSP00000358747:p.Pro534Thr	130	0	0		144	22	0.152778	NM_002557	A0AV19|B9EGE1|Q15841	Missense_Mutation	SNP	ENST00000369732.3	37	CCDS834.1	.	.	.	.	.	.	.	.	.	.	G	9.491	1.100669	0.20552	.	.	ENSG00000085465	ENST00000369732;ENST00000369728;ENST00000434331	T	0.19105	2.17	2.35	-0.421	0.12332	.	.	.	.	.	T	0.03608	0.0103	N	0.22421	0.69	0.09310	N	1	B;B	0.13145	0.007;0.0	B;B	0.06405	0.002;0.0	T	0.42999	-0.9418	9	0.36615	T	0.2	9.8099	5.0173	0.14343	0.4538:0.0:0.5462:0.0	.	534;598	Q12889;Q59HH5	OVGP1_HUMAN;.	T	534;598;342	ENSP00000358747:P534T	ENSP00000358743:P598T	P	-	1	0	OVGP1	111759046	0.000000	0.05858	0.001000	0.08648	0.112000	0.19704	-1.483000	0.02318	-0.296000	0.08947	0.460000	0.39030	CCT	G|1.000;A|0.000	.	alt		0.537	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557		T	111957523	G	T	111957523	3	4	15	1	0	0	0	0	1	0	0	0	11334	1232	43	4	440	4	OVGP1	1	111957523	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	14409519	111957523	137293098	6	1927											
FMO5	2330	hgsc.bcm.edu	37	chr1	146656089	146656089	+	IGR	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttatgtctccttaggcccCtttattccgggacaatttct	6	17	7	11	1	2	0	0	0	2	0	4	1	3	1	4	2	0	1	4	2	4	6			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:146656089C>T	ENST00000254090.4	-	0	2632				RP11-337C18.8_ENST00000606757.1_RNA|FMO5_ENST00000441068.2_Silent_p.K459K|RP11-337C18.10_ENST00000606856.1_RNA|RP11-337C18.8_ENST00000607149.1_RNA	NM_001461.2	NP_001452.2	P49326	FMO5_HUMAN	flavin containing monooxygenase 5							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)			breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(9)|ovary(3)|upper_aerodigestive_tract(1)	25	all_hematologic(923;0.0487)					ccttaggcccctttattccgg	0.348																																					p.K459K		Atlas-SNP	.											.	FMO5	94	.	0			c.G1377A						PASS	.						98	87	90					1																	146656089		692	1591	2283	SO:0001628	intergenic_variant	2330	exon9			AGGCCCCTTTATT	Z47553	CCDS926.1, CCDS44209.1, CCDS44210.1	1q21.1	2011-08-04			ENSG00000131781	ENSG00000131781			3773	protein-coding gene	gene with protein product		603957				8786146, 9119381	Standard	NM_001461		Approved		uc001epi.2	P49326	OTTHUMG00000014607		1.37:g.146656089C>T		120	0	0		76	4	0.0526316	NM_001144829	B2RBG1|C9JJD1|Q8IV22	Silent	SNP	ENST00000254090.4	37	CCDS926.1																																																																																			.	.	none		0.348	FMO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040373.2	NM_001461		T	146656089	C	T	146656089	1	4	15	0	1	0	0	0	0	0	0	0	5966	680	24	2		2	FMO5	1	146656089	IGR	SNP	C	TCGA-FF-8061-01A-11D-2210-10	34698566	146656089	102594532	7	1928											
HIST2H2BE	8349	hgsc.bcm.edu	37	chr1	149857830	149857830	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacttggagctggtgtactTggtgaccgccttggtgccct	4	13	13	11	1	1	1	1	1	0	0	1	2	1	2	3	4	3	2	3	4	1	4			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:149857830T>C	ENST00000369155.2	-	1	402	c.361A>G	c.(361-363)Aag>Gag	p.K121E	HIST2H2AC_ENST00000331380.2_5'Flank|BOLA1_ENST00000369153.2_5'Flank	NM_003528.2	NP_003519.1	Q16778	H2B2E_HUMAN	histone cluster 2, H2be	121					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)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	14	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			CTGGTGTACTTGGTGACCGCC	0.667																																					p.K121E		Atlas-SNP	.											.	HIST2H2BE	33	.	0			c.A361G						PASS	.						30	35	33					1																	149857830		2202	4299	6501	SO:0001583	missense	8349	exon1			TGTACTTGGTGAC	AY131979	CCDS936.1	1q21.2	2011-01-27	2006-10-11	2003-03-07	ENSG00000184678	ENSG00000184678		"Histones / Replication-dependent"	4760	protein-coding gene	gene with protein product		601831	"H2B histone family, member Q", "histone 2, H2be"	H2B, H2BFQ		1469070, 12408966	Standard	NM_003528		Approved	H2B/q, H2B.1	uc001etc.3	Q16778	OTTHUMG00000012095	ENST00000369155.2:c.361A>G	1.37:g.149857830T>C	ENSP00000358151:p.Lys121Glu	80	0	0		117	38	0.324786	NM_003528	A3KMC7|A8K110|Q4KMY1|Q5QNX0|Q9UE88	Missense_Mutation	SNP	ENST00000369155.2	37	CCDS936.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.909008	0.92107	.	.	ENSG00000184678	ENST00000369155	T	0.46063	0.88	6.07	6.07	0.98685	Histone-fold (2);	0.000000	0.85682	D	0.000000	T	0.54078	0.1836	H	0.98664	4.295	0.38928	D	0.957879	P	0.52842	0.956	B	0.40329	0.326	T	0.76302	-0.3009	10	0.87932	D	0	.	15.47	0.75434	0.0:0.0:0.0:1.0	.	121	Q16778	H2B2E_HUMAN	E	121	ENSP00000358151:K121E	ENSP00000358151:K121E	K	-	1	0	HIST2H2BE	148124454	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.924000	0.87555	2.330000	0.79161	0.477000	0.44152	AAG	.	.	none		0.667	HIST2H2BE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033455.1	NM_003528		C	149857830	T	C	149857830	3	2	15	1	0	0	0	0	1	0	0	0	7188	1821	63	3	23	3	HIST2H2BE	1	149857830	Missense_Mutation	SNP	T	TCGA-FF-8061-01A-11D-2210-10	3201741	149857830	99392791	8	1929											
PFDN2	5202	hgsc.bcm.edu	37	chr1	161071920	161071920	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctccaaccatgcggtagcacTtacgagtttcatctacctcc	9	11	6	15	2	2	0	1	0	1	0	4	1	4	0	4	1	5	3	4	1	4	4			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:161071920T>G	ENST00000368010.3	-	3	290	c.206A>C	c.(205-207)aAg>aCg	p.K69T	PFDN2_ENST00000468311.1_Intron	NM_012394.3	NP_036526.2	Q9UHV9	PFD2_HUMAN	prefoldin subunit 2	69					'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)			GCGGTAGCACTTACGAGTTTC	0.517																																					p.K69T		Atlas-SNP	.											.	PFDN2	10	.	0			c.A206C						PASS	.						134	116	122					1																	161071920		2203	4300	6503	SO:0001583	missense	5202	exon3			TAGCACTTACGAG	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.206A>C	1.37:g.161071920T>G	ENSP00000356989:p.Lys69Thr	144	0	0		123	9	0.0731707	NM_012394	Q9P0P7|Q9UN05	Missense_Mutation	SNP	ENST00000368010.3	37	CCDS1217.1	.	.	.	.	.	.	.	.	.	.	T	20.5	3.994360	0.74703	.	.	ENSG00000143256	ENST00000368010	T	0.48522	0.81	5.15	2.82	0.32997	Prefoldin beta-like (1);Prefoldin (1);	0.088219	0.85682	D	0.000000	T	0.53190	0.1781	M	0.79011	2.435	0.80722	D	1	D	0.89917	1.0	D	0.70487	0.969	T	0.56571	-0.7957	10	0.59425	D	0.04	-14.807	8.0692	0.30678	0.0:0.1676:0.0:0.8324	.	69	Q9UHV9	PFD2_HUMAN	T	69	ENSP00000356989:K69T	ENSP00000356989:K69T	K	-	2	0	PFDN2	159338544	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	1.467000	0.35321	0.423000	0.26033	0.459000	0.35465	AAG	.	.	none		0.517	PFDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077100.1	NM_012394		G	161071920	T	G	161071920	3	3	15	1	0	0	0	0	1	0	0	0	11765	1609	56	5	266	5	PFDN2	1	161071920	Missense_Mutation	SNP	T	TCGA-FF-8061-01A-11D-2210-10	11214090	161071920	88178701	9	1930											
CFH	3075	hgsc.bcm.edu	37	chr1	196648799	196648799	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataaatggatctcctatatcTcagaagattatttataagga	16	14	6	5	0	2	2	1	0	2	2	4	4	2	4	1	2	0	0	1	2	8	7			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:196648799T>C	ENST00000359637.2	+	5	536	c.474T>C	c.(472-474)tcT>tcC	p.S158S	CFH_ENST00000367429.4_Silent_p.S222S|CFH_ENST00000439155.2_Silent_p.S222S			P08603	CFAH_HUMAN	complement factor H	222	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						CTCCTATATCTCAGAAGATTA	0.308																																					p.S222S		Atlas-SNP	.											.	CFH	251	.	0			c.T666C						PASS	.						54	58	57					1																	196648799		2203	4297	6500	SO:0001819	synonymous_variant	3075	exon6			TATATCTCAGAAG	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.474T>C	1.37:g.196648799T>C		118	0	0		88	29	0.329545	NM_001014975	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Silent	SNP	ENST00000359637.2	37																																																																																				.	.	none		0.308	CFH-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000087502.1	NM_000186		C	196648799	T	C	196648799	2	2	15	1	0	0	0	0	0	0	0	1	3285	1538	54	3		3	CFH	1	196648799	Silent	SNP	T	TCGA-FF-8061-01A-11D-2210-10	35576879	196648799	52601822	10	1931											
BTG2	7832	hgsc.bcm.edu	37	chr1	203276256	203276256	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctacaaacaccactggtttcCcgaaaagccgtccaagggct	12	7	8	14	2	0	0	0	0	0	0	2	1	2	0	4	2	3	2	4	2	5	2			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:203276256C>T	ENST00000290551.4	+	2	238	c.167C>T	c.(166-168)cCc>cTc	p.P56L	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	56					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			CACTGGTTTCCCGAAAAGCCG	0.592																																					p.P56L		Atlas-SNP	.											.	BTG2	16	.	0			c.C167T						PASS	.						41	43	43					1																	203276256		2203	4300	6503	SO:0001583	missense	7832	exon2			GGTTTCCCGAAAA		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.167C>T	1.37:g.203276256C>T	ENSP00000290551:p.Pro56Leu	84	0	0		106	40	0.377358	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	C	19.48	3.836232	0.71373	.	.	ENSG00000159388	ENST00000290551	T	0.31510	1.49	4.53	2.64	0.31445	Anti-proliferative protein (4);	0.073067	0.53938	D	0.000041	T	0.58047	0.2095	M	0.90369	3.11	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.61004	-0.7150	10	0.87932	D	0	-46.4298	8.7979	0.34890	0.0:0.7636:0.1512:0.0852	.	56	P78543	BTG2_HUMAN	L	56	ENSP00000290551:P56L	ENSP00000290551:P56L	P	+	2	0	BTG2	201542879	1.000000	0.71417	0.819000	0.32651	0.843000	0.47879	5.614000	0.67695	0.527000	0.28560	0.313000	0.20887	CCC	.	.	none		0.592	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		T	203276256	C	T	203276256	3	4	15	1	0	0	0	0	1	0	0	0	1556	623	22	2	173	2	BTG2	1	203276256	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	6627457	203276256	45974365	11	1932											
FCAMR	83953	hgsc.bcm.edu	37	chr1	207140994	207140994	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctcttcctctcctcaccacTtcctgtttgcagaaggggaa	7	13	7	14	0	3	1	1	0	2	1	7	2	5	2	4	2	1	2	4	2	2	3			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:207140994T>C	ENST00000324852.4	-	2	516	c.42A>G	c.(40-42)gaA>gaG	p.E14E	FCAMR_ENST00000400962.3_Silent_p.E14E|FCAMR_ENST00000450945.2_Silent_p.E14E	NM_001170631.1	NP_001164102.1	Q8WWV6	FCAMR_HUMAN	Fc receptor, IgA, IgM, high affinity	315					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						TCCTCACCACTTCCTGTTTGC	0.428																																					p.E14E	Ovarian(199;1883 2142 16966 44409 45154)	Atlas-SNP	.											.	FCAMR	125	.	0			c.A42G						PASS	.						169	143	151					1																	207140994		1568	3582	5150	SO:0001819	synonymous_variant	83953	exon2			CACCACTTCCTGT	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.42A>G	1.37:g.207140994T>C		117	0	0		139	6	0.0431655	NM_001170631	Q32M82|Q8WWV5|Q96SA2	Silent	SNP	ENST00000324852.4	37	CCDS53468.1																																																																																			.	.	none		0.428	FCAMR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088969.2	NM_032029		C	207140994	T	C	207140994	2	2	15	1	0	0	0	0	0	0	0	1	5780	1606	56	3		3	FCAMR	1	207140994	Silent	SNP	T	TCGA-FF-8061-01A-11D-2210-10	3864738	207140994	42109627	12	1933											
PLXNA2	5362	hgsc.bcm.edu	37	chr1	208216497	208216497	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccaggtaagggattcctgagCggtccaggtcactggtcaac	9	8	13	11	1	2	1	2	1	0	0	4	2	4	2	3	5	2	1	3	5	2	2	rs572241200		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:208216497C>T	ENST00000367033.3	-	21	4683	c.3926G>A	c.(3925-3927)cGc>cAc	p.R1309H		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	1309					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)		GATTCCTGAGCGGTCCAGGTC	0.582													C|||	1	0.000199681	0.0	0.0	5008	,	,		19355	0.001		0.0	False		,,,				2504	0.0				p.R1309H		Atlas-SNP	.											PLXNA2,NS,carcinoma,0,1	PLXNA2	178	1	0			c.G3926A						PASS	.						94	89	91					1																	208216497		2203	4300	6503	SO:0001583	missense	5362	exon21			CCTGAGCGGTCCA	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.3926G>A	1.37:g.208216497C>T	ENSP00000356000:p.Arg1309His	110	0	0		117	38	0.324786	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	37	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	C	36	5.774387	0.96922	.	.	ENSG00000076356	ENST00000367033	T	0.00932	5.53	5.42	5.42	0.78866	.	0.048395	0.85682	D	0.000000	T	0.01835	0.0058	N	0.24115	0.695	0.80722	D	1	D	0.67145	0.996	P	0.50970	0.655	T	0.70963	-0.4729	10	0.87932	D	0	.	19.2386	0.93873	0.0:1.0:0.0:0.0	.	1309	O75051	PLXA2_HUMAN	H	1309	ENSP00000356000:R1309H	ENSP00000356000:R1309H	R	-	2	0	PLXNA2	206283120	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.454000	0.80714	2.543000	0.85770	0.650000	0.86243	CGC	.	.	none		0.582	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		T	208216497	C	T	208216497	3	4	15	1	0	0	0	0	1	0	0	0	12129	768	27	1	1806	1	PLXNA2	1	208216497	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	1075503	208216497	41034124	13	1934											
USH2A	7399	hgsc.bcm.edu	37	chr1	216495278	216495278	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaggcatctatatggctggcTtgttgtgtcgcagttatcgg	6	14	14	7	2	1	0	0	0	1	0	3	1	1	0	0	4	0	6	0	4	3	5			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr1:216495278T>G	ENST00000307340.3	-	9	1977	c.1591A>C	c.(1591-1593)Agc>Cgc	p.S531R	USH2A_ENST00000366943.2_Missense_Mutation_p.S531R|USH2A_ENST00000366942.3_Missense_Mutation_p.S531R	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	531	Laminin EGF-like 1. {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)		TATGGCTGGCTTGTTGTGTCG	0.413										HNSCC(13;0.011)																											p.S531R		Atlas-SNP	.											.	USH2A	1168	.	0			c.A1591C						PASS	.						145	133	137					1																	216495278		2203	4300	6503	SO:0001583	missense	7399	exon9			GCTGGCTTGTTGT	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.1591A>C	1.37:g.216495278T>G	ENSP00000305941:p.Ser531Arg	172	0	0		151	9	0.0596026	NM_007123	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	T	6.897	0.535088	0.13188	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.63913	-0.07;-0.07;-0.07	5.65	2.07	0.26955	EGF-like, laminin (3);	0.596017	0.14863	N	0.293961	T	0.45994	0.1370	L	0.33189	0.99	0.09310	N	1	B;B	0.15473	0.012;0.013	B;B	0.17433	0.005;0.018	T	0.27872	-1.0061	10	0.15952	T	0.53	.	8.4255	0.32727	0.0:0.2872:0.0:0.7128	.	531;531	O75445-2;O75445	.;USH2A_HUMAN	R	531	ENSP00000305941:S531R;ENSP00000355910:S531R;ENSP00000355909:S531R	ENSP00000305941:S531R	S	-	1	0	USH2A	214561901	0.000000	0.05858	0.024000	0.17045	0.041000	0.13682	0.201000	0.17276	0.097000	0.17492	0.455000	0.32223	AGC	.	.	none		0.413	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		G	216495278	T	G	216495278	3	3	15	1	0	0	0	0	1	0	0	0	17051	1609	56	5	14287	5	USH2A	1	216495278	Missense_Mutation	SNP	T	TCGA-FF-8061-01A-11D-2210-10	8278781	216495278	32755343	14	1935											
SH3YL1	26751	hgsc.bcm.edu	37	chr2	218939	218939	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tccagcttgaaaattcaaatCcccaggctgctgtccttcaa	11	11	6	13	0	2	1	2	1	0	0	5	1	5	1	4	1	2	3	4	1	4	3			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:218939C>T	ENST00000405430.1	-	12	1277	c.901G>A	c.(901-903)Gat>Aat	p.D301N	SH3YL1_ENST00000415006.2_Missense_Mutation_p.D205N|SH3YL1_ENST00000356150.5_Missense_Mutation_p.D301N|SH3YL1_ENST00000468321.1_5'UTR|SH3YL1_ENST00000403658.1_Missense_Mutation_p.D186N|SH3YL1_ENST00000403657.1_Missense_Mutation_p.D186N|SH3YL1_ENST00000403712.2_Missense_Mutation_p.D282N			Q96HL8	SH3Y1_HUMAN	SH3 and SYLF domain containing 1	301	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)		AAATTCAAATCCCCAGGCTGC	0.373																																					p.D301N		Atlas-SNP	.											.	SH3YL1	49	.	0			c.G901A						PASS	.						102	93	96					2																	218939		1826	4079	5905	SO:0001583	missense	26751	exon10			TCAAATCCCCAGG		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.901G>A	2.37:g.218939C>T	ENSP00000384269:p.Asp301Asn	111	0	0		94	43	0.457447	NM_015677	A8K8E7|B7WNJ4|B7WPL6|Q8NEL2|Q9H5X4|Q9Y3V5	Missense_Mutation	SNP	ENST00000405430.1	37		.	.	.	.	.	.	.	.	.	.	C	32	5.170694	0.94807	.	.	ENSG00000035115	ENST00000415006;ENST00000403712;ENST00000403657;ENST00000405430;ENST00000356150;ENST00000403658;ENST00000451005	T;T;T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85;0.85;0.85	6.03	6.03	0.97812	Src homology-3 domain (5);	0.108509	0.64402	D	0.000010	T	0.81969	0.4935	H	0.98487	4.245	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.97110	1.0;1.0;0.997;0.998	D	0.88284	0.2938	10	0.87932	D	0	-11.8105	18.0605	0.89375	0.0:1.0:0.0:0.0	.	186;282;301;205	Q96HL8-4;Q96HL8-2;Q96HL8;Q96HL8-3	.;.;SH3Y1_HUMAN;.	N	205;282;186;301;301;186;214	ENSP00000404143:D205N;ENSP00000384276:D282N;ENSP00000385668:D186N;ENSP00000384269:D301N;ENSP00000348471:D301N;ENSP00000383928:D186N;ENSP00000416312:D214N	ENSP00000348471:D301N	D	-	1	0	SH3YL1	208939	1.000000	0.71417	0.981000	0.43875	0.982000	0.71751	6.441000	0.73439	2.854000	0.98071	0.655000	0.94253	GAT	.	.	none		0.373	SH3YL1-003	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000322352.1	NM_015677		T	218939	C	T	218939	3	4	15	1	0	0	0	0	1	0	0	0	14278	855	30	2	131	2	SH3YL1	2	218939	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10		218939	242980434	15	1936											
AUP1	27429	hgsc.bcm.edu	37	chr2	74756500	74756500	+	5'Flank	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgtcggaacctgcgaaggacGctgtctggcagcgcgcagct	7	6	15	13	6	1	0	0	0	1	0	2	3	1	2	1	3	4	4	1	3	2	0			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:74756500G>A	ENST00000258080.3	+	0	0				AUP1_ENST00000377526.3_Silent_p.S59S|HTRA2_ENST00000352222.3_5'Flank	NM_013247.4	NP_037379.1	O43464	HTRA2_HUMAN	HtrA serine peptidase 2						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						TGCGAAGGACGCTGTCTGGCA	0.652																																					p.S59S		Atlas-SNP	.											.	AUP1	29	.	0			c.C177T						PASS	.						21	28	26					2																	74756500		2101	4228	6329	SO:0001631	upstream_gene_variant	550	exon2			AAGGACGCTGTCT		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		2.37:g.74756500G>A	Exception_encountered	117	0	0		77	57	0.74026	NM_181575	Q9HBZ4|Q9P0Y3|Q9P0Y4	Silent	SNP	ENST00000258080.3	37	CCDS1951.1																																																																																			.	.	none		0.652	HTRA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252219.2	NM_013247		A	74756500	G	A	74756500	1	1	15	0	1	0	0	0	0	0	0	0	1220	1078	38	1		1	AUP1	2	74756500	5'Flank	SNP	G	TCGA-FF-8061-01A-11D-2210-10	74537561	74756500	168442873	16	1937											
DNAH6	1768	hgsc.bcm.edu	37	chr2	84785000	84785000	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaacctgtggaactgggccaAgtttagcagcagtatttgag	12	10	12	7	0	0	1	0	1	0	0	0	2	0	2	2	2	4	4	2	2	5	4			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:84785000A>G	ENST00000237449.6	+	10	1752	c.1744A>G	c.(1744-1746)Agt>Ggt	p.S582G	DNAH6_ENST00000389394.3_Missense_Mutation_p.S582G|DNAH6_ENST00000398278.2_Missense_Mutation_p.S582G			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	582	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						AACTGGGCCAAGTTTAGCAGC	0.338																																					p.S582G		Atlas-SNP	.											.	DNAH6	194	.	0			c.A1744G						PASS	.						90	89	89					2																	84785000		2203	4300	6503	SO:0001583	missense	1768	exon11			GGGCCAAGTTTAG	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.1744A>G	2.37:g.84785000A>G	ENSP00000237449:p.Ser582Gly	70	0	0		51	18	0.352941	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	37	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	A	11.56	1.675857	0.29783	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.25749	1.78;1.91;1.78	5.09	5.09	0.68999	.	0.000000	0.64402	D	0.000007	T	0.30479	0.0766	M	0.61703	1.905	0.23920	N	0.996469	B;P	0.38827	0.0;0.649	B;B	0.41510	0.0;0.359	T	0.16837	-1.0389	10	0.25106	T	0.35	.	13.8456	0.63466	1.0:0.0:0.0:0.0	.	582;161	Q9C0G6;Q9C0G6-3	DYH6_HUMAN;.	G	582	ENSP00000374045:S582G;ENSP00000381326:S582G;ENSP00000237449:S582G	ENSP00000237449:S582G	S	+	1	0	DNAH6	84638511	1.000000	0.71417	0.627000	0.29227	0.457000	0.32468	5.904000	0.69886	1.914000	0.55421	0.459000	0.35465	AGT	.	.	none		0.338	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		G	84785000	A	G	84785000	3	3	15	1	0	0	0	0	1	0	0	0	4607	72	3	3	1782	3	DNAH6	2	84785000	Missense_Mutation	SNP	A	TCGA-FF-8061-01A-11D-2210-10	10028500	84785000	158414373	17	1938											
DUSP2	1844	hgsc.bcm.edu	37	chr2	96809900	96809900	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgcccccttaccaatgaaGcctatggcctcctggaacca	9	8	9	15	0	0	1	0	1	0	0	1	2	1	2	7	3	4	0	7	3	5	2			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:96809900G>C	ENST00000288943.4	-	3	808	c.723C>G	c.(721-723)ggC>ggG	p.G241G	AC012307.2_ENST00000449242.1_lincRNA	NM_004418.3	NP_004409.1	Q05923	DUS2_HUMAN	dual specificity phosphatase 2	241	Tyrosine-protein phosphatase.				endoderm formation (GO:0001706)|inactivation of MAPK activity (GO:0000188)|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)|protein tyrosine/threonine phosphatase activity (GO:0008330)			NS(1)|breast(1)|lung(2)|skin(1)	5		Ovarian(717;0.0228)				TACCAATGAAGCCTATGGCCT	0.592																																					p.G241G		Atlas-SNP	.											DUSP2,NS,lymphoid_neoplasm,-1,1	DUSP2	20	1	0			c.C723G						PASS	.						66	58	61					2																	96809900		2203	4300	6503	SO:0001819	synonymous_variant	1844	exon3			AATGAAGCCTATG	L11329	CCDS2016.1	2q11	2011-06-09			ENSG00000158050	ENSG00000158050		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3068	protein-coding gene	gene with protein product		603068				7806236, 7590752, 12673251	Standard	NM_004418		Approved	PAC-1	uc002svk.4	Q05923	OTTHUMG00000130456	ENST00000288943.4:c.723C>G	2.37:g.96809900G>C		60	0	0		60	25	0.416667	NM_004418	Q53T45	Silent	SNP	ENST00000288943.4	37	CCDS2016.1																																																																																			.	.	none		0.592	DUSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252847.1	NM_004418		C	96809900	G	C	96809900	2	2	15	1	0	0	0	0	0	0	0	1	4821	958	34	4		4	DUSP2	2	96809900	Silent	SNP	G	TCGA-FF-8061-01A-11D-2210-10	12024900	96809900	146389473	18	1939											
DUSP2	1844	hgsc.bcm.edu	37	chr2	96810590	96810590	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggggcctcagagcacagatcGggacagcagccctggaagcc	10	3	15	13	1	1	2	1	0	0	2	2	4	1	4	3	4	4	2	3	4	1	0	rs187607778		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:96810590G>C	ENST00000288943.4	-	2	505	c.420C>G	c.(418-420)ccC>ccG	p.P140P	AC012307.2_ENST00000449242.1_lincRNA	NM_004418.3	NP_004409.1	Q05923	DUS2_HUMAN	dual specificity phosphatase 2	140	Rhodanese. {ECO:0000255|PROSITE- ProRule:PRU00173}.				endoderm formation (GO:0001706)|inactivation of MAPK activity (GO:0000188)|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)|protein tyrosine/threonine phosphatase activity (GO:0008330)			NS(1)|breast(1)|lung(2)|skin(1)	5		Ovarian(717;0.0228)				AGCACAGATCGGGACAGCAGC	0.672													G|||	1	0.000199681	0.0	0.0014	5008	,	,		10971	0.0		0.0	False		,,,				2504	0.0				p.P140P		Atlas-SNP	.											DUSP2,NS,carcinoma,0,1	DUSP2	20	1	0			c.C420G						PASS	.						15	20	18					2																	96810590		2129	4223	6352	SO:0001819	synonymous_variant	1844	exon2			CAGATCGGGACAG	L11329	CCDS2016.1	2q11	2011-06-09			ENSG00000158050	ENSG00000158050		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3068	protein-coding gene	gene with protein product		603068				7806236, 7590752, 12673251	Standard	NM_004418		Approved	PAC-1	uc002svk.4	Q05923	OTTHUMG00000130456	ENST00000288943.4:c.420C>G	2.37:g.96810590G>C		84	0	0		97	48	0.494845	NM_004418	Q53T45	Silent	SNP	ENST00000288943.4	37	CCDS2016.1																																																																																			C|0.000;G|1.000	0.000	strong		0.672	DUSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252847.1	NM_004418		C	96810590	G	C	96810590	2	2	15	1	0	0	0	0	0	0	0	1	4821	1103	39	4		4	DUSP2	2	96810590	Silent	SNP	G	TCGA-FF-8061-01A-11D-2210-10	690	96810590	146388783	19	1940											
ZAP70	7535	hgsc.bcm.edu	37	chr2	98340878	98340878	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgccatggtgcgtgactacGtgcgccagacgtggaagctg	8	7	15	11	5	0	2	0	1	0	1	0	3	0	3	2	2	4	1	2	2	2	1			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:98340878G>A	ENST00000264972.5	+	3	594	c.379G>A	c.(379-381)Gtg>Atg	p.V127M	ZAP70_ENST00000442208.1_5'Flank	NM_001079.3	NP_001070.2	P43403	ZAP70_HUMAN	zeta-chain (TCR) associated protein kinase 70kDa	127	Interdomain A.				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						GCGTGACTACGTGCGCCAGAC	0.706																																					p.V127M		Atlas-SNP	.											.	ZAP70	77	.	0			c.G379A						PASS	.						5	6	6					2																	98340878		2020	4011	6031	SO:0001583	missense	7535	exon3			GACTACGTGCGCC	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.379G>A	2.37:g.98340878G>A	ENSP00000264972:p.Val127Met	11	0	0		30	16	0.533333	NM_001079	A6NFP4|Q6PIA4|Q8IXD6|Q9UBS6	Missense_Mutation	SNP	ENST00000264972.5	37	CCDS33254.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.687188	0.88639	.	.	ENSG00000115085	ENST00000264972	T	0.26660	1.72	4.9	4.9	0.64082	Tyrosine-protein kinase SYK/ZAP-70, inter-SH2 domain (1);	0.308316	0.22701	N	0.056684	T	0.43765	0.1262	L	0.57536	1.79	0.80722	D	1	D;D	0.76494	0.997;0.999	P;P	0.58928	0.848;0.836	T	0.38178	-0.9673	10	0.72032	D	0.01	.	15.9444	0.79782	0.0:0.0:1.0:0.0	.	127;127	B4E0E2;P43403	.;ZAP70_HUMAN	M	127	ENSP00000264972:V127M	ENSP00000264972:V127M	V	+	1	0	ZAP70	97707310	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.289000	0.72696	2.449000	0.82847	0.467000	0.42956	GTG	.	.	none		0.706	ZAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329278.1			A	98340878	G	A	98340878	3	1	15	1	0	0	0	0	1	0	0	0	17529	1145	40	1	381	1	ZAP70	2	98340878	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	1530288	98340878	144858495	20	1941											
IWS1	55677	hgsc.bcm.edu	37	chr2	128263223	128263223	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gtccttttgcctgtgaagctCctcactttcagagtcactag	7	14	8	12	0	3	2	3	1	0	1	5	2	5	2	3	0	2	1	3	0	2	4			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:128263223C>T	ENST00000295321.4	-	3	515	c.256G>A	c.(256-258)Gag>Aag	p.E86K	AC010976.2_ENST00000599001.1_RNA|IWS1_ENST00000455721.2_Missense_Mutation_p.E93K|IWS1_ENST00000486662.1_5'UTR	NM_017969.2	NP_060439.2	Q96ST2	IWS1_HUMAN	IWS1 homolog (S. cerevisiae)	86	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)		CTGTGAAGCTCCTCACTTTCA	0.483																																					p.E86K		Atlas-SNP	.											.	IWS1	61	.	0			c.G256A						PASS	.						168	169	168					2																	128263223		2203	4300	6503	SO:0001583	missense	55677	exon3			GAAGCTCCTCACT	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.256G>A	2.37:g.128263223C>T	ENSP00000295321:p.Glu86Lys	129	0	0		175	55	0.314286	NM_017969	Q2TB65|Q6P157|Q8N3E8|Q96MI7|Q9NV97|Q9NWH8	Missense_Mutation	SNP	ENST00000295321.4	37	CCDS2146.1	.	.	.	.	.	.	.	.	.	.	C	15.67	2.901973	0.52227	.	.	ENSG00000163166	ENST00000295321;ENST00000455721;ENST00000409725	T;T	0.33438	1.46;1.41	5.4	5.4	0.78164	.	0.301427	0.32608	N	0.005872	T	0.30916	0.0780	L	0.58101	1.795	0.25294	N	0.98934	B	0.21606	0.058	B	0.12837	0.008	T	0.13282	-1.0515	10	0.19590	T	0.45	-3.4505	16.0792	0.80989	0.0:1.0:0.0:0.0	.	86	Q96ST2	IWS1_HUMAN	K	86;93;91	ENSP00000295321:E86K;ENSP00000399245:E93K	ENSP00000295321:E86K	E	-	1	0	IWS1	127979693	0.993000	0.37304	1.000000	0.80357	0.869000	0.49853	3.916000	0.56416	2.524000	0.85096	0.491000	0.48974	GAG	.	.	none		0.483	IWS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254384.2	NM_017969		T	128263223	C	T	128263223	3	4	15	1	0	0	0	0	1	0	0	0	7940	864	30	2	2251	2	IWS1	2	128263223	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	29922345	128263223	114936150	21	1942											
MGAT5	4249	hgsc.bcm.edu	37	chr2	135102520	135102520	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaatcatgaagaaggttgtaGgaaaccgatctggctgccca	13	8	12	8	1	2	2	1	1	1	1	2	5	2	3	2	3	2	3	2	3	5	2			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:135102520G>A	ENST00000409645.1	+	9	1249	c.997G>A	c.(997-999)Gga>Aga	p.G333R	MGAT5_ENST00000281923.2_Missense_Mutation_p.G333R			Q09328	MGT5A_HUMAN	mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase	333					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)		GAAGGTTGTAGGAAACCGATC	0.378																																					p.G333R		Atlas-SNP	.											.	MGAT5	84	.	0			c.G997A						PASS	.						125	122	123					2																	135102520		2203	4300	6503	SO:0001583	missense	4249	exon8			GTTGTAGGAAACC	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.997G>A	2.37:g.135102520G>A	ENSP00000386377:p.Gly333Arg	86	0	0		90	32	0.355556	NM_002410	D3DP70	Missense_Mutation	SNP	ENST00000409645.1	37	CCDS2171.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.578283	0.86645	.	.	ENSG00000152127	ENST00000409645;ENST00000281923	.	.	.	5.38	5.38	0.77491	.	0.050300	0.85682	D	0.000000	T	0.76666	0.4019	L	0.55481	1.735	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75428	-0.3321	9	0.46703	T	0.11	-14.1382	19.4972	0.95079	0.0:0.0:1.0:0.0	.	333	Q09328	MGT5A_HUMAN	R	333	.	ENSP00000281923:G333R	G	+	1	0	MGAT5	134818990	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	9.758000	0.98927	2.668000	0.90789	0.563000	0.77884	GGA	.	.	none		0.378	MGAT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254584.3	NM_002410		A	135102520	G	A	135102520	3	1	15	1	0	0	0	0	1	0	0	0	9557	1001	35	2	1027	2	MGAT5	2	135102520	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	6839297	135102520	108096853	22	1943											
NEB	4703	hgsc.bcm.edu	37	chr2	152470904	152470904	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgcttacaaggatctgacaCttcttggccagcaccacccc	9	9	7	16	1	2	1	0	1	2	0	3	2	2	2	4	2	2	2	4	2	2	3			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:152470904C>T	ENST00000172853.10	-	73	10905	c.10758G>A	c.(10756-10758)aaG>aaA	p.K3586K	NEB_ENST00000427231.2_Silent_p.K3829K|NEB_ENST00000604864.1_Silent_p.K3829K|NEB_ENST00000409198.1_Silent_p.K3586K|NEB_ENST00000397345.3_Silent_p.K3829K|NEB_ENST00000603639.1_Silent_p.K3829K			P20929	NEBU_HUMAN	nebulin	3586					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)		GGATCTGACACTTCTTGGCCA	0.527																																					p.K3829K		Atlas-SNP	.											.	NEB	1697	.	0			c.G11487A						PASS	.						242	237	239					2																	152470904		2063	4213	6276	SO:0001819	synonymous_variant	4703	exon77			CTGACACTTCTTG	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.10758G>A	2.37:g.152470904C>T		210	0	0		237	94	0.396624	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				.	.	none		0.527	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152470904	C	T	152470904	2	4	15	1	0	0	0	0	0	0	0	1	10311	564	20	2		2	NEB	2	152470904	Silent	SNP	C	TCGA-FF-8061-01A-11D-2210-10	17368384	152470904	90728469	23	1944											
ZNF804A	91752	hgsc.bcm.edu	37	chr2	185463692	185463692	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcggcggctgccccatggaGtgttactacattgtcatcag	7	10	13	11	2	2	0	2	0	0	0	2	1	2	1	2	4	3	2	2	4	2	3			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:185463692G>A	ENST00000302277.6	+	1	600	c.6G>A	c.(4-6)gaG>gaA	p.E2E		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	2							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						gcCCCATGGAGTGTTACTACA	0.657																																					p.E2E		Atlas-SNP	.											.	ZNF804A	322	.	0			c.G6A						PASS	.						61	60	60					2																	185463692		2203	4300	6503	SO:0001819	synonymous_variant	91752	exon1			CATGGAGTGTTAC	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.6G>A	2.37:g.185463692G>A		42	0	0		45	19	0.422222	NM_194250	A7E253|Q6ZN26	Silent	SNP	ENST00000302277.6	37	CCDS2291.1																																																																																			.	.	none		0.657	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		A	185463692	G	A	185463692	2	1	15	1	0	0	0	0	0	0	0	1	18185	1020	36	2		2	ZNF804A	2	185463692	Silent	SNP	G	TCGA-FF-8061-01A-11D-2210-10	32992788	185463692	57735681	24	1945											
COL3A1	1281	hgsc.bcm.edu	37	chr2	189849577	189849577	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaatatgtgtctgtgactcAggatccgttctctgcgatga	9	13	10	9	2	3	2	1	2	2	0	5	4	4	3	1	1	1	1	1	1	2	2			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:189849577A>G	ENST00000304636.3	+	2	341	c.171A>G	c.(169-171)tcA>tcG	p.S57S	COL3A1_ENST00000317840.5_Silent_p.S57S	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	57	VWFC. {ECO:0000255|PROSITE- ProRule:PRU00220}.				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)	TCTGTGACTCAGGATCCGTTC	0.463																																					p.S57S		Atlas-SNP	.											.	COL3A1	292	.	0			c.A171G						PASS	.						168	145	153					2																	189849577		2203	4299	6502	SO:0001819	synonymous_variant	1281	exon2			TGACTCAGGATCC	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.171A>G	2.37:g.189849577A>G		124	0	0		122	42	0.344262	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Silent	SNP	ENST00000304636.3	37	CCDS2297.1																																																																																			.	.	none		0.463	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090		G	189849577	A	G	189849577	2	3	15	1	0	0	0	0	0	0	0	1	3690	175	7	3		3	COL3A1	2	189849577	Silent	SNP	A	TCGA-FF-8061-01A-11D-2210-10	4385885	189849577	53349796	25	1946											
ZDBF2	57683	hgsc.bcm.edu	37	chr2	207174869	207174869	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaaagtttcttcgaaggggAaaaaaaaggttacctgggct	16	9	11	5	1	1	0	0	0	1	0	2	2	1	1	1	4	1	3	1	4	8	3			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:207174869A>G	ENST00000374423.3	+	5	6003	c.5617A>G	c.(5617-5619)Aaa>Gaa	p.K1873E		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1873							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						TTCGAAGGGGAAAAAAAAGGT	0.413																																					p.K1873E		Atlas-SNP	.											ZDBF2_ENST00000374423,caecum,carcinoma,0,2	ZDBF2	531	2	0			c.A5617G						PASS	.						58	57	57					2																	207174869		1921	4134	6055	SO:0001583	missense	57683	exon5			AAGGGGAAAAAAA	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.5617A>G	2.37:g.207174869A>G	ENSP00000363545:p.Lys1873Glu	95	0	0		77	26	0.337662	NM_020923	Q6ZNP7|Q6ZSN8	Missense_Mutation	SNP	ENST00000374423.3	37	CCDS46501.1	.	.	.	.	.	.	.	.	.	.	A	4.072	0.011280	0.07912	.	.	ENSG00000204186	ENST00000374423	T	0.38887	1.11	5.48	2.13	0.27403	.	.	.	.	.	T	0.12817	0.0311	N	0.01048	-1.04	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.30268	-0.9984	9	0.12766	T	0.61	.	5.7718	0.18257	0.2703:0.1494:0.5803:0.0	.	1873	Q9HCK1	ZDBF2_HUMAN	E	1873	ENSP00000363545:K1873E	ENSP00000363545:K1873E	K	+	1	0	ZDBF2	206883114	0.934000	0.31675	0.002000	0.10522	0.026000	0.11368	2.260000	0.43267	1.234000	0.43709	0.451000	0.29950	AAA	.	.	none		0.413	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		G	207174869	A	G	207174869	3	3	15	1	0	0	0	0	1	0	0	0	17614	247	9	3	5627	3	ZDBF2	2	207174869	Missense_Mutation	SNP	A	TCGA-FF-8061-01A-11D-2210-10	17325292	207174869	36024504	26	1947											
FN1	2335	hgsc.bcm.edu	37	chr2	216289966	216289966	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggctgggggtgaggctgcGgttggtaaacagctgcacga	8	7	19	7	2	0	1	0	1	0	0	0	3	0	1	0	6	4	6	0	6	2	2	rs145123731	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:216289966G>A	ENST00000359671.1	-	7	1152	c.887C>T	c.(886-888)cCg>cTg	p.P296L	FN1_ENST00000432072.2_Missense_Mutation_p.P296L|FN1_ENST00000446046.1_Missense_Mutation_p.P296L|FN1_ENST00000356005.4_Missense_Mutation_p.P296L|FN1_ENST00000426059.1_Missense_Mutation_p.P296L|FN1_ENST00000354785.4_Missense_Mutation_p.P296L|FN1_ENST00000357009.2_Missense_Mutation_p.P296L|FN1_ENST00000336916.4_Missense_Mutation_p.P296L|FN1_ENST00000323926.6_Missense_Mutation_p.P296L|FN1_ENST00000346544.3_Missense_Mutation_p.P296L|FN1_ENST00000421182.1_Missense_Mutation_p.P296L|FN1_ENST00000345488.5_Missense_Mutation_p.P296L|FN1_ENST00000357867.4_Missense_Mutation_p.P296L|FN1_ENST00000443816.1_Missense_Mutation_p.P296L			P02751	FINC_HUMAN	fibronectin 1	296					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)	GTGAGGCTGCGGTTGGTAAAC	0.517																																					p.P296L		Atlas-SNP	.											FN1_ENST00000354785,colon,carcinoma,+1,2	FN1	521	2	0			c.C887T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	6,4400	12.9+/-30.5	0,6,2197	122	119	120		887,887,887,887,887,887	5.8	1	2	dbSNP_134	120	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense	FN1	NM_002026.2,NM_054034.2,NM_212474.1,NM_212476.1,NM_212478.1,NM_212482.1	98,98,98,98,98,98	0,6,6497	AA,AG,GG		0.0,0.1362,0.0461	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	296/2356,296/658,296/2177,296/2297,296/2331,296/2478	216289966	6,13000	2203	4300	6503	SO:0001583	missense	2335	exon7			GGCTGCGGTTGGT		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.887C>T	2.37:g.216289966G>A	ENSP00000352696:p.Pro296Leu	117	0	0		96	33	0.34375	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	37		.	.	.	.	.	.	.	.	.	.	G	24.1	4.491508	0.84962	0.001362	0.0	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	0.48836	0.8;2.19;2.34;0.88;2.4;2.04;2.39;2.04;2.34;2.08;1.57;0.88;1.47;1.46	5.83	5.83	0.93111	.	0.000000	0.64402	D	0.000002	T	0.68100	0.2964	L	0.59436	1.845	0.80722	D	1	D;D;P;D;D;D;D;D;D;D;P	0.89917	0.989;1.0;0.885;0.982;1.0;1.0;1.0;1.0;1.0;1.0;0.936	P;D;P;P;D;D;D;D;D;D;B	0.91635	0.592;0.998;0.477;0.688;0.999;0.998;0.983;0.996;0.999;0.999;0.396	T	0.68108	-0.5496	10	0.72032	D	0.01	.	20.1374	0.98035	0.0:0.0:1.0:0.0	.	296;296;296;296;296;296;296;296;296;296;296	E9PG29;P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.;.	L	296	ENSP00000394423:P296L;ENSP00000323534:P296L;ENSP00000338200:P296L;ENSP00000350534:P296L;ENSP00000346839:P296L;ENSP00000352696:P296L;ENSP00000265312:P296L;ENSP00000273049:P296L;ENSP00000349509:P296L;ENSP00000410422:P296L;ENSP00000415018:P296L;ENSP00000399538:P296L;ENSP00000348285:P296L;ENSP00000398907:P296L	ENSP00000265313:P296L	P	-	2	0	FN1	215998211	1.000000	0.71417	0.999000	0.59377	0.682000	0.39822	2.458000	0.45014	2.763000	0.94921	0.563000	0.77884	CCG	G|1.000;A|0.000	0.000	strong		0.517	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		A	216289966	G	A	216289966	3	1	15	1	0	0	0	0	1	0	0	0	5970	1116	39	1	6739	1	FN1	2	216289966	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	9115097	216289966	26909407	27	1948											
C2orf24	27013	hgsc.bcm.edu	37	chr2	220041491	220041491	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccccactcaccgtgaagtcCtggaagccggcgagggagaa	10	4	13	14	3	1	2	1	1	0	1	2	5	2	3	5	3	1	0	5	3	3	0			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:220041491C>T	ENST00000409789.1	-	2	487	c.60G>A	c.(58-60)caG>caA	p.Q20Q	CNPPD1_ENST00000360507.5_Silent_p.Q20Q|FAM134A_ENST00000430297.2_5'Flank			Q9BV87	CNPD1_HUMAN	cyclin Pas1/PHO80 domain containing 1	20					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						CCGTGAAGTCCTGGAAGCCGG	0.726																																					p.Q20Q		Atlas-SNP	.											.	CNPPD1	22	.	0			c.G60A						PASS	.						18	19	18					2																	220041491		2167	4262	6429	SO:0001819	synonymous_variant	27013	exon1			GAAGTCCTGGAAG	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.60G>A	2.37:g.220041491C>T		46	0	0		75	4	0.0533333	NM_015680	B2RC77|O75548|Q9H4N0|Q9UQN0	Silent	SNP	ENST00000409789.1	37	CCDS2433.1																																																																																			.	.	none		0.726	CNPPD1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336220.1	NM_015680		T	220041491	C	T	220041491	2	4	15	1	0	0	0	0	0	0	0	1	2161	680	24	2		2	C2orf24	2	220041491	Silent	SNP	C	TCGA-FF-8061-01A-11D-2210-10	3751525	220041491	23157882	28	1949											
STK11IP	114790	hgsc.bcm.edu	37	chr2	220474114	220474114	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgtgttgaccccagtcacCaatgtggctcgggaacagct	8	8	12	13	2	1	1	1	1	0	0	2	2	1	2	4	2	2	3	4	2	2	1			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:220474114C>T	ENST00000456909.1	+	17	2046	c.1956C>T	c.(1954-1956)acC>acT	p.T652T	STK11IP_ENST00000295641.10_Silent_p.T663T			Q8N1F8	S11IP_HUMAN	serine/threonine kinase 11 interacting protein	663					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)		CCCCAGTCACCAATGTGGCTC	0.637																																					p.T663T		Atlas-SNP	.											.	STK11IP	152	.	0			c.C1989T						PASS	.						31	37	35					2																	220474114		2041	4196	6237	SO:0001819	synonymous_variant	114790	exon17			AGTCACCAATGTG	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.1956C>T	2.37:g.220474114C>T		72	0	0		77	4	0.0519481	NM_052902	Q8NAW9|Q8WXE4|Q96CN3|Q96PY9	Silent	SNP	ENST00000456909.1	37																																																																																				.	.	none		0.637	STK11IP-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000131432.1	NM_052902		T	220474114	C	T	220474114	2	4	15	1	0	0	0	0	0	0	0	1	15303	581	21	2		2	STK11IP	2	220474114	Silent	SNP	C	TCGA-FF-8061-01A-11D-2210-10	432623	220474114	22725259	29	1950											
NMUR1	10316	hgsc.bcm.edu	37	chr2	232389859	232389859	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cacagggtgctgcctgtggtCatcctgctgaggctgtggga	5	10	16	10	0	1	1	1	1	0	0	2	2	2	2	2	4	3	3	2	4	0	0			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:232389859C>T	ENST00000305141.4	-	3	1309	c.1176G>A	c.(1174-1176)atG>atA	p.M392I		NM_006056.4	NP_006047.3	Q9HB89	NMUR1_HUMAN	neuromedin U receptor 1	392					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)		TGCCTGTGGTCATCCTGCTGA	0.672																																					p.M392I		Atlas-SNP	.											.	NMUR1	46	.	0			c.G1176A						PASS	.						39	40	39					2																	232389859		2203	4300	6503	SO:0001583	missense	10316	exon3			TGTGGTCATCCTG	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.1176G>A	2.37:g.232389859C>T	ENSP00000305877:p.Met392Ile	125	0	0		157	60	0.382166	NM_006056	O43664|Q7LDP6|Q8NE20	Missense_Mutation	SNP	ENST00000305141.4	37	CCDS2486.1	.	.	.	.	.	.	.	.	.	.	C	13.40	2.224634	0.39300	.	.	ENSG00000171596	ENST00000305141	T	0.37235	1.21	4.27	3.36	0.38483	.	1.558880	0.04572	N	0.393532	T	0.21103	0.0508	N	0.08118	0	0.20074	N	0.999931	B	0.02656	0.0	B	0.01281	0.0	T	0.16928	-1.0386	10	0.27785	T	0.31	-2.4681	6.9443	0.24510	0.0:0.5308:0.373:0.0962	.	392	Q9HB89	NMUR1_HUMAN	I	392	ENSP00000305877:M392I	ENSP00000305877:M392I	M	-	3	0	NMUR1	232098103	0.995000	0.38212	0.869000	0.34112	0.940000	0.58332	1.786000	0.38694	1.119000	0.41883	0.456000	0.33151	ATG	.	.	none		0.672	NMUR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256961.1	NM_006056		T	232389859	C	T	232389859	3	4	15	1	0	0	0	0	1	0	0	0	10515	826	29	2	108	2	NMUR1	2	232389859	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	11915745	232389859	10809514	30	1951											
ESPNL	339768	hgsc.bcm.edu	37	chr2	239040089	239040089	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgacgaggtggccgccggcCgccgggcctggaccgacggc	4	2	18	17	8	0	0	0	0	0	0	0	4	0	1	7	6	0	0	7	6	0	0	rs199724430	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr2:239040089C>T	ENST00000343063.3	+	9	2997	c.2734C>T	c.(2734-2736)Cgc>Tgc	p.R912C	ESPNL_ENST00000477241.1_3'UTR|ESPNL_ENST00000409506.1_Missense_Mutation_p.R544C|ESPNL_ENST00000409169.1_Missense_Mutation_p.R868C	NM_194312.2	NP_919288.2	Q6ZVH7	ESPNL_HUMAN	espin-like	912										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)		GGCCGCCGGCCGCCGGGCCTG	0.692													C|||	11	0.00219649	0.0	0.0	5008	,	,		13571	0.0109		0.0	False		,,,				2504	0.0				p.R912C		Atlas-SNP	.											ESPNL,NS,carcinoma,-1,1	ESPNL	63	1	0			c.C2734T						scavenged	.	C	CYS/ARG	2,4188		0,2,2093	9	12	11		2734	2.9	0.9	2		11	0,8228		0,0,4114	no	missense	ESPNL	NM_194312.2	180	0,2,6207	TT,TC,CC		0.0,0.0477,0.0161	probably-damaging	912/1006	239040089	2,12416	2095	4114	6209	SO:0001583	missense	339768	exon9			GCCGGCCGCCGGG	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.2734C>T	2.37:g.239040089C>T	ENSP00000339115:p.Arg912Cys	1	1	1		11	6	0.545455	NM_194312	Q66K27|Q6ZVG1|Q8IVU2	Missense_Mutation	SNP	ENST00000343063.3	37	CCDS2525.1	4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	C	17.11	3.304542	0.60305	4.77E-4	0.0	ENSG00000144488	ENST00000343063;ENST00000409169;ENST00000409506	T;T;T	0.70749	-0.51;0.58;0.22	4.72	2.87	0.33458	.	0.258957	0.31897	N	0.006898	T	0.72137	0.3423	M	0.68593	2.085	0.46823	D	0.999212	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.959	T	0.73430	-0.3985	10	0.87932	D	0	-35.1335	4.8076	0.13328	0.1532:0.6129:0.1486:0.0853	.	868;912	Q6ZVH7-2;Q6ZVH7	.;ESPNL_HUMAN	C	912;868;544	ENSP00000339115:R912C;ENSP00000386577:R868C;ENSP00000386579:R544C	ENSP00000339115:R912C	R	+	1	0	ESPNL	238704828	0.042000	0.20092	0.896000	0.35187	0.865000	0.49528	1.688000	0.37690	0.401000	0.25424	0.460000	0.39030	CGC	C|0.998;T|0.002	0.002	strong		0.692	ESPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257164.2	NM_194312		T	239040089	C	T	239040089	3	4	15	1	0	0	0	0	1	0	0	0	5257	652	23	1	2768	1	ESPNL	2	239040089	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	6650230	239040089	4159284	31	1952											
NUP210	23225	hgsc.bcm.edu	37	chr3	13379381	13379381	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgggggcgcggatcctcaCggcccttagcagcagcacct	7	6	14	14	3	1	0	1	0	0	0	2	2	2	1	3	4	3	3	3	4	1	1			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr3:13379381C>T	ENST00000254508.5	-	26	3590	c.3508G>A	c.(3508-3510)Gtg>Atg	p.V1170M	NUP210_ENST00000485755.1_Intron	NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	1170					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)					CGGATCCTCACGGCCCTTAGC	0.642																																					p.V1170M		Atlas-SNP	.											.	NUP210	182	.	0			c.G3508A						PASS	.						53	46	49					3																	13379381		2203	4300	6503	SO:0001583	missense	23225	exon26			TCCTCACGGCCCT	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.3508G>A	3.37:g.13379381C>T	ENSP00000254508:p.Val1170Met	26	0	0		42	18	0.428571	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	37	CCDS33704.1	.	.	.	.	.	.	.	.	.	.	C	13.87	2.365480	0.41902	.	.	ENSG00000132182	ENST00000254508	T	0.09163	3.01	4.86	4.86	0.63082	.	0.073766	0.56097	D	0.000034	T	0.17874	0.0429	M	0.70595	2.14	0.50313	D	0.999868	D	0.60160	0.987	P	0.45881	0.496	T	0.03051	-1.1078	10	0.30078	T	0.28	-20.1592	15.1051	0.72315	0.0:1.0:0.0:0.0	.	1170	Q8TEM1	PO210_HUMAN	M	1170	ENSP00000254508:V1170M	ENSP00000254508:V1170M	V	-	1	0	NUP210	13354381	0.987000	0.35691	0.941000	0.38009	0.017000	0.09413	2.662000	0.46766	2.408000	0.81797	0.655000	0.94253	GTG	.	.	none		0.642	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923		T	13379381	C	T	13379381	3	4	15	1	0	0	0	0	1	0	0	0	10769	536	19	1	2215	1	NUP210	3	13379381	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10		13379381	184643049	32	1953											
RNF123	63891	hgsc.bcm.edu	37	chr3	49757994	49757994	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agatccctgcttccagctacGctcaatatgctatctcctgg	8	12	7	14	1	2	1	1	0	1	1	5	1	4	1	3	1	4	4	3	1	4	4			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr3:49757994G>A	ENST00000327697.6	+	36	3695	c.3551G>A	c.(3550-3552)cGc>cAc	p.R1184H	RNF123_ENST00000433785.1_Missense_Mutation_p.R296H|AMIGO3_ENST00000535833.1_5'UTR|AMIGO3_ENST00000320431.7_5'Flank|GMPPB_ENST00000308375.6_3'UTR|GMPPB_ENST00000480687.1_3'UTR|RNF123_ENST00000497099.1_3'UTR	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	1184					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)		TTCCAGCTACGCTCAATATGC	0.617																																					p.R1184H		Atlas-SNP	.											.	RNF123	100	.	0			c.G3551A						PASS	.						56	50	52					3																	49757994		2203	4300	6503	SO:0001583	missense	63891	exon36			AGCTACGCTCAAT	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.3551G>A	3.37:g.49757994G>A	ENSP00000328287:p.Arg1184His	78	0	0		105	42	0.4	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	37	CCDS33758.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.877886	0.51801	.	.	ENSG00000164068	ENST00000327697;ENST00000389066;ENST00000433785	T	0.72725	-0.68	5.29	5.29	0.74685	.	0.059077	0.64402	D	0.000001	T	0.65207	0.2669	L	0.40543	1.245	0.53688	D	0.999979	B	0.15473	0.013	B	0.08055	0.003	T	0.61734	-0.7002	10	0.59425	D	0.04	-23.7591	18.1046	0.89516	0.0:0.0:1.0:0.0	.	1184	Q5XPI4	RN123_HUMAN	H	1184;1184;296	ENSP00000328287:R1184H	ENSP00000328287:R1184H	R	+	2	0	RNF123	49732998	0.990000	0.36364	0.988000	0.46212	0.910000	0.53928	3.769000	0.55303	2.756000	0.94617	0.561000	0.74099	CGC	.	.	none		0.617	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064		A	49757994	G	A	49757994	3	1	15	1	0	0	0	0	1	0	0	0	13448	1087	38	1	3689	1	RNF123	3	49757994	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	36378613	49757994	148264436	33	1954											
CADM2	253559	hgsc.bcm.edu	37	chr3	85932591	85932591	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaggcatatctcaccgttcTgggtaagtgcaagggactaa	12	9	11	9	1	2	0	1	0	2	0	3	1	2	1	1	3	1	4	1	3	5	4			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr3:85932591T>G	ENST00000407528.2	+	3	424	c.362T>G	c.(361-363)cTg>cGg	p.L121R	CADM2_ENST00000383699.3_Missense_Mutation_p.L130R|CADM2_ENST00000405615.2_Missense_Mutation_p.L123R	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	121					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)		CTCACCGTTCTGGGTAAGTGC	0.353																																					p.L130R		Atlas-SNP	.											.	CADM2	195	.	0			c.T389G						PASS	.						78	66	70					3																	85932591		2203	4300	6503	SO:0001583	missense	253559	exon4			CCGTTCTGGGTAA	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.362T>G	3.37:g.85932591T>G	ENSP00000384575:p.Leu121Arg	79	0	0		59	22	0.372881	NM_001167675	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Missense_Mutation	SNP	ENST00000407528.2	37	CCDS54614.1	.	.	.	.	.	.	.	.	.	.	T	16.95	3.262776	0.59431	.	.	ENSG00000175161	ENST00000383699;ENST00000407528;ENST00000405615	T;T;T	0.29142	1.58;1.58;1.58	5.54	5.54	0.83059	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.62889	0.2465	M	0.89414	3.03	0.58432	D	0.999998	D;D;D	0.89917	1.0;0.999;0.999	D;D;D	0.87578	0.995;0.997;0.998	T	0.70684	-0.4804	10	0.72032	D	0.01	.	15.9801	0.80102	0.0:0.0:0.0:1.0	.	123;130;121	Q8N3J6-3;G3XHN4;Q8N3J6	.;.;CADM2_HUMAN	R	130;121;123	ENSP00000373200:L130R;ENSP00000384575:L121R;ENSP00000384193:L123R	ENSP00000373200:L130R	L	+	2	0	CADM2	86015281	1.000000	0.71417	1.000000	0.80357	0.251000	0.25915	7.655000	0.83696	2.230000	0.72887	0.528000	0.53228	CTG	.	.	none		0.353	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184		G	85932591	T	G	85932591	3	3	15	1	0	0	0	0	1	0	0	0	2569	1580	55	5	443	5	CADM2	3	85932591	Missense_Mutation	SNP	T	TCGA-FF-8061-01A-11D-2210-10	36174597	85932591	112089839	34	1955											
ZBED2	79413	hgsc.bcm.edu	37	chr3	111312927	111312927	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggggcattggagtgggcataGcactcacaaaagggccaacc	12	5	14	10	0	1	0	1	0	0	0	1	1	1	1	2	5	2	3	2	5	4	2			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr3:111312927G>A	ENST00000317012.4	-	2	1130	c.122C>T	c.(121-123)gCt>gTt	p.A41V	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	41							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|lung(1)|skin(2)	6						AGTGGGCATAGCACTCACAAA	0.532																																					p.A41V		Atlas-SNP	.											.	ZBED2	22	.	0			c.C122T						PASS	.						243	203	217					3																	111312927		2203	4300	6503	SO:0001583	missense	79413	exon2			GGCATAGCACTCA	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.122C>T	3.37:g.111312927G>A	ENSP00000321370:p.Ala41Val	154	0	0		190	76	0.4	NM_024508	D3DN62	Missense_Mutation	SNP	ENST00000317012.4	37	CCDS2960.2	.	.	.	.	.	.	.	.	.	.	G	4.764	0.142084	0.09083	.	.	ENSG00000177494	ENST00000317012	.	.	.	3.16	2.27	0.28462	.	.	.	.	.	T	0.25005	0.0607	N	0.24115	0.695	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.19844	-1.0293	8	0.22706	T	0.39	.	6.0802	0.19936	0.1484:0.0:0.8516:0.0	.	41	Q9BTP6	ZBED2_HUMAN	V	41	.	ENSP00000321370:A41V	A	-	2	0	ZBED2	112795617	0.000000	0.05858	0.002000	0.10522	0.053000	0.15095	0.323000	0.19593	0.654000	0.30846	0.563000	0.77884	GCT	.	.	none		0.532	ZBED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157228.2	NM_024508		A	111312927	G	A	111312927	3	1	15	1	0	0	0	0	1	0	0	0	17533	971	34	2	538	2	ZBED2	3	111312927	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	25380336	111312927	86709503	35	1956											
PLCH1	23007	hgsc.bcm.edu	37	chr3	155205862	155205862	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgtgtacaaatatggatgcTtctgtcagtccttccaaata	12	14	7	8	0	2	0	1	0	1	0	4	1	4	1	2	1	2	2	2	1	5	5			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr3:155205862T>G	ENST00000340059.7	-	20	2537	c.2538A>C	c.(2536-2538)gaA>gaC	p.E846D	PLCH1_ENST00000494598.1_Missense_Mutation_p.E846D|PLCH1_ENST00000460012.1_Missense_Mutation_p.E828D|PLCH1_ENST00000447496.2_Missense_Mutation_p.E846D|PLCH1_ENST00000334686.6_Missense_Mutation_p.E828D|PLCH1-AS2_ENST00000472913.1_RNA|PLCH1_ENST00000414191.1_Missense_Mutation_p.E828D	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	846					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)			ATATGGATGCTTCTGTCAGTC	0.363																																					p.E846D		Atlas-SNP	.											.	PLCH1	406	.	0			c.A2538C						PASS	.						132	130	130					3																	155205862		2203	4300	6503	SO:0001583	missense	23007	exon20			GGATGCTTCTGTC	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.2538A>C	3.37:g.155205862T>G	ENSP00000345988:p.Glu846Asp	80	0	0		84	7	0.0833333	NM_001130960	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Missense_Mutation	SNP	ENST00000340059.7	37	CCDS46939.1	.	.	.	.	.	.	.	.	.	.	T	18.56	3.650690	0.67472	.	.	ENSG00000114805	ENST00000494598;ENST00000460012;ENST00000447496;ENST00000340059;ENST00000334686;ENST00000414191	T;T;T;T;T;T	0.12984	2.63;2.63;2.63;2.63;2.63;2.63	5.18	1.45	0.22620	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.30448	0.0765	M	0.73962	2.25	0.54753	D	0.999989	D;D;D	0.71674	0.996;0.998;0.984	D;D;P	0.69824	0.966;0.926;0.888	T	0.00953	-1.1502	10	0.36615	T	0.2	.	8.9787	0.35953	0.0:0.2141:0.0:0.7859	.	828;846;846	Q4KWH8-2;Q4KWH8;Q4KWH8-3	.;PLCH1_HUMAN;.	D	846;828;846;846;828;828	ENSP00000419100:E846D;ENSP00000417502:E828D;ENSP00000402759:E846D;ENSP00000345988:E846D;ENSP00000335469:E828D;ENSP00000412977:E828D	ENSP00000335469:E828D	E	-	3	2	PLCH1	156688556	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	1.763000	0.38461	0.013000	0.14918	-0.250000	0.11733	GAA	.	.	none		0.363	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996		G	155205862	T	G	155205862	3	3	15	1	0	0	0	0	1	0	0	0	12046	1606	56	5	2574	5	PLCH1	3	155205862	Missense_Mutation	SNP	T	TCGA-FF-8061-01A-11D-2210-10	43892935	155205862	42816568	36	1957											
SLITRK3	22865	hgsc.bcm.edu	37	chr3	164907346	164907346	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaaattccaaaaatcagaacGgtatattttctgaatcagat	18	12	5	6	1	3	3	2	1	1	2	4	3	4	3	1	1	1	1	1	1	8	5			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr3:164907346G>T	ENST00000475390.1	-	2	1716	c.1273C>A	c.(1273-1275)Cgt>Agt	p.R425S	SLITRK3_ENST00000241274.3_Missense_Mutation_p.R425S			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	425					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						AAATCAGAACGGTATATTTTC	0.398										HNSCC(40;0.11)																											p.R425S		Atlas-SNP	.											SLITRK3,NS,carcinoma,+1,1	SLITRK3	263	1	0			c.C1273A						scavenged	.						54	56	55					3																	164907346		2203	4300	6503	SO:0001583	missense	22865	exon2			CAGAACGGTATAT	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.1273C>A	3.37:g.164907346G>T	ENSP00000420091:p.Arg425Ser	65	0	0		49	3	0.0612245	NM_014926	Q1RMY6	Missense_Mutation	SNP	ENST00000475390.1	37	CCDS3197.1	.	.	.	.	.	.	.	.	.	.	G	14.08	2.429477	0.43122	.	.	ENSG00000121871	ENST00000475390;ENST00000241274	T;T	0.53206	0.63;0.63	5.58	5.58	0.84498	.	0.000000	0.38436	N	0.001696	T	0.42517	0.1206	L	0.44542	1.39	0.51012	D	0.999905	P	0.48998	0.918	P	0.44477	0.451	T	0.10660	-1.0620	10	0.17369	T	0.5	-15.343	14.2462	0.65990	0.0:0.0:0.851:0.149	.	425	O94933	SLIK3_HUMAN	S	425	ENSP00000420091:R425S;ENSP00000241274:R425S	ENSP00000241274:R425S	R	-	1	0	SLITRK3	166390040	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.906000	0.69900	2.906000	0.99361	0.655000	0.94253	CGT	.	.	none		0.398	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926		T	164907346	G	T	164907346	3	4	15	1	0	0	0	0	1	0	0	0	14759	1116	39	4	1664	4	SLITRK3	3	164907346	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	9701484	164907346	33115084	37	1958											
ETV5	2119	hgsc.bcm.edu	37	chr3	185797673	185797673	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caggggctgatgtggtggtcGggggaccgcaaatgtttgct	6	10	18	7	2	0	1	0	1	0	0	1	2	0	2	1	6	1	4	1	6	1	1			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr3:185797673G>A	ENST00000306376.5	-	7	829	c.583C>T	c.(583-585)Cga>Tga	p.R195*	ETV5_ENST00000537818.1_Nonsense_Mutation_p.R237*|ETV5-AS1_ENST00000453370.1_RNA|ETV5_ENST00000434744.1_Nonsense_Mutation_p.R195*	NM_004454.2	NP_004445.1	P41161	ETV5_HUMAN	ets variant 5	195					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)			TGTGGTGGTCGGGGGACCGCA	0.587			T	"TMPRSS2, SCL45A3"	Prostate																																p.R195X		Atlas-SNP	.		Dom	yes		3	3q28	2119	ets variant gene 5		E	.	ETV5	106	.	0			c.C583T						PASS	.						120	118	119					3																	185797673		2203	4300	6503	SO:0001587	stop_gained	2119	exon7			GTGGTCGGGGGAC	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.583C>T	3.37:g.185797673G>A	ENSP00000306894:p.Arg195*	145	0	0		166	74	0.445783	NM_004454	A6NH46|B7Z7D7|Q6IBN5	Nonsense_Mutation	SNP	ENST00000306376.5	37	CCDS33906.1	.	.	.	.	.	.	.	.	.	.	G	39	7.294772	0.98192	.	.	ENSG00000244405	ENST00000306376;ENST00000434744;ENST00000537818	.	.	.	5.34	3.39	0.38822	.	0.818906	0.11352	N	0.572821	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	.	11.3294	0.49467	0.0:0.0:0.6711:0.3289	.	.	.	.	X	195;195;237	.	ENSP00000306894:R195X	R	-	1	2	ETV5	187280367	1.000000	0.71417	0.996000	0.52242	0.984000	0.73092	5.489000	0.66875	1.201000	0.43203	0.563000	0.77884	CGA	.	.	none		0.587	ETV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344947.1	NM_004454		A	185797673	G	A	185797673	4	1	15	1	0	0	0	0	0	1	0	0	5284	1124	39	1	977	1	ETV5	3	185797673	Nonsense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	20890327	185797673	12224757	38	1959											
CRMP1	1400	hgsc.bcm.edu	37	chr4	5868477	5868477	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccacctttgatgaggagtcGgtcactctgcaaagcaaggc	10	9	11	11	1	2	2	1	2	1	0	4	3	3	3	2	3	2	2	2	3	2	1			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr4:5868477G>A	ENST00000397890.2	-	2	260	c.46C>T	c.(46-48)Cga>Tga	p.R16*	CRMP1_ENST00000324989.7_Nonsense_Mutation_p.R130*|CRMP1_ENST00000511535.1_5'UTR|CRMP1_ENST00000512574.1_Nonsense_Mutation_p.R14*	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	16					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)		ATGAGGAGTCGGTCACTCTGC	0.383																																					p.R130X		Atlas-SNP	.											CRMP1,NS,carcinoma,+1,1	CRMP1	118	1	0			c.C388T						scavenged	.						102	88	93					4																	5868477		2203	4300	6503	SO:0001587	stop_gained	1400	exon2			GGAGTCGGTCACT	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.46C>T	4.37:g.5868477G>A	ENSP00000380987:p.Arg16*	100	1	0.01		83	24	0.289157	NM_001014809	A0EJG6|Q13024|Q4W5F1|Q96TC8	Nonsense_Mutation	SNP	ENST00000397890.2	37	CCDS43207.1	.	.	.	.	.	.	.	.	.	.	G	41	8.922703	0.99004	.	.	ENSG00000072832	ENST00000324989;ENST00000397890;ENST00000534845;ENST00000512574	.	.	.	4.26	4.26	0.50523	.	0.237948	0.33772	N	0.004567	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-23.8303	15.8244	0.78686	0.0:0.0:1.0:0.0	.	.	.	.	X	130;16;16;14	.	ENSP00000321606:R130X	R	-	1	2	CRMP1	5919378	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	4.469000	0.60169	2.194000	0.70268	0.563000	0.77884	CGA	.	.	none		0.383	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313		A	5868477	G	A	5868477	4	1	15	1	0	0	0	0	0	1	0	0	3892	1124	39	1	1724	1	CRMP1	4	5868477	Nonsense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10		5868477	185285799	39	1960											
BOD1L	259282	hgsc.bcm.edu	37	chr4	13602085	13602085	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcgaattcttcccctatgcTtgtggaaatcatggcacact	9	14	7	11	1	2	0	1	0	1	0	4	2	3	1	2	2	1	2	2	2	3	5			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr4:13602085T>C	ENST00000040738.5	-	10	6574	c.6439A>G	c.(6439-6441)Agc>Ggc	p.S2147G		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	2147						nucleus (GO:0005634)	DNA binding (GO:0003677)	p.S2147G(1)									TCCCCTATGCTTGTGGAAATC	0.502																																					p.S2147G		Atlas-SNP	.											BOD1L,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	kidney(1)	c.A6439G						scavenged	.						83	73	77					4																	13602085		2203	4300	6503	SO:0001583	missense	259282	exon10			CTATGCTTGTGGA	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.6439A>G	4.37:g.13602085T>C	ENSP00000040738:p.Ser2147Gly	65	0	0		65	3	0.0461538	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	T	20.9	4.072314	0.76415	.	.	ENSG00000038219	ENST00000040738	T	0.16457	2.34	5.5	5.5	0.81552	.	0.000000	0.64402	D	0.000001	T	0.43411	0.1246	M	0.78456	2.415	0.40176	D	0.977236	D	0.76494	0.999	D	0.78314	0.991	T	0.47368	-0.9123	10	0.87932	D	0	-5.3309	14.1665	0.65480	0.0:0.0:0.0:1.0	.	2147	Q8NFC6	BOD1L_HUMAN	G	2147	ENSP00000040738:S2147G	ENSP00000040738:S2147G	S	-	1	0	BOD1L	13211183	1.000000	0.71417	0.997000	0.53966	0.856000	0.48823	4.896000	0.63222	2.083000	0.62718	0.454000	0.30748	AGC	.	.	none		0.502	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		C	13602085	T	C	13602085	3	2	15	1	0	0	0	0	1	0	0	0	1483	1609	56	3	2784	3	BOD1L	4	13602085	Missense_Mutation	SNP	T	TCGA-FF-8061-01A-11D-2210-10	7733608	13602085	177552191	40	1961											
TECRL	253017	hgsc.bcm.edu	37	chr4	65188493	65188493	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	actttgaatggtaatgtagtCcttcaaaaaaggcccgccta	13	11	8	9	1	1	1	1	1	0	0	2	1	2	1	3	2	0	2	3	2	7	5			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr4:65188493C>T	ENST00000381210.3	-	4	459	c.349G>A	c.(349-351)Gac>Aac	p.D117N	TECRL_ENST00000507440.1_Missense_Mutation_p.D117N|TECRL_ENST00000513125.1_5'Flank	NM_001010874.4	NP_001010874.2	Q5HYJ1	TECRL_HUMAN	trans-2,3-enoyl-CoA reductase-like	117					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						GTAATGTAGTCCTTCAAAAAA	0.323																																					p.D117N		Atlas-SNP	.											.	TECRL	106	.	0			c.G349A						PASS	.						58	58	58					4																	65188493		2203	4300	6503	SO:0001583	missense	253017	exon4			TGTAGTCCTTCAA	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.349G>A	4.37:g.65188493C>T	ENSP00000370607:p.Asp117Asn	128	0	0		98	4	0.0408163	NM_001010874		Missense_Mutation	SNP	ENST00000381210.3	37	CCDS33990.1	.	.	.	.	.	.	.	.	.	.	C	12.66	2.005165	0.35415	.	.	ENSG00000205678	ENST00000507440;ENST00000381210;ENST00000509536	T;T;T	0.48522	0.81;0.81;0.81	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.68100	0.2964	M	0.73962	2.25	0.53005	D	0.999963	D;D	0.89917	1.0;0.993	D;D	0.87578	0.998;0.984	T	0.65861	-0.6065	10	0.37606	T	0.19	0.1933	15.4919	0.75611	0.0:1.0:0.0:0.0	.	117;117	Q6IN47;Q5HYJ1	.;TECRL_HUMAN	N	117	ENSP00000426043:D117N;ENSP00000370607:D117N;ENSP00000422497:D117N	ENSP00000370607:D117N	D	-	1	0	TECRL	64871088	1.000000	0.71417	0.996000	0.52242	0.018000	0.09664	4.729000	0.62008	2.728000	0.93425	0.585000	0.79938	GAC	.	.	none		0.323	TECRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361705.4	NM_001010874		T	65188493	C	T	65188493	3	4	15	1	0	0	0	0	1	0	0	0	15761	855	30	2	778	2	TECRL	4	65188493	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	51586408	65188493	125965783	41	1962											
GRID2	2895	hgsc.bcm.edu	37	chr4	94376883	94376883	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtggtggactttacgacacGttacatggactactcagtgg	9	12	12	8	2	1	0	1	0	0	0	1	3	1	2	0	4	3	1	0	4	3	4			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr4:94376883G>A	ENST00000282020.4	+	11	1874	c.1616G>A	c.(1615-1617)cGt>cAt	p.R539H	GRID2_ENST00000510992.1_Missense_Mutation_p.R444H	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	539					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)		TTTACGACACGTTACATGGAC	0.443																																					p.R539H		Atlas-SNP	.											GRID2,NS,carcinoma,+1,1	GRID2	233	1	0			c.G1616A						PASS	.						160	144	149					4																	94376883		2203	4300	6503	SO:0001583	missense	2895	exon11			CGACACGTTACAT	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.1616G>A	4.37:g.94376883G>A	ENSP00000282020:p.Arg539His	147	0	0		180	62	0.344444	NM_001510	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Missense_Mutation	SNP	ENST00000282020.4	37	CCDS3637.1	.	.	.	.	.	.	.	.	.	.	G	31	5.086141	0.94100	.	.	ENSG00000152208	ENST00000282020;ENST00000510992	T;T	0.27402	1.67;1.67	5.97	5.97	0.96955	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	T	0.59851	0.2224	M	0.74881	2.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.59198	-0.7499	10	0.66056	D	0.02	.	20.4387	0.99107	0.0:0.0:1.0:0.0	.	444;539	E9PH24;O43424	.;GRID2_HUMAN	H	539;444	ENSP00000282020:R539H;ENSP00000421257:R444H	ENSP00000282020:R539H	R	+	2	0	GRID2	94595906	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	9.869000	0.99810	2.836000	0.97738	0.655000	0.94253	CGT	.	.	none		0.443	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2			A	94376883	G	A	94376883	3	1	15	1	0	0	0	0	1	0	0	0	6781	1145	40	1	1658	1	GRID2	4	94376883	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	29188390	94376883	96777393	42	1963											
C4orf37	285555	hgsc.bcm.edu	37	chr4	98893436	98893436	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtatgaatgtattacctgatAatcagcaggtccaggggtag	12	11	12	6	0	1	2	1	2	0	0	2	2	2	2	2	3	2	4	2	3	6	5			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr4:98893436A>C	ENST00000295268.3	-	7	1017	c.928T>G	c.(928-930)Tat>Gat	p.Y310D		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	310																	ATTACCTGATAATCAGCAGGT	0.353																																					p.Y310D		Atlas-SNP	.											.	.	.	.	0			c.T928G						PASS	.						72	74	73					4																	98893436		2203	4300	6503	SO:0001583	missense	285555	exon7			CCTGATAATCAGC	BC036870	CCDS3645.1	4q22.3-q23	2013-10-11	2012-07-30	2012-07-30	ENSG00000163116	ENSG00000163116			28712	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 37"	C4orf37		23031811	Standard	NM_174952		Approved	MGC46496	uc003htt.2	Q8N412	OTTHUMG00000131009	ENST00000295268.3:c.928T>G	4.37:g.98893436A>C	ENSP00000295268:p.Tyr310Asp	162	0	0		175	66	0.377143	NM_174952		Missense_Mutation	SNP	ENST00000295268.3	37	CCDS3645.1	.	.	.	.	.	.	.	.	.	.	A	15.42	2.828153	0.50845	.	.	ENSG00000163116	ENST00000522676;ENST00000295268	T;T	0.77877	-1.13;1.39	5.45	5.45	0.79879	.	0.000000	0.64402	D	0.000001	D	0.82879	0.5133	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.84923	0.0855	10	0.87932	D	0	-16.3241	14.4978	0.67700	1.0:0.0:0.0:0.0	.	310	Q8N412	CD037_HUMAN	D	24;310	ENSP00000428346:Y24D;ENSP00000295268:Y310D	ENSP00000295268:Y310D	Y	-	1	0	C4orf37	99112459	1.000000	0.71417	0.985000	0.45067	0.357000	0.29423	5.252000	0.65445	2.066000	0.61787	0.455000	0.32223	TAT	.	.	none		0.353	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952		C	98893436	A	C	98893436	3	2	15	1	0	0	0	0	1	0	0	0	2269	362	13	5	471	5	C4orf37	4	98893436	Missense_Mutation	SNP	A	TCGA-FF-8061-01A-11D-2210-10	4516553	98893436	92260840	43	1964											
TET2	54790	hgsc.bcm.edu	37	chr4	106193850	106193850	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtggaagctcaggaggagAaaaaacggagtggtgccatt	13	7	16	5	1	1	1	1	0	0	1	1	5	1	4	1	5	3	1	1	5	4	1			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr4:106193850A>T	ENST00000540549.1	+	10	5172	c.4312A>T	c.(4312-4314)Aaa>Taa	p.K1438*	TET2_ENST00000380013.4_Nonsense_Mutation_p.K1438*|TET2_ENST00000545826.1_3'UTR|TET2_ENST00000513237.1_Nonsense_Mutation_p.K1459*			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1438					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)		TCAGGAGGAGAAAAAACGGAG	0.473			"Mis N, F"		MDS																																p.K1438X		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	0			c.A4312T						PASS	.						161	152	155					4																	106193850		692	1591	2283	SO:0001587	stop_gained	54790	exon10			GAGGAGAAAAAAC	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.4312A>T	4.37:g.106193850A>T	ENSP00000442788:p.Lys1438*	106	0	0		130	108	0.830769	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Nonsense_Mutation	SNP	ENST00000540549.1	37	CCDS47120.1	.	.	.	.	.	.	.	.	.	.	A	50	16.191500	0.99857	.	.	ENSG00000168769	ENST00000540549;ENST00000513237;ENST00000380013	.	.	.	5.23	5.23	0.72850	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.9501	15.5771	0.76400	1.0:0.0:0.0:0.0	.	.	.	.	X	1438;1459;1438	.	ENSP00000369351:K1438X	K	+	1	0	TET2	106413299	1.000000	0.71417	0.996000	0.52242	0.835000	0.47333	6.960000	0.76036	2.324000	0.78689	0.533000	0.62120	AAA	.	.	none		0.473	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		T	106193850	A	T	106193850	4	4	15	1	0	0	0	0	0	1	0	0	15785	247	9	5	4431	5	TET2	4	106193850	Nonsense_Mutation	SNP	A	TCGA-FF-8061-01A-11D-2210-10	7300414	106193850	84960426	44	1965											
NPY2R	4887	hgsc.bcm.edu	37	chr4	156135863	156135863	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcctggagctgcaaatgacCactaccatcagcgaaggcaa	13	6	10	12	1	1	1	1	1	0	0	2	3	2	2	3	2	4	3	3	2	4	1			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr4:156135863C>T	ENST00000329476.3	+	2	1261	c.772C>T	c.(772-774)Cac>Tac	p.H258Y	NPY2R_ENST00000506608.1_Missense_Mutation_p.H258Y	NM_000910.2	NP_000901.1	P49146	NPY2R_HUMAN	neuropeptide Y receptor Y2	258					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)	TGCAAATGACCACTACCATCA	0.483																																					p.H258Y		Atlas-SNP	.											.	NPY2R	87	.	0			c.C772T						PASS	.						105	106	106					4																	156135863		2203	4300	6503	SO:0001583	missense	4887	exon2			AATGACCACTACC	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.772C>T	4.37:g.156135863C>T	ENSP00000332591:p.His258Tyr	117	0	0		96	41	0.427083	NM_000910	Q13281|Q13457|Q4W5G7|Q6AZZ6|Q9UE67	Missense_Mutation	SNP	ENST00000329476.3	37	CCDS3791.1	.	.	.	.	.	.	.	.	.	.	C	12.90	2.077872	0.36662	.	.	ENSG00000185149	ENST00000329476;ENST00000506608	T;T	0.37058	1.22;1.22	5.8	5.8	0.92144	GPCR, rhodopsin-like superfamily (1);	0.295033	0.37577	N	0.002031	T	0.34571	0.0902	L	0.39085	1.19	0.42996	D	0.994507	B	0.32939	0.391	B	0.34590	0.186	T	0.06197	-1.0840	10	0.36615	T	0.2	.	19.0326	0.92963	0.0:1.0:0.0:0.0	.	258	P49146	NPY2R_HUMAN	Y	258	ENSP00000332591:H258Y;ENSP00000426366:H258Y	ENSP00000332591:H258Y	H	+	1	0	NPY2R	156355313	1.000000	0.71417	1.000000	0.80357	0.587000	0.36485	2.361000	0.44160	2.742000	0.94016	0.643000	0.83706	CAC	.	.	none		0.483	NPY2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365128.1	NM_000910		T	156135863	C	T	156135863	3	4	15	1	0	0	0	0	1	0	0	0	10618	594	21	2	774	2	NPY2R	4	156135863	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	49942013	156135863	35018413	45	1966											
GUCY1A3	2982	hgsc.bcm.edu	37	chr4	156634257	156634257	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttccttcataggttatggAcctcaaaggccaaatgatct	11	13	7	10	0	3	1	2	1	1	0	4	2	4	2	3	3	0	1	3	3	4	4			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr4:156634257A>G	ENST00000296518.7	+	7	1303	c.1094A>G	c.(1093-1095)gAc>gGc	p.D365G	GUCY1A3_ENST00000506455.1_Missense_Mutation_p.D365G|GUCY1A3_ENST00000455639.2_Missense_Mutation_p.D365G|GUCY1A3_ENST00000513574.1_Missense_Mutation_p.D365G|GUCY1A3_ENST00000511108.1_Missense_Mutation_p.D365G|GUCY1A3_ENST00000393832.3_Missense_Mutation_p.D107G|GUCY1A3_ENST00000511507.1_Missense_Mutation_p.D365G			Q02108	GCYA3_HUMAN	guanylate cyclase 1, soluble, alpha 3	365					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)		TAGGTTATGGACCTCAAAGGC	0.408																																					p.D365G		Atlas-SNP	.											.	GUCY1A3	133	.	0			c.A1094G						PASS	.						63	61	61					4																	156634257		2203	4300	6503	SO:0001583	missense	2982	exon7			TTATGGACCTCAA		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.1094A>G	4.37:g.156634257A>G	ENSP00000296518:p.Asp365Gly	119	0	0		113	39	0.345133	NM_001130687	D3DP19|D6RDW3|O43843|Q8TAH3	Missense_Mutation	SNP	ENST00000296518.7	37	CCDS34085.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.681155	0.88542	.	.	ENSG00000164116	ENST00000506455;ENST00000511108;ENST00000511507;ENST00000455639;ENST00000393832;ENST00000296518;ENST00000513574	D;D;D;D;D;D;D	0.88354	-2.37;-2.37;-2.37;-2.37;-2.37;-2.37;-2.37	6.03	6.03	0.97812	Haem NO binding associated (1);	0.000000	0.64402	D	0.000003	D	0.90546	0.7037	L	0.40543	1.245	0.80722	D	1	P;P	0.46142	0.873;0.873	P;P	0.56088	0.791;0.791	D	0.90068	0.4161	10	0.42905	T	0.14	.	16.5582	0.84512	1.0:0.0:0.0:0.0	.	365;365	B3KU69;Q02108	.;GCYA3_HUMAN	G	365;365;365;365;107;365;365	ENSP00000424361:D365G;ENSP00000421493:D365G;ENSP00000426968:D365G;ENSP00000412201:D365G;ENSP00000377418:D107G;ENSP00000296518:D365G;ENSP00000426040:D365G	ENSP00000296518:D365G	D	+	2	0	GUCY1A3	156853707	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	8.930000	0.92872	2.308000	0.77769	0.533000	0.62120	GAC	.	.	none		0.408	GUCY1A3-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365786.2			G	156634257	A	G	156634257	3	3	15	1	0	0	0	0	1	0	0	0	6903	275	10	3	1127	3	GUCY1A3	4	156634257	Missense_Mutation	SNP	A	TCGA-FF-8061-01A-11D-2210-10	498394	156634257	34520019	46	1967											
PDGFC	56034	hgsc.bcm.edu	37	chr4	157689051	157689051	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccagaaaatggtatcggtTctctttagttcttcccttat	8	16	8	9	1	2	1	0	0	2	1	5	1	3	1	2	3	0	3	2	3	5	7			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr4:157689051T>A	ENST00000502773.1	-	5	1285	c.795A>T	c.(793-795)agA>agT	p.R265S	PDGFC_ENST00000542208.1_Missense_Mutation_p.R110S|PDGFC_ENST00000541126.1_Missense_Mutation_p.R102S|PDGFC_ENST00000422544.2_Intron|PDGFC_ENST00000504672.1_Intron	NM_016205.2	NP_057289.1	Q9NRA1	PDGFC_HUMAN	platelet derived growth factor C	265					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)		TGGTATCGGTTCTCTTTAGTT	0.453																																					p.R265S		Atlas-SNP	.											.	PDGFC	46	.	0			c.A795T						PASS	.						187	171	176					4																	157689051		2203	4299	6502	SO:0001583	missense	56034	exon5			ATCGGTTCTCTTT	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.795A>T	4.37:g.157689051T>A	ENSP00000422464:p.Arg265Ser	110	0	0		94	38	0.404255	NM_016205	B4DU34|B9EGR8|Q4W5M9|Q9UL22	Missense_Mutation	SNP	ENST00000502773.1	37	CCDS3795.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.076337	0.76415	.	.	ENSG00000145431	ENST00000502773;ENST00000541126;ENST00000542208	T;T;T	0.42131	2.56;1.0;0.98	5.35	1.63	0.23807	Platelet-derived growth factor (PDGF) (3);	0.098787	0.64402	D	0.000003	T	0.51398	0.1672	M	0.63428	1.95	0.48087	D	0.999582	D;B	0.57571	0.98;0.124	P;B	0.57846	0.828;0.247	T	0.50154	-0.8861	10	0.56958	D	0.05	-15.9159	9.5005	0.39015	0.0:0.4019:0.0:0.5981	.	110;265	B4E3A5;Q9NRA1	.;PDGFC_HUMAN	S	265;102;110	ENSP00000422464:R265S;ENSP00000442943:R102S;ENSP00000439728:R110S	ENSP00000422464:R265S	R	-	3	2	PDGFC	157908501	0.987000	0.35691	1.000000	0.80357	0.999000	0.98932	0.193000	0.17116	0.369000	0.24510	0.533000	0.62120	AGA	.	.	none		0.453	PDGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366123.1			A	157689051	T	A	157689051	3	1	15	1	0	0	0	0	1	0	0	0	11668	1780	62	5	250	5	PDGFC	4	157689051	Missense_Mutation	SNP	T	TCGA-FF-8061-01A-11D-2210-10	1054794	157689051	33465225	47	1968											
FNIP2	57600	hgsc.bcm.edu	37	chr4	159789387	159789387	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgctctgagctacaagagaaCcagctgacctggagtggcaa	12	7	12	10	0	1	3	0	2	1	1	1	5	1	4	2	2	5	4	2	2	4	1			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr4:159789387C>T	ENST00000264433.6	+	13	1674	c.1599C>T	c.(1597-1599)aaC>aaT	p.N533N	FNIP2_ENST00000379346.3_Silent_p.N556N	NM_020840.1	NP_065891.1	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2	533					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)		TACAAGAGAACCAGCTGACCT	0.493																																					p.N533N		Atlas-SNP	.											.	FNIP2	90	.	0			c.C1599T						PASS	.						92	94	94					4																	159789387		2077	4216	6293	SO:0001819	synonymous_variant	57600	exon13			AGAGAACCAGCTG	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.1599C>T	4.37:g.159789387C>T		80	0	0		78	4	0.0512821	NM_020840	Q05DC3|Q96I31|Q9H994	Silent	SNP	ENST00000264433.6	37	CCDS47155.1																																																																																			.	.	none		0.493	FNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366602.1	NM_020840		T	159789387	C	T	159789387	2	4	15	1	0	0	0	0	0	0	0	1	5984	506	18	2		2	FNIP2	4	159789387	Silent	SNP	C	TCGA-FF-8061-01A-11D-2210-10	2100336	159789387	31364889	48	1969											
TLL1	7092	hgsc.bcm.edu	37	chr4	166913969	166913969	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctttaaggtggacttggagaCcatgctatgtcaaagaagcg	12	10	12	7	1	1	2	1	0	0	2	1	4	1	3	1	3	2	1	1	3	4	4	rs377042841		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr4:166913969C>T	ENST00000061240.2	+	3	941	c.294C>T	c.(292-294)gaC>gaT	p.D98D	TLL1_ENST00000513213.1_Silent_p.D98D|TLL1_ENST00000507499.1_Silent_p.D98D	NM_012464.4	NP_036596.3	O43897	TLL1_HUMAN	tolloid-like 1	98					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)		GACTTGGAGACCATGCTATGT	0.363																																					p.D98D		Atlas-SNP	.											.	TLL1	194	.	0			c.C294T						PASS	.						131	129	130					4																	166913969		2203	4299	6502	SO:0001819	synonymous_variant	7092	exon3			TGGAGACCATGCT	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.294C>T	4.37:g.166913969C>T		91	0	0		80	4	0.05	NM_001204760	B2RMU2|Q96AN3|Q9NQS4	Silent	SNP	ENST00000061240.2	37	CCDS3811.1																																																																																			.	.	alt		0.363	TLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363821.1			T	166913969	C	T	166913969	2	4	15	1	0	0	0	0	0	0	0	1	15960	506	18	2		2	TLL1	4	166913969	Silent	SNP	C	TCGA-FF-8061-01A-11D-2210-10	7124582	166913969	24240307	49	1970											
RNASEN	29102	hgsc.bcm.edu	37	chr5	31521306	31521306	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgtctcgatgcctgtgtcTctcccgttctcgctctctta	2	17	8	14	3	4	0	0	0	4	0	9	1	5	0	2	0	1	3	2	0	1	3			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr5:31521306T>C	ENST00000511367.2	-	5	1115	c.871A>G	c.(871-873)Aga>Gga	p.R291G	DROSHA_ENST00000442743.1_Missense_Mutation_p.R291G|DROSHA_ENST00000513349.1_Missense_Mutation_p.R291G|DROSHA_ENST00000344624.3_Missense_Mutation_p.R291G	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	291	Arg-rich.				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						TGCCTGTGTCTCTCCCGTTCT	0.398																																					p.R291G		Atlas-SNP	.											.	DROSHA	130	.	0			c.A871G						PASS	.						256	236	242					5																	31521306		1899	4117	6016	SO:0001583	missense	29102	exon5			TGTGTCTCTCCCG	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.871A>G	5.37:g.31521306T>C	ENSP00000425979:p.Arg291Gly	144	0	0		107	5	0.046729	NM_013235	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Missense_Mutation	SNP	ENST00000511367.2	37	CCDS47195.1	.	.	.	.	.	.	.	.	.	.	T	16.64	3.179709	0.57800	.	.	ENSG00000113360	ENST00000511367;ENST00000344624;ENST00000442743;ENST00000513349;ENST00000382188	T;T;T;T	0.54071	0.59;0.59;0.59;0.59	5.95	4.73	0.59995	.	0.000000	0.85682	D	0.000000	T	0.55513	0.1925	N	0.24115	0.695	0.58432	D	0.999999	D;D	0.54601	0.967;0.967	D;D	0.63597	0.916;0.916	T	0.56117	-0.8032	10	0.44086	T	0.13	-20.9464	12.9148	0.58200	0.0:0.0:0.1352:0.8648	.	291;291	E7EMP9;Q9NRR4	.;RNC_HUMAN	G	291;291;291;291;284	ENSP00000425979:R291G;ENSP00000339845:R291G;ENSP00000409335:R291G;ENSP00000424161:R291G	ENSP00000339845:R291G	R	-	1	2	DROSHA	31557063	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.481000	0.53179	2.279000	0.76181	0.533000	0.62120	AGA	.	.	none		0.398	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235		C	31521306	T	C	31521306	3	2	15	1	0	0	0	0	1	0	0	0	13432	1559	54	3	3377	3	RNASEN	5	31521306	Missense_Mutation	SNP	T	TCGA-FF-8061-01A-11D-2210-10		31521306	149393954	50	1971											
PCDHA10	56139	hgsc.bcm.edu	37	chr5	140236835	140236835	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caagctggtgtccacctacaAgaattactactcattggtgc	11	11	8	11	0	1	1	1	0	0	1	2	1	2	1	2	2	5	1	2	2	6	4			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr5:140236835A>G	ENST00000307360.5	+	1	1202	c.1202A>G	c.(1201-1203)aAg>aGg	p.K401R	PCDHA7_ENST00000525929.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000506939.2_Missense_Mutation_p.K401R|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	401	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)	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)			TCCACCTACAAGAATTACTAC	0.597																																					p.K401R		Atlas-SNP	.											.	PCDHA10	358	.	0			c.A1202G						PASS	.						144	129	134					5																	140236835		2197	4275	6472	SO:0001583	missense	56139	exon1			CCTACAAGAATTA	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.1202A>G	5.37:g.140236835A>G	ENSP00000304234:p.Lys401Arg	130	0	0		189	77	0.407407	NM_031859	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	37	CCDS54921.1	.	.	.	.	.	.	.	.	.	.	A	9.832	1.188630	0.21954	.	.	ENSG00000250120	ENST00000506939;ENST00000307360	T;T	0.51817	4.64;0.69	4.0	1.57	0.23409	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.39036	0.1063	L	0.46819	1.47	0.21325	N	0.999726	B;B;B	0.26809	0.086;0.029;0.16	B;B;B	0.32928	0.085;0.03;0.155	T	0.34976	-0.9807	9	0.39692	T	0.17	.	5.0725	0.14613	0.6033:0.1492:0.2475:0.0	.	401;401;401	Q9Y5I2-3;Q9Y5I2;Q9Y5I2-2	.;PCDAA_HUMAN;.	R	401	ENSP00000421030:K401R;ENSP00000304234:K401R	ENSP00000304234:K401R	K	+	2	0	PCDHA10	140217019	0.000000	0.05858	0.999000	0.59377	0.741000	0.42261	0.427000	0.21379	0.653000	0.30826	0.459000	0.35465	AAG	.	.	none		0.597	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		G	140236835	A	G	140236835	3	3	15	1	0	0	0	0	1	0	0	0	11529	72	3	3	1204	3	PCDHA10	5	140236835	Missense_Mutation	SNP	A	TCGA-FF-8061-01A-11D-2210-10	108715529	140236835	40678425	51	1972											
TLX3	30012	hgsc.bcm.edu	37	chr5	170736474	170736474	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggacagcgcacccgccccGcggggccccgacggcgccag	6	0	15	20	7	0	0	0	0	0	0	0	2	0	1	6	4	1	1	6	4	0	0	rs2303742	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr5:170736474G>A	ENST00000296921.5	+	1	187	c.105G>A	c.(103-105)ccG>ccA	p.P35P		NM_021025.2	NP_066305.2	O43711	TLX3_HUMAN	T-cell leukemia homeobox 3	35					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)			CACCCGCCCCGCGGGGCCCCG	0.766			T	BCL11B	T-ALL								G|||	14	0.00279553	0.0	0.0	5008	,	,		10162	0.0139		0.0	False		,,,				2504	0.0				p.P35P	Esophageal Squamous(33;43 807 3116 3348 30094)	Atlas-SNP	.		Dom	yes		5	5q35.1	30012	"T-cell leukemia, homeobox 3 (HOX11L2)"		L	TLX3_ENST00000296921,NS,carcinoma,+2,1	TLX3	23	1	0			c.G105A						scavenged	.						7	10	9					5																	170736474		2127	4181	6308	SO:0001819	synonymous_variant	30012	exon1			CGCCCCGCGGGGC	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.105G>A	5.37:g.170736474G>A		4	2	0.5		14	12	0.857143	NM_021025	Q96AD3	Silent	SNP	ENST00000296921.5	37	CCDS34288.1																																																																																			G|0.995;A|0.005	0.005	strong		0.766	TLX3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372076.3			A	170736474	G	A	170736474	2	1	15	1	0	0	0	0	0	0	0	1	15977	1074	38	1		1	TLX3	5	170736474	Silent	SNP	G	TCGA-FF-8061-01A-11D-2210-10	30499639	170736474	10178786	52	1973											
ADAMTS2	9509	hgsc.bcm.edu	37	chr5	178552090	178552090	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cacggagcgggtggtgttgtCgtgtagcggctgaatgcagc	6	9	18	8	4	0	1	0	1	0	0	1	2	0	2	0	4	4	4	0	4	2	2			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr5:178552090C>T	ENST00000251582.7	-	19	2943	c.2842G>A	c.(2842-2844)Gac>Aac	p.D948N		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	948	TSP type-1 3. {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)		GTGGTGTTGTCGTGTAGCGGC	0.692																																					p.D948N		Atlas-SNP	.											ADAMTS2,caecum,carcinoma,0,2	ADAMTS2	190	2	0			c.G2842A						scavenged	.						112	113	113					5																	178552090		2203	4300	6503	SO:0001583	missense	9509	exon19			TGTTGTCGTGTAG	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.2842G>A	5.37:g.178552090C>T	ENSP00000251582:p.Asp948Asn	74	1	0.0135135		121	5	0.0413223	NM_014244		Missense_Mutation	SNP	ENST00000251582.7	37	CCDS4444.1	.	.	.	.	.	.	.	.	.	.	C	0.743	-0.775731	0.02951	.	.	ENSG00000087116	ENST00000251582	T	0.53857	0.6	5.31	2.0	0.26442	.	0.301971	0.27792	N	0.017833	T	0.26774	0.0655	N	0.12422	0.21	0.80722	D	1	B	0.24317	0.101	B	0.22601	0.04	T	0.10730	-1.0617	10	0.06757	T	0.87	.	8.4694	0.32975	0.0:0.7177:0.0:0.2823	.	948	O95450	ATS2_HUMAN	N	948	ENSP00000251582:D948N	ENSP00000251582:D948N	D	-	1	0	ADAMTS2	178484696	0.966000	0.33281	0.957000	0.39632	0.030000	0.12068	1.550000	0.36223	0.026000	0.15269	-1.140000	0.01884	GAC	.	.	none		0.692	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244		T	178552090	C	T	178552090	3	4	15	1	0	0	0	0	1	0	0	0	265	884	31	1	809	1	ADAMTS2	5	178552090	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	7815616	178552090	2363170	53	1974											
DEK	7913	hgsc.bcm.edu	37	chr6	18249894	18249894	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tattttacctcctcttcactTtctttatcttcatcatctga	7	21	1	12	0	7	1	3	1	4	0	8	1	8	1	2	0	1	0	2	0	3	8			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:18249894T>G	ENST00000397239.3	-	7	1197	c.750A>C	c.(748-750)gaA>gaC	p.E250D	DEK_ENST00000244776.7_Missense_Mutation_p.E216D	NM_003472.3	NP_003463.1	P35659	DEK_HUMAN	DEK proto-oncogene	250	Asp/Glu-rich (acidic).				chromatin modification (GO:0016568)|regulation of double-strand break repair (GO:2000779)|regulation of double-strand break repair via nonhomologous end joining (GO:2001032)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	7	Ovarian(93;0.00769)|Breast(50;0.0495)	all_hematologic(90;0.053)	OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332)			CCTCTTCACTTTCTTTATCTT	0.328			T	NUP214	AML																																p.E250D		Atlas-SNP	.		Dom	yes		6	6p23	7913	DEK oncogene (DNA binding)		L	DEK,NS,carcinoma,0,1	DEK	31	1	0			c.A750C						PASS	.						67	63	64					6																	18249894		2201	4298	6499	SO:0001583	missense	7913	exon7			TTCACTTTCTTTA	X64229	CCDS34344.1, CCDS47382.1	6p23	2014-06-25	2014-06-25		ENSG00000124795	ENSG00000124795			2768	protein-coding gene	gene with protein product		125264	"DEK oncogene (DNA binding)", "DEK oncogene"			1549122	Standard	NM_003472		Approved	D6S231E	uc003ncr.1	P35659	OTTHUMG00000014319	ENST00000397239.3:c.750A>C	6.37:g.18249894T>G	ENSP00000380414:p.Glu250Asp	124	0	0		89	33	0.370787	NM_003472	B2R6K6|B4DN37|Q5TGV4|Q5TGV5	Missense_Mutation	SNP	ENST00000397239.3	37	CCDS34344.1	.	.	.	.	.	.	.	.	.	.	T	15.14	2.745676	0.49151	.	.	ENSG00000124795	ENST00000397239;ENST00000244776;ENST00000507591	T;T	0.52754	0.68;0.65	6.17	3.8	0.43715	.	0.698644	0.14633	N	0.307696	T	0.21307	0.0513	L	0.44542	1.39	0.37002	D	0.895305	P;P	0.50443	0.935;0.935	B;B	0.42462	0.388;0.388	T	0.03945	-1.0990	10	0.14252	T	0.57	-0.8892	10.6274	0.45516	0.0:0.1285:0.0:0.8715	.	216;250	B4DN37;P35659	.;DEK_HUMAN	D	250;216;26	ENSP00000380414:E250D;ENSP00000244776:E216D	ENSP00000244776:E216D	E	-	3	2	DEK	18357873	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.118000	0.31246	0.572000	0.29383	-0.256000	0.11100	GAA	.	.	none		0.328	DEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039962.4			G	18249894	T	G	18249894	3	3	15	1	0	0	0	0	1	0	0	0	4426	1838	64	5	397	5	DEK	6	18249894	Missense_Mutation	SNP	T	TCGA-FF-8061-01A-11D-2210-10		18249894	152865173	54	1975											
HIST1H1C	3006	hgsc.bcm.edu	37	chr6	26056233	26056233	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cttcggagttgcgccgccagCcgccttcttgggcttcttgg	2	12	13	14	4	2	0	0	0	2	0	3	1	2	1	4	3	2	2	4	3	0	6			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:26056233C>T	ENST00000343677.2	-	1	466	c.424G>A	c.(424-426)Gct>Act	p.A142T		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	142					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						GCGCCGCCAGCCGCCTTCTTG	0.577																																					p.A142T		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.G424A						PASS	.						61	74	69					6																	26056233		2197	4295	6492	SO:0001583	missense	3006	exon1			CGCCAGCCGCCTT	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.424G>A	6.37:g.26056233C>T	ENSP00000339566:p.Ala142Thr	179	0	0		152	9	0.0592105	NM_005319	A8K4I2	Missense_Mutation	SNP	ENST00000343677.2	37	CCDS4577.1	.	.	.	.	.	.	.	.	.	.	C	0.704	-0.789557	0.02884	.	.	ENSG00000187837	ENST00000343677	T	0.14022	2.54	5.54	-9.61	0.00550	.	0.479745	0.21639	N	0.071371	T	0.00936	0.0031	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.34725	-0.9817	10	0.02654	T	1	-4.9914	14.0678	0.64841	0.2008:0.6751:0.0:0.1241	.	142	P16403	H12_HUMAN	T	142	ENSP00000339566:A142T	ENSP00000339566:A142T	A	-	1	0	HIST1H1C	26164212	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.462000	0.02364	-1.623000	0.01558	-0.238000	0.12139	GCT	.	.	none		0.577	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319		T	26056233	C	T	26056233	3	4	15	1	0	0	0	0	1	0	0	0	7133	739	26	2	221	2	HIST1H1C	6	26056233	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	7806339	26056233	145058834	55	1976											
HIST1H1B	3009	hgsc.bcm.edu	37	chr6	27834991	27834991	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tcttgttgagtttaaaggagCcagaagcaccagtgcccttg	10	11	11	9	0	1	2	0	1	1	1	1	3	1	3	3	1	3	3	3	1	3	5			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:27834991C>G	ENST00000331442.3	-	1	368	c.317G>C	c.(316-318)gGc>gCc	p.G106A		NM_005322.2	NP_005313.1	P16401	H15_HUMAN	histone cluster 1, H1b	106	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				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						TTTAAAGGAGCCAGAAGCACC	0.602																																					p.G106A		Atlas-SNP	.											.	HIST1H1B	54	.	0			c.G317C						PASS	.						113	126	121					6																	27834991		2203	4300	6503	SO:0001583	missense	3009	exon1			AAGGAGCCAGAAG	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.317G>C	6.37:g.27834991C>G	ENSP00000330074:p.Gly106Ala	132	0	0		99	43	0.434343	NM_005322	Q14529|Q3MJ42	Missense_Mutation	SNP	ENST00000331442.3	37	CCDS4635.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.578219	0.86645	.	.	ENSG00000184357	ENST00000331442	T	0.58060	0.36	5.3	4.42	0.53409	Histone H1/H5 (2);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.71576	0.3356	M	0.90977	3.165	0.80722	D	1	D	0.60575	0.988	D	0.67725	0.953	T	0.80647	-0.1289	10	0.87932	D	0	-16.951	15.3154	0.74074	0.0:0.8595:0.1405:0.0	.	106	P16401	H15_HUMAN	A	106	ENSP00000330074:G106A	ENSP00000330074:G106A	G	-	2	0	HIST1H1B	27942970	1.000000	0.71417	0.993000	0.49108	0.886000	0.51366	5.792000	0.69052	1.353000	0.45828	0.563000	0.77884	GGC	.	.	none		0.602	HIST1H1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043371.1	NM_005322		G	27834991	C	G	27834991	3	3	15	1	0	0	0	0	1	0	0	0	7132	739	26	4	367	4	HIST1H1B	6	27834991	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	1778758	27834991	143280076	56	1977											
GPX5	2880	hgsc.bcm.edu	37	chr6	28500106	28500106	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcttgttgcaggtatgtccGtccagggggaggatttgtac	6	12	16	7	1	0	0	0	0	0	0	2	2	2	2	2	5	2	5	2	5	2	5	rs138279209		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:28500106G>A	ENST00000412168.2	+	4	457	c.368G>A	c.(367-369)cGt>cAt	p.R123H	GPX5_ENST00000442674.2_3'UTR|GPX5_ENST00000469384.1_Missense_Mutation_p.V84I	NM_001509.2	NP_001500.1	O75715	GPX5_HUMAN	glutathione peroxidase 5 (epididymal androgen-related protein)	123					lipid metabolic process (GO:0006629)|response to oxidative stress (GO:0006979)	extracellular region (GO:0005576)	glutathione peroxidase activity (GO:0004602)			endometrium(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16					Glutathione(DB00143)	AGGTATGTCCGTCCAGGGGGA	0.423																																					p.R123H		Atlas-SNP	.											.	GPX5	42	.	0			c.G368A						PASS	.	G	HIS/ARG,ILE/VAL	0,4406		0,0,2203	139	126	130		368,250	4.2	1	6	dbSNP_134	130	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	GPX5	NM_001509.2,NM_003996.3	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	123/222,84/101	28500106	1,13005	2203	4300	6503	SO:0001583	missense	2880	exon4			ATGTCCGTCCAGG	AJ005277	CCDS4652.1, CCDS4653.1	6p22.1	2008-02-05			ENSG00000224586	ENSG00000224586	1.11.1.9		4557	protein-coding gene	gene with protein product		603435				9639555	Standard	NM_001509		Approved		uc003nll.2	O75715	OTTHUMG00000016307	ENST00000412168.2:c.368G>A	6.37:g.28500106G>A	ENSP00000392398:p.Arg123His	125	0	0		121	95	0.785124	NM_001509	A1A4Y0	Missense_Mutation	SNP	ENST00000412168.2	37	CCDS4652.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.91|17.91	3.503579|3.503579	0.64298|0.64298	0.0|0.0	1.16E-4|1.16E-4	ENSG00000224586|ENSG00000224586	ENST00000412168|ENST00000469384	T|T	0.04156|0.10192	3.69|2.9	4.16|4.16	4.16|4.16	0.48862|0.48862	Thioredoxin-like fold (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.03564|0.03564	0.0102|0.0102	.|.	.|.	.|.	0.22581|0.22581	N|N	0.998967|0.998967	D|P	0.89917|0.39847	1.0|0.691	D|B	0.80764|0.28465	0.994|0.09	T|T	0.26744|0.26744	-1.0094|-1.0094	9|8	0.87932|0.66056	D|D	0|0.02	-14.4515|-14.4515	14.7712|14.7712	0.69679|0.69679	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	123|84	O75715|A1A4Y0	GPX5_HUMAN|.	H|I	123|84	ENSP00000392398:R123H|ENSP00000419935:V84I	ENSP00000392398:R123H|ENSP00000419935:V84I	R|V	+|+	2|1	0|0	GPX5|GPX5	28608085|28608085	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.996000|0.996000	0.88848|0.88848	8.310000|8.310000	0.89971|0.89971	2.597000|2.597000	0.87782|0.87782	0.655000|0.655000	0.94253|0.94253	CGT|GTC	G|1.000;A|0.000	0.000	weak		0.423	GPX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043672.2			A	28500106	G	A	28500106	3	1	15	1	0	0	0	0	1	0	0	0	6752	1145	40	1	382	1	GPX5	6	28500106	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	665115	28500106	142614961	57	1978											
C6orf127	340204	hgsc.bcm.edu	37	chr6	35754842	35754842	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgccaacgtgctccagacaAttgcgagtcgcactgcgcgg	8	7	12	14	5	0	1	0	0	0	1	2	2	1	1	2	1	5	2	2	1	2	1			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:35754842A>G	ENST00000373861.5	+	2	261	c.167A>G	c.(166-168)aAt>aGt	p.N56S	CLPSL1_ENST00000542261.1_Missense_Mutation_p.N55S			A2RUU4	COLL1_HUMAN	colipase-like 1	56					digestion (GO:0007586)|lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	enzyme activator activity (GO:0008047)										GCTCCAGACAATTGCGAGTCG	0.657																																					p.N56S		Atlas-SNP	.											.	.	.	.	0			c.A167G						PASS	.						23	31	28					6																	35754842		2159	4255	6414	SO:0001583	missense	340204	exon2			CAGACAATTGCGA		CCDS43456.1	6p21.31	2014-01-28	2012-02-06	2012-02-06	ENSG00000204140	ENSG00000204140			21251	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 127"	C6orf127			Standard	NM_001010886		Approved	dJ510O8.6	uc003old.4	A2RUU4	OTTHUMG00000014582	ENST00000373861.5:c.167A>G	6.37:g.35754842A>G	ENSP00000362968:p.Asn56Ser	38	0	0		41	10	0.243902	NM_001010886	A7E2T6|B2RPE2|B5G4V2|B6ZDM9|Q5T9G1	Missense_Mutation	SNP	ENST00000373861.5	37	CCDS43456.1	.	.	.	.	.	.	.	.	.	.	A	0.108	-1.141934	0.01728	.	.	ENSG00000204140	ENST00000373861;ENST00000373860;ENST00000542261;ENST00000428710	T;T	0.31247	1.5;1.5	2.05	-4.09	0.03951	.	2.100700	0.03133	U	0.165408	T	0.03608	0.0103	N	0.14661	0.345	0.09310	N	1	B	0.12013	0.005	B	0.14023	0.01	T	0.12477	-1.0546	10	0.33940	T	0.23	.	0.212	0.00157	0.3332:0.2323:0.2143:0.2202	.	56	A2RUU4	CF127_HUMAN	S	56;56;55;9	ENSP00000362968:N56S;ENSP00000438478:N55S	ENSP00000362967:N56S	N	+	2	0	C6orf127	35862820	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-2.569000	0.00915	-3.437000	0.00163	-3.063000	0.00068	AAT	.	.	none		0.657	CLPSL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040317.2	NM_001010886		G	35754842	A	G	35754842	3	3	15	1	0	0	0	0	1	0	0	0	2329	101	4	3	173	3	C6orf127	6	35754842	Missense_Mutation	SNP	A	TCGA-FF-8061-01A-11D-2210-10	7254736	35754842	135360225	58	1979											
PIM1	5292	hgsc.bcm.edu	37	chr6	37138355	37138355	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acatcctggaggttgggatgCtcttgtccaaaatcaactcg	10	11	10	10	1	2	0	1	0	1	0	5	2	4	2	2	3	2	2	2	3	3	2			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:37138355C>T	ENST00000373509.5	+	1	377	c.4C>T	c.(4-6)Ctc>Ttc	p.L2F		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	93					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)	p.L2V(1)|p.L2F(1)		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)	GGTTGGGATGCTCTTGTCCAA	0.701			T	BCL6	NHL																																p.L93F		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,0,3	PIM1	71	3	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.C277T						PASS	.						30	30	30					6																	37138355		2201	4298	6499	SO:0001583	missense	5292	exon1			GGGATGCTCTTGT		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.4C>T	6.37:g.37138355C>T	ENSP00000362608:p.Leu2Phe	29	0	0		33	10	0.30303	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.693535	0.88735	.	.	ENSG00000137193	ENST00000373509	T	0.71222	-0.55	4.05	4.05	0.47172	.	0.000000	0.32147	N	0.006517	T	0.61899	0.2384	N	0.08118	0	0.48830	D	0.999711	D	0.76494	0.999	D	0.66196	0.942	T	0.73933	-0.3826	10	0.72032	D	0.01	.	16.7252	0.85419	0.0:1.0:0.0:0.0	.	93	P11309	PIM1_HUMAN	F	2	ENSP00000362608:L2F	ENSP00000362608:L2F	L	+	1	0	PIM1	37246333	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.672000	0.61597	2.211000	0.71520	0.542000	0.68232	CTC	.	.	none		0.701	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37138355	C	T	37138355	3	4	15	1	0	0	0	0	1	0	0	0	11936	797	28	2	6	2	PIM1	6	37138355	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	1383513	37138355	133976712	59	1980											
PIM1	5292	hgsc.bcm.edu	37	chr6	37138424	37138424	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acgacctgcacgccaccaagCtggcgcccggtgagagcacc	9	3	12	17	4	0	1	0	1	0	1	0	3	0	1	5	2	3	3	5	2	1	0			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:37138424C>T	ENST00000373509.5	+	1	446	c.73C>T	c.(73-75)Ctg>Ttg	p.L25L		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	116					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)	p.L25V(1)		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)	CGCCACCAAGCTGGCGCCCGG	0.726			T	BCL6	NHL																																p.L116L		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,0,1	PIM1	71	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C346T						scavenged	.						22	24	24					6																	37138424		2196	4289	6485	SO:0001819	synonymous_variant	5292	exon1			ACCAAGCTGGCGC		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.73C>T	6.37:g.37138424C>T		11	0	0		12	3	0.25	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.726	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37138424	C	T	37138424	2	4	15	1	0	0	0	0	0	0	0	1	11936	796	28	2		2	PIM1	6	37138424	Silent	SNP	C	TCGA-FF-8061-01A-11D-2210-10	69	37138424	133976643	60	1981											
NFKBIE	4794	hgsc.bcm.edu	37	chr6	44229533	44229533	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctggcccccttcagcaccAgtgcccgaactgcgcccggt	5	6	12	18	3	1	0	1	0	0	0	1	1	1	0	5	3	4	2	5	3	1	1			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:44229533A>T	ENST00000275015.5	-	3	937	c.938T>A	c.(937-939)cTg>cAg	p.L313Q		NM_004556.2	NP_004547.2	O00221	IKBE_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, epsilon	313					cytoplasmic sequestering of transcription factor (GO:0042994)|D-serine transport (GO:0042942)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|urinary_tract(1)	10	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)			CTTCAGCACCAGTGCCCGAAC	0.647																																					p.L313Q		Atlas-SNP	.											.	NFKBIE	31	.	0			c.T938A						PASS	.						30	30	30					6																	44229533		2203	4300	6503	SO:0001583	missense	4794	exon3			AGCACCAGTGCCC	U91616	CCDS34463.1	6p21.1	2013-01-10			ENSG00000146232	ENSG00000146232		"Ankyrin repeat domain containing"	7799	protein-coding gene	gene with protein product		604548				9135156	Standard	NM_004556		Approved	IKBE	uc003oxe.1	O00221	OTTHUMG00000014762	ENST00000275015.5:c.938T>A	6.37:g.44229533A>T	ENSP00000275015:p.Leu313Gln	50	0	0		56	24	0.428571	NM_004556	Q5T9V9	Missense_Mutation	SNP	ENST00000275015.5	37	CCDS34463.1	.	.	.	.	.	.	.	.	.	.	A	14.62	2.589276	0.46214	.	.	ENSG00000146232	ENST00000275015	T	0.71579	-0.58	5.28	5.28	0.74379	Ankyrin repeat-containing domain (3);	0.083592	0.49916	D	0.000132	D	0.88934	0.6572	H	0.98629	4.285	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93185	0.6578	10	0.87932	D	0	-19.4802	14.894	0.70630	1.0:0.0:0.0:0.0	.	313	O00221	IKBE_HUMAN	Q	313	ENSP00000275015:L313Q	ENSP00000275015:L313Q	L	-	2	0	NFKBIE	44337511	1.000000	0.71417	0.985000	0.45067	0.980000	0.70556	9.339000	0.96797	2.000000	0.58554	0.533000	0.62120	CTG	.	.	none		0.647	NFKBIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040733.2			T	44229533	A	T	44229533	3	4	15	1	0	0	0	0	1	0	0	0	10389	188	7	5	580	5	NFKBIE	6	44229533	Missense_Mutation	SNP	A	TCGA-FF-8061-01A-11D-2210-10	7091109	44229533	126885534	61	1982											
NFKBIE	4794	hgsc.bcm.edu	37	chr6	44229563	44229564	+	In_Frame_Ins	INS	-	-	GTACAGCCAGATGGA																															tgcgcccggttggtccagatINSgtacagccagatggagtgct																								rs375743668		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:44229563_44229564insGTACAGCCAGATGGA	ENST00000275015.5	-	3	906_907	c.907_908insTCCATCTGGCTGTAC	c.(907-909)cat>cTCCATCTGGCTGTACat	p.302_303insLHLAV		NM_004556.2	NP_004547.2	O00221	IKBE_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, epsilon	302					cytoplasmic sequestering of transcription factor (GO:0042994)|D-serine transport (GO:0042942)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|urinary_tract(1)	10	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)			TTGGTCCAGATGTACAGCCAGA	0.614																																					p.H303delinsLHLAVH		Pindel	.											.	NFKBIE	31	.	0			c.908_909insTCCATCTGGCTGTAC						PASS	.																																			SO:0001652	inframe_insertion	4794	exon3			.	U91616	CCDS34463.1	6p21.1	2013-01-10			ENSG00000146232	ENSG00000146232		"Ankyrin repeat domain containing"	7799	protein-coding gene	gene with protein product		604548				9135156	Standard	NM_004556		Approved	IKBE	uc003oxe.1	O00221	OTTHUMG00000014762	ENST00000275015.5:c.893_907dupTCCATCTGGCTGTAC	6.37:g.44229563_44229564insGTACAGCCAGATGGA	ENSP00000275015:p.Leu298_Val302dup	35	0	.		36	10	0.278	NM_004556	Q5T9V9	In_Frame_Ins	INS	ENST00000275015.5	37	CCDS34463.1																																																																																			.	.	none		0.614	NFKBIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040733.2			GTACAGCCAGATGGA	44229564	-	GTACAGCCAGATGGA	44229563	7	5	15	1	0	1	1	0	0	0	0	0	10389	1464	51	0	610	0	NFKBIE	6	44229563	In_Frame_Ins	INS	-	TCGA-FF-8061-01A-11D-2210-10	30	44229563	126885504	62	1983											
COL21A1	81578	hgsc.bcm.edu	37	chr6	55922465	55922465	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcatcagacactaatagtttGgtccttttctgaacggatct	10	14	8	9	1	3	2	1	1	2	1	4	3	4	3	1	2	1	2	1	2	3	5			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:55922465G>A	ENST00000244728.5	-	30	3261	c.2864C>T	c.(2863-2865)cCa>cTa	p.P955L	COL21A1_ENST00000370819.1_Missense_Mutation_p.P952L|COL21A1_ENST00000370808.2_Missense_Mutation_p.P321L|COL21A1_ENST00000535941.1_Missense_Mutation_p.P955L|COL21A1_ENST00000467045.1_5'UTR	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	955					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)			CTAATAGTTTGGTCCTTTTCT	0.468																																					p.P955L		Atlas-SNP	.											.	COL21A1	201	.	0			c.C2864T						PASS	.						84	79	81					6																	55922465		1908	4133	6041	SO:0001583	missense	81578	exon30			TAGTTTGGTCCTT	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.2864C>T	6.37:g.55922465G>A	ENSP00000244728:p.Pro955Leu	102	0	0		106	15	0.141509	NM_030820	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Missense_Mutation	SNP	ENST00000244728.5	37	CCDS55025.1	.	.	.	.	.	.	.	.	.	.	G	14.67	2.604681	0.46423	.	.	ENSG00000124749	ENST00000244728;ENST00000370819;ENST00000535941;ENST00000370811;ENST00000370808	D;D;D;D	0.91792	-2.52;-2.47;-2.51;-2.91	4.62	4.62	0.57501	.	0.000000	0.56097	D	0.000039	D	0.95736	0.8613	M	0.80616	2.505	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;0.997;0.997;0.997	D	0.96364	0.9268	10	0.87932	D	0	.	17.8313	0.88683	0.0:0.0:1.0:0.0	.	321;955;955;312	Q96P44-2;B7ZLK3;Q96P44;B3KU30	.;.;COLA1_HUMAN;.	L	955;952;955;952;321	ENSP00000244728:P955L;ENSP00000359855:P952L;ENSP00000444384:P955L;ENSP00000359844:P321L	ENSP00000244728:P955L	P	-	2	0	COL21A1	56030424	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	8.527000	0.90594	2.275000	0.75901	0.655000	0.94253	CCA	.	.	none		0.468	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2			A	55922465	G	A	55922465	3	1	15	1	0	0	0	0	1	0	0	0	3682	1348	47	2	13	2	COL21A1	6	55922465	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	11692902	55922465	115192602	63	1984											
TTK	7272	hgsc.bcm.edu	37	chr6	80744802	80744802	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgatagttaccggaacgaaaTagcttatttgaataaactac	16	12	7	6	2	0	2	0	2	0	0	0	4	0	3	1	1	5	2	1	1	10	7			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:80744802T>A	ENST00000369798.2	+	15	1826	c.1715T>A	c.(1714-1716)aTa>aAa	p.I572K	TTK_ENST00000509894.1_Missense_Mutation_p.I571K|TTK_ENST00000230510.3_Missense_Mutation_p.I571K	NM_001166691.1|NM_003318.4	NP_001160163.1|NP_003309.2	P33981	TTK_HUMAN	TTK protein kinase	572	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)		CGGAACGAAATAGCTTATTTG	0.279																																					p.I572K		Atlas-SNP	.											.	TTK	199	.	0			c.T1715A						PASS	.						77	83	81					6																	80744802		2199	4288	6487	SO:0001583	missense	7272	exon15			ACGAAATAGCTTA		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.1715T>A	6.37:g.80744802T>A	ENSP00000358813:p.Ile572Lys	190	0	0		127	49	0.385827	NM_003318	A8K8U5|B2RDW2|E1P543|Q15272|Q5TCS0|Q9BW51|Q9NTM0	Missense_Mutation	SNP	ENST00000369798.2	37	CCDS4993.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.135303	0.77662	.	.	ENSG00000112742	ENST00000509894;ENST00000230510;ENST00000369798	T;T;T	0.76448	-1.02;-1.02;-1.02	5.67	4.49	0.54785	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.043215	0.85682	D	0.000000	T	0.76506	0.3997	L	0.39085	1.19	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.999;1.0	T	0.80013	-0.1560	10	0.66056	D	0.02	.	12.1537	0.54064	0.0:0.0:0.1433:0.8567	.	572;571	P33981;A8K8U5	TTK_HUMAN;.	K	571;571;572	ENSP00000422936:I571K;ENSP00000230510:I571K;ENSP00000358813:I572K	ENSP00000230510:I571K	I	+	2	0	TTK	80801521	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	0.959000	0.37980	0.455000	0.32223	ATA	.	.	none		0.279	TTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041316.2			A	80744802	T	A	80744802	3	1	15	1	0	0	0	0	1	0	0	0	16735	1406	49	5	1769	5	TTK	6	80744802	Missense_Mutation	SNP	T	TCGA-FF-8061-01A-11D-2210-10	24822337	80744802	90370265	64	1985											
PGM3	5238	hgsc.bcm.edu	37	chr6	83898451	83898451	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcatttgctaaacaggtggCatgttcctcccaggatggtg	9	11	12	9	0	0	0	0	0	0	0	2	1	2	1	2	4	3	4	2	4	2	3			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:83898451C>T	ENST00000283977.4	-	2	154	c.28G>A	c.(28-30)Gcc>Acc	p.A10T	PGM3_ENST00000506587.1_Missense_Mutation_p.A119T|PGM3_ENST00000512866.1_Missense_Mutation_p.A91T|PGM3_ENST00000513973.1_Missense_Mutation_p.A91T					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)		AAACAGGTGGCATGTTCCTCC	0.413																																					p.A119T		Atlas-SNP	.											.	PGM3	39	.	0			c.G355A						PASS	.						148	120	129					6																	83898451		2203	4300	6503	SO:0001583	missense	5238	exon4			AGGTGGCATGTTC	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.28G>A	6.37:g.83898451C>T	ENSP00000283977:p.Ala10Thr	108	0	0		90	34	0.377778	NM_001199917		Missense_Mutation	SNP	ENST00000283977.4	37		.	.	.	.	.	.	.	.	.	.	C	32	5.185099	0.94885	.	.	ENSG00000013375	ENST00000513973;ENST00000512866;ENST00000283977;ENST00000506587;ENST00000510258;ENST00000507554;ENST00000508748	T;T;T;T;T;T	0.63096	-0.02;-0.02;0.59;-0.02;-0.02;-0.02	5.82	5.82	0.92795	Alpha-D-phosphohexomutase, alpha/beta/alpha domain I (1);Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III (2);	0.000000	0.85682	D	0.000000	D	0.84083	0.5394	H	0.94582	3.555	0.80722	D	1	D;D;D	0.76494	0.999;0.99;0.999	D;D;D	0.74348	0.983;0.955;0.974	D	0.87601	0.2497	10	0.87932	D	0	-9.7285	20.0851	0.97797	0.0:1.0:0.0:0.0	.	119;119;91	E9PF86;B4DX94;O95394	.;.;AGM1_HUMAN	T	91;91;10;119;10;91;119	ENSP00000424874:A91T;ENSP00000421565:A91T;ENSP00000283977:A10T;ENSP00000425809:A119T;ENSP00000425558:A91T;ENSP00000424865:A119T	ENSP00000283977:A10T	A	-	1	0	PGM3	83955170	1.000000	0.71417	0.811000	0.32455	0.624000	0.37722	7.487000	0.81328	2.758000	0.94735	0.650000	0.86243	GCC	.	.	none		0.413	PGM3-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000366385.2	NM_015599		T	83898451	C	T	83898451	3	4	15	1	0	0	0	0	1	0	0	0	11809	710	25	2	1401	2	PGM3	6	83898451	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	3153649	83898451	87216616	65	1986											
RFX6	222546	hgsc.bcm.edu	37	chr6	117248414	117248414	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atagcaccagctctaactacCagactgtgtttagggcacag	12	9	9	11	0	1	1	0	0	1	1	1	1	1	1	2	1	4	4	2	1	4	5			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:117248414C>T	ENST00000332958.2	+	17	2126	c.2110C>T	c.(2110-2112)Cag>Tag	p.Q704*		NM_173560.3	NP_775831.2	Q8HWS3	RFX6_HUMAN	regulatory factor X, 6	704					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						CTCTAACTACCAGACTGTGTT	0.507																																					p.Q704X		Atlas-SNP	.											.	RFX6	141	.	0			c.C2110T						PASS	.						137	129	131					6																	117248414		2203	4300	6503	SO:0001587	stop_gained	222546	exon17			AACTACCAGACTG	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.2110C>T	6.37:g.117248414C>T	ENSP00000332208:p.Gln704*	130	0	0		114	55	0.482456	NM_173560	Q5T6B3	Nonsense_Mutation	SNP	ENST00000332958.2	37	CCDS5113.1	.	.	.	.	.	.	.	.	.	.	C	37	6.417248	0.97550	.	.	ENSG00000185002	ENST00000332958	.	.	.	5.15	5.15	0.70609	.	0.122893	0.56097	D	0.000027	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	-14.9498	13.1466	0.59465	0.0:0.9235:0.0:0.0765	.	.	.	.	X	704	.	ENSP00000332208:Q704X	Q	+	1	0	RFX6	117355107	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.039000	0.64185	2.682000	0.91365	0.655000	0.94253	CAG	.	.	none		0.507	RFX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041970.2	NM_173560		T	117248414	C	T	117248414	4	4	15	1	0	0	0	0	0	1	0	0	13282	595	21	2	2176	2	RFX6	6	117248414	Nonsense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	33349963	117248414	53866653	66	1987											
LAMA2	3908	hgsc.bcm.edu	37	chr6	129636794	129636794	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttccagaacaatttgaaggAaagaaggtaagcacaagaac	19	6	9	7	0	0	4	0	1	0	3	1	5	1	5	1	2	3	2	1	2	8	3			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:129636794A>G	ENST00000421865.2	+	25	3778	c.3729A>G	c.(3727-3729)ggA>ggG	p.G1243G		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1243	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)		AATTTGAAGGAAAGAAGGTAA	0.348																																					p.G1243G		Atlas-SNP	.											.	LAMA2	481	.	0			c.A3729G						PASS	.						97	94	95					6																	129636794		2203	4300	6503	SO:0001819	synonymous_variant	3908	exon25			TGAAGGAAAGAAG	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.3729A>G	6.37:g.129636794A>G		78	0	0		95	4	0.0421053	NM_000426	Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	37	CCDS5138.1																																																																																			.	.	none		0.348	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			G	129636794	A	G	129636794	2	3	15	1	0	0	0	0	0	0	0	1	8615	233	9	3		3	LAMA2	6	129636794	Silent	SNP	A	TCGA-FF-8061-01A-11D-2210-10	12388380	129636794	41478273	67	1988											
SGK1	6446	hgsc.bcm.edu	37	chr6	134494230	134494230	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggaaagagaagtgaaggccCaccaggaaagggtgcttcac	14	5	14	8	0	1	2	1	1	0	1	1	5	1	4	2	4	1	1	2	4	4	1			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:134494230C>A	ENST00000237305.7	-	6	568	c.480G>T	c.(478-480)gtG>gtT	p.V160V	SGK1_ENST00000413996.3_Silent_p.V174V|SGK1_ENST00000367857.5_Silent_p.V150V|SGK1_ENST00000528577.1_Silent_p.V188V|SGK1_ENST00000367858.5_Silent_p.V255V|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000475719.2_Intron	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	160	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)		AGTGAAGGCCCACCAGGAAAG	0.443																																					p.V255V		Atlas-SNP	.											.	SGK1	387	.	0			c.G765T						PASS	.						96	96	96					6																	134494230		2203	4300	6503	SO:0001819	synonymous_variant	6446	exon8			AAGGCCCACCAGG	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.480G>T	6.37:g.134494230C>A		188	0	0		212	28	0.132075	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Silent	SNP	ENST00000237305.7	37	CCDS5170.1																																																																																			.	.	none		0.443	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			A	134494230	C	A	134494230	2	1	15	1	0	0	0	0	0	0	0	1	14222	581	21	4		4	SGK1	6	134494230	Silent	SNP	C	TCGA-FF-8061-01A-11D-2210-10	4857436	134494230	36620837	68	1989											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152679666	152679666	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagtttttcagacttggttaCggcttcctataattagcatt	10	17	7	7	1	1	1	1	0	0	1	2	1	2	1	1	2	2	4	1	2	5	9	rs550088683		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr6:152679666C>T	ENST00000367255.5	-	66	11051	c.10450G>A	c.(10450-10452)Gta>Ata	p.V3484I	SYNE1_ENST00000423061.1_Missense_Mutation_p.V3491I|SYNE1_ENST00000265368.4_Missense_Mutation_p.V3484I|SYNE1_ENST00000341594.5_Missense_Mutation_p.V3455I|SYNE1_ENST00000448038.1_Missense_Mutation_p.V3491I	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	3484					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)		GACTTGGTTACGGCTTCCTAT	0.363										HNSCC(10;0.0054)			C|||	1	0.000199681	0.0	0.0	5008	,	,		16527	0.0		0.0	False		,,,				2504	0.001				p.V3491I		Atlas-SNP	.											SYNE1_ENST00000423061,NS,carcinoma,0,3	SYNE1	3227	3	0			c.G10471A						scavenged	.						95	88	90					6																	152679666		2203	4300	6503	SO:0001583	missense	23345	exon66			TGGTTACGGCTTC	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.10450G>A	6.37:g.152679666C>T	ENSP00000356224:p.Val3484Ile	135	1	0.00740741		127	39	0.307087	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	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	11.39	1.624999	0.28889	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.53423	0.72;1.37;0.62;1.37;0.64	5.35	3.57	0.40892	.	0.254853	0.27544	N	0.018893	T	0.20536	0.0494	L	0.52364	1.645	0.80722	D	1	B;B;B;B	0.26577	0.04;0.04;0.04;0.153	B;B;B;B	0.22152	0.017;0.017;0.017;0.038	T	0.04216	-1.0968	10	0.28530	T	0.3	.	7.9553	0.30038	0.0:0.6903:0.0:0.3097	.	3484;3484;3484;3491	B7ZBC3;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	I	3484;3491;3484;3491;3455	ENSP00000356224:V3484I;ENSP00000396024:V3491I;ENSP00000265368:V3484I;ENSP00000390975:V3491I;ENSP00000341887:V3455I	ENSP00000265368:V3484I	V	-	1	0	SYNE1	152721359	1.000000	0.71417	0.457000	0.27056	0.881000	0.50899	2.800000	0.47900	0.647000	0.30713	0.561000	0.74099	GTA	.	.	none		0.363	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152679666	C	T	152679666	3	4	15	1	0	0	0	0	1	0	0	0	15460	536	19	1	16340	1	SYNE1	6	152679666	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	18185436	152679666	18435401	69	1990											
CARD11	84433	hgsc.bcm.edu	37	chr7	2977605	2977605	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttcatgcggtgcttgtacAtttcacagtcctttcccagg	6	15	9	11	1	2	0	2	0	0	0	4	0	4	0	2	2	3	3	2	2	1	5			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr7:2977605A>G	ENST00000396946.4	-	8	1482	c.1079T>C	c.(1078-1080)aTg>aCg	p.M360T		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	360					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.M353T(1)|p.M353K(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)		GTGCTTGTACATTTCACAGTC	0.592			Mis		DLBCL																																p.M360T		Atlas-SNP	.		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	CARD11,colon,carcinoma,-1,4	CARD11	339	4	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.T1079C						PASS	.						143	116	125					7																	2977605		2203	4300	6503	SO:0001583	missense	84433	exon8			TTGTACATTTCAC	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.1079T>C	7.37:g.2977605A>G	ENSP00000380150:p.Met360Thr	52	0	0		69	33	0.478261	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	A	18.62	3.663818	0.67700	.	.	ENSG00000198286	ENST00000396946	T	0.32988	1.43	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.32406	0.0828	L	0.54323	1.7	0.58432	D	0.999999	B	0.24823	0.112	B	0.27715	0.082	T	0.12578	-1.0542	10	0.54805	T	0.06	-50.9525	13.8813	0.63684	1.0:0.0:0.0:0.0	.	360	Q9BXL7	CAR11_HUMAN	T	360	ENSP00000380150:M360T	ENSP00000380150:M360T	M	-	2	0	CARD11	2944131	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	9.048000	0.93830	1.878000	0.54408	0.482000	0.46254	ATG	.	.	none		0.592	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		G	2977605	A	G	2977605	3	3	15	1	0	0	0	0	1	0	0	0	2647	217	8	3	2457	3	CARD11	7	2977605	Missense_Mutation	SNP	A	TCGA-FF-8061-01A-11D-2210-10		2977605	156161058	70	1991											
PCLO	27445	hgsc.bcm.edu	37	chr7	82545106	82545106	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atccttttcatgaaggctaaAtgcggtgcttaatgccgctg	9	13	10	9	2	1	1	1	1	0	0	2	1	2	1	2	2	3	3	2	2	4	4			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr7:82545106A>G	ENST00000333891.9	-	7	12533	c.12196T>C	c.(12196-12198)Ttt>Ctt	p.F4066L	PCLO_ENST00000423517.2_Missense_Mutation_p.F4066L|PCLO_ENST00000437081.1_Missense_Mutation_p.F786L	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						TGAAGGCTAAATGCGGTGCTT	0.438																																					p.F4066L		Atlas-SNP	.											.	PCLO	1506	.	0			c.T12196C						PASS	.						94	83	86					7																	82545106		1946	4159	6105	SO:0001583	missense	27445	exon7			GGCTAAATGCGGT	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.12196T>C	7.37:g.82545106A>G	ENSP00000334319:p.Phe4066Leu	99	0	0		78	31	0.397436	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	A	16.24	3.067747	0.55539	.	.	ENSG00000186472	ENST00000333891;ENST00000423517;ENST00000437081	T;T	0.16457	2.34;2.34	5.84	5.84	0.93424	.	.	.	.	.	T	0.31040	0.0784	L	0.59436	1.845	0.51482	D	0.999927	P;D;D	0.61697	0.78;0.99;0.99	B;P;P	0.52514	0.192;0.701;0.701	T	0.02378	-1.1168	9	0.87932	D	0	.	16.2109	0.82158	1.0:0.0:0.0:0.0	.	3997;4066;4066	Q9Y6V0;Q9Y6V0-5;Q9Y6V0-6	PCLO_HUMAN;.;.	L	4066;4066;786	ENSP00000334319:F4066L;ENSP00000388393:F4066L	ENSP00000334319:F4066L	F	-	1	0	PCLO	82383042	1.000000	0.71417	0.984000	0.44739	0.968000	0.65278	9.339000	0.96797	2.230000	0.72887	0.455000	0.32223	TTT	.	.	none		0.438	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		G	82545106	A	G	82545106	3	3	15	1	0	0	0	0	1	0	0	0	11592	101	4	3	3325	3	PCLO	7	82545106	Missense_Mutation	SNP	A	TCGA-FF-8061-01A-11D-2210-10	79567501	82545106	76593557	71	1992											
AKAP9	10142	hgsc.bcm.edu	37	chr7	91625060	91625060	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gattatcagaaaaagaaagaAgacttcacaatgcaaattag	21	8	7	5	0	2	4	2	0	0	4	2	5	2	4	0	0	1	1	0	0	8	3			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr7:91625060A>C	ENST00000359028.2	+	8	1137	c.912A>C	c.(910-912)gaA>gaC	p.E304D	AKAP9_ENST00000394564.1_Missense_Mutation_p.E292D|AKAP9_ENST00000358100.2_Missense_Mutation_p.E304D|AKAP9_ENST00000356239.3_Missense_Mutation_p.E292D			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	304					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)			AAAAGAAAGAAGACTTCACAA	0.343			T	BRAF	papillary thyroid																																p.E292D		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	AKAP9_ENST00000356239,NS,carcinoma,+2,2	AKAP9	788	2	0			c.A876C						PASS	.						67	63	64					7																	91625060		2203	4300	6503	SO:0001583	missense	10142	exon7			GAAAGAAGACTTC	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.912A>C	7.37:g.91625060A>C	ENSP00000351922:p.Glu304Asp	68	0	0		38	15	0.394737	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		.	.	.	.	.	.	.	.	.	.	A	13.26	2.183510	0.38609	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394565;ENST00000394564	T;T;T;T	0.34472	1.36;1.36;1.36;1.36	5.1	2.75	0.32379	.	0.000000	0.42682	D	0.000674	T	0.50000	0.1590	L	0.59436	1.845	0.36863	D	0.888493	B;B;D;B	0.69078	0.42;0.42;0.997;0.011	B;B;D;B	0.69654	0.087;0.087;0.965;0.009	T	0.54268	-0.8319	10	0.56958	D	0.05	.	8.6538	0.34051	0.8413:0.0:0.1587:0.0	.	292;292;304;292	Q99996-2;Q99996-3;A4D1E4;Q6PJH3	.;.;.;.	D	292;304;304;304;304;292	ENSP00000348573:E292D;ENSP00000351922:E304D;ENSP00000350813:E304D;ENSP00000378065:E292D	ENSP00000348573:E292D	E	+	3	2	AKAP9	91462996	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.124000	0.42006	0.384000	0.24942	0.533000	0.62120	GAA	.	.	none		0.343	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		C	91625060	A	C	91625060	3	2	15	1	0	0	0	0	1	0	0	0	459	69	3	5	902	5	AKAP9	7	91625060	Missense_Mutation	SNP	A	TCGA-FF-8061-01A-11D-2210-10	9079954	91625060	67513603	72	1993											
RNF133	168433	hgsc.bcm.edu	37	chr7	122338692	122338692	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aggtctctgagtactttgatCggctgaaaatggtattggga	10	13	13	5	1	1	3	0	3	1	0	3	4	1	4	0	4	1	3	0	4	4	4			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr7:122338692C>T	ENST00000340112.2	-	1	518	c.281G>A	c.(280-282)cGa>cAa	p.R94Q	CADPS2_ENST00000334010.7_Intron|CADPS2_ENST00000412584.2_Intron|CADPS2_ENST00000449022.2_Intron|CADPS2_ENST00000313070.7_Intron	NM_139175.1	NP_631914.1	Q8WVZ7	RN133_HUMAN	ring finger protein 133	94	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						GTACTTTGATCGGCTGAAAAT	0.458																																					p.R94Q	Colon(198;1778 2057 7449 19869 45985)	Atlas-SNP	.											.	RNF133	41	.	0			c.G281A						PASS	.						157	168	164					7																	122338692		2203	4299	6502	SO:0001583	missense	168433	exon1			TTTGATCGGCTGA	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.281G>A	7.37:g.122338692C>T	ENSP00000344489:p.Arg94Gln	112	0	0		73	26	0.356164	NM_139175	A4D0W2|Q8N7G7	Missense_Mutation	SNP	ENST00000340112.2	37	CCDS5784.1	.	.	.	.	.	.	.	.	.	.	C	11.50	1.656505	0.29425	.	.	ENSG00000188050	ENST00000340112	T	0.14516	2.5	5.79	-5.14	0.02875	.	1.811660	0.03352	N	0.196336	T	0.13200	0.0320	M	0.66939	2.045	0.09310	N	1	P	0.50943	0.94	B	0.43867	0.434	T	0.39820	-0.9595	10	0.14252	T	0.57	.	2.5082	0.04650	0.1832:0.2353:0.0878:0.4937	.	94	Q8WVZ7	RN133_HUMAN	Q	94	ENSP00000344489:R94Q	ENSP00000344489:R94Q	R	-	2	0	RNF133	122125928	0.000000	0.05858	0.000000	0.03702	0.956000	0.61745	-0.849000	0.04322	-1.082000	0.03101	0.655000	0.94253	CGA	.	.	none		0.458	RNF133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347413.1	NM_139175		T	122338692	C	T	122338692	3	4	15	1	0	0	0	0	1	0	0	0	13454	884	31	1	853	1	RNF133	7	122338692	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	30713632	122338692	36799971	73	1994											
LYN	4067	hgsc.bcm.edu	37	chr8	56910951	56910951	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcggaagaactacattcaccGggacctgcgagcagctaatg	12	6	12	11	3	1	1	1	0	0	1	1	4	1	3	2	2	5	2	2	2	4	3			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr8:56910951G>A	ENST00000519728.1	+	11	1393	c.1097G>A	c.(1096-1098)cGg>cAg	p.R366Q	LYN_ENST00000420292.1_3'UTR|LYN_ENST00000520220.2_Missense_Mutation_p.R345Q	NM_002350.3	NP_002341.1	P07948	LYN_HUMAN	LYN proto-oncogene, Src family tyrosine kinase	366	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to extracellular stimulus (GO:0031668)|cellular response to heat (GO:0034605)|cellular response to retinoic acid (GO:0071300)|cytokine secretion (GO:0050663)|dendritic cell differentiation (GO:0097028)|erythrocyte differentiation (GO:0030218)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|Fc receptor mediated stimulatory signaling pathway (GO:0002431)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|histamine secretion by mast cell (GO:0002553)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|leukocyte migration (GO:0050900)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of immune response (GO:0050777)|negative regulation of intracellular signal transduction (GO:1902532)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mast cell proliferation (GO:0070667)|negative regulation of myeloid leukocyte differentiation (GO:0002762)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|neuron projection development (GO:0031175)|oligodendrocyte development (GO:0014003)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of B cell receptor signaling pathway (GO:0050861)|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 dendritic cell apoptotic process (GO:2000670)|positive regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060369)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oligodendrocyte progenitor proliferation (GO:0070447)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of stress-activated protein kinase signaling cascade (GO:0070304)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of B cell apoptotic process (GO:0002902)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cytokine production (GO:0001817)|regulation of cytokine secretion (GO:0050707)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of erythrocyte differentiation (GO:0045646)|regulation of inflammatory response (GO:0050727)|regulation of mast cell activation (GO:0033003)|regulation of mast cell degranulation (GO:0043304)|regulation of monocyte chemotaxis (GO:0090025)|regulation of platelet aggregation (GO:0090330)|regulation of protein phosphorylation (GO:0001932)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to amino acid (GO:0043200)|response to axon injury (GO:0048678)|response to carbohydrate (GO:0009743)|response to drug (GO:0042493)|response to hormone (GO:0009725)|response to insulin (GO:0032868)|response to organic cyclic compound (GO:0014070)|response to sterol depletion (GO:0006991)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|T cell costimulation (GO:0031295)|tolerance induction to self antigen (GO:0002513)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integrin alpha2-beta1 complex (GO:0034666)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|mitochondrial crista (GO:0030061)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycosphingolipid binding (GO:0043208)|ion channel binding (GO:0044325)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22		all_lung(136;0.0555)|Lung NSC(129;0.0726)|all_epithelial(80;0.0772)	Epithelial(17;0.000834)|all cancers(17;0.00598)		Bosutinib(DB06616)|Ponatinib(DB08901)	TACATTCACCGGGACCTGCGA	0.448																																					p.R366Q		Atlas-SNP	.											.	LYN	54	.	0			c.G1097A						PASS	.						115	110	112					8																	56910951		2203	4300	6503	SO:0001583	missense	4067	exon11			TTCACCGGGACCT	M16038	CCDS6162.1, CCDS47859.1	8q13	2014-06-25	2014-06-25		ENSG00000254087	ENSG00000254087		"SH2 domain containing"	6735	protein-coding gene	gene with protein product		165120	"v-yes-1 Yamaguchi sarcoma viral related oncogene homolog"			3561390	Standard	NM_002350		Approved	JTK8	uc003xsk.4	P07948	OTTHUMG00000044345	ENST00000519728.1:c.1097G>A	8.37:g.56910951G>A	ENSP00000428924:p.Arg366Gln	194	0	0		187	65	0.347594	NM_002350	A0AVQ5	Missense_Mutation	SNP	ENST00000519728.1	37	CCDS6162.1	.	.	.	.	.	.	.	.	.	.	G	36	5.851905	0.97023	.	.	ENSG00000254087	ENST00000519728;ENST00000520220	D;D	0.88354	-2.37;-2.37	5.52	5.52	0.82312	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	0.97099	0.9052	H	0.98507	4.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.99	D	0.98468	1.0599	10	0.87932	D	0	.	19.4505	0.94865	0.0:0.0:1.0:0.0	.	436;366	Q6NUK7;P07948	.;LYN_HUMAN	Q	366;345	ENSP00000428924:R366Q;ENSP00000428424:R345Q	ENSP00000428924:R366Q	R	+	2	0	LYN	57073505	1.000000	0.71417	0.688000	0.30117	0.945000	0.59286	9.869000	0.99810	2.597000	0.87782	0.655000	0.94253	CGG	.	.	none		0.448	LYN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378155.1	NM_002350		A	56910951	G	A	56910951	3	1	15	1	0	0	0	0	1	0	0	0	9116	1116	39	1	1135	1	LYN	8	56910951	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10		56910951	89453071	74	1995											
CLVS1	157807	hgsc.bcm.edu	37	chr8	62289218	62289218	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgtcattggaagtcctaatCgaagatccggagcttcagat	11	11	10	9	2	2	2	2	0	0	2	5	5	4	4	2	2	1	1	2	2	3	3			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr8:62289218C>T	ENST00000519846.1	+	4	982	c.510C>T	c.(508-510)atC>atT	p.I170I	CLVS1_ENST00000518592.1_5'UTR|CLVS1_ENST00000325897.4_Silent_p.I170I			Q8IUQ0	CLVS1_HUMAN	clavesin 1	170	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)			endometrium(3)|kidney(4)|large_intestine(4)|lung(21)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	41						AAGTCCTAATCGAAGATCCGG	0.438																																					p.I170I		Atlas-SNP	.											CLVS1,NS,carcinoma,+2,1	CLVS1	74	1	0			c.C510T						PASS	.						112	106	108					8																	62289218		2203	4300	6503	SO:0001819	synonymous_variant	157807	exon3			CCTAATCGAAGAT	AY094971	CCDS6176.1	8q12.1	2009-10-14	2009-10-14	2009-10-14		ENSG00000177182			23139	protein-coding gene	gene with protein product		611292	"retinaldehyde binding protein 1-like 1"	RLBP1L1		16802092, 19651769	Standard	NM_173519		Approved	MGC34646, CRALBPL, C6orf212L	uc003xuh.3	Q8IUQ0		ENST00000519846.1:c.510C>T	8.37:g.62289218C>T		85	0	0		89	32	0.359551	NM_173519	B2R7M5|C8UZT3|Q8NB32	Silent	SNP	ENST00000519846.1	37	CCDS6176.1																																																																																			.	.	none		0.438	CLVS1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378323.1	NM_173519		T	62289218	C	T	62289218	2	4	15	1	0	0	0	0	0	0	0	1	3573	874	31	1		1	CLVS1	8	62289218	Silent	SNP	C	TCGA-FF-8061-01A-11D-2210-10	5378267	62289218	84074804	75	1996											
NBN	4683	hgsc.bcm.edu	37	chr8	90967770	90967770	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gactttgatttcttttggccTttcactcaaatccctgtaga	8	17	6	10	0	3	2	2	1	1	1	4	3	4	2	2	1	0	1	2	1	2	6			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr8:90967770T>C	ENST00000265433.3	-	10	1292	c.1138A>G	c.(1138-1140)Agg>Ggg	p.R380G	NBN_ENST00000409330.1_Missense_Mutation_p.R298G	NM_002485.4	NP_002476.2	O60934	NBN_HUMAN	nibrin	380	Interaction with MTOR, MAPKAP1 and RICTOR.				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)			TCTTTTGGCCTTTCACTCAAA	0.338								Homologous recombination																													p.R380G		Atlas-SNP	.											.	NBN	86	.	0			c.A1138G						PASS	.						74	69	71					8																	90967770		2202	4298	6500	SO:0001583	missense	4683	exon10			TTGGCCTTTCACT	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.1138A>G	8.37:g.90967770T>C	ENSP00000265433:p.Arg380Gly	71	0	0		78	4	0.0512821	NM_002485	B2R626|B2RNC5|O60672|Q32NF7|Q53FM6|Q63HR6|Q7LDM2	Missense_Mutation	SNP	ENST00000265433.3	37	CCDS6249.1	.	.	.	.	.	.	.	.	.	.	T	8.917	0.960201	0.18507	.	.	ENSG00000104320	ENST00000265433;ENST00000409330;ENST00000452387	T;T	0.59083	1.95;0.29	5.45	5.45	0.79879	.	1.198520	0.05445	N	0.548399	T	0.54902	0.1887	L	0.51422	1.61	0.32695	N	0.513694	B;B	0.27450	0.179;0.179	B;B	0.24269	0.036;0.052	T	0.48080	-0.9066	10	0.24483	T	0.36	-0.1736	11.9007	0.52682	0.0:0.0:0.0:1.0	.	380;380	A6H8Y5;O60934	.;NBN_HUMAN	G	380;298;380	ENSP00000265433:R380G;ENSP00000386924:R298G	ENSP00000265433:R380G	R	-	1	2	NBN	91036946	0.946000	0.32159	0.941000	0.38009	0.575000	0.36095	1.542000	0.36137	2.063000	0.61619	0.528000	0.53228	AGG	.	.	none		0.338	NBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331583.3	NM_001024688		C	90967770	T	C	90967770	3	2	15	1	0	0	0	0	1	0	0	0	10200	1608	56	3	1154	3	NBN	8	90967770	Missense_Mutation	SNP	T	TCGA-FF-8061-01A-11D-2210-10	28678552	90967770	55396252	76	1997											
RIMS2	9699	hgsc.bcm.edu	37	chr8	104513174	104513174	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcccggcggcctctcagccGcctctgcagcccgagatgcc	5	6	11	19	4	2	1	1	0	2	1	4	2	3	1	6	2	4	1	6	2	0	0			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr8:104513174G>A	ENST00000406091.3	+	1	60	c.60G>A	c.(58-60)ccG>ccA	p.P20P	RP11-1C8.4_ENST00000523422.1_RNA|RP11-1C8.4_ENST00000517376.1_RNA	NM_001100117.2	NP_001093587.1	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	20					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)			CCTCTCAGCCGCCTCTGCAGC	0.647										HNSCC(12;0.0054)																											p.P20P		Atlas-SNP	.											.	RIMS2	1357	.	0			c.G60A						PASS	.						22	25	24					8																	104513174		1877	4089	5966	SO:0001819	synonymous_variant	9699	exon1			TCAGCCGCCTCTG	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.60G>A	8.37:g.104513174G>A		71	0	0		93	6	0.0645161	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Silent	SNP	ENST00000406091.3	37	CCDS55269.1																																																																																			.	.	none		0.647	RIMS2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001100117		A	104513174	G	A	104513174	2	1	15	1	0	0	0	0	0	0	0	1	13383	1074	38	1		1	RIMS2	8	104513174	Silent	SNP	G	TCGA-FF-8061-01A-11D-2210-10	13545404	104513174	41850848	77	1998											
BAI1	575	hgsc.bcm.edu	37	chr8	143625724	143625724	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggagtgggagaggtcgggCgccacgatcccgctggtggg	5	6	21	9	4	0	1	0	0	0	1	2	4	1	2	2	6	0	1	2	6	0	0			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr8:143625724C>T	ENST00000517894.1	+	31	5595	c.4701C>T	c.(4699-4701)ggC>ggT	p.G1567G	BAI1_ENST00000323289.5_Silent_p.G1567G			O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	1567	Necessary for interaction with MAGI1.				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)					AGAGGTCGGGCGCCACGATCC	0.706																																					p.G1567G		Atlas-SNP	.											.	BAI1	146	.	0			c.C4701T						PASS	.						13	23	19					8																	143625724		1749	3389	5138	SO:0001819	synonymous_variant	575	exon30			GTCGGGCGCCACG	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.4701C>T	8.37:g.143625724C>T		12	0	0		43	20	0.465116	NM_001702		Silent	SNP	ENST00000517894.1	37																																																																																				.	.	none		0.706	BAI1-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379963.3	NM_001702		T	143625724	C	T	143625724	2	4	15	1	0	0	0	0	0	0	0	1	1298	755	27	1		1	BAI1	8	143625724	Silent	SNP	C	TCGA-FF-8061-01A-11D-2210-10	39112550	143625724	2738298	78	1999											
KANK1	23189	hgsc.bcm.edu	37	chr9	731215	731215	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaagaagaaagatggtaacaAagattcaaatggcgcaaaaa	22	5	10	4	1	1	4	1	0	0	4	1	5	1	4	0	2	1	2	0	2	8	2			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr9:731215A>G	ENST00000382303.1	+	9	3606	c.2954A>G	c.(2953-2955)aAa>aGa	p.K985R	KANK1_ENST00000382297.2_Missense_Mutation_p.K985R|KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382293.3_Missense_Mutation_p.K827R	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	985	Nuclear localization signal 2 (NLS 2).				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)		GATGGTAACAAAGATTCAAAT	0.378																																					p.K985R		Atlas-SNP	.											.	KANK1	231	.	0			c.A2954G						PASS	.						142	127	132					9																	731215		2203	4300	6503	SO:0001583	missense	23189	exon9			GTAACAAAGATTC	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.2954A>G	9.37:g.731215A>G	ENSP00000371740:p.Lys985Arg	126	0	0		153	69	0.45098	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	37	CCDS34976.1	.	.	.	.	.	.	.	.	.	.	A	11.99	1.804544	0.31869	.	.	ENSG00000107104	ENST00000382303;ENST00000397976;ENST00000382297;ENST00000382293	T;T;T	0.17528	2.27;2.27;2.27	5.76	-2.74	0.05932	.	0.345964	0.24791	N	0.035577	T	0.12433	0.0302	L	0.57536	1.79	0.09310	N	0.999999	B	0.10296	0.003	B	0.09377	0.004	T	0.29731	-1.0002	10	0.21540	T	0.41	.	6.4346	0.21817	0.5965:0.0:0.2984:0.1051	.	985	Q14678	KANK1_HUMAN	R	985;8;985;827	ENSP00000371740:K985R;ENSP00000371734:K985R;ENSP00000371730:K827R	ENSP00000371730:K827R	K	+	2	0	KANK1	721215	0.072000	0.21174	0.004000	0.12327	0.888000	0.51559	1.007000	0.29860	-0.570000	0.06022	0.528000	0.53228	AAA	.	.	none		0.378	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158		G	731215	A	G	731215	3	3	15	1	0	0	0	0	1	0	0	0	7985	14	1	3	2968	3	KANK1	9	731215	Missense_Mutation	SNP	A	TCGA-FF-8061-01A-11D-2210-10		731215	140482216	79	2000											
UHRF2	115426	hgsc.bcm.edu	37	chr9	6413558	6413558	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgaggacgtgtctcgcaaagCcacgattgaggagctgcgcg	9	7	15	10	5	1	2	0	2	1	0	2	5	1	4	1	2	3	2	1	2	1	1			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr9:6413558C>G	ENST00000276893.5	+	1	236	c.68C>G	c.(67-69)gCc>gGc	p.A23G	UHRF2_ENST00000381373.3_Missense_Mutation_p.A23G|RP11-307L3.4_ENST00000411561.1_RNA	NM_152896.2	NP_690856.1	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase	23	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				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)		TCTCGCAAAGCCACGATTGAG	0.632																																					p.A23G		Atlas-SNP	.											.	UHRF2	50	.	0			c.C68G						PASS	.						52	52	52					9																	6413558		2203	4300	6503	SO:0001583	missense	115426	exon1			GCAAAGCCACGAT	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.68C>G	9.37:g.6413558C>G	ENSP00000276893:p.Ala23Gly	82	0	0		108	28	0.259259	NM_152896	Q5VYR1|Q5VYR3|Q659C8|Q8TAG7	Missense_Mutation	SNP	ENST00000276893.5	37	CCDS6469.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.045016	0.75846	.	.	ENSG00000147854	ENST00000276893;ENST00000381373	T;T	0.73575	-0.76;-0.76	4.83	3.0	0.34707	Ubiquitin supergroup (1);Ubiquitin (2);	0.198751	0.42964	D	0.000626	T	0.67683	0.2919	L	0.31476	0.935	0.36395	D	0.86274	B	0.32893	0.389	B	0.41894	0.369	T	0.72520	-0.4268	10	0.87932	D	0	-7.1406	10.6553	0.45671	0.0:0.8436:0.0:0.1564	.	23	Q96PU4	UHRF2_HUMAN	G	23	ENSP00000276893:A23G;ENSP00000370778:A23G	ENSP00000276893:A23G	A	+	2	0	UHRF2	6403558	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	6.968000	0.76086	0.645000	0.30675	-0.258000	0.10820	GCC	.	.	none		0.632	UHRF2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051665.3	NM_152306		G	6413558	C	G	6413558	3	3	15	1	0	0	0	0	1	0	0	0	16985	739	26	4	70	4	UHRF2	9	6413558	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	5682343	6413558	134799873	80	2001											
HRCT1	646962	hgsc.bcm.edu	37	chr9	35906583	35906583	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgccacacccctcaccaccTccaccaccaccaccaccccc	9	2	1	29	1	1	0	1	0	0	0	2	0	2	0	13	0	0	0	13	0	0	0	rs112821450|rs143611048|rs79156963	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr9:35906583T>A	ENST00000354323.2	+	1	395	c.299T>A	c.(298-300)cTc>cAc	p.L100H	LINC00961_ENST00000443779.1_lincRNA	NM_001039792.1	NP_001034881.1	Q6UXD1	HRCT1_HUMAN	histidine rich carboxyl terminus 1	100	His-rich.					integral component of membrane (GO:0016021)		p.L100H(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(1)	4						cctcaccacctccaccaccac	0.667																																					p.L100H		Atlas-SNP	.											HRCT1,NS,malignant_melanoma,0,1	HRCT1	14	1	1	Substitution - Missense(1)	NS(1)	c.T299A						scavenged	.						13	10	11					9																	35906583		1961	3863	5824	SO:0001583	missense	646962	exon1			ACCACCTCCACCA		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.299T>A	9.37:g.35906583T>A	ENSP00000346283:p.Leu100His	25	1	0.04		31	3	0.0967742	NM_001039792	B7ZBJ1	Missense_Mutation	SNP	ENST00000354323.2	37	CCDS35012.1	.	.	.	.	.	.	.	.	.	.	T	9.866	1.197686	0.22037	.	.	ENSG00000196196	ENST00000354323	.	.	.	3.43	-0.386	0.12466	.	.	.	.	.	T	0.09730	0.0239	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.25117	-1.0141	8	0.87932	D	0	-5.7925	0.5802	0.00711	0.4571:0.1878:0.1238:0.2312	.	100	Q6UXD1	HRCT1_HUMAN	H	100	.	ENSP00000346283:L100H	L	+	2	0	HRCT1	35896583	0.000000	0.05858	0.107000	0.21349	0.466000	0.32739	-0.309000	0.08145	-0.078000	0.12730	-0.376000	0.06991	CTC	T|0.500;A|0.500	0.500	weak		0.667	HRCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334099.1	NM_001039792		A	35906583	T	A	35906583	3	1	15	1	0	0	0	0	1	0	0	0	7362	1551	54	5	301	5	HRCT1	9	35906583	Missense_Mutation	SNP	T	TCGA-FF-8061-01A-11D-2210-10	29493025	35906583	105306848	81	2002											
C5	727	hgsc.bcm.edu	37	chr9	123719614	123719614	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtacttgacaaaaacattttCtacagtgatggatgtgatgc	13	13	9	6	0	1	3	0	3	1	0	1	4	1	4	0	1	4	1	0	1	4	5			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr9:123719614C>T	ENST00000223642.1	-	39	4740	c.4711G>A	c.(4711-4713)Gaa>Aaa	p.E1571K		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	1571	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)	AAAACATTTTCTACAGTGATG	0.348																																					p.E1571K		Atlas-SNP	.											.	C5	124	.	0			c.G4711A						PASS	.						197	191	193					9																	123719614		2203	4300	6503	SO:0001583	missense	727	exon39			CATTTTCTACAGT	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.4711G>A	9.37:g.123719614C>T	ENSP00000223642:p.Glu1571Lys	92	0	0		83	5	0.060241	NM_001735	Q14CJ0|Q27I61	Missense_Mutation	SNP	ENST00000223642.1	37	CCDS6826.1	.	.	.	.	.	.	.	.	.	.	C	17.31	3.357662	0.61293	.	.	ENSG00000106804	ENST00000223642	T	0.22336	1.96	5.86	4.96	0.65561	Tissue inhibitor of metalloproteinases-like, OB-fold (1);Netrin domain (1);Netrin module, non-TIMP type (2);	0.150336	0.64402	D	0.000016	T	0.29061	0.0722	L	0.43923	1.385	0.38310	D	0.943213	D	0.61080	0.989	P	0.57620	0.824	T	0.09596	-1.0667	10	0.21014	T	0.42	.	10.9448	0.47294	0.0:0.9142:0.0:0.0858	.	1571	P01031	CO5_HUMAN	K	1571	ENSP00000223642:E1571K	ENSP00000223642:E1571K	E	-	1	0	C5	122759435	1.000000	0.71417	0.920000	0.36463	0.417000	0.31264	4.611000	0.61162	1.486000	0.48398	0.655000	0.94253	GAA	.	.	none		0.348	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735		T	123719614	C	T	123719614	3	4	15	1	0	0	0	0	1	0	0	0	2282	922	32	2	331	2	C5	9	123719614	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	87813031	123719614	17493817	82	2003											
OR5C1	392391	hgsc.bcm.edu	37	chr9	125551542	125551542	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agatgtttgtctttgcaggtCtggctgatactgagtgttgc	6	16	13	6	0	2	3	0	2	2	1	2	3	2	3	0	2	3	4	0	2	1	4	rs201755571		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr9:125551542C>T	ENST00000373680.2	+	1	393	c.331C>T	c.(331-333)Ctg>Ttg	p.L111L		NM_001001923.1	NP_001001923.1	Q8NGR4	OR5C1_HUMAN	olfactory receptor, family 5, subfamily C, member 1	111						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(5)|lung(6)|pancreas(1)|prostate(5)|skin(1)	20						CTTTGCAGGTCTGGCTGATAC	0.567																																					p.L111L		Atlas-SNP	.											.	OR5C1	45	.	0			c.C331T						PASS	.						136	121	126					9																	125551542		2203	4300	6503	SO:0001819	synonymous_variant	392391	exon1			GCAGGTCTGGCTG	AF399514	CCDS35131.1	9q34.2	2012-08-09			ENSG00000148215	ENSG00000148215		"GPCR / Class A : Olfactory receptors"	8331	protein-coding gene	gene with protein product				OR5C2P			Standard	NM_001001923		Approved	OR9-F, hRPK-465_F_21	uc011lzd.2	Q8NGR4	OTTHUMG00000020622	ENST00000373680.2:c.331C>T	9.37:g.125551542C>T		91	0	0		81	4	0.0493827	NM_001001923	B2RN54|B9EGT0|Q96RC4	Silent	SNP	ENST00000373680.2	37	CCDS35131.1																																																																																			C|1.000;A|0.000	.	alt		0.567	OR5C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053953.1			T	125551542	C	T	125551542	2	4	15	1	0	0	0	0	0	0	0	1	11162	912	32	2		2	OR5C1	9	125551542	Silent	SNP	C	TCGA-FF-8061-01A-11D-2210-10	1831928	125551542	15661889	83	2004											
ADO	84890	hgsc.bcm.edu	37	chr10	64565347	64565347	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgcgttcgcgggccgagtaCaccgaggccagcggcccctg	5	5	15	16	6	0	0	0	0	0	0	1	2	0	0	5	3	3	2	5	3	1	2			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr10:64565347C>G	ENST00000373783.1	+	1	832	c.528C>G	c.(526-528)taC>taG	p.Y176*	RP11-436D10.3_ENST00000425290.1_RNA	NM_032804.5	NP_116193.2	Q96SZ5	AEDO_HUMAN	2-aminoethanethiol (cysteamine) dioxygenase	176						mitochondrion (GO:0005739)	cysteamine dioxygenase activity (GO:0047800)|metal ion binding (GO:0046872)			lung(2)	2	Prostate(12;0.0297)|all_hematologic(501;0.228)					GGGCCGAGTACACCGAGGCCA	0.741																																					p.Y176X		Atlas-SNP	.											.	ADO	10	.	0			c.C528G						PASS	.						16	15	15					10																	64565347		2184	4278	6462	SO:0001587	stop_gained	84890	exon1			CGAGTACACCGAG	BC028589	CCDS7266.2	10q21.3	2007-08-28	2007-08-28	2007-08-28	ENSG00000181915	ENSG00000181915	1.13.11.19		23506	protein-coding gene	gene with protein product	"cysteamine dioxygenase"	611392	"chromosome 10 open reading frame 22"	C10orf22		17581819	Standard	NM_032804		Approved	FLJ14547	uc001jmg.3	Q96SZ5	OTTHUMG00000018306	ENST00000373783.1:c.528C>G	10.37:g.64565347C>G	ENSP00000362888:p.Tyr176*	26	0	0		22	4	0.181818	NM_032804	B1AL29	Nonsense_Mutation	SNP	ENST00000373783.1	37	CCDS7266.2	.	.	.	.	.	.	.	.	.	.	C	40	7.980773	0.98594	.	.	ENSG00000181915	ENST00000373783	.	.	.	4.93	4.0	0.46444	.	0.396168	0.26293	N	0.025215	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.37	12.6806	0.56920	0.0:0.6815:0.3185:0.0	.	.	.	.	X	176	.	ENSP00000362888:Y176X	Y	+	3	2	ADO	64235353	1.000000	0.71417	0.929000	0.37066	0.937000	0.57800	2.542000	0.45744	1.002000	0.39104	0.655000	0.94253	TAC	.	.	none		0.741	ADO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048243.2	NM_032804		G	64565347	C	G	64565347	4	3	15	1	0	0	0	0	0	1	0	0	325	489	17	4	530	4	ADO	10	64565347	Nonsense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10		64565347	70969400	84	2005											
CCAR1	55749	hgsc.bcm.edu	37	chr10	70549639	70549639	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acaatcagaaacttatctacGgtaatggatgaaatccacac	17	9	6	9	1	2	2	1	1	1	1	3	3	3	3	1	2	2	1	1	2	6	3			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr10:70549639G>A	ENST00000265872.6	+	24	3479	c.3360G>A	c.(3358-3360)acG>acA	p.T1120T	CCAR1_ENST00000543719.1_Silent_p.T1105T|CCAR1_ENST00000535016.1_Silent_p.T1105T	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	1120					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						ACTTATCTACGGTAATGGATG	0.284																																					p.T1120T		Atlas-SNP	.											.	CCAR1	118	.	0			c.G3360A						PASS	.						45	48	47					10																	70549639		2201	4293	6494	SO:0001819	synonymous_variant	55749	exon24			ATCTACGGTAATG	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.3360G>A	10.37:g.70549639G>A		158	0	0		167	8	0.0479042	NM_018237	A0JLT7|A1L4P7|A8K9D4|B4DNP8|B4DRK8|Q32NE3|Q5EBM3|Q5VUP6|Q6PIZ0|Q6X935|Q9H8N4|Q9NVA7|Q9NVQ0|Q9NWM6	Silent	SNP	ENST00000265872.6	37	CCDS7282.1																																																																																			.	.	none		0.284	CCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048356.2	NM_018237		A	70549639	G	A	70549639	2	1	15	1	0	0	0	0	0	0	0	1	2732	1103	39	1		1	CCAR1	10	70549639	Silent	SNP	G	TCGA-FF-8061-01A-11D-2210-10	5984292	70549639	64985108	85	2006											
HTR7	3363	hgsc.bcm.edu	37	chr10	92509323	92509323	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccattctgcctcacagggtAtgtgaggggccttgtgatcc	6	11	12	12	0	2	2	1	2	1	0	3	2	3	2	4	3	1	1	4	3	1	3	rs560218001		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr10:92509323A>G	ENST00000336152.3	-	2	594	c.568T>C	c.(568-570)Tac>Cac	p.Y190H	HTR7_ENST00000371719.2_Missense_Mutation_p.Y190H|HTR7_ENST00000371721.3_Missense_Mutation_p.Y190H|HTR7_ENST00000277874.6_Missense_Mutation_p.Y190H	NM_019859.3	NP_062873.1	P34969	5HT7R_HUMAN	5-hydroxytryptamine (serotonin) receptor 7, adenylate cyclase-coupled	190					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)	CTCACAGGGTATGTGAGGGGC	0.517																																					p.Y190H		Atlas-SNP	.											.	HTR7	122	.	0			c.T568C						PASS	.						104	106	106					10																	92509323		2203	4300	6503	SO:0001583	missense	3363	exon2			CAGGGTATGTGAG	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.568T>C	10.37:g.92509323A>G	ENSP00000337949:p.Tyr190His	83	0	0		87	4	0.045977	NM_019860	B5BUP6|P78336|P78372|P78516|Q5VX01|Q5VX02|Q5VX03	Missense_Mutation	SNP	ENST00000336152.3	37	CCDS7408.1	.	.	.	.	.	.	.	.	.	.	A	18.25	3.581537	0.65992	.	.	ENSG00000148680	ENST00000336152;ENST00000277874;ENST00000371719;ENST00000371721	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	5.44	5.44	0.79542	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.61540	0.2355	M	0.87269	2.87	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.68119	-0.5493	10	0.62326	D	0.03	.	15.6519	0.77104	1.0:0.0:0.0:0.0	.	190;190	P34969;P34969-2	5HT7R_HUMAN;.	H	190	ENSP00000337949:Y190H;ENSP00000277874:Y190H;ENSP00000360784:Y190H;ENSP00000360786:Y190H	ENSP00000277874:Y190H	Y	-	1	0	HTR7	92499303	1.000000	0.71417	0.969000	0.41365	0.409000	0.31022	9.139000	0.94554	2.285000	0.76669	0.528000	0.53228	TAC	.	.	none		0.517	HTR7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049343.1	NM_000872		G	92509323	A	G	92509323	3	3	15	1	0	0	0	0	1	0	0	0	7461	449	16	3	887	3	HTR7	10	92509323	Missense_Mutation	SNP	A	TCGA-FF-8061-01A-11D-2210-10	21959684	92509323	43025424	86	2007											
MYOF	26509	hgsc.bcm.edu	37	chr10	95089487	95089487	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggaatcggttttccagatcaAtaattgtttctcctactttt	9	18	6	8	1	2	1	1	0	1	1	5	2	3	2	2	2	1	2	2	2	4	8			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr10:95089487A>G	ENST00000359263.4	-	44	4915	c.4916T>C	c.(4915-4917)aTt>aCt	p.I1639T	MYOF_ENST00000358334.5_Missense_Mutation_p.I1626T|MYOF_ENST00000371502.4_Missense_Mutation_p.I1658T|MYOF_ENST00000371501.4_Missense_Mutation_p.I1639T|MYOF_ENST00000485212.1_5'UTR	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	1639					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						TTCCAGATCAATAATTGTTTC	0.433																																					p.I1639T		Atlas-SNP	.											.	MYOF	177	.	0			c.T4916C						PASS	.						127	123	124					10																	95089487		1858	4102	5960	SO:0001583	missense	26509	exon44			AGATCAATAATTG	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.4916T>C	10.37:g.95089487A>G	ENSP00000352208:p.Ile1639Thr	131	0	0		143	63	0.440559	NM_013451	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Missense_Mutation	SNP	ENST00000359263.4	37	CCDS41551.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.166718	0.78339	.	.	ENSG00000138119	ENST00000358334;ENST00000359263;ENST00000371501;ENST00000371502	T;T;T;T	0.50001	0.76;0.76;0.76;0.76	5.3	5.3	0.74995	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.097327	0.64402	D	0.000002	T	0.74183	0.3683	M	0.92923	3.36	0.80722	D	1	D;P	0.57571	0.98;0.954	D;P	0.63957	0.92;0.701	T	0.81597	-0.0860	10	0.87932	D	0	-7.8203	15.4031	0.74858	1.0:0.0:0.0:0.0	.	1626;1639	Q9NZM1-6;Q9NZM1	.;MYOF_HUMAN	T	1626;1639;1639;1658	ENSP00000351094:I1626T;ENSP00000352208:I1639T;ENSP00000360556:I1639T;ENSP00000360557:I1658T	ENSP00000351094:I1626T	I	-	2	0	MYOF	95079477	1.000000	0.71417	0.794000	0.32065	0.854000	0.48673	8.723000	0.91458	2.232000	0.73038	0.454000	0.30748	ATT	.	.	none		0.433	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451		G	95089487	A	G	95089487	3	3	15	1	0	0	0	0	1	0	0	0	10098	101	4	3	1313	3	MYOF	10	95089487	Missense_Mutation	SNP	A	TCGA-FF-8061-01A-11D-2210-10	2580164	95089487	40445260	87	2008											
SWAP70	23075	hgsc.bcm.edu	37	chr11	9685820	9685820	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcaaggtctccaagtcccagCtcaaggtgggcgcctcctga	8	7	12	14	1	2	1	1	1	1	0	5	1	4	1	4	3	1	2	4	3	3	0			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr11:9685820C>T	ENST00000318950.6	+	1	197	c.94C>T	c.(94-96)Ctc>Ttc	p.L32F	SWAP70_ENST00000447399.2_Missense_Mutation_p.L32F	NM_015055.2	NP_055870.2	Q9UH65	SWP70_HUMAN	SWAP switching B-cell complex 70kDa subunit	32					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)		CAAGTCCCAGCTCAAGGTGGG	0.692																																					p.L32F		Atlas-SNP	.											.	SWAP70	40	.	0			c.C94T						PASS	.						30	24	26					11																	9685820		2179	4272	6451	SO:0001583	missense	23075	exon1			TCCCAGCTCAAGG	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.94C>T	11.37:g.9685820C>T	ENSP00000315630:p.Leu32Phe	121	0	0		222	97	0.436937	NM_015055	D3DQV1|O75135|Q7LCY6|Q9P061|Q9P0Z8	Missense_Mutation	SNP	ENST00000318950.6	37	CCDS31426.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.750499	0.89753	.	.	ENSG00000133789	ENST00000447399;ENST00000318950	D;T	0.86865	-2.18;2.55	5.5	5.5	0.81552	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.93943	0.8061	M	0.81497	2.545	0.80722	D	1	D;P;D	0.76494	0.998;0.891;0.999	D;P;D	0.85130	0.996;0.49;0.997	D	0.94379	0.7603	10	0.87932	D	0	-6.5908	19.0354	0.92974	0.0:1.0:0.0:0.0	.	32;32;32	E7EMB1;Q9UH65;B3KUB9	.;SWP70_HUMAN;.	F	32	ENSP00000399056:L32F;ENSP00000315630:L32F	ENSP00000315630:L32F	L	+	1	0	SWAP70	9642396	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.705000	0.54823	2.584000	0.87258	0.563000	0.77884	CTC	.	.	none		0.692	SWAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386766.2	NM_015055		T	9685820	C	T	9685820	3	4	15	1	0	0	0	0	1	0	0	0	15440	797	28	2	96	2	SWAP70	11	9685820	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10		9685820	125320696	88	2009											
OR5B3	441608	hgsc.bcm.edu	37	chr11	58170412	58170412	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agactaaatgtgtccccagtGtggatggaggcattcaggaa	12	9	13	7	0	1	1	1	0	0	1	2	4	2	4	2	4	0	1	2	4	3	2			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr11:58170412G>A	ENST00000309403.2	-	1	470	c.471C>T	c.(469-471)caC>caT	p.H157H		NM_001005469.1	NP_001005469.1	Q8NH48	OR5B3_HUMAN	olfactory receptor, family 5, subfamily B, member 3	157						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(4)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(6)|upper_aerodigestive_tract(1)	34	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				TGTCCCCAGTGTGGATGGAGG	0.468																																					p.H157H		Atlas-SNP	.											OR5B3,right_upper_lobe,carcinoma,-2,1	OR5B3	65	1	0			c.C471T						PASS	.						114	106	109					11																	58170412		2201	4295	6496	SO:0001819	synonymous_variant	441608	exon1			CCCAGTGTGGATG	AB065545	CCDS31549.1	11q12.1	2012-08-09			ENSG00000172769	ENSG00000172769		"GPCR / Class A : Olfactory receptors"	8324	protein-coding gene	gene with protein product				OR5B13			Standard	NM_001005469		Approved	OST129	uc010rkf.2	Q8NH48	OTTHUMG00000167516	ENST00000309403.2:c.471C>T	11.37:g.58170412G>A		89	0	0		100	4	0.04	NM_001005469	Q6IEV6	Silent	SNP	ENST00000309403.2	37	CCDS31549.1																																																																																			.	.	none		0.468	OR5B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394886.1	NM_001005469		A	58170412	G	A	58170412	2	1	15	1	0	0	0	0	0	0	0	1	11161	1368	48	2		2	OR5B3	11	58170412	Silent	SNP	G	TCGA-FF-8061-01A-11D-2210-10	48484592	58170412	76836104	89	2010											
PPP2R5B	5526	hgsc.bcm.edu	37	chr11	64700699	64700699	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgatgagctcacagcctccTacaagctggaaaagcagcag	13	7	10	11	0	1	2	1	2	0	0	2	3	2	3	2	1	6	4	2	1	4	2			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr11:64700699T>C	ENST00000164133.2	+	13	1949	c.1327T>C	c.(1327-1329)Tac>Cac	p.Y443H		NM_006244.3	NP_006235.1	Q15173	2A5B_HUMAN	protein phosphatase 2, regulatory subunit B', beta	443					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						CACAGCCTCCTACAAGCTGGA	0.552																																					p.Y443H		Atlas-SNP	.											.	PPP2R5B	47	.	0			c.T1327C						PASS	.						96	81	87					11																	64700699		2201	4297	6498	SO:0001583	missense	5526	exon13			GCCTCCTACAAGC	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.1327T>C	11.37:g.64700699T>C	ENSP00000164133:p.Tyr443His	54	0	0		64	4	0.0625	NM_006244	Q13853	Missense_Mutation	SNP	ENST00000164133.2	37	CCDS8085.1	.	.	.	.	.	.	.	.	.	.	T	18.88	3.717126	0.68844	.	.	ENSG00000068971	ENST00000164133;ENST00000527441	.	.	.	4.04	4.04	0.47022	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.71316	0.3325	M	0.70108	2.13	0.58432	D	0.999999	P	0.44195	0.828	P	0.53912	0.737	T	0.74878	-0.3514	9	0.66056	D	0.02	-16.1599	11.5916	0.50949	0.0:0.0:0.0:1.0	.	443	Q15173	2A5B_HUMAN	H	443	.	ENSP00000164133:Y443H	Y	+	1	0	PPP2R5B	64457275	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.508000	0.81686	2.054000	0.61138	0.459000	0.35465	TAC	.	.	none		0.552	PPP2R5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385465.1	NM_006244		C	64700699	T	C	64700699	3	2	15	1	0	0	0	0	1	0	0	0	12405	1522	53	3	1373	3	PPP2R5B	11	64700699	Missense_Mutation	SNP	T	TCGA-FF-8061-01A-11D-2210-10	6530287	64700699	70305817	90	2011											
NPAS4	266743	hgsc.bcm.edu	37	chr11	66191437	66191437	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggaagagtgctccagcaCtaacccactcttcaccgcag	11	6	8	16	1	2	1	1	0	1	1	3	2	3	2	4	1	3	3	4	1	2	2	rs145746289		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr11:66191437C>A	ENST00000311034.2	+	7	1252	c.1076C>A	c.(1075-1077)aCt>aAt	p.T359N		NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	359					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						TGCTCCAGCACTAACCCACTC	0.557																																					p.T359N		Atlas-SNP	.											.	NPAS4	133	.	0			c.C1076A						PASS	.						148	153	152					11																	66191437		2200	4295	6495	SO:0001583	missense	266743	exon7			CCAGCACTAACCC	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.1076C>A	11.37:g.66191437C>A	ENSP00000311196:p.Thr359Asn	48	0	0		49	17	0.346939	NM_178864	B7ZL81|Q8N8S5|Q8N9Q9	Missense_Mutation	SNP	ENST00000311034.2	37	CCDS8138.1	.	.	.	.	.	.	.	.	.	.	C	11.71	1.720846	0.30503	.	.	ENSG00000174576	ENST00000311034	T	0.43688	0.94	4.81	3.88	0.44766	.	0.870088	0.09718	N	0.764833	T	0.25494	0.0620	N	0.08118	0	0.22468	N	0.999071	B	0.14438	0.01	B	0.13407	0.009	T	0.16482	-1.0401	10	0.23302	T	0.38	0.8502	12.7895	0.57526	0.0:0.8339:0.1661:0.0	.	359	Q8IUM7	NPAS4_HUMAN	N	359	ENSP00000311196:T359N	ENSP00000311196:T359N	T	+	2	0	NPAS4	65948013	0.994000	0.37717	0.903000	0.35520	0.977000	0.68977	3.604000	0.54081	1.219000	0.43474	0.563000	0.77884	ACT	C|1.000;T|0.000	.	alt		0.557	NPAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392634.1	NM_178864		A	66191437	C	A	66191437	3	1	15	1	0	0	0	0	1	0	0	0	10574	565	20	4	1102	4	NPAS4	11	66191437	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	1490738	66191437	68815079	91	2012											
NPAS4	266743	hgsc.bcm.edu	37	chr11	66191694	66191694	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagcctccatgagcccttcCagacccatttgcccacccca	8	8	5	20	0	1	2	1	1	0	1	3	2	3	2	8	0	3	0	8	0	0	2			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr11:66191694C>T	ENST00000311034.2	+	7	1509	c.1333C>T	c.(1333-1335)Cag>Tag	p.Q445*		NM_178864.3	NP_849195.2	Q8IUM7	NPAS4_HUMAN	neuronal PAS domain protein 4	445					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						TGAGCCCTTCCAGACCCATTT	0.562																																					p.Q445X		Atlas-SNP	.											.	NPAS4	133	.	0			c.C1333T						PASS	.						187	184	185					11																	66191694		2200	4295	6495	SO:0001587	stop_gained	266743	exon7			CCCTTCCAGACCC	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.1333C>T	11.37:g.66191694C>T	ENSP00000311196:p.Gln445*	65	0	0		74	4	0.0540541	NM_178864	B7ZL81|Q8N8S5|Q8N9Q9	Nonsense_Mutation	SNP	ENST00000311034.2	37	CCDS8138.1	.	.	.	.	.	.	.	.	.	.	C	33	5.203210	0.95033	.	.	ENSG00000174576	ENST00000311034	.	.	.	4.71	4.71	0.59529	.	0.000000	0.47455	D	0.000227	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	-8.3061	13.0275	0.58823	0.0:1.0:0.0:0.0	.	.	.	.	X	445	.	ENSP00000311196:Q445X	Q	+	1	0	NPAS4	65948270	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.401000	0.34589	2.455000	0.83008	0.563000	0.77884	CAG	.	.	none		0.562	NPAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392634.1	NM_178864		T	66191694	C	T	66191694	4	4	15	1	0	0	0	0	0	1	0	0	10574	595	21	2	1359	2	NPAS4	11	66191694	Nonsense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	257	66191694	68814822	92	2013											
RBM14	10432	hgsc.bcm.edu	37	chr11	66391989	66391989	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccttctttggtcgcgaccgCagccctctgcgccgttcacc	3	10	9	19	5	3	0	1	0	2	0	4	1	3	0	5	1	2	2	5	1	0	3			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr11:66391989C>A	ENST00000310137.4	+	2	781	c.642C>A	c.(640-642)cgC>cgA	p.R214R	RBM4_ENST00000503028.2_Intron|RBM14_ENST00000409738.4_Intron|RBM14-RBM4_ENST00000412278.2_Intron|RBM14_ENST00000393979.3_Intron|RBM14-RBM4_ENST00000500635.2_Intron|RBM14_ENST00000409372.1_3'UTR|RBM4_ENST00000514361.3_Intron|RBM14-RBM4_ENST00000511114.1_Intron	NM_006328.3	NP_006319.1	Q96PK6	RBM14_HUMAN	RNA binding motif protein 14	214					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						GTCGCGACCGCAGCCCTCTGC	0.642																																					p.R214R		Atlas-SNP	.											RBM14,rectum,carcinoma,+1,1	RBM14	59	1	0			c.C642A						scavenged	.						43	44	44					11																	66391989		2200	4295	6495	SO:0001819	synonymous_variant	10432	exon2			CGACCGCAGCCCT	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.642C>A	11.37:g.66391989C>A		42	1	0.0238095		50	2	0.04	NM_006328	B0LM41|B3KMN4|D6RGD8|O75932|Q2PYN1|Q53GV1|Q68DQ9|Q96PK5	Silent	SNP	ENST00000310137.4	37	CCDS8147.1																																																																																			.	.	none		0.642	RBM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277128.1	NM_006328		A	66391989	C	A	66391989	2	1	15	1	0	0	0	0	0	0	0	1	13130	697	25	4		4	RBM14	11	66391989	Silent	SNP	C	TCGA-FF-8061-01A-11D-2210-10	200295	66391989	68614527	93	2014											
LRRC32	2615	hgsc.bcm.edu	37	chr11	76371849	76371849	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtagatgagtctcgggagcGcggccaggtcggggaaatgg	8	6	20	7	4	1	2	0	1	1	1	3	4	1	4	1	7	1	1	1	7	2	1	rs201402758		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr11:76371849G>A	ENST00000407242.2	-	3	1030	c.788C>T	c.(787-789)gCg>gTg	p.A263V	LRRC32_ENST00000260061.5_Missense_Mutation_p.A263V|LRRC32_ENST00000464145.1_Intron|LRRC32_ENST00000404995.1_Missense_Mutation_p.A263V|AP001189.4_ENST00000447519.1_RNA	NM_005512.2	NP_005503.1	Q14392	LRC32_HUMAN	leucine rich repeat containing 32	263					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						TCTCGGGAGCGCGGCCAGGTC	0.632																																					p.A263V		Atlas-SNP	.											.	LRRC32	74	.	0			c.C788T						PASS	.						59	59	59					11																	76371849		2200	4292	6492	SO:0001583	missense	2615	exon3			GGGAGCGCGGCCA	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.788C>T	11.37:g.76371849G>A	ENSP00000384126:p.Ala263Val	121	0	0		174	59	0.33908	NM_005512	Q86V06	Missense_Mutation	SNP	ENST00000407242.2	37	CCDS8245.1	.	.	.	.	.	.	.	.	.	.	G	1.050	-0.676017	0.03378	.	.	ENSG00000137507	ENST00000260061;ENST00000407242;ENST00000404995	T;T;T	0.79653	-1.29;-1.29;-1.29	4.55	1.48	0.22813	.	0.688404	0.14657	N	0.306188	T	0.60792	0.2296	L	0.28274	0.84	0.09310	N	1	B	0.15719	0.014	B	0.04013	0.001	T	0.34129	-0.9841	10	0.16420	T	0.52	.	2.0366	0.03541	0.102:0.2514:0.3483:0.2982	.	263	Q14392	LRC32_HUMAN	V	263	ENSP00000260061:A263V;ENSP00000384126:A263V;ENSP00000385766:A263V	ENSP00000260061:A263V	A	-	2	0	LRRC32	76049497	0.000000	0.05858	0.133000	0.22050	0.150000	0.21749	0.012000	0.13287	1.116000	0.41820	0.555000	0.69702	GCG	.	.	weak		0.632	LRRC32-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257926.2	NM_005512		A	76371849	G	A	76371849	3	1	15	1	0	0	0	0	1	0	0	0	8996	1087	38	1	1204	1	LRRC32	11	76371849	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	9979860	76371849	58634667	94	2015											
GDPD4	220032	hgsc.bcm.edu	37	chr11	76996151	76996151	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtcaaagttaaagtattcaCtggatgtttctatccacagg	13	13	8	7	0	3	0	2	0	1	0	4	1	4	1	1	2	0	3	1	2	5	5			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr11:76996151C>T	ENST00000376217.2	-	2	282	c.32G>A	c.(31-33)aGt>aAt	p.S11N	GDPD4_ENST00000527489.1_5'UTR|GDPD4_ENST00000315938.4_Missense_Mutation_p.S11N			Q6W3E5	GDPD4_HUMAN	glycerophosphodiester phosphodiesterase domain containing 4	11					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						AAAGTATTCACTGGATGTTTC	0.383																																					p.S11N		Atlas-SNP	.											.	GDPD4	49	.	0			c.G32A						PASS	.						76	67	70					11																	76996151		2200	4292	6492	SO:0001583	missense	220032	exon2			TATTCACTGGATG	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.32G>A	11.37:g.76996151C>T	ENSP00000365390:p.Ser11Asn	67	0	0		88	26	0.295455	NM_182833	Q7Z5B0	Missense_Mutation	SNP	ENST00000376217.2	37		.	.	.	.	.	.	.	.	.	.	c	0.018	-1.481167	0.01027	.	.	ENSG00000178795	ENST00000376217;ENST00000315938	T;T	0.19669	2.13;2.13	3.94	2.82	0.32997	.	0.095444	0.64402	N	0.000002	T	0.02727	0.0082	N	0.00056	-2.365	0.19775	N	0.99995	B	0.02656	0.0	B	0.01281	0.0	T	0.42085	-0.9472	10	0.02654	T	1	-15.0283	6.3686	0.21469	0.0:0.111:0.0:0.889	.	11	Q6W3E5-2	.	N	11	ENSP00000365390:S11N;ENSP00000320815:S11N	ENSP00000320815:S11N	S	-	2	0	GDPD4	76673799	0.998000	0.40836	1.000000	0.80357	0.434000	0.31775	1.836000	0.39191	0.855000	0.35359	-0.374000	0.07098	AGT	.	.	none		0.383	GDPD4-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382075.1	NM_182833		T	76996151	C	T	76996151	3	4	15	1	0	0	0	0	1	0	0	0	6334	565	20	2	1590	2	GDPD4	11	76996151	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	624302	76996151	58010365	95	2016											
KIAA1377	57562	hgsc.bcm.edu	37	chr11	101834043	101834043	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agagcaaaaataattagaaaAccaggatctgcaaaagtcca	21	6	7	7	0	1	2	0	0	1	2	2	3	2	3	2	1	3	2	2	1	8	2			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr11:101834043A>C	ENST00000263468.8	+	6	2547	c.2277A>C	c.(2275-2277)aaA>aaC	p.K759N	KIAA1377_ENST00000537689.1_Missense_Mutation_p.K560N	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	759										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)		TAATTAGAAAACCAGGATCTG	0.378																																					p.K759N		Atlas-SNP	.											.	KIAA1377	111	.	0			c.A2277C						PASS	.						65	72	70					11																	101834043		2203	4299	6502	SO:0001583	missense	57562	exon6			TAGAAAACCAGGA	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.2277A>C	11.37:g.101834043A>C	ENSP00000263468:p.Lys759Asn	69	0	0		80	9	0.1125	NM_020802	Q4G0U6	Missense_Mutation	SNP	ENST00000263468.8	37	CCDS31658.1	.	.	.	.	.	.	.	.	.	.	A	8.638	0.895225	0.17613	.	.	ENSG00000110318	ENST00000263468;ENST00000537689	T;T	0.07327	3.2;3.2	5.23	5.23	0.72850	.	0.157535	0.45867	D	0.000338	T	0.06645	0.0170	N	0.22421	0.69	0.27731	N	0.944796	B	0.32467	0.372	B	0.29077	0.098	T	0.18903	-1.0322	10	0.72032	D	0.01	-14.8212	11.7668	0.51935	0.8685:0.0:0.0:0.1315	.	759	Q9P2H0	K1377_HUMAN	N	759;560	ENSP00000263468:K759N;ENSP00000443184:K560N	ENSP00000263468:K759N	K	+	3	2	KIAA1377	101339253	0.995000	0.38212	0.714000	0.30535	0.134000	0.20937	3.343000	0.52167	2.093000	0.63338	0.533000	0.62120	AAA	.	.	none		0.378	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802		C	101834043	A	C	101834043	3	2	15	1	0	0	0	0	1	0	0	0	8236	40	2	5	2299	5	KIAA1377	11	101834043	Missense_Mutation	SNP	A	TCGA-FF-8061-01A-11D-2210-10	24837892	101834043	33172473	96	2017											
CACNA1C	775	hgsc.bcm.edu	37	chr12	2676736	2676736	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctctcctgggcctgccagaCacggcaaacaaggccctgct	8	6	10	17	1	1	1	0	0	1	1	2	1	1	1	5	3	3	2	5	3	2	0			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr12:2676736C>T	ENST00000347598.4	+	13	1671	c.1671C>T	c.(1669-1671)gaC>gaT	p.D557D	CACNA1C_ENST00000399595.1_Splice_Site_p.D557D|CACNA1C_ENST00000399629.1_Splice_Site_p.D557D|CACNA1C_ENST00000399606.1_Splice_Site_p.D557D|CACNA1C_ENST00000399621.1_Splice_Site_p.D557D|CACNA1C_ENST00000399638.1_Splice_Site_p.D557D|CACNA1C_ENST00000399641.1_Splice_Site_p.D557D|CACNA1C_ENST00000480911.1_Splice_Site_p.D557D|CACNA1C_ENST00000327702.7_Splice_Site_p.D557D|CACNA1C_ENST00000335762.5_Splice_Site_p.D582D|CACNA1C_ENST00000399634.1_Splice_Site_p.D557D|CACNA1C_ENST00000399617.1_Splice_Site_p.D557D|CACNA1C_ENST00000406454.3_Splice_Site_p.D557D|CACNA1C_ENST00000399603.1_Splice_Site_p.D557D|CACNA1C_ENST00000399597.1_Splice_Site_p.D557D|CACNA1C_ENST00000399644.1_Splice_Site_p.D557D|CACNA1C_ENST00000399591.1_Splice_Site_p.D557D|CACNA1C_ENST00000399601.1_Splice_Site_p.D557D|CACNA1C_ENST00000402845.3_Splice_Site_p.D557D|CACNA1C_ENST00000399649.1_Splice_Site_p.D557D|CACNA1C_ENST00000344100.3_Splice_Site_p.D557D|CACNA1C_ENST00000399655.1_Splice_Site_p.D557D|CACNA1C_ENST00000399637.1_Splice_Site_p.D557D	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	557					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)	GCCTGCCAGACACGGCAAACA	0.567																																					p.D557D		Atlas-SNP	.											.	CACNA1C	1023	.	0			c.C1671T						PASS	.						18	20	19					12																	2676736		2095	4247	6342	SO:0001630	splice_region_variant	775	exon13			GCCAGACACGGCA	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.1670-1C>T	12.37:g.2676736C>T		41	0	0		38	16	0.421053	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	37	CCDS44788.1																																																																																			.	.	none		0.567	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719	Silent	T	2676736	C	T	2676736	5	4	15	1	0	0	0	0	0	0	1	0	2542	492	17	2	1829	2	CACNA1C	12	2676736	Splice_Site	SNP	C	TCGA-FF-8061-01A-11D-2210-10		2676736	131175159	97	2018											
C12orf53	196500	hgsc.bcm.edu	37	chr12	6806573	6806573	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tggggttgcgagcccatgagGggctgcaaaaccatagtcca	10	7	14	10	1	0	1	0	1	0	0	1	2	1	1	3	4	4	3	3	4	3	2			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr12:6806573G>T	ENST00000540656.1	-	3	741	c.403C>A	c.(403-405)Cct>Act	p.P135T	PIANP_ENST00000320591.5_Missense_Mutation_p.P135T|PIANP_ENST00000534837.1_Missense_Mutation_p.P135T	NM_001244015.1	NP_001230944.1	Q8IYJ0	PIANP_HUMAN	PILR alpha associated neural protein	135						integral component of membrane (GO:0016021)											AGCCCATGAGGGGCTGCAAAA	0.602																																					p.P135T		Atlas-SNP	.											.	.	.	.	0			c.C403A						PASS	.						50	54	53					12																	6806573		1940	4123	6063	SO:0001583	missense	196500	exon3			CATGAGGGGCTGC	BC035736	CCDS44818.1, CCDS58205.1	12p13.31	2012-08-17	2012-08-17	2012-08-17	ENSG00000139200	ENSG00000139200			25338	protein-coding gene	gene with protein product	"PILR-associating neural protein"		"chromosome 12 open reading frame 53"	C12orf53		12975309	Standard	NM_153685		Approved	DKFZp547D2210, PANP	uc001qqf.2	Q8IYJ0	OTTHUMG00000168664	ENST00000540656.1:c.403C>A	12.37:g.6806573G>T	ENSP00000442157:p.Pro135Thr	101	0	0		109	5	0.0458716	NM_001244014	A8K0T3|B3KPF7|B3KRI6|Q6UX35	Missense_Mutation	SNP	ENST00000540656.1	37	CCDS44818.1	.	.	.	.	.	.	.	.	.	.	G	16.53	3.148879	0.57151	.	.	ENSG00000139200	ENST00000540656;ENST00000320591;ENST00000534837;ENST00000439553;ENST00000545917	T;T;T;T	0.39056	1.1;1.1;1.1;1.1	4.05	4.05	0.47172	.	0.135360	0.50627	D	0.000106	T	0.19846	0.0477	N	0.14661	0.345	0.31623	N	0.650026	P	0.40282	0.711	B	0.27887	0.084	T	0.28650	-1.0037	10	0.72032	D	0.01	-9.1833	8.2372	0.31634	0.1749:0.0:0.8251:0.0	.	135	Q8IYJ0	CL053_HUMAN	T	135;135;135;109;135	ENSP00000442157:P135T;ENSP00000317818:P135T;ENSP00000443919:P135T;ENSP00000444605:P135T	ENSP00000317818:P135T	P	-	1	0	C12orf53	6676834	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.423000	0.59861	1.802000	0.52723	0.305000	0.20034	CCT	.	.	none		0.602	PIANP-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400524.1	NM_153685		T	6806573	G	T	6806573	3	4	15	1	0	0	0	0	1	0	0	0	1700	1232	43	4	461	4	C12orf53	12	6806573	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	4129837	6806573	127045322	98	2019											
BTG1	694	hgsc.bcm.edu	37	chr12	92539304	92539304	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tggcggcccgggtgtagaagGgatgcatgggggcggcgtgc	5	6	22	8	4	0	1	0	0	0	1	0	2	0	2	1	7	2	2	1	7	2	1			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr12:92539304G>C	ENST00000256015.3	-	1	369	c.8C>G	c.(7-9)cCc>cGc	p.P3R	RP11-796E2.4_ENST00000501008.2_RNA|RP11-796E2.4_ENST00000499685.2_RNA|C12orf79_ENST00000551563.2_5'Flank|C12orf79_ENST00000546975.1_5'Flank|C12orf79_ENST00000549802.1_5'Flank	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	3					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)			haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				GGTGTAGAAGGGATGCATggg	0.746			T	MYC	BCLL																																p.P3R		Atlas-SNP	.		Dom	yes		12	12q22	694	"B-cell translocation gene 1, anti-proliferative"		L	.	BTG1	30	.	0			c.C8G						PASS	.						25	29	28					12																	92539304		2199	4292	6491	SO:0001583	missense	694	exon1			TAGAAGGGATGCA		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.8C>G	12.37:g.92539304G>C	ENSP00000256015:p.Pro3Arg	57	0	0		83	39	0.46988	NM_001731	P31607	Missense_Mutation	SNP	ENST00000256015.3	37	CCDS9043.1	.	.	.	.	.	.	.	.	.	.	G	17.75	3.465474	0.63513	.	.	ENSG00000133639	ENST00000256015	T	0.21361	2.01	3.71	3.71	0.42584	.	0.119071	0.56097	D	0.000026	T	0.15219	0.0367	L	0.29908	0.895	0.45718	D	0.998629	B	0.33694	0.421	B	0.24541	0.054	T	0.09707	-1.0662	10	0.51188	T	0.08	-4.5437	15.638	0.76970	0.0:0.0:1.0:0.0	.	3	P62324	BTG1_HUMAN	R	3	ENSP00000256015:P3R	ENSP00000256015:P3R	P	-	2	0	BTG1	91063435	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.824000	0.86668	1.883000	0.54544	0.455000	0.32223	CCC	.	.	none		0.746	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1			C	92539304	G	C	92539304	3	2	15	1	0	0	0	0	1	0	0	0	1555	1232	43	4	515	4	BTG1	12	92539304	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	85732731	92539304	41312591	99	2020											
WSCD2	9671	hgsc.bcm.edu	37	chr12	108620920	108620920	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggactcctagttacttcattGtgtaccagacacaagtccaa	12	11	7	11	0	1	1	1	0	0	1	3	2	3	2	3	1	2	2	3	1	5	5			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr12:108620920G>A	ENST00000332082.4	+	7	1776	c.958G>A	c.(958-960)Gtg>Atg	p.V320M	WSCD2_ENST00000547525.1_Missense_Mutation_p.V320M|WSCD2_ENST00000261400.3_Missense_Mutation_p.V320M|WSCD2_ENST00000549903.1_Missense_Mutation_p.V320M			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	320	WSC 2. {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						TTACTTCATTGTGTACCAGAC	0.587																																					p.V320M		Atlas-SNP	.											.	WSCD2	125	.	0			c.G958A						PASS	.						59	63	61					12																	108620920		2041	4193	6234	SO:0001583	missense	9671	exon6			TTCATTGTGTACC		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.958G>A	12.37:g.108620920G>A	ENSP00000331933:p.Val320Met	106	0	0		102	17	0.166667	NM_014653	B2RN48|B4DES1|Q8IY35|Q9Y4B7	Missense_Mutation	SNP	ENST00000332082.4	37	CCDS41828.1	.	.	.	.	.	.	.	.	.	.	G	19.83	3.899521	0.72754	.	.	ENSG00000075035	ENST00000547525;ENST00000261400;ENST00000332082;ENST00000549903	T;T;T;T	0.38401	1.14;4.62;1.14;4.62	5.22	5.22	0.72569	Carbohydrate-binding WSC (1);Carbohydrate-binding WSC, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.60599	0.2281	M	0.72894	2.215	0.80722	D	1	P;D	0.71674	0.587;0.998	B;D	0.78314	0.146;0.991	T	0.60692	-0.7213	10	0.52906	T	0.07	-25.5959	17.9638	0.89093	0.0:0.0:1.0:0.0	.	320;320	Q2TBF2-2;Q2TBF2	.;WSCD2_HUMAN	M	320	ENSP00000448047:V320M;ENSP00000261400:V320M;ENSP00000331933:V320M;ENSP00000447272:V320M	ENSP00000261400:V320M	V	+	1	0	WSCD2	107145050	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.078000	0.71282	2.725000	0.93324	0.655000	0.94253	GTG	.	.	none		0.587	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405554.1	NM_014653		A	108620920	G	A	108620920	3	1	15	1	0	0	0	0	1	0	0	0	17422	1377	48	2	976	2	WSCD2	12	108620920	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	16081616	108620920	25230975	100	2021											
CIT	11113	hgsc.bcm.edu	37	chr12	120295436	120295436	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaagtgaccacaacctacaAgacttctgacttcgaagtcc	14	8	6	13	1	1	3	0	2	1	1	3	4	2	3	3	0	2	0	3	0	5	3			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr12:120295436A>G	ENST00000261833.7	-	4	357	c.305T>C	c.(304-306)cTt>cCt	p.L102P	CIT_ENST00000392521.2_Missense_Mutation_p.L102P	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	102	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)		ACAACCTACAAGACTTCTGAC	0.473																																					p.L102P		Atlas-SNP	.											.	CIT	535	.	0			c.T305C						PASS	.						190	190	190					12																	120295436		2203	4300	6503	SO:0001583	missense	11113	exon4			CCTACAAGACTTC	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.305T>C	12.37:g.120295436A>G	ENSP00000261833:p.Leu102Pro	104	0	0		110	33	0.3	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Missense_Mutation	SNP	ENST00000261833.7	37	CCDS9192.1	.	.	.	.	.	.	.	.	.	.	A	16.83	3.231625	0.58777	.	.	ENSG00000122966	ENST00000392521;ENST00000261833;ENST00000536325	T;T;T	0.42513	0.97;0.97;3.04	5.4	5.4	0.78164	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.089941	0.42294	D	0.000735	T	0.38772	0.1053	L	0.44542	1.39	0.80722	D	1	P;B	0.40107	0.703;0.0	B;B	0.37650	0.255;0.014	T	0.39663	-0.9603	10	0.87932	D	0	.	15.7159	0.77667	1.0:0.0:0.0:0.0	.	102;102	Q2M5E1;O14578	.;CTRO_HUMAN	P	102;102;19	ENSP00000376306:L102P;ENSP00000261833:L102P;ENSP00000443199:L19P	ENSP00000261833:L102P	L	-	2	0	CIT	118779819	1.000000	0.71417	0.975000	0.42487	0.992000	0.81027	9.027000	0.93706	2.170000	0.68504	0.482000	0.46254	CTT	.	.	none		0.473	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174		G	120295436	A	G	120295436	3	3	15	1	0	0	0	0	1	0	0	0	3440	72	3	3	5954	3	CIT	12	120295436	Missense_Mutation	SNP	A	TCGA-FF-8061-01A-11D-2210-10	11674516	120295436	13556459	101	2022											
RIMBP2	23504	hgsc.bcm.edu	37	chr12	130892335	130892335	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagggccaccattctccgcGtcgataccgaatgacgcctg	9	7	10	15	5	1	1	0	1	1	0	3	3	1	1	5	1	1	0	5	1	2	2			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr12:130892335G>A	ENST00000261655.4	-	16	3024	c.2861C>T	c.(2860-2862)aCg>aTg	p.T954M		NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	954	SH3 3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				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)		CATTCTCCGCGTCGATACCGA	0.512																																					p.T954M		Atlas-SNP	.											RIMBP2,NS,carcinoma,+1,1	RIMBP2	220	1	0			c.C2861T						PASS	.						290	222	245					12																	130892335		2203	4300	6503	SO:0001583	missense	23504	exon16			CTCCGCGTCGATA	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.2861C>T	12.37:g.130892335G>A	ENSP00000261655:p.Thr954Met	128	0	0		121	42	0.347107	NM_015347	Q96ID2	Missense_Mutation	SNP	ENST00000261655.4	37	CCDS31925.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.189429	0.78789	.	.	ENSG00000060709	ENST00000261655;ENST00000536632	T;T	0.29397	1.57;1.57	4.61	4.61	0.57282	Src homology-3 domain (2);	0.054336	0.64402	D	0.000001	T	0.44201	0.1282	L	0.31371	0.925	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.36504	-0.9745	10	0.40728	T	0.16	-14.8894	17.447	0.87580	0.0:0.0:1.0:0.0	.	954	O15034	RIMB2_HUMAN	M	954;91	ENSP00000261655:T954M;ENSP00000439030:T91M	ENSP00000261655:T954M	T	-	2	0	RIMBP2	129458288	1.000000	0.71417	0.018000	0.16275	0.034000	0.12701	9.767000	0.98960	2.102000	0.63906	0.555000	0.69702	ACG	.	.	none		0.512	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347		A	130892335	G	A	130892335	3	1	15	1	0	0	0	0	1	0	0	0	13378	1145	40	1	313	1	RIMBP2	12	130892335	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	10596899	130892335	2959560	102	2023											
PDS5B	23047	hgsc.bcm.edu	37	chr13	33316792	33316792	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaaataatcacagtaaatcaGgaacttctaccttaagattg	18	11	5	7	0	3	1	2	0	1	1	3	2	3	2	1	1	2	1	1	1	8	6			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr13:33316792G>A	ENST00000315596.10	+	23	2725	c.2539G>A	c.(2539-2541)Gga>Aga	p.G847R		NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	847					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)		CAGTAAATCAGGAACTTCTAC	0.338																																					p.G847R		Atlas-SNP	.											.	PDS5B	141	.	0			c.G2539A						PASS	.						136	127	129					13																	33316792		1863	4106	5969	SO:0001583	missense	23047	exon23			AAATCAGGAACTT	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.2539G>A	13.37:g.33316792G>A	ENSP00000313851:p.Gly847Arg	115	0	0		123	38	0.308943	NM_015032	Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	Missense_Mutation	SNP	ENST00000315596.10	37	CCDS41878.1	.	.	.	.	.	.	.	.	.	.	G	33	5.204381	0.95033	.	.	ENSG00000083642	ENST00000315596;ENST00000421084	.	.	.	5.84	5.84	0.93424	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.72614	0.3482	L	0.43152	1.355	0.80722	D	1	D	0.61697	0.99	P	0.60949	0.881	T	0.72283	-0.4339	9	0.56958	D	0.05	-8.6067	20.1294	0.97995	0.0:0.0:1.0:0.0	.	847	Q9NTI5	PDS5B_HUMAN	R	847	.	ENSP00000313851:G847R	G	+	1	0	PDS5B	32214792	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.756000	0.98918	2.758000	0.94735	0.591000	0.81541	GGA	.	.	none		0.338	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044428.3	NM_015032		A	33316792	G	A	33316792	3	1	15	1	0	0	0	0	1	0	0	0	11701	1001	35	2	2625	2	PDS5B	13	33316792	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10		33316792	81853086	103	2024											
NBEA	26960	hgsc.bcm.edu	37	chr13	35782857	35782857	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagtgttgtggtgcctgtaaAgaaaccacctccaggtagtt	10	11	12	8	0	0	1	0	0	0	1	1	2	1	1	4	2	2	4	4	2	4	4			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr13:35782857A>G	ENST00000400445.3	+	32	5921	c.5387A>G	c.(5386-5388)aAg>aGg	p.K1796R	NBEA_ENST00000540320.1_Missense_Mutation_p.K1796R|NBEA_ENST00000310336.4_Missense_Mutation_p.K1796R|NBEA_ENST00000379939.2_Missense_Mutation_p.K1793R	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1796					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)		GTGCCTGTAAAGAAACCACCT	0.428																																					p.K1796R		Atlas-SNP	.											.	NBEA	340	.	0			c.A5387G						PASS	.						63	60	61					13																	35782857		1837	4085	5922	SO:0001583	missense	26960	exon32			CTGTAAAGAAACC	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.5387A>G	13.37:g.35782857A>G	ENSP00000383295:p.Lys1796Arg	89	0	0		68	26	0.382353	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	37	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	A	18.84	3.708964	0.68615	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336;ENST00000422518	T;T;T;T	0.60171	0.21;0.22;0.22;0.21	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.54854	0.1884	M	0.65975	2.015	0.80722	D	1	P;P	0.42409	0.779;0.666	B;B	0.34346	0.141;0.18	T	0.61768	-0.6995	10	0.52906	T	0.07	.	16.056	0.80805	1.0:0.0:0.0:0.0	.	1796;1793	Q8NFP9;Q5T321	NBEA_HUMAN;.	R	1796;1796;1793;1796;423	ENSP00000440951:K1796R;ENSP00000383295:K1796R;ENSP00000369271:K1793R;ENSP00000308534:K1796R	ENSP00000308534:K1796R	K	+	2	0	NBEA	34680857	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.855000	0.92236	2.178000	0.69098	0.533000	0.62120	AAG	.	.	none		0.428	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		G	35782857	A	G	35782857	3	3	15	1	0	0	0	0	1	0	0	0	10196	72	3	3	5513	3	NBEA	13	35782857	Missense_Mutation	SNP	A	TCGA-FF-8061-01A-11D-2210-10	2466065	35782857	79387021	104	2025											
DHRS12	79758	hgsc.bcm.edu	37	chr13	52345982	52345982	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgtcggcccagccaggatgCatggaagaaaaatggatggc	12	6	15	8	1	0	1	0	0	0	1	1	4	0	4	2	5	2	1	2	5	3	0			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr13:52345982C>T	ENST00000444610.2	-	8	694	c.681G>A	c.(679-681)atG>atA	p.M227I	DHRS12_ENST00000218981.1_Missense_Mutation_p.M178I|DHRS12_ENST00000280056.2_Missense_Mutation_p.M178I|DHRS12_ENST00000490949.1_5'UTR	NM_001270424.1	NP_001257353.1	A0PJE2	DHR12_HUMAN	dehydrogenase/reductase (SDR family) member 12	227							oxidoreductase activity (GO:0016491)			cervix(1)|large_intestine(1)|lung(2)|skin(2)|urinary_tract(1)	7		Breast(56;0.00173)|Prostate(109;0.00899)|Lung NSC(96;0.0199)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.81e-08)		AGCCAGGATGCATGGAAGAAA	0.557																																					p.M227I		Atlas-SNP	.											.	DHRS12	28	.	0			c.G681A						PASS	.						93	101	99					13																	52345982		2203	4300	6503	SO:0001583	missense	79758	exon8			AGGATGCATGGAA	AK023701	CCDS9430.1, CCDS31976.1, CCDS58292.1	13q14.3	2013-10-11			ENSG00000102796	ENSG00000102796		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	25832	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 40C, member 1"					19027726	Standard	NM_001031719		Approved	FLJ13639, SDR40C1	uc001vfq.4	A0PJE2	OTTHUMG00000016952	ENST00000444610.2:c.681G>A	13.37:g.52345982C>T	ENSP00000411565:p.Met227Ile	125	0	0		142	34	0.239437	NM_001270424	Q96GB2|Q9H8H1	Missense_Mutation	SNP	ENST00000444610.2	37	CCDS58292.1	.	.	.	.	.	.	.	.	.	.	C	17.04	3.286334	0.59867	.	.	ENSG00000102796	ENST00000444610;ENST00000218981;ENST00000280056	T;T;T	0.17054	2.3;2.3;3.33	4.57	0.634	0.17718	NAD(P)-binding domain (1);	0.046421	0.85682	D	0.000000	T	0.26810	0.0656	L	0.55213	1.73	0.30247	N	0.794416	B;D;D	0.69078	0.34;0.997;0.997	B;D;D	0.66847	0.171;0.947;0.932	T	0.07404	-1.0774	10	0.62326	D	0.03	.	4.3567	0.11181	0.1627:0.541:0.0:0.2963	.	178;178;227	A0PJE2-3;A0PJE2-2;A0PJE2	.;.;DHR12_HUMAN	I	227;178;178	ENSP00000411565:M227I;ENSP00000218981:M178I;ENSP00000280056:M178I	ENSP00000218981:M178I	M	-	3	0	DHRS12	51243983	1.000000	0.71417	0.007000	0.13788	0.080000	0.17528	1.538000	0.36094	0.539000	0.28788	-0.262000	0.10625	ATG	.	.	none		0.557	DHRS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045036.3	NM_024705		T	52345982	C	T	52345982	3	4	15	1	0	0	0	0	1	0	0	0	4490	710	25	2	463	2	DHRS12	13	52345982	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	16563125	52345982	62823896	105	2026											
PCDH17	27253	hgsc.bcm.edu	37	chr13	58207600	58207600	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cggcctaatccgtgtgaaggGcaatctggactatgaggaaa	12	8	13	8	2	1	2	0	2	1	0	2	4	2	4	2	4	0	1	2	4	5	2			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr13:58207600G>A	ENST00000377918.3	+	1	946	c.920G>A	c.(919-921)gGc>gAc	p.G307D		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	307	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)		CGTGTGAAGGGCAATCTGGAC	0.582																																					p.G307D	Melanoma(72;952 1291 1619 12849 33676)	Atlas-SNP	.											PCDH17,NS,carcinoma,+1,1	PCDH17	304	1	0			c.G920A						PASS	.						64	61	62					13																	58207600		2203	4300	6503	SO:0001583	missense	27253	exon1			TGAAGGGCAATCT	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.920G>A	13.37:g.58207600G>A	ENSP00000367151:p.Gly307Asp	66	0	0		66	15	0.227273	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Missense_Mutation	SNP	ENST00000377918.3	37	CCDS31986.1	.	.	.	.	.	.	.	.	.	.	G	18.62	3.663894	0.67700	.	.	ENSG00000118946	ENST00000377918	T	0.51817	0.69	5.57	4.67	0.58626	Cadherin (4);Cadherin-like (1);	0.044369	0.85682	D	0.000000	T	0.59046	0.2165	L	0.39467	1.215	0.80722	D	1	D;D	0.67145	0.995;0.996	D;D	0.76071	0.978;0.987	T	0.54774	-0.8243	9	.	.	.	.	15.9011	0.79377	0.0:0.1353:0.8647:0.0	.	307;307	O14917-2;O14917	.;PCD17_HUMAN	D	307	ENSP00000367151:G307D	.	G	+	2	0	PCDH17	57105601	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.693000	0.74582	2.640000	0.89533	0.650000	0.86243	GGC	.	.	none		0.582	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		A	58207600	G	A	58207600	3	1	15	1	0	0	0	0	1	0	0	0	11521	1203	42	2	922	2	PCDH17	13	58207600	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	5861618	58207600	56962278	106	2027											
RNF219	79596	hgsc.bcm.edu	37	chr13	79219011	79219011	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccttacctataatttctttgCaaggattttcaggagtgatg	10	16	8	7	0	2	1	1	1	1	0	2	3	2	3	2	2	2	1	2	2	4	7			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr13:79219011C>G	ENST00000282003.6	-	2	252	c.194G>C	c.(193-195)tGc>tCc	p.C65S		NM_024546.3	NP_078822.3	Q5W0B1	RN219_HUMAN	ring finger protein 219	65							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)		AATTTCTTTGCAAGGATTTTC	0.353																																					p.C65S		Atlas-SNP	.											.	RNF219	94	.	0			c.G194C						PASS	.						109	111	110					13																	79219011		2203	4300	6503	SO:0001583	missense	79596	exon2			TCTTTGCAAGGAT	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.194G>C	13.37:g.79219011C>G	ENSP00000282003:p.Cys65Ser	63	0	0		66	19	0.287879	NM_024546	B2RN99|Q8TBY2|Q9H0T2|Q9H8M0	Missense_Mutation	SNP	ENST00000282003.6	37	CCDS31997.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.477267	0.84640	.	.	ENSG00000152193	ENST00000282003	.	.	.	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.67107	0.2858	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.70197	-0.4938	9	0.59425	D	0.04	-5.6669	19.0489	0.93034	0.0:1.0:0.0:0.0	.	65	Q5W0B1	RN219_HUMAN	S	65	.	ENSP00000282003:C65S	C	-	2	0	RNF219	78117012	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.294000	0.78760	2.489000	0.83994	0.655000	0.94253	TGC	.	.	none		0.353	RNF219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045363.1	NM_024546		G	79219011	C	G	79219011	3	3	15	1	0	0	0	0	1	0	0	0	13497	710	25	4	2006	4	RNF219	13	79219011	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	21011411	79219011	35950867	107	2028											
TMTC4	84899	hgsc.bcm.edu	37	chr13	101287349	101287349	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acagtacccaacgctggggaGgtagaggacacgctctgcga	11	5	14	11	3	1	1	0	0	1	1	1	4	1	3	1	4	3	4	1	4	3	2			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr13:101287349G>A	ENST00000376234.3	-	10	1435	c.1246C>T	c.(1246-1248)Ctc>Ttc	p.L416F	TMTC4_ENST00000342624.5_Missense_Mutation_p.L435F|TMTC4_ENST00000328767.5_Missense_Mutation_p.L305F|TMTC4_ENST00000462211.1_5'UTR	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	416						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)					ACGCTGGGGAGGTAGAGGACA	0.537																																					p.L435F		Atlas-SNP	.											.	TMTC4	103	.	0			c.C1303T						PASS	.						77	71	73					13																	101287349		2203	4300	6503	SO:0001583	missense	84899	exon11			TGGGGAGGTAGAG		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.1246C>T	13.37:g.101287349G>A	ENSP00000365408:p.Leu416Phe	117	0	0		108	37	0.342593	NM_032813	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Missense_Mutation	SNP	ENST00000376234.3	37	CCDS41904.1	.	.	.	.	.	.	.	.	.	.	G	16.06	3.015661	0.54468	.	.	ENSG00000125247	ENST00000376234;ENST00000342624;ENST00000328767	T;T;T	0.69175	-0.38;-0.38;-0.38	5.5	4.66	0.58398	.	0.000000	0.85682	D	0.000000	T	0.81403	0.4815	M	0.83692	2.655	0.58432	D	0.999998	P;D;D;D	0.89917	0.908;0.999;0.999;1.0	P;D;D;D	0.78314	0.692;0.991;0.98;0.991	D	0.83482	0.0065	10	0.72032	D	0.01	.	11.3755	0.49726	0.1445:0.0:0.8555:0.0	.	305;416;416;435	B7Z666;Q5T4D3-2;Q5T4D3;Q5T4D3-3	.;.;TMTC4_HUMAN;.	F	416;435;305	ENSP00000365408:L416F;ENSP00000343871:L435F;ENSP00000365409:L305F	ENSP00000365409:L305F	L	-	1	0	TMTC4	100085350	1.000000	0.71417	1.000000	0.80357	0.283000	0.27025	3.246000	0.51414	1.332000	0.45431	-0.251000	0.11542	CTC	.	.	none		0.537	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813		A	101287349	G	A	101287349	3	1	15	1	0	0	0	0	1	0	0	0	16278	1000	35	2	1015	2	TMTC4	13	101287349	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	22068338	101287349	13882529	108	2029											
NFKBIA	4792	hgsc.bcm.edu	37	chr14	35871695	35871695	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaggttttctagtgtcagctGgcccagctgctgctgtatcc	6	13	11	11	0	2	0	1	0	1	0	3	0	3	0	2	2	4	6	2	2	3	4			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr14:35871695G>A	ENST00000216797.5	-	5	912	c.811C>T	c.(811-813)Cag>Tag	p.Q271*	NFKBIA_ENST00000557100.1_5'UTR|NFKBIA_ENST00000557140.1_Nonsense_Mutation_p.Q228*|NFKBIA_ENST00000557389.1_Nonsense_Mutation_p.Q181*	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)	AGTGTCAGCTGGCCCAGCTGC	0.562																																					p.Q271X		Atlas-SNP	.											.	NFKBIA	28	.	0			c.C811T						PASS	.						88	91	90					14																	35871695		2203	4300	6503	SO:0001587	stop_gained	4792	exon5			TCAGCTGGCCCAG		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.811C>T	14.37:g.35871695G>A	ENSP00000216797:p.Gln271*	142	0	0		180	46	0.255556	NM_020529	B2R8L6	Nonsense_Mutation	SNP	ENST00000216797.5	37	CCDS9656.1	.	.	.	.	.	.	.	.	.	.	G	38	7.053020	0.98029	.	.	ENSG00000100906	ENST00000216797;ENST00000557140;ENST00000557389	.	.	.	5.76	5.76	0.90799	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	-12.2413	15.4515	0.75277	0.0:0.1382:0.8618:0.0	.	.	.	.	X	271;228;181	.	ENSP00000216797:Q271X	Q	-	1	0	NFKBIA	34941446	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.992000	0.40737	2.719000	0.93026	0.655000	0.94253	CAG	.	.	none		0.562	NFKBIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276683.1	NM_020529		A	35871695	G	A	35871695	4	1	15	1	0	0	0	0	0	1	0	0	10386	1357	47	2	150	2	NFKBIA	14	35871695	Nonsense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10		35871695	71477845	109	2030											
C14orf149	112849	hgsc.bcm.edu	37	chr14	59950587	59950587	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cggtccgtggctgcggccgtCctcgcatgccacgaaggcgg	4	6	16	15	7	0	0	0	0	0	0	3	1	2	0	4	5	2	2	4	5	1	0	rs548137663		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr14:59950587C>T	ENST00000247194.4	-	1	561	c.448G>A	c.(448-450)Gac>Aac	p.D150N	JKAMP_ENST00000425728.2_5'Flank|JKAMP_ENST00000554271.1_5'Flank|RP11-701B16.2_ENST00000554253.1_RNA|JKAMP_ENST00000556985.1_5'Flank|L3HYPDH_ENST00000487285.1_5'Flank|JKAMP_ENST00000261247.9_5'Flank|JKAMP_ENST00000356057.5_5'Flank	NM_144581.1	NP_653182.1	Q96EM0	T3HPD_HUMAN	L-3-hydroxyproline dehydratase (trans-)	150					metabolic process (GO:0008152)		hydro-lyase activity (GO:0016836)|trans-L-3-hydroxyproline dehydratase activity (GO:0050346)									L-Proline(DB00172)	CTGCGGCCGTCCTCGCATGCC	0.711											OREG0022712	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	1	0.000199681	0.0	0.0	5008	,	,		14809	0.001		0.0	False		,,,				2504	0.0				p.D150N		Atlas-SNP	.											.	.	.	.	0			c.G448A						PASS	.						6	7	7					14																	59950587		2110	4104	6214	SO:0001583	missense	112849	exon1			GGCCGTCCTCGCA	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.448G>A	14.37:g.59950587C>T	ENSP00000247194:p.Asp150Asn	9	0	0	1042	16	8	0.5	NM_144581	Q96LJ5	Missense_Mutation	SNP	ENST00000247194.4	37	CCDS9739.1	.	.	.	.	.	.	.	.	.	.	C	13.37	2.216802	0.39201	.	.	ENSG00000126790	ENST00000247194	T	0.17370	2.28	5.58	3.77	0.43336	.	0.421261	0.27227	N	0.020326	T	0.12178	0.0296	L	0.28458	0.855	0.58432	D	0.999993	B;B	0.16166	0.016;0.001	B;B	0.18263	0.021;0.003	T	0.09443	-1.0674	10	0.15952	T	0.53	.	11.8035	0.52141	0.0:0.8581:0.0:0.1419	.	150;150	B4DGY8;Q96EM0	.;PRCM_HUMAN	N	150	ENSP00000247194:D150N	ENSP00000247194:D150N	D	-	1	0	C14orf149	59020340	0.816000	0.29132	0.851000	0.33527	0.692000	0.40212	1.630000	0.37081	0.726000	0.32339	0.561000	0.74099	GAC	.	.	none		0.711	L3HYPDH-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072254.5	NM_144581		T	59950587	C	T	59950587	3	4	15	1	0	0	0	0	1	0	0	0	1754	855	30	2	636	2	C14orf149	14	59950587	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	24078892	59950587	47398953	110	2031											
C14orf50	145376	hgsc.bcm.edu	37	chr14	65053990	65053990	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagagattgaagaagaagtaGggagactctttcgtaccaat	15	9	11	6	1	1	5	0	1	1	4	2	7	1	5	1	1	1	2	1	1	6	4			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr14:65053990G>A	ENST00000298705.1	+	10	886	c.790G>A	c.(790-792)Ggg>Agg	p.G264R	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	264					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										AGAAGAAGTAGGGAGACTCTT	0.413																																					p.G264R		Atlas-SNP	.											.	.	.	.	0			c.G790A						PASS	.						153	144	147					14																	65053990		2203	4300	6503	SO:0001583	missense	145376	exon10			GAAGTAGGGAGAC		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.790G>A	14.37:g.65053990G>A	ENSP00000298705:p.Gly264Arg	197	0	0		154	72	0.467532	NM_172365	Q6NTH6	Missense_Mutation	SNP	ENST00000298705.1	37	CCDS9767.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.356036	0.82243	.	.	ENSG00000165807	ENST00000298705	T	0.30981	1.51	5.55	5.55	0.83447	.	0.000000	0.64402	D	0.000005	T	0.57359	0.2048	M	0.79475	2.455	0.43708	D	0.996177	D	0.89917	1.0	D	0.97110	1.0	T	0.61083	-0.7134	10	0.87932	D	0	-21.7724	15.0284	0.71687	0.0:0.0:1.0:0.0	.	264	Q96LQ0	PPR36_HUMAN	R	264	ENSP00000298705:G264R	ENSP00000298705:G264R	G	+	1	0	C14orf50	64123743	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	5.068000	0.64364	2.596000	0.87737	0.655000	0.94253	GGG	.	.	none		0.413	PPP1R36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280667.1	NM_172365		A	65053990	G	A	65053990	3	1	15	1	0	0	0	0	1	0	0	0	1779	1000	35	2	828	2	C14orf50	14	65053990	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	5103403	65053990	42295550	111	2032											
TCL1A	8115	hgsc.bcm.edu	37	chr14	96180291	96180291	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aagctggctgtacctcgatgGttaagggcagccaggcgtgc	8	8	15	10	2	0	0	0	0	0	0	1	1	0	0	2	4	4	5	2	4	3	2	rs201228671	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr14:96180291G>A	ENST00000402399.1	-	1	242	c.113C>T	c.(112-114)aCc>aTc	p.T38I	TCL1A_ENST00000554012.1_Missense_Mutation_p.T38I|RP11-164H13.1_ENST00000553445.1_RNA|TCL1A_ENST00000555202.1_Missense_Mutation_p.T38I|RP11-164H13.1_ENST00000547644.2_RNA|RP11-164H13.1_ENST00000556386.1_RNA|TCL1A_ENST00000556450.1_Missense_Mutation_p.T38I	NM_021966.2	NP_068801.1	P56279	TCL1A_HUMAN	T-cell leukemia/lymphoma 1A	38					multicellular organismal development (GO:0007275)|stem cell maintenance (GO:0019827)	cell cortex (GO:0005938)|endoplasmic reticulum (GO:0005783)|pronucleus (GO:0045120)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(5)|prostate(1)|skin(1)	12		all_cancers(154;0.103)		COAD - Colon adenocarcinoma(157;0.205)|Epithelial(152;0.248)		TACCTCGATGGTTAAGGGCAG	0.647			T	TRA@	T-CLL																																p.T38I	Ovarian(96;1068 2019 35393 39316)	Atlas-SNP	.		Dom	yes		14	14q32.1	8115	T-cell leukemia/lymphoma 1A		L	.	TCL1A	26	.	0			c.C113T						PASS	.						86	81	83					14																	96180291		2203	4300	6503	SO:0001583	missense	8115	exon1			TCGATGGTTAAGG	X82240	CCDS9941.1	14q32.1	2008-07-03				ENSG00000100721			11648	protein-coding gene	gene with protein product		186960				2783489, 7809072	Standard	NM_021966		Approved	TCL1	uc001yfb.4	P56279		ENST00000402399.1:c.113C>T	14.37:g.96180291G>A	ENSP00000385036:p.Thr38Ile	59	0	0		61	32	0.52459	NM_001098725	Q6IBK7	Missense_Mutation	SNP	ENST00000402399.1	37	CCDS9941.1	.	.	.	.	.	.	.	.	.	.	G	10.04	1.242016	0.22796	.	.	ENSG00000100721	ENST00000554012;ENST00000402399;ENST00000556450;ENST00000555202	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	3.15	-2.77	0.05877	.	1.693040	0.03527	N	0.221932	T	0.20170	0.0485	N	0.22421	0.69	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.22487	-1.0215	10	0.31617	T	0.26	-11.297	7.6786	0.28500	0.4562:0.0:0.5438:0.0	.	38	P56279	TCL1A_HUMAN	I	38	ENSP00000451506:T38I;ENSP00000385036:T38I;ENSP00000450701:T38I;ENSP00000450496:T38I	ENSP00000385036:T38I	T	-	2	0	TCL1A	95250044	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.190000	0.03058	-0.453000	0.07076	-1.090000	0.02178	ACC	G|0.999;C|0.001	.	alt		0.647	TCL1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413246.1			A	96180291	G	A	96180291	3	1	15	1	0	0	0	0	1	0	0	0	15719	1261	44	2	243	2	TCL1A	14	96180291	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	31126301	96180291	11169249	112	2033											
ATP10A	57194	hgsc.bcm.edu	37	chr15	25969147	25969147	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgacttcttctcttgatacCgccatatccacagtccatgt	9	14	5	13	1	2	2	0	2	2	0	5	2	4	2	4	0	1	0	4	0	2	5	rs144743073	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr15:25969147C>T	ENST00000356865.6	-	6	1112	c.1001G>A	c.(1000-1002)cGg>cAg	p.R334Q		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	334					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)		CTCTTGATACCGCCATATCCA	0.358													C|||	2	0.000399361	0.0015	0.0	5008	,	,		19965	0.0		0.0	False		,,,				2504	0.0				p.R334Q		Atlas-SNP	.											.	ATP10A	270	.	0			c.G1001A						PASS	.	C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	136	136	136		1001	2.4	0	15	dbSNP_134	136	0,8600		0,0,4300	no	missense	ATP10A	NM_024490.3	43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	334/1500	25969147	1,13005	2203	4300	6503	SO:0001583	missense	57194	exon6			TGATACCGCCATA	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.1001G>A	15.37:g.25969147C>T	ENSP00000349325:p.Arg334Gln	124	0	0		83	31	0.373494	NM_024490	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	.	.	.	.	.	.	.	.	.	.	C	4.862	0.160142	0.09287	2.27E-4	0.0	ENSG00000206190	ENST00000356865	T	0.45668	0.89	5.3	2.36	0.29203	ATPase, P-type, ATPase-associated domain (1);	0.118743	0.56097	D	0.000021	T	0.20129	0.0484	N	0.12637	0.245	0.35235	D	0.777281	B	0.21520	0.057	B	0.18561	0.022	T	0.14755	-1.0461	10	0.18710	T	0.47	-27.5818	7.1544	0.25628	0.0:0.5527:0.0:0.4473	.	334	O60312	AT10A_HUMAN	Q	334	ENSP00000349325:R334Q	ENSP00000349325:R334Q	R	-	2	0	ATP10A	23520240	1.000000	0.71417	0.035000	0.18076	0.036000	0.12997	4.520000	0.60524	0.748000	0.32831	-0.251000	0.11542	CGG	C|1.000;T|0.000	0.000	weak		0.358	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		T	25969147	C	T	25969147	3	4	15	1	0	0	0	0	1	0	0	0	1116	652	23	1	3562	1	ATP10A	15	25969147	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10		25969147	76562245	113	2034											
ARHGAP11A	9824	hgsc.bcm.edu	37	chr15	32926229	32926229	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaaattcaatctagggaaaaAtggcagagaagtagtaagtt	18	9	11	3	0	2	1	1	0	1	1	2	4	2	2	0	2	0	4	0	2	8	5			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr15:32926229A>T	ENST00000361627.3	+	10	2053	c.1331A>T	c.(1330-1332)aAt>aTt	p.N444I	ARHGAP11A_ENST00000565905.1_Missense_Mutation_p.N255I|ARHGAP11A_ENST00000567348.1_Missense_Mutation_p.N444I|ARHGAP11A_ENST00000543522.1_Missense_Mutation_p.N255I|ARHGAP11A_ENST00000563864.1_Missense_Mutation_p.N416I	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	444					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)		CTAGGGAAAAATGGCAGAGAA	0.353																																					p.N444I	Colon(45;757 1134 30003 36652)	Atlas-SNP	.											.	ARHGAP11A	84	.	0			c.A1331T						PASS	.						36	35	35					15																	32926229		2201	4300	6501	SO:0001583	missense	9824	exon10			GGAAAAATGGCAG	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.1331A>T	15.37:g.32926229A>T	ENSP00000355090:p.Asn444Ile	282	0	0		237	48	0.202532	NM_199357	B4DZN9|Q6PI96|Q9Y3S6	Missense_Mutation	SNP	ENST00000361627.3	37	CCDS10028.1	.	.	.	.	.	.	.	.	.	.	.	17.09	3.300482	0.60195	.	.	ENSG00000198826	ENST00000361627;ENST00000543522	T	0.10288	2.89	5.51	-3.26	0.05064	.	0.454459	0.22141	N	0.064049	T	0.15478	0.0373	L	0.44542	1.39	0.32060	N	0.595807	P;D	0.57571	0.901;0.98	B;P	0.54312	0.296;0.748	T	0.06844	-1.0804	10	0.87932	D	0	.	13.7577	0.62946	0.3388:0.0:0.6612:0.0	.	444;255	Q6P4F7;B4DZN9	RHGBA_HUMAN;.	I	444;255	ENSP00000355090:N444I	ENSP00000355090:N444I	N	+	2	0	ARHGAP11A	30713521	1.000000	0.71417	0.899000	0.35326	0.825000	0.46686	1.904000	0.39868	-0.528000	0.06366	-0.290000	0.09829	AAT	.	.	none		0.353	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783		T	32926229	A	T	32926229	3	4	15	1	0	0	0	0	1	0	0	0	863	101	4	5	1369	5	ARHGAP11A	15	32926229	Missense_Mutation	SNP	A	TCGA-FF-8061-01A-11D-2210-10	6957082	32926229	69605163	114	2035											
B2M	567	hgsc.bcm.edu	37	chr15	45003779	45003779	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggccttagctgtgctcgcgcTactctctctttctggcctgg	2	14	11	14	2	3	0	0	0	3	0	5	0	3	0	2	3	3	3	2	3	2	3			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr15:45003779T>C	ENST00000558401.1	+	1	105	c.35T>C	c.(34-36)cTa>cCa	p.L12P	PATL2_ENST00000558573.1_5'Flank|B2M_ENST00000559916.1_Missense_Mutation_p.L12P|B2M_ENST00000544417.1_Missense_Mutation_p.L12P	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	12					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 exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|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 T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|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)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)	p.A11fs*42(1)|p.L12Q(1)		breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		GTGCTCGCGCTACTCTCTCTT	0.617																																					p.L12P		Atlas-SNP	.											B2M,colon,carcinoma,0,2	B2M	99	2	2	Substitution - Missense(1)|Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(2)	c.T35C						PASS	.						132	94	107					15																	45003779		2198	4298	6496	SO:0001583	missense	567	exon1			TCGCGCTACTCTC	AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"Immunoglobulin superfamily / C1-set domain containing"	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.35T>C	15.37:g.45003779T>C	ENSP00000452780:p.Leu12Pro	104	0	0		99	76	0.767677	NM_004048	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Missense_Mutation	SNP	ENST00000558401.1	37	CCDS10113.1	.	.	.	.	.	.	.	.	.	.	T	17.66	3.443926	0.63067	.	.	ENSG00000166710	ENST00000349264;ENST00000544417;ENST00000396754	T	0.01388	4.95	5.35	5.35	0.76521	.	9.011740	0.00721	U	0.000881	T	0.10809	0.0264	M	0.74647	2.275	0.29321	N	0.867335	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	T	0.17107	-1.0380	10	0.87932	D	0	.	11.9001	0.52678	0.0:0.0:0.0:1.0	.	12;12;12	F5H6I0;A6XMH4;P61769	.;.;B2MG_HUMAN	P	12	ENSP00000437604:L12P	ENSP00000340858:L12P	L	+	2	0	B2M	42791071	0.253000	0.23982	0.051000	0.19133	0.007000	0.05969	3.556000	0.53734	2.371000	0.80710	0.533000	0.62120	CTA	.	.	none		0.617	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048		C	45003779	T	C	45003779	3	2	15	1	0	0	0	0	1	0	0	0	1244	1522	53	3	37	3	B2M	15	45003779	Missense_Mutation	SNP	T	TCGA-FF-8061-01A-11D-2210-10	12077550	45003779	57527613	115	2036											
TLN2	83660	hgsc.bcm.edu	37	chr15	63017221	63017221	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aatcgattcagctctgaataCggtgcagacgcttaagaatg	13	10	10	8	3	2	3	1	1	1	2	3	4	2	3	0	1	3	3	0	1	5	3			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr15:63017221C>T	ENST00000561311.1	+	26	3403	c.3173C>T	c.(3172-3174)aCg>aTg	p.T1058M	TLN2_ENST00000306829.6_Missense_Mutation_p.T1058M			Q9Y4G6	TLN2_HUMAN	talin 2	1058	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						GCTCTGAATACGGTGCAGACG	0.527																																					p.T1058M		Atlas-SNP	.											.	TLN2	253	.	0			c.C3173T						PASS	.						72	68	69					15																	63017221		2203	4300	6503	SO:0001583	missense	83660	exon24			TGAATACGGTGCA	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.3173C>T	15.37:g.63017221C>T	ENSP00000453508:p.Thr1058Met	36	0	0		37	31	0.837838	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	37	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	C	10.97	1.501273	0.26861	.	.	ENSG00000171914	ENST00000306829	T	0.67865	-0.29	5.54	5.54	0.83059	.	0.136037	0.64402	D	0.000002	T	0.54208	0.1844	N	0.17082	0.46	0.39663	D	0.970632	B	0.22746	0.074	B	0.14578	0.011	T	0.50285	-0.8846	10	0.40728	T	0.16	-16.3734	19.8379	0.96666	0.0:1.0:0.0:0.0	.	1058	Q9Y4G6	TLN2_HUMAN	M	1058	ENSP00000303476:T1058M	ENSP00000303476:T1058M	T	+	2	0	TLN2	60804513	0.998000	0.40836	0.927000	0.36925	0.015000	0.08874	4.850000	0.62889	2.765000	0.95021	0.655000	0.94253	ACG	.	.	none		0.527	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			T	63017221	C	T	63017221	3	4	15	1	0	0	0	0	1	0	0	0	15963	536	19	1	3267	1	TLN2	15	63017221	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	18013442	63017221	39514171	116	2037											
CPLX3	594855	hgsc.bcm.edu	37	chr15	75119053	75119053	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggcgaagaccatggcgttCatggtgaagaccatggtggg	9	7	16	9	3	1	3	1	1	0	2	1	4	1	3	3	5	0	1	3	5	2	1			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr15:75119053C>A	ENST00000395018.4	+	1	166	c.9C>A	c.(7-9)ttC>ttA	p.F3L	RP11-414J4.2_ENST00000564823.1_RNA	NM_001030005.2	NP_001025176.1	Q8WVH0	CPLX3_HUMAN	complexin 3	3					insulin secretion (GO:0030073)|regulation of neurotransmitter secretion (GO:0046928)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|synapse (GO:0045202)	neurotransmitter transporter activity (GO:0005326)			large_intestine(2)|lung(2)	4						CCATGGCGTTCATGGTGAAGA	0.672																																					p.F3L		Atlas-SNP	.											.	CPLX3	12	.	0			c.C9A						PASS	.						36	40	39					15																	75119053		2197	4295	6492	SO:0001583	missense	594855	exon1			GGCGTTCATGGTG	BC018026	CCDS32294.1	15q24.1	2005-08-09			ENSG00000213578	ENSG00000213578			27652	protein-coding gene	gene with protein product		609585				15911881	Standard	NM_001030005		Approved	CPX-III	uc002ayu.1	Q8WVH0	OTTHUMG00000142816	ENST00000395018.4:c.9C>A	15.37:g.75119053C>A	ENSP00000378464:p.Phe3Leu	26	0	0		55	45	0.818182	NM_001030005	D3DW66|Q8TEM6|Q9H818	Missense_Mutation	SNP	ENST00000395018.4	37	CCDS32294.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.225855	0.79576	.	.	ENSG00000213578	ENST00000395018	.	.	.	4.3	3.38	0.38709	.	0.000000	0.64402	U	0.000001	T	0.75057	0.3798	M	0.71036	2.16	0.41174	D	0.986185	D	0.57257	0.979	D	0.71414	0.973	T	0.75227	-0.3392	9	0.66056	D	0.02	-10.3249	10.8632	0.46839	0.0:0.8306:0.0:0.1694	.	3	Q8WVH0	CPLX3_HUMAN	L	3	.	ENSP00000378464:F3L	F	+	3	2	CPLX3	72906106	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	1.306000	0.33505	0.461000	0.27071	-1.164000	0.01763	TTC	.	.	none		0.672	CPLX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286402.2	NM_001030005		A	75119053	C	A	75119053	3	1	15	1	0	0	0	0	1	0	0	0	3808	825	29	4	11	4	CPLX3	15	75119053	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	12101832	75119053	27412339	117	2038											
GP2	2813	hgsc.bcm.edu	37	chr16	20329589	20329589	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttcctcaacaccaggttaaAccgggaggtgtccccttgtt	8	11	10	12	1	1	0	1	0	0	0	3	1	3	1	5	3	2	3	5	3	3	4			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr16:20329589A>C	ENST00000381362.4	-	8	1256	c.1180T>G	c.(1180-1182)Ttt>Gtt	p.F394V	GP2_ENST00000302555.5_Missense_Mutation_p.F391V|GP2_ENST00000381360.5_Missense_Mutation_p.F247V|GP2_ENST00000341642.5_Missense_Mutation_p.F244V|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)	394	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				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						ACCAGGTTAAACCGGGAGGTG	0.498																																					p.F394V		Atlas-SNP	.											.	GP2	122	.	0			c.T1180G						PASS	.						203	164	178					16																	20329589		2203	4300	6503	SO:0001583	missense	2813	exon8			GGTTAAACCGGGA	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.1180T>G	16.37:g.20329589A>C	ENSP00000370767:p.Phe394Val	199	0	0		184	37	0.201087	NM_001007240	A6NFM9|A6NJA8|Q13338|Q9UIF1	Missense_Mutation	SNP	ENST00000381362.4	37	CCDS42128.1	.	.	.	.	.	.	.	.	.	.	A	16.89	3.246113	0.59103	.	.	ENSG00000169347	ENST00000302555;ENST00000381362;ENST00000381360;ENST00000341642;ENST00000537520	D;D;D;D	0.83419	-1.72;-1.72;-1.72;-1.72	5.8	4.69	0.59074	Endoglin/CD105 antigen conserved site (1);Endoglin/CD105 antigen subgroup (1);Zona pellucida sperm-binding protein (3);	.	.	.	.	D	0.91620	0.7352	M	0.90595	3.13	0.09310	N	0.999993	D;D;D;D	0.89917	0.999;1.0;1.0;0.999	D;D;D;D	0.85130	0.987;0.997;0.997;0.995	D	0.83676	0.0169	9	0.41790	T	0.15	-14.0034	10.2265	0.43229	0.9209:0.0:0.0791:0.0	.	244;372;391;394	P55259-4;B7Z1G2;P55259-3;P55259	.;.;.;GP2_HUMAN	V	391;394;247;244;372	ENSP00000304044:F391V;ENSP00000370767:F394V;ENSP00000370765:F247V;ENSP00000343861:F244V	ENSP00000304044:F391V	F	-	1	0	GP2	20237090	0.853000	0.29707	0.007000	0.13788	0.754000	0.42855	1.836000	0.39191	0.989000	0.38761	0.528000	0.53228	TTT	.	.	none		0.498	GP2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436920.1	NM_016295		C	20329589	A	C	20329589	3	2	15	1	0	0	0	0	1	0	0	0	6590	43	2	5	453	5	GP2	16	20329589	Missense_Mutation	SNP	A	TCGA-FF-8061-01A-11D-2210-10		20329589	70025164	118	2039											
PRKCB	5579	hgsc.bcm.edu	37	chr16	24183630	24183630	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tggagtacgtgaatgggggcGacctcatgtatcacatccag	10	9	13	9	2	2	1	2	1	0	0	3	3	3	2	2	3	1	2	2	3	3	2			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr16:24183630G>A	ENST00000321728.7	+	11	1454	c.1279G>A	c.(1279-1281)Gac>Aac	p.D427N	PRKCB_ENST00000303531.7_Missense_Mutation_p.D427N	NM_212535.2	NP_997700.1	P05771	KPCB_HUMAN	protein kinase C, beta	427	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)	GAATGGGGGCGACCTCATGTA	0.527																																					p.D427N		Atlas-SNP	.											PRKCB_ENST00000321728,caecum,carcinoma,0,3	PRKCB	383	3	0			c.G1279A						scavenged	.						125	103	110					16																	24183630		2197	4300	6497	SO:0001583	missense	5579	exon11			GGGGGCGACCTCA	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.1279G>A	16.37:g.24183630G>A	ENSP00000318315:p.Asp427Asn	193	1	0.00518135		170	59	0.347059	NM_212535	C5IFJ8|D3DWF5|O43744|P05127|Q15138|Q93060|Q9UE49|Q9UE50|Q9UEH8|Q9UJ30|Q9UJ33	Missense_Mutation	SNP	ENST00000321728.7	37	CCDS10618.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.795660	0.90453	.	.	ENSG00000166501	ENST00000321728;ENST00000303531	T;T	0.27402	1.67;1.67	5.25	5.25	0.73442	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	0.56093	0.1962	M	0.69358	2.11	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.58521	-0.7622	10	0.87932	D	0	.	18.1787	0.89769	0.0:0.0:1.0:0.0	.	427;427	P05771-2;P05771	.;KPCB_HUMAN	N	427	ENSP00000318315:D427N;ENSP00000305355:D427N	ENSP00000305355:D427N	D	+	1	0	PRKCB	24091131	1.000000	0.71417	0.958000	0.39756	0.462000	0.32619	9.768000	0.98965	2.606000	0.88127	0.557000	0.71058	GAC	.	.	none		0.527	PRKCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254504.2	NM_212535		A	24183630	G	A	24183630	3	1	15	1	0	0	0	0	1	0	0	0	12520	1058	37	1	1321	1	PRKCB	16	24183630	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	3854041	24183630	66171123	119	2040											
RPGRIP1L	23322	hgsc.bcm.edu	37	chr16	53730084	53730084	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttaattttatcctcctgcTtgcgggcatgctgtttaagt	6	19	8	8	1	0	0	0	0	0	0	2	0	2	0	2	1	3	4	2	1	3	7			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr16:53730084T>G	ENST00000379925.3	-	3	259	c.209A>C	c.(208-210)aAg>aCg	p.K70T	RPGRIP1L_ENST00000262135.4_Missense_Mutation_p.K70T|RPGRIP1L_ENST00000564374.1_Missense_Mutation_p.K70T|RPGRIP1L_ENST00000568653.3_Missense_Mutation_p.K70T|RPGRIP1L_ENST00000563746.1_Missense_Mutation_p.K70T|RPGRIP1L_ENST00000566096.1_Missense_Mutation_p.K70T	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	70					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)				ATCCTCCTGCTTGCGGGCATG	0.368																																					p.K70T		Atlas-SNP	.											.	RPGRIP1L	118	.	0			c.A209C						PASS	.						118	123	121					16																	53730084		2198	4300	6498	SO:0001583	missense	23322	exon3			TCCTGCTTGCGGG		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.209A>C	16.37:g.53730084T>G	ENSP00000369257:p.Lys70Thr	86	0	0		80	37	0.4625	NM_001127897	A0PJ88|Q9Y2K8	Missense_Mutation	SNP	ENST00000379925.3	37	CCDS32447.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.313073	0.81358	.	.	ENSG00000103494	ENST00000379925;ENST00000262135	T;T	0.68765	-0.35;-0.35	5.73	5.73	0.89815	.	0.052346	0.64402	D	0.000001	T	0.78729	0.4329	L	0.58969	1.84	0.48236	D	0.999616	D;D;P;D	0.76494	0.991;0.991;0.5;0.999	P;P;B;D	0.70716	0.894;0.776;0.173;0.97	T	0.79308	-0.1857	10	0.51188	T	0.08	-19.9813	16.0142	0.80425	0.0:0.0:0.0:1.0	.	70;70;70;70	B4E3M8;B7ZKJ9;Q68CZ1;Q68CZ1-2	.;.;FTM_HUMAN;.	T	70	ENSP00000369257:K70T;ENSP00000262135:K70T	ENSP00000262135:K70T	K	-	2	0	RPGRIP1L	52287585	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.371000	0.73119	2.187000	0.69744	0.460000	0.39030	AAG	.	.	none		0.368	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272		G	53730084	T	G	53730084	3	3	15	1	0	0	0	0	1	0	0	0	13565	1609	56	5	3838	5	RPGRIP1L	16	53730084	Missense_Mutation	SNP	T	TCGA-FF-8061-01A-11D-2210-10	29546454	53730084	36624669	120	2041											
ZFHX3	463	hgsc.bcm.edu	37	chr16	72830766	72830766	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggtggcgttccctctggcatCtgaagcaatgcgtggaggga	7	9	16	9	2	2	1	0	1	2	0	3	3	3	3	1	5	2	3	1	5	2	1			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr16:72830766C>T	ENST00000268489.5	-	9	6487	c.5815G>A	c.(5815-5817)Gat>Aat	p.D1939N	ZFHX3_ENST00000397992.5_Missense_Mutation_p.D1025N	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	1939					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)				CCTCTGGCATCTGAAGCAATG	0.517																																					p.D1939N		Atlas-SNP	.											ZFHX3,NS,carcinoma,0,1	ZFHX3	404	1	0			c.G5815A						PASS	.						97	96	97					16																	72830766		2198	4300	6498	SO:0001583	missense	463	exon9			TGGCATCTGAAGC	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.5815G>A	16.37:g.72830766C>T	ENSP00000268489:p.Asp1939Asn	135	0	0		130	49	0.376923	NM_006885	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	37	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	C	17.54	3.416295	0.62511	.	.	ENSG00000140836	ENST00000268489;ENST00000397992	T;T	0.74632	-0.86;-0.85	5.73	5.73	0.89815	.	0.000000	0.49916	D	0.000137	T	0.78323	0.4265	L	0.39898	1.24	0.80722	D	1	D	0.60575	0.988	P	0.57204	0.815	T	0.72701	-0.4214	10	0.21014	T	0.42	.	19.9064	0.97008	0.0:1.0:0.0:0.0	.	1939	Q15911	ZFHX3_HUMAN	N	1939;1025	ENSP00000268489:D1939N;ENSP00000438926:D1025N	ENSP00000268489:D1939N	D	-	1	0	ZFHX3	71388267	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	7.810000	0.86072	2.693000	0.91896	0.655000	0.94253	GAT	.	.	none		0.517	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		T	72830766	C	T	72830766	3	4	15	1	0	0	0	0	1	0	0	0	17649	913	32	2	5304	2	ZFHX3	16	72830766	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	19100682	72830766	17523987	121	2042											
CDH13	1012	hgsc.bcm.edu	37	chr16	83813610	83813610	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcactgggactttgctgatAaccctggaggacgtgaatga	10	9	14	8	1	0	3	0	3	0	0	0	6	0	6	1	4	2	2	1	4	2	2			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr16:83813610A>G	ENST00000566620.1	+	12	2009	c.1719A>G	c.(1717-1719)atA>atG	p.I573M	CDH13_ENST00000268613.10_Missense_Mutation_p.I620M|CDH13_ENST00000428848.3_Missense_Mutation_p.I534M	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	573	Cadherin 4. {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)		CTTTGCTGATAACCCTGGAGG	0.488																																					p.I620M		Atlas-SNP	.											.	CDH13	97	.	0			c.A1860G						PASS	.						92	86	88					16																	83813610		1936	4181	6117	SO:0001583	missense	1012	exon13			GCTGATAACCCTG	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.1719A>G	16.37:g.83813610A>G	ENSP00000454435:p.Ile573Met	89	0	0		80	17	0.2125	NM_001220488	A8W476|A8W477|B7Z590|C9JRI6|J3KN62|Q6GTW4|Q8TBX3	Missense_Mutation	SNP	ENST00000566620.1	37	CCDS58486.1	.	.	.	.	.	.	.	.	.	.	A	14.93	2.681211	0.47886	.	.	ENSG00000140945	ENST00000268613;ENST00000428848;ENST00000536143;ENST00000538855;ENST00000539548;ENST00000540531	T	0.61040	0.14	5.52	-11.0	0.00169	Cadherin (5);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.73690	0.3619	M	0.92077	3.27	0.80722	D	1	D;D;D	0.58970	0.971;0.971;0.984	P;P;P	0.62435	0.868;0.902;0.813	D	0.88936	0.3376	9	0.87932	D	0	.	14.1687	0.65495	0.1048:0.6952:0.0618:0.1382	.	534;620;573	B7Z590;B7Z9B1;P55290	.;.;CAD13_HUMAN	M	620;573;534;275;132;263	ENSP00000268613:I620M	ENSP00000268613:I620M	I	+	3	3	CDH13	82371111	0.000000	0.05858	0.159000	0.22649	0.522000	0.34438	-2.440000	0.01016	-3.003000	0.00275	-1.236000	0.01555	ATA	.	.	none		0.488	CDH13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432917.1	NM_001257		G	83813610	A	G	83813610	3	3	15	1	0	0	0	0	1	0	0	0	3101	352	13	3	1765	3	CDH13	16	83813610	Missense_Mutation	SNP	A	TCGA-FF-8061-01A-11D-2210-10	10982844	83813610	6541143	122	2043											
ALOX15	246	hgsc.bcm.edu	37	chr17	4544856	4544856	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcccgagcgccgcctcccCgtgctggccgaccagccaca	5	5	10	21	5	0	0	0	0	0	0	2	2	2	0	8	1	3	1	8	1	0	1	rs145573801	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr17:4544856C>T	ENST00000570836.1	-	2	187	c.91G>A	c.(91-93)Ggg>Agg	p.G31R	ALOX15_ENST00000545513.1_Missense_Mutation_p.G53R|ALOX15_ENST00000293761.3_Missense_Mutation_p.G31R|ALOX15_ENST00000574640.1_Missense_Mutation_p.G31R			P16050	LOX15_HUMAN	arachidonate 15-lipoxygenase	31	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				apoptotic cell clearance (GO:0043277)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|cellular response to calcium ion (GO:0071277)|cellular response to interleukin-13 (GO:0035963)|hepoxilin biosynthetic process (GO:0051122)|inflammatory response (GO:0006954)|leukotriene metabolic process (GO:0006691)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxygenase pathway (GO:0019372)|negative regulation of adaptive immune response (GO:0002820)|ossification (GO:0001503)|phosphatidylethanolamine biosynthetic process (GO:0006646)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of engulfment of apoptotic cell (GO:1901074)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|lipid particle (GO:0005811)|membrane (GO:0016020)|plasma membrane (GO:0005886)	arachidonate 12-lipoxygenase activity (GO:0004052)|arachidonate 15-lipoxygenase activity (GO:0050473)|eoxin A4 synthase activity (GO:0097260)|iron ion binding (GO:0005506)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(5)	20				READ - Rectum adenocarcinoma(115;0.0327)		GCCGCCTCCCCGTGCTGGCCG	0.687																																					p.G31R		Atlas-SNP	.											.	ALOX15	70	.	0			c.G91A						PASS	.						23	23	23					17																	4544856		2194	4291	6485	SO:0001583	missense	246	exon1			CCTCCCCGTGCTG	M23892	CCDS11049.1	17p13.3	2010-09-24			ENSG00000161905	ENSG00000161905	1.13.11.33	"Arachidonate lipoxygenases"	433	protein-coding gene	gene with protein product		152392				1570320	Standard	NM_001140		Approved	15-LOX-1	uc002fyh.3	P16050	OTTHUMG00000090746	ENST00000570836.1:c.91G>A	17.37:g.4544856C>T	ENSP00000458832:p.Gly31Arg	60	0	0		95	5	0.0526316	NM_001140	A8K2P4|B7ZA11|Q8N6R7|Q99657	Missense_Mutation	SNP	ENST00000570836.1	37	CCDS11049.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.133041	0.77662	.	.	ENSG00000161905	ENST00000293761;ENST00000545513	T;T	0.73047	-0.71;-0.71	5.33	2.14	0.27477	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	0.071907	0.53938	D	0.000048	T	0.69486	0.3116	L	0.60904	1.88	0.37169	D	0.902979	D;P;D	0.60160	0.987;0.792;0.972	B;B;P	0.47206	0.406;0.176;0.541	T	0.72858	-0.4165	10	0.42905	T	0.14	-18.9916	13.5218	0.61572	0.0:0.5739:0.4261:0.0	.	53;31;31	F5H0G8;B7ZA11;P16050	.;.;LOX15_HUMAN	R	31;53	ENSP00000293761:G31R;ENSP00000439855:G53R	ENSP00000293761:G31R	G	-	1	0	ALOX15	4491605	0.682000	0.27624	0.783000	0.31826	0.940000	0.58332	0.928000	0.28831	0.218000	0.20820	0.655000	0.94253	GGG	C|1.000;G|0.000	.	alt		0.687	ALOX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207487.2			T	4544856	C	T	4544856	3	4	15	1	0	0	0	0	1	0	0	0	538	652	23	1	1953	1	ALOX15	17	4544856	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10		4544856	76650354	123	2044											
PITPNM3	83394	hgsc.bcm.edu	37	chr17	6358850	6358850	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcaggaactctggctgcgcGtgcagcccgaagctgccctt	6	7	13	15	4	1	0	0	0	1	0	1	2	1	1	2	2	6	4	2	2	2	1			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr17:6358850G>A	ENST00000262483.8	-	20	2820	c.2733C>T	c.(2731-2733)caC>caT	p.H911H	PITPNM3_ENST00000576664.1_5'UTR|PITPNM3_ENST00000421306.3_Silent_p.H875H	NM_031220.3	NP_112497.2	Q9BZ71	PITM3_HUMAN	PITPNM family member 3	911					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)		CTGGCTGCGCGTGCAGCCCGA	0.697																																					p.H911H		Atlas-SNP	.											.	PITPNM3	91	.	0			c.C2733T						PASS	.						23	27	26					17																	6358850		2195	4299	6494	SO:0001819	synonymous_variant	83394	exon20			CTGCGCGTGCAGC	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.2733C>T	17.37:g.6358850G>A		42	0	0		42	16	0.380952	NM_031220	A1A5D0|F8WEW5|Q59GH9|Q9NPQ4	Silent	SNP	ENST00000262483.8	37	CCDS11076.1																																																																																			.	.	none		0.697	PITPNM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219824.2	NM_031220		A	6358850	G	A	6358850	2	1	15	1	0	0	0	0	0	0	0	1	11961	1136	40	1		1	PITPNM3	17	6358850	Silent	SNP	G	TCGA-FF-8061-01A-11D-2210-10	1813994	6358850	74836360	124	2045											
CDRT1	374286	hgsc.bcm.edu	37	chr17	15519066	15519066	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agacttgtgaggtcgcagacTtggagctgtggtctttctca	7	13	13	8	1	2	3	1	1	2	2	4	4	2	4	0	3	1	2	0	3	0	3			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr17:15519066T>G	ENST00000395906.3	-	2	562	c.563A>C	c.(562-564)aAg>aCg	p.K188T	RP11-385D13.1_ENST00000455584.2_Missense_Mutation_p.K498T	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	188										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)		GGTCGCAGACTTGGAGCTGTG	0.483																																					p.K188T		Atlas-SNP	.											.	CDRT1	83	.	0			c.A563C						PASS	.						55	56	56					17																	15519066		2200	4278	6478	SO:0001583	missense	374286	exon2			GCAGACTTGGAGC	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.563A>C	17.37:g.15519066T>G	ENSP00000379242:p.Lys188Thr	208	0	0		231	18	0.0779221	NM_006382	O43848|O95611	Missense_Mutation	SNP	ENST00000395906.3	37	CCDS45619.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	4.808|4.808	0.150194|0.150194	0.09185|0.09185	.|.	.|.	ENSG00000251537|ENSG00000251537	ENST00000261644;ENST00000395906|ENST00000455584	T|.	0.23950|.	1.88|.	3.68|3.68	-5.28|-5.28	0.02755|0.02755	.|.	0.556354|.	0.17795|.	N|.	0.161741|.	T|T	0.12008|0.12008	0.0292|0.0292	N|N	0.03115|0.03115	-0.41|-0.41	0.09310|0.09310	N|N	1|1	B;B|.	0.12013|.	0.005;0.002|.	B;B|.	0.08055|.	0.003;0.001|.	T|T	0.30679|0.30679	-0.9970|-0.9970	10|5	0.27082|.	T|.	0.32|.	.|.	7.1977|7.1977	0.25862|0.25862	0.2497:0.0:0.5367:0.2136|0.2497:0.0:0.5367:0.2136	.|.	188;512|.	O95170;Q59EB2|.	CDRT1_HUMAN;.|.	T|R	188|513	ENSP00000379242:K188T|.	ENSP00000261644:K188T|.	K|S	-|-	2|1	0|0	RP11-385D13.1|RP11-385D13.1	15459791|15459791	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.005000|0.005000	0.04900|0.04900	0.192000|0.192000	0.17096|0.17096	-1.167000|-1.167000	0.02779|0.02779	-0.501000|-0.501000	0.04562|0.04562	AAG|AGT	.	.	none		0.483	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382		G	15519066	T	G	15519066	3	3	15	1	0	0	0	0	1	0	0	0	3176	1609	56	5	1739	5	CDRT1	17	15519066	Missense_Mutation	SNP	T	TCGA-FF-8061-01A-11D-2210-10	9160216	15519066	65676144	125	2046											
TLCD1	116238	hgsc.bcm.edu	37	chr17	27052991	27052991	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gcaggttgtgccagcgccagGtgcgcagggggtcggcgcgc	4	5	20	12	5	0	0	0	0	0	0	1	0	0	0	2	5	3	3	2	5	0	1			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr17:27052991G>A	ENST00000292090.3	-	1	235	c.125C>T	c.(124-126)aCc>aTc	p.T42I	AC010761.14_ENST00000587898.1_RNA|NEK8_ENST00000268766.6_5'Flank|TLCD1_ENST00000394933.3_Intron|SNORD42A_ENST00000459584.1_RNA|SNORD4B_ENST00000459083.1_RNA	NM_138463.3	NP_612472.1	Q96CP7	TLCD1_HUMAN	TLC domain containing 1	42	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(2)|lung(2)	7	Lung NSC(42;0.00431)					CCAGCGCCAGGTGCGCAGGGG	0.697																																					p.T42I		Atlas-SNP	.											.	TLCD1	15	.	0			c.C125T						PASS	.						22	23	22					17																	27052991		2201	4298	6499	SO:0001583	missense	116238	exon1			CGCCAGGTGCGCA	BC014072	CCDS11242.1, CCDS54102.1	17q11.2	2007-03-23			ENSG00000160606	ENSG00000160606			25177	protein-coding gene	gene with protein product						12151215	Standard	NM_138463		Approved		uc002hco.3	Q96CP7	OTTHUMG00000132683	ENST00000292090.3:c.125C>T	17.37:g.27052991G>A	ENSP00000292090:p.Thr42Ile	60	0	0		63	4	0.0634921	NM_138463	A8MYP9	Missense_Mutation	SNP	ENST00000292090.3	37	CCDS11242.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.480642	0.84747	.	.	ENSG00000160606	ENST00000292090	.	.	.	4.6	4.6	0.57074	TRAM/LAG1/CLN8 homology domain (2);	0.205916	0.42821	D	0.000648	T	0.41465	0.1160	N	0.19112	0.55	0.80722	D	1	B	0.26744	0.158	B	0.20767	0.031	T	0.39035	-0.9633	9	0.49607	T	0.09	-2.0919	12.7767	0.57453	0.0:0.0:1.0:0.0	.	42	Q96CP7	TLCD1_HUMAN	I	42	.	ENSP00000292090:T42I	T	-	2	0	TLCD1	24077118	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.514000	0.45503	2.385000	0.81259	0.555000	0.69702	ACC	.	.	none		0.697	TLCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255973.1	NM_138463		A	27052991	G	A	27052991	3	1	15	1	0	0	0	0	1	0	0	0	15952	1261	44	2	634	2	TLCD1	17	27052991	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	11533925	27052991	54142219	126	2047											
ATAD5	79915	hgsc.bcm.edu	37	chr17	29221631	29221635	+	Frame_Shift_Del	DEL	TCTCT	TCTCT	-																															aaagtgtattttcgagtcgaTctcttctctatgtgggtaat																										TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	TCTCT	TCTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr17:29221631_29221635delTCTCT	ENST00000321990.4	+	22	5725_5729	c.5347_5351delTCTCT	c.(5347-5352)tctcttfs	p.SL1783fs	TEFM_ENST00000579183.1_5'Flank	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1783					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)				TTCGAGTCGATCTCTTCTCTATGTG	0.341																																					p.1782_1784del		Pindel,Atlas-Indel	.											.	ATAD5	150	.	0			c.5346_5350del						PASS	.																																			SO:0001589	frameshift_variant	79915	exon22			.		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.5347_5351delTCTCT	17.37:g.29221636_29221640delTCTCT	ENSP00000313171:p.Ser1783fs	65	0	.		55	14	0.255	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Frame_Shift_Del	DEL	ENST00000321990.4	37	CCDS11260.1																																																																																			.	.	none		0.341	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		-	29221635	TCTCT	-	29221631	7	5	15	1	0	1	0	1	0	0	0	0	1076	1435	50	0	5433	0	ATAD5	17	29221631	Frame_Shift_Del	DEL	TCTCT	TCGA-FF-8061-01A-11D-2210-10	2168640	29221631	51973579	127	2048											
MYO1D	4642	hgsc.bcm.edu	37	chr17	30932257	30932257	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggagacactcagaccagtCaactgcaaagagaaaatgca	17	6	9	9	0	2	3	2	0	0	3	2	5	2	3	1	1	3	2	1	1	4	1			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr17:30932257C>A	ENST00000318217.5	-	21	3016	c.2712G>T	c.(2710-2712)ttG>ttT	p.L904F	MYO1D_ENST00000579584.1_Missense_Mutation_p.L904F|MYO1D_ENST00000394649.4_Missense_Mutation_p.L816F	NM_015194.1	NP_056009.1	O94832	MYO1D_HUMAN	myosin ID	904	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)			TCAGACCAGTCAACTGCAAAG	0.418																																					p.L904F		Atlas-SNP	.											.	MYO1D	93	.	0			c.G2712T						PASS	.						92	81	85					17																	30932257		2203	4300	6503	SO:0001583	missense	4642	exon21			ACCAGTCAACTGC	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.2712G>T	17.37:g.30932257C>A	ENSP00000324527:p.Leu904Phe	119	0	0		103	43	0.417476	NM_015194	A6H8V3|Q8NHP9	Missense_Mutation	SNP	ENST00000318217.5	37	CCDS32615.1	.	.	.	.	.	.	.	.	.	.	C	12.32	1.903118	0.33628	.	.	ENSG00000176658	ENST00000318217;ENST00000394649	T	0.41400	1.0	4.94	3.92	0.45320	Myosin tail 2 (1);	0.000000	0.32503	U	0.006009	T	0.35537	0.0935	L	0.43923	1.385	0.80722	D	1	B;B	0.17852	0.014;0.024	B;B	0.19666	0.026;0.026	T	0.23511	-1.0186	10	0.87932	D	0	.	10.4809	0.44693	0.0:0.8966:0.0:0.1034	.	815;904	Q7Z3N6;O94832	.;MYO1D_HUMAN	F	904;96	ENSP00000324527:L904F	ENSP00000324527:L904F	L	-	3	2	MYO1D	27956370	1.000000	0.71417	1.000000	0.80357	0.647000	0.38526	1.952000	0.40343	1.124000	0.41980	-0.345000	0.07892	TTG	.	.	none		0.418	MYO1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447457.1			A	30932257	C	A	30932257	3	1	15	1	0	0	0	0	1	0	0	0	10080	825	29	4	316	4	MYO1D	17	30932257	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	1710626	30932257	50262953	128	2049											
KRTAP9-9	81870	hgsc.bcm.edu	37	chr17	39411694	39411694	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tgctgcaggaccacctgctgGaagcccaccactgtgaccac	9	6	10	16	0	0	1	0	1	0	0	0	3	0	3	5	2	4	3	5	2	1	0			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr17:39411694G>C	ENST00000394008.1	+	1	59	c.57G>C	c.(55-57)tgG>tgC	p.W19C		NM_030975.2	NP_112237.2	Q9BYP9	KRA99_HUMAN	keratin associated protein 9-9	24	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)			CCACCTGCTGGAAGCCCACCA	0.622																																					p.W19C		Atlas-SNP	.											KRTAP9-9,NS,carcinoma,+2,1	KRTAP9-9	24	1	0			c.G57C						scavenged	.																																			SO:0001583	missense	81870	exon1			CTGCTGGAAGCCC	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.57G>C	17.37:g.39411694G>C	ENSP00000377576:p.Trp19Cys	24	2	0.0833333		15	2	0.133333	NM_030975	B5MDD6|Q9BYQ1	Missense_Mutation	SNP	ENST00000394008.1	37	CCDS54127.1	.	.	.	.	.	.	.	.	.	.	.	0.100	-1.153249	0.01700	.	.	ENSG00000198083	ENST00000394008	T	0.00711	5.8	3.04	-5.55	0.02536	.	.	.	.	.	T	0.00210	0.0006	N	0.00152	-1.975	0.20196	N	0.999925	B	0.02656	0.0	B	0.04013	0.001	T	0.42865	-0.9426	9	0.02654	T	1	.	6.8781	0.24158	0.0:0.2867:0.1571:0.5562	.	24	Q9BYP9	KRA99_HUMAN	C	19	ENSP00000377576:W19C	ENSP00000377576:W19C	W	+	3	0	KRTAP9-9	36665220	0.000000	0.05858	0.005000	0.12908	0.435000	0.31806	-0.843000	0.04350	-1.036000	0.03287	0.456000	0.33151	TGG	.	.	none		0.622	KRTAP9-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257710.1	NM_030975		C	39411694	G	C	39411694	3	2	15	1	0	0	0	0	1	0	0	0	8586	1183	41	4	59	4	KRTAP9-9	17	39411694	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	8479437	39411694	41783516	129	2050											
GAST	2520	hgsc.bcm.edu	37	chr17	39872062	39872064	+	In_Frame_Del	DEL	GAA	GAA	-																															agcagggaccatggctggagGaagaagaagaagcctatgga																										TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr17:39872062_39872064delGAA	ENST00000329402.3	+	3	311_313	c.244_246delGAA	c.(244-246)gaadel	p.E85del	JUP_ENST00000540235.1_Intron|RNA5SP442_ENST00000365050.1_RNA	NM_000805.4	NP_000796.1	P01350	GAST_HUMAN	gastrin	85					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)			ATGGCTGGAGGAAGAAGAAGAAG	0.562																																					p.81_82del		Atlas-Indel	.											.	GAST	13	.	0			c.243_245del						PASS	.																																			SO:0001651	inframe_deletion	2520	exon3			.		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.244_246delGAA	17.37:g.39872071_39872073delGAA	ENSP00000331358:p.Glu85del	94	0	0		113	15	0.132743	NM_000805	P78463|P78464	In_Frame_Del	DEL	ENST00000329402.3	37	CCDS11404.1																																																																																			.	.	none		0.562	GAST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257409.1			-	39872064	GAA	-	39872062	7	5	15	1	0	1	0	1	0	0	0	0	6260	1175	41	0	250	0	GAST	17	39872062	In_Frame_Del	DEL	GAA	TCGA-FF-8061-01A-11D-2210-10	460368	39872062	41323148	130	2051											
STAT3	6774	hgsc.bcm.edu	37	chr17	40474470	40474470	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaatgacatgttgttcagcTgctgctttgtgtatggttcc	7	16	10	8	0	1	1	1	1	0	0	2	1	2	1	1	1	3	7	1	1	2	5			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr17:40474470T>C	ENST00000264657.5	-	21	2243	c.1931A>G	c.(1930-1932)cAg>cGg	p.Q644R	STAT3_ENST00000404395.3_Missense_Mutation_p.Q644R|STAT3_ENST00000585517.1_Missense_Mutation_p.Q644R|STAT3_ENST00000389272.3_Missense_Mutation_p.Q546R|STAT3_ENST00000588969.1_Missense_Mutation_p.Q644R	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)	644	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.		Missing (in AD-HIES). {ECO:0000269|PubMed:17881745}.		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)		GTTGTTCAGCTGCTGCTTTGT	0.458									Hyperimmunoglobulin E Recurrent Infection Syndrome																												p.Q644R		Atlas-SNP	.											.	STAT3	268	.	0			c.A1931G	GRCh37	CM083172	STAT3	M		PASS	.						255	223	234					17																	40474470		2203	4300	6503	SO:0001583	missense	6774	exon21	Familial Cancer Database	HIES, Hyper IgE syndrome, autosomal dominant (Job syndrome) / recessive	TTCAGCTGCTGCT	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.1931A>G	17.37:g.40474470T>C	ENSP00000264657:p.Gln644Arg	237	0	0		283	137	0.484099	NM_003150	A8K7B8|K7ENL3|O14916|Q9BW54	Missense_Mutation	SNP	ENST00000264657.5	37	CCDS32656.1	.	.	.	.	.	.	.	.	.	.	T	16.96	3.266403	0.59540	.	.	ENSG00000168610	ENST00000264657;ENST00000389272;ENST00000404395	D;D;D	0.88354	-2.37;-2.37;-2.37	4.64	4.64	0.57946	SH2 motif (4);	0.000000	0.85682	D	0.000000	D	0.87557	0.6207	N	0.11313	0.125	0.58432	D	0.999996	P;P;P	0.49559	0.908;0.925;0.925	D;D;D	0.67900	0.922;0.954;0.954	D	0.87438	0.2393	10	0.33141	T	0.24	-36.6451	14.2314	0.65895	0.0:0.0:0.0:1.0	.	644;644;644	P40763-2;P40763;B5BTZ6	.;STAT3_HUMAN;.	R	644;546;644	ENSP00000264657:Q644R;ENSP00000373923:Q546R;ENSP00000384943:Q644R	ENSP00000264657:Q644R	Q	-	2	0	STAT3	37727996	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	6.128000	0.71650	1.953000	0.56701	0.460000	0.39030	CAG	.	.	none		0.458	STAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319353.3	NM_139276, NM_003150		C	40474470	T	C	40474470	3	2	15	1	0	0	0	0	1	0	0	0	15281	1580	55	3	397	3	STAT3	17	40474470	Missense_Mutation	SNP	T	TCGA-FF-8061-01A-11D-2210-10	602408	40474470	40720740	131	2052			1	15		2	2	13	T		6.628396e-05
STAT3	6774	hgsc.bcm.edu	37	chr17	40474482	40474482	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgttcagctgctgctttgtgTatggttccacggactggatc	5	15	12	9	1	1	0	1	0	0	0	3	2	2	2	1	3	3	6	1	3	1	4			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	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_ENST00000585517.1_Missense_Mutation_p.Y640F|STAT3_ENST00000389272.3_Missense_Mutation_p.Y542F|STAT3_ENST00000588969.1_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	46	0			c.A1919T						PASS	.						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	17.37:g.40474482T>A	ENSP00000264657:p.Tyr640Phe	228	0	0		271	137	0.505535	NM_003150	A8K7B8|K7ENL3|O14916|Q9BW54	Missense_Mutation	SNP	ENST00000264657.5	37	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	.	.	none		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	15	1	0	0	0	0	1	0	0	0	15281	1638	57	5	409	5	STAT3	17	40474482	Missense_Mutation	SNP	T	TCGA-FF-8061-01A-11D-2210-10	12	40474482	40720728	132	2053			1	15		2	2	13	T		6.628396e-05
NGFR	4804	hgsc.bcm.edu	37	chr17	47572823	47572823	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccatggacgggccgcgccTgctgctgttgctgcttctgg	2	10	15	14	4	1	0	0	0	1	0	1	1	1	1	3	3	4	5	3	3	0	2			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr17:47572823T>C	ENST00000172229.3	+	1	169	c.44T>C	c.(43-45)cTg>cCg	p.L15P	NGFR_ENST00000504201.1_5'Flank	NM_002507.3	NP_002498.1	P08138	TNR16_HUMAN	nerve growth factor receptor	15					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)					GGGCCGCGCCTGCTGCTGTTG	0.711																																					p.L15P		Atlas-SNP	.											.	NGFR	46	.	0			c.T44C						PASS	.						4	7	6					17																	47572823		1842	3757	5599	SO:0001583	missense	4804	exon1			CGCGCCTGCTGCT	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.44T>C	17.37:g.47572823T>C	ENSP00000172229:p.Leu15Pro	7	0	0		13	5	0.384615	NM_002507	B2R961|B4E096	Missense_Mutation	SNP	ENST00000172229.3	37	CCDS11549.1	.	.	.	.	.	.	.	.	.	.	T	14.20	2.463454	0.43736	.	.	ENSG00000064300	ENST00000172229	D	0.91631	-2.88	4.54	4.54	0.55810	.	1.870110	0.02589	N	0.099734	D	0.90652	0.7068	N	0.24115	0.695	0.80722	D	1	P	0.48834	0.916	P	0.49140	0.601	T	0.80696	-0.1267	10	0.45353	T	0.12	-3.3729	10.5353	0.45000	0.0:0.0:0.0:1.0	.	15	P08138	TNR16_HUMAN	P	15	ENSP00000172229:L15P	ENSP00000172229:L15P	L	+	2	0	NGFR	44927822	1.000000	0.71417	1.000000	0.80357	0.465000	0.32709	3.325000	0.52030	1.804000	0.52760	0.443000	0.29094	CTG	.	.	none		0.711	NGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365150.1			C	47572823	T	C	47572823	3	2	15	1	0	0	0	0	1	0	0	0	10405	1580	55	3	46	3	NGFR	17	47572823	Missense_Mutation	SNP	T	TCGA-FF-8061-01A-11D-2210-10	7098341	47572823	33622387	133	2054											
LLGL2	3993	hgsc.bcm.edu	37	chr17	73552167	73552167	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gcaccagcccagcgccctcgGctacagcccgtccctgcgca	6	4	10	21	4	0	0	0	0	0	0	2	0	1	0	5	1	5	3	5	1	1	1			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr17:73552167G>A	ENST00000392550.3	+	3	233	c.116G>A	c.(115-117)gGc>gAc	p.G39D	LLGL2_ENST00000375227.4_Missense_Mutation_p.G39D|LLGL2_ENST00000578363.1_Missense_Mutation_p.G39D|LLGL2_ENST00000577200.1_Missense_Mutation_p.G39D|LLGL2_ENST00000167462.5_Missense_Mutation_p.G39D	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	39					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)			AGCGCCCTCGGCTACAGCCCG	0.687																																					p.G39D		Atlas-SNP	.											.	LLGL2	155	.	0			c.G116A						PASS	.						75	64	68					17																	73552167		2202	4300	6502	SO:0001583	missense	3993	exon3			CCCTCGGCTACAG	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.116G>A	17.37:g.73552167G>A	ENSP00000376333:p.Gly39Asp	28	0	0		50	24	0.48	NM_001015002	Q14521|Q9BR62	Missense_Mutation	SNP	ENST00000392550.3	37	CCDS32733.1	.	.	.	.	.	.	.	.	.	.	G	13.01	2.109326	0.37242	.	.	ENSG00000073350	ENST00000167462;ENST00000392550;ENST00000375227	T;T;T	0.61742	1.7;1.7;0.08	4.68	4.68	0.58851	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.051374	0.85682	D	0.000000	T	0.53465	0.1798	L	0.36672	1.1	0.49687	D	0.999815	B;B;B	0.27971	0.169;0.124;0.196	B;B;B	0.33799	0.049;0.049;0.17	T	0.56649	-0.7944	10	0.56958	D	0.05	-7.1885	17.7752	0.88505	0.0:0.0:1.0:0.0	.	39;39;39	Q6P1M3-2;Q6P1M3;Q6P1M3-3	.;L2GL2_HUMAN;.	D	39	ENSP00000167462:G39D;ENSP00000376333:G39D;ENSP00000364375:G39D	ENSP00000167462:G39D	G	+	2	0	LLGL2	71063762	1.000000	0.71417	1.000000	0.80357	0.670000	0.39368	3.755000	0.55197	2.431000	0.82371	0.563000	0.77884	GGC	.	.	none		0.687	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524		A	73552167	G	A	73552167	3	1	15	1	0	0	0	0	1	0	0	0	8843	1203	42	2	122	2	LLGL2	17	73552167	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	25979344	73552167	7643043	134	2055											
KIAA0802	23255	hgsc.bcm.edu	37	chr18	8806921	8806921	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accagcagctgttcagcgccTtcaaggccttgctggaggac	8	8	12	13	1	2	0	2	0	0	0	2	2	2	2	3	3	4	4	3	3	1	3			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr18:8806921T>C	ENST00000306329.11	+	9	3424	c.3424T>C	c.(3424-3426)Ttc>Ctc	p.F1142L	SOGA2_ENST00000359865.3_Missense_Mutation_p.F823L|SOGA2_ENST00000400050.3_Missense_Mutation_p.F782L|SOGA2_ENST00000306285.7_Missense_Mutation_p.F138L|SOGA2_ENST00000518815.1_Missense_Mutation_p.F138L|SOGA2_ENST00000517570.1_Missense_Mutation_p.F782L																							GTTCAGCGCCTTCAAGGCCTT	0.587																																					p.F823L		Atlas-SNP	.											CCDC165,NS,carcinoma,-2,1	.	.	1	0			c.T2467C						scavenged	.						70	61	64					18																	8806921		2203	4300	6503	SO:0001583	missense	23255	exon11			AGCGCCTTCAAGG																												ENST00000306329.11:c.3424T>C	18.37:g.8806921T>C	ENSP00000305027:p.Phe1142Leu	58	0	0		62	3	0.0483871	NM_015210		Missense_Mutation	SNP	ENST00000306329.11	37		.	.	.	.	.	.	.	.	.	.	T	0.201	-1.045061	0.01997	.	.	ENSG00000168502	ENST00000306329;ENST00000517570;ENST00000359865;ENST00000400050;ENST00000306285	T;T;T;T	0.21543	2.0;2.0;2.0;2.0	5.54	4.67	0.58626	.	0.145473	0.32444	N	0.006085	T	0.04543	0.0124	N	0.00621	-1.32	0.23704	N	0.997068	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.39418	-0.9615	10	0.02654	T	1	-19.4729	6.0193	0.19620	0.0:0.6353:0.1402:0.2244	.	1133;823	Q9Y4B5;Q9Y4B5-3	CC165_HUMAN;.	L	844;782;823;782;138	ENSP00000429556:F782L;ENSP00000352927:F823L;ENSP00000382924:F782L;ENSP00000303670:F138L	ENSP00000303670:F138L	F	+	1	0	CCDC165	8796921	0.802000	0.28943	0.123000	0.21794	0.132000	0.20833	1.531000	0.36018	1.461000	0.47929	-0.242000	0.12053	TTC	.	.	none		0.587	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1			C	8806921	T	C	8806921	3	2	15	1	0	0	0	0	1	0	0	0	8203	1609	56	3	2501	3	KIAA0802	18	8806921	Missense_Mutation	SNP	T	TCGA-FF-8061-01A-11D-2210-10		8806921	69270327	135	2056											
SERPINB10	5273	hgsc.bcm.edu	37	chr18	61600364	61600364	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaagccaaaagcagtgggccTtcaactctactacaaaagcc	16	6	7	12	0	2	0	1	0	1	0	2	0	2	0	3	1	6	1	3	1	8	3			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr18:61600364T>G	ENST00000238508.3	+	7	775	c.716T>G	c.(715-717)cTt>cGt	p.L239R		NM_005024.1	NP_005015.1	P48595	SPB10_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 10	239					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)				GCAGTGGGCCTTCAACTCTAC	0.383																																					p.L239R		Atlas-SNP	.											.	SERPINB10	53	.	0			c.T716G						PASS	.						118	130	126					18																	61600364		2203	4300	6503	SO:0001583	missense	5273	exon6			TGGGCCTTCAACT	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.716T>G	18.37:g.61600364T>G	ENSP00000238508:p.Leu239Arg	81	0	0		61	12	0.196721	NM_005024	Q4VAX4|Q4VAX7	Missense_Mutation	SNP	ENST00000238508.3	37	CCDS11990.1	.	.	.	.	.	.	.	.	.	.	T	16.41	3.116431	0.56505	.	.	ENSG00000242550	ENST00000238508	D	0.86694	-2.16	5.95	5.95	0.96441	Serpin domain (3);	0.219993	0.40385	N	0.001119	D	0.96175	0.8753	H	0.98646	4.29	0.47153	D	0.999333	D	0.89917	1.0	D	0.69824	0.966	D	0.97755	1.0217	10	0.87932	D	0	.	15.61	0.76707	0.0:0.0:0.0:1.0	.	239	P48595	SPB10_HUMAN	R	239	ENSP00000238508:L239R	ENSP00000238508:L239R	L	+	2	0	SERPINB10	59751344	0.981000	0.34729	0.564000	0.28396	0.115000	0.19883	5.005000	0.63972	2.282000	0.76494	0.533000	0.62120	CTT	.	.	none		0.383	SERPINB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134012.3	NM_005024		G	61600364	T	G	61600364	3	3	15	1	0	0	0	0	1	0	0	0	14112	1609	56	5	738	5	SERPINB10	18	61600364	Missense_Mutation	SNP	T	TCGA-FF-8061-01A-11D-2210-10	52793443	61600364	16476884	136	2057											
PARD6G	84552	hgsc.bcm.edu	37	chr18	77960661	77960661	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccttgcagaagttgtcatcaTtgttgatgggcagcaggtct	8	13	12	8	0	3	2	2	1	1	1	3	2	3	2	1	2	2	5	1	2	1	4			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr18:77960661T>C	ENST00000353265.3	-	2	424	c.227A>G	c.(226-228)aAt>aGt	p.N76S	PARD6G_ENST00000470488.2_Missense_Mutation_p.N76S|AC139100.3_ENST00000588950.1_RNA	NM_032510.3	NP_115899.1	Q9BYG4	PAR6G_HUMAN	par-6 family cell polarity regulator gamma	76	OPR.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	8		all_cancers(4;5.63e-22)|all_epithelial(4;5.86e-15)|all_lung(4;1.32e-05)|Ovarian(4;1.33e-05)|Lung NSC(4;2.77e-05)|Esophageal squamous(42;0.0157)|all_hematologic(56;0.13)|Melanoma(33;0.144)		Epithelial(2;1.48e-13)|all cancers(1;5.77e-13)|OV - Ovarian serous cystadenocarcinoma(15;2.74e-10)|BRCA - Breast invasive adenocarcinoma(31;0.00166)|STAD - Stomach adenocarcinoma(84;0.18)|Lung(128;0.23)		GTTGTCATCATTGTTGATGGG	0.498																																					p.N76S		Atlas-SNP	.											.	PARD6G	20	.	0			c.A227G						PASS	.						108	100	103					18																	77960661		2203	4300	6503	SO:0001583	missense	84552	exon2			TCATCATTGTTGA		CCDS12022.1	18q23	2013-08-28	2013-08-28		ENSG00000178184	ENSG00000178184			16076	protein-coding gene	gene with protein product		608976	"par-6 (partitioning defective 6, C.elegans) homolog gamma", "par-6 partitioning defective 6 homolog gamma (C. elegans)"			11260256	Standard	NM_032510		Approved	PAR-6G, PAR6gamma	uc002lny.3	Q9BYG4	OTTHUMG00000132922	ENST00000353265.3:c.227A>G	18.37:g.77960661T>C	ENSP00000343144:p.Asn76Ser	136	0	0		91	42	0.461538	NM_032510	A8QM57	Missense_Mutation	SNP	ENST00000353265.3	37	CCDS12022.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.311065	0.81358	.	.	ENSG00000178184	ENST00000353265	T	0.16324	2.35	5.43	5.43	0.79202	Phox/Bem1p (2);	0.000000	0.85682	D	0.000000	T	0.46464	0.1394	M	0.85197	2.74	0.80722	D	1	D;D	0.89917	0.992;1.0	P;D	0.91635	0.829;0.999	T	0.50355	-0.8838	9	.	.	.	-32.4304	14.5927	0.68378	0.0:0.0:0.0:1.0	.	76;76	A8QM57;Q9BYG4	.;PAR6G_HUMAN	S	76	ENSP00000343144:N76S	.	N	-	2	0	PARD6G	76061652	1.000000	0.71417	0.931000	0.37212	0.850000	0.48378	6.824000	0.75288	2.282000	0.76494	0.533000	0.62120	AAT	.	.	none		0.498	PARD6G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256435.2	NM_032510		C	77960661	T	C	77960661	3	2	15	1	0	0	0	0	1	0	0	0	11456	1493	52	3	911	3	PARD6G	18	77960661	Missense_Mutation	SNP	T	TCGA-FF-8061-01A-11D-2210-10	16360297	77960661	116587	137	2058											
ADAMTSL5	339366	hgsc.bcm.edu	37	chr19	1510692	1510692	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcccgcaggagctggagcagCgggtccaggacacccacggg	8	2	17	14	3	0	0	0	0	0	0	1	3	1	3	3	5	3	3	3	5	0	0	rs550092054		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:1510692C>T	ENST00000413997.2	-	3	166	c.167G>A	c.(166-168)cGc>cAc	p.R56H	ADAMTSL5_ENST00000330475.4_Missense_Mutation_p.R46H|ADAMTSL5_ENST00000590562.1_5'UTR|CTB-25B13.9_ENST00000590252.1_RNA|ADAMTSL5_ENST00000395467.2_5'UTR			Q6ZMM2	ATL5_HUMAN	ADAMTS-like 5	56	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)		GCTGGAGCAGCGGGTCCAGGA	0.741																																					p.R46H		Atlas-SNP	.											.	ADAMTSL5	24	.	0			c.G137A						PASS	.						4	4	4					19																	1510692		1835	3619	5454	SO:0001583	missense	339366	exon3			GAGCAGCGGGTCC	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.167G>A	19.37:g.1510692C>T	ENSP00000399364:p.Arg56His	27	0	0		43	16	0.372093	NM_213604	B4DXK7|Q8IW95	Missense_Mutation	SNP	ENST00000413997.2	37		.	.	.	.	.	.	.	.	.	.	C	16.83	3.230248	0.58777	.	.	ENSG00000185761	ENST00000413997;ENST00000330475	T;T	0.53206	0.63;0.63	3.43	1.08	0.20341	.	0.329393	0.27206	N	0.020425	T	0.30916	0.0780	N	0.11698	0.16	0.80722	D	1	D;D	0.63046	0.992;0.992	P;P	0.51918	0.684;0.594	T	0.14980	-1.0453	10	0.44086	T	0.13	.	2.1487	0.03794	0.1977:0.4922:0.1932:0.1169	.	56;46	B4DXK7;Q6ZMM2	.;ATL5_HUMAN	H	56;46	ENSP00000399364:R56H;ENSP00000327608:R46H	ENSP00000327608:R46H	R	-	2	0	ADAMTSL5	1461692	0.015000	0.18098	0.987000	0.45799	0.871000	0.50021	0.129000	0.15830	0.129000	0.18514	0.456000	0.33151	CGC	.	.	none		0.741	ADAMTSL5-202	KNOWN	basic	protein_coding	protein_coding		XM_294919		T	1510692	C	T	1510692	3	4	15	1	0	0	0	0	1	0	0	0	278	768	27	1	1318	1	ADAMTSL5	19	1510692	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10		1510692	57618291	138	2059											
MKNK2	2872	hgsc.bcm.edu	37	chr19	2041911	2041911	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcccacgaagggcgggtaGccgctgagtaggatatacaa	11	5	15	10	4	0	1	0	1	0	0	0	3	0	2	2	4	2	3	2	4	6	4			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:2041911G>A	ENST00000591601.1	-	10	908	c.873C>T	c.(871-873)ggC>ggT	p.G291G	MKNK2_ENST00000591142.1_Silent_p.G35G|MKNK2_ENST00000591588.1_Silent_p.G35G|MKNK2_ENST00000250896.3_Silent_p.G291G|MKNK2_ENST00000309340.7_Silent_p.G291G|MKNK2_ENST00000588014.1_Silent_p.G35G|MKNK2_ENST00000541165.1_Silent_p.G160G			Q9HBH9	MKNK2_HUMAN	MAP kinase interacting serine/threonine kinase 2	291	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)		AGGGCGGGTAGCCGCTGAGTA	0.697																																					p.G291G		Atlas-SNP	.											.	MKNK2	56	.	0			c.C873T						PASS	.						24	20	22					19																	2041911		2102	4136	6238	SO:0001819	synonymous_variant	2872	exon11			CGGGTAGCCGCTG	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.873C>T	19.37:g.2041911G>A		35	0	0		38	5	0.131579	NM_017572	Q6GPI3|Q9HBH8|Q9UHR0|Q9Y2N6	Silent	SNP	ENST00000591601.1	37	CCDS12080.1																																																																																			.	.	none		0.697	MKNK2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449312.1	NM_199054		A	2041911	G	A	2041911	2	1	15	1	0	0	0	0	0	0	0	1	9614	958	34	2		2	MKNK2	19	2041911	Silent	SNP	G	TCGA-FF-8061-01A-11D-2210-10	531219	2041911	57087072	139	2060											
C3	718	hgsc.bcm.edu	37	chr19	6714453	6714453	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcttgaccgggatgccttccGggttctgtgggaggcaggag	5	9	18	9	2	1	1	0	1	1	0	2	4	2	4	3	5	1	3	3	5	0	3			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:6714453G>A	ENST00000245907.6	-	5	601	c.509C>T	c.(508-510)cCg>cTg	p.P170L		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	170					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)	GATGCCTTCCGGGTTCTGTGG	0.567																																					p.P170L		Atlas-SNP	.											.	C3	192	.	0			c.C509T						PASS	.						57	48	51					19																	6714453		2203	4299	6502	SO:0001583	missense	718	exon5			CCTTCCGGGTTCT	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.509C>T	19.37:g.6714453G>A	ENSP00000245907:p.Pro170Leu	87	0	0		61	26	0.42623	NM_000064	A7E236	Missense_Mutation	SNP	ENST00000245907.6	37	CCDS32883.1	.	.	.	.	.	.	.	.	.	.	g	16.30	3.085611	0.55861	.	.	ENSG00000125730	ENST00000245907	T	0.78481	-1.18	4.97	4.97	0.65823	Alpha-2-macroglobulin, N-terminal (1);	0.168178	0.53938	D	0.000053	D	0.91717	0.7381	H	0.96142	3.775	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.94274	0.7513	10	0.87932	D	0	.	15.7294	0.77790	0.0:0.0:1.0:0.0	.	170	P01024	CO3_HUMAN	L	170	ENSP00000245907:P170L	ENSP00000245907:P170L	P	-	2	0	C3	6665453	1.000000	0.71417	0.904000	0.35570	0.061000	0.15899	6.362000	0.73077	2.297000	0.77311	0.509000	0.49947	CCG	.	.	none		0.567	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064		A	6714453	G	A	6714453	3	1	15	1	0	0	0	0	1	0	0	0	2206	1116	39	1	4630	1	C3	19	6714453	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	4672542	6714453	52414530	140	2061											
SYCE2	256126	hgsc.bcm.edu	37	chr19	13010850	13010850	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcagccacagaagaaacgaAcacgtctgggggctgtgagt	12	7	13	9	2	2	3	1	1	1	2	2	4	2	3	1	2	3	1	1	2	3	1			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:13010850A>G	ENST00000293695.7	-	5	598	c.580T>C	c.(580-582)Ttc>Ctc	p.F194L	GCDH_ENST00000588242.2_3'UTR	NM_001105578.1	NP_001099048.1	Q6PIF2	SYCE2_HUMAN	synaptonemal complex central element protein 2	194					synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(1)	8						GAAGAAACGAACACGTCTGGG	0.532																																					p.F194L		Atlas-SNP	.											.	SYCE2	19	.	0			c.T580C						PASS	.						56	63	61					19																	13010850		1915	4123	6038	SO:0001583	missense	256126	exon5			AAACGAACACGTC	AK097443	CCDS42509.1	19p13.13	2008-02-05				ENSG00000161860			27411	protein-coding gene	gene with protein product	"central element synaptonemal complex 1"	611487				15944401	Standard	NM_001105578		Approved	CESC1	uc002mvr.2	Q6PIF2		ENST00000293695.7:c.580T>C	19.37:g.13010850A>G	ENSP00000293695:p.Phe194Leu	87	0	0		84	5	0.0595238	NM_001105578	B4DYD3	Missense_Mutation	SNP	ENST00000293695.7	37	CCDS42509.1	.	.	.	.	.	.	.	.	.	.	A	11.35	1.612603	0.28712	.	.	ENSG00000161860	ENST00000293695	D	0.85629	-2.01	3.46	-3.27	0.05048	.	.	.	.	.	T	0.71160	0.3307	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.56757	-0.7926	9	0.87932	D	0	.	5.1896	0.15203	0.2862:0.0:0.5364:0.1775	.	194	Q6PIF2	SYCE2_HUMAN	L	194	ENSP00000293695:F194L	ENSP00000293695:F194L	F	-	1	0	SYCE2	12871850	0.000000	0.05858	0.000000	0.03702	0.052000	0.14988	-1.037000	0.03557	-0.830000	0.04262	-0.464000	0.05259	TTC	.	.	none		0.532	SYCE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451913.1	XM_497609		G	13010850	A	G	13010850	3	3	15	1	0	0	0	0	1	0	0	0	15444	43	2	3	84	3	SYCE2	19	13010850	Missense_Mutation	SNP	A	TCGA-FF-8061-01A-11D-2210-10	6296397	13010850	46118133	141	2062											
PRKACA	5566	hgsc.bcm.edu	37	chr19	14204559	14204559	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atctacctgcaggaggttccGcagcaggtccttcaagtcag	9	9	11	12	1	3	0	2	0	1	0	5	1	5	1	3	3	3	4	3	3	2	3			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:14204559G>A	ENST00000308677.4	-	9	1007	c.811C>T	c.(811-813)Cgg>Tgg	p.R271W	SAMD1_ENST00000541938.1_5'Flank|PRKACA_ENST00000350356.3_5'UTR|PRKACA_ENST00000589994.1_Missense_Mutation_p.R263W|PRKACA_ENST00000590853.1_Intron	NM_002730.3	NP_002721.1	P17612	KAPCA_HUMAN	protein kinase, cAMP-dependent, catalytic, alpha	271	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						AGGAGGTTCCGCAGCAGGTCC	0.547																																					p.R271W		Atlas-SNP	.											.	PRKACA	65	.	0			c.C811T						PASS	.						97	88	91					19																	14204559		2203	4300	6503	SO:0001583	missense	5566	exon9			GGTTCCGCAGCAG		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.811C>T	19.37:g.14204559G>A	ENSP00000309591:p.Arg271Trp	152	0	0		162	67	0.41358	NM_002730	Q32P54|Q9H2Y0|Q9NRB4|Q9NRH9	Missense_Mutation	SNP	ENST00000308677.4	37	CCDS12304.1	.	.	.	.	.	.	.	.	.	.	G	19.56	3.850706	0.71719	.	.	ENSG00000072062	ENST00000308677;ENST00000350356;ENST00000535695	T	0.66815	-0.23	4.89	4.89	0.63831	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	0.48286	D	0.000193	T	0.82190	0.4983	M	0.88906	2.99	0.42130	D	0.991466	D;D	0.67145	0.995;0.996	D;D	0.69307	0.963;0.918	D	0.85403	0.1132	10	0.87932	D	0	.	10.785	0.46401	0.0:0.0:0.8106:0.1894	.	271;263	P17612;P17612-2	KAPCA_HUMAN;.	W	271;263;271	ENSP00000309591:R271W	ENSP00000309591:R271W	R	-	1	2	PRKACA	14065559	0.994000	0.37717	1.000000	0.80357	0.989000	0.77384	2.068000	0.41471	2.271000	0.75665	0.491000	0.48974	CGG	.	.	none		0.547	PRKACA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459004.1	NM_002730		A	14204559	G	A	14204559	3	1	15	1	0	0	0	0	1	0	0	0	12509	1086	38	1	252	1	PRKACA	19	14204559	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	1193709	14204559	44924424	142	2063											
LPHN1	22859	hgsc.bcm.edu	37	chr19	14261777	14261777	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagccctcgtggctaggacGccgcacctggtagtagccct	6	8	13	14	3	0	0	0	0	0	0	1	1	0	1	4	3	2	5	4	3	4	4	rs375528213		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:14261777G>A	ENST00000340736.6	-	24	4630	c.4333C>T	c.(4333-4335)Cgt>Tgt	p.R1445C	LPHN1_ENST00000361434.3_Missense_Mutation_p.R1440C|CTB-55O6.12_ENST00000588387.1_RNA|CTB-55O6.12_ENST00000588658.1_RNA	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	1445					calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|heterophilic cell-cell adhesion (GO:0007157)|neuropeptide signaling pathway (GO:0007218)|positive regulation of synapse maturation (GO:0090129)	axon (GO:0030424)|cell junction (GO:0030054)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TGGCTAGGACGCCGCACCTGG	0.711																																					p.R1445C		Atlas-SNP	.											.	LPHN1	107	.	0			c.C4333T						PASS	.	G	CYS/ARG,CYS/ARG	0,4282		0,0,2141	9	10	10		4333,4318	0.2	1	19		10	1,8383		0,1,4191	no	missense,missense	LPHN1	NM_001008701.2,NM_014921.4	180,180	0,1,6332	AA,AG,GG		0.0119,0.0,0.0079	probably-damaging,probably-damaging	1445/1475,1440/1470	14261777	1,12665	2141	4192	6333	SO:0001583	missense	22859	exon24			TAGGACGCCGCAC	AB020628	CCDS12307.1, CCDS32928.1	19p13.2	2014-08-08				ENSG00000072071		"-", "GPCR / Class B : Orphans"	20973	protein-coding gene	gene with protein product						10994649	Standard	NM_014921		Approved	KIAA0821, CIRL1, LEC2	uc010xnn.2	O94910		ENST00000340736.6:c.4333C>T	19.37:g.14261777G>A	ENSP00000340688:p.Arg1445Cys	39	0	0		110	41	0.372727	NM_001008701	Q96IE7|Q9BU07|Q9HAR3	Missense_Mutation	SNP	ENST00000340736.6	37	CCDS32928.1	.	.	.	.	.	.	.	.	.	.	G	15.35	2.806701	0.50421	0.0	1.19E-4	ENSG00000072071	ENST00000340736;ENST00000361434	T;T	0.79454	-1.27;-1.27	3.94	0.249	0.15531	GPCR, family 2, latrophilin, C-terminal (1);	0.194324	0.31450	N	0.007633	D	0.82568	0.5065	M	0.65975	2.015	0.43913	D	0.996557	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.969	T	0.78700	-0.2102	10	0.87932	D	0	.	5.6925	0.17837	0.1007:0.0:0.5742:0.3251	.	1440;1445	O94910-2;O94910	.;LPHN1_HUMAN	C	1445;1440	ENSP00000340688:R1445C;ENSP00000355328:R1440C	ENSP00000340688:R1445C	R	-	1	0	LPHN1	14122777	0.997000	0.39634	0.996000	0.52242	0.857000	0.48899	0.527000	0.22987	-0.153000	0.11137	0.205000	0.17691	CGT	.	.	weak		0.711	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921		A	14261777	G	A	14261777	3	1	15	1	0	0	0	0	1	0	0	0	8924	1087	38	1	95	1	LPHN1	19	14261777	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	57218	14261777	44867206	143	2064											
RHPN2	85415	hgsc.bcm.edu	37	chr19	33517507	33517507	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagctcagctccagccgcaCttgctcccgcacctttgagt	7	9	9	16	2	1	1	1	1	0	0	3	2	3	1	4	0	4	5	4	0	1	2			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:33517507C>T	ENST00000254260.3	-	3	252	c.217G>A	c.(217-219)Gtg>Atg	p.V73M	RHPN2_ENST00000400226.4_De_novo_Start_OutOfFrame	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	73					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)		p.V73M(2)		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)					TCCAGCCGCACTTGCTCCCGC	0.552																																					p.V73M		Atlas-SNP	.											RHPN2,face,carcinoma,0,2	RHPN2	107	2	2	Substitution - Missense(2)	NS(1)|skin(1)	c.G217A						scavenged	.						84	83	83					19																	33517507		2203	4300	6503	SO:0001583	missense	85415	exon3			GCCGCACTTGCTC	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.217G>A	19.37:g.33517507C>T	ENSP00000254260:p.Val73Met	34	1	0.0294118		37	3	0.0810811	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	C	18.08	3.542997	0.65198	.	.	ENSG00000131941	ENST00000254260	T	0.39787	1.06	3.88	3.88	0.44766	.	0.000000	0.85682	D	0.000000	T	0.64853	0.2636	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.71984	-0.4427	10	0.87932	D	0	11.9954	16.025	0.80536	0.0:1.0:0.0:0.0	.	73	Q8IUC4	RHPN2_HUMAN	M	73	ENSP00000254260:V73M	ENSP00000254260:V73M	V	-	1	0	RHPN2	38209347	1.000000	0.71417	1.000000	0.80357	0.343000	0.28985	7.267000	0.78462	2.167000	0.68274	0.557000	0.71058	GTG	.	.	none		0.552	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103		T	33517507	C	T	33517507	3	4	15	1	0	0	0	0	1	0	0	0	13366	565	20	2	1895	2	RHPN2	19	33517507	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	19255730	33517507	25611476	144	2065											
DMKN	93099	hgsc.bcm.edu	37	chr19	36002412	36002412	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccgccactgctgctgccactGctgctgccaccactgctgct	4	9	9	19	1	0	0	0	0	0	0	0	0	0	0	5	0	8	6	5	0	0	0	rs56743379|rs111543270		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:36002412G>A	ENST00000339686.3	-	5	995	c.819C>T	c.(817-819)agC>agT	p.S273S	DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000418261.1_Silent_p.S273S|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000447113.2_Silent_p.S273S|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000424570.2_Silent_p.S273S|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000440396.1_Silent_p.S273S|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000451297.2_Silent_p.S273S|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000492341.2_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	273	Gly-rich.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.S274_S290del(1)		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)			tgctgccactgctgctgccac	0.657																																					p.S273S		Atlas-SNP	.											.	DMKN	116	.	1	Deletion - In frame(1)	ovary(1)	c.C819T						PASS	.						29	22	24					19																	36002412		2184	4248	6432	SO:0001819	synonymous_variant	93099	exon5			GCCACTGCTGCTG	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.819C>T	19.37:g.36002412G>A		29	0	0		36	4	0.111111	NM_001126058	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Silent	SNP	ENST00000339686.3	37	CCDS12463.1																																																																																			.	.	none		0.657	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317		A	36002412	G	A	36002412	2	1	15	1	0	0	0	0	0	0	0	1	4584	1310	46	2		2	DMKN	19	36002412	Silent	SNP	G	TCGA-FF-8061-01A-11D-2210-10	2484905	36002412	23126571	145	2066											
PSG4	5672	hgsc.bcm.edu	37	chr19	43708388	43708388	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagttgtgggcggattccagAagtttaaaagtgatgctagg	11	11	14	5	1	0	2	0	1	0	1	1	3	1	3	1	3	1	3	1	3	4	5			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:43708388A>C	ENST00000405312.3	-	2	317	c.80T>G	c.(79-81)tTc>tGc	p.F27C	PSG4_ENST00000244295.9_Missense_Mutation_p.F27C|PSG4_ENST00000433626.2_Missense_Mutation_p.F27C	NM_002780.3	NP_002771.2	Q00888	PSG4_HUMAN	pregnancy specific beta-1-glycoprotein 4	27					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)				CGGATTCCAGAAGTTTAAAAG	0.468																																					p.X27X		Atlas-SNP	.											.	PSG4	129	.	0			c.G80G						PASS	.						107	121	116					19																	43708388		2144	4269	6413	SO:0001583	missense	5672	exon2			TTCCAGAAGTTTA		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.80T>G	19.37:g.43708388A>C	ENSP00000384770:p.Phe27Cys	200	0	0		190	74	0.389474	NM_002780	E7EX79|Q13047|Q13048|Q15234|Q15240|Q9UQ76	Silent	SNP	ENST00000405312.3	37	CCDS46093.1	.	.	.	.	.	.	.	.	.	.	N	7.311	0.615088	0.14129	.	.	ENSG00000243137	ENST00000244295;ENST00000405312;ENST00000433626;ENST00000451895	T;T;T;T	0.50813	1.16;0.73;1.87;3.24	1.65	0.446	0.16602	.	.	.	.	.	T	0.34193	0.0889	L	0.33624	1.015	0.09310	N	1	B;B;B	0.28324	0.207;0.154;0.012	B;B;B	0.33254	0.091;0.16;0.033	T	0.36962	-0.9726	9	0.72032	D	0.01	.	3.5161	0.07726	0.6473:0.0:0.0:0.3527	.	27;27;27	E7EX79;Q00888-2;Q00888	.;.;PSG4_HUMAN	C	27;27;27;43	ENSP00000244295:F27C;ENSP00000384770:F27C;ENSP00000387864:F27C;ENSP00000388134:F43C	ENSP00000244295:F27C	F	-	2	0	PSG4	48400228	0.058000	0.20735	0.279000	0.24732	0.035000	0.12851	-0.188000	0.09642	0.069000	0.16605	0.145000	0.16022	TTC	.	.	none		0.468	PSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323073.1	NM_213633		C	43708388	A	C	43708388	3	2	15	1	0	0	0	0	1	0	0	0	12669	246	9	5	1199	5	PSG4	19	43708388	Missense_Mutation	SNP	A	TCGA-FF-8061-01A-11D-2210-10	7705976	43708388	15420595	146	2067											
ZNF223	7766	hgsc.bcm.edu	37	chr19	44570830	44570831	+	Frame_Shift_Del	DEL	AG	AG	-																															aaacatcagagaattcacacAggggagaagccattcaaatg																								rs568496344	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:44570830_44570831delAG	ENST00000434772.3	+	5	1104_1105	c.849_850delAG	c.(847-852)acagggfs	p.G284fs	ZNF223_ENST00000591793.1_Frame_Shift_Del_p.G394fs	NM_013361.4	NP_037493.3	Q9UK11	ZN223_HUMAN	zinc finger protein 223	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)			endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18		Prostate(69;0.0352)				GAATTCACACAGGGGAGAAGCC	0.421														7	0.00139776	0.0	0.0	5008	,	,		22779	0.0069		0.0	False		,,,				2504	0.0				p.283_283del		Pindel,Atlas-Indel	.											.	ZNF223	61	.	0			c.848_849del						PASS	.																																			SO:0001589	frameshift_variant	7766	exon5			.	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.849_850delAG	19.37:g.44570830_44570831delAG	ENSP00000401947:p.Gly284fs	91	0	.		226	39	0.173	NM_013361	Q15736|Q8TBJ3|Q9HCA9	Frame_Shift_Del	DEL	ENST00000434772.3	37	CCDS12635.1																																																																																			.	.	none		0.421	ZNF223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460469.2			-	44570831	AG	-	44570830	7	5	15	1	0	1	0	1	0	0	0	0	17792	175	7	0	863	0	ZNF223	19	44570830	Frame_Shift_Del	DEL	AG	TCGA-FF-8061-01A-11D-2210-10	862442	44570830	14558153	147	2068											
ZNF223	7766	hgsc.bcm.edu	37	chr19	44571010	44571010	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atccacacaggagagaaaccAtataattgtaaagaatgtgg	18	8	9	6	0	0	2	0	0	0	2	1	4	1	3	2	2	1	1	2	2	6	4	rs141349301		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:44571010A>G	ENST00000434772.3	+	5	1284	c.1029A>G	c.(1027-1029)ccA>ccG	p.P343P	ZNF223_ENST00000591793.1_Silent_p.P453P	NM_013361.4	NP_037493.3	Q9UK11	ZN223_HUMAN	zinc finger protein 223	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)			endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18		Prostate(69;0.0352)				GAGAGAAACCATATAATTGTA	0.438																																					p.P343P		Atlas-SNP	.											.	ZNF223	61	.	0			c.A1029G						PASS	.						102	106	105					19																	44571010		2203	4300	6503	SO:0001819	synonymous_variant	7766	exon5			GAAACCATATAAT	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.1029A>G	19.37:g.44571010A>G		58	0	0		68	15	0.220588	NM_013361	Q15736|Q8TBJ3|Q9HCA9	Silent	SNP	ENST00000434772.3	37	CCDS12635.1																																																																																			A|1.000;T|0.000	.	alt		0.438	ZNF223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460469.2			G	44571010	A	G	44571010	2	3	15	1	0	0	0	0	0	0	0	1	17792	204	8	3		3	ZNF223	19	44571010	Silent	SNP	A	TCGA-FF-8061-01A-11D-2210-10	180	44571010	14557973	148	2069											
SNRPD2	6633	hgsc.bcm.edu	37	chr19	46191649	46191649	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aggacccagcactcacctatCgaaggccttcacgcggccca	10	5	9	17	3	2	0	2	0	0	0	3	2	2	1	4	3	1	1	4	3	2	2			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:46191649C>T	ENST00000342669.3	-	2	622	c.178G>A	c.(178-180)Gat>Aat	p.D60N	SNRPD2_ENST00000391932.3_Missense_Mutation_p.D50N|SNRPD2_ENST00000587367.1_Missense_Mutation_p.D50N|SNRPD2_ENST00000588599.1_Missense_Mutation_p.D50N|SNRPD2_ENST00000590212.1_Missense_Mutation_p.D60N|SNRPD2_ENST00000585392.1_5'UTR|SNRPD2_ENST00000588301.1_Missense_Mutation_p.D60N	NM_004597.5	NP_004588.1	P62316	SMD2_HUMAN	small nuclear ribonucleoprotein D2 polypeptide 16.5kDa	60					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|spliceosomal snRNP assembly (GO:0000387)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|methylosome (GO:0034709)|nucleoplasm (GO:0005654)|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)	poly(A) RNA binding (GO:0044822)			breast(1)|large_intestine(1)|lung(2)	4		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00546)|GBM - Glioblastoma multiforme(486;0.0807)|Epithelial(262;0.194)		ACTCACCTATCGAAGGCCTTC	0.562																																					p.D60N		Atlas-SNP	.											.	SNRPD2	7	.	0			c.G178A						PASS	.						100	87	92					19																	46191649		2203	4300	6503	SO:0001583	missense	6633	exon2			ACCTATCGAAGGC		CCDS33053.1, CCDS54281.1	19q13.2-q13.3	2011-10-11	2002-08-29		ENSG00000125743	ENSG00000125743			11159	protein-coding gene	gene with protein product	"snRNP core protein D2"	601061	"small nuclear ribonucleoprotein D2 polypeptide (16.5kD)"	SNRPD1		7527560, 1701240	Standard	NM_004597		Approved	Sm-D2	uc002pcw.3	P62316		ENST00000342669.3:c.178G>A	19.37:g.46191649C>T	ENSP00000342374:p.Asp60Asn	169	0	0		209	80	0.382775	NM_004597	A8K797|J3KPM5|P43330	Missense_Mutation	SNP	ENST00000342669.3	37	CCDS33053.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.631630	0.87660	.	.	ENSG00000125743	ENST00000342669;ENST00000391932	T;T	0.80480	-1.38;-1.38	5.85	5.85	0.93711	Like-Sm ribonucleoprotein (LSM) domain, eukaryotic/archaea-type (1);Like-Sm ribonucleoprotein (LSM) domain (1);Like-Sm ribonucleoprotein (LSM)-related domain (1);	0.000000	0.85682	D	0.000000	D	0.85737	0.5766	H	0.95574	3.69	0.80722	D	1	P	0.41710	0.76	B	0.33799	0.17	D	0.89638	0.3860	10	0.87932	D	0	.	17.6515	0.88165	0.0:1.0:0.0:0.0	.	60	P62316	SMD2_HUMAN	N	60;50	ENSP00000342374:D60N;ENSP00000375798:D50N	ENSP00000342374:D60N	D	-	1	0	SNRPD2	50883489	1.000000	0.71417	0.998000	0.56505	0.956000	0.61745	5.436000	0.66538	2.767000	0.95098	0.655000	0.94253	GAT	.	.	none		0.562	SNRPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459648.1	NM_004597		T	46191649	C	T	46191649	3	4	15	1	0	0	0	0	1	0	0	0	14880	884	31	1	186	1	SNRPD2	19	46191649	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	1620639	46191649	12937334	149	2070											
NOSIP	51070	hgsc.bcm.edu	37	chr19	50063941	50063941	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggtgcagttcttgccatgcCgcgtcatcctagggaggaag	7	9	14	11	3	2	0	1	0	1	0	3	2	3	2	3	3	3	2	3	3	2	3			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:50063941C>T	ENST00000596358.1	-	2	66	c.8G>A	c.(7-9)cGg>cAg	p.R3Q	NOSIP_ENST00000339093.3_Missense_Mutation_p.R3Q|NOSIP_ENST00000391853.3_Missense_Mutation_p.R3Q	NM_001270960.1	NP_001257889.1	Q9Y314	NOSIP_HUMAN	nitric oxide synthase interacting protein	3					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)		CTTGCCATGCCGCGTCATCCT	0.632																																					p.R3Q		Atlas-SNP	.											.	NOSIP	28	.	0			c.G8A						PASS	.						85	60	68					19																	50063941		2203	4299	6502	SO:0001583	missense	51070	exon3			CCATGCCGCGTCA	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.8G>A	19.37:g.50063941C>T	ENSP00000470034:p.Arg3Gln	45	0	0		59	18	0.305085	NM_015953	Q96FD2	Missense_Mutation	SNP	ENST00000596358.1	37	CCDS12772.1	.	.	.	.	.	.	.	.	.	.	C	34	5.315578	0.95655	.	.	ENSG00000142546	ENST00000339093;ENST00000391853	T;T	0.78595	-1.19;-1.19	5.41	2.1	0.27182	.	0.000000	0.85682	D	0.000000	D	0.87006	0.6070	M	0.86805	2.84	0.45718	D	0.998623	D	0.89917	1.0	D	0.85130	0.997	D	0.85312	0.1079	10	0.87932	D	0	-23.987	7.983	0.30194	0.0:0.7195:0.1321:0.1484	.	3	Q9Y314	NOSIP_HUMAN	Q	3	ENSP00000343497:R3Q;ENSP00000375726:R3Q	ENSP00000343497:R3Q	R	-	2	0	NOSIP	54755753	1.000000	0.71417	0.003000	0.11579	0.601000	0.36947	6.534000	0.73833	0.268000	0.21939	0.655000	0.94253	CGG	.	.	none		0.632	NOSIP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465423.1			T	50063941	C	T	50063941	3	4	15	1	0	0	0	0	1	0	0	0	10554	652	23	1	929	1	NOSIP	19	50063941	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	3872292	50063941	9065042	150	2071											
ZNF761	147804	hgsc.bcm.edu	37	chr19	53950528	53950528	+	RNA	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caaaggagtcagggatggctTtttctcaggtgagatgatat	11	12	13	5	0	2	2	2	2	1	1	3	5	2	4	0	4	0	1	0	4	2	3			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr19:53950528T>G	ENST00000424846.3	+	0	2920				ZNF761_ENST00000454407.1_RNA	NR_003148.3				tropomyosin 3 pseudogene 9																		AGGGATGGCTTTTTCTCAGGT	0.443																																					p.F3V		Atlas-SNP	.											.	ZNF761	104	.	0			c.T7G						PASS	.						131	125	127					19																	53950528		876	1991	2867			388561	exon4			ATGGCTTTTTCTC			19q13.42	2012-07-04			ENSG00000241015	ENSG00000241015			44142	pseudogene	pseudogene							Standard	NR_003148		Approved				OTTHUMG00000157312		19.37:g.53950528T>G		21	0	0		34	12	0.352941	NM_001008401		Missense_Mutation	SNP	ENST00000424846.3	37																																																																																				.	.	none		0.443	TPM3P9-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000347070.1	NR_003148		G	53950528	T	G	53950528	1	3	15	0	1	0	0	0	0	0	0	0	18151	1841	64	5		5	ZNF761	19	53950528	RNA	SNP	T	TCGA-FF-8061-01A-11D-2210-10	3886587	53950528	5178455	151	2072											
ZNF343	79175	hgsc.bcm.edu	37	chr20	2473385	2473385	+	Frame_Shift_Del	DEL	T	T	-																															taattctccagcatcacttcTttgtatagattcctctgctc																										TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr20:2473385delT	ENST00000278772.4	-	5	751	c.264delA	c.(262-264)aaafs	p.K88fs	ZNF343_ENST00000358413.2_Frame_Shift_Del_p.K88fs|ZNF343_ENST00000381253.1_Frame_Shift_Del_p.K88fs|RP4-734P14.4_ENST00000461548.1_Frame_Shift_Del_p.K88fs	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	88	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						GCATCACTTCTTTGTATAGAT	0.408																																					p.E89fs		Atlas-Indel	.											ZNF343,NS,carcinoma,0,1	ZNF343	47	1	0			c.265delG						PASS	.						234	216	222					20																	2473385		2203	4300	6503	SO:0001589	frameshift_variant	79175	exon5			.	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.264delA	20.37:g.2473385delT	ENSP00000278772:p.Lys88fs	88	0	0		116	15	0.12931	NM_024325	Q5JXU8|Q5JXU9|Q8N8F2|Q96EX8|Q96NA5|Q9BQB0	Frame_Shift_Del	DEL	ENST00000278772.4	37	CCDS13028.1																																																																																			.	.	none		0.408	ZNF343-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077617.1	NM_024325		-	2473385	T	-	2473385	7	5	15	1	0	1	0	1	0	0	0	0	17873	1606	56	0	1543	0	ZNF343	20	2473385	Frame_Shift_Del	DEL	T	TCGA-FF-8061-01A-11D-2210-10		2473385	60552135	152	2073											
ZNF337	26152	hgsc.bcm.edu	37	chr20	25656946	25656946	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gacttattagtatagcctcgCccacactccttgcacacaaa	12	10	5	14	1	0	0	0	0	0	0	2	1	1	0	3	0	2	2	3	0	5	5			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr20:25656946C>T	ENST00000376436.1	-	4	1517	c.978G>A	c.(976-978)ggG>ggA	p.G326G	ZNF337_ENST00000252979.5_Silent_p.G326G|RP4-694B14.5_ENST00000455791.1_RNA|RP4-694B14.5_ENST00000421829.1_RNA|RP4-694B14.5_ENST00000439498.1_RNA|ZNF337_ENST00000538750.1_Silent_p.G294G|ZNF337_ENST00000481610.1_5'Flank|RP4-694B14.5_ENST00000414393.1_RNA|RP4-694B14.5_ENST00000428254.1_RNA			Q9Y3M9	ZN337_HUMAN	zinc finger protein 337	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)			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						TATAGCCTCGCCCACACTCCT	0.483																																					p.G326G		Atlas-SNP	.											.	ZNF337	65	.	0			c.G978A						PASS	.						105	100	102					20																	25656946		2203	4300	6503	SO:0001819	synonymous_variant	26152	exon5			GCCTCGCCCACAC		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.978G>A	20.37:g.25656946C>T		95	0	0		106	8	0.0754717	NM_015655	B4DSM2|Q9Y3Y5	Silent	SNP	ENST00000376436.1	37	CCDS13174.1																																																																																			.	.	none		0.483	ZNF337-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078454.1			T	25656946	C	T	25656946	2	4	15	1	0	0	0	0	0	0	0	1	17868	726	26	2		2	ZNF337	20	25656946	Silent	SNP	C	TCGA-FF-8061-01A-11D-2210-10	23183561	25656946	37368574	153	2074											
SLC17A9	63910	hgsc.bcm.edu	37	chr20	61594979	61594979	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcagcctgctccttcttcAtcctcctctcctggctgccc	2	13	6	20	0	3	0	1	0	2	0	7	0	6	0	6	1	4	3	6	1	0	2			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr20:61594979A>G	ENST00000370351.4	+	7	900	c.769A>G	c.(769-771)Atc>Gtc	p.I257V	SLC17A9_ENST00000488738.1_3'UTR|SLC17A9_ENST00000370349.3_Missense_Mutation_p.I251V	NM_022082.3	NP_071365	Q9BYT1	S17A9_HUMAN	solute carrier family 17 (vesicular nucleotide transporter), member 9	257					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						CTCCTTCTTCATCCTCCTCTC	0.677																																					p.I257V		Atlas-SNP	.											.	SLC17A9	54	.	0			c.A769G						PASS	.						54	59	58					20																	61594979		2148	4249	6397	SO:0001583	missense	63910	exon7			TTCTTCATCCTCC	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.769A>G	20.37:g.61594979A>G	ENSP00000359376:p.Ile257Val	110	0	0		131	63	0.480916	NM_022082	B3KTF2|Q5W198|Q8TB07|Q8TBP4|Q8TEL5|Q9BYT0|Q9BYT2	Missense_Mutation	SNP	ENST00000370351.4	37	CCDS42901.1	.	.	.	.	.	.	.	.	.	.	a	0.269	-0.994082	0.02145	.	.	ENSG00000101194	ENST00000370351;ENST00000370349	T;T	0.59224	0.28;0.28	4.86	2.62	0.31277	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.162450	0.52532	N	0.000066	T	0.40247	0.1109	N	0.20574	0.59	0.28715	N	0.903358	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.11329	0.006;0.005;0.005	T	0.22626	-1.0211	10	0.30078	T	0.28	.	11.9672	0.53042	0.9221:0.0:0.0779:0.0	.	277;257;251	B4DPU8;Q9BYT1;Q9BYT1-2	.;S17A9_HUMAN;.	V	257;251	ENSP00000359376:I257V;ENSP00000359374:I251V	ENSP00000359374:I251V	I	+	1	0	SLC17A9	61065424	1.000000	0.71417	0.996000	0.52242	0.054000	0.15201	2.976000	0.49289	0.231000	0.21079	-0.741000	0.03529	ATC	.	.	none		0.677	SLC17A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080100.1	NM_022082		G	61594979	A	G	61594979	3	3	15	1	0	0	0	0	1	0	0	0	14439	217	8	3	795	3	SLC17A9	20	61594979	Missense_Mutation	SNP	A	TCGA-FF-8061-01A-11D-2210-10	35938033	61594979	1430541	154	2075											
ADAMTS5	11096	hgsc.bcm.edu	37	chr21	28327094	28327094	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgaaggctgcgtggaggcCatcgtcttcaatcacagcac	10	8	12	11	2	3	1	2	1	1	0	4	2	3	2	1	3	2	2	1	3	2	1			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr21:28327094C>T	ENST00000284987.5	-	2	1322	c.1201G>A	c.(1201-1203)Ggc>Agc	p.G401S	MIR4759_ENST00000584048.1_RNA	NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	401	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				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						GCGTGGAGGCCATCGTCTTCA	0.512																																					p.G401S	Esophageal Squamous(53;683 1080 10100 14424 45938)	Atlas-SNP	.											.	ADAMTS5	184	.	0			c.G1201A						PASS	.						123	112	116					21																	28327094		2203	4300	6503	SO:0001583	missense	11096	exon2			GGAGGCCATCGTC	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.1201G>A	21.37:g.28327094C>T	ENSP00000284987:p.Gly401Ser	73	0	0		58	14	0.241379	NM_007038	Q52LV4|Q9UKP2	Missense_Mutation	SNP	ENST00000284987.5	37	CCDS13579.1	.	.	.	.	.	.	.	.	.	.	C	35	5.419488	0.96111	.	.	ENSG00000154736	ENST00000284987	D	0.86694	-2.16	5.05	5.05	0.67936	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.85682	D	0.000000	D	0.93119	0.7809	M	0.72624	2.21	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93653	0.6975	10	0.87932	D	0	.	18.5978	0.91235	0.0:1.0:0.0:0.0	.	401	Q9UNA0	ATS5_HUMAN	S	401	ENSP00000284987:G401S	ENSP00000284987:G401S	G	-	1	0	ADAMTS5	27248965	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.651000	0.83577	2.641000	0.89580	0.557000	0.71058	GGC	.	.	none		0.512	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1			T	28327094	C	T	28327094	3	4	15	1	0	0	0	0	1	0	0	0	269	594	21	2	1619	2	ADAMTS5	21	28327094	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10		28327094	19802801	155	2076											
ITSN1	6453	hgsc.bcm.edu	37	chr21	35190669	35190669	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	aaaaatgatgtcatcaccgtCctggaacagcaagacatgtg	15	8	9	9	1	2	2	2	1	0	1	3	3	3	3	2	1	2	1	2	1	4	0			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr21:35190669C>T	ENST00000381318.3	+	23	3114	c.2826C>T	c.(2824-2826)gtC>gtT	p.V942V	ITSN1_ENST00000399352.1_Silent_p.V937V|ITSN1_ENST00000399353.1_Silent_p.V900V|ITSN1_ENST00000399326.3_Silent_p.V937V|ITSN1_ENST00000399349.1_Silent_p.V937V|ITSN1_ENST00000381285.4_Silent_p.V942V|ITSN1_ENST00000399355.2_Silent_p.V942V|ITSN1_ENST00000399367.3_Silent_p.V937V|ITSN1_ENST00000437442.2_Silent_p.V937V|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000381291.4_Silent_p.V942V|ITSN1_ENST00000379960.5_Intron	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	942	SH3 2. {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						TCATCACCGTCCTGGAACAGC	0.453																																					p.V942V		Atlas-SNP	.											.	ITSN1	166	.	0			c.C2826T						PASS	.						176	169	171					21																	35190669		2203	4300	6503	SO:0001819	synonymous_variant	6453	exon23			CACCGTCCTGGAA	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.2826C>T	21.37:g.35190669C>T		155	0	0		142	60	0.422535	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	Silent	SNP	ENST00000381318.3	37	CCDS33545.1																																																																																			.	.	none		0.453	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024		T	35190669	C	T	35190669	2	4	15	1	0	0	0	0	0	0	0	1	7935	842	30	2		2	ITSN1	21	35190669	Silent	SNP	C	TCGA-FF-8061-01A-11D-2210-10	6863575	35190669	12939226	156	2077											
C21orf2	755	hgsc.bcm.edu	37	chr21	45753031	45753031	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacagcacccgcagacgcggCagccccttcaggtagaagag	11	3	12	15	3	1	3	1	0	0	3	1	3	1	3	3	2	2	4	3	2	2	2			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr21:45753031C>T	ENST00000339818.4	-	4	465	c.258G>A	c.(256-258)ctG>ctA	p.L86L	AP001062.7_ENST00000448927.1_RNA|C21orf2_ENST00000397956.3_Silent_p.L86L|C21orf2_ENST00000496321.1_5'UTR|C21orf2_ENST00000325223.7_Silent_p.L86L	NM_001271440.1|NM_004928.2	NP_001258369.1|NP_004919.1	O43822	CU002_HUMAN	chromosome 21 open reading frame 2	86					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)		GCAGACGCGGCAGCCCCTTCA	0.697																																					p.L86L		Atlas-SNP	.											.	C21orf2	10	.	0			c.G258A						PASS	.						18	20	20					21																	45753031		2201	4295	6496	SO:0001819	synonymous_variant	755	exon4			ACGCGGCAGCCCC	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.258G>A	21.37:g.45753031C>T		63	0	0		100	4	0.04	NM_004928	A8MPS9|O14993|Q8N5X6|Q99837|Q99838	Silent	SNP	ENST00000339818.4	37	CCDS13709.1																																																																																			.	.	none		0.697	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195799.1	NM_004928		T	45753031	C	T	45753031	2	4	15	1	0	0	0	0	0	0	0	1	2125	697	25	2		2	C21orf2	21	45753031	Silent	SNP	C	TCGA-FF-8061-01A-11D-2210-10	10562362	45753031	2376864	157	2078											
KRTAP10-11	386678	hgsc.bcm.edu	37	chr21	46067104	46067104	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtccctcctctgccacccCgtgtgcaggtccacctgctg	3	10	10	18	1	1	0	0	0	1	0	4	0	4	0	7	1	3	2	7	1	0	0	rs75548048	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr21:46067104C>T	ENST00000334670.8	+	1	774	c.729C>T	c.(727-729)ccC>ccT	p.P243P	TSPEAR_ENST00000323084.4_Intron	NM_198692.2	NP_941965.2	P60412	KR10B_HUMAN	keratin associated protein 10-11	243	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						TCTGCCACCCCGTGTGCAGGT	0.687													C|||	125	0.0249601	0.0915	0.0058	5008	,	,		20784	0.0		0.0	False		,,,				2504	0.0				p.P243P		Atlas-SNP	.											.	KRTAP10-11	36	.	0			c.C729T						PASS	.	C	,	313,4093	167.3+/-198.3	16,281,1906	94	104	101		,729	-0.6	0.7	21	dbSNP_131	101	1,8599		0,1,4299	no	intron,coding-synonymous	TSPEAR,KRTAP10-11	NM_144991.2,NM_198692.2	,	16,282,6205	TT,TC,CC		0.0116,7.1039,2.4143	,	,243/299	46067104	314,12692	2203	4300	6503	SO:0001819	synonymous_variant	386678	exon1			CCACCCCGTGTGC	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.729C>T	21.37:g.46067104C>T		88	0	0		111	10	0.0900901	NM_198692	A2RRF9	Silent	SNP	ENST00000334670.8	37	CCDS42962.1																																																																																			C|0.980;T|0.020	0.020	strong		0.687	KRTAP10-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128029.1	NM_198692		T	46067104	C	T	46067104	2	4	15	1	0	0	0	0	0	0	0	1	8516	639	23	1		1	KRTAP10-11	21	46067104	Silent	SNP	C	TCGA-FF-8061-01A-11D-2210-10	314073	46067104	2062791	158	2079											
KRTAP10-11	386678	hgsc.bcm.edu	37	chr21	46067193	46067193	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctgccgcccggcctcctGcgtgtccctcctctgccgcc	0	9	10	22	4	1	0	0	0	1	0	4	0	4	0	8	1	4	1	8	1	0	0			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr21:46067193G>C	ENST00000334670.8	+	1	863	c.818G>C	c.(817-819)tGc>tCc	p.C273S	TSPEAR_ENST00000323084.4_Intron	NM_198692.2	NP_941965.2	P60412	KR10B_HUMAN	keratin associated protein 10-11	273						keratin filament (GO:0045095)				NS(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)	12						CCGGCCTCCTGCGTGTCCCTC	0.677																																					p.C273S		Atlas-SNP	.											KRTAP10-11,NS,carcinoma,-1,1	KRTAP10-11	36	1	0			c.G818C						PASS	.						41	52	48					21																	46067193		2200	4292	6492	SO:0001583	missense	386678	exon1			CCTCCTGCGTGTC	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.818G>C	21.37:g.46067193G>C	ENSP00000334197:p.Cys273Ser	80	0	0		134	6	0.0447761	NM_198692	A2RRF9	Missense_Mutation	SNP	ENST00000334670.8	37	CCDS42962.1	.	.	.	.	.	.	.	.	.	.	g	10.35	1.326226	0.24080	.	.	ENSG00000243489	ENST00000334670	T	0.00648	5.99	3.93	1.85	0.25348	.	.	.	.	.	T	0.00724	0.0024	L	0.45051	1.395	0.21527	N	0.999652	B	0.21071	0.051	B	0.24541	0.054	T	0.44314	-0.9336	9	0.16896	T	0.51	.	7.0501	0.25069	0.1131:0.3795:0.5075:0.0	.	273	P60412	KR10B_HUMAN	S	273	ENSP00000334197:C273S	ENSP00000334197:C273S	C	+	2	0	KRTAP10-11	44891621	0.000000	0.05858	0.035000	0.18076	0.597000	0.36814	-0.005000	0.12855	0.627000	0.30340	0.462000	0.41574	TGC	.	.	none		0.677	KRTAP10-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128029.1	NM_198692		C	46067193	G	C	46067193	3	2	15	1	0	0	0	0	1	0	0	0	8516	1319	46	4	820	4	KRTAP10-11	21	46067193	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	89	46067193	2062702	159	2080											
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230312	23230312	+	Missense_Mutation	SNP	C	C	G																															ccaggcagcgctggcccctgCtgctgctgggtctggccatg																										TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr22:23230312C>G	ENST00000526893.1	+	1	353	c.79C>G	c.(79-81)Ctg>Gtg	p.L27V	IGLL5_ENST00000531372.1_Missense_Mutation_p.L27V|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Missense_Mutation_p.L27V	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	27						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CTGGCCCCTGCTGCTGCTGGG	0.667																																					p.L27V		Atlas-SNP	.											IGLL5,NS,lymphoid_neoplasm,-2,1	IGLL5	26	1	0			c.C79G						PASS	.																																			SO:0001583	missense	100423062	exon1			CCCCTGCTGCTGC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.79C>G	22.37:g.23230312C>G	ENSP00000431254:p.Leu27Val	108	0	0		142	61	0.429577	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	C	10.18	1.278851	0.23307	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00626	6.13;6.14	3.81	-2.69	0.06022	.	.	.	.	.	T	0.00524	0.0017	L	0.29908	0.895	0.09310	N	1	P	0.37061	0.58	B	0.28232	0.087	T	0.47032	-0.9148	9	0.72032	D	0.01	.	7.0435	0.25033	0.3778:0.5232:0.0:0.099	.	27	B9A064	IGLL5_HUMAN	V	27	ENSP00000436353:L27V;ENSP00000431254:L27V	ENSP00000431254:L27V	L	+	1	2	IGLL5	21560312	0.000000	0.05858	0.000000	0.03702	0.067000	0.16453	-1.733000	0.01850	-0.440000	0.07211	-0.165000	0.13383	CTG	.	.	none		0.667	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		G	23230312	C	G	23230312	3	3	15	1	0	0	0	0	1	0	0	0	7603	796	28	4	81	4	IGLL5	22	23230312	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10		23230312	28074254	160	2081	26	2	2	16		6	4	101	N	G_C	2.724311e-11
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230315	23230315	+	Silent	SNP	C	C	T																															ggcagcgctggcccctgctgCtgctgggtctggccatggtc																								rs148489860	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr22:23230315C>T	ENST00000526893.1	+	1	356	c.82C>T	c.(82-84)Ctg>Ttg	p.L28L	IGLL5_ENST00000531372.1_Silent_p.L28L|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Silent_p.L28L	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	28						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GCCCCTGCTGCTGCTGGGTCT	0.662													C|||	11	0.00219649	0.0045	0.0	5008	,	,		12566	0.003		0.001	False		,,,				2504	0.001				p.L28L		Atlas-SNP	.											.	IGLL5	26	.	0			c.C82T						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			CTGCTGCTGCTGG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.82C>T	22.37:g.23230315C>T		108	0	0		140	60	0.428571	NM_001178126		Silent	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			C|1.000;T|0.000	0.000	strong		0.662	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		T	23230315	C	T	23230315	2	4	15	1	0	0	0	0	0	0	0	1	7603	796	28	2		2	IGLL5	22	23230315	Silent	SNP	C	TCGA-FF-8061-01A-11D-2210-10	3	23230315	28074251	161	2082	26	2	2	16		6	4	101	N	G_C	2.724311e-11
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230333	23230333	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgctgctgggtctggccatgGtcgcccatggcctgctgcgc	2	10	15	14	2	1	0	0	0	1	0	2	0	1	0	3	4	4	3	3	4	0	0			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr22:23230333G>A	ENST00000526893.1	+	1	374	c.100G>A	c.(100-102)Gtc>Atc	p.V34I	IGLL5_ENST00000531372.1_Missense_Mutation_p.V34I|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Missense_Mutation_p.V34I	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	34						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						TCTGGCCATGGTCGCCCATGG	0.667																																					p.V34I		Atlas-SNP	.											.	IGLL5	26	.	0			c.G100A						PASS	.																																			SO:0001583	missense	100423062	exon1			GCCATGGTCGCCC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.100G>A	22.37:g.23230333G>A	ENSP00000431254:p.Val34Ile	108	0	0		126	50	0.396825	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	10.08	1.252980	0.22965	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00581	6.42;6.42	3.55	1.39	0.22231	.	.	.	.	.	T	0.00384	0.0012	N	0.19112	0.55	0.09310	N	1	B	0.34061	0.436	B	0.21708	0.036	T	0.45160	-0.9280	9	0.28530	T	0.3	.	4.2734	0.10797	0.121:0.0:0.654:0.225	.	34	B9A064	IGLL5_HUMAN	I	34	ENSP00000436353:V34I;ENSP00000431254:V34I	ENSP00000431254:V34I	V	+	1	0	IGLL5	21560333	0.005000	0.15991	0.001000	0.08648	0.001000	0.01503	0.741000	0.26202	0.464000	0.27142	-0.196000	0.12772	GTC	.	.	none		0.667	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		A	23230333	G	A	23230333	3	1	15	1	0	0	0	0	1	0	0	0	7603	1261	44	2	102	2	IGLL5	22	23230333	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	18	23230333	28074233	162	2083			2	16		6	4	101	N	G_C	2.724311e-11
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230364	23230364	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctgctgcgcccaatggttgCaccgcaaagcggggacccag	8	5	13	15	3	0	0	0	0	0	0	0	1	0	1	4	3	4	4	4	3	2	1	rs538723125	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr22:23230364C>A	ENST00000526893.1	+	1	405	c.131C>A	c.(130-132)gCa>gAa	p.A44E	IGLL5_ENST00000531372.1_Missense_Mutation_p.A44E|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Missense_Mutation_p.A44E	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	44						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CCAATGGTTGCACCGCAAAGC	0.682																																					p.A44E		Atlas-SNP	.											.	IGLL5	26	.	0			c.C131A						PASS	.																																			SO:0001583	missense	100423062	exon1			TGGTTGCACCGCA	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.131C>A	22.37:g.23230364C>A	ENSP00000431254:p.Ala44Glu	109	0	0		142	58	0.408451	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	C	14.63	2.592719	0.46214	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00686	5.85;5.86	3.92	-0.956	0.10353	.	.	.	.	.	T	0.00580	0.0019	L	0.29908	0.895	0.09310	N	1	P	0.44877	0.845	B	0.38655	0.278	T	0.48091	-0.9065	9	0.15952	T	0.53	.	4.4817	0.11771	0.0:0.4301:0.3576:0.2123	.	44	B9A064	IGLL5_HUMAN	E	44	ENSP00000436353:A44E;ENSP00000431254:A44E	ENSP00000431254:A44E	A	+	2	0	IGLL5	21560364	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.266000	0.18534	-0.052000	0.13311	0.643000	0.83706	GCA	.	.	none		0.682	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		A	23230364	C	A	23230364	3	1	15	1	0	0	0	0	1	0	0	0	7603	710	25	4	133	4	IGLL5	22	23230364	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	31	23230364	28074202	163	2084			2	16		6	4	101	N	G_C	2.724311e-11
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230402	23230402	+	Missense_Mutation	SNP	G	G	A																															cagaccctggagcctcagttGgaagcagccgatccagcctg																										TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr22:23230402G>A	ENST00000526893.1	+	1	443	c.169G>A	c.(169-171)Gga>Aga	p.G57R	IGLL5_ENST00000531372.1_Missense_Mutation_p.G57R|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Missense_Mutation_p.G57R	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	57						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						AGCCTCAGTTGGAAGCAGCCG	0.662																																					p.G57R		Atlas-SNP	.											.	IGLL5	26	.	0			c.G169A						PASS	.																																			SO:0001583	missense	100423062	exon1			TCAGTTGGAAGCA	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.169G>A	22.37:g.23230402G>A	ENSP00000431254:p.Gly57Arg	101	0	0		146	61	0.417808	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	14.96	2.690900	0.48097	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00587	6.39;6.38	3.92	-1.17	0.09648	.	.	.	.	.	T	0.00496	0.0016	L	0.32530	0.975	0.09310	N	1	B	0.15719	0.014	B	0.11329	0.006	T	0.40079	-0.9582	9	0.37606	T	0.19	.	5.1199	0.14854	0.2033:0.4108:0.3859:0.0	.	57	B9A064	IGLL5_HUMAN	R	57	ENSP00000436353:G57R;ENSP00000431254:G57R	ENSP00000431254:G57R	G	+	1	0	IGLL5	21560402	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.250000	0.08830	-0.072000	0.12864	-0.189000	0.12847	GGA	.	.	none		0.662	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		A	23230402	G	A	23230402	3	1	15	1	0	0	0	0	1	0	0	0	7603	1349	47	2	171	2	IGLL5	22	23230402	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	38	23230402	28074164	164	2085	27	2	2	16		6	4	101	N	G_C	2.724311e-11
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230412	23230412	+	Missense_Mutation	SNP	G	G	C																															agcctcagttggaagcagccGatccagcctgcggagcctgt																										TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr22:23230412G>C	ENST00000526893.1	+	1	453	c.179G>C	c.(178-180)cGa>cCa	p.R60P	IGLL5_ENST00000531372.1_Missense_Mutation_p.R60P|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Missense_Mutation_p.R60P	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	60						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GGAAGCAGCCGATCCAGCCTG	0.652																																					p.R60P		Atlas-SNP	.											.	IGLL5	26	.	0			c.G179C						PASS	.																																			SO:0001583	missense	100423062	exon1			GCAGCCGATCCAG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.179G>C	22.37:g.23230412G>C	ENSP00000431254:p.Arg60Pro	94	0	0		148	64	0.432432	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.919402	0.33908	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00622	6.17;6.16	3.92	-7.84	0.01196	.	.	.	.	.	T	0.00496	0.0016	L	0.29908	0.895	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.47341	-0.9125	9	0.62326	D	0.03	.	2.9625	0.05897	0.0917:0.3589:0.1664:0.3831	.	60	B9A064	IGLL5_HUMAN	P	60	ENSP00000436353:R60P;ENSP00000431254:R60P	ENSP00000431254:R60P	R	+	2	0	IGLL5	21560412	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.219000	0.00553	-1.485000	0.01854	0.643000	0.83706	CGA	.	.	none		0.652	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		C	23230412	G	C	23230412	3	2	15	1	0	0	0	0	1	0	0	0	7603	1058	37	4	181	4	IGLL5	22	23230412	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	10	23230412	28074154	165	2086	27	2	2	16		6	4	101	N	G_C	2.724311e-11
MYO18B	84700	hgsc.bcm.edu	37	chr22	26422889	26422889	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccctggaaatcgaaggggccGctggtggtctcttgaggtcc	6	9	15	11	2	1	1	0	1	1	0	4	3	2	2	3	6	0	1	3	6	2	1	rs187337528		TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr22:26422889G>A	ENST00000407587.2	+	43	7121	c.6952G>A	c.(6952-6954)Gct>Act	p.A2318T	MYO18B_ENST00000536101.1_Missense_Mutation_p.A2317T|MYO18B_ENST00000335473.7_Missense_Mutation_p.A2317T			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2317						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.A2318T(2)		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						CGAAGGGGCCGCTGGTGGTCT	0.587													G|||	1	0.000199681	0.0	0.0	5008	,	,		16066	0.001		0.0	False		,,,				2504	0.0				p.A2317T		Atlas-SNP	.											MYO18B,NS,haematopoietic_neoplasm,0,2	MYO18B	322	2	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.G6949A						PASS	.						28	34	32					22																	26422889		1894	4096	5990	SO:0001583	missense	84700	exon43			GGGGCCGCTGGTG	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.6952G>A	22.37:g.26422889G>A	ENSP00000386096:p.Ala2318Thr	31	0	0		38	13	0.342105	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	0.012	-1.691334	0.00731	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.86956	-2.17;-2.17;-2.19	4.43	-7.52	0.01341	.	7739.210000	0.00166	N	0.000002	T	0.64294	0.2585	N	0.03608	-0.345	0.09310	N	1	B;B;B;B;B	0.06786	0.0;0.001;0.001;0.001;0.001	B;B;B;B;B	0.04013	0.0;0.0;0.0;0.001;0.001	T	0.58284	-0.7663	10	0.23891	T	0.37	.	0.11	0.00055	0.3104:0.2229:0.2234:0.2433	.	1830;2319;2317;2318;2317	Q8IUG5-2;B0QYF5;Q8IUG5;F5GXR6;F5GYU7	.;.;MY18B_HUMAN;.;.	T	2317;2317;2318	ENSP00000441229:A2317T;ENSP00000334563:A2317T;ENSP00000386096:A2318T	ENSP00000334563:A2317T	A	+	1	0	MYO18B	24752889	0.000000	0.05858	0.000000	0.03702	0.055000	0.15305	-1.861000	0.01654	-1.216000	0.02607	-0.448000	0.05591	GCT	G|1.000;A|0.000	0.000	strong		0.587	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		A	26422889	G	A	26422889	3	1	15	1	0	0	0	0	1	0	0	0	10075	1087	38	1	7115	1	MYO18B	22	26422889	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	3192477	26422889	24881677	166	2087											
NAGA	4668	hgsc.bcm.edu	37	chr22	42463804	42463804	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggaatgccatgagggaagcGcttgggatccggcatcaggc	10	6	16	9	2	1	1	1	1	0	0	2	4	2	4	2	5	2	2	2	5	2	1	rs140775168	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chr22:42463804G>T	ENST00000396398.3	-	3	821	c.289C>A	c.(289-291)Cgc>Agc	p.R97S	NAGA_ENST00000402937.1_Missense_Mutation_p.R97S|NAGA_ENST00000403363.1_Missense_Mutation_p.R97S	NM_000262.2	NP_000253.1	P17050	NAGAB_HUMAN	N-acetylgalactosaminidase, alpha-	97					carbohydrate catabolic process (GO:0016052)|glycolipid catabolic process (GO:0019377)|glycoside catabolic process (GO:0016139)|glycosylceramide catabolic process (GO:0046477)|oligosaccharide metabolic process (GO:0009311)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-galactosidase activity (GO:0004557)|alpha-N-acetylgalactosaminidase activity (GO:0008456)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	11						TGAGGGAAGCGCTTGGGATCC	0.607																																					p.R97S		Atlas-SNP	.											.	NAGA	26	.	0			c.C289A						PASS	.						130	112	118					22																	42463804		2203	4300	6503	SO:0001583	missense	4668	exon3			GGAAGCGCTTGGG		CCDS14030.1	22q13.2	2010-07-09			ENSG00000198951	ENSG00000198951	3.2.1.49		7631	protein-coding gene	gene with protein product		104170					Standard	NM_000262		Approved	D22S674	uc003bbw.4	P17050	OTTHUMG00000151276	ENST00000396398.3:c.289C>A	22.37:g.42463804G>T	ENSP00000379680:p.Arg97Ser	58	0	0		80	32	0.4	NM_000262		Missense_Mutation	SNP	ENST00000396398.3	37	CCDS14030.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.210448	0.79240	.	.	ENSG00000198951	ENST00000396398;ENST00000403363;ENST00000402937	D;D;D	0.99820	-6.93;-6.93;-6.93	4.66	3.59	0.41128	Aldolase-type TIM barrel (1);Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.99768	0.9905	M	0.87097	2.86	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96983	0.9716	10	0.72032	D	0.01	-23.1156	10.2175	0.43177	0.0:0.0:0.5995:0.4005	.	97	P17050	NAGAB_HUMAN	S	97	ENSP00000379680:R97S;ENSP00000385283:R97S;ENSP00000384603:R97S	ENSP00000379680:R97S	R	-	1	0	NAGA	40793750	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.394000	0.34509	2.441000	0.82636	0.561000	0.74099	CGC	G|1.000;C|0.000	.	alt		0.607	NAGA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322056.1			T	42463804	G	T	42463804	3	4	15	1	0	0	0	0	1	0	0	0	10150	1087	38	4	974	4	NAGA	22	42463804	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10	16040915	42463804	8840762	167	2088											
P2RY8	286530	hgsc.bcm.edu	37	chrX	1585217	1585217	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gttgcaatggtagtagatttGgaaaggcaacacgctggcca	12	9	13	7	1	0	1	0	0	0	1	0	2	0	2	1	4	2	6	1	4	5	4			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chrX:1585217G>T	ENST00000381297.4	-	2	445	c.235C>A	c.(235-237)Caa>Aaa	p.Q79K	P2RY8_ENST00000460672.1_5'Flank	NM_178129.4	NP_835230.1	Q86VZ1	P2RY8_HUMAN	purinergic receptor P2Y, G-protein coupled, 8	79						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(13)|prostate(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)				TAGTAGATTTGGAAAGGCAAC	0.572			T	CRLF2	"B-ALL, Downs associated ALL"																																p.Q79K		Atlas-SNP	.		Dom	yes		"X,Y"	Xp22.3; Yp11.3	286530	"purinergic receptor P2Y, G-protein coupled, 8"		L	.	P2RY8	53	.	0			c.C235A						PASS	.						141	127	132					X																	1585217		2203	4296	6499	SO:0001583	missense	286530	exon2			AGATTTGGAAAGG	AA804531	CCDS14115.1	Xp22.33 and Yp11.3	2012-08-08			ENSG00000182162	ENSG00000182162		"Pseudoautosomal regions / PAR1", "Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	15524	protein-coding gene	gene with protein product		300525				11004484	Standard	NM_178129		Approved	P2Y8	uc004cpz.2	Q86VZ1	OTTHUMG00000021060	ENST00000381297.4:c.235C>A	X.37:g.1585217G>T	ENSP00000370697:p.Gln79Lys	218	0	0		260	105	0.403846	NM_178129		Missense_Mutation	SNP	ENST00000381297.4	37	CCDS14115.1	.	.	.	.	.	.	.	.	.	.	g	3.768	-0.048128	0.07407	.	.	ENSG00000182162	ENST00000381297	T	0.71461	-0.57	2.1	2.1	0.27182	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	U	0.000002	T	0.65015	0.2651	N	0.16066	0.365	0.09310	N	0.999999	D	0.76494	0.999	D	0.87578	0.998	T	0.58244	-0.7670	10	0.02654	T	1	.	12.2776	0.54744	0.0:0.0:1.0:0.0	.	79	Q86VZ1	P2RY8_HUMAN	K	79	ENSP00000370697:Q79K	ENSP00000370697:Q79K	Q	-	1	0	P2RY8	1545217	1.000000	0.71417	0.577000	0.28562	0.017000	0.09413	5.642000	0.67888	0.637000	0.30526	0.279000	0.19357	CAA	.	.	none		0.572	P2RY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055602.1	NM_178129		T	1585217	G	T	1585217	3	4	15	1	0	0	0	0	1	0	0	0	11364	1357	47	4	848	4	P2RY8	23	1585217	Missense_Mutation	SNP	G	TCGA-FF-8061-01A-11D-2210-10		1585217	153685343	168	2089											
TSPYL2	64061	hgsc.bcm.edu	37	chrX	53112146	53112146	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gtagcgcagtggggtgggcgCcccagaggttagttgacccg	6	7	18	10	3	0	2	0	1	0	1	0	2	0	2	3	4	1	4	3	4	2	3	rs144264921	byFrequency	TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chrX:53112146C>T	ENST00000375442.4	+	1	598	c.466C>T	c.(466-468)Ccc>Tcc	p.P156S		NM_022117.3	NP_071400.1	Q9H2G4	TSYL2_HUMAN	TSPY-like 2	156					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						GGGGTGGGCGCCCCAGAGGTT	0.587													C|||	3	0.000794702	0.0015	0.0	3775	,	,		10753	0.0		0.001	False		,,,				2504	0.0				p.P156S		Atlas-SNP	.											.	TSPYL2	53	.	0			c.C466T						PASS	.		SER/PRO	6,3828		0,6,0,1626,570	25	24	24		466	-0.7	0.4	X	dbSNP_134	24	3,6724		0,1,2,2427,1869	yes	missense	TSPYL2	NM_022117.3	74	0,7,2,4053,2439	TT,TC,T,CC,C		0.0446,0.1565,0.0852	benign	156/694	53112146	9,10552	2202	4299	6501	SO:0001583	missense	64061	exon1			TGGGCGCCCCAGA	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.466C>T	X.37:g.53112146C>T	ENSP00000364591:p.Pro156Ser	66	0	0		85	4	0.0470588	NM_022117	O94799|Q96DG7|Q9BZW6	Missense_Mutation	SNP	ENST00000375442.4	37	CCDS14350.1	.	.	.	.	.	.	.	.	.	.	C	1.215	-0.628646	0.03610	0.001565	4.46E-4	ENSG00000184205	ENST00000375442	T	0.19532	2.14	3.48	-0.742	0.11108	.	1.020780	0.07854	N	0.965098	T	0.07234	0.0183	N	0.02916	-0.46	0.20821	N	0.999844	B;B	0.14438	0.01;0.01	B;B	0.08055	0.003;0.003	T	0.40251	-0.9573	10	0.09590	T	0.72	-10.5495	6.56	0.22481	0.0:0.5958:0.0:0.4042	.	156;156	Q9H2G4;A8K8U7	TSYL2_HUMAN;.	S	156	ENSP00000364591:P156S	ENSP00000364591:P156S	P	+	1	0	TSPYL2	53128871	0.006000	0.16342	0.447000	0.26932	0.809000	0.45718	-0.888000	0.04148	-0.236000	0.09753	0.519000	0.50382	CCC	C|0.998;T|0.002	0.002	strong		0.587	TSPYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056718.1	NM_022117		T	53112146	C	T	53112146	3	4	15	1	0	0	0	0	1	0	0	0	16675	739	26	2	468	2	TSPYL2	23	53112146	Missense_Mutation	SNP	C	TCGA-FF-8061-01A-11D-2210-10	51526929	53112146	102158414	169	2090											
P2RY10	27334	hgsc.bcm.edu	37	chrX	78216808	78216808	+	Frame_Shift_Del	DEL	T	T	-																															tccctatcatattaactttaTtttttacaccatggtaaagg																										TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chrX:78216808delT	ENST00000171757.2	+	4	1071	c.791delT	c.(790-792)attfs	p.I264fs	P2RY10_ENST00000544091.1_Frame_Shift_Del_p.I264fs	NM_014499.2	NP_055314.1	O00398	P2Y10_HUMAN	purinergic receptor P2Y, G-protein coupled, 10	264						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						ATTAACTTTATTTTTTACACC	0.458																																					p.I264fs		Pindel,Atlas-Indel	.											.	P2RY10	99	.	0			c.790delA						PASS	.						145	137	140					X																	78216808		2203	4300	6503	SO:0001589	frameshift_variant	27334	exon2			.	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.791delT	X.37:g.78216808delT	ENSP00000171757:p.Ile264fs	25	0	.		36	20	0.556	NM_198333	D3DTE5|Q4VBN7|Q86V16	Frame_Shift_Del	DEL	ENST00000171757.2	37	CCDS14442.1																																																																																			.	.	none		0.458	P2RY10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057323.1			-	78216808	T	-	78216808	7	5	15	1	0	1	0	1	0	0	0	0	11356	1493	52	0	793	0	P2RY10	23	78216808	Frame_Shift_Del	DEL	T	TCGA-FF-8061-01A-11D-2210-10	25104662	78216808	77053752	170	2091											
ARMCX5	64860	hgsc.bcm.edu	37	chrX	101858323	101858323	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gctggactgaaattactaggGcacttgagtataaaatttga	14	12	10	5	0	0	3	0	3	0	0	0	4	0	4	0	2	1	3	0	2	6	6			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chrX:101858323G>A	ENST00000604957.1	+	1	3876	c.1254G>A	c.(1252-1254)ggG>ggA	p.G418G	ARMCX5_ENST00000537008.1_Silent_p.G418G|ARMCX5_ENST00000246174.2_Silent_p.G418G|ARMCX5_ENST00000372742.1_Silent_p.G418G|RP4-769N13.7_ENST00000602441.1_RNA|ARMCX5_ENST00000536530.1_Silent_p.G418G|RP4-769N13.6_ENST00000476910.2_RNA|ARMCX5_ENST00000541409.1_Silent_p.G418G	NM_001168478.1	NP_001161950.1	Q6P1M9	ARMX5_HUMAN	armadillo repeat containing, X-linked 5	418										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	22						AATTACTAGGGCACTTGAGTA	0.388																																					p.G418G		Atlas-SNP	.											.	ARMCX5	55	.	0			c.G1254A						PASS	.						53	53	53					X																	101858323		2203	4300	6503	SO:0001819	synonymous_variant	64860	exon3			ACTAGGGCACTTG		CCDS14500.1	Xq22.1-q22.3	2014-03-21			ENSG00000125962	ENSG00000125962		"Armadillo repeat containing"	25772	protein-coding gene	gene with protein product						16221301, 22569362	Standard	NM_022838		Approved	FLJ12969, GASP5	uc004ejh.3	Q6P1M9	OTTHUMG00000022062	ENST00000604957.1:c.1254G>A	X.37:g.101858323G>A		97	0	0		92	11	0.119565	NM_022838	B3KU88|D3DX99|Q68DB4|Q9BVZ3|Q9H969	Silent	SNP	ENST00000604957.1	37	CCDS14500.1																																																																																			.	.	none		0.388	ARMCX5-013	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000469659.1	NM_022838		A	101858323	G	A	101858323	2	1	15	1	0	0	0	0	0	0	0	1	962	1190	42	2		2	ARMCX5	23	101858323	Silent	SNP	G	TCGA-FF-8061-01A-11D-2210-10	23641515	101858323	53412237	171	2092											
ZCCHC12	170261	hgsc.bcm.edu	37	chrX	117959875	117959875	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagggaggaagaggattgggAtgatgcttttattaaacgga	14	10	15	2	1	0	2	0	1	0	1	0	7	0	7	0	5	2	1	0	5	5	4			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chrX:117959875A>G	ENST00000310164.2	+	4	1175	c.668A>G	c.(667-669)gAt>gGt	p.D223G		NM_173798.2	NP_776159.1	Q6PEW1	ZCH12_HUMAN	zinc finger, CCHC domain containing 12	223					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						GAGGATTGGGATGATGCTTTT	0.483																																					p.D223G		Atlas-SNP	.											.	ZCCHC12	60	.	0			c.A668G						PASS	.						59	52	55					X																	117959875		2203	4300	6503	SO:0001583	missense	170261	exon4			ATTGGGATGATGC	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	ENST00000310164.2:c.668A>G	X.37:g.117959875A>G	ENSP00000308921:p.Asp223Gly	66	0	0		77	4	0.0519481	NM_173798	B3KV48|Q6PID5|Q8N1C1	Missense_Mutation	SNP	ENST00000310164.2	37	CCDS14574.1	.	.	.	.	.	.	.	.	.	.	A	7.022	0.558807	0.13436	.	.	ENSG00000174460	ENST00000310164	T	0.34472	1.36	3.0	3.0	0.34707	.	.	.	.	.	T	0.36908	0.0984	M	0.72479	2.2	0.26670	N	0.971746	B	0.33612	0.419	B	0.35413	0.202	T	0.36187	-0.9758	9	0.59425	D	0.04	-9.0207	6.8214	0.23859	1.0:0.0:0.0:0.0	.	223	Q6PEW1	ZCH12_HUMAN	G	223	ENSP00000308921:D223G	ENSP00000308921:D223G	D	+	2	0	ZCCHC12	117843903	1.000000	0.71417	0.968000	0.41197	0.127000	0.20565	3.563000	0.53784	1.412000	0.46977	0.486000	0.48141	GAT	.	.	none		0.483	ZCCHC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058014.1	NM_173798		G	117959875	A	G	117959875	3	3	15	1	0	0	0	0	1	0	0	0	17596	333	12	3	670	3	ZCCHC12	23	117959875	Missense_Mutation	SNP	A	TCGA-FF-8061-01A-11D-2210-10	16101552	117959875	37310685	172	2093											
PLXNB3	5365	hgsc.bcm.edu	37	chrX	153035889	153035889	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtgccgtccaggccttggAggcggctgccccgtgagtcc	4	7	15	15	3	0	1	0	1	0	0	2	2	2	2	6	4	2	1	6	4	0	1			TCGA-FF-8061-01A-11D-2210-10	TCGA-FF-8061-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a29278af-7ecf-403e-b6a9-623ea7879d05	08470796-8ff6-4e18-98d5-f9ee0d079517	g.chrX:153035889A>G	ENST00000361971.5	+	9	1997	c.1883A>G	c.(1882-1884)gAg>gGg	p.E628G	PLXNB3_ENST00000538776.1_Missense_Mutation_p.E281G|PLXNB3_ENST00000538543.1_Missense_Mutation_p.E178G|PLXNB3_ENST00000538282.1_Missense_Mutation_p.E238G|PLXNB3_ENST00000538966.1_Missense_Mutation_p.E651G	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	628	PSI 2.				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)					CAGGCCTTGGAGGCGGCTGCC	0.657																																					p.E651G		Atlas-SNP	.											.	PLXNB3	208	.	0			c.A1952G						PASS	.						57	43	47					X																	153035889		2193	4296	6489	SO:0001583	missense	5365	exon10			CCTTGGAGGCGGC	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.1883A>G	X.37:g.153035889A>G	ENSP00000355378:p.Glu628Gly	118	0	0		132	6	0.0454545	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Missense_Mutation	SNP	ENST00000361971.5	37	CCDS14729.1	.	.	.	.	.	.	.	.	.	.	a	5.600	0.295469	0.10622	.	.	ENSG00000198753	ENST00000538966;ENST00000361971;ENST00000538776;ENST00000538543;ENST00000538282	T;T;T;T;T	0.68624	5.21;5.17;4.6;1.91;-0.34	5.1	3.86	0.44501	.	0.274152	0.33591	N	0.004748	T	0.54631	0.1870	L	0.56769	1.78	0.23204	N	0.99813	B;B;B;B;B	0.28233	0.075;0.204;0.058;0.035;0.025	B;B;B;B;B	0.25614	0.021;0.055;0.04;0.062;0.045	T	0.39292	-0.9621	10	0.24483	T	0.36	.	4.6981	0.12813	0.6145:0.1945:0.0:0.191	.	281;310;178;651;628	B7Z3H9;B7Z9A5;F5GZZ4;F5H773;Q9ULL4	.;.;.;.;PLXB3_HUMAN	G	651;628;281;178;238	ENSP00000442736:E651G;ENSP00000355378:E628G;ENSP00000445569:E281G;ENSP00000444086:E178G;ENSP00000441919:E238G	ENSP00000355378:E628G	E	+	2	0	PLXNB3	152689083	0.004000	0.15560	0.572000	0.28498	0.065000	0.16274	0.309000	0.19332	1.683000	0.51011	0.427000	0.28365	GAG	.	.	none		0.657	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1			G	153035889	A	G	153035889	3	3	15	1	0	0	0	0	1	0	0	0	12134	304	11	3	2031	3	PLXNB3	23	153035889	Missense_Mutation	SNP	A	TCGA-FF-8061-01A-11D-2210-10	35076014	153035889	2234671	173	2094											
TNFRSF14	8764	hgsc.bcm.edu	37	chr1	2491336	2491336	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcagcccaggccacttcTgcatcgtccaggacggggac	7	6	13	15	2	1	0	0	0	1	0	3	2	2	2	3	4	3	3	3	4	0	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr1:2491336T>C	ENST00000355716.4	+	4	678	c.379T>C	c.(379-381)Tgc>Cgc	p.C127R	RP3-395M20.8_ENST00000416860.2_RNA|RP3-395M20.8_ENST00000452793.1_RNA|TNFRSF14_ENST00000409119.1_Missense_Mutation_p.C127R	NM_003820.2	NP_003811.2	Q92956	TNR14_HUMAN	tumor necrosis factor receptor superfamily, member 14	127					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)		AGGCCACTTCTGCATCGTCCA	0.692			"Mis, N, F"		follicular lymphoma																																p.C127R		Atlas-SNP	.		Rec	yes		1	1p36.32	8764	"tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)"		L	.	TNFRSF14	89	.	0			c.T379C						PASS	.						35	36	35					1																	2491336		2193	4297	6490	SO:0001583	missense	8764	exon4			CACTTCTGCATCG	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.379T>C	1.37:g.2491336T>C	ENSP00000347948:p.Cys127Arg	357	1	0.00280112		113	39	0.345133	NM_003820	B3KW30|B9DI89|Q6IB95|Q8N634|Q8WXR1|Q96J31|Q9UM65	Missense_Mutation	SNP	ENST00000355716.4	37	CCDS44046.1	.	.	.	.	.	.	.	.	.	.	T	13.73	2.325399	0.41197	.	.	ENSG00000157873	ENST00000426449;ENST00000434817;ENST00000435221;ENST00000451778;ENST00000409119;ENST00000355716	T;T;T;T;T;T	0.63255	-0.03;-0.03;-0.03;-0.03;-0.03;-0.03	3.57	3.57	0.40892	TNFR/CD27/30/40/95 cysteine-rich region (1);	.	.	.	.	T	0.79358	0.4432	M	0.88704	2.975	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.81549	-0.0882	9	0.87932	D	0	-11.917	8.7123	0.34391	0.0:0.0:0.0:1.0	.	127	Q92956	TNR14_HUMAN	R	127	ENSP00000411854:C127R;ENSP00000415254:C127R;ENSP00000399292:C127R;ENSP00000399533:C127R;ENSP00000386859:C127R;ENSP00000347948:C127R	ENSP00000347948:C127R	C	+	1	0	TNFRSF14	2483082	0.009000	0.17119	0.985000	0.45067	0.221000	0.24807	0.389000	0.20751	1.642000	0.50584	0.379000	0.24179	TGC	.	.	none		0.692	TNFRSF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002088.1			C	2491336	T	C	2491336	3	2	16	1	0	0	0	0	1	0	0	0	16304	1580	55	3	393	3	TNFRSF14	1	2491336	Missense_Mutation	SNP	T	TCGA-FF-8062-01A-11D-2210-10		2491336	246759285	1	2095											
PIK3CD	5293	hgsc.bcm.edu	37	chr1	9787030	9787030	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acttccgagtgaagtttaacGaagccctccgtgagagctgg	10	9	12	10	3	0	2	0	2	0	1	2	5	2	2	3	1	3	2	3	1	3	3	rs397518423		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr1:9787030G>A	ENST00000377346.4	+	24	3256	c.3061G>A	c.(3061-3063)Gaa>Aaa	p.E1021K	PIK3CD_ENST00000361110.2_Missense_Mutation_p.E1045K|CLSTN1_ENST00000477264.1_5'Flank|PIK3CD_ENST00000536656.1_Missense_Mutation_p.E1045K	NM_005026.3	NP_005017.3	O00329	PK3CD_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit delta	1021	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.		E -> K (in APDS; results in gain of function causing enhanced membrane association and kinase activity). {ECO:0000269|PubMed:24136356}.		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)	GAAGTTTAACGAAGCCCTCCG	0.567																																					p.E1021K		Atlas-SNP	.											PIK3CD,NS,lymphoid_neoplasm,0,2	PIK3CD	86	2	0			c.G3061A	GRCh37	CM067447	PIK3CD	M		PASS	.						79	71	74					1																	9787030		2203	4300	6503	SO:0001583	missense	5293	exon24			TTTAACGAAGCCC		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.3061G>A	1.37:g.9787030G>A	ENSP00000366563:p.Glu1021Lys	109	0	0		117	59	0.504274	NM_005026	A6NCG0|G1FFP1|O15445|Q5SR49	Missense_Mutation	SNP	ENST00000377346.4	37	CCDS104.1	.	.	.	.	.	.	.	.	.	.	G	15.36	2.810780	0.50421	.	.	ENSG00000171608	ENST00000536656;ENST00000377346;ENST00000361110;ENST00000360563	T;T;T	0.81415	-1.49;-1.49;-1.49	4.65	3.72	0.42706	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.85682	D	0.000000	D	0.86431	0.5931	L	0.53729	1.69	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;P;D	0.74674	0.984;0.876;0.941	D	0.87336	0.2328	10	0.87932	D	0	-17.4746	14.041	0.64674	0.0:0.0:0.8477:0.1523	.	1020;1045;1021	B7ZM44;Q5SR50;O00329	.;.;PK3CD_HUMAN	K	1045;1021;1045;1045	ENSP00000446444:E1045K;ENSP00000366563:E1021K;ENSP00000354410:E1045K	ENSP00000353766:E1045K	E	+	1	0	PIK3CD	9709617	1.000000	0.71417	0.115000	0.21578	0.699000	0.40488	9.865000	0.99609	0.945000	0.37605	-0.187000	0.12897	GAA	.	.	none		0.567	PIK3CD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004235.1	NM_005026		A	9787030	G	A	9787030	3	1	16	1	0	0	0	0	1	0	0	0	11924	1059	37	1	3147	1	PIK3CD	1	9787030	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	7295694	9787030	239463591	2	2096											
CTBS	1486	hgsc.bcm.edu	37	chr1	85040024	85040024	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagcagcgccagcagcgcCagcagcgctagacccgggac	9	1	14	17	4	0	1	0	0	0	1	0	2	0	2	4	1	6	4	4	1	1	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr1:85040024C>T	ENST00000370630.5	-	1	123	c.75G>A	c.(73-75)ctG>ctA	p.L25L	CTBS_ENST00000477677.1_5'UTR	NM_004388.2	NP_004379.1	Q01459	DIAC_HUMAN	chitobiase, di-N-acetyl-	25					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)		ccagcagcgccagcagcgcTA	0.726																																					p.L25L		Atlas-SNP	.											CTBS,NS,carcinoma,0,1	CTBS	24	1	0			c.G75A						scavenged	.						3	4	4					1																	85040024		1689	3502	5191	SO:0001819	synonymous_variant	1486	exon1			CAGCGCCAGCAGC	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.75G>A	1.37:g.85040024C>T		6	0	0		3	2	0.666667	NM_004388	Q5VX50	Silent	SNP	ENST00000370630.5	37	CCDS698.1																																																																																			.	.	none		0.726	CTBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027457.2	NM_004388		T	85040024	C	T	85040024	2	4	16	1	0	0	0	0	0	0	0	1	4001	581	21	2		2	CTBS	1	85040024	Silent	SNP	C	TCGA-FF-8062-01A-11D-2210-10	75252994	85040024	164210597	3	2097											
SSX2IP	117178	hgsc.bcm.edu	37	chr1	85128001	85128001	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctgcattttccattaggatTtgtttctgacgatattcata	9	19	6	7	1	3	1	1	1	2	0	4	3	4	2	1	1	1	2	1	1	3	8			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr1:85128001T>G	ENST00000342203.3	-	8	1070	c.807A>C	c.(805-807)caA>caC	p.Q269H	SSX2IP_ENST00000370612.4_Missense_Mutation_p.Q269H|SSX2IP_ENST00000437941.2_Missense_Mutation_p.Q242H|SSX2IP_ENST00000603677.1_Intron|SSX2IP_ENST00000605755.1_Missense_Mutation_p.Q242H	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	269					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)		CCATTAGGATTTGTTTCTGAC	0.323																																					p.Q269H		Atlas-SNP	.											.	SSX2IP	53	.	0			c.A807C						PASS	.						113	124	120					1																	85128001		2203	4300	6503	SO:0001583	missense	117178	exon9			TAGGATTTGTTTC		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.807A>C	1.37:g.85128001T>G	ENSP00000340279:p.Gln269His	127	0	0		131	8	0.0610687	NM_001166417	A8K8W0|B4DFE3|D3DT13|J3KR02|Q6P2P8|Q6ULS1|Q7L168|Q9UIX0	Missense_Mutation	SNP	ENST00000342203.3	37	CCDS699.1	.	.	.	.	.	.	.	.	.	.	T	18.44	3.624299	0.66901	.	.	ENSG00000117155	ENST00000342203;ENST00000437941;ENST00000544699;ENST00000370612	T;T	0.47869	0.85;0.83	5.65	4.53	0.55603	.	0.219097	0.49305	D	0.000151	T	0.46405	0.1391	M	0.63428	1.95	0.41120	D	0.985803	D;D;D	0.64830	0.994;0.994;0.994	P;P;P	0.58820	0.846;0.783;0.783	T	0.53865	-0.8378	10	0.87932	D	0	-3.6859	7.8139	0.29247	0.0:0.2925:0.0:0.7075	.	265;269;242	F5H549;Q9Y2D8;B4DFE3	.;ADIP_HUMAN;.	H	269;242;265;269	ENSP00000340279:Q269H;ENSP00000412781:Q242H	ENSP00000340279:Q269H	Q	-	3	2	SSX2IP	84900589	0.991000	0.36638	1.000000	0.80357	0.996000	0.88848	0.235000	0.17948	0.994000	0.38892	0.482000	0.46254	CAA	.	.	none		0.323	SSX2IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027469.1	NM_014021		G	85128001	T	G	85128001	3	3	16	1	0	0	0	0	1	0	0	0	15219	1838	64	5	1065	5	SSX2IP	1	85128001	Missense_Mutation	SNP	T	TCGA-FF-8062-01A-11D-2210-10	87977	85128001	164122620	4	2098											
COL11A1	1301	hgsc.bcm.edu	37	chr1	103364535	103364535	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgtcttccctctgcacctgCagctccaggaggaccctata	7	11	8	15	0	2	0	0	0	2	0	4	2	4	2	4	2	3	3	4	2	2	4			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr1:103364535C>A	ENST00000370096.3	-	55	4414	c.4102G>T	c.(4102-4104)Gca>Tca	p.A1368S	COL11A1_ENST00000358392.2_Missense_Mutation_p.A1380S|COL11A1_ENST00000353414.4_Missense_Mutation_p.A1329S|COL11A1_ENST00000512756.1_Missense_Mutation_p.A1252S	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	1368	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)		TCTGCACCTGCAGCTCCAGGA	0.274																																					p.A1380S		Atlas-SNP	.											.	COL11A1	972	.	0			c.G4138T						PASS	.						44	45	44					1																	103364535		2201	4298	6499	SO:0001583	missense	1301	exon55			CACCTGCAGCTCC	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.4102G>T	1.37:g.103364535C>A	ENSP00000359114:p.Ala1368Ser	79	0	0		101	46	0.455446	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	37	CCDS778.1	.	.	.	.	.	.	.	.	.	.	C	12.00	1.807087	0.31961	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000370090;ENST00000512756	D;D;D;D	0.94330	-3.4;-3.4;-3.4;-3.4	6.06	1.46	0.22682	.	0.409732	0.27509	N	0.019059	D	0.84543	0.5495	L	0.43152	1.355	0.24453	N	0.994478	B;B;P;B;B	0.37708	0.043;0.073;0.606;0.0;0.03	B;B;P;B;B	0.49012	0.027;0.059;0.598;0.001;0.037	T	0.77130	-0.2701	10	0.20519	T	0.43	.	4.6044	0.12371	0.1589:0.3328:0.0:0.5083	.	1252;1329;1380;1368;588	E9PCU0;P12107-3;P12107-2;P12107;F5H5Z5	.;.;.;COBA1_HUMAN;.	S	1368;1380;1329;588;1252	ENSP00000359114:A1368S;ENSP00000351163:A1380S;ENSP00000302551:A1329S;ENSP00000426533:A1252S	ENSP00000302551:A1329S	A	-	1	0	COL11A1	103137123	0.906000	0.30813	0.990000	0.47175	0.983000	0.72400	0.385000	0.20685	-0.012000	0.14223	0.650000	0.86243	GCA	.	.	none		0.274	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		A	103364535	C	A	103364535	3	1	16	1	0	0	0	0	1	0	0	0	3669	710	25	4	1370	4	COL11A1	1	103364535	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	18236534	103364535	145886086	5	2099											
BAT2L2	23215	hgsc.bcm.edu	37	chr1	171557627	171557628	+	Frame_Shift_Del	DEL	AC	AC	-																															gaatgacacaaccatttcctAcacagtttgcaccccaggtg																										TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr1:171557627_171557628delAC	ENST00000338920.4	+	33	8413_8414	c.8176_8177delAC	c.(8176-8178)acafs	p.T2726fs	PRRC2C_ENST00000426496.2_Frame_Shift_Del_p.T2661fs|PRRC2C_ENST00000392078.3_Frame_Shift_Del_p.T2728fs|PRRC2C_ENST00000367742.3_Frame_Shift_Del_p.T2728fs	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	2726					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										ACCATTTCCTACACAGTTTGCA	0.396																																					p.2725_2726del		Atlas-Indel	.											BAT2D1_ENST00000392078,NS,carcinoma,+2,2	.	.	2	0			c.8175_8176del						PASS	.																																			SO:0001589	frameshift_variant	23215	exon33			.	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.8176_8177delAC	1.37:g.171557629_171557630delAC	ENSP00000343629:p.Thr2726fs	104	0	0		118	20	0.169492	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Frame_Shift_Del	DEL	ENST00000338920.4	37	CCDS1296.2																																																																																			.	.	none		0.396	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		-	171557628	AC	-	171557627	7	5	16	1	0	1	0	1	0	0	0	0	1321	391	14	0	8194	0	BAT2L2	1	171557627	Frame_Shift_Del	DEL	AC	TCGA-FF-8062-01A-11D-2210-10	68193092	171557627	77692994	6	2100											
TOR1AIP1	26092	hgsc.bcm.edu	37	chr1	179852022	179852022	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagacgcgaaggactaccCgccttcagcagcagcactca	12	5	10	14	3	2	2	2	1	0	1	2	4	2	3	2	1	4	3	2	1	3	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr1:179852022C>T	ENST00000606911.2	+	1	576	c.385C>T	c.(385-387)Cgc>Tgc	p.R129C	TOR1AIP1_ENST00000528443.2_Missense_Mutation_p.R129C|TOR1AIP1_ENST00000271583.3_Missense_Mutation_p.R129C|RP11-533E19.7_ENST00000610272.1_lincRNA|TOR1AIP1_ENST00000435319.4_Missense_Mutation_p.R8C			Q5JTV8	TOIP1_HUMAN	torsin A interacting protein 1	129					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						AAGGACTACCCGCCTTCAGCA	0.597																																					p.R129C		Atlas-SNP	.											.	TOR1AIP1	58	.	0			c.C385T						PASS	.						36	42	40					1																	179852022		2203	4300	6503	SO:0001583	missense	26092	exon1			ACTACCCGCCTTC		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.385C>T	1.37:g.179852022C>T	ENSP00000476687:p.Arg129Cys	101	0	0		92	4	0.0434783	NM_001267578	A8K630|B0QZ57|Q5JTV6|Q8IZ65|Q9H8Y6|Q9HAJ1|Q9NV52|Q9Y3X5	Missense_Mutation	SNP	ENST00000606911.2	37	CCDS1335.1	.	.	.	.	.	.	.	.	.	.	C	15.00	2.703232	0.48412	.	.	ENSG00000143337	ENST00000528443;ENST00000325993;ENST00000271583;ENST00000435319	T;T;T	0.26810	1.71;1.71;1.71	3.48	1.49	0.22878	.	0.353873	0.20615	N	0.088900	T	0.38506	0.1043	M	0.61703	1.905	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.65773	0.91;0.938	T	0.12426	-1.0548	10	0.72032	D	0.01	-0.3755	4.6478	0.12580	0.0:0.6448:0.2268:0.1284	.	129;129	Q5JTV8;E9PKD1	TOIP1_HUMAN;.	C	129	ENSP00000435365:R129C;ENSP00000271583:R129C;ENSP00000393292:R129C	ENSP00000271583:R129C	R	+	1	0	TOR1AIP1	178118645	0.004000	0.15560	0.005000	0.12908	0.019000	0.09904	1.565000	0.36386	0.267000	0.21916	0.563000	0.77884	CGC	.	.	none		0.597	TOR1AIP1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000100313.4	NM_015602		T	179852022	C	T	179852022	3	4	16	1	0	0	0	0	1	0	0	0	16387	652	23	1	387	1	TOR1AIP1	1	179852022	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	8294395	179852022	69398599	7	2101											
ARL8A	127829	hgsc.bcm.edu	37	chr1	202113679	202113679	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggccttgaaccagtccagcaGcttgttgaacaaagcgatca	12	8	10	11	1	1	2	1	2	0	0	2	3	2	2	3	1	5	3	3	1	3	3			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr1:202113679G>A	ENST00000272217.2	-	1	190	c.22C>T	c.(22-24)Ctg>Ttg	p.L8L		NM_001256129.1|NM_138795.3	NP_001243058.1|NP_620150.1	Q96BM9	ARL8A_HUMAN	ADP-ribosylation factor-like 8A	8					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						CAGTCCAGCAGCTTGTTGAAC	0.677																																					p.L8L		Atlas-SNP	.											.	ARL8A	14	.	0			c.C22T						PASS	.						79	63	69					1																	202113679		2203	4300	6503	SO:0001819	synonymous_variant	127829	exon1			CCAGCAGCTTGTT	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.22C>T	1.37:g.202113679G>A		25	0	0		29	7	0.241379	NM_138795	B3KXD0	Silent	SNP	ENST00000272217.2	37	CCDS1421.1																																																																																			.	.	none		0.677	ARL8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087493.1	NM_138795		A	202113679	G	A	202113679	2	1	16	1	0	0	0	0	0	0	0	1	946	962	34	2		2	ARL8A	1	202113679	Silent	SNP	G	TCGA-FF-8062-01A-11D-2210-10	22261657	202113679	47136942	8	2102											
SYT14	255928	hgsc.bcm.edu	37	chr1	210334267	210334267	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agcatgaaaagaaaagagatGataggctggatttctttagg	16	10	12	3	0	1	4	0	2	1	2	1	6	1	5	0	3	1	2	0	3	6	4			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr1:210334267G>C	ENST00000472886.1	+	8	1562	c.1548G>C	c.(1546-1548)atG>atC	p.M516I	SYT14_ENST00000367015.1_Missense_Mutation_p.M478I|SYT14_ENST00000422431.1_Missense_Mutation_p.M580I|SYT14_ENST00000271745.7_3'UTR|SYT14_ENST00000399639.2_3'UTR|SYT14_ENST00000534859.1_Missense_Mutation_p.M542I|SYT14_ENST00000537238.1_Missense_Mutation_p.M478I|SYT14_ENST00000367019.1_Missense_Mutation_p.M535I			Q8NB59	SYT14_HUMAN	synaptotagmin XIV	516	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)		GAAAAGAGATGATAGGCTGGA	0.398																																					p.M580I		Atlas-SNP	.											.	SYT14	89	.	0			c.G1740C						PASS	.						139	134	135					1																	210334267		2203	4300	6503	SO:0001583	missense	255928	exon10			AGAGATGATAGGC	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.1548G>C	1.37:g.210334267G>C	ENSP00000418901:p.Met516Ile	121	0	0		151	26	0.172185	NM_001146261	B1AJU0|B1AJU1|F5H426|Q5THX7|Q707N3|Q707N4|Q707N5|Q707N6|Q707N7	Missense_Mutation	SNP	ENST00000472886.1	37	CCDS31014.1	.	.	.	.	.	.	.	.	.	.	G	15.15	2.747320	0.49257	.	.	ENSG00000143469	ENST00000422431;ENST00000534859;ENST00000537238;ENST00000367019;ENST00000472886;ENST00000367015	T;T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21;-0.21	5.54	5.54	0.83059	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.039837	0.85682	D	0.000000	T	0.61999	0.2392	L	0.39397	1.21	0.80722	D	1	B;B;B;B	0.24426	0.1;0.057;0.103;0.082	B;B;B;B	0.29077	0.098;0.042;0.059;0.087	T	0.55250	-0.8170	10	0.21014	T	0.42	-22.5444	19.8284	0.96626	0.0:0.0:1.0:0.0	.	563;516;535;580	A1L3Y1;Q8NB59;Q8NB59-6;F5H426	.;SYT14_HUMAN;.;.	I	580;542;478;535;516;478	ENSP00000389039:M580I;ENSP00000442891:M542I;ENSP00000437423:M478I;ENSP00000355986:M535I;ENSP00000418901:M516I;ENSP00000355982:M478I	ENSP00000355982:M478I	M	+	3	0	SYT14	208400890	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.338000	0.96553	2.751000	0.94390	0.585000	0.79938	ATG	.	.	none		0.398	SYT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089124.1	NM_153262		C	210334267	G	C	210334267	3	2	16	1	0	0	0	0	1	0	0	0	15485	1290	45	4	1778	4	SYT14	1	210334267	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	8220588	210334267	38916354	9	2103											
PARP1	142	hgsc.bcm.edu	37	chr1	226573325	226573325	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagaccagctgacccgagcaTtcctcgcagggaaggagggc	11	4	14	12	2	0	2	0	1	0	1	2	5	1	4	3	3	2	3	3	3	2	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr1:226573325T>C	ENST00000366794.5	-	7	1034	c.891A>G	c.(889-891)gaA>gaG	p.E297E		NM_001618.3	NP_001609.2	P09874	PARP1_HUMAN	poly (ADP-ribose) polymerase 1	297					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)		GACCCGAGCATTCCTCGCAGG	0.562								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																													p.E297E		Atlas-SNP	.											.	PARP1	100	.	0			c.A891G						PASS	.						115	98	103					1																	226573325		2203	4300	6503	SO:0001819	synonymous_variant	142	exon7			CGAGCATTCCTCG	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.891A>G	1.37:g.226573325T>C		98	0	0		108	5	0.0462963	NM_001618	B1ANJ4|Q8IUZ9	Silent	SNP	ENST00000366794.5	37	CCDS1554.1																																																																																			.	.	none		0.562	PARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091519.1	NM_001618		C	226573325	T	C	226573325	2	2	16	1	0	0	0	0	0	0	0	1	11463	1490	52	3		3	PARP1	1	226573325	Silent	SNP	T	TCGA-FF-8062-01A-11D-2210-10	16239058	226573325	22677296	10	2104											
C1orf57	84284	hgsc.bcm.edu	37	chr1	233113956	233113956	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgccagatatcgtgacgtgCgtgcagagcagcaggaagtg	10	7	15	9	3	0	3	0	1	0	2	1	4	0	4	1	1	5	3	1	1	2	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr1:233113956C>T	ENST00000366628.5	+	5	639	c.552C>T	c.(550-552)tgC>tgT	p.C184C	NTPCR_ENST00000490098.1_3'UTR	NM_032324.1	NP_115700.1	Q9BSD7	NTPCR_HUMAN	nucleoside-triphosphatase, cancer-related	184						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						TCGTGACGTGCGTGCAGAGCA	0.537																																					p.C184C		Atlas-SNP	.											.	NTPCR	15	.	0			c.C552T						PASS	.						111	88	96					1																	233113956		2203	4300	6503	SO:0001819	synonymous_variant	84284	exon5			GACGTGCGTGCAG	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.552C>T	1.37:g.233113956C>T		110	0	0		89	4	0.0449438	NM_032324		Silent	SNP	ENST00000366628.5	37	CCDS1597.1																																																																																			.	.	none		0.537	NTPCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092324.2	NM_032324		T	233113956	C	T	233113956	2	4	16	1	0	0	0	0	0	0	0	1	2051	776	27	1		1	C1orf57	1	233113956	Silent	SNP	C	TCGA-FF-8062-01A-11D-2210-10	6540631	233113956	16136665	11	2105											
KRTCAP3	200634	hgsc.bcm.edu	37	chr2	27666008	27666008	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgcctgctccctgggcctccTtcttgctgtgtcactcactg	2	14	9	16	0	3	0	2	0	1	0	5	0	5	0	4	1	3	2	4	1	0	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr2:27666008T>C	ENST00000543753.1	+	4	388	c.341T>C	c.(340-342)cTt>cCt	p.L114P	KRTCAP3_ENST00000288873.3_Missense_Mutation_p.L114P|KRTCAP3_ENST00000407293.1_Missense_Mutation_p.L96P	NM_001168364.1	NP_001161836.1	Q53RY4	KCP3_HUMAN	keratinocyte associated protein 3	114						integral component of membrane (GO:0016021)				large_intestine(1)|lung(2)	3	Acute lymphoblastic leukemia(172;0.155)					CTGGGCCTCCTTCTTGCTGTG	0.627																																					p.L114P		Atlas-SNP	.											.	KRTCAP3	12	.	0			c.T341C						PASS	.						138	144	142					2																	27666008		2203	4300	6503	SO:0001583	missense	200634	exon4			GCCTCCTTCTTGC	AY157576	CCDS1754.1	2p23.3	2008-02-05			ENSG00000157992	ENSG00000157992			28943	protein-coding gene	gene with protein product							Standard	NM_173853		Approved	KCP3	uc002rks.3	Q53RY4	OTTHUMG00000097782	ENST00000543753.1:c.341T>C	2.37:g.27666008T>C	ENSP00000442400:p.Leu114Pro	127	0	0		100	4	0.04	NM_173853	B7ZL49|Q6UW42|Q8IWS5	Missense_Mutation	SNP	ENST00000543753.1	37	CCDS1754.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.014958	0.75161	.	.	ENSG00000157992	ENST00000543753;ENST00000288873;ENST00000407293	T;T;T	0.51071	0.72;0.72;0.72	5.77	5.77	0.91146	.	0.187045	0.47093	D	0.000255	T	0.64461	0.2600	M	0.65498	2.005	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.67925	-0.5544	10	0.87932	D	0	-14.8246	10.1184	0.42605	0.0:0.0789:0.0:0.9211	.	114	Q53RY4	KCP3_HUMAN	P	114;114;96	ENSP00000442400:L114P;ENSP00000288873:L114P;ENSP00000384689:L96P	ENSP00000288873:L114P	L	+	2	0	KRTCAP3	27519512	0.998000	0.40836	0.993000	0.49108	0.893000	0.52053	3.967000	0.56802	2.201000	0.70794	0.459000	0.35465	CTT	.	.	none		0.627	KRTCAP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215025.1	NM_173853		C	27666008	T	C	27666008	3	2	16	1	0	0	0	0	1	0	0	0	8588	1609	56	3	355	3	KRTCAP3	2	27666008	Missense_Mutation	SNP	T	TCGA-FF-8062-01A-11D-2210-10		27666008	215533365	12	2106											
LTBP1	4052	hgsc.bcm.edu	37	chr2	33614282	33614282	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cagctgtgtaacatccccgtGacgggacgccggcagccata	9	6	12	14	4	0	1	0	1	0	0	1	2	1	2	4	2	3	3	4	2	2	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr2:33614282G>C	ENST00000404816.2	+	32	5096	c.4743G>C	c.(4741-4743)gtG>gtC	p.V1581V	LTBP1_ENST00000407925.1_Silent_p.V1255V|LTBP1_ENST00000418533.2_Silent_p.V1213V|LTBP1_ENST00000272273.5_Silent_p.V479V|LTBP1_ENST00000402934.1_Silent_p.V1200V|LTBP1_ENST00000404525.1_Silent_p.V1202V|LTBP1_ENST00000390003.4_Silent_p.V1256V|LTBP1_ENST00000354476.3_Silent_p.V1582V			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1581					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)				ACATCCCCGTGACGGGACGCC	0.562																																					p.V1581V		Atlas-SNP	.											.	LTBP1	317	.	0			c.G4743C						PASS	.						115	103	107					2																	33614282		2203	4300	6503	SO:0001819	synonymous_variant	4052	exon32			CCCCGTGACGGGA		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.4743G>C	2.37:g.33614282G>C		136	0	0		148	48	0.324324	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Silent	SNP	ENST00000404816.2	37	CCDS33177.2																																																																																			.	.	none		0.562	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		C	33614282	G	C	33614282	2	2	16	1	0	0	0	0	0	0	0	1	9082	1277	45	4		4	LTBP1	2	33614282	Silent	SNP	G	TCGA-FF-8062-01A-11D-2210-10	5948274	33614282	209585091	13	2107											
UXS1	80146	hgsc.bcm.edu	37	chr2	106729179	106729179	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcatgtgcatgcgtggccCaaaggtgttgaagattctgg	8	12	14	7	1	2	2	1	1	1	1	2	2	2	2	1	3	2	3	1	3	2	3			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr2:106729179C>T	ENST00000409501.3	-	10	844	c.787G>A	c.(787-789)Ggg>Agg	p.G263R	UXS1_ENST00000409032.1_Missense_Mutation_p.G95R|UXS1_ENST00000540130.1_Missense_Mutation_p.G206R|UXS1_ENST00000283148.7_Missense_Mutation_p.G268R|UXS1_ENST00000428048.2_Missense_Mutation_p.G107R			Q8NBZ7	UXS1_HUMAN	UDP-glucuronate decarboxylase 1	263					protein tetramerization (GO:0051262)|UDP-D-xylose biosynthetic process (GO:0033320)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	NAD+ binding (GO:0070403)|protein homodimerization activity (GO:0042803)|UDP-glucuronate decarboxylase activity (GO:0048040)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)	17						ATGCGTGGCCCAAAGGTGTTG	0.602																																					p.G268R		Atlas-SNP	.											.	UXS1	75	.	0			c.G802A						PASS	.						72	74	74					2																	106729179		2106	4232	6338	SO:0001583	missense	80146	exon10			GTGGCCCAAAGGT	AK027244	CCDS46378.1, CCDS58720.1, CCDS58721.1	2q12.2	2012-02-22			ENSG00000115652	ENSG00000115652	4.1.1.35	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	17729	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 6E, member 12"	609749				19027726	Standard	NM_001253875		Approved	FLJ23591, UGD, SDR6E1	uc002tdn.3	Q8NBZ7	OTTHUMG00000153150	ENST00000409501.3:c.787G>A	2.37:g.106729179C>T	ENSP00000387019:p.Gly263Arg	92	0	0		65	10	0.153846	NM_001253875	Q8NBX3|Q9H5C2	Missense_Mutation	SNP	ENST00000409501.3	37	CCDS46378.1	.	.	.	.	.	.	.	.	.	.	C	31	5.081668	0.94050	.	.	ENSG00000115652	ENST00000283148;ENST00000540130;ENST00000409501;ENST00000409032;ENST00000428048;ENST00000441952;ENST00000416298;ENST00000444193	D;D;D;D;D;D;D;D	0.98649	-5.05;-5.05;-5.05;-5.05;-5.05;-5.05;-5.05;-5.05	5.25	5.25	0.73442	NAD-dependent epimerase/dehydratase (1);	0.000000	0.85682	D	0.000000	D	0.99677	0.9879	H	0.99964	5.085	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	0.96850	0.9624	10	0.87932	D	0	.	18.4398	0.90662	0.0:1.0:0.0:0.0	.	107;268;263	B4E3U7;Q8NBZ7-2;Q8NBZ7	.;.;UXS1_HUMAN	R	268;206;263;95;107;107;95;95	ENSP00000283148:G268R;ENSP00000438265:G206R;ENSP00000387019:G263R;ENSP00000387096:G95R;ENSP00000394334:G107R;ENSP00000416656:G107R;ENSP00000403612:G95R;ENSP00000404468:G95R	ENSP00000283148:G268R	G	-	1	0	UXS1	106095611	1.000000	0.71417	0.986000	0.45419	0.950000	0.60333	6.730000	0.74780	2.452000	0.82932	0.561000	0.74099	GGG	.	.	none		0.602	UXS1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329778.1	NM_025076.3		T	106729179	C	T	106729179	3	4	16	1	0	0	0	0	1	0	0	0	17124	594	21	2	499	2	UXS1	2	106729179	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	73114897	106729179	136470194	14	2108											
LIMS1	3987	hgsc.bcm.edu	37	chr2	109300340	109300340	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttataattttttgtctttaGgaataagtttgtggagtttg	9	22	9	1	0	1	0	0	0	1	0	1	2	1	2	0	2	0	2	0	2	5	11			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr2:109300340G>A	ENST00000393310.1	+	10	1030		c.e10-1		LIMS1_ENST00000410093.1_Splice_Site|LIMS1_ENST00000544547.1_Splice_Site|LIMS1_ENST00000409441.1_Splice_Site|LIMS1_ENST00000332345.6_Splice_Site|LIMS1_ENST00000338045.3_Splice_Site|LIMS1_ENST00000542845.1_Splice_Site	NM_001193488.1	NP_001180417.1	P48059	LIMS1_HUMAN	LIM and senescent cell antigen-like domains 1						cell aging (GO:0007569)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-matrix adhesion (GO:0007160)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chordate embryonic development (GO:0043009)|establishment or maintenance of cell polarity (GO:0007163)|negative regulation of apoptotic process (GO:0043066)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|protein heterooligomerization (GO:0051291)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)	10						TTTGTCTTTAGGAATAAGTTT	0.323																																					.		Atlas-SNP	.											.	LIMS1	38	.	0			c.900-1G>A						PASS	.						52	55	54					2																	109300340		2200	4299	6499	SO:0001630	splice_region_variant	3987	exon10			TCTTTAGGAATAA		CCDS2078.1, CCDS54382.1, CCDS54383.1, CCDS54384.1, CCDS54385.1	2q12.3	2008-05-23			ENSG00000169756	ENSG00000169756			6616	protein-coding gene	gene with protein product		602567				7517666, 10022929	Standard	NM_001193482		Approved	PINCH, PINCH1	uc002tek.4	P48059	OTTHUMG00000130983	ENST00000393310.1:c.864-1G>A	2.37:g.109300340G>A		154	0	0		202	46	0.227723	NM_001193483	B2RAJ4|B7Z483|B7Z7R3|B7Z907|Q53TE0|Q9BS44	Splice_Site	SNP	ENST00000393310.1	37	CCDS2078.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.573303	0.86542	.	.	ENSG00000169756	ENST00000544547;ENST00000332345;ENST00000393310;ENST00000410093;ENST00000409441;ENST00000338045;ENST00000542845	.	.	.	6.04	6.04	0.98038	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.5948	0.99439	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	LIMS1	108666772	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	9.827000	0.99397	2.873000	0.98535	0.563000	0.77884	.	.	.	none		0.323	LIMS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253596.1	NM_004987	Intron	A	109300340	G	A	109300340	5	1	16	1	0	0	0	0	0	0	1	0	8812	1014	35	2	897	2	LIMS1	2	109300340	Splice_Site	SNP	G	TCGA-FF-8062-01A-11D-2210-10	2571161	109300340	133899033	15	2109											
INHBB	3625	hgsc.bcm.edu	37	chr2	121107185	121107185	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctcatcggctggaacgactGgatcatagcacccaccggct	9	7	10	15	3	2	0	2	0	0	0	3	3	2	2	3	4	2	3	3	4	2	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr2:121107185G>A	ENST00000295228.3	+	2	1005	c.959G>A	c.(958-960)tGg>tAg	p.W320*		NM_002193.2	NP_002184.2	P09529	INHBB_HUMAN	inhibin, beta B	320					activin receptor signaling pathway (GO:0032924)|cell differentiation (GO:0030154)|cellular response to insulin stimulus (GO:0032869)|cellular response to leptin stimulus (GO:0044320)|cellular response to starvation (GO:0009267)|defense response (GO:0006952)|fat cell differentiation (GO:0045444)|growth (GO:0040007)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of hepatocyte growth factor biosynthetic process (GO:0048178)|negative regulation of insulin secretion (GO:0046676)|oocyte development (GO:0048599)|ovarian follicle development (GO:0001541)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|positive regulation of ovulation (GO:0060279)|response to mechanical stimulus (GO:0009612)	extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	cytokine activity (GO:0005125)|hormone activity (GO:0005179)|host cell surface receptor binding (GO:0046789)|protein homodimerization activity (GO:0042803)			NS(1)|breast(1)|endometrium(2)|large_intestine(3)|lung(4)|pancreas(2)|skin(2)	15		Prostate(154;0.122)				TGGAACGACTGGATCATAGCA	0.622																																					p.W320X		Atlas-SNP	.											INHBB,NS,malignant_melanoma,-1,1	INHBB	29	1	0			c.G959A						PASS	.						78	75	76					2																	121107185		2203	4300	6503	SO:0001587	stop_gained	3625	exon2			ACGACTGGATCAT		CCDS2132.1	2q14.2	2014-01-30	2007-07-30		ENSG00000163083	ENSG00000163083		"Endogenous ligands"	6067	protein-coding gene	gene with protein product		147390	"inhibin, beta B (activin AB beta polypeptide)"			3345731	Standard	NM_002193		Approved		uc002tmn.2	P09529	OTTHUMG00000131437	ENST00000295228.3:c.959G>A	2.37:g.121107185G>A	ENSP00000295228:p.Trp320*	142	0	0		100	4	0.04	NM_002193	Q53T31|Q8N1D3	Nonsense_Mutation	SNP	ENST00000295228.3	37	CCDS2132.1	.	.	.	.	.	.	.	.	.	.	G	16.51	3.144622	0.57044	.	.	ENSG00000163083	ENST00000295228	.	.	.	4.51	4.51	0.55191	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.61	16.4938	0.84209	0.0:0.0:1.0:0.0	.	.	.	.	X	320	.	ENSP00000295228:W320X	W	+	2	0	INHBB	120823655	1.000000	0.71417	1.000000	0.80357	0.066000	0.16364	9.507000	0.97996	2.495000	0.84180	0.563000	0.77884	TGG	.	.	none		0.622	INHBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254234.1			A	121107185	G	A	121107185	4	1	16	1	0	0	0	0	0	1	0	0	7751	1357	47	2	965	2	INHBB	2	121107185	Nonsense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	11806845	121107185	122092188	16	2110											
HECW2	57520	hgsc.bcm.edu	37	chr2	197092929	197092929	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataatatgggttaaagagttCtctggataccaggaagaaaa	17	10	10	4	0	1	2	0	0	1	2	2	4	1	4	1	3	1	2	1	3	8	5			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr2:197092929C>A	ENST00000260983.3	-	22	3996	c.3814G>T	c.(3814-3816)Gaa>Taa	p.E1272*	HECW2_ENST00000409111.1_Nonsense_Mutation_p.E916*	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	1272	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						TTAAAGAGTTCTCTGGATACC	0.348																																					p.E1272X		Atlas-SNP	.											.	HECW2	239	.	0			c.G3814T						PASS	.						83	86	85					2																	197092929		2203	4300	6503	SO:0001587	stop_gained	57520	exon22			AGAGTTCTCTGGA	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.3814G>T	2.37:g.197092929C>A	ENSP00000260983:p.Glu1272*	144	0	0		216	60	0.277778	NM_020760	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Nonsense_Mutation	SNP	ENST00000260983.3	37	CCDS33354.1	.	.	.	.	.	.	.	.	.	.	C	45	11.371157	0.99552	.	.	ENSG00000138411	ENST00000409111;ENST00000260983	.	.	.	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.4587	0.94906	0.0:1.0:0.0:0.0	.	.	.	.	X	916;1272	.	ENSP00000260983:E1272X	E	-	1	0	HECW2	196801174	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.651000	0.83577	2.828000	0.97474	0.655000	0.94253	GAA	.	.	none		0.348	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760		A	197092929	C	A	197092929	4	1	16	1	0	0	0	0	0	1	0	0	7052	922	32	4	936	4	HECW2	2	197092929	Nonsense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	75985744	197092929	46106444	17	2111											
TTLL4	9654	hgsc.bcm.edu	37	chr2	219602439	219602439	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcactatagtattggcctcCgccagaaaaacagcttcaag	14	8	8	11	1	1	1	1	0	0	1	2	1	2	1	3	1	3	3	3	1	6	5			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr2:219602439C>T	ENST00000392102.1	+	3	380	c.40C>T	c.(40-42)Cgc>Tgc	p.R14C	TTLL4_ENST00000258398.4_Missense_Mutation_p.R14C|TTLL4_ENST00000457313.1_Intron|TTLL4_ENST00000442769.1_Missense_Mutation_p.R14C	NM_014640.4	NP_055455.3	Q14679	TTLL4_HUMAN	tubulin tyrosine ligase-like family, member 4	14					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)		TATTGGCCTCCGCCAGAAAAA	0.592																																					p.R14C	GBM(172;1818 2053 15407 20943 49753)	Atlas-SNP	.											.	TTLL4	96	.	0			c.C40T						PASS	.						57	57	57					2																	219602439		2203	4300	6503	SO:0001583	missense	9654	exon3			GGCCTCCGCCAGA		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.40C>T	2.37:g.219602439C>T	ENSP00000375951:p.Arg14Cys	119	0	0		120	17	0.141667	NM_014640	A8K6V5|Q8WW29	Missense_Mutation	SNP	ENST00000392102.1	37	CCDS2422.1	.	.	.	.	.	.	.	.	.	.	c	7.873	0.728577	0.15507	.	.	ENSG00000135912	ENST00000415717;ENST00000392102;ENST00000437755;ENST00000442769;ENST00000424644;ENST00000258398	T;T;T;T;T;T	0.24908	1.83;1.83;1.83;1.83;1.83;1.83	5.32	0.493	0.16878	.	0.620848	0.15371	N	0.265860	T	0.14141	0.0342	N	0.20986	0.625	0.28758	N	0.901088	B;B	0.13145	0.004;0.007	B;B	0.04013	0.001;0.001	T	0.14476	-1.0471	10	0.87932	D	0	.	4.2465	0.10674	0.1639:0.4106:0.0:0.4255	.	14;14	E7EX20;Q14679	.;TTLL4_HUMAN	C	14	ENSP00000411228:R14C;ENSP00000375951:R14C;ENSP00000391342:R14C;ENSP00000396555:R14C;ENSP00000405485:R14C;ENSP00000258398:R14C	ENSP00000258398:R14C	R	+	1	0	TTLL4	219310683	0.139000	0.22563	0.923000	0.36655	0.461000	0.32589	-0.000000	0.12993	0.011000	0.14865	-0.970000	0.02610	CGC	.	.	none		0.592	TTLL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256726.1	NM_014640		T	219602439	C	T	219602439	3	4	16	1	0	0	0	0	1	0	0	0	16744	652	23	1	42	1	TTLL4	2	219602439	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	22509510	219602439	23596934	18	2112											
SP140	11262	hgsc.bcm.edu	37	chr2	231102990	231102990	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgatgtattgtgtactcagTgaactggagaagacatttgg	11	13	13	4	0	1	4	1	2	0	2	1	5	1	4	0	2	2	2	0	2	4	4			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr2:231102990T>G	ENST00000392045.3	+	3	414	c.300T>G	c.(298-300)agT>agG	p.S100R	SP140_ENST00000343805.6_Missense_Mutation_p.S100R|SP140_ENST00000350136.5_Missense_Mutation_p.S80R|SP140_ENST00000544128.1_3'UTR|SP140_ENST00000420434.3_Missense_Mutation_p.S100R|SP140_ENST00000417495.3_Missense_Mutation_p.S100R|SP140_ENST00000486687.2_Missense_Mutation_p.S100R|SP140_ENST00000373645.3_Missense_Mutation_p.S100R	NM_007237.4	NP_009168.4	Q13342	SP140_HUMAN	SP140 nuclear body protein	100	HSR. {ECO:0000255|PROSITE- ProRule:PRU00747}.				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)		GTGTACTCAGTGAACTGGAGA	0.388																																					p.S100R		Atlas-SNP	.											.	SP140	121	.	0			c.T300G						PASS	.						127	117	120					2																	231102990		2203	4300	6503	SO:0001583	missense	11262	exon3			ACTCAGTGAACTG	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.300T>G	2.37:g.231102990T>G	ENSP00000375899:p.Ser100Arg	181	0	0		230	51	0.221739	NM_007237	E7ESH9|E7EUR5|E9PFJ6|Q0VGE5|Q13341|Q3KR17|Q4ZG66|Q53TG1|Q6NSG4|Q92881|Q96TG3	Missense_Mutation	SNP	ENST00000392045.3	37	CCDS42831.1	.	.	.	.	.	.	.	.	.	.	T	12.17	1.856712	0.32791	.	.	ENSG00000079263	ENST00000537563;ENST00000486687;ENST00000392044;ENST00000350136;ENST00000392045;ENST00000417495;ENST00000343805;ENST00000420434;ENST00000373645	D;D;D;D;D;D	0.94931	-3.56;-3.56;-3.56;-3.56;-3.56;-3.56	3.7	-4.24	0.03777	Sp100 (2);	.	.	.	.	D	0.92792	0.7708	M	0.68317	2.08	0.09310	N	1	B;B;B;P;B;B	0.41232	0.288;0.288;0.244;0.743;0.45;0.122	B;B;B;P;B;B	0.50192	0.148;0.148;0.092;0.634;0.243;0.063	D	0.85321	0.1084	9	0.87932	D	0	-2.9298	0.0805	0.00031	0.3142:0.2021:0.1609:0.3228	.	100;100;100;100;100;100	E7EUR5;E7ESH9;E9PFJ6;Q13342;E7EX75;Q6NSG4	.;.;.;LY10_HUMAN;.;.	R	100;100;100;80;100;100;100;100;100	ENSP00000440107:S100R;ENSP00000345846:S80R;ENSP00000375899:S100R;ENSP00000342096:S100R;ENSP00000398210:S100R;ENSP00000362749:S100R	ENSP00000342096:S100R	S	+	3	2	SP140	230811234	0.000000	0.05858	0.001000	0.08648	0.793000	0.44817	-0.731000	0.04909	-0.792000	0.04480	0.533000	0.62120	AGT	.	.	none		0.388	SP140-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000332015.1	NM_007237		G	231102990	T	G	231102990	3	3	16	1	0	0	0	0	1	0	0	0	14977	1693	59	5	310	5	SP140	2	231102990	Missense_Mutation	SNP	T	TCGA-FF-8062-01A-11D-2210-10	11500551	231102990	12096383	19	2113											
RAF1	5894	hgsc.bcm.edu	37	chr3	12627290	12627290	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cactgttaagccttcatggaGaaatatatctcaatgcttgt	12	14	7	8	0	2	1	2	0	1	1	3	2	2	1	1	1	2	2	1	1	5	5			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr3:12627290G>A	ENST00000251849.4	-	14	1865	c.1426C>T	c.(1426-1428)Ctc>Ttc	p.L476F	RAF1_ENST00000442415.2_Missense_Mutation_p.L496F|RAF1_ENST00000542177.1_Missense_Mutation_p.L395F|RAF1_ENST00000534997.1_Missense_Mutation_p.L261F	NM_002880.3	NP_002871.1	P04049	RAF1_HUMAN	Raf-1 proto-oncogene, serine/threonine kinase	476	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		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)	CCTTCATGGAGAAATATATCT	0.388			T	SRGAP3	pilocytic astrocytoma				Noonan syndrome																												p.L476F		Atlas-SNP	.		Dom	yes		3	3p25	5894	v-raf-1 murine leukemia viral oncogene homolog 1		M	.	RAF1	66	.	0			c.C1426T						PASS	.						96	95	95					3																	12627290		2203	4300	6503	SO:0001583	missense	5894	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	CATGGAGAAATAT	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.1426C>T	3.37:g.12627290G>A	ENSP00000251849:p.Leu476Phe	58	0	0		61	15	0.245902	NM_002880	B0LPH8|B2R5N3|Q15278|Q9UC20	Missense_Mutation	SNP	ENST00000251849.4	37	CCDS2612.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.160558	0.78226	.	.	ENSG00000132155	ENST00000251849;ENST00000442415;ENST00000432427;ENST00000534997;ENST00000542177	D;D;D;D;D	0.85955	-2.05;-2.05;-2.05;-2.05;-2.05	5.26	5.26	0.73747	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.93106	0.7805	M	0.82923	2.615	0.80722	D	1	D;D;D	0.89917	0.985;0.985;1.0	D;D;D	0.87578	0.983;0.946;0.998	D	0.93639	0.6963	10	0.87932	D	0	.	19.0661	0.93110	0.0:0.0:1.0:0.0	.	395;261;476	B4E0X2;B4E1N6;P04049	.;.;RAF1_HUMAN	F	476;496;355;261;395	ENSP00000251849:L476F;ENSP00000401888:L496F;ENSP00000398591:L355F;ENSP00000441186:L261F;ENSP00000443567:L395F	ENSP00000251849:L476F	L	-	1	0	RAF1	12602290	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.135000	0.71696	2.746000	0.94184	0.655000	0.94253	CTC	.	.	none		0.388	RAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252015.2	NM_002880		A	12627290	G	A	12627290	3	1	16	1	0	0	0	0	1	0	0	0	13017	942	33	2	536	2	RAF1	3	12627290	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10		12627290	185395140	20	2114											
RAF1	5894	hgsc.bcm.edu	37	chr3	12645694	12645694	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgtggacattaggtgtggAtgtcgacctctgcctctggg	6	12	14	9	1	2	0	0	0	2	0	3	3	2	2	2	4	1	0	2	4	1	1	rs3730271		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr3:12645694A>G	ENST00000251849.4	-	7	1214	c.775T>C	c.(775-777)Tcc>Ccc	p.S259P	RAF1_ENST00000442415.2_Missense_Mutation_p.S259P|RAF1_ENST00000542177.1_Missense_Mutation_p.S178P|RAF1_ENST00000534997.1_Missense_Mutation_p.S44P	NM_002880.3	NP_002871.1	P04049	RAF1_HUMAN	Raf-1 proto-oncogene, serine/threonine kinase	259			S -> A (in an ovarian serous carcinoma sample; somatic mutation; increased ERK activation). {ECO:0000269|PubMed:17344846}.|S -> F (in NS5). {ECO:0000269|PubMed:17603483}.		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.S259A(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)	TTAGGTGTGGATGTCGACCTC	0.512			T	SRGAP3	pilocytic astrocytoma				Noonan syndrome																												p.S259P		Atlas-SNP	.		Dom	yes		3	3p25	5894	v-raf-1 murine leukemia viral oncogene homolog 1		M	RAF1,caecum,carcinoma,0,3	RAF1	66	3	1	Substitution - Missense(1)	ovary(1)	c.T775C	GRCh37	CM086899	RAF1	M	rs3730271	PASS	.						155	138	144					3																	12645694		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	GTGTGGATGTCGA	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.775T>C	3.37:g.12645694A>G	ENSP00000251849:p.Ser259Pro	126	0	0		165	37	0.224242	NM_002880	B0LPH8|B2R5N3|Q15278|Q9UC20	Missense_Mutation	SNP	ENST00000251849.4	37	CCDS2612.1	.	.	.	.	.	.	.	.	.	.	A	16.40	3.111444	0.56398	.	.	ENSG00000132155	ENST00000251849;ENST00000442415;ENST00000432427;ENST00000534997;ENST00000542177	T;T;T;T;T	0.77877	-1.1;-1.13;-1.06;-0.98;-1.08	5.73	5.73	0.89815	.	0.094049	0.85682	D	0.000000	D	0.88288	0.6396	M	0.81802	2.56	0.80722	D	1	P;D;B	0.76494	0.633;0.999;0.205	B;D;B	0.70487	0.349;0.969;0.111	D	0.89783	0.3962	10	0.87932	D	0	.	16.3123	0.82883	1.0:0.0:0.0:0.0	rs3730271;rs3730271	178;44;259	B4E0X2;B4E1N6;P04049	.;.;RAF1_HUMAN	P	259;259;138;44;178	ENSP00000251849:S259P;ENSP00000401888:S259P;ENSP00000398591:S138P;ENSP00000441186:S44P;ENSP00000443567:S178P	ENSP00000251849:S259P	S	-	1	0	RAF1	12620694	1.000000	0.71417	0.984000	0.44739	0.289000	0.27227	9.282000	0.95840	2.308000	0.77769	0.533000	0.62120	TCC	A|1.000;|0.000	.	weak		0.512	RAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252015.2	NM_002880		G	12645694	A	G	12645694	3	3	16	1	0	0	0	0	1	0	0	0	13017	333	12	3	1215	3	RAF1	3	12645694	Missense_Mutation	SNP	A	TCGA-FF-8062-01A-11D-2210-10	18404	12645694	185376736	21	2115											
SLC6A6	6533	hgsc.bcm.edu	37	chr3	14523273	14523273	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattgggctgggctggagccTggccctttcctccatgctct	3	12	12	14	0	1	0	0	0	1	0	3	1	3	1	4	4	2	3	4	4	0	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr3:14523273T>C	ENST00000454876.2	+	14	1975	c.1646T>C	c.(1645-1647)cTg>cCg	p.L549P	SLC6A6_ENST00000360861.3_Missense_Mutation_p.L549P			P31641	SC6A6_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 6	549					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						GGCTGGAGCCTGGCCCTTTCC	0.592																																					p.L549P		Atlas-SNP	.											.	SLC6A6	58	.	0			c.T1646C						PASS	.						136	119	125					3																	14523273		2203	4300	6503	SO:0001583	missense	6533	exon14			GGAGCCTGGCCCT		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.1646T>C	3.37:g.14523273T>C	ENSP00000398063:p.Leu549Pro	127	0	0		85	14	0.164706	NM_003043	B2RNU7|Q9BRI2|Q9BXB0	Missense_Mutation	SNP	ENST00000454876.2	37	CCDS33705.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.350042	0.82132	.	.	ENSG00000131389	ENST00000454876;ENST00000360861	T;T	0.80123	-1.34;-1.34	4.5	4.5	0.54988	.	0.074225	0.51477	D	0.000099	D	0.91713	0.7380	M	0.93763	3.455	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.93800	0.7100	10	0.87932	D	0	.	14.1214	0.65189	0.0:0.0:0.0:1.0	.	549	P31641	SC6A6_HUMAN	P	549	ENSP00000398063:L549P;ENSP00000354107:L549P	ENSP00000354107:L549P	L	+	2	0	SLC6A6	14498277	1.000000	0.71417	0.997000	0.53966	0.937000	0.57800	7.988000	0.88194	1.789000	0.52484	0.377000	0.23210	CTG	.	.	none		0.592	SLC6A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340507.1	NM_003043		C	14523273	T	C	14523273	3	2	16	1	0	0	0	0	1	0	0	0	14703	1580	55	3	1696	3	SLC6A6	3	14523273	Missense_Mutation	SNP	T	TCGA-FF-8062-01A-11D-2210-10	1877579	14523273	183499157	22	2116											
RFTN1	23180	hgsc.bcm.edu	37	chr3	16419279	16419279	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgctctccggtccatccaGtgtcttgctcaccccctgtg	3	13	9	16	1	3	0	1	0	2	0	6	0	5	0	5	1	2	3	5	1	0	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr3:16419279G>A	ENST00000334133.4	-	5	1044	c.772C>T	c.(772-774)Ctg>Ttg	p.L258L	RFTN1_ENST00000432519.1_Silent_p.L222L	NM_015150.1	NP_055965.1	Q14699	RFTN1_HUMAN	raftlin, lipid raft linker 1	258					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						GGTCCATCCAGTGTCTTGCTC	0.587																																					p.L258L		Atlas-SNP	.											.	RFTN1	79	.	0			c.C772T						PASS	.						70	74	73					3																	16419279		2203	4300	6503	SO:0001819	synonymous_variant	23180	exon5			CATCCAGTGTCTT	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.772C>T	3.37:g.16419279G>A		113	0	0		82	28	0.341463	NM_015150	Q0D2G0|Q496Y2|Q4QQI7|Q5JB48|Q7Z7P2	Silent	SNP	ENST00000334133.4	37	CCDS33712.1																																																																																			.	.	none		0.587	RFTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346908.1	NM_015150		A	16419279	G	A	16419279	2	1	16	1	0	0	0	0	0	0	0	1	13273	1020	36	2		2	RFTN1	3	16419279	Silent	SNP	G	TCGA-FF-8062-01A-11D-2210-10	1896006	16419279	181603151	23	2117											
THRB	7068	hgsc.bcm.edu	37	chr3	24231681	24231681	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagtggtctggatgagatgtGgcgacgactgttcatttttc	8	14	13	6	2	2	1	1	1	1	1	3	5	2	2	0	3	0	1	0	3	1	3			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr3:24231681G>A	ENST00000356447.4	-	4	451	c.167C>T	c.(166-168)cCa>cTa	p.P56L	THRB_ENST00000396671.2_Missense_Mutation_p.P56L|THRB_ENST00000416420.1_Missense_Mutation_p.P56L	NM_000461.4|NM_001128177.1	NP_000452.2|NP_001121649.1	P10828	THB_HUMAN	thyroid hormone receptor, beta	56	Modulating.				female courtship behavior (GO:0008050)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of female receptivity (GO:0007621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart contraction (GO:0008016)|sensory perception of sound (GO:0007605)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|Type I pneumocyte differentiation (GO:0060509)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone binding (GO:0070324)|thyroid hormone receptor activity (GO:0004887)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(6)|pancreas(2)|prostate(1)|skin(3)	19					Dextrothyroxine(DB00509)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	GATGAGATGTGGCGACGACTG	0.502																																					p.P56L	Melanoma(21;896 1043 15021 37958)	Atlas-SNP	.											.	THRB	52	.	0			c.C167T						PASS	.						247	234	239					3																	24231681		2203	4300	6503	SO:0001583	missense	7068	exon4			AGATGTGGCGACG		CCDS2641.1	3p24.2	2013-01-16	2011-05-19		ENSG00000151090	ENSG00000151090		"Nuclear hormone receptors"	11799	protein-coding gene	gene with protein product	"avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 2", "oncogene ERBA2", "generalized resistance to thyroid hormone", "thyroid hormone receptor beta 1"	190160	"thyroid hormone receptor, beta (avian erythroblastic leukemia viral (v-erb-a) oncogene homolog 2)", "pituitary resistance to thyroid hormone", "thyroid hormone receptor, beta (erythroblastic leukemia viral (v-erb-a) oncogene homolog 2, avian)"	ERBA2, PRTH		1973914, 8040303	Standard	NM_000461		Approved	THRB1, THRB2, NR1A2, THR1, ERBA-BETA, GRTH	uc003ccy.4	P10828	OTTHUMG00000130478	ENST00000356447.4:c.167C>T	3.37:g.24231681G>A	ENSP00000348827:p.Pro56Leu	204	0	0		246	48	0.195122	NM_000461	B3KU79|P37243|Q13986|Q3KP35|Q6WGL2|Q9UD41	Missense_Mutation	SNP	ENST00000356447.4	37	CCDS2641.1	.	.	.	.	.	.	.	.	.	.	G	10.73	1.433453	0.25813	.	.	ENSG00000151090	ENST00000396671;ENST00000356447;ENST00000416420;ENST00000413780;ENST00000415021;ENST00000447875;ENST00000453729;ENST00000431815;ENST00000447414;ENST00000428492;ENST00000418247	D;D;D;D	0.96427	-3.13;-3.13;-3.13;-4.01	5.81	4.0	0.46444	.	.	.	.	.	D	0.91372	0.7278	N	0.24115	0.695	0.09310	N	0.999996	B	0.02656	0.0	B	0.01281	0.0	D	0.84018	0.0352	9	0.59425	D	0.04	.	6.734	0.23399	0.0673:0.1301:0.667:0.1356	.	56	P10828	THB_HUMAN	L	56;56;56;25;56;56;56;56;56;56;56	ENSP00000379904:P56L;ENSP00000348827:P56L;ENSP00000414444:P56L;ENSP00000414100:P25L	ENSP00000348827:P56L	P	-	2	0	THRB	24206685	0.034000	0.19679	0.421000	0.26609	0.342000	0.28953	1.173000	0.31920	0.781000	0.33589	0.655000	0.94253	CCA	.	.	none		0.502	THRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252877.3	NM_000461		A	24231681	G	A	24231681	3	1	16	1	0	0	0	0	1	0	0	0	15890	1348	47	2	1246	2	THRB	3	24231681	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	7812402	24231681	173790749	24	2118											
RBMS3	27303	hgsc.bcm.edu	37	chr3	29938966	29938966	+	Splice_Site	SNP	G	G	T																															tcccctgtctccacataccaGgtatgtccaatttacctgca																								rs13060292		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr3:29938966G>T	ENST00000383767.2	+	9	1224	c.888G>T	c.(886-888)caG>caT	p.Q296H	RBMS3_ENST00000434693.2_Splice_Site_p.Q295H|RBMS3_ENST00000383766.2_Splice_Site_p.Q295H|RBMS3_ENST00000452462.1_Splice_Site_p.Q296H|RBMS3_ENST00000456853.1_Splice_Site_p.Q309H|RBMS3_ENST00000273139.9_Splice_Site_p.Q296H|RBMS3_ENST00000396583.3_Splice_Site_p.Q309H			Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting protein 3	296					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)				CCACATACCAGGTATGTCCAA	0.403																																					p.Q309H		Atlas-SNP	.											.	RBMS3	62	.	0			c.G927T						PASS	.						204	184	191					3																	29938966		2203	4300	6503	SO:0001630	splice_region_variant	27303	exon10			ATACCAGGTATGT	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.888+1G>T	3.37:g.29938966G>T		146	0	0		175	39	0.222857	NM_001177712	A8K9S4|B7ZL17|G5E9J9|O75876|Q17RI0|Q6XE23	Missense_Mutation	SNP	ENST00000383767.2	37	CCDS33724.1	.	.	.	.	.	.	.	.	.	.	G	31	5.100850	0.94245	.	.	ENSG00000144642	ENST00000434693;ENST00000396583;ENST00000383767;ENST00000273139;ENST00000383766;ENST00000452462;ENST00000456853	T;T;T;T;T;T;T	0.30182	1.54;1.59;1.56;1.58;1.67;1.57;1.59	5.21	5.21	0.72293	.	0.000000	0.85682	D	0.000000	T	0.61677	0.2366	M	0.85373	2.75	0.80722	D	1	D;D;P;D	0.89917	1.0;0.999;0.756;0.999	D;D;P;D	0.76071	0.987;0.981;0.644;0.971	T	0.66524	-0.5902	9	.	.	.	.	18.754	0.91825	0.0:0.0:1.0:0.0	.	296;309;295;296	G5E9J9;Q6XE24-2;Q6XE24-3;Q6XE24	.;.;.;RBMS3_HUMAN	H	295;309;296;296;295;296;309	ENSP00000395592:Q295H;ENSP00000379828:Q309H;ENSP00000373277:Q296H;ENSP00000273139:Q296H;ENSP00000373276:Q295H;ENSP00000397926:Q296H;ENSP00000400519:Q309H	.	Q	+	3	2	RBMS3	29913970	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.433000	0.82419	0.655000	0.94253	CAG	.	.	alt		0.403	RBMS3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341306.1	NM_001003792	Missense_Mutation	T	29938966	G	T	29938966	5	4	16	1	0	0	0	0	0	0	1	0	13165	1014	35	4	965	4	RBMS3	3	29938966	Splice_Site	SNP	G	TCGA-FF-8062-01A-11D-2210-10	5707285	29938966	168083464	25	2119	28	2									
RBMS3	27303	hgsc.bcm.edu	37	chr3	29938967	29938967	+	Splice_Site	SNP	G	G	T																															cccctgtctccacataccagGtatgtccaatttacctgcac																										TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr3:29938967G>T	ENST00000383767.2	+	9	1224		c.e9+1		RBMS3_ENST00000434693.2_Splice_Site|RBMS3_ENST00000383766.2_Splice_Site|RBMS3_ENST00000452462.1_Splice_Site|RBMS3_ENST00000456853.1_Splice_Site|RBMS3_ENST00000273139.9_Splice_Site|RBMS3_ENST00000396583.3_Splice_Site			Q6XE24	RBMS3_HUMAN	RNA binding motif, single stranded interacting protein 3						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)				CACATACCAGGTATGTCCAAT	0.398																																					.		Atlas-SNP	.											.	RBMS3	62	.	0			c.927+1G>T						PASS	.						204	183	190					3																	29938967		2203	4300	6503	SO:0001630	splice_region_variant	27303	exon10			TACCAGGTATGTC	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.888+1G>T	3.37:g.29938967G>T		143	0	0		177	41	0.231638	NM_001177712	A8K9S4|B7ZL17|G5E9J9|O75876|Q17RI0|Q6XE23	Splice_Site	SNP	ENST00000383767.2	37	CCDS33724.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.872761	0.91587	.	.	ENSG00000144642	ENST00000434693;ENST00000396583;ENST00000383767;ENST00000273139;ENST00000383766;ENST00000452462;ENST00000456853	.	.	.	5.21	5.21	0.72293	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.754	0.91825	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RBMS3	29913971	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.433000	0.82419	0.655000	0.94253	.	.	.	none		0.398	RBMS3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341306.1	NM_001003792	Intron	T	29938967	G	T	29938967	5	4	16	1	0	0	0	0	0	0	1	0	13165	1275	44	4	966	4	RBMS3	3	29938967	Splice_Site	SNP	G	TCGA-FF-8062-01A-11D-2210-10	1	29938967	168083463	26	2120	28	2									
SCN11A	11280	hgsc.bcm.edu	37	chr3	38924723	38924723	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cacaagacaatgatgatttaCcagtgccccactgctcagca	13	8	7	13	0	1	3	1	2	0	1	1	3	1	3	3	0	4	2	3	0	3	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr3:38924723C>T	ENST00000302328.3	-	18	3418		c.e18+1		SCN11A_ENST00000450244.1_Splice_Site|SCN11A_ENST00000456224.3_Splice_Site|SCN11A_ENST00000444237.2_Splice_Site	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit						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)	TGATGATTTACCAGTGCCCCA	0.488																																					.		Atlas-SNP	.											.	SCN11A	296	.	0			c.3219+1G>A						PASS	.						93	83	87					3																	38924723		2203	4300	6503	SO:0001630	splice_region_variant	11280	exon19			GATTTACCAGTGC	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.3219+1G>A	3.37:g.38924723C>T		72	0	0		82	4	0.0487805	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Splice_Site	SNP	ENST00000302328.3	37	CCDS33737.1	.	.	.	.	.	.	.	.	.	.	C	31	5.080272	0.94050	.	.	ENSG00000168356	ENST00000302328;ENST00000450244;ENST00000456224;ENST00000444237	.	.	.	5.69	5.69	0.88448	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.776	0.96393	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SCN11A	38899727	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.453000	0.80700	2.840000	0.97914	0.655000	0.94253	.	.	.	none		0.488	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139	Intron	T	38924723	C	T	38924723	5	4	16	1	0	0	0	0	0	0	1	0	13928	521	18	2	2191	2	SCN11A	3	38924723	Splice_Site	SNP	C	TCGA-FF-8062-01A-11D-2210-10	8985756	38924723	159097707	27	2121											
DOCK3	1795	hgsc.bcm.edu	37	chr3	51394558	51394558	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagctgtcaatggaggcattGcacgctatcaggaggtaagc	11	8	13	9	1	2	0	2	0	0	0	2	2	2	2	0	4	3	5	0	4	3	3			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr3:51394558G>A	ENST00000266037.9	+	44	4692	c.4669G>A	c.(4669-4671)Gca>Aca	p.A1557T		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	1557	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)		TGGAGGCATTGCACGCTATCA	0.522																																					p.A1557T		Atlas-SNP	.											.	DOCK3	397	.	0			c.G4669A						PASS	.						100	94	96					3																	51394558		2067	4226	6293	SO:0001583	missense	1795	exon44			GGCATTGCACGCT	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.4669G>A	3.37:g.51394558G>A	ENSP00000266037:p.Ala1557Thr	87	0	0		93	23	0.247312	NM_004947	O15017	Missense_Mutation	SNP	ENST00000266037.9	37	CCDS46835.1	.	.	.	.	.	.	.	.	.	.	G	16.48	3.135619	0.56828	.	.	ENSG00000088538	ENST00000266037;ENST00000402669	T	0.17370	2.28	5.84	5.84	0.93424	.	0.052235	0.85682	D	0.000000	T	0.16599	0.0399	L	0.38838	1.175	0.58432	D	0.999998	B	0.26672	0.156	B	0.29267	0.1	T	0.03130	-1.1069	10	0.34782	T	0.22	.	14.9171	0.70807	0.0:0.0:0.8569:0.1431	.	1557	Q8IZD9	DOCK3_HUMAN	T	1557;353	ENSP00000266037:A1557T	ENSP00000266037:A1557T	A	+	1	0	DOCK3	51369598	1.000000	0.71417	0.861000	0.33841	0.989000	0.77384	7.871000	0.87180	2.765000	0.95021	0.655000	0.94253	GCA	.	.	none		0.522	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		A	51394558	G	A	51394558	3	1	16	1	0	0	0	0	1	0	0	0	4690	1319	46	2	4843	2	DOCK3	3	51394558	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	12469835	51394558	146627872	28	2122											
EPHA3	2042	hgsc.bcm.edu	37	chr3	89390951	89390951	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atctctaatataaacgagacCtcagttatcctggactggag	13	11	8	9	1	2	1	1	0	1	1	4	4	3	3	2	2	1	1	2	2	5	4			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr3:89390951C>T	ENST00000336596.2	+	5	1242	c.1017C>T	c.(1015-1017)acC>acT	p.T339T	EPHA3_ENST00000494014.1_Silent_p.T339T|EPHA3_ENST00000452448.2_Silent_p.T339T	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	339	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		TAAACGAGACCTCAGTTATCC	0.403										TSP Lung(6;0.00050)																											p.T339T		Atlas-SNP	.											.	EPHA3	501	.	0			c.C1017T						PASS	.						76	79	78					3																	89390951		2203	4300	6503	SO:0001819	synonymous_variant	2042	exon5			CGAGACCTCAGTT	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.1017C>T	3.37:g.89390951C>T		83	0	0		93	4	0.0430108	NM_005233	Q9H2V3|Q9H2V4	Silent	SNP	ENST00000336596.2	37	CCDS2922.1																																																																																			.	.	none		0.403	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		T	89390951	C	T	89390951	2	4	16	1	0	0	0	0	0	0	0	1	5170	668	24	2		2	EPHA3	3	89390951	Silent	SNP	C	TCGA-FF-8062-01A-11D-2210-10	37996393	89390951	108631479	29	2123											
EPHA6	285220	hgsc.bcm.edu	37	chr3	97251298	97251298	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaaaggtggccacatggatcGgcaaagaagagattttctaa	15	8	12	6	1	1	2	0	0	1	2	2	5	1	3	1	4	0	1	1	4	4	3			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr3:97251298G>A	ENST00000514100.1	+	8	715	c.473G>A	c.(472-474)cGg>cAg	p.R158Q	EPHA6_ENST00000442602.2_Missense_Mutation_p.R132Q|EPHA6_ENST00000502694.1_Missense_Mutation_p.R158Q|EPHA6_ENST00000389672.5_Missense_Mutation_p.R766Q	NM_001278300.1	NP_001265229.1	Q9UF33	EPHA6_HUMAN	EPH receptor A6	672	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						CACATGGATCGGCAAAGAAGA	0.438																																					p.R766Q		Atlas-SNP	.											EPHA6,NS,carcinoma,+1,1	EPHA6	439	1	0			c.G2297A						scavenged	.						93	90	91					3																	97251298		1862	4119	5981	SO:0001583	missense	285220	exon11			TGGATCGGCAAAG	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.473G>A	3.37:g.97251298G>A	ENSP00000421711:p.Arg158Gln	96	1	0.0104167		122	27	0.221311	NM_001080448	D6RAL5	Missense_Mutation	SNP	ENST00000514100.1	37		.	.	.	.	.	.	.	.	.	.	G	20.5	3.999696	0.74818	.	.	ENSG00000080224	ENST00000389672;ENST00000514100;ENST00000502694;ENST00000442602	D;D;D;D	0.82255	-1.59;-1.59;-1.59;-1.59	5.85	5.85	0.93711	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.81889	0.4918	N	0.20304	0.555	0.51767	D	0.999937	P;B;D;P	0.62365	0.508;0.04;0.991;0.568	B;B;P;B	0.52109	0.073;0.019;0.69;0.039	D	0.83686	0.0174	9	0.59425	D	0.04	.	20.1542	0.98100	0.0:0.0:1.0:0.0	.	132;671;158;158	B4DXQ6;Q9UF33;Q9UF33-2;D6RAL5	.;EPHA6_HUMAN;.;.	Q	766;158;158;132	ENSP00000374323:R766Q;ENSP00000421711:R158Q;ENSP00000423950:R158Q;ENSP00000403100:R132Q	ENSP00000374323:R766Q	R	+	2	0	EPHA6	98733988	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.613000	0.54152	2.767000	0.95098	0.563000	0.77884	CGG	.	.	none		0.438	EPHA6-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000359997.1	NM_001080448		A	97251298	G	A	97251298	3	1	16	1	0	0	0	0	1	0	0	0	5173	1116	39	1	2407	1	EPHA6	3	97251298	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	7860347	97251298	100771132	30	2124											
OR5H6	79295	hgsc.bcm.edu	37	chr3	97983269	97983269	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataccgctcttcctggcattCttggtaatatatctcatcac	9	15	5	12	1	4	0	2	0	3	0	6	0	5	0	2	2	1	3	2	2	4	7			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr3:97983269C>A	ENST00000383696.2	+	1	182	c.141C>A	c.(139-141)ttC>ttA	p.F47L	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)	47						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						TCCTGGCATTCTTGGTAATAT	0.413																																					p.F47L		Atlas-SNP	.											OR5H6,bladder,carcinoma,0,1	OR5H6	89	1	0			c.C141A						PASS	.						207	217	213					3																	97983269		2203	4299	6502	SO:0001583	missense	79295	exon1			GGCATTCTTGGTA	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.141C>A	3.37:g.97983269C>A	ENSP00000373196:p.Phe47Leu	261	0	0		296	74	0.25	NM_001005479	Q6IF88	Missense_Mutation	SNP	ENST00000383696.2	37	CCDS33800.1	.	.	.	.	.	.	.	.	.	.	-	13.32	2.202696	0.38905	.	.	ENSG00000230301	ENST00000383696	T	0.04454	3.62	2.19	0.231	0.15377	.	0.000000	0.44902	D	0.000416	T	0.13756	0.0333	M	0.66297	2.02	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.02533	-1.1145	10	0.72032	D	0.01	.	6.0007	0.19519	0.0:0.6814:0.0:0.3186	.	47	Q8NGV6	OR5H6_HUMAN	L	47	ENSP00000373196:F47L	ENSP00000373196:F47L	F	+	3	2	OR5H6	99465959	0.000000	0.05858	0.002000	0.10522	0.058000	0.15608	-0.601000	0.05687	0.251000	0.21505	0.194000	0.17425	TTC	.	.	none		0.413	OR5H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359111.2			A	97983269	C	A	97983269	3	1	16	1	0	0	0	0	1	0	0	0	11172	912	32	4	143	4	OR5H6	3	97983269	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	731971	97983269	100039161	31	2125											
PLXNA1	5361	hgsc.bcm.edu	37	chr3	126733600	126733600	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctccgtgcgtgcccatgacGccctggtggaggtgtgtgtg	3	10	17	11	3	0	1	0	1	0	0	1	2	1	2	3	3	2	1	3	3	0	0			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr3:126733600G>A	ENST00000393409.2	+	13	2803	c.2803G>A	c.(2803-2805)Gcc>Acc	p.A935T	PLXNA1_ENST00000251772.4_Missense_Mutation_p.A912T	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	935	IPT/TIG 1.				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)		TGCCCATGACGCCCTGGTGGA	0.697																																					p.A935T		Atlas-SNP	.											.	PLXNA1	185	.	0			c.G2803A						PASS	.						62	46	52					3																	126733600		2202	4299	6501	SO:0001583	missense	5361	exon13			CATGACGCCCTGG	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.2803G>A	3.37:g.126733600G>A	ENSP00000377061:p.Ala935Thr	99	0	0		67	13	0.19403	NM_032242		Missense_Mutation	SNP	ENST00000393409.2	37	CCDS33847.2	.	.	.	.	.	.	.	.	.	.	G	23.3	4.402308	0.83230	.	.	ENSG00000114554	ENST00000393409;ENST00000251772	T;T	0.77098	-1.07;-1.07	4.21	4.21	0.49690	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000008	D	0.84088	0.5395	L	0.55743	1.74	0.58432	D	0.999999	D	0.60575	0.988	D	0.63488	0.915	D	0.84986	0.0891	10	0.48119	T	0.1	.	16.7531	0.85492	0.0:0.0:1.0:0.0	.	935	Q9UIW2	PLXA1_HUMAN	T	935;912	ENSP00000377061:A935T;ENSP00000251772:A912T	ENSP00000251772:A912T	A	+	1	0	PLXNA1	128216290	1.000000	0.71417	0.927000	0.36925	0.341000	0.28922	7.032000	0.76498	2.184000	0.69523	0.484000	0.47621	GCC	.	.	none		0.697	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242		A	126733600	G	A	126733600	3	1	16	1	0	0	0	0	1	0	0	0	12128	1087	38	1	2853	1	PLXNA1	3	126733600	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	28750331	126733600	71288830	32	2126											
SGEF	26084	hgsc.bcm.edu	37	chr3	153842198	153842199	+	Splice_Site	INS	-	-	A																															tacttttttttgtctcttagINSaaaaaaatgctgaaaggaca																										TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr3:153842198_153842199insA	ENST00000356448.4	+	3	1367_1368		c.e3-1		ARHGEF26_ENST00000465093.1_Splice_Site|ARHGEF26_ENST00000465817.1_Splice_Site	NM_001251962.1	NP_001238891.1	Q96DR7	ARHGQ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 26						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						ttGTCTCTTAGAAAAAAATGCT	0.267																																					.	GBM(163;191 2003 24758 29593 48540)|Ovarian(152;631 1885 20165 22910 51013)	Atlas-Indel	.											.	ARHGEF26	158	.	0			c.1084-1->A						PASS	.																																			SO:0001630	splice_region_variant	26084	exon3			.	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.1084-1->A	3.37:g.153842205_153842205dupA		23	0	0		31	10	0.322581	NM_001251962	B3KVP8|E9PBD0|Q68CL1|Q6AZ96|Q6Q8Q8|Q96AW8|Q96DR6|Q9H9D7|Q9H9R2|Q9UFW5	Splice_Site	INS	ENST00000356448.4	37	CCDS46938.1																																																																																			.	.	none		0.267	ARHGEF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353287.3	NM_015595	Intron	A	153842199	-	A	153842198	8	5	16	1	0	1	1	0	0	0	1	0	14220	956	33	0	1089	0	SGEF	3	153842198	Splice_Site	INS	-	TCGA-FF-8062-01A-11D-2210-10	27108598	153842198	44180232	33	2127											
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178916936	178916936	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aattgaaccagtaggcaaccGtgaagaaaagatcctcaatc	17	7	8	9	1	1	4	1	2	0	2	3	4	2	4	3	1	2	2	3	1	8	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr3:178916936G>T	ENST00000263967.3	+	2	480	c.323G>T	c.(322-324)cGt>cTt	p.R108L		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	108					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.R108H(11)|p.R108L(2)|p.G106_R108delGNR(2)|p.G106_R108del(2)|p.R108P(1)|p.R108del(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)	GTAGGCAACCGTGAAGAAAAG	0.338		57	Mis		"colorectal, gastric, gliobastoma, breast"					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.R108L	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,colon,carcinoma,0,39	PIK3CA	8460	39	19	Substitution - Missense(14)|Deletion - In frame(5)	endometrium(7)|large_intestine(5)|lung(4)|breast(2)|central_nervous_system(1)	c.G323T						scavenged	.						87	82	84					3																	178916936		1822	4071	5893	SO:0001583	missense	5290	exon2			GCAACCGTGAAGA		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.323G>T	3.37:g.178916936G>T	ENSP00000263967:p.Arg108Leu	67	0	0		59	3	0.0508475	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.594124	0.86953	.	.	ENSG00000121879	ENST00000263967;ENST00000468036	T;T	0.74002	0.83;-0.8	5.52	5.52	0.82312	Phosphatidylinositol 3-kinase, p85-binding (2);	0.000000	0.85682	D	0.000000	T	0.81545	0.4845	M	0.64404	1.975	0.80722	D	1	D	0.56035	0.974	P	0.54460	0.753	T	0.80502	-0.1354	9	.	.	.	-11.9048	19.4271	0.94746	0.0:0.0:1.0:0.0	.	108	P42336	PK3CA_HUMAN	L	108	ENSP00000263967:R108L;ENSP00000417479:R108L	.	R	+	2	0	PIK3CA	180399630	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.630000	0.83225	2.584000	0.87258	0.555000	0.69702	CGT	.	.	none		0.338	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			T	178916936	G	T	178916936	3	4	16	1	0	0	0	0	1	0	0	0	11922	1145	40	4	325	4	PIK3CA	3	178916936	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	25074738	178916936	19105494	34	2128											
KLHL6	89857	hgsc.bcm.edu	37	chr3	183209942	183209942	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gataccgcagctggcccgctCgtggctgagctgggtcacca	6	7	14	14	3	1	1	1	1	0	0	2	2	1	1	3	3	3	5	3	3	1	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr3:183209942C>G	ENST00000341319.3	-	7	1674	c.1639G>C	c.(1639-1641)Gag>Cag	p.E547Q		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	547					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)			CTGGCCCGCTCGTGGCTGAGC	0.657																																					p.E547Q		Atlas-SNP	.											.	KLHL6	100	.	0			c.G1639C						PASS	.						39	39	39					3																	183209942		2202	4299	6501	SO:0001583	missense	89857	exon7			CCCGCTCGTGGCT	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.1639G>C	3.37:g.183209942C>G	ENSP00000341342:p.Glu547Gln	174	0	0		152	27	0.177632	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Missense_Mutation	SNP	ENST00000341319.3	37	CCDS3245.2	.	.	.	.	.	.	.	.	.	.	C	20.1	3.940006	0.73557	.	.	ENSG00000172578	ENST00000341319	T	0.66815	-0.23	5.8	5.8	0.92144	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.73489	0.3593	L	0.33668	1.02	0.50467	D	0.999877	D	0.60575	0.988	D	0.66497	0.944	T	0.67245	-0.5719	10	0.22706	T	0.39	.	20.029	0.97531	0.0:1.0:0.0:0.0	.	547	Q8WZ60	KLHL6_HUMAN	Q	547	ENSP00000341342:E547Q	ENSP00000341342:E547Q	E	-	1	0	KLHL6	184692636	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.907000	0.69908	2.742000	0.94016	0.591000	0.81541	GAG	.	.	none		0.657	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446		G	183209942	C	G	183209942	3	3	16	1	0	0	0	0	1	0	0	0	8402	893	31	4	230	4	KLHL6	3	183209942	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	4293006	183209942	14812488	35	2129											
ANKRD56	345079	hgsc.bcm.edu	37	chr4	77818940	77818940	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctcagcaaggcagcgttggtCacgcggcccccagcctggca	7	5	13	16	3	2	0	2	0	0	0	2	0	2	0	3	4	3	4	3	4	1	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr4:77818940C>T	ENST00000334306.2	-	1	62	c.63G>A	c.(61-63)gtG>gtA	p.V21V		NM_001029870.1	NP_001025041.1	A6NEL2	SWAHB_HUMAN	sosondowah ankyrin repeat domain family member B	21																	CAGCGTTGGTCACGCGGCCCC	0.657																																					p.V21V		Atlas-SNP	.											.	.	.	.	0			c.G63A						PASS	.						24	26	25					4																	77818940		2201	4300	6501	SO:0001819	synonymous_variant	345079	exon1			GTTGGTCACGCGG		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.63G>A	4.37:g.77818940C>T		31	0	0		41	10	0.243902	NM_001029870	B2RP29	Silent	SNP	ENST00000334306.2	37	CCDS34017.1																																																																																			.	.	none		0.657	SOWAHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362762.1	NM_001029870		T	77818940	C	T	77818940	2	4	16	1	0	0	0	0	0	0	0	1	682	813	29	2		2	ANKRD56	4	77818940	Silent	SNP	C	TCGA-FF-8062-01A-11D-2210-10		77818940	113335336	36	2130											
MAPK10	5602	hgsc.bcm.edu	37	chr4	87022299	87022299	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	atgaagcttgtgcctgctgtCctggccagtccaaagtccag	8	10	11	12	0	0	1	0	1	0	0	3	1	3	1	5	1	3	2	5	1	2	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr4:87022299C>T	ENST00000359221.3	-	8	1162	c.636G>A	c.(634-636)agG>agA	p.R212R	MAPK10_ENST00000395166.1_Silent_p.R174R|MAPK10_ENST00000361569.2_Silent_p.R212R|MAPK10_ENST00000449047.2_Silent_p.R67R|MAPK10_ENST00000395161.2_Silent_p.R212R|MAPK10_ENST00000513839.1_5'Flank|MAPK10_ENST00000395160.3_Silent_p.R67R|MAPK10_ENST00000395157.3_Silent_p.R67R|MAPK10_ENST00000395169.3_Silent_p.R174R			P53779	MK10_HUMAN	mitogen-activated protein kinase 10	212	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)	p.R212S(1)|p.R67S(1)		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)		TGCCTGCTGTCCTGGCCAGTC	0.448																																					p.R212R		Atlas-SNP	.											MAPK10_ENST00000449047,NS,carcinoma,0,1	MAPK10	106	1	2	Substitution - Missense(2)	lung(2)	c.G636A						PASS	.						119	100	107					4																	87022299		2203	4300	6503	SO:0001819	synonymous_variant	5602	exon8			TGCTGTCCTGGCC	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.636G>A	4.37:g.87022299C>T		124	0	0		174	45	0.258621	NM_002753	A6NFS3|A6NG28|B3KQ94|Q15707|Q49AP1	Silent	SNP	ENST00000359221.3	37	CCDS34026.1	.	.	.	.	.	.	.	.	.	.	C	10.65	1.409014	0.25378	.	.	ENSG00000109339	ENST00000515400	.	.	.	5.84	3.2	0.36748	.	.	.	.	.	T	0.59487	0.2197	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55153	-0.8185	4	.	.	.	-18.4515	9.8477	0.41037	0.0:0.7294:0.0:0.2706	.	.	.	.	N	125	.	.	D	-	1	0	MAPK10	87241323	0.997000	0.39634	1.000000	0.80357	0.998000	0.95712	0.528000	0.23002	0.822000	0.34565	0.557000	0.71058	GAC	.	.	none		0.448	MAPK10-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000361363.2			T	87022299	C	T	87022299	2	4	16	1	0	0	0	0	0	0	0	1	9281	854	30	2		2	MAPK10	4	87022299	Silent	SNP	C	TCGA-FF-8062-01A-11D-2210-10	9203359	87022299	104131977	37	2131											
TACR3	6870	hgsc.bcm.edu	37	chr4	104511045	104511045	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtcacggtgtacatactgcTttgccggtttggatgaaacc	8	12	12	9	2	1	1	1	1	0	0	1	2	1	2	2	4	5	3	2	4	3	4			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr4:104511045T>C	ENST00000304883.2	-	5	1332	c.1192A>G	c.(1192-1194)Agc>Ggc	p.S398G	RP11-297P16.3_ENST00000502936.1_RNA|RP11-297P16.3_ENST00000512401.1_RNA	NM_001059.2	NP_001050.1	P29371	NK3R_HUMAN	tachykinin receptor 3	398					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)		TACATACTGCTTTGCCGGTTT	0.507																																					p.S398G		Atlas-SNP	.											.	TACR3	102	.	0			c.A1192G						PASS	.						207	193	198					4																	104511045		2203	4300	6503	SO:0001583	missense	6870	exon5			TACTGCTTTGCCG	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.1192A>G	4.37:g.104511045T>C	ENSP00000303325:p.Ser398Gly	195	0	0		252	58	0.230159	NM_001059	Q0P510	Missense_Mutation	SNP	ENST00000304883.2	37	CCDS3664.1	.	.	.	.	.	.	.	.	.	.	T	14.99	2.701190	0.48307	.	.	ENSG00000169836	ENST00000304883	T	0.66460	-0.21	5.81	4.64	0.57946	.	0.043074	0.85682	N	0.000000	T	0.57110	0.2031	L	0.45422	1.42	0.47476	D	0.999437	B	0.11235	0.004	B	0.10450	0.005	T	0.51068	-0.8752	10	0.33141	T	0.24	.	11.0731	0.48014	0.0:0.072:0.0:0.928	.	398	P29371	NK3R_HUMAN	G	398	ENSP00000303325:S398G	ENSP00000303325:S398G	S	-	1	0	TACR3	104730494	1.000000	0.71417	0.974000	0.42286	0.982000	0.71751	5.850000	0.69473	1.034000	0.39945	0.482000	0.46254	AGC	.	.	none		0.507	TACR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253804.1	NM_001059		C	104511045	T	C	104511045	3	2	16	1	0	0	0	0	1	0	0	0	15522	1609	56	3	209	3	TACR3	4	104511045	Missense_Mutation	SNP	T	TCGA-FF-8062-01A-11D-2210-10	17488746	104511045	86643231	38	2132											
TET2	54790	hgsc.bcm.edu	37	chr4	106158250	106158259	+	Frame_Shift_Del	DEL	CAGAAGCAAG	CAGAAGCAAG	-																															aggctcttactctcaaatcaCagaagcaagtaaaagttgaa																										TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	CAGAAGCAAG	CAGAAGCAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr4:106158250_106158259delCAGAAGCAAG	ENST00000540549.1	+	3	4011_4020	c.3151_3160delCAGAAGCAAG	c.(3151-3162)cagaagcaagtafs	p.QKQV1051fs	TET2_ENST00000380013.4_Frame_Shift_Del_p.QKQV1051fs|TET2_ENST00000513237.1_Frame_Shift_Del_p.QKQV1072fs|TET2_ENST00000413648.2_Frame_Shift_Del_p.QKQV1051fs|TET2_ENST00000545826.1_Frame_Shift_Del_p.QKQV1051fs|TET2_ENST00000394764.1_Frame_Shift_Del_p.QKQV1051fs|TET2_ENST00000305737.2_Frame_Shift_Del_p.QKQV1051fs			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1051					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)	p.Q1053*(2)|p.Q1051*(1)		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)		TCTCAAATCACAGAAGCAAGTAAAAGTTGA	0.443			"Mis N, F"		MDS																																p.1050_1053del		Pindel,Atlas-Indel	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	3	Substitution - Nonsense(3)	haematopoietic_and_lymphoid_tissue(3)	c.3150_3159del						PASS	.																																			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	ENST00000540549.1:c.3151_3160delCAGAAGCAAG	4.37:g.106158250_106158259delCAGAAGCAAG	ENSP00000442788:p.Gln1051fs	86	0	.		133	23	0.173	NM_017628	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Frame_Shift_Del	DEL	ENST00000540549.1	37	CCDS47120.1																																																																																			.	.	none		0.443	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		-	106158259	CAGAAGCAAG	-	106158250	7	5	16	1	0	1	0	1	0	0	0	0	15785	479	17	0	3153	0	TET2	4	106158250	Frame_Shift_Del	DEL	CAGAAGCAAG	TCGA-FF-8062-01A-11D-2210-10	1647205	106158250	84996026	39	2133											
TET2	54790	hgsc.bcm.edu	37	chr4	106182925	106182925	+	Frame_Shift_Del	DEL	C	C	-																															actttatacaggaagagaaaCtggagtctcatttgcaaaac																										TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr4:106182925delC	ENST00000540549.1	+	8	4824	c.3964delC	c.(3964-3966)ctgfs	p.L1322fs	TET2_ENST00000380013.4_Frame_Shift_Del_p.L1322fs|TET2_ENST00000513237.1_Frame_Shift_Del_p.L1343fs|TET2_ENST00000545826.1_3'UTR			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1322					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)		GGAAGAGAAACTGGAGTCTCA	0.313			"Mis N, F"		MDS																																p.K1321fs		Pindel,Atlas-Indel	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	0			c.3963delA						PASS	.						87	74	78					4																	106182925		692	1588	2280	SO:0001589	frameshift_variant	54790	exon8			.	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.3964delC	4.37:g.106182925delC	ENSP00000442788:p.Leu1322fs	229	0	.		251	39	0.155	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Frame_Shift_Del	DEL	ENST00000540549.1	37	CCDS47120.1																																																																																			.	.	none		0.313	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		-	106182925	C	-	106182925	7	5	16	1	0	1	0	1	0	0	0	0	15785	564	20	0	4075	0	TET2	4	106182925	Frame_Shift_Del	DEL	C	TCGA-FF-8062-01A-11D-2210-10	24675	106182925	84971351	40	2134											
ANK2	287	hgsc.bcm.edu	37	chr4	114294465	114294465	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctaggaaaatcattaggcggTatgtatcctctgaaggcaca	13	10	10	8	1	2	1	1	1	1	0	3	2	3	2	1	4	0	3	1	4	7	4			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr4:114294465T>G	ENST00000357077.4	+	45	11772	c.11719T>G	c.(11719-11721)Tat>Gat	p.Y3907D	ANK2_ENST00000509550.1_Missense_Mutation_p.Y998D|ANK2_ENST00000394537.3_Missense_Mutation_p.Y1822D|ANK2_ENST00000264366.6_Missense_Mutation_p.Y3874D|ANK2_ENST00000506722.1_Missense_Mutation_p.Y1813D|ANK2_ENST00000510275.2_Missense_Mutation_p.Y505D	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	3907					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)		CATTAGGCGGTATGTATCCTC	0.383																																					p.Y3907D		Atlas-SNP	.											.	ANK2	576	.	0			c.T11719G						PASS	.						84	84	84					4																	114294465		2203	4300	6503	SO:0001583	missense	287	exon45			AGGCGGTATGTAT	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.11719T>G	4.37:g.114294465T>G	ENSP00000349588:p.Tyr3907Asp	85	0	0		148	25	0.168919	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.5|24.5	4.542868|4.542868	0.86022|0.86022	.|.	.|.	ENSG00000145362|ENSG00000145362	ENST00000514960|ENST00000506722;ENST00000431447;ENST00000394537;ENST00000357077;ENST00000264366;ENST00000343056;ENST00000509550;ENST00000510275;ENST00000505342	.|T;T;T;T;T;D;D	.|0.96491	.|-0.33;-0.31;-0.37;-0.38;-1.08;-2.04;-4.03	6.06|6.06	6.06|6.06	0.98353|0.98353	.|.	.|0.135690	.|0.33553	.|N	.|0.004794	D|D	0.97626|0.97626	0.9222|0.9222	M|M	0.70595|0.70595	2.14|2.14	0.46317|0.46317	D|D	0.998987|0.998987	.|D;D;D;P;D;D	.|0.71674	.|0.963;0.996;0.979;0.892;0.998;0.984	.|P;D;P;P;D;D	.|0.64506	.|0.642;0.919;0.642;0.643;0.917;0.926	D|D	0.97950|0.97950	1.0331|1.0331	5|10	.|0.56958	.|D	.|0.05	.|.	16.6093|16.6093	0.84858|0.84858	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|998;888;854;1822;3907;1813	.|E9PCH6;F8W694;Q7Z344;Q01484-2;Q01484-4;Q01484-5	.|.;.;.;.;.;.	G|D	854|1813;888;1822;3907;3874;1813;998;505;917	.|ENSP00000421067:Y1813D;ENSP00000378044:Y1822D;ENSP00000349588:Y3907D;ENSP00000264366:Y3874D;ENSP00000426944:Y998D;ENSP00000421023:Y505D;ENSP00000422498:Y917D	.|ENSP00000264366:Y3874D	V|Y	+|+	2|1	0|0	ANK2|ANK2	114513914|114513914	0.979000|0.979000	0.34478|0.34478	0.749000|0.749000	0.31150|0.31150	0.846000|0.846000	0.48090|0.48090	4.663000|4.663000	0.61532|0.61532	2.324000|2.324000	0.78689|0.78689	0.533000|0.533000	0.62120|0.62120	GTA|TAT	.	.	none		0.383	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		G	114294465	T	G	114294465	3	3	16	1	0	0	0	0	1	0	0	0	621	1638	57	5	11962	5	ANK2	4	114294465	Missense_Mutation	SNP	T	TCGA-FF-8062-01A-11D-2210-10	8111540	114294465	76859811	41	2135											
PDE5A	8654	hgsc.bcm.edu	37	chr4	120460116	120460116	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaagaaagaggataattaccGctaacgactgtagctctctt	15	10	8	8	2	1	2	0	0	1	2	2	4	1	3	1	1	3	3	1	1	6	5	rs142017762		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr4:120460116G>A	ENST00000354960.3	-	11	1950	c.1631C>T	c.(1630-1632)gCg>gTg	p.A544V	PDE5A_ENST00000512739.1_5'UTR|PDE5A_ENST00000394439.1_Splice_Site_p.A492V|PDE5A_ENST00000264805.5_Splice_Site_p.A502V|RP11-33B1.1_ENST00000498873.1_RNA	NM_001083.3	NP_001074.2	O76074	PDE5A_HUMAN	phosphodiesterase 5A, cGMP-specific	544					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)	GATAATTACCGCTAACGACTG	0.343																																					p.A544V		Atlas-SNP	.											.	PDE5A	83	.	0			c.C1631T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA	0,4406		0,0,2203	137	152	147		1631,1505,1475	4.9	1	4	dbSNP_134	147	1,8599	1.2+/-3.3	0,1,4299	no	missense-near-splice,missense-near-splice,missense-near-splice	PDE5A	NM_001083.3,NM_033430.2,NM_033437.3	64,64,64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign	544/876,502/834,492/824	120460116	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	8654	exon11			ATTACCGCTAACG	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.1632+1C>T	4.37:g.120460116G>A		86	0	0		127	16	0.125984	NM_001083	A0AV69|A8K2C4|O75026|O75887|Q86UI0|Q86V66|Q9Y6Z6	Missense_Mutation	SNP	ENST00000354960.3	37	CCDS3713.1	.	.	.	.	.	.	.	.	.	.	G	15.44	2.832877	0.50951	0.0	1.16E-4	ENSG00000138735	ENST00000354960;ENST00000394439;ENST00000264805	T;T;T	0.62941	-0.01;0.04;0.04	5.8	4.94	0.65067	.	0.317482	0.32655	N	0.005809	T	0.46483	0.1395	N	0.16478	0.41	0.47737	D	0.999504	B;B	0.13145	0.007;0.002	B;B	0.04013	0.0;0.001	T	0.30794	-0.9966	10	0.23302	T	0.38	.	15.7381	0.77863	0.0:0.0:0.8623:0.1377	.	544;502	O76074;O76074-2	PDE5A_HUMAN;.	V	544;492;502	ENSP00000347046:A544V;ENSP00000377957:A492V;ENSP00000264805:A502V	ENSP00000264805:A502V	A	-	2	0	PDE5A	120679564	1.000000	0.71417	0.998000	0.56505	0.947000	0.59692	4.056000	0.57448	1.411000	0.46957	0.650000	0.86243	GCG	G|1.000;A|0.000	0.000	weak		0.343	PDE5A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256529.1	NM_001083	Missense_Mutation	A	120460116	G	A	120460116	5	1	16	1	0	0	0	0	0	0	1	0	11653	1101	38	1	1040	1	PDE5A	4	120460116	Splice_Site	SNP	G	TCGA-FF-8062-01A-11D-2210-10	6165651	120460116	70694160	42	2136											
TMEM184C	55751	hgsc.bcm.edu	37	chr4	148539118	148539118	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcgaaaacatgccttgcaCttgtacctggaggaactgga	11	9	12	9	1	0	0	0	0	0	0	0	4	0	3	2	3	6	2	2	3	4	3			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr4:148539118C>T	ENST00000296582.3	+	1	585	c.11C>T	c.(10-12)aCt>aTt	p.T4I	RP11-425A23.1_ENST00000508072.1_RNA|TMEM184C_ENST00000508208.1_Missense_Mutation_p.T4I	NM_018241.2	NP_060711.2	Q9NVA4	T184C_HUMAN	transmembrane protein 184C	4						integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(2)|prostate(1)	16						ATGCCTTGCACTTGTACCTGG	0.478											OREG0016353	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T4I		Atlas-SNP	.											.	TMEM184C	25	.	0			c.C11T						PASS	.						264	246	252					4																	148539118		2203	4300	6503	SO:0001583	missense	55751	exon1			CTTGCACTTGTAC	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.11C>T	4.37:g.148539118C>T	ENSP00000296582:p.Thr4Ile	205	0	0	1718	220	51	0.231818	NM_018241	D3DP04|Q86X84|Q969I7|Q9NXM2	Missense_Mutation	SNP	ENST00000296582.3	37	CCDS3770.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.374141	0.82573	.	.	ENSG00000164168	ENST00000296582;ENST00000508208	.	.	.	5.45	5.45	0.79879	.	0.138744	0.48767	D	0.000162	T	0.57621	0.2066	L	0.43152	1.355	0.51233	D	0.999917	B	0.31680	0.335	B	0.28139	0.086	T	0.58951	-0.7545	9	0.56958	D	0.05	-10.0523	19.6609	0.95871	0.0:1.0:0.0:0.0	.	4	Q9NVA4	T184C_HUMAN	I	4	.	ENSP00000296582:T4I	T	+	2	0	TMEM184C	148758568	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	7.185000	0.77714	2.720000	0.93068	0.557000	0.71058	ACT	.	.	none		0.478	TMEM184C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364644.1	NM_018241		T	148539118	C	T	148539118	3	4	16	1	0	0	0	0	1	0	0	0	16121	565	20	2	13	2	TMEM184C	4	148539118	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	28079002	148539118	42615158	43	2137											
FBXL7	23194	hgsc.bcm.edu	37	chr5	15928178	15928178	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacacacccgctcatccggCtcgcctccagaccccagaag	9	5	7	20	3	2	2	2	0	0	2	5	2	4	2	6	1	0	2	6	1	1	0			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr5:15928178C>A	ENST00000504595.1	+	3	788	c.307C>A	c.(307-309)Ctc>Atc	p.L103I	FBXL7_ENST00000510662.1_Missense_Mutation_p.L56I|FBXL7_ENST00000329673.7_Missense_Mutation_p.L91I	NM_001278317.1|NM_012304.3	NP_001265246.1|NP_036436.1	Q9UJT9	FBXL7_HUMAN	F-box and leucine-rich repeat protein 7	103					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						GCTCATCCGGCTCGCCTCCAG	0.677																																					p.L103I		Atlas-SNP	.											FBXL7,NS,carcinoma,-2,1	FBXL7	138	1	0			c.C307A						PASS	.						19	25	23					5																	15928178		2032	4180	6212	SO:0001583	missense	23194	exon3			ATCCGGCTCGCCT	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.307C>A	5.37:g.15928178C>A	ENSP00000423630:p.Leu103Ile	47	0	0		54	15	0.277778	NM_012304	B9EGF1|D6RDY7|O94926	Missense_Mutation	SNP	ENST00000504595.1	37	CCDS54833.1	.	.	.	.	.	.	.	.	.	.	C	10.92	1.486928	0.26686	.	.	ENSG00000183580	ENST00000504595;ENST00000510662;ENST00000329673	T;T;T	0.10573	2.89;2.86;2.89	5.52	4.65	0.58169	.	0.324591	0.29868	N	0.011000	T	0.06781	0.0173	N	0.19112	0.55	0.38780	D	0.954745	B	0.09022	0.002	B	0.04013	0.001	T	0.26467	-1.0102	10	0.37606	T	0.19	.	6.5028	0.22178	0.1505:0.7051:0.0:0.1444	.	103	Q9UJT9	FBXL7_HUMAN	I	103;56;91	ENSP00000423630:L103I;ENSP00000425184:L56I;ENSP00000329632:L91I	ENSP00000329632:L91I	L	+	1	0	FBXL7	15981178	0.998000	0.40836	0.893000	0.35052	0.928000	0.56348	1.263000	0.33004	1.324000	0.45282	-0.311000	0.09066	CTC	.	.	none		0.677	FBXL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366117.1	NM_012304		A	15928178	C	A	15928178	3	1	16	1	0	0	0	0	1	0	0	0	5732	797	28	4	317	4	FBXL7	5	15928178	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10		15928178	164987082	44	2138											
PRDM9	56979	hgsc.bcm.edu	37	chr5	23526430	23526430	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacatgtagaacgcaatcaCtcctctcagaacttcccagg	13	8	6	14	1	2	2	2	0	1	2	5	2	4	2	2	1	3	2	2	1	5	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr5:23526430C>T	ENST00000296682.3	+	11	1415	c.1233C>T	c.(1231-1233)caC>caT	p.H411H		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	411					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						AACGCAATCACTCCTCTCAGA	0.483										HNSCC(3;0.000094)																											p.H411H		Atlas-SNP	.											.	PRDM9	344	.	0			c.C1233T						PASS	.						131	123	126					5																	23526430		2203	4300	6503	SO:0001819	synonymous_variant	56979	exon11			CAATCACTCCTCT	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.1233C>T	5.37:g.23526430C>T		240	0	0		231	38	0.164502	NM_020227	B4DX22|Q27Q50	Silent	SNP	ENST00000296682.3	37	CCDS43307.1																																																																																			.	.	none		0.483	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		T	23526430	C	T	23526430	2	4	16	1	0	0	0	0	0	0	0	1	12475	564	20	2		2	PRDM9	5	23526430	Silent	SNP	C	TCGA-FF-8062-01A-11D-2210-10	7598252	23526430	157388830	45	2139											
CDH10	1008	hgsc.bcm.edu	37	chr5	24593514	24593514	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctttgctgtggcacaggcGtccttctgaacattatttct	6	17	8	10	1	3	1	0	1	3	0	4	1	4	1	1	2	2	2	1	2	2	5	rs140810299		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr5:24593514G>A	ENST00000264463.4	-	2	593	c.86C>T	c.(85-87)aCg>aTg	p.T29M	RP11-116O11.1_ENST00000510391.1_RNA	NM_006727.3	NP_006718.2	Q9Y6N8	CAD10_HUMAN	cadherin 10, type 2 (T2-cadherin)	29					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)		TGGCACAGGCGTCCTTCTGAA	0.403										HNSCC(23;0.051)			G|||	1	0.000199681	0.0	0.0	5008	,	,		16405	0.0		0.001	False		,,,				2504	0.0				p.T29M		Atlas-SNP	.											.	CDH10	391	.	0			c.C86T						PASS	.	G	MET/THR	1,4405	2.1+/-5.4	0,1,2202	105	98	101		86	2.5	1	5	dbSNP_134	101	0,8598		0,0,4299	no	missense	CDH10	NM_006727.3	81	0,1,6501	AA,AG,GG		0.0,0.0227,0.0077	benign	29/789	24593514	1,13003	2203	4299	6502	SO:0001583	missense	1008	exon2			ACAGGCGTCCTTC	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.86C>T	5.37:g.24593514G>A	ENSP00000264463:p.Thr29Met	145	0	0		185	36	0.194595	NM_006727	Q9ULB3	Missense_Mutation	SNP	ENST00000264463.4	37	CCDS3892.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	10.53	1.375184	0.24857	2.27E-4	0.0	ENSG00000040731	ENST00000264463	T	0.56103	0.48	4.36	2.53	0.30540	.	0.543154	0.19943	N	0.102617	T	0.43897	0.1268	L	0.50333	1.59	0.28771	N	0.900348	B	0.17852	0.024	B	0.14578	0.011	T	0.41787	-0.9489	10	0.45353	T	0.12	.	9.2453	0.37523	0.1795:0.0:0.8205:0.0	.	29	Q9Y6N8	CAD10_HUMAN	M	29	ENSP00000264463:T29M	ENSP00000264463:T29M	T	-	2	0	CDH10	24629271	1.000000	0.71417	0.993000	0.49108	0.503000	0.33858	6.687000	0.74552	0.962000	0.38057	-0.244000	0.11960	ACG	G|1.000;A|0.000	0.000	strong		0.403	CDH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207345.2	NM_006727		A	24593514	G	A	24593514	3	1	16	1	0	0	0	0	1	0	0	0	3098	1145	40	1	2324	1	CDH10	5	24593514	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	1067084	24593514	156321746	46	2140											
CAMK4	814	hgsc.bcm.edu	37	chr5	110560276	110560276	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgcgagcctcgtcccggattActggatcgacggctccaaca	8	7	11	15	6	0	0	0	0	0	0	4	4	2	2	3	3	3	1	3	3	2	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr5:110560276A>T	ENST00000282356.4	+	1	493	c.95A>T	c.(94-96)tAc>tTc	p.Y32F	CAMK4_ENST00000512453.1_Missense_Mutation_p.Y32F	NM_001744.4	NP_001735.1	Q16566	KCC4_HUMAN	calcium/calmodulin-dependent protein kinase IV	32					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|long-term memory (GO:0007616)|myeloid dendritic cell differentiation (GO:0043011)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleocytoplasmic transport (GO:0006913)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of osteoclast differentiation (GO:0045670)|regulation of T cell differentiation in thymus (GO:0033081)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	30		all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109)		GTCCCGGATTACTGGATCGAC	0.682																																					p.Y32F		Atlas-SNP	.											.	CAMK4	77	.	0			c.A95T						PASS	.						27	30	29					5																	110560276		2202	4300	6502	SO:0001583	missense	814	exon1			CGGATTACTGGAT	D30742	CCDS4103.1	5q22.1	2012-09-20			ENSG00000152495	ENSG00000152495	2.7.11.17		1464	protein-coding gene	gene with protein product	"brain Ca++-calmodulin-dependent protein kinase type IV", "calcium/calmodulin-dependent protein kinase type IV catalytic chain", "CAM kinase IV", "CAM kinase- GR"	114080				2536634	Standard	NM_001744		Approved	CaMK-GR	uc003kpf.3	Q16566	OTTHUMG00000128792	ENST00000282356.4:c.95A>T	5.37:g.110560276A>T	ENSP00000282356:p.Tyr32Phe	145	0	0		141	30	0.212766	NM_001744	D3DSZ7	Missense_Mutation	SNP	ENST00000282356.4	37	CCDS4103.1	.	.	.	.	.	.	.	.	.	.	A	15.17	2.753876	0.49362	.	.	ENSG00000152495	ENST00000508074;ENST00000512453;ENST00000282356	T;T;T	0.66995	0.73;-0.24;-0.24	4.16	4.16	0.48862	Protein kinase-like domain (1);	0.074149	0.56097	D	0.000028	T	0.51126	0.1656	N	0.19112	0.55	0.41715	D	0.989476	B	0.18610	0.029	B	0.18871	0.023	T	0.51348	-0.8717	10	0.48119	T	0.1	.	12.4796	0.55833	1.0:0.0:0.0:0.0	.	32	Q16566	KCC4_HUMAN	F	32	ENSP00000426940:Y32F;ENSP00000422634:Y32F;ENSP00000282356:Y32F	ENSP00000282356:Y32F	Y	+	2	0	CAMK4	110588175	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.960000	0.56752	1.649000	0.50652	0.377000	0.23210	TAC	.	.	none		0.682	CAMK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250719.2	NM_001744		T	110560276	A	T	110560276	3	4	16	1	0	0	0	0	1	0	0	0	2607	391	14	5	97	5	CAMK4	5	110560276	Missense_Mutation	SNP	A	TCGA-FF-8062-01A-11D-2210-10	85966762	110560276	70354984	47	2141											
EPB41L4A	64097	hgsc.bcm.edu	37	chr5	111500817	111500818	+	Splice_Site	INS	-	-	AAAAT																															tttagacccatttcttctctINSaaaatatatttgaaaaatgt																								rs369027426		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr5:111500817_111500818insAAAAT	ENST00000261486.5	-	23	2209		c.e23-2		EPB41L4A-AS1_ENST00000413221.2_lincRNA|EPB41L4A_ENST00000507810.1_Intron	NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A							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)		ATTTCTTCTCTAAAATATATTT	0.312																																					.		Atlas-Indel	.											.	EPB41L4A	130	.	0			c.1933-2->ATTTT						PASS	.																																			SO:0001630	splice_region_variant	64097	exon24			.	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.1933-2->ATTTT	5.37:g.111500818_111500822dupAAAAT		83	0	0		130	11	0.0846154	NM_022140	A4FUI6	Splice_Site	INS	ENST00000261486.5	37	CCDS43350.1																																																																																			.	.	alt		0.312	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1		Intron	AAAAT	111500818	-	AAAAT	111500817	8	5	16	1	0	1	1	0	0	0	1	0	5157	1536	53	0	133	0	EPB41L4A	5	111500817	Splice_Site	INS	-	TCGA-FF-8062-01A-11D-2210-10	940541	111500817	69414443	48	2142											
RBM27	54439	hgsc.bcm.edu	37	chr5	145613242	145613242	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtccaggtcctggccatagTatgagacttcctgttcccca	7	11	10	13	0	0	1	0	1	0	1	4	2	4	1	6	3	0	2	6	3	2	4			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr5:145613242T>G	ENST00000265271.5	+	7	1246	c.1080T>G	c.(1078-1080)agT>agG	p.S360R	RBM27_ENST00000506502.1_Missense_Mutation_p.S360R	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	360	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)			CTGGCCATAGTATGAGACTTC	0.562																																					p.S360R		Atlas-SNP	.											.	RBM27	119	.	0			c.T1080G						PASS	.						41	42	42					5																	145613242		1568	3582	5150	SO:0001583	missense	54439	exon7			CCATAGTATGAGA	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.1080T>G	5.37:g.145613242T>G	ENSP00000265271:p.Ser360Arg	100	0	0		106	31	0.292453	NM_018989	Q8IYW9	Missense_Mutation	SNP	ENST00000265271.5	37	CCDS43378.1	.	.	.	.	.	.	.	.	.	.	T	14.01	2.406658	0.42715	.	.	ENSG00000091009	ENST00000265271	T	0.46451	0.87	5.52	1.85	0.25348	.	0.476754	0.24611	N	0.037051	T	0.20414	0.0491	N	0.08118	0	0.27233	N	0.959348	B;B	0.23058	0.001;0.079	B;B	0.21546	0.001;0.035	T	0.19257	-1.0311	10	0.20519	T	0.43	-1.2398	10.0623	0.42282	0.0:0.3859:0.0:0.6141	.	360;360	Q9P2N5;B3KY61	RBM27_HUMAN;.	R	360	ENSP00000265271:S360R	ENSP00000265271:S360R	S	+	3	2	RBM27	145593435	0.269000	0.24143	0.979000	0.43373	0.998000	0.95712	-0.066000	0.11598	0.139000	0.18822	0.533000	0.62120	AGT	.	.	none		0.562	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128		G	145613242	T	G	145613242	3	3	16	1	0	0	0	0	1	0	0	0	13142	1635	57	5	1106	5	RBM27	5	145613242	Missense_Mutation	SNP	T	TCGA-FF-8062-01A-11D-2210-10	34112425	145613242	35302018	49	2143											
TRIM38	10475	hgsc.bcm.edu	37	chr6	25983696	25983696	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtgcaaaaagaaaggctaTgtagcacttacttctccccc	12	10	7	12	0	1	1	0	0	1	1	2	1	1	1	2	1	3	4	2	1	6	4			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr6:25983696T>A	ENST00000357085.3	+	8	1655	c.1179T>A	c.(1177-1179)taT>taA	p.Y393*	TRIM38_ENST00000349458.3_Nonsense_Mutation_p.Y393*|U91328.21_ENST00000608931.1_RNA	NM_006355.3	NP_006346.1	O00635	TRI38_HUMAN	tripartite motif containing 38	393	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				negative regulation of defense response to virus (GO:0050687)|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)|positive regulation of viral entry into host cell (GO:0046598)|positive regulation of viral genome replication (GO:0045070)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|regulation of interferon-beta production (GO:0032648)|signal transduction (GO:0007165)	intracellular (GO:0005622)	signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	23						AGAAAGGCTATGTAGCACTTA	0.478																																					p.Y393X		Atlas-SNP	.											.	TRIM38	50	.	0			c.T1179A						PASS	.						124	122	123					6																	25983696		2203	4300	6503	SO:0001587	stop_gained	10475	exon8			AGGCTATGTAGCA	U90547	CCDS4568.1	6p21.3	2011-04-20	2011-01-25	2002-06-07	ENSG00000112343	ENSG00000112343		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10059	protein-coding gene	gene with protein product			"ring finger protein 15", "tripartite motif-containing 38"	RNF15			Standard	XR_241880		Approved	RORET	uc003nfm.4	O00635	OTTHUMG00000014414	ENST00000357085.3:c.1179T>A	6.37:g.25983696T>A	ENSP00000349596:p.Tyr393*	138	0	0		170	61	0.358824	NM_006355	B2R862	Nonsense_Mutation	SNP	ENST00000357085.3	37	CCDS4568.1	.	.	.	.	.	.	.	.	.	.	t	27.6	4.847153	0.91277	.	.	ENSG00000112343	ENST00000540262;ENST00000349458;ENST00000357085	.	.	.	4.25	0.426	0.16479	.	0.336568	0.21891	N	0.067596	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.4119	0.27021	0.0:0.455:0.0:0.545	.	.	.	.	X	393	.	ENSP00000230099:Y393X	Y	+	3	2	TRIM38	26091675	0.000000	0.05858	0.001000	0.08648	0.227000	0.25037	-0.723000	0.04952	0.067000	0.16545	0.533000	0.62120	TAT	.	.	none		0.478	TRIM38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040076.2			A	25983696	T	A	25983696	4	1	16	1	0	0	0	0	0	1	0	0	16527	1471	51	5	1201	5	TRIM38	6	25983696	Nonsense_Mutation	SNP	T	TCGA-FF-8062-01A-11D-2210-10		25983696	145131371	50	2144											
HIST1H1A	3024	hgsc.bcm.edu	37	chr6	26017331	26017331	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atttactttttcttgggtgcCgctttcttgggtttggcagt	3	20	11	7	1	2	0	0	0	2	0	2	0	2	0	1	3	2	3	1	3	1	8			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr6:26017331C>T	ENST00000244573.3	-	1	709	c.630G>A	c.(628-630)gcG>gcA	p.A210A		NM_005325.3	NP_005316.1	Q02539	H11_HUMAN	histone cluster 1, H1a	210					nucleosome assembly (GO:0006334)|spermatogenesis (GO:0007283)	nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|ovary(3)|prostate(1)	13						TCTTGGGTGCCGCTTTCTTGG	0.463																																					p.A210A		Atlas-SNP	.											.	HIST1H1A	25	.	0			c.G630A						PASS	.						106	109	108					6																	26017331		2203	4300	6503	SO:0001819	synonymous_variant	3024	exon1			GGGTGCCGCTTTC	AF531299	CCDS4569.1	6p22.1	2012-11-16	2006-10-11	2003-02-21	ENSG00000124610	ENSG00000124610		"Histones / Replication-dependent"	4715	protein-coding gene	gene with protein product		142709	"H1 histone family, member 1", "histone 1, H1a"	H1F1		2759094, 12408966	Standard	NM_005325		Approved	H1.1, H1a	uc003nfo.3	Q02539	OTTHUMG00000016413	ENST00000244573.3:c.630G>A	6.37:g.26017331C>T		252	0	0		245	104	0.42449	NM_005325	Q3MJ34	Silent	SNP	ENST00000244573.3	37	CCDS4569.1																																																																																			.	.	none		0.463	HIST1H1A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043884.1	NM_005325		T	26017331	C	T	26017331	2	4	16	1	0	0	0	0	0	0	0	1	7131	639	23	1		1	HIST1H1A	6	26017331	Silent	SNP	C	TCGA-FF-8062-01A-11D-2210-10	33635	26017331	145097736	51	2145											
BAT1	7919	hgsc.bcm.edu	37	chr6	31500627	31500627	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgttgtccttcagtttcacgTagtactgctgcaacccatgc	7	13	8	13	2	2	0	2	0	0	0	3	0	3	0	2	0	5	6	2	0	3	5			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr6:31500627T>C	ENST00000396172.1	-	7	1427	c.797A>G	c.(796-798)tAc>tGc	p.Y266C	DDX39B_ENST00000376177.2_Missense_Mutation_p.Y266C|DDX39B_ENST00000417556.2_Missense_Mutation_p.Y281C|DDX39B_ENST00000462421.1_5'Flank|DDX39B_ENST00000415382.2_Missense_Mutation_p.Y188C|DDX39B_ENST00000458640.1_Missense_Mutation_p.Y266C|ATP6V1G2-DDX39B_ENST00000376185.1_3'UTR	NM_004640.6	NP_004631.1	Q13838	DX39B_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	266	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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						CAGTTTCACGTAGTACTGCTG	0.552																																					p.Y266C		Atlas-SNP	.											.	DDX39B	38	.	0			c.A797G						PASS	.						125	100	109					6																	31500627		1511	2709	4220	SO:0001583	missense	7919	exon7			TTCACGTAGTACT	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.797A>G	6.37:g.31500627T>C	ENSP00000379475:p.Tyr266Cys	189	0	0		208	93	0.447115	NM_004640	B0S8C0|O43496|Q0EFA1|Q2L6F9|Q53GL9|Q5RJ64|Q5RJ66|Q5ST94|Q5STB4|Q5STB5|Q5STB7|Q5STB8|Q5STU4|Q5STU5|Q5STU6|Q5STU8|Q71V76	Missense_Mutation	SNP	ENST00000396172.1	37	CCDS4697.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.74|19.74	3.883915|3.883915	0.72410|0.72410	.|.	.|.	ENSG00000198563|ENSG00000198563	ENST00000417023|ENST00000376177;ENST00000458640;ENST00000396172;ENST00000417556;ENST00000415382;ENST00000431908;ENST00000427214	.|D;T;T;T;T;T;T	.|0.92752	.|-3.1;3.44;3.44;3.44;3.44;3.44;3.33	5.46|5.46	4.28|4.28	0.50868|0.50868	.|Helicase, C-terminal (1);	.|0.079694	.|0.51477	.|D	.|0.000087	D|D	0.95053|0.95053	0.8398|0.8398	M|M	0.86740|0.86740	2.835|2.835	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;0.988	.|D;D;D;P	.|0.91635	.|0.999;0.999;0.994;0.693	D|D	0.95212|0.95212	0.8326|0.8326	5|10	.|0.87932	.|D	.|0	-12.1399|-12.1399	10.7351|10.7351	0.46120|0.46120	0.0:0.0:0.1602:0.8398|0.0:0.0:0.1602:0.8398	.|.	.|188;266;266;281	.|B4DP52;Q13838;Q5STU3;F8VQ10	.|.;DX39B_HUMAN;.;.	A|C	30|266;266;266;281;188;188;266	.|ENSP00000365347:Y266C;ENSP00000416269:Y266C;ENSP00000379475:Y266C;ENSP00000412582:Y281C;ENSP00000392669:Y188C;ENSP00000408000:Y188C;ENSP00000399371:Y266C	.|ENSP00000365347:Y266C	T|Y	-|-	1|2	0|0	DDX39B|DDX39B	31608606|31608606	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.673000|7.673000	0.83973|0.83973	0.886000|0.886000	0.36113|0.36113	0.533000|0.533000	0.62120|0.62120	ACG|TAC	.	.	none		0.552	DDX39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259083.1	NM_004640		C	31500627	T	C	31500627	3	2	16	1	0	0	0	0	1	0	0	0	1318	1638	57	3	509	3	BAT1	6	31500627	Missense_Mutation	SNP	T	TCGA-FF-8062-01A-11D-2210-10	5483296	31500627	139614440	52	2146											
TNF	7124	hgsc.bcm.edu	37	chr6	31543635	31543635	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctcagcctcttctccttcctGatcgtggcaggcgccaccac	5	10	8	18	2	3	1	1	1	2	0	6	1	4	1	5	2	1	1	5	2	0	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr6:31543635G>A	ENST00000449264.2	+	1	292	c.117G>A	c.(115-117)ctG>ctA	p.L39L		NM_000594.3	NP_000585.2	P01375	TNFA_HUMAN	tumor necrosis factor	39		Cleavage; by SPPL2A or SPPL2B.			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|calcium-mediated signaling (GO:0019722)|cell activation (GO:0001775)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nicotine (GO:0071316)|cellular response to organic cyclic compound (GO:0071407)|chronic inflammatory response to antigenic stimulus (GO:0002439)|defense response to Gram-positive bacterium (GO:0050830)|embryonic digestive tract development (GO:0048566)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|glucose metabolic process (GO:0006006)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|JNK cascade (GO:0007254)|leukocyte tethering or rolling (GO:0050901)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|necroptotic signaling pathway (GO:0097527)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of branching involved in lung morphogenesis (GO:0061048)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of glucose import (GO:0046325)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of L-glutamate transport (GO:0002037)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of lipid storage (GO:0010888)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein complex disassembly (GO:0043242)|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)|organ morphogenesis (GO:0009887)|osteoclast differentiation (GO:0030316)|positive regulation of apoptotic process (GO:0043065)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of chronic inflammatory response to antigenic stimulus (GO:0002876)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fever generation (GO:0031622)|positive regulation of gene expression (GO:0010628)|positive regulation of hair follicle development (GO:0051798)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|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 interferon-gamma production (GO:0032729)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mitosis (GO:0045840)|positive regulation of mononuclear cell migration (GO:0071677)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of podosome assembly (GO:0071803)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein transport (GO:0051222)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of synaptic transmission (GO:0050806)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translational initiation by iron (GO:0045994)|positive regulation of vitamin D biosynthetic process (GO:0060557)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|receptor biosynthetic process (GO:0032800)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of immunoglobulin secretion (GO:0051023)|regulation of insulin secretion (GO:0050796)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to salt stress (GO:0009651)|response to virus (GO:0009615)|sequestering of triglyceride (GO:0030730)|skeletal muscle contraction (GO:0003009)|transformed cell apoptotic process (GO:0006927)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	cytokine activity (GO:0005125)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|transcription regulatory region DNA binding (GO:0044212)|tumor necrosis factor receptor binding (GO:0005164)			large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|skin(3)	8		Ovarian(999;0.00556)			Adalimumab(DB00051)|Amrinone(DB01427)|Certolizumab pegol(DB08904)|Chloroquine(DB00608)|Clenbuterol(DB01407)|Epinephrine(DB00668)|Etanercept(DB00005)|Glucosamine(DB01296)|golimumab(DB06674)|Infliximab(DB00065)|Pomalidomide(DB08910)|Pranlukast(DB01411)|Pseudoephedrine(DB00852)|Thalidomide(DB01041)	TCTCCTTCCTGATCGTGGCAG	0.652									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of																												p.L39L		Atlas-SNP	.											.	TNF	15	.	0			c.G117A						PASS	.						66	67	67					6																	31543635		2203	4300	6503	SO:0001819	synonymous_variant	7124	exon1	Familial Cancer Database	incl.: Familial Head and Neck Cancer	CTTCCTGATCGTG	X02910	CCDS4702.1	6p21.3	2013-05-22	2010-05-04		ENSG00000232810	ENSG00000232810		"Tumor necrosis factor (ligand) superfamily"	11892	protein-coding gene	gene with protein product	"TNF superfamily, member 2"	191160	"tumor necrosis factor (TNF superfamily, member 2)"	TNFA		2413547, 6392892	Standard	NM_000594		Approved	TNFSF2, DIF, TNF-alpha	uc003nui.4	P01375	OTTHUMG00000031194	ENST00000449264.2:c.117G>A	6.37:g.31543635G>A		75	0	0		69	25	0.362319	NM_000594	O43647|Q9P1Q2|Q9UIV3	Silent	SNP	ENST00000449264.2	37	CCDS4702.1																																																																																			.	.	none		0.652	TNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076390.2			A	31543635	G	A	31543635	2	1	16	1	0	0	0	0	0	0	0	1	16286	1277	45	2		2	TNF	6	31543635	Silent	SNP	G	TCGA-FF-8062-01A-11D-2210-10	43008	31543635	139571432	53	2147											
TNF	7124	hgsc.bcm.edu	37	chr6	31543674	31543674	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgctcttctgcctgctgcaCtttggagtgatcggccccca	5	11	10	15	2	2	1	0	1	2	0	3	2	2	2	3	2	3	3	3	2	0	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr6:31543674C>G	ENST00000449264.2	+	1	331	c.156C>G	c.(154-156)caC>caG	p.H52Q		NM_000594.3	NP_000585.2	P01375	TNFA_HUMAN	tumor necrosis factor	52		Cleavage; by SPPL2A or SPPL2B.			activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|calcium-mediated signaling (GO:0019722)|cell activation (GO:0001775)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nicotine (GO:0071316)|cellular response to organic cyclic compound (GO:0071407)|chronic inflammatory response to antigenic stimulus (GO:0002439)|defense response to Gram-positive bacterium (GO:0050830)|embryonic digestive tract development (GO:0048566)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|glucose metabolic process (GO:0006006)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|JNK cascade (GO:0007254)|leukocyte tethering or rolling (GO:0050901)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|necroptotic signaling pathway (GO:0097527)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of branching involved in lung morphogenesis (GO:0061048)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of glucose import (GO:0046325)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of L-glutamate transport (GO:0002037)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of lipid storage (GO:0010888)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein complex disassembly (GO:0043242)|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)|organ morphogenesis (GO:0009887)|osteoclast differentiation (GO:0030316)|positive regulation of apoptotic process (GO:0043065)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of chronic inflammatory response to antigenic stimulus (GO:0002876)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fever generation (GO:0031622)|positive regulation of gene expression (GO:0010628)|positive regulation of hair follicle development (GO:0051798)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|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 interferon-gamma production (GO:0032729)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mitosis (GO:0045840)|positive regulation of mononuclear cell migration (GO:0071677)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of podosome assembly (GO:0071803)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein transport (GO:0051222)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of synaptic transmission (GO:0050806)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translational initiation by iron (GO:0045994)|positive regulation of vitamin D biosynthetic process (GO:0060557)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|receptor biosynthetic process (GO:0032800)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of immunoglobulin secretion (GO:0051023)|regulation of insulin secretion (GO:0050796)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to salt stress (GO:0009651)|response to virus (GO:0009615)|sequestering of triglyceride (GO:0030730)|skeletal muscle contraction (GO:0003009)|transformed cell apoptotic process (GO:0006927)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	cytokine activity (GO:0005125)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|transcription regulatory region DNA binding (GO:0044212)|tumor necrosis factor receptor binding (GO:0005164)			large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|skin(3)	8		Ovarian(999;0.00556)			Adalimumab(DB00051)|Amrinone(DB01427)|Certolizumab pegol(DB08904)|Chloroquine(DB00608)|Clenbuterol(DB01407)|Epinephrine(DB00668)|Etanercept(DB00005)|Glucosamine(DB01296)|golimumab(DB06674)|Infliximab(DB00065)|Pomalidomide(DB08910)|Pranlukast(DB01411)|Pseudoephedrine(DB00852)|Thalidomide(DB01041)	GCCTGCTGCACTTTGGAGTGA	0.627									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of																												p.H52Q		Atlas-SNP	.											.	TNF	15	.	0			c.C156G						PASS	.						45	45	45					6																	31543674		2203	4300	6503	SO:0001583	missense	7124	exon1	Familial Cancer Database	incl.: Familial Head and Neck Cancer	GCTGCACTTTGGA	X02910	CCDS4702.1	6p21.3	2013-05-22	2010-05-04		ENSG00000232810	ENSG00000232810		"Tumor necrosis factor (ligand) superfamily"	11892	protein-coding gene	gene with protein product	"TNF superfamily, member 2"	191160	"tumor necrosis factor (TNF superfamily, member 2)"	TNFA		2413547, 6392892	Standard	NM_000594		Approved	TNFSF2, DIF, TNF-alpha	uc003nui.4	P01375	OTTHUMG00000031194	ENST00000449264.2:c.156C>G	6.37:g.31543674C>G	ENSP00000398698:p.His52Gln	100	0	0		78	24	0.307692	NM_000594	O43647|Q9P1Q2|Q9UIV3	Missense_Mutation	SNP	ENST00000449264.2	37	CCDS4702.1	.	.	.	.	.	.	.	.	.	.	C	13.50	2.256573	0.39896	.	.	ENSG00000232810	ENST00000449264	T	0.74737	-0.87	5.77	3.99	0.46301	.	0.294531	0.38058	N	0.001824	T	0.50120	0.1597	L	0.58583	1.82	0.51767	D	0.999937	B	0.18166	0.026	B	0.18871	0.023	T	0.51004	-0.8760	10	0.23302	T	0.38	.	6.9811	0.24704	0.0:0.743:0.0:0.257	.	52	P01375	TNFA_HUMAN	Q	52	ENSP00000398698:H52Q	ENSP00000398698:H52Q	H	+	3	2	TNF	31651653	0.998000	0.40836	1.000000	0.80357	0.943000	0.58893	0.436000	0.21526	1.445000	0.47624	0.655000	0.94253	CAC	.	.	none		0.627	TNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076390.2			G	31543674	C	G	31543674	3	3	16	1	0	0	0	0	1	0	0	0	16286	564	20	4	158	4	TNF	6	31543674	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	39	31543674	139571393	54	2148											
C6orf27	80737	hgsc.bcm.edu	37	chr6	31744405	31744405	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtgacgttgagcgctgccTcctcagttaggtcttggtgg	4	12	16	9	2	2	2	1	2	1	0	3	2	3	2	2	4	2	3	2	4	1	3			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr6:31744405T>C	ENST00000375688.4	-	2	352	c.152A>G	c.(151-153)gAg>gGg	p.E51G	VWA7_ENST00000375686.3_Missense_Mutation_p.E51G|VWA7_ENST00000447450.1_Missense_Mutation_p.E51G|Y_RNA_ENST00000364685.1_RNA|VWA7_ENST00000467576.1_5'UTR			Q9Y334	VWA7_HUMAN	von Willebrand factor A domain containing 7	51						extracellular region (GO:0005576)											GAGCGCTGCCTCCTCAGTTAG	0.642																																					p.E51G		Atlas-SNP	.											.	.	.	.	0			c.A152G						PASS	.						19	9	13					6																	31744405		1410	2507	3917	SO:0001583	missense	80737	exon2			GCTGCCTCCTCAG		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.152A>G	6.37:g.31744405T>C	ENSP00000364840:p.Glu51Gly	177	0	0		158	67	0.424051	NM_025258	A2BEX8|A6NHR6|B0V041|Q5SSR5|Q96QC8|Q9UMP9	Missense_Mutation	SNP	ENST00000375688.4	37	CCDS4721.2	.	.	.	.	.	.	.	.	.	.	T	17.59	3.427819	0.62733	.	.	ENSG00000204396	ENST00000375688;ENST00000375686;ENST00000447450	T;T;T	0.13778	2.56;2.56;2.56	4.92	3.74	0.42951	.	0.199559	0.41823	D	0.000801	T	0.05914	0.0154	L	0.50333	1.59	0.31474	N	0.667961	B	0.29646	0.253	B	0.31337	0.128	T	0.13737	-1.0498	10	0.51188	T	0.08	-10.4076	10.0134	0.42001	0.0:0.0:0.1703:0.8297	.	51	Q9Y334	G7C_HUMAN	G	51	ENSP00000364840:E51G;ENSP00000364838:E51G;ENSP00000390554:E51G	ENSP00000364838:E51G	E	-	2	0	C6orf27	31852384	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.464000	0.53057	0.881000	0.35993	0.455000	0.32223	GAG	.	.	none		0.642	VWA7-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076233.2	NM_025258		C	31744405	T	C	31744405	3	2	16	1	0	0	0	0	1	0	0	0	2364	1551	54	3	2586	3	C6orf27	6	31744405	Missense_Mutation	SNP	T	TCGA-FF-8062-01A-11D-2210-10	200731	31744405	139370662	55	2149											
ZBTB12	221527	hgsc.bcm.edu	37	chr6	31868698	31868698	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctctttgaggcctattttggGctcaatgaactggctgaggg	7	13	13	8	0	2	3	1	3	1	0	2	3	2	3	1	4	1	2	1	4	3	4			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr6:31868698G>A	ENST00000375527.2	-	2	560	c.385C>T	c.(385-387)Ccc>Tcc	p.P129S	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	129					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						CCTATTTTGGGCTCAATGAAC	0.582																																					p.P129S		Atlas-SNP	.											.	ZBTB12	25	.	0			c.C385T						PASS	.						74	73	74					6																	31868698		2203	4300	6503	SO:0001583	missense	221527	exon2			TTTTGGGCTCAAT	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.385C>T	6.37:g.31868698G>A	ENSP00000364677:p.Pro129Ser	127	0	0		101	51	0.504951	NM_181842	B0UY00|Q5JQ98	Missense_Mutation	SNP	ENST00000375527.2	37	CCDS4727.1	.	.	.	.	.	.	.	.	.	.	G	16.96	3.266422	0.59540	.	.	ENSG00000204366	ENST00000375527	T	0.14766	2.48	4.38	3.51	0.40186	.	0.071421	0.56097	U	0.000028	T	0.09335	0.0230	N	0.19112	0.55	0.45066	D	0.998089	D	0.69078	0.997	D	0.68765	0.96	T	0.19289	-1.0310	10	0.19590	T	0.45	.	11.2674	0.49118	0.0928:0.0:0.9072:0.0	.	129	Q9Y330	ZBT12_HUMAN	S	129	ENSP00000364677:P129S	ENSP00000364677:P129S	P	-	1	0	ZBTB12	31976677	1.000000	0.71417	0.991000	0.47740	0.967000	0.64934	6.542000	0.73869	0.823000	0.34589	0.423000	0.28283	CCC	.	.	none		0.582	ZBTB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076315.2	NM_181842		A	31868698	G	A	31868698	3	1	16	1	0	0	0	0	1	0	0	0	17540	1203	42	2	998	2	ZBTB12	6	31868698	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	124293	31868698	139246369	56	2150											
RNGTT	8732	hgsc.bcm.edu	37	chr6	89554108	89554108	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acagatgtcaaaaaacggctTatttctgacgctaaatggtt	14	12	8	7	2	2	2	1	1	1	1	2	2	2	2	0	2	1	3	0	2	6	4			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr6:89554108T>A	ENST00000369485.4	-	11	1423	c.1237A>T	c.(1237-1239)Aag>Tag	p.K413*	RNGTT_ENST00000538899.1_Nonsense_Mutation_p.K353*|RNGTT_ENST00000369475.3_Nonsense_Mutation_p.K413*|RNGTT_ENST00000265607.6_Nonsense_Mutation_p.K413*	NM_003800.3	NP_003791.3	O60942	MCE1_HUMAN	RNA guanylyltransferase and 5'-phosphatase	413	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)		AAAAACGGCTTATTTCTGACG	0.333																																					p.K413X		Atlas-SNP	.											.	RNGTT	52	.	0			c.A1237T						PASS	.						137	136	137					6																	89554108		2203	4300	6503	SO:0001587	stop_gained	8732	exon11			ACGGCTTATTTCT	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.1237A>T	6.37:g.89554108T>A	ENSP00000358497:p.Lys413*	61	0	0		67	16	0.238806	NM_003800	E1P513|E1P514|O43483|O60257|O60351|Q5TCW8|Q8WUM8	Nonsense_Mutation	SNP	ENST00000369485.4	37	CCDS5017.1	.	.	.	.	.	.	.	.	.	.	T	40	7.950168	0.98577	.	.	ENSG00000111880	ENST00000369485;ENST00000265607;ENST00000538899;ENST00000536746;ENST00000369475	.	.	.	5.7	5.7	0.88788	.	0.119116	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.5296	15.9509	0.79835	0.0:0.0:0.0:1.0	.	.	.	.	X	413;413;353;384;413	.	ENSP00000265607:K413X	K	-	1	0	RNGTT	89610827	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	7.953000	0.87836	2.175000	0.68902	0.460000	0.39030	AAG	.	.	none		0.333	RNGTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041469.1			A	89554108	T	A	89554108	4	1	16	1	0	0	0	0	0	1	0	0	13518	1763	61	5	580	5	RNGTT	6	89554108	Nonsense_Mutation	SNP	T	TCGA-FF-8062-01A-11D-2210-10	57685410	89554108	81560959	57	2151											
LAMA4	3910	hgsc.bcm.edu	37	chr6	112537639	112537639	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cgcagggcacacattctcccGacagggtgtgaaagaatcca	12	6	11	12	2	1	2	0	1	1	1	3	3	2	2	2	2	0	2	2	2	2	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr6:112537639G>A	ENST00000230538.7	-	3	624	c.227C>T	c.(226-228)tCg>tTg	p.S76L	RP1-142L7.9_ENST00000603682.1_lincRNA|LAMA4_ENST00000522006.1_Missense_Mutation_p.S76L|LAMA4_ENST00000524032.1_5'UTR|LAMA4_ENST00000389463.4_Missense_Mutation_p.S76L|LAMA4_ENST00000431543.2_Missense_Mutation_p.S76L|LAMA4_ENST00000424408.2_Missense_Mutation_p.S76L	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	76					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)		ACATTCTCCCGACAGGGTGTG	0.433																																					p.S76L		Atlas-SNP	.											.	LAMA4	227	.	0			c.C227T						PASS	.						111	93	99					6																	112537639		2203	4300	6503	SO:0001583	missense	3910	exon3			TCTCCCGACAGGG		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.227C>T	6.37:g.112537639G>A	ENSP00000230538:p.Ser76Leu	78	0	0		100	25	0.25	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Missense_Mutation	SNP	ENST00000230538.7	37	CCDS43491.1	.	.	.	.	.	.	.	.	.	.	G	15.39	2.819282	0.50633	.	.	ENSG00000112769	ENST00000230538;ENST00000522006;ENST00000389463;ENST00000424408;ENST00000454881;ENST00000521398;ENST00000542588;ENST00000368639;ENST00000519932;ENST00000431543;ENST00000243219;ENST00000521690	T;T;T;T;T;D;D	0.97731	2.5;2.49;2.49;2.49;1.6;-4.51;-4.51	5.84	5.84	0.93424	.	0.216402	0.41001	D	0.000980	D	0.96917	0.8993	N	0.24115	0.695	0.80722	D	1	D;P;D	0.89917	1.0;0.916;0.998	D;P;D	0.74023	0.964;0.541;0.982	D	0.96804	0.9591	10	0.38643	T	0.18	.	17.6392	0.88130	0.0:0.0:1.0:0.0	.	76;76;76	Q6LET9;Q16363;Q16363-2	.;LAMA4_HUMAN;.	L	76	ENSP00000230538:S76L;ENSP00000429488:S76L;ENSP00000374114:S76L;ENSP00000416470:S76L;ENSP00000430336:S76L;ENSP00000428583:S76L;ENSP00000412136:S76L	ENSP00000230538:S76L	S	-	2	0	LAMA4	112644332	0.998000	0.40836	0.238000	0.24106	0.008000	0.06430	6.253000	0.72453	2.748000	0.94277	0.650000	0.86243	TCG	.	.	none		0.433	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206		A	112537639	G	A	112537639	3	1	16	1	0	0	0	0	1	0	0	0	8617	1059	37	1	5392	1	LAMA4	6	112537639	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	22983531	112537639	58577428	58	2152											
TMEM200A	114801	hgsc.bcm.edu	37	chr6	130761752	130761752	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ccggctttattccccatctgGtttttttcttattttaggag	5	20	7	9	1	2	0	0	0	2	0	3	1	3	1	3	3	0	2	3	3	3	9			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr6:130761752G>T	ENST00000296978.3	+	3	1056	c.185G>T	c.(184-186)gGt>gTt	p.G62V	TMEM200A_ENST00000545622.1_Missense_Mutation_p.G62V|TMEM200A_ENST00000392429.1_Missense_Mutation_p.G62V	NM_001258276.1|NM_001258277.1|NM_001258278.1	NP_001245205.1|NP_001245206.1|NP_001245207.1	Q86VY9	T200A_HUMAN	transmembrane protein 200A	62						integral component of membrane (GO:0016021)		p.G62A(2)		NS(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(30)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52				GBM - Glioblastoma multiforme(226;0.0139)|OV - Ovarian serous cystadenocarcinoma(155;0.12)		TCCCCATCTGGTTTTTTTCTT	0.473																																					p.G62V		Atlas-SNP	.											TMEM200A,NS,carcinoma,0,2	TMEM200A	108	2	2	Substitution - Missense(2)	kidney(2)	c.G185T						PASS	.						113	115	114					6																	130761752		2203	4300	6503	SO:0001583	missense	114801	exon3			CATCTGGTTTTTT	AB067500	CCDS5140.1	6q23.1	2009-09-04	2007-12-18	2007-12-18	ENSG00000164484	ENSG00000164484			21075	protein-coding gene	gene with protein product			"KIAA1913"	KIAA1913		15722956	Standard	NM_001258276		Approved	TTMC	uc010kfh.4	Q86VY9	OTTHUMG00000015557	ENST00000296978.3:c.185G>T	6.37:g.130761752G>T	ENSP00000296978:p.Gly62Val	162	0	0		207	37	0.178744	NM_001258277	Q96PX5	Missense_Mutation	SNP	ENST00000296978.3	37	CCDS5140.1	.	.	.	.	.	.	.	.	.	.	G	19.23	3.787946	0.70337	.	.	ENSG00000164484	ENST00000296978;ENST00000545622;ENST00000392429	.	.	.	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.76147	0.3947	M	0.73217	2.22	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.78499	-0.2180	9	0.87932	D	0	.	19.305	0.94157	0.0:0.0:1.0:0.0	.	62	Q86VY9	T200A_HUMAN	V	62	.	ENSP00000296978:G62V	G	+	2	0	TMEM200A	130803445	1.000000	0.71417	0.950000	0.38849	0.599000	0.36880	9.809000	0.99208	2.547000	0.85894	0.655000	0.94253	GGT	.	.	none		0.473	TMEM200A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042201.1	NM_052913		T	130761752	G	T	130761752	3	4	16	1	0	0	0	0	1	0	0	0	16138	1261	44	4	187	4	TMEM200A	6	130761752	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	18224113	130761752	40353315	59	2153											
SGK1	6446	hgsc.bcm.edu	37	chr6	134493825	134493825	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aacgatgttcagtgaatgcaGgtagcccaaggcactggcta	12	8	12	9	1	1	1	1	1	0	0	1	2	1	1	1	3	3	5	1	3	5	3			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr6:134493825G>A	ENST00000237305.7	-	7	725	c.637C>T	c.(637-639)Ctg>Ttg	p.L213L	SGK1_ENST00000367858.5_Silent_p.L308L|SGK1_ENST00000475719.2_Silent_p.L169L|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000528577.1_Silent_p.L241L|SGK1_ENST00000367857.5_Silent_p.L203L|SGK1_ENST00000413996.3_Silent_p.L227L	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	213	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)		AGTGAATGCAGGTAGCCCAAG	0.502																																					p.L308L		Atlas-SNP	.											SGK1_ENST00000528577,NS,carcinoma,0,5	SGK1	387	5	0			c.C922T						PASS	.						71	63	66					6																	134493825		2203	4300	6503	SO:0001819	synonymous_variant	6446	exon9			AATGCAGGTAGCC	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.637C>T	6.37:g.134493825G>A		96	0	0		108	15	0.138889	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Silent	SNP	ENST00000237305.7	37	CCDS5170.1																																																																																			.	.	none		0.502	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			A	134493825	G	A	134493825	2	1	16	1	0	0	0	0	0	0	0	1	14222	991	35	2		2	SGK1	6	134493825	Silent	SNP	G	TCGA-FF-8062-01A-11D-2210-10	3732073	134493825	36621242	60	2154			1	17		8	6	1887	N	G_C	6.584007e-13
SGK1	6446	hgsc.bcm.edu	37	chr6	134494426	134494426	+	Missense_Mutation	SNP	G	G	C																															tcatacctctttctttttcaGgattgctttcttctgtaaaa																										TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr6:134494426G>C	ENST00000237305.7	-	5	491	c.403C>G	c.(403-405)Ctg>Gtg	p.L135V	SGK1_ENST00000367858.5_Missense_Mutation_p.L230V|SGK1_ENST00000475719.2_Missense_Mutation_p.L135V|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000528577.1_Missense_Mutation_p.L163V|SGK1_ENST00000367857.5_Missense_Mutation_p.L125V|SGK1_ENST00000413996.3_Missense_Mutation_p.L149V	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	135	Glu/Lys-rich.|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)		TTCTTTTTCAGGATTGCTTTC	0.378																																					p.L230V		Atlas-SNP	.											.	SGK1	387	.	0			c.C688G						PASS	.						114	113	113					6																	134494426		2203	4300	6503	SO:0001583	missense	6446	exon7			TTTTCAGGATTGC	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.403C>G	6.37:g.134494426G>C	ENSP00000237305:p.Leu135Val	153	0	0		149	27	0.181208	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	10.79	1.450776	0.26074	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719	T;T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16;1.88	6.17	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	T	0.36799	0.0980	L	0.33753	1.03	0.80722	D	1	B;B;B;B;B;B	0.27140	0.007;0.169;0.017;0.002;0.013;0.003	B;B;B;B;B;B	0.31442	0.01;0.13;0.1;0.006;0.035;0.01	T	0.31280	-0.9949	10	0.16896	T	0.51	.	15.9715	0.80025	0.0648:0.0:0.9352:0.0	.	163;149;135;125;230;135	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	V	230;149;135;125;163;135	ENSP00000356832:L230V;ENSP00000396242:L149V;ENSP00000237305:L135V;ENSP00000356831:L125V;ENSP00000434450:L163V;ENSP00000434302:L135V	ENSP00000237305:L135V	L	-	1	2	SGK1	134536119	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.089000	0.57685	1.599000	0.50093	0.655000	0.94253	CTG	.	.	none		0.378	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			C	134494426	G	C	134494426	3	2	16	1	0	0	0	0	1	0	0	0	14222	991	35	4	924	4	SGK1	6	134494426	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	601	134494426	36620641	61	2155	29	2	1	17		8	6	1887	N	G_C	6.584007e-13
SGK1	6446	hgsc.bcm.edu	37	chr6	134494432	134494432	+	Missense_Mutation	SNP	C	C	G																															ctctttctttttcaggattgCtttcttctgtaaaactttga																										TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr6:134494432C>G	ENST00000237305.7	-	5	485	c.397G>C	c.(397-399)Gca>Cca	p.A133P	SGK1_ENST00000367858.5_Missense_Mutation_p.A228P|SGK1_ENST00000475719.2_Missense_Mutation_p.A133P|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000528577.1_Missense_Mutation_p.A161P|SGK1_ENST00000367857.5_Missense_Mutation_p.A123P|SGK1_ENST00000413996.3_Missense_Mutation_p.A147P	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	133	Glu/Lys-rich.|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)		TTCAGGATTGCTTTCTTCTGT	0.383																																					p.A228P		Atlas-SNP	.											.	SGK1	387	.	0			c.G682C						PASS	.						114	114	114					6																	134494432		2203	4300	6503	SO:0001583	missense	6446	exon7			GGATTGCTTTCTT	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.397G>C	6.37:g.134494432C>G	ENSP00000237305:p.Ala133Pro	148	0	0		157	21	0.133758	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.565036	0.86439	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719	T;T;T;T;T;T	0.65916	-0.18;-0.18;-0.18;-0.18;-0.18;1.81	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);	0.096985	0.64402	D	0.000001	T	0.61702	0.2368	N	0.24115	0.695	0.80722	D	1	D;D;P;P;D;P	0.67145	0.977;0.979;0.907;0.936;0.996;0.948	P;P;P;P;P;P	0.60117	0.706;0.578;0.864;0.578;0.869;0.703	T	0.64326	-0.6434	10	0.62326	D	0.03	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	161;147;133;123;228;133	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	P	228;147;133;123;161;133	ENSP00000356832:A228P;ENSP00000396242:A147P;ENSP00000237305:A133P;ENSP00000356831:A123P;ENSP00000434450:A161P;ENSP00000434302:A133P	ENSP00000237305:A133P	A	-	1	0	SGK1	134536125	1.000000	0.71417	0.994000	0.49952	0.999000	0.98932	5.920000	0.70017	2.941000	0.99782	0.655000	0.94253	GCA	.	.	none		0.383	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			G	134494432	C	G	134494432	3	3	16	1	0	0	0	0	1	0	0	0	14222	797	28	4	930	4	SGK1	6	134494432	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	6	134494432	36620635	62	2156	29	2	1	17		8	6	1887	N	G_C	6.584007e-13
SGK1	6446	hgsc.bcm.edu	37	chr6	134495159	134495159	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ttactggaggagaagggttgGcattcataagctcaggctcc	10	10	13	8	0	2	1	2	0	0	1	3	3	3	2	1	5	2	4	1	5	3	4			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr6:134495159G>A	ENST00000237305.7	-	3	300	c.212C>T	c.(211-213)gCc>gTc	p.A71V	SGK1_ENST00000367858.5_Missense_Mutation_p.A166V|SGK1_ENST00000475719.2_Missense_Mutation_p.A71V|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000528577.1_Missense_Mutation_p.A99V|SGK1_ENST00000367857.5_Missense_Mutation_p.A61V|SGK1_ENST00000413996.3_Missense_Mutation_p.A85V	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	71					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)		AGAAGGGTTGGCATTCATAAG	0.453																																					p.A166V		Atlas-SNP	.											SGK1_ENST00000528577,NS,lymphoid_neoplasm,0,5	SGK1	387	5	0			c.C497T						PASS	.						152	146	148					6																	134495159		2203	4300	6503	SO:0001583	missense	6446	exon5			GGGTTGGCATTCA	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.212C>T	6.37:g.134495159G>A	ENSP00000237305:p.Ala71Val	92	0	0		64	11	0.171875	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	14.85	2.658406	0.47467	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T	0.72835	-0.68;-0.68;-0.68;-0.66;-0.66;-0.69	5.99	5.12	0.69794	.	0.399737	0.30076	N	0.010479	T	0.37293	0.0998	N	0.14661	0.345	0.80722	D	1	B;B;B;B;B;B	0.12630	0.001;0.001;0.001;0.001;0.006;0.0	B;B;B;B;B;B	0.14578	0.004;0.003;0.002;0.005;0.011;0.001	T	0.26950	-1.0088	10	0.25106	T	0.35	.	14.2908	0.66275	0.0:0.0:0.7295:0.2705	.	99;85;71;61;166;71	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	V	166;85;71;61;99;71;135	ENSP00000356832:A166V;ENSP00000396242:A85V;ENSP00000237305:A71V;ENSP00000356831:A61V;ENSP00000434450:A99V;ENSP00000434302:A71V	ENSP00000237305:A71V	A	-	2	0	SGK1	134536852	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.654000	0.54453	1.523000	0.49018	0.655000	0.94253	GCC	.	.	none		0.453	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			A	134495159	G	A	134495159	3	1	16	1	0	0	0	0	1	0	0	0	14222	1203	42	2	1123	2	SGK1	6	134495159	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	727	134495159	36619908	63	2157			1	17		8	6	1887	N	G_C	6.584007e-13
SGK1	6446	hgsc.bcm.edu	37	chr6	134495170	134495170	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaagggttggcattcataagCtcaggctcctgaggttggga	9	10	15	7	0	2	1	2	1	0	0	3	3	3	2	1	5	1	5	1	5	2	4			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr6:134495170C>G	ENST00000237305.7	-	3	289	c.201G>C	c.(199-201)gaG>gaC	p.E67D	SGK1_ENST00000367858.5_Missense_Mutation_p.E162D|SGK1_ENST00000475719.2_Missense_Mutation_p.E67D|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000528577.1_Missense_Mutation_p.E95D|SGK1_ENST00000367857.5_Missense_Mutation_p.E57D|SGK1_ENST00000413996.3_Missense_Mutation_p.E81D	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	67					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)		CATTCATAAGCTCAGGCTCCT	0.483																																					p.E162D		Atlas-SNP	.											.	SGK1	387	.	0			c.G486C						PASS	.						150	144	146					6																	134495170		2203	4300	6503	SO:0001583	missense	6446	exon5			CATAAGCTCAGGC	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.201G>C	6.37:g.134495170C>G	ENSP00000237305:p.Glu67Asp	94	0	0		71	5	0.0704225	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	C	15.64	2.893621	0.52121	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T	0.72725	-0.68;-0.68;-0.66;-0.66;-0.64;-0.64	5.99	4.2	0.49525	.	0.000000	0.85682	D	0.000000	T	0.42720	0.1215	L	0.45137	1.4	0.80722	D	1	B;B;B;B;B;B	0.18461	0.005;0.028;0.001;0.013;0.017;0.001	B;B;B;B;B;B	0.21917	0.012;0.011;0.001;0.007;0.037;0.003	T	0.36383	-0.9750	10	0.30854	T	0.27	.	7.4903	0.27458	0.0:0.6523:0.0:0.3477	.	95;81;67;57;162;67	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	D	162;81;67;57;95;67;131	ENSP00000356832:E162D;ENSP00000396242:E81D;ENSP00000237305:E67D;ENSP00000356831:E57D;ENSP00000434450:E95D;ENSP00000434302:E67D	ENSP00000237305:E67D	E	-	3	2	SGK1	134536863	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.890000	0.39728	0.848000	0.35191	0.655000	0.94253	GAG	.	.	none		0.483	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			G	134495170	C	G	134495170	3	3	16	1	0	0	0	0	1	0	0	0	14222	796	28	4	1134	4	SGK1	6	134495170	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	11	134495170	36619897	64	2158			1	17		8	6	1887	N	G_C	6.584007e-13
SGK1	6446	hgsc.bcm.edu	37	chr6	134495211	134495211	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gatcttcaagatggactgaaCttcagggctgcagggaataa	13	9	12	7	0	3	2	2	1	1	1	3	5	3	4	0	3	2	2	0	3	4	3			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr6:134495211C>G	ENST00000237305.7	-	3	248	c.160G>C	c.(160-162)Gtt>Ctt	p.V54L	SGK1_ENST00000367858.5_Missense_Mutation_p.V149L|SGK1_ENST00000475719.2_Missense_Mutation_p.V54L|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000528577.1_Missense_Mutation_p.V82L|SGK1_ENST00000367857.5_Missense_Mutation_p.V44L|SGK1_ENST00000413996.3_Missense_Mutation_p.V68L	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	54	Necessary for localization to the mitochondria.				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)		ATGGACTGAACTTCAGGGCTG	0.498																																					p.V149L		Atlas-SNP	.											SGK1_ENST00000528577,NS,lymphoid_neoplasm,0,5	SGK1	387	5	0			c.G445C						PASS	.						122	115	117					6																	134495211		2203	4300	6503	SO:0001583	missense	6446	exon5			ACTGAACTTCAGG	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.160G>C	6.37:g.134495211C>G	ENSP00000237305:p.Val54Leu	85	0	0		73	6	0.0821918	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.408672	0.83340	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T;T	0.38077	1.71;1.71;1.71;1.71;1.71;1.71;1.16	5.99	5.99	0.97316	.	0.000000	0.85682	D	0.000000	T	0.57636	0.2067	M	0.76574	2.34	0.80722	D	1	P;D;B;B;B;B	0.67145	0.529;0.996;0.117;0.289;0.262;0.19	B;D;B;B;B;B	0.76071	0.17;0.987;0.056;0.105;0.276;0.056	T	0.56890	-0.7904	10	0.59425	D	0.04	.	20.4777	0.99188	0.0:1.0:0.0:0.0	.	82;68;54;44;149;54	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	L	149;68;54;44;82;54;118	ENSP00000356832:V149L;ENSP00000396242:V68L;ENSP00000237305:V54L;ENSP00000356831:V44L;ENSP00000434450:V82L;ENSP00000434302:V54L;ENSP00000435577:V118L	ENSP00000237305:V54L	V	-	1	0	SGK1	134536904	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.487000	0.81328	2.840000	0.97914	0.655000	0.94253	GTT	.	.	none		0.498	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			G	134495211	C	G	134495211	3	3	16	1	0	0	0	0	1	0	0	0	14222	565	20	4	1175	4	SGK1	6	134495211	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	41	134495211	36619856	65	2159			1	17		8	6	1887	N	G_C	6.584007e-13
SGK1	6446	hgsc.bcm.edu	37	chr6	134495706	134495706	+	Missense_Mutation	SNP	C	C	T																															taaagtcgttcagacccatcCtcctctgcttcatgaaagct																										TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr6:134495706C>T	ENST00000237305.7	-	2	183	c.95G>A	c.(94-96)aGg>aAg	p.R32K	SGK1_ENST00000367858.5_Missense_Mutation_p.R127K|SGK1_ENST00000475719.2_Missense_Mutation_p.R32K|SGK1_ENST00000489458.2_5'Flank|SGK1_ENST00000528577.1_Missense_Mutation_p.R60K|SGK1_ENST00000367857.5_Missense_Mutation_p.R22K|SGK1_ENST00000413996.3_Missense_Mutation_p.R46K	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	32	Necessary for localization to the mitochondria.				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)	p.R32M(1)|p.R127M(1)		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)		CAGACCCATCCTCCTCTGCTT	0.428											OREG0017675	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R127K		Atlas-SNP	.											SGK1_ENST00000367858,NS,lymphoid_neoplasm,0,2	SGK1	387	2	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.G380A						PASS	.						79	79	79					6																	134495706		2203	4300	6503	SO:0001583	missense	6446	exon4			CCCATCCTCCTCT	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.95G>A	6.37:g.134495706C>T	ENSP00000237305:p.Arg32Lys	76	0	0	1611	48	12	0.25	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	C	19.42	3.823755	0.71143	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T;T	0.43688	1.39;1.39;1.39;1.39;1.39;1.39;0.94	5.89	5.89	0.94794	.	0.083857	0.85682	D	0.000000	T	0.27559	0.0677	L	0.37630	1.12	0.80722	D	1	B;B;B;B;B;B	0.15719	0.014;0.001;0.011;0.004;0.014;0.003	B;B;B;B;B;B	0.25405	0.03;0.002;0.02;0.03;0.06;0.007	T	0.03545	-1.1026	10	0.40728	T	0.16	.	20.2576	0.98430	0.0:1.0:0.0:0.0	.	60;46;32;22;127;32	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	K	127;46;32;22;60;32;96	ENSP00000356832:R127K;ENSP00000396242:R46K;ENSP00000237305:R32K;ENSP00000356831:R22K;ENSP00000434450:R60K;ENSP00000434302:R32K;ENSP00000435577:R96K	ENSP00000237305:R32K	R	-	2	0	SGK1	134537399	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.276000	0.51646	2.783000	0.95769	0.655000	0.94253	AGG	.	.	none		0.428	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			T	134495706	C	T	134495706	3	4	16	1	0	0	0	0	1	0	0	0	14222	681	24	2	1244	2	SGK1	6	134495706	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	495	134495706	36619361	66	2160	30	2	1	17		8	6	1887	N	G_C	6.584007e-13
SGK1	6446	hgsc.bcm.edu	37	chr6	134495711	134495711	+	Silent	SNP	C	C	T																															tcgttcagacccatcctcctCtgcttcatgaaagctgtgga																										TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr6:134495711C>T	ENST00000237305.7	-	2	178	c.90G>A	c.(88-90)caG>caA	p.Q30Q	SGK1_ENST00000367858.5_Silent_p.Q125Q|SGK1_ENST00000475719.2_Silent_p.Q30Q|SGK1_ENST00000489458.2_5'Flank|SGK1_ENST00000528577.1_Silent_p.Q58Q|SGK1_ENST00000367857.5_Silent_p.Q20Q|SGK1_ENST00000413996.3_Silent_p.Q44Q	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	30	Necessary for localization to the mitochondria.				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)		CCATCCTCCTCTGCTTCATGA	0.433											OREG0017675	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q125Q		Atlas-SNP	.											.	SGK1	387	.	0			c.G375A						PASS	.						76	76	76					6																	134495711		2203	4300	6503	SO:0001819	synonymous_variant	6446	exon4			CCTCCTCTGCTTC	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.90G>A	6.37:g.134495711C>T		78	0	0	1611	47	13	0.276596	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Silent	SNP	ENST00000237305.7	37	CCDS5170.1																																																																																			.	.	none		0.433	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			T	134495711	C	T	134495711	2	4	16	1	0	0	0	0	0	0	0	1	14222	912	32	2		2	SGK1	6	134495711	Silent	SNP	C	TCGA-FF-8062-01A-11D-2210-10	5	134495711	36619356	67	2161	30	2	1	17		8	6	1887	N	G_C	6.584007e-13
ZBTB2	57621	hgsc.bcm.edu	37	chr6	151687092	151687092	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggcttttctggataaatttgCgtccacatattgtgcactcg	8	15	9	9	2	1	0	0	0	1	0	3	1	2	1	1	2	2	2	1	2	3	6			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr6:151687092C>T	ENST00000325144.4	-	3	1249	c.1109G>A	c.(1108-1110)cGc>cAc	p.R370H		NM_020861.1	NP_065912.1	Q8N680	ZBTB2_HUMAN	zinc finger and BTB domain containing 2	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)			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)		GATAAATTTGCGTCCACATAT	0.527																																					p.R370H		Atlas-SNP	.											.	ZBTB2	30	.	0			c.G1109A						PASS	.						114	111	112					6																	151687092		2203	4300	6503	SO:0001583	missense	57621	exon3			AATTTGCGTCCAC	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.1109G>A	6.37:g.151687092C>T	ENSP00000323183:p.Arg370His	354	0	0		333	14	0.042042	NM_020861	A8K7C7|Q5SZ81|Q9P245	Missense_Mutation	SNP	ENST00000325144.4	37	CCDS5231.1	.	.	.	.	.	.	.	.	.	.	C	16.55	3.155967	0.57259	.	.	ENSG00000181472	ENST00000325144	T	0.61510	0.1	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	0.61565	0.2357	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.66268	-0.5966	10	0.87932	D	0	-41.439	19.976	0.97309	0.0:1.0:0.0:0.0	.	370	Q8N680	ZBTB2_HUMAN	H	370	ENSP00000323183:R370H	ENSP00000323183:R370H	R	-	2	0	ZBTB2	151728785	1.000000	0.71417	0.998000	0.56505	0.912000	0.54170	7.704000	0.84595	2.713000	0.92767	0.655000	0.94253	CGC	.	.	none		0.527	ZBTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042715.1	NM_020861		T	151687092	C	T	151687092	3	4	16	1	0	0	0	0	1	0	0	0	17543	768	27	1	439	1	ZBTB2	6	151687092	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	17191381	151687092	19427975	68	2162											
TIAM2	26230	hgsc.bcm.edu	37	chr6	155458711	155458711	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaagcttgagctggtggcacGaaggaaatggaaacagtact	14	7	14	6	1	0	1	0	1	0	0	0	5	0	3	0	4	4	4	0	4	5	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr6:155458711G>A	ENST00000461783.3	+	7	2868	c.1595G>A	c.(1594-1596)cGa>cAa	p.R532Q	TIAM2_ENST00000318981.5_Missense_Mutation_p.R532Q|TIAM2_ENST00000456144.1_Missense_Mutation_p.R532Q|TIAM2_ENST00000367174.2_5'UTR|TIAM2_ENST00000360366.4_Missense_Mutation_p.R532Q|TIAM2_ENST00000529824.2_Missense_Mutation_p.R532Q			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	532	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)		CTGGTGGCACGAAGGAAATGG	0.572																																					p.R532Q		Atlas-SNP	.											TIAM2,NS,malignant_melanoma,0,1	TIAM2	161	1	0			c.G1595A						scavenged	.						71	74	73					6																	155458711		2203	4300	6503	SO:0001583	missense	26230	exon4			TGGCACGAAGGAA		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.1595G>A	6.37:g.155458711G>A	ENSP00000437188:p.Arg532Gln	20	0	0		25	6	0.24	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Missense_Mutation	SNP	ENST00000461783.3	37	CCDS34558.1	.	.	.	.	.	.	.	.	.	.	G	36	5.662895	0.96734	.	.	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000528535;ENST00000456144;ENST00000318981;ENST00000360366;ENST00000529824	T;T;T;T;T;T	0.75367	-0.93;-0.93;-0.93;-0.93;-0.93;-0.93	6.08	6.08	0.98989	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.82176	0.4980	L	0.51422	1.61	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.79784	0.989;0.993	T	0.82076	-0.0636	10	0.87932	D	0	.	20.6634	0.99662	0.0:0.0:1.0:0.0	.	532;532	Q8IVF5-2;Q8IVF5	.;TIAM2_HUMAN	Q	532;778;532;532;532;532;532	ENSP00000437188:R532Q;ENSP00000434901:R532Q;ENSP00000407746:R532Q;ENSP00000327315:R532Q;ENSP00000353528:R532Q;ENSP00000433348:R532Q	ENSP00000327315:R532Q	R	+	2	0	TIAM2	155500403	1.000000	0.71417	0.992000	0.48379	0.967000	0.64934	9.476000	0.97823	2.894000	0.99253	0.655000	0.94253	CGA	.	.	none		0.572	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454		A	155458711	G	A	155458711	3	1	16	1	0	0	0	0	1	0	0	0	15906	1058	37	1	1601	1	TIAM2	6	155458711	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	3771619	155458711	15656356	69	2163											
CCR6	1235	hgsc.bcm.edu	37	chr6	167550741	167550741	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggtgtgtgagaaggaagtaCaagtcctcaggcttctcctg	9	11	13	8	0	2	1	1	1	1	1	4	3	3	2	2	3	1	2	2	3	4	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr6:167550741C>A	ENST00000341935.5	+	3	1575	c.1023C>A	c.(1021-1023)taC>taA	p.Y341*	CCR6_ENST00000349984.4_Nonsense_Mutation_p.Y341*|CCR6_ENST00000400926.2_Nonsense_Mutation_p.Y341*|RP11-517H2.6_ENST00000609590.1_RNA	NM_031409.3	NP_113597.2	P51684	CCR6_HUMAN	chemokine (C-C motif) receptor 6	341					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)		GAAGGAAGTACAAGTCCTCAG	0.493																																					p.Y341X		Atlas-SNP	.											.	CCR6	36	.	0			c.C1023A						PASS	.						75	73	74					6																	167550741		2203	4300	6503	SO:0001587	stop_gained	1235	exon3			GAAGTACAAGTCC	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.1023C>A	6.37:g.167550741C>A	ENSP00000343952:p.Tyr341*	115	0	0		137	27	0.19708	NM_004367	E1P5C6|P78553|Q92846	Nonsense_Mutation	SNP	ENST00000341935.5	37	CCDS5298.1	.	.	.	.	.	.	.	.	.	.	C	34	5.358683	0.95854	.	.	ENSG00000112486	ENST00000400926;ENST00000341935;ENST00000349984	.	.	.	4.64	0.654	0.17833	.	6.339280	0.01476	U	0.016474	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.9574	0.19281	0.0:0.5143:0.1513:0.3344	.	.	.	.	X	341	.	ENSP00000343952:Y341X	Y	+	3	2	CCR6	167470731	0.636000	0.27207	0.000000	0.03702	0.011000	0.07611	0.126000	0.15769	0.122000	0.18314	0.655000	0.94253	TAC	.	.	none		0.493	CCR6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043118.1			A	167550741	C	A	167550741	4	1	16	1	0	0	0	0	0	1	0	0	2947	489	17	4	1029	4	CCR6	6	167550741	Nonsense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	12092030	167550741	3564326	70	2164											
HECW1	23072	hgsc.bcm.edu	37	chr7	43283515	43283515	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgggtcattatgctgctgcAcctgtgtagtgtgaaggtca	7	13	14	7	0	2	1	2	1	0	0	2	1	2	1	1	2	3	4	1	2	3	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr7:43283515A>G	ENST00000395891.2	+	3	616	c.11A>G	c.(10-12)cAc>cGc	p.H4R	AC004692.4_ENST00000458680.1_RNA|AC004692.4_ENST00000458590.1_RNA|AC004692.4_ENST00000457315.1_RNA|HECW1_ENST00000453890.1_Missense_Mutation_p.H4R	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	4					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						ATGCTGCTGCACCTGTGTAGT	0.448																																					p.H4R		Atlas-SNP	.											.	HECW1	540	.	0			c.A11G						PASS	.						235	234	234					7																	43283515		2082	4218	6300	SO:0001583	missense	23072	exon3			TGCTGCACCTGTG	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.11A>G	7.37:g.43283515A>G	ENSP00000379228:p.His4Arg	249	0	0		222	52	0.234234	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Missense_Mutation	SNP	ENST00000395891.2	37	CCDS5469.2	.	.	.	.	.	.	.	.	.	.	A	6.186	0.402502	0.11696	.	.	ENSG00000002746	ENST00000395891;ENST00000453890	T;T	0.34472	1.36;1.36	4.67	4.67	0.58626	.	2.499770	0.02291	U	0.070289	T	0.49983	0.1589	N	0.22421	0.69	0.31746	N	0.635233	D;D	0.57899	0.981;0.981	D;D	0.69824	0.966;0.966	T	0.46133	-0.9213	10	0.20519	T	0.43	.	14.1181	0.65167	1.0:0.0:0.0:0.0	.	4;4	B4DH42;Q76N89	.;HECW1_HUMAN	R	4	ENSP00000379228:H4R;ENSP00000407774:H4R	ENSP00000379228:H4R	H	+	2	0	HECW1	43250040	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.982000	0.76173	1.742000	0.51746	0.460000	0.39030	CAC	.	.	none		0.448	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		G	43283515	A	G	43283515	3	3	16	1	0	0	0	0	1	0	0	0	7051	159	6	3	13	3	HECW1	7	43283515	Missense_Mutation	SNP	A	TCGA-FF-8062-01A-11D-2210-10		43283515	115855148	71	2165											
STK17A	9263	hgsc.bcm.edu	37	chr7	43664438	43664438	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	attccaggagaatttatctaCtgagcaatatttccctttag	12	15	6	8	0	1	2	0	1	1	1	3	3	3	2	2	1	2	1	2	1	6	8			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr7:43664438C>G	ENST00000319357.5	+	7	1421	c.1242C>G	c.(1240-1242)taC>taG	p.Y414*		NM_004760.2	NP_004751.2	Q9UEE5	ST17A_HUMAN	serine/threonine kinase 17a	414					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						AATTTATCTACTGAGCAATAT	0.348																																					p.Y414X		Atlas-SNP	.											.	STK17A	31	.	0			c.C1242G						PASS	.						37	39	38					7																	43664438		2200	4298	6498	SO:0001587	stop_gained	9263	exon7			TATCTACTGAGCA	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.1242C>G	7.37:g.43664438C>G	ENSP00000319192:p.Tyr414*	26	0	0		23	9	0.391304	NM_004760	A4D1V6|Q8IVC8	Nonsense_Mutation	SNP	ENST00000319357.5	37	CCDS5470.1	.	.	.	.	.	.	.	.	.	.	C	38	6.861793	0.97893	.	.	ENSG00000164543	ENST00000319357	.	.	.	4.94	4.94	0.65067	.	0.000000	0.43260	D	0.000582	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.1523	0.89678	0.0:1.0:0.0:0.0	.	.	.	.	X	414	.	ENSP00000319192:Y414X	Y	+	3	2	STK17A	43630963	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.531000	0.53546	2.259000	0.74868	0.557000	0.71058	TAC	.	.	none		0.348	STK17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250902.1	NM_004760		G	43664438	C	G	43664438	4	3	16	1	0	0	0	0	0	1	0	0	15305	576	20	4	1268	4	STK17A	7	43664438	Nonsense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	380923	43664438	115474225	72	2166											
PCLO	27445	hgsc.bcm.edu	37	chr7	82595469	82595469	+	Frame_Shift_Del	DEL	T	T	-																															ttttttcttcagggagtggcTttttttcttgaagagctgaa																										TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr7:82595469delT	ENST00000333891.9	-	4	3972	c.3635delA	c.(3634-3636)aagfs	p.K1212fs	PCLO_ENST00000423517.2_Frame_Shift_Del_p.K1212fs	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						AGGGAGTGGCTTTTTTTCTTG	0.368																																					p.K1212fs		Pindel,Atlas-Indel	.											.	PCLO	1506	.	0			c.3636delG						PASS	.						164	155	158					7																	82595469		1796	4076	5872	SO:0001589	frameshift_variant	27445	exon4			.	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.3635delA	7.37:g.82595469delT	ENSP00000334319:p.Lys1212fs	189	0	.		259	39	0.151	NM_014510		Frame_Shift_Del	DEL	ENST00000333891.9	37	CCDS47630.1																																																																																			.	.	none		0.368	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		-	82595469	T	-	82595469	7	5	16	1	0	1	0	1	0	0	0	0	11592	1609	56	0	11898	0	PCLO	7	82595469	Frame_Shift_Del	DEL	T	TCGA-FF-8062-01A-11D-2210-10	38931031	82595469	76543194	73	2167											
SEMA3A	10371	hgsc.bcm.edu	37	chr7	83610791	83610791	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgttgaaccaatatatagttGttgctgtggaaagagtttac	12	14	10	5	1	0	2	0	1	0	1	0	3	0	3	1	1	3	5	1	1	7	8			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr7:83610791G>A	ENST00000265362.4	-	14	1812	c.1498C>T	c.(1498-1500)Caa>Taa	p.Q500*	SEMA3A_ENST00000436949.1_Nonsense_Mutation_p.Q500*	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	500	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						ATATATAGTTGTTGCTGTGGA	0.418																																					p.Q500X		Atlas-SNP	.											.	SEMA3A	121	.	0			c.C1498T						PASS	.						55	56	56					7																	83610791		2203	4300	6503	SO:0001587	stop_gained	10371	exon14			ATAGTTGTTGCTG	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.1498C>T	7.37:g.83610791G>A	ENSP00000265362:p.Gln500*	77	0	0		90	14	0.155556	NM_006080		Nonsense_Mutation	SNP	ENST00000265362.4	37	CCDS5599.1	.	.	.	.	.	.	.	.	.	.	G	40	8.476428	0.98827	.	.	ENSG00000075213	ENST00000265362;ENST00000436949	.	.	.	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.51188	T	0.08	.	19.8579	0.96771	0.0:0.0:1.0:0.0	.	.	.	.	X	500	.	ENSP00000265362:Q500X	Q	-	1	0	SEMA3A	83448727	1.000000	0.71417	0.996000	0.52242	0.707000	0.40811	9.807000	0.99171	2.687000	0.91594	0.655000	0.94253	CAA	.	.	none		0.418	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		A	83610791	G	A	83610791	4	1	16	1	0	0	0	0	0	1	0	0	14039	1386	48	2	833	2	SEMA3A	7	83610791	Nonsense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	1015322	83610791	75527872	74	2168											
FLNC	2318	hgsc.bcm.edu	37	chr7	128483878	128483878	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggcagtgacagtgacttatgGcggggaccctgtccccaaga	9	7	14	11	1	0	3	0	2	0	1	1	4	1	4	3	4	0	1	3	4	2	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr7:128483878G>A	ENST00000325888.8	+	19	3101	c.2840G>A	c.(2839-2841)gGc>gAc	p.G947D	FLNC_ENST00000346177.6_Missense_Mutation_p.G947D	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	947					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						GTGACTTATGGCGGGGACCCT	0.532																																					p.G947D		Atlas-SNP	.											.	FLNC	339	.	0			c.G2840A						PASS	.						85	87	86					7																	128483878		1932	4140	6072	SO:0001583	missense	2318	exon19			CTTATGGCGGGGA	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.2840G>A	7.37:g.128483878G>A	ENSP00000327145:p.Gly947Asp	154	0	0		114	37	0.324561	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Missense_Mutation	SNP	ENST00000325888.8	37	CCDS43644.1	.	.	.	.	.	.	.	.	.	.	G	19.02	3.746324	0.69418	.	.	ENSG00000128591	ENST00000325888;ENST00000346177	D;D	0.91521	-2.86;-2.86	5.32	5.32	0.75619	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.95108	0.8415	M	0.71920	2.185	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	D	0.95440	0.8524	10	0.87932	D	0	.	18.9962	0.92813	0.0:0.0:1.0:0.0	.	947;947	Q14315-2;Q14315	.;FLNC_HUMAN	D	947	ENSP00000327145:G947D;ENSP00000344002:G947D	ENSP00000327145:G947D	G	+	2	0	FLNC	128271114	1.000000	0.71417	1.000000	0.80357	0.453000	0.32348	9.783000	0.99037	2.481000	0.83766	0.561000	0.74099	GGC	.	.	none		0.532	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			A	128483878	G	A	128483878	3	1	16	1	0	0	0	0	1	0	0	0	5943	1203	42	2	2914	2	FLNC	7	128483878	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	44873087	128483878	30654785	75	2169											
C8orf45	157777	hgsc.bcm.edu	37	chr8	67796149	67796149	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtttgttgatgagtctagtAcagacaactgaccgtaacaa	13	12	9	7	1	1	4	0	3	1	1	1	4	1	4	1	0	3	4	1	0	5	5			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr8:67796149A>G	ENST00000422365.2	+	9	1164	c.993A>G	c.(991-993)gtA>gtG	p.V331V	MCMDC2_ENST00000313616.5_Silent_p.V331V|MCMDC2_ENST00000492775.1_Silent_p.V331V|MCMDC2_ENST00000541540.1_Silent_p.V268V|MCMDC2_ENST00000396592.3_Silent_p.V331V	NM_173518.4	NP_775789.3	Q4G0Z9	MCMD2_HUMAN	minichromosome maintenance domain containing 2	331					DNA replication (GO:0006260)		ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(2)|kidney(2)|lung(5)	9						TGAGTCTAGTACAGACAACTG	0.378																																					p.V331V		Atlas-SNP	.											.	MCMDC2	84	.	0			c.A993G						PASS	.						75	71	72					8																	67796149		2203	4300	6503	SO:0001819	synonymous_variant	157777	exon9			TCTAGTACAGACA	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.993A>G	8.37:g.67796149A>G		92	0	0		103	5	0.0485437	NM_173518	B4DYZ3|B4DZM4|B4E293|Q6P533|Q7Z3P4	Silent	SNP	ENST00000422365.2	37	CCDS6197.2																																																																																			.	.	none		0.378	MCMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347350.1	NM_173518		G	67796149	A	G	67796149	2	3	16	1	0	0	0	0	0	0	0	1	2432	378	14	3		3	C8orf45	8	67796149	Silent	SNP	A	TCGA-FF-8062-01A-11D-2210-10		67796149	78567873	76	2170											
SULF1	23213	hgsc.bcm.edu	37	chr8	70512971	70512971	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tccagactttgatgtcagtgGatgattctgtggagagggta	9	13	14	5	0	2	4	1	2	1	2	3	6	3	5	1	3	0	1	1	3	1	3			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr8:70512971G>A	ENST00000260128.4	+	9	1585	c.868G>A	c.(868-870)Gat>Aat	p.D290N	SULF1_ENST00000521946.1_3'UTR|SULF1_ENST00000458141.2_Missense_Mutation_p.D290N|SULF1_ENST00000402687.4_Missense_Mutation_p.D290N|SULF1_ENST00000419716.3_Missense_Mutation_p.D290N	NM_015170.2	NP_055985.2	Q8IWU6	SULF1_HUMAN	sulfatase 1	290					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)			GATGTCAGTGGATGATTCTGT	0.438																																					p.D290N		Atlas-SNP	.											.	SULF1	153	.	0			c.G868A						PASS	.						163	155	158					8																	70512971		2203	4300	6503	SO:0001583	missense	23213	exon9			TCAGTGGATGATT	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.868G>A	8.37:g.70512971G>A	ENSP00000260128:p.Asp290Asn	89	0	0		106	22	0.207547	NM_001128205	Q86YV8|Q8NCA2|Q9UPS5	Missense_Mutation	SNP	ENST00000260128.4	37	CCDS6204.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.929844	0.92389	.	.	ENSG00000137573	ENST00000458141;ENST00000260128;ENST00000402687;ENST00000419716	D;D;D;D	0.99842	-7.1;-7.1;-7.1;-7.1	6.16	6.16	0.99307	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.042703	0.85682	D	0.000000	D	0.99869	0.9938	M	0.90082	3.085	0.80722	D	1	D	0.76494	0.999	D	0.76575	0.988	D	0.97261	0.9904	10	0.87932	D	0	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	290	Q8IWU6	SULF1_HUMAN	N	290	ENSP00000403040:D290N;ENSP00000260128:D290N;ENSP00000385704:D290N;ENSP00000390315:D290N	ENSP00000260128:D290N	D	+	1	0	SULF1	70675525	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.905000	0.87416	2.937000	0.99478	0.650000	0.86243	GAT	.	.	none		0.438	SULF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378885.2	NM_015170		A	70512971	G	A	70512971	3	1	16	1	0	0	0	0	1	0	0	0	15385	1174	41	2	886	2	SULF1	8	70512971	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	2716822	70512971	75851051	77	2171											
PI15	51050	hgsc.bcm.edu	37	chr8	75737657	75737657	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggatatccccaaagccaggcGgaagcgctacatttcgcaga	12	6	11	12	3	0	1	0	0	0	1	2	3	1	3	3	3	3	2	3	3	4	3	rs141788887	byFrequency	TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr8:75737657G>A	ENST00000260113.2	+	2	352	c.173G>A	c.(172-174)cGg>cAg	p.R58Q	RP11-758M4.4_ENST00000523860.1_RNA|RP11-758M4.4_ENST00000518128.1_RNA|PI15_ENST00000523773.1_Missense_Mutation_p.R58Q	NM_015886.3	NP_056970.1	O43692	PI15_HUMAN	peptidase inhibitor 15	58						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)			AAAGCCAGGCGGAAGCGCTAC	0.448													G|||	10	0.00199681	0.0068	0.0014	5008	,	,		17888	0.0		0.0	False		,,,				2504	0.0				p.R58Q		Atlas-SNP	.											.	PI15	73	.	0			c.G173A						PASS	.	G	GLN/ARG	28,4378	35.2+/-66.4	0,28,2175	85	76	79		173	4.4	1	8	dbSNP_134	79	1,8599	1.2+/-3.3	0,1,4299	yes	missense	PI15	NM_015886.3	43	0,29,6474	AA,AG,GG		0.0116,0.6355,0.223	probably-damaging	58/259	75737657	29,12977	2203	4300	6503	SO:0001583	missense	51050	exon2			CCAGGCGGAAGCG	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.173G>A	8.37:g.75737657G>A	ENSP00000260113:p.Arg58Gln	70	0	0		87	14	0.16092	NM_015886	Q68CY1	Missense_Mutation	SNP	ENST00000260113.2	37	CCDS6218.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	13.03	2.115943	0.37339	0.006355	1.16E-4	ENSG00000137558	ENST00000260113;ENST00000523773	T;T	0.09630	2.96;2.96	5.35	4.45	0.53987	CAP domain (2);	0.169477	0.49916	D	0.000123	T	0.07773	0.0195	M	0.68593	2.085	0.48040	D	0.999577	P	0.49559	0.925	B	0.34301	0.179	T	0.28713	-1.0035	10	0.13108	T	0.6	.	16.2838	0.82709	0.0:0.1326:0.8674:0.0	.	58	O43692	PI15_HUMAN	Q	58	ENSP00000260113:R58Q;ENSP00000428567:R58Q	ENSP00000260113:R58Q	R	+	2	0	PI15	75900212	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.032000	0.64140	1.585000	0.49928	0.655000	0.94253	CGG	G|0.997;A|0.003	0.003	strong		0.448	PI15-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379115.1	NM_015886		A	75737657	G	A	75737657	3	1	16	1	0	0	0	0	1	0	0	0	11877	1116	39	1	175	1	PI15	8	75737657	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	5224686	75737657	70626365	78	2172											
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77776035	77776035	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagccgcaaaactccaacgAtgcttcagaaacaaaggaag	17	4	8	12	2	1	1	1	0	0	1	2	3	2	2	3	1	5	2	3	1	6	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr8:77776035A>T	ENST00000521891.2	+	11	10533	c.10085A>T	c.(10084-10086)gAt>gTt	p.D3362V	ZFHX4_ENST00000455469.2_Missense_Mutation_p.D3317V|ZFHX4_ENST00000050961.6_Missense_Mutation_p.D3313V|ZFHX4_ENST00000518282.1_Missense_Mutation_p.D3336V	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	3313					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)			AACTCCAACGATGCTTCAGAA	0.433										HNSCC(33;0.089)																											p.D3362V		Atlas-SNP	.											.	ZFHX4	878	.	0			c.A10085T						PASS	.						21	21	21					8																	77776035		1851	3991	5842	SO:0001583	missense	79776	exon11			CCAACGATGCTTC		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.10085A>T	8.37:g.77776035A>T	ENSP00000430497:p.Asp3362Val	51	0	0		48	8	0.166667	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	A	2.721	-0.266537	0.05754	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.54479	0.57;0.62;0.61;0.58	4.5	4.5	0.54988	.	0.932477	0.08819	U	0.889077	T	0.39989	0.1099	N	0.11560	0.145	0.48762	D	0.999701	B	0.20459	0.045	B	0.25614	0.062	T	0.17745	-1.0359	10	0.72032	D	0.01	.	13.9762	0.64275	1.0:0.0:0.0:0.0	.	3317	Q86UP3-4	.	V	3362;3346;3317;3313;3336	ENSP00000430497:D3362V;ENSP00000399605:D3317V;ENSP00000050961:D3313V;ENSP00000430848:D3336V	ENSP00000050961:D3313V	D	+	2	0	ZFHX4	77938590	1.000000	0.71417	0.644000	0.29465	0.313000	0.28021	7.047000	0.76599	1.907000	0.55213	0.496000	0.49642	GAT	.	.	none		0.433	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77776035	A	T	77776035	3	4	16	1	0	0	0	0	1	0	0	0	17650	333	12	5	10123	5	ZFHX4	8	77776035	Missense_Mutation	SNP	A	TCGA-FF-8062-01A-11D-2210-10	2038378	77776035	68587987	79	2173											
RALYL	138046	hgsc.bcm.edu	37	chr8	85774611	85774611	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcccagagtggcagtcacaaCgactcgcagggggaaaggag	12	4	15	10	2	1	1	1	0	0	1	3	4	2	3	1	4	1	2	1	4	2	0			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr8:85774611C>T	ENST00000521268.1	+	6	1599	c.494C>T	c.(493-495)aCg>aTg	p.T165M	RALYL_ENST00000521376.1_Missense_Mutation_p.T76M|RALYL_ENST00000522455.1_Missense_Mutation_p.T165M|RALYL_ENST00000523850.1_Missense_Mutation_p.T92M|RALYL_ENST00000517638.1_Missense_Mutation_p.T178M|RALYL_ENST00000518566.1_Missense_Mutation_p.T154M|RALYL_ENST00000521695.1_Missense_Mutation_p.T165M	NM_173848.5	NP_776247.3	Q86SE5	RALYL_HUMAN	RALY RNA binding protein-like	165							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)	24						GCAGTCACAACGACTCGCAGG	0.483																																					p.T178M		Atlas-SNP	.											.	RALYL	123	.	0			c.C533T						PASS	.						56	61	59					8																	85774611		1929	4136	6065	SO:0001583	missense	138046	exon6			TCACAACGACTCG		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.494C>T	8.37:g.85774611C>T	ENSP00000430367:p.Thr165Met	57	0	0		53	13	0.245283	NM_001100391	B3KTH2|G3V129|Q6ZW87|Q8N1C2	Missense_Mutation	SNP	ENST00000521268.1	37	CCDS55253.1	.	.	.	.	.	.	.	.	.	.	C	18.00	3.526572	0.64860	.	.	ENSG00000184672	ENST00000522455;ENST00000521695;ENST00000521268;ENST00000518566;ENST00000517638;ENST00000523850;ENST00000521376	T;T;T;T;T;T;T	0.18657	2.83;2.83;2.83;2.85;2.83;2.42;2.2	5.1	5.1	0.69264	.	0.214143	0.49305	D	0.000143	T	0.35941	0.0949	M	0.61703	1.905	0.09310	N	1	P;D;P;P;D	0.60160	0.791;0.987;0.939;0.93;0.987	B;P;B;P;P	0.51016	0.336;0.588;0.337;0.656;0.588	T	0.19192	-1.0313	10	0.62326	D	0.03	-3.4988	18.8851	0.92375	0.0:1.0:0.0:0.0	.	154;165;92;178;165	B3KT61;B3KSX3;Q86SE5-2;G3V129;Q86SE5	.;.;.;.;RALYL_HUMAN	M	165;165;165;154;178;92;76	ENSP00000430394:T165M;ENSP00000428667:T165M;ENSP00000430367:T165M;ENSP00000430065:T154M;ENSP00000430128:T178M;ENSP00000428807:T92M;ENSP00000428310:T76M	ENSP00000430128:T178M	T	+	2	0	RALYL	85937166	0.679000	0.27596	0.011000	0.14972	0.798000	0.45092	5.613000	0.67688	2.511000	0.84671	0.551000	0.68910	ACG	.	.	none		0.483	RALYL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379448.1			T	85774611	C	T	85774611	3	4	16	1	0	0	0	0	1	0	0	0	13035	536	19	1	555	1	RALYL	8	85774611	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	7998576	85774611	60589411	80	2174											
ZNF572	137209	hgsc.bcm.edu	37	chr8	125989722	125989722	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catctcattagacatcagagAacacatacaggagaaaaacc	19	6	6	10	0	2	3	2	0	1	3	3	5	2	3	1	1	3	0	1	1	5	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr8:125989722A>G	ENST00000319286.5	+	3	1366	c.1212A>G	c.(1210-1212)agA>agG	p.R404R		NM_152412.2	NP_689625.2	Q7Z3I7	ZN572_HUMAN	zinc finger protein 572	404					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)			GACATCAGAGAACACATACAG	0.423										HNSCC(60;0.17)																											p.R404R		Atlas-SNP	.											ZNF572,colon,carcinoma,+1,1	ZNF572	82	1	0			c.A1212G						PASS	.						83	80	81					8																	125989722		2203	4300	6503	SO:0001819	synonymous_variant	137209	exon3			TCAGAGAACACAT	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.1212A>G	8.37:g.125989722A>G		57	0	0		65	4	0.0615385	NM_152412	A1L4F1|Q8N1Q0	Silent	SNP	ENST00000319286.5	37	CCDS6354.1																																																																																			.	.	none		0.423	ZNF572-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381359.1	NM_152412		G	125989722	A	G	125989722	2	3	16	1	0	0	0	0	0	0	0	1	18019	243	9	3		3	ZNF572	8	125989722	Silent	SNP	A	TCGA-FF-8062-01A-11D-2210-10	40215111	125989722	20374300	81	2175											
ZFAT	57623	hgsc.bcm.edu	37	chr8	135613905	135613905	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccccaccaccagctactggaGggaggaggtctgaggcctca	9	5	13	14	0	2	1	1	1	1	0	2	4	2	4	5	5	2	1	5	5	1	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr8:135613905G>A	ENST00000377838.3	-	6	2231	c.2057C>T	c.(2056-2058)cCt>cTt	p.P686L	ZFAT_ENST00000520727.1_Missense_Mutation_p.P674L|ZFAT_ENST00000523399.1_Missense_Mutation_p.P624L|ZFAT_ENST00000520356.1_Missense_Mutation_p.P674L|ZFAT_ENST00000520214.1_Missense_Mutation_p.P674L|ZFAT_ENST00000429442.2_Missense_Mutation_p.P674L|ZFAT-AS1_ENST00000505776.1_RNA	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	686					hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|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)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			AGCTACTGGAGGGAGGAGGTC	0.597																																					p.P686L		Atlas-SNP	.											.	ZFAT	265	.	0			c.C2057T						PASS	.						68	73	72					8																	135613905		2041	4199	6240	SO:0001583	missense	57623	exon6			ACTGGAGGGAGGA	BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827		"Zinc fingers, C2H2-type"	19899	protein-coding gene	gene with protein product		610931	"zinc finger protein 406"	ZNF406, ZFAT1		10819331, 18329245	Standard	NM_020863		Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.2057C>T	8.37:g.135613905G>A	ENSP00000367069:p.Pro686Leu	131	0	0		111	5	0.045045	NM_020863	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Missense_Mutation	SNP	ENST00000377838.3	37	CCDS47924.1	.	.	.	.	.	.	.	.	.	.	G	10.02	1.235411	0.22626	.	.	ENSG00000066827	ENST00000520356;ENST00000520727;ENST00000429442;ENST00000377838;ENST00000520214;ENST00000318135;ENST00000523399;ENST00000398946	T;T;T;T;T;T	0.09911	3.0;2.93;2.93;2.93;2.93;2.96	5.0	4.12	0.48240	.	0.066393	0.64402	D	0.000013	T	0.07683	0.0193	L	0.27053	0.805	0.09310	N	0.999997	B;B;B;B	0.25272	0.016;0.004;0.122;0.001	B;B;B;B	0.28305	0.009;0.004;0.088;0.002	T	0.33445	-0.9868	10	0.24483	T	0.36	-8.8579	8.1168	0.30948	0.2492:0.0:0.7508:0.0	.	624;674;674;686	E9PER3;E9PBN4;Q9P243-3;Q9P243	.;.;.;ZFAT_HUMAN	L	674;674;674;686;674;573;624;674	ENSP00000427879:P674L;ENSP00000427831:P674L;ENSP00000394501:P674L;ENSP00000367069:P686L;ENSP00000428483:P674L;ENSP00000429091:P624L	ENSP00000326997:P573L	P	-	2	0	ZFAT	135683087	0.003000	0.15002	0.039000	0.18376	0.809000	0.45718	1.438000	0.35002	1.327000	0.45338	0.561000	0.74099	CCT	.	.	none		0.597	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939		A	135613905	G	A	135613905	3	1	16	1	0	0	0	0	1	0	0	0	17647	1000	35	2	1718	2	ZFAT	8	135613905	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	9624183	135613905	10750117	82	2176											
MSMP	692094	hgsc.bcm.edu	37	chr9	35753722	35753722	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaacagtccttgcggagccaAgactcacccagggtaaaata	15	6	9	11	1	1	1	1	0	0	1	2	2	2	2	3	2	3	1	3	2	5	3			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr9:35753722A>G	ENST00000436428.2	-	2	313	c.174T>C	c.(172-174)tcT>tcC	p.S58S	RGP1_ENST00000378078.4_3'UTR|MSMP_ENST00000414286.1_5'UTR|RP11-112J3.15_ENST00000425499.2_RNA	NM_001044264.2	NP_001037729.1	Q1L6U9	MSMP_HUMAN	microseminoprotein, prostate associated	58						cytoplasm (GO:0005737)|extracellular space (GO:0005615)				endometrium(2)|kidney(1)|lung(3)|prostate(3)	9						TGCGGAGCCAAGACTCACCCA	0.527																																					p.S58S		Atlas-SNP	.											.	MSMP	15	.	0			c.T174C						PASS	.						44	46	45					9																	35753722		2045	4202	6247	SO:0001819	synonymous_variant	692094	exon2			GAGCCAAGACTCA	DQ012170	CCDS43797.1	9p13.3	2012-10-02			ENSG00000215183	ENSG00000215183			29663	protein-coding gene	gene with protein product		612191				17338636	Standard	NM_001044264		Approved	PC-3, PSMP	uc003zyb.2	Q1L6U9	OTTHUMG00000019882	ENST00000436428.2:c.174T>C	9.37:g.35753722A>G		146	0	0		133	34	0.255639	NM_001044264		Silent	SNP	ENST00000436428.2	37	CCDS43797.1																																																																																			.	.	none		0.527	MSMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052384.2	NM_001044264		G	35753722	A	G	35753722	2	3	16	1	0	0	0	0	0	0	0	1	9893	59	3	3		3	MSMP	9	35753722	Silent	SNP	A	TCGA-FF-8062-01A-11D-2210-10		35753722	105459709	83	2177											
MUSK	4593	hgsc.bcm.edu	37	chr9	113496632	113496632	+	Frame_Shift_Del	DEL	A	A	-																															gcattcctgtccccaccatcAcctggattgaaaacggaaat																										TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr9:113496632delA	ENST00000374448.4	+	6	864	c.730delA	c.(730-732)accfs	p.T244fs	MUSK_ENST00000416899.2_Frame_Shift_Del_p.T244fs|MUSK_ENST00000189978.5_Frame_Shift_Del_p.T244fs	NM_001166281.1|NM_005592.3	NP_001159753.1|NP_005583.1	O15146	MUSK_HUMAN	muscle, skeletal, receptor tyrosine kinase	244	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						CCCCACCATCACCTGGATTGA	0.507																																					p.I253fs		Pindel,Atlas-Indel	.											.	MUSK	112	.	0			c.759delC						PASS	.						140	128	132					9																	113496632		2052	4215	6267	SO:0001589	frameshift_variant	4593	exon7			.	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.730delA	9.37:g.113496632delA	ENSP00000363571:p.Thr244fs	98	0	.		105	17	0.162	NM_001166280	Q32MJ8|Q32MJ9|Q5VZW7|Q5VZW8	Frame_Shift_Del	DEL	ENST00000374448.4	37	CCDS48005.1																																																																																			.	.	none		0.507	MUSK-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				-	113496632	A	-	113496632	7	5	16	1	0	1	0	1	0	0	0	0	9998	159	6	0	786	0	MUSK	9	113496632	Frame_Shift_Del	DEL	A	TCGA-FF-8062-01A-11D-2210-10	77742910	113496632	27716799	84	2178											
BAT2L1	84726	hgsc.bcm.edu	37	chr9	134322483	134322483	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atgtttcagatgtgttcgccGaagtcatcagaaaaccaggg	12	10	11	8	2	3	2	3	0	0	2	4	3	3	2	2	1	1	2	2	1	3	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr9:134322483G>A	ENST00000357304.4	+	7	922	c.867G>A	c.(865-867)ccG>ccA	p.P289P	PRRC2B_ENST00000372249.1_5'Flank|PRRC2B_ENST00000458550.1_Silent_p.P289P|PRRC2B_ENST00000405995.1_Silent_p.P289P	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	289							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						TGTGTTCGCCGAAGTCATCAG	0.428																																					p.P289P		Atlas-SNP	.											.	PRRC2B	266	.	0			c.G867A						PASS	.						108	103	105					9																	134322483		1937	4141	6078	SO:0001819	synonymous_variant	84726	exon7			TTCGCCGAAGTCA	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.867G>A	9.37:g.134322483G>A		131	0	0		146	25	0.171233	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Silent	SNP	ENST00000357304.4	37	CCDS48044.1																																																																																			.	.	none		0.428	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	134322483	G	A	134322483	2	1	16	1	0	0	0	0	0	0	0	1	1320	1045	37	1		1	BAT2L1	9	134322483	Silent	SNP	G	TCGA-FF-8062-01A-11D-2210-10	20825851	134322483	6890948	85	2179											
ARHGAP22	58504	hgsc.bcm.edu	37	chr10	49654625	49654625	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagttcttcttctaaccgggAcattcgttttctcaggtcag	7	15	8	11	2	5	0	2	0	4	0	7	1	5	1	1	2	1	2	1	2	1	7			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr10:49654625A>G	ENST00000249601.4	-	10	2202	c.1906T>C	c.(1906-1908)Tcc>Ccc	p.S636P	ARHGAP22_ENST00000374170.1_Missense_Mutation_p.S477P|ARHGAP22_ENST00000417912.2_Missense_Mutation_p.S652P|ARHGAP22_ENST00000435790.2_Missense_Mutation_p.S642P|ARHGAP22_ENST00000374172.1_Missense_Mutation_p.S527P|ARHGAP22_ENST00000417247.2_Missense_Mutation_p.S546P|ARHGAP22_ENST00000477708.2_Missense_Mutation_p.S469P	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	636					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						TCTAACCGGGACATTCGTTTT	0.502																																					p.S652P		Atlas-SNP	.											.	ARHGAP22	94	.	0			c.T1954C						PASS	.						126	115	118					10																	49654625		2203	4300	6503	SO:0001583	missense	58504	exon10			ACCGGGACATTCG	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.1906T>C	10.37:g.49654625A>G	ENSP00000249601:p.Ser636Pro	269	0	0		231	55	0.238095	NM_001256024	A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Missense_Mutation	SNP	ENST00000249601.4	37	CCDS7227.1	.	.	.	.	.	.	.	.	.	.	A	10.90	1.482037	0.26598	.	.	ENSG00000128805	ENST00000249601;ENST00000374172;ENST00000374170;ENST00000477708;ENST00000417247;ENST00000435790;ENST00000417912	T;T;T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98;0.98;0.98	4.42	0.456	0.16655	.	0.502966	0.20316	N	0.094726	T	0.49881	0.1583	L	0.51422	1.61	0.09310	N	0.999995	B;P;P;P;P;D	0.64830	0.337;0.475;0.744;0.475;0.744;0.994	B;B;B;B;B;P	0.59703	0.063;0.099;0.26;0.099;0.134;0.862	T	0.45877	-0.9231	10	0.44086	T	0.13	.	12.1264	0.53919	0.4414:0.5586:0.0:0.0	.	642;636;652;636;546;469	B4DED8;A6NDI7;Q7Z5H3-2;Q7Z5H3;Q7Z5H3-3;D6R9V6	.;.;.;RHG22_HUMAN;.;.	P	636;527;477;469;546;642;652	ENSP00000249601:S636P;ENSP00000363287:S527P;ENSP00000363285:S477P;ENSP00000422868:S469P;ENSP00000410054:S546P;ENSP00000416701:S642P;ENSP00000412461:S652P	ENSP00000249601:S636P	S	-	1	0	ARHGAP22	49324631	0.002000	0.14202	0.014000	0.15608	0.008000	0.06430	-0.001000	0.12947	0.080000	0.16959	0.459000	0.35465	TCC	.	.	none		0.502	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226		G	49654625	A	G	49654625	3	3	16	1	0	0	0	0	1	0	0	0	872	275	10	3	194	3	ARHGAP22	10	49654625	Missense_Mutation	SNP	A	TCGA-FF-8062-01A-11D-2210-10		49654625	85880122	86	2180											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1258274	1258274	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aacagctggaagctctccccCtcctgcccggacgccctggc	6	6	10	19	2	1	0	0	0	1	0	3	2	2	2	5	3	4	2	5	3	2	0			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr11:1258274C>T	ENST00000529681.1	+	25	3235	c.3177C>T	c.(3175-3177)ccC>ccT	p.P1059P	MUC5B_ENST00000447027.1_Silent_p.P1062P	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1059	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)		AGCTCTCCCCCTCCTGCCCGG	0.657																																					p.P1059P		Atlas-SNP	.											.	MUC5B	473	.	0			c.C3177T						PASS	.						42	59	53					11																	1258274		2100	4204	6304	SO:0001819	synonymous_variant	727897	exon25			CTCCCCCTCCTGC	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.3177C>T	11.37:g.1258274C>T		62	0	0		59	4	0.0677966	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			.	.	none		0.657	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		T	1258274	C	T	1258274	2	4	16	1	0	0	0	0	0	0	0	1	9988	668	24	2		2	MUC5B	11	1258274	Silent	SNP	C	TCGA-FF-8062-01A-11D-2210-10		1258274	133748242	87	2181											
CKAP5	9793	hgsc.bcm.edu	37	chr11	46831321	46831321	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catctccaccagcagactgtTgttgttccaatttagcttct	8	15	6	12	0	2	1	0	0	2	1	4	1	3	1	3	0	2	5	3	0	2	6			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr11:46831321T>A	ENST00000529230.1	-	6	780	c.734A>T	c.(733-735)cAa>cTa	p.Q245L	CKAP5_ENST00000312055.5_Missense_Mutation_p.Q245L|CKAP5_ENST00000415402.1_Missense_Mutation_p.Q245L|CKAP5_ENST00000354558.3_Missense_Mutation_p.Q245L			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	245					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						AGCAGACTGTTGTTGTTCCAA	0.428																																					p.Q245L	Ovarian(4;85 273 2202 4844 13323)	Atlas-SNP	.											.	CKAP5	134	.	0			c.A734T						PASS	.						214	203	207					11																	46831321		2201	4299	6500	SO:0001583	missense	9793	exon6			GACTGTTGTTGTT		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.734A>T	11.37:g.46831321T>A	ENSP00000432768:p.Gln245Leu	194	0	0		222	38	0.171171	NM_001008938	Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	Missense_Mutation	SNP	ENST00000529230.1	37	CCDS31477.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.232689	0.79688	.	.	ENSG00000175216	ENST00000529230;ENST00000415402;ENST00000312055;ENST00000378629;ENST00000354558	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	5.78	3.39	0.38822	Armadillo-like helical (1);Armadillo-type fold (1);	0.052954	0.85682	D	0.000000	T	0.49830	0.1580	L	0.46157	1.445	0.58432	D	0.999998	P;B;D	0.54772	0.908;0.062;0.968	D;B;P	0.64144	0.922;0.055;0.449	T	0.33111	-0.9881	10	0.31617	T	0.26	-16.6184	8.6638	0.34108	0.0:0.0672:0.1296:0.8032	.	245;245;245	Q14008-3;Q14008-2;Q14008	.;.;CKAP5_HUMAN	L	245	ENSP00000432768:Q245L;ENSP00000395302:Q245L;ENSP00000310227:Q245L;ENSP00000346566:Q245L	ENSP00000310227:Q245L	Q	-	2	0	CKAP5	46787897	1.000000	0.71417	0.958000	0.39756	0.988000	0.76386	7.607000	0.82883	0.418000	0.25898	-0.297000	0.09499	CAA	.	.	none		0.428	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1	NM_014756		A	46831321	T	A	46831321	3	1	16	1	0	0	0	0	1	0	0	0	3447	1812	63	5	5520	5	CKAP5	11	46831321	Missense_Mutation	SNP	T	TCGA-FF-8062-01A-11D-2210-10	45573047	46831321	88175195	88	2182											
OR5W2	390148	hgsc.bcm.edu	37	chr11	55681542	55681542	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagaagaaatgattaatctCattagacccacagaagcata	19	8	6	8	0	1	5	1	1	1	4	2	5	1	5	1	0	1	1	1	0	6	3			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr11:55681542C>A	ENST00000344514.1	-	1	516	c.517G>T	c.(517-519)Gag>Tag	p.E173*		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	173						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						TGATTAATCTCATTAGACCCA	0.418																																					p.E173X	Melanoma(48;171 1190 15239 43886 49348)	Atlas-SNP	.											OR5W2,colon,carcinoma,+2,1	OR5W2	112	1	0			c.G517T						PASS	.						84	77	79					11																	55681542		2201	4296	6497	SO:0001587	stop_gained	390148	exon1			TAATCTCATTAGA	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.517G>T	11.37:g.55681542C>A	ENSP00000342448:p.Glu173*	52	0	0		69	15	0.217391	NM_001001960		Nonsense_Mutation	SNP	ENST00000344514.1	37	CCDS31513.1	.	.	.	.	.	.	.	.	.	.	C	19.62	3.861330	0.71949	.	.	ENSG00000187612	ENST00000344514	.	.	.	5.0	4.09	0.47781	.	0.000000	0.40818	N	0.001006	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	11.1192	0.48279	0.0:0.9092:0.0:0.0908	.	.	.	.	X	173	.	ENSP00000342448:E173X	E	-	1	0	OR5W2	55438118	0.000000	0.05858	0.625000	0.29200	0.981000	0.71138	-0.662000	0.05305	1.097000	0.41459	0.542000	0.68232	GAG	.	.	none		0.418	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960		A	55681542	C	A	55681542	4	1	16	1	0	0	0	0	0	1	0	0	11194	835	29	4	417	4	OR5W2	11	55681542	Nonsense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	8850221	55681542	79324974	89	2183											
OR5AK2	390181	hgsc.bcm.edu	37	chr11	56756917	56756917	+	Frame_Shift_Del	DEL	T	T	-																															agtccaatagcatcaatcacTttttctgtgatgttccccct																										TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr11:56756917delT	ENST00000326855.2	+	1	571	c.529delT	c.(529-531)tttfs	p.F178fs		NM_001005323.1	NP_001005323.1	Q8NH90	O5AK2_HUMAN	olfactory receptor, family 5, subfamily AK, member 2	178						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(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21						CATCAATCACTTTTTCTGTGA	0.398																																					p.H176fs		Atlas-Indel	.											.	OR5AK2	45	.	0			c.528delC						PASS	.						346	311	323					11																	56756917		2201	4296	6497	SO:0001589	frameshift_variant	390181	exon1			.	AB065496	CCDS31538.1	11q11	2012-08-09			ENSG00000181273	ENSG00000181273		"GPCR / Class A : Olfactory receptors"	15251	protein-coding gene	gene with protein product							Standard	NM_001005323		Approved		uc010rjp.2	Q8NH90	OTTHUMG00000167019	ENST00000326855.2:c.529delT	11.37:g.56756917delT	ENSP00000322784:p.Phe178fs	250	0	0		294	47	0.159864	NM_001005323	B2RNZ9	Frame_Shift_Del	DEL	ENST00000326855.2	37	CCDS31538.1																																																																																			.	.	none		0.398	OR5AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392446.1	NM_001005323		-	56756917	T	-	56756917	7	5	16	1	0	1	0	1	0	0	0	0	11151	1609	56	0	531	0	OR5AK2	11	56756917	Frame_Shift_Del	DEL	T	TCGA-FF-8062-01A-11D-2210-10	1075375	56756917	78249599	90	2184											
FAU	740	hgsc.bcm.edu	37	chr11	64889279	64889279	+	5'Flank	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcctgggcgcggacaaagaGctgcatattggcgactgagt	9	8	14	10	3	0	2	0	1	0	1	1	4	1	3	1	3	2	2	1	3	2	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr11:64889279G>C	ENST00000279242.2	+	0	0				MRPL49_ENST00000526171.1_5'Flank|FAU_ENST00000434372.2_Missense_Mutation_p.L3V|FAU_ENST00000525297.1_Missense_Mutation_p.L3V|FAU_ENST00000529639.1_Missense_Mutation_p.L3V|MRPL49_ENST00000534078.1_5'Flank|FAU_ENST00000527548.1_Missense_Mutation_p.L3V|FAU_ENST00000279259.3_Missense_Mutation_p.L3V|FAU_ENST00000529259.1_Missense_Mutation_p.L3V|MRPL49_ENST00000531705.1_5'Flank|FAU_ENST00000531743.1_Missense_Mutation_p.L3V	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						CGGACAAAGAGCTGCATATTG	0.537																																					p.L3V		Atlas-SNP	.											FAU,NS,carcinoma,+2,1	FAU	17	1	0			c.C7G						PASS	.						67	61	63					11																	64889279		2201	4297	6498	SO:0001631	upstream_gene_variant	2197	exon2			CAAAGAGCTGCAT		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		11.37:g.64889279G>C	Exception_encountered	89	0	0		87	22	0.252874	NM_001997	B2R4G6	Missense_Mutation	SNP	ENST00000279242.2	37	CCDS8096.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.409753	0.83340	.	.	ENSG00000149806	ENST00000529639;ENST00000531743;ENST00000525297;ENST00000527548;ENST00000279259;ENST00000529259;ENST00000526555;ENST00000434372	T;T;T;T;T;T;T;T	0.60548	1.11;1.11;0.18;1.11;1.11;1.11;1.11;1.11	5.92	4.99	0.66335	Ubiquitin supergroup (1);Ubiquitin (1);	0.058047	0.64402	N	0.000001	T	0.57607	0.2065	M	0.71920	2.185	0.80722	D	1	P;P	0.41393	0.461;0.748	B;B	0.37480	0.181;0.251	T	0.64647	-0.6358	10	0.72032	D	0.01	-4.6526	14.7826	0.69776	0.0:0.145:0.8549:0.0	.	3;3	E9PMS9;P35544	.;UBIM_HUMAN	V	3	ENSP00000435370:L3V;ENSP00000431822:L3V;ENSP00000436110:L3V;ENSP00000434440:L3V;ENSP00000279259:L3V;ENSP00000434680:L3V;ENSP00000433139:L3V;ENSP00000413848:L3V	ENSP00000279259:L3V	L	-	1	0	FAU	64645855	1.000000	0.71417	0.994000	0.49952	0.853000	0.48598	4.503000	0.60407	1.476000	0.48215	0.650000	0.86243	CTC	.	.	none		0.537	MRPL49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385293.1	NM_004927		C	64889279	G	C	64889279	1	2	16	0	1	0	0	0	0	0	0	0	5702	971	34	4		4	FAU	11	64889279	5'Flank	SNP	G	TCGA-FF-8062-01A-11D-2210-10	8132362	64889279	70117237	91	2185											
RBM14	10432	hgsc.bcm.edu	37	chr11	66392639	66392640	+	In_Frame_Ins	INS	-	-	CTA																															tactcttcccaacctgctgcINSctatgtggcacagccagcca																										TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr11:66392639_66392640insCTA	ENST00000310137.4	+	2	1431_1432	c.1292_1293insCTA	c.(1291-1296)gcctat>gcCTActat	p.432_433insY	RBM14-RBM4_ENST00000511114.1_Intron|RBM14_ENST00000409738.4_Intron|RBM4_ENST00000503028.2_Intron|RBM14-RBM4_ENST00000500635.2_Intron|RBM4_ENST00000514361.3_Intron|RBM14-RBM4_ENST00000412278.2_Intron|RBM14_ENST00000393979.3_Intron	NM_006328.3	NP_006319.1	Q96PK6	RBM14_HUMAN	RNA binding motif protein 14	432	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						CAACCTGCTGCCTATGTGGCAC	0.614																																					p.A431delinsAY		Pindel,Atlas-Indel	.											.	RBM14	59	.	0			c.1292_1293insCTA						PASS	.																																			SO:0001652	inframe_insertion	10432	exon2			.	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.1293_1295dupCTA	11.37:g.66392640_66392642dupCTA	ENSP00000311747:p.Tyr432_Tyr432dup	80	0	.		70	12	0.171	NM_006328	B0LM41|B3KMN4|D6RGD8|O75932|Q2PYN1|Q53GV1|Q68DQ9|Q96PK5	In_Frame_Ins	INS	ENST00000310137.4	37	CCDS8147.1																																																																																			.	.	none		0.614	RBM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277128.1	NM_006328		CTA	66392640	-	CTA	66392639	7	5	16	1	0	1	1	0	0	0	0	0	13130	739	26	0	1298	0	RBM14	11	66392639	In_Frame_Ins	INS	-	TCGA-FF-8062-01A-11D-2210-10	1503360	66392639	68613877	92	2186											
ODZ4	26011	hgsc.bcm.edu	37	chr11	78380664	78380664	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccagccgagtgatgcggtcGcggatgtcataccgtagtgg	7	8	15	11	5	1	1	1	1	0	0	2	3	1	2	3	3	3	1	3	3	2	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr11:78380664G>A	ENST00000278550.7	-	32	7188	c.6726C>T	c.(6724-6726)cgC>cgT	p.R2242R		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	2242					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)										TGATGCGGTCGCGGATGTCAT	0.572																																					p.R2242R		Atlas-SNP	.											ODZ4_ENST00000278550,colon,carcinoma,-1,2	.	.	2	0			c.C6726T						PASS	.						170	174	173					11																	78380664		2171	4252	6423	SO:0001819	synonymous_variant	26011	exon32			GCGGTCGCGGATG	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.6726C>T	11.37:g.78380664G>A		141	0	0		143	37	0.258741	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Silent	SNP	ENST00000278550.7	37	CCDS44688.1																																																																																			.	.	none		0.572	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			A	78380664	G	A	78380664	2	1	16	1	0	0	0	0	0	0	0	1	10846	1074	38	1		1	ODZ4	11	78380664	Silent	SNP	G	TCGA-FF-8062-01A-11D-2210-10	11988025	78380664	56625852	93	2187											
SYTL2	54843	hgsc.bcm.edu	37	chr11	85447546	85447546	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cataaaaataatatttacccTcttttgaagtctgaaataaa	18	14	3	6	0	2	2	0	2	2	0	2	2	2	2	1	0	1	0	1	0	10	8			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr11:85447546T>C	ENST00000528231.1	-	5	858	c.581A>G	c.(580-582)gAg>gGg	p.E194G	SYTL2_ENST00000316356.4_Missense_Mutation_p.E195G|SYTL2_ENST00000389960.4_Missense_Mutation_p.E194G|SYTL2_ENST00000524452.1_Missense_Mutation_p.E194G|SYTL2_ENST00000527523.1_Missense_Mutation_p.E146G	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	194					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)		ATATTTACCCTCTTTTGAAGT	0.328																																					p.E195G		Atlas-SNP	.											.	SYTL2	231	.	0			c.A584G						PASS	.						84	84	84					11																	85447546		2202	4297	6499	SO:0001583	missense	54843	exon5			TTACCCTCTTTTG	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.581A>G	11.37:g.85447546T>C	ENSP00000431701:p.Glu194Gly	73	0	0		88	4	0.0454545	NM_001162953	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	37	CCDS53688.1	.	.	.	.	.	.	.	.	.	.	T	16.53	3.147895	0.57151	.	.	ENSG00000137501	ENST00000389960;ENST00000316356;ENST00000528231;ENST00000527523;ENST00000524452	T;T;T;T;T	0.27720	1.73;1.75;1.75;1.65;1.73	5.93	5.93	0.95920	.	.	.	.	.	T	0.37489	0.1005	L	0.54323	1.7	0.80722	D	1	P;P;P;P;P	0.40834	0.73;0.546;0.611;0.546;0.554	P;B;B;B;B	0.45406	0.479;0.208;0.05;0.156;0.299	T	0.07290	-1.0780	8	.	.	.	.	14.6214	0.68588	0.0:0.0:0.0:1.0	.	146;194;194;195;52	Q9HCH5-14;Q9HCH5-6;Q9HCH5;Q9HCH5-13;Q9HCH5-15	.;.;SYTL2_HUMAN;.;.	G	194;195;194;146;194	ENSP00000374610:E194G;ENSP00000318803:E195G;ENSP00000431701:E194G;ENSP00000434010:E146G;ENSP00000435238:E194G	.	E	-	2	0	SYTL2	85125194	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.569000	0.60865	2.271000	0.75665	0.533000	0.62120	GAG	.	.	none		0.328	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927		C	85447546	T	C	85447546	3	2	16	1	0	0	0	0	1	0	0	0	15498	1551	54	3	4760	3	SYTL2	11	85447546	Missense_Mutation	SNP	T	TCGA-FF-8062-01A-11D-2210-10	7066882	85447546	49558970	94	2188											
ALKBH8	91801	hgsc.bcm.edu	37	chr11	107423860	107423860	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ataatggcttatctttatctAcattgttgttctcatagtgg	9	19	7	6	0	3	0	1	0	3	0	4	0	3	0	0	2	1	3	0	2	5	9			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr11:107423860A>T	ENST00000428149.2	-	5	720	c.569T>A	c.(568-570)gTa>gAa	p.V190E	ALKBH8_ENST00000389568.3_Missense_Mutation_p.V190E|ALKBH8_ENST00000530933.1_5'Flank|ALKBH8_ENST00000417449.2_Missense_Mutation_p.V193E|ALKBH8_ENST00000429370.1_Missense_Mutation_p.V190E	NM_138775.2	NP_620130.2	Q96BT7	ALKB8_HUMAN	alkB, alkylation repair homolog 8 (E. coli)	190					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)	p.V190A(2)		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)		ATCTTTATCTACATTGTTGTT	0.308																																					p.V190E		Atlas-SNP	.											ALKBH8_ENST00000428149,colon,carcinoma,0,2	ALKBH8	88	2	2	Substitution - Missense(2)	large_intestine(2)	c.T569A						scavenged	.						139	128	132					11																	107423860		2200	4294	6494	SO:0001583	missense	91801	exon5			TTATCTACATTGT	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.569T>A	11.37:g.107423860A>T	ENSP00000415885:p.Val190Glu	99	0	0		74	3	0.0405405	NM_138775	B1Q2M0|B4DEF6|Q8N989	Missense_Mutation	SNP	ENST00000428149.2	37	CCDS8337.2	.	.	.	.	.	.	.	.	.	.	A	25.1	4.602662	0.87157	.	.	ENSG00000137760	ENST00000428149;ENST00000429370;ENST00000389568;ENST00000417449	T;T;T;T	0.31769	1.48;1.48;1.48;1.48	5.52	5.52	0.82312	.	0.062750	0.64402	D	0.000007	T	0.56411	0.1983	M	0.76170	2.325	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.61182	-0.7114	10	0.87932	D	0	-25.9757	14.8123	0.70006	1.0:0.0:0.0:0.0	.	190	Q96BT7	ALKB8_HUMAN	E	190;190;190;193	ENSP00000415885:V190E;ENSP00000391225:V190E;ENSP00000374219:V190E;ENSP00000397673:V193E	ENSP00000260318:V190E	V	-	2	0	ALKBH8	106929070	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	8.572000	0.90756	2.095000	0.63458	0.482000	0.46254	GTA	.	.	none		0.308	ALKBH8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347071.2	NM_138775		T	107423860	A	T	107423860	3	4	16	1	0	0	0	0	1	0	0	0	533	391	14	5	1457	5	ALKBH8	11	107423860	Missense_Mutation	SNP	A	TCGA-FF-8062-01A-11D-2210-10	21976314	107423860	27582656	95	2189											
GRIK4	2900	hgsc.bcm.edu	37	chr11	120831697	120831697	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ccgtgcagcgcatggatgtgCccattgagtcagtggatgac	8	9	14	10	2	1	2	1	2	0	0	1	4	1	4	2	2	3	2	2	2	0	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr11:120831697C>T	ENST00000527524.2	+	17	2241	c.1954C>T	c.(1954-1956)Ccc>Tcc	p.P652S	GRIK4_ENST00000438375.2_Missense_Mutation_p.P652S	NM_001282470.1	NP_001269399.1	Q16099	GRIK4_HUMAN	glutamate receptor, ionotropic, kainate 4	652					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)		CATGGATGTGCCCATTGAGTC	0.532																																					p.P652S		Atlas-SNP	.											GRIK4,NS,carcinoma,-1,1	GRIK4	149	1	0			c.C1954T						PASS	.						140	111	121					11																	120831697		2203	4299	6502	SO:0001583	missense	2900	exon15			GATGTGCCCATTG	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.1954C>T	11.37:g.120831697C>T	ENSP00000435648:p.Pro652Ser	130	0	0		130	31	0.238462	NM_014619	A8K9L1	Missense_Mutation	SNP	ENST00000527524.2	37	CCDS8433.1	.	.	.	.	.	.	.	.	.	.	C	34	5.386043	0.95967	.	.	ENSG00000149403	ENST00000527524;ENST00000438375	T;T	0.11495	2.77;2.77	5.51	5.51	0.81932	Ionotropic glutamate receptor (2);	0.000000	0.85682	D	0.000000	T	0.35278	0.0926	M	0.70595	2.14	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.03240	-1.1057	10	0.66056	D	0.02	.	19.0461	0.93020	0.0:1.0:0.0:0.0	.	652;652	A6H8K8;Q16099	.;GRIK4_HUMAN	S	652	ENSP00000435648:P652S;ENSP00000404063:P652S	ENSP00000404063:P652S	P	+	1	0	GRIK4	120336907	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.593000	0.87608	0.655000	0.94253	CCC	.	.	none		0.532	GRIK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109760.4	NM_014619		T	120831697	C	T	120831697	3	4	16	1	0	0	0	0	1	0	0	0	6785	739	26	2	2012	2	GRIK4	11	120831697	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	13407837	120831697	14174819	96	2190											
LST-3TM12	338821	hgsc.bcm.edu	37	chr12	21201693	21201693	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttggcatgttttcaggaggaTatatcattaaaaaattcaaa	16	14	7	4	0	3	0	3	0	0	0	3	2	3	2	0	3	0	2	0	3	6	7	rs370821380		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr12:21201693T>A	ENST00000421593.2	+	8	1042	c.1042T>A	c.(1042-1044)Tat>Aat	p.Y348N	SLCO1B7_ENST00000554957.1_Missense_Mutation_p.Y395N|LST3_ENST00000540229.1_Intron|SLCO1B3_ENST00000553473.1_Intron|LST3_ENST00000381541.3_Missense_Mutation_p.Y395N	NM_001009562.4	NP_001009562.3	G3V0H7	SO1B7_HUMAN	solute carrier organic anion transporter family, member 1B7 (non-functional)	348						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						TTCAGGAGGATATATCATTAA	0.353																																					p.Y348N		Atlas-SNP	.											.	SLCO1B7	85	.	0			c.T1042A						PASS	.						48	48	48					12																	21201693		2014	4205	6219	SO:0001583	missense	338821	exon8			GGAGGATATATCA	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	ENST00000421593.2:c.1042T>A	12.37:g.21201693T>A	ENSP00000394168:p.Tyr348Asn	103	0	0		176	46	0.261364	NM_001009562	Q71QF0	Missense_Mutation	SNP	ENST00000421593.2	37	CCDS44843.1	.	.	.	.	.	.	.	.	.	.	.	13.38	2.220808	0.39201	.	.	ENSG00000257046;ENSG00000205754;ENSG00000205754	ENST00000381541;ENST00000554957;ENST00000421593	T;T;T	0.81415	-1.41;-1.41;-1.49	3.45	3.45	0.39498	.	0.479354	0.21186	N	0.078723	D	0.85898	0.5804	M	0.83012	2.62	0.25795	N	0.984577	D;P	0.54397	0.966;0.942	P;P	0.58873	0.847;0.847	T	0.77723	-0.2481	10	0.72032	D	0.01	.	5.4437	0.16523	0.0:0.1313:0.0:0.8687	.	348;395	G3V0H7;F5H094	.;.	N	395;395;348	ENSP00000370952:Y395N;ENSP00000452013:Y395N;ENSP00000394168:Y348N	ENSP00000370952:Y395N	Y	+	1	0	SLCO1B7;RP11-545J16.1	21092960	0.369000	0.25039	0.990000	0.47175	0.727000	0.41649	0.316000	0.19469	1.554000	0.49487	0.416000	0.27883	TAT	.	.	alt		0.353	SLCO1B7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402066.1	NM_001009562		A	21201693	T	A	21201693	3	1	16	1	0	0	0	0	1	0	0	0	9075	1406	49	5	1072	5	LST-3TM12	12	21201693	Missense_Mutation	SNP	T	TCGA-FF-8062-01A-11D-2210-10		21201693	112650202	97	2191											
SLC16A7	9194	hgsc.bcm.edu	37	chr12	60173423	60173423	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	taacgtcaaagtttcaaatgCacagagtgtaacctcagaaa	17	9	7	8	1	3	2	3	0	0	2	3	2	3	2	1	0	3	3	1	0	5	3			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr12:60173423C>T	ENST00000261187.4	+	5	1564	c.1400C>T	c.(1399-1401)gCa>gTa	p.A467V	SLC16A7_ENST00000543448.1_Missense_Mutation_p.A368V|SLC16A7_ENST00000552024.1_Missense_Mutation_p.A467V|SLC16A7_ENST00000547379.1_Missense_Mutation_p.A467V|SLC16A7_ENST00000552432.1_Missense_Mutation_p.A467V	NM_004731.4	NP_004722.2	O60669	MOT2_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 7	467					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)	GTTTCAAATGCACAGAGTGTA	0.358																																					p.A467V		Atlas-SNP	.											.	SLC16A7	82	.	0			c.C1400T						PASS	.						75	72	73					12																	60173423		2203	4300	6503	SO:0001583	missense	9194	exon6			CAAATGCACAGAG	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.1400C>T	12.37:g.60173423C>T	ENSP00000261187:p.Ala467Val	89	0	0		97	4	0.0412371	NM_001270622	Q8NEM3|Q9UPB3	Missense_Mutation	SNP	ENST00000261187.4	37	CCDS8961.1	.	.	.	.	.	.	.	.	.	.	C	9.231	1.035740	0.19590	.	.	ENSG00000118596	ENST00000552432;ENST00000547379;ENST00000552024;ENST00000261187;ENST00000543448	T;T;T;T;T	0.17691	2.4;2.4;2.4;2.4;2.26	5.05	1.63	0.23807	.	4.485940	0.00687	N	0.000717	T	0.09774	0.0240	N	0.11560	0.145	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.23119	-1.0197	9	.	.	.	.	4.8693	0.13624	0.0:0.5139:0.1597:0.3264	.	467	O60669	MOT2_HUMAN	V	467;467;467;467;368	ENSP00000449547:A467V;ENSP00000448071:A467V;ENSP00000448742:A467V;ENSP00000261187:A467V;ENSP00000443731:A368V	.	A	+	2	0	SLC16A7	58459690	0.000000	0.05858	0.006000	0.13384	0.006000	0.05464	0.432000	0.21461	0.622000	0.30249	0.467000	0.42956	GCA	.	.	none		0.358	SLC16A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406587.1	NM_004731		T	60173423	C	T	60173423	3	4	16	1	0	0	0	0	1	0	0	0	14428	710	25	2	1414	2	SLC16A7	12	60173423	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	38971730	60173423	73678472	98	2192											
ZFC3H1	196441	hgsc.bcm.edu	37	chr12	72017233	72017233	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcagtgttaacaattcttgAaggattatcattagatggat	13	16	8	4	0	3	2	2	1	1	1	3	4	3	4	0	2	1	1	0	2	5	6			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr12:72017233A>G	ENST00000378743.3	-	24	5009	c.4651T>C	c.(4651-4653)Tca>Cca	p.S1551P		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	1551					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						ACAATTCTTGAAGGATTATCA	0.343																																					p.S1551P		Atlas-SNP	.											.	ZFC3H1	172	.	0			c.T4651C						PASS	.						103	93	96					12																	72017233		1834	4087	5921	SO:0001583	missense	196441	exon24			TTCTTGAAGGATT	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.4651T>C	12.37:g.72017233A>G	ENSP00000368017:p.Ser1551Pro	74	0	0		90	4	0.0444444	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Missense_Mutation	SNP	ENST00000378743.3	37	CCDS41813.1	.	.	.	.	.	.	.	.	.	.	A	18.44	3.623719	0.66901	.	.	ENSG00000133858	ENST00000378743	T	0.34072	1.38	4.98	4.98	0.66077	.	0.170588	0.39985	N	0.001204	T	0.48409	0.1498	L	0.34521	1.04	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.45116	-0.9283	10	0.44086	T	0.13	.	14.6713	0.68945	1.0:0.0:0.0:0.0	.	1551	O60293	ZC3H1_HUMAN	P	1551	ENSP00000368017:S1551P	ENSP00000368017:S1551P	S	-	1	0	ZFC3H1	70303500	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	4.627000	0.61276	1.868000	0.54150	0.460000	0.39030	TCA	.	.	none		0.343	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982		G	72017233	A	G	72017233	3	3	16	1	0	0	0	0	1	0	0	0	17648	246	9	3	1366	3	ZFC3H1	12	72017233	Missense_Mutation	SNP	A	TCGA-FF-8062-01A-11D-2210-10	11843810	72017233	61834662	99	2193											
C12orf51	283450	hgsc.bcm.edu	37	chr12	112622063	112622063	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agggaagtgactgtgtacatGgagcccatgtccgacaccga	11	7	13	10	2	0	1	0	1	0	0	1	5	1	3	3	2	2	1	3	2	2	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr12:112622063G>A	ENST00000430131.2	-	60	10586	c.9441C>T	c.(9439-9441)tcC>tcT	p.S3147S	HECTD4_ENST00000550722.1_Silent_p.S3423S|HECTD4_ENST00000377560.5_Silent_p.S3397S			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3147					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)										CTGTGTACATGGAGCCCATGT	0.637																																					p.S3435S		Atlas-SNP	.											.	.	.	.	0			c.C10305T						PASS	.						74	85	82					12																	112622063		1990	4157	6147	SO:0001819	synonymous_variant	283450	exon61			GTACATGGAGCCC	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.9441C>T	12.37:g.112622063G>A		130	0	0		82	18	0.219512	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	37																																																																																				.	.	none		0.637	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		A	112622063	G	A	112622063	2	1	16	1	0	0	0	0	0	0	0	1	1698	1335	47	2		2	C12orf51	12	112622063	Silent	SNP	G	TCGA-FF-8062-01A-11D-2210-10	40604830	112622063	21229832	100	2194											
MTUS2	23281	hgsc.bcm.edu	37	chr13	30054459	30054459	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgcgcctgcaggaggagcaCggtgaccagctgctgagcat	8	5	16	12	3	0	2	0	2	0	0	0	4	0	4	2	3	5	5	2	3	0	0			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr13:30054459C>T	ENST00000380808.2	+	3	510	c.294C>T	c.(292-294)caC>caT	p.H98H	MTUS2_ENST00000431530.3_Silent_p.H1129H|MTUS2-AS1_ENST00000587588.1_RNA|MTUS2_ENST00000542829.1_Silent_p.H8H|MTUS2-AS1_ENST00000323380.5_RNA	NM_015233.5	NP_056048.1	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	1119						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						AGGAGGAGCACGGTGACCAGC	0.667																																					p.H1129H		Atlas-SNP	.											.	MTUS2	279	.	0			c.C3387T						PASS	.						11	15	14					13																	30054459		2064	4188	6252	SO:0001819	synonymous_variant	23281	exon8			GGAGCACGGTGAC	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.294C>T	13.37:g.30054459C>T		169	0	0		168	26	0.154762	NM_001033602	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Silent	SNP	ENST00000380808.2	37	CCDS41874.1																																																																																			.	.	none		0.667	MTUS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044335.2	XM_166270		T	30054459	C	T	30054459	2	4	16	1	0	0	0	0	0	0	0	1	9975	535	19	1		1	MTUS2	13	30054459	Silent	SNP	C	TCGA-FF-8062-01A-11D-2210-10		30054459	85115419	101	2195											
NBEA	26960	hgsc.bcm.edu	37	chr13	35632915	35632915	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgcaaatagggtattctgtgGtcaacttggtgccgtgtatg	8	14	13	6	1	2	0	1	0	1	0	2	0	2	0	1	3	3	3	1	3	5	5			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr13:35632915G>A	ENST00000400445.3	+	8	1688	c.1154G>A	c.(1153-1155)gGt>gAt	p.G385D	NBEA_ENST00000540320.1_Missense_Mutation_p.G385D|NBEA_ENST00000379939.2_Missense_Mutation_p.G385D|NBEA_ENST00000310336.4_Missense_Mutation_p.G385D	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	385					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)		GTATTCTGTGGTCAACTTGGT	0.358																																					p.G385D		Atlas-SNP	.											.	NBEA	340	.	0			c.G1154A						PASS	.						34	31	32					13																	35632915		1799	4063	5862	SO:0001583	missense	26960	exon8			TCTGTGGTCAACT	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.1154G>A	13.37:g.35632915G>A	ENSP00000383295:p.Gly385Asp	344	0	0		395	68	0.172152	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	37	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.004746	0.93287	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	D;D;D;D	0.86297	-2.1;-2.1;-2.1;-2.1	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	D	0.94608	0.8262	M	0.86420	2.815	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94886	0.8043	10	0.72032	D	0.01	.	19.6016	0.95566	0.0:0.0:1.0:0.0	.	385	Q5T321	.	D	385	ENSP00000440951:G385D;ENSP00000383295:G385D;ENSP00000369271:G385D;ENSP00000308534:G385D	ENSP00000308534:G385D	G	+	2	0	NBEA	34530915	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.813000	0.99286	2.718000	0.92993	0.650000	0.86243	GGT	.	.	none		0.358	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678		A	35632915	G	A	35632915	3	1	16	1	0	0	0	0	1	0	0	0	10196	1261	44	2	1184	2	NBEA	13	35632915	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	5578456	35632915	79536963	102	2196											
PCDH9	5101	hgsc.bcm.edu	37	chr13	66879059	66879059	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggggtgttgatatggacccaAgccaggaggcatccagcaat	11	7	14	9	0	0	1	0	1	0	0	1	3	1	3	3	5	2	3	3	5	3	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr13:66879059A>C	ENST00000377865.2	-	4	3576	c.3442T>G	c.(3442-3444)Ttg>Gtg	p.L1148V	PCDH9_ENST00000328454.5_Missense_Mutation_p.L1114V|PCDH9-AS1_ENST00000430861.1_RNA|PCDH9_ENST00000456367.1_Missense_Mutation_p.L1114V|PCDH9_ENST00000544246.1_Missense_Mutation_p.L1148V			Q9HC56	PCDH9_HUMAN	protocadherin 9	1148					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)		TATGGACCCAAGCCAGGAGGC	0.517																																					p.L1148V		Atlas-SNP	.											.	PCDH9	252	.	0			c.T3442G						PASS	.						121	105	111					13																	66879059		2203	4300	6503	SO:0001583	missense	5101	exon5			GACCCAAGCCAGG	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.3442T>G	13.37:g.66879059A>C	ENSP00000367096:p.Leu1148Val	94	0	0		112	20	0.178571	NM_203487	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Missense_Mutation	SNP	ENST00000377865.2	37	CCDS9444.1	.	.	.	.	.	.	.	.	.	.	A	15.23	2.771484	0.49680	.	.	ENSG00000184226	ENST00000544246;ENST00000377865;ENST00000456367;ENST00000328454	T;T;T;T	0.54675	0.64;0.64;0.56;0.56	6.16	5.03	0.67393	.	0.000000	0.38217	N	0.001780	T	0.43122	0.1233	L	0.39898	1.24	0.30218	N	0.797123	P;P;P	0.46859	0.85;0.885;0.85	B;B;B	0.43301	0.301;0.415;0.301	T	0.51100	-0.8748	10	0.45353	T	0.12	.	7.8316	0.29347	0.7928:0.0:0.2072:0.0	.	1106;1114;1148	B7ZM79;Q9HC56-2;Q9HC56	.;.;PCDH9_HUMAN	V	1148;1148;1114;1114	ENSP00000442186:L1148V;ENSP00000367096:L1148V;ENSP00000401699:L1114V;ENSP00000332060:L1114V	ENSP00000332060:L1114V	L	-	1	2	PCDH9	65777060	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.940000	0.40223	2.367000	0.80283	0.528000	0.53228	TTG	.	.	none		0.517	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487		C	66879059	A	C	66879059	3	2	16	1	0	0	0	0	1	0	0	0	11527	69	3	5	275	5	PCDH9	13	66879059	Missense_Mutation	SNP	A	TCGA-FF-8062-01A-11D-2210-10	31246144	66879059	48290819	103	2197											
LMO7	4008	hgsc.bcm.edu	37	chr13	76381767	76381767	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctatagaagagatgacctcGagatggcagccctggatcct	11	8	12	10	1	0	4	0	1	0	3	2	7	1	5	3	2	1	2	3	2	3	2	rs534047308		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr13:76381767G>A	ENST00000321797.8	+	8	1370	c.649G>A	c.(649-651)Gag>Aag	p.E217K	RP11-29G8.3_ENST00000563635.1_RNA|LMO7_ENST00000357063.3_Missense_Mutation_p.E502K|LMO7_ENST00000377534.3_Missense_Mutation_p.E502K|LMO7_ENST00000526202.1_Intron|LMO7_ENST00000341547.4_Intron|LMO7_ENST00000465261.2_Missense_Mutation_p.E217K			Q8WWI1	LMO7_HUMAN	LIM domain 7	502					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)		AGATGACCTCGAGATGGCAGC	0.453													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18167	0.0		0.0	False		,,,				2504	0.0				p.E217K		Atlas-SNP	.											.	LMO7	334	.	0			c.G649A						PASS	.						93	86	88					13																	76381767		1568	3582	5150	SO:0001583	missense	4008	exon7			GACCTCGAGATGG	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.649G>A	13.37:g.76381767G>A	ENSP00000317802:p.Glu217Lys	67	0	0		92	4	0.0434783	NM_015842	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000321797.8	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.44|13.44	2.238724|2.238724	0.39598|0.39598	.|.	.|.	ENSG00000136153|ENSG00000136153	ENST00000357063;ENST00000377534;ENST00000321797;ENST00000465261;ENST00000526528|ENST00000447038	T;T;T;T|.	0.54279|.	0.58;0.58;0.58;0.58|.	5.83|5.83	4.11|4.11	0.48088|0.48088	.|.	0.288711|.	0.37304|.	N|.	0.002146|.	T|T	0.54515|0.54515	0.1863|0.1863	M|M	0.64997|0.64997	1.995|1.995	0.19300|0.19300	N|N	0.999977|0.999977	B;B|.	0.23735|.	0.09;0.022|.	B;B|.	0.11329|.	0.006;0.006|.	T|T	0.45041|0.45041	-0.9288|-0.9288	10|5	0.66056|.	D|.	0.02|.	-4.5653|-4.5653	12.5045|12.5045	0.55973|0.55973	0.1331:0.0:0.8669:0.0|0.1331:0.0:0.8669:0.0	.|.	502;217|.	Q8WWI1;E9PLH4|.	LMO7_HUMAN;.|.	K|Q	502;502;217;217;123|125	ENSP00000349571:E502K;ENSP00000366757:E502K;ENSP00000317802:E217K;ENSP00000433352:E217K|.	ENSP00000317802:E217K|.	E|R	+|+	1|2	0|0	LMO7|LMO7	75279768|75279768	1.000000|1.000000	0.71417|0.71417	0.004000|0.004000	0.12327|0.12327	0.032000|0.032000	0.12392|0.12392	4.278000|4.278000	0.58946|0.58946	0.814000|0.814000	0.34374|0.34374	0.655000|0.655000	0.94253|0.94253	GAG|CGA	.	.	none		0.453	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358		A	76381767	G	A	76381767	3	1	16	1	0	0	0	0	1	0	0	0	8864	1059	37	1	1546	1	LMO7	13	76381767	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	9502708	76381767	38788111	104	2198											
LMO7	4008	hgsc.bcm.edu	37	chr13	76415865	76415865	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagggtccaagtcttcagaCagagaaggaacccgagcagg	14	4	14	9	1	2	2	1	0	1	2	3	6	3	3	2	3	2	1	2	3	4	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr13:76415865C>A	ENST00000321797.8	+	22	3799	c.3078C>A	c.(3076-3078)gaC>gaA	p.D1026E	LMO7_ENST00000357063.3_Missense_Mutation_p.D1311E|LMO7_ENST00000377534.3_Missense_Mutation_p.D1311E|LMO7_ENST00000526202.1_Missense_Mutation_p.D903E|LMO7_ENST00000341547.4_Missense_Mutation_p.D977E|LMO7_ENST00000465261.2_Missense_Mutation_p.D1026E			Q8WWI1	LMO7_HUMAN	LIM domain 7	1311					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)		AGTCTTCAGACAGAGAAGGAA	0.527																																					p.D1026E		Atlas-SNP	.											.	LMO7	334	.	0			c.C3078A						PASS	.						96	97	96					13																	76415865		2203	4300	6503	SO:0001583	missense	4008	exon21			TTCAGACAGAGAA	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.3078C>A	13.37:g.76415865C>A	ENSP00000317802:p.Asp1026Glu	71	0	0		93	30	0.322581	NM_015842	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000321797.8	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.74|14.74	2.624220|2.624220	0.46840|0.46840	.|.	.|.	ENSG00000136153|ENSG00000136153	ENST00000341547;ENST00000357063;ENST00000377534;ENST00000377499;ENST00000321797;ENST00000526202;ENST00000465261|ENST00000447038;ENST00000525914	T;T;T;T;T;T;T|.	0.39997|.	1.65;1.63;1.64;1.06;1.06;1.07;1.05|.	5.95|5.95	4.09|4.09	0.47781|0.47781	.|.	0.607412|.	0.18332|.	N|.	0.144459|.	T|T	0.43389|0.43389	0.1245|0.1245	L|L	0.45581|0.45581	1.43|1.43	0.31577|0.31577	N|N	0.655654|0.655654	B;B;B;B;B|.	0.31318|.	0.06;0.319;0.012;0.06;0.119|.	B;B;B;B;B|.	0.26416|.	0.018;0.069;0.007;0.031;0.052|.	T|T	0.47837|0.47837	-0.9086|-0.9086	10|5	0.14656|.	T|.	0.56|.	-25.6026|-25.6026	4.7211|4.7211	0.12918|0.12918	0.1534:0.6166:0.1482:0.0818|0.1534:0.6166:0.1482:0.0818	.|.	903;977;1311;1026;1259|.	E9PMS6;Q8WWI1-3;Q8WWI1;E9PLH4;F8J2B5|.	.;.;LMO7_HUMAN;.;.|.	E|K	977;1311;1311;925;1026;903;1026|935;195	ENSP00000342112:D977E;ENSP00000349571:D1311E;ENSP00000366757:D1311E;ENSP00000366719:D925E;ENSP00000317802:D1026E;ENSP00000431129:D903E;ENSP00000433352:D1026E|.	ENSP00000317802:D1026E|.	D|Q	+|+	3|1	2|0	LMO7|LMO7	75313866|75313866	0.914000|0.914000	0.31030|0.31030	0.999000|0.999000	0.59377|0.59377	0.914000|0.914000	0.54420|0.54420	0.510000|0.510000	0.22723|0.22723	2.825000|2.825000	0.97269|0.97269	0.655000|0.655000	0.94253|0.94253	GAC|CAG	.	.	none		0.527	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358		A	76415865	C	A	76415865	3	1	16	1	0	0	0	0	1	0	0	0	8864	477	17	4	4031	4	LMO7	13	76415865	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	34098	76415865	38754013	105	2199											
FAM70B	348013	hgsc.bcm.edu	37	chr13	114514733	114514733	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gcagccgcttcccagttgcgCcctcctctgccctggcttcg	2	10	10	19	3	1	0	0	0	1	0	4	0	3	0	5	1	3	4	5	1	0	3			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr13:114514733C>G	ENST00000375353.3	+	9	865	c.838C>G	c.(838-840)Ccc>Gcc	p.P280A	TMEM255B_ENST00000467169.1_3'UTR	NM_182614.2	NP_872420.1	Q8WV15	T255B_HUMAN	transmembrane protein 255B	280	Pro-rich.					integral component of membrane (GO:0016021)											CCCAGTTGCGCCCTCCTCTGC	0.647																																					p.P280A		Atlas-SNP	.											.	.	.	.	0			c.C838G						PASS	.						47	53	51					13																	114514733		2203	4300	6503	SO:0001583	missense	348013	exon9			GTTGCGCCCTCCT	BC018995	CCDS45071.1	13q34	2012-11-30	2012-11-30	2012-11-30	ENSG00000184497	ENSG00000184497			28297	protein-coding gene	gene with protein product			"family with sequence similarity 70, member B"	FAM70B		12477932	Standard	NM_182614		Approved	MGC20579	uc001vuh.3	Q8WV15	OTTHUMG00000017398	ENST00000375353.3:c.838C>G	13.37:g.114514733C>G	ENSP00000364502:p.Pro280Ala	145	0	0		110	15	0.136364	NM_182614		Missense_Mutation	SNP	ENST00000375353.3	37	CCDS45071.1	.	.	.	.	.	.	.	.	.	.	C	4.207	0.037268	0.08148	.	.	ENSG00000184497	ENST00000375353	T	0.40225	1.04	4.35	-5.0	0.03001	.	.	.	.	.	T	0.28400	0.0702	L	0.50333	1.59	0.09310	N	1	B	0.09022	0.002	B	0.11329	0.006	T	0.30268	-0.9984	9	0.46703	T	0.11	-1.715	1.5609	0.02594	0.1161:0.2033:0.1673:0.5134	.	280	Q8WV15	FA70B_HUMAN	A	280	ENSP00000364502:P280A	ENSP00000364502:P280A	P	+	1	0	FAM70B	113599210	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.015000	0.12634	-1.335000	0.02241	0.484000	0.47621	CCC	.	.	none		0.647	TMEM255B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045953.4	NM_182614		G	114514733	C	G	114514733	3	3	16	1	0	0	0	0	1	0	0	0	5614	739	26	4	872	4	FAM70B	13	114514733	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	38098868	114514733	655145	106	2200											
CHD8	57680	hgsc.bcm.edu	37	chr14	21870201	21870201	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctggtcaatgtcctcttcaCaaaacttggagccttcatca	10	13	6	12	0	6	0	4	0	2	0	7	1	7	1	2	2	2	0	2	2	3	3			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr14:21870201C>T	ENST00000557364.1	-	20	4240	c.3977G>A	c.(3976-3978)tGt>tAt	p.C1326Y	CHD8_ENST00000430710.3_Missense_Mutation_p.C1047Y|CHD8_ENST00000399982.2_Missense_Mutation_p.C1326Y|CHD8_ENST00000555962.1_5'UTR			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1326					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)		GTCCTCTTCACAAAACTTGGA	0.403																																					p.C1326Y		Atlas-SNP	.											.	CHD8	339	.	0			c.G3977A						PASS	.						163	157	159					14																	21870201		2037	4224	6261	SO:0001583	missense	57680	exon19			TCTTCACAAAACT	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.3977G>A	14.37:g.21870201C>T	ENSP00000451601:p.Cys1326Tyr	142	0	0		197	31	0.15736	NM_001170629	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Missense_Mutation	SNP	ENST00000557364.1	37	CCDS53885.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.109408	0.77096	.	.	ENSG00000100888	ENST00000430710;ENST00000399982;ENST00000262707;ENST00000557364	D;D;D	0.85702	-2.02;-2.02;-2.02	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.91835	0.7416	M	0.69358	2.11	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.89666	0.3880	10	0.38643	T	0.18	-18.0066	19.6509	0.95805	0.0:1.0:0.0:0.0	.	1326;1047	Q9HCK8;Q9HCK8-2	CHD8_HUMAN;.	Y	1047;1326;1046;1326	ENSP00000406288:C1047Y;ENSP00000382863:C1326Y;ENSP00000451601:C1326Y	ENSP00000262707:C1046Y	C	-	2	0	CHD8	20940041	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.776000	0.85560	2.941000	0.99782	0.655000	0.94253	TGT	.	.	none		0.403	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920		T	21870201	C	T	21870201	3	4	16	1	0	0	0	0	1	0	0	0	3333	478	17	2	3844	2	CHD8	14	21870201	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10		21870201	85479339	107	2201											
TTC9	23508	hgsc.bcm.edu	37	chr14	71109098	71109098	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcaaataccaccgggcgttGctggagctgaaggggctgct	8	7	16	10	2	0	1	0	1	0	0	0	2	0	2	2	5	4	6	2	5	3	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr14:71109098G>A	ENST00000256367.2	+	1	595	c.252G>A	c.(250-252)ttG>ttA	p.L84L	CTD-2540L5.6_ENST00000500016.1_lincRNA|CTD-2540L5.5_ENST00000553982.1_lincRNA	NM_015351.1	NP_056166.1	Q92623	TTC9A_HUMAN	tetratricopeptide repeat domain 9	84										skin(1)	1				all cancers(60;0.00545)|BRCA - Breast invasive adenocarcinoma(234;0.00747)|OV - Ovarian serous cystadenocarcinoma(108;0.0538)		ACCGGGCGTTGCTGGAGCTGA	0.682																																					p.L84L		Atlas-SNP	.											.	TTC9	11	.	0			c.G252A						PASS	.						10	12	11					14																	71109098		1871	4083	5954	SO:0001819	synonymous_variant	23508	exon1			GGCGTTGCTGGAG	D86980	CCDS45132.1	14q24.2	2014-08-12			ENSG00000133985			"Tetratricopeptide (TTC) repeat domain containing"	20267	protein-coding gene	gene with protein product		610488					Standard	NM_015351		Approved	KIAA0227, TTC9A	uc001xmi.2	Q92623	OTTHUMG00000172133	ENST00000256367.2:c.252G>A	14.37:g.71109098G>A		79	0	0		64	6	0.09375	NM_015351	Q86WT2	Silent	SNP	ENST00000256367.2	37	CCDS45132.1																																																																																			.	.	none		0.682	TTC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417024.1	XM_027236		A	71109098	G	A	71109098	2	1	16	1	0	0	0	0	0	0	0	1	16730	1310	46	2		2	TTC9	14	71109098	Silent	SNP	G	TCGA-FF-8062-01A-11D-2210-10	49238897	71109098	36240442	108	2202											
KCNK10	54207	hgsc.bcm.edu	37	chr14	88652049	88652049	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctcctcctctttcttctcctCgtccagggagtaattccgga	5	14	7	15	2	3	0	0	0	3	0	9	2	7	2	5	2	0	1	5	2	1	4			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr14:88652049C>T	ENST00000340700.5	-	7	1898	c.1447G>A	c.(1447-1449)Gag>Aag	p.E483K	KCNK10_ENST00000319231.5_Missense_Mutation_p.E488K|KCNK10_ENST00000312350.5_Missense_Mutation_p.E488K	NM_021161.4	NP_066984.1	P57789	KCNKA_HUMAN	potassium channel, subfamily K, member 10	483					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						TTCTTCTCCTCGTCCAGGGAG	0.502																																					p.E488K		Atlas-SNP	.											.	KCNK10	273	.	0			c.G1462A						PASS	.						149	148	148					14																	88652049		2203	4300	6503	SO:0001583	missense	54207	exon7			TCTCCTCGTCCAG	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.1447G>A	14.37:g.88652049C>T	ENSP00000343104:p.Glu483Lys	252	0	0		275	68	0.247273	NM_138318	B2R8T4|B2RCT3|B5TJL4|Q6B014|Q8TDK7|Q8TDK8|Q9HB59	Missense_Mutation	SNP	ENST00000340700.5	37	CCDS9880.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.944729	0.73672	.	.	ENSG00000100433	ENST00000340700;ENST00000312350;ENST00000319231	D;D;D	0.94232	-3.36;-3.37;-3.38	5.5	5.5	0.81552	.	0.667612	0.15589	N	0.254476	D	0.90930	0.7149	L	0.46157	1.445	0.51767	D	0.999937	B;B;B	0.29612	0.251;0.251;0.251	B;B;B	0.15052	0.012;0.008;0.012	D	0.88801	0.3285	10	0.72032	D	0.01	.	18.3984	0.90507	0.0:1.0:0.0:0.0	.	483;488;488	P57789;B2R8T4;Q6B014	KCNKA_HUMAN;.;.	K	483;488;488	ENSP00000343104:E483K;ENSP00000310568:E488K;ENSP00000312811:E488K	ENSP00000310568:E488K	E	-	1	0	KCNK10	87721802	1.000000	0.71417	0.929000	0.37066	0.786000	0.44442	7.294000	0.78760	2.599000	0.87857	0.655000	0.94253	GAG	.	.	none		0.502	KCNK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410167.1	NM_021161		T	88652049	C	T	88652049	3	4	16	1	0	0	0	0	1	0	0	0	8068	893	31	1	173	1	KCNK10	14	88652049	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	17542951	88652049	18697491	109	2203											
BTBD7	55727	hgsc.bcm.edu	37	chr14	93709220	93709221	+	Frame_Shift_Ins	INS	-	-	T																															tggattttctctggtgtctgINSttttttgctctagtgtgtgt																										TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr14:93709220_93709221insT	ENST00000334746.5	-	11	3104_3105	c.2797_2798insA	c.(2797-2799)acafs	p.T933fs	BTBD7_ENST00000554565.1_Frame_Shift_Ins_p.T582fs|BTBD7_ENST00000393170.2_Frame_Shift_Ins_p.T507fs	NM_001002860.2	NP_001002860.2	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7	933					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)		TCTGGTGTCTGTTTTTTGCTCT	0.485																																					p.T933fs		Pindel,Atlas-Indel	.											.	BTBD7	112	.	0			c.2798_2799insA						PASS	.																																			SO:0001589	frameshift_variant	55727	exon11			.	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.2798dupA	14.37:g.93709226_93709226dupT	ENSP00000335615:p.Thr933fs	279	0	.		367	68	0.185	NM_001002860	A8K5V7|Q69Z05|Q7Z308|Q86TS0|Q9HAA4|Q9NVM0	Frame_Shift_Ins	INS	ENST00000334746.5	37	CCDS32146.1																																																																																			.	.	none		0.485	BTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412701.1	NM_001002860		T	93709221	-	T	93709220	7	5	16	1	0	1	1	0	0	0	0	0	1548	1377	48	0	604	0	BTBD7	14	93709220	Frame_Shift_Ins	INS	-	TCGA-FF-8062-01A-11D-2210-10	5057171	93709220	13640320	110	2204											
BCL11B	64919	hgsc.bcm.edu	37	chr14	99641016	99641016	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aaggggtccttcatgaagtgCcgcgacgccgcgtagcccac	8	6	13	14	5	1	1	1	1	0	0	2	2	2	1	4	2	2	1	4	2	3	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr14:99641016C>G	ENST00000357195.3	-	4	2166	c.2157G>C	c.(2155-2157)cgG>cgC	p.R719R	BCL11B_ENST00000345514.2_Silent_p.R648R|BCL11B_ENST00000443726.2_Silent_p.R525R	NM_001282237.1|NM_138576.2	NP_001269166.1|NP_612808.1	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B (zinc finger protein)	719					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)		TCATGAAGTGCCGCGACGCCG	0.667			T	TLX3	T-ALL																																p.R719R		Atlas-SNP	.		Dom	yes		14	14q32.1	64919	B-cell CLL/lymphoma 11B  (CTIP2)		L	BCL11B,NS,carcinoma,-2,1	BCL11B	108	1	0			c.G2157C						PASS	.						23	20	21					14																	99641016		2198	4295	6493	SO:0001819	synonymous_variant	64919	exon4			GAAGTGCCGCGAC	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.2157G>C	14.37:g.99641016C>G		61	0	0		28	7	0.25	NM_138576	Q9H162	Silent	SNP	ENST00000357195.3	37	CCDS9950.1																																																																																			.	.	none		0.667	BCL11B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000072332.2	NM_138576		G	99641016	C	G	99641016	2	3	16	1	0	0	0	0	0	0	0	1	1364	726	26	4		4	BCL11B	14	99641016	Silent	SNP	C	TCGA-FF-8062-01A-11D-2210-10	5931796	99641016	7708524	111	2205											
B2M	567	hgsc.bcm.edu	37	chr15	45003764	45003764	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatgtctcgctccgtggcctTagctgtgctcgcgctactct	3	13	11	14	4	2	0	0	0	2	0	5	1	3	0	2	1	3	4	2	1	2	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr15:45003764T>C	ENST00000558401.1	+	1	90	c.20T>C	c.(19-21)tTa>tCa	p.L7S	PATL2_ENST00000558573.1_5'Flank|B2M_ENST00000559916.1_Missense_Mutation_p.L7S|B2M_ENST00000544417.1_Missense_Mutation_p.L7S	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	7					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 exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|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 T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|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)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)	p.L7S(1)		breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		TCCGTGGCCTTAGCTGTGCTC	0.607																																					p.L7S		Atlas-SNP	.											B2M,NS,lymphoid_neoplasm,0,1	B2M	99	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.T20C						scavenged	.						131	95	107					15																	45003764		2198	4298	6496	SO:0001583	missense	567	exon1			TGGCCTTAGCTGT	AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"Immunoglobulin superfamily / C1-set domain containing"	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.20T>C	15.37:g.45003764T>C	ENSP00000452780:p.Leu7Ser	118	1	0.00847458		104	24	0.230769	NM_004048	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Missense_Mutation	SNP	ENST00000558401.1	37	CCDS10113.1	.	.	.	.	.	.	.	.	.	.	T	11.97	1.798275	0.31777	.	.	ENSG00000166710	ENST00000349264;ENST00000544417;ENST00000396754	T	0.01422	4.91	5.35	4.22	0.49857	.	2.541080	0.03331	U	0.193423	T	0.04227	0.0117	M	0.73598	2.24	0.09310	N	1	P;P;P	0.46512	0.879;0.808;0.808	P;B;B	0.44394	0.448;0.368;0.368	T	0.44097	-0.9350	10	0.40728	T	0.16	.	8.1935	0.31383	0.0:0.0892:0.0:0.9108	.	7;7;7	F5H6I0;A6XMH4;P61769	.;.;B2MG_HUMAN	S	7	ENSP00000437604:L7S	ENSP00000340858:L7S	L	+	2	0	B2M	42791056	0.006000	0.16342	0.001000	0.08648	0.002000	0.02628	0.889000	0.28282	1.144000	0.42321	0.533000	0.62120	TTA	.	.	none		0.607	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048		C	45003764	T	C	45003764	3	2	16	1	0	0	0	0	1	0	0	0	1244	1764	61	3	22	3	B2M	15	45003764	Missense_Mutation	SNP	T	TCGA-FF-8062-01A-11D-2210-10		45003764	57527628	112	2206											
LACTB	114294	hgsc.bcm.edu	37	chr15	63433784	63433784	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aaggaaacaaacgtatggttCgtgtagaaagcaacggcatt	16	8	11	6	3	0	1	0	0	0	1	1	2	0	2	0	3	4	5	0	3	7	4	rs556545187		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr15:63433784C>T	ENST00000261893.4	+	6	1496	c.1424C>T	c.(1423-1425)tCg>tTg	p.S475L	RPS27L_ENST00000559763.1_Intron	NM_032857.3	NP_116246.2	P83111	LACTB_HUMAN	lactamase, beta	475						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						ACGTATGGTTCGTGTAGAAAG	0.483													C|||	1	0.000199681	0.0	0.0	5008	,	,		20385	0.0		0.0	False		,,,				2504	0.001				p.S475L	Melanoma(85;443 1381 6215 27308 35583)	Atlas-SNP	.											LACTB,NS,carcinoma,-1,1	LACTB	29	1	0			c.C1424T						PASS	.						77	66	70					15																	63433784		2203	4300	6503	SO:0001583	missense	114294	exon6			ATGGTTCGTGTAG	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.1424C>T	15.37:g.63433784C>T	ENSP00000261893:p.Ser475Leu	144	0	0		163	39	0.239264	NM_032857	P83096	Missense_Mutation	SNP	ENST00000261893.4	37	CCDS10182.1	.	.	.	.	.	.	.	.	.	.	C	2.400	-0.337917	0.05278	.	.	ENSG00000103642	ENST00000261893	T	0.40476	1.03	5.64	5.64	0.86602	Beta-lactamase/transpeptidase-like (2);Beta-lactamase-related (1);	0.334872	0.37178	N	0.002209	T	0.20373	0.0490	N	0.22421	0.69	0.23838	N	0.996708	P	0.37500	0.597	B	0.30782	0.12	T	0.17561	-1.0365	10	0.11485	T	0.65	-11.5505	5.3675	0.16121	0.1481:0.6328:0.1427:0.0764	.	475	P83111	LACTB_HUMAN	L	475	ENSP00000261893:S475L	ENSP00000261893:S475L	S	+	2	0	LACTB	61220837	0.996000	0.38824	0.874000	0.34290	0.217000	0.24651	2.416000	0.44644	2.817000	0.96982	0.563000	0.77884	TCG	.	.	none		0.483	LACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256224.1	NM_032857		T	63433784	C	T	63433784	3	4	16	1	0	0	0	0	1	0	0	0	8606	893	31	1	1450	1	LACTB	15	63433784	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	18430020	63433784	39097608	113	2207											
MAP2K1	5604	hgsc.bcm.edu	37	chr15	66727441	66727441	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcgaaagcgccttgaggccTttcttacccagaagcagaag	12	7	11	11	2	1	3	0	1	1	2	1	4	1	3	3	1	4	1	3	1	4	3			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr15:66727441T>C	ENST00000307102.5	+	2	688	c.157T>C	c.(157-159)Ttt>Ctt	p.F53L		NM_002755.3	NP_002746.1	Q02750	MP2K1_HUMAN	mitogen-activated protein kinase kinase 1	53			F -> S (in CFC3). {ECO:0000269|PubMed:16439621}.		activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cellular senescence (GO:0090398)|chemotaxis (GO:0006935)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|Golgi inheritance (GO:0048313)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|keratinocyte differentiation (GO:0030216)|labyrinthine layer development (GO:0060711)|MAPK cascade (GO:0000165)|melanosome transport (GO:0032402)|mitotic nuclear division (GO:0007067)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell proliferation (GO:0008285)|negative regulation of homotypic cell-cell adhesion (GO:0034111)|neurotrophin TRK receptor signaling pathway (GO:0048011)|placenta blood vessel development (GO:0060674)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|protein heterooligomerization (GO:0051291)|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)|regulation of vascular smooth muscle contraction (GO:0003056)|response to axon injury (GO:0048678)|response to glucocorticoid (GO:0051384)|response to oxidative stress (GO:0006979)|signal transduction (GO:0007165)|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)|vesicle transport along microtubule (GO:0047496)	cell cortex (GO:0005938)|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)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase activity (GO:0004672)|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)|receptor signaling protein tyrosine phosphatase activity (GO:0004728)	p.F53L(2)|p.F53S(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(8)|urinary_tract(1)	20					Bosutinib(DB06616)|Trametinib(DB08911)	CCTTGAGGCCTTTCTTACCCA	0.547																																					p.F53L		Atlas-SNP	.											MAP2K1,rectum,carcinoma,0,3	MAP2K1	115	3	3	Substitution - Missense(3)	lung(2)|large_intestine(1)	c.T157C						scavenged	.						155	146	149					15																	66727441		2201	4299	6500	SO:0001583	missense	5604	exon2			GAGGCCTTTCTTA	L11284	CCDS10216.1	15q22.1-q22.33	2014-09-17			ENSG00000169032	ENSG00000169032	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6840	protein-coding gene	gene with protein product		176872		PRKMK1		9465908, 8388392	Standard	NM_002755		Approved	MEK1, MAPKK1	uc010bhq.3	Q02750	OTTHUMG00000133196	ENST00000307102.5:c.157T>C	15.37:g.66727441T>C	ENSP00000302486:p.Phe53Leu	88	1	0.0113636		94	26	0.276596	NM_002755		Missense_Mutation	SNP	ENST00000307102.5	37	CCDS10216.1	.	.	.	.	.	.	.	.	.	.	T	35	5.500444	0.96355	.	.	ENSG00000169032	ENST00000307102	D	0.93019	-3.15	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	D	0.95188	0.8440	M	0.76170	2.325	0.80722	D	1	D;D	0.61080	0.989;0.98	P;P	0.59115	0.852;0.805	D	0.93980	0.7257	10	0.26408	T	0.33	-14.6287	14.0473	0.64712	0.0:0.0:0.0:1.0	.	31;53	B4DFY5;Q02750	.;MP2K1_HUMAN	L	53	ENSP00000302486:F53L	ENSP00000302486:F53L	F	+	1	0	MAP2K1	64514495	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.924000	0.87555	1.911000	0.55334	0.383000	0.25322	TTT	.	.	none		0.547	MAP2K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256906.4			C	66727441	T	C	66727441	3	2	16	1	0	0	0	0	1	0	0	0	9245	1609	56	3	163	3	MAP2K1	15	66727441	Missense_Mutation	SNP	T	TCGA-FF-8062-01A-11D-2210-10	3293657	66727441	35803951	114	2208											
ULK3	25989	hgsc.bcm.edu	37	chr15	75131687	75131687	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaatccccctcctggtcttTcttcacagcctgcaccacca	7	11	5	18	0	3	1	1	1	2	0	5	1	5	1	6	1	2	1	6	1	1	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr15:75131687T>C	ENST00000440863.2	-	8	971	c.880A>G	c.(880-882)Aaa>Gaa	p.K294E	ULK3_ENST00000569437.1_Missense_Mutation_p.K294E|ULK3_ENST00000568667.1_Missense_Mutation_p.K305E	NM_001099436.1	NP_001092906	Q6PHR2	ULK3_HUMAN	unc-51 like kinase 3	294	MIT 1.				autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|cellular senescence (GO:0090398)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of smoothened signaling pathway (GO:0045880)|protein autophosphorylation (GO:0046777)|regulation of autophagy (GO:0010506)	ATG1/UKL1 signaling complex (GO:0034273)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|pre-autophagosomal structure (GO:0000407)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)	2						TCCTGGTCTTTCTTCACAGCC	0.592																																					p.K294E		Atlas-SNP	.											.	ULK3	30	.	0			c.A880G						PASS	.						38	42	41					15																	75131687		1947	4121	6068	SO:0001583	missense	25989	exon8			GGTCTTTCTTCAC	BC048289		15q24.1	2013-07-02	2013-07-02			ENSG00000140474			19703	protein-coding gene	gene with protein product		613472	"unc-51-like kinase 3 (C. elegans)"				Standard	XM_005254289		Approved	DKFZP434C131, FLJ90566	uc010bkf.1	Q6PHR2		ENST00000440863.2:c.880A>G	15.37:g.75131687T>C	ENSP00000400312:p.Lys294Glu	155	0	0		118	10	0.0847458	NM_001099436	B2RXK3|B4DRQ7|D3DW68|Q9NPN5|Q9UFS4	Missense_Mutation	SNP	ENST00000440863.2	37	CCDS45305.1	.	.	.	.	.	.	.	.	.	.	T	14.52	2.560326	0.45590	.	.	ENSG00000140474	ENST00000440863;ENST00000418051	T	0.68903	-0.36	5.05	5.05	0.67936	MIT (2);	.	.	.	.	T	0.50343	0.1610	N	0.17082	0.46	0.46061	D	0.998848	B;B;B;B	0.31680	0.335;0.335;0.199;0.11	B;B;B;B	0.31290	0.127;0.127;0.072;0.031	T	0.50250	-0.8850	9	0.30854	T	0.27	-15.4837	13.6385	0.62235	0.0:0.0:0.0:1.0	.	305;204;294;294	B4DFT0;B4DFS6;Q6PHR2;Q6PHR2-3	.;.;ULK3_HUMAN;.	E	294;305	ENSP00000400312:K294E	ENSP00000393658:K305E	K	-	1	0	ULK3	72918740	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	5.864000	0.69575	1.907000	0.55213	0.402000	0.26972	AAA	.	.	none		0.592	ULK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421734.4	NM_015518		C	75131687	T	C	75131687	3	2	16	1	0	0	0	0	1	0	0	0	16992	1792	62	3	574	3	ULK3	15	75131687	Missense_Mutation	SNP	T	TCGA-FF-8062-01A-11D-2210-10	8404246	75131687	27399705	115	2209											
RHBDF1	64285	hgsc.bcm.edu	37	chr16	112797	112797	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcaaagaaggatgtgtccagCtcatcggggaaatcagttgt	12	9	13	7	1	2	1	2	0	0	1	4	3	3	3	1	3	1	3	1	3	3	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr16:112797C>A	ENST00000262316.6	-	6	913	c.771G>T	c.(769-771)gaG>gaT	p.E257D	RHBDF1_ENST00000454039.2_Missense_Mutation_p.E257D	NM_022450.3	NP_071895.3	Q96CC6	RHDF1_HUMAN	rhomboid 5 homolog 1 (Drosophila)	257					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)				ATGTGTCCAGCTCATCGGGGA	0.602																																					p.E257D		Atlas-SNP	.											.	RHBDF1	54	.	0			c.G771T						PASS	.						112	118	116					16																	112797		2203	4300	6503	SO:0001583	missense	64285	exon6			GTCCAGCTCATCG	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.771G>T	16.37:g.112797C>A	ENSP00000262316:p.Glu257Asp	102	0	0		95	18	0.189474	NM_022450	Q04842|Q1W6H2|Q4TT59|Q96S34|Q9H6E1	Missense_Mutation	SNP	ENST00000262316.6	37	CCDS32344.1	.	.	.	.	.	.	.	.	.	.	.	10.61	1.397914	0.25205	.	.	ENSG00000007384	ENST00000262316;ENST00000454039	T;T	0.64260	-0.09;-0.09	4.56	3.57	0.40892	.	0.102644	0.64402	D	0.000003	T	0.44074	0.1276	N	0.20401	0.57	0.47621	D	0.999476	B;B;B	0.29481	0.085;0.245;0.002	B;B;B	0.36608	0.074;0.229;0.02	T	0.22591	-1.0212	10	0.09590	T	0.72	-35.6303	8.8488	0.35188	0.0:0.8267:0.0:0.1733	.	257;280;257	F5GWL4;B4E3Q0;Q96CC6	.;.;RHDF1_HUMAN	D	257	ENSP00000262316:E257D;ENSP00000392133:E257D	ENSP00000262316:E257D	E	-	3	2	RHBDF1	52797	0.997000	0.39634	0.999000	0.59377	0.981000	0.71138	0.894000	0.28350	2.359000	0.80004	0.462000	0.41574	GAG	.	.	none		0.602	RHBDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134178.2	NM_022450		A	112797	C	A	112797	3	1	16	1	0	0	0	0	1	0	0	0	13334	796	28	4	1848	4	RHBDF1	16	112797	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10		112797	90241956	116	2210											
PIGQ	9091	hgsc.bcm.edu	37	chr16	632296	632296	+	Intron	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaggccggcaggcccctccGcctcctgatgcaggtgaggc	5	5	15	16	3	0	2	0	2	0	0	2	3	2	2	6	5	1	2	6	5	0	0			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr16:632296G>A	ENST00000026218.5	+	10	1619				PIGQ_ENST00000409527.2_Missense_Mutation_p.R527H|PIGQ_ENST00000321878.5_Missense_Mutation_p.R527H	NM_148920.2	NP_683721.1	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Q						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)				AGGCCCCTCCGCCTCCTGATG	0.692																																					p.R527H		Atlas-SNP	.											.	PIGQ	43	.	0			c.G1580A						PASS	.						23	23	23					16																	632296		2195	4293	6488	SO:0001627	intron_variant	9091	exon10			CCCTCCGCCTCCT	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.1532-587G>A	16.37:g.632296G>A		145	0	0		107	44	0.411215	NM_004204	A2IDE1|D3DU52|O14927|Q96G00|Q96S22|Q9UJH4	Missense_Mutation	SNP	ENST00000026218.5	37	CCDS10411.1	.	.	.	.	.	.	.	.	.	.	G	11.43	1.635080	0.29068	.	.	ENSG00000007541	ENST00000409527;ENST00000321878;ENST00000540241	T;T	0.44482	0.92;0.92	5.08	5.08	0.68730	.	.	.	.	.	T	0.32041	0.0816	L	0.28400	0.85	0.80722	D	1	B	0.23377	0.084	B	0.17098	0.017	T	0.09509	-1.0671	9	0.14656	T	0.56	.	17.4349	0.87548	0.0:0.0:1.0:0.0	.	527	Q9BRB3-2	.	H	527;527;85	ENSP00000386760:R527H;ENSP00000326674:R527H	ENSP00000326674:R527H	R	+	2	0	PIGQ	572297	1.000000	0.71417	1.000000	0.80357	0.355000	0.29361	4.179000	0.58290	2.361000	0.80049	0.561000	0.74099	CGC	.	.	none		0.692	PIGQ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000239270.2	NM_004204		A	632296	G	A	632296	1	1	16	0	1	0	0	0	0	0	0	0	11905	1087	38	1		1	PIGQ	16	632296	Intron	SNP	G	TCGA-FF-8062-01A-11D-2210-10	519499	632296	89722457	117	2211											
ABCA3	21	hgsc.bcm.edu	37	chr16	2339491	2339491	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gatgagggctccaatgccgtCggaggggtccatggccccac	7	6	15	13	2	0	1	0	1	0	0	3	3	2	2	5	5	1	1	5	5	1	0	rs145565697	byFrequency	TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr16:2339491C>T	ENST00000301732.5	-	20	3344	c.2644G>A	c.(2644-2646)Gac>Aac	p.D882N	ABCA3_ENST00000382381.3_Missense_Mutation_p.D824N	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	882					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)	CCAATGCCGTCGGAGGGGTCC	0.687													C|||	2	0.000399361	0.0015	0.0	5008	,	,		17193	0.0		0.0	False		,,,				2504	0.0				p.D882N		Atlas-SNP	.											.	ABCA3	176	.	0			c.G2644A						PASS	.	C	ASN/ASP	10,4380		0,10,2185	32	29	30		2644	0.5	0	16	dbSNP_134	30	0,8598		0,0,4299	yes	missense	ABCA3	NM_001089.2	23	0,10,6484	TT,TC,CC		0.0,0.2278,0.077	benign	882/1705	2339491	10,12978	2195	4299	6494	SO:0001583	missense	21	exon20			TGCCGTCGGAGGG	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.2644G>A	16.37:g.2339491C>T	ENSP00000301732:p.Asp882Asn	98	0	0		90	4	0.0444444	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Missense_Mutation	SNP	ENST00000301732.5	37	CCDS10466.1	.	.	.	.	.	.	.	.	.	.	C	10.43	1.348915	0.24426	0.002278	0.0	ENSG00000167972	ENST00000301732;ENST00000382381	D	0.91740	-2.9	4.68	0.543	0.17179	.	0.223978	0.44688	N	0.000432	D	0.84813	0.5555	L	0.36672	1.1	0.52099	D	0.999942	B;B;B	0.09022	0.001;0.002;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.72360	-0.4317	10	0.30854	T	0.27	.	8.3806	0.32468	0.0:0.673:0.0:0.327	.	882;886;882	A7MBM9;Q4LE27;Q99758	.;.;ABCA3_HUMAN	N	882;886	ENSP00000301732:D882N	ENSP00000301732:D882N	D	-	1	0	ABCA3	2279492	0.951000	0.32395	0.000000	0.03702	0.215000	0.24574	2.187000	0.42602	-0.026000	0.13895	0.561000	0.74099	GAC	C|0.998;T|0.002	0.002	strong		0.687	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089		T	2339491	C	T	2339491	3	4	16	1	0	0	0	0	1	0	0	0	33	884	31	1	2526	1	ABCA3	16	2339491	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	1707195	2339491	88015262	118	2212											
NLRC3	197358	hgsc.bcm.edu	37	chr16	3614077	3614077	+	RNA	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	atctcctcctcgttaaagccCcggatctccgtcatccggtc	6	11	7	17	4	3	0	1	0	2	0	9	1	5	1	6	2	1	1	6	2	2	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr16:3614077C>T	ENST00000301749.7	-	0	1266				NLRC3_ENST00000324659.8_RNA|NLRC3_ENST00000448023.2_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000603507.1_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CGTTAAAGCCCCGGATCTCCG	0.607																																					p.R287R		Atlas-SNP	.											NLRC3,NS,carcinoma,-2,1	NLRC3	103	1	0			c.G861A						PASS	.						47	53	51					16																	3614077		2025	4166	6191			197358	exon5			AAAGCCCCGGATC	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"Nucleotide-binding domain and leucine rich repeat containing"	29889	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3", "NOD-like receptor C3"	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3614077C>T		43	0	0		28	11	0.392857	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Silent	SNP	ENST00000301749.7	37																																																																																				.	.	none		0.607	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844		T	3614077	C	T	3614077	1	4	16	0	1	0	0	0	0	0	0	0	10477	610	22	2		2	NLRC3	16	3614077	RNA	SNP	C	TCGA-FF-8062-01A-11D-2210-10	1274586	3614077	86740676	119	2213											
MYH11	4629	hgsc.bcm.edu	37	chr16	15880586	15880586	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttttcccggctccagactcGcctctgaaagacacgggaac	9	8	10	14	3	1	3	0	1	1	2	4	4	3	4	3	2	1	2	3	2	2	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr16:15880586G>A	ENST00000300036.5	-	5	643	c.534C>T	c.(532-534)ggC>ggT	p.G178G	MYH11_ENST00000576790.2_Silent_p.G178G|MYH11_ENST00000396324.3_Silent_p.G178G|MYH11_ENST00000452625.2_Silent_p.G178G	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	178	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						CTCCAGACTCGCCTCTGAAAG	0.522			T	CBFB	AML																																p.G178G		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	.	MYH11	520	.	0			c.C534T						PASS	.						107	86	93					16																	15880586		2197	4300	6497	SO:0001819	synonymous_variant	4629	exon5			AGACTCGCCTCTG	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.534C>T	16.37:g.15880586G>A		160	0	0		178	47	0.264045	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																			.	.	none		0.522	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		A	15880586	G	A	15880586	2	1	16	1	0	0	0	0	0	0	0	1	10040	1074	38	1		1	MYH11	16	15880586	Silent	SNP	G	TCGA-FF-8062-01A-11D-2210-10	12266509	15880586	74474167	120	2214											
SMG1	23049	hgsc.bcm.edu	37	chr16	18847712	18847712	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttgtgtgcttatctcttgaaGcaagcttgcaagctgtgttg	7	16	11	7	0	1	1	0	1	1	0	2	1	1	1	0	0	5	6	0	0	4	5			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr16:18847712G>A	ENST00000446231.2	-	47	8159	c.7747C>T	c.(7747-7749)Ctt>Ttt	p.L2583F	SMG1_ENST00000389467.3_Missense_Mutation_p.L2583F			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2583					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						ATCTCTTGAAGCAAGCTTGCA	0.383																																					p.L2583F		Atlas-SNP	.											.	SMG1	401	.	0			c.C7747T						PASS	.						125	115	118					16																	18847712		1903	4133	6036	SO:0001583	missense	23049	exon47			CTTGAAGCAAGCT	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.7747C>T	16.37:g.18847712G>A	ENSP00000402515:p.Leu2583Phe	98	0	0		125	22	0.176	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	37	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	G	18.74	3.688557	0.68271	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.01215	5.16;5.16	6.17	6.17	0.99709	Armadillo-type fold (1);	0.000000	0.64402	D	0.000010	T	0.02888	0.0086	N	0.19112	0.55	0.45427	D	0.998404	D	0.58620	0.983	P	0.56474	0.799	T	0.63782	-0.6559	10	0.72032	D	0.01	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	2583	Q96Q15	SMG1_HUMAN	F	2583	ENSP00000402515:L2583F;ENSP00000374118:L2583F	ENSP00000374118:L2583F	L	-	1	0	SMG1	18755213	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	7.862000	0.87013	2.941000	0.99782	0.655000	0.94253	CTT	.	.	none		0.383	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		A	18847712	G	A	18847712	3	1	16	1	0	0	0	0	1	0	0	0	14810	971	34	2	3306	2	SMG1	16	18847712	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	2967126	18847712	71507041	121	2215											
TMC5	79838	hgsc.bcm.edu	37	chr16	19498605	19498605	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttcttgctctttttcccaTccttcaccggggtcttgtgc	2	18	7	14	1	5	0	1	0	4	0	7	0	7	0	3	2	2	1	3	2	0	6			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr16:19498605T>C	ENST00000396229.2	+	17	3279	c.2530T>C	c.(2530-2532)Tcc>Ccc	p.S844P	TMC5_ENST00000381414.4_Missense_Mutation_p.S844P|TMC5_ENST00000561503.1_Missense_Mutation_p.S485P|TMC5_ENST00000219821.5_Missense_Mutation_p.S598P|TMC5_ENST00000542583.2_Missense_Mutation_p.S844P|CTA-363E6.6_ENST00000561762.1_RNA|TMC5_ENST00000541464.1_Missense_Mutation_p.S792P|TMC5_ENST00000564959.1_Missense_Mutation_p.S527P	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5	844					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						CTTTTTCCCATCCTTCACCGG	0.532																																					p.S844P		Atlas-SNP	.											.	TMC5	169	.	0			c.T2530C						PASS	.						75	65	69					16																	19498605		2197	4300	6497	SO:0001583	missense	79838	exon17			TTCCCATCCTTCA	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.2530T>C	16.37:g.19498605T>C	ENSP00000379531:p.Ser844Pro	78	0	0		98	17	0.173469	NM_001105249	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	Missense_Mutation	SNP	ENST00000396229.2	37	CCDS45431.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.499431	0.85069	.	.	ENSG00000103534	ENST00000541464;ENST00000381414;ENST00000396229;ENST00000542583;ENST00000219821;ENST00000440743	T;T;T;T;T	0.71817	-0.34;-0.28;-0.48;-0.48;-0.6	5.72	5.72	0.89469	.	0.165964	0.56097	D	0.000036	D	0.84982	0.5593	M	0.84948	2.725	0.44862	D	0.997878	D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;0.999;0.999	D;D;D;D;D;D	0.87578	0.998;0.979;0.994;0.992;0.991;0.996	D	0.85275	0.1058	10	0.37606	T	0.19	-27.6788	14.9732	0.71249	0.0:0.0:0.0:1.0	.	792;527;598;598;844;844	F5GYU8;E7EU57;Q6UXY8-3;B3KUQ8;Q6UXY8;Q6UXY8-2	.;.;.;.;TMC5_HUMAN;.	P	792;844;844;844;598;527	ENSP00000441227:S792P;ENSP00000370822:S844P;ENSP00000379531:S844P;ENSP00000446274:S844P;ENSP00000219821:S598P	ENSP00000219821:S598P	S	+	1	0	TMC5	19406106	1.000000	0.71417	0.957000	0.39632	0.995000	0.86356	5.372000	0.66156	2.176000	0.68965	0.533000	0.62120	TCC	.	.	none		0.532	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	NM_024780		C	19498605	T	C	19498605	3	2	16	1	0	0	0	0	1	0	0	0	16003	1435	50	3	2902	3	TMC5	16	19498605	Missense_Mutation	SNP	T	TCGA-FF-8062-01A-11D-2210-10	650893	19498605	70856148	122	2216											
ZNF423	23090	hgsc.bcm.edu	37	chr16	49670344	49670344	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cggccggatattgtggtcccGcagccggtgattctgcagca	6	9	14	12	4	1	1	0	1	1	0	2	2	2	2	3	4	3	3	3	4	1	3	rs544721667		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr16:49670344G>A	ENST00000561648.1	-	4	2772	c.2719C>T	c.(2719-2721)Cgg>Tgg	p.R907W	ZNF423_ENST00000567169.1_Missense_Mutation_p.R790W|ZNF423_ENST00000562520.1_Missense_Mutation_p.R847W|ZNF423_ENST00000563137.2_Missense_Mutation_p.R847W|ZNF423_ENST00000535559.1_Missense_Mutation_p.R790W|ZNF423_ENST00000262383.2_Missense_Mutation_p.R907W|ZNF423_ENST00000562871.1_Missense_Mutation_p.R847W	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	907					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)				TTGTGGTCCCGCAGCCGGTGA	0.592													G|||	1	0.000199681	0.0	0.0	5008	,	,		20967	0.0		0.0	False		,,,				2504	0.001				p.R907W		Atlas-SNP	.											ZNF423_ENST00000262383,NS,carcinoma,+2,2	ZNF423	463	2	0			c.C2719T						PASS	.						61	59	60					16																	49670344		2198	4300	6498	SO:0001583	missense	23090	exon4			GGTCCCGCAGCCG	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.2719C>T	16.37:g.49670344G>A	ENSP00000455426:p.Arg907Trp	124	0	0		119	23	0.193277	NM_015069	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	37	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	G	16.73	3.204654	0.58234	.	.	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.10382	2.88;2.93	4.81	2.74	0.32292	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.85682	D	0.000000	T	0.27063	0.0663	M	0.62723	1.935	0.43540	D	0.995834	D	0.89917	1.0	D	0.72625	0.978	T	0.01574	-1.1321	9	.	.	.	-25.0868	13.064	0.59022	0.0:0.0:0.463:0.537	.	907	Q2M1K9	ZN423_HUMAN	W	907;790	ENSP00000262383:R907W;ENSP00000442321:R790W	.	R	-	1	2	ZNF423	48227845	0.829000	0.29322	0.997000	0.53966	0.985000	0.73830	0.897000	0.28390	1.028000	0.39785	-0.268000	0.10319	CGG	.	.	none		0.592	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		A	49670344	G	A	49670344	3	1	16	1	0	0	0	0	1	0	0	0	17913	1086	38	1	1155	1	ZNF423	16	49670344	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	30171739	49670344	40684409	123	2217											
CDH16	1014	hgsc.bcm.edu	37	chr16	66944286	66944286	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccactcacgatcaagccatGgtcttggcggggtgtgcaga	8	9	13	11	2	3	1	2	0	1	1	4	2	4	1	2	4	2	1	2	4	1	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr16:66944286G>A	ENST00000299752.4	-	15	2237	c.2044C>T	c.(2044-2046)Cat>Tat	p.H682Y	CDH16_ENST00000568632.1_Missense_Mutation_p.H585Y|CDH16_ENST00000565796.1_Missense_Mutation_p.H643Y|CDH16_ENST00000570262.1_Missense_Mutation_p.H602Y|CDH16_ENST00000394055.3_Missense_Mutation_p.H660Y	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	682	Ectodomain G.				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)		ATCAAGCCATGGTCTTGGCGG	0.632																																					p.H682Y		Atlas-SNP	.											.	CDH16	91	.	0			c.C2044T						PASS	.						111	113	112					16																	66944286		2200	4300	6500	SO:0001583	missense	1014	exon15			AGCCATGGTCTTG	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.2044C>T	16.37:g.66944286G>A	ENSP00000299752:p.His682Tyr	143	0	0		135	25	0.185185	NM_004062	B4DPA8|H3BPD3|Q6UW93	Missense_Mutation	SNP	ENST00000299752.4	37	CCDS10823.1	.	.	.	.	.	.	.	.	.	.	G	0.692	-0.794195	0.02862	.	.	ENSG00000166589	ENST00000394055;ENST00000299752;ENST00000544875	T;T	0.55234	0.53;0.53	4.61	2.56	0.30785	.	0.293204	0.32884	N	0.005525	T	0.29491	0.0735	L	0.31294	0.92	0.25809	N	0.984415	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.002;0.001;0.001	T	0.26538	-1.0100	10	0.02654	T	1	-0.7022	4.7712	0.13157	0.3365:0.0:0.6635:0.0	.	660;682;682	O75309-2;B2R7S8;O75309	.;.;CAD16_HUMAN	Y	660;682;646	ENSP00000377619:H660Y;ENSP00000299752:H682Y	ENSP00000299752:H682Y	H	-	1	0	CDH16	65501787	0.596000	0.26866	0.456000	0.27044	0.193000	0.23685	1.826000	0.39092	0.477000	0.27464	0.455000	0.32223	CAT	.	.	none		0.632	CDH16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268839.2	NM_004062		A	66944286	G	A	66944286	3	1	16	1	0	0	0	0	1	0	0	0	3103	1348	47	2	461	2	CDH16	16	66944286	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	17273942	66944286	23410467	124	2218											
ATP2C2	9914	hgsc.bcm.edu	37	chr16	84473085	84473085	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggactctgactgccaatgaAatgacagtgacccagcttgt	11	9	11	10	0	1	4	0	4	1	0	1	5	1	5	2	1	2	1	2	1	2	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr16:84473085A>T	ENST00000262429.4	+	13	1253	c.1164A>T	c.(1162-1164)gaA>gaT	p.E388D	ATP2C2_ENST00000416219.2_Missense_Mutation_p.E388D|ATP2C2_ENST00000420010.2_3'UTR	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2	388					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						CTGCCAATGAAATGACAGTGA	0.512																																					p.E388D		Atlas-SNP	.											.	ATP2C2	75	.	0			c.A1164T						PASS	.						234	245	242					16																	84473085		2145	4254	6399	SO:0001583	missense	9914	exon13			CAATGAAATGACA	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.1164A>T	16.37:g.84473085A>T	ENSP00000262429:p.Glu388Asp	144	0	0		161	35	0.217391	NM_014861	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	Missense_Mutation	SNP	ENST00000262429.4	37	CCDS42207.1	.	.	.	.	.	.	.	.	.	.	A	17.65	3.441104	0.63067	.	.	ENSG00000064270	ENST00000416219;ENST00000262429;ENST00000420010	D;D	0.96619	-4.07;-4.07	4.91	-5.36	0.02689	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	0.000003	D	0.97620	0.9220	M	0.90198	3.095	0.40064	D	0.975936	D;D;D;P	0.58970	0.984;0.975;0.963;0.946	P;D;P;D	0.64237	0.898;0.923;0.883;0.923	D	0.97061	0.9771	10	0.87932	D	0	.	15.4601	0.75349	0.2567:0.0:0.7433:0.0	.	388;237;405;388	E7ES94;F8WAA5;O75185-2;O75185	.;.;.;AT2C2_HUMAN	D	388;388;237	ENSP00000397925:E388D;ENSP00000262429:E388D	ENSP00000262429:E388D	E	+	3	2	ATP2C2	83030586	1.000000	0.71417	0.830000	0.32933	0.244000	0.25665	0.514000	0.22786	-0.979000	0.03529	-0.441000	0.05720	GAA	.	.	none		0.512	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861		T	84473085	A	T	84473085	3	4	16	1	0	0	0	0	1	0	0	0	1144	11	1	5	1214	5	ATP2C2	16	84473085	Missense_Mutation	SNP	A	TCGA-FF-8062-01A-11D-2210-10	17528799	84473085	5881668	125	2219											
RNF166	115992	hgsc.bcm.edu	37	chr16	88766062	88766062	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatgtgggcaccacggggaCgaacttggggcagttggcca	8	7	17	9	2	0	1	0	1	0	0	0	3	0	2	2	6	1	3	2	6	1	2	rs144508728		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr16:88766062C>T	ENST00000312838.4	-	3	486	c.391G>A	c.(391-393)Gtc>Atc	p.V131I	RNF166_ENST00000541206.2_Missense_Mutation_p.V22I|RNF166_ENST00000537718.2_Missense_Mutation_p.V22I|RNF166_ENST00000568683.1_Missense_Mutation_p.V22I|RNF166_ENST00000562499.1_5'Flank|RP5-1142A6.5_ENST00000561699.1_RNA|RNF166_ENST00000567844.1_Missense_Mutation_p.V50I	NM_178841.3	NP_849163.1	Q96A37	RN166_HUMAN	ring finger protein 166	131							zinc ion binding (GO:0008270)			endometrium(1)	1				BRCA - Breast invasive adenocarcinoma(80;0.0476)		ACCACGGGGACGAACTTGGGG	0.622																																					p.V131I		Atlas-SNP	.											.	RNF166	3	.	0			c.G391A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL	1,4393	2.1+/-5.4	0,1,2196	135	105	115		148,64,391	4.6	1	16	dbSNP_134	115	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense,missense	RNF166	NM_001171815.1,NM_001171816.1,NM_178841.3	29,29,29	0,2,6494	TT,TC,CC		0.0116,0.0228,0.0154	benign,benign,benign	50/157,22/129,131/238	88766062	2,12990	2197	4299	6496	SO:0001583	missense	115992	exon3			CGGGGACGAACTT	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.391G>A	16.37:g.88766062C>T	ENSP00000326095:p.Val131Ile	145	0	0		99	4	0.040404	NM_178841	B3KQ03|D3DX75|H3BTU8|Q96DM0	Missense_Mutation	SNP	ENST00000312838.4	37	CCDS10969.1	.	.	.	.	.	.	.	.	.	.	C	15.68	2.905259	0.52333	2.28E-4	1.16E-4	ENSG00000158717	ENST00000312838;ENST00000537718;ENST00000541206	T	0.15718	2.4	4.57	4.57	0.56435	.	0.136393	0.49305	D	0.000153	T	0.07954	0.0199	N	0.14661	0.345	0.44309	D	0.997187	P	0.44659	0.84	B	0.25405	0.06	T	0.35500	-0.9786	10	0.18710	T	0.47	-28.0268	16.9747	0.86310	0.0:1.0:0.0:0.0	.	131	Q96A37	RN166_HUMAN	I	131;50;22	ENSP00000326095:V131I	ENSP00000326095:V131I	V	-	1	0	RNF166	87293563	0.998000	0.40836	0.987000	0.45799	0.967000	0.64934	3.918000	0.56432	2.115000	0.64714	0.313000	0.20887	GTC	C|1.000;T|0.000	0.000	weak		0.622	RNF166-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269544.1	NM_178841		T	88766062	C	T	88766062	3	4	16	1	0	0	0	0	1	0	0	0	13472	536	19	1	338	1	RNF166	16	88766062	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	4292977	88766062	1588691	126	2220											
SOX15	6665	hgsc.bcm.edu	37	chr17	7492686	7492686	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtgtcgggcgcggagccgCttggcctcctccacgaaggg	5	6	17	13	5	0	0	0	0	0	0	3	2	2	1	4	5	1	1	4	5	1	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr17:7492686C>T	ENST00000250055.2	-	1	802	c.309G>A	c.(307-309)aaG>aaA	p.K103K	SOX15_ENST00000570788.1_Silent_p.K103K|MPDU1_ENST00000423172.2_Intron|FXR2_ENST00000573057.1_5'Flank|SOX15_ENST00000538513.2_Silent_p.K103K	NM_006942.1	NP_008873.1	O60248	SOX15_HUMAN	SRY (sex determining region Y)-box 15	103					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						CGCGGAGCCGCTTGGCCTCCT	0.682											OREG0024139	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.K103K		Atlas-SNP	.											.	SOX15	10	.	0			c.G309A						PASS	.						24	27	26					17																	7492686		2202	4299	6501	SO:0001819	synonymous_variant	6665	exon1			GAGCCGCTTGGCC	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.309G>A	17.37:g.7492686C>T		155	0	0	642	79	11	0.139241	NM_006942	B4DWU7|D3DTQ0|P35717|Q9Y6W7	Silent	SNP	ENST00000250055.2	37	CCDS32549.1																																																																																			.	.	none		0.682	SOX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440757.1	NM_006942		T	7492686	C	T	7492686	2	4	16	1	0	0	0	0	0	0	0	1	14961	796	28	2		2	SOX15	17	7492686	Silent	SNP	C	TCGA-FF-8062-01A-11D-2210-10		7492686	73702524	127	2221											
MAPK7	5598	hgsc.bcm.edu	37	chr17	19285517	19285517	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtaccccagcctgcctgccCaccccctggccctgcacccc	4	6	7	24	0	0	0	0	0	0	0	0	0	0	0	10	1	5	2	10	1	1	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr17:19285517C>T	ENST00000308406.5	+	5	2287	c.1901C>T	c.(1900-1902)cCa>cTa	p.P634L	MAPK7_ENST00000395604.3_Missense_Mutation_p.P634L|MAPK7_ENST00000299612.7_Missense_Mutation_p.P495L|MAPK7_ENST00000571657.1_Intron|MFAP4_ENST00000574313.2_5'Flank|MAPK7_ENST00000395602.4_Missense_Mutation_p.P634L	NM_139033.2	NP_620602.2	Q13164	MK07_HUMAN	mitogen-activated protein kinase 7	634	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)					CCTGCCTGCCCACCCCCTGGC	0.706																																					p.P634L		Atlas-SNP	.											.	MAPK7	72	.	0			c.C1901T						PASS	.						17	18	18					17																	19285517		2190	4285	6475	SO:0001583	missense	5598	exon5			CCTGCCCACCCCC	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.1901C>T	17.37:g.19285517C>T	ENSP00000311005:p.Pro634Leu	128	0	0		59	13	0.220339	NM_002749	Q16634|Q59F50|Q6QLU7|Q7L4P4|Q969G1|Q96G51	Missense_Mutation	SNP	ENST00000308406.5	37	CCDS11206.1	.	.	.	.	.	.	.	.	.	.	C	9.264	1.043860	0.19748	.	.	ENSG00000166484	ENST00000308406;ENST00000299612;ENST00000395604;ENST00000395602	T;T;T;T	0.77489	-0.78;-1.1;-0.78;-0.78	4.87	2.72	0.32119	.	0.502080	0.21467	N	0.074080	T	0.55130	0.1901	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.49952	-0.8884	10	0.59425	D	0.04	-0.6152	6.3873	0.21568	0.1809:0.7178:0.0:0.1013	.	634	Q13164	MK07_HUMAN	L	634;495;634;634	ENSP00000311005:P634L;ENSP00000299612:P495L;ENSP00000378968:P634L;ENSP00000378966:P634L	ENSP00000299612:P495L	P	+	2	0	MAPK7	19226110	0.001000	0.12720	0.025000	0.17156	0.710000	0.40934	0.264000	0.18497	1.174000	0.42811	0.313000	0.20887	CCA	.	.	none		0.706	MAPK7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132506.1	NM_139033		T	19285517	C	T	19285517	3	4	16	1	0	0	0	0	1	0	0	0	9291	594	21	2	1915	2	MAPK7	17	19285517	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	11792831	19285517	61909693	128	2222											
NF1	4763	hgsc.bcm.edu	37	chr17	29667603	29667603	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtcaacttgtattcagcaggTaccgcacttcttgaacaaaa	13	11	7	10	1	3	1	2	1	1	0	3	1	3	1	1	1	4	4	1	1	6	6			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr17:29667603T>G	ENST00000358273.4	+	47	7385	c.7002T>G	c.(7000-7002)ggT>ggG	p.G2334G	NF1_ENST00000356175.3_Silent_p.G2313G|NF1_ENST00000417592.2_Silent_p.G47G|NF1_ENST00000444181.2_Silent_p.G127G	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	2334					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)		ATTCAGCAGGTACCGCACTTC	0.438			"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.G2334G		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.T7002G						PASS	.						122	108	113					17																	29667603		2203	4300	6503	SO:0001819	synonymous_variant	4763	exon47	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	AGCAGGTACCGCA		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.7002T>G	17.37:g.29667603T>G		151	0	0		155	22	0.141935	NM_001042492	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	37	CCDS42292.1																																																																																			.	.	none		0.438	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		G	29667603	T	G	29667603	2	3	16	1	0	0	0	0	0	0	0	1	10365	1625	57	5		5	NF1	17	29667603	Silent	SNP	T	TCGA-FF-8062-01A-11D-2210-10	10382086	29667603	51527607	129	2223											
DDX52	11056	hgsc.bcm.edu	37	chr17	35979827	35979827	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtaccttagtagtttctgAaaaccttttatgtattctgg	9	19	7	6	0	2	1	0	1	2	0	2	1	2	1	2	1	2	4	2	1	7	9			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr17:35979827A>C	ENST00000349699.2	-	13	1678	c.1635T>G	c.(1633-1635)ttT>ttG	p.F545L	DDX52_ENST00000394367.3_Missense_Mutation_p.F437L	NM_007010.3	NP_008941.2	Q9Y2R4	DDX52_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52	545	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.|Lys-rich.					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)				GTAGTTTCTGAAAACCTTTTA	0.338																																					p.F545L		Atlas-SNP	.											.	DDX52	40	.	0			c.T1635G						PASS	.						96	99	98					17																	35979827		2203	4300	6503	SO:0001583	missense	11056	exon13			TTTCTGAAAACCT	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.1635T>G	17.37:g.35979827A>C	ENSP00000268854:p.Phe545Leu	159	0	0		179	40	0.223464	NM_007010	Q86YG1|Q8N213|Q9NVE0|Q9Y482	Missense_Mutation	SNP	ENST00000349699.2	37	CCDS11323.1	.	.	.	.	.	.	.	.	.	.	A	4.181	0.032244	0.08101	.	.	ENSG00000141141	ENST00000349699;ENST00000394367	T;T	0.13307	2.6;2.63	5.87	0.492	0.16872	Helicase, C-terminal (1);	0.095278	0.64402	N	0.000001	T	0.02494	0.0076	N	0.01015	-1.05	0.38208	D	0.940389	B	0.02656	0.0	B	0.04013	0.001	T	0.37731	-0.9693	10	0.06365	T	0.9	.	1.6637	0.02797	0.3737:0.1278:0.3671:0.1314	.	545	Q9Y2R4	DDX52_HUMAN	L	545;437	ENSP00000268854:F545L;ENSP00000377893:F437L	ENSP00000268854:F545L	F	-	3	2	DDX52	33053940	0.998000	0.40836	0.991000	0.47740	0.741000	0.42261	0.324000	0.19610	-0.090000	0.12462	-0.242000	0.12053	TTT	.	.	none		0.338	DDX52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256795.1	NM_152300		C	35979827	A	C	35979827	3	2	16	1	0	0	0	0	1	0	0	0	4372	243	9	5	176	5	DDX52	17	35979827	Missense_Mutation	SNP	A	TCGA-FF-8062-01A-11D-2210-10	6312224	35979827	45215383	130	2224											
COASY	80347	hgsc.bcm.edu	37	chr17	40716156	40716156	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtcagcgaggagacctatcGtggggggatggccatcaacc	9	6	16	10	2	2	1	2	0	0	1	3	4	2	2	3	6	2	0	3	6	2	1	rs367865615		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr17:40716156G>A	ENST00000393818.2	+	2	1334	c.878G>A	c.(877-879)cGt>cAt	p.R293H	MLX_ENST00000346833.4_5'Flank|RP11-400F19.8_ENST00000585572.1_RNA|MLX_ENST00000246912.4_5'Flank|COASY_ENST00000420359.1_Missense_Mutation_p.R293H|COASY_ENST00000590958.1_Missense_Mutation_p.R322H|MLX_ENST00000435881.2_5'Flank|COASY_ENST00000421097.2_Missense_Mutation_p.R293H|COASY_ENST00000449624.1_5'UTR	NM_025233.6	NP_079509.5	Q13057	COASY_HUMAN	CoA synthase	293	Phosphopantetheine adenylyltransferase.				cell death (GO:0008219)|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)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)	ATP binding (GO:0005524)|dephospho-CoA kinase activity (GO:0004140)|pantetheine-phosphate adenylyltransferase activity (GO:0004595)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)	21		all_cancers(22;1.06e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)		GAGACCTATCGTGGGGGGATG	0.622																																					p.R322H		Atlas-SNP	.											.	COASY	45	.	0			c.G965A						PASS	.						39	41	40					17																	40716156		2203	4300	6503	SO:0001583	missense	80347	exon4			CCTATCGTGGGGG	AF453478	CCDS11429.1, CCDS45685.1	17q12-q21	2010-04-30	2010-04-30			ENSG00000068120	2.7.7.3		29932	protein-coding gene	gene with protein product		609855	"Coenzyme A synthase"			11923312, 11980892	Standard	NM_025233		Approved	DPCK, NBP, CoASY, PPAT	uc010cyj.4	Q13057		ENST00000393818.2:c.878G>A	17.37:g.40716156G>A	ENSP00000377406:p.Arg293His	187	0	0		153	41	0.267974	NM_001042532	B2RA78|B4DLU0|Q6GS23|Q8NBM7|Q8NEW1|Q8WXD4|Q9NRM3	Missense_Mutation	SNP	ENST00000393818.2	37	CCDS11429.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.500814	0.85176	.	.	ENSG00000068120	ENST00000421097;ENST00000420359;ENST00000393818	D;D;D	0.96459	-4.01;-4.02;-4.02	5.23	5.23	0.72850	Cytidylyltransferase (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.106801	0.64402	D	0.000014	D	0.97498	0.9181	M	0.62266	1.93	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.71870	0.975;0.973	D	0.97758	1.0219	10	0.87932	D	0	-11.0142	16.6827	0.85297	0.0:0.0:1.0:0.0	.	322;293	Q13057-2;Q13057	.;COASY_HUMAN	H	322;293;293	ENSP00000393564:R322H;ENSP00000413338:R293H;ENSP00000377406:R293H	ENSP00000377406:R293H	R	+	2	0	COASY	37969682	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.983000	0.40648	2.882000	0.98803	0.655000	0.94253	CGT	.	.	alt		0.622	COASY-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450409.1	NM_025233		A	40716156	G	A	40716156	3	1	16	1	0	0	0	0	1	0	0	0	3654	1145	40	1	975	1	COASY	17	40716156	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	4736329	40716156	40479054	131	2225											
B4GALNT2	124872	hgsc.bcm.edu	37	chr17	47246178	47246178	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccagctgcgtggtgaccagtGgcgtggtcaacttcttcctg	5	11	13	12	2	2	1	1	1	1	0	3	1	3	1	3	3	3	1	3	3	1	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr17:47246178G>T	ENST00000300404.2	+	10	1470	c.1411G>T	c.(1411-1413)Ggc>Tgc	p.G471C	B4GALNT2_ENST00000393354.2_Missense_Mutation_p.G411C|B4GALNT2_ENST00000504681.1_Missense_Mutation_p.G385C	NM_153446.2	NP_703147.2	Q8NHY0	B4GN2_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 2	471					lipid glycosylation (GO:0030259)|negative regulation of cell-cell adhesion (GO:0022408)|protein glycosylation (GO:0006486)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)			endometrium(3)|large_intestine(6)|liver(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	24			all cancers(6;0.000316)			GGTGACCAGTGGCGTGGTCAA	0.567																																					p.G471C	GBM(124;244 1635 8663 18097 33175)	Atlas-SNP	.											B4GALNT2,colon,carcinoma,-2,1	B4GALNT2	67	1	0			c.G1411T						PASS	.						81	59	66					17																	47246178		2203	4300	6503	SO:0001583	missense	124872	exon10			ACCAGTGGCGTGG	AJ517770	CCDS11544.1, CCDS54139.1, CCDS54140.1	17q21.33	2013-02-22	2006-01-08	2006-01-08	ENSG00000167080	ENSG00000167080	2.4.1.-	"Beta 4-glycosyltransferases", "Glycosyltransferase family 2 domain containing"	24136	protein-coding gene	gene with protein product		111730	"UDP-GalNAc:Neu5Acalpha2-3Galbeta-R beta1,4-N-acetylgalactosaminyltransferase"	GALGT2		8782649, 12678917	Standard	NM_153446		Approved	Sda, Cad	uc002ion.2	Q8NHY0	OTTHUMG00000161307	ENST00000300404.2:c.1411G>T	17.37:g.47246178G>T	ENSP00000300404:p.Gly471Cys	99	0	0		95	4	0.0421053	NM_153446	B4DZE4|Q14CP1|Q86Y40	Missense_Mutation	SNP	ENST00000300404.2	37	CCDS11544.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.716785	0.89205	.	.	ENSG00000167080	ENST00000504681;ENST00000393354;ENST00000300404	T;T;T	0.25749	1.78;1.78;1.78	5.28	5.28	0.74379	.	0.000000	0.64402	D	0.000001	T	0.53238	0.1784	M	0.77103	2.36	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.51756	-0.8665	10	0.38643	T	0.18	-22.868	17.6682	0.88209	0.0:0.0:1.0:0.0	.	411;471	Q8NHY0-2;Q8NHY0	.;B4GN2_HUMAN	C	385;411;471	ENSP00000425510:G385C;ENSP00000377022:G411C;ENSP00000300404:G471C	ENSP00000300404:G471C	G	+	1	0	B4GALNT2	44601177	1.000000	0.71417	0.626000	0.29213	0.892000	0.51952	8.715000	0.91416	2.450000	0.82876	0.561000	0.74099	GGC	.	.	none		0.567	B4GALNT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364477.1	NM_153446		T	47246178	G	T	47246178	3	4	16	1	0	0	0	0	1	0	0	0	1267	1348	47	4	1467	4	B4GALNT2	17	47246178	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	6530022	47246178	33949032	132	2226											
BRIP1	83990	hgsc.bcm.edu	37	chr17	59760682	59760682	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taaaaccaggaaacatgcctTtatttttggaaggagatggt	14	12	10	5	0	0	1	0	0	0	1	0	4	0	3	2	4	3	0	2	4	5	5			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr17:59760682T>G	ENST00000259008.2	-	20	3992	c.3725A>C	c.(3724-3726)aAa>aCa	p.K1242T		NM_032043.2	NP_114432.2	Q9BX63	FANCJ_HUMAN	BRCA1 interacting protein C-terminal helicase 1	1242					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						AAACATGCCTTTATTTTTGGA	0.284			"F, N, Mis"			"AML, leukemia, breast"		Involved in tolerance or repair of DNA crosslinks																													p.K1242T		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.A3725C						PASS	.						63	66	65					17																	59760682		2202	4292	6494	SO:0001583	missense	83990	exon20			ATGCCTTTATTTT	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.3725A>C	17.37:g.59760682T>G	ENSP00000259008:p.Lys1242Thr	73	0	0		102	20	0.196078	NM_032043	Q3MJE2|Q8NCI5	Missense_Mutation	SNP	ENST00000259008.2	37	CCDS11631.1	.	.	.	.	.	.	.	.	.	.	T	12.26	1.883513	0.33255	.	.	ENSG00000136492	ENST00000259008	T	0.77620	-1.11	4.35	4.35	0.52113	.	.	.	.	.	T	0.63010	0.2475	N	0.19112	0.55	0.80722	D	1	P	0.40970	0.734	B	0.39617	0.305	T	0.61153	-0.7120	8	.	.	.	.	11.1816	0.48631	0.0:0.0:0.0:1.0	.	1242	Q9BX63	FANCJ_HUMAN	T	1242	ENSP00000259008:K1242T	.	K	-	2	0	BRIP1	57115464	1.000000	0.71417	0.914000	0.36105	0.079000	0.17450	2.496000	0.45346	1.710000	0.51325	0.383000	0.25322	AAA	.	.	none		0.284	BRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445362.1	NM_032043		G	59760682	T	G	59760682	3	3	16	1	0	0	0	0	1	0	0	0	1516	1841	64	5	28	5	BRIP1	17	59760682	Missense_Mutation	SNP	T	TCGA-FF-8062-01A-11D-2210-10	12514504	59760682	21434528	133	2227											
GH2	2689	hgsc.bcm.edu	37	chr17	61957782	61957782	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagtagagcagcccgtagtTcttgagcagtgcgtcatcgt	8	10	13	10	3	2	2	1	1	1	1	3	2	2	2	1	0	4	6	1	0	2	4			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr17:61957782T>A	ENST00000423893.2	-	5	614	c.553A>T	c.(553-555)Aac>Tac	p.N185Y	GH2_ENST00000456543.2_Missense_Mutation_p.R183S|GH2_ENST00000332800.7_3'UTR|GH2_ENST00000449787.2_Missense_Mutation_p.N170Y			P01242	SOM2_HUMAN	growth hormone 2	185					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						AGCCCGTAGTTCTTGAGCAGT	0.557																																					p.N185Y		Atlas-SNP	.											.	GH2	73	.	0			c.A553T						PASS	.						201	164	177					17																	61957782		2203	4300	6503	SO:0001583	missense	2689	exon5			CGTAGTTCTTGAG	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.553A>T	17.37:g.61957782T>A	ENSP00000409294:p.Asn185Tyr	460	0	0		412	95	0.230583	NM_002059	B1A4H5|B1A4H7|O14643|O14644|P09587	Missense_Mutation	SNP	ENST00000423893.2	37	CCDS11647.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	12.27|12.27	1.886442|1.886442	0.33348|0.33348	.|.	.|.	ENSG00000136487|ENSG00000136487	ENST00000423893;ENST00000449787|ENST00000456543	D;D|D	0.88664|0.88896	-2.41;-2.41|-2.44	2.74|2.74	2.74|2.74	0.32292|0.32292	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);|.	.|.	.|.	.|.	.|.	D|D	0.93115|0.93115	0.7808|0.7808	M|M	0.93939|0.93939	3.475|3.475	0.80722|0.80722	D|D	1|1	D;D|P	0.89917|0.52170	1.0;1.0|0.951	D;D|P	0.97110|0.56088	1.0;0.998|0.791	D|D	0.91600|0.91600	0.5294|0.5294	9|9	0.87932|0.48119	D|T	0|0.1	.|.	5.5287|5.5287	0.16972|0.16972	0.0:0.1365:0.0:0.8635|0.0:0.1365:0.0:0.8635	.|.	185;170|183	P01242;O14643|O14644	SOM2_HUMAN;.|.	Y|S	185;170|183	ENSP00000409294:N185Y;ENSP00000410618:N170Y|ENSP00000394122:R183S	ENSP00000409294:N185Y|ENSP00000394122:R183S	N|R	-|-	1|3	0|2	GH2|GH2	59311514|59311514	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.020000|0.020000	0.10135|0.10135	3.546000|3.546000	0.53656|0.53656	1.255000|1.255000	0.44051|0.44051	0.254000|0.254000	0.18369|0.18369	AAC|AGA	.	.	none		0.557	GH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417665.1	NM_002059		A	61957782	T	A	61957782	3	1	16	1	0	0	0	0	1	0	0	0	6376	1783	62	5	192	5	GH2	17	61957782	Missense_Mutation	SNP	T	TCGA-FF-8062-01A-11D-2210-10	2197100	61957782	19237428	134	2228											
FAM59A	64762	hgsc.bcm.edu	37	chr18	29850212	29850212	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctgaagaatagtaggacaaGgtggggctgggagagcgagt	12	6	18	5	1	0	3	0	1	0	2	0	6	0	4	1	5	1	2	1	5	5	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr18:29850212G>A	ENST00000269209.6	-	5	1704	c.1701C>T	c.(1699-1701)acC>acT	p.T567T	GAREM_ENST00000399218.4_Silent_p.T567T			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	567					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)										AGTAGGACAAGGTGGGGCTGG	0.557																																					p.T567T		Atlas-SNP	.											.	.	.	.	0			c.C1701T						PASS	.						154	129	137					18																	29850212		2203	4300	6503	SO:0001819	synonymous_variant	64762	exon5			GGACAAGGTGGGG	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.1701C>T	18.37:g.29850212G>A		192	0	0		185	53	0.286486	NM_022751	Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	Silent	SNP	ENST00000269209.6	37	CCDS56057.1																																																																																			.	.	none		0.557	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255365.1	NM_022751		A	29850212	G	A	29850212	2	1	16	1	0	0	0	0	0	0	0	1	5600	987	35	2		2	FAM59A	18	29850212	Silent	SNP	G	TCGA-FF-8062-01A-11D-2210-10		29850212	48227036	135	2229											
FHOD3	80206	hgsc.bcm.edu	37	chr18	34340708	34340708	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccgtggaggacgccaccccCgcgctgggcgtccgcacacg	5	4	14	18	7	0	0	0	0	0	0	2	2	2	2	5	3	0	2	5	3	0	0	rs200423151		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr18:34340708C>T	ENST00000359247.4	+	22	3987	c.3987C>T	c.(3985-3987)ccC>ccT	p.P1329P	FHOD3_ENST00000445677.1_Silent_p.P1308P|FHOD3_ENST00000257209.4_Silent_p.P1346P|FHOD3_ENST00000591635.1_Silent_p.P542P|FHOD3_ENST00000592128.1_Silent_p.P325P|FHOD3_ENST00000590592.1_Silent_p.P1529P	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	1329					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)				ACGCCACCCCCGCGCTGGGCG	0.687													C|||	1	0.000199681	0.0008	0.0	5008	,	,		13615	0.0		0.0	False		,,,				2504	0.0				p.P1346P		Atlas-SNP	.											.	FHOD3	210	.	0			c.C4038T						PASS	.						23	22	22					18																	34340708		2193	4295	6488	SO:0001819	synonymous_variant	80206	exon23			CACCCCCGCGCTG	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.3987C>T	18.37:g.34340708C>T		24	0	0		22	5	0.227273	NM_025135	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Silent	SNP	ENST00000359247.4	37																																																																																				C|1.000;T|0.000	0.000	strong		0.687	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114		T	34340708	C	T	34340708	2	4	16	1	0	0	0	0	0	0	0	1	5891	639	23	1		1	FHOD3	18	34340708	Silent	SNP	C	TCGA-FF-8062-01A-11D-2210-10	4490496	34340708	43736540	136	2230											
DSEL	92126	hgsc.bcm.edu	37	chr18	65180867	65180867	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attggaatctgctatacccaCagttctttggaagccaggta	11	12	9	9	0	2	0	0	0	2	0	2	2	2	2	2	3	3	3	2	3	5	6			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr18:65180867C>A	ENST00000310045.7	-	2	2482	c.1009G>T	c.(1009-1011)Gtg>Ttg	p.V337L	CTD-2541J13.2_ENST00000583493.1_RNA|RP11-638L3.1_ENST00000583687.1_lincRNA|CTD-2541J13.2_ENST00000581951.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	327					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)				GCTATACCCACAGTTCTTTGG	0.383																																					p.V337L		Atlas-SNP	.											.	DSEL	196	.	0			c.G1009T						PASS	.						69	74	72					18																	65180867		2203	4300	6503	SO:0001583	missense	92126	exon2			TACCCACAGTTCT	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.1009G>T	18.37:g.65180867C>A	ENSP00000310565:p.Val337Leu	78	0	0		72	13	0.180556	NM_032160	Q17RH1|Q6P5Z3	Missense_Mutation	SNP	ENST00000310045.7	37	CCDS11995.1	.	.	.	.	.	.	.	.	.	.	C	15.14	2.743918	0.49151	.	.	ENSG00000171451	ENST00000310045;ENST00000397964	T	0.27402	1.67	4.9	4.9	0.64082	.	0.000000	0.64402	U	0.000002	T	0.31231	0.0790	M	0.71581	2.175	0.44694	D	0.997686	P	0.37955	0.612	B	0.33960	0.173	T	0.11665	-1.0578	10	0.39692	T	0.17	-13.9785	11.9105	0.52737	0.0:0.9195:0.0:0.0805	.	327	Q8IZU8	DSEL_HUMAN	L	337;327	ENSP00000310565:V337L	ENSP00000310565:V337L	V	-	1	0	DSEL	63331847	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.819000	0.62664	2.460000	0.83146	0.563000	0.77884	GTG	.	.	none		0.383	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160		A	65180867	C	A	65180867	3	1	16	1	0	0	0	0	1	0	0	0	4777	478	17	4	2663	4	DSEL	18	65180867	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	30840159	65180867	12896381	137	2231											
ZNF181	339318	hgsc.bcm.edu	37	chr19	35232117	35232117	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggaagacttttagccatggCtcatcccttacacgacatct	10	11	8	12	1	2	1	1	0	1	1	3	3	3	2	2	2	2	1	2	2	3	3	rs200927726		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr19:35232117C>T	ENST00000492450.1	+	4	920	c.831C>T	c.(829-831)ggC>ggT	p.G277G	ZNF181_ENST00000459757.2_Silent_p.G276G|ZNF181_ENST00000392232.3_Silent_p.G321G			Q2M3W8	ZN181_HUMAN	zinc finger protein 181	277					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.G213G(1)		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)			TTAGCCATGGCTCATCCCTTA	0.443																																					p.G277G		Atlas-SNP	.											ZNF181,NS,carcinoma,+2,2	ZNF181	65	2	1	Substitution - coding silent(1)	kidney(1)	c.C831T						scavenged	.						90	95	93					19																	35232117		2203	4300	6503	SO:0001819	synonymous_variant	339318	exon4			CCATGGCTCATCC	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.831C>T	19.37:g.35232117C>T		92	2	0.0217391		73	4	0.0547945	NM_001029997	B7ZKX3|Q49A75	Silent	SNP	ENST00000492450.1	37	CCDS32990.2																																																																																			C|0.999;T|0.001	0.001	weak		0.443	ZNF181-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349005.3	NM_001029997		T	35232117	C	T	35232117	2	4	16	1	0	0	0	0	0	0	0	1	17764	784	28	2		2	ZNF181	19	35232117	Silent	SNP	C	TCGA-FF-8062-01A-11D-2210-10		35232117	23896866	138	2232											
PRKD2	25865	hgsc.bcm.edu	37	chr19	47204071	47204071	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tatacctctgggccttgcctCcctcgccttcctcctcctca	3	13	5	20	1	2	0	1	0	1	0	7	0	6	0	8	1	2	0	8	1	2	4			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr19:47204071C>T	ENST00000291281.4	-	7	1331	c.1106G>A	c.(1105-1107)gGa>gAa	p.G369E	PRKD2_ENST00000600194.1_Missense_Mutation_p.G212E|PRKD2_ENST00000433867.1_Missense_Mutation_p.G369E|PRKD2_ENST00000601806.1_Missense_Mutation_p.G212E|PRKD2_ENST00000595515.1_Missense_Mutation_p.G369E			Q9BZL6	KPCD2_HUMAN	protein kinase D2	369					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)		GGCCTTGCCTCCCTCGCCTTC	0.572																																					p.G369E		Atlas-SNP	.											.	PRKD2	94	.	0			c.G1106A						PASS	.						62	50	54					19																	47204071		2203	4300	6503	SO:0001583	missense	25865	exon7			TTGCCTCCCTCGC	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.1106G>A	19.37:g.47204071C>T	ENSP00000291281:p.Gly369Glu	86	0	0		69	4	0.057971	NM_016457	Q8TB08|Q9P0T6|Q9Y3X8	Missense_Mutation	SNP	ENST00000291281.4	37	CCDS12689.1	.	.	.	.	.	.	.	.	.	.	C	5.174	0.217694	0.09810	.	.	ENSG00000105287	ENST00000291281;ENST00000433867	T;T	0.63744	-0.06;-0.06	4.28	-0.572	0.11745	.	1.007170	0.07985	N	0.986164	T	0.44767	0.1309	L	0.47716	1.5	0.24460	N	0.99445	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.33007	-0.9885	10	0.05436	T	0.98	-3.4373	4.0249	0.09683	0.0:0.415:0.1761:0.4089	.	369;369	E7ER94;Q9BZL6	.;KPCD2_HUMAN	E	369	ENSP00000291281:G369E;ENSP00000393978:G369E	ENSP00000291281:G369E	G	-	2	0	PRKD2	51895911	0.359000	0.24955	0.792000	0.32020	0.882000	0.50991	0.493000	0.22451	0.198000	0.20407	0.555000	0.69702	GGA	.	.	none		0.572	PRKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466591.1	NM_016457		T	47204071	C	T	47204071	3	4	16	1	0	0	0	0	1	0	0	0	12531	855	30	2	1578	2	PRKD2	19	47204071	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	11971954	47204071	11924912	139	2233											
KLK6	5653	hgsc.bcm.edu	37	chr19	51466703	51466703	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgtcctggtcatggctggcGgcatcatagtcagggtggat	7	11	15	8	1	3	0	3	0	0	0	4	1	4	1	1	6	0	2	1	6	1	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr19:51466703G>A	ENST00000376851.3	-	4	739	c.300C>T	c.(298-300)gcC>gcT	p.A100A	KLK6_ENST00000456750.2_5'Flank|KLK6_ENST00000376853.4_Intron|KLK6_ENST00000391808.1_5'UTR|KLK6_ENST00000310157.2_Silent_p.A100A|CTB-147C22.8_ENST00000601506.1_RNA|KLK6_ENST00000594641.1_Silent_p.A100A	NM_001012964.1	NP_001012982.1	Q92876	KLK6_HUMAN	kallikrein-related peptidase 6	100	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)		CATGGCTGGCGGCATCATAGT	0.582																																					p.A100A		Atlas-SNP	.											.	KLK6	35	.	0			c.C300T						PASS	.						81	63	69					19																	51466703		2203	4300	6503	SO:0001819	synonymous_variant	5653	exon4			GCTGGCGGCATCA	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.300C>T	19.37:g.51466703G>A		147	0	0		133	28	0.210526	NM_001012964	A6NJA1|A8MW09|Q6H301	Silent	SNP	ENST00000376851.3	37	CCDS12811.1																																																																																			.	.	none		0.582	KLK6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465060.1	NM_002774		A	51466703	G	A	51466703	2	1	16	1	0	0	0	0	0	0	0	1	8417	1103	39	1		1	KLK6	19	51466703	Silent	SNP	G	TCGA-FF-8062-01A-11D-2210-10	4262632	51466703	7662280	140	2234											
CPXM1	56265	hgsc.bcm.edu	37	chr20	2775239	2775239	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgacagcgtcagcaatcccaAgctccgtgtccttgtccctc	7	10	8	16	2	1	1	1	1	0	0	6	1	5	1	4	0	3	2	4	0	2	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr20:2775239A>T	ENST00000380605.2	-	13	1971	c.1907T>A	c.(1906-1908)cTt>cAt	p.L636H		NM_001184699.1|NM_019609.4	NP_001171628.1|NP_062555.1	Q96SM3	CPXM1_HUMAN	carboxypeptidase X (M14 family), member 1	636					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						AGCAATCCCAAGCTCCGTGTC	0.587																																					p.L636H		Atlas-SNP	.											.	CPXM1	107	.	0			c.T1907A						PASS	.						183	117	140					20																	2775239		2203	4300	6503	SO:0001583	missense	56265	exon13			ATCCCAAGCTCCG	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.1907T>A	20.37:g.2775239A>T	ENSP00000369979:p.Leu636His	54	0	0		55	16	0.290909	NM_019609	Q6P4G8|Q6UW65|Q9NUB5	Missense_Mutation	SNP	ENST00000380605.2	37	CCDS13033.1	.	.	.	.	.	.	.	.	.	.	A	10.31	1.314694	0.23908	.	.	ENSG00000088882	ENST00000380605;ENST00000421947	T	0.42131	0.98	5.53	1.79	0.24919	Peptidase M14, carboxypeptidase A (1);Carboxypeptidase-like, regulatory domain (1);Carboxypeptidase, regulatory domain (1);	0.516425	0.19628	N	0.109747	T	0.25005	0.0607	L	0.27053	0.805	0.09310	N	1	B	0.11235	0.004	B	0.10450	0.005	T	0.13202	-1.0518	10	0.44086	T	0.13	-3.0776	4.3529	0.11163	0.4832:0.0:0.0892:0.4276	.	636	Q96SM3	CPXM1_HUMAN	H	636;332	ENSP00000369979:L636H	ENSP00000369979:L636H	L	-	2	0	CPXM1	2723239	0.000000	0.05858	0.155000	0.22561	0.974000	0.67602	-0.008000	0.12788	0.507000	0.28148	0.533000	0.62120	CTT	.	.	none		0.587	CPXM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077643.2	NM_019609		T	2775239	A	T	2775239	3	4	16	1	0	0	0	0	1	0	0	0	3839	72	3	5	305	5	CPXM1	20	2775239	Missense_Mutation	SNP	A	TCGA-FF-8062-01A-11D-2210-10		2775239	60250281	141	2235											
CD93	22918	hgsc.bcm.edu	37	chr20	23065878	23065878	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcccatggggtcccaggaCgcacgtggcccccccacgac	6	6	11	18	3	0	0	0	0	0	0	2	2	2	1	5	4	0	1	5	4	0	1	rs140540216		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr20:23065878C>T	ENST00000246006.4	-	1	1099	c.952G>A	c.(952-954)Gtc>Atc	p.V318I		NM_012072.3	NP_036204.2	Q9NPY3	C1QR1_HUMAN	CD93 molecule	318	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.		V -> A. {ECO:0000269|PubMed:11781389}.		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)					GGTCCCAGGACGCACGTGGCC	0.637																																					p.V318I		Atlas-SNP	.											CD93,colon,carcinoma,0,1	CD93	84	1	0			c.G952A						PASS	.						39	43	42					20																	23065878		2203	4300	6503	SO:0001583	missense	22918	exon1			CCAGGACGCACGT	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.952G>A	20.37:g.23065878C>T	ENSP00000246006:p.Val318Ile	167	0	0		150	27	0.18	NM_012072	O00274	Missense_Mutation	SNP	ENST00000246006.4	37	CCDS13149.1	.	.	.	.	.	.	.	.	.	.	T	1.767	-0.485219	0.04352	.	.	ENSG00000125810	ENST00000246006	D	0.87412	-2.25	5.42	-2.28	0.06826	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	1.855870	0.02965	N	0.143707	T	0.75591	0.3870	N	0.25647	0.755	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.59215	-0.7496	10	0.12103	T	0.63	-4.8249	3.9396	0.09321	0.0988:0.4634:0.0974:0.3404	.	318	Q9NPY3	C1QR1_HUMAN	I	318	ENSP00000246006:V318I	ENSP00000246006:V318I	V	-	1	0	CD93	23013878	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.089000	0.01357	-0.557000	0.06126	-1.014000	0.02459	GTC	C|1.000;A|0.000	.	alt		0.637	CD93-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078312.2	NM_012072		T	23065878	C	T	23065878	3	4	16	1	0	0	0	0	1	0	0	0	3049	536	19	1	1014	1	CD93	20	23065878	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	20290639	23065878	39959642	142	2236											
SCAND1	51282	hgsc.bcm.edu	37	chr20	34542105	34542105	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcagcgaggagcccacacaGttacgctcaggggctgagct	9	5	15	12	2	1	1	1	1	0	0	1	3	1	2	1	4	4	5	1	4	1	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr20:34542105G>C	ENST00000373991.3	-	3	1172	c.102C>G	c.(100-102)aaC>aaG	p.N34K	SCAND1_ENST00000305978.2_Missense_Mutation_p.N34K			P57086	SCND1_HUMAN	SCAN domain containing 1	34					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)					AGCCCACACAGTTACGCTCAG	0.697																																					p.N97K		Atlas-SNP	.											.	SCAND1	2	.	0			c.C291G						PASS	.						11	12	12					20																	34542105		2173	4249	6422	SO:0001583	missense	51282	exon2			CACACAGTTACGC	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.102C>G	20.37:g.34542105G>C	ENSP00000363103:p.Asn34Lys	93	0	0		69	5	0.0724638	NM_033630	Q6IAG7	Missense_Mutation	SNP	ENST00000373991.3	37	CCDS13269.1	.	.	.	.	.	.	.	.	.	.	G	12.91	2.078518	0.36662	.	.	ENSG00000171222	ENST00000305978;ENST00000373991	T;T	0.08370	3.1;3.1	4.31	1.19	0.21007	.	0.828409	0.10092	N	0.717113	T	0.05823	0.0152	N	0.24115	0.695	0.09310	N	1	B	0.19583	0.037	B	0.21546	0.035	T	0.47169	-0.9138	10	0.17369	T	0.5	.	8.3967	0.32561	0.2657:0.0:0.7343:0.0	.	34	P57086	SCND1_HUMAN	K	34	ENSP00000301995:N34K;ENSP00000363103:N34K	ENSP00000301995:N34K	N	-	3	2	SCAND1	34005519	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.103000	0.10940	0.182000	0.20032	0.561000	0.74099	AAC	.	.	none		0.697	SCAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078958.2	NM_016558		C	34542105	G	C	34542105	3	2	16	1	0	0	0	0	1	0	0	0	13890	1020	36	4	441	4	SCAND1	20	34542105	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	11476227	34542105	28483415	143	2237											
FAM83D	81610	hgsc.bcm.edu	37	chr20	37555095	37555095	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgagcgccgccatggctctgCtgtccgagggcctggacgag	5	6	16	14	5	1	0	0	0	1	0	2	4	2	1	4	3	2	2	4	3	0	0	rs542789388		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr20:37555095C>G	ENST00000217429.4	+	1	141	c.100C>G	c.(100-102)Ctg>Gtg	p.L34V		NM_030919.2	NP_112181.2	Q9H4H8	FA83D_HUMAN	family with sequence similarity 83, member D	4					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)				CATGGCTCTGCTGTCCGAGGG	0.672																																					p.L34V		Atlas-SNP	.											.	FAM83D	60	.	0			c.C100G						PASS	.						13	17	15					20																	37555095		1906	4100	6006	SO:0001583	missense	81610	exon1			GCTCTGCTGTCCG	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.100C>G	20.37:g.37555095C>G	ENSP00000217429:p.Leu34Val	34	0	0		29	6	0.206897	NM_030919	B4E1I7|Q5THR2|Q68EN1|Q6P457|Q7Z6H0|Q96DF5|Q96N89|Q9BVM8	Missense_Mutation	SNP	ENST00000217429.4	37	CCDS42872.1	.	.	.	.	.	.	.	.	.	.	C	14.22	2.471206	0.43942	.	.	ENSG00000101447	ENST00000217429;ENST00000424027	T	0.12255	2.7	5.48	-0.0886	0.13672	.	6.575320	0.00481	N	0.000125	T	0.08268	0.0206	N	0.14661	0.345	0.09310	N	1	B;B	0.31548	0.22;0.328	B;B	0.31101	0.058;0.124	T	0.22836	-1.0205	10	0.19590	T	0.45	.	5.1809	0.15160	0.2481:0.5461:0.0:0.2058	.	4;4	Q9H4H8;Q9H4H8-2	FA83D_HUMAN;.	V	34;4	ENSP00000217429:L34V	ENSP00000217429:L34V	L	+	1	2	FAM83D	36988509	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.197000	0.17197	0.029000	0.15352	0.655000	0.94253	CTG	.	.	none		0.672	FAM83D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079211.1			G	37555095	C	G	37555095	3	3	16	1	0	0	0	0	1	0	0	0	5644	796	28	4	102	4	FAM83D	20	37555095	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	3012990	37555095	25470425	144	2238											
CYYR1	116159	hgsc.bcm.edu	37	chr21	27945186	27945186	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccgccgccctccgtcactgaCctgcgtagacaaagagcagg	9	5	11	16	4	1	3	1	1	0	2	2	3	2	3	5	1	2	2	5	1	2	1	rs576125420		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr21:27945186C>T	ENST00000299340.4	-	1	417		c.e1+1		CYYR1_ENST00000400043.3_Splice_Site|CYYR1_ENST00000435845.2_Splice_Site	NM_052954.2	NP_443186.1	Q96J86	CYYR1_HUMAN	cysteine/tyrosine-rich 1							integral component of membrane (GO:0016021)				large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	15						CCGTCACTGACCTGCGTAGAC	0.662																																					.		Atlas-SNP	.											.	CYYR1	38	.	0			c.73+1G>A						PASS	.						58	58	58					21																	27945186		2203	4299	6502	SO:0001630	splice_region_variant	116159	exon2			CACTGACCTGCGT	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.73+1G>A	21.37:g.27945186C>T		69	0	0		104	20	0.192308	NM_052954	A0A059TD09|A8MTU9|B2R845|Q53ER3|Q5JPD0|Q96NV7|R9QAJ4|W8CQB3	Splice_Site	SNP	ENST00000299340.4	37	CCDS13578.1	.	.	.	.	.	.	.	.	.	.	C	19.94	3.919627	0.73098	.	.	ENSG00000166265	ENST00000299340;ENST00000435845;ENST00000400043	.	.	.	4.59	4.59	0.56863	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.227	0.59921	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CYYR1	26867057	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	3.229000	0.51278	2.835000	0.97688	0.650000	0.86243	.	.	.	none		0.662	CYYR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171654.2	NM_052954	Intron	T	27945186	C	T	27945186	5	4	16	1	0	0	0	0	0	0	1	0	4213	521	18	2	406	2	CYYR1	21	27945186	Splice_Site	SNP	C	TCGA-FF-8062-01A-11D-2210-10		27945186	20184709	145	2239											
DSCR4	10281	hgsc.bcm.edu	37	chr21	39493346	39493346	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcgtcaagatgattaacgAcatggacacacatgggtgag	13	9	11	8	2	2	3	1	2	1	1	3	5	2	4	0	2	1	0	0	2	2	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr21:39493346A>G	ENST00000328264.3	-	1	108	c.4T>C	c.(4-6)Tcg>Ccg	p.S2P	DSCR4_ENST00000398948.1_Missense_Mutation_p.S2P|DSCR8_ENST00000357704.4_5'Flank|DSCR8_ENST00000400477.3_5'Flank	NM_005867.2	NP_005858.1	P56555	DSCR4_HUMAN	Down syndrome critical region gene 4	2										large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	6						atgattaacgacatggacaca	0.498																																					p.S2P		Atlas-SNP	.											.	DSCR4	20	.	0			c.T4C						PASS	.						95	84	88					21																	39493346		2203	4300	6503	SO:0001583	missense	10281	exon1			TTAACGACATGGA	AB000099	CCDS33554.1	21q22.2	2012-04-19			ENSG00000184029	ENSG00000184029			3045	protein-coding gene	gene with protein product		604829				9455479	Standard	NM_005867		Approved	DCRB	uc002ywp.3	P56555	OTTHUMG00000086673	ENST00000328264.3:c.4T>C	21.37:g.39493346A>G	ENSP00000328676:p.Ser2Pro	48	0	0		58	15	0.258621	NM_005867	Q4VB31	Missense_Mutation	SNP	ENST00000328264.3	37	CCDS33554.1	.	.	.	.	.	.	.	.	.	.	A	6.972	0.549360	0.13374	.	.	ENSG00000184029	ENST00000398948;ENST00000328264	.	.	.	0.235	0.235	0.15431	.	.	.	.	.	T	0.51210	0.1661	.	.	.	0.09310	N	1	P	0.51449	0.945	P	0.57425	0.82	T	0.40156	-0.9578	6	0.87932	D	0	.	.	.	.	.	2	P56555	DSCR4_HUMAN	P	2	.	ENSP00000328676:S2P	S	-	1	0	DSCR4	38415216	0.003000	0.15002	0.015000	0.15790	0.015000	0.08874	-0.597000	0.05713	0.263000	0.21812	0.260000	0.18958	TCG	.	.	none		0.498	DSCR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000194834.1	NM_005867		G	39493346	A	G	39493346	3	3	16	1	0	0	0	0	1	0	0	0	4774	275	10	3	364	3	DSCR4	21	39493346	Missense_Mutation	SNP	A	TCGA-FF-8062-01A-11D-2210-10	11548160	39493346	8636549	146	2240											
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230348	23230348	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccatggtcgcccatggcctgCtgcgcccaatggttgcaccg	5	8	12	16	3	0	0	0	0	0	0	1	0	0	0	5	3	3	3	5	3	1	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr22:23230348C>T	ENST00000526893.1	+	1	389	c.115C>T	c.(115-117)Ctg>Ttg	p.L39L	IGLL5_ENST00000532223.2_Silent_p.L39L|IGLL5_ENST00000531372.1_Silent_p.L39L|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	39						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CCATGGCCTGCTGCGCCCAAT	0.687																																					p.L39L		Atlas-SNP	.											.	IGLL5	26	.	0			c.C115T						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			GGCCTGCTGCGCC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.115C>T	22.37:g.23230348C>T		151	0	0		118	5	0.0423729	NM_001178126		Silent	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.687	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		T	23230348	C	T	23230348	2	4	16	1	0	0	0	0	0	0	0	1	7603	796	28	2		2	IGLL5	22	23230348	Silent	SNP	C	TCGA-FF-8062-01A-11D-2210-10		23230348	28074218	147	2241			2	18		2	2	18	N	C_A	8.62135e-05
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230365	23230365	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctgcgcccaatggttgcAccgcaaagcggggacccaga	9	5	13	14	3	0	1	0	0	0	1	0	2	0	2	3	3	4	4	3	3	2	1	rs559053132	byFrequency	TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr22:23230365A>T	ENST00000526893.1	+	1	406	c.132A>T	c.(130-132)gcA>gcT	p.A44A	IGLL5_ENST00000532223.2_Silent_p.A44A|IGLL5_ENST00000531372.1_Silent_p.A44A|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	44						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CAATGGTTGCACCGCAAAGCG	0.677																																					p.H9L		Atlas-SNP	.											.	IGLL5	26	.	0			c.A26T						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			GGTTGCACCGCAA	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.132A>T	22.37:g.23230365A>T		157	0	0		114	28	0.245614	NM_001256296		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.677	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		T	23230365	A	T	23230365	2	4	16	1	0	0	0	0	0	0	0	1	7603	146	6	5		5	IGLL5	22	23230365	Silent	SNP	A	TCGA-FF-8062-01A-11D-2210-10	17	23230365	28074201	148	2242			2	18		2	2	18	N	C_A	8.62135e-05
TRIOBP	11078	hgsc.bcm.edu	37	chr22	38122289	38122289	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gacctagcgttcctggcaccCtcaccttcaccgggcagctc	6	8	9	18	2	2	0	2	0	0	0	4	1	3	0	5	2	2	4	5	2	1	3			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr22:38122289C>T	ENST00000406386.3	+	7	3981	c.3726C>T	c.(3724-3726)ccC>ccT	p.P1242P		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	1242					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)					TCCTGGCACCCTCACCTTCAC	0.701																																					p.P1242P		Atlas-SNP	.											.	TRIOBP	262	.	0			c.C3726T						PASS	.						27	35	32					22																	38122289		1912	4097	6009	SO:0001819	synonymous_variant	11078	exon7			GGCACCCTCACCT	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.3726C>T	22.37:g.38122289C>T		112	0	0		82	4	0.0487805	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Silent	SNP	ENST00000406386.3	37	CCDS43015.1																																																																																			.	.	none		0.701	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			T	38122289	C	T	38122289	2	4	16	1	0	0	0	0	0	0	0	1	16568	668	24	2		2	TRIOBP	22	38122289	Silent	SNP	C	TCGA-FF-8062-01A-11D-2210-10	14891924	38122289	13182277	149	2243											
ARHGAP8	23779	hgsc.bcm.edu	37	chr22	45221390	45221390	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagaagctccagagcctgcaCgagggccggacgccgcctcc	8	3	14	16	4	0	2	0	0	0	2	2	5	2	3	6	2	3	2	6	2	1	0	rs368897846		TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr22:45221390C>T	ENST00000389774.2	+	8	747	c.606C>T	c.(604-606)caC>caT	p.H202H	PRR5-ARHGAP8_ENST00000361473.5_Silent_p.H302H|PRR5-ARHGAP8_ENST00000352766.7_Silent_p.H381H|ARHGAP8_ENST00000336963.4_Silent_p.H171H|ARHGAP8_ENST00000517296.3_Silent_p.H381H|ARHGAP8_ENST00000356099.6_Silent_p.H171H|ARHGAP8_ENST00000389773.5_Silent_p.H293H	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	202					positive regulation of ERK1 and ERK2 cascade (GO:0070374)|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)	Rho GTPase activator activity (GO:0005100)	p.H202Q(1)|p.H207Q(1)		breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(9)|prostate(1)|skin(7)	29		all_neural(38;0.00409)|Ovarian(80;0.00976)|Glioma(61;0.0649)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0204)		AGAGCCTGCACGAGGGCCGGA	0.662																																					p.H293H		Atlas-SNP	.											PRR5-ARHGAP8,NS,carcinoma,0,2	PRR5-ARHGAP8	53	2	2	Substitution - Missense(2)	lung(2)	c.C879T						PASS	.	C	,,,	0,4404		0,0,2202	35	37	36		606,513,879,513	1	0	22		36	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ARHGAP8,PRR5-ARHGAP8	NM_001017526.1,NM_001198726.1,NM_181334.4,NM_181335.2	,,,	0,1,6500	TT,TC,CC		0.0116,0.0,0.0077	,,,	202/465,171/306,293/556,171/434	45221390	1,13001	2202	4299	6501	SO:0001819	synonymous_variant	553158	exon10			CCTGCACGAGGGC	AF177331	CCDS14060.2, CCDS33664.1, CCDS56233.1	22q13.3	2010-05-11			ENSG00000241484	ENSG00000241484		"Rho GTPase activating proteins"	677	protein-coding gene	gene with protein product		609405				10591208	Standard	NM_001198726		Approved	FLJ20185, BPGAP1		P85298	OTTHUMG00000030234	ENST00000389774.2:c.606C>T	22.37:g.45221390C>T		175	0	0		99	18	0.181818	NM_181334	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Silent	SNP	ENST00000389774.2	37	CCDS33664.1	.	.	.	.	.	.	.	.	.	.	c	4.721	0.134002	0.09032	0.0	1.16E-4	ENSG00000248405	ENST00000515632	.	.	.	4.46	1.03	0.20045	.	.	.	.	.	T	0.33498	0.0865	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.26744	-1.0094	4	.	.	.	.	8.4748	0.33007	0.3768:0.4931:0.1301:0.0	.	.	.	.	M	225	.	.	T	+	2	0	PRR5-ARHGAP8	43600054	0.233000	0.23772	0.026000	0.17262	0.101000	0.19017	0.419000	0.21247	1.055000	0.40461	0.556000	0.70494	ACG	.	.	weak		0.662	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701		T	45221390	C	T	45221390	2	4	16	1	0	0	0	0	0	0	0	1	888	535	19	1		1	ARHGAP8	22	45221390	Silent	SNP	C	TCGA-FF-8062-01A-11D-2210-10	7099101	45221390	6083176	150	2244											
PLXNB2	23654	hgsc.bcm.edu	37	chr22	50728063	50728063	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccatcttggcgtgcaccttGtccagcgggaacaggcagag	8	8	13	12	2	1	1	0	0	1	1	3	2	3	2	3	3	3	2	3	3	1	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr22:50728063G>A	ENST00000449103.1	-	3	1091	c.951C>T	c.(949-951)gaC>gaT	p.D317D	PLXNB2_ENST00000359337.4_Silent_p.D317D			O15031	PLXB2_HUMAN	plexin B2	317	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)		CGTGCACCTTGTCCAGCGGGA	0.642																																					p.D317D		Atlas-SNP	.											.	PLXNB2	172	.	0			c.C951T						PASS	.						42	51	48					22																	50728063		1949	4160	6109	SO:0001819	synonymous_variant	23654	exon3			CACCTTGTCCAGC		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.951C>T	22.37:g.50728063G>A		65	0	0		42	10	0.238095	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Silent	SNP	ENST00000449103.1	37	CCDS43035.1																																																																																			.	.	none		0.642	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401		A	50728063	G	A	50728063	2	1	16	1	0	0	0	0	0	0	0	1	12133	1368	48	2		2	PLXNB2	22	50728063	Silent	SNP	G	TCGA-FF-8062-01A-11D-2210-10	5506673	50728063	576503	151	2245											
ADM2	79924	hgsc.bcm.edu	37	chr22	50921164	50921164	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccaacactcgggcccccgAagacactcgggcccccgcag	8	2	11	20	5	0	1	0	0	0	1	2	2	0	1	5	2	1	1	5	2	2	0	rs72438078|rs3840963	byFrequency	TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chr22:50921164A>C	ENST00000395738.2	+	2	571	c.279A>C	c.(277-279)cgA>cgC	p.R93R	ADM2_ENST00000362068.2_Missense_Mutation_p.E10A|ADM2_ENST00000395737.1_Silent_p.R93R	NM_001253845.1|NM_024866.5	NP_001240774.1|NP_079142.2	Q7Z4H4	ADM2_HUMAN	adrenomedullin 2	93					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)	p.H95_R100delHSGPRR(1)		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)		CGGGCCCCCGAAGACACTCGG	0.697																																					p.R93R		Atlas-SNP	.											ADM2,rectum,carcinoma,0,2	ADM2	15	2	1	Deletion - In frame(1)	breast(1)	c.A279C						PASS	.																																			SO:0001819	synonymous_variant	79924	exon2			CCCCCGAAGACAC	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.279A>C	22.37:g.50921164A>C		47	0	0		36	10	0.277778	NM_024866	Q3LFQ0	Silent	SNP	ENST00000395738.2	37	CCDS33682.1	.	.	.	.	.	.	.	.	.	.	A	16.21	3.058801	0.55325	.	.	ENSG00000128165	ENST00000362068	.	.	.	4.21	-5.89	0.02282	.	.	.	.	.	T	0.08670	0.0215	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.35151	-0.9800	5	0.08381	T	0.77	.	0.8616	0.01194	0.2188:0.3176:0.2553:0.2083	.	.	.	.	A	10	.	ENSP00000354955:E10A	E	+	2	0	ADM2	49268030	0.000000	0.05858	0.002000	0.10522	0.479000	0.33129	-1.143000	0.03200	-0.430000	0.07318	0.368000	0.22195	GAA	.	.	none		0.697	ADM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316816.1	NM_024866		C	50921164	A	C	50921164	2	2	16	1	0	0	0	0	0	0	0	1	322	233	9	5		5	ADM2	22	50921164	Silent	SNP	A	TCGA-FF-8062-01A-11D-2210-10	193101	50921164	383402	152	2246											
TMSB4X	7114	hgsc.bcm.edu	37	chrX	12994912	12994912	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acagcgattgaacaggagaaGcaagcaggcgaatcgtaatg	16	5	13	7	3	0	2	0	1	0	1	1	5	0	2	0	2	4	3	0	2	5	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chrX:12994912G>C	ENST00000380635.1	+	3	333	c.117G>C	c.(115-117)aaG>aaC	p.K39N	TMSB4X_ENST00000380633.1_Missense_Mutation_p.K39N|TMSB4X_ENST00000451311.2_Missense_Mutation_p.K39N|TMSB4X_ENST00000380636.1_Missense_Mutation_p.K39N			P62328	TYB4_HUMAN	thymosin beta 4, X-linked	39					actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|sequestering of actin monomers (GO:0042989)	cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	poly(A) RNA binding (GO:0044822)			upper_aerodigestive_tract(1)	1						AACAGGAGAAGCAAGCAGGCG	0.393																																					p.K39N		Atlas-SNP	.											.	TMSB4X	3	.	0			c.G117C						PASS	.						56	60	59					X																	12994912		2187	4236	6423	SO:0001583	missense	7114	exon3			GGAGAAGCAAGCA		CCDS35202.1	Xp22.2	2013-05-14	2008-02-25		ENSG00000205542	ENSG00000205542			11881	protein-coding gene	gene with protein product		300159	"thymosin, beta 4, X chromosome"	TMSB4		2677145, 9381176	Standard	NM_021109		Approved	TB4X	uc004cvf.3	P62328	OTTHUMG00000021144	ENST00000380635.1:c.117G>C	X.37:g.12994912G>C	ENSP00000370009:p.Lys39Asn	71	0	0		81	15	0.185185	NM_021109	P01253|P01254|Q546P5|Q63576|Q9UE55	Missense_Mutation	SNP	ENST00000380635.1	37	CCDS35202.1	.	.	.	.	.	.	.	.	.	.	G	14.65	2.598583	0.46318	.	.	ENSG00000205542	ENST00000451311;ENST00000380636;ENST00000380635;ENST00000380633	T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22	4.8	4.8	0.61643	.	0.082982	0.46145	U	0.000307	T	0.72590	0.3479	.	.	.	0.39812	D	0.972719	P	0.44260	0.83	P	0.53062	0.717	T	0.76729	-0.2852	9	0.87932	D	0	-4.3082	8.5344	0.33355	0.1781:0.0:0.8219:0.0	.	39	P62328	TYB4_HUMAN	N	39	ENSP00000414376:K39N;ENSP00000370010:K39N;ENSP00000370009:K39N;ENSP00000370007:K39N	ENSP00000370007:K39N	K	+	3	2	TMSB4X	12904833	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.475000	0.66787	2.129000	0.65627	0.600000	0.82982	AAG	.	.	none		0.393	TMSB4X-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000055779.1	NM_021109		C	12994912	G	C	12994912	3	2	16	1	0	0	0	0	1	0	0	0	16272	962	34	4	123	4	TMSB4X	23	12994912	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10		12994912	142275648	153	2247											
ZFX	7543	hgsc.bcm.edu	37	chrX	24229366	24229366	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agatgcctcaggctttaaacGgcacgttatttccattcaca	11	12	7	11	2	2	1	2	0	0	1	3	1	3	1	2	2	2	3	2	2	3	5			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chrX:24229366G>A	ENST00000379177.1	+	11	2718	c.2291G>A	c.(2290-2292)cGg>cAg	p.R764Q	ZFX_ENST00000304543.5_Missense_Mutation_p.R764Q|ZFX_ENST00000540034.1_Missense_Mutation_p.R803Q|ZFX_ENST00000338565.3_Missense_Mutation_p.R714Q|ZFX_ENST00000379188.3_Missense_Mutation_p.R764Q|ZFX_ENST00000539115.1_Missense_Mutation_p.R535Q	NM_001178085.1|NM_003410.3	NP_001171556.1|NP_003401.2	P17010	ZFX_HUMAN	zinc finger protein, X-linked	764					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						GGCTTTAAACGGCACGTTATT	0.448																																					p.R764Q	Esophageal Squamous(20;306 562 7346 32868 37983)	Atlas-SNP	.											.	ZFX	61	.	0			c.G2291A						PASS	.						178	149	158					X																	24229366		2203	4300	6503	SO:0001583	missense	7543	exon10			TTAAACGGCACGT		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.2291G>A	X.37:g.24229366G>A	ENSP00000368475:p.Arg764Gln	205	0	0		240	53	0.220833	NM_003410	B9EG97|O43668|Q8WYJ8	Missense_Mutation	SNP	ENST00000379177.1	37	CCDS14211.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.961282	0.74016	.	.	ENSG00000005889	ENST00000539115;ENST00000379188;ENST00000535562;ENST00000379177;ENST00000304543;ENST00000540034;ENST00000338565	T;T;T;T;T;T	0.15952	2.38;2.38;2.38;2.38;2.38;2.38	5.19	5.19	0.71726	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000014	T	0.36771	0.0979	L	0.48362	1.52	0.54753	D	0.999989	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.998;0.999;0.993	T	0.03433	-1.1037	10	0.42905	T	0.14	-6.7851	18.0792	0.89437	0.0:0.0:1.0:0.0	.	803;486;764	B9EG97;F5GYV7;P17010	.;.;ZFX_HUMAN	Q	535;764;486;764;764;803;714	ENSP00000438233:R535Q;ENSP00000368486:R764Q;ENSP00000368475:R764Q;ENSP00000304985:R764Q;ENSP00000441382:R803Q;ENSP00000343384:R714Q	ENSP00000304985:R764Q	R	+	2	0	ZFX	24139287	1.000000	0.71417	0.924000	0.36721	0.948000	0.59901	9.813000	0.99286	2.291000	0.77112	0.594000	0.82650	CGG	.	.	none		0.448	ZFX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056084.1	NM_003410		A	24229366	G	A	24229366	3	1	16	1	0	0	0	0	1	0	0	0	17676	1116	39	1	2376	1	ZFX	23	24229366	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	11234454	24229366	131041194	154	2248											
DDX3X	1654	hgsc.bcm.edu	37	chrX	41206198	41206198	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttgaagctaaacaagaagtgCcgtcttggttagaaaacatg	15	10	10	6	1	1	3	0	1	1	2	1	3	1	3	1	1	4	2	1	1	8	4			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chrX:41206198C>T	ENST00000399959.2	+	15	2557	c.1702C>T	c.(1702-1704)Ccg>Tcg	p.P568S	DDX3X_ENST00000457138.2_Missense_Mutation_p.P552S|DDX3X_ENST00000478993.1_3'UTR|DDX3X_ENST00000441189.2_Intron|RN7SL15P_ENST00000582825.1_RNA	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	568	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.|Interaction with GSK3B.				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						ACAAGAAGTGCCGTCTTGGTT	0.403										HNSCC(61;0.18)																											p.P568S		Atlas-SNP	.											.	DDX3X	138	.	0			c.C1702T						PASS	.						93	90	91					X																	41206198		2172	4275	6447	SO:0001583	missense	1654	exon15			GAAGTGCCGTCTT	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.1702C>T	X.37:g.41206198C>T	ENSP00000382840:p.Pro568Ser	248	0	0		241	15	0.0622407	NM_001193416	A8K538|B4E3E8|O15536	Missense_Mutation	SNP	ENST00000399959.2	37	CCDS43931.1	.	.	.	.	.	.	.	.	.	.	C	26.9	4.782891	0.90282	.	.	ENSG00000215301	ENST00000399959;ENST00000457138	T;T	0.27402	1.67;1.69	5.28	5.28	0.74379	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.58221	0.2107	M	0.76002	2.32	0.80722	D	1	B;D;D;D	0.89917	0.002;1.0;1.0;1.0	B;D;D;D	0.97110	0.0;0.936;1.0;1.0	T	0.63404	-0.6645	10	0.87932	D	0	-8.1884	18.0954	0.89488	0.0:1.0:0.0:0.0	.	438;552;580;568	B4DLU5;B4E3E8;Q59GX6;O00571	.;.;.;DDX3X_HUMAN	S	568;552	ENSP00000382840:P568S;ENSP00000392494:P552S	ENSP00000382840:P568S	P	+	1	0	DDX3X	41091142	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.773000	0.85462	2.209000	0.71365	0.529000	0.55759	CCG	.	.	none		0.403	DDX3X-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056253.1	NM_024005		T	41206198	C	T	41206198	3	4	16	1	0	0	0	0	1	0	0	0	4360	739	26	2	1760	2	DDX3X	23	41206198	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	16976832	41206198	114064362	155	2249											
ALAS2	212	hgsc.bcm.edu	37	chrX	55041425	55041425	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acgggtgctggcaatgtagcCgcccacacagccaaaggcct	10	5	12	14	2	0	0	0	0	0	0	0	0	0	0	4	3	3	3	4	3	3	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chrX:55041425C>T	ENST00000330807.5	-	9	1329	c.1192G>A	c.(1192-1194)Ggc>Agc	p.G398S	ALAS2_ENST00000498636.1_5'UTR|ALAS2_ENST00000396198.3_Missense_Mutation_p.G385S|ALAS2_ENST00000335854.4_Missense_Mutation_p.G361S	NM_000032.4	NP_000023.2	P22557	HEM0_HUMAN	aminolevulinate, delta-, synthase 2	398					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)	GCAATGTAGCCGCCCACACAG	0.532																																					p.G398S		Atlas-SNP	.											.	ALAS2	163	.	0			c.G1192A						PASS	.						32	31	32					X																	55041425		2203	4300	6503	SO:0001583	missense	212	exon9			TGTAGCCGCCCAC		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.1192G>A	X.37:g.55041425C>T	ENSP00000332369:p.Gly398Ser	88	0	0		109	17	0.155963	NM_000032	A8K3F0|A8K6C4|Q13735|Q5JZF5|Q8N6H3	Missense_Mutation	SNP	ENST00000330807.5	37	CCDS14366.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.630705	0.87660	.	.	ENSG00000158578	ENST00000330807;ENST00000396198;ENST00000335854	D;D;D	0.98684	-5.07;-5.07;-5.07	5.64	5.64	0.86602	Aminotransferase, class I/classII (1);Tetrapyrrole biosynthesis, 5-aminolevulinic acid synthase (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.093208	0.64402	D	0.000001	D	0.99501	0.9822	H	0.97682	4.055	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.995;0.995;0.997	D	0.98150	1.0441	10	0.87932	D	0	-10.8077	17.643	0.88142	0.0:1.0:0.0:0.0	.	361;385;398	A8K6C4;Q5JZF5;P22557	.;.;HEM0_HUMAN	S	398;385;361	ENSP00000332369:G398S;ENSP00000379501:G385S;ENSP00000337131:G361S	ENSP00000332369:G398S	G	-	1	0	ALAS2	55058150	1.000000	0.71417	0.910000	0.35882	0.622000	0.37654	7.818000	0.86416	2.524000	0.85096	0.600000	0.82982	GGC	.	.	none		0.532	ALAS2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056843.3	NM_000032		T	55041425	C	T	55041425	3	4	16	1	0	0	0	0	1	0	0	0	485	652	23	1	583	1	ALAS2	23	55041425	Missense_Mutation	SNP	C	TCGA-FF-8062-01A-11D-2210-10	13835227	55041425	100229135	156	2250											
FAM123B	139285	hgsc.bcm.edu	37	chrX	63411917	63411917	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccaggttcatattgggccgtGgatacatttgggcagtttcc	7	13	12	9	1	1	0	1	0	0	0	2	1	2	1	3	4	1	3	3	4	2	6			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chrX:63411917G>A	ENST00000330258.3	-	2	1522	c.1250C>T	c.(1249-1251)cCa>cTa	p.P417L	AMER1_ENST00000403336.1_Missense_Mutation_p.P417L|AMER1_ENST00000374869.3_Missense_Mutation_p.P417L	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	417					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)									ATTGGGCCGTGGATACATTTG	0.517																																					p.P417L		Atlas-SNP	.											.	.	.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.C1250T						PASS	.						219	200	207					X																	63411917		2203	4300	6503	SO:0001583	missense	139285	exon2			GGCCGTGGATACA	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.1250C>T	X.37:g.63411917G>A	ENSP00000329117:p.Pro417Leu	198	0	0		190	35	0.184211	NM_152424	A2IB86|Q8N885	Missense_Mutation	SNP	ENST00000330258.3	37	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	G	0.352	-0.944210	0.02322	.	.	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	T;T;T	0.29917	1.55;1.55;1.55	4.64	2.68	0.31781	.	0.510469	0.18585	N	0.136891	T	0.25306	0.0615	L	0.46157	1.445	0.27490	N	0.952304	B	0.10296	0.003	B	0.14578	0.011	T	0.16453	-1.0402	10	0.44086	T	0.13	-0.1509	8.3007	0.32012	0.2172:0.0:0.7828:0.0	.	417	Q5JTC6	F123B_HUMAN	L	417	ENSP00000364003:P417L;ENSP00000329117:P417L;ENSP00000384722:P417L	ENSP00000329117:P417L	P	-	2	0	FAM123B	63328642	0.138000	0.22547	0.195000	0.23364	0.065000	0.16274	1.140000	0.31516	0.559000	0.29153	0.600000	0.82982	CCA	.	.	none		0.517	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		A	63411917	G	A	63411917	3	1	16	1	0	0	0	0	1	0	0	0	5428	1348	47	2	2161	2	FAM123B	23	63411917	Missense_Mutation	SNP	G	TCGA-FF-8062-01A-11D-2210-10	8370492	63411917	91858643	157	2251											
IRS4	8471	hgsc.bcm.edu	37	chrX	107976167	107976167	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcggcgagcgcggaggcCgcagctacaacttggctgag	7	5	17	12	5	0	1	0	1	0	0	0	3	0	2	1	4	5	4	1	4	2	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chrX:107976167C>T	ENST00000372129.2	-	1	3484	c.3408G>A	c.(3406-3408)gcG>gcA	p.A1136A	RP6-24A23.6_ENST00000563887.1_5'Flank	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	1136	Ala-rich.				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						GCGCGGAGGCCGCAGCTACAA	0.642																																					p.A1136A		Atlas-SNP	.											.	IRS4	253	.	0			c.G3408A						PASS	.						30	35	34					X																	107976167		2196	4283	6479	SO:0001819	synonymous_variant	8471	exon1			GGAGGCCGCAGCT	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.3408G>A	X.37:g.107976167C>T		21	0	0		15	7	0.466667	NM_003604		Silent	SNP	ENST00000372129.2	37	CCDS14544.1																																																																																			.	.	none		0.642	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604		T	107976167	C	T	107976167	2	4	16	1	0	0	0	0	0	0	0	1	7851	639	23	1		1	IRS4	23	107976167	Silent	SNP	C	TCGA-FF-8062-01A-11D-2210-10	44564250	107976167	47294393	158	2252											
ODZ1	10178	hgsc.bcm.edu	37	chrX	123870854	123870854	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggacccagctgttatgcagAtggactgaatcctgcgtgct	9	10	12	10	1	0	2	0	1	0	1	1	4	1	4	2	2	4	4	2	2	2	1			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chrX:123870854A>G	ENST00000371130.3	-	4	792	c.729T>C	c.(727-729)caT>caC	p.H243H	TENM1_ENST00000422452.2_Silent_p.H243H	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	243	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)										TGTTATGCAGATGGACTGAAT	0.532																																					p.H243H		Atlas-SNP	.											.	.	.	.	0			c.T729C						PASS	.						178	161	166					X																	123870854		2203	4300	6503	SO:0001819	synonymous_variant	10178	exon4			ATGCAGATGGACT	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.729T>C	X.37:g.123870854A>G		80	0	0		86	14	0.162791	NM_001163278	B2RTR5|Q5JZ17	Silent	SNP	ENST00000371130.3	37	CCDS14609.1																																																																																			.	.	none		0.532	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		G	123870854	A	G	123870854	2	3	16	1	0	0	0	0	0	0	0	1	10843	330	12	3		3	ODZ1	23	123870854	Silent	SNP	A	TCGA-FF-8062-01A-11D-2210-10	15894687	123870854	31399706	159	2253											
MAGEC1	9947	hgsc.bcm.edu	37	chrX	140995472	140995472	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttccccagagtttccctgAgagtcctcagagtcctcctg	6	12	8	15	0	2	3	1	1	1	3	7	4	7	3	6	0	0	1	6	0	0	2			TCGA-FF-8062-01A-11D-2210-10	TCGA-FF-8062-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	bd403458-5154-488b-931a-a7e737a6bf8c	1edee53e-5b0f-44c1-93e4-ad0778e1e147	g.chrX:140995472A>G	ENST00000285879.4	+	4	2568	c.2282A>G	c.(2281-2283)gAg>gGg	p.E761G	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	761										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)					AGTTTCCCTGAGAGTCCTCAG	0.542										HNSCC(15;0.026)																											p.E761G		Atlas-SNP	.											.	MAGEC1	317	.	0			c.A2282G						PASS	.						129	141	137					X																	140995472		2203	4300	6503	SO:0001583	missense	9947	exon4			TCCCTGAGAGTCC	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.2282A>G	X.37:g.140995472A>G	ENSP00000285879:p.Glu761Gly	101	0	0		82	12	0.146341	NM_005462	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	.	.	.	.	.	.	.	.	.	.	-	8.918	0.960479	0.18583	.	.	ENSG00000155495	ENST00000285879	T	0.02552	4.25	1.2	-2.4	0.06583	.	.	.	.	.	T	0.02380	0.0073	N	0.24115	0.695	0.09310	N	1	P	0.39094	0.659	B	0.42959	0.403	T	0.39375	-0.9617	9	0.72032	D	0.01	.	1.9049	0.03275	0.2872:0.2437:0.0:0.4691	.	761	O60732	MAGC1_HUMAN	G	761	ENSP00000285879:E761G	ENSP00000285879:E761G	E	+	2	0	MAGEC1	140823138	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.560000	0.05964	-0.662000	0.05338	0.235000	0.17854	GAG	.	.	none		0.542	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462		G	140995472	A	G	140995472	3	3	16	1	0	0	0	0	1	0	0	0	9189	304	11	3	2288	3	MAGEC1	23	140995472	Missense_Mutation	SNP	A	TCGA-FF-8062-01A-11D-2210-10	17124618	140995472	14275088	160	2254											
MMEL1	79258	hgsc.bcm.edu	37	chr1	2527447	2527447	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgacctctgcgagccacataCcttctcctgcgccttcttct	5	13	6	17	2	4	1	0	1	4	0	5	2	4	1	5	0	4	0	5	0	1	4			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr1:2527447C>A	ENST00000378412.3	-	15	1662		c.e15+1		MMEL1_ENST00000502556.1_Splice_Site|MMEL1_ENST00000288709.6_Splice_Site			Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1							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)		GAGCCACATACCTTCTCCTGC	0.632																																					.		Atlas-SNP	.											.	MMEL1	64	.	0			c.1500+1G>T						PASS	.						202	163	176					1																	2527447		2203	4300	6503	SO:0001630	splice_region_variant	79258	exon16			CACATACCTTCTC	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.1500+1G>T	1.37:g.2527447C>A		120	0	0		109	28	0.256881	NM_033467	B9DI79|Q495T7|Q495T8|Q5SZS6|Q96PH9	Splice_Site	SNP	ENST00000378412.3	37	CCDS30569.2	.	.	.	.	.	.	.	.	.	.	C	15.17	2.754525	0.49362	.	.	ENSG00000142606	ENST00000378411;ENST00000288709;ENST00000378412;ENST00000502556	.	.	.	5.25	5.25	0.73442	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.7647	0.88475	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MMEL1	2517307	1.000000	0.71417	0.998000	0.56505	0.154000	0.21943	7.444000	0.80532	2.606000	0.88127	0.655000	0.94253	.	.	.	none		0.632	MMEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002395.2	NM_033467	Intron	A	2527447	C	A	2527447	5	1	17	1	0	0	0	0	0	0	1	0	9655	521	18	4	878	4	MMEL1	1	2527447	Splice_Site	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10		2527447	246723174	1	2255											
TMEM54	113452	hgsc.bcm.edu	37	chr1	33363889	33363889	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accaggcctgtcttcatcagCaccttccggaagtcgcccac	8	8	8	17	2	3	0	2	0	1	0	5	1	4	1	5	2	1	1	5	2	1	2			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr1:33363889C>T	ENST00000373463.3	-	2	167	c.48G>A	c.(46-48)gtG>gtA	p.V16V	TMEM54_ENST00000475208.1_5'UTR|TMEM54_ENST00000329151.5_Silent_p.V16V	NM_033504.2	NP_277039.1	Q969K7	TMM54_HUMAN	transmembrane protein 54	16						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)				TCTTCATCAGCACCTTCCGGA	0.632																																					p.V16V		Atlas-SNP	.											.	TMEM54	12	.	0			c.G48A						PASS	.						92	80	84					1																	33363889		2203	4300	6503	SO:0001819	synonymous_variant	113452	exon2			CATCAGCACCTTC		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.48G>A	1.37:g.33363889C>T		90	0	0		68	21	0.308824	NM_033504	Q6UV18|Q8IVD0|Q9UM12	Silent	SNP	ENST00000373463.3	37	CCDS371.1																																																																																			.	.	none		0.632	TMEM54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011474.1	NM_033504		T	33363889	C	T	33363889	2	4	17	1	0	0	0	0	0	0	0	1	16195	697	25	2		2	TMEM54	1	33363889	Silent	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	30836442	33363889	215886732	2	2256											
LRRC7	57554	hgsc.bcm.edu	37	chr1	70501838	70501838	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tccagctaatgaaatgaggaTtggggaacttcacccttcat	12	11	9	9	0	2	2	2	2	0	0	3	4	3	4	2	3	2	1	2	3	3	4			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr1:70501838T>C	ENST00000035383.5	+	17	1946	c.1916T>C	c.(1915-1917)aTt>aCt	p.I639T	LRRC7_ENST00000310961.5_Missense_Mutation_p.I644T|LRRC7_ENST00000415775.2_Intron	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	639						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						GAAATGAGGATTGGGGAACTT	0.413																																					p.I639T		Atlas-SNP	.											.	LRRC7	400	.	0			c.T1916C						PASS	.						95	97	96					1																	70501838		2203	4300	6503	SO:0001583	missense	57554	exon17			TGAGGATTGGGGA		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.1916T>C	1.37:g.70501838T>C	ENSP00000035383:p.Ile639Thr	136	0	0		153	46	0.300654	NM_020794	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	ENST00000035383.5	37	CCDS645.1	.	.	.	.	.	.	.	.	.	.	T	16.22	3.061856	0.55432	.	.	ENSG00000033122	ENST00000310961;ENST00000035383;ENST00000370957	T;T	0.55052	0.54;0.63	6.06	6.06	0.98353	.	0.050444	0.85682	D	0.000000	T	0.29061	0.0722	L	0.29908	0.895	0.80722	D	1	P	0.36282	0.546	B	0.32980	0.156	T	0.25813	-1.0121	10	0.52906	T	0.07	.	15.8056	0.78506	0.0:0.0:0.0:1.0	.	639	Q96NW7	LRRC7_HUMAN	T	644;639;462	ENSP00000309245:I644T;ENSP00000035383:I639T	ENSP00000035383:I639T	I	+	2	0	LRRC7	70274426	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.426000	0.66476	2.323000	0.78572	0.528000	0.53228	ATT	.	.	none		0.413	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1	NM_020794		C	70501838	T	C	70501838	3	2	17	1	0	0	0	0	1	0	0	0	9029	1493	52	3	1982	3	LRRC7	1	70501838	Missense_Mutation	SNP	T	TCGA-FF-A7CQ-01A-11D-A382-10	37137949	70501838	178748783	3	2257											
VCAM1	7412	hgsc.bcm.edu	37	chr1	101200181	101200181	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gataatcctgaagaaaaaagCggagacaggagacacagtac	19	4	11	7	1	0	4	0	1	0	3	1	7	1	4	1	2	2	1	1	2	6	2	rs369761581		TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr1:101200181C>T	ENST00000294728.2	+	8	2017	c.1916C>T	c.(1915-1917)gCg>gTg	p.A639V	VCAM1_ENST00000370119.4_Missense_Mutation_p.A577V|VCAM1_ENST00000370115.1_Missense_Mutation_p.A440V|VCAM1_ENST00000347652.2_Missense_Mutation_p.A547V	NM_001078.3	NP_001069.1	P19320	VCAM1_HUMAN	vascular cell adhesion molecule 1	639	Ig-like C2-type 7.				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)	AAGAAAAAAGCGGAGACAGGA	0.418																																					p.A639V		Atlas-SNP	.											VCAM1,NS,carcinoma,0,1	VCAM1	111	1	0			c.C1916T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA	0,4406		0,0,2203	82	85	84		1640,1730,1916	4	0.9	1		84	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	VCAM1	NM_080682.2,NM_001199834.1,NM_001078.3	64,64,64	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	547/648,577/678,639/740	101200181	1,13005	2203	4300	6503	SO:0001583	missense	7412	exon8			AAAAAGCGGAGAC	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.1916C>T	1.37:g.101200181C>T	ENSP00000294728:p.Ala639Val	161	0	0		165	47	0.284848	NM_001078	A8K6R7|B4DKS4|E9PDD1|Q6NUP8	Missense_Mutation	SNP	ENST00000294728.2	37	CCDS773.1	.	.	.	.	.	.	.	.	.	.	C	10.02	1.237173	0.22711	0.0	1.16E-4	ENSG00000162692	ENST00000370119;ENST00000347652;ENST00000294728;ENST00000370115	T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09	5.87	4.0	0.46444	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.656371	0.16226	N	0.223805	T	0.24005	0.0581	L	0.28192	0.835	0.09310	N	1	B;P;B	0.35411	0.372;0.5;0.032	B;B;B	0.30401	0.069;0.115;0.053	T	0.07309	-1.0779	10	0.59425	D	0.04	-8.8298	5.0828	0.14666	0.1619:0.6436:0.0:0.1945	.	577;547;639	E9PDD1;P19320-2;P19320	.;.;VCAM1_HUMAN	V	577;547;639;440	ENSP00000359137:A577V;ENSP00000304611:A547V;ENSP00000294728:A639V;ENSP00000359133:A440V	ENSP00000294728:A639V	A	+	2	0	VCAM1	100972769	0.001000	0.12720	0.908000	0.35775	0.636000	0.38137	0.201000	0.17276	0.922000	0.37019	0.655000	0.94253	GCG	.	.	none		0.418	VCAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030213.1	NM_001078		T	101200181	C	T	101200181	3	4	17	1	0	0	0	0	1	0	0	0	17152	768	27	1	1946	1	VCAM1	1	101200181	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	30698343	101200181	148050440	4	2258											
CD58	965	hgsc.bcm.edu	37	chr1	117087138	117087139	+	Frame_Shift_Del	DEL	CT	CT	-																															ttttgttttttccataggacCtcttttaaaggcacattgct																										TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr1:117087138_117087139delCT	ENST00000369489.5	-	2	224_225	c.158_159delAG	c.(157-159)gagfs	p.E53fs	CD58_ENST00000457047.2_Frame_Shift_Del_p.E53fs|CD58_ENST00000369487.3_Frame_Shift_Del_p.E53fs	NM_001779.2	NP_001770.1	P19256	LFA3_HUMAN	CD58 molecule	53	Ig-like.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular response to interferon-gamma (GO:0071346)|cellular response to tumor necrosis factor (GO:0071356)|heterotypic cell-cell adhesion (GO:0034113)|leukocyte migration (GO:0050900)|positive regulation of interleukin-8 secretion (GO:2000484)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(3)|urinary_tract(1)	9	Lung SC(450;0.225)	all_cancers(81;0.000363)|all_lung(203;0.000118)|all_epithelial(167;0.000149)|Lung NSC(69;0.000577)		Lung(183;0.0086)|LUSC - Lung squamous cell carcinoma(189;0.0528)|Colorectal(144;0.0775)|all cancers(265;0.109)|Epithelial(280;0.118)|COAD - Colon adenocarcinoma(174;0.121)		TCCATAGGACCTCTTTTAAAGG	0.347																																					p.53_54del		Pindel,Atlas-Indel	.											.	CD58	40	.	0			c.159_160del						PASS	.																																			SO:0001589	frameshift_variant	965	exon2			.	BC005930	CCDS888.1, CCDS44199.1	1p13	2008-02-05	2006-03-28		ENSG00000116815	ENSG00000116815		"CD molecules"	1688	protein-coding gene	gene with protein product		153420	"CD58 antigen, (lymphocyte function-associated antigen 3)"	LFA3		9510189	Standard	NM_001144822		Approved		uc001egm.3	P19256	OTTHUMG00000022749	ENST00000369489.5:c.158_159delAG	1.37:g.117087140_117087141delCT	ENSP00000358501:p.Glu53fs	276	0	.		203	45	0.222	NM_001144822	A8K7G5|Q5U053|Q6IB65|Q96KI9	Frame_Shift_Del	DEL	ENST00000369489.5	37	CCDS888.1																																																																																			.	.	none		0.347	CD58-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059036.1	NM_001779		-	117087139	CT	-	117087138	7	5	17	1	0	1	0	1	0	0	0	0	3027	680	24	0	617	0	CD58	1	117087138	Frame_Shift_Del	DEL	CT	TCGA-FF-A7CQ-01A-11D-A382-10	15886957	117087138	132163483	5	2259											
ZNF648	127665	hgsc.bcm.edu	37	chr1	182026466	182026466	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtactttcctgctgttccgcGcttttgccaggaccgcggca	4	12	11	14	4	0	0	0	0	0	0	2	1	2	1	4	2	3	5	4	2	1	5			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr1:182026466G>A	ENST00000339948.3	-	2	887	c.680C>T	c.(679-681)gCg>gTg	p.A227V		NM_001009992.1	NP_001009992.1	Q5T619	ZN648_HUMAN	zinc finger protein 648	227					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						GCTGTTCCGCGCTTTTGCCAG	0.701																																					p.A227V	NSCLC(71;908 1374 5429 20458 35642)	Atlas-SNP	.											.	ZNF648	111	.	0			c.C680T						PASS	.						19	21	21					1																	182026466		2197	4292	6489	SO:0001583	missense	127665	exon2			TTCCGCGCTTTTG	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.680C>T	1.37:g.182026466G>A	ENSP00000344129:p.Ala227Val	69	0	0		64	20	0.3125	NM_001009992	B2RP16	Missense_Mutation	SNP	ENST00000339948.3	37	CCDS30952.1	.	.	.	.	.	.	.	.	.	.	G	9.025	0.985833	0.18889	.	.	ENSG00000179930	ENST00000339948	T	0.08008	3.14	2.77	-5.54	0.02544	.	.	.	.	.	T	0.03348	0.0097	N	0.12746	0.255	0.09310	N	1	B	0.12630	0.006	B	0.06405	0.002	T	0.39603	-0.9606	9	0.48119	T	0.1	.	1.1984	0.01880	0.3631:0.2567:0.2507:0.1295	.	227	Q5T619	ZN648_HUMAN	V	227	ENSP00000344129:A227V	ENSP00000344129:A227V	A	-	2	0	ZNF648	180293089	0.000000	0.05858	0.002000	0.10522	0.031000	0.12232	-0.098000	0.11024	-1.907000	0.01087	-0.150000	0.13652	GCG	.	.	none		0.701	ZNF648-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090794.1	XM_060597		A	182026466	G	A	182026466	3	1	17	1	0	0	0	0	1	0	0	0	18078	1087	38	1	1030	1	ZNF648	1	182026466	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	64939328	182026466	67224155	6	2260											
KCNT2	343450	hgsc.bcm.edu	37	chr1	196451484	196451484	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taagccccacaaaggtagacTtctgttcacccaaaagatat	15	9	6	11	0	2	2	1	0	1	2	2	2	2	2	3	1	1	2	3	1	6	5			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr1:196451484T>A	ENST00000294725.9	-	4	1216	c.301A>T	c.(301-303)Agt>Tgt	p.S101C	KCNT2_ENST00000367433.5_Missense_Mutation_p.S101C|KCNT2_ENST00000451324.2_De_novo_Start_InFrame|KCNT2_ENST00000367431.4_Missense_Mutation_p.S101C|KCNT2_ENST00000609185.1_Missense_Mutation_p.S101C			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	101					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						AAAGGTAGACTTCTGTTCACC	0.289																																					p.S101C		Atlas-SNP	.											.	KCNT2	243	.	0			c.A301T						PASS	.						59	55	56					1																	196451484		2202	4300	6502	SO:0001583	missense	343450	exon4			GTAGACTTCTGTT	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.301A>T	1.37:g.196451484T>A	ENSP00000294725:p.Ser101Cys	227	0	0		229	53	0.231441	NM_198503	Q3SY59|Q5VTN1|Q6ZMT3	Missense_Mutation	SNP	ENST00000294725.9	37	CCDS1384.1	.	.	.	.	.	.	.	.	.	.	T	17.74	3.464348	0.63513	.	.	ENSG00000162687	ENST00000367433;ENST00000367431;ENST00000294725	T;T;T	0.19105	2.18;2.17;2.43	5.44	4.25	0.50352	.	0.079635	0.53938	D	0.000052	T	0.26376	0.0644	L	0.42245	1.32	0.80722	D	1	D;P;P;D	0.55800	0.973;0.711;0.945;0.973	P;P;P;P	0.51550	0.474;0.673;0.673;0.474	T	0.01099	-1.1452	10	0.48119	T	0.1	-21.5096	11.4097	0.49919	0.1351:0.0:0.0:0.8649	.	101;101;101;101	A9LNM6;Q6UVM3-2;Q6UVM3-3;Q6UVM3	.;.;.;KCNT2_HUMAN	C	101	ENSP00000356403:S101C;ENSP00000356401:S101C;ENSP00000294725:S101C	ENSP00000294725:S101C	S	-	1	0	KCNT2	194718107	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.280000	0.43443	2.183000	0.69458	0.533000	0.62120	AGT	.	.	none		0.289	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503		A	196451484	T	A	196451484	3	1	17	1	0	0	0	0	1	0	0	0	8101	1609	56	5	3206	5	KCNT2	1	196451484	Missense_Mutation	SNP	T	TCGA-FF-A7CQ-01A-11D-A382-10	14425018	196451484	52799137	7	2261											
BTG2	7832	hgsc.bcm.edu	37	chr1	203276261	203276261	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aacaccactggtttcccgaaAagccgtccaagggctccggc	10	6	10	15	3	0	0	0	0	0	0	3	1	3	0	5	3	2	2	5	3	4	1			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr1:203276261A>C	ENST00000290551.4	+	2	243	c.172A>C	c.(172-174)Aag>Cag	p.K58Q	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	58					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			GTTTCCCGAAAAGCCGTCCAA	0.597																																					p.K58Q		Atlas-SNP	.											.	BTG2	16	.	0			c.A172C						PASS	.						42	44	43					1																	203276261		2203	4300	6503	SO:0001583	missense	7832	exon2			CCCGAAAAGCCGT		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.172A>C	1.37:g.203276261A>C	ENSP00000290551:p.Lys58Gln	57	0	0		63	16	0.253968	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	A	14.75	2.629108	0.46944	.	.	ENSG00000159388	ENST00000290551	T	0.23950	1.88	4.53	3.39	0.38822	Anti-proliferative protein (4);	0.065881	0.64402	D	0.000016	T	0.21881	0.0527	L	0.51853	1.615	0.45439	D	0.998419	B	0.30511	0.282	B	0.25506	0.061	T	0.03433	-1.1037	10	0.44086	T	0.13	-25.7358	10.3	0.43646	0.8338:0.1662:0.0:0.0	.	58	P78543	BTG2_HUMAN	Q	58	ENSP00000290551:K58Q	ENSP00000290551:K58Q	K	+	1	0	BTG2	201542884	1.000000	0.71417	0.630000	0.29268	0.848000	0.48234	4.716000	0.61916	0.752000	0.32923	0.260000	0.18958	AAG	.	.	none		0.597	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		C	203276261	A	C	203276261	3	2	17	1	0	0	0	0	1	0	0	0	1556	15	1	5	178	5	BTG2	1	203276261	Missense_Mutation	SNP	A	TCGA-FF-A7CQ-01A-11D-A382-10	6824777	203276261	45974360	8	2262											
RAB3GAP2	25782	hgsc.bcm.edu	37	chr1	220326665	220326665	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggtctttcccaaaaggagtGggtgtggcctcttctgtggg	5	13	15	8	0	3	0	0	0	3	0	4	1	4	1	2	5	0	0	2	5	2	2			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr1:220326665G>A	ENST00000358951.2	-	33	3845	c.3729C>T	c.(3727-3729)ccC>ccT	p.P1243P		NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN	RAB3 GTPase activating protein subunit 2 (non-catalytic)	1243					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)		CAAAAGGAGTGGGTGTGGCCT	0.468																																					p.P1243P		Atlas-SNP	.											.	RAB3GAP2	120	.	0			c.C3729T						PASS	.						211	202	205					1																	220326665		2203	4300	6503	SO:0001819	synonymous_variant	25782	exon33			AGGAGTGGGTGTG	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.3729C>T	1.37:g.220326665G>A		295	0	0		284	72	0.253521	NM_012414	A6H8V0|O75872|Q9HAB0|Q9UFJ7|Q9UQ15	Silent	SNP	ENST00000358951.2	37	CCDS31028.1																																																																																			.	.	none		0.468	RAB3GAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090205.2	NM_012414		A	220326665	G	A	220326665	2	1	17	1	0	0	0	0	0	0	0	1	12951	1335	47	2		2	RAB3GAP2	1	220326665	Silent	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	17050404	220326665	28923956	9	2263											
OR2L8	391190	hgsc.bcm.edu	37	chr1	248112303	248112303	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctgtccatgattcttctcatCttcttggacacccatctcca	7	15	4	15	0	5	1	1	1	5	0	8	2	6	2	3	1	0	0	3	1	0	4			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr1:248112303C>G	ENST00000357191.3	+	1	144	c.144C>G	c.(142-144)atC>atG	p.I48M	OR2L13_ENST00000366478.2_Intron	NM_001001963.1	NP_001001963.1	Q8NGY9	OR2L8_HUMAN	olfactory receptor, family 2, subfamily L, member 8 (gene/pseudogene)	48						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)			TTCTTCTCATCTTCTTGGACA	0.418																																					p.I48M		Atlas-SNP	.											OR2L8,right_lower_lobe,carcinoma,0,1	OR2L8	92	1	0			c.C144G						PASS	.						337	303	314					1																	248112303		2203	4300	6503	SO:0001583	missense	391190	exon1			TCTCATCTTCTTG	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.144C>G	1.37:g.248112303C>G	ENSP00000349719:p.Ile48Met	405	0	0		358	99	0.276536	NM_001001963	Q6IF03	Missense_Mutation	SNP	ENST00000357191.3	37	CCDS31101.1	.	.	.	.	.	.	.	.	.	.	C	10.44	1.351760	0.24512	.	.	ENSG00000196936	ENST00000357191	T	0.08458	3.09	1.48	1.48	0.22813	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.30135	0.0755	M	0.93106	3.38	0.09310	N	1	D	0.89917	1.0	D	0.83275	0.996	T	0.11155	-1.0599	9	0.87932	D	0	.	2.7963	0.05402	0.4476:0.3804:0.0:0.172	.	48	Q8NGY9	OR2L8_HUMAN	M	48	ENSP00000349719:I48M	ENSP00000349719:I48M	I	+	3	3	OR2L8	246178926	0.000000	0.05858	0.013000	0.15412	0.267000	0.26476	-4.229000	0.00270	0.803000	0.34113	0.298000	0.19748	ATC	.	.	none		0.418	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2			G	248112303	C	G	248112303	3	3	17	1	0	0	0	0	1	0	0	0	11018	903	32	4	146	4	OR2L8	1	248112303	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	27785638	248112303	1138318	10	2264											
AUP1	27429	hgsc.bcm.edu	37	chr2	74756626	74756626	+	5'UTR	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aggaagcagtcacccggaagCctgggggcgagaggcgaagt	11	3	18	9	3	1	1	1	0	0	1	1	5	1	3	2	5	2	1	2	5	3	0			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr2:74756626C>T	ENST00000258080.3	+	0	123				AUP1_ENST00000377526.3_Splice_Site_p.R17R|HTRA2_ENST00000352222.3_5'Flank	NM_013247.4	NP_037379.1	O43464	HTRA2_HUMAN	HtrA serine peptidase 2						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						CACCCGGAAGCCTGGGGGCGA	0.662																																					p.R17R		Atlas-SNP	.											.	AUP1	29	.	0			c.G51A						PASS	.						21	33	29					2																	74756626		2093	4161	6254	SO:0001623	5_prime_UTR_variant	550	exon2			CGGAAGCCTGGGG		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.-508C>T	2.37:g.74756626C>T		91	0	0		93	21	0.225806	NM_181575	Q9HBZ4|Q9P0Y3|Q9P0Y4	Silent	SNP	ENST00000258080.3	37	CCDS1951.1																																																																																			.	.	none		0.662	HTRA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252219.2	NM_013247		T	74756626	C	T	74756626	1	4	17	0	1	0	0	0	0	0	0	0	1220	753	26	2		2	AUP1	2	74756626	5'UTR	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10		74756626	168442747	11	2265											
SEMA4C	54910	hgsc.bcm.edu	37	chr2	97531445	97531445	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaggcgtaggtgccacagacGtacaggtgggaggcattgta	11	7	16	7	2	0	1	0	0	0	1	0	2	0	2	1	5	2	4	1	5	4	4	rs139208590	byFrequency	TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr2:97531445G>A	ENST00000305476.5	-	5	510	c.378C>T	c.(376-378)taC>taT	p.Y126Y		NM_017789.4	NP_060259.4	Q9C0C4	SEM4C_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C	126	Dominant negative effect on myogenic differentiation. {ECO:0000250}.|Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell migration in hindbrain (GO:0021535)|cerebellum development (GO:0021549)|muscle cell differentiation (GO:0042692)|neural tube closure (GO:0001843)|positive regulation of stress-activated MAPK cascade (GO:0032874)|semaphorin-plexin signaling pathway (GO:0071526)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synaptic vesicle membrane (GO:0030672)	receptor activity (GO:0004872)			NS(1)|kidney(1)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	17						TGCCACAGACGTACAGGTGGG	0.632													G|||	2	0.000399361	0.0008	0.0014	5008	,	,		20427	0.0		0.0	False		,,,				2504	0.0				p.Y126Y		Atlas-SNP	.											.	SEMA4C	56	.	0			c.C378T						PASS	.	G		3,4403	6.2+/-15.9	0,3,2200	142	126	131		378	-4.7	0.2	2	dbSNP_134	131	0,8600		0,0,4300	no	coding-synonymous	SEMA4C	NM_017789.4		0,3,6500	AA,AG,GG		0.0,0.0681,0.0231		126/834	97531445	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	54910	exon5			ACAGACGTACAGG	AB051526	CCDS2029.1	2q11.2	2013-01-11			ENSG00000168758	ENSG00000168758		"Semaphorins", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	10731	protein-coding gene	gene with protein product	"M-Sema F"	604462		SEMAI		7656991	Standard	NM_017789		Approved	Semacl1, Semaf	uc002sxh.4	Q9C0C4	OTTHUMG00000130535	ENST00000305476.5:c.378C>T	2.37:g.97531445G>A		92	0	0		93	28	0.301075	NM_017789	Q32MJ3|Q7Z5X0	Silent	SNP	ENST00000305476.5	37	CCDS2029.1																																																																																			G|1.000;A|0.000	0.000	strong		0.632	SEMA4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252957.1	NM_017789		A	97531445	G	A	97531445	2	1	17	1	0	0	0	0	0	0	0	1	14048	1140	40	1		1	SEMA4C	2	97531445	Silent	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	22774819	97531445	145667928	12	2266											
ARHGEF4	50649	hgsc.bcm.edu	37	chr2	131799003	131799003	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtaccctctgcagctggcCgagctgctcaaatacacgca	11	7	9	14	2	2	0	1	0	1	0	2	1	2	0	2	1	6	6	2	1	4	2	rs374604987		TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr2:131799003C>T	ENST00000326016.5	+	9	1824	c.1305C>T	c.(1303-1305)gcC>gcT	p.A435A	ARHGEF4_ENST00000525839.1_Silent_p.A435A|ARHGEF4_ENST00000392953.3_Silent_p.A435A|ARHGEF4_ENST00000409303.1_Silent_p.A375A|ARHGEF4_ENST00000355771.3_Silent_p.A364A|ARHGEF4_ENST00000428230.2_Intron	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	435	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				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)		TGCAGCTGGCCGAGCTGCTCA	0.607																																					p.A435A		Atlas-SNP	.											.	ARHGEF4	89	.	0			c.C1305T						PASS	.	C	,	0,4406		0,0,2203	38	35	36		1305,1305	-10.7	0	2		36	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	ARHGEF4	NM_015320.2,NM_032995.1	,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,	435/691,435/671	131799003	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	50649	exon9			GCTGGCCGAGCTG	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.1305C>T	2.37:g.131799003C>T		66	0	0		42	9	0.214286	NM_032995	Q9HDC6|Q9UPP0	Silent	SNP	ENST00000326016.5	37	CCDS2165.1	.	.	.	.	.	.	.	.	.	.	C	9.771	1.172725	0.21704	0.0	2.33E-4	ENSG00000136002	ENST00000532720	.	.	.	5.33	-10.7	0.00240	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999998	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.6524	0.17625	0.2674:0.4363:0.2018:0.0946	.	.	.	.	X	52	.	.	R	+	1	2	ARHGEF4	131515473	0.000000	0.05858	0.015000	0.15790	0.994000	0.84299	-9.239000	0.00012	-4.865000	0.00029	-0.367000	0.07326	CGA	.	.	weak		0.607	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254554.4			T	131799003	C	T	131799003	2	4	17	1	0	0	0	0	0	0	0	1	908	639	23	1		1	ARHGEF4	2	131799003	Silent	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	34267558	131799003	111400370	13	2267											
SDPR	8436	hgsc.bcm.edu	37	chr2	192700851	192700851	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttactccccctggaggtcGccttctcagcagcctcctct	5	11	8	17	1	2	0	1	0	2	0	6	1	4	1	5	2	3	2	5	2	1	2			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr2:192700851G>A	ENST00000304141.4	-	2	1405	c.1076C>T	c.(1075-1077)gCg>gTg	p.A359V		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)			CCTGGAGGTCGCCTTCTCAGC	0.567																																					p.A359V		Atlas-SNP	.											SDPR,right_upper_lobe,carcinoma,+1,1	SDPR	67	1	0			c.C1076T						scavenged	.						124	118	120					2																	192700851		2203	4300	6503	SO:0001583	missense	8436	exon2			GAGGTCGCCTTCT	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.1076C>T	2.37:g.192700851G>A	ENSP00000305675:p.Ala359Val	136	1	0.00735294		154	43	0.279221	NM_004657		Missense_Mutation	SNP	ENST00000304141.4	37	CCDS2313.1	.	.	.	.	.	.	.	.	.	.	G	10.15	1.271428	0.23221	.	.	ENSG00000168497	ENST00000304141	T	0.64438	-0.1	4.99	-8.5	0.00927	.	2.243020	0.01630	N	0.023474	T	0.46092	0.1375	L	0.44542	1.39	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.21518	-1.0243	10	0.39692	T	0.17	-0.367	2.1987	0.03917	0.3415:0.0673:0.271:0.3202	.	359	O95810	SDPR_HUMAN	V	359	ENSP00000305675:A359V	ENSP00000305675:A359V	A	-	2	0	SDPR	192409096	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.817000	0.04472	-2.474000	0.00527	-1.119000	0.02030	GCG	.	.	none		0.567	SDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334791.2	NM_004657		A	192700851	G	A	192700851	3	1	17	1	0	0	0	0	1	0	0	0	13985	1087	38	1	205	1	SDPR	2	192700851	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	60901848	192700851	50498522	14	2268											
FN1	2335	hgsc.bcm.edu	37	chr2	216257691	216257691	+	Intron	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagtaggggcactctcgccGccattaatgagagtgataac	11	9	12	9	2	1	2	0	2	1	1	2	3	1	2	2	2	1	3	2	2	4	4			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr2:216257691G>A	ENST00000359671.1	-	25	4062				FN1_ENST00000323926.6_Silent_p.G1344G|FN1_ENST00000354785.4_Silent_p.G1344G|FN1_ENST00000432072.2_Silent_p.G1344G|FN1_ENST00000443816.1_Intron|FN1_ENST00000356005.4_Intron|FN1_ENST00000421182.1_Intron|FN1_ENST00000357867.4_Intron|FN1_ENST00000446046.1_Intron|FN1_ENST00000357009.2_Intron|FN1_ENST00000345488.5_Intron|FN1_ENST00000336916.4_Intron|FN1_ENST00000346544.3_Intron			P02751	FINC_HUMAN	fibronectin 1						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)	CACTCTCGCCGCCATTAATGA	0.463																																					p.G1344G		Atlas-SNP	.											.	FN1	521	.	0			c.C4032T						PASS	.						71	71	71					2																	216257691		1917	4131	6048	SO:0001627	intron_variant	2335	exon25			CTCGCCGCCATTA		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.3797-1154C>T	2.37:g.216257691G>A		135	0	0		126	31	0.246032	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	37																																																																																				.	.	none		0.463	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		A	216257691	G	A	216257691	1	1	17	0	1	0	0	0	0	0	0	0	5970	1074	38	1		1	FN1	2	216257691	Intron	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	23556840	216257691	26941682	15	2269											
DGKD	8527	hgsc.bcm.edu	37	chr2	234363499	234363499	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gactttaacaacaagcgcgaTgagcacccagagaagtgcag	15	5	11	10	2	0	2	0	1	0	1	0	5	0	2	1	0	5	2	1	0	4	2			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr2:234363499T>A	ENST00000264057.2	+	19	2367	c.2355T>A	c.(2353-2355)gaT>gaA	p.D785E	DGKD_ENST00000409813.3_Missense_Mutation_p.D741E	NM_152879.2	NP_690618.2	Q16760	DGKD_HUMAN	diacylglycerol kinase, delta 130kDa	785					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)	ACAAGCGCGATGAGCACCCAG	0.478																																					p.D785E		Atlas-SNP	.											.	DGKD	106	.	0			c.T2355A						PASS	.						141	118	126					2																	234363499		2203	4300	6503	SO:0001583	missense	8527	exon19			GCGCGATGAGCAC	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.2355T>A	2.37:g.234363499T>A	ENSP00000264057:p.Asp785Glu	46	0	0		53	10	0.188679	NM_152879	Q14158|Q6PK55|Q8NG53	Missense_Mutation	SNP	ENST00000264057.2	37	CCDS2504.1	.	.	.	.	.	.	.	.	.	.	T	0.034	-1.317972	0.01320	.	.	ENSG00000077044	ENST00000264057;ENST00000409813	T;T	0.26223	1.75;1.75	3.57	-4.83	0.03161	Diacylglycerol kinase, accessory domain (2);	0.000000	0.64402	D	0.000003	T	0.04634	0.0126	N	0.00303	-1.675	0.35588	D	0.806807	B;B;B	0.26081	0.001;0.141;0.005	B;B;B	0.28139	0.013;0.086;0.085	T	0.36866	-0.9730	10	0.02654	T	1	.	12.6652	0.56837	0.0:0.1334:0.0:0.8666	.	669;741;785	Q53SE4;Q16760-2;Q16760	.;.;DGKD_HUMAN	E	785;741	ENSP00000264057:D785E;ENSP00000386455:D741E	ENSP00000264057:D785E	D	+	3	2	DGKD	234028238	0.000000	0.05858	0.342000	0.25602	0.228000	0.25075	-2.627000	0.00874	-1.028000	0.03321	-0.304000	0.09214	GAT	.	.	none		0.478	DGKD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257072.2	NM_003648		A	234363499	T	A	234363499	3	1	17	1	0	0	0	0	1	0	0	0	4469	1461	51	5	2453	5	DGKD	2	234363499	Missense_Mutation	SNP	T	TCGA-FF-A7CQ-01A-11D-A382-10	18105808	234363499	8835874	16	2270											
EFHB	151651	hgsc.bcm.edu	37	chr3	19974810	19974810	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ccactcctgattcaatgtttCcagcctcctttctctgttca	6	16	4	15	0	3	1	2	1	1	0	7	1	6	1	5	0	1	2	5	0	1	4			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr3:19974810C>T	ENST00000295824.9	-	1	862	c.701G>A	c.(700-702)gGa>gAa	p.G234E	EFHB_ENST00000344838.4_Missense_Mutation_p.G104E|EFHB_ENST00000498089.1_5'UTR	NM_144715.3	NP_653316.3	Q8N7U6	EFHB_HUMAN	EF-hand domain family, member B	234							calcium ion binding (GO:0005509)			breast(2)|endometrium(4)|kidney(1)|lung(17)|prostate(1)|urinary_tract(1)	26						TTCAATGTTTCCAGCCTCCTT	0.478																																					p.G234E		Atlas-SNP	.											.	EFHB	186	.	0			c.G701A						PASS	.						107	102	104					3																	19974810		2203	4300	6503	SO:0001583	missense	151651	exon1			ATGTTTCCAGCCT	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.701G>A	3.37:g.19974810C>T	ENSP00000295824:p.Gly234Glu	152	0	0		122	38	0.311475	NM_144715	A6ND25|A8MPR3|Q6ZWK9|Q8IV58|Q96LQ6	Missense_Mutation	SNP	ENST00000295824.9	37	CCDS33715.2	.	.	.	.	.	.	.	.	.	.	C	0.205	-1.041511	0.02013	.	.	ENSG00000163576	ENST00000295824;ENST00000344838;ENST00000389256	T;T;T	0.19938	2.11;2.11;2.38	5.0	-4.58	0.03410	.	0.774623	0.11571	N	0.550800	T	0.04092	0.0114	N	0.00926	-1.1	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.37663	-0.9696	9	.	.	.	-4.4587	2.2528	0.04048	0.1215:0.2865:0.123:0.469	.	104;234	Q8N7U6-3;Q8N7U6	.;EFHB_HUMAN	E	234;104;234	ENSP00000295824:G234E;ENSP00000342263:G104E;ENSP00000373908:G234E	.	G	-	2	0	EFHB	19949814	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.311000	0.08124	-0.692000	0.05128	-0.136000	0.14681	GGA	.	.	none		0.478	EFHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318673.2	NM_144715		T	19974810	C	T	19974810	3	4	17	1	0	0	0	0	1	0	0	0	4947	855	30	2	1852	2	EFHB	3	19974810	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10		19974810	178047620	17	2271											
OSBPL10	114884	hgsc.bcm.edu	37	chr3	32022624	32022624	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cggctgctgctgcggctgctGctgttgctacccccgccgcc	1	9	13	18	4	0	0	0	0	0	0	0	0	0	0	4	2	7	8	4	2	1	2			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr3:32022624G>A	ENST00000396556.2	-	1	170	c.48C>T	c.(46-48)agC>agT	p.S16S	OSBPL10_ENST00000438237.2_Silent_p.S16S|ZNF860_ENST00000360311.4_5'Flank	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	16					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)		tgcggctgctgctgttgctAC	0.791																																					p.S16S		Atlas-SNP	.											.	OSBPL10	160	.	0			c.C48T						PASS	.						2	3	2					3																	32022624		674	1482	2156	SO:0001819	synonymous_variant	114884	exon1			GCTGCTGCTGTTG	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.48C>T	3.37:g.32022624G>A		128	0	0		114	38	0.333333	NM_017784	B4E212|Q9BTU5	Silent	SNP	ENST00000396556.2	37	CCDS2651.1																																																																																			.	.	none		0.791	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2			A	32022624	G	A	32022624	2	1	17	1	0	0	0	0	0	0	0	1	11284	1310	46	2		2	OSBPL10	3	32022624	Silent	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	12047814	32022624	165999806	18	2272											
DOCK3	1795	hgsc.bcm.edu	37	chr3	51315142	51315142	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaatcgcacgctcaggaggCggtaagagggcagcggtgcc	10	4	16	11	4	1	1	1	0	0	1	2	2	1	2	1	5	2	4	1	5	2	1			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr3:51315142C>T	ENST00000266037.9	+	26	2803	c.2780C>T	c.(2779-2781)gCg>gTg	p.A927V		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	927					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.A927V(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)		GCTCAGGAGGCGGTAAGAGGG	0.547																																					p.A927V		Atlas-SNP	.											DOCK3_ENST00000266037,colon,carcinoma,0,1	DOCK3	397	1	1	Substitution - Missense(1)	large_intestine(1)	c.C2780T						PASS	.						42	44	44					3																	51315142		2052	4183	6235	SO:0001583	missense	1795	exon26			AGGAGGCGGTAAG	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.2780C>T	3.37:g.51315142C>T	ENSP00000266037:p.Ala927Val	242	0	0		255	62	0.243137	NM_004947	O15017	Missense_Mutation	SNP	ENST00000266037.9	37	CCDS46835.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.936315	0.73442	.	.	ENSG00000088538	ENST00000266037	T	0.66460	-0.21	5.25	5.25	0.73442	.	0.203179	0.53938	D	0.000060	T	0.54679	0.1873	L	0.41236	1.265	0.58432	D	0.999996	P	0.47350	0.894	B	0.32864	0.154	T	0.57808	-0.7747	10	0.29301	T	0.29	.	19.2367	0.93864	0.0:1.0:0.0:0.0	.	927	Q8IZD9	DOCK3_HUMAN	V	927	ENSP00000266037:A927V	ENSP00000266037:A927V	A	+	2	0	DOCK3	51290182	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.089000	0.71384	2.637000	0.89404	0.585000	0.79938	GCG	.	.	none		0.547	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		T	51315142	C	T	51315142	3	4	17	1	0	0	0	0	1	0	0	0	4690	768	27	1	2882	1	DOCK3	3	51315142	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	19292518	51315142	146707288	19	2273											
PCBP4	57060	hgsc.bcm.edu	37	chr3	51994890	51994890	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctccatcctcacctgctcccGgattcgctttacagtctcgc	5	12	6	18	3	2	0	1	0	1	0	7	1	5	1	4	1	2	2	4	1	1	3			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr3:51994890G>T	ENST00000461554.1	-	5	461	c.130C>A	c.(130-132)Cgg>Agg	p.R44R	PCBP4_ENST00000484633.1_Silent_p.R44R|PCBP4_ENST00000471622.1_Silent_p.R44R|RP11-155D18.14_ENST00000489595.2_Silent_p.R44R|PCBP4_ENST00000395013.3_5'UTR|PCBP4_ENST00000428823.2_Silent_p.R44R|PCBP4_ENST00000322099.7_Silent_p.R44R|RP11-155D18.12_ENST00000488257.1_RNA|PCBP4_ENST00000395014.2_5'Flank|PCBP4_ENST00000355852.2_Silent_p.R44R	NM_001174100.1	NP_001167571.1	P57723	PCBP4_HUMAN	poly(rC) binding protein 4	44	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.					cytoplasm (GO:0005737)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(2)|large_intestine(2)|lung(2)|prostate(1)|stomach(1)	8				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000534)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		ACCTGCTCCCGGATTCGCTTT	0.562																																					p.R44R		Atlas-SNP	.											.	PCBP4	35	.	0			c.C130A						PASS	.						188	203	198					3																	51994890		2203	4300	6503	SO:0001819	synonymous_variant	57060	exon4			GCTCCCGGATTCG	AF176330	CCDS2839.1, CCDS2840.1, CCDS2840.2	3p21	2013-07-16	2001-11-28		ENSG00000090097	ENSG00000090097			8652	protein-coding gene	gene with protein product	"RNA binding protein MCG10", "LYST-interacting protein", "alphaCP-4 protein"	608503	"poly(rC)-binding protein 4"			10936052	Standard	NM_033008		Approved	MCG10, LIP4	uc003dch.2	P57723	OTTHUMG00000157366	ENST00000461554.1:c.130C>A	3.37:g.51994890G>T		91	0	0		73	4	0.0547945	NM_033008	Q96AH7	Silent	SNP	ENST00000461554.1	37	CCDS2839.1																																																																																			.	.	none		0.562	PCBP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348597.1	NM_020418		T	51994890	G	T	51994890	2	4	17	1	0	0	0	0	0	0	0	1	11512	1115	39	4		4	PCBP4	3	51994890	Silent	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	679748	51994890	146027540	20	2274											
CRYBG3	131544	hgsc.bcm.edu	37	chr3	97607289	97607289	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaatgaaatcattacatcCgcttcaaatggtaagcaaat	18	10	6	7	1	2	2	2	1	0	1	3	2	3	2	1	1	2	3	1	1	6	3			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr3:97607289C>T	ENST00000182096.4	+	6	1614	c.1550C>T	c.(1549-1551)cCg>cTg	p.P517L		NM_153605.3	NP_705833.3	Q68DQ2	CRBG3_HUMAN	beta-gamma crystallin domain containing 3	2465							carbohydrate binding (GO:0030246)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(10)|stomach(1)|upper_aerodigestive_tract(2)	32						TCATTACATCCGCTTCAAATG	0.373																																					p.P2465L		Atlas-SNP	.											CRYBG3,NS,carcinoma,-1,1	CRYBG3	86	1	0			c.C7394T						scavenged	.						49	45	46					3																	97607289		1824	4083	5907	SO:0001583	missense	131544	exon9			TACATCCGCTTCA			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.1550C>T	3.37:g.97607289C>T	ENSP00000182096:p.Pro517Leu	261	2	0.00766284		276	50	0.181159	NM_153605	B4DLE8|F6VHI2|Q4G0V8|Q7Z4R9|Q86VD0|Q8N262|Q8N7F1|Q8NDQ8	Missense_Mutation	SNP	ENST00000182096.4	37		.	.	.	.	.	.	.	.	.	.	C	22.3	4.276340	0.80580	.	.	ENSG00000080200	ENST00000182096	D	0.81579	-1.51	5.54	5.54	0.83059	Beta/gamma crystallin (2);Gamma-crystallin-related (1);	0.536580	0.18498	N	0.139438	T	0.78641	0.4315	L	0.54323	1.7	0.80722	D	1	P	0.43431	0.807	B	0.39185	0.293	T	0.81762	-0.0784	10	0.72032	D	0.01	.	17.2707	0.87101	0.0:1.0:0.0:0.0	.	517	Q68DQ2	CRBG3_HUMAN	L	517	ENSP00000182096:P517L	ENSP00000182096:P517L	P	+	2	0	CRYBG3	99089979	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.933000	0.63484	2.611000	0.88343	0.655000	0.94253	CCG	.	.	none		0.373	CRYBG3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353751.1	NM_153605		T	97607289	C	T	97607289	3	4	17	1	0	0	0	0	1	0	0	0	3915	652	23	1	1572	1	CRYBG3	3	97607289	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	45612399	97607289	100415141	21	2275											
MAEA	10296	hgsc.bcm.edu	37	chr4	1326571	1326571	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagaaagcacttcagccaagCagaagggagccagctggacg	15	3	13	10	1	1	2	1	0	0	2	1	4	1	4	2	2	5	3	2	2	4	1			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr4:1326571C>T	ENST00000303400.4	+	6	746	c.683C>T	c.(682-684)gCa>gTa	p.A228V	MAEA_ENST00000505177.2_Missense_Mutation_p.A266V|MAEA_ENST00000264750.6_Missense_Mutation_p.A187V|MAEA_ENST00000505839.1_Missense_Mutation_p.A180V|MAEA_ENST00000510794.1_Missense_Mutation_p.A227V|MAEA_ENST00000512289.1_3'UTR|MAEA_ENST00000514708.1_Silent_p.S161S|MAEA_ENST00000452175.2_Missense_Mutation_p.A149V	NM_001017405.1	NP_001017405.1	Q7L5Y9	MAEA_HUMAN	macrophage erythroblast attacher	228					cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|cytoskeleton organization (GO:0007010)|enucleate erythrocyte development (GO:0048822)|erythrocyte maturation (GO:0043249)|negative regulation of myeloid cell apoptotic process (GO:0033033)|regulation of mitotic cell cycle (GO:0007346)	actomyosin contractile ring (GO:0005826)|cytoskeleton (GO:0005856)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(23;0.0201)		WF10(DB05389)	TTCAGCCAAGCAGAAGGGAGC	0.517																																					p.A228V		Atlas-SNP	.											.	MAEA	39	.	0			c.C683T						PASS	.						50	44	46					4																	1326571		2203	4300	6503	SO:0001583	missense	10296	exon6			GCCAAGCAGAAGG	AF084928	CCDS33936.1, CCDS33937.1, CCDS75090.1	4p16.3	2012-07-20			ENSG00000090316	ENSG00000090316			13731	protein-coding gene	gene with protein product	"GID complex subunit 9, FYV10 homolog (S. cerevisiae)"	606801				9763581	Standard	XM_005272243		Approved	EMP, GID9	uc003gda.3	Q7L5Y9	OTTHUMG00000160169	ENST00000303400.4:c.683C>T	4.37:g.1326571C>T	ENSP00000302830:p.Ala228Val	136	0	0		122	40	0.327869	NM_001017405	O95285|Q5JB54|Q6ZRD6|Q9BQ11|Q9H9V6|Q9H9Z4|Q9NW84	Missense_Mutation	SNP	ENST00000303400.4	37	CCDS33936.1	.	.	.	.	.	.	.	.	.	.	C	16.70	3.196643	0.58126	.	.	ENSG00000090316	ENST00000303400;ENST00000505177;ENST00000264750;ENST00000539495;ENST00000502558;ENST00000452175;ENST00000510794;ENST00000505839	T;T;T;T;T;T	0.43688	0.95;0.94;0.98;0.96;0.98;0.94	5.35	5.35	0.76521	Ran binding protein-like, CRA domain (1);	0.000000	0.85682	D	0.000000	T	0.37183	0.0994	L	0.27053	0.805	0.80722	D	1	B;B;B;B	0.29766	0.071;0.256;0.2;0.073	B;B;B;B	0.33960	0.05;0.173;0.047;0.065	T	0.17592	-1.0364	10	0.44086	T	0.13	-15.0804	19.04	0.92995	0.0:1.0:0.0:0.0	.	227;266;187;228	B4DVN3;E7ESC7;Q7L5Y9-3;Q7L5Y9	.;.;.;MAEA_HUMAN	V	228;266;187;207;160;149;227;180	ENSP00000302830:A228V;ENSP00000422215:A266V;ENSP00000264750:A187V;ENSP00000426903:A160V;ENSP00000411415:A149V;ENSP00000426807:A227V	ENSP00000264750:A187V	A	+	2	0	MAEA	1316571	1.000000	0.71417	0.963000	0.40424	0.989000	0.77384	7.433000	0.80362	2.487000	0.83934	0.655000	0.94253	GCA	.	.	none		0.517	MAEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359511.1	NM_005882		T	1326571	C	T	1326571	3	4	17	1	0	0	0	0	1	0	0	0	9162	710	25	2	705	2	MAEA	4	1326571	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10		1326571	189827705	22	2276											
PPP2R2C	5522	hgsc.bcm.edu	37	chr4	6325285	6325285	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggtgttccgatcgaacatgCggaagaagttgttgtaggcc	9	11	14	7	3	0	1	0	0	0	1	2	4	1	2	2	3	2	4	2	3	4	4			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr4:6325285C>T	ENST00000382599.4	-	9	1304	c.1088G>A	c.(1087-1089)cGc>cAc	p.R363H	PPP2R2C_ENST00000507294.1_Missense_Mutation_p.R356H|PPP2R2C_ENST00000506140.1_Missense_Mutation_p.R356H|PPP2R2C_ENST00000335585.5_Missense_Mutation_p.R363H|PPP2R2C_ENST00000515571.1_Missense_Mutation_p.R346H			Q9Y2T4	2ABG_HUMAN	protein phosphatase 2, regulatory subunit B, gamma	363					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						ATCGAACATGCGGAAGAAGTT	0.617																																					p.R363H		Atlas-SNP	.											.	PPP2R2C	63	.	0			c.G1088A						PASS	.						55	48	51					4																	6325285		2202	4300	6502	SO:0001583	missense	5522	exon9			AACATGCGGAAGA	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.1088G>A	4.37:g.6325285C>T	ENSP00000372042:p.Arg363His	93	0	0		65	17	0.261538	NM_181876	A8MSY7|B7Z3Y1|Q7Z4V7|Q8NEC4|Q9H3G7	Missense_Mutation	SNP	ENST00000382599.4	37		.	.	.	.	.	.	.	.	.	.	C	17.53	3.413163	0.62511	.	.	ENSG00000074211	ENST00000335585;ENST00000506140;ENST00000515571;ENST00000382599;ENST00000507294	T;T;T;T;T	0.32988	1.43;1.43;1.43;1.43;1.43	4.45	4.45	0.53987	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.23210	0.0561	L	0.39147	1.195	0.80722	D	1	B;P;B;B	0.35793	0.037;0.521;0.037;0.347	B;B;B;B	0.26864	0.074;0.074;0.074;0.074	T	0.05517	-1.0880	10	0.24483	T	0.36	-43.8669	16.2691	0.82606	0.0:1.0:0.0:0.0	.	356;363;346;363	B7Z3Y1;Q9Y2T4;Q9Y2T4-3;Q9Y2T4-2	.;2ABG_HUMAN;.;.	H	363;356;346;363;356	ENSP00000335083:R363H;ENSP00000423649:R356H;ENSP00000422374:R346H;ENSP00000372042:R363H;ENSP00000425247:R356H	ENSP00000335083:R363H	R	-	2	0	PPP2R2C	6376186	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.711000	0.74675	2.304000	0.77564	0.555000	0.69702	CGC	.	.	none		0.617	PPP2R2C-001	NOVEL	overlapping_uORF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206889.2	NM_181876		T	6325285	C	T	6325285	3	4	17	1	0	0	0	0	1	0	0	0	12398	768	27	1	259	1	PPP2R2C	4	6325285	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	4998714	6325285	184828991	23	2277											
PCDH7	5099	hgsc.bcm.edu	37	chr4	30724220	30724221	+	Frame_Shift_Ins	INS	-	-	C																															tggcccgcgaccgcgggcagINSccccccaagaccgacaaggc																										TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr4:30724220_30724221insC	ENST00000361762.2	+	1	2184_2185	c.1176_1177insC	c.(1177-1179)cccfs	p.P393fs	PCDH7_ENST00000543491.1_Frame_Shift_Ins_p.P393fs	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	393	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						ACCGCGGGCAGCCCCCCAAGAC	0.634																																					p.Q392fs		Pindel,Atlas-Indel	.											.	PCDH7	215	.	0			c.1176_1177insC						PASS	.																																			SO:0001589	frameshift_variant	5099	exon1			.	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.1182dupC	4.37:g.30724226_30724226dupC	ENSP00000355243:p.Pro393fs	103	0	.		86	13	0.151	NM_032457	O60246|O60247|Q4W5C4	Frame_Shift_Ins	INS	ENST00000361762.2	37	CCDS33971.1																																																																																			.	.	none		0.634	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589		C	30724221	-	C	30724220	7	5	17	1	0	1	1	0	0	0	0	0	11525	962	34	0	1178	0	PCDH7	4	30724220	Frame_Shift_Ins	INS	-	TCGA-FF-A7CQ-01A-11D-A382-10	24398935	30724220	160430056	24	2278											
IGJ	3512	hgsc.bcm.edu	37	chr4	71522967	71522967	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	caaatctggttctcaatggtGaggtgggatcagagatattc	11	12	12	6	0	3	2	2	1	2	1	5	4	3	3	0	4	0	1	0	4	3	3			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr4:71522967G>A	ENST00000254801.4	-	3	399	c.230C>T	c.(229-231)tCa>tTa	p.S77L	IGJ_ENST00000543780.1_Missense_Mutation_p.S93L|ENAM_ENST00000472903.1_Intron	NM_144646.3	NP_653247.1	P01591	IGJ_HUMAN	immunoglobulin J polypeptide, linker protein for immunoglobulin alpha and mu polypeptides	77					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)			TCTCAATGGTGAGGTGGGATC	0.308																																					p.S77L		Atlas-SNP	.											.	IGJ	13	.	0			c.C230T						PASS	.						103	96	98					4																	71522967		2203	4298	6501	SO:0001583	missense	3512	exon3			AATGGTGAGGTGG	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.230C>T	4.37:g.71522967G>A	ENSP00000254801:p.Ser77Leu	91	0	0		87	18	0.206897	NM_144646		Missense_Mutation	SNP	ENST00000254801.4	37	CCDS3545.1	.	.	.	.	.	.	.	.	.	.	G	24.2	4.506896	0.85282	.	.	ENSG00000132465	ENST00000254801;ENST00000510437;ENST00000543780;ENST00000510614;ENST00000391614	.	.	.	5.5	5.5	0.81552	.	0.000000	0.52532	D	0.000080	T	0.69387	0.3105	L	0.36672	1.1	0.42993	D	0.99449	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	T	0.72312	-0.4331	9	0.87932	D	0	.	18.181	0.89777	0.0:0.0:1.0:0.0	.	93;77	D6RHJ6;P01591	.;IGJ_HUMAN	L	77;77;93;86;93	.	ENSP00000254801:S77L	S	-	2	0	IGJ	71741831	1.000000	0.71417	0.991000	0.47740	0.919000	0.55068	4.942000	0.63547	2.588000	0.87417	0.655000	0.94253	TCA	.	.	none		0.308	IGJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252160.1	NM_144646		A	71522967	G	A	71522967	3	1	17	1	0	0	0	0	1	0	0	0	7601	1294	45	2	257	2	IGJ	4	71522967	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	40798747	71522967	119631309	25	2279											
DSPP	1834	hgsc.bcm.edu	37	chr4	88533881	88533881	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatgtcgctgttgtccaagaAgatggacctcaagtagctgg	10	10	13	8	1	1	2	1	0	0	2	3	4	2	3	2	2	1	4	2	2	4	2			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr4:88533881A>T	ENST00000282478.7	+	3	576	c.543A>T	c.(541-543)gaA>gaT	p.E181D	DSPP_ENST00000399271.1_Missense_Mutation_p.E181D|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	181					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)		TTGTCCAAGAAGATGGACCTC	0.408																																					p.E181D		Atlas-SNP	.											.	DSPP	174	.	0			c.A543T						PASS	.						113	110	111					4																	88533881		2033	4191	6224	SO:0001583	missense	1834	exon4			CCAAGAAGATGGA	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.543A>T	4.37:g.88533881A>T	ENSP00000282478:p.Glu181Asp	141	0	0		124	42	0.33871	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	A	14.33	2.504048	0.44558	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.94417	-3.42;-3.42	4.94	-0.955	0.10356	.	0.000000	0.33515	N	0.004829	D	0.86243	0.5886	L	0.34521	1.04	0.09310	N	1	B	0.27229	0.172	B	0.23716	0.048	T	0.76008	-0.3116	10	0.51188	T	0.08	-12.5992	1.7214	0.02912	0.4096:0.2621:0.0771:0.2512	.	181	Q9NZW4	DSPP_HUMAN	D	181	ENSP00000382213:E181D;ENSP00000282478:E181D	ENSP00000282478:E181D	E	+	3	2	DSPP	88752905	0.300000	0.24435	0.021000	0.16686	0.237000	0.25408	0.236000	0.17967	0.036000	0.15547	0.455000	0.32223	GAA	.	.	none		0.408	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		T	88533881	A	T	88533881	3	4	17	1	0	0	0	0	1	0	0	0	4784	69	3	5	553	5	DSPP	4	88533881	Missense_Mutation	SNP	A	TCGA-FF-A7CQ-01A-11D-A382-10	17010914	88533881	102620395	26	2280											
UBE2D3	7323	hgsc.bcm.edu	37	chr4	103720570	103720570	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tttaacatacttacttatctCtgtctgttttatagatccgt	9	20	4	8	1	2	1	0	0	2	1	4	1	3	1	1	0	3	1	1	0	6	8			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr4:103720570C>T	ENST00000453744.2	-	7	905	c.392G>A	c.(391-393)aGa>aAa	p.R131K	UBE2D3_ENST00000394801.4_Missense_Mutation_p.R131K|UBE2D3_ENST00000350435.7_Missense_Mutation_p.R125K|UBE2D3_ENST00000343106.5_Missense_Mutation_p.R131K|UBE2D3_ENST00000502404.1_Missense_Mutation_p.R102K|UBE2D3_ENST00000394803.5_Missense_Mutation_p.R131K|UBE2D3_ENST00000349311.8_Missense_Mutation_p.R131K|UBE2D3_ENST00000505207.1_Missense_Mutation_p.R102K|UBE2D3_ENST00000357194.6_Missense_Mutation_p.R133K|UBE2D3_ENST00000394804.2_Missense_Mutation_p.R131K|UBE2D3_ENST00000338145.3_Missense_Mutation_p.R131K|UBE2D3_ENST00000321805.7_Missense_Mutation_p.R131K|UBE2D3_ENST00000507845.1_Missense_Mutation_p.R102K|UBE2D3_ENST00000504211.1_Missense_Mutation_p.R102K	NM_181891.1	NP_871620.1	P61077	UB2D3_HUMAN	ubiquitin-conjugating enzyme E2D 3	131					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)		TTACTTATCTCTGTCTGTTTT	0.353																																					p.R133K		Atlas-SNP	.											.	UBE2D3	25	.	0			c.G398A						PASS	.						57	57	57					4																	103720570		2203	4299	6502	SO:0001583	missense	7323	exon6			TTATCTCTGTCTG	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.392G>A	4.37:g.103720570C>T	ENSP00000396901:p.Arg131Lys	512	1	0.00195312		505	137	0.271287	NM_181893	A6NJ93|A6NJB1|A6NM99|P47986|Q6IB88|Q6NXS4|Q8N924	Missense_Mutation	SNP	ENST00000453744.2	37	CCDS3660.1	.	.	.	.	.	.	.	.	.	.	C	16.64	3.178726	0.57692	.	.	ENSG00000109332	ENST00000453744;ENST00000394801;ENST00000394803;ENST00000394804;ENST00000343106;ENST00000321805;ENST00000350435;ENST00000338145;ENST00000349311;ENST00000504211;ENST00000357194;ENST00000505207;ENST00000507845;ENST00000502404	T;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;1.19	5.89	5.89	0.94794	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.358712	0.35525	N	0.003152	T	0.32071	0.0817	L	0.27053	0.805	0.49582	D	0.999802	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.19148	0.003;0.024;0.002	T	0.03524	-1.1028	10	0.41790	T	0.15	.	20.2361	0.98357	0.0:1.0:0.0:0.0	.	133;131;131	P61077-3;P61077;P61077-2	.;UB2D3_HUMAN;.	K	131;131;131;131;131;131;125;131;131;102;133;102;102;102	ENSP00000396901:R131K;ENSP00000378280:R131K;ENSP00000378282:R131K;ENSP00000378283:R131K;ENSP00000345285:R131K;ENSP00000318494:R131K;ENSP00000337262:R125K;ENSP00000337208:R131K;ENSP00000344069:R131K;ENSP00000426620:R102K;ENSP00000349722:R133K;ENSP00000426586:R102K;ENSP00000424359:R102K;ENSP00000421904:R102K	ENSP00000318494:R131K	R	-	2	0	UBE2D3	103939682	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.584000	0.60971	2.791000	0.96007	0.591000	0.81541	AGA	.	.	none		0.353	UBE2D3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253791.2	NM_181893		T	103720570	C	T	103720570	3	4	17	1	0	0	0	0	1	0	0	0	16865	913	32	2	112	2	UBE2D3	4	103720570	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	15186689	103720570	87433706	27	2281											
INTS12	57117	hgsc.bcm.edu	37	chr4	106621116	106621116	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttgaatgcaagaaacctagtGctttcaaaaaaatgggatca	17	10	8	6	0	2	2	2	1	0	1	2	3	2	3	1	1	3	2	1	1	7	3			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr4:106621116G>A	ENST00000451321.2	-	2	526	c.47C>T	c.(46-48)gCa>gTa	p.A16V	INTS12_ENST00000394735.1_Missense_Mutation_p.A16V|INTS12_ENST00000340139.5_Missense_Mutation_p.A16V	NM_001142471.1	NP_001135943.1	Q96CB8	INT12_HUMAN	integrator complex subunit 12	16					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)		GAAACCTAGTGCTTTCAAAAA	0.398																																					p.A16V		Atlas-SNP	.											.	INTS12	35	.	0			c.C47T						PASS	.						123	133	130					4																	106621116		2203	4300	6503	SO:0001583	missense	57117	exon3			CCTAGTGCTTTCA		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.47C>T	4.37:g.106621116G>A	ENSP00000415433:p.Ala16Val	112	0	0		113	27	0.238938	NM_020395	B2RC48|Q3B6Z3|Q9HD71	Missense_Mutation	SNP	ENST00000451321.2	37	CCDS3671.1	.	.	.	.	.	.	.	.	.	.	G	17.74	3.464285	0.63513	.	.	ENSG00000138785	ENST00000394735;ENST00000340139;ENST00000451321;ENST00000503746;ENST00000420368;ENST00000416543;ENST00000433009;ENST00000510876;ENST00000515819	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	5.9	5.9	0.94986	.	0.098342	0.64402	D	0.000001	T	0.65688	0.2715	L	0.56769	1.78	0.54753	D	0.999987	D	0.76494	0.999	P	0.62491	0.903	T	0.65647	-0.6117	10	0.72032	D	0.01	-15.9342	20.2789	0.98501	0.0:0.0:1.0:0.0	.	16	Q96CB8	INT12_HUMAN	V	16;16;16;16;16;16;16;29;16	ENSP00000378221:A16V;ENSP00000340737:A16V;ENSP00000415433:A16V;ENSP00000423618:A16V;ENSP00000412317:A16V;ENSP00000396309:A16V;ENSP00000396729:A16V;ENSP00000422856:A29V;ENSP00000422048:A16V	ENSP00000340737:A16V	A	-	2	0	INTS12	106840565	1.000000	0.71417	0.995000	0.50966	0.990000	0.78478	4.588000	0.60999	2.788000	0.95919	0.650000	0.86243	GCA	.	.	none		0.398	INTS12-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318624.1	NM_020395		A	106621116	G	A	106621116	3	1	17	1	0	0	0	0	1	0	0	0	7786	1319	46	2	1365	2	INTS12	4	106621116	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	2900546	106621116	84533160	28	2282											
FAT4	79633	hgsc.bcm.edu	37	chr4	126242688	126242688	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gagcatgtctttacctggtgGatgtttatgccatagaaaaa	12	13	10	6	0	1	1	0	0	1	1	1	3	1	2	2	2	3	2	2	2	5	5			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr4:126242688G>A	ENST00000394329.3	+	1	5135	c.5122G>A	c.(5122-5124)Gat>Aat	p.D1708N		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1708	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						TTACCTGGTGGATGTTTATGC	0.398																																					p.D1708N		Atlas-SNP	.											.	FAT4	1752	.	0			c.G5122A						PASS	.						77	74	75					4																	126242688		1888	4124	6012	SO:0001583	missense	79633	exon1			CTGGTGGATGTTT	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.5122G>A	4.37:g.126242688G>A	ENSP00000377862:p.Asp1708Asn	147	0	0		126	26	0.206349	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	29.0	4.971544	0.92919	.	.	ENSG00000196159	ENST00000394329	T	0.37411	1.2	5.27	5.27	0.74061	Cadherin (3);Cadherin-like (1);	0.000000	0.35378	U	0.003259	T	0.24044	0.0582	N	0.20845	0.615	0.80722	D	1	P	0.38922	0.651	B	0.32677	0.15	T	0.04373	-1.0956	10	0.18710	T	0.47	.	18.9064	0.92464	0.0:0.0:1.0:0.0	.	1708	Q6V0I7	FAT4_HUMAN	N	1708	ENSP00000377862:D1708N	ENSP00000377862:D1708N	D	+	1	0	FAT4	126462138	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.666000	0.83877	2.466000	0.83321	0.655000	0.94253	GAT	.	.	none		0.398	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126242688	G	A	126242688	3	1	17	1	0	0	0	0	1	0	0	0	5700	1174	41	2	5124	2	FAT4	4	126242688	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	19621572	126242688	64911588	29	2283											
POU4F2	5458	hgsc.bcm.edu	37	chr4	147560457	147560457	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctcgagcaacgctggtggTggcggcggcggcggcggcgg	4	4	22	11	8	0	0	0	0	0	0	1	1	0	0	0	9	3	3	0	9	1	0	rs530695040|rs5862765		TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr4:147560457T>C	ENST00000281321.3	+	1	413	c.165T>C	c.(163-165)ggT>ggC	p.G55G	AC093887.1_ENST00000584185.1_RNA	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN	POU class 4 homeobox 2	55	Poly-Gly.				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)					ACGCTggtggtggcggcggcg	0.761																																					p.G55G		Atlas-SNP	.											.	POU4F2	83	.	0			c.T165C						PASS	.						3	3	3					4																	147560457		1733	3503	5236	SO:0001819	synonymous_variant	5458	exon1			TGGTGGTGGCGGC	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.165T>C	4.37:g.147560457T>C		105	0	0		81	5	0.0617284	NM_004575	B1PJR6|B2RC84|Q13883|Q14987	Silent	SNP	ENST00000281321.3	37	CCDS34074.1																																																																																			.	.	none		0.761	POU4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367020.1	NM_004575		C	147560457	T	C	147560457	2	2	17	1	0	0	0	0	0	0	0	1	12288	1683	59	3		3	POU4F2	4	147560457	Silent	SNP	T	TCGA-FF-A7CQ-01A-11D-A382-10	21317769	147560457	43593819	30	2284											
NR3C2	4306	hgsc.bcm.edu	37	chr4	149002555	149002555	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tccaccttgggcagctggtcGctgatgatctccaccagcat	7	10	10	14	1	1	2	0	2	1	0	4	2	2	2	4	2	2	4	4	2	0	1			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr4:149002555G>A	ENST00000358102.3	-	9	3257	c.2895C>T	c.(2893-2895)agC>agT	p.S965S	NR3C2_ENST00000355292.3_Silent_p.S969S|NR3C2_ENST00000511528.1_Silent_p.S969S|NR3C2_ENST00000344721.4_Silent_p.S965S|NR3C2_ENST00000512865.1_Silent_p.S848S	NM_000901.4|NM_001166104.1	NP_000892.2|NP_001159576.1	P08235	MCR_HUMAN	nuclear receptor subfamily 3, group C, member 2	965	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)	p.S965S(1)		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)	GCAGCTGGTCGCTGATGATCT	0.577																																					p.S965S	Melanoma(27;428 957 40335 51025 51111)	Atlas-SNP	.											NR3C2,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	NR3C2	94	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C2895T						PASS	.						65	60	62					4																	149002555		2203	4300	6503	SO:0001819	synonymous_variant	4306	exon9			CTGGTCGCTGATG	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.2895C>T	4.37:g.149002555G>A		110	0	0		103	36	0.349515	NM_000901	B0ZBF5|B0ZBF7|Q2NKL1|Q96KQ8|Q96KQ9	Silent	SNP	ENST00000358102.3	37	CCDS3772.1																																																																																			.	.	none		0.577	NR3C2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364986.1			A	149002555	G	A	149002555	2	1	17	1	0	0	0	0	0	0	0	1	10640	1078	38	1		1	NR3C2	4	149002555	Silent	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	1442098	149002555	42151721	31	2285											
WDR70	55100	hgsc.bcm.edu	37	chr5	37703146	37703146	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caaacttgttttctttgagcGtaggactttccaaagggtgt	9	15	10	7	1	1	1	0	1	1	0	2	2	2	2	1	2	2	2	1	2	3	6			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr5:37703146G>A	ENST00000265107.4	+	13	1529	c.1373G>A	c.(1372-1374)cGt>cAt	p.R458H	RNU6-484P_ENST00000384016.1_RNA	NM_018034.2	NP_060504.1	Q9NW82	WDR70_HUMAN	WD repeat domain 70	458							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)			TTCTTTGAGCGTAGGACTTTC	0.423																																					p.R458H		Atlas-SNP	.											.	WDR70	76	.	0			c.G1373A						PASS	.						126	114	118					5																	37703146		2203	4300	6503	SO:0001583	missense	55100	exon13			TTGAGCGTAGGAC	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.1373G>A	5.37:g.37703146G>A	ENSP00000265107:p.Arg458His	188	0	0		194	44	0.226804	NM_018034	Q9H053	Missense_Mutation	SNP	ENST00000265107.4	37	CCDS34147.1	.	.	.	.	.	.	.	.	.	.	G	17.99	3.523092	0.64747	.	.	ENSG00000082068	ENST00000265107	T	0.01335	5.0	5.76	5.76	0.90799	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.246635	0.34223	N	0.004145	T	0.02533	0.0077	M	0.74647	2.275	0.80722	D	1	B	0.33841	0.428	B	0.20577	0.03	T	0.52162	-0.8612	10	0.38643	T	0.18	-35.416	14.7489	0.69511	0.0:0.0:0.8553:0.1447	.	458	Q9NW82	WDR70_HUMAN	H	458	ENSP00000265107:R458H	ENSP00000265107:R458H	R	+	2	0	WDR70	37738903	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.761000	0.68801	2.880000	0.98712	0.650000	0.86243	CGT	.	.	none		0.423	WDR70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368294.1	NM_018034		A	37703146	G	A	37703146	3	1	17	1	0	0	0	0	1	0	0	0	17336	1145	40	1	1423	1	WDR70	5	37703146	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10		37703146	143212114	32	2286											
ANKHD1	54882	hgsc.bcm.edu	37	chr5	139818110	139818110	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctgaggtactccggagactGacatcctcagttagttgtgc	8	11	11	11	1	1	3	1	2	0	1	3	4	3	3	3	2	2	3	3	2	2	3			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr5:139818110G>A	ENST00000360839.2	+	3	679	c.525G>A	c.(523-525)ctG>ctA	p.L175L	ANKHD1_ENST00000394722.3_Silent_p.L164L|ANKHD1_ENST00000297183.6_Silent_p.L175L|ANKHD1-EIF4EBP3_ENST00000532219.1_Silent_p.L175L|ANKHD1_ENST00000394723.3_Silent_p.L175L	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	175			L -> M (in dbSNP:rs17850570). {ECO:0000269|PubMed:15489334}.			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)			TCCGGAGACTGACATCCTCAG	0.473																																					p.L175L		Atlas-SNP	.											.	ANKHD1	233	.	0			c.G525A						PASS	.						212	189	197					5																	139818110		2203	4300	6503	SO:0001819	synonymous_variant	54882	exon3			GAGACTGACATCC	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.525G>A	5.37:g.139818110G>A		127	0	0		109	19	0.174312	NM_024668	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Silent	SNP	ENST00000360839.2	37	CCDS4225.1																																																																																			.	.	none		0.473	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		A	139818110	G	A	139818110	2	1	17	1	0	0	0	0	0	0	0	1	628	1277	45	2		2	ANKHD1	5	139818110	Silent	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	102114964	139818110	41097150	33	2287											
PPP2R2B	5521	hgsc.bcm.edu	37	chr5	145979852	145979852	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgggtgcctggggttctatAcctggtaagtctcgatgggg	6	12	16	7	1	2	0	0	0	2	0	3	1	2	0	2	6	2	2	2	6	3	4			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr5:145979852A>C	ENST00000394413.3	-	7	1531		c.e7+1		PPP2R2B_ENST00000508545.2_Splice_Site|PPP2R2B_ENST00000453001.1_Splice_Site|PPP2R2B_ENST00000336640.6_Splice_Site|PPP2R2B_ENST00000394409.3_Splice_Site|PPP2R2B_ENST00000394410.2_Splice_Site|CTB-99A3.1_ENST00000512730.1_RNA|PPP2R2B_ENST00000394414.1_Splice_Site|PPP2R2B_ENST00000504198.1_Splice_Site|PPP2R2B_ENST00000356826.3_Splice_Site|PPP2R2B_ENST00000530902.1_Splice_Site|PPP2R2B_ENST00000394411.4_Splice_Site			Q00005	2ABB_HUMAN	protein phosphatase 2, regulatory subunit B, beta						apoptotic process (GO:0006915)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(9)|ovary(1)|prostate(4)|skin(3)	32			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGGGTTCTATACCTGGTAAGT	0.483																																					.		Atlas-SNP	.											.	PPP2R2B	271	.	0			c.927+2T>G						PASS	.						153	150	151					5																	145979852		2203	4300	6503	SO:0001630	splice_region_variant	5521	exon9			TTCTATACCTGGT	M64930	CCDS4283.1, CCDS4284.1, CCDS43380.1, CCDS4284.2, CCDS64282.1	5q32	2013-01-10	2010-04-14		ENSG00000156475	ENSG00000156475	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits", "WD repeat domain containing"	9305	protein-coding gene	gene with protein product	"PP2A subunit B isoform beta"	604325	"spinocerebellar ataxia 12", "protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), beta isoform", "protein phosphatase 2 (formerly 2A), regulatory subunit B, beta isoform"	SCA12		1849734, 10581021	Standard	NM_181674		Approved	PR55-BETA, PR52B	uc003log.5	Q00005	OTTHUMG00000163381	ENST00000394413.3:c.960+1T>G	5.37:g.145979852A>C		210	0	0		131	36	0.274809	NM_001271948	A6NEJ2|A8K102|B3KPD0|B7Z2F2|B7Z304|D3DQF7|D3DQF8|G3V149	Splice_Site	SNP	ENST00000394413.3	37	CCDS4284.1	.	.	.	.	.	.	.	.	.	.	A	19.43	3.825202	0.71143	.	.	ENSG00000156475	ENST00000394413;ENST00000508545;ENST00000394414;ENST00000394411;ENST00000356826;ENST00000453001;ENST00000394410;ENST00000336640;ENST00000504198;ENST00000394409;ENST00000512984	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8924	0.79309	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	AC011357.1	145960045	1.000000	0.71417	0.994000	0.49952	0.838000	0.47535	9.287000	0.95975	2.219000	0.72066	0.533000	0.62120	.	.	.	none		0.483	PPP2R2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251893.2	NM_181678	Intron	C	145979852	A	C	145979852	5	2	17	1	0	0	0	0	0	0	1	0	12397	405	14	5	381	5	PPP2R2B	5	145979852	Splice_Site	SNP	A	TCGA-FF-A7CQ-01A-11D-A382-10	6161742	145979852	34935408	34	2288											
IRF4	3662	hgsc.bcm.edu	37	chr6	393206	393206	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcggcatgagcgcggtgagCtgcggcaacgggaagctccg	7	6	17	11	6	0	2	0	2	0	0	2	3	1	3	1	4	5	4	1	4	2	1			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr6:393206C>G	ENST00000380956.4	+	2	180	c.54C>G	c.(52-54)agC>agG	p.S18R	IRF4_ENST00000495137.1_Intron	NM_001195286.1|NM_002460.3	NP_001182215.1|NP_002451.2	Q15306	IRF4_HUMAN	interferon regulatory factor 4	18					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)	p.S18R(1)		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)		GCGCGGTGAGCTGCGGCAACG	0.706			T	IGH@	MM																																p.S18R		Atlas-SNP	.		Dom	yes		6	6p25-p23	3662	interferon regulatory factor 4		L	IRF4_ENST00000380956,NS,carcinoma,+2,4	IRF4	65	4	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C54G						scavenged	.						29	32	31					6																	393206		2179	4264	6443	SO:0001583	missense	3662	exon2			GGTGAGCTGCGGC	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.54C>G	6.37:g.393206C>G	ENSP00000370343:p.Ser18Arg	89	1	0.011236		67	22	0.328358	NM_001195286	Q5VUI7|Q99660	Missense_Mutation	SNP	ENST00000380956.4	37	CCDS4469.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.064151	0.76187	.	.	ENSG00000137265	ENST00000380956;ENST00000412334	D	0.97752	-4.52	4.48	3.51	0.40186	Interferon regulatory factor DNA-binding domain (1);	0.429735	0.29579	N	0.011746	D	0.96775	0.8947	L	0.53729	1.69	0.58432	D	0.999998	D;D;D	0.89917	0.996;1.0;1.0	P;D;D	0.69824	0.893;0.966;0.959	D	0.94663	0.7850	10	0.27785	T	0.31	-18.6481	7.4654	0.27318	0.0:0.7502:0.0:0.2498	.	18;18;18	F2Z3D5;Q15306-2;Q15306	.;.;IRF4_HUMAN	R	18;48	ENSP00000370343:S18R	ENSP00000370343:S18R	S	+	3	2	IRF4	338206	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	3.305000	0.51873	2.339000	0.79563	0.306000	0.20318	AGC	.	.	none		0.706	IRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043638.1			G	393206	C	G	393206	3	3	17	1	0	0	0	0	1	0	0	0	7841	796	28	4	56	4	IRF4	6	393206	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10		393206	170721861	35	2289			1	19		4	3	155	N	G_C_A	2.013301e-07
IRF4	3662	hgsc.bcm.edu	37	chr6	393328	393328	+	Missense_Mutation	SNP	A	A	G																															cccctggaagcacgcgggcaAgcaggactacaaccgcgagg																										TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr6:393328A>G	ENST00000380956.4	+	2	302	c.176A>G	c.(175-177)aAg>aGg	p.K59R	IRF4_ENST00000495137.1_Intron	NM_001195286.1|NM_002460.3	NP_001182215.1|NP_002451.2	Q15306	IRF4_HUMAN	interferon regulatory factor 4	59					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)		CACGCGGGCAAGCAGGACTAC	0.692			T	IGH@	MM																																p.K59R		Atlas-SNP	.		Dom	yes		6	6p25-p23	3662	interferon regulatory factor 4		L	.	IRF4	65	.	0			c.A176G						PASS	.						29	26	27					6																	393328		2201	4300	6501	SO:0001583	missense	3662	exon2			CGGGCAAGCAGGA	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.176A>G	6.37:g.393328A>G	ENSP00000370343:p.Lys59Arg	83	0	0		68	20	0.294118	NM_001195286	Q5VUI7|Q99660	Missense_Mutation	SNP	ENST00000380956.4	37	CCDS4469.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.376789	0.82682	.	.	ENSG00000137265	ENST00000380956;ENST00000412334	D	0.97328	-4.34	4.58	4.58	0.56647	Interferon regulatory factor, conserved site (1);Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (4);	0.097786	0.64402	D	0.000001	D	0.94318	0.8174	L	0.27944	0.81	0.80722	D	1	P;P;D	0.54207	0.93;0.914;0.965	D;D;D	0.69307	0.945;0.909;0.963	D	0.92833	0.6282	10	0.05959	T	0.93	-29.4556	14.1683	0.65493	1.0:0.0:0.0:0.0	.	59;59;59	F2Z3D5;Q15306-2;Q15306	.;.;IRF4_HUMAN	R	59;89	ENSP00000370343:K59R	ENSP00000370343:K59R	K	+	2	0	IRF4	338328	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.258000	0.89853	1.943000	0.56356	0.254000	0.18369	AAG	.	.	none		0.692	IRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043638.1			G	393328	A	G	393328	3	3	17	1	0	0	0	0	1	0	0	0	7841	72	3	3	178	3	IRF4	6	393328	Missense_Mutation	SNP	A	TCGA-FF-A7CQ-01A-11D-A382-10	122	393328	170721739	36	2290	31	2	1	19		4	3	155	N	G_C_A	2.013301e-07
IRF4	3662	hgsc.bcm.edu	37	chr6	393329	393329	+	Silent	SNP	G	G	A																															ccctggaagcacgcgggcaaGcaggactacaaccgcgagga																										TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr6:393329G>A	ENST00000380956.4	+	2	303	c.177G>A	c.(175-177)aaG>aaA	p.K59K	IRF4_ENST00000495137.1_Intron	NM_001195286.1|NM_002460.3	NP_001182215.1|NP_002451.2	Q15306	IRF4_HUMAN	interferon regulatory factor 4	59					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)		ACGCGGGCAAGCAGGACTACA	0.692			T	IGH@	MM																																p.K59K		Atlas-SNP	.		Dom	yes		6	6p25-p23	3662	interferon regulatory factor 4		L	.	IRF4	65	.	0			c.G177A						PASS	.						29	26	27					6																	393329		2201	4300	6501	SO:0001819	synonymous_variant	3662	exon2			GGGCAAGCAGGAC	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.177G>A	6.37:g.393329G>A		81	0	0		68	19	0.279412	NM_001195286	Q5VUI7|Q99660	Silent	SNP	ENST00000380956.4	37	CCDS4469.1																																																																																			.	.	none		0.692	IRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043638.1			A	393329	G	A	393329	2	1	17	1	0	0	0	0	0	0	0	1	7841	962	34	2		2	IRF4	6	393329	Silent	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	1	393329	170721738	37	2291	31	2	1	19		4	3	155	N	G_C_A	2.013301e-07
IRF4	3662	hgsc.bcm.edu	37	chr6	393360	393360	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accgcgaggaggacgccgcgCtcttcaaggtctccggcctc	6	6	13	16	6	3	0	1	0	2	0	5	3	3	2	4	4	0	1	4	4	1	1			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr6:393360C>G	ENST00000380956.4	+	2	334	c.208C>G	c.(208-210)Ctc>Gtc	p.L70V	IRF4_ENST00000495137.1_Intron	NM_001195286.1|NM_002460.3	NP_001182215.1|NP_002451.2	Q15306	IRF4_HUMAN	interferon regulatory factor 4	70					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)		GGACGCCGCGCTCTTCAAGGT	0.731			T	IGH@	MM																																p.L70V		Atlas-SNP	.		Dom	yes		6	6p25-p23	3662	interferon regulatory factor 4		L	.	IRF4	65	.	0			c.C208G						PASS	.						16	15	15					6																	393360		2194	4295	6489	SO:0001583	missense	3662	exon2			GCCGCGCTCTTCA	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.208C>G	6.37:g.393360C>G	ENSP00000370343:p.Leu70Val	57	0	0		46	14	0.304348	NM_001195286	Q5VUI7|Q99660	Missense_Mutation	SNP	ENST00000380956.4	37	CCDS4469.1	.	.	.	.	.	.	.	.	.	.	C	32	5.127190	0.94429	.	.	ENSG00000137265	ENST00000380956;ENST00000412334	D	0.97791	-4.54	4.58	4.58	0.56647	Interferon regulatory factor, conserved site (1);Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (4);	0.117485	0.64402	D	0.000014	D	0.97266	0.9106	L	0.37800	1.135	0.80722	D	1	P;P;P	0.41597	0.756;0.713;0.701	P;P;P	0.59948	0.866;0.789;0.866	D	0.97866	1.0283	10	0.48119	T	0.1	-23.7921	17.6301	0.88104	0.0:1.0:0.0:0.0	.	70;70;70	F2Z3D5;Q15306-2;Q15306	.;.;IRF4_HUMAN	V	70;100	ENSP00000370343:L70V	ENSP00000370343:L70V	L	+	1	0	IRF4	338360	1.000000	0.71417	0.997000	0.53966	0.957000	0.61999	5.239000	0.65371	2.399000	0.81585	0.306000	0.20318	CTC	.	.	none		0.731	IRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043638.1			G	393360	C	G	393360	3	3	17	1	0	0	0	0	1	0	0	0	7841	797	28	4	210	4	IRF4	6	393360	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	31	393360	170721707	38	2292			1	19		4	3	155	N	G_C_A	2.013301e-07
FOXC1	2296	hgsc.bcm.edu	37	chr6	1610821	1610821	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccggcccccatgagcgtgtaCtcgcaccctgcgcacgccga	6	5	11	19	6	0	1	0	1	0	0	1	2	0	1	5	1	3	3	5	1	1	1	rs372857241		TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr6:1610821C>G	ENST00000380874.2	+	1	141	c.141C>G	c.(139-141)taC>taG	p.Y47*		NM_001453.2	NP_001444.2	Q12948	FOXC1_HUMAN	forkhead box C1	47					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)		TGAGCGTGTACTCGCACCCTG	0.751																																					p.Y47X	Pancreas(133;719 1821 3197 26645 35015)	Atlas-SNP	.											.	FOXC1	19	.	0			c.C141G						PASS	.						10	11	10					6																	1610821		2182	4269	6451	SO:0001587	stop_gained	2296	exon1			CGTGTACTCGCAC	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.141C>G	6.37:g.1610821C>G	ENSP00000370256:p.Tyr47*	39	0	0		32	10	0.3125	NM_001453	Q86UP7|Q9BYM1|Q9NUE5|Q9UDD0|Q9UP06	Nonsense_Mutation	SNP	ENST00000380874.2	37	CCDS4473.1	.	.	.	.	.	.	.	.	.	.	c	36	5.748035	0.96882	.	.	ENSG00000054598	ENST00000541209;ENST00000380874	.	.	.	3.33	3.33	0.38152	.	0.000000	0.64402	U	0.000005	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.7782	0.69746	0.0:1.0:0.0:0.0	.	.	.	.	X	47	.	ENSP00000370256:Y47X	Y	+	3	2	FOXC1	1555820	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	1.697000	0.37784	1.842000	0.53543	0.457000	0.33378	TAC	.	.	alt		0.751	FOXC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043450.1			G	1610821	C	G	1610821	4	3	17	1	0	0	0	0	0	1	0	0	6002	576	20	4	143	4	FOXC1	6	1610821	Nonsense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	1217461	1610821	169504246	39	2293											
HIST1H2BC	8347	hgsc.bcm.edu	37	chr6	26123915	26123915	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggaagcctcgcccgcgatgCgctcaaatatgtcgttaacg	9	8	12	12	6	1	0	1	0	0	0	3	2	1	1	2	1	3	2	2	1	4	2			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr6:26123915C>T	ENST00000314332.5	-	1	223	c.218G>A	c.(217-219)cGc>cAc	p.R73H	HIST1H2BC_ENST00000396984.1_Missense_Mutation_p.R73H|HIST1H2AC_ENST00000377791.2_5'Flank|HIST1H2AC_ENST00000602637.1_5'Flank			P62807	H2B1C_HUMAN	histone cluster 1, H2bc	73					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)			NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)	16						GCCCGCGATGCGCTCAAATAT	0.577																																					p.R73H		Atlas-SNP	.											.	HIST1H2BC	35	.	0			c.G218A						PASS	.						125	122	123					6																	26123915		2203	4300	6503	SO:0001583	missense	8347	exon1			GCGATGCGCTCAA	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.218G>A	6.37:g.26123915C>T	ENSP00000321744:p.Arg73His	126	0	0		109	11	0.100917	NM_003526	P02278|Q3B872|Q4VB69|Q93078|Q93080	Missense_Mutation	SNP	ENST00000314332.5	37	CCDS4584.1	.	.	.	.	.	.	.	.	.	.	.	18.43	3.621236	0.66787	.	.	ENSG00000180596	ENST00000314332;ENST00000396984	T;T	0.69561	-0.41;-0.41	5.61	5.61	0.85477	Histone-fold (2);Histone core (1);	.	.	.	.	T	0.50650	0.1628	.	.	.	0.47862	D	0.999531	B	0.23316	0.083	B	0.19148	0.024	T	0.49093	-0.8975	8	0.49607	T	0.09	.	18.9929	0.92801	0.0:1.0:0.0:0.0	.	73	P62807	H2B1C_HUMAN	H	73	ENSP00000321744:R73H;ENSP00000380180:R73H	ENSP00000321744:R73H	R	-	2	0	HIST1H2BC	26231894	1.000000	0.71417	1.000000	0.80357	0.359000	0.29487	7.638000	0.83328	2.799000	0.96334	0.650000	0.86243	CGC	.	.	none		0.577	HIST1H2BC-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468022.1	NM_003526		T	26123915	C	T	26123915	3	4	17	1	0	0	0	0	1	0	0	0	7151	768	27	1	166	1	HIST1H2BC	6	26123915	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	24513094	26123915	144991152	40	2294											
HIST1H1E	3008	hgsc.bcm.edu	37	chr6	26157108	26157108	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggcgaagaagccggctgcaGctgctggagccaaaaaagcg	13	3	15	10	3	0	1	0	0	0	1	0	3	0	2	2	3	6	4	2	3	5	0	rs201935674	byFrequency	TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr6:26157108G>A	ENST00000304218.3	+	1	550	c.490G>A	c.(490-492)Gct>Act	p.A164T	HIST1H2BD_ENST00000377777.4_5'Flank|HIST1H2BD_ENST00000289316.2_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	164					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)	p.A164P(1)		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						GCCGGCTGCAGCTGCTGGAGC	0.597													G|||	2	0.000399361	0.0	0.0	5008	,	,		12111	0.0		0.002	False		,,,				2504	0.0				p.A164T		Atlas-SNP	.											HIST1H1E,NS,lymphoid_neoplasm,-1,3	HIST1H1E	69	3	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G490A						PASS	.						15	21	19					6																	26157108		2192	4287	6479	SO:0001583	missense	3008	exon1			GCTGCAGCTGCTG	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.490G>A	6.37:g.26157108G>A	ENSP00000307705:p.Ala164Thr	102	0	0		70	20	0.285714	NM_005321	Q4VB25	Missense_Mutation	SNP	ENST00000304218.3	37	CCDS4586.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	.	13.33	2.206374	0.39003	.	.	ENSG00000168298	ENST00000304218	T	0.04862	3.54	5.49	5.49	0.81192	.	0.133164	0.49916	D	0.000129	T	0.04543	0.0124	L	0.37697	1.125	0.49798	D	0.99982	P	0.48911	0.917	P	0.51297	0.665	T	0.11324	-1.0592	10	0.02654	T	1	-2.5382	18.7205	0.91691	0.0:0.0:1.0:0.0	.	164	P10412	H14_HUMAN	T	164	ENSP00000307705:A164T	ENSP00000307705:A164T	A	+	1	0	HIST1H1E	26265087	0.970000	0.33590	0.822000	0.32727	0.970000	0.65996	2.285000	0.43487	2.723000	0.93209	0.655000	0.94253	GCT	G|0.999;A|0.001	0.001	strong		0.597	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321		A	26157108	G	A	26157108	3	1	17	1	0	0	0	0	1	0	0	0	7135	971	34	2	492	2	HIST1H1E	6	26157108	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	33193	26157108	144957959	41	2295											
HIST1H2AI	8329	hgsc.bcm.edu	37	chr6	27776072	27776072	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccgggcttcagtttcccgtaGgccgagtgcatcgcctgctc	4	10	12	15	4	1	0	1	0	0	0	4	1	2	0	4	2	2	5	4	2	1	3			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr6:27776072G>A	ENST00000358739.3	+	1	174	c.85G>A	c.(85-87)Ggc>Agc	p.G29S	HIST1H2BL_ENST00000377401.2_5'Flank|HIST1H3H_ENST00000369163.2_5'Flank	NM_003509.2	NP_003500.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2ai	29						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)			lung(3)	3						GTTTCCCGTAGGCCGAGTGCA	0.652																																					p.G29S		Atlas-SNP	.											.	HIST1H2AI	9	.	0			c.G85A						PASS	.						30	37	34					6																	27776072		2184	4292	6476	SO:0001583	missense	8329	exon1			CCCGTAGGCCGAG	Z83742	CCDS4626.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000196747	ENSG00000196747		"Histones / Replication-dependent"	4725	protein-coding gene	gene with protein product		602787	"H2A histone family, member C", "histone 1, H2ai"	H2AFC		9439656, 12408966	Standard	NM_003509		Approved	H2A/c		P0C0S8	OTTHUMG00000014484	ENST00000358739.3:c.85G>A	6.37:g.27776072G>A	ENSP00000351589:p.Gly29Ser	224	0	0		272	20	0.0735294	NM_003509	P02261|Q2M1R2|Q76PA6	Missense_Mutation	SNP	ENST00000358739.3	37	CCDS4626.1	.	.	.	.	.	.	.	.	.	.	.	18.23	3.577988	0.65878	.	.	ENSG00000196747	ENST00000358739	T	0.44083	0.93	4.53	4.53	0.55603	.	0.000000	0.41001	D	0.000970	T	0.54647	0.1871	.	.	.	0.47905	D	0.999543	.	.	.	.	.	.	T	0.61128	-0.7125	7	0.87932	D	0	.	17.2005	0.86904	0.0:0.0:1.0:0.0	.	.	.	.	S	29	ENSP00000351589:G29S	ENSP00000351589:G29S	G	+	1	0	HIST1H2AI	27884051	1.000000	0.71417	0.998000	0.56505	0.144000	0.21451	8.900000	0.92551	2.458000	0.83093	0.556000	0.70494	GGC	.	.	none		0.652	HIST1H2AI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040152.1	NM_003509		A	27776072	G	A	27776072	3	1	17	1	0	0	0	0	1	0	0	0	7144	1000	35	2	87	2	HIST1H2AI	6	27776072	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	1618964	27776072	143338995	42	2296											
TNF	7124	hgsc.bcm.edu	37	chr6	31544592	31544592	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gcctgtagcccatgttgtagGtaagagctctgaggatgtgt	8	12	14	7	0	1	2	0	1	1	1	1	3	1	3	2	2	2	5	2	2	3	4			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr6:31544592G>C	ENST00000449264.2	+	3	455		c.e3+1			NM_000594.3	NP_000585.2	P01375	TNFA_HUMAN	tumor necrosis factor						activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|calcium-mediated signaling (GO:0019722)|cell activation (GO:0001775)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nicotine (GO:0071316)|cellular response to organic cyclic compound (GO:0071407)|chronic inflammatory response to antigenic stimulus (GO:0002439)|defense response to Gram-positive bacterium (GO:0050830)|embryonic digestive tract development (GO:0048566)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|glucose metabolic process (GO:0006006)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|JNK cascade (GO:0007254)|leukocyte tethering or rolling (GO:0050901)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|necroptotic signaling pathway (GO:0097527)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of branching involved in lung morphogenesis (GO:0061048)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of glucose import (GO:0046325)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of L-glutamate transport (GO:0002037)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of lipid storage (GO:0010888)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein complex disassembly (GO:0043242)|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)|organ morphogenesis (GO:0009887)|osteoclast differentiation (GO:0030316)|positive regulation of apoptotic process (GO:0043065)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of chronic inflammatory response to antigenic stimulus (GO:0002876)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fever generation (GO:0031622)|positive regulation of gene expression (GO:0010628)|positive regulation of hair follicle development (GO:0051798)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|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 interferon-gamma production (GO:0032729)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mitosis (GO:0045840)|positive regulation of mononuclear cell migration (GO:0071677)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of podosome assembly (GO:0071803)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein transport (GO:0051222)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of synaptic transmission (GO:0050806)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translational initiation by iron (GO:0045994)|positive regulation of vitamin D biosynthetic process (GO:0060557)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|receptor biosynthetic process (GO:0032800)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of immunoglobulin secretion (GO:0051023)|regulation of insulin secretion (GO:0050796)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to salt stress (GO:0009651)|response to virus (GO:0009615)|sequestering of triglyceride (GO:0030730)|skeletal muscle contraction (GO:0003009)|transformed cell apoptotic process (GO:0006927)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	cytokine activity (GO:0005125)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|transcription regulatory region DNA binding (GO:0044212)|tumor necrosis factor receptor binding (GO:0005164)			large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|skin(3)	8		Ovarian(999;0.00556)			Adalimumab(DB00051)|Amrinone(DB01427)|Certolizumab pegol(DB08904)|Chloroquine(DB00608)|Clenbuterol(DB01407)|Epinephrine(DB00668)|Etanercept(DB00005)|Glucosamine(DB01296)|golimumab(DB06674)|Infliximab(DB00065)|Pomalidomide(DB08910)|Pranlukast(DB01411)|Pseudoephedrine(DB00852)|Thalidomide(DB01041)	CATGTTGTAGGTAAGAGCTCT	0.483									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of																												.		Atlas-SNP	.											.	TNF	15	.	0			c.280+1G>C						PASS	.						192	191	191					6																	31544592		1511	2709	4220	SO:0001630	splice_region_variant	7124	exon3	Familial Cancer Database	incl.: Familial Head and Neck Cancer	TTGTAGGTAAGAG	X02910	CCDS4702.1	6p21.3	2013-05-22	2010-05-04		ENSG00000232810	ENSG00000232810		"Tumor necrosis factor (ligand) superfamily"	11892	protein-coding gene	gene with protein product	"TNF superfamily, member 2"	191160	"tumor necrosis factor (TNF superfamily, member 2)"	TNFA		2413547, 6392892	Standard	NM_000594		Approved	TNFSF2, DIF, TNF-alpha	uc003nui.4	P01375	OTTHUMG00000031194	ENST00000449264.2:c.280+1G>C	6.37:g.31544592G>C		243	0	0		164	61	0.371951	NM_000594	O43647|Q9P1Q2|Q9UIV3	Splice_Site	SNP	ENST00000449264.2	37	CCDS4702.1	.	.	.	.	.	.	.	.	.	.	G	18.64	3.666938	0.67814	.	.	ENSG00000232810	ENST00000449264	.	.	.	4.77	4.77	0.60923	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1679	0.59581	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TNF	31652571	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.530000	0.60595	2.490000	0.84030	0.655000	0.94253	.	.	.	none		0.483	TNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076390.2		Intron	C	31544592	G	C	31544592	5	2	17	1	0	0	0	0	0	0	1	0	16286	1275	44	4	291	4	TNF	6	31544592	Splice_Site	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	3768520	31544592	139570475	43	2297											
C6orf48	50854	hgsc.bcm.edu	37	chr6	31805113	31805113	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaatctccccctcatggagaGaagctttgtatggctgtcat	9	12	10	10	0	3	1	2	0	1	1	4	4	3	2	2	2	1	3	2	2	3	2			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr6:31805113G>A	ENST00000375640.3	+	3	735	c.8G>A	c.(7-9)aGa>aAa	p.R3K	C6orf48_ENST00000375638.3_Missense_Mutation_p.R3K|C6orf48_ENST00000395788.3_Missense_Mutation_p.R3K|SNORD48_ENST00000364953.1_RNA|C6orf48_ENST00000375633.1_Missense_Mutation_p.R3K|C6orf48_ENST00000375639.2_Missense_Mutation_p.R3K|C6orf48_ENST00000375642.2_Missense_Mutation_p.R3K|C6orf48_ENST00000395789.1_Missense_Mutation_p.R3K|SNORD52_ENST00000364884.1_RNA|C6orf48_ENST00000375641.2_Missense_Mutation_p.R3K|C6orf48_ENST00000375635.2_Missense_Mutation_p.R3K	NM_001040438.1	NP_001035528.1	Q9UBA6	G8_HUMAN	chromosome 6 open reading frame 48	3										breast(1)|large_intestine(1)|lung(1)|skin(1)	4						CTCATGGAGAGAAGCTTTGTA	0.502																																					p.R3K		Atlas-SNP	.											.	C6orf48	8	.	0			c.G8A						PASS	.						219	180	193					6																	31805113		2203	4300	6503	SO:0001583	missense	50854	exon4			TGGAGAGAAGCTT	AJ249732	CCDS34416.1	6p21.33	2011-12-13			ENSG00000204387	ENSG00000204387			19078	protein-coding gene	gene with protein product		605447				8096093	Standard	NM_001287483		Approved	D6S57, G8	uc003rjy.2	Q9UBA6	OTTHUMG00000031175	ENST00000375640.3:c.8G>A	6.37:g.31805113G>A	ENSP00000364791:p.Arg3Lys	258	0	0		258	69	0.267442	NM_001040437	Q9BW21|Q9UBA7|Q9UBA8	Missense_Mutation	SNP	ENST00000375640.3	37	CCDS34416.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.554|8.554	0.876186|0.876186	0.17395|0.17395	.|.	.|.	ENSG00000204387|ENSG00000204387	ENST00000375636|ENST00000375640;ENST00000375641;ENST00000375639;ENST00000375638;ENST00000375635;ENST00000375642;ENST00000395789;ENST00000375633;ENST00000395788	.|.	.|.	.|.	3.29|3.29	-1.64|-1.64	0.08318|0.08318	.|.	.|.	.|.	.|.	.|.	T|T	0.11750|0.11750	0.0286|0.0286	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|B	.|0.14438	.|0.01	.|B	.|0.06405	.|0.002	T|T	0.35895|0.35895	-0.9770|-0.9770	4|7	.|0.87932	.|D	.|0	.|.	5.6811|5.6811	0.17776|0.17776	0.4984:0.3626:0.139:0.0|0.4984:0.3626:0.139:0.0	.|.	.|3	.|Q9UBA6	.|G8_HUMAN	K|K	118|3	.|.	.|ENSP00000364784:R3K	E|R	+|+	1|2	0|0	C6orf48|C6orf48	31913092|31913092	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.151000|0.151000	0.16283|0.16283	-0.327000|-0.327000	0.08551|0.08551	-0.165000|-0.165000	0.13383|0.13383	GAA|AGA	.	.	none		0.502	C6orf48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076332.2	NM_001040437		A	31805113	G	A	31805113	3	1	17	1	0	0	0	0	1	0	0	0	2367	942	33	2	10	2	C6orf48	6	31805113	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	260521	31805113	139309954	44	2298											
FKBP5	2289	hgsc.bcm.edu	37	chr6	35610531	35610531	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcttttttggaggtaataTcctctccctgctcagcaaca	8	15	7	11	0	3	0	1	0	2	0	5	1	4	1	2	2	3	3	2	2	3	5			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr6:35610531T>G	ENST00000539068.1	-	2	273	c.71A>C	c.(70-72)gAt>gCt	p.D24A	FKBP5_ENST00000540787.1_Intron|FKBP5_ENST00000542713.1_Missense_Mutation_p.D24A|FKBP5_ENST00000536438.1_Missense_Mutation_p.D24A|FKBP5_ENST00000357266.4_Missense_Mutation_p.D24A	NM_001145776.1	NP_001139248.1	Q13451	FKBP5_HUMAN	FK506 binding protein 5	24					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						GGAGGTAATATCCTCTCCCTG	0.438																																					p.D24A		Atlas-SNP	.											.	FKBP5	64	.	0			c.A71C						PASS	.						196	191	192					6																	35610531		2203	4300	6503	SO:0001583	missense	2289	exon3			GTAATATCCTCTC	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.71A>C	6.37:g.35610531T>G	ENSP00000441205:p.Asp24Ala	228	0	0		278	111	0.399281	NM_001145775	F5H7R1|Q59EB8|Q5TGM6	Missense_Mutation	SNP	ENST00000539068.1	37	CCDS4808.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	17.54|17.54|17.54	3.415111|3.415111|3.415111	0.62511|0.62511|0.62511	.|.|.	.|.|.	ENSG00000096060|ENSG00000096060|ENSG00000096060	ENST00000543400|ENST00000536438;ENST00000357266;ENST00000539068;ENST00000337746;ENST00000542713|ENST00000373875	.|D;D;D;T|.	.|0.83250|.	.|-1.7;-1.7;-1.7;-1.44|.	5.95|5.95|5.95	5.95|5.95|5.95	0.96441|0.96441|0.96441	.|.|.	.|0.108693|.	.|0.64402|.	.|D|.	.|0.000006|.	.|T|T	.|0.61974|0.61974	.|0.2390|0.2390	M|M|M	0.63843|0.63843|0.63843	1.955|1.955|1.955	0.54753|0.54753|0.54753	D|D|D	0.999985|0.999985|0.999985	.|B;B|.	.|0.26512|.	.|0.001;0.151|.	.|B;B|.	.|0.20184|.	.|0.002;0.028|.	.|T|T	.|0.62163|0.62163	.|-0.6912|-0.6912	.|10|6	.|0.54805|0.34782	.|T|T	.|0.06|0.22	.|-2.376|-2.376	13.9469|13.9469|13.9469	0.64091|0.64091|0.64091	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.|.	.|24;24|.	.|F5H7R1;Q13451|.	.|.;FKBP5_HUMAN|.	.|A|L	-1|24|23	.|ENSP00000444810:D24A;ENSP00000349811:D24A;ENSP00000441205:D24A;ENSP00000442340:D24A|.	.|ENSP00000338160:D24A|ENSP00000362982:I23L	.|D|I	-|-|-	.|2|1	.|0|0	FKBP5|FKBP5|FKBP5	35718509|35718509|35718509	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.903000|0.903000|0.903000	0.53119|0.53119|0.53119	6.180000|6.180000|6.180000	0.71981|0.71981|0.71981	2.279000|2.279000|2.279000	0.76181|0.76181|0.76181	0.533000|0.533000|0.533000	0.62120|0.62120|0.62120	.|GAT|ATA	.	.	none		0.438	FKBP5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040309.2			G	35610531	T	G	35610531	3	3	17	1	0	0	0	0	1	0	0	0	5919	1435	50	5	1400	5	FKBP5	6	35610531	Missense_Mutation	SNP	T	TCGA-FF-A7CQ-01A-11D-A382-10	3805418	35610531	135504536	45	2299											
PIM1	5292	hgsc.bcm.edu	37	chr6	37138392	37138392	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctcgcttgcccacctgcgcgCcgcgccctgcaacgacctgc	4	6	10	21	6	0	0	0	0	0	0	1	1	0	0	5	0	5	2	5	0	1	1			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr6:37138392C>T	ENST00000373509.5	+	1	414	c.41C>T	c.(40-42)gCc>gTc	p.A14V		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	105					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)	CACCTGCGCGCCGCGCCCTGC	0.716			T	BCL6	NHL																																p.A105V		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,right_lower_lobe,carcinoma,-1,1	PIM1	71	1	0			c.C314T						scavenged	.						27	28	28					6																	37138392		2201	4297	6498	SO:0001583	missense	5292	exon1			TGCGCGCCGCGCC		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.41C>T	6.37:g.37138392C>T	ENSP00000362608:p.Ala14Val	79	1	0.0126582		98	30	0.306122	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.936460	0.52972	.	.	ENSG00000137193	ENST00000373509	T	0.69435	-0.4	4.2	4.2	0.49525	.	0.605746	0.14689	N	0.304266	T	0.21186	0.0510	N	0.08118	0	0.32695	N	0.513601	P	0.38020	0.615	B	0.24006	0.05	T	0.02844	-1.1103	10	0.16420	T	0.52	.	12.2313	0.54490	0.1706:0.8294:0.0:0.0	.	105	P11309	PIM1_HUMAN	V	14	ENSP00000362608:A14V	ENSP00000362608:A14V	A	+	2	0	PIM1	37246370	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.287000	0.51732	2.289000	0.77006	0.542000	0.68232	GCC	.	.	none		0.716	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37138392	C	T	37138392	3	4	17	1	0	0	0	0	1	0	0	0	11936	739	26	2	43	2	PIM1	6	37138392	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	1527861	37138392	133976675	46	2300			2	20	36745032	9	8	812	N	G_C_-	9.190863e-22
PIM1	5292	hgsc.bcm.edu	37	chr6	37138416	37138416	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gccctgcaacgacctgcacgCcaccaagctggcgcccggtg	7	4	12	18	4	0	0	0	0	0	0	0	1	0	0	5	2	4	3	5	2	2	0			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr6:37138416C>T	ENST00000373509.5	+	1	438	c.65C>T	c.(64-66)gCc>gTc	p.A22V		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	113					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)	GACCTGCACGCCACCAAGCTG	0.736			T	BCL6	NHL																																p.A113V		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C338T						PASS	.						24	26	26					6																	37138416		2199	4293	6492	SO:0001583	missense	5292	exon1			TGCACGCCACCAA		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.65C>T	6.37:g.37138416C>T	ENSP00000362608:p.Ala22Val	70	0	0		80	12	0.15	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	11.18	1.562878	0.27915	.	.	ENSG00000137193	ENST00000373509	T	0.69175	-0.38	4.2	3.32	0.38043	.	0.485099	0.18021	N	0.154227	T	0.22551	0.0544	N	0.08118	0	0.28270	N	0.924459	B	0.25441	0.126	B	0.17979	0.02	T	0.05818	-1.0862	10	0.20046	T	0.44	.	10.0767	0.42364	0.0:0.9018:0.0:0.0982	.	113	P11309	PIM1_HUMAN	V	22	ENSP00000362608:A22V	ENSP00000362608:A22V	A	+	2	0	PIM1	37246394	0.226000	0.23696	0.998000	0.56505	0.958000	0.62258	1.274000	0.33132	2.289000	0.77006	0.542000	0.68232	GCC	.	.	none		0.736	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37138416	C	T	37138416	3	4	17	1	0	0	0	0	1	0	0	0	11936	739	26	2	67	2	PIM1	6	37138416	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	24	37138416	133976651	47	2301			2	20	36745032	9	8	812	N	G_C_-	9.190863e-22
PIM1	5292	hgsc.bcm.edu	37	chr6	37138609	37138609	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cccgctactgggcagcggcgGcttcggctcggtctactcag	4	8	14	15	5	2	0	1	0	1	0	4	0	2	0	1	5	3	4	1	5	2	3			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr6:37138609G>A	ENST00000373509.5	+	2	516	c.143G>A	c.(142-144)gGc>gAc	p.G48D		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	139					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)	GGCAGCGGCGGCTTCGGCTCG	0.736			T	BCL6	NHL																																p.G139D		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.G416A						PASS	.						20	30	27					6																	37138609		2169	4264	6433	SO:0001583	missense	5292	exon2			GCGGCGGCTTCGG		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.143G>A	6.37:g.37138609G>A	ENSP00000362608:p.Gly48Asp	99	0	0		106	19	0.179245	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.111530	0.77210	.	.	ENSG00000137193	ENST00000373509	T	0.16073	2.37	4.64	2.82	0.32997	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	0.28001	0.0690	H	0.95294	3.65	0.48762	D	0.999708	P	0.43826	0.818	P	0.49387	0.609	T	0.17684	-1.0361	10	0.87932	D	0	.	9.1477	0.36944	0.0781:0.0:0.7761:0.1459	.	139	P11309	PIM1_HUMAN	D	48	ENSP00000362608:G48D	ENSP00000362608:G48D	G	+	2	0	PIM1	37246587	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.992000	0.70609	0.485000	0.27652	0.549000	0.68633	GGC	.	.	none		0.736	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			A	37138609	G	A	37138609	3	1	17	1	0	0	0	0	1	0	0	0	11936	1203	42	2	149	2	PIM1	6	37138609	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	193	37138609	133976458	48	2302			2	20	36745032	9	8	812	N	G_C_-	9.190863e-22
PIM1	5292	hgsc.bcm.edu	37	chr6	37138908	37138908	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctcgcccctgcagcctaatgGcactcgagtgcccatggaag	8	7	11	15	2	0	0	0	0	0	0	2	2	0	1	4	2	3	2	4	2	2	1			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr6:37138908G>A	ENST00000373509.5	+	4	621	c.248G>A	c.(247-249)gGc>gAc	p.G83D		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	174					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)	CAGCCTAATGGCACTCGAGTG	0.662			T	BCL6	NHL																																p.G174D		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,0,1	PIM1	71	1	0			c.G521A						PASS	.						50	57	54					6																	37138908		2203	4300	6503	SO:0001583	missense	5292	exon4			CTAATGGCACTCG		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.248G>A	6.37:g.37138908G>A	ENSP00000362608:p.Gly83Asp	54	0	0		61	14	0.229508	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	G	17.92	3.506654	0.64410	.	.	ENSG00000137193	ENST00000373509	T	0.64991	-0.13	4.28	4.28	0.50868	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.315172	0.28327	N	0.015753	T	0.38026	0.1025	N	0.25485	0.75	0.58432	D	0.999999	B	0.18166	0.026	B	0.20184	0.028	T	0.34304	-0.9834	10	0.45353	T	0.12	.	16.8746	0.86048	0.0:0.0:1.0:0.0	.	174	P11309	PIM1_HUMAN	D	83	ENSP00000362608:G83D	ENSP00000362608:G83D	G	+	2	0	PIM1	37246886	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.484000	0.81180	2.371000	0.80710	0.549000	0.68633	GGC	.	.	none		0.662	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			A	37138908	G	A	37138908	3	1	17	1	0	0	0	0	1	0	0	0	11936	1203	42	2	262	2	PIM1	6	37138908	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	299	37138908	133976159	49	2303			2	20	36745032	9	8	812	N	G_C_-	9.190863e-22
PIM1	5292	hgsc.bcm.edu	37	chr6	37138919	37138919	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agcctaatggcactcgagtgCccatggaagtggtcctgctg	8	9	13	11	1	0	0	0	0	0	0	2	2	1	1	3	3	3	2	3	3	2	1			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr6:37138919C>T	ENST00000373509.5	+	4	632	c.259C>T	c.(259-261)Ccc>Tcc	p.P87S		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	178					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)	CACTCGAGTGCCCATGGAAGT	0.657			T	BCL6	NHL																																p.P178S		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C532T						PASS	.						58	66	63					6																	37138919		2203	4300	6503	SO:0001583	missense	5292	exon4			CGAGTGCCCATGG		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.259C>T	6.37:g.37138919C>T	ENSP00000362608:p.Pro87Ser	53	0	0		63	11	0.174603	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.182069	0.78677	.	.	ENSG00000137193	ENST00000373509	T	0.13307	2.6	4.28	3.41	0.39046	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.065293	0.64402	N	0.000006	T	0.15696	0.0378	L	0.52905	1.665	0.58432	D	0.999994	P	0.51537	0.946	P	0.56612	0.802	T	0.01042	-1.1471	10	0.87932	D	0	.	12.2367	0.54520	0.0:0.9151:0.0:0.0849	.	178	P11309	PIM1_HUMAN	S	87	ENSP00000362608:P87S	ENSP00000362608:P87S	P	+	1	0	PIM1	37246897	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.764000	0.68826	1.146000	0.42352	0.549000	0.68633	CCC	.	.	none		0.657	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37138919	C	T	37138919	3	4	17	1	0	0	0	0	1	0	0	0	11936	739	26	2	273	2	PIM1	6	37138919	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	11	37138919	133976148	50	2304			2	20	36745032	9	8	812	N	G_C_-	9.190863e-22
PIM1	5292	hgsc.bcm.edu	37	chr6	37139042	37139042	+	Missense_Mutation	SNP	G	G	A																															agaggcccgagccggtgcaaGatctcttcgacttcatcacg																										TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr6:37139042G>A	ENST00000373509.5	+	4	755	c.382G>A	c.(382-384)Gat>Aat	p.D128N		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	219					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)	GCCGGTGCAAGATCTCTTCGA	0.622			T	BCL6	NHL																																p.D219N		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.G655A						PASS	.						81	95	91					6																	37139042		2203	4300	6503	SO:0001583	missense	5292	exon4			GTGCAAGATCTCT		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.382G>A	6.37:g.37139042G>A	ENSP00000362608:p.Asp128Asn	111	0	0		125	57	0.456	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.857582	0.91433	.	.	ENSG00000137193	ENST00000373509	T	0.15603	2.41	4.28	4.28	0.50868	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	0.24005	0.0581	L	0.42008	1.315	0.80722	D	1	D	0.53745	0.962	P	0.62885	0.908	T	0.02081	-1.1217	10	0.87932	D	0	.	16.8746	0.86048	0.0:0.0:1.0:0.0	.	219	P11309	PIM1_HUMAN	N	128	ENSP00000362608:D128N	ENSP00000362608:D128N	D	+	1	0	PIM1	37247020	1.000000	0.71417	1.000000	0.80357	0.773000	0.43773	9.149000	0.94659	2.371000	0.80710	0.549000	0.68633	GAT	.	.	none		0.622	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			A	37139042	G	A	37139042	3	1	17	1	0	0	0	0	1	0	0	0	11936	942	33	2	396	2	PIM1	6	37139042	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	123	37139042	133976025	51	2305	32	2	2	20	36745032	9	8	812	N	G_C_-	9.190863e-22
PIM1	5292	hgsc.bcm.edu	37	chr6	37139046	37139047	+	In_Frame_Ins	INS	-	-	CTTCGA																															cccgagccggtgcaagatctINScttcgacttcatcacggaaa																										TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr6:37139046_37139047insCTTCGA	ENST00000373509.5	+	4	759_760	c.386_387insCTTCGA	c.(385-390)ctcttc>ctCTTCGActtc	p.132_133insDF		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	223	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)	GTGCAAGATCTCTTCGACTTCA	0.634			T	BCL6	NHL																																p.L220delinsLFD		Atlas-Indel	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.659_660insCTTCGA						PASS	.																																			SO:0001652	inframe_insertion	5292	exon4			.		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.387_392dupCTTCGA	6.37:g.37139047_37139052dupCTTCGA	ENSP00000362608:p.Asp131_Phe132dup	110	0	0		123	14	0.113821	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	In_Frame_Ins	INS	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.634	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			CTTCGA	37139047	-	CTTCGA	37139046	7	5	17	1	0	1	1	0	0	0	0	0	11936	1551	54	0	400	0	PIM1	6	37139046	In_Frame_Ins	INS	-	TCGA-FF-A7CQ-01A-11D-A382-10	4	37139046	133976021	52	2306	32	2	2	20	36745032	9	8	812	N	G_C_-	9.190863e-22
PIM1	5292	hgsc.bcm.edu	37	chr6	37139063	37139063	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	atctcttcgacttcatcacgGaaaggggagccctgcaagag	11	8	11	11	2	3	1	2	0	1	1	5	4	3	3	1	3	2	1	1	3	2	2	rs200523275	byFrequency	TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr6:37139063G>A	ENST00000373509.5	+	4	776	c.403G>A	c.(403-405)Gaa>Aaa	p.E135K		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	226	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)	CTTCATCACGGAAAGGGGAGC	0.637			T	BCL6	NHL								G|||	2	0.000399361	0.0	0.0	5008	,	,		15869	0.002		0.0	False		,,,				2504	0.0				p.E226K		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,0,2	PIM1	71	2	0			c.G676A						PASS	.						75	88	84					6																	37139063		2203	4300	6503	SO:0001583	missense	5292	exon4			ATCACGGAAAGGG		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.403G>A	6.37:g.37139063G>A	ENSP00000362608:p.Glu135Lys	120	0	0		125	22	0.176	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	15.05	2.719704	0.48728	.	.	ENSG00000137193	ENST00000373509	T	0.64991	-0.13	4.58	4.58	0.56647	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.128681	0.50627	D	0.000105	T	0.32675	0.0837	N	0.03253	-0.375	0.54753	D	0.999988	B	0.23128	0.08	B	0.34093	0.175	T	0.45991	-0.9223	10	0.72032	D	0.01	.	17.1751	0.86839	0.0:0.0:1.0:0.0	.	226	P11309	PIM1_HUMAN	K	135	ENSP00000362608:E135K	ENSP00000362608:E135K	E	+	1	0	PIM1	37247041	1.000000	0.71417	0.929000	0.37066	0.060000	0.15804	9.205000	0.95048	2.371000	0.80710	0.549000	0.68633	GAA	G|1.000;A|0.000	0.000	strong		0.637	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			A	37139063	G	A	37139063	3	1	17	1	0	0	0	0	1	0	0	0	11936	1175	41	2	417	2	PIM1	6	37139063	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	17	37139063	133976004	53	2307			2	20	36745032	9	8	812	N	G_C_-	9.190863e-22
PIM1	5292	hgsc.bcm.edu	37	chr6	37139203	37139203	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcgacctcaatcgcggcgaGctcaagctcatcgacttcgg	9	8	10	14	6	3	0	3	0	0	0	7	3	3	0	1	2	2	2	1	2	2	1			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr6:37139203G>A	ENST00000373509.5	+	4	916	c.543G>A	c.(541-543)gaG>gaA	p.E181E		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	272	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)	p.E181D(1)		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)	ATCGCGGCGAGCTCAAGCTCA	0.637			T	BCL6	NHL																																p.E272E		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,0,1	PIM1	71	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G816A						PASS	.						32	33	32					6																	37139203		2203	4300	6503	SO:0001819	synonymous_variant	5292	exon4			CGGCGAGCTCAAG		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.543G>A	6.37:g.37139203G>A		85	0	0		96	21	0.21875	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.637	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			A	37139203	G	A	37139203	2	1	17	1	0	0	0	0	0	0	0	1	11936	962	34	2		2	PIM1	6	37139203	Silent	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	140	37139203	133975864	54	2308			2	20	36745032	9	8	812	N	G_C_-	9.190863e-22
MDGA1	266727	hgsc.bcm.edu	37	chr6	37605198	37605198	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcccccacagctgtgggctGgactggcagggggctccact	5	6	16	14	0	0	0	0	0	0	0	1	1	1	1	3	6	1	4	3	6	0	0			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr6:37605198G>A	ENST00000434837.3	-	17	3992	c.2814C>T	c.(2812-2814)tcC>tcT	p.S938S	MDGA1_ENST00000297153.7_Silent_p.S942S	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	938					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						GCTGTGGGCTGGACTGGCAGG	0.652																																					p.S938S		Atlas-SNP	.											.	MDGA1	104	.	0			c.C2814T						PASS	.						38	43	41					6																	37605198		2029	4182	6211	SO:0001819	synonymous_variant	266727	exon17			TGGGCTGGACTGG	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.2814C>T	6.37:g.37605198G>A		94	0	0		105	47	0.447619	NM_153487	A6NHG0|Q8NBE3	Silent	SNP	ENST00000434837.3	37	CCDS47417.1																																																																																			.	.	none		0.652	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3			A	37605198	G	A	37605198	2	1	17	1	0	0	0	0	0	0	0	1	9415	1335	47	2		2	MDGA1	6	37605198	Silent	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	465995	37605198	133509869	55	2309											
NFYA	4800	hgsc.bcm.edu	37	chr6	41060751	41060751	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctacgtgaatgccaaacaatAccaccgtattcttaagagga	15	9	7	10	2	1	2	0	1	1	1	1	3	1	3	3	1	4	1	3	1	7	5			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr6:41060751A>G	ENST00000341376.6	+	8	1016	c.815A>G	c.(814-816)tAc>tGc	p.Y272C	NFYA_ENST00000353205.5_Missense_Mutation_p.Y243C|OARD1_ENST00000480585.1_Intron	NM_002505.4	NP_002496.1	P23511	NFYA_HUMAN	nuclear transcription factor Y, alpha	272					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)					GCCAAACAATACCACCGTATT	0.478																																					p.Y272C		Atlas-SNP	.											.	NFYA	33	.	0			c.A815G						PASS	.						108	102	104					6																	41060751		2203	4300	6503	SO:0001583	missense	4800	exon8			AACAATACCACCG		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.815A>G	6.37:g.41060751A>G	ENSP00000345702:p.Tyr272Cys	76	0	0		127	53	0.417323	NM_002505	Q8IXU0	Missense_Mutation	SNP	ENST00000341376.6	37	CCDS4849.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.674529	0.88445	.	.	ENSG00000001167	ENST00000341376;ENST00000353205	.	.	.	5.88	5.88	0.94601	CCAAT-binding factor, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.83036	0.5167	M	0.91038	3.17	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	D	0.87194	0.2236	9	0.87932	D	0	0.0035	15.4635	0.75381	1.0:0.0:0.0:0.0	.	243;272	P23511-2;P23511	.;NFYA_HUMAN	C	272;243	.	ENSP00000345702:Y272C	Y	+	2	0	NFYA	41168729	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.237000	0.95368	2.250000	0.74265	0.533000	0.62120	TAC	.	.	none		0.478	NFYA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040496.1			G	41060751	A	G	41060751	3	3	17	1	0	0	0	0	1	0	0	0	10398	391	14	3	841	3	NFYA	6	41060751	Missense_Mutation	SNP	A	TCGA-FF-A7CQ-01A-11D-A382-10	3455553	41060751	130054316	56	2310											
TRDN	10345	hgsc.bcm.edu	37	chr6	123869636	123869636	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaccatcatcatcttcttcAtcttcagatgagatgatgtc	10	15	5	11	0	8	3	5	2	3	2	9	4	8	3	1	0	0	0	1	0	0	3			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr6:123869636A>G	ENST00000398178.3	-	3	375	c.354T>C	c.(352-354)gaT>gaC	p.D118D	TRDN_ENST00000546248.1_Silent_p.D118D|TRDN_ENST00000542443.1_Silent_p.D118D|TRDN_ENST00000334268.4_Silent_p.D118D	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin	118					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)		CATCTTCTTCATCTTCAGATG	0.378																																					p.D118D		Atlas-SNP	.											.	TRDN	88	.	0			c.T354C						PASS	.						61	60	60					6																	123869636		1871	4103	5974	SO:0001819	synonymous_variant	10345	exon3			TTCTTCATCTTCA	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.354T>C	6.37:g.123869636A>G		99	0	0		103	26	0.252427	NM_001256022	A5D6W5|F5H2W7|Q6NSB8	Silent	SNP	ENST00000398178.3	37	CCDS55053.1																																																																																			.	.	none		0.378	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				G	123869636	A	G	123869636	2	3	17	1	0	0	0	0	0	0	0	1	16483	214	8	3		3	TRDN	6	123869636	Silent	SNP	A	TCGA-FF-A7CQ-01A-11D-A382-10	82808885	123869636	47245431	57	2311											
IL22RA2	116379	hgsc.bcm.edu	37	chr6	137468925	137468926	+	Frame_Shift_Ins	INS	-	-	T																															agtaatcttctatagatacaINStttttttccttttggtatct																										TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr6:137468925_137468926insT	ENST00000296980.2	-	6	875_876	c.575_576insA	c.(574-576)aatfs	p.N192fs	IL22RA2_ENST00000349184.4_Frame_Shift_Ins_p.N160fs|IL22RA2_ENST00000339602.3_Intron	NM_052962.2	NP_443194.1	Q969J5	I22R2_HUMAN	interleukin 22 receptor, alpha 2	192	Fibronectin type-III 3.				cytokine-mediated signaling pathway (GO:0019221)|negative regulation of inflammatory response (GO:0050728)|regulation of tyrosine phosphorylation of Stat3 protein (GO:0042516)	cytosol (GO:0005829)|extracellular space (GO:0005615)	interleukin-22 binding (GO:0042017)|interleukin-22 receptor activity (GO:0042018)			endometrium(1)|large_intestine(1)|lung(3)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000313)|OV - Ovarian serous cystadenocarcinoma(155;0.00407)		CTATAGATACATTTTTTTCCTT	0.292																																					p.N192fs		Atlas-Indel	.											.	IL22RA2	17	.	0			c.576_577insA						PASS	.																																			SO:0001589	frameshift_variant	116379	exon6			.	AY044429	CCDS5182.1, CCDS5183.1, CCDS5184.1	6q24.1-q24.2	2008-02-05			ENSG00000164485	ENSG00000164485		"Interleukins and interleukin receptors"	14901	protein-coding gene	gene with protein product		606648				11481447, 11390454	Standard	NM_181309		Approved	CRF2-S1, IL-22BP	uc003qhl.3	Q969J5	OTTHUMG00000015655	ENST00000296980.2:c.576dupA	6.37:g.137468932_137468932dupT	ENSP00000296980:p.Asn192fs	238	0	0		248	51	0.205645	NM_052962	Q08AH7|Q6UWM1|Q96A41|Q96QR0	Frame_Shift_Ins	INS	ENST00000296980.2	37	CCDS5182.1																																																																																			.	.	none		0.292	IL22RA2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042399.1			T	137468926	-	T	137468925	7	5	17	1	0	1	1	0	0	0	0	0	7683	214	8	0	223	0	IL22RA2	6	137468925	Frame_Shift_Ins	INS	-	TCGA-FF-A7CQ-01A-11D-A382-10	13599289	137468925	33646142	58	2312											
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138528237	138528237	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaagaatgtgaagctggccCaacatgctttggcagggatg	11	8	13	9	0	0	2	0	1	0	1	0	3	0	3	2	3	3	3	2	3	4	1			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr6:138528237C>A	ENST00000251691.4	+	3	362	c.196C>A	c.(196-198)Caa>Aaa	p.Q66K		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)		GAAGCTGGCCCAACATGCTTT	0.453																																					p.Q66K		Atlas-SNP	.											.	KIAA1244	236	.	0			c.C196A						PASS	.						91	78	82					6																	138528237		2203	4300	6503	SO:0001583	missense	57221	exon3			CTGGCCCAACATG	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.196C>A	6.37:g.138528237C>A	ENSP00000251691:p.Gln66Lys	101	0	0		85	18	0.211765	NM_020340		Missense_Mutation	SNP	ENST00000251691.4	37	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	C	23.4	4.414067	0.83449	.	.	ENSG00000112379	ENST00000251691	T	0.17370	2.28	5.77	5.77	0.91146	.	.	.	.	.	T	0.22742	0.0549	L	0.29908	0.895	0.58432	D	0.999997	D	0.63880	0.993	D	0.67548	0.952	T	0.01156	-1.1434	9	0.41790	T	0.15	-13.1881	19.9944	0.97379	0.0:1.0:0.0:0.0	.	66	Q5TH69	BIG3_HUMAN	K	66	ENSP00000251691:Q66K	ENSP00000251691:Q66K	Q	+	1	0	KIAA1244	138569930	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.262000	0.78410	2.720000	0.93068	0.557000	0.71058	CAA	.	.	none		0.453	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		A	138528237	C	A	138528237	3	1	17	1	0	0	0	0	1	0	0	0	8226	595	21	4	206	4	KIAA1244	6	138528237	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	1059312	138528237	32586830	59	2313											
SDK1	221935	hgsc.bcm.edu	37	chr7	4153851	4153851	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgcagatgcaggccttcaaCgccgtcggggctgggccgtg	5	7	16	13	4	1	1	1	0	0	1	2	1	1	1	3	4	3	3	3	4	1	1	rs549888988	byFrequency	TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr7:4153851C>T	ENST00000404826.2	+	25	3907	c.3768C>T	c.(3766-3768)aaC>aaT	p.N1256N	SDK1_ENST00000389531.3_Silent_p.N1256N	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1256	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)		AGGCCTTCAACGCCGTCGGGG	0.632													C|||	2	0.000399361	0.0	0.0	5008	,	,		16102	0.0		0.0	False		,,,				2504	0.002				p.N1256N		Atlas-SNP	.											.	SDK1	361	.	0			c.C3768T						PASS	.						36	35	35					7																	4153851		2203	4300	6503	SO:0001819	synonymous_variant	221935	exon25			CTTCAACGCCGTC	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.3768C>T	7.37:g.4153851C>T		101	0	0		94	32	0.340426	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	ENST00000404826.2	37	CCDS34590.1																																																																																			.	.	none		0.632	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		T	4153851	C	T	4153851	2	4	17	1	0	0	0	0	0	0	0	1	13983	535	19	1		1	SDK1	7	4153851	Silent	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10		4153851	154984812	60	2314											
ZNF498	221785	hgsc.bcm.edu	37	chr7	99219100	99219100	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gaggtcaagcctgaatggggGatgccccctggggaaggagt	9	6	18	8	0	1	1	1	1	0	0	1	5	1	4	3	6	2	0	3	6	3	0			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr7:99219100G>A	ENST00000394152.2	+	5	819	c.492G>A	c.(490-492)ggG>ggA	p.G164G	ZSCAN25_ENST00000466948.1_Intron|ZSCAN25_ENST00000334715.3_Silent_p.G164G|ZSCAN25_ENST00000262941.6_Silent_p.G164G	NM_145115.2	NP_660090.2	Q6NSZ9	ZSC25_HUMAN	zinc finger and SCAN domain containing 25	164					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)										CTGAATGGGGGATGCCCCCTG	0.627																																					p.G164G		Atlas-SNP	.											.	.	.	.	0			c.G492A						PASS	.						65	61	62					7																	99219100		2203	4300	6503	SO:0001819	synonymous_variant	221785	exon5			ATGGGGGATGCCC	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.492G>A	7.37:g.99219100G>A		55	0	0		83	31	0.373494	NM_145115	A4D290|D6W5T5|Q14C82|Q14C99|Q5EBM9|Q6DJZ0|Q6N032|Q6ZML3	Silent	SNP	ENST00000394152.2	37	CCDS5671.2																																																																																			.	.	none		0.627	ZSCAN25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157203.4	NM_145115		A	99219100	G	A	99219100	2	1	17	1	0	0	0	0	0	0	0	1	17962	1161	41	2		2	ZNF498	7	99219100	Silent	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	95065249	99219100	59919563	61	2315											
TMEM168	64418	hgsc.bcm.edu	37	chr7	112415375	112415375	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaaaattccatttgttggcTaaaagaaatccaaaacatgt	18	11	6	6	0	0	2	0	0	0	2	2	2	2	2	2	1	1	2	2	1	7	4			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr7:112415375T>C	ENST00000312814.6	-	3	1689		c.e3-2		TMEM168_ENST00000454074.1_Splice_Site|TMEM168_ENST00000480969.1_Splice_Site	NM_022484.4	NP_071929.3	Q9H0V1	TM168_HUMAN	transmembrane protein 168							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						ATTTGTTGGCTAAAAGAAATC	0.338																																					.		Atlas-SNP	.											.	TMEM168	84	.	0			c.1129-2A>G						PASS	.						59	54	56					7																	112415375		2203	4300	6503	SO:0001630	splice_region_variant	64418	exon4			GTTGGCTAAAAGA		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.1129-2A>G	7.37:g.112415375T>C		67	0	0		72	4	0.0555556	NM_022484	A4D0T9|B4DDS0|Q8NEK4|Q9H8J2	Splice_Site	SNP	ENST00000312814.6	37	CCDS5757.1	.	.	.	.	.	.	.	.	.	.	T	22.2	4.262067	0.80358	.	.	ENSG00000146802	ENST00000312814;ENST00000454074;ENST00000418785;ENST00000441474	.	.	.	5.31	5.31	0.75309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.556	0.76192	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	TMEM168	112202611	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.101000	0.76997	2.146000	0.66826	0.533000	0.62120	.	.	.	none		0.338	TMEM168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338696.4	NM_022484	Intron	C	112415375	T	C	112415375	5	2	17	1	0	0	0	0	0	0	1	0	16098	1536	53	3	978	3	TMEM168	7	112415375	Splice_Site	SNP	T	TCGA-FF-A7CQ-01A-11D-A382-10	13196275	112415375	46723288	62	2316											
AKR1B15	441282	hgsc.bcm.edu	37	chr7	134260279	134260279	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaacctggactgaaatataaAccagtgactaaccaggtaaa	19	7	7	8	0	0	2	0	2	0	0	0	3	0	3	3	2	3	1	3	2	8	4			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr7:134260279A>T	ENST00000457545.2	+	7	881	c.621A>T	c.(619-621)aaA>aaT	p.K207N	AKR1B15_ENST00000423958.1_Missense_Mutation_p.K179N	NM_001080538.2	NP_001074007.2	C9JRZ8	AK1BF_HUMAN	aldo-keto reductase family 1, member B15	207							oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|urinary_tract(1)	18						TGAAATATAAACCAGTGACTA	0.468																																					p.K207N		Atlas-SNP	.											.	AKR1B15	105	.	0			c.A621T						PASS	.						69	75	73					7																	134260279		2202	4300	6502	SO:0001583	missense	441282	exon7			ATATAAACCAGTG		CCDS47715.1, CCDS47715.2	7q33	2009-09-09			ENSG00000227471	ENSG00000227471		"Aldo-keto reductases"	37281	protein-coding gene	gene with protein product							Standard	NM_001080538		Approved		uc011kpr.2	C9JRZ8	OTTHUMG00000155376	ENST00000457545.2:c.621A>T	7.37:g.134260279A>T	ENSP00000389289:p.Lys207Asn	103	0	0		92	40	0.434783	NM_001080538	C9J3V2	Missense_Mutation	SNP	ENST00000457545.2	37	CCDS47715.2	.	.	.	.	.	.	.	.	.	.	A	15.77	2.930250	0.52866	.	.	ENSG00000227471	ENST00000457545;ENST00000423958	T;T	0.28069	1.63;1.63	3.82	-4.68	0.03309	NADP-dependent oxidoreductase domain (3);	.	.	.	.	T	0.46658	0.1404	H	0.94847	3.59	0.49130	D	0.999758	P;P	0.51653	0.609;0.947	B;P	0.44860	0.286;0.462	T	0.71646	-0.4530	9	0.87932	D	0	.	15.1895	0.73032	0.1808:0.0:0.8192:0.0	.	179;207	C9JRZ8-2;C9JRZ8	.;AK1BF_HUMAN	N	207;179	ENSP00000389289:K207N;ENSP00000397009:K179N	ENSP00000397009:K179N	K	+	3	2	AKR1B15	133910819	0.067000	0.21026	0.376000	0.26042	0.690000	0.40134	-0.684000	0.05173	-0.911000	0.03843	-0.451000	0.05528	AAA	.	.	none		0.468	AKR1B15-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339726.2			T	134260279	A	T	134260279	3	4	17	1	0	0	0	0	1	0	0	0	468	40	2	5	639	5	AKR1B15	7	134260279	Missense_Mutation	SNP	A	TCGA-FF-A7CQ-01A-11D-A382-10	21844904	134260279	24878384	63	2317											
ZNF425	155054	hgsc.bcm.edu	37	chr7	148801430	148801430	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcaggtgctgcgtgagccgCgactgctgagaaaaggtctt	8	10	14	9	3	2	2	1	2	1	1	2	4	2	2	1	2	4	2	1	2	2	2	rs575584712		TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr7:148801430C>T	ENST00000378061.2	-	4	1665	c.1533G>A	c.(1531-1533)tcG>tcA	p.S511S		NM_001001661.2	NP_001001661.1	Q6IV72	ZN425_HUMAN	zinc finger protein 425	511					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(6)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	50	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			GCGTGAGCCGCGACTGCTGAG	0.627													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18036	0.0		0.0	False		,,,				2504	0.0				p.S511S		Atlas-SNP	.											ZNF425,NS,carcinoma,0,1	ZNF425	99	1	0			c.G1533A						PASS	.						48	39	42					7																	148801430		2203	4300	6503	SO:0001819	synonymous_variant	155054	exon4			GAGCCGCGACTGC	AK056498	CCDS34773.1	7q36.1	2013-01-08			ENSG00000204947	ENSG00000204947		"Zinc fingers, C2H2-type", "-"	20690	protein-coding gene	gene with protein product							Standard	NM_001001661		Approved		uc003wfj.3	Q6IV72	OTTHUMG00000158971	ENST00000378061.2:c.1533G>A	7.37:g.148801430C>T		84	0	0		74	27	0.364865	NM_001001661	B3KPM1|Q08AG3	Silent	SNP	ENST00000378061.2	37	CCDS34773.1																																																																																			.	.	none		0.627	ZNF425-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352726.1	XM_088140		T	148801430	C	T	148801430	2	4	17	1	0	0	0	0	0	0	0	1	17914	755	27	1		1	ZNF425	7	148801430	Silent	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	14541151	148801430	10337233	64	2318											
XKR4	114786	hgsc.bcm.edu	37	chr8	56270330	56270330	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaaaatggtatatgagtatgCggatgtgagtatgctgcatt	12	13	13	3	1	0	2	0	2	0	0	0	4	0	3	0	2	3	5	0	2	6	5			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr8:56270330C>T	ENST00000327381.6	+	2	999	c.899C>T	c.(898-900)gCg>gTg	p.A300V		NM_052898.1	NP_443130.1	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related family, member 4	300						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)			TATGAGTATGCGGATGTGAGT	0.453																																					p.A300V		Atlas-SNP	.											XKR4,colon,carcinoma,0,1	XKR4	104	1	0			c.C899T						PASS	.						178	159	165					8																	56270330		2203	4300	6503	SO:0001583	missense	114786	exon2			AGTATGCGGATGT	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.899C>T	8.37:g.56270330C>T	ENSP00000328326:p.Ala300Val	231	0	0		219	56	0.255708	NM_052898	Q96PZ8	Missense_Mutation	SNP	ENST00000327381.6	37	CCDS34893.1	.	.	.	.	.	.	.	.	.	.	C	16.89	3.248401	0.59103	.	.	ENSG00000206579	ENST00000327381;ENST00000543752	T	0.66280	-0.2	5.96	5.96	0.96718	.	0.054071	0.64402	D	0.000001	T	0.79511	0.4458	M	0.65975	2.015	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.78191	-0.2300	10	0.54805	T	0.06	-14.25	20.4192	0.99033	0.0:1.0:0.0:0.0	.	300	Q5GH76	XKR4_HUMAN	V	300	ENSP00000328326:A300V	ENSP00000328326:A300V	A	+	2	0	XKR4	56432884	1.000000	0.71417	0.984000	0.44739	0.293000	0.27360	7.818000	0.86416	2.831000	0.97527	0.650000	0.86243	GCG	.	.	none		0.453	XKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378129.2	NM_052898		T	56270330	C	T	56270330	3	4	17	1	0	0	0	0	1	0	0	0	17448	768	27	1	905	1	XKR4	8	56270330	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10		56270330	90093692	65	2319											
CNBD1	168975	hgsc.bcm.edu	37	chr8	88298781	88298781	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttaggaaaaaataaaactTgaaaatatgcaaaagttgaa	22	11	6	2	0	0	2	0	2	0	0	0	3	0	3	0	1	2	2	0	1	12	6			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr8:88298781T>A	ENST00000518476.1	+	8	975	c.924T>A	c.(922-924)ctT>ctA	p.L308L		NM_173538.2	NP_775809.1	Q8NA66	CNBD1_HUMAN	cyclic nucleotide binding domain containing 1	308										breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(4)|urinary_tract(1)	32						AAATAAAACTTGAAAATATGC	0.274																																					p.L308L		Atlas-SNP	.											.	CNBD1	206	.	0			c.T924A						PASS	.						39	35	36					8																	88298781		1760	3999	5759	SO:0001819	synonymous_variant	168975	exon8			AAAACTTGAAAAT	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.924T>A	8.37:g.88298781T>A		82	0	0		70	19	0.271429	NM_173538		Silent	SNP	ENST00000518476.1	37	CCDS55259.1																																																																																			.	.	none		0.274	CNBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375113.2	NM_173538		A	88298781	T	A	88298781	2	1	17	1	0	0	0	0	0	0	0	1	3593	1799	63	5		5	CNBD1	8	88298781	Silent	SNP	T	TCGA-FF-A7CQ-01A-11D-A382-10	32028451	88298781	58065241	66	2320											
VPS13B	157680	hgsc.bcm.edu	37	chr8	100887760	100887760	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cttccatgcaaataccatgcCctgtggtggctgcagaacct	9	10	9	13	0	0	1	0	0	0	1	1	1	1	1	4	2	5	3	4	2	3	2			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr8:100887760C>T	ENST00000358544.2	+	62	12046	c.11935C>T	c.(11935-11937)Cct>Tct	p.P3979S	VPS13B_ENST00000357162.2_Missense_Mutation_p.P3954S|VPS13B_ENST00000395996.1_3'UTR	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	3979					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)			AATACCATGCCCTGTGGTGGC	0.478																																					p.P3979S	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.C11935T						PASS	.						152	130	137					8																	100887760		2203	4300	6503	SO:0001583	missense	157680	exon62			CCATGCCCTGTGG	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.11935C>T	8.37:g.100887760C>T	ENSP00000351346:p.Pro3979Ser	172	0	0		162	61	0.376543	NM_017890	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	C	3.563	-0.089224	0.07097	.	.	ENSG00000132549	ENST00000357162;ENST00000358544	T;T	0.67171	-0.25;-0.25	5.65	3.84	0.44239	.	0.292622	0.31949	N	0.006813	T	0.44932	0.1317	N	0.14661	0.345	0.80722	D	1	B;B	0.09022	0.001;0.002	B;B	0.09377	0.004;0.002	T	0.20605	-1.0270	10	0.10902	T	0.67	.	11.2147	0.48819	0.0:0.8027:0.1284:0.0689	.	3954;3979	Q7Z7G8-2;Q7Z7G8	.;VP13B_HUMAN	S	3954;3979	ENSP00000349685:P3954S;ENSP00000351346:P3979S	ENSP00000349685:P3954S	P	+	1	0	VPS13B	100956936	0.012000	0.17670	0.980000	0.43619	0.612000	0.37316	1.690000	0.37711	0.729000	0.32403	0.655000	0.94253	CCT	.	.	none		0.478	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		T	100887760	C	T	100887760	3	4	17	1	0	0	0	0	1	0	0	0	17205	623	22	2	12371	2	VPS13B	8	100887760	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	12588979	100887760	45476262	67	2321											
HAS2	3037	hgsc.bcm.edu	37	chr8	122641110	122641110	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtgactcatctgtctcaccGggacccttttcgtggaagtt	6	14	10	11	2	3	1	2	1	2	0	5	3	3	3	2	2	0	1	2	2	1	3			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr8:122641110G>A	ENST00000303924.4	-	2	1008	c.471C>T	c.(469-471)ccC>ccT	p.P157P		NM_005328.2	NP_005319.1	Q92819	HYAS2_HUMAN	hyaluronan synthase 2	157					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)			CTGTCTCACCGGGACCCTTTT	0.433																																					p.P157P		Atlas-SNP	.											.	HAS2	87	.	0			c.C471T						PASS	.						324	290	302					8																	122641110		2203	4300	6503	SO:0001819	synonymous_variant	3037	exon2			CTCACCGGGACCC	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.471C>T	8.37:g.122641110G>A		213	0	0		172	42	0.244186	NM_005328	Q32MM3	Silent	SNP	ENST00000303924.4	37	CCDS6335.1																																																																																			.	.	none		0.433	HAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381150.2	NM_005328		A	122641110	G	A	122641110	2	1	17	1	0	0	0	0	0	0	0	1	6971	1103	39	1		1	HAS2	8	122641110	Silent	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	21753350	122641110	23722912	68	2322											
ZNF707	286075	hgsc.bcm.edu	37	chr8	144775926	144775926	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacgtgcggcgagaaagagcCagggaaggaagcagctttag	13	4	16	8	3	0	2	0	0	0	2	0	5	0	4	1	3	4	2	1	3	4	2			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr8:144775926C>T	ENST00000532205.1	+	8	1241	c.342C>T	c.(340-342)gcC>gcT	p.A114A	ZNF707_ENST00000532158.1_Silent_p.A114A|ZNF707_ENST00000358656.4_Silent_p.A114A|RP11-429J17.2_ENST00000531565.1_RNA|ZNF707_ENST00000418203.2_Silent_p.A114A|ZNF707_ENST00000454097.1_Silent_p.A114A			Q96C28	ZN707_HUMAN	zinc finger protein 707	114					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)			GAGAAAGAGCCAGGGAAGGAA	0.582																																					p.A114A		Atlas-SNP	.											.	ZNF707	21	.	0			c.C342T						PASS	.						55	60	59					8																	144775926		2012	4175	6187	SO:0001819	synonymous_variant	286075	exon6			AAGAGCCAGGGAA	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.342C>T	8.37:g.144775926C>T		102	0	0		111	27	0.243243	NM_001100598	A8K317|B3KNY1|D3DWK7	Silent	SNP	ENST00000532205.1	37	CCDS47932.1	.	.	.	.	.	.	.	.	.	.	C	1.036	-0.680439	0.03353	.	.	ENSG00000181135	ENST00000530574	T	0.01548	4.78	1.76	0.866	0.19079	.	.	.	.	.	T	0.02230	0.0069	.	.	.	0.21105	N	0.99979	.	.	.	.	.	.	T	0.47873	-0.9083	6	0.44086	T	0.13	.	6.2605	0.20897	0.0:0.8249:0.0:0.1751	.	.	.	.	L	111	ENSP00000436362:P111L	ENSP00000436362:P111L	P	+	2	0	ZNF707	144847914	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.747000	0.26290	0.300000	0.22699	-0.253000	0.11424	CCA	.	.	none		0.582	ZNF707-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382197.1	NM_173831		T	144775926	C	T	144775926	2	4	17	1	0	0	0	0	0	0	0	1	18126	581	21	2		2	ZNF707	8	144775926	Silent	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	22134816	144775926	1588096	69	2323											
STOML2	30968	hgsc.bcm.edu	37	chr9	35100654	35100654	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cagtaggatagtgttggagtCcttggccagtttggagaacg	9	11	15	6	1	0	1	0	0	0	1	1	4	1	3	2	4	1	3	2	4	3	5			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr9:35100654C>T	ENST00000356493.5	-	9	936	c.874G>A	c.(874-876)Gac>Aac	p.D292N	RP11-182N22.8_ENST00000431804.1_RNA|STOML2_ENST00000487490.1_5'Flank|STOML2_ENST00000452248.2_Missense_Mutation_p.D247N	NM_013442.1	NP_038470.1	Q9UJZ1	STML2_HUMAN	stomatin (EPB72)-like 2	292					CD4-positive, alpha-beta T cell activation (GO:0035710)|cellular calcium ion homeostasis (GO:0006874)|interleukin-2 production (GO:0032623)|lipid localization (GO:0010876)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|mitochondrial calcium ion transport (GO:0006851)|mitochondrial protein processing (GO:0034982)|mitochondrion organization (GO:0007005)|positive regulation of cardiolipin metabolic process (GO:1900210)|positive regulation of mitochondrial DNA replication (GO:0090297)|positive regulation of mitochondrial membrane potential (GO:0010918)|protein oligomerization (GO:0051259)|stress-induced mitochondrial fusion (GO:1990046)|T cell receptor signaling pathway (GO:0050852)	cytoskeleton (GO:0005856)|extrinsic component of plasma membrane (GO:0019897)|membrane raft (GO:0045121)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)	cardiolipin binding (GO:1901612)|receptor binding (GO:0005102)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|prostate(1)	16			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			GTGTTGGAGTCCTTGGCCAGT	0.542																																					p.D292N		Atlas-SNP	.											.	STOML2	27	.	0			c.G874A						PASS	.						215	190	199					9																	35100654		2203	4300	6503	SO:0001583	missense	30968	exon9			TGGAGTCCTTGGC	AF190167	CCDS6577.1, CCDS69588.1, CCDS75830.1	9p13.1	2008-02-05			ENSG00000165283	ENSG00000165283			14559	protein-coding gene	gene with protein product		608292				10713127, 17121834	Standard	NM_001287031		Approved	SLP-2, HSPC108	uc003zwi.3	Q9UJZ1	OTTHUMG00000019851	ENST00000356493.5:c.874G>A	9.37:g.35100654C>T	ENSP00000348886:p.Asp292Asn	113	0	0		129	12	0.0930233	NM_013442	B4E1K7|D3DRN3|O60376|Q53G29|Q96FY2|Q9P042	Missense_Mutation	SNP	ENST00000356493.5	37	CCDS6577.1	.	.	.	.	.	.	.	.	.	.	C	17.19	3.325674	0.60743	.	.	ENSG00000165283	ENST00000356493;ENST00000452248	D;D	0.98090	-3.44;-4.71	5.51	5.51	0.81932	.	0.237450	0.43110	D	0.000605	D	0.94771	0.8312	N	0.24115	0.695	0.54753	D	0.999986	B;B	0.26318	0.006;0.146	B;B	0.28465	0.004;0.09	D	0.92340	0.5881	9	.	.	.	-17.448	19.403	0.94639	0.0:1.0:0.0:0.0	.	247;292	B4E1K7;Q9UJZ1	.;STML2_HUMAN	N	292;247	ENSP00000348886:D292N;ENSP00000395743:D247N	.	D	-	1	0	STOML2	35090654	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.893000	0.69798	2.590000	0.87494	0.563000	0.77884	GAC	.	.	none		0.542	STOML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052273.1	NM_013442		T	35100654	C	T	35100654	3	4	17	1	0	0	0	0	1	0	0	0	15329	855	30	2	204	2	STOML2	9	35100654	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10		35100654	106112777	70	2324											
VPS13A	23230	hgsc.bcm.edu	37	chr9	79875041	79875041	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttacctcttatttctttacgAatctcagataaaaaactaca	15	15	2	9	1	3	1	1	0	3	1	4	2	3	1	1	0	4	0	1	0	8	7			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr9:79875041A>T	ENST00000360280.3	+	23	2588	c.2328A>T	c.(2326-2328)cgA>cgT	p.R776R	VPS13A_ENST00000376636.3_Silent_p.R776R|VPS13A_ENST00000357409.5_Silent_p.R776R|VPS13A_ENST00000376634.4_Silent_p.R776R	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	776					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						TTTCTTTACGAATCTCAGATA	0.308																																					p.R776R		Atlas-SNP	.											VPS13A_ENST00000376634,colon,carcinoma,+2,3	VPS13A	735	3	0			c.A2328T						PASS	.						47	47	47					9																	79875041		2203	4297	6500	SO:0001819	synonymous_variant	23230	exon23			TTTACGAATCTCA	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.2328A>T	9.37:g.79875041A>T		223	0	0		315	55	0.174603	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Silent	SNP	ENST00000360280.3	37	CCDS6655.1																																																																																			.	.	none		0.308	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		T	79875041	A	T	79875041	2	4	17	1	0	0	0	0	0	0	0	1	17204	233	9	5		5	VPS13A	9	79875041	Silent	SNP	A	TCGA-FF-A7CQ-01A-11D-A382-10	44774387	79875041	61338390	71	2325											
BAAT	570	hgsc.bcm.edu	37	chr9	104125078	104125078	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttgagttgtctcaaaagtgcGatagagctctagtaacccca	12	11	9	9	1	2	2	1	1	2	1	3	3	2	2	2	0	3	3	2	0	5	5			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr9:104125078G>A	ENST00000395051.3	-	3	959	c.889C>T	c.(889-891)Cgc>Tgc	p.R297C	BAAT_ENST00000259407.2_Missense_Mutation_p.R297C			Q14032	BAAT_HUMAN	bile acid CoA:amino acid N-acyltransferase	297					acyl-CoA metabolic process (GO:0006637)|bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid conjugation (GO:0002152)|bile acid metabolic process (GO:0008206)|fatty acid metabolic process (GO:0006631)|glycine metabolic process (GO:0006544)|liver development (GO:0001889)|organ regeneration (GO:0031100)|small molecule metabolic process (GO:0044281)|taurine metabolic process (GO:0019530)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carboxylic ester hydrolase activity (GO:0052689)|glycine N-choloyltransferase activity (GO:0047963)|long-chain acyl-CoA hydrolase activity (GO:0052816)|medium-chain acyl-CoA hydrolase activity (GO:0052815)|N-acyltransferase activity (GO:0016410)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|very long chain acyl-CoA hydrolase activity (GO:0052817)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		Acute lymphoblastic leukemia(62;0.0559)			Glycine(DB00145)	TCAAAAGTGCGATAGAGCTCT	0.453																																					p.R297C		Atlas-SNP	.											BAAT,NS,carcinoma,+1,2	BAAT	52	2	0			c.C889T						PASS	.						105	106	105					9																	104125078		2203	4300	6503	SO:0001583	missense	570	exon4			AAGTGCGATAGAG	L34081	CCDS6752.1	9q22.3	2014-06-24	2014-06-24		ENSG00000136881	ENSG00000136881	2.3.1.65		932	protein-coding gene	gene with protein product	"glycine N-choloyltransferase"	602938	"bile acid Coenzyme A:amino acid N-acyltransferase (glycine N-choloyltransferase)", "bile acid CoA: amino acid N-acyltransferase (glycine N-choloyltransferase)"				Standard	NM_001701		Approved	BAT	uc010mtd.3	Q14032	OTTHUMG00000020377	ENST00000395051.3:c.889C>T	9.37:g.104125078G>A	ENSP00000378491:p.Arg297Cys	170	0	0		171	31	0.181287	NM_001127610	Q3B7W9|Q96L31	Missense_Mutation	SNP	ENST00000395051.3	37	CCDS6752.1	.	.	.	.	.	.	.	.	.	.	G	16.69	3.193049	0.58017	.	.	ENSG00000136881	ENST00000259407;ENST00000395051	T;T	0.32023	1.47;1.47	4.96	-5.2	0.02823	BAAT/Acyl-CoA thioester hydrolase C-terminal (1);	2.307260	0.01179	N	0.007052	T	0.27798	0.0684	N	0.19112	0.55	0.09310	N	1	D	0.65815	0.995	P	0.56916	0.809	T	0.35773	-0.9775	10	0.72032	D	0.01	1.8351	1.2033	0.01890	0.1891:0.3271:0.153:0.3308	.	297	Q14032	BAAT_HUMAN	C	297	ENSP00000259407:R297C;ENSP00000378491:R297C	ENSP00000259407:R297C	R	-	1	0	BAAT	103164899	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.138000	0.01303	-0.582000	0.05929	0.655000	0.94253	CGC	.	.	none		0.453	BAAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053433.1			A	104125078	G	A	104125078	3	1	17	1	0	0	0	0	1	0	0	0	1280	1058	37	1	371	1	BAAT	9	104125078	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	24250037	104125078	37088353	72	2326											
PPP3R2	116443	hgsc.bcm.edu	37	chr9	104357008	104357008	+	Intron	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagtccacttctccatcacCgtcggtgtcgaagacgtcga	9	9	10	13	5	2	1	1	0	1	1	7	4	3	1	3	1	0	0	3	1	2	1	rs202237297		TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr9:104357008C>T	ENST00000361820.3	-	7	3367				PPP3R2_ENST00000374806.1_Missense_Mutation_p.G69S	NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A						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)	TCTCCATCACCGTCGGTGTCG	0.572																																					p.G69S		Atlas-SNP	.											.	PPP3R2	38	.	0			c.G205A						PASS	.	C	,SER/GLY	0,4406		0,0,2203	90	87	88		,205	3.8	0.3	9		88	7,8593	5.7+/-21.5	0,7,4293	yes	intron,missense	PPP3R2,GRIN3A	NM_133445.2,NM_147180.2	,56	0,7,6496	TT,TC,CC		0.0814,0.0,0.0538	,probably-damaging	,69/174	104357008	7,12999	2203	4300	6503	SO:0001627	intron_variant	5535	exon1			CATCACCGTCGGT		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.2767-15366G>A	9.37:g.104357008C>T		76	0	0		87	7	0.0804598	NM_147180	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	37	CCDS6758.1	.	.	.	.	.	.	.	.	.	.	C	17.45	3.393870	0.62066	0.0	8.14E-4	ENSG00000188386	ENST00000374806;ENST00000541976	T	0.74737	-0.87	3.8	3.8	0.43715	EF-hand-like domain (1);	0.000000	0.40728	N	0.001028	T	0.76147	0.3947	M	0.79258	2.445	0.48236	D	0.999619	P	0.46621	0.881	B	0.43478	0.421	T	0.82016	-0.0666	10	0.87932	D	0	-25.0681	13.968	0.64221	0.0:1.0:0.0:0.0	.	66	Q96LZ3	CANB2_HUMAN	S	69	ENSP00000363939:G69S	ENSP00000363939:G69S	G	-	1	0	PPP3R2	103396829	1.000000	0.71417	0.305000	0.25099	0.163000	0.22366	5.776000	0.68924	2.399000	0.81585	0.563000	0.77884	GGT	.	.	weak		0.572	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1			T	104357008	C	T	104357008	1	4	17	0	1	0	0	0	0	0	0	0	12413	652	23	1		1	PPP3R2	9	104357008	Intron	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	231930	104357008	36856423	73	2327											
PCDH15	65217	hgsc.bcm.edu	37	chr10	55663021	55663021	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	accttcactctgagtacagaAgtaaacattcttgcatcttc	12	13	5	11	0	4	2	1	1	3	1	5	2	4	2	1	0	3	3	1	0	4	6			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr10:55663021A>G	ENST00000320301.6	-	26	3877	c.3483T>C	c.(3481-3483)acT>acC	p.T1161T	PCDH15_ENST00000395430.1_Silent_p.T1161T|PCDH15_ENST00000395433.1_Silent_p.T1139T|PCDH15_ENST00000414778.1_Silent_p.T1166T|PCDH15_ENST00000395432.2_Silent_p.T1124T|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395445.1_Silent_p.T1168T|PCDH15_ENST00000373965.2_Silent_p.T1168T|PCDH15_ENST00000395438.1_Silent_p.T1161T|PCDH15_ENST00000437009.1_Silent_p.T1090T|PCDH15_ENST00000409834.1_Silent_p.T772T|PCDH15_ENST00000361849.3_Silent_p.T1161T|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000463095.1_5'UTR	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1161	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)				TGAGTACAGAAGTAAACATTC	0.353										HNSCC(58;0.16)																											p.T1166T		Atlas-SNP	.											.	PCDH15	1715	.	0			c.T3498C						PASS	.						85	81	82					10																	55663021		2203	4300	6503	SO:0001819	synonymous_variant	65217	exon27			TACAGAAGTAAAC	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.3483T>C	10.37:g.55663021A>G		173	0	0		121	29	0.239669	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	ENST00000320301.6	37	CCDS7248.1																																																																																			.	.	none		0.353	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		G	55663021	A	G	55663021	2	3	17	1	0	0	0	0	0	0	0	1	11520	59	3	3		3	PCDH15	10	55663021	Silent	SNP	A	TCGA-FF-A7CQ-01A-11D-A382-10		55663021	79871726	74	2328											
PDZD8	118987	hgsc.bcm.edu	37	chr10	119133946	119133946	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gatgatggaggtgagctgggGcatgggccgcccttcaaact	8	8	16	9	1	1	2	1	2	0	0	1	4	1	3	2	5	2	2	2	5	1	1			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr10:119133946G>A	ENST00000334464.5	-	1	1032	c.793C>T	c.(793-795)Ccc>Tcc	p.P265S		NM_173791.3	NP_776152.1	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	265					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)		GTGAGCTGGGGCATGGGCCGC	0.582																																					p.P265S		Atlas-SNP	.											.	PDZD8	85	.	0			c.C793T						PASS	.						64	69	68					10																	119133946		2203	4300	6503	SO:0001583	missense	118987	exon1			GCTGGGGCATGGG	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.793C>T	10.37:g.119133946G>A	ENSP00000334642:p.Pro265Ser	90	0	0		70	16	0.228571	NM_173791	Q86WE0|Q86WE5|Q9UFF1	Missense_Mutation	SNP	ENST00000334464.5	37	CCDS7600.1	.	.	.	.	.	.	.	.	.	.	G	15.37	2.813834	0.50527	.	.	ENSG00000165650	ENST00000334464	D	0.87029	-2.2	4.87	3.96	0.45880	.	0.000000	0.85682	D	0.000000	D	0.91064	0.7188	L	0.54323	1.7	0.58432	D	0.999998	D	0.89917	1.0	D	0.85130	0.997	D	0.89811	0.3982	10	0.37606	T	0.19	-2.6702	14.5263	0.67892	0.0:0.0:0.8523:0.1477	.	265	Q8NEN9	PDZD8_HUMAN	S	265	ENSP00000334642:P265S	ENSP00000334642:P265S	P	-	1	0	PDZD8	119123936	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	7.425000	0.80255	1.015000	0.39444	0.655000	0.94253	CCC	.	.	none		0.582	PDZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050565.1	NM_173791		A	119133946	G	A	119133946	3	1	17	1	0	0	0	0	1	0	0	0	11714	1203	42	2	2691	2	PDZD8	10	119133946	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	63470925	119133946	16400801	75	2329											
PDZD8	118987	hgsc.bcm.edu	37	chr10	119133982	119133982	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaactgggagcgcacctcgaAgtcgatcagcgggtcttcca	10	7	12	12	4	2	0	1	0	1	0	5	3	3	1	2	2	3	1	2	2	2	1			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr10:119133982A>G	ENST00000334464.5	-	1	996	c.757T>C	c.(757-759)Ttc>Ctc	p.F253L		NM_173791.3	NP_776152.1	Q8NEN9	PDZD8_HUMAN	PDZ domain containing 8	253					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)		CGCACCTCGAAGTCGATCAGC	0.597																																					p.F253L		Atlas-SNP	.											.	PDZD8	85	.	0			c.T757C						PASS	.						57	58	57					10																	119133982		2203	4300	6503	SO:0001583	missense	118987	exon1			CCTCGAAGTCGAT	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.757T>C	10.37:g.119133982A>G	ENSP00000334642:p.Phe253Leu	92	0	0		70	14	0.2	NM_173791	Q86WE0|Q86WE5|Q9UFF1	Missense_Mutation	SNP	ENST00000334464.5	37	CCDS7600.1	.	.	.	.	.	.	.	.	.	.	A	4.086	0.014013	0.07959	.	.	ENSG00000165650	ENST00000334464	D	0.84370	-1.84	4.87	3.72	0.42706	.	0.063697	0.64402	D	0.000005	T	0.69744	0.3145	N	0.16478	0.41	0.49299	D	0.999774	B	0.15930	0.015	B	0.15052	0.012	T	0.57306	-0.7834	10	0.20046	T	0.44	-9.6398	6.3359	0.21296	0.7806:0.0:0.0778:0.1416	.	253	Q8NEN9	PDZD8_HUMAN	L	253	ENSP00000334642:F253L	ENSP00000334642:F253L	F	-	1	0	PDZD8	119123972	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.781000	0.68964	0.677000	0.31305	0.533000	0.62120	TTC	.	.	none		0.597	PDZD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050565.1	NM_173791		G	119133982	A	G	119133982	3	3	17	1	0	0	0	0	1	0	0	0	11714	72	3	3	2727	3	PDZD8	10	119133982	Missense_Mutation	SNP	A	TCGA-FF-A7CQ-01A-11D-A382-10	36	119133982	16400765	76	2330											
EIF3A	8661	hgsc.bcm.edu	37	chr10	120824953	120824953	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtgtcggtggggcttgaagAcctagtagtgttgcaaggcg	7	10	17	7	3	0	2	0	1	0	1	1	2	0	2	1	4	1	4	1	4	4	4			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr10:120824953A>C	ENST00000369144.3	-	7	1207	c.1080T>G	c.(1078-1080)ggT>ggG	p.G360G	EIF3A_ENST00000541549.1_Silent_p.G326G	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)		GGGCTTGAAGACCTAGTAGTG	0.418																																					p.G360G		Atlas-SNP	.											.	EIF3A	142	.	0			c.T1080G						PASS	.						135	127	130					10																	120824953		2203	4300	6503	SO:0001819	synonymous_variant	8661	exon7			TTGAAGACCTAGT	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.1080T>G	10.37:g.120824953A>C		136	0	0		129	35	0.271318	NM_003750	B7ZBG9|Q6IBN8|Q96TD5	Silent	SNP	ENST00000369144.3	37	CCDS7608.1																																																																																			.	.	none		0.418	EIF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050634.1	NM_003750		C	120824953	A	C	120824953	2	2	17	1	0	0	0	0	0	0	0	1	5014	262	10	5		5	EIF3A	10	120824953	Silent	SNP	A	TCGA-FF-A7CQ-01A-11D-A382-10	1690971	120824953	14709794	77	2331											
EPS8L2	64787	hgsc.bcm.edu	37	chr11	726654	726655	+	Frame_Shift_Ins	INS	-	-	GCTC																															ggcatcctgaccgggccgcaINSgctcttctccctcaacaagg																										TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr11:726654_726655insGCTC	ENST00000533256.1	+	21	2345_2346	c.1970_1971insGCTC	c.(1969-1974)cagctcfs	p.-658fs	EPS8L2_ENST00000526198.1_Frame_Shift_Ins_p.-674fs|EPS8L2_ENST00000530636.1_Frame_Shift_Ins_p.-658fs|EPS8L2_ENST00000534449.1_3'UTR|AP006621.9_ENST00000527021.2_RNA|EPS8L2_ENST00000318562.8_Frame_Shift_Ins_p.-658fs			Q9H6S3	ES8L2_HUMAN	EPS8-like 2						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)		ACCGGGCCGCAGCTCTTCTCCC	0.678																																					p.Q657fs		Pindel,Atlas-Indel	.											.	EPS8L2	42	.	0			c.1970_1971insGCTC						PASS	.																																			SO:0001589	frameshift_variant	64787	exon20			.	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.1971_1974dupGCTC	11.37:g.726655_726658dupGCTC	ENSP00000435585:p.Leu658fs	103	0	.		106	18	0.17	NM_022772	B3KSX1|B7ZKL3|Q53GM8|Q8WYW7|Q96K06|Q9H6K9	Frame_Shift_Ins	INS	ENST00000533256.1	37	CCDS31328.1																																																																																			.	.	none		0.678	EPS8L2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382344.1	NM_022772		GCTC	726655	-	GCTC	726654	7	5	17	1	0	1	1	0	0	0	0	0	5198	188	7	0	2044	0	EPS8L2	11	726654	Frame_Shift_Ins	INS	-	TCGA-FF-A7CQ-01A-11D-A382-10		726654	134279862	78	2332											
C11orf40	143501	hgsc.bcm.edu	37	chr11	4592708	4592708	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaagtagaacacgatccataCagtttttccctgcaaagacc	14	9	7	11	1	0	2	0	0	0	2	2	4	2	2	3	0	3	3	3	0	5	4	rs67037861|rs71280817|rs79804156		TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr11:4592708C>G	ENST00000307616.1	-	4	598	c.599G>C	c.(598-600)tGt>tCt	p.C200S		NM_144663.1	NP_653264.1	Q8WZ69	CK040_HUMAN	chromosome 11 open reading frame 40	200										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)		acgatccatacagtttttccC	0.428																																					p.C200S		Atlas-SNP	.											.	C11orf40	37	.	0			c.G599C						PASS	.						87	75	79					11																	4592708		2133	4180	6313	SO:0001583	missense	143501	exon4			TCCATACAGTTTT		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.599G>C	11.37:g.4592708C>G	ENSP00000302918:p.Cys200Ser	132	0	0		125	11	0.088	NM_144663		Missense_Mutation	SNP	ENST00000307616.1	37	CCDS31354.1	.	.	.	.	.	.	.	.	.	.	C	1.174	-0.640091	0.03557	.	.	ENSG00000171987	ENST00000307616	T	0.54866	0.55	0.56	-1.12	0.09808	.	.	.	.	.	T	0.27524	0.0676	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.17349	-1.0372	8	0.87932	D	0	.	.	.	.	.	200	Q8WZ69	CK040_HUMAN	S	200	ENSP00000302918:C200S	ENSP00000302918:C200S	C	-	2	0	C11orf40	4549284	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	-1.580000	0.02121	-0.348000	0.08286	-1.125000	0.01998	TGT	.	.	weak		0.428	C11orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383529.1	NM_144663		G	4592708	C	G	4592708	3	3	17	1	0	0	0	0	1	0	0	0	1641	478	17	4	57	4	C11orf40	11	4592708	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	3866054	4592708	130413808	79	2333											
MPEG1	219972	hgsc.bcm.edu	37	chr11	58978697	58978697	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagagacggtgcccctaaatCtctggatatagcaggatcta	12	9	10	10	1	2	1	0	0	2	1	3	4	2	3	2	3	2	1	2	3	5	4			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr11:58978697C>T	ENST00000361050.3	-	1	1727	c.1642G>A	c.(1642-1644)Gat>Aat	p.D548N		NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	548						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)				GCCCCTAAATCTCTGGATATA	0.557																																					p.D548N		Atlas-SNP	.											.	MPEG1	72	.	0			c.G1642A						PASS	.						40	43	42					11																	58978697		1844	4086	5930	SO:0001583	missense	219972	exon1			CTAAATCTCTGGA	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.1642G>A	11.37:g.58978697C>T	ENSP00000354335:p.Asp548Asn	77	0	0		64	16	0.25	NM_001039396	Q2M1T6|Q8TEF8	Missense_Mutation	SNP	ENST00000361050.3	37	CCDS41650.1	.	.	.	.	.	.	.	.	.	.	C	4.924	0.171623	0.09391	.	.	ENSG00000197629	ENST00000361050	T	0.22539	1.95	5.83	4.74	0.60224	.	0.250875	0.28560	N	0.014904	T	0.20210	0.0486	L	0.48362	1.52	0.09310	N	1	B	0.18310	0.027	B	0.17433	0.018	T	0.07888	-1.0749	10	0.44086	T	0.13	-21.4942	12.7616	0.57367	0.0:0.9095:0.0:0.0905	.	548	Q2M385	MPEG1_HUMAN	N	548	ENSP00000354335:D548N	ENSP00000354335:D548N	D	-	1	0	MPEG1	58735273	0.182000	0.23173	0.069000	0.20011	0.065000	0.16274	0.596000	0.24044	2.767000	0.95098	0.655000	0.94253	GAT	.	.	none		0.557	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396		T	58978697	C	T	58978697	3	4	17	1	0	0	0	0	1	0	0	0	9732	913	32	2	512	2	MPEG1	11	58978697	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	54385989	58978697	76027819	80	2334											
MPEG1	219972	hgsc.bcm.edu	37	chr11	58980009	58980009	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgttgatggagtaggaggtGctactctggtaatttgccca	8	13	14	6	0	1	1	0	1	1	0	1	3	1	3	1	4	3	4	1	4	3	5			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr11:58980009G>A	ENST00000361050.3	-	1	415	c.330C>T	c.(328-330)agC>agT	p.S110S	RN7SL42P_ENST00000579786.1_RNA	NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	110	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)				AGTAGGAGGTGCTACTCTGGT	0.453																																					p.S110S		Atlas-SNP	.											.	MPEG1	72	.	0			c.C330T						PASS	.						200	187	191					11																	58980009		1918	4125	6043	SO:0001819	synonymous_variant	219972	exon1			GGAGGTGCTACTC	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.330C>T	11.37:g.58980009G>A		121	0	0		133	45	0.338346	NM_001039396	Q2M1T6|Q8TEF8	Silent	SNP	ENST00000361050.3	37	CCDS41650.1																																																																																			.	.	none		0.453	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396		A	58980009	G	A	58980009	2	1	17	1	0	0	0	0	0	0	0	1	9732	1310	46	2		2	MPEG1	11	58980009	Silent	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	1312	58980009	76026507	81	2335											
SHANK2	22941	hgsc.bcm.edu	37	chr11	70332437	70332437	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgttgtccagcttagtggCgtccacggtgtgcaccatca	6	10	13	12	3	1	0	1	0	0	0	3	0	3	0	3	3	2	3	3	3	1	2	rs555445178		TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr11:70332437C>T	ENST00000423696.2	-	15	2860	c.2824G>A	c.(2824-2826)Gcc>Acc	p.A942T	SHANK2_ENST00000409161.1_Missense_Mutation_p.A725T|SHANK2_ENST00000449833.2_Missense_Mutation_p.A726T|SHANK2_ENST00000338508.4_Missense_Mutation_p.A1322T			Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	942					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)			AGCTTAGTGGCGTCCACGGTG	0.592																																					p.A733T		Atlas-SNP	.											.	SHANK2	340	.	0			c.G2197A						PASS	.						119	105	110					11																	70332437		2200	4294	6494	SO:0001583	missense	22941	exon10			TAGTGGCGTCCAC	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.2824G>A	11.37:g.70332437C>T	ENSP00000394536:p.Ala942Thr	114	0	0		86	26	0.302326	NM_133266	C0SPG8|C0SPG9|Q3Y8G9|Q52LK2|Q9UKP1	Missense_Mutation	SNP	ENST00000423696.2	37		.	.	.	.	.	.	.	.	.	.	C	1.958	-0.439660	0.04636	.	.	ENSG00000162105	ENST00000449833;ENST00000409161;ENST00000424924;ENST00000338508;ENST00000423696;ENST00000433693;ENST00000294018	T;T;T;T;T;T	0.17691	2.26;2.26;2.26;2.26;2.26;2.26	4.98	0.842	0.18927	.	0.465316	0.25863	N	0.027802	T	0.07818	0.0196	N	0.13043	0.29	0.09310	N	0.999999	B;B;B	0.10296	0.003;0.003;0.002	B;B;B	0.08055	0.003;0.003;0.002	T	0.41413	-0.9510	10	0.10902	T	0.67	.	8.9408	0.35729	0.0:0.455:0.0:0.545	.	942;1321;726	Q9UPX8;Q9UPX8-3;Q9UPX8-4	SHAN2_HUMAN;.;.	T	726;725;600;1322;942;960;945	ENSP00000399423:A726T;ENSP00000386491:A725T;ENSP00000402944:A600T;ENSP00000345193:A1322T;ENSP00000394536:A942T;ENSP00000294018:A945T	ENSP00000294018:A945T	A	-	1	0	SHANK2	70010085	0.010000	0.17322	0.079000	0.20413	0.912000	0.54170	0.683000	0.25349	-0.107000	0.12088	0.561000	0.74099	GCC	.	.	none		0.592	SHANK2-203	KNOWN	basic	protein_coding	protein_coding		NM_012309		T	70332437	C	T	70332437	3	4	17	1	0	0	0	0	1	0	0	0	14280	768	27	1	1596	1	SHANK2	11	70332437	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	11352428	70332437	64674079	82	2336											
MTNR1B	4544	hgsc.bcm.edu	37	chr11	92703057	92703057	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaccaccgccgtggacgtcGtgggcaacctcctggtgatc	6	8	12	15	4	1	1	1	1	0	0	4	2	2	2	5	3	1	1	5	3	1	0	rs148309052		TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr11:92703057G>A	ENST00000257068.2	+	1	172	c.166G>A	c.(166-168)Gtg>Atg	p.V56M		NM_005959.3	NP_005950.1	P49286	MTR1B_HUMAN	melatonin receptor 1B	56					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)	CGTGGACGTCGTGGGCAACCT	0.692																																					p.V56M		Atlas-SNP	.											.	MTNR1B	75	.	0			c.G166A						PASS	.	G	MET/VAL	0,4396		0,0,2198	35	28	30		166	-1.4	0	11	dbSNP_134	30	2,8588		0,2,4293	no	missense	MTNR1B	NM_005959.3	21	0,2,6491	AA,AG,GG		0.0233,0.0,0.0154	benign	56/363	92703057	2,12984	2198	4295	6493	SO:0001583	missense	4544	exon1			GACGTCGTGGGCA	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.166G>A	11.37:g.92703057G>A	ENSP00000257068:p.Val56Met	57	0	0		52	11	0.211538	NM_005959		Missense_Mutation	SNP	ENST00000257068.2	37	CCDS8290.1	.	.	.	.	.	.	.	.	.	.	G	4.668	0.124122	0.08931	0.0	2.33E-4	ENSG00000134640	ENST00000257068	T	0.40225	1.04	4.57	-1.37	0.09056	.	0.534882	0.16009	N	0.233911	T	0.19967	0.0480	L	0.29908	0.895	0.19775	N	0.999956	P	0.35982	0.531	B	0.26310	0.068	T	0.09185	-1.0686	10	0.34782	T	0.22	-0.2663	3.6257	0.08112	0.1518:0.353:0.3793:0.1159	.	56	P49286	MTR1B_HUMAN	M	56	ENSP00000257068:V56M	ENSP00000257068:V56M	V	+	1	0	MTNR1B	92342705	0.012000	0.17670	0.023000	0.16930	0.042000	0.13812	0.085000	0.14912	-0.236000	0.09753	-0.142000	0.14014	GTG	G|1.000;A|0.000	0.000	weak		0.692	MTNR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394323.1			A	92703057	G	A	92703057	3	1	17	1	0	0	0	0	1	0	0	0	9961	1145	40	1	168	1	MTNR1B	11	92703057	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	22370620	92703057	42303459	83	2337											
TAS2R30	259293	hgsc.bcm.edu	37	chr12	11286093	11286093	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttttccagcctcccaaaatTacaaactgatatgatcatgg	13	12	5	11	0	1	2	1	2	0	0	3	2	3	2	3	1	3	0	3	1	5	4			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr12:11286093T>G	ENST00000539585.1	-	1	1150	c.751A>C	c.(751-753)Aat>Cat	p.N251H	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_001097643.1	NP_001091112.1	P59541	T2R30_HUMAN	taste receptor, type 2, member 30	251					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)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	13						CTCCCAAAATTACAAACTGAT	0.413																																					p.N251H		Atlas-SNP	.											.	TAS2R30	28	.	0			c.A751C						PASS	.						134	142	139					12																	11286093		2203	4299	6502	SO:0001583	missense	259293	exon1			CAAAATTACAAAC	AX097746, AF494233	CCDS53750.1	12p13.2	2012-08-22				ENSG00000256188		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	19112	protein-coding gene	gene with protein product		613963	"taste receptor, type 2, member 47"	TAS2R47			Standard	NM_001097643		Approved	T2R30	uc009zhs.1	P59541		ENST00000539585.1:c.751A>C	12.37:g.11286093T>G	ENSP00000444736:p.Asn251His	170	0	0		178	41	0.230337	NM_001097643	Q645X7	Missense_Mutation	SNP	ENST00000539585.1	37	CCDS53750.1	.	.	.	.	.	.	.	.	.	.	-	7.335	0.619790	0.14193	.	.	ENSG00000256188	ENST00000539585	T	0.00737	5.76	2.6	-2.21	0.06973	.	.	.	.	.	T	0.00845	0.0028	L	0.56340	1.77	0.09310	N	1	B	0.17038	0.02	B	0.23716	0.048	T	0.44574	-0.9319	9	0.23891	T	0.37	.	3.172	0.06555	0.4197:0.0:0.2144:0.3658	.	251	P59541	T2R30_HUMAN	H	251	ENSP00000444736:N251H	ENSP00000444736:N251H	N	-	1	0	TAS2R30	11177360	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.332000	0.07904	-0.617000	0.05664	0.260000	0.18958	AAT	.	.	none		0.413	TAS2R30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400238.1	NM_001097643		G	11286093	T	G	11286093	3	3	17	1	0	0	0	0	1	0	0	0	15588	1754	61	5	212	5	TAS2R30	12	11286093	Missense_Mutation	SNP	T	TCGA-FF-A7CQ-01A-11D-A382-10		11286093	122565802	84	2338											
SRGAP1	57522	hgsc.bcm.edu	37	chr12	64485076	64485076	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcctccaaatgttccccctaAgccccagaaacacaggaagt	13	6	7	15	0	0	1	0	0	0	1	2	2	2	2	6	1	2	1	6	1	4	2			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr12:64485076A>C	ENST00000355086.3	+	12	1981	c.1457A>C	c.(1456-1458)aAg>aCg	p.K486T	RP11-196H14.2_ENST00000535594.1_RNA|SRGAP1_ENST00000543397.1_Intron|SRGAP1_ENST00000357825.3_Intron	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	486	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)		GTTCCCCCTAAGCCCCAGAAA	0.428																																					p.K486T		Atlas-SNP	.											.	SRGAP1	146	.	0			c.A1457C						PASS	.						85	87	86					12																	64485076		2203	4300	6503	SO:0001583	missense	57522	exon12			CCCCTAAGCCCCA	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.1457A>C	12.37:g.64485076A>C	ENSP00000347198:p.Lys486Thr	73	0	0		61	11	0.180328	NM_020762	Q9H8A3|Q9P2P2	Missense_Mutation	SNP	ENST00000355086.3	37	CCDS8967.1	.	.	.	.	.	.	.	.	.	.	A	17.07	3.294486	0.60086	.	.	ENSG00000196935	ENST00000355086	T	0.08720	3.06	5.75	5.75	0.90469	.	0.000000	0.36591	U	0.002508	T	0.08714	0.0216	L	0.49126	1.545	0.80722	D	1	P	0.37781	0.608	B	0.27608	0.081	T	0.21177	-1.0253	9	.	.	.	.	15.5468	0.76108	1.0:0.0:0.0:0.0	.	486	Q7Z6B7	SRGP1_HUMAN	T	486	ENSP00000347198:K486T	.	K	+	2	0	SRGAP1	62771343	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.299000	0.59073	2.326000	0.78906	0.533000	0.62120	AAG	.	.	none		0.428	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1			C	64485076	A	C	64485076	3	2	17	1	0	0	0	0	1	0	0	0	15160	72	3	5	1503	5	SRGAP1	12	64485076	Missense_Mutation	SNP	A	TCGA-FF-A7CQ-01A-11D-A382-10	53198983	64485076	69366819	85	2339											
POSTN	10631	hgsc.bcm.edu	37	chr13	38158888	38158888	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacctgatcaatcaaatggAtcacaccattatttgtcaca	14	11	6	10	0	4	1	4	1	0	0	4	3	4	3	2	2	0	0	2	2	3	2			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr13:38158888A>G	ENST00000379747.4	-	8	1190	c.1073T>C	c.(1072-1074)aTc>aCc	p.I358T	POSTN_ENST00000541481.1_Missense_Mutation_p.I358T|POSTN_ENST00000379743.4_Missense_Mutation_p.I358T|POSTN_ENST00000379742.4_Missense_Mutation_p.I358T|POSTN_ENST00000379749.4_Missense_Mutation_p.I358T|POSTN_ENST00000541179.1_Missense_Mutation_p.I358T	NM_006475.2	NP_006466.2	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor	358	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)		AATCAAATGGATCACACCATT	0.313																																					p.I358T		Atlas-SNP	.											POSTN,colon,carcinoma,0,1	POSTN	161	1	0			c.T1073C						scavenged	.						235	199	212					13																	38158888		2203	4300	6503	SO:0001583	missense	10631	exon8			AAATGGATCACAC	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.1073T>C	13.37:g.38158888A>G	ENSP00000369071:p.Ile358Thr	234	2	0.00854701		217	59	0.271889	NM_006475	B1ALD8|C0IMJ1|C0IMJ2|C0IMJ4|D2KRH7|F5H628|Q15064|Q29XZ0|Q3KPJ5|Q5VSY5|Q8IZF9	Missense_Mutation	SNP	ENST00000379747.4	37	CCDS9364.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.193128	0.78902	.	.	ENSG00000133110	ENST00000541179;ENST00000379749;ENST00000379747;ENST00000379743;ENST00000379742;ENST00000541481	D;D;D;D;D;D	0.94723	-3.5;-3.5;-3.5;-3.5;-3.5;-3.5	5.41	5.41	0.78517	FAS1 domain (5);	0.000000	0.85682	D	0.000000	D	0.98074	0.9365	H	0.95712	3.71	0.58432	D	0.999998	D;D;D;D;D;D;D	0.89917	0.998;0.995;1.0;0.997;0.987;0.999;1.0	D;D;D;D;D;D;D	0.91635	0.997;0.995;0.999;0.995;0.976;0.979;0.999	D	0.99395	1.0926	10	0.87932	D	0	.	15.1264	0.72486	1.0:0.0:0.0:0.0	.	358;358;358;358;358;358;358	C0IMJ4;F5H628;B1ALD8;Q15063-3;Q15063-4;Q15063-2;Q15063	.;.;.;.;.;.;POSTN_HUMAN	T	358	ENSP00000437959:I358T;ENSP00000369073:I358T;ENSP00000369071:I358T;ENSP00000369067:I358T;ENSP00000369066:I358T;ENSP00000437953:I358T	ENSP00000369066:I358T	I	-	2	0	POSTN	37056888	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.926000	0.92839	2.043000	0.60533	0.533000	0.62120	ATC	.	.	none		0.313	POSTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044566.2	NM_006475		G	38158888	A	G	38158888	3	3	17	1	0	0	0	0	1	0	0	0	12268	333	12	3	1501	3	POSTN	13	38158888	Missense_Mutation	SNP	A	TCGA-FF-A7CQ-01A-11D-A382-10		38158888	77010990	86	2340											
AKAP11	11215	hgsc.bcm.edu	37	chr13	42876626	42876626	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgcctacttttttaaacccCtcagacgaaaatttgaaaac	14	12	4	11	2	1	2	1	1	0	1	2	3	1	2	3	0	3	0	3	0	7	5			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr13:42876626C>A	ENST00000025301.2	+	8	3919	c.3744C>A	c.(3742-3744)ccC>ccA	p.P1248P		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	1248					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)		TTTTAAACCCCTCAGACGAAA	0.368																																					p.P1248P		Atlas-SNP	.											.	AKAP11	146	.	0			c.C3744A						PASS	.						65	69	68					13																	42876626		2203	4300	6503	SO:0001819	synonymous_variant	11215	exon8			AAACCCCTCAGAC	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.3744C>A	13.37:g.42876626C>A		104	0	0		97	26	0.268041	NM_016248	O75124|Q9NUK7	Silent	SNP	ENST00000025301.2	37	CCDS9383.1																																																																																			.	.	none		0.368	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248		A	42876626	C	A	42876626	2	1	17	1	0	0	0	0	0	0	0	1	447	668	24	4		4	AKAP11	13	42876626	Silent	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	4717738	42876626	72293252	87	2341											
HS6ST3	266722	hgsc.bcm.edu	37	chr13	96743654	96743654	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	agccttgtagctgcaaagcgGgtcagaagaagtgcacctgc	11	7	13	10	1	1	2	1	0	0	2	1	2	1	2	2	1	6	4	2	1	4	2			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr13:96743654G>A	ENST00000376705.2	+	1	562	c.538G>A	c.(538-540)Ggt>Agt	p.G180S		NM_153456.3	NP_703157.2	Q8IZP7	H6ST3_HUMAN	heparan sulfate 6-O-sulfotransferase 3	180					heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)	integral component of membrane (GO:0016021)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)			NS(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|skin(1)	20	all_neural(89;0.0878)|Medulloblastoma(90;0.163)					CTGCAAAGCGGGTCAGAAGAA	0.637																																					p.G180S		Atlas-SNP	.											.	HS6ST3	54	.	0			c.G538A						PASS	.						32	30	31					13																	96743654		2203	4300	6503	SO:0001583	missense	266722	exon1			AAAGCGGGTCAGA	AF539426	CCDS9481.1	13q32.2	2007-12-04			ENSG00000185352	ENSG00000185352		"Sulfotransferases, membrane-bound"	19134	protein-coding gene	gene with protein product		609401					Standard	NM_153456		Approved		uc001vmw.4	Q8IZP7	OTTHUMG00000017232	ENST00000376705.2:c.538G>A	13.37:g.96743654G>A	ENSP00000365895:p.Gly180Ser	22	0	0		35	15	0.428571	NM_153456	Q5W0L0|Q68CW6	Missense_Mutation	SNP	ENST00000376705.2	37	CCDS9481.1	.	.	.	.	.	.	.	.	.	.	g	19.57	3.852748	0.71719	.	.	ENSG00000185352	ENST00000376705	T	0.44083	0.93	5.29	3.52	0.40303	.	0.000000	0.85682	D	0.000000	T	0.65995	0.2745	M	0.85542	2.76	0.47183	D	0.999344	D	0.89917	1.0	D	0.97110	1.0	T	0.68834	-0.5304	10	0.59425	D	0.04	-15.837	12.193	0.54282	0.0:0.1303:0.7341:0.1357	.	180	Q8IZP7	H6ST3_HUMAN	S	180	ENSP00000365895:G180S	ENSP00000365895:G180S	G	+	1	0	HS6ST3	95541655	1.000000	0.71417	0.943000	0.38184	0.809000	0.45718	7.241000	0.78201	0.586000	0.29626	0.645000	0.84053	GGT	.	.	none		0.637	HS6ST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045517.2	NM_153456		A	96743654	G	A	96743654	3	1	17	1	0	0	0	0	1	0	0	0	7381	1232	43	2	540	2	HS6ST3	13	96743654	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	53867028	96743654	18426224	88	2342											
FAM179B	23116	hgsc.bcm.edu	37	chr14	45535938	45535938	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttttatcagatacagaaaatAatcaagaccttgttgttgga	15	14	7	5	0	2	3	2	0	0	3	2	4	2	4	1	1	1	2	1	1	6	7			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr14:45535938A>G	ENST00000361577.3	+	16	4772	c.4558A>G	c.(4558-4560)Aat>Gat	p.N1520D	FAM179B_ENST00000382233.2_3'UTR|FAM179B_ENST00000361462.2_Missense_Mutation_p.N1573D	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	1520										endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						TACAGAAAATAATCAAGACCT	0.368																																					p.N1520D		Atlas-SNP	.											.	FAM179B	115	.	0			c.A4558G						PASS	.						77	81	79					14																	45535938		2203	4300	6503	SO:0001583	missense	23116	exon16			GAAAATAATCAAG	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.4558A>G	14.37:g.45535938A>G	ENSP00000355045:p.Asn1520Asp	113	0	0		106	31	0.292453	NM_015091	Q68D66|Q6PG27	Missense_Mutation	SNP	ENST00000361577.3	37	CCDS9681.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.183215	0.78677	.	.	ENSG00000198718	ENST00000361577;ENST00000361462	T;T	0.22336	1.96;1.96	5.59	4.43	0.53597	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.41858	0.1177	M	0.65498	2.005	0.80722	D	1	D;D	0.71674	0.994;0.998	D;D	0.70935	0.949;0.971	T	0.23726	-1.0180	10	0.59425	D	0.04	-14.0258	11.3311	0.49477	0.8479:0.1521:0.0:0.0	.	1573;1520	G3XAE9;Q9Y4F4	.;F179B_HUMAN	D	1520;1573	ENSP00000355045:N1520D;ENSP00000354917:N1573D	ENSP00000354917:N1573D	N	+	1	0	FAM179B	44605688	1.000000	0.71417	0.997000	0.53966	0.986000	0.74619	7.279000	0.78599	0.929000	0.37192	0.459000	0.35465	AAT	.	.	none		0.368	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781		G	45535938	A	G	45535938	3	3	17	1	0	0	0	0	1	0	0	0	5511	362	13	3	4620	3	FAM179B	14	45535938	Missense_Mutation	SNP	A	TCGA-FF-A7CQ-01A-11D-A382-10		45535938	61813602	89	2343											
PRKCH	5583	hgsc.bcm.edu	37	chr14	61857975	61857975	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccagaggggaaagtatttgtGgtaataacccttaccgggag	12	9	13	7	1	0	1	0	0	0	1	0	3	0	3	3	4	2	2	3	4	5	5			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr14:61857975G>T	ENST00000332981.5	+	2	781	c.396G>T	c.(394-396)gtG>gtT	p.V132V	PRKCH_ENST00000555082.1_5'UTR	NM_006255.3	NP_006246.2	P24723	KPCL_HUMAN	protein kinase C, eta	132					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)		AAGTATTTGTGGTAATAACCC	0.338																																					p.V132V	Melanoma(135;863 1779 8064 14443 26348)	Atlas-SNP	.											.	PRKCH	89	.	0			c.G396T						PASS	.						87	85	86					14																	61857975		2203	4300	6503	SO:0001819	synonymous_variant	5583	exon2			ATTTGTGGTAATA	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.396G>T	14.37:g.61857975G>T		106	0	0		106	29	0.273585	NM_006255	B4DJN5|Q16246|Q8NE03	Silent	SNP	ENST00000332981.5	37	CCDS9752.1																																																																																			.	.	none		0.338	PRKCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276974.2	NM_006255		T	61857975	G	T	61857975	2	4	17	1	0	0	0	0	0	0	0	1	12525	1335	47	4		4	PRKCH	14	61857975	Silent	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	16322037	61857975	45491565	90	2344											
RGS6	9628	hgsc.bcm.edu	37	chr14	72943455	72943455	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgcttcttctcctagtccgtGtatggcgtgactgaagagtc	6	14	11	10	2	2	3	0	2	2	1	5	3	3	3	2	1	1	2	2	1	3	4			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr14:72943455G>A	ENST00000553530.1	+	11	906	c.699G>A	c.(697-699)gtG>gtA	p.V233V	RGS6_ENST00000406236.4_Silent_p.V233V|RGS6_ENST00000402788.2_Silent_p.V233V|RGS6_ENST00000556437.1_Silent_p.V233V|RGS6_ENST00000434263.2_Silent_p.V164V|RGS6_ENST00000555571.1_Silent_p.V233V|RGS6_ENST00000553525.1_Silent_p.V233V|RGS6_ENST00000404301.2_Silent_p.V233V|RGS6_ENST00000407322.4_Silent_p.V233V|RGS6_ENST00000355512.6_Silent_p.V233V|RGS6_ENST00000554782.1_Silent_p.V94V|RGS6_ENST00000343854.6_Silent_p.V233V	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	233					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)		CCTAGTCCGTGTATGGCGTGA	0.507																																					p.V233V	Ovarian(143;1926 2468 21071 48641)	Atlas-SNP	.											RGS6,NS,carcinoma,+1,1	RGS6	92	1	0			c.G699A						PASS	.						117	100	106					14																	72943455		2203	4300	6503	SO:0001819	synonymous_variant	9628	exon11			GTCCGTGTATGGC	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.699G>A	14.37:g.72943455G>A		112	0	0		92	13	0.141304	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	37	CCDS9808.1																																																																																			.	.	none		0.507	RGS6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413033.2			A	72943455	G	A	72943455	2	1	17	1	0	0	0	0	0	0	0	1	13324	1364	48	2		2	RGS6	14	72943455	Silent	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	11085480	72943455	34406085	91	2345											
MAGEL2	54551	hgsc.bcm.edu	37	chr15	23889331	23889331	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctggtttccaggaatgctcGagggccccagaggaactcat	9	8	13	11	1	1	1	1	0	0	1	3	4	2	3	3	4	2	3	3	4	2	1	rs368965952		TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr15:23889331G>A	ENST00000532292.1	-	1	1844	c.1750C>T	c.(1750-1752)Cga>Tga	p.R584*		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2	467					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)		AGGAATGCTCGAGGGCCCCAG	0.507																																					p.R1187X		Atlas-SNP	.											.	MAGEL2	108	.	0			c.C3559T						PASS	.						52	53	53					15																	23889331		1908	4117	6025	SO:0001587	stop_gained	54551	exon1			ATGCTCGAGGGCC	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.1750C>T	15.37:g.23889331G>A	ENSP00000433433:p.Arg584*	97	0	0		87	26	0.298851	NM_019066		Nonsense_Mutation	SNP	ENST00000532292.1	37																																																																																				.	.	alt		0.507	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395182.2	NM_019066		A	23889331	G	A	23889331	4	1	17	1	0	0	0	0	0	1	0	0	9198	1066	37	1	194	1	MAGEL2	15	23889331	Nonsense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10		23889331	78642061	92	2346											
FEM1B	10116	hgsc.bcm.edu	37	chr15	68583506	68583506	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcaagtgcctggctgcccgaGcagttcgggctaatgacatt	8	10	12	11	2	1	1	1	1	0	0	2	2	1	1	2	2	3	4	2	2	2	3			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr15:68583506G>A	ENST00000306917.4	+	2	2425	c.1810G>A	c.(1810-1812)Gca>Aca	p.A604T		NM_015322.4	NP_056137.1	Q9UK73	FEM1B_HUMAN	fem-1 homolog b (C. elegans)	604					apoptotic process (GO:0006915)|branching involved in prostate gland morphogenesis (GO:0060442)|epithelial cell maturation involved in prostate gland development (GO:0060743)|regulation of DNA damage checkpoint (GO:2000001)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of ubiquitin-protein transferase activity (GO:0051438)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	death receptor binding (GO:0005123)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|urinary_tract(1)	9						GGCTGCCCGAGCAGTTCGGGC	0.408																																					p.A604T		Atlas-SNP	.											.	FEM1B	38	.	0			c.G1810A						PASS	.						57	57	57					15																	68583506		2200	4298	6498	SO:0001583	missense	10116	exon2			GCCCGAGCAGTTC		CCDS10228.1	15q22	2013-02-19	2001-11-28		ENSG00000169018	ENSG00000169018		"Ankyrin repeat domain containing"	3649	protein-coding gene	gene with protein product		613539	"FEM-1 (C. elegans) homolog b"			10623617	Standard	NM_015322		Approved		uc002arg.3	Q9UK73	OTTHUMG00000133285	ENST00000306917.4:c.1810G>A	15.37:g.68583506G>A	ENSP00000307298:p.Ala604Thr	135	0	0		109	26	0.238532	NM_015322	O43146	Missense_Mutation	SNP	ENST00000306917.4	37	CCDS10228.1	.	.	.	.	.	.	.	.	.	.	G	19.16	3.773911	0.69992	.	.	ENSG00000169018	ENST00000306917	T	0.45276	0.9	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	T	0.34135	0.0887	L	0.33339	1.005	0.80722	D	1	P	0.40660	0.726	B	0.34590	0.186	T	0.10730	-1.0617	10	0.40728	T	0.16	-34.5384	18.7742	0.91904	0.0:0.0:1.0:0.0	.	604	Q9UK73	FEM1B_HUMAN	T	604	ENSP00000307298:A604T	ENSP00000307298:A604T	A	+	1	0	FEM1B	66370560	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.793000	0.99091	2.685000	0.91497	0.491000	0.48974	GCA	.	.	none		0.408	FEM1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257065.1			A	68583506	G	A	68583506	3	1	17	1	0	0	0	0	1	0	0	0	5818	971	34	2	1816	2	FEM1B	15	68583506	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	44694175	68583506	33947886	93	2347											
MESP2	145873	hgsc.bcm.edu	37	chr15	90320149	90320149	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gggcaagggcaggggcagggGcaggggcaagggcaggggca	9	0	25	7	0	0	0	0	0	0	0	0	0	0	0	0	11	0	7	0	11	2	0			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr15:90320149G>A	ENST00000341735.3	+	1	561	c.561G>A	c.(559-561)ggG>ggA	p.G187G	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	187	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)			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)			aggggcaggggcaggggcaag	0.781																																					p.G187G		Atlas-SNP	.											.	MESP2	20	.	0			c.G561A						PASS	.						2	3	3					15																	90320149		1334	3199	4533	SO:0001819	synonymous_variant	145873	exon1			GCAGGGGCAGGGG		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.561G>A	15.37:g.90320149G>A		43	0	0		26	11	0.423077	NM_001039958	Q7RTU2	Silent	SNP	ENST00000341735.3	37	CCDS42078.1																																																																																			.	.	none		0.781	MESP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416421.1	XM_085261		A	90320149	G	A	90320149	2	1	17	1	0	0	0	0	0	0	0	1	9492	1190	42	2		2	MESP2	15	90320149	Silent	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	21736643	90320149	12211243	94	2348											
PRSS33	260429	hgsc.bcm.edu	37	chr16	2835579	2835579	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcgcacgggcaccgagagcGtgcggggcgaggtggagccc	6	3	20	12	6	0	1	0	0	0	1	1	4	0	2	2	5	3	2	2	5	0	0	rs7202954	byFrequency	TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr16:2835579G>A	ENST00000293851.5	-	4	470	c.311C>T	c.(310-312)aCg>aTg	p.T104M	PRSS33_ENST00000576886.1_Intron|PRSS33_ENST00000570702.1_Missense_Mutation_p.T104M	NM_152891.2	NP_690851.2	Q8NF86	PRS33_HUMAN	protease, serine, 33	104	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular space (GO:0005615)	serine-type endopeptidase activity (GO:0004252)	p.T104M(1)		prostate(1)	1						CACCGAGAGCGTGCGGGGCGA	0.746													G|||	643	0.128395	0.4145	0.0677	5008	,	,		12173	0.0139		0.005	False		,,,				2504	0.0297				p.T104M	NSCLC(194;489 2153 16702 19171 27758)	Atlas-SNP	.											PRSS33,NS,carcinoma,0,1	PRSS33	7	1	1	Substitution - Missense(1)	prostate(1)	c.C311T						scavenged	.		MET/THR	600,2138		28,544,797	2	2	2		311	0.1	0	16	dbSNP_116	2	47,5743		1,45,2849	no	missense	PRSS33	NM_152891.2	81	29,589,3646	AA,AG,GG		0.8117,21.9138,7.5868	possibly-damaging	104/281	2835579	647,7881	1369	2895	4264	SO:0001583	missense	260429	exon4			GAGAGCGTGCGGG	AF536382	CCDS42110.1	16p13.3	2014-09-04			ENSG00000103355	ENSG00000103355		"Serine peptidases / Serine peptidases"	30405	protein-coding gene	gene with protein product		613797				12795636	Standard	NM_152891		Approved	EOS	uc002cro.1	Q8NF86	OTTHUMG00000177360	ENST00000293851.5:c.311C>T	16.37:g.2835579G>A	ENSP00000293851:p.Thr104Met	2	2	1		11	6	0.545455	NM_152891	A6NNQ3|Q8N171	Missense_Mutation	SNP	ENST00000293851.5	37	CCDS42110.1	217	0.09935897435897435	187	0.3800813008130081	23	0.06353591160220995	6	0.01048951048951049	1	0.0013192612137203166	G	10.39	1.336851	0.24253	0.219138	0.008117	ENSG00000103355	ENST00000293851	D	0.88896	-2.44	4.74	0.141	0.14811	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.637530	0.14568	N	0.311635	T	0.00012	0.0000	L	0.43152	1.355	0.80722	P	0.0	P	0.35612	0.512	B	0.33568	0.166	T	0.03981	-1.0987	9	0.45353	T	0.12	.	2.8287	0.05492	0.0871:0.2745:0.3404:0.298	rs7202954	104	Q8NF86	PRS33_HUMAN	M	104	ENSP00000293851:T104M	ENSP00000293851:T104M	T	-	2	0	PRSS33	2775580	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.357000	0.20199	-0.204000	0.10235	-0.492000	0.04666	ACG	G|0.887;A|0.113	0.113	strong		0.746	PRSS33-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436446.1	NM_152891		A	2835579	G	A	2835579	3	1	17	1	0	0	0	0	1	0	0	0	12635	1145	40	1	543	1	PRSS33	16	2835579	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10		2835579	87519174	95	2349											
ALOXE3	59344	hgsc.bcm.edu	37	chr17	8012556	8012556	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagttggggatagccaggaCgccgcgggcccgcaggctgt	6	6	18	11	4	0	0	0	0	0	0	0	2	0	2	3	5	1	4	3	5	2	3	rs121434232		TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr17:8012556C>T	ENST00000448843.2	-	12	1838	c.1498G>A	c.(1498-1500)Gtc>Atc	p.V500I	ALOXE3_ENST00000380149.1_Missense_Mutation_p.V656I|ALOXE3_ENST00000318227.3_Missense_Mutation_p.V632I	NM_021628.2	NP_067641.2	Q9BYJ1	LOXE3_HUMAN	arachidonate lipoxygenase 3	500	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.		V -> F (in ARCI3; complete loss of the enzyme activity). {ECO:0000269|PubMed:11773004}.		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						ATAGCCAGGACGCCGCGGGCC	0.652																																					p.V632I		Atlas-SNP	.											.	ALOXE3	145	.	0			c.G1894A	GRCh37	CM020012	ALOXE3	M	rs121434232	PASS	.						60	56	57					17																	8012556		2203	4300	6503	SO:0001583	missense	59344	exon12			CCAGGACGCCGCG	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.1498G>A	17.37:g.8012556C>T	ENSP00000400581:p.Val500Ile	44	0	0		51	16	0.313726	NM_001165960	B2R981|B7Z3W0|Q3ZB74|Q9H4F2|Q9HC22	Missense_Mutation	SNP	ENST00000448843.2	37	CCDS11130.1	.	.	.	.	.	.	.	.	.	.	c	25.8	4.677504	0.88445	.	.	ENSG00000179148	ENST00000380149;ENST00000318227;ENST00000448843	T;T;T	0.77620	-1.11;-1.11;-1.11	5.06	4.08	0.47627	Lipoxygenase, C-terminal (3);	0.061563	0.64402	D	0.000003	T	0.81688	0.4875	M	0.71296	2.17	0.41900	D	0.990418	P;P;P	0.45594	0.554;0.862;0.862	B;P;P	0.50136	0.312;0.632;0.632	D	0.84169	0.0433	10	0.72032	D	0.01	-22.8779	12.9038	0.58141	0.0:0.9196:0.0:0.0804	.	632;500;500	B7Z3W0;Q9BYJ1;B3KVD2	.;LOXE3_HUMAN;.	I	656;632;500	ENSP00000369494:V656I;ENSP00000314879:V632I;ENSP00000400581:V500I	ENSP00000314879:V632I	V	-	1	0	ALOXE3	7953281	0.229000	0.23729	0.393000	0.26258	0.960000	0.62799	0.696000	0.25541	1.369000	0.46134	0.556000	0.70494	GTC	.	.	alt		0.652	ALOXE3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441475.1			T	8012556	C	T	8012556	3	4	17	1	0	0	0	0	1	0	0	0	542	536	19	1	657	1	ALOXE3	17	8012556	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10		8012556	73182654	96	2350											
TTLL6	284076	hgsc.bcm.edu	37	chr17	46847276	46847276	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttgtgggcagaaaagattTtaacattttcttctgggtta	10	18	9	4	0	2	2	0	0	2	2	2	2	2	2	0	2	1	2	0	2	4	8			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr17:46847276T>C	ENST00000393382.3	-	14	2365	c.2224A>G	c.(2224-2226)Aaa>Gaa	p.K742E	TTLL6_ENST00000433608.2_Missense_Mutation_p.K435E	NM_001130918.1	NP_001124390.1			tubulin tyrosine ligase-like family, member 6											endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						AGAAAAGATTTTAACATTTTC	0.468																																					p.K742E		Atlas-SNP	.											.	TTLL6	113	.	0			c.A2224G						PASS	.						85	85	85					17																	46847276		2203	4300	6503	SO:0001583	missense	284076	exon14			AAGATTTTAACAT	AK093127	CCDS11537.2, CCDS45724.1	17q21.32	2013-02-14			ENSG00000170703	ENSG00000170703		"Tubulin tyrosine ligase-like family"	26664	protein-coding gene	gene with protein product		610849				15890843	Standard	NM_173623		Approved	FLJ35808	uc021tzm.1	Q8N841	OTTHUMG00000156978	ENST00000393382.3:c.2224A>G	17.37:g.46847276T>C	ENSP00000377043:p.Lys742Glu	440	0	0		420	120	0.285714	NM_001130918		Missense_Mutation	SNP	ENST00000393382.3	37	CCDS45724.1	.	.	.	.	.	.	.	.	.	.	T	12.22	1.872466	0.33069	.	.	ENSG00000170703	ENST00000440941;ENST00000305326;ENST00000433608;ENST00000393382	T	0.19394	2.15	3.94	1.63	0.23807	.	7739.210000	0.00166	U	0.000000	T	0.25419	0.0618	L	0.59436	1.845	0.09310	N	1	P;P	0.43094	0.799;0.728	B;B	0.39339	0.162;0.297	T	0.27905	-1.0060	10	0.46703	T	0.11	.	8.1135	0.30928	0.0:0.0:0.4101:0.5899	.	694;435	Q8N841;G5E937	TTLL6_HUMAN;.	E	742;435;420;694	ENSP00000399211:K420E	ENSP00000302547:K435E	K	-	1	0	TTLL6	44202275	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	0.571000	0.23669	0.308000	0.22923	0.533000	0.62120	AAA	.	.	none		0.468	TTLL6-003	KNOWN	downstream_ATG|non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346939.3	NM_173623		C	46847276	T	C	46847276	3	2	17	1	0	0	0	0	1	0	0	0	16746	1850	64	3	459	3	TTLL6	17	46847276	Missense_Mutation	SNP	T	TCGA-FF-A7CQ-01A-11D-A382-10	38834720	46847276	34347934	97	2351											
CCDC47	57003	hgsc.bcm.edu	37	chr17	61833644	61833644	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gacttctcccatctctgacaGgatggccaaagagtccggca	10	8	10	13	1	2	2	0	1	2	1	5	4	3	3	3	3	0	1	3	3	1	1			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr17:61833644G>C	ENST00000225726.5	-	8	1286	c.904C>G	c.(904-906)Ctg>Gtg	p.L302V	CCDC47_ENST00000403162.3_Missense_Mutation_p.L302V|CCDC47_ENST00000582252.1_Missense_Mutation_p.L302V	NM_020198.2	NP_064583.2	Q96A33	CCD47_HUMAN	coiled-coil domain containing 47	302					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						ATCTCTGACAGGATGGCCAAA	0.438																																					p.L302V		Atlas-SNP	.											.	CCDC47	34	.	0			c.C904G						PASS	.						118	110	113					17																	61833644		2203	4300	6503	SO:0001583	missense	57003	exon8			CTGACAGGATGGC	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.904C>G	17.37:g.61833644G>C	ENSP00000225726:p.Leu302Val	159	0	0		171	40	0.233918	NM_020198	B2RAS8|D3DU20|Q96D00|Q96JZ7|Q9H3E4|Q9NRG3	Missense_Mutation	SNP	ENST00000225726.5	37	CCDS11643.1	.	.	.	.	.	.	.	.	.	.	G	10.51	1.369969	0.24771	.	.	ENSG00000108588	ENST00000225726;ENST00000403162	.	.	.	5.54	3.45	0.39498	.	0.000000	0.85682	D	0.000000	T	0.66228	0.2768	L	0.49350	1.555	0.58432	D	0.999999	D;P	0.67145	0.996;0.788	D;P	0.75484	0.986;0.448	T	0.64901	-0.6298	9	0.44086	T	0.13	-11.4654	9.1184	0.36773	0.2579:0.0:0.7421:0.0	.	302;302	Q96A33-2;Q96A33	.;CCD47_HUMAN	V	302	.	ENSP00000225726:L302V	L	-	1	2	CCDC47	59187376	1.000000	0.71417	1.000000	0.80357	0.810000	0.45777	3.121000	0.50438	1.392000	0.46585	0.655000	0.94253	CTG	.	.	none		0.438	CCDC47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444016.2	NM_020198		C	61833644	G	C	61833644	3	2	17	1	0	0	0	0	1	0	0	0	2820	991	35	4	571	4	CCDC47	17	61833644	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	14986368	61833644	19361566	98	2352											
CD79B	974	hgsc.bcm.edu	37	chr17	62006798	62006798	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgcccctctccttacctcgTaggtgtgatcttcctccatg	4	14	7	16	1	2	1	0	1	2	0	6	1	4	1	6	1	2	1	6	1	2	3			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr17:62006798T>C	ENST00000006750.3	-	5	679	c.587A>G	c.(586-588)tAc>tGc	p.Y196C	CD79B_ENST00000349817.2_Missense_Mutation_p.Y92C|CD79B_ENST00000392795.3_Missense_Mutation_p.Y197C	NM_000626.2|NM_021602.2	NP_000617.1|NP_067613.1	P40259	CD79B_HUMAN	CD79b molecule, immunoglobulin-associated beta	196	ITAM. {ECO:0000255|PROSITE- ProRule:PRU00379}.				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)	p.Y196C(1)|p.Y196F(1)|p.Y196S(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	15						CCTTACCTCGTAGGTGTGATC	0.632			"Mis, O"		DLBCL																																p.Y197C		Atlas-SNP	.		Dom	yes		17	17q23	974	"CD79b molecule, immunoglobulin-associated beta"		L	CD79B,NS,lymphoid_neoplasm,-1,13	CD79B	38	13	3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	c.A590G						PASS	.						93	74	81					17																	62006798		2203	4300	6503	SO:0001583	missense	974	exon5			ACCTCGTAGGTGT	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.587A>G	17.37:g.62006798T>C	ENSP00000006750:p.Tyr196Cys	74	0	0		72	24	0.333333	NM_001039933	Q53FS2|Q9BU06	Missense_Mutation	SNP	ENST00000006750.3	37	CCDS11655.1	.	.	.	.	.	.	.	.	.	.	T	13.15	2.151836	0.38021	.	.	ENSG00000007312	ENST00000349817;ENST00000392795;ENST00000006750	D;D;D	0.96651	-4.08;-4.08;-4.08	4.2	4.2	0.49525	.	0.000000	0.64402	D	0.000002	D	0.95601	0.8570	N	0.24115	0.695	0.53005	D	0.999969	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	D	0.95387	0.8478	10	0.87932	D	0	-12.4743	9.5968	0.39578	0.0:0.0:0.0:1.0	.	92;196	P40259-2;P40259	.;CD79B_HUMAN	C	92;197;196	ENSP00000245862:Y92C;ENSP00000376544:Y197C;ENSP00000006750:Y196C	ENSP00000006750:Y196C	Y	-	2	0	CD79B	59360530	0.997000	0.39634	0.977000	0.42913	0.245000	0.25701	3.902000	0.56310	1.782000	0.52362	0.358000	0.22013	TAC	.	.	none		0.632	CD79B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417711.1			C	62006798	T	C	62006798	3	2	17	1	0	0	0	0	1	0	0	0	3039	1638	57	3	110	3	CD79B	17	62006798	Missense_Mutation	SNP	T	TCGA-FF-A7CQ-01A-11D-A382-10	173154	62006798	19188412	99	2353											
CD79B	974	hgsc.bcm.edu	37	chr17	62007630	62007635	+	In_Frame_Del	DEL	CCAGAG	CCAGAG	-																															ttctcgtccatctcctgcttCcagagccagctcacattgcc																										TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	CCAGAG	CCAGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr17:62007630_62007635delCCAGAG	ENST00000006750.3	-	3	321_326	c.229_234delCTCTGG	c.(229-234)ctctggdel	p.LW77del	CD79B_ENST00000349817.2_Intron|CD79B_ENST00000392795.3_In_Frame_Del_p.LW78del	NM_000626.2|NM_021602.2	NP_000617.1|NP_067613.1	P40259	CD79B_HUMAN	CD79b molecule, immunoglobulin-associated beta	77	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						TCTCCTGCTTCCAGAGCCAGCTCACA	0.573			"Mis, O"		DLBCL																																p.78_80del		Pindel,Atlas-Indel	.		Dom	yes		17	17q23	974	"CD79b molecule, immunoglobulin-associated beta"		L	.	CD79B	38	.	0			c.233_238del						PASS	.																																			SO:0001651	inframe_deletion	974	exon3			.	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.229_234delCTCTGG	17.37:g.62007630_62007635delCCAGAG	ENSP00000006750:p.Leu77_Trp78del	104	0	.		67	11	0.164	NM_001039933	Q53FS2|Q9BU06	In_Frame_Del	DEL	ENST00000006750.3	37	CCDS11655.1																																																																																			.	.	none		0.573	CD79B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417711.1			-	62007635	CCAGAG	-	62007630	7	5	17	1	0	1	0	1	0	0	0	0	3039	856	30	0	471	0	CD79B	17	62007630	In_Frame_Del	DEL	CCAGAG	TCGA-FF-A7CQ-01A-11D-A382-10	832	62007630	19187580	100	2354											
ITGB4	3691	hgsc.bcm.edu	37	chr17	73727034	73727034	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	acatcgtggagctgctggagGaggccttcaatgtgagggca	9	8	16	8	1	1	1	1	1	0	0	2	4	1	4	1	5	2	3	1	5	1	1			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr17:73727034G>A	ENST00000200181.3	+	9	1268	c.1081G>A	c.(1081-1083)Gag>Aag	p.E361K	ITGB4_ENST00000579662.1_Missense_Mutation_p.E361K|ITGB4_ENST00000584558.1_3'UTR|ITGB4_ENST00000339591.3_Missense_Mutation_p.E361K|ITGB4_ENST00000450894.3_Missense_Mutation_p.E361K|ITGB4_ENST00000449880.2_Missense_Mutation_p.E361K	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	361					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)			GCTGCTGGAGGAGGCCTTCAA	0.612																																					p.E361K		Atlas-SNP	.											.	ITGB4	165	.	0			c.G1081A						PASS	.						84	84	84					17																	73727034		2203	4300	6503	SO:0001583	missense	3691	exon9			CTGGAGGAGGCCT		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.1081G>A	17.37:g.73727034G>A	ENSP00000200181:p.Glu361Lys	36	0	0		37	8	0.216216	NM_001005731	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Missense_Mutation	SNP	ENST00000200181.3	37	CCDS11727.1	.	.	.	.	.	.	.	.	.	.	G	13.14	2.148655	0.37923	.	.	ENSG00000132470	ENST00000450894;ENST00000200181;ENST00000339591;ENST00000449880	D;D;D	0.97752	-4.52;-4.52;-4.52	5.42	5.42	0.78866	Integrin beta subunit, N-terminal (2);	0.679936	0.14303	N	0.328121	D	0.94525	0.8237	L	0.28556	0.865	0.09310	N	1	B;B;B;B	0.33448	0.081;0.2;0.238;0.412	B;B;B;B	0.34242	0.061;0.047;0.114;0.178	D	0.88349	0.2980	10	0.24483	T	0.36	.	12.1854	0.54236	0.1235:0.0:0.8765:0.0	.	361;361;361;361	P16144-5;P16144-3;A0AVL6;P16144	.;.;.;ITB4_HUMAN	K	277;361;361;361	ENSP00000200181:E361K;ENSP00000344079:E361K;ENSP00000400217:E361K	ENSP00000200181:E361K	E	+	1	0	ITGB4	71238629	0.214000	0.23563	1.000000	0.80357	0.949000	0.60115	1.951000	0.40333	2.545000	0.85829	0.557000	0.71058	GAG	.	.	none		0.612	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			A	73727034	G	A	73727034	3	1	17	1	0	0	0	0	1	0	0	0	7906	1175	41	2	1111	2	ITGB4	17	73727034	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	11719404	73727034	7468176	101	2355											
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2732488	2732491	+	Splice_Site	DEL	AAAG	AAAG	-																															cagctttagcagaaaaaattAaagtaagtatctctaacaga																										TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	AAAG	AAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr18:2732488_2732491delAAAG	ENST00000320876.6	+	25	3612_3614	c.3274_3276delAAAG	c.(3274-3276)aaadel	p.K1092fs	SMCHD1_ENST00000261598.8_Splice_Site_p.K1092fs|RP11-703M24.5_ENST00000583546.1_RNA	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1092					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						AGAAAAAATTAAAGTAAGTATCTC	0.284																																					p.1091_1092del		Atlas-Indel	.											.	SMCHD1	88	.	0			c.3273_3276del						PASS	.																																			SO:0001630	splice_region_variant	23347	exon25			.	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.3276+1AAAG>-	18.37:g.2732488_2732491delAAAG		84	0	0		144	16	0.111111	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Frame_Shift_Del	DEL	ENST00000320876.6	37	CCDS45822.1																																																																																			.	.	none		0.284	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2		Frame_Shift_Del	-	2732491	AAAG	-	2732488	8	5	17	1	0	1	0	1	0	0	1	0	14803	363	13	0	3372	0	SMCHD1	18	2732488	Splice_Site	DEL	AAAG	TCGA-FF-A7CQ-01A-11D-A382-10		2732488	75344760	102	2356											
TGIF1	7050	hgsc.bcm.edu	37	chr18	3451989	3451989	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtttcgaggatggttctagcGcagagccgggtgtctgccgg	5	10	17	9	4	2	1	0	0	2	1	3	3	2	2	2	4	3	3	2	4	1	3			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr18:3451989G>A	ENST00000330513.5	+	1	315	c.12G>A	c.(10-12)gcG>gcA	p.A4A	TGIF1_ENST00000345133.5_Intron|TGIF1_ENST00000401449.1_Intron|TGIF1_ENST00000551541.1_Intron|TGIF1_ENST00000551402.1_Intron|TGIF1_ENST00000400167.2_5'Flank|TGIF1_ENST00000577543.1_Intron|TGIF1_ENST00000405385.3_Intron|TGIF1_ENST00000407501.2_Intron|TGIF1_ENST00000548489.2_Intron|TGIF1_ENST00000343820.5_Intron	NM_170695.2	NP_733796.2	Q15583	TGIF1_HUMAN	TGFB-induced factor homeobox 1	4					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)				TGGTTCTAGCGCAGAGCCGGG	0.652																																					p.A4A		Atlas-SNP	.											.	TGIF1	41	.	0			c.G12A						PASS	.						31	35	34					18																	3451989		2203	4300	6503	SO:0001819	synonymous_variant	7050	exon1			TCTAGCGCAGAGC	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	ENST00000330513.5:c.12G>A	18.37:g.3451989G>A		152	0	0		226	28	0.123894	NM_170695	A6NE42|A6NLU7|F8VZB6|Q6ICR0|Q8N5X9|Q9NRS0	Silent	SNP	ENST00000330513.5	37	CCDS11834.1																																																																																			.	.	none		0.652	TGIF1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254368.4	NM_170695		A	3451989	G	A	3451989	2	1	17	1	0	0	0	0	0	0	0	1	15840	1074	38	1		1	TGIF1	18	3451989	Silent	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	719501	3451989	74625259	103	2357											
KLHL14	57565	hgsc.bcm.edu	37	chr18	30350266	30350266	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcctcctgcggcggcggctGctgctgctgtgacggctgct	1	10	15	15	4	0	1	0	1	0	0	2	1	2	1	2	4	5	6	2	4	0	0			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr18:30350266G>A	ENST00000359358.4	-	2	727	c.289C>T	c.(289-291)Cag>Tag	p.Q97*	KLHL14_ENST00000358095.4_Nonsense_Mutation_p.Q97*|AC012123.1_ENST00000426194.1_Intron	NM_020805.1	NP_065856.1	Q9P2G3	KLH14_HUMAN	kelch-like family member 14	97	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						ggcggcggctgctgctgctgt	0.736																																					p.Q97X		Atlas-SNP	.											.	KLHL14	92	.	0			c.C289T						PASS	.						13	19	17					18																	30350266		2140	4213	6353	SO:0001587	stop_gained	57565	exon2			GCGGCTGCTGCTG	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.289C>T	18.37:g.30350266G>A	ENSP00000352314:p.Gln97*	165	0	0		204	38	0.186275	NM_020805	A6NNW1|B4DHA0|Q8WU41	Nonsense_Mutation	SNP	ENST00000359358.4	37	CCDS32813.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.136803	0.77662	.	.	ENSG00000197705	ENST00000359358;ENST00000358095	.	.	.	4.14	4.14	0.48551	.	0.341802	0.26338	N	0.024957	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	.	11.7742	0.51977	0.0:0.0:1.0:0.0	.	.	.	.	X	97	.	ENSP00000350808:Q97X	Q	-	1	0	KLHL14	28604264	0.999000	0.42202	0.955000	0.39395	0.984000	0.73092	0.703000	0.25646	2.141000	0.66446	0.460000	0.39030	CAG	.	.	none		0.736	KLHL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448376.1			A	30350266	G	A	30350266	4	1	17	1	0	0	0	0	0	1	0	0	8379	1328	46	2	1629	2	KLHL14	18	30350266	Nonsense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	26898277	30350266	47726982	104	2358											
C18orf34	374864	hgsc.bcm.edu	37	chr18	30950118	30950118	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tacggcacagctgtgacgtcGacatgggtagctaaagtaaa	13	8	12	8	3	0	1	0	1	0	0	1	2	0	1	0	2	3	5	0	2	6	4			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr18:30950118G>A	ENST00000383096.3	-	6	426	c.244C>T	c.(244-246)Cga>Tga	p.R82*	CCDC178_ENST00000406524.2_Nonsense_Mutation_p.R82*|CCDC178_ENST00000579947.1_Nonsense_Mutation_p.R82*|CCDC178_ENST00000579916.1_Nonsense_Mutation_p.R82*|CCDC178_ENST00000403303.1_Nonsense_Mutation_p.R82*|CCDC178_ENST00000402325.1_Nonsense_Mutation_p.R82*|CCDC178_ENST00000583930.1_Nonsense_Mutation_p.R82*|CCDC178_ENST00000300227.8_Nonsense_Mutation_p.R82*			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178	82																	CTGTGACGTCGACATGGGTAG	0.368																																					p.R82X		Atlas-SNP	.											.	.	.	.	0			c.C244T						PASS	.						74	66	69					18																	30950118		2203	4300	6503	SO:0001587	stop_gained	374864	exon5			GACGTCGACATGG	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.244C>T	18.37:g.30950118G>A	ENSP00000372576:p.Arg82*	126	0	0		129	41	0.317829	NM_001105528	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Nonsense_Mutation	SNP	ENST00000383096.3	37	CCDS42424.1	.	.	.	.	.	.	.	.	.	.	G	16.53	3.148756	0.57151	.	.	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000300227;ENST00000406524;ENST00000402325;ENST00000399177	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.4729	14.8979	0.70656	0.0:0.0:1.0:0.0	.	.	.	.	X	82	.	ENSP00000300227:R82X	R	-	1	2	C18orf34	29204116	0.978000	0.34361	0.949000	0.38748	0.248000	0.25809	1.567000	0.36407	2.589000	0.87451	0.555000	0.69702	CGA	.	.	none		0.368	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995		A	30950118	G	A	30950118	4	1	17	1	0	0	0	0	0	1	0	0	1904	1066	37	1	2431	1	C18orf34	18	30950118	Nonsense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	599852	30950118	47127130	105	2359											
CDH20	28316	hgsc.bcm.edu	37	chr18	59203733	59203733	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgtttctgcagatactccAttgatagaagcagtgaccct	11	12	8	10	0	1	4	0	2	1	2	2	4	2	4	2	0	3	3	2	0	3	4			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr18:59203733A>C	ENST00000262717.4	+	8	1677	c.1279A>C	c.(1279-1281)Att>Ctt	p.I427L	CDH20_ENST00000536675.2_Missense_Mutation_p.I427L|CDH20_ENST00000538374.1_Missense_Mutation_p.I427L			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	427	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(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				CAGATACTCCATTGATAGAAG	0.423																																					p.I427L		Atlas-SNP	.											.	CDH20	117	.	0			c.A1279C						PASS	.						220	201	207					18																	59203733		2203	4300	6503	SO:0001583	missense	28316	exon7			TACTCCATTGATA	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.1279A>C	18.37:g.59203733A>C	ENSP00000262717:p.Ile427Leu	126	0	0		252	41	0.162698	NM_031891	Q495S3	Missense_Mutation	SNP	ENST00000262717.4	37	CCDS11977.1	.	.	.	.	.	.	.	.	.	.	A	17.50	3.405638	0.62288	.	.	ENSG00000101542	ENST00000536675;ENST00000538374;ENST00000262717	T;T;T	0.55413	0.52;0.52;0.52	5.36	5.36	0.76844	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.49847	0.1581	L	0.45137	1.4	0.58432	D	0.999996	B	0.21753	0.06	B	0.31101	0.124	T	0.46105	-0.9215	10	0.41790	T	0.15	.	15.641	0.77001	1.0:0.0:0.0:0.0	.	427	Q9HBT6	CAD20_HUMAN	L	427	ENSP00000444767:I427L;ENSP00000442226:I427L;ENSP00000262717:I427L	ENSP00000262717:I427L	I	+	1	0	CDH20	57354713	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.669000	0.91163	2.158000	0.67659	0.523000	0.50628	ATT	.	.	none		0.423	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891		C	59203733	A	C	59203733	3	2	17	1	0	0	0	0	1	0	0	0	3108	217	8	5	1305	5	CDH20	18	59203733	Missense_Mutation	SNP	A	TCGA-FF-A7CQ-01A-11D-A382-10	28253615	59203733	18873515	106	2360											
CDH7	1005	hgsc.bcm.edu	37	chr18	63527021	63527021	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacttcagcttaacaacggaTgcaacaaataaccacaactt	17	9	4	11	1	1	0	1	0	0	0	1	1	1	1	1	1	8	2	1	1	7	5			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr18:63527021T>C	ENST00000397968.2	+	10	1998	c.1572T>C	c.(1570-1572)gaT>gaC	p.D524D	CDH7_ENST00000536984.2_Silent_p.D524D|CDH7_ENST00000323011.3_Silent_p.D524D	NM_004361.2	NP_004352.2	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2	524	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)			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)				TAACAACGGATGCAACAAATA	0.358																																					p.D524D		Atlas-SNP	.											.	CDH7	362	.	0			c.T1572C						PASS	.						104	86	92					18																	63527021		2203	4299	6502	SO:0001819	synonymous_variant	1005	exon10			AACGGATGCAACA	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.1572T>C	18.37:g.63527021T>C		95	0	0		161	19	0.118012	NM_004361	Q9H157	Silent	SNP	ENST00000397968.2	37	CCDS11993.1																																																																																			.	.	none		0.358	CDH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256217.2	NM_033646		C	63527021	T	C	63527021	2	2	17	1	0	0	0	0	0	0	0	1	3117	1461	51	3		3	CDH7	18	63527021	Silent	SNP	T	TCGA-FF-A7CQ-01A-11D-A382-10	4323288	63527021	14550227	107	2361											
STAP2	55620	hgsc.bcm.edu	37	chr19	4328706	4328706	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgcgtggtgaccgacacgcCgtcggcgccgtccccgctgg	3	5	15	18	9	0	1	0	1	0	0	2	2	1	1	6	3	0	1	6	3	0	0			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr19:4328706C>T	ENST00000594605.1	-	6	679	c.556G>A	c.(556-558)Ggc>Agc	p.G186S	STAP2_ENST00000600324.1_Missense_Mutation_p.G186S|STAP2_ENST00000597593.1_5'Flank	NM_001013841.1	NP_001013863.1	Q9UGK3	STAP2_HUMAN	signal transducing adaptor family member 2	186	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.					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)		ACCGACACGCCGTCGGCGCCG	0.716																																					p.G186S		Atlas-SNP	.											.	STAP2	38	.	0			c.G556A						PASS	.																																			SO:0001583	missense	55620	exon6			ACACGCCGTCGGC	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.556G>A	19.37:g.4328706C>T	ENSP00000471052:p.Gly186Ser	102	0	0		114	36	0.315789	NM_001013841	A6NKK3|Q9NXI2	Missense_Mutation	SNP	ENST00000594605.1	37	CCDS45926.1	.	.	.	.	.	.	.	.	.	.	C	3.199	-0.164145	0.06502	.	.	ENSG00000178078	ENST00000314714;ENST00000424810	.	.	.	4.47	0.897	0.19258	SH2 motif (3);	1.373150	0.05071	N	0.481758	T	0.17746	0.0426	N	0.03608	-0.345	0.19945	N	0.999944	B;B	0.14012	0.009;0.002	B;B	0.12837	0.008;0.004	T	0.25779	-1.0122	9	0.87932	D	0	-8.0506	4.4444	0.11589	0.0:0.5903:0.1844:0.2253	.	186;186	Q9UGK3-2;Q9UGK3	.;STAP2_HUMAN	S	186	.	ENSP00000317912:G186S	G	-	1	0	STAP2	4279706	0.000000	0.05858	0.170000	0.22879	0.499000	0.33736	0.007000	0.13174	0.282000	0.22254	0.479000	0.44913	GGC	.	.	none		0.716	STAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458114.2	NM_001013841		T	4328706	C	T	4328706	3	4	17	1	0	0	0	0	1	0	0	0	15268	652	23	1	825	1	STAP2	19	4328706	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10		4328706	54800277	108	2362											
RFX2	5990	hgsc.bcm.edu	37	chr19	6016117	6016117	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacctggtgcccagccgccGcgttctcagccccataaaca	8	6	8	19	3	1	0	1	0	1	0	2	0	1	0	7	1	4	1	7	1	2	2			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr19:6016117G>A	ENST00000303657.5	-	7	912	c.763C>T	c.(763-765)Cgg>Tgg	p.R255W	RFX2_ENST00000592546.1_Missense_Mutation_p.R230W|RFX2_ENST00000359161.3_Missense_Mutation_p.R255W|CTC-232P5.1_ENST00000587836.1_RNA	NM_000635.3	NP_000626.2	P48378	RFX2_HUMAN	regulatory factor X, 2 (influences HLA class II expression)	255					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						CCCAGCCGCCGCGTTCTCAGC	0.577																																					p.R255W	Colon(38;171 817 19800 47433 48051)	Atlas-SNP	.											.	RFX2	60	.	0			c.C763T						PASS	.						72	67	68					19																	6016117		2203	4300	6503	SO:0001583	missense	5990	exon7			GCCGCCGCGTTCT		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.763C>T	19.37:g.6016117G>A	ENSP00000306335:p.Arg255Trp	54	0	0		69	20	0.289855	NM_000635	A8K581|B3KNC4|Q6IQ44|Q8SNA2	Missense_Mutation	SNP	ENST00000303657.5	37	CCDS12157.1	.	.	.	.	.	.	.	.	.	.	G	18.20	3.570825	0.65765	.	.	ENSG00000087903	ENST00000303657;ENST00000359161	D	0.92348	-3.02	4.55	2.16	0.27623	Winged helix-turn-helix transcription repressor DNA-binding (1);DNA-binding RFX (1);	0.000000	0.85682	D	0.000000	D	0.96688	0.8919	H	0.94698	3.57	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.96970	0.9708	10	0.87932	D	0	-29.2202	12.3587	0.55190	0.0:0.0:0.6993:0.3007	.	230;255	P48378-2;P48378	.;RFX2_HUMAN	W	255;230	ENSP00000306335:R255W	ENSP00000306335:R255W	R	-	1	2	RFX2	5967117	1.000000	0.71417	0.918000	0.36340	0.578000	0.36192	5.299000	0.65716	0.996000	0.38943	0.561000	0.74099	CGG	.	.	none		0.577	RFX2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452687.1	NM_000635		A	6016117	G	A	6016117	3	1	17	1	0	0	0	0	1	0	0	0	13278	1086	38	1	1456	1	RFX2	19	6016117	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	1687411	6016117	53112866	109	2363											
ELAVL1	1994	hgsc.bcm.edu	37	chr19	8046064	8046064	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcacaaagccatagcccaagCtgtgtcctgtgcaagagaac	13	7	9	12	0	1	1	1	0	0	1	2	2	2	1	3	0	5	2	3	0	5	1			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr19:8046064C>T	ENST00000407627.2	-	3	308	c.179G>A	c.(178-180)aGc>aAc	p.S60N	ELAVL1_ENST00000596459.1_Missense_Mutation_p.S60N|ELAVL1_ENST00000351593.5_Missense_Mutation_p.S87N|ELAVL1_ENST00000593807.1_Missense_Mutation_p.S60N	NM_001419.2	NP_001410.2	Q15717	ELAV1_HUMAN	ELAV like RNA binding protein 1	60	RRM 1. {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						ATAGCCCAAGCTGTGTCCTGT	0.527																																					p.S60N		Atlas-SNP	.											.	ELAVL1	44	.	0			c.G179A						PASS	.						164	118	133					19																	8046064		2203	4300	6503	SO:0001583	missense	1994	exon3			CCCAAGCTGTGTC	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.179G>A	19.37:g.8046064C>T	ENSP00000385269:p.Ser60Asn	90	0	0		86	26	0.302326	NM_001419	B4DVB8|Q53XN6|Q9BTT1	Missense_Mutation	SNP	ENST00000407627.2	37	CCDS12193.1	.	.	.	.	.	.	.	.	.	.	C	35	5.460172	0.96240	.	.	ENSG00000066044	ENST00000407627;ENST00000351593	T;T	0.78481	-1.18;-1.18	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	0.78773	0.4336	L	0.61218	1.895	0.80722	D	1	P	0.38729	0.644	B	0.40101	0.319	T	0.80997	-0.1132	10	0.87932	D	0	.	17.4906	0.87702	0.0:1.0:0.0:0.0	.	60	Q15717	ELAV1_HUMAN	N	60;87	ENSP00000385269:S60N;ENSP00000264073:S87N	ENSP00000264073:S87N	S	-	2	0	ELAVL1	7952064	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.225000	0.78051	2.719000	0.93026	0.655000	0.94253	AGC	.	.	none		0.527	ELAVL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461494.3	NM_001419		T	8046064	C	T	8046064	3	4	17	1	0	0	0	0	1	0	0	0	5051	797	28	2	817	2	ELAVL1	19	8046064	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	2029947	8046064	51082919	110	2364											
MUC16	94025	hgsc.bcm.edu	37	chr19	8993393	8993393	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cattgacatagagactgtccCtgtccagtgtgtaggggccc	8	10	12	11	0	0	2	0	1	0	1	2	3	2	2	3	2	0	1	3	2	2	3	rs376237412		TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr19:8993393C>A	ENST00000397910.4	-	66	41899	c.41696G>T	c.(41695-41697)aGg>aTg	p.R13899M	MUC16_ENST00000380951.5_Missense_Mutation_p.R540M	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13902	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						GAGACTGTCCCTGTCCAGTGT	0.562																																					p.R13899M		Atlas-SNP	.											.	MUC16	4315	.	0			c.G41696T						PASS	.						157	145	149					19																	8993393		2058	4191	6249	SO:0001583	missense	94025	exon66			CTGTCCCTGTCCA	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.41696G>T	19.37:g.8993393C>A	ENSP00000381008:p.Arg13899Met	115	0	0		114	28	0.245614	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	12.61|12.61	1.988656|1.988656	0.35131|0.35131	.|.	.|.	ENSG00000181143|ENSG00000181143	ENST00000542240|ENST00000397910;ENST00000380951	.|T;T	.|0.25579	.|1.79;1.79	3.61|3.61	-6.75|-6.75	0.01738|0.01738	.|.	.|2.513830	.|0.02296	.|U	.|0.070703	T|T	0.46541|0.46541	0.1398|0.1398	M|M	0.74881|0.74881	2.28|2.28	.|.	.|.	.|.	.|P;D	.|0.60575	.|0.79;0.988	.|B;D	.|0.78314	.|0.339;0.991	T|T	0.60752|0.60752	-0.7201|-0.7201	4|9	.|0.66056	.|D	.|0.02	.|.	7.8879|7.8879	0.29661|0.29661	0.0:0.1805:0.1386:0.6809|0.0:0.1805:0.1386:0.6809	.|.	.|21544;13899	.|Q8WXI7;B5ME49	.|MUC16_HUMAN;.	W|M	739|13899;540	.|ENSP00000381008:R13899M;ENSP00000370338:R540M	.|ENSP00000370338:R540M	G|R	-|-	1|2	0|0	MUC16|MUC16	8854393|8854393	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.009000|0.009000	0.06853|0.06853	-0.619000|-0.619000	0.05572|0.05572	-1.236000|-1.236000	0.02542|0.02542	-1.011000|-1.011000	0.02470|0.02470	GGG|AGG	.	.	alt		0.562	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	8993393	C	A	8993393	3	1	17	1	0	0	0	0	1	0	0	0	9982	681	24	4	1903	4	MUC16	19	8993393	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	947329	8993393	50135590	111	2365											
OR7G1	125962	hgsc.bcm.edu	37	chr19	9226244	9226244	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	acagatgtcagtaaaggagaGattaaagagaaggaagtaca	20	6	12	3	0	1	3	1	0	0	3	1	7	1	5	0	2	1	2	0	2	7	3			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr19:9226244G>C	ENST00000541538.1	-	1	195	c.196C>G	c.(196-198)Ctc>Gtc	p.L66V	OR7G1_ENST00000293614.1_Missense_Mutation_p.L66V	NM_001005192.2	NP_001005192.2	Q8NGA0	OR7G1_HUMAN	olfactory receptor, family 7, subfamily G, member 1	66						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)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	20						GTAAAGGAGAGATTAAAGAGA	0.493																																					p.L66V		Atlas-SNP	.											.	OR7G1	53	.	0			c.C196G						PASS	.						162	159	160					19																	9226244		2203	4300	6503	SO:0001583	missense	125962	exon1			AGGAGAGATTAAA		CCDS32898.1, CCDS32898.2	19p13.2	2013-09-24			ENSG00000161807	ENSG00000161807		"GPCR / Class A : Olfactory receptors"	8465	protein-coding gene	gene with protein product				OR7G1P			Standard	NM_001005192		Approved	OR19-15	uc021uoi.1	Q8NGA0	OTTHUMG00000168067	ENST00000541538.1:c.196C>G	19.37:g.9226244G>C	ENSP00000444134:p.Leu66Val	107	0	0		135	42	0.311111	NM_001005192	Q6IFJ5|Q96RA1	Missense_Mutation	SNP	ENST00000541538.1	37	CCDS32898.2	.	.	.	.	.	.	.	.	.	.	g	12.27	1.888842	0.33348	.	.	ENSG00000161807	ENST00000293614;ENST00000541538	T;T	0.00587	6.38;6.38	2.98	2.98	0.34508	GPCR, rhodopsin-like superfamily (1);	0.000000	0.31566	U	0.007425	T	0.03959	0.0111	H	0.98866	4.355	0.26521	N	0.974429	D	0.60160	0.987	P	0.58721	0.844	T	0.13098	-1.0522	10	0.87932	D	0	.	7.8169	0.29265	0.1236:0.0:0.8764:0.0	.	66	Q8NGA0	OR7G1_HUMAN	V	66	ENSP00000293614:L66V;ENSP00000444134:L66V	ENSP00000293614:L66V	L	-	1	0	OR7G1	9087244	0.000000	0.05858	0.405000	0.26409	0.111000	0.19643	-0.465000	0.06680	1.978000	0.57642	0.411000	0.27672	CTC	.	.	none		0.493	OR7G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397912.1			C	9226244	G	C	9226244	3	2	17	1	0	0	0	0	1	0	0	0	11231	942	33	4	813	4	OR7G1	19	9226244	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	232851	9226244	49902739	112	2366											
KANK2	25959	hgsc.bcm.edu	37	chr19	11289041	11289041	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccgccgttgacccccacgaaCtggaggctcctccggtgggc	5	6	13	17	4	0	1	0	1	0	0	2	3	2	2	6	4	1	2	6	4	1	1			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr19:11289041C>T	ENST00000586659.1	-	6	1814	c.1500G>A	c.(1498-1500)caG>caA	p.Q500Q	KANK2_ENST00000589359.1_Silent_p.Q508Q|KANK2_ENST00000355150.5_Silent_p.Q500Q|KANK2_ENST00000589894.1_Silent_p.Q500Q|KANK2_ENST00000432929.2_Silent_p.Q508Q			Q63ZY3	KANK2_HUMAN	KN motif and ankyrin repeat domains 2	500					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						CCCCCACGAACTGGAGGCTCC	0.652																																					p.Q508Q		Atlas-SNP	.											.	KANK2	47	.	0			c.G1524A						PASS	.						18	21	20					19																	11289041		2203	4297	6500	SO:0001819	synonymous_variant	25959	exon4			CACGAACTGGAGG	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.1500G>A	19.37:g.11289041C>T		63	0	0		82	20	0.243902	NM_015493	B0I1P4|Q3KQZ3|Q6GUF5|Q9H8S4|Q9NUP0|Q9P210	Silent	SNP	ENST00000586659.1	37	CCDS12255.1																																																																																			.	.	none		0.652	KANK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453066.2	NM_015493		T	11289041	C	T	11289041	2	4	17	1	0	0	0	0	0	0	0	1	7986	564	20	2		2	KANK2	19	11289041	Silent	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	2062797	11289041	47839942	113	2367											
CPAMD8	27151	hgsc.bcm.edu	37	chr19	17081795	17081795	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgtagaggccaccgtcctGccggtggttcaggctcactc	5	9	14	13	2	2	1	2	0	0	1	4	1	3	1	4	5	1	3	4	5	1	2			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr19:17081795G>A	ENST00000443236.1	-	18	2291	c.2260C>T	c.(2260-2262)Cag>Tag	p.Q754*	CPAMD8_ENST00000388925.4_Missense_Mutation_p.A496V	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	707						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						CCACCGTCCTGCCGGTGGTTC	0.627																																					p.Q754X		Atlas-SNP	.											CPAMD8,right_upper_lobe,carcinoma,+1,1	CPAMD8	192	1	0			c.C2260T						PASS	.						56	61	59					19																	17081795		2069	4191	6260	SO:0001587	stop_gained	27151	exon18			CGTCCTGCCGGTG	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.2260C>T	19.37:g.17081795G>A	ENSP00000402505:p.Gln754*	43	0	0		43	11	0.255814	NM_015692	Q8NC09|Q9ULD7	Nonsense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	39|39	7.759309|7.759309	0.98474|0.98474	.|.	.|.	ENSG00000160111|ENSG00000160111	ENST00000388925|ENST00000291440	T|.	0.54071|.	0.59|.	3.18|3.18	3.18|3.18	0.36537|0.36537	.|.	.|0.227351	.|0.29178	.|U	.|0.012906	T|.	0.37571|.	0.1008|.	.|.	.|.	.|.	0.36263|0.36263	D|D	0.854687|0.854687	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.31392|.	-0.9945|.	6|.	0.39692|0.06365	T|T	0.17|0.9	.|.	14.3292|14.3292	0.66541|0.66541	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	V|X	496|754	ENSP00000373577:A496V|.	ENSP00000373577:A496V|ENSP00000291440:Q754X	A|Q	-|-	2|1	0|0	CPAMD8|CPAMD8	16942795|16942795	1.000000|1.000000	0.71417|0.71417	0.996000|0.996000	0.52242|0.52242	0.933000|0.933000	0.57130|0.57130	6.082000|6.082000	0.71318|0.71318	1.331000|1.331000	0.45412|0.45412	0.650000|0.650000	0.86243|0.86243	GCA|CAG	.	.	none		0.627	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692		A	17081795	G	A	17081795	4	1	17	1	0	0	0	0	0	1	0	0	3797	1328	46	2	3638	2	CPAMD8	19	17081795	Nonsense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	5792754	17081795	42047188	114	2368											
LOC729991-MEF2B	100271849	hgsc.bcm.edu	37	chr19	19261528	19261529	+	Frame_Shift_Ins	INS	-	-	T																															caggatgcgggagatctggaINStttttttcctccccatcgtc																										TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr19:19261528_19261529insT	ENST00000602424.2	-	4	742_743	c.16_17insA	c.(16-18)atcfs	p.I6fs	MEF2BNB-MEF2B_ENST00000444486.3_Frame_Shift_Ins_p.I6fs|MEF2B_ENST00000162023.5_Frame_Shift_Ins_p.I6fs|MEF2B_ENST00000409447.2_Frame_Shift_Ins_p.I6fs|MEF2BNB-MEF2B_ENST00000514819.3_Frame_Shift_Ins_p.I23fs|MEF2B_ENST00000424583.2_Frame_Shift_Ins_p.I6fs|MEF2B_ENST00000410050.1_Frame_Shift_Ins_p.I6fs|MEF2B_ENST00000409224.1_Frame_Shift_Ins_p.I6fs|MEF2BNB-MEF2B_ENST00000602276.1_5'UTR	NM_005919.3	NP_005910.1	Q02080	MEF2B_HUMAN	myocyte enhancer factor 2B	6	Lys-rich (basic).|MADS-box. {ECO:0000255|PROSITE- ProRule:PRU00251}.				muscle organ development (GO:0007517)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cell junction (GO:0030054)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|haematopoietic_and_lymphoid_tissue(21)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(5;0.00011)|Epithelial(12;0.00412)			GGAGATCTGGATTTTTTTCCTC	0.564																																					p.I6fs		Pindel,Atlas-Indel	.											.	MEF2BNB-MEF2B	29	.	0			c.17_18insA						PASS	.																																			SO:0001589	frameshift_variant	4207	exon4			.	X63380	CCDS12394.1, CCDS46024.1	19p13.11	2010-05-12	2007-04-24					"Myocyte enhancer factors"	6995	protein-coding gene	gene with protein product		600661				1516833, 8575763	Standard	NM_001145785		Approved	RSRFR2	uc002nll.2	Q02080		ENST00000602424.2:c.17dupA	19.37:g.19261535_19261535dupT	ENSP00000473308:p.Ile6fs	154	0	.		180	37	0.206	NM_005919	A0AV80|B4DVH7|B7ZVY1|G5E9M1	Frame_Shift_Ins	INS	ENST00000602424.2	37	CCDS12394.1																																																																																			.	.	none		0.564	MEF2B-202	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_005919		T	19261529	-	T	19261528	7	5	17	1	0	1	1	0	0	0	0	0	8898	333	12	0	1108	0	LOC729991-MEF2B	19	19261528	Frame_Shift_Ins	INS	-	TCGA-FF-A7CQ-01A-11D-A382-10	2179733	19261528	39867455	115	2369											
MYH14	79784	hgsc.bcm.edu	37	chr19	50753007	50753007	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagcaggaggagtaccagcGtgagggcatcccctggacct	9	5	16	11	1	0	1	0	1	0	0	1	5	1	5	4	5	3	3	4	5	1	1			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr19:50753007G>A	ENST00000596571.1	+	12	1559	c.1559G>A	c.(1558-1560)cGt>cAt	p.R520H	MYH14_ENST00000440075.2_Missense_Mutation_p.R528H|MYH14_ENST00000262269.8_Missense_Mutation_p.R528H|MYH14_ENST00000425460.1_Missense_Mutation_p.R528H|MYH14_ENST00000376970.2_Missense_Mutation_p.R520H|MYH14_ENST00000601313.1_Missense_Mutation_p.R528H|MYH14_ENST00000598205.1_Missense_Mutation_p.R528H			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	520	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)		GAGTACCAGCGTGAGGGCATC	0.622																																					p.R528H		Atlas-SNP	.											MYH14_ENST00000262269,NS,carcinoma,+1,2	MYH14	261	2	0			c.G1583A						PASS	.						177	150	159					19																	50753007		2203	4300	6503	SO:0001583	missense	79784	exon14			ACCAGCGTGAGGG	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.1559G>A	19.37:g.50753007G>A	ENSP00000472819:p.Arg520His	105	0	0		96	28	0.291667	NM_001077186	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	37	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.893565	0.91889	.	.	ENSG00000105357	ENST00000301415;ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	T;T;T;T	0.73363	-0.74;-0.74;-0.74;-0.74	4.37	4.37	0.52481	Myosin head, motor domain (2);	.	.	.	.	D	0.88923	0.6569	M	0.93241	3.395	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.72075	0.976;0.965;0.913	D	0.91720	0.5388	9	0.87932	D	0	.	14.7979	0.69891	0.0:0.0:1.0:0.0	.	528;520;528	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	H	520;528;520;528;520;528	ENSP00000406273:R528H;ENSP00000366169:R520H;ENSP00000407879:R528H;ENSP00000262269:R528H	ENSP00000262269:R528H	R	+	2	0	MYH14	55444819	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.602000	0.82796	2.429000	0.82318	0.655000	0.94253	CGT	.	.	none		0.622	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		A	50753007	G	A	50753007	3	1	17	1	0	0	0	0	1	0	0	0	10042	1145	40	1	1633	1	MYH14	19	50753007	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	31491479	50753007	8375976	116	2370											
ZNF677	342926	hgsc.bcm.edu	37	chr19	53740528	53740528	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcagtacatttgtaaggtttCtctccagtatgagttctctg	8	17	8	8	0	3	1	1	1	2	0	6	1	4	1	1	1	1	5	1	1	3	6			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr19:53740528C>G	ENST00000598513.1	-	5	1602	c.1452G>C	c.(1450-1452)gaG>gaC	p.E484D	ZNF677_ENST00000333952.4_Missense_Mutation_p.E484D	NM_182609.2	NP_872415.1	Q86XU0	ZN677_HUMAN	zinc finger protein 677	484					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.E484D(1)		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)		TGTAAGGTTTCTCTCCAGTAT	0.358																																					p.E484D		Atlas-SNP	.											ZNF677,colon,carcinoma,0,2	ZNF677	94	2	1	Substitution - Missense(1)	large_intestine(1)	c.G1452C						PASS	.						70	69	70					19																	53740528		2203	4300	6503	SO:0001583	missense	342926	exon5			AGGTTTCTCTCCA	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.1452G>C	19.37:g.53740528C>G	ENSP00000469391:p.Glu484Asp	139	0	0		139	46	0.330935	NM_182609		Missense_Mutation	SNP	ENST00000598513.1	37	CCDS12861.1	.	.	.	.	.	.	.	.	.	.	C	15.06	2.720032	0.48728	.	.	ENSG00000197928	ENST00000333952	T	0.26810	1.71	2.21	1.06	0.20224	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35677	N	0.003049	T	0.23926	0.0579	L	0.37630	1.12	0.24758	N	0.992942	P	0.49185	0.92	P	0.50192	0.634	T	0.06499	-1.0823	10	0.72032	D	0.01	.	6.2797	0.21001	0.0:0.8126:0.0:0.1874	.	484	Q86XU0	ZN677_HUMAN	D	484	ENSP00000334394:E484D	ENSP00000334394:E484D	E	-	3	2	ZNF677	58432340	0.810000	0.29049	0.999000	0.59377	0.915000	0.54546	0.297000	0.19101	0.413000	0.25759	-0.345000	0.07892	GAG	.	.	none		0.358	ZNF677-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464189.1	NM_182609		G	53740528	C	G	53740528	3	3	17	1	0	0	0	0	1	0	0	0	18099	912	32	4	306	4	ZNF677	19	53740528	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	2987521	53740528	5388455	117	2371											
EPS8L1	54869	hgsc.bcm.edu	37	chr19	55593906	55593906	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	atgccgtggcgctgctgcggGacaacgtcactccacgtgaa	8	7	13	13	5	1	1	1	1	0	0	2	2	2	2	2	2	4	2	2	2	2	0			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr19:55593906G>A	ENST00000201647.6	+	12	1206	c.1150G>A	c.(1150-1152)Gac>Aac	p.D384N	EPS8L1_ENST00000540810.1_Missense_Mutation_p.D320N|EPS8L1_ENST00000592824.1_3'UTR|EPS8L1_ENST00000245618.5_Missense_Mutation_p.D257N|EPS8L1_ENST00000586329.1_Missense_Mutation_p.D366N|EPS8L1_ENST00000588359.1_Missense_Mutation_p.D38N	NM_133180.2	NP_573441.2	Q8TE68	ES8L1_HUMAN	EPS8-like 1	384					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)		GCTGCTGCGGGACAACGTCAC	0.692																																					p.D384N	Ovarian(149;255 1863 3636 27051 29647)	Atlas-SNP	.											.	EPS8L1	122	.	0			c.G1150A						PASS	.						14	12	13					19																	55593906		2175	4264	6439	SO:0001583	missense	54869	exon12			CTGCGGGACAACG	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.1150G>A	19.37:g.55593906G>A	ENSP00000201647:p.Asp384Asn	74	0	0		64	14	0.21875	NM_133180	Q71RE2|Q8NC10|Q96BB7|Q9BSQ2|Q9GZQ2|Q9NXH0	Missense_Mutation	SNP	ENST00000201647.6	37	CCDS12914.1	.	.	.	.	.	.	.	.	.	.	G	8.107	0.777937	0.16120	.	.	ENSG00000131037	ENST00000310075;ENST00000201647;ENST00000540810;ENST00000245618;ENST00000539118	T;T;T	0.21734	1.99;1.99;1.99	4.05	4.05	0.47172	.	0.303746	0.34435	N	0.003973	T	0.07954	0.0199	N	0.04880	-0.145	0.27125	N	0.962039	B;B;B;B;B	0.33694	0.421;0.004;0.002;0.002;0.002	B;B;B;B;B	0.29785	0.107;0.004;0.007;0.002;0.003	T	0.23332	-1.0191	10	0.02654	T	1	-29.3165	11.9005	0.52680	0.0:0.0:1.0:0.0	.	320;366;131;257;384	B4DKV7;Q8TE68-3;Q8TE68-4;Q8TE68-2;Q8TE68	.;.;.;.;ES8L1_HUMAN	N	366;384;320;257;38	ENSP00000201647:D384N;ENSP00000437541:D320N;ENSP00000245618:D257N	ENSP00000201647:D384N	D	+	1	0	EPS8L1	60285718	0.353000	0.24904	0.976000	0.42696	0.927000	0.56198	2.970000	0.49240	2.262000	0.75019	0.561000	0.74099	GAC	.	.	none		0.692	EPS8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451713.1	NM_017729		A	55593906	G	A	55593906	3	1	17	1	0	0	0	0	1	0	0	0	5197	1174	41	2	1244	2	EPS8L1	19	55593906	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	1853378	55593906	3535077	118	2372											
NLRP9	338321	hgsc.bcm.edu	37	chr19	56244737	56244737	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggttgtttttccaattccatCaggaccttccaggaccacag	9	12	8	12	0	1	0	1	0	0	0	4	2	4	2	5	3	0	2	5	3	1	5			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr19:56244737C>T	ENST00000332836.2	-	2	487	c.460G>A	c.(460-462)Gat>Aat	p.D154N		NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	154	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)		CCAATTCCATCAGGACCTTCC	0.408																																					p.D154N		Atlas-SNP	.											.	NLRP9	163	.	0			c.G460A						PASS	.						84	80	81					19																	56244737		2203	4300	6503	SO:0001583	missense	338321	exon2			TTCCATCAGGACC	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.460G>A	19.37:g.56244737C>T	ENSP00000331857:p.Asp154Asn	163	0	0		138	41	0.297101	NM_176820	B2RN12|Q86W27	Missense_Mutation	SNP	ENST00000332836.2	37	CCDS12934.1	.	.	.	.	.	.	.	.	.	.	C	6.868	0.529542	0.13127	.	.	ENSG00000185792	ENST00000332836;ENST00000333452	T	0.61392	0.11	2.63	-5.25	0.02781	NACHT nucleoside triphosphatase (1);	.	.	.	.	T	0.43853	0.1266	N	0.22421	0.69	0.09310	N	1	B	0.29432	0.244	B	0.41135	0.348	T	0.51585	-0.8687	9	0.33141	T	0.24	.	7.3965	0.26939	0.0:0.2139:0.574:0.2121	.	154	Q7RTR0	NALP9_HUMAN	N	154	ENSP00000331857:D154N	ENSP00000331857:D154N	D	-	1	0	NLRP9	60936549	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.209000	0.09358	-1.401000	0.02058	-0.178000	0.13098	GAT	.	.	none		0.408	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453653.1	NM_176820		T	56244737	C	T	56244737	3	4	17	1	0	0	0	0	1	0	0	0	10493	826	29	2	2547	2	NLRP9	19	56244737	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	650831	56244737	2884246	119	2373											
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385790	58385790	+	Missense_Mutation	SNP	G	G	T																															cacattctccacattcataaGgtcttttcccagtgtgaact																								rs111727691		TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr19:58385790G>T	ENST00000435989.2	-	3	1202	c.968C>A	c.(967-969)cCt>cAt	p.P323H	ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000595295.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	323					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						ACATTCATAAGGTCTTTTCCC	0.358																																					p.P323H		Atlas-SNP	.											.	ZNF814	93	.	0			c.C968A						PASS	.						15	12	13					19																	58385790		688	1563	2251	SO:0001583	missense	730051	exon3			TCATAAGGTCTTT		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.968C>A	19.37:g.58385790G>T	ENSP00000410545:p.Pro323His	218	0	0		214	29	0.135514	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	8.139	0.784825	0.16189	.	.	ENSG00000204514	ENST00000435989	T	0.29397	1.57	2.27	1.18	0.20946	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.57080	0.2029	M	0.90019	3.08	0.20764	N	0.999853	D	0.89917	1.0	D	0.67231	0.95	T	0.46247	-0.9205	9	0.66056	D	0.02	.	9.258	0.37595	0.0:0.0:0.7811:0.2189	.	323	B7Z6K7	ZN814_HUMAN	H	323	ENSP00000410545:P323H	ENSP00000410545:P323H	P	-	2	0	ZNF814	63077602	0.000000	0.05858	0.028000	0.17463	0.016000	0.09150	-0.439000	0.06897	0.330000	0.23485	-1.407000	0.01130	CCT	G|0.500;T|0.500	0.500	weak		0.358	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		T	58385790	G	T	58385790	3	4	17	1	0	0	0	0	1	0	0	0	18191	1000	35	4	1603	4	ZNF814	19	58385790	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	2141053	58385790	743193	120	2374	33	2									
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385793	58385793	+	Missense_Mutation	SNP	C	C	T																															attctccacattcataaggtCttttcccagtgtgaactctc																								rs113623532		TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr19:58385793C>T	ENST00000435989.2	-	3	1199	c.965G>A	c.(964-966)aGa>aAa	p.R322K	ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000595295.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	322					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						TTCATAAGGTCTTTTCCCAGT	0.358																																					p.R322K		Atlas-SNP	.											.	ZNF814	93	.	0			c.G965A						PASS	.						15	12	13					19																	58385793		687	1562	2249	SO:0001583	missense	730051	exon3			TAAGGTCTTTTCC		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.965G>A	19.37:g.58385793C>T	ENSP00000410545:p.Arg322Lys	216	0	0		203	28	0.137931	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	0.023	-1.395361	0.01175	.	.	ENSG00000204514	ENST00000435989	T	0.12361	2.69	2.27	9.47E-4	0.14044	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03608	0.0103	N	0.02225	-0.63	0.09310	N	0.999999	B	0.29301	0.241	B	0.28916	0.096	T	0.40534	-0.9558	9	0.02654	T	1	.	4.6969	0.12808	0.0:0.4166:0.0:0.5834	.	322	B7Z6K7	ZN814_HUMAN	K	322	ENSP00000410545:R322K	ENSP00000410545:R322K	R	-	2	0	ZNF814	63077605	0.000000	0.05858	0.024000	0.17045	0.009000	0.06853	-1.883000	0.01623	0.331000	0.23511	-1.381000	0.01174	AGA	C|0.500;T|0.500	0.500	weak		0.358	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		T	58385793	C	T	58385793	3	4	17	1	0	0	0	0	1	0	0	0	18191	913	32	2	1606	2	ZNF814	19	58385793	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	3	58385793	743190	121	2375	33	2									
PLCB1	23236	hgsc.bcm.edu	37	chr20	8130945	8130945	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcttacatttctaggactCaactattgttactccaatta	11	17	3	10	0	3	0	1	0	2	0	4	1	4	1	1	1	3	1	1	1	7	8			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr20:8130945C>A	ENST00000338037.6	+	2	131	c.104C>A	c.(103-105)tCa>tAa	p.S35*	PLCB1_ENST00000378641.3_Nonsense_Mutation_p.S35*|PLCB1_ENST00000378637.2_Nonsense_Mutation_p.S35*	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	35					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						TTCTAGGACTCAACTATTGTT	0.328																																					p.V35D		Atlas-SNP	.											.	PLCB1	394	.	0			c.T104A						PASS	.						73	71	72					20																	8130945		2203	4291	6494	SO:0001587	stop_gained	23236	exon2			AGGACTCAACTAT	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.104C>A	20.37:g.8130945C>A	ENSP00000338185:p.Ser35*	311	0	0		263	61	0.231939	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Missense_Mutation	SNP	ENST00000338037.6	37	CCDS13102.1	.	.	.	.	.	.	.	.	.	.	C	42	9.746884	0.99253	.	.	ENSG00000182621	ENST00000378641;ENST00000338037;ENST00000378637;ENST00000404098	.	.	.	5.76	5.76	0.90799	.	0.148595	0.45126	D	0.000393	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.5213	0.90954	0.0:1.0:0.0:0.0	.	.	.	.	X	35;35;35;34	.	ENSP00000338185:S35X	S	+	2	0	PLCB1	8078945	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.576000	0.67437	2.715000	0.92844	0.561000	0.74099	TCA	.	.	none		0.328	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3			A	8130945	C	A	8130945	4	1	17	1	0	0	0	0	0	1	0	0	12036	838	29	4	110	4	PLCB1	20	8130945	Nonsense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10		8130945	54894575	122	2376											
FOXA2	3170	hgsc.bcm.edu	37	chr20	22562836	22562836	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggtgggccgcggcctgctgCtgctgcccgggagagggcgc	3	5	20	13	4	0	1	0	0	0	1	0	2	0	1	3	5	4	3	3	5	0	0			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr20:22562836C>T	ENST00000377115.4	-	3	1207	c.1026G>A	c.(1024-1026)caG>caA	p.Q342Q	FOXA2_ENST00000419308.2_Silent_p.Q348Q	NM_153675.2	NP_710141.1	Q9Y261	FOXA2_HUMAN	forkhead box A2	342					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)					CGGCCTGCTGCTGCTGCCCGG	0.756																																					p.Q348Q		Atlas-SNP	.											.	FOXA2	48	.	0			c.G1044A						PASS	.						14	12	13					20																	22562836		1999	3801	5800	SO:0001819	synonymous_variant	3170	exon2			CTGCTGCTGCTGC	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.1026G>A	20.37:g.22562836C>T		99	0	0		74	20	0.27027	NM_021784	Q8WUW4|Q96DF7	Silent	SNP	ENST00000377115.4	37	CCDS13147.1																																																																																			.	.	none		0.756	FOXA2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078289.1			T	22562836	C	T	22562836	2	4	17	1	0	0	0	0	0	0	0	1	5998	796	28	2		2	FOXA2	20	22562836	Silent	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	14431891	22562836	40462684	123	2377											
PHF20	51230	hgsc.bcm.edu	37	chr20	34458897	34458897	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cccaggaaaagtcaaaaaacTactcggaaaacactgacaaa	21	4	6	10	1	1	1	1	1	0	0	2	3	1	3	1	2	3	0	1	2	9	1			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr20:34458897T>G	ENST00000374012.3	+	8	1072	c.943T>G	c.(943-945)Tac>Gac	p.Y315D	PHF20_ENST00000481202.1_3'UTR|PHF20_ENST00000439301.1_3'UTR			Q9BVI0	PHF20_HUMAN	PHD finger protein 20	315					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)					GTCAAAAAACTACTCGGAAAA	0.428																																					p.Y315D		Atlas-SNP	.											.	PHF20	94	.	0			c.T943G						PASS	.						82	77	79					20																	34458897		2203	4300	6503	SO:0001583	missense	51230	exon8			AAAAACTACTCGG	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.943T>G	20.37:g.34458897T>G	ENSP00000363124:p.Tyr315Asp	51	0	0		67	20	0.298507	NM_016436	A7E235|B2RB56|E1P5S3|Q566Q2|Q5JWY9|Q66K49|Q9BWV4|Q9BXA3|Q9BZW3|Q9H421|Q9H4J6|Q9NZ22	Missense_Mutation	SNP	ENST00000374012.3	37	CCDS13268.1	.	.	.	.	.	.	.	.	.	.	T	11.05	1.524349	0.27299	.	.	ENSG00000025293	ENST00000374012;ENST00000339089;ENST00000374000	T;T;T	0.43294	1.55;0.95;0.95	5.11	2.67	0.31697	.	0.743446	0.13065	N	0.416564	T	0.25005	0.0607	N	0.22421	0.69	0.21841	N	0.999515	B;B	0.28128	0.037;0.201	B;B	0.25759	0.014;0.063	T	0.13953	-1.0490	10	0.33141	T	0.24	.	5.4595	0.16610	0.0:0.093:0.1751:0.7319	.	315;315	Q9BVI0;Q66K49	PHF20_HUMAN;.	D	315	ENSP00000363124:Y315D;ENSP00000341900:Y315D;ENSP00000363112:Y315D	ENSP00000341900:Y315D	Y	+	1	0	PHF20	33922311	0.030000	0.19436	0.314000	0.25224	0.996000	0.88848	1.520000	0.35899	0.905000	0.36596	0.482000	0.46254	TAC	.	.	none		0.428	PHF20-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078949.2	NM_016436		G	34458897	T	G	34458897	3	3	17	1	0	0	0	0	1	0	0	0	11840	1522	53	5	969	5	PHF20	20	34458897	Missense_Mutation	SNP	T	TCGA-FF-A7CQ-01A-11D-A382-10	11896061	34458897	28566623	124	2378											
ADAMTS1	9510	hgsc.bcm.edu	37	chr21	28214839	28214839	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccaccaggctaactgaattaCgaatgctggggtgtttgtac	10	11	11	9	1	0	1	0	1	0	0	0	2	0	1	2	3	4	4	2	3	5	4			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr21:28214839C>A	ENST00000284984.3	-	2	1350	c.896G>T	c.(895-897)cGt>cTt	p.R299L		NM_006988.3	NP_008919.3	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 1	299	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				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)		AACTGAATTACGAATGCTGGG	0.517																																					p.R299L		Atlas-SNP	.											.	ADAMTS1	131	.	0			c.G896T						PASS	.						101	84	89					21																	28214839		2203	4300	6503	SO:0001583	missense	9510	exon2			GAATTACGAATGC	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.896G>T	21.37:g.28214839C>A	ENSP00000284984:p.Arg299Leu	120	0	0		139	40	0.28777	NM_006988	D3DSD5|Q9NSJ8|Q9P2K0|Q9UH83|Q9UP80	Missense_Mutation	SNP	ENST00000284984.3	37	CCDS33524.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.76|15.76	2.928654|2.928654	0.52759|0.52759	.|.	.|.	ENSG00000154734|ENSG00000154734	ENST00000284984;ENST00000517777;ENST00000517452|ENST00000451462	T;T;T|.	0.63580|.	-0.05;-0.05;-0.05|.	5.44|5.44	5.44|5.44	0.79542|0.79542	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);|.	.|.	.|.	.|.	.|.	T|T	0.50326|0.50326	0.1609|0.1609	N|N	0.12611|0.12611	0.24|0.24	0.58432|0.58432	D|D	0.999996|0.999996	B|.	0.19817|.	0.039|.	B|.	0.16289|.	0.015|.	T|T	0.42916|0.42916	-0.9423|-0.9423	9|5	0.40728|.	T|.	0.16|.	.|.	19.4587|19.4587	0.94906|0.94906	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	299|.	Q9UHI8|.	ATS1_HUMAN|.	L|L	299;37;61|81	ENSP00000284984:R299L;ENSP00000429557:R37L;ENSP00000431065:R61L|.	ENSP00000284984:R299L|.	R|V	-|-	2|1	0|0	ADAMTS1|ADAMTS1	27136710|27136710	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.994000|0.994000	0.84299|0.84299	5.510000|5.510000	0.67018|0.67018	2.828000|2.828000	0.97474|0.97474	0.655000|0.655000	0.94253|0.94253	CGT|GTA	.	.	none		0.517	ADAMTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171650.2			A	28214839	C	A	28214839	3	1	17	1	0	0	0	0	1	0	0	0	255	536	19	4	2039	4	ADAMTS1	21	28214839	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10		28214839	19915056	125	2379											
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230278	23230278	+	Silent	SNP	G	G	A																															ggttgtgagacccctgaggaGctgggccctggtcccaggca																								rs544778929	byFrequency	TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr22:23230278G>A	ENST00000526893.1	+	1	319	c.45G>A	c.(43-45)gaG>gaA	p.E15E	IGLL5_ENST00000531372.1_Silent_p.E15E|IGLL5_ENST00000532223.2_Silent_p.E15E|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	15						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CCCCTGAGGAGCTGGGCCCTG	0.672													G|||	6	0.00119808	0.0023	0.0029	5008	,	,		13267	0.0		0.0	False		,,,				2504	0.001				p.E15E		Atlas-SNP	.											IGLL5,NS,lymphoid_neoplasm,0,1	IGLL5	26	1	0			c.G45A						scavenged	.																																			SO:0001819	synonymous_variant	100423062	exon1			TGAGGAGCTGGGC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.45G>A	22.37:g.23230278G>A		171	1	0.00584795		103	35	0.339806	NM_001178126		Silent	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.672	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		A	23230278	G	A	23230278	2	1	17	1	0	0	0	0	0	0	0	1	7603	962	34	2		2	IGLL5	22	23230278	Silent	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10		23230278	28074288	126	2380	34	2									
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230279	23230279	+	Silent	SNP	C	C	T																															gttgtgagacccctgaggagCtgggccctggtcccaggcag																								rs564743210	byFrequency	TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr22:23230279C>T	ENST00000526893.1	+	1	320	c.46C>T	c.(46-48)Ctg>Ttg	p.L16L	IGLL5_ENST00000531372.1_Silent_p.L16L|IGLL5_ENST00000532223.2_Silent_p.L16L|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	16						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CCCTGAGGAGCTGGGCCCTGG	0.667													C|||	3	0.000599042	0.0023	0.0	5008	,	,		13145	0.0		0.0	False		,,,				2504	0.0				p.L16L		Atlas-SNP	.											.	IGLL5	26	.	0			c.C46T						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			GAGGAGCTGGGCC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.46C>T	22.37:g.23230279C>T		166	0	0		102	34	0.333333	NM_001178126		Silent	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.667	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		T	23230279	C	T	23230279	2	4	17	1	0	0	0	0	0	0	0	1	7603	796	28	2		2	IGLL5	22	23230279	Silent	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	1	23230279	28074287	127	2381	34	2									
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23235883	23235884	+	Frame_Shift_Del	DEL	CC	CC	-																															cccgtcatgcccagcaggctCctgctccagcccagccccca																										TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr22:23235883_23235884delCC	ENST00000526893.1	+	2	484_485	c.210_211delCC	c.(208-213)ctcctgfs	p.LL70fs	IGLL5_ENST00000531372.1_Intron|IGLJ1_ENST00000390320.2_RNA|IGLC1_ENST00000390321.2_RNA|IGLL5_ENST00000532223.2_Frame_Shift_Del_p.LL71fs	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	70						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CCAGCAGGCTCCTGCTCCAGCC	0.658																																					p.70_70del		Atlas-Indel	.											.	IGLL5	26	.	0			c.209_210del						PASS	.																																			SO:0001589	frameshift_variant	100423062	exon2			.	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.210_211delCC	22.37:g.23235883_23235884delCC	ENSP00000431254:p.Leu70fs	48	0	0		26	12	0.461538	NM_001178126		Frame_Shift_Del	DEL	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.658	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		-	23235884	CC	-	23235883	7	5	17	1	0	1	0	1	0	0	0	0	7603	842	30	0	216	0	IGLL5	22	23235883	Frame_Shift_Del	DEL	CC	TCGA-FF-A7CQ-01A-11D-A382-10	5604	23235883	28068683	128	2382	35	2									
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23235887	23235887	+	Missense_Mutation	SNP	C	C	G																															tcatgcccagcaggctcctgCtccagcccagcccccagaga																										TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr22:23235887C>G	ENST00000526893.1	+	2	488	c.214C>G	c.(214-216)Ctc>Gtc	p.L72V	IGLL5_ENST00000531372.1_Intron|IGLJ1_ENST00000390320.2_RNA|IGLC1_ENST00000390321.2_RNA|IGLL5_ENST00000532223.2_Missense_Mutation_p.L73V	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	72						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CAGGCTCCTGCTCCAGCCCAG	0.657																																					p.L72V		Atlas-SNP	.											.	IGLL5	26	.	0			c.C214G						PASS	.						39	43	42					22																	23235887		691	1590	2281	SO:0001583	missense	100423062	exon2			CTCCTGCTCCAGC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.214C>G	22.37:g.23235887C>G	ENSP00000431254:p.Leu72Val	49	0	0		28	13	0.464286	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	C	8.638	0.895344	0.17613	.	.	ENSG00000254709	ENST00000532223;ENST00000526893	T;T	0.00571	6.5;6.5	2.5	-2.87	0.05700	.	.	.	.	.	T	0.00468	0.0015	L	0.50333	1.59	0.09310	N	1	B	0.28026	0.198	B	0.24541	0.054	T	0.39781	-0.9597	9	0.54805	T	0.06	.	3.482	0.07606	0.0:0.3311:0.3656:0.3033	.	72	B9A064	IGLL5_HUMAN	V	73;72	ENSP00000436353:L73V;ENSP00000431254:L72V	ENSP00000417505:L6V	L	+	1	0	IGLL5	21565887	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.207000	0.03008	-0.350000	0.08262	0.491000	0.48974	CTC	.	.	none		0.657	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		G	23235887	C	G	23235887	3	3	17	1	0	0	0	0	1	0	0	0	7603	797	28	4	220	4	IGLL5	22	23235887	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	4	23235887	28068679	129	2383	35	2									
CRYBB3	1417	hgsc.bcm.edu	37	chr22	25603042	25603042	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctatgagttccccggctacCgtgggcgccagtacgtgttt	5	11	13	12	4	0	1	0	1	0	0	1	1	1	1	4	2	2	5	4	2	3	5			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr22:25603042C>T	ENST00000215855.2	+	6	579	c.499C>T	c.(499-501)Cgt>Tgt	p.R167C	CRYBB3_ENST00000404334.1_3'UTR	NM_004076.3	NP_004067.1	P26998	CRBB3_HUMAN	crystallin, beta B3	167	Beta/gamma crystallin 'Greek key' 4. {ECO:0000255|PROSITE-ProRule:PRU00028}.				visual perception (GO:0007601)		structural constituent of eye lens (GO:0005212)			large_intestine(2)|lung(2)|prostate(1)	5						CCCCGGCTACCGTGGGCGCCA	0.642																																					p.P167S		Atlas-SNP	.											.	CRYBB3	13	.	0			c.C499T						PASS	.						64	57	59					22																	25603042		2201	4299	6500	SO:0001583	missense	1417	exon6			GGCTACCGTGGGC		CCDS13830.1	22q11.23	2008-06-10			ENSG00000100053	ENSG00000100053			2400	protein-coding gene	gene with protein product		123630		CRYB3		8999933	Standard	NM_004076		Approved		uc003abo.2	P26998	OTTHUMG00000150869	ENST00000215855.2:c.499C>T	22.37:g.25603042C>T	ENSP00000215855:p.Arg167Cys	68	0	0		73	17	0.232877	NM_004076	Q3B7S9|Q3T1B7|Q6ISK6|Q92965|Q9UH09	Missense_Mutation	SNP	ENST00000215855.2	37	CCDS13830.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.987958	0.74589	.	.	ENSG00000100053	ENST00000215855	T	0.78707	-1.2	4.87	4.87	0.63330	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.000000	0.85682	D	0.000000	D	0.86091	0.5850	M	0.81112	2.525	0.80722	D	1	D	0.62365	0.991	P	0.61940	0.896	D	0.87862	0.2665	10	0.87932	D	0	.	11.7789	0.52001	0.1759:0.8241:0.0:0.0	.	167	P26998	CRBB3_HUMAN	C	167	ENSP00000215855:R167C	ENSP00000215855:R167C	R	+	1	0	CRYBB3	23933042	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.684000	0.37649	2.223000	0.72356	0.561000	0.74099	CGT	.	.	none		0.642	CRYBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320352.1	NM_004076		T	25603042	C	T	25603042	3	4	17	1	0	0	0	0	1	0	0	0	3914	652	23	1	517	1	CRYBB3	22	25603042	Missense_Mutation	SNP	C	TCGA-FF-A7CQ-01A-11D-A382-10	2367155	25603042	25701524	130	2384											
GAL3ST1	9514	hgsc.bcm.edu	37	chr22	30951371	30951371	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggcacgggcgagtcgcggcGggcgttgagcttgaagtaga	7	6	19	9	7	0	3	0	2	0	1	1	4	0	3	0	4	1	4	0	4	2	3			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr22:30951371G>A	ENST00000402321.1	-	3	1158	c.841C>T	c.(841-843)Cgc>Tgc	p.R281C	GAL3ST1_ENST00000338911.5_Missense_Mutation_p.R281C|GAL3ST1_ENST00000401975.1_Missense_Mutation_p.R281C|GAL3ST1_ENST00000406955.1_Missense_Mutation_p.R281C|GAL3ST1_ENST00000402369.1_Missense_Mutation_p.R281C|GAL3ST1_ENST00000443111.2_Missense_Mutation_p.R281C|GAL3ST1_ENST00000406361.1_Missense_Mutation_p.R281C			Q99999	G3ST1_HUMAN	galactose-3-O-sulfotransferase 1	281				RR -> LN (in Ref. 1; AA sequence). {ECO:0000305}.	galactosylceramide biosynthetic process (GO:0006682)|glycosphingolipid metabolic process (GO:0006687)|myelination (GO:0042552)|protein N-linked glycosylation (GO:0006487)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|sphingolipid metabolic process (GO:0006665)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	galactosylceramide sulfotransferase activity (GO:0001733)|sulfotransferase activity (GO:0008146)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	21						GAGTCGCGGCGGGCGTTGAGC	0.652																																					p.R281C		Atlas-SNP	.											.	GAL3ST1	44	.	0			c.C841T						PASS	.						39	44	42					22																	30951371		2203	4300	6503	SO:0001583	missense	9514	exon4			CGCGGCGGGCGTT	D88667	CCDS13879.1	22q12.2	2007-04-02			ENSG00000128242	ENSG00000128242		"Sulfotransferases, membrane-bound"	24240	protein-coding gene	gene with protein product	"cerebroside (3' phosphoadenylylsulfate:galactosylceramide 3') sulfotransferase"	602300				9847074, 9030544	Standard	NM_004861		Approved	CST	uc003aii.1	Q99999	OTTHUMG00000151200	ENST00000402321.1:c.841C>T	22.37:g.30951371G>A	ENSP00000385735:p.Arg281Cys	40	0	0		31	10	0.322581	NM_004861	Q96C63	Missense_Mutation	SNP	ENST00000402321.1	37	CCDS13879.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.200716	0.79015	.	.	ENSG00000128242	ENST00000406955;ENST00000402321;ENST00000402369;ENST00000401975;ENST00000338911;ENST00000406361;ENST00000443111	T;T;T;T;T;T;T	0.26660	1.72;1.72;1.72;1.72;1.72;1.72;1.72	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.61961	0.2389	M	0.90977	3.165	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.71464	-0.4585	10	0.87932	D	0	-8.8903	18.6705	0.91508	0.0:0.0:1.0:0.0	.	281	Q99999	G3ST1_HUMAN	C	281	ENSP00000385825:R281C;ENSP00000385735:R281C;ENSP00000384122:R281C;ENSP00000384388:R281C;ENSP00000343234:R281C;ENSP00000385207:R281C;ENSP00000402587:R281C	ENSP00000343234:R281C	R	-	1	0	GAL3ST1	29281371	1.000000	0.71417	0.995000	0.50966	0.835000	0.47333	4.470000	0.60175	2.523000	0.85059	0.561000	0.74099	CGC	.	.	none		0.652	GAL3ST1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321745.1	NM_004861		A	30951371	G	A	30951371	3	1	17	1	0	0	0	0	1	0	0	0	6205	1116	39	1	434	1	GAL3ST1	22	30951371	Missense_Mutation	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10	5348329	30951371	20353195	131	2385											
PLXNB2	23654	hgsc.bcm.edu	37	chr22	50720155	50720155	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctcctgcagcgtcatcgccTtgttcagattggtgccctgg	4	12	11	14	2	2	1	2	0	0	1	4	1	3	1	4	2	3	2	4	2	0	3			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chr22:50720155T>A	ENST00000449103.1	-	21	3502	c.3362A>T	c.(3361-3363)aAg>aTg	p.K1121M	PLXNB2_ENST00000359337.4_Missense_Mutation_p.K1121M|PLXNB2_ENST00000496720.1_5'Flank			O15031	PLXB2_HUMAN	plexin B2	1121					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)		CGTCATCGCCTTGTTCAGATT	0.672																																					p.K1121M		Atlas-SNP	.											.	PLXNB2	172	.	0			c.A3362T						PASS	.						21	25	24					22																	50720155		2147	4255	6402	SO:0001583	missense	23654	exon21			ATCGCCTTGTTCA		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.3362A>T	22.37:g.50720155T>A	ENSP00000409171:p.Lys1121Met	69	0	0		53	14	0.264151	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Missense_Mutation	SNP	ENST00000449103.1	37	CCDS43035.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.16|14.16	2.453769|2.453769	0.43531|0.43531	.|.	.|.	ENSG00000196576|ENSG00000196576	ENST00000449103;ENST00000359337|ENST00000427829	T;T|.	0.03553|.	3.89;3.89|.	4.47|4.47	4.47|4.47	0.54385|0.54385	Immunoglobulin-like fold (1);|.	0.530450|.	0.16890|.	N|.	0.195334|.	T|T	0.53449|0.53449	0.1797|0.1797	L|L	0.38838|0.38838	1.175|1.175	0.38197|0.38197	D|D	0.940066|0.940066	P|.	0.38473|.	0.633|.	B|.	0.34489|.	0.184|.	T|T	0.54899|0.54899	-0.8224|-0.8224	10|5	0.34782|.	T|.	0.22|.	.|.	10.1523|10.1523	0.42801|0.42801	0.0:0.0:0.1676:0.8324|0.0:0.0:0.1676:0.8324	.|.	1121|.	O15031|.	PLXB2_HUMAN|.	M|W	1121|139	ENSP00000409171:K1121M;ENSP00000352288:K1121M|.	ENSP00000352288:K1121M|.	K|R	-|-	2|1	0|2	PLXNB2|PLXNB2	49062282|49062282	0.800000|0.800000	0.28916|0.28916	1.000000|1.000000	0.80357|0.80357	0.952000|0.952000	0.60782|0.60782	0.495000|0.495000	0.22483|0.22483	1.882000|1.882000	0.54519|0.54519	0.402000|0.402000	0.26972|0.26972	AAG|AGG	.	.	none		0.672	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401		A	50720155	T	A	50720155	3	1	17	1	0	0	0	0	1	0	0	0	12133	1609	56	5	2222	5	PLXNB2	22	50720155	Missense_Mutation	SNP	T	TCGA-FF-A7CQ-01A-11D-A382-10	19768784	50720155	584411	132	2386											
FAM47C	442444	hgsc.bcm.edu	37	chrX	37028925	37028925	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgggtgtccagtctctgcccGgagcctaccaagaccggagc	7	6	13	15	3	1	1	0	0	1	1	3	3	2	3	5	3	4	0	5	3	2	1			TCGA-FF-A7CQ-01A-11D-A382-10	TCGA-FF-A7CQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2e4fe50f-0ee6-46c2-9795-2e2c1c8a86bf	5f7ab27c-4bb5-430c-a173-433d42f767d5	g.chrX:37028925G>A	ENST00000358047.3	+	1	2494	c.2442G>A	c.(2440-2442)ccG>ccA	p.P814P		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	814										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						GTCTCTGCCCGGAGCCTACCA	0.557																																					p.P814P		Atlas-SNP	.											.	FAM47C	267	.	0			c.G2442A						PASS	.						51	52	51					X																	37028925		2202	4300	6502	SO:0001819	synonymous_variant	442444	exon1			CTGCCCGGAGCCT	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.2442G>A	X.37:g.37028925G>A		79	0	0		68	35	0.514706	NM_001013736	Q6ZU46	Silent	SNP	ENST00000358047.3	37	CCDS35227.1																																																																																			.	.	none		0.557	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736		A	37028925	G	A	37028925	2	1	17	1	0	0	0	0	0	0	0	1	5579	1103	39	1		1	FAM47C	23	37028925	Silent	SNP	G	TCGA-FF-A7CQ-01A-11D-A382-10		37028925	118241635	133	2387											
ANGPTL7	10218	hgsc.bcm.edu	37	chr1	11253778	11253778	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gggacttctggctggggaacGaacacatccaccggctctcc	8	7	12	14	2	2	0	0	0	2	0	4	3	3	2	3	5	2	2	3	5	2	1	rs376924013		TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr1:11253778G>A	ENST00000376819.3	+	3	858	c.619G>A	c.(619-621)Gaa>Aaa	p.E207K	ANGPTL7_ENST00000476934.1_3'UTR|MTOR_ENST00000361445.4_Intron	NM_021146.2	NP_066969.1	O43827	ANGL7_HUMAN	angiopoietin-like 7	207	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				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)		GCTGGGGAACGAACACATCCA	0.597																																					p.E207K		Atlas-SNP	.											.	ANGPTL7	23	.	0			c.G619A						PASS	.	G	,LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	84	76	79		,619	5.8	0.7	1		79	0,8600		0,0,4300	no	intron,missense	MTOR,ANGPTL7	NM_004958.3,NM_021146.2	,56	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,benign	,207/347	11253778	1,13005	2203	4300	6503	SO:0001583	missense	10218	exon3			GGGAACGAACACA	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.619G>A	1.37:g.11253778G>A	ENSP00000366015:p.Glu207Lys	44	0	0		55	7	0.127273	NM_021146	B2R9B2|F1T0A6|Q4ZGK4	Missense_Mutation	SNP	ENST00000376819.3	37	CCDS128.1	.	.	.	.	.	.	.	.	.	.	G	32	5.130708	0.94473	2.27E-4	0.0	ENSG00000171819	ENST00000376819	D	0.84660	-1.88	5.81	5.81	0.92471	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.089808	0.85682	D	0.000000	D	0.86301	0.5900	M	0.77103	2.36	0.80722	D	1	P	0.46656	0.882	B	0.39465	0.3	D	0.87083	0.2167	10	0.46703	T	0.11	.	20.0833	0.97789	0.0:0.0:1.0:0.0	.	207	O43827	ANGL7_HUMAN	K	207	ENSP00000366015:E207K	ENSP00000366015:E207K	E	+	1	0	ANGPTL7	11176365	1.000000	0.71417	0.698000	0.30274	0.938000	0.57974	8.031000	0.88826	2.756000	0.94617	0.655000	0.94253	GAA	.	.	none		0.597	ANGPTL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005564.1	NM_021146		A	11253778	G	A	11253778	3	1	18	1	0	0	0	0	1	0	0	0	619	1059	37	1	629	1	ANGPTL7	1	11253778	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10		11253778	237996843	1	2388											
PLEKHM2	23207	hgsc.bcm.edu	37	chr1	16054583	16054583	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggccctcacagagtagacaaCaatcacctgctcctgctcat	11	8	7	15	0	3	2	3	0	0	2	4	2	4	2	3	1	3	3	3	1	3	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr1:16054583C>T	ENST00000375799.3	+	10	1997	c.1770C>T	c.(1768-1770)aaC>aaT	p.N590N	PLEKHM2_ENST00000375793.2_Silent_p.N570N|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	590					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)		GAGTAGACAACAATCACCTGC	0.577																																					p.N590N		Atlas-SNP	.											.	PLEKHM2	94	.	0			c.C1770T						PASS	.						60	63	62					1																	16054583		2179	4272	6451	SO:0001819	synonymous_variant	23207	exon10			AGACAACAATCAC	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.1770C>T	1.37:g.16054583C>T		134	0	0		164	32	0.195122	NM_015164	O94928|Q5VT65|Q6NUH9|Q7L8G1|Q8IVT7|Q8N2T4|Q96AY0|Q9NTF7	Silent	SNP	ENST00000375799.3	37	CCDS44063.1																																																																																			.	.	none		0.577	PLEKHM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008463.1	NM_015164		T	16054583	C	T	16054583	2	4	18	1	0	0	0	0	0	0	0	1	12090	477	17	2		2	PLEKHM2	1	16054583	Silent	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	4800805	16054583	233196038	2	2389											
UBR4	23352	hgsc.bcm.edu	37	chr1	19494536	19494536	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttacacaataagatctccaGtcaacctgaccagtgagagg	14	8	8	11	0	2	3	1	2	1	2	3	4	2	3	3	1	2	0	3	1	4	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr1:19494536G>A	ENST00000375254.3	-	28	3911	c.3884C>T	c.(3883-3885)aCt>aTt	p.T1295I	UBR4_ENST00000375217.2_Missense_Mutation_p.T1295I|UBR4_ENST00000375226.2_Missense_Mutation_p.T1295I|UBR4_ENST00000375267.2_Missense_Mutation_p.T1295I	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	1295					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)		AAGATCTCCAGTCAACCTGAC	0.483																																					p.T1295I		Atlas-SNP	.											.	UBR4	415	.	0			c.C3884T						PASS	.						123	121	122					1																	19494536		2203	4300	6503	SO:0001583	missense	23352	exon28			TCTCCAGTCAACC	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.3884C>T	1.37:g.19494536G>A	ENSP00000364403:p.Thr1295Ile	79	0	0		70	18	0.257143	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	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	G	16.55	3.153495	0.57259	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000417040;ENST00000419533	T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15	5.82	4.9	0.64082	.	0.000000	0.85682	D	0.000000	T	0.44435	0.1293	N	0.11927	0.2	0.80722	D	1	P	0.42039	0.769	B	0.41299	0.353	T	0.36986	-0.9725	10	0.09843	T	0.71	.	15.8923	0.79309	0.0:0.0:0.8634:0.1366	.	1295	Q5T4S7	UBR4_HUMAN	I	1295;1295;1295;1295;5;511	ENSP00000364403:T1295I;ENSP00000364416:T1295I;ENSP00000364365:T1295I;ENSP00000364374:T1295I	ENSP00000364365:T1295I	T	-	2	0	UBR4	19367123	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.633000	0.83260	1.434000	0.47414	0.655000	0.94253	ACT	.	.	none		0.483	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		A	19494536	G	A	19494536	3	1	18	1	0	0	0	0	1	0	0	0	16919	1029	36	2	11983	2	UBR4	1	19494536	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	3439953	19494536	229756085	3	2390											
SRRM1	10250	hgsc.bcm.edu	37	chr1	24996752	24996752	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtctacaaactggtcaccAgctgtaccggtcaaaaaggc	12	7	9	13	2	3	0	2	0	1	0	3	0	3	0	3	3	4	2	3	3	5	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr1:24996752A>T	ENST00000323848.9	+	15	2661	c.2346A>T	c.(2344-2346)ccA>ccT	p.P782P	SRRM1_ENST00000374389.4_Silent_p.P791P|SRRM1_ENST00000479034.1_3'UTR|SRRM1_ENST00000447431.2_Silent_p.P794P	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	782	Pro-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)		ACTGGTCACCAGCTGTACCGG	0.527																																					p.P782P	Ovarian(68;897 1494 3282 17478)	Atlas-SNP	.											.	SRRM1	81	.	0			c.A2346T						PASS	.						104	100	101					1																	24996752		2203	4300	6503	SO:0001819	synonymous_variant	10250	exon15			GTCACCAGCTGTA	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.2346A>T	1.37:g.24996752A>T		222	0	0		202	57	0.282178	NM_005839	O60585|Q5VVN4	Silent	SNP	ENST00000323848.9	37	CCDS255.1																																																																																			.	.	none		0.527	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839		T	24996752	A	T	24996752	2	4	18	1	0	0	0	0	0	0	0	1	15183	175	7	5		5	SRRM1	1	24996752	Silent	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10	5502216	24996752	224253869	4	2391											
EIF2B3	8891	hgsc.bcm.edu	37	chr1	45341356	45341356	+	Missense_Mutation	SNP	C	C	A																															tctggacagagagcagacagCaatttgggcaccttaaggac																										TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr1:45341356C>A	ENST00000360403.2	-	9	1113	c.987G>T	c.(985-987)ttG>ttT	p.L329F	EIF2B3_ENST00000372183.3_Missense_Mutation_p.L329F	NM_001261418.1|NM_020365.4	NP_001248347.1|NP_065098.1	Q9NR50	EI2BG_HUMAN	eukaryotic translation initiation factor 2B, subunit 3 gamma, 58kDa	329					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)					GAGCAGACAGCAATTTGGGCA	0.522																																					p.L329F	Colon(26;357 658 2581 11857 12657)	Atlas-SNP	.											.	EIF2B3	43	.	0			c.G987T						PASS	.						151	137	142					1																	45341356		2203	4300	6503	SO:0001583	missense	8891	exon9			AGACAGCAATTTG	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.987G>T	1.37:g.45341356C>A	ENSP00000353575:p.Leu329Phe	95	0	0		125	8	0.064	NM_020365	B2RBH8|D3DPZ2|Q5QP89|Q5QP90|Q8NDB5|Q8WV57|Q9H850	Missense_Mutation	SNP	ENST00000360403.2	37	CCDS517.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.69|16.69	3.192156|3.192156	0.58017|0.58017	.|.	.|.	ENSG00000070785|ENSG00000070785	ENST00000439363|ENST00000360403;ENST00000372183	.|T;D	.|0.94232	.|0.51;-3.38	5.4|5.4	5.4|5.4	0.78164|0.78164	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.91181|0.91181	0.7222|0.7222	M|M	0.65975|0.65975	2.015|2.015	0.53688|0.53688	D|D	0.999975|0.999975	.|B;P	.|0.36712	.|0.171;0.566	.|B;B	.|0.40901	.|0.124;0.343	D|D	0.86913|0.86913	0.2062|0.2062	5|10	.|0.10377	.|T	.|0.69	-1.4932|-1.4932	9.8482|9.8482	0.41039|0.41039	0.0:0.8458:0.0:0.1542|0.0:0.8458:0.0:0.1542	.|.	.|329;329	.|Q9NR50-2;Q9NR50	.|.;EI2BG_HUMAN	F|F	150|329	.|ENSP00000353575:L329F;ENSP00000361257:L329F	.|ENSP00000353575:L329F	C|L	-|-	2|3	0|2	EIF2B3|EIF2B3	45113943|45113943	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	1.969000|1.969000	0.40510|0.40510	2.528000|2.528000	0.85240|0.85240	0.655000|0.655000	0.94253|0.94253	TGC|TTG	.	.	none		0.522	EIF2B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023724.1	NM_020365		A	45341356	C	A	45341356	3	1	18	1	0	0	0	0	1	0	0	0	5004	709	25	4	424	4	EIF2B3	1	45341356	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	20344604	45341356	203909265	5	2392	36	2									
EIF2B3	8891	hgsc.bcm.edu	37	chr1	45341357	45341357	+	Missense_Mutation	SNP	A	A	G																															ctggacagagagcagacagcAatttgggcaccttaaggaca																										TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr1:45341357A>G	ENST00000360403.2	-	9	1112	c.986T>C	c.(985-987)tTg>tCg	p.L329S	EIF2B3_ENST00000372183.3_Missense_Mutation_p.L329S	NM_001261418.1|NM_020365.4	NP_001248347.1|NP_065098.1	Q9NR50	EI2BG_HUMAN	eukaryotic translation initiation factor 2B, subunit 3 gamma, 58kDa	329					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)					AGCAGACAGCAATTTGGGCAC	0.527																																					p.L329S	Colon(26;357 658 2581 11857 12657)	Atlas-SNP	.											.	EIF2B3	43	.	0			c.T986C						PASS	.						148	136	140					1																	45341357		2203	4300	6503	SO:0001583	missense	8891	exon9			GACAGCAATTTGG	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.986T>C	1.37:g.45341357A>G	ENSP00000353575:p.Leu329Ser	92	0	0		125	7	0.056	NM_020365	B2RBH8|D3DPZ2|Q5QP89|Q5QP90|Q8NDB5|Q8WV57|Q9H850	Missense_Mutation	SNP	ENST00000360403.2	37	CCDS517.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.19|15.19	2.758999|2.758999	0.49468|0.49468	.|.	.|.	ENSG00000070785|ENSG00000070785	ENST00000439363|ENST00000360403;ENST00000372183	.|T;D	.|0.94138	.|0.54;-3.36	5.4|5.4	5.4|5.4	0.78164|0.78164	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.92583|0.92583	0.7644|0.7644	M|M	0.77103|0.77103	2.36|2.36	0.54753|0.54753	D|D	0.999987|0.999987	.|B;B	.|0.27192	.|0.171;0.006	.|B;B	.|0.34991	.|0.193;0.017	D|D	0.88823|0.88823	0.3300|0.3300	5|10	.|0.06365	.|T	.|0.9	-1.4932|-1.4932	15.0974|15.0974	0.72247|0.72247	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|329;329	.|Q9NR50-2;Q9NR50	.|.;EI2BG_HUMAN	R|S	150|329	.|ENSP00000353575:L329S;ENSP00000361257:L329S	.|ENSP00000353575:L329S	C|L	-|-	1|2	0|0	EIF2B3|EIF2B3	45113944|45113944	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	6.176000|6.176000	0.71955|0.71955	2.045000|2.045000	0.60652|0.60652	0.533000|0.533000	0.62120|0.62120	TGC|TTG	.	.	none		0.527	EIF2B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023724.1	NM_020365		G	45341357	A	G	45341357	3	3	18	1	0	0	0	0	1	0	0	0	5004	131	5	3	425	3	EIF2B3	1	45341357	Missense_Mutation	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10	1	45341357	203909264	6	2393	36	2									
BEND5	79656	hgsc.bcm.edu	37	chr1	49208438	49208438	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tactttttccagatcaatggCgggacctaggcagttaagaa	12	11	10	8	1	1	2	1	0	0	2	2	3	2	3	2	3	1	2	2	3	5	5			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr1:49208438C>T	ENST00000371833.3	-	4	837	c.751G>A	c.(751-753)Gcc>Acc	p.A251T	BEND5_ENST00000476096.1_Intron|AGBL4_ENST00000371838.1_Intron|AGBL4_ENST00000371839.1_Intron	NM_024603.2	NP_078879.2	Q7L4P6	BEND5_HUMAN	BEN domain containing 5	251						Golgi apparatus (GO:0005794)				large_intestine(5)|lung(2)|skin(1)	8						AGATCAATGGCGGGACCTAGG	0.443																																					p.A251T		Atlas-SNP	.											.	BEND5	93	.	0			c.G751A						PASS	.						61	62	61					1																	49208438		2203	4300	6503	SO:0001583	missense	79656	exon4			CAATGGCGGGACC	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.751G>A	1.37:g.49208438C>T	ENSP00000360899:p.Ala251Thr	97	0	0		98	7	0.0714286	NM_024603	D3DQ27|Q96A62|Q9HAI3	Missense_Mutation	SNP	ENST00000371833.3	37	CCDS552.2	.	.	.	.	.	.	.	.	.	.	C	15.38	2.817313	0.50633	.	.	ENSG00000162373	ENST00000371833	.	.	.	5.45	5.45	0.79879	.	0.297443	0.39544	N	0.001321	T	0.36138	0.0956	N	0.12182	0.205	0.42004	D	0.990908	B	0.21147	0.052	B	0.08055	0.003	T	0.21586	-1.0241	8	.	.	.	-28.0768	11.8067	0.52158	0.0:0.9211:0.0:0.0789	.	251	Q7L4P6	BEND5_HUMAN	T	251	.	.	A	-	1	0	BEND5	48981025	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.067000	0.57527	2.838000	0.97847	0.591000	0.81541	GCC	.	.	none		0.443	BEND5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022323.1	NM_024603		T	49208438	C	T	49208438	3	4	18	1	0	0	0	0	1	0	0	0	1401	768	27	1	526	1	BEND5	1	49208438	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	3867081	49208438	200042183	7	2394											
FAF1	11124	hgsc.bcm.edu	37	chr1	51121170	51121170	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taattggtggcgaacggggaTacttgtaaggtcatacacat	12	11	12	6	2	1	0	1	0	0	0	1	2	1	1	0	5	3	1	0	5	5	6			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr1:51121170T>A	ENST00000396153.2	-	8	1139	c.688A>T	c.(688-690)Atc>Ttc	p.I230F	FAF1_ENST00000371778.4_Missense_Mutation_p.I230F	NM_007051.2	NP_008982.1	Q9UNN5	FAF1_HUMAN	Fas (TNFRSF6) associated factor 1	230					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)	p.0?(1)		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)		CGAACGGGGATACTTGTAAGG	0.368																																					p.I230F		Atlas-SNP	.											.	FAF1	64	.	1	Whole gene deletion(1)	thyroid(1)	c.A688T						PASS	.						125	118	121					1																	51121170		2203	4300	6503	SO:0001583	missense	11124	exon8			CGGGGATACTTGT	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.688A>T	1.37:g.51121170T>A	ENSP00000379457:p.Ile230Phe	90	0	0		83	20	0.240964	NM_007051	Q549F0|Q9UF34|Q9UNT3|Q9Y2Z3	Missense_Mutation	SNP	ENST00000396153.2	37	CCDS554.1	.	.	.	.	.	.	.	.	.	.	T	28.2	4.901931	0.92035	.	.	ENSG00000185104	ENST00000396153;ENST00000371778	T;T	0.33216	1.42;1.42	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.58061	0.2096	M	0.75085	2.285	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.61103	-0.7130	10	0.87932	D	0	-11.8054	16.8222	0.85835	0.0:0.0:0.0:1.0	.	230	Q9UNN5	FAF1_HUMAN	F	230	ENSP00000379457:I230F;ENSP00000360843:I230F	ENSP00000360843:I230F	I	-	1	0	FAF1	50893758	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	6.615000	0.74201	2.371000	0.80710	0.533000	0.62120	ATC	.	.	none		0.368	FAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021807.1	NM_007051		A	51121170	T	A	51121170	3	1	18	1	0	0	0	0	1	0	0	0	5374	1406	49	5	1312	5	FAF1	1	51121170	Missense_Mutation	SNP	T	TCGA-FF-A7CR-01A-11D-A382-10	1912732	51121170	198129451	8	2395											
ATG4C	84938	hgsc.bcm.edu	37	chr1	63282305	63282305	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tagaggatcacgtaattgcaGgaaatgtagaagaatttcgt	15	11	11	4	2	1	3	1	0	0	3	2	5	1	5	0	2	1	3	0	2	6	5			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr1:63282305G>A	ENST00000317868.4	+	4	427	c.220G>A	c.(220-222)Gga>Aga	p.G74R	ATG4C_ENST00000371120.3_Missense_Mutation_p.G74R	NM_032852.3	NP_116241.2	Q96DT6	ATG4C_HUMAN	autophagy related 4C, cysteine peptidase	74					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						CGTAATTGCAGGAAATGTAGA	0.373																																					p.G74R		Atlas-SNP	.											ATG4C_ENST00000317868,NS,carcinoma,-1,4	ATG4C	96	4	0			c.G220A						PASS	.						74	73	74					1																	63282305		2203	4300	6503	SO:0001583	missense	84938	exon4			ATTGCAGGAAATG	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.220G>A	1.37:g.63282305G>A	ENSP00000322159:p.Gly74Arg	126	0	0		142	33	0.232394	NM_178221	A6NLR8|D3DQ58|Q96K04	Missense_Mutation	SNP	ENST00000317868.4	37	CCDS623.1	.	.	.	.	.	.	.	.	.	.	G	16.55	3.155852	0.57259	.	.	ENSG00000125703	ENST00000317868;ENST00000371120;ENST00000443289;ENST00000540025;ENST00000371118	T;T;T;T	0.44083	0.93;0.93;0.93;0.93	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.31638	0.0803	M	0.69248	2.105	0.80722	D	1	B	0.24092	0.097	B	0.30105	0.111	T	0.15983	-1.0418	10	0.42905	T	0.14	-25.7434	13.6326	0.62204	0.0745:0.0:0.9255:0.0	.	74	Q96DT6	ATG4C_HUMAN	R	74	ENSP00000322159:G74R;ENSP00000360161:G74R;ENSP00000396614:G74R;ENSP00000360159:G74R	ENSP00000322159:G74R	G	+	1	0	ATG4C	63054893	1.000000	0.71417	0.989000	0.46669	0.904000	0.53231	7.605000	0.82844	2.631000	0.89168	0.655000	0.94253	GGA	.	.	none		0.373	ATG4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025332.2	NM_032852		A	63282305	G	A	63282305	3	1	18	1	0	0	0	0	1	0	0	0	1098	1001	35	2	230	2	ATG4C	1	63282305	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	12161135	63282305	185968316	9	2396											
NEGR1	257194	hgsc.bcm.edu	37	chr1	72400774	72400774	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atacataccttgcacagttaGatgcacctgcattgttctgg	10	13	8	10	0	1	1	0	0	1	1	1	1	1	1	2	1	5	5	2	1	3	6			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr1:72400774G>T	ENST00000357731.5	-	2	636	c.397C>A	c.(397-399)Cta>Ata	p.L133I	NEGR1_ENST00000306821.3_Missense_Mutation_p.L5I|NEGR1_ENST00000434200.1_Missense_Mutation_p.L131I|NEGR1_ENST00000467479.1_5'UTR	NM_173808.2	NP_776169.2	Q7Z3B1	NEGR1_HUMAN	neuronal growth regulator 1	133	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)		TGCACAGTTAGATGCACCTGC	0.388																																					p.L133I		Atlas-SNP	.											.	NEGR1	60	.	0			c.C397A						PASS	.						100	90	94					1																	72400774		2203	4300	6503	SO:0001583	missense	257194	exon2			CAGTTAGATGCAC	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.397C>A	1.37:g.72400774G>T	ENSP00000350364:p.Leu133Ile	134	0	0		167	33	0.197605	NM_173808	Q5VT21|Q6UY06|Q8N440|Q8NAQ3	Missense_Mutation	SNP	ENST00000357731.5	37	CCDS661.1	.	.	.	.	.	.	.	.	.	.	G	17.55	3.418704	0.62622	.	.	ENSG00000172260	ENST00000357731;ENST00000306821;ENST00000434200	T;T;T	0.57436	0.4;1.15;0.4	5.71	3.71	0.42584	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	T	0.59432	0.2193	M	0.73753	2.245	0.52099	D	0.999944	D;D	0.69078	0.995;0.997	D;D	0.67382	0.951;0.951	T	0.64462	-0.6402	10	0.59425	D	0.04	-6.5201	10.2474	0.43350	0.2176:0.0:0.7824:0.0	.	131;133	B4DI94;Q7Z3B1	.;NEGR1_HUMAN	I	133;5;131	ENSP00000350364:L133I;ENSP00000305938:L5I;ENSP00000413294:L131I	ENSP00000305938:L5I	L	-	1	2	NEGR1	72173362	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	1.024000	0.30077	1.349000	0.45751	0.655000	0.94253	CTA	.	.	none		0.388	NEGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026722.4	NM_173808		T	72400774	G	T	72400774	3	4	18	1	0	0	0	0	1	0	0	0	10326	933	33	4	691	4	NEGR1	1	72400774	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	9118469	72400774	176849847	10	2397											
LPPR5	163404	hgsc.bcm.edu	37	chr1	99470000	99470000	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccgggcttaccacgagcacGgggaccccggcggccagcga	7	2	15	17	6	0	0	0	0	0	0	0	3	0	1	5	5	3	2	5	5	1	1	rs148163708	byFrequency	TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr1:99470000G>A	ENST00000263177.4	-	1	449	c.228C>T	c.(226-228)ccC>ccT	p.P76P	LPPR5_ENST00000534652.1_5'UTR|LPPR5_ENST00000370188.3_Silent_p.P76P|RP5-896L10.1_ENST00000425113.1_RNA	NM_001037317.1	NP_001032394.1	Q32ZL2	LPPR5_HUMAN		76						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)										CCACGAGCACGGGGACCCCGG	0.721																																					p.P76P		Atlas-SNP	.											.	.	.	.	0			c.C228T						PASS	.						12	14	14					1																	99470000		2197	4283	6480	SO:0001819	synonymous_variant	0	exon1			GAGCACGGGGACC																												ENST00000263177.4:c.228C>T	1.37:g.99470000G>A		67	0	0		66	17	0.257576	NM_001037317	A8MPX4|B7UCH3|Q32ZD0|Q3ZCU7	Silent	SNP	ENST00000263177.4	37	CCDS30778.1																																																																																			G|1.000;T|0.000	.	alt		0.721	LPPR5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393221.1			A	99470000	G	A	99470000	2	1	18	1	0	0	0	0	0	0	0	1	8937	1103	39	1		1	LPPR5	1	99470000	Silent	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	27069226	99470000	149780621	11	2398											
AHCYL1	10768	hgsc.bcm.edu	37	chr1	110561015	110561015	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaataagaatgtagtgacaCgggagcacttggatcgcatg	14	8	13	6	2	0	2	0	1	0	1	1	5	0	4	0	2	1	3	0	2	4	3			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr1:110561015C>T	ENST00000369799.5	+	12	1511	c.1144C>T	c.(1144-1146)Cgg>Tgg	p.R382W	AHCYL1_ENST00000393614.4_Missense_Mutation_p.R335W|AHCYL1_ENST00000359172.3_Missense_Mutation_p.R335W	NM_001242673.1|NM_001242674.1|NM_006621.5	NP_001229602.1|NP_001229603.1|NP_006612.2	O43865	SAHH2_HUMAN	adenosylhomocysteinase-like 1	382	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)		TGTAGTGACACGGGAGCACTT	0.443																																					p.R382W		Atlas-SNP	.											.	AHCYL1	49	.	0			c.C1144T						PASS	.						87	75	79					1																	110561015		2203	4300	6503	SO:0001583	missense	10768	exon12			GTGACACGGGAGC	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.1144C>T	1.37:g.110561015C>T	ENSP00000358814:p.Arg382Trp	129	0	0		139	32	0.230216	NM_006621	B4E168|Q2TAJ6|Q502W8|Q5VSM0|Q6P171|Q96PK4|Q9UG84	Missense_Mutation	SNP	ENST00000369799.5	37	CCDS818.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.070240	0.76301	.	.	ENSG00000168710	ENST00000369799;ENST00000359172;ENST00000393614	T;T;T	0.78126	-1.15;-1.13;-1.13	5.62	4.69	0.59074	S-adenosyl-L-homocysteine hydrolase, NAD binding (1);	0.000000	0.85682	D	0.000000	D	0.87958	0.6309	M	0.93328	3.405	0.80722	D	1	D	0.65815	0.995	D	0.67900	0.954	D	0.90425	0.4420	10	0.56958	D	0.05	-15.4423	13.7117	0.62672	0.3369:0.6631:0.0:0.0	.	382	O43865	SAHH2_HUMAN	W	382;335;335	ENSP00000358814:R382W;ENSP00000352092:R335W;ENSP00000377238:R335W	ENSP00000352092:R335W	R	+	1	2	AHCYL1	110362538	0.997000	0.39634	0.982000	0.44146	0.998000	0.95712	3.533000	0.53561	1.328000	0.45358	0.655000	0.94253	CGG	.	.	none		0.443	AHCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032243.1			T	110561015	C	T	110561015	3	4	18	1	0	0	0	0	1	0	0	0	410	527	19	1	1190	1	AHCYL1	1	110561015	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	11091015	110561015	138689606	12	2399											
HIST2H2AC	8338	hgsc.bcm.edu	37	chr1	149858804	149858804	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccatccgcaacgacgaggaaCtgaacaagctgctgggcaaa	14	4	11	12	3	0	1	0	1	0	0	1	4	1	2	2	2	5	4	2	2	5	0			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr1:149858804C>G	ENST00000331380.2	+	1	280	c.280C>G	c.(280-282)Ctg>Gtg	p.L94V	HIST2H2BE_ENST00000369155.2_5'Flank|BOLA1_ENST00000369153.2_5'Flank	NM_003517.2	NP_003508.1	Q16777	H2A2C_HUMAN	histone cluster 2, H2ac	94						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)			CGACGAGGAACTGAACAAGCT	0.592																																					p.L94V		Atlas-SNP	.											HIST2H2AC,NS,carcinoma,-2,3	HIST2H2AC	75	3	0			c.C280G						PASS	.						70	71	70					1																	149858804		2203	4298	6501	SO:0001583	missense	8338	exon1			GAGGAACTGAACA	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.280C>G	1.37:g.149858804C>G	ENSP00000332194:p.Leu94Val	219	0	0		272	68	0.25	NM_003517	Q6DRA7|Q8IUE5	Missense_Mutation	SNP	ENST00000331380.2	37	CCDS937.1	.	.	.	.	.	.	.	.	.	.	C	7.491	0.650732	0.14516	.	.	ENSG00000184260	ENST00000331380	T	0.52983	0.64	5.67	3.82	0.43975	Histone-fold (2);Histone H2A (1);	0.000000	0.38778	N	0.001568	T	0.68997	0.3062	H	0.95917	3.74	0.33693	D	0.613536	D	0.71674	0.998	D	0.80764	0.994	T	0.78391	-0.2222	10	0.87932	D	0	.	11.0346	0.47793	0.0:0.8491:0.0:0.1509	.	94	Q16777	H2A2C_HUMAN	V	94	ENSP00000332194:L94V	ENSP00000332194:L94V	L	+	1	2	HIST2H2AC	148125428	1.000000	0.71417	0.199000	0.23439	0.005000	0.04900	5.888000	0.69758	0.771000	0.33359	-0.136000	0.14681	CTG	.	.	none		0.592	HIST2H2AC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087128.1	NM_003517		G	149858804	C	G	149858804	3	3	18	1	0	0	0	0	1	0	0	0	7187	564	20	4	282	4	HIST2H2AC	1	149858804	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	39297789	149858804	99391817	13	2400											
HRNR	388697	hgsc.bcm.edu	37	chr1	152187485	152187485	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atgggccacggctggaagaaCgacctgagccagacccatgt	11	5	13	12	2	0	3	0	1	0	2	0	5	0	4	4	3	2	1	4	3	2	0	rs571489109	byFrequency	TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr1:152187485C>T	ENST00000368801.2	-	3	6695	c.6620G>A	c.(6619-6621)cGt>cAt	p.R2207H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2207					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)			GCTGGAAGAACGACCTGAGCC	0.597													c|||	3	0.000599042	0.0008	0.0014	5008	,	,		38924	0.0		0.0	False		,,,				2504	0.001				p.R2207H		Atlas-SNP	.											HRNR,trunk,malignant_melanoma,-1,1	HRNR	403	1	0			c.G6620A						scavenged	.						24	37	32					1																	152187485		2153	4277	6430	SO:0001583	missense	388697	exon3			GAAGAACGACCTG	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.6620G>A	1.37:g.152187485C>T	ENSP00000357791:p.Arg2207His	261	0	0		272	16	0.0588235	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	-	7.903	0.734868	0.15574	.	.	ENSG00000197915	ENST00000368801	T	0.17854	2.25	3.18	-2.56	0.06268	.	.	.	.	.	T	0.03178	0.0093	L	0.29908	0.895	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.44159	-0.9346	9	0.45353	T	0.12	.	4.6072	0.12383	0.0:0.3414:0.1691:0.4895	.	2207	Q86YZ3	HORN_HUMAN	H	2207	ENSP00000357791:R2207H	ENSP00000357791:R2207H	R	-	2	0	HRNR	150454109	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.838000	0.04372	-0.349000	0.08274	-0.506000	0.04501	CGT	.	.	none		0.597	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		T	152187485	C	T	152187485	3	4	18	1	0	0	0	0	1	0	0	0	7368	536	19	1	1936	1	HRNR	1	152187485	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	2328681	152187485	97063136	14	2401											
CACNA1E	777	hgsc.bcm.edu	37	chr1	181689418	181689418	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatcagtttgcttttcctcCtcttcctcttcatcgttgtc	3	20	4	14	1	5	0	3	0	2	0	10	0	8	0	3	0	1	3	3	0	0	6			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr1:181689418C>T	ENST00000367573.2	+	14	1828	c.1828C>T	c.(1828-1830)Ctc>Ttc	p.L610F	CACNA1E_ENST00000357570.5_Missense_Mutation_p.L561F|CACNA1E_ENST00000360108.3_Missense_Mutation_p.L610F|CACNA1E_ENST00000358338.5_Missense_Mutation_p.L561F|CACNA1E_ENST00000367570.1_Missense_Mutation_p.L610F|CACNA1E_ENST00000526775.1_Missense_Mutation_p.L610F|CACNA1E_ENST00000367567.4_Missense_Mutation_p.L217F	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	610					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						GCTTTTCCTCCTCTTCCTCTT	0.463																																					p.L610F		Atlas-SNP	.											.	CACNA1E	778	.	0			c.C1828T						PASS	.						230	205	213					1																	181689418		1997	4164	6161	SO:0001583	missense	777	exon14			TTCCTCCTCTTCC	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.1828C>T	1.37:g.181689418C>T	ENSP00000356545:p.Leu610Phe	293	0	0		262	38	0.145038	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Missense_Mutation	SNP	ENST00000367573.2	37	CCDS55664.1	.	.	.	.	.	.	.	.	.	.	C	32	5.182207	0.94885	.	.	ENSG00000198216	ENST00000367570;ENST00000526775;ENST00000357570;ENST00000358338;ENST00000367567;ENST00000360108;ENST00000367573	D;D;D;D;D;D;D	0.98732	-5.1;-5.1;-5.1;-5.1;-5.1;-5.1;-5.1	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	D	0.99263	0.9743	M	0.88105	2.93	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.996	D	0.99285	1.0897	10	0.87932	D	0	.	18.2263	0.89918	0.0:1.0:0.0:0.0	.	610;610	Q15878-2;Q15878-3	.;.	F	610;610;561;561;217;610;610	ENSP00000356542:L610F;ENSP00000434814:L610F;ENSP00000350183:L561F;ENSP00000351101:L561F;ENSP00000356539:L217F;ENSP00000353222:L610F;ENSP00000356545:L610F	ENSP00000350183:L561F	L	+	1	0	CACNA1E	179956041	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.711000	0.84669	2.391000	0.81399	0.563000	0.77884	CTC	.	.	none		0.463	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		T	181689418	C	T	181689418	3	4	18	1	0	0	0	0	1	0	0	0	2544	681	24	2	1882	2	CACNA1E	1	181689418	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	29501933	181689418	67561203	15	2402											
BTG2	7832	hgsc.bcm.edu	37	chr1	203274867	203274867	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tcagcggggcgctccaggagGcactcacaggtgagcgcatg	8	5	16	12	3	2	1	2	1	0	0	3	2	3	2	1	5	2	3	1	5	0	0			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr1:203274867G>C	ENST00000290551.4	+	1	204	c.133G>C	c.(133-135)Gca>Cca	p.A45P	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	45					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.A45T(1)		haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			GCTCCAGGAGGCACTCACAGG	0.706																																					p.A45P		Atlas-SNP	.											BTG2,lymph_node,lymphoid_neoplasm,-1,2	BTG2	16	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G133C						PASS	.						11	13	13					1																	203274867		2020	3950	5970	SO:0001583	missense	7832	exon1			CAGGAGGCACTCA		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.133G>C	1.37:g.203274867G>C	ENSP00000290551:p.Ala45Pro	56	0	0		86	15	0.174419	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.163593	0.78226	.	.	ENSG00000159388	ENST00000290551	T	0.25085	1.82	4.4	4.4	0.53042	Anti-proliferative protein (3);	0.078518	0.49916	D	0.000121	T	0.52008	0.1708	M	0.82630	2.6	0.47374	D	0.999406	D	0.62365	0.991	D	0.64687	0.928	T	0.58222	-0.7674	10	0.51188	T	0.08	-33.413	15.7078	0.77598	0.0:0.0:1.0:0.0	.	45	P78543	BTG2_HUMAN	P	45	ENSP00000290551:A45P	ENSP00000290551:A45P	A	+	1	0	BTG2	201541490	1.000000	0.71417	0.991000	0.47740	0.943000	0.58893	4.326000	0.59241	2.282000	0.76494	0.471000	0.43371	GCA	.	.	none		0.706	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		C	203274867	G	C	203274867	3	2	18	1	0	0	0	0	1	0	0	0	1556	1203	42	4	135	4	BTG2	1	203274867	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	21585449	203274867	45975754	16	2403			1	21		3	3	1421	N	T_G_C	3.387568e-05
BTG2	7832	hgsc.bcm.edu	37	chr1	203274878	203274878	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccaggaggcactcacaggTgagcgcatgccgaggggcct	8	5	15	13	2	1	1	1	1	0	0	2	3	2	2	3	5	2	2	3	5	0	0			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr1:203274878T>C	ENST00000290551.4	+	1	213		c.e1+2		RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2						anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			CACTCACAGGTGAGCGCATGC	0.706																																					.		Atlas-SNP	.											.	BTG2	16	.	0			c.142+2T>C						PASS	.						10	12	12					1																	203274878		1987	3852	5839	SO:0001630	splice_region_variant	7832	exon1			CACAGGTGAGCGC		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.142+2T>C	1.37:g.203274878T>C		51	0	0		79	14	0.177215	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Splice_Site	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	T	16.34	3.094946	0.56075	.	.	ENSG00000159388	ENST00000290551	.	.	.	4.23	4.23	0.50019	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2923	0.54825	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	BTG2	201541501	1.000000	0.71417	1.000000	0.80357	0.498000	0.33706	6.849000	0.75414	1.785000	0.52413	0.386000	0.25728	.	.	.	none		0.706	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763	Intron	C	203274878	T	C	203274878	5	2	18	1	0	0	0	0	0	0	1	0	1556	1710	59	3	146	3	BTG2	1	203274878	Splice_Site	SNP	T	TCGA-FF-A7CR-01A-11D-A382-10	11	203274878	45975743	17	2404			1	21		3	3	1421	N	T_G_C	3.387568e-05
BTG2	7832	hgsc.bcm.edu	37	chr1	203276287	203276287	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaagggctccggctaccgCtgcattcgcatcaaccacaa	10	7	8	16	3	1	0	1	0	0	0	4	0	3	0	4	2	3	5	4	2	4	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr1:203276287C>G	ENST00000290551.4	+	2	269	c.198C>G	c.(196-198)cgC>cgG	p.R66R	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	66					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			CCGGCTACCGCTGCATTCGCA	0.612																																					p.R66R		Atlas-SNP	.											BTG2,NS,carcinoma,+2,1	BTG2	16	1	0			c.C198G						PASS	.						46	48	47					1																	203276287		2203	4300	6503	SO:0001819	synonymous_variant	7832	exon2			CTACCGCTGCATT		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.198C>G	1.37:g.203276287C>G		58	0	0		66	14	0.212121	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Silent	SNP	ENST00000290551.4	37	CCDS1437.1																																																																																			.	.	none		0.612	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		G	203276287	C	G	203276287	2	3	18	1	0	0	0	0	0	0	0	1	1556	784	28	4		4	BTG2	1	203276287	Silent	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	1409	203276287	45974334	18	2405			1	21		3	3	1421	N	T_G_C	3.387568e-05
MAPKAPK2	9261	hgsc.bcm.edu	37	chr1	206858801	206858801	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cctggggctgggcatcaacgGcaaagttttgcagatcttca	9	10	12	10	1	3	1	2	0	1	1	3	1	3	1	1	4	2	5	1	4	2	3			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr1:206858801G>A	ENST00000367103.3	+	1	420	c.227G>A	c.(226-228)gGc>gAc	p.G76D	MAPKAPK2_ENST00000294981.4_Missense_Mutation_p.G76D	NM_004759.4|NM_032960.3	NP_004750.1|NP_116584.2	P49137	MAPK2_HUMAN	mitogen-activated protein kinase-activated protein kinase 2	76	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|activation of MAPK activity (GO:0000187)|arachidonic acid metabolic process (GO:0019369)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|G2 DNA damage checkpoint (GO:0031572)|gene expression (GO:0010467)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|leukotriene metabolic process (GO:0006691)|macropinocytosis (GO:0044351)|MAPK cascade (GO:0000165)|mRNA metabolic process (GO:0016071)|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)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of interleukin-6 production (GO:0032675)|regulation of tumor necrosis factor production (GO:0032680)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)|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)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	19	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.211)			GGCATCAACGGCAAAGTTTTG	0.607																																					p.G76D		Atlas-SNP	.											.	MAPKAPK2	45	.	0			c.G227A						PASS	.						46	48	47					1																	206858801		2203	4300	6503	SO:0001583	missense	9261	exon1			TCAACGGCAAAGT	U12779	CCDS1466.1, CCDS31001.1	1q32	2008-02-05			ENSG00000162889	ENSG00000162889			6887	protein-coding gene	gene with protein product		602006				8179591, 8280084	Standard	NM_004759		Approved		uc001hem.2	P49137	OTTHUMG00000036342	ENST00000367103.3:c.227G>A	1.37:g.206858801G>A	ENSP00000356070:p.Gly76Asp	50	0	0		78	18	0.230769	NM_004759	Q5SY30|Q5SY41|Q8IYD6	Missense_Mutation	SNP	ENST00000367103.3	37	CCDS31001.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.252052	0.80135	.	.	ENSG00000162889	ENST00000294981;ENST00000367103	T;T	0.80738	-1.41;-1.41	3.52	3.52	0.40303	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.92136	0.7507	H	0.95850	3.73	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93986	0.7262	9	0.87932	D	0	-15.4357	12.5833	0.56403	0.0:0.0:1.0:0.0	.	76;76	P49137;P49137-2	MAPK2_HUMAN;.	D	76	ENSP00000294981:G76D;ENSP00000356070:G76D	ENSP00000294981:G76D	G	+	2	0	MAPKAPK2	204925424	1.000000	0.71417	0.999000	0.59377	0.740000	0.42216	8.642000	0.91036	1.789000	0.52484	0.195000	0.17529	GGC	.	.	none		0.607	MAPKAPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088465.1	NM_004759		A	206858801	G	A	206858801	3	1	18	1	0	0	0	0	1	0	0	0	9298	1203	42	2	229	2	MAPKAPK2	1	206858801	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	3582514	206858801	42391820	19	2406											
AIDA	64853	hgsc.bcm.edu	37	chr1	222885628	222885628	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcctaaaactggcgccccagCgctgcagcagactccgggtc	8	6	11	16	3	0	1	0	0	0	1	3	1	2	1	4	2	4	3	4	2	2	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr1:222885628C>T	ENST00000340020.6	-	1	238	c.32G>A	c.(31-33)cGc>cAc	p.R11H	AIDA_ENST00000355727.2_Missense_Mutation_p.R11H|BROX_ENST00000537020.1_5'Flank|AIDA_ENST00000541237.1_Intron|BROX_ENST00000340934.5_5'Flank|AIDA_ENST00000474863.1_5'UTR|BROX_ENST00000539697.1_5'Flank	NM_022831.2	NP_073742.2	Q96BJ3	AIDA_HUMAN	axin interactor, dorsalization associated	11					dorsal/ventral pattern formation (GO:0009953)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|regulation of protein homodimerization activity (GO:0043496)	cytoplasm (GO:0005737)				kidney(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	10						GGCGCCCCAGCGCTGCAGCAG	0.672																																					p.R11H		Atlas-SNP	.											.	AIDA	23	.	0			c.G32A						PASS	.						14	13	14					1																	222885628		2197	4265	6462	SO:0001583	missense	64853	exon1			CCCCAGCGCTGCA	BC043142	CCDS1533.1	1q41	2008-05-22	2008-05-22	2008-05-22	ENSG00000186063	ENSG00000186063			25761	protein-coding gene	gene with protein product	"axin interaction partner and dorsalization antagonist"	612375	"chromosome 1 open reading frame 80"	C1orf80		8619474, 9110174, 17681137	Standard	NM_022831		Approved	FLJ12806	uc001hnn.3	Q96BJ3	OTTHUMG00000037653	ENST00000340020.6:c.32G>A	1.37:g.222885628C>T	ENSP00000339161:p.Arg11His	168	0	0		175	35	0.2	NM_022831	A8K1F0|Q49A81|Q5JRA4|Q658P1|Q9H9E8	Missense_Mutation	SNP	ENST00000340020.6	37	CCDS1533.1	.	.	.	.	.	.	.	.	.	.	C	17.38	3.375314	0.61735	.	.	ENSG00000186063	ENST00000340020;ENST00000355727	.	.	.	5.19	5.19	0.71726	Axin interactor, dorsalization-associated protein, N-terminal (2);	0.063428	0.64402	D	0.000002	T	0.52725	0.1752	L	0.29908	0.895	0.80722	D	1	B	0.31077	0.307	B	0.41666	0.363	T	0.56583	-0.7955	9	0.59425	D	0.04	.	11.8464	0.52387	0.0:0.9189:0.0:0.0811	.	11	Q96BJ3	AIDA_HUMAN	H	11	.	ENSP00000339161:R11H	R	-	2	0	AIDA	220952251	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.068000	0.41471	2.435000	0.82474	0.549000	0.68633	CGC	.	.	none		0.672	AIDA-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091818.1	NM_022831		T	222885628	C	T	222885628	3	4	18	1	0	0	0	0	1	0	0	0	423	768	27	1	928	1	AIDA	1	222885628	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	16026827	222885628	26364993	20	2407											
C1orf65	164127	hgsc.bcm.edu	37	chr1	223567173	223567173	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gacaggaaccaagccccgccCggcttggcagccgcagaccc	9	2	12	18	3	0	1	0	0	0	1	0	3	0	2	6	3	3	3	6	3	2	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr1:223567173C>T	ENST00000366875.3	+	1	459	c.356C>T	c.(355-357)cCg>cTg	p.P119L		NM_152610.2	NP_689823.2	Q8N715	CC185_HUMAN		119	Pro-rich.									breast(4)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|skin(3)	29				GBM - Glioblastoma multiforme(131;0.0704)		AAGCCCCGCCCGGCTTGGCAG	0.726																																					p.P119L		Atlas-SNP	.											.	C1orf65	71	.	0			c.C356T						PASS	.						4	6	6					1																	223567173		1859	3868	5727	SO:0001583	missense	164127	exon1			CCCGCCCGGCTTG																												ENST00000366875.3:c.356C>T	1.37:g.223567173C>T	ENSP00000355840:p.Pro119Leu	29	0	0		30	6	0.2	NM_152610	Q8N746|Q8NA93	Missense_Mutation	SNP	ENST00000366875.3	37	CCDS1537.1	.	.	.	.	.	.	.	.	.	.	C	10.55	1.382072	0.24944	.	.	ENSG00000178395	ENST00000366875	T	0.17854	2.25	4.48	-4.17	0.03857	.	.	.	.	.	T	0.07728	0.0194	N	0.24115	0.695	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.36065	-0.9763	9	0.33141	T	0.24	.	0.34	0.00332	0.279:0.29:0.1491:0.2819	.	119	Q8N715	CA065_HUMAN	L	119	ENSP00000355840:P119L	ENSP00000355840:P119L	P	+	2	0	C1orf65	221633796	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.205000	0.01232	-0.870000	0.04047	-0.230000	0.12252	CCG	.	.	none		0.726	C1orf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092718.1			T	223567173	C	T	223567173	3	4	18	1	0	0	0	0	1	0	0	0	2057	652	23	1	358	1	C1orf65	1	223567173	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	681545	223567173	25683448	21	2408											
TTC13	79573	hgsc.bcm.edu	37	chr1	231093993	231093993	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actcttcatttgtgctgtcaTtatcagtggcaaacgggaat	10	14	9	8	1	4	0	3	0	1	0	4	1	4	1	0	2	2	2	0	2	3	3			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr1:231093993T>C	ENST00000366661.4	-	3	426	c.419A>G	c.(418-420)aAt>aGt	p.N140S	TTC13_ENST00000414259.1_Missense_Mutation_p.N140S|TTC13_ENST00000366662.4_Missense_Mutation_p.N140S	NM_024525.4	NP_078801.3	Q8NBP0	TTC13_HUMAN	tetratricopeptide repeat domain 13	140										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)		TGTGCTGTCATTATCAGTGGC	0.373																																					p.N140S		Atlas-SNP	.											.	TTC13	74	.	0			c.A419G						PASS	.						132	123	126					1																	231093993		2203	4300	6503	SO:0001583	missense	79573	exon3			CTGTCATTATCAG		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.419A>G	1.37:g.231093993T>C	ENSP00000355621:p.Asn140Ser	167	0	0		168	27	0.160714	NM_001122835	B1AQI1|B1AQI2|Q8IVP8|Q8NBI0|Q8ND20	Missense_Mutation	SNP	ENST00000366661.4	37	CCDS1588.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.57|13.57	2.276579|2.276579	0.40294|0.40294	.|.	.|.	ENSG00000143643|ENSG00000143643	ENST00000522821|ENST00000366661;ENST00000366662;ENST00000414259	.|T;T;T	.|0.53206	.|0.85;0.65;0.63	5.95|5.95	5.95|5.95	0.96441|0.96441	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.29556|0.29556	0.0737|0.0737	N|N	0.19112|0.19112	0.55|0.55	0.49389|0.49389	D|D	0.99978|0.99978	.|P;P;P	.|0.46395	.|0.877;0.739;0.495	.|B;B;B	.|0.36464	.|0.192;0.225;0.084	T|T	0.12863|0.12863	-1.0531|-1.0531	5|10	.|0.11182	.|T	.|0.66	-0.015|-0.015	15.4063|15.4063	0.74881|0.74881	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|140;140;140	.|E9PGV4;Q8NBP0-2;Q8NBP0	.|.;.;TTC13_HUMAN	V|S	129|140	.|ENSP00000355621:N140S;ENSP00000355622:N140S;ENSP00000416631:N140S	.|ENSP00000355621:N140S	M|N	-|-	1|2	0|0	TTC13|TTC13	229160616|229160616	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	5.206000|5.206000	0.65192|0.65192	2.279000|2.279000	0.76181|0.76181	0.533000|0.533000	0.62120|0.62120	ATG|AAT	.	.	none		0.373	TTC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092229.2	NM_024525		C	231093993	T	C	231093993	3	2	18	1	0	0	0	0	1	0	0	0	16695	1493	52	3	2247	3	TTC13	1	231093993	Missense_Mutation	SNP	T	TCGA-FF-A7CR-01A-11D-A382-10	7526820	231093993	18156628	22	2409											
CHRM3	1131	hgsc.bcm.edu	37	chr1	240072488	240072488	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taccagcagagacagtcggtCatttttcacaagcgcgcacc	11	8	9	13	3	2	1	2	0	0	1	3	2	2	1	2	1	3	2	2	1	2	3			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr1:240072488C>A	ENST00000255380.4	+	5	2516	c.1737C>A	c.(1735-1737)gtC>gtA	p.V579V		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	579					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)	GACAGTCGGTCATTTTTCACA	0.488																																					p.V579V		Atlas-SNP	.											.	CHRM3	118	.	0			c.C1737A						PASS	.						43	44	44					1																	240072488		2203	4300	6503	SO:0001819	synonymous_variant	1131	exon5			GTCGGTCATTTTT	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.1737C>A	1.37:g.240072488C>A		106	0	0		120	29	0.241667	NM_000740	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Silent	SNP	ENST00000255380.4	37	CCDS1616.1																																																																																			.	.	none		0.488	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740		A	240072488	C	A	240072488	2	1	18	1	0	0	0	0	0	0	0	1	3380	813	29	4		4	CHRM3	1	240072488	Silent	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	8978495	240072488	9178133	23	2410											
SLC8A1	6546	hgsc.bcm.edu	37	chr2	40655834	40655834	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggtcatcatcaaaaatagtTacagtggcagtggagggaga	14	9	13	5	0	3	1	3	0	0	1	3	3	3	2	0	4	1	2	0	4	4	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr2:40655834T>C	ENST00000403092.1	-	2	1620	c.1587A>G	c.(1585-1587)gtA>gtG	p.V529V	SLC8A1_ENST00000405901.3_Silent_p.V529V|SLC8A1_ENST00000406391.2_Silent_p.V529V|SLC8A1_ENST00000542756.1_Silent_p.V529V|SLC8A1_ENST00000402441.1_Silent_p.V529V|SLC8A1_ENST00000542024.1_Silent_p.V529V|SLC8A1_ENST00000405269.1_Silent_p.V529V|SLC8A1_ENST00000406785.2_Silent_p.V529V|SLC8A1_ENST00000408028.2_Silent_p.V529V|SLC8A1_ENST00000332839.4_Silent_p.V529V			P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 1	529	Calx-beta 2.				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)	CAAAAATAGTTACAGTGGCAG	0.438																																					p.V529V		Atlas-SNP	.											.	SLC8A1	221	.	0			c.A1587G						PASS	.						111	110	111					2																	40655834		2203	4300	6503	SO:0001819	synonymous_variant	6546	exon1			AATAGTTACAGTG		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.1587A>G	2.37:g.40655834T>C		168	0	0		152	37	0.243421	NM_001252624	A8K6N1|D6W595|O95849|Q4QQG6|Q587I6|Q59GN4|Q9UBL8|Q9UD55|Q9UDN1|Q9UDN2|Q9UKX6	Silent	SNP	ENST00000403092.1	37	CCDS1806.1																																																																																			.	.	none		0.438	SLC8A1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326065.1	NM_021097		C	40655834	T	C	40655834	2	2	18	1	0	0	0	0	0	0	0	1	14721	1741	61	3		3	SLC8A1	2	40655834	Silent	SNP	T	TCGA-FF-A7CR-01A-11D-A382-10		40655834	202543539	24	2411											
BCL11A	53335	hgsc.bcm.edu	37	chr2	60689133	60689133	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgggaggctccatagccattGgattcaaccgcagcaccctg	9	7	11	14	2	1	0	1	0	0	0	2	2	2	2	4	3	3	3	4	3	2	3			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr2:60689133G>A	ENST00000335712.6	-	4	1141	c.914C>T	c.(913-915)cCa>cTa	p.P305L	BCL11A_ENST00000477659.1_5'UTR|BCL11A_ENST00000358510.4_Missense_Mutation_p.P271L|BCL11A_ENST00000538214.1_Missense_Mutation_p.P271L|BCL11A_ENST00000537768.1_Intron|BCL11A_ENST00000356842.4_Missense_Mutation_p.P305L|BCL11A_ENST00000359629.5_Intron	NM_022893.3	NP_075044.2	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A (zinc finger protein)	305	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)			CATAGCCATTGGATTCAACCG	0.632			T	IGH@	B-CLL																																p.P305L		Atlas-SNP	.		Dom	yes		2	2p13	53335	B-cell CLL/lymphoma 11A		L	BCL11A_ENST00000356842,caecum,carcinoma,0,5	BCL11A	298	5	0			c.C914T						PASS	.						50	56	54					2																	60689133		2203	4300	6503	SO:0001583	missense	53335	exon4			GCCATTGGATTCA	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.914C>T	2.37:g.60689133G>A	ENSP00000338774:p.Pro305Leu	56	0	0		54	18	0.333333	NM_018014	D6W5D7|Q86W14|Q8WU92|Q96JL6|Q9H163|Q9H164|Q9H3G9|Q9NWA7	Missense_Mutation	SNP	ENST00000335712.6	37	CCDS1862.1	.	.	.	.	.	.	.	.	.	.	G	14.96	2.691230	0.48097	.	.	ENSG00000119866	ENST00000356842;ENST00000378117;ENST00000538214;ENST00000335712;ENST00000358510	T;T;T;T	0.12569	2.87;2.67;2.83;2.68	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.35480	0.0933	L	0.58101	1.795	0.80722	D	1	D;P;P;D	0.67145	0.983;0.728;0.83;0.996	D;B;P;P	0.64410	0.925;0.277;0.49;0.889	T	0.01053	-1.1467	10	0.66056	D	0.02	-0.8491	20.139	0.98050	0.0:0.0:1.0:0.0	.	271;271;305;305	F5H2Y4;Q9H165-6;Q9H165;D9YZV9	.;.;BC11A_HUMAN;.	L	305;341;271;305;271	ENSP00000349300:P305L;ENSP00000438303:P271L;ENSP00000338774:P305L;ENSP00000351307:P271L	ENSP00000338774:P305L	P	-	2	0	BCL11A	60542637	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.764000	0.94973	0.655000	0.94253	CCA	.	.	none		0.632	BCL11A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251579.2	NM_022893		A	60689133	G	A	60689133	3	1	18	1	0	0	0	0	1	0	0	0	1363	1348	47	2	1703	2	BCL11A	2	60689133	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	20033299	60689133	182510240	25	2412											
ETAA1	54465	hgsc.bcm.edu	37	chr2	67630426	67630426	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tttgataaaaatatggaagaGctagatgtgattcaagagca	17	11	10	3	0	1	5	1	2	0	3	1	6	1	6	0	1	2	2	0	1	7	5			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr2:67630426G>A	ENST00000272342.5	+	5	742	c.612G>A	c.(610-612)gaG>gaA	p.E204E	ETAA1_ENST00000462772.1_Intron	NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	204						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						ATATGGAAGAGCTAGATGTGA	0.259																																					p.E204E		Atlas-SNP	.											.	ETAA1	88	.	0			c.G612A						PASS	.						29	36	34					2																	67630426		2180	4273	6453	SO:0001819	synonymous_variant	54465	exon5			GGAAGAGCTAGAT	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.612G>A	2.37:g.67630426G>A		171	0	0		160	34	0.2125	NM_019002	Q05BT7|Q53SC4	Silent	SNP	ENST00000272342.5	37	CCDS1882.1																																																																																			.	.	none		0.259	ETAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251735.1	NM_019002		A	67630426	G	A	67630426	2	1	18	1	0	0	0	0	0	0	0	1	5269	962	34	2		2	ETAA1	2	67630426	Silent	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	6941293	67630426	175568947	26	2413											
SULT1C2	6819	hgsc.bcm.edu	37	chr2	108917339	108917339	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctccacggatactaaagaCtcacctttccactcagctgc	10	10	5	16	1	3	1	2	0	1	1	5	2	4	2	3	1	3	1	3	1	3	3			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr2:108917339C>G	ENST00000437390.2	+	4	542	c.365C>G	c.(364-366)aCt>aGt	p.T122S	SULT1C2_ENST00000251481.6_Missense_Mutation_p.T108S|SULT1C2_ENST00000409880.1_Intron|SULT1C2_ENST00000326853.5_Intron			O75897	ST1C4_HUMAN	sulfotransferase family, cytosolic, 1C, member 2	114					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)			NS(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20						ATACTAAAGACTCACCTTTCC	0.478																																					p.T108S		Atlas-SNP	.											.	SULT1C2	82	.	0			c.C323G						PASS	.						180	200	194					2																	108917339		2203	4300	6503	SO:0001583	missense	6819	exon4			TAAAGACTCACCT	U66036, AF186255	CCDS2075.1, CCDS2076.1	2q12.3	2010-09-30	2007-03-16	2007-03-16	ENSG00000198203	ENSG00000198203		"Sulfotransferases, cytosolic"	11456	protein-coding gene	gene with protein product		602385	"sulfotransferase family, cytosolic, 1C, member 1"	SULT1C1		9169148, 10783263	Standard	NM_001056		Approved	ST1C1	uc002tdx.3	O00338	OTTHUMG00000153215	ENST00000437390.2:c.365C>G	2.37:g.108917339C>G	ENSP00000399651:p.Thr122Ser	108	0	0		113	34	0.300885	NM_001056	Q069I8|Q08AS5|Q53S63	Missense_Mutation	SNP	ENST00000437390.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.75|15.75	2.925506|2.925506	0.52759|0.52759	.|.	.|.	ENSG00000198203|ENSG00000198203	ENST00000409067|ENST00000251481;ENST00000437390	.|D;D	.|0.84516	.|-1.86;-1.86	4.31|4.31	4.31|4.31	0.51392|0.51392	.|Sulfotransferase domain (1);	.|.	.|.	.|.	.|.	T|T	0.81912|0.81912	0.4923|0.4923	L|L	0.47016|0.47016	1.485|1.485	0.36646|0.36646	D|D	0.877121|0.877121	.|B;B	.|0.13594	.|0.008;0.002	.|B;B	.|0.27715	.|0.082;0.03	T|T	0.79773|0.79773	-0.1662|-0.1662	5|9	.|0.23891	.|T	.|0.37	.|.	15.9394|15.9394	0.79743|0.79743	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|122;108	.|B4DLP0;O00338	.|.;ST1C2_HUMAN	E|S	104|108;122	.|ENSP00000251481:T108S;ENSP00000399651:T122S	.|ENSP00000251481:T108S	D|T	+|+	3|2	2|0	SULT1C2|SULT1C2	108283771|108283771	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.891000|0.891000	0.51852|0.51852	4.926000|4.926000	0.63433|0.63433	2.225000|2.225000	0.72522|0.72522	0.591000|0.591000	0.81541|0.81541	GAC|ACT	.	.	none		0.478	SULT1C2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000329969.2	NM_176825		G	108917339	C	G	108917339	3	3	18	1	0	0	0	0	1	0	0	0	15392	565	20	4	432	4	SULT1C2	2	108917339	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	41286913	108917339	134282034	27	2414											
MERTK	10461	hgsc.bcm.edu	37	chr2	112779062	112779062	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctaagaagatttacagtggCgattattaccgccaaggccg	12	10	10	9	3	1	2	0	0	1	2	1	3	1	2	3	2	2	0	3	2	6	5	rs149178674		TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr2:112779062C>T	ENST00000295408.4	+	17	2510	c.2253C>T	c.(2251-2253)ggC>ggT	p.G751G	MERTK_ENST00000409780.1_Silent_p.G575G|MERTK_ENST00000421804.2_Silent_p.G751G			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	751	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)	p.G751G(1)		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						TTTACAGTGGCGATTATTACC	0.478																																					p.G751G		Atlas-SNP	.											MERTK,colon,carcinoma,0,1	MERTK	112	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C2253T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	151	145	147		2253	-10.5	0.1	2	dbSNP_134	147	0,8600		0,0,4300	no	coding-synonymous	MERTK	NM_006343.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		751/1000	112779062	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	10461	exon17			CAGTGGCGATTAT	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.2253C>T	2.37:g.112779062C>T		72	0	0		88	20	0.227273	NM_006343	Q9HBB4	Silent	SNP	ENST00000295408.4	37	CCDS2094.1																																																																																			C|1.000;T|0.000	0.000	weak		0.478	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2			T	112779062	C	T	112779062	2	4	18	1	0	0	0	0	0	0	0	1	9488	755	27	1		1	MERTK	2	112779062	Silent	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	3861723	112779062	130420311	28	2415											
CXCR4	7852	hgsc.bcm.edu	37	chr2	136873448	136873448	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tggagtcatagtcccctgagCccatttcctcggtgtagtta	7	13	10	11	1	1	1	1	1	0	0	4	2	3	2	4	2	1	2	4	2	3	4			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr2:136873448C>T	ENST00000241393.3	-	2	154	c.50G>A	c.(49-51)gGc>gAc	p.G17D	CXCR4_ENST00000466288.1_5'UTR|CXCR4_ENST00000409817.1_Missense_Mutation_p.G21D	NM_003467.2	NP_003458.1	P61073	CXCR4_HUMAN	chemokine (C-X-C motif) receptor 4	17	Important for chemokine binding, signaling and HIV-1 coreceptor activity.				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)	GTCCCCTGAGCCCATTTCCTC	0.403																																					p.G21D		Atlas-SNP	.											.	CXCR4	51	.	0			c.G62A						PASS	.						74	79	78					2																	136873448		2203	4300	6503	SO:0001583	missense	7852	exon1			CCTGAGCCCATTT	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.50G>A	2.37:g.136873448C>T	ENSP00000241393:p.Gly17Asp	99	0	0		126	39	0.309524	NM_001008540	B2R5N0|O60835|P30991|P56438|Q53S69|Q9BXA0|Q9UKN2	Missense_Mutation	SNP	ENST00000241393.3	37	CCDS46420.1	.	.	.	.	.	.	.	.	.	.	C	17.06	3.291560	0.59976	.	.	ENSG00000121966	ENST00000409817;ENST00000241393	T;T	0.59502	0.26;0.26	5.88	5.88	0.94601	CXC chemokine receptor, type 4, N-terminal (1);	0.151224	0.50627	D	0.000111	T	0.48607	0.1509	L	0.27053	0.805	0.80722	D	1	B;B	0.15930	0.006;0.015	B;B	0.16289	0.015;0.011	T	0.30534	-0.9975	10	0.27082	T	0.32	.	20.2228	0.98330	0.0:1.0:0.0:0.0	.	17;21	P61073;P61073-2	CXCR4_HUMAN;.	D	21;17	ENSP00000386884:G21D;ENSP00000241393:G17D	ENSP00000241393:G17D	G	-	2	0	CXCR4	136589918	1.000000	0.71417	1.000000	0.80357	0.813000	0.45954	5.359000	0.66074	2.789000	0.95967	0.655000	0.94253	GGC	.	.	none		0.403	CXCR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331732.1			T	136873448	C	T	136873448	3	4	18	1	0	0	0	0	1	0	0	0	4095	739	26	2	1012	2	CXCR4	2	136873448	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	24094386	136873448	106325925	29	2416											
GPD2	2820	hgsc.bcm.edu	37	chr2	157407178	157407178	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacctttcacggactctgtGcgcaaaatggatgataaaga	13	9	11	8	2	2	2	1	1	1	1	2	5	2	5	1	3	1	1	1	3	4	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr2:157407178G>T	ENST00000310454.6	+	8	1263	c.891G>T	c.(889-891)gtG>gtT	p.V297V	GPD2_ENST00000409674.1_Silent_p.V297V|GPD2_ENST00000409125.4_Silent_p.V70V|GPD2_ENST00000540309.1_Silent_p.V297V|GPD2_ENST00000438166.2_Silent_p.V297V	NM_001083112.2	NP_001076581.2	P43304	GPDM_HUMAN	glycerol-3-phosphate dehydrogenase 2 (mitochondrial)	297					camera-type eye development (GO:0043010)|cellular lipid metabolic process (GO:0044255)|gluconeogenesis (GO:0006094)|glycerol catabolic process (GO:0019563)|glycerol-3-phosphate metabolic process (GO:0006072)|multicellular organism growth (GO:0035264)|small molecule metabolic process (GO:0044281)	glycerol-3-phosphate dehydrogenase complex (GO:0009331)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|glycerol-3-phosphate dehydrogenase activity (GO:0004368)|sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity (GO:0052591)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(1)|stomach(1)	22						CGGACTCTGTGCGCAAAATGG	0.468																																					p.V297V		Atlas-SNP	.											.	GPD2	59	.	0			c.G891T						PASS	.						126	111	116					2																	157407178		2203	4300	6503	SO:0001819	synonymous_variant	2820	exon8			CTCTGTGCGCAAA		CCDS2202.1	2q24.1	2013-01-10			ENSG00000115159	ENSG00000115159	1.1.1.8	"EF-hand domain containing"	4456	protein-coding gene	gene with protein product		138430					Standard	NM_001083112		Approved		uc002tzd.4	P43304	OTTHUMG00000131951	ENST00000310454.6:c.891G>T	2.37:g.157407178G>T		104	0	0		119	25	0.210084	NM_001083112	A8K4V0|B3KSA9|Q59FR1|Q9HAP9	Silent	SNP	ENST00000310454.6	37	CCDS2202.1																																																																																			.	.	none		0.468	GPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254910.3			T	157407178	G	T	157407178	2	4	18	1	0	0	0	0	0	0	0	1	6614	1306	46	4		4	GPD2	2	157407178	Silent	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	20533730	157407178	85792195	30	2417											
SCN7A	6332	hgsc.bcm.edu	37	chr2	167313511	167313511	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagtatgcctaagaacaaacTtgccatataaaaggaaaaca	21	7	6	7	0	0	1	0	0	0	1	0	2	0	2	2	1	5	1	2	1	10	5			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr2:167313511T>C	ENST00000409855.1	-	10	1285	c.1159A>G	c.(1159-1161)Agt>Ggt	p.S387G		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	387					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)	p.S387G(2)		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)	AAGAACAAACTTGCCATATAA	0.353																																					p.S387G		Atlas-SNP	.											SCN7A_ENST00000409855,NS,lymphoid_neoplasm,0,2	SCN7A	410	2	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.A1159G						PASS	.						76	65	68					2																	167313511		1818	4080	5898	SO:0001583	missense	6332	exon10			ACAAACTTGCCAT	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.1159A>G	2.37:g.167313511T>C	ENSP00000386796:p.Ser387Gly	147	0	0		187	44	0.235294	NM_002976		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.687193	0.88639	.	.	ENSG00000136546	ENST00000409855;ENST00000259060;ENST00000419992;ENST00000441411	D;D;D	0.98550	-4.99;-4.99;-4.99	5.35	5.35	0.76521	Ion transport (1);	0.201865	0.35262	N	0.003327	D	0.98220	0.9411	L	0.46157	1.445	0.37219	D	0.905164	D	0.63046	0.992	D	0.76071	0.987	D	0.99956	1.1628	10	0.87932	D	0	.	13.2728	0.60170	0.0:0.0:0.0:1.0	.	387	Q01118	SCN7A_HUMAN	G	387	ENSP00000386796:S387G;ENSP00000413699:S387G;ENSP00000403846:S387G	ENSP00000259060:S387G	S	-	1	0	SCN7A	167021757	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	7.937000	0.87672	2.006000	0.58801	0.454000	0.30748	AGT	.	.	none		0.353	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1			C	167313511	T	C	167313511	3	2	18	1	0	0	0	0	1	0	0	0	13938	1609	56	3	3953	3	SCN7A	2	167313511	Missense_Mutation	SNP	T	TCGA-FF-A7CR-01A-11D-A382-10	9906333	167313511	75885862	31	2418											
ITGAV	3685	hgsc.bcm.edu	37	chr2	187521026	187521026	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcaaaagggagcaattcgAcgagcactgtttctctacag	14	8	10	9	2	1	0	0	0	1	0	3	3	1	1	0	1	4	4	0	1	5	3			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr2:187521026A>C	ENST00000261023.3	+	17	1891	c.1617A>C	c.(1615-1617)cgA>cgC	p.R539R	AC017101.10_ENST00000453665.1_RNA|ITGAV_ENST00000433736.2_Silent_p.R493R|ITGAV_ENST00000374907.3_Silent_p.R503R	NM_002210.3	NP_002201	P06756	ITAV_HUMAN	integrin, alpha V	539					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)	GAGCAATTCGACGAGCACTGT	0.423																																					p.R539R	Melanoma(58;108 1995 6081)	Atlas-SNP	.											ITGAV,rectum,carcinoma,+2,1	ITGAV	124	1	0			c.A1617C						PASS	.						199	197	198					2																	187521026		2203	4300	6503	SO:0001819	synonymous_variant	3685	exon17			AATTCGACGAGCA		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.1617A>C	2.37:g.187521026A>C		143	0	0		192	36	0.1875	NM_002210	A0AV67|B0LPF4|B7Z883|B7ZLX0|D3DPG8|E7EWZ6|Q53SK4|Q59EB7|Q6LD15	Silent	SNP	ENST00000261023.3	37	CCDS2292.1																																																																																			.	.	none		0.423	ITGAV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255882.2	NM_002210		C	187521026	A	C	187521026	2	2	18	1	0	0	0	0	0	0	0	1	7897	262	10	5		5	ITGAV	2	187521026	Silent	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10	20207515	187521026	55678347	32	2419											
ITPR1	3708	hgsc.bcm.edu	37	chr3	4722294	4722294	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcctcctgtgtatatttaagCgagagtttgatgaaagcaat	12	13	10	6	1	0	3	0	2	0	1	1	4	1	3	2	0	2	3	2	0	5	5			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr3:4722294C>T	ENST00000443694.2	+	22	2980	c.2980C>T	c.(2980-2982)Cga>Tga	p.R994*	ITPR1_ENST00000354582.6_Nonsense_Mutation_p.R1009*|ITPR1_ENST00000423119.2_Nonsense_Mutation_p.R1000*|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000302640.8_Nonsense_Mutation_p.R994*|ITPR1_ENST00000357086.4_Nonsense_Mutation_p.R1000*|ITPR1_ENST00000456211.2_Nonsense_Mutation_p.R985*			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	1009					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)	p.R985*(1)		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)	TATATTTAAGCGAGAGTTTGA	0.398																																					p.R1000X		Atlas-SNP	.											ITPR1,rectum,carcinoma,0,1	ITPR1	659	1	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2998T						scavenged	.						110	107	108					3																	4722294		1874	4092	5966	SO:0001587	stop_gained	3708	exon25			TTTAAGCGAGAGT	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.2980C>T	3.37:g.4722294C>T	ENSP00000401671:p.Arg994*	101	1	0.00990099		103	26	0.252427	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Nonsense_Mutation	SNP	ENST00000443694.2	37	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	C	41	8.817682	0.98964	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	.	.	.	4.62	3.74	0.42951	.	0.449318	0.22299	N	0.061883	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	.	12.1324	0.53950	0.3112:0.6888:0.0:0.0	.	.	.	.	X	1009;994;1009;1000;1000;985;994	.	ENSP00000306253:R994X	R	+	1	2	ITPR1	4697294	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	0.841000	0.27613	1.141000	0.42275	0.491000	0.48974	CGA	.	.	none		0.398	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		T	4722294	C	T	4722294	4	4	18	1	0	0	0	0	0	1	0	0	7929	760	27	1	3115	1	ITPR1	3	4722294	Nonsense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10		4722294	193300136	33	2420											
OSBPL10	114884	hgsc.bcm.edu	37	chr3	32022601	32022601	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcgaggagcccgccgaggtaGcacggctgctgctgcggctg	5	5	18	13	5	0	0	0	0	0	0	0	3	0	1	2	4	5	6	2	4	1	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr3:32022601G>A	ENST00000396556.2	-	1	193	c.71C>T	c.(70-72)gCt>gTt	p.A24V	OSBPL10_ENST00000438237.2_Missense_Mutation_p.A24V|ZNF860_ENST00000360311.4_5'Flank	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	24					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)		CGCCGAGGTAGCACGgctgct	0.781																																					p.A24V		Atlas-SNP	.											.	OSBPL10	160	.	0			c.C71T						PASS	.						2	2	2					3																	32022601		815	1738	2553	SO:0001583	missense	114884	exon1			GAGGTAGCACGGC	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.71C>T	3.37:g.32022601G>A	ENSP00000379804:p.Ala24Val	86	0	0		114	32	0.280702	NM_017784	B4E212|Q9BTU5	Missense_Mutation	SNP	ENST00000396556.2	37	CCDS2651.1	.	.	.	.	.	.	.	.	.	.	G	15.53	2.860887	0.51482	.	.	ENSG00000144645	ENST00000396556;ENST00000438237	T;T	0.22539	1.95;2.28	4.02	3.12	0.35913	.	1.483920	0.05400	N	0.540468	T	0.15652	0.0377	N	0.14661	0.345	0.27329	N	0.956829	B;B	0.12630	0.006;0.006	B;B	0.09377	0.002;0.004	T	0.24657	-1.0154	10	0.49607	T	0.09	-5.9363	10.905	0.47076	0.0:0.0:0.8107:0.1893	.	24;24	B4E212;Q9BXB5	.;OSB10_HUMAN	V	24	ENSP00000379804:A24V;ENSP00000406124:A24V	ENSP00000379804:A24V	A	-	2	0	OSBPL10	31997605	0.989000	0.36119	1.000000	0.80357	0.924000	0.55760	1.025000	0.30090	1.010000	0.39314	0.298000	0.19748	GCT	.	.	none		0.781	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2			A	32022601	G	A	32022601	3	1	18	1	0	0	0	0	1	0	0	0	11284	971	34	2	2271	2	OSBPL10	3	32022601	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	27300307	32022601	165999829	34	2421											
OSBPL10	114884	hgsc.bcm.edu	37	chr3	32022625	32022625	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggctgctgctgcggctgctgCtgttgctacccccgccgccg	1	9	14	17	4	0	0	0	0	0	0	0	0	0	0	4	2	7	8	4	2	1	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr3:32022625C>G	ENST00000396556.2	-	1	169	c.47G>C	c.(46-48)aGc>aCc	p.S16T	OSBPL10_ENST00000438237.2_Missense_Mutation_p.S16T|ZNF860_ENST00000360311.4_5'Flank	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	16					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)		gcggctgctgctgttgctACC	0.791																																					p.S16T		Atlas-SNP	.											.	OSBPL10	160	.	0			c.G47C						PASS	.						2	3	2					3																	32022625		679	1485	2164	SO:0001583	missense	114884	exon1			CTGCTGCTGTTGC	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.47G>C	3.37:g.32022625C>G	ENSP00000379804:p.Ser16Thr	113	0	0		148	33	0.222973	NM_017784	B4E212|Q9BTU5	Missense_Mutation	SNP	ENST00000396556.2	37	CCDS2651.1	.	.	.	.	.	.	.	.	.	.	C	14.90	2.672276	0.47781	.	.	ENSG00000144645	ENST00000396556;ENST00000438237	T;T	0.23552	1.9;2.21	3.91	3.91	0.45181	.	0.842884	0.09989	N	0.729989	T	0.16685	0.0401	N	0.14661	0.345	0.27041	N	0.964015	P;P	0.51791	0.948;0.948	B;B	0.40534	0.332;0.332	T	0.05971	-1.0853	10	0.28530	T	0.3	.	13.8256	0.63348	0.0:1.0:0.0:0.0	.	16;16	B4E212;Q9BXB5	.;OSB10_HUMAN	T	16	ENSP00000379804:S16T;ENSP00000406124:S16T	ENSP00000379804:S16T	S	-	2	0	OSBPL10	31997629	1.000000	0.71417	1.000000	0.80357	0.785000	0.44390	2.735000	0.47377	2.196000	0.70406	0.298000	0.19748	AGC	.	.	none		0.791	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2			G	32022625	C	G	32022625	3	3	18	1	0	0	0	0	1	0	0	0	11284	797	28	4	2295	4	OSBPL10	3	32022625	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	24	32022625	165999805	35	2422											
C3orf35	339883	hgsc.bcm.edu	37	chr3	37458937	37458937	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcagatgggcctgcagggCagtgctcagcatttcaacat	10	8	13	10	0	2	1	2	0	0	1	2	2	2	1	1	2	5	5	1	2	1	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr3:37458937C>T	ENST00000328376.5	+	5	1159	c.180C>T	c.(178-180)ggC>ggT	p.G60G	C3orf35_ENST00000426078.1_Silent_p.G60G|C3orf35_ENST00000452017.2_Silent_p.G60G|C3orf35_ENST00000481400.1_Intron|C3orf35_ENST00000425564.2_Silent_p.G60G|C3orf35_ENST00000425932.1_Silent_p.G60G	NM_178339.2	NP_848029.2	Q8IVJ8	APRG1_HUMAN	chromosome 3 open reading frame 35	60						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						GCCTGCAGGGCAGTGCTCAGC	0.463																																					p.G60G		Atlas-SNP	.											C3orf35,NS,carcinoma,+2,1	C3orf35	21	1	0			c.C180T						PASS	.						116	112	113					3																	37458937		1902	4110	6012	SO:0001819	synonymous_variant	339883	exon5			GCAGGGCAGTGCT	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.180C>T	3.37:g.37458937C>T		161	0	0		145	29	0.2	NM_178342	B7ZMA0|Q8IVJ5|Q8IVJ9	Silent	SNP	ENST00000328376.5	37	CCDS43065.1																																																																																			.	.	none		0.463	C3orf35-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342344.2	NM_178338		T	37458937	C	T	37458937	2	4	18	1	0	0	0	0	0	0	0	1	2227	697	25	2		2	C3orf35	3	37458937	Silent	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	5436312	37458937	160563493	36	2423											
MYD88	4615	hgsc.bcm.edu	37	chr3	38182337	38182337	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atttgcactcagcctctctcCaggtaagctcaaccctgctc	8	11	6	16	0	3	0	2	0	1	0	6	0	4	0	3	1	5	4	3	1	2	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr3:38182337C>T	ENST00000495303.1	+	2	462	c.457C>T	c.(457-459)Cag>Tag	p.Q153*	MYD88_ENST00000481122.1_3'UTR|MYD88_ENST00000396334.3_Missense_Mutation_p.P258L|MYD88_ENST00000424893.1_Missense_Mutation_p.P213L|MYD88_ENST00000443433.2_Nonsense_Mutation_p.Q198*|MYD88_ENST00000417037.2_Missense_Mutation_p.P266L	NM_001172566.1	NP_001166037.1	Q99836	MYD88_HUMAN	myeloid differentiation primary response 88	0	Intermediate domain. {ECO:0000250}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|cell surface receptor signaling pathway (GO:0007166)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-positive bacterium (GO:0050830)|establishment of endothelial intestinal barrier (GO:0090557)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of apoptotic process (GO:0043066)|negative regulation of growth of symbiont in host (GO:0044130)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-23 production (GO:0032747)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of lymphocyte proliferation (GO:0050671)|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 tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)|response to molecule of fungal origin (GO:0002238)|response to peptidoglycan (GO:0032494)|response to virus (GO:0009615)|signal transduction (GO:0007165)|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)|type I interferon biosynthetic process (GO:0045351)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)	death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|TIR domain binding (GO:0070976)			breast(1)|haematopoietic_and_lymphoid_tissue(226)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	237				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		AGCCTCTCTCCAGGTAAGCTC	0.552			Mis		ABC-DLBCL																																p.Q198X		Atlas-SNP	.		Dom	yes		3	3p22	4615	myeloid differentiation primary response gene (88)		L	.	MYD88	900	.	0			c.C592T						PASS	.						125	119	121					3																	38182337		2203	4300	6503	SO:0001587	stop_gained	4615	exon3			TCTCTCCAGGTAA	U84408	CCDS2674.2, CCDS54565.1, CCDS54566.1, CCDS54567.1, CCDS54568.1	3p22	2014-09-17	2012-11-15		ENSG00000172936	ENSG00000172936			7562	protein-coding gene	gene with protein product		602170	"myeloid differentiation primary response gene (88)"			9013863	Standard	NM_002468		Approved		uc003chx.3	Q99836	OTTHUMG00000131083	ENST00000495303.1:c.457C>T	3.37:g.38182337C>T	ENSP00000417848:p.Gln153*	120	0	0		96	45	0.46875	NM_001172569	B4DKH8|B4DKU4|B4DQ60|B4DQ72|J3KPU4|J3KQ87|J3KQJ6|P78397|Q53XS7	Nonsense_Mutation	SNP	ENST00000495303.1	37	CCDS54568.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	32|32	5.149061|5.149061	0.94645|0.94645	.|.	.|.	ENSG00000172936|ENSG00000172936	ENST00000417037;ENST00000396334;ENST00000424893;ENST00000421516;ENST00000415158|ENST00000495303;ENST00000443433	T;T;T;T|.	0.07216|.	3.49;3.21;3.21;3.49|.	5.61|5.61	5.61|5.61	0.85477|0.85477	Toll/interleukin-1 receptor homology (TIR) domain (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.79028|.	0.4377|.	.|.	.|.	.|.	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|.	0.80730|.	-0.1252|.	9|.	0.02654|0.87932	T|D	1|0	-8.5502|-8.5502	18.9993|18.9993	0.92826|0.92826	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	200;245;234|.	Q99836-2;Q99836;B4E3D6|.	.;MYD88_HUMAN;.|.	L|X	266;258;213;265;234|153;198	ENSP00000401399:P266L;ENSP00000379625:P258L;ENSP00000389979:P213L;ENSP00000391753:P265L|.	ENSP00000379625:P258L|ENSP00000390565:Q198X	P|Q	+|+	2|1	0|0	MYD88|MYD88	38157341|38157341	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	7.375000|7.375000	0.79646|0.79646	2.815000|2.815000	0.96918|0.96918	0.561000|0.561000	0.74099|0.74099	CCA|CAG	.	.	none		0.552	MYD88-008	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000342700.1	NM_002468		T	38182337	C	T	38182337	4	4	18	1	0	0	0	0	0	1	0	0	10032	595	21	2	811	2	MYD88	3	38182337	Nonsense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	723400	38182337	159840093	37	2424											
KLHL18	23276	hgsc.bcm.edu	37	chr3	47385186	47385186	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctctggcttcctcagcattGccgagatgtacagctctgtg	6	12	11	12	1	3	1	1	0	2	1	4	2	4	1	2	1	4	5	2	1	1	3			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr3:47385186G>A	ENST00000232766.5	+	10	1500	c.1480G>A	c.(1480-1482)Gcc>Acc	p.A494T	KLHL18_ENST00000455924.2_Missense_Mutation_p.A382T	NM_025010.4	NP_079286.2	O94889	KLH18_HUMAN	kelch-like family member 18	494										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)		CCTCAGCATTGCCGAGATGTA	0.642																																					p.A494T		Atlas-SNP	.											.	KLHL18	46	.	0			c.G1480A						PASS	.						83	84	84					3																	47385186		2203	4300	6503	SO:0001583	missense	23276	exon10			AGCATTGCCGAGA	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.1480G>A	3.37:g.47385186G>A	ENSP00000232766:p.Ala494Thr	55	0	0		57	12	0.210526	NM_025010	A8K612|Q7Z3E8|Q8N125	Missense_Mutation	SNP	ENST00000232766.5	37	CCDS33749.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.737796	0.89573	.	.	ENSG00000114648	ENST00000232766;ENST00000455924	T;T	0.77489	-1.1;-1.1	5.06	5.06	0.68205	Galactose oxidase, beta-propeller (1);	0.056309	0.64402	D	0.000001	T	0.73513	0.3596	L	0.39633	1.23	0.80722	D	1	P	0.42161	0.772	B	0.40982	0.345	T	0.78145	-0.2318	10	0.87932	D	0	.	17.6032	0.88031	0.0:0.0:1.0:0.0	.	494	O94889	KLH18_HUMAN	T	494;382	ENSP00000232766:A494T;ENSP00000405585:A382T	ENSP00000232766:A494T	A	+	1	0	KLHL18	47360190	1.000000	0.71417	0.876000	0.34364	0.904000	0.53231	7.711000	0.84669	2.636000	0.89361	0.491000	0.48974	GCC	.	.	none		0.642	KLHL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344493.1	NM_025010		A	47385186	G	A	47385186	3	1	18	1	0	0	0	0	1	0	0	0	8382	1319	46	2	1518	2	KLHL18	3	47385186	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	9202849	47385186	150637244	38	2425											
GRM2	2912	hgsc.bcm.edu	37	chr3	51749480	51749480	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccaggagtacatccgctgggGcgatgcctgggctgtgggac	6	7	17	11	2	0	0	0	0	0	0	1	3	1	2	3	5	2	3	3	5	1	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr3:51749480G>T	ENST00000395052.3	+	4	1925	c.1691G>T	c.(1690-1692)gGc>gTc	p.G564V	GRM2_ENST00000475478.1_3'UTR|GRM2_ENST00000442933.2_Intron	NM_000839.3	NP_000830.2	Q14416	GRM2_HUMAN	glutamate receptor, metabotropic 2	564					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)		ATCCGCTGGGGCGATGCCTGG	0.622																																					p.G564V		Atlas-SNP	.											GRM2,caecum,carcinoma,-1,1	GRM2	91	1	0			c.G1691T						PASS	.						48	44	45					3																	51749480		2202	4300	6502	SO:0001583	missense	2912	exon4			GCTGGGGCGATGC	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.1691G>T	3.37:g.51749480G>T	ENSP00000378492:p.Gly564Val	57	0	0		75	18	0.24	NM_000839	B0M0K7|Q14CU5|Q52MC6|Q9H3N6	Missense_Mutation	SNP	ENST00000395052.3	37	CCDS2834.1	.	.	.	.	.	.	.	.	.	.	G	10.15	1.272267	0.23221	.	.	ENSG00000164082	ENST00000395052	D	0.89123	-2.47	5.3	4.43	0.53597	.	0.113989	0.64402	D	0.000013	D	0.83133	0.5188	L	0.43923	1.385	0.80722	D	1	B	0.20887	0.049	B	0.14023	0.01	T	0.78650	-0.2121	10	0.41790	T	0.15	.	9.2087	0.37304	0.2103:0.0:0.7897:0.0	.	564	Q14416	GRM2_HUMAN	V	564	ENSP00000378492:G564V	ENSP00000378492:G564V	G	+	2	0	GRM2	51724520	0.997000	0.39634	0.990000	0.47175	0.837000	0.47467	3.121000	0.50438	1.398000	0.46701	0.561000	0.74099	GGC	.	.	none		0.622	GRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346542.1			T	51749480	G	T	51749480	3	4	18	1	0	0	0	0	1	0	0	0	6806	1203	42	4	1701	4	GRM2	3	51749480	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	4364294	51749480	146272950	39	2426											
EPHA3	2042	hgsc.bcm.edu	37	chr3	89499497	89499497	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggaatcccggcagcctgaaGatcatcaccagtgcagccgc	10	5	11	15	3	2	2	2	1	0	1	3	3	3	3	4	2	3	2	4	2	2	0			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr3:89499497G>T	ENST00000336596.2	+	15	2892	c.2667G>T	c.(2665-2667)aaG>aaT	p.K889N	EPHA3_ENST00000494014.1_Missense_Mutation_p.K889N	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	889					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.K889K(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)		GCAGCCTGAAGATCATCACCA	0.438										TSP Lung(6;0.00050)																											p.K889N		Atlas-SNP	.											EPHA3,NS,carcinoma,0,1	EPHA3	501	1	1	Substitution - coding silent(1)	ovary(1)	c.G2667T						PASS	.						68	63	65					3																	89499497		2203	4300	6503	SO:0001583	missense	2042	exon15			CCTGAAGATCATC	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.2667G>T	3.37:g.89499497G>T	ENSP00000337451:p.Lys889Asn	103	0	0		120	32	0.266667	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	G	15.16	2.751796	0.49362	.	.	ENSG00000044524	ENST00000336596;ENST00000494014	T;T	0.62232	0.04;0.04	5.66	4.67	0.58626	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.71525	0.3350	M	0.72353	2.195	0.80722	D	1	D	0.71674	0.998	D	0.75020	0.985	T	0.73043	-0.4107	9	.	.	.	.	3.6688	0.08266	0.3385:0.0:0.6615:0.0	.	889	P29320	EPHA3_HUMAN	N	889	ENSP00000337451:K889N;ENSP00000419190:K889N	.	K	+	3	2	EPHA3	89582187	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.415000	0.52700	2.673000	0.90976	0.650000	0.86243	AAG	.	.	none		0.438	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		T	89499497	G	T	89499497	3	4	18	1	0	0	0	0	1	0	0	0	5170	933	33	4	2751	4	EPHA3	3	89499497	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	37750017	89499497	108522933	40	2427											
ARL13B	200894	hgsc.bcm.edu	37	chr3	93768309	93768309	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaaccaccgggtagaaccaCttaatatagatgactgtgct	13	9	10	9	1	0	3	0	1	0	2	0	4	0	4	3	2	3	2	3	2	6	4			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr3:93768309C>G	ENST00000394222.3	+	8	1359	c.1084C>G	c.(1084-1086)Ctt>Gtt	p.L362V	ARL13B_ENST00000471138.1_Missense_Mutation_p.L362V|DHFRL1_ENST00000481631.1_Intron|ARL13B_ENST00000303097.7_Missense_Mutation_p.L255V|ARL13B_ENST00000535334.1_Missense_Mutation_p.L259V|ARL13B_ENST00000539730.1_Missense_Mutation_p.L83V	NM_001174150.1	NP_001167621.1	Q3SXY8	AR13B_HUMAN	ADP-ribosylation factor-like 13B	362					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						GGTAGAACCACTTAATATAGA	0.373																																					p.L362V		Atlas-SNP	.											.	ARL13B	52	.	0			c.C1084G						PASS	.						84	83	83					3																	93768309		2203	4300	6503	SO:0001583	missense	200894	exon8			GAACCACTTAATA	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.1084C>G	3.37:g.93768309C>G	ENSP00000377769:p.Leu362Val	420	0	0		416	92	0.221154	NM_182896	D3DN29|G3V1S8|Q504W8|Q8TCL5	Missense_Mutation	SNP	ENST00000394222.3	37	CCDS2925.1	.	.	.	.	.	.	.	.	.	.	C	0.018	-1.484787	0.01027	.	.	ENSG00000169379	ENST00000535334;ENST00000303097;ENST00000394222;ENST00000471138;ENST00000539730	T;T;T;T;T	0.62498	1.74;0.02;0.22;0.22;1.06	5.12	-1.85	0.07784	.	0.388487	0.26424	N	0.024448	T	0.24236	0.0587	N	0.03324	-0.35	0.53005	D	0.999964	B;B;B;B	0.10296	0.003;0.0;0.001;0.001	B;B;B;B	0.08055	0.003;0.002;0.002;0.003	T	0.32877	-0.9890	10	0.02654	T	1	-4.0133	3.8052	0.08774	0.1835:0.3115:0.4052:0.0998	.	259;362;255;362	G3V1S8;B4DLH1;Q3SXY8-2;Q3SXY8	.;.;.;AR13B_HUMAN	V	259;255;362;362;83	ENSP00000445145:L259V;ENSP00000306225:L255V;ENSP00000377769:L362V;ENSP00000420780:L362V;ENSP00000437977:L83V	ENSP00000306225:L255V	L	+	1	0	ARL13B	95250999	0.391000	0.25221	0.952000	0.39060	0.483000	0.33249	0.432000	0.21461	-0.084000	0.12595	-1.058000	0.02302	CTT	.	.	none		0.373	ARL13B-005	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352904.1	NM_182896		G	93768309	C	G	93768309	3	3	18	1	0	0	0	0	1	0	0	0	929	565	20	4	1114	4	ARL13B	3	93768309	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	4268812	93768309	104254121	41	2428											
CASR	846	hgsc.bcm.edu	37	chr3	122003487	122003487	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcgccgcagcaacgtctccCgcaagcggtccagcagcctt	7	6	11	17	5	1	0	0	0	1	0	3	0	2	0	4	1	6	4	4	1	2	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr3:122003487C>T	ENST00000490131.1	+	7	3058	c.2686C>T	c.(2686-2688)Cgc>Tgc	p.R896C	CASR_ENST00000296154.5_Missense_Mutation_p.R896C|CASR_ENST00000498619.1_Missense_Mutation_p.R906C|AC068754.1_ENST00000408547.1_RNA	NM_000388.3	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor	896	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)			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)	CAACGTCTCCCGCAAGCGGTC	0.657																																					p.R906C		Atlas-SNP	.											CASR,colon,carcinoma,0,1	CASR	190	1	0			c.C2716T						PASS	.						30	31	31					3																	122003487		2203	4299	6502	SO:0001583	missense	846	exon7			GTCTCCCGCAAGC	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.2686C>T	3.37:g.122003487C>T	ENSP00000418685:p.Arg896Cys	65	0	0		61	13	0.213115	NM_001178065	Q13912|Q16108|Q16109|Q16110|Q16379|Q2M1T0|Q4PJ19	Missense_Mutation	SNP	ENST00000490131.1	37	CCDS3010.1	.	.	.	.	.	.	.	.	.	.	C	17.04	3.288301	0.59976	.	.	ENSG00000036828	ENST00000490131;ENST00000498619;ENST00000296154	D;D;D	0.89810	-2.57;-2.57;-2.57	5.89	4.94	0.65067	.	0.051558	0.64402	D	0.000001	D	0.89469	0.6724	L	0.32530	0.975	0.58432	D	0.999999	D;D	0.76494	0.999;0.999	P;P	0.56088	0.791;0.791	D	0.90626	0.4563	10	0.87932	D	0	.	16.9209	0.86164	0.1363:0.8637:0.0:0.0	.	906;896	E7ENE0;P41180	.;CASR_HUMAN	C	896;906;896	ENSP00000418685:R896C;ENSP00000420194:R906C;ENSP00000296154:R896C	ENSP00000296154:R896C	R	+	1	0	CASR	123486177	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.573000	0.60893	2.793000	0.96121	0.561000	0.74099	CGC	.	.	none		0.657	CASR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355761.1	NM_000388		T	122003487	C	T	122003487	3	4	18	1	0	0	0	0	1	0	0	0	2684	652	23	1	2738	1	CASR	3	122003487	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	28235178	122003487	76018943	42	2429											
PLXNA1	5361	hgsc.bcm.edu	37	chr3	126747903	126747903	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtcaccaccaagattgacaaCgattggaagaggctgaacac	15	6	10	10	1	1	4	1	2	0	2	1	6	1	5	2	2	2	1	2	2	4	2	rs369457038		TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr3:126747903C>T	ENST00000393409.2	+	25	4737	c.4737C>T	c.(4735-4737)aaC>aaT	p.N1579N	PLXNA1_ENST00000251772.4_Silent_p.N1556N	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	1579					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)		AGATTGACAACGATTGGAAGA	0.672																																					p.N1579N		Atlas-SNP	.											PLXNA1,NS,carcinoma,0,1	PLXNA1	185	1	0			c.C4737T						PASS	.	C		0,4406		0,0,2203	144	97	113		4737	-3.6	1	3		113	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PLXNA1	NM_032242.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		1579/1897	126747903	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	5361	exon25			TGACAACGATTGG	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.4737C>T	3.37:g.126747903C>T		59	0	0		46	15	0.326087	NM_032242		Silent	SNP	ENST00000393409.2	37	CCDS33847.2																																																																																			.	.	weak		0.672	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242		T	126747903	C	T	126747903	2	4	18	1	0	0	0	0	0	0	0	1	12128	535	19	1		1	PLXNA1	3	126747903	Silent	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	4744416	126747903	71274527	43	2430											
AMOTL2	51421	hgsc.bcm.edu	37	chr3	134089710	134089710	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtggggggccctgctggttgCgggccagctgtgggaagctg	3	8	21	9	1	0	0	0	0	0	0	0	1	0	1	2	6	4	4	2	6	1	1	rs554025750	byFrequency	TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr3:134089710C>T	ENST00000422605.2	-	2	732	c.566G>A	c.(565-567)cGc>cAc	p.R189H	AMOTL2_ENST00000513145.1_Missense_Mutation_p.R189H|AMOTL2_ENST00000511759.1_Intron|AMOTL2_ENST00000514516.1_Missense_Mutation_p.R247H|AMOTL2_ENST00000249883.5_Missense_Mutation_p.R189H			Q9Y2J4	AMOL2_HUMAN	angiomotin like 2	189					hippo signaling (GO:0035329)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|tight junction (GO:0005923)				endometrium(8)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	19						CTGCTGGTTGCGGGCCAGCTG	0.667													C|||	2	0.000399361	0.0	0.0029	5008	,	,		14670	0.0		0.0	False		,,,				2504	0.0				p.R189H		Atlas-SNP	.											.	AMOTL2	52	.	0			c.G566A						PASS	.						22	28	26					3																	134089710		2201	4295	6496	SO:0001583	missense	51421	exon2			TGGTTGCGGGCCA	AF175966	CCDS33860.1, CCDS63783.1, CCDS63784.1	3q21-q22	2008-07-18			ENSG00000114019	ENSG00000114019			17812	protein-coding gene	gene with protein product	"Leman coiled-coil protein", "angiomotin-like protein 2"	614658					Standard	NM_016201		Approved	LCCP	uc003eqg.1	Q9Y2J4	OTTHUMG00000159777	ENST00000422605.2:c.566G>A	3.37:g.134089710C>T	ENSP00000409999:p.Arg189His	51	0	0		69	14	0.202899	NM_016201	A8K6F1|B7Z5Q1|E9PHW3|Q53EP1|Q96F99|Q9UKB4	Missense_Mutation	SNP	ENST00000422605.2	37		.	.	.	.	.	.	.	.	.	.	C	20.6	4.015558	0.75161	.	.	ENSG00000114019	ENST00000249883;ENST00000422605;ENST00000514516;ENST00000513145;ENST00000510560	T;T;T;T;T	0.15834	2.39;2.39;2.39;2.39;2.39	4.52	4.52	0.55395	.	0.281504	0.36066	N	0.002805	T	0.14184	0.0343	L	0.40543	1.245	0.41298	D	0.987023	P;P;P	0.37352	0.591;0.591;0.456	B;B;B	0.28139	0.086;0.086;0.039	T	0.08472	-1.0720	10	0.30078	T	0.28	-17.0703	17.6366	0.88124	0.0:1.0:0.0:0.0	.	189;189;247	Q9Y2J4-3;Q9Y2J4-2;E9PHW3	.;.;.	H	189;189;247;189;189	ENSP00000249883:R189H;ENSP00000409999:R189H;ENSP00000424765:R247H;ENSP00000425475:R189H;ENSP00000427184:R189H	ENSP00000249883:R189H	R	-	2	0	AMOTL2	135572400	0.910000	0.30920	1.000000	0.80357	0.740000	0.42216	4.318000	0.59190	2.207000	0.71202	0.455000	0.32223	CGC	.	.	none		0.667	AMOTL2-014	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000358149.1	NM_016201		T	134089710	C	T	134089710	3	4	18	1	0	0	0	0	1	0	0	0	584	768	27	1	1812	1	AMOTL2	3	134089710	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	7341807	134089710	63932720	44	2431											
GPR149	344758	hgsc.bcm.edu	37	chr3	154139229	154139229	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtgctattttataaatccCataacttttttggaatgata	13	18	5	5	0	0	1	0	1	0	0	1	2	1	2	1	1	2	1	1	1	7	9			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr3:154139229C>T	ENST00000389740.2	-	3	1321	c.1222G>A	c.(1222-1224)Ggg>Agg	p.G408R		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	408					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)			TTATAAATCCCATAACTTTTT	0.313																																					p.G408R		Atlas-SNP	.											.	GPR149	134	.	0			c.G1222A						PASS	.						41	39	40					3																	154139229		1801	4065	5866	SO:0001583	missense	344758	exon3			AAATCCCATAACT	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.1222G>A	3.37:g.154139229C>T	ENSP00000374390:p.Gly408Arg	133	0	0		134	26	0.19403	NM_001038705		Missense_Mutation	SNP	ENST00000389740.2	37	CCDS43162.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.239708	0.79800	.	.	ENSG00000174948	ENST00000389740	.	.	.	4.77	4.77	0.60923	.	0.000000	0.85682	D	0.000000	T	0.78214	0.4248	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81086	-0.1092	9	0.87932	D	0	-15.4694	17.8046	0.88598	0.0:1.0:0.0:0.0	.	408	Q86SP6	GP149_HUMAN	R	408	.	ENSP00000374390:G408R	G	-	1	0	GPR149	155621923	1.000000	0.71417	0.997000	0.53966	0.984000	0.73092	6.717000	0.74707	2.392000	0.81423	0.454000	0.30748	GGG	.	.	none		0.313	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580		T	154139229	C	T	154139229	3	4	18	1	0	0	0	0	1	0	0	0	6662	594	21	2	981	2	GPR149	3	154139229	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	20049519	154139229	43883201	45	2432											
ZNF141	7700	hgsc.bcm.edu	37	chr4	367062	367062	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	acataagagaattcatgctgGagagaaacccatcacatgtg	16	8	9	8	0	2	2	2	0	0	2	2	5	2	3	1	1	2	1	1	1	3	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr4:367062G>A	ENST00000240499.7	+	4	985	c.836G>A	c.(835-837)gGa>gAa	p.G279E	ZNF141_ENST00000505939.1_Intron|ZNF141_ENST00000512994.1_Intron	NM_003441.2	NP_003432.1	Q15928	ZN141_HUMAN	zinc finger protein 141	279					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						ATTCATGCTGGAGAGAAACCC	0.358																																					p.G279E		Atlas-SNP	.											.	ZNF141	48	.	0			c.G836A						PASS	.						73	83	80					4																	367062		2203	4300	6503	SO:0001583	missense	7700	exon4			ATGCTGGAGAGAA	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.836G>A	4.37:g.367062G>A	ENSP00000240499:p.Gly279Glu	104	0	0		118	24	0.20339	NM_003441	Q6DK07	Missense_Mutation	SNP	ENST00000240499.7	37	CCDS33931.1	.	.	.	.	.	.	.	.	.	.	G	9.811	1.183068	0.21870	.	.	ENSG00000131127	ENST00000240499	T	0.25749	1.78	1.23	-0.229	0.13094	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.23014	0.0556	L	0.39633	1.23	0.31083	N	0.711687	P	0.46020	0.871	P	0.47786	0.557	T	0.25152	-1.0140	8	.	.	.	.	5.6773	0.17755	0.0:0.0:0.6827:0.3173	.	279	Q15928	ZN141_HUMAN	E	279	ENSP00000240499:G279E	.	G	+	2	0	ZNF141	357062	0.755000	0.28372	0.043000	0.18650	0.306000	0.27790	0.515000	0.22801	-0.424000	0.07382	0.305000	0.20034	GGA	.	.	none		0.358	ZNF141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357710.1	NM_003441		A	367062	G	A	367062	3	1	18	1	0	0	0	0	1	0	0	0	17745	1174	41	2	850	2	ZNF141	4	367062	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10		367062	190787214	46	2433											
ZNF721	170960	hgsc.bcm.edu	37	chr4	435533	435533	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaattttcttatgtgcataaAgatttgcagactgtctaaag	13	15	8	5	0	2	2	0	0	2	2	2	3	2	2	0	0	2	2	0	0	6	6			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr4:435533A>G	ENST00000338977.5	-	2	2735	c.2687T>C	c.(2686-2688)cTt>cCt	p.L896P	ZNF721_ENST00000506646.1_Intron|ZNF721_ENST00000507078.1_Intron|ZNF721_ENST00000511833.2_Missense_Mutation_p.L908P|ABCA11P_ENST00000451020.2_RNA			Q8TF20	ZN721_HUMAN	zinc finger protein 721	896					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						ATGTGCATAAAGATTTGCAGA	0.368																																					p.I908T		Atlas-SNP	.											.	ZNF721	205	.	0			c.T2723C						PASS	.						62	65	64					4																	435533		2011	4220	6231	SO:0001583	missense	170960	exon3			GCATAAAGATTTG	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.2687T>C	4.37:g.435533A>G	ENSP00000340524:p.Leu896Pro	111	0	0		135	38	0.281481	NM_133474	Q69YG7	Missense_Mutation	SNP	ENST00000338977.5	37		.	.	.	.	.	.	.	.	.	.	A	10.93	1.489800	0.26686	.	.	ENSG00000182903	ENST00000338977;ENST00000511833	T;T	0.42900	0.96;0.96	0.539	-1.08	0.09936	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.67325	0.2881	H	0.96430	3.82	0.09310	N	0.999993	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.70716	0.934;0.934;0.97	T	0.56347	-0.7994	9	0.72032	D	0.01	.	3.4437	0.07473	0.654:0.0:0.0:0.346	.	896;908;908	Q8TF20;D9N162;Q8TF20-2	ZN721_HUMAN;.;.	P	896;908	ENSP00000340524:L896P;ENSP00000428878:L908P	ENSP00000340524:L896P	L	-	2	0	ZNF721	425533	0.792000	0.28813	0.001000	0.08648	0.017000	0.09413	6.207000	0.72159	-0.660000	0.05352	0.172000	0.16884	CTT	.	.	none		0.368	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474		G	435533	A	G	435533	3	3	18	1	0	0	0	0	1	0	0	0	18137	72	3	3	52	3	ZNF721	4	435533	Missense_Mutation	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10	68471	435533	190718743	47	2434											
TADA2B	93624	hgsc.bcm.edu	37	chr4	7056150	7056150	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccacgtggacatgtacgtgcGgaagctgaaagagagacagc	13	5	14	9	3	0	3	0	1	0	2	0	6	0	5	1	2	4	2	1	2	3	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr4:7056150G>A	ENST00000310074.7	+	2	821	c.632G>A	c.(631-633)cGg>cAg	p.R211Q	TADA2B_ENST00000512388.1_Missense_Mutation_p.R136Q|TADA2B_ENST00000515646.1_Missense_Mutation_p.R119Q	NM_152293.2	NP_689506.2	Q86TJ2	TAD2B_HUMAN	transcriptional adaptor 2B	211					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)			breast(3)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)	18						ATGTACGTGCGGAAGCTGAAA	0.582																																					p.R211Q		Atlas-SNP	.											TADA2B,rectum,carcinoma,-1,1	TADA2B	29	1	0			c.G632A						PASS	.						83	89	87					4																	7056150		2034	4200	6234	SO:0001583	missense	93624	exon2			ACGTGCGGAAGCT	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.632G>A	4.37:g.7056150G>A	ENSP00000308022:p.Arg211Gln	101	0	0		81	22	0.271605	NM_152293	A0AUJ8|A4QMR7|B3KSN0|B3KU86|Q6MZG9	Missense_Mutation	SNP	ENST00000310074.7	37	CCDS47007.1	.	.	.	.	.	.	.	.	.	.	G	17.00	3.277741	0.59758	.	.	ENSG00000173011	ENST00000506692;ENST00000310074;ENST00000512388;ENST00000515646;ENST00000510704	T;T;T;T;T	0.44881	0.91;0.99;0.99;0.99;0.99	5.29	4.41	0.53225	.	0.000000	0.85682	D	0.000000	T	0.52725	0.1752	L	0.39633	1.23	0.80722	D	1	D;D	0.89917	1.0;0.975	D;B	0.70227	0.968;0.31	T	0.44590	-0.9318	10	0.24483	T	0.36	-38.7557	14.8658	0.70416	0.0:0.0:0.8552:0.1448	.	136;211	Q86TJ2-2;Q86TJ2	.;TAD2B_HUMAN	Q	119;211;136;119;119	ENSP00000422398:R119Q;ENSP00000308022:R211Q;ENSP00000423947:R136Q;ENSP00000423181:R119Q;ENSP00000425731:R119Q	ENSP00000308022:R211Q	R	+	2	0	TADA2B	7107051	1.000000	0.71417	0.990000	0.47175	0.995000	0.86356	9.325000	0.96381	1.163000	0.42636	0.561000	0.74099	CGG	.	.	none		0.582	TADA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358687.2	NM_152293		A	7056150	G	A	7056150	3	1	18	1	0	0	0	0	1	0	0	0	15526	1116	39	1	638	1	TADA2B	4	7056150	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	6620617	7056150	184098126	48	2435											
LIMCH1	22998	hgsc.bcm.edu	37	chr4	41648713	41648713	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccaatcccatgaaatacctgCggcaacagtcactgcctcca	12	7	6	16	1	1	1	1	1	0	0	3	1	3	1	5	1	4	1	5	1	4	1	rs143733086		TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr4:41648713C>T	ENST00000313860.7	+	12	1522	c.1468C>T	c.(1468-1470)Cgg>Tgg	p.R490W	LIMCH1_ENST00000511496.1_Missense_Mutation_p.R331W|LIMCH1_ENST00000508501.1_Missense_Mutation_p.R490W|LIMCH1_ENST00000396595.3_Missense_Mutation_p.R336W|LIMCH1_ENST00000512632.1_Missense_Mutation_p.R490W|LIMCH1_ENST00000513024.1_Missense_Mutation_p.R319W|LIMCH1_ENST00000514096.1_Missense_Mutation_p.R331W|LIMCH1_ENST00000381753.4_Missense_Mutation_p.R324W|LIMCH1_ENST00000509277.1_Missense_Mutation_p.R324W|LIMCH1_ENST00000512946.1_Missense_Mutation_p.R490W|LIMCH1_ENST00000512820.1_Missense_Mutation_p.R478W|LIMCH1_ENST00000503057.1_Missense_Mutation_p.R875W	NM_014988.2	NP_055803.2	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1	490					actomyosin structure organization (GO:0031032)		zinc ion binding (GO:0008270)	p.R875W(1)|p.R490W(1)		central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(5)	41						GAAATACCTGCGGCAACAGTC	0.498													C|||	1	0.000199681	0.0	0.0	5008	,	,		20033	0.001		0.0	False		,,,				2504	0.0				p.R490W		Atlas-SNP	.											LIMCH1_ENST00000503057,NS,carcinoma,0,1	LIMCH1	233	1	2	Substitution - Missense(2)	prostate(2)	c.C1468T						PASS	.						220	224	223					4																	41648713		2203	4300	6503	SO:0001583	missense	22998	exon12			TACCTGCGGCAAC	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.1468C>T	4.37:g.41648713C>T	ENSP00000316891:p.Arg490Trp	174	0	0		150	8	0.0533333	NM_014988	A8MXC3|E9PHM7|Q503B5|Q5CZB1|Q5CZB6|Q5H9S8|Q68E07|Q6PJ44|Q7Z3G5|Q8N3S9|Q8N6M2	Missense_Mutation	SNP	ENST00000313860.7	37	CCDS33977.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	18.78	3.697333	0.68386	.	.	ENSG00000064042	ENST00000513024;ENST00000508501;ENST00000512946;ENST00000313860;ENST00000512632;ENST00000512820;ENST00000503057;ENST00000511496;ENST00000313875;ENST00000514096;ENST00000509277;ENST00000396595;ENST00000381753	T;T;T;T;T;T;T;T;T;T;T;T	0.55930	0.94;1.15;1.1;1.16;0.94;1.16;0.52;0.49;0.52;0.94;0.94;0.53	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.70133	0.3189	M	0.68952	2.095	0.80722	D	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	0.91635	0.982;0.982;0.987;0.995;0.996;0.997;0.995;0.999;0.997;0.999;0.997	T	0.72384	-0.4310	10	0.87932	D	0	-18.4384	13.7854	0.63105	0.2558:0.7442:0.0:0.0	.	241;324;490;324;336;875;319;478;490;490;490	B7Z3G0;E9PDJ9;D6RD46;Q9UPQ0-9;Q9UPQ0-6;G5EA03;Q9UPQ0-5;Q9UPQ0-4;E9PHM7;Q9UPQ0-2;Q9UPQ0	.;.;.;.;.;.;.;.;.;.;LIMC1_HUMAN	W	319;490;490;490;490;478;875;331;874;331;324;336;324	ENSP00000425222:R319W;ENSP00000424825:R490W;ENSP00000424645:R490W;ENSP00000316891:R490W;ENSP00000427045:R490W;ENSP00000424437:R478W;ENSP00000425631:R875W;ENSP00000421242:R331W;ENSP00000426334:R331W;ENSP00000422864:R324W;ENSP00000379840:R336W;ENSP00000371172:R324W	ENSP00000316891:R490W	R	+	1	2	LIMCH1	41343470	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.662000	0.37418	2.675000	0.91044	0.591000	0.81541	CGG	C|1.000;T|0.000	0.000	strong		0.498	LIMCH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361249.2	NM_014988		T	41648713	C	T	41648713	3	4	18	1	0	0	0	0	1	0	0	0	8806	759	27	1	1542	1	LIMCH1	4	41648713	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	34592563	41648713	149505563	49	2436											
UGT2B15	7367	hgsc.bcm.edu	37	chr4	69433904	69433904	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaaatgtattttttgaaataCtatatgtccatctatcgaac	15	16	4	6	1	1	1	0	1	1	0	3	2	2	1	1	0	2	1	1	0	9	8			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr4:69433904C>T	ENST00000317746.2	-	1	341	c.299G>A	c.(298-300)aGt>aAt	p.S100N		NM_001077.3	NP_001068.1	O75795	UDB17_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B17	100					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)	TTTTGAAATACTATATGTCCA	0.264																																					p.S100N	Melanoma(18;649 833 28984 37818 38500)	Atlas-SNP	.											.	UGT2B17	34	.	0			c.G299A						PASS	.						44	49	47					4																	69433904		2056	3898	5954	SO:0001583	missense	7367	exon1			GAAATACTATATG	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.299G>A	4.37:g.69433904C>T	ENSP00000320401:p.Ser100Asn	306	0	0		366	88	0.240437	NM_001077		Missense_Mutation	SNP	ENST00000317746.2	37	CCDS3523.1	.	.	.	.	.	.	.	.	.	.	c	2.171	-0.389799	0.04932	.	.	ENSG00000197888	ENST00000317746	T	0.58940	0.3	2.41	1.19	0.21007	.	0.508000	0.17225	U	0.182199	T	0.24509	0.0594	N	0.02802	-0.49	0.09310	N	1	.	.	.	.	.	.	T	0.13495	-1.0507	8	0.22109	T	0.4	.	4.3641	0.11216	0.0:0.3431:0.0:0.6569	.	.	.	.	N	100	ENSP00000320401:S100N	ENSP00000320401:S100N	S	-	2	0	UGT2B17	69116499	0.001000	0.12720	0.001000	0.08648	0.017000	0.09413	0.888000	0.28268	0.205000	0.20568	-0.451000	0.05528	AGT	.	.	none		0.264	UGT2B17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251436.1	NM_001077		T	69433904	C	T	69433904	3	4	18	1	0	0	0	0	1	0	0	0	16973	565	20	2	1317	2	UGT2B15	4	69433904	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	27785191	69433904	121720372	50	2437											
NAA11	84779	hgsc.bcm.edu	37	chr4	80246356	80246356	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	catgctctaggaggtggaatCcgagctttctgagctgtcct	7	12	12	10	1	2	1	0	1	2	0	4	4	4	3	2	3	3	3	2	3	2	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr4:80246356C>T	ENST00000286794.4	-	1	848	c.676G>A	c.(676-678)Gat>Aat	p.D226N	NAA11_ENST00000513733.1_5'UTR	NM_032693.2	NP_116082.1	Q9BSU3	NAA11_HUMAN	N(alpha)-acetyltransferase 11, NatA catalytic subunit	226					N-terminal protein amino acid acetylation (GO:0006474)	NatA complex (GO:0031415)|nucleus (GO:0005634)	peptide alpha-N-acetyltransferase activity (GO:0004596)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|pancreas(1)|skin(2)	23						GAGGTGGAATCCGAGCTTTCT	0.527																																					p.D226N		Atlas-SNP	.											.	NAA11	43	.	0			c.G676A						PASS	.						59	60	60					4																	80246356		2081	4216	6297	SO:0001583	missense	84779	exon1			TGGAATCCGAGCT		CCDS47084.1	4q21.23	2010-05-07	2010-01-14	2010-01-14		ENSG00000156269	2.3.1.88	"N(alpha)-acetyltransferase subunits"	28125	protein-coding gene	gene with protein product			"ARD1 homolog B (S. cerevisiae)"	ARD1B		16638120, 19660095	Standard	NM_032693		Approved	ARD2, hARD2	uc003hlt.4	Q9BSU3		ENST00000286794.4:c.676G>A	4.37:g.80246356C>T	ENSP00000286794:p.Asp226Asn	196	0	0		171	38	0.222222	NM_032693	Q66K19|Q6P479	Missense_Mutation	SNP	ENST00000286794.4	37	CCDS47084.1	.	.	.	.	.	.	.	.	.	.	C	6.267	0.417331	0.11870	.	.	ENSG00000156269	ENST00000286794	T	0.60040	0.22	4.95	0.0217	0.14130	.	0.589208	0.15884	N	0.239915	T	0.41949	0.1181	L	0.42245	1.32	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.21280	-1.0250	10	0.28530	T	0.3	-1.0315	5.6297	0.17504	0.0:0.4997:0.2646:0.2357	.	226	Q9BSU3	NAA11_HUMAN	N	226	ENSP00000286794:D226N	ENSP00000286794:D226N	D	-	1	0	NAA11	80465380	0.373000	0.25073	0.001000	0.08648	0.002000	0.02628	0.690000	0.25451	-0.135000	0.11495	0.655000	0.94253	GAT	.	.	none		0.527	NAA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362922.1			T	80246356	C	T	80246356	3	4	18	1	0	0	0	0	1	0	0	0	10126	855	30	2	17	2	NAA11	4	80246356	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	10812452	80246356	110907920	51	2438											
GRID2	2895	hgsc.bcm.edu	37	chr4	94376873	94376873	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atcgtgaaaatgtggtggacTttacgacacgttacatggac	12	11	11	7	3	0	1	0	1	0	0	1	4	0	3	0	3	2	1	0	3	4	3			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr4:94376873T>G	ENST00000282020.4	+	11	1864	c.1606T>G	c.(1606-1608)Ttt>Gtt	p.F536V	GRID2_ENST00000510992.1_Missense_Mutation_p.F441V	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	536					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)		TGTGGTGGACTTTACGACACG	0.433																																					p.F536V		Atlas-SNP	.											.	GRID2	233	.	0			c.T1606G						PASS	.						143	131	135					4																	94376873		2203	4300	6503	SO:0001583	missense	2895	exon11			GTGGACTTTACGA	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.1606T>G	4.37:g.94376873T>G	ENSP00000282020:p.Phe536Val	178	0	0		184	47	0.255435	NM_001510	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Missense_Mutation	SNP	ENST00000282020.4	37	CCDS3637.1	.	.	.	.	.	.	.	.	.	.	T	28.4	4.913732	0.92178	.	.	ENSG00000152208	ENST00000282020;ENST00000510992	T;T	0.54479	0.57;0.57	5.97	5.97	0.96955	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	D	0.82761	0.5107	H	0.97516	4.02	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.85130	0.997;0.997	D	0.88958	0.3391	10	0.87932	D	0	.	16.4608	0.84044	0.0:0.0:0.0:1.0	.	441;536	E9PH24;O43424	.;GRID2_HUMAN	V	536;441	ENSP00000282020:F536V;ENSP00000421257:F441V	ENSP00000282020:F536V	F	+	1	0	GRID2	94595896	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.040000	0.89188	2.288000	0.76882	0.533000	0.62120	TTT	.	.	none		0.433	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2			G	94376873	T	G	94376873	3	3	18	1	0	0	0	0	1	0	0	0	6781	1609	56	5	1648	5	GRID2	4	94376873	Missense_Mutation	SNP	T	TCGA-FF-A7CR-01A-11D-A382-10	14130517	94376873	96777403	52	2439											
NHEDC2	133308	hgsc.bcm.edu	37	chr4	103966055	103966055	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tatttctttcacctggtcacGgcttggaaagtactgaatga	10	14	9	8	1	3	2	2	2	1	0	3	3	3	3	1	3	1	2	1	3	4	5			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr4:103966055G>A	ENST00000394785.3	-	8	1619	c.988C>T	c.(988-990)Cgt>Tgt	p.R330C	SLC9B2_ENST00000503103.1_Missense_Mutation_p.R273C|SLC9B2_ENST00000339611.4_Missense_Mutation_p.R330C|SLC9B2_ENST00000362026.3_Missense_Mutation_p.R330C|SLC9B2_ENST00000503230.1_Missense_Mutation_p.R273C	NM_178833.4	NP_849155.2	Q86UD5	SL9B2_HUMAN	solute carrier family 9, subfamily B (NHA2, cation proton antiporter 2), member 2	330					ion transmembrane transport (GO:0034220)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	solute:proton antiporter activity (GO:0015299)										ACCTGGTCACGGCTTGGAAAG	0.408																																					p.R330C		Atlas-SNP	.											NHEDC2,colon,carcinoma,+1,2	.	.	2	0			c.C988T						PASS	.						143	156	151					4																	103966055		2203	4300	6503	SO:0001583	missense	133308	exon8			GGTCACGGCTTGG	AK172823	CCDS3662.1, CCDS75173.1, CCDS75174.1	4q24	2013-05-22	2012-03-22	2011-08-03	ENSG00000164038	ENSG00000164038		"Solute carriers"	25143	protein-coding gene	gene with protein product		611789	"Na+/H+ exchanger domain containing 2", "solute carrier family 9, subfamily B (cation proton antiporter 2), member 2"	NHEDC2		18600791	Standard	XM_005262758		Approved	FLJ23984, NHA2	uc003hwy.3	Q86UD5	OTTHUMG00000131125	ENST00000394785.3:c.988C>T	4.37:g.103966055G>A	ENSP00000378265:p.Arg330Cys	358	0	0		383	76	0.198433	NM_178833	B5ME52|Q6ZMD8|Q96D95	Missense_Mutation	SNP	ENST00000394785.3	37	CCDS3662.1	.	.	.	.	.	.	.	.	.	.	G	16.27	3.076292	0.55753	.	.	ENSG00000164038	ENST00000362026;ENST00000506288;ENST00000339611;ENST00000394785;ENST00000503103;ENST00000503230	T;T;T;T;T;T	0.16897	2.31;2.31;2.31;2.31;2.31;2.31	5.03	-2.47	0.06442	.	1.386590	0.04153	N	0.321639	T	0.26991	0.0661	L	0.56199	1.76	0.23287	N	0.997975	D;D;B;D	0.64830	0.994;0.971;0.146;0.98	P;P;B;P	0.57244	0.816;0.697;0.04;0.553	T	0.29640	-1.0005	10	0.54805	T	0.06	-0.6348	4.0241	0.09678	0.1963:0.0649:0.4217:0.3172	.	273;273;330;330	B7Z676;E9PE63;Q86UD5-2;Q86UD5	.;.;.;SL9B2_HUMAN	C	330;230;330;330;273;273	ENSP00000354574:R330C;ENSP00000421943:R230C;ENSP00000345241:R330C;ENSP00000378265:R330C;ENSP00000425385:R273C;ENSP00000422477:R273C	ENSP00000345241:R330C	R	-	1	0	SLC9B2	104185504	0.504000	0.26123	0.964000	0.40570	0.872000	0.50106	0.737000	0.26144	-0.290000	0.09025	-0.671000	0.03813	CGT	.	.	none		0.408	SLC9B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253805.1	NM_178833		A	103966055	G	A	103966055	3	1	18	1	0	0	0	0	1	0	0	0	10410	1116	39	1	645	1	NHEDC2	4	103966055	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	9589182	103966055	87188221	53	2440											
MAML3	55534	hgsc.bcm.edu	37	chr4	140811112	140811123	+	In_Frame_Del	DEL	TGCTGCTGCTGT	TGCTGCTGCTGT	-																															gctgctgctgctgctgctgcTgctgctgctgttgctgttgc																								rs62344938|rs62344939		TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	TGCTGCTGCTGT	TGCTGCTGCTGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr4:140811112_140811123delTGCTGCTGCTGT	ENST00000509479.2	-	2	2323_2334	c.1467_1478delACAGCAGCAGCA	c.(1465-1479)caacagcagcagcag>cag	p.489_493QQQQQ>Q	MAML3_ENST00000398940.1_In_Frame_Del_p.28_32QQQQQ>Q|MAML3_ENST00000327122.5_In_Frame_Del_p.333_337QQQQQ>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						PASS	.			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	4.37:g.140811112_140811123delTGCTGCTGCTGT	ENSP00000421180:p.Gln505_Gln508del	92	0	0		120	23	0.191667	NM_018717		In_Frame_Del	DEL	ENST00000509479.2	37	CCDS54805.1																																																																																			.	.	alt		0.547	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			-	140811123	TGCTGCTGCTGT	-	140811112	7	5	18	1	0	1	0	1	0	0	0	0	9216	1580	55	0	1946	0	MAML3	4	140811112	In_Frame_Del	DEL	TGCTGCTGCTGT	TCGA-FF-A7CR-01A-11D-A382-10	36845057	140811112	50343164	54	2441											
INPP4B	8821	hgsc.bcm.edu	37	chr4	143044563	143044563	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataaaaccacaaaccaatccAgcaagctgaaaaaaaaatat	24	5	3	9	0	0	1	0	1	0	0	1	1	1	1	3	0	4	2	3	0	10	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr4:143044563A>C	ENST00000513000.1	-	21	2332	c.1899T>G	c.(1897-1899)gcT>gcG	p.A633A	INPP4B_ENST00000508116.1_Silent_p.A633A|INPP4B_ENST00000308502.4_Silent_p.A633A|INPP4B_ENST00000262992.4_Silent_p.A633A|INPP4B_ENST00000509777.1_Silent_p.A633A	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa	633					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)					AAACCAATCCAGCAAGCTGAA	0.358																																					p.A633A		Atlas-SNP	.											.	INPP4B	132	.	0			c.T1899G						PASS	.						69	67	68					4																	143044563		2203	4300	6503	SO:0001819	synonymous_variant	8821	exon21			CAATCCAGCAAGC	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.1899T>G	4.37:g.143044563A>C		76	0	0		96	25	0.260417	NM_003866	Q2TAI2|Q5XLE7|Q6IN59|Q6PJB4	Silent	SNP	ENST00000513000.1	37	CCDS3757.1																																																																																			.	.	none		0.358	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	NM_003866		C	143044563	A	C	143044563	2	2	18	1	0	0	0	0	0	0	0	1	7762	175	7	5		5	INPP4B	4	143044563	Silent	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10	2233451	143044563	48109713	55	2442											
HHIP	64399	hgsc.bcm.edu	37	chr4	145658962	145658962	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggaggtgtctgtgttagaccGaacaagtgcctctgtaaaaa	12	10	12	7	1	2	1	0	0	2	1	2	3	2	2	2	2	2	2	2	2	6	2	rs35379077	byFrequency	TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr4:145658962G>A	ENST00000296575.3	+	13	2611	c.1956G>A	c.(1954-1956)ccG>ccA	p.P652P		NM_022475.2	NP_071920.1	Q96QV1	HHIP_HUMAN	hedgehog interacting protein	652	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)		GTGTTAGACCGAACAAGTGCC	0.448																																					p.P652P		Atlas-SNP	.											.	HHIP	100	.	0			c.G1956A						PASS	.	G		0,4406		0,0,2203	145	123	131		1956	-10.8	0.2	4	dbSNP_126	131	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	HHIP	NM_022475.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		652/701	145658962	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	64399	exon13			TAGACCGAACAAG	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.1956G>A	4.37:g.145658962G>A		132	0	0		134	35	0.261194	NM_022475	Q6PK09|Q8NCI7|Q9BXK3|Q9H1J4|Q9H7E7	Silent	SNP	ENST00000296575.3	37	CCDS3762.1																																																																																			G|1.000;A|0.000	0.000	strong		0.448	HHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364887.2			A	145658962	G	A	145658962	2	1	18	1	0	0	0	0	0	0	0	1	7101	1045	37	1		1	HHIP	4	145658962	Silent	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	2614399	145658962	45495314	56	2443											
DNAH5	1767	hgsc.bcm.edu	37	chr5	13845064	13845064	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcaggatctgagacgaagAaaaaccgaggaaagcacagt	17	3	14	7	2	1	2	0	1	1	2	1	7	1	4	1	3	2	2	1	3	4	0			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr5:13845064A>G	ENST00000265104.4	-	32	5257	c.5153T>C	c.(5152-5154)tTc>tCc	p.F1718S		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1718	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)					TGAGACGAAGAAAAACCGAGG	0.438									Kartagener syndrome																												p.F1718S		Atlas-SNP	.											DNAH5,scalp,malignant_melanoma,-1,1	DNAH5	868	1	0			c.T5153C						scavenged	.						76	78	77					5																	13845064		2203	4300	6503	SO:0001583	missense	1767	exon32	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	ACGAAGAAAAACC	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.5153T>C	5.37:g.13845064A>G	ENSP00000265104:p.Phe1718Ser	78	1	0.0128205		82	28	0.341463	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.068037	0.76301	.	.	ENSG00000039139	ENST00000265104	T	0.65549	-0.16	4.85	4.85	0.62838	Dynein heavy chain, domain-2 (1);	0.052439	0.85682	D	0.000000	D	0.84822	0.5557	H	0.97707	4.06	0.80722	D	1	P	0.42735	0.788	P	0.58013	0.831	D	0.89587	0.3825	10	0.87932	D	0	.	14.5198	0.67842	1.0:0.0:0.0:0.0	.	1718	Q8TE73	DYH5_HUMAN	S	1718	ENSP00000265104:F1718S	ENSP00000265104:F1718S	F	-	2	0	DNAH5	13898064	1.000000	0.71417	1.000000	0.80357	0.484000	0.33280	9.141000	0.94612	1.840000	0.53500	0.529000	0.55759	TTC	.	.	none		0.438	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		G	13845064	A	G	13845064	3	3	18	1	0	0	0	0	1	0	0	0	4606	246	9	3	8913	3	DNAH5	5	13845064	Missense_Mutation	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10		13845064	167070196	57	2444											
SLC45A2	51151	hgsc.bcm.edu	37	chr5	33964023	33964023	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtgagcaccaatgcagagaAgaagaacatgacctggaatt	17	6	11	7	0	0	5	0	2	0	3	0	7	0	6	2	1	3	2	2	1	5	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr5:33964023A>C	ENST00000296589.4	-	3	807	c.661T>G	c.(661-663)Ttc>Gtc	p.F221V	SLC45A2_ENST00000509381.1_Intron|SLC45A2_ENST00000342059.3_Missense_Mutation_p.F162V|SLC45A2_ENST00000345083.5_Intron|SLC45A2_ENST00000382102.3_Missense_Mutation_p.F221V	NM_016180.3	NP_057264	Q9UMX9	S45A2_HUMAN	solute carrier family 45, member 2	221			Missing (in OCA4). {ECO:0000269|PubMed:14722913}.		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(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(25)|ovary(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48						AATGCAGAGAAGAAGAACATG	0.498																																					p.F221V	Ovarian(31;380 859 8490 22203 49048)	Atlas-SNP	.											.	SLC45A2	100	.	0			c.T661G						PASS	.						112	109	110					5																	33964023		2203	4300	6503	SO:0001583	missense	51151	exon3			CAGAGAAGAAGAA	AF172849	CCDS3901.1, CCDS43308.1, CCDS75232.1	5p13.3	2013-08-06	2005-10-06	2005-10-06	ENSG00000164175	ENSG00000164175		"Solute carriers"	16472	protein-coding gene	gene with protein product		606202	"membrane associated transporter"	MATP		11916009, 11574907	Standard	NM_001012509		Approved	AIM-1, OCA4	uc003jid.3	Q9UMX9	OTTHUMG00000090719	ENST00000296589.4:c.661T>G	5.37:g.33964023A>C	ENSP00000296589:p.Phe221Val	105	0	0		125	23	0.184	NM_016180	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000296589.4	37	CCDS3901.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.579386	0.86645	.	.	ENSG00000164175	ENST00000296589;ENST00000342059;ENST00000382102;ENST00000510600	D;T;D;D	0.92495	-3.05;-1.29;-3.05;-3.05	5.93	5.93	0.95920	Major facilitator superfamily domain, general substrate transporter (1);	0.045176	0.85682	D	0.000000	D	0.94663	0.8279	M	0.75884	2.315	0.80722	D	1	P;B	0.50066	0.931;0.443	P;B	0.59115	0.852;0.326	D	0.93153	0.6551	10	0.22706	T	0.39	-18.1182	15.3582	0.74443	1.0:0.0:0.0:0.0	.	221;221	Q9UMX9-4;Q9UMX9	.;S45A2_HUMAN	V	221;162;221;46	ENSP00000296589:F221V;ENSP00000341014:F162V;ENSP00000371534:F221V;ENSP00000424010:F46V	ENSP00000296589:F221V	F	-	1	0	SLC45A2	33999780	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	4.984000	0.63838	2.270000	0.75569	0.460000	0.39030	TTC	.	.	none		0.498	SLC45A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207443.2	NM_016180		C	33964023	A	C	33964023	3	2	18	1	0	0	0	0	1	0	0	0	14656	72	3	5	966	5	SLC45A2	5	33964023	Missense_Mutation	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10	20118959	33964023	146951237	58	2445											
PLK2	10769	hgsc.bcm.edu	37	chr5	57755718	57755718	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtccgctccgcaacccttGcccagcgcctgctcgcacat	6	7	9	19	4	0	0	0	0	0	0	3	1	2	0	5	0	4	4	5	0	1	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr5:57755718G>A	ENST00000274289.3	-	1	369	c.69C>T	c.(67-69)ggC>ggT	p.G23G	PLK2_ENST00000502671.1_5'Flank	NM_001252226.1|NM_006622.3	NP_001239155.1|NP_006613.2	Q9NYY3	PLK2_HUMAN	polo-like kinase 2	23					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)		CGCAACCCTTGCCCAGCGCCT	0.697																																					p.G23G		Atlas-SNP	.											.	PLK2	71	.	0			c.C69T						PASS	.						18	21	20					5																	57755718		2203	4294	6497	SO:0001819	synonymous_variant	10769	exon1			ACCCTTGCCCAGC		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.69C>T	5.37:g.57755718G>A		106	0	0		151	29	0.192053	NM_006622	O60679|Q96CV7|Q9UE61	Silent	SNP	ENST00000274289.3	37	CCDS3974.1																																																																																			.	.	none		0.697	PLK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214150.1	NM_006622		A	57755718	G	A	57755718	2	1	18	1	0	0	0	0	0	0	0	1	12105	1306	46	2		2	PLK2	5	57755718	Silent	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	23791695	57755718	123159542	59	2446											
MAST4	375449	hgsc.bcm.edu	37	chr5	66462402	66462402	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ctgagctgctcctccagcttCcctgaaaccagggccggagt	7	8	11	15	1	0	2	0	2	0	0	3	3	3	3	5	2	4	3	5	2	1	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr5:66462402C>T	ENST00000403625.2	+	29	7690	c.7395C>T	c.(7393-7395)ttC>ttT	p.F2465F	MAST4_ENST00000403666.1_Silent_p.F2276F|MAST4_ENST00000404260.3_Silent_p.F2468F|MAST4_ENST00000405643.1_Silent_p.F2286F|MAST4_ENST00000261569.7_Silent_p.F2271F	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	2468						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)		CCTCCAGCTTCCCTGAAACCA	0.632											OREG0016638	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F2465F		Atlas-SNP	.											.	MAST4	218	.	0			c.C7395T						PASS	.						17	21	20					5																	66462402		2005	4179	6184	SO:0001819	synonymous_variant	375449	exon29			CAGCTTCCCTGAA	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.7395C>T	5.37:g.66462402C>T		99	0	0	1092	136	36	0.264706	NM_001164664	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Silent	SNP	ENST00000403625.2	37	CCDS54861.1	.	.	.	.	.	.	.	.	.	.	C	2.439	-0.328963	0.05314	.	.	ENSG00000069020	ENST00000443808	.	.	.	4.94	-2.72	0.05968	.	.	.	.	.	T	0.57710	0.2072	.	.	.	0.44207	D	0.997031	.	.	.	.	.	.	T	0.57046	-0.7878	4	.	.	.	-8.1125	12.3345	0.55058	0.0:0.7809:0.0:0.2191	.	.	.	.	S	1522	.	.	P	+	1	0	MAST4	66498158	0.030000	0.19436	0.223000	0.23860	0.279000	0.26890	0.023000	0.13533	-0.391000	0.07763	-0.379000	0.06801	CCC	.	.	none		0.632	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			T	66462402	C	T	66462402	2	4	18	1	0	0	0	0	0	0	0	1	9336	854	30	2		2	MAST4	5	66462402	Silent	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	8706684	66462402	114452858	60	2447											
GIN1	54826	hgsc.bcm.edu	37	chr5	102442522	102442522	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gctccactgtcattttcatgGcattctcttaagactttctt	7	18	5	11	0	4	1	2	0	2	1	6	1	5	1	1	1	0	2	1	1	1	6			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr5:102442522G>A	ENST00000399004.2	-	3	325	c.231C>T	c.(229-231)tgC>tgT	p.C77C	GIN1_ENST00000511400.1_5'Flank|GIN1_ENST00000508629.1_Silent_p.C77C	NM_017676.2	NP_060146.2	Q9NXP7	GIN1_HUMAN	gypsy retrotransposon integrase 1	77					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)		CATTTTCATGGCATTCTCTTA	0.353																																					p.C77C		Atlas-SNP	.											.	GIN1	53	.	0			c.C231T						PASS	.						103	95	98					5																	102442522		1844	4092	5936	SO:0001819	synonymous_variant	54826	exon3			TTCATGGCATTCT	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.231C>T	5.37:g.102442522G>A		430	0	0		492	31	0.0630081	NM_017676	B2RXF7|B4DIV4|Q6AI03|Q96BR2	Silent	SNP	ENST00000399004.2	37	CCDS43349.1																																																																																			.	.	none		0.353	GIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370478.3	NM_017676		A	102442522	G	A	102442522	2	1	18	1	0	0	0	0	0	0	0	1	6394	1195	42	2		2	GIN1	5	102442522	Silent	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	35980120	102442522	78472738	61	2448											
NDST1	3340	hgsc.bcm.edu	37	chr5	149901306	149901306	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtactgtgtggcctacggcGtgggcatcattggcttcttc	5	13	13	10	2	2	0	1	0	1	0	3	0	2	0	1	4	2	3	1	4	2	5			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr5:149901306G>A	ENST00000261797.6	+	2	992	c.490G>A	c.(490-492)Gtg>Atg	p.V164M	NDST1_ENST00000523767.1_Missense_Mutation_p.V164M	NM_001543.4	NP_001534.1	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	164	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)			GGCCTACGGCGTGGGCATCAT	0.542																																					p.V164M		Atlas-SNP	.											.	NDST1	79	.	0			c.G490A						PASS	.						89	90	90					5																	149901306		2203	4300	6503	SO:0001583	missense	3340	exon2			TACGGCGTGGGCA	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.490G>A	5.37:g.149901306G>A	ENSP00000261797:p.Val164Met	33	0	0		31	9	0.290323	NM_001543	Q96E57	Missense_Mutation	SNP	ENST00000261797.6	37	CCDS34277.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.949559	0.92660	.	.	ENSG00000070614	ENST00000523767;ENST00000261797	T;T	0.58210	0.35;0.69	4.96	4.96	0.65561	.	0.185114	0.46145	D	0.000313	T	0.77883	0.4197	M	0.91612	3.225	0.80722	D	1	D;D;D	0.64830	0.994;0.984;0.994	D;P;D	0.65010	0.931;0.704;0.931	T	0.82653	-0.0351	9	.	.	.	.	18.7747	0.91907	0.0:0.0:1.0:0.0	.	164;164;164	E7EVJ3;P52848-2;P52848	.;.;NDST1_HUMAN	M	164	ENSP00000428604:V164M;ENSP00000261797:V164M	.	V	+	1	0	NDST1	149881499	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.539000	0.98076	2.733000	0.93635	0.655000	0.94253	GTG	.	.	none		0.542	NDST1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374314.2	NM_001543		A	149901306	G	A	149901306	3	1	18	1	0	0	0	0	1	0	0	0	10264	1145	40	1	492	1	NDST1	5	149901306	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	47458784	149901306	31013954	62	2449											
IRF4	3662	hgsc.bcm.edu	37	chr6	393318	393318	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcttccgcatcccctggaagCacgcgggcaagcaggactac	9	6	11	15	3	1	0	0	0	1	0	3	2	3	2	3	3	3	4	3	3	3	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr6:393318C>T	ENST00000380956.4	+	2	292	c.166C>T	c.(166-168)Cac>Tac	p.H56Y	IRF4_ENST00000495137.1_Intron	NM_001195286.1|NM_002460.3	NP_001182215.1|NP_002451.2	Q15306	IRF4_HUMAN	interferon regulatory factor 4	56					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)		CCCCTGGAAGCACGCGGGCAA	0.687			T	IGH@	MM																																p.H56Y		Atlas-SNP	.		Dom	yes		6	6p25-p23	3662	interferon regulatory factor 4		L	.	IRF4	65	.	0			c.C166T						PASS	.						32	30	30					6																	393318		2202	4299	6501	SO:0001583	missense	3662	exon2			TGGAAGCACGCGG	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.166C>T	6.37:g.393318C>T	ENSP00000370343:p.His56Tyr	68	0	0		101	20	0.19802	NM_001195286	Q5VUI7|Q99660	Missense_Mutation	SNP	ENST00000380956.4	37	CCDS4469.1	.	.	.	.	.	.	.	.	.	.	C	31	5.080588	0.94050	.	.	ENSG00000137265	ENST00000380956;ENST00000412334	D	0.98493	-4.96	4.58	4.58	0.56647	Interferon regulatory factor, conserved site (1);Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (4);	0.092628	0.85682	D	0.000000	D	0.99272	0.9746	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;1.0	D	0.98982	1.0805	10	0.87932	D	0	-31.5343	17.6301	0.88104	0.0:1.0:0.0:0.0	.	56;56;56	F2Z3D5;Q15306-2;Q15306	.;.;IRF4_HUMAN	Y	56;86	ENSP00000370343:H56Y	ENSP00000370343:H56Y	H	+	1	0	IRF4	338318	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.954000	0.76001	2.399000	0.81585	0.306000	0.20318	CAC	.	.	none		0.687	IRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043638.1			T	393318	C	T	393318	3	4	18	1	0	0	0	0	1	0	0	0	7841	710	25	2	168	2	IRF4	6	393318	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10		393318	170721749	63	2450											
FOXC1	2296	hgsc.bcm.edu	37	chr6	1610903	1610903	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cgccgcagccgcagcccaagGacatggtgaagccgccctat	9	4	12	16	4	0	1	0	1	0	0	0	2	0	2	5	2	3	2	5	2	3	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr6:1610903G>A	ENST00000380874.2	+	1	223	c.223G>A	c.(223-225)Gac>Aac	p.D75N		NM_001453.2	NP_001444.2	Q12948	FOXC1_HUMAN	forkhead box C1	75				QPQPKDMV -> RSRSPRHG (in Ref. 5; AAK13575). {ECO:0000305}.	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)		GCAGCCCAAGGACATGGTGAA	0.652																																					p.D75N	Pancreas(133;719 1821 3197 26645 35015)	Atlas-SNP	.											.	FOXC1	19	.	0			c.G223A						PASS	.						46	48	47					6																	1610903		2203	4300	6503	SO:0001583	missense	2296	exon1			CCCAAGGACATGG	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.223G>A	6.37:g.1610903G>A	ENSP00000370256:p.Asp75Asn	61	0	0		47	13	0.276596	NM_001453	Q86UP7|Q9BYM1|Q9NUE5|Q9UDD0|Q9UP06	Missense_Mutation	SNP	ENST00000380874.2	37	CCDS4473.1	.	.	.	.	.	.	.	.	.	.	g	28.2	4.901869	0.92035	.	.	ENSG00000054598	ENST00000541209;ENST00000380874	D	0.93076	-3.16	3.86	3.86	0.44501	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.41500	U	0.000880	D	0.95465	0.8527	M	0.72894	2.215	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	D	0.96071	0.9046	10	0.72032	D	0.01	.	15.7496	0.77972	0.0:0.0:1.0:0.0	.	75	Q12948	FOXC1_HUMAN	N	75	ENSP00000370256:D75N	ENSP00000370256:D75N	D	+	1	0	FOXC1	1555902	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.589000	0.90817	1.842000	0.53543	0.457000	0.33378	GAC	.	.	none		0.652	FOXC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043450.1			A	1610903	G	A	1610903	3	1	18	1	0	0	0	0	1	0	0	0	6002	1174	41	2	225	2	FOXC1	6	1610903	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	1217585	1610903	169504164	64	2451											
HIST1H1C	3006	hgsc.bcm.edu	37	chr6	26056463	26056463	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catagccggcggcagccaacGcttttttcagagcagccaga	10	7	11	13	3	1	2	1	0	0	2	1	2	1	2	3	2	5	3	3	2	2	4	rs79562358		TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr6:26056463G>A	ENST00000343677.2	-	1	236	c.194C>T	c.(193-195)gCg>gTg	p.A65V		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	65	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				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						GGCAGCCAACGCTTTTTTCAG	0.562													G|||	1	0.000199681	0.0008	0.0	5008	,	,		15415	0.0		0.0	False		,,,				2504	0.0				p.A65V		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.C194T						PASS	.	G	VAL/ALA	0,4406		0,0,2203	82	91	88		194	5.7	1	6	dbSNP_131	88	1,8599	1.2+/-3.3	0,1,4299	no	missense	HIST1H1C	NM_005319.3	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	65/214	26056463	1,13005	2203	4300	6503	SO:0001583	missense	3006	exon1			GCCAACGCTTTTT	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.194C>T	6.37:g.26056463G>A	ENSP00000339566:p.Ala65Val	171	0	0		182	72	0.395604	NM_005319	A8K4I2	Missense_Mutation	SNP	ENST00000343677.2	37	CCDS4577.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	18.31	3.594901	0.66219	0.0	1.16E-4	ENSG00000187837	ENST00000343677	T	0.22134	1.97	5.73	5.73	0.89815	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.111844	0.64402	D	0.000013	T	0.39036	0.1063	M	0.85099	2.735	0.58432	D	0.999992	D	0.62365	0.991	P	0.55667	0.781	T	0.27806	-1.0063	10	0.51188	T	0.08	-17.4652	19.2479	0.93909	0.0:0.0:1.0:0.0	.	65	P16403	H12_HUMAN	V	65	ENSP00000339566:A65V	ENSP00000339566:A65V	A	-	2	0	HIST1H1C	26164442	1.000000	0.71417	1.000000	0.80357	0.011000	0.07611	5.446000	0.66600	2.861000	0.98227	0.655000	0.94253	GCG	G|0.999;A|0.001	0.001	strong		0.562	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319		A	26056463	G	A	26056463	3	1	18	1	0	0	0	0	1	0	0	0	7133	1087	38	1	451	1	HIST1H1C	6	26056463	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	24445560	26056463	145058604	65	2452											
HIST1H4K	8362	hgsc.bcm.edu	37	chr6	27799065	27799065	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacatccatggcggtgaccgTcttgcgcttggcgtgctctg	4	11	13	13	4	2	1	0	1	2	0	3	1	3	1	2	3	2	2	2	3	0	2	rs561516608	byFrequency	TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr6:27799065T>C	ENST00000357549.2	-	1	240	c.241A>G	c.(241-243)Acg>Gcg	p.T81A		NM_003541.2	NP_003532.1	P62805	H4_HUMAN	histone cluster 1, H4k	81					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(1)|endometrium(1)|lung(3)|ovary(1)|prostate(1)	7						GCGGTGACCGTCTTGCGCTTG	0.607																																					p.T81A		Atlas-SNP	.											.	HIST1H4K	15	.	0			c.A241G						PASS	.						24	27	26					6																	27799065		2199	4276	6475	SO:0001583	missense	8362	exon1			TGACCGTCTTGCG	X60483	CCDS4631.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197914	ENSG00000273542		"Histones / Replication-dependent"	4784	protein-coding gene	gene with protein product		602825	"H4 histone family, member D", "histone 1, H4k"	H4FD		9439656, 12408966	Standard	NM_003541		Approved	H4/d, H4F2iii, dJ160A22.1	uc003njr.3	P62805	OTTHUMG00000014488	ENST00000357549.2:c.241A>G	6.37:g.27799065T>C	ENSP00000350159:p.Thr81Ala	353	1	0.00283286		341	128	0.375367	NM_003541	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000357549.2	37	CCDS4631.1	.	.	.	.	.	.	.	.	.	.	.	28.3	4.910440	0.92107	.	.	ENSG00000197914	ENST00000357549	T	0.78003	-1.14	4.25	4.25	0.50352	.	0.000000	0.53938	U	0.000047	T	0.78824	0.4344	.	.	.	0.36651	D	0.877411	.	.	.	.	.	.	T	0.82376	-0.0488	7	0.62326	D	0.03	.	12.857	0.57890	0.0:0.0:0.0:1.0	.	.	.	.	A	81	ENSP00000350159:T81A	ENSP00000350159:T81A	T	-	1	0	HIST1H4K	27907044	1.000000	0.71417	0.992000	0.48379	0.939000	0.58152	7.204000	0.77872	1.679000	0.50963	0.528000	0.53228	ACG	.	.	none		0.607	HIST1H4K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040156.1	NM_003541		C	27799065	T	C	27799065	3	2	18	1	0	0	0	0	1	0	0	0	7184	1667	58	3	74	3	HIST1H4K	6	27799065	Missense_Mutation	SNP	T	TCGA-FF-A7CR-01A-11D-A382-10	1742602	27799065	143316002	66	2453											
PIM1	5292	hgsc.bcm.edu	37	chr6	37138355	37138355	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acatcctggaggttgggatgCtcttgtccaaaatcaactcg	10	11	10	10	1	2	0	1	0	1	0	5	2	4	2	2	3	2	2	2	3	3	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr6:37138355C>T	ENST00000373509.5	+	1	377	c.4C>T	c.(4-6)Ctc>Ttc	p.L2F		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	93					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)	p.L2V(1)|p.L2F(1)		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)	GGTTGGGATGCTCTTGTCCAA	0.701			T	BCL6	NHL																																p.L93F		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,0,3	PIM1	71	3	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.C277T						PASS	.						30	30	30					6																	37138355		2201	4298	6499	SO:0001583	missense	5292	exon1			GGGATGCTCTTGT		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.4C>T	6.37:g.37138355C>T	ENSP00000362608:p.Leu2Phe	65	0	0		64	19	0.296875	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.693535	0.88735	.	.	ENSG00000137193	ENST00000373509	T	0.71222	-0.55	4.05	4.05	0.47172	.	0.000000	0.32147	N	0.006517	T	0.61899	0.2384	N	0.08118	0	0.48830	D	0.999711	D	0.76494	0.999	D	0.66196	0.942	T	0.73933	-0.3826	10	0.72032	D	0.01	.	16.7252	0.85419	0.0:1.0:0.0:0.0	.	93	P11309	PIM1_HUMAN	F	2	ENSP00000362608:L2F	ENSP00000362608:L2F	L	+	1	0	PIM1	37246333	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.672000	0.61597	2.211000	0.71520	0.542000	0.68232	CTC	.	.	none		0.701	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37138355	C	T	37138355	3	4	18	1	0	0	0	0	1	0	0	0	11936	797	28	2	6	2	PIM1	6	37138355	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	9339290	37138355	133976712	67	2454			2	22		9	9	2513	N	G_C_A	5.015395e-20
PIM1	5292	hgsc.bcm.edu	37	chr6	37138380	37138380	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gtccaaaatcaactcgcttgCccacctgcgcgccgcgccct	7	7	8	19	5	1	0	1	0	0	0	3	0	2	0	5	0	3	1	5	0	3	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr6:37138380C>T	ENST00000373509.5	+	1	402	c.29C>T	c.(28-30)gCc>gTc	p.A10V		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	101					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)	AACTCGCTTGCCCACCTGCGC	0.731			T	BCL6	NHL																																p.A101V		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,0,1	PIM1	71	1	0			c.C302T						scavenged	.						30	31	31					6																	37138380		2202	4297	6499	SO:0001583	missense	5292	exon1			CGCTTGCCCACCT		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.29C>T	6.37:g.37138380C>T	ENSP00000362608:p.Ala10Val	60	0	0		65	8	0.123077	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	16.80	3.223561	0.58668	.	.	ENSG00000137193	ENST00000373509	T	0.69806	-0.43	4.2	4.2	0.49525	.	0.229124	0.22580	N	0.058236	T	0.33206	0.0855	N	0.08118	0	0.45439	D	0.998418	P	0.40834	0.73	B	0.34779	0.189	T	0.49579	-0.8925	10	0.52906	T	0.07	.	17.0668	0.86561	0.0:1.0:0.0:0.0	.	101	P11309	PIM1_HUMAN	V	10	ENSP00000362608:A10V	ENSP00000362608:A10V	A	+	2	0	PIM1	37246358	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.592000	0.46171	2.289000	0.77006	0.542000	0.68232	GCC	.	.	none		0.731	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37138380	C	T	37138380	3	4	18	1	0	0	0	0	1	0	0	0	11936	739	26	2	31	2	PIM1	6	37138380	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	25	37138380	133976687	68	2455			2	22		9	9	2513	N	G_C_A	5.015395e-20
PIM1	5292	hgsc.bcm.edu	37	chr6	37138420	37138420	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcaacgacctgcacgccacCaagctggcgcccggtgagag	9	4	13	15	4	0	1	0	1	0	1	0	3	0	1	4	2	4	3	4	2	2	0			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr6:37138420C>T	ENST00000373509.5	+	1	442	c.69C>T	c.(67-69)acC>acT	p.T23T		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	114					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)	TGCACGCCACCAAGCTGGCGC	0.731			T	BCL6	NHL																																p.T114T		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C342T						PASS	.						23	26	25					6																	37138420		2198	4290	6488	SO:0001819	synonymous_variant	5292	exon1			CGCCACCAAGCTG		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.69C>T	6.37:g.37138420C>T		66	0	0		66	26	0.393939	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.731	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37138420	C	T	37138420	2	4	18	1	0	0	0	0	0	0	0	1	11936	581	21	2		2	PIM1	6	37138420	Silent	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	40	37138420	133976647	69	2456			2	22		9	9	2513	N	G_C_A	5.015395e-20
PIM1	5292	hgsc.bcm.edu	37	chr6	37138625	37138625	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggcggcttcggctcggtctaCtcaggcatccgcgtctccga	4	9	13	15	6	3	0	1	0	2	0	7	1	4	0	2	5	1	3	2	5	1	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr6:37138625C>G	ENST00000373509.5	+	2	532	c.159C>G	c.(157-159)taC>taG	p.Y53*		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	144					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)	p.Y53Y(1)		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)	GCTCGGTCTACTCAGGCATCC	0.721			T	BCL6	NHL																																p.Y144X		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,carcinoma,+2,2	PIM1	71	2	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C432G						PASS	.						20	29	26					6																	37138625		2183	4281	6464	SO:0001587	stop_gained	5292	exon2			GGTCTACTCAGGC		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.159C>G	6.37:g.37138625C>G	ENSP00000362608:p.Tyr53*	85	0	0		82	42	0.512195	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Nonsense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	39	7.820184	0.98507	.	.	ENSG00000137193	ENST00000373509	.	.	.	4.64	3.49	0.39957	.	0.347466	0.27618	N	0.018561	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.3647	0.32380	0.0:0.7776:0.0:0.2224	.	.	.	.	X	53	.	ENSP00000362608:Y53X	Y	+	3	2	PIM1	37246603	0.705000	0.27846	0.996000	0.52242	0.994000	0.84299	0.438000	0.21559	2.294000	0.77228	0.549000	0.68633	TAC	.	.	none		0.721	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			G	37138625	C	G	37138625	4	3	18	1	0	0	0	0	0	1	0	0	11936	576	20	4	165	4	PIM1	6	37138625	Nonsense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	205	37138625	133976442	70	2457			2	22		9	9	2513	N	G_C_A	5.015395e-20
PIM1	5292	hgsc.bcm.edu	37	chr6	37138901	37138901	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cggccccctcgcccctgcagCctaatggcactcgagtgccc	5	6	10	20	3	0	0	0	0	0	0	2	1	0	0	6	2	3	2	6	2	1	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr6:37138901C>A	ENST00000373509.5	+	4	614	c.241C>A	c.(241-243)Cct>Act	p.P81T		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	172					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)	GCCCCTGCAGCCTAATGGCAC	0.667			T	BCL6	NHL																																p.P172T		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C514A						PASS	.						45	52	50					6																	37138901		2203	4299	6502	SO:0001630	splice_region_variant	5292	exon4			CTGCAGCCTAATG		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.241-1C>A	6.37:g.37138901C>A		46	0	0		52	28	0.538462	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	12.57	1.977235	0.34848	.	.	ENSG00000137193	ENST00000373509	T	0.62941	-0.01	4.28	4.28	0.50868	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.230218	0.35525	N	0.003156	T	0.33673	0.0871	L	0.28608	0.87	0.41062	D	0.98538	B	0.10296	0.003	B	0.11329	0.006	T	0.15521	-1.0434	9	.	.	.	.	15.0358	0.71744	0.0:1.0:0.0:0.0	.	172	P11309	PIM1_HUMAN	T	81	ENSP00000362608:P81T	.	P	+	1	0	PIM1	37246879	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	4.378000	0.59568	2.371000	0.80710	0.549000	0.68633	CCT	.	.	none		0.667	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		Missense_Mutation	A	37138901	C	A	37138901	5	1	18	1	0	0	0	0	0	0	1	0	11936	753	26	4	255	4	PIM1	6	37138901	Splice_Site	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	276	37138901	133976166	71	2458			2	22		9	9	2513	N	G_C_A	5.015395e-20
PIM1	5292	hgsc.bcm.edu	37	chr6	37138946	37138946	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aagtggtcctgctgaagaagGtgagctcgggtttctccggc	7	10	15	9	2	1	3	0	2	1	1	4	3	2	3	2	4	2	3	2	4	3	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr6:37138946G>A	ENST00000373509.5	+	4	659	c.286G>A	c.(286-288)Gtg>Atg	p.V96M		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	187					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)	GCTGAAGAAGGTGAGCTCGGG	0.652			T	BCL6	NHL																																p.V187M		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.G559A						PASS	.						80	89	86					6																	37138946		2203	4300	6503	SO:0001583	missense	5292	exon4			AAGAAGGTGAGCT		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.286G>A	6.37:g.37138946G>A	ENSP00000362608:p.Val96Met	59	0	0		58	18	0.310345	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.518058	0.85495	.	.	ENSG00000137193	ENST00000373509	T	0.66638	-0.22	4.14	4.14	0.48551	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.077156	0.51477	D	0.000084	T	0.54191	0.1843	N	0.25426	0.745	0.54753	D	0.999985	P	0.37015	0.578	P	0.46076	0.503	T	0.65327	-0.6195	10	0.87932	D	0	.	16.5618	0.84568	0.0:0.0:1.0:0.0	.	187	P11309	PIM1_HUMAN	M	96	ENSP00000362608:V96M	ENSP00000362608:V96M	V	+	1	0	PIM1	37246924	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.549000	0.98106	2.283000	0.76528	0.549000	0.68633	GTG	.	.	none		0.652	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			A	37138946	G	A	37138946	3	1	18	1	0	0	0	0	1	0	0	0	11936	1261	44	2	300	2	PIM1	6	37138946	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	45	37138946	133976121	72	2459			2	22		9	9	2513	N	G_C_A	5.015395e-20
PIM1	5292	hgsc.bcm.edu	37	chr6	37139038	37139038	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctggagaggcccgagccggtGcaagatctcttcgacttcat	8	9	12	12	3	2	2	1	0	1	2	4	5	2	2	2	3	2	1	2	3	1	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr6:37139038G>T	ENST00000373509.5	+	4	751	c.378G>T	c.(376-378)gtG>gtT	p.V126V		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	217					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)	CCGAGCCGGTGCAAGATCTCT	0.617			T	BCL6	NHL																																p.V217V		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.G651T						PASS	.						80	94	89					6																	37139038		2203	4300	6503	SO:0001819	synonymous_variant	5292	exon4			GCCGGTGCAAGAT		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.378G>T	6.37:g.37139038G>T		100	0	0		87	12	0.137931	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.617	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37139038	G	T	37139038	2	4	18	1	0	0	0	0	0	0	0	1	11936	1306	46	4		4	PIM1	6	37139038	Silent	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	92	37139038	133976029	73	2460			2	22		9	9	2513	N	G_C_A	5.015395e-20
PIM1	5292	hgsc.bcm.edu	37	chr6	37139191	37139191	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaaaacatccttatcgacctCaatcgcggcgagctcaagct	12	8	8	13	4	2	0	2	0	0	0	5	3	3	0	2	1	3	2	2	1	5	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr6:37139191C>T	ENST00000373509.5	+	4	904	c.531C>T	c.(529-531)ctC>ctT	p.L177L		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	268	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)	TTATCGACCTCAATCGCGGCG	0.637			T	BCL6	NHL																																p.L268L		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C804T						PASS	.						37	38	37					6																	37139191		2203	4300	6503	SO:0001819	synonymous_variant	5292	exon4			CGACCTCAATCGC		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.531C>T	6.37:g.37139191C>T		101	0	0		90	28	0.311111	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.637	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37139191	C	T	37139191	2	4	18	1	0	0	0	0	0	0	0	1	11936	813	29	2		2	PIM1	6	37139191	Silent	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	153	37139191	133975876	74	2461			2	22		9	9	2513	N	G_C_A	5.015395e-20
PIM1	5292	hgsc.bcm.edu	37	chr6	37140867	37140867	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggggatcctgctgtatgatAtggtgtgtggagatattcct	7	15	14	5	0	0	2	0	1	0	1	2	4	2	3	2	4	1	2	2	4	3	4			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr6:37140867A>T	ENST00000373509.5	+	5	1076	c.703A>T	c.(703-705)Atg>Ttg	p.M235L	PIM1_ENST00000468243.1_3'UTR	NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	326	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)	GCTGTATGATATGGTGTGTGG	0.552			T	BCL6	NHL																																p.M326L		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,trunk,malignant_melanoma,-2,1	PIM1	71	1	0			c.A976T						PASS	.						143	132	136					6																	37140867		2203	4300	6503	SO:0001583	missense	5292	exon5			TATGATATGGTGT		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.703A>T	6.37:g.37140867A>T	ENSP00000362608:p.Met235Leu	172	0	0		155	80	0.516129	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	A	35	5.493129	0.96339	.	.	ENSG00000137193	ENST00000373509	T	0.10573	2.86	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);	0.042575	0.85682	D	0.000000	T	0.03390	0.0098	N	0.04387	-0.21	0.54753	D	0.999985	P	0.34934	0.476	B	0.40101	0.319	T	0.48937	-0.8990	10	0.49607	T	0.09	.	14.5991	0.68427	1.0:0.0:0.0:0.0	.	326	P11309	PIM1_HUMAN	L	235	ENSP00000362608:M235L	ENSP00000362608:M235L	M	+	1	0	PIM1	37248845	1.000000	0.71417	0.945000	0.38365	0.975000	0.68041	8.930000	0.92872	2.149000	0.67028	0.482000	0.46254	ATG	.	.	none		0.552	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37140867	A	T	37140867	3	4	18	1	0	0	0	0	1	0	0	0	11936	449	16	5	721	5	PIM1	6	37140867	Missense_Mutation	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10	1676	37140867	133974200	75	2462			2	22		9	9	2513	N	G_C_A	5.015395e-20
TNFAIP3	7128	hgsc.bcm.edu	37	chr6	138200459	138200460	+	Frame_Shift_Del	DEL	TG	TG	-																															aaacaagggcttttgcacacTgtgtttcatcgagtacagag																										TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr6:138200459_138200460delTG	ENST00000237289.4	+	7	1943_1944	c.1877_1878delTG	c.(1876-1878)ctgfs	p.L626fs		NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	626	Interaction with TNIP1. {ECO:0000250}.|Required for proteosomal degradation of UBE2N and UBE2D3, TRAF6 deubiquitination, and TAX1BP1 interaction with UBE2N. {ECO:0000250}.|Sufficient for inhibitory activity of TNF-induced NF-kappa-B activity. {ECO:0000250}.				apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|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 interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|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 protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)|p.C627fs*44(1)|p.L626fs*45(1)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		TTTTGCACACTGTGTTTCATCG	0.51			"D, N, F"		"marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"																																p.626_626del	GBM(130;153 1739 22295 28918 47987)	Atlas-Indel	.		Rec	yes		6	6q23	7128	"tumor necrosis factor, alpha-induced protein 3"		L	.	TNFAIP3	340	.	27	Whole gene deletion(25)|Deletion - Frameshift(2)	haematopoietic_and_lymphoid_tissue(27)	c.1876_1877del						PASS	.																																			SO:0001589	frameshift_variant	7128	exon7			.	M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"OTU domain containing"	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.1877_1878delTG	6.37:g.138200461_138200462delTG	ENSP00000237289:p.Leu626fs	63	0	0		91	17	0.186813	NM_001270508	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Frame_Shift_Del	DEL	ENST00000237289.4	37	CCDS5187.1																																																																																			.	.	none		0.51	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1			-	138200460	TG	-	138200459	7	5	18	1	0	1	0	1	0	0	0	0	16289	1580	55	0	1899	0	TNFAIP3	6	138200459	Frame_Shift_Del	DEL	TG	TCGA-FF-A7CR-01A-11D-A382-10	101059592	138200459	32914608	76	2463											
PARK2	5071	hgsc.bcm.edu	37	chr6	162206824	162206824	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ccacacaaggcagggagtagCcaagttgagggtcgtgaaca	13	5	14	9	1	0	2	0	2	0	0	1	3	0	3	2	3	2	3	2	3	4	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr6:162206824C>G	ENST00000366898.1	-	7	953	c.851G>C	c.(850-852)gGc>gCc	p.G284A	PARK2_ENST00000338468.3_Missense_Mutation_p.G93A|PARK2_ENST00000366892.1_Missense_Mutation_p.G284A|PARK2_ENST00000366896.1_Missense_Mutation_p.G135A|PARK2_ENST00000366894.1_Missense_Mutation_p.G93A|PARK2_ENST00000366897.1_Missense_Mutation_p.G256A	NM_004562.2	NP_004553.2	O60260	PRKN2_HUMAN	parkin RBR E3 ubiquitin protein ligase	284	SYT11 binding 2.		G -> R (in PARK2).		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)		CAGGGAGTAGCCAAGTTGAGG	0.433																																					p.G284A		Atlas-SNP	.											.	PARK2	96	.	0			c.G851C						PASS	.						94	82	86					6																	162206824		2203	4300	6503	SO:0001583	missense	5071	exon7			GAGTAGCCAAGTT		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.851G>C	6.37:g.162206824C>G	ENSP00000355865:p.Gly284Ala	75	0	0		96	15	0.15625	NM_004562	A3FG77|A8K975|D3JZW7|D3K2X0|Q5TFV8|Q5VVX4|Q6Q2I6|Q8NI41|Q8NI43|Q8NI44|Q8WW07	Missense_Mutation	SNP	ENST00000366898.1	37	CCDS5281.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.514696	0.85389	.	.	ENSG00000185345	ENST00000366898;ENST00000366897;ENST00000366896;ENST00000366894;ENST00000338468;ENST00000392134;ENST00000366892;ENST00000366895	D;D;D;D;D;D	0.99828	-6.99;-6.99;-6.99;-6.99;-6.99;-6.99	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	D	0.99819	0.9920	M	0.82056	2.57	0.58432	D	0.999994	D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.996;0.999;0.999;0.999	D	0.97538	1.0084	10	0.49607	T	0.09	.	17.7106	0.88321	0.0:1.0:0.0:0.0	.	284;135;256;284;93	O60260-5;Q5VVX3;Q5VVX4;O60260;Q8NI42	.;.;.;PRKN2_HUMAN;.	A	284;256;135;93;93;93;284;205	ENSP00000355865:G284A;ENSP00000355863:G256A;ENSP00000355862:G135A;ENSP00000355860:G93A;ENSP00000343589:G93A;ENSP00000355858:G284A	ENSP00000343589:G93A	G	-	2	0	PARK2	162126814	1.000000	0.71417	0.983000	0.44433	0.791000	0.44710	6.554000	0.73923	2.717000	0.92951	0.650000	0.86243	GGC	.	.	none		0.433	PARK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042995.1			G	162206824	C	G	162206824	3	3	18	1	0	0	0	0	1	0	0	0	11458	739	26	4	570	4	PARK2	6	162206824	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	24006365	162206824	8908243	77	2464											
POM121L12	285877	hgsc.bcm.edu	37	chr7	53104001	53104001	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaggcggaacctgcagcccCggccctctgccttcaagccc	6	5	11	19	2	2	0	1	0	1	0	2	1	2	1	6	3	5	2	6	3	2	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr7:53104001C>T	ENST00000408890.4	+	1	653	c.637C>T	c.(637-639)Cgg>Tgg	p.R213W		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	213										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						CCTGCAGCCCCGGCCCTCTGC	0.672																																					p.R213W		Atlas-SNP	.											POM121L12,NS,carcinoma,-2,1	POM121L12	146	1	0			c.C637T						PASS	.						45	55	52					7																	53104001		1974	4130	6104	SO:0001583	missense	285877	exon1			CAGCCCCGGCCCT		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.637C>T	7.37:g.53104001C>T	ENSP00000386133:p.Arg213Trp	54	0	0		51	15	0.294118	NM_182595	Q8NDI9	Missense_Mutation	SNP	ENST00000408890.4	37	CCDS43584.1	.	.	.	.	.	.	.	.	.	.	C	7.515	0.655388	0.14580	.	.	ENSG00000221900	ENST00000408890	T	0.11277	2.79	1.8	0.644	0.17776	.	.	.	.	.	T	0.17450	0.0419	L	0.34521	1.04	0.09310	N	1	D	0.89917	1.0	D	0.79784	0.993	T	0.13602	-1.0503	9	0.87932	D	0	.	4.709	0.12863	0.627:0.373:0.0:0.0	.	213	Q8N7R1	P1L12_HUMAN	W	213	ENSP00000386133:R213W	ENSP00000386133:R213W	R	+	1	2	POM121L12	53071495	0.000000	0.05858	0.069000	0.20011	0.053000	0.15095	-0.015000	0.12634	0.178000	0.19917	-0.397000	0.06425	CGG	.	.	none		0.672	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595		T	53104001	C	T	53104001	3	4	18	1	0	0	0	0	1	0	0	0	12250	643	23	1	639	1	POM121L12	7	53104001	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10		53104001	106034662	78	2465											
UPK3B	80761	hgsc.bcm.edu	37	chr7	76143285	76143285	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagacccccggatccatcgAcacctggccagggcggcgaa	10	3	13	15	4	0	1	0	0	0	1	2	5	1	2	5	4	0	0	5	4	2	0			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr7:76143285A>G	ENST00000257632.5	+	3	776	c.648A>G	c.(646-648)cgA>cgG	p.R216R	UPK3B_ENST00000419923.2_Silent_p.R216R|UPK3B_ENST00000394849.1_Silent_p.R161R|UPK3B_ENST00000448265.3_Silent_p.R216R|UPK3B_ENST00000443097.2_Missense_Mutation_p.D188G|UPK3B_ENST00000334348.3_Missense_Mutation_p.D188G			Q9BT76	UPK3B_HUMAN	uroplakin 3B	216					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)				GGATCCATCGACACCTGGCCA	0.647																																					p.D188G		Atlas-SNP	.											.	UPK3B	15	.	0			c.A563G						PASS	.						169	121	137					7																	76143285		2203	4300	6503	SO:0001819	synonymous_variant	80761	exon5			CCATCGACACCTG	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.648A>G	7.37:g.76143285A>G		85	0	0		112	30	0.267857	NM_182684	A6NHH5|A8K231|A8MZA8|B3KPU5|Q75MM5|Q86W06	Missense_Mutation	SNP	ENST00000257632.5	37	CCDS5588.1	.	.	.	.	.	.	.	.	.	.	.	13.57	2.275948	0.40294	.	.	ENSG00000243566	ENST00000334348;ENST00000443097	T;T	0.58940	0.3;0.3	4.87	4.87	0.63330	.	.	.	.	.	T	0.60945	0.2308	.	.	.	0.34163	D	0.668931	P	0.39282	0.666	P	0.47134	0.539	T	0.71965	-0.4433	8	0.45353	T	0.12	.	11.8846	0.52594	1.0:0.0:0.0:0.0	.	188	A6NHH5	.	G	188	ENSP00000334938:D188G;ENSP00000444585:D188G	ENSP00000334938:D188G	D	+	2	0	UPK3B	75981221	1.000000	0.71417	1.000000	0.80357	0.217000	0.24651	4.525000	0.60559	1.831000	0.53308	0.260000	0.18958	GAC	.	.	none		0.647	UPK3B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000313978.2	NM_030570		G	76143285	A	G	76143285	2	3	18	1	0	0	0	0	0	0	0	1	17026	275	10	3		3	UPK3B	7	76143285	Silent	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10	23039284	76143285	82995378	79	2466											
CYP3A43	64816	hgsc.bcm.edu	37	chr7	99453289	99453290	+	Frame_Shift_Ins	INS	-	-	A																															aaagatgttacccattttttINSaaaaaattccattgaaagga																										TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr7:99453289_99453290insA	ENST00000354829.2	+	8	849_850	c.746_747insA	c.(745-750)ttaaaafs	p.LK249fs	CYP3A43_ENST00000444905.1_Intron|CYP3A43_ENST00000342499.4_Intron|CYP3A43_ENST00000312017.5_Frame_Shift_Ins_p.LK249fs|CYP3A43_ENST00000415413.1_Intron|CYP3A43_ENST00000222382.5_Frame_Shift_Ins_p.LK249fs|CYP3A43_ENST00000417625.1_Frame_Shift_Ins_p.LK139fs|CYP3A43_ENST00000477658.1_3'UTR	NM_022820.3|NM_057095.1	NP_073731.1|NP_476436.1	Q9HB55	CP343_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 43	249			Missing (in allele CYP3A43*2).		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)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(1)	19	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)				Dexamethasone(DB01234)|Dolutegravir(DB08930)|Ethosuximide(DB00593)|Oxazepam(DB00842)|Phenelzine(DB00780)|Praziquantel(DB01058)|Rifampicin(DB01045)|Rifapentine(DB01201)|Testosterone(DB00624)|Troleandomycin(DB01361)|Zalcitabine(DB00943)	ACCCATTTTTTAAAAAATTCCA	0.312																																					p.L249fs		Atlas-Indel	.											CYP3A43,NS,carcinoma,0,1	CYP3A43	52	1	0			c.746_747insA						PASS	.																																			SO:0001589	frameshift_variant	64816	exon8			.	AF319634	CCDS5675.1, CCDS5676.1, CCDS5677.1, CCDS64723.1	7q21.1	2007-12-14	2003-01-14		ENSG00000021461	ENSG00000021461		"Cytochrome P450s"	17450	protein-coding gene	gene with protein product		606534	"cytochrome P450, subfamily IIIA, polypeptide 43"			11160876, 11266076	Standard	NM_022820		Approved		uc003ury.1	Q9HB55	OTTHUMG00000156498	ENST00000354829.2:c.752dupA	7.37:g.99453295_99453295dupA	ENSP00000346887:p.Leu249fs	89	0	0		128	31	0.242188	NM_022820	Q495Y1|Q75MK2|Q75MK3|Q9HB52|Q9HB53|Q9HB54|Q9HB57	Frame_Shift_Ins	INS	ENST00000354829.2	37	CCDS5676.1																																																																																			.	.	none		0.312	CYP3A43-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000344379.1			A	99453290	-	A	99453289	7	5	18	1	0	1	1	0	0	0	0	0	4181	1764	61	0	776	0	CYP3A43	7	99453289	Frame_Shift_Ins	INS	-	TCGA-FF-A7CR-01A-11D-A382-10	23310004	99453289	59685374	80	2467											
TRIM4	89122	hgsc.bcm.edu	37	chr7	99507230	99507230	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acttctacatcctgtaaatgCatgactttcttcatcttggc	9	16	5	11	0	4	1	1	1	3	0	5	1	5	1	1	1	2	2	1	1	3	6	rs188783002		TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr7:99507230C>T	ENST00000355947.2	-	3	654	c.525G>A	c.(523-525)atG>atA	p.M175I	TRIM4_ENST00000349062.2_Missense_Mutation_p.M149I|TRIM4_ENST00000354241.5_Missense_Mutation_p.M149I	NM_033017.3	NP_148977.2	Q9C037	TRIM4_HUMAN	tripartite motif containing 4	175					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)				CCTGTAAATGCATGACTTTCT	0.453																																					p.M175I		Atlas-SNP	.											.	TRIM4	33	.	0			c.G525A						PASS	.						250	204	220					7																	99507230		2203	4300	6503	SO:0001583	missense	89122	exon3			TAAATGCATGACT	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.525G>A	7.37:g.99507230C>T	ENSP00000348216:p.Met175Ile	125	0	0		141	25	0.177305	NM_033017	A4D298|Q75MK1|Q96F06|Q9C036	Missense_Mutation	SNP	ENST00000355947.2	37	CCDS5679.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	1.528|1.528	-0.545076|-0.545076	0.04024|0.04024	.|.	.|.	ENSG00000146833|ENSG00000146833	ENST00000447480|ENST00000355947;ENST00000349062;ENST00000542799;ENST00000354241	.|T;T;T	.|0.66995	.|-0.11;-0.08;-0.24	2.55|2.55	-0.256|-0.256	0.12984|0.12984	.|.	.|.	.|.	.|.	.|.	T|T	0.46983|0.46983	0.1421|0.1421	N|N	0.25647|0.25647	0.755|0.755	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.02656	.|0.0;0.0;0.0	.|B;B;B	.|0.09377	.|0.004;0.0;0.0	T|T	0.26258|0.26258	-1.0108|-1.0108	5|9	.|0.33141	.|T	.|0.24	.|.	5.0163|5.0163	0.14337|0.14337	0.0:0.5468:0.0:0.4532|0.0:0.5468:0.0:0.4532	.|.	.|149;149;175	.|Q9C037-3;Q9C037-2;Q9C037	.|.;.;TRIM4_HUMAN	T|I	51|175;149;5;149	.|ENSP00000348216:M175I;ENSP00000275736:M149I;ENSP00000346186:M149I	.|ENSP00000275736:M149I	A|M	-|-	1|3	0|0	TRIM4|TRIM4	99345166|99345166	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	-0.579000|-0.579000	0.05834|0.05834	-0.071000|-0.071000	0.12886|0.12886	-0.262000|-0.262000	0.10625|0.10625	GCA|ATG	C|1.000;A|0.000	.	alt		0.453	TRIM4-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345050.1	NM_033017		T	99507230	C	T	99507230	3	4	18	1	0	0	0	0	1	0	0	0	16529	710	25	2	997	2	TRIM4	7	99507230	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	53941	99507230	59631433	81	2468											
NRF1	4899	hgsc.bcm.edu	37	chr7	129330335	129330335	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggaggttaactcagaactGccgcctctcaccatcgacgg	10	7	10	14	3	2	1	2	0	1	1	4	3	2	2	3	3	3	1	3	3	2	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr7:129330335G>T	ENST00000393232.1	+	5	672	c.555G>T	c.(553-555)ctG>ctT	p.L185L	NRF1_ENST00000393231.3_Silent_p.L185L|NRF1_ENST00000223190.4_Silent_p.L185L|NRF1_ENST00000311967.2_Silent_p.L185L|NRF1_ENST00000539636.1_Silent_p.L24L|NRF1_ENST00000393230.2_Silent_p.L185L|NRF1_ENST00000353868.4_Silent_p.L185L	NM_005011.3	NP_005002.3	Q16656	NRF1_HUMAN	nuclear respiratory factor 1	185					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						ACTCAGAACTGCCGCCTCTCA	0.562																																					p.L185L		Atlas-SNP	.											.	NRF1	40	.	0			c.G555T						PASS	.						102	84	90					7																	129330335		2203	4300	6503	SO:0001819	synonymous_variant	4899	exon5			AGAACTGCCGCCT	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.555G>T	7.37:g.129330335G>T		79	0	0		102	28	0.27451	NM_005011	A8K4C6|B4DDV6|Q15305|Q96AN2	Silent	SNP	ENST00000393232.1	37	CCDS5813.2																																																																																			.	.	none		0.562	NRF1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289813.1	NM_001040110		T	129330335	G	T	129330335	2	4	18	1	0	0	0	0	0	0	0	1	10655	1306	46	4		4	NRF1	7	129330335	Silent	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	29823105	129330335	29808328	82	2469											
MYOM2	9172	hgsc.bcm.edu	37	chr8	2057240	2057240	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttttgataaggggcgggttcGcttctggctccaggctgagc	5	12	15	9	2	1	2	0	2	1	0	3	2	2	2	1	5	1	4	1	5	1	5			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr8:2057240G>T	ENST00000262113.4	+	25	3239	c.3098G>T	c.(3097-3099)cGc>cTc	p.R1033L	MYOM2_ENST00000523438.1_Missense_Mutation_p.R458L	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	1033					muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)	p.R1033H(1)		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)		GGGCGGGTTCGCTTCTGGCTC	0.443																																					p.R1033L		Atlas-SNP	.											MYOM2,NS,carcinoma,0,1	MYOM2	251	1	1	Substitution - Missense(1)	lung(1)	c.G3098T						PASS	.						81	79	80					8																	2057240		2203	4300	6503	SO:0001583	missense	9172	exon25			GGGTTCGCTTCTG		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.3098G>T	8.37:g.2057240G>T	ENSP00000262113:p.Arg1033Leu	171	0	0		190	38	0.2	NM_003970	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	37	CCDS5957.1	.	.	.	.	.	.	.	.	.	.	g	34	5.316100	0.95655	.	.	ENSG00000036448	ENST00000262113;ENST00000523438	T;T	0.41065	1.01;1.01	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.68577	0.3016	M	0.81497	2.545	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.66999	-0.5781	10	0.41790	T	0.15	.	20.0285	0.97531	0.0:0.0:1.0:0.0	.	1033	P54296	MYOM2_HUMAN	L	1033;458	ENSP00000262113:R1033L;ENSP00000428396:R458L	ENSP00000262113:R1033L	R	+	2	0	MYOM2	2044647	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	9.512000	0.98008	2.727000	0.93392	0.645000	0.84053	CGC	.	.	none		0.443	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970		T	2057240	G	T	2057240	3	4	18	1	0	0	0	0	1	0	0	0	10101	1087	38	4	3192	4	MYOM2	8	2057240	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10		2057240	144306782	83	2470											
DLC1	10395	hgsc.bcm.edu	37	chr8	12957770	12957770	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aagatgggcccgctgatgatCaaccccagctttgagggcgc	9	7	13	12	2	1	4	1	3	0	1	1	4	1	4	3	2	2	2	3	2	2	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr8:12957770C>T	ENST00000276297.4	-	9	2485	c.2076G>A	c.(2074-2076)ttG>ttA	p.L692L	DLC1_ENST00000358919.2_Silent_p.L255L|DLC1_ENST00000512044.2_Silent_p.L289L|DLC1_ENST00000520226.1_Silent_p.L181L	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	692					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						CGCTGATGATCAACCCCAGCT	0.572																																					p.L692L		Atlas-SNP	.											.	DLC1	411	.	0			c.G2076A						PASS	.						88	83	84					8																	12957770		2203	4300	6503	SO:0001819	synonymous_variant	10395	exon9			GATGATCAACCCC	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.2076G>A	8.37:g.12957770C>T		83	0	0		103	21	0.203883	NM_182643	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Silent	SNP	ENST00000276297.4	37	CCDS5989.1																																																																																			.	.	none		0.572	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		T	12957770	C	T	12957770	2	4	18	1	0	0	0	0	0	0	0	1	4552	825	29	2		2	DLC1	8	12957770	Silent	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	10900530	12957770	133406252	84	2471											
DLC1	10395	hgsc.bcm.edu	37	chr8	13356598	13356598	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttggttatctgtgggttccTgggtggccagggtctccttt	2	16	14	9	0	2	0	0	0	2	0	4	0	3	0	3	5	0	2	3	5	1	4			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr8:13356598T>C	ENST00000276297.4	-	2	1392	c.983A>G	c.(982-984)cAg>cGg	p.Q328R	DLC1_ENST00000511869.1_Missense_Mutation_p.Q328R|DLC1_ENST00000316609.5_Missense_Mutation_p.Q328R	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	328					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						TGTGGGTTCCTGGGTGGCCAG	0.408																																					p.Q328R		Atlas-SNP	.											DLC1_ENST00000511869,colon,carcinoma,+1,3	DLC1	411	3	0			c.A983G						PASS	.						134	119	124					8																	13356598		2203	4300	6503	SO:0001583	missense	10395	exon2			GGTTCCTGGGTGG	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.983A>G	8.37:g.13356598T>C	ENSP00000276297:p.Gln328Arg	162	0	0		188	34	0.180851	NM_182643	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Missense_Mutation	SNP	ENST00000276297.4	37	CCDS5989.1	.	.	.	.	.	.	.	.	.	.	T	19.33	3.807054	0.70797	.	.	ENSG00000164741	ENST00000276297;ENST00000316609;ENST00000511869	T;T;T	0.13538	3.49;2.58;2.6	4.97	4.97	0.65823	.	0.197118	0.25361	N	0.031236	T	0.31263	0.0791	L	0.54323	1.7	0.31199	N	0.69997	D;D;B	0.76494	0.977;0.999;0.079	P;D;B	0.68943	0.73;0.961;0.025	T	0.12630	-1.0540	10	0.48119	T	0.1	.	14.7808	0.69766	0.0:0.0:0.0:1.0	.	328;328;328	E9PF76;Q96QB1-3;Q96QB1	.;.;RHG07_HUMAN	R	328	ENSP00000276297:Q328R;ENSP00000321034:Q328R;ENSP00000425878:Q328R	ENSP00000276297:Q328R	Q	-	2	0	DLC1	13400969	0.997000	0.39634	1.000000	0.80357	0.996000	0.88848	2.786000	0.47790	2.228000	0.72767	0.533000	0.62120	CAG	.	.	none		0.408	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		C	13356598	T	C	13356598	3	2	18	1	0	0	0	0	1	0	0	0	4552	1580	55	3	3756	3	DLC1	8	13356598	Missense_Mutation	SNP	T	TCGA-FF-A7CR-01A-11D-A382-10	398828	13356598	133007424	85	2472											
SLC7A2	6542	hgsc.bcm.edu	37	chr8	17406346	17406346	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcaaaaatatatcagcaaGtgccaggtaaaatatttgag	17	11	7	6	0	2	1	2	1	1	0	3	1	2	1	1	1	2	2	1	1	8	5			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr8:17406346G>C	ENST00000494857.1	+	5	910	c.692G>C	c.(691-693)aGt>aCt	p.S231T	SLC7A2_ENST00000522656.1_Missense_Mutation_p.S231T|SLC7A2_ENST00000004531.10_Missense_Mutation_p.S271T|SLC7A2_ENST00000470360.1_Missense_Mutation_p.S271T|SLC7A2_ENST00000398090.3_Missense_Mutation_p.S271T	NM_001008539.3	NP_001008539.3	P52569	CTR2_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	231					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)	ATATCAGCAAGTGCCAGGTAA	0.323																																					p.S271T		Atlas-SNP	.											.	SLC7A2	157	.	0			c.G812C						PASS	.						118	125	123					8																	17406346		2203	4300	6503	SO:0001583	missense	6542	exon4			CAGCAAGTGCCAG	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.692G>C	8.37:g.17406346G>C	ENSP00000419140:p.Ser231Thr	165	0	0		211	49	0.232227	NM_001164771	B7ZL54|O15291|O15292|Q14CQ6|Q6NSZ7|Q86TC6	Missense_Mutation	SNP	ENST00000494857.1	37	CCDS34852.1	.	.	.	.	.	.	.	.	.	.	G	1.700	-0.501731	0.04261	.	.	ENSG00000003989	ENST00000494857;ENST00000522656;ENST00000470360;ENST00000004531;ENST00000398090	D;D;D;D;D	0.88046	-2.17;-2.17;-2.33;-2.18;-2.33	4.68	-4.3	0.03710	Amino acid permease domain (1);	1.206210	0.05361	N	0.533658	T	0.72622	0.3483	N	0.20401	0.57	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.09377	0.004;0.004;0.004	T	0.55471	-0.8136	10	0.25106	T	0.35	.	3.0652	0.06212	0.2122:0.4456:0.1431:0.1991	.	271;271;231	P52569-3;P52569-2;P52569	.;.;CTR2_HUMAN	T	231;231;271;271;271	ENSP00000419140:S231T;ENSP00000430464:S231T;ENSP00000419873:S271T;ENSP00000004531:S271T;ENSP00000381164:S271T	ENSP00000004531:S271T	S	+	2	0	SLC7A2	17450725	0.000000	0.05858	0.163000	0.22734	0.993000	0.82548	-1.404000	0.02494	-0.607000	0.05738	0.650000	0.86243	AGT	.	.	none		0.323	SLC7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253367.3	NM_003046		C	17406346	G	C	17406346	3	2	18	1	0	0	0	0	1	0	0	0	14712	1029	36	4	826	4	SLC7A2	8	17406346	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	4049748	17406346	128957676	86	2473											
DOCK5	80005	hgsc.bcm.edu	37	chr8	25181469	25181469	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgatctggtggtttataaggTggtgctaacagaaaatggct	11	12	13	5	1	1	1	0	0	1	1	1	2	1	1	0	5	2	3	0	5	5	4			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr8:25181469T>C	ENST00000276440.7	+	17	1763		c.e17+2			NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5						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)		GTTTATAAGGTGGTGCTAACA	0.443																																					.	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											.	DOCK5	167	.	0			c.1719+2T>C						PASS	.						69	61	63					8																	25181469		2203	4300	6503	SO:0001630	splice_region_variant	80005	exon17			ATAAGGTGGTGCT		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.1719+2T>C	8.37:g.25181469T>C		94	0	0		79	14	0.177215	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Splice_Site	SNP	ENST00000276440.7	37	CCDS6047.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.581236	0.86748	.	.	ENSG00000147459	ENST00000276440;ENST00000444569	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9649	0.79961	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	DOCK5	25237386	1.000000	0.71417	0.989000	0.46669	0.962000	0.63368	7.997000	0.88414	2.232000	0.73038	0.533000	0.62120	.	.	.	none		0.443	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	Intron	C	25181469	T	C	25181469	5	2	18	1	0	0	0	0	0	0	1	0	4692	1710	59	3	1787	3	DOCK5	8	25181469	Splice_Site	SNP	T	TCGA-FF-A7CR-01A-11D-A382-10	7775123	25181469	121182553	87	2474											
TOX	9760	hgsc.bcm.edu	37	chr8	59750643	59750643	+	Frame_Shift_Del	DEL	T	T	-																															cactgggaatcccttacctgTttttgctcttctcctaaacc																										TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr8:59750643delT	ENST00000361421.1	-	5	1141	c.921delA	c.(919-921)aaafs	p.K307fs		NM_014729.2	NP_055544.1	O94900	TOX_HUMAN	thymocyte selection-associated high mobility group box	307						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)				CCCTTACCTGTTTTTGCTCTT	0.473																																					p.Q308fs	Pancreas(161;610 1969 17913 21374 22725)	Pindel,Atlas-Indel	.											.	TOX	83	.	0			c.922delC						PASS	.						90	89	90					8																	59750643		2203	4300	6503	SO:0001589	frameshift_variant	9760	exon5			.		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.921delA	8.37:g.59750643delT	ENSP00000354842:p.Lys307fs	112	0	.		83	19	0.229	NM_014729	Q96AV5	Frame_Shift_Del	DEL	ENST00000361421.1	37	CCDS34897.1																																																																																			.	.	none		0.473	TOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378307.1	NM_014729		-	59750643	T	-	59750643	7	5	18	1	0	1	0	1	0	0	0	0	16392	1722	60	0	679	0	TOX	8	59750643	Frame_Shift_Del	DEL	T	TCGA-FF-A7CR-01A-11D-A382-10	34569174	59750643	86613379	88	2475											
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77765620	77765620	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgacattaataattctccaAgtgaagaacagatccaggaa	17	10	7	7	0	1	4	0	2	1	2	3	5	2	5	2	1	1	0	2	1	6	4			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr8:77765620A>G	ENST00000521891.2	+	10	6911	c.6463A>G	c.(6463-6465)Agt>Ggt	p.S2155G	ZFHX4_ENST00000455469.2_Missense_Mutation_p.S2110G|ZFHX4_ENST00000518282.1_Missense_Mutation_p.S2129G|ZFHX4_ENST00000050961.6_Missense_Mutation_p.S2110G	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2110					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)			TAATTCTCCAAGTGAAGAACA	0.383										HNSCC(33;0.089)																											p.S2155G		Atlas-SNP	.											.	ZFHX4	878	.	0			c.A6463G						PASS	.						51	51	51					8																	77765620		1838	4076	5914	SO:0001583	missense	79776	exon10			TCTCCAAGTGAAG		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.6463A>G	8.37:g.77765620A>G	ENSP00000430497:p.Ser2155Gly	50	0	0		69	12	0.173913	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	A	12.86	2.063687	0.36373	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	D;D;D;D	0.92495	-3.05;-3.05;-3.05;-3.05	3.92	3.92	0.45320	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.52532	U	0.000072	D	0.89375	0.6697	L	0.48260	1.515	0.48395	D	0.999648	B;B;B	0.30179	0.271;0.229;0.229	B;B;B	0.34652	0.187;0.117;0.117	D	0.88251	0.2916	10	0.45353	T	0.12	.	13.2107	0.59822	1.0:0.0:0.0:0.0	.	2110;2110;2155	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	G	2155;2139;2110;2110;2129	ENSP00000430497:S2155G;ENSP00000399605:S2110G;ENSP00000050961:S2110G;ENSP00000430848:S2129G	ENSP00000050961:S2110G	S	+	1	0	ZFHX4	77928175	1.000000	0.71417	0.944000	0.38274	0.926000	0.56050	7.202000	0.77856	1.784000	0.52394	0.374000	0.22700	AGT	.	.	none		0.383	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		G	77765620	A	G	77765620	3	3	18	1	0	0	0	0	1	0	0	0	17650	72	3	3	6497	3	ZFHX4	8	77765620	Missense_Mutation	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10	18014977	77765620	68598402	89	2476											
MTSS1	9788	hgsc.bcm.edu	37	chr8	125565316	125565318	+	In_Frame_Del	DEL	CTC	CTC	-																															gatggcgttcagcatgtcttCtccttgtggagtatcccttg																										TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr8:125565316_125565318delCTC	ENST00000518547.1	-	14	2656_2658	c.2183_2185delGAG	c.(2182-2187)ggagaa>gaa	p.G728del	MTSS1_ENST00000524090.1_In_Frame_Del_p.G618del|MTSS1_ENST00000325064.5_In_Frame_Del_p.G732del|NDUFB9_ENST00000522532.1_Intron|MTSS1_ENST00000354184.4_In_Frame_Del_p.G446del|MTSS1_ENST00000431961.2_In_Frame_Del_p.G446del|MTSS1_ENST00000378017.3_In_Frame_Del_p.G703del|MTSS1_ENST00000523587.1_5'UTR|MTSS1_ENST00000395508.2_In_Frame_Del_p.G502del	NM_001282971.1|NM_014751.4	NP_001269900.1|NP_055566.3	O43312	MTSS1_HUMAN	metastasis suppressor 1	728	WH2. {ECO:0000255|PROSITE- ProRule:PRU00406}.				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)			AGCATGTCTTCTCCTTGTGGAGT	0.562																																					p.728_729del	Esophageal Squamous(160;622 1893 3862 8546 12509)	Pindel,Atlas-Indel	.											.	MTSS1	79	.	0			c.2184_2186del						PASS	.																																			SO:0001651	inframe_deletion	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.2183_2185delGAG	8.37:g.125565316_125565318delCTC	ENSP00000429064:p.Gly728del	204	0	.		220	43	0.195	NM_014751	J3KNK6|Q8TCA2|Q96RX2	In_Frame_Del	DEL	ENST00000518547.1	37	CCDS6353.1																																																																																			.	.	none		0.562	MTSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109625.3	NM_014751		-	125565318	CTC	-	125565316	7	5	18	1	0	1	0	1	0	0	0	0	9971	922	32	0	86	0	MTSS1	8	125565316	In_Frame_Del	DEL	CTC	TCGA-FF-A7CR-01A-11D-A382-10	47799696	125565316	20798706	90	2477											
OC90	729330	hgsc.bcm.edu	37	chr8	133045291	133045291	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgcttctgctcaccttttTcagtggtctcctcaggatca	6	15	7	13	0	6	0	4	0	2	0	7	1	6	1	2	2	2	2	2	2	0	3			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr8:133045291T>C	ENST00000443356.2	-	12	988	c.902A>G	c.(901-903)gAa>gGa	p.E301G	OC90_ENST00000603859.1_Missense_Mutation_p.E285G|OC90_ENST00000254627.3_Missense_Mutation_p.E285G|OC90_ENST00000262283.5_Missense_Mutation_p.E497G			Q02509	OC90_HUMAN	otoconin 90	301					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)			CTCACCTTTTTCAGTGGTCTC	0.493																																					p.E285G		Atlas-SNP	.											OC90_ENST00000262283,NS,carcinoma,-1,2	OC90	163	2	0			c.A854G						PASS	.						69	75	73					8																	133045291		2013	4178	6191	SO:0001583	missense	729330	exon11			CCTTTTTCAGTGG	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.902A>G	8.37:g.133045291T>C	ENSP00000390050:p.Glu301Gly	80	0	0		64	9	0.140625	NM_001080399	B4DNG8	Missense_Mutation	SNP	ENST00000443356.2	37		.	.	.	.	.	.	.	.	.	.	T	0.567	-0.842871	0.02671	.	.	ENSG00000253117;ENSG00000253117;ENSG00000258417	ENST00000254627;ENST00000443356;ENST00000262283	T;T;T	0.30182	1.61;1.57;1.54	4.67	1.77	0.24775	.	1.009930	0.07936	N	0.978315	T	0.09024	0.0223	N	0.01168	-0.975	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.0	T	0.32322	-0.9911	10	0.02654	T	1	-0.7969	6.2646	0.20919	0.0:0.5341:0.3643:0.1016	.	285;301	Q02509-2;Q02509	.;OC90_HUMAN	G	285;301;497	ENSP00000254627:E285G;ENSP00000390050:E301G;ENSP00000262283:E497G	ENSP00000254627:E285G	E	-	2	0	RP11-240B13.2;OC90	133114473	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.862000	0.27899	0.395000	0.25257	-0.242000	0.12053	GAA	.	.	none		0.493	OC90-201	KNOWN	basic	protein_coding	protein_coding		NM_001080399		C	133045291	T	C	133045291	3	2	18	1	0	0	0	0	1	0	0	0	10823	1783	62	3	595	3	OC90	8	133045291	Missense_Mutation	SNP	T	TCGA-FF-A7CR-01A-11D-A382-10	7479975	133045291	13318731	91	2478											
SLA	6503	hgsc.bcm.edu	37	chr8	134057342	134057342	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctttacctgcctgtgtctcAccgacagtgagtaaaaccct	9	11	8	13	1	1	1	1	1	1	0	2	2	1	1	4	0	3	2	4	0	3	3			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr8:134057342A>G	ENST00000338087.5	-	7	1190	c.371T>C	c.(370-372)gTg>gCg	p.V124A	SLA_ENST00000427060.2_Missense_Mutation_p.V164A|SLA_ENST00000517648.1_Intron|TG_ENST00000519543.1_Intron|TG_ENST00000542445.1_Intron|TG_ENST00000377869.1_Intron|SLA_ENST00000395352.3_Missense_Mutation_p.V141A|SLA_ENST00000524345.1_Missense_Mutation_p.V16A|TG_ENST00000220616.4_Intron	NM_001045556.2	NP_001039021.1	Q13239	SLAP1_HUMAN	Src-like-adaptor	124	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)			CCTGTGTCTCACCGACAGTGA	0.572																																					p.V164A		Atlas-SNP	.											.	SLA	63	.	0			c.T491C						PASS	.						124	100	108					8																	134057342		2203	4300	6503	SO:0001583	missense	6503	exon5			TGTCTCACCGACA		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.371T>C	8.37:g.134057342A>G	ENSP00000337548:p.Val124Ala	112	0	0		86	27	0.313953	NM_006748	B7Z4J2|B7Z4L6|Q6FI01|Q9UMQ8	Missense_Mutation	SNP	ENST00000338087.5	37	CCDS6370.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.568259	0.86439	.	.	ENSG00000155926	ENST00000338087;ENST00000427060;ENST00000395352;ENST00000524345;ENST00000522119	D;D;D;D;D	0.91068	-2.78;-2.78;-2.78;-2.78;-2.78	5.77	5.77	0.91146	SH2 motif (5);	0.000000	0.85682	D	0.000000	D	0.95837	0.8645	M	0.88979	2.995	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;1.0	D	0.96457	0.9338	10	0.87932	D	0	-32.0528	14.0378	0.64656	1.0:0.0:0.0:0.0	.	124;124;124	Q6FI01;Q5TZW1;Q13239	.;.;SLAP1_HUMAN	A	124;164;141;16;124	ENSP00000337548:V124A;ENSP00000394049:V164A;ENSP00000378759:V141A;ENSP00000427928:V16A;ENSP00000430596:V124A	ENSP00000337548:V124A	V	-	2	0	SLA	134126524	1.000000	0.71417	0.976000	0.42696	0.953000	0.61014	8.526000	0.90588	2.210000	0.71456	0.459000	0.35465	GTG	.	.	none		0.572	SLA-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378771.1			G	134057342	A	G	134057342	3	3	18	1	0	0	0	0	1	0	0	0	14378	159	6	3	471	3	SLA	8	134057342	Missense_Mutation	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10	1012051	134057342	12306680	92	2479											
DENND3	22898	hgsc.bcm.edu	37	chr8	142178188	142178188	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agcaagtgcgtgcaggcataCcatgcccactttgtctccat	9	10	9	13	1	1	0	0	0	1	0	2	0	1	0	3	1	5	3	3	1	2	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr8:142178188C>T	ENST00000262585.2	+	13	1877	c.1599C>T	c.(1597-1599)taC>taT	p.Y533Y	DENND3_ENST00000519811.1_Silent_p.Y613Y|DENND3_ENST00000424248.1_Silent_p.Y481Y	NM_014957.2	NP_055772.2	A2RUS2	DEND3_HUMAN	DENN/MADD domain containing 3	533					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)			TGCAGGCATACCATGCCCACT	0.537																																					p.Y533Y		Atlas-SNP	.											.	DENND3	127	.	0			c.C1599T						PASS	.						136	122	126					8																	142178188		2203	4300	6503	SO:0001819	synonymous_variant	22898	exon13			GGCATACCATGCC	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.1599C>T	8.37:g.142178188C>T		146	0	0		163	12	0.0736196	NM_014957	B7ZM28|O94947|Q2TAM7|Q6ZMS6|Q96DK3	Silent	SNP	ENST00000262585.2	37	CCDS34947.1	.	.	.	.	.	.	.	.	.	.	C	0.032	-1.328256	0.01309	.	.	ENSG00000105339	ENST00000518668	.	.	.	5.36	1.0	0.19881	.	.	.	.	.	T	0.58308	0.2113	.	.	.	0.53688	D	0.999971	.	.	.	.	.	.	T	0.52902	-0.8513	4	.	.	.	-9.2619	10.3492	0.43924	0.0:0.6493:0.0:0.3507	.	.	.	.	S	538	.	.	P	+	1	0	DENND3	142247370	0.999000	0.42202	0.004000	0.12327	0.001000	0.01503	0.623000	0.24447	0.272000	0.22027	-0.379000	0.06801	CCA	.	.	none		0.537	DENND3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_014957		T	142178188	C	T	142178188	2	4	18	1	0	0	0	0	0	0	0	1	4434	518	18	2		2	DENND3	8	142178188	Silent	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	8120846	142178188	4185834	93	2480											
ARC	23237	hgsc.bcm.edu	37	chr8	143695199	143695199	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcccacggaaacggtgtggCgggctgactcgctgcccacc	6	5	14	16	5	0	1	0	1	0	0	1	2	0	2	3	4	2	2	3	4	1	0			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr8:143695199C>T	ENST00000356613.2	-	1	1634	c.434G>A	c.(433-435)cGc>cAc	p.R145H	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)				AACGGTGTGGCGGGCTGACTC	0.701																																					p.R145H		Atlas-SNP	.											.	ARC	34	.	0			c.G434A						PASS	.						7	9	8					8																	143695199		2139	4195	6334	SO:0001583	missense	23237	exon1			GTGTGGCGGGCTG	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.434G>A	8.37:g.143695199C>T	ENSP00000349022:p.Arg145His	31	0	0		27	6	0.222222	NM_015193	B4DFL0|O60937	Missense_Mutation	SNP	ENST00000356613.2	37	CCDS34950.1	.	.	.	.	.	.	.	.	.	.	C	18.39	3.614323	0.66672	.	.	ENSG00000198576	ENST00000356613	T	0.35789	1.29	4.56	3.68	0.42216	.	0.231396	0.26075	N	0.026492	T	0.24314	0.0589	L	0.27053	0.805	0.31343	N	0.683397	B	0.20459	0.045	B	0.11329	0.006	T	0.18524	-1.0334	10	0.87932	D	0	.	8.138	0.31067	0.0:0.7901:0.0:0.2099	.	145	Q7LC44	ARC_HUMAN	H	145	ENSP00000349022:R145H	ENSP00000349022:R145H	R	-	2	0	ARC	143692201	0.998000	0.40836	0.992000	0.48379	0.736000	0.42039	0.684000	0.25364	0.899000	0.36444	0.462000	0.41574	CGC	.	.	none		0.701	ARC-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259274.2			T	143695199	C	T	143695199	3	4	18	1	0	0	0	0	1	0	0	0	841	768	27	1	760	1	ARC	8	143695199	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	1517011	143695199	2668823	94	2481											
C9orf93	203238	hgsc.bcm.edu	37	chr9	15745534	15745534	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acatcaaaaggagcagttgcGttgtttacaagcgctcagtt	12	11	10	8	2	2	0	2	0	0	0	2	1	2	1	0	1	4	6	0	1	4	5	rs570101221		TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr9:15745534G>A	ENST00000380701.3	+	18	2904	c.2576G>A	c.(2575-2577)cGt>cAt	p.R859H	CCDC171_ENST00000297641.3_Missense_Mutation_p.R859H	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	859																	GAGCAGTTGCGTTGTTTACAA	0.343													G|||	1	0.000199681	0.0	0.0	5008	,	,		14338	0.0		0.0	False		,,,				2504	0.001				p.R859H		Atlas-SNP	.											.	.	.	.	0			c.G2576A						PASS	.						187	183	185					9																	15745534		2203	4300	6503	SO:0001583	missense	203238	exon18			AGTTGCGTTGTTT	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.2576G>A	9.37:g.15745534G>A	ENSP00000370077:p.Arg859His	93	0	0		101	20	0.19802	NM_173550	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Missense_Mutation	SNP	ENST00000380701.3	37	CCDS6481.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.33|19.33	3.806863|3.806863	0.70797|0.70797	.|.	.|.	ENSG00000164989|ENSG00000164989	ENST00000297641;ENST00000380689;ENST00000380701|ENST00000449575	T;T|.	0.15952|.	2.38;2.38|.	5.03|5.03	4.12|4.12	0.48240|0.48240	.|.	0.205040|.	0.41712|.	D|.	0.000833|.	T|T	0.43322|0.43322	0.1242|0.1242	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	D|D	1|1	B;B;B|.	0.25007|.	0.116;0.071;0.049|.	B;B;B|.	0.19391|.	0.025;0.011;0.017|.	T|T	0.24657|0.24657	-1.0154|-1.0154	10|5	0.38643|.	T|.	0.18|.	-7.835|-7.835	11.9773|11.9773	0.53100|0.53100	0.1426:0.0:0.8574:0.0|0.1426:0.0:0.8574:0.0	.|.	867;126;859|.	B7ZM22;A6NK04;Q6TFL3|.	.;.;CI093_HUMAN|.	H|I	859;126;859|99	ENSP00000297641:R859H;ENSP00000370077:R859H|.	ENSP00000297641:R859H|.	R|V	+|+	2|1	0|0	C9orf93|C9orf93	15735534|15735534	0.688000|0.688000	0.27680|0.27680	1.000000|1.000000	0.80357|0.80357	0.978000|0.978000	0.69477|0.69477	1.853000|1.853000	0.39358|0.39358	2.351000|2.351000	0.79841|0.79841	0.591000|0.591000	0.81541|0.81541	CGT|GTT	.	.	none		0.343	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550		A	15745534	G	A	15745534	3	1	18	1	0	0	0	0	1	0	0	0	2508	1145	40	1	2642	1	C9orf93	9	15745534	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10		15745534	125467897	95	2482											
GRHPR	9380	hgsc.bcm.edu	37	chr9	37424860	37424860	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	agctgtgaggtggagcagtgGgactcggatgagcccatccc	8	7	16	10	1	0	2	0	2	0	0	2	5	1	5	2	4	3	2	2	4	0	0	rs180177304		TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr9:37424860G>T	ENST00000318158.6	+	2	187	c.102G>T	c.(100-102)tgG>tgT	p.W34C	GRHPR_ENST00000493368.1_3'UTR|GRHPR_ENST00000607784.1_Missense_Mutation_p.W34C	NM_012203.1	NP_036335.1	Q9UBQ7	GRHPR_HUMAN	glyoxylate reductase/hydroxypyruvate reductase	34					cellular nitrogen compound metabolic process (GO:0034641)|dicarboxylic acid metabolic process (GO:0043648)|excretion (GO:0007588)|glyoxylate metabolic process (GO:0046487)|metabolic process (GO:0008152)|oxidation-reduction process (GO:0055114)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisomal matrix (GO:0005782)	carboxylic acid binding (GO:0031406)|glycerate dehydrogenase activity (GO:0008465)|glyoxylate reductase (NADP) activity (GO:0030267)|hydroxypyruvate reductase activity (GO:0016618)|NAD binding (GO:0051287)|NADPH binding (GO:0070402)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12				GBM - Glioblastoma multiforme(29;0.00687)		TGGAGCAGTGGGACTCGGATG	0.677																																					p.W34C		Atlas-SNP	.											.	GRHPR	35	.	0			c.G102T						PASS	.						46	43	44					9																	37424860		2203	4300	6503	SO:0001583	missense	9380	exon2			GCAGTGGGACTCG	AF134895	CCDS6609.1	9q12	2012-07-13			ENSG00000137106	ENSG00000137106	1.1.1.79, 1.1.1.81		4570	protein-coding gene	gene with protein product	"primary hyperoxaluria type 2"	604296		GLXR		10524214, 10484776	Standard	XM_005251631		Approved	PH2	uc003zzu.1	Q9UBQ7	OTTHUMG00000019914	ENST00000318158.6:c.102G>T	9.37:g.37424860G>T	ENSP00000313432:p.Trp34Cys	55	0	0		46	18	0.391304	NM_012203	Q5T945|Q9H3E9|Q9H636|Q9UKX1	Missense_Mutation	SNP	ENST00000318158.6	37	CCDS6609.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.399816	0.83120	.	.	ENSG00000137106	ENST00000377824;ENST00000318158	D;D	0.83755	-1.76;-1.76	5.74	5.74	0.90152	D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.87390	0.6165	M	0.86178	2.8	0.80722	D	1	P	0.43287	0.802	B	0.43478	0.421	D	0.87612	0.2504	10	0.44086	T	0.13	.	19.5878	0.95496	0.0:0.0:1.0:0.0	.	34	Q9UBQ7	GRHPR_HUMAN	C	34	ENSP00000367055:W34C;ENSP00000313432:W34C	ENSP00000313432:W34C	W	+	3	0	GRHPR	37414860	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	9.016000	0.93645	2.745000	0.94114	0.650000	0.86243	TGG	.	.	alt		0.677	GRHPR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052442.1	NM_012203		T	37424860	G	T	37424860	3	4	18	1	0	0	0	0	1	0	0	0	6775	1241	43	4	108	4	GRHPR	9	37424860	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	21679326	37424860	103788571	96	2483											
GRHPR	9380	hgsc.bcm.edu	37	chr9	37424900	37424900	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgccaaggagctagagcgaGgtgtggcgggggcccacggc	7	4	19	11	3	0	1	0	0	0	1	0	3	0	2	2	6	3	1	2	6	2	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr9:37424900G>C	ENST00000318158.6	+	2	227	c.142G>C	c.(142-144)Ggt>Cgt	p.G48R	GRHPR_ENST00000493368.1_3'UTR|GRHPR_ENST00000607784.1_Missense_Mutation_p.G48R	NM_012203.1	NP_036335.1	Q9UBQ7	GRHPR_HUMAN	glyoxylate reductase/hydroxypyruvate reductase	48					cellular nitrogen compound metabolic process (GO:0034641)|dicarboxylic acid metabolic process (GO:0043648)|excretion (GO:0007588)|glyoxylate metabolic process (GO:0046487)|metabolic process (GO:0008152)|oxidation-reduction process (GO:0055114)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisomal matrix (GO:0005782)	carboxylic acid binding (GO:0031406)|glycerate dehydrogenase activity (GO:0008465)|glyoxylate reductase (NADP) activity (GO:0030267)|hydroxypyruvate reductase activity (GO:0016618)|NAD binding (GO:0051287)|NADPH binding (GO:0070402)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12				GBM - Glioblastoma multiforme(29;0.00687)		GCTAGAGCGAGGTGTGGCGGG	0.662																																					p.G48R		Atlas-SNP	.											.	GRHPR	35	.	0			c.G142C						PASS	.						50	47	48					9																	37424900		2203	4300	6503	SO:0001583	missense	9380	exon2			GAGCGAGGTGTGG	AF134895	CCDS6609.1	9q12	2012-07-13			ENSG00000137106	ENSG00000137106	1.1.1.79, 1.1.1.81		4570	protein-coding gene	gene with protein product	"primary hyperoxaluria type 2"	604296		GLXR		10524214, 10484776	Standard	XM_005251631		Approved	PH2	uc003zzu.1	Q9UBQ7	OTTHUMG00000019914	ENST00000318158.6:c.142G>C	9.37:g.37424900G>C	ENSP00000313432:p.Gly48Arg	58	0	0		41	18	0.439024	NM_012203	Q5T945|Q9H3E9|Q9H636|Q9UKX1	Missense_Mutation	SNP	ENST00000318158.6	37	CCDS6609.1	.	.	.	.	.	.	.	.	.	.	G	9.113	1.007054	0.19199	.	.	ENSG00000137106	ENST00000377824;ENST00000318158	D;D	0.82803	-1.65;-1.65	5.98	-1.73	0.08081	D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain (1);NAD(P)-binding domain (1);	0.355960	0.35805	N	0.002974	T	0.55417	0.1919	N	0.02379	-0.575	0.18873	N	0.999986	B	0.11235	0.004	B	0.23150	0.044	T	0.49995	-0.8879	10	0.15066	T	0.55	-4.7328	8.5821	0.33634	0.1811:0.4099:0.409:0.0	.	48	Q9UBQ7	GRHPR_HUMAN	R	48	ENSP00000367055:G48R;ENSP00000313432:G48R	ENSP00000313432:G48R	G	+	1	0	GRHPR	37414900	0.001000	0.12720	0.000000	0.03702	0.006000	0.05464	0.078000	0.14761	-0.336000	0.08438	-0.181000	0.13052	GGT	.	.	none		0.662	GRHPR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052442.1	NM_012203		C	37424900	G	C	37424900	3	2	18	1	0	0	0	0	1	0	0	0	6775	1000	35	4	148	4	GRHPR	9	37424900	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	40	37424900	103788531	97	2484											
SLC28A3	64078	hgsc.bcm.edu	37	chr9	86917281	86917281	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gtgaaagttcagcacacaggCcgaaatcaccataaccagat	16	6	8	11	1	2	2	2	1	0	1	2	3	2	2	3	1	2	2	3	1	3	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr9:86917281C>T	ENST00000376238.4	-	5	407	c.358G>A	c.(358-360)Gcc>Acc	p.A120T	SLC28A3_ENST00000495823.1_5'Flank|SLC28A3_ENST00000537648.1_Missense_Mutation_p.A51T	NM_001199633.1|NM_022127.2	NP_001186562.1|NP_071410.1	Q9HAS3	S28A3_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 3	120					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)			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)	AGCACACAGGCCGAAATCACC	0.502																																					p.A120T	Ovarian(106;425 1539 34835 42413 43572)	Atlas-SNP	.											.	SLC28A3	72	.	0			c.G358A						PASS	.						81	66	71					9																	86917281		2203	4300	6503	SO:0001583	missense	64078	exon5			CACAGGCCGAAAT	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.358G>A	9.37:g.86917281C>T	ENSP00000365413:p.Ala120Thr	46	0	0		37	10	0.27027	NM_001199633	A8K9Y4|B1AML0|B2RA51|B4E2S8|F5GYE3	Missense_Mutation	SNP	ENST00000376238.4	37	CCDS6670.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.751503	0.89753	.	.	ENSG00000197506	ENST00000376238;ENST00000537648	D;D	0.84070	-1.8;-1.8	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	D	0.91352	0.7272	M	0.80422	2.495	0.47183	D	0.99934	D;D	0.69078	0.997;0.997	D;D	0.74348	0.983;0.983	D	0.91859	0.5498	10	0.66056	D	0.02	-18.4347	17.9616	0.89087	0.0:1.0:0.0:0.0	.	51;120	B4E2S8;Q9HAS3	.;S28A3_HUMAN	T	120;51	ENSP00000365413:A120T;ENSP00000446438:A51T	ENSP00000365413:A120T	A	-	1	0	SLC28A3	86107101	1.000000	0.71417	0.999000	0.59377	0.883000	0.51084	5.949000	0.70257	2.775000	0.95449	0.655000	0.94253	GCC	.	.	none		0.502	SLC28A3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052874.1	NM_022127		T	86917281	C	T	86917281	3	4	18	1	0	0	0	0	1	0	0	0	14548	739	26	2	1773	2	SLC28A3	9	86917281	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	49492381	86917281	54296150	98	2485											
C9orf30	91283	hgsc.bcm.edu	37	chr9	103204249	103204249	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	caacgaaattataaagcctgCcaaatacttctcagaattgg	16	10	6	9	1	1	1	1	0	1	1	2	2	1	1	2	1	4	0	2	1	8	5			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr9:103204249C>T	ENST00000395067.2	+	2	300	c.29C>T	c.(28-30)gCc>gTc	p.A10V	MSANTD3-TMEFF1_ENST00000502978.1_5'Flank|MSANTD3_ENST00000374885.1_Missense_Mutation_p.A10V|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	10										endometrium(2)|lung(2)	4						ATAAAGCCTGCCAAATACTTC	0.393																																					p.A10V		Atlas-SNP	.											.	MSANTD3	10	.	0			c.C29T						PASS	.						59	56	57					9																	103204249		2203	4300	6503	SO:0001583	missense	91283	exon2			AGCCTGCCAAATA	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.29C>T	9.37:g.103204249C>T	ENSP00000378506:p.Ala10Val	58	0	0		69	18	0.26087	NM_001198805	B2RC35|Q5T726|Q5T727|Q5T728	Missense_Mutation	SNP	ENST00000395067.2	37	CCDS6749.1	.	.	.	.	.	.	.	.	.	.	C	27.1	4.798673	0.90538	.	.	ENSG00000066697	ENST00000395067;ENST00000398977;ENST00000374885;ENST00000374886	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	T	0.74612	0.3739	L	0.43923	1.385	0.47905	D	0.999541	D	0.65815	0.995	D	0.76071	0.987	T	0.73895	-0.3838	8	0.54805	T	0.06	-10.9805	19.1261	0.93384	0.0:1.0:0.0:0.0	.	10	Q96H12	CI030_HUMAN	V	10	.	ENSP00000364020:A10V	A	+	2	0	C9orf30	102244070	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.267000	0.65530	2.779000	0.95612	0.655000	0.94253	GCC	.	.	none		0.393	MSANTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053410.1	NM_080655		T	103204249	C	T	103204249	3	4	18	1	0	0	0	0	1	0	0	0	2480	739	26	2	31	2	C9orf30	9	103204249	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	16286968	103204249	38009182	99	2486											
KLF4	9314	hgsc.bcm.edu	37	chr9	110250112	110250112	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctcacgtcgttgatgtccGccaggttgaagggagccgtc	6	9	15	11	4	1	2	1	2	0	0	4	3	2	3	3	3	1	3	3	3	1	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr9:110250112G>A	ENST00000374672.4	-	3	1036	c.563C>T	c.(562-564)gCg>gTg	p.A188V		NM_004235.4	NP_004226.3	O43474	KLF4_HUMAN	Kruppel-like factor 4 (gut)	188	Pro-rich.				cellular response to cycloheximide (GO:0071409)|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 peptide (GO:1901653)|epidermal cell differentiation (GO:0009913)|epidermis morphogenesis (GO:0048730)|fat cell differentiation (GO:0045444)|mesodermal cell fate determination (GO:0007500)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000342)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of muscle hyperplasia (GO:0014740)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of response to cytokine stimulus (GO:0060761)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of hemoglobin biosynthetic process (GO:0046985)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic camera-type eye development (GO:0031077)|post-embryonic hemopoiesis (GO:0035166)|regulation of cell differentiation (GO:0045595)|response to retinoic acid (GO:0032526)|stem cell maintenance (GO:0019827)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|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)|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)|sequence-specific DNA binding transcription factor recruiting transcription factor activity (GO:0001010)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(5)|large_intestine(1)|lung(3)|pancreas(1)|prostate(2)	16						GTTGATGTCCGCCAGGTTGAA	0.731																																					p.A188V		Atlas-SNP	.											.	KLF4	106	.	0			c.C563T						PASS	.						4	4	4					9																	110250112		2029	4039	6068	SO:0001583	missense	9314	exon3			ATGTCCGCCAGGT	AF022184	CCDS6770.2	9q31	2013-01-08			ENSG00000136826	ENSG00000136826		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	6348	protein-coding gene	gene with protein product		602253				9422764, 16372018	Standard	NM_004235		Approved	EZF, GKLF	uc004bdg.3	O43474	OTTHUMG00000020449	ENST00000374672.4:c.563C>T	9.37:g.110250112G>A	ENSP00000363804:p.Ala188Val	63	0	0		39	12	0.307692	NM_004235	B2R8S4|B3KT79|L0R3I6|L0R4N5|P78338|Q5T3J8|Q5T3J9|Q8N717|Q9UNP3	Missense_Mutation	SNP	ENST00000374672.4	37	CCDS6770.2	.	.	.	.	.	.	.	.	.	.	G	21.3	4.133999	0.77662	.	.	ENSG00000136826	ENST00000374672;ENST00000411706	T	0.05513	3.43	4.42	3.5	0.40072	.	0.000000	0.42964	D	0.000640	T	0.09379	0.0231	N	0.19112	0.55	0.30455	N	0.774841	D;D	0.69078	0.997;0.994	P;P	0.55161	0.77;0.652	T	0.03684	-1.1013	10	0.46703	T	0.11	.	13.8448	0.63461	0.0:0.1545:0.8455:0.0	.	188;188	O43474;O43474-1	KLF4_HUMAN;.	V	188;179	ENSP00000363804:A188V	ENSP00000363804:A188V	A	-	2	0	KLF4	109289933	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	8.439000	0.90308	1.031000	0.39867	0.655000	0.94253	GCG	.	.	none		0.731	KLF4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053556.2	NM_004235		A	110250112	G	A	110250112	3	1	18	1	0	0	0	0	1	0	0	0	8357	1087	38	1	888	1	KLF4	9	110250112	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	7045863	110250112	30963319	100	2487											
CEP110	11064	hgsc.bcm.edu	37	chr9	123922502	123922502	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtgaaagaaaaactcaacttAcacttataaagcaggaaatt	20	9	6	6	0	1	2	1	1	0	1	1	3	1	3	0	1	4	1	0	1	9	4			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr9:123922502A>G	ENST00000373855.1	+	32	5271	c.5011A>G	c.(5011-5013)Aca>Gca	p.T1671A	CNTRL_ENST00000373850.1_Missense_Mutation_p.T1119A|CNTRL_ENST00000373844.1_Missense_Mutation_p.T116A|CNTRL_ENST00000238341.5_Missense_Mutation_p.T1671A|CNTRL_ENST00000373845.2_3'UTR			Q7Z7A1	CNTRL_HUMAN	centriolin	1671					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						AACTCAACTTACACTTATAAA	0.308																																					p.T1671A		Atlas-SNP	.											.	CNTRL	161	.	0			c.A5011G						PASS	.						68	78	74					9																	123922502		2203	4291	6494	SO:0001583	missense	11064	exon30			CAACTTACACTTA	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.5011A>G	9.37:g.123922502A>G	ENSP00000362962:p.Thr1671Ala	297	0	0		385	89	0.231169	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	37	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	A	6.384	0.438895	0.12104	.	.	ENSG00000119397	ENST00000373855;ENST00000238341;ENST00000454238;ENST00000439778;ENST00000373850;ENST00000431571;ENST00000373845;ENST00000373844	T;T;T	0.28454	1.61;1.61;1.61	5.62	-2.39	0.06602	.	.	.	.	.	T	0.10637	0.0260	N	0.04880	-0.145	0.20821	N	0.999849	B	0.02656	0.0	B	0.01281	0.0	T	0.36672	-0.9738	9	0.08179	T	0.78	.	5.5625	0.17152	0.3011:0.0:0.4108:0.2881	.	1671	Q7Z7A1	CNTRL_HUMAN	A	1671;1671;1671;427;1119;340;353;116	ENSP00000362962:T1671A;ENSP00000238341:T1671A;ENSP00000362956:T1119A	ENSP00000238341:T1671A	T	+	1	0	CNTRL	122962323	0.022000	0.18835	0.991000	0.47740	0.958000	0.62258	-0.238000	0.08977	-0.267000	0.09325	-0.462000	0.05337	ACA	.	.	none		0.308	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018		G	123922502	A	G	123922502	3	3	18	1	0	0	0	0	1	0	0	0	3247	391	14	3	5129	3	CEP110	9	123922502	Missense_Mutation	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10	13672390	123922502	17290929	101	2488											
ABL1	25	hgsc.bcm.edu	37	chr9	133729485	133729485	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagtagcatctgactttgaGcctcagggtctgagtgaagc	9	10	12	10	0	3	4	1	4	2	0	3	4	3	4	2	1	3	2	2	1	2	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr9:133729485G>A	ENST00000318560.5	+	2	495	c.114G>A	c.(112-114)gaG>gaA	p.E38E		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	38	CAP.				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)	CTGACTTTGAGCCTCAGGGTC	0.463			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"																																p.E57E		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.G171A						PASS	.						99	103	102					9																	133729485		2203	4300	6503	SO:0001819	synonymous_variant	25	exon2			CTTTGAGCCTCAG	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.114G>A	9.37:g.133729485G>A		90	0	0		116	21	0.181034	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																			.	.	none		0.463	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		A	133729485	G	A	133729485	2	1	18	1	0	0	0	0	0	0	0	1	92	962	34	2		2	ABL1	9	133729485	Silent	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	9806983	133729485	7483946	102	2489											
UAP1L1	91373	hgsc.bcm.edu	37	chr9	139973009	139973009	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cggccgagttcttcagggagCacaacttcttccacctggac	8	9	10	14	2	3	0	1	0	2	0	4	3	4	2	3	3	2	2	3	3	1	4			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr9:139973009C>T	ENST00000409858.3	+	3	582	c.550C>T	c.(550-552)Cac>Tac	p.H184Y	UAP1L1_ENST00000476184.1_3'UTR|UAP1L1_ENST00000360271.3_Missense_Mutation_p.H61Y	NM_207309.2	NP_997192.2	Q3KQV9	UAP1L_HUMAN	UDP-N-acetylglucosamine pyrophosphorylase 1 like 1	184							uridylyltransferase activity (GO:0070569)			kidney(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8	all_cancers(76;0.0926)	Myeloproliferative disorder(178;0.0821)	STAD - Stomach adenocarcinoma(284;0.0878)	OV - Ovarian serous cystadenocarcinoma(145;2.96e-05)|Epithelial(140;0.000486)		CTTCAGGGAGCACAACTTCTT	0.622																																					p.H184Y		Atlas-SNP	.											.	UAP1L1	46	.	0			c.C550T						PASS	.						80	65	70					9																	139973009		2203	4300	6503	SO:0001583	missense	91373	exon3			AGGGAGCACAACT	AK022632	CCDS7028.2	9q34.3	2014-07-31	2014-07-31		ENSG00000197355	ENSG00000197355			28082	protein-coding gene	gene with protein product							Standard	NM_207309		Approved		uc010ncb.3	Q3KQV9	OTTHUMG00000020962	ENST00000409858.3:c.550C>T	9.37:g.139973009C>T	ENSP00000386935:p.His184Tyr	82	0	0		78	16	0.205128	NM_207309	A2AMJ8|Q5SPZ2|Q69YQ3|Q6ZR38	Missense_Mutation	SNP	ENST00000409858.3	37	CCDS7028.2	.	.	.	.	.	.	.	.	.	.	C	17.70	3.454287	0.63290	.	.	ENSG00000197355	ENST00000409858;ENST00000360271	T;T	0.16897	2.31;2.31	5.01	2.9	0.33743	.	0.272139	0.42053	D	0.000779	T	0.47728	0.1461	M	0.93062	3.375	0.22017	N	0.99942	D;D	0.63880	0.993;0.978	D;P	0.64144	0.922;0.689	T	0.52283	-0.8596	10	0.87932	D	0	.	14.3374	0.66600	0.2808:0.7192:0.0:0.0	.	184;61	Q3KQV9;Q3KQV9-2	UAP1L_HUMAN;.	Y	184;61	ENSP00000386935:H184Y;ENSP00000353409:H61Y	ENSP00000353409:H61Y	H	+	1	0	UAP1L1	139092830	0.204000	0.23447	0.634000	0.29324	0.941000	0.58515	0.800000	0.27042	1.104000	0.41587	0.561000	0.74099	CAC	.	.	none		0.622	UAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055216.2	XM_038063		T	139973009	C	T	139973009	3	4	18	1	0	0	0	0	1	0	0	0	16841	710	25	2	560	2	UAP1L1	9	139973009	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	6243524	139973009	1240422	103	2490											
ARHGAP21	57584	hgsc.bcm.edu	37	chr10	24910129	24910129	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gtgtcagtactggtgtactgGtttgctgtttgctcaatgat	6	17	12	6	0	2	1	2	1	0	0	2	1	2	1	0	2	4	6	0	2	3	4			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr10:24910129G>C	ENST00000396432.2	-	9	1181	c.695C>G	c.(694-696)aCc>aGc	p.T232S	ARHGAP21_ENST00000320481.6_Missense_Mutation_p.T19S	NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	231					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						TGGTGTACTGGTTTGCTGTTT	0.488																																					p.T232S		Atlas-SNP	.											ARHGAP21,NS,carcinoma,+1,1	ARHGAP21	185	1	0			c.C695G						PASS	.						103	91	95					10																	24910129		2203	4300	6503	SO:0001583	missense	57584	exon9			GTACTGGTTTGCT	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.695C>G	10.37:g.24910129G>C	ENSP00000379709:p.Thr232Ser	304	0	0		357	87	0.243697	NM_020824	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000396432.2	37	CCDS7144.2	.	.	.	.	.	.	.	.	.	.	G	1.164	-0.642809	0.03531	.	.	ENSG00000107863	ENST00000396432;ENST00000447364;ENST00000320481;ENST00000376410;ENST00000446003;ENST00000445703	T;T;T;T	0.43294	2.92;2.92;0.95;0.97	5.35	2.34	0.29019	.	1.015580	0.07822	N	0.959901	T	0.31638	0.0803	L	0.31294	0.92	0.09310	N	0.999997	B;B	0.13145	0.007;0.005	B;B	0.17722	0.019;0.008	T	0.26155	-1.0111	10	0.27082	T	0.32	.	9.346	0.38109	0.1111:0.2519:0.637:0.0	.	222;231	F8W9U9;Q5T5U3	.;RHG21_HUMAN	S	232;221;19;222;232;67	ENSP00000379709:T232S;ENSP00000365604:T19S;ENSP00000365592:T222S;ENSP00000405018:T232S	ENSP00000365604:T19S	T	-	2	0	ARHGAP21	24950135	0.930000	0.31532	0.329000	0.25429	0.430000	0.31655	1.225000	0.32551	0.713000	0.32060	0.650000	0.86243	ACC	.	.	none		0.488	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824		C	24910129	G	C	24910129	3	2	18	1	0	0	0	0	1	0	0	0	871	1261	44	4	5253	4	ARHGAP21	10	24910129	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10		24910129	110624618	104	2491											
PPYR1	5540	hgsc.bcm.edu	37	chr10	47086871	47086871	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccctgggcaccccatacaacTtctctgaacattgccaggat	10	9	7	15	0	1	1	0	1	1	0	2	2	1	2	4	2	4	1	4	2	3	3			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr10:47086871T>G	ENST00000395716.1	+	2	173	c.88T>G	c.(88-90)Ttc>Gtc	p.F30V	NPY4R_ENST00000374312.1_Missense_Mutation_p.F30V			P50391	NPY4R_HUMAN	neuropeptide Y receptor Y4	30					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)										CCCATACAACTTCTCTGAACA	0.517																																					p.F30V		Atlas-SNP	.											PPYR1,NS,carcinoma,-2,1	PPYR1	54	1	0			c.T88G						scavenged	.						162	149	153					10																	47086871		2203	4300	6503	SO:0001583	missense	5540	exon3			TACAACTTCTCTG		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.88T>G	10.37:g.47086871T>G	ENSP00000379066:p.Phe30Val	219	1	0.00456621		228	32	0.140351	NM_005972	Q13456|Q5ISU3|Q5T2X9|Q6FH06	Missense_Mutation	SNP	ENST00000395716.1	37	CCDS31193.1	.	.	.	.	.	.	.	.	.	.	T	7.764	0.706034	0.15172	.	.	ENSG00000204174	ENST00000374312;ENST00000395716	T;T	0.35421	1.31;1.31	4.78	2.33	0.28932	.	0.515322	0.21459	N	0.074187	T	0.27384	0.0672	L	0.60455	1.87	0.26222	N	0.979144	B	0.33022	0.394	B	0.23716	0.048	T	0.11817	-1.0572	10	0.31617	T	0.26	.	7.1302	0.25496	0.0:0.1902:0.0:0.8098	.	30	P50391	NPY4R_HUMAN	V	30	ENSP00000363431:F30V;ENSP00000379066:F30V	ENSP00000363431:F30V	F	+	1	0	PPYR1	46506877	0.994000	0.37717	0.987000	0.45799	0.266000	0.26442	1.294000	0.33365	0.357000	0.24183	-0.290000	0.09829	TTC	.	.	none		0.517	NPY4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047837.1			G	47086871	T	G	47086871	3	3	18	1	0	0	0	0	1	0	0	0	12428	1609	56	5	90	5	PPYR1	10	47086871	Missense_Mutation	SNP	T	TCGA-FF-A7CR-01A-11D-A382-10	22176742	47086871	88447876	105	2492											
RHOBTB1	9886	hgsc.bcm.edu	37	chr10	62631996	62631996	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggagcatacactgttgtagTtggtgcagatgtggtgcaaa	10	12	14	5	0	0	1	0	0	0	1	0	2	0	2	0	3	4	6	0	3	3	4			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr10:62631996T>G	ENST00000337910.5	-	10	2205	c.1868A>C	c.(1867-1869)aAc>aCc	p.N623T	RHOBTB1_ENST00000490827.1_5'UTR|RHOBTB1_ENST00000357917.4_Missense_Mutation_p.N623T	NM_001242359.1|NM_014836.4	NP_001229288.1|NP_055651.1	O94844	RHBT1_HUMAN	Rho-related BTB domain containing 1	623					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)					ACTGTTGTAGTTGGTGCAGAT	0.483																																					p.N623T		Atlas-SNP	.											.	RHOBTB1	61	.	0			c.A1868C						PASS	.						163	153	156					10																	62631996		2203	4300	6503	SO:0001583	missense	9886	exon10			TTGTAGTTGGTGC	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.1868A>C	10.37:g.62631996T>G	ENSP00000338671:p.Asn623Thr	116	0	0		104	24	0.230769	NM_014836		Missense_Mutation	SNP	ENST00000337910.5	37	CCDS7261.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.771859	0.90108	.	.	ENSG00000072422	ENST00000357917;ENST00000337910	T;T	0.22743	1.94;1.94	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.43545	0.1252	M	0.88775	2.98	0.80722	D	1	P	0.45078	0.85	P	0.48770	0.589	T	0.53872	-0.8377	10	0.87932	D	0	.	15.7833	0.78281	0.0:0.0:0.0:1.0	.	623	O94844	RHBT1_HUMAN	T	623	ENSP00000350595:N623T;ENSP00000338671:N623T	ENSP00000338671:N623T	N	-	2	0	RHOBTB1	62302002	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.036000	0.88901	2.133000	0.65898	0.459000	0.35465	AAC	.	.	none		0.483	RHOBTB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048220.1			G	62631996	T	G	62631996	3	3	18	1	0	0	0	0	1	0	0	0	13348	1725	60	5	230	5	RHOBTB1	10	62631996	Missense_Mutation	SNP	T	TCGA-FF-A7CR-01A-11D-A382-10	15545125	62631996	72902751	106	2493											
NHLRC2	374354	hgsc.bcm.edu	37	chr10	115636657	115636657	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagtagaccaagttactgatAgattggtaatagcagacact	15	10	9	7	0	0	4	0	1	0	3	0	4	0	4	1	1	2	4	1	1	6	6			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr10:115636657A>C	ENST00000369301.3	+	3	921	c.709A>C	c.(709-711)Aga>Cga	p.R237R		NM_198514.3	NP_940916.2	Q8NBF2	NHLC2_HUMAN	NHL repeat containing 2	237										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)		AGTTACTGATAGATTGGTAAT	0.353																																					p.R237R		Atlas-SNP	.											.	NHLRC2	56	.	0			c.A709C						PASS	.						58	60	59					10																	115636657		2185	4291	6476	SO:0001819	synonymous_variant	374354	exon3			ACTGATAGATTGG	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.709A>C	10.37:g.115636657A>C		82	0	0		75	13	0.173333	NM_198514	Q8N1H1|Q8N5A6	Silent	SNP	ENST00000369301.3	37	CCDS7585.1																																																																																			.	.	none		0.353	NHLRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050446.1	NM_198514		C	115636657	A	C	115636657	2	2	18	1	0	0	0	0	0	0	0	1	10415	412	15	5		5	NHLRC2	10	115636657	Silent	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10	53004661	115636657	19898090	107	2494											
MUC6	4588	hgsc.bcm.edu	37	chr11	1017576	1017576	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggatgtagaggttttggccGtgctaaatgagcttcgggat	8	12	16	5	2	0	2	0	1	0	1	1	4	0	4	1	4	2	4	1	4	3	5	rs372353242		TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr11:1017576G>T	ENST00000421673.2	-	31	5275	c.5225C>A	c.(5224-5226)aCg>aAg	p.T1742K		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1742	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)		GGTTTTGGCCGTGCTAAATGA	0.537																																					p.T1742K		Atlas-SNP	.											MUC6_ENST00000421673,NS,carcinoma,+1,2	MUC6	408	2	0			c.C5225A						PASS	.						688	670	676					11																	1017576		2188	4282	6470	SO:0001583	missense	4588	exon31			TTGGCCGTGCTAA	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.5225C>A	11.37:g.1017576G>T	ENSP00000406861:p.Thr1742Lys	501	0	0		566	48	0.0848057	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	-	7.936	0.741705	0.15642	.	.	ENSG00000184956	ENST00000421673	T	0.25414	1.8	2.32	-2.37	0.06643	.	.	.	.	.	T	0.38532	0.1044	M	0.62723	1.935	0.09310	N	1	D	0.89917	1.0	D	0.79108	0.992	T	0.23547	-1.0185	9	0.59425	D	0.04	.	3.4316	0.07430	0.3783:0.0:0.4408:0.1809	.	1742	Q6W4X9	MUC6_HUMAN	K	1742	ENSP00000406861:T1742K	ENSP00000406861:T1742K	T	-	2	0	MUC6	1007576	0.010000	0.17322	0.000000	0.03702	0.004000	0.04260	0.978000	0.29488	-0.611000	0.05709	-0.643000	0.03959	ACG	.	.	alt		0.537	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		T	1017576	G	T	1017576	3	4	18	1	0	0	0	0	1	0	0	0	9989	1145	40	4	2106	4	MUC6	11	1017576	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10		1017576	133988940	108	2495											
HIPK3	10114	hgsc.bcm.edu	37	chr11	33374879	33374879	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	accagtggcccacctgttagCctctccgtgtacctcaagac	8	9	8	16	1	2	1	1	0	1	1	3	1	2	1	6	1	2	2	6	1	3	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr11:33374879C>T	ENST00000303296.4	+	17	3718	c.3413C>T	c.(3412-3414)gCc>gTc	p.A1138V	HIPK3_ENST00000456517.1_Missense_Mutation_p.A1117V|HIPK3_ENST00000525975.1_Missense_Mutation_p.A1117V|AL122015.1_ENST00000411202.1_RNA|HIPK3_ENST00000379016.3_Missense_Mutation_p.A1117V	NM_005734.3	NP_005725.3	Q9H422	HIPK3_HUMAN	homeodomain interacting protein kinase 3	1138					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						CACCTGTTAGCCTCTCCGTGT	0.522																																					p.A1138V		Atlas-SNP	.											.	HIPK3	92	.	0			c.C3413T						PASS	.						220	181	194					11																	33374879		2202	4298	6500	SO:0001583	missense	10114	exon17			TGTTAGCCTCTCC	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.3413C>T	11.37:g.33374879C>T	ENSP00000304226:p.Ala1138Val	242	0	0		261	54	0.206897	NM_005734	O14632|Q2PBG4|Q2PBG5|Q92632|Q9HAS2	Missense_Mutation	SNP	ENST00000303296.4	37	CCDS7884.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.618437	0.87359	.	.	ENSG00000110422	ENST00000525975;ENST00000303296;ENST00000379016;ENST00000456517	T;T;T;T	0.61274	0.12;0.15;0.12;0.12	6.16	5.25	0.73442	.	0.000000	0.64402	D	0.000013	T	0.74207	0.3686	M	0.61703	1.905	0.58432	D	0.999994	D;D	0.76494	0.999;0.985	D;P	0.72075	0.976;0.871	T	0.77395	-0.2604	10	0.72032	D	0.01	.	17.5986	0.88020	0.0:0.8766:0.1234:0.0	.	1117;1138	Q9H422-2;Q9H422	.;HIPK3_HUMAN	V	1117;1138;1117;1117	ENSP00000431710:A1117V;ENSP00000304226:A1138V;ENSP00000368301:A1117V;ENSP00000398241:A1117V	ENSP00000304226:A1138V	A	+	2	0	HIPK3	33331455	1.000000	0.71417	1.000000	0.80357	0.720000	0.41350	7.263000	0.78421	1.605000	0.50152	-0.181000	0.13052	GCC	.	.	none		0.522	HIPK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255358.1	NM_005734		T	33374879	C	T	33374879	3	4	18	1	0	0	0	0	1	0	0	0	7127	739	26	2	3475	2	HIPK3	11	33374879	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	32357303	33374879	101631637	109	2496											
OR5L1	219437	hgsc.bcm.edu	37	chr11	55579421	55579421	+	Missense_Mutation	SNP	T	T	C																															ggtgtgttctctgattcattTgtgcttagctcttaggatcc																										TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr11:55579421T>C	ENST00000333973.2	+	1	568	c.479T>C	c.(478-480)tTg>tCg	p.L160S		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	160						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)				CTGATTCATTTGTGCTTAGCT	0.443																																					p.L160S		Atlas-SNP	.											.	OR5L1	145	.	0			c.T479C						PASS	.						218	191	200					11																	55579421		2200	4296	6496	SO:0001583	missense	219437	exon1			TTCATTTGTGCTT	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.479T>C	11.37:g.55579421T>C	ENSP00000335529:p.Leu160Ser	407	0	0		404	57	0.141089	NM_001004738	B2RNK6|Q6IFD0	Missense_Mutation	SNP	ENST00000333973.2	37	CCDS31509.1	.	.	.	.	.	.	.	.	.	.	t	9.888	1.203401	0.22121	.	.	ENSG00000186117	ENST00000333973	T	0.00130	8.69	4.18	-3.36	0.04913	GPCR, rhodopsin-like superfamily (1);	0.749235	0.11513	N	0.556535	T	0.00109	0.0003	N	0.13272	0.32	0.09310	N	1	B	0.25105	0.118	B	0.33392	0.163	T	0.10154	-1.0642	10	0.62326	D	0.03	-5.254	7.8224	0.29294	0.1535:0.6254:0.0:0.2211	.	160	Q8NGL2	OR5L1_HUMAN	S	160	ENSP00000335529:L160S	ENSP00000335529:L160S	L	+	2	0	OR5L1	55335997	0.000000	0.05858	0.000000	0.03702	0.068000	0.16541	-0.162000	0.10012	-0.600000	0.05790	0.358000	0.22013	TTG	.	.	none		0.443	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738		C	55579421	T	C	55579421	3	2	18	1	0	0	0	0	1	0	0	0	11179	1821	63	3	481	3	OR5L1	11	55579421	Missense_Mutation	SNP	T	TCGA-FF-A7CR-01A-11D-A382-10	22204542	55579421	79427095	110	2497	37	2									
OR5L1	219437	hgsc.bcm.edu	37	chr11	55579424	55579424	+	Missense_Mutation	SNP	G	G	C																															gtgttctctgattcatttgtGcttagctcttaggatcccct																										TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr11:55579424G>C	ENST00000333973.2	+	1	571	c.482G>C	c.(481-483)tGc>tCc	p.C161S		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	161						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)				ATTCATTTGTGCTTAGCTCTT	0.448																																					p.C161S		Atlas-SNP	.											.	OR5L1	145	.	0			c.G482C						PASS	.						219	193	202					11																	55579424		2200	4296	6496	SO:0001583	missense	219437	exon1			ATTTGTGCTTAGC	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.482G>C	11.37:g.55579424G>C	ENSP00000335529:p.Cys161Ser	413	0	0		403	61	0.151365	NM_001004738	B2RNK6|Q6IFD0	Missense_Mutation	SNP	ENST00000333973.2	37	CCDS31509.1	.	.	.	.	.	.	.	.	.	.	g	7.397	0.632046	0.14322	.	.	ENSG00000186117	ENST00000333973	T	0.35789	1.29	4.18	0.752	0.18398	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000023	T	0.14700	0.0355	N	0.02751	-0.505	0.09310	N	1	B	0.25105	0.118	B	0.33392	0.163	T	0.30707	-0.9969	10	0.21540	T	0.41	-20.2258	7.1232	0.25456	0.0:0.1433:0.3172:0.5395	.	161	Q8NGL2	OR5L1_HUMAN	S	161	ENSP00000335529:C161S	ENSP00000335529:C161S	C	+	2	0	OR5L1	55336000	0.000000	0.05858	0.000000	0.03702	0.056000	0.15407	-0.323000	0.07997	0.187000	0.20147	0.435000	0.28638	TGC	.	.	none		0.448	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738		C	55579424	G	C	55579424	3	2	18	1	0	0	0	0	1	0	0	0	11179	1319	46	4	484	4	OR5L1	11	55579424	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	3	55579424	79427092	111	2498	37	2									
OR5D16	390144	hgsc.bcm.edu	37	chr11	55606497	55606497	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctggtgaacctggttgtagaAgatagaaccatttcattctc	11	13	9	8	0	2	4	1	1	1	3	3	4	2	4	2	2	2	2	2	2	5	5			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr11:55606497A>T	ENST00000378396.1	+	1	270	c.270A>T	c.(268-270)gaA>gaT	p.E90D		NM_001005496.1	NP_001005496.1	Q8NGK9	OR5DG_HUMAN	olfactory receptor, family 5, subfamily D, member 16	90						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)				TGGTTGTAGAAGATAGAACCA	0.418																																					p.E90D		Atlas-SNP	.											OR5D16,NS,carcinoma,+2,1	OR5D16	94	1	0			c.A270T						scavenged	.						199	195	196					11																	55606497		2201	4296	6497	SO:0001583	missense	390144	exon1			TGTAGAAGATAGA	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.270A>T	11.37:g.55606497A>T	ENSP00000367649:p.Glu90Asp	306	2	0.00653595		317	70	0.22082	NM_001005496	Q6IF65|Q96RB4	Missense_Mutation	SNP	ENST00000378396.1	37	CCDS31512.1	.	.	.	.	.	.	.	.	.	.	.	11.61	1.689090	0.29962	.	.	ENSG00000205029	ENST00000378396	T	0.09817	2.94	4.05	1.4	0.22301	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.08670	0.0215	L	0.39566	1.225	0.09310	N	1	B	0.21452	0.056	B	0.28784	0.094	T	0.37572	-0.9700	9	0.45353	T	0.12	-3.3486	1.9721	0.03408	0.5741:0.1682:0.0953:0.1625	.	90	Q8NGK9	OR5DG_HUMAN	D	90	ENSP00000367649:E90D	ENSP00000367649:E90D	E	+	3	2	OR5D16	55363073	0.000000	0.05858	0.355000	0.25773	0.899000	0.52679	-1.669000	0.01958	0.553000	0.29044	0.433000	0.28618	GAA	.	.	none		0.418	OR5D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334506.1	NM_001005496		T	55606497	A	T	55606497	3	4	18	1	0	0	0	0	1	0	0	0	11165	69	3	5	272	5	OR5D16	11	55606497	Missense_Mutation	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10	27073	55606497	79400019	112	2499											
OR5M10	390167	hgsc.bcm.edu	37	chr11	56345100	56345100	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagtgtgattaggtagatcGccaggaacaccccaaacagg	13	6	11	11	1	0	2	0	1	0	1	1	3	0	3	4	3	2	1	4	3	4	2	rs182443406	byFrequency	TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr11:56345100G>A	ENST00000526812.2	-	1	163	c.98C>T	c.(97-99)gCg>gTg	p.A33V		NM_001004741.1	NP_001004741.1	Q6IEU7	OR5MA_HUMAN	olfactory receptor, family 5, subfamily M, member 10	33						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						TAGGTAGATCGCCAGGAACAC	0.488																																					p.A33V		Atlas-SNP	.											.	OR5M10	56	.	0			c.C98T						PASS	.						172	164	166					11																	56345100		1943	4142	6085	SO:0001583	missense	390167	exon1			TAGATCGCCAGGA	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.98C>T	11.37:g.56345100G>A	ENSP00000436004:p.Ala33Val	221	0	0		193	54	0.279793	NM_001004741	B9EIL9	Missense_Mutation	SNP	ENST00000526812.2	37	CCDS53630.1	.	.	.	.	.	.	.	.	.	.	G	0.508	-0.867878	0.02590	.	.	ENSG00000254834	ENST00000526812	T	0.01304	5.03	4.04	-3.41	0.04839	.	.	.	.	.	T	0.00440	0.0014	N	0.00538	-1.39	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46020	-0.9221	9	0.02654	T	1	.	6.0359	0.19708	0.4:0.3341:0.266:0.0	.	33	Q6IEU7	OR5MA_HUMAN	V	33	ENSP00000436004:A33V	ENSP00000436004:A33V	A	-	2	0	OR5M10	56101676	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.474000	0.06607	-0.336000	0.08438	-1.035000	0.02400	GCG	G|0.999;T|0.001	.	alt		0.488	OR5M10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391609.1	NM_001004741		A	56345100	G	A	56345100	3	1	18	1	0	0	0	0	1	0	0	0	11182	1087	38	1	853	1	OR5M10	11	56345100	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	738603	56345100	78661416	113	2500											
OR10Q1	219960	hgsc.bcm.edu	37	chr11	57995634	57995634	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gtggagaaggcccggcggcgGccctcggcagaacggatgct	7	4	18	12	5	0	2	0	0	0	2	1	4	0	3	2	7	2	2	2	7	2	0			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr11:57995634G>T	ENST00000316770.2	-	1	756	c.714C>A	c.(712-714)ggC>ggA	p.G238G		NM_001004471.2	NP_001004471.1	Q8NGQ4	O10Q1_HUMAN	olfactory receptor, family 10, subfamily Q, member 1	238						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)				CCCGGCGGCGGCCCTCGGCAG	0.627																																					p.G238G		Atlas-SNP	.											.	OR10Q1	79	.	0			c.C714A						PASS	.						56	52	54					11																	57995634		2201	4295	6496	SO:0001819	synonymous_variant	219960	exon1			GCGGCGGCCCTCG	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.714C>A	11.37:g.57995634G>T		62	0	0		70	12	0.171429	NM_001004471	Q6IFG4	Silent	SNP	ENST00000316770.2	37	CCDS31547.1																																																																																			.	.	none		0.627	OR10Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394706.1	NM_001004471		T	57995634	G	T	57995634	2	4	18	1	0	0	0	0	0	0	0	1	10925	1190	42	4		4	OR10Q1	11	57995634	Silent	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	1650534	57995634	77010882	114	2501											
MPEG1	219972	hgsc.bcm.edu	37	chr11	58978306	58978306	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tcttcttgaacttccgggtgCcgtagatggccaaggtgata	8	12	12	9	2	2	3	0	2	2	1	3	3	3	3	3	3	2	1	3	3	4	5			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr11:58978306C>T	ENST00000361050.3	-	1	2118	c.2033G>A	c.(2032-2034)gGc>gAc	p.G678D		NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	678						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)				CTTCCGGGTGCCGTAGATGGC	0.547																																					p.G678D		Atlas-SNP	.											MPEG1,NS,carcinoma,-1,1	MPEG1	72	1	0			c.G2033A						PASS	.						133	135	134					11																	58978306		2039	4175	6214	SO:0001583	missense	219972	exon1			CGGGTGCCGTAGA	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.2033G>A	11.37:g.58978306C>T	ENSP00000354335:p.Gly678Asp	158	0	0		208	57	0.274038	NM_001039396	Q2M1T6|Q8TEF8	Missense_Mutation	SNP	ENST00000361050.3	37	CCDS41650.1	.	.	.	.	.	.	.	.	.	.	C	16.17	3.047131	0.55110	.	.	ENSG00000197629	ENST00000361050	T	0.23950	1.88	5.54	4.61	0.57282	.	0.370520	0.28510	N	0.015081	T	0.41396	0.1157	M	0.64997	1.995	0.34444	D	0.699936	D	0.59767	0.986	P	0.56398	0.797	T	0.59273	-0.7485	10	0.66056	D	0.02	-20.5924	12.8488	0.57846	0.1634:0.8366:0.0:0.0	.	678	Q2M385	MPEG1_HUMAN	D	678	ENSP00000354335:G678D	ENSP00000354335:G678D	G	-	2	0	MPEG1	58734882	0.025000	0.19082	0.349000	0.25694	0.852000	0.48524	2.436000	0.44819	1.286000	0.44565	0.655000	0.94253	GGC	.	.	none		0.547	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396		T	58978306	C	T	58978306	3	4	18	1	0	0	0	0	1	0	0	0	9732	739	26	2	121	2	MPEG1	11	58978306	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	982672	58978306	76028210	115	2502											
MPEG1	219972	hgsc.bcm.edu	37	chr11	58979064	58979064	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tggttgtaaccctcctcgtgGatctgggataacaggtgcac	8	11	12	10	1	1	0	0	0	1	0	3	2	2	2	2	4	3	3	2	4	2	3			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr11:58979064G>A	ENST00000361050.3	-	1	1360	c.1275C>T	c.(1273-1275)atC>atT	p.I425I	RN7SL42P_ENST00000579786.1_RNA	NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	425						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)				CCTCCTCGTGGATCTGGGATA	0.542																																					p.I425I		Atlas-SNP	.											.	MPEG1	72	.	0			c.C1275T						PASS	.						75	72	73					11																	58979064		1934	4148	6082	SO:0001819	synonymous_variant	219972	exon1			CTCGTGGATCTGG	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.1275C>T	11.37:g.58979064G>A		65	0	0		73	16	0.219178	NM_001039396	Q2M1T6|Q8TEF8	Silent	SNP	ENST00000361050.3	37	CCDS41650.1																																																																																			.	.	none		0.542	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396		A	58979064	G	A	58979064	2	1	18	1	0	0	0	0	0	0	0	1	9732	1164	41	2		2	MPEG1	11	58979064	Silent	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	758	58979064	76027452	116	2503											
CDC42BPG	55561	hgsc.bcm.edu	37	chr11	64591992	64591992	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tagggggaggcttcggggccGttctgagacctgcaggagaa	8	7	18	8	2	1	2	0	1	1	2	2	5	1	3	2	6	1	3	2	6	2	3	rs138706676		TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr11:64591992G>A	ENST00000342711.5	-	37	4608	c.4609C>T	c.(4609-4611)Cgg>Tgg	p.R1537W		NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)											central_nervous_system(1)|lung(3)	4						CTTCGGGGCCGTTCTGAGACC	0.582																																					p.R1537W		Atlas-SNP	.											.	CDC42BPG	101	.	0			c.C4609T						PASS	.	G	TRP/ARG	1,4401	2.1+/-5.4	0,1,2200	45	49	48		4609	2.2	1	11	dbSNP_134	48	0,8594		0,0,4297	no	missense	CDC42BPG	NM_017525.2	101	0,1,6497	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	1537/1552	64591992	1,12995	2201	4297	6498	SO:0001583	missense	55561	exon37			GGGGCCGTTCTGA	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.4609C>T	11.37:g.64591992G>A	ENSP00000345133:p.Arg1537Trp	134	0	0		137	29	0.211679	NM_017525		Missense_Mutation	SNP	ENST00000342711.5	37	CCDS31601.1	.	.	.	.	.	.	.	.	.	.	G	13.78	2.338643	0.41398	2.27E-4	0.0	ENSG00000171219	ENST00000342711	T	0.71579	-0.58	4.33	2.24	0.28232	.	0.238745	0.21940	N	0.066899	T	0.64735	0.2625	L	0.36672	1.1	0.26162	N	0.979986	D	0.76494	0.999	P	0.50082	0.63	T	0.58042	-0.7706	10	0.59425	D	0.04	.	8.9266	0.35643	0.0:0.0:0.5967:0.4033	.	1537	Q6DT37	MRCKG_HUMAN	W	1537	ENSP00000345133:R1537W	ENSP00000345133:R1537W	R	-	1	2	CDC42BPG	64348568	0.951000	0.32395	0.989000	0.46669	0.948000	0.59901	1.490000	0.35573	0.939000	0.37446	0.555000	0.69702	CGG	G|1.000;A|0.000	0.000	weak		0.582	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516		A	64591992	G	A	64591992	3	1	18	1	0	0	0	0	1	0	0	0	3076	1144	40	1	50	1	CDC42BPG	11	64591992	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	5612928	64591992	70414524	117	2504											
NUDT8	254552	hgsc.bcm.edu	37	chr11	67395800	67395800	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atcccccagctcacctcctcCgagttgggcctgaggctctg	5	9	10	17	1	2	1	1	1	1	0	5	2	5	1	6	2	1	3	6	2	0	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr11:67395800C>T	ENST00000376693.2	-	3	408	c.399G>A	c.(397-399)tcG>tcA	p.S133S	NUDT8_ENST00000301490.4_Silent_p.S133S|RP11-655M14.13_ENST00000533311.1_lincRNA	NM_001243750.1	NP_001230679.1	Q8WV74	NUDT8_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 8	133	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.					mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			endometrium(1)|lung(1)|prostate(1)|skin(1)	4						TCACCTCCTCCGAGTTGGGCC	0.622																																					p.S133S		Atlas-SNP	.											.	NUDT8	12	.	0			c.G399A						PASS	.						122	91	102					11																	67395800		2200	4294	6494	SO:0001819	synonymous_variant	254552	exon3			CTCCTCCGAGTTG	AI743601	CCDS8174.1, CCDS58151.1	11q13.2	2008-07-21			ENSG00000167799	ENSG00000167799		"Nudix motif containing"	8055	protein-coding gene	gene with protein product						11415433	Standard	NM_181843		Approved	FLJ41567	uc001omo.2	Q8WV74	OTTHUMG00000167292	ENST00000376693.2:c.399G>A	11.37:g.67395800C>T		30	0	0		49	12	0.244898	NM_181843	Q6ZW59	Silent	SNP	ENST00000376693.2	37	CCDS58151.1																																																																																			.	.	none		0.622	NUDT8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394036.1	NM_181843		T	67395800	C	T	67395800	2	4	18	1	0	0	0	0	0	0	0	1	10754	639	23	1		1	NUDT8	11	67395800	Silent	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	2803808	67395800	67610716	118	2505											
NOX4	50507	hgsc.bcm.edu	37	chr11	89177362	89177362	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcactgtaattcactgagaAgttgagggcattcaccagat	12	12	9	8	0	3	3	3	2	0	2	3	4	3	3	1	1	0	3	1	1	2	5			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr11:89177362A>G	ENST00000263317.4	-	5	626	c.388T>C	c.(388-390)Ttc>Ctc	p.F130L	NOX4_ENST00000531342.1_Intron|NOX4_ENST00000527956.1_Missense_Mutation_p.F106L|NOX4_ENST00000424319.1_Missense_Mutation_p.F106L|NOX4_ENST00000534731.1_Missense_Mutation_p.F130L|NOX4_ENST00000542487.1_Missense_Mutation_p.F106L|NOX4_ENST00000375979.3_Intron|NOX4_ENST00000532825.1_Missense_Mutation_p.F106L|NOX4_ENST00000343727.5_Missense_Mutation_p.F106L|NOX4_ENST00000525196.1_Missense_Mutation_p.F130L|NOX4_ENST00000535633.1_Missense_Mutation_p.F106L|NOX4_ENST00000413594.2_Missense_Mutation_p.F151L|NOX4_ENST00000528341.1_Missense_Mutation_p.F105L|NOX4_ENST00000527626.1_Intron			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4	130	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)				TTCACTGAGAAGTTGAGGGCA	0.453																																					p.F130L		Atlas-SNP	.											NOX4,NS,carcinoma,+1,1	NOX4	101	1	0			c.T388C						PASS	.						137	117	124					11																	89177362		2201	4299	6500	SO:0001583	missense	50507	exon5			CTGAGAAGTTGAG	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.388T>C	11.37:g.89177362A>G	ENSP00000263317:p.Phe130Leu	103	0	0		104	28	0.269231	NM_001143836	A8K715|B7Z520|E7EMD7|Q5K3R4|Q5K3R5|Q5K3R6|Q5K3R8|Q7Z7G3|Q86V92	Missense_Mutation	SNP	ENST00000263317.4	37	CCDS8285.1	.	.	.	.	.	.	.	.	.	.	A	17.40	3.379180	0.61735	.	.	ENSG00000086991	ENST00000424319;ENST00000535633;ENST00000343727;ENST00000534731;ENST00000525196;ENST00000263317;ENST00000532825;ENST00000527956;ENST00000542487;ENST00000528341;ENST00000413594	D;D;D;D;D;D;D;D;D;D;D	0.90620	-2.7;-2.7;-2.7;-2.7;-2.7;-2.7;-2.7;-2.7;-2.7;-2.7;-2.7	5.16	5.16	0.70880	Flavoprotein transmembrane component (1);	0.113019	0.64402	D	0.000011	D	0.91452	0.7302	L	0.31526	0.94	0.58432	D	0.999991	B;B;D;B;B	0.57257	0.017;0.395;0.979;0.01;0.144	B;B;D;B;B	0.71414	0.057;0.249;0.973;0.008;0.269	D	0.90606	0.4548	9	.	.	.	-16.4589	14.2622	0.66092	1.0:0.0:0.0:0.0	.	106;105;130;130;130	E9PMY6;E9PPP2;E9PI95;Q9NPH5-6;Q9NPH5	.;.;.;.;NOX4_HUMAN	L	106;106;106;130;130;130;106;106;106;105;151	ENSP00000412446:F106L;ENSP00000440172:F106L;ENSP00000344747:F106L;ENSP00000436892:F130L;ENSP00000436716:F130L;ENSP00000263317:F130L;ENSP00000434924:F106L;ENSP00000433797:F106L;ENSP00000439373:F106L;ENSP00000436970:F105L;ENSP00000405705:F151L	.	F	-	1	0	NOX4	88817010	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.714000	0.84703	2.070000	0.61991	0.460000	0.39030	TTC	.	.	none		0.453	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	NM_016931		G	89177362	A	G	89177362	3	3	18	1	0	0	0	0	1	0	0	0	10567	72	3	3	1404	3	NOX4	11	89177362	Missense_Mutation	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10	21781562	89177362	45829154	119	2506											
SORL1	6653	hgsc.bcm.edu	37	chr11	121323082	121323082	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	agggagtcgcgactcccgttCctattcaccctggtcgcact	6	10	10	15	4	1	0	1	0	0	0	5	2	3	1	3	2	0	2	3	2	1	3			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr11:121323082C>A	ENST00000260197.7	+	1	171	c.42C>A	c.(40-42)ttC>ttA	p.F14L	RP11-730K11.1_ENST00000501964.1_RNA|RP11-730K11.1_ENST00000529160.1_RNA	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	14					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)		GACTCCCGTTCCTATTCACCC	0.697																																					p.F14L		Atlas-SNP	.											.	SORL1	218	.	0			c.C42A						PASS	.						12	11	12					11																	121323082		2181	4277	6458	SO:0001583	missense	6653	exon1			CCCGTTCCTATTC	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.42C>A	11.37:g.121323082C>A	ENSP00000260197:p.Phe14Leu	53	0	0		55	12	0.218182	NM_003105	B2RNX7|Q92856	Missense_Mutation	SNP	ENST00000260197.7	37	CCDS8436.1	.	.	.	.	.	.	.	.	.	.	C	15.41	2.826352	0.50739	.	.	ENSG00000137642	ENST00000260197	D	0.90444	-2.67	3.8	3.8	0.43715	.	0.671312	0.13420	N	0.389241	T	0.78861	0.4350	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.70861	-0.4757	10	0.13470	T	0.59	.	11.0822	0.48066	0.0:1.0:0.0:0.0	.	14	Q92673	SORL_HUMAN	L	14	ENSP00000260197:F14L	ENSP00000260197:F14L	F	+	3	2	SORL1	120828292	1.000000	0.71417	0.996000	0.52242	0.978000	0.69477	1.878000	0.39608	1.985000	0.57927	0.442000	0.29010	TTC	.	.	none		0.697	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105		A	121323082	C	A	121323082	3	1	18	1	0	0	0	0	1	0	0	0	14949	854	30	4	44	4	SORL1	11	121323082	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	32145720	121323082	13683434	120	2507											
OR8B2	26595	hgsc.bcm.edu	37	chr11	124252524	124252524	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgacatgagagctacaagtaCtgaaggcttttgatcttcct	11	13	9	8	0	1	4	0	4	1	1	2	5	2	4	1	1	3	3	1	1	4	5			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr11:124252524C>A	ENST00000375013.2	-	1	734	c.716G>T	c.(715-717)aGt>aTt	p.S239I		NM_001005468.1	NP_001005468.1	Q96RD0	OR8B2_HUMAN	olfactory receptor, family 8, subfamily B, member 2	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)|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)		GCTACAAGTACTGAAGGCTTT	0.383																																					p.S239I		Atlas-SNP	.											.	OR8B2	42	.	0			c.G716T						PASS	.						56	61	59					11																	124252524		2196	4280	6476	SO:0001583	missense	26595	exon1			CAAGTACTGAAGG	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.716G>T	11.37:g.124252524C>A	ENSP00000364152:p.Ser239Ile	383	0	0		357	69	0.193277	NM_001005468	Q8NGH2	Missense_Mutation	SNP	ENST00000375013.2	37	CCDS31708.1	.	.	.	.	.	.	.	.	.	.	c	17.43	3.388312	0.61956	.	.	ENSG00000204293	ENST00000375013	T	0.00302	8.2	3.81	3.81	0.43845	GPCR, rhodopsin-like superfamily (1);	0.080815	0.53938	D	0.000051	T	0.00695	0.0023	H	0.95151	3.63	0.19300	N	0.999979	P	0.51933	0.949	P	0.54210	0.745	T	0.13176	-1.0519	10	0.87932	D	0	.	10.3825	0.44121	0.0:0.6742:0.3258:0.0	.	239	Q96RD0	OR8B2_HUMAN	I	239	ENSP00000364152:S239I	ENSP00000364152:S239I	S	-	2	0	OR8B2	123757734	0.105000	0.21958	0.391000	0.26233	0.558000	0.35554	0.590000	0.23954	2.126000	0.65437	0.505000	0.49811	AGT	.	.	none		0.383	OR8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387290.1	NM_001005468		A	124252524	C	A	124252524	3	1	18	1	0	0	0	0	1	0	0	0	11236	565	20	4	228	4	OR8B2	11	124252524	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	2929442	124252524	10753992	121	2508											
CCND2	894	hgsc.bcm.edu	37	chr12	4383227	4383227	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atggagctgctgtgccacgaGgtggacccggtccgcagggc	6	6	17	12	3	0	0	0	0	0	0	1	3	1	2	3	5	3	3	3	5	0	0			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr12:4383227G>A	ENST00000261254.3	+	1	290	c.21G>A	c.(19-21)gaG>gaA	p.E7E	RP11-264F23.3_ENST00000539135.1_RNA|RP11-264F23.4_ENST00000537370.1_RNA	NM_001759.3	NP_001750.1	P30279	CCND2_HUMAN	cyclin D2	7					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)			TGTGCCACGAGGTGGACCCGG	0.637			T	IGL@	"NHL,CLL"																																p.E7E		Atlas-SNP	.		Dom	yes		12	12p13	894	cyclin D2		L	.	CCND2	50	.	0			c.G21A						PASS	.						29	28	28					12																	4383227		2202	4298	6500	SO:0001819	synonymous_variant	894	exon1			CCACGAGGTGGAC	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.21G>A	12.37:g.4383227G>A		68	0	0		83	21	0.253012	NM_001759	A8K531|Q13955|Q5U035	Silent	SNP	ENST00000261254.3	37	CCDS8524.1																																																																																			.	.	none		0.637	CCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398287.1	NM_001759		A	4383227	G	A	4383227	2	1	18	1	0	0	0	0	0	0	0	1	2919	991	35	2		2	CCND2	12	4383227	Silent	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10		4383227	129468668	122	2509											
MLL2	8085	hgsc.bcm.edu	37	chr12	49435941	49435941	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggtgagatggtggacagctGgcccaactcctcatccttct	8	10	11	12	0	2	1	1	1	1	1	4	3	4	2	3	4	2	1	3	4	1	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr12:49435941G>A	ENST00000301067.7	-	28	6039	c.6040C>T	c.(6040-6042)Cag>Tag	p.Q2014*		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2014					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)										GTGGACAGCTGGCCCAACTCC	0.577																																					p.Q2014X		Atlas-SNP	.											MLL2_ENST00000301067,bladder,carcinoma,0,2	MLL2	1173	2	0			c.C6040T						PASS	.						50	54	53					12																	49435941		2121	4221	6342	SO:0001587	stop_gained	8085	exon28			ACAGCTGGCCCAA	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.6040C>T	12.37:g.49435941G>A	ENSP00000301067:p.Gln2014*	65	0	0		69	16	0.231884	NM_003482	O14687	Nonsense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	45	11.794231	0.99604	.	.	ENSG00000167548	ENST00000301067	.	.	.	5.34	5.34	0.76211	.	0.000000	0.36338	N	0.002643	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	13.1167	0.59303	0.0:0.2705:0.7295:0.0	.	.	.	.	X	2014	.	ENSP00000301067:Q2014X	Q	-	1	0	MLL2	47722208	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	4.514000	0.60482	2.686000	0.91538	0.561000	0.74099	CAG	.	.	none		0.577	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49435941	G	A	49435941	4	1	18	1	0	0	0	0	0	1	0	0	9630	1357	47	2	10681	2	MLL2	12	49435941	Nonsense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	45052714	49435941	84415954	123	2510											
PAN2	10330	hgsc.bcm.edu	37	chr12	56712936	56712936	+	5'Flank	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cggggcatatggaacaggtaGacagtgtcaaggacttggtc	11	8	15	7	1	1	1	1	0	0	1	2	3	1	3	0	6	1	2	0	6	4	3			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr12:56712936G>C	ENST00000273308.4	-	0	0				PAN2_ENST00000548043.1_Silent_p.V1104V|PAN2_ENST00000440411.3_Silent_p.V1100V|PAN2_ENST00000549090.1_Intron|PAN2_ENST00000257931.5_Silent_p.V1103V|PAN2_ENST00000425394.2_Silent_p.V1104V	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						GGAACAGGTAGACAGTGTCAA	0.493																																					p.V1104V		Atlas-SNP	.											.	PAN2	107	.	0			c.C3312G						PASS	.						100	92	95					12																	56712936		2203	4300	6503	SO:0001631	upstream_gene_variant	9924	exon24			CAGGTAGACAGTG	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		12.37:g.56712936G>C	Exception_encountered	97	0	0		131	30	0.229008	NM_001127460	B2R7B9|Q9UHE9	Silent	SNP	ENST00000273308.4	37	CCDS8914.1																																																																																			.	.	none		0.493	CNPY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408546.1	NM_014255		C	56712936	G	C	56712936	1	2	18	0	1	0	0	0	0	0	0	0	11423	929	33	4		4	PAN2	12	56712936	5'Flank	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	7276995	56712936	77138959	124	2511											
NAV3	89795	hgsc.bcm.edu	37	chr12	78571048	78571048	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	caagttaccccataatgctgGtgactgtggctcagcatcca	10	10	9	12	0	1	1	1	1	0	0	2	1	2	1	3	2	3	4	3	2	3	2	rs555983392		TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr12:78571048G>T	ENST00000397909.2	+	27	5425	c.5252G>T	c.(5251-5253)gGt>gTt	p.G1751V	NAV3_ENST00000266692.7_Missense_Mutation_p.G1574V|NAV3_ENST00000228327.6_Missense_Mutation_p.G1751V|NAV3_ENST00000536525.2_Missense_Mutation_p.G1751V			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1751						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						CATAATGCTGGTGACTGTGGC	0.443										HNSCC(70;0.22)			G|||	1	0.000199681	0.0008	0.0	5008	,	,		17214	0.0		0.0	False		,,,				2504	0.0				p.G1751V		Atlas-SNP	.											.	NAV3	506	.	0			c.G5252T						PASS	.						121	112	115					12																	78571048		1909	4132	6041	SO:0001583	missense	89795	exon27			ATGCTGGTGACTG	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.5252G>T	12.37:g.78571048G>T	ENSP00000381007:p.Gly1751Val	136	0	0		171	68	0.397661	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.01|12.01	1.808147|1.808147	0.31961|0.31961	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692;ENST00000378640;ENST00000550788|ENST00000552895	D;D;D;D;D|.	0.93076|.	-3.16;-3.16;-3.16;-3.16;-3.16|.	5.95|5.95	5.01|5.01	0.66863|0.66863	.|.	0.000000|.	0.40818|.	U|.	0.001019|.	T|T	0.52468|0.52468	0.1736|0.1736	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	D|D	1|1	P;B;P;B|.	0.50617|.	0.57;0.001;0.937;0.017|.	B;B;B;B|.	0.43536|.	0.147;0.003;0.423;0.008|.	T|T	0.43147|0.43147	-0.9409|-0.9409	10|5	0.56958|.	D|.	0.05|.	-13.5845|-13.5845	10.0624|10.0624	0.42284|0.42284	0.0709:0.1386:0.7906:0.0|0.0709:0.1386:0.7906:0.0	.|.	1751;1574;1751;1751|.	E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2|.	.;.;NAV3_HUMAN;.|.	V|C	1751;1751;1751;1574;365;373|645	ENSP00000446132:G1751V;ENSP00000381007:G1751V;ENSP00000228327:G1751V;ENSP00000266692:G1574V;ENSP00000448303:G373V|.	ENSP00000228327:G1751V|.	G|W	+|+	2|3	0|0	NAV3|NAV3	77095179|77095179	0.914000|0.914000	0.31030|0.31030	0.895000|0.895000	0.35142|0.35142	0.183000|0.183000	0.23260|0.23260	2.930000|2.930000	0.48924|0.48924	2.824000|2.824000	0.97209|0.97209	0.655000|0.655000	0.94253|0.94253	GGT|TGG	.	.	none		0.443	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		T	78571048	G	T	78571048	3	4	18	1	0	0	0	0	1	0	0	0	10194	1261	44	4	5358	4	NAV3	12	78571048	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	21858112	78571048	55280847	125	2512											
BTG1	694	hgsc.bcm.edu	37	chr12	92537899	92537899	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtagtttttggaagggctcGttctgcccaagagaagttcc	8	13	12	8	1	1	1	0	0	1	1	3	3	2	2	2	2	1	5	2	2	4	5	rs544927217		TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr12:92537899G>A	ENST00000256015.3	-	2	834	c.473C>T	c.(472-474)aCg>aTg	p.T158M	RP11-796E2.4_ENST00000501008.2_RNA|C12orf79_ENST00000551563.2_5'Flank|RP11-796E2.4_ENST00000499685.2_RNA|C12orf79_ENST00000551843.1_5'Flank|C12orf79_ENST00000546975.1_5'Flank|C12orf79_ENST00000549802.1_5'Flank	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	158					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)			haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				GGAAGGGCTCGTTCTGCCCAA	0.428			T	MYC	BCLL						OREG0022024	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T158M		Atlas-SNP	.		Dom	yes		12	12q22	694	"B-cell translocation gene 1, anti-proliferative"		L	.	BTG1	30	.	0			c.C473T						PASS	.						94	81	85					12																	92537899		2203	4300	6503	SO:0001583	missense	694	exon2			GGGCTCGTTCTGC		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.473C>T	12.37:g.92537899G>A	ENSP00000256015:p.Thr158Met	92	0	0	1291	146	18	0.123288	NM_001731	P31607	Missense_Mutation	SNP	ENST00000256015.3	37	CCDS9043.1	.	.	.	.	.	.	.	.	.	.	G	18.66	3.671909	0.67928	.	.	ENSG00000133639	ENST00000256015;ENST00000552315	T;T	0.36878	1.81;1.23	5.27	5.27	0.74061	Anti-proliferative protein (1);	0.000000	0.85682	D	0.000000	T	0.49712	0.1573	L	0.46157	1.445	0.80722	D	1	D	0.76494	0.999	P	0.56216	0.794	T	0.50233	-0.8852	10	0.87932	D	0	-3.6362	19.0956	0.93249	0.0:0.0:1.0:0.0	.	158	P62324	BTG1_HUMAN	M	158;83	ENSP00000256015:T158M;ENSP00000447551:T83M	ENSP00000256015:T158M	T	-	2	0	BTG1	91062030	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.601000	0.82783	2.733000	0.93635	0.650000	0.86243	ACG	.	.	none		0.428	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1			A	92537899	G	A	92537899	3	1	18	1	0	0	0	0	1	0	0	0	1555	1145	40	1	46	1	BTG1	12	92537899	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	13966851	92537899	41313996	126	2513											
BTG1	694	hgsc.bcm.edu	37	chr12	92537992	92537992	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgctacctcctgctggtgagGcttcatacagcacacagatg	9	10	10	12	0	1	2	1	1	0	1	2	2	2	2	2	2	5	4	2	2	2	3			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr12:92537992G>A	ENST00000256015.3	-	2	741	c.380C>T	c.(379-381)gCc>gTc	p.A127V	RP11-796E2.4_ENST00000501008.2_RNA|C12orf79_ENST00000551563.2_5'Flank|RP11-796E2.4_ENST00000499685.2_RNA|C12orf79_ENST00000551843.1_5'Flank|C12orf79_ENST00000546975.1_5'Flank|C12orf79_ENST00000549802.1_5'Flank	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	127					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)			haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				TGCTGGTGAGGCTTCATACAG	0.517			T	MYC	BCLL						OREG0022024	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A127V		Atlas-SNP	.		Dom	yes		12	12q22	694	"B-cell translocation gene 1, anti-proliferative"		L	.	BTG1	30	.	0			c.C380T						PASS	.						111	99	103					12																	92537992		2203	4300	6503	SO:0001583	missense	694	exon2			GGTGAGGCTTCAT		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.380C>T	12.37:g.92537992G>A	ENSP00000256015:p.Ala127Val	93	0	0	1291	158	33	0.208861	NM_001731	P31607	Missense_Mutation	SNP	ENST00000256015.3	37	CCDS9043.1	.	.	.	.	.	.	.	.	.	.	G	15.27	2.783019	0.49891	.	.	ENSG00000133639	ENST00000256015;ENST00000552315	T;T	0.31769	1.89;1.48	5.8	5.8	0.92144	Anti-proliferative protein (1);	0.052045	0.85682	D	0.000000	T	0.47875	0.1469	L	0.51422	1.61	0.40184	D	0.977322	P	0.37688	0.605	P	0.51297	0.665	T	0.33189	-0.9878	10	0.52906	T	0.07	-8.3568	20.0608	0.97674	0.0:0.0:1.0:0.0	.	127	P62324	BTG1_HUMAN	V	127;52	ENSP00000256015:A127V;ENSP00000447551:A52V	ENSP00000256015:A127V	A	-	2	0	BTG1	91062123	1.000000	0.71417	1.000000	0.80357	0.748000	0.42578	9.413000	0.97351	2.733000	0.93635	0.650000	0.86243	GCC	.	.	none		0.517	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1			A	92537992	G	A	92537992	3	1	18	1	0	0	0	0	1	0	0	0	1555	1203	42	2	139	2	BTG1	12	92537992	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	93	92537992	41313903	127	2514											
DTX1	1840	hgsc.bcm.edu	37	chr12	113496132	113496132	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ccctacacggccaccgtgtgCcaccacattgagaacgtgct	9	7	9	16	3	0	1	0	1	0	1	0	2	0	1	5	1	4	1	5	1	2	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr12:113496132C>T	ENST00000257600.3	+	1	638	c.135C>T	c.(133-135)tgC>tgT	p.C45C		NM_004416.2	NP_004407.2	Q86Y01	DTX1_HUMAN	deltex 1, E3 ubiquitin ligase	45	WWE 1. {ECO:0000255|PROSITE- ProRule:PRU00248}.				cell surface receptor signaling pathway (GO:0007166)|glial cell differentiation (GO:0010001)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of T cell differentiation (GO:0045581)|Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)|regulation of Notch signaling pathway (GO:0008593)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Notch binding (GO:0005112)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	32						CCACCGTGTGCCACCACATTG	0.647																																					p.C45C		Atlas-SNP	.											.	DTX1	83	.	0			c.C135T						PASS	.						103	90	94					12																	113496132		2203	4300	6503	SO:0001819	synonymous_variant	1840	exon1			CGTGTGCCACCAC	AF053700	CCDS9164.1	12q24	2014-01-28	2014-01-28			ENSG00000135144			3060	protein-coding gene	gene with protein product		602582	"deltex homolog 1 (Drosophila)"			9590294, 12670957	Standard	NM_004416		Approved	hDx-1	uc001tuk.1	Q86Y01	OTTHUMG00000169610	ENST00000257600.3:c.135C>T	12.37:g.113496132C>T		71	0	0		89	10	0.11236	NM_004416	O60630|Q9BS04	Silent	SNP	ENST00000257600.3	37	CCDS9164.1																																																																																			.	.	none		0.647	DTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405045.2			T	113496132	C	T	113496132	2	4	18	1	0	0	0	0	0	0	0	1	4795	747	26	2		2	DTX1	12	113496132	Silent	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	20958140	113496132	20355763	128	2515											
TBX5	6910	hgsc.bcm.edu	37	chr12	114836488	114836488	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtctgggtgcacgtacaggcGgccaggcatggcgggctcag	6	6	18	11	3	2	0	1	0	1	0	2	0	2	0	1	6	2	4	1	6	1	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr12:114836488G>A	ENST00000310346.4	-	5	1066	c.400C>T	c.(400-402)Cgc>Tgc	p.R134C	TBX5_ENST00000526441.1_Missense_Mutation_p.R134C|TBX5_ENST00000349716.5_Missense_Mutation_p.R84C|TBX5_ENST00000405440.2_Missense_Mutation_p.R134C|TBX5_ENST00000552726.1_5'UTR	NM_000192.3	NP_000183.2	Q99593	TBX5_HUMAN	T-box 5	134					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)		ACGTACAGGCGGCCAGGCATG	0.622																																					p.R134C	NSCLC(152;1358 1980 4050 23898 40356)	Atlas-SNP	.											.	TBX5	188	.	0			c.C400T						PASS	.						48	41	43					12																	114836488		2203	4300	6503	SO:0001583	missense	6910	exon5			ACAGGCGGCCAGG	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.400C>T	12.37:g.114836488G>A	ENSP00000309913:p.Arg134Cys	86	0	0		118	51	0.432203	NM_000192	A6ND77|O15301|Q96TB0|Q9Y4I2	Missense_Mutation	SNP	ENST00000310346.4	37	CCDS9173.1	.	.	.	.	.	.	.	.	.	.	G	17.00	3.275640	0.59649	.	.	ENSG00000089225	ENST00000349716;ENST00000310346;ENST00000448888;ENST00000405440;ENST00000526441	D;D;D;D	0.90732	-2.72;-2.72;-2.72;-2.72	4.56	3.66	0.41972	p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.93864	0.8037	M	0.73430	2.235	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.973;1.0	D	0.92576	0.6070	10	0.38643	T	0.18	.	10.5224	0.44927	0.0:0.1237:0.6601:0.2162	.	134;134	Q99593-2;Q99593	.;TBX5_HUMAN	C	84;134;31;134;134	ENSP00000337723:R84C;ENSP00000309913:R134C;ENSP00000384152:R134C;ENSP00000433292:R134C	ENSP00000309913:R134C	R	-	1	0	TBX5	113320871	0.990000	0.36364	0.980000	0.43619	0.586000	0.36452	2.065000	0.41442	1.231000	0.43661	0.655000	0.94253	CGC	.	.	none		0.622	TBX5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388297.1	NM_080717		A	114836488	G	A	114836488	3	1	18	1	0	0	0	0	1	0	0	0	15676	1116	39	1	1243	1	TBX5	12	114836488	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	1340356	114836488	19015407	129	2516											
TSC22D1	8848	hgsc.bcm.edu	37	chr13	45009000	45009000	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttctctgaccgcatacatcAaatggcttttcactagatcc	10	13	5	13	1	3	2	2	1	1	1	5	2	4	2	2	1	1	2	2	1	3	5			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr13:45009000A>C	ENST00000458659.2	-	3	3474	c.2984T>G	c.(2983-2985)tTg>tGg	p.L995W	TSC22D1_ENST00000501704.2_Intron|RP11-71C5.2_ENST00000426579.2_RNA|TSC22D1_ENST00000261489.2_Missense_Mutation_p.L66W	NM_183422.3	NP_904358.2	Q15714	T22D1_HUMAN	TSC22 domain family, member 1	995					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)		CGCATACATCAAATGGCTTTT	0.378																																					p.L995W		Atlas-SNP	.											.	TSC22D1	88	.	0			c.T2984G						PASS	.						104	113	110					13																	45009000		2203	4300	6503	SO:0001583	missense	8848	exon3			TACATCAAATGGC	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.2984T>G	13.37:g.45009000A>C	ENSP00000397435:p.Leu995Trp	202	0	0		187	57	0.304813	NM_183422	B3KRL7|B9EGI0|O00666|Q6AHX5|Q6IBU1|Q8NCN1|Q96JS5	Missense_Mutation	SNP	ENST00000458659.2	37	CCDS31966.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.977062	0.74360	.	.	ENSG00000102804	ENST00000458659;ENST00000261489	D	0.83075	-1.68	5.72	5.72	0.89469	.	0.569269	0.14836	N	0.295563	D	0.90783	0.7106	M	0.76938	2.355	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.71870	0.975;0.937	D	0.90788	0.4684	10	0.87932	D	0	.	14.02	0.64547	1.0:0.0:0.0:0.0	.	995;66	Q15714;Q15714-2	T22D1_HUMAN;.	W	995;66	ENSP00000397435:L995W	ENSP00000261489:L66W	L	-	2	0	TSC22D1	43907000	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	9.287000	0.95975	2.188000	0.69820	0.529000	0.55759	TTG	.	.	none		0.378	TSC22D1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044743.2	NM_006022		C	45009000	A	C	45009000	3	2	18	1	0	0	0	0	1	0	0	0	16622	131	5	5	241	5	TSC22D1	13	45009000	Missense_Mutation	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10		45009000	70160878	130	2517											
HECTD1	25831	hgsc.bcm.edu	37	chr14	31626395	31626395	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatccaggacagttgcagtGatttccactagtattgtagg	10	13	11	7	0	0	2	0	2	0	0	2	3	2	3	2	2	1	4	2	2	3	6			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr14:31626395G>T	ENST00000399332.1	-	11	2225	c.1737C>A	c.(1735-1737)atC>atA	p.I579I	HECTD1_ENST00000553700.1_Silent_p.I579I	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	579					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)		CAGTTGCAGTGATTTCCACTA	0.323																																					p.I579I		Atlas-SNP	.											.	HECTD1	159	.	0			c.C1737A						PASS	.						181	171	174					14																	31626395		1847	4099	5946	SO:0001819	synonymous_variant	25831	exon11			TGCAGTGATTTCC	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.1737C>A	14.37:g.31626395G>T		194	0	0		320	79	0.246875	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Silent	SNP	ENST00000399332.1	37	CCDS41939.1																																																																																			.	.	none		0.323	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			T	31626395	G	T	31626395	2	4	18	1	0	0	0	0	0	0	0	1	7048	1280	45	4		4	HECTD1	14	31626395	Silent	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10		31626395	75723145	131	2518											
C14orf4	64207	hgsc.bcm.edu	37	chr14	77493791	77493791	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgctgctgctgctgctgctgCtgttgctgctgctgctgctg	0	15	14	12	0	0	0	0	0	0	0	0	0	0	0	0	0	12	13	0	0	0	1	rs377151545		TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr14:77493791C>T	ENST00000238647.3	-	1	1243	c.345G>A	c.(343-345)caG>caA	p.Q115Q		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	115	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						gctgctgctgctgttgctgct	0.697																																					p.Q115Q		Atlas-SNP	.											.	IRF2BPL	40	.	0			c.G345A						PASS	.						2	2	2					14																	77493791		1245	2269	3514	SO:0001819	synonymous_variant	64207	exon1			CTGCTGCTGTTGC	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.345G>A	14.37:g.77493791C>T		37	0	0		46	10	0.217391	NM_024496	Q8NDQ2|Q96JG2|Q9H3I7	Silent	SNP	ENST00000238647.3	37	CCDS9854.1																																																																																			.	.	none		0.697	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1	NM_024496		T	77493791	C	T	77493791	2	4	18	1	0	0	0	0	0	0	0	1	1775	796	28	2		2	C14orf4	14	77493791	Silent	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	45867396	77493791	29855749	132	2519											
ADCK1	57143	hgsc.bcm.edu	37	chr14	78392248	78392248	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgcctgcatgctgacggcgCgatcgtgggactcggtcaac	6	9	14	12	5	1	1	1	1	0	0	3	3	1	2	1	3	4	2	1	3	1	1	rs142956948	byFrequency	TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr14:78392248C>T	ENST00000238561.5	+	9	1249	c.1150C>T	c.(1150-1152)Cga>Tga	p.R384*	ADCK1_ENST00000556560.1_3'UTR|ADCK1_ENST00000341211.5_Nonsense_Mutation_p.R316*	NM_020421.3	NP_065154.2	Q86TW2	ADCK1_HUMAN	aarF domain containing kinase 1	391	Protein kinase.					extracellular region (GO:0005576)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.R316*(1)		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)		GCTGACGGCGCGATCGTGGGA	0.602													C|||	2	0.000399361	0.0	0.0	5008	,	,		17780	0.0		0.002	False		,,,				2504	0.0				p.R384X		Atlas-SNP	.											ADCK1,colon,carcinoma,0,1	ADCK1	81	1	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1150T						scavenged	.						150	153	152					14																	78392248		2203	4300	6503	SO:0001587	stop_gained	57143	exon9			ACGGCGCGATCGT	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.1150C>T	14.37:g.78392248C>T	ENSP00000238561:p.Arg384*	84	1	0.0119048		92	17	0.184783	NM_020421	B3KUD5|Q6PD65|Q9UIE6	Nonsense_Mutation	SNP	ENST00000238561.5	37	CCDS9869.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	21.1	4.096859	0.76870	.	.	ENSG00000063761	ENST00000238561;ENST00000341211	.	.	.	5.26	4.38	0.52667	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-41.0779	13.4374	0.61092	0.3432:0.6568:0.0:0.0	.	.	.	.	X	384;316	.	ENSP00000238561:R384X	R	+	1	2	ADCK1	77462001	1.000000	0.71417	0.911000	0.35937	0.100000	0.18952	4.008000	0.57103	1.215000	0.43411	-0.165000	0.13383	CGA	C|0.999;T|0.001	0.001	strong		0.602	ADCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413864.1	NM_020421		T	78392248	C	T	78392248	4	4	18	1	0	0	0	0	0	1	0	0	288	760	27	1	1180	1	ADCK1	14	78392248	Nonsense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	898457	78392248	28957292	133	2520											
C15orf43	145645	hgsc.bcm.edu	37	chr15	45270701	45270701	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttgtaggttatatatcaattGatgccatgaagaaattcctt	13	16	7	5	0	1	3	1	2	0	1	2	3	2	3	2	1	1	2	2	1	7	8			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr15:45270701G>A	ENST00000340827.3	+	7	555	c.538G>A	c.(538-540)Gat>Aat	p.D180N		NM_152448.2	NP_689661.1	Q8NHR7	CO043_HUMAN	chromosome 15 open reading frame 43	180										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)		TATATCAATTGATGCCATGAA	0.299																																					p.D180N		Atlas-SNP	.											.	C15orf43	19	.	0			c.G538A						PASS	.						47	50	49					15																	45270701		2193	4284	6477	SO:0001583	missense	145645	exon7			TCAATTGATGCCA	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.538G>A	15.37:g.45270701G>A	ENSP00000340644:p.Asp180Asn	397	0	0		498	109	0.218875	NM_152448		Missense_Mutation	SNP	ENST00000340827.3	37	CCDS10115.1	.	.	.	.	.	.	.	.	.	.	G	14.83	2.653183	0.47362	.	.	ENSG00000167014	ENST00000340827	T	0.67523	-0.27	4.05	3.12	0.35913	.	0.199441	0.32106	N	0.006577	T	0.68220	0.2977	L	0.29908	0.895	0.26427	N	0.976005	D	0.67145	0.996	D	0.77557	0.99	T	0.57825	-0.7744	10	0.52906	T	0.07	.	7.923	0.29857	0.1204:0.0:0.8796:0.0	.	180	Q8NHR7	CO043_HUMAN	N	180	ENSP00000340644:D180N	ENSP00000340644:D180N	D	+	1	0	C15orf43	43057993	1.000000	0.71417	1.000000	0.80357	0.644000	0.38419	2.150000	0.42254	0.813000	0.34350	0.298000	0.19748	GAT	.	.	none		0.299	C15orf43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254032.1	NM_152448		A	45270701	G	A	45270701	3	1	18	1	0	0	0	0	1	0	0	0	1799	1290	45	2	564	2	C15orf43	15	45270701	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10		45270701	57260691	134	2521											
DUOX2	50506	hgsc.bcm.edu	37	chr15	45404810	45404810	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcaggccggctatgccccgCgtggctgcgttgctgagccg	3	7	17	14	5	0	1	0	1	0	0	0	1	0	1	4	4	4	5	4	4	1	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr15:45404810C>T	ENST00000603300.1	-	4	469	c.267G>A	c.(265-267)acG>acA	p.T89T	DUOXA2_ENST00000323030.5_5'Flank|DUOX2_ENST00000389039.6_Silent_p.T89T	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	89	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)		CTATGCCCCGCGTGGCTGCGT	0.672																																					p.T89T		Atlas-SNP	.											.	DUOX2	137	.	0			c.G267A						PASS	.						26	30	29					15																	45404810		2191	4277	6468	SO:0001819	synonymous_variant	50506	exon4			GCCCCGCGTGGCT	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.267G>A	15.37:g.45404810C>T		90	0	0		82	16	0.195122	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Silent	SNP	ENST00000603300.1	37	CCDS10117.1																																																																																			.	.	none		0.672	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080		T	45404810	C	T	45404810	2	4	18	1	0	0	0	0	0	0	0	1	4803	755	27	1		1	DUOX2	15	45404810	Silent	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	134109	45404810	57126582	135	2522											
DUOX1	53905	hgsc.bcm.edu	37	chr15	45427482	45427482	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acggagtcccagcaatccccGggacccggtgaggcggggaa	9	3	16	13	4	0	1	0	1	0	0	2	4	2	4	4	6	1	1	4	6	2	0			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr15:45427482G>A	ENST00000321429.4	+	6	895	c.488G>A	c.(487-489)cGg>cAg	p.R163Q	DUOX1_ENST00000389037.3_Missense_Mutation_p.R163Q	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	163	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)		AGCAATCCCCGGGACCCGGTG	0.736																																					p.R163Q		Atlas-SNP	.											.	DUOX1	125	.	0			c.G488A						PASS	.						8	10	9					15																	45427482		2133	4212	6345	SO:0001583	missense	53905	exon6			ATCCCCGGGACCC	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.488G>A	15.37:g.45427482G>A	ENSP00000317997:p.Arg163Gln	59	0	0		77	16	0.207792	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Missense_Mutation	SNP	ENST00000321429.4	37	CCDS32221.1	.	.	.	.	.	.	.	.	.	.	.	29.0	4.966816	0.92855	.	.	ENSG00000137857	ENST00000431588;ENST00000321429;ENST00000389037	T;T	0.72394	-0.65;-0.65	3.55	3.55	0.40652	.	0.000000	0.85682	D	0.000000	D	0.87684	0.6239	H	0.95712	3.71	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91007	0.4847	10	0.87932	D	0	-29.494	13.0686	0.59048	0.0:0.0:1.0:0.0	.	163	Q9NRD9	DUOX1_HUMAN	Q	163	ENSP00000317997:R163Q;ENSP00000373689:R163Q	ENSP00000317997:R163Q	R	+	2	0	DUOX1	43214774	1.000000	0.71417	0.994000	0.49952	0.739000	0.42172	4.852000	0.62904	1.976000	0.57569	0.454000	0.30748	CGG	.	.	none		0.736	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434		A	45427482	G	A	45427482	3	1	18	1	0	0	0	0	1	0	0	0	4802	1116	39	1	502	1	DUOX1	15	45427482	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	22672	45427482	57103910	136	2523											
ISLR	3671	hgsc.bcm.edu	37	chr15	74468257	74468257	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccggtgagggtggtgaggAcacactggggcgcaggttcc	6	6	19	10	2	0	2	0	2	0	0	1	3	1	3	2	7	0	2	2	7	0	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr15:74468257A>G	ENST00000249842.3	+	2	1415	c.1058A>G	c.(1057-1059)gAc>gGc	p.D353G	ISLR_ENST00000395118.1_Missense_Mutation_p.D353G|RP11-665J16.1_ENST00000561647.1_RNA	NM_005545.3	NP_005536.1	O14498	ISLR_HUMAN	immunoglobulin superfamily containing leucine-rich repeat	353					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						GGTGGTGAGGACACACTGGGG	0.627																																					p.D353G		Atlas-SNP	.											.	ISLR	49	.	0			c.A1058G						PASS	.						92	75	81					15																	74468257		2198	4297	6495	SO:0001583	missense	3671	exon2			GTGAGGACACACT	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.1058A>G	15.37:g.74468257A>G	ENSP00000249842:p.Asp353Gly	45	0	0		53	11	0.207547	NM_201526		Missense_Mutation	SNP	ENST00000249842.3	37	CCDS10260.1	.	.	.	.	.	.	.	.	.	.	A	6.017	0.371486	0.11409	.	.	ENSG00000129009	ENST00000249842;ENST00000395118	T;T	0.64260	-0.09;-0.09	4.54	4.54	0.55810	.	0.000000	0.44902	U	0.000416	T	0.39784	0.1091	N	0.08118	0	0.34788	D	0.735477	B	0.30793	0.295	B	0.27608	0.081	T	0.50693	-0.8798	10	0.21014	T	0.42	.	13.8818	0.63686	1.0:0.0:0.0:0.0	.	353	O14498	ISLR_HUMAN	G	353	ENSP00000249842:D353G;ENSP00000378550:D353G	ENSP00000249842:D353G	D	+	2	0	ISLR	72255310	0.998000	0.40836	0.339000	0.25562	0.004000	0.04260	4.428000	0.59894	1.687000	0.51057	0.402000	0.26972	GAC	.	.	none		0.627	ISLR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269044.1	NM_005545		G	74468257	A	G	74468257	3	3	18	1	0	0	0	0	1	0	0	0	7867	275	10	3	1060	3	ISLR	15	74468257	Missense_Mutation	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10	29040775	74468257	28063135	137	2524											
MESDC2	23184	hgsc.bcm.edu	37	chr15	81271769	81271769	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtccttgatctcccaggcgtAgctcccatcgcgaagcatga	8	9	10	14	3	1	2	0	2	1	0	5	3	3	2	3	1	2	3	3	1	2	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr15:81271769A>C	ENST00000261758.4	-	3	582	c.496T>G	c.(496-498)Tac>Gac	p.Y166D	MESDC2_ENST00000560244.1_5'Flank	NM_015154.1	NP_055969.1	Q14696	MESD_HUMAN	mesoderm development candidate 2	166	Escort domain. {ECO:0000250}.				mesoderm development (GO:0007498)|protein folding (GO:0006457)|protein localization to cell surface (GO:0034394)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)				cervix(1)|large_intestine(5)|ovary(1)|urinary_tract(1)	8						TCCCAGGCGTAGCTCCCATCG	0.532																																					p.Y166D		Atlas-SNP	.											.	MESDC2	23	.	0			c.T496G						PASS	.						75	70	72					15																	81271769		2203	4300	6503	SO:0001583	missense	23184	exon3			AGGCGTAGCTCCC	D42039	CCDS32308.1	15q13	2008-07-18							13520	protein-coding gene	gene with protein product		607783				7788527, 11247670	Standard	NM_015154		Approved	KIAA0081, BOCA, MESD	uc002bfy.1	Q14696		ENST00000261758.4:c.496T>G	15.37:g.81271769A>C	ENSP00000261758:p.Tyr166Asp	62	0	0		50	17	0.34	NM_015154	B4DW84|D3DW96|Q969U1	Missense_Mutation	SNP	ENST00000261758.4	37	CCDS32308.1	.	.	.	.	.	.	.	.	.	.	A	17.53	3.413065	0.62511	.	.	ENSG00000117899	ENST00000261758	.	.	.	5.9	5.9	0.94986	.	0.142736	0.48286	D	0.000198	T	0.58075	0.2097	L	0.56769	1.78	0.50171	D	0.999853	P	0.41232	0.743	B	0.41174	0.349	T	0.58393	-0.7644	9	0.37606	T	0.19	-5.1443	16.378	0.83412	1.0:0.0:0.0:0.0	.	166	Q14696	MESD_HUMAN	D	166	.	ENSP00000261758:Y166D	Y	-	1	0	MESDC2	79058824	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.304000	0.51866	2.277000	0.76020	0.529000	0.55759	TAC	.	.	none		0.532	MESDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417673.2	NM_015154		C	81271769	A	C	81271769	3	2	18	1	0	0	0	0	1	0	0	0	9490	420	15	5	212	5	MESDC2	15	81271769	Missense_Mutation	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10	6803512	81271769	21259623	138	2525											
SV2B	9899	hgsc.bcm.edu	37	chr15	91835705	91835705	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccaaagtggtccccatccttCtggctgctgcttctctggtt	4	14	9	14	0	2	0	0	0	2	0	5	0	4	0	4	3	2	4	4	3	1	3			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr15:91835705C>T	ENST00000394232.1	+	13	2445	c.1975C>T	c.(1975-1977)Ctg>Ttg	p.L659L	SV2B_ENST00000330276.4_Silent_p.L659L|SV2B_ENST00000545111.2_Silent_p.L508L	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	659					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)			CCCCATCCTTCTGGCTGCTGC	0.507																																					p.L659L		Atlas-SNP	.											.	SV2B	98	.	0			c.C1975T						PASS	.						133	124	127					15																	91835705		2198	4298	6496	SO:0001819	synonymous_variant	9899	exon14			ATCCTTCTGGCTG	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.1975C>T	15.37:g.91835705C>T		211	0	0		218	53	0.243119	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Silent	SNP	ENST00000394232.1	37	CCDS10370.1																																																																																			.	.	none		0.507	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848		T	91835705	C	T	91835705	2	4	18	1	0	0	0	0	0	0	0	1	15433	912	32	2		2	SV2B	15	91835705	Silent	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	10563936	91835705	10695687	139	2526											
SRRM2	23524	hgsc.bcm.edu	37	chr16	2816224	2816224	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcaccagtcagccggagaCggtcaaggtccaggacttca	10	7	11	13	2	4	1	4	0	0	1	5	3	5	2	3	4	1	0	3	4	1	2	rs151100831	byFrequency	TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr16:2816224C>T	ENST00000301740.8	+	11	6244	c.5695C>T	c.(5695-5697)Cgg>Tgg	p.R1899W		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	1899	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						CAGCCGGAGACGGTCAAGGTC	0.592																																					p.R1899W		Atlas-SNP	.											SRRM2,colon,carcinoma,0,1	SRRM2	263	1	0			c.C5695T						PASS	.						104	100	101					16																	2816224		2198	4300	6498	SO:0001583	missense	23524	exon11			CGGAGACGGTCAA	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.5695C>T	16.37:g.2816224C>T	ENSP00000301740:p.Arg1899Trp	39	0	0		73	42	0.575342	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	37	CCDS32373.1	.	.	.	.	.	.	.	.	.	.	C	0.854	-0.737664	0.03111	.	.	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933	T	0.26373	1.74	5.46	3.27	0.37495	.	0.000000	0.56097	D	0.000040	T	0.25717	0.0626	N	0.08118	0	0.31050	N	0.715362	D	0.89917	1.0	D	0.77557	0.99	T	0.10222	-1.0639	10	0.72032	D	0.01	-8.5524	7.212	0.25939	0.3166:0.5967:0.0:0.0867	.	1899	Q9UQ35	SRRM2_HUMAN	W	1899;1899;1151	ENSP00000301740:R1899W	ENSP00000301740:R1899W	R	+	1	2	SRRM2	2756225	0.982000	0.34865	0.993000	0.49108	0.970000	0.65996	1.597000	0.36729	1.280000	0.44463	0.650000	0.86243	CGG	C|0.999;A|0.001	.	alt		0.592	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			T	2816224	C	T	2816224	3	4	18	1	0	0	0	0	1	0	0	0	15184	527	19	1	5733	1	SRRM2	16	2816224	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10		2816224	87538529	140	2527											
UBN1	29855	hgsc.bcm.edu	37	chr16	4910954	4910954	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggacttggagcatctgctcAgtgagtctccagaaggaagt	10	10	13	8	0	3	2	1	1	2	1	4	5	3	5	1	3	2	2	1	3	2	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr16:4910954A>G	ENST00000396658.4	+	6	1664	c.961A>G	c.(961-963)Agt>Ggt	p.S321G	UBN1_ENST00000262376.6_Missense_Mutation_p.S321G|UBN1_ENST00000590769.1_Missense_Mutation_p.S321G|UBN1_ENST00000545171.1_Missense_Mutation_p.S321G|UBN1_ENST00000585857.1_3'UTR	NM_016936.3	NP_058632.2	Q9NPG3	UBN1_HUMAN	ubinuclein 1	321					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						GCATCTGCTCAGTGAGTCTCC	0.552																																					p.S321G		Atlas-SNP	.											.	UBN1	88	.	0			c.A961G						PASS	.						110	99	102					16																	4910954		2197	4300	6497	SO:0001583	missense	29855	exon7			CTGCTCAGTGAGT	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.961A>G	16.37:g.4910954A>G	ENSP00000379894:p.Ser321Gly	67	0	0		100	53	0.53	NM_001079514	B7Z6D3|D3DUE8|Q13079|Q9P1P7	Missense_Mutation	SNP	ENST00000396658.4	37	CCDS10525.1	.	.	.	.	.	.	.	.	.	.	A	11.90	1.775994	0.31411	.	.	ENSG00000118900	ENST00000262376;ENST00000545171;ENST00000396658	T;T;T	0.46451	1.46;0.87;1.46	5.77	5.77	0.91146	.	0.199192	0.56097	D	0.000028	T	0.29945	0.0749	L	0.28274	0.84	0.32091	N	0.591818	B;B	0.22346	0.063;0.068	B;B	0.15484	0.013;0.009	T	0.31641	-0.9936	10	0.33141	T	0.24	-9.2052	12.0518	0.53511	0.871:0.0:0.0:0.129	.	321;321	Q9NPG3-2;Q9NPG3	.;UBN1_HUMAN	G	321	ENSP00000262376:S321G;ENSP00000442379:S321G;ENSP00000379894:S321G	ENSP00000262376:S321G	S	+	1	0	UBN1	4850955	0.822000	0.29219	1.000000	0.80357	0.997000	0.91878	1.248000	0.32827	2.326000	0.78906	0.533000	0.62120	AGT	.	.	none		0.552	UBN1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251719.1	NM_016936		G	4910954	A	G	4910954	3	3	18	1	0	0	0	0	1	0	0	0	16907	188	7	3	983	3	UBN1	16	4910954	Missense_Mutation	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10	2094730	4910954	85443799	141	2528											
A2BP1	54715	hgsc.bcm.edu	37	chr16	7759118	7759118	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttgctccagcccccacctaCggcgttggtgccatggtgag	5	9	12	15	2	0	1	0	1	0	0	1	1	1	1	5	3	4	2	5	3	1	3	rs372365163		TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr16:7759118C>T	ENST00000550418.1	+	15	2044	c.1056C>T	c.(1054-1056)taC>taT	p.Y352Y	RBFOX1_ENST00000311745.5_Silent_p.Y373Y|RBFOX1_ENST00000547338.1_Silent_p.Y352Y|RBFOX1_ENST00000340209.4_Silent_p.Y357Y|RBFOX1_ENST00000355637.4_Missense_Mutation_p.T391M|RBFOX1_ENST00000436368.2_Silent_p.Y373Y|RBFOX1_ENST00000535565.2_Missense_Mutation_p.T327M|RBFOX1_ENST00000552089.1_Missense_Mutation_p.T387M|RBFOX1_ENST00000547372.1_Missense_Mutation_p.T413M|RBFOX1_ENST00000422070.4_Silent_p.Y395Y|RBFOX1_ENST00000553186.1_Silent_p.Y325Y	NM_018723.3	NP_061193.2	Q9NWB1	RFOX1_HUMAN	RNA binding protein, fox-1 homolog (C. elegans) 1	352					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						CCCCCACCTACGGCGTTGGTG	0.547																																					p.T391M	Ovarian(157;934 2567 15163 39509)	Atlas-SNP	.											RBFOX1_ENST00000550418,NS,carcinoma,0,3	RBFOX1	341	3	0			c.C1172T						PASS	.	C	,,,,,MET/THR	0,4394		0,0,2197	161	145	151		975,1056,1056,1119,1119,1172	5.7	1	16		151	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,missense	RBFOX1	NM_001142333.1,NM_001142334.1,NM_018723.3,NM_145891.2,NM_145892.2,NM_145893.2	,,,,,81	0,1,6496	TT,TC,CC		0.0116,0.0,0.0077	,,,,,	325/371,352/398,352/398,373/419,373/393,391/396	7759118	1,12993	2197	4300	6497	SO:0001819	synonymous_variant	54715	exon13			CACCTACGGCGTT	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.1056C>T	16.37:g.7759118C>T		155	0	0		193	96	0.497409	NM_145893	Q7Z7I7|Q8TAE3|Q8TAF2|Q8WYB2|Q9NS20	Missense_Mutation	SNP	ENST00000550418.1	37	CCDS55983.1	.	.	.	.	.	.	.	.	.	.	C	18.26	3.585513	0.66105	0.0	1.16E-4	ENSG00000078328	ENST00000547372;ENST00000535565;ENST00000552089;ENST00000355637	T;T	0.32515	1.45;1.68	5.65	5.65	0.86999	.	.	.	.	.	T	0.61286	0.2335	.	.	.	0.80722	D	1	D;P	0.89917	1.0;0.94	D;B	0.83275	0.996;0.37	T	0.64816	-0.6318	8	0.87932	D	0	-6.3857	19.7329	0.96190	0.0:1.0:0.0:0.0	.	327;391	F5H0M1;Q9NWB1-5	.;.	M	413;327;387;391	ENSP00000446842:T413M;ENSP00000347855:T391M	ENSP00000347855:T391M	T	+	2	0	RBFOX1	7699119	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.476000	0.66793	2.661000	0.90470	0.557000	0.71058	ACG	.	.	weak		0.547	RBFOX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409492.2	NM_145891		T	7759118	C	T	7759118	2	4	18	1	0	0	0	0	0	0	0	1	3	548	19	1		1	A2BP1	16	7759118	Silent	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	2848164	7759118	82595635	142	2529											
GGA2	23062	hgsc.bcm.edu	37	chr16	23521643	23521643	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ggcctgccaggctactcactGagccacagctccagcgacgc	8	5	11	17	2	1	1	1	1	0	0	2	2	2	1	4	2	5	2	4	2	1	1	rs17844840|rs1071685	byFrequency	TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr16:23521643G>C	ENST00000309859.4	-	1	172	c.90C>G	c.(88-90)ctC>ctG	p.L30L	GGA2_ENST00000567468.1_Splice_Site_p.L30L	NM_015044.4	NP_055859.1	Q9UJY4	GGA2_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 2	30					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)		GCTACTCACTGAGCCACAGCT	0.781													G|||	3460	0.690895	0.5756	0.7291	5008	,	,		7234	0.6964		0.8131	False		,,,				2504	0.6881				p.L30L		Atlas-SNP	.											.	GGA2	49	.	0			c.C90G						PASS	.						1	1	1					16																	23521643		725	1470	2195	SO:0001630	splice_region_variant	23062	exon1			CTCACTGAGCCAC	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.91+1C>G	16.37:g.23521643G>C		5	0	0		13	7	0.538462	NM_015044	D3DWF0|O14564|Q9NYN2|Q9UPS2	Silent	SNP	ENST00000309859.4	37	CCDS10611.1																																																																																			G|0.291;C|0.709	0.709	strong		0.781	GGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214019.1		Silent	C	23521643	G	C	23521643	5	2	18	1	0	0	0	0	0	0	1	0	6361	1304	45	4	1819	4	GGA2	16	23521643	Splice_Site	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	15762525	23521643	66833110	143	2530											
CCDC102A	92922	hgsc.bcm.edu	37	chr16	57562804	57562804	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcagtgcagtccgaccaccGgcgcatggtcttctccatct	6	9	11	15	3	3	0	0	0	3	0	5	1	4	0	4	3	1	3	4	3	0	1	rs12935069		TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr16:57562804G>A	ENST00000258214.2	-	2	532	c.286C>T	c.(286-288)Cgg>Tgg	p.R96W		NM_033212.3	NP_149989.2	Q96A19	C102A_HUMAN	coiled-coil domain containing 102A	96				R -> W (in Ref. 2; AAH08285/AAH09941). {ECO:0000305}.						endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)	8						TCCGACCACCGGCGCATGGTC	0.731													A|||	5008	1.0	1.0	1.0	5008	,	,		3757	1.0		1.0	False		,,,				2504	1.0				p.R96W		Atlas-SNP	.											.	CCDC102A	22	.	0			c.C286T						PASS	.						8	10	9					16																	57562804		1834	3717	5551	SO:0001583	missense	92922	exon2			ACCACCGGCGCAT	BC008285	CCDS10784.1	16q13	2008-02-05			ENSG00000135736	ENSG00000135736			28097	protein-coding gene	gene with protein product						12477932	Standard	NM_033212		Approved	MGC10992	uc002elw.3	Q96A19	OTTHUMG00000133472	ENST00000258214.2:c.286C>T	16.37:g.57562804G>A	ENSP00000258214:p.Arg96Trp	0	0	.		6	6	1	NM_033212	Q9BT74	Missense_Mutation	SNP	ENST00000258214.2	37	CCDS10784.1	2180	0.9981684981684982	492	1.0	360	0.994475138121547	570	0.9965034965034965	758	1.0	A	10.17	1.277909	0.23307	.	.	ENSG00000135736	ENST00000258214	T	0.37752	1.18	4.82	4.82	0.62117	.	0.000000	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00049	-2.415	0.40217	P	0.022302999999999962	B	0.02656	0.0	B	0.01281	0.0	T	0.44787	-0.9305	9	0.33141	T	0.24	-23.2491	9.5348	0.39216	0.9152:0.0:0.0848:0.0	rs12935069;rs12935069	96	Q96A19	C102A_HUMAN	W	96	ENSP00000258214:R96W	ENSP00000258214:R96W	R	-	1	2	CCDC102A	56120305	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	6.801000	0.75170	0.698000	0.31739	-0.556000	0.04195	CGG	G|0.001;A|0.999	0.999	strong		0.731	CCDC102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257348.1	NM_033212		A	57562804	G	A	57562804	3	1	18	1	0	0	0	0	1	0	0	0	2738	1115	39	1	1398	1	CCDC102A	16	57562804	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	34041161	57562804	32791949	144	2531											
RPL13	6137	hgsc.bcm.edu	37	chr16	89629371	89629371	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctagtctccgtatggcccGtgccaacgcccggctcttcg	4	9	11	17	6	2	0	0	0	2	0	4	0	2	0	4	2	2	3	4	2	3	3	rs139252401		TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr16:89629371G>A	ENST00000393099.3	+	5	806	c.557G>A	c.(556-558)cGt>cAt	p.R186H	RPL13_ENST00000567815.1_Missense_Mutation_p.R186H|RPL13_ENST00000311528.5_Missense_Mutation_p.R186H|RPL13_ENST00000452368.3_Missense_Mutation_p.R139H|SNORD68_ENST00000363214.1_RNA	NM_033251.2	NP_150254.1	P26373	RL13_HUMAN	ribosomal protein L13	186					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)		CGTATGGCCCGTGCCAACGCC	0.493																																					p.R186H		Atlas-SNP	.											.	RPL13	11	.	0			c.G557A						PASS	.	G	HIS/ARG,HIS/ARG	0,4396		0,0,2198	33	37	35		557,557	3.6	0.9	16	dbSNP_134	35	1,8593	1.2+/-3.3	0,1,4296	no	missense,missense	RPL13	NM_000977.3,NM_033251.2	29,29	0,1,6494	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	186/212,186/212	89629371	1,12989	2198	4297	6495	SO:0001583	missense	6137	exon6			TGGCCCGTGCCAA	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.557G>A	16.37:g.89629371G>A	ENSP00000376811:p.Arg186His	100	0	0		148	46	0.310811	NM_000977	B4DLX3|F5H1S2|Q3KQT8|Q567Q8|Q9BPX0	Missense_Mutation	SNP	ENST00000393099.3	37	CCDS10979.1	.	.	.	.	.	.	.	.	.	.	G	19.25	3.791435	0.70452	0.0	1.16E-4	ENSG00000167526	ENST00000311528;ENST00000452368;ENST00000393099	T;T;T	0.56103	1.22;0.48;1.22	4.52	3.57	0.40892	.	0.000000	0.85682	U	0.000000	T	0.52484	0.1737	L	0.55834	1.745	0.80722	D	1	P;B	0.49559	0.925;0.362	P;B	0.46144	0.505;0.091	T	0.57236	-0.7846	10	0.62326	D	0.03	-12.1465	12.6145	0.56569	0.0813:0.0:0.9187:0.0	.	139;186	F5H1S2;P26373	.;RL13_HUMAN	H	186;139;186	ENSP00000307889:R186H;ENSP00000438959:R139H;ENSP00000376811:R186H	ENSP00000307889:R186H	R	+	2	0	RPL13	88156872	1.000000	0.71417	0.886000	0.34754	0.819000	0.46315	9.688000	0.98670	1.041000	0.40125	0.462000	0.41574	CGT	G|1.000;A|0.000	0.000	weak		0.493	RPL13-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258294.2	NM_000977		A	89629371	G	A	89629371	3	1	18	1	0	0	0	0	1	0	0	0	13574	1145	40	1	575	1	RPL13	16	89629371	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	32066567	89629371	725382	145	2532											
C1QBP	708	hgsc.bcm.edu	37	chr17	5336352	5336352	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctctactggctcttgacaaAactcttgaggtcttcaagaa	11	12	8	10	0	5	3	1	2	4	1	5	3	5	3	0	2	2	2	0	2	5	4			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr17:5336352A>C	ENST00000225698.4	-	6	913	c.832T>G	c.(832-834)Ttt>Gtt	p.F278V	C1QBP_ENST00000574444.1_Missense_Mutation_p.F174V|CTC-524C5.2_ENST00000575890.1_RNA	NM_001212.3	NP_001203.1	Q07021	C1QBP_HUMAN	complement component 1, q subcomponent binding protein	278					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)|mature ribosome assembly (GO:0042256)|mRNA processing (GO:0006397)|negative regulation of defense response to virus (GO:0050687)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of MDA-5 signaling pathway (GO:0039534)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of mitochondrial translation (GO:0070131)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of trophoblast cell migration (GO:1901165)|regulation of complement activation (GO:0030449)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	adrenergic receptor binding (GO:0031690)|complement component C1q binding (GO:0001849)|hyaluronic acid binding (GO:0005540)|kininogen binding (GO:0030984)|mitochondrial ribosome binding (GO:0097177)|mRNA binding (GO:0003729)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			lung(2)|ovary(1)	3					Hyaluronan(DB08818)	CTCTTGACAAAACTCTTGAGG	0.493																																					p.F278V		Atlas-SNP	.											.	C1QBP	12	.	0			c.T832G						PASS	.						78	76	77					17																	5336352		2203	4300	6503	SO:0001583	missense	708	exon6			TGACAAAACTCTT	X75913	CCDS11071.1	17p13.3	2009-05-07				ENSG00000108561			1243	protein-coding gene	gene with protein product	"C1q globular domain-binding protein", "hyaluronan-binding protein 1", "splicing factor SF2-associated protein"	601269		HABP1		8567680, 8195709	Standard	NM_001212		Approved	gC1Q-R, gC1qR, p32, SF2p32	uc002gby.1	Q07021		ENST00000225698.4:c.832T>G	17.37:g.5336352A>C	ENSP00000225698:p.Phe278Val	68	0	0		93	24	0.258065	NM_001212	Q2HXR8|Q9NNY8	Missense_Mutation	SNP	ENST00000225698.4	37	CCDS11071.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.140421	0.77775	.	.	ENSG00000108561	ENST00000225698	.	.	.	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.84759	0.5543	M	0.90309	3.105	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	D	0.88015	0.2765	9	0.87932	D	0	-7.3523	15.1895	0.73032	1.0:0.0:0.0:0.0	.	278	Q07021	C1QBP_HUMAN	V	278	.	ENSP00000225698:F278V	F	-	1	0	C1QBP	5277076	1.000000	0.71417	0.974000	0.42286	0.385000	0.30292	9.186000	0.94906	2.181000	0.69327	0.533000	0.62120	TTT	.	.	none		0.493	C1QBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439388.1	NM_001212		C	5336352	A	C	5336352	3	2	18	1	0	0	0	0	1	0	0	0	1958	14	1	5	20	5	C1QBP	17	5336352	Missense_Mutation	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10		5336352	75858858	146	2533											
MYH8	4626	hgsc.bcm.edu	37	chr17	10304053	10304053	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctccgctttggctcgggacGccctctctgcctcgatttct	2	14	9	16	4	3	0	0	0	3	0	7	2	3	1	3	2	1	2	3	2	0	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr17:10304053G>A	ENST00000403437.2	-	27	3483	c.3389C>T	c.(3388-3390)gCg>gTg	p.A1130V	RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	1130					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						GGCTCGGGACGCCCTCTCTGC	0.552									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																												p.A1130V		Atlas-SNP	.											.	MYH8	346	.	0			c.C3389T						PASS	.						45	51	49					17																	10304053		2203	4300	6503	SO:0001583	missense	4626	exon27	Familial Cancer Database	Carney Complex Variant	CGGGACGCCCTCT		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.3389C>T	17.37:g.10304053G>A	ENSP00000384330:p.Ala1130Val	74	0	0		106	14	0.132075	NM_002472	Q14910	Missense_Mutation	SNP	ENST00000403437.2	37	CCDS11153.1	.	.	.	.	.	.	.	.	.	.	G	15.55	2.867713	0.51588	.	.	ENSG00000133020	ENST00000252173;ENST00000403437	T	0.79554	-1.28	5.38	5.38	0.77491	Myosin tail (1);	0.171371	0.27595	U	0.018674	D	0.83834	0.5340	M	0.82132	2.575	0.53688	D	0.999977	B	0.22146	0.065	B	0.27170	0.077	T	0.81955	-0.0696	10	0.72032	D	0.01	.	19.3244	0.94256	0.0:0.0:1.0:0.0	.	1130	P13535	MYH8_HUMAN	V	1130	ENSP00000384330:A1130V	ENSP00000252173:A1130V	A	-	2	0	MYH8	10244778	1.000000	0.71417	1.000000	0.80357	0.280000	0.26924	9.499000	0.97975	2.794000	0.96219	0.655000	0.94253	GCG	.	.	none		0.552	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472		A	10304053	G	A	10304053	3	1	18	1	0	0	0	0	1	0	0	0	10050	1087	38	1	2480	1	MYH8	17	10304053	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	4967701	10304053	70891157	147	2534											
FAM83G	644815	hgsc.bcm.edu	37	chr17	18907061	18907061	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccgccccgctggcttcctcGccgtcgccgaccccattgtc	2	9	9	21	6	0	0	0	0	0	0	5	1	2	0	8	1	0	2	8	1	0	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr17:18907061G>A	ENST00000388995.6	-	2	517	c.294C>T	c.(292-294)ggC>ggT	p.G98G	SLC5A10_ENST00000395645.3_Intron|FAM83G_ENST00000345041.4_Silent_p.G98G|SLC5A10_ENST00000317977.6_Intron|SLC5A10_ENST00000395642.1_Intron|SLC5A10_ENST00000417251.2_Intron|FAM83G_ENST00000585154.2_Silent_p.G98G|SLC5A10_ENST00000395643.2_Intron|SLC5A10_ENST00000395647.2_Intron			A6ND36	FA83G_HUMAN	family with sequence similarity 83, member G	98					BMP signaling pathway (GO:0030509)	cytosol (GO:0005829)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(3)|stomach(1)	22						TGGCTTCCTCGCCGTCGCCGA	0.716																																					p.G98G		Atlas-SNP	.											.	FAM83G	51	.	0			c.C294T						PASS	.						10	12	11					17																	18907061		1868	4050	5918	SO:0001819	synonymous_variant	644815	exon2			TTCCTCGCCGTCG	AK123558	CCDS42276.1	17p11.2	2014-05-01	2006-03-22		ENSG00000188522	ENSG00000188522			32554	protein-coding gene	gene with protein product	"protein associated with SMAD1"	615886				24554596	Standard	NM_001039999		Approved	FLJ41564, PAWS1	uc002guw.3	A6ND36	OTTHUMG00000059411	ENST00000388995.6:c.294C>T	17.37:g.18907061G>A		66	0	0		76	17	0.223684	NM_001039999	Q3KQZ4|Q6ZW60	Silent	SNP	ENST00000388995.6	37	CCDS42276.1																																																																																			.	.	none		0.716	FAM83G-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253108.4			A	18907061	G	A	18907061	2	1	18	1	0	0	0	0	0	0	0	1	5647	1074	38	1		1	FAM83G	17	18907061	Silent	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	8603008	18907061	62288149	148	2535											
CD79B	974	hgsc.bcm.edu	37	chr17	62006799	62006799	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgcccctctccttacctcgtAggtgtgatcttcctccatgc	4	14	7	16	1	2	1	0	1	2	0	6	1	4	1	6	1	3	1	6	1	2	3			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr17:62006799A>G	ENST00000006750.3	-	5	678	c.586T>C	c.(586-588)Tac>Cac	p.Y196H	CD79B_ENST00000392795.3_Missense_Mutation_p.Y197H|CD79B_ENST00000349817.2_Missense_Mutation_p.Y92H	NM_000626.2|NM_021602.2	NP_000617.1|NP_067613.1	P40259	CD79B_HUMAN	CD79b molecule, immunoglobulin-associated beta	196	ITAM. {ECO:0000255|PROSITE- ProRule:PRU00379}.				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)	p.Y196H(2)|p.Y196N(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	15						CTTACCTCGTAGGTGTGATCT	0.632			"Mis, O"		DLBCL																																p.Y197H		Atlas-SNP	.		Dom	yes		17	17q23	974	"CD79b molecule, immunoglobulin-associated beta"		L	CD79B,NS,lymphoid_neoplasm,0,13	CD79B	38	13	3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	c.T589C						scavenged	.						94	74	81					17																	62006799		2203	4300	6503	SO:0001583	missense	974	exon5			CCTCGTAGGTGTG	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.586T>C	17.37:g.62006799A>G	ENSP00000006750:p.Tyr196His	67	1	0.0149254		77	36	0.467532	NM_001039933	Q53FS2|Q9BU06	Missense_Mutation	SNP	ENST00000006750.3	37	CCDS11655.1	.	.	.	.	.	.	.	.	.	.	A	14.26	2.482264	0.44147	.	.	ENSG00000007312	ENST00000349817;ENST00000392795;ENST00000006750	D;D;D	0.96651	-4.08;-4.08;-4.08	4.2	4.2	0.49525	.	0.000000	0.64402	D	0.000002	D	0.95601	0.8570	N	0.24115	0.695	0.45172	D	0.998183	D;D	0.89917	0.999;1.0	D;D	0.91635	0.996;0.999	D	0.95387	0.8478	10	0.87932	D	0	-12.4743	9.5967	0.39578	1.0:0.0:0.0:0.0	.	92;196	P40259-2;P40259	.;CD79B_HUMAN	H	92;197;196	ENSP00000245862:Y92H;ENSP00000376544:Y197H;ENSP00000006750:Y196H	ENSP00000006750:Y196H	Y	-	1	0	CD79B	59360531	1.000000	0.71417	0.995000	0.50966	0.298000	0.27526	4.559000	0.60796	1.782000	0.52362	0.358000	0.22013	TAC	.	.	none		0.632	CD79B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417711.1			G	62006799	A	G	62006799	3	3	18	1	0	0	0	0	1	0	0	0	3039	420	15	3	111	3	CD79B	17	62006799	Missense_Mutation	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10	43099738	62006799	19188411	149	2536											
TTYH2	94015	hgsc.bcm.edu	37	chr17	72233625	72233625	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tggagctgaccaagctatccGaccagactggctacgtggag	10	7	13	11	2	0	2	0	1	0	1	1	5	1	4	3	3	3	3	3	3	3	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr17:72233625G>A	ENST00000269346.4	+	4	681	c.607G>A	c.(607-609)Gac>Aac	p.D203N	TTYH2_ENST00000529107.1_Missense_Mutation_p.D182N	NM_032646.5	NP_116035.5	Q9BSA4	TTYH2_HUMAN	tweety family member 2	203						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						CAAGCTATCCGACCAGACTGG	0.577																																					p.D203N		Atlas-SNP	.											.	TTYH2	63	.	0			c.G607A						PASS	.						68	61	64					17																	72233625		2203	4300	6503	SO:0001583	missense	94015	exon4			CTATCCGACCAGA		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.607G>A	17.37:g.72233625G>A	ENSP00000269346:p.Asp203Asn	37	0	0		45	25	0.555556	NM_032646	B3KX97|Q3B7H8|Q3B7R9|Q6AWB4|Q8NBB7|Q96PK1	Missense_Mutation	SNP	ENST00000269346.4	37	CCDS32717.1	.	.	.	.	.	.	.	.	.	.	G	10.09	1.256174	0.22965	.	.	ENSG00000141540	ENST00000269346;ENST00000529107	T;T	0.11063	2.81;2.81	5.52	-5.84	0.02318	.	0.886322	0.10208	N	0.702443	T	0.05868	0.0153	N	0.20610	0.595	0.09310	N	1	B;B	0.26975	0.165;0.011	B;B	0.22601	0.04;0.014	T	0.33929	-0.9849	10	0.41790	T	0.15	-7.3003	10.3533	0.43950	0.6543:0.1034:0.2424:0.0	.	182;203	B4DKD1;Q9BSA4	.;TTYH2_HUMAN	N	203;182	ENSP00000269346:D203N;ENSP00000433089:D182N	ENSP00000269346:D203N	D	+	1	0	TTYH2	69745220	0.006000	0.16342	0.038000	0.18304	0.152000	0.21847	0.352000	0.20113	-0.870000	0.04047	-0.734000	0.03567	GAC	.	.	none		0.577	TTYH2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387459.1			A	72233625	G	A	72233625	3	1	18	1	0	0	0	0	1	0	0	0	16755	1058	37	1	621	1	TTYH2	17	72233625	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	10226826	72233625	8961585	150	2537											
RHBDF2	79651	hgsc.bcm.edu	37	chr17	74471179	74471179	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgtgcaaatcaccagcagcGtgatgatgacatggacgaag	14	6	12	9	3	1	3	1	3	0	0	1	5	1	4	1	1	3	2	1	1	2	0			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr17:74471179G>A	ENST00000313080.4	-	10	1520	c.1247C>T	c.(1246-1248)aCg>aTg	p.T416M	RHBDF2_ENST00000389760.4_Missense_Mutation_p.T387M|RHBDF2_ENST00000591885.1_Missense_Mutation_p.T387M	NM_024599.5	NP_078875.4	Q6PJF5	RHDF2_HUMAN	rhomboid 5 homolog 2 (Drosophila)	416					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)	p.T416M(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(4)|skin(1)	27						CACCAGCAGCGTGATGATGAC	0.622																																					p.T416M		Atlas-SNP	.											RHBDF2,colon,carcinoma,0,1	RHBDF2	57	1	1	Substitution - Missense(1)	large_intestine(1)	c.C1247T						PASS	.						93	66	75					17																	74471179		2202	4299	6501	SO:0001583	missense	79651	exon10			AGCAGCGTGATGA	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.1247C>T	17.37:g.74471179G>A	ENSP00000322775:p.Thr416Met	61	0	0		69	8	0.115942	NM_024599	A6NEM3|A8K801|Q5U607|Q5YGQ8|Q9H6E9	Missense_Mutation	SNP	ENST00000313080.4	37	CCDS32743.1	.	.	.	.	.	.	.	.	.	.	G	14.91	2.676691	0.47886	.	.	ENSG00000129667	ENST00000313080;ENST00000389760;ENST00000389762	T;T	0.11604	2.76;2.76	5.1	3.11	0.35812	.	0.051498	0.85682	D	0.000000	T	0.08358	0.0208	N	0.26092	0.79	0.58432	D	0.999997	D;D;P;P	0.55800	0.967;0.973;0.908;0.723	B;B;B;B	0.43052	0.268;0.406;0.223;0.131	T	0.31024	-0.9958	10	0.33940	T	0.23	-6.9882	10.8119	0.46551	0.1535:0.0:0.8465:0.0	.	387;362;416;387	B7Z8H4;Q6ZWP8;Q6PJF5;Q6PJF5-2	.;.;RHDF2_HUMAN;.	M	416;387;362	ENSP00000322775:T416M;ENSP00000374410:T387M	ENSP00000322775:T416M	T	-	2	0	RHBDF2	71982774	1.000000	0.71417	0.995000	0.50966	0.987000	0.75469	4.708000	0.61859	1.157000	0.42530	0.462000	0.41574	ACG	.	.	none		0.622	RHBDF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450134.1	NM_024599		A	74471179	G	A	74471179	3	1	18	1	0	0	0	0	1	0	0	0	13335	1145	40	1	1363	1	RHBDF2	17	74471179	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	2237554	74471179	6724031	151	2538											
ACTG1	71	hgsc.bcm.edu	37	chr17	79478964	79478964	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctgttggccttggggttcaGgggggcctcggtcagcagca	4	10	17	10	1	3	0	2	0	1	0	4	0	3	0	2	7	2	4	2	7	0	3			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr17:79478964G>C	ENST00000575842.1	-	2	754	c.328C>G	c.(328-330)Ctg>Gtg	p.L110V	RP13-766D20.2_ENST00000430912.1_RNA|ACTG1_ENST00000575087.1_Missense_Mutation_p.L110V|AC139149.1_ENST00000584254.1_RNA|ACTG1_ENST00000331925.2_Missense_Mutation_p.L110V|ACTG1_ENST00000573283.1_Missense_Mutation_p.L110V			P63261	ACTG_HUMAN	actin, gamma 1	110					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)			TTGGGGTTCAGGGGGGCCTCG	0.627																																					p.L110V		Atlas-SNP	.											.	ACTG1	55	.	0			c.C328G						PASS	.						43	54	50					17																	79478964		2203	4298	6501	SO:0001583	missense	71	exon3			GGTTCAGGGGGGC		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.328C>G	17.37:g.79478964G>C	ENSP00000458162:p.Leu110Val	131	0	0		154	7	0.0454545	NM_001614	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000575842.1	37	CCDS11782.1	.	.	.	.	.	.	.	.	.	.	G	8.995	0.978682	0.18812	.	.	ENSG00000184009	ENST00000331925;ENST00000447294	D	0.94793	-3.52	4.51	0.962	0.19643	Actin/actin-like conserved site (1);	0.000000	0.53938	D	0.000044	D	0.97851	0.9294	H	0.97611	4.04	0.35790	D	0.822304	P	0.39748	0.686	D	0.68353	0.957	D	0.97599	1.0122	10	0.87932	D	0	.	6.7442	0.23453	0.4546:0.0:0.5454:0.0	.	110	P63261	ACTG_HUMAN	V	110	ENSP00000331514:L110V	ENSP00000331514:L110V	L	-	1	2	ACTG1	77093559	1.000000	0.71417	0.952000	0.39060	0.162000	0.22319	2.494000	0.45329	0.371000	0.24564	-0.217000	0.12591	CTG	.	.	none		0.627	ACTG1-012	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439935.2	NM_001614		C	79478964	G	C	79478964	3	2	18	1	0	0	0	0	1	0	0	0	196	991	35	4	815	4	ACTG1	17	79478964	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	5007785	79478964	1716246	152	2539											
DSG3	1830	hgsc.bcm.edu	37	chr18	29052745	29052745	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atggagccgatttcatggaaAgttctggtaagtggacataa	13	11	12	5	1	2	0	1	0	1	0	2	4	2	3	1	4	1	2	1	4	3	4			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr18:29052745A>G	ENST00000257189.4	+	14	2178	c.2095A>G	c.(2095-2097)Agt>Ggt	p.S699G		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	699					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)			TTTCATGGAAAGTTCTGGTAA	0.323																																					p.S699G		Atlas-SNP	.											.	DSG3	172	.	0			c.A2095G						PASS	.						82	80	81					18																	29052745		2203	4300	6503	SO:0001583	missense	1830	exon14			ATGGAAAGTTCTG	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.2095A>G	18.37:g.29052745A>G	ENSP00000257189:p.Ser699Gly	156	0	0		186	40	0.215054	NM_001944	A8K2V2	Missense_Mutation	SNP	ENST00000257189.4	37	CCDS11898.1	.	.	.	.	.	.	.	.	.	.	A	14.10	2.433730	0.43224	.	.	ENSG00000134757	ENST00000257189	T	0.46451	0.87	6.08	6.08	0.98989	.	0.216111	0.31784	N	0.007067	T	0.36303	0.0962	L	0.46157	1.445	0.29335	N	0.866406	B	0.21606	0.058	B	0.15052	0.012	T	0.35001	-0.9806	10	0.52906	T	0.07	.	10.6629	0.45712	0.8399:0.1601:0.0:0.0	.	699	P32926	DSG3_HUMAN	G	699	ENSP00000257189:S699G	ENSP00000257189:S699G	S	+	1	0	DSG3	27306743	0.925000	0.31364	1.000000	0.80357	0.988000	0.76386	2.357000	0.44125	2.333000	0.79357	0.482000	0.46254	AGT	.	.	none		0.323	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944		G	29052745	A	G	29052745	3	3	18	1	0	0	0	0	1	0	0	0	4780	72	3	3	2149	3	DSG3	18	29052745	Missense_Mutation	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10		29052745	49024503	153	2540											
CDH7	1005	hgsc.bcm.edu	37	chr18	63529970	63529970	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aacaatcagtttactatctgCcaattttcattgtggacagt	12	15	6	8	0	3	0	2	0	1	0	3	1	3	1	1	1	3	1	1	1	5	6			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr18:63529970C>A	ENST00000397968.2	+	11	2107	c.1681C>A	c.(1681-1683)Cca>Aca	p.P561T	CDH7_ENST00000536984.2_Missense_Mutation_p.P561T|CDH7_ENST00000323011.3_Missense_Mutation_p.P561T|RP11-389J22.1_ENST00000581987.1_RNA	NM_004361.2	NP_004352.2	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2	561	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)			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)				TTACTATCTGCCAATTTTCAT	0.498																																					p.P561T		Atlas-SNP	.											.	CDH7	362	.	0			c.C1681A						PASS	.						145	117	127					18																	63529970		2203	4300	6503	SO:0001583	missense	1005	exon11			TATCTGCCAATTT	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.1681C>A	18.37:g.63529970C>A	ENSP00000381058:p.Pro561Thr	114	0	0		167	30	0.179641	NM_004361	Q9H157	Missense_Mutation	SNP	ENST00000397968.2	37	CCDS11993.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.129597	0.77549	.	.	ENSG00000081138	ENST00000323011;ENST00000536984;ENST00000397966;ENST00000397968	T;T;T	0.42900	0.96;0.96;0.96	5.37	5.37	0.77165	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.60676	0.2287	L	0.46885	1.475	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.62732	-0.6792	10	0.87932	D	0	.	19.0909	0.93227	0.0:1.0:0.0:0.0	.	561;561	F5H5X9;Q9ULB5	.;CADH7_HUMAN	T	561	ENSP00000319166:P561T;ENSP00000443030:P561T;ENSP00000381058:P561T	ENSP00000319166:P561T	P	+	1	0	CDH7	61680950	1.000000	0.71417	0.991000	0.47740	0.476000	0.33039	7.792000	0.85828	2.528000	0.85240	0.591000	0.81541	CCA	.	.	none		0.498	CDH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256217.2	NM_033646		A	63529970	C	A	63529970	3	1	18	1	0	0	0	0	1	0	0	0	3117	739	26	4	1719	4	CDH7	18	63529970	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	34477225	63529970	14547278	154	2541											
RAB3D	9545	hgsc.bcm.edu	37	chr19	11446354	11446354	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cactcaccagtcctgcacagCggcaaaggattcctgattgg	10	8	10	13	1	1	1	1	1	0	0	3	2	3	2	3	3	2	2	3	3	1	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr19:11446354C>T	ENST00000222120.3	-	3	594	c.334G>A	c.(334-336)Gct>Act	p.A112T	RAB3D_ENST00000589655.1_Missense_Mutation_p.A112T	NM_004283.3	NP_004274.1	O95716	RAB3D_HUMAN	RAB3D, member RAS oncogene family	112					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						TCCTGCACAGCGGCAAAGGAT	0.602																																					p.A112T		Atlas-SNP	.											RAB3D,NS,carcinoma,+1,1	RAB3D	24	1	0			c.G334A						PASS	.						137	127	130					19																	11446354		2203	4300	6503	SO:0001583	missense	9545	exon3			GCACAGCGGCAAA	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.334G>A	19.37:g.11446354C>T	ENSP00000222120:p.Ala112Thr	47	0	0		71	15	0.211268	NM_004283		Missense_Mutation	SNP	ENST00000222120.3	37	CCDS12257.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.485743	0.84854	.	.	ENSG00000105514	ENST00000222120	T	0.76839	-1.05	4.64	4.64	0.57946	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.80701	0.4673	N	0.21194	0.64	0.80722	D	1	D	0.76494	0.999	D	0.70935	0.971	D	0.83509	0.0079	10	0.72032	D	0.01	.	16.7878	0.85578	0.0:1.0:0.0:0.0	.	112	O95716	RAB3D_HUMAN	T	112	ENSP00000222120:A112T	ENSP00000222120:A112T	A	-	1	0	RAB3D	11307354	1.000000	0.71417	0.635000	0.29338	0.771000	0.43674	7.499000	0.81566	2.584000	0.87258	0.462000	0.41574	GCT	.	.	none		0.602	RAB3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453211.1	NM_004283		T	11446354	C	T	11446354	3	4	18	1	0	0	0	0	1	0	0	0	12949	768	27	1	337	1	RAB3D	19	11446354	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10		11446354	47682629	155	2542											
RGL3	57139	hgsc.bcm.edu	37	chr19	11508197	11508197	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcctccgagctctgctgcGccgggagggggattcgaggg	4	6	20	11	4	1	0	0	0	1	0	3	4	2	2	3	5	3	2	3	5	0	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr19:11508197G>A	ENST00000380456.3	-	17	1886	c.1823C>T	c.(1822-1824)gCg>gTg	p.A608V	RGL3_ENST00000568628.1_5'UTR|RGL3_ENST00000393423.3_Missense_Mutation_p.A614V	NM_001035223.2|NM_001161616.1	NP_001030300.2|NP_001155088.1	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation stimulator-like 3	608					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						GCTCTGCTGCGCCGGGAGGGG	0.677																																					p.A614V	GBM(174;751 2067 17998 27979 33959)	Atlas-SNP	.											RGL3_ENST00000380456,NS,carcinoma,0,2	RGL3	100	2	0			c.C1841T						PASS	.						17	19	19					19																	11508197		2199	4287	6486	SO:0001583	missense	57139	exon17			TGCTGCGCCGGGA	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.1823C>T	19.37:g.11508197G>A	ENSP00000369823:p.Ala608Val	51	0	0		71	25	0.352113	NM_001161616	B5ME84|B7ZL22|Q0P6G0	Missense_Mutation	SNP	ENST00000380456.3	37	CCDS32910.1	.	.	.	.	.	.	.	.	.	.	G	8.583	0.882799	0.17467	.	.	ENSG00000205517	ENST00000342684;ENST00000393423;ENST00000380456	T;T	0.44083	0.93;0.93	4.48	1.04	0.20106	.	0.474496	0.23534	N	0.047147	T	0.17874	0.0429	N	0.14661	0.345	0.09310	N	0.999998	B;B;B;P	0.52692	0.037;0.037;0.021;0.955	B;B;B;B	0.35655	0.007;0.007;0.004;0.207	T	0.19484	-1.0304	10	0.59425	D	0.04	.	4.9404	0.13963	0.0:0.4382:0.3657:0.1961	.	608;614;614;405	Q3MIN7;B5ME84;B7ZL22;Q8TEP0	RGL3_HUMAN;.;.;.	V	405;614;608	ENSP00000377075:A614V;ENSP00000369823:A608V	ENSP00000344665:A405V	A	-	2	0	RGL3	11369197	0.572000	0.26668	0.198000	0.23420	0.011000	0.07611	1.182000	0.32029	0.214000	0.20742	-0.321000	0.08615	GCG	.	.	none		0.677	RGL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421208.3	XM_290867		A	11508197	G	A	11508197	3	1	18	1	0	0	0	0	1	0	0	0	13293	1087	38	1	321	1	RGL3	19	11508197	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	61843	11508197	47620786	156	2543											
MAST1	22983	hgsc.bcm.edu	37	chr19	12980018	12980018	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgctcccccatcaccatccAgcgctcgggcaagaagtatg	9	6	9	17	3	1	1	1	0	0	1	4	1	3	1	5	1	1	4	5	1	3	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr19:12980018A>T	ENST00000251472.4	+	22	2951	c.2912A>T	c.(2911-2913)cAg>cTg	p.Q971L		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						ATCACCATCCAGCGCTCGGGC	0.582																																					p.Q971L		Atlas-SNP	.											.	MAST1	214	.	0			c.A2912T						PASS	.						89	76	81					19																	12980018		2203	4300	6503	SO:0001583	missense	22983	exon22			CCATCCAGCGCTC	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.2912A>T	19.37:g.12980018A>T	ENSP00000251472:p.Gln971Leu	120	0	0		117	30	0.25641	NM_014975		Missense_Mutation	SNP	ENST00000251472.4	37	CCDS32921.1	.	.	.	.	.	.	.	.	.	.	A	17.67	3.447174	0.63178	.	.	ENSG00000105613	ENST00000251472	T	0.39997	1.05	5.01	5.01	0.66863	PDZ/DHR/GLGF (2);	0.066047	0.64402	D	0.000008	T	0.31358	0.0794	N	0.24115	0.695	0.58432	D	0.999999	B	0.09022	0.002	B	0.18561	0.022	T	0.12116	-1.0560	10	0.72032	D	0.01	-15.0771	12.6691	0.56857	1.0:0.0:0.0:0.0	.	971	Q9Y2H9	MAST1_HUMAN	L	971	ENSP00000251472:Q971L	ENSP00000251472:Q971L	Q	+	2	0	MAST1	12841018	1.000000	0.71417	1.000000	0.80357	0.768000	0.43524	6.242000	0.72376	1.886000	0.54624	0.379000	0.24179	CAG	.	.	none		0.582	MAST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451733.2	NM_014975		T	12980018	A	T	12980018	3	4	18	1	0	0	0	0	1	0	0	0	9333	188	7	5	2998	5	MAST1	19	12980018	Missense_Mutation	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10	1471821	12980018	46148965	157	2544											
ZNF208	7757	hgsc.bcm.edu	37	chr19	22157027	22157027	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcttatgtttagtaaggattGcagattggttaaaagccttg	11	16	10	4	0	1	1	0	0	1	1	1	2	1	2	1	2	2	4	1	2	5	8			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr19:22157027G>T	ENST00000397126.4	-	4	957	c.809C>A	c.(808-810)gCa>gAa	p.A270E	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	270					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)				AGTAAGGATTGCAGATTGGTT	0.363																																					p.A270E		Atlas-SNP	.											.	ZNF208	817	.	0			c.C809A						PASS	.						33	36	35					19																	22157027		2135	4259	6394	SO:0001583	missense	7757	exon4			AGGATTGCAGATT	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.809C>A	19.37:g.22157027G>T	ENSP00000380315:p.Ala270Glu	58	0	0		97	5	0.0515464	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	G	10.36	1.329450	0.24167	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.15372	2.43	2.89	0.112	0.14623	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12008	0.0292	.	.	.	0.09310	N	1	B	0.31125	0.309	B	0.20577	0.03	T	0.18241	-1.0343	8	0.66056	D	0.02	.	10.6065	0.45398	0.0:0.3727:0.6273:0.0	.	270	O43345	ZN208_HUMAN	E	270	ENSP00000380315:A270E	ENSP00000380315:A270E	A	-	2	0	ZNF208	21948867	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.059000	0.14322	0.166000	0.19597	0.306000	0.20318	GCA	.	.	none		0.363	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		T	22157027	G	T	22157027	3	4	18	1	0	0	0	0	1	0	0	0	17781	1319	46	4	3037	4	ZNF208	19	22157027	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	9177009	22157027	36971956	158	2545											
HKR1	284459	hgsc.bcm.edu	37	chr19	37853921	37853921	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agacacaagaggacacattcAggagagaagccttacatttg	16	7	10	8	0	1	3	1	0	0	3	1	6	1	5	1	2	2	0	1	2	3	3			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr19:37853921A>T	ENST00000324411.4	+	6	1493	c.1224A>T	c.(1222-1224)tcA>tcT	p.S408S	HKR1_ENST00000541583.2_Silent_p.S347S|HKR1_ENST00000591471.1_Silent_p.S135S|HKR1_ENST00000589392.1_Silent_p.S390S|HKR1_ENST00000591134.1_Intron|HKR1_ENST00000392153.3_Silent_p.S389S|HKR1_ENST00000544914.1_Silent_p.S135S	NM_181786.2	NP_861451.1	P10072	HKR1_HUMAN	HKR1, GLI-Kruppel zinc finger family member	408					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)			GGACACATTCAGGAGAGAAGC	0.522																																					p.S408S		Atlas-SNP	.											.	HKR1	74	.	0			c.A1224T						PASS	.						99	102	101					19																	37853921		2203	4300	6503	SO:0001819	synonymous_variant	284459	exon6			ACATTCAGGAGAG	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.1224A>T	19.37:g.37853921A>T		43	0	0		53	16	0.301887	NM_181786	A8MRS7|Q6PJD0|Q9BSW9|Q9UM09	Silent	SNP	ENST00000324411.4	37	CCDS12502.1																																																																																			.	.	none		0.522	HKR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458375.1	NM_181786		T	37853921	A	T	37853921	2	4	18	1	0	0	0	0	0	0	0	1	7203	175	7	5		5	HKR1	19	37853921	Silent	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10	15696894	37853921	21275062	159	2546											
HAS1	3036	hgsc.bcm.edu	37	chr19	52222861	52222861	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcctcctggtaggcggagatGgtcagcgccacactgcgcgc	6	7	14	14	4	1	1	1	0	0	1	3	2	3	1	3	4	2	1	3	4	1	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr19:52222861G>A	ENST00000222115.1	-	2	334	c.300C>T	c.(298-300)acC>acT	p.T100T	HAS1_ENST00000601714.1_Silent_p.T107T|HAS1_ENST00000540069.2_Silent_p.T99T|HAS1_ENST00000594621.1_5'Flank	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	100					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)		AGGCGGAGATGGTCAGCGCCA	0.761																																					p.T100T	NSCLC(132;636 2450 45807 47979)	Atlas-SNP	.											.	HAS1	61	.	0			c.C300T						PASS	.						4	5	5					19																	52222861		1881	3592	5473	SO:0001819	synonymous_variant	3036	exon2			GGAGATGGTCAGC	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.300C>T	19.37:g.52222861G>A		53	0	0		70	27	0.385714	NM_001523	Q14470|Q9NS49	Silent	SNP	ENST00000222115.1	37	CCDS12838.1																																																																																			.	.	none		0.761	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523		A	52222861	G	A	52222861	2	1	18	1	0	0	0	0	0	0	0	1	6970	1335	47	2		2	HAS1	19	52222861	Silent	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	14368940	52222861	6906122	160	2547											
CSNK2A1	1457	hgsc.bcm.edu	37	chr20	470463	470463	+	Frame_Shift_Del	DEL	C	C	-																															ccatggaaaaatggctccttCcgaaagatcatacttgccag																										TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr20:470463delC	ENST00000217244.3	-	10	1059	c.684delG	c.(682-684)cggfs	p.R228fs	CSNK2A1_ENST00000400227.3_Frame_Shift_Del_p.R228fs|CSNK2A1_ENST00000400217.2_Frame_Shift_Del_p.R92fs|CSNK2A1_ENST00000349736.5_Frame_Shift_Del_p.R228fs	NM_177559.2	NP_808227.1	P68400	CSK21_HUMAN	casein kinase 2, alpha 1 polypeptide	228	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)			ATGGCTCCTTCCGAAAGATCA	0.373																																					p.K229fs		Pindel,Atlas-Indel	.											.	CSNK2A1	36	.	0			c.685delA						PASS	.						103	92	96					20																	470463		2203	4300	6503	SO:0001589	frameshift_variant	1457	exon9			.	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.684delG	20.37:g.470463delC	ENSP00000217244:p.Arg228fs	79	0	.		91	18	0.198	NM_001895	B4DYS6|D3DVV8|P19138|P20426|Q14013|Q5U065	Frame_Shift_Del	DEL	ENST00000217244.3	37	CCDS13003.1																																																																																			.	.	none		0.373	CSNK2A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077466.1	NM_001895		-	470463	C	-	470463	7	5	18	1	0	1	0	1	0	0	0	0	3959	842	30	0	511	0	CSNK2A1	20	470463	Frame_Shift_Del	DEL	C	TCGA-FF-A7CR-01A-11D-A382-10		470463	62555057	161	2548											
PCSK2	5126	hgsc.bcm.edu	37	chr20	17240884	17240884	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtctacttgactctccacaGcttccctttgctgaaggtct	6	15	7	13	0	3	2	0	2	3	0	5	2	4	2	2	1	3	2	2	1	2	4			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr20:17240884G>T	ENST00000262545.2	+	2	492		c.e2-1		PCSK2_ENST00000536609.1_Intron|PCSK2_ENST00000377899.1_Splice_Site	NM_002594.3	NP_002585.2	P16519	NEC2_HUMAN	proprotein convertase subtilisin/kexin type 2						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)"	ACTCTCCACAGCTTCCCTTTG	0.552																																					.		Atlas-SNP	.											.	PCSK2	112	.	0			c.121-1G>T						PASS	.						145	128	134					20																	17240884		2203	4300	6503	SO:0001630	splice_region_variant	5126	exon3			TCCACAGCTTCCC	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.178-1G>T	20.37:g.17240884G>T		43	0	0		50	10	0.2	NM_001201528	B1ANH9|B4DFQ3|Q14927|Q5JYQ1|Q8IWA8|Q9NQG3|Q9NUG1|Q9UJC6	Splice_Site	SNP	ENST00000262545.2	37	CCDS13125.1	.	.	.	.	.	.	.	.	.	.	G	13.59	2.282721	0.40394	.	.	ENSG00000125851	ENST00000377899;ENST00000262545	.	.	.	5.37	5.37	0.77165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5997	0.68432	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PCSK2	17188884	1.000000	0.71417	1.000000	0.80357	0.420000	0.31355	6.453000	0.73488	2.513000	0.84729	0.655000	0.94253	.	.	.	none		0.552	PCSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078120.2	NM_002594	Intron	T	17240884	G	T	17240884	5	4	18	1	0	0	0	0	0	0	1	0	11610	985	34	4	183	4	PCSK2	20	17240884	Splice_Site	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	16770421	17240884	45784636	162	2549											
C20orf118	140711	hgsc.bcm.edu	37	chr20	35517718	35517718	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaagctccccttgcccgaccTtcaacaacgaggtgctggcc	8	7	10	16	2	1	0	1	0	0	0	2	3	2	0	5	2	5	2	5	2	3	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr20:35517718T>C	ENST00000217320.3	+	6	621	c.577T>C	c.(577-579)Ttc>Ctc	p.F193L	TLDC2_ENST00000602922.1_Missense_Mutation_p.F193L	NM_080628.1	NP_542195.1	A0PJX2	TLDC2_HUMAN	TBC/LysM-associated domain containing 2	193	TLD.																TTGCCCGACCTTCAACAACGA	0.617																																					p.F193L		Atlas-SNP	.											C20orf118,NS,carcinoma,-2,1	C20orf118	21	1	0			c.T577C						PASS	.						77	68	71					20																	35517718		2203	4300	6503	SO:0001583	missense	140711	exon6			CCGACCTTCAACA	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.577T>C	20.37:g.35517718T>C	ENSP00000217320:p.Phe193Leu	74	0	0		119	5	0.0420168	NM_080628	B3KVU8	Missense_Mutation	SNP	ENST00000217320.3	37	CCDS33465.1	.	.	.	.	.	.	.	.	.	.	T	21.4	4.149620	0.78001	.	.	ENSG00000101342	ENST00000217320	T	0.57595	0.39	5.41	5.41	0.78517	TLDc (2);	0.000000	0.85682	D	0.000000	T	0.80166	0.4573	H	0.95504	3.68	0.53005	D	0.999964	D	0.89917	1.0	D	0.83275	0.996	D	0.86032	0.1514	10	0.87932	D	0	-19.3697	13.6557	0.62338	0.0:0.0:0.0:1.0	.	193	A0PJX2	CT118_HUMAN	L	193	ENSP00000217320:F193L	ENSP00000217320:F193L	F	+	1	0	C20orf118	34951132	1.000000	0.71417	1.000000	0.80357	0.330000	0.28571	6.242000	0.72376	2.044000	0.60594	0.533000	0.62120	TTC	.	.	none		0.617	TLDC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079060.2	NM_080628		C	35517718	T	C	35517718	3	2	18	1	0	0	0	0	1	0	0	0	2086	1609	56	3	599	3	C20orf118	20	35517718	Missense_Mutation	SNP	T	TCGA-FF-A7CR-01A-11D-A382-10	18276834	35517718	27507802	163	2550											
RBM38	55544	hgsc.bcm.edu	37	chr20	55967801	55967801	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggccaacgtgaacctggcatAtctgggcgccaagccgcgga	9	5	14	13	4	1	1	0	1	1	0	1	2	1	2	4	4	3	1	4	4	4	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr20:55967801A>C	ENST00000356208.5	+	2	504	c.329A>C	c.(328-330)tAt>tCt	p.Y110S	RP4-800J21.3_ENST00000417346.1_RNA|RBM38_ENST00000440234.2_Missense_Mutation_p.Y110S|RBM38_ENST00000371219.2_Missense_Mutation_p.Y29S	NM_017495.5	NP_059965.2	Q9H0Z9	RBM38_HUMAN	RNA binding motif protein 38	110	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|cell cycle (GO:0007049)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|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)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|regulation of myotube differentiation (GO:0010830)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			large_intestine(3)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9	Lung NSC(12;0.00242)|all_lung(29;0.00767)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;1.55e-12)|Epithelial(14;9.49e-09)|all cancers(14;5.01e-08)			AACCTGGCATATCTGGGCGCC	0.617																																					p.Y110S		Atlas-SNP	.											.	RBM38	19	.	0			c.A329C						PASS	.						48	58	55					20																	55967801		1976	4180	6156	SO:0001583	missense	55544	exon2			TGGCATATCTGGG	X75314	CCDS46617.1, CCDS46618.1	20q13.31	2013-02-12	2006-07-11	2006-07-11	ENSG00000132819	ENSG00000132819		"RNA binding motif (RRM) containing"	15818	protein-coding gene	gene with protein product		612428	"RNA-binding region (RNP1, RRM) containing 1"	RNPC1			Standard	NM_017495		Approved	HSRNASEB, SEB4D, seb4B, dJ800J21.2	uc010zzj.2	Q9H0Z9	OTTHUMG00000032820	ENST00000356208.5:c.329A>C	20.37:g.55967801A>C	ENSP00000348538:p.Tyr110Ser	138	0	0		125	35	0.28	NM_183425	A6NDK1|A6NMU6|Q15350|Q15351|Q9BYK3|Q9BYK4	Missense_Mutation	SNP	ENST00000356208.5	37	CCDS46617.1	.	.	.	.	.	.	.	.	.	.	A	19.73	3.881598	0.72294	.	.	ENSG00000132819	ENST00000356208;ENST00000440234;ENST00000371219	T;T;T	0.73789	-0.78;-0.78;2.07	5.11	5.11	0.69529	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (1);	0.000000	0.85682	D	0.000000	T	0.50599	0.1625	N	0.02247	-0.625	0.80722	D	1	B	0.13145	0.007	B	0.20184	0.028	T	0.48864	-0.8997	10	0.21014	T	0.42	3.4076	14.5578	0.68113	1.0:0.0:0.0:0.0	.	110	Q9H0Z9	RBM38_HUMAN	S	110;110;29	ENSP00000348538:Y110S;ENSP00000407848:Y110S;ENSP00000360263:Y29S	ENSP00000345248:Y87S	Y	+	2	0	RBM38	55401207	1.000000	0.71417	0.988000	0.46212	0.980000	0.70556	8.638000	0.91019	1.915000	0.55452	0.533000	0.62120	TAT	.	.	none		0.617	RBM38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079843.4	NM_183425		C	55967801	A	C	55967801	3	2	18	1	0	0	0	0	1	0	0	0	13147	449	16	5	94	5	RBM38	20	55967801	Missense_Mutation	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10	20450083	55967801	7057719	164	2551											
CDH26	60437	hgsc.bcm.edu	37	chr20	58569512	58569512	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggacaatacctggggaaatgCggaggacacatggaagttgg	13	6	16	6	1	0	0	0	0	0	0	0	5	0	5	1	7	2	1	1	7	4	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr20:58569512C>T	ENST00000244047.5	+	11	1945	c.1634C>T	c.(1633-1635)gCg>gTg	p.A545V	CDH26_ENST00000244049.3_5'Flank|CDH26_ENST00000350849.6_5'Flank|CDH26_ENST00000348616.4_Missense_Mutation_p.A545V|CDH26_ENST00000497614.1_3'UTR			Q8IXH8	CAD26_HUMAN	cadherin 26	545					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)			TGGGGAAATGCGGAGGACACA	0.483																																					p.A545V		Atlas-SNP	.											CDH26_ENST00000244047,caecum,carcinoma,-1,2	CDH26	229	2	0			c.C1634T						PASS	.						47	45	45					20																	58569512		2203	4300	6503	SO:0001583	missense	60437	exon11			GAAATGCGGAGGA	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.1634C>T	20.37:g.58569512C>T	ENSP00000244047:p.Ala545Val	44	0	0		50	10	0.2	NM_177980	A2A2M5|B3KNX3|Q6P5Y6|Q8TCH3|Q9BQN4|Q9NRU1	Missense_Mutation	SNP	ENST00000244047.5	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.035|8.035	0.762688|0.762688	0.15914|0.15914	.|.	.|.	ENSG00000124215|ENSG00000124215	ENST00000244047;ENST00000348616|ENST00000370991	T;T|.	0.60797|.	0.16;0.16|.	4.14|4.14	-2.75|-2.75	0.05914|0.05914	Cadherin-like (1);|.	1.199730|.	0.06092|.	N|.	0.663775|.	T|T	0.12817|0.12817	0.0311|0.0311	N|N	0.05199|0.05199	-0.095|-0.095	0.09310|0.09310	N|N	1|1	B;B|.	0.20368|.	0.044;0.019|.	B;B|.	0.16289|.	0.015;0.01|.	T|T	0.25328|0.25328	-1.0135|-1.0135	10|5	0.05525|.	T|.	0.97|.	.|.	3.2617|3.2617	0.06851|0.06851	0.2957:0.3011:0.0:0.4032|0.2957:0.3011:0.0:0.4032	.|.	545;545|.	Q8IXH8;Q8IXH8-4|.	CAD26_HUMAN;.|.	V|W	545|137	ENSP00000244047:A545V;ENSP00000339390:A545V|.	ENSP00000244047:A545V|.	A|R	+|+	2|1	0|2	CDH26|CDH26	58002907|58002907	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.004000|0.004000	0.04260|0.04260	-1.140000|-1.140000	0.03210|0.03210	-0.411000|-0.411000	0.07530|0.07530	0.655000|0.655000	0.94253|0.94253	GCG|CGG	.	.	none		0.483	CDH26-201	KNOWN	basic	protein_coding	protein_coding		NM_177980		T	58569512	C	T	58569512	3	4	18	1	0	0	0	0	1	0	0	0	3112	768	27	1	1676	1	CDH26	20	58569512	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	2601711	58569512	4456008	165	2552											
UCKL1	54963	hgsc.bcm.edu	37	chr20	62576008	62576008	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccctcgatgtcccggccgCgctcactgatgtcccggcgc	4	7	11	19	6	1	1	1	1	0	0	4	2	3	1	4	2	0	1	4	2	0	0			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr20:62576008C>T	ENST00000354216.6	-	6	776	c.734G>A	c.(733-735)cGc>cAc	p.R245H	UCKL1_ENST00000369892.3_Missense_Mutation_p.R245H|UCKL1_ENST00000492660.1_5'Flank|MIR647_ENST00000384823.1_RNA|UCKL1_ENST00000358711.3_Missense_Mutation_p.R245H|UCKL1_ENST00000369908.5_Missense_Mutation_p.R230H	NM_017859.3	NP_060329.2	Q9NWZ5	UCKL1_HUMAN	uridine-cytidine kinase 1-like 1	245					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)					GTCCCGGCCGCGCTCACTGAT	0.607																																					p.R245H		Atlas-SNP	.											.	UCKL1	28	.	0			c.G734A						PASS	.						133	83	100					20																	62576008		2198	4298	6496	SO:0001583	missense	54963	exon6			CGGCCGCGCTCAC	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.734G>A	20.37:g.62576008C>T	ENSP00000346155:p.Arg245His	121	0	0		132	38	0.287879	NM_017859	B7Z8N2|Q5JWV0|Q70AQ5|Q8N524|Q9H3Z2	Missense_Mutation	SNP	ENST00000354216.6	37	CCDS13547.1	.	.	.	.	.	.	.	.	.	.	C	33	5.253488	0.95336	.	.	ENSG00000198276	ENST00000354216;ENST00000369892;ENST00000358711;ENST00000369908	.	.	.	5.84	4.9	0.64082	Phosphoribulokinase/uridine kinase (1);	0.000000	0.85682	D	0.000000	D	0.91399	0.7286	H	0.99758	4.755	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.995	D	0.95029	0.8167	9	0.87932	D	0	-20.8731	14.9695	0.71223	0.0:0.9316:0.0:0.0684	.	230;245	B7Z8N2;Q9NWZ5	.;UCKL1_HUMAN	H	245;245;245;230	.	ENSP00000346155:R245H	R	-	2	0	UCKL1	62046452	1.000000	0.71417	0.322000	0.25334	0.878000	0.50629	5.657000	0.67996	1.489000	0.48450	0.561000	0.74099	CGC	.	.	none		0.607	UCKL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080236.1	NM_017859		T	62576008	C	T	62576008	3	4	18	1	0	0	0	0	1	0	0	0	16940	768	27	1	952	1	UCKL1	20	62576008	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	4006496	62576008	449512	166	2553											
ERG	2078	hgsc.bcm.edu	37	chr21	39775625	39775625	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catggtctgtactccatagcGtaggatctgaaaggggtggg	9	10	15	7	1	2	1	0	1	2	0	3	2	3	2	1	5	2	2	1	5	4	3	rs140222241		TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr21:39775625G>A	ENST00000417133.2	-	6	601	c.416C>T	c.(415-417)aCg>aTg	p.T139M	ERG_ENST00000398897.1_Missense_Mutation_p.T40M|ERG_ENST00000398919.2_Missense_Mutation_p.T139M|ERG_ENST00000398907.1_Missense_Mutation_p.T132M|ERG_ENST00000398905.1_Missense_Mutation_p.T132M|ERG_ENST00000398910.1_Missense_Mutation_p.T139M|ERG_ENST00000288319.7_Missense_Mutation_p.T132M|ERG_ENST00000442448.1_Missense_Mutation_p.T139M|ERG_ENST00000398911.1_Missense_Mutation_p.T139M|ERG_ENST00000453032.2_Missense_Mutation_p.T40M|ERG_ENST00000429727.2_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	PAC. {ECO:0000255|PROSITE- ProRule:PRU00141}.				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)	ACTCCATAGCGTAGGATCTGA	0.517			T	"EWSR1, TMPRSS2, ELF4, FUS, HERPUD1, NDRG1"	"Ewing sarcoma, prostate, AML"																																p.T139M	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.C416T						PASS	.	G	MET/THR,MET/THR,MET/THR,MET/THR	0,4406		0,0,2203	75	66	69		416,119,416,395	3.7	0.1	21	dbSNP_134	69	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	ERG	NM_001136154.1,NM_001136155.1,NM_004449.4,NM_182918.3	81,81,81,81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign,benign	139/487,40/388,139/463,132/480	39775625	1,13005	2203	4300	6503	SO:0001583	missense	2078	exon6			CATAGCGTAGGAT		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.416C>T	21.37:g.39775625G>A	ENSP00000414150:p.Thr139Met	76	0	0		97	27	0.278351	NM_001243432	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Missense_Mutation	SNP	ENST00000417133.2	37	CCDS46648.1	.	.	.	.	.	.	.	.	.	.	G	15.13	2.740833	0.49151	0.0	1.16E-4	ENSG00000157554	ENST00000398905;ENST00000398907;ENST00000288319;ENST00000398897;ENST00000398911;ENST00000417133;ENST00000398910;ENST00000442448;ENST00000453032;ENST00000398919	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	4.55	3.66	0.41972	Sterile alpha motif/pointed domain (2);Pointed domain (3);	0.111389	0.64402	D	0.000011	T	0.37376	0.1001	N	0.24115	0.695	0.53688	D	0.999971	P;D;P;P;B	0.76494	0.776;0.999;0.741;0.547;0.338	P;D;B;B;B	0.66196	0.505;0.942;0.207;0.084;0.07	T	0.10894	-1.0610	10	0.39692	T	0.17	.	13.0918	0.59171	0.0784:0.0:0.9216:0.0	.	139;132;139;139;132	P11308;B5MDW0;P11308-6;P11308-1;P11308-4	ERG_HUMAN;.;.;.;.	M	132;132;132;40;139;139;139;139;40;139	ENSP00000381877:T132M;ENSP00000381879:T132M;ENSP00000288319:T132M;ENSP00000381871:T40M;ENSP00000381882:T139M;ENSP00000414150:T139M;ENSP00000381881:T139M;ENSP00000394694:T139M;ENSP00000396268:T40M;ENSP00000381891:T139M	ENSP00000288319:T132M	T	-	2	0	ERG	38697495	1.000000	0.71417	0.106000	0.21319	0.686000	0.39977	4.789000	0.62446	1.043000	0.40175	0.655000	0.94253	ACG	G|1.000;A|0.000	0.000	weak		0.517	ERG-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207532.2	NM_182918		A	39775625	G	A	39775625	3	1	18	1	0	0	0	0	1	0	0	0	5224	1145	40	1	1072	1	ERG	21	39775625	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10		39775625	8354270	167	2554											
U2AF1	7307	hgsc.bcm.edu	37	chr21	44513242	44513242	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccagatctttcacgatctctCgaccgcctcctgtcacgctc	6	11	6	18	4	4	1	2	0	2	1	8	3	5	1	4	0	0	1	4	0	0	1	rs560573558	byFrequency	TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr21:44513242C>T	ENST00000291552.4	-	8	785	c.693G>A	c.(691-693)tcG>tcA	p.S231S	U2AF1_ENST00000459639.1_Silent_p.S158S|U2AF1_ENST00000380276.2_Silent_p.S231S|U2AF1_ENST00000486519.1_5'Flank|U2AF1_ENST00000398137.1_Silent_p.S158S	NM_006758.2	NP_006749.1	Q01081	U2AF1_HUMAN	U2 small nuclear RNA auxiliary factor 1	231	Arg/Gly/Ser-rich (RS domain).				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)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(111)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	126						CACGATCTCTCGACCGCCTCC	0.577			Mis		"CLL, MDS"																																p.S231S		Atlas-SNP	.		Dom	yes		21	21q22.3	7307	U2 small nuclear RNA auxiliary factor 1		L	U2AF1_ENST00000380276,NS,neuroblastoma,-1,4	U2AF1	322	4	0			c.G693A						PASS	.						52	55	54					21																	44513242		2203	4300	6503	SO:0001819	synonymous_variant	7307	exon8			ATCTCTCGACCGC	BC001177	CCDS13694.1, CCDS33574.1, CCDS42948.1	21q22.3	2014-09-17	2006-04-11		ENSG00000160201	ENSG00000160201		"RNA binding motif (RRM) containing"	12453	protein-coding gene	gene with protein product		191317	"U2(RNU2) small nuclear RNA auxiliary factor binding protein", "U2(RNU2) small nuclear RNA auxiliary factor 1"	U2AFBP		8660980, 7956352	Standard	NM_006758		Approved	U2AF35, RNU2AF1, RN	uc002zdb.1	Q01081	OTTHUMG00000086836	ENST00000291552.4:c.693G>A	21.37:g.44513242C>T		61	0	0		62	8	0.129032	NM_001025203	Q701P4|Q71RF1	Silent	SNP	ENST00000291552.4	37	CCDS13694.1																																																																																			.	.	none		0.577	U2AF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195541.1	NM_006758		T	44513242	C	T	44513242	2	4	18	1	0	0	0	0	0	0	0	1	16836	871	31	1		1	U2AF1	21	44513242	Silent	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	4737617	44513242	3616653	168	2555											
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230310	23230310	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccaggcagcgctggccccTgctgctgctgggtctggcca	3	8	14	16	1	1	0	0	0	1	0	2	0	2	0	4	4	4	5	4	4	0	0			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr22:23230310T>A	ENST00000526893.1	+	1	351	c.77T>A	c.(76-78)cTg>cAg	p.L26Q	IGLL5_ENST00000531372.1_Missense_Mutation_p.L26Q|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Missense_Mutation_p.L26Q	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	26						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CGCTGGCCCCTGCTGCTGCTG	0.662																																					p.L26Q		Atlas-SNP	.											.	IGLL5	26	.	0			c.T77A						PASS	.																																			SO:0001583	missense	100423062	exon1			GGCCCCTGCTGCT	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.77T>A	22.37:g.23230310T>A	ENSP00000431254:p.Leu26Gln	140	0	0		107	20	0.186916	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	T	14.31	2.497679	0.44455	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00792	5.69;5.7	3.81	1.57	0.23409	.	.	.	.	.	T	0.01124	0.0037	L	0.32530	0.975	0.09310	N	1	D	0.76494	0.999	P	0.61800	0.894	T	0.26121	-1.0112	9	0.02654	T	1	.	3.9146	0.09217	0.0:0.1156:0.2159:0.6685	.	26	B9A064	IGLL5_HUMAN	Q	26	ENSP00000436353:L26Q;ENSP00000431254:L26Q	ENSP00000431254:L26Q	L	+	2	0	IGLL5	21560310	0.019000	0.18553	0.000000	0.03702	0.079000	0.17450	2.550000	0.45811	0.262000	0.21774	0.523000	0.50628	CTG	.	.	none		0.662	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		A	23230310	T	A	23230310	3	1	18	1	0	0	0	0	1	0	0	0	7603	1580	55	5	79	5	IGLL5	22	23230310	Missense_Mutation	SNP	T	TCGA-FF-A7CR-01A-11D-A382-10		23230310	28074256	169	2556			3	23		10	6	5690	N	T_G_C	3.205253e-10
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230348	23230348	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccatggtcgcccatggcctgCtgcgcccaatggttgcaccg	5	8	12	16	3	0	0	0	0	0	0	1	0	0	0	5	3	3	3	5	3	1	1			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr22:23230348C>T	ENST00000526893.1	+	1	389	c.115C>T	c.(115-117)Ctg>Ttg	p.L39L	IGLL5_ENST00000531372.1_Silent_p.L39L|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Silent_p.L39L	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	39						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CCATGGCCTGCTGCGCCCAAT	0.687																																					p.L39L		Atlas-SNP	.											.	IGLL5	26	.	0			c.C115T						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			GGCCTGCTGCGCC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.115C>T	22.37:g.23230348C>T		135	0	0		113	19	0.168142	NM_001178126		Silent	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.687	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		T	23230348	C	T	23230348	2	4	18	1	0	0	0	0	0	0	0	1	7603	796	28	2		2	IGLL5	22	23230348	Silent	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	38	23230348	28074218	170	2557			3	23		10	6	5690	N	T_G_C	3.205253e-10
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230386	23230386	+	Silent	SNP	C	C	T																															ccgcaaagcggggacccagaCcctggagcctcagttggaag																										TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr22:23230386C>T	ENST00000526893.1	+	1	427	c.153C>T	c.(151-153)gaC>gaT	p.D51D	IGLL5_ENST00000531372.1_Silent_p.D51D|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Silent_p.D51D	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	51						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GGGACCCAGACCCTGGAGCCT	0.677																																					p.T16I		Atlas-SNP	.											.	IGLL5	26	.	0			c.C47T						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			CCCAGACCCTGGA	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.153C>T	22.37:g.23230386C>T		132	0	0		95	14	0.147368	NM_001256296		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.677	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		T	23230386	C	T	23230386	2	4	18	1	0	0	0	0	0	0	0	1	7603	506	18	2		2	IGLL5	22	23230386	Silent	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	38	23230386	28074180	171	2558	38	2	3	23		10	6	5690	N	T_G_C	3.205253e-10
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230394	23230394	+	Missense_Mutation	SNP	C	C	T																															cggggacccagaccctggagCctcagttggaagcagccgat																										TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr22:23230394C>T	ENST00000526893.1	+	1	435	c.161C>T	c.(160-162)gCc>gTc	p.A54V	IGLL5_ENST00000531372.1_Missense_Mutation_p.A54V|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Missense_Mutation_p.A54V	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	54						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GACCCTGGAGCCTCAGTTGGA	0.667																																					p.A54V		Atlas-SNP	.											.	IGLL5	26	.	0			c.C161T						PASS	.																																			SO:0001583	missense	100423062	exon1			CTGGAGCCTCAGT	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.161C>T	22.37:g.23230394C>T	ENSP00000431254:p.Ala54Val	126	0	0		92	13	0.141304	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	C	15.92	2.975826	0.53720	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00617	6.19;6.19	3.92	-1.07	0.09968	.	.	.	.	.	T	0.00552	0.0018	L	0.29908	0.895	0.09310	N	1	B	0.21821	0.061	B	0.11329	0.006	T	0.47071	-0.9145	9	0.87932	D	0	.	2.5676	0.04787	0.1918:0.3543:0.3485:0.1053	.	54	B9A064	IGLL5_HUMAN	V	54	ENSP00000436353:A54V;ENSP00000431254:A54V	ENSP00000431254:A54V	A	+	2	0	IGLL5	21560394	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.197000	0.17197	-0.079000	0.12707	-0.152000	0.13540	GCC	.	.	none		0.667	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		T	23230394	C	T	23230394	3	4	18	1	0	0	0	0	1	0	0	0	7603	739	26	2	163	2	IGLL5	22	23230394	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	8	23230394	28074172	172	2559	38	2	3	23		10	6	5690	N	T_G_C	3.205253e-10
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230419	23230419	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gttggaagcagccgatccagCctgcggagcctgtggggcag	7	6	17	11	2	0	0	0	0	0	0	1	3	1	2	4	4	5	3	4	4	1	1	rs554734650	byFrequency	TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr22:23230419C>T	ENST00000526893.1	+	1	460	c.186C>T	c.(184-186)agC>agT	p.S62S	IGLL5_ENST00000531372.1_Silent_p.S62S|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Silent_p.S62S	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	62						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GCCGATCCAGCCTGCGGAGCC	0.647													C|||	3	0.000599042	0.0008	0.0	5008	,	,		11441	0.001		0.001	False		,,,				2504	0.0				p.A27V		Atlas-SNP	.											.	IGLL5	26	.	0			c.C80T						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			ATCCAGCCTGCGG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.186C>T	22.37:g.23230419C>T		111	0	0		81	24	0.296296	NM_001256296		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.647	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		T	23230419	C	T	23230419	2	4	18	1	0	0	0	0	0	0	0	1	7603	738	26	2		2	IGLL5	22	23230419	Silent	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	25	23230419	28074147	173	2560			3	23		10	6	5690	N	T_G_C	3.205253e-10
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230436	23230436	+	Missense_Mutation	SNP	G	G	A																															cagcctgcggagcctgtgggGcaggtaaggggcaagagatt																								rs541593342	byFrequency	TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr22:23230436G>A	ENST00000526893.1	+	1	477	c.203G>A	c.(202-204)gGc>gAc	p.G68D	IGLL5_ENST00000531372.1_Missense_Mutation_p.G68D|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Missense_Mutation_p.G68D	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	68						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						AGCCTGTGGGGCAGGTAAGGG	0.642													G|||	6	0.00119808	0.0023	0.0029	5008	,	,		11793	0.0		0.001	False		,,,				2504	0.0				p.G68D		Atlas-SNP	.											.	IGLL5	26	.	0			c.G203A						PASS	.																																			SO:0001583	missense	100423062	exon1			TGTGGGGCAGGTA	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.203G>A	22.37:g.23230436G>A	ENSP00000431254:p.Gly68Asp	97	0	0		66	7	0.106061	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	9.760	1.169735	0.21621	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00638	6.04;6.53	3.92	-2.62	0.06152	.	.	.	.	.	T	0.00524	0.0017	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46062	-0.9218	9	0.56958	D	0.05	.	1.8547	0.03176	0.21:0.1724:0.4462:0.1715	.	68	B9A064	IGLL5_HUMAN	D	68	ENSP00000436353:G68D;ENSP00000431254:G68D	ENSP00000431254:G68D	G	+	2	0	IGLL5	21560436	0.005000	0.15991	0.008000	0.14137	0.042000	0.13812	0.008000	0.13197	-0.478000	0.06823	-0.195000	0.12781	GGC	.	.	none		0.642	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		A	23230436	G	A	23230436	3	1	18	1	0	0	0	0	1	0	0	0	7603	1203	42	2	205	2	IGLL5	22	23230436	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	17	23230436	28074130	174	2561	39	3	3	23		10	6	5690	N	T_G_C	3.205253e-10
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230439	23230439	+	Splice_Site	SNP	G	G	A																															cctgcggagcctgtggggcaGgtaaggggcaagagattcca																										TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr22:23230439G>A	ENST00000526893.1	+	1	480	c.206G>A	c.(205-207)aGg>aAg	p.R69K	IGLL5_ENST00000531372.1_Splice_Site_p.R69K|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Splice_Site_p.S69N	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	69						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CTGTGGGGCAGGTAAGGGGCA	0.627																																					p.R69K		Atlas-SNP	.											.	IGLL5	26	.	0			c.G206A						PASS	.																																			SO:0001630	splice_region_variant	100423062	exon1			GGGGCAGGTAAGG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.206+1G>A	22.37:g.23230439G>A		94	0	0		64	15	0.234375	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.883|9.883	1.202015|1.202015	0.22121|0.22121	.|.	.|.	ENSG00000254709|ENSG00000254709	ENST00000526893;ENST00000531372|ENST00000532223	T|T	0.00801|0.00561	5.68|6.59	3.92|3.92	3.92|3.92	0.45320|0.45320	.|.	.|.	.|.	.|.	.|.	T|T	0.00637|0.00637	0.0021|0.0021	L|L	0.27053|0.27053	0.805|0.805	0.45718|0.45718	D|D	0.99862|0.99862	D|.	0.57571|.	0.98|.	D|.	0.67548|.	0.952|.	D|D	0.86314|0.86314	0.1688|0.1688	9|7	0.66056|0.28530	D|T	0.02|0.3	.|.	11.74|11.74	0.51788|0.51788	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	69|.	B9A064|.	IGLL5_HUMAN|.	K|N	69|69	ENSP00000431254:R69K|ENSP00000436353:S69N	ENSP00000431254:R69K|ENSP00000436353:S69N	R|S	+|+	2|2	0|0	IGLL5|IGLL5	21560439|21560439	0.985000|0.985000	0.35326|0.35326	1.000000|1.000000	0.80357|0.80357	0.199000|0.199000	0.23934|0.23934	1.700000|1.700000	0.37815|0.37815	2.481000|2.481000	0.83766|0.83766	0.643000|0.643000	0.83706|0.83706	AGG|AGC	.	.	none		0.627	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	Missense_Mutation	A	23230439	G	A	23230439	5	1	18	1	0	0	0	0	0	0	1	0	7603	1014	35	2	208	2	IGLL5	22	23230439	Splice_Site	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	3	23230439	28074127	175	2562	39	3	3	23		10	6	5690	N	T_G_C	3.205253e-10
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230440	23230440	+	Splice_Site	SNP	G	G	A																															ctgcggagcctgtggggcagGtaaggggcaagagattccag																										TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr22:23230440G>A	ENST00000526893.1	+	1	480		c.e1+1		IGLL5_ENST00000531372.1_Splice_Site|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Splice_Site	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5							extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						TGTGGGGCAGGTAAGGGGCAA	0.627																																					.		Atlas-SNP	.											.	IGLL5	26	.	0			c.100+1G>A						PASS	.																																			SO:0001630	splice_region_variant	100423062	exon1			GGGCAGGTAAGGG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.206+1G>A	22.37:g.23230440G>A		94	0	0		61	14	0.229508	NM_001256296		Splice_Site	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	10.15	1.271539	0.23221	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	.	.	.	3.92	3.92	0.45320	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.74	0.51788	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	IGLL5	21560440	1.000000	0.71417	1.000000	0.80357	0.199000	0.23934	1.700000	0.37815	2.481000	0.83766	0.643000	0.83706	.	.	.	none		0.627	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	Intron	A	23230440	G	A	23230440	5	1	18	1	0	0	0	0	0	0	1	0	7603	1275	44	2	209	2	IGLL5	22	23230440	Splice_Site	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	1	23230440	28074126	176	2563	39	3	3	23		10	6	5690	N	T_G_C	3.205253e-10
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23235998	23235998	+	Splice_Site	SNP	G	G	A																															ggaccaaggtcaccgtcctaGgtaagtggctctcaaccttt																								rs201857114	byFrequency	TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr22:23235998G>A	ENST00000526893.1	+	2	599	c.325G>A	c.(325-327)Ggt>Agt	p.G109S	IGLL5_ENST00000531372.1_Intron|IGLJ1_ENST00000390320.2_RNA|IGLL5_ENST00000532223.2_Splice_Site_p.G110S|IGLC1_ENST00000390321.2_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	109	J region (By similarity to lambda light- chain).					extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CACCGTCCTAGGTAAGTGGCT	0.592													G|||	4	0.000798722	0.0023	0.0	5008	,	,		12894	0.001		0.0	False		,,,				2504	0.0				p.G109S		Atlas-SNP	.											.	IGLL5	26	.	0			c.G325A						PASS	.	G	SER/GLY	0,4270		0,0,2135	88	100	96		325	2.4	1	22		96	1,8505		0,1,4252	yes	missense-near-splice	IGLL5	NM_001178126.1	56	0,1,6387	AA,AG,GG		0.0118,0.0,0.0078	benign	109/215	23235998	1,12775	2135	4253	6388	SO:0001630	splice_region_variant	100423062	exon2			GTCCTAGGTAAGT	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.325+1G>A	22.37:g.23235998G>A		66	0	0		74	20	0.27027	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	10.60	1.395359	0.25205	0.0	1.18E-4	ENSG00000254709	ENST00000532223;ENST00000526893	T;T	0.00570	6.51;6.51	3.51	2.43	0.29744	Immunoglobulin-like fold (1);	.	.	.	.	T	0.00580	0.0019	.	.	.	0.80722	D	1	B	0.25772	0.134	B	0.32624	0.149	T	0.67356	-0.5691	8	0.52906	T	0.07	.	8.0064	0.30327	0.0:0.0:0.7569:0.2431	.	109	B9A064	IGLL5_HUMAN	S	110;109	ENSP00000436353:G110S;ENSP00000431254:G109S	ENSP00000431254:G109S	G	+	1	0	IGLL5	21565998	0.993000	0.37304	0.977000	0.42913	0.289000	0.27227	2.340000	0.43974	0.781000	0.33589	0.491000	0.48974	GGT	.	.	weak		0.592	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	Missense_Mutation	A	23235998	G	A	23235998	5	1	18	1	0	0	0	0	0	0	1	0	7603	1014	35	2	331	2	IGLL5	22	23235998	Splice_Site	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	5558	23235998	28068568	177	2564	40	2	3	23		10	6	5690	N	T_G_C	3.205253e-10
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23235999	23235999	+	Splice_Site	SNP	G	G	C																															gaccaaggtcaccgtcctagGtaagtggctctcaacctttc																										TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr22:23235999G>C	ENST00000526893.1	+	2	599		c.e2+1		IGLL5_ENST00000531372.1_Intron|IGLJ1_ENST00000390320.2_RNA|IGLL5_ENST00000532223.2_Splice_Site|IGLC1_ENST00000390321.2_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5							extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						ACCGTCCTAGGTAAGTGGCTC	0.587																																					.		Atlas-SNP	.											.	IGLL5	26	.	0			c.325+1G>C						PASS	.						88	100	96					22																	23235999		2136	4255	6391	SO:0001630	splice_region_variant	100423062	exon2			TCCTAGGTAAGTG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.325+1G>C	22.37:g.23235999G>C		64	0	0		75	21	0.28	NM_001178126		Splice_Site	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	9.342	1.063224	0.19987	.	.	ENSG00000254709	ENST00000532223;ENST00000526893	.	.	.	3.51	3.51	0.40186	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.7103	0.45980	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	IGLL5	21565999	1.000000	0.71417	0.997000	0.53966	0.297000	0.27493	4.982000	0.63825	1.990000	0.58119	0.491000	0.48974	.	.	.	none		0.587	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	Intron	C	23235999	G	C	23235999	5	2	18	1	0	0	0	0	0	0	1	0	7603	1275	44	4	332	4	IGLL5	22	23235999	Splice_Site	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	1	23235999	28068567	178	2565	40	2	3	23		10	6	5690	N	T_G_C	3.205253e-10
MCHR1	2847	hgsc.bcm.edu	37	chr22	41076964	41076964	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgtccccaggatcacctcctCgcacggggagcatctcctac	7	8	9	17	2	2	0	1	0	1	0	6	2	4	2	5	3	2	2	5	3	1	1	rs200627010		TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chr22:41076964C>T	ENST00000249016.4	+	2	997	c.301C>T	c.(301-303)Cgc>Tgc	p.R101C	MCHR1_ENST00000498400.1_3'UTR|MCHR1_ENST00000381433.2_Missense_Mutation_p.R101C	NM_005297.3	NP_005288.3	Q99705	MCHR1_HUMAN	melanin-concentrating hormone receptor 1	101					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						ATCACCTCCTCGCACGGGGAG	0.577																																					p.R101C		Atlas-SNP	.											MCHR1,NS,carcinoma,0,1	MCHR1	45	1	0			c.C301T						scavenged	.						123	95	105					22																	41076964		2203	4300	6503	SO:0001583	missense	2847	exon2			CCTCCTCGCACGG		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.301C>T	22.37:g.41076964C>T	ENSP00000249016:p.Arg101Cys	77	1	0.012987		82	21	0.256098	NM_005297	B2RBX6|Q5R3J1|Q96S47|Q9BV08	Missense_Mutation	SNP	ENST00000249016.4	37	CCDS14004.1	.	.	.	.	.	.	.	.	.	.	C	10.96	1.498061	0.26861	.	.	ENSG00000128285	ENST00000249016;ENST00000381433	T;T	0.36520	1.25;1.25	5.36	5.36	0.76844	.	0.229124	0.38959	N	0.001519	T	0.24928	0.0605	L	0.27053	0.805	0.22639	N	0.998904	B	0.22414	0.069	B	0.16722	0.016	T	0.10042	-1.0647	10	0.36615	T	0.2	.	10.3991	0.44218	0.0:0.9107:0.0:0.0893	.	101	Q99705	MCHR1_HUMAN	C	101	ENSP00000249016:R101C;ENSP00000370841:R101C	ENSP00000249016:R101C	R	+	1	0	MCHR1	39406910	0.001000	0.12720	0.423000	0.26634	0.033000	0.12548	0.312000	0.19397	2.669000	0.90835	0.655000	0.94253	CGC	.	.	weak		0.577	MCHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317142.1	NM_005297		T	41076964	C	T	41076964	3	4	18	1	0	0	0	0	1	0	0	0	9391	884	31	1	307	1	MCHR1	22	41076964	Missense_Mutation	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	17840965	41076964	10227602	179	2566											
ZBED1	9189	hgsc.bcm.edu	37	chrX	2408513	2408513	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcttcacgcatctgctccGtgttgctcttgacgaactcg	6	12	10	13	4	3	1	1	1	2	0	5	2	4	1	1	1	3	5	1	1	1	3			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chrX:2408513G>A	ENST00000381223.4	-	2	451	c.248C>T	c.(247-249)aCg>aTg	p.T83M	ZBED1_ENST00000381218.3_Missense_Mutation_p.T83M|DHRSX_ENST00000334651.5_Intron|ZBED1_ENST00000515319.1_5'Flank|ZBED1_ENST00000381222.2_Missense_Mutation_p.T83M	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	83					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)				CATCTGCTCCGTGTTGCTCTT	0.632																																					p.T83M		Atlas-SNP	.											.	ZBED1	64	.	0			c.C248T						PASS	.						195	174	181					X																	2408513		2203	4296	6499	SO:0001583	missense	9189	exon2			TGCTCCGTGTTGC	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.248C>T	X.37:g.2408513G>A	ENSP00000370621:p.Thr83Met	291	0	0		299	29	0.09699	NM_001171135	Q96BY4	Missense_Mutation	SNP	ENST00000381223.4	37	CCDS14118.1	.	.	.	.	.	.	.	.	.	.	G	16.60	3.169287	0.57584	.	.	ENSG00000214717	ENST00000381223;ENST00000381222;ENST00000381218;ENST00000461691	.	.	.	2.62	2.62	0.31277	.	0.172732	0.35207	U	0.003379	T	0.63082	0.2481	.	.	.	0.09310	N	1	D	0.89917	1.0	D	0.70935	0.971	T	0.55842	-0.8077	8	0.48119	T	0.1	-26.8773	13.0583	0.58992	0.0:0.0:1.0:0.0	.	83	O96006	ZBED1_HUMAN	M	83	.	ENSP00000370616:T83M	T	-	2	0	ZBED1	2418513	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	6.339000	0.72969	1.086000	0.41228	0.425000	0.28330	ACG	.	.	none		0.632	ZBED1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144310.3	NM_004729		A	2408513	G	A	2408513	3	1	18	1	0	0	0	0	1	0	0	0	17532	1145	40	1	1840	1	ZBED1	23	2408513	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10		2408513	152862047	180	2567											
MAGEB6	158809	hgsc.bcm.edu	37	chrX	26212458	26212458	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcaggtgtttcaggctcaaaAtatgatgtggctgccgaggg	9	10	15	7	1	2	1	2	1	0	0	2	2	2	1	1	4	1	4	1	4	3	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chrX:26212458A>T	ENST00000379034.1	+	2	644	c.495A>T	c.(493-495)aaA>aaT	p.K165N		NM_173523.2	NP_775794.2	Q8N7X4	MAGB6_HUMAN	melanoma antigen family B, 6	165										breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(18)|ovary(3)|prostate(2)	33						CAGGCTCAAAATATGATGTGG	0.488																																					p.K165N		Atlas-SNP	.											.	MAGEB6	91	.	0			c.A495T						PASS	.						53	48	50					X																	26212458		2202	4300	6502	SO:0001583	missense	158809	exon2			CTCAAAATATGAT	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.495A>T	X.37:g.26212458A>T	ENSP00000368320:p.Lys165Asn	73	0	0		65	30	0.461538	NM_173523	Q6GS19|Q9H219	Missense_Mutation	SNP	ENST00000379034.1	37	CCDS14217.1	.	.	.	.	.	.	.	.	.	.	A	6.511	0.462510	0.12342	.	.	ENSG00000176746	ENST00000379034	T	0.01947	4.54	1.74	-3.48	0.04739	.	.	.	.	.	T	0.01353	0.0044	N	0.24115	0.695	0.09310	N	1	P	0.47677	0.899	B	0.40009	0.316	T	0.31251	-0.9950	9	0.35671	T	0.21	.	0.7658	0.01015	0.2468:0.3792:0.1733:0.2007	.	165	Q8N7X4	MAGB6_HUMAN	N	165	ENSP00000368320:K165N	ENSP00000368320:K165N	K	+	3	2	MAGEB6	26122379	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.010000	0.12743	-1.568000	0.01670	0.376000	0.23039	AAA	.	.	none		0.488	MAGEB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056123.1	NM_173523		T	26212458	A	T	26212458	3	4	18	1	0	0	0	0	1	0	0	0	9188	98	4	5	497	5	MAGEB6	23	26212458	Missense_Mutation	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10	23803945	26212458	129058102	181	2568											
USP9X	8239	hgsc.bcm.edu	37	chrX	41056722	41056722	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcaaacttctgagaaaaaaTttcatattggttgtgaaaaa	17	14	6	4	0	3	2	2	2	1	1	3	3	3	2	0	1	1	1	0	1	7	6			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chrX:41056722T>A	ENST00000324545.8	+	29	4972	c.4339T>A	c.(4339-4341)Ttt>Att	p.F1447I	USP9X_ENST00000378308.2_Missense_Mutation_p.F1447I	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	1447					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						TGAGAAAAAATTTCATATTGG	0.363																																					p.F1447I	Ovarian(172;1807 2695 35459 49286)	Atlas-SNP	.											.	USP9X	385	.	0			c.T4339A						PASS	.						72	71	72					X																	41056722		2050	4201	6251	SO:0001583	missense	8239	exon29			AAAAAATTTCATA	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.4339T>A	X.37:g.41056722T>A	ENSP00000316357:p.Phe1447Ile	155	0	0		157	71	0.452229	NM_001039591	O75550|Q8WWT3|Q8WX12	Missense_Mutation	SNP	ENST00000324545.8	37	CCDS43930.1	.	.	.	.	.	.	.	.	.	.	T	16.70	3.194592	0.58017	.	.	ENSG00000124486	ENST00000378308;ENST00000324545	T;T	0.02787	4.16;4.16	5.3	5.3	0.74995	.	0.105859	0.64402	D	0.000002	T	0.02494	0.0076	N	0.14661	0.345	0.40695	D	0.982439	B;B	0.16166	0.016;0.002	B;B	0.20384	0.029;0.008	T	0.57136	-0.7863	10	0.21540	T	0.41	.	14.4424	0.67327	0.0:0.0:0.0:1.0	.	1447;1447	Q93008-1;Q93008	.;USP9X_HUMAN	I	1447	ENSP00000367558:F1447I;ENSP00000316357:F1447I	ENSP00000316357:F1447I	F	+	1	0	USP9X	40941666	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.694000	0.84235	1.859000	0.53934	0.339000	0.21740	TTT	.	.	none		0.363	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652		A	41056722	T	A	41056722	3	1	18	1	0	0	0	0	1	0	0	0	17105	1493	52	5	4449	5	USP9X	23	41056722	Missense_Mutation	SNP	T	TCGA-FF-A7CR-01A-11D-A382-10	14844264	41056722	114213838	182	2569											
WAS	7454	hgsc.bcm.edu	37	chrX	48547156	48547156	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtccactgccccctgtacctTtggggattgccccaccccca	5	9	8	19	0	0	0	0	0	0	0	1	1	1	1	8	2	3	1	8	2	1	3			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chrX:48547156T>C	ENST00000376701.4	+	10	1114	c.1039T>C	c.(1039-1041)Ttg>Ctg	p.L347L		NM_000377.2	NP_000368.1	P42768	WASP_HUMAN	Wiskott-Aldrich syndrome	347					actin filament polymerization (GO:0030041)|actin filament-based movement (GO:0030048)|actin polymerization or depolymerization (GO:0008154)|blood coagulation (GO:0007596)|defense response (GO:0006952)|endosomal transport (GO:0016197)|epidermis development (GO:0008544)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|protein complex assembly (GO:0006461)|regulation of catalytic activity (GO:0050790)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|vesicle membrane (GO:0012506)	identical protein binding (GO:0042802)|phospholipase binding (GO:0043274)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|small GTPase regulator activity (GO:0005083)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	28		all_lung(315;1.27e-10)				CCCTGTACCTTTGGGGATTGC	0.701			"Mis, N, F, S"			lymphoma																															p.L347L		Atlas-SNP	.		X-linked recessive		Wiskott-Aldrich syndrome	X	Xp11.23-p11.22	7454	Wiskott-Aldrich syndrome		L	.	WAS	51	.	0			c.T1039C						PASS	.						7	7	7					X																	48547156		2147	4185	6332	SO:0001819	synonymous_variant	7454	exon10			GTACCTTTGGGGA	AF115548	CCDS14303.1	Xp11.4-p11.21	2014-09-17	2012-07-12		ENSG00000015285	ENSG00000015285			12731	protein-coding gene	gene with protein product	"eczema-thrombocytopenia"	300392	"thrombocytopenia 1 (X-linked)", "Wiskott-Aldrich syndrome (eczema-thrombocytopenia)"	IMD2, THC		7795648	Standard	NM_000377		Approved	WASP	uc004dkm.4	P42768	OTTHUMG00000034483	ENST00000376701.4:c.1039T>C	X.37:g.48547156T>C		149	0	0		184	95	0.516304	NM_000377	Q9BU11|Q9UNJ9	Silent	SNP	ENST00000376701.4	37	CCDS14303.1																																																																																			.	.	none		0.701	WAS-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083379.1	NM_000377		C	48547156	T	C	48547156	2	2	18	1	0	0	0	0	0	0	0	1	17266	1838	64	3		3	WAS	23	48547156	Silent	SNP	T	TCGA-FF-A7CR-01A-11D-A382-10	7490434	48547156	106723404	183	2570											
CACNA1F	778	hgsc.bcm.edu	37	chrX	49083586	49083586	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttctctctctccttggagaaCtccctgagggaggaggatag	8	11	12	10	0	2	2	0	1	2	1	6	6	4	5	2	4	1	0	2	4	2	3			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chrX:49083586C>T	ENST00000376265.2	-	9	1183	c.1122G>A	c.(1120-1122)gaG>gaA	p.E374E	CACNA1F_ENST00000323022.5_Silent_p.E374E|CACNA1F_ENST00000376251.1_Silent_p.E309E	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	374					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)	CCTTGGAGAACTCCCTGAGGG	0.562																																					p.E374E		Atlas-SNP	.											.	CACNA1F	218	.	0			c.G1122A						PASS	.						18	14	15					X																	49083586		2185	4254	6439	SO:0001819	synonymous_variant	778	exon9			GGAGAACTCCCTG	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.1122G>A	X.37:g.49083586C>T		41	0	0		45	18	0.4	NM_001256789	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Silent	SNP	ENST00000376265.2	37	CCDS35253.1																																																																																			.	.	none		0.562	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183		T	49083586	C	T	49083586	2	4	18	1	0	0	0	0	0	0	0	1	2545	564	20	2		2	CACNA1F	23	49083586	Silent	SNP	C	TCGA-FF-A7CR-01A-11D-A382-10	536430	49083586	106186974	184	2571											
HEPH	9843	hgsc.bcm.edu	37	chrX	65480101	65480101	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcttcactgttttttctcgaAcaggtaagtcctaacttccc	8	16	5	12	1	3	0	1	0	2	0	6	1	5	0	2	1	2	2	2	1	3	7			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chrX:65480101A>G	ENST00000343002.2	+	18	3860	c.3196A>G	c.(3196-3198)Aca>Gca	p.T1066A	HEPH_ENST00000441993.2_Missense_Mutation_p.T1069A|HEPH_ENST00000519389.1_Missense_Mutation_p.T1120A|HEPH_ENST00000419594.1_Missense_Mutation_p.T877A|HEPH_ENST00000374727.3_Missense_Mutation_p.T1069A|HEPH_ENST00000336279.5_Missense_Mutation_p.T799A			Q9BQS7	HEPH_HUMAN	hephaestin	1066	Plastocyanin-like 6.				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						TTTTTCTCGAACAGGTAAGTC	0.473																																					p.T1120A		Atlas-SNP	.											.	HEPH	224	.	0			c.A3358G						PASS	.						92	74	80					X																	65480101		2203	4300	6503	SO:0001583	missense	9843	exon19			TCTCGAACAGGTA	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.3196A>G	X.37:g.65480101A>G	ENSP00000343939:p.Thr1066Ala	36	0	0		56	30	0.535714	NM_138737	B1AJX8|D3DVT7|E9PHN8|O75180|Q6UW45|Q9C058	Missense_Mutation	SNP	ENST00000343002.2	37		.	.	.	.	.	.	.	.	.	.	A	4.208	0.037327	0.08148	.	.	ENSG00000089472	ENST00000519389;ENST00000374727;ENST00000336279;ENST00000441993;ENST00000419594;ENST00000343002	D;D;D;D;D;D	0.99245	-5.62;-5.61;-5.62;-5.58;-5.62;-5.61	4.81	-0.296	0.12824	Cupredoxin (1);	1.165000	0.06166	N	0.676881	D	0.94434	0.8209	N	0.03608	-0.345	0.09310	N	1	B;B;B	0.14805	0.001;0.011;0.0	B;B;B	0.06405	0.0;0.002;0.002	D	0.92975	0.6401	10	0.09338	T	0.73	.	4.6493	0.12587	0.3017:0.2357:0.4627:0.0	.	1120;877;1066	E9PHN8;E7ES21;Q9BQS7	.;.;HEPH_HUMAN	A	1120;1069;799;1069;877;1066	ENSP00000430620:T1120A;ENSP00000363859:T1069A;ENSP00000337418:T799A;ENSP00000411687:T1069A;ENSP00000413211:T877A;ENSP00000343939:T1066A	ENSP00000337418:T799A	T	+	1	0	HEPH	65396826	0.000000	0.05858	0.021000	0.16686	0.161000	0.22273	0.012000	0.13287	-0.060000	0.13132	0.486000	0.48141	ACA	.	.	none		0.473	HEPH-002	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000056995.1	NM_138737		G	65480101	A	G	65480101	3	3	18	1	0	0	0	0	1	0	0	0	7063	43	2	3	3432	3	HEPH	23	65480101	Missense_Mutation	SNP	A	TCGA-FF-A7CR-01A-11D-A382-10	16396515	65480101	89790459	185	2572											
DGAT2L6	347516	hgsc.bcm.edu	37	chrX	69424319	69424319	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatggccggggcttcactcGcggatcctggggcttcctgc	3	9	14	15	3	1	0	1	0	0	0	4	1	3	1	4	6	1	2	4	6	0	2			TCGA-FF-A7CR-01A-11D-A382-10	TCGA-FF-A7CR-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f8b1d5ee-a86d-4505-96f8-3e8b0c050946	2bbed379-b7b8-4107-afe0-bfd42b041bb3	g.chrX:69424319G>A	ENST00000333026.3	+	6	912	c.812G>A	c.(811-813)cGc>cAc	p.R271H		NM_198512.1	NP_940914.1	Q6ZPD8	DG2L6_HUMAN	diacylglycerol O-acyltransferase 2-like 6	271					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						GGCTTCACTCGCGGATCCTGG	0.502																																					p.R271H		Atlas-SNP	.											.	DGAT2L6	40	.	0			c.G812A						PASS	.						74	69	71					X																	69424319		2203	4300	6503	SO:0001583	missense	347516	exon6			TCACTCGCGGATC	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.812G>A	X.37:g.69424319G>A	ENSP00000328036:p.Arg271His	100	0	0		79	32	0.405063	NM_198512	Q6IEE2	Missense_Mutation	SNP	ENST00000333026.3	37	CCDS14397.1	.	.	.	.	.	.	.	.	.	.	G	4.247	0.044849	0.08196	.	.	ENSG00000184210	ENST00000333026	T	0.14022	2.54	4.98	1.3	0.21679	.	0.760798	0.11324	N	0.575729	T	0.10809	0.0264	L	0.39245	1.2	0.09310	N	1	B	0.09022	0.002	B	0.14023	0.01	T	0.32693	-0.9897	10	0.42905	T	0.14	-13.1803	5.2833	0.15688	0.2715:0.0:0.5826:0.1459	.	271	Q6ZPD8	DG2L6_HUMAN	H	271	ENSP00000328036:R271H	ENSP00000328036:R271H	R	+	2	0	DGAT2L6	69341044	0.000000	0.05858	0.750000	0.31169	0.053000	0.15095	-1.212000	0.02994	-0.055000	0.13244	-1.016000	0.02456	CGC	.	.	none		0.502	DGAT2L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057067.1	NM_198512		A	69424319	G	A	69424319	3	1	18	1	0	0	0	0	1	0	0	0	4461	1087	38	1	834	1	DGAT2L6	23	69424319	Missense_Mutation	SNP	G	TCGA-FF-A7CR-01A-11D-A382-10	3944218	69424319	85846241	186	2573											
HSPG2	3339	hgsc.bcm.edu	37	chr1	22182158	22182158	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccttcgcagggagctggccGccggggccccctgacgagta	5	5	16	15	4	0	1	0	1	0	0	1	3	0	2	5	4	1	3	5	4	1	2			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr1:22182158G>A	ENST00000374695.3	-	46	5791	c.5712C>T	c.(5710-5712)ggC>ggT	p.G1904G	HSPG2_ENST00000430507.1_5'Flank	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	1904	Ig-like C2-type 4.				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)	GGAGCTGGCCGCCGGGGCCCC	0.672																																					p.G1904G		Atlas-SNP	.											.	HSPG2	311	.	0			c.C5712T						PASS	.						12	13	12					1																	22182158		2193	4281	6474	SO:0001819	synonymous_variant	3339	exon46			CTGGCCGCCGGGG	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.5712C>T	1.37:g.22182158G>A		58	0	0		39	8	0.205128	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																			.	.	none		0.672	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		A	22182158	G	A	22182158	2	1	19	1	0	0	0	0	0	0	0	1	7439	1074	38	1		1	HSPG2	1	22182158	Silent	SNP	G	TCGA-FF-A7CW-01A-11D-A382-10		22182158	227068463	1	2574											
RC3H1	149041	hgsc.bcm.edu	37	chr1	173951933	173951933	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agttttagaggcttgaggaaAccgtggctccaatctttgca	10	12	11	8	1	1	2	0	1	1	1	2	3	2	3	2	3	2	4	2	3	3	4			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr1:173951933A>T	ENST00000367696.2	-	5	1051	c.700T>A	c.(700-702)Ttt>Att	p.F234I	RC3H1_ENST00000367694.2_Missense_Mutation_p.F234I|RC3H1_ENST00000258349.4_Missense_Mutation_p.F234I			Q5TC82	RC3H1_HUMAN	ring finger and CCCH-type domains 1	234					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						GCTTGAGGAAACCGTGGCTCC	0.433																																					p.F234I		Atlas-SNP	.											.	RC3H1	110	.	0			c.T700A						PASS	.						103	103	103					1																	173951933		2203	4300	6503	SO:0001583	missense	149041	exon4			GAGGAAACCGTGG	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.700T>A	1.37:g.173951933A>T	ENSP00000356669:p.Phe234Ile	155	0	0		158	73	0.462025	NM_172071	B3KVK1|Q5W180|Q5W181|Q8IVE6|Q8N9V1	Missense_Mutation	SNP	ENST00000367696.2	37	CCDS30940.1	.	.	.	.	.	.	.	.	.	.	A	35	5.463575	0.96257	.	.	ENSG00000135870	ENST00000367696;ENST00000258349;ENST00000367694	D;D;D	0.95412	-3.7;-3.7;-3.7	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	D	0.97558	0.9200	M	0.78801	2.425	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;1.0;1.0	D;D;D;D	0.83275	0.991;0.991;0.996;0.982	D	0.98323	1.0529	10	0.87932	D	0	-16.8265	16.0858	0.81049	1.0:0.0:0.0:0.0	.	234;234;234;234	B9EGU6;B7ZMB3;Q5TC82-2;Q5TC82	.;.;.;RC3H1_HUMAN	I	234	ENSP00000356669:F234I;ENSP00000258349:F234I;ENSP00000356667:F234I	ENSP00000258349:F234I	F	-	1	0	RC3H1	172218556	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	2.264000	0.75181	0.533000	0.62120	TTT	.	.	none		0.433	RC3H1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090733.2	NM_172071		T	173951933	A	T	173951933	3	4	19	1	0	0	0	0	1	0	0	0	13181	43	2	5	2765	5	RC3H1	1	173951933	Missense_Mutation	SNP	A	TCGA-FF-A7CW-01A-11D-A382-10	151769775	173951933	75298688	2	2575											
CAMSAP1L1	23271	hgsc.bcm.edu	37	chr1	200818866	200818866	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aaaaataacacctttgaatcGaaccttgacacctcctcggt	14	10	5	12	2	0	2	0	2	0	0	3	3	1	2	4	1	2	0	4	1	5	3			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr1:200818866G>A	ENST00000236925.4	+	12	3051	c.3002G>A	c.(3001-3003)cGa>cAa	p.R1001Q	CAMSAP2_ENST00000358823.2_Missense_Mutation_p.R990Q|CAMSAP2_ENST00000413307.2_Missense_Mutation_p.R974Q			Q08AD1	CAMP2_HUMAN	calmodulin regulated spectrin-associated protein family, member 2	1001					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)										CCTTTGAATCGAACCTTGACA	0.418																																					p.R990Q		Atlas-SNP	.											CAMSAP1L1,NS,carcinoma,+1,1	.	.	1	0			c.G2969A						PASS	.						100	105	103					1																	200818866		2203	4300	6503	SO:0001583	missense	23271	exon11			TGAATCGAACCTT	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.3002G>A	1.37:g.200818866G>A	ENSP00000236925:p.Arg1001Gln	153	0	0		185	97	0.524324	NM_203459	B1APG6|Q08AD2|Q6PGN8|Q96FB3|Q9UG20|Q9UPS4	Missense_Mutation	SNP	ENST00000236925.4	37		.	.	.	.	.	.	.	.	.	.	G	23.4	4.407876	0.83340	.	.	ENSG00000118200	ENST00000358823;ENST00000413307;ENST00000236925	T;T;T	0.35973	1.32;1.28;1.32	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.62429	0.2427	M	0.73217	2.22	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.992;0.951;0.999	T	0.58070	-0.7701	10	0.44086	T	0.13	-15.275	20.3214	0.98679	0.0:0.0:1.0:0.0	.	974;1001;990	Q08AD1-2;Q08AD1;Q08AD1-3	.;CAMP2_HUMAN;.	Q	990;974;1001	ENSP00000351684:R990Q;ENSP00000416800:R974Q;ENSP00000236925:R1001Q	ENSP00000236925:R1001Q	R	+	2	0	CAMSAP1L1	199085489	1.000000	0.71417	0.991000	0.47740	0.996000	0.88848	7.844000	0.86867	2.804000	0.96469	0.655000	0.94253	CGA	.	.	none		0.418	CAMSAP2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086956.2	NM_203459		A	200818866	G	A	200818866	3	1	19	1	0	0	0	0	1	0	0	0	2614	1058	37	1	3011	1	CAMSAP1L1	1	200818866	Missense_Mutation	SNP	G	TCGA-FF-A7CW-01A-11D-A382-10	26866933	200818866	48431755	3	2576											
TPO	7173	hgsc.bcm.edu	37	chr2	1491693	1491693	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgacggaaaggctctttgtGctgtccaattccagcacctt	8	12	9	12	1	1	1	0	1	1	0	3	2	3	2	3	2	2	3	3	2	2	3			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr2:1491693G>A	ENST00000345913.4	+	10	1789	c.1698G>A	c.(1696-1698)gtG>gtA	p.V566V	TPO_ENST00000346956.3_Silent_p.V566V|TPO_ENST00000349624.3_Silent_p.V393V|TPO_ENST00000382201.3_Intron|TPO_ENST00000497517.2_Intron|TPO_ENST00000329066.4_Silent_p.V566V|TPO_ENST00000337415.3_Silent_p.V566V|TPO_ENST00000382198.1_Silent_p.V393V	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	566					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)	GGCTCTTTGTGCTGTCCAATT	0.577																																					p.V566V		Atlas-SNP	.											.	TPO	224	.	0			c.G1698A						PASS	.						139	118	125					2																	1491693		2203	4300	6503	SO:0001819	synonymous_variant	7173	exon10			CTTTGTGCTGTCC		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.1698G>A	2.37:g.1491693G>A		75	0	0		62	21	0.33871	NM_001206744	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Silent	SNP	ENST00000345913.4	37	CCDS1643.1																																																																																			.	.	none		0.577	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		A	1491693	G	A	1491693	2	1	19	1	0	0	0	0	0	0	0	1	16425	1306	46	2		2	TPO	2	1491693	Silent	SNP	G	TCGA-FF-A7CW-01A-11D-A382-10		1491693	241707680	4	2577											
CTNNA2	1496	hgsc.bcm.edu	37	chr2	80801387	80801387	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagttcatcgatgcctctcGcctggtgtatgatggcgttc	5	14	12	10	3	2	2	1	2	1	0	5	3	2	2	2	2	1	3	2	2	1	3			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr2:80801387G>A	ENST00000402739.4	+	12	1846	c.1841G>A	c.(1840-1842)cGc>cAc	p.R614H	AC008067.2_ENST00000430876.1_RNA|CTNNA2_ENST00000541047.1_Missense_Mutation_p.R614H|CTNNA2_ENST00000343114.3_Missense_Mutation_p.R293H|CTNNA2_ENST00000466387.1_Missense_Mutation_p.R614H|AC008067.2_ENST00000609950.1_RNA|CTNNA2_ENST00000496558.1_Missense_Mutation_p.R614H|CTNNA2_ENST00000361291.4_Missense_Mutation_p.R648H|CTNNA2_ENST00000540488.1_Missense_Mutation_p.R614H	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	614					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)	p.R614H(1)		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						GATGCCTCTCGCCTGGTGTAT	0.527																																					p.R614H		Atlas-SNP	.											CTNNA2_ENST00000466387,NS,carcinoma,+1,3	CTNNA2	462	3	1	Substitution - Missense(1)	prostate(1)	c.G1841A						PASS	.						172	164	167					2																	80801387		2149	4276	6425	SO:0001583	missense	1496	exon13			CCTCTCGCCTGGT		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.1841G>A	2.37:g.80801387G>A	ENSP00000384638:p.Arg614His	127	0	0		106	29	0.273585	NM_001164883	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Missense_Mutation	SNP	ENST00000402739.4	37		.	.	.	.	.	.	.	.	.	.	G	35	5.472512	0.96274	.	.	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488;ENST00000343114	T;T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95;0.95	5.75	5.75	0.90469	.	0.061993	0.64402	D	0.000005	T	0.67655	0.2916	M	0.80183	2.485	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	P;D;D;D	0.79784	0.791;0.993;0.987;0.987	T	0.68187	-0.5475	9	.	.	.	.	18.1307	0.89600	0.0:0.0:1.0:0.0	.	246;614;614;614	F6KRI5;P26232;P26232-3;P26232-2	.;CTNA2_HUMAN;.;.	H	614;614;648;614;614;614;293	ENSP00000418191:R614H;ENSP00000419295:R614H;ENSP00000355398:R648H;ENSP00000384638:R614H;ENSP00000444675:R614H;ENSP00000441705:R614H;ENSP00000341500:R293H	.	R	+	2	0	CTNNA2	80654898	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.799000	0.99117	2.732000	0.93576	0.655000	0.94253	CGC	.	.	none		0.527	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389		A	80801387	G	A	80801387	3	1	19	1	0	0	0	0	1	0	0	0	4015	1087	38	1	1679	1	CTNNA2	2	80801387	Missense_Mutation	SNP	G	TCGA-FF-A7CW-01A-11D-A382-10	79309694	80801387	162397986	5	2578											
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160285738	160285738	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaatggaatacgcagttcaCgttcatctgttactcttctt	9	15	6	11	2	5	0	2	0	3	0	5	1	5	1	1	1	2	4	1	1	4	6			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr2:160285738C>T	ENST00000392783.2	-	11	2723	c.2228G>A	c.(2227-2229)cGt>cAt	p.R743H	BAZ2B_ENST00000343439.5_Missense_Mutation_p.R643H|BAZ2B_ENST00000392782.1_Missense_Mutation_p.R741H|BAZ2B_ENST00000355831.2_Missense_Mutation_p.R743H	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	743	MBD. {ECO:0000255|PROSITE- ProRule:PRU00338}.				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						ACGCAGTTCACGTTCATCTGT	0.274																																					p.R743H		Atlas-SNP	.											BAZ2B,NS,carcinoma,-1,1	BAZ2B	196	1	0			c.G2228A						scavenged	.						89	84	86					2																	160285738		1807	4073	5880	SO:0001583	missense	29994	exon11			AGTTCACGTTCAT	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.2228G>A	2.37:g.160285738C>T	ENSP00000376534:p.Arg743His	561	2	0.00356506		463	102	0.220302	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	37	CCDS2209.2	.	.	.	.	.	.	.	.	.	.	C	15.17	2.753579	0.49362	.	.	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439	D;D;D;D	0.99479	-5.98;-5.98;-5.98;-2.02	5.05	3.23	0.37069	Methyl-CpG DNA binding (3);DNA-binding, integrase-type (1);	0.467765	0.15641	N	0.251909	D	0.97932	0.9320	L	0.50333	1.59	0.27152	N	0.961373	B;B;B;B	0.32245	0.039;0.167;0.067;0.361	B;B;B;B	0.26202	0.02;0.04;0.008;0.067	D	0.96004	0.8996	10	0.66056	D	0.02	-0.6977	10.7496	0.46200	0.0:0.8427:0.0:0.1573	.	547;643;741;743	Q9UIF8-4;Q9UIF8-2;Q9UIF8-5;Q9UIF8	.;.;.;BAZ2B_HUMAN	H	741;743;743;643	ENSP00000376533:R741H;ENSP00000376534:R743H;ENSP00000348087:R743H;ENSP00000339670:R643H	ENSP00000339670:R643H	R	-	2	0	BAZ2B	159993984	0.697000	0.27767	0.895000	0.35142	0.990000	0.78478	1.322000	0.33689	0.635000	0.30488	-0.142000	0.14014	CGT	.	.	none		0.274	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			T	160285738	C	T	160285738	3	4	19	1	0	0	0	0	1	0	0	0	1332	536	19	1	4386	1	BAZ2B	2	160285738	Missense_Mutation	SNP	C	TCGA-FF-A7CW-01A-11D-A382-10	79484351	160285738	82913635	6	2579											
MAGI1	9223	hgsc.bcm.edu	37	chr3	65425591	65425591	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgctgctgctgctgctgctgTtgctgctgctgttgctgctg	0	16	14	11	0	0	0	0	0	0	0	0	0	0	0	0	0	11	13	0	0	0	2	rs374381483|rs79701778		TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr3:65425591T>C	ENST00000497477.2	-	9	1232	c.1233A>G	c.(1231-1233)caA>caG	p.Q411Q	MAGI1_ENST00000470990.1_5'UTR|MAGI1_ENST00000402939.2_Silent_p.Q411Q|MAGI1_ENST00000483466.1_Silent_p.Q411Q|MAGI1_ENST00000330909.8_Silent_p.Q411Q			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	411	Poly-Gln.				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)		gctgctgctgttgctgctgct	0.542											OREG0015658	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q411Q		Atlas-SNP	.											MAGI1_ENST00000402939,NS,carcinoma,0,3	MAGI1	481	3	0			c.A1233G						scavenged	.						61	60	61					3																	65425591		2191	4267	6458	SO:0001819	synonymous_variant	9223	exon9			CTGCTGTTGCTGC	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.1233A>G	3.37:g.65425591T>C		90	2	0.0222222	1084	93	5	0.0537634	NM_001033057	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Silent	SNP	ENST00000497477.2	37		.	.	.	.	.	.	.	.	.	.	T	1.469	-0.560380	0.03939	.	.	ENSG00000151276	ENST00000460329	.	.	.	2.82	-5.65	0.02459	.	.	.	.	.	T	0.27313	0.0670	.	.	.	0.21445	N	0.999683	.	.	.	.	.	.	T	0.31558	-0.9939	4	.	.	.	.	7.6202	0.28181	0.0:0.2714:0.1222:0.6064	.	.	.	.	S	292	.	.	N	-	2	0	MAGI1	65400631	0.067000	0.21026	0.000000	0.03702	0.001000	0.01503	-1.642000	0.02006	-1.408000	0.02040	-1.740000	0.00687	AAC	T|0.500;C|0.500	0.500	weak		0.542	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742		C	65425591	T	C	65425591	2	2	19	1	0	0	0	0	0	0	0	1	9199	1722	60	3		3	MAGI1	3	65425591	Silent	SNP	T	TCGA-FF-A7CW-01A-11D-A382-10		65425591	132596839	7	2580											
EBLN2	55096	hgsc.bcm.edu	37	chr3	73111480	73111480	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atttgagctatctgggaaaaAcagacagtatccactggatg	14	10	10	7	0	1	2	0	1	1	1	2	4	2	4	1	2	2	2	1	2	4	3			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr3:73111480A>C	ENST00000533473.1	+	1	671	c.248A>C	c.(247-249)aAc>aCc	p.N83T	PPP4R2_ENST00000356692.5_Intron|PPP4R2_ENST00000295862.9_Intron|PPP4R2_ENST00000394284.3_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						TCTGGGAAAAACAGACAGTAT	0.483																																					p.N83T		Atlas-SNP	.											.	EBLN2	18	.	0			c.A248C						PASS	.						34	34	34					3																	73111480		1943	4138	6081	SO:0001583	missense	55096	exon1			GGAAAAACAGACA		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.248A>C	3.37:g.73111480A>C	ENSP00000432104:p.Asn83Thr	150	0	0		144	8	0.0555556	NM_018029	Q8WWH3|Q9NW89	Missense_Mutation	SNP	ENST00000533473.1	37	CCDS54608.1	.	.	.	.	.	.	.	.	.	.	A	2.477	-0.320603	0.05386	.	.	ENSG00000255423	ENST00000533473	.	.	.	0.458	-0.848	0.10727	P40 nucleoprotein, subdomain 1, Borna disease virus (1);	.	.	.	.	T	0.14917	0.0360	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.10450	0.005	T	0.28038	-1.0056	7	0.20046	T	0.44	.	.	.	.	.	83	Q6P2I7	EBLN2_HUMAN	T	83	.	ENSP00000432104:N83T	N	+	2	0	EBLN2	73194170	0.030000	0.19436	0.004000	0.12327	0.004000	0.04260	-1.980000	0.01492	-0.352000	0.08237	-0.354000	0.07668	AAC	.	.	none		0.483	EBLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386932.1	NM_018029		C	73111480	A	C	73111480	3	2	19	1	0	0	0	0	1	0	0	0	4886	43	2	5	250	5	EBLN2	3	73111480	Missense_Mutation	SNP	A	TCGA-FF-A7CW-01A-11D-A382-10	7685889	73111480	124910950	8	2581											
CLSTN2	64084	hgsc.bcm.edu	37	chr3	140275464	140275464	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caactccaggcagttcccaaCggcgggtgtgcggcgcctca	7	6	13	15	4	1	0	1	0	0	0	3	0	3	0	3	4	3	2	3	4	2	1	rs368537354		TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr3:140275464C>T	ENST00000458420.3	+	11	1974	c.1784C>T	c.(1783-1785)aCg>aTg	p.T595M		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	595					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)	p.T595M(1)		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						CAGTTCCCAACGGCGGGTGTG	0.572										HNSCC(16;0.037)																											p.T595M	GBM(45;858 913 3709 36904 37282)	Atlas-SNP	.											CLSTN2,caecum,carcinoma,-1,2	CLSTN2	190	2	1	Substitution - Missense(1)	large_intestine(1)	c.C1784T						PASS	.	C	MET/THR	0,4406		0,0,2203	114	102	106		1784	5.4	0.1	3		106	1,8599	1.2+/-3.3	0,1,4299	no	missense	CLSTN2	NM_022131.2	81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	595/956	140275464	1,13005	2203	4300	6503	SO:0001583	missense	64084	exon11			TCCCAACGGCGGG	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.1784C>T	3.37:g.140275464C>T	ENSP00000402460:p.Thr595Met	99	0	0		89	13	0.146067	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Missense_Mutation	SNP	ENST00000458420.3	37	CCDS3112.1	.	.	.	.	.	.	.	.	.	.	C	18.10	3.547528	0.65311	0.0	1.16E-4	ENSG00000158258	ENST00000458420	T	0.35973	1.28	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	T	0.65176	0.2666	M	0.86178	2.8	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.68526	-0.5385	9	.	.	.	-12.9896	16.9972	0.86371	0.0:1.0:0.0:0.0	.	595	Q9H4D0	CSTN2_HUMAN	M	595	ENSP00000402460:T595M	.	T	+	2	0	CLSTN2	141758154	1.000000	0.71417	0.082000	0.20525	0.276000	0.26787	7.776000	0.85560	2.692000	0.91855	0.563000	0.77884	ACG	.	.	weak		0.572	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131		T	140275464	C	T	140275464	3	4	19	1	0	0	0	0	1	0	0	0	3564	536	19	1	1826	1	CLSTN2	3	140275464	Missense_Mutation	SNP	C	TCGA-FF-A7CW-01A-11D-A382-10	67163984	140275464	57746966	9	2582											
GPR171	29909	hgsc.bcm.edu	37	chr3	150916504	150916504	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtggtcactaaaagtatgtTgatgagagcctttttcacat	11	14	9	7	1	2	2	2	2	0	1	2	3	2	2	1	1	1	2	1	1	3	5			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr3:150916504T>C	ENST00000309180.5	-	3	900	c.670A>G	c.(670-672)Aac>Gac	p.N224D	MED12L_ENST00000273432.4_Intron|MED12L_ENST00000474524.1_Intron	NM_013308.3	NP_037440.3	O14626	GP171_HUMAN	G protein-coupled receptor 171	224					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)			AAAAGTATGTTGATGAGAGCC	0.388																																					p.N224D		Atlas-SNP	.											.	GPR171	36	.	0			c.A670G						PASS	.						90	88	89					3																	150916504		2203	4300	6503	SO:0001583	missense	29909	exon3			GTATGTTGATGAG	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.670A>G	3.37:g.150916504T>C	ENSP00000308479:p.Asn224Asp	231	0	0		242	39	0.161157	NM_013308	D3DNJ4|Q8IV06	Missense_Mutation	SNP	ENST00000309180.5	37	CCDS3155.1	.	.	.	.	.	.	.	.	.	.	T	11.80	1.746709	0.30955	.	.	ENSG00000174946	ENST00000309180	T	0.37235	1.21	5.61	4.43	0.53597	GPCR, rhodopsin-like superfamily (1);	0.478447	0.21746	N	0.069745	T	0.38585	0.1046	L	0.58810	1.83	0.24759	N	0.992934	B	0.21905	0.062	B	0.30716	0.119	T	0.31586	-0.9938	10	0.42905	T	0.14	-9.7024	12.6935	0.56990	0.0:0.0:0.3884:0.6116	.	224	O14626	GP171_HUMAN	D	224	ENSP00000308479:N224D	ENSP00000308479:N224D	N	-	1	0	GPR171	152399194	0.979000	0.34478	0.581000	0.28614	0.653000	0.38743	2.825000	0.48096	0.910000	0.36722	0.528000	0.53228	AAC	.	.	none		0.388	GPR171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357793.1	NM_013308		C	150916504	T	C	150916504	3	2	19	1	0	0	0	0	1	0	0	0	6676	1812	63	3	293	3	GPR171	3	150916504	Missense_Mutation	SNP	T	TCGA-FF-A7CW-01A-11D-A382-10	10641040	150916504	47105926	10	2583											
KLHL6	89857	hgsc.bcm.edu	37	chr3	183273174	183273174	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atagttgctggctgcggcaaGcaccacgcggtggcaggaga	9	6	16	10	3	0	1	0	0	0	1	0	2	0	1	1	5	3	6	1	5	2	2	rs548549593	byFrequency	TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr3:183273174G>A	ENST00000341319.3	-	1	303	c.268C>T	c.(268-270)Ctt>Ttt	p.L90F		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	90	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				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)			GCTGCGGCAAGCACCACGCGG	0.507													G|||	2	0.000399361	0.0015	0.0	5008	,	,		15549	0.0		0.0	False		,,,				2504	0.0				p.L90F		Atlas-SNP	.											.	KLHL6	100	.	0			c.C268T						PASS	.						99	89	92					3																	183273174		2203	4300	6503	SO:0001583	missense	89857	exon1			CGGCAAGCACCAC	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.268C>T	3.37:g.183273174G>A	ENSP00000341342:p.Leu90Phe	160	0	0		152	66	0.434211	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Missense_Mutation	SNP	ENST00000341319.3	37	CCDS3245.2	.	.	.	.	.	.	.	.	.	.	G	28.2	4.901455	0.92035	.	.	ENSG00000172578	ENST00000341319	D	0.89681	-2.55	5.56	5.56	0.83823	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.96876	0.8980	H	0.97659	4.05	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98014	1.0367	10	0.87932	D	0	.	19.5245	0.95199	0.0:0.0:1.0:0.0	.	90	Q8WZ60	KLHL6_HUMAN	F	90	ENSP00000341342:L90F	ENSP00000341342:L90F	L	-	1	0	KLHL6	184755868	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.900000	0.87376	2.608000	0.88229	0.655000	0.94253	CTT	.	.	none		0.507	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446		A	183273174	G	A	183273174	3	1	19	1	0	0	0	0	1	0	0	0	8402	971	34	2	1625	2	KLHL6	3	183273174	Missense_Mutation	SNP	G	TCGA-FF-A7CW-01A-11D-A382-10	32356670	183273174	14749256	11	2584											
GPR125	166647	hgsc.bcm.edu	37	chr4	22446632	22446632	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctgcttcacgcctgtgactgGttgggcctgcagtgacttag	5	12	13	11	1	1	2	1	2	0	0	1	2	1	2	2	2	2	3	2	2	1	3			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr4:22446632G>T	ENST00000334304.5	-	6	939	c.670C>A	c.(670-672)Cca>Aca	p.P224T	GPR125_ENST00000282943.5_5'UTR|GPR125_ENST00000502482.1_Missense_Mutation_p.P224T|GPR125_ENST00000508133.1_5'Flank	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	224	LRRCT.				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)				CCTGTGACTGGTTGGGCCTGC	0.463																																					p.P224T		Atlas-SNP	.											GPR125,NS,carcinoma,+2,1	GPR125	118	1	0			c.C670A						PASS	.						130	114	119					4																	22446632		2203	4300	6503	SO:0001583	missense	166647	exon6			TGACTGGTTGGGC	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.670C>A	4.37:g.22446632G>T	ENSP00000334952:p.Pro224Thr	189	0	0		142	28	0.197183	NM_145290	Q6UXK9|Q86SQ5|Q8TC55	Missense_Mutation	SNP	ENST00000334304.5	37	CCDS33964.1	.	.	.	.	.	.	.	.	.	.	G	13.77	2.336957	0.41398	.	.	ENSG00000152990	ENST00000334304;ENST00000502482	T;T	0.57273	0.56;0.41	5.83	5.83	0.93111	Cysteine-rich flanking region, C-terminal (1);	0.107611	0.64402	D	0.000007	T	0.42607	0.1210	N	0.25485	0.75	0.48288	D	0.999629	B;B;B	0.09022	0.002;0.001;0.0	B;B;B	0.12837	0.005;0.008;0.002	T	0.18903	-1.0322	10	0.42905	T	0.14	-3.1626	15.7745	0.78204	0.0:0.0:0.8556:0.1444	.	99;224;224	Q8IWK6-3;Q8IWK6-2;Q8IWK6	.;.;GP125_HUMAN	T	224	ENSP00000334952:P224T;ENSP00000421006:P224T	ENSP00000334952:P224T	P	-	1	0	GPR125	22055730	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.556000	0.53734	2.763000	0.94921	0.585000	0.79938	CCA	.	.	none		0.463	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3			T	22446632	G	T	22446632	3	4	19	1	0	0	0	0	1	0	0	0	6647	1261	44	4	3351	4	GPR125	4	22446632	Missense_Mutation	SNP	G	TCGA-FF-A7CW-01A-11D-A382-10		22446632	168707644	12	2585											
UGT2B7	7364	hgsc.bcm.edu	37	chr4	69978319	69978319	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gcagcccacgacctcacctgGttccagtaccactctttgga	8	9	8	16	1	2	0	1	0	1	0	3	2	3	1	5	2	2	3	5	2	1	3			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr4:69978319G>A	ENST00000305231.7	+	6	1501	c.1455G>A	c.(1453-1455)tgG>tgA	p.W485*	UGT2B7_ENST00000508661.1_3'UTR	NM_001074.2	NP_001065.2	P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	485					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)	ACCTCACCTGGTTCCAGTACC	0.483																																					p.W485X		Atlas-SNP	.											.	UGT2B7	79	.	0			c.G1455A						PASS	.						177	167	170					4																	69978319		2203	4300	6503	SO:0001587	stop_gained	7364	exon6			CACCTGGTTCCAG	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	ENST00000305231.7:c.1455G>A	4.37:g.69978319G>A	ENSP00000304811:p.Trp485*	140	0	0		112	35	0.3125	NM_001074	B2R810|Q6GTW0	Nonsense_Mutation	SNP	ENST00000305231.7	37	CCDS3526.1	.	.	.	.	.	.	.	.	.	.	G	14.01	2.407084	0.42715	.	.	ENSG00000171234	ENST00000305231	.	.	.	2.13	2.13	0.27403	.	0.000000	0.64402	U	0.000004	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.956	0.41666	0.0:0.0:1.0:0.0	.	.	.	.	X	485	.	.	W	+	3	0	UGT2B7	70012908	1.000000	0.71417	0.982000	0.44146	0.254000	0.26022	8.547000	0.90665	1.192000	0.43071	0.306000	0.20318	TGG	.	.	none		0.483	UGT2B7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251560.1	NM_001074		A	69978319	G	A	69978319	4	1	19	1	0	0	0	0	0	1	0	0	16977	1270	44	2	1477	2	UGT2B7	4	69978319	Nonsense_Mutation	SNP	G	TCGA-FF-A7CW-01A-11D-A382-10	47531687	69978319	121175957	13	2586											
FRAS1	80144	hgsc.bcm.edu	37	chr4	79176419	79176419	+	Frame_Shift_Del	DEL	G	G	-																															cctgttcctatgaaggccatGtgtttcaggatggggaggac																										TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr4:79176419delG	ENST00000325942.6	+	6	933	c.493delG	c.(493-495)gtgfs	p.V165fs	FRAS1_ENST00000264899.6_Frame_Shift_Del_p.V165fs|FRAS1_ENST00000264895.6_Frame_Shift_Del_p.V165fs	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	165	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						TGAAGGCCATGTGTTTCAGGA	0.537																																					p.H164fs		Atlas-Indel	.											.	FRAS1	779	.	0			c.492delT						PASS	.						54	55	55					4																	79176419		1937	4123	6060	SO:0001589	frameshift_variant	80144	exon6			.	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.493delG	4.37:g.79176419delG	ENSP00000326330:p.Val165fs	194	0	0		133	27	0.203008	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Frame_Shift_Del	DEL	ENST00000325942.6	37	CCDS54772.1																																																																																			.	.	none		0.537	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			-	79176419	G	-	79176419	7	5	19	1	0	1	0	1	0	0	0	0	6050	1377	48	0	515	0	FRAS1	4	79176419	Frame_Shift_Del	DEL	G	TCGA-FF-A7CW-01A-11D-A382-10	9198100	79176419	111977857	14	2587											
SLC9A3	6550	hgsc.bcm.edu	37	chr5	480029	480029	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggtctcgagacttctgggcCgaccgtctcatgaggaccct	6	9	12	14	4	3	2	1	1	3	1	5	5	3	3	3	3	0	0	3	3	0	1	rs147340203	byFrequency	TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr5:480029C>T	ENST00000264938.3	-	10	1578	c.1569G>A	c.(1567-1569)tcG>tcA	p.S523S	SLC9A3_ENST00000514375.1_Silent_p.S514S|CTD-2228K2.7_ENST00000607286.1_RNA|CTD-2228K2.7_ENST00000607005.1_RNA|CTD-2228K2.7_ENST00000606288.1_RNA	NM_004174.2	NP_004165.2	P48764	SL9A3_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	523					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)			ACTTCTGGGCCGACCGTCTCA	0.592													C|||	5	0.000998403	0.0038	0.0	5008	,	,		17863	0.0		0.0	False		,,,				2504	0.0				p.S523S		Atlas-SNP	.											.	SLC9A3	89	.	0			c.G1569A						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	117	114	115		1569	-9.9	0	5	dbSNP_134	115	0,8600		0,0,4300	no	coding-synonymous	SLC9A3	NM_004174.2		0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		523/835	480029	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	6550	exon10			CTGGGCCGACCGT		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.1569G>A	5.37:g.480029C>T		50	0	0		35	7	0.2	NM_004174	B7ZKR2|E9PF67|Q3MIW3	Silent	SNP	ENST00000264938.3	37	CCDS3855.1																																																																																			C|1.000;T|0.000	0.000	strong		0.592	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174		T	480029	C	T	480029	2	4	19	1	0	0	0	0	0	0	0	1	14728	639	23	1		1	SLC9A3	5	480029	Silent	SNP	C	TCGA-FF-A7CW-01A-11D-A382-10		480029	180435231	15	2588											
HEATR7B2	133558	hgsc.bcm.edu	37	chr5	41054902	41054902	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacccatgacgattttgacTgttctttctattgaaatgat	10	17	6	8	1	3	4	1	4	2	0	3	5	3	4	1	0	0	1	1	0	2	6			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr5:41054902T>G	ENST00000399564.4	-	11	1524	c.1074A>C	c.(1072-1074)acA>acC	p.T358T	MROH2B_ENST00000506092.2_Intron	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	358																	CGATTTTGACTGTTCTTTCTA	0.368																																					p.T358T		Atlas-SNP	.											.	.	.	.	0			c.A1074C						PASS	.						147	138	141					5																	41054902		1834	4081	5915	SO:0001819	synonymous_variant	133558	exon11			TTTGACTGTTCTT		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.1074A>C	5.37:g.41054902T>G		192	0	0		154	44	0.285714	NM_173489	Q68DM1|Q7Z4U4|Q8N7X3	Silent	SNP	ENST00000399564.4	37	CCDS47202.1																																																																																			.	.	none		0.368	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489		G	41054902	T	G	41054902	2	3	19	1	0	0	0	0	0	0	0	1	7044	1567	55	5		5	HEATR7B2	5	41054902	Silent	SNP	T	TCGA-FF-A7CW-01A-11D-A382-10	40574873	41054902	139860358	16	2589											
HIST1H1E	3008	hgsc.bcm.edu	37	chr6	26157030	26157030	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cagcaggagcggcgaagaagCccaagaaggcgacgggggcg	12	0	19	10	5	0	2	0	0	0	2	0	5	0	3	1	5	3	1	1	5	4	0			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr6:26157030C>T	ENST00000304218.3	+	1	472	c.412C>T	c.(412-414)Ccc>Tcc	p.P138S	HIST1H2BD_ENST00000289316.2_5'Flank|HIST1H2BD_ENST00000377777.4_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	138					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						GGCGAAGAAGCCCAAGAAGGC	0.607																																					p.P138S		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.C412T						PASS	.						13	20	18					6																	26157030		2197	4290	6487	SO:0001583	missense	3008	exon1			AAGAAGCCCAAGA	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.412C>T	6.37:g.26157030C>T	ENSP00000307705:p.Pro138Ser	100	0	0		72	16	0.222222	NM_005321	Q4VB25	Missense_Mutation	SNP	ENST00000304218.3	37	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	3.287	-0.145748	0.06627	.	.	ENSG00000168298	ENST00000304218	T	0.27890	1.64	5.51	2.29	0.28610	.	0.547850	0.18939	N	0.126986	T	0.07863	0.0197	L	0.34521	1.04	0.50039	D	0.999848	B	0.06786	0.001	B	0.04013	0.001	T	0.18524	-1.0334	10	0.11182	T	0.66	-0.7372	10.3673	0.44033	0.0:0.6:0.3296:0.0704	.	138	P10412	H14_HUMAN	S	138	ENSP00000307705:P138S	ENSP00000307705:P138S	P	+	1	0	HIST1H1E	26265009	0.597000	0.26874	0.998000	0.56505	0.708000	0.40852	0.204000	0.17335	0.191000	0.20236	0.561000	0.74099	CCC	.	.	none		0.607	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321		T	26157030	C	T	26157030	3	4	19	1	0	0	0	0	1	0	0	0	7135	739	26	2	414	2	HIST1H1E	6	26157030	Missense_Mutation	SNP	C	TCGA-FF-A7CW-01A-11D-A382-10		26157030	144958037	17	2590											
MUC21	394263	hgsc.bcm.edu	37	chr6	30955191	30955191	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aactctgagtccagcacagtGtccagtggggccagcactgc	9	7	12	13	0	1	1	0	1	1	0	3	1	3	1	3	2	4	2	3	2	1	0	rs56644482		TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr6:30955191G>C	ENST00000376296.3	+	2	1480	c.1239G>C	c.(1237-1239)gtG>gtC	p.V413V	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	413	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						CCAGCACAGTGTCCAGTGGGG	0.627																																					p.V413V		Atlas-SNP	.											MUC21,NS,carcinoma,0,2	MUC21	98	2	0			c.G1239C						scavenged	.						145	140	142					6																	30955191		2203	4300	6503	SO:0001819	synonymous_variant	394263	exon2			CACAGTGTCCAGT	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.1239G>C	6.37:g.30955191G>C		72	0	0		48	3	0.0625	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																			.	.	none		0.627	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909		C	30955191	G	C	30955191	2	2	19	1	0	0	0	0	0	0	0	1	9986	1364	48	4		4	MUC21	6	30955191	Silent	SNP	G	TCGA-FF-A7CW-01A-11D-A382-10	4798161	30955191	140159876	18	2591											
CARD11	84433	hgsc.bcm.edu	37	chr7	2977662	2977662	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggtcctccttctcctccAggtactgtgaaccacacaga	9	9	7	16	0	1	2	0	1	1	1	5	2	4	2	6	2	2	1	6	2	2	2			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr7:2977662A>T	ENST00000396946.4	-	8	1425	c.1022T>A	c.(1021-1023)cTg>cAg	p.L341Q		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	341					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)		CTTCTCCTCCAGGTACTGTGA	0.542			Mis		DLBCL																																p.L341Q		Atlas-SNP	.		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	.	CARD11	339	.	0			c.T1022A						PASS	.						146	128	134					7																	2977662		2203	4300	6503	SO:0001583	missense	84433	exon8			TCCTCCAGGTACT	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.1022T>A	7.37:g.2977662A>T	ENSP00000380150:p.Leu341Gln	76	0	0		62	14	0.225806	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	A	14.15	2.450208	0.43531	.	.	ENSG00000198286	ENST00000396946	T	0.38401	1.14	5.0	5.0	0.66597	.	0.000000	0.64402	D	0.000006	T	0.51415	0.1673	L	0.52905	1.665	0.53005	D	0.99996	D	0.76494	0.999	D	0.75020	0.985	T	0.53662	-0.8407	10	0.72032	D	0.01	-21.9678	9.3257	0.37990	0.8401:0.0:0.0:0.1599	.	341	Q9BXL7	CAR11_HUMAN	Q	341	ENSP00000380150:L341Q	ENSP00000380150:L341Q	L	-	2	0	CARD11	2944188	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.059000	0.76684	1.878000	0.54408	0.482000	0.46254	CTG	.	.	none		0.542	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		T	2977662	A	T	2977662	3	4	19	1	0	0	0	0	1	0	0	0	2647	188	7	5	2514	5	CARD11	7	2977662	Missense_Mutation	SNP	A	TCGA-FF-A7CW-01A-11D-A382-10		2977662	156161001	19	2592											
MAGI2	9863	hgsc.bcm.edu	37	chr7	79082348	79082348	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctctcaccttgcttgacacActtgagccggagggggtcct	6	10	12	13	1	1	2	1	2	1	0	3	3	2	3	3	3	2	2	3	3	0	3			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr7:79082348A>T	ENST00000354212.4	-	1	542	c.289T>A	c.(289-291)Tgt>Agt	p.C97S	MAGI2-AS3_ENST00000424477.1_RNA|MAGI2-AS3_ENST00000451809.1_RNA|MAGI2-AS3_ENST00000429408.1_RNA|MAGI2-AS3_ENST00000422093.1_RNA|MAGI2_ENST00000419488.1_Missense_Mutation_p.C97S|MAGI2-AS3_ENST00000414797.1_RNA|MAGI2-AS3_ENST00000448195.1_RNA|MAGI2-AS3_ENST00000446159.1_RNA|MAGI2_ENST00000522391.1_Missense_Mutation_p.C97S|MAGI2-AS3_ENST00000426835.1_RNA	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	97	PDZ 1. {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)				TGCTTGACACACTTGAGCCGG	0.647																																					p.C97S		Atlas-SNP	.											.	MAGI2	246	.	0			c.T289A						PASS	.						45	48	47					7																	79082348		2203	4300	6503	SO:0001583	missense	9863	exon1			TGACACACTTGAG	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.289T>A	7.37:g.79082348A>T	ENSP00000346151:p.Cys97Ser	30	0	0		27	12	0.444444	NM_012301	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Missense_Mutation	SNP	ENST00000354212.4	37	CCDS5594.1	.	.	.	.	.	.	.	.	.	.	A	18.90	3.720746	0.68959	.	.	ENSG00000187391	ENST00000419488;ENST00000354212;ENST00000536298;ENST00000522391	T;T;T	0.10005	3.03;3.03;2.92	5.39	5.39	0.77823	PDZ/DHR/GLGF (3);	.	.	.	.	T	0.15435	0.0372	L	0.50919	1.6	0.80722	D	1	P;P	0.49358	0.923;0.454	P;B	0.48454	0.578;0.192	T	0.01739	-1.1284	9	0.35671	T	0.21	.	10.6966	0.45903	0.8401:0.1599:0.0:0.0	.	97;97	Q86UL8-2;Q86UL8	.;MAGI2_HUMAN	S	97	ENSP00000405766:C97S;ENSP00000346151:C97S;ENSP00000428389:C97S	ENSP00000346151:C97S	C	-	1	0	MAGI2	78920284	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.133000	0.77259	2.033000	0.60031	0.402000	0.26972	TGT	.	.	none		0.647	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		T	79082348	A	T	79082348	3	4	19	1	0	0	0	0	1	0	0	0	9200	159	6	5	4166	5	MAGI2	7	79082348	Missense_Mutation	SNP	A	TCGA-FF-A7CW-01A-11D-A382-10	76104686	79082348	80056315	20	2593											
CLCN1	1180	hgsc.bcm.edu	37	chr7	143049009	143049009	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggccgacatcttgcagggccCcagcctgcgatccacagacg	8	5	12	16	3	1	1	0	0	1	1	2	3	2	1	5	2	3	1	5	2	0	1			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr7:143049009C>T	ENST00000343257.2	+	23	3005	c.2918C>T	c.(2917-2919)cCc>cTc	p.P973L		NM_000083.2	NP_000074	P35523	CLCN1_HUMAN	chloride channel, voltage-sensitive 1	973					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)					TTGCAGGGCCCCAGCCTGCGA	0.632																																					p.P973L		Atlas-SNP	.											.	CLCN1	141	.	0			c.C2918T						PASS	.						76	77	77					7																	143049009		2203	4300	6503	SO:0001583	missense	1180	exon23			AGGGCCCCAGCCT	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.2918C>T	7.37:g.143049009C>T	ENSP00000339867:p.Pro973Leu	114	0	0		102	16	0.156863	NM_000083	A4D2H5|Q2M202	Missense_Mutation	SNP	ENST00000343257.2	37	CCDS5881.1	.	.	.	.	.	.	.	.	.	.	C	17.45	3.392032	0.62066	.	.	ENSG00000188037	ENST00000343257	D	0.85088	-1.94	4.49	4.49	0.54785	.	0.191462	0.34002	N	0.004352	D	0.89008	0.6593	M	0.62723	1.935	0.43065	D	0.994695	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	D	0.88115	0.2828	10	0.46703	T	0.11	.	7.2092	0.25925	0.0:0.8406:0.0:0.1594	.	172;973	Q75L28;P35523	.;CLCN1_HUMAN	L	973	ENSP00000339867:P973L	ENSP00000339867:P973L	P	+	2	0	CLCN1	142759131	0.998000	0.40836	1.000000	0.80357	0.974000	0.67602	2.063000	0.41423	2.202000	0.70862	0.561000	0.74099	CCC	.	.	none		0.632	CLCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327420.1	NM_000083		T	143049009	C	T	143049009	3	4	19	1	0	0	0	0	1	0	0	0	3464	623	22	2	3008	2	CLCN1	7	143049009	Missense_Mutation	SNP	C	TCGA-FF-A7CW-01A-11D-A382-10	63966661	143049009	16089654	21	2594											
OR2F2	135948	hgsc.bcm.edu	37	chr7	143633276	143633276	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttaacatccaagctgggaacTtgactcatgaacattacttt	13	13	6	9	0	1	2	1	2	0	0	2	3	2	3	1	1	5	1	1	1	5	4			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr7:143633276T>C	ENST00000408955.2	+	1	1018	c.951T>C	c.(949-951)acT>acC	p.T317T		NM_001004685.1	NP_001004685.1	O95006	OR2F2_HUMAN	olfactory receptor, family 2, subfamily F, 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(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)					AGCTGGGAACTTGACTCATGA	0.433																																					p.T317T		Atlas-SNP	.											.	OR2F2	63	.	0			c.T951C						PASS	.						32	31	31					7																	143633276		1968	4195	6163	SO:0001819	synonymous_variant	135948	exon1			GGGAACTTGACTC		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.951T>C	7.37:g.143633276T>C		40	0	0		56	4	0.0714286	NM_001004685	A4D2G0|Q6IFP8	Silent	SNP	ENST00000408955.2	37	CCDS43666.1																																																																																			.	.	none		0.433	OR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349570.1			C	143633276	T	C	143633276	2	2	19	1	0	0	0	0	0	0	0	1	11006	1596	56	3		3	OR2F2	7	143633276	Silent	SNP	T	TCGA-FF-A7CW-01A-11D-A382-10	584267	143633276	15505387	22	2595											
COL14A1	7373	hgsc.bcm.edu	37	chr8	121282320	121282320	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtatttatggtggatggatcCtggagcattggagatgaaaa	12	12	14	3	0	0	2	0	1	0	1	1	6	1	5	1	5	1	2	1	5	4	4			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr8:121282320C>A	ENST00000297848.3	+	26	3390	c.3120C>A	c.(3118-3120)tcC>tcA	p.S1040S	COL14A1_ENST00000247781.3_Silent_p.S945S|COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000309791.4_Silent_p.S1040S	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)			TGGATGGATCCTGGAGCATTG	0.428																																					p.S1040S		Atlas-SNP	.											COL14A1,NS,carcinoma,+1,1	COL14A1	292	1	0			c.C3120A						PASS	.						135	123	127					8																	121282320		2203	4299	6502	SO:0001819	synonymous_variant	7373	exon26			TGGATCCTGGAGC		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.3120C>A	8.37:g.121282320C>A		84	0	0		65	16	0.246154	NM_021110		Silent	SNP	ENST00000297848.3	37	CCDS34938.1																																																																																			.	.	none		0.428	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		A	121282320	C	A	121282320	2	1	19	1	0	0	0	0	0	0	0	1	3673	668	24	4		4	COL14A1	8	121282320	Silent	SNP	C	TCGA-FF-A7CW-01A-11D-A382-10		121282320	25081702	23	2596											
ABCA1	19	hgsc.bcm.edu	37	chr9	107571802	107571802	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagggtctttggtgagggCgtttaagagttccagggttc	6	12	16	7	1	1	2	0	1	1	1	3	2	2	2	2	4	0	3	2	4	1	5	rs189206655		TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr9:107571802C>T	ENST00000374736.3	-	30	4613	c.4219G>A	c.(4219-4221)Gcc>Acc	p.A1407T		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	1407			A -> T (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		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)	p.A1407T(1)		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)	TTGGTGAGGGCGTTTAAGAGT	0.517													C|||	1	0.000199681	0.0	0.0014	5008	,	,		14853	0.0		0.0	False		,,,				2504	0.0				p.A1407T		Atlas-SNP	.											ABCA1,caecum,carcinoma,0,4	ABCA1	244	4	1	Substitution - Missense(1)	large_intestine(1)	c.G4219A						scavenged	.						110	106	107					9																	107571802		2203	4300	6503	SO:0001583	missense	19	exon30			TGAGGGCGTTTAA	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.4219G>A	9.37:g.107571802C>T	ENSP00000363868:p.Ala1407Thr	169	1	0.00591716		136	22	0.161765	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Missense_Mutation	SNP	ENST00000374736.3	37	CCDS6762.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	18.47	3.630940	0.67015	.	.	ENSG00000165029	ENST00000374736	D	0.95949	-3.86	5.68	5.68	0.88126	.	0.046614	0.85682	D	0.000000	D	0.93979	0.8072	L	0.49699	1.58	0.80722	D	1	B	0.24186	0.099	B	0.30716	0.119	D	0.90832	0.4717	10	0.18276	T	0.48	.	19.8476	0.96716	0.0:1.0:0.0:0.0	.	1407	O95477	ABCA1_HUMAN	T	1407	ENSP00000363868:A1407T	ENSP00000363868:A1407T	A	-	1	0	ABCA1	106611623	0.995000	0.38212	0.947000	0.38551	0.336000	0.28762	3.225000	0.51246	2.704000	0.92352	0.650000	0.86243	GCC	C|1.000;T|0.000	0.000	strong		0.517	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		T	107571802	C	T	107571802	3	4	19	1	0	0	0	0	1	0	0	0	28	768	27	1	2650	1	ABCA1	9	107571802	Missense_Mutation	SNP	C	TCGA-FF-A7CW-01A-11D-A382-10		107571802	33641629	24	2597											
PTCHD3	374308	hgsc.bcm.edu	37	chr10	27703150	27703150	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgggcttctgctccggcccCggcctgggcttgggctccac	1	10	14	16	2	1	0	0	0	1	0	3	0	3	0	5	5	1	4	5	5	0	3	rs369428695		TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr10:27703150C>T	ENST00000438700.3	-	1	147	c.30G>A	c.(28-30)ccG>ccA	p.P10P		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	10					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						GCTCCGGCCCCGGCCTGGGCT	0.622																																					p.P10P		Atlas-SNP	.											.	PTCHD3	140	.	0			c.G30A						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	42	51	48		30	-0.9	0	10		48	0,8598		0,0,4299	no	coding-synonymous	PTCHD3	NM_001034842.3		0,1,6501	TT,TC,CC		0.0,0.0227,0.0077		10/768	27703150	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	374308	exon1			CGGCCCCGGCCTG	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.30G>A	10.37:g.27703150C>T		87	0	0		55	18	0.327273	NM_001034842	I3L499|Q6ZU28	Silent	SNP	ENST00000438700.3	37	CCDS31173.1																																																																																			.	.	none		0.622	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541		T	27703150	C	T	27703150	2	4	19	1	0	0	0	0	0	0	0	1	12746	639	23	1		1	PTCHD3	10	27703150	Silent	SNP	C	TCGA-FF-A7CW-01A-11D-A382-10		27703150	107831597	25	2598											
MPP7	143098	hgsc.bcm.edu	37	chr10	28420542	28420542	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttttactgagtcttcctcatCgtcaatatcttcaggcatag	9	16	6	10	1	5	1	3	1	2	0	7	1	6	1	1	1	1	1	1	1	4	6			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr10:28420542C>T	ENST00000375732.1	-	6	653	c.394G>A	c.(394-396)Gat>Aat	p.D132N	MPP7_ENST00000337532.5_Missense_Mutation_p.D132N|MPP7_ENST00000375719.3_Missense_Mutation_p.D132N|MPP7_ENST00000540098.1_Missense_Mutation_p.D132N|MPP7_ENST00000481244.1_5'UTR|MPP7_ENST00000445954.2_Missense_Mutation_p.D7N			Q5T2T1	MPP7_HUMAN	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	132					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						TCTTCCTCATCGTCAATATCT	0.413																																					p.D132N		Atlas-SNP	.											.	MPP7	60	.	0			c.G394A						PASS	.						132	119	123					10																	28420542		2203	4300	6503	SO:0001583	missense	143098	exon8			CCTCATCGTCAAT	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.394G>A	10.37:g.28420542C>T	ENSP00000364884:p.Asp132Asn	85	0	0		97	24	0.247423	NM_173496	B2RCC9|B4DWL9|B5MDZ3|D3DRW3|Q5T2T0|Q8IY28	Missense_Mutation	SNP	ENST00000375732.1	37	CCDS7158.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.939983	0.73557	.	.	ENSG00000150054	ENST00000375732;ENST00000337532;ENST00000540098;ENST00000375719;ENST00000445954	T;T;T;T;T	0.23147	2.72;2.72;2.72;2.72;1.92	5.74	4.84	0.62591	PDZ/DHR/GLGF (1);	0.221823	0.52532	N	0.000062	T	0.22513	0.0543	L	0.39633	1.23	0.80722	D	1	B	0.23854	0.092	B	0.18871	0.023	T	0.02404	-1.1164	10	0.33141	T	0.24	.	14.4397	0.67306	0.0:0.9287:0.0:0.0713	.	132	Q5T2T1	MPP7_HUMAN	N	132;132;132;132;7	ENSP00000364884:D132N;ENSP00000337907:D132N;ENSP00000438693:D132N;ENSP00000364871:D132N;ENSP00000405397:D7N	ENSP00000337907:D132N	D	-	1	0	MPP7	28460548	1.000000	0.71417	0.883000	0.34634	0.991000	0.79684	4.814000	0.62627	1.442000	0.47568	0.561000	0.74099	GAT	.	.	none		0.413	MPP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047345.1	NM_173496		T	28420542	C	T	28420542	3	4	19	1	0	0	0	0	1	0	0	0	9748	884	31	1	1384	1	MPP7	10	28420542	Missense_Mutation	SNP	C	TCGA-FF-A7CW-01A-11D-A382-10	717392	28420542	107114205	26	2599											
PRKG1	5592	hgsc.bcm.edu	37	chr10	54048530	54048530	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatgaaaacctataacatcaTattgagggggattgacatga	16	11	9	5	0	1	4	1	4	0	0	1	5	1	5	1	2	2	0	1	2	6	6			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr10:54048530T>C	ENST00000401604.2	+	15	1903	c.1709T>C	c.(1708-1710)aTa>aCa	p.I570T	PRKG1_ENST00000373975.2_Missense_Mutation_p.I288T|PRKG1-AS1_ENST00000426785.2_RNA|PRKG1-AS1_ENST00000452247.2_RNA|PRKG1_ENST00000373980.4_Missense_Mutation_p.I585T|PRKG1_ENST00000373985.1_Missense_Mutation_p.I558T			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	570	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)		TATAACATCATATTGAGGGGG	0.348																																					p.I585T		Atlas-SNP	.											.	PRKG1	167	.	0			c.T1754C						PASS	.						100	103	102					10																	54048530		2203	4300	6503	SO:0001583	missense	5592	exon15			ACATCATATTGAG		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.1709T>C	10.37:g.54048530T>C	ENSP00000384200:p.Ile570Thr	167	0	0		136	33	0.242647	NM_006258	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Missense_Mutation	SNP	ENST00000401604.2	37	CCDS44399.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.377284	0.82682	.	.	ENSG00000185532	ENST00000401604;ENST00000373985;ENST00000373980;ENST00000332193;ENST00000373975	T;T;T	0.11821	2.74;2.74;2.74	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	0.36963	0.0986	M	0.85299	2.745	0.80722	D	1	P;D;D	0.56521	0.806;0.97;0.976	P;P;P	0.57283	0.702;0.721;0.817	T	0.37572	-0.9700	10	0.66056	D	0.02	-16.6233	14.8289	0.70132	0.0:0.0:0.0:1.0	.	288;585;570	B3KSF3;Q13976-2;Q13976	.;.;KGP1_HUMAN	T	570;558;585;288;182	ENSP00000384200:I570T;ENSP00000363097:I558T;ENSP00000363092:I585T	ENSP00000327642:I288T	I	+	2	0	PRKG1	53718536	1.000000	0.71417	0.999000	0.59377	0.957000	0.61999	8.040000	0.89188	1.978000	0.57642	0.533000	0.62120	ATA	.	.	none		0.348	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	54048530	T	C	54048530	3	2	19	1	0	0	0	0	1	0	0	0	12534	1406	49	3	2082	3	PRKG1	10	54048530	Missense_Mutation	SNP	T	TCGA-FF-A7CW-01A-11D-A382-10	25627988	54048530	81486217	27	2600											
TLL2	7093	hgsc.bcm.edu	37	chr10	98157024	98157024	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagccggctgtccgtggagaCgaggggctccgggatcttat	6	8	17	10	4	1	1	0	0	1	1	3	5	3	2	3	5	1	2	3	5	1	1			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr10:98157024C>T	ENST00000357947.3	-	11	1528	c.1303G>A	c.(1303-1305)Gtc>Atc	p.V435I	TLL2_ENST00000469598.1_5'UTR	NM_012465.3	NP_036597.1	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	435	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)		TCCGTGGAGACGAGGGGCTCC	0.577																																					p.V435I		Atlas-SNP	.											.	TLL2	122	.	0			c.G1303A						PASS	.						58	52	54					10																	98157024		2203	4300	6503	SO:0001583	missense	7093	exon11			TGGAGACGAGGGG	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.1303G>A	10.37:g.98157024C>T	ENSP00000350630:p.Val435Ile	62	0	0		46	14	0.304348	NM_012465	A6NDK0|Q2M1H1|Q6PJN5|Q9UQ00	Missense_Mutation	SNP	ENST00000357947.3	37	CCDS7449.1	.	.	.	.	.	.	.	.	.	.	C	0.647	-0.810936	0.02798	.	.	ENSG00000095587	ENST00000357947	T	0.34472	1.36	5.11	-8.58	0.00897	CUB (5);	1.421770	0.05282	N	0.519613	T	0.12774	0.0310	N	0.13168	0.305	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.25813	-1.0121	10	0.02654	T	1	.	2.9319	0.05802	0.0942:0.1609:0.3118:0.433	.	435	Q9Y6L7	TLL2_HUMAN	I	435	ENSP00000350630:V435I	ENSP00000350630:V435I	V	-	1	0	TLL2	98147014	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.251000	0.08818	-1.951000	0.01029	-1.275000	0.01399	GTC	.	.	none		0.577	TLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049608.1			T	98157024	C	T	98157024	3	4	19	1	0	0	0	0	1	0	0	0	15961	536	19	1	1788	1	TLL2	10	98157024	Missense_Mutation	SNP	C	TCGA-FF-A7CW-01A-11D-A382-10	44108494	98157024	37377723	28	2601											
C11orf84	144097	hgsc.bcm.edu	37	chr11	63585573	63585573	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtggccctcttgcaagacGtgagagctgagcagccgtcc	7	7	15	12	2	1	3	0	2	1	2	2	4	2	3	3	2	4	3	3	2	1	1	rs373118347		TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr11:63585573G>A	ENST00000294244.4	+	2	723	c.424G>A	c.(424-426)Gtg>Atg	p.V142M		NM_138471.1	NP_612480.1	Q9BUA3	CK084_HUMAN	chromosome 11 open reading frame 84	142										endometrium(3)|kidney(1)|lung(3)|skin(1)	8						CTTGCAAGACGTGAGAGCTGA	0.587																																					p.V142M		Atlas-SNP	.											.	C11orf84	33	.	0			c.G424A						PASS	.	G	MET/VAL	3,4399	6.2+/-15.9	0,3,2198	69	72	71		424	-6.3	0	11		71	0,8596		0,0,4298	no	missense	C11orf84	NM_138471.1	21	0,3,6496	AA,AG,GG		0.0,0.0682,0.0231	benign	142/382	63585573	3,12995	2201	4298	6499	SO:0001583	missense	144097	exon2			CAAGACGTGAGAG	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.424G>A	11.37:g.63585573G>A	ENSP00000294244:p.Val142Met	55	0	0		43	11	0.255814	NM_138471	Q68CV7|Q6PHS2|Q96IH0	Missense_Mutation	SNP	ENST00000294244.4	37	CCDS31594.1	.	.	.	.	.	.	.	.	.	.	G	13.23	2.175663	0.38413	6.82E-4	0.0	ENSG00000168005	ENST00000294244	T	0.47177	0.85	5.38	-6.3	0.02007	.	1.609270	0.03598	N	0.232943	T	0.18173	0.0436	N	0.08118	0	0.09310	N	1	P	0.46656	0.882	B	0.33690	0.168	T	0.30268	-0.9984	10	0.87932	D	0	-6.9248	1.2292	0.01940	0.4312:0.105:0.1743:0.2896	.	142	Q9BUA3	CK084_HUMAN	M	142	ENSP00000294244:V142M	ENSP00000294244:V142M	V	+	1	0	C11orf84	63342149	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-1.225000	0.02956	-0.942000	0.03695	-0.254000	0.11334	GTG	.	.	weak		0.587	C11orf84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396084.1	NM_138471		A	63585573	G	A	63585573	3	1	19	1	0	0	0	0	1	0	0	0	1669	1145	40	1	430	1	C11orf84	11	63585573	Missense_Mutation	SNP	G	TCGA-FF-A7CW-01A-11D-A382-10		63585573	71420943	29	2602											
MLL2	8085	hgsc.bcm.edu	37	chr12	49435033	49435033	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccagtccaaaggggtcctGcgaaggcacttgggcgggca	8	5	17	11	2	0	0	0	0	0	0	2	1	2	0	3	6	1	2	3	6	2	1			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr12:49435033G>A	ENST00000301067.7	-	31	6519	c.6520C>T	c.(6520-6522)Cag>Tag	p.Q2174*		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2174	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)	p.Q2174*(1)|p.Q1904*(1)									AAGGGGTCCTGCGAAGGCACT	0.706																																					p.Q2174X		Atlas-SNP	.											MLL2_ENST00000301067,NS,lymphoid_neoplasm,0,2	MLL2	1173	2	2	Substitution - Nonsense(2)	haematopoietic_and_lymphoid_tissue(2)	c.C6520T						PASS	.						6	9	8					12																	49435033		1816	3965	5781	SO:0001587	stop_gained	8085	exon31			GGTCCTGCGAAGG	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.6520C>T	12.37:g.49435033G>A	ENSP00000301067:p.Gln2174*	42	0	0		29	10	0.344828	NM_003482	O14687	Nonsense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	45	11.616333	0.99583	.	.	ENSG00000167548	ENST00000301067	.	.	.	4.09	4.09	0.47781	.	0.000000	0.31381	N	0.007760	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	15.9318	0.79668	0.0:0.0:1.0:0.0	.	.	.	.	X	2174	.	ENSP00000301067:Q2174X	Q	-	1	0	MLL2	47721300	0.995000	0.38212	1.000000	0.80357	0.891000	0.51852	2.306000	0.43673	2.210000	0.71456	0.561000	0.74099	CAG	.	.	none		0.706	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49435033	G	A	49435033	4	1	19	1	0	0	0	0	0	1	0	0	9630	1328	46	2	10189	2	MLL2	12	49435033	Nonsense_Mutation	SNP	G	TCGA-FF-A7CW-01A-11D-A382-10		49435033	84416862	30	2603											
BRAP	8315	hgsc.bcm.edu	37	chr12	112103531	112103531	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	attcacagactcgtccatgcGctccagacacaccgtgcact	10	8	7	16	3	1	2	1	0	0	2	4	2	3	2	3	0	2	2	3	0	0	1			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr12:112103531G>A	ENST00000327551.6	-	6	858	c.718C>T	c.(718-720)Cgc>Tgc	p.R240C	BRAP_ENST00000419234.4_Missense_Mutation_p.R270C|BRAP_ENST00000539060.1_Missense_Mutation_p.R91C			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						TCGTCCATGCGCTCCAGACAC	0.557																																					p.R270C	Pancreas(146;846 1904 7830 25130 26065)	Atlas-SNP	.											.	BRAP	42	.	0			c.C808T						PASS	.						161	105	124					12																	112103531		2203	4300	6503	SO:0001583	missense	8315	exon6			CCATGCGCTCCAG	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.718C>T	12.37:g.112103531G>A	ENSP00000330813:p.Arg240Cys	113	0	0		78	17	0.217949	NM_006768	B4DTT1|F4NAR0|F4NAR1|Q6ZMG5|Q7Z356|Q8IZ35	Missense_Mutation	SNP	ENST00000327551.6	37		.	.	.	.	.	.	.	.	.	.	G	19.21	3.783685	0.70222	.	.	ENSG00000089234	ENST00000419234;ENST00000539060;ENST00000327551;ENST00000547043	T;T;T	0.43294	0.95;0.95;0.95	5.22	4.25	0.50352	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	0.53190	0.1781	L	0.35593	1.075	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.993;0.997	T	0.57493	-0.7802	10	0.87932	D	0	-12.2466	14.8944	0.70633	0.0:0.0:0.8067:0.1933	.	91;270	B4DRM1;Q7Z569	.;BRAP_HUMAN	C	270;91;240;52	ENSP00000403524:R270C;ENSP00000441659:R91C;ENSP00000330813:R240C	ENSP00000330813:R240C	R	-	1	0	BRAP	110587914	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	3.515000	0.53429	2.431000	0.82371	0.305000	0.20034	CGC	.	.	none		0.557	BRAP-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404994.2			A	112103531	G	A	112103531	3	1	19	1	0	0	0	0	1	0	0	0	1499	1087	38	1	998	1	BRAP	12	112103531	Missense_Mutation	SNP	G	TCGA-FF-A7CW-01A-11D-A382-10	62668498	112103531	21748364	31	2604											
MLXIP	22877	hgsc.bcm.edu	37	chr12	122612486	122612486	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgacacccctggacggctctGtggacgtagacgagcaccgc	8	6	13	14	4	1	2	0	1	1	1	1	5	1	4	3	3	1	3	3	3	1	1			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr12:122612486G>T	ENST00000319080.7	+	3	709	c.577G>T	c.(577-579)Gtg>Ttg	p.V193L						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)		GGACGGCTCTGTGGACGTAGA	0.607																																					p.V193L	Esophageal Squamous(105;787 1493 16200 18566 52466)	Atlas-SNP	.											.	MLXIP	46	.	0			c.G577T						PASS	.						113	120	118					12																	122612486		2014	4189	6203	SO:0001583	missense	22877	exon3			GGCTCTGTGGACG	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.577G>T	12.37:g.122612486G>T	ENSP00000312834:p.Val193Leu	57	0	0		41	13	0.317073	NM_014938		Missense_Mutation	SNP	ENST00000319080.7	37		.	.	.	.	.	.	.	.	.	.	G	22.8	4.334205	0.81801	.	.	ENSG00000175727	ENST00000319080	T	0.14766	2.48	5.53	5.53	0.82687	.	0.068042	0.64402	D	0.000013	T	0.27524	0.0676	.	.	.	0.80722	D	1	P	0.49961	0.93	P	0.49887	0.625	T	0.00697	-1.1605	9	0.59425	D	0.04	-19.7812	19.4566	0.94895	0.0:0.0:1.0:0.0	.	193	Q9HAP2	MLXIP_HUMAN	L	193	ENSP00000312834:V193L	ENSP00000312834:V193L	V	+	1	0	MLXIP	121178440	0.989000	0.36119	0.990000	0.47175	0.674000	0.39518	1.896000	0.39789	2.590000	0.87494	0.655000	0.94253	GTG	.	.	none		0.607	MLXIP-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401718.2	NM_014938		T	122612486	G	T	122612486	3	4	19	1	0	0	0	0	1	0	0	0	9645	1377	48	4	587	4	MLXIP	12	122612486	Missense_Mutation	SNP	G	TCGA-FF-A7CW-01A-11D-A382-10	10508955	122612486	11239409	32	2605											
CSK	1445	hgsc.bcm.edu	37	chr15	75093927	75093927	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggcggagactgtctcctcaAgttctcgctgtgagtgaagc	7	10	14	10	2	3	3	1	2	2	1	5	4	3	3	1	2	1	2	1	2	2	1			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr15:75093927A>G	ENST00000220003.9	+	10	1607	c.878A>G	c.(877-879)aAg>aGg	p.K293R	CSK_ENST00000439220.2_Missense_Mutation_p.K293R|CSK_ENST00000309470.9_Missense_Mutation_p.K293R|CSK_ENST00000567571.1_Missense_Mutation_p.K293R	NM_004383.2	NP_004374.1	P41240	CSK_HUMAN	c-src tyrosine kinase	293	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adherens junction organization (GO:0034332)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cellular response to peptide hormone stimulus (GO:0071375)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of bone resorption (GO:0045779)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of kinase activity (GO:0033673)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of phagocytosis (GO:0050765)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|positive regulation of MAP kinase activity (GO:0043406)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060368)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein C-terminus binding (GO:0008022)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|lung(2)	3						TGTCTCCTCAAGTTCTCGCTG	0.627																																					p.K293R		Atlas-SNP	.											.	CSK	43	.	0			c.A878G						PASS	.						106	86	93					15																	75093927		2197	4296	6493	SO:0001583	missense	1445	exon11			TCCTCAAGTTCTC		CCDS10269.1	15q24.1	2013-02-14			ENSG00000103653	ENSG00000103653	2.7.10.1	"SH2 domain containing"	2444	protein-coding gene	gene with protein product		124095				1377109	Standard	NM_004383		Approved		uc010bka.3	P41240	OTTHUMG00000142814	ENST00000220003.9:c.878A>G	15.37:g.75093927A>G	ENSP00000220003:p.Lys293Arg	71	0	0		69	8	0.115942	NM_001127190	Q2M3N2|Q6FGZ6	Missense_Mutation	SNP	ENST00000220003.9	37	CCDS10269.1	.	.	.	.	.	.	.	.	.	.	a	13.88	2.368850	0.42003	.	.	ENSG00000103653	ENST00000220003;ENST00000439220;ENST00000451345;ENST00000309470	D;D;D	0.82984	-1.67;-1.67;-1.67	5.27	5.27	0.74061	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.207772	0.48767	D	0.000163	T	0.64193	0.2576	N	0.02111	-0.68	0.42521	D	0.993006	B	0.33280	0.405	B	0.32928	0.155	T	0.72228	-0.4354	10	0.87932	D	0	-24.1195	14.1618	0.65452	1.0:0.0:0.0:0.0	.	293	P41240	CSK_HUMAN	R	293;293;242;293	ENSP00000220003:K293R;ENSP00000414764:K293R;ENSP00000438808:K293R	ENSP00000220003:K293R	K	+	2	0	CSK	72880980	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.845000	0.69437	1.990000	0.58119	0.529000	0.55759	AAG	.	.	none		0.627	CSK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286398.2	NM_004383		G	75093927	A	G	75093927	3	3	19	1	0	0	0	0	1	0	0	0	3945	72	3	3	912	3	CSK	15	75093927	Missense_Mutation	SNP	A	TCGA-FF-A7CW-01A-11D-A382-10		75093927	27437465	33	2606											
MESP2	145873	hgsc.bcm.edu	37	chr15	90320144	90320144	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcaggggcaagggcaggggCaggggcaggggcaagggcag	9	0	25	7	0	0	0	0	0	0	0	0	0	0	0	0	11	0	7	0	11	2	0	rs56192595|rs200021459|rs199821487	byFrequency	TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr15:90320144C>G	ENST00000341735.3	+	1	556	c.556C>G	c.(556-558)Cag>Gag	p.Q186E	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	186	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)			agggcaggggcaggggcaggg	0.786																																					p.Q186E		Atlas-SNP	.											.	MESP2	20	.	1	Deletion - In frame(1)	upper_aerodigestive_tract(1)	c.C556G						PASS	.						2	2	2					15																	90320144		1033	2283	3316	SO:0001583	missense	145873	exon1			CAGGGGCAGGGGC		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.556C>G	15.37:g.90320144C>G	ENSP00000342392:p.Gln186Glu	9	0	0		18	6	0.333333	NM_001039958	Q7RTU2	Missense_Mutation	SNP	ENST00000341735.3	37	CCDS42078.1	.	.	.	.	.	.	.	.	.	.	-	2.714	-0.268135	0.05716	.	.	ENSG00000188095	ENST00000341735	T	0.81163	-1.46	1.25	0.212	0.15240	.	.	.	.	.	T	0.56963	0.2021	N	0.08118	0	0.09310	N	1	B	0.17852	0.024	B	0.21360	0.034	T	0.41680	-0.9495	9	0.14252	T	0.57	.	5.4957	0.16802	0.0:0.5895:0.4105:0.0	.	186	Q0VG99	MESP2_HUMAN	E	186	ENSP00000342392:Q186E	ENSP00000342392:Q186E	Q	+	1	0	MESP2	88121148	0.038000	0.19896	0.001000	0.08648	0.006000	0.05464	0.044000	0.13992	0.112000	0.17975	0.297000	0.19635	CAG	.	.	none		0.786	MESP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416421.1	XM_085261		G	90320144	C	G	90320144	3	3	19	1	0	0	0	0	1	0	0	0	9492	711	25	4	558	4	MESP2	15	90320144	Missense_Mutation	SNP	C	TCGA-FF-A7CW-01A-11D-A382-10	15226217	90320144	12211248	34	2607											
ZC3H7A	29066	hgsc.bcm.edu	37	chr16	11855353	11855353	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acatcactctcatcgcacgcCggtctttggtccacctaaga	9	10	7	15	3	3	1	2	0	2	1	6	1	4	1	3	2	0	1	3	2	1	2			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr16:11855353C>T	ENST00000396516.2	-	18	2425	c.2228G>A	c.(2227-2229)cGg>cAg	p.R743Q	ZC3H7A_ENST00000355758.4_Missense_Mutation_p.R743Q|ZC3H7A_ENST00000575984.1_5'Flank			Q8IWR0	Z3H7A_HUMAN	zinc finger CCCH-type containing 7A	743						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						CATCGCACGCCGGTCTTTGGT	0.428																																					p.R743Q		Atlas-SNP	.											ZC3H7A,NS,carcinoma,-1,1	ZC3H7A	72	1	0			c.G2228A						PASS	.						124	121	122					16																	11855353		2197	4300	6497	SO:0001583	missense	29066	exon19			GCACGCCGGTCTT	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.2228G>A	16.37:g.11855353C>T	ENSP00000379773:p.Arg743Gln	113	0	0		106	40	0.377358	NM_014153	D3DUG5|Q9NPE9	Missense_Mutation	SNP	ENST00000396516.2	37	CCDS10550.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.235201	0.79800	.	.	ENSG00000122299	ENST00000355758;ENST00000396516	T;T	0.11385	2.78;2.78	5.66	5.66	0.87406	.	0.149940	0.56097	D	0.000027	T	0.16428	0.0395	L	0.61218	1.895	0.80722	D	1	P;P	0.48764	0.89;0.915	P;P	0.45276	0.454;0.475	T	0.00275	-1.1856	10	0.56958	D	0.05	.	12.1063	0.53813	0.0:0.9222:0.0:0.0778	.	464;743	Q9NXC8;Q8IWR0	.;Z3H7A_HUMAN	Q	743	ENSP00000347999:R743Q;ENSP00000379773:R743Q	ENSP00000347999:R743Q	R	-	2	0	ZC3H7A	11762854	0.996000	0.38824	0.911000	0.35937	0.989000	0.77384	3.366000	0.52343	2.665000	0.90641	0.563000	0.77884	CGG	.	.	none		0.428	ZC3H7A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437066.1	NM_014153		T	11855353	C	T	11855353	3	4	19	1	0	0	0	0	1	0	0	0	17587	652	23	1	707	1	ZC3H7A	16	11855353	Missense_Mutation	SNP	C	TCGA-FF-A7CW-01A-11D-A382-10		11855353	78499400	35	2608											
GLP2R	9340	hgsc.bcm.edu	37	chr17	9745901	9745901	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atatttggcaggatgactccGaatgctccgagaaccacagc	12	8	10	11	2	0	2	0	1	0	1	2	5	2	3	3	2	3	2	3	2	3	2			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr17:9745901G>A	ENST00000262441.5	+	4	985	c.472G>A	c.(472-474)Gaa>Aaa	p.E158K	GLP2R_ENST00000574745.1_5'UTR	NM_004246.1	NP_004237.1	O95838	GLP2R_HUMAN	glucagon-like peptide 2 receptor	158					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)	p.E158K(1)		endometrium(4)|large_intestine(7)|lung(22)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	44					Glucagon recombinant(DB00040)|Teduglutide(DB08900)	GGATGACTCCGAATGCTCCGA	0.547																																					p.E158K		Atlas-SNP	.											GLP2R,rectum,carcinoma,0,1	GLP2R	90	1	1	Substitution - Missense(1)	large_intestine(1)	c.G472A						PASS	.						130	104	113					17																	9745901		2203	4300	6503	SO:0001583	missense	9340	exon4			GACTCCGAATGCT	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.472G>A	17.37:g.9745901G>A	ENSP00000262441:p.Glu158Lys	50	0	0		33	7	0.212121	NM_004246	Q4VAT3	Missense_Mutation	SNP	ENST00000262441.5	37	CCDS11150.1	.	.	.	.	.	.	.	.	.	.	G	35	5.538263	0.96460	.	.	ENSG00000065325	ENST00000396206;ENST00000304773;ENST00000262441	T	0.37915	1.17	5.06	5.06	0.68205	GPCR, family 2, extracellular hormone receptor domain (1);	0.000000	0.39341	N	0.001387	T	0.54711	0.1875	M	0.74258	2.255	0.53688	D	0.999978	P	0.50156	0.932	P	0.54026	0.74	T	0.59621	-0.7420	10	0.72032	D	0.01	.	17.3704	0.87376	0.0:0.0:1.0:0.0	.	158	O95838	GLP2R_HUMAN	K	158;133;158	ENSP00000262441:E158K	ENSP00000262441:E158K	E	+	1	0	GLP2R	9686626	1.000000	0.71417	0.997000	0.53966	0.995000	0.86356	6.102000	0.71486	2.643000	0.89663	0.655000	0.94253	GAA	.	.	none		0.547	GLP2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252601.4			A	9745901	G	A	9745901	3	1	19	1	0	0	0	0	1	0	0	0	6461	1059	37	1	486	1	GLP2R	17	9745901	Missense_Mutation	SNP	G	TCGA-FF-A7CW-01A-11D-A382-10		9745901	71449309	36	2609											
COLEC12	81035	hgsc.bcm.edu	37	chr18	333015	333015	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tggcaggcatacctgttcctCtctagtgtttatgaaaacaa	11	13	8	9	0	1	1	0	1	1	0	3	1	2	1	2	2	2	4	2	2	6	5			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr18:333015C>T	ENST00000400256.3	-	7	2152	c.1945G>A	c.(1945-1947)Gag>Aag	p.E649K		NM_130386.2	NP_569057	Q5KU26	COL12_HUMAN	collectin sub-family member 12	649	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				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)				ACCTGTTCCTCTCTAGTGTTT	0.368																																					p.E649K		Atlas-SNP	.											.	COLEC12	121	.	0			c.G1945A						PASS	.						75	81	79					18																	333015		2203	4300	6503	SO:0001583	missense	81035	exon7			GTTCCTCTCTAGT	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.1945G>A	18.37:g.333015C>T	ENSP00000383115:p.Glu649Lys	156	0	0		172	20	0.116279	NM_130386	Q6P9F2|Q8TCR2|Q8WZA4|Q9BY85|Q9BYH7	Missense_Mutation	SNP	ENST00000400256.3	37	CCDS32782.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.318823	0.81469	.	.	ENSG00000158270	ENST00000400256	T	0.20598	2.06	5.68	5.68	0.88126	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.85682	D	0.000000	T	0.27063	0.0663	M	0.74881	2.28	0.80722	D	1	P	0.41008	0.735	B	0.38156	0.266	T	0.02877	-1.1099	10	0.39692	T	0.17	-25.494	14.0139	0.64513	0.0:0.9279:0.0:0.0721	.	649	Q5KU26	COL12_HUMAN	K	649	ENSP00000383115:E649K	ENSP00000383115:E649K	E	-	1	0	COLEC12	323015	1.000000	0.71417	0.959000	0.39883	0.647000	0.38526	5.691000	0.68249	2.686000	0.91538	0.650000	0.86243	GAG	.	.	none		0.368	COLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440746.1			T	333015	C	T	333015	3	4	19	1	0	0	0	0	1	0	0	0	3714	922	32	2	299	2	COLEC12	18	333015	Missense_Mutation	SNP	C	TCGA-FF-A7CW-01A-11D-A382-10		333015	77744233	37	2610											
LAMA1	284217	hgsc.bcm.edu	37	chr18	6978310	6978310	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agccccgccacgtccctcagCgtgctcaccgcgctctggct	4	7	10	20	5	3	0	2	0	1	0	4	0	4	0	5	1	3	3	5	1	0	0			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr18:6978310C>T	ENST00000389658.3	-	43	6168	c.6075G>A	c.(6073-6075)acG>acA	p.T2025T		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2025	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)				CGTCCCTCAGCGTGCTCACCG	0.537																																					p.T2025T		Atlas-SNP	.											LAMA1,NS,carcinoma,-1,1	LAMA1	458	1	0			c.G6075A						PASS	.						113	102	106					18																	6978310		2203	4300	6503	SO:0001819	synonymous_variant	284217	exon43			CCTCAGCGTGCTC	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.6075G>A	18.37:g.6978310C>T		123	0	0		151	29	0.192053	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																			.	.	none		0.537	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		T	6978310	C	T	6978310	2	4	19	1	0	0	0	0	0	0	0	1	8614	755	27	1		1	LAMA1	18	6978310	Silent	SNP	C	TCGA-FF-A7CW-01A-11D-A382-10	6645295	6978310	71098938	38	2611											
LAMA3	3909	hgsc.bcm.edu	37	chr18	21508671	21508671	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	acctactgaccacctccaggCctcatttggatttcagacct	9	11	6	15	0	2	2	2	1	0	1	3	3	3	3	6	2	1	0	6	2	1	3			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr18:21508671C>T	ENST00000313654.9	+	64	8619	c.8378C>T	c.(8377-8379)gCc>gTc	p.A2793V	LAMA3_ENST00000399516.3_Missense_Mutation_p.A2737V|LAMA3_ENST00000587184.1_Missense_Mutation_p.A1128V|LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000269217.6_Missense_Mutation_p.A1184V	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2793	Laminin G-like 3. {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)					CACCTCCAGGCCTCATTTGGA	0.428																																					p.A2793V		Atlas-SNP	.											.	LAMA3	397	.	0			c.C8378T						PASS	.						188	161	170					18																	21508671		2203	4300	6503	SO:0001583	missense	3909	exon64			TCCAGGCCTCATT	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.8378C>T	18.37:g.21508671C>T	ENSP00000324532:p.Ala2793Val	130	0	0		174	20	0.114943	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	37	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	C	6.801	0.516865	0.13005	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000269217	T;T;T	0.14766	2.48;2.48;2.48	5.84	3.09	0.35607	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);	.	.	.	.	T	0.08268	0.0206	L	0.33485	1.01	0.24198	N	0.995527	P;P;B;B	0.40431	0.666;0.717;0.002;0.028	B;B;B;B	0.37480	0.194;0.251;0.004;0.01	T	0.13361	-1.0512	9	0.05959	T	0.93	.	7.515	0.27596	0.0:0.659:0.0:0.341	.	1128;1184;2737;2793	Q6VU69;B0YJ33;Q6VU67;Q16787	.;.;.;LAMA3_HUMAN	V	2793;2737;1184	ENSP00000324532:A2793V;ENSP00000382432:A2737V;ENSP00000269217:A1184V	ENSP00000269217:A1184V	A	+	2	0	LAMA3	19762669	0.827000	0.29292	0.996000	0.52242	0.815000	0.46073	0.444000	0.21661	0.378000	0.24764	-0.136000	0.14681	GCC	.	.	none		0.428	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		T	21508671	C	T	21508671	3	4	19	1	0	0	0	0	1	0	0	0	8616	739	26	2	8807	2	LAMA3	18	21508671	Missense_Mutation	SNP	C	TCGA-FF-A7CW-01A-11D-A382-10	14530361	21508671	56568577	39	2612											
ASXL3	80816	hgsc.bcm.edu	37	chr18	31324277	31324277	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctccagtttgtctctgactGtctccgttgaaagctcagaa	8	13	8	12	1	3	3	1	2	2	1	6	3	4	3	3	0	1	3	3	0	2	2	rs576992025		TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr18:31324277G>A	ENST00000269197.5	+	12	4465	c.4465G>A	c.(4465-4467)Gtc>Atc	p.V1489I		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	1489					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						GTCTCTGACTGTCTCCGTTGA	0.562											OREG0024911	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V1489I		Atlas-SNP	.											.	ASXL3	405	.	0			c.G4465A						PASS	.						47	50	49					18																	31324277		2202	4300	6502	SO:0001583	missense	80816	exon12			CTGACTGTCTCCG	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.4465G>A	18.37:g.31324277G>A	ENSP00000269197:p.Val1489Ile	67	0	0	823	55	22	0.4	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	37	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	G	14.24	2.477762	0.44044	.	.	ENSG00000141431	ENST00000269197	T	0.15487	2.42	6.16	6.16	0.99307	.	.	.	.	.	T	0.13372	0.0324	L	0.27053	0.805	0.27072	N	0.963301	B	0.23540	0.087	B	0.20577	0.03	T	0.08289	-1.0729	9	0.46703	T	0.11	.	10.2745	0.43501	0.0701:0.0:0.7846:0.1453	.	1489	Q9C0F0	ASXL3_HUMAN	I	1489	ENSP00000269197:V1489I	ENSP00000269197:V1489I	V	+	1	0	ASXL3	29578275	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.272000	0.43373	2.937000	0.99478	0.650000	0.86243	GTC	.	.	none		0.562	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			A	31324277	G	A	31324277	3	1	19	1	0	0	0	0	1	0	0	0	1068	1377	48	2	4511	2	ASXL3	18	31324277	Missense_Mutation	SNP	G	TCGA-FF-A7CW-01A-11D-A382-10	9815606	31324277	46752971	40	2613											
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43514836	43514836	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagagctgctgcaggttctcGctctccacctggtgcatgag	6	10	13	12	1	2	2	0	1	2	1	4	3	2	2	2	2	4	6	2	2	0	1			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr18:43514836G>A	ENST00000282041.5	-	11	2230	c.2196C>T	c.(2194-2196)agC>agT	p.S732S		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	732					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						GCAGGTTCTCGCTCTCCACCT	0.597																																					p.S732S		Atlas-SNP	.											.	EPG5	199	.	0			c.C2196T						PASS	.						56	59	58					18																	43514836		2028	4189	6217	SO:0001819	synonymous_variant	57724	exon11			GTTCTCGCTCTCC	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.2196C>T	18.37:g.43514836G>A		126	0	0		156	28	0.179487	NM_020964	A2BDF3|Q9H8C8	Silent	SNP	ENST00000282041.5	37	CCDS11926.2																																																																																			.	.	none		0.597	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		A	43514836	G	A	43514836	2	1	19	1	0	0	0	0	0	0	0	1	8258	1078	38	1		1	KIAA1632	18	43514836	Silent	SNP	G	TCGA-FF-A7CW-01A-11D-A382-10	12190559	43514836	34562412	41	2614											
NCOA3	8202	hgsc.bcm.edu	37	chr20	46254225	46254225	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttaggaccgcttttacttcaGgcaagtataaagattttaac	13	14	7	7	1	1	1	1	0	0	1	1	2	1	2	1	2	2	3	1	2	7	8			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chr20:46254225G>T	ENST00000371998.3	+	5	548	c.357G>T	c.(355-357)caG>caT	p.Q119H	NCOA3_ENST00000341724.6_Splice_Site_p.Q119H|NCOA3_ENST00000372004.3_Splice_Site_p.Q119H|NCOA3_ENST00000371997.3_Splice_Site_p.Q119H			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	119	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						TTTTACTTCAGGCAAGTATAA	0.343																																					p.Q119H		Atlas-SNP	.											.	NCOA3	156	.	0			c.G357T						PASS	.						76	71	73					20																	46254225		2203	4300	6503	SO:0001630	splice_region_variant	8202	exon5			ACTTCAGGCAAGT	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.357+1G>T	20.37:g.46254225G>T		110	0	0		83	4	0.0481928	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Missense_Mutation	SNP	ENST00000371998.3	37	CCDS13407.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.672296	0.88348	.	.	ENSG00000124151	ENST00000340189;ENST00000341724;ENST00000372004;ENST00000371998;ENST00000371997	T;T;T;T	0.02606	4.23;4.39;4.39;4.24	5.62	5.62	0.85841	PAS (2);PAS fold (1);	0.000000	0.85682	D	0.000000	T	0.18425	0.0442	M	0.79926	2.475	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;0.983;0.998	T	0.00077	-1.2116	10	0.87932	D	0	-11.5155	19.6585	0.95853	0.0:0.0:1.0:0.0	.	119;123;119;119;119	Q9Y6Q9-3;Q59EE8;Q0IIN7;Q9Y6Q9-5;Q9Y6Q9	.;.;.;.;NCOA3_HUMAN	H	119	ENSP00000342123:Q119H;ENSP00000361073:Q119H;ENSP00000361066:Q119H;ENSP00000361065:Q119H	ENSP00000345671:Q119H	Q	+	3	2	NCOA3	45687632	1.000000	0.71417	1.000000	0.80357	0.727000	0.41649	8.004000	0.88535	2.657000	0.90304	0.467000	0.42956	CAG	.	.	none		0.343	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	Missense_Mutation	T	46254225	G	T	46254225	5	4	19	1	0	0	0	0	0	0	1	0	10239	1014	35	4	367	4	NCOA3	20	46254225	Splice_Site	SNP	G	TCGA-FF-A7CW-01A-11D-A382-10		46254225	16771295	42	2615											
ACE2	59272	hgsc.bcm.edu	37	chrX	15612969	15612969	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaatgttcacaaacgtaccCgtttgctcttgtcttctgag	10	14	7	10	2	4	1	1	1	3	0	4	1	4	1	1	0	3	4	1	0	4	5	rs201900069		TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chrX:15612969C>T	ENST00000252519.3	-	2	446	c.344G>A	c.(343-345)cGg>cAg	p.R115Q	ACE2_ENST00000427411.1_Splice_Site_p.R115Q			Q9BYF1	ACE2_HUMAN	angiotensin I converting enzyme 2	115					angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|angiotensin-mediated drinking behavior (GO:0003051)|cellular protein metabolic process (GO:0044267)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|receptor biosynthetic process (GO:0032800)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of cell proliferation (GO:0042127)|regulation of cytokine production (GO:0001817)|regulation of inflammatory response (GO:0050727)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)|regulation of vasoconstriction (GO:0019229)|regulation of vasodilation (GO:0042312)|response to virus (GO:0009615)|viral entry into host cell (GO:0046718)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	carboxypeptidase activity (GO:0004180)|endopeptidase activity (GO:0004175)|glycoprotein binding (GO:0001948)|peptide hormone binding (GO:0017046)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(10)|lung(10)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	32	Hepatocellular(33;0.183)				Lisinopril(DB00722)|Moexipril(DB00691)	CAAACGTACCCGTTTGCTCTT	0.388													C|||	1	0.000264901	0.0	0.0	3775	,	,		13925	0.001		0.0	False		,,,				2504	0.0				p.R115Q		Atlas-SNP	.											.	ACE2	87	.	0			c.G344A						PASS	.	C	GLN/ARG	0,3835		0,0,1632,571	180	167	172		344	-3.8	0	X		172	1,6727		0,1,2427,1872	no	missense-near-splice	ACE2	NM_021804.2	43	0,1,4059,2443	TT,TC,CC,C		0.0149,0.0,0.0095	benign	115/806	15612969	1,10562	2203	4300	6503	SO:0001630	splice_region_variant	59272	exon3			CGTACCCGTTTGC	AF291820	CCDS14169.1	Xp22	2013-06-12	2013-06-12		ENSG00000130234	ENSG00000130234	3.4.17.23		13557	protein-coding gene	gene with protein product	"peptidyl-dipeptidase A"	300335	"angiotensin I converting enzyme (peptidyl-dipeptidase A) 2"			10969042	Standard	NM_021804		Approved		uc004cxb.2	Q9BYF1	OTTHUMG00000021177	ENST00000252519.3:c.345+1G>A	X.37:g.15612969C>T		57	0	0		58	33	0.568965	NM_021804	C7ECU1|Q6UWP0|Q86WT0|Q9NRA7|Q9UFZ6	Missense_Mutation	SNP	ENST00000252519.3	37	CCDS14169.1	1	6.027727546714888E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	4.400	0.073831	0.08485	0.0	1.49E-4	ENSG00000130234	ENST00000252519;ENST00000427411	T;T	0.34072	1.38;1.38	6.02	-3.77	0.04346	.	0.724147	0.13392	N	0.391291	T	0.16769	0.0403	N	0.16266	0.395	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.21518	-1.0243	10	0.20046	T	0.44	-2.3109	7.4188	0.27061	0.1206:0.2584:0.0:0.6211	.	115	Q9BYF1	ACE2_HUMAN	Q	115	ENSP00000252519:R115Q;ENSP00000389326:R115Q	ENSP00000252519:R115Q	R	-	2	0	ACE2	15522890	0.018000	0.18449	0.005000	0.12908	0.151000	0.21798	0.082000	0.14847	-1.172000	0.02762	-1.013000	0.02462	CGG	C|0.999;T|0.001	0.001	strong		0.388	ACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055867.1		Missense_Mutation	T	15612969	C	T	15612969	5	4	19	1	0	0	0	0	0	0	1	0	137	666	23	1	2141	1	ACE2	23	15612969	Splice_Site	SNP	C	TCGA-FF-A7CW-01A-11D-A382-10		15612969	139657591	43	2616											
FAM48B1	100130302	hgsc.bcm.edu	37	chrX	24382417	24382418	+	IGR	INS	-	-	CTGCTGCTC																															tgctgctgctgctgctgctgINSctgctgctgctcctgctcct																								rs185449787		TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chrX:24382417_24382418insCTGCTGCTC								AC004552.1 (15394 upstream) : PDK3 (100919 downstream)																							tgctgctgctgctgctgctgct	0.619																																					p.A514delinsAAAP		Atlas-Indel	.											.	.	.	.	0			c.1540_1541insCTGCTGCTC						PASS	.																																			SO:0001628	intergenic_variant	100130302	exon1			.																													X.37:g.24382417_24382418insCTGCTGCTC		91	0	0		80	40	0.5	NM_001136234		In_Frame_Ins	INS		37																																																																																				.	.	alt	0	0.619									CTGCTGCTC	24382418	-	CTGCTGCTC	24382417	6	5	19	0	1	1	1	0	0	0	0	0	5581	1319	46	0		0	FAM48B1	23	24382417	IGR	INS	-	TCGA-FF-A7CW-01A-11D-A382-10	8769448	24382417	130888143	44	2617											
SLC35A2	7355	hgsc.bcm.edu	37	chrX	48762343	48762346	+	Frame_Shift_Del	DEL	GCCG	GCCG	-																															accacagccaccagtagcccGccgaaggcctggttgagcac																										TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	GCCG	GCCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chrX:48762343_48762346delGCCG	ENST00000247138.5	-	4	843_846	c.840_843delCGGC	c.(838-843)ttcggcfs	p.FG280fs	SLC35A2_ENST00000452555.2_Frame_Shift_Del_p.FG308fs|SLC35A2_ENST00000376529.3_Intron|SLC35A2_ENST00000376521.1_Frame_Shift_Del_p.FG280fs|SLC35A2_ENST00000376515.3_Intron|SLC35A2_ENST00000413561.2_Frame_Shift_Del_p.FG219fs|SLC35A2_ENST00000445167.2_Intron	NM_005660.1	NP_005651.1	P78381	S35A2_HUMAN	solute carrier family 35 (UDP-galactose transporter), member A2	280					galactose metabolic process (GO:0006012)|transmembrane transport (GO:0055085)|UDP-galactose transport (GO:0015785)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	sugar:proton symporter activity (GO:0005351)|UDP-galactose transmembrane transporter activity (GO:0005459)			breast(1)|endometrium(4)|kidney(2)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(2)	15						CCAGTAGCCCGCCGAAGGCCTGGT	0.603																																					p.281_282del		Pindel,Atlas-Indel	.											.	SLC35A2	46	.	0			c.841_844del						PASS	.																																			SO:0001589	frameshift_variant	7355	exon4			.	D88146	CCDS14311.1, CCDS35247.1, CCDS43937.1, CCDS65253.1, CCDS65254.1, CCDS75973.1, CCDS75974.1, CCDS75975.1	Xp11.23-p11.22	2013-05-22			ENSG00000102100	ENSG00000102100		"Solute carriers"	11022	protein-coding gene	gene with protein product		314375	"solute carrier family 35 (UDP-galactose transporter), member 2"	UGALT		8128316	Standard	NM_001042498		Approved	UGAT, UGT, UGT1, UGT2, UGTL	uc004dlo.1	P78381	OTTHUMG00000024129	ENST00000247138.5:c.840_843delCGGC	X.37:g.48762343_48762346delGCCG	ENSP00000247138:p.Phe280fs	54	0	.		47	13	0.277	NM_001042498	A8K2L9|A8K9V1|B4DE11|B4DPT2|E7EW45|Q8IV21|Q92553	Frame_Shift_Del	DEL	ENST00000247138.5	37	CCDS14311.1																																																																																			.	.	none		0.603	SLC35A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060790.1	NM_005660		-	48762346	GCCG	-	48762343	7	5	19	1	0	1	0	1	0	0	0	0	14586	1074	38	0	511	0	SLC35A2	23	48762343	Frame_Shift_Del	DEL	GCCG	TCGA-FF-A7CW-01A-11D-A382-10	24379926	48762343	106508217	45	2618											
RPS6KA6	27330	hgsc.bcm.edu	37	chrX	83357092	83357092	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatggagttaagagaagtcCattttctcctcgaagttgtt	10	14	10	7	1	1	1	0	0	1	1	4	4	2	2	2	1	0	4	2	1	3	5			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chrX:83357092C>A	ENST00000262752.2	-	18	1736	c.1729G>T	c.(1729-1731)Gga>Tga	p.G577*	RPS6KA6_ENST00000543399.1_Nonsense_Mutation_p.G577*|RPS6KA6_ENST00000495332.1_5'UTR	NM_014496.4	NP_055311.1	Q9UK32	KS6A6_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 6	577	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						AAGAGAAGTCCATTTTCTCCT	0.358																																					p.G577X		Atlas-SNP	.											.	RPS6KA6	116	.	0			c.G1729T						PASS	.						135	115	122					X																	83357092		2203	4300	6503	SO:0001587	stop_gained	27330	exon18			GAAGTCCATTTTC	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.1729G>T	X.37:g.83357092C>A	ENSP00000262752:p.Gly577*	248	0	0		178	92	0.516854	NM_014496	B2R854|B7ZL90|Q6FHX2|Q8WX28|Q9H4S6	Nonsense_Mutation	SNP	ENST00000262752.2	37	CCDS14451.1	.	.	.	.	.	.	.	.	.	.	C	39	7.488025	0.98316	.	.	ENSG00000072133	ENST00000262752;ENST00000543399	.	.	.	5.11	5.11	0.69529	.	0.055100	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	17.9644	0.89096	0.0:1.0:0.0:0.0	.	.	.	.	X	577	.	ENSP00000262752:G577X	G	-	1	0	RPS6KA6	83243748	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.597000	0.82733	2.263000	0.75096	0.523000	0.50628	GGA	.	.	none		0.358	RPS6KA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057372.1	NM_014496		A	83357092	C	A	83357092	4	1	19	1	0	0	0	0	0	1	0	0	13670	603	21	4	528	4	RPS6KA6	23	83357092	Nonsense_Mutation	SNP	C	TCGA-FF-A7CW-01A-11D-A382-10	34594749	83357092	71913468	46	2619											
POF1B	79983	hgsc.bcm.edu	37	chrX	84586012	84586012	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gatatagatccgtattcttaCggctcagatcagcaagcaac	13	10	8	10	2	3	2	2	0	1	2	4	3	4	2	1	1	4	4	1	1	6	5			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chrX:84586012C>T	ENST00000262753.4	-	7	942	c.797G>A	c.(796-798)cGt>cAt	p.R266H	POF1B_ENST00000373145.3_Missense_Mutation_p.R266H	NM_024921.3	NP_079197.3	Q8WVV4	POF1B_HUMAN	premature ovarian failure, 1B	266						tight junction (GO:0005923)				central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|liver(2)|lung(17)|ovary(1)|prostate(1)	35						CGTATTCTTACGGCTCAGATC	0.383																																					p.R266H		Atlas-SNP	.											.	POF1B	77	.	0			c.G797A						PASS	.						108	91	97					X																	84586012		2203	4300	6503	SO:0001583	missense	79983	exon7			TTCTTACGGCTCA	BC017500	CCDS14452.1	Xq21.2	2008-02-05			ENSG00000124429	ENSG00000124429			13711	protein-coding gene	gene with protein product		300603				11299520	Standard	NM_024921		Approved	POF, FLJ22792	uc004eer.2	Q8WVV4	OTTHUMG00000021934	ENST00000262753.4:c.797G>A	X.37:g.84586012C>T	ENSP00000262753:p.Arg266His	200	0	0		185	93	0.502703	NM_024921	A8K2U5|Q5H9E9|Q5H9F0|Q8NG12|Q9H5Y2|Q9H738|Q9H744	Missense_Mutation	SNP	ENST00000262753.4	37	CCDS14452.1	.	.	.	.	.	.	.	.	.	.	C	17.34	3.365477	0.61513	.	.	ENSG00000124429	ENST00000262753;ENST00000373145;ENST00000276124	T;T	0.26067	1.76;1.76	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.48466	0.1501	L	0.58101	1.795	0.53688	D	0.999974	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.41680	-0.9495	10	0.54805	T	0.06	-0.0188	16.0996	0.81163	0.0:1.0:0.0:0.0	.	266;266	Q8WVV4-1;Q8WVV4	.;POF1B_HUMAN	H	266	ENSP00000262753:R266H;ENSP00000362238:R266H	ENSP00000262753:R266H	R	-	2	0	POF1B	84472668	1.000000	0.71417	0.845000	0.33349	0.209000	0.24338	4.530000	0.60595	2.404000	0.81709	0.600000	0.82982	CGT	.	.	none		0.383	POF1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057391.2	NM_024921		T	84586012	C	T	84586012	3	4	19	1	0	0	0	0	1	0	0	0	12191	536	19	1	1016	1	POF1B	23	84586012	Missense_Mutation	SNP	C	TCGA-FF-A7CW-01A-11D-A382-10	1228920	84586012	70684548	47	2620											
SPANXN2	494119	hgsc.bcm.edu	37	chrX	142795338	142795338	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccttcagatgagtccaggtCttcgtcctcctgtgaagatc	7	13	9	12	1	2	4	1	2	1	2	8	4	6	4	4	1	0	0	4	1	1	2			TCGA-FF-A7CW-01A-11D-A382-10	TCGA-FF-A7CW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	422d5ebf-9d30-4c11-b1fe-c437822f0143	22d154b9-2ceb-409b-94d1-8f44d359d3a3	g.chrX:142795338C>A	ENST00000370498.1	-	2	1093	c.340G>T	c.(340-342)Gac>Tac	p.D114Y		NM_001009615.1	NP_001009615.1	Q5MJ10	SPXN2_HUMAN	SPANX family, member N2	114										NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(17)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	27	Acute lymphoblastic leukemia(192;6.56e-05)					GAGTCCAGGTCTTCGTCCTCC	0.527																																					p.D114Y		Atlas-SNP	.											.	SPANXN2	67	.	0			c.G340T						PASS	.						56	53	54					X																	142795338		2199	4293	6492	SO:0001583	missense	494119	exon2			CCAGGTCTTCGTC		CCDS35419.1	Xq27.3	2012-06-12			ENSG00000203924	ENSG00000268988			33175	protein-coding gene	gene with protein product	"cancer/testis antigen family 11, member 7"	300665				14973187, 17012309	Standard	NM_001009615		Approved	SPANX-N2, CT11.7	uc004fbz.3	Q5MJ10	OTTHUMG00000022583	ENST00000370498.1:c.340G>T	X.37:g.142795338C>A	ENSP00000359529:p.Asp114Tyr	183	0	0		139	37	0.266187	NM_001009615	Q0ZNM2	Missense_Mutation	SNP	ENST00000370498.1	37	CCDS35419.1	.	.	.	.	.	.	.	.	.	.	c	4.402	0.074349	0.08485	.	.	ENSG00000203924	ENST00000370498	T	0.08984	3.03	0.755	-1.51	0.08664	.	.	.	.	.	T	0.05181	0.0138	L	0.55481	1.735	0.09310	N	1	P	0.42993	0.797	B	0.25291	0.059	T	0.20042	-1.0287	8	0.87932	D	0	.	.	.	.	.	114	Q5MJ10	SPXN2_HUMAN	Y	114	ENSP00000359529:D114Y	ENSP00000359529:D114Y	D	-	1	0	SPANXN2	142623004	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	0.082000	0.14847	-1.317000	0.02292	0.173000	0.16961	GAC	.	.	none		0.527	SPANXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058621.2	NM_001009615		A	142795338	C	A	142795338	3	1	19	1	0	0	0	0	1	0	0	0	15006	913	32	4	206	4	SPANXN2	23	142795338	Missense_Mutation	SNP	C	TCGA-FF-A7CW-01A-11D-A382-10	58209326	142795338	12475222	48	2621											
KIAA0562	9731	hgsc.bcm.edu	37	chr1	3742332	3742332	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggcctgacctgtttgcagTggtcacatcttgtcagcatg	6	13	11	11	0	3	1	2	1	1	0	3	1	3	1	2	2	2	3	2	2	0	2			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr1:3742332T>C	ENST00000378230.3	-	18	2678	c.2354A>G	c.(2353-2355)cAc>cGc	p.H785R		NM_014704.3	NP_055519.1	O60308	CE104_HUMAN	centrosomal protein 104kDa	785						centriole (GO:0005814)	glutamate binding (GO:0016595)|glycine binding (GO:0016594)|thienylcyclohexylpiperidine binding (GO:0016596)			breast(2)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(14)|lung(8)|prostate(1)|skin(3)	39						CTGTTTGCAGTGGTCACATCT	0.507																																					p.H785R		Atlas-SNP	.											.	CEP104	79	.	0			c.A2354G						PASS	.						117	102	107					1																	3742332		2203	4300	6503	SO:0001583	missense	9731	exon18			TTGCAGTGGTCAC	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.2354A>G	1.37:g.3742332T>C	ENSP00000367476:p.His785Arg	90	0	0		57	26	0.45614	NM_014704	Q5JSQ3|Q5SR24|Q5SR25|Q6PKF5|Q86W32|Q86X14	Missense_Mutation	SNP	ENST00000378230.3	37	CCDS30571.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.82|13.82	2.352613|2.352613	0.41700|0.41700	.|.	.|.	ENSG00000116198|ENSG00000116198	ENST00000378230|ENST00000438539	T|.	0.31247|.	1.5|.	4.84|4.84	2.5|2.5	0.30297|0.30297	.|.	0.537894|.	0.19901|.	N|.	0.103507|.	T|T	0.63534|0.63534	0.2519|0.2519	M|M	0.72894|0.72894	2.215|2.215	0.80722|0.80722	D|D	1|1	P|.	0.46220|.	0.874|.	P|.	0.45712|.	0.491|.	T|T	0.58261|0.58261	-0.7667|-0.7667	10|5	0.45353|.	T|.	0.12|.	.|.	8.4447|8.4447	0.32834|0.32834	0.0:0.1613:0.0:0.8387|0.0:0.1613:0.0:0.8387	.|.	785|.	O60308|.	CE104_HUMAN|.	R|A	785|82	ENSP00000367476:H785R|.	ENSP00000367476:H785R|.	H|T	-|-	2|1	0|0	CEP104|CEP104	3732192|3732192	1.000000|1.000000	0.71417|0.71417	0.385000|0.385000	0.26158|0.26158	0.725000|0.725000	0.41563|0.41563	3.962000|3.962000	0.56766|0.56766	0.225000|0.225000	0.20959|0.20959	0.533000|0.533000	0.62120|0.62120	CAC|ACT	.	.	none		0.507	CEP104-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009747.3	NM_014704		C	3742332	T	C	3742332	3	2	20	1	0	0	0	0	1	0	0	0	8193	1696	59	3	443	3	KIAA0562	1	3742332	Missense_Mutation	SNP	T	TCGA-FF-A7CX-01A-12D-A382-10		3742332	245508289	1	2622											
EPHA2	1969	hgsc.bcm.edu	37	chr1	16475116	16475116	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcttgtagtagacacggaCggagagcagcgccacacagg	11	6	13	11	3	1	2	0	0	1	2	1	4	1	3	1	3	2	3	1	3	2	4			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr1:16475116C>T	ENST00000358432.5	-	3	734	c.580G>A	c.(580-582)Gtc>Atc	p.V194I	EPHA2_ENST00000461614.1_5'UTR	NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2	194	Cys-rich.|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)	TAGACACGGACGGAGAGCAGC	0.647																																					p.V194I		Atlas-SNP	.											.	EPHA2	102	.	0			c.G580A						PASS	.						63	61	62					1																	16475116		2203	4300	6503	SO:0001583	missense	1969	exon3			CACGGACGGAGAG	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.580G>A	1.37:g.16475116C>T	ENSP00000351209:p.Val194Ile	30	0	0		41	21	0.512195	NM_004431	B5A968|Q8N3Z2	Missense_Mutation	SNP	ENST00000358432.5	37	CCDS169.1	.	.	.	.	.	.	.	.	.	.	C	16.69	3.193575	0.58017	.	.	ENSG00000142627	ENST00000358432	T	0.05513	3.43	5.14	5.14	0.70334	Tyrosine-protein kinase, receptor class V, conserved site (1);Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.49305	D	0.000150	T	0.14013	0.0339	M	0.68317	2.08	0.58432	D	0.999996	P;P	0.41978	0.767;0.674	P;B	0.44946	0.465;0.353	T	0.00423	-1.1748	10	0.87932	D	0	.	16.0881	0.81073	0.0:1.0:0.0:0.0	.	194;194	B5A968;P29317	.;EPHA2_HUMAN	I	194	ENSP00000351209:V194I	ENSP00000351209:V194I	V	-	1	0	EPHA2	16347703	1.000000	0.71417	0.997000	0.53966	0.944000	0.59088	6.023000	0.70848	2.393000	0.81446	0.561000	0.74099	GTC	.	.	none		0.647	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	NM_004431		T	16475116	C	T	16475116	3	4	20	1	0	0	0	0	1	0	0	0	5169	536	19	1	2410	1	EPHA2	1	16475116	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	12732784	16475116	232775505	2	2623											
EPHA8	2046	hgsc.bcm.edu	37	chr1	22915717	22915717	+	Intron	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggtaggcggagaaactccGtcccgcagcgtcctggtccc	7	6	13	15	4	0	1	0	0	0	1	4	2	4	1	4	4	2	2	4	4	2	1	rs199679973		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr1:22915717G>A	ENST00000166244.3	+	5	1387				EPHA8_ENST00000374644.4_Missense_Mutation_p.V445I|EPHA8_ENST00000538803.1_Missense_Mutation_p.V445I	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)	p.V445I(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)		GAGAAACTCCGTCCCGCAGCG	0.667																																					p.V445I		Atlas-SNP	.											EPHA8_ENST00000374644,colon,carcinoma,0,1	EPHA8	221	1	1	Substitution - Missense(1)	large_intestine(1)	c.G1333A						PASS	.						35	35	35					1																	22915717		2203	4300	6503	SO:0001627	intron_variant	2046	exon5			AACTCCGTCCCGC	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.1315+18G>A	1.37:g.22915717G>A		80	0	0		72	34	0.472222	NM_001006943	Q6IN80|Q8IUX6|Q9NUA9|Q9P269	Missense_Mutation	SNP	ENST00000166244.3	37	CCDS225.1	.	.	.	.	.	.	.	.	.	.	G	10.79	1.450212	0.26074	.	.	ENSG00000070886	ENST00000374644;ENST00000538803	T;T	0.01304	5.03;5.03	4.52	0.0827	0.14430	.	.	.	.	.	T	0.00845	0.0028	.	.	.	0.09310	N	1	B	0.26935	0.164	B	0.14023	0.01	T	0.48479	-0.9032	7	.	.	.	.	2.9702	0.05920	0.1737:0.1401:0.5431:0.1431	.	445	P29322-2	.	I	445	ENSP00000363775:V445I;ENSP00000440274:V445I	.	V	+	1	0	EPHA8	22788304	0.000000	0.05858	0.006000	0.13384	0.026000	0.11368	0.211000	0.17474	0.225000	0.20959	0.436000	0.28706	GTC	G|0.999;A|0.001	0.001	weak		0.667	EPHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008085.1	NM_020526		A	22915717	G	A	22915717	1	1	20	0	1	0	0	0	0	0	0	0	5175	1145	40	1		1	EPHA8	1	22915717	Intron	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	6440601	22915717	226334904	3	2624											
ID3	3399	hgsc.bcm.edu	37	chr1	23885712	23885712	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtcgatgacgcgctgtaggAtttccacctggctaagctga	9	10	12	10	3	0	2	0	2	0	0	2	4	1	3	2	2	1	4	2	2	2	3			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr1:23885712A>G	ENST00000374561.5	-	1	573	c.206T>C	c.(205-207)aTc>aCc	p.I69T	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	69	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				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)		GCGCTGTAGGATTTCCACCTG	0.627																																					p.I69T		Atlas-SNP	.											.	ID3	29	.	0			c.T206C						PASS	.						59	64	62					1																	23885712		2203	4300	6503	SO:0001583	missense	3399	exon1			TGTAGGATTTCCA	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.206T>C	1.37:g.23885712A>G	ENSP00000363689:p.Ile69Thr	130	0	0		112	61	0.544643	NM_002167	A8K1T8|O75641	Missense_Mutation	SNP	ENST00000374561.5	37	CCDS237.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.401635	0.83120	.	.	ENSG00000117318	ENST00000374561	D	0.98633	-5.04	5.6	5.6	0.85130	Helix-loop-helix DNA-binding (5);	0.000000	0.85682	D	0.000000	D	0.98707	0.9566	L	0.53671	1.685	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99886	1.1123	10	0.87932	D	0	-20.0651	14.6048	0.68469	1.0:0.0:0.0:0.0	.	69	Q02535	ID3_HUMAN	T	69	ENSP00000363689:I69T	ENSP00000363689:I69T	I	-	2	0	ID3	23758299	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.339000	0.96797	2.126000	0.65437	0.482000	0.46254	ATC	.	.	none		0.627	ID3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008904.1	NM_002167		G	23885712	A	G	23885712	3	3	20	1	0	0	0	0	1	0	0	0	7500	333	12	3	161	3	ID3	1	23885712	Missense_Mutation	SNP	A	TCGA-FF-A7CX-01A-12D-A382-10	969995	23885712	225364909	4	2625											
DLGAP3	58512	hgsc.bcm.edu	37	chr1	35351360	35351360	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cggggcctggcttcccggcgGgatggggggcggggcctttc	1	7	21	12	4	0	0	0	0	0	0	2	1	1	1	3	10	0	1	3	10	0	2			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr1:35351360G>A	ENST00000373347.1	-	7	1901	c.1633C>T	c.(1633-1635)Ccg>Tcg	p.P545S	DLGAP3_ENST00000235180.4_Missense_Mutation_p.P545S			O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated protein 3	545					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)				CTTCCCGGCGGGATGGGGGGC	0.756																																					p.P545S		Atlas-SNP	.											.	DLGAP3	107	.	0			c.C1633T						PASS	.						2	3	2					1																	35351360		1432	3197	4629	SO:0001583	missense	58512	exon5			CCGGCGGGATGGG	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.1633C>T	1.37:g.35351360G>A	ENSP00000362444:p.Pro545Ser	52	0	0		45	20	0.444444	NM_001080418	Q5TDD5|Q9H3X7	Missense_Mutation	SNP	ENST00000373347.1	37	CCDS30670.1	.	.	.	.	.	.	.	.	.	.	G	34	5.393254	0.96009	.	.	ENSG00000116544	ENST00000373347;ENST00000235180	T;T	0.59224	0.28;0.28	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.77961	0.4209	M	0.83118	2.625	0.80722	D	1	D	0.89917	1.0	D	0.66716	0.946	T	0.80155	-0.1500	10	0.56958	D	0.05	-13.9072	18.8995	0.92437	0.0:0.0:1.0:0.0	.	545	O95886	DLGP3_HUMAN	S	545	ENSP00000362444:P545S;ENSP00000235180:P545S	ENSP00000235180:P545S	P	-	1	0	DLGAP3	35123947	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.369000	0.79578	2.684000	0.91462	0.561000	0.74099	CCG	.	.	none		0.756	DLGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011554.1	NM_021234		A	35351360	G	A	35351360	3	1	20	1	0	0	0	0	1	0	0	0	4563	1232	43	2	1330	2	DLGAP3	1	35351360	Missense_Mutation	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	11465648	35351360	213899261	5	2626											
PTPRF	5792	hgsc.bcm.edu	37	chr1	44085859	44085859	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gagcacaattccaccatcatCgtcatgctgaccaagcttcg	11	9	7	14	2	2	1	2	1	0	0	5	2	3	1	3	0	3	3	3	0	2	2			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr1:44085859C>T	ENST00000359947.4	+	30	5545	c.5205C>T	c.(5203-5205)atC>atT	p.I1735I	PTPRF_ENST00000372413.3_Silent_p.I1726I|PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000372414.3_Silent_p.I1735I|PTPRF_ENST00000438120.1_Silent_p.I1726I|PTPRF_ENST00000422171.2_Silent_p.I1094I	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1735	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				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)				CCACCATCATCGTCATGCTGA	0.612																																					p.I1735I		Atlas-SNP	.											.	PTPRF	172	.	0			c.C5205T						PASS	.						128	121	123					1																	44085859		2203	4300	6503	SO:0001819	synonymous_variant	5792	exon30			CATCATCGTCATG	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.5205C>T	1.37:g.44085859C>T		198	0	0		176	81	0.460227	NM_002840	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	37	CCDS489.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.027|7.027	0.559821|0.559821	0.13436|0.13436	.|.	.|.	ENSG00000142949|ENSG00000142949	ENST00000412568;ENST00000414879|ENST00000429895	.|.	.|.	.|.	4.97|4.97	1.84|1.84	0.25277|0.25277	.|.	.|.	.|.	.|.	.|.	T|T	0.53948|0.53948	0.1828|0.1828	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.46582|0.46582	-0.9181|-0.9181	4|4	.|.	.|.	.|.	.|.	6.315|6.315	0.21186|0.21186	0.0:0.4855:0.3251:0.1893|0.0:0.4855:0.3251:0.1893	.|.	.|.	.|.	.|.	C|L	1119;1160|1381	.|.	.|.	R|S	+|+	1|2	0|0	PTPRF|PTPRF	43858446|43858446	0.996000|0.996000	0.38824|0.38824	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	0.303000|0.303000	0.19210|0.19210	0.769000|0.769000	0.33313|0.33313	0.563000|0.563000	0.77884|0.77884	CGT|TCG	.	.	none		0.612	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1			T	44085859	C	T	44085859	2	4	20	1	0	0	0	0	0	0	0	1	12816	874	31	1		1	PTPRF	1	44085859	Silent	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	8734499	44085859	205164762	6	2627											
NRD1	4898	hgsc.bcm.edu	37	chr1	52306079	52306079	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcatcttcttcttcttccTccacctcctcttcttcttca	4	19	0	18	0	9	0	2	0	7	0	12	0	12	0	4	0	0	0	4	0	0	7	rs62648104		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	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_ENST00000539524.1_Missense_Mutation_p.E18V|NRD1_ENST00000485608.1_5'UTR|NRD1_ENST00000544028.1_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						PASS	.						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	1.37:g.52306079T>A	ENSP00000346890:p.Glu150Val	346	0	0		414	40	0.0966184	NM_001101662	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Missense_Mutation	SNP	ENST00000354831.7	37	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	0.976	weak		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	20	1	0	0	0	0	1	0	0	0	10654	1551	54	5	3338	5	NRD1	1	52306079	Missense_Mutation	SNP	T	TCGA-FF-A7CX-01A-12D-A382-10	8220220	52306079	196944542	7	2628											
DAB1	1600	hgsc.bcm.edu	37	chr1	57480789	57480789	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccattttctgcctgggcttgTcggtctgtggacttgacctg	3	15	12	11	1	2	1	0	1	2	0	3	2	2	2	3	3	1	1	3	3	0	4			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr1:57480789T>G	ENST00000371231.1	-	13	1344	c.1310A>C	c.(1309-1311)gAc>gCc	p.D437A	DAB1_ENST00000485760.1_5'UTR|DAB1_ENST00000371234.4_Missense_Mutation_p.D404A|DAB1_ENST00000439789.2_Missense_Mutation_p.D318A|DAB1_ENST00000420954.2_Missense_Mutation_p.D402A|DAB1_ENST00000371236.2_Missense_Mutation_p.D404A|DAB1_ENST00000414851.2_Missense_Mutation_p.D386A			O75553	DAB1_HUMAN	Dab, reelin signal transducer, homolog 1 (Drosophila)	437					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						CCTGGGCTTGTCGGTCTGTGG	0.607																																					p.D404A		Atlas-SNP	.											.	DAB1	129	.	0			c.A1211C						PASS	.						76	72	74					1																	57480789		2203	4300	6503	SO:0001583	missense	1600	exon14			GGCTTGTCGGTCT	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.1310A>C	1.37:g.57480789T>G	ENSP00000360275:p.Asp437Ala	126	0	0		98	38	0.387755	NM_021080	A4FU90|B3KTG3|Q4LE59|Q5T6M6|Q5T6M9|Q5T835|Q5T836|Q5T837|Q6NWS9|Q6NWT0|Q6NWT1|Q9NYA8	Missense_Mutation	SNP	ENST00000371231.1	37		.	.	.	.	.	.	.	.	.	.	T	13.46	2.242995	0.39697	.	.	ENSG00000173406	ENST00000371236;ENST00000371233;ENST00000371234;ENST00000420954;ENST00000414851;ENST00000439789;ENST00000371231	T;T;T;T;T;T	0.56611	0.45;0.45;0.48;0.52;1.56;0.5	5.54	4.41	0.53225	.	0.250480	0.47093	D	0.000257	T	0.32585	0.0834	N	0.08118	0	0.38346	D	0.944219	B;B;B;B;B	0.29988	0.264;0.002;0.023;0.006;0.007	B;B;B;B;B	0.29785	0.107;0.017;0.029;0.009;0.029	T	0.29761	-1.0001	10	0.48119	T	0.1	-22.3082	11.5505	0.50719	0.0:0.0695:0.0:0.9305	.	386;437;404;318;402	O75553-4;O75553;O75553-6;O75553-3;O75553-5	.;DAB1_HUMAN;.;.;.	A	404;404;404;402;386;318;437	ENSP00000360280:D404A;ENSP00000360278:D404A;ENSP00000395296:D402A;ENSP00000387581:D386A;ENSP00000409328:D318A;ENSP00000360275:D437A	ENSP00000360275:D437A	D	-	2	0	DAB1	57253377	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.749000	0.47492	1.114000	0.41781	0.528000	0.53228	GAC	.	.	none		0.607	DAB1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000027962.1	NM_021080		G	57480789	T	G	57480789	3	3	20	1	0	0	0	0	1	0	0	0	4219	1667	58	5	468	5	DAB1	1	57480789	Missense_Mutation	SNP	T	TCGA-FF-A7CX-01A-12D-A382-10	5174710	57480789	191769832	8	2629											
DAB1	1600	hgsc.bcm.edu	37	chr1	57481087	57481087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccagaaggacgggaggacagCgcccattgcaacgtaacctg	12	4	13	12	3	0	1	0	0	0	1	0	4	0	4	3	3	4	2	3	3	3	2			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr1:57481087C>T	ENST00000371231.1	-	13	1046	c.1012G>A	c.(1012-1014)Gct>Act	p.A338T	DAB1_ENST00000485760.1_5'UTR|DAB1_ENST00000371234.4_Missense_Mutation_p.A305T|DAB1_ENST00000439789.2_Missense_Mutation_p.A219T|DAB1_ENST00000420954.2_Missense_Mutation_p.A303T|DAB1_ENST00000371236.2_Missense_Mutation_p.A305T|DAB1_ENST00000414851.2_Missense_Mutation_p.A287T			O75553	DAB1_HUMAN	Dab, reelin signal transducer, homolog 1 (Drosophila)	338					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						GGGAGGACAGCGCCCATTGCA	0.577																																					p.A305T		Atlas-SNP	.											.	DAB1	129	.	0			c.G913A						PASS	.						24	27	26					1																	57481087		2199	4292	6491	SO:0001583	missense	1600	exon14			GGACAGCGCCCAT	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.1012G>A	1.37:g.57481087C>T	ENSP00000360275:p.Ala338Thr	73	0	0		59	5	0.0847458	NM_021080	A4FU90|B3KTG3|Q4LE59|Q5T6M6|Q5T6M9|Q5T835|Q5T836|Q5T837|Q6NWS9|Q6NWT0|Q6NWT1|Q9NYA8	Missense_Mutation	SNP	ENST00000371231.1	37		.	.	.	.	.	.	.	.	.	.	C	13.22	2.173250	0.38413	.	.	ENSG00000173406	ENST00000371236;ENST00000371233;ENST00000371234;ENST00000420954;ENST00000414851;ENST00000439789;ENST00000371231;ENST00000371232	T;T;T;T;T;T;T	0.54675	0.63;0.63;0.78;0.66;1.79;0.76;0.56	5.54	3.7	0.42460	.	0.145096	0.64402	N	0.000008	T	0.29783	0.0744	N	0.14661	0.345	0.58432	D	0.999996	P;B;B;B;P	0.42078	0.77;0.005;0.014;0.014;0.77	B;B;B;B;B	0.32149	0.141;0.052;0.015;0.008;0.141	T	0.05989	-1.0852	10	0.30078	T	0.28	-23.0659	12.5109	0.56005	0.0:0.8654:0.0:0.1346	.	287;338;305;219;303	O75553-4;O75553;O75553-6;O75553-3;O75553-5	.;DAB1_HUMAN;.;.;.	T	305;305;305;303;287;219;338;219	ENSP00000360280:A305T;ENSP00000360278:A305T;ENSP00000395296:A303T;ENSP00000387581:A287T;ENSP00000409328:A219T;ENSP00000360275:A338T;ENSP00000360276:A219T	ENSP00000360275:A338T	A	-	1	0	DAB1	57253675	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.349000	0.44054	0.915000	0.36847	-0.133000	0.14855	GCT	.	.	none		0.577	DAB1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000027962.1	NM_021080		T	57481087	C	T	57481087	3	4	20	1	0	0	0	0	1	0	0	0	4219	768	27	1	766	1	DAB1	1	57481087	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	298	57481087	191769534	9	2630											
DOCK7	85440	hgsc.bcm.edu	37	chr1	62962115	62962115	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcattaaaattctgagatgtGcccaccaaggaggatagtga	14	10	10	7	0	2	2	1	2	1	1	2	5	2	4	2	2	1	0	2	2	4	3			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr1:62962115G>T	ENST00000340370.5	-	37	4742	c.4725C>A	c.(4723-4725)ggC>ggA	p.G1575G	DOCK7_ENST00000251157.5_Silent_p.G1597G	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	1606					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						TCTGAGATGTGCCCACCAAGG	0.358																																					p.G1597G		Atlas-SNP	.											.	DOCK7	184	.	0			c.C4791A						PASS	.						85	84	85					1																	62962115		2203	4300	6503	SO:0001819	synonymous_variant	85440	exon38			AGATGTGCCCACC		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.4725C>A	1.37:g.62962115G>T		247	1	0.00404858		248	105	0.423387	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Silent	SNP	ENST00000340370.5	37	CCDS30734.1	.	.	.	.	.	.	.	.	.	.	G	9.022	0.985117	0.18889	.	.	ENSG00000116641	ENST00000454575	.	.	.	5.97	0.57	0.17347	.	.	.	.	.	T	0.43255	0.1239	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.22243	-1.0222	4	.	.	.	.	2.6339	0.04952	0.2263:0.3704:0.296:0.1073	.	.	.	.	N	769	.	.	H	-	1	0	DOCK7	62734703	0.998000	0.40836	0.999000	0.59377	0.995000	0.86356	0.554000	0.23407	0.111000	0.17947	0.585000	0.79938	CAC	.	.	none		0.358	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		T	62962115	G	T	62962115	2	4	20	1	0	0	0	0	0	0	0	1	4694	1306	46	4		4	DOCK7	1	62962115	Silent	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	5481028	62962115	186288506	10	2631											
NOTCH2	4853	hgsc.bcm.edu	37	chr1	120529632	120529635	+	Frame_Shift_Del	DEL	ACAA	ACAA	-																															taagtgttgaccccatccacAcaaacccctccattctgaca																										TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	ACAA	ACAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr1:120529632_120529635delACAA	ENST00000256646.2	-	5	1041_1044	c.822_825delTTGT	c.(820-825)gtttgtfs	p.VC274fs		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	274	EGF-like 7; 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)		CCCCATCCACACAAACCCCTCCAT	0.471			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome																												p.275_276del		Pindel,Atlas-Indel	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.823_826del						PASS	.																																			SO:0001589	frameshift_variant	4853	exon5	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.822_825delTTGT	1.37:g.120529632_120529635delACAA	ENSP00000256646:p.Val274fs	69	0	.		77	25	0.325	NM_024408	Q5T3X7|Q99734|Q9H240	Frame_Shift_Del	DEL	ENST00000256646.2	37	CCDS908.1																																																																																			.	.	none		0.471	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		-	120529635	ACAA	-	120529632	7	5	20	1	0	1	0	1	0	0	0	0	10557	157	6	0	6710	0	NOTCH2	1	120529632	Frame_Shift_Del	DEL	ACAA	TCGA-FF-A7CX-01A-12D-A382-10	57567517	120529632	128720989	11	2632											
KRTCAP2	80128	hgsc.bcm.edu	37	chr1	155145757	155145757	+	5'Flank	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caagaaaggcgagctgaaccGggtgcggttagctatgcgca	11	6	15	9	4	0	2	0	1	0	1	0	3	0	2	1	3	5	4	1	3	5	2	rs551900242		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr1:155145757G>A	ENST00000334634.4	+	0	0				TRIM46_ENST00000368385.4_5'Flank|TRIM46_ENST00000392451.2_5'Flank|KRTCAP2_ENST00000490672.1_5'UTR|RP11-201K10.3_ENST00000473363.2_Intron|KRTCAP2_ENST00000295682.4_Missense_Mutation_p.R8W|TRIM46_ENST00000543729.1_5'Flank|TRIM46_ENST00000368382.1_5'Flank|TRIM46_ENST00000545012.1_5'Flank|TRIM46_ENST00000368383.3_5'Flank	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)			GAGCTGAACCGGGTGCGGTTA	0.637											OREG0013854	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R8W		Atlas-SNP	.											.	KRTCAP2	15	.	0			c.C22T						PASS	.						35	33	34					1																	155145757		2203	4300	6503	SO:0001631	upstream_gene_variant	200185	exon1			TGAACCGGGTGCG		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		1.37:g.155145757G>A	Exception_encountered	98	0	0	1768	92	83	0.902174	NM_173852	A0AVI6|B1AVQ4|Q5VT60|Q5VT62|Q6NT17|Q6NT41|Q6ZRL7|Q9H5P2	Missense_Mutation	SNP	ENST00000334634.4	37	CCDS1097.1	.	.	.	.	.	.	.	.	.	.	G	13.15	2.150951	0.38021	.	.	ENSG00000163463	ENST00000295682	T	0.52295	0.67	5.7	0.335	0.15953	.	1.897460	0.02605	N	0.101423	T	0.10252	0.0251	N	0.08118	0	0.09310	N	1	B;B	0.11235	0.004;0.002	B;B	0.04013	0.001;0.001	T	0.21075	-1.0256	10	0.87932	D	0	8.0E-4	2.6567	0.05014	0.1567:0.2687:0.4403:0.1343	.	8;8	B3KNA5;Q8N6L1	.;KTAP2_HUMAN	W	8	ENSP00000295682:R8W	ENSP00000295682:R8W	R	-	1	2	KRTCAP2	153412381	0.169000	0.23002	0.002000	0.10522	0.000000	0.00434	-0.175000	0.09825	-0.102000	0.12197	-0.899000	0.02877	CGG	.	.	none		0.637	TRIM46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086728.1	NM_025058		A	155145757	G	A	155145757	1	1	20	0	1	0	0	0	0	0	0	0	8587	1115	39	1		1	KRTCAP2	1	155145757	5'Flank	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	34616125	155145757	94104864	12	2633											
NEK7	140609	hgsc.bcm.edu	37	chr1	198288596	198288596	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atccagagaagcgaccagacGtcacctatgtttatgacgta	13	9	9	10	3	1	3	1	1	0	2	2	5	2	3	3	0	1	2	3	0	4	4	rs114884409		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr1:198288596G>A	ENST00000367385.4	+	10	1195	c.853G>A	c.(853-855)Gtc>Atc	p.V285I	NEK7_ENST00000538004.1_Missense_Mutation_p.V285I	NM_133494.2	NP_598001.1	Q8TDX7	NEK7_HUMAN	NIMA-related kinase 7	285	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokinesis (GO:0000910)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle (GO:0007346)|spindle assembly (GO:0051225)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)	p.V285I(1)		endometrium(3)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	21						GCGACCAGACGTCACCTATGT	0.388													G|||	1	0.000199681	0.0	0.0	5008	,	,		20820	0.001		0.0	False		,,,				2504	0.0				p.V285I		Atlas-SNP	.											NEK7,NS,carcinoma,0,1	NEK7	42	1	1	Substitution - Missense(1)	stomach(1)	c.G853A						PASS	.						109	99	102					1																	198288596		2203	4300	6503	SO:0001583	missense	140609	exon10			CCAGACGTCACCT	AB062450	CCDS1394.1	1q31.3	2012-11-15	2012-11-15		ENSG00000151414	ENSG00000151414			13386	protein-coding gene	gene with protein product		606848	"NIMA (never in mitosis gene a)-related kinase 7"			11701951	Standard	NM_133494		Approved		uc001gun.4	Q8TDX7	OTTHUMG00000035658	ENST00000367385.4:c.853G>A	1.37:g.198288596G>A	ENSP00000356355:p.Val285Ile	108	0	0		118	40	0.338983	NM_133494	A6NGT8	Missense_Mutation	SNP	ENST00000367385.4	37	CCDS1394.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	0.544	-0.852228	0.02651	.	.	ENSG00000151414	ENST00000367385;ENST00000538004	T;T	0.38887	1.11;1.11	5.54	3.25	0.37280	Serine/threonine-protein kinase-like domain (1);Serine-threonine/tyrosine-protein kinase (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.101356	0.64402	N	0.000003	T	0.11836	0.0288	N	0.01109	-1.01	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.25328	-1.0135	10	0.02654	T	1	.	7.8419	0.29403	0.7675:0.0:0.2325:0.0	.	285	Q8TDX7	NEK7_HUMAN	I	285	ENSP00000356355:V285I;ENSP00000444621:V285I	ENSP00000356355:V285I	V	+	1	0	NEK7	196555219	1.000000	0.71417	0.998000	0.56505	0.334000	0.28698	3.529000	0.53532	0.407000	0.25591	-0.312000	0.09012	GTC	G|0.999;A|0.001	0.001	strong		0.388	NEK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086550.2	NM_133494		A	198288596	G	A	198288596	3	1	20	1	0	0	0	0	1	0	0	0	10338	1145	40	1	887	1	NEK7	1	198288596	Missense_Mutation	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	43142839	198288596	50962025	13	2634											
OR2T4	127074	hgsc.bcm.edu	37	chr1	248525640	248525640	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcaagctcctatttactcaTcctcctcaccatccacggga	9	12	4	16	1	3	0	3	0	0	0	7	1	7	1	5	1	2	1	5	1	3	4			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr1:248525640T>C	ENST00000366475.1	+	1	758	c.758T>C	c.(757-759)aTc>aCc	p.I253T		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	253						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)			TATTTACTCATCCTCCTCACC	0.517																																					p.I253T		Atlas-SNP	.											OR2T4,brain,glioma,+1,1	OR2T4	126	1	0			c.T758C						scavenged	.						135	130	132					1																	248525640		2203	4300	6503	SO:0001583	missense	127074	exon1			TACTCATCCTCCT	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.758T>C	1.37:g.248525640T>C	ENSP00000355431:p.Ile253Thr	12	2	0.166667		64	28	0.4375	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	37	CCDS31113.1	.	.	.	.	.	.	.	.	.	.	T	10.31	1.315398	0.23908	.	.	ENSG00000196944	ENST00000366475	T	0.00402	7.56	3.09	1.94	0.25998	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	D	0.000219	T	0.01523	0.0049	H	0.95151	3.63	0.33277	D	0.561816	D	0.89917	1.0	D	0.85130	0.997	T	0.11299	-1.0593	10	0.87932	D	0	.	7.6506	0.28346	0.0:0.1075:0.0:0.8925	.	253	Q8NH00	OR2T4_HUMAN	T	253	ENSP00000355431:I253T	ENSP00000355431:I253T	I	+	2	0	OR2T4	246592263	1.000000	0.71417	0.061000	0.19648	0.014000	0.08584	4.666000	0.61554	0.295000	0.22570	-0.361000	0.07541	ATC	.	.	none		0.517	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696		C	248525640	T	C	248525640	3	2	20	1	0	0	0	0	1	0	0	0	11036	1435	50	3	760	3	OR2T4	1	248525640	Missense_Mutation	SNP	T	TCGA-FF-A7CX-01A-12D-A382-10	50237044	248525640	724981	14	2635											
PXDN	7837	hgsc.bcm.edu	37	chr2	1680761	1680761	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctctgcaggtgaagtacacGgtgttccccgaggtcacatc	8	9	12	12	2	2	1	1	1	1	0	4	2	3	1	2	3	2	4	2	3	2	2			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr2:1680761G>A	ENST00000252804.4	-	8	836	c.786C>T	c.(784-786)acC>acT	p.T262T	PXDN_ENST00000483018.1_5'Flank	NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	262	Ig-like C2-type 1.				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)		TGAAGTACACGGTGTTCCCCG	0.547																																					p.T262T		Atlas-SNP	.											.	PXDN	255	.	0			c.C786T						PASS	.						65	73	70					2																	1680761		1993	4173	6166	SO:0001819	synonymous_variant	7837	exon8			GTACACGGTGTTC	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.786C>T	2.37:g.1680761G>A		176	0	0		160	71	0.44375	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Silent	SNP	ENST00000252804.4	37	CCDS46221.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	3.453|3.453	-0.111536|-0.111536	0.06881|0.06881	.|.	.|.	ENSG00000130508|ENSG00000130508	ENST00000433670|ENST00000447941	.|.	.|.	.|.	4.77|4.77	-9.54|-9.54	0.00572|0.00572	.|.	.|.	.|.	.|.	.|.	T|T	0.30947|0.30947	0.0781|0.0781	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.39418|0.39418	-0.9615|-0.9615	4|4	.|.	.|.	.|.	-26.0331|-26.0331	0.3493|0.3493	0.00346|0.00346	0.3348:0.2419:0.1617:0.2616|0.3348:0.2419:0.1617:0.2616	.|.	.|.	.|.	.|.	L|C	258|186	.|.	.|.	P|R	-|-	2|1	0|0	PXDN|PXDN	1659768|1659768	0.000000|0.000000	0.05858|0.05858	0.500000|0.500000	0.27589|0.27589	0.539000|0.539000	0.34962|0.34962	-3.664000|-3.664000	0.00399|0.00399	-2.386000|-2.386000	0.00590|0.00590	-1.553000|-1.553000	0.00894|0.00894	CCG|CGT	.	.	none		0.547	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		A	1680761	G	A	1680761	2	1	20	1	0	0	0	0	0	0	0	1	12862	1103	39	1		1	PXDN	2	1680761	Silent	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10		1680761	241518612	15	2636											
STRN	6801	hgsc.bcm.edu	37	chr2	37193498	37193498	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggccgcccccgccgcagccgCcccgtcgccggccgcggcag	2	1	15	23	9	0	0	0	0	0	0	1	0	0	0	9	3	1	2	9	3	0	0			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr2:37193498C>T	ENST00000263918.4	-	1	117	c.109G>A	c.(109-111)Gcg>Acg	p.A37T	STRN_ENST00000379213.2_Intron	NM_003162.3	NP_003153.2	O43815	STRN_HUMAN	striatin, calmodulin binding protein	37					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)				gccgcagccgccccgtcgccg	0.751																																					p.A37T		Atlas-SNP	.											.	STRN	71	.	0			c.G109A						PASS	.						3	3	3					2																	37193498		1371	3032	4403	SO:0001583	missense	6801	exon1			CAGCCGCCCCGTC	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.109G>A	2.37:g.37193498C>T	ENSP00000263918:p.Ala37Thr	52	0	0		65	27	0.415385	NM_003162	Q3KP65|Q53TQ8|Q9NP38	Missense_Mutation	SNP	ENST00000263918.4	37	CCDS1784.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.261212	0.80246	.	.	ENSG00000115808	ENST00000263918	T	0.64618	-0.11	3.47	3.47	0.39725	.	0.423459	0.19848	N	0.104710	T	0.36771	0.0979	N	0.08118	0	0.80722	D	1	B	0.28470	0.213	B	0.21151	0.033	T	0.21724	-1.0237	10	0.25751	T	0.34	-0.3364	10.1491	0.42782	0.0:0.7949:0.2051:0.0	.	37	O43815	STRN_HUMAN	T	37	ENSP00000263918:A37T	ENSP00000263918:A37T	A	-	1	0	STRN	37047002	0.987000	0.35691	0.998000	0.56505	0.984000	0.73092	3.812000	0.55628	1.747000	0.51819	0.484000	0.47621	GCG	.	.	none		0.751	STRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218568.1			T	37193498	C	T	37193498	3	4	20	1	0	0	0	0	1	0	0	0	15344	739	26	2	2305	2	STRN	2	37193498	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	35512737	37193498	206005875	16	2637											
MAP4K3	8491	hgsc.bcm.edu	37	chr2	39552696	39552696	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaaatcatggtaagtggaaTgatctggattatttacttta	13	15	9	4	1	2	1	1	1	1	0	2	4	2	3	0	3	1	1	0	3	6	6			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr2:39552696T>A	ENST00000263881.3	-	12	1205	c.881A>T	c.(880-882)cAt>cTt	p.H294L	MAP4K3_ENST00000536018.1_5'UTR|RP11-449G16.1_ENST00000609671.1_RNA|MAP4K3_ENST00000437545.1_Missense_Mutation_p.H231L|MAP4K3_ENST00000341681.5_Missense_Mutation_p.H294L	NM_003618.3	NP_003609.2	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase kinase 3	294					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)				GTAAGTGGAATGATCTGGATT	0.353																																					p.H294L		Atlas-SNP	.											.	MAP4K3	109	.	0			c.A881T						PASS	.						107	105	106					2																	39552696		2203	4300	6503	SO:0001583	missense	8491	exon12			GTGGAATGATCTG	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.881A>T	2.37:g.39552696T>A	ENSP00000263881:p.His294Leu	253	1	0.00395257		252	102	0.404762	NM_001270425	Q6IQ39|Q8IVH7|Q9UDM5|Q9Y6R5	Missense_Mutation	SNP	ENST00000263881.3	37	CCDS1803.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.375916	0.82682	.	.	ENSG00000011566	ENST00000263881;ENST00000437545;ENST00000341681	T;T;T	0.25250	1.81;1.81;1.81	5.86	5.86	0.93980	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.31451	0.0797	M	0.71581	2.175	0.80722	D	1	B;B	0.12630	0.0;0.006	B;B	0.12837	0.003;0.008	T	0.05920	-1.0856	9	.	.	.	.	16.2405	0.82405	0.0:0.0:0.0:1.0	.	294;294	Q8IVH8-3;Q8IVH8	.;M4K3_HUMAN	L	294;231;294	ENSP00000263881:H294L;ENSP00000416958:H231L;ENSP00000345434:H294L	.	H	-	2	0	MAP4K3	39406200	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.509000	0.81698	2.238000	0.73509	0.477000	0.44152	CAT	.	.	none		0.353	MAP4K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219966.2	NM_003618		A	39552696	T	A	39552696	3	1	20	1	0	0	0	0	1	0	0	0	9270	1464	51	5	1895	5	MAP4K3	2	39552696	Missense_Mutation	SNP	T	TCGA-FF-A7CX-01A-12D-A382-10	2359198	39552696	203646677	17	2638											
C2orf86	51057	hgsc.bcm.edu	37	chr2	63661025	63661025	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acagttgatagctagatgtcGctctgttgtcttgtttattg	7	18	10	6	1	2	2	0	1	2	1	3	2	2	2	0	0	1	5	0	0	3	8			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr2:63661025G>A	ENST00000272321.7	-	9	1206	c.679C>T	c.(679-681)Cga>Tga	p.R227*	WDPCP_ENST00000398544.3_Nonsense_Mutation_p.R68*|WDPCP_ENST00000409120.1_Nonsense_Mutation_p.R35*|WDPCP_ENST00000409199.1_Nonsense_Mutation_p.R35*|WDPCP_ENST00000409835.1_5'UTR|WDPCP_ENST00000409562.3_Nonsense_Mutation_p.R227*	NM_015910.5	NP_056994.3	O95876	FRITZ_HUMAN	WD repeat containing planar cell polarity effector	227					auditory receptor cell morphogenesis (GO:0002093)|camera-type eye development (GO:0043010)|cardiovascular system development (GO:0072358)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|digestive system development (GO:0055123)|embryonic digit morphogenesis (GO:0042733)|establishment of protein localization (GO:0045184)|glomerular visceral epithelial cell migration (GO:0090521)|kidney development (GO:0001822)|palate development (GO:0060021)|regulation of embryonic cell shape (GO:0016476)|regulation of establishment of cell polarity (GO:2000114)|regulation of fibroblast migration (GO:0010762)|regulation of focal adhesion assembly (GO:0051893)|regulation of protein localization (GO:0032880)|regulation of ruffle assembly (GO:1900027)|respiratory system development (GO:0060541)|septin cytoskeleton organization (GO:0032185)|smoothened signaling pathway (GO:0007224)	axonemal basal plate (GO:0097541)|axoneme (GO:0005930)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(19)|ovary(1)|skin(1)	35						GCTAGATGTCGCTCTGTTGTC	0.393																																					p.R227X		Atlas-SNP	.											WDPCP,colon,carcinoma,+1,3	WDPCP	79	3	0			c.C679T						scavenged	.						73	70	71					2																	63661025		1885	4097	5982	SO:0001587	stop_gained	51057	exon9			GATGTCGCTCTGT		CCDS42688.1, CCDS46301.1	2p15	2014-04-24	2011-02-01	2011-02-01	ENSG00000143951	ENSG00000143951			28027	protein-coding gene	gene with protein product		613580	"chromosome 2 open reading frame 86"	C2orf86		15654087, 20671153	Standard	NM_015910		Approved	hFrtz, fritz, BBS15	uc002sch.3	O95876	OTTHUMG00000152566	ENST00000272321.7:c.679C>T	2.37:g.63661025G>A	ENSP00000272321:p.Arg227*	222	1	0.0045045		163	64	0.392638	NM_015910	Q53RW4|Q7Z2Z3	Nonsense_Mutation	SNP	ENST00000272321.7	37	CCDS42688.1	.	.	.	.	.	.	.	.	.	.	G	57	29.697367	0.99976	.	.	ENSG00000143951	ENST00000272321;ENST00000409199;ENST00000409120;ENST00000398544;ENST00000409562	.	.	.	5.43	3.64	0.41730	.	0.062767	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-0.8926	11.2324	0.48920	0.1489:0.0:0.8511:0.0	.	.	.	.	X	227;35;35;68;227	.	ENSP00000272321:R227X	R	-	1	2	WDPCP	63514529	1.000000	0.71417	0.134000	0.22075	0.811000	0.45836	3.598000	0.54038	0.674000	0.31244	0.563000	0.77884	CGA	.	.	none		0.393	WDPCP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326820.1	NM_015910		A	63661025	G	A	63661025	4	1	20	1	0	0	0	0	0	1	0	0	2203	1095	38	1	1601	1	C2orf86	2	63661025	Nonsense_Mutation	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	24108329	63661025	179538348	18	2639											
LRRTM4	80059	hgsc.bcm.edu	37	chr2	77745577	77745577	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggaattcatttgtctttcaGactctctggcctttttccgc	5	17	8	11	1	4	1	2	0	2	1	6	2	5	2	2	2	0	0	2	2	1	5			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr2:77745577G>T	ENST00000409093.1	-	3	1754	c.1418C>A	c.(1417-1419)tCt>tAt	p.S473Y	LRRTM4_ENST00000409282.1_Missense_Mutation_p.S474Y|LRRTM4_ENST00000409088.3_Missense_Mutation_p.S473Y|LRRTM4_ENST00000409911.1_Missense_Mutation_p.S474Y|LRRTM4_ENST00000409884.1_Missense_Mutation_p.S473Y			Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	473					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)		TTGTCTTTCAGACTCTCTGGC	0.468																																					p.S473Y		Atlas-SNP	.											.	LRRTM4	334	.	0			c.C1418A						PASS	.						82	81	82					2																	77745577		1898	4120	6018	SO:0001583	missense	80059	exon3			CTTTCAGACTCTC	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.1418C>A	2.37:g.77745577G>T	ENSP00000386357:p.Ser473Tyr	191	0	0		141	43	0.304965	NM_024993	Q4FZ98|Q6UXJ7	Missense_Mutation	SNP	ENST00000409093.1	37	CCDS46346.1	.	.	.	.	.	.	.	.	.	.	G	14.29	2.492072	0.44352	.	.	ENSG00000176204	ENST00000409911;ENST00000409884;ENST00000409093;ENST00000409088;ENST00000409282	T;T;T;T;T	0.74842	-0.88;-0.88;-0.88;-0.88;-0.88	5.68	5.68	0.88126	.	0.330675	0.33457	N	0.004881	T	0.75882	0.3910	L	0.43152	1.355	0.41973	D	0.990766	P;P;P	0.46395	0.877;0.811;0.877	B;P;P	0.48227	0.367;0.571;0.504	T	0.78800	-0.2062	10	0.87932	D	0	.	18.3564	0.90358	0.0:0.0:1.0:0.0	.	474;473;473	Q4KMX1;Q86VH4-2;Q86VH4	.;.;LRRT4_HUMAN	Y	474;473;473;473;474	ENSP00000387228:S474Y;ENSP00000387297:S473Y;ENSP00000386357:S473Y;ENSP00000386236:S473Y;ENSP00000386286:S474Y	ENSP00000386236:S473Y	S	-	2	0	LRRTM4	77599085	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.308000	0.72820	2.670000	0.90874	0.655000	0.94253	TCT	.	.	none		0.468	LRRTM4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328225.1	NM_024993		T	77745577	G	T	77745577	3	4	20	1	0	0	0	0	1	0	0	0	9051	942	33	4	368	4	LRRTM4	2	77745577	Missense_Mutation	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	14084552	77745577	165453796	19	2640											
TUBA3D	113457	hgsc.bcm.edu	37	chr2	132238015	132238015	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttgatggggccctgaatgTggacttgacggaattccaga	10	11	13	7	1	0	4	0	3	0	1	1	6	1	6	2	4	0	0	2	4	2	3			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr2:132238015T>A	ENST00000321253.6	+	4	856	c.749T>A	c.(748-750)gTg>gAg	p.V250E		NM_080386.3	NP_525125.2	Q13748	TBA3C_HUMAN	tubulin, alpha 3d	250					'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)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	32				BRCA - Breast invasive adenocarcinoma(221;0.13)		GCCCTGAATGTGGACTTGACG	0.577																																					p.V250E	Ovarian(137;2059 2432 35543 39401)	Atlas-SNP	.											.	TUBA3D	60	.	0			c.T749A						PASS	.						82	116	105					2																	132238015		2022	4288	6310	SO:0001583	missense	113457	exon4			TGAATGTGGACTT	K03460	CCDS33290.1	2q21.1	2007-03-16			ENSG00000075886	ENSG00000075886		"Tubulins"	24071	protein-coding gene	gene with protein product	"alpha-tubulin isotype H2-alpha"					3785200	Standard	NM_080386		Approved	H2-ALPHA	uc002tsu.4	Q13748	OTTHUMG00000153600	ENST00000321253.6:c.749T>A	2.37:g.132238015T>A	ENSP00000326042:p.Val250Glu	133	0	0		140	62	0.442857	NM_080386	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Missense_Mutation	SNP	ENST00000321253.6	37	CCDS33290.1	.	.	.	.	.	.	.	.	.	.	t	9.448	1.089784	0.20390	.	.	ENSG00000075886	ENST00000321253;ENST00000341158	D	0.84944	-1.92	2.24	2.24	0.28232	Tubulin/FtsZ, 2-layer sandwich domain (1);Tubulin/FtsZ, GTPase domain (1);Tubulin/FtsZ, C-terminal (1);	0.000000	0.41194	U	0.000924	D	0.93976	0.8071	H	0.98068	4.14	0.46774	D	0.999198	D	0.67145	0.996	D	0.74023	0.982	D	0.93074	0.6485	10	0.87932	D	0	.	8.0376	0.30502	0.0:0.0:0.0:1.0	.	250	Q13748	TBA3C_HUMAN	E	250	ENSP00000326042:V250E	ENSP00000326042:V250E	V	+	2	0	TUBA3D	131954485	1.000000	0.71417	0.967000	0.41034	0.146000	0.21551	6.744000	0.74854	1.023000	0.39654	0.163000	0.16589	GTG	.	.	none		0.577	TUBA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331800.2	NM_080386		A	132238015	T	A	132238015	3	1	20	1	0	0	0	0	1	0	0	0	16762	1696	59	5	763	5	TUBA3D	2	132238015	Missense_Mutation	SNP	T	TCGA-FF-A7CX-01A-12D-A382-10	54492438	132238015	110961358	20	2641											
LRP1B	53353	hgsc.bcm.edu	37	chr2	141571285	141571285	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcattgactcgattacttctAaattaccaccatccaggttg	11	14	5	11	1	2	1	1	1	1	0	4	2	3	1	3	1	2	1	3	1	4	6			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr2:141571285A>G	ENST00000389484.3	-	32	6271	c.5300T>C	c.(5299-5301)tTa>tCa	p.L1767S		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1767					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)		GATTACTTCTAAATTACCACC	0.353										TSP Lung(27;0.18)																											p.L1767S	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.T5300C						PASS	.						169	148	155					2																	141571285		2203	4299	6502	SO:0001583	missense	53353	exon32			ACTTCTAAATTAC	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.5300T>C	2.37:g.141571285A>G	ENSP00000374135:p.Leu1767Ser	289	0	0		278	96	0.345324	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	A	18.77	3.695623	0.68386	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.91792	-2.91	5.83	5.83	0.93111	Six-bladed beta-propeller, TolB-like (1);	0.098626	0.40554	N	0.001061	D	0.90665	0.7072	L	0.39898	1.24	0.43971	D	0.996656	D	0.54047	0.964	P	0.49140	0.601	D	0.88943	0.3381	10	0.23891	T	0.37	.	16.1982	0.82046	1.0:0.0:0.0:0.0	.	1767	Q9NZR2	LRP1B_HUMAN	S	1767;1705	ENSP00000374135:L1767S	ENSP00000374135:L1767S	L	-	2	0	LRP1B	141287755	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.282000	0.95840	2.226000	0.72624	0.533000	0.62120	TTA	.	.	none		0.353	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		G	141571285	A	G	141571285	3	3	20	1	0	0	0	0	1	0	0	0	8964	372	13	3	8739	3	LRP1B	2	141571285	Missense_Mutation	SNP	A	TCGA-FF-A7CX-01A-12D-A382-10	9333270	141571285	101628088	21	2642											
MBD5	55777	hgsc.bcm.edu	37	chr2	149226791	149226791	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggagtcatgtacaaagagttCagcattcagcttcaacctcc	12	10	8	11	0	4	1	4	0	0	1	5	2	5	2	2	1	4	4	2	1	3	4			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr2:149226791C>T	ENST00000407073.1	+	9	2276	c.1279C>T	c.(1279-1281)Cag>Tag	p.Q427*	MBD5_ENST00000404807.1_Nonsense_Mutation_p.Q427*	NM_018328.4	NP_060798.2	Q9P267	MBD5_HUMAN	methyl-CpG binding domain protein 5	427					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)		ACAAAGAGTTCAGCATTCAGC	0.498																																					p.Q427X		Atlas-SNP	.											.	MBD5	164	.	0			c.C1279T						PASS	.						113	110	111					2																	149226791		2203	4300	6503	SO:0001587	stop_gained	55777	exon9			AGAGTTCAGCATT	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.1279C>T	2.37:g.149226791C>T	ENSP00000386049:p.Gln427*	138	0	0		130	51	0.392308	NM_018328	A5HMQ4|A7E2B1|Q53SR1|Q9NUV6	Nonsense_Mutation	SNP	ENST00000407073.1	37	CCDS33302.1	.	.	.	.	.	.	.	.	.	.	C	47	12.983514	0.99711	.	.	ENSG00000204406	ENST00000407073;ENST00000404807	.	.	.	5.18	5.18	0.71444	.	0.230777	0.30658	N	0.009142	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	-0.0931	19.0722	0.93143	0.0:1.0:0.0:0.0	.	.	.	.	X	427	.	ENSP00000384672:Q427X	Q	+	1	0	MBD5	148943261	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.384000	0.79751	2.595000	0.87683	0.655000	0.94253	CAG	.	.	none		0.498	MBD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318111.2			T	149226791	C	T	149226791	4	4	20	1	0	0	0	0	0	1	0	0	9356	827	29	2	1293	2	MBD5	2	149226791	Nonsense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	7655506	149226791	93972582	22	2643											
XIRP2	129446	hgsc.bcm.edu	37	chr2	168100213	168100213	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggagatgtaagaacagcaCggtggatgtttgaaacacag	15	7	14	5	1	0	3	0	1	0	2	0	5	0	4	0	3	3	3	0	3	3	2	rs548985321		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr2:168100213C>T	ENST00000409195.1	+	9	2400	c.2311C>T	c.(2311-2313)Cgg>Tgg	p.R771W	XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.R771W|XIRP2_ENST00000409273.1_Missense_Mutation_p.R549W|XIRP2_ENST00000409756.2_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	596					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.R771W(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						AAGAACAGCACGGTGGATGTT	0.388													C|||	1	0.000199681	0.0	0.0	5008	,	,		19204	0.0		0.0	False		,,,				2504	0.001				p.R771W		Atlas-SNP	.											XIRP2,colon,carcinoma,0,1	XIRP2	914	1	1	Substitution - Missense(1)	large_intestine(1)	c.C2311T						PASS	.						72	67	69					2																	168100213		1863	4091	5954	SO:0001583	missense	129446	exon9			ACAGCACGGTGGA	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.2311C>T	2.37:g.168100213C>T	ENSP00000386840:p.Arg771Trp	222	0	0		150	68	0.453333	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	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	C	17.07	3.296005	0.60086	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.39229	1.09;1.09;1.09	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.63355	0.2504	M	0.77486	2.375	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	0.66492	-0.5910	10	0.87932	D	0	-10.5946	10.2698	0.43477	0.135:0.7957:0.0:0.0693	.	596;596;549	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	W	771;771;549	ENSP00000386840:R771W;ENSP00000295237:R771W;ENSP00000387255:R549W	ENSP00000295237:R771W	R	+	1	2	XIRP2	167808459	0.994000	0.37717	1.000000	0.80357	0.997000	0.91878	1.731000	0.38135	2.810000	0.96702	0.650000	0.86243	CGG	.	.	none		0.388	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		T	168100213	C	T	168100213	3	4	20	1	0	0	0	0	1	0	0	0	17445	527	19	1	2341	1	XIRP2	2	168100213	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	18873422	168100213	75099160	23	2644											
OSBPL6	114880	hgsc.bcm.edu	37	chr2	179255816	179255816	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggtgaattattggaattCtaacatgaatgaagtccagg	14	11	10	6	0	1	3	0	3	1	0	2	4	2	4	2	3	1	0	2	3	6	4			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr2:179255816C>A	ENST00000190611.4	+	22	2694	c.2318C>A	c.(2317-2319)tCt>tAt	p.S773Y	OSBPL6_ENST00000409045.3_Missense_Mutation_p.S742Y|OSBPL6_ENST00000392505.2_Missense_Mutation_p.S798Y|OSBPL6_ENST00000359685.3_Missense_Mutation_p.S737Y|OSBPL6_ENST00000315022.2_Missense_Mutation_p.S777Y|OSBPL6_ENST00000409631.1_Missense_Mutation_p.S737Y	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	773					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)			TATTGGAATTCTAACATGAAT	0.428																																					p.S798Y		Atlas-SNP	.											OSBPL6,NS,carcinoma,-1,1	OSBPL6	178	1	0			c.C2393A						PASS	.						129	127	128					2																	179255816		2203	4300	6503	SO:0001583	missense	114880	exon23			GGAATTCTAACAT	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.2318C>A	2.37:g.179255816C>A	ENSP00000190611:p.Ser773Tyr	184	0	0		158	75	0.474684	NM_001201480	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Missense_Mutation	SNP	ENST00000190611.4	37	CCDS2277.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.259546	0.80246	.	.	ENSG00000079156	ENST00000392505;ENST00000359685;ENST00000409045;ENST00000190611;ENST00000409631;ENST00000315022	T;T;T;T;T;T	0.32515	1.45;1.45;1.45;1.45;1.45;1.45	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	T	0.61324	0.2338	M	0.84219	2.685	0.80722	D	1	D;D;D;D;D	0.89917	0.957;0.994;0.958;1.0;0.997	P;D;P;D;D	0.87578	0.905;0.963;0.867;0.998;0.973	T	0.67585	-0.5633	10	0.87932	D	0	-11.6467	18.8281	0.92127	0.0:1.0:0.0:0.0	.	742;777;737;798;773	Q9BZF3-4;Q9BZF3-3;Q9BZF3-2;Q9BZF3-5;Q9BZF3	.;.;.;.;OSBL6_HUMAN	Y	798;737;742;773;737;777	ENSP00000376293:S798Y;ENSP00000352713:S737Y;ENSP00000387248:S742Y;ENSP00000190611:S773Y;ENSP00000386885:S737Y;ENSP00000318723:S777Y	ENSP00000190611:S773Y	S	+	2	0	OSBPL6	178964062	1.000000	0.71417	0.983000	0.44433	0.698000	0.40448	7.625000	0.83145	2.514000	0.84764	0.462000	0.41574	TCT	.	.	none		0.428	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523		A	179255816	C	A	179255816	3	1	20	1	0	0	0	0	1	0	0	0	11290	913	32	4	2518	4	OSBPL6	2	179255816	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	11155603	179255816	63943557	24	2645											
DNAJC10	54431	hgsc.bcm.edu	37	chr2	183627529	183627529	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	atttctacgaaagagcaaagGtatgtccagactttcctctg	12	12	8	9	1	2	2	0	0	2	2	4	3	4	2	2	1	2	2	2	1	4	4			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr2:183627529G>A	ENST00000264065.7	+	22	2680		c.e22+1			NM_018981.1	NP_061854.1	Q8IXB1	DJC10_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 10						cell redox homeostasis (GO:0045454)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of ATPase activity (GO:0032781)|protein folding in endoplasmic reticulum (GO:0034975)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum chaperone complex (GO:0034663)|endoplasmic reticulum lumen (GO:0005788)|membrane (GO:0016020)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|chaperone binding (GO:0051087)|disulfide oxidoreductase activity (GO:0015036)|Hsp70 protein binding (GO:0030544)|misfolded protein binding (GO:0051787)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide oxidoreductase activity (GO:0015035)			breast(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(15)|ovary(1)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			AAGAGCAAAGGTATGTCCAGA	0.413																																					.	Pancreas(56;860 1183 25669 35822 48585)	Atlas-SNP	.											.	DNAJC10	76	.	0			c.2265+1G>A						PASS	.						116	113	114					2																	183627529		2203	4300	6503	SO:0001630	splice_region_variant	54431	exon22			GCAAAGGTATGTC		CCDS33345.1, CCDS74613.1	2q32.1	2011-11-23			ENSG00000077232	ENSG00000077232		"Heat shock proteins / DNAJ (HSP40)", "Protein disulfide isomerases"	24637	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 19"	607987				12411443, 12446677	Standard	NM_018981		Approved	ERdj5, PDIA19	uc002uow.2	Q8IXB1	OTTHUMG00000154209	ENST00000264065.7:c.2265+1G>A	2.37:g.183627529G>A		272	0	0		266	136	0.511278	NM_018981	Q17RJ6|Q3B7W8|Q4ZG06|Q53QT7|Q6UWZ6|Q86T61|Q8NC82|Q8TD87|Q96K38|Q96K44|Q96K54|Q9NSY6	Splice_Site	SNP	ENST00000264065.7	37	CCDS33345.1	.	.	.	.	.	.	.	.	.	.	G	12.58	1.980875	0.34942	.	.	ENSG00000077232	ENST00000264065;ENST00000392392	.	.	.	5.94	5.94	0.96194	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.5399	0.91024	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	DNAJC10	183335774	1.000000	0.71417	0.999000	0.59377	0.097000	0.18754	7.235000	0.78143	2.816000	0.96949	0.563000	0.77884	.	.	.	none		0.413	DNAJC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334418.2	NM_018981	Intron	A	183627529	G	A	183627529	5	1	20	1	0	0	0	0	0	0	1	0	4631	1275	44	2	2344	2	DNAJC10	2	183627529	Splice_Site	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	4371713	183627529	59571844	25	2646											
NDUFS1	4719	hgsc.bcm.edu	37	chr2	207017231	207017231	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttgctgctgtggcagttgttCgaactgaccatcaaagatat	10	13	10	8	1	1	2	1	1	0	1	2	3	1	2	1	1	3	5	1	1	3	4			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr2:207017231C>T	ENST00000233190.6	-	3	331	c.65G>A	c.(64-66)cGa>cAa	p.R22Q	NDUFS1_ENST00000432169.1_Intron|NDUFS1_ENST00000423725.1_Intron|NDUFS1_ENST00000455934.2_Missense_Mutation_p.R36Q|NDUFS1_ENST00000449699.1_Missense_Mutation_p.R22Q|NDUFS1_ENST00000457011.1_Intron|NDUFS1_ENST00000440274.1_Missense_Mutation_p.R22Q	NM_005006.6	NP_004997.4	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzyme Q reductase)	22					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						GGCAGTTGTTCGAACTGACCA	0.388																																					p.R36Q		Atlas-SNP	.											NDUFS1,NS,carcinoma,-1,3	NDUFS1	82	3	0			c.G107A						PASS	.						110	92	98					2																	207017231		2203	4300	6503	SO:0001583	missense	4719	exon3			GTTGTTCGAACTG		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.65G>A	2.37:g.207017231C>T	ENSP00000233190:p.Arg22Gln	210	0	0		209	84	0.401914	NM_001199984	B4DIN9|B4DJA0|B4DPG1|B4DUC1|E7ENF3|Q53TR8|Q8N1C4|Q8TCC9	Missense_Mutation	SNP	ENST00000233190.6	37	CCDS2366.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.397368	0.83120	.	.	ENSG00000023228	ENST00000233190;ENST00000440274;ENST00000455934;ENST00000449699;ENST00000454195	D;D;D;D;T	0.88664	-2.32;-2.41;-2.32;-2.32;-1.18	5.9	5.9	0.94986	.	0.318441	0.28332	N	0.015736	D	0.86138	0.5861	M	0.63169	1.94	0.80722	D	1	B;P;B	0.42993	0.063;0.797;0.028	B;B;B	0.26969	0.022;0.075;0.007	D	0.87780	0.2611	10	0.62326	D	0.03	.	20.2723	0.98479	0.0:1.0:0.0:0.0	.	22;36;22	E7ENF3;B4DJA0;P28331	.;.;NDUS1_HUMAN	Q	22;22;36;22;22	ENSP00000233190:R22Q;ENSP00000409766:R22Q;ENSP00000392709:R36Q;ENSP00000399912:R22Q;ENSP00000389413:R22Q	ENSP00000233190:R22Q	R	-	2	0	NDUFS1	206725476	1.000000	0.71417	0.999000	0.59377	0.839000	0.47603	6.841000	0.75374	2.793000	0.96121	0.563000	0.77884	CGA	.	.	none		0.388	NDUFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256391.4	NM_005006		T	207017231	C	T	207017231	3	4	20	1	0	0	0	0	1	0	0	0	10300	884	31	1	2186	1	NDUFS1	2	207017231	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	23389702	207017231	36182142	26	2647											
COL4A3	1285	hgsc.bcm.edu	37	chr2	228125811	228125811	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ttcccaggtcccagtggtccCcccggagttcctggaagtcc	5	9	11	16	1	0	0	0	0	0	0	5	2	5	2	7	4	0	1	7	4	1	2			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr2:228125811C>T	ENST00000396578.3	+	20	1290	c.1128C>T	c.(1126-1128)ccC>ccT	p.P376P	AC097662.2_ENST00000437673.1_RNA|AC097662.2_ENST00000606119.1_RNA|AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000396588.2_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	376	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)		CCAGTGGTCCCCCCGGAGTTC	0.383																																					p.P376P		Atlas-SNP	.											.	COL4A3	293	.	0			c.C1128T						PASS	.						76	77	77					2																	228125811		1809	4076	5885	SO:0001819	synonymous_variant	1285	exon20			TGGTCCCCCCGGA		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.1128C>T	2.37:g.228125811C>T		81	0	0		72	31	0.430556	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Silent	SNP	ENST00000396578.3	37	CCDS42829.1																																																																																			.	.	none		0.383	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091		T	228125811	C	T	228125811	2	4	20	1	0	0	0	0	0	0	0	1	3693	610	22	2		2	COL4A3	2	228125811	Silent	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	21108580	228125811	15073562	27	2648											
SLC19A3	80704	hgsc.bcm.edu	37	chr2	228564154	228564154	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaacaacagcagcagccaggTaatgatgaaactgatacctt	17	7	8	9	0	0	3	0	3	0	0	0	3	0	3	2	1	7	3	2	1	5	3			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr2:228564154T>G	ENST00000258403.3	-	3	348	c.277A>C	c.(277-279)Acc>Ccc	p.T93P	SLC19A3_ENST00000409287.1_Intron|SLC19A3_ENST00000541617.1_Missense_Mutation_p.T89P	NM_025243.3	NP_079519.1	Q9BZV2	S19A3_HUMAN	solute carrier family 19 (thiamine transporter), member 3	93					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)	AGCAGCCAGGTAATGATGAAA	0.522																																					p.T93P		Atlas-SNP	.											.	SLC19A3	62	.	0			c.A277C						PASS	.						154	153	153					2																	228564154		2203	4300	6503	SO:0001583	missense	80704	exon3			GCCAGGTAATGAT	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.277A>C	2.37:g.228564154T>G	ENSP00000258403:p.Thr93Pro	97	0	0		101	44	0.435644	NM_025243		Missense_Mutation	SNP	ENST00000258403.3	37	CCDS2468.1	.	.	.	.	.	.	.	.	.	.	T	18.69	3.678458	0.68042	.	.	ENSG00000135917	ENST00000258403;ENST00000541617;ENST00000456524	T;T;T	0.80909	-1.43;-1.43;0.3	5.91	2.01	0.26516	Major facilitator superfamily domain, general substrate transporter (1);	0.282882	0.44483	D	0.000455	D	0.89553	0.6748	M	0.89904	3.07	0.42819	D	0.99398	P;D	0.64830	0.915;0.994	P;D	0.69142	0.812;0.962	D	0.88648	0.3180	10	0.56958	D	0.05	-16.2265	11.0935	0.48130	0.4754:0.0:0.0:0.5246	.	89;93	F5H2M8;Q9BZV2	.;S19A3_HUMAN	P	93;89;93	ENSP00000258403:T93P;ENSP00000445519:T89P;ENSP00000399001:T93P	ENSP00000258403:T93P	T	-	1	0	SLC19A3	228272398	0.421000	0.25465	0.038000	0.18304	0.965000	0.64279	2.170000	0.42443	0.088000	0.17205	0.533000	0.62120	ACC	.	.	none		0.522	SLC19A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256894.1			G	228564154	T	G	228564154	3	3	20	1	0	0	0	0	1	0	0	0	14445	1638	57	5	1229	5	SLC19A3	2	228564154	Missense_Mutation	SNP	T	TCGA-FF-A7CX-01A-12D-A382-10	438343	228564154	14635219	28	2649											
DNER	92737	hgsc.bcm.edu	37	chr2	230312065	230312065	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatttgtagctggtgcccaCgctgcggcacgtgccatgag	6	9	14	12	3	0	1	0	1	0	0	0	1	0	1	2	2	4	5	2	2	1	2			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr2:230312065C>T	ENST00000341772.4	-	8	1587	c.1453G>A	c.(1453-1455)Gtg>Atg	p.V485M		NM_139072.3	NP_620711.3	Q8NFT8	DNER_HUMAN	delta/notch-like EGF repeat containing	485	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)		CTGGTGCCCACGCTGCGGCAC	0.552																																					p.V485M		Atlas-SNP	.											.	DNER	129	.	0			c.G1453A						PASS	.						41	38	39					2																	230312065		2202	4299	6501	SO:0001583	missense	92737	exon8			TGCCCACGCTGCG	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.1453G>A	2.37:g.230312065C>T	ENSP00000345229:p.Val485Met	262	0	0		209	111	0.5311	NM_139072	A6NP39|Q53R88|Q53TP7|Q53TQ5|Q8IYT0|Q8TB42|Q9NTF1|Q9UDM2	Missense_Mutation	SNP	ENST00000341772.4	37	CCDS33390.1	.	.	.	.	.	.	.	.	.	.	C	15.51	2.855442	0.51376	.	.	ENSG00000187957	ENST00000341772;ENST00000543700	D	0.87729	-2.29	4.94	2.97	0.34412	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.182021	0.48767	D	0.000169	D	0.84138	0.5406	N	0.16130	0.375	0.47994	D	0.999568	D	0.76494	0.999	D	0.66847	0.947	T	0.81052	-0.1107	10	0.31617	T	0.26	.	8.7086	0.34369	0.0:0.6322:0.2908:0.077	.	485	Q8NFT8	DNER_HUMAN	M	485;203	ENSP00000345229:V485M	ENSP00000345229:V485M	V	-	1	0	DNER	230020309	0.978000	0.34361	0.996000	0.52242	0.924000	0.55760	1.900000	0.39828	1.188000	0.43014	0.655000	0.94253	GTG	.	.	none		0.552	DNER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331902.1	NM_139072		T	230312065	C	T	230312065	3	4	20	1	0	0	0	0	1	0	0	0	4669	536	19	1	784	1	DNER	2	230312065	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	1747911	230312065	12887308	29	2650											
DNAJB3	54578	hgsc.bcm.edu	37	chr2	234652351	234652351	+	Intron	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagccgccctccgcccccGcctcgccatagcggtcatag	5	6	10	20	5	1	0	1	0	0	0	3	0	2	0	7	1	3	1	7	1	2	2			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr2:234652351G>A	ENST00000305139.6	+	2	1000				UGT1A3_ENST00000482026.1_Intron|UGT1A4_ENST00000373409.3_Intron|UGT1A10_ENST00000373445.1_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A1_ENST00000609767.1_Intron|UGT1A6_ENST00000406651.1_Intron|DNAJB3_ENST00000449667.1_RNA|UGT1A9_ENST00000354728.4_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A6_ENST00000373424.1_Intron	NM_001072.3	NP_001063.2	P19224	UD16_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A6						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)	CTCCGCCCCCGCCTCGCCATA	0.627																																					p.A71V		Atlas-SNP	.											.	.	.	.	0			c.C212T						PASS	.						97	108	105					2																	234652351		2007	4180	6187	SO:0001627	intron_variant	414061	exon1			GCCCCCGCCTCGC	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.862-23329G>A	2.37:g.234652351G>A		107	0	0		97	41	0.42268	NM_001001394	A6NKK6|B8K289|Q96TE7	Missense_Mutation	SNP	ENST00000305139.6	37	CCDS2507.1																																																																																			.	.	none		0.627	UGT1A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130988.1	NM_205862		A	234652351	G	A	234652351	1	1	20	0	1	0	0	0	0	0	0	0	4623	1087	38	1		1	DNAJB3	2	234652351	Intron	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	4340286	234652351	8547022	30	2651											
MYD88	4615	hgsc.bcm.edu	37	chr3	38182292	38182292	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctctgatgattacctgcagaGcaaggaatgtgacttccaga	12	10	10	9	0	1	5	0	3	1	2	2	6	2	6	2	1	3	2	2	1	3	2			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr3:38182292G>A	ENST00000495303.1	+	2	417	c.412G>A	c.(412-414)Gca>Aca	p.A138T	MYD88_ENST00000424893.1_Missense_Mutation_p.S198N|MYD88_ENST00000443433.2_Missense_Mutation_p.A183T|MYD88_ENST00000417037.2_Missense_Mutation_p.S251N|MYD88_ENST00000396334.3_Missense_Mutation_p.S243N|MYD88_ENST00000481122.1_3'UTR	NM_001172566.1	NP_001166037.1	Q99836	MYD88_HUMAN	myeloid differentiation primary response 88	0	Intermediate domain. {ECO:0000250}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|cell surface receptor signaling pathway (GO:0007166)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-positive bacterium (GO:0050830)|establishment of endothelial intestinal barrier (GO:0090557)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of apoptotic process (GO:0043066)|negative regulation of growth of symbiont in host (GO:0044130)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-23 production (GO:0032747)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of lymphocyte proliferation (GO:0050671)|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 tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)|response to molecule of fungal origin (GO:0002238)|response to peptidoglycan (GO:0032494)|response to virus (GO:0009615)|signal transduction (GO:0007165)|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)|type I interferon biosynthetic process (GO:0045351)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)	death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|TIR domain binding (GO:0070976)	p.S243N(7)		breast(1)|haematopoietic_and_lymphoid_tissue(226)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	237				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		TACCTGCAGAGCAAGGAATGT	0.552			Mis		ABC-DLBCL																																p.S251N		Atlas-SNP	.		Dom	yes		3	3p22	4615	myeloid differentiation primary response gene (88)		L	MYD88,NS,lymphoid_neoplasm,0,8	MYD88	900	8	7	Substitution - Missense(7)	haematopoietic_and_lymphoid_tissue(7)	c.G752A						PASS	.						175	167	170					3																	38182292		2203	4300	6503	SO:0001583	missense	4615	exon4			TGCAGAGCAAGGA	U84408	CCDS2674.2, CCDS54565.1, CCDS54566.1, CCDS54567.1, CCDS54568.1	3p22	2014-09-17	2012-11-15		ENSG00000172936	ENSG00000172936			7562	protein-coding gene	gene with protein product		602170	"myeloid differentiation primary response gene (88)"			9013863	Standard	NM_002468		Approved		uc003chx.3	Q99836	OTTHUMG00000131083	ENST00000495303.1:c.412G>A	3.37:g.38182292G>A	ENSP00000417848:p.Ala138Thr	130	0	0		124	53	0.427419	NM_001172567	B4DKH8|B4DKU4|B4DQ60|B4DQ72|J3KPU4|J3KQ87|J3KQJ6|P78397|Q53XS7	Missense_Mutation	SNP	ENST00000495303.1	37	CCDS54568.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.3|26.3	4.725497|4.725497	0.89298|0.89298	.|.	.|.	ENSG00000172936|ENSG00000172936	ENST00000495303;ENST00000443433|ENST00000417037;ENST00000396334;ENST00000424893;ENST00000421516;ENST00000415158	.|T;T;T;T	.|0.36878	.|1.23;1.23;1.23;1.23	5.74|5.74	5.74|5.74	0.90152|0.90152	.|Toll/interleukin-1 receptor homology (TIR) domain (4);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.63943|0.63943	0.2554|0.2554	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	P;P|D;D;D	0.45348|0.89917	0.856;0.7|0.999;1.0;0.999	B;B|D;D;D	0.33890|0.97110	0.172;0.172|0.999;0.999;1.0	T|T	0.63466|0.63466	-0.6631|-0.6631	7|9	0.72032|0.54805	D|T	0.01|0.06	-26.8793|-26.8793	19.2995|19.2995	0.94138|0.94138	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	138;183|185;230;219	B4DQ60;B4DQ72|Q99836-2;Q99836;B4E3D6	.;.|.;MYD88_HUMAN;.	T|N	138;183|251;243;198;250;219	.|ENSP00000401399:S251N;ENSP00000379625:S243N;ENSP00000389979:S198N;ENSP00000391753:S250N	ENSP00000390565:A183T|ENSP00000379625:S243N	A|S	+|+	1|2	0|0	MYD88|MYD88	38157296|38157296	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.939000|0.939000	0.58152|0.58152	9.285000|9.285000	0.95894|0.95894	2.884000|2.884000	0.98904|0.98904	0.655000|0.655000	0.94253|0.94253	GCA|AGC	.	.	none		0.552	MYD88-008	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000342700.1	NM_002468		A	38182292	G	A	38182292	3	1	20	1	0	0	0	0	1	0	0	0	10032	971	34	2	766	2	MYD88	3	38182292	Missense_Mutation	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10		38182292	159840138	31	2652											
ZIC1	7545	hgsc.bcm.edu	37	chr3	147128137	147128137	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctgcggccctgggccatCaccatcacccgggccacgtc	5	6	11	19	3	2	0	2	0	0	0	3	0	2	0	5	3	2	1	5	3	0	0			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr3:147128137C>A	ENST00000282928.4	+	1	967	c.238C>A	c.(238-240)Cac>Aac	p.H80N		NM_003412.3	NP_003403.2	Q15915	ZIC1_HUMAN	Zic family member 1	80	Poly-His.				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						CCTGGGCCATCACCATCACCC	0.687																																					p.H80N		Atlas-SNP	.											.	ZIC1	141	.	0			c.C238A						PASS	.						13	16	15					3																	147128137		2147	4278	6425	SO:0001583	missense	7545	exon1			GGCCATCACCATC	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.238C>A	3.37:g.147128137C>A	ENSP00000282928:p.His80Asn	60	0	0		54	14	0.259259	NM_003412	Q2M3N1	Missense_Mutation	SNP	ENST00000282928.4	37	CCDS3136.1	.	.	.	.	.	.	.	.	.	.	C	18.80	3.700350	0.68501	.	.	ENSG00000152977	ENST00000282928	D	0.86497	-2.13	3.51	3.51	0.40186	.	0.000000	0.85682	D	0.000000	D	0.91150	0.7213	L	0.53249	1.67	0.80722	D	1	D	0.61697	0.99	D	0.77004	0.989	D	0.91653	0.5336	10	0.52906	T	0.07	.	15.2119	0.73230	0.0:1.0:0.0:0.0	.	80	Q15915	ZIC1_HUMAN	N	80	ENSP00000282928:H80N	ENSP00000282928:H80N	H	+	1	0	ZIC1	148610827	1.000000	0.71417	0.999000	0.59377	0.946000	0.59487	5.752000	0.68728	1.806000	0.52798	0.442000	0.29010	CAC	.	.	none		0.687	ZIC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355497.1	NM_003412		A	147128137	C	A	147128137	3	1	20	1	0	0	0	0	1	0	0	0	17693	826	29	4	240	4	ZIC1	3	147128137	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	108945845	147128137	50894293	32	2653											
GHSR	2693	hgsc.bcm.edu	37	chr3	172163205	172163205	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatttggaaaataaatatcGccctacgtggaaggggagcc	13	8	13	7	2	0	0	0	0	0	0	1	4	0	4	2	5	2	0	2	5	7	4	rs148371213		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr3:172163205G>A	ENST00000241256.2	-	2	889	c.847C>T	c.(847-849)Cga>Tga	p.R283*		NM_198407.2	NP_940799.1	Q92847	GHSR_HUMAN	growth hormone secretagogue receptor	283					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)			AATAAATATCGCCCTACGTGG	0.488																																					p.R283X	Esophageal Squamous(93;641 1401 20883 29581 34638)	Atlas-SNP	.											.	GHSR	104	.	0			c.C847T						PASS	.	G	stop/ARG	0,4406		0,0,2203	63	64	64		847	3.8	0.9	3	dbSNP_134	64	2,8598	2.2+/-6.3	0,2,4298	yes	stop-gained	GHSR	NM_198407.2		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		283/367	172163205	2,13004	2203	4300	6503	SO:0001587	stop_gained	2693	exon2			AATATCGCCCTAC	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.847C>T	3.37:g.172163205G>A	ENSP00000241256:p.Arg283*	85	0	0		84	41	0.488095	NM_198407	Q14D12|Q6ISR8|Q92848|Q96RJ7	Nonsense_Mutation	SNP	ENST00000241256.2	37	CCDS3218.1	.	.	.	.	.	.	.	.	.	.	G	33	5.290630	0.95546	0.0	2.33E-4	ENSG00000121853	ENST00000241256	.	.	.	5.64	3.76	0.43208	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.2887	14.1574	0.65426	0.0:0.0:0.6792:0.3208	.	.	.	.	X	283	.	ENSP00000241256:R283X	R	-	1	2	GHSR	173645899	1.000000	0.71417	0.886000	0.34754	0.789000	0.44602	3.165000	0.50778	0.843000	0.35070	0.650000	0.86243	CGA	G|1.000;A|0.000	0.000	weak		0.488	GHSR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346728.1	NM_004122		A	172163205	G	A	172163205	4	1	20	1	0	0	0	0	0	1	0	0	6383	1095	38	1	257	1	GHSR	3	172163205	Nonsense_Mutation	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	25035068	172163205	25859225	33	2654											
KCTD8	386617	hgsc.bcm.edu	37	chr4	44450163	44450163	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcgcgcagcagccgctccttCtcggggaagtgctccggcag	5	7	14	15	5	1	0	0	0	1	0	5	1	3	1	3	3	3	5	3	3	1	1			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr4:44450163C>T	ENST00000360029.3	-	1	661	c.378G>A	c.(376-378)gaG>gaA	p.E126E	AC131951.1_ENST00000584757.1_RNA	NM_198353.2	NP_938167.1	Q6ZWB6	KCTD8_HUMAN	potassium channel tetramerization domain containing 8	126					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						GCCGCTCCTTCTCGGGGAAGT	0.617										HNSCC(17;0.042)																											p.E126E		Atlas-SNP	.											.	KCTD8	96	.	0			c.G378A						PASS	.						23	22	23					4																	44450163		2170	4255	6425	SO:0001819	synonymous_variant	386617	exon1			CTCCTTCTCGGGG	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.378G>A	4.37:g.44450163C>T		81	0	0		67	36	0.537313	NM_198353	A2RU39	Silent	SNP	ENST00000360029.3	37	CCDS3467.1																																																																																			.	.	none		0.617	KCTD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216868.1			T	44450163	C	T	44450163	2	4	20	1	0	0	0	0	0	0	0	1	8124	912	32	2		2	KCTD8	4	44450163	Silent	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10		44450163	146704113	34	2655											
EPHA5	2044	hgsc.bcm.edu	37	chr4	66356412	66356412	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	taacatttgagatggcattcCgaggagcagaggggggtcct	10	9	15	7	1	0	2	0	1	0	2	2	5	2	3	2	5	2	2	2	5	1	3			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr4:66356412C>T	ENST00000273854.3	-	5	1685	c.1085G>A	c.(1084-1086)cGg>cAg	p.R362Q	EPHA5_ENST00000432638.2_Intron|EPHA5_ENST00000511294.1_Missense_Mutation_p.R362Q|EPHA5_ENST00000354839.4_Missense_Mutation_p.R362Q	NM_001281765.1|NM_004439.5	NP_001268694.1|NP_004430.4	P54756	EPHA5_HUMAN	EPH receptor A5	362	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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						GATGGCATTCCGAGGAGCAGA	0.398										TSP Lung(17;0.13)																											p.R362Q		Atlas-SNP	.											.	EPHA5	315	.	0			c.G1085A						PASS	.						45	44	44					4																	66356412		2203	4300	6503	SO:0001583	missense	2044	exon5			GCATTCCGAGGAG	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.1085G>A	4.37:g.66356412C>T	ENSP00000273854:p.Arg362Gln	146	0	0		120	55	0.458333	NM_004439	Q7Z3F2	Missense_Mutation	SNP	ENST00000273854.3	37	CCDS3513.1	.	.	.	.	.	.	.	.	.	.	C	14.15	2.450707	0.43531	.	.	ENSG00000145242	ENST00000273854;ENST00000354839;ENST00000511294	T;T;T	0.57273	0.41;0.41;0.41	5.86	5.86	0.93980	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.53938	D	0.000052	T	0.68155	0.2970	L	0.53780	1.695	0.53688	D	0.999976	D;P;D;P	0.76494	0.999;0.659;0.998;0.568	D;B;D;B	0.67382	0.951;0.153;0.918;0.024	T	0.60352	-0.7280	10	0.26408	T	0.33	.	20.1859	0.98214	0.0:1.0:0.0:0.0	.	362;362;362;362	B7ZKW7;B7ZKJ3;P54756-2;P54756	.;.;.;EPHA5_HUMAN	Q	362	ENSP00000273854:R362Q;ENSP00000346899:R362Q;ENSP00000427638:R362Q	ENSP00000273854:R362Q	R	-	2	0	EPHA5	66039007	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.058000	0.57463	2.777000	0.95525	0.591000	0.81541	CGG	.	.	none		0.398	EPHA5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251388.2	NM_004439		T	66356412	C	T	66356412	3	4	20	1	0	0	0	0	1	0	0	0	5172	652	23	1	2084	1	EPHA5	4	66356412	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	21906249	66356412	124797864	35	2656											
THAP6	152815	hgsc.bcm.edu	37	chr4	76452235	76452235	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaattagatcatgtgatcggCgagctagaggatacaaagga	16	8	12	5	2	1	3	1	1	0	2	2	6	1	5	0	3	2	1	0	3	5	3			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr4:76452235C>T	ENST00000311638.3	+	5	548	c.480C>T	c.(478-480)ggC>ggT	p.G160G	THAP6_ENST00000507557.1_Intron|THAP6_ENST00000380837.3_Silent_p.G118G|THAP6_ENST00000507885.1_Intron|THAP6_ENST00000507556.1_Intron|THAP6_ENST00000504190.1_Intron|THAP6_ENST00000514480.1_Silent_p.G160G|THAP6_ENST00000502620.1_Intron	NM_144721.4	NP_653322.1	Q8TBB0	THAP6_HUMAN	THAP domain containing 6	160						microtubule cytoskeleton (GO:0015630)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			lung(5)	5			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			ATGTGATCGGCGAGCTAGAGG	0.353																																					p.G160G		Atlas-SNP	.											THAP6,NS,carcinoma,0,1	THAP6	14	1	0			c.C480T						PASS	.						70	70	70					4																	76452235		2203	4300	6503	SO:0001819	synonymous_variant	152815	exon5			GATCGGCGAGCTA	BC022989	CCDS3568.1	4q21.21	2013-01-25			ENSG00000174796	ENSG00000174796		"THAP (C2CH-type zinc finger) domain containing"	23189	protein-coding gene	gene with protein product		612535				12575992	Standard	NM_144721		Approved	MGC30052	uc003him.3	Q8TBB0	OTTHUMG00000130108	ENST00000311638.3:c.480C>T	4.37:g.76452235C>T		207	0	0		225	95	0.422222	NM_144721	B4E146|Q5HYJ7|Q5JPC6	Silent	SNP	ENST00000311638.3	37	CCDS3568.1																																																																																			.	.	none		0.353	THAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252414.1	NM_144721		T	76452235	C	T	76452235	2	4	20	1	0	0	0	0	0	0	0	1	15863	755	27	1		1	THAP6	4	76452235	Silent	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	10095823	76452235	114702041	36	2657											
PRDM9	56979	hgsc.bcm.edu	37	chr5	23526712	23526712	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaacaggccagaaagtgaaTccagggaacacaggcaaatt	18	4	11	8	0	0	3	0	1	0	2	1	4	1	4	2	3	2	1	2	3	5	1			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr5:23526712T>C	ENST00000296682.3	+	11	1697	c.1515T>C	c.(1513-1515)aaT>aaC	p.N505N		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	505					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						AGAAAGTGAATCCAGGGAACA	0.438										HNSCC(3;0.000094)																											p.N505N		Atlas-SNP	.											.	PRDM9	344	.	0			c.T1515C						PASS	.						78	76	77					5																	23526712		1987	4170	6157	SO:0001819	synonymous_variant	56979	exon11			AGTGAATCCAGGG	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.1515T>C	5.37:g.23526712T>C		98	0	0		85	45	0.529412	NM_020227	B4DX22|Q27Q50	Silent	SNP	ENST00000296682.3	37	CCDS43307.1																																																																																			.	.	none		0.438	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		C	23526712	T	C	23526712	2	2	20	1	0	0	0	0	0	0	0	1	12475	1432	50	3		3	PRDM9	5	23526712	Silent	SNP	T	TCGA-FF-A7CX-01A-12D-A382-10		23526712	157388548	37	2658											
SLCO6A1	133482	hgsc.bcm.edu	37	chr5	101834271	101834271	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cacagcaggtgctgactaagCagcccaaaccacagggctgc	12	4	11	14	0	0	1	0	1	0	0	0	1	0	1	2	2	6	4	2	2	2	1			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr5:101834271C>T	ENST00000506729.1	-	1	449	c.278G>A	c.(277-279)tGc>tAc	p.C93Y	RP11-58B2.1_ENST00000502494.1_RNA|SLCO6A1_ENST00000513675.1_Missense_Mutation_p.C93Y|SLCO6A1_ENST00000389019.3_Missense_Mutation_p.C93Y|SLCO6A1_ENST00000379810.1_Missense_Mutation_p.C93Y|SLCO6A1_ENST00000514551.1_5'UTR|SLCO6A1_ENST00000379807.3_Missense_Mutation_p.C93Y			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	93	Cys-rich.					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)		GCTGACTAAGCAGCCCAAACC	0.502																																					p.C93Y		Atlas-SNP	.											.	SLCO6A1	153	.	0			c.G278A						PASS	.						105	107	106					5																	101834271		2203	4300	6503	SO:0001583	missense	133482	exon1			ACTAAGCAGCCCA	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.278G>A	5.37:g.101834271C>T	ENSP00000421339:p.Cys93Tyr	121	0	0		125	49	0.392	NM_173488	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Missense_Mutation	SNP	ENST00000506729.1	37	CCDS34206.1	.	.	.	.	.	.	.	.	.	.	C	12.22	1.871154	0.33069	.	.	ENSG00000205359	ENST00000506729;ENST00000379807;ENST00000389019;ENST00000513675;ENST00000379810	T;T;T;T;T	0.47177	0.91;0.91;0.93;0.85;0.85	3.52	2.6	0.31112	.	0.609562	0.14883	N	0.292850	T	0.49115	0.1538	L	0.32530	0.975	0.09310	N	1	D;D;D	0.89917	0.998;1.0;0.996	P;D;P	0.68192	0.904;0.956;0.804	T	0.33650	-0.9860	10	0.11794	T	0.64	.	8.6	0.33738	0.0:0.7635:0.2365:0.0	.	93;93;93	Q86UG4-2;C9J020;Q86UG4	.;.;SO6A1_HUMAN	Y	93	ENSP00000421339:C93Y;ENSP00000369135:C93Y;ENSP00000373671:C93Y;ENSP00000421990:C93Y;ENSP00000369138:C93Y	ENSP00000369135:C93Y	C	-	2	0	SLCO6A1	101862170	0.002000	0.14202	0.007000	0.13788	0.004000	0.04260	0.712000	0.25779	0.994000	0.38892	0.484000	0.47621	TGC	.	.	none		0.502	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488		T	101834271	C	T	101834271	3	4	20	1	0	0	0	0	1	0	0	0	14747	710	25	2	1933	2	SLCO6A1	5	101834271	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	78307559	101834271	79080989	38	2659											
PCDHA3	56145	hgsc.bcm.edu	37	chr5	140180941	140180941	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cgcatcgcgcaggacctgggGctggagctggcggagctggt	5	6	19	11	4	0	0	0	0	0	0	1	3	0	3	1	7	2	5	1	7	0	0	rs201478898	byFrequency	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr5:140180941G>A	ENST00000522353.2	+	1	159	c.159G>A	c.(157-159)ggG>ggA	p.G53G	PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000520672.2_Intron|PCDHA3_ENST00000532566.2_Silent_p.G53G|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	53	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)			AGGACCTGGGGCTGGAGCTGG	0.637																																					p.G53G		Atlas-SNP	.											PCDHA3_ENST00000522353,NS,haematopoietic_neoplasm,0,2	PCDHA3	396	2	0			c.G159A						scavenged	.																																			SO:0001819	synonymous_variant	56145	exon1			CCTGGGGCTGGAG	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.159G>A	5.37:g.140180941G>A		82	2	0.0243902		102	13	0.127451	NM_031497	O75286	Silent	SNP	ENST00000522353.2	37	CCDS54915.1																																																																																			G|0.926;A|0.074	0.074	strong		0.637	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906		A	140180941	G	A	140180941	2	1	20	1	0	0	0	0	0	0	0	1	11534	1190	42	2		2	PCDHA3	5	140180941	Silent	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	38346670	140180941	40734319	39	2660											
PCDH1	5097	hgsc.bcm.edu	37	chr5	141243763	141243763	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggggcagtgatatagggtgcGttgtcattctcgtccagcac	7	11	14	9	2	2	1	1	1	1	0	4	1	3	1	1	3	2	3	1	3	2	4	rs374090402		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr5:141243763G>C	ENST00000394536.3	-	3	2272	c.2133C>G	c.(2131-2133)aaC>aaG	p.N711K	PCDH1_ENST00000456271.1_Missense_Mutation_p.N699K|PCDH1_ENST00000287008.3_Missense_Mutation_p.N711K|PCDH1_ENST00000511044.1_5'UTR|PCDH1_ENST00000536585.1_Missense_Mutation_p.N689K|PCDH1_ENST00000503492.1_Intron	NM_001278613.1|NM_001278615.1	NP_001265542.1|NP_001265544.1	Q08174	PCDH1_HUMAN	protocadherin 1	711	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)		TATAGGGTGCGTTGTCATTCT	0.567																																					p.N711K	Ovarian(132;1609 1739 4190 14731 45037)	Atlas-SNP	.											.	PCDH1	119	.	0			c.C2133G						PASS	.						146	130	135					5																	141243763		2203	4300	6503	SO:0001583	missense	5097	exon3			GGGTGCGTTGTCA	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.2133C>G	5.37:g.141243763G>C	ENSP00000378043:p.Asn711Lys	85	0	0		60	17	0.283333	NM_032420	Q8IUP2	Missense_Mutation	SNP	ENST00000394536.3	37	CCDS43375.1	.	.	.	.	.	.	.	.	.	.	g	7.871	0.728137	0.15507	.	.	ENSG00000156453	ENST00000287008;ENST00000394536;ENST00000456271;ENST00000357517;ENST00000536585	T;T;T;T;T	0.31247	1.5;4.66;4.66;4.66;4.66	5.25	-8.9	0.00782	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	0.000000	0.53938	D	0.000057	T	0.61135	0.2323	H	0.95437	3.67	0.44469	D	0.997404	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.81540	-0.0886	10	0.87932	D	0	.	18.2689	0.90062	0.3802:0.0:0.6198:0.0	.	711;711	Q08174;Q08174-2	PCDH1_HUMAN;.	K	711;711;699;722;689	ENSP00000287008:N711K;ENSP00000378043:N711K;ENSP00000403497:N699K;ENSP00000350122:N722K;ENSP00000438825:N689K	ENSP00000287008:N711K	N	-	3	2	PCDH1	141223947	0.000000	0.05858	0.098000	0.21074	0.327000	0.28475	-1.247000	0.02893	-2.573000	0.00466	-1.884000	0.00543	AAC	.	.	alt		0.567	PCDH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251862.1	NM_032420		C	141243763	G	C	141243763	3	2	20	1	0	0	0	0	1	0	0	0	11515	1136	40	4	1676	4	PCDH1	5	141243763	Missense_Mutation	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	1062822	141243763	39671497	40	2661											
CSNK1A1	1452	hgsc.bcm.edu	37	chr5	148930448	148930448	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ccaaatagatgtccccgaagGagccagacccgatcttccgt	11	7	9	14	3	1	2	0	0	1	2	3	5	3	3	6	1	1	0	6	1	3	2			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr5:148930448G>C	ENST00000377843.2	-	1	559	c.80C>G	c.(79-81)tCc>tGc	p.S27C	CSNK1A1_ENST00000515748.2_Missense_Mutation_p.S27C|CSNK1A1_ENST00000515768.1_Missense_Mutation_p.S27C|CSNK1A1_ENST00000515435.1_5'Flank|CSNK1A1_ENST00000504676.1_5'Flank|CSNK1A1_ENST00000261798.5_Missense_Mutation_p.S27C	NM_001025105.1|NM_001892.4	NP_001020276.1|NP_001883.4	P48729	KC1A_HUMAN	casein kinase 1, alpha 1	27	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)		GTCCCCGAAGGAGCCAGACCC	0.537																																					p.S27C	Colon(5;64 69 1309 10383)	Atlas-SNP	.											.	CSNK1A1	63	.	0			c.C80G						PASS	.						101	112	109					5																	148930448		2152	4284	6436	SO:0001583	missense	1452	exon1			CCGAAGGAGCCAG	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.80C>G	5.37:g.148930448G>C	ENSP00000367074:p.Ser27Cys	106	0	0		95	90	0.947368	NM_001025105	D3DQG0|D3DQG1|Q4JJA0|Q5U046|Q5U047|Q6FGA2|Q71TU5|Q96HD2|Q9UDK3	Missense_Mutation	SNP	ENST00000377843.2	37	CCDS47303.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.668650	0.88348	.	.	ENSG00000113712	ENST00000261798;ENST00000377843;ENST00000322237;ENST00000515768;ENST00000515748	T;T;T;T	0.23754	1.89;1.89;1.89;1.89	5.08	5.08	0.68730	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	U	0.000000	T	0.68531	0.3011	H	0.99312	4.51	0.80722	D	1	D;D;D	0.62365	0.989;0.974;0.991	P;P;P	0.61397	0.888;0.749;0.877	D	0.83643	0.0151	10	0.87932	D	0	.	18.6698	0.91507	0.0:0.0:1.0:0.0	.	27;27;27	Q71TU5;P48729;P48729-2	.;KC1A_HUMAN;.	C	27	ENSP00000261798:S27C;ENSP00000367074:S27C;ENSP00000421689:S27C;ENSP00000421268:S27C	ENSP00000261798:S27C	S	-	2	0	CSNK1A1	148910641	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.596000	0.82721	2.634000	0.89283	0.561000	0.74099	TCC	.	.	none		0.537	CSNK1A1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001892		C	148930448	G	C	148930448	3	2	20	1	0	0	0	0	1	0	0	0	3952	1174	41	4	1061	4	CSNK1A1	5	148930448	Missense_Mutation	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	7686685	148930448	31984812	41	2662											
ZNF454	285676	hgsc.bcm.edu	37	chr5	178391738	178391738	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttggatcaatggacaataaaGgaaagattcagtagcagtag	17	9	11	4	0	2	1	2	0	0	1	2	4	2	4	0	3	1	3	0	3	7	5			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr5:178391738G>T	ENST00000320129.3	+	5	636	c.333G>T	c.(331-333)aaG>aaT	p.K111N	ZNF454_ENST00000519564.1_Missense_Mutation_p.K111N	NM_001178090.1|NM_182594.2	NP_001171561.1|NP_872400.2	Q8N9F8	ZN454_HUMAN	zinc finger protein 454	111					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(2)|large_intestine(11)|lung(18)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	46	all_cancers(89;0.000904)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.225)|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;0.234)		GGACAATAAAGGAAAGATTCA	0.453																																					p.K111N		Atlas-SNP	.											.	ZNF454	99	.	0			c.G333T						PASS	.						66	65	66					5																	178391738		2203	4300	6503	SO:0001583	missense	285676	exon5			AATAAAGGAAAGA	AK094763	CCDS4441.1	5q35.3	2013-01-08			ENSG00000178187	ENSG00000178187		"Zinc fingers, C2H2-type", "-"	21200	protein-coding gene	gene with protein product							Standard	NM_182594		Approved	FLJ37444	uc021yjc.1	Q8N9F8	OTTHUMG00000130891	ENST00000320129.3:c.333G>T	5.37:g.178391738G>T	ENSP00000326249:p.Lys111Asn	173	0	0		160	151	0.94375	NM_001178089	Q2M1P2|Q2M323	Missense_Mutation	SNP	ENST00000320129.3	37	CCDS4441.1	.	.	.	.	.	.	.	.	.	.	G	8.312	0.822243	0.16678	.	.	ENSG00000178187	ENST00000320129;ENST00000519564	T;T	0.08008	3.14;3.14	4.94	4.08	0.47627	.	0.376195	0.19376	N	0.115794	T	0.04318	0.0119	N	0.08118	0	0.09310	N	0.999996	P	0.37781	0.608	B	0.37943	0.261	T	0.41858	-0.9485	10	0.18710	T	0.47	-13.6803	8.7625	0.34683	0.101:0.0:0.899:0.0	.	111	Q8N9F8	ZN454_HUMAN	N	111	ENSP00000326249:K111N;ENSP00000430354:K111N	ENSP00000326249:K111N	K	+	3	2	ZNF454	178324344	0.074000	0.21230	0.230000	0.23976	0.066000	0.16364	0.745000	0.26259	1.304000	0.44892	0.650000	0.86243	AAG	.	.	none		0.453	ZNF454-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253476.2	XM_209718		T	178391738	G	T	178391738	3	4	20	1	0	0	0	0	1	0	0	0	17938	991	35	4	347	4	ZNF454	5	178391738	Missense_Mutation	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	29461290	178391738	2523522	42	2663											
HIST1H3B	8358	hgsc.bcm.edu	37	chr6	26031883	26031883	+	Frame_Shift_Del	DEL	C	C	-																															aaagtgactttacatttacgCtctttctccgcgaatgcggc																										TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr6:26031883delC	ENST00000244661.2	-	1	405	c.406delG	c.(406-408)gcgfs	p.A136fs		NM_003537.3	NP_003528.1	P68431	H31_HUMAN	histone cluster 1, H3b	136					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						TACATTTACGCTCTTTCTCCG	0.448																																					p.A136fs		Pindel,Atlas-Indel	.											HIST1H3B,NS,lymphoid_neoplasm,-1,3	HIST1H3B	59	3	0			c.407delC						PASS	.						55	59	57					6																	26031883		2203	4300	6503	SO:0001589	frameshift_variant	8358	exon1			.	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.406delG	6.37:g.26031883delC	ENSP00000244661:p.Ala136fs	85	0	.		95	35	0.368	NM_003537	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Frame_Shift_Del	DEL	ENST00000244661.2	37	CCDS4573.1																																																																																			.	.	none		0.448	HIST1H3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040077.1	NM_003537		-	26031883	C	-	26031883	7	5	20	1	0	1	0	1	0	0	0	0	7165	797	28	0	8	0	HIST1H3B	6	26031883	Frame_Shift_Del	DEL	C	TCGA-FF-A7CX-01A-12D-A382-10		26031883	145083184	43	2664											
PRSS16	10279	hgsc.bcm.edu	37	chr6	27219672	27219672	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caggcggagctgttgggggcGctgcaggcactggtgggagg	5	6	22	8	2	0	0	0	0	0	0	0	2	0	2	0	8	2	5	0	8	0	1			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr6:27219672G>A	ENST00000230582.3	+	8	876	c.861G>A	c.(859-861)gcG>gcA	p.A287A	PRSS16_ENST00000377456.2_3'UTR|PRSS16_ENST00000421826.2_Intron	NM_005865.3	NP_005856.1	Q9NQE7	TSSP_HUMAN	protease, serine, 16 (thymus)	287					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						TGTTGGGGGCGCTGCAGGCAC	0.701																																					p.A287A	NSCLC(178;1118 2105 17078 23587 44429)	Atlas-SNP	.											.	PRSS16	66	.	0			c.G861A						PASS	.						15	18	17					6																	27219672		2176	4276	6452	SO:0001819	synonymous_variant	10279	exon8			GGGGGCGCTGCAG	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.861G>A	6.37:g.27219672G>A		132	0	0		142	63	0.443662	NM_005865	O75416	Silent	SNP	ENST00000230582.3	37	CCDS4623.1																																																																																			.	.	none		0.701	PRSS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043418.2			A	27219672	G	A	27219672	2	1	20	1	0	0	0	0	0	0	0	1	12628	1074	38	1		1	PRSS16	6	27219672	Silent	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	1187789	27219672	143895395	44	2665											
GABBR1	2550	hgsc.bcm.edu	37	chr6	29578720	29578720	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccaatccatttatctgttttGgaccaggaaagatcatcctt	11	14	6	10	0	2	1	1	0	1	1	4	3	4	3	4	2	0	1	4	2	3	5			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr6:29578720G>T	ENST00000377034.4	-	14	2024	c.1689C>A	c.(1687-1689)tcC>tcA	p.S563S	GABBR1_ENST00000377012.4_Silent_p.S446S|GABBR1_ENST00000377016.4_Silent_p.S501S|GABBR1_ENST00000355973.3_Silent_p.S446S|GABBR1_ENST00000376977.3_Silent_p.S563S	NM_001470.2	NP_001461.1	Q9UBS5	GABR1_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 1	563					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)	TATCTGTTTTGGACCAGGAAA	0.458																																					p.S563S		Atlas-SNP	.											.	GABBR1	95	.	0			c.C1689A						PASS	.						190	151	165					6																	29578720		1511	2709	4220	SO:0001819	synonymous_variant	2550	exon14			TGTTTTGGACCAG	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.1689C>A	6.37:g.29578720G>T		90	0	0		84	11	0.130952	NM_001470	B0UXY7|O95375|O95468|O95975|O96022|Q5STL4|Q5SUJ8|Q5SUL3|Q71SG6|Q86W60|Q9UQQ0	Silent	SNP	ENST00000377034.4	37	CCDS4663.1																																																																																			.	.	none		0.458	GABBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076141.3			T	29578720	G	T	29578720	2	4	20	1	0	0	0	0	0	0	0	1	6163	1335	47	4		4	GABBR1	6	29578720	Silent	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	2359048	29578720	141536347	45	2666											
MUC21	394263	hgsc.bcm.edu	37	chr6	30954870	30954870	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccaccaactctgagtccagTacgacctccagtggggccaa	10	6	10	15	1	1	1	0	1	1	0	3	2	3	1	6	2	2	1	6	2	3	1	rs9262377		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr6:30954870T>C	ENST00000376296.3	+	2	1159	c.918T>C	c.(916-918)agT>agC	p.S306S	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	306	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						CTGAGTCCAGTACGACCTCCA	0.597																																					p.S306S		Atlas-SNP	.											MUC21,rectum,carcinoma,0,1	MUC21	98	1	0			c.T918C						scavenged	.						171	164	167					6																	30954870		2203	4300	6503	SO:0001819	synonymous_variant	394263	exon2			GTCCAGTACGACC	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.918T>C	6.37:g.30954870T>C		30	1	0.0333333		45	5	0.111111	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																			.	.	weak		0.597	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909		C	30954870	T	C	30954870	2	2	20	1	0	0	0	0	0	0	0	1	9986	1635	57	3		3	MUC21	6	30954870	Silent	SNP	T	TCGA-FF-A7CX-01A-12D-A382-10	1376150	30954870	140160197	46	2667											
ANKS1A	23294	hgsc.bcm.edu	37	chr6	34957033	34957033	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacctccagcaaagccaccGcccgatgaagaggaagaaga	15	2	10	14	2	0	4	0	1	0	3	1	6	1	5	6	1	2	1	6	1	4	0			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr6:34957033G>A	ENST00000360359.3	+	9	1380	c.1242G>A	c.(1240-1242)ccG>ccA	p.P414P	ANKS1A_ENST00000535627.1_Intron	NM_015245.2	NP_056060.2	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1A	414					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)		p.P414P(1)		cervix(2)|endometrium(3)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						CAAAGCCACCGCCCGATGAAG	0.413																																					p.P414P		Atlas-SNP	.											ANKS1A,NS,carcinoma,0,1	ANKS1A	123	1	1	Substitution - coding silent(1)	lung(1)	c.G1242A						PASS	.						163	160	161					6																	34957033		2203	4300	6503	SO:0001819	synonymous_variant	23294	exon9			GCCACCGCCCGAT	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.1242G>A	6.37:g.34957033G>A		152	0	0		142	67	0.471831	NM_015245	A2RUC1|B4DQW8|Q5JYI9|Q5SYR2|Q86WQ7	Silent	SNP	ENST00000360359.3	37	CCDS4798.1																																																																																			.	.	none		0.413	ANKS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040262.1	XM_166478		A	34957033	G	A	34957033	2	1	20	1	0	0	0	0	0	0	0	1	688	1074	38	1		1	ANKS1A	6	34957033	Silent	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	4002163	34957033	136158034	47	2668											
TFAP2B	7021	hgsc.bcm.edu	37	chr6	50791293	50791293	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	taccaccagagccaggacccCtactcccacgtcaacgaccc	11	4	6	20	2	1	1	1	0	0	1	2	3	2	2	7	1	4	0	7	1	3	2			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr6:50791293C>A	ENST00000393655.3	+	2	424	c.255C>A	c.(253-255)ccC>ccA	p.P85P	TFAP2B_ENST00000489228.1_3'UTR|TFAP2B_ENST00000263046.4_Silent_p.P94P	NM_003221.3	NP_003212.2	Q92481	AP2B_HUMAN	transcription factor AP-2 beta (activating enhancer binding protein 2 beta)	85	Gln/Pro-rich (transactivation domain).				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)					GCCAGGACCCCTACTCCCACG	0.687																																					p.P85P	Pancreas(116;1373 2332 5475 10752)	Atlas-SNP	.											.	TFAP2B	91	.	0			c.C255A						PASS	.						65	71	69					6																	50791293		2203	4300	6503	SO:0001819	synonymous_variant	7021	exon2			GGACCCCTACTCC	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.255C>A	6.37:g.50791293C>A		160	0	0		121	56	0.46281	NM_003221	Q5JYX6|Q9NQ63|Q9NU99|Q9UJI7|Q9Y214|Q9Y3K3	Silent	SNP	ENST00000393655.3	37	CCDS4934.2																																																																																			.	.	none		0.687	TFAP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040886.3	NM_003221		A	50791293	C	A	50791293	2	1	20	1	0	0	0	0	0	0	0	1	15803	668	24	4		4	TFAP2B	6	50791293	Silent	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	15834260	50791293	120323774	48	2669											
CCNC	892	hgsc.bcm.edu	37	chr6	99998133	99998133	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcttcttggcccatgtccTgcacatactggagcaaaggt	8	12	10	11	0	2	0	0	0	2	0	3	1	3	1	2	3	3	2	2	3	2	3			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr6:99998133T>G	ENST00000520429.1	-	8	936	c.491A>C	c.(490-492)cAg>cCg	p.Q164P	CCNC_ENST00000518714.1_Missense_Mutation_p.Q164P|CCNC_ENST00000369220.4_Missense_Mutation_p.Q164P|CCNC_ENST00000521017.1_5'Flank|CCNC_ENST00000523985.1_Missense_Mutation_p.Q79P|CCNC_ENST00000523799.1_Missense_Mutation_p.Q79P|CCNC_ENST00000520371.1_Missense_Mutation_p.Q164P	NM_001013399.1|NM_005190.3	NP_001013417.1|NP_005181.2	P24863	CCNC_HUMAN	cyclin C	164					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)		GCCCATGTCCTGCACATACTG	0.338																																					p.Q164P	GBM(57;273 1020 40094 44454 49348)	Atlas-SNP	.											.	CCNC	23	.	0			c.A491C						PASS	.						141	118	126					6																	99998133		2203	4300	6503	SO:0001583	missense	892	exon8			ATGTCCTGCACAT		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.491A>C	6.37:g.99998133T>G	ENSP00000428982:p.Gln164Pro	155	0	0		83	67	0.807229	NM_005190	B4DPZ1|Q9H543	Missense_Mutation	SNP	ENST00000520429.1	37	CCDS34502.1	.	.	.	.	.	.	.	.	.	.	T	18.61	3.661964	0.67700	.	.	ENSG00000112237	ENST00000520429;ENST00000369220;ENST00000520371;ENST00000523799;ENST00000486428;ENST00000523985;ENST00000518714;ENST00000524049	T;T;T;T;T;T;T;T	0.33654	1.84;1.83;1.83;1.42;1.4;1.42;1.83;1.44	5.63	5.63	0.86233	Cyclin-like (3);	0.000000	0.85682	D	0.000000	T	0.24470	0.0593	M	0.71920	2.185	0.80722	D	1	P;P	0.36171	0.541;0.541	B;B	0.30029	0.11;0.11	T	0.07481	-1.0770	9	.	.	.	-5.2956	16.1988	0.82053	0.0:0.0:0.0:1.0	.	164;164	Q7Z4L3;P24863	.;CCNC_HUMAN	P	164;164;164;79;110;79;164;79	ENSP00000428982:Q164P;ENSP00000358222:Q164P;ENSP00000430381:Q164P;ENSP00000430014:Q79P;ENSP00000430077:Q110P;ENSP00000430119:Q79P;ENSP00000430294:Q164P;ENSP00000427885:Q79P	.	Q	-	2	0	CCNC	100104854	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.994000	0.88315	2.284000	0.76573	0.529000	0.55759	CAG	.	.	none		0.338	CCNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041613.2	NM_005190		G	99998133	T	G	99998133	3	3	20	1	0	0	0	0	1	0	0	0	2917	1580	55	5	380	5	CCNC	6	99998133	Missense_Mutation	SNP	T	TCGA-FF-A7CX-01A-12D-A382-10	49206840	99998133	71116934	49	2670											
TNFAIP3	7128	hgsc.bcm.edu	37	chr6	138192658	138192659	+	Splice_Site	INS	-	-	GG																															ttgtggcgctgaaaacgaacINSggtaagacttgttctgttgt																								rs146004919		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr6:138192658_138192659insGG	ENST00000237289.4	+	2	360_361	c.294_295insGG	c.(295-297)ggt>GGggt	p.G99fs		NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	99	OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.|TRAF-binding.				apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|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 interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|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 protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)|p.G99fs*2(1)|p.?(1)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		TGAAAACGAACGGTAAGACTTG	0.495			"D, N, F"		"marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"																																p.N98fs	GBM(130;153 1739 22295 28918 47987)	Pindel,Atlas-Indel	.		Rec	yes		6	6q23	7128	"tumor necrosis factor, alpha-induced protein 3"		L	.	TNFAIP3	340	.	27	Whole gene deletion(25)|Insertion - Frameshift(1)|Unknown(1)	haematopoietic_and_lymphoid_tissue(27)	c.294_295insGG						PASS	.																																			SO:0001630	splice_region_variant	7128	exon2			.	M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"OTU domain containing"	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.295+1->GG	6.37:g.138192659_138192660dupGG		46	0	.		18	10	0.556	NM_001270507	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Frame_Shift_Ins	INS	ENST00000237289.4	37	CCDS5187.1																																																																																			.	.	none		0.495	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1		Frame_Shift_Ins	GG	138192659	-	GG	138192658	8	5	20	1	0	1	1	0	0	0	1	0	16289	550	19	0	296	0	TNFAIP3	6	138192658	Splice_Site	INS	-	TCGA-FF-A7CX-01A-12D-A382-10	38194525	138192658	32922409	50	2671											
CARD11	84433	hgsc.bcm.edu	37	chr7	2987283	2987283	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctgctcatcaatgaccttaCactgacgcaggtagggcgtg	9	9	11	12	2	2	2	2	2	0	0	2	2	2	2	2	2	2	3	2	2	3	2			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr7:2987283C>T	ENST00000396946.4	-	3	549	c.146G>A	c.(145-147)tGt>tAt	p.C49Y	AC004906.3_ENST00000423194.1_RNA	NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	49	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				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.C42Y(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)		AATGACCTTACACTGACGCAG	0.527			Mis		DLBCL																																p.C49Y		Atlas-SNP	.		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	CARD11,colon,carcinoma,+1,2	CARD11	339	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G146A						scavenged	.						281	212	236					7																	2987283		2203	4300	6503	SO:0001583	missense	84433	exon3			ACCTTACACTGAC	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.146G>A	7.37:g.2987283C>T	ENSP00000380150:p.Cys49Tyr	200	1	0.005		227	54	0.237885	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	C	27.2	4.807258	0.90623	.	.	ENSG00000198286	ENST00000396946;ENST00000356408	T;T	0.21031	2.03;2.03	5.31	5.31	0.75309	DEATH-like (2);Caspase Recruitment (2);	0.000000	0.85682	D	0.000000	T	0.50633	0.1627	M	0.80183	2.485	0.80722	D	1	D	0.65815	0.995	D	0.69654	0.965	T	0.55704	-0.8099	10	0.87932	D	0	-43.4909	19.0497	0.93038	0.0:1.0:0.0:0.0	.	49	Q9BXL7	CAR11_HUMAN	Y	49	ENSP00000380150:C49Y;ENSP00000348779:C49Y	ENSP00000348779:C49Y	C	-	2	0	CARD11	2953809	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.267000	0.78462	2.516000	0.84829	0.556000	0.70494	TGT	.	.	none		0.527	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		T	2987283	C	T	2987283	3	4	20	1	0	0	0	0	1	0	0	0	2647	478	17	2	3410	2	CARD11	7	2987283	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10		2987283	156151380	51	2672											
HOXA9	3205	hgsc.bcm.edu	37	chr7	27204938	27204938	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cgggctgaagtcggggtgctCggccagcgtcgccgcctgcc	3	6	17	15	6	0	1	0	1	0	0	3	1	0	1	4	4	3	2	4	4	1	0			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr7:27204938C>T	ENST00000343483.6	-	1	211	c.139G>A	c.(139-141)Gag>Aag	p.E47K	HOXA9_ENST00000497089.1_Intron|HOXA9_ENST00000396345.1_Missense_Mutation_p.E47K|RP1-170O19.20_ENST00000470747.4_Intron|RP1-170O19.20_ENST00000465941.1_Intron	NM_152739.3	NP_689952.1	P31269	HXA9_HUMAN	homeobox A9	47					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)			central_nervous_system(1)|endometrium(1)|lung(5)|prostate(1)	8						TCGGGGTGCTCGGCCAGCGTC	0.731			T	"NUP98, MSI2"	AML*																																p.E47K		Atlas-SNP	.		Dom	yes		7	7p15-p14.2	3205	homeo box A9		L	.	HOXA9	20	.	0			c.G139A						PASS	.						8	9	9					7																	27204938		2092	4040	6132	SO:0001583	missense	3205	exon1			GGTGCTCGGCCAG		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.139G>A	7.37:g.27204938C>T	ENSP00000343619:p.Glu47Lys	61	0	0		58	21	0.362069	NM_152739	O43369|O43429|Q99820	Missense_Mutation	SNP	ENST00000343483.6	37	CCDS5409.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.406924	0.83230	.	.	ENSG00000078399	ENST00000343483;ENST00000242050;ENST00000396345	D	0.93811	-3.29	5.46	4.58	0.56647	Hox9, N-terminal activation domain (1);	0.210905	0.32884	N	0.005532	D	0.96380	0.8819	M	0.87097	2.86	0.80722	D	1	D	0.67145	0.996	P	0.61070	0.883	D	0.96715	0.9528	10	0.72032	D	0.01	.	14.1396	0.65311	0.0:0.9275:0.0:0.0725	.	47	P31269	HXA9_HUMAN	K	47;41;47	ENSP00000343619:E47K	ENSP00000242050:E41K	E	-	1	0	HOXA9	27171463	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.325000	0.59234	1.308000	0.44962	0.655000	0.94253	GAG	.	.	none		0.731	HOXA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358706.2			T	27204938	C	T	27204938	3	4	20	1	0	0	0	0	1	0	0	0	7307	893	31	1	687	1	HOXA9	7	27204938	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	24217655	27204938	131933725	52	2673											
TFR2	7036	hgsc.bcm.edu	37	chr7	100226979	100226979	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	catgcatccctctgggccccGatgacaacgtagtgatctgg	8	9	11	13	2	2	2	0	2	2	0	3	3	3	2	3	2	2	2	3	2	2	1			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr7:100226979G>A	ENST00000462107.1	-	11	1574	c.1287C>T	c.(1285-1287)atC>atT	p.I429I	TFR2_ENST00000544242.1_5'UTR|TFR2_ENST00000431692.1_Missense_Mutation_p.R344W|TFR2_ENST00000223051.3_Silent_p.I429I			Q9UP52	TFR2_HUMAN	transferrin receptor 2	429					cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transferrin receptor activity (GO:0004998)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)				Gallium nitrate(DB05260)	TCTGGGCCCCGATGACAACGT	0.612																																					p.I429I		Atlas-SNP	.											.	TFR2	53	.	0			c.C1287T						PASS	.						85	74	77					7																	100226979		2203	4300	6503	SO:0001819	synonymous_variant	7036	exon10			GGCCCCGATGACA	AF053356	CCDS34707.1	7q22	2003-01-27			ENSG00000106327	ENSG00000106327			11762	protein-coding gene	gene with protein product		604720				9799793, 12130528	Standard	NM_003227		Approved	HFE3, TFRC2	uc003uvv.1	Q9UP52	OTTHUMG00000159598	ENST00000462107.1:c.1287C>T	7.37:g.100226979G>A		37	0	0		33	22	0.666667	NM_003227	A6NGM7|O75422|Q1HE13|Q9HA99|Q9NX67	Silent	SNP	ENST00000462107.1	37	CCDS34707.1	.	.	.	.	.	.	.	.	.	.	G	11.43	1.635636	0.29068	.	.	ENSG00000106327	ENST00000431692	T	0.57595	0.39	4.39	-7.68	0.01268	.	.	.	.	.	T	0.48589	0.1508	.	.	.	0.25491	N	0.987645	.	.	.	.	.	.	T	0.59451	-0.7452	6	0.87932	D	0	-13.3063	10.2135	0.43156	0.7308:0.105:0.1641:0.0	.	.	.	.	W	344	ENSP00000413905:R344W	ENSP00000413905:R344W	R	-	1	2	TFR2	100064915	0.002000	0.14202	0.842000	0.33263	0.867000	0.49689	-1.543000	0.02194	-1.638000	0.01529	-0.291000	0.09656	CGG	.	.	none		0.612	TFR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356392.3	NM_003227		A	100226979	G	A	100226979	2	1	20	1	0	0	0	0	0	0	0	1	15826	1048	37	1		1	TFR2	7	100226979	Silent	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	73022041	100226979	58911684	53	2674											
MLL3	58508	hgsc.bcm.edu	37	chr7	151896389	151896389	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gttccagattttgttggagcCgaggatgaactaagtagtgg	10	12	14	5	1	0	2	0	1	0	1	1	5	1	4	2	3	2	3	2	3	3	6	rs200269228		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr7:151896389C>T	ENST00000262189.6	-	27	4466	c.4248G>A	c.(4246-4248)tcG>tcA	p.S1416S	KMT2C_ENST00000355193.2_Silent_p.S1416S	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1416					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)										TTGTTGGAGCCGAGGATGAAC	0.333													C|||	1	0.000199681	0.0008	0.0	5008	,	,		16515	0.0		0.0	False		,,,				2504	0.0				p.S1416S		Atlas-SNP	.											.	MLL3	1564	.	0			c.G4248A						PASS	.						72	71	71					7																	151896389		2203	4300	6503	SO:0001819	synonymous_variant	58508	exon27			TGGAGCCGAGGAT	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.4248G>A	7.37:g.151896389C>T		218	0	0		198	79	0.39899	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Silent	SNP	ENST00000262189.6	37	CCDS5931.1																																																																																			C|1.000;T|0.000	0.000	strong		0.333	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			T	151896389	C	T	151896389	2	4	20	1	0	0	0	0	0	0	0	1	9631	639	23	1		1	MLL3	7	151896389	Silent	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	51669410	151896389	7242274	54	2675											
ARC	23237	hgsc.bcm.edu	37	chr8	143695095	143695095	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgcccgggcagctcgccagCggctgggggcggggtgatgg	3	5	21	12	4	0	1	0	1	0	0	1	1	0	1	2	7	3	3	2	7	0	0			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr8:143695095C>T	ENST00000356613.2	-	1	1738	c.538G>A	c.(538-540)Gct>Act	p.A180T	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)				AGCTCGCCAGCGGCTGGGGGC	0.736																																					p.A180T		Atlas-SNP	.											.	ARC	34	.	0			c.G538A						PASS	.						4	7	6					8																	143695095		1831	3772	5603	SO:0001583	missense	23237	exon1			CGCCAGCGGCTGG	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.538G>A	8.37:g.143695095C>T	ENSP00000349022:p.Ala180Thr	20	0	0		21	17	0.809524	NM_015193	B4DFL0|O60937	Missense_Mutation	SNP	ENST00000356613.2	37	CCDS34950.1	.	.	.	.	.	.	.	.	.	.	c	2.551	-0.304065	0.05495	.	.	ENSG00000198576	ENST00000356613	T	0.30448	1.53	4.55	0.643	0.17770	.	0.623272	0.12914	N	0.428666	T	0.10852	0.0265	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.34875	-0.9811	10	0.15066	T	0.55	.	5.5167	0.16910	0.0:0.5043:0.1484:0.3473	.	180	Q7LC44	ARC_HUMAN	T	180	ENSP00000349022:A180T	ENSP00000349022:A180T	A	-	1	0	ARC	143692097	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	-0.311000	0.08124	0.043000	0.15746	-0.461000	0.05368	GCT	.	.	none		0.736	ARC-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259274.2			T	143695095	C	T	143695095	3	4	20	1	0	0	0	0	1	0	0	0	841	768	27	1	656	1	ARC	8	143695095	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10		143695095	2668927	55	2676											
MAF1	84232	hgsc.bcm.edu	37	chr8	145160665	145160665	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctggagatgcccacatcattGgcaggtgaggcaggctgggg	8	7	17	9	0	1	2	1	1	0	1	1	3	1	2	1	7	1	3	1	7	0	1			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr8:145160665G>T	ENST00000322428.5	+	2	483	c.79G>T	c.(79-81)Ggc>Tgc	p.G27C	MAF1_ENST00000532522.1_Missense_Mutation_p.G27C|MAF1_ENST00000534585.1_Missense_Mutation_p.G27C|SHARPIN_ENST00000398712.2_5'Flank|KIAA1875_ENST00000323662.8_5'Flank|SHARPIN_ENST00000533948.1_5'Flank	NM_032272.4	NP_115648.2	Q9H063	MAF1_HUMAN	MAF1 homolog (S. cerevisiae)	27					negative regulation of transcription from RNA polymerase III promoter (GO:0016480)|transcription, DNA-templated (GO:0006351)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	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)			central_nervous_system(1)|lung(8)|urinary_tract(1)	10	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;3.1e-42)|Epithelial(56;1.23e-40)|all cancers(56;4.84e-36)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CCACATCATTGGCAGGTGAGG	0.572																																					p.G27C		Atlas-SNP	.											.	MAF1	16	.	0			c.G79T						PASS	.						67	65	66					8																	145160665		2203	4300	6503	SO:0001583	missense	84232	exon2			ATCATTGGCAGGT		CCDS6416.1	8q24.3	2012-10-29			ENSG00000179632	ENSG00000179632			24966	protein-coding gene	gene with protein product		610210				11230166, 11438659	Standard	NM_032272		Approved	DKFZp586G1123	uc003zbc.1	Q9H063	OTTHUMG00000165244	ENST00000322428.5:c.79G>T	8.37:g.145160665G>T	ENSP00000318604:p.Gly27Cys	38	0	0		49	43	0.877551	NM_032272	D3DWL4	Missense_Mutation	SNP	ENST00000322428.5	37	CCDS6416.1	.	.	.	.	.	.	.	.	.	.	G	17.02	3.281555	0.59758	.	.	ENSG00000179632	ENST00000322428;ENST00000534585;ENST00000532522;ENST00000527572;ENST00000527058	T;T;T	0.56103	0.59;0.48;0.59	4.94	4.94	0.65067	.	0.061031	0.64402	D	0.000004	T	0.69797	0.3151	M	0.88704	2.975	0.80722	D	1	D	0.55172	0.97	P	0.53861	0.736	T	0.76063	-0.3096	10	0.54805	T	0.06	-43.3794	13.6671	0.62403	0.0:0.0:1.0:0.0	.	27	Q9H063	MAF1_HUMAN	C	27	ENSP00000318604:G27C;ENSP00000433979:G27C;ENSP00000436720:G27C	ENSP00000318604:G27C	G	+	1	0	MAF1	145232653	1.000000	0.71417	0.998000	0.56505	0.301000	0.27625	5.450000	0.66626	2.285000	0.76669	0.462000	0.41574	GGC	.	.	none		0.572	MAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382910.1	NM_032272		T	145160665	G	T	145160665	3	4	20	1	0	0	0	0	1	0	0	0	9165	1348	47	4	81	4	MAF1	8	145160665	Missense_Mutation	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	1465570	145160665	1203357	56	2677											
KIAA1529	100499483	hgsc.bcm.edu	37	chr9	100071801	100071801	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgaagaaggtggagactcctGaaggggaggtgatgtctccc	10	8	16	7	0	1	5	0	3	1	2	3	7	2	6	2	5	0	0	2	5	3	0			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr9:100071801G>A	ENST00000357054.1	+	17	1659	c.724G>A	c.(724-726)Gaa>Aaa	p.E242K	CCDC180_ENST00000411667.2_Missense_Mutation_p.E103K|RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000375202.2_Missense_Mutation_p.E103K|CCDC180_ENST00000460482.2_3'UTR|CCDC180_ENST00000529487.1_Missense_Mutation_p.E103K|CCDC180_ENST00000395220.1_Missense_Mutation_p.E242K			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180	242						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											GGAGACTCCTGAAGGGGAGGT	0.587																																					p.E103K		Atlas-SNP	.											.	.	.	.	0			c.G307A						PASS	.						90	76	81					9																	100071801		2203	4300	6503	SO:0001583	missense	0	exon3			ACTCCTGAAGGGG	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.724G>A	9.37:g.100071801G>A	ENSP00000349562:p.Glu242Lys	76	0	0		71	35	0.492958	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Missense_Mutation	SNP	ENST00000357054.1	37		.	.	.	.	.	.	.	.	.	.	G	11.03	1.520367	0.27211	.	.	ENSG00000197816	ENST00000357054;ENST00000395220;ENST00000375202;ENST00000411667;ENST00000541524;ENST00000529487	T;T;T;T;T	0.19394	2.98;2.15;2.99;2.62;2.99	4.71	1.65	0.23941	.	0.386006	0.19087	N	0.123067	T	0.27134	0.0665	M	0.65975	2.015	0.09310	N	1	D;P;D;P	0.54207	0.965;0.884;0.965;0.884	P;P;P;P	0.58077	0.832;0.482;0.832;0.482	T	0.17992	-1.0351	10	0.07482	T	0.82	-4.6043	4.0123	0.09627	0.215:0.1986:0.5864:0.0	.	103;242;103;242	F5H149;B7ZMG3;Q9P1Z9-2;Q9P1Z9	.;.;.;CI174_HUMAN	K	242;242;103;103;126;103	ENSP00000349562:E242K;ENSP00000378646:E242K;ENSP00000364348:E103K;ENSP00000414000:E103K;ENSP00000434727:E103K	ENSP00000349562:E242K	E	+	1	0	C9orf174	99111622	0.049000	0.20398	0.401000	0.26359	0.065000	0.16274	0.405000	0.21015	1.128000	0.42052	-0.258000	0.10820	GAA	.	.	none		0.587	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893		A	100071801	G	A	100071801	3	1	20	1	0	0	0	0	1	0	0	0	8249	1291	45	2	746	2	KIAA1529	9	100071801	Missense_Mutation	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10		100071801	41141630	57	2678											
RGS3	5998	hgsc.bcm.edu	37	chr9	116346320	116346320	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggggcagagcagggctgctcGggagatgaggaggatgcaga	10	4	21	6	1	0	4	0	1	0	3	1	7	0	6	0	6	3	5	0	6	0	0			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr9:116346320G>T	ENST00000374140.2	+	21	2837	c.2628G>T	c.(2626-2628)tcG>tcT	p.S876S	RP11-168K11.2_ENST00000428429.1_RNA|RGS3_ENST00000342620.5_Intron|RGS3_ENST00000462143.1_Silent_p.S197S|RGS3_ENST00000394646.3_Intron|RGS3_ENST00000374134.3_Silent_p.S197S|RGS3_ENST00000343817.5_Silent_p.S595S|RGS3_ENST00000350696.5_Silent_p.S876S	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	876					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						AGGGCTGCTCGGGAGATgagg	0.657																																					p.S876S		Atlas-SNP	.											.	RGS3	251	.	0			c.G2628T						PASS	.						75	65	69					9																	116346320		2203	4299	6502	SO:0001819	synonymous_variant	5998	exon21			CTGCTCGGGAGAT	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.2628G>T	9.37:g.116346320G>T		64	0	0		74	22	0.297297	NM_144488	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Silent	SNP	ENST00000374140.2	37	CCDS43869.1																																																																																			.	.	none		0.657	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790		T	116346320	G	T	116346320	2	4	20	1	0	0	0	0	0	0	0	1	13321	1103	39	4		4	RGS3	9	116346320	Silent	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	16274519	116346320	24867111	58	2679											
SH3GLB2	56904	hgsc.bcm.edu	37	chr9	131790419	131790419	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcgtccgacgccagcttcttCatgttgaagtccatggcgtg	6	11	12	12	4	2	1	1	1	1	0	4	2	4	1	3	1	1	2	3	1	1	3			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr9:131790419C>T	ENST00000372564.3	-	1	160	c.15G>A	c.(13-15)atG>atA	p.M5I	SH3GLB2_ENST00000416629.1_Missense_Mutation_p.M5I|SH3GLB2_ENST00000372559.1_Missense_Mutation_p.M5I|SH3GLB2_ENST00000372554.4_Missense_Mutation_p.M5I|SH3GLB2_ENST00000417224.1_Missense_Mutation_p.M5I	NM_020145.2	NP_064530.1	Q9NR46	SHLB2_HUMAN	SH3-domain GRB2-like endophilin B2	5	Membrane-binding amphipathic helix. {ECO:0000250}.					cytoplasm (GO:0005737)				NS(1)|kidney(1)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)	12						CCAGCTTCTTCATGTTGAAGT	0.781																																					p.M5I		Atlas-SNP	.											.	SH3GLB2	32	.	0			c.G15A						PASS	.						5	4	5					9																	131790419		1641	3025	4666	SO:0001583	missense	56904	exon1			CTTCTTCATGTTG	AF257319	CCDS6916.1, CCDS69680.1	9q34	2008-02-05	2001-12-04		ENSG00000148341	ENSG00000148341			10834	protein-coding gene	gene with protein product		609288	"SH3-domain, GRB2-like, endophilin B2"			11161816	Standard	NM_020145		Approved	KIAA1848	uc004bwv.3	Q9NR46	OTTHUMG00000020769	ENST00000372564.3:c.15G>A	9.37:g.131790419C>T	ENSP00000361645:p.Met5Ile	28	0	0		41	17	0.414634	NM_020145	A6NC47|A8MPS4|Q8WY61|Q96JH9	Missense_Mutation	SNP	ENST00000372564.3	37	CCDS6916.1	.	.	.	.	.	.	.	.	.	.	C	17.93	3.509061	0.64410	.	.	ENSG00000148341	ENST00000372564;ENST00000372559;ENST00000543311;ENST00000372554;ENST00000417224;ENST00000416629	T;T;T;T;T	0.16324	2.35;2.35;2.37;2.36;2.38	4.19	3.29	0.37713	.	0.109396	0.64402	D	0.000007	T	0.14013	0.0339	L	0.36672	1.1	0.37175	D	0.903204	B;B	0.14438	0.01;0.003	B;B	0.15052	0.009;0.012	T	0.07693	-1.0759	10	0.51188	T	0.08	.	10.6936	0.45886	0.0:0.9034:0.0:0.0966	.	5;5	Q9NR46-2;Q9NR46	.;SHLB2_HUMAN	I	5	ENSP00000361645:M5I;ENSP00000361640:M5I;ENSP00000361634:M5I;ENSP00000402566:M5I;ENSP00000388282:M5I	ENSP00000361634:M5I	M	-	3	0	SH3GLB2	130830240	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	1.778000	0.38614	0.964000	0.38108	0.544000	0.68410	ATG	.	.	none		0.781	SH3GLB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054535.2			T	131790419	C	T	131790419	3	4	20	1	0	0	0	0	1	0	0	0	14269	826	29	2	1216	2	SH3GLB2	9	131790419	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	15444099	131790419	9423012	59	2680											
PLXDC2	84898	hgsc.bcm.edu	37	chr10	20432282	20432282	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagccacacagtacatagcAcctttaatggcaaatttcga	15	9	6	11	1	0	0	0	0	0	0	1	1	0	0	2	1	3	3	2	1	4	5			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr10:20432282A>T	ENST00000377252.4	+	5	1441	c.600A>T	c.(598-600)gcA>gcT	p.A200A	PLXDC2_ENST00000377238.2_3'UTR|PLXDC2_ENST00000377242.3_Silent_p.A151A	NM_001282736.1|NM_032812.7	NP_001269665.1|NP_116201.7	Q6UX71	PXDC2_HUMAN	plexin domain containing 2	200					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						AGTACATAGCACCTTTAATGG	0.358																																					p.A200A		Atlas-SNP	.											PLXDC2,NS,carcinoma,+1,2	PLXDC2	108	2	0			c.A600T						scavenged	.						173	163	166					10																	20432282		2203	4300	6503	SO:0001819	synonymous_variant	84898	exon5			CATAGCACCTTTA	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.600A>T	10.37:g.20432282A>T		215	2	0.00930233		210	83	0.395238	NM_032812	Q96E59|Q96PD9|Q96SU9	Silent	SNP	ENST00000377252.4	37	CCDS7132.1																																																																																			.	.	none		0.358	PLXDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047101.2	NM_032812		T	20432282	A	T	20432282	2	4	20	1	0	0	0	0	0	0	0	1	12127	146	6	5		5	PLXDC2	10	20432282	Silent	SNP	A	TCGA-FF-A7CX-01A-12D-A382-10		20432282	115102465	60	2681											
SEC24C	9632	hgsc.bcm.edu	37	chr10	75526107	75526107	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	taacaatgtcaccttctacaGggagggtggggcagaagagt	12	8	14	7	0	2	2	1	0	1	2	2	3	2	3	1	4	2	1	1	4	4	3			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr10:75526107G>A	ENST00000339365.2	+	13	1769		c.e13-1		SEC24C_ENST00000535742.1_Intron|SEC24C_ENST00000411652.2_Splice_Site|SEC24C_ENST00000546025.1_Splice_Site|SEC24C_ENST00000345254.4_Splice_Site|SEC24C_ENST00000540668.1_Intron	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C						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)					ACCTTCTACAGGGAGGGTGGG	0.498																																					.		Atlas-SNP	.											.	SEC24C	86	.	0			c.1608-1G>A						PASS	.						91	73	79					10																	75526107		2203	4300	6503	SO:0001630	splice_region_variant	9632	exon13			TCTACAGGGAGGG	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.1608-1G>A	10.37:g.75526107G>A		86	0	0		85	30	0.352941	NM_004922	B4DZT4|Q8WV25	Splice_Site	SNP	ENST00000339365.2	37	CCDS7332.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.982734	0.74474	.	.	ENSG00000176986	ENST00000546025;ENST00000345254;ENST00000339365;ENST00000411652	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.3409	0.98764	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SEC24C	75196113	1.000000	0.71417	0.999000	0.59377	0.878000	0.50629	9.869000	0.99810	2.814000	0.96858	0.655000	0.94253	.	.	.	none		0.498	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1		Intron	A	75526107	G	A	75526107	5	1	20	1	0	0	0	0	0	0	1	0	14011	1014	35	2	1649	2	SEC24C	10	75526107	Splice_Site	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	55093825	75526107	60008640	61	2682											
ANXA11	311	hgsc.bcm.edu	37	chr10	81932570	81932570	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaccctcttacctggtgcAgctggtgggtagccacctgg	6	9	13	13	0	1	1	0	0	1	1	1	1	1	1	4	4	4	3	4	4	2	2			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr10:81932570A>T	ENST00000438331.1	-	4	530	c.48T>A	c.(46-48)gcT>gcA	p.A16A	ANXA11_ENST00000372231.3_Silent_p.A16A|ANXA11_ENST00000535999.1_Silent_p.A16A|ANXA11_ENST00000360615.4_Silent_p.A16A|ANXA11_ENST00000463657.1_5'Flank|ANXA11_ENST00000265447.4_Silent_p.A16A|ANXA11_ENST00000422982.3_Silent_p.A16A|ANXA11_ENST00000537102.1_5'UTR	NM_145869.1	NP_665876.1	P50995	ANX11_HUMAN	annexin A11	16					cytokinesis, completion of separation (GO:0007109)|phagocytosis (GO:0006909)|response to calcium ion (GO:0051592)	azurophil granule (GO:0042582)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|specific granule (GO:0042581)|spindle (GO:0005819)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|MHC class II protein complex binding (GO:0023026)|phosphatidylethanolamine binding (GO:0008429)|poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)			endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|urinary_tract(1)	17	Prostate(51;0.00985)|all_epithelial(25;0.0951)		Colorectal(32;0.109)			TACCTGGTGCAGCTGGTGGGT	0.592																																					p.A16A		Atlas-SNP	.											.	ANXA11	32	.	0			c.T48A						PASS	.						78	79	79					10																	81932570		2203	4300	6503	SO:0001819	synonymous_variant	311	exon3			TGGTGCAGCTGGT	L19605	CCDS7364.1, CCDS60576.1	10q22.3	2005-11-09			ENSG00000122359	ENSG00000122359		"Annexins"	535	protein-coding gene	gene with protein product		602572		ANX11		7508441, 9503022	Standard	NM_001157		Approved		uc001kbt.1	P50995	OTTHUMG00000018604	ENST00000438331.1:c.48T>A	10.37:g.81932570A>T		55	0	0		46	6	0.130435	NM_145868	B4DVE7	Silent	SNP	ENST00000438331.1	37	CCDS7364.1																																																																																			.	.	none		0.592	ANXA11-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049044.1	NM_145869		T	81932570	A	T	81932570	2	4	20	1	0	0	0	0	0	0	0	1	716	175	7	5		5	ANXA11	10	81932570	Silent	SNP	A	TCGA-FF-A7CX-01A-12D-A382-10	6406463	81932570	53602177	62	2683											
CNNM1	26507	hgsc.bcm.edu	37	chr10	101090081	101090081	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgccgggcttcgggggcaccGgggaagactacagcgaagag	9	3	18	11	5	0	2	0	0	0	2	1	4	0	3	2	5	2	2	2	5	3	2			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr10:101090081G>A	ENST00000356713.4	+	1	1226	c.937G>A	c.(937-939)Ggg>Agg	p.G313R	CNNM1_ENST00000370528.3_Missense_Mutation_p.G242R|CNNM1_ENST00000446890.1_Missense_Mutation_p.G242R|CNNM1_ENST00000370534.4_5'UTR	NM_020348.2	NP_065081.2	Q9NRU3	CNNM1_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 1	313	DUF21.				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)		CGGGGGCACCGGGGAAGACTA	0.687																																					p.G313R		Atlas-SNP	.											CNNM1_ENST00000356713,NS,carcinoma,-1,1	CNNM1	101	1	0			c.G937A						PASS	.						7	11	10					10																	101090081		1994	4112	6106	SO:0001583	missense	26507	exon1			GGCACCGGGGAAG	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.937G>A	10.37:g.101090081G>A	ENSP00000349147:p.Gly313Arg	102	0	0		104	8	0.0769231	NM_020348	Q4QQG7|Q4QQH8|Q4QQP9|Q9NT45	Missense_Mutation	SNP	ENST00000356713.4	37	CCDS7478.2	.	.	.	.	.	.	.	.	.	.	G	11.34	1.610067	0.28712	.	.	ENSG00000119946	ENST00000356713;ENST00000446890;ENST00000370528	D;D;D	0.88741	-2.42;-2.42;-2.42	4.33	3.4	0.38934	Domain of unknown function DUF21 (1);	.	.	.	.	D	0.89234	0.6657	L	0.29908	0.895	0.80722	D	1	P;D	0.76494	0.941;0.999	B;D	0.76071	0.232;0.987	D	0.85675	0.1297	9	0.22706	T	0.39	-21.3627	12.086	0.53698	0.0:0.0:0.8264:0.1736	.	313;313	Q9NRU3-2;Q9NRU3	.;CNNM1_HUMAN	R	313;242;242	ENSP00000349147:G313R;ENSP00000406492:G242R;ENSP00000359559:G242R	ENSP00000349147:G313R	G	+	1	0	CNNM1	101080071	0.799000	0.28903	0.429000	0.26710	0.155000	0.21991	0.917000	0.28665	1.001000	0.39076	0.462000	0.41574	GGG	.	.	none		0.687	CNNM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049792.2	NM_020348		A	101090081	G	A	101090081	3	1	20	1	0	0	0	0	1	0	0	0	3614	1116	39	1	939	1	CNNM1	10	101090081	Missense_Mutation	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	19157511	101090081	34444666	63	2684											
GPR26	2849	hgsc.bcm.edu	37	chr10	125426000	125426002	+	In_Frame_Del	DEL	TGC	TGC	-																															gctgctgtccaacgcgctggTgctgctctgcctgctgcaca																										TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	TGC	TGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr10:125426000_125426002delTGC	ENST00000284674.1	+	1	130_132	c.77_79delTGC	c.(76-81)gtgctg>gtg	p.L28del		NM_153442.3	NP_703143.1	Q8NDV2	GPR26_HUMAN	G protein-coupled receptor 26	28					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)			breast(3)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	20		Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)				AACGCGCTGGTGCTGCTCTGCCT	0.709																																					p.26_26del		Pindel,Atlas-Indel	.											.	GPR26	47	.	0			c.76_78del						PASS	.																																			SO:0001651	inframe_deletion	2849	exon1			.		CCDS7636.1	10q26.2-q26.3	2012-08-21			ENSG00000154478	ENSG00000154478		"GPCR / Class A : Orphans"	4481	protein-coding gene	gene with protein product		604847					Standard	NM_153442		Approved		uc001lhh.3	Q8NDV2	OTTHUMG00000019204	ENST00000284674.1:c.77_79delTGC	10.37:g.125426003_125426005delTGC	ENSP00000284674:p.Leu28del	81	0	.		70	24	0.343	NM_153442	Q2M2E2	In_Frame_Del	DEL	ENST00000284674.1	37	CCDS7636.1																																																																																			.	.	none		0.709	GPR26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050850.1			-	125426002	TGC	-	125426000	7	5	20	1	0	1	0	1	0	0	0	0	6692	1696	59	0	79	0	GPR26	10	125426000	In_Frame_Del	DEL	TGC	TCGA-FF-A7CX-01A-12D-A382-10	24335919	125426000	10108747	64	2685											
DCHS1	8642	hgsc.bcm.edu	37	chr11	6652558	6652558	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ataccagttagcgtgtacaaGatggtcccattctccccctc	9	11	7	14	1	1	1	0	0	1	1	4	1	2	1	4	1	3	2	4	1	4	4			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr11:6652558G>A	ENST00000299441.3	-	8	4167	c.3756C>T	c.(3754-3756)atC>atT	p.I1252I	RP11-732A19.6_ENST00000526633.1_RNA	NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	1252	Cadherin 12. {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)		GCGTGTACAAGATGGTCCCAT	0.592																																					p.I1252I		Atlas-SNP	.											.	DCHS1	277	.	0			c.C3756T						PASS	.						221	175	190					11																	6652558		2201	4296	6497	SO:0001819	synonymous_variant	8642	exon8			GTACAAGATGGTC	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.3756C>T	11.37:g.6652558G>A		114	0	0		139	11	0.0791367	NM_003737	O15098	Silent	SNP	ENST00000299441.3	37	CCDS7771.1																																																																																			.	.	none		0.592	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		A	6652558	G	A	6652558	2	1	20	1	0	0	0	0	0	0	0	1	4289	932	33	2		2	DCHS1	11	6652558	Silent	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10		6652558	128353958	65	2686											
MRVI1	10335	hgsc.bcm.edu	37	chr11	10655535	10655535	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgttggccaggtttttgtcGgtttctccttctggtgaagt	3	18	12	8	1	2	1	0	1	2	0	4	1	2	1	2	4	0	3	2	4	1	5	rs373779712		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr11:10655535G>A	ENST00000436272.1	-	2	360	c.282C>T	c.(280-282)acC>acT	p.T94T	MRVI1_ENST00000532037.1_5'UTR|MRVI1_ENST00000558540.1_Intron|MRVI1_ENST00000424001.1_Intron|MRVI1_ENST00000527509.2_Silent_p.T12T|MRVI1_ENST00000421747.1_Silent_p.T94T|MRVI1_ENST00000534266.2_5'UTR|MRVI1_ENST00000423302.2_Silent_p.T103T|MRVI1_ENST00000531107.1_Silent_p.T94T|MRVI1_ENST00000545852.1_5'UTR|MRVI1_ENST00000541483.1_Silent_p.T103T|MRVI1_ENST00000552103.1_Silent_p.T12T|MRVI1_ENST00000547195.1_Silent_p.T12T			Q9Y6F6	MRVI1_HUMAN	murine retrovirus integration site 1 homolog	94					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)		GGTTTTTGTCGGTTTCTCCTT	0.468																																					p.T103T		Atlas-SNP	.											.	MRVI1	113	.	0			c.C309T						PASS	.	G	,,,,,	1,3817		0,1,1908	82	79	80		282,36,,309,,309	-7.2	0	11		80	0,8256		0,0,4128	no	coding-synonymous,coding-synonymous,intron,coding-synonymous,utr-5,coding-synonymous	MRVI1	NM_001098579.2,NM_001100163.2,NM_001100167.2,NM_001206880.1,NM_001206881.1,NM_130385.3	,,,,,	0,1,6036	AA,AG,GG		0.0,0.0262,0.0083	,,,,,	94/905,12/822,,103/707,,103/913	10655535	1,12073	1909	4128	6037	SO:0001819	synonymous_variant	10335	exon3			TTTGTCGGTTTCT	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.282C>T	11.37:g.10655535G>A		249	0	0		202	74	0.366337	NM_001206880	B7Z3T4|B7Z6I2|B7Z9A3|E9PQY6|F5H6A1|J3KQZ7|Q17S00|Q9UNY1	Silent	SNP	ENST00000436272.1	37																																																																																				.	.	weak		0.468	MRVI1-203	KNOWN	basic	protein_coding	protein_coding		NM_001098579		A	10655535	G	A	10655535	2	1	20	1	0	0	0	0	0	0	0	1	9862	1103	39	1		1	MRVI1	11	10655535	Silent	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	4002977	10655535	124350981	66	2687											
MUC15	143662	hgsc.bcm.edu	37	chr11	26582712	26582712	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatcattcaaagttggattgTagtagctagaattcccaaaa	16	12	7	6	0	2	1	2	0	0	1	3	2	3	2	1	1	1	4	1	1	8	7			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr11:26582712T>C	ENST00000455601.2	-	4	1023	c.905A>G	c.(904-906)tAc>tGc	p.Y302C	ANO3_ENST00000531568.1_Intron|MUC15_ENST00000436318.2_Missense_Mutation_p.Y329C|ANO3_ENST00000529242.1_Intron|MUC15_ENST00000529533.1_Missense_Mutation_p.Y329C|MUC15_ENST00000527569.1_Missense_Mutation_p.Y279C|ANO3_ENST00000525139.1_Intron|ANO3_ENST00000256737.3_Intron|ANO3_ENST00000537978.1_Intron|MUC15_ENST00000281268.8_Missense_Mutation_p.Y279C	NM_145650.3	NP_663625.2	Q8N387	MUC15_HUMAN	mucin 15, cell surface associated	302					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)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	25						AGTTGGATTGTAGTAGCTAGA	0.383																																					p.Y329C		Atlas-SNP	.											.	MUC15	88	.	0			c.A986G						PASS	.						151	138	142					11																	26582712		2203	4300	6503	SO:0001583	missense	143662	exon5			GGATTGTAGTAGC	AJ417818	CCDS7859.1, CCDS44556.1, CCDS44557.1	11p14.3	2007-01-17	2006-03-14					"Mucins"	14956	protein-coding gene	gene with protein product		608566				12047385	Standard	NM_145650		Approved		uc001mqw.3	Q8N387		ENST00000455601.2:c.905A>G	11.37:g.26582712T>C	ENSP00000397339:p.Tyr302Cys	295	0	0		283	22	0.0777385	NM_001135091	B3KY00|E9PII6|F8W945|Q6UWS3|Q8IXI8|Q8WW41	Missense_Mutation	SNP	ENST00000455601.2	37	CCDS7859.1	.	.	.	.	.	.	.	.	.	.	T	17.44	3.389236	0.61956	.	.	ENSG00000169550	ENST00000455601;ENST00000436318;ENST00000281268;ENST00000529533;ENST00000527569	T;T;T;T;T	0.48201	0.86;0.82;0.87;0.82;0.87	5.43	4.23	0.50019	.	0.000000	0.45361	D	0.000370	T	0.55386	0.1917	L	0.32530	0.975	0.33656	D	0.609055	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	T	0.66614	-0.5879	10	0.62326	D	0.03	-5.9356	11.3819	0.49763	0.1354:0.0:0.0:0.8646	.	279;302;329	F8W945;Q8N387;E9PII6	.;MUC15_HUMAN;.	C	302;329;279;329;279	ENSP00000397339:Y302C;ENSP00000416753:Y329C;ENSP00000281268:Y279C;ENSP00000431983:Y329C;ENSP00000431945:Y279C	ENSP00000281268:Y279C	Y	-	2	0	MUC15	26539288	1.000000	0.71417	0.986000	0.45419	0.780000	0.44128	2.385000	0.44371	2.187000	0.69744	0.482000	0.46254	TAC	.	.	none		0.383	MUC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387866.1	NM_145650		C	26582712	T	C	26582712	3	2	20	1	0	0	0	0	1	0	0	0	9981	1638	57	3	103	3	MUC15	11	26582712	Missense_Mutation	SNP	T	TCGA-FF-A7CX-01A-12D-A382-10	15927177	26582712	108423804	67	2688											
C11orf41	25758	hgsc.bcm.edu	37	chr11	33667420	33667420	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcctggcatccgcgggccaCgcaggccagagccggcacca	8	2	14	17	4	0	1	0	0	0	1	1	1	1	1	6	4	2	3	6	4	0	0			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr11:33667420C>T	ENST00000321505.4	+	16	4887	c.4707C>T	c.(4705-4707)caC>caT	p.H1569H	KIAA1549L_ENST00000389726.3_Silent_p.H1575H			Q6ZVL6	K154L_HUMAN	KIAA1549-like	1569						integral component of membrane (GO:0016021)											CCGCGGGCCACGCAGGCCAGA	0.682																																					p.H1569H		Atlas-SNP	.											.	.	.	.	0			c.C4707T						PASS	.						21	26	24					11																	33667420		2111	4216	6327	SO:0001819	synonymous_variant	25758	exon16			GGGCCACGCAGGC	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.4707C>T	11.37:g.33667420C>T		126	0	0		128	64	0.5	NM_012194	B0QYU0	Silent	SNP	ENST00000321505.4	37	CCDS44565.2																																																																																			.	.	none		0.682	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194		T	33667420	C	T	33667420	2	4	20	1	0	0	0	0	0	0	0	1	1642	535	19	1		1	C11orf41	11	33667420	Silent	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	7084708	33667420	101339096	68	2689											
SLC29A2	3177	hgsc.bcm.edu	37	chr11	66133453	66133453	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtcccagccagtccatgatgTtgaagaggaggaagcagcag	12	6	14	9	0	0	3	0	2	0	1	2	5	2	5	3	2	3	3	3	2	2	1			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr11:66133453T>C	ENST00000357440.2	-	10	1241	c.1013A>G	c.(1012-1014)aAc>aGc	p.N338S	SLC29A2_ENST00000311161.7_Silent_p.Q293Q|SLC29A2_ENST00000546034.1_Missense_Mutation_p.N338S|SLC29A2_ENST00000544554.1_Missense_Mutation_p.N338S	NM_001532.2	NP_001523.2	Q14542	S29A2_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 2	338					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)	GTCCATGATGTTGAAGAGGAG	0.572																																					p.N338S		Atlas-SNP	.											.	SLC29A2	24	.	0			c.A1013G						PASS	.						107	101	103					11																	66133453		2200	4295	6495	SO:0001583	missense	3177	exon10			ATGATGTTGAAGA	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.1013A>G	11.37:g.66133453T>C	ENSP00000350024:p.Asn338Ser	89	0	0		58	23	0.396552	NM_001532	B3KPY7|O43530|Q52M84|Q96R00|Q9UPE0	Missense_Mutation	SNP	ENST00000357440.2	37	CCDS8137.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.803190	0.90623	.	.	ENSG00000174669	ENST00000357440;ENST00000544554;ENST00000546034	T;T;T	0.80738	-1.41;-1.41;-1.41	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.88485	0.6449	M	0.72118	2.19	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	D	0.89435	0.3719	10	0.66056	D	0.02	-24.3104	13.6825	0.62493	0.0:0.0:0.0:1.0	.	338	Q14542	S29A2_HUMAN	S	338	ENSP00000350024:N338S;ENSP00000439456:N338S;ENSP00000440329:N338S	ENSP00000350024:N338S	N	-	2	0	SLC29A2	65890029	1.000000	0.71417	0.989000	0.46669	0.996000	0.88848	6.135000	0.71696	2.123000	0.65237	0.529000	0.55759	AAC	.	.	none		0.572	SLC29A2-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402093.1	NM_001532		C	66133453	T	C	66133453	3	2	20	1	0	0	0	0	1	0	0	0	14550	1725	60	3	369	3	SLC29A2	11	66133453	Missense_Mutation	SNP	T	TCGA-FF-A7CX-01A-12D-A382-10	32466033	66133453	68873063	69	2690											
MTNR1B	4544	hgsc.bcm.edu	37	chr11	92714681	92714681	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctacccctacccgctaatcCtcgtggccatcttctatgac	7	12	5	17	2	3	1	0	1	3	0	5	1	4	1	5	1	2	1	5	1	4	5			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr11:92714681C>A	ENST00000257068.2	+	2	298	c.292C>A	c.(292-294)Ctc>Atc	p.L98I		NM_005959.3	NP_005950.1	P49286	MTR1B_HUMAN	melatonin receptor 1B	98					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)	CCCGCTAATCCTCGTGGCCAT	0.567																																					p.L98I		Atlas-SNP	.											.	MTNR1B	75	.	0			c.C292A						PASS	.						217	213	214					11																	92714681		2201	4298	6499	SO:0001583	missense	4544	exon2			CTAATCCTCGTGG	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.292C>A	11.37:g.92714681C>A	ENSP00000257068:p.Leu98Ile	123	0	0		139	10	0.0719424	NM_005959		Missense_Mutation	SNP	ENST00000257068.2	37	CCDS8290.1	.	.	.	.	.	.	.	.	.	.	C	19.59	3.856263	0.71834	.	.	ENSG00000134640	ENST00000257068	T	0.44083	0.93	3.97	3.97	0.46021	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000001	T	0.64305	0.2586	M	0.74258	2.255	0.58432	D	0.999991	P	0.51351	0.944	D	0.70227	0.968	T	0.68322	-0.5439	10	0.52906	T	0.07	-25.9064	16.6059	0.84828	0.0:1.0:0.0:0.0	.	98	P49286	MTR1B_HUMAN	I	98	ENSP00000257068:L98I	ENSP00000257068:L98I	L	+	1	0	MTNR1B	92354329	1.000000	0.71417	0.824000	0.32777	0.966000	0.64601	5.183000	0.65065	2.220000	0.72140	0.491000	0.48974	CTC	.	.	none		0.567	MTNR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394323.1			A	92714681	C	A	92714681	3	1	20	1	0	0	0	0	1	0	0	0	9961	681	24	4	298	4	MTNR1B	11	92714681	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	26581228	92714681	42291835	70	2691											
ARID2	196528	hgsc.bcm.edu	37	chr12	46244016	46244016	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atgctccagtgactgtcattCaaagtaaagctccaattcct	12	12	6	11	0	2	1	2	1	0	0	5	1	5	1	3	0	2	3	3	0	4	3			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr12:46244016C>T	ENST00000334344.6	+	15	2282	c.2110C>T	c.(2110-2112)Caa>Taa	p.Q704*	ARID2_ENST00000457135.1_5'Flank|ARID2_ENST00000444670.1_Nonsense_Mutation_p.Q314*|ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000422737.1_Nonsense_Mutation_p.Q555*	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	704					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)		GACTGTCATTCAAAGTAAAGC	0.428			"N, S, F"		hepatocellular carcinoma																																p.Q704X		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	ARID2,lower_third,carcinoma,0,1	ARID2	311	1	0			c.C2110T						PASS	.						143	138	139					12																	46244016		2203	4300	6503	SO:0001587	stop_gained	196528	exon15			GTCATTCAAAGTA		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.2110C>T	12.37:g.46244016C>T	ENSP00000335044:p.Gln704*	211	0	0		182	78	0.428571	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Nonsense_Mutation	SNP	ENST00000334344.6	37	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	C	40	8.047537	0.98627	.	.	ENSG00000189079	ENST00000334344;ENST00000422737;ENST00000444670	.	.	.	5.79	5.79	0.91817	.	0.344788	0.32204	N	0.006435	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.30854	T	0.27	-5.712	20.0413	0.97592	0.0:1.0:0.0:0.0	.	.	.	.	X	704;555;314	.	ENSP00000335044:Q704X	Q	+	1	0	ARID2	44530283	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.036000	0.70948	2.751000	0.94390	0.650000	0.86243	CAA	.	.	none		0.428	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		T	46244016	C	T	46244016	4	4	20	1	0	0	0	0	0	1	0	0	915	827	29	2	2168	2	ARID2	12	46244016	Nonsense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10		46244016	87607879	71	2692											
GNS	2799	hgsc.bcm.edu	37	chr12	65153012	65153012	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	caggagggcaggtggcggggGctgccccgccggagccgacc	5	2	20	14	4	0	0	0	0	0	0	0	3	0	2	5	7	2	2	5	7	0	0			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr12:65153012G>A	ENST00000258145.3	-	1	215	c.45C>T	c.(43-45)agC>agT	p.S15S	GNS_ENST00000542058.1_Silent_p.S15S|RP11-629N8.3_ENST00000434563.3_RNA|snoU13_ENST00000458789.1_RNA|GNS_ENST00000543646.1_Silent_p.S15S	NM_002076.3	NP_002067.1	P15586	GNS_HUMAN	glucosamine (N-acetyl)-6-sulfatase	15					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	metal ion binding (GO:0046872)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)|sulfuric ester hydrolase activity (GO:0008484)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(4)	15	Lung NSC(1;7.25e-14)|all_lung(1;1.25e-12)		LUAD - Lung adenocarcinoma(6;0.115)	GBM - Glioblastoma multiforme(28;0.0435)		GGTGGCGGGGGCTGCCCCGCC	0.751																																					p.S15S		Atlas-SNP	.											.	GNS	41	.	0			c.C45T						PASS	.						3	4	4					12																	65153012		1794	3465	5259	SO:0001819	synonymous_variant	2799	exon1			GCGGGGGCTGCCC		CCDS8970.1	12q14	2010-05-04	2008-08-01		ENSG00000135677	ENSG00000135677	3.1.6.14		4422	protein-coding gene	gene with protein product	"Sanfilippo disease IIID", "N-acetylglucosamine-6-sulfatase"	607664					Standard	NM_002076		Approved		uc001ssg.4	P15586	OTTHUMG00000168819	ENST00000258145.3:c.45C>T	12.37:g.65153012G>A		44	0	0		32	14	0.4375	NM_002076	B4DYH8|Q53F05	Silent	SNP	ENST00000258145.3	37	CCDS8970.1																																																																																			.	.	none		0.751	GNS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401195.2			A	65153012	G	A	65153012	2	1	20	1	0	0	0	0	0	0	0	1	6558	1194	42	2		2	GNS	12	65153012	Silent	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	18908996	65153012	68698883	72	2693											
BTG1	694	hgsc.bcm.edu	37	chr12	92539174	92539174	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccctgctcacctgccagcagCtcctgcaggctctggctgaa	6	8	10	17	0	2	1	1	1	1	0	3	1	3	1	4	2	5	6	4	2	1	0	rs200623021		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr12:92539174C>G	ENST00000256015.3	-	1	499	c.138G>C	c.(136-138)gaG>gaC	p.E46D	C12orf79_ENST00000549802.1_5'Flank|RP11-796E2.4_ENST00000499685.2_RNA|C12orf79_ENST00000551563.2_5'Flank|RP11-796E2.4_ENST00000501008.2_RNA|C12orf79_ENST00000546975.1_5'Flank	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	46					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)	p.E46D(1)		haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				CTGCCAGCAGCTCCTGCAGGC	0.701			T	MYC	BCLL																																p.E46D		Atlas-SNP	.		Dom	yes		12	12q22	694	"B-cell translocation gene 1, anti-proliferative"		L	BTG1,NS,lymphoid_neoplasm,0,1	BTG1	30	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G138C						PASS	.						29	32	31					12																	92539174		2201	4299	6500	SO:0001583	missense	694	exon1			CAGCAGCTCCTGC		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.138G>C	12.37:g.92539174C>G	ENSP00000256015:p.Glu46Asp	124	0	0		132	68	0.515152	NM_001731	P31607	Missense_Mutation	SNP	ENST00000256015.3	37	CCDS9043.1	.	.	.	.	.	.	.	.	.	.	C	12.85	2.062147	0.36373	.	.	ENSG00000133639	ENST00000256015	T	0.23552	1.9	3.6	1.62	0.23740	Anti-proliferative protein (3);	0.185807	0.46145	D	0.000307	T	0.18718	0.0449	L	0.39245	1.2	0.42552	D	0.993111	B	0.06786	0.001	B	0.09377	0.004	T	0.06972	-1.0797	10	0.30854	T	0.27	-8.7689	9.9123	0.41413	0.0:0.8212:0.0:0.1788	.	46	P62324	BTG1_HUMAN	D	46	ENSP00000256015:E46D	ENSP00000256015:E46D	E	-	3	2	BTG1	91063305	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.415000	0.34748	0.663000	0.31027	0.455000	0.32223	GAG	C|1.000;T|0.000	.	alt		0.701	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1			G	92539174	C	G	92539174	3	3	20	1	0	0	0	0	1	0	0	0	1555	796	28	4	385	4	BTG1	12	92539174	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	27386162	92539174	41312721	73	2694											
HVCN1	84329	hgsc.bcm.edu	37	chr12	111089042	111089042	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cattgatgatccgggccaccCgccacagccggagcagaatc	10	5	11	15	3	0	3	0	2	0	1	2	4	1	4	5	2	2	1	5	2	1	1			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr12:111089042C>T	ENST00000356742.5	-	5	1376	c.623G>A	c.(622-624)cGg>cAg	p.R208Q	HVCN1_ENST00000242607.8_Missense_Mutation_p.R208Q|HVCN1_ENST00000548312.1_Missense_Mutation_p.R208Q|HVCN1_ENST00000439744.2_Missense_Mutation_p.R188Q			Q96D96	HVCN1_HUMAN	hydrogen voltage-gated channel 1	208					cellular response to pH (GO:0071467)|cellular response to zinc ion (GO:0071294)|multicellular organism reproduction (GO:0032504)|proton transport (GO:0015992)|response to pH (GO:0009268)|response to zinc ion (GO:0010043)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	voltage-gated cation channel activity (GO:0022843)|voltage-gated proton channel activity (GO:0030171)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	19						CCGGGCCACCCGCCACAGCCG	0.607																																					p.R208Q		Atlas-SNP	.											HVCN1,caecum,carcinoma,-1,2	HVCN1	38	2	0			c.G623A						PASS	.						64	54	57					12																	111089042		2203	4300	6503	SO:0001583	missense	84329	exon6			GCCACCCGCCACA	BC007277	CCDS31900.1, CCDS58278.1	12q24.11	2011-12-09	2006-03-24	2006-03-24	ENSG00000122986	ENSG00000122986		"Voltage-gated ion channels / Hydrogen voltage-gated channel"	28240	protein-coding gene	gene with protein product	"voltage sensor domain-only protein"	611227				20961760, 16556803, 18356202, 22020278	Standard	NM_032369		Approved	MGC15619, Hv1, VSOP	uc001trs.2	Q96D96		ENST00000356742.5:c.623G>A	12.37:g.111089042C>T	ENSP00000349181:p.Arg208Gln	71	0	0		87	35	0.402299	NM_032369	A8MQ37|B4DEB3|F8WCH5|Q6UW11|Q96IS5	Missense_Mutation	SNP	ENST00000356742.5	37	CCDS31900.1	.	.	.	.	.	.	.	.	.	.	c	37	6.074823	0.97262	.	.	ENSG00000122986	ENST00000548312;ENST00000242607;ENST00000356742;ENST00000439744	D;D;D;D	0.98777	-5.13;-5.13;-5.13;-5.13	5.61	5.61	0.85477	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99435	0.9800	H	0.94503	3.545	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	D	0.98591	1.0654	10	0.87932	D	0	-30.045	19.6266	0.95679	0.0:1.0:0.0:0.0	.	208;208	Q96D96;Q96D96-3	HVCN1_HUMAN;.	Q	208;208;208;188	ENSP00000449601:R208Q;ENSP00000242607:R208Q;ENSP00000349181:R208Q;ENSP00000412052:R188Q	ENSP00000242607:R208Q	R	-	2	0	HVCN1	109573425	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.792000	0.85828	2.648000	0.89879	0.556000	0.70494	CGG	.	.	none		0.607	HVCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404653.1	NM_032369		T	111089042	C	T	111089042	3	4	20	1	0	0	0	0	1	0	0	0	7471	652	23	1	210	1	HVCN1	12	111089042	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	18549868	111089042	22762853	74	2695											
C12orf52	84934	hgsc.bcm.edu	37	chr12	113624824	113624824	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tcaaggggcagcacccccacCctcacaccaaggaagaagaa	15	2	9	15	0	2	2	2	0	0	2	2	3	2	3	4	3	1	2	4	3	5	0			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr12:113624824C>T	ENST00000548278.1	+	3	965	c.273C>T	c.(271-273)acC>acT	p.T91T	RP11-545P7.4_ENST00000552525.1_RNA|DDX54_ENST00000306014.5_5'Flank|C12orf52_ENST00000552495.1_Silent_p.T115T|DDX54_ENST00000314045.7_5'Flank|C12orf52_ENST00000549621.1_Silent_p.T91T	NM_032848.1	NP_116237.1	Q96K30	RITA1_HUMAN		91					negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurogenesis (GO:0022008)|Notch signaling pathway (GO:0007219)|nuclear export (GO:0051168)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	tubulin binding (GO:0015631)	p.L92F(1)		large_intestine(2)|lung(1)|prostate(1)|urinary_tract(1)	5						GCACCCCCACCCTCACACCAA	0.562																																					p.T91T		Atlas-SNP	.											.	C12orf52	19	.	1	Substitution - Missense(1)	lung(1)	c.C273T						PASS	.						35	39	37					12																	113624824		2197	4296	6493	SO:0001819	synonymous_variant	84934	exon3			CCCCACCCTCACA																												ENST00000548278.1:c.273C>T	12.37:g.113624824C>T		36	0	0		56	23	0.410714	NM_032848	B3KVZ4|C9JIN1|F8VRG5|Q53GM3|Q96K25	Silent	SNP	ENST00000548278.1	37	CCDS9166.1																																																																																			.	.	none		0.562	C12orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405239.1			T	113624824	C	T	113624824	2	4	20	1	0	0	0	0	0	0	0	1	1699	610	22	2		2	C12orf52	12	113624824	Silent	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	2535782	113624824	20227071	75	2696											
COL4A1	1282	hgsc.bcm.edu	37	chr13	110831690	110831690	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gcctggtaccccaatgctccCcttctccccgggtgtgccag	4	9	10	18	1	1	0	0	0	1	0	3	0	2	0	8	2	3	2	8	2	2	2			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr13:110831690C>T	ENST00000375820.4	-	30	2393	c.2272G>A	c.(2272-2274)Ggg>Agg	p.G758R		NM_001845.4	NP_001836.2	P02462	CO4A1_HUMAN	collagen, type IV, alpha 1	758	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)			CCAATGCTCCCCTTCTCCCCG	0.587																																					p.G758R		Atlas-SNP	.											.	COL4A1	372	.	0			c.G2272A						PASS	.						79	82	81					13																	110831690		2203	4300	6503	SO:0001583	missense	1282	exon30			TGCTCCCCTTCTC	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.2272G>A	13.37:g.110831690C>T	ENSP00000364979:p.Gly758Arg	78	0	0		72	68	0.944444	NM_001845	A7E2W4|B1AM70|Q1P9S9|Q5VWF6|Q86X41|Q8NF88|Q9NYC5	Missense_Mutation	SNP	ENST00000375820.4	37	CCDS9511.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.078077	0.76528	.	.	ENSG00000187498	ENST00000375820	D	0.99353	-5.77	4.7	4.7	0.59300	.	0.000000	0.85682	D	0.000000	D	0.99648	0.9870	H	0.96720	3.87	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97434	1.0017	10	0.87932	D	0	.	18.0343	0.89294	0.0:1.0:0.0:0.0	.	758	P02462	CO4A1_HUMAN	R	758	ENSP00000364979:G758R	ENSP00000364979:G758R	G	-	1	0	COL4A1	109629691	1.000000	0.71417	0.986000	0.45419	0.351000	0.29236	6.933000	0.75874	2.328000	0.79073	0.655000	0.94253	GGG	.	.	none		0.587	COL4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045759.3			T	110831690	C	T	110831690	3	4	20	1	0	0	0	0	1	0	0	0	3691	623	22	2	2829	2	COL4A1	13	110831690	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10		110831690	4338188	76	2697											
SSTR1	6751	hgsc.bcm.edu	37	chr14	38679760	38679760	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacctgcacgtcccggatcaCgacgctctgagcccgggcca	7	5	11	18	5	2	1	1	1	1	0	3	3	3	2	4	2	2	2	4	2	0	0			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr14:38679760C>T	ENST00000267377.2	+	3	1783	c.1166C>T	c.(1165-1167)aCg>aTg	p.T389M		NM_001049.2	NP_001040.1	P30872	SSR1_HUMAN	somatostatin receptor 1	389					cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cerebellum development (GO:0021549)|digestion (GO:0007586)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glutamate receptor signaling pathway (GO:0007215)|negative regulation of cell proliferation (GO:0008285)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29	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;0.00444)	Octreotide(DB00104)|Pasireotide(DB06663)	TCCCGGATCACGACGCTCTGA	0.657																																					p.T389M		Atlas-SNP	.											.	SSTR1	66	.	0			c.C1166T						PASS	.						20	21	20					14																	38679760		2201	4299	6500	SO:0001583	missense	6751	exon3			GGATCACGACGCT		CCDS9666.1	14q13	2012-08-08			ENSG00000139874	ENSG00000139874		"GPCR / Class A : Somatostatin receptors"	11330	protein-coding gene	gene with protein product		182451				8449518	Standard	NM_001049		Approved		uc001wul.1	P30872	OTTHUMG00000140249	ENST00000267377.2:c.1166C>T	14.37:g.38679760C>T	ENSP00000267377:p.Thr389Met	37	0	0		42	13	0.309524	NM_001049		Missense_Mutation	SNP	ENST00000267377.2	37	CCDS9666.1	.	.	.	.	.	.	.	.	.	.	C	13.99	2.402583	0.42613	.	.	ENSG00000139874	ENST00000267377	T	0.71341	-0.56	4.97	3.01	0.34805	.	0.297808	0.23327	N	0.049396	T	0.53867	0.1823	N	0.22421	0.69	0.35543	D	0.803255	P	0.50066	0.931	B	0.37422	0.249	T	0.69510	-0.5126	10	0.87932	D	0	.	13.6077	0.62056	0.0:0.6722:0.3278:0.0	.	389	P30872	SSR1_HUMAN	M	389	ENSP00000267377:T389M	ENSP00000267377:T389M	T	+	2	0	SSTR1	37749511	0.997000	0.39634	0.873000	0.34254	0.617000	0.37484	3.465000	0.53064	1.290000	0.44636	0.561000	0.74099	ACG	.	.	none		0.657	SSTR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409930.2			T	38679760	C	T	38679760	3	4	20	1	0	0	0	0	1	0	0	0	15212	536	19	1	1168	1	SSTR1	14	38679760	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10		38679760	68669780	77	2698											
SIX6	4990	hgsc.bcm.edu	37	chr14	60976600	60976600	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagcaaaaaacgtgagctcGcccaggcaaccggactgacc	13	3	10	15	3	0	2	0	2	0	0	1	3	0	3	4	2	4	3	4	2	4	0			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr14:60976600G>A	ENST00000327720.5	+	1	932	c.484G>A	c.(484-486)Gcc>Acc	p.A162T		NM_007374.2	NP_031400.2	O95475	SIX6_HUMAN	SIX homeobox 6	162					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)		ACGTGAGCTCGCCCAGGCAAC	0.597																																					p.A162T		Atlas-SNP	.											.	SIX6	27	.	0			c.G484A						PASS	.						48	42	44					14																	60976600		2201	4300	6501	SO:0001583	missense	4990	exon1			GAGCTCGCCCAGG	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.484G>A	14.37:g.60976600G>A	ENSP00000328596:p.Ala162Thr	88	0	0		91	42	0.461538	NM_007374	Q6NT42|Q9P1X8	Missense_Mutation	SNP	ENST00000327720.5	37	CCDS9747.1	.	.	.	.	.	.	.	.	.	.	G	34	5.296643	0.95574	.	.	ENSG00000184302	ENST00000327720	D	0.98164	-4.76	5.38	5.38	0.77491	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99533	0.9833	H	0.99675	4.695	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97712	1.0191	10	0.72032	D	0.01	.	18.3062	0.90182	0.0:0.0:1.0:0.0	.	162	O95475	SIX6_HUMAN	T	162	ENSP00000328596:A162T	ENSP00000328596:A162T	A	+	1	0	SIX6	60046353	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	9.657000	0.98554	2.804000	0.96469	0.462000	0.41574	GCC	.	.	none		0.597	SIX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276952.2			A	60976600	G	A	60976600	3	1	20	1	0	0	0	0	1	0	0	0	14366	1087	38	1	486	1	SIX6	14	60976600	Missense_Mutation	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	22296840	60976600	46372940	78	2699											
FNTB	2342	hgsc.bcm.edu	37	chr14	65520040	65520040	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gatgtgctgccagtgccctgCgggggggcttctggataaac	6	9	16	10	1	1	0	0	0	1	0	1	2	1	1	2	4	5	2	2	4	2	2	rs374785351		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr14:65520040C>T	ENST00000246166.2	+	10	1274	c.1040C>T	c.(1039-1041)gCg>gTg	p.A347V	CHURC1-FNTB_ENST00000549987.1_Missense_Mutation_p.A382V|MAX_ENST00000341653.2_Intron|FNTB_ENST00000542227.1_Missense_Mutation_p.A301V|FNTB_ENST00000447296.2_Missense_Mutation_p.A381V	NM_002028.3	NP_002019.1	P49356	FNTB_HUMAN	farnesyltransferase, CAAX box, beta	347					negative regulation of cell proliferation (GO:0008285)|phototransduction, visible light (GO:0007603)|positive regulation of cell cycle (GO:0045787)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|protein farnesylation (GO:0018343)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|response to cytokine (GO:0034097)|response to inorganic substance (GO:0010035)|response to organic cyclic compound (GO:0014070)|rhodopsin mediated signaling pathway (GO:0016056)|wound healing (GO:0042060)	cytosol (GO:0005829)|microtubule associated complex (GO:0005875)|protein farnesyltransferase complex (GO:0005965)	farnesyltranstransferase activity (GO:0004311)|protein farnesyltransferase activity (GO:0004660)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(2)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	14				all cancers(60;0.00115)|OV - Ovarian serous cystadenocarcinoma(108;0.00412)|BRCA - Breast invasive adenocarcinoma(234;0.011)		CAGTGCCCTGCGGGGGGGCTT	0.597																																					p.A408V		Atlas-SNP	.											FNTB,rectum,carcinoma,-1,1	.	.	1	0			c.C1223T						PASS	.	C	,VAL/ALA,VAL/ALA,VAL/ALA	0,4406		0,0,2203	34	34	34		,1040,1223,902	5.3	0.1	14		34	1,8599	1.2+/-3.3	0,1,4299	no	intron,missense,missense,missense	FNTB,MAX,CHURC1-FNTB	NM_197957.2,NM_002028.3,NM_001202559.1,NM_001202558.1	,64,64,64	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,benign,benign,benign	,347/438,408/499,301/392	65520040	1,13005	2203	4300	6503	SO:0001583	missense	100529261	exon12			GCCCTGCGGGGGG		CCDS9769.1	14q23.3	2011-09-28			ENSG00000257365	ENSG00000257365			3785	protein-coding gene	gene with protein product		134636				8276393	Standard	NM_002028		Approved	FPTB		P49356	OTTHUMG00000142811	ENST00000246166.2:c.1040C>T	14.37:g.65520040C>T	ENSP00000246166:p.Ala347Val	53	0	0		59	26	0.440678	NM_001202559	B2RDX6|B4E1A0	Missense_Mutation	SNP	ENST00000246166.2	37	CCDS9769.1	.	.	.	.	.	.	.	.	.	.	C	12.60	1.986392	0.35036	0.0	1.16E-4	ENSG00000125954;ENSG00000125954;ENSG00000125954;ENSG00000125954;ENSG00000257365	ENST00000542227;ENST00000549987;ENST00000447296;ENST00000448390;ENST00000246166	T;T;T;T;T	0.39997	1.05;1.05;1.05;1.05;1.05	5.31	5.31	0.75309	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.369639	0.31051	N	0.008345	T	0.19846	0.0477	N	0.15975	0.35	0.80722	D	1	B;B;P;B	0.42123	0.046;0.37;0.771;0.227	B;B;B;B	0.21151	0.011;0.016;0.027;0.033	T	0.07539	-1.0767	10	0.33141	T	0.24	-7.8543	12.9217	0.58237	0.1624:0.8376:0.0:0.0	.	350;301;381;347	Q86TX8;B4E1A0;B4DL54;P49356	.;.;.;FNTB_HUMAN	V	301;382;381;103;347	ENSP00000443140:A301V;ENSP00000447121:A382V;ENSP00000406393:A381V;ENSP00000399362:A103V;ENSP00000246166:A347V	ENSP00000246166:A347V	A	+	2	0	FNTB;AL139022.1	64589793	0.055000	0.20627	0.094000	0.20943	0.797000	0.45037	2.346000	0.44027	2.767000	0.95098	0.561000	0.74099	GCG	.	.	weak		0.597	FNTB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000286392.1	NM_002028		T	65520040	C	T	65520040	3	4	20	1	0	0	0	0	1	0	0	0	5986	768	27	1	1078	1	FNTB	14	65520040	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	4543440	65520040	41829500	79	2700											
C14orf118	55668	hgsc.bcm.edu	37	chr14	76620825	76620825	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acagcagaggcggcagcttcGgaaacgccgaggtcggaagc	11	3	16	11	5	0	1	0	0	0	1	2	4	0	3	1	5	4	3	1	5	2	1			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr14:76620825G>A	ENST00000261530.7	+	2	185	c.119G>A	c.(118-120)cGg>cAg	p.R40Q	GPATCH2L_ENST00000557263.1_Missense_Mutation_p.R40Q|GPATCH2L_ENST00000556663.1_Missense_Mutation_p.R40Q|GPATCH2L_ENST00000312858.5_Missense_Mutation_p.R40Q	NM_017926.2	NP_060396.2	Q9NWQ4	GPT2L_HUMAN	G patch domain containing 2-like	40	Arg-rich.																CGGCAGCTTCGGAAACGCCGA	0.587																																					p.R40Q		Atlas-SNP	.											.	.	.	.	0			c.G119A						PASS	.						48	48	48					14																	76620825		2203	4300	6503	SO:0001583	missense	55668	exon2			AGCTTCGGAAACG	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.119G>A	14.37:g.76620825G>A	ENSP00000261530:p.Arg40Gln	99	0	0		71	34	0.478873	NM_017926	B3KN42|Q6PEJ7|Q9H3M3|Q9NWH0|Q9ULR8	Missense_Mutation	SNP	ENST00000261530.7	37	CCDS9848.1	.	.	.	.	.	.	.	.	.	.	G	36	5.619242	0.96649	.	.	ENSG00000089916	ENST00000336993;ENST00000557542;ENST00000557263;ENST00000312858;ENST00000261530;ENST00000556663	T;T;T;T	0.61392	0.19;0.18;0.11;0.19	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.73489	0.3593	L	0.56199	1.76	0.80722	D	1	D;D;D	0.89917	1.0;0.997;0.999	D;D;D	0.81914	0.995;0.964;0.99	T	0.74928	-0.3497	10	0.66056	D	0.02	-16.1396	19.2547	0.93941	0.0:0.0:1.0:0.0	.	40;40;40	Q9NWQ4-1;Q9NWQ4-4;Q9NWQ4	.;.;CN118_HUMAN	Q	40	ENSP00000451587:R40Q;ENSP00000323775:R40Q;ENSP00000261530:R40Q;ENSP00000450657:R40Q	ENSP00000261530:R40Q	R	+	2	0	C14orf118	75690578	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	9.378000	0.97191	2.553000	0.86117	0.561000	0.74099	CGG	.	.	none		0.587	GPATCH2L-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000413698.2	NM_017926		A	76620825	G	A	76620825	3	1	20	1	0	0	0	0	1	0	0	0	1743	1116	39	1	121	1	C14orf118	14	76620825	Missense_Mutation	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	11100785	76620825	30728715	80	2701											
EML1	2009	hgsc.bcm.edu	37	chr14	100402447	100402447	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caacgggaggaagtacacgcGagtgggcaagtgctcggtaa	12	5	16	8	4	0	0	0	0	0	0	1	3	0	2	0	4	3	4	0	4	5	2			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr14:100402447G>A	ENST00000262233.6	+	18	2130	c.1991G>A	c.(1990-1992)cGa>cAa	p.R664Q	EML1_ENST00000327921.9_Missense_Mutation_p.R652Q|EML1_ENST00000334192.4_Missense_Mutation_p.R683Q	NM_004434.2	NP_004425.2	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1	664	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)				AAGTACACGCGAGTGGGCAAG	0.463																																					p.R683Q		Atlas-SNP	.											.	EML1	97	.	0			c.G2048A						PASS	.						103	100	101					14																	100402447		2203	4300	6503	SO:0001583	missense	2009	exon19			ACACGCGAGTGGG	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.1991G>A	14.37:g.100402447G>A	ENSP00000262233:p.Arg664Gln	136	0	0		134	61	0.455224	NM_001008707	Q86U15|Q8N536|Q8N5C4|Q8WWL6	Missense_Mutation	SNP	ENST00000262233.6	37	CCDS32155.1	.	.	.	.	.	.	.	.	.	.	G	16.99	3.274587	0.59649	.	.	ENSG00000066629	ENST00000327921;ENST00000262233;ENST00000334192;ENST00000542138	T;T;T	0.39406	1.08;1.08;1.08	5.2	5.2	0.72013	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	0.69124	0.3076	M	0.92317	3.295	0.51767	D	0.999939	D;P;D	0.71674	0.998;0.94;0.979	P;P;P	0.57244	0.816;0.507;0.487	T	0.78881	-0.2029	10	0.87932	D	0	-16.2349	17.709	0.88316	0.0:0.0:1.0:0.0	.	652;664;683	F8W717;O00423;O00423-3	.;EMAL1_HUMAN;.	Q	652;664;683;683	ENSP00000327384:R652Q;ENSP00000262233:R664Q;ENSP00000334314:R683Q	ENSP00000262233:R664Q	R	+	2	0	EML1	99472200	0.997000	0.39634	0.071000	0.20095	0.038000	0.13279	7.691000	0.84191	2.429000	0.82318	0.561000	0.74099	CGA	.	.	none		0.463	EML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413943.1	NM_001008707		A	100402447	G	A	100402447	3	1	20	1	0	0	0	0	1	0	0	0	5098	1058	37	1	2122	1	EML1	14	100402447	Missense_Mutation	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	23781622	100402447	6947093	81	2702											
TYRO3	7301	hgsc.bcm.edu	37	chr15	41859646	41859646	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gctccgggacctggtgcctgCcaccaactacagcctcaggg	7	6	12	16	1	1	0	1	0	0	0	2	1	2	1	6	3	5	1	6	3	2	1			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr15:41859646C>T	ENST00000263798.3	+	7	1096	c.872C>T	c.(871-873)gCc>gTc	p.A291V	TYRO3_ENST00000559066.1_Missense_Mutation_p.A246V	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase	291	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		CTGGTGCCTGCCACCAACTAC	0.622																																					p.A291V		Atlas-SNP	.											.	TYRO3	169	.	0			c.C872T						PASS	.						95	97	97					15																	41859646		2203	4300	6503	SO:0001583	missense	7301	exon7			TGCCTGCCACCAA	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.872C>T	15.37:g.41859646C>T	ENSP00000263798:p.Ala291Val	65	0	0		70	34	0.485714	NM_006293	O14953|Q86VR3	Missense_Mutation	SNP	ENST00000263798.3	37	CCDS10080.1	.	.	.	.	.	.	.	.	.	.	C	15.54	2.864830	0.51482	.	.	ENSG00000092445	ENST00000540218;ENST00000263798	T	0.57595	0.39	4.64	4.64	0.57946	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.42294	D	0.000740	T	0.41396	0.1157	L	0.29908	0.895	0.33717	D	0.616478	P	0.46578	0.88	B	0.42462	0.388	T	0.50608	-0.8808	10	0.18710	T	0.47	-16.5648	14.5246	0.67878	0.0:1.0:0.0:0.0	.	291	Q06418	TYRO3_HUMAN	V	223;291	ENSP00000263798:A291V	ENSP00000263798:A291V	A	+	2	0	TYRO3	39646938	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.491000	0.45303	2.417000	0.82017	0.655000	0.94253	GCC	.	.	none		0.622	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2			T	41859646	C	T	41859646	3	4	20	1	0	0	0	0	1	0	0	0	16829	739	26	2	898	2	TYRO3	15	41859646	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10		41859646	60671746	82	2703											
MYO5C	55930	hgsc.bcm.edu	37	chr15	52487626	52487626	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcttctcaaagtcatctataGgtgtgtatgaattaaggatc	12	15	8	6	0	4	1	2	1	3	0	6	2	4	2	0	2	0	1	0	2	6	5			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr15:52487626G>A	ENST00000261839.7	-	40	5185	c.5024C>T	c.(5023-5025)cCt>cTt	p.P1675L	RP11-430B1.2_ENST00000560518.1_lincRNA	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	1675	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.					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)		GTCATCTATAGGTGTGTATGA	0.353																																					p.P1675L		Atlas-SNP	.											.	MYO5C	162	.	0			c.C5024T						PASS	.						83	82	82					15																	52487626		1853	4081	5934	SO:0001583	missense	55930	exon40			TCTATAGGTGTGT	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.5024C>T	15.37:g.52487626G>A	ENSP00000261839:p.Pro1675Leu	189	0	0		221	99	0.447964	NM_018728	Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	37	CCDS42036.1	.	.	.	.	.	.	.	.	.	.	G	31	5.063602	0.93898	.	.	ENSG00000128833	ENST00000261839	D	0.90133	-2.62	5.62	5.62	0.85841	Dilute (1);Dil domain (1);	0.000000	0.85682	D	0.000000	D	0.95714	0.8606	M	0.80746	2.51	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95790	0.8824	10	0.87932	D	0	.	19.661	0.95871	0.0:0.0:1.0:0.0	.	1675	Q9NQX4	MYO5C_HUMAN	L	1675	ENSP00000261839:P1675L	ENSP00000261839:P1675L	P	-	2	0	MYO5C	50274918	1.000000	0.71417	1.000000	0.80357	0.887000	0.51463	9.869000	0.99810	2.659000	0.90383	0.655000	0.94253	CCT	.	.	none		0.353	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728		A	52487626	G	A	52487626	3	1	20	1	0	0	0	0	1	0	0	0	10089	1000	35	2	212	2	MYO5C	15	52487626	Missense_Mutation	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	10627980	52487626	50043766	83	2704											
ABCC1	4363	hgsc.bcm.edu	37	chr16	16146585	16146585	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctttccttccttagaatcTgggcccttccgtcctggctg	3	15	8	15	1	1	1	0	0	1	1	6	1	6	1	6	2	0	1	6	2	2	4			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr16:16146585T>C	ENST00000399410.3	+	11	1560	c.1385T>C	c.(1384-1386)cTg>cCg	p.L462P	ABCC1_ENST00000351154.5_Missense_Mutation_p.L462P|ABCC1_ENST00000399408.2_Missense_Mutation_p.L462P|ABCC1_ENST00000349029.5_Missense_Mutation_p.L462P|ABCC1_ENST00000346370.5_Missense_Mutation_p.L462P|ABCC1_ENST00000345148.5_Missense_Mutation_p.L462P	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	462	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				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)	CCTTAGAATCTGGGCCCTTCC	0.552																																					p.L462P		Atlas-SNP	.											.	ABCC1	156	.	0			c.T1385C						PASS	.						126	127	127					16																	16146585		2108	4218	6326	SO:0001583	missense	4363	exon11			AGAATCTGGGCCC	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.1385T>C	16.37:g.16146585T>C	ENSP00000382342:p.Leu462Pro	124	0	0		127	52	0.409449	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Missense_Mutation	SNP	ENST00000399410.3	37	CCDS42122.1	.	.	.	.	.	.	.	.	.	.	T	16.30	3.085088	0.55861	.	.	ENSG00000103222	ENST00000399410;ENST00000399408;ENST00000346370;ENST00000351154;ENST00000345148;ENST00000349029;ENST00000536381	D;D;D;D;D;D	0.90900	-2.75;-2.75;-2.75;-2.75;-2.75;-2.75	5.12	5.12	0.69794	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.073654	0.56097	D	0.000030	D	0.96756	0.8941	H	0.96015	3.755	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.998;1.0;0.999;1.0	D;D;D;D;D;D;D	0.91635	0.999;0.999;0.994;0.986;0.999;0.992;0.99	D	0.97898	1.0301	10	0.87932	D	0	-15.4369	14.0882	0.64973	0.0:0.0:0.0:1.0	.	462;462;462;462;462;462;462	P33527-6;P33527-5;P33527-4;P33527-3;P33527-2;P33527;P33527-9	.;.;.;.;.;MRP1_HUMAN;.	P	462;462;462;462;462;462;136	ENSP00000382342:L462P;ENSP00000382340:L462P;ENSP00000263019:L462P;ENSP00000263017:L462P;ENSP00000263014:L462P;ENSP00000263016:L462P	ENSP00000263014:L462P	L	+	2	0	ABCC1	16054086	1.000000	0.71417	1.000000	0.80357	0.129000	0.20672	7.659000	0.83766	1.913000	0.55393	0.402000	0.26972	CTG	.	.	none		0.552	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996		C	16146585	T	C	16146585	3	2	20	1	0	0	0	0	1	0	0	0	49	1580	55	3	1427	3	ABCC1	16	16146585	Missense_Mutation	SNP	T	TCGA-FF-A7CX-01A-12D-A382-10		16146585	74208168	84	2705											
CDIPT	10423	hgsc.bcm.edu	37	chr16	29870830	29870830	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agctcattcccagcacacaaGgtgaacagagcaggctgcac	13	5	10	13	0	1	2	1	1	0	1	2	2	2	2	1	2	5	5	1	2	2	1			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr16:29870830G>T	ENST00000219789.6	-	5	1307	c.429C>A	c.(427-429)acC>acA	p.T143T	CDIPT_ENST00000570016.1_Silent_p.T143T|CDIPT_ENST00000563415.1_Intron|CDIPT_ENST00000561555.1_Silent_p.T167T|CDIPT_ENST00000566113.1_Silent_p.T98T|CDIPT_ENST00000569956.1_Silent_p.T143T|CDIPT_ENST00000567459.1_5'Flank	NM_006319.3	NP_006310.1	O14735	CDIPT_HUMAN	CDP-diacylglycerol--inositol 3-phosphatidyltransferase	143					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						CAGCACACAAGGTGAACAGAG	0.572																																					p.T143T		Atlas-SNP	.											.	CDIPT	15	.	0			c.C429A						PASS	.						86	71	76					16																	29870830		2197	4300	6497	SO:0001819	synonymous_variant	10423	exon5			ACACAAGGTGAAC	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.429C>A	16.37:g.29870830G>T		90	0	0		95	5	0.0526316	NM_006319	B4DUV0|H3BTV1|Q6FGU1|Q6ZN70	Silent	SNP	ENST00000219789.6	37	CCDS10657.1																																																																																			.	.	none		0.572	CDIPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255147.3	NM_006319		T	29870830	G	T	29870830	2	4	20	1	0	0	0	0	0	0	0	1	3125	987	35	4		4	CDIPT	16	29870830	Silent	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	13724245	29870830	60483923	85	2706											
ABCC11	85320	hgsc.bcm.edu	37	chr16	48209258	48209258	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgatgctgcaaatgtccacGccgtcaatgagaatccggcc	10	7	10	14	4	1	1	1	1	0	1	3	3	3	1	5	1	2	2	5	1	3	0			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr16:48209258G>A	ENST00000394747.1	-	25	3958	c.3609C>T	c.(3607-3609)ggC>ggT	p.G1203G	ABCC11_ENST00000394748.1_Silent_p.G1203G|ABCC11_ENST00000356608.2_Silent_p.G1203G|ABCC11_ENST00000565329.1_5'UTR|ABCC11_ENST00000353782.5_Silent_p.G1203G	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	1203	ABC transporter 2. {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)	AAATGTCCACGCCGTCAATGA	0.607																																					p.G1203G		Atlas-SNP	.											ABCC11,right_upper_lobe,carcinoma,-2,1	ABCC11	177	1	0			c.C3609T						scavenged	.						72	60	64					16																	48209258		2201	4300	6501	SO:0001819	synonymous_variant	85320	exon25			GTCCACGCCGTCA	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.3609C>T	16.37:g.48209258G>A		77	1	0.012987		95	45	0.473684	NM_033151	Q8TDJ0|Q96JA6|Q9BX80	Silent	SNP	ENST00000394747.1	37	CCDS10732.1																																																																																			.	.	none		0.607	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583		A	48209258	G	A	48209258	2	1	20	1	0	0	0	0	0	0	0	1	51	1074	38	1		1	ABCC11	16	48209258	Silent	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	18338428	48209258	42145495	86	2707											
CPNE2	221184	hgsc.bcm.edu	37	chr16	57171163	57171163	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caaccacgtggcccggtttgCggcccaggccacacaacagc	9	4	11	17	3	0	0	0	0	0	0	0	0	0	0	4	4	4	1	4	4	2	1			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr16:57171163C>G	ENST00000535318.2	+	15	1632	c.1271C>G	c.(1270-1272)gCg>gGg	p.A424G	CPNE2_ENST00000537605.1_Missense_Mutation_p.A322G|CPNE2_ENST00000565874.1_Missense_Mutation_p.A424G|CPNE2_ENST00000290776.8_Missense_Mutation_p.A424G|CPNE2_ENST00000565951.1_Intron			Q96FN4	CPNE2_HUMAN	copine II	424	VWFA.					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)				GCCCGGTTTGCGGCCCAGGCC	0.622																																					p.A424G		Atlas-SNP	.											.	CPNE2	48	.	0			c.C1271G						PASS	.						84	55	65					16																	57171163		2198	4300	6498	SO:0001583	missense	221184	exon14			GGTTTGCGGCCCA		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.1271C>G	16.37:g.57171163C>G	ENSP00000439018:p.Ala424Gly	78	0	0		58	30	0.517241	NM_152727	Q68D19|Q719H8|Q86XP9	Missense_Mutation	SNP	ENST00000535318.2	37	CCDS10774.1	.	.	.	.	.	.	.	.	.	.	C	36	5.784801	0.96937	.	.	ENSG00000140848	ENST00000290776;ENST00000537605;ENST00000535318	T;T;T	0.28255	1.62;1.62;1.62	5.88	5.88	0.94601	von Willebrand factor, type A (1);Copine (1);	0.000000	0.85682	D	0.000000	T	0.67040	0.2851	M	0.91612	3.225	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.73173	-0.4066	10	0.72032	D	0.01	-30.9625	20.2422	0.98381	0.0:1.0:0.0:0.0	.	424;424	A8K8A4;Q96FN4	.;CPNE2_HUMAN	G	424;322;424	ENSP00000290776:A424G;ENSP00000445468:A322G;ENSP00000439018:A424G	ENSP00000290776:A424G	A	+	2	0	CPNE2	55728664	1.000000	0.71417	0.980000	0.43619	0.917000	0.54804	7.788000	0.85771	2.782000	0.95742	0.655000	0.94253	GCG	.	.	none		0.622	CPNE2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432986.2	NM_152727		G	57171163	C	G	57171163	3	3	20	1	0	0	0	0	1	0	0	0	3814	768	27	4	1321	4	CPNE2	16	57171163	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	8961905	57171163	33183590	87	2708											
MYH8	4626	hgsc.bcm.edu	37	chr17	10293802	10293802	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgatttttgtgtgaacctctCggctcttcactcgcaatttg	6	17	8	10	2	3	2	1	2	2	0	5	2	3	2	1	1	1	2	1	1	2	4			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr17:10293802C>T	ENST00000403437.2	-	40	5877	c.5783G>A	c.(5782-5784)cGa>cAa	p.R1928Q	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	1928					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						GTGAACCTCTCGGCTCTTCAC	0.473									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																												p.R1928Q		Atlas-SNP	.											.	MYH8	346	.	0			c.G5783A						PASS	.						149	142	145					17																	10293802		2203	4300	6503	SO:0001583	missense	4626	exon40	Familial Cancer Database	Carney Complex Variant	ACCTCTCGGCTCT		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.5783G>A	17.37:g.10293802C>T	ENSP00000384330:p.Arg1928Gln	327	0	0		325	145	0.446154	NM_002472	Q14910	Missense_Mutation	SNP	ENST00000403437.2	37	CCDS11153.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.792275	0.90453	.	.	ENSG00000133020	ENST00000252173;ENST00000403437	D	0.83755	-1.76	5.05	4.09	0.47781	Myosin tail (1);	0.000000	0.35903	U	0.002906	D	0.89167	0.6638	M	0.94142	3.5	0.50039	D	0.999841	P	0.46277	0.875	P	0.45971	0.499	D	0.91641	0.5327	10	0.72032	D	0.01	.	13.789	0.63128	0.0:0.926:0.0:0.074	.	1928	P13535	MYH8_HUMAN	Q	1928	ENSP00000384330:R1928Q	ENSP00000252173:R1928Q	R	-	2	0	MYH8	10234527	1.000000	0.71417	0.990000	0.47175	0.862000	0.49288	5.827000	0.69300	1.353000	0.45828	0.650000	0.86243	CGA	.	.	none		0.473	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472		T	10293802	C	T	10293802	3	4	20	1	0	0	0	0	1	0	0	0	10050	884	31	1	34	1	MYH8	17	10293802	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10		10293802	70901408	88	2709											
KRT25	147183	hgsc.bcm.edu	37	chr17	38906791	38906791	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgatctgagcctggatctgcGccagctgcgcacagtagttg	7	9	13	12	3	2	1	0	1	2	0	2	3	2	2	2	1	4	4	2	1	1	2			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr17:38906791G>C	ENST00000312150.4	-	6	1076	c.1016C>G	c.(1015-1017)gCg>gGg	p.A339G		NM_181534.3	NP_853512.1			keratin 25									p.A339V(1)		endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(4)	16		Breast(137;0.00526)				CTGGATCTGCGCCAGCTGCGC	0.562																																					p.A339G		Atlas-SNP	.											KRT25,NS,carcinoma,0,4	KRT25	63	4	1	Substitution - Missense(1)	prostate(1)	c.C1016G						PASS	.						138	140	139					17																	38906791		2203	4300	6503	SO:0001583	missense	147183	exon6			ATCTGCGCCAGCT	AK129503	CCDS11373.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000204897	ENSG00000204897		"-", "Intermediate filaments type I, keratins (acidic)"	30839	protein-coding gene	gene with protein product			"keratin 25A"	KRT25A		16831889	Standard	NM_181534		Approved		uc002hve.3	Q7Z3Z0	OTTHUMG00000133373	ENST00000312150.4:c.1016C>G	17.37:g.38906791G>C	ENSP00000310573:p.Ala339Gly	184	0	0		180	66	0.366667	NM_181534		Missense_Mutation	SNP	ENST00000312150.4	37	CCDS11373.1	.	.	.	.	.	.	.	.	.	.	G	17.38	3.374955	0.61735	.	.	ENSG00000204897	ENST00000394042;ENST00000312150	D	0.88586	-2.4	5.52	5.52	0.82312	Filament (1);	0.213774	0.33040	N	0.005356	D	0.83760	0.5324	L	0.28192	0.835	0.09310	N	1	B	0.15141	0.012	B	0.22753	0.041	T	0.75042	-0.3457	10	0.54805	T	0.06	.	15.7677	0.78141	0.0:0.0:0.8633:0.1367	.	339	Q7Z3Z0	K1C25_HUMAN	G	268;339	ENSP00000310573:A339G	ENSP00000310573:A339G	A	-	2	0	KRT25	36160317	0.243000	0.23878	0.929000	0.37066	0.713000	0.41058	3.072000	0.50049	2.566000	0.86566	0.655000	0.94253	GCG	.	.	none		0.562	KRT25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257218.1	NM_181534		C	38906791	G	C	38906791	3	2	20	1	0	0	0	0	1	0	0	0	8471	1087	38	4	348	4	KRT25	17	38906791	Missense_Mutation	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	28612989	38906791	42288419	89	2710											
KRTAP4-11	653240	hgsc.bcm.edu	37	chr17	39274360	39274360	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgacagcagctggagatgcAgcatctggggcggcagcagg	9	4	18	10	2	1	1	0	0	1	1	1	3	1	1	0	5	5	6	0	5	0	0			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr17:39274360A>T	ENST00000391413.2	-	1	246	c.208T>A	c.(208-210)Tgc>Agc	p.C70S		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	70	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].		Missing (in allele KAP4.14). {ECO:0000269|PubMed:15955084}.			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)			CTGGAGATGCAGCATCTGGGG	0.667																																					p.C70S		Atlas-SNP	.											KRTAP4-11,NS,carcinoma,0,1	KRTAP4-11	94	1	0			c.T208A						scavenged	.						7	12	11					17																	39274360		677	1580	2257	SO:0001583	missense	653240	exon1			AGATGCAGCATCT	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.208T>A	17.37:g.39274360A>T	ENSP00000375232:p.Cys70Ser	68	0	0		85	4	0.0470588	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	13.38	2.219303	0.39201	.	.	ENSG00000212721	ENST00000391413	T	0.02280	4.36	3.77	1.34	0.21922	.	0.000000	0.36972	U	0.002304	T	0.04770	0.0129	M	0.90252	3.1	0.23636	N	0.997233	B	0.17268	0.021	B	0.17722	0.019	T	0.23048	-1.0199	10	0.54805	T	0.06	.	4.9719	0.14119	0.7038:0.1861:0.1101:0.0	.	70	Q9BYQ6	KR411_HUMAN	S	70	ENSP00000375232:C70S	ENSP00000375232:C70S	C	-	1	0	KRTAP4-11	36527886	0.844000	0.29557	0.494000	0.27515	0.120000	0.20174	1.052000	0.30429	0.644000	0.30656	0.496000	0.49642	TGC	.	.	none		0.667	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1			T	39274360	A	T	39274360	3	4	20	1	0	0	0	0	1	0	0	0	8558	188	7	5	383	5	KRTAP4-11	17	39274360	Missense_Mutation	SNP	A	TCGA-FF-A7CX-01A-12D-A382-10	367569	39274360	41920850	90	2711											
KRT19	3880	hgsc.bcm.edu	37	chr17	39681516	39681516	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggagttctcaatggtggCaccaagaatctggaaggcag	11	8	13	9	0	2	1	1	0	2	1	3	3	2	3	2	5	0	3	2	5	4	1			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr17:39681516C>T	ENST00000361566.3	-	2	490	c.430G>A	c.(430-432)Gcc>Acc	p.A144T	KRT15_ENST00000254043.3_5'Flank	NM_002276.4	NP_002267.2	P08727	K1C19_HUMAN	keratin 19	144	Coil 1B.|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)				TCAATGGTGGCACCAAGAATC	0.537																																					p.A144T		Atlas-SNP	.											.	KRT19	41	.	0			c.G430A						PASS	.						106	102	104					17																	39681516		2203	4300	6503	SO:0001583	missense	3880	exon2			TGGTGGCACCAAG		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.430G>A	17.37:g.39681516C>T	ENSP00000355124:p.Ala144Thr	75	0	0		54	34	0.62963	NM_002276	B2R874|Q5XG83|Q6NW33|Q7L5M9|Q96A53|Q96FV1|Q9BYF9|Q9P1Y4	Missense_Mutation	SNP	ENST00000361566.3	37	CCDS11399.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.528656	0.85706	.	.	ENSG00000171345	ENST00000361566;ENST00000455635	D;D	0.88975	-2.45;-2.45	5.0	5.0	0.66597	Filament (1);	0.000000	0.46758	D	0.000268	D	0.92018	0.7471	L	0.54908	1.71	0.80722	D	1	D;P	0.76494	0.999;0.857	D;P	0.68943	0.961;0.732	D	0.88520	0.3095	10	0.13108	T	0.6	.	18.4827	0.90818	0.0:1.0:0.0:0.0	.	307;144	B4DE59;P08727	.;K1C19_HUMAN	T	144;113	ENSP00000355124:A144T;ENSP00000408759:A113T	ENSP00000355124:A144T	A	-	1	0	KRT19	36935042	1.000000	0.71417	0.986000	0.45419	0.994000	0.84299	4.663000	0.61532	2.599000	0.87857	0.561000	0.74099	GCC	.	.	none		0.537	KRT19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257285.1	NM_002276		T	39681516	C	T	39681516	3	4	20	1	0	0	0	0	1	0	0	0	8465	710	25	2	792	2	KRT19	17	39681516	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	407156	39681516	41513694	91	2712											
KRT17	3872	hgsc.bcm.edu	37	chr17	39775873	39775873	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggtctggtggacctgctcGcgggaggagatgaccttgcc	5	9	17	10	2	1	2	0	1	1	1	2	5	1	4	3	5	2	1	3	5	0	1	rs575174355		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr17:39775873G>A	ENST00000311208.8	-	8	1339	c.1272C>T	c.(1270-1272)cgC>cgT	p.R424R	JUP_ENST00000540235.1_Silent_p.R583R	NM_000422.2	NP_000413.1	Q04695	K1C17_HUMAN	keratin 17	424	Tail.				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)				GGACCTGCTCGCGGGAGGAGA	0.652													g|||	1	0.000199681	0.0	0.0	5008	,	,		17112	0.0		0.0	False		,,,				2504	0.001				p.R424R	Pancreas(92;1242 2086 39193 50508)	Atlas-SNP	.											.	KRT17	57	.	0			c.C1272T						PASS	.						93	92	92					17																	39775873		2203	4300	6503	SO:0001819	synonymous_variant	3872	exon8			CTGCTCGCGGGAG	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.1272C>T	17.37:g.39775873G>A		354	0	0		358	157	0.438547	NM_000422	A5Z1M9|A5Z1N0|A5Z1N1|A5Z1N2|A6NDV6|A6NKQ2|Q6IP98|Q8N1P6	Silent	SNP	ENST00000311208.8	37	CCDS11402.1																																																																																			.	.	none		0.652	KRT17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257460.1	NM_000422		A	39775873	G	A	39775873	2	1	20	1	0	0	0	0	0	0	0	1	8463	1074	38	1		1	KRT17	17	39775873	Silent	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	94357	39775873	41419337	92	2713											
VEZF1	7716	hgsc.bcm.edu	37	chr17	56058015	56058016	+	Frame_Shift_Ins	INS	-	-	T																															ttgatactttggctctgcccINSatgagtctttaagtggctgg																										TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr17:56058015_56058016insT	ENST00000581208.1	-	4	964_965	c.924_925insA	c.(922-927)catgggfs	p.G309fs	VEZF1_ENST00000584396.1_Frame_Shift_Ins_p.G300fs	NM_007146.2	NP_009077.2	Q14119	VEZF1_HUMAN	vascular endothelial zinc finger 1	309					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						TGGCTCTGCCCATGAGTCTTTA	0.436																																					p.G309fs		Atlas-Indel	.											.	VEZF1	50	.	0			c.925_926insA						PASS	.																																			SO:0001589	frameshift_variant	7716	exon4			.	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.924_925insA	17.37:g.56058015_56058016insT	ENSP00000462337:p.Gly309fs	277	0	0		200	37	0.185	NM_007146		Frame_Shift_Ins	INS	ENST00000581208.1	37	CCDS32687.1																																																																																			.	.	none		0.436	VEZF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443321.1			T	56058016	-	T	56058015	7	5	20	1	0	1	1	0	0	0	0	0	17170	594	21	0	652	0	VEZF1	17	56058015	Frame_Shift_Ins	INS	-	TCGA-FF-A7CX-01A-12D-A382-10	16282142	56058015	25137195	93	2714	41	2									
VEZF1	7716	hgsc.bcm.edu	37	chr17	56058016	56058016	+	Missense_Mutation	SNP	A	A	T																															ttgatactttggctctgcccAtgagtctttaagtggctggt																										TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr17:56058016A>T	ENST00000581208.1	-	4	964	c.924T>A	c.(922-924)caT>caA	p.H308Q	VEZF1_ENST00000584396.1_Missense_Mutation_p.H299Q	NM_007146.2	NP_009077.2	Q14119	VEZF1_HUMAN	vascular endothelial zinc finger 1	308					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						GGCTCTGCCCATGAGTCTTTA	0.438																																					p.H308Q		Atlas-SNP	.											VEZF1,NS,carcinoma,-2,1	VEZF1	50	1	0			c.T924A						scavenged	.						172	138	149					17																	56058016		2203	4300	6503	SO:0001583	missense	7716	exon4			CTGCCCATGAGTC	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.924T>A	17.37:g.56058016A>T	ENSP00000462337:p.His308Gln	280	1	0.00357143		197	37	0.187817	NM_007146		Missense_Mutation	SNP	ENST00000581208.1	37	CCDS32687.1	.	.	.	.	.	.	.	.	.	.	A	18.49	3.634518	0.67130	.	.	ENSG00000136451	ENST00000258963	.	.	.	5.69	0.944	0.19537	Zinc finger, C2H2-like (1);	0.000000	0.85682	D	0.000000	T	0.80586	0.4651	H	0.94734	3.575	0.58432	D	0.999996	D	0.69078	0.997	D	0.64144	0.922	T	0.81265	-0.1011	9	0.87932	D	0	-2.1035	10.2282	0.43238	0.6257:0.0:0.3743:0.0	.	308	Q14119	VEZF1_HUMAN	Q	308	.	ENSP00000258963:H308Q	H	-	3	2	VEZF1	53413015	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	1.069000	0.30641	-0.115000	0.11915	-0.269000	0.10298	CAT	.	.	none		0.438	VEZF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443321.1			T	56058016	A	T	56058016	3	4	20	1	0	0	0	0	1	0	0	0	17170	214	8	5	653	5	VEZF1	17	56058016	Missense_Mutation	SNP	A	TCGA-FF-A7CX-01A-12D-A382-10	1	56058016	25137194	94	2715	41	2									
HELZ	9931	hgsc.bcm.edu	37	chr17	65116527	65116527	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaagtacaacttaccatttcGattttgctcatgttgatcct	10	16	6	9	1	1	1	1	1	0	0	3	3	2	1	2	0	4	3	2	0	4	6			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr17:65116527G>A	ENST00000358691.5	-	27	3998	c.3832C>T	c.(3832-3834)Cga>Tga	p.R1278*	HELZ_ENST00000580168.1_Nonsense_Mutation_p.R1279*	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	1278						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)					TTACCATTTCGATTTTGCTCA	0.418																																					p.R1278X		Atlas-SNP	.											.	HELZ	160	.	0			c.C3832T						PASS	.						251	216	227					17																	65116527		1990	4185	6175	SO:0001587	stop_gained	9931	exon27			CATTTCGATTTTG	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.3832C>T	17.37:g.65116527G>A	ENSP00000351524:p.Arg1278*	437	0	0		446	195	0.43722	NM_014877	I6L9H4	Nonsense_Mutation	SNP	ENST00000358691.5	37	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	G	43	10.302058	0.99379	.	.	ENSG00000198265	ENST00000358691	.	.	.	5.78	4.8	0.61643	.	0.055330	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.0796	16.2698	0.82608	0.0:0.0:0.8664:0.1336	.	.	.	.	X	1278	.	ENSP00000351524:R1278X	R	-	1	2	HELZ	62546989	1.000000	0.71417	0.954000	0.39281	0.821000	0.46438	1.433000	0.34947	1.430000	0.47334	0.655000	0.94253	CGA	.	.	none		0.418	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		A	65116527	G	A	65116527	4	1	20	1	0	0	0	0	0	1	0	0	7058	1066	37	1	2024	1	HELZ	17	65116527	Nonsense_Mutation	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	9058511	65116527	16078683	95	2716											
THOC1	9984	hgsc.bcm.edu	37	chr18	216549	216549	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tctggtaaacttttaaactgCtggttggttggctggaagaa	10	14	12	5	0	1	1	0	0	1	1	1	2	1	2	0	5	3	5	0	5	6	5			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr18:216549C>T	ENST00000261600.6	-	19	1546	c.1539G>A	c.(1537-1539)caG>caA	p.Q513Q		NM_005131.2	NP_005122.2	Q96FV9	THOC1_HUMAN	THO complex 1	513					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)				TTTTAAACTGCTGGTTGGTTG	0.393																																					p.Q513Q		Atlas-SNP	.											.	THOC1	43	.	0			c.G1539A						PASS	.						188	190	189					18																	216549		1841	4093	5934	SO:0001819	synonymous_variant	9984	exon19			AAACTGCTGGTTG	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.1539G>A	18.37:g.216549C>T		252	0	0		100	79	0.79	NM_005131	B2RBP6|Q15219|Q64I72|Q64I73	Silent	SNP	ENST00000261600.6	37	CCDS45820.1																																																																																			.	.	none		0.393	THOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440348.5	NM_005131		T	216549	C	T	216549	2	4	20	1	0	0	0	0	0	0	0	1	15879	796	28	2		2	THOC1	18	216549	Silent	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10		216549	77860699	96	2717											
CDH2	1000	hgsc.bcm.edu	37	chr18	25572711	25572711	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gccactgattctgtacactgCgttccaggctggtgtatggg	6	12	13	10	1	1	1	0	1	1	0	2	1	2	1	2	3	2	4	2	3	2	4	rs200263846		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr18:25572711C>T	ENST00000269141.3	-	9	1675	c.1252G>A	c.(1252-1254)Gca>Aca	p.A418T	CDH2_ENST00000399380.3_Missense_Mutation_p.A387T	NM_001792.3	NP_001783.2	P19022	CADH2_HUMAN	cadherin 2, type 1, N-cadherin (neuronal)	418	Cadherin 3. {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						CTGTACACTGCGTTCCAGGCT	0.502																																					p.A418T		Atlas-SNP	.											.	CDH2	194	.	0			c.G1252A						PASS	.	C	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	229	176	194		1252	5.4	0.6	18		194	0,8600		0,0,4300	no	missense	CDH2	NM_001792.3	58	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	418/907	25572711	1,13005	2203	4300	6503	SO:0001583	missense	1000	exon9			ACACTGCGTTCCA	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.1252G>A	18.37:g.25572711C>T	ENSP00000269141:p.Ala418Thr	155	0	0		152	12	0.0789474	NM_001792	A8MWK3|B0YIY6|Q14923|Q8N173	Missense_Mutation	SNP	ENST00000269141.3	37	CCDS11891.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.262284	0.80358	2.27E-4	0.0	ENSG00000170558	ENST00000269141;ENST00000399380	T;T	0.54279	0.58;0.58	5.39	5.39	0.77823	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.73776	0.3630	M	0.74467	2.265	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.988	T	0.74748	-0.3560	10	0.54805	T	0.06	.	19.5228	0.95192	0.0:1.0:0.0:0.0	.	387;418	A8MWK3;P19022	.;CADH2_HUMAN	T	418;387	ENSP00000269141:A418T;ENSP00000382312:A387T	ENSP00000269141:A418T	A	-	1	0	CDH2	23826709	1.000000	0.71417	0.551000	0.28230	0.257000	0.26127	6.052000	0.71080	2.674000	0.91012	0.655000	0.94253	GCA	.	.	weak		0.502	CDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133246.3	NM_001792		T	25572711	C	T	25572711	3	4	20	1	0	0	0	0	1	0	0	0	3107	768	27	1	1500	1	CDH2	18	25572711	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	25356162	25572711	52504537	97	2718											
KIAA1012	22878	hgsc.bcm.edu	37	chr18	29511319	29511319	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gttaaggtcataatctcctgCtgtaatcacattagctacta	12	14	6	9	0	3	0	2	0	1	0	4	0	3	0	1	1	3	4	1	1	6	6			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr18:29511319C>T	ENST00000283351.4	-	2	660	c.325G>A	c.(325-327)Gca>Aca	p.A109T	TRAPPC8_ENST00000582513.1_Missense_Mutation_p.A109T|TRAPPC8_ENST00000582539.1_Missense_Mutation_p.A55T|TRAPPC8_ENST00000584876.1_5'UTR	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	109					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						TAATCTCCTGCTGTAATCACA	0.408																																					p.A109T		Atlas-SNP	.											.	TRAPPC8	126	.	0			c.G325A						PASS	.						129	123	125					18																	29511319		2203	4300	6503	SO:0001583	missense	22878	exon2			CTCCTGCTGTAAT	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.325G>A	18.37:g.29511319C>T	ENSP00000283351:p.Ala109Thr	196	0	0		188	90	0.478723	NM_014939	A0JP15|B3KME5|Q9H0L2	Missense_Mutation	SNP	ENST00000283351.4	37	CCDS11901.1	.	.	.	.	.	.	.	.	.	.	C	17.15	3.315881	0.60524	.	.	ENSG00000153339	ENST00000283351	T	0.08807	3.05	5.98	5.98	0.97165	.	0.062021	0.64402	D	0.000005	T	0.09379	0.0231	L	0.40543	1.245	0.51012	D	0.999907	B;B	0.20780	0.048;0.048	B;B	0.21360	0.012;0.034	T	0.25572	-1.0128	10	0.11485	T	0.65	.	18.6326	0.91366	0.0:1.0:0.0:0.0	.	109;109	Q6PCC9;Q9Y2L5	.;TPPC8_HUMAN	T	109	ENSP00000283351:A109T	ENSP00000283351:A109T	A	-	1	0	TRAPPC8	27765317	1.000000	0.71417	0.921000	0.36526	0.990000	0.78478	6.733000	0.74796	2.838000	0.97847	0.591000	0.81541	GCA	.	.	none		0.408	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939		T	29511319	C	T	29511319	3	4	20	1	0	0	0	0	1	0	0	0	8213	797	28	2	4094	2	KIAA1012	18	29511319	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	3938608	29511319	48565929	98	2719											
SMAD7	4092	hgsc.bcm.edu	37	chr18	46448230	46448230	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cgtcttctcctcccagtatgCcaccacgcaccagtgtgacc	7	9	7	18	2	2	1	0	1	2	0	4	1	3	1	6	0	1	2	6	0	1	2			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr18:46448230C>T	ENST00000262158.2	-	4	1079	c.793G>A	c.(793-795)Gca>Aca	p.A265T	SMAD7_ENST00000589634.1_Missense_Mutation_p.A264T|SMAD7_ENST00000591805.1_Missense_Mutation_p.A50T|SMAD7_ENST00000585986.1_5'UTR	NM_001190821.1|NM_005904.3	NP_001177750.1|NP_005895.1	O15105	SMAD7_HUMAN	SMAD family member 7	265	MH2. {ECO:0000255|PROSITE- ProRule:PRU00439}.				adherens junction assembly (GO:0034333)|artery morphogenesis (GO:0048844)|BMP signaling pathway (GO:0030509)|cellular protein complex localization (GO:0034629)|cellular response to transforming growth factor beta stimulus (GO:0071560)|gene expression (GO:0010467)|negative regulation of BMP signaling pathway (GO:0030514)|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 peptidyl-serine phosphorylation (GO:0033137)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription by competitive promoter binding (GO:0010944)|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 ubiquitin-protein transferase activity (GO:0051444)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein stabilization (GO:0050821)|regulation of activin receptor signaling pathway (GO:0032925)|regulation of cardiac muscle contraction (GO:0055117)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|response to laminar fluid shear stress (GO:0034616)|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)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	activin binding (GO:0048185)|beta-catenin binding (GO:0008013)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|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 transforming growth factor beta receptor binding (GO:0034713)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	10	Colorectal(1;0.0518)					TCCCAGTATGCCACCACGCAC	0.537																																					p.A265T		Atlas-SNP	.											.	SMAD7	22	.	0			c.G793A						PASS	.						51	56	54					18																	46448230		2201	4299	6500	SO:0001583	missense	4092	exon4			AGTATGCCACCAC	AF010193	CCDS11936.1, CCDS54186.1, CCDS59317.1	18q21.1	2006-11-06	2006-11-06	2004-05-26	ENSG00000101665	ENSG00000101665		"SMADs"	6773	protein-coding gene	gene with protein product		602932	"MAD, mothers against decapentaplegic homolog 7 (Drosophila)", "SMAD, mothers against DPP homolog 7 (Drosophila)"	MADH8, MADH7		9256479, 9730599	Standard	NM_005904		Approved		uc002ldg.3	O15105	OTTHUMG00000132655	ENST00000262158.2:c.793G>A	18.37:g.46448230C>T	ENSP00000262158:p.Ala265Thr	42	0	0		46	21	0.456522	NM_005904	B7Z773|K7EQ10|O14740|Q6DK23	Missense_Mutation	SNP	ENST00000262158.2	37	CCDS11936.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.602452	0.87157	.	.	ENSG00000101665	ENST00000545051;ENST00000262158	D	0.98937	-5.25	5.62	5.62	0.85841	SMAD domain-like (1);SMAD/FHA domain (1);SMAD domain, Dwarfin-type (3);	0.102280	0.64402	D	0.000002	D	0.98905	0.9629	M	0.63428	1.95	0.80722	D	1	D;D	0.89917	0.994;1.0	D;D	0.91635	0.954;0.999	D	0.99900	1.1158	10	0.87932	D	0	.	17.8377	0.88704	0.0:1.0:0.0:0.0	.	265;77	O15105;B3KYA8	SMAD7_HUMAN;.	T	50;265	ENSP00000262158:A265T	ENSP00000262158:A265T	A	-	1	0	SMAD7	44702228	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.818000	0.86416	2.643000	0.89663	0.591000	0.81541	GCA	.	.	none		0.537	SMAD7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255906.1	NM_005904		T	46448230	C	T	46448230	3	4	20	1	0	0	0	0	1	0	0	0	14778	739	26	2	491	2	SMAD7	18	46448230	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	16936911	46448230	31629018	99	2720											
DSEL	92126	hgsc.bcm.edu	37	chr18	65178778	65178778	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctatgtacaatgccctcatcGaagctcctaaaacttcctga	12	11	5	13	1	1	1	1	1	0	0	4	2	3	1	3	0	4	2	3	0	6	4			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr18:65178778G>T	ENST00000310045.7	-	2	4571	c.3098C>A	c.(3097-3099)tCg>tAg	p.S1033*	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	1023					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)				TGCCCTCATCGAAGCTCCTAA	0.408																																					p.S1033X		Atlas-SNP	.											DSEL,colon,carcinoma,0,2	DSEL	196	2	0			c.C3098A						PASS	.						81	86	84					18																	65178778		2203	4300	6503	SO:0001587	stop_gained	92126	exon2			CTCATCGAAGCTC	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.3098C>A	18.37:g.65178778G>T	ENSP00000310565:p.Ser1033*	87	0	0		81	32	0.395062	NM_032160	Q17RH1|Q6P5Z3	Nonsense_Mutation	SNP	ENST00000310045.7	37	CCDS11995.1	.	.	.	.	.	.	.	.	.	.	G	51	18.544858	0.99907	.	.	ENSG00000171451	ENST00000310045;ENST00000397964	.	.	.	4.94	4.94	0.65067	.	0.084010	0.50627	U	0.000119	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.1601	18.2215	0.89903	0.0:0.0:1.0:0.0	.	.	.	.	X	1033;1023	.	ENSP00000310565:S1033X	S	-	2	0	DSEL	63329758	1.000000	0.71417	0.820000	0.32676	0.993000	0.82548	9.733000	0.98818	2.292000	0.77174	0.558000	0.71614	TCG	.	.	none		0.408	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160		T	65178778	G	T	65178778	4	4	20	1	0	0	0	0	0	1	0	0	4777	1059	37	4	574	4	DSEL	18	65178778	Nonsense_Mutation	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	18730548	65178778	12898470	100	2721											
MED16	10025	hgsc.bcm.edu	37	chr19	880103	880103	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatggtctgcagtgagagcCggtgcacgatgtggacgctg	7	8	16	10	3	1	1	0	1	1	1	1	4	1	2	2	3	3	3	2	3	0	0			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr19:880103C>T	ENST00000589119.1	-	7	1186	c.1187G>A	c.(1186-1188)cGg>cAg	p.R396Q	MED16_ENST00000312090.6_Missense_Mutation_p.R396Q|MED16_ENST00000325464.1_Missense_Mutation_p.R396Q|MED16_ENST00000269814.4_Missense_Mutation_p.R396Q|MED16_ENST00000395808.3_Missense_Mutation_p.R396Q|MED16_ENST00000606828.1_Intron			Q9Y2X0	MED16_HUMAN	mediator complex subunit 16	396					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)		CAGTGAGAGCCGGTGCACGAT	0.721																																					p.R396Q		Atlas-SNP	.											.	MED16	61	.	0			c.G1187A						PASS	.						20	21	21					19																	880103		2169	4279	6448	SO:0001583	missense	10025	exon8			GAGAGCCGGTGCA	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.1187G>A	19.37:g.880103C>T	ENSP00000464810:p.Arg396Gln	102	0	0		98	37	0.377551	NM_005481	Q6PJT2|Q96AD4|Q96I35|Q9Y652	Missense_Mutation	SNP	ENST00000589119.1	37	CCDS12047.1	.	.	.	.	.	.	.	.	.	.	C	32	5.154168	0.94645	.	.	ENSG00000175221	ENST00000325464;ENST00000312090;ENST00000395808;ENST00000269814;ENST00000534906;ENST00000537596;ENST00000540679;ENST00000538572;ENST00000424039	T;T;T;T	0.51325	0.71;0.71;0.71;0.71	3.94	3.94	0.45596	WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.65831	0.2729	M	0.65498	2.005	0.80722	D	1	D;D;D;D;D	0.71674	0.998;0.998;0.998;0.998;0.998	D;D;D;D;D	0.79108	0.986;0.988;0.986;0.986;0.992	T	0.69720	-0.5069	10	0.54805	T	0.06	-6.181	15.3215	0.74126	0.0:1.0:0.0:0.0	.	396;396;396;396;396	Q9Y2X0-2;E7ETV0;Q9Y2X0-4;Q9Y2X0-3;Q9Y2X0	.;.;.;.;MED16_HUMAN	Q	396;396;396;396;396;252;157;155;396	ENSP00000325612:R396Q;ENSP00000308528:R396Q;ENSP00000379153:R396Q;ENSP00000269814:R396Q	ENSP00000269814:R396Q	R	-	2	0	MED16	831103	1.000000	0.71417	0.994000	0.49952	0.760000	0.43138	6.990000	0.76225	1.910000	0.55303	0.561000	0.74099	CGG	.	.	none		0.721	MED16-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457902.3	NM_005481		T	880103	C	T	880103	3	4	20	1	0	0	0	0	1	0	0	0	9443	652	23	1	1482	1	MED16	19	880103	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10		880103	58248880	101	2722											
PDE4A	5141	hgsc.bcm.edu	37	chr19	10571742	10571742	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgccatccacgatgtggaTcaccctggggtctccaacca	8	8	10	15	1	2	0	1	0	1	0	4	2	3	1	5	3	2	1	5	3	1	0			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr19:10571742T>A	ENST00000352831.6	+	11	1538	c.1428T>A	c.(1426-1428)gaT>gaA	p.D476E	PDE4A_ENST00000380702.2_Missense_Mutation_p.D454E|PDE4A_ENST00000344979.3_Missense_Mutation_p.D237E|PDE4A_ENST00000293683.5_Missense_Mutation_p.D450E|PDE4A_ENST00000592685.1_Missense_Mutation_p.D454E|PDE4A_ENST00000440014.2_Missense_Mutation_p.D415E	NM_001111307.1	NP_001104777.1	P27815	PDE4A_HUMAN	phosphodiesterase 4A, cAMP-specific	476	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)	ACGATGTGGATCACCCTGGGG	0.612																																					p.D476E		Atlas-SNP	.											.	PDE4A	236	.	0			c.T1428A						PASS	.						50	43	45					19																	10571742		2203	4300	6503	SO:0001583	missense	5141	exon11			TGTGGATCACCCT		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.1428T>A	19.37:g.10571742T>A	ENSP00000270474:p.Asp476Glu	36	0	0		81	30	0.37037	NM_001111307	O75522|O76092|Q16255|Q16691|Q5DM53|Q6PMT2|Q8IVA7|Q8WUQ3|Q9H3H2	Missense_Mutation	SNP	ENST00000352831.6	37	CCDS45961.1	.	.	.	.	.	.	.	.	.	.	T	15.72	2.915647	0.52546	.	.	ENSG00000065989	ENST00000380702;ENST00000352831;ENST00000293683;ENST00000440014;ENST00000344979;ENST00000380686	T;T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68;-0.68	4.15	3.08	0.35506	Metal-dependent phosphohydrolase, HD domain (1);-cyclic nucleotide phosphodiesterase, conserved site (1);5&apos (3);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (3);	0.000000	0.85682	D	0.000000	T	0.80037	0.4550	M	0.74467	2.265	0.58432	D	0.999996	B;D;D;P;P	0.63046	0.062;0.992;0.992;0.47;0.695	B;P;D;B;B	0.68943	0.021;0.81;0.961;0.164;0.253	T	0.79685	-0.1700	10	0.87932	D	0	.	7.8314	0.29344	0.0:0.8623:0.0:0.1377	.	142;237;415;450;476	P27815-5;P27815-4;P27815-6;P27815-2;P27815	.;.;.;.;PDE4A_HUMAN	E	454;476;450;415;237;142	ENSP00000370078:D454E;ENSP00000270474:D476E;ENSP00000293683:D450E;ENSP00000394754:D415E;ENSP00000341007:D237E	ENSP00000293683:D450E	D	+	3	2	PDE4A	10432742	0.999000	0.42202	0.998000	0.56505	0.831000	0.47069	0.703000	0.25646	0.867000	0.35654	0.454000	0.30748	GAT	.	.	none		0.612	PDE4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451244.1			A	10571742	T	A	10571742	3	1	20	1	0	0	0	0	1	0	0	0	11648	1432	50	5	1927	5	PDE4A	19	10571742	Missense_Mutation	SNP	T	TCGA-FF-A7CX-01A-12D-A382-10	9691639	10571742	48557241	102	2723											
KRI1	65095	hgsc.bcm.edu	37	chr19	10671051	10671051	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctcctcctcatagcgtttgTtgaggatgtaatcccgcagg	7	12	10	12	2	1	1	1	1	0	0	4	2	4	2	4	2	1	4	4	2	2	4			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr19:10671051T>C	ENST00000312962.6	-	9	774	c.755A>G	c.(754-756)aAc>aGc	p.N252S	KRI1_ENST00000361821.5_Missense_Mutation_p.N248S|KRI1_ENST00000537964.1_5'Flank	NM_023008.3	NP_075384.3	Q8N9T8	KRI1_HUMAN	KRI1 homolog (S. cerevisiae)	246	Glu-rich.			E -> G (in Ref. 1; BAB14357). {ECO:0000305}.		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)			ATAGCGTTTGTTGAGGATGTA	0.547																																					p.N252S		Atlas-SNP	.											.	KRI1	65	.	0			c.A755G						PASS	.						81	68	72					19																	10671051		2203	4300	6503	SO:0001583	missense	65095	exon9			CGTTTGTTGAGGA		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.755A>G	19.37:g.10671051T>C	ENSP00000320917:p.Asn252Ser	32	0	0		24	6	0.25	NM_023008	Q2M1R5|Q2M1R7|Q7L5J7|Q96G92|Q9BU50|Q9H6I1|Q9H978	Missense_Mutation	SNP	ENST00000312962.6	37	CCDS12242.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	26.1|26.1	4.707279|4.707279	0.89018|0.89018	.|.	.|.	ENSG00000129347|ENSG00000129347	ENST00000312962;ENST00000361821;ENST00000541101|ENST00000543682	T;T|.	0.11712|.	2.91;2.75|.	5.36|5.36	5.36|5.36	0.76844|0.76844	.|.	0.096297|.	0.64402|.	D|.	0.000002|.	T|T	0.60418|0.60418	0.2267|0.2267	L|L	0.42686|0.42686	1.345|1.345	0.51233|0.51233	D|D	0.99991|0.99991	D;D|.	0.71674|.	0.998;0.998|.	D;D|.	0.68039|.	0.955;0.955|.	T|T	0.57849|0.57849	-0.7740|-0.7740	10|5	0.26408|.	T|.	0.33|.	-68.9122|-68.9122	14.3212|14.3212	0.66487|0.66487	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	252;248|.	Q8N9T8;D3YTE0|.	KRI1_HUMAN;.|.	S|A	252;248;252|190	ENSP00000320917:N252S;ENSP00000355366:N248S|.	ENSP00000320917:N252S|.	N|T	-|-	2|1	0|0	KRI1|KRI1	10532051|10532051	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	4.214000|4.214000	0.58527|0.58527	2.035000|2.035000	0.60131|0.60131	0.460000|0.460000	0.39030|0.39030	AAC|ACA	.	.	none		0.547	KRI1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317705.1	NM_023008		C	10671051	T	C	10671051	3	2	20	1	0	0	0	0	1	0	0	0	8453	1725	60	3	1418	3	KRI1	19	10671051	Missense_Mutation	SNP	T	TCGA-FF-A7CX-01A-12D-A382-10	99309	10671051	48457932	103	2724											
LOC55908	55908	hgsc.bcm.edu	37	chr19	11350375	11350375	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggtgacccggcctgcctcagCggcccccatgggcggcccag	4	4	15	18	3	1	1	1	1	0	0	1	1	1	1	6	5	2	0	6	5	0	0	rs368909299		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr19:11350375C>T	ENST00000252453.8	+	1	81	c.62C>T	c.(61-63)gCg>gTg	p.A21V	C19orf80_ENST00000591200.1_Intron|DOCK6_ENST00000294618.7_Intron|DOCK6_ENST00000319867.7_5'Flank	NM_018687.6	NP_061157.3	Q6UXH0	BETAT_HUMAN	chromosome 19 open reading frame 80	21					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						CCTGCCTCAGCGGCCCCCATG	0.642																																					p.A21V		Atlas-SNP	.											.	C19orf80	8	.	0			c.C62T						PASS	.	C	,VAL/ALA	0,3976		0,0,1988	26	28	28		,62	-1	0	19		28	1,8303		0,1,4151	no	intron,missense	C19orf80,DOCK6	NM_020812.2,NM_018687.6	,64	0,1,6139	TT,TC,CC		0.012,0.0,0.0081	,benign	,21/199	11350375	1,12279	1988	4152	6140	SO:0001583	missense	55908	exon1			CCTCAGCGGCCCC		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.62C>T	19.37:g.11350375C>T	ENSP00000252453:p.Ala21Val	108	0	0		81	25	0.308642	NM_018687	Q9NQZ1	Missense_Mutation	SNP	ENST00000252453.8	37	CCDS54220.1	.	.	.	.	.	.	.	.	.	.	C	7.645	0.681793	0.14907	0.0	1.2E-4	ENSG00000130173	ENST00000252453	T	0.29917	1.55	3.95	-0.984	0.10259	.	1.345480	0.05125	N	0.491383	T	0.08758	0.0217	N	0.01576	-0.805	0.09310	N	1	B	0.13145	0.007	B	0.06405	0.002	T	0.25813	-1.0121	10	0.02654	T	1	-25.4118	3.7785	0.08671	0.1661:0.3986:0.0:0.4353	.	21	Q6UXH0	TD26_HUMAN	V	21	ENSP00000252453:A21V	ENSP00000252453:A21V	A	+	2	0	C19orf80	11211375	0.000000	0.05858	0.000000	0.03702	0.048000	0.14542	0.032000	0.13732	-0.346000	0.08312	-0.657000	0.03884	GCG	.	.	weak		0.642	C19orf80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453175.1	NM_018687		T	11350375	C	T	11350375	3	4	20	1	0	0	0	0	1	0	0	0	8890	768	27	1	64	1	LOC55908	19	11350375	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	679324	11350375	47778608	104	2725											
KLF2	10365	hgsc.bcm.edu	37	chr19	16436026	16436026	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccattgccctgtcgcccgcaGcgctggccgcgcgccgaacc	4	5	12	20	7	0	0	0	0	0	0	1	1	0	0	6	1	3	2	6	1	1	1			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr19:16436026G>A	ENST00000248071.5	+	2	182		c.e2-1		KLF2_ENST00000592003.1_Intron|CTD-2562J15.6_ENST00000588799.1_RNA	NM_016270.2	NP_057354.1	Q9Y5W3	KLF2_HUMAN	Kruppel-like factor 2						cell morphogenesis (GO:0000902)|cellular response to cycloheximide (GO:0071409)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to peptide (GO:1901653)|cellular response to tumor necrosis factor (GO:0071356)|erythrocyte maturation (GO:0043249)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of interleukin-6 production (GO:0032715)|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 gene expression, epigenetic (GO:0040029)|transcription, DNA-templated (GO:0006351)|Type I pneumocyte differentiation (GO:0060509)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			haematopoietic_and_lymphoid_tissue(3)|lung(1)|skin(1)	5						GTCGCCCGCAGCGCTGGCCGC	0.721																																					.		Atlas-SNP	.											.	KLF2	10	.	0			c.76-1G>A						PASS	.						2	2	2					19																	16436026		1274	2633	3907	SO:0001630	splice_region_variant	10365	exon2			CCCGCAGCGCTGG	AF123344	CCDS12343.1	19p13.11	2013-10-15	2013-10-15		ENSG00000127528	ENSG00000127528		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	6347	protein-coding gene	gene with protein product		602016	"Kruppel-like factor 2 (lung)"			10217429, 10458913	Standard	NM_016270		Approved	LKLF	uc002ndw.3	Q9Y5W3	OTTHUMG00000182330	ENST00000248071.5:c.76-1G>A	19.37:g.16436026G>A		83	0	0		70	28	0.4	NM_016270	Q6IPC4|Q9UJS5|Q9UKR6	Splice_Site	SNP	ENST00000248071.5	37	CCDS12343.1	.	.	.	.	.	.	.	.	.	.	G	1.494	-0.553859	0.03996	.	.	ENSG00000127528	ENST00000248071	.	.	.	2.41	1.33	0.21861	.	.	.	.	.	.	.	.	.	.	.	0.19575	N	0.999965	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.5609	0.27851	0.0:0.0:0.745:0.255	.	.	.	.	.	-1	.	.	.	+	.	.	KLF2	16297026	1.000000	0.71417	0.983000	0.44433	0.017000	0.09413	3.047000	0.49854	0.231000	0.21079	-1.767000	0.00664	.	.	.	none		0.721	KLF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460562.1		Intron	A	16436026	G	A	16436026	5	1	20	1	0	0	0	0	0	0	1	0	8355	985	34	2	81	2	KLF2	19	16436026	Splice_Site	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	5085651	16436026	42692957	105	2726											
SUPT5H	6829	hgsc.bcm.edu	37	chr19	39950582	39950582	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgatgcgcaagttcattgcCtaccagttcacagacacggt	10	11	9	11	2	2	2	2	1	0	1	2	2	2	2	2	1	3	3	2	1	2	5			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr19:39950582C>A	ENST00000599117.1	+	11	973	c.606C>A	c.(604-606)gcC>gcA	p.A202A	SUPT5H_ENST00000359191.6_Silent_p.A198A|SUPT5H_ENST00000598725.1_Silent_p.A202A|SUPT5H_ENST00000402194.2_Silent_p.A198A|SUPT5H_ENST00000432763.2_Silent_p.A202A			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	202	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)			AGTTCATTGCCTACCAGTTCA	0.537																																					p.A202A		Atlas-SNP	.											.	SUPT5H	119	.	0			c.C606A						PASS	.						97	82	87					19																	39950582		2203	4300	6503	SO:0001819	synonymous_variant	6829	exon9			CATTGCCTACCAG	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.606C>A	19.37:g.39950582C>A		52	0	0		33	17	0.515152	NM_003169	O43279|Q59G52|Q99639	Silent	SNP	ENST00000599117.1	37	CCDS12536.1																																																																																			.	.	none		0.537	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464918.1	NM_003169		A	39950582	C	A	39950582	2	1	20	1	0	0	0	0	0	0	0	1	15414	668	24	4		4	SUPT5H	19	39950582	Silent	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	23514556	39950582	19178401	106	2727											
PHLDB3	653583	hgsc.bcm.edu	37	chr19	44006279	44006279	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctcagctccttcctctggcGctgtagctccttcactcgct	3	13	7	18	2	3	0	2	0	1	0	7	0	6	0	4	1	2	5	4	1	1	3			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr19:44006279G>A	ENST00000292140.5	-	3	730	c.370C>T	c.(370-372)Cgc>Tgc	p.R124C	PHLDB3_ENST00000599242.1_Missense_Mutation_p.R124C	NM_198850.3	NP_942147.3	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B, member 3	124							enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|lung(5)	7		Prostate(69;0.0153)				TTCCTCTGGCGCTGTAGCTCC	0.657																																					p.R124C		Atlas-SNP	.											Q96HZ0_HUMAN,rectum,carcinoma,0,4	PHLDB3	30	4	0			c.C370T						PASS	.						26	28	27					19																	44006279		2202	4295	6497	SO:0001583	missense	653583	exon3			TCTGGCGCTGTAG		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.370C>T	19.37:g.44006279G>A	ENSP00000292140:p.Arg124Cys	132	0	0		125	61	0.488	NM_198850	Q8N7Z4	Missense_Mutation	SNP	ENST00000292140.5	37	CCDS12621.2	.	.	.	.	.	.	.	.	.	.	G	24.0	4.483661	0.84854	.	.	ENSG00000176531	ENST00000292140	T	0.47528	0.84	4.11	4.11	0.48088	.	0.938103	0.08873	N	0.881237	T	0.62732	0.2452	L	0.47716	1.5	0.39113	D	0.961502	D;D	0.89917	1.0;1.0	D;P	0.72338	0.977;0.848	T	0.59558	-0.7432	10	0.72032	D	0.01	.	12.2619	0.54655	0.0:0.0:1.0:0.0	.	124;124	Q6NSJ2-2;Q6NSJ2	.;PHLB3_HUMAN	C	124	ENSP00000292140:R124C	ENSP00000292140:R124C	R	-	1	0	PHLDB3	48698119	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	4.602000	0.61098	2.040000	0.60383	0.306000	0.20318	CGC	.	.	none		0.657	PHLDB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319643.2			A	44006279	G	A	44006279	3	1	20	1	0	0	0	0	1	0	0	0	11862	1087	38	1	1608	1	PHLDB3	19	44006279	Missense_Mutation	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	4055697	44006279	15122704	107	2728											
C19orf41	126123	hgsc.bcm.edu	37	chr19	50657864	50657864	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggatgactcacgagaccaCgatgaccacgaagacaaaga	18	3	10	10	3	1	5	1	2	0	3	1	9	1	6	2	1	0	0	2	1	3	0	rs189762069		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr19:50657864C>T	ENST00000293405.3	-	6	616	c.616G>A	c.(616-618)Gtg>Atg	p.V206M		NM_152358.2	NP_689571.2	Q6UXV1	IZUM2_HUMAN	IZUMO family member 2	206						integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	7						CACGAGACCACGATGACCACG	0.577													C|||	1	0.000199681	0.0	0.0	5008	,	,		13120	0.001		0.0	False		,,,				2504	0.0				p.V206M		Atlas-SNP	.											.	IZUMO2	26	.	0			c.G616A						PASS	.	C	MET/VAL	1,4263		0,1,2131	117	135	129		616	-0.5	0	19		129	0,8488		0,0,4244	yes	missense	IZUMO2	NM_152358.2	21	0,1,6375	TT,TC,CC		0.0,0.0235,0.0078	probably-damaging	206/222	50657864	1,12751	2132	4244	6376	SO:0001583	missense	126123	exon6			AGACCACGATGAC	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.616G>A	19.37:g.50657864C>T	ENSP00000293405:p.Val206Met	37	0	0		32	13	0.40625	NM_152358	Q5GRG3|Q5GRG4|Q6ZNM5|Q8NHR8	Missense_Mutation	SNP	ENST00000293405.3	37	CCDS12792.2	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	C	11.80	1.747698	0.30955	2.35E-4	0.0	ENSG00000161652	ENST00000293405	T	0.53640	0.61	3.32	-0.489	0.12052	.	.	.	.	.	T	0.35595	0.0937	L	0.29908	0.895	0.09310	N	1	D	0.63880	0.993	P	0.46253	0.509	T	0.23797	-1.0178	9	0.62326	D	0.03	.	6.0335	0.19692	0.0:0.5467:0.313:0.1403	.	206	Q6UXV1	IZUM2_HUMAN	M	206	ENSP00000293405:V206M	ENSP00000293405:V206M	V	-	1	0	IZUMO2	55349676	0.025000	0.19082	0.006000	0.13384	0.356000	0.29392	-0.553000	0.06012	0.009000	0.14813	0.305000	0.20034	GTG	C|0.999;T|0.001	0.001	strong		0.577	IZUMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157232.1	NM_152358		T	50657864	C	T	50657864	3	4	20	1	0	0	0	0	1	0	0	0	1926	536	19	1	57	1	C19orf41	19	50657864	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	6651585	50657864	8471119	108	2729											
SHANK1	50944	hgsc.bcm.edu	37	chr19	51170329	51170329	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgggtcagggtggccacctCgctgtcataggatgtcaggc	6	9	15	11	1	3	0	3	0	0	0	4	1	3	1	2	5	0	1	2	5	1	1			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr19:51170329C>T	ENST00000293441.1	-	22	4906	c.4888G>A	c.(4888-4890)Gag>Aag	p.E1630K	SHANK1_ENST00000391813.1_Missense_Mutation_p.E1017K|SHANK1_ENST00000391814.1_Missense_Mutation_p.E1638K|SYT3_ENST00000544769.1_Intron|SHANK1_ENST00000359082.3_Missense_Mutation_p.E1621K	NM_016148.2	NP_057232.2	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	1630					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)		GTGGCCACCTCGCTGTCATAG	0.741																																					p.E1630K		Atlas-SNP	.											.	SHANK1	210	.	0			c.G4888A						PASS	.						7	8	8					19																	51170329		2135	4176	6311	SO:0001583	missense	50944	exon22			CCACCTCGCTGTC	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.4888G>A	19.37:g.51170329C>T	ENSP00000293441:p.Glu1630Lys	37	0	0		47	26	0.553191	NM_016148	A8MXP5|B7WNY6|Q9NYW9	Missense_Mutation	SNP	ENST00000293441.1	37	CCDS12799.1	.	.	.	.	.	.	.	.	.	.	C	11.02	1.514991	0.27123	.	.	ENSG00000161681	ENST00000293441;ENST00000391813;ENST00000359082;ENST00000391814	T;T;T;T	0.45668	1.02;1.48;1.0;0.89	2.39	1.29	0.21616	.	0.428107	0.19862	U	0.104406	T	0.37348	0.1000	N	0.13235	0.315	0.40588	D	0.981464	P;D	0.76494	0.875;0.999	B;P	0.61132	0.176;0.884	T	0.30534	-0.9975	10	0.59425	D	0.04	.	7.5315	0.27685	0.0:0.8515:0.0:0.1485	.	1630;1017	Q9Y566;Q9Y566-2	SHAN1_HUMAN;.	K	1630;1017;1621;1638	ENSP00000293441:E1630K;ENSP00000375689:E1017K;ENSP00000351984:E1621K;ENSP00000375690:E1638K	ENSP00000293441:E1630K	E	-	1	0	SHANK1	55862141	0.879000	0.30193	0.999000	0.59377	0.763000	0.43281	1.238000	0.32707	1.043000	0.40175	0.205000	0.17691	GAG	.	.	none		0.741	SHANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268071.1	NM_016148		T	51170329	C	T	51170329	3	4	20	1	0	0	0	0	1	0	0	0	14279	893	31	1	1605	1	SHANK1	19	51170329	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	512465	51170329	7958654	109	2730											
NLRP5	126206	hgsc.bcm.edu	37	chr19	56538497	56538497	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggctctagccagaaggatcGtgctgtgctgggcgcaaggt	7	8	16	10	3	1	1	0	0	1	1	2	2	1	2	1	4	3	4	1	4	3	1			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr19:56538497G>A	ENST00000390649.3	+	7	898	c.898G>A	c.(898-900)Gtg>Atg	p.V300M		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	300	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				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)		CAGAAGGATCGTGCTGTGCTG	0.572																																					p.V300M		Atlas-SNP	.											.	NLRP5	217	.	0			c.G898A						PASS	.						47	53	51					19																	56538497		2103	4219	6322	SO:0001583	missense	126206	exon7			AGGATCGTGCTGT	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.898G>A	19.37:g.56538497G>A	ENSP00000375063:p.Val300Met	72	0	0		75	30	0.4	NM_153447	A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	37	CCDS12938.1	.	.	.	.	.	.	.	.	.	.	G	0.069	-1.205920	0.01568	.	.	ENSG00000171487	ENST00000390649	D	0.81908	-1.55	3.35	-0.145	0.13436	NACHT nucleoside triphosphatase (1);	1.025170	0.07825	N	0.960488	T	0.57917	0.2086	N	0.04116	-0.275	0.09310	N	1	B	0.30634	0.288	B	0.30782	0.12	T	0.51718	-0.8670	10	0.02654	T	1	.	5.3187	0.15870	0.2998:0.5492:0.151:0.0	.	300	P59047	NALP5_HUMAN	M	300	ENSP00000375063:V300M	ENSP00000375063:V300M	V	+	1	0	NLRP5	61230309	1.000000	0.71417	0.001000	0.08648	0.007000	0.05969	1.986000	0.40677	-0.028000	0.13850	-0.302000	0.09304	GTG	.	.	none		0.572	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447		A	56538497	G	A	56538497	3	1	20	1	0	0	0	0	1	0	0	0	10489	1145	40	1	924	1	NLRP5	19	56538497	Missense_Mutation	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	5368168	56538497	2590486	110	2731											
TMEM90B	79953	hgsc.bcm.edu	37	chr20	24565617	24565617	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgggcatcgcagccttctaCttgtcccatgaggtaaggcc	7	10	11	13	1	1	1	0	1	1	0	3	1	2	1	3	3	2	3	3	3	2	4			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr20:24565617C>T	ENST00000376862.3	+	3	1239	c.606C>T	c.(604-606)taC>taT	p.Y202Y	SYNDIG1_ENST00000482637.1_3'UTR	NM_024893.1	NP_079169.1	Q9H7V2	SYNG1_HUMAN	synapse differentiation inducing 1	202					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)			breast(2)|endometrium(1)|large_intestine(3)|lung(14)|prostate(1)|skin(3)	24						CAGCCTTCTACTTGTCCCATG	0.617																																					p.Y202Y		Atlas-SNP	.											.	SYNDIG1	58	.	0			c.C606T						PASS	.						137	124	128					20																	24565617		2203	4300	6503	SO:0001819	synonymous_variant	79953	exon3			CTTCTACTTGTCC	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.606C>T	20.37:g.24565617C>T		131	0	0		105	52	0.495238	NM_024893	Q6IA30|Q9H514	Silent	SNP	ENST00000376862.3	37	CCDS13164.1																																																																																			.	.	none		0.617	SYNDIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078376.1	NM_024893		T	24565617	C	T	24565617	2	4	20	1	0	0	0	0	0	0	0	1	16234	576	20	2		2	TMEM90B	20	24565617	Silent	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10		24565617	38459903	111	2732											
CDH22	64405	hgsc.bcm.edu	37	chr20	44845551	44845551	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaggccacccagctgacccGccatgtctgtggcctggatc	7	7	12	15	1	1	2	0	1	1	1	2	3	1	3	5	3	1	1	5	3	0	0			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr20:44845551G>A	ENST00000372262.3	-	4	1152	c.752C>T	c.(751-753)gCg>gTg	p.A251V	CDH22_ENST00000537909.1_Missense_Mutation_p.A251V|CDH22_ENST00000474438.1_5'UTR	NM_021248.1	NP_067071.1	Q9UJ99	CAD22_HUMAN	cadherin 22, type 2	251	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)				CAGCTGACCCGCCATGTCTGT	0.637																																					p.A251V		Atlas-SNP	.											.	CDH22	112	.	0			c.C752T						PASS	.						93	80	84					20																	44845551		2203	4300	6503	SO:0001583	missense	64405	exon5			TGACCCGCCATGT	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.752C>T	20.37:g.44845551G>A	ENSP00000361336:p.Ala251Val	33	0	0		28	12	0.428571	NM_021248	B9EGK7|O43205	Missense_Mutation	SNP	ENST00000372262.3	37	CCDS13395.1	.	.	.	.	.	.	.	.	.	.	g	18.36	3.606840	0.66558	.	.	ENSG00000149654	ENST00000372262;ENST00000537909	T;T	0.59638	0.25;0.25	4.17	4.17	0.49024	Cadherin (5);Cadherin-like (1);	0.185956	0.46145	N	0.000310	T	0.62744	0.2453	M	0.80422	2.495	0.44890	D	0.997901	P	0.47962	0.903	B	0.43838	0.433	T	0.67436	-0.5671	10	0.33141	T	0.24	.	16.2392	0.82399	0.0:0.0:1.0:0.0	.	251	Q9UJ99	CAD22_HUMAN	V	251	ENSP00000361336:A251V;ENSP00000437790:A251V	ENSP00000361336:A251V	A	-	2	0	CDH22	44278958	0.996000	0.38824	0.986000	0.45419	0.995000	0.86356	2.338000	0.43957	2.379000	0.81126	0.525000	0.51046	GCG	.	.	none		0.637	CDH22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080491.1	NM_021248		A	44845551	G	A	44845551	3	1	20	1	0	0	0	0	1	0	0	0	3109	1087	38	1	1766	1	CDH22	20	44845551	Missense_Mutation	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	20279934	44845551	18179969	112	2733											
CYYR1	116159	hgsc.bcm.edu	37	chr21	27938630	27938630	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtaggagcaacagtagggcGtggttccatcacagcagtaa	13	7	13	8	1	1	0	1	0	0	0	2	1	2	1	1	3	3	6	1	3	4	4	rs79874795	byFrequency	TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr21:27938630G>A	ENST00000299340.4	-	2	474	c.131C>T	c.(130-132)aCg>aTg	p.T44M	CYYR1_ENST00000435845.2_Missense_Mutation_p.T152M|CYYR1_ENST00000400043.3_Missense_Mutation_p.T44M|AP001597.1_ENST00000357401.3_RNA	NM_052954.2	NP_443186.1	Q96J86	CYYR1_HUMAN	cysteine/tyrosine-rich 1	44						integral component of membrane (GO:0016021)				large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	15						ACAGTAGGGCGTGGTTCCATC	0.423													G|||	44	0.00878594	0.0318	0.0014	5008	,	,		18472	0.001		0.0	False		,,,				2504	0.0				p.T44M		Atlas-SNP	.											.	CYYR1	38	.	0			c.C131T						PASS	.	G	MET/THR	103,4303	79.9+/-118.3	2,99,2102	143	122	129		131	4.1	0.3	21	dbSNP_131	129	0,8600		0,0,4300	yes	missense	CYYR1	NM_052954.2	81	2,99,6402	AA,AG,GG		0.0,2.3377,0.7919	probably-damaging	44/155	27938630	103,12903	2203	4300	6503	SO:0001583	missense	116159	exon2			TAGGGCGTGGTTC	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.131C>T	21.37:g.27938630G>A	ENSP00000299340:p.Thr44Met	108	0	0		102	57	0.558824	NM_052954	A0A059TD09|A8MTU9|B2R845|Q53ER3|Q5JPD0|Q96NV7|R9QAJ4|W8CQB3	Missense_Mutation	SNP	ENST00000299340.4	37	CCDS13578.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	G	16.74	3.207186	0.58343	0.023377	0.0	ENSG00000166265	ENST00000299340;ENST00000435845;ENST00000400043	T;T;T	0.34275	1.37;1.37;1.37	5.05	4.09	0.47781	.	0.293803	0.38381	N	0.001715	T	0.28830	0.0715	L	0.44542	1.39	0.09310	N	1	D;D	0.69078	0.997;0.997	P;P	0.58077	0.742;0.832	T	0.09952	-1.0651	10	0.62326	D	0.03	-12.2221	13.1121	0.59278	0.0:0.1628:0.8372:0.0	.	44;44	Q96J86-2;Q96J86	.;CYYR1_HUMAN	M	44;152;44	ENSP00000299340:T44M;ENSP00000401313:T152M;ENSP00000382918:T44M	ENSP00000299340:T44M	T	-	2	0	CYYR1	26860501	1.000000	0.71417	0.274000	0.24659	0.976000	0.68499	4.318000	0.59190	2.731000	0.93534	0.591000	0.81541	ACG	G|0.994;A|0.006	0.006	strong		0.423	CYYR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171654.2	NM_052954		A	27938630	G	A	27938630	3	1	20	1	0	0	0	0	1	0	0	0	4213	1145	40	1	345	1	CYYR1	21	27938630	Missense_Mutation	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10		27938630	20191265	113	2734											
DGCR8	54487	hgsc.bcm.edu	37	chr22	20077332	20077332	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcttgggaacgggaagcataCgggtaggggaggcatcagtc	10	7	17	7	2	2	0	1	0	1	0	3	3	2	3	0	6	3	3	0	6	4	3			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr22:20077332C>T	ENST00000351989.3	+	4	1450	c.1021C>T	c.(1021-1023)Cgg>Tgg	p.R341W	DGCR8_ENST00000383024.2_Missense_Mutation_p.R341W|DGCR8_ENST00000407755.1_Missense_Mutation_p.R341W	NM_022720.6	NP_073557.3	Q8WYQ5	DGCR8_HUMAN	DGCR8 microprocessor complex subunit	341	Necessary for heme-binding and pri-miRNA processing.|Necessary for interaction with NCL.				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)					GGGAAGCATACGGGTAGGGGA	0.547																																					p.R341W		Atlas-SNP	.											.	DGCR8	53	.	0			c.C1021T						PASS	.						140	127	131					22																	20077332		2203	4300	6503	SO:0001583	missense	54487	exon4			AGCATACGGGTAG	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.1021C>T	22.37:g.20077332C>T	ENSP00000263209:p.Arg341Trp	117	0	0		130	59	0.453846	NM_001190326	B2R8G1|Q6DCB2|Q6MZE9|Q6Y2L0|Q96G39|Q96GP8|Q9H6L8|Q9H6T7|Q9NRW2	Missense_Mutation	SNP	ENST00000351989.3	37	CCDS13773.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.454739	0.84209	.	.	ENSG00000128191	ENST00000351989;ENST00000383024;ENST00000407755	T;T;T	0.53640	0.66;0.61;0.61	5.68	3.51	0.40186	.	0.048535	0.85682	D	0.000000	T	0.66005	0.2746	M	0.82823	2.61	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.981	T	0.68250	-0.5458	10	0.87932	D	0	-10.7924	6.7678	0.23576	0.3527:0.5557:0.0:0.0916	.	341;341	Q8WYQ5-3;Q8WYQ5	.;DGCR8_HUMAN	W	341	ENSP00000263209:R341W;ENSP00000372488:R341W;ENSP00000384726:R341W	ENSP00000263209:R341W	R	+	1	2	DGCR8	18457332	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.304000	0.51866	1.401000	0.46761	0.650000	0.86243	CGG	.	.	none		0.547	DGCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318654.1			T	20077332	C	T	20077332	3	4	20	1	0	0	0	0	1	0	0	0	4466	527	19	1	1031	1	DGCR8	22	20077332	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10		20077332	31227234	114	2735											
APOBEC3D	140564	hgsc.bcm.edu	37	chr22	39421643	39421643	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caaattcgatgacaattatgCatccctgcaccgcacgctaa	13	9	6	13	3	0	1	0	1	0	0	2	2	1	1	2	0	2	4	2	0	4	3			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr22:39421643C>T	ENST00000216099.8	+	4	979	c.572C>T	c.(571-573)gCa>gTa	p.A191V	APOBEC3D_ENST00000427494.2_Intron|APOBEC3D_ENST00000381568.4_Missense_Mutation_p.A191V	NM_152426.3	NP_689639.2	Q96AK3	ABC3D_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D	191					defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|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)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines (GO:0016814)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)	11	Melanoma(58;0.04)					GACAATTATGCATCCCTGCAC	0.517																																					p.A191V		Atlas-SNP	.											.	APOBEC3D	61	.	0			c.C572T						PASS	.						325	281	296					22																	39421643		2203	4300	6503	SO:0001583	missense	140564	exon4			ATTATGCATCCCT	BF832090	CCDS46709.1	22q13.1	2012-10-19	2008-05-01		ENSG00000243811	ENSG00000243811		"Apolipoprotein B mRNA editing enzymes"	17354	protein-coding gene	gene with protein product		609900	"apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3D (putative)", "apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3E pseudogene"	APOBEC3E		11863358	Standard	NM_152426		Approved	ARP6, APOBEC3DE	uc003awt.4	Q96AK3	OTTHUMG00000151084	ENST00000216099.8:c.572C>T	22.37:g.39421643C>T	ENSP00000216099:p.Ala191Val	192	0	0		160	66	0.4125	NM_152426	Q5JZ91|Q7Z2N2|Q7Z2N5|Q7Z2N6	Missense_Mutation	SNP	ENST00000216099.8	37	CCDS46709.1	.	.	.	.	.	.	.	.	.	.	.	9.818	1.184973	0.21870	.	.	ENSG00000243811	ENST00000381568;ENST00000216099	T;T	0.66638	-0.22;-0.22	2.44	-4.88	0.03113	APOBEC-like, C-terminal (1);	.	.	.	.	T	0.59729	0.2215	N	0.19112	0.55	0.09310	N	0.999994	D	0.76494	0.999	D	0.83275	0.996	T	0.51490	-0.8699	9	0.30078	T	0.28	.	2.9123	0.05740	0.1786:0.1616:0.5051:0.1547	.	191	Q96AK3	ABC3D_HUMAN	V	191	ENSP00000370980:A191V;ENSP00000216099:A191V	ENSP00000216099:A191V	A	+	2	0	APOBEC3D	37751589	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.396000	0.07278	-1.845000	0.01176	-1.262000	0.01453	GCA	.	.	none		0.517	APOBEC3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321232.2	NM_152426		T	39421643	C	T	39421643	3	4	20	1	0	0	0	0	1	0	0	0	792	710	25	2	586	2	APOBEC3D	22	39421643	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	19344311	39421643	11882923	115	2736											
CPT1B	1375	hgsc.bcm.edu	37	chr22	51012005	51012005	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccaggctgaggtggggagggGtcgtccaggatcctctggaa	7	7	18	9	1	1	1	0	1	1	0	4	4	3	4	3	8	0	1	3	8	1	0			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chr22:51012005G>A	ENST00000360719.2	-	10	1247	c.1110C>T	c.(1108-1110)gaC>gaT	p.D370D	CPT1B_ENST00000395650.2_Silent_p.D370D|CPT1B_ENST00000434492.2_Silent_p.D167D|CPT1B_ENST00000440709.1_Intron|CPT1B_ENST00000312108.7_Silent_p.D370D|CPT1B_ENST00000457250.1_Silent_p.D336D|CHKB-CPT1B_ENST00000453634.1_3'UTR|CPT1B_ENST00000405237.3_Silent_p.D370D	NM_001145135.1|NM_152245.2	NP_001138607.1|NP_689451.1	Q92523	CPT1B_HUMAN	carnitine palmitoyltransferase 1B (muscle)	370					carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		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)		all cancers(3;3.56e-77)|OV - Ovarian serous cystadenocarcinoma(4;5.39e-74)|Epithelial(4;5.58e-70)|GBM - Glioblastoma multiforme(4;5.59e-08)|LUAD - Lung adenocarcinoma(64;0.0016)|Lung(4;0.00942)|BRCA - Breast invasive adenocarcinoma(115;0.207)		GTGGGGAGGGGTCGTCCAGGA	0.607																																					p.D370D	Esophageal Squamous(170;988 1933 25577 30295 48163)	Atlas-SNP	.											.	CPT1B	61	.	0			c.C1110T						PASS	.						59	60	60					22																	51012005		2203	4300	6503	SO:0001819	synonymous_variant	1375	exon10			GGAGGGGTCGTCC	U62733	CCDS14098.1, CCDS46734.1	22q13.33	2007-07-26			ENSG00000205560	ENSG00000205560			2329	protein-coding gene	gene with protein product		601987				9070950	Standard	NM_152245		Approved	M-CPT1, CPT1-M	uc003bmm.3	Q92523	OTTHUMG00000137390	ENST00000360719.2:c.1110C>T	22.37:g.51012005G>A		30	0	0		37	17	0.459459	NM_001145135	B7Z4U4|B7Z5T8|E9PCP2|Q13389|Q99655|Q9BY90	Silent	SNP	ENST00000360719.2	37	CCDS14098.1																																																																																			.	.	none		0.607	CPT1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317264.5	NM_152246		A	51012005	G	A	51012005	2	1	20	1	0	0	0	0	0	0	0	1	3834	1252	44	2		2	CPT1B	22	51012005	Silent	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	11590362	51012005	292561	116	2737											
P2RY8	286530	hgsc.bcm.edu	37	chrX	1585333	1585333	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cccacagagagaagaggttgCccgggatgctgaccgccgcc	9	4	14	14	3	0	4	0	1	0	3	0	6	0	5	5	2	2	2	5	2	1	1			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chrX:1585333C>T	ENST00000381297.4	-	2	329	c.119G>A	c.(118-120)gGc>gAc	p.G40D	P2RY8_ENST00000460672.1_5'UTR	NM_178129.4	NP_835230.1	Q86VZ1	P2RY8_HUMAN	purinergic receptor P2Y, G-protein coupled, 8	40						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(13)|prostate(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)				GAAGAGGTTGCCCGGGATGCT	0.677			T	CRLF2	"B-ALL, Downs associated ALL"																																p.G40D		Atlas-SNP	.		Dom	yes		"X,Y"	Xp22.3; Yp11.3	286530	"purinergic receptor P2Y, G-protein coupled, 8"		L	.	P2RY8	53	.	0			c.G119A						PASS	.						45	46	46					X																	1585333		2203	4296	6499	SO:0001583	missense	286530	exon2			AGGTTGCCCGGGA	AA804531	CCDS14115.1	Xp22.33 and Yp11.3	2012-08-08			ENSG00000182162	ENSG00000182162		"Pseudoautosomal regions / PAR1", "Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	15524	protein-coding gene	gene with protein product		300525				11004484	Standard	NM_178129		Approved	P2Y8	uc004cpz.2	Q86VZ1	OTTHUMG00000021060	ENST00000381297.4:c.119G>A	X.37:g.1585333C>T	ENSP00000370697:p.Gly40Asp	84	0	0		40	34	0.85	NM_178129		Missense_Mutation	SNP	ENST00000381297.4	37	CCDS14115.1	.	.	.	.	.	.	.	.	.	.	c	12.05	1.820917	0.32237	.	.	ENSG00000182162	ENST00000381297	T	0.57107	0.42	2.1	2.1	0.27182	GPCR, rhodopsin-like superfamily (1);	0.165149	0.39274	U	0.001406	T	0.73505	0.3595	M	0.89478	3.035	0.19575	N	0.999967	D	0.89917	1.0	D	0.79784	0.993	T	0.66256	-0.5969	10	0.54805	T	0.06	.	12.2776	0.54744	0.0:1.0:0.0:0.0	.	40	Q86VZ1	P2RY8_HUMAN	D	40	ENSP00000370697:G40D	ENSP00000370697:G40D	G	-	2	0	P2RY8	1545333	0.995000	0.38212	0.099000	0.21106	0.036000	0.12997	4.100000	0.57762	0.637000	0.30526	0.279000	0.19357	GGC	.	.	none		0.677	P2RY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055602.1	NM_178129		T	1585333	C	T	1585333	3	4	20	1	0	0	0	0	1	0	0	0	11364	739	26	2	964	2	P2RY8	23	1585333	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10		1585333	153685227	117	2738											
NDP	4693	hgsc.bcm.edu	37	chrX	43809178	43809178	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggcagcagtgacaggaggaaCggaagggttgcttgaggaca	12	5	18	6	1	0	2	0	2	0	0	0	6	0	6	0	6	3	4	0	6	2	2	rs104894867		TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chrX:43809178C>T	ENST00000378062.5	-	3	676	c.269G>A	c.(268-270)cGt>cAt	p.R90H	NDP-AS1_ENST00000435093.1_RNA|NDP_ENST00000470584.1_5'UTR	NM_000266.3	NP_000257.1	Q00604	NDP_HUMAN	Norrie disease (pseudoglioma)	90	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039}.		R -> C (in ND). {ECO:0000269|PubMed:14635119}.|R -> P (in ND). {ECO:0000269|PubMed:1307245}.		canonical Wnt signaling pathway (GO:0060070)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|extracellular matrix-cell signaling (GO:0035426)|nervous system development (GO:0007399)|placenta development (GO:0001890)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|vacuole organization (GO:0007033)|visual perception (GO:0007601)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)	frizzled binding (GO:0005109)|growth factor activity (GO:0008083)|protein homodimerization activity (GO:0042803)			kidney(1)|lung(2)	3						ACAGGAGGAACGGAAGGGTTG	0.642											OREG0019744	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R90H		Atlas-SNP	.											.	NDP	12	.	0			c.G269A	GRCh37	CI056488|CM920503	NDP	I|M	rs104894867	PASS	.						60	42	48					X																	43809178		2203	4298	6501	SO:0001583	missense	4693	exon3			GAGGAACGGAAGG	X65882	CCDS14262.1	Xp11.4-p11.3	2013-02-26			ENSG00000124479	ENSG00000124479		"Endogenous ligands"	7678	protein-coding gene	gene with protein product		300658	"exudative vitreoretinopathy 2 (X-linked)"	EVR2		8252044	Standard	NM_000266		Approved	norrin	uc004dga.3	Q00604	OTTHUMG00000021391	ENST00000378062.5:c.269G>A	X.37:g.43809178C>T	ENSP00000367301:p.Arg90His	95	0	0	919	74	69	0.932432	NM_000266	B2R8K6|Q5JYH5	Missense_Mutation	SNP	ENST00000378062.5	37	CCDS14262.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.633579	0.87660	.	.	ENSG00000124479	ENST00000378062	D	0.90900	-2.75	5.96	5.96	0.96718	Cystine knot (1);Cystine knot, C-terminal (2);	0.063268	0.64402	D	0.000007	D	0.89921	0.6855	N	0.14661	0.345	0.47441	D	0.999423	D	0.71674	0.998	P	0.56788	0.806	D	0.91752	0.5413	10	0.72032	D	0.01	-23.3466	19.3572	0.94420	0.0:1.0:0.0:0.0	.	90	Q00604	NDP_HUMAN	H	90	ENSP00000367301:R90H	ENSP00000367301:R90H	R	-	2	0	NDP	43694122	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.656000	0.54467	2.524000	0.85096	0.600000	0.82982	CGT	.	.	alt		0.642	NDP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056309.1	NM_000266		T	43809178	C	T	43809178	3	4	20	1	0	0	0	0	1	0	0	0	10259	536	19	1	136	1	NDP	23	43809178	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	42223845	43809178	111461382	118	2739											
ASB12	142689	hgsc.bcm.edu	37	chrX	63444983	63444983	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgcggccaaatagagggggCcagaacatgaagctatgttt	12	8	13	8	1	0	3	0	1	0	2	0	3	0	3	2	3	3	2	2	3	5	3			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chrX:63444983C>T	ENST00000396130.2	-	1	520	c.521G>A	c.(520-522)gGc>gAc	p.G174D	ASB12_ENST00000362002.2_Missense_Mutation_p.G183D|MTMR8_ENST00000453546.1_Missense_Mutation_p.G558D			Q8WXK4	ASB12_HUMAN	ankyrin repeat and SOCS box containing 12	174					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						ATAGAGGGGGCCAGAACATGA	0.562																																					p.G183D		Atlas-SNP	.											.	ASB12	102	.	2	Whole gene deletion(2)	ovary(1)|large_intestine(1)	c.G548A						PASS	.						76	68	71					X																	63444983		2203	4300	6503	SO:0001583	missense	142689	exon2			AGGGGGCCAGAAC	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.521G>A	X.37:g.63444983C>T	ENSP00000379435:p.Gly174Asp	90	0	0		71	64	0.901408	NM_130388	J3KP57|Q2M3D5|Q52LK4|Q6ISF9|Q8N8F5	Missense_Mutation	SNP	ENST00000396130.2	37		.	.	.	.	.	.	.	.	.	.	C	20.9	4.066306	0.76187	.	.	ENSG00000198881;ENSG00000198881;ENSG00000198881;ENSG00000102043	ENST00000362002;ENST00000396130;ENST00000361287;ENST00000453546	T;T;T	0.76578	0.01;0.04;-1.03	4.0	4.0	0.46444	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.80691	0.4671	L	0.27053	0.805	0.36377	D	0.861693	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.85746	0.1340	10	0.66056	D	0.02	-2.8088	14.2368	0.65932	0.0:1.0:0.0:0.0	.	558;174	B4DQL0;Q8WXK4	.;ASB12_HUMAN	D	183;174;183;558	ENSP00000355195:G183D;ENSP00000379435:G174D;ENSP00000394003:G558D	ENSP00000354626:G183D	G	-	2	0	ASB12;MTMR8	63361708	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.023000	0.76437	1.986000	0.57962	0.468000	0.43344	GGC	.	.	none		0.562	ASB12-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding				T	63444983	C	T	63444983	3	4	20	1	0	0	0	0	1	0	0	0	1016	739	26	2	416	2	ASB12	23	63444983	Missense_Mutation	SNP	C	TCGA-FF-A7CX-01A-12D-A382-10	19635805	63444983	91825577	119	2740											
AWAT2	158835	hgsc.bcm.edu	37	chrX	69261726	69261726	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgctggtcaaacagtttacGtagggcatcaatatagagtg	13	11	11	6	1	2	1	2	0	0	1	2	1	2	1	0	2	3	4	0	2	6	5			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chrX:69261726G>A	ENST00000276101.3	-	7	939	c.934C>T	c.(934-936)Cgt>Tgt	p.R312C		NM_001002254.1	NP_001002254.1	Q6E213	AWAT2_HUMAN	acyl-CoA wax alcohol acyltransferase 2	312					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						AACAGTTTACGTAGGGCATCA	0.502																																					p.R312C	NSCLC(80;1334 1436 9350 24214 26427)	Atlas-SNP	.											.	AWAT2	36	.	0			c.C934T						PASS	.						165	127	140					X																	69261726		2203	4300	6503	SO:0001583	missense	158835	exon7			GTTTACGTAGGGC	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.934C>T	X.37:g.69261726G>A	ENSP00000421172:p.Arg312Cys	123	0	0		108	89	0.824074	NM_001002254	Q6IEE3|Q6P437	Missense_Mutation	SNP	ENST00000276101.3	37	CCDS35320.1	.	.	.	.	.	.	.	.	.	.	G	3.291	-0.144980	0.06627	.	.	ENSG00000147160	ENST00000276101	D	0.93366	-3.21	4.94	-0.467	0.12150	.	0.674304	0.14683	N	0.304642	D	0.84660	0.5521	N	0.21240	0.645	0.09310	N	1	B	0.25486	0.127	B	0.23419	0.046	T	0.73285	-0.4031	10	0.49607	T	0.09	.	4.6613	0.12643	0.3968:0.0:0.4605:0.1427	.	312	Q6E213	AWAT2_HUMAN	C	312	ENSP00000421172:R312C	ENSP00000421172:R312C	R	-	1	0	AWAT2	69178451	0.002000	0.14202	0.000000	0.03702	0.087000	0.18053	1.168000	0.31859	-0.386000	0.07821	-0.190000	0.12839	CGT	.	.	none		0.502	AWAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358738.1	NM_001002254		A	69261726	G	A	69261726	3	1	20	1	0	0	0	0	1	0	0	0	1235	1145	40	1	71	1	AWAT2	23	69261726	Missense_Mutation	SNP	G	TCGA-FF-A7CX-01A-12D-A382-10	5816743	69261726	86008834	120	2741											
SLC6A14	11254	hgsc.bcm.edu	37	chrX	115584183	115584183	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatcatacatgtttcgtaggTtttgatttggcattcattgc	8	19	8	6	1	2	1	2	1	0	0	3	1	2	1	0	2	2	4	0	2	3	9			TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chrX:115584183T>A	ENST00000371900.4	+	9	1249	c.1161T>A	c.(1159-1161)ggT>ggA	p.G387G		NM_007231.3	NP_009162.1	Q9UN76	S6A14_HUMAN	solute carrier family 6 (amino acid transporter), member 14	387					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)	GTTTCGTAGGTTTTGATTTGG	0.318																																					p.G387G		Atlas-SNP	.											.	SLC6A14	56	.	0			c.T1161A						PASS	.						131	114	120					X																	115584183		2203	4300	6503	SO:0001630	splice_region_variant	11254	exon9			CGTAGGTTTTGAT	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.1160-1T>A	X.37:g.115584183T>A		157	1	0.00636943		111	91	0.81982	NM_007231	Q5H942	Silent	SNP	ENST00000371900.4	37	CCDS14570.1																																																																																			.	.	none		0.318	SLC6A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057986.1		Silent	A	115584183	T	A	115584183	5	1	20	1	0	0	0	0	0	0	1	0	14692	1739	60	5	1195	5	SLC6A14	23	115584183	Splice_Site	SNP	T	TCGA-FF-A7CX-01A-12D-A382-10	46322457	115584183	39686377	121	2742											
SLC6A14	11254	hgsc.bcm.edu	37	chrX	115584299	115584299	+	Frame_Shift_Del	DEL	C	C	-																															gggtctcgattctcagtttgCttcgattggtaagtaatact																										TCGA-FF-A7CX-01A-12D-A382-10	TCGA-FF-A7CX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4d394512-e495-472b-89e0-bb402f714949	3a9f03ca-8618-47eb-80a8-120d835ab714	g.chrX:115584299delC	ENST00000371900.4	+	9	1365	c.1277delC	c.(1276-1278)gctfs	p.A426fs		NM_007231.3	NP_009162.1	Q9UN76	S6A14_HUMAN	solute carrier family 6 (amino acid transporter), member 14	426					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)	TCTCAGTTTGCTTCGATTGGT	0.378																																					p.A426fs		Pindel,Atlas-Indel	.											.	SLC6A14	56	.	0			c.1276delG						PASS	.						159	134	142					X																	115584299		2203	4300	6503	SO:0001589	frameshift_variant	11254	exon9			.	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.1277delC	X.37:g.115584299delC	ENSP00000360967:p.Ala426fs	162	0	.		113	64	0.566	NM_007231	Q5H942	Frame_Shift_Del	DEL	ENST00000371900.4	37	CCDS14570.1																																																																																			.	.	none		0.378	SLC6A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057986.1			-	115584299	C	-	115584299	7	5	20	1	0	1	0	1	0	0	0	0	14692	797	28	0	1311	0	SLC6A14	23	115584299	Frame_Shift_Del	DEL	C	TCGA-FF-A7CX-01A-12D-A382-10	116	115584299	39686261	122	2743											
PRAMEF4	400735	hgsc.bcm.edu	37	chr1	12942173	12942173	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcctcttggcattgaggaagCacccatgggccatagcttca	9	10	10	12	0	2	1	1	1	1	0	3	2	3	2	3	3	2	3	3	3	2	4	rs201789683		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	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	1	0			c.G377C						scavenged	.						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	1.37:g.12942173C>G	ENSP00000235349:p.Cys126Ser	61	0	0		33	4	0.121212	NM_001009611	Q5LJB5	Missense_Mutation	SNP	ENST00000235349.5	37	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	0.500	weak		0.493	PRAMEF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005518.1	NM_001009611		G	12942173	C	G	12942173	3	3	21	1	0	0	0	0	1	0	0	0	12449	710	25	4	1067	4	PRAMEF4	1	12942173	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10		12942173	236308448	1	2744											
ARID1A	8289	hgsc.bcm.edu	37	chr1	27056217	27056217	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctaacccatactcgcagcaaCagggacctccgtcaggaccg	11	5	9	16	3	1	0	1	0	0	0	3	2	2	2	4	2	4	2	4	2	3	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr1:27056217C>T	ENST00000324856.7	+	2	1584	c.1213C>T	c.(1213-1215)Cag>Tag	p.Q405*	ARID1A_ENST00000457599.2_Nonsense_Mutation_p.Q405*|ARID1A_ENST00000374152.2_Nonsense_Mutation_p.Q22*	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	405					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.Q405*(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)		CTCGCAGCAACAGGGACCTCC	0.577			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.Q405X		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	ARID1A,NS,carcinoma,0,1	ARID1A	842	1	1	Substitution - Nonsense(1)	endometrium(1)	c.C1213T						PASS	.						90	93	92					1																	27056217		2203	4300	6503	SO:0001587	stop_gained	8289	exon2			CAGCAACAGGGAC	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.1213C>T	1.37:g.27056217C>T	ENSP00000320485:p.Gln405*	376	1	0.00265957		269	99	0.36803	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Nonsense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	C	37	6.467169	0.97590	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000524572;ENST00000374152	.	.	.	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	-7.4344	20.8598	0.99761	0.0:1.0:0.0:0.0	.	.	.	.	X	405;405;22;22	.	ENSP00000320485:Q405X	Q	+	1	0	ARID1A	26928804	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.752000	0.68728	2.937000	0.99478	0.650000	0.86243	CAG	.	.	none		0.577	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		T	27056217	C	T	27056217	4	4	21	1	0	0	0	0	0	1	0	0	913	479	17	2	1219	2	ARID1A	1	27056217	Nonsense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	14114044	27056217	222194404	2	2745											
ZSCAN20	7579	hgsc.bcm.edu	37	chr1	33959918	33959918	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgtcctacagaagctgtttgCcaacctcttgactggggaga	9	11	11	10	0	1	3	0	1	1	2	2	4	2	3	3	2	4	2	3	2	3	3			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr1:33959918C>T	ENST00000361328.3	+	8	2127	c.1974C>T	c.(1972-1974)tgC>tgT	p.C658C		NM_145238.3	NP_660281	P17040	ZSC20_HUMAN	zinc finger and SCAN domain containing 20	658					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)				AAGCTGTTTGCCAACCTCTTG	0.448																																					p.C658C		Atlas-SNP	.											.	ZSCAN20	107	.	0			c.C1974T						PASS	.						71	70	70					1																	33959918		1865	4109	5974	SO:0001819	synonymous_variant	7579	exon8			TGTTTGCCAACCT	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.1974C>T	1.37:g.33959918C>T		240	0	0		169	73	0.431953	NM_145238	A8K2D0|B1ALI4|B1ALI5|B1ALI6|Q6ZN23|Q96FA9|Q96H84	Silent	SNP	ENST00000361328.3	37	CCDS41300.1																																																																																			.	.	none		0.448	ZSCAN20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277003.2	NM_145238		T	33959918	C	T	33959918	2	4	21	1	0	0	0	0	0	0	0	1	18247	747	26	2		2	ZSCAN20	1	33959918	Silent	SNP	C	TCGA-FM-8000-01A-11D-2210-10	6903701	33959918	215290703	3	2746											
GJA9	81025	hgsc.bcm.edu	37	chr1	39341674	39341674	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tacacccagaacaagcattcGaaatatgaacaggatggtga	17	7	9	8	1	0	3	0	2	0	1	1	5	0	4	1	2	4	1	1	2	6	3			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr1:39341674G>A	ENST00000360786.3	-	1	349	c.97C>T	c.(97-99)Cga>Tga	p.R33*	RP5-864K19.4_ENST00000456813.1_RNA|RP5-864K19.4_ENST00000433671.2_RNA|RP5-864K19.4_ENST00000443161.1_RNA|GJA9_ENST00000454994.2_Nonsense_Mutation_p.R33*|MYCBP_ENST00000397572.2_5'Flank|GJA9_ENST00000357771.3_Nonsense_Mutation_p.R33*|MYCBP_ENST00000489803.1_5'UTR			P57773	CXA9_HUMAN	gap junction protein, alpha 9, 59kDa	33					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)			ACAAGCATTCGAAATATGAAC	0.463																																					p.R33X		Atlas-SNP	.											GJA9,NS,carcinoma,+1,2	GJA9	55	2	0			c.C97T						PASS	.						232	234	234					1																	39341674		2203	4300	6503	SO:0001587	stop_gained	81025	exon2			GCATTCGAAATAT	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.97C>T	1.37:g.39341674G>A	ENSP00000354020:p.Arg33*	105	0	0		88	32	0.363636	NM_030772	B2R722|B3KVQ2|Q5TA63|Q96KG0	Nonsense_Mutation	SNP	ENST00000360786.3	37	CCDS432.1	.	.	.	.	.	.	.	.	.	.	G	37	6.181663	0.97352	.	.	ENSG00000131233	ENST00000454994;ENST00000357771;ENST00000360786	.	.	.	4.56	1.49	0.22878	.	0.000000	0.64402	U	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.2658	0.20925	0.1684:0.0:0.6824:0.1491	.	.	.	.	X	33	.	ENSP00000350415:R33X	R	-	1	2	GJA9	39114261	1.000000	0.71417	0.990000	0.47175	0.995000	0.86356	3.814000	0.55643	0.198000	0.20407	0.655000	0.94253	CGA	.	.	none		0.463	GJA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001205.1	NM_030772		A	39341674	G	A	39341674	4	1	21	1	0	0	0	0	0	1	0	0	6414	1066	37	1	1454	1	GJA9	1	39341674	Nonsense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	5381756	39341674	209908947	4	2747											
PTBP2	58155	hgsc.bcm.edu	37	chr1	97243142	97243142	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acataatcttaatttccagcGtgctcaggcagttcttcaag	11	13	7	10	1	4	0	2	0	2	0	5	0	5	0	1	1	2	3	1	1	3	5			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr1:97243142G>A	ENST00000426398.2	+	6	477	c.434G>A	c.(433-435)cGt>cAt	p.R145H	PTBP2_ENST00000541987.1_Splice_Site_p.R114H|PTBP2_ENST00000370198.1_Splice_Site_p.R145H|PTBP2_ENST00000482253.1_3'UTR|PTBP2_ENST00000370197.1_Splice_Site_p.R145H|PTBP2_ENST00000609116.1_Splice_Site_p.R145H|PTBP2_ENST00000394184.3_Splice_Site_p.R156H	NM_021190.2	NP_067013.1	Q9UKA9	PTBP2_HUMAN	polypyrimidine tract binding protein 2	145					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)		AATTTCCAGCGTGCTCAGGCA	0.438																																					p.R145H		Atlas-SNP	.											.	PTBP2	62	.	0			c.G434A						PASS	.						68	66	67					1																	97243142		2203	4300	6503	SO:0001630	splice_region_variant	58155	exon6			TCCAGCGTGCTCA	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.433-1G>A	1.37:g.97243142G>A		332	0	0		216	98	0.453704	NM_021190	Q8N0Z1|Q8N160|Q8NFB0|Q8NFB1|Q969N9|Q96Q76	Missense_Mutation	SNP	ENST00000426398.2	37	CCDS754.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.813104	0.90707	.	.	ENSG00000117569	ENST00000236228;ENST00000370198;ENST00000370197;ENST00000426398;ENST00000394184;ENST00000541987;ENST00000394176	T;T;T;T;T;T	0.77750	0.89;0.86;0.86;0.89;0.87;-1.12	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	D	0.86100	0.5852	M	0.69463	2.115	0.80722	D	1	B;D;D;B;B;B	0.76494	0.069;0.999;0.999;0.276;0.227;0.397	B;D;D;B;B;B	0.76071	0.059;0.987;0.984;0.049;0.03;0.071	D	0.84408	0.0564	10	0.52906	T	0.07	-2.5786	20.5632	0.99335	0.0:0.0:1.0:0.0	.	153;156;145;145;145;145	B4DSU5;B4DSS8;Q9UKA9-4;Q9UKA9;Q9UKA9-2;Q9UKA9-3	.;.;.;PTBP2_HUMAN;.;.	H	145;145;145;145;156;114;135	ENSP00000236228:R145H;ENSP00000359217:R145H;ENSP00000359216:R145H;ENSP00000412788:R145H;ENSP00000377738:R156H;ENSP00000442475:R114H	ENSP00000236228:R145H	R	+	2	0	PTBP2	97015730	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.143000	0.94623	2.937000	0.99478	0.650000	0.86243	CGT	.	.	none		0.438	PTBP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029453.1		Missense_Mutation	A	97243142	G	A	97243142	5	1	21	1	0	0	0	0	0	0	1	0	12738	1159	40	1	456	1	PTBP2	1	97243142	Splice_Site	SNP	G	TCGA-FM-8000-01A-11D-2210-10	57901468	97243142	152007479	5	2748											
VANGL1	81839	hgsc.bcm.edu	37	chr1	116206595	116206595	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gacctgggcactttttttccGcaagcggagagctgacatgc	8	10	12	11	2	0	2	0	1	0	1	1	4	1	2	2	2	3	3	2	2	1	3	rs148341022		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr1:116206595G>A	ENST00000355485.2	+	4	789	c.518G>A	c.(517-519)cGc>cAc	p.R173H	VANGL1_ENST00000310260.3_Missense_Mutation_p.R173H|VANGL1_ENST00000369509.1_Missense_Mutation_p.R173H|VANGL1_ENST00000369510.4_Missense_Mutation_p.R171H	NM_001172411.1|NM_138959.2	NP_001165882.1|NP_620409.1	Q8TAA9	VANG1_HUMAN	VANGL planar cell polarity protein 1	173					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)		p.F171fs*93(1)		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)		CTTTTTTTCCGCAAGCGGAGA	0.493													G|||	1	0.000199681	0.0	0.0014	5008	,	,		18866	0.0		0.0	False		,,,				2504	0.0				p.R173H		Atlas-SNP	.											.	VANGL1	65	.	1	Deletion - Frameshift(1)	kidney(1)	c.G518A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG	0,4406		0,0,2203	157	164	162		512,518,518	4.4	1	1	dbSNP_134	162	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	VANGL1	NM_001172411.1,NM_001172412.1,NM_138959.2	29,29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	171/523,173/525,173/525	116206595	1,13005	2203	4300	6503	SO:0001583	missense	81839	exon4			TTTTCCGCAAGCG	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.518G>A	1.37:g.116206595G>A	ENSP00000347672:p.Arg173His	344	1	0.00290698		214	82	0.383178	NM_138959	Q5T1D3|Q5T1D4|Q86WG8|Q8N559	Missense_Mutation	SNP	ENST00000355485.2	37	CCDS883.1	.	.	.	.	.	.	.	.	.	.	G	18.45	3.625876	0.66901	0.0	1.16E-4	ENSG00000173218	ENST00000355485;ENST00000369510;ENST00000310260;ENST00000369509	D;D;D;D	0.87179	-2.22;-2.22;-2.22;-2.22	5.34	4.43	0.53597	.	0.000000	0.85682	D	0.000000	D	0.92355	0.7574	M	0.84511	2.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.979;0.988	D	0.93638	0.6962	10	0.72032	D	0.01	-0.2344	14.2916	0.66281	0.0719:0.0:0.9281:0.0	.	171;173	Q8TAA9-2;Q8TAA9	.;VANG1_HUMAN	H	173;171;173;173	ENSP00000347672:R173H;ENSP00000358523:R171H;ENSP00000310800:R173H;ENSP00000358522:R173H	ENSP00000310800:R173H	R	+	2	0	VANGL1	116008118	1.000000	0.71417	1.000000	0.80357	0.414000	0.31173	9.476000	0.97823	1.397000	0.46682	-0.142000	0.14014	CGC	G|1.000;A|0.000	0.000	weak		0.493	VANGL1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033096.1			A	116206595	G	A	116206595	3	1	21	1	0	0	0	0	1	0	0	0	17134	1087	38	1	528	1	VANGL1	1	116206595	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	18963453	116206595	133044026	6	2749											
ANKRD35	148741	hgsc.bcm.edu	37	chr1	145561654	145561654	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gacagcaactgactaccaatGgggcacagacctttggccct	11	7	10	13	0	0	2	0	1	0	1	0	3	0	2	3	3	3	2	3	3	3	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr1:145561654G>A	ENST00000355594.4	+	10	1429	c.1342G>A	c.(1342-1344)Ggg>Agg	p.G448R		NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	448										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)					GACTACCAATGGGGCACAGAC	0.572																																					p.G448R	Melanoma(9;127 754 22988 51047)	Atlas-SNP	.											.	ANKRD35	96	.	0			c.G1342A						PASS	.						61	70	67					1																	145561654		2203	4300	6503	SO:0001583	missense	148741	exon10			ACCAATGGGGCAC	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.1342G>A	1.37:g.145561654G>A	ENSP00000347802:p.Gly448Arg	124	0	0		148	44	0.297297	NM_144698	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	37	CCDS919.1	.	.	.	.	.	.	.	.	.	.	G	2.695	-0.272176	0.05716	.	.	ENSG00000198483	ENST00000453670;ENST00000355594	D	0.81821	-1.54	5.08	1.06	0.20224	.	0.359955	0.20369	N	0.093688	T	0.51601	0.1684	L	0.57536	1.79	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.41752	-0.9491	10	0.22706	T	0.39	-7.101	4.7491	0.13052	0.2659:0.1576:0.5765:0.0	.	448	Q8N283	ANR35_HUMAN	R	357;448	ENSP00000347802:G448R	ENSP00000347802:G448R	G	+	1	0	ANKRD35	144273011	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.130000	0.15850	0.012000	0.14892	0.655000	0.94253	GGG	.	.	none		0.572	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698		A	145561654	G	A	145561654	3	1	21	1	0	0	0	0	1	0	0	0	664	1348	47	2	1380	2	ANKRD35	1	145561654	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	29355059	145561654	103688967	7	2750											
KPRP	448834	hgsc.bcm.edu	37	chr1	152732767	152732767	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccctgtgtgccccagtgcCagacccagggctcctatggg	5	8	13	15	0	0	1	0	0	0	1	2	1	2	1	6	2	2	1	6	2	1	1	rs569937176		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr1:152732767C>T	ENST00000606109.1	+	1	731	c.703C>T	c.(703-705)Cag>Tag	p.Q235*	KPRP_ENST00000368773.1_Nonsense_Mutation_p.Q235*			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	235						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)			GCCCCAGTGCCAGACCCAGGG	0.602													C|||	1	0.000199681	0.0	0.0014	5008	,	,		17686	0.0		0.0	False		,,,				2504	0.0				p.Q235X		Atlas-SNP	.											.	KPRP	152	.	0			c.C703T						PASS	.						76	81	80					1																	152732767		2203	4300	6503	SO:0001587	stop_gained	448834	exon2			CAGTGCCAGACCC	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.703C>T	1.37:g.152732767C>T	ENSP00000475216:p.Gln235*	142	0	0		129	30	0.232558	NM_001025231		Nonsense_Mutation	SNP	ENST00000606109.1	37	CCDS30862.1	.	.	.	.	.	.	.	.	.	.	C	17.23	3.336488	0.60963	.	.	ENSG00000203786	ENST00000368773	.	.	.	5.78	2.71	0.32032	.	0.165834	0.29152	N	0.012987	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-4.1297	4.9823	0.14172	0.1513:0.6187:0.1469:0.083	.	.	.	.	X	235	.	ENSP00000357762:Q235X	Q	+	1	0	KPRP	150999391	0.001000	0.12720	0.141000	0.22245	0.397000	0.30659	0.391000	0.20784	0.885000	0.36088	0.655000	0.94253	CAG	.	.	none		0.602	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231		T	152732767	C	T	152732767	4	4	21	1	0	0	0	0	0	1	0	0	8445	595	21	2	705	2	KPRP	1	152732767	Nonsense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	7171113	152732767	96517854	8	2751											
USF1	7391	hgsc.bcm.edu	37	chr1	161012436	161012436	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggcaatagccacactggttGggtcttccccagtagccact	8	10	10	13	0	1	0	0	0	1	0	2	0	2	0	4	3	2	3	4	3	3	4			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr1:161012436G>A	ENST00000368021.3	-	4	287	c.83C>T	c.(82-84)cCa>cTa	p.P28L	USF1_ENST00000368020.1_Missense_Mutation_p.P28L|USF1_ENST00000368019.1_Missense_Mutation_p.P28L|USF1_ENST00000435396.1_5'UTR	NM_007122.3	NP_009053.1	P22415	USF1_HUMAN	upstream transcription factor 1	28					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)			CACACTGGTTGGGTCTTCCCC	0.522																																					p.P28L		Atlas-SNP	.											.	USF1	29	.	0			c.C83T						PASS	.						54	53	54					1																	161012436		2203	4300	6503	SO:0001583	missense	7391	exon4			CTGGTTGGGTCTT	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.83C>T	1.37:g.161012436G>A	ENSP00000357000:p.Pro28Leu	148	0	0		145	31	0.213793	NM_001276373	B2RBZ4|Q5SY46|Q7Z5Y1	Missense_Mutation	SNP	ENST00000368021.3	37	CCDS1214.1	.	.	.	.	.	.	.	.	.	.	G	18.00	3.526071	0.64860	.	.	ENSG00000158773	ENST00000368020;ENST00000368021;ENST00000368019;ENST00000531842	D;D;D;D	0.93076	-3.14;-3.14;-3.16;-2.74	4.74	4.74	0.60224	.	0.000000	0.85682	D	0.000000	D	0.90051	0.6893	L	0.58101	1.795	0.80722	D	1	P	0.43938	0.822	B	0.42555	0.391	D	0.91114	0.4924	10	0.52906	T	0.07	-14.642	15.2652	0.73654	0.0:0.0:1.0:0.0	.	28	P22415	USF1_HUMAN	L	28	ENSP00000356999:P28L;ENSP00000357000:P28L;ENSP00000356998:P28L;ENSP00000435005:P28L	ENSP00000356998:P28L	P	-	2	0	USF1	159279060	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.478000	0.60230	2.450000	0.82876	0.655000	0.94253	CCA	.	.	none		0.522	USF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077050.1	NM_007122		A	161012436	G	A	161012436	3	1	21	1	0	0	0	0	1	0	0	0	17047	1348	47	2	881	2	USF1	1	161012436	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	8279669	161012436	88238185	9	2752											
PIGC	5279	hgsc.bcm.edu	37	chr1	172411314	172411314	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcatgaagactgacatggcaTagatggtgtcagtgctgaca	12	9	13	7	0	1	5	1	3	0	2	1	5	1	5	0	2	1	3	0	2	2	1			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr1:172411314T>C	ENST00000367728.1	-	1	1912	c.449A>G	c.(448-450)tAt>tGt	p.Y150C	PIGC_ENST00000484368.1_Intron|PIGC_ENST00000344529.4_Missense_Mutation_p.Y150C|PIGC_ENST00000258324.1_Missense_Mutation_p.Y150C|C1orf105_ENST00000367727.4_Intron			Q92535	PIGC_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class C	150					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						TGACATGGCATAGATGGTGTC	0.468																																					p.Y150C		Atlas-SNP	.											.	PIGC	24	.	0			c.A449G						PASS	.						71	61	64					1																	172411314		2203	4300	6503	SO:0001583	missense	5279	exon2			ATGGCATAGATGG	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.449A>G	1.37:g.172411314T>C	ENSP00000356702:p.Tyr150Cys	123	0	0		114	61	0.535088	NM_153747	O14491	Missense_Mutation	SNP	ENST00000367728.1	37	CCDS1302.1	.	.	.	.	.	.	.	.	.	.	T	19.00	3.741330	0.69304	.	.	ENSG00000135845	ENST00000344529;ENST00000367728;ENST00000258324	T;T;T	0.45668	0.89;0.89;0.89	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	T	0.59542	0.2201	M	0.83118	2.625	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.67448	-0.5668	10	0.72032	D	0.01	-6.9131	13.6827	0.62496	0.0:0.0:0.0:1.0	.	150	Q92535	PIGC_HUMAN	C	150	ENSP00000356701:Y150C;ENSP00000356702:Y150C;ENSP00000258324:Y150C	ENSP00000258324:Y150C	Y	-	2	0	PIGC	170677937	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.528000	0.81941	1.917000	0.55516	0.528000	0.53228	TAT	.	.	none		0.468	PIGC-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084068.1	NM_153747		C	172411314	T	C	172411314	3	2	21	1	0	0	0	0	1	0	0	0	11895	1406	49	3	448	3	PIGC	1	172411314	Missense_Mutation	SNP	T	TCGA-FM-8000-01A-11D-2210-10	11398878	172411314	76839307	10	2753											
TSEN15	116461	hgsc.bcm.edu	37	chr1	184020964	184020964	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcggtgttcgcggctttggCgacggcggtggagctccttc	2	10	18	11	6	0	0	0	0	0	0	3	2	1	1	1	7	1	3	1	7	0	3			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr1:184020964C>A	ENST00000361641.1	+	1	154	c.75C>A	c.(73-75)ggC>ggA	p.G25G	TSEN15_ENST00000533373.1_Silent_p.G25G|TSEN15_ENST00000423085.2_Silent_p.G25G	NM_052965.2	NP_443197.1	Q8WW01	SEN15_HUMAN	TSEN15 tRNA splicing endonuclease subunit	25					mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	nucleus (GO:0005634)	tRNA-intron endonuclease activity (GO:0000213)			breast(1)|kidney(3)|large_intestine(2)|lung(2)	8						GCGGCTTTGGCGACGGCGGTG	0.746																																					p.G25G		Atlas-SNP	.											.	TSEN15	19	.	0			c.C75A						PASS	.						6	9	8					1																	184020964		2080	4114	6194	SO:0001819	synonymous_variant	116461	exon1			CTTTGGCGACGGC	AF288394	CCDS1361.1, CCDS44286.1, CCDS72993.1	1q25	2013-08-06	2013-08-06	2008-06-12	ENSG00000198860	ENSG00000198860		"tRNA splicing endonuclease subunits"	16791	protein-coding gene	gene with protein product		608756	"chromosome 1 open reading frame 19", "tRNA splicing endonuclease 15 homolog (S. cerevisiae)"	C1orf19		11318611, 17166513	Standard	XM_006711148		Approved		uc001gqt.4	Q8WW01	OTTHUMG00000035461	ENST00000361641.1:c.75C>A	1.37:g.184020964C>A		38	0	0		41	13	0.317073	NM_001127394	B4DKP0|Q9BZQ5	Silent	SNP	ENST00000361641.1	37	CCDS1361.1																																																																																			.	.	none		0.746	TSEN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086132.1			A	184020964	C	A	184020964	2	1	21	1	0	0	0	0	0	0	0	1	16626	755	27	4		4	TSEN15	1	184020964	Silent	SNP	C	TCGA-FM-8000-01A-11D-2210-10	11609650	184020964	65229657	11	2754											
PRG4	10216	hgsc.bcm.edu	37	chr1	186277976	186277979	+	Frame_Shift_Del	DEL	GAGT	GAGT	-																															aaagccaaaaacaatgcctaGagtgagaaaaccaaagacga																										TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	GAGT	GAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr1:186277976_186277979delGAGT	ENST00000445192.2	+	7	3170_3173	c.3125_3128delGAGT	c.(3124-3129)agagtgfs	p.RV1042fs	PRG4_ENST00000367484.3_Frame_Shift_Del_p.RV571fs|RNU6-1240P_ENST00000365155.1_RNA|PRG4_ENST00000367483.4_Frame_Shift_Del_p.RV1001fs|PRG4_ENST00000367486.3_Frame_Shift_Del_p.RV999fs|PRG4_ENST00000367485.4_Frame_Shift_Del_p.RV949fs	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	1042					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						ACAATGCCTAGAGTGAGAAAACCA	0.446																																					p.1042_1043del		Pindel,Atlas-Indel	.											PRG4,NS,adenoma,-1,1	PRG4	259	1	0			c.3124_3127del	GRCh37	CD061459	PRG4	D		PASS	.																																			SO:0001589	frameshift_variant	10216	exon7			.	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.3125_3128delGAGT	1.37:g.186277976_186277979delGAGT	ENSP00000399679:p.Arg1042fs	118	0	.		105	18	0.171	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Frame_Shift_Del	DEL	ENST00000445192.2	37	CCDS1369.1																																																																																			.	.	none		0.446	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		-	186277979	GAGT	-	186277976	7	5	21	1	0	1	0	1	0	0	0	0	12493	942	33	0	3147	0	PRG4	1	186277976	Frame_Shift_Del	DEL	GAGT	TCGA-FM-8000-01A-11D-2210-10	2257012	186277976	62972645	12	2755											
OR2L8	391190	hgsc.bcm.edu	37	chr1	248112914	248112914	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgtagtaactttctactatgCaccttttgtctacacttatc	9	18	4	10	0	2	0	0	0	2	0	3	0	2	0	1	0	4	3	1	0	6	9			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr1:248112914C>A	ENST00000357191.3	+	1	755	c.755C>A	c.(754-756)gCa>gAa	p.A252E	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.A252E		Atlas-SNP	.											OR2L8,right_upper_lobe,carcinoma,0,1	OR2L8	92	1	0			c.C755A						PASS	.						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>A	1.37:g.248112914C>A	ENSP00000349719:p.Ala252Glu	234	0	0		208	45	0.216346	NM_001001963	Q6IF03	Missense_Mutation	SNP	ENST00000357191.3	37	CCDS31101.1	.	.	.	.	.	.	.	.	.	.	.	6.378	0.437845	0.12104	.	.	ENSG00000196936	ENST00000357191	T	0.38887	1.11	1.8	-0.381	0.12485	GPCR, rhodopsin-like superfamily (1);	0.590255	0.12675	U	0.448469	T	0.44265	0.1285	L	0.60067	1.865	0.09310	N	1	P	0.45126	0.851	P	0.51550	0.673	T	0.36359	-0.9751	10	0.87932	D	0	.	3.7754	0.08657	0.0:0.3475:0.3505:0.302	.	252	Q8NGY9	OR2L8_HUMAN	E	252	ENSP00000349719:A252E	ENSP00000349719:A252E	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	.	.	none		0.478	OR2L8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096853.2			A	248112914	C	A	248112914	3	1	21	1	0	0	0	0	1	0	0	0	11018	710	25	4	757	4	OR2L8	1	248112914	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	61834938	248112914	1137707	13	2756											
XPO1	7514	hgsc.bcm.edu	37	chr2	61726851	61726851	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acataattattacttgcctgTcttttaaatgcttagatttg	11	19	5	6	0	1	1	0	0	1	1	1	1	1	1	1	0	3	1	1	0	6	8			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr2:61726851T>A	ENST00000401558.2	-	7	1314	c.587A>T	c.(586-588)gAc>gTc	p.D196V	XPO1_ENST00000406957.1_Missense_Mutation_p.D196V|XPO1_ENST00000404992.2_Missense_Mutation_p.D196V	NM_003400.3	NP_003391.1	O14980	XPO1_HUMAN	exportin 1	196	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)			TACTTGCCTGTCTTTTAAATG	0.289			Mis		CLL																																p.D196V		Atlas-SNP	.	-'	Dom	yes		2	2p15	7514	"exportin 1 (CRM1 homolog, yeast)"		L	.	XPO1	108	.	0			c.A587T						PASS	.						50	52	51					2																	61726851		2202	4299	6501	SO:0001583	missense	7514	exon7			TGCCTGTCTTTTA	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.587A>T	2.37:g.61726851T>A	ENSP00000384863:p.Asp196Val	104	0	0		201	144	0.716418	NM_003400	A6NL14|A8K1K5|D6W5E2|Q63HP8|Q68CP3|Q99433	Missense_Mutation	SNP	ENST00000401558.2	37	CCDS33205.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.562341	0.86335	.	.	ENSG00000082898	ENST00000401558;ENST00000404992;ENST00000406957	T;T;T	0.52057	0.68;0.68;0.68	5.95	5.95	0.96441	Exportin-1/Importin-beta-like (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.69762	0.3147	M	0.83118	2.625	0.80722	D	1	D	0.61080	0.989	D	0.65323	0.934	T	0.71310	-0.4631	10	0.40728	T	0.16	.	16.4025	0.83647	0.0:0.0:0.0:1.0	.	196	O14980	XPO1_HUMAN	V	196	ENSP00000384863:D196V;ENSP00000385942:D196V;ENSP00000385559:D196V	ENSP00000384863:D196V	D	-	2	0	XPO1	61580355	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.027000	0.88791	2.268000	0.75426	0.533000	0.62120	GAC	.	.	none		0.289	XPO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325872.3	NM_003400		A	61726851	T	A	61726851	3	1	21	1	0	0	0	0	1	0	0	0	17460	1667	58	5	2704	5	XPO1	2	61726851	Missense_Mutation	SNP	T	TCGA-FM-8000-01A-11D-2210-10		61726851	181472522	14	2757											
MYO7B	4648	hgsc.bcm.edu	37	chr2	128350377	128350377	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gtccgcccacagctgttcgaCcgggagctgtgcctgcggca	5	7	14	15	4	0	0	0	0	0	0	2	2	1	1	4	2	4	4	4	2	0	1			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr2:128350377C>G	ENST00000409816.2	+	16	2033	c.2001C>G	c.(1999-2001)gaC>gaG	p.D667E	MYO7B_ENST00000389524.4_Missense_Mutation_p.D667E|MYO7B_ENST00000428314.1_Missense_Mutation_p.D667E			Q6PIF6	MYO7B_HUMAN	myosin VIIB	667	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)		AGCTGTTCGACCGGGAGCTGT	0.682																																					p.D667E		Atlas-SNP	.											.	MYO7B	359	.	0			c.C2001G						PASS	.						16	23	21					2																	128350377		2021	4165	6186	SO:0001583	missense	4648	exon17			GTTCGACCGGGAG		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.2001C>G	2.37:g.128350377C>G	ENSP00000386461:p.Asp667Glu	116	0	0		63	22	0.349206	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.163986	0.78339	.	.	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	D;D;D	0.89196	-2.48;-2.48;-2.48	4.93	2.71	0.32032	Myosin head, motor domain (2);	0.058193	0.64402	D	0.000003	D	0.88265	0.6390	L	0.48877	1.53	0.47441	D	0.999428	D	0.55800	0.973	P	0.59889	0.865	D	0.83912	0.0296	10	0.22109	T	0.4	.	6.5587	0.22474	0.0:0.5804:0.0:0.4196	.	667	Q6PIF6	MYO7B_HUMAN	E	667	ENSP00000374175:D667E;ENSP00000415090:D667E;ENSP00000386461:D667E	ENSP00000374175:D667E	D	+	3	2	MYO7B	128066847	1.000000	0.71417	0.999000	0.59377	0.965000	0.64279	1.575000	0.36493	1.215000	0.43411	-0.136000	0.14681	GAC	.	.	none		0.682	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001		G	128350377	C	G	128350377	3	3	21	1	0	0	0	0	1	0	0	0	10092	506	18	4	2063	4	MYO7B	2	128350377	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	66623526	128350377	114848996	15	2758											
NCKAP5	344148	hgsc.bcm.edu	37	chr2	133542832	133542832	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccttccagaaagtgttttcTgtttgtctcccagccaaaca	9	13	7	12	0	2	1	0	0	2	1	4	1	3	1	4	0	2	2	4	0	2	4			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr2:133542832T>C	ENST00000409261.1	-	14	1925	c.1552A>G	c.(1552-1554)Aga>Gga	p.R518G	NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000317721.6_Missense_Mutation_p.R518G|NCKAP5_ENST00000405974.3_Intron	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	518										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						AAGTGTTTTCTGTTTGTCTCC	0.493																																					p.R518G		Atlas-SNP	.											.	NCKAP5	322	.	0			c.A1552G						PASS	.						124	124	124					2																	133542832		1962	4173	6135	SO:0001583	missense	344148	exon14			GTTTTCTGTTTGT	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.1552A>G	2.37:g.133542832T>C	ENSP00000387128:p.Arg518Gly	157	0	0		129	46	0.356589	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	.	.	.	.	.	.	.	.	.	.	t	0.068	-1.208267	0.01568	.	.	ENSG00000176771	ENST00000409261;ENST00000317721	T;T	0.10099	2.91;2.91	5.38	0.0287	0.14159	.	0.509237	0.13975	N	0.349882	T	0.05181	0.0138	N	0.12746	0.255	0.25358	N	0.988806	B	0.02656	0.0	B	0.06405	0.002	T	0.45425	-0.9262	10	0.12766	T	0.61	.	9.6561	0.39928	0.0:0.3315:0.0:0.6685	.	518	O14513	NCKP5_HUMAN	G	518	ENSP00000387128:R518G;ENSP00000380603:R518G	ENSP00000380603:R518G	R	-	1	2	NCKAP5	133259302	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.118000	0.10692	-0.187000	0.10516	-0.424000	0.05967	AGA	.	.	none		0.493	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481		C	133542832	T	C	133542832	3	2	21	1	0	0	0	0	1	0	0	0	10232	1588	55	3	4205	3	NCKAP5	2	133542832	Missense_Mutation	SNP	T	TCGA-FM-8000-01A-11D-2210-10	5192455	133542832	109656541	16	2759											
SCN7A	6332	hgsc.bcm.edu	37	chr2	167313460	167313461	+	Frame_Shift_Del	DEL	CT	CT	-																															cttcttagatatttcaccaaCtctctgcttttcttcttcat																										TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr2:167313460_167313461delCT	ENST00000409855.1	-	10	1335_1336	c.1209_1210delAG	c.(1207-1212)agagttfs	p.RV403fs		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	403					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)	ATTTCACCAACTCTCTGCTTTT	0.332																																					p.404_404del		Pindel,Atlas-Indel	.											.	SCN7A	410	.	0			c.1210_1211del						PASS	.																																			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.1209_1210delAG	2.37:g.167313464_167313465delCT	ENSP00000386796:p.Arg403fs	159	0	.		151	39	0.258	NM_002976		Frame_Shift_Del	DEL	ENST00000409855.1	37	CCDS46442.1																																																																																			.	.	none		0.332	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1			-	167313461	CT	-	167313460	7	5	21	1	0	1	0	1	0	0	0	0	13938	565	20	0	3902	0	SCN7A	2	167313460	Frame_Shift_Del	DEL	CT	TCGA-FM-8000-01A-11D-2210-10	33770628	167313460	75885913	17	2760											
LRP2	4036	hgsc.bcm.edu	37	chr2	170127524	170127524	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caaagaaagaaggattccccGaaactggaaccatgacatct	17	6	8	10	1	1	3	0	1	1	2	2	6	2	5	3	2	2	0	3	2	5	1	rs201860953		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr2:170127524G>A	ENST00000263816.3	-	16	2495	c.2210C>T	c.(2209-2211)tCg>tTg	p.S737L	LRP2_ENST00000443831.1_Intron	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	737					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)	p.S737L(2)		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)"	AGGATTCCCCGAAACTGGAAC	0.413																																					p.S737L		Atlas-SNP	.											LRP2,rectum,carcinoma,0,2	LRP2	751	2	2	Substitution - Missense(2)	large_intestine(2)	c.C2210T						PASS	.	G	LEU/SER	0,4406		0,0,2203	122	106	111		2210	4.9	0.2	2		111	6,8594	5.0+/-18.6	0,6,4294	yes	missense	LRP2	NM_004525.2	145	0,6,6497	AA,AG,GG		0.0698,0.0,0.0461	benign	737/4656	170127524	6,13000	2203	4300	6503	SO:0001583	missense	4036	exon16			TTCCCCGAAACTG		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.2210C>T	2.37:g.170127524G>A	ENSP00000263816:p.Ser737Leu	142	0	0		97	36	0.371134	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	G	13.97	2.397079	0.42512	0.0	6.98E-4	ENSG00000081479	ENST00000263816	D	0.90788	-2.73	5.77	4.9	0.64082	Six-bladed beta-propeller, TolB-like (1);	0.101407	0.64402	D	0.000003	T	0.80363	0.4609	N	0.20685	0.6	0.80722	D	1	B	0.33120	0.398	B	0.22152	0.038	T	0.78288	-0.2262	10	0.07813	T	0.8	.	15.2561	0.73585	0.0675:0.0:0.9325:0.0	.	737	P98164	LRP2_HUMAN	L	737	ENSP00000263816:S737L	ENSP00000263816:S737L	S	-	2	0	LRP2	169835770	1.000000	0.71417	0.229000	0.23960	0.126000	0.20510	7.917000	0.87498	1.581000	0.49865	0.655000	0.94253	TCG	G|0.999;A|0.001	0.001	weak		0.413	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		A	170127524	G	A	170127524	3	1	21	1	0	0	0	0	1	0	0	0	8965	1059	37	1	12013	1	LRP2	2	170127524	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	2814064	170127524	73071849	18	2761											
HOXD4	3233	hgsc.bcm.edu	37	chr2	177016724	177016724	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtccgaccccaagcagccGccctccgggacggcactcaa	9	3	10	19	4	1	0	1	0	0	0	3	2	3	1	6	2	2	2	6	2	2	0			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr2:177016724G>A	ENST00000306324.3	+	1	775	c.363G>A	c.(361-363)ccG>ccA	p.P121P	MIR10B_ENST00000385011.1_RNA|HOXD3_ENST00000468418.3_5'UTR	NM_014621.2	NP_055436.2	P09016	HXD4_HUMAN	homeobox D4	121					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)		CCAAGCAGCCGCCCTCCGGGA	0.682																																					p.P121P		Atlas-SNP	.											.	HOXD4	32	.	0			c.G363A						PASS	.						28	35	33					2																	177016724		2125	4262	6387	SO:0001819	synonymous_variant	3233	exon1			GCAGCCGCCCTCC		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.363G>A	2.37:g.177016724G>A		29	0	0		18	11	0.611111	NM_014621	B2R9R3|Q96AU0	Silent	SNP	ENST00000306324.3	37	CCDS2269.1																																																																																			.	.	none		0.682	HOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255697.2			A	177016724	G	A	177016724	2	1	21	1	0	0	0	0	0	0	0	1	7333	1074	38	1		1	HOXD4	2	177016724	Silent	SNP	G	TCGA-FM-8000-01A-11D-2210-10	6889200	177016724	66182649	19	2762											
SATB2	23314	hgsc.bcm.edu	37	chr2	200193545	200193545	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacttctggcagattgaggAaattctgcatggccctcagg	9	10	11	11	0	3	2	1	1	2	1	3	3	3	3	2	4	1	2	2	4	1	3			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr2:200193545A>G	ENST00000417098.1	-	8	2078	c.1262T>C	c.(1261-1263)tTc>tCc	p.F421S	RP11-486F17.1_ENST00000489557.2_RNA|SATB2_ENST00000443023.1_Missense_Mutation_p.F362S|SATB2_ENST00000260926.5_Missense_Mutation_p.F421S|SATB2_ENST00000428695.1_Missense_Mutation_p.F303S|SATB2_ENST00000457245.1_Missense_Mutation_p.F421S	NM_001172509.1	NP_001165980.1	Q9UPW6	SATB2_HUMAN	SATB homeobox 2	421					cartilage development (GO:0051216)|cellular response to organic substance (GO:0071310)|chromatin remodeling (GO:0006338)|embryonic pattern specification (GO:0009880)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|osteoblast development (GO:0002076)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(40)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						CAGATTGAGGAAATTCTGCAT	0.517																																					p.F421S	Colon(30;262 767 11040 24421 36230)	Atlas-SNP	.											SATB2,NS,carcinoma,+1,1	SATB2	134	1	0			c.T1262C						PASS	.						111	99	103					2																	200193545		2203	4300	6503	SO:0001583	missense	23314	exon9			TTGAGGAAATTCT	AB028957	CCDS2327.1	2q33.1	2011-06-20	2007-02-15		ENSG00000119042	ENSG00000119042		"Homeoboxes / CUT class"	21637	protein-coding gene	gene with protein product		608148	"SATB family member 2"				Standard	NM_015265		Approved	KIAA1034, FLJ21474	uc002uva.2	Q9UPW6	OTTHUMG00000132767	ENST00000417098.1:c.1262T>C	2.37:g.200193545A>G	ENSP00000401112:p.Phe421Ser	137	0	0		76	33	0.434211	NM_015265	A8K5Z8|Q3ZB87|Q4V763	Missense_Mutation	SNP	ENST00000417098.1	37	CCDS2327.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.643706	0.87859	.	.	ENSG00000119042	ENST00000417098;ENST00000443023;ENST00000260926;ENST00000428695;ENST00000457245	T;T;T;T;T	0.61158	0.18;0.19;0.18;0.13;0.18	4.98	4.98	0.66077	Homeodomain protein CUT (2);Lambda repressor-like, DNA-binding (2);	0.000000	0.85682	D	0.000000	T	0.75466	0.3853	M	0.74258	2.255	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.996;0.999	T	0.79112	-0.1937	10	0.87932	D	0	-16.206	15.1355	0.72562	1.0:0.0:0.0:0.0	.	303;421	Q3ZB87;Q9UPW6	.;SATB2_HUMAN	S	421;362;421;303;421	ENSP00000401112:F421S;ENSP00000388764:F362S;ENSP00000260926:F421S;ENSP00000388581:F303S;ENSP00000405420:F421S	ENSP00000260926:F421S	F	-	2	0	SATB2	199901790	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.087000	0.94110	2.218000	0.71995	0.528000	0.53228	TTC	.	.	none		0.517	SATB2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256140.1	NM_015265		G	200193545	A	G	200193545	3	3	21	1	0	0	0	0	1	0	0	0	13869	246	9	3	955	3	SATB2	2	200193545	Missense_Mutation	SNP	A	TCGA-FM-8000-01A-11D-2210-10	23176821	200193545	43005828	20	2763											
ADAM23	8745	hgsc.bcm.edu	37	chr2	207437855	207437855	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcagtttcagccacgagggtAtgaatgccgggatgctgtga	9	9	15	8	2	1	2	1	2	0	0	1	4	1	3	2	2	3	4	2	2	2	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr2:207437855A>G	ENST00000264377.3	+	18	2001	c.1673A>G	c.(1672-1674)tAt>tGt	p.Y558C	ADAM23_ENST00000374416.1_Missense_Mutation_p.Y558C|ADAM23_ENST00000374415.3_Missense_Mutation_p.Y558C	NM_003812.2	NP_003803.1	O75077	ADA23_HUMAN	ADAM metallopeptidase domain 23	558	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)		CCACGAGGGTATGAATGCCGG	0.373																																					p.Y558C	Melanoma(194;1127 2130 19620 24042 27855)	Atlas-SNP	.											.	ADAM23	239	.	0			c.A1673G						PASS	.						232	210	218					2																	207437855		2203	4300	6503	SO:0001583	missense	8745	exon18			GAGGGTATGAATG	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.1673A>G	2.37:g.207437855A>G	ENSP00000264377:p.Tyr558Cys	119	0	0		100	4	0.04	NM_003812	A2RU59	Missense_Mutation	SNP	ENST00000264377.3	37	CCDS2369.1	.	.	.	.	.	.	.	.	.	.	A	16.89	3.247881	0.59103	.	.	ENSG00000114948	ENST00000264377;ENST00000374416;ENST00000431817;ENST00000374415	T;T;T	0.11385	2.78;2.78;2.78	5.99	5.99	0.97316	Blood coagulation inhibitor, Disintegrin (5);	0.107594	0.41712	D	0.000829	T	0.29158	0.0725	M	0.76838	2.35	0.58432	D	0.999999	D	0.57571	0.98	P	0.59115	0.852	T	0.01858	-1.1259	10	0.62326	D	0.03	.	11.9424	0.52909	0.855:0.145:0.0:0.0	.	558	O75077	ADA23_HUMAN	C	558;558;452;558	ENSP00000264377:Y558C;ENSP00000363537:Y558C;ENSP00000363536:Y558C	ENSP00000264377:Y558C	Y	+	2	0	ADAM23	207146100	1.000000	0.71417	0.992000	0.48379	0.994000	0.84299	4.789000	0.62446	2.304000	0.77564	0.529000	0.55759	TAT	.	.	none		0.373	ADAM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256431.2	NM_003812		G	207437855	A	G	207437855	3	3	21	1	0	0	0	0	1	0	0	0	245	449	16	3	1743	3	ADAM23	2	207437855	Missense_Mutation	SNP	A	TCGA-FM-8000-01A-11D-2210-10	7244310	207437855	35761518	21	2764											
COL6A3	1293	hgsc.bcm.edu	37	chr2	238277339	238277339	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	actgtgaagaccagtctgggGtcattggtgatggtctgcag	8	11	15	7	0	3	3	1	2	2	1	3	3	3	3	1	4	1	1	1	4	1	1			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr2:238277339G>A	ENST00000295550.4	-	10	5219	c.4767C>T	c.(4765-4767)gaC>gaT	p.D1589D	COL6A3_ENST00000346358.4_Silent_p.D1389D|COL6A3_ENST00000347401.3_Silent_p.D1388D|COL6A3_ENST00000472056.1_Silent_p.D982D|COL6A3_ENST00000409809.1_Silent_p.D1383D|COL6A3_ENST00000353578.4_Silent_p.D1383D	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1589	Nonhelical region.|VWFA 8. {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)		CCAGTCTGGGGTCATTGGTGA	0.542																																					p.D1589D		Atlas-SNP	.											.	COL6A3	608	.	0			c.C4767T						PASS	.						198	175	182					2																	238277339		2203	4300	6503	SO:0001819	synonymous_variant	1293	exon10			TCTGGGGTCATTG	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.4767C>T	2.37:g.238277339G>A		159	0	0		110	42	0.381818	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			.	.	none		0.542	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		A	238277339	G	A	238277339	2	1	21	1	0	0	0	0	0	0	0	1	3703	1252	44	2		2	COL6A3	2	238277339	Silent	SNP	G	TCGA-FM-8000-01A-11D-2210-10	30839484	238277339	4922034	22	2765											
SLC6A11	6538	hgsc.bcm.edu	37	chr3	10976837	10976837	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcctccatgctctgcatcccGctctggatctgcatcacagt	6	12	7	16	1	4	0	1	0	3	0	7	1	7	1	3	1	3	4	3	1	0	0	rs138273152		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr3:10976837G>A	ENST00000254488.2	+	13	1764	c.1698G>A	c.(1696-1698)ccG>ccA	p.P566P		NM_014229.1	NP_055044.1	P48066	S6A11_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 11	566					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)	TCTGCATCCCGCTCTGGATCT	0.607																																					p.P566P		Atlas-SNP	.											SLC6A11,NS,carcinoma,+1,2	SLC6A11	87	2	0			c.G1698A						PASS	.	G		4,4402	8.1+/-20.4	0,4,2199	162	145	150		1698	-8.4	0.4	3	dbSNP_134	150	0,8600		0,0,4300	no	coding-synonymous	SLC6A11	NM_014229.1		0,4,6499	AA,AG,GG		0.0,0.0908,0.0308		566/633	10976837	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	6538	exon13			CATCCCGCTCTGG	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.1698G>A	3.37:g.10976837G>A		207	0	0		133	28	0.210526	NM_014229	B2R6U6|Q8IYC9	Silent	SNP	ENST00000254488.2	37	CCDS2602.1																																																																																			G|1.000;A|0.000	0.000	weak		0.607	SLC6A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251927.1	NM_014229		A	10976837	G	A	10976837	2	1	21	1	0	0	0	0	0	0	0	1	14689	1074	38	1		1	SLC6A11	3	10976837	Silent	SNP	G	TCGA-FM-8000-01A-11D-2210-10		10976837	187045593	23	2766											
GNAI2	2771	hgsc.bcm.edu	37	chr3	50294169	50294169	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctgcaggatgtttgatgtggGtggtcagcggtctgagcgga	6	11	18	6	2	2	2	1	2	1	0	2	4	2	4	0	5	3	2	0	5	0	1			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr3:50294169G>A	ENST00000313601.6	+	6	992	c.608G>A	c.(607-609)gGt>gAt	p.G203D	GNAI2_ENST00000440628.1_Missense_Mutation_p.G151D|GNAI2_ENST00000536647.1_Missense_Mutation_p.G122D|GNAI2_ENST00000422163.1_Missense_Mutation_p.G187D|GNAI2_ENST00000451956.1_Missense_Mutation_p.G166D|GNAI2_ENST00000266027.5_Missense_Mutation_p.G187D|GNAI2_ENST00000491100.1_3'UTR	NM_002070.2	NP_002061.1	P04899	GNAI2_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 2	203					activation of MAPKK activity (GO:0000186)|adenosine receptor signaling pathway (GO:0001973)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of synaptic transmission (GO:0050805)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|regulation of calcium ion transport (GO:0051924)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|membrane (GO:0016020)|membrane raft (GO:0045121)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	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)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|liver(2)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(193;0.000288)|KIRC - Kidney renal clear cell carcinoma(197;0.00571)|Kidney(197;0.00651)		TTTGATGTGGGTGGTCAGCGG	0.542																																					p.G203D		Atlas-SNP	.											.	GNAI2	42	.	0			c.G608A						PASS	.						166	156	159					3																	50294169		2203	4300	6503	SO:0001583	missense	2771	exon6			ATGTGGGTGGTCA	X04828	CCDS2813.1, CCDS54587.1, CCDS63642.1, CCDS63644.1	3p21.31	2010-08-27			ENSG00000114353	ENSG00000114353			4385	protein-coding gene	gene with protein product	"GTP-binding regulatory protein Gi alpha-2 chain"	139360		GNAI2B		3100330, 1733849	Standard	NM_001166425		Approved	GIP	uc003cyq.1	P04899	OTTHUMG00000156940	ENST00000313601.6:c.608G>A	3.37:g.50294169G>A	ENSP00000312999:p.Gly203Asp	283	0	0		191	76	0.397906	NM_002070	B3KTZ0|B4DYA0|B4E2X5|Q6B6N3|Q8IZ71	Missense_Mutation	SNP	ENST00000313601.6	37	CCDS2813.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.738764	0.89573	.	.	ENSG00000114353	ENST00000422163;ENST00000313601;ENST00000536647;ENST00000540560;ENST00000440628;ENST00000451956;ENST00000266027	D;D;D;D;D;D	0.95690	-3.78;-3.78;-3.78;-3.78;-3.78;-3.78	4.97	4.1	0.47936	.	0.000000	0.85682	D	0.000000	D	0.98592	0.9529	H	0.98936	4.375	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	0.98640	1.0675	10	0.87932	D	0	.	11.6416	0.51235	0.0865:0.0:0.9135:0.0	.	166;203;187;187	B4DYA0;P04899;B3KTZ0;P04899-2	.;GNAI2_HUMAN;.;.	D	187;203;122;203;151;166;187	ENSP00000406871:G187D;ENSP00000312999:G203D;ENSP00000444360:G122D;ENSP00000395736:G151D;ENSP00000406369:G166D;ENSP00000266027:G187D	ENSP00000266027:G187D	G	+	2	0	GNAI2	50269173	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	9.596000	0.98267	1.479000	0.48272	0.655000	0.94253	GGT	.	.	none		0.542	GNAI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346688.1	NM_002070		A	50294169	G	A	50294169	3	1	21	1	0	0	0	0	1	0	0	0	6513	1261	44	2	641	2	GNAI2	3	50294169	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	39317332	50294169	147728261	24	2767											
IQCF2	389123	hgsc.bcm.edu	37	chr3	51897174	51897174	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacggcaggcagctctgatcGcctacgcaaccagagagagg	12	4	13	12	3	1	3	0	1	1	2	2	4	1	3	2	3	4	4	2	3	3	1	rs369181892		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr3:51897174G>A	ENST00000333127.3	+	3	312	c.283G>A	c.(283-285)Gcc>Acc	p.A95T	IQCF2_ENST00000429548.1_3'UTR	NM_203424.1	NP_982248.1	Q8IXL9	IQCF2_HUMAN	IQ motif containing F2	95								p.A95T(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	10				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.000537)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		AGCTCTGATCGCCTACGCAAC	0.582																																					p.A95T		Atlas-SNP	.											IQCF2,mouth,carcinoma,0,1	IQCF2	21	1	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.G283A						scavenged	.	G	THR/ALA	0,4406		0,0,2203	115	111	113		283	-4.6	0	3		113	1,8599	1.2+/-3.3	0,1,4299	no	missense	IQCF2	NM_203424.1	58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	95/165	51897174	1,13005	2203	4300	6503	SO:0001583	missense	389123	exon3			CTGATCGCCTACG	AK128883	CCDS2835.1	3p21.31	2008-02-05			ENSG00000184345	ENSG00000184345			31815	protein-coding gene	gene with protein product							Standard	NM_203424		Approved		uc003dbt.1	Q8IXL9	OTTHUMG00000156914	ENST00000333127.3:c.283G>A	3.37:g.51897174G>A	ENSP00000329904:p.Ala95Thr	134	1	0.00746269		60	3	0.05	NM_203424		Missense_Mutation	SNP	ENST00000333127.3	37	CCDS2835.1	.	.	.	.	.	.	.	.	.	.	G	10.92	1.488097	0.26686	0.0	1.16E-4	ENSG00000184345	ENST00000333127	T	0.29917	1.55	4.95	-4.59	0.03400	.	2.430730	0.01286	N	0.009898	T	0.07098	0.0180	N	0.00517	-1.405	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.13899	-1.0492	10	0.18710	T	0.47	0.3689	0.6435	0.00814	0.3204:0.1226:0.3097:0.2474	.	95	Q8IXL9	IQCF2_HUMAN	T	95	ENSP00000329904:A95T	ENSP00000329904:A95T	A	+	1	0	IQCF2	51872214	0.000000	0.05858	0.000000	0.03702	0.303000	0.27691	-0.149000	0.10204	-0.609000	0.05724	-0.367000	0.07326	GCC	.	.	weak		0.582	IQCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346594.1	NM_203424		A	51897174	G	A	51897174	3	1	21	1	0	0	0	0	1	0	0	0	7817	1087	38	1	293	1	IQCF2	3	51897174	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	1603005	51897174	146125256	25	2768											
DNAH1	25981	hgsc.bcm.edu	37	chr3	52409342	52409342	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaccgtcaccccgcggctgAtgcgtcacttcaactacctg	8	8	8	17	4	3	1	3	1	0	0	3	1	3	1	4	1	3	1	4	1	2	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr3:52409342A>G	ENST00000420323.2	+	45	7333	c.7072A>G	c.(7072-7074)Atg>Gtg	p.M2358V		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	2358	AAA 3. {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)		CCCGCGGCTGATGCGTCACTT	0.572																																					p.M2358V		Atlas-SNP	.											.	DNAH1	534	.	0			c.A7072G						PASS	.						52	53	53					3																	52409342		2088	4207	6295	SO:0001583	missense	25981	exon45			CGGCTGATGCGTC	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.7072A>G	3.37:g.52409342A>G	ENSP00000401514:p.Met2358Val	78	0	0		36	17	0.472222	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	.	.	.	.	.	.	.	.	.	.	A	6.771	0.511200	0.12883	.	.	ENSG00000114841	ENST00000420323	T	0.34667	1.35	5.71	5.71	0.89125	.	0.396398	0.21139	N	0.079506	T	0.24661	0.0598	N	0.16602	0.42	0.23869	N	0.996616	B	0.06786	0.001	B	0.09377	0.004	T	0.10359	-1.0633	10	0.17832	T	0.49	.	15.9779	0.80083	1.0:0.0:0.0:0.0	.	2358	C9JXH6	.	V	2358	ENSP00000401514:M2358V	ENSP00000401514:M2358V	M	+	1	0	DNAH1	52384382	0.995000	0.38212	0.987000	0.45799	0.158000	0.22134	3.572000	0.53849	2.183000	0.69458	0.454000	0.30748	ATG	.	.	none		0.572	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		G	52409342	A	G	52409342	3	3	21	1	0	0	0	0	1	0	0	0	4599	333	12	3	7246	3	DNAH1	3	52409342	Missense_Mutation	SNP	A	TCGA-FM-8000-01A-11D-2210-10	512168	52409342	145613088	26	2769											
SPCS1	28972	hgsc.bcm.edu	37	chr3	52741760	52741760	+	Frame_Shift_Del	DEL	C	C	-																															ctctcaagtggttacctgttCaagaatcaagcacagacgac																										TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr3:52741760delC	ENST00000602728.1	+	4	410	c.241delC	c.(241-243)caafs	p.Q81fs	GLT8D1_ENST00000407584.3_5'Flank|GLT8D1_ENST00000266014.5_5'Flank|GLT8D1_ENST00000478968.2_5'Flank|SPCS1_ENST00000233025.7_Frame_Shift_Del_p.Q148fs|SPCS1_ENST00000423431.1_Frame_Shift_Del_p.Q59fs|GLT8D1_ENST00000491606.1_5'Flank			Q9Y6A9	SPCS1_HUMAN	signal peptidase complex subunit 1 homolog (S. cerevisiae)	81					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|proteolysis (GO:0006508)|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 endoplasmic reticulum membrane (GO:0030176)|signal peptidase complex (GO:0005787)	peptidase activity (GO:0008233)			kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)	6				BRCA - Breast invasive adenocarcinoma(193;6.51e-05)|Kidney(197;0.000583)|KIRC - Kidney renal clear cell carcinoma(197;0.000751)|OV - Ovarian serous cystadenocarcinoma(275;0.0469)		GTTACCTGTTCAAGAATCAAG	0.413																																					p.V147fs		Pindel,Atlas-Indel	.											.	SPCS1	20	.	0			c.441delT						PASS	.						123	126	125					3																	52741760		2203	4300	6503	SO:0001589	frameshift_variant	28972	exon4			.	AF092138	CCDS33769.2	3p21.31	2005-01-05			ENSG00000114902	ENSG00000114902			23401	protein-coding gene	gene with protein product		610358				8632014	Standard	NM_014041		Approved	SPC12, HSPC033, YJR010C-A, SPC1	uc011bei.2	Q9Y6A9	OTTHUMG00000154930	ENST00000602728.1:c.241delC	3.37:g.52741760delC	ENSP00000473265:p.Gln81fs	331	0	.		202	43	0.213	NM_014041	B3KNF8|Q9BVW1	Frame_Shift_Del	DEL	ENST00000602728.1	37																																																																																				.	.	none		0.413	SPCS1-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467759.1	NM_014041		-	52741760	C	-	52741760	7	5	21	1	0	1	0	1	0	0	0	0	15038	827	29	0	456	0	SPCS1	3	52741760	Frame_Shift_Del	DEL	C	TCGA-FM-8000-01A-11D-2210-10	332418	52741760	145280670	27	2770											
ERC2	26059	hgsc.bcm.edu	37	chr3	56052950	56052950	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagagcttcctctagcgtcGccagtgcagtatctgtatta	9	12	9	11	2	2	1	0	0	2	1	4	1	3	1	2	0	3	4	2	0	4	5	rs201400364		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr3:56052950G>A	ENST00000288221.6	-	8	2006	c.1751C>T	c.(1750-1752)gCg>gTg	p.A584V		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	584						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)		CTCTAGCGTCGCCAGTGCAGT	0.468													G|||	1	0.000199681	0.0	0.0	5008	,	,		17318	0.0		0.001	False		,,,				2504	0.0				p.A584V		Atlas-SNP	.											.	ERC2	221	.	0			c.C1751T						PASS	.						143	125	131					3																	56052950		1958	4155	6113	SO:0001583	missense	26059	exon8			AGCGTCGCCAGTG	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.1751C>T	3.37:g.56052950G>A	ENSP00000288221:p.Ala584Val	212	0	0		148	57	0.385135	NM_015576	Q2T9F6|Q86TK4	Missense_Mutation	SNP	ENST00000288221.6	37	CCDS46851.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	G|G	13.84|13.84	2.357442|2.357442	0.41801|0.41801	.|.	.|.	ENSG00000187672|ENSG00000187672	ENST00000288221|ENST00000492584	T|.	0.45276|.	0.9|.	5.28|5.28	5.28|5.28	0.74379|0.74379	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.68320|.	0.2988|.	L|L	0.44542|0.44542	1.39|1.39	0.53688|0.53688	D|D	0.999973|0.999973	P|.	0.35923|.	0.528|.	B|.	0.30029|.	0.11|.	T|.	0.63734|.	-0.6570|.	10|.	0.49607|.	T|.	0.09|.	-10.6087|-10.6087	19.2601|19.2601	0.93964|0.93964	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	584|.	O15083|.	ERC2_HUMAN|.	V|X	584|223	ENSP00000288221:A584V|.	ENSP00000288221:A584V|.	A|R	-|-	2|1	0|2	ERC2|ERC2	56027990|56027990	1.000000|1.000000	0.71417|0.71417	0.616000|0.616000	0.29078|0.29078	0.002000|0.002000	0.02628|0.02628	9.715000|9.715000	0.98748|0.98748	2.641000|2.641000	0.89580|0.89580	0.650000|0.650000	0.86243|0.86243	GCG|CGA	G|1.000;A|0.000	0.000	strong		0.468	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576		A	56052950	G	A	56052950	3	1	21	1	0	0	0	0	1	0	0	0	5213	1087	38	1	1152	1	ERC2	3	56052950	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	3311190	56052950	141969480	28	2771											
FRMD4B	23150	hgsc.bcm.edu	37	chr3	69230472	69230472	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtcacactctgcatagggtGtgtacccggcaatgtagtaa	11	10	11	9	1	2	0	1	0	1	0	2	0	2	0	1	2	2	5	1	2	5	4			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr3:69230472G>A	ENST00000398540.3	-	21	2512	c.2429C>T	c.(2428-2430)aCa>aTa	p.T810I	FRMD4B_ENST00000542259.1_Missense_Mutation_p.T756I|FRMD4B_ENST00000478263.1_Missense_Mutation_p.T462I	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	810					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)		TGCATAGGGTGTGTACCCGGC	0.483																																					p.T810I		Atlas-SNP	.											.	FRMD4B	90	.	0			c.C2429T						PASS	.						60	61	61					3																	69230472		1950	4148	6098	SO:0001583	missense	23150	exon21			TAGGGTGTGTACC	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.2429C>T	3.37:g.69230472G>A	ENSP00000381549:p.Thr810Ile	92	0	0		87	45	0.517241	NM_015123	Q8TAI3	Missense_Mutation	SNP	ENST00000398540.3	37	CCDS46863.1	.	.	.	.	.	.	.	.	.	.	G	14.43	2.534382	0.45073	.	.	ENSG00000114541	ENST00000398540;ENST00000542259;ENST00000478263	D;D	0.83250	-1.7;-1.7	5.83	4.94	0.65067	.	0.763911	0.12619	N	0.453162	T	0.71634	0.3363	N	0.08118	0	0.09310	N	1	B;B	0.18166	0.026;0.02	B;B	0.13407	0.009;0.009	T	0.64257	-0.6450	10	0.87932	D	0	0.0843	16.0743	0.80958	0.0:0.0:0.8649:0.1351	.	654;810	B4DHD5;Q9Y2L6	.;FRM4B_HUMAN	I	810;756;462	ENSP00000381549:T810I;ENSP00000437658:T756I	ENSP00000381549:T810I	T	-	2	0	FRMD4B	69313162	0.427000	0.25514	0.002000	0.10522	0.958000	0.62258	3.999000	0.57031	1.424000	0.47217	0.591000	0.81541	ACA	.	.	none		0.483	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1			A	69230472	G	A	69230472	3	1	21	1	0	0	0	0	1	0	0	0	6060	1377	48	2	687	2	FRMD4B	3	69230472	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	13177522	69230472	128791958	29	2772											
COL6A5	256076	hgsc.bcm.edu	37	chr3	130159037	130159037	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttttccaaatgcttgcattcGagaggctttcttacctgaag	9	15	8	9	1	1	2	0	1	1	1	3	3	2	2	2	1	3	3	2	1	3	6			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr3:130159037G>A	ENST00000432398.2	+	35	6349	c.5855G>A	c.(5854-5856)cGa>cAa	p.R1952Q	COL6A5_ENST00000265379.6_Missense_Mutation_p.R1952Q	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1952	Nonhelical region.|VWFA 8. {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						GCTTGCATTCGAGAGGCTTTC	0.393																																					p.R1952Q		Atlas-SNP	.											.	COL6A5	205	.	0			c.G5855A						PASS	.						71	65	67					3																	130159037		1876	4103	5979	SO:0001583	missense	256076	exon35			GCATTCGAGAGGC	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.5855G>A	3.37:g.130159037G>A	ENSP00000390895:p.Arg1952Gln	146	0	0		117	52	0.444444	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		.	.	.	.	.	.	.	.	.	.	G	5.461	0.270143	0.10349	.	.	ENSG00000172752	ENST00000432398;ENST00000265379	D;D	0.88586	-2.32;-2.4	5.63	-2.94	0.05581	.	.	.	.	.	T	0.62732	0.2452	N	0.00841	-1.15	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.57700	-0.7766	9	0.13470	T	0.59	.	6.1151	0.20122	0.5337:0.0:0.3505:0.1158	.	1952	A8TX70-2	.	Q	1952	ENSP00000390895:R1952Q;ENSP00000265379:R1952Q	ENSP00000265379:R1952Q	R	+	2	0	COL6A5	131641727	0.451000	0.25705	0.007000	0.13788	0.227000	0.25037	1.081000	0.30791	-0.396000	0.07703	-0.414000	0.06135	CGA	.	.	none		0.393	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		A	130159037	G	A	130159037	3	1	21	1	0	0	0	0	1	0	0	0	3704	1058	37	1	5989	1	COL6A5	3	130159037	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	60928565	130159037	67863393	30	2773											
FAIM	55179	hgsc.bcm.edu	37	chr3	138341028	138341028	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atttttctgttttattatgtAggaagagataagaaaagagt	15	16	9	1	0	1	3	0	0	1	3	1	5	1	4	0	1	0	2	0	1	7	7			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr3:138341028A>G	ENST00000393035.2	+	3	220		c.e3-1		FAIM_ENST00000338446.4_Splice_Site|FAIM_ENST00000360570.3_Splice_Site|FAIM_ENST00000393034.2_Splice_Site|FAIM_ENST00000464668.1_Splice_Site	NM_001033032.1	NP_001028204.1	Q9NVQ4	FAIM1_HUMAN	Fas apoptotic inhibitory molecule						apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)	cytoplasm (GO:0005737)				kidney(1)|upper_aerodigestive_tract(1)	2						TTTATTATGTAGGAAGAGATA	0.303																																					.		Atlas-SNP	.											.	FAIM	27	.	0			c.112-2A>G						PASS	.						40	42	41					3																	138341028		2202	4299	6501	SO:0001630	splice_region_variant	55179	exon3			TTATGTAGGAAGA	AK001444	CCDS3103.1, CCDS33864.1, CCDS33865.1	3q23	2008-07-18			ENSG00000158234	ENSG00000158234			18703	protein-coding gene	gene with protein product						10075978	Standard	NM_018147		Approved	FLJ10582, FAIM1	uc003esq.3	Q9NVQ4	OTTHUMG00000159885	ENST00000393035.2:c.112-1A>G	3.37:g.138341028A>G		26	0	0		24	6	0.25	NM_001033032	Q6IAN2	Splice_Site	SNP	ENST00000393035.2	37	CCDS3103.1	.	.	.	.	.	.	.	.	.	.	A	16.32	3.089156	0.55968	.	.	ENSG00000158234	ENST00000338446;ENST00000360570;ENST00000393035;ENST00000393034;ENST00000464668;ENST00000479848	.	.	.	5.91	5.91	0.95273	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.2885	0.66260	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FAIM	139823718	1.000000	0.71417	0.968000	0.41197	0.640000	0.38277	9.295000	0.96095	2.252000	0.74401	0.528000	0.53228	.	.	.	none		0.303	FAIM-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357979.1	NM_001033032	Intron	G	138341028	A	G	138341028	5	3	21	1	0	0	0	0	0	0	1	0	5380	434	15	3	270	3	FAIM	3	138341028	Splice_Site	SNP	A	TCGA-FM-8000-01A-11D-2210-10	8181991	138341028	59681402	31	2774											
TRIM42	287015	hgsc.bcm.edu	37	chr3	140406661	140406661	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaaaagagatcagaaatggCtttctcaagttgcgcagcat	14	9	10	8	2	2	2	2	0	1	2	3	4	2	2	0	1	2	4	0	1	4	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr3:140406661C>T	ENST00000286349.3	+	3	1328	c.1137C>T	c.(1135-1137)ggC>ggT	p.G379G		NM_152616.4	NP_689829.3	Q8IWZ5	TRI42_HUMAN	tripartite motif containing 42	379						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						TCAGAAATGGCTTTCTCAAGT	0.383																																					p.G379G		Atlas-SNP	.											.	TRIM42	143	.	0			c.C1137T						PASS	.						75	74	75					3																	140406661		2203	4300	6503	SO:0001819	synonymous_variant	287015	exon3			AAATGGCTTTCTC	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.1137C>T	3.37:g.140406661C>T		174	0	0		126	57	0.452381	NM_152616	A1L4B4|Q8N832|Q8NDL3	Silent	SNP	ENST00000286349.3	37	CCDS3113.1																																																																																			.	.	none		0.383	TRIM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359531.2	NM_152616		T	140406661	C	T	140406661	2	4	21	1	0	0	0	0	0	0	0	1	16532	784	28	2		2	TRIM42	3	140406661	Silent	SNP	C	TCGA-FM-8000-01A-11D-2210-10	2065633	140406661	57615769	32	2775											
KLHL6	89857	hgsc.bcm.edu	37	chr3	183273173	183273173	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatagttgctggctgcggcaAgcaccacgcggtggcaggag	9	6	16	10	3	0	0	0	0	0	0	0	1	0	1	1	5	3	6	1	5	3	2	rs140971016		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr3:183273173A>G	ENST00000341319.3	-	1	304	c.269T>C	c.(268-270)cTt>cCt	p.L90P		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	90	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				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)			GGCTGCGGCAAGCACCACGCG	0.507													A|||	1	0.000199681	0.0	0.0	5008	,	,		15531	0.0		0.0	False		,,,				2504	0.001				p.L90P		Atlas-SNP	.											.	KLHL6	100	.	0			c.T269C						PASS	.	A	PRO/LEU	0,4406		0,0,2203	98	88	92		269	5.6	1	3	dbSNP_134	92	1,8599		0,1,4299	no	missense	KLHL6	NM_130446.2	98	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	probably-damaging	90/622	183273173	1,13005	2203	4300	6503	SO:0001583	missense	89857	exon1			GCGGCAAGCACCA	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.269T>C	3.37:g.183273173A>G	ENSP00000341342:p.Leu90Pro	206	0	0		147	58	0.394558	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Missense_Mutation	SNP	ENST00000341319.3	37	CCDS3245.2	.	.	.	.	.	.	.	.	.	.	A	23.2	4.386970	0.82902	0.0	1.16E-4	ENSG00000172578	ENST00000341319	D	0.90004	-2.6	5.56	5.56	0.83823	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.96972	0.9011	H	0.99011	4.4	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98701	1.0700	10	0.87932	D	0	.	15.7124	0.77641	1.0:0.0:0.0:0.0	.	90	Q8WZ60	KLHL6_HUMAN	P	90	ENSP00000341342:L90P	ENSP00000341342:L90P	L	-	2	0	KLHL6	184755867	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.483000	0.81158	2.108000	0.64289	0.533000	0.62120	CTT	A|1.000;G|0.000	0.000	weak		0.507	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446		G	183273173	A	G	183273173	3	3	21	1	0	0	0	0	1	0	0	0	8402	72	3	3	1624	3	KLHL6	3	183273173	Missense_Mutation	SNP	A	TCGA-FM-8000-01A-11D-2210-10	42866512	183273173	14749257	33	2776											
BCL6	604	hgsc.bcm.edu	37	chr3	187442783	187442783	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tggctcttcagagtctgaagGtgccggaaacgggtgccaca	9	8	14	10	2	3	2	1	1	2	1	3	3	3	3	2	4	3	1	2	4	2	1			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr3:187442783G>T	ENST00000406870.2	-	9	2289	c.1923C>A	c.(1921-1923)caC>caA	p.H641Q	BCL6_ENST00000450123.2_Missense_Mutation_p.H585Q|RP11-211G3.3_ENST00000437407.1_Intron|RP11-211G3.3_ENST00000449623.1_Intron|BCL6_ENST00000232014.4_Missense_Mutation_p.H641Q	NM_001706.4	NP_001697.2	P41182	BCL6_HUMAN	B-cell CLL/lymphoma 6	641					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)		GAGTCTGAAGGTGCCGGAAAC	0.562			"T, Mis"	"IG loci, ZNFN1A1, LCP1, PIM1, TFRC, CIITA, NACA, HSPCB, HSPCA, HIST1H4I, IL21R,  POU2AF1, ARHH, EIF4A2, SFRS3"	"NHL, CLL"																																p.H641Q		Atlas-SNP	.		Dom	yes		3	3q27	604	B-cell CLL/lymphoma 6		L	.	BCL6	107	.	0			c.C1923A						PASS	.						112	109	110					3																	187442783		2203	4300	6503	SO:0001583	missense	604	exon9			CTGAAGGTGCCGG		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.1923C>A	3.37:g.187442783G>T	ENSP00000384371:p.His641Gln	143	0	0		88	32	0.363636	NM_001706	A7E241|B8PSA7|D3DNV5	Missense_Mutation	SNP	ENST00000406870.2	37	CCDS3289.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.213582	0.79352	.	.	ENSG00000113916	ENST00000406870;ENST00000232014;ENST00000450123	T;T;T	0.18338	2.22;2.22;2.22	5.78	4.9	0.64082	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	0.23766	0.0575	N	0.16602	0.42	0.51233	D	0.999912	D;D	0.69078	0.975;0.997	P;D	0.81914	0.857;0.995	T	0.07424	-1.0773	10	0.19590	T	0.45	.	13.9219	0.63937	0.0728:0.0:0.9272:0.0	.	585;641	B8PSA7;P41182	.;BCL6_HUMAN	Q	641;641;585	ENSP00000384371:H641Q;ENSP00000232014:H641Q;ENSP00000413122:H585Q	ENSP00000232014:H641Q	H	-	3	2	BCL6	188925477	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.762000	0.68809	1.441000	0.47550	0.655000	0.94253	CAC	.	.	none		0.562	BCL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344202.1	NM_138931		T	187442783	G	T	187442783	3	4	21	1	0	0	0	0	1	0	0	0	1376	1252	44	4	205	4	BCL6	3	187442783	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	4169610	187442783	10579647	34	2777											
SLC10A4	201780	hgsc.bcm.edu	37	chr4	48490448	48490448	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	aattttctattactaggtttCcctgtggtctctgctagtga	7	18	8	8	0	2	1	0	1	2	0	4	1	3	1	1	2	2	2	1	2	5	7			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr4:48490448C>T	ENST00000273861.4	+	3	1025	c.806C>T	c.(805-807)tCc>tTc	p.S269F	ZAR1_ENST00000327939.4_5'Flank	NM_152679.3	NP_689892.1	Q96EP9	NTCP4_HUMAN	solute carrier family 10, member 4	269						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bile acid:sodium symporter activity (GO:0008508)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	6						TACTAGGTTTCCCTGTGGTCT	0.453																																					p.S269F		Atlas-SNP	.											.	SLC10A4	23	.	0			c.C806T						PASS	.						152	157	155					4																	48490448		2203	4300	6503	SO:0001583	missense	201780	exon3			AGGTTTCCCTGTG	BC012048	CCDS3482.1	4p12	2013-07-18	2013-07-18		ENSG00000145248	ENSG00000145248		"Solute carriers"	22980	protein-coding gene	gene with protein product							Standard	NM_152679		Approved	MGC29802	uc003gyc.2	Q96EP9	OTTHUMG00000102092	ENST00000273861.4:c.806C>T	4.37:g.48490448C>T	ENSP00000273861:p.Ser269Phe	61	0	0		44	14	0.318182	NM_152679	Q8WUZ2	Missense_Mutation	SNP	ENST00000273861.4	37	CCDS3482.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.640924	0.87859	.	.	ENSG00000145248	ENST00000273861	T	0.15372	2.43	5.55	5.55	0.83447	.	0.096024	0.85682	D	0.000000	T	0.29458	0.0734	L	0.31120	0.905	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	T	0.02126	-1.1209	10	0.10111	T	0.7	0.371	19.8809	0.96899	0.0:1.0:0.0:0.0	.	269	Q96EP9	NTCP4_HUMAN	F	269	ENSP00000273861:S269F	ENSP00000273861:S269F	S	+	2	0	SLC10A4	48185205	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	7.445000	0.80570	2.771000	0.95319	0.561000	0.74099	TCC	.	.	none		0.453	SLC10A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219926.3	NM_152679		T	48490448	C	T	48490448	3	4	21	1	0	0	0	0	1	0	0	0	14391	855	30	2	816	2	SLC10A4	4	48490448	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10		48490448	142663828	35	2778											
ATOH1	474	hgsc.bcm.edu	37	chr4	94750977	94750977	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttctcgactttcgaggacagCgccctgacagcgatgatggc	8	9	12	12	4	1	2	0	2	1	0	3	6	1	3	1	2	2	0	1	2	0	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr4:94750977C>T	ENST00000306011.3	+	1	936	c.900C>T	c.(898-900)agC>agT	p.S300S		NM_005172.1	NP_005163.1	Q92858	ATOH1_HUMAN	atonal homolog 1 (Drosophila)	300					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)		TCGAGGACAGCGCCCTGACAG	0.607																																					p.S300S		Atlas-SNP	.											.	ATOH1	40	.	0			c.C900T						PASS	.						66	71	69					4																	94750977		2203	4300	6503	SO:0001819	synonymous_variant	474	exon1			GGACAGCGCCCTG	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.900C>T	4.37:g.94750977C>T		44	0	0		37	13	0.351351	NM_005172	Q14CT9	Silent	SNP	ENST00000306011.3	37	CCDS3638.1																																																																																			.	.	none		0.607	ATOH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253585.1	NM_005172		T	94750977	C	T	94750977	2	4	21	1	0	0	0	0	0	0	0	1	1112	767	27	1		1	ATOH1	4	94750977	Silent	SNP	C	TCGA-FM-8000-01A-11D-2210-10	46260529	94750977	96403299	36	2779											
NUDT6	11162	hgsc.bcm.edu	37	chr4	123814096	123814096	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cacagtcaggtcaattttgtCaaacccttctctgtacccat	10	13	5	13	0	4	0	3	0	1	0	5	0	4	0	2	1	2	1	2	1	3	4			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr4:123814096C>T	ENST00000304430.5	-	5	871	c.838G>A	c.(838-840)Gac>Aac	p.D280N	FGF2_ENST00000608478.1_3'UTR|NUDT6_ENST00000339154.2_Missense_Mutation_p.D111N|FGF2_ENST00000264498.3_3'UTR|NUDT6_ENST00000608639.1_5'Flank|NUDT6_ENST00000502270.1_Missense_Mutation_p.D111N	NM_007083.4	NP_009014.2	P53370	NUDT6_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 6	280						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						TCAATTTTGTCAAACCCTTCT	0.423																																					p.D280N		Atlas-SNP	.											.	NUDT6	50	.	0			c.G838A						PASS	.						94	93	93					4																	123814096		2203	4300	6503	SO:0001583	missense	11162	exon5			TTTTGTCAAACCC	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.838G>A	4.37:g.123814096C>T	ENSP00000306070:p.Asp280Asn	118	0	0		96	34	0.354167	NM_007083	A8K756|O95097|Q9UQD9	Missense_Mutation	SNP	ENST00000304430.5	37	CCDS43268.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.936405	0.52972	.	.	ENSG00000170917	ENST00000304430;ENST00000339154;ENST00000502270	T;T;T	0.29655	1.56;1.56;1.56	5.11	5.11	0.69529	NUDIX hydrolase domain-like (1);	0.313784	0.34314	N	0.004066	T	0.34164	0.0888	M	0.71581	2.175	0.37755	D	0.926118	P	0.34462	0.454	B	0.31290	0.127	T	0.42899	-0.9424	10	0.59425	D	0.04	-23.1859	14.2122	0.65771	0.0:0.8508:0.1492:0.0	.	280	P53370	NUDT6_HUMAN	N	280;111;111	ENSP00000306070:D280N;ENSP00000344011:D111N;ENSP00000424117:D111N	ENSP00000306070:D280N	D	-	1	0	NUDT6	124033546	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.142000	0.50601	2.380000	0.81148	0.650000	0.86243	GAC	.	.	none		0.423	NUDT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095331.3	NM_007083		T	123814096	C	T	123814096	3	4	21	1	0	0	0	0	1	0	0	0	10752	826	29	2	116	2	NUDT6	4	123814096	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	29063119	123814096	67340180	37	2780											
FAT4	79633	hgsc.bcm.edu	37	chr4	126412678	126412678	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acggtcgcagggccgagggaGgacctgtgggcacccaggca	8	3	18	12	3	0	0	0	0	0	0	1	3	0	2	3	6	0	3	3	6	0	0			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr4:126412678G>A	ENST00000394329.3	+	17	14714	c.14701G>A	c.(14701-14703)Gga>Aga	p.G4901R	FAT4_ENST00000335110.5_Missense_Mutation_p.G3142R	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4901					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						GGCCGAGGGAGGACCTGTGGG	0.537																																					p.G4901R		Atlas-SNP	.											.	FAT4	1752	.	0			c.G14701A						PASS	.						60	58	59					4																	126412678		2203	4300	6503	SO:0001583	missense	79633	exon17			GAGGGAGGACCTG	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.14701G>A	4.37:g.126412678G>A	ENSP00000377862:p.Gly4901Arg	148	0	0		141	60	0.425532	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	17.97	3.518282	0.64634	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	D;D	0.89617	-2.38;-2.54	5.19	5.19	0.71726	.	0.000000	0.33875	U	0.004462	D	0.93818	0.8023	M	0.79123	2.44	0.52501	D	0.999958	D;D;D	0.69078	0.99;0.997;0.99	P;P;P	0.62382	0.901;0.881;0.901	D	0.94568	0.7768	10	0.87932	D	0	.	17.7328	0.88383	0.0:0.0:1.0:0.0	.	3142;4901;4900	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	R	4901;3142	ENSP00000377862:G4901R;ENSP00000335169:G3142R	ENSP00000335169:G3142R	G	+	1	0	FAT4	126632128	1.000000	0.71417	0.824000	0.32777	0.750000	0.42670	5.265000	0.65519	2.425000	0.82216	0.491000	0.48974	GGA	.	.	none		0.537	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126412678	G	A	126412678	3	1	21	1	0	0	0	0	1	0	0	0	5700	1001	35	2	14767	2	FAT4	4	126412678	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	2598582	126412678	64741598	38	2781											
GRIA2	2891	hgsc.bcm.edu	37	chr4	158257596	158257596	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaggtgattgacttctcaaAgcccttcatgagcctcggga	10	10	11	10	1	2	4	2	3	1	1	4	5	2	5	2	2	2	0	2	2	1	3			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr4:158257596A>C	ENST00000264426.9	+	11	1820	c.1541A>C	c.(1540-1542)aAg>aCg	p.K514T	GRIA2_ENST00000507898.1_Missense_Mutation_p.K467T|GRIA2_ENST00000393815.2_Missense_Mutation_p.K467T|GRIA2_ENST00000449365.1_Missense_Mutation_p.K467T|GRIA2_ENST00000296526.7_Missense_Mutation_p.K514T	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	514					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)	GACTTCTCAAAGCCCTTCATG	0.408																																					p.K514T		Atlas-SNP	.											.	GRIA2	358	.	0			c.A1541C						PASS	.						172	171	171					4																	158257596		2203	4300	6503	SO:0001583	missense	2891	exon11			TCTCAAAGCCCTT		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.1541A>C	4.37:g.158257596A>C	ENSP00000264426:p.Lys514Thr	270	1	0.0037037		197	84	0.426396	NM_000826	A8MT92|I6L997|Q96FP6	Missense_Mutation	SNP	ENST00000264426.9	37	CCDS43274.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.013329	0.75161	.	.	ENSG00000120251	ENST00000507898;ENST00000393815;ENST00000296526;ENST00000264426;ENST00000449365	T;T;T;T;T	0.37584	1.19;1.19;1.19;1.19;1.19	5.46	5.46	0.80206	Ionotropic glutamate receptor (1);	0.000000	0.85682	D	0.000000	T	0.47985	0.1475	L	0.27975	0.815	0.80722	D	1	P;D;D	0.89917	0.94;1.0;0.993	B;D;D	0.91635	0.346;0.999;0.968	T	0.48151	-0.9060	10	0.51188	T	0.08	.	15.8204	0.78638	1.0:0.0:0.0:0.0	.	514;514;467	P42262;P42262-2;A8MT92	GRIA2_HUMAN;.;.	T	467;467;514;514;467	ENSP00000426845:K467T;ENSP00000377403:K467T;ENSP00000296526:K514T;ENSP00000264426:K514T;ENSP00000389837:K467T	ENSP00000264426:K514T	K	+	2	0	GRIA2	158477046	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.287000	0.95975	2.196000	0.70406	0.533000	0.62120	AAG	.	.	none		0.408	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2			C	158257596	A	C	158257596	3	2	21	1	0	0	0	0	1	0	0	0	6777	72	3	5	1583	5	GRIA2	4	158257596	Missense_Mutation	SNP	A	TCGA-FM-8000-01A-11D-2210-10	31844918	158257596	32896680	39	2782											
SLC6A3	6531	hgsc.bcm.edu	37	chr5	1406387	1406387	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcatctgctggatgtcgtcGctgaactgcccaacacctga	8	10	10	13	2	2	2	1	2	1	0	4	3	2	3	2	1	4	2	2	1	2	0	rs114563841		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr5:1406387G>A	ENST00000270349.9	-	12	1642	c.1515C>T	c.(1513-1515)agC>agT	p.S505S	SLC6A3_ENST00000453492.2_Silent_p.S505S	NM_001044.4	NP_001035.1	Q01959	SC6A3_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 3	505					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)	GGATGTCGTCGCTGAACTGCC	0.642													g|||	1	0.000199681	0.0008	0.0	5008	,	,		17793	0.0		0.0	False		,,,				2504	0.0				p.S505S		Atlas-SNP	.											.	SLC6A3	102	.	0			c.C1515T						PASS	.						76	71	72					5																	1406387		2203	4300	6503	SO:0001819	synonymous_variant	6531	exon12			GTCGTCGCTGAAC		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.1515C>T	5.37:g.1406387G>A		160	0	0		84	26	0.309524	NM_001044	A2RUN4|Q14996	Silent	SNP	ENST00000270349.9	37	CCDS3863.1																																																																																			G|0.995;A|0.005	0.005	strong		0.642	SLC6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253650.3	NM_001044		A	1406387	G	A	1406387	2	1	21	1	0	0	0	0	0	0	0	1	14700	1078	38	1		1	SLC6A3	5	1406387	Silent	SNP	G	TCGA-FM-8000-01A-11D-2210-10		1406387	179508873	40	2783											
ADCY2	108	hgsc.bcm.edu	37	chr5	7826845	7826845	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttctaggttaccgaggagaCgagcctcgtcctgcagaccc	8	8	11	14	3	1	2	0	0	1	2	3	5	2	2	4	2	3	2	4	2	2	3			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr5:7826845C>T	ENST00000338316.4	+	25	3226	c.3137C>T	c.(3136-3138)aCg>aTg	p.T1046M	ADCY2_ENST00000537121.1_Missense_Mutation_p.T866M	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	1046					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						ACCGAGGAGACGAGCCTCGTC	0.488																																					p.T1046M		Atlas-SNP	.											.	ADCY2	337	.	0			c.C3137T						PASS	.						103	92	96					5																	7826845		2203	4300	6503	SO:0001583	missense	108	exon25			AGGAGACGAGCCT	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.3137C>T	5.37:g.7826845C>T	ENSP00000342952:p.Thr1046Met	104	0	0		60	22	0.366667	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	37	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	C	12.50	1.957024	0.34565	.	.	ENSG00000078295	ENST00000338316;ENST00000382532;ENST00000541993;ENST00000537121	D;D	0.84516	-1.86;-1.86	5.43	4.56	0.56223	Adenylyl cyclase class-3/4/guanylyl cyclase (4);	0.053234	0.85682	D	0.000000	D	0.92557	0.7636	M	0.85299	2.745	0.50171	D	0.999853	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92270	0.5824	10	0.37606	T	0.19	.	15.5943	0.76566	0.1387:0.8613:0.0:0.0	.	866;1046	B7Z2C1;Q08462	.;ADCY2_HUMAN	M	1046;158;879;866	ENSP00000342952:T1046M;ENSP00000444803:T866M	ENSP00000342952:T1046M	T	+	2	0	ADCY2	7879845	1.000000	0.71417	0.683000	0.30040	0.075000	0.17131	5.871000	0.69628	1.275000	0.44379	0.591000	0.81541	ACG	.	.	none		0.488	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		T	7826845	C	T	7826845	3	4	21	1	0	0	0	0	1	0	0	0	294	536	19	1	3235	1	ADCY2	5	7826845	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	6420458	7826845	173088415	41	2784											
AQPEP	206338	hgsc.bcm.edu	37	chr5	115299001	115299001	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacgtctacaccgaccagggCgagcgcaggtaagggctgta	11	5	14	11	4	1	0	0	0	1	0	1	2	1	0	2	3	3	4	2	3	4	3			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr5:115299001C>T	ENST00000357872.4	+	1	811	c.687C>T	c.(685-687)ggC>ggT	p.G229G	AQPEP_ENST00000395528.2_5'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		229						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										CCGACCAGGGCGAGCGCAGGT	0.662																																					p.G229G		Atlas-SNP	.											.	.	.	.	0			c.C687T						PASS	.						13	15	14					5																	115299001		2141	4234	6375	SO:0001819	synonymous_variant	0	exon1			CCAGGGCGAGCGC																												ENST00000357872.4:c.687C>T	5.37:g.115299001C>T		59	0	0		38	16	0.421053	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Silent	SNP	ENST00000357872.4	37	CCDS4124.1																																																																																			.	.	none		0.662	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1			T	115299001	C	T	115299001	2	4	21	1	0	0	0	0	0	0	0	1	834	755	27	1		1	AQPEP	5	115299001	Silent	SNP	C	TCGA-FM-8000-01A-11D-2210-10	107472156	115299001	65616259	42	2785											
ZNF608	57507	hgsc.bcm.edu	37	chr5	123984038	123984038	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaactgtctaacgcagccGtcatgttggagattactgga	11	10	11	9	2	2	1	1	0	1	1	2	3	2	2	1	2	5	3	1	2	3	3	rs186374145		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr5:123984038G>A	ENST00000306315.5	-	4	2474	c.2039C>T	c.(2038-2040)aCg>aTg	p.T680M	ZNF608_ENST00000504926.1_Missense_Mutation_p.T253M	NM_020747.2	NP_065798.2	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	680							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)		TAACGCAGCCGTCATGTTGGA	0.458													G|||	1	0.000199681	0.0	0.0	5008	,	,		17651	0.0		0.001	False		,,,				2504	0.0				p.T680M		Atlas-SNP	.											.	ZNF608	117	.	0			c.C2039T						PASS	.						117	120	119					5																	123984038		2203	4300	6503	SO:0001583	missense	57507	exon4			GCAGCCGTCATGT	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.2039C>T	5.37:g.123984038G>A	ENSP00000307746:p.Thr680Met	185	0	0		147	71	0.482993	NM_020747	A7E2W9|Q3SYM6|Q68D12|Q8IY05|Q9Y5A1	Missense_Mutation	SNP	ENST00000306315.5	37	CCDS34219.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	13.84	2.356303	0.41700	.	.	ENSG00000168916	ENST00000504926;ENST00000306315;ENST00000509799;ENST00000513986	T;T	0.50277	0.75;0.75	5.88	5.88	0.94601	.	0.336013	0.35235	N	0.003341	T	0.41766	0.1173	N	0.14661	0.345	0.35596	D	0.807501	D	0.57899	0.981	P	0.47015	0.534	T	0.51919	-0.8644	10	0.51188	T	0.08	-7.3927	20.2315	0.98350	0.0:0.0:1.0:0.0	.	680	Q9ULD9	ZN608_HUMAN	M	253;680;680;680	ENSP00000427657:T253M;ENSP00000307746:T680M	ENSP00000307746:T680M	T	-	2	0	ZNF608	124011937	0.997000	0.39634	0.999000	0.59377	0.904000	0.53231	6.509000	0.73725	2.784000	0.95788	0.551000	0.68910	ACG	G|1.000;A|0.000	0.000	strong		0.458	ZNF608-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371300.1	XM_114432		A	123984038	G	A	123984038	3	1	21	1	0	0	0	0	1	0	0	0	18049	1145	40	1	2523	1	ZNF608	5	123984038	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	8685037	123984038	56931222	43	2786											
PKD2L2	27039	hgsc.bcm.edu	37	chr5	137228235	137228235	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatgtcatctctatttttggAcacttctgtgcctggtgaag	7	17	9	8	0	3	1	1	1	2	0	4	2	3	2	1	2	1	0	1	2	3	5			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr5:137228235A>T	ENST00000508883.1	+	3	226	c.200A>T	c.(199-201)gAc>gTc	p.D67V	PKD2L2_ENST00000502810.1_Missense_Mutation_p.D67V|PKD2L2_ENST00000290431.5_Missense_Mutation_p.D67V|PKD2L2_ENST00000508638.1_Missense_Mutation_p.D67V|PKD2L2_ENST00000350250.4_Missense_Mutation_p.D33V			Q9NZM6	PK2L2_HUMAN	polycystic kidney disease 2-like 2	67					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)			CTATTTTTGGACACTTCTGTG	0.338																																					p.D67V		Atlas-SNP	.											.	PKD2L2	68	.	0			c.A200T						PASS	.						147	140	142					5																	137228235		1857	4103	5960	SO:0001583	missense	27039	exon3			TTTTGGACACTTC	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.200A>T	5.37:g.137228235A>T	ENSP00000424725:p.Asp67Val	122	0	0		86	34	0.395349	NM_001258448	A6NK98|B4DXD2|E9PC91|E9PDG4|Q86YB4|Q9UNJ0	Missense_Mutation	SNP	ENST00000508883.1	37		.	.	.	.	.	.	.	.	.	.	A	18.53	3.644784	0.67358	.	.	ENSG00000078795	ENST00000350250;ENST00000508638;ENST00000502810;ENST00000508883;ENST00000290431	T;T;T;T;T	0.72835	-0.31;0.23;-0.69;-0.23;-0.24	5.84	5.84	0.93424	.	0.078484	0.53938	D	0.000050	T	0.67487	0.2898	L	0.52905	1.665	0.80722	D	1	B;P;B	0.40731	0.036;0.728;0.328	B;B;B	0.37601	0.09;0.254;0.155	T	0.72308	-0.4332	10	0.72032	D	0.01	-18.009	15.8841	0.79226	1.0:0.0:0.0:0.0	.	67;67;67	Q9NZM6;E9PC91;Q9NZM6-5	PK2L2_HUMAN;.;.	V	33;67;67;67;67	ENSP00000344177:D33V;ENSP00000423382:D67V;ENSP00000425513:D67V;ENSP00000424725:D67V;ENSP00000290431:D67V	ENSP00000290431:D67V	D	+	2	0	PKD2L2	137256134	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.333000	0.90026	2.233000	0.73108	0.496000	0.49642	GAC	.	.	none		0.338	PKD2L2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372521.1	NM_014386		T	137228235	A	T	137228235	3	4	21	1	0	0	0	0	1	0	0	0	11977	275	10	5	210	5	PKD2L2	5	137228235	Missense_Mutation	SNP	A	TCGA-FM-8000-01A-11D-2210-10	13244197	137228235	43687025	44	2787											
PCDHA6	56142	hgsc.bcm.edu	37	chr5	140209668	140209668	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcgctgacagcgacggccacGgttctggtgtcgctggtgga	5	8	17	11	5	1	1	0	1	1	0	2	3	1	2	1	5	1	3	1	5	0	1	rs141570762	byFrequency	TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr5:140209668G>A	ENST00000529310.1	+	1	2106	c.1992G>A	c.(1990-1992)acG>acA	p.T664T	PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000512229.2_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	664	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)			CGACGGCCACGGTTCTGGTGT	0.692																																					p.T664T		Atlas-SNP	.											.	PCDHA6	442	.	0			c.G1992A						PASS	.						37	44	42					5																	140209668		2202	4297	6499	SO:0001819	synonymous_variant	56142	exon1			GGCCACGGTTCTG	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.1992G>A	5.37:g.140209668G>A		94	0	0		56	29	0.517857	NM_018909	O75283|Q9NRT8	Silent	SNP	ENST00000529310.1	37	CCDS47281.1																																																																																			G|0.998;C|0.002	.	alt		0.692	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909		A	140209668	G	A	140209668	2	1	21	1	0	0	0	0	0	0	0	1	11537	1103	39	1		1	PCDHA6	5	140209668	Silent	SNP	G	TCGA-FM-8000-01A-11D-2210-10	2981433	140209668	40705592	45	2788											
PCDHA13	56136	hgsc.bcm.edu	37	chr5	140263476	140263476	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgagcgcgcgcgactctggCgtgccgcctctgggcagcaa	5	6	16	14	6	2	1	0	1	2	0	2	2	2	1	2	2	3	2	2	2	1	0			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr5:140263476C>T	ENST00000289272.2	+	1	1623	c.1623C>T	c.(1621-1623)ggC>ggT	p.G541G	PCDHA8_ENST00000531613.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA13_ENST00000409494.1_Silent_p.G541G|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA7_ENST00000525929.1_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	541	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)|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)			GCGACTCTGGCGTGCCGCCTC	0.692																																					p.G541G	Melanoma(147;1739 1852 5500 27947 37288)	Atlas-SNP	.											.	PCDHA13	213	.	0			c.C1623T						PASS	.						73	79	77					5																	140263476		2203	4299	6502	SO:0001819	synonymous_variant	56136	exon1			CTCTGGCGTGCCG	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.1623C>T	5.37:g.140263476C>T		55	0	0		24	14	0.583333	NM_031865	O75277	Silent	SNP	ENST00000289272.2	37	CCDS4240.1																																																																																			.	.	none		0.692	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		T	140263476	C	T	140263476	2	4	21	1	0	0	0	0	0	0	0	1	11532	755	27	1		1	PCDHA13	5	140263476	Silent	SNP	C	TCGA-FM-8000-01A-11D-2210-10	53808	140263476	40651784	46	2789											
PCDHGA1	56114	hgsc.bcm.edu	37	chr5	140711925	140711925	+	Silent	SNP	C	C	T																															ctgctggaccagaacgacaaCgcgcccgagatcctgtaccc																										TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr5:140711925C>T	ENST00000517417.1	+	1	1674	c.1674C>T	c.(1672-1674)aaC>aaT	p.N558N	PCDHGA1_ENST00000378105.3_Silent_p.N558N	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	558	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.N558N(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)			AGAACGACAACGCGCCCGAGA	0.647																																					p.N558N		Atlas-SNP	.											PCDHGA1_ENST00000517417,NS,carcinoma,0,4	PCDHGA1	397	4	2	Substitution - coding silent(2)	lung(2)	c.C1674T						scavenged	.						140	153	149					5																	140711925		2203	4300	6503	SO:0001819	synonymous_variant	56114	exon1			CGACAACGCGCCC	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.1674C>T	5.37:g.140711925C>T		133	1	0.0075188		65	20	0.307692	NM_018912	Q2M273|Q9Y5D6	Silent	SNP	ENST00000517417.1	37	CCDS54922.1																																																																																			.	.	none		0.647	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912		T	140711925	C	T	140711925	2	4	21	1	0	0	0	0	0	0	0	1	11559	535	19	1		1	PCDHGA1	5	140711925	Silent	SNP	C	TCGA-FM-8000-01A-11D-2210-10	448449	140711925	40203335	47	2790	42	2									
PCDHGA1	56114	hgsc.bcm.edu	37	chr5	140711926	140711926	+	Missense_Mutation	SNP	G	G	A																															tgctggaccagaacgacaacGcgcccgagatcctgtacccc																										TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr5:140711926G>A	ENST00000517417.1	+	1	1675	c.1675G>A	c.(1675-1677)Gcg>Acg	p.A559T	PCDHGA1_ENST00000378105.3_Missense_Mutation_p.A559T	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	559	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)			GAACGACAACGCGCCCGAGAT	0.647																																					p.A559T		Atlas-SNP	.											PCDHGA1_ENST00000517417,NS,carcinoma,0,4	PCDHGA1	397	4	0			c.G1675A						scavenged	.						135	148	144					5																	140711926		2203	4300	6503	SO:0001583	missense	56114	exon1			GACAACGCGCCCG	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.1675G>A	5.37:g.140711926G>A	ENSP00000431083:p.Ala559Thr	132	0	0		65	3	0.0461538	NM_018912	Q2M273|Q9Y5D6	Missense_Mutation	SNP	ENST00000517417.1	37	CCDS54922.1	.	.	.	.	.	.	.	.	.	.	C	3.266	-0.150071	0.06585	.	.	ENSG00000204956	ENST00000517417;ENST00000378105	T;T	0.61742	0.08;0.08	3.92	-2.88	0.05682	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	0.462493	0.17896	N	0.158361	T	0.42268	0.1195	L	0.53617	1.68	0.09310	N	1	B;B	0.27559	0.026;0.181	B;B	0.15870	0.013;0.014	T	0.18304	-1.0341	10	0.28530	T	0.3	.	7.8166	0.29263	0.2962:0.1121:0.5917:0.0	.	559;559	Q9Y5H4-2;Q9Y5H4	.;PCDG1_HUMAN	T	559	ENSP00000431083:A559T;ENSP00000367345:A559T	ENSP00000367345:A559T	A	+	1	0	PCDHGA1	140692110	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.397000	0.00485	-0.867000	0.04063	-2.215000	0.00298	GCG	.	.	none		0.647	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912		A	140711926	G	A	140711926	3	1	21	1	0	0	0	0	1	0	0	0	11559	1087	38	1	1677	1	PCDHGA1	5	140711926	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	1	140711926	40203334	48	2791	42	2									
HIST1H3D	8351	hgsc.bcm.edu	37	chr6	26197212	26197212	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctcctgcagcgccatcacCgccgagctctgaaaacgcag	9	5	10	17	4	2	1	1	1	1	0	3	2	3	1	5	0	4	3	5	0	2	0			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr6:26197212C>G	ENST00000356476.2	-	1	266	c.267G>C	c.(265-267)gcG>gcC	p.A89A	HIST1H3D_ENST00000377831.5_Silent_p.A89A|HIST1H2BF_ENST00000359985.1_5'Flank			P68431	H31_HUMAN	histone cluster 1, H3d	89					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)			NS(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)	14		all_hematologic(11;0.196)				GCGCCATCACCGCCGAGCTCT	0.582																																					p.A89A	GBM(108;3816 4467)	Atlas-SNP	.											HIST1H3D,colon,carcinoma,0,1	HIST1H3D	31	1	0			c.G267C						PASS	.						76	73	74					6																	26197212		2203	4300	6503	SO:0001819	synonymous_variant	8351	exon2			CATCACCGCCGAG	Z80784	CCDS4590.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197409	ENSG00000197409		"Histones / Replication-dependent"	4767	protein-coding gene	gene with protein product		602811	"H3 histone family, member B", "histone 1, H3d"	H3FB		9119399, 12408966	Standard	NM_003530		Approved	H3/b	uc003ngv.4	P68431	OTTHUMG00000014433	ENST00000356476.2:c.267G>C	6.37:g.26197212C>G		186	0	0		109	36	0.330275	NM_003530	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000356476.2	37	CCDS4590.1																																																																																			.	.	none		0.582	HIST1H3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040096.1	NM_003530		G	26197212	C	G	26197212	2	3	21	1	0	0	0	0	0	0	0	1	7167	639	23	4		4	HIST1H3D	6	26197212	Silent	SNP	C	TCGA-FM-8000-01A-11D-2210-10		26197212	144917855	49	2792											
LTB	4050	hgsc.bcm.edu	37	chr6	31550123	31550123	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcaccagagaagtggctccTgccacagctagcaggaggga	11	5	14	11	0	1	1	1	0	0	1	2	4	2	3	3	3	3	3	3	3	2	1			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr6:31550123T>C	ENST00000429299.2	-	1	79	c.72A>G	c.(70-72)gcA>gcG	p.A24A	LTB_ENST00000446745.2_Silent_p.A24A|LTB_ENST00000483972.1_Intron	NM_002341.1	NP_002332.1	Q06643	TNFC_HUMAN	lymphotoxin beta (TNF superfamily, member 3)	24					cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|signal transduction (GO:0007165)|skin development (GO:0043588)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	9						AAGTGGCTCCTGCCACAGCTA	0.647																																					p.A24A		Atlas-SNP	.											.	LTB	19	.	0			c.A72G						PASS	.						69	50	57					6																	31550123		1509	2708	4217	SO:0001819	synonymous_variant	4050	exon1			GGCTCCTGCCACA	L11015	CCDS4703.1, CCDS4704.1	6p21.3	2013-05-22			ENSG00000227507	ENSG00000227507		"Tumor necrosis factor (ligand) superfamily"	6711	protein-coding gene	gene with protein product		600978		TNFC		7916655, 1714477	Standard	NM_002341		Approved	p33, TNFSF3	uc003nuk.3	Q06643	OTTHUMG00000031136	ENST00000429299.2:c.72A>G	6.37:g.31550123T>C		251	0	0		164	63	0.384146	NM_002341	P78370|Q52LU8|Q99761	Silent	SNP	ENST00000429299.2	37	CCDS4703.1																																																																																			.	.	none		0.647	LTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076239.3			C	31550123	T	C	31550123	2	2	21	1	0	0	0	0	0	0	0	1	9079	1567	55	3		3	LTB	6	31550123	Silent	SNP	T	TCGA-FM-8000-01A-11D-2210-10	5352911	31550123	139564944	50	2793											
DAAM2	23500	hgsc.bcm.edu	37	chr6	39832772	39832772	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagatgcagagtctgtacgCgtttgatgaggaggagacgg	10	9	16	6	3	2	5	1	2	1	3	2	7	2	6	0	3	2	3	0	3	1	2	rs574596379	byFrequency	TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr6:39832772C>T	ENST00000398904.2	+	5	532	c.350C>T	c.(349-351)gCg>gTg	p.A117V	DAAM2_ENST00000538976.1_Missense_Mutation_p.A117V|DAAM2_ENST00000274867.4_Missense_Mutation_p.A117V|DAAM2_ENST00000494405.1_3'UTR			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	117	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)					AGTCTGTACGCGTTTGATGAG	0.572											OREG0017416	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2	0.000399361	0.0	0.0029	5008	,	,		17783	0.0		0.0	False		,,,				2504	0.0				p.A117V		Atlas-SNP	.											.	DAAM2	101	.	0			c.C350T						PASS	.						83	97	92					6																	39832772		2092	4212	6304	SO:0001583	missense	23500	exon5			TGTACGCGTTTGA	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.350C>T	6.37:g.39832772C>T	ENSP00000381876:p.Ala117Val	189	0	0	888	105	37	0.352381	NM_015345	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	37	CCDS56426.1	.	.	.	.	.	.	.	.	.	.	C	14.78	2.638456	0.47153	.	.	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976	T;T;T	0.77620	-1.11;-1.11;-1.11	5.69	1.47	0.22746	GTPase-binding/formin homology 3 (1);Armadillo-type fold (1);Diaphanous GTPase-binding (1);	0.460055	0.23541	N	0.047078	T	0.52451	0.1735	L	0.48362	1.52	0.80722	D	1	B;B	0.13594	0.007;0.008	B;B	0.08055	0.002;0.003	T	0.52102	-0.8620	10	0.36615	T	0.2	.	9.0456	0.36345	0.3782:0.5537:0.0:0.0681	.	117;117	G5EA45;Q86T65	.;DAAM2_HUMAN	V	117	ENSP00000274867:A117V;ENSP00000381876:A117V;ENSP00000437808:A117V	ENSP00000274867:A117V	A	+	2	0	DAAM2	39940750	0.840000	0.29493	0.012000	0.15200	0.795000	0.44927	1.720000	0.38022	0.695000	0.31675	0.655000	0.94253	GCG	.	.	none		0.572	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1			T	39832772	C	T	39832772	3	4	21	1	0	0	0	0	1	0	0	0	4218	768	27	1	364	1	DAAM2	6	39832772	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	8282649	39832772	131282295	51	2794											
GSTA3	2940	hgsc.bcm.edu	37	chr6	52764808	52764808	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcatctttttcctcaggtCgacataagggcagaagaagg	11	10	12	8	1	2	2	1	0	1	2	4	3	3	2	1	4	0	2	1	4	3	3	rs45602042	byFrequency	TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr6:52764808C>A	ENST00000211122.3	-	5	403	c.338G>T	c.(337-339)cGa>cTa	p.R113L	GSTA3_ENST00000370968.1_Missense_Mutation_p.R63L	NM_000847.4	NP_000838.3	Q16772	GSTA3_HUMAN	glutathione S-transferase alpha 3	113	GST C-terminal.		R -> Q (in dbSNP:rs45602042). {ECO:0000269|Ref.3}.	RP -> PA (in Ref. 1; AAA74634). {ECO:0000305}.	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)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(2)	10	Lung NSC(77;0.0912)				Glutathione(DB00143)	TTCCTCAGGTCGACATAAGGG	0.388																																					p.R113L		Atlas-SNP	.											GSTA3,caecum,carcinoma,-1,1	GSTA3	21	1	0			c.G338T						PASS	.						194	177	183					6																	52764808		2203	4300	6503	SO:0001583	missense	2940	exon5			TCAGGTCGACATA	AF020919	CCDS4947.1	6p12.2	2012-06-21	2008-11-26		ENSG00000174156	ENSG00000174156	2.5.1.18	"Glutathione S-transferases / Soluble"	4628	protein-coding gene	gene with protein product		605449	"glutathione S-transferase A3"			8307579, 9480897	Standard	NM_000847		Approved		uc003pbb.3	Q16772	OTTHUMG00000014865	ENST00000211122.3:c.338G>T	6.37:g.52764808C>A	ENSP00000211122:p.Arg113Leu	175	0	0		147	55	0.37415	NM_000847	O43468|Q068V6|Q8WWA8|Q9H415	Missense_Mutation	SNP	ENST00000211122.3	37	CCDS4947.1	.	.	.	.	.	.	.	.	.	.	C	8.320	0.824098	0.16678	.	.	ENSG00000174156	ENST00000370968;ENST00000211122;ENST00000431899	T;T;T	0.06849	4.49;4.49;3.25	3.91	1.91	0.25777	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.290327	0.31461	N	0.007611	T	0.01320	0.0043	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47262	-0.9131	10	0.48119	T	0.1	.	8.2476	0.31698	0.0:0.1509:0.579:0.2701	.	113	Q16772	GSTA3_HUMAN	L	63;113;63	ENSP00000360007:R63L;ENSP00000211122:R113L;ENSP00000399142:R63L	ENSP00000211122:R113L	R	-	2	0	GSTA3	52872767	0.352000	0.24895	0.008000	0.14137	0.007000	0.05969	2.182000	0.42556	0.971000	0.38288	-0.340000	0.08031	CGA	C|0.989;T|0.011	.	alt		0.388	GSTA3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040933.1			A	52764808	C	A	52764808	3	1	21	1	0	0	0	0	1	0	0	0	6841	884	31	4	342	4	GSTA3	6	52764808	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	12932036	52764808	118350259	52	2795											
HCRTR2	3062	hgsc.bcm.edu	37	chr6	55113583	55113583	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgagacctggttttttggaCagtccctttgcaaagtgatt	8	15	10	8	0	0	2	0	2	0	1	1	4	1	3	2	2	1	2	2	2	1	5			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr6:55113583C>A	ENST00000370862.3	+	2	706	c.370C>A	c.(370-372)Cag>Aag	p.Q124K		NM_001526.3	NP_001517.2	O43614	OX2R_HUMAN	hypocretin (orexin) receptor 2	124					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)			GTTTTTTGGACAGTCCCTTTG	0.433																																					p.Q124K		Atlas-SNP	.											.	HCRTR2	112	.	0			c.C370A						PASS	.						255	237	243					6																	55113583		2203	4299	6502	SO:0001583	missense	3062	exon2			TTTGGACAGTCCC	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.370C>A	6.37:g.55113583C>A	ENSP00000359899:p.Gln124Lys	211	0	0		142	59	0.415493	NM_001526	Q5VTM0	Missense_Mutation	SNP	ENST00000370862.3	37	CCDS4956.1	.	.	.	.	.	.	.	.	.	.	C	8.432	0.848733	0.17034	.	.	ENSG00000137252	ENST00000370862	T	0.71579	-0.58	4.65	3.7	0.42460	GPCR, rhodopsin-like superfamily (1);	0.238432	0.43747	D	0.000534	T	0.31544	0.0800	N	0.25825	0.765	0.36022	D	0.838786	B;B	0.02656	0.0;0.0	B;B	0.12837	0.008;0.008	T	0.10245	-1.0638	10	0.05959	T	0.93	.	9.4903	0.38955	0.1417:0.6016:0.2567:0.0	.	124;124	Q548Y0;O43614	.;OX2R_HUMAN	K	124	ENSP00000359899:Q124K	ENSP00000359899:Q124K	Q	+	1	0	HCRTR2	55221542	0.690000	0.27699	1.000000	0.80357	0.994000	0.84299	0.404000	0.20999	2.282000	0.76494	0.555000	0.69702	CAG	.	.	none		0.433	HCRTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043392.1			A	55113583	C	A	55113583	3	1	21	1	0	0	0	0	1	0	0	0	7011	479	17	4	376	4	HCRTR2	6	55113583	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	2348775	55113583	116001484	53	2796											
MDN1	23195	hgsc.bcm.edu	37	chr6	90437660	90437660	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acaggtagatctgctccaaaCaggtctgtgatgtcctttga	10	12	10	9	0	2	3	0	2	2	1	4	3	4	3	2	2	2	2	2	2	2	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr6:90437660C>T	ENST00000369393.3	-	37	5479	c.5364G>A	c.(5362-5364)ctG>ctA	p.L1788L	MDN1_ENST00000428876.1_Silent_p.L1788L			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	1788					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)		CTGCTCCAAACAGGTCTGTGA	0.448																																					p.L1788L		Atlas-SNP	.											.	MDN1	478	.	0			c.G5364A						PASS	.						128	111	116					6																	90437660		2203	4300	6503	SO:0001819	synonymous_variant	23195	exon37			TCCAAACAGGTCT	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.5364G>A	6.37:g.90437660C>T		79	0	0		61	28	0.459016	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	37	CCDS5024.1																																																																																			.	.	none		0.448	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			T	90437660	C	T	90437660	2	4	21	1	0	0	0	0	0	0	0	1	9424	465	17	2		2	MDN1	6	90437660	Silent	SNP	C	TCGA-FM-8000-01A-11D-2210-10	35324077	90437660	80677407	54	2797											
EPHA7	2045	hgsc.bcm.edu	37	chr6	93982068	93982068	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgactccattgggatgctctGgttcctgccaggaaagctcg	7	11	12	11	1	1	1	0	1	1	0	4	3	3	3	3	3	3	3	3	3	1	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr6:93982068G>C	ENST00000369303.4	-	6	1581	c.1397C>G	c.(1396-1398)cCa>cGa	p.P466R		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	466	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		GGGATGCTCTGGTTCCTGCCA	0.448																																					p.P466R		Atlas-SNP	.											.	EPHA7	251	.	0			c.C1397G						PASS	.						275	254	261					6																	93982068		2203	4300	6503	SO:0001583	missense	2045	exon6			TGCTCTGGTTCCT	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.1397C>G	6.37:g.93982068G>C	ENSP00000358309:p.Pro466Arg	278	1	0.00359712		208	75	0.360577	NM_004440	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Missense_Mutation	SNP	ENST00000369303.4	37	CCDS5031.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.949958	0.73787	.	.	ENSG00000135333	ENST00000369303	T	0.74737	-0.87	5.58	5.58	0.84498	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.93291	0.7862	H	0.99811	4.8	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	D	0.95956	0.8958	10	0.87932	D	0	.	19.9439	0.97175	0.0:0.0:1.0:0.0	.	466;466;466	Q15375-4;Q15375-2;Q15375	.;.;EPHA7_HUMAN	R	466	ENSP00000358309:P466R	ENSP00000358309:P466R	P	-	2	0	EPHA7	94038789	1.000000	0.71417	0.923000	0.36655	0.990000	0.78478	9.420000	0.97426	2.797000	0.96272	0.561000	0.74099	CCA	.	.	none		0.448	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1			C	93982068	G	C	93982068	3	2	21	1	0	0	0	0	1	0	0	0	5174	1348	47	4	1647	4	EPHA7	6	93982068	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	3544408	93982068	77132999	55	2798											
REV3L	5980	hgsc.bcm.edu	37	chr6	111694135	111694135	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tggctgagtcaagagactgtCccatttcttttctggtgtga	7	15	11	8	0	3	3	1	2	2	1	4	4	4	3	1	2	0	1	1	2	1	3			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr6:111694135C>T	ENST00000358835.3	-	14	5877	c.5423G>A	c.(5422-5424)gGa>gAa	p.G1808E	REV3L_ENST00000435970.1_Missense_Mutation_p.G1730E|REV3L_ENST00000368805.1_Missense_Mutation_p.G1808E|REV3L_ENST00000368802.3_Missense_Mutation_p.G1808E			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	1808					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)		AAGAGACTGTCCCATTTCTTT	0.428								DNA polymerases (catalytic subunits)																													p.G1808E		Atlas-SNP	.											.	REV3L	386	.	0			c.G5423A						PASS	.						148	135	139					6																	111694135		2203	4300	6503	SO:0001583	missense	5980	exon13			GACTGTCCCATTT	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.5423G>A	6.37:g.111694135C>T	ENSP00000351697:p.Gly1808Glu	100	0	0		70	32	0.457143	NM_002912	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	37	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	C	0.014	-1.600138	0.00849	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	T;T;T;T	0.01406	5.02;5.02;5.02;4.93	5.93	0.909	0.19332	Ribonuclease H-like (1);	1.297520	0.04829	N	0.438371	T	0.00271	0.0008	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36768	-0.9734	10	0.02654	T	1	-0.0059	2.2054	0.03934	0.1225:0.4906:0.1189:0.268	.	1808	O60673	DPOLZ_HUMAN	E	1808;1808;1808;1730	ENSP00000357792:G1808E;ENSP00000357795:G1808E;ENSP00000351697:G1808E;ENSP00000402003:G1730E	ENSP00000351697:G1808E	G	-	2	0	REV3L	111800828	0.032000	0.19561	0.030000	0.17652	0.264000	0.26372	-0.020000	0.12525	0.116000	0.18110	0.655000	0.94253	GGA	.	.	none		0.428	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		T	111694135	C	T	111694135	3	4	21	1	0	0	0	0	1	0	0	0	13255	855	30	2	4049	2	REV3L	6	111694135	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	17712067	111694135	59420932	56	2799											
RSPO3	84870	hgsc.bcm.edu	37	chr6	127476585	127476585	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtcagaagggagaacgaggTacaatcataataacaaaatg	19	7	10	5	1	2	2	2	0	0	2	2	4	2	2	0	2	3	1	0	2	8	3			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr6:127476585T>C	ENST00000356698.4	+	4	1223		c.e4+2		RSPO3_ENST00000368317.3_Splice_Site	NM_032784.3	NP_116173.2	Q9BXY4	RSPO3_HUMAN	R-spondin 3						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)		GAGAACGAGGTACAATCATAA	0.368																																					.		Atlas-SNP	.											RSPO3,NS,carcinoma,+2,1	RSPO3	32	1	0			c.634+2T>C						PASS	.						63	53	56					6																	127476585		2203	4300	6503	SO:0001630	splice_region_variant	84870	exon4			ACGAGGTACAATC	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.634+2T>C	6.37:g.127476585T>C		59	0	0		50	24	0.48	NM_032784	B2RC27|Q5VTV4|Q96K87	Splice_Site	SNP	ENST00000356698.4	37	CCDS5135.1	.	.	.	.	.	.	.	.	.	.	T	17.32	3.359375	0.61403	.	.	ENSG00000146374	ENST00000356698;ENST00000368317	.	.	.	5.54	5.54	0.83059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.6555	0.51315	0.0:0.0:0.1481:0.8519	.	.	.	.	.	-1	.	.	.	+	.	.	RSPO3	127518278	1.000000	0.71417	0.998000	0.56505	0.976000	0.68499	3.139000	0.50577	2.124000	0.65301	0.455000	0.32223	.	.	.	none		0.368	RSPO3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042111.1	NM_032784	Intron	C	127476585	T	C	127476585	5	2	21	1	0	0	0	0	0	0	1	0	13726	1652	57	3	650	3	RSPO3	6	127476585	Splice_Site	SNP	T	TCGA-FM-8000-01A-11D-2210-10	15782450	127476585	43638482	57	2800											
KIAA0408	9729	hgsc.bcm.edu	37	chr6	127768258	127768258	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttacttacatgaagatcaggAtgagatttagcagggtgatc	13	12	11	5	0	1	4	1	3	0	2	2	6	1	5	0	2	3	1	0	2	4	4			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr6:127768258A>G	ENST00000483725.3	-	5	1542	c.1206T>C	c.(1204-1206)caT>caC	p.H402H	SOGA3_ENST00000556132.1_3'UTR|SOGA3_ENST00000481848.2_3'UTR	NM_014702.4	NP_055517.3	Q6ZU52	K0408_HUMAN	KIAA0408	402										endometrium(3)|large_intestine(7)|lung(15)|ovary(1)|pancreas(1)|skin(1)	28				GBM - Glioblastoma multiforme(226;0.0217)|all cancers(137;0.13)		GAAGATCAGGATGAGATTTAG	0.438																																					p.H402H		Atlas-SNP	.											.	KIAA0408	61	.	0			c.T1206C						PASS	.						80	80	80					6																	127768258		2203	4300	6503	SO:0001819	synonymous_variant	9729	exon5			ATCAGGATGAGAT	AB007868	CCDS34531.1	6q22.33	2012-11-29			ENSG00000189367	ENSG00000189367			21636	protein-coding gene	gene with protein product							Standard	NM_014702		Approved		uc011ebs.2	Q6ZU52	OTTHUMG00000166439	ENST00000483725.3:c.1206T>C	6.37:g.127768258A>G		77	0	0		80	31	0.3875	NM_014702	B3KRE5|E1P573|O43158|Q5TF20|Q7L2M2	Silent	SNP	ENST00000483725.3	37	CCDS34531.1																																																																																			.	.	none		0.438	KIAA0408-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042145.3	NM_014702		G	127768258	A	G	127768258	2	3	21	1	0	0	0	0	0	0	0	1	8183	330	12	3		3	KIAA0408	6	127768258	Silent	SNP	A	TCGA-FM-8000-01A-11D-2210-10	291673	127768258	43346809	58	2801											
AVL9	23080	hgsc.bcm.edu	37	chr7	32620454	32620454	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggcaaaaaaattggaaacGtcatggtcacaactagccgg	15	7	11	8	2	2	0	2	0	0	0	2	1	2	1	1	4	3	1	1	4	6	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr7:32620454G>A	ENST00000318709.4	+	15	2004	c.1783G>A	c.(1783-1785)Gtc>Atc	p.V595I	AVL9_ENST00000404479.1_Intron|AVL9_ENST00000409301.1_Missense_Mutation_p.V577I	NM_015060.1	NP_055875.1	Q8NBF6	AVL9_HUMAN	AVL9 homolog (S. cerevisiase)	595					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						AATTGGAAACGTCATGGTCAC	0.368																																					p.V595I		Atlas-SNP	.											.	AVL9	66	.	0			c.G1783A						PASS	.						92	86	88					7																	32620454		2203	4300	6503	SO:0001583	missense	23080	exon15			GGAAACGTCATGG	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.1783G>A	7.37:g.32620454G>A	ENSP00000315568:p.Val595Ile	159	0	0		178	33	0.185393	NM_015060	Q92573	Missense_Mutation	SNP	ENST00000318709.4	37	CCDS34613.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.390565	0.82902	.	.	ENSG00000105778	ENST00000318709;ENST00000409301;ENST00000329714	T;T	0.45276	0.96;0.9	5.89	5.89	0.94794	.	0.126361	0.52532	D	0.000065	T	0.32496	0.0831	L	0.29908	0.895	0.80722	D	1	P	0.36733	0.567	B	0.21708	0.036	T	0.22312	-1.0220	10	0.87932	D	0	-15.1738	20.2617	0.98447	0.0:0.0:1.0:0.0	.	595	Q8NBF6	AVL9_HUMAN	I	595;577;537	ENSP00000315568:V595I;ENSP00000387011:V577I	ENSP00000315568:V595I	V	+	1	0	AVL9	32586979	1.000000	0.71417	0.995000	0.50966	0.990000	0.78478	9.202000	0.95026	2.793000	0.96121	0.655000	0.94253	GTC	.	.	none		0.368	AVL9-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328643.1	NM_015060		A	32620454	G	A	32620454	3	1	21	1	0	0	0	0	1	0	0	0	1228	1145	40	1	1841	1	AVL9	7	32620454	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10		32620454	126518209	59	2802											
ABCA13	154664	hgsc.bcm.edu	37	chr7	48314642	48314642	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accaaggaagacttcgcaatTgtgataaaaattcttttgga	15	12	8	6	1	1	2	0	1	1	1	2	4	1	4	1	2	0	1	1	2	6	6			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr7:48314642T>A	ENST00000435803.1	+	17	5403	c.5379T>A	c.(5377-5379)atT>atA	p.I1793I		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						ACTTCGCAATTGTGATAAAAA	0.378																																					p.I1793I		Atlas-SNP	.											.	ABCA13	1192	.	0			c.T5379A						PASS	.						43	41	41					7																	48314642		1844	4104	5948	SO:0001819	synonymous_variant	154664	exon17			CGCAATTGTGATA	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.5379T>A	7.37:g.48314642T>A		123	0	0		157	44	0.280255	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1																																																																																			.	.	none		0.378	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48314642	T	A	48314642	2	1	21	1	0	0	0	0	0	0	0	1	31	1800	63	5		5	ABCA13	7	48314642	Silent	SNP	T	TCGA-FM-8000-01A-11D-2210-10	15694188	48314642	110824021	60	2803											
EGFR	1956	hgsc.bcm.edu	37	chr7	55214404	55214404	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgactttctcagcaacatgtCgatggacttccagaaccacc	11	10	7	13	1	1	2	1	1	1	1	4	4	2	3	3	1	3	1	3	1	2	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr7:55214404C>T	ENST00000275493.2	+	4	707	c.530C>T	c.(529-531)tCg>tTg	p.S177L	EGFR_ENST00000442591.1_Missense_Mutation_p.S177L|EGFR_ENST00000455089.1_Intron|EGFR_ENST00000342916.3_Missense_Mutation_p.S177L|EGFR_ENST00000344576.2_Missense_Mutation_p.S177L|EGFR_ENST00000454757.2_Missense_Mutation_p.S124L|EGFR_ENST00000420316.2_Missense_Mutation_p.S177L	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	177			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)	AGCAACATGTCGATGGACTTC	0.582		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																											p.S177L		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.C530T						PASS	.						128	101	110					7																	55214404		2203	4300	6503	SO:0001583	missense	1956	exon4	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	ACATGTCGATGGA		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.530C>T	7.37:g.55214404C>T	ENSP00000275493:p.Ser177Leu	97	0	0		69	16	0.231884	NM_201283	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	C	13.28	2.191545	0.38707	.	.	ENSG00000146648	ENST00000342916;ENST00000395504;ENST00000344576;ENST00000420316;ENST00000275493;ENST00000442591;ENST00000450046;ENST00000454757	D;D;D;D;D;T;D	0.81739	-1.53;-1.53;-1.53;-1.53;-1.53;-1.06;-1.53	5.6	5.6	0.85130	.	0.578375	0.18102	N	0.151642	T	0.78110	0.4232	L	0.51422	1.61	0.37607	D	0.920783	B;B;B;B	0.17038	0.003;0.02;0.012;0.007	B;B;B;B	0.14023	0.006;0.01;0.007;0.002	T	0.75637	-0.3249	10	0.51188	T	0.08	.	17.1089	0.86670	0.0:1.0:0.0:0.0	.	177;177;177;177	P00533;P00533-3;P00533-4;P00533-2	EGFR_HUMAN;.;.;.	L	177;47;177;177;177;177;124;124	ENSP00000342376:S177L;ENSP00000345973:S177L;ENSP00000413843:S177L;ENSP00000275493:S177L;ENSP00000410031:S177L;ENSP00000413354:S124L;ENSP00000395243:S124L	ENSP00000275493:S177L	S	+	2	0	EGFR	55181898	0.008000	0.16893	0.978000	0.43139	0.094000	0.18550	1.093000	0.30939	2.630000	0.89119	0.655000	0.94253	TCG	.	.	none		0.582	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		T	55214404	C	T	55214404	3	4	21	1	0	0	0	0	1	0	0	0	4969	893	31	1	544	1	EGFR	7	55214404	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	6899762	55214404	103924259	61	2804											
RELN	5649	hgsc.bcm.edu	37	chr7	103236931	103236931	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgaagtctgaaaagtacaTctctgctagcaggtgccact	11	10	10	10	0	2	2	0	2	2	0	3	2	2	2	1	1	4	4	1	1	5	2	rs374443790		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr7:103236931T>G	ENST00000428762.1	-	25	3670	c.3511A>C	c.(3511-3513)Atg>Ctg	p.M1171L	RELN_ENST00000343529.5_Missense_Mutation_p.M1171L|RELN_ENST00000424685.2_Missense_Mutation_p.M1171L	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1171					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)		GAAAAGTACATCTCTGCTAGC	0.493																																					p.M1171L	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.A3511C						PASS	.						183	167	172					7																	103236931		2203	4300	6503	SO:0001583	missense	5649	exon25			AGTACATCTCTGC		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.3511A>C	7.37:g.103236931T>G	ENSP00000392423:p.Met1171Leu	188	0	0		187	46	0.245989	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	T	17.56	3.419022	0.62622	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.37752	2.09;1.18;2.09	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.25531	0.0621	N	0.19112	0.55	0.44771	D	0.997776	P;B	0.35468	0.503;0.272	B;B	0.35931	0.214;0.032	T	0.06698	-1.0812	10	0.13470	T	0.59	.	16.1652	0.81750	0.0:0.0:0.0:1.0	.	1171;1171	P78509-2;P78509	.;RELN_HUMAN	L	1171	ENSP00000392423:M1171L;ENSP00000345694:M1171L;ENSP00000388446:M1171L	ENSP00000345694:M1171L	M	-	1	0	RELN	103024167	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.653000	0.67967	2.230000	0.72887	0.528000	0.53228	ATG	.	.	alt		0.493	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		G	103236931	T	G	103236931	3	3	21	1	0	0	0	0	1	0	0	0	13235	1435	50	5	7035	5	RELN	7	103236931	Missense_Mutation	SNP	T	TCGA-FM-8000-01A-11D-2210-10	48022527	103236931	55901732	62	2805											
EZH2	2146	hgsc.bcm.edu	37	chr7	148507460	148507460	+	Missense_Mutation	SNP	T	T	C																															acagaaagctgcacatgtatTtatcatacactttccctctt																										TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr7:148507460T>C	ENST00000460911.1	-	17	2067	c.1979A>G	c.(1978-1980)aAa>aGa	p.K660R	EZH2_ENST00000350995.2_Missense_Mutation_p.K621R|EZH2_ENST00000478654.1_Missense_Mutation_p.K609R|EZH2_ENST00000476773.1_Missense_Mutation_p.K609R|EZH2_ENST00000483967.1_Missense_Mutation_p.K651R|EZH2_ENST00000320356.2_Missense_Mutation_p.K665R|EZH2_ENST00000541220.1_Missense_Mutation_p.K609R			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	660	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)	p.K665_Y666del(1)		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)			GCACATGTATTTATCATACAC	0.428			Mis		DLBCL																																p.K665R		Atlas-SNP	.		Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	.	EZH2	823	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.A1994G						PASS	.						110	91	98					7																	148507460		2202	4300	6502	SO:0001583	missense	2146	exon17			ATGTATTTATCAT		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.1979A>G	7.37:g.148507460T>C	ENSP00000419711:p.Lys660Arg	79	0	0		61	22	0.360656	NM_004456	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Missense_Mutation	SNP	ENST00000460911.1	37	CCDS56516.1	.	.	.	.	.	.	.	.	.	.	t	29.6	5.021682	0.93462	.	.	ENSG00000106462	ENST00000478654;ENST00000320356;ENST00000460911;ENST00000350995;ENST00000541220;ENST00000476773;ENST00000483967	T;T;T;T;T;T;T	0.81247	-1.47;-1.32;-1.32;-1.32;-1.47;-1.47;-1.32	5.45	5.45	0.79879	SET domain (3);	0.000000	0.85682	D	0.000000	D	0.84611	0.5510	L	0.39566	1.225	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.994	T	0.81705	-0.0811	10	0.21014	T	0.42	.	15.542	0.76057	0.0:0.0:0.0:1.0	.	651;609;660;621;665	Q15910-4;Q15910-5;Q15910;Q15910-3;Q15910-2	.;.;EZH2_HUMAN;.;.	R	609;665;660;621;609;609;651	ENSP00000417062:K609R;ENSP00000320147:K665R;ENSP00000419711:K660R;ENSP00000223193:K621R;ENSP00000443219:K609R;ENSP00000419050:K609R;ENSP00000419856:K651R	ENSP00000320147:K665R	K	-	2	0	EZH2	148138393	1.000000	0.71417	0.995000	0.50966	0.993000	0.82548	7.789000	0.85783	2.064000	0.61679	0.533000	0.62120	AAA	.	.	none		0.428	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456		C	148507460	T	C	148507460	3	2	21	1	0	0	0	0	1	0	0	0	5336	1841	64	3	277	3	EZH2	7	148507460	Missense_Mutation	SNP	T	TCGA-FM-8000-01A-11D-2210-10	45270529	148507460	10631203	63	2806	43	2									
EZH2	2146	hgsc.bcm.edu	37	chr7	148507461	148507461	+	Missense_Mutation	SNP	T	T	C																															cagaaagctgcacatgtattTatcatacactttccctcttc																										TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr7:148507461T>C	ENST00000460911.1	-	17	2066	c.1978A>G	c.(1978-1980)Aaa>Gaa	p.K660E	EZH2_ENST00000350995.2_Missense_Mutation_p.K621E|EZH2_ENST00000478654.1_Missense_Mutation_p.K609E|EZH2_ENST00000476773.1_Missense_Mutation_p.K609E|EZH2_ENST00000483967.1_Missense_Mutation_p.K651E|EZH2_ENST00000320356.2_Missense_Mutation_p.K665E|EZH2_ENST00000541220.1_Missense_Mutation_p.K609E			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	660	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)	p.K665_Y666del(1)		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)			CACATGTATTTATCATACACT	0.428			Mis		DLBCL																																p.K665E		Atlas-SNP	.		Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	.	EZH2	823	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.A1993G						PASS	.						109	91	97					7																	148507461		2202	4300	6502	SO:0001583	missense	2146	exon17			TGTATTTATCATA		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.1978A>G	7.37:g.148507461T>C	ENSP00000419711:p.Lys660Glu	78	0	0		63	23	0.365079	NM_004456	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Missense_Mutation	SNP	ENST00000460911.1	37	CCDS56516.1	.	.	.	.	.	.	.	.	.	.	t	29.7	5.031157	0.93575	.	.	ENSG00000106462	ENST00000478654;ENST00000320356;ENST00000460911;ENST00000350995;ENST00000541220;ENST00000476773;ENST00000483967	D;T;T;T;D;D;T	0.81659	-1.52;-1.32;-1.32;-1.32;-1.52;-1.52;-1.32	5.45	5.45	0.79879	SET domain (3);	0.000000	0.85682	D	0.000000	D	0.86439	0.5933	L	0.46567	1.45	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.994	D	0.86978	0.2102	10	0.52906	T	0.07	.	15.542	0.76057	0.0:0.0:0.0:1.0	.	651;609;660;621;665	Q15910-4;Q15910-5;Q15910;Q15910-3;Q15910-2	.;.;EZH2_HUMAN;.;.	E	609;665;660;621;609;609;651	ENSP00000417062:K609E;ENSP00000320147:K665E;ENSP00000419711:K660E;ENSP00000223193:K621E;ENSP00000443219:K609E;ENSP00000419050:K609E;ENSP00000419856:K651E	ENSP00000320147:K665E	K	-	1	0	EZH2	148138394	1.000000	0.71417	0.995000	0.50966	0.993000	0.82548	7.789000	0.85783	2.064000	0.61679	0.533000	0.62120	AAA	.	.	none		0.428	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456		C	148507461	T	C	148507461	3	2	21	1	0	0	0	0	1	0	0	0	5336	1763	61	3	278	3	EZH2	7	148507461	Missense_Mutation	SNP	T	TCGA-FM-8000-01A-11D-2210-10	1	148507461	10631202	64	2807	43	2									
EZH2	2146	hgsc.bcm.edu	37	chr7	148508727	148508727	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtgccttacctctccacagTattctgagatgaattcattt	10	15	6	10	0	3	2	1	2	2	1	4	3	3	2	3	0	2	1	3	0	3	5	rs267601394		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr7:148508727T>A	ENST00000460911.1	-	16	2010	c.1922A>T	c.(1921-1923)tAc>tTc	p.Y641F	EZH2_ENST00000350995.2_Missense_Mutation_p.Y602F|EZH2_ENST00000478654.1_Missense_Mutation_p.Y590F|EZH2_ENST00000476773.1_Missense_Mutation_p.Y590F|EZH2_ENST00000483967.1_Missense_Mutation_p.Y632F|EZH2_ENST00000320356.2_Missense_Mutation_p.Y646F|EZH2_ENST00000541220.1_Missense_Mutation_p.Y590F			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	641	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.		Y -> C (in a patient with diffuse large B-cell lymphoma; somatic mutation). {ECO:0000269|PubMed:20081860}.|Y -> F (found in patients with follicular lymphoma; also in diffuse large B-cell lymphoma; somatic mutation). {ECO:0000269|PubMed:20081860}.|Y -> H (found in patients with follicular lymphoma; also in diffuse large B-cell lymphoma; somatic mutation). {ECO:0000269|PubMed:20081860}.|Y -> N (found in patients with follicular lymphoma; also in diffuse large B-cell lymphoma; somatic mutation). {ECO:0000269|PubMed:20081860}.|Y -> S (found in patients with follicular lymphoma; also in diffuse large B-cell lymphoma; somatic mutation). {ECO:0000269|PubMed:20081860}.		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)	p.Y646F(59)|p.Y646S(22)|p.Y602F(8)|p.Y646C(6)|p.Y602S(4)		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)			CTCTCCACAGTATTCTGAGAT	0.378			Mis		DLBCL																																p.Y646F		Atlas-SNP	.		Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	EZH2_ENST00000350995,face,carcinoma,-1,214	EZH2	823	214	99	Substitution - Missense(99)	haematopoietic_and_lymphoid_tissue(99)	c.A1937T						PASS	.						96	89	91					7																	148508727		2203	4300	6503	SO:0001583	missense	2146	exon16			CCACAGTATTCTG		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.1922A>T	7.37:g.148508727T>A	ENSP00000419711:p.Tyr641Phe	31	0	0		36	14	0.388889	NM_004456	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Missense_Mutation	SNP	ENST00000460911.1	37	CCDS56516.1	.	.	.	.	.	.	.	.	.	.	t	28.3	4.907221	0.92107	.	.	ENSG00000106462	ENST00000478654;ENST00000320356;ENST00000460911;ENST00000350995;ENST00000541220;ENST00000476773;ENST00000483967	D;D;D;D;D;D;D	0.92965	-3.14;-1.9;-1.9;-1.9;-3.14;-3.14;-1.9	5.63	5.63	0.86233	SET domain (3);	0.000000	0.85682	D	0.000000	D	0.96990	0.9017	M	0.93328	3.405	0.80722	D	1	D;D;D;D;P	0.76494	0.999;0.997;0.964;0.999;0.817	D;D;D;D;B	0.71656	0.974;0.956;0.912;0.974;0.367	D	0.98006	1.0363	10	0.87932	D	0	.	15.87	0.79108	0.0:0.0:0.0:1.0	.	632;590;641;602;646	Q15910-4;Q15910-5;Q15910;Q15910-3;Q15910-2	.;.;EZH2_HUMAN;.;.	F	590;646;641;602;590;590;632	ENSP00000417062:Y590F;ENSP00000320147:Y646F;ENSP00000419711:Y641F;ENSP00000223193:Y602F;ENSP00000443219:Y590F;ENSP00000419050:Y590F;ENSP00000419856:Y632F	ENSP00000320147:Y646F	Y	-	2	0	EZH2	148139660	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.789000	0.85783	2.145000	0.66743	0.533000	0.62120	TAC	.	.	none		0.378	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456		A	148508727	T	A	148508727	3	1	21	1	0	0	0	0	1	0	0	0	5336	1638	57	5	338	5	EZH2	7	148508727	Missense_Mutation	SNP	T	TCGA-FM-8000-01A-11D-2210-10	1266	148508727	10629936	65	2808											
ACCN3	9311	hgsc.bcm.edu	37	chr7	150746203	150746203	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccaccagactgccctggaTgagcgagaaagccaccggct	11	4	11	15	2	0	3	0	1	0	2	0	5	0	4	5	2	3	1	5	2	1	0			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr7:150746203T>G	ENST00000349064.5	+	1	429	c.231T>G	c.(229-231)gaT>gaG	p.D77E	ASIC3_ENST00000297512.8_Missense_Mutation_p.D77E|ASIC3_ENST00000357922.4_Missense_Mutation_p.D77E	NM_004769.3|NM_020321.3	NP_004760.1|NP_064717.1	Q9UHC3	ASIC3_HUMAN	acid-sensing (proton-gated) ion channel 3	77					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)										CTGCCCTGGATGAGCGAGAAA	0.642																																					p.D77E		Atlas-SNP	.											.	.	.	.	0			c.T231G						PASS	.						112	89	97					7																	150746203		2203	4300	6503	SO:0001583	missense	9311	exon1			CCTGGATGAGCGA	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.231T>G	7.37:g.150746203T>G	ENSP00000344838:p.Asp77Glu	62	0	0		36	15	0.416667	NM_020322	B2R9V0|O60263|O75906|Q59FN9|Q9UER8|Q9UHC4	Missense_Mutation	SNP	ENST00000349064.5	37	CCDS5916.1	.	.	.	.	.	.	.	.	.	.	T	15.96	2.985752	0.53934	.	.	ENSG00000213199	ENST00000357922;ENST00000349064;ENST00000297512	T;T;T	0.64085	-0.08;-0.08;-0.08	5.11	-4.68	0.03309	.	0.214262	0.21995	N	0.066087	T	0.45756	0.1358	L	0.49513	1.565	0.22648	N	0.998896	B;B;B	0.22604	0.072;0.003;0.01	B;B;B	0.25291	0.059;0.003;0.047	T	0.35301	-0.9794	10	0.20519	T	0.43	-12.6316	7.4624	0.27302	0.0:0.2523:0.2205:0.5272	.	77;77;77	Q9UHC3-2;Q9UHC3-3;Q9UHC3	.;.;ACCN3_HUMAN	E	77	ENSP00000350600:D77E;ENSP00000344838:D77E;ENSP00000297512:D77E	ENSP00000297512:D77E	D	+	3	2	ACCN3	150377136	0.001000	0.12720	0.892000	0.35008	0.965000	0.64279	-1.636000	0.02016	-0.937000	0.03719	-0.441000	0.05720	GAT	.	.	none		0.642	ASIC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351725.1	NM_004769		G	150746203	T	G	150746203	3	3	21	1	0	0	0	0	1	0	0	0	130	1461	51	5	233	5	ACCN3	7	150746203	Missense_Mutation	SNP	T	TCGA-FM-8000-01A-11D-2210-10	2237476	150746203	8392460	66	2809											
MLL3	58508	hgsc.bcm.edu	37	chr7	151970845	151970845	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcaggaagatgtgactgaaAtcctgaaaggtgccggctcc	12	7	13	9	1	0	4	0	3	0	1	2	5	2	5	3	3	2	2	3	3	3	0			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr7:151970845A>T	ENST00000262189.6	-	7	1175	c.957T>A	c.(955-957)gaT>gaA	p.D319E	KMT2C_ENST00000355193.2_Missense_Mutation_p.D319E	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	319					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)										TGTGACTGAAATCCTGAAAGG	0.413																																					p.D319E		Atlas-SNP	.											MLL3_ENST00000355193,NS,carcinoma,-1,2	MLL3	1564	2	0			c.T957A						PASS	.						260	243	249					7																	151970845		2203	4300	6503	SO:0001583	missense	58508	exon7			ACTGAAATCCTGA	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.957T>A	7.37:g.151970845A>T	ENSP00000262189:p.Asp319Glu	704	0	0		404	21	0.0519802	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	A	17.78	3.474094	0.63737	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	T;T	0.69175	-0.38;-0.38	4.87	-3.2	0.05156	Zinc finger, PHD-type (1);Protein kinase C-like, phorbol ester/diacylglycerol binding (1);	0.000000	0.44902	U	0.000409	T	0.68787	0.3039	L	0.43598	1.365	0.80722	D	1	D	0.71674	0.998	D	0.83275	0.996	T	0.65384	-0.6181	10	0.23302	T	0.38	.	12.0041	0.53248	0.8755:0.0:0.1245:0.0	.	319	Q8NEZ4	MLL3_HUMAN	E	319	ENSP00000262189:D319E;ENSP00000347325:D319E	ENSP00000262189:D319E	D	-	3	2	MLL3	151601778	1.000000	0.71417	0.830000	0.32933	0.993000	0.82548	1.285000	0.33261	-0.549000	0.06191	0.528000	0.53228	GAT	.	.	none		0.413	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			T	151970845	A	T	151970845	3	4	21	1	0	0	0	0	1	0	0	0	9631	98	4	5	13990	5	MLL3	7	151970845	Missense_Mutation	SNP	A	TCGA-FM-8000-01A-11D-2210-10	1224642	151970845	7167818	67	2810											
SHH	6469	hgsc.bcm.edu	37	chr7	155599176	155599176	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gccatcttcgtcccagccctCggtcacccgcagtttcactc	5	10	7	19	3	3	0	2	0	1	0	7	0	4	0	4	1	1	2	4	1	0	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr7:155599176C>T	ENST00000297261.2	-	2	526	c.376G>A	c.(376-378)Gag>Aag	p.E126K	SHH_ENST00000472308.1_5'Flank	NM_000193.2	NP_000184.1	Q15465	SHH_HUMAN	sonic hedgehog	126					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)		TCCCAGCCCTCGGTCACCCGC	0.612																																					p.E126K		Atlas-SNP	.											.	SHH	34	.	0			c.G376A						PASS	.						105	77	87					7																	155599176		2203	4300	6503	SO:0001583	missense	6469	exon2			AGCCCTCGGTCAC		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.376G>A	7.37:g.155599176C>T	ENSP00000297261:p.Glu126Lys	151	0	0		94	4	0.0425532	NM_000193	A4D247|Q75MC9	Missense_Mutation	SNP	ENST00000297261.2	37	CCDS5942.1	.	.	.	.	.	.	.	.	.	.	C	32	5.149394	0.94645	.	.	ENSG00000164690	ENST00000297261;ENST00000430104	D;D	0.99578	-6.21;-6.21	3.55	3.55	0.40652	Hedgehog/DD-peptidase (2);Hedgehog, N-terminal signaling domain (1);	0.000000	0.85682	D	0.000000	D	0.99641	0.9868	M	0.89904	3.07	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;1.0;0.998	D	0.97386	0.9986	10	0.87932	D	0	.	15.6723	0.77289	0.0:1.0:0.0:0.0	.	126;129;39	Q15465;D9ZGF9;C9JC48	SHH_HUMAN;.;.	K	126;39	ENSP00000297261:E126K;ENSP00000396621:E39K	ENSP00000297261:E126K	E	-	1	0	SHH	155291937	1.000000	0.71417	0.993000	0.49108	0.992000	0.81027	7.409000	0.80053	1.967000	0.57214	0.561000	0.74099	GAG	.	.	none		0.612	SHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322327.1	NM_000193		T	155599176	C	T	155599176	3	4	21	1	0	0	0	0	1	0	0	0	14294	893	31	1	1020	1	SHH	7	155599176	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	3628331	155599176	3539487	68	2811											
DLGAP2	9228	hgsc.bcm.edu	37	chr8	1497731	1497731	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtacctgaagcgcagctcctGgtctacgctgacggtcagcc	7	8	12	14	3	2	2	1	2	1	0	3	2	3	2	3	2	5	4	3	2	3	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr8:1497731G>A	ENST00000421627.2	+	2	1006	c.872G>A	c.(871-873)tGg>tAg	p.W291*		NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	370					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)		CGCAGCTCCTGGTCTACGCTG	0.647																																					p.W291X		Atlas-SNP	.											.	DLGAP2	292	.	0			c.G872A						PASS	.						18	21	20					8																	1497731		2180	4277	6457	SO:0001587	stop_gained	9228	exon2			GCTCCTGGTCTAC	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.872G>A	8.37:g.1497731G>A	ENSP00000400258:p.Trp291*	86	0	0		65	13	0.2	NM_004745	A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	Nonsense_Mutation	SNP	ENST00000421627.2	37	CCDS47760.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	39|39	7.817673|7.817673	0.98507|0.98507	.|.	.|.	ENSG00000198010|ENSG00000198010	ENST00000520901|ENST00000356067;ENST00000421627	.|.	.|.	.|.	5.3|5.3	5.3|5.3	0.74995|0.74995	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.46852|.	0.1414|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.39418|.	-0.9615|.	3|.	.|0.02654	.|T	.|1	-10.1825|-10.1825	18.9482|18.9482	0.92630|0.92630	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	S|X	308|336;291	.|.	.|ENSP00000348366:W336X	G|W	+|+	1|2	0|0	DLGAP2|DLGAP2	1485138|1485138	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.966000|0.966000	0.64601|0.64601	8.917000|8.917000	0.92751|0.92751	2.463000|2.463000	0.83235|0.83235	0.655000|0.655000	0.94253|0.94253	GGT|TGG	.	.	none		0.647	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374478.1	NM_004745		A	1497731	G	A	1497731	4	1	21	1	0	0	0	0	0	1	0	0	4562	1357	47	2	874	2	DLGAP2	8	1497731	Nonsense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10		1497731	144866291	69	2812											
CSMD1	64478	hgsc.bcm.edu	37	chr8	4494914	4494914	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccatcgtaaactgataaaatAtcaaaatcttcttcaagagc	17	11	4	9	1	4	2	2	1	2	1	5	2	4	2	1	0	2	1	1	0	8	5			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr8:4494914A>G	ENST00000520002.1	-	2	807	c.252T>C	c.(250-252)gaT>gaC	p.D84D	CSMD1_ENST00000539096.1_Silent_p.D84D|CSMD1_ENST00000537824.1_Silent_p.D84D|CSMD1_ENST00000602723.1_Silent_p.D84D|CSMD1_ENST00000542608.1_Silent_p.D84D|CSMD1_ENST00000400186.3_Silent_p.D84D|CSMD1_ENST00000602557.1_Silent_p.D84D			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	84	CUB 1. {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)		CTGATAAAATATCAAAATCTT	0.398																																					p.D84D		Atlas-SNP	.											.	CSMD1	1469	.	0			c.T252C						PASS	.						121	121	121					8																	4494914		1894	4130	6024	SO:0001819	synonymous_variant	64478	exon2			TAAAATATCAAAA			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.252T>C	8.37:g.4494914A>G		109	0	0		64	34	0.53125	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37																																																																																				.	.	none		0.398	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		G	4494914	A	G	4494914	2	3	21	1	0	0	0	0	0	0	0	1	3946	446	16	3		3	CSMD1	8	4494914	Silent	SNP	A	TCGA-FM-8000-01A-11D-2210-10	2997183	4494914	141869108	70	2813											
CSMD1	64478	hgsc.bcm.edu	37	chr8	4494939	4494939	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aatcttcttcaagagcaaagGtatggaaggacaactgtatc	15	10	9	7	0	3	1	1	0	2	1	4	3	3	3	0	3	2	3	0	3	7	4	rs562417147		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr8:4494939G>T	ENST00000520002.1	-	2	782	c.227C>A	c.(226-228)aCc>aAc	p.T76N	CSMD1_ENST00000539096.1_Missense_Mutation_p.T76N|CSMD1_ENST00000537824.1_Missense_Mutation_p.T76N|CSMD1_ENST00000602723.1_Missense_Mutation_p.T76N|CSMD1_ENST00000542608.1_Missense_Mutation_p.T76N|CSMD1_ENST00000400186.3_Missense_Mutation_p.T76N|CSMD1_ENST00000602557.1_Missense_Mutation_p.T76N			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	76	CUB 1. {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)		AAGAGCAAAGGTATGGAAGGA	0.423													G|||	1	0.000199681	0.0	0.0	5008	,	,		14473	0.001		0.0	False		,,,				2504	0.0				p.T76N		Atlas-SNP	.											.	CSMD1	1469	.	0			c.C227A						PASS	.						132	131	131					8																	4494939		1923	4156	6079	SO:0001583	missense	64478	exon2			GCAAAGGTATGGA			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.227C>A	8.37:g.4494939G>T	ENSP00000430733:p.Thr76Asn	144	0	0		78	39	0.5	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	G	14.03	2.413876	0.42817	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.17854	2.25;2.25;2.25;2.25;2.25	5.12	5.12	0.69794	.	.	.	.	.	T	0.13286	0.0322	N	0.12569	0.235	0.29907	N	0.823931	P	0.34587	0.458	B	0.43052	0.406	T	0.14309	-1.0477	9	0.26408	T	0.33	.	9.6543	0.39917	0.0954:0.0:0.9046:0.0	.	76	E5RIG2	.	N	76	ENSP00000383047:T76N;ENSP00000430733:T76N;ENSP00000441462:T76N;ENSP00000446243:T76N;ENSP00000441675:T76N	ENSP00000383047:T76N	T	-	2	0	CSMD1	4482347	1.000000	0.71417	0.951000	0.38953	0.965000	0.64279	5.671000	0.68095	2.401000	0.81631	0.585000	0.79938	ACC	.	.	none		0.423	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		T	4494939	G	T	4494939	3	4	21	1	0	0	0	0	1	0	0	0	3946	1261	44	4	10556	4	CSMD1	8	4494939	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	25	4494939	141869083	71	2814											
KIAA1967	57805	hgsc.bcm.edu	37	chr8	22464810	22464810	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cagttgatcttccagcctcaCcggattcccccactctttcc	6	12	5	18	1	3	1	1	1	2	0	6	2	6	2	6	1	1	1	6	1	0	4			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr8:22464810C>T	ENST00000308511.4	+	6	708	c.459C>T	c.(457-459)caC>caT	p.H153H	CCAR2_ENST00000520861.1_5'UTR|CCAR2_ENST00000389279.3_Silent_p.H153H			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	153					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage checkpoint (GO:2000003)|regulation of circadian rhythm (GO:0042752)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of protein stability (GO:0031647)|response to UV (GO:0009411)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|DBIRD complex (GO:0044609)|mitochondrial matrix (GO:0005759)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)										TCCAGCCTCACCGGATTCCCC	0.547																																					p.H153H		Atlas-SNP	.											KIAA1967,NS,carcinoma,+2,1	KIAA1967	72	1	0			c.C459T						scavenged	.						82	68	73					8																	22464810		2203	4300	6503	SO:0001819	synonymous_variant	57805	exon6			GCCTCACCGGATT	AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941			23360	protein-coding gene	gene with protein product	"deleted in breast cancer"	607359	"KIAA1967"	KIAA1967		12370419	Standard	NM_021174		Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.459C>T	8.37:g.22464810C>T		30	0	0		15	2	0.133333	NM_021174	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Silent	SNP	ENST00000308511.4	37	CCDS34863.1	.	.	.	.	.	.	.	.	.	.	C	7.746	0.702375	0.15172	.	.	ENSG00000158941	ENST00000523801;ENST00000518989	.	.	.	5.96	0.261	0.15592	.	.	.	.	.	T	0.54464	0.1860	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45948	-0.9226	4	.	.	.	-25.3158	7.9306	0.29899	0.0:0.4073:0.0:0.5927	.	.	.	.	S	161;106	.	.	P	+	1	0	KIAA1967	22520755	0.998000	0.40836	0.998000	0.56505	0.997000	0.91878	0.425000	0.21346	0.097000	0.17492	-0.150000	0.13652	CCG	.	.	none		0.547	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174		T	22464810	C	T	22464810	2	4	21	1	0	0	0	0	0	0	0	1	8274	506	18	2		2	KIAA1967	8	22464810	Silent	SNP	C	TCGA-FM-8000-01A-11D-2210-10	17969871	22464810	123899212	72	2815											
MCM4	4173	hgsc.bcm.edu	37	chr8	48875553	48875553	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtgaactgtgaacacatcAaatcatttgacaaaaatttg	17	12	6	6	0	2	3	2	3	0	0	2	3	2	3	0	0	2	0	0	0	5	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr8:48875553A>T	ENST00000262105.2	+	6	855	c.646A>T	c.(646-648)Aaa>Taa	p.K216*	PRKDC_ENST00000338368.3_5'Flank|PRKDC_ENST00000314191.2_5'Flank|MCM4_ENST00000523944.1_Nonsense_Mutation_p.K216*|PRKDC_ENST00000523565.1_5'Flank	NM_005914.3	NP_005905.2	P33991	MCM4_HUMAN	minichromosome maintenance complex component 4	216					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)				TGAACACATCAAATCATTTGA	0.274																																					p.K216X		Atlas-SNP	.											.	MCM4	97	.	0			c.A646T						PASS	.						61	65	64					8																	48875553		2202	4299	6501	SO:0001587	stop_gained	4173	exon7			CACATCAAATCAT		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.646A>T	8.37:g.48875553A>T	ENSP00000262105:p.Lys216*	153	0	0		111	31	0.279279	NM_182746	Q8NEH1|Q99658	Nonsense_Mutation	SNP	ENST00000262105.2	37	CCDS6143.1	.	.	.	.	.	.	.	.	.	.	A	33	5.216530	0.95104	.	.	ENSG00000104738	ENST00000523944;ENST00000262105;ENST00000396826;ENST00000429229;ENST00000519170	.	.	.	5.64	3.16	0.36331	.	0.515689	0.24332	N	0.039454	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.6873	12.5614	0.56283	0.7376:0.2624:0.0:0.0	.	.	.	.	X	216;216;203;176;166	.	ENSP00000262105:K216X	K	+	1	0	MCM4	49038106	1.000000	0.71417	0.921000	0.36526	0.971000	0.66376	3.376000	0.52417	0.379000	0.24794	0.379000	0.24179	AAA	.	.	none		0.274	MCM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377791.1	NM_005914		T	48875553	A	T	48875553	4	4	21	1	0	0	0	0	0	1	0	0	9398	131	5	5	668	5	MCM4	8	48875553	Nonsense_Mutation	SNP	A	TCGA-FM-8000-01A-11D-2210-10	26410743	48875553	97488469	73	2816											
CYP7A1	1581	hgsc.bcm.edu	37	chr8	59409213	59409213	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctggaatggtgtttgcttgCgatgcccagaggaccacgag	8	9	15	9	2	0	1	0	0	0	1	0	5	0	3	2	3	3	3	2	3	1	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr8:59409213C>T	ENST00000301645.3	-	3	995	c.858G>A	c.(856-858)tcG>tcA	p.S286S		NM_000780.3	NP_000771.2	P22680	CP7A1_HUMAN	cytochrome P450, family 7, subfamily A, polypeptide 1	286					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)				TGTTTGCTTGCGATGCCCAGA	0.423									Neonatal Giant Cell Hepatitis																												p.S286S		Atlas-SNP	.											CYP7A1,NS,carcinoma,-1,2	CYP7A1	76	2	0			c.G858A						PASS	.						124	120	121					8																	59409213		2203	4300	6503	SO:0001819	synonymous_variant	1581	exon3	Familial Cancer Database	Neonatal Hemochromatosis	TGCTTGCGATGCC	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.858G>A	8.37:g.59409213C>T		80	0	0		64	4	0.0625	NM_000780	P78454|Q3MIL8|Q7KZ19	Silent	SNP	ENST00000301645.3	37	CCDS6171.1																																																																																			.	.	none		0.423	CYP7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378190.1	NM_000780		T	59409213	C	T	59409213	2	4	21	1	0	0	0	0	0	0	0	1	4198	755	27	1		1	CYP7A1	8	59409213	Silent	SNP	C	TCGA-FM-8000-01A-11D-2210-10	10533660	59409213	86954809	74	2817											
VPS13B	157680	hgsc.bcm.edu	37	chr8	100789120	100789120	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggtttgtcccatccctttgCgtttctttccagtttgctca	3	19	7	12	1	2	0	1	0	1	0	5	0	5	0	3	1	2	4	3	1	0	5			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr8:100789120C>T	ENST00000358544.2	+	41	7551	c.7440C>T	c.(7438-7440)tgC>tgT	p.C2480C	VPS13B_ENST00000395996.1_3'UTR|VPS13B_ENST00000357162.2_Silent_p.C2455C	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	2480					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)			CATCCCTTTGCGTTTCTTTCC	0.458																																					p.C2480C	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.C7440T						PASS	.						285	226	246					8																	100789120		2203	4300	6503	SO:0001819	synonymous_variant	157680	exon41			CCTTTGCGTTTCT	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.7440C>T	8.37:g.100789120C>T		292	1	0.00342466		203	76	0.374384	NM_017890	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Silent	SNP	ENST00000358544.2	37	CCDS6280.1																																																																																			.	.	none		0.458	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		T	100789120	C	T	100789120	2	4	21	1	0	0	0	0	0	0	0	1	17205	776	27	1		1	VPS13B	8	100789120	Silent	SNP	C	TCGA-FM-8000-01A-11D-2210-10	41379907	100789120	45574902	75	2818											
CSMD3	114788	hgsc.bcm.edu	37	chr8	114031393	114031393	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgataattggtggtggtatAttcattccagataacctgaa	12	14	9	6	0	1	3	1	2	0	1	2	3	2	3	2	3	1	1	2	3	5	7			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr8:114031393A>T	ENST00000297405.5	-	6	1177	c.933T>A	c.(931-933)aaT>aaA	p.N311K	CSMD3_ENST00000352409.3_Missense_Mutation_p.N311K|CSMD3_ENST00000455883.2_Missense_Mutation_p.N311K|CSMD3_ENST00000343508.3_Missense_Mutation_p.N271K	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	311	CUB 2. {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						GTGGTGGTATATTCATTCCAG	0.358										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.N311K		Atlas-SNP	.											.	CSMD3	2325	.	0			c.T933A						PASS	.						182	167	172					8																	114031393		2203	4300	6503	SO:0001583	missense	114788	exon6			TGGTATATTCATT	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.933T>A	8.37:g.114031393A>T	ENSP00000297405:p.Asn311Lys	220	0	0		146	54	0.369863	NM_052900	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	a	15.30	2.793743	0.50102	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000455883;ENST00000352409	D;D;D;D	0.93547	-3.24;-3.24;-3.24;-3.24	5.6	1.85	0.25348	CUB (5);	0.000000	0.64402	D	0.000001	D	0.90373	0.6987	N	0.25094	0.71	0.28935	N	0.891307	P;B;D;P	0.89917	0.952;0.002;1.0;0.5	B;B;D;B	0.87578	0.419;0.004;0.998;0.376	T	0.82222	-0.0564	10	0.05959	T	0.93	.	5.9155	0.19052	0.7421:0.0:0.135:0.1228	.	311;311;311;271	Q7Z407-3;Q7Z407-4;Q7Z407;Q7Z407-2	.;.;CSMD3_HUMAN;.	K	271;311;311;311	ENSP00000345799:N271K;ENSP00000297405:N311K;ENSP00000412263:N311K;ENSP00000343124:N311K	ENSP00000297405:N311K	N	-	3	2	CSMD3	114100569	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	1.922000	0.40045	0.076000	0.16826	-0.545000	0.04230	AAT	.	.	none		0.358	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	114031393	A	T	114031393	3	4	21	1	0	0	0	0	1	0	0	0	3948	446	16	5	10454	5	CSMD3	8	114031393	Missense_Mutation	SNP	A	TCGA-FM-8000-01A-11D-2210-10	13242273	114031393	32332629	76	2819											
RFX3	5991	hgsc.bcm.edu	37	chr9	3225259	3225259	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagttcttcatccatttcaCtttctacttcactgccttca	7	17	2	15	0	6	0	4	0	2	0	7	0	7	0	3	0	2	1	3	0	1	7			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr9:3225259C>T	ENST00000382004.3	-	18	2344	c.2033G>A	c.(2032-2034)aGt>aAt	p.S678N		NM_001282116.1|NM_134428.1	NP_001269045.1|NP_602304.1	P48380	RFX3_HUMAN	regulatory factor X, 3 (influences HLA class II expression)	678					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)		ATCCATTTCACTTTCTACTTC	0.418																																					p.S678N		Atlas-SNP	.											RFX3_ENST00000382004,NS,carcinoma,+1,1	RFX3	156	1	0			c.G2033A						PASS	.						95	91	93					9																	3225259		2203	4300	6503	SO:0001583	missense	5991	exon18			ATTTCACTTTCTA	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.2033G>A	9.37:g.3225259C>T	ENSP00000371434:p.Ser678Asn	94	0	0		61	24	0.393443	NM_134428	A8K0H5|D3DRH8|D3DRH9|Q5JTL7|Q5JTL8|Q6NW13|Q8WTU4|Q95HL5|Q95HL6	Missense_Mutation	SNP	ENST00000382004.3	37	CCDS6449.1	.	.	.	.	.	.	.	.	.	.	C	17.04	3.288405	0.59976	.	.	ENSG00000080298	ENST00000382004	T	0.45276	0.9	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.41880	0.1178	L	0.57536	1.79	0.80722	D	1	P	0.44734	0.842	B	0.36922	0.236	T	0.33574	-0.9863	10	0.33940	T	0.23	-14.4178	19.8344	0.96650	0.0:1.0:0.0:0.0	.	678	P48380	RFX3_HUMAN	N	678	ENSP00000371434:S678N	ENSP00000371434:S678N	S	-	2	0	RFX3	3215259	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.448000	0.73469	2.686000	0.91538	0.643000	0.83706	AGT	.	.	none		0.418	RFX3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051545.1	NM_002919		T	3225259	C	T	3225259	3	4	21	1	0	0	0	0	1	0	0	0	13279	565	20	2	220	2	RFX3	9	3225259	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10		3225259	137988172	77	2820											
HAUS6	54801	hgsc.bcm.edu	37	chr9	19058226	19058226	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggtaagattcttccctttTcttggaaagagatttcttca	10	16	8	7	0	4	2	1	0	3	2	5	5	5	3	1	2	0	1	1	2	2	8	rs201053056		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr9:19058226T>G	ENST00000380502.3	-	16	3006	c.2539A>C	c.(2539-2541)Aaa>Caa	p.K847Q	HAUS6_ENST00000380496.1_Missense_Mutation_p.K711Q	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	847					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						TCTTCCCTTTTCTTGGAAAGA	0.428																																					p.K847Q		Atlas-SNP	.											.	HAUS6	66	.	0			c.A2539C						PASS	.						149	147	148					9																	19058226		2203	4300	6503	SO:0001583	missense	54801	exon16			CCCTTTTCTTGGA	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.2539A>C	9.37:g.19058226T>G	ENSP00000369871:p.Lys847Gln	197	0	0		135	57	0.422222	NM_017645	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Missense_Mutation	SNP	ENST00000380502.3	37	CCDS6489.1	.	.	.	.	.	.	.	.	.	.	T	0.794	-0.757692	0.03019	.	.	ENSG00000147874	ENST00000380502;ENST00000380496	T;T	0.26660	1.73;1.72	5.27	0.291	0.15732	.	0.706131	0.13913	N	0.354089	T	0.12561	0.0305	N	0.17474	0.49	0.09310	N	1	B;B;B	0.20052	0.041;0.041;0.023	B;B;B	0.17433	0.018;0.012;0.012	T	0.26815	-1.0092	10	0.28530	T	0.3	-0.407	5.0616	0.14560	0.0:0.2258:0.3007:0.4735	.	812;711;847	Q7Z4H7-3;Q5VY60;Q7Z4H7	.;.;HAUS6_HUMAN	Q	847;711	ENSP00000369871:K847Q;ENSP00000369865:K711Q	ENSP00000369865:K711Q	K	-	1	0	HAUS6	19048226	0.001000	0.12720	0.069000	0.20011	0.046000	0.14306	0.201000	0.17276	-0.090000	0.12462	-0.456000	0.05471	AAA	T|1.000;C|0.000	.	alt		0.428	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645		G	19058226	T	G	19058226	3	3	21	1	0	0	0	0	1	0	0	0	6979	1792	62	5	336	5	HAUS6	9	19058226	Missense_Mutation	SNP	T	TCGA-FM-8000-01A-11D-2210-10	15832967	19058226	122155205	78	2821											
HAUS6	54801	hgsc.bcm.edu	37	chr9	19058365	19058365	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ataggactatttggctccagTttaaaattggcctctgaact	11	14	8	8	0	1	1	0	1	1	0	2	2	2	2	2	3	1	2	2	3	5	6			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr9:19058365T>C	ENST00000380502.3	-	16	2867	c.2400A>G	c.(2398-2400)aaA>aaG	p.K800K	HAUS6_ENST00000380496.1_Silent_p.K664K	NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	800					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						TTGGCTCCAGTTTAAAATTGG	0.398																																					p.K800K		Atlas-SNP	.											.	HAUS6	66	.	0			c.A2400G						PASS	.						68	72	71					9																	19058365		2203	4299	6502	SO:0001819	synonymous_variant	54801	exon16			CTCCAGTTTAAAA	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.2400A>G	9.37:g.19058365T>C		196	0	0		132	49	0.371212	NM_017645	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Silent	SNP	ENST00000380502.3	37	CCDS6489.1																																																																																			.	.	none		0.398	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645		C	19058365	T	C	19058365	2	2	21	1	0	0	0	0	0	0	0	1	6979	1722	60	3		3	HAUS6	9	19058365	Silent	SNP	T	TCGA-FM-8000-01A-11D-2210-10	139	19058365	122155066	79	2822											
HINT2	84681	hgsc.bcm.edu	37	chr9	35813717	35813717	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	agatggttggggctgctcccCcaggagttgcctgctgggcc	4	9	16	12	0	0	1	0	0	0	1	1	2	1	2	4	5	3	5	4	5	0	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr9:35813717C>T	ENST00000259667.5	-	2	187	c.146G>A	c.(145-147)gGg>gAg	p.G49E	SPAG8_ENST00000479751.1_5'Flank|TMEM8B_ENST00000377996.1_5'Flank|SPAG8_ENST00000340291.2_5'Flank|SPAG8_ENST00000396638.2_5'Flank|SPAG8_ENST00000484764.1_5'Flank|AL133410.1_ENST00000582432.1_RNA|HINT2_ENST00000474908.1_5'UTR	NM_032593.2	NP_115982.1	Q9BX68	HINT2_HUMAN	histidine triad nucleotide binding protein 2	49					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)			GGCTGCTCCCCCAGGAGTTGC	0.582											OREG0019179	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G49E	GBM(185;1694 2122 5473 25431 37228)	Atlas-SNP	.											.	HINT2	15	.	0			c.G146A						PASS	.						48	43	45					9																	35813717		2203	4300	6503	SO:0001583	missense	84681	exon2			GCTCCCCCAGGAG	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.146G>A	9.37:g.35813717C>T	ENSP00000259667:p.Gly49Glu	120	0	0	858	76	30	0.394737	NM_032593	Q5TCW3	Missense_Mutation	SNP	ENST00000259667.5	37	CCDS6594.1	.	.	.	.	.	.	.	.	.	.	C	12.40	1.926970	0.34002	.	.	ENSG00000137133	ENST00000259667	T	0.73897	-0.79	5.08	4.18	0.49190	.	0.267851	0.36234	N	0.002713	T	0.48943	0.1528	N	0.19112	0.55	0.31821	N	0.625982	P	0.46952	0.887	B	0.26202	0.067	T	0.60895	-0.7172	10	0.49607	T	0.09	-14.0947	7.7201	0.28727	0.0:0.7473:0.1635:0.0893	.	49	Q9BX68	HINT2_HUMAN	E	49	ENSP00000259667:G49E	ENSP00000259667:G49E	G	-	2	0	HINT2	35803717	0.001000	0.12720	0.998000	0.56505	0.981000	0.71138	1.243000	0.32767	1.261000	0.44149	0.561000	0.74099	GGG	.	.	none		0.582	HINT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052390.1	NM_032593		T	35813717	C	T	35813717	3	4	21	1	0	0	0	0	1	0	0	0	7121	623	22	2	361	2	HINT2	9	35813717	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	16755352	35813717	105399714	80	2823											
FAM102A	399665	hgsc.bcm.edu	37	chr9	130742408	130742408	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aatttcttcttcttcatcaaGaaagccatgagcgagttccc	11	13	6	11	1	5	2	2	1	3	1	6	3	6	2	2	0	2	1	2	0	3	5			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr9:130742408G>A	ENST00000373095.1	-	1	384	c.9C>T	c.(7-9)ttC>ttT	p.F3F		NM_001035254.2	NP_001030331.1	Q5T9C2	F102A_HUMAN	family with sequence similarity 102, member A	3										breast(1)|cervix(1)|large_intestine(3)|lung(1)|ovary(4)	10						TCTTCATCAAGAAAGCCATGA	0.527																																					p.F3F		Atlas-SNP	.											.	FAM102A	32	.	0			c.C9T						PASS	.						93	106	101					9																	130742408		2203	4300	6503	SO:0001819	synonymous_variant	399665	exon1			CATCAAGAAAGCC		CCDS6888.1, CCDS35150.1	9q34.11	2012-11-05	2005-11-17	2005-11-17	ENSG00000167106	ENSG00000167106			31419	protein-coding gene	gene with protein product	"sym-3 homolog A (C. elegans)"	610891	"chromosome 9 open reading frame 132"	C9orf132			Standard	NM_001035254		Approved	Eeig1, bA203J24.7, SYM-3A	uc004bsx.2	Q5T9C2	OTTHUMG00000020720	ENST00000373095.1:c.9C>T	9.37:g.130742408G>A		82	0	0		59	25	0.423729	NM_001035254	A2A329|Q8TEL4	Silent	SNP	ENST00000373095.1	37	CCDS35150.1																																																																																			.	.	none		0.527	FAM102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054298.2			A	130742408	G	A	130742408	2	1	21	1	0	0	0	0	0	0	0	1	5387	933	33	2		2	FAM102A	9	130742408	Silent	SNP	G	TCGA-FM-8000-01A-11D-2210-10	94928691	130742408	10471023	81	2824											
SEC16A	9919	hgsc.bcm.edu	37	chr9	139371030	139371030	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcccccagtgggtggtgcgtAcggttttctgggctatctcc	3	12	14	12	2	2	0	0	0	2	0	3	0	2	0	3	4	2	3	3	4	2	4			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr9:139371030A>C	ENST00000371706.3	-	1	537	c.504T>G	c.(502-504)cgT>cgG	p.R168R	SEC16A_ENST00000431893.2_Silent_p.R168R|SEC16A_ENST00000313050.7_Silent_p.R346R|SEC16A_ENST00000290037.6_Silent_p.R168R			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	168					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)		GGTGGTGCGTACGGTTTTCTG	0.632																																					p.R346R		Atlas-SNP	.											.	SEC16A	249	.	0			c.T1038G						PASS	.						20	22	21					9																	139371030		1852	4093	5945	SO:0001819	synonymous_variant	9919	exon3			GTGCGTACGGTTT	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.504T>G	9.37:g.139371030A>C		96	0	0		87	40	0.45977	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Silent	SNP	ENST00000371706.3	37																																																																																				.	.	none		0.632	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459		C	139371030	A	C	139371030	2	2	21	1	0	0	0	0	0	0	0	1	14001	378	14	5		5	SEC16A	9	139371030	Silent	SNP	A	TCGA-FM-8000-01A-11D-2210-10	8628622	139371030	1842401	82	2825											
GPR158	57512	hgsc.bcm.edu	37	chr10	25701364	25701364	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtgtatgctgctcgacttcGttagcatgctggtggtctac	5	15	12	9	2	1	0	0	0	1	0	3	1	1	0	0	2	5	6	0	2	3	4			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr10:25701364G>A	ENST00000376351.3	+	4	1656	c.1297G>A	c.(1297-1299)Gtt>Att	p.V433I		NM_020752.2	NP_065803.2	Q5T848	GP158_HUMAN	G protein-coupled receptor 158	433					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						GCTCGACTTCGTTAGCATGCT	0.473																																					p.V433I		Atlas-SNP	.											.	GPR158	255	.	0			c.G1297A						PASS	.						195	167	177					10																	25701364		2203	4300	6503	SO:0001583	missense	57512	exon4			GACTTCGTTAGCA	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.1297G>A	10.37:g.25701364G>A	ENSP00000365529:p.Val433Ile	159	0	0		88	35	0.397727	NM_020752	Q6QR81|Q9ULT3	Missense_Mutation	SNP	ENST00000376351.3	37	CCDS31166.1	.	.	.	.	.	.	.	.	.	.	G	5.850	0.341062	0.11069	.	.	ENSG00000151025	ENST00000376351	D	0.87729	-2.29	6.16	-9.35	0.00633	GPCR, family 3, C-terminal (2);	0.949110	0.08702	N	0.906239	T	0.65688	0.2715	N	0.04355	-0.22	0.09310	N	1	B	0.15473	0.013	B	0.14023	0.01	T	0.60944	-0.7162	10	0.02654	T	1	.	15.4514	0.75277	0.7301:0.0789:0.1909:0.0	.	433	Q5T848	GP158_HUMAN	I	433	ENSP00000365529:V433I	ENSP00000365529:V433I	V	+	1	0	GPR158	25741370	0.208000	0.23494	0.004000	0.12327	0.915000	0.54546	0.141000	0.16076	-2.012000	0.00950	-2.218000	0.00297	GTT	.	.	none		0.473	GPR158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047248.2	XM_166110		A	25701364	G	A	25701364	3	1	21	1	0	0	0	0	1	0	0	0	6671	1145	40	1	1311	1	GPR158	10	25701364	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10		25701364	109833383	83	2826											
ZNF438	220929	hgsc.bcm.edu	37	chr10	31138094	31138094	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttggggatcattttttactcTttctttaccatctctacact	7	20	4	10	0	4	0	1	0	3	0	5	1	4	1	1	2	3	0	1	2	3	8			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr10:31138094T>G	ENST00000361310.3	-	6	1569	c.1240A>C	c.(1240-1242)Aga>Cga	p.R414R	ZNF438_ENST00000375311.1_5'UTR|ZNF438_ENST00000331737.6_Silent_p.R404R|ZNF438_ENST00000442986.1_Silent_p.R414R|ZNF438_ENST00000436087.2_Silent_p.R414R|ZNF438_ENST00000413025.1_Silent_p.R414R|ZNF438_ENST00000444692.2_Silent_p.R404R|ZNF438_ENST00000538351.2_Silent_p.R365R|ZNF438_ENST00000452305.1_Silent_p.R404R			Q7Z4V0	ZN438_HUMAN	zinc finger protein 438	414					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)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(15)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		Prostate(175;0.0587)				TTTTTTACTCTTTCTTTACCA	0.373																																					p.R414R		Atlas-SNP	.											.	ZNF438	90	.	0			c.A1240C						PASS	.						66	73	70					10																	31138094		2203	4298	6501	SO:0001819	synonymous_variant	220929	exon7			TTACTCTTTCTTT	AK057323	CCDS7168.1, CCDS44369.1, CCDS53504.1	10p11.23	2006-02-15			ENSG00000183621	ENSG00000183621		"Zinc fingers, C2H2-type"	21029	protein-coding gene	gene with protein product							Standard	NM_182755		Approved	bA330O11.1	uc010qeb.2	Q7Z4V0	OTTHUMG00000017904	ENST00000361310.3:c.1240A>C	10.37:g.31138094T>G		57	0	0		64	29	0.453125	NM_182755	A2A3J4|A8K9L5|Q5T426|Q658Q4|Q6ZN65	Silent	SNP	ENST00000361310.3	37	CCDS7168.1																																																																																			.	.	none		0.373	ZNF438-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277006.1	NM_182755		G	31138094	T	G	31138094	2	3	21	1	0	0	0	0	0	0	0	1	17925	1617	56	5		5	ZNF438	10	31138094	Silent	SNP	T	TCGA-FM-8000-01A-11D-2210-10	5436730	31138094	104396653	84	2827											
ZNF485	220992	hgsc.bcm.edu	37	chr10	44112510	44112510	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	atctttcaggtatagctcatCctttgctggtcatcagaaaa	11	14	7	9	0	5	1	4	0	1	1	6	1	6	1	1	2	2	3	1	2	4	4			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr10:44112510C>G	ENST00000361807.3	+	5	1213	c.1019C>G	c.(1018-1020)tCc>tGc	p.S340C	ZNF485_ENST00000374435.3_Missense_Mutation_p.S340C|ZNF485_ENST00000374437.2_Missense_Mutation_p.S249C	NM_145312.3	NP_660355.2	Q8NCK3	ZN485_HUMAN	zinc finger protein 485	340					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						TATAGCTCATCCTTTGCTGGT	0.428																																					p.S340C		Atlas-SNP	.											.	ZNF485	102	.	0			c.C1019G						PASS	.						122	117	119					10																	44112510		2203	4300	6503	SO:0001583	missense	220992	exon5			GCTCATCCTTTGC	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.1019C>G	10.37:g.44112510C>G	ENSP00000354694:p.Ser340Cys	70	0	0		34	13	0.382353	NM_145312	B4DSE6|Q96CL0	Missense_Mutation	SNP	ENST00000361807.3	37	CCDS7205.2	.	.	.	.	.	.	.	.	.	.	C	9.435	1.086676	0.20390	.	.	ENSG00000198298	ENST00000361807;ENST00000374437;ENST00000374435	T;T;T	0.08008	3.14;3.14;3.14	1.86	1.86	0.25419	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17704	0.0425	L	0.56124	1.755	0.09310	N	1	P	0.52842	0.956	P	0.57776	0.827	T	0.04811	-1.0925	9	0.62326	D	0.03	.	9.7485	0.40462	0.0:1.0:0.0:0.0	.	340	Q8NCK3	ZN485_HUMAN	C	340;249;340	ENSP00000354694:S340C;ENSP00000363560:S249C;ENSP00000363558:S340C	ENSP00000354694:S340C	S	+	2	0	ZNF485	43432516	0.000000	0.05858	0.680000	0.29994	0.951000	0.60555	-1.275000	0.02817	1.337000	0.45525	0.313000	0.20887	TCC	.	.	none		0.428	ZNF485-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047719.2	NM_145312		G	44112510	C	G	44112510	3	3	21	1	0	0	0	0	1	0	0	0	17953	855	30	4	1033	4	ZNF485	10	44112510	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	12974416	44112510	91422237	85	2828											
PCDH15	65217	hgsc.bcm.edu	37	chr10	55782809	55782811	+	In_Frame_Del	DEL	ACA	ACA	-																															gtactgctccatctgttgccAcaacaacaagttcatagtag																								rs483352837		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	ACA	ACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr10:55782809_55782811delACA	ENST00000320301.6	-	19	2761_2763	c.2367_2369delTGT	c.(2365-2370)gttgtg>gtg	p.789_790VV>V	PCDH15_ENST00000395445.1_In_Frame_Del_p.796_797VV>V|PCDH15_ENST00000395438.1_In_Frame_Del_p.789_790VV>V|PCDH15_ENST00000373965.2_In_Frame_Del_p.796_797VV>V|PCDH15_ENST00000437009.1_In_Frame_Del_p.718_719VV>V|PCDH15_ENST00000373955.1_In_Frame_Del_p.789_790VV>V|PCDH15_ENST00000395430.1_In_Frame_Del_p.789_790VV>V|PCDH15_ENST00000395432.2_In_Frame_Del_p.752_753VV>V|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000409834.1_In_Frame_Del_p.400_401VV>V|PCDH15_ENST00000395433.1_In_Frame_Del_p.767_768VV>V|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000361849.3_In_Frame_Del_p.789_790VV>V|PCDH15_ENST00000414778.1_In_Frame_Del_p.794_795VV>V|PCDH15_ENST00000395442.1_Intron	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	789	Cadherin 7. {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)	p.V790L(2)|p.V795L(2)		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)				ATCTGTTGCCACAACAACAAGTT	0.414										HNSCC(58;0.16)																											p.795_795del		Pindel,Atlas-Indel	.											PCDH15_ENST00000417177,NS,carcinoma,-2,4	PCDH15	1715	4	4	Substitution - Missense(4)	lung(4)	c.2383_2385del						PASS	.		,,,,,,,,,,,	6,4258		3,0,2129					,,,,,,,,,,,	4.9	1			181	21,8233		10,1,4116	no	coding,coding,coding,coding,coding,coding,coding,coding,coding,coding,coding,coding	PCDH15	NM_033056.3,NM_001142773.1,NM_001142772.1,NM_001142771.1,NM_001142770.1,NM_001142769.1,NM_001142768.1,NM_001142767.1,NM_001142766.1,NM_001142765.1,NM_001142764.1,NM_001142763.1	,,,,,,,,,,,	13,1,6245	A1A1,A1R,RR		0.2544,0.1407,0.2157	,,,,,,,,,,,	,,,,,,,,,,,		27,12491				SO:0001651	inframe_deletion	65217	exon20			.	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.2367_2369delTGT	10.37:g.55782815_55782817delACA	ENSP00000322604:p.Val790del	171	0	.		134	37	0.276	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	In_Frame_Del	DEL	ENST00000320301.6	37	CCDS7248.1																																																																																			.	.	none		0.414	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		-	55782811	ACA	-	55782809	7	5	21	1	0	1	0	1	0	0	0	0	11520	159	6	0	5177	0	PCDH15	10	55782809	In_Frame_Del	DEL	ACA	TCGA-FM-8000-01A-11D-2210-10	11670299	55782809	79751938	86	2829											
ANK3	288	hgsc.bcm.edu	37	chr10	61946498	61946498	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgctcaggttcacattcgcaTttctaccgaggagcagcgac	9	10	10	12	3	3	0	2	0	1	0	4	3	3	1	1	2	4	4	1	2	1	4			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr10:61946498T>C	ENST00000280772.2	-	17	2251	c.2060A>G	c.(2059-2061)aAt>aGt	p.N687S	ANK3_ENST00000373827.2_Missense_Mutation_p.N681S|ANK3_ENST00000503366.1_Missense_Mutation_p.N670S	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	687					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						CACATTCGCATTTCTACCGAG	0.517																																					p.N687S		Atlas-SNP	.											.	ANK3	703	.	0			c.A2060G						PASS	.						201	148	166					10																	61946498		2203	4300	6503	SO:0001583	missense	288	exon17			TTCGCATTTCTAC	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.2060A>G	10.37:g.61946498T>C	ENSP00000280772:p.Asn687Ser	136	0	0		100	55	0.55	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Missense_Mutation	SNP	ENST00000280772.2	37	CCDS7258.1	.	.	.	.	.	.	.	.	.	.	T	14.85	2.659040	0.47467	.	.	ENSG00000151150	ENST00000280772;ENST00000373827;ENST00000503366;ENST00000395299;ENST00000395293;ENST00000395304;ENST00000536348	T;T;T	0.15256	2.44;2.44;2.44	6.17	6.17	0.99709	Ankyrin repeat-containing domain (4);	0.000000	0.44902	D	0.000401	T	0.15176	0.0366	L	0.37630	1.12	0.80722	D	1	B;B;B;B;B	0.21071	0.002;0.001;0.005;0.025;0.051	B;B;B;B;B	0.19946	0.005;0.009;0.023;0.021;0.027	T	0.03773	-1.1005	10	0.46703	T	0.11	.	11.0511	0.47889	0.0:0.0685:0.0:0.9315	.	670;348;231;681;687	E9PE32;E7EMJ1;Q59G01;Q5CZH9;Q12955	.;.;.;.;ANK3_HUMAN	S	687;681;670;649;348;348;231	ENSP00000280772:N687S;ENSP00000362933:N681S;ENSP00000425236:N670S	ENSP00000280772:N687S	N	-	2	0	ANK3	61616504	1.000000	0.71417	0.998000	0.56505	0.626000	0.37791	4.282000	0.58971	2.371000	0.80710	0.533000	0.62120	AAT	.	.	none		0.517	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		C	61946498	T	C	61946498	3	2	21	1	0	0	0	0	1	0	0	0	622	1493	52	3	11514	3	ANK3	10	61946498	Missense_Mutation	SNP	T	TCGA-FM-8000-01A-11D-2210-10	6163689	61946498	73588249	87	2830											
RUFY2	55680	hgsc.bcm.edu	37	chr10	70143622	70143622	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatttcatctagcccctgaCgagaatgcttatatgtttga	11	14	7	9	1	2	3	1	2	1	1	2	4	2	3	2	0	2	2	2	0	4	5			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr10:70143622C>T	ENST00000602465.1	-	10	972	c.872G>A	c.(871-873)cGt>cAt	p.R291H	RUFY2_ENST00000454950.2_Missense_Mutation_p.R233H|RUFY2_ENST00000472394.2_5'UTR|RUFY2_ENST00000399200.2_Missense_Mutation_p.R257H|RUFY2_ENST00000388768.2_Missense_Mutation_p.R326H			Q8WXA3	RUFY2_HUMAN	RUN and FYVE domain containing 2	340						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						TAGCCCCTGACGAGAATGCTT	0.353																																					p.R326H		Atlas-SNP	.											.	RUFY2	58	.	0			c.G977A						PASS	.						143	129	133					10																	70143622		1866	4102	5968	SO:0001583	missense	55680	exon10			CCCTGACGAGAAT	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.872G>A	10.37:g.70143622C>T	ENSP00000473462:p.Arg291His	103	0	0		74	41	0.554054	NM_017987	B3KXB2|B4DFR0|Q5TC48|Q8IW33|Q96P51|Q9P1Z1	Missense_Mutation	SNP	ENST00000602465.1	37		.	.	.	.	.	.	.	.	.	.	C	32	5.126953	0.94429	.	.	ENSG00000204130	ENST00000388768;ENST00000399200;ENST00000454950	T;T;T	0.54479	0.57;1.78;1.36	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	T	0.70622	0.3245	M	0.65975	2.015	0.80722	D	1	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.80764	0.987;0.994;0.991;0.994	T	0.70970	-0.4727	10	0.49607	T	0.09	.	16.8596	0.86014	0.0:1.0:0.0:0.0	.	233;291;257;326	B4DFR0;Q8WXA3-2;Q8WXA3-4;Q8WXA3-3	.;.;.;.	H	326;257;233	ENSP00000373420:R326H;ENSP00000382151:R257H;ENSP00000404986:R233H	ENSP00000373420:R326H	R	-	2	0	RUFY2	69813628	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.004000	0.76317	2.647000	0.89833	0.585000	0.79938	CGT	.	.	none		0.353	RUFY2-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467567.1	NM_017987		T	70143622	C	T	70143622	3	4	21	1	0	0	0	0	1	0	0	0	13754	536	19	1	1097	1	RUFY2	10	70143622	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	8197124	70143622	65391125	88	2831											
LOXL4	84171	hgsc.bcm.edu	37	chr10	100017842	100017842	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccacctgtggtcacagaccGtgccccactggcggttcatg	6	9	11	15	2	2	1	2	0	0	1	3	1	3	1	5	3	1	1	5	3	0	1			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr10:100017842G>A	ENST00000260702.3	-	7	1151	c.1001C>T	c.(1000-1002)aCg>aTg	p.T334M	RP11-34A14.3_ENST00000433374.1_RNA	NM_032211.6	NP_115587.6	Q96JB6	LOXL4_HUMAN	lysyl oxidase-like 4	334	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)		GTCACAGACCGTGCCCCACTG	0.682																																					p.T334M		Atlas-SNP	.											.	LOXL4	60	.	0			c.C1001T						PASS	.						70	64	66					10																	100017842		2203	4300	6503	SO:0001583	missense	84171	exon7			CAGACCGTGCCCC	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.1001C>T	10.37:g.100017842G>A	ENSP00000260702:p.Thr334Met	118	0	0		72	25	0.347222	NM_032211	Q5W0B3|Q96DY1|Q96PC0|Q9H6T5	Missense_Mutation	SNP	ENST00000260702.3	37	CCDS7473.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.952441	0.92660	.	.	ENSG00000138131	ENST00000260702	T	0.39229	1.09	4.94	4.94	0.65067	Speract/scavenger receptor (4);Speract/scavenger receptor-related (2);	0.000000	0.85682	D	0.000000	T	0.77136	0.4086	H	0.96662	3.86	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85790	0.1367	10	0.66056	D	0.02	.	18.1558	0.89690	0.0:0.0:1.0:0.0	.	334	Q96JB6	LOXL4_HUMAN	M	334	ENSP00000260702:T334M	ENSP00000260702:T334M	T	-	2	0	LOXL4	100007832	1.000000	0.71417	0.929000	0.37066	0.949000	0.60115	9.869000	0.99810	2.283000	0.76528	0.549000	0.68633	ACG	.	.	none		0.682	LOXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049766.1	NM_032211		A	100017842	G	A	100017842	3	1	21	1	0	0	0	0	1	0	0	0	8911	1145	40	1	1305	1	LOXL4	10	100017842	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	29874220	100017842	35516905	89	2832											
PNLIPRP1	5407	hgsc.bcm.edu	37	chr10	118351352	118351352	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctggggcgggacagcaatcaGgcccctgaaaattctcccct	9	7	11	14	1	2	1	1	1	1	0	3	2	2	2	4	4	1	1	4	4	3	1			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr10:118351352G>A	ENST00000528052.1	+	3	190	c.119G>A	c.(118-120)aGg>aAg	p.R40K	PNLIPRP1_ENST00000442761.1_Missense_Mutation_p.R40K|PNLIPRP1_ENST00000534537.1_Missense_Mutation_p.R40K|PNLIPRP1_ENST00000358834.4_Missense_Mutation_p.R40K|PNLIPRP1_ENST00000480870.2_3'UTR			P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1	40					lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|triglyceride lipase activity (GO:0004806)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	38				all cancers(201;0.0161)		ACAGCAATCAGGCCCCTGAAA	0.512																																					p.R40K		Atlas-SNP	.											.	PNLIPRP1	82	.	0			c.G119A						PASS	.						111	118	116					10																	118351352		2203	4300	6503	SO:0001583	missense	5407	exon3			CAATCAGGCCCCT	BC025784	CCDS7595.1	10q26.12	2006-07-04			ENSG00000187021	ENSG00000187021			9156	protein-coding gene	gene with protein product		604422				1379598	Standard	NM_006229		Approved	PLRP1	uc001lco.1	P54315	OTTHUMG00000019109	ENST00000528052.1:c.119G>A	10.37:g.118351352G>A	ENSP00000433933:p.Arg40Lys	89	0	0		61	20	0.327869	NM_006229	Q68D83|Q68DR6|Q8TAU2|Q9BS82	Missense_Mutation	SNP	ENST00000528052.1	37	CCDS7595.1	.	.	.	.	.	.	.	.	.	.	G	17.00	3.277781	0.59758	.	.	ENSG00000187021	ENST00000531984;ENST00000358834;ENST00000528052;ENST00000442761;ENST00000530319;ENST00000527980;ENST00000471549;ENST00000534537	D;D;D;D;D;D;D;D	0.91237	-2.81;-2.81;-2.81;-2.81;-2.81;-2.81;-2.81;-2.81	5.51	4.59	0.56863	Lipase, N-terminal (1);	0.128417	0.53938	D	0.000050	D	0.96636	0.8902	H	0.95328	3.655	0.45995	D	0.998805	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.996	D	0.97514	1.0068	10	0.72032	D	0.01	-8.5798	14.5305	0.67923	0.0:0.0:0.852:0.148	.	40;40	P54315;P54315-2	LIPR1_HUMAN;.	K	40	ENSP00000436123:R40K;ENSP00000351695:R40K;ENSP00000433933:R40K;ENSP00000400963:R40K;ENSP00000437263:R40K;ENSP00000433785:R40K;ENSP00000431207:R40K;ENSP00000434159:R40K	ENSP00000351695:R40K	R	+	2	0	PNLIPRP1	118341342	1.000000	0.71417	0.937000	0.37676	0.979000	0.70002	6.886000	0.75611	1.304000	0.44892	0.655000	0.94253	AGG	.	.	none		0.512	PNLIPRP1-011	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384633.1	NM_006229		A	118351352	G	A	118351352	3	1	21	1	0	0	0	0	1	0	0	0	12159	1000	35	2	125	2	PNLIPRP1	10	118351352	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	18333510	118351352	17183395	90	2833											
MUC2	4583	hgsc.bcm.edu	37	chr11	1092950	1092950	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacacccatcaccaccaccaCtacggtgaccccaaccccaa	13	3	4	21	1	1	1	1	1	0	0	1	2	1	1	8	1	2	0	8	1	3	1	rs199605832		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr11:1092950C>T	ENST00000441003.2	+	30	4796	c.4769C>T	c.(4768-4770)aCt>aTt	p.T1590I	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Missense_Mutation_p.T1591I	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)		p.T1591I(1)|p.T1590I(1)		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)	accaccaccactacggtgacc	0.632																																					p.T1590I		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	2	Substitution - Missense(2)	endometrium(2)	c.C4769T						scavenged	.	C	ILE/THR	6,3646		0,6,1820	56	90	78		4766	-3.5	0	11		78	4,6702		0,4,3349	no	missense	MUC2	NM_002457.2	89	0,10,5169	TT,TC,CC		0.0596,0.1643,0.0965	possibly-damaging	1589/2813	1092950	10,10348	1826	3353	5179	SO:0001583	missense	4583	exon30			CCACCACTACGGT	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.4769C>T	11.37:g.1092950C>T	ENSP00000415183:p.Thr1590Ile	149	1	0.00671141		55	3	0.0545455	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	4.282	0.051491	0.08291	0.001643	5.96E-4	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.15372	2.43;2.75	1.75	-3.51	0.04696	.	79.651400	0.00166	U	0.000017	T	0.09113	0.0225	.	.	.	0.09310	N	1	P	0.49090	0.919	B	0.31686	0.134	T	0.33954	-0.9848	9	0.51188	T	0.08	.	5.4287	0.16440	0.2102:0.3762:0.4136:0.0	.	1590	E7EUV1	.	I	1590;1591	ENSP00000415183:T1590I;ENSP00000351956:T1591I	ENSP00000351956:T1591I	T	+	2	0	MUC2	1082950	0.003000	0.15002	0.000000	0.03702	0.181000	0.23173	1.844000	0.39269	-1.047000	0.03242	0.121000	0.15741	ACT	.	.	weak		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1092950	C	T	1092950	3	4	21	1	0	0	0	0	1	0	0	0	9984	565	20	2	4887	2	MUC2	11	1092950	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10		1092950	133913566	91	2834											
OR10A5	144124	hgsc.bcm.edu	37	chr11	6866966	6866966	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttatcctcatgagcttctCttccctacctactgaaatac	10	15	3	13	0	2	2	1	2	1	0	5	2	4	2	3	0	4	1	3	0	5	7			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr11:6866966C>A	ENST00000299454.4	+	1	84	c.53C>A	c.(52-54)tCt>tAt	p.S18Y	OR10A5_ENST00000379831.2_Missense_Mutation_p.S22Y			Q9H207	O10A5_HUMAN	olfactory receptor, family 10, subfamily A, member 5	18					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)		ATGAGCTTCTCTTCCCTACCT	0.413																																					p.S18Y	Pancreas(44;21 1072 25662 28041 45559)	Atlas-SNP	.											.	OR10A5	48	.	0			c.C53A						PASS	.						185	192	190					11																	6866966		2201	4296	6497	SO:0001583	missense	144124	exon1			GCTTCTCTTCCCT	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.53C>A	11.37:g.6866966C>A	ENSP00000299454:p.Ser18Tyr	273	0	0		220	85	0.386364	NM_178168	O95223|Q52M66|Q96R21|Q96R22	Missense_Mutation	SNP	ENST00000299454.4	37	CCDS7773.1	.	.	.	.	.	.	.	.	.	.	.	14.86	2.662395	0.47572	.	.	ENSG00000166363	ENST00000299454;ENST00000379831	T;T	0.01106	5.33;5.33	3.46	3.46	0.39613	.	0.000000	0.50627	D	0.000101	T	0.07234	0.0183	M	0.93550	3.43	0.32884	D	0.510957	P	0.44776	0.843	P	0.53954	0.738	T	0.01087	-1.1456	10	0.72032	D	0.01	.	13.2073	0.59805	0.0:1.0:0.0:0.0	.	18	Q9H207	O10A5_HUMAN	Y	18;22	ENSP00000299454:S18Y;ENSP00000369159:S22Y	ENSP00000299454:S18Y	S	+	2	0	OR10A5	6823542	0.749000	0.28305	0.976000	0.42696	0.745000	0.42441	3.177000	0.50871	2.225000	0.72522	0.591000	0.81541	TCT	.	.	none		0.413	OR10A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385983.1	NM_178168		A	6866966	C	A	6866966	3	1	21	1	0	0	0	0	1	0	0	0	10902	913	32	4	55	4	OR10A5	11	6866966	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	5774016	6866966	128139550	92	2835											
OR4C16	219428	hgsc.bcm.edu	37	chr11	55340486	55340486	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaatacagaagtgaaaagtGccatgaggaagctttggagc	16	7	13	5	0	0	4	0	2	0	2	0	6	0	6	1	2	4	1	1	2	6	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr11:55340486G>A	ENST00000314634.3	+	1	883	c.883G>A	c.(883-885)Gcc>Acc	p.A295T		NM_001004701.2	NP_001004701.2	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C, member 16 (gene/pseudogene)	295						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)				AGTGAAAAGTGCCATGAGGAA	0.368																																					p.A295T		Atlas-SNP	.											.	OR4C16	104	.	0			c.G883A						PASS	.						45	43	44					11																	55340486		2201	4296	6497	SO:0001583	missense	219428	exon1			AAAAGTGCCATGA	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.883G>A	11.37:g.55340486G>A	ENSP00000324913:p.Ala295Thr	62	0	0		65	24	0.369231	NM_001004701	Q6IEV8	Missense_Mutation	SNP	ENST00000314634.3	37	CCDS31502.1	.	.	.	.	.	.	.	.	.	.	G	11.96	1.795312	0.31777	.	.	ENSG00000181935	ENST00000314634	T	0.42131	0.98	4.68	3.77	0.43336	.	0.000000	0.64402	D	0.000016	T	0.38904	0.1058	L	0.47716	1.5	0.26601	N	0.973018	B	0.32338	0.365	B	0.37239	0.244	T	0.40059	-0.9583	10	0.66056	D	0.02	.	10.7693	0.46312	0.0931:0.0:0.9069:0.0	.	295	Q8NGL9	OR4CG_HUMAN	T	295	ENSP00000324913:A295T	ENSP00000324913:A295T	A	+	1	0	OR4C16	55097062	0.004000	0.15560	0.990000	0.47175	0.345000	0.29048	1.157000	0.31724	1.203000	0.43233	0.549000	0.68633	GCC	.	.	none		0.368	OR4C16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382627.1	NM_001004701		A	55340486	G	A	55340486	3	1	21	1	0	0	0	0	1	0	0	0	11058	1319	46	2	885	2	OR4C16	11	55340486	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	48473520	55340486	79666030	93	2836											
BCO2	83875	hgsc.bcm.edu	37	chr11	112071462	112071462	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgggaaccccagtgtaataCgcggtttcatgtggtggaaa	10	10	13	8	2	1	0	1	0	0	0	1	2	1	2	2	4	2	2	2	4	4	3	rs141269805		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr11:112071462C>T	ENST00000357685.5	+	7	1127	c.992C>T	c.(991-993)aCg>aTg	p.T331M	BCO2_ENST00000526088.1_Missense_Mutation_p.T297M|BCO2_ENST00000361053.4_Missense_Mutation_p.T258M|BCO2_ENST00000438022.1_Missense_Mutation_p.T297M|BCO2_ENST00000532593.1_Missense_Mutation_p.T226M|BCO2_ENST00000393032.2_Missense_Mutation_p.T297M|BCO2_ENST00000531169.1_Missense_Mutation_p.T297M			Q9BYV7	BCDO2_HUMAN	beta-carotene oxygenase 2	331					carotene catabolic process (GO:0016121)|carotene metabolic process (GO:0016119)|carotenoid metabolic process (GO:0016116)|oxidation-reduction process (GO:0055114)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of reactive oxygen species metabolic process (GO:2000377)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)	intracellular (GO:0005622)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			NS(1)|breast(1)|kidney(3)|large_intestine(1)|lung(9)|skin(1)	16						CAGTGTAATACGCGGTTTCAT	0.398																																					p.T331M	GBM(177;1916 2099 21049 29541 39946)	Atlas-SNP	.											.	BCO2	44	.	0			c.C992T						PASS	.	C	MET/THR,MET/THR	1,4401	2.1+/-5.4	0,1,2200	121	124	123		890,992	5.4	0.9	11	dbSNP_134	123	0,8594		0,0,4297	no	missense,missense	BCO2	NM_001037290.1,NM_031938.4	81,81	0,1,6497	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	297/546,331/580	112071462	1,12995	2201	4297	6498	SO:0001583	missense	83875	exon7			GTAATACGCGGTT	AJ290393	CCDS8358.2, CCDS41716.1, CCDS58181.1, CCDS58182.1, CCDS58183.1	11q23.1	2014-05-12	2008-04-15	2008-04-15	ENSG00000197580	ENSG00000197580	1.13.11.71		18503	protein-coding gene	gene with protein product	"beta-carotene 9',10' oxygenase", "carotenoid-9',10'-cleaving dioxygenase"	611740	"beta-carotene dioxygenase 2"	BCDO2		11278918, 15983114, 15949678	Standard	NM_031938		Approved	FLJ34464, B-DIOX-II	uc001pnf.3	Q9BYV7	OTTHUMG00000167155	ENST00000357685.5:c.992C>T	11.37:g.112071462C>T	ENSP00000350314:p.Thr331Met	80	0	0		92	33	0.358696	NM_031938	B0YIX5|B4DNC3|E9PBI8|E9PJJ1|Q8IUS0|Q96JC8|Q96JY5	Missense_Mutation	SNP	ENST00000357685.5	37	CCDS8358.2	.	.	.	.	.	.	.	.	.	.	C	17.30	3.354480	0.61293	2.27E-4	0.0	ENSG00000197580	ENST00000357685;ENST00000393032;ENST00000361053;ENST00000438022;ENST00000526088;ENST00000532593;ENST00000531169	D;D;D;D;D;D;D	0.95588	-3.75;-3.75;-3.75;-3.75;-3.75;-3.75;-3.75	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	D	0.98140	0.9386	M	0.89353	3.025	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;0.993	D	0.98900	1.0776	10	0.87932	D	0	-17.1853	19.2802	0.94050	0.0:1.0:0.0:0.0	.	308;258;331;158	C9JEZ9;E9PBI8;Q9BYV7;Q8NAZ7	.;.;BCDO2_HUMAN;.	M	331;297;258;297;297;226;297	ENSP00000350314:T331M;ENSP00000376752:T297M;ENSP00000354338:T258M;ENSP00000414843:T297M;ENSP00000436615:T297M;ENSP00000431802:T226M;ENSP00000437053:T297M	ENSP00000350314:T331M	T	+	2	0	BCO2	111576672	1.000000	0.71417	0.948000	0.38648	0.108000	0.19459	5.274000	0.65569	2.579000	0.87056	0.585000	0.79938	ACG	C|1.000;T|0.000	0.000	weak		0.398	BCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256570.3	NM_001037290		T	112071462	C	T	112071462	3	4	21	1	0	0	0	0	1	0	0	0	1385	536	19	1	1018	1	BCO2	11	112071462	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	56730976	112071462	22935054	94	2837											
HTR3A	3359	hgsc.bcm.edu	37	chr11	113848285	113848285	+	Intron	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tcctgtcaatgaatgcatagGtcctttctacaaggtaatac	12	13	7	9	0	2	1	1	1	1	0	4	1	4	1	2	2	3	2	2	2	7	5			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr11:113848285G>A	ENST00000504030.2	+	2	512				HTR3A_ENST00000299961.5_Silent_p.R3R|HTR3A_ENST00000535865.1_Intron|HTR3A_ENST00000375498.2_Intron|HTR3A_ENST00000506841.2_Intron|HTR3A_ENST00000355556.2_Intron			P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A, ionotropic						cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cellular response to growth factor stimulus (GO:0071363)|digestion (GO:0007586)|ion transmembrane transport (GO:0034220)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	36		all_cancers(61;2.31e-17)|all_epithelial(67;2.1e-10)|all_hematologic(158;4.64e-05)|Melanoma(852;0.000312)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0294)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.71e-06)|Epithelial(105;2.58e-05)|all cancers(92;0.000238)|OV - Ovarian serous cystadenocarcinoma(223;0.191)	Alosetron(DB00969)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Chloroprocaine(DB01161)|Cisapride(DB00604)|Clozapine(DB00363)|Dolasetron(DB00757)|Ergoloid mesylate(DB01049)|Granisetron(DB00889)|Loxapine(DB00408)|Memantine(DB01043)|Methadone(DB00333)|Metoclopramide(DB01233)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Ondansetron(DB00904)|Palonosetron(DB00377)|Procaine(DB00721)|Quetiapine(DB01224)|Rocuronium(DB00728)|Tapentadol(DB06204)|Trimipramine(DB00726)|Tubocurarine(DB01199)|Ziprasidone(DB00246)	GAATGCATAGGTCCTTTCTAC	0.423																																					p.R3R		Atlas-SNP	.											.	HTR3A	93	.	0			c.G9A						PASS	.						167	137	146					11																	113848285		692	1591	2283	SO:0001627	intron_variant	3359	exon1			GCATAGGTCCTTT	D49394	CCDS8365.1, CCDS8366.1, CCDS8365.2, CCDS8366.2, CCDS53710.1	11q23.1-q23.2	2012-05-22	2012-02-03					"5-HT (serotonin) receptors", "Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"	5297	protein-coding gene	gene with protein product		182139	"5-hydroxytryptamine (serotonin) receptor 3A"	HTR3		8530095, 12867984	Standard	NM_000869		Approved	5-HT3R, 5-HT3A	uc010rxb.2	P46098		ENST00000504030.2:c.68-208G>A	11.37:g.113848285G>A		73	0	0		63	24	0.380952	NM_001161772	B4DSY6|G5E986|O60854|Q7KZM7|Q99918|Q9BSZ9	Silent	SNP	ENST00000504030.2	37																																																																																				.	.	none		0.423	HTR3A-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000360822.2	NM_000869		A	113848285	G	A	113848285	1	1	21	0	1	0	0	0	0	0	0	0	7453	1252	44	2		2	HTR3A	11	113848285	Intron	SNP	G	TCGA-FM-8000-01A-11D-2210-10	1776823	113848285	21158231	95	2838											
PATE1	160065	hgsc.bcm.edu	37	chr11	125616559	125616559	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctttttttttccaacagcatTatctggatcactttcaatga	10	18	4	9	0	3	1	2	1	1	0	4	2	4	2	1	1	2	1	1	1	3	6			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr11:125616559T>C	ENST00000305738.5	+	2	68	c.56T>C	c.(55-57)tTa>tCa	p.L19S	PATE1_ENST00000437148.2_Missense_Mutation_p.L19S	NM_138294.2	NP_612151.1	Q8WXA2	PATE1_HUMAN	prostate and testis expressed 1	19						extracellular region (GO:0005576)				large_intestine(1)|lung(5)	6						CCAACAGCATTATCTGGATCA	0.418																																					p.L19S		Atlas-SNP	.											.	PATE1	21	.	0			c.T56C						PASS	.						132	132	132					11																	125616559		2201	4299	6500	SO:0001583	missense	160065	exon2			CAGCATTATCTGG	AF462605	CCDS8464.1	11q24.2	2008-12-17				ENSG00000171053		"PATE family"	24664	protein-coding gene	gene with protein product	"expressed in prostate and testis"	606861				11880645, 15798027	Standard	NM_138294		Approved	PATE	uc001qct.3	Q8WXA2		ENST00000305738.5:c.56T>C	11.37:g.125616559T>C	ENSP00000307164:p.Leu19Ser	174	0	0		128	44	0.34375	NM_138294	Q3KNX2	Missense_Mutation	SNP	ENST00000305738.5	37	CCDS8464.1	.	.	.	.	.	.	.	.	.	.	T	3.058	-0.193988	0.06259	.	.	ENSG00000171053	ENST00000305738;ENST00000437148	T;T	0.31247	1.5;1.5	3.7	0.0174	0.14112	.	1.465370	0.05162	N	0.498016	T	0.19327	0.0464	N	0.12182	0.205	0.09310	N	1	P;P	0.47762	0.739;0.9	B;P	0.44477	0.305;0.451	T	0.12167	-1.0558	10	0.72032	D	0.01	-10.9707	3.1939	0.06626	0.0:0.2353:0.2167:0.548	.	19;19	Q8WXA2-2;Q8WXA2	.;PATE1_HUMAN	S	19	ENSP00000307164:L19S;ENSP00000396056:L19S	ENSP00000307164:L19S	L	+	2	0	PATE1	125121769	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.289000	0.18957	-0.012000	0.14223	0.459000	0.35465	TTA	.	.	none		0.418	PATE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386726.2	NM_138294		C	125616559	T	C	125616559	3	2	21	1	0	0	0	0	1	0	0	0	11482	1764	61	3	62	3	PATE1	11	125616559	Missense_Mutation	SNP	T	TCGA-FM-8000-01A-11D-2210-10	11768274	125616559	9389957	96	2839											
FAM118B	79607	hgsc.bcm.edu	37	chr11	126110774	126110774	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtgctgcagttgcgccccaAgttccagccctcaaatcctg	8	9	9	15	1	1	0	1	0	0	0	3	0	3	0	5	0	4	4	5	0	2	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr11:126110774A>G	ENST00000533050.1	+	4	667	c.174A>G	c.(172-174)caA>caG	p.Q58Q	FAM118B_ENST00000360194.4_Silent_p.Q58Q|FAM118B_ENST00000525728.1_3'UTR|FAM118B_ENST00000529731.1_Silent_p.Q58Q	NM_024556.3	NP_078832.1	Q9BPY3	F118B_HUMAN	family with sequence similarity 118, member B	58								p.Q58H(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)	13	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;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0784)		TTGCGCCCCAAGTTCCAGCCC	0.438																																					p.Q58Q		Atlas-SNP	.											FAM118B,caecum,carcinoma,0,1	FAM118B	29	1	1	Substitution - Missense(1)	large_intestine(1)	c.A174G						scavenged	.						192	206	201					11																	126110774		2201	4299	6500	SO:0001819	synonymous_variant	79607	exon4			GCCCCAAGTTCCA	BC001340	CCDS8470.1	11q24.2	2014-03-13				ENSG00000197798			26110	protein-coding gene	gene with protein product						24569877	Standard	NM_024556		Approved	FLJ21103	uc001qdf.3	Q9BPY3		ENST00000533050.1:c.174A>G	11.37:g.126110774A>G		146	1	0.00684932		71	33	0.464789	NM_024556	Q9H7B0	Silent	SNP	ENST00000533050.1	37	CCDS8470.1																																																																																			.	.	none		0.438	FAM118B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386346.1	NM_024556		G	126110774	A	G	126110774	2	3	21	1	0	0	0	0	0	0	0	1	5417	69	3	3		3	FAM118B	11	126110774	Silent	SNP	A	TCGA-FM-8000-01A-11D-2210-10	494215	126110774	8895742	97	2840											
TIRAP	114609	hgsc.bcm.edu	37	chr11	126162924	126162924	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggccctgatggtggctttcGtcaagtcaaagaagctgtca	9	10	13	9	1	3	2	3	1	0	1	4	2	3	2	1	3	1	2	1	3	3	1	rs199561634		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr11:126162924G>A	ENST00000392680.2	+	5	1025	c.620G>A	c.(619-621)cGt>cAt	p.R207H	TIRAP_ENST00000392678.3_Missense_Mutation_p.R207H|RP11-712L6.5_ENST00000528876.1_5'Flank|TIRAP_ENST00000392679.1_Missense_Mutation_p.R207H|RP11-712L6.7_ENST00000533378.1_RNA	NM_001039661.1	NP_001034750.1	P58753	TIRAP_HUMAN	toll-interleukin 1 receptor (TIR) domain containing adaptor protein	207	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)		GGTGGCTTTCGTCAAGTCAAA	0.537																																					p.R207H		Atlas-SNP	.											.	TIRAP	37	.	0			c.G620A						PASS	.						57	62	60					11																	126162924		2193	4291	6484	SO:0001583	missense	114609	exon5			GCTTTCGTCAAGT	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.620G>A	11.37:g.126162924G>A	ENSP00000376447:p.Arg207His	90	0	0		77	36	0.467532	NM_148910	B3KW65|Q56UH9|Q56UI0|Q8N5E5	Missense_Mutation	SNP	ENST00000392680.2	37	CCDS8472.1	.	.	.	.	.	.	.	.	.	.	G	10.49	1.365402	0.24684	.	.	ENSG00000150455	ENST00000392679;ENST00000279992;ENST00000392678;ENST00000392680	T;T;T	0.02472	4.28;4.28;4.28	5.83	-9.57	0.00562	Toll/interleukin-1 receptor homology (TIR) domain (1);	1.158350	0.06092	N	0.663909	T	0.02267	0.0070	L	0.31294	0.92	0.09310	N	1	B;B	0.10296	0.0;0.003	B;B	0.01281	0.0;0.0	T	0.43327	-0.9398	9	.	.	.	-12.1802	13.0157	0.58754	0.2329:0.0818:0.6853:0.0	.	207;207	P58753;Q56UH9	TIRAP_HUMAN;.	H	207	ENSP00000376446:R207H;ENSP00000376445:R207H;ENSP00000376447:R207H	.	R	+	2	0	TIRAP	125668134	0.000000	0.05858	0.284000	0.24805	0.924000	0.55760	-0.924000	0.03996	-1.520000	0.01773	-0.290000	0.09829	CGT	G|0.999;A|0.001	0.001	weak		0.537	TIRAP-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000277092.1	NM_148910		A	126162924	G	A	126162924	3	1	21	1	0	0	0	0	1	0	0	0	15942	1145	40	1	626	1	TIRAP	11	126162924	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	52150	126162924	8843592	98	2841											
ETS1	2113	hgsc.bcm.edu	37	chr11	128442997	128442997	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgagtaagggacggggctgCtcccagcagaatccacaaag	12	5	13	11	1	0	2	0	1	0	1	2	3	2	3	2	3	2	4	2	3	3	1			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr11:128442997C>T	ENST00000392668.4	-	2	113	c.29G>A	c.(28-30)aGc>aAc	p.S10N	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)		GACGGGGCTGCTCCCAGCAGA	0.577																																					p.S10N		Atlas-SNP	.											.	ETS1	123	.	0			c.G29A						PASS	.						46	53	51					11																	128442997		1565	3577	5142	SO:0001583	missense	2113	exon2			GGGCTGCTCCCAG		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.29G>A	11.37:g.128442997C>T	ENSP00000376436:p.Ser10Asn	101	0	0		70	21	0.3	NM_001143820	A9UL17|F5GYX9|Q14278|Q16080|Q6N087|Q96AC5	Missense_Mutation	SNP	ENST00000392668.4	37	CCDS44767.1	.	.	.	.	.	.	.	.	.	.	C	11.62	1.693001	0.30052	.	.	ENSG00000134954	ENST00000392668	T	0.12569	2.67	5.25	3.4	0.38934	.	0.224065	0.36034	N	0.002835	T	0.08313	0.0207	.	.	.	0.09310	N	0.99999	B	0.02656	0.0	B	0.01281	0.0	T	0.32188	-0.9916	9	0.24483	T	0.36	.	7.9729	0.30138	0.0:0.8177:0.0:0.1823	.	10	Q6N087	.	N	10	ENSP00000376436:S10N	ENSP00000376436:S10N	S	-	2	0	ETS1	127948207	0.002000	0.14202	0.002000	0.10522	0.012000	0.07955	1.224000	0.32539	0.915000	0.36847	-0.136000	0.14681	AGC	.	.	none		0.577	ETS1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386267.2	NM_005238		T	128442997	C	T	128442997	3	4	21	1	0	0	0	0	1	0	0	0	5277	797	28	2	1550	2	ETS1	11	128442997	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	2280073	128442997	6563519	99	2842											
MLL2	8085	hgsc.bcm.edu	37	chr12	49433749	49433750	+	Frame_Shift_Del	DEL	CT	CT	-																															ggacagcccatagctctcccCtgtggacccgctgctgggcc																										TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr12:49433749_49433750delCT	ENST00000301067.7	-	31	7802_7803	c.7803_7804delAG	c.(7801-7806)acagggfs	p.G2602fs	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2602	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)										TAGCTCTCCCCTGTGGACCCGC	0.663																																					p.2602_2602del		Pindel,Atlas-Indel	.											.	MLL2	1173	.	0			c.7804_7805del						PASS	.																																			SO:0001589	frameshift_variant	8085	exon31			.	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.7803_7804delAG	12.37:g.49433749_49433750delCT	ENSP00000301067:p.Gly2602fs	85	0	.		54	18	0.333	NM_003482	O14687	Frame_Shift_Del	DEL	ENST00000301067.7	37	CCDS44873.1																																																																																			.	.	none		0.663	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			-	49433750	CT	-	49433749	7	5	21	1	0	1	0	1	0	0	0	0	9630	681	24	0	8905	0	MLL2	12	49433749	Frame_Shift_Del	DEL	CT	TCGA-FM-8000-01A-11D-2210-10		49433749	84418146	100	2843											
PRPF40B	25766	hgsc.bcm.edu	37	chr12	50026835	50026835	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgtggccccagatgggcgCatctactactacaatgctga	10	9	10	12	1	1	2	0	1	1	1	1	2	1	2	2	2	4	2	2	2	4	3			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr12:50026835C>T	ENST00000380281.1	+	6	385	c.321C>T	c.(319-321)cgC>cgT	p.R107R	PRPF40B_ENST00000261897.1_Silent_p.R101R|PRPF40B_ENST00000548825.2_Silent_p.R129R			Q6NWY9	PR40B_HUMAN	PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae)	107	WW 1. {ECO:0000255|PROSITE- ProRule:PRU00224}.				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						CAGATGGGCGCATCTACTACT	0.612																																					p.R129R		Atlas-SNP	.											.	PRPF40B	83	.	0			c.C387T						PASS	.						35	31	32					12																	50026835		2203	4299	6502	SO:0001819	synonymous_variant	25766	exon7			TGGGCGCATCTAC	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.321C>T	12.37:g.50026835C>T		86	0	0		61	17	0.278689	NM_001031698	O75401|Q6PI09|Q6ZWB3|Q8NCZ1|Q9H5G4|Q9NT95	Silent	SNP	ENST00000380281.1	37																																																																																				.	.	none		0.612	PRPF40B-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000404838.1	NM_012272		T	50026835	C	T	50026835	2	4	21	1	0	0	0	0	0	0	0	1	12584	697	25	2		2	PRPF40B	12	50026835	Silent	SNP	C	TCGA-FM-8000-01A-11D-2210-10	593086	50026835	83825060	101	2844											
R3HDM2	22864	hgsc.bcm.edu	37	chr12	57690294	57690294	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tacccggtgtaatagcatccGgtgatatgaggtcatctgag	10	11	12	8	2	2	3	1	3	1	0	3	3	3	3	2	3	2	2	2	3	4	4			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr12:57690294G>A	ENST00000347140.3	-	9	991	c.601C>T	c.(601-603)Cgg>Tgg	p.R201W	RP11-123K3.4_ENST00000548184.1_5'Flank|R3HDM2_ENST00000358907.2_Missense_Mutation_p.R201W|R3HDM2_ENST00000403821.2_Missense_Mutation_p.R201W|R3HDM2_ENST00000413953.2_5'Flank|R3HDM2_ENST00000402412.1_Missense_Mutation_p.R201W			Q9Y2K5	R3HD2_HUMAN	R3H domain containing 2	201	R3H. {ECO:0000255|PROSITE- ProRule:PRU00382}.					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						AATAGCATCCGGTGATATGAG	0.408																																					p.R201W		Atlas-SNP	.											.	R3HDM2	125	.	0			c.C601T						PASS	.						118	92	100					12																	57690294		692	1591	2283	SO:0001583	missense	22864	exon7			GCATCCGGTGATA	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.601C>T	12.37:g.57690294G>A	ENSP00000317903:p.Arg201Trp	134	0	0		69	17	0.246377	NM_014925	Q2M1T9|Q3ZCT5	Missense_Mutation	SNP	ENST00000347140.3	37	CCDS8937.2	.	.	.	.	.	.	.	.	.	.	G	21.7	4.185177	0.78677	.	.	ENSG00000179912	ENST00000347140;ENST00000402412;ENST00000358907;ENST00000403821;ENST00000547262	D;D;D;D;D	0.99098	-5.42;-5.42;-5.42;-5.42;-5.42	4.79	4.79	0.61399	Single-stranded nucleic acid binding R3H (3);	0.000000	0.85682	D	0.000000	D	0.99239	0.9735	M	0.88105	2.93	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.98758	1.0723	9	.	.	.	-20.0351	10.7182	0.46026	0.0:0.0:0.7054:0.2946	.	201;201	B5MCU0;Q9Y2K5	.;R3HD2_HUMAN	W	201;201;201;201;89	ENSP00000317903:R201W;ENSP00000385839:R201W;ENSP00000351784:R201W;ENSP00000385169:R201W;ENSP00000450411:R89W	.	R	-	1	2	R3HDM2	55976561	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.007000	0.49536	2.653000	0.90120	0.655000	0.94253	CGG	.	.	none		0.408	R3HDM2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326570.2	NM_014925		A	57690294	G	A	57690294	3	1	21	1	0	0	0	0	1	0	0	0	12903	1115	39	1	2393	1	R3HDM2	12	57690294	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	7663459	57690294	76161601	102	2845											
CEP290	80184	hgsc.bcm.edu	37	chr12	88483187	88483187	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgactccaacttaccaagAgcagtagcctcactcagttg	12	10	7	12	0	2	2	2	1	0	1	3	2	3	2	3	0	4	3	3	0	4	4			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr12:88483187A>G	ENST00000552810.1	-	31	3994	c.3651T>C	c.(3649-3651)gcT>gcC	p.A1217A	CEP290_ENST00000397838.3_Silent_p.A277A|CEP290_ENST00000547691.2_Silent_p.A277A|CEP290_ENST00000309041.7_Silent_p.A1219A	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	1217					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						ACTTACCAAGAGCAGTAGCCT	0.393																																					p.A1217A		Atlas-SNP	.											.	CEP290	195	.	0			c.T3651C						PASS	.						54	52	52					12																	88483187		1885	4119	6004	SO:0001819	synonymous_variant	80184	exon31			ACCAAGAGCAGTA	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.3651T>C	12.37:g.88483187A>G		132	0	0		100	4	0.04	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Silent	SNP	ENST00000552810.1	37	CCDS55858.1																																																																																			.	.	none		0.393	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		G	88483187	A	G	88483187	2	3	21	1	0	0	0	0	0	0	0	1	3255	291	11	3		3	CEP290	12	88483187	Silent	SNP	A	TCGA-FM-8000-01A-11D-2210-10	30792893	88483187	45368708	103	2846											
TMPO	7112	hgsc.bcm.edu	37	chr12	98931352	98931352	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagagttgagcacaatcaggTatctttagttttattaccac	13	14	7	7	0	2	2	1	1	1	1	2	2	2	2	1	1	2	4	1	1	6	7			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr12:98931352T>C	ENST00000556029.1	+	4	1019		c.e4+2		TMPO_ENST00000343315.5_Splice_Site|TMPO_ENST00000393053.2_Splice_Site|TMPO_ENST00000261210.5_Missense_Mutation_p.V222A	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						CACAATCAGGTATCTTTAGTT	0.413																																					.		Atlas-SNP	.											.	TMPO	111	.	0			c.663+2T>C						PASS	.						95	88	90					12																	98931352		2203	4300	6503	SO:0001630	splice_region_variant	7112	exon4			ATCAGGTATCTTT		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.663+2T>C	12.37:g.98931352T>C		71	0	0		68	27	0.397059	NM_001032284	A2T926|Q14861	Splice_Site	SNP	ENST00000556029.1	37	CCDS31879.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.7|20.7	4.038827|4.038827	0.75617|0.75617	.|.	.|.	ENSG00000120802|ENSG00000120802	ENST00000556029;ENST00000343315;ENST00000393053;ENST00000556678|ENST00000261210	.|T	.|0.75589	.|-0.95	5.76|5.76	5.76|5.76	0.90799|0.90799	.|.	.|.	.|.	.|.	.|.	.|D	.|0.85754	.|0.5770	.|.	.|.	.|.	0.30616|0.30616	N|N	0.759|0.759	.|D	.|0.69078	.|0.997	.|D	.|0.72625	.|0.978	.|D	.|0.84747	.|0.0754	.|7	.|.	.|.	.|.	.|.	16.0796|16.0796	0.80995|0.80995	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|222	.|A2T926	.|.	.|A	-1|222	.|ENSP00000261210:V222A	.|.	.|V	+|+	.|2	.|0	TMPO|TMPO	97455483|97455483	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.893000|0.893000	0.52053|0.52053	5.448000|5.448000	0.66612|0.66612	2.195000|2.195000	0.70347|0.70347	0.528000|0.528000	0.53228|0.53228	.|GTA	.	.	none		0.413	TMPO-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407973.2	NM_003276	Intron	C	98931352	T	C	98931352	5	2	21	1	0	0	0	0	0	0	1	0	16252	1652	57	3	2203	3	TMPO	12	98931352	Splice_Site	SNP	T	TCGA-FM-8000-01A-11D-2210-10	10448165	98931352	34920543	104	2847											
KSR2	283455	hgsc.bcm.edu	37	chr12	117962801	117962801	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctctcaatgtcaatcagcCggatggccacctcgccatgc	8	8	8	17	2	3	0	3	0	1	0	5	1	3	1	5	2	2	0	5	2	2	0			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr12:117962801C>T	ENST00000339824.5	-	14	2802	c.2075G>A	c.(2074-2076)cGg>cAg	p.R692Q	KSR2_ENST00000545002.1_5'UTR|KSR2_ENST00000425217.1_Missense_Mutation_p.R663Q|KSR2_ENST00000302438.5_Missense_Mutation_p.R389Q			Q6VAB6	KSR2_HUMAN	kinase suppressor of ras 2	692	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)					GTCAATCAGCCGGATGGCCAC	0.597																																					p.R663Q		Atlas-SNP	.											.	KSR2	208	.	0			c.G1988A						PASS	.						54	58	56					12																	117962801		2111	4213	6324	SO:0001583	missense	283455	exon14			ATCAGCCGGATGG	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.2075G>A	12.37:g.117962801C>T	ENSP00000339952:p.Arg692Gln	139	0	0		84	38	0.452381	NM_173598	A0PJT2|Q3B828|Q8N775	Missense_Mutation	SNP	ENST00000339824.5	37		.	.	.	.	.	.	.	.	.	.	C	28.4	4.917300	0.92249	.	.	ENSG00000171435	ENST00000425217;ENST00000339824;ENST00000302438;ENST00000542378	D;D;D	0.89681	-2.55;-2.55;-2.55	4.98	4.09	0.47781	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.91898	0.7435	L	0.48362	1.52	0.53688	D	0.99997	D	0.89917	1.0	D	0.97110	1.0	D	0.92456	0.5974	10	0.72032	D	0.01	.	13.6616	0.62370	0.0:0.9254:0.0:0.0746	.	692	Q6VAB6	KSR2_HUMAN	Q	663;692;389;364	ENSP00000389715:R663Q;ENSP00000339952:R692Q;ENSP00000305466:R389Q	ENSP00000305466:R389Q	R	-	2	0	KSR2	116447184	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	5.933000	0.70130	1.328000	0.45358	-0.143000	0.13931	CGG	.	.	none		0.597	KSR2-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401987.2	NM_173598		T	117962801	C	T	117962801	3	4	21	1	0	0	0	0	1	0	0	0	8591	652	23	1	805	1	KSR2	12	117962801	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	19031449	117962801	15889094	105	2848											
MBNL2	10150	hgsc.bcm.edu	37	chr13	97928659	97928660	+	Frame_Shift_Ins	INS	-	-	AA																															attgcctgctttgattccctINSaaaggtaagagaatgcgttt																								rs139620750		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr13:97928659_97928660insAA	ENST00000376673.3	+	2	951_952	c.170_171insAA	c.(169-174)ctaaagfs	p.LK57fs	MBNL2_ENST00000397601.1_Frame_Shift_Ins_p.LK57fs|MBNL2_ENST00000445661.2_Frame_Shift_Ins_p.LK57fs|MBNL2_ENST00000345429.6_Frame_Shift_Ins_p.LK57fs|MBNL2_ENST00000343600.4_Frame_Shift_Ins_p.LK57fs			Q5VZF2	MBNL2_HUMAN	muscleblind-like splicing regulator 2	57					mRNA processing (GO:0006397)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(4)|lung(7)|prostate(1)|skin(1)	17	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.218)			TTTGATTCCCTAAAGGTAAGAG	0.371																																					p.L57fs		Pindel,Atlas-Indel	.											.	MBNL2	84	.	0			c.170_171insAA						PASS	.																																			SO:0001589	frameshift_variant	10150	exon2			.	AF061261	CCDS9483.1, CCDS9484.1	13q31.1	2013-01-18	2012-02-23		ENSG00000139793	ENSG00000139793		"Zinc fingers, CCCH-type domain containing"	16746	protein-coding gene	gene with protein product		607327	"muscleblind-like 2 (Drosophila)"			11929853	Standard	NM_207304		Approved	MBLL, MBLL39	uc001vmz.4	Q5VZF2	OTTHUMG00000017239	ENST00000376673.3:c.171_172dupAA	13.37:g.97928660_97928661dupAA	ENSP00000365861:p.Leu57fs	147	0	.		106	37	0.349	NM_207304	Q3SXY5|Q58F19|Q8NEV3|Q8TD82	Frame_Shift_Ins	INS	ENST00000376673.3	37																																																																																				.	.	none		0.371	MBNL2-202	KNOWN	basic	protein_coding	protein_coding		NM_144778		AA	97928660	-	AA	97928659	7	5	21	1	0	1	1	0	0	0	0	0	9363	1522	53	0	172	0	MBNL2	13	97928659	Frame_Shift_Ins	INS	-	TCGA-FM-8000-01A-11D-2210-10		97928659	17241219	106	2849											
ERCC5	2073	hgsc.bcm.edu	37	chr13	103515306	103515306	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtagataatgtggaaaatGtggtgtcatttaatgctaaa	15	13	10	3	0	1	1	1	0	0	1	1	2	1	2	0	2	1	2	0	2	7	5			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr13:103515306G>A	ENST00000355739.4	+	8	3230	c.1807G>A	c.(1807-1809)Gtg>Atg	p.V603M	ERCC5_ENST00000375954.1_5'Flank|BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.C1028Y	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	603					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)					TGTGGAAAATGTGGTGTCATT	0.408			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.V1057M		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.G3169A						PASS	.						79	76	77					13																	103515306		2203	4300	6503	SO:0001583	missense	0	exon16	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	GAAAATGTGGTGT	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.1807G>A	13.37:g.103515306G>A	ENSP00000347978:p.Val603Met	124	0	0		95	30	0.315789	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Missense_Mutation	SNP	ENST00000355739.4	37	CCDS32004.1	.	.	.	.	.	.	.	.	.	.	G	16.21	3.058536	0.55325	.	.	ENSG00000134899	ENST00000418659;ENST00000355739;ENST00000375955	T	0.05081	3.5	5.72	4.01	0.46588	.	1.630770	0.03085	N	0.158987	T	0.10723	0.0262	L	0.43152	1.355	0.09310	N	0.999999	P;P;P	0.46395	0.868;0.744;0.877	P;B;B	0.45506	0.483;0.31;0.365	T	0.26155	-1.0111	10	0.40728	T	0.16	-0.086	7.6996	0.28615	0.2635:0.0:0.7365:0.0	.	603;603;1028	B4DSI5;P28715;Q59FZ7	.;ERCC5_HUMAN;.	M	1028;603;435	ENSP00000347978:V603M	ENSP00000347978:V603M	V	+	1	0	ERCC5	102313307	0.000000	0.05858	0.002000	0.10522	0.455000	0.32408	0.187000	0.16998	0.791000	0.33826	-0.186000	0.12905	GTG	.	.	none		0.408	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1			A	103515306	G	A	103515306	3	1	21	1	0	0	0	0	1	0	0	0	5218	1377	48	2	1837	2	ERCC5	13	103515306	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	5586647	103515306	11654572	107	2850											
C14orf28	122525	hgsc.bcm.edu	37	chr14	45370114	45370114	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gagttactgttccaactggcGatgcccaactcgagtgcagg	9	9	12	11	2	0	0	0	0	0	0	2	3	1	0	2	2	5	3	2	2	3	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr14:45370114G>A	ENST00000325192.3	+	2	751	c.476G>A	c.(475-477)cGa>cAa	p.R159Q	C14orf28_ENST00000557112.1_Missense_Mutation_p.R159Q|C14orf28_ENST00000553841.1_3'UTR|RP11-857B24.5_ENST00000555157.1_RNA	NM_001017923.1	NP_001017923.1	Q4W4Y0	CN028_HUMAN	chromosome 14 open reading frame 28	159								p.R159L(1)		endometrium(1)|large_intestine(3)|liver(1)|lung(4)|ovary(2)	11						TCCAACTGGCGATGCCCAACT	0.343																																					p.R159Q		Atlas-SNP	.											C14orf28,NS,carcinoma,0,1	C14orf28	32	1	1	Substitution - Missense(1)	lung(1)	c.G476A						PASS	.						70	72	72					14																	45370114		2203	4300	6503	SO:0001583	missense	122525	exon2			ACTGGCGATGCCC	AA496212	CCDS32069.1	14q21.2	2012-08-16			ENSG00000179476	ENSG00000179476			19834	protein-coding gene	gene with protein product	"dopamine receptor interacting protein 1"						Standard	XM_005267316		Approved	DRIP-1	uc001wvo.3	Q4W4Y0	OTTHUMG00000170722	ENST00000325192.3:c.476G>A	14.37:g.45370114G>A	ENSP00000326846:p.Arg159Gln	88	0	0		85	31	0.364706	NM_001017923		Missense_Mutation	SNP	ENST00000325192.3	37	CCDS32069.1	.	.	.	.	.	.	.	.	.	.	G	13.22	2.173338	0.38413	.	.	ENSG00000179476	ENST00000325192;ENST00000557112	T;T	0.30714	1.52;1.52	5.86	4.96	0.65561	.	0.227351	0.44285	D	0.000467	T	0.12433	0.0302	N	0.08118	0	0.27714	N	0.945356	P	0.37176	0.586	B	0.21360	0.034	T	0.09907	-1.0653	10	0.40728	T	0.16	.	9.7082	0.40229	0.1595:0.0:0.8405:0.0	.	159	Q4W4Y0	CN028_HUMAN	Q	159	ENSP00000326846:R159Q;ENSP00000451791:R159Q	ENSP00000326846:R159Q	R	+	2	0	C14orf28	44439864	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.525000	0.53502	1.592000	0.50018	0.650000	0.86243	CGA	.	.	none		0.343	C14orf28-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410086.1	NM_001017923		A	45370114	G	A	45370114	3	1	21	1	0	0	0	0	1	0	0	0	1772	1058	37	1	478	1	C14orf28	14	45370114	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10		45370114	61979426	108	2851											
PRPF39	55015	hgsc.bcm.edu	37	chr14	45579854	45579854	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aagtttagaacgacggcatgGaaatctggaagaagctgaac	16	7	12	6	2	1	3	0	1	1	2	1	6	1	5	0	3	3	3	0	3	7	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr14:45579854G>A	ENST00000355765.6	+	10	1576	c.1406G>A	c.(1405-1407)gGa>gAa	p.G469E	SNORD127_ENST00000458892.1_RNA	NM_017922.3	NP_060392.3	Q86UA1	PRP39_HUMAN	pre-mRNA processing factor 39	469					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(4)|lung(3)|ovary(1)	12						CGACGGCATGGAAATCTGGAA	0.368																																					p.G469E		Atlas-SNP	.											.	PRPF39	46	.	0			c.G1406A						PASS	.						46	39	41					14																	45579854		2202	4299	6501	SO:0001583	missense	55015	exon10			GGCATGGAAATCT	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.1406G>A	14.37:g.45579854G>A	ENSP00000348010:p.Gly469Glu	194	0	0		135	62	0.459259	NM_017922	Q08AL1|Q08AL2|Q9NUU5	Missense_Mutation	SNP	ENST00000355765.6	37	CCDS9682.2	.	.	.	.	.	.	.	.	.	.	G	24.2	4.510464	0.85389	.	.	ENSG00000185246	ENST00000355765	T	0.38722	1.12	5.53	5.53	0.82687	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.64260	0.2582	M	0.78456	2.415	0.80722	D	1	D;D	0.89917	1.0;0.995	D;P	0.87578	0.998;0.844	T	0.59579	-0.7428	10	0.09843	T	0.71	-13.7778	19.0642	0.93103	0.0:0.0:1.0:0.0	.	73;469	Q86UA1-2;Q86UA1	.;PRP39_HUMAN	E	469	ENSP00000348010:G469E	ENSP00000348010:G469E	G	+	2	0	PRPF39	44649604	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.824000	0.99380	2.607000	0.88179	0.563000	0.77884	GGA	.	.	none		0.368	PRPF39-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319683.2			A	45579854	G	A	45579854	3	1	21	1	0	0	0	0	1	0	0	0	12581	1174	41	2	1440	2	PRPF39	14	45579854	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	209740	45579854	61769686	109	2852											
MAP4K5	11183	hgsc.bcm.edu	37	chr14	50901153	50901153	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgaagatgcagagttcaaaTtgattgtctcaaactgaact	15	12	8	6	0	2	5	2	3	1	2	3	5	2	5	0	0	3	2	0	0	4	3			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr14:50901153T>C	ENST00000013125.4	-	27	2441	c.2123A>G	c.(2122-2124)aAt>aGt	p.N708S		NM_006575.4|NM_198794.2	NP_006566.2|NP_942089.1	Q9Y4K4	M4K5_HUMAN	mitogen-activated protein kinase kinase kinase kinase 5	708	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)					AGAGTTCAAATTGATTGTCTC	0.348																																					p.N708S		Atlas-SNP	.											.	MAP4K5	48	.	0			c.A2123G						PASS	.						85	73	77					14																	50901153		1864	4096	5960	SO:0001583	missense	11183	exon27			TTCAAATTGATTG	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.2123A>G	14.37:g.50901153T>C	ENSP00000013125:p.Asn708Ser	88	0	0		68	32	0.470588	NM_006575	Q8IYF6	Missense_Mutation	SNP	ENST00000013125.4	37		.	.	.	.	.	.	.	.	.	.	T	21.9	4.222735	0.79464	.	.	ENSG00000012983	ENST00000013125	T	0.05025	3.51	4.96	4.96	0.65561	Citron-like (3);	0.000000	0.85682	D	0.000000	T	0.27454	0.0674	M	0.82823	2.61	0.80722	D	1	D;D	0.76494	0.995;0.999	D;D	0.79108	0.958;0.992	T	0.03662	-1.1015	10	0.62326	D	0.03	.	14.6592	0.68858	0.0:0.0:0.0:1.0	.	708;708	B2R928;Q9Y4K4	.;M4K5_HUMAN	S	708	ENSP00000013125:N708S	ENSP00000013125:N708S	N	-	2	0	MAP4K5	49970903	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.991000	0.88244	1.861000	0.53984	0.454000	0.30748	AAT	.	.	none		0.348	MAP4K5-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000410880.1	NM_006575		C	50901153	T	C	50901153	3	2	21	1	0	0	0	0	1	0	0	0	9272	1493	52	3	441	3	MAP4K5	14	50901153	Missense_Mutation	SNP	T	TCGA-FM-8000-01A-11D-2210-10	5321299	50901153	56448387	110	2853											
SMOC1	64093	hgsc.bcm.edu	37	chr14	70459149	70459149	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcagatgacgggtctaagcCgacacccacgatggagaccc	11	6	11	13	3	2	3	1	1	1	2	2	6	2	3	3	2	1	0	3	2	1	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr14:70459149C>T	ENST00000381280.4	+	6	795	c.542C>T	c.(541-543)cCg>cTg	p.P181L	SMOC1_ENST00000361956.3_Missense_Mutation_p.P181L	NM_001034852.2|NM_022137.5	NP_001030024.1|NP_071420.1	Q9H4F8	SMOC1_HUMAN	SPARC related modular calcium binding 1	181					cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|eye development (GO:0001654)|limb development (GO:0060173)|positive regulation of cell-substrate adhesion (GO:0010811)|regulation of osteoblast differentiation (GO:0045667)|signal transduction (GO:0007165)	basement membrane (GO:0005604)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	21				all cancers(60;0.00417)|BRCA - Breast invasive adenocarcinoma(234;0.0119)|OV - Ovarian serous cystadenocarcinoma(108;0.028)		GGGTCTAAGCCGACACCCACG	0.438																																					p.P181L		Atlas-SNP	.											.	SMOC1	61	.	0			c.C542T						PASS	.						146	147	146					14																	70459149		2203	4300	6503	SO:0001583	missense	64093	exon6			CTAAGCCGACACC	AJ249900	CCDS9798.1, CCDS32110.1	14q24.1	2010-08-05			ENSG00000198732	ENSG00000198732			20318	protein-coding gene	gene with protein product		608488				12130637	Standard	NM_001034852		Approved		uc001xlt.2	Q9H4F8		ENST00000381280.4:c.542C>T	14.37:g.70459149C>T	ENSP00000370680:p.Pro181Leu	110	0	0		79	4	0.0506329	NM_001034852	A8K1S3|B2R7P5|Q96F78	Missense_Mutation	SNP	ENST00000381280.4	37	CCDS9798.1	.	.	.	.	.	.	.	.	.	.	C	19.90	3.912646	0.72983	.	.	ENSG00000198732	ENST00000361956;ENST00000381280	T;T	0.57273	0.41;0.41	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.60534	0.2276	L	0.29908	0.895	0.80722	D	1	P;D	0.89917	0.519;1.0	B;D	0.85130	0.175;0.997	T	0.52305	-0.8593	10	0.11485	T	0.65	-15.2578	18.9026	0.92449	0.0:1.0:0.0:0.0	.	181;181	Q9H4F8-2;Q9H4F8	.;SMOC1_HUMAN	L	181	ENSP00000355110:P181L;ENSP00000370680:P181L	ENSP00000355110:P181L	P	+	2	0	SMOC1	69528902	1.000000	0.71417	0.999000	0.59377	0.980000	0.70556	7.703000	0.84585	2.478000	0.83669	0.555000	0.69702	CCG	.	.	none		0.438	SMOC1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000412467.1			T	70459149	C	T	70459149	3	4	21	1	0	0	0	0	1	0	0	0	14816	652	23	1	564	1	SMOC1	14	70459149	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	19557996	70459149	36890391	111	2854											
SIPA1L1	26037	hgsc.bcm.edu	37	chr14	72190600	72190600	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgtgggatttatggacacgaGaaagtaagagttactttcct	12	12	11	6	2	0	2	0	0	0	2	1	5	1	4	1	2	1	2	1	2	4	5			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr14:72190600G>A	ENST00000555818.1	+	16	4856	c.4508G>A	c.(4507-4509)aGa>aAa	p.R1503K	SIPA1L1_ENST00000554874.1_3'UTR|SIPA1L1_ENST00000381232.3_Missense_Mutation_p.R1482K|SIPA1L1_ENST00000537413.1_Missense_Mutation_p.R957K|SIPA1L1_ENST00000358550.2_Missense_Mutation_p.R1482K	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	1503					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)		ATGGACACGAGAAAGTAAGAG	0.473																																					p.R1503K		Atlas-SNP	.											.	SIPA1L1	219	.	0			c.G4508A						PASS	.						62	69	67					14																	72190600		2203	4300	6503	SO:0001583	missense	26037	exon16			ACACGAGAAAGTA	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.4508G>A	14.37:g.72190600G>A	ENSP00000450832:p.Arg1503Lys	61	0	0		37	12	0.324324	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Missense_Mutation	SNP	ENST00000555818.1	37	CCDS9807.1	.	.	.	.	.	.	.	.	.	.	G	12.78	2.041335	0.35989	.	.	ENSG00000197555	ENST00000381232;ENST00000555818;ENST00000358550;ENST00000537413	T;T;T;D	0.83673	-0.92;-0.91;-0.92;-1.75	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	D	0.82614	0.5075	N	0.16368	0.405	0.80722	D	1	P;P;B;P;B	0.52842	0.885;0.956;0.063;0.942;0.127	P;P;B;P;B	0.62184	0.465;0.899;0.034;0.573;0.161	T	0.77635	-0.2514	10	0.12430	T	0.62	-26.2712	19.4992	0.95086	0.0:0.0:1.0:0.0	.	957;1503;957;1482;1503	F5GYF8;A6H8W6;B4DYX7;O43166-2;O43166	.;.;.;.;SI1L1_HUMAN	K	1482;1503;1482;957	ENSP00000370630:R1482K;ENSP00000450832:R1503K;ENSP00000351352:R1482K;ENSP00000440682:R957K	ENSP00000351352:R1503K	R	+	2	0	SIPA1L1	71260353	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.184000	0.94893	2.689000	0.91719	0.655000	0.94253	AGA	.	.	none		0.473	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		A	72190600	G	A	72190600	3	1	21	1	0	0	0	0	1	0	0	0	14344	942	33	2	4566	2	SIPA1L1	14	72190600	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	1731451	72190600	35158940	112	2855											
CCDC88C	440193	hgsc.bcm.edu	37	chr14	91770135	91770135	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagggcctcgtactcggccGattgccgctcgtgcagcgtg	4	9	15	13	6	0	1	0	1	0	0	3	2	0	1	3	2	4	3	3	2	1	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr14:91770135G>T	ENST00000389857.6	-	20	3631	c.3545C>A	c.(3544-3546)tCg>tAg	p.S1182*		NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	1182					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)				GTACTCGGCCGATTGCCGCTC	0.637																																					p.S1182X		Atlas-SNP	.											CCDC88C_ENST00000389857,caecum,carcinoma,+1,2	CCDC88C	192	2	0			c.C3545A						PASS	.						52	56	55					14																	91770135		2129	4235	6364	SO:0001587	stop_gained	440193	exon20			TCGGCCGATTGCC		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.3545C>A	14.37:g.91770135G>T	ENSP00000374507:p.Ser1182*	84	0	0		71	29	0.408451	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Nonsense_Mutation	SNP	ENST00000389857.6	37	CCDS45151.1	.	.	.	.	.	.	.	.	.	.	G	44	10.628605	0.99440	.	.	ENSG00000015133	ENST00000389857	.	.	.	5.37	4.47	0.54385	.	0.141481	0.32563	U	0.005935	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	-16.2203	15.9444	0.79782	0.0:0.1467:0.8533:0.0	.	.	.	.	X	1182	.	ENSP00000374507:S1182X	S	-	2	0	CCDC88C	90839888	1.000000	0.71417	0.851000	0.33527	0.827000	0.46813	7.740000	0.84986	1.376000	0.46267	0.561000	0.74099	TCG	.	.	none		0.637	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353		T	91770135	G	T	91770135	4	4	21	1	0	0	0	0	0	1	0	0	2867	1059	37	4	2585	4	CCDC88C	14	91770135	Nonsense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	19579535	91770135	15579405	113	2856											
HERC2	8924	hgsc.bcm.edu	37	chr15	28366537	28366537	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggccatgctgacgatcgcgTaccatagttgcttgtactac	8	11	11	11	3	0	1	0	1	0	0	1	2	0	1	2	1	5	5	2	1	4	6			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr15:28366537T>C	ENST00000261609.7	-	86	13335	c.13227A>G	c.(13225-13227)gtA>gtG	p.V4409V		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)		GACGATCGCGTACCATAGTTG	0.468																																					p.V4409V		Atlas-SNP	.											.	HERC2	501	.	0			c.A13227G						PASS	.						135	124	128					15																	28366537		2203	4300	6503	SO:0001819	synonymous_variant	8924	exon86			ATCGCGTACCATA	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.13227A>G	15.37:g.28366537T>C		115	0	0		75	4	0.0533333	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			.	.	none		0.468	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		C	28366537	T	C	28366537	2	2	21	1	0	0	0	0	0	0	0	1	7067	1625	57	3		3	HERC2	15	28366537	Silent	SNP	T	TCGA-FM-8000-01A-11D-2210-10		28366537	74164855	114	2857											
B2M	567	hgsc.bcm.edu	37	chr15	45007681	45007681	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatggaaagtcaaatttccTgaattgctatgtgtctgggt	11	14	11	5	0	2	1	1	1	1	0	3	3	3	2	1	2	1	1	1	2	5	3			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr15:45007681T>G	ENST00000558401.1	+	2	198	c.128T>G	c.(127-129)cTg>cGg	p.L43R	B2M_ENST00000559916.1_Missense_Mutation_p.L43R|B2M_ENST00000544417.1_Missense_Mutation_p.L43R|B2M_ENST00000559220.1_Intron	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	43	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 exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|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 T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|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)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)	p.L43P(1)		breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		TCAAATTTCCTGAATTGCTAT	0.408																																					p.L43R		Atlas-SNP	.											B2M,colon,carcinoma,0,2	B2M	99	2	1	Substitution - Missense(1)	breast(1)	c.T128G						PASS	.						176	180	178					15																	45007681		2198	4298	6496	SO:0001583	missense	567	exon2			ATTTCCTGAATTG	AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"Immunoglobulin superfamily / C1-set domain containing"	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.128T>G	15.37:g.45007681T>G	ENSP00000452780:p.Leu43Arg	109	0	0		81	67	0.82716	NM_004048	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Missense_Mutation	SNP	ENST00000558401.1	37	CCDS10113.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.001047	0.74818	.	.	ENSG00000166710	ENST00000349264;ENST00000544417;ENST00000396754	T	0.22539	1.95	6.03	6.03	0.97812	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.595751	0.18761	N	0.131892	T	0.63954	0.2555	H	0.98594	4.275	0.58432	D	0.99999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.76777	-0.2834	10	0.87932	D	0	.	12.95	0.58394	0.0:0.0:0.0:1.0	.	43;43;43	F5H6I0;A6XMH4;P61769	.;.;B2MG_HUMAN	R	43	ENSP00000437604:L43R	ENSP00000340858:L43R	L	+	2	0	B2M	42794973	0.971000	0.33674	0.101000	0.21167	0.672000	0.39443	4.264000	0.58859	2.308000	0.77769	0.533000	0.62120	CTG	.	.	none		0.408	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048		G	45007681	T	G	45007681	3	3	21	1	0	0	0	0	1	0	0	0	1244	1580	55	5	134	5	B2M	15	45007681	Missense_Mutation	SNP	T	TCGA-FM-8000-01A-11D-2210-10	16641144	45007681	57523711	115	2858											
B2M	567	hgsc.bcm.edu	37	chr15	45007710	45007710	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtgtctgggtttcatccaTccgacattgaagttgactta	9	15	9	8	1	2	2	1	2	1	0	4	3	4	2	2	1	0	2	2	1	2	4			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr15:45007710T>A	ENST00000558401.1	+	2	227	c.157T>A	c.(157-159)Tcc>Acc	p.S53T	B2M_ENST00000559916.1_Missense_Mutation_p.S53T|B2M_ENST00000544417.1_Missense_Mutation_p.S53T|B2M_ENST00000559220.1_Intron	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	53	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 exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|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 T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|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)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		GTTTCATCCATCCGACATTGA	0.403																																					p.S53T		Atlas-SNP	.											B2M,colon,carcinoma,-2,1	B2M	99	1	0			c.T157A						PASS	.						187	191	189					15																	45007710		2198	4298	6496	SO:0001583	missense	567	exon2			CATCCATCCGACA	AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"Immunoglobulin superfamily / C1-set domain containing"	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.157T>A	15.37:g.45007710T>A	ENSP00000452780:p.Ser53Thr	123	0	0		103	87	0.84466	NM_004048	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Missense_Mutation	SNP	ENST00000558401.1	37	CCDS10113.1	.	.	.	.	.	.	.	.	.	.	T	12.86	2.065633	0.36470	.	.	ENSG00000166710	ENST00000349264;ENST00000544417;ENST00000396754	T	0.09073	3.02	6.03	4.15	0.48705	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.101727	0.64402	D	0.000001	T	0.13798	0.0334	L	0.52573	1.65	0.26086	N	0.981025	P;P;B	0.38992	0.653;0.594;0.302	B;P;B	0.47645	0.418;0.553;0.173	T	0.04360	-1.0957	10	0.87932	D	0	.	8.9614	0.35849	0.0:0.8383:0.0:0.1617	.	53;53;53	F5H6I0;A6XMH4;P61769	.;.;B2MG_HUMAN	T	53	ENSP00000437604:S53T	ENSP00000340858:S53T	S	+	1	0	B2M	42795002	0.901000	0.30685	0.893000	0.35052	0.090000	0.18270	2.330000	0.43885	0.866000	0.35629	-0.912000	0.02778	TCC	.	.	none		0.403	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048		A	45007710	T	A	45007710	3	1	21	1	0	0	0	0	1	0	0	0	1244	1435	50	5	163	5	B2M	15	45007710	Missense_Mutation	SNP	T	TCGA-FM-8000-01A-11D-2210-10	29	45007710	57523682	116	2859											
UNKL	64718	hgsc.bcm.edu	37	chr16	1417803	1417803	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcaggatgggggaggggcTgggggagaagctgccggaaa	10	4	21	6	1	1	1	1	0	0	1	1	5	1	4	1	8	2	2	1	8	2	0			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr16:1417803T>C	ENST00000389221.4	-	13	1632	c.1633A>G	c.(1633-1635)Agc>Ggc	p.S545G	UNKL_ENST00000402641.2_Missense_Mutation_p.S47G|UNKL_ENST00000391893.2_Missense_Mutation_p.S44G|UNKL_ENST00000508903.2_Missense_Mutation_p.S548G|UNKL_ENST00000248104.7_Missense_Mutation_p.S44G|UNKL_ENST00000403703.1_Missense_Mutation_p.S47G|UNKL_ENST00000397464.1_Missense_Mutation_p.S47G	NM_001193388.1	NP_001180317	Q9H9P5	UNKL_HUMAN	unkempt family zinc finger-like	545	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)				GGGGAGGGGCTGGGGGAGAAG	0.652																																					p.S548G		Atlas-SNP	.											.	UNKL	46	.	0			c.A1642G						PASS	.						9	9	9					16																	1417803		2180	4274	6454	SO:0001583	missense	64718	exon13			AGGGGCTGGGGGA	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.1633A>G	16.37:g.1417803T>C	ENSP00000373873:p.Ser545Gly	146	0	0		127	73	0.574803	NM_001193388	B0QYN6|B1GXI8|Q96EV1|Q96RZ1|Q9BWL5|Q9H5K0|Q9UJJ8	Missense_Mutation	SNP	ENST00000389221.4	37	CCDS53981.1	.	.	.	.	.	.	.	.	.	.	t	16.06	3.015598	0.54468	.	.	ENSG00000059145	ENST00000248104;ENST00000389221;ENST00000403703;ENST00000391893;ENST00000397464;ENST00000402641;ENST00000508903;ENST00000513783	T;T	0.68331	-0.22;-0.32	4.67	4.67	0.58626	.	.	.	.	.	T	0.74566	0.3733	L	0.49455	1.56	0.80722	D	1	D;D;D	0.76494	0.996;0.999;0.982	P;D;D	0.85130	0.836;0.997;0.952	T	0.71130	-0.4682	9	0.23891	T	0.37	.	12.1563	0.54079	0.0:0.0:0.0:1.0	.	545;44;548	Q9H9P5;Q9H9P5-3;E9PDK2	UNKL_HUMAN;.;.	G	44;545;47;44;47;47;548;47	ENSP00000373873:S545G;ENSP00000380606:S47G	ENSP00000248104:S44G	S	-	1	0	UNKL	1357804	1.000000	0.71417	1.000000	0.80357	0.543000	0.35085	5.503000	0.66962	1.760000	0.52011	0.445000	0.29226	AGC	.	.	none		0.652	UNKL-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001037125		C	1417803	T	C	1417803	3	2	21	1	0	0	0	0	1	0	0	0	17016	1580	55	3	571	3	UNKL	16	1417803	Missense_Mutation	SNP	T	TCGA-FM-8000-01A-11D-2210-10		1417803	88936950	117	2860											
KREMEN2	79412	hgsc.bcm.edu	37	chr16	3014557	3014557	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ctgcagggcttcctctttctCctcttcctcccgctgctgca	2	14	7	18	1	3	0	0	0	3	0	7	0	6	0	4	1	3	5	4	1	0	3			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr16:3014557C>T	ENST00000303746.5	+	1	613	c.36C>T	c.(34-36)ctC>ctT	p.L12L	KREMEN2_ENST00000572045.1_Silent_p.L12L|KREMEN2_ENST00000575885.1_Silent_p.L12L|KREMEN2_ENST00000575769.1_Silent_p.L12L|KREMEN2_ENST00000319500.6_Silent_p.L12L|KREMEN2_ENST00000571007.1_Silent_p.L12L			Q8NCW0	KREM2_HUMAN	kringle containing transmembrane protein 2	12					Wnt signaling pathway (GO:0016055)	integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(1)|large_intestine(1)	4						TCCTCTTTCTCCTCTTCCTCC	0.687																																					p.L12L		Atlas-SNP	.											.	KREMEN2	13	.	0			c.C36T						PASS	.						58	63	61					16																	3014557		2198	4300	6498	SO:0001819	synonymous_variant	79412	exon1			CTTTCTCCTCTTC	BC003533	CCDS10483.1, CCDS10484.1, CCDS58412.1, CCDS58413.1	16p13.11	2008-08-04			ENSG00000131650	ENSG00000131650			18797	protein-coding gene	gene with protein product		609899				12050670	Standard	NM_172229		Approved	MGC10791, KRM2	uc002csg.3	Q8NCW0	OTTHUMG00000128976	ENST00000303746.5:c.36C>T	16.37:g.3014557C>T		144	0	0		136	35	0.257353	NM_001253725	B4DXF6|I3L2S2|Q8N2J4|Q8NCW1|Q96GL8|Q9BTP9	Silent	SNP	ENST00000303746.5	37	CCDS10483.1																																																																																			.	.	none		0.687	KREMEN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250964.2	NM_145347		T	3014557	C	T	3014557	2	4	21	1	0	0	0	0	0	0	0	1	8452	842	30	2		2	KREMEN2	16	3014557	Silent	SNP	C	TCGA-FM-8000-01A-11D-2210-10	1596754	3014557	87340196	118	2861											
ADCY9	115	hgsc.bcm.edu	37	chr16	4016487	4016487	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcgcggtgttcagccctgaCgccgccatgtacgtggctcc	4	9	13	15	5	1	1	1	1	0	0	2	1	2	1	4	2	3	3	4	2	1	2	rs371159341		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr16:4016487C>T	ENST00000294016.3	-	11	3889	c.3351G>A	c.(3349-3351)gcG>gcA	p.A1117A		NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	1117	Guanylate cyclase 2. {ECO:0000255|PROSITE-ProRule:PRU00099}.				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						TCAGCCCTGACGCCGCCATGT	0.617																																					p.A1117A		Atlas-SNP	.											.	ADCY9	151	.	0			c.G3351A						PASS	.	C		0,4394		0,0,2197	87	75	79		3351	-10.2	0.1	16		79	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ADCY9	NM_001116.3		0,1,6496	TT,TC,CC		0.0116,0.0,0.0077		1117/1354	4016487	1,12993	2197	4300	6497	SO:0001819	synonymous_variant	115	exon11			CCCTGACGCCGCC	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.3351G>A	16.37:g.4016487C>T		80	0	0		76	20	0.263158	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Silent	SNP	ENST00000294016.3	37	CCDS32382.1																																																																																			.	.	weak		0.617	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1			T	4016487	C	T	4016487	2	4	21	1	0	0	0	0	0	0	0	1	301	523	19	1		1	ADCY9	16	4016487	Silent	SNP	C	TCGA-FM-8000-01A-11D-2210-10	1001930	4016487	86338266	119	2862											
ITPRIPL2	162073	hgsc.bcm.edu	37	chr16	19126354	19126354	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcttgtggcgctggagccaCggagcctgggcgaggagcca	6	5	18	12	4	0	0	0	0	0	0	0	4	0	3	3	5	3	2	3	5	0	1			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr16:19126354C>T	ENST00000381440.3	+	1	1101	c.571C>T	c.(571-573)Cgg>Tgg	p.R191W	CTD-2349B8.1_ENST00000564808.2_Intron	NM_001034841.3	NP_001030013.1	Q3MIP1	IPIL2_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein-like 2	191						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						GCTGGAGCCACGGAGCCTGGG	0.716											OREG0023657	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R191W		Atlas-SNP	.											.	ITPRIPL2	40	.	0			c.C571T						PASS	.						9	13	11					16																	19126354		2072	4098	6170	SO:0001583	missense	162073	exon1			GAGCCACGGAGCC		CCDS32395.1	16p12.3	2011-04-28	2011-04-28		ENSG00000205730	ENSG00000205730			27257	protein-coding gene	gene with protein product			"inositol 1,4,5-triphosphate receptor interacting protein-like 2"				Standard	NM_001034841		Approved	FLJ22994, MGC126798, MGC126800, LOC162073	uc002dfu.4	Q3MIP1		ENST00000381440.3:c.571C>T	16.37:g.19126354C>T	ENSP00000370849:p.Arg191Trp	5	0	0	730	4	4	1	NM_001034841		Missense_Mutation	SNP	ENST00000381440.3	37	CCDS32395.1	.	.	.	.	.	.	.	.	.	.	C	17.10	3.301907	0.60195	.	.	ENSG00000205730	ENST00000381440	T	0.15603	2.41	4.67	3.67	0.42095	.	0.000000	0.29508	U	0.011950	T	0.25044	0.0608	N	0.24115	0.695	0.37413	D	0.913301	D	0.89917	1.0	D	0.66979	0.948	T	0.14783	-1.0460	10	0.59425	D	0.04	-13.6348	12.7941	0.57551	0.1644:0.8356:0.0:0.0	.	191	Q3MIP1	IPIL2_HUMAN	W	191	ENSP00000370849:R191W	ENSP00000370849:R191W	R	+	1	2	ITPRIPL2	19033855	0.145000	0.22656	0.938000	0.37757	0.804000	0.45430	1.856000	0.39389	2.137000	0.66172	0.655000	0.94253	CGG	.	.	none		0.716	ITPRIPL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435827.3	NM_001034841		T	19126354	C	T	19126354	3	4	21	1	0	0	0	0	1	0	0	0	7934	527	19	1	573	1	ITPRIPL2	16	19126354	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	15109867	19126354	71228399	120	2863											
TBC1D10B	26000	hgsc.bcm.edu	37	chr16	30369466	30369486	+	In_Frame_Del	DEL	CCGCTCCTTCTCCTGTTTCTG	CCGCTCCTTCTCCTGTTTCTG	-																															tgcttctgccgctccttctcCcgctccttctcctgtttctg																								rs144176745|rs549120802		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	CCGCTCCTTCTCCTGTTTCTG	CCGCTCCTTCTCCTGTTTCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr16:30369466_30369486delCCGCTCCTTCTCCTGTTTCTG	ENST00000409939.3	-	9	2286_2306	c.2206_2226delCAGAAACAGGAGAAGGAGCGG	c.(2206-2226)cagaaacaggagaaggagcggdel	p.QKQEKER736del	CD2BP2_ENST00000305596.3_5'Flank|RP11-347C12.10_ENST00000563252.1_lincRNA	NM_015527.3	NP_056342.3	Q4KMP7	TB10B_HUMAN	TBC1 domain family, member 10B	736					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)			gctccttctcccgctccttctcctgtttctgccgctccttc	0.584																																					p.736_743del		Pindel,Atlas-Indel	.											.	TBC1D10B	32	.	0			c.2207_2227del						PASS	.																																			SO:0001651	inframe_deletion	26000	exon9			.	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.2206_2226delCAGAAACAGGAGAAGGAGCGG	16.37:g.30369466_30369486delCCGCTCCTTCTCCTGTTTCTG	ENSP00000386538:p.Gln736_Arg742del	284	0	.		131	21	0.16	NM_015527	B9A6L0|Q6IN54|Q6P530|Q71RG7|Q86VC5|Q9H8Z2|Q9NUN6|Q9UFP2	In_Frame_Del	DEL	ENST00000409939.3	37	CCDS10676.2																																																																																			.	.	none		0.584	TBC1D10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255527.3	NM_015527		-	30369486	CCGCTCCTTCTCCTGTTTCTG	-	30369466	7	5	21	1	0	1	0	1	0	0	0	0	15614	610	22	0	204	0	TBC1D10B	16	30369466	In_Frame_Del	DEL	CCGCTCCTTCTCCTGTTTCTG	TCGA-FM-8000-01A-11D-2210-10	11243112	30369466	59985287	121	2864											
NLRC5	84166	hgsc.bcm.edu	37	chr16	57060777	57060777	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcccctatcaactgccctTccacaatttcccactgacct	8	11	2	20	0	1	1	1	1	0	0	4	1	4	1	7	0	2	0	7	0	3	3			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr16:57060777T>G	ENST00000262510.6	+	6	2147	c.1922T>G	c.(1921-1923)tTc>tGc	p.F641C	NLRC5_ENST00000308149.7_Missense_Mutation_p.F641C|NLRC5_ENST00000436936.1_Missense_Mutation_p.F641C|NLRC5_ENST00000539144.1_Missense_Mutation_p.F641C	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	641					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)				CAACTGCCCTTCCACAATTTC	0.582																																					p.F641C		Atlas-SNP	.											.	NLRC5	186	.	0			c.T1922G						PASS	.						135	104	114					16																	57060777		2198	4300	6498	SO:0001583	missense	84166	exon5			TGCCCTTCCACAA	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.1922T>G	16.37:g.57060777T>G	ENSP00000262510:p.Phe641Cys	145	0	0		161	103	0.639752	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Missense_Mutation	SNP	ENST00000262510.6	37	CCDS10773.1	.	.	.	.	.	.	.	.	.	.	T	16.13	3.035554	0.54896	.	.	ENSG00000140853	ENST00000262510;ENST00000308149;ENST00000436936;ENST00000327982;ENST00000539144;ENST00000538110	T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58	5.52	5.52	0.82312	.	0.000000	0.36200	N	0.002731	T	0.71660	0.3366	M	0.78049	2.395	0.30726	N	0.747709	D;D;D;D	0.89917	1.0;1.0;1.0;0.997	D;D;D;D	0.85130	0.997;0.997;0.996;0.971	T	0.73849	-0.3853	10	0.42905	T	0.14	.	13.3563	0.60629	0.0:0.0:0.0:1.0	.	641;641;641;641	Q86WI3-5;Q86WI3-4;Q86WI3-6;Q86WI3	.;.;.;NLRC5_HUMAN	C	641;641;641;115;641;148	ENSP00000262510:F641C;ENSP00000308886:F641C;ENSP00000389739:F641C;ENSP00000441727:F641C;ENSP00000441597:F148C	ENSP00000262510:F641C	F	+	2	0	NLRC5	55618278	1.000000	0.71417	0.996000	0.52242	0.574000	0.36063	4.416000	0.59815	2.096000	0.63516	0.459000	0.35465	TTC	.	.	none		0.582	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206		G	57060777	T	G	57060777	3	3	21	1	0	0	0	0	1	0	0	0	10479	1783	62	5	1936	5	NLRC5	16	57060777	Missense_Mutation	SNP	T	TCGA-FM-8000-01A-11D-2210-10	26691311	57060777	33293976	122	2865											
ZNF319	57567	hgsc.bcm.edu	37	chr16	58032032	58032032	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggatgccatagacggcacaGcccagggggttctccgccgt	8	6	14	13	3	1	1	0	0	1	1	2	2	1	2	4	4	2	2	4	4	1	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr16:58032032G>T	ENST00000299237.2	-	2	760	c.138C>A	c.(136-138)ggC>ggA	p.G46G	USB1_ENST00000561743.1_5'Flank	NM_020807.1	NP_065858.1	Q9P2F9	ZN319_HUMAN	zinc finger protein 319	46	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)			large_intestine(2)|lung(4)|ovary(1)|urinary_tract(1)	8						AGACGGCACAGCCCAGGGGGT	0.706																																					p.G46G		Atlas-SNP	.											.	ZNF319	42	.	0			c.C138A						PASS	.						42	43	43					16																	58032032		2197	4299	6496	SO:0001819	synonymous_variant	57567	exon2			GGCACAGCCCAGG	AB037809	CCDS32462.1	16q21	2013-01-08				ENSG00000166188		"Zinc fingers, C2H2-type"	13644	protein-coding gene	gene with protein product						10718198, 11161788	Standard	XM_005256069		Approved	KIAA1388, Zfp319	uc002emx.1	Q9P2F9		ENST00000299237.2:c.138C>A	16.37:g.58032032G>T		40	0	0		32	9	0.28125	NM_020807	Q52LH8	Silent	SNP	ENST00000299237.2	37	CCDS32462.1																																																																																			.	.	none		0.706	ZNF319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430317.1			T	58032032	G	T	58032032	2	4	21	1	0	0	0	0	0	0	0	1	17852	958	34	4		4	ZNF319	16	58032032	Silent	SNP	G	TCGA-FM-8000-01A-11D-2210-10	971255	58032032	32322721	123	2866											
PLD2	5338	hgsc.bcm.edu	37	chr17	4718855	4718855	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggctatagcaagagggcgCtgatgctgctgcaccccaac	9	7	13	12	1	0	2	0	1	0	1	0	2	0	2	2	2	5	6	2	2	4	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr17:4718855C>T	ENST00000263088.6	+	13	1389	c.1258C>T	c.(1258-1260)Ctg>Ttg	p.L420L	PLD2_ENST00000572940.1_Silent_p.L420L	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2	420					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)	CAAGAGGGCGCTGATGCTGCT	0.582											OREG0024105	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L420L		Atlas-SNP	.											PLD2_ENST00000263088,bladder,carcinoma,-2,2	PLD2	138	2	0			c.C1258T						PASS	.						250	220	230					17																	4718855		2203	4300	6503	SO:0001819	synonymous_variant	5338	exon13			AGGGCGCTGATGC	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.1258C>T	17.37:g.4718855C>T		156	0	0	621	115	48	0.417391	NM_001243108	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Silent	SNP	ENST00000263088.6	37	CCDS11057.1																																																																																			.	.	none		0.582	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663		T	4718855	C	T	4718855	2	4	21	1	0	0	0	0	0	0	0	1	12055	796	28	2		2	PLD2	17	4718855	Silent	SNP	C	TCGA-FM-8000-01A-11D-2210-10		4718855	76476355	124	2867											
MINK1	50488	hgsc.bcm.edu	37	chr17	4797860	4797860	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aaaggcccctggcaagagctCgttcacgatgtttgtggatc	9	10	12	10	2	1	1	1	0	0	1	3	3	1	2	2	3	1	4	2	3	2	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr17:4797860C>T	ENST00000355280.6	+	24	3045	c.2849C>T	c.(2848-2850)tCg>tTg	p.S950L	MINK1_ENST00000347992.7_Missense_Mutation_p.S921L|MINK1_ENST00000453408.3_Missense_Mutation_p.S930L	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						GGCAAGAGCTCGTTCACGATG	0.602																																					p.S950L		Atlas-SNP	.											.	MINK1	110	.	0			c.C2849T						PASS	.						57	62	60					17																	4797860		2116	4245	6361	SO:0001583	missense	50488	exon24			AGAGCTCGTTCAC	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.2849C>T	17.37:g.4797860C>T	ENSP00000347427:p.Ser950Leu	108	0	0		75	4	0.0533333	NM_153827		Missense_Mutation	SNP	ENST00000355280.6	37	CCDS45588.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.952243	0.92660	.	.	ENSG00000141503	ENST00000355280;ENST00000453408;ENST00000347992	D;D;D	0.83591	-1.74;-1.74;-1.71	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	D	0.90079	0.6901	M	0.73598	2.24	0.58432	D	0.999999	D;D;D;D	0.69078	0.996;0.997;0.994;0.997	P;D;P;D	0.66847	0.658;0.947;0.885;0.947	D	0.91106	0.4918	10	0.87932	D	0	.	15.884	0.79226	0.0:1.0:0.0:0.0	.	913;930;950;921	Q8N4C8-2;Q8N4C8-4;Q8N4C8;Q8N4C8-3	.;.;MINK1_HUMAN;.	L	950;930;921	ENSP00000347427:S950L;ENSP00000406487:S930L;ENSP00000269296:S921L	ENSP00000269296:S921L	S	+	2	0	MINK1	4738636	1.000000	0.71417	0.928000	0.36995	0.990000	0.78478	6.788000	0.75105	2.620000	0.88729	0.655000	0.94253	TCG	.	.	none		0.602	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439801.1	NM_015716		T	4797860	C	T	4797860	3	4	21	1	0	0	0	0	1	0	0	0	9596	893	31	1	2710	1	MINK1	17	4797860	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	79005	4797860	76397350	125	2868											
PFN1	5216	hgsc.bcm.edu	37	chr17	4849259	4849259	+	Missense_Mutation	SNP	T	T	G																															tcttgttgatcaaaccaccgTggacaccttctttgcccatc																										TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr17:4849259T>G	ENST00000225655.5	-	3	978	c.359A>C	c.(358-360)cAc>cCc	p.H120P	PFN1_ENST00000574872.1_Missense_Mutation_p.H84P	NM_005022.3	NP_005013.1	P07737	PROF1_HUMAN	profilin 1	120					actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cell death (GO:0008219)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of ATPase activity (GO:0032781)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of ruffle assembly (GO:1900029)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	actin binding (GO:0003779)|adenyl-nucleotide exchange factor activity (GO:0000774)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|poly(A) RNA binding (GO:0044822)|proline-rich region binding (GO:0070064)			NS(1)|endometrium(1)|lung(2)|upper_aerodigestive_tract(1)	5						CAAACCACCGTGGACACCTTC	0.557																																					p.H120P		Atlas-SNP	.											.	PFN1	6	.	0			c.A359C						PASS	.						107	81	90					17																	4849259		2203	4300	6503	SO:0001583	missense	5216	exon3			CCACCGTGGACAC	BC057828	CCDS11061.1	17p13.2	2010-07-09			ENSG00000108518	ENSG00000108518			8881	protein-coding gene	gene with protein product		176610				3356709, 1968707	Standard	NM_005022		Approved		uc002gaa.4	P07737	OTTHUMG00000099396	ENST00000225655.5:c.359A>C	17.37:g.4849259T>G	ENSP00000225655:p.His120Pro	331	0	0		195	71	0.364103	NM_005022	Q53Y44	Missense_Mutation	SNP	ENST00000225655.5	37	CCDS11061.1	.	.	.	.	.	.	.	.	.	.	T	12.80	2.045910	0.36085	.	.	ENSG00000108518	ENST00000225655	D	0.85955	-2.05	4.01	4.01	0.46588	.	0.000000	0.64402	D	0.000001	D	0.90184	0.6932	M	0.69823	2.125	0.53688	D	0.999975	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.88931	0.3373	10	0.35671	T	0.21	.	11.2225	0.48864	0.0:0.0:0.0:1.0	.	120;120	P07737;Q53Y44	PROF1_HUMAN;.	P	120	ENSP00000225655:H120P	ENSP00000225655:H120P	H	-	2	0	PFN1	4790004	1.000000	0.71417	0.998000	0.56505	0.619000	0.37552	6.169000	0.71913	1.815000	0.52974	0.247000	0.18012	CAC	.	.	alt		0.557	PFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216853.1	NM_005022		G	4849259	T	G	4849259	3	3	21	1	0	0	0	0	1	0	0	0	11776	1696	59	5	67	5	PFN1	17	4849259	Missense_Mutation	SNP	T	TCGA-FM-8000-01A-11D-2210-10	51399	4849259	76345951	126	2869	44	2									
PFN1	5216	hgsc.bcm.edu	37	chr17	4849260	4849260	+	Missense_Mutation	SNP	G	G	C																															cttgttgatcaaaccaccgtGgacaccttctttgcccatca																										TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr17:4849260G>C	ENST00000225655.5	-	3	977	c.358C>G	c.(358-360)Cac>Gac	p.H120D	PFN1_ENST00000574872.1_Missense_Mutation_p.H84D	NM_005022.3	NP_005013.1	P07737	PROF1_HUMAN	profilin 1	120					actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cell death (GO:0008219)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of ATPase activity (GO:0032781)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of ruffle assembly (GO:1900029)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	actin binding (GO:0003779)|adenyl-nucleotide exchange factor activity (GO:0000774)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|poly(A) RNA binding (GO:0044822)|proline-rich region binding (GO:0070064)			NS(1)|endometrium(1)|lung(2)|upper_aerodigestive_tract(1)	5						AAACCACCGTGGACACCTTCT	0.552																																					p.H120D		Atlas-SNP	.											.	PFN1	6	.	0			c.C358G						PASS	.						107	81	90					17																	4849260		2203	4300	6503	SO:0001583	missense	5216	exon3			CACCGTGGACACC	BC057828	CCDS11061.1	17p13.2	2010-07-09			ENSG00000108518	ENSG00000108518			8881	protein-coding gene	gene with protein product		176610				3356709, 1968707	Standard	NM_005022		Approved		uc002gaa.4	P07737	OTTHUMG00000099396	ENST00000225655.5:c.358C>G	17.37:g.4849260G>C	ENSP00000225655:p.His120Asp	330	0	0		196	72	0.367347	NM_005022	Q53Y44	Missense_Mutation	SNP	ENST00000225655.5	37	CCDS11061.1	.	.	.	.	.	.	.	.	.	.	G	19.32	3.805916	0.70682	.	.	ENSG00000108518	ENST00000225655	D	0.85702	-2.02	4.14	4.14	0.48551	.	0.000000	0.64402	D	0.000001	D	0.91878	0.7429	M	0.83953	2.67	0.53688	D	0.999977	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.91227	0.5011	10	0.35671	T	0.21	.	14.3076	0.66395	0.0:0.0:1.0:0.0	.	120;120	P07737;Q53Y44	PROF1_HUMAN;.	D	120	ENSP00000225655:H120D	ENSP00000225655:H120D	H	-	1	0	PFN1	4790005	1.000000	0.71417	1.000000	0.80357	0.660000	0.38997	7.593000	0.82686	2.300000	0.77407	0.448000	0.29417	CAC	.	.	none		0.552	PFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216853.1	NM_005022		C	4849260	G	C	4849260	3	2	21	1	0	0	0	0	1	0	0	0	11776	1348	47	4	68	4	PFN1	17	4849260	Missense_Mutation	SNP	G	TCGA-FM-8000-01A-11D-2210-10	1	4849260	76345950	127	2870	44	2									
NLRP1	22861	hgsc.bcm.edu	37	chr17	5440172	5440172	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttctgggtccccccttaccGtctgctgaagatgagcagct	6	11	11	13	1	2	3	0	2	2	1	3	3	3	3	4	1	4	4	4	1	2	2	rs199748129		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr17:5440172G>A	ENST00000572272.1	-	8	2958	c.2959C>T	c.(2959-2961)Cgg>Tgg	p.R987W	NLRP1_ENST00000577119.1_Intron|NLRP1_ENST00000269280.4_Splice_Site_p.R987W|NLRP1_ENST00000571307.1_5'UTR|NLRP1_ENST00000354411.3_Intron|NLRP1_ENST00000345221.3_Splice_Site_p.R987W|NLRP1_ENST00000262467.5_Splice_Site_p.R987W			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	987					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)	p.R987W(1)		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)				CCCCCTTACCGTCTGCTGAAG	0.587																																					p.R987W		Atlas-SNP	.											NLRP1,colon,carcinoma,0,1	NLRP1	358	1	1	Substitution - Missense(1)	large_intestine(1)	c.C2959T						PASS	.						74	61	65					17																	5440172		2203	4300	6503	SO:0001630	splice_region_variant	22861	exon8			CTTACCGTCTGCT	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.2960+1C>T	17.37:g.5440172G>A		53	0	0		37	11	0.297297	NM_014922	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	37	CCDS42246.1	.	.	.	.	.	.	.	.	.	.	G	5.855	0.342015	0.11069	.	.	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000345221;ENST00000537069	T;T;T;T	0.71222	-0.55;-0.55;-0.54;-0.54	2.69	-5.38	0.02673	.	0.838313	0.09764	N	0.758830	T	0.37892	0.1020	N	0.03294	-0.36	0.09310	N	1	B;B;B;B	0.10296	0.003;0.0;0.002;0.001	B;B;B;B	0.06405	0.002;0.0;0.0;0.0	T	0.12502	-1.0545	10	0.49607	T	0.09	.	2.3958	0.04389	0.2437:0.1575:0.4437:0.1551	.	253;987;987;987	F5H042;Q9C000;Q9C000-2;E9PE50	.;NALP1_HUMAN;.;.	W	987;987;987;987;253	ENSP00000442029:R987W;ENSP00000262467:R987W;ENSP00000269280:R987W;ENSP00000324366:R987W	ENSP00000262467:R987W	R	-	1	2	NLRP1	5380896	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.179000	0.03090	-1.788000	0.01266	-2.377000	0.00234	CGG	.	.	weak		0.587	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004	Missense_Mutation	A	5440172	G	A	5440172	5	1	21	1	0	0	0	0	0	0	1	0	10480	1159	40	1	1577	1	NLRP1	17	5440172	Splice_Site	SNP	G	TCGA-FM-8000-01A-11D-2210-10	590912	5440172	75755038	128	2871											
SLFN12	55106	hgsc.bcm.edu	37	chr17	33738875	33738875	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcttcacatattaattgctTaagtccttcatgttgtaaga	11	18	5	7	0	3	1	2	0	1	1	4	1	4	1	1	0	1	3	1	0	4	9			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr17:33738875T>G	ENST00000394562.1	-	6	1742	c.1219A>C	c.(1219-1221)Aag>Cag	p.K407Q	SLFN12_ENST00000304905.5_Missense_Mutation_p.K407Q|RP11-686D22.8_ENST00000587012.1_RNA|SLFN12_ENST00000452764.3_Missense_Mutation_p.K407Q|SLFN12_ENST00000460530.1_5'UTR			Q8IYM2	SLN12_HUMAN	schlafen family member 12	407							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)		ATTAATTGCTTAAGTCCTTCA	0.383																																					p.K407Q		Atlas-SNP	.											SLFN12,colon,carcinoma,+2,1	SLFN12	56	1	0			c.A1219C						PASS	.						103	107	106					17																	33738875		2203	4300	6503	SO:0001583	missense	55106	exon4			ATTGCTTAAGTCC	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.1219A>C	17.37:g.33738875T>G	ENSP00000378063:p.Lys407Gln	74	0	0		47	18	0.382979	NM_018042	A8K711|Q9NP47	Missense_Mutation	SNP	ENST00000394562.1	37	CCDS11295.1	.	.	.	.	.	.	.	.	.	.	T	4.983	0.182542	0.09495	.	.	ENSG00000172123	ENST00000394562;ENST00000304905;ENST00000452764	T;T;T	0.03920	3.76;3.76;3.76	3.05	-0.252	0.12999	.	.	.	.	.	T	0.02610	0.0079	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43877	-0.9364	9	0.51188	T	0.08	.	3.4293	0.07422	0.0:0.5168:0.2174:0.2659	.	407	Q8IYM2	SLN12_HUMAN	Q	407	ENSP00000378063:K407Q;ENSP00000302077:K407Q;ENSP00000394903:K407Q	ENSP00000302077:K407Q	K	-	1	0	SLFN12	30762988	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-2.299000	0.01139	-0.137000	0.11455	-2.169000	0.00324	AAG	.	.	none		0.383	SLFN12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256491.1	NM_018042		G	33738875	T	G	33738875	3	3	21	1	0	0	0	0	1	0	0	0	14749	1763	61	5	521	5	SLFN12	17	33738875	Missense_Mutation	SNP	T	TCGA-FM-8000-01A-11D-2210-10	28298703	33738875	47456335	129	2872											
AATK	9625	hgsc.bcm.edu	37	chr17	79098649	79098649	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagtcacgaagtagtcctcCtgttggcacagggacgggtc	8	8	14	11	2	1	0	1	0	0	0	4	2	3	1	2	3	0	4	2	3	2	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr17:79098649C>T	ENST00000326724.4	-	9	865		c.e9-1		AATK_ENST00000417379.1_Splice_Site|MIR338_ENST00000390137.2_RNA|MIR657_ENST00000385003.1_RNA|AATK_ENST00000572339.1_5'Flank	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase						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)			AGTAGTCCTCCTGTTGGCACA	0.667																																					.		Atlas-SNP	.											.	AATK	102	.	0			c.841-1G>A						PASS	.						33	38	36					17																	79098649		2147	4246	6393	SO:0001630	splice_region_variant	9625	exon10			GTCCTCCTGTTGG	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.841-1G>A	17.37:g.79098649C>T		186	0	0		99	46	0.464646	NM_001080395	O75136|Q6ZN31|Q86X28	Splice_Site	SNP	ENST00000326724.4	37	CCDS45807.1	.	.	.	.	.	.	.	.	.	.	C	13.52	2.262080	0.39995	.	.	ENSG00000181409	ENST00000326724;ENST00000417379;ENST00000374792	.	.	.	3.66	3.66	0.41972	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6471	0.68769	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	AATK	76713244	1.000000	0.71417	0.999000	0.59377	0.276000	0.26787	7.002000	0.76304	2.041000	0.60428	0.591000	0.81541	.	.	.	none		0.667	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920	Intron	T	79098649	C	T	79098649	5	4	21	1	0	0	0	0	0	0	1	0	26	695	24	2	3308	2	AATK	17	79098649	Splice_Site	SNP	C	TCGA-FM-8000-01A-11D-2210-10	45359774	79098649	2096561	130	2873											
DSG2	1829	hgsc.bcm.edu	37	chr18	29098213	29098213	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	attttacagatctgctttaaCgttggaagtggacttcactt	10	16	8	7	1	2	1	1	0	1	1	2	3	2	3	0	2	3	2	0	2	3	7	rs587780925		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr18:29098213C>T	ENST00000261590.8	+	2	266	c.57C>T	c.(55-57)aaC>aaT	p.N19N	DSG2_ENST00000585206.1_Silent_p.N19N	NM_001943.3	NP_001934.2	Q14126	DSG2_HUMAN	desmoglein 2	19					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)			TCTGCTTTAACGTTGGAAGTG	0.368																																					p.N19N		Atlas-SNP	.											.	DSG2	115	.	0			c.C57T						PASS	.						105	100	102					18																	29098213		1839	4087	5926	SO:0001819	synonymous_variant	1829	exon2			CTTTAACGTTGGA	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.57C>T	18.37:g.29098213C>T		83	0	0		69	32	0.463768	NM_001943	Q4KKU6	Silent	SNP	ENST00000261590.8	37	CCDS42423.1																																																																																			.	.	none		0.368	DSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447506.1	NM_001943		T	29098213	C	T	29098213	2	4	21	1	0	0	0	0	0	0	0	1	4779	535	19	1		1	DSG2	18	29098213	Silent	SNP	C	TCGA-FM-8000-01A-11D-2210-10		29098213	48979035	131	2874											
DCC	1630	hgsc.bcm.edu	37	chr18	50832066	50832066	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatggaaacactggagccaaAcaacctctggtacctattca	14	8	8	11	0	2	0	1	0	1	0	2	3	2	2	3	3	5	1	3	3	5	3			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr18:50832066A>G	ENST00000442544.2	+	13	2646	c.2030A>G	c.(2029-2031)aAc>aGc	p.N677S	DCC_ENST00000581580.1_Missense_Mutation_p.N332S|DCC_ENST00000412726.1_Missense_Mutation_p.N525S	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	677	Fibronectin type-III 3. {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)		CTGGAGCCAAACAACCTCTGG	0.428																																					p.N677S		Atlas-SNP	.											.	DCC	360	.	0			c.A2030G						PASS	.						99	104	102					18																	50832066		2203	4300	6503	SO:0001583	missense	1630	exon13			AGCCAAACAACCT	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.2030A>G	18.37:g.50832066A>G	ENSP00000389140:p.Asn677Ser	121	0	0		88	35	0.397727	NM_005215		Missense_Mutation	SNP	ENST00000442544.2	37	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	A	14.76	2.631843	0.46944	.	.	ENSG00000187323	ENST00000442544;ENST00000304775;ENST00000412726	T;T	0.56776	0.44;0.44	5.58	5.58	0.84498	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.30603	0.0770	N	0.05383	-0.06	0.52099	D	0.999944	B;B;B	0.15141	0.007;0.003;0.012	B;B;B	0.20767	0.031;0.031;0.018	T	0.19712	-1.0297	10	0.05620	T	0.96	.	15.0365	0.71751	1.0:0.0:0.0:0.0	.	525;525;677	E7EQM8;B4DYX2;P43146	.;.;DCC_HUMAN	S	677;610;525	ENSP00000389140:N677S;ENSP00000397322:N525S	ENSP00000304146:N610S	N	+	2	0	DCC	49086064	1.000000	0.71417	0.985000	0.45067	0.977000	0.68977	8.773000	0.91762	2.239000	0.73571	0.533000	0.62120	AAC	.	.	none		0.428	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		G	50832066	A	G	50832066	3	3	21	1	0	0	0	0	1	0	0	0	4284	43	2	3	2080	3	DCC	18	50832066	Missense_Mutation	SNP	A	TCGA-FM-8000-01A-11D-2210-10	21733853	50832066	27245182	132	2875											
BCL2	596	hgsc.bcm.edu	37	chr18	60985444	60985444	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acacacatgaccccaccgaaCtcaaagaaggccacaatcct	16	4	5	16	1	1	2	1	1	0	1	2	3	2	2	5	1	1	0	5	1	4	0			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr18:60985444C>T	ENST00000398117.1	-	1	1917	c.456G>A	c.(454-456)gaG>gaA	p.E152E	BCL2_ENST00000589955.1_Silent_p.E152E|BCL2_ENST00000444484.1_Silent_p.E152E|BCL2_ENST00000333681.4_Silent_p.E152E	NM_000633.2	NP_000624.2	P10415	BCL2_HUMAN	B-cell CLL/lymphoma 2	152					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)	CCCCACCGAACTCAAAGAAGG	0.627			T	IGH@	"NHL, CLL"																																p.E152E		Atlas-SNP	.		Dom	yes		18	18q21.3	596	B-cell CLL/lymphoma 2		L	.	BCL2	272	.	0			c.G456A						PASS	.						139	148	145					18																	60985444		2203	4300	6503	SO:0001819	synonymous_variant	596	exon2			ACCGAACTCAAAG	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.456G>A	18.37:g.60985444C>T		190	0	0		128	50	0.390625	NM_000633	C9JHD5|P10416|Q13842|Q16197	Silent	SNP	ENST00000398117.1	37	CCDS11981.1																																																																																			.	.	none		0.627	BCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256199.1	NM_000633, NM_000657		T	60985444	C	T	60985444	2	4	21	1	0	0	0	0	0	0	0	1	1365	564	20	2		2	BCL2	18	60985444	Silent	SNP	C	TCGA-FM-8000-01A-11D-2210-10	10153378	60985444	17091804	133	2876											
SERPINB7	8710	hgsc.bcm.edu	37	chr18	61471521	61471521	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	atggaatggaccaatccaagGcgaatgacctctaagtatgt	14	9	10	8	1	1	1	0	1	1	0	2	4	2	3	3	3	0	1	3	3	6	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr18:61471521G>A	ENST00000398019.2	+	8	1120	c.795G>A	c.(793-795)agG>agA	p.R265R	SERPINB7_ENST00000540675.1_Silent_p.R248R|SERPINB7_ENST00000336429.2_Silent_p.R265R|SERPINB7_ENST00000546027.1_Silent_p.R265R	NM_003784.3	NP_003775.1	O75635	SPB7_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 7	265					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)				CCAATCCAAGGCGAATGACCT	0.333																																					p.R265R		Atlas-SNP	.											.	SERPINB7	66	.	0			c.G795A						PASS	.						45	44	44					18																	61471521		2203	4300	6503	SO:0001819	synonymous_variant	8710	exon8			TCCAAGGCGAATG	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.795G>A	18.37:g.61471521G>A		22	0	0		19	7	0.368421	NM_001261830	B4DUW8|F5GZC0|Q1ED45|Q3KPG4	Silent	SNP	ENST00000398019.2	37	CCDS11988.1																																																																																			.	.	none		0.333	SERPINB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134007.1	NM_003784		A	61471521	G	A	61471521	2	1	21	1	0	0	0	0	0	0	0	1	14121	1194	42	2		2	SERPINB7	18	61471521	Silent	SNP	G	TCGA-FM-8000-01A-11D-2210-10	486077	61471521	16605727	134	2877											
DAZAP1	26528	hgsc.bcm.edu	37	chr19	1434902	1434902	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gtgcaagggttccacccctaCcgacgctagcccgcggcgcc	6	5	12	18	5	0	0	0	0	0	0	1	1	1	0	6	2	3	3	6	2	3	3			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr19:1434902C>G	ENST00000233078.4	+	12	1376	c.1215C>G	c.(1213-1215)taC>taG	p.Y405*	DAZAP1_ENST00000336761.6_3'UTR	NM_018959.2	NP_061832.2	Q96EP5	DAZP1_HUMAN	DAZ associated protein 1	405					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)		TCCACCCCTACCGACGCTAGC	0.677																																					p.Y405X		Atlas-SNP	.											.	DAZAP1	52	.	0			c.C1215G						PASS	.						10	11	10					19																	1434902		2142	4191	6333	SO:0001587	stop_gained	26528	exon12			CCCCTACCGACGC		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.1215C>G	19.37:g.1434902C>G	ENSP00000233078:p.Tyr405*	15	0	0		12	5	0.416667	NM_018959	Q96MJ3|Q9NRR9	Nonsense_Mutation	SNP	ENST00000233078.4	37	CCDS12065.1	.	.	.	.	.	.	.	.	.	.	C	37	6.251811	0.97412	.	.	ENSG00000071626	ENST00000233078	.	.	.	5.26	2.98	0.34508	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.0207	0.42041	0.0:0.7804:0.0:0.2196	.	.	.	.	X	405	.	ENSP00000233078:Y405X	Y	+	3	2	DAZAP1	1385902	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.278000	0.33179	1.215000	0.43411	0.561000	0.74099	TAC	.	.	none		0.677	DAZAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449522.3	NM_170711		G	1434902	C	G	1434902	4	3	21	1	0	0	0	0	0	1	0	0	4246	518	18	4	1354	4	DAZAP1	19	1434902	Nonsense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10		1434902	57694081	135	2878											
FUT5	2527	hgsc.bcm.edu	37	chr19	5867725	5867725	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgtggcttggctgggccCaggggatccatgggtcagag	6	8	17	10	0	1	1	1	0	0	1	2	2	2	2	2	6	0	2	2	6	0	1			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr19:5867725C>T	ENST00000586349.1	-	4	406	c.407G>A	c.(406-408)tGg>tAg	p.W136*	FUT5_ENST00000252675.5_Silent_p.L4L|FUT5_ENST00000588525.1_Silent_p.L4L																							TGGCTGGGCCCAGGGGATCCA	0.602																																					p.L4L		Atlas-SNP	.											.	FUT5	29	.	0			c.G12A						PASS	.						22	25	24					19																	5867725		2200	4289	6489	SO:0001587	stop_gained	2527	exon2			TGGGCCCAGGGGA																												ENST00000586349.1:c.407G>A	19.37:g.5867725C>T	ENSP00000466639:p.Trp136*	223	0	0		107	32	0.299065	NM_002034		Silent	SNP	ENST00000586349.1	37																																																																																				.	.	none		0.602	AC024592.12-002	PUTATIVE	mRNA_start_NF|mRNA_end_NF|cds_start_NF|cds_end_NF|basic|appris_candidate_longest|readthrough_transcript|exp_conf	protein_coding	protein_coding	OTTHUMT00000452249.1			T	5867725	C	T	5867725	4	4	21	1	0	0	0	0	0	1	0	0	6115	581	21	2	1116	2	FUT5	19	5867725	Nonsense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	4432823	5867725	53261258	136	2879											
MLLT1	4298	hgsc.bcm.edu	37	chr19	6230658	6230658	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttctcgcagcgcaggtggtTcacgggcgggttgccttcca	4	10	14	13	4	2	0	1	0	1	0	4	0	3	0	2	4	2	4	2	4	0	4			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr19:6230658T>A	ENST00000252674.7	-	4	506	c.343A>T	c.(343-345)Aac>Tac	p.N115Y		NM_005934.3	NP_005925.2	Q03111	ENL_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1	115					negative regulation of protein kinase activity (GO:0006469)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	DNA binding (GO:0003677)			endometrium(3)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|skin(2)	17						CGCAGGTGGTTCACGGGCGGG	0.612			T	MLL	AL																																p.N115Y		Atlas-SNP	.		Dom	yes		19	19p13.3	4298	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1 (ENL)"		L	MLLT1,NS,carcinoma,+2,1	MLLT1	47	1	0			c.A343T						PASS	.						168	167	167					19																	6230658		2203	4300	6503	SO:0001583	missense	4298	exon4			GGTGGTTCACGGG		CCDS12160.1	19p13.3	2012-10-04	2001-11-28		ENSG00000130382	ENSG00000130382			7134	protein-coding gene	gene with protein product		159556	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 1"				Standard	XM_005259561		Approved	ENL, LTG19, YEATS1	uc002mek.3	Q03111	OTTHUMG00000180757	ENST00000252674.7:c.343A>T	19.37:g.6230658T>A	ENSP00000252674:p.Asn115Tyr	78	0	0		39	26	0.666667	NM_005934	Q14768	Missense_Mutation	SNP	ENST00000252674.7	37	CCDS12160.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.187892	0.78789	.	.	ENSG00000130382	ENST00000252674	.	.	.	4.7	4.7	0.59300	.	0.000000	0.85682	D	0.000000	T	0.77287	0.4108	M	0.83692	2.655	0.80722	D	1	D	0.60575	0.988	P	0.61132	0.884	T	0.81398	-0.0951	9	0.72032	D	0.01	-55.4765	13.1576	0.59527	0.0:0.0:0.0:1.0	.	115	Q03111	ENL_HUMAN	Y	115	.	ENSP00000252674:N115Y	N	-	1	0	MLLT1	6181658	1.000000	0.71417	0.948000	0.38648	0.719000	0.41307	7.727000	0.84838	1.966000	0.57179	0.533000	0.62120	AAC	.	.	none		0.612	MLLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452909.1	NM_005934		A	6230658	T	A	6230658	3	1	21	1	0	0	0	0	1	0	0	0	9634	1783	62	5	1372	5	MLLT1	19	6230658	Missense_Mutation	SNP	T	TCGA-FM-8000-01A-11D-2210-10	362933	6230658	52898325	137	2880											
ZNF559	84527	hgsc.bcm.edu	37	chr19	9449245	9449245	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatggtggctgggtggttgaCaaattactctcaggtaagta	10	12	14	5	0	1	1	1	1	1	0	2	2	1	1	0	5	1	4	0	5	4	4	rs35591059		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr19:9449245C>G	ENST00000393883.2	+	3	668	c.20C>G	c.(19-21)aCa>aGa	p.T7R	ZNF177_ENST00000602738.1_5'UTR|ZNF559_ENST00000603380.1_Missense_Mutation_p.T7R|ZNF559_ENST00000586255.1_Missense_Mutation_p.T35R|ZNF177_ENST00000602856.1_Intron|ZNF559_ENST00000317221.7_Missense_Mutation_p.T7R|ZNF559_ENST00000538743.1_Intron|ZNF177_ENST00000605471.1_Intron|ZNF177_ENST00000541595.2_5'UTR|ZNF559_ENST00000592504.1_Missense_Mutation_p.T7R|ZNF559_ENST00000585352.1_Missense_Mutation_p.T7R|ZNF177_ENST00000446085.4_Intron|ZNF559_ENST00000592896.1_Missense_Mutation_p.T35R|ZNF559_ENST00000587557.1_Missense_Mutation_p.T71R	NM_001202412.1	NP_001189341.1	Q9BR84	ZN559_HUMAN	zinc finger protein 559	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)			endometrium(2)|large_intestine(7)|lung(15)|ovary(1)|urinary_tract(1)	26						GGGTGGTTGACAAATTACTCT	0.393																																					p.T71R		Atlas-SNP	.											.	ZNF559	77	.	0			c.C212G						PASS	.						190	180	183					19																	9449245		2203	4300	6503	SO:0001583	missense	84527	exon3			GGTTGACAAATTA	AL389937	CCDS12211.1, CCDS59349.1, CCDS62531.1, CCDS62532.1	19p13.2	2013-09-20			ENSG00000188321	ENSG00000188321		"Zinc fingers, C2H2-type", "-"	28197	protein-coding gene	gene with protein product						12477932	Standard	NM_001202406		Approved	MGC13105	uc002mle.4	Q9BR84	OTTHUMG00000179942	ENST00000393883.2:c.20C>G	19.37:g.9449245C>G	ENSP00000377461:p.Thr7Arg	157	1	0.00636943		119	98	0.823529	NM_001202408	K7EMG6	Missense_Mutation	SNP	ENST00000393883.2	37	CCDS12211.1	.	.	.	.	.	.	.	.	.	.	C	10.08	1.252616	0.22880	.	.	ENSG00000188321	ENST00000317221;ENST00000393883	T;T	0.06687	4.85;3.27	2.47	-1.11	0.09840	Krueppel-associated box (1);	.	.	.	.	T	0.02342	0.0072	N	0.03983	-0.305	0.09310	N	1	B	0.33964	0.434	B	0.30572	0.117	T	0.39921	-0.9590	9	0.09590	T	0.72	.	2.3148	0.04196	0.2411:0.4635:0.0:0.2955	.	7	Q9BR84	ZN559_HUMAN	R	7	ENSP00000325393:T7R;ENSP00000377461:T7R	ENSP00000325393:T7R	T	+	2	0	ZNF559	9310245	0.000000	0.05858	0.000000	0.03702	0.444000	0.32077	-0.799000	0.04560	-0.164000	0.10927	0.462000	0.41574	ACA	.	.	none		0.393	ZNF559-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449021.1	NM_032497		G	9449245	C	G	9449245	3	3	21	1	0	0	0	0	1	0	0	0	18005	478	17	4	22	4	ZNF559	19	9449245	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	3218587	9449245	49679738	138	2881											
ILF3	3609	hgsc.bcm.edu	37	chr19	10795539	10795539	+	Intron	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgtcttaatttacagcaggTtttgtatgaatttttaacct	10	20	6	5	0	1	1	0	1	1	0	1	1	1	1	1	1	3	3	1	1	5	10			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr19:10795539T>G	ENST00000590261.1	+	16	2059				ILF3_ENST00000449870.1_Intron|ILF3_ENST00000588657.1_Intron|ILF3_ENST00000407004.3_3'UTR|ILF3_ENST00000592763.1_3'UTR|ILF3_ENST00000318511.3_Intron|ILF3_ENST00000420083.1_Silent_p.G688G|ILF3_ENST00000250241.8_Silent_p.G688G			Q12906	ILF3_HUMAN	interleukin enhancer binding factor 3, 90kDa						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)			TTACAGCAGGTTTTGTATGAA	0.358																																					p.G688G		Atlas-SNP	.											.	ILF3	99	.	0			c.T2064G						PASS	.						102	93	95					19																	10795539		1844	4079	5923	SO:0001627	intron_variant	3609	exon18			AGCAGGTTTTGTA	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.2059+893T>G	19.37:g.10795539T>G		119	0	0		94	76	0.808511	NM_153464	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	37	CCDS12246.1																																																																																			.	.	none		0.358	ILF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452074.1			G	10795539	T	G	10795539	1	3	21	0	1	0	0	0	0	0	0	0	7721	1712	60	5		5	ILF3	19	10795539	Intron	SNP	T	TCGA-FM-8000-01A-11D-2210-10	1346294	10795539	48333444	139	2882											
LOC729991-MEF2B	100271849	hgsc.bcm.edu	37	chr19	19260045	19260045	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggggtacctcgaggatgTcagtgttggtgcggctctcg	4	11	16	10	3	2	0	1	0	1	0	4	2	2	1	2	5	2	3	2	5	1	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr19:19260045T>G	ENST00000602424.2	-	5	974	c.248A>C	c.(247-249)gAc>gCc	p.D83A	MEF2BNB-MEF2B_ENST00000514819.3_Missense_Mutation_p.D100A|MEF2B_ENST00000424583.2_Missense_Mutation_p.D83A|MEF2B_ENST00000410050.1_Missense_Mutation_p.D83A|MEF2B_ENST00000409224.1_Missense_Mutation_p.D83A|MEF2BNB-MEF2B_ENST00000602276.1_5'UTR|MEF2B_ENST00000409447.2_Missense_Mutation_p.D83A|MEF2B_ENST00000162023.5_Missense_Mutation_p.D83A|MEF2BNB-MEF2B_ENST00000444486.3_Missense_Mutation_p.D83A	NM_005919.3	NP_005910.1	Q02080	MEF2B_HUMAN	myocyte enhancer factor 2B	83					muscle organ development (GO:0007517)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cell junction (GO:0030054)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D83V(11)|p.D83A(2)		breast(1)|haematopoietic_and_lymphoid_tissue(21)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(5;0.00011)|Epithelial(12;0.00412)			CTCGAGGATGTCAGTGTTGGT	0.607																																					p.D83A		Atlas-SNP	.											MEF2BNB-MEF2B,NS,lymphoid_neoplasm,0,15	MEF2BNB-MEF2B	29	15	13	Substitution - Missense(13)	haematopoietic_and_lymphoid_tissue(13)	c.A248C						scavenged	.						126	63	84					19																	19260045		2203	4300	6503	SO:0001583	missense	4207	exon5			AGGATGTCAGTGT	X63380	CCDS12394.1, CCDS46024.1	19p13.11	2010-05-12	2007-04-24					"Myocyte enhancer factors"	6995	protein-coding gene	gene with protein product		600661				1516833, 8575763	Standard	NM_001145785		Approved	RSRFR2	uc002nll.2	Q02080		ENST00000602424.2:c.248A>C	19.37:g.19260045T>G	ENSP00000473308:p.Asp83Ala	172	2	0.0116279		97	70	0.721649	NM_005919	A0AV80|B4DVH7|B7ZVY1|G5E9M1	Missense_Mutation	SNP	ENST00000602424.2	37	CCDS12394.1	.	.	.	.	.	.	.	.	.	.	T	19.93	3.917436	0.73098	.	.	ENSG00000213999	ENST00000409224;ENST00000424583;ENST00000410050;ENST00000444486;ENST00000409447;ENST00000162023	D;D;D;D;D	0.83591	-1.74;-1.74;-1.74;-1.74;-1.74	5.33	5.33	0.75918	Transcription factor, MADS-box (1);	0.000000	0.85682	D	0.000000	D	0.90092	0.6905	M	0.74467	2.265	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	0.987;0.978;0.996;0.999;0.997	D	0.90697	0.4617	10	0.56958	D	0.05	-31.0539	13.2359	0.59969	0.0:0.0:0.0:1.0	.	83;130;83;83;83	Q02080;B8ZZJ5;C9J4J4;G5E9M1;B3KQ23	MEF2B_HUMAN;.;.;.;.	A	83;83;83;83;130;83	ENSP00000386480:D83A;ENSP00000402154:D83A;ENSP00000386374:D83A;ENSP00000390762:D83A;ENSP00000162023:D83A	ENSP00000162023:D83A	D	-	2	0	MEF2B	19121045	1.000000	0.71417	0.999000	0.59377	0.518000	0.34316	7.923000	0.87546	2.024000	0.59613	0.459000	0.35465	GAC	.	.	none		0.607	MEF2B-202	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_005919		G	19260045	T	G	19260045	3	3	21	1	0	0	0	0	1	0	0	0	8898	1667	58	5	873	5	LOC729991-MEF2B	19	19260045	Missense_Mutation	SNP	T	TCGA-FM-8000-01A-11D-2210-10	8464506	19260045	39868938	140	2883											
ZNF676	163223	hgsc.bcm.edu	37	chr19	22363817	22363817	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtaaggattgaggatcgattAaaagctttgccacattcttc	12	13	9	7	1	1	1	0	1	1	0	3	4	1	3	1	2	2	2	1	2	3	6			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr19:22363817A>G	ENST00000397121.2	-	3	1019	c.702T>C	c.(700-702)ttT>ttC	p.F234F		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	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)			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)				AGGATCGATTAAAAGCTTTGC	0.368																																					p.F234F		Atlas-SNP	.											ZNF676,NS,carcinoma,-1,2	ZNF676	146	2	0			c.T702C						scavenged	.						75	83	80					19																	22363817		2176	4287	6463	SO:0001819	synonymous_variant	163223	exon3			TCGATTAAAAGCT	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.702T>C	19.37:g.22363817A>G		26	1	0.0384615		24	3	0.125	NM_001001411	A8MVX5	Silent	SNP	ENST00000397121.2	37	CCDS42539.1																																																																																			.	.	none		0.368	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411		G	22363817	A	G	22363817	2	3	21	1	0	0	0	0	0	0	0	1	18098	359	13	3		3	ZNF676	19	22363817	Silent	SNP	A	TCGA-FM-8000-01A-11D-2210-10	3103772	22363817	36765166	141	2884											
ZNF675	171392	hgsc.bcm.edu	37	chr19	23869831	23869831	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtcgcacccgtaactctcAccatttctaggcttccaggg	8	11	8	14	2	2	0	1	0	2	0	5	0	3	0	3	2	1	3	3	2	2	4			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr19:23869831A>C	ENST00000359788.4	-	1	172		c.e1+1		ZNF675_ENST00000601935.1_Splice_Site|ZNF675_ENST00000601010.1_Splice_Site|ZNF675_ENST00000596211.1_Splice_Site|ZNF675_ENST00000600313.1_Splice_Site|ZNF675_ENST00000599168.1_Splice_Site	NM_138330.2	NP_612203.2	Q8TD23	ZN675_HUMAN	zinc finger protein 675						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)				CGTAACTCTCACCATTTCTAG	0.602																																					.		Atlas-SNP	.											.	ZNF675	88	.	0			c.3+2T>G						PASS	.						87	81	83					19																	23869831		2203	4300	6503	SO:0001630	splice_region_variant	171392	exon2			ACTCTCACCATTT		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.3+1T>G	19.37:g.23869831A>C		59	0	0		26	7	0.269231	NM_138330	Q8N211	Splice_Site	SNP	ENST00000359788.4	37	CCDS32981.1	.	.	.	.	.	.	.	.	.	.	.	3.188	-0.166399	0.06461	.	.	ENSG00000197372	ENST00000359788	.	.	.	0.458	0.458	0.16670	.	.	.	.	.	.	.	.	.	.	.	0.24824	N	0.992563	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	-1	.	.	.	-	.	.	ZNF675	23661671	0.065000	0.20965	0.013000	0.15412	0.013000	0.08279	0.320000	0.19540	0.407000	0.25591	0.397000	0.26171	.	.	.	none		0.602	ZNF675-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466433.1	NM_138330	Intron	C	23869831	A	C	23869831	5	2	21	1	0	0	0	0	0	0	1	0	18097	173	6	5	1717	5	ZNF675	19	23869831	Splice_Site	SNP	A	TCGA-FM-8000-01A-11D-2210-10	1506014	23869831	35259152	142	2885											
MAG	4099	hgsc.bcm.edu	37	chr19	35793379	35793379	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tggaagccaacagtgaacggGacaatggtggccgtagaggg	12	5	17	7	2	0	2	0	1	0	1	0	4	0	4	2	5	3	1	2	5	5	1			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr19:35793379G>A	ENST00000392213.3	+	7	1158	c.999G>A	c.(997-999)ggG>ggA	p.G333G	MAG_ENST00000537831.2_Silent_p.G308G|MAG_ENST00000361922.4_Silent_p.G333G	NM_002361.3	NP_002352.1	P20916	MAG_HUMAN	myelin associated glycoprotein	333	Ig-like C2-type 3.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|negative regulation of axonogenesis (GO:0050771)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of axonogenesis (GO:0050770)|substantia nigra development (GO:0021762)	integral component of membrane (GO:0016021)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)	carbohydrate binding (GO:0030246)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(10)|lung(11)|skin(2)|upper_aerodigestive_tract(2)	34	all_lung(56;2.37e-08)|Lung NSC(56;3.66e-08)|Esophageal squamous(110;0.162)	Renal(1328;0.242)	Epithelial(14;3.14e-19)|OV - Ovarian serous cystadenocarcinoma(14;1.5e-18)|all cancers(14;1.5e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			CAGTGAACGGGACAATGGTGG	0.572																																					p.G333G		Atlas-SNP	.											.	MAG	172	.	0			c.G999A						PASS	.						86	73	77					19																	35793379		2203	4300	6503	SO:0001819	synonymous_variant	4099	exon7			GAACGGGACAATG	M29273	CCDS12455.1, CCDS12456.1, CCDS56090.1	19q13.1	2013-01-29			ENSG00000105695	ENSG00000105695		"Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6783	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 4A"	159460		GMA		2476987, 8432525	Standard	NM_080600		Approved	SIGLEC4A, SIGLEC-4A, S-MAG	uc002nyy.2	P20916		ENST00000392213.3:c.999G>A	19.37:g.35793379G>A		55	0	0		29	22	0.758621	NM_080600	B7Z2E5|F5GYC0|Q567S4	Silent	SNP	ENST00000392213.3	37	CCDS12455.1																																																																																			.	.	none		0.572	MAG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466071.1	NM_080600		A	35793379	G	A	35793379	2	1	21	1	0	0	0	0	0	0	0	1	9171	1161	41	2		2	MAG	19	35793379	Silent	SNP	G	TCGA-FM-8000-01A-11D-2210-10	11923548	35793379	23335604	143	2886											
SPRED3	399473	hgsc.bcm.edu	37	chr19	38882747	38882747	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctggctgcgctggccgcactGggtcgaggtgagcagcccag	5	6	17	13	3	0	1	0	1	0	0	1	2	0	1	2	4	3	4	2	4	0	0			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr19:38882747G>A	ENST00000338502.4	+	2	442	c.339G>A	c.(337-339)ctG>ctA	p.L113L	SPRED3_ENST00000587564.2_3'UTR|SPRED3_ENST00000586301.1_Silent_p.L113L|SPRED3_ENST00000587013.1_Silent_p.L157L	NM_001042522.2	NP_001035987.1	Q2MJR0	SPRE3_HUMAN	sprouty-related, EVH1 domain containing 3	113	WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}.				inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)	plasma membrane (GO:0005886)				central_nervous_system(2)|large_intestine(1)|lung(5)|skin(1)	9	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			TGGCCGCACTGGGTCGAGGTG	0.627																																					p.L113L		Atlas-SNP	.											.	SPRED3	47	.	0			c.G339A						PASS	.						81	88	86					19																	38882747		2051	4190	6241	SO:0001819	synonymous_variant	399473	exon2			CGCACTGGGTCGA		CCDS42560.1	19q13	2007-10-05				ENSG00000188766			31041	protein-coding gene	gene with protein product		609293				14618415	Standard	NM_001042522		Approved		uc002oim.4	Q2MJR0		ENST00000338502.4:c.339G>A	19.37:g.38882747G>A		110	0	0		79	35	0.443038	NM_001042522	Q2MJR1	Silent	SNP	ENST00000338502.4	37	CCDS42560.1																																																																																			.	.	none		0.627	SPRED3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459216.1	XM_351191		A	38882747	G	A	38882747	2	1	21	1	0	0	0	0	0	0	0	1	15109	1335	47	2		2	SPRED3	19	38882747	Silent	SNP	G	TCGA-FM-8000-01A-11D-2210-10	3089368	38882747	20246236	144	2887											
USP29	57663	hgsc.bcm.edu	37	chr19	57640529	57640529	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catgtgaaaaaggggatattAgaaaatcaaggtgggaaggg	17	7	15	2	0	1	2	1	1	0	1	1	4	1	4	0	5	0	0	0	5	8	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr19:57640529A>G	ENST00000254181.4	+	4	940	c.486A>G	c.(484-486)ttA>ttG	p.L162L	USP29_ENST00000598197.1_Silent_p.L162L	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	162					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)		AGGGGATATTAGAAAATCAAG	0.358																																					p.L162L		Atlas-SNP	.											.	USP29	186	.	0			c.A486G						PASS	.						87	86	87					19																	57640529		2203	4300	6503	SO:0001819	synonymous_variant	57663	exon4			GATATTAGAAAAT		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.486A>G	19.37:g.57640529A>G		101	0	0		106	81	0.764151	NM_020903		Silent	SNP	ENST00000254181.4	37	CCDS33124.1																																																																																			.	.	none		0.358	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1			G	57640529	A	G	57640529	2	3	21	1	0	0	0	0	0	0	0	1	17074	417	15	3		3	USP29	19	57640529	Silent	SNP	A	TCGA-FM-8000-01A-11D-2210-10	18757782	57640529	1488454	145	2888											
MZF1	7593	hgsc.bcm.edu	37	chr19	59073591	59073591	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcggaaggccttgccacactCagggcatgcgtagggccgtt	7	7	15	12	3	1	0	1	0	0	0	1	1	1	1	3	4	2	3	3	4	2	3			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr19:59073591C>T	ENST00000215057.2	-	6	2613	c.2053G>A	c.(2053-2055)Gag>Aag	p.E685K	AC016629.8_ENST00000593642.1_RNA|AC016629.8_ENST00000600726.1_RNA|AC016629.8_ENST00000600534.1_RNA|MZF1_ENST00000594234.1_3'UTR|MZF1_ENST00000599369.1_Missense_Mutation_p.E685K	NM_001267033.1|NM_198055.1	NP_001253962.1|NP_932172.1	P28698	MZF1_HUMAN	myeloid zinc finger 1	685					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)	p.E685K(1)		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)		TTGCCACACTCAGGGCATGCG	0.697																																					p.E685K		Atlas-SNP	.											MZF1,NS,carcinoma,0,1	MZF1	37	1	1	Substitution - Missense(1)	endometrium(1)	c.G2053A						PASS	.						57	44	48					19																	59073591		2202	4298	6500	SO:0001583	missense	7593	exon6			CACACTCAGGGCA	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.2053G>A	19.37:g.59073591C>T	ENSP00000215057:p.Glu685Lys	94	0	0		47	23	0.489362	NM_198055	M0QXU0|Q7Z729|Q96I71|Q9NRY0|Q9UBW2	Missense_Mutation	SNP	ENST00000215057.2	37	CCDS12988.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.949631	0.73787	.	.	ENSG00000099326	ENST00000215057	T	0.16597	2.33	3.06	3.06	0.35304	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12944	0.0314	N	0.21142	0.635	0.35830	D	0.825217	P	0.43542	0.81	B	0.40506	0.331	T	0.27468	-1.0073	9	0.72032	D	0.01	-17.6756	12.3439	0.55109	0.0:1.0:0.0:0.0	.	685	P28698	MZF1_HUMAN	K	685	ENSP00000215057:E685K	ENSP00000215057:E685K	E	-	1	0	MZF1	63765403	0.000000	0.05858	0.996000	0.52242	0.941000	0.58515	-0.144000	0.10280	2.014000	0.59158	0.462000	0.41574	GAG	.	.	none		0.697	MZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467112.1	NM_198055		T	59073591	C	T	59073591	3	4	21	1	0	0	0	0	1	0	0	0	10117	835	29	2	155	2	MZF1	19	59073591	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	1433062	59073591	55392	146	2889											
ADRA1D	146	hgsc.bcm.edu	37	chr20	4229009	4229009	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggtacttgagtgagtggCgcacgcccacgtaccggtcc	6	8	14	13	4	0	2	0	2	0	0	1	2	1	2	3	3	2	3	3	3	2	3			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr20:4229009C>T	ENST00000379453.4	-	1	712	c.596G>A	c.(595-597)cGc>cAc	p.R199H		NM_000678.3	NP_000669.1	P25100	ADA1D_HUMAN	adrenoceptor alpha 1D	199					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)	p.R199H(1)		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)	GAGTGAGTGGCGCACGCCCAC	0.682																																					p.R199H		Atlas-SNP	.											ADRA1D,NS,carcinoma,0,1	ADRA1D	36	1	1	Substitution - Missense(1)	lung(1)	c.G596A						PASS	.						33	36	35					20																	4229009		2196	4296	6492	SO:0001583	missense	146	exon1			GAGTGGCGCACGC	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.596G>A	20.37:g.4229009C>T	ENSP00000368766:p.Arg199His	135	0	0		83	32	0.385542	NM_000678	Q9NPY0	Missense_Mutation	SNP	ENST00000379453.4	37	CCDS13079.1	.	.	.	.	.	.	.	.	.	.	c	18.46	3.627986	0.66901	.	.	ENSG00000171873	ENST00000379453	T	0.19806	2.12	4.49	4.49	0.54785	GPCR, rhodopsin-like superfamily (1);	0.055353	0.64402	D	0.000004	T	0.34513	0.0900	L	0.48260	1.515	0.31054	N	0.714891	D	0.76494	0.999	D	0.73380	0.98	T	0.24977	-1.0145	10	0.59425	D	0.04	.	8.376	0.32442	0.0:0.8943:0.0:0.1057	.	199	P25100	ADA1D_HUMAN	H	199	ENSP00000368766:R199H	ENSP00000368766:R199H	R	-	2	0	ADRA1D	4177009	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.625000	0.46452	2.339000	0.79563	0.552000	0.68991	CGC	.	.	none		0.682	ADRA1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077812.2	NM_000678		T	4229009	C	T	4229009	3	4	21	1	0	0	0	0	1	0	0	0	336	768	27	1	1130	1	ADRA1D	20	4229009	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10		4229009	58796511	147	2890											
MACROD2	140733	hgsc.bcm.edu	37	chr20	15967421	15967421	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ataaaaattgaaacagaatcGcagagctcatatatggaaac	20	8	7	6	1	1	3	1	1	0	2	2	4	1	4	0	1	3	2	0	1	8	4			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr20:15967421G>A	ENST00000310348.4	+	14	1035	c.1035G>A	c.(1033-1035)tcG>tcA	p.S345S	MACROD2_ENST00000378058.3_Silent_p.S110S|MACROD2_ENST00000402914.1_Silent_p.S110S|MACROD2_ENST00000407045.3_5'UTR|MACROD2_ENST00000217246.4_Silent_p.S345S			A1Z1Q3	MACD2_HUMAN	MACRO domain containing 2	345	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)				AAACAGAATCGCAGAGCTCAT	0.318																																					p.S345S		Atlas-SNP	.											MACROD2,colon,carcinoma,+2,2	MACROD2	34	2	0			c.G1035A						PASS	.						71	67	69					20																	15967421		2203	4300	6503	SO:0001819	synonymous_variant	140733	exon14			AGAATCGCAGAGC	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.1035G>A	20.37:g.15967421G>A		178	0	0		121	50	0.413223	NM_080676	A6NFF7|B0QZ39|B3KWV0|Q0P6D5|Q495E0|Q5W199|Q6ZN71	Silent	SNP	ENST00000310348.4	37	CCDS13120.2																																																																																			.	.	none		0.318	MACROD2-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_080676		A	15967421	G	A	15967421	2	1	21	1	0	0	0	0	0	0	0	1	9155	1074	38	1		1	MACROD2	20	15967421	Silent	SNP	G	TCGA-FM-8000-01A-11D-2210-10	11738412	15967421	47058099	148	2891											
ATP9A	10079	hgsc.bcm.edu	37	chr20	50313972	50313972	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	attctgctcaccttttcaacGatgataaggtctccaacttg	10	14	6	11	1	4	1	2	1	2	0	5	2	4	1	2	1	3	1	2	1	3	5	rs376498362		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr20:50313972G>A	ENST00000338821.5	-	5	750	c.486C>T	c.(484-486)atC>atT	p.I162I	ATP9A_ENST00000311637.5_Intron|ATP9A_ENST00000402822.1_Intron	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	162					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						CCTTTTCAACGATGATAAGGT	0.413																																					p.I162I		Atlas-SNP	.											.	ATP9A	135	.	0			c.C486T						PASS	.						278	258	265					20																	50313972		2203	4300	6503	SO:0001819	synonymous_variant	10079	exon5			TTCAACGATGATA	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.486C>T	20.37:g.50313972G>A		143	0	0		94	34	0.361702	NM_006045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Silent	SNP	ENST00000338821.5	37	CCDS33489.1																																																																																			.	.	weak		0.413	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045		A	50313972	G	A	50313972	2	1	21	1	0	0	0	0	0	0	0	1	1198	1048	37	1		1	ATP9A	20	50313972	Silent	SNP	G	TCGA-FM-8000-01A-11D-2210-10	34346551	50313972	12711548	149	2892											
AURKA	116151	hgsc.bcm.edu	37	chr20	54945628	54945628	+	IGR	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tcatagcaaagaactccaagGctccagagatccaccttctc	13	8	6	14	0	2	2	1	0	1	2	6	3	5	2	4	1	2	2	4	1	4	2			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr20:54945628G>C	ENST00000371384.3	+	0	3046				AURKA_ENST00000395909.4_Missense_Mutation_p.S314R|AURKA_ENST00000347343.2_Missense_Mutation_p.S314R|AURKA_ENST00000371356.2_Missense_Mutation_p.S314R|AURKA_ENST00000395915.3_Missense_Mutation_p.S314R|AURKA_ENST00000395913.3_Missense_Mutation_p.S314R|AURKA_ENST00000395911.1_Missense_Mutation_p.S314R|AURKA_ENST00000395914.1_Missense_Mutation_p.S314R|AURKA_ENST00000395907.1_Missense_Mutation_p.S314R|AURKA_ENST00000312783.6_Missense_Mutation_p.S314R	NM_080821.2	NP_543011.2	Q96KR6	F210B_HUMAN	family with sequence similarity 210, member B							integral component of membrane (GO:0016021)											GAACTCCAAGGCTCCAGAGAT	0.483																																					p.S314R		Atlas-SNP	.											.	AURKA	42	.	0			c.C942G						PASS	.						86	85	85					20																	54945628		2203	4300	6503	SO:0001628	intergenic_variant	6790	exon8			TCCAAGGCTCCAG	AL121914	CCDS13450.1	20q13.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000124098	ENSG00000124098			16102	protein-coding gene	gene with protein product	"hypothetical protein LOC116151"		"chromosome 20 open reading frame 108"	C20orf108		11780052	Standard	NM_080821		Approved	dJ1167H4.1, DKFZP434A1114	uc002xxc.3	Q96KR6	OTTHUMG00000032793		20.37:g.54945628G>C		126	0	0		92	31	0.336957	NM_198437	B2RBQ9|E1P5Y7|Q8WVN2|Q9BYL6|Q9H418	Missense_Mutation	SNP	ENST00000371384.3	37	CCDS13450.1	.	.	.	.	.	.	.	.	.	.	G	17.95	3.514015	0.64522	.	.	ENSG00000087586	ENST00000395909;ENST00000395914;ENST00000347343;ENST00000395915;ENST00000312783;ENST00000371356;ENST00000395913;ENST00000395911;ENST00000395907	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	5.01	2.65	0.31530	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	0.58921	0.2156	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	0.87578	0.996;0.998;0.998;0.998	T	0.71344	-0.4621	10	0.72032	D	0.01	-11.5994	10.6203	0.45476	0.2568:0.0:0.7432:0.0	.	246;314;314;314	B4DX16;A3KFJ0;B2R6Z3;O14965	.;.;.;AURKA_HUMAN	R	314	ENSP00000379245:S314R;ENSP00000379250:S314R;ENSP00000216911:S314R;ENSP00000379251:S314R;ENSP00000321591:S314R;ENSP00000360407:S314R;ENSP00000379249:S314R;ENSP00000379247:S314R;ENSP00000379243:S314R	ENSP00000321591:S314R	S	-	3	2	AURKA	54379035	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.239000	0.32719	1.239000	0.43787	0.650000	0.86243	AGC	.	.	none		0.483	FAM210B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079800.2	NM_080821		C	54945628	G	C	54945628	1	2	21	0	1	0	0	0	0	0	0	0	1221	1194	42	4		4	AURKA	20	54945628	IGR	SNP	G	TCGA-FM-8000-01A-11D-2210-10	4631656	54945628	8079892	150	2893											
KRTAP21-1	337977	hgsc.bcm.edu	37	chr21	32127679	32127679	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccatagccacaggagttgccGtagtagttgcaacacatgtt	11	10	10	10	1	0	0	0	0	0	0	0	1	0	1	3	1	4	6	3	1	4	6	rs147444076		TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr21:32127679G>A	ENST00000335093.3	-	1	67	c.18C>T	c.(16-18)taC>taT	p.Y6Y		NM_181619.1	NP_853650.1	Q3LI58	KR211_HUMAN	keratin associated protein 21-1	6						intermediate filament (GO:0005882)				breast(1)|endometrium(1)|lung(4)|urinary_tract(1)	7						agGAGTTGCCGTAGTAGTTGC	0.517													g|||	1	0.000199681	0.0	0.0	5008	,	,		18266	0.0		0.001	False		,,,				2504	0.0				p.Y6Y		Atlas-SNP	.											KRTAP21-1,NS,carcinoma,0,1	KRTAP21-1	23	1	0			c.C18T						PASS	.	G		0,4406		0,0,2203	125	118	121		18	-2.4	0.1	21	dbSNP_134	121	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KRTAP21-1	NM_181619.1		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		6/80	32127679	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	337977	exon1			GTTGCCGTAGTAG	AP001709	CCDS13606.1	21q22.1	2006-03-13			ENSG00000187005	ENSG00000187005		"Keratin associated proteins"	18945	protein-coding gene	gene with protein product						12359730	Standard	NM_181619		Approved	KAP21.1	uc011adi.2	Q3LI58	OTTHUMG00000057777	ENST00000335093.3:c.18C>T	21.37:g.32127679G>A		41	0	0		34	19	0.558824	NM_181619		Silent	SNP	ENST00000335093.3	37	CCDS13606.1																																																																																			G|1.000;A|0.000	0.000	strong		0.517	KRTAP21-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128229.2			A	32127679	G	A	32127679	2	1	21	1	0	0	0	0	0	0	0	1	8547	1140	40	1		1	KRTAP21-1	21	32127679	Silent	SNP	G	TCGA-FM-8000-01A-11D-2210-10		32127679	16002216	151	2894											
CHEK2	11200	hgsc.bcm.edu	37	chr22	29107902	29107902	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tttattggtacttactgcctCtcttgctgaaccaatagcaa	10	15	6	10	0	1	1	0	1	1	0	2	1	1	1	2	1	6	3	2	1	7	7			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chr22:29107902C>T	ENST00000405598.1	-	7	978	c.787G>A	c.(787-789)Gag>Aag	p.E263K	CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000382566.1_Missense_Mutation_p.E263K|CHEK2_ENST00000382580.2_Missense_Mutation_p.E306K|CHEK2_ENST00000464581.1_5'UTR|CHEK2_ENST00000348295.3_Missense_Mutation_p.E263K|CHEK2_ENST00000544772.1_Missense_Mutation_p.E42K|CHEK2_ENST00000402731.1_Missense_Mutation_p.E263K|CHEK2_ENST00000382578.1_Missense_Mutation_p.E172K|CHEK2_ENST00000404276.1_Missense_Mutation_p.E263K|CHEK2_ENST00000403642.1_Missense_Mutation_p.E172K|CHEK2_ENST00000328354.6_Missense_Mutation_p.E263K			O96017	CHK2_HUMAN	checkpoint kinase 2	263	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						CTTACTGCCTCTCTTGCTGAA	0.368			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																													p.E306K		Atlas-SNP	.	yes	Rec		familial breast cancer	22	22q12.1	11200	CHK2 checkpoint homolog (S. pombe)		E	.	CHEK2	438	.	0			c.G916A						PASS	.						166	135	145					22																	29107902		2203	4300	6503	SO:0001583	missense	11200	exon7			CTGCCTCTCTTGC	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.787G>A	22.37:g.29107902C>T	ENSP00000386087:p.Glu263Lys	102	0	0		65	4	0.0615385	NM_001005735	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Missense_Mutation	SNP	ENST00000405598.1	37	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	C	13.96	2.392506	0.42410	.	.	ENSG00000183765	ENST00000348295;ENST00000382578;ENST00000544772;ENST00000382566;ENST00000328354;ENST00000404276;ENST00000405598;ENST00000382580;ENST00000403642;ENST00000402731;ENST00000447421;ENST00000425190;ENST00000439200	D;T;T;T;T;T;T;T;T;D;T;T;D	0.93712	-1.65;-0.14;-0.14;-0.14;-0.14;-0.14;-0.14;-0.14;-0.14;-1.65;-0.14;-0.14;-3.27	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);	0.185810	0.47455	D	0.000221	D	0.85566	0.5726	N	0.13198	0.31	0.42139	D	0.991506	B;B;B;B;B;B;B	0.28933	0.002;0.228;0.008;0.101;0.082;0.039;0.137	B;B;B;B;B;B;B	0.27796	0.009;0.083;0.012;0.061;0.036;0.079;0.076	T	0.82928	-0.0214	10	0.10902	T	0.67	-1.9415	15.167	0.72837	0.0:1.0:0.0:0.0	.	263;172;42;263;263;263;306	O96017-7;O96017-4;Q9HBS5;A8JZZ5;O96017-12;O96017;O96017-9	.;.;.;.;.;CHK2_HUMAN;.	K	263;172;42;263;263;263;263;306;172;263;196;42;294	ENSP00000329012:E263K;ENSP00000372021:E172K;ENSP00000442458:E42K;ENSP00000372007:E263K;ENSP00000329178:E263K;ENSP00000385747:E263K;ENSP00000386087:E263K;ENSP00000372023:E306K;ENSP00000384919:E172K;ENSP00000384835:E263K;ENSP00000397478:E196K;ENSP00000390244:E42K;ENSP00000408065:E294K	ENSP00000329178:E263K	E	-	1	0	CHEK2	27437902	0.978000	0.34361	0.162000	0.22713	0.680000	0.39746	2.867000	0.48428	2.339000	0.79563	0.591000	0.81541	GAG	.	.	none		0.368	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		T	29107902	C	T	29107902	3	4	21	1	0	0	0	0	1	0	0	0	3337	922	32	2	884	2	CHEK2	22	29107902	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10		29107902	22196664	152	2895											
MXRA5	25878	hgsc.bcm.edu	37	chrX	3242042	3242042	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atataccatgcggtccatttCatccctcacttgagcaatgc	10	12	6	13	1	2	1	2	1	0	0	4	1	4	1	3	1	4	1	3	1	3	4			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chrX:3242042C>A	ENST00000217939.6	-	5	1838	c.1684G>T	c.(1684-1686)Gaa>Taa	p.E562*		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	562	Ig-like C2-type 1.					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)				CGGTCCATTTCATCCCTCACT	0.527																																					p.E562X		Atlas-SNP	.											.	MXRA5	815	.	0			c.G1684T						PASS	.						53	39	44					X																	3242042		2203	4300	6503	SO:0001587	stop_gained	25878	exon5			CCATTTCATCCCT	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.1684G>T	X.37:g.3242042C>A	ENSP00000217939:p.Glu562*	387	1	0.00258398		282	101	0.358156	NM_015419	Q6P1M7|Q9Y3Y8	Nonsense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	C	36	5.738582	0.96865	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	.	.	.	3.76	3.76	0.43208	.	0.000000	0.41194	U	0.000936	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	.	10.7443	0.46170	0.1902:0.8098:0.0:0.0	.	.	.	.	X	562	.	ENSP00000217939:E562X	E	-	1	0	MXRA5	3252042	1.000000	0.71417	0.055000	0.19348	0.387000	0.30353	6.358000	0.73055	1.507000	0.48752	0.525000	0.51046	GAA	.	.	none		0.527	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		A	3242042	C	A	3242042	4	1	21	1	0	0	0	0	0	1	0	0	10012	835	29	4	6814	4	MXRA5	23	3242042	Nonsense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10		3242042	152028518	153	2896											
PCYT1B	9468	hgsc.bcm.edu	37	chrX	24608245	24608245	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgtatctctcggcttcattCatcacggtgaaacctttgaa	9	14	7	11	3	4	2	3	2	1	0	7	2	4	2	1	2	1	2	1	2	3	4			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chrX:24608245C>A	ENST00000379144.2	-	4	511	c.381G>T	c.(379-381)atG>atT	p.M127I	PCYT1B_ENST00000379145.1_Missense_Mutation_p.M109I|PCYT1B_ENST00000356768.4_Missense_Mutation_p.M127I	NM_004845.4	NP_004836.2	Q9Y5K3	PCY1B_HUMAN	phosphate cytidylyltransferase 1, choline, beta	127					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|ovarian follicle development (GO:0001541)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)	choline-phosphate cytidylyltransferase activity (GO:0004105)			breast(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)	17					Choline(DB00122)	CGGCTTCATTCATCACGGTGA	0.473																																					p.M127I		Atlas-SNP	.											.	PCYT1B	88	.	0			c.G381T						PASS	.						142	109	121					X																	24608245		2203	4300	6503	SO:0001583	missense	9468	exon4			TTCATTCATCACG	AF052510	CCDS14213.1, CCDS55391.1, CCDS55392.1	Xp22	2008-02-05	2005-09-05		ENSG00000102230	ENSG00000102230	2.7.7.15		8755	protein-coding gene	gene with protein product		604926	"phosphate cytidylyltransferase 1, choline, beta isoform"			9593753	Standard	NM_004845		Approved	CCT-beta, CTB	uc004dbi.3	Q9Y5K3	OTTHUMG00000021270	ENST00000379144.2:c.381G>T	X.37:g.24608245C>A	ENSP00000368439:p.Met127Ile	130	0	0		114	43	0.377193	NM_004845	A8IX00|B2RCX8|B4DK10|E9PD84|O60621|Q86XC9	Missense_Mutation	SNP	ENST00000379144.2	37	CCDS14213.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.743164	0.89663	.	.	ENSG00000102230	ENST00000379145;ENST00000379144;ENST00000356768	D;D;D	0.96041	-3.89;-3.89;-3.89	5.44	5.44	0.79542	Cytidylyltransferase (1);Rossmann-like alpha/beta/alpha sandwich fold (1);Cytidyltransferase-related (1);	0.000000	0.85682	D	0.000000	D	0.96830	0.8965	M	0.62016	1.91	0.80722	D	1	D;P;P	0.56968	0.978;0.877;0.746	P;P;P	0.60236	0.871;0.823;0.686	D	0.97087	0.9788	10	0.62326	D	0.03	-23.8847	18.3331	0.90277	0.0:1.0:0.0:0.0	.	127;109;127	Q9Y5K3-2;E9PD84;Q9Y5K3	.;.;PCY1B_HUMAN	I	109;127;127	ENSP00000368440:M109I;ENSP00000368439:M127I;ENSP00000349211:M127I	ENSP00000349211:M127I	M	-	3	0	PCYT1B	24518166	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.320000	0.79064	2.524000	0.85096	0.600000	0.82982	ATG	.	.	none		0.473	PCYT1B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056103.1	NM_004845		A	24608245	C	A	24608245	3	1	21	1	0	0	0	0	1	0	0	0	11620	826	29	4	785	4	PCYT1B	23	24608245	Missense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	21366203	24608245	130662315	154	2897											
CACNA1F	778	hgsc.bcm.edu	37	chrX	49088337	49088337	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gggggcccggggcacagcccCcattcgggaccagggcctgc	5	3	17	16	2	0	0	0	0	0	0	1	1	0	1	5	6	2	1	5	6	0	1			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chrX:49088337C>T	ENST00000376265.2	-	2	139	c.78G>A	c.(76-78)tgG>tgA	p.W26*	CACNA1F_ENST00000376251.1_Intron|CACNA1F_ENST00000323022.5_Nonsense_Mutation_p.W26*	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	26					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)	GGCACAGCCCCCATTCGGGAC	0.612																																					p.W26X		Atlas-SNP	.											.	CACNA1F	218	.	0			c.G78A						PASS	.						22	19	20					X																	49088337		2173	4252	6425	SO:0001587	stop_gained	778	exon2			CAGCCCCCATTCG	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.78G>A	X.37:g.49088337C>T	ENSP00000365441:p.Trp26*	102	0	0		70	19	0.271429	NM_001256789	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Nonsense_Mutation	SNP	ENST00000376265.2	37	CCDS35253.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.891730	0.91889	.	.	ENSG00000102001	ENST00000323022;ENST00000376265	.	.	.	4.85	4.85	0.62838	.	0.890957	0.09424	N	0.804021	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.9927	0.41881	0.0:0.9014:0.0:0.0986	.	.	.	.	X	26	.	.	W	-	3	0	CACNA1F	48975281	0.139000	0.22563	1.000000	0.80357	0.747000	0.42532	0.576000	0.23744	2.155000	0.67459	0.436000	0.28706	TGG	.	.	none		0.612	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183		T	49088337	C	T	49088337	4	4	21	1	0	0	0	0	0	1	0	0	2545	624	22	2	6043	2	CACNA1F	23	49088337	Nonsense_Mutation	SNP	C	TCGA-FM-8000-01A-11D-2210-10	24480092	49088337	106182223	155	2898											
MTMR8	55613	hgsc.bcm.edu	37	chrX	63574801	63574801	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttataagaaaaagcataaagAtcttcaggtaatgctggaga	18	10	9	4	0	2	3	1	0	1	3	2	4	2	3	0	2	2	3	0	2	7	5			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chrX:63574801A>T	ENST00000374852.3	-	4	391	c.324T>A	c.(322-324)gaT>gaA	p.D108E	MTMR8_ENST00000453546.1_Missense_Mutation_p.D108E	NM_017677.3	NP_060147.2	Q96EF0	MTMR8_HUMAN	myotubularin related protein 8	108						nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.0?(1)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|skin(3)	37						AAGCATAAAGATCTTCAGGTA	0.363																																					p.D108E		Atlas-SNP	.											.	MTMR8	178	.	1	Whole gene deletion(1)	ovary(1)	c.T324A						PASS	.						61	48	52					X																	63574801		2203	4300	6503	SO:0001583	missense	55613	exon4			ATAAAGATCTTCA	AK000133	CCDS14379.1	Xq11.2-q12	2013-01-11			ENSG00000102043	ENSG00000102043		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	16825	protein-coding gene	gene with protein product						11275328	Standard	NM_017677		Approved	FLJ20126	uc004dvs.3	Q96EF0	OTTHUMG00000021707	ENST00000374852.3:c.324T>A	X.37:g.63574801A>T	ENSP00000363985:p.Asp108Glu	83	0	0		63	30	0.47619	NM_017677	Q5JT99|Q9NXP6	Missense_Mutation	SNP	ENST00000374852.3	37	CCDS14379.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	8.868|8.868	0.948526|0.948526	0.18356|0.18356	.|.	.|.	ENSG00000102043|ENSG00000102043	ENST00000453546;ENST00000374852;ENST00000247400|ENST00000442913	T;T|.	0.81247|.	-1.47;-1.47|.	2.78|2.78	1.59|1.59	0.23543|0.23543	.|.	0.113616|.	0.32868|.	U|.	0.005558|.	T|T	0.08758|0.08758	0.0217|0.0217	N|N	0.01771|0.01771	-0.73|-0.73	0.27265|0.27265	N|N	0.958517|0.958517	B;B|.	0.06786|.	0.001;0.001|.	B;B|.	0.08055|.	0.001;0.003|.	T|T	0.29397|0.29397	-1.0013|-1.0013	10|5	0.10902|.	T|.	0.67|.	.|.	2.1307|2.1307	0.03749|0.03749	0.4848:0.0:0.2795:0.2356|0.4848:0.0:0.2795:0.2356	.|.	108;108|.	B4DQL0;Q96EF0|.	.;MTMR8_HUMAN|.	E|T	108;108;107|25	ENSP00000394003:D108E;ENSP00000363985:D108E|.	ENSP00000247400:D107E|.	D|S	-|-	3|1	2|0	MTMR8|MTMR8	63491526|63491526	0.857000|0.857000	0.29778|0.29778	0.998000|0.998000	0.56505|0.56505	0.978000|0.978000	0.69477|0.69477	-0.122000|-0.122000	0.10627|0.10627	0.349000|0.349000	0.23975|0.23975	-0.453000|-0.453000	0.05500|0.05500	GAT|TCT	.	.	none		0.363	MTMR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056949.2	NM_017677		T	63574801	A	T	63574801	3	4	21	1	0	0	0	0	1	0	0	0	9958	330	12	5	1834	5	MTMR8	23	63574801	Missense_Mutation	SNP	A	TCGA-FM-8000-01A-11D-2210-10	14486464	63574801	91695759	156	2899											
RBMX2	51634	hgsc.bcm.edu	37	chrX	129545348	129545348	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaagaactatccgagtggaTcatgtgtctaactatcgggc	11	10	12	8	2	2	1	1	0	1	1	4	4	3	3	1	3	2	0	1	3	5	3			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chrX:129545348T>C	ENST00000305536.6	+	5	394	c.330T>C	c.(328-330)gaT>gaC	p.D110D	RBMX2_ENST00000469953.1_3'UTR	NM_016024.2	NP_057108.2	Q9Y388	RBMX2_HUMAN	RNA binding motif protein, X-linked 2	110	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.						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						TCCGAGTGGATCATGTGTCTA	0.478																																					p.D110D		Atlas-SNP	.											.	RBMX2	46	.	0			c.T330C						PASS	.						152	138	143					X																	129545348		1914	4108	6022	SO:0001819	synonymous_variant	51634	exon5			AGTGGATCATGTG	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.330T>C	X.37:g.129545348T>C		107	0	0		99	48	0.484848	NM_016024	A8K9Z0|Q5JY82|Q9Y3I8	Silent	SNP	ENST00000305536.6	37	CCDS43993.1																																																																																			.	.	none		0.478	RBMX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058265.1	NM_016024		C	129545348	T	C	129545348	2	2	21	1	0	0	0	0	0	0	0	1	13167	1432	50	3		3	RBMX2	23	129545348	Silent	SNP	T	TCGA-FM-8000-01A-11D-2210-10	65970547	129545348	25725212	157	2900											
L1CAM	3897	hgsc.bcm.edu	37	chrX	153128162	153128162	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgggggaagtggcccctgAgctgtcattgccccctgccg	5	8	15	13	1	1	1	1	1	0	0	1	3	1	2	5	3	3	1	5	3	1	1			TCGA-FM-8000-01A-11D-2210-10	TCGA-FM-8000-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	68ab7686-eb0b-4bdd-8e60-132917be4063	b1ed3024-96f1-49e2-bde2-851174877525	g.chrX:153128162A>G	ENST00000370060.1	-	29	3919	c.3730T>C	c.(3730-3732)Tca>Cca	p.S1244P	L1CAM_ENST00000370057.3_Missense_Mutation_p.S1244P|L1CAM_ENST00000361981.3_Missense_Mutation_p.S1235P|L1CAM_ENST00000361699.4_Missense_Mutation_p.S1240P|L1CAM_ENST00000370055.1_Missense_Mutation_p.S1235P|L1CAM_ENST00000538883.1_Missense_Mutation_p.S1242P|L1CAM_ENST00000543994.1_Missense_Mutation_p.S1246P	NM_001278116.1	NP_001265045.1	P32004	L1CAM_HUMAN	L1 cell adhesion molecule	1244					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)					GTGGCCCCTGAGCTGTCATTG	0.602																																					p.S1244P		Atlas-SNP	.											.	L1CAM	189	.	0			c.T3730C						PASS	.						82	68	73					X																	153128162		2203	4300	6503	SO:0001583	missense	3897	exon28			CCCCTGAGCTGTC	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.3730T>C	X.37:g.153128162A>G	ENSP00000359077:p.Ser1244Pro	163	0	0		98	29	0.295918	NM_000425	A0AV65|A4ZYW4|B2RMU7|G3XAF4|Q8TA87	Missense_Mutation	SNP	ENST00000370060.1	37	CCDS14733.1	.	.	.	.	.	.	.	.	.	.	A	19.92	3.916391	0.73098	.	.	ENSG00000198910	ENST00000370060;ENST00000543994;ENST00000370057;ENST00000538883;ENST00000361981;ENST00000370055;ENST00000370058;ENST00000361699	T;T;T;T;T;T;D;T	0.85773	-0.16;-0.15;-0.16;-0.12;-0.1;-0.1;-2.03;-0.14	4.7	4.7	0.59300	.	0.000000	0.46758	D	0.000276	D	0.89058	0.6607	L	0.48362	1.52	0.46927	D	0.999252	D;P;P	0.89917	1.0;0.513;0.757	D;B;P	0.87578	0.998;0.395;0.45	D	0.89887	0.4034	10	0.87932	D	0	.	12.2435	0.54558	1.0:0.0:0.0:0.0	.	1235;1240;1244	G3XAF4;P32004-2;P32004	.;.;L1CAM_HUMAN	P	1244;1246;1244;1242;1235;1235;140;1240	ENSP00000359077:S1244P;ENSP00000438430:S1246P;ENSP00000359074:S1244P;ENSP00000439645:S1242P;ENSP00000354712:S1235P;ENSP00000359072:S1235P;ENSP00000359075:S140P;ENSP00000355380:S1240P	ENSP00000355380:S1240P	S	-	1	0	L1CAM	152781356	1.000000	0.71417	1.000000	0.80357	0.756000	0.42949	5.828000	0.69307	1.732000	0.51606	0.430000	0.28490	TCA	.	.	none		0.602	L1CAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061094.2	NM_024003		G	153128162	A	G	153128162	3	3	21	1	0	0	0	0	1	0	0	0	8597	304	11	3	47	3	L1CAM	23	153128162	Missense_Mutation	SNP	A	TCGA-FM-8000-01A-11D-2210-10	23582814	153128162	2142398	158	2901											
NOC2L	26155	hgsc.bcm.edu	37	chr1	889421	889421	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtaagccttgatgtccacaCgaagcttcccccagagcggg	9	7	12	13	2	0	2	0	1	0	1	2	3	2	2	4	2	3	2	4	2	2	3	rs3828050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:889421C>T	ENST00000327044.6	-	7	789	c.740G>A	c.(739-741)cGt>cAt	p.R247H	NOC2L_ENST00000487214.1_5'Flank	NM_015658.3	NP_056473	Q9Y3T9	NOC2L_HUMAN	nucleolar complex associated 2 homolog (S. cerevisiae)	247					apoptotic process (GO:0006915)|cellular response to UV (GO:0034644)|chromatin assembly (GO:0031497)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of histone acetylation (GO:0035067)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleolus to nucleoplasm transport (GO:0032066)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|nucleosome binding (GO:0031491)|poly(A) RNA binding (GO:0044822)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)	p.R247L(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	16	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;1.86e-38)|OV - Ovarian serous cystadenocarcinoma(86;6.08e-23)|Colorectal(212;0.000161)|COAD - Colon adenocarcinoma(227;0.000194)|BRCA - Breast invasive adenocarcinoma(365;0.000475)|Kidney(185;0.00231)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0344)|Lung(427;0.2)		GATGTCCACACGAAGCTTCCC	0.647													C|||	2	0.000399361	0.0	0.0	5008	,	,		16641	0.002		0.0	False		,,,				2504	0.0				p.R247H		Atlas-SNP	.											NOC2L,NS,carcinoma,0,1	NOC2L	42	1	1	Substitution - Missense(1)	lung(1)	c.G740A						PASS	.						87	84	85					1																	889421		2203	4300	6503	SO:0001583	missense	26155	exon7			TCCACACGAAGCT	AL050019	CCDS3.1	1p36.33	2014-06-12			ENSG00000188976	ENSG00000188976			24517	protein-coding gene	gene with protein product	"novel INHAT repressor", "protein phosphatase 1, regulatory subunit 12"	610770					Standard	NM_015658		Approved	DKFZP564C186, NET7, NET15, NIR, PPP1R112	uc001abz.4	Q9Y3T9	OTTHUMG00000040720	ENST00000327044.6:c.740G>A	1.37:g.889421C>T	ENSP00000317992:p.Arg247His	288	1	0.00347222		275	143	0.52	NM_015658	Q5SVA3|Q9BTN6	Missense_Mutation	SNP	ENST00000327044.6	37	CCDS3.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	C	11.92	1.783028	0.31593	.	.	ENSG00000188976	ENST00000327044	T	0.67698	-0.28	4.11	4.11	0.48088	Armadillo-type fold (1);	0.152310	0.44688	D	0.000440	T	0.62732	0.2452	L	0.53249	1.67	0.51767	D	0.99993	B;B;B	0.22146	0.065;0.065;0.031	B;B;B	0.18561	0.022;0.022;0.01	T	0.65730	-0.6097	10	0.66056	D	0.02	-17.7817	15.5423	0.76062	0.0:1.0:0.0:0.0	rs3828050	247;247;14	B3KNC3;Q9Y3T9;Q9H9J5	.;NOC2L_HUMAN;.	H	247	ENSP00000317992:R247H	ENSP00000317992:R247H	R	-	2	0	NOC2L	879284	0.999000	0.42202	0.993000	0.49108	0.561000	0.35649	4.286000	0.58995	2.135000	0.66039	0.306000	0.20318	CGT	C|0.999;T|0.001	0.001	strong		0.647	NOC2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097869.1	NM_015658		T	889421	C	T	889421	3	4	22	1	0	0	0	0	1	0	0	0	10522	536	19	1	1561	1	NOC2L	1	889421	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10		889421	248361200	1	2902											
AGRN	375790	hgsc.bcm.edu	37	chr1	978804	978804	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacggcctgtaccctcgggCgggagatccaggtggcgcgc	5	5	16	15	5	0	1	0	0	0	1	2	2	1	1	4	5	1	1	4	5	1	1	rs144164397	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:978804C>T	ENST00000379370.2	+	8	1620	c.1570C>T	c.(1570-1572)Cgg>Tgg	p.R524W		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	524	Kazal-like 5. {ECO:0000255|PROSITE- ProRule:PRU00798}.				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)		TACCCTCGGGCGGGAGATCCA	0.687													C|||	6	0.00119808	0.003	0.0029	5008	,	,		13574	0.0		0.0	False		,,,				2504	0.0				p.R524W		Atlas-SNP	.											.	AGRN	110	.	0			c.C1570T						PASS	.	C	TRP/ARG	12,4360		0,12,2174	32	33	32		1570	3.8	0.6	1	dbSNP_134	32	0,8582		0,0,4291	yes	missense	AGRN	NM_198576.3	101	0,12,6465	TT,TC,CC		0.0,0.2745,0.0926	probably-damaging	524/2046	978804	12,12942	2186	4291	6477	SO:0001583	missense	375790	exon8			CTCGGGCGGGAGA	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.1570C>T	1.37:g.978804C>T	ENSP00000368678:p.Arg524Trp	65	0	0		76	38	0.5	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Missense_Mutation	SNP	ENST00000379370.2	37	CCDS30551.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	15.96	2.987733	0.53934	0.002745	0.0	ENSG00000188157	ENST00000379370	T	0.04454	3.62	4.76	3.76	0.43208	Proteinase inhibitor I1, Kazal (1);Protease inhibitor, Kazal-type (1);	0.533856	0.15977	N	0.235503	T	0.20941	0.0504	M	0.82433	2.59	0.37536	D	0.918126	D	0.89917	1.0	D	0.77557	0.99	T	0.02275	-1.1184	10	0.87932	D	0	-11.7757	9.9656	0.41723	0.4775:0.5225:0.0:0.0	.	524	O00468	AGRIN_HUMAN	W	524	ENSP00000368678:R524W	ENSP00000368678:R524W	R	+	1	2	AGRN	968667	0.998000	0.40836	0.597000	0.28824	0.014000	0.08584	3.246000	0.51414	2.195000	0.70347	0.655000	0.94253	CGG	C|0.999;T|0.001	0.001	strong		0.687	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576		T	978804	C	T	978804	3	4	22	1	0	0	0	0	1	0	0	0	397	759	27	1	1600	1	AGRN	1	978804	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	89383	978804	248271817	2	2903											
TNFRSF18	8784	hgsc.bcm.edu	37	chr1	1141824	1141824	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagcgcgcgtccgttcccGtcccaagcaggaggcgccca	7	4	13	17	6	0	0	0	0	0	0	3	1	3	1	4	2	3	3	4	2	1	1	rs11466676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1141824G>C	ENST00000379268.2	-	1	247	c.128C>G	c.(127-129)aCg>aGg	p.T43R	TNFRSF18_ENST00000328596.6_Missense_Mutation_p.T43R|TNFRSF18_ENST00000486728.1_5'Flank|TNFRSF18_ENST00000379265.5_Missense_Mutation_p.T43R	NM_004195.2|NM_148902.1	NP_004186.1|NP_683700.1	Q9Y5U5	TNR18_HUMAN	tumor necrosis factor receptor superfamily, member 18	43			T -> R (in dbSNP:rs11466676).		apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	tumor necrosis factor-activated receptor activity (GO:0005031)			lung(1)	1	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;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|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)		GTCCGTTCCCGTCCCAAGCAG	0.716													g|||	238	0.047524	0.1702	0.0173	5008	,	,		12979	0.0		0.001	False		,,,				2504	0.0				p.T43R	GBM(157;472 1934 13810 14591 35952)	Atlas-SNP	.											.	TNFRSF18	13	.	0			c.C128G						PASS	.	G	ARG/THR,ARG/THR,ARG/THR	308,3220		10,288,1466	4	5	5		128,128,128	2.1	0	1	dbSNP_120	5	2,7088		0,2,3543	no	missense,missense,missense	TNFRSF18	NM_004195.2,NM_148901.1,NM_148902.1	71,71,71	10,290,5009	CC,CG,GG		0.0282,8.7302,2.9196	benign,benign,benign	43/242,43/256,43/235	1141824	310,10308	1764	3545	5309	SO:0001583	missense	8784	exon1			GTTCCCGTCCCAA	AF125304	CCDS9.1, CCDS10.1, CCDS30552.1	1p36.3	2011-08-11			ENSG00000186891	ENSG00000186891		"Tumor necrosis factor receptor superfamily", "CD molecules"	11914	protein-coding gene	gene with protein product		603905				9177197, 10037686	Standard	NM_004195		Approved	AITR, GITR, CD357	uc001add.3	Q9Y5U5	OTTHUMG00000001414	ENST00000379268.2:c.128C>G	1.37:g.1141824G>C	ENSP00000368570:p.Thr43Arg	33	0	0		22	9	0.409091	NM_148902	B1AME1|O95851|Q5U0I4|Q9NYJ9	Missense_Mutation	SNP	ENST00000379268.2	37	CCDS10.1	84	0.038461538461538464	75	0.1524390243902439	6	0.016574585635359115	2	0.0034965034965034965	1	0.0013192612137203166	G	12.07	1.828233	0.32329	0.087302	2.82E-4	ENSG00000186891	ENST00000328596;ENST00000379268;ENST00000379265	T;T;T	0.60171	1.64;0.31;0.21	3.1	2.14	0.27477	.	0.907582	0.08998	U	0.863377	T	0.00524	0.0017	L	0.50333	1.59	0.80722	P	0.0	D;D;D	0.57571	0.98;0.98;0.98	P;P;P	0.52309	0.695;0.673;0.582	T	0.11084	-1.0602	9	0.87932	D	0	-4.6596	8.7668	0.34708	0.0:0.233:0.767:0.0	rs11466676	43;43;43	Q9Y5U5-2;Q9Y5U5;B1AME3	.;TNR18_HUMAN;.	R	43	ENSP00000328207:T43R;ENSP00000368570:T43R;ENSP00000368567:T43R	ENSP00000328207:T43R	T	-	2	0	TNFRSF18	1131687	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.161000	0.10026	0.563000	0.29222	0.462000	0.41574	ACG	G|0.955;C|0.045	0.045	strong		0.716	TNFRSF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004083.2	NM_004195		C	1141824	G	C	1141824	3	2	22	1	0	0	0	0	1	0	0	0	16306	1145	40	4	870	4	TNFRSF18	1	1141824	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	163020	1141824	248108797	3	2904											
TAS1R3	83756	hgsc.bcm.edu	37	chr1	1269488	1269488	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagcttcggcctagcgcacGccaccaatgccacgctggcc	7	6	10	18	4	1	0	1	0	0	0	2	0	1	0	5	2	3	3	5	2	2	2	rs112507608	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1269488G>A	ENST00000339381.5	+	6	2235	c.2203G>A	c.(2203-2205)Gcc>Acc	p.A735T		NM_152228.1	NP_689414	Q7RTX0	TS1R3_HUMAN	taste receptor, type 1, member 3	735					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of sweet taste (GO:0050916)|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)			kidney(2)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	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;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.88e-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;0.146)		CCTAGCGCACGCCACCAATGC	0.677													g|||	299	0.0597045	0.2148	0.0202	5008	,	,		18080	0.0		0.001	False		,,,				2504	0.0				p.A735T		Atlas-SNP	.											.	TAS1R3	39	.	0			c.G2203A						PASS	.	G	THR/ALA	825,3533		76,673,1430	31	17	22		2203	-1	0	1	dbSNP_132	22	6,8566		0,6,4280	yes	missense	TAS1R3	NM_152228.1	58	76,679,5710	AA,AG,GG		0.07,18.9307,6.4269	benign	735/853	1269488	831,12099	2179	4286	6465	SO:0001583	missense	83756	exon6			GCGCACGCCACCA	AC026283	CCDS30556.1	1p36	2012-08-22			ENSG00000169962	ENSG00000169962		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	15661	protein-coding gene	gene with protein product		605865				11319557	Standard	XM_006710939		Approved	T1R3	uc010nyk.2	Q7RTX0	OTTHUMG00000003071	ENST00000339381.5:c.2203G>A	1.37:g.1269488G>A	ENSP00000344411:p.Ala735Thr	71	0	0		61	29	0.47541	NM_152228	Q5TA49|Q8NGW9	Missense_Mutation	SNP	ENST00000339381.5	37	CCDS30556.1	110	0.05036630036630037	102	0.2073170731707317	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	G	5.972	0.363238	0.11296	0.189307	7.0E-4	ENSG00000169962	ENST00000339381	D	0.88741	-2.42	4.35	-1.05	0.10036	GPCR, family 3, C-terminal (2);	0.499914	0.20112	N	0.098990	T	0.00210	0.0006	L	0.33485	1.01	0.80722	P	0.0	B	0.18166	0.026	B	0.14578	0.011	T	0.24119	-1.0169	9	0.62326	D	0.03	.	9.7028	0.40198	0.4805:0.0:0.5195:0.0	.	735	Q7RTX0	TS1R3_HUMAN	T	735	ENSP00000344411:A735T	ENSP00000344411:A735T	A	+	1	0	TAS1R3	1259351	0.001000	0.12720	0.001000	0.08648	0.011000	0.07611	0.420000	0.21263	-0.093000	0.12396	0.456000	0.33151	GCC	G|0.933;A|0.067	0.067	strong		0.677	TAS1R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008493.1			A	1269488	G	A	1269488	3	1	22	1	0	0	0	0	1	0	0	0	15579	1087	38	1	2225	1	TAS1R3	1	1269488	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	127664	1269488	247981133	4	2905											
DVL1	1855	hgsc.bcm.edu	37	chr1	1277183	1277183	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggtgcccattggtccgggCggctgtgggggcagcaggtt	3	9	20	9	2	0	0	0	0	0	0	1	0	1	0	2	7	2	4	2	7	0	2	rs61735963	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1277183C>T	ENST00000378888.5	-	5	753	c.469G>A	c.(469-471)Gcc>Acc	p.A157T	DVL1_ENST00000378891.5_Missense_Mutation_p.A157T			O14640	DVL1_HUMAN	dishevelled segment polarity protein 1	157				A -> P (in Ref. 1; AAB65242). {ECO:0000305}.	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)		TTGGTCCGGGCGGCTGTGGGG	0.687													c|||	329	0.0656949	0.2375	0.0202	5008	,	,		17330	0.0		0.001	False		,,,				2504	0.0				p.A157T		Atlas-SNP	.											.	DVL1	36	.	0			c.G469A						PASS	.	C	THR/ALA	898,3474		85,728,1373	14	14	14		469	-3.4	0	1	dbSNP_129	14	9,8557		0,9,4274	yes	missense	DVL1	NM_004421.2	58	85,737,5647	TT,TC,CC		0.1051,20.5398,7.0104	benign	157/671	1277183	907,12031	2186	4283	6469	SO:0001583	missense	1855	exon5			TCCGGGCGGCTGT	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.469G>A	1.37:g.1277183C>T	ENSP00000368166:p.Ala157Thr	88	0	0		107	50	0.46729	NM_004421	Q5TA33|Q5TA35	Missense_Mutation	SNP	ENST00000378888.5	37		122	0.055860805860805864	114	0.23170731707317074	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	C	8.305	0.820817	0.16678	0.205398	0.001051	ENSG00000107404	ENST00000378891;ENST00000378888;ENST00000345100	T;T	0.04917	3.53;3.53	4.02	-3.44	0.04796	.	0.469288	0.22130	N	0.064219	T	0.00012	0.0000	N	0.04880	-0.145	0.45621	P	0.0014420000000000543	B	0.02656	0.0	B	0.04013	0.001	T	0.37572	-0.9700	9	0.07813	T	0.8	.	0.2996	0.00271	0.3245:0.167:0.1548:0.3536	.	157	O14640-2	.	T	157	ENSP00000368169:A157T;ENSP00000368166:A157T	ENSP00000340031:A157T	A	-	1	0	DVL1	1267046	0.188000	0.23250	0.019000	0.16419	0.398000	0.30690	0.396000	0.20867	-0.463000	0.06973	0.205000	0.17691	GCC	C|0.931;T|0.069	0.069	strong		0.687	DVL1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000008490.1	NM_004421		T	1277183	C	T	1277183	3	4	22	1	0	0	0	0	1	0	0	0	4837	768	27	1	1587	1	DVL1	1	1277183	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	7695	1277183	247973438	5	2906											
MXRA8	54587	hgsc.bcm.edu	37	chr1	1290408	1290408	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccagtgcaccacctgttgAgcctcctccacgtgccggtc	5	9	9	18	2	0	1	0	1	0	0	4	1	3	1	7	1	3	2	7	1	0	1	rs147996767	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1290408A>G	ENST00000309212.6	-	5	633	c.603T>C	c.(601-603)gcT>gcC	p.A201A	MXRA8_ENST00000477278.2_Silent_p.A192A|MXRA8_ENST00000342753.4_Silent_p.A100A|MXRA8_ENST00000445648.2_Silent_p.A201A	NM_001282582.1|NM_032348.2	NP_001269511.1|NP_115724.1	Q9BRK3	MXRA8_HUMAN	matrix-remodelling associated 8	201	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)		CCACCTGTTGAGCCTCCTCCA	0.751													-|||	361	0.0720847	0.2579	0.0274	5008	,	,		8344	0.0		0.001	False		,,,				2504	0.0				p.A201A		Atlas-SNP	.											.	MXRA8	28	.	0			c.T603C						PASS	.			722,3238		65,592,1323	7	9	9		603	-0.7	1	1	dbSNP_134	9	6,7864		0,6,3929	no	coding-synonymous	MXRA8	NM_032348.2		65,598,5252	GG,GA,AA		0.0762,18.2323,6.1538		201/443	1290408	728,11102	1980	3935	5915	SO:0001819	synonymous_variant	54587	exon5			CTGTTGAGCCTCC	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.603T>C	1.37:g.1290408A>G		11	0	0		14	7	0.5	NM_032348	B3KTR6|B4DE34|Q5TA39|Q96KC3	Silent	SNP	ENST00000309212.6	37	CCDS24.1																																																																																			A|0.939;G|0.061	0.061	strong		0.751	MXRA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008282.2	NM_032348		G	1290408	A	G	1290408	2	3	22	1	0	0	0	0	0	0	0	1	10014	291	11	3		3	MXRA8	1	1290408	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	13225	1290408	247960213	6	2907											
ATAD3C	219293	hgsc.bcm.edu	37	chr1	1403894	1403894	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggcctgggcccgaggacgAgcaaccctcatcctgagtcc	8	5	13	15	2	1	1	1	1	0	0	3	5	3	2	5	3	2	1	5	3	1	0	rs145079480	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1403894A>G	ENST00000378785.2	+	12	2215	c.1220A>G	c.(1219-1221)gAg>gGg	p.E407G		NM_001039211.2	NP_001034300.2	Q5T2N8	ATD3C_HUMAN	ATPase family, AAA domain containing 3C	407							ATP binding (GO:0005524)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|lung(4)	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;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)		CCCGAGGACGAGCAACCCTCA	0.642													N|||	127	0.0253594	0.0923	0.0072	5008	,	,		14787	0.0		0.0	False		,,,				2504	0.0				p.E407G		Atlas-SNP	.											.	ATAD3C	23	.	0			c.A1220G						PASS	.	A	GLY/GLU	425,3979		20,385,1797	22	25	24		1220	-0.4	0	1	dbSNP_134	24	0,8590		0,0,4295	no	missense	ATAD3C	NM_001039211.2	98	20,385,6092	GG,GA,AA		0.0,9.6503,3.2707	benign	407/412	1403894	425,12569	2202	4295	6497	SO:0001583	missense	219293	exon12			AGGACGAGCAACC	AK091918	CCDS44039.1	1p36.33	2010-04-21		2007-02-08	ENSG00000215915	ENSG00000215915		"ATPases / AAA-type"	32151	protein-coding gene	gene with protein product							Standard	NM_001039211		Approved	FLJ34599	uc001aft.2	Q5T2N8	OTTHUMG00000000531	ENST00000378785.2:c.1220A>G	1.37:g.1403894A>G	ENSP00000368062:p.Glu407Gly	290	0	0		276	108	0.391304	NM_001039211	Q8N1Z5	Missense_Mutation	SNP	ENST00000378785.2	37	CCDS44039.1	60	0.027472527472527472	56	0.11382113821138211	4	0.011049723756906077	0	0.0	0	0.0	.	5.440	0.266325	0.10294	0.096503	0.0	ENSG00000215915	ENST00000378785	D	0.94184	-3.37	1.1	-0.358	0.12575	.	.	.	.	.	T	0.13329	0.0323	L	0.36672	1.1	0.80722	P	0.0	B	0.22480	0.07	B	0.19148	0.024	T	0.57980	-0.7717	8	0.34782	T	0.22	.	4.8484	0.13524	0.6826:0.3174:0.0:0.0	.	407	Q5T2N8	ATD3C_HUMAN	G	407	ENSP00000368062:E407G	ENSP00000368062:E407G	E	+	2	0	ATAD3C	1393757	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	0.745000	0.26259	-0.095000	0.12351	0.163000	0.16589	GAG	A|0.972;G|0.028	0.028	strong		0.642	ATAD3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001279.3	NM_001039211		G	1403894	A	G	1403894	3	3	22	1	0	0	0	0	1	0	0	0	1075	304	11	3	1266	3	ATAD3C	1	1403894	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	113486	1403894	247846727	7	2908											
ATAD3A	55210	hgsc.bcm.edu	37	chr1	1458915	1458915	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gccggcggctcctcagtcgaCcccaggacgcgctggagggt	5	5	16	15	5	1	0	1	0	0	0	3	3	2	2	4	5	0	2	4	5	0	0	rs113107431	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1458915C>T	ENST00000378755.5	+	9	1169	c.1075C>T	c.(1075-1077)Ccc>Tcc	p.P359S	ATAD3A_ENST00000536055.1_Missense_Mutation_p.P232S|ATAD3A_ENST00000378756.3_Missense_Mutation_p.P311S	NM_018188.3	NP_060658.3	Q9NVI7	ATD3A_HUMAN	ATPase family, AAA domain containing 3A	359					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)		CCTCAGTCGACCCCAGGACGC	0.706													c|||	108	0.0215655	0.0756	0.0115	5008	,	,		12132	0.0		0.0	False		,,,				2504	0.0				p.P359S		Atlas-SNP	.											.	ATAD3A	35	.	0			c.C1075T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO	341,4065	171.6+/-201.8	11,319,1873	48	47	47		931,694,1075	4.8	0.8	1	dbSNP_132	47	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense	ATAD3A	NM_001170535.1,NM_001170536.1,NM_018188.3	74,74,74	11,321,6171	TT,TC,CC		0.0233,7.7394,2.6372	benign,benign,benign	311/587,232/508,359/635	1458915	343,12663	2203	4300	6503	SO:0001583	missense	55210	exon9			AGTCGACCCCAGG	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.1075C>T	1.37:g.1458915C>T	ENSP00000368030:p.Pro359Ser	131	0	0		181	102	0.563536	NM_018188	B3KPB3|D2K8Q1|G3V1I6|Q5SV23|Q8N275|Q96A50	Missense_Mutation	SNP	ENST00000378755.5	37	CCDS31.1	55|55	0.025183150183150184|0.025183150183150184	49|49	0.09959349593495935|0.09959349593495935	6|6	0.016574585635359115|0.016574585635359115	0|0	0.0|0.0	0|0	0.0|0.0	c|c	9.414|9.414	1.081264|1.081264	0.20309|0.20309	0.077394|0.077394	2.33E-4|2.33E-4	ENSG00000197785|ENSG00000197785	ENST00000378756;ENST00000378755;ENST00000536055|ENST00000339113	D;D;D|.	0.94723|.	-3.25;-3.12;-3.5|.	4.8|4.8	4.8|4.8	0.61643|0.61643	.|.	0.325455|.	0.33895|.	N|.	0.004457|.	T|T	0.01835|0.01835	0.0058|0.0058	L|L	0.41906|0.41906	1.305|1.305	0.34198|0.34198	D|D	0.672866|0.672866	B;B|.	0.28439|.	0.047;0.212|.	B;B|.	0.22601|.	0.027;0.04|.	T|T	0.30416|0.30416	-0.9979|-0.9979	10|5	0.33940|.	T|.	0.23|.	.|.	8.613|8.613	0.33815|0.33815	0.1587:0.665:0.1764:0.0|0.1587:0.665:0.1764:0.0	.|.	311;359|.	D2K8Q1;Q9NVI7|.	.;ATD3A_HUMAN|.	S|I	311;359;232|296	ENSP00000368031:P311S;ENSP00000368030:P359S;ENSP00000439290:P232S|.	ENSP00000368030:P359S|.	P|T	+|+	1|2	0|0	ATAD3A|ATAD3A	1448778|1448778	1.000000|1.000000	0.71417|0.71417	0.842000|0.842000	0.33263|0.33263	0.047000|0.047000	0.14425|0.14425	3.205000|3.205000	0.51090|0.51090	2.220000|2.220000	0.72140|0.72140	0.556000|0.556000	0.70494|0.70494	CCC|ACC	C|0.972;T|0.028	0.028	strong		0.706	ATAD3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000001365.1	NM_018188		T	1458915	C	T	1458915	3	4	22	1	0	0	0	0	1	0	0	0	1073	507	18	2	1109	2	ATAD3A	1	1458915	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	55021	1458915	247791706	8	2909											
ATAD3A	55210	hgsc.bcm.edu	37	chr1	1458944	1458944	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcgctggagggtgttgtgctCagtgtaagtcggtgtgcctg	4	12	18	7	2	1	0	1	0	0	0	2	1	1	1	1	3	2	4	1	3	1	2	rs112145664	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1458944C>T	ENST00000378755.5	+	9	1198	c.1104C>T	c.(1102-1104)ctC>ctT	p.L368L	ATAD3A_ENST00000536055.1_Silent_p.L241L|ATAD3A_ENST00000378756.3_Silent_p.L320L	NM_018188.3	NP_060658.3	Q9NVI7	ATD3A_HUMAN	ATPase family, AAA domain containing 3A	368					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)		GTGTTGTGCTCAGTGTAAGTC	0.711													N|||	109	0.0217652	0.0756	0.0115	5008	,	,		12972	0.001		0.0	False		,,,				2504	0.0				p.L368L		Atlas-SNP	.											.	ATAD3A	35	.	0			c.C1104T						PASS	.	G	,,	346,4060	177.3+/-206.3	11,324,1868	57	56	56		960,723,1104	2.9	0.9	1	dbSNP_132	56	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	ATAD3A	NM_001170535.1,NM_001170536.1,NM_018188.3	,,	11,326,6166	TT,TC,CC		0.0233,7.8529,2.6757	,,	320/587,241/508,368/635	1458944	348,12658	2203	4300	6503	SO:0001819	synonymous_variant	55210	exon9			TGTGCTCAGTGTA	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.1104C>T	1.37:g.1458944C>T		139	0	0		186	106	0.569892	NM_018188	B3KPB3|D2K8Q1|G3V1I6|Q5SV23|Q8N275|Q96A50	Silent	SNP	ENST00000378755.5	37	CCDS31.1	43	0.019688644688644688	37	0.07520325203252033	6	0.016574585635359115	0	0.0	0	0.0	c	0.686	-0.796159	0.02862	0.078529	2.33E-4	ENSG00000197785	ENST00000339113	.	.	.	4.8	2.93	0.34026	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.355	0.66730	0.0:0.5744:0.4256:0.0	.	.	.	.	X	306	.	.	Q	+	1	0	ATAD3A	1448807	1.000000	0.71417	0.865000	0.33974	0.004000	0.04260	0.553000	0.23391	0.465000	0.27167	-1.655000	0.00754	CAG	C|0.974;T|0.026	0.026	strong		0.711	ATAD3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000001365.1	NM_018188		T	1458944	C	T	1458944	2	4	22	1	0	0	0	0	0	0	0	1	1073	813	29	2		2	ATAD3A	1	1458944	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	29	1458944	247791677	9	2910											
NADK	65220	hgsc.bcm.edu	37	chr1	1688719	1688719	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttggggacttgttccacgtCagccgctggctcgcggggtc	3	11	15	12	4	1	0	1	0	0	0	4	1	2	1	2	5	1	3	2	5	0	3	rs78921781	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1688719C>A	ENST00000341426.5	-	4	515	c.294G>T	c.(292-294)ctG>ctT	p.L98L	NADK_ENST00000492768.1_5'UTR|NADK_ENST00000342348.5_Silent_p.L66L|NADK_ENST00000344463.4_Silent_p.L202L|NADK_ENST00000378625.1_Silent_p.L202L|NADK_ENST00000341991.3_Silent_p.L98L	NM_023018.4	NP_075394.3	O95544	NADK_HUMAN	NAD kinase	98					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)		TGTTCCACGTCAGCCGCTGGC	0.552													C|||	27	0.00539137	0.0159	0.0014	5008	,	,		10189	0.001		0.004	False		,,,				2504	0.0				p.L202L		Atlas-SNP	.											.	NADK	79	.	0			c.G606T						PASS	.	C	,,,	69,4337	62.3+/-99.4	1,67,2135	97	98	98		294,606,198,294	5.7	1	1	dbSNP_133	98	7,8593	6.4+/-24.3	1,5,4294	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NADK	NM_001198993.1,NM_001198994.1,NM_001198995.1,NM_023018.4	,,,	2,72,6429	AA,AC,CC		0.0814,1.566,0.5843	,,,	98/447,202/592,66/415,98/447	1688719	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	65220	exon6			CCACGTCAGCCGC	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.294G>T	1.37:g.1688719C>A		71	0	0		73	39	0.534247	NM_001198994	A6NNN3|A8K296|B7Z434|F5GXR5|Q5QPS4|Q9H2P2|Q9H931	Silent	SNP	ENST00000341426.5	37	CCDS30565.1																																																																																			C|0.995;A|0.005	0.005	strong		0.552	NADK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002769.1	NM_023018		A	1688719	C	A	1688719	2	1	22	1	0	0	0	0	0	0	0	1	10146	813	29	4		4	NADK	1	1688719	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	229775	1688719	247561902	10	2911											
PRDM16	63976	hgsc.bcm.edu	37	chr1	3322139	3322139	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcccacgcctgccccgactgCgggaagaccttcgccacgtc	6	5	11	19	5	0	1	0	0	0	1	2	3	0	2	6	1	2	0	6	1	1	1	rs61745281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:3322139C>T	ENST00000270722.5	+	8	1162	c.1113C>T	c.(1111-1113)tgC>tgT	p.C371C	PRDM16_ENST00000378398.3_Silent_p.C372C|PRDM16_ENST00000514189.1_Silent_p.C372C|PRDM16_ENST00000441472.2_Silent_p.C371C|PRDM16_ENST00000442529.2_Silent_p.C371C|PRDM16_ENST00000511072.1_Silent_p.C372C|PRDM16_ENST00000378391.2_Silent_p.C371C|PRDM16_ENST00000512462.1_3'UTR			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	371					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)		GCCCCGACTGCGGGAAGACCT	0.657			T	EVI1	"MDS, AML"								c|||	139	0.0277556	0.0998	0.0101	5008	,	,		14941	0.0		0.0	False		,,,				2504	0.0				p.C371C		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.C1113T						PASS	.	C	,	363,4035		14,335,1850	41	48	46		1113,1113	-4	1	1	dbSNP_129	46	6,8576		0,6,4285	no	coding-synonymous,coding-synonymous	PRDM16	NM_022114.3,NM_199454.2	,	14,341,6135	TT,TC,CC		0.0699,8.2538,2.8428	,	371/1277,371/1258	3322139	369,12611	2199	4291	6490	SO:0001819	synonymous_variant	63976	exon8			CGACTGCGGGAAG	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.1113C>T	1.37:g.3322139C>T		56	0	0		66	36	0.545455	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Silent	SNP	ENST00000270722.5	37	CCDS41236.2																																																																																			C|0.984;T|0.016	0.016	strong		0.657	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114		T	3322139	C	T	3322139	2	4	22	1	0	0	0	0	0	0	0	1	12469	776	27	1		1	PRDM16	1	3322139	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1633420	3322139	245928482	11	2912											
NPHP4	261734	hgsc.bcm.edu	37	chr1	5965824	5965824	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cttccaggtgggagataccgGcctccaacgggaactcctgc	8	7	12	14	2	0	1	0	0	0	1	3	3	3	2	5	4	4	0	5	4	3	2	rs12093500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:5965824G>C	ENST00000378156.4	-	14	1896	c.1631C>G	c.(1630-1632)gCc>gGc	p.A544G	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	544			A -> G (in dbSNP:rs12093500). {ECO:0000269|PubMed:15776426}.		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)		GGAGATACCGGCCTCCAACGG	0.572													C|||	127	0.0253594	0.0877	0.0115	5008	,	,		18214	0.0		0.003	False		,,,				2504	0.0				p.A544G		Atlas-SNP	.											.	NPHP4	119	.	0			c.C1631G						PASS	.	C	GLY/ALA	306,3584		10,286,1649	28	31	30		1631	4.5	0.3	1	dbSNP_120	30	14,8254		0,14,4120	yes	missense	NPHP4	NM_015102.3	60	10,300,5769	CC,CG,GG		0.1693,7.8663,2.632	benign	544/1427	5965824	320,11838	1945	4134	6079	SO:0001583	missense	261734	exon14			ATACCGGCCTCCA	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.1631C>G	1.37:g.5965824G>C	ENSP00000367398:p.Ala544Gly	101	0	0		132	64	0.484848	NM_015102	Q8IWC0	Missense_Mutation	SNP	ENST00000378156.4	37	CCDS44052.1	39	0.017857142857142856	30	0.06097560975609756	6	0.016574585635359115	0	0.0	3	0.00395778364116095	C	0.007	-1.936935	0.00484	0.078663	0.001693	ENSG00000131697	ENST00000378156	D	0.87334	-2.24	5.42	4.5	0.54988	.	0.527792	0.18448	N	0.140932	T	0.08626	0.0214	N	0.00436	-1.5	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.06643	-1.0815	10	0.10377	T	0.69	.	16.1591	0.81686	0.0:0.6272:0.3728:0.0	rs12093500;rs61332996;rs12093500	544	O75161	NPHP4_HUMAN	G	544	ENSP00000367398:A544G	ENSP00000367398:A544G	A	-	2	0	NPHP4	5888411	.	.	0.285000	0.24819	0.013000	0.08279	.	.	0.644000	0.30656	-0.216000	0.12614	GCC	G|0.980;C|0.020	0.020	strong		0.572	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2			C	5965824	G	C	5965824	3	2	22	1	0	0	0	0	1	0	0	0	10590	1203	42	4	2717	4	NPHP4	1	5965824	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2643685	5965824	243284797	12	2913											
RNF207	388591	hgsc.bcm.edu	37	chr1	6267523	6267523	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggacagctcaggggatggCgtggaggcggtgcgctgtgc	5	7	21	8	3	1	0	1	0	0	0	1	3	1	3	0	7	3	2	0	7	0	0	rs58587405	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:6267523C>T	ENST00000377939.4	+	3	403	c.276C>T	c.(274-276)ggC>ggT	p.G92G	RP1-120G22.11_ENST00000455744.1_RNA|RNF207_ENST00000377948.2_5'UTR	NM_207396.2	NP_997279.2	Q6ZRF8	RN207_HUMAN	ring finger protein 207	92						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(2)	16	Ovarian(185;0.0634)	all_cancers(23;1.22e-38)|all_epithelial(116;4.25e-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;4.84e-38)|GBM - Glioblastoma multiforme(13;5.77e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.88e-19)|Colorectal(212;6.9e-08)|COAD - Colon adenocarcinoma(227;8.13e-06)|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;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		CAGGGGATGGCGTGGAGGCGG	0.692													C|||	152	0.0303514	0.1059	0.0144	5008	,	,		10633	0.0		0.002	False		,,,				2504	0.0				p.G92G		Atlas-SNP	.											.	RNF207	45	.	0			c.C276T						PASS	.	C		427,3971		22,383,1794	23	26	25		276	3.6	0.4	1	dbSNP_129	25	5,8589		0,5,4292	no	coding-synonymous	RNF207	NM_207396.2		22,388,6086	TT,TC,CC		0.0582,9.709,3.3251		92/635	6267523	432,12560	2199	4297	6496	SO:0001819	synonymous_variant	388591	exon3			GGATGGCGTGGAG	AK128246	CCDS59.2	1p36.31	2008-11-19			ENSG00000158286	ENSG00000158286		"RING-type (C3HC4) zinc fingers"	32947	protein-coding gene	gene with protein product	"OTTHUMG00000001089"		"chromosome 1 open reading frame 188"	C1orf188			Standard	NM_207396		Approved	FLJ46380, FLJ32096	uc001amg.3	Q6ZRF8	OTTHUMG00000001089	ENST00000377939.4:c.276C>T	1.37:g.6267523C>T		214	0	0		294	152	0.517007	NM_207396	A2VCM8|B4DFR6|Q5TGS6|Q6ZS63|Q96MP2	Silent	SNP	ENST00000377939.4	37	CCDS59.2																																																																																			C|0.966;T|0.034	0.034	strong		0.692	RNF207-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003669.2	NM_207396		T	6267523	C	T	6267523	2	4	22	1	0	0	0	0	0	0	0	1	13489	755	27	1		1	RNF207	1	6267523	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	301699	6267523	242983098	13	2914											
RNF207	388591	hgsc.bcm.edu	37	chr1	6278425	6278425	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaggaacaacgcggcctcaGccaggtaaagcaagtctctc	12	5	11	13	2	2	0	1	0	1	0	4	1	2	1	2	3	4	3	2	3	5	1	rs61746089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:6278425G>A	ENST00000377939.4	+	17	1856	c.1729G>A	c.(1729-1731)Gcc>Acc	p.A577T	RNF207_ENST00000483336.1_3'UTR|RNF207_ENST00000377948.2_3'UTR	NM_207396.2	NP_997279.2	Q6ZRF8	RN207_HUMAN	ring finger protein 207	577						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(2)	16	Ovarian(185;0.0634)	all_cancers(23;1.22e-38)|all_epithelial(116;4.25e-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;4.84e-38)|GBM - Glioblastoma multiforme(13;5.77e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.88e-19)|Colorectal(212;6.9e-08)|COAD - Colon adenocarcinoma(227;8.13e-06)|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;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		CGCGGCCTCAGCCAGGTAAAG	0.577													G|||	29	0.00579073	0.0204	0.0029	5008	,	,		20029	0.0		0.0	False		,,,				2504	0.0				p.A577T		Atlas-SNP	.											.	RNF207	45	.	0			c.G1729A						PASS	.	G	THR/ALA	79,4175		0,79,2048	59	70	66		1729	-1.1	0.7	1	dbSNP_129	66	0,8490		0,0,4245	yes	missense	RNF207	NM_207396.2	58	0,79,6293	AA,AG,GG		0.0,1.8571,0.6199	benign	577/635	6278425	79,12665	2127	4245	6372	SO:0001583	missense	388591	exon17			GCCTCAGCCAGGT	AK128246	CCDS59.2	1p36.31	2008-11-19			ENSG00000158286	ENSG00000158286		"RING-type (C3HC4) zinc fingers"	32947	protein-coding gene	gene with protein product	"OTTHUMG00000001089"		"chromosome 1 open reading frame 188"	C1orf188			Standard	NM_207396		Approved	FLJ46380, FLJ32096	uc001amg.3	Q6ZRF8	OTTHUMG00000001089	ENST00000377939.4:c.1729G>A	1.37:g.6278425G>A	ENSP00000367173:p.Ala577Thr	91	0	0		96	51	0.53125	NM_207396	A2VCM8|B4DFR6|Q5TGS6|Q6ZS63|Q96MP2	Missense_Mutation	SNP	ENST00000377939.4	37	CCDS59.2	17	0.007783882783882784	15	0.03048780487804878	2	0.0055248618784530384	0	0.0	0	0.0	G	12.17	1.856674	0.32791	0.018571	0.0	ENSG00000158286	ENST00000377939	T	0.17691	2.26	5.1	-1.12	0.09808	.	1.899990	0.03308	N	0.190106	T	0.02807	0.0084	N	0.16478	0.41	0.53005	D	0.999968	B	0.06786	0.001	B	0.08055	0.003	T	0.39502	-0.9611	10	0.13470	T	0.59	-18.452	4.6334	0.12513	0.3114:0.3955:0.293:0.0	rs61746089	577	Q6ZRF8	RN207_HUMAN	T	577	ENSP00000367173:A577T	ENSP00000367173:A577T	A	+	1	0	RNF207	6201012	0.008000	0.16893	0.657000	0.29651	0.042000	0.13812	-0.175000	0.09825	0.123000	0.18342	-0.222000	0.12452	GCC	G|0.991;A|0.009	0.009	strong		0.577	RNF207-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003669.2	NM_207396		A	6278425	G	A	6278425	3	1	22	1	0	0	0	0	1	0	0	0	13489	971	34	2	1791	2	RNF207	1	6278425	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	10902	6278425	242972196	14	2915											
ACOT7	11332	hgsc.bcm.edu	37	chr1	6324747	6324747	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagcgcttcttctcgtcctcGgtctcgggctgtggaccaca	5	11	11	14	4	3	0	0	0	3	0	7	1	4	1	2	3	1	2	2	3	1	2	rs61739537	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:6324747G>A	ENST00000377855.2	-	9	1199	c.1053C>T	c.(1051-1053)acC>acT	p.T351T	ACOT7_ENST00000608083.1_Silent_p.T309T|ACOT7_ENST00000377845.3_Silent_p.T321T|ACOT7_ENST00000545482.1_Silent_p.T236T|ACOT7_ENST00000361521.4_Silent_p.T341T|ACOT7_ENST00000377842.3_Silent_p.T300T	NM_181864.2	NP_863654.1	O00154	BACH_HUMAN	acyl-CoA thioesterase 7	351					coenzyme A biosynthetic process (GO:0015937)|fatty acid catabolic process (GO:0009062)|long-chain fatty-acyl-CoA catabolic process (GO:0036116)|medium-chain fatty acid biosynthetic process (GO:0051792)|medium-chain fatty-acyl-CoA catabolic process (GO:0036114)|palmitic acid biosynthetic process (GO:1900535)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)	carboxylic ester hydrolase activity (GO:0052689)|fatty-acyl-CoA binding (GO:0000062)|long-chain fatty acyl-CoA binding (GO:0036042)|palmitoyl-CoA hydrolase activity (GO:0016290)|protein homodimerization activity (GO:0042803)	p.T341T(1)		kidney(1)|large_intestine(3)|lung(10)|pancreas(1)|prostate(1)	16	Ovarian(185;0.0634)|all_lung(157;0.175)	all_cancers(23;1.42e-38)|all_epithelial(116;3.96e-23)|all_lung(118;3.69e-08)|Lung NSC(185;8.52e-07)|all_hematologic(16;6.92e-06)|Colorectal(325;4.53e-05)|Acute lymphoblastic leukemia(12;5e-05)|all_neural(13;0.000164)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;9.16e-37)|GBM - Glioblastoma multiforme(13;5.89e-29)|OV - Ovarian serous cystadenocarcinoma(86;7.63e-19)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;2.06e-05)|Kidney(185;7.74e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00129)|BRCA - Breast invasive adenocarcinoma(365;0.00132)|STAD - Stomach adenocarcinoma(132;0.00195)|READ - Rectum adenocarcinoma(331;0.0481)		TCTCGTCCTCGGTCTCGGGCT	0.647													G|||	99	0.0197684	0.062	0.0086	5008	,	,		19936	0.0		0.0089	False		,,,				2504	0.002				p.T351T	GBM(74;673 1226 4974 11850 13190)	Atlas-SNP	.											ACOT7,NS,carcinoma,0,1	ACOT7	71	1	1	Substitution - coding silent(1)	pancreas(1)	c.C1053T						PASS	.	G	,,,	244,4160	138.4+/-174.2	9,226,1967	143	102	116		1023,1053,963,900	-7.1	0.9	1	dbSNP_129	116	69,8531	40.3+/-97.0	1,67,4232	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ACOT7	NM_007274.3,NM_181864.2,NM_181865.2,NM_181866.2	,,,	10,293,6199	AA,AG,GG		0.8023,5.5404,2.407	,,,	341/371,351/381,321/351,300/330	6324747	313,12691	2202	4300	6502	SO:0001819	synonymous_variant	11332	exon9			GTCCTCGGTCTCG	AB074417	CCDS65.1, CCDS66.1, CCDS67.1, CCDS30573.1	1p36	2008-08-14			ENSG00000097021	ENSG00000097021		"Acyl CoA thioesterases"	24157	protein-coding gene	gene with protein product	"brain acyl CoA hydrolase"	602587				10578051, 16103133, 16940157	Standard	XM_005263427		Approved	BACH, ACH1, ACT, CTE-II, LACH1, MGC1126, hBACH	uc001amt.3	O00154	OTTHUMG00000001295	ENST00000377855.2:c.1053C>T	1.37:g.6324747G>A		47	0	0		78	34	0.435897	NM_181864	A8K0K7|A8K232|A8K6B8|A8K837|B3KQ12|O43703|Q53Y78|Q5JYL2|Q5JYL3|Q5JYL4|Q5JYL5|Q5JYL6|Q5TGR4|Q9UJM9|Q9Y539|Q9Y540	Silent	SNP	ENST00000377855.2	37	CCDS65.1																																																																																			G|0.972;A|0.028	0.028	strong		0.647	ACOT7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003773.1	NM_007274		A	6324747	G	A	6324747	2	1	22	1	0	0	0	0	0	0	0	1	155	1103	39	1		1	ACOT7	1	6324747	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	46322	6324747	242925874	15	2916											
TNFRSF25	8718	hgsc.bcm.edu	37	chr1	6524649	6524649	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cggtgcagggccccgcagtcTaggcatggttggcagtagaa	8	7	16	10	2	1	1	0	0	1	1	1	1	1	1	2	5	1	6	2	5	3	3	rs35137293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:6524649T>C	ENST00000356876.3	-	4	513	c.426A>G	c.(424-426)ctA>ctG	p.L142L	TNFRSF25_ENST00000348333.3_Silent_p.L97L|TNFRSF25_ENST00000461703.2_5'UTR|TNFRSF25_ENST00000377782.3_Silent_p.L142L|TNFRSF25_ENST00000351748.3_Intron|TNFRSF25_ENST00000351959.5_Silent_p.L142L	NM_003790.2|NM_148967.1	NP_003781.1|NP_683868.1	Q93038	TNR25_HUMAN	tumor necrosis factor receptor superfamily, member 25	142					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)		CCCCGCAGTCTAGGCATGGTT	0.627													t|||	104	0.0207668	0.0734	0.0072	5008	,	,		16978	0.0		0.002	False		,,,				2504	0.0				p.L142L		Atlas-SNP	.											.	TNFRSF25	22	.	0			c.A426G						PASS	.	T	,,,,,	262,4144	147.6+/-182.1	5,252,1946	52	56	54		426,426,426,426,291,	-6.5	0	1	dbSNP_126	54	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron	TNFRSF25	NM_001039664.1,NM_003790.2,NM_148965.1,NM_148966.1,NM_148967.1,NM_148970.1	,,,,,	5,258,6240	CC,CT,TT		0.0698,5.9464,2.0606	,,,,,	142/182,142/418,142/427,142/381,97/373,	6524649	268,12738	2203	4300	6503	SO:0001819	synonymous_variant	8718	exon4			GCAGTCTAGGCAT	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.426A>G	1.37:g.6524649T>C		131	0	0		110	50	0.454545	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	37	CCDS71.1																																																																																			T|0.978;C|0.022	0.022	strong		0.627	TNFRSF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002259.1	NM_148965		C	6524649	T	C	6524649	2	2	22	1	0	0	0	0	0	0	0	1	16311	1509	53	3		3	TNFRSF25	1	6524649	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	199902	6524649	242725972	16	2917											
TNFRSF25	8718	hgsc.bcm.edu	37	chr1	6525257	6525257	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggagttgccgcagggctcCgtgcaaggggccttcaggta	6	8	17	10	2	1	0	1	0	0	0	2	1	2	1	3	5	2	5	3	5	2	3	rs45438594	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:6525257C>T	ENST00000356876.3	-	3	273	c.186G>A	c.(184-186)acG>acA	p.T62T	TNFRSF25_ENST00000348333.3_Intron|TNFRSF25_ENST00000461703.2_5'UTR|TNFRSF25_ENST00000377782.3_Silent_p.T62T|TNFRSF25_ENST00000351748.3_Intron|TNFRSF25_ENST00000351959.5_Silent_p.T62T	NM_003790.2|NM_148967.1	NP_003781.1|NP_683868.1	Q93038	TNR25_HUMAN	tumor necrosis factor receptor superfamily, member 25	62					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)		CGCAGGGCTCCGTGCAAGGGG	0.647													c|||	186	0.0371406	0.1135	0.0115	5008	,	,		16887	0.0		0.004	False		,,,				2504	0.0245				p.T62T		Atlas-SNP	.											.	TNFRSF25	22	.	0			c.G186A						PASS	.		,,,,,	397,4009	194.0+/-219.0	16,365,1822	45	43	44		186,186,186,186,,	-3.9	0.5	1	dbSNP_127	44	11,8589	7.1+/-27.0	0,11,4289	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron,intron	TNFRSF25	NM_001039664.1,NM_003790.2,NM_148965.1,NM_148966.1,NM_148967.1,NM_148970.1	,,,,,	16,376,6111	TT,TC,CC		0.1279,9.0104,3.137	,,,,,	62/182,62/418,62/427,62/381,,	6525257	408,12598	2203	4300	6503	SO:0001819	synonymous_variant	8718	exon3			GGGCTCCGTGCAA	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.186G>A	1.37:g.6525257C>T		115	0	0		88	49	0.556818	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	37	CCDS71.1																																																																																			C|0.965;T|0.035	0.035	strong		0.647	TNFRSF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002259.1	NM_148965		T	6525257	C	T	6525257	2	4	22	1	0	0	0	0	0	0	0	1	16311	639	23	1		1	TNFRSF25	1	6525257	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	608	6525257	242725364	17	2918											
PER3	8863	hgsc.bcm.edu	37	chr1	7880585	7880585	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccaacaaatggacggtccatAgacacaggaggaggagctcc	14	4	12	11	1	0	1	0	0	0	1	2	5	2	5	3	5	2	1	3	5	3	1	rs17031601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:7880585A>T	ENST00000361923.2	+	15	1993	c.1818A>T	c.(1816-1818)atA>atT	p.I606I	PER3_ENST00000377532.3_Silent_p.I614I|RP3-467L1.4_ENST00000451646.1_RNA	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	606	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)		GACGGTCCATAGACACAGGAG	0.507													A|||	67	0.0133786	0.0477	0.0058	5008	,	,		18040	0.0		0.0	False		,,,				2504	0.0				p.I606I		Atlas-SNP	.											.	PER3	95	.	0			c.A1818T						PASS	.	A		174,4232	115.4+/-153.4	3,168,2032	79	65	70		1818	-0.2	0	1	dbSNP_123	70	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	PER3	NM_016831.1		3,171,6329	TT,TA,AA		0.0349,3.9492,1.3609		606/1202	7880585	177,12829	2203	4300	6503	SO:0001819	synonymous_variant	8863	exon15			GTCCATAGACACA	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.1818A>T	1.37:g.7880585A>T		183	0	0		213	113	0.530516	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Silent	SNP	ENST00000361923.2	37	CCDS89.1																																																																																			A|0.985;T|0.015	0.015	strong		0.507	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831		T	7880585	A	T	7880585	2	4	22	1	0	0	0	0	0	0	0	1	11740	410	15	5		5	PER3	1	7880585	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1355328	7880585	241370036	18	2919											
PER3	8863	hgsc.bcm.edu	37	chr1	7887234	7887234	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcaggaaagggaagcacaagCggaagaagctgccggagccg	14	1	17	9	3	0	1	0	0	0	1	0	5	0	5	2	4	5	3	2	4	5	0	rs35687686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:7887234C>T	ENST00000361923.2	+	17	2396	c.2221C>T	c.(2221-2223)Cgg>Tgg	p.R741W	PER3_ENST00000377532.3_Missense_Mutation_p.R749W|RP3-467L1.4_ENST00000451646.1_RNA	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	741	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)		GAAGCACAAGCGGAAGAAGCT	0.597													C|||	30	0.00599042	0.0197	0.0058	5008	,	,		15161	0.0		0.0	False		,,,				2504	0.0				p.R741W		Atlas-SNP	.											PER3,colon,carcinoma,0,1	PER3	95	1	0			c.C2221T						PASS	.	C	TRP/ARG	70,4246		1,68,2089	19	24	22		2221	1.6	0.1	1	dbSNP_126	22	1,8501		0,1,4250	yes	missense	PER3	NM_016831.1	101	1,69,6339	TT,TC,CC		0.0118,1.6219,0.5539	probably-damaging	741/1202	7887234	71,12747	2158	4251	6409	SO:0001583	missense	8863	exon17			CACAAGCGGAAGA	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.2221C>T	1.37:g.7887234C>T	ENSP00000355031:p.Arg741Trp	80	0	0		74	34	0.459459	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	12	0.005494505494505495	10	0.02032520325203252	2	0.0055248618784530384	0	0.0	0	0.0	C	10.54	1.377888	0.24944	0.016219	1.18E-4	ENSG00000049246	ENST00000377532;ENST00000361923	T;T	0.13778	2.56;2.6	4.52	1.64	0.23874	.	2.148170	0.02588	N	0.099653	T	0.06188	0.0160	L	0.42529	1.33	0.09310	N	1	B;P;P;B	0.40180	0.179;0.581;0.705;0.179	B;B;B;B	0.31686	0.019;0.063;0.134;0.019	T	0.32161	-0.9917	10	0.87932	D	0	.	7.6166	0.28160	0.0:0.7331:0.0:0.2669	rs35687686	741;749;749;741	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	W	749;741	ENSP00000366755:R749W;ENSP00000355031:R741W	ENSP00000355031:R741W	R	+	1	2	PER3	7809821	0.991000	0.36638	0.061000	0.19648	0.054000	0.15201	0.501000	0.22578	0.181000	0.19994	0.561000	0.74099	CGG	C|0.993;T|0.007	0.007	strong		0.597	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831		T	7887234	C	T	7887234	3	4	22	1	0	0	0	0	1	0	0	0	11740	759	27	1	2287	1	PER3	1	7887234	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6649	7887234	241363387	19	2920											
PER3	8863	hgsc.bcm.edu	37	chr1	7887499	7887499	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcctgcatgggctgccctTgtccgagggcttgcagcctt	4	10	14	13	1	0	0	0	0	0	0	1	1	1	0	4	3	4	4	4	3	0	3	rs35899625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:7887499T>G	ENST00000361923.2	+	17	2661	c.2486T>G	c.(2485-2487)tTg>tGg	p.L829W	PER3_ENST00000377532.3_Missense_Mutation_p.L837W|RP3-467L1.4_ENST00000451646.1_RNA	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	829	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)		GGGCTGCCCTTGTCCGAGGGC	0.592													T|||	12	0.00239617	0.0083	0.0014	5008	,	,		17848	0.0		0.0	False		,,,				2504	0.0				p.L829W		Atlas-SNP	.											.	PER3	95	.	0			c.T2486G						PASS	.	T	TRP/LEU	46,4360	48.2+/-83.0	1,44,2158	104	104	104		2486	-1.6	0	1	dbSNP_126	104	0,8600		0,0,4300	yes	missense	PER3	NM_016831.1	61	1,44,6458	GG,GT,TT		0.0,1.044,0.3537	possibly-damaging	829/1202	7887499	46,12960	2203	4300	6503	SO:0001583	missense	8863	exon17			TGCCCTTGTCCGA	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.2486T>G	1.37:g.7887499T>G	ENSP00000355031:p.Leu829Trp	144	0	0		207	116	0.560386	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	T	14.56	2.570910	0.45798	0.01044	0.0	ENSG00000049246	ENST00000377532;ENST00000361923;ENST00000539773	T;T	0.11063	2.81;2.81	3.82	-1.61	0.08399	.	2.355770	0.02257	N	0.067230	T	0.10981	0.0268	N	0.14661	0.345	0.09310	N	1	D;D;D;D	0.60575	0.979;0.983;0.988;0.979	P;P;P;P	0.62089	0.793;0.842;0.898;0.793	T	0.32666	-0.9898	10	0.38643	T	0.18	.	9.3251	0.37988	0.0:0.4119:0.0:0.5881	rs35899625	829;837;837;829	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	W	837;829;40	ENSP00000366755:L837W;ENSP00000355031:L829W	ENSP00000355031:L829W	L	+	2	0	PER3	7810086	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.331000	0.07914	-0.204000	0.10235	-0.337000	0.08149	TTG	T|0.995;G|0.005	0.005	strong		0.592	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831		G	7887499	T	G	7887499	3	3	22	1	0	0	0	0	1	0	0	0	11740	1821	63	5	2552	5	PER3	1	7887499	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	265	7887499	241363122	20	2921											
RERE	473	hgsc.bcm.edu	37	chr1	8415621	8415621	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gtgggctgctgacatgggggGtgggatggccccaggcaggt	5	7	21	8	0	0	1	0	1	0	0	0	2	0	2	2	8	1	3	2	8	0	0			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:8415621G>A	ENST00000337907.3	-	23	5159	c.4525C>T	c.(4525-4527)Ccc>Tcc	p.P1509S	RERE_ENST00000476556.1_Missense_Mutation_p.P955S|RERE_ENST00000400908.2_Missense_Mutation_p.P1509S|RERE_ENST00000400907.2_Missense_Mutation_p.P527S|RERE_ENST00000377464.1_Missense_Mutation_p.P1241S	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	1509	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)		GACATGGGGGGTGGGATGGCC	0.652																																					p.P1509S		Atlas-SNP	.											.	RERE	129	.	0			c.C4525T						PASS	.						15	17	16					1																	8415621		2198	4291	6489	SO:0001583	missense	473	exon23			TGGGGGGTGGGAT	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.4525C>T	1.37:g.8415621G>A	ENSP00000338629:p.Pro1509Ser	43	0	0		58	36	0.62069	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Missense_Mutation	SNP	ENST00000337907.3	37	CCDS95.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.870072	0.91587	.	.	ENSG00000142599	ENST00000337907;ENST00000377464;ENST00000400907;ENST00000476556;ENST00000400908;ENST00000505225	T;T;T	0.47177	0.85;0.85;0.85	5.98	5.98	0.97165	.	.	.	.	.	T	0.64450	0.2599	L	0.60455	1.87	0.80722	D	1	D	0.54772	0.968	P	0.60117	0.869	T	0.61855	-0.6977	9	0.52906	T	0.07	-25.8584	19.4247	0.94737	0.0:0.0:1.0:0.0	.	1509	Q9P2R6	RERE_HUMAN	S	1509;1241;527;955;1509;165	ENSP00000338629:P1509S;ENSP00000366684:P1241S;ENSP00000383700:P1509S	ENSP00000338629:P1509S	P	-	1	0	RERE	8338208	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.807000	0.99171	2.843000	0.97960	0.585000	0.79938	CCC	.	.	none		0.652	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1			A	8415621	G	A	8415621	3	1	22	1	0	0	0	0	1	0	0	0	13246	1261	44	2	183	2	RERE	1	8415621	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	528122	8415621	240835000	21	2922											
RERE	473	hgsc.bcm.edu	37	chr1	8420966	8420966	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aggccaaagggctgtgggggGcctgggtgctgcagcagggg	6	5	22	8	0	0	0	0	0	0	0	0	0	0	0	2	8	3	4	2	8	1	0	rs77608355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:8420966G>A	ENST00000337907.3	-	19	3235	c.2601C>T	c.(2599-2601)ggC>ggT	p.G867G	RERE_ENST00000476556.1_Silent_p.G313G|RERE_ENST00000400908.2_Silent_p.G867G|RERE_ENST00000400907.2_Intron|RERE_ENST00000377464.1_Silent_p.G599G	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	867	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)		GCTGTGGGGGGCCTGGGTGCT	0.726													G|||	162	0.0323482	0.1165	0.0115	5008	,	,		10147	0.0		0.0	False		,,,				2504	0.0				p.G867G		Atlas-SNP	.											.	RERE	129	.	0			c.C2601T						PASS	.	G	,,	201,3379		0,201,1589	3	3	3		2601,939,2601	-10.4	0.5	1	dbSNP_131	3	2,7358		0,2,3678	no	coding-synonymous,coding-synonymous,coding-synonymous	RERE	NM_001042681.1,NM_001042682.1,NM_012102.3	,,	0,203,5267	AA,AG,GG		0.0272,5.6145,1.8556	,,	867/1567,313/1013,867/1567	8420966	203,10737	1790	3680	5470	SO:0001819	synonymous_variant	473	exon19			TGGGGGGCCTGGG	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.2601C>T	1.37:g.8420966G>A		10	0	0		11	9	0.818182	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Silent	SNP	ENST00000337907.3	37	CCDS95.1																																																																																			G|0.972;A|0.028	0.028	strong		0.726	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1			A	8420966	G	A	8420966	2	1	22	1	0	0	0	0	0	0	0	1	13246	1190	42	2		2	RERE	1	8420966	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5345	8420966	240829655	22	2923											
CA6	765	hgsc.bcm.edu	37	chr1	9009452	9009452	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggggctcaatatgacaggCtatgagacccaggcagggga	13	5	15	8	0	1	2	1	2	0	1	1	4	1	3	1	6	0	3	1	6	4	2	rs61746465	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:9009452C>T	ENST00000377443.2	+	2	214	c.210C>T	c.(208-210)ggC>ggT	p.G70G	CA6_ENST00000480186.3_Silent_p.G70G|CA6_ENST00000476083.1_Intron|CA6_ENST00000377442.2_Intron|CA6_ENST00000377436.3_Silent_p.G70G	NM_001215.3	NP_001206.2	P23280	CAH6_HUMAN	carbonic anhydrase VI	70			G -> A (in dbSNP:rs2274329).		bicarbonate transport (GO:0015701)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|skin(5)	16	Ovarian(185;0.112)|all_lung(157;0.143)	all_epithelial(116;1.02e-19)|all_lung(118;3.6e-06)|Lung NSC(185;7.94e-06)|Renal(390;0.000147)|Breast(348;0.00123)|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;6.9e-07)|COAD - Colon adenocarcinoma(227;8.28e-05)|Kidney(185;0.000268)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|STAD - Stomach adenocarcinoma(132;0.00184)|BRCA - Breast invasive adenocarcinoma(304;0.00192)|READ - Rectum adenocarcinoma(331;0.0649)	Mafenide(DB06795)|Zonisamide(DB00909)	ATATGACAGGCTATGAGACCC	0.607													C|||	61	0.0121805	0.0439	0.0029	5008	,	,		20134	0.0		0.001	False		,,,				2504	0.0				p.G70G		Atlas-SNP	.											.	CA6	47	.	0			c.C210T						PASS	.	C		149,4257	102.1+/-140.7	5,139,2059	59	48	52		210	4.4	0.9	1	dbSNP_129	52	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	CA6	NM_001215.2		5,141,6357	TT,TC,CC		0.0233,3.3818,1.161		70/309	9009452	151,12855	2203	4300	6503	SO:0001819	synonymous_variant	765	exon2			GACAGGCTATGAG	M57892	CCDS30578.1, CCDS57970.1, CCDS57971.1	1p36.2	2008-02-05			ENSG00000131686	ENSG00000131686	4.2.1.1	"Carbonic anhydrases"	1380	protein-coding gene	gene with protein product		114780				9691177	Standard	NM_001215		Approved		uc031plc.1	P23280	OTTHUMG00000001763	ENST00000377443.2:c.210C>T	1.37:g.9009452C>T		102	0	0		111	64	0.576577	NM_001270500	E7EMQ1|Q5FBW3|Q5FC00|Q96QX8|Q9UF03	Silent	SNP	ENST00000377443.2	37	CCDS30578.1																																																																																			C|0.988;T|0.012	0.012	strong		0.607	CA6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000004911.1			T	9009452	C	T	9009452	2	4	22	1	0	0	0	0	0	0	0	1	2523	784	28	2		2	CA6	1	9009452	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	588486	9009452	240241169	23	2924											
SLC2A7	155184	hgsc.bcm.edu	37	chr1	9083094	9083094	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttcccgtccatgaatgttGcgtgtcgctcaaagtaggtt	7	13	11	10	3	1	1	1	1	0	0	4	1	3	1	2	1	1	5	2	1	3	4	rs61744620	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:9083094G>T	ENST00000400906.1	-	3	193	c.194C>A	c.(193-195)gCa>gAa	p.A65E		NM_207420.2	NP_997303.2	Q6PXP3	GTR7_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 7	65					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)		CATGAATGTTGCGTGTCGCTC	0.502													G|||	118	0.0235623	0.0847	0.0086	5008	,	,		20374	0.0		0.0	False		,,,				2504	0.0				p.A65E		Atlas-SNP	.											SLC2A7,rectum,carcinoma,-1,2	SLC2A7	56	2	0			c.C194A						PASS	.	G	GLU/ALA	324,4082	172.3+/-202.3	18,288,1897	171	158	162		194	1.6	0	1	dbSNP_129	162	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SLC2A7	NM_207420.2	107	18,289,6196	TT,TG,GG		0.0116,7.3536,2.4988	benign	65/513	9083094	325,12681	2203	4300	6503	SO:0001583	missense	155184	exon3			AATGTTGCGTGTC	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.194C>A	1.37:g.9083094G>T	ENSP00000383698:p.Ala65Glu	77	0	0		83	45	0.542169	NM_207420	A2A333	Missense_Mutation	SNP	ENST00000400906.1	37	CCDS98.2	56	0.02564102564102564	52	0.10569105691056911	4	0.011049723756906077	0	0.0	0	0.0	G	13.62	2.292105	0.40594	0.073536	1.16E-4	ENSG00000197241	ENST00000400906	T	0.73047	-0.71	4.68	1.57	0.23409	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.305652	0.30210	N	0.010158	T	0.01287	0.0042	N	0.04994	-0.135	0.09310	N	1	B	0.10296	0.003	B	0.14578	0.011	T	0.03086	-1.1074	10	0.44086	T	0.13	.	15.0439	0.71813	0.0:0.5434:0.4566:0.0	.	65	Q6PXP3	GTR7_HUMAN	E	65	ENSP00000383698:A65E	ENSP00000383698:A65E	A	-	2	0	SLC2A7	9005681	0.000000	0.05858	0.002000	0.10522	0.305000	0.27757	1.115000	0.31209	0.567000	0.29293	0.556000	0.70494	GCA	G|0.974;T|0.026	0.026	strong		0.502	SLC2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127768.3	NM_207420		T	9083094	G	T	9083094	3	4	22	1	0	0	0	0	1	0	0	0	14565	1319	46	4	1384	4	SLC2A7	1	9083094	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	73642	9083094	240167527	24	2925											
H6PD	9563	hgsc.bcm.edu	37	chr1	9322194	9322194	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgacggaggtcctcaccctCgtggccatggagctgcccca	6	7	12	16	2	1	1	1	1	0	0	3	3	2	3	5	4	2	1	5	4	0	0	rs145706807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:9322194C>T	ENST00000377403.2	+	4	1124	c.822C>T	c.(820-822)ctC>ctT	p.L274L	H6PD_ENST00000602477.1_Silent_p.L285L	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	274	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)		TCCTCACCCTCGTGGCCATGG	0.637													C|||	2	0.000399361	0.0015	0.0	5008	,	,		19119	0.0		0.0	False		,,,				2504	0.0				p.L274L		Atlas-SNP	.											.	H6PD	71	.	0			c.C822T						PASS	.	C		7,4399	14.3+/-33.2	0,7,2196	68	63	65		822	-10.5	0.2	1	dbSNP_134	65	0,8600		0,0,4300	no	coding-synonymous	H6PD	NM_004285.3		0,7,6496	TT,TC,CC		0.0,0.1589,0.0538		274/792	9322194	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	9563	exon4			CACCCTCGTGGCC	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.822C>T	1.37:g.9322194C>T		195	0	0		213	126	0.591549	NM_004285	Q4TT33|Q66I35|Q68DT3	Silent	SNP	ENST00000377403.2	37	CCDS101.1																																																																																			C|0.999;T|0.001	0.001	strong		0.637	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	NM_004285		T	9322194	C	T	9322194	2	4	22	1	0	0	0	0	0	0	0	1	6945	871	31	1		1	H6PD	1	9322194	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	239100	9322194	239928427	25	2926											
TMEM201	199953	hgsc.bcm.edu	37	chr1	9671935	9671935	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggggctgctcggaggaggcCgccacctggagaggtctgta	7	6	18	10	2	1	1	0	0	1	1	2	4	1	3	3	7	1	3	3	7	1	1	rs4073292	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:9671935C>T	ENST00000340381.6	+	10	1899	c.1890C>T	c.(1888-1890)gcC>gcT	p.A630A	TMEM201_ENST00000377376.4_Silent_p.A606A	NM_001130924.2	NP_001124396.2	Q5SNT2	TM201_HUMAN	transmembrane protein 201	630					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)		CGGAGGAGGCCGCCACCTGGA	0.642													C|||	355	0.0708866	0.2564	0.0202	5008	,	,		15597	0.0		0.002	False		,,,				2504	0.0				p.A630A		Atlas-SNP	.											.	TMEM201	63	.	0			c.C1890T						PASS	.	C		298,1086		35,228,429	21	21	21		1890	-2.5	0	1	dbSNP_108	21	4,3178		0,4,1587	no	coding-synonymous	TMEM201	NM_001130924.2		35,232,2016	TT,TC,CC		0.1257,21.5318,6.6141		630/667	9671935	302,4264	692	1591	2283	SO:0001819	synonymous_variant	199953	exon10			GGAGGCCGCCACC		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.1890C>T	1.37:g.9671935C>T		82	0	0		86	44	0.511628	NM_001130924	B9EH90|Q5SNT3	Silent	SNP	ENST00000340381.6	37	CCDS44055.2	154	0.07051282051282051	145	0.29471544715447157	8	0.022099447513812154	0	0.0	1	0.0013192612137203166	C	0.113	-1.136063	0.01742	0.215318	0.001257	ENSG00000188807	ENST00000416541	.	.	.	5.28	-2.46	0.06461	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.34304	-0.9834	3	.	.	.	-6.4317	7.9697	0.30119	0.0:0.4376:0.1547:0.4077	rs4073292;rs17034220;rs4073292	.	.	.	C	516	.	.	R	+	1	0	TMEM201	9594522	0.000000	0.05858	0.011000	0.14972	0.058000	0.15608	-0.270000	0.08584	-0.319000	0.08652	-1.134000	0.01955	CGC	C|0.934;T|0.066	0.066	strong		0.642	TMEM201-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127672.1	NM_001010866		T	9671935	C	T	9671935	2	4	22	1	0	0	0	0	0	0	0	1	16141	639	23	1		1	TMEM201	1	9671935	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	349741	9671935	239578686	26	2927											
UBE4B	10277	hgsc.bcm.edu	37	chr1	10211588	10211588	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catcctctctccaccaagttGttggtaccttccctgatgaa	8	13	6	14	0	1	2	0	2	1	0	5	2	4	2	5	1	1	3	5	1	3	4	rs149899336	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:10211588G>A	ENST00000253251.8	+	20	3347	c.2508G>A	c.(2506-2508)ttG>ttA	p.L836L	UBE4B_ENST00000377157.3_Silent_p.L720L|UBE4B_ENST00000343090.6_Silent_p.L965L					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)		CCACCAAGTTGTTGGTACCTT	0.453													G|||	3	0.000599042	0.0023	0.0	5008	,	,		22768	0.0		0.0	False		,,,				2504	0.0				p.L965L		Atlas-SNP	.											.	UBE4B	233	.	0			c.G2895A						PASS	.	G	,	15,4391	22.3+/-47.3	0,15,2188	166	152	157		2895,2508	4.2	0.9	1	dbSNP_134	157	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	UBE4B	NM_001105562.2,NM_006048.4	,	0,15,6488	AA,AG,GG		0.0,0.3404,0.1153	,	965/1303,836/1174	10211588	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	10277	exon21			CAAGTTGTTGGTA	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.2508G>A	1.37:g.10211588G>A		179	0	0		179	86	0.480447	NM_001105562		Silent	SNP	ENST00000253251.8	37	CCDS110.1																																																																																			G|0.999;A|0.001	0.001	strong		0.453	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048		A	10211588	G	A	10211588	2	1	22	1	0	0	0	0	0	0	0	1	16898	1368	48	2		2	UBE4B	1	10211588	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	539653	10211588	239039033	27	2928											
PEX14	5195	hgsc.bcm.edu	37	chr1	10684422	10684422	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagttacagacgaccctcgcCtccgtccaggagctgctgat	8	8	10	15	3	0	2	0	1	0	1	3	4	2	3	4	1	3	3	4	1	1	1	rs35046754	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:10684422C>A	ENST00000356607.4	+	7	593	c.513C>A	c.(511-513)gcC>gcA	p.A171A	PEX14_ENST00000538836.1_Silent_p.A107A	NM_004565.2	NP_004556.1	O75381	PEX14_HUMAN	peroxisomal biogenesis factor 14	171					microtubule anchoring (GO:0034453)|negative regulation of protein binding (GO:0032091)|negative regulation of protein homotetramerization (GO:1901094)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peroxisome organization (GO:0007031)|peroxisome transport along microtubule (GO:0036250)|protein complex assembly (GO:0006461)|protein homooligomerization (GO:0051260)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, substrate release (GO:0044721)|protein import into peroxisome matrix, translocation (GO:0016561)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|protein N-terminus binding (GO:0047485)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)			breast(3)|endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	13	Ovarian(185;0.203)	all_lung(284;6.02e-06)|Lung NSC(185;9.62e-06)|Renal(390;0.000147)|Breast(348;0.000932)|Colorectal(325;0.00215)|Hepatocellular(190;0.00913)|Ovarian(437;0.023)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0292)|Colorectal(212;9.13e-08)|COAD - Colon adenocarcinoma(227;2.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000482)|Kidney(185;0.00174)|KIRC - Kidney renal clear cell carcinoma(229;0.00457)|STAD - Stomach adenocarcinoma(132;0.0249)|READ - Rectum adenocarcinoma(331;0.0419)		CGACCCTCGCCTCCGTCCAGG	0.622													C|||	63	0.0125799	0.0469	0.0014	5008	,	,		15967	0.0		0.0	False		,,,				2504	0.0				p.A171A		Atlas-SNP	.											.	PEX14	40	.	0			c.C513A						PASS	.	C		209,4197	127.4+/-164.3	9,191,2003	75	76	76		513	2.9	1	1	dbSNP_126	76	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	PEX14	NM_004565.2		9,193,6301	AA,AC,CC		0.0233,4.7435,1.6223		171/378	10684422	211,12795	2203	4300	6503	SO:0001819	synonymous_variant	5195	exon7			CCTCGCCTCCGTC	AF045186	CCDS30582.1	1p36.22	2008-05-14			ENSG00000142655	ENSG00000142655			8856	protein-coding gene	gene with protein product		601791				9653144	Standard	NM_004565		Approved		uc001arn.3	O75381	OTTHUMG00000001908	ENST00000356607.4:c.513C>A	1.37:g.10684422C>A		311	0	0		314	171	0.544586	NM_004565	B2R7N1|B3KML6|B7Z1N2|Q8WX51	Silent	SNP	ENST00000356607.4	37	CCDS30582.1																																																																																			C|0.986;A|0.014	0.014	strong		0.622	PEX14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005414.1			A	10684422	C	A	10684422	2	1	22	1	0	0	0	0	0	0	0	1	11751	668	24	4		4	PEX14	1	10684422	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	472834	10684422	238566199	28	2929											
C1orf127	148345	hgsc.bcm.edu	37	chr1	11008102	11008102	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	taggaagaactgccaggggcGctgccagcctcaccctgggc	8	5	14	14	1	1	1	1	0	0	1	1	2	1	2	4	4	4	1	4	4	3	1	rs1281018	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11008102G>A	ENST00000377008.4	-	11	2035	c.1589C>T	c.(1588-1590)gCg>gTg	p.A530V	C1orf127_ENST00000377004.4_Missense_Mutation_p.A697V			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	530			A -> V (in dbSNP:rs1281018).							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)		TGCCAGGGGCGCTGCCAGCCT	0.622													G|||	442	0.0882588	0.2542	0.0245	5008	,	,		18073	0.0069		0.0447	False		,,,				2504	0.0378				p.A697V		Atlas-SNP	.											.	C1orf127	134	.	0			c.C2090T						PASS	.	G	VAL/ALA	809,3597	299.6+/-285.9	81,647,1475	36	38	37		2090	-2	0	1	dbSNP_87	37	346,8254	112.3+/-172.5	4,338,3958	yes	missense	C1orf127	NM_001170754.1	64	85,985,5433	AA,AG,GG		4.0233,18.3613,8.8805	possibly-damaging	697/824	11008102	1155,11851	2203	4300	6503	SO:0001583	missense	148345	exon12			AGGGGCGCTGCCA	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.1589C>T	1.37:g.11008102G>A	ENSP00000366207:p.Ala530Val	93	0	0		114	52	0.45614	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Missense_Mutation	SNP	ENST00000377008.4	37		165|165	0.07554945054945054|0.07554945054945054	115|115	0.23373983739837398|0.23373983739837398	8|8	0.022099447513812154|0.022099447513812154	2|2	0.0034965034965034965|0.0034965034965034965	40|40	0.052770448548812667|0.052770448548812667	G|G	7.224|7.224	0.597877|0.597877	0.13939|0.13939	0.183613|0.183613	0.040233|0.040233	ENSG00000175262|ENSG00000175262	ENST00000377004;ENST00000377008|ENST00000418570;ENST00000520253	T;T|.	0.33865|.	1.39;1.39|.	3.9|3.9	-2.05|-2.05	0.07321|0.07321	.|.	0.523531|.	0.14669|.	N|.	0.305451|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.14661|0.14661	0.345|0.345	0.80722|0.80722	P|P	0.0|0.0	P;P;P|.	0.42961|.	0.795;0.795;0.795|.	B;B;B|.	0.31390|.	0.129;0.129;0.081|.	T|T	0.35051|0.35051	-0.9804|-0.9804	9|4	0.18276|.	T|.	0.48|.	-0.422|-0.422	0.9467|0.9467	0.01367|0.01367	0.2137:0.3268:0.2711:0.1885|0.2137:0.3268:0.2711:0.1885	rs1281018;rs1281018|rs1281018;rs1281018	548;522;530|.	B7ZLG7;Q8N9H9-2;Q8N9H9|.	.;.;CA127_HUMAN|.	V|C	697;530|532;649	ENSP00000366203:A697V;ENSP00000366207:A530V|.	ENSP00000366203:A697V|.	A|R	-|-	2|1	0|0	C1orf127|C1orf127	10930689|10930689	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.030000|0.030000	0.12068|0.12068	-2.362000|-2.362000	0.01082|0.01082	-0.266000|-0.266000	0.09339|0.09339	-0.474000|-0.474000	0.04947|0.04947	GCG|CGC	G|0.914;A|0.086	0.086	strong		0.622	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507		A	11008102	G	A	11008102	3	1	22	1	0	0	0	0	1	0	0	0	1996	1087	38	1	385	1	C1orf127	1	11008102	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	323680	11008102	238242519	29	2930											
C1orf127	148345	hgsc.bcm.edu	37	chr1	11008594	11008594	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtgacagatggtcctgagAccagaagtgattcaggtcgt	10	9	15	7	1	1	5	1	3	0	3	3	6	2	5	2	3	0	0	2	3	1	1	rs1281016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11008594A>T	ENST00000377008.4	-	11	1543	c.1097T>A	c.(1096-1098)gTc>gAc	p.V366D	C1orf127_ENST00000377004.4_Missense_Mutation_p.V533D			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	366			V -> D (in dbSNP:rs1281016).							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)		TGGTCCTGAGACCAGAAGTGA	0.612													A|||	346	0.0690895	0.2035	0.0144	5008	,	,		19200	0.004		0.0427	False		,,,				2504	0.0204				p.V533D		Atlas-SNP	.											.	C1orf127	134	.	0			c.T1598A						PASS	.	A	ASP/VAL	735,3671	303.5+/-288.0	65,605,1533	56	53	54		1598	0.5	0	1	dbSNP_87	54	343,8257	116.3+/-176.0	4,335,3961	yes	missense	C1orf127	NM_001170754.1	152	69,940,5494	TT,TA,AA		3.9884,16.6818,8.2885	probably-damaging	533/824	11008594	1078,11928	2203	4300	6503	SO:0001583	missense	148345	exon12			CCTGAGACCAGAA	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.1097T>A	1.37:g.11008594A>T	ENSP00000366207:p.Val366Asp	199	0	0		179	86	0.480447	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Missense_Mutation	SNP	ENST00000377008.4	37		167|167	0.07646520146520147|0.07646520146520147	123|123	0.25|0.25	4|4	0.011049723756906077|0.011049723756906077	1|1	0.0017482517482517483|0.0017482517482517483	39|39	0.051451187335092345|0.051451187335092345	A|A	13.05|13.05	2.122259|2.122259	0.37436|0.37436	0.166818|0.166818	0.039884|0.039884	ENSG00000175262|ENSG00000175262	ENST00000418570;ENST00000520253|ENST00000377004;ENST00000377008	.|T;T	.|0.26518	.|1.73;1.73	4.15|4.15	0.48|0.48	0.16804|0.16804	.|.	.|0.956786	.|0.08574	.|N	.|0.925628	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.24115|0.24115	0.695|0.695	0.80722|0.80722	P|P	0.0|0.0	.|P;P;P	.|0.46512	.|0.879;0.879;0.879	.|B;B;B	.|0.42163	.|0.378;0.378;0.378	T|T	0.19484|0.19484	-1.0304|-1.0304	4|9	.|0.15952	.|T	.|0.53	-5.9143|-5.9143	0.8883|0.8883	0.01249|0.01249	0.3866:0.3152:0.136:0.1622|0.3866:0.3152:0.136:0.1622	rs1281016;rs52819154;rs1281016|rs1281016;rs52819154;rs1281016	.|384;358;366	.|B7ZLG7;Q8N9H9-2;Q8N9H9	.|.;.;CA127_HUMAN	T|D	368;485|533;366	.|ENSP00000366203:V533D;ENSP00000366207:V366D	.|ENSP00000366203:V533D	S|V	-|-	1|2	0|0	C1orf127|C1orf127	10931181|10931181	0.000000|0.000000	0.05858|0.05858	0.008000|0.008000	0.14137|0.14137	0.057000|0.057000	0.15508|0.15508	-0.110000|-0.110000	0.10824|0.10824	0.317000|0.317000	0.23160|0.23160	0.402000|0.402000	0.26972|0.26972	TCT|GTC	A|0.922;T|0.078	0.078	strong		0.612	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507		T	11008594	A	T	11008594	3	4	22	1	0	0	0	0	1	0	0	0	1996	275	10	5	877	5	C1orf127	1	11008594	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	492	11008594	238242027	30	2931											
C1orf127	148345	hgsc.bcm.edu	37	chr1	11009679	11009679	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaggatgcagccatagacgtGctttggccagtgcgtcggaa	9	8	15	9	3	0	1	0	0	0	1	1	4	0	3	2	3	4	2	2	3	2	2	rs1281013	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11009679G>A	ENST00000377008.4	-	10	1236		c.e10+1		C1orf127_ENST00000377004.4_Splice_Site			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127											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)		CCATAGACGTGCTTTGGCCAG	0.612													G|||	346	0.0690895	0.2035	0.0144	5008	,	,		17717	0.004		0.0427	False		,,,				2504	0.0204				.		Atlas-SNP	.											.	C1orf127	134	.	0			c.1290+2C>T						PASS	.	G		719,3679		64,591,1544	34	29	31			-0.6	0	1	dbSNP_87	31	331,8269		4,323,3973	yes	splice-5	C1orf127	NM_001170754.1		68,914,5517	AA,AG,GG		3.8488,16.3483,8.0782			11009679	1050,11948	2199	4300	6499	SO:0001630	splice_region_variant	148345	exon12			AGACGTGCTTTGG	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.789+1C>T	1.37:g.11009679G>A		103	0	0		100	51	0.51	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Splice_Site	SNP	ENST00000377008.4	37		166	0.076007326007326	122	0.24796747967479674	4	0.011049723756906077	1	0.0017482517482517483	39	0.051451187335092345	G	2.596	-0.293985	0.05568	0.163483	0.038488	ENSG00000175262	ENST00000418570;ENST00000377004;ENST00000377008	.	.	.	3.68	-0.578	0.11724	.	.	.	.	.	.	.	.	.	.	.	0.51012	P	9.899999999996023E-5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1.2328	0.01946	0.2149:0.1807:0.4347:0.1697	rs1281013;rs1281013	.	.	.	.	-1	.	.	.	-	.	.	C1orf127	10932266	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.106000	0.15354	-0.247000	0.09597	-0.354000	0.07668	.	G|0.907;A|0.093	0.093	strong		0.612	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	Intron	A	11009679	G	A	11009679	5	1	22	1	0	0	0	0	0	0	1	0	1996	1333	46	2	1187	2	C1orf127	1	11009679	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1085	11009679	238240942	31	2932											
C1orf127	148345	hgsc.bcm.edu	37	chr1	11009703	11009703	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggccagtgcgtcggaaggcCggtgcaggaggtcccgagaa	8	5	18	10	4	0	1	0	0	0	1	2	4	1	3	3	6	2	1	3	6	2	0	rs1281012	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11009703C>T	ENST00000377008.4	-	10	1213	c.767G>A	c.(766-768)cGg>cAg	p.R256Q	C1orf127_ENST00000377004.4_Missense_Mutation_p.R423Q			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	256	Pro-rich.		R -> Q (in dbSNP:rs1281012).							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)		GTCGGAAGGCCGGTGCAGGAG	0.622													C|||	347	0.0692891	0.2042	0.0144	5008	,	,		17273	0.004		0.0427	False		,,,				2504	0.0204				p.R423Q		Atlas-SNP	.											.	C1orf127	134	.	0			c.G1268A						PASS	.	C	GLN/ARG	725,3675		66,593,1541	40	34	36		1268	-6.4	0	1	dbSNP_87	36	333,8267		4,325,3971	yes	missense	C1orf127	NM_001170754.1	43	70,918,5512	TT,TC,CC		3.8721,16.4773,8.1385	benign	423/824	11009703	1058,11942	2200	4300	6500	SO:0001583	missense	148345	exon11			GAAGGCCGGTGCA	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.767G>A	1.37:g.11009703C>T	ENSP00000366207:p.Arg256Gln	118	0	0		121	60	0.495868	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Missense_Mutation	SNP	ENST00000377008.4	37		167|167	0.07646520146520147|0.07646520146520147	123|123	0.25|0.25	4|4	0.011049723756906077|0.011049723756906077	1|1	0.0017482517482517483|0.0017482517482517483	39|39	0.051451187335092345|0.051451187335092345	C|C	1.843|1.843	-0.467033|-0.467033	0.04476|0.04476	0.164773|0.164773	0.038721|0.038721	ENSG00000175262|ENSG00000175262	ENST00000418570|ENST00000377004;ENST00000377008	.|T;T	.|0.29142	.|1.58;1.58	3.98|3.98	-6.39|-6.39	0.01951|0.01951	.|.	.|6.202500	.|0.00166	.|N	.|0.000011	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02539|0.02539	-0.55|-0.55	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.09022	.|0.002;0.002	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.18999|0.18999	-1.0319|-1.0319	4|9	.|0.23891	.|T	.|0.37	.|.	2.3424|2.3424	0.04263|0.04263	0.1182:0.3558:0.1181:0.4079|0.1182:0.3558:0.1181:0.4079	rs1281012;rs1281012|rs1281012;rs1281012	.|274;256	.|B7ZLG7;Q8N9H9	.|.;CA127_HUMAN	S|Q	258|423;256	.|ENSP00000366203:R423Q;ENSP00000366207:R256Q	.|ENSP00000366203:R423Q	G|R	-|-	1|2	0|0	C1orf127|C1orf127	10932290|10932290	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-1.451000|-1.451000	0.02387|0.02387	-1.615000|-1.615000	0.01573|0.01573	-1.314000|-1.314000	0.01303|0.01303	GGC|CGG	C|0.907;T|0.093	0.093	strong		0.622	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507		T	11009703	C	T	11009703	3	4	22	1	0	0	0	0	1	0	0	0	1996	652	23	1	1211	1	C1orf127	1	11009703	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	24	11009703	238240918	32	2933											
MASP2	10747	hgsc.bcm.edu	37	chr1	11087687	11087687	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atatacgccctcctgttgtgCgggctgatagtccacaaact	9	11	9	12	2	0	1	0	1	0	0	2	1	2	1	3	1	3	2	3	1	4	4	rs12085877	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11087687C>T	ENST00000400897.3	-	11	1331	c.1316G>A	c.(1315-1317)cGc>cAc	p.R439H	RP4-635E18.8_ENST00000607145.1_RNA	NM_006610.3	NP_006601.2	O00187	MASP2_HUMAN	mannan-binding lectin serine peptidase 2	439			R -> H (in dbSNP:rs12085877).		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)		TCCTGTTGTGCGGGCTGATAG	0.443													C|||	144	0.028754	0.1036	0.0101	5008	,	,		19654	0.0		0.0	False		,,,				2504	0.0				p.R439H	GBM(35;611 746 20780 22741 36496)	Atlas-SNP	.											MASP2,NS,carcinoma,-1,1	MASP2	71	1	0			c.G1316A						PASS	.	C	HIS/ARG	413,3987		16,381,1803	59	62	61		1316	-0.5	0	1	dbSNP_120	61	3,8595		0,3,4296	yes	missense	MASP2	NM_006610.3	29	16,384,6099	TT,TC,CC		0.0349,9.3864,3.2005	benign	439/687	11087687	416,12582	2200	4299	6499	SO:0001583	missense	10747	exon11			GTTGTGCGGGCTG	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.1316G>A	1.37:g.11087687C>T	ENSP00000383690:p.Arg439His	104	0	0		100	44	0.44	NM_006610	A8K458|A8MWJ2|O75754|Q5TEQ5|Q5TER0|Q96QG4|Q9BZH0|Q9H498|Q9H499|Q9UBP3|Q9UC48|Q9ULC7|Q9UMV3|Q9Y270	Missense_Mutation	SNP	ENST00000400897.3	37	CCDS123.1	54	0.024725274725274724	50	0.1016260162601626	4	0.011049723756906077	0	0.0	0	0.0	C	11.07	1.530812	0.27387	0.093864	3.49E-4	ENSG00000009724	ENST00000400897	D	0.92858	-3.12	5.45	-0.488	0.12056	Peptidase cysteine/serine, trypsin-like (1);Complement control module (1);	0.541857	0.18692	N	0.133825	T	0.12050	0.0293	L	0.28400	0.85	0.21802	N	0.99953	B	0.11235	0.004	B	0.06405	0.002	T	0.50363	-0.8837	10	0.35671	T	0.21	.	0.5192	0.00609	0.2067:0.2927:0.1873:0.3133	rs12085877;rs52829987;rs12085877	439	O00187	MASP2_HUMAN	H	439	ENSP00000383690:R439H	ENSP00000383690:R439H	R	-	2	0	MASP2	11010274	0.000000	0.05858	0.005000	0.12908	0.027000	0.11550	-0.560000	0.05964	0.002000	0.14630	0.563000	0.77884	CGC	C|0.971;T|0.029	0.029	strong		0.443	MASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006072.1	NM_006610		T	11087687	C	T	11087687	3	4	22	1	0	0	0	0	1	0	0	0	9332	768	27	1	748	1	MASP2	1	11087687	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	77984	11087687	238162934	33	2934											
MASP2	10747	hgsc.bcm.edu	37	chr1	11106648	11106648	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggcctcgaaccccgtgaacGgcttctcgttggagtagtcg	7	9	13	12	5	1	1	0	1	1	0	4	3	1	2	3	3	2	3	3	3	3	3	rs56392418	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11106648G>A	ENST00000400897.3	-	3	392	c.377C>T	c.(376-378)cCg>cTg	p.P126L	MASP2_ENST00000400898.3_Missense_Mutation_p.P126L	NM_006610.3	NP_006601.2	O00187	MASP2_HUMAN	mannan-binding lectin serine peptidase 2	126	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.		P -> L (in MASPD; dbSNP:rs56392418). {ECO:0000269|PubMed:16029433, ECO:0000269|PubMed:17252003}.		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)		CCCCGTGAACGGCTTCTCGTT	0.607													G|||	181	0.0361422	0.1316	0.0101	5008	,	,		19642	0.0		0.0	False		,,,				2504	0.0				p.P126L	GBM(35;611 746 20780 22741 36496)	Atlas-SNP	.											.	MASP2	71	.	0			c.C377T	GRCh37	CM073192	MASP2	M	rs56392418	PASS	.	G	LEU/PRO,LEU/PRO	505,3901	231.7+/-245.5	22,461,1720	52	45	47		377,377	2.8	1	1	dbSNP_129	47	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	MASP2	NM_006610.3,NM_139208.2	98,98	22,463,6018	AA,AG,GG		0.0233,11.4616,3.8982	possibly-damaging,possibly-damaging	126/687,126/186	11106648	507,12499	2203	4300	6503	SO:0001583	missense	10747	exon3			GTGAACGGCTTCT	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.377C>T	1.37:g.11106648G>A	ENSP00000383690:p.Pro126Leu	109	0	0		130	50	0.384615	NM_139208	A8K458|A8MWJ2|O75754|Q5TEQ5|Q5TER0|Q96QG4|Q9BZH0|Q9H498|Q9H499|Q9UBP3|Q9UC48|Q9ULC7|Q9UMV3|Q9Y270	Missense_Mutation	SNP	ENST00000400897.3	37	CCDS123.1	70	0.03205128205128205	66	0.13414634146341464	4	0.011049723756906077	0	0.0	0	0.0	G	17.33	3.361797	0.61403	0.114616	2.33E-4	ENSG00000009724	ENST00000400897;ENST00000400898	T;T	0.26660	1.72;1.72	4.87	2.75	0.32379	CUB (5);	0.752220	0.12578	N	0.456686	T	0.00178	0.0005	L	0.33485	1.01	0.49051	D	0.999741	B;P	0.36183	0.179;0.542	B;B	0.33196	0.016;0.159	T	0.18461	-1.0336	10	0.66056	D	0.02	.	7.2086	0.25921	0.0979:0.0:0.6342:0.2678	rs56392418;rs61747086	126;126	O00187-2;O00187	.;MASP2_HUMAN	L	126	ENSP00000383690:P126L;ENSP00000383691:P126L	ENSP00000383690:P126L	P	-	2	0	MASP2	11029235	0.099000	0.21834	0.984000	0.44739	0.939000	0.58152	0.769000	0.26604	1.046000	0.40249	-0.251000	0.11542	CCG	G|0.964;A|0.036	0.036	strong		0.607	MASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006072.1	NM_006610		A	11106648	G	A	11106648	3	1	22	1	0	0	0	0	1	0	0	0	9332	1116	39	1	1737	1	MASP2	1	11106648	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	18961	11106648	238143973	34	2935											
FBXO44	93611	hgsc.bcm.edu	37	chr1	11721321	11721321	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agcatcaccatcgggcccccGctgccctgacaccccctgag	7	5	9	20	2	1	2	1	2	0	0	2	2	1	2	6	1	2	2	6	1	0	0	rs12057383	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11721321G>A	ENST00000251547.5	+	6	841	c.759G>A	c.(757-759)ccG>ccA	p.P253P	FBXO44_ENST00000376762.4_Missense_Mutation_p.A212T|FBXO6_ENST00000376753.4_5'Flank|FBXO44_ENST00000376760.1_Missense_Mutation_p.A212T|FBXO44_ENST00000376770.1_Silent_p.P253P|FBXO44_ENST00000251546.4_Missense_Mutation_p.A212T|FBXO44_ENST00000376768.1_Missense_Mutation_p.A244T	NM_033182.5	NP_149438.2	Q9H4M3	FBX44_HUMAN	F-box protein 44	253						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)		TCGGGCCCCCGCTGCCCTGAC	0.637													G|||	406	0.0810703	0.2784	0.0187	5008	,	,		15749	0.002		0.007	False		,,,				2504	0.0164				p.A212T		Atlas-SNP	.											.	FBXO44	20	.	0			c.G634A						PASS	.	G	,,THR/ALA,THR/ALA	1089,3317	394.7+/-329.4	130,829,1244	66	70	69		759,759,634,634	-4.8	0.9	1	dbSNP_120	69	33,8567	22.8+/-68.1	0,33,4267	yes	coding-synonymous,coding-synonymous,missense,missense	FBXO44	NM_001014765.1,NM_033182.5,NM_183412.2,NM_183413.2	,,58,58	130,862,5511	AA,AG,GG		0.3837,24.7163,8.6268	,,,	253/256,253/256,212/225,212/225	11721321	1122,11884	2203	4300	6503	SO:0001819	synonymous_variant	93611	exon5			GCCCCCGCTGCCC	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.759G>A	1.37:g.11721321G>A		128	0	0		141	66	0.468085	NM_183412	B3KNZ2|B7Z743|Q5TGX2|Q5TGX4|Q5TGX5|Q68DJ9|Q8WWY2	Missense_Mutation	SNP	ENST00000251547.5	37	CCDS132.1	145	0.06639194139194139	135	0.27439024390243905	4	0.011049723756906077	0	0.0	6	0.0079155672823219	G	11.75	1.732499	0.30684	0.247163	0.003837	ENSG00000132879	ENST00000251546;ENST00000376768;ENST00000376762;ENST00000376760	T;T;T;T	0.38401	1.2;1.14;1.2;1.2	4.82	-4.76	0.03229	.	0.998809	0.08102	N	0.997570	T	0.00012	0.0000	.	.	.	0.23696	P	0.9970848	B;B	0.10296	0.0;0.003	B;B	0.06405	0.001;0.002	T	0.31251	-0.9950	8	0.62326	D	0.03	-13.878	10.7614	0.46266	0.1572:0.1065:0.7363:0.0	rs12057383;rs56815691	244;212	B7Z1P2;Q9H4M3-2	.;.	T	212;244;212;212	ENSP00000251546:A212T;ENSP00000365959:A244T;ENSP00000365953:A212T;ENSP00000365951:A212T	ENSP00000251546:A212T	A	+	1	0	FBXO44	11643908	0.000000	0.05858	0.924000	0.36721	0.260000	0.26232	-0.672000	0.05244	-1.124000	0.02936	-0.258000	0.10820	GCT	G|0.924;A|0.076	0.076	strong		0.637	FBXO44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005761.1	NM_183412		A	11721321	G	A	11721321	2	1	22	1	0	0	0	0	0	0	0	1	5761	1087	38	1		1	FBXO44	1	11721321	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	614673	11721321	237529300	35	2936											
CLCN6	1185	hgsc.bcm.edu	37	chr1	11876692	11876692	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaaggtcgaagatatgaggcGgtgaagtggatggtggtgtt	11	10	18	2	2	0	3	0	2	0	1	1	5	0	4	0	6	0	1	0	6	4	2	rs57044879	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11876692G>A	ENST00000346436.6	+	4	286	c.234G>A	c.(232-234)gcG>gcA	p.A78A	CLCN6_ENST00000376492.3_3'UTR|CLCN6_ENST00000376496.3_Silent_p.A78A|CLCN6_ENST00000376487.3_Silent_p.A56A|CLCN6_ENST00000376497.3_Silent_p.A78A|CLCN6_ENST00000312413.6_Silent_p.A78A	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6	78					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)		GATATGAGGCGGTGAAGTGGA	0.532													G|||	135	0.0269569	0.0938	0.0058	5008	,	,		19754	0.004		0.001	False		,,,				2504	0.002				p.A78A		Atlas-SNP	.											.	CLCN6	77	.	0			c.G234A						PASS	.	G	,,,	483,3923	220.7+/-238.1	24,435,1744	134	103	114		234,234,234,234	1.6	1	1	dbSNP_129	114	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CLCN6	NM_001286.2,NM_021735.2,NM_021736.2,NM_021737.2	,,,	24,443,6036	AA,AG,GG		0.093,10.9623,3.7752	,,,	78/870,78/321,78/354,78/309	11876692	491,12515	2203	4300	6503	SO:0001819	synonymous_variant	1185	exon4			TGAGGCGGTGAAG	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.234G>A	1.37:g.11876692G>A		158	0	0		192	111	0.578125	NM_001286	A8K1T4|B4DGT7|F8W9R3|O60818|O60819|O60820|O60821|P78520|P78521|Q17R81|Q5SNW2|Q5SNW3|Q5SNX1|Q5SNX2|Q5SNX3|Q99427|Q99428|Q99429	Silent	SNP	ENST00000346436.6	37	CCDS138.1																																																																																			G|0.971;A|0.029	0.029	strong		0.532	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2	NM_001286		A	11876692	G	A	11876692	2	1	22	1	0	0	0	0	0	0	0	1	3469	1103	39	1		1	CLCN6	1	11876692	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	155371	11876692	237373929	36	2937											
CLCN6	1185	hgsc.bcm.edu	37	chr1	11884586	11884586	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccatgatccacagtggttcGgtggtgggagctggcctccc	5	9	14	13	1	0	1	0	1	0	0	3	2	2	2	4	5	1	2	4	5	0	1	rs60602304	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11884586G>A	ENST00000346436.6	+	8	676	c.624G>A	c.(622-624)tcG>tcA	p.S208S	CLCN6_ENST00000376492.3_3'UTR|CLCN6_ENST00000376496.3_Silent_p.S208S|CLCN6_ENST00000376487.3_Silent_p.S186S|CLCN6_ENST00000312413.6_Silent_p.S208S	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6	208					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)		ACAGTGGTTCGGTGGTGGGAG	0.597													G|||	115	0.0229633	0.0794	0.0043	5008	,	,		18300	0.004		0.001	False		,,,				2504	0.002				p.S208S		Atlas-SNP	.											.	CLCN6	77	.	0			c.G624A						PASS	.	G	,,,	421,3985	204.8+/-226.9	19,383,1801	75	68	71		624,624,624,624	-11.6	0.1	1	dbSNP_129	71	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CLCN6	NM_001286.2,NM_021735.2,NM_021736.2,NM_021737.2	,,,	19,391,6093	AA,AG,GG		0.093,9.5552,3.2985	,,,	208/870,208/321,208/354,208/309	11884586	429,12577	2203	4300	6503	SO:0001819	synonymous_variant	1185	exon8			TGGTTCGGTGGTG	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.624G>A	1.37:g.11884586G>A		105	0	0		99	53	0.535354	NM_001286	A8K1T4|B4DGT7|F8W9R3|O60818|O60819|O60820|O60821|P78520|P78521|Q17R81|Q5SNW2|Q5SNW3|Q5SNX1|Q5SNX2|Q5SNX3|Q99427|Q99428|Q99429	Silent	SNP	ENST00000346436.6	37	CCDS138.1																																																																																			G|0.970;A|0.030	0.030	strong		0.597	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2	NM_001286		A	11884586	G	A	11884586	2	1	22	1	0	0	0	0	0	0	0	1	3469	1103	39	1		1	CLCN6	1	11884586	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	7894	11884586	237366035	37	2938											
TNFRSF1B	7133	hgsc.bcm.edu	37	chr1	12253003	12253003	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cacccggagtatggccccagGggcagtacacttaccccagc	9	5	11	16	1	0	0	0	0	0	0	0	1	0	1	5	4	3	3	5	4	3	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12253003G>A	ENST00000376259.3	+	6	724	c.635G>A	c.(634-636)gGg>gAg	p.G212E	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	212					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)	ATGGCCCCAGGGGCAGTACAC	0.617																																					p.G212E		Atlas-SNP	.											.	TNFRSF1B	28	.	0			c.G635A						PASS	.						165	121	136					1																	12253003		2203	4300	6503	SO:0001583	missense	7133	exon6			CCCCAGGGGCAGT	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.635G>A	1.37:g.12253003G>A	ENSP00000365435:p.Gly212Glu	76	0	0		110	58	0.527273	NM_001066	B1AJZ3|Q16042|Q6YI29|Q9UIH1	Missense_Mutation	SNP	ENST00000376259.3	37	CCDS145.1	.	.	.	.	.	.	.	.	.	.	G	3.321	-0.138774	0.06669	.	.	ENSG00000028137	ENST00000376259;ENST00000400863	D	0.86097	-2.07	3.31	-0.714	0.11219	.	2.871980	0.01167	N	0.006766	T	0.75273	0.3827	L	0.38953	1.18	0.09310	N	1	B	0.15473	0.013	B	0.12837	0.008	T	0.60840	-0.7183	10	0.02654	T	1	0.0033	6.2978	0.21095	0.4784:0.0:0.5216:0.0	.	212	P20333	TNR1B_HUMAN	E	212	ENSP00000365435:G212E	ENSP00000365435:G212E	G	+	2	0	TNFRSF1B	12175590	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.169000	0.09911	-0.138000	0.11434	-0.812000	0.03155	GGG	.	.	none		0.617	TNFRSF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005133.1	NM_001066		A	12253003	G	A	12253003	3	1	22	1	0	0	0	0	1	0	0	0	16309	1232	43	2	657	2	TNFRSF1B	1	12253003	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	368417	12253003	236997618	38	2939											
C1orf158	93190	hgsc.bcm.edu	37	chr1	12819401	12819401	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgctgtggctgccagagaaGtctgactttccccttcttgg	5	14	11	11	0	2	2	0	1	2	1	3	3	3	2	3	2	2	2	3	2	1	4	rs115263357	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12819401G>A	ENST00000288048.5	+	3	600	c.384G>A	c.(382-384)aaG>aaA	p.K128K	C1orf158_ENST00000376210.3_Silent_p.K90K	NM_152290.2	NP_689503.2	Q8N1D5	CA158_HUMAN	chromosome 1 open reading frame 158	128										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)		TGCCAGAGAAGTCTGACTTTC	0.522													G|||	33	0.00658946	0.0227	0.0043	5008	,	,		20187	0.0		0.0	False		,,,				2504	0.0				p.K128K		Atlas-SNP	.											.	C1orf158	28	.	0			c.G384A						PASS	.	G		78,4328		0,78,2125	86	88	87		384	1.4	0.3	1	dbSNP_132	87	0,8600		0,0,4300	no	coding-synonymous	C1orf158	NM_152290.2		0,78,6425	AA,AG,GG		0.0,1.7703,0.5997		128/195	12819401	78,12928	2203	4300	6503	SO:0001819	synonymous_variant	93190	exon3			AGAGAAGTCTGAC	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.384G>A	1.37:g.12819401G>A		111	0	0		107	53	0.495327	NM_152290	Q5VUY4	Silent	SNP	ENST00000288048.5	37	CCDS147.1																																																																																			G|0.993;A|0.007	0.007	strong		0.522	C1orf158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005325.1	NM_152290		A	12819401	G	A	12819401	2	1	22	1	0	0	0	0	0	0	0	1	2009	1020	36	2		2	C1orf158	1	12819401	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	566398	12819401	236431220	39	2940											
PRAMEF2	65122	hgsc.bcm.edu	37	chr1	12918903	12918903	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccgagactactggagctggcGgggcagagcctgctgagaga	9	5	17	10	2	0	4	0	1	0	3	0	7	0	5	2	4	4	3	2	4	1	1	rs17038644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12918903G>A	ENST00000240189.2	+	2	126	c.39G>A	c.(37-39)gcG>gcA	p.A13A		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	13					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)		TGGAGCTGGCGGGGCAGAGCC	0.562													.|||	197	0.0393371	0.0908	0.0144	5008	,	,		19026	0.0298		0.0189	False		,,,				2504	0.0184				p.A13A		Atlas-SNP	.											.	PRAMEF2	85	.	0			c.G39A						PASS	.	A		276,4126	143.8+/-178.8	19,238,1944	88	99	95		39	-1.7	0	1	dbSNP_123	95	7,8587		0,7,4290	no	coding-synonymous	PRAMEF2	NM_023014.1		19,245,6234	AA,AG,GG		0.0815,6.2699,2.1776		13/475	12918903	283,12713	2201	4297	6498	SO:0001819	synonymous_variant	65122	exon2			GCTGGCGGGGCAG		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.39G>A	1.37:g.12918903G>A		358	1	0.0027933		452	227	0.502212	NM_023014		Silent	SNP	ENST00000240189.2	37	CCDS149.1																																																																																			G|0.978;A|0.022	0.022	strong		0.562	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014		A	12918903	G	A	12918903	2	1	22	1	0	0	0	0	0	0	0	1	12447	1103	39	1		1	PRAMEF2	1	12918903	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	99502	12918903	236331718	40	2941											
CTRC	11330	hgsc.bcm.edu	37	chr1	15767036	15767036	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgtggaggcatacgtgtggCgggactttgattgctagcaa	9	10	15	7	3	0	1	0	1	0	0	0	3	0	3	0	4	3	3	0	4	3	4	rs497078	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:15767036C>A	ENST00000375949.4	+	3	206	c.180C>A	c.(178-180)ggC>ggA	p.G60G	CTRC_ENST00000483406.1_3'UTR|CTRC_ENST00000375943.2_Intron	NM_007272.2	NP_009203.2	Q99895	CTRC_HUMAN	chymotrypsin C (caldecrin)	60	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)		peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)	13		Breast(348;0.000207)|all_lung(284;0.00021)|Colorectal(325;0.000257)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)|Hepatocellular(190;0.0634)		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)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		ATACGTGTGGCGGGACTTTGA	0.627													C|||	90	0.0179712	0.0651	0.0058	5008	,	,		14713	0.0		0.0	False		,,,				2504	0.0				p.G60G		Atlas-SNP	.											.	CTRC	28	.	0			c.C180A						PASS	.						144	95	111					1																	15767036		2203	4300	6503	SO:0001819	synonymous_variant	11330	exon3			GTGTGGCGGGACT	BC015118	CCDS156.1	1p36.21	2009-02-18			ENSG00000162438	ENSG00000162438	3.4.21.2		2523	protein-coding gene	gene with protein product	"elastase 4"	601405				8635596	Standard	NM_007272		Approved	CLCR, ELA4	uc001awi.1	Q99895	OTTHUMG00000002255	ENST00000375949.4:c.180C>A	1.37:g.15767036C>A		105	0	0		108	40	0.37037	NM_007272	A8K082|O00765|Q9NUH5	Silent	SNP	ENST00000375949.4	37	CCDS156.1																																																																																			A|0.000;C|0.887;T|0.113	0.000	strong		0.627	CTRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006435.1	NM_007272		A	15767036	C	A	15767036	2	1	22	1	0	0	0	0	0	0	0	1	4029	755	27	4		4	CTRC	1	15767036	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2848133	15767036	233483585	41	2942											
TMEM82	388595	hgsc.bcm.edu	37	chr1	16069664	16069664	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgagttctccctccgggccgTgtccacgctgctgtccctgg	2	10	12	17	4	1	0	0	0	1	0	5	1	4	0	5	2	1	3	5	2	0	1	rs61740067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:16069664T>C	ENST00000375782.1	+	3	449	c.311T>C	c.(310-312)gTg>gCg	p.V104A	TMEM82_ENST00000465575.1_3'UTR|RP11-169K16.4_ENST00000418525.1_RNA	NM_001013641.1	NP_001013663.1	A0PJX8	TMM82_HUMAN	transmembrane protein 82	104	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)		CTCCGGGCCGTGTCCACGCTG	0.701													T|||	115	0.0229633	0.0817	0.0101	5008	,	,		13676	0.0		0.0	False		,,,				2504	0.0				p.V104A		Atlas-SNP	.											.	TMEM82	30	.	0			c.T311C						PASS	.	T	ALA/VAL	248,4156	138.4+/-174.2	7,234,1961	39	37	38		311	4.4	0.8	1	dbSNP_129	38	0,8594		0,0,4297	yes	missense	TMEM82	NM_001013641.1	64	7,234,6258	CC,CT,TT		0.0,5.6312,1.908	benign	104/344	16069664	248,12750	2202	4297	6499	SO:0001583	missense	388595	exon3			GGGCCGTGTCCAC		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.311T>C	1.37:g.16069664T>C	ENSP00000364938:p.Val104Ala	67	0	0		80	29	0.3625	NM_001013641	B2RP27|Q5VVD4	Missense_Mutation	SNP	ENST00000375782.1	37	CCDS30608.1	53	0.024267399267399268	48	0.0975609756097561	5	0.013812154696132596	0	0.0	0	0.0	T	18.43	3.622000	0.66787	0.056312	0.0	ENSG00000162460	ENST00000375782	T	0.57595	0.39	4.44	4.44	0.53790	.	0.248154	0.34002	N	0.004349	T	0.01976	0.0062	M	0.72894	2.215	0.32890	D	0.511731	P	0.49559	0.925	B	0.38264	0.269	T	0.49370	-0.8947	10	0.66056	D	0.02	-21.6084	13.99	0.64359	0.0:0.0:0.0:1.0	rs61740067	104	A0PJX8	TMM82_HUMAN	A	104	ENSP00000364938:V104A	ENSP00000364938:V104A	V	+	2	0	TMEM82	15942251	0.731000	0.28111	0.774000	0.31636	0.905000	0.53344	3.834000	0.55798	1.763000	0.52060	0.459000	0.35465	GTG	T|0.982;C|0.018	0.018	strong		0.701	TMEM82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008471.2	NM_001013641		C	16069664	T	C	16069664	3	2	22	1	0	0	0	0	1	0	0	0	16221	1696	59	3	321	3	TMEM82	1	16069664	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	302628	16069664	233180957	42	2943											
FBLIM1	54751	hgsc.bcm.edu	37	chr1	16091700	16091700	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agagctgcagccacagtgccGgctgcacctatgcagctctt	8	8	11	14	1	1	1	0	0	1	1	1	1	1	1	3	1	7	6	3	1	1	2	rs61733331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:16091700G>A	ENST00000375766.3	+	3	862	c.222G>A	c.(220-222)ccG>ccA	p.P74P	FBLIM1_ENST00000441801.2_Silent_p.P74P|FBLIM1_ENST00000332305.5_Silent_p.P74P|FBLIM1_ENST00000400773.1_Silent_p.P74P|FBLIM1_ENST00000375771.1_Silent_p.P74P	NM_017556.2	NP_060026.2	Q8WUP2	FBLI1_HUMAN	filamin binding LIM protein 1	74	Intrinsically disordered.|Pro-rich.				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)		CCACAGTGCCGGCTGCACCTA	0.662													A|||	84	0.0167732	0.0477	0.0043	5008	,	,		13729	0.0069		0.002	False		,,,				2504	0.0092				p.P74P		Atlas-SNP	.											.	FBLIM1	46	.	0			c.G222A						PASS	.	A	,,	157,4227		2,153,2037	21	24	23		222,222,222	-2.8	0	1	dbSNP_129	23	18,8566		0,18,4274	no	coding-synonymous,coding-synonymous,coding-synonymous	FBLIM1	NM_001024215.1,NM_001024216.1,NM_017556.2	,,	2,171,6311	AA,AG,GG		0.2097,3.5812,1.3495	,,	74/375,74/277,74/374	16091700	175,12793	2192	4292	6484	SO:0001819	synonymous_variant	54751	exon2			AGTGCCGGCTGCA		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.222G>A	1.37:g.16091700G>A		117	0	0		123	67	0.544715	NM_001024215	B3KNY0|Q5VVE0|Q5VVE1|Q8IX23|Q96T00|Q9UFD6	Silent	SNP	ENST00000375766.3	37	CCDS163.1																																																																																			G|0.988;A|0.012	0.012	strong		0.662	FBLIM1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008511.3	NM_001024215		A	16091700	G	A	16091700	2	1	22	1	0	0	0	0	0	0	0	1	5705	1103	39	1		1	FBLIM1	1	16091700	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	22036	16091700	233158921	43	2944											
FBXO42	54455	hgsc.bcm.edu	37	chr1	16577948	16577948	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatatggcctgtacaggactGtccaaagaagagccacccac	13	6	10	12	0	0	2	0	0	0	2	1	4	1	3	4	2	2	1	4	2	4	2	rs61731119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:16577948G>A	ENST00000375592.3	-	10	1587	c.1371C>T	c.(1369-1371)gaC>gaT	p.D457D		NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	457										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)		GTACAGGACTGTCCAAAGAAG	0.552													G|||	149	0.0297524	0.1074	0.0101	5008	,	,		17306	0.0		0.0	False		,,,				2504	0.0				p.D457D		Atlas-SNP	.											.	FBXO42	53	.	0			c.C1371T						PASS	.	G		386,4020	179.7+/-208.2	17,352,1834	29	33	32		1371	5.5	1	1	dbSNP_129	32	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	FBXO42	NM_018994.1		17,356,6130	AA,AG,GG		0.0465,8.7608,2.9986		457/718	16577948	390,12616	2203	4300	6503	SO:0001819	synonymous_variant	54455	exon10			AGGACTGTCCAAA	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.1371C>T	1.37:g.16577948G>A		181	0	0		159	87	0.54717	NM_018994	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	Silent	SNP	ENST00000375592.3	37	CCDS30613.1																																																																																			G|0.973;A|0.027	0.027	strong		0.552	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006285.1			A	16577948	G	A	16577948	2	1	22	1	0	0	0	0	0	0	0	1	5759	1368	48	2		2	FBXO42	1	16577948	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	486248	16577948	232672673	44	2945											
PADI2	11240	hgsc.bcm.edu	37	chr1	17413127	17413127	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agctccgcggagccacccgtGtacttgaccacatggtagag	9	7	12	13	3	0	2	0	1	0	1	1	3	1	3	4	2	3	3	4	2	2	3	rs35184728	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17413127G>A	ENST00000375486.4	-	7	786	c.723C>T	c.(721-723)taC>taT	p.Y241Y	PADI2_ENST00000444885.2_Missense_Mutation_p.T160I|PADI2_ENST00000375481.1_Silent_p.Y241Y	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	241					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)	AGCCACCCGTGTACTTGACCA	0.602													G|||	105	0.0209665	0.0635	0.0072	5008	,	,		17470	0.0159		0.0	False		,,,				2504	0.0				p.Y241Y		Atlas-SNP	.											PADI2,NS,malignant_melanoma,-1,1	PADI2	72	1	0			c.C723T						PASS	.	G		290,4116	159.2+/-191.8	8,274,1921	81	85	84		723	2.6	1	1	dbSNP_126	84	0,8600		0,0,4300	no	coding-synonymous	PADI2	NM_007365.2		8,274,6221	AA,AG,GG		0.0,6.5819,2.2297		241/666	17413127	290,12716	2203	4300	6503	SO:0001819	synonymous_variant	11240	exon7			ACCCGTGTACTTG	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.723C>T	1.37:g.17413127G>A		84	0	0		110	62	0.563636	NM_007365	Q96DA7|Q9UPN2	Silent	SNP	ENST00000375486.4	37	CCDS177.1	42	0.019230769230769232	28	0.056910569105691054	2	0.0055248618784530384	12	0.02097902097902098	0	0.0	G	11.73	1.726689	0.30593	0.065819	0.0	ENSG00000117115	ENST00000444885	T	0.05258	3.47	4.56	2.62	0.31277	.	.	.	.	.	T	0.00328	0.0010	.	.	.	0.24587	N	0.993841	B	0.02656	0.0	B	0.06405	0.002	T	0.45818	-0.9235	8	0.20519	T	0.43	-30.2651	8.7762	0.34762	0.2513:0.0:0.7487:0.0	rs35184728	160	B4DIU3	.	I	160	ENSP00000405894:T160I	ENSP00000405894:T160I	T	-	2	0	PADI2	17285714	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	3.058000	0.49939	1.124000	0.41980	0.460000	0.39030	ACA	G|0.976;A|0.024	0.024	strong		0.602	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1			A	17413127	G	A	17413127	2	1	22	1	0	0	0	0	0	0	0	1	11387	1372	48	2		2	PADI2	1	17413127	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	835179	17413127	231837494	45	2946											
PADI4	23569	hgsc.bcm.edu	37	chr1	17668508	17668508	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcactacctgatggtcccCggtggaaagcacaacatgga	11	8	10	12	1	1	1	1	1	1	0	3	3	2	3	3	4	3	1	3	4	3	1	rs16825565	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17668508C>T	ENST00000375448.4	+	7	749	c.723C>T	c.(721-723)ccC>ccT	p.P241P	AC004824.2_ENST00000602074.1_Intron	NM_012387.2	NP_036519.2	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV	241					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)	TGATGGTCCCCGGTGGAAAGC	0.602													C|||	74	0.0147764	0.0537	0.0043	5008	,	,		17108	0.0		0.0	False		,,,				2504	0.0				p.P241P		Atlas-SNP	.											.	PADI4	70	.	0			c.C723T						PASS	.	C		190,4216	119.6+/-157.3	6,178,2019	85	78	81		723	-9.9	0	1	dbSNP_123	81	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	PADI4	NM_012387.2		6,180,6317	TT,TC,CC		0.0233,4.3123,1.4762		241/664	17668508	192,12814	2203	4300	6503	SO:0001819	synonymous_variant	23569	exon7			GGTCCCCGGTGGA	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.723C>T	1.37:g.17668508C>T		143	0	0		122	54	0.442623	NM_012387	A8K392|B2RBW0|Q5VTZ8|Q70SX4	Silent	SNP	ENST00000375448.4	37	CCDS180.1																																																																																			C|0.984;T|0.016	0.016	strong		0.602	PADI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006799.1	NM_012387		T	17668508	C	T	17668508	2	4	22	1	0	0	0	0	0	0	0	1	11389	639	23	1		1	PADI4	1	17668508	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	255381	17668508	231582113	46	2947											
PADI6	353238	hgsc.bcm.edu	37	chr1	17727847	17727847	+	RNA	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcatcaatgactttgactgTtacctgacagaggtcggaga	11	12	10	8	1	2	5	2	3	0	2	3	6	2	5	1	2	1	1	1	2	2	3	rs183565903	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17727847T>C	ENST00000434762.2	+	0	2049							Q6TGC4	PADI6_HUMAN	peptidyl arginine deiminase, type VI						cytoplasm organization (GO:0007028)|cytoskeleton organization (GO:0007010)|protein citrullination (GO:0018101)|regulation of translation by machinery localization (GO:0043143)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(2)	29		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;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	ACTTTGACTGTTACCTGACAG	0.552													T|||	4	0.000798722	0.0015	0.0029	5008	,	,		19527	0.0		0.0	False		,,,				2504	0.0				p.C666C		Atlas-SNP	.											.	PADI6	51	.	0			c.T1998C						PASS	.	T		5,3961		0,5,1978	60	64	63		1999	-1.8	0.9	1		63	0,8346		0,0,4173	no	coding-synonymous	PADI6	NM_207421.3		0,5,6151	CC,CT,TT		0.0,0.1261,0.0406		666/695	17727847	5,12307	1983	4173	6156			353238	exon17			TGACTGTTACCTG	AY422079	CCDS72715.1	1p36.13	2014-07-10			ENSG00000256049	ENSG00000276747	3.5.3.15	"Peptidyl arginine deiminases"	20449	protein-coding gene	gene with protein product		610363				15087120	Standard	NM_207421		Approved		uc001bak.1	Q6TGC4	OTTHUMG00000002372		1.37:g.17727847T>C		128	0	0		121	52	0.429752	NM_207421	Q330K5|Q70SX3	Silent	SNP	ENST00000434762.2	37																																																																																				T|1.000;C|0.000	0.000	strong		0.552	PADI6-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000006804.4	NM_207421		C	17727847	T	C	17727847	1	2	22	0	1	0	0	0	0	0	0	0	11390	1731	60	3		3	PADI6	1	17727847	RNA	SNP	T	TCGA-G8-6324-01A-11D-2210-10	59339	17727847	231522774	47	2948											
TAS1R2	80834	hgsc.bcm.edu	37	chr1	19166100	19166100	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaccggatggcactagtccCtcctcatggtgtagccctgg	6	9	11	15	1	1	0	1	0	0	0	3	1	3	1	5	4	1	2	5	4	2	2	rs9988418	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19166100C>T	ENST00000375371.3	-	6	2534	c.2513G>A	c.(2512-2514)aGg>aAg	p.R838K		NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	838			R -> K (in dbSNP:rs9988418).		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)	GCACTAGTCCCTCCTCATGGT	0.612													c|||	288	0.057508	0.1944	0.0303	5008	,	,		15986	0.001		0.003	False		,,,				2504	0.0061				p.R838K		Atlas-SNP	.											.	TAS1R2	134	.	0			c.G2513A						PASS	.		LYS/ARG	613,3793	264.1+/-265.8	43,527,1633	64	51	55		2513	-5.4	0	1	dbSNP_119	55	60,8540	35.9+/-90.5	1,58,4241	yes	missense	TAS1R2	NM_152232.2	26	44,585,5874	TT,TC,CC		0.6977,13.9128,5.1745	benign	838/840	19166100	673,12333	2203	4300	6503	SO:0001583	missense	80834	exon6			TAGTCCCTCCTCA		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.2513G>A	1.37:g.19166100C>T	ENSP00000364520:p.Arg838Lys	134	0	0		186	83	0.446237	NM_152232	Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	37	CCDS187.1	91	0.041666666666666664	71	0.1443089430894309	16	0.04419889502762431	1	0.0017482517482517483	3	0.00395778364116095	C	0.013	-1.638637	0.00799	0.139128	0.006977	ENSG00000179002	ENST00000375371	D	0.87650	-2.28	5.19	-5.36	0.02689	.	0.573210	0.15415	N	0.263527	T	0.00608	0.0020	N	0.01576	-0.805	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.34279	-0.9835	9	0.02654	T	1	.	6.9586	0.24585	0.135:0.5063:0.0:0.3587	rs9988418;rs52814741;rs9988418	838	Q8TE23	TS1R2_HUMAN	K	838	ENSP00000364520:R838K	ENSP00000364520:R838K	R	-	2	0	TAS1R2	19038687	0.002000	0.14202	0.003000	0.11579	0.095000	0.18619	-0.049000	0.11924	-1.382000	0.02109	-0.364000	0.07487	AGG	C|0.950;T|0.050	0.050	strong		0.612	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1			T	19166100	C	T	19166100	3	4	22	1	0	0	0	0	1	0	0	0	15578	681	24	2	10	2	TAS1R2	1	19166100	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1438253	19166100	230084521	48	2949											
TAS1R2	80834	hgsc.bcm.edu	37	chr1	19166894	19166894	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgctgaggaagcccagggcGgccagcagggccacagcgat	9	3	17	12	2	0	1	0	1	0	0	0	3	0	2	3	4	4	2	3	4	1	0	rs11805253	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19166894G>A	ENST00000375371.3	-	6	1740	c.1719C>T	c.(1717-1719)gcC>gcT	p.A573A		NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	573					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)	AGCCCAGGGCGGCCAGCAGGG	0.612													G|||	262	0.0523163	0.1747	0.0303	5008	,	,		18191	0.001		0.003	False		,,,				2504	0.0061				p.A573A		Atlas-SNP	.											.	TAS1R2	134	.	0			c.C1719T						PASS	.	G		529,3877	237.7+/-249.4	32,465,1706	49	51	50		1719	-7.5	0	1	dbSNP_120	50	61,8539	36.9+/-92.0	1,59,4240	no	coding-synonymous	TAS1R2	NM_152232.2		33,524,5946	AA,AG,GG		0.7093,12.0064,4.5364		573/840	19166894	590,12416	2203	4300	6503	SO:0001819	synonymous_variant	80834	exon6			CAGGGCGGCCAGC		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.1719C>T	1.37:g.19166894G>A		140	0	0		125	63	0.504	NM_152232	Q5TZ19	Silent	SNP	ENST00000375371.3	37	CCDS187.1																																																																																			G|0.959;A|0.041	0.041	strong		0.612	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1			A	19166894	G	A	19166894	2	1	22	1	0	0	0	0	0	0	0	1	15578	1103	39	1		1	TAS1R2	1	19166894	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	794	19166894	230083727	49	2950											
UBR4	23352	hgsc.bcm.edu	37	chr1	19403331	19403331	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcttcgtagatgggcatgtcGttgtggcggatgtactcagc	6	12	15	8	3	1	1	1	0	0	1	3	2	1	2	0	3	2	5	0	3	2	4	rs142064832	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19403331G>A	ENST00000375254.3	-	105	15417	c.15390C>T	c.(15388-15390)aaC>aaT	p.N5130N	UBR4_ENST00000375217.2_Silent_p.N5123N|UBR4_ENST00000543981.1_Silent_p.N794N|UBR4_ENST00000375226.2_Silent_p.N5106N|UBR4_ENST00000429347.2_Silent_p.N653N|UBR4_ENST00000375224.1_Silent_p.N837N|UBR4_ENST00000375225.3_Silent_p.N205N|RP5-1126H10.2_ENST00000606379.1_RNA|UBR4_ENST00000375267.2_Silent_p.N5151N	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	5130					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)		TGGGCATGTCGTTGTGGCGGA	0.552													G|||	14	0.00279553	0.0106	0.0	5008	,	,		19899	0.0		0.0	False		,,,				2504	0.0				p.N5130N		Atlas-SNP	.											.	UBR4	415	.	0			c.C15390T						PASS	.	G		14,4392	22.3+/-47.3	0,14,2189	199	172	181		15390	-4.1	1	1	dbSNP_134	181	0,8600		0,0,4300	no	coding-synonymous	UBR4	NM_020765.2		0,14,6489	AA,AG,GG		0.0,0.3177,0.1076		5130/5184	19403331	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	23352	exon105			CATGTCGTTGTGG	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.15390C>T	1.37:g.19403331G>A		195	0	0		193	88	0.455959	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	37	CCDS189.1																																																																																			G|0.999;A|0.001	0.001	strong		0.552	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		A	19403331	G	A	19403331	2	1	22	1	0	0	0	0	0	0	0	1	16919	1136	40	1		1	UBR4	1	19403331	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	236437	19403331	229847290	50	2951											
UBR4	23352	hgsc.bcm.edu	37	chr1	19451090	19451090	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caggaggtgggattcgagaaTtggtgtcagtaatctttttg	9	14	14	4	1	2	1	1	0	1	1	3	4	2	3	0	4	0	1	0	4	2	5	rs183578825	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19451090T>C	ENST00000375254.3	-	65	9560	c.9533A>G	c.(9532-9534)aAt>aGt	p.N3178S	UBR4_ENST00000375217.2_Missense_Mutation_p.N3171S|UBR4_ENST00000375226.2_Missense_Mutation_p.N3154S|UBR4_ENST00000375267.2_Missense_Mutation_p.N3178S	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	3178					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)		GATTCGAGAATTGGTGTCAGT	0.468													T|||	3	0.000599042	0.0023	0.0	5008	,	,		19837	0.0		0.0	False		,,,				2504	0.0				p.N3178S		Atlas-SNP	.											UBR4,NS,carcinoma,0,1	UBR4	415	1	0			c.A9533G						PASS	.						201	183	189					1																	19451090		2203	4300	6503	SO:0001583	missense	23352	exon65			CGAGAATTGGTGT	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.9533A>G	1.37:g.19451090T>C	ENSP00000364403:p.Asn3178Ser	164	0	0		167	79	0.473054	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	37	CCDS189.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	T	13.60	2.286447	0.40494	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000425413;ENST00000417040	T;T;T;T	0.21543	2.0;2.0;2.01;2.01	6.07	3.29	0.37713	.	0.196102	0.52532	N	0.000075	T	0.07999	0.0200	N	0.03608	-0.345	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.24693	-1.0153	10	0.16896	T	0.51	.	7.8597	0.29504	0.0:0.303:0.0:0.697	.	3178	Q5T4S7	UBR4_HUMAN	S	3178;3178;3171;3154;786;1864	ENSP00000364403:N3178S;ENSP00000364416:N3178S;ENSP00000364365:N3171S;ENSP00000364374:N3154S	ENSP00000364365:N3171S	N	-	2	0	UBR4	19323677	1.000000	0.71417	0.990000	0.47175	0.842000	0.47809	3.890000	0.56220	0.348000	0.23949	0.533000	0.62120	AAT	T|0.999;C|0.001	0.001	strong		0.468	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		C	19451090	T	C	19451090	3	2	22	1	0	0	0	0	1	0	0	0	16919	1493	52	3	6186	3	UBR4	1	19451090	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	47759	19451090	229799531	51	2952											
UBR4	23352	hgsc.bcm.edu	37	chr1	19467322	19467322	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agggttcctgcgtccagagaGgaagagctgggtgcctggcc	7	7	17	10	1	0	2	0	0	0	2	2	4	2	3	4	4	3	2	4	4	1	1	rs139618268	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19467322G>A	ENST00000375254.3	-	58	8580	c.8553C>T	c.(8551-8553)tcC>tcT	p.S2851S	UBR4_ENST00000375217.2_Intron|UBR4_ENST00000375226.2_Intron|UBR4_ENST00000375267.2_Silent_p.S2851S	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	2851					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)		CGTCCAGAGAGGAAGAGCTGG	0.622													G|||	3	0.000599042	0.0023	0.0	5008	,	,		19916	0.0		0.0	False		,,,				2504	0.0				p.S2851S		Atlas-SNP	.											.	UBR4	415	.	0			c.C8553T						PASS	.	G		17,4389	22.3+/-47.3	0,17,2186	66	60	62		8553	4.8	1	1	dbSNP_134	62	0,8600		0,0,4300	no	coding-synonymous	UBR4	NM_020765.2		0,17,6486	AA,AG,GG		0.0,0.3858,0.1307		2851/5184	19467322	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	23352	exon58			CAGAGAGGAAGAG	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.8553C>T	1.37:g.19467322G>A		57	0	0		67	34	0.507463	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	37	CCDS189.1																																																																																			G|0.999;A|0.001	0.001	strong		0.622	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		A	19467322	G	A	19467322	2	1	22	1	0	0	0	0	0	0	0	1	16919	987	35	2		2	UBR4	1	19467322	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	16232	19467322	229783299	52	2953											
UBR4	23352	hgsc.bcm.edu	37	chr1	19482788	19482788	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aacaaagtctgcggtgacaaTtgctaactcggtctgtgaac	12	10	10	9	2	2	2	0	2	2	0	3	2	2	2	0	2	5	1	0	2	5	2	rs145733997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19482788T>C	ENST00000375254.3	-	42	6076	c.6049A>G	c.(6049-6051)Att>Gtt	p.I2017V	UBR4_ENST00000375217.2_Missense_Mutation_p.I2017V|UBR4_ENST00000375226.2_Missense_Mutation_p.I2017V|UBR4_ENST00000375267.2_Missense_Mutation_p.I2017V	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	2017					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)		GCGGTGACAATTGCTAACTCG	0.433													T|||	15	0.00299521	0.0106	0.0	5008	,	,		21210	0.0		0.0	False		,,,				2504	0.001				p.I2017V		Atlas-SNP	.											.	UBR4	415	.	0			c.A6049G						PASS	.	T	VAL/ILE	11,4395	19.1+/-41.9	0,11,2192	132	119	123		6049	5.4	1	1	dbSNP_134	123	0,8600		0,0,4300	yes	missense	UBR4	NM_020765.2	29	0,11,6492	CC,CT,TT		0.0,0.2497,0.0846	benign	2017/5184	19482788	11,12995	2203	4300	6503	SO:0001583	missense	23352	exon42			TGACAATTGCTAA	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.6049A>G	1.37:g.19482788T>C	ENSP00000364403:p.Ile2017Val	204	0	0		192	95	0.494792	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	37	CCDS189.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	11.40	1.626757	0.28978	0.002497	0.0	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000417040;ENST00000419533	T;T;T;T;T	0.14391	2.51;2.51;2.51;2.51;3.45	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.08980	0.0222	N	0.01482	-0.84	0.80722	D	1	P	0.35745	0.518	P	0.47827	0.558	T	0.47636	-0.9102	10	0.09590	T	0.72	.	15.6048	0.76658	0.0:0.0:0.0:1.0	.	2017	Q5T4S7	UBR4_HUMAN	V	2017;2017;2017;2017;727;1233	ENSP00000364403:I2017V;ENSP00000364416:I2017V;ENSP00000364365:I2017V;ENSP00000364374:I2017V;ENSP00000404897:I727V	ENSP00000364365:I2017V	I	-	1	0	UBR4	19355375	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	5.563000	0.67352	2.270000	0.75569	0.482000	0.46254	ATT	T|0.999;C|0.001	0.001	strong		0.433	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		C	19482788	T	C	19482788	3	2	22	1	0	0	0	0	1	0	0	0	16919	1493	52	3	9762	3	UBR4	1	19482788	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	15466	19482788	229767833	53	2954											
UBR4	23352	hgsc.bcm.edu	37	chr1	19500830	19500830	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taccaaggctgttacattctTgttttcctttctcctaactg	7	18	5	11	0	2	0	0	0	2	0	4	0	3	0	3	1	3	3	3	1	4	8	rs143098074	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19500830T>G	ENST00000375254.3	-	22	2992	c.2965A>C	c.(2965-2967)Aag>Cag	p.K989Q	UBR4_ENST00000375217.2_Missense_Mutation_p.K989Q|UBR4_ENST00000375226.2_Missense_Mutation_p.K989Q|UBR4_ENST00000375267.2_Missense_Mutation_p.K989Q	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	989					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)		GTTACATTCTTGTTTTCCTTT	0.423													T|||	9	0.00179712	0.0068	0.0	5008	,	,		19353	0.0		0.0	False		,,,				2504	0.0				p.K989Q		Atlas-SNP	.											.	UBR4	415	.	0			c.A2965C						PASS	.	T	GLN/LYS	7,4399	12.9+/-30.5	0,7,2196	155	131	139		2965	5.8	1	1	dbSNP_134	139	0,8600		0,0,4300	yes	missense	UBR4	NM_020765.2	53	0,7,6496	GG,GT,TT		0.0,0.1589,0.0538	benign	989/5184	19500830	7,12999	2203	4300	6503	SO:0001583	missense	23352	exon22			CATTCTTGTTTTC	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.2965A>C	1.37:g.19500830T>G	ENSP00000364403:p.Lys989Gln	49	0	0		68	34	0.5	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	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	T	16.68	3.189502	0.57909	0.001589	0.0	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000419533	T;T;T;T	0.25912	1.78;1.78;1.78;1.77	5.76	5.76	0.90799	.	0.104877	0.64402	D	0.000006	T	0.21921	0.0528	L	0.36672	1.1	0.80722	D	1	P	0.34522	0.455	B	0.31869	0.137	T	0.02885	-1.1098	10	0.29301	T	0.29	.	15.7251	0.77751	0.0:0.0:0.0:1.0	.	989	Q5T4S7	UBR4_HUMAN	Q	989;989;989;989;205	ENSP00000364403:K989Q;ENSP00000364416:K989Q;ENSP00000364365:K989Q;ENSP00000364374:K989Q	ENSP00000364365:K989Q	K	-	1	0	UBR4	19373417	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.368000	0.79567	2.197000	0.70478	0.533000	0.62120	AAG	T|0.999;G|0.001	0.001	strong		0.423	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		G	19500830	T	G	19500830	3	3	22	1	0	0	0	0	1	0	0	0	16919	1821	63	5	12926	5	UBR4	1	19500830	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	18042	19500830	229749791	54	2955											
UBR4	23352	hgsc.bcm.edu	37	chr1	19518855	19518855	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagcaccaagcacccagcaaTtggaaattctgatagtgctg	14	8	9	10	0	1	1	0	1	1	0	1	2	1	2	2	1	4	4	2	1	5	3	rs147313932	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19518855T>C	ENST00000375254.3	-	11	1248	c.1221A>G	c.(1219-1221)caA>caG	p.Q407Q	UBR4_ENST00000375217.2_Silent_p.Q407Q|UBR4_ENST00000375226.2_Silent_p.Q407Q|UBR4_ENST00000375267.2_Silent_p.Q407Q	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	407					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)		CACCCAGCAATTGGAAATTCT	0.428													T|||	15	0.00299521	0.0106	0.0	5008	,	,		19894	0.001		0.0	False		,,,				2504	0.0				p.Q407Q		Atlas-SNP	.											.	UBR4	415	.	0			c.A1221G						PASS	.	T		13,4393	21.2+/-45.6	0,13,2190	79	81	80		1221	-11.2	0	1	dbSNP_134	80	0,8600		0,0,4300	no	coding-synonymous	UBR4	NM_020765.2		0,13,6490	CC,CT,TT		0.0,0.2951,0.1		407/5184	19518855	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	23352	exon11			CAGCAATTGGAAA	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.1221A>G	1.37:g.19518855T>C		76	0	0		78	37	0.474359	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	37	CCDS189.1																																																																																			T|0.999;C|0.001	0.001	strong		0.428	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		C	19518855	T	C	19518855	2	2	22	1	0	0	0	0	0	0	0	1	16919	1490	52	3		3	UBR4	1	19518855	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	18025	19518855	229731766	55	2956											
KIAA0090	23065	hgsc.bcm.edu	37	chr1	19549250	19549250	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagggagctgaaggcggtggCgttgtattgctcagtgccct	6	10	16	9	2	1	1	1	1	0	0	1	2	1	2	1	4	3	4	1	4	2	3	rs371524055	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19549250C>T	ENST00000477853.1	-	20	2497	c.2455G>A	c.(2455-2457)Gcc>Acc	p.A819T	EMC1_ENST00000375208.3_Missense_Mutation_p.A797T|RP1-43E13.2_ENST00000437898.1_RNA|EMC1_ENST00000375199.3_Missense_Mutation_p.A818T|EMC1_ENST00000480380.1_5'Flank	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	819						ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)											AAGGCGGTGGCGTTGTATTGC	0.602													C|||	4	0.000798722	0.003	0.0	5008	,	,		18529	0.0		0.0	False		,,,				2504	0.0				p.A819T		Atlas-SNP	.											.	.	.	.	0			c.G2455A						PASS	.	C	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	121	107	111		2455	6	1	1		111	0,8600		0,0,4300	no	missense	KIAA0090	NM_015047.1	58	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	819/994	19549250	1,13005	2203	4300	6503	SO:0001583	missense	23065	exon20			CGGTGGCGTTGTA		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.2455G>A	1.37:g.19549250C>T	ENSP00000420608:p.Ala819Thr	191	0	0		199	105	0.527638	NM_015047	A8K6F3|Q14700|Q5TG62|Q63HL0|Q63HL3|Q8NBH8	Missense_Mutation	SNP	ENST00000477853.1	37	CCDS190.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.93|14.93	2.680976|2.680976	0.47886|0.47886	2.27E-4|2.27E-4	0.0|0.0	ENSG00000127463|ENSG00000127463	ENST00000477853;ENST00000375199;ENST00000375208;ENST00000486405|ENST00000375197	T;T;T|.	0.24723|.	1.84;1.84;1.84|.	5.98|5.98	5.98|5.98	0.97165|0.97165	Domain of unknown function DUF1620 (1);|.	0.085825|.	0.85682|.	D|.	0.000000|.	T|T	0.51856|0.51856	0.1699|0.1699	N|N	0.26092|0.26092	0.79|0.79	0.80722|0.80722	D|D	1|1	B;B;P;P|.	0.39520|.	0.334;0.101;0.625;0.676|.	B;B;B;B|.	0.32289|.	0.063;0.063;0.088;0.143|.	T|T	0.45160|0.45160	-0.9280|-0.9280	10|5	0.21014|.	T|.	0.42|.	-26.1445|-26.1445	12.3448|12.3448	0.55114|0.55114	0.0:0.9228:0.0:0.0772|0.0:0.9228:0.0:0.0772	.|.	797;818;818;819|.	Q8N766-4;Q8N766-2;Q8N766-3;Q8N766|.	.;.;.;K0090_HUMAN|.	T|H	819;818;797;64|552	ENSP00000420608:A819T;ENSP00000364345:A818T;ENSP00000364354:A797T|.	ENSP00000364345:A818T|.	A|R	-|-	1|2	0|0	KIAA0090|KIAA0090	19421837|19421837	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.732000|0.732000	0.41865|0.41865	5.405000|5.405000	0.66351|0.66351	2.838000|2.838000	0.97847|0.97847	0.655000|0.655000	0.94253|0.94253	GCC|CGC	.	.	none		0.602	EMC1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007076.2	NM_015047		T	19549250	C	T	19549250	3	4	22	1	0	0	0	0	1	0	0	0	8162	768	27	1	542	1	KIAA0090	1	19549250	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	30395	19549250	229701371	56	2957											
TMCO4	255104	hgsc.bcm.edu	37	chr1	20009837	20009837	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cggagggcaggcagcctgggGccagcaagagccccttctcg	7	4	16	14	2	1	1	0	0	1	1	2	2	1	2	4	5	3	3	4	5	1	1	rs116650784	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:20009837G>C	ENST00000294543.6	-	16	1842	c.1601C>G	c.(1600-1602)gCc>gGc	p.A534G	TMCO4_ENST00000375122.2_Missense_Mutation_p.A494G|TMCO4_ENST00000489814.1_5'UTR|TMCO4_ENST00000375127.1_Missense_Mutation_p.A534G	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)		GCAGCCTGGGGCCAGCAAGAG	0.672													G|||	115	0.0229633	0.0802	0.013	5008	,	,		16781	0.0		0.0	False		,,,				2504	0.0				p.A534G		Atlas-SNP	.											.	TMCO4	46	.	0			c.C1601G						PASS	.	G	GLY/ALA	310,4096	135.3+/-171.4	14,282,1907	30	33	32		1601	5.1	1	1	dbSNP_132	32	6,8594	5.0+/-18.6	0,6,4294	no	missense	TMCO4	NM_181719.4	60	14,288,6201	CC,CG,GG		0.0698,7.0359,2.4296	possibly-damaging	534/635	20009837	316,12690	2203	4300	6503	SO:0001583	missense	255104	exon16			CCTGGGGCCAGCA		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.1601C>G	1.37:g.20009837G>C	ENSP00000294543:p.Ala534Gly	175	0	0		201	95	0.472637	NM_181719	Q5TGY2|Q6MZN5|Q7Z6K6|Q9UQP4|Q9Y3K1	Missense_Mutation	SNP	ENST00000294543.6	37	CCDS198.1	41	0.018772893772893772	36	0.07317073170731707	5	0.013812154696132596	0	0.0	0	0.0	G	14.56	2.573196	0.45902	0.070359	6.98E-4	ENSG00000162542	ENST00000294543;ENST00000375127;ENST00000375122	T;T;T	0.34275	1.39;1.41;1.37	5.11	5.11	0.69529	.	0.134780	0.33959	N	0.004400	T	0.02047	0.0064	L	0.32530	0.975	0.31140	N	0.706765	P;P;B	0.43231	0.473;0.801;0.42	B;B;B	0.35353	0.056;0.201;0.061	T	0.02070	-1.1219	10	0.39692	T	0.17	-0.7187	15.6348	0.76944	0.0:0.0:1.0:0.0	.	118;534;494	Q6ZSC6;Q5TGY1;Q5TGY1-2	.;TMCO4_HUMAN;.	G	534;534;494	ENSP00000294543:A534G;ENSP00000364269:A534G;ENSP00000364264:A494G	ENSP00000294543:A534G	A	-	2	0	TMCO4	19882424	1.000000	0.71417	1.000000	0.80357	0.792000	0.44763	2.016000	0.40971	2.532000	0.85374	0.563000	0.77884	GCC	G|0.975;C|0.025	0.025	strong		0.672	TMCO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007658.1	NM_181719		C	20009837	G	C	20009837	3	2	22	1	0	0	0	0	1	0	0	0	16013	1203	42	4	307	4	TMCO4	1	20009837	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	460587	20009837	229240784	57	2958											
PINK1	65018	hgsc.bcm.edu	37	chr1	20975047	20975047	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttggctgctgcctggctgaTgagagcatcggcctgcagtt	5	12	14	10	1	0	2	0	2	0	1	1	3	0	2	2	3	4	6	2	3	0	2	rs45499398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:20975047T>C	ENST00000321556.4	+	6	1267	c.1173T>C	c.(1171-1173)gaT>gaC	p.D391D	PINK1-AS_ENST00000451424.1_RNA|PINK1_ENST00000492302.1_3'UTR	NM_032409.2	NP_115785.1	Q9BXM7	PINK1_HUMAN	PTEN induced putative kinase 1	391	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.				activation of protein kinase B activity (GO:0032148)|cell death (GO:0008219)|cellular response to hypoxia (GO:0071456)|cellular response to toxic substance (GO:0097237)|intracellular signal transduction (GO:0035556)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of gene expression (GO:0010629)|negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway (GO:1903384)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|peptidyl-serine autophosphorylation (GO:0036289)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial electron transport, NADH to ubiquinone (GO:1902958)|positive regulation of peptidase activity (GO:0010952)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of mitochondrion degradation (GO:1903146)|regulation of protein complex assembly (GO:0043254)|regulation of protein ubiquitination (GO:0031396)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|TORC2 signaling (GO:0038203)|ubiquitin-dependent protein catabolic process (GO:0006511)	astrocyte projection (GO:0097449)|axon (GO:0030424)|cell body (GO:0044297)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of mitochondrial outer membrane (GO:0031307)|Lewy body (GO:0097413)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|C3HC4-type RING finger domain binding (GO:0055131)|calcium-dependent protein kinase activity (GO:0010857)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)|protein kinase B binding (GO:0043422)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)	14		all_lung(284;2.72e-05)|Lung NSC(340;2.94e-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;0.0182)|COAD - Colon adenocarcinoma(152;1.21e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000146)|Kidney(64;0.000182)|GBM - Glioblastoma multiforme(114;0.000497)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GCCTGGCTGATGAGAGCATCG	0.607													T|||	50	0.00998403	0.0356	0.0043	5008	,	,		19352	0.0		0.0	False		,,,				2504	0.0				p.D391D	Esophageal Squamous(145;853 1803 8146 34412 35011)	Atlas-SNP	.											.	PINK1	37	.	0			c.T1173C						PASS	.	T		157,4249	107.8+/-146.2	6,145,2052	65	57	60		1173	-5.2	0	1	dbSNP_127	60	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	PINK1	NM_032409.2		6,147,6350	CC,CT,TT		0.0233,3.5633,1.2225		391/582	20975047	159,12847	2203	4300	6503	SO:0001819	synonymous_variant	65018	exon6			GGCTGATGAGAGC	AB053323	CCDS211.1	1p36.12	2011-07-21			ENSG00000158828	ENSG00000158828		"Parkinson disease"	14581	protein-coding gene	gene with protein product		608309	"Parkinson disease (autosomal recessive) 6"	PARK6		11494141, 15349860	Standard	NM_032409		Approved		uc001bdm.3	Q9BXM7	OTTHUMG00000002841	ENST00000321556.4:c.1173T>C	1.37:g.20975047T>C		81	0	0		101	52	0.514852	NM_032409	Q8N6T9|Q8NBU3|Q96DE4	Silent	SNP	ENST00000321556.4	37	CCDS211.1																																																																																			T|0.989;C|0.011	0.011	strong		0.607	PINK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007954.1	NM_032409		C	20975047	T	C	20975047	2	2	22	1	0	0	0	0	0	0	0	1	11941	1461	51	3		3	PINK1	1	20975047	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	965210	20975047	228275574	58	2959											
KIF17	57576	hgsc.bcm.edu	37	chr1	21030956	21030956	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ccacctgacaggctgctgggGctcatctgctgtgtcaggat	6	10	13	12	0	3	1	2	1	1	0	3	2	3	2	2	4	2	4	2	4	0	0	rs56750936	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:21030956G>T	ENST00000247986.2	-	5	1417	c.1107C>A	c.(1105-1107)agC>agA	p.S369R	KIF17_ENST00000375044.1_Missense_Mutation_p.S269R|KIF17_ENST00000400463.3_Missense_Mutation_p.S369R			Q9P2E2	KIF17_HUMAN	kinesin family member 17	369			S -> R (in dbSNP:rs56750936).		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)		GGCTGCTGGGGCTCATCTGCT	0.607													G|||	135	0.0269569	0.0961	0.0101	5008	,	,		14173	0.0		0.0	False		,,,				2504	0.001				p.S369R		Atlas-SNP	.											.	KIF17	130	.	0			c.C1107A						PASS	.	G	ARG/SER,ARG/SER	369,4037	188.5+/-214.9	14,341,1848	85	73	77		1107,1107	3.4	1	1	dbSNP_129	77	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	KIF17	NM_001122819.1,NM_020816.2	110,110	14,347,6142	TT,TG,GG		0.0698,8.3749,2.8833	benign,benign	369/1029,369/1030	21030956	375,12631	2203	4300	6503	SO:0001583	missense	57576	exon5			GCTGGGGCTCATC	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.1107C>A	1.37:g.21030956G>T	ENSP00000247986:p.Ser369Arg	107	0	0		126	121	0.960317	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Missense_Mutation	SNP	ENST00000247986.2	37	CCDS213.1	61	0.027930402930402932	57	0.11585365853658537	4	0.011049723756906077	0	0.0	0	0.0	G	2.171	-0.389993	0.04932	0.083749	6.98E-4	ENSG00000117245	ENST00000375044;ENST00000400463;ENST00000247986	T;T;T	0.70986	-0.53;-0.44;-0.44	5.26	3.4	0.38934	.	0.959805	0.08472	U	0.940858	T	0.01287	0.0042	N	0.22421	0.69	0.09310	N	1	B;B	0.30406	0.278;0.007	B;B	0.33960	0.173;0.011	T	0.01762	-1.1279	10	0.19590	T	0.45	.	8.9324	0.35680	0.2408:0.0:0.7592:0.0	rs56750936;rs61731590	369;369	Q9P2E2-3;Q9P2E2	.;KIF17_HUMAN	R	269;369;369	ENSP00000364184:S269R;ENSP00000383311:S369R;ENSP00000247986:S369R	ENSP00000247986:S369R	S	-	3	2	KIF17	20903543	0.011000	0.17503	0.984000	0.44739	0.078000	0.17371	0.251000	0.18257	0.733000	0.32492	-0.448000	0.05591	AGC	G|0.968;T|0.032	0.032	strong		0.607	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816		T	21030956	G	T	21030956	3	4	22	1	0	0	0	0	1	0	0	0	8288	1194	42	4	2026	4	KIF17	1	21030956	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	55909	21030956	228219665	59	2960											
EIF4G3	8672	hgsc.bcm.edu	37	chr1	21177800	21177800	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagtgctgttcctctccacAtccacacctcctgtgagctg	6	12	7	16	0	2	1	1	1	1	0	6	1	5	1	5	0	2	3	5	0	0	1	rs2230572	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:21177800A>T	ENST00000264211.8	-	22	3749	c.3555T>A	c.(3553-3555)gaT>gaA	p.D1185E	EIF4G3_ENST00000536266.1_Missense_Mutation_p.D789E|EIF4G3_ENST00000602326.1_Missense_Mutation_p.D1191E|EIF4G3_ENST00000374937.3_Missense_Mutation_p.D1191E|EIF4G3_ENST00000374935.3_Missense_Mutation_p.D905E|EIF4G3_ENST00000400422.1_Missense_Mutation_p.D1185E|EIF4G3_ENST00000537738.1_Missense_Mutation_p.D675E	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	1185			D -> E (in dbSNP:rs2230572).		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)		TCCTCTCCACATCCACACCTC	0.498													A|||	14	0.00279553	0.0091	0.0029	5008	,	,		16789	0.0		0.0	False		,,,				2504	0.0				p.D1221E		Atlas-SNP	.											EIF4G3_ENST00000374937,NS,carcinoma,-2,2	EIF4G3	300	2	0			c.T3663A						PASS	.	A	GLU/ASP,GLU/ASP,GLU/ASP	50,4356	52.9+/-88.7	0,50,2153	163	147	152		3663,3573,3555	-7.4	0	1	dbSNP_98	152	0,8600		0,0,4300	yes	missense,missense,missense	EIF4G3	NM_001198801.1,NM_001198802.1,NM_003760.4	45,45,45	0,50,6453	TT,TA,AA		0.0,1.1348,0.3844	benign,benign,benign	1221/1622,1191/1592,1185/1586	21177800	50,12956	2203	4300	6503	SO:0001583	missense	8672	exon26			CTCCACATCCACA	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.3555T>A	1.37:g.21177800A>T	ENSP00000264211:p.Asp1185Glu	172	0	0		197	101	0.51269	NM_001198801	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Missense_Mutation	SNP	ENST00000264211.8	37	CCDS214.1	10	0.004578754578754579	8	0.016260162601626018	2	0.0055248618784530384	0	0.0	0	0.0	A	14.94	2.685816	0.47991	0.011348	0.0	ENSG00000075151	ENST00000264211;ENST00000400415;ENST00000400422;ENST00000374935;ENST00000537738;ENST00000374937;ENST00000536266	T;T;T;T;T;T	0.06849	3.87;3.87;3.68;3.25;3.87;3.55	5.73	-7.44	0.01379	.	0.243758	0.46758	N	0.000265	T	0.01222	0.0040	N	0.14661	0.345	0.26519	N	0.974465	B;B;B;B;B	0.06786	0.001;0.0;0.0;0.001;0.0	B;B;B;B;B	0.09377	0.001;0.001;0.001;0.004;0.002	T	0.39035	-0.9633	10	0.07644	T	0.81	-6.5184	6.1684	0.20404	0.2584:0.1981:0.4652:0.0783	rs2230572;rs35634957	1380;905;789;1191;1185	Q59GJ0;Q504Z1;F5H564;B9EGQ7;O43432	.;.;.;.;IF4G3_HUMAN	E	1185;1381;1185;905;675;1191;789	ENSP00000264211:D1185E;ENSP00000383274:D1185E;ENSP00000364071:D905E;ENSP00000442010:D675E;ENSP00000364073:D1191E;ENSP00000444693:D789E	ENSP00000264211:D1185E	D	-	3	2	EIF4G3	21050387	0.000000	0.05858	0.006000	0.13384	0.482000	0.33219	-2.045000	0.01410	-1.357000	0.02180	0.482000	0.46254	GAT	A|0.995;T|0.005	0.005	strong		0.498	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760		T	21177800	A	T	21177800	3	4	22	1	0	0	0	0	1	0	0	0	5040	214	8	5	1242	5	EIF4G3	1	21177800	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	146844	21177800	228072821	60	2961											
NBPF3	84224	hgsc.bcm.edu	37	chr1	21795287	21795287	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctagaaatcaacaagaaatcGcgcccccagctggcagagaa	16	4	9	12	2	1	3	1	0	0	3	2	4	1	3	2	1	2	2	2	1	6	1	rs10157037	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:21795287G>A	ENST00000318249.5	+	3	590	c.240G>A	c.(238-240)tcG>tcA	p.S80S	NBPF3_ENST00000318220.6_Silent_p.S24S|NBPF3_ENST00000342104.5_Silent_p.S80S|NBPF3_ENST00000454000.2_Intron	NM_032264.3	NP_115640.1	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3	80						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)		ACAAGAAATCGCGCCCCCAGC	0.502											OREG0013205	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	.|||	267	0.0533147	0.1467	0.0951	5008	,	,		17981	0.001		0.002	False		,,,				2504	0.0041				p.K80K		Atlas-SNP	.											.	NBPF3	55	.	0			c.A240A						PASS	.	G		498,3908		32,434,1737	85	99	94		240	-2.3	0	1	dbSNP_119	94	57,8543		1,55,4244	no	coding-synonymous	NBPF3	NM_032264.2		33,489,5981	AA,AG,GG		0.6628,11.3028,4.2673		80/634	21795287	555,12451	2203	4300	6503	SO:0001819	synonymous_variant	84224	exon3			GAAATCGCGCCCC	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.240G>A	1.37:g.21795287G>A		195	0	0	751	191	95	0.497382	NM_001256416	A8K965|B4DSP2|I3L0I8|Q3BBW1|Q5VTG2|Q5VTG3|Q5VTG4|Q8IX78|Q8ND86|Q8TC96	Silent	SNP	ENST00000318249.5	37	CCDS216.1																																																																																			G|0.953;A|0.047	0.047	strong		0.502	NBPF3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_032264		A	21795287	G	A	21795287	2	1	22	1	0	0	0	0	0	0	0	1	10206	1074	38	1		1	NBPF3	1	21795287	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	617487	21795287	227455334	61	2962											
NBPF3	84224	hgsc.bcm.edu	37	chr1	21801436	21801444	+	Splice_Site	DEL	GTCTCCCAG	GTCTCCCAG	-																															gaggaagaaaaagggccagtGtctcccaggtaatgccatgg																								rs139002241|rs570380722|rs372317136	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GTCTCCCAG	GTCTCCCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:21801436_21801444delGTCTCCCAG	ENST00000318249.5	+	8	1334_1342	c.984_992delGTCTCCCAG	c.(982-993)gtgtctcccagg>gtg	p.SPR329del	NBPF3_ENST00000318220.6_Splice_Site_p.SPR273del|NBPF3_ENST00000342104.5_Splice_Site_p.SPR329del|NBPF3_ENST00000454000.2_Splice_Site_p.SPR259del	NM_032264.3	NP_115640.1	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3	329	NBPF 2. {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)		AAGGGCCAGTGTCTCCCAGGTAATGCCAT	0.388														277	0.0553115	0.1551	0.0937	5008	,	,		21818	0.001		0.002	False		,,,				2504	0.0041				p.328_331del		Pindel,Atlas-Indel	.											.	NBPF3	55	.	0			c.983_991del						PASS	.			506,3760		32,442,1659						-1.6	0		dbSNP_134	214	59,8193		1,57,4068	no	coding-near-splice	NBPF3	NM_032264.2		33,499,5727	A1A1,A1R,RR		0.715,11.8612,4.5135				565,11953				SO:0001630	splice_region_variant	84224	exon8			.	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.992+1GTCTCCCAG>-	1.37:g.21801436_21801444delGTCTCCCAG		85	0	.		88	17	0.193	NM_032264	A8K965|B4DSP2|I3L0I8|Q3BBW1|Q5VTG2|Q5VTG3|Q5VTG4|Q8IX78|Q8ND86|Q8TC96	In_Frame_Del	DEL	ENST00000318249.5	37	CCDS216.1																																																																																			GTCTCCCAG|0.948;-|0.052	0.052	strong		0.388	NBPF3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_032264	In_Frame_Del	-	21801444	GTCTCCCAG	-	21801436	8	5	22	1	0	1	0	1	0	0	1	0	10206	1364	48	0	1010	0	NBPF3	1	21801436	Splice_Site	DEL	GTCTCCCAG	TCGA-G8-6324-01A-11D-2210-10	6149	21801436	227449185	62	2963											
RAP1GAP	5909	hgsc.bcm.edu	37	chr1	21932598	21932598	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aggtcggggttgttgggcgcGaagctcccgctgtggctggt	3	10	19	9	4	0	0	0	0	0	0	2	1	1	0	1	6	1	5	1	6	1	2	rs150973141	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:21932598G>A	ENST00000374765.4	-	18	1589	c.1389C>T	c.(1387-1389)ttC>ttT	p.F463F	RAP1GAP_ENST00000290101.4_Silent_p.F527F|RAP1GAP_ENST00000374761.2_Silent_p.F494F|RAP1GAP_ENST00000374763.2_Silent_p.F463F|RAP1GAP_ENST00000542643.2_Silent_p.F463F	NM_002885.2	NP_002876.2	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein	463					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)		TGTTGGGCGCGAAGCTCCCGC	0.682																																					p.F527F		Atlas-SNP	.											.	RAP1GAP	119	.	0			c.C1581T						PASS	.	G	,,	7,4383		0,7,2188	55	33	40		1389,1581,1389	-2.1	0.1	1	dbSNP_134	40	0,8592		0,0,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	RAP1GAP	NM_001145657.1,NM_001145658.1,NM_002885.2	,,	0,7,6484	AA,AG,GG		0.0,0.1595,0.0539	,,	463/682,527/728,463/664	21932598	7,12975	2195	4296	6491	SO:0001819	synonymous_variant	5909	exon18			GGGCGCGAAGCTC	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.1389C>T	1.37:g.21932598G>A		106	0	0		114	50	0.438596	NM_001145658	J3QSS6|O75062|Q5T3S9|Q5T3T4|Q7Z5S8|Q9UQ51	Silent	SNP	ENST00000374765.4	37	CCDS218.1																																																																																			G|0.999;A|0.001	0.001	strong		0.682	RAP1GAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019759.2	NM_002885		A	21932598	G	A	21932598	2	1	22	1	0	0	0	0	0	0	0	1	13052	1049	37	1		1	RAP1GAP	1	21932598	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	131162	21932598	227318023	63	2964											
CELA3A	10136	hgsc.bcm.edu	37	chr1	22328207	22328207	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gttccctcctccttgtggccGttggtaagaccccaacctgt	5	12	9	15	1	0	1	0	0	0	1	3	1	3	1	7	2	1	3	7	2	2	4	rs11541414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:22328207G>A	ENST00000290122.3	+	1	59	c.40G>A	c.(40-42)Gtt>Att	p.V14I	CELA3A_ENST00000374663.1_Missense_Mutation_p.V14I|RN7SL768P_ENST00000584415.1_RNA	NM_005747.4	NP_005738.4	P09093	CEL3A_HUMAN	chymotrypsin-like elastase family, member 3A	14					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						CCTTGTGGCCGTTGGTAAGAC	0.537													G|||	284	0.0567093	0.1755	0.0187	5008	,	,		18400	0.0258		0.0109	False		,,,				2504	0.002				p.V14I		Atlas-SNP	.											.	CELA3A	35	.	0			c.G40A						PASS	.	G	ILE/VAL	543,3853	244.7+/-253.9	48,447,1703	198	197	197		40	1.4	1	1	dbSNP_120	197	97,8503	54.8+/-115.7	2,93,4205	no	missense	CELA3A	NM_005747.4	29	50,540,5908	AA,AG,GG		1.1279,12.3521,4.9246		14/271	22328207	640,12356	2198	4300	6498	SO:0001583	missense	10136	exon1			GTGGCCGTTGGTA	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.40G>A	1.37:g.22328207G>A	ENSP00000290122:p.Val14Ile	270	0	0		264	135	0.511364	NM_005747	B1AQ53|Q9BRW4	Missense_Mutation	SNP	ENST00000290122.3	37	CCDS220.1	121	0.0554029304029304	91	0.18495934959349594	5	0.013812154696132596	21	0.03671328671328671	4	0.005277044854881266	G	4.477	0.088340	0.08583	0.123521	0.011279	ENSG00000142789	ENST00000290122;ENST00000374663	D;D	0.92911	-2.37;-3.13	3.38	1.44	0.22558	.	.	.	.	.	T	0.00552	0.0018	N	0.13098	0.295	0.58432	P	6.999999999979245E-6	B	0.16802	0.019	B	0.04013	0.001	T	0.21211	-1.0252	8	0.22706	T	0.39	-4.0293	4.8356	0.13464	0.0:0.6486:0.224:0.1274	rs11541414;rs12129372	14	P09093	CEL3A_HUMAN	I	14	ENSP00000290122:V14I;ENSP00000363795:V14I	ENSP00000290122:V14I	V	+	1	0	CELA3A	22200794	0.882000	0.30256	0.999000	0.59377	0.226000	0.24999	-0.001000	0.12947	0.265000	0.21872	-1.210000	0.01631	GTT	G|0.950;A|0.050	0.050	strong		0.537	CELA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007791.1	NM_005747		A	22328207	G	A	22328207	3	1	22	1	0	0	0	0	1	0	0	0	3215	1145	40	1	42	1	CELA3A	1	22328207	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	395609	22328207	226922414	64	2965											
WNT4	54361	hgsc.bcm.edu	37	chr1	22446768	22446768	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgtcctgctcacagaagtcGgggctaggctccaagtacac	10	8	11	12	1	1	1	1	0	0	1	4	1	3	1	2	3	2	4	2	3	4	2	rs34228276	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:22446768G>A	ENST00000290167.6	-	5	874	c.831C>T	c.(829-831)ccC>ccT	p.P277P	WNT4_ENST00000542383.1_Silent_p.P222P	NM_030761.4	NP_110388.2	P56705	WNT4_HUMAN	wingless-type MMTV integration site family, member 4	277			P -> L (in dbSNP:rs34228276).		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)		CACAGAAGTCGGGGCTAGGCT	0.647													G|||	117	0.0233626	0.0582	0.0173	5008	,	,		19089	0.003		0.0229	False		,,,				2504	0.002				p.P277P		Atlas-SNP	.											.	WNT4	33	.	0			c.C831T						PASS	.	G		288,4118	158.9+/-191.5	8,272,1923	121	102	108		831	-6.9	0.9	1	dbSNP_126	108	180,8420	82.0+/-144.6	0,180,4120	no	coding-synonymous	WNT4	NM_030761.4		8,452,6043	AA,AG,GG		2.093,6.5365,3.5983		277/352	22446768	468,12538	2203	4300	6503	SO:0001819	synonymous_variant	54361	exon5			GAAGTCGGGGCTA	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.831C>T	1.37:g.22446768G>A		179	0	0		204	103	0.504902	NM_030761	B4DJF9|Q5TZQ0|Q96T81|Q9BXF5|Q9H1J8|Q9UJM2	Silent	SNP	ENST00000290167.6	37	CCDS223.1																																																																																			G|0.968;A|0.032	0.032	strong		0.647	WNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008088.2			A	22446768	G	A	22446768	2	1	22	1	0	0	0	0	0	0	0	1	17405	1103	39	1		1	WNT4	1	22446768	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	118561	22446768	226803853	65	2966											
ZBTB40	9923	hgsc.bcm.edu	37	chr1	22816687	22816687	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaaatgatgtacacgggcaaActacctgtgggcaagcacaa	15	6	11	9	1	0	1	0	1	0	0	0	2	0	1	1	2	4	4	1	2	6	2	rs115103344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:22816687A>G	ENST00000375647.4	+	2	453	c.246A>G	c.(244-246)aaA>aaG	p.K82K	ZBTB40_ENST00000374651.4_Silent_p.K82K|ZBTB40_ENST00000404138.1_Silent_p.K82K	NM_014870.3	NP_055685.3	Q9NUA8	ZBT40_HUMAN	zinc finger and BTB domain containing 40	82	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				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)		ACACGGGCAAACTACCTGTGG	0.473													A|||	31	0.0061901	0.0204	0.0043	5008	,	,		21552	0.0		0.001	False		,,,				2504	0.0				p.K82K		Atlas-SNP	.											.	ZBTB40	87	.	0			c.A246G						PASS	.	A	,	74,4332	65.3+/-102.7	0,74,2129	90	85	87		246,246	-3	0.6	1	dbSNP_132	87	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ZBTB40	NM_001083621.1,NM_014870.3	,	0,75,6428	GG,GA,AA		0.0116,1.6795,0.5767	,	82/1240,82/1240	22816687	75,12931	2203	4300	6503	SO:0001819	synonymous_variant	9923	exon3			GGGCAAACTACCT	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.246A>G	1.37:g.22816687A>G		107	0	0		122	62	0.508197	NM_001083621	O75066|Q5TFU5|Q8N1R1	Silent	SNP	ENST00000375647.4	37	CCDS224.1																																																																																			A|0.993;G|0.007	0.007	strong		0.473	ZBTB40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008094.1	NM_014870		G	22816687	A	G	22816687	2	3	22	1	0	0	0	0	0	0	0	1	17557	40	2	3		3	ZBTB40	1	22816687	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	369919	22816687	226433934	66	2967											
EPHB2	2048	hgsc.bcm.edu	37	chr1	23222008	23222008	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gagaagttgccactcatcatCggctcctcggccgctggcct	6	9	11	15	3	2	1	2	0	0	1	5	2	3	1	4	3	1	3	4	3	1	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:23222008C>T	ENST00000400191.3	+	8	1653	c.1635C>T	c.(1633-1635)atC>atT	p.I545I	EPHB2_ENST00000374630.3_Silent_p.I545I|EPHB2_ENST00000465676.1_3'UTR|EPHB2_ENST00000374627.1_Silent_p.I540I|EPHB2_ENST00000374632.3_Silent_p.I545I	NM_004442.6|NM_017449.3	NP_004433.2|NP_059145.2	P29323	EPHB2_HUMAN	EPH receptor B2	545					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)		CACTCATCATCGGCTCCTCGG	0.592																																					p.I545I		Atlas-SNP	.											.	EPHB2	257	.	0			c.C1635T						PASS	.						139	120	126					1																	23222008		2203	4300	6503	SO:0001819	synonymous_variant	2048	exon8			CATCATCGGCTCC	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.1635C>T	1.37:g.23222008C>T		103	0	0		115	59	0.513043	NM_004442	O43477|Q5T0U6|Q5T0U7|Q5T0U8	Silent	SNP	ENST00000400191.3	37																																																																																				.	.	none		0.592	EPHB2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000008060.2	NM_017449		T	23222008	C	T	23222008	2	4	22	1	0	0	0	0	0	0	0	1	5177	874	31	1		1	EPHB2	1	23222008	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	405321	23222008	226028613	67	2968											
KDM1A	23028	hgsc.bcm.edu	37	chr1	23395037	23395037	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acttcggattttcaggttccTaaagagaaagatgaaatggt	14	12	10	5	1	1	3	1	1	0	2	3	5	2	4	1	3	0	1	1	3	4	5	rs145865107	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:23395037T>C	ENST00000356634.3	+	9	1262	c.1113T>C	c.(1111-1113)ccT>ccC	p.P371P	KDM1A_ENST00000542151.1_Silent_p.P395P|RP1-184J9.2_ENST00000427154.1_RNA|KDM1A_ENST00000400181.4_Silent_p.P395P	NM_015013.3	NP_055828.2	O60341	KDM1A_HUMAN	lysine (K)-specific demethylase 1A	371	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						TTCAGGTTCCTAAAGAGAAAG	0.348													T|||	22	0.00439297	0.0151	0.0029	5008	,	,		18338	0.0		0.0	False		,,,				2504	0.0				p.P395P		Atlas-SNP	.											.	KDM1A	49	.	0			c.T1185C						PASS	.	T	,	41,4365	43.8+/-77.6	0,41,2162	72	68	69		1185,1113	0.5	1	1	dbSNP_134	69	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	KDM1A	NM_001009999.2,NM_015013.3	,	0,42,6461	CC,CT,TT		0.0116,0.9305,0.3229	,	395/877,371/853	23395037	42,12964	2203	4300	6503	SO:0001819	synonymous_variant	23028	exon11			GGTTCCTAAAGAG	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.1113T>C	1.37:g.23395037T>C		98	0	0		130	71	0.546154	NM_001009999	A8MWP9|Q5TH94|Q5TH95|Q86VT7|Q8IXK4|Q8NDP6|Q8TAZ3|Q96AW4	Silent	SNP	ENST00000356634.3	37	CCDS30627.1																																																																																			T|0.998;C|0.002	0.002	strong		0.348	KDM1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008880.3	NM_015013		C	23395037	T	C	23395037	2	2	22	1	0	0	0	0	0	0	0	1	8131	1509	53	3		3	KDM1A	1	23395037	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	173029	23395037	225855584	68	2969											
KDM1A	23028	hgsc.bcm.edu	37	chr1	23409674	23409674	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctttttcccctaaaatagccGattccacgactcttctttgc	8	15	4	14	2	2	0	0	0	2	0	4	2	4	0	4	0	2	0	4	0	3	7	rs137940710	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:23409674G>A	ENST00000356634.3	+	19	2525	c.2376G>A	c.(2374-2376)ccG>ccA	p.P792P	KDM1A_ENST00000542151.1_Silent_p.P816P|RP1-184J9.2_ENST00000427154.1_RNA|KDM1A_ENST00000400181.4_Silent_p.P816P	NM_015013.3	NP_055828.2	O60341	KDM1A_HUMAN	lysine (K)-specific demethylase 1A	792	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						TAAAATAGCCGATTCCACGAC	0.438													G|||	21	0.00419329	0.0144	0.0029	5008	,	,		19038	0.0		0.0	False		,,,				2504	0.0				p.P816P		Atlas-SNP	.											.	KDM1A	49	.	0			c.G2448A						PASS	.	G	,	24,4382	30.8+/-60.4	0,24,2179	75	71	72		2448,2376	-1.3	1	1	dbSNP_134	72	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	KDM1A	NM_001009999.2,NM_015013.3	,	0,24,6479	AA,AG,GG		0.0,0.5447,0.1845	,	816/877,792/853	23409674	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	23028	exon21			ATAGCCGATTCCA	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.2376G>A	1.37:g.23409674G>A		318	1	0.00314465		279	140	0.501792	NM_001009999	A8MWP9|Q5TH94|Q5TH95|Q86VT7|Q8IXK4|Q8NDP6|Q8TAZ3|Q96AW4	Silent	SNP	ENST00000356634.3	37	CCDS30627.1																																																																																			G|0.999;A|0.001	0.001	strong		0.438	KDM1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008880.3	NM_015013		A	23409674	G	A	23409674	2	1	22	1	0	0	0	0	0	0	0	1	8131	1045	37	1		1	KDM1A	1	23409674	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	14637	23409674	225840947	69	2970											
KDM1A	23028	hgsc.bcm.edu	37	chr1	23409803	23409803	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tttttgggggccatgtatacGctgcctcgccaggccacacc	6	10	11	14	2	0	0	0	0	0	0	1	0	0	0	5	3	2	2	5	3	2	4	rs150794224	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:23409803G>A	ENST00000356634.3	+	19	2654	c.2505G>A	c.(2503-2505)acG>acA	p.T835T	KDM1A_ENST00000542151.1_Silent_p.T859T|RP1-184J9.2_ENST00000427154.1_RNA|KDM1A_ENST00000400181.4_Silent_p.T859T	NM_015013.3	NP_055828.2	O60341	KDM1A_HUMAN	lysine (K)-specific demethylase 1A	835	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						CCATGTATACGCTGCCTCGCC	0.562													G|||	23	0.00459265	0.0159	0.0029	5008	,	,		18489	0.0		0.0	False		,,,				2504	0.0				p.T859T		Atlas-SNP	.											.	KDM1A	49	.	0			c.G2577A						PASS	.	G	,	43,4363	46.7+/-81.2	0,43,2160	84	70	75		2577,2505	-6.8	0	1	dbSNP_134	75	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	KDM1A	NM_001009999.2,NM_015013.3	,	0,44,6459	AA,AG,GG		0.0116,0.9759,0.3383	,	859/877,835/853	23409803	44,12962	2203	4300	6503	SO:0001819	synonymous_variant	23028	exon21			GTATACGCTGCCT	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.2505G>A	1.37:g.23409803G>A		89	0	0		69	43	0.623188	NM_001009999	A8MWP9|Q5TH94|Q5TH95|Q86VT7|Q8IXK4|Q8NDP6|Q8TAZ3|Q96AW4	Silent	SNP	ENST00000356634.3	37	CCDS30627.1																																																																																			G|0.997;A|0.003	0.003	strong		0.562	KDM1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008880.3	NM_015013		A	23409803	G	A	23409803	2	1	22	1	0	0	0	0	0	0	0	1	8131	1074	38	1		1	KDM1A	1	23409803	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	129	23409803	225840818	70	2971											
LUZP1	7798	hgsc.bcm.edu	37	chr1	23415518	23415518	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgcagttgcctgtagacaCtgagtgtacagtcttcccct	7	13	10	11	0	1	2	0	1	1	1	2	2	2	2	3	0	3	4	3	0	2	4	rs12066671	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:23415518C>T	ENST00000302291.4	-	5	3902	c.3101G>A	c.(3100-3102)aGt>aAt	p.S1034N	LUZP1_ENST00000418342.1_Missense_Mutation_p.S1034N|LUZP1_ENST00000374623.3_Missense_Mutation_p.S1034N|RP1-184J9.2_ENST00000427154.1_RNA			Q86V48	LUZP1_HUMAN	leucine zipper protein 1	1034			S -> N (in dbSNP:rs12066671).		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)		CCTGTAGACACTGAGTGTACA	0.552													C|||	381	0.0760783	0.2693	0.0331	5008	,	,		19540	0.0		0.002	False		,,,				2504	0.0				p.S1034N		Atlas-SNP	.											.	LUZP1	83	.	0			c.G3101A						PASS	.	C	ASN/SER,ASN/SER	921,3485	353.1+/-312.0	102,717,1384	117	109	112		3101,3101	2.3	0	1	dbSNP_120	112	8,8592	6.4+/-24.3	0,8,4292	yes	missense,missense	LUZP1	NM_001142546.1,NM_033631.3	46,46	102,725,5676	TT,TC,CC		0.093,20.9033,7.1429	benign,benign	1034/1077,1034/1077	23415518	929,12077	2203	4300	6503	SO:0001583	missense	7798	exon5			TAGACACTGAGTG	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.3101G>A	1.37:g.23415518C>T	ENSP00000303758:p.Ser1034Asn	273	0	0		328	166	0.506098	NM_033631	Q5TH93|Q8N4X3|Q8TEH1	Missense_Mutation	SNP	ENST00000302291.4	37	CCDS30628.1	125	0.05723443223443223	115	0.23373983739837398	10	0.027624309392265192	0	0.0	0	0.0	C	7.770	0.707239	0.15239	0.209033	9.3E-4	ENSG00000169641	ENST00000418342;ENST00000374623;ENST00000302291	T;T;T	0.13420	2.59;2.59;2.59	5.53	2.34	0.29019	.	0.527164	0.17464	N	0.173327	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.30281	0.275	B	0.27076	0.076	T	0.44697	-0.9311	9	0.39692	T	0.17	.	9.0334	0.36273	0.1575:0.5558:0.2867:0.0	rs12066671;rs52805088;rs12066671	1034	Q86V48	LUZP1_HUMAN	N	1034	ENSP00000393460:S1034N;ENSP00000363752:S1034N;ENSP00000303758:S1034N	ENSP00000303758:S1034N	S	-	2	0	LUZP1	23288105	0.000000	0.05858	0.008000	0.14137	0.279000	0.26890	0.390000	0.20768	0.750000	0.32877	0.655000	0.94253	AGT	C|0.925;T|0.075	0.075	strong		0.552	LUZP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008900.3	NM_033631		T	23415518	C	T	23415518	3	4	22	1	0	0	0	0	1	0	0	0	9095	565	20	2	133	2	LUZP1	1	23415518	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	5715	23415518	225835103	71	2972											
LUZP1	7798	hgsc.bcm.edu	37	chr1	23418576	23418576	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtatctgggagctccatggTattggtggaggctctgacag	7	11	16	7	0	2	1	0	1	2	0	3	3	3	3	1	6	1	4	1	6	2	3	rs144862656	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:23418576T>C	ENST00000302291.4	-	4	2980	c.2179A>G	c.(2179-2181)Acc>Gcc	p.T727A	LUZP1_ENST00000314174.5_Missense_Mutation_p.T727A|LUZP1_ENST00000418342.1_Missense_Mutation_p.T727A|LUZP1_ENST00000374623.3_Missense_Mutation_p.T727A			Q86V48	LUZP1_HUMAN	leucine zipper protein 1	727					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)		AGCTCCATGGTATTGGTGGAG	0.493													C|||	23	0.00459265	0.0159	0.0029	5008	,	,		20483	0.0		0.0	False		,,,				2504	0.0				p.T727A		Atlas-SNP	.											.	LUZP1	83	.	0			c.A2179G						PASS	.	C	ALA/THR,ALA/THR	41,4365	799.2+/-415.5	0,41,2162	182	199	193		2179,2179	3.8	0.4	1	dbSNP_134	193	1,8599	812.4+/-407.1	0,1,4299	yes	missense,missense	LUZP1	NM_001142546.1,NM_033631.3	58,58	0,42,6461	CC,CT,TT		0.0116,0.9305,0.3229	benign,benign	727/1077,727/1077	23418576	42,12964	2203	4300	6503	SO:0001583	missense	7798	exon4			CCATGGTATTGGT	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.2179A>G	1.37:g.23418576T>C	ENSP00000303758:p.Thr727Ala	108	0	0		126	59	0.468254	NM_033631	Q5TH93|Q8N4X3|Q8TEH1	Missense_Mutation	SNP	ENST00000302291.4	37	CCDS30628.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	C	0.005	-2.197318	0.00299	0.009305	1.16E-4	ENSG00000169641	ENST00000418342;ENST00000374623;ENST00000302291;ENST00000314174	T;T;T;T	0.12039	2.94;2.94;2.94;2.72	4.74	3.81	0.43845	.	0.350958	0.20869	N	0.084207	T	0.01905	0.0060	N	0.00347	-1.61	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38628	-0.9652	10	0.23891	T	0.37	.	4.1464	0.10217	0.3497:0.476:0.0:0.1743	.	727;727	Q86V48-2;Q86V48	.;LUZP1_HUMAN	A	727	ENSP00000393460:T727A;ENSP00000363752:T727A;ENSP00000303758:T727A;ENSP00000313705:T727A	ENSP00000303758:T727A	T	-	1	0	LUZP1	23291163	0.087000	0.21565	0.421000	0.26609	0.137000	0.21094	0.043000	0.13971	0.605000	0.29947	-0.330000	0.08379	ACC	T|0.997;C|0.003	0.003	strong		0.493	LUZP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008900.3	NM_033631		C	23418576	T	C	23418576	3	2	22	1	0	0	0	0	1	0	0	0	9095	1638	57	3	1059	3	LUZP1	1	23418576	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	3058	23418576	225832045	72	2973											
LUZP1	7798	hgsc.bcm.edu	37	chr1	23419806	23419806	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaaggtcgttatttttggActtcattttcttaagctctt	7	20	7	7	1	3	1	1	1	2	0	4	2	3	2	0	2	1	2	0	2	3	8	rs12091554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:23419806A>C	ENST00000302291.4	-	4	1750	c.949T>G	c.(949-951)Tcc>Gcc	p.S317A	LUZP1_ENST00000314174.5_Missense_Mutation_p.S317A|LUZP1_ENST00000418342.1_Missense_Mutation_p.S317A|LUZP1_ENST00000374623.3_Missense_Mutation_p.S317A			Q86V48	LUZP1_HUMAN	leucine zipper protein 1	317			S -> A (in dbSNP:rs12091554).		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)		TTATTTTTGGACTTCATTTTC	0.338													C|||	242	0.0483227	0.1702	0.0245	5008	,	,		21716	0.0		0.0	False		,,,				2504	0.0				p.S317A		Atlas-SNP	.											.	LUZP1	83	.	0			c.T949G						PASS	.	C	ALA/SER,ALA/SER	637,3769	765.9+/-413.4	65,507,1631	164	156	159		949,949	5.2	1	1	dbSNP_120	159	12,8588	818.3+/-406.9	0,12,4288	yes	missense,missense	LUZP1	NM_001142546.1,NM_033631.3	99,99	65,519,5919	CC,CA,AA		0.1395,14.4576,4.99	benign,benign	317/1077,317/1077	23419806	649,12357	2203	4300	6503	SO:0001583	missense	7798	exon4			TTTTGGACTTCAT	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.949T>G	1.37:g.23419806A>C	ENSP00000303758:p.Ser317Ala	216	0	0		169	79	0.467456	NM_033631	Q5TH93|Q8N4X3|Q8TEH1	Missense_Mutation	SNP	ENST00000302291.4	37	CCDS30628.1	82	0.037545787545787544	73	0.1483739837398374	9	0.024861878453038673	0	0.0	0	0.0	C	1.368	-0.586747	0.03827	0.144576	0.001395	ENSG00000169641	ENST00000418342;ENST00000374623;ENST00000302291;ENST00000314174	T;T;T;T	0.12361	2.92;2.92;2.92;2.69	6.08	5.16	0.70880	.	0.000000	0.48286	N	0.000191	T	0.00039	0.0001	N	0.00729	-1.24	0.47065	P	6.960000000000299E-4	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.34453	-0.9828	9	0.11485	T	0.65	.	10.4106	0.44291	0.1361:0.7953:0.0:0.0686	rs12091554;rs52806883;rs12091554	317;317	Q86V48-2;Q86V48	.;LUZP1_HUMAN	A	317	ENSP00000393460:S317A;ENSP00000363752:S317A;ENSP00000303758:S317A;ENSP00000313705:S317A	ENSP00000303758:S317A	S	-	1	0	LUZP1	23292393	1.000000	0.71417	1.000000	0.80357	0.771000	0.43674	3.887000	0.56197	1.603000	0.50134	-0.121000	0.15023	TCC	A|0.952;C|0.048	0.048	strong		0.338	LUZP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008900.3	NM_033631		C	23419806	A	C	23419806	3	2	22	1	0	0	0	0	1	0	0	0	9095	275	10	5	2289	5	LUZP1	1	23419806	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1230	23419806	225830815	73	2974											
LUZP1	7798	hgsc.bcm.edu	37	chr1	23419914	23419914	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttgttgtcttcctgattgcGgttcttttcattttctgatt	3	24	7	7	1	4	2	1	2	3	0	5	2	5	2	1	1	1	2	1	1	0	10	rs142425004	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:23419914G>A	ENST00000302291.4	-	4	1642	c.841C>T	c.(841-843)Cgc>Tgc	p.R281C	LUZP1_ENST00000314174.5_Missense_Mutation_p.R281C|LUZP1_ENST00000418342.1_Missense_Mutation_p.R281C|LUZP1_ENST00000374623.3_Missense_Mutation_p.R281C			Q86V48	LUZP1_HUMAN	leucine zipper protein 1	281					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)		TCCTGATTGCGGTTCTTTTCA	0.388													G|||	20	0.00399361	0.0106	0.0014	5008	,	,		20491	0.005		0.0	False		,,,				2504	0.0				p.R281C		Atlas-SNP	.											LUZP1,NS,carcinoma,+1,1	LUZP1	83	1	0			c.C841T						PASS	.	G	CYS/ARG,CYS/ARG	28,4378	35.2+/-66.4	0,28,2175	217	203	208		841,841	4.1	1	1	dbSNP_134	208	0,8600		0,0,4300	yes	missense,missense	LUZP1	NM_001142546.1,NM_033631.3	180,180	0,28,6475	AA,AG,GG		0.0,0.6355,0.2153	probably-damaging,probably-damaging	281/1077,281/1077	23419914	28,12978	2203	4300	6503	SO:0001583	missense	7798	exon4			GATTGCGGTTCTT	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.841C>T	1.37:g.23419914G>A	ENSP00000303758:p.Arg281Cys	341	0	0		313	147	0.469649	NM_033631	Q5TH93|Q8N4X3|Q8TEH1	Missense_Mutation	SNP	ENST00000302291.4	37	CCDS30628.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	16.53	3.149333	0.57151	0.006355	0.0	ENSG00000169641	ENST00000418342;ENST00000374623;ENST00000302291;ENST00000314174	T;T;T;T	0.15372	2.64;2.64;2.64;2.43	6.08	4.13	0.48395	.	0.000000	0.39909	N	0.001226	T	0.08980	0.0222	L	0.42245	1.32	0.42205	D	0.991782	P;P	0.41929	0.765;0.765	B;B	0.28139	0.086;0.086	T	0.08046	-1.0741	10	0.44086	T	0.13	.	13.9909	0.64367	0.0:0.0:0.5289:0.4711	.	281;281	Q86V48-2;Q86V48	.;LUZP1_HUMAN	C	281	ENSP00000393460:R281C;ENSP00000363752:R281C;ENSP00000303758:R281C;ENSP00000313705:R281C	ENSP00000303758:R281C	R	-	1	0	LUZP1	23292501	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	1.802000	0.38853	1.554000	0.49487	0.655000	0.94253	CGC	G|0.999;A|0.001	0.001	strong		0.388	LUZP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008900.3	NM_033631		A	23419914	G	A	23419914	3	1	22	1	0	0	0	0	1	0	0	0	9095	1116	39	1	2397	1	LUZP1	1	23419914	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	108	23419914	225830707	74	2975											
TCEB3	6924	hgsc.bcm.edu	37	chr1	24077554	24077554	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacggtcatgagaggagagaTgagagaaagaggtgtcacag	15	5	16	5	1	2	5	2	2	0	4	2	9	2	6	0	3	0	0	0	3	1	0	rs35397069	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:24077554T>C	ENST00000418390.2	+	4	808	c.537T>C	c.(535-537)gaT>gaC	p.D179D	TCEB3_ENST00000609199.1_Silent_p.D153D	NM_003198.2	NP_003189.2	Q14241	ELOA1_HUMAN	transcription elongation factor B (SIII), polypeptide 3 (110kDa, elongin A)	179					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)		AGAGGAGAGATGAGAGAAAGA	0.498													C|||	487	0.0972444	0.351	0.0303	5008	,	,		19697	0.0		0.001	False		,,,				2504	0.001				p.D179D		Atlas-SNP	.											.	TCEB3	61	.	0			c.T537C						PASS	.	C		1242,3164	704.4+/-407.1	172,898,1133	105	97	100		537	-11.1	0.1	1	dbSNP_126	100	22,8578	818.3+/-406.9	0,22,4278	no	coding-synonymous	TCEB3	NM_003198.2		172,920,5411	CC,CT,TT		0.2558,28.1888,9.7186		179/799	24077554	1264,11742	2203	4300	6503	SO:0001819	synonymous_variant	6924	exon4			GAGAGATGAGAGA	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.537T>C	1.37:g.24077554T>C		148	0	0		159	68	0.427673	NM_003198	B2R7Q8|Q8IXH1	Silent	SNP	ENST00000418390.2	37	CCDS239.2																																																																																			T|0.913;C|0.087	0.087	strong		0.498	TCEB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000008230.2	NM_003198		C	24077554	T	C	24077554	2	2	22	1	0	0	0	0	0	0	0	1	15696	1461	51	3		3	TCEB3	1	24077554	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	657640	24077554	225173067	75	2976											
TCEB3	6924	hgsc.bcm.edu	37	chr1	24078234	24078234	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggaaagtcaaaactaattTggatagaaagtcactgggct	16	9	11	5	0	2	1	2	0	0	1	2	3	2	3	0	3	1	1	0	3	6	3	rs34394004	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:24078234T>C	ENST00000418390.2	+	4	1488	c.1217T>C	c.(1216-1218)tTg>tCg	p.L406S	TCEB3_ENST00000609199.1_Missense_Mutation_p.L380S	NM_003198.2	NP_003189.2	Q14241	ELOA1_HUMAN	transcription elongation factor B (SIII), polypeptide 3 (110kDa, elongin A)	406					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)		AAAACTAATTTGGATAGAAAG	0.448											OREG0013232	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	279	0.0557109	0.202	0.0144	5008	,	,		18505	0.0		0.001	False		,,,				2504	0.001				p.L406S		Atlas-SNP	.											.	TCEB3	61	.	0			c.T1217C						PASS	.	C	SER/LEU	741,3665	746.0+/-411.7	66,609,1528	97	109	105		1217	-2.6	0	1	dbSNP_126	105	16,8584	812.1+/-407.1	0,16,4284	yes	missense	TCEB3	NM_003198.2	145	66,625,5812	CC,CT,TT		0.186,16.818,5.8204	benign	406/799	24078234	757,12249	2203	4300	6503	SO:0001583	missense	6924	exon4			CTAATTTGGATAG	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.1217T>C	1.37:g.24078234T>C	ENSP00000395574:p.Leu406Ser	63	0	0	768	74	36	0.486486	NM_003198	B2R7Q8|Q8IXH1	Missense_Mutation	SNP	ENST00000418390.2	37	CCDS239.2	102	0.046703296703296704	94	0.1910569105691057	8	0.022099447513812154	0	0.0	0	0.0	C	0.011	-1.697264	0.00725	0.16818	0.00186	ENSG00000011007	ENST00000418390	T	0.06768	3.26	5.85	-2.64	0.06114	.	1.391920	0.04481	N	0.377838	T	0.00012	0.0000	N	0.01003	-1.06	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45116	-0.9283	9	0.11794	T	0.64	2.5335	6.9989	0.24799	0.1849:0.3127:0.0:0.5025	rs34394004	406	Q14241	ELOA1_HUMAN	S	406	ENSP00000395574:L406S	ENSP00000395574:L406S	L	+	2	0	TCEB3	23950821	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.017000	0.01445	-1.183000	0.02723	-1.073000	0.02249	TTG	T|0.935;C|0.065	0.065	strong		0.448	TCEB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000008230.2	NM_003198		C	24078234	T	C	24078234	3	2	22	1	0	0	0	0	1	0	0	0	15696	1821	63	3	1231	3	TCEB3	1	24078234	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	680	24078234	225172387	76	2977											
FUCA1	2517	hgsc.bcm.edu	37	chr1	24189740	24189740	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aaccactctaagagtgagtgGtatagtccatagcggatgtt	12	11	11	7	1	1	2	0	1	1	1	2	3	2	3	2	2	2	2	2	2	5	5	rs541724746		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:24189740G>A	ENST00000374479.3	-	3	553	c.546C>T	c.(544-546)taC>taT	p.Y182Y		NM_000147.4	NP_000138.2	P04066	FUCO_HUMAN	fucosidase, alpha-L- 1, tissue	182					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)		AGAGTGAGTGGTATAGTCCAT	0.358													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17635	0.0		0.0	False		,,,				2504	0.0				p.Y182Y		Atlas-SNP	.											.	FUCA1	24	.	0			c.C546T						PASS	.						94	88	90					1																	24189740		2203	4300	6503	SO:0001819	synonymous_variant	2517	exon3			TGAGTGGTATAGT	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.546C>T	1.37:g.24189740G>A		63	0	0		74	36	0.486486	NM_000147	B2RBG3|Q14334|Q14335|Q3LID0|Q8NAC2	Silent	SNP	ENST00000374479.3	37	CCDS244.2																																																																																			.	.	none		0.358	FUCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008259.2	NM_000147		A	24189740	G	A	24189740	2	1	22	1	0	0	0	0	0	0	0	1	6102	1256	44	2		2	FUCA1	1	24189740	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	111506	24189740	225060881	77	2978											
MYOM3	127294	hgsc.bcm.edu	37	chr1	24383873	24383873	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtcacatgctcttcagctccTtgggctcgtccccgtgcttg	3	13	10	15	2	3	0	2	0	1	0	6	0	5	0	3	1	3	4	3	1	0	3	rs59805085	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:24383873T>C	ENST00000374434.3	-	37	4457	c.4295A>G	c.(4294-4296)aAg>aGg	p.K1432R	RP11-293P20.2_ENST00000439239.2_RNA|MYOM3_ENST00000330966.7_Missense_Mutation_p.K1435R|MYOM3_ENST00000338909.5_Missense_Mutation_p.K325R	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	1432						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)		CTTCAGCTCCTTGGGCTCGTC	0.577													T|||	277	0.0553115	0.2005	0.0159	5008	,	,		21478	0.0		0.001	False		,,,				2504	0.0				p.K1432R		Atlas-SNP	.											.	MYOM3	131	.	0			c.A4295G						PASS	.	T	ARG/LYS	524,3714		36,452,1631	75	74	74		4295	2.9	1	1	dbSNP_129	74	9,8473		0,9,4232	yes	missense	MYOM3	NM_152372.3	26	36,461,5863	CC,CT,TT		0.1061,12.3643,4.1903	benign	1432/1438	24383873	533,12187	2119	4241	6360	SO:0001583	missense	127294	exon37			AGCTCCTTGGGCT	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.4295A>G	1.37:g.24383873T>C	ENSP00000363557:p.Lys1432Arg	147	0	0		158	83	0.525316	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Missense_Mutation	SNP	ENST00000374434.3	37	CCDS41281.1	85	0.03891941391941392	77	0.1565040650406504	8	0.022099447513812154	0	0.0	0	0.0	T	1.496	-0.553376	0.03996	0.123643	0.001061	ENSG00000142661	ENST00000338909;ENST00000374434;ENST00000330966;ENST00000374442	T;T;T	0.56103	0.48;0.56;0.56	5.24	2.88	0.33553	.	0.543380	0.19217	N	0.119765	T	0.00109	0.0003	N	0.22421	0.69	0.41520	P	0.01160899999999998	B;B	0.20459	0.01;0.045	B;B	0.17722	0.004;0.019	T	0.09707	-1.0662	9	0.06494	T	0.89	.	3.3931	0.07297	0.1436:0.0766:0.1321:0.6476	rs59805085	1432;325	Q5VTT5;Q5VTT5-3	MYOM3_HUMAN;.	R	325;1432;1435;326	ENSP00000342689:K325R;ENSP00000363557:K1432R;ENSP00000332670:K1435R	ENSP00000332670:K1435R	K	-	2	0	MYOM3	24256460	0.000000	0.05858	0.997000	0.53966	0.370000	0.29829	0.160000	0.16462	0.795000	0.33922	0.533000	0.62120	AAG	T|0.975;C|0.025	0.025	strong		0.577	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372		C	24383873	T	C	24383873	3	2	22	1	0	0	0	0	1	0	0	0	10102	1609	56	3	22	3	MYOM3	1	24383873	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	194133	24383873	224866748	78	2979											
GRHL3	57822	hgsc.bcm.edu	37	chr1	24664220	24664220	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaaaggccagttctaccccGtcaccctgcggaccccagca	10	5	8	18	2	2	0	1	0	1	0	2	1	2	1	6	2	3	2	6	2	2	2	rs145470039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:24664220G>A	ENST00000350501.5	+	6	908	c.781G>A	c.(781-783)Gtc>Atc	p.V261I	GRHL3_ENST00000342072.4_Missense_Mutation_p.V168I|GRHL3_ENST00000356046.2_Missense_Mutation_p.V215I|GRHL3_ENST00000236255.4_Missense_Mutation_p.V266I|GRHL3_ENST00000361548.4_Missense_Mutation_p.V261I	NM_198174.2	NP_937817.3	Q8TE85	GRHL3_HUMAN	grainyhead-like 3 (Drosophila)	261					central nervous system development (GO:0007417)|cochlea morphogenesis (GO:0090103)|ectoderm development (GO:0007398)|epidermis development (GO:0008544)|establishment of planar polarity (GO:0001736)|eyelid development in camera-type eye (GO:0061029)|pattern specification process (GO:0007389)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.V266I(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00171)|all_lung(284;0.00226)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;8.72e-25)|Colorectal(126;4.38e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00377)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.143)		GTTCTACCCCGTCACCCTGCG	0.587													G|||	9	0.00179712	0.0061	0.0014	5008	,	,		20270	0.0		0.0	False		,,,				2504	0.0				p.V266I		Atlas-SNP	.											GRHL3_ENST00000350501,NS,carcinoma,0,4	GRHL3	69	4	1	Substitution - Missense(1)	ovary(1)	c.G796A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	16,4390	23.3+/-48.9	0,16,2187	98	84	89		781,781,796,643	4.1	0.8	1	dbSNP_134	89	0,8600		0,0,4300	yes	missense,missense,missense,missense	GRHL3	NM_198174.2,NM_198173.2,NM_021180.3,NM_001195010.1	29,29,29,29	0,16,6487	AA,AG,GG		0.0,0.3631,0.123	benign,benign,benign,benign	261/627,261/603,266/608,215/557	24664220	16,12990	2203	4300	6503	SO:0001583	missense	57822	exon6			TACCCCGTCACCC	AY231161	CCDS251.1, CCDS252.1, CCDS44088.1, CCDS252.2, CCDS53284.1	1p36	2008-02-05	2005-07-11	2005-07-11	ENSG00000158055	ENSG00000158055			25839	protein-coding gene	gene with protein product		608317	"transcription factor CP2-like 4"	TFCP2L4		12549979	Standard	NM_021180		Approved	SOM	uc021oiw.1	Q8TE85	OTTHUMG00000003040	ENST00000350501.5:c.781G>A	1.37:g.24664220G>A	ENSP00000288955:p.Val261Ile	93	0	0		79	37	0.468354	NM_021180	A2A297|B2RCL1|G3XAF0|Q5TH78|Q86Y06|Q8N407	Missense_Mutation	SNP	ENST00000350501.5	37	CCDS252.2	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	4.028	0.002793	0.07866	0.003631	0.0	ENSG00000158055	ENST00000361548;ENST00000342072;ENST00000350501;ENST00000356046;ENST00000236255	T;T;T;T;T	0.15017	2.46;2.46;2.46;2.46;2.46	5.97	4.12	0.48240	.	0.237878	0.42964	N	0.000623	T	0.03390	0.0098	N	0.02103	-0.685	0.32683	N	0.515251	B;B;B	0.18310	0.013;0.003;0.027	B;B;B	0.14578	0.008;0.006;0.011	T	0.30937	-0.9961	10	0.02654	T	1	-28.162	9.5371	0.39229	0.2343:0.0:0.7657:0.0	.	215;266;261	A2A297;Q8TE85-2;G3XAF0	.;.;.	I	261;168;261;215;266	ENSP00000354943:V261I;ENSP00000340543:V168I;ENSP00000288955:V261I;ENSP00000348333:V215I;ENSP00000236255:V266I	ENSP00000236255:V266I	V	+	1	0	GRHL3	24536807	0.796000	0.28864	0.822000	0.32727	0.992000	0.81027	1.375000	0.34295	0.868000	0.35678	0.655000	0.94253	GTC	G|0.997;A|0.003	0.003	strong		0.587	GRHL3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000009047.2	NM_021180		A	24664220	G	A	24664220	3	1	22	1	0	0	0	0	1	0	0	0	6774	1145	40	1	839	1	GRHL3	1	24664220	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	280347	24664220	224586401	79	2980											
TMEM57	55219	hgsc.bcm.edu	37	chr1	25757607	25757607	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggatgaagcggcggaacgcCgactgcagtaagctccgccg	10	4	15	12	6	0	1	0	1	0	0	1	4	1	3	3	3	4	3	3	3	3	1	rs114403991	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:25757607C>T	ENST00000374343.4	+	1	197	c.18C>T	c.(16-18)gcC>gcT	p.A6A	TMEM57_ENST00000399763.3_Silent_p.A6A|TMEM57_ENST00000399766.3_Silent_p.A6A|RHCE_ENST00000349320.3_5'Flank	NM_018202.4	NP_060672.2	Q8N5G2	MACOI_HUMAN	transmembrane protein 57	6					brain development (GO:0007420)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuron projection terminus (GO:0044306)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|synapse (GO:0045202)				breast(3)|endometrium(2)|kidney(2)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	27		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.00715)|all_lung(284;0.00989)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0675)|all_neural(195;0.201)		UCEC - Uterine corpus endometrioid carcinoma (279;0.042)|OV - Ovarian serous cystadenocarcinoma(117;1.85e-26)|Colorectal(126;2.99e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|STAD - Stomach adenocarcinoma(196;0.000766)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|GBM - Glioblastoma multiforme(114;0.0191)|READ - Rectum adenocarcinoma(331;0.0649)		GGCGGAACGCCGACTGCAGTA	0.761													C|||	56	0.0111821	0.0371	0.0086	5008	,	,		5510	0.0		0.001	False		,,,				2504	0.0				p.A6A		Atlas-SNP	.											.	TMEM57	72	.	0			c.C18T						PASS	.	C		61,4291		0,61,2115	11	13	12		18	-0.5	1	1	dbSNP_132	12	1,8539		0,1,4269	no	coding-synonymous	TMEM57	NM_018202.4		0,62,6384	TT,TC,CC		0.0117,1.4017,0.4809		6/665	25757607	62,12830	2176	4270	6446	SO:0001819	synonymous_variant	55219	exon1			GAACGCCGACTGC	AK001609	CCDS30638.1, CCDS60034.1	1p36.11	2008-02-05			ENSG00000204178	ENSG00000204178			25572	protein-coding gene	gene with protein product		610301				12459264, 15255972	Standard	XM_005245931		Approved	FLJ10747	uc001bkk.3	Q8N5G2	OTTHUMG00000003473	ENST00000374343.4:c.18C>T	1.37:g.25757607C>T		36	0	0		55	34	0.618182	NM_018202	B1AK00|Q2TLX5|Q2TLX6|Q9NVG6	Silent	SNP	ENST00000374343.4	37	CCDS30638.1																																																																																			C|0.992;T|0.008	0.008	strong		0.761	TMEM57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009659.2	NM_018202		T	25757607	C	T	25757607	2	4	22	1	0	0	0	0	0	0	0	1	16199	639	23	1		1	TMEM57	1	25757607	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1093387	25757607	223493014	80	2981											
CNKSR1	10256	hgsc.bcm.edu	37	chr1	26508997	26508997	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacgtggctgggatctgccaCaacatcctggtctgctgccc	6	9	11	15	1	2	0	0	0	2	0	3	1	3	1	3	3	4	2	3	3	1	0	rs2802347	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:26508997C>T	ENST00000374253.5	+	6	585	c.546C>T	c.(544-546)caC>caT	p.H182H	CNKSR1_ENST00000480348.2_3'UTR|CNKSR1_ENST00000361530.6_Silent_p.H182H|CNKSR1_ENST00000531191.1_5'UTR	NM_006314.2	NP_006305.2	Q969H4	CNKR1_HUMAN	connector enhancer of kinase suppressor of Ras 1	182					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)		GGATCTGCCACAACATCCTGG	0.652													C|||	259	0.0517173	0.1846	0.0202	5008	,	,		17396	0.0		0.001	False		,,,				2504	0.0				p.H182H	NSCLC(180;1396 2109 28270 30756 34275)	Atlas-SNP	.											.	CNKSR1	66	.	0			c.C546T						PASS	.	C		702,3704	293.3+/-282.5	64,574,1565	65	65	65		546	2.4	1	1	dbSNP_100	65	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	CNKSR1	NM_006314.2		64,578,5861	TT,TC,CC		0.0465,15.9328,5.4283		182/714	26508997	706,12300	2203	4300	6503	SO:0001819	synonymous_variant	10256	exon6			CTGCCACAACATC	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.546C>T	1.37:g.26508997C>T		156	0	0		182	93	0.510989	NM_006314	B1AMW9|O95381	Silent	SNP	ENST00000374253.5	37		108	0.04945054945054945	98	0.1991869918699187	10	0.027624309392265192	0	0.0	0	0.0	C	13.82	2.352119	0.41700	0.159328	4.65E-4	ENSG00000142675	ENST00000422547	.	.	.	4.47	2.37	0.29283	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.999999889351	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	-2.2956	5.5452	0.17059	0.0:0.4831:0.4021:0.1148	rs2802347	.	.	.	X	170	.	ENSP00000390945:Q170X	Q	+	1	0	CNKSR1	26381584	0.230000	0.23740	0.998000	0.56505	0.271000	0.26615	0.419000	0.21247	1.068000	0.40764	0.650000	0.86243	CAA	C|0.940;T|0.060	0.060	strong		0.652	CNKSR1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000089943.2	NM_006314		T	26508997	C	T	26508997	2	4	22	1	0	0	0	0	0	0	0	1	3608	477	17	2		2	CNKSR1	1	26508997	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	751390	26508997	222741624	81	2982											
CCDC21	64793	hgsc.bcm.edu	37	chr1	26581981	26581981	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	catgaaagacaagaagaggcGaggaagtttgatattcctag	16	8	12	5	1	0	5	0	2	0	3	1	7	1	6	1	2	0	1	1	2	6	4	rs34867486	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:26581981G>A	ENST00000252992.4	+	4	659	c.528G>A	c.(526-528)gcG>gcA	p.A176A	CEP85_ENST00000451429.2_Silent_p.A125A	NM_001281517.1|NM_022778.2	NP_001268446.1|NP_073615.2	Q6P2H3	CEP85_HUMAN	centrosomal protein 85kDa	176						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						AAGAAGAGGCGAGGAAGTTTG	0.473													G|||	105	0.0209665	0.0749	0.0086	5008	,	,		21433	0.0		0.0	False		,,,				2504	0.0				p.A176A		Atlas-SNP	.											CEP85,NS,carcinoma,+2,1	CEP85	61	1	0			c.G528A						PASS	.	G		236,4170	141.1+/-176.5	3,230,1970	87	85	86		528	3.6	0.7	1	dbSNP_126	86	3,8597	3.0+/-9.4	0,3,4297	yes	coding-synonymous	CEP85	NM_022778.2		3,233,6267	AA,AG,GG		0.0349,5.3563,1.8376		176/763	26581981	239,12767	2203	4300	6503	SO:0001819	synonymous_variant	64793	exon4			AGAGGCGAGGAAG	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.528G>A	1.37:g.26581981G>A		110	0	0		114	58	0.508772	NM_022778	B4DRL1|D3DPK4|F8W7K4|Q5VY68|Q5VY70|Q9H6Q1|Q9H828|Q9UF52	Silent	SNP	ENST00000252992.4	37	CCDS277.1																																																																																			G|0.979;A|0.021	0.021	strong		0.473	CEP85-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009492.2	NM_022778		A	26581981	G	A	26581981	2	1	22	1	0	0	0	0	0	0	0	1	2798	1045	37	1		1	CCDC21	1	26581981	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	72984	26581981	222668640	82	2983											
UBXN11	91544	hgsc.bcm.edu	37	chr1	26620761	26620761	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctctgagactgtcttgctcTctgagtcctcctggtccatg	4	14	10	13	0	3	2	0	2	3	1	7	3	6	2	3	1	1	2	3	1	0	1	rs6695966	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:26620761T>C	ENST00000374222.1	-	9	958	c.494A>G	c.(493-495)gAg>gGg	p.E165G	UBXN11_ENST00000374223.1_Intron|UBXN11_ENST00000374217.2_Missense_Mutation_p.E132G|UBXN11_ENST00000535108.1_Missense_Mutation_p.E7G|UBXN11_ENST00000374221.3_Missense_Mutation_p.E165G|UBXN11_ENST00000357089.4_Missense_Mutation_p.E132G|UBXN11_ENST00000436301.2_Missense_Mutation_p.E90G|UBXN11_ENST00000314675.7_Intron			Q5T124	UBX11_HUMAN	UBX domain protein 11	165			E -> G (in dbSNP:rs6695966).			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						TGTCTTGCTCTCTGAGTCCTC	0.607													T|||	98	0.0195687	0.0696	0.0086	5008	,	,		18835	0.0		0.0	False		,,,				2504	0.0				p.E165G		Atlas-SNP	.											.	UBXN11	54	.	0			c.A494G						PASS	.	T	,GLY/GLU,GLY/GLU	200,3930		2,196,1867	99	98	98		,395,494	4.5	0.1	1	dbSNP_116	98	3,8407		0,3,4202	yes	intron,missense,missense	UBXN11	NM_001077262.1,NM_145345.2,NM_183008.2	,98,98	2,199,6069	CC,CT,TT		0.0357,4.8426,1.6188	,possibly-damaging,possibly-damaging	,132/488,165/521	26620761	203,12337	2065	4205	6270	SO:0001583	missense	91544	exon9			TTGCTCTCTGAGT	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.494A>G	1.37:g.26620761T>C	ENSP00000363339:p.Glu165Gly	97	0	0		77	36	0.467532	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Missense_Mutation	SNP	ENST00000374222.1	37	CCDS41288.1	32	0.014652014652014652	29	0.05894308943089431	3	0.008287292817679558	0	0.0	0	0.0	T	20.1	3.936518	0.73442	0.048426	3.57E-4	ENSG00000158062	ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217;ENST00000389235;ENST00000535108;ENST00000436301;ENST00000374215;ENST00000452980;ENST00000442942;ENST00000450041;ENST00000423664	T;T;T;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;0.56;0.56;0.56	4.47	4.47	0.54385	.	0.322809	0.32655	N	0.005820	T	0.11965	0.0291	M	0.61703	1.905	0.18873	N	0.999983	P;P;P;P;P	0.44139	0.734;0.799;0.827;0.827;0.799	B;B;P;P;B	0.46758	0.398;0.272;0.526;0.526;0.214	T	0.22277	-1.0221	10	0.72032	D	0.01	-25.9901	10.3196	0.43758	0.0:0.0:0.0:1.0	rs6695966;rs52794001;rs6695966	7;90;132;127;165	B7Z1T8;B7Z3N8;Q5T124-2;Q5T124-4;Q5T124	.;.;.;.;UBX11_HUMAN	G	132;165;165;132;132;7;90;127;132;132;90;127	ENSP00000349601:E132G;ENSP00000363338:E165G;ENSP00000363339:E165G;ENSP00000363334:E132G;ENSP00000446034:E7G;ENSP00000393858:E90G;ENSP00000363332:E127G;ENSP00000410357:E132G;ENSP00000404956:E132G;ENSP00000413448:E90G;ENSP00000394036:E127G	ENSP00000349601:E132G	E	-	2	0	UBXN11	26493348	0.829000	0.29322	0.059000	0.19551	0.483000	0.33249	2.735000	0.47377	2.013000	0.59113	0.459000	0.35465	GAG	T|0.974;C|0.026	0.026	strong		0.607	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345		C	26620761	T	C	26620761	3	2	22	1	0	0	0	0	1	0	0	0	16928	1551	54	3	1100	3	UBXN11	1	26620761	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	38780	26620761	222629860	83	2984											
ARID1A	8289	hgsc.bcm.edu	37	chr1	27097616	27097618	+	In_Frame_Del	DEL	AAG	AAG	-																															gtttggttatacaggtcaacAagaacaaaaaatggcgggaa																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:27097616_27097618delAAG	ENST00000324856.7	+	12	3576_3578	c.3205_3207delAAG	c.(3205-3207)aagdel	p.K1069del	ARID1A_ENST00000457599.2_In_Frame_Del_p.K1069del|ARID1A_ENST00000540690.1_5'Flank|ARID1A_ENST00000374152.2_In_Frame_Del_p.K686del	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1069	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				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)		ACAGGTCAACAAGAACAAAAAAT	0.483			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.1068_1069del		Pindel,Atlas-Indel	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.3204_3206del						PASS	.																																			SO:0001651	inframe_deletion	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.3205_3207delAAG	1.37:g.27097616_27097618delAAG	ENSP00000320485:p.Lys1069del	81	0	.		79	16	0.203	NM_139135	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	In_Frame_Del	DEL	ENST00000324856.7	37	CCDS285.1																																																																																			.	.	none		0.483	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		-	27097618	AAG	-	27097616	7	5	22	1	0	1	0	1	0	0	0	0	913	131	5	0	3251	0	ARID1A	1	27097616	In_Frame_Del	DEL	AAG	TCGA-G8-6324-01A-11D-2210-10	476855	27097616	222153005	84	2985											
SMPDL3B	27293	hgsc.bcm.edu	37	chr1	28285123	28285123	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catgcacacagtgctggaccGcatcgctggcgaccagagca	10	5	12	14	3	0	1	0	0	0	1	1	3	0	2	2	2	3	5	2	2	0	0	rs34560878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:28285123G>A	ENST00000373894.3	+	8	1333	c.1142G>A	c.(1141-1143)cGc>cAc	p.R381H	XKR8_ENST00000373884.5_5'Flank|RP11-460I13.2_ENST00000448015.1_RNA|SMPDL3B_ENST00000549094.1_Missense_Mutation_p.R333H	NM_014474.2	NP_055289.2	Q92485	ASM3B_HUMAN	sphingomyelin phosphodiesterase, acid-like 3B	381			R -> H (in dbSNP:rs34560878).		sphingomyelin catabolic process (GO:0006685)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	16		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000431)|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;5.68e-24)|Colorectal(126;1.65e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00587)|READ - Rectum adenocarcinoma(331;0.055)		GTGCTGGACCGCATCGCTGGC	0.642													G|||	73	0.0145767	0.0507	0.0086	5008	,	,		19689	0.0		0.0	False		,,,				2504	0.0				p.R381H		Atlas-SNP	.											.	SMPDL3B	54	.	0			c.G1142A						PASS	.	G	HIS/ARG	188,4218	120.0+/-157.7	4,180,2019	69	64	65		1142	-1.2	0	1	dbSNP_126	65	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SMPDL3B	NM_014474.2	29	4,181,6318	AA,AG,GG		0.0116,4.2669,1.4532	benign	381/456	28285123	189,12817	2203	4300	6503	SO:0001583	missense	27293	exon8			TGGACCGCATCGC	Y08134	CCDS30655.1, CCDS30656.1	1p35.3	2008-02-05			ENSG00000130768	ENSG00000130768			21416	protein-coding gene	gene with protein product							Standard	NM_014474		Approved	ASML3B	uc001bpg.3	Q92485	OTTHUMG00000003910	ENST00000373894.3:c.1142G>A	1.37:g.28285123G>A	ENSP00000363001:p.Arg381His	146	0	0		173	86	0.49711	NM_014474	B7ZB35|Q5T0Z0|Q96CB7	Missense_Mutation	SNP	ENST00000373894.3	37	CCDS30655.1	19	0.0086996336996337	15	0.03048780487804878	4	0.011049723756906077	0	0.0	0	0.0	G	11.15	1.553282	0.27739	0.042669	1.16E-4	ENSG00000130768	ENST00000373894;ENST00000549094	D;D	0.90732	-2.72;-2.72	5.09	-1.23	0.09465	.	0.392324	0.27043	N	0.021217	T	0.65491	0.2696	M	0.73962	2.25	0.20074	N	0.999932	B;B	0.20887	0.049;0.029	B;B	0.17098	0.017;0.007	T	0.71331	-0.4625	10	0.52906	T	0.07	-4.737	5.5703	0.17192	0.488:0.0:0.3824:0.1296	rs34560878	333;381	F8VWW8;Q92485	.;ASM3B_HUMAN	H	381;333	ENSP00000363001:R381H;ENSP00000449450:R333H	ENSP00000363001:R381H	R	+	2	0	SMPDL3B	28157710	0.916000	0.31088	0.009000	0.14445	0.001000	0.01503	0.985000	0.29578	-0.071000	0.12886	-1.288000	0.01363	CGC	G|0.986;A|0.014	0.014	strong		0.642	SMPDL3B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011170.1	NM_014474		A	28285123	G	A	28285123	3	1	22	1	0	0	0	0	1	0	0	0	14824	1087	38	1	1289	1	SMPDL3B	1	28285123	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1187507	28285123	220965498	85	2986											
PTAFR	5724	hgsc.bcm.edu	37	chr1	28476520	28476520	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggactaatttttgagggaaTtgccagggatctggttgaat	10	13	14	4	0	1	2	0	2	1	0	1	5	1	5	1	4	1	1	1	4	3	5	rs5939	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:28476520T>C	ENST00000373857.3	-	2	1647	c.1013A>G	c.(1012-1014)aAt>aGt	p.N338S	PTAFR_ENST00000539896.1_Missense_Mutation_p.N338S|PTAFR_ENST00000305392.3_Missense_Mutation_p.N338S	NM_000952.4|NM_001164722.2|NM_001164723.2	NP_000943.1|NP_001158194.1|NP_001158195.1	P25105	PTAFR_HUMAN	platelet-activating factor receptor	338			N -> S (in dbSNP:rs5939). {ECO:0000269|PubMed:10391209}.		chemotaxis (GO:0006935)|cytokine production (GO:0001816)|cytokine-mediated signaling pathway (GO:0019221)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|inositol trisphosphate biosynthetic process (GO:0032959)|interferon-gamma-mediated signaling pathway (GO:0060333)|phosphatidylinositol-mediated signaling (GO:0048015)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|phospholipid binding (GO:0005543)|platelet activating factor receptor activity (GO:0004992)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|stomach(1)	15		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00715)|all_lung(284;0.00732)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.215)|OV - Ovarian serous cystadenocarcinoma(117;6e-22)|Colorectal(126;3.04e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00279)|BRCA - Breast invasive adenocarcinoma(304;0.00595)|STAD - Stomach adenocarcinoma(196;0.00678)|READ - Rectum adenocarcinoma(331;0.0649)		TTTGAGGGAATTGCCAGGGAT	0.527													T|||	120	0.0239617	0.0862	0.0086	5008	,	,		21965	0.0		0.0	False		,,,				2504	0.0				p.N338S		Atlas-SNP	.											.	PTAFR	30	.	0			c.A1013G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN,SER/ASN	324,4082	173.4+/-203.2	12,300,1891	100	107	105		1013,1013,1013,1013	-1.5	0	1	dbSNP_52	105	7,8593	5.7+/-21.5	0,7,4293	yes	missense,missense,missense,missense	PTAFR	NM_000952.4,NM_001164721.1,NM_001164722.2,NM_001164723.2	46,46,46,46	12,307,6184	CC,CT,TT		0.0814,7.3536,2.545	benign,benign,benign,benign	338/343,338/343,338/343,338/343	28476520	331,12675	2203	4300	6503	SO:0001583	missense	5724	exon3			AGGGAATTGCCAG	BC063000	CCDS318.1	1p35-p34.3	2012-08-20			ENSG00000169403	ENSG00000169403		"GPCR / Class A : Platelet-activating factor receptors"	9582	protein-coding gene	gene with protein product		173393				1322356	Standard	NM_001164721		Approved		uc001bpl.3	P25105	OTTHUMG00000003953	ENST00000373857.3:c.1013A>G	1.37:g.28476520T>C	ENSP00000362965:p.Asn338Ser	121	0	0		151	68	0.450331	NM_001164723	A3KMC8|A8K2H5	Missense_Mutation	SNP	ENST00000373857.3	37	CCDS318.1	30	0.013736263736263736	26	0.052845528455284556	4	0.011049723756906077	0	0.0	0	0.0	T	3.748	-0.052169	0.07362	0.073536	8.14E-4	ENSG00000169403	ENST00000373857;ENST00000539896;ENST00000305392	T;T;T	0.70399	-0.48;-0.48;-0.48	5.38	-1.47	0.08772	.	1.433670	0.04726	N	0.420206	T	0.04363	0.0120	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.04495	-1.0947	10	0.07813	T	0.8	.	1.6592	0.02787	0.1391:0.3175:0.1355:0.408	rs5939;rs5939	338	P25105	PTAFR_HUMAN	S	338	ENSP00000362965:N338S;ENSP00000442658:N338S;ENSP00000301974:N338S	ENSP00000301974:N338S	N	-	2	0	PTAFR	28349107	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-0.242000	0.08928	-0.555000	0.06142	-0.418000	0.06021	AAT	T|0.975;C|0.025	0.025	strong		0.527	PTAFR-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011258.1	NM_000952		C	28476520	T	C	28476520	3	2	22	1	0	0	0	0	1	0	0	0	12735	1493	52	3	19	3	PTAFR	1	28476520	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	191397	28476520	220774101	86	2987											
EPB41	2035	hgsc.bcm.edu	37	chr1	29391505	29391505	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	caactgtaggatttagacaaGagtcaagaggagatcaaaaa	19	7	10	5	0	2	4	2	0	0	4	2	6	2	5	0	2	1	1	0	2	7	3	rs79677225	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:29391505G>A	ENST00000343067.4	+	16	2146	c.2019G>A	c.(2017-2019)aaG>aaA	p.K673K	EPB41_ENST00000349460.4_Silent_p.K450K|EPB41_ENST00000373797.1_Silent_p.K659K|EPB41_ENST00000373800.3_Silent_p.K431K|EPB41_ENST00000398863.2_Silent_p.K619K|EPB41_ENST00000356093.2_Silent_p.K640K|EPB41_ENST00000347529.3_Silent_p.K584K|EPB41_ENST00000373798.1_Silent_p.K673K	NM_001166005.1	NP_001159477.1	P11171	41_HUMAN	erythrocyte membrane protein band 4.1	673	Spectrin--actin-binding.				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)		ATTTAGACAAGAGTCAAGAGG	0.433													G|||	46	0.0091853	0.0325	0.0043	5008	,	,		19618	0.0		0.0	False		,,,				2504	0.0				p.K673K		Atlas-SNP	.											.	EPB41	118	.	0			c.G2019A						PASS	.	G	,,,,,	99,4307	79.3+/-117.8	2,95,2106	98	92	94		2019,1977,1230,1293,1350,1752	-0.5	1	1	dbSNP_132	94	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	EPB41	NM_001166005.1,NM_001166006.1,NM_001166007.1,NM_004437.3,NM_203342.2,NM_203343.2	,,,,,	2,95,6406	AA,AG,GG		0.0,2.2469,0.7612	,,,,,	673/865,659/721,410/602,431/589,450/642,584/776	29391505	99,12907	2203	4300	6503	SO:0001819	synonymous_variant	2035	exon16			AGACAAGAGTCAA	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.2019G>A	1.37:g.29391505G>A		79	0	0		62	25	0.403226	NM_001166005	B1ALH8|B1ALH9|D3DPM9|D3DPN0|P11176|Q14245|Q5TB35|Q5VXN8|Q8IXV9|Q9Y578|Q9Y579	Silent	SNP	ENST00000343067.4	37	CCDS53288.1																																																																																			G|0.991;A|0.009	0.009	strong		0.433	EPB41-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010312.1	NM_203342		A	29391505	G	A	29391505	2	1	22	1	0	0	0	0	0	0	0	1	5153	933	33	2		2	EPB41	1	29391505	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	914985	29391505	219859116	87	2988											
TMEM200B	399474	hgsc.bcm.edu	37	chr1	29447765	29447765	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggtgaagtaccccgacgcggGgacgggtcccagatttctgg	7	7	16	11	4	1	2	0	1	1	1	2	4	2	3	3	5	1	1	3	5	2	2	rs115927590	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:29447765G>T	ENST00000420504.2	-	2	733	c.576C>A	c.(574-576)tcC>tcA	p.S192S	TMEM200B_ENST00000521452.1_Silent_p.S192S	NM_001171868.1	NP_001165339.1	Q69YZ2	T200B_HUMAN	transmembrane protein 200B	192	Pro-rich.					integral component of membrane (GO:0016021)				ovary(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.00765)|Lung NSC(340;0.0153)|all_lung(284;0.0173)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;7.32e-08)|COAD - Colon adenocarcinoma(152;4.92e-06)|STAD - Stomach adenocarcinoma(196;0.00618)|BRCA - Breast invasive adenocarcinoma(304;0.0501)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.126)		CCCGACGCGGGGACGGGTCCC	0.692													G|||	46	0.0091853	0.0325	0.0043	5008	,	,		14044	0.0		0.0	False		,,,				2504	0.0				p.S192S		Atlas-SNP	.											.	TMEM200B	9	.	0			c.C576A						PASS	.	G	,	98,4306		2,94,2106	16	17	17		576,576	1.4	1	1	dbSNP_132	17	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous	TMEM200B	NM_001003682.3,NM_001171868.1	,	2,94,6404	TT,TG,GG		0.0,2.2252,0.7538	,	192/308,192/308	29447765	98,12902	2202	4298	6500	SO:0001819	synonymous_variant	399474	exon2			ACGCGGGGACGGG		CCDS30658.1	1p35	2007-12-18			ENSG00000253304	ENSG00000253304			33785	protein-coding gene	gene with protein product						15722956	Standard	NM_001003682		Approved	TTMB	uc001brn.2	Q69YZ2	OTTHUMG00000003658	ENST00000420504.2:c.576C>A	1.37:g.29447765G>T		72	0	0		56	23	0.410714	NM_001171868	Q6P2G8|Q6P2Q5	Silent	SNP	ENST00000420504.2	37	CCDS30658.1																																																																																			G|0.990;T|0.010	0.010	strong		0.692	TMEM200B-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010377.2	NM_001003682		T	29447765	G	T	29447765	2	4	22	1	0	0	0	0	0	0	0	1	16139	1219	43	4		4	TMEM200B	1	29447765	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	56260	29447765	219802856	88	2989											
SDC3	9672	hgsc.bcm.edu	37	chr1	31349795	31349795	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtagccatggtagtggagacGgtggtggctctctggctggg	5	10	19	7	1	1	1	0	0	1	1	2	2	1	1	1	7	1	4	1	7	2	2	rs142879690	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:31349795G>A	ENST00000339394.6	-	3	648	c.474C>T	c.(472-474)acC>acT	p.T158T	SDC3_ENST00000471567.1_5'UTR|SDC3_ENST00000336798.7_Silent_p.T100T	NM_014654.3	NP_055469.3	O75056	SDC3_HUMAN	syndecan 3	158	Ser/Thr-rich (mucin-like).				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)		TAGTGGAGACGGTGGTGGCTC	0.667													G|||	5	0.000998403	0.0038	0.0	5008	,	,		12182	0.0		0.0	False		,,,				2504	0.0				p.T158T		Atlas-SNP	.											.	SDC3	45	.	0			c.C474T						PASS	.	G		21,4385	25.3+/-52.1	0,21,2182	36	38	37		474	-1	0.3	1	dbSNP_134	37	0,8598		0,0,4299	no	coding-synonymous	SDC3	NM_014654.3		0,21,6481	AA,AG,GG		0.0,0.4766,0.1615		158/443	31349795	21,12983	2203	4299	6502	SO:0001819	synonymous_variant	9672	exon3			GGAGACGGTGGTG	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.474C>T	1.37:g.31349795G>A		119	0	0		141	70	0.496454	NM_014654	Q5T1Z6|Q5T1Z7|Q96CT3|Q96PR8	Silent	SNP	ENST00000339394.6	37	CCDS30661.1																																																																																			G|0.998;A|0.002	0.002	strong		0.667	SDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102017.1	NM_014654		A	31349795	G	A	31349795	2	1	22	1	0	0	0	0	0	0	0	1	13968	1103	39	1		1	SDC3	1	31349795	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1902030	31349795	217900826	89	2990											
DCDC2B	149069	hgsc.bcm.edu	37	chr1	32677370	32677370	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	catgggtttcagggtcctccCgtgactcgccacttgtgtga	5	12	12	12	2	1	2	1	2	0	0	4	2	3	2	3	2	0	1	3	2	0	2	rs182464428	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:32677370C>T	ENST00000409358.1	+	3	327	c.327C>T	c.(325-327)ccC>ccT	p.P109P		NM_001099434.1	NP_001092904.1	A2VCK2	DCD2B_HUMAN	doublecortin domain containing 2B	109					intracellular signal transduction (GO:0035556)					breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)	11		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				AGGGTCCTCCCGTGACTCGCC	0.617													C|||	5	0.000998403	0.0038	0.0	5008	,	,		15943	0.0		0.0	False		,,,				2504	0.0				p.P109P		Atlas-SNP	.											.	DCDC2B	24	.	0			c.C327T						PASS	.	C		18,4196		0,18,2089	36	38	38		327	-6.6	0	1		38	0,8482		0,0,4241	no	coding-synonymous	DCDC2B	NM_001099434.1		0,18,6330	TT,TC,CC		0.0,0.4271,0.1418		109/350	32677370	18,12678	2107	4241	6348	SO:0001819	synonymous_variant	149069	exon3			TCCTCCCGTGACT	BC128073	CCDS44100.1	1p35.1	2008-05-13			ENSG00000222046	ENSG00000222046			32576	protein-coding gene	gene with protein product							Standard	NM_001099434		Approved		uc001bun.2	A2VCK2	OTTHUMG00000005741	ENST00000409358.1:c.327C>T	1.37:g.32677370C>T		85	0	0		76	36	0.473684	NM_001099434	B7ZBC6	Silent	SNP	ENST00000409358.1	37	CCDS44100.1																																																																																			C|0.998;T|0.002	0.002	strong		0.617	DCDC2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328293.1	XM_940631		T	32677370	C	T	32677370	2	4	22	1	0	0	0	0	0	0	0	1	4288	639	23	1		1	DCDC2B	1	32677370	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1327575	32677370	216573251	90	2991											
TSSK3	81629	hgsc.bcm.edu	37	chr1	32829261	32829261	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctggaccacaagaacatcAtccaggtgtatgagatgctg	12	8	10	11	0	1	2	1	1	0	2	2	4	2	3	3	2	2	2	3	2	3	1	rs35508255	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:32829261A>G	ENST00000373534.3	+	2	716	c.211A>G	c.(211-213)Atc>Gtc	p.I71V	FAM229A_ENST00000415596.1_Intron|FAM229A_ENST00000432622.1_5'Flank	NM_052841.3	NP_443073.1	Q96PN8	TSSK3_HUMAN	testis-specific serine kinase 3	71	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		I -> V (in dbSNP:rs35508255).		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)				CAAGAACATCATCCAGGTGTA	0.562													A|||	81	0.0161741	0.0582	0.0058	5008	,	,		19728	0.0		0.0	False		,,,				2504	0.0				p.I71V		Atlas-SNP	.											.	TSSK3	22	.	0			c.A211G						PASS	.	A	VAL/ILE	208,4198	128.2+/-165.1	5,198,2000	79	84	82		211	1.9	1	1	dbSNP_126	82	3,8597	3.0+/-9.4	0,3,4297	yes	missense	TSSK3	NM_052841.3	29	5,201,6297	GG,GA,AA		0.0349,4.7208,1.6223	benign	71/269	32829261	211,12795	2203	4300	6503	SO:0001583	missense	81629	exon2			AACATCATCCAGG	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.211A>G	1.37:g.32829261A>G	ENSP00000362634:p.Ile71Val	120	0	0		147	82	0.557823	NM_052841	Q5TEE5	Missense_Mutation	SNP	ENST00000373534.3	37	CCDS362.1	39	0.017857142857142856	36	0.07317073170731707	3	0.008287292817679558	0	0.0	0	0.0	A	9.836	1.189629	0.21954	0.047208	3.49E-4	ENSG00000162526	ENST00000373534	T	0.15372	2.43	5.42	1.88	0.25563	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.086426	0.49916	N	0.000121	T	0.00496	0.0016	N	0.02379	-0.575	0.80722	D	1	P	0.45715	0.865	P	0.45232	0.474	T	0.45512	-0.9256	10	0.13470	T	0.59	.	8.5454	0.33417	0.7713:0.0:0.2287:0.0	rs35508255;rs61742632	71	Q96PN8	TSSK3_HUMAN	V	71	ENSP00000362634:I71V	ENSP00000362634:I71V	I	+	1	0	TSSK3	32601848	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.475000	0.35409	0.456000	0.26937	-0.274000	0.10170	ATC	A|0.981;G|0.019	0.019	strong		0.562	TSSK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020049.1			G	32829261	A	G	32829261	3	3	22	1	0	0	0	0	1	0	0	0	16685	217	8	3	217	3	TSSK3	1	32829261	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	151891	32829261	216421360	91	2992											
RBBP4	5928	hgsc.bcm.edu	37	chr1	33134865	33134865	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaaacaatacttccaaaccAagccactcagttgatgctca	15	9	4	13	0	3	1	3	1	0	0	4	1	4	1	3	0	5	2	3	0	5	3	rs11551266	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:33134865A>C	ENST00000373493.5	+	7	954	c.795A>C	c.(793-795)ccA>ccC	p.P265P	RBBP4_ENST00000373485.1_Silent_p.P265P|RBBP4_ENST00000544435.1_Silent_p.P13P|RBBP4_ENST00000458695.2_Silent_p.P230P|RBBP4_ENST00000414241.3_Silent_p.P264P	NM_001135255.1|NM_005610.2	NP_001128727.1|NP_005601.1	Q09028	RBBP4_HUMAN	retinoblastoma binding protein 4	265					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)				CTTCCAAACCAAGCCACTCAG	0.383													A|||	409	0.0816693	0.2927	0.0303	5008	,	,		17140	0.0		0.001	False		,,,				2504	0.0				p.P265P		Atlas-SNP	.											.	RBBP4	38	.	0			c.A795C						PASS	.	A	,,	1061,3345	373.0+/-320.6	139,783,1281	63	62	62		792,690,795	4.1	1	1	dbSNP_120	62	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous,coding-synonymous,coding-synonymous	RBBP4	NM_001135255.1,NM_001135256.1,NM_005610.2	,,	139,794,5570	CC,CA,AA		0.1279,24.0808,8.2423	,,	264/425,230/391,265/426	33134865	1072,11934	2203	4300	6503	SO:0001819	synonymous_variant	5928	exon7			CAAACCAAGCCAC	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.795A>C	1.37:g.33134865A>C		236	1	0.00423729		215	94	0.437209	NM_005610	B2R6G9|B4DRH0|D3DPQ3|P31149|Q53H02|Q96BV9	Silent	SNP	ENST00000373493.5	37	CCDS366.1	158|158	0.07234432234432235|0.07234432234432235	151|151	0.30691056910569103|0.30691056910569103	7|7	0.019337016574585635|0.019337016574585635	0|0	0.0|0.0	0|0	0.0|0.0	A|A	8.870|8.870	0.948970|0.948970	0.18356|0.18356	0.240808|0.240808	0.001279|0.001279	ENSG00000162521|ENSG00000162521	ENST00000475321|ENST00000463378	.|.	.|.	.|.	5.23|5.23	4.08|4.08	0.47627|0.47627	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.34153|0.34153	-0.9840|-0.9840	3|3	.|.	.|.	.|.	.|.	6.6964|6.6964	0.23201|0.23201	0.5947:0.2729:0.0:0.1324|0.5947:0.2729:0.0:0.1324	rs11551266;rs17849722;rs56732244|rs11551266;rs17849722;rs56732244	.|.	.|.	.|.	Q|P	68|25	.|.	.|.	K|Q	+|+	1|2	0|0	RBBP4|RBBP4	32907452|32907452	0.838000|0.838000	0.29461|0.29461	1.000000|1.000000	0.80357|0.80357	0.954000|0.954000	0.61252|0.61252	0.081000|0.081000	0.14823|0.14823	0.910000|0.910000	0.36722|0.36722	0.402000|0.402000	0.26972|0.26972	AAG|CAA	A|0.925;C|0.075	0.075	strong		0.383	RBBP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021957.3	NM_005610		C	33134865	A	C	33134865	2	2	22	1	0	0	0	0	0	0	0	1	13116	117	5	5		5	RBBP4	1	33134865	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	305604	33134865	216115756	92	2993											
ZNF362	149076	hgsc.bcm.edu	37	chr1	33745781	33745781	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttctgagtcaagcgcgggcGcgggcacgggcacgggtacc	6	5	17	13	6	2	1	1	1	1	0	2	1	2	1	1	4	2	3	1	4	2	2	rs143005937	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:33745781G>A	ENST00000539719.1	+	5	576	c.406G>A	c.(406-408)Gcg>Acg	p.A136T	ZNF362_ENST00000373428.5_Missense_Mutation_p.A136T	NM_152493.2	NP_689706.2	Q5T0B9	ZN362_HUMAN	zinc finger protein 362	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)			endometrium(3)|kidney(1)|large_intestine(4)|lung(2)	10		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				AAGCGCGGGCGCGGGCACGGG	0.697													G|||	40	0.00798722	0.0272	0.0058	5008	,	,		11977	0.0		0.0	False		,,,				2504	0.0				p.A136T	Pancreas(162;1431 2676 35353 38425)	Atlas-SNP	.											.	ZNF362	31	.	0			c.G406A						PASS	.	G	THR/ALA	138,4266	98.5+/-137.1	6,126,2070	53	59	57		406	1.2	0	1	dbSNP_134	57	0,8596		0,0,4298	yes	missense	ZNF362	NM_152493.2	58	6,126,6368	AA,AG,GG		0.0,3.1335,1.0615	benign	136/421	33745781	138,12862	2202	4298	6500	SO:0001583	missense	149076	exon5			GCGGGCGCGGGCA		CCDS377.1	1p35.1	2013-01-08			ENSG00000160094	ENSG00000160094		"Zinc fingers, C2H2-type"	18079	protein-coding gene	gene with protein product	"rotund homolog (Drosophila)"						Standard	NM_152493		Approved	FLJ25476, lin-29, RN	uc001bxc.1	Q5T0B9	OTTHUMG00000004124	ENST00000539719.1:c.406G>A	1.37:g.33745781G>A	ENSP00000446335:p.Ala136Thr	103	0	0		137	81	0.591241	NM_152493	Q8WYU4	Missense_Mutation	SNP	ENST00000539719.1	37	CCDS377.1	9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	G	0.389	-0.924363	0.02377	0.031335	0.0	ENSG00000160094	ENST00000483388;ENST00000539719;ENST00000373428	T;T	0.07567	3.18;3.18	2.39	1.17	0.20885	.	1.192330	0.06286	N	0.698320	T	0.01222	0.0040	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.45687	-0.9244	10	0.12766	T	0.61	.	4.807	0.13325	0.8237:0.0:0.1763:0.0	.	136	Q5T0B9	ZN362_HUMAN	T	123;136;136	ENSP00000446335:A136T;ENSP00000362527:A136T	ENSP00000362527:A136T	A	+	1	0	ZNF362	33518368	0.998000	0.40836	0.007000	0.13788	0.438000	0.31896	0.857000	0.27831	0.111000	0.17947	-0.839000	0.03059	GCG	G|0.989;A|0.011	0.011	strong		0.697	ZNF362-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011857.2	NM_152493		A	33745781	G	A	33745781	3	1	22	1	0	0	0	0	1	0	0	0	17883	1087	38	1	420	1	ZNF362	1	33745781	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	610916	33745781	215504840	93	2994											
PHC2	1912	hgsc.bcm.edu	37	chr1	33820520	33820520	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggggtgtggggcacgccctcGggatgtccattctgaggccc	4	8	17	12	2	1	1	0	1	1	0	3	2	2	2	3	6	0	1	3	6	0	1	rs79627057	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:33820520G>A	ENST00000257118.5	-	7	1364	c.1311C>T	c.(1309-1311)ccC>ccT	p.P437P	PHC2_ENST00000373422.3_Silent_p.P42P|RP11-415J8.5_ENST00000432703.1_RNA|PHC2_ENST00000419414.2_Silent_p.P437P|PHC2_ENST00000373416.1_5'UTR|PHC2_ENST00000431992.1_Silent_p.P408P	NM_198040.2	NP_932157.1	Q8IXK0	PHC2_HUMAN	polyhomeotic homolog 2 (Drosophila)	437					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)				GCACGCCCTCGGGATGTCCAT	0.607													G|||	94	0.01877	0.0651	0.0115	5008	,	,		18903	0.0		0.0	False		,,,				2504	0.0				p.P437P		Atlas-SNP	.											.	PHC2	78	.	0			c.C1311T						PASS	.	G		237,4169	140.4+/-175.9	12,213,1978	72	69	70		1311	-8.6	0.4	1	dbSNP_131	70	0,8600		0,0,4300	no	coding-synonymous	PHC2	NM_198040.2		12,213,6278	AA,AG,GG		0.0,5.379,1.8222		437/859	33820520	237,12769	2203	4300	6503	SO:0001819	synonymous_variant	1912	exon7			GCCCTCGGGATGT	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.1311C>T	1.37:g.33820520G>A		90	0	0		110	46	0.418182	NM_198040	A1L4Q1|A8KA40|D3DPR2|Q2TAL3|Q5T0C1|Q6NUJ6|Q6ZQR1|Q8N306|Q8TAG8|Q96BL4|Q9Y4Y7	Silent	SNP	ENST00000257118.5	37	CCDS378.1																																																																																			G|0.981;A|0.019	0.019	strong		0.607	PHC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000011895.1	NM_198040		A	33820520	G	A	33820520	2	1	22	1	0	0	0	0	0	0	0	1	11826	1103	39	1		1	PHC2	1	33820520	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	74739	33820520	215430101	94	2995											
CSMD2	114784	hgsc.bcm.edu	37	chr1	34174737	34174737	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgccctggctttcagctgAattcccttccctggctgggt	5	13	10	13	0	1	1	1	1	0	0	3	1	3	1	3	3	2	3	3	3	2	3	rs10914765	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:34174737A>G	ENST00000373380.1	-	1	367	c.147T>C	c.(145-147)atT>atC	p.I49I	CSMD2_ENST00000373381.4_Silent_p.I1176I|CSMD2_ENST00000373388.2_5'UTR			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1136	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)				CTTTCAGCTGAATTCCCTTCC	0.453													A|||	205	0.0409345	0.087	0.0101	5008	,	,		20724	0.0		0.001	False		,,,				2504	0.0838				p.I1136I		Atlas-SNP	.											.	CSMD2	946	.	0			c.T3408C						PASS	.	A		313,4093	170.1+/-200.6	10,293,1900	132	124	127		3408	4.4	1	1	dbSNP_120	127	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	CSMD2	NM_052896.3		10,297,6196	GG,GA,AA		0.0465,7.1039,2.4373		1136/3488	34174737	317,12689	2203	4300	6503	SO:0001819	synonymous_variant	114784	exon22			CAGCTGAATTCCC	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.147T>C	1.37:g.34174737A>G		94	0	0		105	52	0.495238	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Silent	SNP	ENST00000373380.1	37																																																																																				A|0.972;G|0.028	0.028	strong		0.453	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896		G	34174737	A	G	34174737	2	3	22	1	0	0	0	0	0	0	0	1	3947	242	9	3		3	CSMD2	1	34174737	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	354217	34174737	215075884	95	2996											
GJB4	127534	hgsc.bcm.edu	37	chr1	35227041	35227041	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagcagcccggctgccccaaCgtctgctatgacgagttctt	8	9	10	14	3	2	1	0	1	2	0	2	2	2	1	3	1	5	4	3	1	3	3	rs76188300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:35227041C>T	ENST00000339480.1	+	2	556	c.186C>T	c.(184-186)aaC>aaT	p.N62N	RP1-34M23.5_ENST00000542839.1_RNA	NM_153212.2	NP_694944.1	Q9NTQ9	CXB4_HUMAN	gap junction protein, beta 4, 30.3kDa	62					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)				GCTGCCCCAACGTCTGCTATG	0.612													C|||	181	0.0361422	0.1293	0.013	5008	,	,		21540	0.0		0.001	False		,,,				2504	0.0				p.N62N		Atlas-SNP	.											.	GJB4	51	.	0			c.C186T						PASS	.	C		513,3893	236.5+/-248.6	25,463,1715	177	125	143		186	-6	0.8	1	dbSNP_131	143	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	GJB4	NM_153212.2		25,468,6010	TT,TC,CC		0.0581,11.6432,3.9828		62/267	35227041	518,12488	2203	4300	6503	SO:0001819	synonymous_variant	127534	exon2			CCCCAACGTCTGC		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.186C>T	1.37:g.35227041C>T		148	0	0		166	77	0.463855	NM_153212	B3KQ82	Silent	SNP	ENST00000339480.1	37	CCDS383.1																																																																																			C|0.964;T|0.036	0.036	strong		0.612	GJB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011560.1	NM_153212		T	35227041	C	T	35227041	2	4	22	1	0	0	0	0	0	0	0	1	6418	535	19	1		1	GJB4	1	35227041	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1052304	35227041	214023580	96	2997											
GJB4	127534	hgsc.bcm.edu	37	chr1	35227306	35227306	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttcctctatatcttccacCgcctctacaaggattatgac	9	13	5	14	1	3	1	0	1	3	0	5	2	5	2	4	1	1	1	4	1	5	6	rs78499418	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:35227306C>A	ENST00000339480.1	+	2	821	c.451C>A	c.(451-453)Cgc>Agc	p.R151S	RP1-34M23.5_ENST00000542839.1_RNA	NM_153212.2	NP_694944.1	Q9NTQ9	CXB4_HUMAN	gap junction protein, beta 4, 30.3kDa	151					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)				TATCTTCCACCGCCTCTACAA	0.597													C|||	224	0.0447284	0.0991	0.0807	5008	,	,		20226	0.0317		0.0	False		,,,				2504	0.0051				p.R151S		Atlas-SNP	.											.	GJB4	51	.	0			c.C451A						PASS	.	C	SER/ARG	388,4018	195.7+/-220.2	16,356,1831	61	51	54		451	2.8	1	1	dbSNP_131	54	7,8593	5.0+/-18.6	0,7,4293	yes	missense	GJB4	NM_153212.2	110	16,363,6124	AA,AC,CC		0.0814,8.8062,3.0371	benign	151/267	35227306	395,12611	2203	4300	6503	SO:0001583	missense	127534	exon2			TTCCACCGCCTCT		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.451C>A	1.37:g.35227306C>A	ENSP00000345868:p.Arg151Ser	73	0	0		75	41	0.546667	NM_153212	B3KQ82	Missense_Mutation	SNP	ENST00000339480.1	37	CCDS383.1	110	0.05036630036630037	58	0.11788617886178862	31	0.0856353591160221	21	0.03671328671328671	0	0.0	C	14.68	2.606763	0.46527	0.088062	8.14E-4	ENSG00000189433	ENST00000339480	D	0.95272	-3.66	5.73	2.76	0.32466	Gap junction protein, cysteine-rich domain (1);	0.176980	0.50627	D	0.000107	T	0.12050	0.0293	L	0.45352	1.415	0.53688	P	2.5000000000052758E-5	B	0.20780	0.048	B	0.20577	0.03	T	0.61865	-0.6975	9	0.32370	T	0.25	.	2.7568	0.05295	0.1289:0.5283:0.1251:0.2177	.	151	Q9NTQ9	CXB4_HUMAN	S	151	ENSP00000345868:R151S	ENSP00000345868:R151S	R	+	1	0	GJB4	34999893	0.000000	0.05858	0.951000	0.38953	0.977000	0.68977	-0.582000	0.05814	0.319000	0.23209	0.655000	0.94253	CGC	C|0.966;A|0.034	0.034	strong		0.597	GJB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011560.1	NM_153212		A	35227306	C	A	35227306	3	1	22	1	0	0	0	0	1	0	0	0	6418	652	23	4	453	4	GJB4	1	35227306	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	265	35227306	214023315	97	2998											
GJA4	2701	hgsc.bcm.edu	37	chr1	35260760	35260760	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggacccaccccctcagaatGgccaaaaacccccaagtcgt	12	5	7	17	1	1	1	1	0	0	1	2	2	1	2	6	2	1	0	6	2	4	0	rs140949366	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:35260760G>A	ENST00000342280.4	+	2	1034	c.946G>A	c.(946-948)Ggc>Agc	p.G316S		NM_002060.2	NP_002051.2	P35212	CXA4_HUMAN	gap junction protein, alpha 4, 37kDa	316					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)				CCCTCAGAATGGCCAAAAACC	0.577													G|||	40	0.00798722	0.0295	0.0014	5008	,	,		17399	0.0		0.0	False		,,,				2504	0.0				p.G316S		Atlas-SNP	.											.	GJA4	25	.	0			c.G946A						PASS	.	G	SER/GLY	121,4285	88.7+/-127.4	4,113,2086	42	40	41		946	3.4	0	1	dbSNP_134	41	0,8600		0,0,4300	yes	missense	GJA4	NM_002060.2	56	4,113,6386	AA,AG,GG		0.0,2.7463,0.9303	probably-damaging	316/334	35260760	121,12885	2203	4300	6503	SO:0001583	missense	2701	exon2			CAGAATGGCCAAA	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.946G>A	1.37:g.35260760G>A	ENSP00000343676:p.Gly316Ser	43	0	0		51	25	0.490196	NM_002060	A8K698|D3DPR4|Q9P106|Q9UBL1|Q9UNA9|Q9UNB0|Q9UNB1|Q9Y5N7	Missense_Mutation	SNP	ENST00000342280.4	37	CCDS30669.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	2.239	-0.374329	0.05034	0.027463	0.0	ENSG00000187513	ENST00000342280	D	0.97186	-4.28	5.25	3.39	0.38822	.	0.791228	0.11561	N	0.551774	D	0.85448	0.5699	L	0.44542	1.39	0.09310	N	0.999995	B	0.06786	0.001	B	0.04013	0.001	T	0.78170	-0.2308	10	0.11794	T	0.64	.	7.8674	0.29545	0.1462:0.1332:0.7206:0.0	.	316	P35212	CXA4_HUMAN	S	316	ENSP00000343676:G316S	ENSP00000343676:G316S	G	+	1	0	GJA4	35033347	0.002000	0.14202	0.009000	0.14445	0.026000	0.11368	0.960000	0.29253	0.603000	0.29913	0.561000	0.74099	GGC	G|0.989;A|0.011	0.011	strong		0.577	GJA4-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011556.1	NM_002060		A	35260760	G	A	35260760	3	1	22	1	0	0	0	0	1	0	0	0	6411	1348	47	2	948	2	GJA4	1	35260760	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	33454	35260760	213989861	98	2999											
ZMYM6	9204	hgsc.bcm.edu	37	chr1	35454115	35454115	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctgaacacatttctactaaAtatggtttaattaattcttc	13	18	3	7	0	3	1	0	1	3	0	4	1	3	1	0	1	2	1	0	1	7	9	rs61745582	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:35454115A>G	ENST00000357182.4	-	16	2795	c.2568T>C	c.(2566-2568)taT>taC	p.Y856Y	ZMYM6_ENST00000493328.1_5'UTR|ZMYM6_ENST00000487874.1_Intron|ZMYM6_ENST00000373340.2_Intron	NM_007167.3	NP_009098.3	O95789	ZMYM6_HUMAN	zinc finger, MYM-type 6	856					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)				tttctactaaatatggtttaa	0.338													A|||	214	0.0427316	0.1513	0.0187	5008	,	,		17989	0.0		0.001	False		,,,				2504	0.0				p.Y856Y		Atlas-SNP	.											.	ZMYM6	110	.	0			c.T2568C						PASS	.	A		249,2077		15,219,929	17	16	16		2568	2.4	1	1	dbSNP_129	16	5,5061		0,5,2528	no	coding-synonymous	ZMYM6	NM_007167.3		15,224,3457	GG,GA,AA		0.0987,10.7051,3.4361		856/1326	35454115	254,7138	1163	2533	3696	SO:0001819	synonymous_variant	9204	exon16			TACTAAATATGGT	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.2568T>C	1.37:g.35454115A>G		245	0	0		229	112	0.489083	NM_007167	B4DRJ6|Q32Q23|Q4G108|Q5SVZ9|Q5SW00|Q69YL4|Q96IY0|Q9NWF1|Q9P2J4	Silent	SNP	ENST00000357182.4	37	CCDS387.2																																																																																			A|0.962;G|0.038	0.038	strong		0.338	ZMYM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011999.1	NM_007167		G	35454115	A	G	35454115	2	3	22	1	0	0	0	0	0	0	0	1	17719	108	4	3		3	ZMYM6	1	35454115	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	193355	35454115	213796506	99	3000											
EIF2C3	192669	hgsc.bcm.edu	37	chr1	36521340	36521340	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	accttacgcacaatgtacttCgcttaaatagtccaagtata	14	12	5	10	2	0	0	0	0	0	0	2	0	1	0	2	0	2	4	2	0	9	7	rs61743816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:36521340C>T	ENST00000373191.4	+	19	2926	c.2577C>T	c.(2575-2577)ttC>ttT	p.F859F	AGO3_ENST00000246314.6_Silent_p.F625F	NM_024852.3	NP_079128.2	Q9H9G7	AGO3_HUMAN	argonaute RISC catalytic component 3	859					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)										CAATGTACTTCGCTTAAATAG	0.428													C|||	48	0.00958466	0.034	0.0	5008	,	,		20951	0.0		0.003	False		,,,				2504	0.0				p.F859F		Atlas-SNP	.											.	.	.	.	0			c.C2577T						PASS	.	C	,	105,4301	81.9+/-120.4	2,101,2100	139	115	123		2577,1875	1.9	1	1	dbSNP_129	123	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	EIF2C3	NM_024852.3,NM_177422.2	,	2,106,6395	TT,TC,CC		0.0581,2.3831,0.8458	,	859/861,625/627	36521340	110,12896	2203	4300	6503	SO:0001819	synonymous_variant	192669	exon19			GTACTTCGCTTAA	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.2577C>T	1.37:g.36521340C>T		122	0	0		90	43	0.477778	NM_024852	B1ALI0|Q5TA55|Q9H1U6	Silent	SNP	ENST00000373191.4	37	CCDS399.1																																																																																			C|0.992;T|0.008	0.008	strong		0.428	AGO3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019831.4	NM_024852		T	36521340	C	T	36521340	2	4	22	1	0	0	0	0	0	0	0	1	5009	883	31	1		1	EIF2C3	1	36521340	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1067225	36521340	212729281	100	3001											
TEKT2	27285	hgsc.bcm.edu	37	chr1	36551495	36551495	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctgcctctggatgtggccaTtgagtgcctgaccctgcggg	4	10	14	13	1	1	2	0	2	1	0	1	3	1	3	5	3	3	0	5	3	0	1	rs419653	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:36551495T>C	ENST00000207457.3	+	4	468	c.341T>C	c.(340-342)aTt>aCt	p.I114T	ADPRHL2_ENST00000373178.4_5'Flank	NM_014466.2	NP_055281.2	Q9UIF3	TEKT2_HUMAN	tektin 2 (testicular)	114			I -> T (in dbSNP:rs419653).		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)				GATGTGGCCATTGAGTGCCTG	0.587													T|||	65	0.0129792	0.0484	0.0014	5008	,	,		19232	0.0		0.0	False		,,,				2504	0.0				p.I114T		Atlas-SNP	.											.	TEKT2	32	.	0			c.T341C						PASS	.	T	THR/ILE	134,4272	95.7+/-134.4	5,124,2074	58	53	55		341	5.8	0.7	1	dbSNP_80	55	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TEKT2	NM_014466.2	89	5,125,6373	CC,CT,TT		0.0116,3.0413,1.038	benign	114/431	36551495	135,12871	2203	4300	6503	SO:0001583	missense	27285	exon4			TGGCCATTGAGTG	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.341T>C	1.37:g.36551495T>C	ENSP00000207457:p.Ile114Thr	143	0	0		160	65	0.40625	NM_014466	A6NIS6|O60638	Missense_Mutation	SNP	ENST00000207457.3	37	CCDS401.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	T	11.29	1.595161	0.28445	0.030413	1.16E-4	ENSG00000092850	ENST00000207457	T	0.02177	4.41	5.79	5.79	0.91817	.	0.454845	0.25833	N	0.028007	T	0.00468	0.0015	N	0.12182	0.205	0.33226	D	0.55525	B	0.23990	0.095	B	0.23574	0.047	T	0.49969	-0.8882	10	0.14252	T	0.57	.	16.1354	0.81481	0.0:0.0:0.0:1.0	rs419653;rs419653	114	Q9UIF3	TEKT2_HUMAN	T	114	ENSP00000207457:I114T	ENSP00000207457:I114T	I	+	2	0	TEKT2	36324082	0.589000	0.26807	0.652000	0.29579	0.988000	0.76386	1.835000	0.39181	2.207000	0.71202	0.533000	0.62120	ATT	T|0.990;C|0.010	0.010	strong		0.587	TEKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020200.1	NM_014466		C	36551495	T	C	36551495	3	2	22	1	0	0	0	0	1	0	0	0	15768	1493	52	3	351	3	TEKT2	1	36551495	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	30155	36551495	212699126	101	3002											
THRAP3	9967	hgsc.bcm.edu	37	chr1	36752687	36752687	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcacatcccagatgggctcaActctgccgagtggtgccggg	7	7	14	13	2	2	1	1	0	1	1	3	2	3	1	3	3	3	2	3	3	1	0	rs58840555	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:36752687A>G	ENST00000354618.5	+	4	1080	c.856A>G	c.(856-858)Act>Gct	p.T286A	THRAP3_ENST00000469141.2_Missense_Mutation_p.T286A	NM_005119.3	NP_005110.2	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	286	Ser-rich.				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)				GATGGGCTCAACTCTGCCGAG	0.597			T	USP6	aneurysmal bone cysts								A|||	283	0.0565096	0.1997	0.0274	5008	,	,		19531	0.0		0.0	False		,,,				2504	0.0				p.T286A	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.A856G						PASS	.	A	ALA/THR	773,3633	311.1+/-291.9	88,597,1518	75	77	76		856	-10.2	0.1	1	dbSNP_129	76	9,8591	7.1+/-27.0	0,9,4291	no	missense	THRAP3	NM_005119.3	58	88,606,5809	GG,GA,AA		0.1047,17.5443,6.0126	benign	286/956	36752687	782,12224	2203	4300	6503	SO:0001583	missense	9967	exon4			GGCTCAACTCTGC	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.856A>G	1.37:g.36752687A>G	ENSP00000346634:p.Thr286Ala	115	0	0		121	49	0.404959	NM_005119	D3DPS5|Q5VTK6	Missense_Mutation	SNP	ENST00000354618.5	37	CCDS405.1	101	0.04624542124542125	89	0.18089430894308944	12	0.03314917127071823	0	0.0	0	0.0	A	0.128	-1.116496	0.01799	0.175443	0.001047	ENSG00000054118	ENST00000354618;ENST00000469141	T;T	0.12774	2.65;2.65	5.85	-10.2	0.00374	.	0.656822	0.15045	N	0.283624	T	0.00012	0.0000	N	0.00538	-1.39	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.12967	-1.0527	9	0.06365	T	0.9	0.3741	7.9158	0.29816	0.1879:0.0:0.445:0.3671	rs58840555;rs61732681	286	Q9Y2W1	TR150_HUMAN	A	286	ENSP00000346634:T286A;ENSP00000433825:T286A	ENSP00000346634:T286A	T	+	1	0	THRAP3	36525274	0.000000	0.05858	0.133000	0.22050	0.263000	0.26337	-0.599000	0.05700	-2.368000	0.00604	-2.215000	0.00298	ACT	A|0.946;G|0.054	0.054	strong		0.597	THRAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021688.2	NM_005119		G	36752687	A	G	36752687	3	3	22	1	0	0	0	0	1	0	0	0	15889	43	2	3	862	3	THRAP3	1	36752687	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	201192	36752687	212497934	102	3003											
STK40	83931	hgsc.bcm.edu	37	chr1	36820015	36820015	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggtctctgtgcacgatattTttctgtaaaacaacaggcgt	11	13	9	8	2	2	0	0	0	2	0	3	1	2	0	0	2	3	2	0	2	4	4	rs115120808	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:36820015T>C	ENST00000373129.3	-	7	979	c.573A>G	c.(571-573)aaA>aaG	p.K191K	STK40_ENST00000482458.1_5'Flank|STK40_ENST00000359297.2_Silent_p.K191K|STK40_ENST00000373132.3_Silent_p.K191K|STK40_ENST00000373130.3_Silent_p.K196K	NM_032017.1	NP_114406.1	Q8N2I9	STK40_HUMAN	serine/threonine kinase 40	191	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.			Missing (in Ref. 2; BAC11371). {ECO:0000305}.	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)				GCACGATATTTTTCTGTAAAA	0.527													T|||	55	0.0109824	0.0401	0.0029	5008	,	,		20477	0.0		0.0	False		,,,				2504	0.0				p.K191K		Atlas-SNP	.											.	STK40	53	.	0			c.A573G						PASS	.	T		162,4244	109.1+/-147.4	5,152,2046	189	177	181		573	3	1	1	dbSNP_132	181	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	STK40	NM_032017.1		5,153,6345	CC,CT,TT		0.0116,3.6768,1.2533		191/436	36820015	163,12843	2203	4300	6503	SO:0001819	synonymous_variant	83931	exon7			GATATTTTTCTGT	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.573A>G	1.37:g.36820015T>C		184	0	0		173	81	0.468208	NM_032017	D3DPS8|Q5VTK8|Q5VTK9|Q6ZMN1|Q8N2J8|Q8N3I6|Q96HN6|Q96I44|Q9BSA3|Q9H7H6	Silent	SNP	ENST00000373129.3	37	CCDS407.1																																																																																			T|0.990;C|0.010	0.010	strong		0.527	STK40-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022592.1	NM_032017		C	36820015	T	C	36820015	2	2	22	1	0	0	0	0	0	0	0	1	15322	1838	64	3		3	STK40	1	36820015	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	67328	36820015	212430606	103	3004											
CSF3R	1441	hgsc.bcm.edu	37	chr1	36933493	36933493	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tggctggcagccatgaggtgGatgtgatacagactggcggg	8	8	18	7	1	0	3	0	2	0	1	0	4	0	4	1	6	2	2	1	6	1	1	rs3917998	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:36933493G>A	ENST00000373106.1	-	14	2341	c.1794C>T	c.(1792-1794)atC>atT	p.I598I	CSF3R_ENST00000373104.1_Silent_p.I598I|CSF3R_ENST00000440588.2_Silent_p.I598I|CSF3R_ENST00000338937.5_Silent_p.I598I|CSF3R_ENST00000418048.2_Silent_p.I598I|CSF3R_ENST00000373103.1_Silent_p.I598I|CSF3R_ENST00000487540.2_5'UTR|CSF3R_ENST00000361632.4_Silent_p.I598I|CSF3R_ENST00000331941.5_Silent_p.I598I	NM_000760.3	NP_000751.1	Q99062	CSF3R_HUMAN	colony stimulating factor 3 receptor (granulocyte)	598	Fibronectin type-III 5. {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)	CCATGAGGTGGATGTGATACA	0.632													G|||	39	0.00778754	0.0287	0.0014	5008	,	,		18146	0.0		0.0	False		,,,				2504	0.0				p.I598I		Atlas-SNP	.											.	CSF3R	157	.	0			c.C1794T						PASS	.	G	,,	110,4296	85.3+/-124.0	1,108,2094	62	72	68		1794,1794,1794	0.9	0.8	1	dbSNP_108	68	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	CSF3R	NM_000760.3,NM_156039.3,NM_172313.2	,,	1,113,6389	AA,AG,GG		0.0581,2.4966,0.8842	,,	598/837,598/864,598/784	36933493	115,12891	2203	4300	6503	SO:0001819	synonymous_variant	1441	exon14			GAGGTGGATGTGA	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.1794C>T	1.37:g.36933493G>A		131	0	0		142	69	0.485915	NM_156039		Silent	SNP	ENST00000373106.1	37	CCDS413.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	G	1.164	-0.642824	0.03531	0.024966	5.81E-4	ENSG00000119535	ENST00000464465	.	.	.	5.33	0.847	0.18961	.	.	.	.	.	T	0.37625	0.1010	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31166	-0.9953	4	.	.	.	-20.3197	6.8146	0.23822	0.0808:0.1894:0.6261:0.1037	rs3917998;rs3917998	.	.	.	F	150	.	.	S	-	2	0	CSF3R	36706080	0.985000	0.35326	0.819000	0.32651	0.078000	0.17371	0.083000	0.14871	0.245000	0.21373	-0.797000	0.03246	TCC	G|0.991;A|0.009	0.009	strong		0.632	CSF3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021997.2	NM_156039		A	36933493	G	A	36933493	2	1	22	1	0	0	0	0	0	0	0	1	3939	1164	41	2		2	CSF3R	1	36933493	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	113478	36933493	212317128	104	3005											
C1orf109	54955	hgsc.bcm.edu	37	chr1	38155319	38155319	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggacgatgtcaccagccacCagctgcttacgcctcagccg	9	6	10	16	3	2	0	2	0	0	0	2	2	2	1	5	1	5	2	5	1	1	1	rs61731880	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:38155319C>T	ENST00000358011.4	-	2	423	c.234G>A	c.(232-234)ctG>ctA	p.L78L	CDCA8_ENST00000373055.1_5'Flank|C1orf109_ENST00000464085.1_Silent_p.L78L|CDCA8_ENST00000327331.2_5'Flank	NM_017850.1	NP_060320.1	Q9NX04	CA109_HUMAN	chromosome 1 open reading frame 109	78										lung(2)|prostate(2)	4		Myeloproliferative disorder(586;0.0393)				CACCAGCCACCAGCTGCTTAC	0.547													C|||	196	0.0391374	0.1369	0.0202	5008	,	,		18248	0.0		0.001	False		,,,				2504	0.0				p.L78L		Atlas-SNP	.											.	C1orf109	13	.	0			c.G234A						PASS	.	C		501,3905	225.2+/-241.2	27,447,1729	93	99	97		234	2.7	0.5	1	dbSNP_129	97	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	C1orf109	NM_017850.1		27,450,6026	TT,TC,CC		0.0349,11.3709,3.8751		78/204	38155319	504,12502	2203	4300	6503	SO:0001819	synonymous_variant	54955	exon2			AGCCACCAGCTGC	AK000515	CCDS423.1	1p34.3	2012-06-21			ENSG00000116922	ENSG00000116922			26039	protein-coding gene	gene with protein product		614799				22548824	Standard	XM_005270979		Approved	FLJ20508	uc001cbp.3	Q9NX04	OTTHUMG00000004323	ENST00000358011.4:c.234G>A	1.37:g.38155319C>T		187	0	0		214	103	0.481308	NM_017850	D3DPT1|Q8WVD1	Silent	SNP	ENST00000358011.4	37	CCDS423.1																																																																																			C|0.966;T|0.034	0.034	strong		0.547	C1orf109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012486.1	NM_017850		T	38155319	C	T	38155319	2	4	22	1	0	0	0	0	0	0	0	1	1984	581	21	2		2	C1orf109	1	38155319	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1221826	38155319	211095302	105	3006											
EPHA10	284656	hgsc.bcm.edu	37	chr1	38188736	38188736	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccaaggctcctctccagcGtgacgcttttcgcatccagt	6	11	8	16	3	1	1	0	1	1	0	6	1	4	1	4	1	1	3	4	1	1	2	rs146568133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:38188736G>A	ENST00000373048.4	-	10	1936	c.1937C>T	c.(1936-1938)aCg>aTg	p.T646M	EPHA10_ENST00000330210.7_Missense_Mutation_p.T141M|EPHA10_ENST00000427468.2_Missense_Mutation_p.T646M|EPHA10_ENST00000540011.1_Missense_Mutation_p.T141M|EPHA10_ENST00000446149.2_5'UTR	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	646	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)				CCTCTCCAGCGTGACGCTTTT	0.617													G|||	5	0.000998403	0.003	0.0	5008	,	,		19137	0.0		0.001	False		,,,				2504	0.0				p.T646M		Atlas-SNP	.											.	EPHA10	120	.	0			c.C1937T						PASS	.	G	MET/THR	16,4208		0,16,2096	53	59	57		1937	0.7	0.6	1	dbSNP_134	57	3,8429		0,3,4213	yes	missense	EPHA10	NM_001099439.1	81	0,19,6309	AA,AG,GG		0.0356,0.3788,0.1501	probably-damaging	646/1009	38188736	19,12637	2112	4216	6328	SO:0001583	missense	284656	exon10			TCCAGCGTGACGC	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.1937C>T	1.37:g.38188736G>A	ENSP00000362139:p.Thr646Met	128	0	0		118	57	0.483051	NM_001099439	A4FU89|J3KPB5|Q6NW42	Missense_Mutation	SNP	ENST00000373048.4	37	CCDS41305.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	6.575	0.474435	0.12521	0.003788	3.56E-4	ENSG00000183317	ENST00000330210;ENST00000427468;ENST00000540011;ENST00000373048	D;D;T;D	0.83250	-1.7;-1.7;2.32;-1.7	3.96	0.672	0.17935	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.805996	0.10139	N	0.711048	T	0.66005	0.2746	L	0.41632	1.29	0.21579	N	0.99964	B	0.22851	0.076	B	0.17433	0.018	T	0.60321	-0.7286	10	0.66056	D	0.02	.	3.9999	0.09576	0.2121:0.0:0.4597:0.3283	.	646	Q5JZY3	EPHAA_HUMAN	M	141;646;141;646	ENSP00000330379:T141M;ENSP00000397746:T646M;ENSP00000441822:T141M;ENSP00000362139:T646M	ENSP00000330379:T141M	T	-	2	0	EPHA10	37961323	0.800000	0.28916	0.606000	0.28943	0.055000	0.15305	1.113000	0.31184	0.274000	0.22072	-0.657000	0.03884	ACG	G|0.999;A|0.001	0.001	strong		0.617	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641		A	38188736	G	A	38188736	3	1	22	1	0	0	0	0	1	0	0	0	5168	1145	40	1	1121	1	EPHA10	1	38188736	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	33417	38188736	211061885	106	3007											
EPHA10	284656	hgsc.bcm.edu	37	chr1	38197214	38197214	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtgacggtgactgtgggcGcccctgtcttcaccatggag	5	10	15	11	2	2	2	1	2	1	0	2	3	2	3	3	4	0	0	3	4	0	1	rs141193695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:38197214G>A	ENST00000373048.4	-	7	1531	c.1532C>T	c.(1531-1533)gCg>gTg	p.A511V	EPHA10_ENST00000330210.7_Missense_Mutation_p.A6V|EPHA10_ENST00000427468.2_Missense_Mutation_p.A511V|EPHA10_ENST00000540011.1_Missense_Mutation_p.A6V|EPHA10_ENST00000446149.2_5'UTR	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	511	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)				GACTGTGGGCGCCCCTGTCTT	0.587													G|||	4	0.000798722	0.003	0.0	5008	,	,		15942	0.0		0.0	False		,,,				2504	0.0				p.A511V		Atlas-SNP	.											EPHA10,colon,carcinoma,+1,1	EPHA10	120	1	0			c.C1532T						PASS	.	G	VAL/ALA	16,3888		0,16,1936	106	106	106		1532	2.9	0.3	1	dbSNP_134	106	1,8293		0,1,4146	yes	missense	EPHA10	NM_001099439.1	64	0,17,6082	AA,AG,GG		0.0121,0.4098,0.1394	possibly-damaging	511/1009	38197214	17,12181	1952	4147	6099	SO:0001583	missense	284656	exon7			GTGGGCGCCCCTG	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.1532C>T	1.37:g.38197214G>A	ENSP00000362139:p.Ala511Val	99	0	0		86	38	0.44186	NM_001099439	A4FU89|J3KPB5|Q6NW42	Missense_Mutation	SNP	ENST00000373048.4	37	CCDS41305.1	47	0.02152014652014652	14	0.028455284552845527	4	0.011049723756906077	9	0.015734265734265736	20	0.026385224274406333	G	11.32	1.603665	0.28534	0.004098	1.21E-4	ENSG00000183317	ENST00000330210;ENST00000427468;ENST00000540011;ENST00000373048	T;T;T;T	0.76448	-1.02;0.36;-1.02;0.36	4.77	2.89	0.33648	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.526148	0.16039	N	0.232481	T	0.42268	0.1195	L	0.47016	1.485	0.09310	N	1	B	0.19331	0.035	B	0.10450	0.005	T	0.41305	-0.9516	9	.	.	.	.	5.1724	0.15118	0.172:0.0:0.6615:0.1665	.	511	Q5JZY3	EPHAA_HUMAN	V	6;511;6;511	ENSP00000330379:A6V;ENSP00000397746:A511V;ENSP00000441822:A6V;ENSP00000362139:A511V	.	A	-	2	0	EPHA10	37969801	0.972000	0.33761	0.319000	0.25293	0.345000	0.29048	3.224000	0.51238	0.605000	0.29947	0.563000	0.77884	GCG	G|0.979;A|0.021	0.021	strong		0.587	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641		A	38197214	G	A	38197214	3	1	22	1	0	0	0	0	1	0	0	0	5168	1087	38	1	1538	1	EPHA10	1	38197214	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	8478	38197214	211053407	107	3008											
INPP5B	3633	hgsc.bcm.edu	37	chr1	38411444	38411444	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacgcgtgttcctggccgcCgtgctccaggcggtagcgca	4	8	14	15	6	1	0	1	0	0	0	3	0	3	0	4	3	2	4	4	3	1	2	rs56993041	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:38411444C>T	ENST00000373026.1	-	2	136	c.136G>A	c.(136-138)Ggc>Agc	p.G46S	INPP5B_ENST00000373023.2_Missense_Mutation_p.G46S|INPP5B_ENST00000373021.1_Missense_Mutation_p.G46S|INPP5B_ENST00000373024.3_Missense_Mutation_p.G46S			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	46	PH.		G -> S (in dbSNP:rs56993041).		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)				TCCTGGCCGCCGTGCTCCAGG	0.652													C|||	143	0.0285543	0.1021	0.0115	5008	,	,		15864	0.0		0.0	False		,,,				2504	0.0				p.G46S		Atlas-SNP	.											.	INPP5B	76	.	0			c.G136A						PASS	.	C	SER/GLY	341,3813		12,317,1748	54	65	61		136	4.4	0	1	dbSNP_129	61	0,8390		0,0,4195	yes	missense	INPP5B	NM_005540.2	56	12,317,5943	TT,TC,CC		0.0,8.209,2.7184	possibly-damaging	46/914	38411444	341,12203	2077	4195	6272	SO:0001583	missense	3633	exon3			GGCCGCCGTGCTC	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.136G>A	1.37:g.38411444C>T	ENSP00000362117:p.Gly46Ser	191	1	0.0052356		215	118	0.548837	NM_005540	C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	Missense_Mutation	SNP	ENST00000373026.1	37		47	0.02152014652014652	44	0.08943089430894309	3	0.008287292817679558	0	0.0	0	0.0	C	15.32	2.799766	0.50208	0.08209	0.0	ENSG00000204084	ENST00000373023;ENST00000373029;ENST00000373026;ENST00000373024;ENST00000373021	D;D;D;T	0.91945	-2.93;-2.93;-2.94;0.96	4.43	4.43	0.53597	.	0.993232	0.08181	N	0.985409	T	0.32763	0.0840	L	0.54323	1.7	0.80722	D	1	P	0.39920	0.695	B	0.32149	0.141	T	0.68047	-0.5512	10	0.51188	T	0.08	.	13.2598	0.60098	0.0:1.0:0.0:0.0	rs56993041;rs61744649	46	P32019-2	.	S	46	ENSP00000362114:G46S;ENSP00000362117:G46S;ENSP00000362115:G46S;ENSP00000362112:G46S	ENSP00000362112:G46S	G	-	1	0	INPP5B	38184031	0.009000	0.17119	0.018000	0.16275	0.185000	0.23345	2.347000	0.44036	2.411000	0.81874	0.563000	0.77884	GGC	C|0.978;T|0.022	0.022	strong		0.652	INPP5B-003	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000012968.1	NM_005540		T	38411444	C	T	38411444	3	4	22	1	0	0	0	0	1	0	0	0	7764	652	23	1	2693	1	INPP5B	1	38411444	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	214230	38411444	210839177	108	3009											
SF3A3	10946	hgsc.bcm.edu	37	chr1	38433762	38433762	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acattagcaaagtgagcagtGtttgggatgcccaaacacct	13	9	10	9	0	0	1	0	1	0	0	0	2	0	2	2	1	4	3	2	1	3	2	rs59294668	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:38433762G>A	ENST00000373019.4	-	15	2281	c.1326C>T	c.(1324-1326)aaC>aaT	p.N442N	SF3A3_ENST00000448721.2_Silent_p.N389N	NM_006802.2	NP_006793.1	Q12874	SF3A3_HUMAN	splicing factor 3a, subunit 3, 60kDa	442					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)				AGTGAGCAGTGTTTGGGATGC	0.448													G|||	79	0.0157748	0.0545	0.0101	5008	,	,		22415	0.0		0.0	False		,,,				2504	0.0				p.N442N		Atlas-SNP	.											.	SF3A3	37	.	0			c.C1326T						PASS	.	G		199,4207	123.3+/-160.7	7,185,2011	184	174	177		1326	-0.1	1	1	dbSNP_129	177	0,8600		0,0,4300	no	coding-synonymous	SF3A3	NM_006802.2		7,185,6311	AA,AG,GG		0.0,4.5166,1.5301		442/502	38433762	199,12807	2203	4300	6503	SO:0001819	synonymous_variant	10946	exon15			AGCAGTGTTTGGG	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.1326C>T	1.37:g.38433762G>A		478	2	0.0041841		500	294	0.588	NM_006802	D3DPT5|Q15460|Q5VT87	Silent	SNP	ENST00000373019.4	37	CCDS428.1																																																																																			G|0.983;A|0.017	0.017	strong		0.448	SF3A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012976.1	NM_006802		A	38433762	G	A	38433762	2	1	22	1	0	0	0	0	0	0	0	1	14163	1368	48	2		2	SF3A3	1	38433762	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	22318	38433762	210816859	109	3010											
RRAGC	64121	hgsc.bcm.edu	37	chr1	39325136	39325136	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccatgagcagaatcctcggCttggagctgtcagcgccccc	7	7	11	16	2	1	2	1	1	0	1	3	3	2	3	4	2	3	3	4	2	1	1	rs112925356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:39325136C>T	ENST00000373001.3	-	1	359	c.183G>A	c.(181-183)aaG>aaA	p.K61K	RP5-864K19.4_ENST00000456813.1_RNA|RP5-864K19.4_ENST00000433671.2_RNA	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)				GAATCCTCGGCTTGGAGCTGT	0.726													C|||	139	0.0277556	0.0658	0.0086	5008	,	,		6031	0.001		0.001	False		,,,				2504	0.045				p.K61K		Atlas-SNP	.											.	RRAGC	28	.	0			c.G183A						PASS	.	C		156,3314		2,152,1581	7	8	7		183	5	1	1	dbSNP_132	7	12,6612		0,12,3300	no	coding-synonymous	RRAGC	NM_022157.2		2,164,4881	TT,TC,CC		0.1812,4.4957,1.6644		61/400	39325136	168,9926	1735	3312	5047	SO:0001819	synonymous_variant	64121	exon1			CCTCGGCTTGGAG	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.183G>A	1.37:g.39325136C>T		53	0	0		56	29	0.517857	NM_001271851		Silent	SNP	ENST00000373001.3	37	CCDS430.1																																																																																			C|0.978;T|0.022	0.022	strong		0.726	RRAGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001222.2	NM_022157		T	39325136	C	T	39325136	2	4	22	1	0	0	0	0	0	0	0	1	13689	796	28	2		2	RRAGC	1	39325136	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	891374	39325136	209925485	110	3011											
MACF1	23499	hgsc.bcm.edu	37	chr1	39853163	39853163	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttggttgagctcaaaaaccaTtgggaagagcttagtaaaaa	16	10	10	5	0	1	2	1	1	0	1	1	3	1	3	1	2	3	4	1	2	7	5	rs79901102	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:39853163T>C	ENST00000372915.3	+	57	14751	c.14664T>C	c.(14662-14664)caT>caC	p.H4888H	MACF1_ENST00000564288.1_Silent_p.H4883H|MACF1_ENST00000545844.1_Silent_p.H2821H|MACF1_ENST00000539005.1_Silent_p.H2800H|MACF1_ENST00000317713.7_Silent_p.H2821H|MACF1_ENST00000289893.4_Silent_p.H3323H|MACF1_ENST00000361689.2_Silent_p.H2821H|MACF1_ENST00000567887.1_Silent_p.H4920H			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	4888					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)			TCAAAAACCATTGGGAAGAGC	0.438													T|||	125	0.0249601	0.0885	0.0086	5008	,	,		19483	0.0		0.001	False		,,,				2504	0.001				p.H2821H		Atlas-SNP	.											.	MACF1	909	.	0			c.T8463C						PASS	.	T	,	308,4096	161.1+/-193.3	8,292,1902	73	82	79		8463,9969	-12.3	0	1	dbSNP_131	79	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	MACF1	NM_012090.4,NM_033044.3	,	8,295,6199	CC,CT,TT		0.0349,6.9936,2.3916	,	2821/5431,3323/5939	39853163	311,12693	2202	4300	6502	SO:0001819	synonymous_variant	23499	exon54			AAACCATTGGGAA	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.14664T>C	1.37:g.39853163T>C		74	0	0		66	36	0.545455	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Silent	SNP	ENST00000372915.3	37																																																																																				T|0.975;C|0.025	0.025	strong		0.438	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		C	39853163	T	C	39853163	2	2	22	1	0	0	0	0	0	0	0	1	9153	1490	52	3		3	MACF1	1	39853163	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	528027	39853163	209397458	111	3012											
KIAA0754	643314	hgsc.bcm.edu	37	chr1	39879517	39879517	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ctgtggtggccaccctggagGaacccacttccccggcagct	6	7	12	16	1	0	0	0	0	0	0	1	2	1	2	5	5	2	2	5	5	1	1	rs587523	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:39879517G>A	ENST00000530275.1	+	1	3367	c.3172G>A	c.(3172-3174)Gaa>Aaa	p.E1058K	MACF1_ENST00000564288.1_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000289893.4_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000567887.1_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	1058	Ala-rich.		E -> K (in dbSNP:rs587523).							central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	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)			CACCCTGGAGGAACCCACTTC	0.637													N|||	206	0.0411342	0.1392	0.0187	5008	,	,		13391	0.002		0.004	False		,,,				2504	0.0031				p.E1194K		Atlas-SNP	.											.	KIAA0754	93	.	0			c.G3580A						PASS	.	G	,,LYS/GLU	469,3435		31,407,1514	18	21	20		,,3580	0.1	0	1	dbSNP_83	20	47,8247		0,47,4100	yes	intron,intron,missense	MACF1,KIAA0754	NM_012090.4,NM_033044.3,NM_015038.1	,,56	31,454,5614	AA,AG,GG		0.5667,12.0133,4.2302	,,benign	,,1194/1428	39879517	516,11682	1952	4147	6099	SO:0001583	missense	643314	exon1			CTGGAGGAACCCA			1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.3172G>A	1.37:g.39879517G>A	ENSP00000431179:p.Glu1058Lys	179	0	0		191	96	0.502618	NM_015038	E9PMC2|Q6ZSB2	Missense_Mutation	SNP	ENST00000530275.1	37		81	0.03708791208791209	73	0.1483739837398374	6	0.016574585635359115	0	0.0	2	0.002638522427440633	N	13.03	2.116599	0.37339	0.120133	0.005667	ENSG00000255103	ENST00000530275	T	0.26223	1.75	3.58	0.0671	0.14364	.	.	.	.	.	T	0.00073	0.0002	N	0.14661	0.345	0.09310	N	1	B	0.27351	0.176	B	0.17433	0.018	T	0.32929	-0.9888	9	0.28530	T	0.3	.	7.1222	0.25450	0.0:0.1645:0.4977:0.3378	rs587523;rs587523	1058	O94854	K0754_HUMAN	K	1058	ENSP00000431179:E1058K	ENSP00000431179:E1058K	E	+	1	0	RP4-562N20.1	39652104	0.089000	0.21612	0.001000	0.08648	0.083000	0.17756	2.290000	0.43531	0.013000	0.14918	0.205000	0.17691	GAA	G|0.932;A|0.068	0.068	strong		0.637	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038		A	39879517	G	A	39879517	3	1	22	1	0	0	0	0	1	0	0	0	8201	1175	41	2	3582	2	KIAA0754	1	39879517	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	26354	39879517	209371104	112	3013											
MACF1	23499	hgsc.bcm.edu	37	chr1	39907949	39907949	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaaccactgacagaactcaAacacctctgggagaacctgg	15	5	9	12	0	2	4	1	1	1	3	2	5	2	4	3	2	4	0	3	2	4	0	rs682351	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:39907949A>G	ENST00000372915.3	+	75	18689	c.18602A>G	c.(18601-18603)aAa>aGa	p.K6201R	MACF1_ENST00000564288.1_Missense_Mutation_p.K6302R|MACF1_ENST00000545844.1_Missense_Mutation_p.K4243R|MACF1_ENST00000539005.1_Missense_Mutation_p.K4113R|MACF1_ENST00000317713.7_Missense_Mutation_p.K4243R|MACF1_ENST00000289893.4_Missense_Mutation_p.K4745R|MACF1_ENST00000361689.2_Missense_Mutation_p.K4243R|MACF1_ENST00000567887.1_Missense_Mutation_p.K6339R			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	6201			K -> R (in dbSNP:rs682351).		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)			ACAGAACTCAAACACCTCTGG	0.453													A|||	60	0.0119808	0.0431	0.0043	5008	,	,		19820	0.0		0.0	False		,,,				2504	0.0				p.K4243R		Atlas-SNP	.											.	MACF1	909	.	0			c.A12728G						PASS	.	A	ARG/LYS,ARG/LYS	177,4229	114.6+/-152.6	3,171,2029	54	55	54		14234,12728	6	1	1	dbSNP_83	54	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense	MACF1	NM_033044.3,NM_012090.4	26,26	3,174,6326	GG,GA,AA		0.0349,4.0172,1.384	benign,benign	4745/5939,4243/5431	39907949	180,12826	2203	4300	6503	SO:0001583	missense	23499	exon73			AACTCAAACACCT	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.18602A>G	1.37:g.39907949A>G	ENSP00000362006:p.Lys6201Arg	72	0	0		68	34	0.5	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	A	14.28	2.488881	0.44249	0.040172	3.49E-4	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893	T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82	6.03	6.03	0.97812	.	0.000000	0.64402	D	0.000002	T	0.06781	0.0173	N	0.12637	0.245	0.80722	D	1	B;B	0.31413	0.003;0.322	B;B	0.33454	0.014;0.164	T	0.04128	-1.0975	10	0.38643	T	0.18	.	16.5582	0.84512	1.0:0.0:0.0:0.0	rs682351;rs52811310;rs682351	6201;4243	Q9UPN3;F8W8Q1	MACF1_HUMAN;.	R	4243;6201;4243;4243;4113;4745	ENSP00000439537:K4243R;ENSP00000362006:K6201R;ENSP00000354573:K4243R;ENSP00000313438:K4243R;ENSP00000444364:K4113R;ENSP00000289893:K4745R	ENSP00000289893:K4745R	K	+	2	0	MACF1	39680536	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.094000	0.57721	2.308000	0.77769	0.533000	0.62120	AAA	A|0.986;G|0.014	0.014	strong		0.453	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		G	39907949	A	G	39907949	3	3	22	1	0	0	0	0	1	0	0	0	9153	14	1	3	19165	3	MACF1	1	39907949	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	28432	39907949	209342672	113	3014											
CAP1	5538	hgsc.bcm.edu	37	chr1	40535945	40535945	+	IGR	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaagggcaaaattaactccAttacagtaggtgagtctttg	13	12	9	7	0	2	1	1	1	1	0	3	1	3	1	1	2	2	2	1	2	6	4			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:40535945A>G	ENST00000433473.3	-	0	2740				CAP1_ENST00000372805.3_Missense_Mutation_p.I370V|CAP1_ENST00000479759.1_3'UTR|CAP1_ENST00000340450.3_Missense_Mutation_p.I369V|CAP1_ENST00000372797.3_Missense_Mutation_p.I370V|CAP1_ENST00000372802.1_Missense_Mutation_p.I369V|CAP1_ENST00000372792.2_Missense_Mutation_p.I370V|CAP1_ENST00000372798.1_Missense_Mutation_p.I369V	NM_000310.3	NP_000301.1	P50897	PPT1_HUMAN	palmitoyl-protein thioesterase 1						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)			AATTAACTCCATTACAGTAGG	0.458																																					p.I370V		Atlas-SNP	.											.	CAP1	38	.	0			c.A1108G						PASS	.						81	77	78					1																	40535945		2020	4170	6190	SO:0001628	intergenic_variant	10487	exon10			AACTCCATTACAG	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		1.37:g.40535945A>G		128	0	0		154	82	0.532468	NM_006367	B4DY24|Q6FGQ4	Missense_Mutation	SNP	ENST00000433473.3	37	CCDS447.1	.	.	.	.	.	.	.	.	.	.	A	16.24	3.066402	0.55539	.	.	ENSG00000131236	ENST00000372797;ENST00000372802;ENST00000372792;ENST00000538246;ENST00000372798;ENST00000340450;ENST00000372805	T;T;T;T;T;T	0.08896	3.05;3.04;3.05;3.04;3.04;3.05	5.34	5.34	0.76211	CARP motif (1);Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal (1);Adenylate cyclase-associated CAP, C-terminal (2);C-CAP/cofactor C-like domain (1);	0.000000	0.85682	D	0.000000	T	0.11707	0.0285	L	0.48986	1.54	0.80722	D	1	B;B	0.33807	0.061;0.426	B;B	0.36534	0.149;0.227	T	0.03829	-1.1000	10	0.46703	T	0.11	-17.1934	14.503	0.67734	1.0:0.0:0.0:0.0	.	317;370	E7ENY9;Q01518	.;CAP1_HUMAN	V	370;369;370;347;369;369;370	ENSP00000361883:I370V;ENSP00000361888:I369V;ENSP00000361878:I370V;ENSP00000361884:I369V;ENSP00000344832:I369V;ENSP00000361891:I370V	ENSP00000344832:I369V	I	+	1	0	CAP1	40308532	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.437000	0.80417	1.996000	0.58369	0.528000	0.53228	ATT	.	.	none		0.458	PPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013126.2	NM_000310		G	40535945	A	G	40535945	1	3	22	0	1	0	0	0	0	0	0	0	2621	217	8	3		3	CAP1	1	40535945	IGR	SNP	A	TCGA-G8-6324-01A-11D-2210-10	627996	40535945	208714676	114	3015											
ZNF684	127396	hgsc.bcm.edu	37	chr1	41006341	41006341	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtgctgagagaaccctgtaTtgggatgtgatgttggagaa	10	12	15	4	0	0	4	0	2	0	2	0	7	0	5	1	2	2	3	1	2	3	3	rs74575870	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:41006341T>C	ENST00000372699.3	+	3	350	c.99T>C	c.(97-99)taT>taC	p.Y33Y	ZNF684_ENST00000493756.1_Intron|ZNF684_ENST00000372697.3_Silent_p.Y33Y|ZNF684_ENST00000372696.3_Silent_p.Y33Y	NM_152373.3	NP_689586.3	Q5T5D7	ZN684_HUMAN	zinc finger protein 684	33	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(2)|kidney(2)|lung(3)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	13	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;5.42e-18)			GAACCCTGTATTGGGATGTGA	0.433													T|||	176	0.0351438	0.1278	0.0086	5008	,	,		18203	0.0		0.001	False		,,,				2504	0.0				p.Y33Y		Atlas-SNP	.											.	ZNF684	37	.	0			c.T99C						PASS	.	T		384,4022	194.3+/-219.2	13,358,1832	198	172	181		99	2.7	1	1	dbSNP_132	181	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	ZNF684	NM_152373.3		13,365,6125	CC,CT,TT		0.0814,8.7154,3.0063		33/379	41006341	391,12615	2203	4300	6503	SO:0001819	synonymous_variant	127396	exon3			CCTGTATTGGGAT		CCDS454.1	1p34.2	2013-01-08			ENSG00000117010	ENSG00000117010		"Zinc fingers, C2H2-type", "-"	28418	protein-coding gene	gene with protein product	"hypothetical protein MGC27466"					12477932	Standard	NM_152373		Approved	MGC27466	uc001cft.2	Q5T5D7	OTTHUMG00000007359	ENST00000372699.3:c.99T>C	1.37:g.41006341T>C		287	0	0		311	133	0.427653	NM_152373	Q2NKY4	Silent	SNP	ENST00000372699.3	37	CCDS454.1																																																																																			T|0.973;C|0.027	0.027	strong		0.433	ZNF684-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019260.3	NM_152373		C	41006341	T	C	41006341	2	2	22	1	0	0	0	0	0	0	0	1	18106	1500	52	3		3	ZNF684	1	41006341	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	470396	41006341	208244280	115	3016											
PPCS	79717	hgsc.bcm.edu	37	chr1	42925501	42925501	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcggaaaccaagttattgctAtcagaggaagaaatagaaaa	19	8	9	5	1	1	3	1	0	0	3	2	5	1	5	1	2	2	2	1	2	9	4	rs142078638	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:42925501A>G	ENST00000372561.3	+	3	847	c.840A>G	c.(838-840)ctA>ctG	p.L280L	PPCS_ENST00000372556.3_3'UTR|PPCS_ENST00000372562.1_Silent_p.L107L|PPCS_ENST00000455780.1_Silent_p.L107L|PPCS_ENST00000472013.1_3'UTR	NM_024664.2	NP_078940.2	Q9HAB8	PPCS_HUMAN	phosphopantothenoylcysteine synthetase	280					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)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	phosphopantothenate--cysteine ligase activity (GO:0004632)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|skin(3)	12	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				AGTTATTGCTATCAGAGGAAG	0.388													A|||	6	0.00119808	0.0015	0.0	5008	,	,		17283	0.004		0.0	False		,,,				2504	0.0				p.L280L		Atlas-SNP	.											.	PPCS	30	.	0			c.A840G						PASS	.	A	,	7,3669		0,7,1831	102	98	99		321,840	-10.5	0.6	1	dbSNP_134	99	0,8184		0,0,4092	no	coding-synonymous,coding-synonymous	PPCS	NM_001077447.1,NM_024664.2	,	0,7,5923	GG,GA,AA		0.0,0.1904,0.059	,	107/139,280/312	42925501	7,11853	1838	4092	5930	SO:0001819	synonymous_variant	79717	exon3			ATTGCTATCAGAG	AK021900	CCDS41311.1, CCDS41312.1	1p34.2	2008-02-05			ENSG00000127125	ENSG00000127125	6.3.2.5		25686	protein-coding gene	gene with protein product		609853				11923312	Standard	NM_024664		Approved	FLJ11838	uc001chl.3	Q9HAB8	OTTHUMG00000007332	ENST00000372561.3:c.840A>G	1.37:g.42925501A>G		139	0	0		123	56	0.455285	NM_024664	Q3KQT2|Q5VVM0	Silent	SNP	ENST00000372561.3	37	CCDS41311.1																																																																																			A|0.998;G|0.002	0.002	strong		0.388	PPCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019166.1	NM_024664		G	42925501	A	G	42925501	2	3	22	1	0	0	0	0	0	0	0	1	12314	436	16	3		3	PPCS	1	42925501	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1919160	42925501	206325120	116	3017											
FAM183A	440585	hgsc.bcm.edu	37	chr1	43621973	43621973	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgtggggcttaggagatgatCaccacaagtagcatcccagc	11	7	12	11	1	1	2	1	1	0	1	2	3	2	2	2	3	2	3	2	3	3	2	rs59274667	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:43621973C>T	ENST00000335282.4	+	4	394	c.394C>T	c.(394-396)Cac>Tac	p.H132Y	FAM183A_ENST00000409337.1_3'UTR|FAM183A_ENST00000410048.1_Missense_Mutation_p.H104Y	NM_001101376.2	NP_001094846.2	A6NL82	F183A_HUMAN	family with sequence similarity 183, member A	132										kidney(1)|large_intestine(1)|lung(2)|ovary(3)	7						AGGAGATGATCACCACAAGTA	0.473													C|||	26	0.00519169	0.0197	0.0	5008	,	,		22333	0.0		0.0	False		,,,				2504	0.0				p.H132Y		Atlas-SNP	.											.	FAM183A	28	.	0			c.C394T						PASS	.	C	TYR/HIS	67,3987		1,65,1961	126	127	127		394	-0.6	0	1	dbSNP_129	127	0,8370		0,0,4185	yes	missense	FAM183A	NM_001101376.2	83	1,65,6146	TT,TC,CC		0.0,1.6527,0.5393	benign	132/135	43621973	67,12357	2027	4185	6212	SO:0001583	missense	440585	exon4			GATGATCACCACA	AI192630, AI375550, AL139138	CCDS44126.1	1p34.2	2008-08-11			ENSG00000186973	ENSG00000186973			34347	protein-coding gene	gene with protein product						11181995	Standard	NM_001101376		Approved	LOC440585, hCG23177	uc009vwo.3	A6NL82	OTTHUMG00000007286	ENST00000335282.4:c.394C>T	1.37:g.43621973C>T	ENSP00000334415:p.His132Tyr	99	0	0		120	60	0.5	NM_001101376	B7ZBL8	Missense_Mutation	SNP	ENST00000335282.4	37	CCDS44126.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	C	10.05	1.243842	0.22796	0.016527	0.0	ENSG00000186973	ENST00000409706;ENST00000410048;ENST00000409337;ENST00000410025;ENST00000335282	.	.	.	4.08	-0.601	0.11638	.	1.498380	0.03915	N	0.282630	T	0.10637	0.0260	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.18272	-1.0342	9	0.49607	T	0.09	.	3.0707	0.06230	0.2209:0.3721:0.0:0.4069	rs59274667;rs61738384	132	A6NL82	F183A_HUMAN	Y	132;104;42;80;132	.	ENSP00000334415:H132Y	H	+	1	0	FAM183A	43394560	0.000000	0.05858	0.000000	0.03702	0.129000	0.20672	-0.229000	0.09098	-0.092000	0.12417	-0.768000	0.03414	CAC	C|0.996;T|0.004	0.004	strong		0.473	FAM183A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019024.3	NM_001101376		T	43621973	C	T	43621973	3	4	22	1	0	0	0	0	1	0	0	0	5515	826	29	2	408	2	FAM183A	1	43621973	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	696472	43621973	205628648	117	3018											
EBNA1BP2	10969	hgsc.bcm.edu	37	chr1	43630156	43630156	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctctcttgttcgttttccAggtctcttctacagaaaaag	8	17	6	10	1	4	1	0	0	4	1	8	1	5	1	1	1	1	2	1	1	3	7	rs11559311	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:43630156A>C	ENST00000236051.2	-	9	1020	c.879T>G	c.(877-879)ccT>ccG	p.P293P	EBNA1BP2_ENST00000431635.2_Silent_p.P348P	NM_006824.2	NP_006815.2	Q99848	EBP2_HUMAN	EBNA1 binding protein 2	293					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)				TTCGTTTTCCAGGTCTCTTCT	0.443													A|||	410	0.081869	0.2405	0.0605	5008	,	,		19601	0.001		0.0368	False		,,,				2504	0.0123				p.P348P		Atlas-SNP	.											.	EBNA1BP2	37	.	0			c.T1044G						PASS	.	A	,	913,3493	351.1+/-311.1	102,709,1392	176	155	162		1044,879	-0.3	1	1	dbSNP_120	162	356,8244	119.7+/-179.0	6,344,3950	no	coding-synonymous,coding-synonymous	EBNA1BP2	NM_001159936.1,NM_006824.2	,	108,1053,5342	CC,CA,AA		4.1395,20.7217,9.757	,	348/362,293/307	43630156	1269,11737	2203	4300	6503	SO:0001819	synonymous_variant	10969	exon10			TTTTCCAGGTCTC	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.879T>G	1.37:g.43630156A>C		140	0	0		158	80	0.506329	NM_001159936	Q96A66	Silent	SNP	ENST00000236051.2	37	CCDS478.1																																																																																			A|0.912;C|0.088	0.088	strong		0.443	EBNA1BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019015.1			C	43630156	A	C	43630156	2	2	22	1	0	0	0	0	0	0	0	1	4887	175	7	5		5	EBNA1BP2	1	43630156	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	8183	43630156	205620465	118	3019											
WDR65	149465	hgsc.bcm.edu	37	chr1	43638436	43638436	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgggagatcatgtcagccgtGgtagctcagacgctgcatgt	8	9	14	10	3	3	2	3	0	0	2	3	3	3	2	1	2	3	4	1	2	1	1	rs6695238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:43638436G>T	ENST00000372492.4	+	2	336	c.12G>T	c.(10-12)gtG>gtT	p.V4V	WDR65_ENST00000528956.1_Silent_p.V4V|EBNA1BP2_ENST00000472982.1_5'Flank|EBNA1BP2_ENST00000236051.2_5'Flank|EBNA1BP2_ENST00000431635.2_5'Flank	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		4										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)				TGTCAGCCGTGGTAGCTCAGA	0.547													G|||	341	0.0680911	0.1899	0.0576	5008	,	,		10442	0.001		0.0368	False		,,,				2504	0.0123				p.V4V		Atlas-SNP	.											.	WDR65	76	.	0			c.G12T						PASS	.	G	,,	714,3692	295.6+/-283.7	65,584,1554	116	104	108		12,12,12	2.1	1	1	dbSNP_116	108	354,8246	119.5+/-178.9	6,342,3952	no	coding-synonymous,coding-synonymous,coding-synonymous	WDR65	NM_001167965.1,NM_001167966.1,NM_152498.3	,,	71,926,5506	TT,TG,GG		4.1163,16.2052,8.2116	,,	4/699,4/699,4/699	43638436	1068,11938	2203	4300	6503	SO:0001819	synonymous_variant	149465	exon2			AGCCGTGGTAGCT																												ENST00000372492.4:c.12G>T	1.37:g.43638436G>T		95	0	0		129	66	0.511628	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Silent	SNP	ENST00000372492.4	37																																																																																				G|0.920;T|0.080	0.080	strong		0.547	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1			T	43638436	G	T	43638436	2	4	22	1	0	0	0	0	0	0	0	1	17331	1335	47	4		4	WDR65	1	43638436	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	8280	43638436	205612185	119	3020											
HYI	81888	hgsc.bcm.edu	37	chr1	43917098	43917098	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacctcgaggctgatactcaCagcccacgaagcctttgtag	10	8	9	14	2	1	1	1	1	0	0	2	3	1	1	3	1	3	2	3	1	3	3	rs79439514	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:43917098C>G	ENST00000372425.4	-	7	938	c.743G>C	c.(742-744)tGt>tCt	p.C248S	SZT2_ENST00000562955.1_3'UTR|HYI_ENST00000372434.1_Missense_Mutation_p.C273S|HYI_ENST00000372426.1_Missense_Mutation_p.C200S|HYI_ENST00000372432.1_Splice_Site|HYI_ENST00000583037.1_Missense_Mutation_p.C175S|SZT2_ENST00000372442.1_3'UTR|HYI-AS1_ENST00000444386.1_RNA|HYI_ENST00000486909.1_Missense_Mutation_p.C248S|SZT2-AS1_ENST00000396885.2_RNA			Q5T013	HYI_HUMAN	hydroxypyruvate isomerase (putative)	248							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)				CTGATACTCACAGCCCACGAA	0.627													C|||	146	0.0291534	0.1051	0.0086	5008	,	,		18840	0.0		0.001	False		,,,				2504	0.0				p.C248S		Atlas-SNP	.											.	HYI	23	.	0			c.G743C						PASS	.	C	SER/CYS,,	377,4029	189.5+/-215.6	21,335,1847	61	66	64		743,,	5.5	1	1	dbSNP_131	64	2,8598	2.2+/-6.3	0,2,4298	yes	missense,utr-3,splice-5	SZT2,HYI	NM_001190880.2,NM_015284.3,NM_031207.5	112,,	21,337,6145	GG,GC,CC		0.0233,8.5565,2.914	probably-damaging,,	248/278,,	43917098	379,12627	2203	4300	6503	SO:0001583	missense	81888	exon7			TACTCACAGCCCA		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	ENST00000372425.4:c.743G>C	1.37:g.43917098C>G	ENSP00000361502:p.Cys248Ser	37	0	0		42	18	0.428571	NM_001190880	D3DPX4|D3DPX5|Q5Q9A2|Q7Z778|Q96S83|Q9BZR3|Q9BZR4	Missense_Mutation	SNP	ENST00000372425.4	37	CCDS53309.1	56|56	0.02564102564102564|0.02564102564102564	54|54	0.10975609756097561|0.10975609756097561	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	C|C	20.9|20.9	4.070255|4.070255	0.76301|0.76301	0.085565|0.085565	2.33E-4|2.33E-4	ENSG00000178922|ENSG00000178922	ENST00000372425;ENST00000372434;ENST00000372430;ENST00000372426;ENST00000486909|ENST00000470662	T;T;T|.	0.43294|.	0.95;0.95;0.95|.	5.52|5.52	5.52|5.52	0.82312|0.82312	Xylose isomerase-like, TIM barrel domain (2);|.	.|.	.|.	.|.	.|.	T|T	0.17492|0.17492	0.0420|0.0420	M|M	0.93638|0.93638	3.44|3.44	0.09310|0.09310	P|P	0.9999999792184|0.9999999792184	D|.	0.54601|.	0.967|.	P|.	0.56865|.	0.808|.	T|T	0.69239|0.69239	-0.5197|-0.5197	8|4	0.87932|.	D|.	0|.	.|.	19.8124|19.8124	0.96553|0.96553	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	248|.	Q5T013|.	HYI_HUMAN|.	S|L	248;200;175;200;248|157	ENSP00000361502:C248S;ENSP00000361503:C200S;ENSP00000428399:C248S|.	ENSP00000361502:C248S|.	C|V	-|-	2|1	0|0	HYI|HYI	43689685|43689685	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.785000|0.785000	0.44390|0.44390	7.729000|7.729000	0.84864|0.84864	2.764000|2.764000	0.94973|0.94973	0.563000|0.563000	0.77884|0.77884	TGT|GTG	C|0.974;G|0.026	0.026	strong		0.627	HYI-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031207		G	43917098	C	G	43917098	3	3	22	1	0	0	0	0	1	0	0	0	7477	492	17	4	98	4	HYI	1	43917098	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	278662	43917098	205333523	120	3021											
PTPRF	5792	hgsc.bcm.edu	37	chr1	44019305	44019305	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aaagtcagctcccagcgcttCgaggtgcgtctgtggtggga	7	9	15	10	3	2	0	1	0	1	0	4	2	3	1	1	3	3	2	1	3	1	1	rs6684279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:44019305C>T	ENST00000359947.4	+	4	574	c.234C>T	c.(232-234)ttC>ttT	p.F78F	PTPRF_ENST00000438120.1_Silent_p.F78F|PTPRF_ENST00000372414.3_Silent_p.F78F|PTPRF_ENST00000372413.3_Silent_p.F78F	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	78	Ig-like C2-type 1.				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)				CCCAGCGCTTCGAGGTGCGTC	0.597													C|||	165	0.0329473	0.118	0.0072	5008	,	,		21711	0.0		0.004	False		,,,				2504	0.0				p.F78F		Atlas-SNP	.											.	PTPRF	172	.	0			c.C234T						PASS	.	C	,	440,3966	210.2+/-230.7	23,394,1786	126	121	122		234,234	-9.8	0.6	1	dbSNP_116	122	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	PTPRF	NM_002840.3,NM_130440.2	,	23,395,6085	TT,TC,CC		0.0116,9.9864,3.3907	,	78/1908,78/1899	44019305	441,12565	2203	4300	6503	SO:0001819	synonymous_variant	5792	exon4			GCGCTTCGAGGTG	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.234C>T	1.37:g.44019305C>T		89	0	0		81	41	0.506173	NM_002840	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	37	CCDS489.2																																																																																			C|0.964;T|0.036	0.036	strong		0.597	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1			T	44019305	C	T	44019305	2	4	22	1	0	0	0	0	0	0	0	1	12816	883	31	1		1	PTPRF	1	44019305	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	102207	44019305	205231316	121	3022											
IPO13	9670	hgsc.bcm.edu	37	chr1	44422367	44422367	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accctcaccttctggtacacActgcaggtgtgtctgtgtga	7	12	10	12	0	3	1	1	1	2	0	3	1	3	1	2	2	2	2	2	2	1	2	rs36061711	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:44422367A>G	ENST00000372343.3	+	4	1760	c.1098A>G	c.(1096-1098)acA>acG	p.T366T	IPO13_ENST00000492152.1_3'UTR	NM_014652.3	NP_055467.3	O94829	IPO13_HUMAN	importin 13	366					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)				TCTGGTACACACTGCAGGTGT	0.532													A|||	196	0.0391374	0.1415	0.013	5008	,	,		20746	0.0		0.0	False		,,,				2504	0.0				p.T366T		Atlas-SNP	.											.	IPO13	86	.	0			c.A1098G						PASS	.	A		497,3909	231.4+/-245.2	31,435,1737	125	116	119		1098	-11.5	0.2	1	dbSNP_126	119	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	IPO13	NM_014652.3		31,437,6035	GG,GA,AA		0.0233,11.2801,3.8367		366/964	44422367	499,12507	2203	4300	6503	SO:0001819	synonymous_variant	9670	exon4			GTACACACTGCAG	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.1098A>G	1.37:g.44422367A>G		129	0	0		164	83	0.506098	NM_014652	D3DPY4|Q5T4X3|Q7LC04|Q96HS3|Q9H8N3|Q9UFR1	Silent	SNP	ENST00000372343.3	37	CCDS503.1																																																																																			A|0.964;G|0.036	0.036	strong		0.532	IPO13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022846.1	NM_014652		G	44422367	A	G	44422367	2	3	22	1	0	0	0	0	0	0	0	1	7803	146	6	3		3	IPO13	1	44422367	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	403062	44422367	204828254	122	3023											
IPO13	9670	hgsc.bcm.edu	37	chr1	44424525	44424525	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gatgatcatgaaggccctgaGcttcggaagctgccagtgcc	9	8	13	11	1	1	3	1	3	0	0	2	5	1	4	3	2	4	2	3	2	2	1	rs74073335	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:44424525G>A	ENST00000372343.3	+	11	2654	c.1992G>A	c.(1990-1992)gaG>gaA	p.E664E		NM_014652.3	NP_055467.3	O94829	IPO13_HUMAN	importin 13	664					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)				AAGGCCCTGAGCTTCGGAAGC	0.562													G|||	38	0.00758786	0.0287	0.0	5008	,	,		20073	0.0		0.0	False		,,,				2504	0.0				p.E664E		Atlas-SNP	.											.	IPO13	86	.	0			c.G1992A						PASS	.	G		124,4282	90.6+/-129.3	1,122,2080	84	78	80		1992	3.8	1	1	dbSNP_130	80	0,8600		0,0,4300	no	coding-synonymous	IPO13	NM_014652.3		1,122,6380	AA,AG,GG		0.0,2.8143,0.9534		664/964	44424525	124,12882	2203	4300	6503	SO:0001819	synonymous_variant	9670	exon11			CCCTGAGCTTCGG	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.1992G>A	1.37:g.44424525G>A		165	0	0		166	96	0.578313	NM_014652	D3DPY4|Q5T4X3|Q7LC04|Q96HS3|Q9H8N3|Q9UFR1	Silent	SNP	ENST00000372343.3	37	CCDS503.1																																																																																			G|0.991;A|0.009	0.009	strong		0.562	IPO13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022846.1	NM_014652		A	44424525	G	A	44424525	2	1	22	1	0	0	0	0	0	0	0	1	7803	962	34	2		2	IPO13	1	44424525	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2158	44424525	204826096	123	3024											
IPO13	9670	hgsc.bcm.edu	37	chr1	44433055	44433055	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcctgttcgccctgaacaaGcactgcttcagcctcctgag	8	10	8	15	1	1	2	1	2	0	0	4	2	3	2	4	0	4	3	4	0	2	2	rs34392712	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:44433055G>A	ENST00000372343.3	+	19	3344	c.2682G>A	c.(2680-2682)aaG>aaA	p.K894K	DPH2_ENST00000255108.3_5'Flank|IPO13_ENST00000372339.3_Silent_p.K112K|DPH2_ENST00000396758.2_5'Flank|DPH2_ENST00000412950.2_5'Flank	NM_014652.3	NP_055467.3	O94829	IPO13_HUMAN	importin 13	894					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)				CCCTGAACAAGCACTGCTTCA	0.617													g|||	67	0.0133786	0.0499	0.0014	5008	,	,		18701	0.0		0.0	False		,,,				2504	0.0				p.K894K		Atlas-SNP	.											.	IPO13	86	.	0			c.G2682A						PASS	.			173,4233	110.4+/-148.6	3,167,2033	72	70	71		2682	-0.2	1	1	dbSNP_126	71	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	IPO13	NM_014652.3		3,168,6332	AA,AG,GG		0.0116,3.9265,1.3378		894/964	44433055	174,12832	2203	4300	6503	SO:0001819	synonymous_variant	9670	exon19			GAACAAGCACTGC	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.2682G>A	1.37:g.44433055G>A		98	0	0		117	59	0.504274	NM_014652	D3DPY4|Q5T4X3|Q7LC04|Q96HS3|Q9H8N3|Q9UFR1	Silent	SNP	ENST00000372343.3	37	CCDS503.1																																																																																			G|0.989;A|0.011	0.011	strong		0.617	IPO13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022846.1	NM_014652		A	44433055	G	A	44433055	2	1	22	1	0	0	0	0	0	0	0	1	7803	962	34	2		2	IPO13	1	44433055	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	8530	44433055	204817566	124	3025											
CCDC17	149483	hgsc.bcm.edu	37	chr1	46086588	46086588	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cactcacctgaggaatcccaTtcagctgcccaaggctaagg	11	7	9	14	0	2	1	2	1	0	0	3	2	3	2	3	3	2	2	3	3	3	2	rs16832629	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:46086588T>C	ENST00000528266.1	-	11	1733	c.1586A>G	c.(1585-1587)aAt>aGt	p.N529S	CCDC17_ENST00000343901.2_Missense_Mutation_p.N497S|CCDC17_ENST00000445048.2_Intron|CCDC17_ENST00000421127.2_Missense_Mutation_p.N520S|CCDC17_ENST00000464739.1_5'Flank			Q96LX7	CCD17_HUMAN	coiled-coil domain containing 17	529										kidney(1)|large_intestine(1)|lung(1)|ovary(2)	5	Acute lymphoblastic leukemia(166;0.155)					AGGAATCCCATTCAGCTGCCC	0.577													T|||	32	0.00638978	0.0227	0.0029	5008	,	,		22169	0.0		0.0	False		,,,				2504	0.0				p.N529S		Atlas-SNP	.											.	CCDC17	54	.	0			c.A1586G						PASS	.	T	SER/ASN,SER/ASN	81,4325	68.7+/-106.4	0,81,2122	49	44	46		1586,1559	4.8	0.8	1	dbSNP_123	46	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	CCDC17	NM_001114938.2,NM_001190182.1	46,46	0,82,6421	CC,CT,TT		0.0116,1.8384,0.6305	probably-damaging,probably-damaging	529/623,520/614	46086588	82,12924	2203	4300	6503	SO:0001583	missense	149483	exon11			ATCCCATTCAGCT		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.1586A>G	1.37:g.46086588T>C	ENSP00000432172:p.Asn529Ser	128	0	0		140	57	0.407143	NM_001114938	A1A4Y7|B4DNX7|B4E1Q5|C9J8L2|Q0P683|Q5T629	Missense_Mutation	SNP	ENST00000528266.1	37	CCDS44131.2	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	T	20.8	4.050511	0.75960	0.018384	1.16E-4	ENSG00000159588	ENST00000421127;ENST00000343901;ENST00000528266	T;T;T	0.48201	0.82;0.82;0.82	5.92	4.77	0.60923	.	0.130657	0.52532	D	0.000077	T	0.49389	0.1554	M	0.71581	2.175	0.36900	D	0.890378	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.70227	0.954;0.968;0.954	T	0.68492	-0.5394	10	0.87932	D	0	-5.1285	11.5274	0.50588	0.1344:0.0:0.0:0.8656	rs16832629	529;520;497	Q96LX7;Q96LX7-5;F2Z395	CCD17_HUMAN;.;.	S	520;497;529	ENSP00000389415:N520S;ENSP00000341451:N497S;ENSP00000432172:N529S	ENSP00000341451:N497S	N	-	2	0	CCDC17	45859175	0.991000	0.36638	0.794000	0.32065	0.951000	0.60555	2.283000	0.43470	1.021000	0.39600	0.533000	0.62120	AAT	T|0.993;C|0.007	0.007	strong		0.577	CCDC17-008	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386833.1	NM_152500		C	46086588	T	C	46086588	3	2	22	1	0	0	0	0	1	0	0	0	2795	1493	52	3	294	3	CCDC17	1	46086588	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1653533	46086588	203164033	125	3026											
MAST2	23139	hgsc.bcm.edu	37	chr1	46496368	46496368	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgagtgaggagaaggaggaCcattcagatggcctggcagg	11	6	17	7	0	1	4	1	2	0	2	1	7	1	6	2	6	0	1	2	6	1	1	rs376559790		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:46496368C>T	ENST00000361297.2	+	22	2926	c.2643C>T	c.(2641-2643)gaC>gaT	p.D881D	MAST2_ENST00000372009.2_Silent_p.D811D	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)					AGAAGGAGGACCATTCAGATG	0.642																																					p.D881D		Atlas-SNP	.											.	MAST2	136	.	0			c.C2643T						PASS	.						21	24	23					1																	46496368		2045	4187	6232	SO:0001819	synonymous_variant	23139	exon22			GGAGGACCATTCA	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.2643C>T	1.37:g.46496368C>T		117	0	0		119	5	0.0420168	NM_015112		Silent	SNP	ENST00000361297.2	37	CCDS41326.1																																																																																			.	.	none		0.642	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112		T	46496368	C	T	46496368	2	4	22	1	0	0	0	0	0	0	0	1	9334	506	18	2		2	MAST2	1	46496368	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	409780	46496368	202754253	126	3027											
UQCRH	7388	hgsc.bcm.edu	37	chr1	46775856	46775856	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acaacagtgagagagcaatgCgagcagttggagaaatgtgt	15	7	14	5	1	0	3	0	1	0	2	0	6	0	3	0	1	4	3	0	1	3	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:46775856C>A	ENST00000311672.5	+	3	247	c.111C>A	c.(109-111)tgC>tgA	p.C37*		NM_001089591.1|NM_006004.2	NP_001083060.1|NP_005995.2	P07919	QCR6_HUMAN	ubiquinol-cytochrome c reductase hinge protein	37					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)					GAGAGCAATGCGAGCAGTTGG	0.468																																					p.C37X		Atlas-SNP	.											.	UQCRH	4	.	0			c.C111A						PASS	.						84	85	85					1																	46775856		2203	4300	6503	SO:0001587	stop_gained	7388	exon3			GCAATGCGAGCAG	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.111C>A	1.37:g.46775856C>A	ENSP00000309565:p.Cys37*	182	0	0		193	100	0.518135	NM_006004	B2R4V9|D3DQ18|Q5TDF6|Q6LDB8|Q9BQ91	Nonsense_Mutation	SNP	ENST00000311672.5	37	CCDS30704.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.424984	0.83667	.	.	ENSG00000173660	ENST00000311672	.	.	.	5.23	0.0755	0.14399	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.1407	9.4087	0.38477	0.0:0.3877:0.0:0.6123	.	.	.	.	X	37	.	ENSP00000309565:C37X	C	+	3	2	UQCRH	46548443	0.816000	0.29132	0.998000	0.56505	0.997000	0.91878	-0.075000	0.11431	0.135000	0.18707	0.655000	0.94253	TGC	.	.	none		0.468	UQCRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021451.1	NM_006004		A	46775856	C	A	46775856	4	1	22	1	0	0	0	0	0	1	0	0	17037	776	27	4	121	4	UQCRH	1	46775856	Nonsense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	279488	46775856	202474765	127	3028											
FAAH	2166	hgsc.bcm.edu	37	chr1	46874246	46874246	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caaacagagccttgaggctgCggggcacacggtatgactgc	10	6	14	11	2	0	3	0	2	0	1	0	3	0	3	1	4	4	3	1	4	2	2	rs77101686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:46874246C>T	ENST00000243167.8	+	8	1151	c.1067C>T	c.(1066-1068)gCg>gTg	p.A356V	FAAH_ENST00000493735.1_3'UTR	NM_001441.2	NP_001432.2	O00519	FAAH1_HUMAN	fatty acid amide hydrolase	356					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)	CTTGAGGCTGCGGGGCACACG	0.617													C|||	42	0.00838658	0.0076	0.0	5008	,	,		20191	0.0159		0.0	False		,,,				2504	0.0164				p.A356V		Atlas-SNP	.											FAAH,colon,carcinoma,-1,1	FAAH	36	1	0			c.C1067T						scavenged	.	C	VAL/ALA	8,4398	15.5+/-35.6	0,8,2195	152	156	155		1067	5.4	1	1	dbSNP_131	155	4,8596	3.7+/-12.6	0,4,4296	yes	missense	FAAH	NM_001441.2	64	0,12,6491	TT,TC,CC		0.0465,0.1816,0.0923	probably-damaging	356/580	46874246	12,12994	2203	4300	6503	SO:0001583	missense	2166	exon8			AGGCTGCGGGGCA	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.1067C>T	1.37:g.46874246C>T	ENSP00000243167:p.Ala356Val	59	1	0.0169492		68	43	0.632353	NM_001441	D3DQ19|Q52M86|Q5TDF8	Missense_Mutation	SNP	ENST00000243167.8	37	CCDS535.1	12	0.005494505494505495	1	0.0020325203252032522	0	0.0	11	0.019230769230769232	0	0.0	C	31	5.097033	0.94197	0.001816	4.65E-4	ENSG00000117480	ENST00000243167;ENST00000396325	T	0.56776	0.44	5.4	5.4	0.78164	Amidase signature domain (2);	0.000000	0.85682	D	0.000000	T	0.65238	0.2672	M	0.90425	3.115	0.80722	D	1	D	0.89917	1.0	D	0.65573	0.936	T	0.79065	-0.1956	10	0.87932	D	0	0.6812	19.1897	0.93660	0.0:1.0:0.0:0.0	.	356	O00519	FAAH1_HUMAN	V	356;63	ENSP00000243167:A356V	ENSP00000243167:A356V	A	+	2	0	FAAH	46646833	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.585000	0.67497	2.548000	0.85928	0.655000	0.94253	GCG	C|0.998;T|0.002	0.002	strong		0.617	FAAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021443.1	NM_001441		T	46874246	C	T	46874246	3	4	22	1	0	0	0	0	1	0	0	0	5358	768	27	1	1097	1	FAAH	1	46874246	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	98390	46874246	202376375	128	3029											
FAAH	2166	hgsc.bcm.edu	37	chr1	46876488	46876488	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcgtctgtcctgtgcagctGccaaggctgtcagctttcct	4	13	11	13	1	2	0	1	0	1	0	4	0	4	0	3	1	5	4	3	1	1	1	rs74783386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:46876488G>C	ENST00000243167.8	+	11	1362	c.1278G>C	c.(1276-1278)ctG>ctC	p.L426L		NM_001441.2	NP_001432.2	O00519	FAAH1_HUMAN	fatty acid amide hydrolase	426					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)	CTGTGCAGCTGCCAAGGCTGT	0.617													C|||	42	0.00838658	0.0076	0.0	5008	,	,		18450	0.0159		0.0	False		,,,				2504	0.0164				p.L426L		Atlas-SNP	.											.	FAAH	36	.	0			c.G1278C						PASS	.	C		8,4398	825.1+/-416.5	0,8,2195	93	80	84		1278	1.2	1	1	dbSNP_131	84	4,8596	819.0+/-406.8	0,4,4296	no	coding-synonymous	FAAH	NM_001441.2		0,12,6491	CC,CG,GG		0.0465,0.1816,0.0923		426/580	46876488	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	2166	exon11			GCAGCTGCCAAGG	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.1278G>C	1.37:g.46876488G>C		168	0	0		176	80	0.454545	NM_001441	D3DQ19|Q52M86|Q5TDF8	Silent	SNP	ENST00000243167.8	37	CCDS535.1																																																																																			G|0.998;C|0.002	0.002	strong		0.617	FAAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021443.1	NM_001441		C	46876488	G	C	46876488	2	2	22	1	0	0	0	0	0	0	0	1	5358	1306	46	4		4	FAAH	1	46876488	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2242	46876488	202374133	129	3030											
FAAH	2166	hgsc.bcm.edu	37	chr1	46877885	46877885	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggtgctgacccccatgctggCccctgctctggacttgaatg	5	10	12	14	0	1	2	0	2	1	0	1	3	1	3	4	3	3	3	4	3	1	1	rs75429705	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:46877885C>G	ENST00000243167.8	+	13	1511	c.1427C>G	c.(1426-1428)gCc>gGc	p.A476G		NM_001441.2	NP_001432.2	O00519	FAAH1_HUMAN	fatty acid amide hydrolase	476					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)	CCCATGCTGGCCCCTGCTCTG	0.637													G|||	43	0.00858626	0.0076	0.0	5008	,	,		17547	0.0169		0.0	False		,,,				2504	0.0164				p.A476G		Atlas-SNP	.											.	FAAH	36	.	0			c.C1427G						PASS	.	G	GLY/ALA	6,4354		0,6,2174	73	72	72		1427	4.7	1	1	dbSNP_131	72	4,8536		0,4,4266	no	missense	FAAH	NM_001441.2	60	0,10,6440	GG,GC,CC		0.0468,0.1376,0.0775	benign	476/580	46877885	10,12890	2180	4270	6450	SO:0001583	missense	2166	exon13			TGCTGGCCCCTGC	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.1427C>G	1.37:g.46877885C>G	ENSP00000243167:p.Ala476Gly	207	1	0.00483092		196	107	0.545918	NM_001441	D3DQ19|Q52M86|Q5TDF8	Missense_Mutation	SNP	ENST00000243167.8	37	CCDS535.1	12	0.005494505494505495	1	0.0020325203252032522	0	0.0	11	0.019230769230769232	0	0.0	G	6.661	0.490412	0.12702	0.001376	4.68E-4	ENSG00000117480	ENST00000243167	T	0.64991	-0.13	4.66	4.66	0.58398	Amidase signature domain (2);	0.120287	0.56097	N	0.000022	T	0.22085	0.0532	N	0.04297	-0.235	0.21105	N	0.999789	B	0.02656	0.0	B	0.01281	0.0	T	0.04537	-1.0944	10	0.08599	T	0.76	-24.7092	15.0542	0.71901	0.0:0.1428:0.8572:0.0	.	476	O00519	FAAH1_HUMAN	G	476	ENSP00000243167:A476G	ENSP00000243167:A476G	A	+	2	0	FAAH	46650472	1.000000	0.71417	1.000000	0.80357	0.361000	0.29550	6.705000	0.74644	1.203000	0.43233	-0.120000	0.15030	GCC	C|0.997;G|0.003	0.003	strong		0.637	FAAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021443.1	NM_001441		G	46877885	C	G	46877885	3	3	22	1	0	0	0	0	1	0	0	0	5358	739	26	4	1477	4	FAAH	1	46877885	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1397	46877885	202372736	130	3031											
CYP4B1	1580	hgsc.bcm.edu	37	chr1	47283814	47283814	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccttcaggtctttgactcTctgcgcttttccactgagaa	6	15	7	13	1	3	2	1	2	2	1	6	3	5	2	2	1	1	1	2	1	1	4	rs74072926	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:47283814T>C	ENST00000271153.4	+	11	1317	c.1281T>C	c.(1279-1281)tcT>tcC	p.S427S	CYP4B1_ENST00000371923.4_Silent_p.S428S|CYP4B1_ENST00000452782.2_Silent_p.S265S|CYP4B1_ENST00000371919.4_Silent_p.S413S			P13584	CP4B1_HUMAN	cytochrome P450, family 4, subfamily B, polypeptide 1	427					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)	TCTTTGACTCTCTGCGCTTTT	0.577													T|||	24	0.00479233	0.0166	0.0029	5008	,	,		20927	0.0		0.0	False		,,,				2504	0.0				p.S428S		Atlas-SNP	.											CYP4B1,bladder,carcinoma,+1,2	CYP4B1	81	2	0			c.T1284C						PASS	.	T	,	36,4370	42.3+/-75.8	0,36,2167	147	136	140		1281,1284	-4.7	0.8	1	dbSNP_130	140	2,8598	3.0+/-9.4	0,2,4298	no	coding-synonymous,coding-synonymous	CYP4B1	NM_000779.3,NM_001099772.1	,	0,38,6465	CC,CT,TT		0.0233,0.8171,0.2922	,	427/512,428/513	47283814	38,12968	2203	4300	6503	SO:0001819	synonymous_variant	1580	exon11			TGACTCTCTGCGC	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.1281T>C	1.37:g.47283814T>C		202	0	0		187	95	0.508021	NM_001099772	Q1HBI2|Q8TD85|Q8WWF2|Q8WWU9|Q8WWV0	Silent	SNP	ENST00000271153.4	37	CCDS542.1																																																																																			T|0.995;C|0.005	0.005	strong		0.577	CYP4B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021911.1	NM_000779		C	47283814	T	C	47283814	2	2	22	1	0	0	0	0	0	0	0	1	4187	1538	54	3		3	CYP4B1	1	47283814	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	405929	47283814	201966807	131	3032											
CYP4A22	284541	hgsc.bcm.edu	37	chr1	47603338	47603338	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctccctcccactggctcttcGggcacatccaggaggtaggg	6	8	12	15	1	1	0	0	0	1	0	5	1	4	1	3	5	0	3	3	5	1	2	rs112604161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:47603338G>A	ENST00000371891.3	+	1	212	c.181G>A	c.(181-183)Ggg>Agg	p.G61R	CYP4A22_ENST00000294337.3_Missense_Mutation_p.G61R|CYP4A22_ENST00000485117.1_3'UTR|CYP4A22_ENST00000371890.3_Missense_Mutation_p.G61R|CYP4A22-AS1_ENST00000444042.2_lincRNA	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	61						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						CTGGCTCTTCGGGCACATCCA	0.602													G|||	54	0.0107827	0.0378	0.0014	5008	,	,		19903	0.0		0.003	False		,,,				2504	0.0				p.G61R	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											.	CYP4A22	60	.	0			c.G181A						PASS	.	G	ARG/GLY	153,4253	102.5+/-141.1	4,145,2054	46	40	42		181	2.5	0	1	dbSNP_132	42	1,8599	1.2+/-3.3	0,1,4299	no	missense	CYP4A22	NM_001010969.2	125	4,146,6353	AA,AG,GG		0.0116,3.4725,1.1841	probably-damaging	61/520	47603338	154,12852	2203	4300	6503	SO:0001583	missense	284541	exon1			CTCTTCGGGCACA		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.181G>A	1.37:g.47603338G>A	ENSP00000360958:p.Gly61Arg	110	0	0		171	82	0.479532	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Missense_Mutation	SNP	ENST00000371891.3	37	CCDS30707.1	21	0.009615384615384616	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	g	17.36	3.368930	0.61624	0.034725	1.16E-4	ENSG00000162365	ENST00000371890;ENST00000371891;ENST00000294337	T;T;T	0.78481	-1.08;-1.18;-1.18	2.47	2.47	0.30058	.	0.000000	0.85682	D	0.000000	T	0.75474	0.3854	H	0.96460	3.825	0.53005	D	0.999967	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.86371	0.1723	10	0.87932	D	0	.	13.1509	0.59488	0.0:0.0:1.0:0.0	.	61;61	Q5TCH5;Q5TCH4	.;CP4AM_HUMAN	R	61	ENSP00000360957:G61R;ENSP00000360958:G61R;ENSP00000294337:G61R	ENSP00000294337:G61R	G	+	1	0	CYP4A22	47375925	1.000000	0.71417	0.009000	0.14445	0.114000	0.19823	4.707000	0.61852	1.071000	0.40834	0.205000	0.17691	GGG	G|0.987;A|0.013	0.013	strong		0.602	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213		A	47603338	G	A	47603338	3	1	22	1	0	0	0	0	1	0	0	0	4186	1116	39	1	183	1	CYP4A22	1	47603338	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	319524	47603338	201647283	132	3033											
SLC5A9	200010	hgsc.bcm.edu	37	chr1	48697713	48697713	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaccacctgtcacctcccaCggcccgatgctttccacatt	8	9	5	19	2	1	0	1	0	0	0	3	1	3	0	6	1	1	1	6	1	0	2	rs140292897	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:48697713C>T	ENST00000438567.2	+	7	839	c.787C>T	c.(787-789)Cgg>Tgg	p.R263W	SLC5A9_ENST00000236495.5_Missense_Mutation_p.R288W|SLC5A9_ENST00000420136.2_Intron|SLC5A9_ENST00000533824.1_Missense_Mutation_p.R284W|RP5-1024N4.4_ENST00000606809.1_RNA	NM_001011547.2	NP_001011547.2	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 9	263					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						TCACCTCCCACGGCCCGATGC	0.617													C|||	7	0.00139776	0.0045	0.0	5008	,	,		20299	0.0		0.001	False		,,,				2504	0.0				p.R288W		Atlas-SNP	.											.	SLC5A9	82	.	0			c.C862T						PASS	.	C	TRP/ARG,TRP/ARG	27,4379	34.3+/-65.2	0,27,2176	124	113	117		787,862	5	0.8	1	dbSNP_134	117	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	SLC5A9	NM_001011547.2,NM_001135181.1	101,101	0,30,6473	TT,TC,CC		0.0349,0.6128,0.2307	probably-damaging,probably-damaging	263/682,288/707	48697713	30,12976	2203	4300	6503	SO:0001583	missense	200010	exon8			CTCCCACGGCCCG	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.787C>T	1.37:g.48697713C>T	ENSP00000401730:p.Arg263Trp	248	0	0		233	232	0.995708	NM_001135181	B3KY87|B7ZL45|B7ZL47|E9PAK4|E9PJ08|Q5TET3	Missense_Mutation	SNP	ENST00000438567.2	37	CCDS30709.2	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	28.2	4.897309	0.91962	0.006128	3.49E-4	ENSG00000117834	ENST00000533824;ENST00000438567;ENST00000236495	D;D;D	0.89415	-2.46;-2.44;-2.51	5.95	5.02	0.67125	.	0.000000	0.85682	D	0.000000	D	0.94401	0.8199	M	0.93420	3.415	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.94931	0.8082	10	0.87932	D	0	.	15.4795	0.75514	0.1395:0.8605:0.0:0.0	.	284;263;288	E9PJ08;Q2M3M2;E9PAK4	.;SC5A9_HUMAN;.	W	284;263;288	ENSP00000431900:R284W;ENSP00000401730:R263W;ENSP00000236495:R288W	ENSP00000236495:R288W	R	+	1	2	SLC5A9	48470300	0.998000	0.40836	0.828000	0.32881	0.985000	0.73830	3.906000	0.56340	1.485000	0.48380	0.563000	0.77884	CGG	C|0.998;T|0.002	0.002	strong		0.617	SLC5A9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022061.3	XM_117174		T	48697713	C	T	48697713	3	4	22	1	0	0	0	0	1	0	0	0	14687	527	19	1	892	1	SLC5A9	1	48697713	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1094375	48697713	200552908	133	3034											
AGBL4	84871	hgsc.bcm.edu	37	chr1	49005351	49005351	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aattgccaccttttcaaccaCggggttcagccgataatagt	11	11	8	11	2	2	0	2	0	0	0	2	1	2	0	4	2	3	1	4	2	4	6	rs60977321	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:49005351C>T	ENST00000371839.1	-	12	1443	c.1327G>A	c.(1327-1329)Gtg>Atg	p.V443M	AGBL4_ENST00000334103.7_Missense_Mutation_p.V176M	NM_032785.3	NP_116174.3	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4	443			V -> M (in dbSNP:rs60977321).		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)		TTTTCAACCACGGGGTTCAGC	0.512													C|||	322	0.0642971	0.233	0.0144	5008	,	,		17535	0.0		0.004	False		,,,				2504	0.0				p.V443M		Atlas-SNP	.											.	AGBL4	54	.	0			c.G1327A						PASS	.	C	MET/VAL	287,1097		31,225,436	134	111	118		1327	-2.2	1	1	dbSNP_129	118	4,3178		0,4,1587	yes	missense	AGBL4	NM_032785.3	21	31,229,2023	TT,TC,CC		0.1257,20.737,6.3732	benign	443/504	49005351	291,4275	692	1591	2283	SO:0001583	missense	84871	exon12			CAACCACGGGGTT	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.1327G>A	1.37:g.49005351C>T	ENSP00000360905:p.Val443Met	109	0	0		129	57	0.44186	NM_032785	B3KT26|B4DG37	Missense_Mutation	SNP	ENST00000371839.1	37	CCDS44137.1	103	0.04716117216117216	100	0.2032520325203252	3	0.008287292817679558	0	0.0	0	0.0	C	4.542	0.100554	0.08731	0.20737	0.001257	ENSG00000186094	ENST00000371839;ENST00000411952;ENST00000334103	T;T	0.44881	2.53;0.91	4.65	-2.18	0.07037	.	2.280690	0.01719	N	0.028181	T	0.00012	0.0000	N	0.08118	0	0.52099	P	5.3999999999998494E-5	B;B;B	0.19583	0.0;0.002;0.037	B;B;B	0.08055	0.0;0.001;0.003	T	0.12863	-1.0531	9	0.25751	T	0.34	-0.0068	1.605	0.02682	0.2303:0.0994:0.4078:0.2624	rs60977321	455;176;443	Q5VU57-2;B4DGK1;Q5VU57	.;.;CBPC6_HUMAN	M	443;437;176	ENSP00000360905:V443M;ENSP00000335516:V176M	ENSP00000335516:V176M	V	-	1	0	AGBL4	48777938	0.020000	0.18652	0.992000	0.48379	0.242000	0.25591	-1.494000	0.02296	-0.194000	0.10399	-1.708000	0.00717	GTG	C|0.961;T|0.039	0.039	strong		0.512	AGBL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021346.4	NM_032785		T	49005351	C	T	49005351	3	4	22	1	0	0	0	0	1	0	0	0	377	536	19	1	196	1	AGBL4	1	49005351	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	307638	49005351	200245270	134	3035											
ZFYVE9	9372	hgsc.bcm.edu	37	chr1	52705174	52705174	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgggtgaggtggctccagtAtgggtaccggattctcaggc	6	10	16	9	1	1	1	1	1	1	0	3	2	2	2	2	6	1	3	2	6	2	3	rs34437486	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:52705174A>G	ENST00000371591.1	+	3	2216	c.2085A>G	c.(2083-2085)gtA>gtG	p.V695V	ZFYVE9_ENST00000357206.2_Silent_p.V695V|ZFYVE9_ENST00000287727.3_Silent_p.V695V	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	695					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						TGGCTCCAGTATGGGTACCGG	0.478													A|||	30	0.00599042	0.0227	0.0	5008	,	,		18368	0.0		0.0	False		,,,				2504	0.0				p.V695V		Atlas-SNP	.											.	ZFYVE9	131	.	0			c.A2085G						PASS	.	A	,,	126,4280	93.0+/-131.7	1,124,2078	71	69	70		2085,2085,2085	-7.1	0.7	1	dbSNP_126	70	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	ZFYVE9	NM_004799.2,NM_007323.1,NM_007324.2	,,	1,125,6377	GG,GA,AA		0.0116,2.8597,0.9765	,,	695/1426,695/763,695/1367	52705174	127,12879	2203	4300	6503	SO:0001819	synonymous_variant	9372	exon4			TCCAGTATGGGTA	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.2085A>G	1.37:g.52705174A>G		140	0	0		154	70	0.454545	NM_007323	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Silent	SNP	ENST00000371591.1	37	CCDS563.1																																																																																			A|0.991;G|0.009	0.009	strong		0.478	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324		G	52705174	A	G	52705174	2	3	22	1	0	0	0	0	0	0	0	1	17686	436	16	3		3	ZFYVE9	1	52705174	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	3699823	52705174	196545447	135	3036											
FAM159A	348378	hgsc.bcm.edu	37	chr1	53099242	53099242	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cagctgcccgcggccgggggGcgaggcggccgctgtcttct	2	6	18	15	6	2	0	0	0	2	0	2	1	2	0	3	6	2	2	3	6	0	1	rs182623287	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:53099242G>A	ENST00000517870.1	+	1	227	c.77G>A	c.(76-78)gGc>gAc	p.G26D	FAM159A_ENST00000401050.3_3'UTR	NM_001042693.1	NP_001036158.1	Q6UWV7	F159A_HUMAN	family with sequence similarity 159, member A	26						integral component of membrane (GO:0016021)				endometrium(3)|lung(6)|upper_aerodigestive_tract(1)	10						cggccggggggcgaggcggcc	0.716													G|||	5	0.000998403	0.0008	0.0058	5008	,	,		9747	0.0		0.0	False		,,,				2504	0.0				p.G26D		Atlas-SNP	.											.	FAM159A	22	.	0			c.G77A						PASS	.						14	16	16					1																	53099242		1869	4059	5928	SO:0001583	missense	348378	exon1			CGGGGGGCGAGGC		CCDS41336.1	1p32.3	2008-08-08			ENSG00000182183	ENSG00000182183			28757	protein-coding gene	gene with protein product						12477932	Standard	NM_001042693		Approved	MGC52498	uc001cuf.3	Q6UWV7	OTTHUMG00000008330	ENST00000517870.1:c.77G>A	1.37:g.53099242G>A	ENSP00000429726:p.Gly26Asp	41	0	0		46	23	0.5	NM_001042693	Q6ZRG4	Missense_Mutation	SNP	ENST00000517870.1	37	CCDS41336.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	G	12.99	2.103714	0.37145	.	.	ENSG00000182183	ENST00000517870	.	.	.	3.44	3.44	0.39384	.	0.253016	0.29876	U	0.010972	T	0.22666	0.0547	N	0.03608	-0.345	0.36963	D	0.893453	P	0.34639	0.461	B	0.39562	0.303	T	0.23511	-1.0186	9	0.06625	T	0.88	.	15.773	0.78187	0.0:0.0:1.0:0.0	.	26	Q6UWV7	F159A_HUMAN	D	26	.	ENSP00000429726:G26D	G	+	2	0	FAM159A	52871830	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.263000	0.43293	1.860000	0.53959	0.455000	0.32223	GGC	G|0.999;A|0.001	0.001	strong		0.716	FAM159A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022934.2	NM_001042693		A	53099242	G	A	53099242	3	1	22	1	0	0	0	0	1	0	0	0	5473	1203	42	2	79	2	FAM159A	1	53099242	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	394068	53099242	196151379	136	3037											
ZYG11B	79699	hgsc.bcm.edu	37	chr1	53262456	53262456	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	actgagctcttcattgtcagGgtaagtctataatctcctcc	9	14	7	11	0	5	1	2	1	3	0	7	1	6	1	2	1	1	2	2	1	3	5	rs11206020	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:53262456G>A	ENST00000294353.6	+	8	1630	c.1485G>A	c.(1483-1485)agG>agA	p.R495R	ZYG11B_ENST00000545132.1_Splice_Site_p.R495R|ZYG11B_ENST00000443756.2_Splice_Site_p.R495R	NM_024646.2	NP_078922.1	Q9C0D3	ZY11B_HUMAN	zyg-11 family member B, cell cycle regulator	495										breast(1)|endometrium(1)|kidney(6)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	30						TCATTGTCAGGGTAAGTCTAT	0.328													G|||	201	0.0401358	0.1452	0.0115	5008	,	,		10687	0.0		0.001	False		,,,				2504	0.0				p.R495R		Atlas-SNP	.											.	ZYG11B	61	.	0			c.G1485A						PASS	.	G		532,3874	238.7+/-250.0	28,476,1699	136	126	130		1485	2.2	1	1	dbSNP_120	130	6,8594	3.7+/-12.6	0,6,4294	yes	coding-synonymous-near-splice	ZYG11B	NM_024646.2		28,482,5993	AA,AG,GG		0.0698,12.0744,4.1366		495/745	53262456	538,12468	2203	4300	6503	SO:0001630	splice_region_variant	79699	exon8			TGTCAGGGTAAGT	AB051517	CCDS30717.1	1p32.3	2013-01-17	2012-12-10	2005-07-11	ENSG00000162378	ENSG00000162378		"ZYG11 cell cycle regulator family"	25820	protein-coding gene	gene with protein product			"zyg-11 homolog (C. elegans)", "zyg-11 homolog B (C. elegans)"	ZYG11		11214970	Standard	NM_024646		Approved	FLJ13456	uc001cuj.3	Q9C0D3	OTTHUMG00000008938	ENST00000294353.6:c.1485+1G>A	1.37:g.53262456G>A		126	0	0		131	55	0.419847	NM_024646	Q8N2X3|Q9H8L8	Silent	SNP	ENST00000294353.6	37	CCDS30717.1																																																																																			G|0.962;A|0.038	0.038	strong		0.328	ZYG11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024749.1	NM_024646	Silent	A	53262456	G	A	53262456	5	1	22	1	0	0	0	0	0	0	1	0	18268	1246	43	2	1515	2	ZYG11B	1	53262456	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	163214	53262456	195988165	137	3038											
PODN	127435	hgsc.bcm.edu	37	chr1	53544271	53544271	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcctcaagcggttgcacacGgtgcacctgtacaacaacgc	10	6	11	14	3	1	0	1	0	0	0	1	0	1	0	2	3	6	4	2	3	4	2	rs62000444	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:53544271G>C	ENST00000312553.5	+	8	1240	c.1233G>C	c.(1231-1233)acG>acC	p.T411T	PODN_ENST00000371500.3_Silent_p.T392T|PODN_ENST00000395871.2_Silent_p.T269T|RP11-334A14.5_ENST00000447867.1_RNA	NM_001199081.1|NM_153703.4	NP_001186010.1|NP_714914.2	Q7Z5L7	PODN_HUMAN	podocan	363					negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						GGTTGCACACGGTGCACCTGT	0.662													G|||	54	0.0107827	0.034	0.0115	5008	,	,		19751	0.0		0.001	False		,,,				2504	0.0				p.T411T		Atlas-SNP	.											.	PODN	86	.	0			c.G1233C						PASS	.	G	,,,	95,4311	76.2+/-114.5	1,93,2109	66	61	63		1176,1176,807,1233	-1.9	1	1	dbSNP_129	63	9,8591	6.4+/-24.3	0,9,4291	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PODN	NM_001199080.1,NM_001199081.1,NM_001199082.1,NM_153703.4	,,,	1,102,6400	CC,CG,GG		0.1047,2.1562,0.7996	,,,	392/643,392/643,269/520,411/662	53544271	104,12902	2203	4300	6503	SO:0001819	synonymous_variant	127435	exon8			GCACACGGTGCAC	AY313607	CCDS573.1, CCDS55601.1, CCDS55602.1	1p32.3	2008-02-05			ENSG00000174348	ENSG00000174348		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	23174	protein-coding gene	gene with protein product	"podocan proteoglycan"	608661					Standard	NM_153703		Approved	PCAN, PODOCAN, MGC24995, SLRR5A	uc010onr.2	Q7Z5L7	OTTHUMG00000008934	ENST00000312553.5:c.1233G>C	1.37:g.53544271G>C		97	0	0		120	61	0.508333	NM_153703	B4DKN5|B4E373|Q5VVZ2|Q5VVZ3|Q6PIR3|Q6UXL8|Q8N641	Silent	SNP	ENST00000312553.5	37	CCDS573.1																																																																																			G|0.992;C|0.008	0.008	strong		0.662	PODN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024735.1	NM_153703		C	53544271	G	C	53544271	2	2	22	1	0	0	0	0	0	0	0	1	12187	1103	39	4		4	PODN	1	53544271	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	281815	53544271	195706350	138	3039											
GLIS1	148979	hgsc.bcm.edu	37	chr1	54060107	54060107	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gccctgctggtgaggcccaaAgagctctgaaaactcatccg	10	7	11	13	1	2	3	1	2	1	1	3	3	3	3	3	2	3	2	3	2	3	0	rs34961060	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:54060107A>G	ENST00000312233.2	-	3	1035	c.469T>C	c.(469-471)Ttt>Ctt	p.F157L		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						TGAGGCCCAAAGAGCTCTGAA	0.657													A|||	183	0.0365415	0.1362	0.0029	5008	,	,		14987	0.0		0.001	False		,,,				2504	0.0				p.F157L		Atlas-SNP	.											.	GLIS1	52	.	0			c.T469C						PASS	.	A	LEU/PHE	429,3963		23,383,1790	15	18	17		469	2.4	0.8	1	dbSNP_126	17	4,8562		0,4,4279	yes	missense	GLIS1	NM_147193.2	22	23,387,6069	GG,GA,AA		0.0467,9.7678,3.3416	possibly-damaging	157/621	54060107	433,12525	2196	4283	6479	SO:0001583	missense	148979	exon3			GCCCAAAGAGCTC	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.469T>C	1.37:g.54060107A>G	ENSP00000309653:p.Phe157Leu	68	0	0		63	31	0.492063	NM_147193		Missense_Mutation	SNP	ENST00000312233.2	37	CCDS582.1	79	0.036172161172161175	77	0.1565040650406504	2	0.0055248618784530384	0	0.0	0	0.0	A	16.69	3.192807	0.58017	0.097678	4.67E-4	ENSG00000174332	ENST00000312233	T	0.10573	2.86	5.07	2.43	0.29744	.	0.105911	0.41605	N	0.000847	T	0.00039	0.0001	L	0.29908	0.895	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.39313	-0.9620	9	0.02654	T	1	.	7.8454	0.29422	0.7801:0.0:0.2199:0.0	rs34961060	157	Q8NBF1	GLIS1_HUMAN	L	157	ENSP00000309653:F157L	ENSP00000309653:F157L	F	-	1	0	GLIS1	53832695	1.000000	0.71417	0.814000	0.32528	0.822000	0.46500	2.049000	0.41288	0.888000	0.36160	0.379000	0.24179	TTT	A|0.968;G|0.032	0.032	strong		0.657	GLIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022109.1	NM_147193		G	54060107	A	G	54060107	3	3	22	1	0	0	0	0	1	0	0	0	6453	72	3	3	1425	3	GLIS1	1	54060107	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	515836	54060107	195190514	139	3040											
CDCP2	200008	hgsc.bcm.edu	37	chr1	54610404	54610405	+	Frame_Shift_Del	DEL	TG	TG	-																															acgatcagccagctgcactcTgtgttgtaggggtacagtct																								rs558673127	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:54610404_54610405delTG	ENST00000371330.1	-	2	1008_1009	c.161_162delCA	c.(160-162)acafs	p.T54fs	RP11-446E24.4_ENST00000525949.1_5'UTR|RP11-446E24.4_ENST00000311841.7_3'UTR	NM_201546.2	NP_963840.2	Q5VXM1	CDCP2_HUMAN	CUB domain containing protein 2	54	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.					extracellular region (GO:0005576)				kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|stomach(1)	24						AGCTGCACTCTGTGTTGTAGGG	0.559														3	0.000599042	0.0015	0.0014	5008	,	,		20392	0.0		0.0	False		,,,				2504	0.0				p.54_55del		Pindel,Atlas-Indel	.											.	CDCP2	52	.	0			c.162_163del						PASS	.			66,4200		31,4,2098						4.5	1			74	145,8109		72,1,4054	no	frameshift	CDCP2	NM_201546.2		103,5,6152	A1A1,A1R,RR		1.7567,1.5471,1.6853				211,12309				SO:0001589	frameshift_variant	200008	exon2			.		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.161_162delCA	1.37:g.54610406_54610407delTG	ENSP00000360381:p.Thr54fs	138	0	.		119	33	0.277	NM_201546	Q6ZWJ3	Frame_Shift_Del	DEL	ENST00000371330.1	37	CCDS588.2																																																																																			.	.	none		0.559	CDCP2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000022209.2	NM_201546		-	54610405	TG	-	54610404	7	5	22	1	0	1	0	1	0	0	0	0	3096	1567	55	0	1199	0	CDCP2	1	54610404	Frame_Shift_Del	DEL	TG	TCGA-G8-6324-01A-11D-2210-10	550297	54610404	194640217	140	3041											
SSBP3	23648	hgsc.bcm.edu	37	chr1	54747176	54747176	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggggaatgttgccaagcaCggggctcggggcagctgctg	6	6	20	9	2	0	0	0	0	0	0	1	1	0	1	1	7	4	6	1	7	2	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:54747176C>T	ENST00000371320.3	-	5	711	c.301G>A	c.(301-303)Gtg>Atg	p.V101M	SSBP3_ENST00000417664.2_De_novo_Start_InFrame|SSBP3_ENST00000371319.3_Missense_Mutation_p.V101M|SSBP3_ENST00000357475.4_Missense_Mutation_p.V101M|SSBP3_ENST00000326956.7_5'UTR	NM_145716.2	NP_663768.1	Q9BWW4	SSBP3_HUMAN	single stranded DNA binding protein 3	101	Pro-rich.				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						TTGCCAAGCACGGGGCTCGGG	0.617																																					p.V101M		Atlas-SNP	.											.	SSBP3	65	.	0			c.G301A						PASS	.						16	15	15					1																	54747176		2194	4286	6480	SO:0001583	missense	23648	exon5			CAAGCACGGGGCT		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.301G>A	1.37:g.54747176C>T	ENSP00000360371:p.Val101Met	80	0	0		105	35	0.333333	NM_145716	A8K0A9|Q5T860|Q5T861|Q9BTM0|Q9BWW3	Missense_Mutation	SNP	ENST00000371320.3	37	CCDS591.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.555184	0.86231	.	.	ENSG00000157216	ENST00000371320;ENST00000371319;ENST00000357475	.	.	.	4.83	4.83	0.62350	.	0.000000	0.64402	U	0.000001	T	0.77818	0.4187	M	0.68317	2.08	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.80764	0.994;0.981;0.973	T	0.78311	-0.2253	9	0.46703	T	0.11	-0.63	18.3318	0.90271	0.0:1.0:0.0:0.0	.	101;101;101	Q9BWW4-2;Q9BWW4-3;Q9BWW4	.;.;SSBP3_HUMAN	M	101	.	ENSP00000350067:V101M	V	-	1	0	SSBP3	54519764	1.000000	0.71417	0.977000	0.42913	0.991000	0.79684	7.369000	0.79578	2.409000	0.81822	0.563000	0.77884	GTG	.	.	none		0.617	SSBP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022721.1	NM_018070		T	54747176	C	T	54747176	3	4	22	1	0	0	0	0	1	0	0	0	15196	536	19	1	921	1	SSBP3	1	54747176	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	136772	54747176	194503445	141	3042											
ACOT11	26027	hgsc.bcm.edu	37	chr1	55073630	55073630	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctcagggacccctatgtcatCgcgctgaggtcggtcacgct	6	9	12	14	4	3	1	3	1	0	0	5	2	3	2	2	3	0	2	2	3	1	1	rs78753605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55073630C>T	ENST00000371316.3	+	15	1600	c.1518C>T	c.(1516-1518)atC>atT	p.I506I	ACOT11_ENST00000343744.2_Silent_p.I506I|ACOT11_ENST00000481208.1_3'UTR	NM_015547.3	NP_056362.1	Q8WXI4	ACO11_HUMAN	acyl-CoA thioesterase 11	506	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				fatty acid metabolic process (GO:0006631)|intracellular signal transduction (GO:0035556)|response to cold (GO:0009409)|response to temperature stimulus (GO:0009266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|lipid binding (GO:0008289)			NS(1)|central_nervous_system(1)|endometrium(6)|large_intestine(3)|lung(5)|ovary(1)	17						CCTATGTCATCGCGCTGAGGT	0.642													C|||	83	0.0165735	0.0605	0.0029	5008	,	,		18552	0.001		0.0	False		,,,				2504	0.0				p.I506I	Ovarian(148;1440 1861 22015 32453 51933)	Atlas-SNP	.											.	ACOT11	105	.	0			c.C1518T						PASS	.	C	,	201,4205	126.6+/-163.6	4,193,2006	93	90	91		1518,1518	-6.9	0.9	1	dbSNP_132	91	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ACOT11	NM_015547.3,NM_147161.3	,	4,194,6305	TT,TC,CC		0.0116,4.562,1.5531	,	506/608,506/595	55073630	202,12804	2203	4300	6503	SO:0001819	synonymous_variant	26027	exon15			TGTCATCGCGCTG	AB014607	CCDS592.1, CCDS593.1	1p32.3	2011-09-13	2005-09-08	2005-09-08	ENSG00000162390	ENSG00000162390	3.1.2.-	"Acyl CoA thioesterases", "StAR-related lipid transfer (START) domain containing"	18156	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 14"	606803	"thioesterase, adipose associated"	THEA		11696000, 16103133, 16940157	Standard	NM_015547		Approved	STARD14, BFIT, KIAA0707, BFIT1, THEM1	uc001cxl.2	Q8WXI4	OTTHUMG00000009891	ENST00000371316.3:c.1518C>T	1.37:g.55073630C>T		165	0	0		157	87	0.55414	NM_147161	B1AQ22|D3DQ50|O75187|Q52LP1|Q53ER9|Q96DI1|Q9H883	Silent	SNP	ENST00000371316.3	37	CCDS592.1																																																																																			C|0.984;T|0.016	0.016	strong		0.642	ACOT11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027356.1	NM_015547		T	55073630	C	T	55073630	2	4	22	1	0	0	0	0	0	0	0	1	149	874	31	1		1	ACOT11	1	55073630	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	326454	55073630	194176991	142	3043											
FAM151A	338094	hgsc.bcm.edu	37	chr1	55075334	55075334	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctctgccagccacatggccGgggaccgaaaaactcccgtg	9	6	11	15	3	1	0	0	0	1	0	3	2	2	1	5	3	3	0	5	3	2	0	rs201640566	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55075334G>A	ENST00000302250.2	-	8	1525	c.1365C>T	c.(1363-1365)ccC>ccT	p.P455P	FAM151A_ENST00000371304.2_Intron|ACOT11_ENST00000371316.3_Intron|ACOT11_ENST00000343744.2_3'UTR|ACOT11_ENST00000481208.1_3'UTR	NM_176782.2	NP_788954.2	Q8WW52	F151A_HUMAN	family with sequence similarity 151, member A	455						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						CCACATGGCCGGGGACCGAAA	0.642													g|||	2	0.000399361	0.0008	0.0014	5008	,	,		18259	0.0		0.0	False		,,,				2504	0.0				p.P455P		Atlas-SNP	.											.	FAM151A	58	.	0			c.C1365T						PASS	.						32	35	34					1																	55075334		2202	4300	6502	SO:0001819	synonymous_variant	338094	exon8			ATGGCCGGGGACC	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.1365C>T	1.37:g.55075334G>A		66	0	0		58	29	0.5	NM_176782	Q5VUG5|Q6DKH5|Q6UWV0|Q8NAX9|Q96KY5	Silent	SNP	ENST00000302250.2	37	CCDS594.1																																																																																			G|1.000;A|0.000	0.000	strong		0.642	FAM151A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027342.1	NM_176782		A	55075334	G	A	55075334	2	1	22	1	0	0	0	0	0	0	0	1	5463	1103	39	1		1	FAM151A	1	55075334	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1704	55075334	194175287	143	3044											
TTC4	7268	hgsc.bcm.edu	37	chr1	55188437	55188437	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tagatgccaaagagaagaagCttctggaaatgagggctaaa	17	7	12	5	0	1	4	0	1	1	3	1	6	1	5	1	2	2	2	1	2	7	3	rs62000412	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55188437C>T	ENST00000371281.3	+	5	646	c.559C>T	c.(559-561)Ctt>Ttt	p.L187F	MROH7-TTC4_ENST00000414150.2_3'UTR|TTC4_ENST00000371284.5_3'UTR	NM_004623.4	NP_004614.3	O95801	TTC4_HUMAN	tetratricopeptide repeat domain 4	187										breast(2)|endometrium(3)|kidney(1)|lung(2)|stomach(1)	9						AGAGAAGAAGCTTCTGGAAAT	0.463													C|||	65	0.0129792	0.0484	0.0014	5008	,	,		20967	0.0		0.0	False		,,,				2504	0.0				p.L187F		Atlas-SNP	.											.	TTC4	21	.	0			c.C559T						PASS	.	C	PHE/LEU	192,4214	121.7+/-159.2	4,184,2015	122	115	117		559	5.4	1	1	dbSNP_129	117	2,8598	2.2+/-6.3	0,2,4298	yes	missense	TTC4	NM_004623.4	22	4,186,6313	TT,TC,CC		0.0233,4.3577,1.4916	probably-damaging	187/388	55188437	194,12812	2203	4300	6503	SO:0001583	missense	7268	exon5			AAGAAGCTTCTGG		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.559C>T	1.37:g.55188437C>T	ENSP00000360329:p.Leu187Phe	102	0	0		85	46	0.541176	NM_004623	Q53Y95|Q5TA96|Q9H3I2	Missense_Mutation	SNP	ENST00000371281.3	37	CCDS596.1	21	0.009615384615384616	21	0.042682926829268296	0	0.0	0	0.0	0	0.0	C	21.3	4.125911	0.77436	0.043577	2.33E-4	ENSG00000243725	ENST00000371281;ENST00000371284	T	0.20200	2.09	5.42	5.42	0.78866	Tetratricopeptide-like helical (1);	.	.	.	.	T	0.13841	0.0335	M	0.82716	2.605	0.58432	D	0.999996	P;D	0.64830	0.908;0.994	P;P	0.51945	0.514;0.685	T	0.06320	-1.0833	9	0.48119	T	0.1	-11.5851	18.1602	0.89706	0.0:1.0:0.0:0.0	rs62000412	187;198	O95801;Q5TA95	TTC4_HUMAN;.	F	187;198	ENSP00000360329:L187F	ENSP00000360329:L187F	L	+	1	0	TTC4	54961025	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.354000	0.52254	2.703000	0.92315	0.460000	0.39030	CTT	C|0.986;T|0.014	0.014	strong		0.463	TTC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027432.1	NM_004623		T	55188437	C	T	55188437	3	4	22	1	0	0	0	0	1	0	0	0	16725	797	28	2	577	2	TTC4	1	55188437	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	113103	55188437	194062184	144	3045											
TTC4	7268	hgsc.bcm.edu	37	chr1	55197320	55197320	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agctggcctgtgctctttctGtacccagagtatgcccagtc	6	12	10	13	0	2	1	0	0	2	1	3	1	2	1	3	1	4	4	3	1	2	3	rs1062700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55197320G>A	ENST00000371281.3	+	7	930	c.843G>A	c.(841-843)ctG>ctA	p.L281L	MROH7-TTC4_ENST00000414150.2_3'UTR|TTC4_ENST00000371284.5_3'UTR	NM_004623.4	NP_004614.3	O95801	TTC4_HUMAN	tetratricopeptide repeat domain 4	281										breast(2)|endometrium(3)|kidney(1)|lung(2)|stomach(1)	9						TGCTCTTTCTGTACCCAGAGT	0.557													G|||	248	0.0495208	0.0651	0.0216	5008	,	,		18066	0.004		0.0606	False		,,,				2504	0.0838				p.L281L		Atlas-SNP	.											.	TTC4	21	.	0			c.G843A						PASS	.	G		311,4095	166.5+/-197.7	16,279,1908	79	69	72		843	0.9	1	1	dbSNP_86	72	399,8201	126.8+/-185.2	7,385,3908	no	coding-synonymous	TTC4	NM_004623.4		23,664,5816	AA,AG,GG		4.6395,7.0586,5.459		281/388	55197320	710,12296	2203	4300	6503	SO:0001819	synonymous_variant	7268	exon7			CTTTCTGTACCCA		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.843G>A	1.37:g.55197320G>A		83	0	0		76	29	0.381579	NM_004623	Q53Y95|Q5TA96|Q9H3I2	Silent	SNP	ENST00000371281.3	37	CCDS596.1																																																																																			G|0.946;A|0.054	0.054	strong		0.557	TTC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027432.1	NM_004623		A	55197320	G	A	55197320	2	1	22	1	0	0	0	0	0	0	0	1	16725	1364	48	2		2	TTC4	1	55197320	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	8883	55197320	194053301	145	3046											
C1orf177	163747	hgsc.bcm.edu	37	chr1	55272743	55272743	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggccccatactccacgcgttAttctacccaagtggtgagtt	8	11	9	13	2	1	1	0	1	1	0	2	1	2	1	4	2	2	2	4	2	4	5	rs115158797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55272743A>G	ENST00000371273.3	+	2	194	c.179A>G	c.(178-180)tAt>tGt	p.Y60C	C1orf177_ENST00000358193.3_Missense_Mutation_p.Y60C	NM_001110533.1	NP_001104003	Q3ZCV2	CA177_HUMAN	chromosome 1 open reading frame 177	60										breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(6)|prostate(2)	17						TCCACGCGTTATTCTACCCAA	0.572													A|||	49	0.00978435	0.0363	0.0014	5008	,	,		16140	0.0		0.0	False		,,,				2504	0.0				p.Y60C		Atlas-SNP	.											.	C1orf177	36	.	0			c.A179G						PASS	.	A	CYS/TYR,CYS/TYR	127,4279	93.9+/-132.6	2,123,2078	205	186	192		179,179	1.3	0	1	dbSNP_132	192	0,8600		0,0,4300	yes	missense,missense	C1orf177	NM_001110533.1,NM_152607.2	194,194	2,123,6378	GG,GA,AA		0.0,2.8824,0.9765	possibly-damaging,possibly-damaging	60/419,60/415	55272743	127,12879	2203	4300	6503	SO:0001583	missense	163747	exon2			CGCGTTATTCTAC	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.179A>G	1.37:g.55272743A>G	ENSP00000360320:p.Tyr60Cys	157	0	0		159	78	0.490566	NM_001110533	B7WPL2|Q8N7Y9	Missense_Mutation	SNP	ENST00000371273.3	37	CCDS44153.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	A	10.43	1.348922	0.24426	0.028824	0.0	ENSG00000162398	ENST00000358193;ENST00000371273	T;T	0.26518	1.73;1.73	3.72	1.32	0.21799	.	1.288330	0.05479	N	0.554456	T	0.06462	0.0166	N	0.25647	0.755	0.09310	N	1	D;D	0.57257	0.979;0.979	P;P	0.53313	0.723;0.723	T	0.08249	-1.0731	10	0.39692	T	0.17	.	3.1969	0.06636	0.498:0.0:0.108:0.394	.	60;60	Q3ZCV2;Q3ZCV2-2	CA177_HUMAN;.	C	60	ENSP00000350924:Y60C;ENSP00000360320:Y60C	ENSP00000350924:Y60C	Y	+	2	0	C1orf177	55045331	0.001000	0.12720	0.000000	0.03702	0.013000	0.08279	1.170000	0.31883	0.264000	0.21851	0.379000	0.24179	TAT	A|0.989;G|0.011	0.011	strong		0.572	C1orf177-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027674.1	NM_152607		G	55272743	A	G	55272743	3	3	22	1	0	0	0	0	1	0	0	0	2019	449	16	3	185	3	C1orf177	1	55272743	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	75423	55272743	193977878	146	3047											
C1orf177	163747	hgsc.bcm.edu	37	chr1	55277553	55277553	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctggaaccggtctcattcCgagggcctcatgtgcaggat	7	9	13	12	2	2	0	2	0	1	0	4	3	3	2	4	4	2	1	4	4	1	1	rs61691036	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55277553C>T	ENST00000371273.3	+	5	582	c.567C>T	c.(565-567)tcC>tcT	p.S189S	C1orf177_ENST00000358193.3_Silent_p.S189S	NM_001110533.1	NP_001104003	Q3ZCV2	CA177_HUMAN	chromosome 1 open reading frame 177	189										breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(6)|prostate(2)	17						GGTCTCATTCCGAGGGCCTCA	0.617													C|||	73	0.0145767	0.0522	0.0029	5008	,	,		17175	0.0		0.0	False		,,,				2504	0.002				p.S189S		Atlas-SNP	.											.	C1orf177	36	.	0			c.C567T						PASS	.	C	,	248,4158	145.0+/-179.8	10,228,1965	75	70	71		567,567	-0.4	0.9	1	dbSNP_129	71	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	C1orf177	NM_001110533.1,NM_152607.2	,	10,230,6263	TT,TC,CC		0.0233,5.6287,1.9222	,	189/419,189/415	55277553	250,12756	2203	4300	6503	SO:0001819	synonymous_variant	163747	exon5			TCATTCCGAGGGC	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.567C>T	1.37:g.55277553C>T		142	0	0		214	112	0.523364	NM_001110533	B7WPL2|Q8N7Y9	Silent	SNP	ENST00000371273.3	37	CCDS44153.1																																																																																			C|0.979;T|0.021	0.021	strong		0.617	C1orf177-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027674.1	NM_152607		T	55277553	C	T	55277553	2	4	22	1	0	0	0	0	0	0	0	1	2019	639	23	1		1	C1orf177	1	55277553	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4810	55277553	193973068	147	3048											
USP24	23358	hgsc.bcm.edu	37	chr1	55545240	55545240	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaaggtttcccttcagacaTgaacaacaaggcttctacct	12	11	7	11	0	2	2	1	1	1	1	3	2	3	2	2	2	3	3	2	2	5	5	rs116203669	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55545240T>C	ENST00000294383.6	-	60	7170	c.7171A>G	c.(7171-7173)Atg>Gtg	p.M2391V	USP24_ENST00000407756.1_Missense_Mutation_p.M2231V	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	2391					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						CCTTCAGACATGAACAACAAG	0.433													T|||	23	0.00459265	0.0174	0.0	5008	,	,		20623	0.0		0.0	False		,,,				2504	0.0				p.M2391V		Atlas-SNP	.											.	USP24	323	.	0			c.A7171G						PASS	.	T	VAL/MET	33,3727		0,33,1847	159	154	156		7171	-2	1	1	dbSNP_132	156	0,8242		0,0,4121	yes	missense	USP24	NM_015306.2	21	0,33,5968	CC,CT,TT		0.0,0.8777,0.275	benign	2391/2621	55545240	33,11969	1880	4121	6001	SO:0001583	missense	23358	exon60			CAGACATGAACAA	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.7171A>G	1.37:g.55545240T>C	ENSP00000294383:p.Met2391Val	81	0	0		89	41	0.460674	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Missense_Mutation	SNP	ENST00000294383.6	37	CCDS44154.2	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	T	0.334	-0.954398	0.02285	0.008777	0.0	ENSG00000162402	ENST00000294383;ENST00000407756	T;T	0.01887	4.58;4.58	4.8	-1.97	0.07503	.	0.295167	0.28544	N	0.014980	T	0.00468	0.0015	N	0.02539	-0.55	0.20764	N	0.999858	B	0.02656	0.0	B	0.01281	0.0	T	0.46707	-0.9172	10	0.28530	T	0.3	.	5.8291	0.18570	0.3638:0.0:0.4105:0.2258	.	2231	B7WPF4	.	V	2391;2231	ENSP00000294383:M2391V;ENSP00000385700:M2231V	ENSP00000294383:M2391V	M	-	1	0	USP24	55317828	0.985000	0.35326	0.995000	0.50966	0.984000	0.73092	0.139000	0.16036	-0.284000	0.09102	-0.691000	0.03719	ATG	T|0.996;C|0.004	0.004	strong		0.433	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			C	55545240	T	C	55545240	3	2	22	1	0	0	0	0	1	0	0	0	17070	1464	51	3	727	3	USP24	1	55545240	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	267687	55545240	193705381	148	3049											
C1orf168	199920	hgsc.bcm.edu	37	chr1	57186000	57186000	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgacaataatctctttgtcGtactgaaatgagaaattact	15	14	6	6	1	1	3	0	3	1	1	3	4	1	3	0	0	2	1	0	0	6	4	rs76493848	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:57186000G>A	ENST00000343433.6	-	18	2057	c.1977C>T	c.(1975-1977)taC>taT	p.Y659Y		NM_001004303.4	NP_001004303.3	Q5VWT5	CA168_HUMAN	chromosome 1 open reading frame 168	659										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						TCTCTTTGTCGTACTGAAATG	0.303													G|||	66	0.0131789	0.0469	0.0058	5008	,	,		15674	0.0		0.0	False		,,,				2504	0.0				p.Y659Y		Atlas-SNP	.											.	C1orf168	102	.	0			c.C1977T						PASS	.	G		207,4199	122.5+/-159.9	2,203,1998	52	52	52		1977	-0.1	0.6	1	dbSNP_132	52	3,8587	1.2+/-3.3	0,3,4292	no	coding-synonymous	C1orf168	NM_001004303.4		2,206,6290	AA,AG,GG		0.0349,4.6981,1.6159		659/729	57186000	210,12786	2203	4295	6498	SO:0001819	synonymous_variant	199920	exon18			TTTGTCGTACTGA	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.1977C>T	1.37:g.57186000G>A		103	0	0		86	41	0.476744	NM_001004303	Q63HM3|Q6ZUY6	Silent	SNP	ENST00000343433.6	37	CCDS30729.1																																																																																			G|0.987;A|0.013	0.013	strong		0.303	C1orf168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022751.2	NM_001004303		A	57186000	G	A	57186000	2	1	22	1	0	0	0	0	0	0	0	1	2014	1140	40	1		1	C1orf168	1	57186000	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1640760	57186000	192064621	149	3050											
TACSTD2	4070	hgsc.bcm.edu	37	chr1	59041940	59041940	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgactttctccggttggtgaTcaccaggacggccatgccgg	6	9	13	13	4	2	1	1	1	1	0	3	3	2	2	4	5	1	1	4	5	0	2	rs114373153	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:59041940T>C	ENST00000371225.2	-	1	1226	c.889A>G	c.(889-891)Atc>Gtc	p.I297V		NM_002353.2	NP_002344.2	P09758	TACD2_HUMAN	tumor-associated calcium signal transducer 2	297					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)					CGGTTGGTGATCACCAGgacg	0.622													T|||	149	0.0297524	0.1082	0.0043	5008	,	,		14669	0.0		0.003	False		,,,				2504	0.0				p.I297V		Atlas-SNP	.											.	TACSTD2	6	.	0			c.A889G						PASS	.	T	VAL/ILE	398,4008	195.0+/-219.7	18,362,1823	50	46	47		889	1	0.8	1	dbSNP_132	47	6,8594	4.3+/-15.6	0,6,4294	yes	missense	TACSTD2	NM_002353.2	29	18,368,6117	CC,CT,TT		0.0698,9.0331,3.1063	benign	297/324	59041940	404,12602	2203	4300	6503	SO:0001583	missense	4070	exon1			TGGTGATCACCAG	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.889A>G	1.37:g.59041940T>C	ENSP00000360269:p.Ile297Val	103	0	0		105	61	0.580952	NM_002353	Q15658|Q6FG48|Q7Z7Q4|Q96QD2	Missense_Mutation	SNP	ENST00000371225.2	37	CCDS609.1	61	0.027930402930402932	58	0.11788617886178862	3	0.008287292817679558	0	0.0	0	0.0	T	3.973	-0.008046	0.07773	0.090331	6.98E-4	ENSG00000184292	ENST00000371225	T	0.76448	-1.02	4.59	0.995	0.19838	.	0.178739	0.48286	N	0.000189	T	0.00936	0.0031	N	0.12422	0.21	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.01071	-1.1461	10	0.11182	T	0.66	-9.0532	3.5124	0.07713	0.1616:0.2884:0.0:0.5501	.	297	P09758	TACD2_HUMAN	V	297	ENSP00000360269:I297V	ENSP00000360269:I297V	I	-	1	0	TACSTD2	58814528	0.005000	0.15991	0.797000	0.32132	0.803000	0.45373	-0.133000	0.10451	0.004000	0.14682	0.533000	0.62120	ATC	T|0.965;C|0.035	0.035	strong		0.622	TACSTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027818.1	NM_002353		C	59041940	T	C	59041940	3	2	22	1	0	0	0	0	1	0	0	0	15523	1435	50	3	86	3	TACSTD2	1	59041940	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1855940	59041940	190208681	150	3051											
TM2D1	83941	hgsc.bcm.edu	37	chr1	62190780	62190780	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagacggaccagacggccAggcggccgccatcttggaga	10	3	15	13	4	1	3	0	0	1	3	1	5	1	4	4	5	1	1	4	5	0	1	rs200054903	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:62190780A>G	ENST00000606498.1	-	1	33	c.13T>C	c.(13-15)Tgg>Cgg	p.W5R	TM2D1_ENST00000294613.5_Missense_Mutation_p.W5R|TM2D1_ENST00000371177.2_Missense_Mutation_p.W5R|TM2D1_ENST00000371180.2_Missense_Mutation_p.W67R			Q9BX74	TM2D1_HUMAN	TM2 domain containing 1	5					apoptotic signaling pathway (GO:0097190)	integral component of plasma membrane (GO:0005887)	beta-amyloid binding (GO:0001540)|G-protein coupled receptor activity (GO:0004930)			large_intestine(2)|lung(3)|ovary(1)	6						CCAGACGGCCAGGCGGCCGCC	0.652													A|||	31	0.0061901	0.0219	0.0029	5008	,	,		16840	0.0		0.0	False		,,,				2504	0.0				p.W5R		Atlas-SNP	.											TM2D1_ENST00000371177,right_upper_lobe,carcinoma,+1,3	TM2D1	37	3	0			c.T13C						PASS	.	A	ARG/TRP	54,3760		0,54,1853	35	41	39		13	-6	0	1		39	0,8178		0,0,4089	no	missense	TM2D1	NM_032027.2	101	0,54,5942	GG,GA,AA		0.0,1.4158,0.4503	benign	5/208	62190780	54,11938	1907	4089	5996	SO:0001583	missense	83941	exon1			ACGGCCAGGCGGC	AF353990	CCDS65554.1	1p32.1	2008-02-05			ENSG00000162604	ENSG00000162604			24142	protein-coding gene	gene with protein product		610080				11278849, 12553667	Standard	NM_032027		Approved	BBP	uc001czz.1	Q9BX74	OTTHUMG00000008466	ENST00000606498.1:c.13T>C	1.37:g.62190780A>G	ENSP00000475700:p.Trp5Arg	63	0	0		57	34	0.596491	NM_032027	A6NDA8	Missense_Mutation	SNP	ENST00000606498.1	37		.	.	.	.	.	.	.	.	.	.	A	13.04	2.117243	0.37339	0.014158	0.0	ENSG00000162604	ENST00000371180;ENST00000294613;ENST00000371178;ENST00000371177	.	.	.	4.69	-5.98	0.02220	.	1.041710	0.07590	N	0.921834	T	0.17789	0.0427	L	0.38531	1.155	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33292	-0.9874	9	0.72032	D	0.01	3.1902	0.4995	0.00577	0.1994:0.2683:0.1696:0.3628	.	5	Q9BX74	TM2D1_HUMAN	R	67;5;5;5	.	ENSP00000294613:W5R	W	-	1	0	TM2D1	61963368	0.061000	0.20836	0.000000	0.03702	0.034000	0.12701	-0.222000	0.09190	-0.981000	0.03520	0.379000	0.24179	TGG	.	.	weak		0.652	TM2D1-012	KNOWN	non_canonical_U12|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470779.2	NM_032027		G	62190780	A	G	62190780	3	3	22	1	0	0	0	0	1	0	0	0	15978	188	7	3	634	3	TM2D1	1	62190780	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	3148840	62190780	187059841	151	3052											
INADL	10207	hgsc.bcm.edu	37	chr1	62288730	62288730	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatacattgggtctcctacaGccagaagatgagctgcttga	11	10	11	9	0	1	4	0	2	1	2	2	5	1	4	2	1	5	2	2	1	3	4	rs1286812	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:62288730G>C	ENST00000371158.2	+	15	1911	c.1797G>C	c.(1795-1797)caG>caC	p.Q599H	INADL_ENST00000316485.6_Missense_Mutation_p.Q599H	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	599	PDZ 4. {ECO:0000255|PROSITE- ProRule:PRU00143}.		Q -> H (in dbSNP:rs1286812).		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						GTCTCCTACAGCCAGAAGATG	0.428													G|||	61	0.0121805	0.0454	0.0014	5008	,	,		18625	0.0		0.0	False		,,,				2504	0.0				p.Q599H		Atlas-SNP	.											.	INADL	179	.	0			c.G1797C						PASS	.	G	HIS/GLN	95,4311	76.8+/-115.0	0,95,2108	154	140	145		1797	4	1	1	dbSNP_87	145	0,8600		0,0,4300	yes	missense	INADL	NM_176877.2	24	0,95,6408	CC,CG,GG		0.0,2.1562,0.7304	possibly-damaging	599/1802	62288730	95,12911	2203	4300	6503	SO:0001583	missense	10207	exon15			CCTACAGCCAGAA	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.1797G>C	1.37:g.62288730G>C	ENSP00000360200:p.Gln599His	223	0	0		219	111	0.506849	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	37	CCDS617.2	17	0.007783882783882784	17	0.034552845528455285	0	0.0	0	0.0	0	0.0	G	12.64	1.998539	0.35226	0.021562	0.0	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000255202	T;T	0.27720	1.65;1.65	4.99	4.02	0.46733	PDZ/DHR/GLGF (4);	0.205916	0.32868	N	0.005548	T	0.16041	0.0386	L	0.35644	1.08	0.80722	D	1	D;D;P	0.65815	0.995;0.995;0.808	P;D;B	0.66716	0.894;0.946;0.442	T	0.01496	-1.1340	10	0.39692	T	0.17	.	6.7972	0.23732	0.1259:0.1743:0.6997:0.0	rs1286812;rs1286812	599;599;599	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	H	599	ENSP00000360200:Q599H;ENSP00000326199:Q599H	ENSP00000255202:Q599H	Q	+	3	2	INADL	62061318	0.999000	0.42202	1.000000	0.80357	0.416000	0.31233	0.561000	0.23515	2.322000	0.78497	0.561000	0.74099	CAG	G|0.992;C|0.008	0.008	strong		0.428	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		C	62288730	G	C	62288730	3	2	22	1	0	0	0	0	1	0	0	0	7740	962	34	4	1851	4	INADL	1	62288730	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	97950	62288730	186961891	152	3053											
INADL	10207	hgsc.bcm.edu	37	chr1	62393420	62393420	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	agaggcaaggaactgctccaCcgccaatgaaacttcctcct	12	7	8	14	1	0	2	0	1	0	1	3	3	3	3	5	2	3	2	5	2	4	1	rs61743112	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:62393420C>T	ENST00000371158.2	+	27	3703	c.3589C>T	c.(3589-3591)Ccg>Tcg	p.P1197S	INADL_ENST00000316485.6_Missense_Mutation_p.P1197S	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1197					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						AACTGCTCCACCGCCAATGAA	0.398													C|||	199	0.0397364	0.1415	0.0173	5008	,	,		17651	0.0		0.0	False		,,,				2504	0.0				p.P1197S		Atlas-SNP	.											.	INADL	179	.	0			c.C3589T						PASS	.	C	SER/PRO	478,3928	224.9+/-240.9	21,436,1746	102	94	97		3589	4.4	0.6	1	dbSNP_129	97	2,8598	2.2+/-6.3	0,2,4298	yes	missense	INADL	NM_176877.2	74	21,438,6044	TT,TC,CC		0.0233,10.8488,3.6906	possibly-damaging	1197/1802	62393420	480,12526	2203	4300	6503	SO:0001583	missense	10207	exon27			GCTCCACCGCCAA	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.3589C>T	1.37:g.62393420C>T	ENSP00000360200:p.Pro1197Ser	84	0	0		90	45	0.5	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	37	CCDS617.2	86	0.039377289377289376	81	0.16463414634146342	5	0.013812154696132596	0	0.0	0	0.0	C	11.14	1.550134	0.27652	0.108488	2.33E-4	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513	T;T	0.16073	2.44;2.37	4.45	4.45	0.53987	.	0.000000	0.64402	D	0.000002	T	0.00144	0.0004	M	0.74258	2.255	0.09310	P	1.0	D;P;D	0.89917	0.959;0.726;1.0	P;B;D	0.79108	0.897;0.205;0.992	T	0.09335	-1.0679	9	0.08381	T	0.77	.	12.8308	0.57744	0.0:1.0:0.0:0.0	rs61743112	1197;1197;1197	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	S	1197	ENSP00000360200:P1197S;ENSP00000326199:P1197S	ENSP00000326199:P1197S	P	+	1	0	INADL	62166008	0.949000	0.32298	0.641000	0.29422	0.012000	0.07955	3.927000	0.56499	2.465000	0.83290	0.650000	0.86243	CCG	C|0.959;T|0.041	0.041	strong		0.398	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		T	62393420	C	T	62393420	3	4	22	1	0	0	0	0	1	0	0	0	7740	507	18	2	3691	2	INADL	1	62393420	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	104690	62393420	186857201	153	3054											
INADL	10207	hgsc.bcm.edu	37	chr1	62455982	62455982	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttgtggtgggaattaacccGgaaggacctgctgccgcaga	9	9	14	9	2	0	1	0	0	0	1	0	4	0	4	3	4	3	2	3	4	3	2	rs6681983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:62455982G>A	ENST00000371158.2	+	28	3927	c.3813G>A	c.(3811-3813)ccG>ccA	p.P1271P	INADL_ENST00000316485.6_Silent_p.P1271P|INADL_ENST00000543708.1_Silent_p.P55P|INADL_ENST00000545929.1_5'UTR	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1271	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						GAATTAACCCGGAAGGACCTG	0.433													G|||	99	0.0197684	0.0711	0.0072	5008	,	,		15469	0.0		0.0	False		,,,				2504	0.0				p.P1271P		Atlas-SNP	.											.	INADL	179	.	0			c.G3813A						PASS	.	G		187,4219	119.6+/-157.3	4,179,2020	94	89	90		3813	-11.7	0	1	dbSNP_116	90	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	INADL	NM_176877.2		4,182,6317	AA,AG,GG		0.0349,4.2442,1.4609		1271/1802	62455982	190,12816	2203	4300	6503	SO:0001819	synonymous_variant	10207	exon28			TAACCCGGAAGGA	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.3813G>A	1.37:g.62455982G>A		94	0	0		73	34	0.465753	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Silent	SNP	ENST00000371158.2	37	CCDS617.2																																																																																			G|0.985;A|0.015	0.015	strong		0.433	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605		A	62455982	G	A	62455982	2	1	22	1	0	0	0	0	0	0	0	1	7740	1103	39	1		1	INADL	1	62455982	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	62562	62455982	186794639	154	3055											
DOCK7	85440	hgsc.bcm.edu	37	chr1	63119442	63119442	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgtataacttcttatacagtCtctaacatgtggatccattt	11	17	5	8	0	2	0	0	0	2	0	4	1	3	1	1	1	3	1	1	1	5	7			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:63119442C>T	ENST00000340370.5	-	4	360	c.343G>A	c.(343-345)Gac>Aac	p.D115N	DOCK7_ENST00000404627.2_Missense_Mutation_p.D115N|DOCK7_ENST00000251157.5_Missense_Mutation_p.D115N	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	115					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						CTTATACAGTCTCTAACATGT	0.303																																					p.D115N		Atlas-SNP	.											.	DOCK7	184	.	0			c.G343A						PASS	.						61	62	62					1																	63119442		2203	4297	6500	SO:0001583	missense	85440	exon4			TACAGTCTCTAAC		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.343G>A	1.37:g.63119442C>T	ENSP00000340742:p.Asp115Asn	129	0	0		149	45	0.302013	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Missense_Mutation	SNP	ENST00000340370.5	37	CCDS30734.1	.	.	.	.	.	.	.	.	.	.	C	34	5.339631	0.95783	.	.	ENSG00000116641	ENST00000371140;ENST00000251157;ENST00000340370;ENST00000404627	T;T;T	0.49720	0.77;0.77;0.77	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.64193	0.2576	M	0.78049	2.395	0.80722	D	1	D;D;P;P;D	0.65815	0.992;0.995;0.923;0.923;0.993	D;D;P;P;D	0.66979	0.925;0.948;0.772;0.772;0.913	T	0.64330	-0.6433	10	0.48119	T	0.1	.	18.898	0.92432	0.0:1.0:0.0:0.0	.	115;115;115;115;115	Q96NI0;Q96N67-2;Q96N67-5;Q96N67-4;Q96N67-3	.;.;.;.;.	N	115	ENSP00000251157:D115N;ENSP00000340742:D115N;ENSP00000384446:D115N	ENSP00000251157:D115N	D	-	1	0	DOCK7	62892030	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.651000	0.83577	2.699000	0.92147	0.655000	0.94253	GAC	.	.	none		0.303	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407		T	63119442	C	T	63119442	3	4	22	1	0	0	0	0	1	0	0	0	4694	913	32	2	6170	2	DOCK7	1	63119442	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	663460	63119442	186131179	155	3056											
ROR1	4919	hgsc.bcm.edu	37	chr1	64643650	64643650	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttccagagaaatttactcCgctgattactacagggtcca	11	12	7	11	1	0	2	0	1	0	1	3	3	3	2	3	1	3	1	3	1	4	5	rs35586842	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:64643650C>T	ENST00000371079.1	+	9	2301	c.1926C>T	c.(1924-1926)tcC>tcT	p.S642S	ROR1_ENST00000545203.1_Silent_p.S93S	NM_005012.3	NP_005003.2	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1	642	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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						AAATTTACTCCGCTGATTACT	0.448													C|||	122	0.024361	0.0885	0.0058	5008	,	,		18919	0.0		0.001	False		,,,				2504	0.0				p.S642S		Atlas-SNP	.											.	ROR1	113	.	0			c.C1926T						PASS	.	C		346,4060	177.3+/-206.3	12,322,1869	62	64	64		1926	-11.8	0.3	1	dbSNP_126	64	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	ROR1	NM_005012.2		12,326,6165	TT,TC,CC		0.0465,7.8529,2.6911		642/938	64643650	350,12656	2203	4300	6503	SO:0001819	synonymous_variant	4919	exon9			TTACTCCGCTGAT	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.1926C>T	1.37:g.64643650C>T		121	0	0		126	76	0.603175	NM_005012	Q5VVX6|Q66K77|Q92776	Silent	SNP	ENST00000371079.1	37	CCDS626.1																																																																																			C|0.972;T|0.028	0.028	strong		0.448	ROR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025002.1	NM_005012		T	64643650	C	T	64643650	2	4	22	1	0	0	0	0	0	0	0	1	13541	639	23	1		1	ROR1	1	64643650	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1524208	64643650	184606971	156	3057											
UBE2U	148581	hgsc.bcm.edu	37	chr1	64686577	64686577	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagttacctaaagacccaCgtaaatgtatcaggtaagtt	15	10	9	7	1	1	1	1	0	0	1	1	2	1	2	2	2	1	5	2	2	7	6	rs139887828	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:64686577C>T	ENST00000371076.3	+	6	737	c.493C>T	c.(493-495)Cgt>Tgt	p.R165C	UBE2U_ENST00000464349.1_3'UTR	NM_152489.1	NP_689702.1	Q5VVX9	UBE2U_HUMAN	ubiquitin-conjugating enzyme E2U (putative)	165					protein ubiquitination (GO:0016567)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)			large_intestine(3)|lung(2)|skin(1)	6						TAAAGACCCACGTAAATGTAT	0.284													C|||	38	0.00758786	0.0272	0.0029	5008	,	,		13978	0.0		0.0	False		,,,				2504	0.0				p.R165C		Atlas-SNP	.											.	UBE2U	16	.	0			c.C493T						PASS	.	C	CYS/ARG	138,4268	98.5+/-137.1	0,138,2065	92	99	96		493	-5.5	0	1	dbSNP_134	96	1,8589	1.2+/-3.3	0,1,4294	yes	missense	UBE2U	NM_152489.1	180	0,139,6359	TT,TC,CC		0.0116,3.1321,1.0696	benign	165/227	64686577	139,12857	2203	4295	6498	SO:0001583	missense	148581	exon6			GACCCACGTAAAT	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.493C>T	1.37:g.64686577C>T	ENSP00000360116:p.Arg165Cys	187	0	0		159	78	0.490566	NM_152489	Q8N1D4	Missense_Mutation	SNP	ENST00000371076.3	37	CCDS627.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	C	7.130	0.579790	0.13686	0.031321	1.16E-4	ENSG00000177414	ENST00000371077;ENST00000371076	T;T	0.72942	-0.7;-0.69	4.12	-5.54	0.02544	Ubiquitin-conjugating enzyme/RWD-like (1);	2.859510	0.01357	N	0.012095	T	0.25419	0.0618	N	0.14661	0.345	0.09310	N	1	B	0.24043	0.096	B	0.09377	0.004	T	0.18366	-1.0339	10	0.87932	D	0	.	3.3218	0.07053	0.095:0.4157:0.2415:0.2478	.	165	Q5VVX9	UBE2U_HUMAN	C	165	ENSP00000360117:R165C;ENSP00000360116:R165C	ENSP00000360116:R165C	R	+	1	0	UBE2U	64459165	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.259000	0.08721	-1.248000	0.02503	-0.229000	0.12294	CGT	C|0.991;T|0.009	0.009	strong		0.284	UBE2U-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025005.1	NM_152489		T	64686577	C	T	64686577	3	4	22	1	0	0	0	0	1	0	0	0	16889	536	19	1	515	1	UBE2U	1	64686577	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	42927	64686577	184564044	157	3058											
JAK1	3716	hgsc.bcm.edu	37	chr1	65300305	65300305	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagcttgtccgattggatggTtggaattcccagcatttcct	8	14	10	9	1	0	0	0	0	0	0	3	3	3	2	3	3	2	3	3	3	2	5	rs369143723		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:65300305T>C	ENST00000342505.4	-	25	3653	c.3405A>G	c.(3403-3405)caA>caG	p.Q1135Q		NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	1135	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)	GATTGGATGGTTGGAATTCCC	0.313			Mis		ALL																																p.Q1135Q		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.A3405G						PASS	.	T		1,3603		0,1,1801	104	98	100		3405	-4.4	0.6	1		100	0,8148		0,0,4074	no	coding-synonymous	JAK1	NM_002227.2		0,1,5875	CC,CT,TT		0.0,0.0277,0.0085		1135/1155	65300305	1,11751	1802	4074	5876	SO:0001819	synonymous_variant	3716	exon25			GGATGGTTGGAAT	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.3405A>G	1.37:g.65300305T>C		142	0	0		166	78	0.46988	NM_002227	Q59GQ2|Q9UD26	Silent	SNP	ENST00000342505.4	37	CCDS41346.1																																																																																			.	.	none		0.313	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		C	65300305	T	C	65300305	2	2	22	1	0	0	0	0	0	0	0	1	7946	1722	60	3		3	JAK1	1	65300305	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	613728	65300305	183950316	158	3059											
WDR78	79819	hgsc.bcm.edu	37	chr1	67327986	67327986	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggcagtggacattatgcCtagataaagacacagaaagg	16	6	11	8	0	0	3	0	0	0	3	0	4	0	4	2	3	1	1	2	3	5	3	rs144890566		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:67327986C>G	ENST00000371026.3	-	7	996		c.e7-1		WDR78_ENST00000431318.1_Splice_Site|WDR78_ENST00000371023.3_Splice_Site|WDR78_ENST00000493572.1_5'UTR	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						GACATTATGCCTAGATAAAGA	0.318																																					.		Atlas-SNP	.											.	WDR78	102	.	0			c.941-1G>C						PASS	.	C	,	2,4404	4.2+/-10.8	0,2,2201	65	65	65		,	4.8	0.6	1	dbSNP_134	65	0,8600		0,0,4300	no	splice-3,splice-3	WDR78	NM_024763.4,NM_207014.2	,	0,2,6501	GG,GC,CC		0.0,0.0454,0.0154	,	,	67327986	2,13004	2203	4300	6503	SO:0001630	splice_region_variant	79819	exon8			TTATGCCTAGATA	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.941-1G>C	1.37:g.67327986C>G		196	0	0		178	93	0.522472	NM_024763	A8K9W5|B5MDT3|H7BY80|Q5VTI0|Q8N5G5|Q9H5R9|Q9UF44	Splice_Site	SNP	ENST00000371026.3	37	CCDS635.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.64|17.64	3.440343|3.440343	0.63067|0.63067	4.54E-4|4.54E-4	0.0|0.0	ENSG00000152763|ENSG00000152763	ENST00000371026;ENST00000431318;ENST00000464352;ENST00000371023;ENST00000469450|ENST00000531552	.|T	.|0.55413	.|0.52	5.67|5.67	4.76|4.76	0.60689|0.60689	.|.	.|.	.|.	.|.	.|.	.|T	.|0.47544	.|0.1451	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.47262	.|-0.9131	.|5	.|.	.|.	.|.	.|.	12.3988|12.3988	0.55402|0.55402	0.0:0.9183:0.0:0.0817|0.0:0.9183:0.0:0.0817	.|.	.|.	.|.	.|.	.|R	-1|1	.|ENSP00000433037:G1R	.|.	.|G	-|-	.|1	.|0	WDR78|WDR78	67100574|67100574	1.000000|1.000000	0.71417|0.71417	0.631000|0.631000	0.29282|0.29282	0.826000|0.826000	0.46750|0.46750	4.397000|4.397000	0.59690|0.59690	1.393000|1.393000	0.46605|0.46605	0.591000|0.591000	0.81541|0.81541	.|GGC	C|1.000;G|0.000	0.000	weak		0.318	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025404.1	NM_024763	Intron	G	67327986	C	G	67327986	5	3	22	1	0	0	0	0	0	0	1	0	17343	695	24	4	1707	4	WDR78	1	67327986	Splice_Site	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2027681	67327986	181922635	159	3060											
IL12RB2	3595	hgsc.bcm.edu	37	chr1	67787286	67787286	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catctgtatcttattgcagaTgcgtgcaagagaggcgatgt	10	12	12	7	2	2	2	0	0	2	2	2	4	2	2	0	1	3	3	0	1	3	3	rs2307147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:67787286T>C	ENST00000262345.1	+	3	718	c.78T>C	c.(76-78)gaT>gaC	p.D26D	IL12RB2_ENST00000371000.1_Splice_Site_p.D26D|IL12RB2_ENST00000541374.1_Splice_Site_p.D26D|IL12RB2_ENST00000544434.1_Splice_Site_p.D26D	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	26					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						TTATTGCAGATGCGTGCAAGA	0.388													T|||	324	0.0646965	0.2383	0.013	5008	,	,		20536	0.0		0.0	False		,,,				2504	0.0				p.D26D		Atlas-SNP	.											.	IL12RB2	94	.	0			c.T78C						PASS	.	T		901,3505	347.5+/-309.5	88,725,1390	103	94	97		78	-1.2	1	1	dbSNP_100	97	9,8591	5.7+/-21.5	0,9,4291	yes	coding-synonymous-near-splice	IL12RB2	NM_001559.2		88,734,5681	CC,CT,TT		0.1047,20.4494,6.9968		26/863	67787286	910,12096	2203	4300	6503	SO:0001630	splice_region_variant	3595	exon3			TGCAGATGCGTGC	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.77-1T>C	1.37:g.67787286T>C		56	0	0		78	35	0.448718	NM_001559	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Silent	SNP	ENST00000262345.1	37	CCDS638.1																																																																																			T|0.926;C|0.074	0.074	strong		0.388	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559	Silent	C	67787286	T	C	67787286	5	2	22	1	0	0	0	0	0	0	1	0	7636	1478	51	3	84	3	IL12RB2	1	67787286	Splice_Site	SNP	T	TCGA-G8-6324-01A-11D-2210-10	459300	67787286	181463335	160	3061											
GNG12	55970	hgsc.bcm.edu	37	chr1	68171215	68171215	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaaagggtcactcctggcAtgttcctcacagtaggacat	11	9	10	11	0	2	0	2	0	0	0	4	1	4	1	2	3	1	4	2	3	2	2	rs17130202	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:68171215A>G	ENST00000370982.3	-	4	337	c.138T>C	c.(136-138)caT>caC	p.H46H		NM_018841.5	NP_061329.3	Q9UBI6	GBG12_HUMAN	guanine nucleotide binding protein (G protein), gamma 12	46					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						CACTCCTGGCATGTTCCTCAC	0.393													A|||	54	0.0107827	0.0386	0.0043	5008	,	,		20621	0.0		0.0	False		,,,				2504	0.0				p.H46H		Atlas-SNP	.											.	GNG12	11	.	0			c.T138C						PASS	.	A		138,4268	99.4+/-138.0	2,134,2067	128	119	122		138	-4.2	1	1	dbSNP_123	122	0,8600		0,0,4300	no	coding-synonymous	GNG12	NM_018841.5		2,134,6367	GG,GA,AA		0.0,3.1321,1.061		46/73	68171215	138,12868	2203	4300	6503	SO:0001819	synonymous_variant	55970	exon4			CCTGGCATGTTCC	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.138T>C	1.37:g.68171215A>G		102	0	0		103	42	0.407767	NM_018841	Q69YP5|Q9BRV5	Silent	SNP	ENST00000370982.3	37	CCDS30749.1																																																																																			A|0.991;G|0.009	0.009	strong		0.393	GNG12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026355.2			G	68171215	A	G	68171215	2	3	22	1	0	0	0	0	0	0	0	1	6533	214	8	3		3	GNG12	1	68171215	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	383929	68171215	181079406	161	3062											
RPE65	6121	hgsc.bcm.edu	37	chr1	68904645	68904645	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctttccagcagcagagatcCacaatcagaaacccattgtc	13	8	6	14	0	1	2	1	0	0	2	4	3	3	2	4	0	3	2	4	0	2	2	rs61752907	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:68904645C>A	ENST00000262340.5	-	9	1031	c.978G>T	c.(976-978)gtG>gtT	p.V326V		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	326					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						AGCAGAGATCCACAATCAGAA	0.418													C|||	12	0.00239617	0.0083	0.0	5008	,	,		18772	0.0		0.001	False		,,,				2504	0.0				p.V326V		Atlas-SNP	.											.	RPE65	87	.	0			c.G978T						PASS	.	C		17,4389	25.3+/-52.1	0,17,2186	281	279	280	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	978	3	1	1	dbSNP_129	280	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	RPE65	NM_000329.2		0,21,6482	AA,AC,CC		0.0465,0.3858,0.1615		326/534	68904645	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	6121	exon9			GAGATCCACAATC	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.978G>T	1.37:g.68904645C>A		128	0	0		143	72	0.503497	NM_000329	A8K1L0|Q5T9U3	Silent	SNP	ENST00000262340.5	37	CCDS643.1																																																																																			C|0.998;A|0.002	0.002	strong		0.418	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329		A	68904645	C	A	68904645	2	1	22	1	0	0	0	0	0	0	0	1	13560	581	21	4		4	RPE65	1	68904645	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	733430	68904645	180345976	162	3063											
LRRIQ3	127255	hgsc.bcm.edu	37	chr1	74575141	74575141	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ttgaaaaagagatccttaagGagcttatcttcatacccttt	13	14	6	8	0	2	2	1	1	1	1	3	4	3	3	2	1	2	1	2	1	5	6	rs182798407	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:74575141G>A	ENST00000395089.1	-	4	803	c.804C>T	c.(802-804)ctC>ctT	p.L268L	LRRIQ3_ENST00000468759.1_5'UTR|LRRIQ3_ENST00000370909.2_Silent_p.L160L|LRRIQ3_ENST00000354431.4_Silent_p.L268L			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	268										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						GATCCTTAAGGAGCTTATCTT	0.289													G|||	15	0.00299521	0.0113	0.0	5008	,	,		12152	0.0		0.0	False		,,,				2504	0.0				p.L268L		Atlas-SNP	.											LRRIQ3,right_upper_lobe,carcinoma,-1,1	LRRIQ3	146	1	0			c.C804T						PASS	.	G		41,3525		2,37,1744	100	83	88		804	2	0	1		88	0,8096		0,0,4048	no	coding-synonymous	LRRIQ3	NM_001105659.1		2,37,5792	AA,AG,GG		0.0,1.1497,0.3516		268/625	74575141	41,11621	1783	4048	5831	SO:0001819	synonymous_variant	127255	exon5			CTTAAGGAGCTTA	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.804C>T	1.37:g.74575141G>A		98	0	0		120	59	0.491667	NM_001105659	A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Silent	SNP	ENST00000395089.1	37	CCDS41350.1																																																																																			G|0.997;A|0.003	0.003	strong		0.289	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258		A	74575141	G	A	74575141	2	1	22	1	0	0	0	0	0	0	0	1	9039	1161	41	2		2	LRRIQ3	1	74575141	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5670496	74575141	174675480	163	3064											
LRRIQ3	127255	hgsc.bcm.edu	37	chr1	74649119	74649119	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tctgaaatggctattgcttaCctgatttccatggagatcaa	11	14	8	8	0	2	3	1	2	1	1	3	4	3	3	2	2	2	2	2	2	4	4	rs143858191	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:74649119C>T	ENST00000395089.1	-	1	249		c.e1+1		LRRIQ3_ENST00000370911.3_Splice_Site|LRRIQ3_ENST00000370909.2_Splice_Site|LRRIQ3_ENST00000354431.4_Splice_Site			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3											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						CTATTGCTTACCTGATTTCCA	0.299													C|||	12	0.00239617	0.0091	0.0	5008	,	,		16045	0.0		0.0	False		,,,				2504	0.0				.		Atlas-SNP	.											.	LRRIQ3	146	.	0			c.249+1G>A						PASS	.	C		32,4368	34.3+/-65.2	2,28,2170	61	67	65			5.3	1	1	dbSNP_134	65	0,8588		0,0,4294	yes	splice-5	LRRIQ3	NM_001105659.1		2,28,6464	TT,TC,CC		0.0,0.7273,0.2464			74649119	32,12956	2200	4294	6494	SO:0001630	splice_region_variant	127255	exon3			TGCTTACCTGATT	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.249+1G>A	1.37:g.74649119C>T		131	0	0		119	55	0.462185	NM_001105659	A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Splice_Site	SNP	ENST00000395089.1	37	CCDS41350.1	5	0.0022893772893772895	4	0.008130081300813009	0	0.0	0	0.0	1	0.0013192612137203166	C	17.79	3.476396	0.63737	0.007273	0.0	ENSG00000162620	ENST00000395089;ENST00000354431;ENST00000370909;ENST00000388972;ENST00000444984;ENST00000370911	.	.	.	5.27	5.27	0.74061	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.0114	0.89225	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	LRRIQ3	74421707	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	5.083000	0.64456	2.601000	0.87937	0.655000	0.94253	.	C|0.998;T|0.002	0.002	strong		0.299	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258	Intron	T	74649119	C	T	74649119	5	4	22	1	0	0	0	0	0	0	1	0	9039	521	18	2	1652	2	LRRIQ3	1	74649119	Splice_Site	SNP	C	TCGA-G8-6324-01A-11D-2210-10	73978	74649119	174601502	164	3065											
FPGT	8790	hgsc.bcm.edu	37	chr1	74670277	74670277	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggagaatttgagtttattagGtttgacaaacctggctttac	11	15	10	5	0	0	3	0	2	0	1	0	4	0	3	1	3	2	3	1	3	5	7	rs139749795	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:74670277G>A	ENST00000609362.1	+	4	583	c.546G>A	c.(544-546)agG>agA	p.R182R	FPGT_ENST00000534056.1_Intron|FPGT-TNNI3K_ENST00000533006.1_Intron|FPGT_ENST00000370894.5_Intron|FPGT-TNNI3K_ENST00000370895.1_Intron|FPGT-TNNI3K_ENST00000557284.2_Intron|FPGT_ENST00000467578.2_3'UTR|FPGT_ENST00000524915.1_Intron|FPGT-TNNI3K_ENST00000370899.3_Intron|FPGT-TNNI3K_ENST00000370893.1_Intron|FPGT_ENST00000370898.3_Silent_p.R195R|TNNI3K_ENST00000370891.2_Intron	NM_003838.4	NP_003829.3	O14772	FPGT_HUMAN	fucose-1-phosphate guanylyltransferase	182					fucose metabolic process (GO:0006004)	cytoplasm (GO:0005737)	catalytic activity (GO:0003824)|fucose-1-phosphate guanylyltransferase activity (GO:0047341)|GTP binding (GO:0005525)	p.R182R(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	39						AGTTTATTAGGTTTGACAAAC	0.353													G|||	15	0.00299521	0.0113	0.0	5008	,	,		17320	0.0		0.0	False		,,,				2504	0.0				p.R182R		Atlas-SNP	.											FPGT,NS,carcinoma,0,1	FPGT	77	1	1	Substitution - coding silent(1)	lung(1)	c.G546A						PASS	.	G	,,,,	49,4357	51.6+/-87.1	2,45,2156	113	111	111		,,,,546	-11.1	0	1	dbSNP_134	111	0,8600		0,0,4300	no	intron,intron,intron,intron,coding-synonymous	FPGT,FPGT-TNNI3K	NM_001112808.2,NM_001199327.1,NM_001199328.1,NM_001199329.1,NM_003838.3	,,,,	2,45,6456	AA,AG,GG		0.0,1.1121,0.3767	,,,,	,,,,182/595	74670277	49,12957	2203	4300	6503	SO:0001819	synonymous_variant	8790	exon4			TATTAGGTTTGAC	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.546G>A	1.37:g.74670277G>A		185	0	0		166	78	0.46988	NM_003838	A6NMH3|B4DRX2|B4E2Y7|E9PNQ2|Q8N5J7	Silent	SNP	ENST00000609362.1	37	CCDS663.1																																																																																			G|0.996;A|0.004	0.004	strong		0.353	FPGT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	74670277	G	A	74670277	2	1	22	1	0	0	0	0	0	0	0	1	6045	1252	44	2		2	FPGT	1	74670277	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	21158	74670277	174580344	165	3066											
C1orf173	127254	hgsc.bcm.edu	37	chr1	75038963	75038963	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctctgctgttggcttccacgCcctcaagggagcctcatgaa	7	10	10	14	1	3	1	2	1	1	0	4	2	4	2	3	2	2	3	3	2	2	2	rs75061423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:75038963C>A	ENST00000326665.5	-	14	2649	c.2431G>T	c.(2431-2433)Gcg>Tcg	p.A811S	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		811	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						GGCTTCCACGCCCTCAAGGGA	0.557													c|||	122	0.024361	0.0908	0.0029	5008	,	,		17211	0.0		0.0	False		,,,				2504	0.0				p.A811S		Atlas-SNP	.											.	C1orf173	380	.	0			c.G2431T						PASS	.	C	SER/ALA	345,4061	181.2+/-209.3	12,321,1870	91	88	89		2431	2.6	0	1	dbSNP_131	89	1,8599	1.2+/-3.3	0,1,4299	yes	missense	C1orf173	NM_001002912.4	99	12,322,6169	AA,AC,CC		0.0116,7.8302,2.6603	benign	811/1531	75038963	346,12660	2203	4300	6503	SO:0001583	missense	127254	exon14			TCCACGCCCTCAA																												ENST00000326665.5:c.2431G>T	1.37:g.75038963C>A	ENSP00000322609:p.Ala811Ser	121	0	0		126	60	0.47619	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	37	CCDS30755.1	38	0.0173992673992674	37	0.07520325203252033	1	0.0027624309392265192	0	0.0	0	0.0	C	12.22	1.873823	0.33069	0.078302	1.16E-4	ENSG00000178965	ENST00000326665	T	0.11604	2.76	5.54	2.6	0.31112	.	.	.	.	.	T	0.01870	0.0059	N	0.22421	0.69	0.09310	N	1	B	0.15719	0.014	B	0.15870	0.014	T	0.47686	-0.9098	9	0.15952	T	0.53	-1.3011	7.1998	0.25874	0.0:0.5789:0.2768:0.1442	.	811	Q5RHP9	CA173_HUMAN	S	811	ENSP00000322609:A811S	ENSP00000322609:A811S	A	-	1	0	C1orf173	74811551	0.000000	0.05858	0.005000	0.12908	0.008000	0.06430	-0.211000	0.09332	0.701000	0.31803	0.561000	0.74099	GCG	A|0.022;C|0.978	0.022	strong		0.557	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			A	75038963	C	A	75038963	3	1	22	1	0	0	0	0	1	0	0	0	2016	739	26	4	2165	4	C1orf173	1	75038963	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	368686	75038963	174211658	166	3067											
CRYZ	1429	hgsc.bcm.edu	37	chr1	75175865	75175865	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aacaatcttttgtccttcctCagtaccagcagtgcccaaaa	12	11	5	13	0	2	0	1	0	1	0	4	0	4	0	4	0	4	2	4	0	5	4	rs17095822	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:75175865C>T	ENST00000340866.5	-	6	634	c.547G>A	c.(547-549)Gag>Aag	p.E183K	CRYZ_ENST00000492102.1_5'Flank|CRYZ_ENST00000370871.3_Missense_Mutation_p.E183K|CRYZ_ENST00000370872.3_Missense_Mutation_p.E46K|CRYZ_ENST00000417775.1_Missense_Mutation_p.E183K	NM_001889.3	NP_001880.2	Q08257	QOR_HUMAN	crystallin, zeta (quinone reductase)	183			E -> K (in dbSNP:rs17095822).		protein homotetramerization (GO:0051289)|visual perception (GO:0007601)|xenobiotic catabolic process (GO:0042178)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	mRNA 3'-UTR binding (GO:0003730)|NADPH binding (GO:0070402)|NADPH:quinone reductase activity (GO:0003960)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)	10					Dicoumarol(DB00266)	TGTCCTTCCTCAGTACCAGCA	0.353													C|||	105	0.0209665	0.0756	0.0043	5008	,	,		15672	0.001		0.0	False		,,,				2504	0.001				p.E183K		Atlas-SNP	.											.	CRYZ	28	.	0			c.G547A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	244,4162	141.9+/-177.2	7,230,1966	78	79	79		547,547,136,547	4.6	1	1	dbSNP_123	79	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense	CRYZ	NM_001130042.1,NM_001130043.1,NM_001134759.1,NM_001889.3	56,56,56,56	7,233,6263	TT,TC,CC		0.0349,5.5379,1.8991	benign,benign,benign,benign	183/330,183/296,46/193,183/330	75175865	247,12759	2203	4300	6503	SO:0001583	missense	1429	exon6			CTTCCTCAGTACC		CCDS665.1, CCDS44162.1, CCDS44163.1	1p31.1	2013-02-14			ENSG00000116791	ENSG00000116791			2419	protein-coding gene	gene with protein product		123691					Standard	NM_001889		Approved		uc001dgj.3	Q08257	OTTHUMG00000009620	ENST00000340866.5:c.547G>A	1.37:g.75175865C>T	ENSP00000339399:p.Glu183Lys	229	0	0		303	145	0.478548	NM_001130043	A6NN60|D3DQ76|Q53FT0|Q59EU7|Q5HYE7|Q6NSK9	Missense_Mutation	SNP	ENST00000340866.5	37	CCDS665.1	38	0.0173992673992674	37	0.07520325203252033	1	0.0027624309392265192	0	0.0	0	0.0	C	7.833	0.720290	0.15372	0.055379	3.49E-4	ENSG00000116791	ENST00000340866;ENST00000370872;ENST00000417775;ENST00000370871;ENST00000370870;ENST00000441120	T;T;T;T;T;T	0.32272	3.43;3.43;3.43;1.46;3.43;3.43	5.54	4.63	0.57726	Alcohol dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	0.170547	0.48767	D	0.000162	T	0.18173	0.0436	L	0.54863	1.705	0.42476	D	0.992842	B;B;B	0.27068	0.141;0.167;0.029	B;B;B	0.35114	0.051;0.196;0.027	T	0.05084	-1.0907	10	0.39692	T	0.17	.	9.917	0.41442	0.0:0.7871:0.1388:0.074	rs17095822;rs56573849;rs17095822	46;183;183	Q5HYE7;A6NN60;Q08257	.;.;QOR_HUMAN	K	183;46;183;183;183;183	ENSP00000339399:E183K;ENSP00000359909:E46K;ENSP00000399805:E183K;ENSP00000359908:E183K;ENSP00000359907:E183K;ENSP00000404289:E183K	ENSP00000339399:E183K	E	-	1	0	CRYZ	74948453	0.995000	0.38212	0.965000	0.40720	0.170000	0.22686	2.685000	0.46959	1.464000	0.47987	0.563000	0.77884	GAG	C|0.979;T|0.021	0.021	strong		0.353	CRYZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026514.1			T	75175865	C	T	75175865	3	4	22	1	0	0	0	0	1	0	0	0	3924	835	29	2	458	2	CRYZ	1	75175865	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	136902	75175865	174074756	167	3068											
ST6GALNAC3	256435	hgsc.bcm.edu	37	chr1	76878097	76878097	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttaagaaggaaactgggaaGgacaggtgagccctctctga	13	8	13	7	0	1	3	0	2	1	1	2	6	1	6	1	4	2	0	1	4	4	2	rs17098940	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:76878097G>A	ENST00000328299.3	+	3	766	c.618G>A	c.(616-618)aaG>aaA	p.K206K	ST6GALNAC3_ENST00000464140.1_3'UTR	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	206					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						AAACTGGGAAGGACAGGTGAG	0.383													A|||	213	0.0425319	0.1558	0.0101	5008	,	,		18401	0.0		0.0	False		,,,				2504	0.0				p.K206K		Atlas-SNP	.											.	ST6GALNAC3	71	.	0			c.G618A						PASS	.	A	,	562,3844		36,490,1677	45	43	44		618,618	2.4	1	1	dbSNP_123	44	4,8590		0,4,4293	no	coding-synonymous,coding-synonymous	ST6GALNAC3	NM_001160011.1,NM_152996.2	,	36,494,5970	AA,AG,GG		0.0465,12.7553,4.3538	,	206/211,206/306	76878097	566,12434	2203	4297	6500	SO:0001819	synonymous_variant	256435	exon3			TGGGAAGGACAGG		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.618G>A	1.37:g.76878097G>A		42	0	0		67	35	0.522388	NM_001160011	Q6PCE0|Q6UX29|Q8N259	Silent	SNP	ENST00000328299.3	37	CCDS672.1																																																																																			G|0.955;A|0.045	0.045	strong		0.383	ST6GALNAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026501.1	NM_152996		A	76878097	G	A	76878097	2	1	22	1	0	0	0	0	0	0	0	1	15240	991	35	2		2	ST6GALNAC3	1	76878097	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1702232	76878097	172372524	168	3069											
PTGFR	5737	hgsc.bcm.edu	37	chr1	78959081	78959081	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcccttggtgtttcattgtTgtgcaatgcaatcacaggaa	10	13	10	8	0	2	0	2	0	0	0	2	1	2	1	1	2	3	4	1	2	3	4	rs115994459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:78959081T>C	ENST00000370757.3	+	2	890	c.653T>C	c.(652-654)tTg>tCg	p.L218S	PTGFR_ENST00000370756.3_Missense_Mutation_p.L218S|PTGFR_ENST00000370758.1_Missense_Mutation_p.L218S	NM_000959.3	NP_000950.1	P43088	PF2R_HUMAN	prostaglandin F receptor (FP)	218					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)	GTTTCATTGTTGTGCAATGCA	0.378													T|||	22	0.00439297	0.0129	0.0058	5008	,	,		20200	0.0		0.001	False		,,,				2504	0.0				p.L218S		Atlas-SNP	.											.	PTGFR	121	.	0			c.T653C						PASS	.	T	SER/LEU,SER/LEU	58,4348	58.1+/-94.6	1,56,2146	62	65	64		653,653	4.7	0.6	1	dbSNP_132	64	0,8600		0,0,4300	yes	missense,missense	PTGFR	NM_000959.3,NM_001039585.1	145,145	1,56,6446	CC,CT,TT		0.0,1.3164,0.4459	benign,benign	218/360,218/298	78959081	58,12948	2203	4300	6503	SO:0001583	missense	5737	exon2			CATTGTTGTGCAA	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.653T>C	1.37:g.78959081T>C	ENSP00000359793:p.Leu218Ser	126	0	0		142	61	0.429577	NM_000959	A8K9Y0|Q2KHP3|Q6RYQ6|Q9P1X4	Missense_Mutation	SNP	ENST00000370757.3	37	CCDS686.1	9	0.004120879120879121	6	0.012195121951219513	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	T	12.84	2.059053	0.36373	0.013164	0.0	ENSG00000122420	ENST00000370758;ENST00000370757;ENST00000370756	T;T;T	0.38887	1.11;1.11;1.11	5.85	4.73	0.59995	GPCR, rhodopsin-like superfamily (1);	0.414998	0.24801	N	0.035481	T	0.12817	0.0311	N	0.16903	0.455	0.34244	D	0.677948	B;B	0.16166	0.001;0.016	B;B	0.17433	0.008;0.018	T	0.05784	-1.0864	10	0.33940	T	0.23	-2.4004	11.3546	0.49609	0.0:0.0715:0.0:0.9285	.	218;218	P43088;P43088-2	PF2R_HUMAN;.	S	218	ENSP00000359794:L218S;ENSP00000359793:L218S;ENSP00000359792:L218S	ENSP00000359792:L218S	L	+	2	0	PTGFR	78731669	1.000000	0.71417	0.551000	0.28230	0.878000	0.50629	3.960000	0.56752	1.168000	0.42723	0.533000	0.62120	TTG	T|0.995;C|0.005	0.005	strong		0.378	PTGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026582.1	NM_000959		C	78959081	T	C	78959081	3	2	22	1	0	0	0	0	1	0	0	0	12762	1821	63	3	655	3	PTGFR	1	78959081	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2080984	78959081	170291540	169	3070											
CLCA4	22802	hgsc.bcm.edu	37	chr1	87012929	87012929	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttgttatagatcctagtgtgCcagaagatgaaaaaataatt	16	13	8	4	0	0	4	0	1	0	3	1	4	1	4	2	0	1	1	2	0	8	6	rs2231580	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:87012929C>T	ENST00000370563.3	+	1	169	c.127C>T	c.(127-129)Cca>Tca	p.P43S	CLCA4_ENST00000263723.5_5'UTR	NM_012128.3	NP_036260.2	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	43			P -> S (in dbSNP:rs2231580).		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)		TCCTAGTGTGCCAGAAGATGA	0.289													C|||	197	0.0393371	0.143	0.0115	5008	,	,		17655	0.0		0.0	False		,,,				2504	0.0				p.P43S		Atlas-SNP	.											.	CLCA4	131	.	0			c.C127T						PASS	.	C	SER/PRO	430,3208		15,400,1404	112	103	106		127	2.5	0.9	1	dbSNP_98	106	1,8149		0,1,4074	yes	missense	CLCA4	NM_012128.3	74	15,401,5478	TT,TC,CC		0.0123,11.8197,3.6563	benign	43/920	87012929	431,11357	1819	4075	5894	SO:0001583	missense	22802	exon1			AGTGTGCCAGAAG	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.127C>T	1.37:g.87012929C>T	ENSP00000359594:p.Pro43Ser	95	0	0		94	50	0.531915	NM_012128	A8MQC9|B7Z1Q5|Q6UX81|Q9UNF7	Missense_Mutation	SNP	ENST00000370563.3	37	CCDS41355.1	71	0.03250915750915751	67	0.13617886178861788	4	0.011049723756906077	0	0.0	0	0.0	C	13.02	2.111801	0.37242	0.118197	1.23E-4	ENSG00000016602	ENST00000370563	T	0.15487	2.42	5.51	2.51	0.30379	Chloride channel calcium-activated (1);	0.460669	0.22684	N	0.056907	T	0.11324	0.0276	L	0.50993	1.605	0.80722	D	1	P	0.40534	0.72	P	0.53102	0.718	T	0.17961	-1.0352	10	0.34782	T	0.22	-0.5846	2.8316	0.05502	0.1469:0.5502:0.1426:0.1603	rs2231580;rs52821083;rs60157342;rs2231580	43	Q14CN2	CLCA4_HUMAN	S	43	ENSP00000359594:P43S	ENSP00000359594:P43S	P	+	1	0	CLCA4	86785517	0.986000	0.35501	0.942000	0.38095	0.500000	0.33767	0.870000	0.28010	0.336000	0.23639	0.655000	0.94253	CCA	C|0.971;T|0.029	0.029	strong		0.289	CLCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028292.1	NM_012128		T	87012929	C	T	87012929	3	4	22	1	0	0	0	0	1	0	0	0	3461	739	26	2	129	2	CLCA4	1	87012929	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	8053848	87012929	162237692	170	3071											
CLCA4	22802	hgsc.bcm.edu	37	chr1	87043733	87043733	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccactgaatagagccgcgtaCataccaggctgggtagtgaa	12	7	12	10	2	0	3	0	2	0	1	0	3	0	3	3	2	3	3	3	2	6	4	rs2231601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:87043733C>T	ENST00000370563.3	+	12	2142	c.2100C>T	c.(2098-2100)taC>taT	p.Y700Y	RP4-651E10.4_ENST00000456587.1_RNA	NM_012128.3	NP_036260.2	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	700					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)		GAGCCGCGTACATACCAGGCT	0.403													C|||	204	0.0407348	0.149	0.0101	5008	,	,		17663	0.0		0.0	False		,,,				2504	0.0				p.Y700Y		Atlas-SNP	.											.	CLCA4	131	.	0			c.C2100T						PASS	.	C		472,3276		21,430,1423	42	41	41		2100	-7	0	1	dbSNP_98	41	0,8218		0,0,4109	no	coding-synonymous	CLCA4	NM_012128.3		21,430,5532	TT,TC,CC		0.0,12.5934,3.9445		700/920	87043733	472,11494	1874	4109	5983	SO:0001819	synonymous_variant	22802	exon12			CGCGTACATACCA	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.2100C>T	1.37:g.87043733C>T		125	0	0		91	38	0.417582	NM_012128	A8MQC9|B7Z1Q5|Q6UX81|Q9UNF7	Silent	SNP	ENST00000370563.3	37	CCDS41355.1																																																																																			C|0.976;T|0.024	0.024	strong		0.403	CLCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028292.1	NM_012128		T	87043733	C	T	87043733	2	4	22	1	0	0	0	0	0	0	0	1	3461	489	17	2		2	CLCA4	1	87043733	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	30804	87043733	162206888	171	3072											
CLCA4	22802	hgsc.bcm.edu	37	chr1	87045696	87045696	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gttttgatgatgctcttcaaGtaaatactactgatctgtca	11	16	7	7	0	4	3	2	3	2	0	4	3	4	3	0	0	3	3	0	0	5	6	rs2231604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:87045696G>C	ENST00000370563.3	+	14	2470	c.2428G>C	c.(2428-2430)Gta>Cta	p.V810L	RP4-651E10.4_ENST00000456587.1_RNA	NM_012128.3	NP_036260.2	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	810			V -> L (in dbSNP:rs2231604). {ECO:0000269|PubMed:15489334}.		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)		TGCTCTTCAAGTAAATACTAC	0.333													G|||	275	0.0549121	0.1944	0.0115	5008	,	,		18080	0.005		0.0	False		,,,				2504	0.0051				p.V810L		Atlas-SNP	.											.	CLCA4	131	.	0			c.G2428C						PASS	.	G	LEU/VAL	642,3036		52,538,1249	57	51	53		2428	4.9	0.9	1	dbSNP_98	53	2,8174		0,2,4086	yes	missense	CLCA4	NM_012128.3	32	52,540,5335	CC,CG,GG		0.0245,17.4551,5.4328	probably-damaging	810/920	87045696	644,11210	1839	4088	5927	SO:0001583	missense	22802	exon14			CTTCAAGTAAATA	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.2428G>C	1.37:g.87045696G>C	ENSP00000359594:p.Val810Leu	110	0	0		149	59	0.395973	NM_012128	A8MQC9|B7Z1Q5|Q6UX81|Q9UNF7	Missense_Mutation	SNP	ENST00000370563.3	37	CCDS41355.1	109	0.04990842490842491	102	0.2073170731707317	5	0.013812154696132596	2	0.0034965034965034965	0	0.0	G	14.30	2.494809	0.44352	0.174551	2.45E-4	ENSG00000016602	ENST00000370563	T	0.03717	3.83	5.82	4.91	0.64330	.	0.000000	0.64402	D	0.000001	T	0.04048	0.0113	M	0.80847	2.515	0.09310	P	1.0	P;P	0.47350	0.894;0.894	P;P	0.45071	0.468;0.468	T	0.25398	-1.0133	9	0.44086	T	0.13	-20.4313	10.9104	0.47106	0.071:0.1305:0.7984:0.0	rs2231604;rs52796222;rs2231604	362;810	Q9NXP1;Q14CN2	.;CLCA4_HUMAN	L	810	ENSP00000359594:V810L	ENSP00000359594:V810L	V	+	1	0	CLCA4	86818284	0.999000	0.42202	0.888000	0.34837	0.308000	0.27856	2.265000	0.43311	1.477000	0.48234	-0.237000	0.12165	GTA	G|0.950;C|0.050	0.050	strong		0.333	CLCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028292.1	NM_012128		C	87045696	G	C	87045696	3	2	22	1	0	0	0	0	1	0	0	0	3461	1029	36	4	2482	4	CLCA4	1	87045696	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1963	87045696	162204925	172	3073											
CLCA4	22802	hgsc.bcm.edu	37	chr1	87045903	87045908	+	In_Frame_Del	DEL	CCTACT	CCTACT	-																															ctgatgacattgatcctacaCctactcctactcctactcct																								rs56040873|rs77594462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCTACT	CCTACT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:87045903_87045908delCCTACT	ENST00000370563.3	+	14	2677_2682	c.2635_2640delCCTACT	c.(2635-2640)cctactdel	p.PT885del	RP4-651E10.4_ENST00000456587.1_RNA	NM_012128.3	NP_036260.2	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	885					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)		TGAtcctacacctactcctactccta	0.345																																					p.878_880del		Pindel,Atlas-Indel	.											.	CLCA4	131	.	0			c.2634_2639del						PASS	.			2247,6,1315		606,4,1031,1,0,142						-0.9	0		dbSNP_108	97	5524,10,2288		1973,7,1571,1,1,358	no	codingComplex	CLCA4	NM_012128.3		2579,11,2602,2,1,500	A1A1,A1A2,A1R,A2A2,A2R,RR		29.3787,37.0235,31.7735				7771,16,3603				SO:0001651	inframe_deletion	22802	exon14			.	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.2635_2640delCCTACT	1.37:g.87045909_87045914delCCTACT	ENSP00000359594:p.Pro885_Thr886del	146	0	.		181	46	0.254	NM_012128	A8MQC9|B7Z1Q5|Q6UX81|Q9UNF7	In_Frame_Del	DEL	ENST00000370563.3	37	CCDS41355.1																																																																																			.	.	weak		0.345	CLCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028292.1	NM_012128		-	87045908	CCTACT	-	87045903	7	5	22	1	0	1	0	1	0	0	0	0	3461	507	18	0	2689	0	CLCA4	1	87045903	In_Frame_Del	DEL	CCTACT	TCGA-G8-6324-01A-11D-2210-10	207	87045903	162204718	173	3074											
PKN2	5586	hgsc.bcm.edu	37	chr1	89273241	89273241	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggtttcagtttaatctacAagatttcaggtgttgtgctg	10	16	10	5	0	3	1	2	0	1	1	3	1	3	1	0	2	2	4	0	2	4	6	rs12085658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:89273241A>G	ENST00000370521.3	+	14	2323	c.1964A>G	c.(1963-1965)cAa>cGa	p.Q655R	PKN2_ENST00000370505.3_Missense_Mutation_p.Q498R|PKN2_ENST00000370513.5_Missense_Mutation_p.Q607R|PKN2_ENST00000544045.1_Missense_Mutation_p.Q329R	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	655			Q -> R (in dbSNP:rs12085658).		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)		TTTAATCTACAAGATTTCAGG	0.318													A|||	43	0.00858626	0.0295	0.0058	5008	,	,		16355	0.0		0.0	False		,,,				2504	0.0				p.Q655R		Atlas-SNP	.											.	PKN2	109	.	0			c.A1964G						PASS	.	A	ARG/GLN	90,3516		0,90,1713	150	145	146		1964	5.8	1	1	dbSNP_120	146	0,8134		0,0,4067	yes	missense	PKN2	NM_006256.2	43	0,90,5780	GG,GA,AA		0.0,2.4958,0.7666	benign	655/985	89273241	90,11650	1803	4067	5870	SO:0001583	missense	5586	exon14			ATCTACAAGATTT	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.1964A>G	1.37:g.89273241A>G	ENSP00000359552:p.Gln655Arg	103	0	0		101	50	0.49505	NM_006256	B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	Missense_Mutation	SNP	ENST00000370521.3	37	CCDS714.1	14	0.00641025641025641	12	0.024390243902439025	2	0.0055248618784530384	0	0.0	0	0.0	A	15.07	2.724560	0.48833	0.024958	0.0	ENSG00000065243	ENST00000370521;ENST00000370505;ENST00000370513;ENST00000544045	T;T;T;T	0.24538	1.85;1.85;1.85;1.85	5.75	5.75	0.90469	Protein kinase-like domain (1);	0.162237	0.28612	U	0.014721	T	0.07728	0.0194	N	0.08118	0	0.36654	D	0.877588	B;B;B	0.22683	0.073;0.073;0.025	B;B;B	0.17098	0.017;0.017;0.013	T	0.09773	-1.0659	10	0.54805	T	0.06	.	16.0549	0.80794	1.0:0.0:0.0:0.0	rs12085658;rs52814429;rs12085658	639;607;655	B4DTP5;E7ESL7;Q16513	.;.;PKN2_HUMAN	R	655;498;607;329	ENSP00000359552:Q655R;ENSP00000359536:Q498R;ENSP00000359544:Q607R;ENSP00000439643:Q329R	ENSP00000359536:Q498R	Q	+	2	0	PKN2	89045829	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.711000	0.61881	2.193000	0.70182	0.477000	0.44152	CAA	A|0.992;G|0.008	0.008	strong		0.318	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027828.3	NM_006256		G	89273241	A	G	89273241	3	3	22	1	0	0	0	0	1	0	0	0	11989	130	5	3	2018	3	PKN2	1	89273241	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2227338	89273241	159977380	174	3075											
RBMXL1	494115	hgsc.bcm.edu	37	chr1	89449168	89449168	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccctggttcctccacttccTcctcttccagctccaaaacc	6	11	3	21	0	1	0	0	0	1	0	7	0	7	0	9	1	2	2	9	1	2	3	rs59048247	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:89449168T>A	ENST00000321792.5	-	2	769	c.342A>T	c.(340-342)ggA>ggT	p.G114G	CCBL2_ENST00000446900.2_Intron|RBMXL1_ENST00000413769.1_5'UTR|CCBL2_ENST00000260508.4_Intron|RBMXL1_ENST00000399794.2_Silent_p.G114G|CCBL2_ENST00000370485.2_Intron|CCBL2_ENST00000370491.3_Intron	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	114					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										CTCCACTTCCTCCTCTTCCAG	0.512													.|||	318	0.0634984	0.2292	0.0187	5008	,	,		19592	0.0		0.002	False		,,,				2504	0.0				p.G114G		Atlas-SNP	.											.	.	.	.	0			c.A342T						PASS	.	T	,,,	876,3530	339.1+/-305.6	83,710,1410	90	98	96		,,342,342	-0.4	0.5	1	dbSNP_129	96	10,8590	7.1+/-27.0	0,10,4290	no	intron,intron,coding-synonymous,coding-synonymous	CCBL2,RBMXL1	NM_001008661.2,NM_001008662.2,NM_001162536.2,NM_019610.5	,,,	83,720,5700	AA,AT,TT		0.1163,19.882,6.8122	,,,	,,114/391,114/391	89449168	886,12120	2203	4300	6503	SO:0001819	synonymous_variant	494115	exon3			ACTTCCTCCTCTT	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.342A>T	1.37:g.89449168T>A		394	0	0		338	150	0.443787	NM_001162536		Silent	SNP	ENST00000321792.5	37	CCDS716.1																																																																																			T|0.940;A|0.060	0.060	strong		0.512	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610		A	89449168	T	A	89449168	2	1	22	1	0	0	0	0	0	0	0	1	13168	1538	54	5		5	RBMXL1	1	89449168	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	175927	89449168	159801453	175	3076											
CCBL2	56267	hgsc.bcm.edu	37	chr1	89453966	89453966	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agaatccgaggattttggaaGaagaaattgtcttcaggaat	15	11	11	4	1	2	3	1	0	1	3	3	7	3	6	1	3	0	0	1	3	5	4	rs74100109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:89453966G>A	ENST00000260508.4	-	2	405	c.68C>T	c.(67-69)tCt>tTt	p.S23F	CCBL2_ENST00000446900.2_5'UTR|RBMXL1_ENST00000413769.1_5'UTR|RBMXL1_ENST00000399794.2_5'UTR|CCBL2_ENST00000370485.2_Missense_Mutation_p.S23F|CCBL2_ENST00000370491.3_Intron|RBMXL1_ENST00000321792.5_Intron	NM_001008661.2	NP_001008661.1	Q6YP21	KAT3_HUMAN	cysteine conjugate-beta lyase 2	23					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)		GATTTTGGAAGAAGAAATTGT	0.348													G|||	45	0.00898562	0.0318	0.0043	5008	,	,		17385	0.0		0.0	False		,,,				2504	0.0				p.S23F		Atlas-SNP	.											.	CCBL2	138	.	0			c.C68T						PASS	.	G	PHE/SER,,,	148,4258	96.2+/-134.9	4,140,2059	58	64	62		68,,,	4.6	1	1	dbSNP_130	62	0,8600		0,0,4300	yes	missense,intron,utr-5,intron	CCBL2,RBMXL1	NM_001008661.2,NM_001008662.2,NM_001162536.2,NM_019610.5	155,,,	4,140,6359	AA,AG,GG		0.0,3.3591,1.1379	benign,,,	23/455,,,	89453966	148,12858	2203	4300	6503	SO:0001583	missense	56267	exon2			TTGGAAGAAGAAA	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.68C>T	1.37:g.89453966G>A	ENSP00000260508:p.Ser23Phe	266	0	0		328	159	0.484756	NM_001008661	B3KQ13|O95335|Q5JS27|Q5T9T7|Q5T9T8|Q6AI27|Q6ICW1|Q9BVY5	Missense_Mutation	SNP	ENST00000260508.4	37	CCDS30766.1	13	0.005952380952380952	11	0.022357723577235773	2	0.0055248618784530384	0	0.0	0	0.0	G	9.181	1.023703	0.19433	0.033591	0.0	ENSG00000137944	ENST00000260508;ENST00000370485;ENST00000370486	T;T	0.72725	-0.68;-0.52	5.5	4.58	0.56647	.	0.894418	0.09587	N	0.782010	T	0.43233	0.1238	N	0.22421	0.69	0.80722	D	1	B	0.25169	0.119	B	0.24269	0.052	T	0.42447	-0.9451	10	0.52906	T	0.07	-4.0555	9.248	0.37539	0.0959:0.0:0.9041:0.0	.	23	Q6YP21	KAT3_HUMAN	F	23	ENSP00000260508:S23F;ENSP00000359517:S23F	ENSP00000260508:S23F	S	-	2	0	CCBL2	89226554	0.999000	0.42202	0.970000	0.41538	0.267000	0.26476	3.285000	0.51716	2.588000	0.87417	0.650000	0.86243	TCT	G|0.988;A|0.012	0.012	strong		0.348	CCBL2-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000029300.3	NM_001008661		A	89453966	G	A	89453966	3	1	22	1	0	0	0	0	1	0	0	0	2735	942	33	2	1348	2	CCBL2	1	89453966	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4798	89453966	159796655	176	3077											
GBP7	388646	hgsc.bcm.edu	37	chr1	89615023	89615023	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttatctttgaaggagtactcCatgaagactgcaatggcttc	11	13	9	8	0	1	3	0	2	1	1	3	4	2	4	1	2	2	3	1	2	5	4	rs74098339	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:89615023C>G	ENST00000294671.2	-	7	1242	c.1104G>C	c.(1102-1104)atG>atC	p.M368I		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	368						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)		AGGAGTACTCCATGAAGACTG	0.453													C|||	43	0.00858626	0.0303	0.0043	5008	,	,		17526	0.0		0.0	False		,,,				2504	0.0				p.M368I		Atlas-SNP	.											.	GBP7	57	.	0			c.G1104C						PASS	.	C	ILE/MET	143,4263	99.8+/-138.5	3,137,2063	97	93	95		1104	3.5	1	1	dbSNP_130	95	0,8600		0,0,4300	no	missense	GBP7	NM_207398.2	10	3,137,6363	GG,GC,CC		0.0,3.2456,1.0995	possibly-damaging	368/639	89615023	143,12863	2203	4300	6503	SO:0001583	missense	388646	exon7			GTACTCCATGAAG	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.1104G>C	1.37:g.89615023C>G	ENSP00000294671:p.Met368Ile	202	1	0.00495049		235	120	0.510638	NM_207398		Missense_Mutation	SNP	ENST00000294671.2	37	CCDS720.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	C	8.920	0.960823	0.18583	0.032456	0.0	ENSG00000213512	ENST00000294671	T	0.02369	4.32	3.54	3.54	0.40534	Guanylate-binding protein, C-terminal (3);	0.154247	0.56097	D	0.000024	T	0.02649	0.0080	M	0.70903	2.155	0.34498	D	0.705737	B	0.32324	0.364	B	0.37943	0.261	T	0.22765	-1.0207	10	0.45353	T	0.12	.	12.621	0.56603	0.0:1.0:0.0:0.0	.	368	Q8N8V2	GBP7_HUMAN	I	368	ENSP00000294671:M368I	ENSP00000294671:M368I	M	-	3	0	GBP7	89387611	0.368000	0.25031	1.000000	0.80357	0.063000	0.16089	0.647000	0.24812	1.819000	0.53055	0.523000	0.50628	ATG	C|0.988;G|0.012	0.012	strong		0.453	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398		G	89615023	C	G	89615023	3	3	22	1	0	0	0	0	1	0	0	0	6287	594	21	4	832	4	GBP7	1	89615023	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	161057	89615023	159635598	177	3078											
GBP5	115362	hgsc.bcm.edu	37	chr1	89735229	89735229	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ggggtctgacatgtggatctCtaaagccatgtctaggatgt	9	12	13	7	0	3	1	0	1	3	0	4	3	3	3	1	4	1	0	1	4	3	2	rs17130763	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:89735229C>G	ENST00000370459.3	-	2	137	c.10G>C	c.(10-12)Gag>Cag	p.E4Q	GBP5_ENST00000343435.5_Missense_Mutation_p.E4Q|RP4-620F22.2_ENST00000437128.1_RNA			Q96PP8	GBP5_HUMAN	guanylate binding protein 5	4	GTPase domain (Globular). {ECO:0000250}.		E -> Q (in dbSNP:rs17130763).			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)		ATGTGGATCTCTAAAGCCATG	0.443													C|||	76	0.0151757	0.053	0.0086	5008	,	,		12783	0.0		0.0	False		,,,				2504	0.0				p.E4Q		Atlas-SNP	.											.	GBP5	65	.	0			c.G10C						PASS	.	C	GLN/GLU,GLN/GLU	202,4204	125.3+/-162.5	4,194,2005	169	164	166		10,10	1.5	0	1	dbSNP_123	166	0,8600		0,0,4300	yes	missense,missense	GBP5	NM_001134486.2,NM_052942.3	29,29	4,194,6305	GG,GC,CC		0.0,4.5847,1.5531	benign,benign	4/587,4/587	89735229	202,12804	2203	4300	6503	SO:0001583	missense	115362	exon3			GGATCTCTAAAGC	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.10G>C	1.37:g.89735229C>G	ENSP00000359488:p.Glu4Gln	142	0	0		137	72	0.525547	NM_052942	B2RCE1|Q86TM5	Missense_Mutation	SNP	ENST00000370459.3	37	CCDS722.1	25	0.011446886446886446	21	0.042682926829268296	4	0.011049723756906077	0	0.0	0	0.0	C	11.40	1.626401	0.28978	0.045847	0.0	ENSG00000154451	ENST00000343435;ENST00000370459;ENST00000443807	T;T;T	0.66099	0.36;0.36;-0.19	5.0	1.48	0.22813	.	0.954043	0.08802	N	0.891614	T	0.35008	0.0917	M	0.62154	1.92	0.09310	N	1	B	0.20052	0.041	B	0.22152	0.038	T	0.32693	-0.9897	10	0.33141	T	0.24	-0.4944	5.2406	0.15469	0.1544:0.6219:0.0:0.2237	rs17130763;rs17130763	4	Q96PP8	GBP5_HUMAN	Q	4	ENSP00000340396:E4Q;ENSP00000359488:E4Q;ENSP00000403010:E4Q	ENSP00000340396:E4Q	E	-	1	0	GBP5	89507817	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.226000	0.17776	0.521000	0.28445	0.655000	0.94253	GAG	C|0.976;G|0.024	0.024	strong		0.443	GBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027700.1	NM_052942		G	89735229	C	G	89735229	3	3	22	1	0	0	0	0	1	0	0	0	6285	922	32	4	1790	4	GBP5	1	89735229	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	120206	89735229	159515392	178	3079											
LRRC8B	23507	hgsc.bcm.edu	37	chr1	90049088	90049088	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcgactgttcagttgatgtGcaggcttttacaggatataa	11	14	10	6	1	1	1	1	1	0	0	2	3	1	2	0	2	2	4	0	2	3	6	rs35903285	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:90049088G>A	ENST00000330947.2	+	5	1239	c.879G>A	c.(877-879)gtG>gtA	p.V293V	RP5-1007M22.2_ENST00000443562.1_RNA|LRRC8B_ENST00000358200.4_Silent_p.V293V|LRRC8B_ENST00000439853.1_Silent_p.V293V	NM_001134476.1	NP_001127948.1	Q6P9F7	LRC8B_HUMAN	leucine rich repeat containing 8 family, member B	293					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)		CAGTTGATGTGCAGGCTTTTA	0.353													G|||	110	0.0219649	0.0787	0.0086	5008	,	,		22049	0.0		0.0	False		,,,				2504	0.0				p.V293V		Atlas-SNP	.											.	LRRC8B	49	.	0			c.G879A						PASS	.	G	,	315,4091	167.3+/-198.3	12,291,1900	154	153	153		879,879	-0.2	0.9	1	dbSNP_126	153	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous	LRRC8B	NM_001134476.1,NM_015350.2	,	12,295,6196	AA,AG,GG		0.0465,7.1493,2.4527	,	293/804,293/804	90049088	319,12687	2203	4300	6503	SO:0001819	synonymous_variant	23507	exon5			TGATGTGCAGGCT	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.879G>A	1.37:g.90049088G>A		67	0	0		94	43	0.457447	NM_015350	D3DT28|Q6UY21|Q8N106|Q92627	Silent	SNP	ENST00000330947.2	37	CCDS724.1																																																																																			G|0.976;A|0.024	0.024	strong		0.353	LRRC8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028008.1	NM_015350		A	90049088	G	A	90049088	2	1	22	1	0	0	0	0	0	0	0	1	9031	1306	46	2		2	LRRC8B	1	90049088	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	313859	90049088	159201533	179	3080											
LRRC8C	84230	hgsc.bcm.edu	37	chr1	90179470	90179470	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttgaaatcacagagttgcaAtctctaaaacttgaaatcat	16	13	5	7	0	3	3	2	2	1	1	4	3	3	3	0	0	2	2	0	0	5	4	rs34576461	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:90179470A>G	ENST00000370454.4	+	3	1596	c.1341A>G	c.(1339-1341)caA>caG	p.Q447Q	LRRC8C_ENST00000479252.1_Intron|RP11-302M6.4_ENST00000370453.5_Intron	NM_032270.4	NP_115646	Q8TDW0	LRC8C_HUMAN	leucine rich repeat containing 8 family, member C	447					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)		CAGAGTTGCAATCTCTAAAAC	0.423													A|||	99	0.0197684	0.0703	0.0086	5008	,	,		19984	0.0		0.0	False		,,,				2504	0.0				p.Q447Q		Atlas-SNP	.											.	LRRC8C	73	.	0			c.A1341G						PASS	.	A		281,4125	158.5+/-191.2	11,259,1933	88	84	85		1341	-0.5	1	1	dbSNP_126	85	0,8600		0,0,4300	no	coding-synonymous	LRRC8C	NM_032270.4		11,259,6233	GG,GA,AA		0.0,6.3777,2.1605		447/804	90179470	281,12725	2203	4300	6503	SO:0001819	synonymous_variant	84230	exon3			GTTGCAATCTCTA		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.1341A>G	1.37:g.90179470A>G		81	0	0		68	35	0.514706	NM_032270	B3KXS9|Q29RV6|Q9H075	Silent	SNP	ENST00000370454.4	37	CCDS725.1																																																																																			A|0.979;G|0.021	0.021	strong		0.423	LRRC8C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028435.2	NM_032270		G	90179470	A	G	90179470	2	3	22	1	0	0	0	0	0	0	0	1	9032	98	4	3		3	LRRC8C	1	90179470	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	130382	90179470	159071151	180	3081											
BRDT	676	hgsc.bcm.edu	37	chr1	92445179	92445179	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgaacctgttgagagtatGcctttatgttacatcaaaac	13	14	7	7	0	1	2	1	2	0	1	1	3	1	2	2	0	4	3	2	0	6	6	rs114276662	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:92445179G>A	ENST00000362005.3	+	9	1570	c.1152G>A	c.(1150-1152)atG>atA	p.M384I	BRDT_ENST00000394530.3_Missense_Mutation_p.M338I|BRDT_ENST00000399546.2_Missense_Mutation_p.M384I|BRDT_ENST00000402388.1_Missense_Mutation_p.M384I|BRDT_ENST00000370389.2_Missense_Mutation_p.M311I	NM_001242805.1	NP_001229734	Q58F21	BRDT_HUMAN	bromodomain, testis-specific	384					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)		TTGAGAGTATGCCTTTATGTT	0.348													G|||	22	0.00439297	0.0144	0.0029	5008	,	,		16690	0.0		0.001	False		,,,				2504	0.0				p.M388I		Atlas-SNP	.											.	BRDT	133	.	0			c.G1164A						PASS	.	G	ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET	67,4339	61.7+/-98.7	0,67,2136	103	103	103		1152,1164,1014,1014,933,1152,1152	3.5	0	1	dbSNP_133	103	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense,missense	BRDT	NM_001242805.1,NM_001242806.1,NM_001242807.1,NM_001242808.1,NM_001242810.1,NM_001726.3,NM_207189.2	10,10,10,10,10,10,10	0,67,6436	AA,AG,GG		0.0,1.5207,0.5151	benign,benign,benign,benign,benign,benign,benign	384/948,388/952,338/902,338/902,311/875,384/948,384/948	92445179	67,12939	2203	4300	6503	SO:0001583	missense	676	exon8			GAGTATGCCTTTA	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.1152G>A	1.37:g.92445179G>A	ENSP00000354568:p.Met384Ile	195	0	0		206	92	0.446602	NM_001242806	A6NF68|B7Z811|B7Z890|B7ZAX7|D3DT32|O14789|Q05DQ4|Q6P5T1|Q7Z4A6|Q8IWI6	Missense_Mutation	SNP	ENST00000362005.3	37	CCDS735.1	7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	G	7.998	0.754682	0.15778	0.015207	0.0	ENSG00000137948	ENST00000362005;ENST00000370389;ENST00000399546;ENST00000539070;ENST00000394530;ENST00000426141;ENST00000402388	T;T;T;T;T;T	0.09163	3.33;3.34;3.33;3.38;3.01;3.33	5.41	3.49	0.39957	Bromodomain (1);	0.456653	0.24005	N	0.042435	T	0.02230	0.0069	L	0.29908	0.895	0.09310	N	1	B;B;B;B	0.18863	0.031;0.031;0.0;0.031	B;B;B;B	0.09377	0.004;0.004;0.002;0.002	T	0.43032	-0.9416	10	0.38643	T	0.18	-0.2883	5.9499	0.19239	0.1483:0.0:0.5637:0.288	.	338;338;388;384	B7ZAX7;B7Z811;B7Z890;Q58F21	.;.;.;BRDT_HUMAN	I	384;311;384;384;338;384;384	ENSP00000354568:M384I;ENSP00000359416:M311I;ENSP00000387822:M384I;ENSP00000378038:M338I;ENSP00000404969:M384I;ENSP00000384051:M384I	ENSP00000354568:M384I	M	+	3	0	BRDT	92217767	0.008000	0.16893	0.016000	0.15963	0.543000	0.35085	1.606000	0.36826	0.631000	0.30412	0.655000	0.94253	ATG	G|0.995;A|0.005	0.005	strong		0.348	BRDT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027980.2	NM_207189		A	92445179	G	A	92445179	3	1	22	1	0	0	0	0	1	0	0	0	1510	1319	46	2	1178	2	BRDT	1	92445179	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2265709	92445179	156805442	181	3082											
BRDT	676	hgsc.bcm.edu	37	chr1	92467626	92467626	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtgattctgaacagctctcaAatggcataactgtgatgcat	12	12	9	8	0	2	3	1	3	2	0	3	3	2	3	0	1	4	3	0	1	3	2	rs78267346	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:92467626A>G	ENST00000362005.3	+	17	2726	c.2308A>G	c.(2308-2310)Aat>Gat	p.N770D	BRDT_ENST00000394530.3_Missense_Mutation_p.N724D|BRDT_ENST00000399546.2_Missense_Mutation_p.N770D|BRDT_ENST00000402388.1_Missense_Mutation_p.N770D|BRDT_ENST00000370389.2_Missense_Mutation_p.N697D	NM_001242805.1	NP_001229734	Q58F21	BRDT_HUMAN	bromodomain, testis-specific	770					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)		ACAGCTCTCAAATGGCATAAC	0.333													A|||	56	0.0111821	0.0401	0.0029	5008	,	,		17569	0.0		0.001	False		,,,				2504	0.0				p.N774D		Atlas-SNP	.											.	BRDT	133	.	0			c.A2320G						PASS	.	A	ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN	113,4293	86.8+/-125.4	2,109,2092	113	101	105		2308,2320,2170,2170,2089,2308,2308	1.3	0	1	dbSNP_132	105	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense,missense	BRDT	NM_001242805.1,NM_001242806.1,NM_001242807.1,NM_001242808.1,NM_001242810.1,NM_001726.3,NM_207189.2	23,23,23,23,23,23,23	2,109,6392	GG,GA,AA		0.0,2.5647,0.8688	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	770/948,774/952,724/902,724/902,697/875,770/948,770/948	92467626	113,12893	2203	4300	6503	SO:0001583	missense	676	exon16			CTCTCAAATGGCA	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.2308A>G	1.37:g.92467626A>G	ENSP00000354568:p.Asn770Asp	275	0	0		297	159	0.535354	NM_001242806	A6NF68|B7Z811|B7Z890|B7ZAX7|D3DT32|O14789|Q05DQ4|Q6P5T1|Q7Z4A6|Q8IWI6	Missense_Mutation	SNP	ENST00000362005.3	37	CCDS735.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	A	8.950	0.968040	0.18659	0.025647	0.0	ENSG00000137948	ENST00000362005;ENST00000370389;ENST00000399546;ENST00000394530;ENST00000402388	T;T;T;T;T	0.57107	0.42;0.42;0.42;0.42;0.42	3.71	1.32	0.21799	.	0.438833	0.21441	N	0.074491	T	0.18341	0.0440	L	0.56769	1.78	0.09310	N	1	B;B;B;B	0.33694	0.421;0.421;0.16;0.421	B;B;B;B	0.29862	0.108;0.108;0.045;0.055	T	0.14504	-1.0470	10	0.18710	T	0.47	-3.342	3.8025	0.08764	0.6439:0.235:0.1211:0.0	.	724;724;774;770	B7ZAX7;B7Z811;B7Z890;Q58F21	.;.;.;BRDT_HUMAN	D	770;697;770;724;770	ENSP00000354568:N770D;ENSP00000359416:N697D;ENSP00000387822:N770D;ENSP00000378038:N724D;ENSP00000384051:N770D	ENSP00000354568:N770D	N	+	1	0	BRDT	92240214	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	0.214000	0.17541	0.274000	0.22072	0.533000	0.62120	AAT	A|0.988;G|0.012	0.012	strong		0.333	BRDT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027980.2	NM_207189		G	92467626	A	G	92467626	3	3	22	1	0	0	0	0	1	0	0	0	1510	14	1	3	2366	3	BRDT	1	92467626	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	22447	92467626	156782995	182	3083											
RPL5	6125	hgsc.bcm.edu	37	chr1	93299193	93299193	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tacaggatgatagttcgtgtGacaaacagagatatcatttg	14	12	10	5	1	1	3	1	2	0	1	2	5	1	4	0	1	2	1	0	1	4	5	rs58263806	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:93299193G>A	ENST00000370321.3	+	3	255	c.165G>A	c.(163-165)gtG>gtA	p.V55V		NM_000969.3	NP_000960.2	P46777	RL5_HUMAN	ribosomal protein L5	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)|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)		TAGTTCGTGTGACAAACAGAG	0.368													A|||	121	0.0241613	0.0877	0.0058	5008	,	,		18734	0.0		0.001	False		,,,				2504	0.0				p.V55V		Atlas-SNP	.											.	RPL5	38	.	0			c.G165A						PASS	.	A		313,4093	796.5+/-415.4	11,291,1901	62	68	66		165	1.1	1	1	dbSNP_129	66	4,8596	818.7+/-406.8	0,4,4296	no	coding-synonymous	RPL5	NM_000969.3		11,295,6197	AA,AG,GG		0.0465,7.1039,2.4373		55/298	93299193	317,12689	2203	4300	6503	SO:0001819	synonymous_variant	6125	exon3			TCGTGTGACAAAC	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.165G>A	1.37:g.93299193G>A		67	0	0		70	25	0.357143	NM_000969	Q32LZ3|Q53HH6|Q9H3F4	Silent	SNP	ENST00000370321.3	37	CCDS741.1																																																																																			G|0.977;A|0.023	0.023	strong		0.368	RPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030058.2	NM_000969		A	93299193	G	A	93299193	2	1	22	1	0	0	0	0	0	0	0	1	13612	1277	45	2		2	RPL5	1	93299193	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	831567	93299193	155951428	183	3084											
CCDC18	343099	hgsc.bcm.edu	37	chr1	93720153	93720153	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	attgaaagaacacaacaaagGatgaaagaaatggagagtgt	21	6	11	3	0	0	5	0	2	0	3	0	7	0	6	0	2	2	0	0	2	6	1	rs61729705	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:93720153G>T	ENST00000343253.7	+	24	3823	c.3321G>T	c.(3319-3321)agG>agT	p.R1107S	CCDC18_ENST00000338949.4_3'UTR|CCDC18_ENST00000401026.3_Missense_Mutation_p.R1108S|CCDC18_ENST00000557479.1_Missense_Mutation_p.R1226S|CCDC18_ENST00000334652.5_3'UTR			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	1107										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)		CACAACAAAGGATGAAAGAAA	0.323													G|||	487	0.0972444	0.3366	0.0288	5008	,	,		19033	0.0159		0.002	False		,,,				2504	0.0041				p.R1108S		Atlas-SNP	.											.	CCDC18	93	.	0			c.G3324T						PASS	.	G	SER/ARG	1093,2575		157,779,898	125	131	129		3324	0.4	1	1	dbSNP_129	129	13,8157		1,11,4073	yes	missense	CCDC18	NM_206886.3	110	158,790,4971	TT,TG,GG		0.1591,29.7983,9.3428	benign	1108/1300	93720153	1106,10732	1834	4085	5919	SO:0001583	missense	343099	exon24			ACAAAGGATGAAA			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.3321G>T	1.37:g.93720153G>T	ENSP00000343377:p.Arg1107Ser	217	0	0		200	90	0.45	NM_206886	Q6ZU17	Missense_Mutation	SNP	ENST00000343253.7	37		175|175	0.08012820512820513|0.08012820512820513	150|150	0.3048780487804878|0.3048780487804878	12|12	0.03314917127071823|0.03314917127071823	11|11	0.019230769230769232|0.019230769230769232	2|2	0.002638522427440633|0.002638522427440633	G|G	5.074|5.074	0.199375|0.199375	0.09652|0.09652	0.297983|0.297983	0.001591|0.001591	ENSG00000122483|ENSG00000122483	ENST00000370276|ENST00000343253;ENST00000401026;ENST00000557479	.|.	.|.	.|.	5.02|5.02	0.449|0.449	0.16619|0.16619	.|.	.|0.782786	.|0.12361	.|N	.|0.475673	T|T	0.06462|0.06462	0.0166|0.0166	N|N	0.12182|0.12182	0.205|0.205	0.09310|0.09310	P|P	0.99999902352|0.99999902352	.|P;B	.|0.35575	.|0.51;0.006	.|B;B	.|0.36666	.|0.23;0.005	T|T	0.30149|0.30149	-0.9988|-0.9988	4|8	.|0.21540	.|T	.|0.41	.|.	5.0771|5.0771	0.14638|0.14638	0.5374:0.1787:0.2838:0.0|0.5374:0.1787:0.2838:0.0	rs61729705|rs61729705	.|26;1226	.|Q5T9S4;G3V388	.|.;.	V|S	1161|1107;1108;1226	.|.	.|ENSP00000343377:R1107S	G|R	+|+	2|3	0|2	CCDC18|CCDC18	93492741|93492741	1.000000|1.000000	0.71417|0.71417	0.977000|0.977000	0.42913|0.42913	0.453000|0.453000	0.32348|0.32348	0.703000|0.703000	0.25646|0.25646	0.243000|0.243000	0.21327|0.21327	-0.143000|-0.143000	0.13931|0.13931	GGA|AGG	A|0.000;G|0.947;T|0.053	0.053	strong		0.323	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886		T	93720153	G	T	93720153	3	4	22	1	0	0	0	0	1	0	0	0	2796	1165	41	4	3772	4	CCDC18	1	93720153	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	420960	93720153	155530468	184	3085											
BCAR3	8412	hgsc.bcm.edu	37	chr1	94049576	94049576	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaattccccgaaacataccAatcggcaggtagctctctga	14	8	7	12	2	1	1	0	1	1	0	4	2	2	1	3	2	3	3	3	2	6	3	rs78645541	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:94049576A>G	ENST00000370244.1	-	8	1320	c.1032T>C	c.(1030-1032)atT>atC	p.I344I	BCAR3_ENST00000539242.1_Splice_Site_p.I20I|BCAR3_ENST00000370247.3_Splice_Site_p.I253I|BCAR3_ENST00000466632.1_5'UTR|BCAR3_ENST00000370243.1_Splice_Site_p.I344I|BCAR3_ENST00000260502.6_Splice_Site_p.I344I	NM_001261408.1	NP_001248337.1	O75815	BCAR3_HUMAN	breast cancer anti-estrogen resistance 3	344					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)		GAAACATACCAATCGGCAGGT	0.522													A|||	34	0.00678914	0.025	0.0014	5008	,	,		18298	0.0		0.0	False		,,,				2504	0.0				p.I344I		Atlas-SNP	.											.	BCAR3	62	.	0			c.T1032C						PASS	.	A		122,4284	91.6+/-130.3	1,120,2082	95	93	93		1032	0	0.9	1	dbSNP_131	93	0,8600		0,0,4300	yes	coding-synonymous-near-splice	BCAR3	NM_003567.2		1,120,6382	GG,GA,AA		0.0,2.769,0.938		344/826	94049576	122,12884	2203	4300	6503	SO:0001630	splice_region_variant	8412	exon6			CATACCAATCGGC	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.1033+1T>C	1.37:g.94049576A>G		144	0	0		146	81	0.554795	NM_001261409	D3DT43|Q5TEW3|Q6UW40|Q9BR50	Silent	SNP	ENST00000370244.1	37	CCDS745.1																																																																																			A|0.992;G|0.008	0.008	strong		0.522	BCAR3-003	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028420.1		Silent	G	94049576	A	G	94049576	5	3	22	1	0	0	0	0	0	0	1	0	1349	144	5	3	1473	3	BCAR3	1	94049576	Splice_Site	SNP	A	TCGA-G8-6324-01A-11D-2210-10	329423	94049576	155201045	185	3086											
ABCA4	24	hgsc.bcm.edu	37	chr1	94505604	94505604	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtccagtccttaccatccAggacttgttctggagttagg	7	12	10	12	1	1	0	0	0	1	0	4	2	4	2	5	3	1	2	5	3	2	4	rs61750126	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:94505604A>C	ENST00000370225.3	-	24	3688	c.3602T>G	c.(3601-3603)cTg>cGg	p.L1201R		NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	1201			L -> R (in STGD1; may predispose to develop retinal toxicity after treatment with chloroquine and hydroxychloroquine; dbSNP:rs61750126). {ECO:0000269|PubMed:11384574, 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)		CTTACCATCCAGGACTTGTTC	0.547											OREG0013610	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	146	0.0291534	0.1051	0.0101	5008	,	,		20682	0.0		0.0	False		,,,				2504	0.0				p.L1201R		Atlas-SNP	.											.	ABCA4	275	.	0			c.T3602G	GRCh37	CM990042	ABCA4	M	rs61750126	PASS	.	A	ARG/LEU	412,3994	189.5+/-215.6	25,362,1816	131	106	115	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3602	5.5	1	1	dbSNP_129	115	4,8596	2.2+/-6.3	0,4,4296	yes	missense	ABCA4	NM_000350.2	102	25,366,6112	CC,CA,AA		0.0465,9.3509,3.1985	probably-damaging	1201/2274	94505604	416,12590	2203	4300	6503	SO:0001583	missense	24	exon24			CCATCCAGGACTT	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.3602T>G	1.37:g.94505604A>C	ENSP00000359245:p.Leu1201Arg	92	0	0	1306	89	39	0.438202	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	37	CCDS747.1	46	0.021062271062271064	44	0.08943089430894309	2	0.0055248618784530384	0	0.0	0	0.0	A	12.19	1.864956	0.32977	0.093509	4.65E-4	ENSG00000198691	ENST00000370225	D	0.86562	-2.14	5.54	5.54	0.83059	.	0.077785	0.50627	D	0.000119	T	0.76983	0.4064	L	0.53249	1.67	0.80722	A	1	B	0.18863	0.031	B	0.24269	0.052	T	0.73228	-0.4049	9	0.27082	T	0.32	.	13.1677	0.59581	1.0:0.0:0.0:0.0	rs61750126	1201	P78363	ABCA4_HUMAN	R	1201	ENSP00000359245:L1201R	ENSP00000359245:L1201R	L	-	2	0	ABCA4	94278192	1.000000	0.71417	0.997000	0.53966	0.864000	0.49448	4.771000	0.62318	2.326000	0.78906	0.533000	0.62120	CTG	A|0.968;C|0.032	0.032	strong		0.547	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350		C	94505604	A	C	94505604	3	2	22	1	0	0	0	0	1	0	0	0	34	188	7	5	3327	5	ABCA4	1	94505604	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	456028	94505604	154745017	186	3087											
SNX7	51375	hgsc.bcm.edu	37	chr1	99150590	99150590	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaaagtcatgttactacaatAgaaactttcattacgtatag	16	13	6	6	1	2	1	2	0	0	1	2	2	2	1	0	0	4	2	0	0	9	7			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:99150590A>G	ENST00000306121.3	+	2	339	c.330A>G	c.(328-330)atA>atG	p.I110M	SNX7_ENST00000529992.1_Missense_Mutation_p.I110M|SNX7_ENST00000370189.5_Missense_Mutation_p.I46M	NM_015976.4	NP_057060.2	Q9UNH6	SNX7_HUMAN	sorting nexin 7	46	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				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)		TTACTACAATAGAAACTTTCA	0.318																																					p.I110M		Atlas-SNP	.											.	SNX7	76	.	0			c.A330G						PASS	.						80	73	75					1																	99150590		2203	4300	6503	SO:0001583	missense	51375	exon2			TACAATAGAAACT	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.330A>G	1.37:g.99150590A>G	ENSP00000304429:p.Ile110Met	223	0	0		184	95	0.516304	NM_015976	A8KAF3|D3DT50|Q53FQ3|Q5VT09|Q5VT10|Q86U82|Q8WVD4|Q96FW9|Q9Y3Z7	Missense_Mutation	SNP	ENST00000306121.3	37	CCDS755.2	.	.	.	.	.	.	.	.	.	.	A	5.637	0.302207	0.10678	.	.	ENSG00000162627	ENST00000370189;ENST00000529992;ENST00000306121;ENST00000454199	T;T;T;T	0.39997	1.05;1.05;1.05;1.05	5.39	0.163	0.14986	.	0.106693	0.64402	D	0.000006	T	0.09335	0.0230	N	0.02213	-0.635	0.48135	D	0.999592	P;B;B	0.44260	0.83;0.0;0.001	P;B;B	0.58210	0.835;0.007;0.019	T	0.19712	-1.0297	10	0.02654	T	1	-24.3064	4.5265	0.11983	0.2744:0.137:0.0:0.5886	.	110;110;46	E9PNL2;Q9UNH6-3;Q9UNH6-2	.;.;.	M	46;110;110;46	ENSP00000359208:I46M;ENSP00000434731:I110M;ENSP00000304429:I110M;ENSP00000388266:I46M	ENSP00000304429:I110M	I	+	3	3	SNX7	98923178	0.994000	0.37717	0.996000	0.52242	0.469000	0.32828	0.198000	0.17217	-0.237000	0.09739	-0.451000	0.05528	ATA	.	.	none		0.318	SNX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029609.2			G	99150590	A	G	99150590	3	3	22	1	0	0	0	0	1	0	0	0	14922	410	15	3	336	3	SNX7	1	99150590	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	4644986	99150590	150100031	187	3088											
AGL	178	hgsc.bcm.edu	37	chr1	100353654	100353654	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtcagcccttaaatatgcAggtcttcaaggtaagcaaat	13	11	9	8	0	3	0	2	0	1	0	3	0	3	0	1	3	3	3	1	3	6	4	rs34230588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:100353654A>C	ENST00000294724.4	+	21	3280	c.2802A>C	c.(2800-2802)gcA>gcC	p.A934A	AGL_ENST00000370165.3_Silent_p.A934A|AGL_ENST00000361302.3_Silent_p.A918A|AGL_ENST00000370161.2_Silent_p.A918A|AGL_ENST00000370163.3_Silent_p.A934A|AGL_ENST00000361522.4_Silent_p.A917A|AGL_ENST00000361915.3_Silent_p.A934A	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	934					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)		TTAAATATGCAGGTCTTCAAG	0.418													A|||	27	0.00539137	0.0204	0.0	5008	,	,		17736	0.0		0.0	False		,,,				2504	0.0				p.A934A		Atlas-SNP	.											.	AGL	137	.	0			c.A2802C						PASS	.	A	,,,,,	97,4309	78.8+/-117.2	1,95,2107	121	115	117		2802,2802,2802,2802,2751,2754	1.8	1	1	dbSNP_126	117	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AGL	NM_000028.2,NM_000642.2,NM_000643.2,NM_000644.2,NM_000645.2,NM_000646.2	,,,,,	1,95,6407	CC,CA,AA		0.0,2.2015,0.7458	,,,,,	934/1533,934/1533,934/1533,934/1533,917/1516,918/1517	100353654	97,12909	2203	4300	6503	SO:0001819	synonymous_variant	178	exon21			ATATGCAGGTCTT	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.2802A>C	1.37:g.100353654A>C		61	0	0		50	21	0.42	NM_000644	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Silent	SNP	ENST00000294724.4	37	CCDS759.1																																																																																			A|0.994;C|0.006	0.006	strong		0.418	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028		C	100353654	A	C	100353654	2	2	22	1	0	0	0	0	0	0	0	1	384	175	7	5		5	AGL	1	100353654	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1203064	100353654	148896967	188	3089											
CDC14A	8556	hgsc.bcm.edu	37	chr1	100856380	100856380	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttttgataggtgcctatgcAgtaagtaccttcttcatgat	9	17	8	7	0	2	2	1	2	1	0	2	2	2	2	2	1	3	3	2	1	4	8	rs28361212	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:100856380A>C	ENST00000336454.3	+	4	664	c.309A>C	c.(307-309)gcA>gcC	p.A103A	CDC14A_ENST00000370124.3_Splice_Site_p.A103A|CDC14A_ENST00000542213.1_Splice_Site_p.A45A|CDC14A_ENST00000361544.6_Splice_Site_p.A103A|CDC14A_ENST00000370125.2_Splice_Site_p.A103A|CDC14A_ENST00000544534.1_Splice_Site_p.A103A	NM_003672.3	NP_003663.2	Q9UNH5	CC14A_HUMAN	cell division cycle 14A	103	A.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(5)|kidney(6)|large_intestine(6)|lung(10)|skin(2)|urinary_tract(1)	31		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)		GTGCCTATGCAGTAAGTACCT	0.378													G|||	482	0.096246	0.3533	0.0202	5008	,	,		19271	0.0		0.001	False		,,,				2504	0.0				p.A103A		Atlas-SNP	.											.	CDC14A	65	.	0			c.A309C						PASS	.	G	,,	1374,3032		208,958,1037	99	97	98		309,309,309	-11.2	0.1	1	dbSNP_125	98	3,8597		0,3,4297	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	CDC14A	NM_003672.3,NM_033312.2,NM_033313.2	,,	208,961,5334	CC,CA,AA		0.0349,31.1847,10.5874	,,	103/595,103/624,103/384	100856380	1377,11629	2203	4300	6503	SO:0001630	splice_region_variant	8556	exon4			CTATGCAGTAAGT	AF000367	CCDS769.1, CCDS770.1, CCDS771.1	1p21	2013-01-17	2013-01-17		ENSG00000079335	ENSG00000079335		"Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"	1718	protein-coding gene	gene with protein product		603504	"CDC10 (cell division cycle 10, S. cerevisiae, homolog)", "CDC14 cell division cycle 14 homolog A (S. cerevisiae)"			9367992, 10409437	Standard	NM_033312		Approved	Cdc14A1, Cdc14A2, cdc14	uc001dtf.2	Q9UNH5	OTTHUMG00000010987	ENST00000336454.3:c.309+1A>C	1.37:g.100856380A>C		59	0	0		68	32	0.470588	NM_033313	A6MA65|B1AQ14|B1AQ15|O43171|O60727|O60728|Q52LH9|Q8IXX0	Silent	SNP	ENST00000336454.3	37	CCDS769.1																																																																																			A|0.885;C|0.115	0.115	strong		0.378	CDC14A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000030220.1	NM_033312	Silent	C	100856380	A	C	100856380	5	2	22	1	0	0	0	0	0	0	1	0	3058	202	7	5	323	5	CDC14A	1	100856380	Splice_Site	SNP	A	TCGA-G8-6324-01A-11D-2210-10	502726	100856380	148394241	189	3090											
CDC14A	8556	hgsc.bcm.edu	37	chr1	100928421	100928421	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gagaacaccgaaggggccatCgccgttcactgcaaaggtgt	11	6	13	11	3	1	1	1	0	0	1	2	3	1	1	3	3	2	2	3	3	3	1	rs74667145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:100928421C>T	ENST00000336454.3	+	9	1177	c.822C>T	c.(820-822)atC>atT	p.I274I	CDC14A_ENST00000370124.3_Silent_p.I274I|RP5-837M10.4_ENST00000432210.1_RNA|CDC14A_ENST00000542213.1_Silent_p.I216I|CDC14A_ENST00000361544.6_Silent_p.I274I|CDC14A_ENST00000370125.2_3'UTR|CDC14A_ENST00000544534.1_Silent_p.I274I	NM_003672.3	NP_003663.2	Q9UNH5	CC14A_HUMAN	cell division cycle 14A	274	B.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(5)|kidney(6)|large_intestine(6)|lung(10)|skin(2)|urinary_tract(1)	31		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)		AAGGGGCCATCGCCGTTCACT	0.527													C|||	9	0.00179712	0.0068	0.0	5008	,	,		18751	0.0		0.0	False		,,,				2504	0.0				p.I274I		Atlas-SNP	.											.	CDC14A	65	.	0			c.C822T						PASS	.	C	,,	20,4386	28.1+/-56.4	0,20,2183	60	51	54		822,822,822	-3.7	0.1	1	dbSNP_132	54	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	CDC14A	NM_003672.3,NM_033312.2,NM_033313.2	,,	0,20,6483	TT,TC,CC		0.0,0.4539,0.1538	,,	274/595,274/624,274/384	100928421	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	8556	exon9			GGCCATCGCCGTT	AF000367	CCDS769.1, CCDS770.1, CCDS771.1	1p21	2013-01-17	2013-01-17		ENSG00000079335	ENSG00000079335		"Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"	1718	protein-coding gene	gene with protein product		603504	"CDC10 (cell division cycle 10, S. cerevisiae, homolog)", "CDC14 cell division cycle 14 homolog A (S. cerevisiae)"			9367992, 10409437	Standard	NM_033312		Approved	Cdc14A1, Cdc14A2, cdc14	uc001dtf.2	Q9UNH5	OTTHUMG00000010987	ENST00000336454.3:c.822C>T	1.37:g.100928421C>T		70	0	0		73	35	0.479452	NM_033313	A6MA65|B1AQ14|B1AQ15|O43171|O60727|O60728|Q52LH9|Q8IXX0	Silent	SNP	ENST00000336454.3	37	CCDS769.1																																																																																			C|0.999;T|0.001	0.001	strong		0.527	CDC14A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000030220.1	NM_033312		T	100928421	C	T	100928421	2	4	22	1	0	0	0	0	0	0	0	1	3058	874	31	1		1	CDC14A	1	100928421	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	72041	100928421	148322200	190	3091											
CDC14A	8556	hgsc.bcm.edu	37	chr1	100933576	100933576	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaacactacaggtttacacaTgctgaaataattgcttggat	15	12	7	7	0	0	1	0	1	0	0	0	2	0	2	0	2	5	3	0	2	5	6	rs17122597	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:100933576T>C	ENST00000336454.3	+	10	1258	c.903T>C	c.(901-903)caT>caC	p.H301H	CDC14A_ENST00000370124.3_Silent_p.H301H|RP5-837M10.4_ENST00000432210.1_RNA|CDC14A_ENST00000542213.1_Silent_p.H243H|CDC14A_ENST00000361544.6_Silent_p.H301H|CDC14A_ENST00000370125.2_3'UTR|CDC14A_ENST00000544534.1_Silent_p.H301H	NM_003672.3	NP_003663.2	Q9UNH5	CC14A_HUMAN	cell division cycle 14A	301	B.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(5)|kidney(6)|large_intestine(6)|lung(10)|skin(2)|urinary_tract(1)	31		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)		GGTTTACACATGCTGAAATAA	0.398													C|||	302	0.0603035	0.2216	0.0086	5008	,	,		20803	0.0		0.003	False		,,,				2504	0.0				p.H301H		Atlas-SNP	.											.	CDC14A	65	.	0			c.T903C						PASS	.	C	,,	894,3512	741.8+/-411.3	94,706,1403	159	159	159		903,903,903	-7.4	0.3	1	dbSNP_123	159	5,8595	819.1+/-406.8	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	CDC14A	NM_003672.3,NM_033312.2,NM_033313.2	,,	94,711,5698	CC,CT,TT		0.0581,20.2905,6.9122	,,	301/595,301/624,301/384	100933576	899,12107	2203	4300	6503	SO:0001819	synonymous_variant	8556	exon10			TACACATGCTGAA	AF000367	CCDS769.1, CCDS770.1, CCDS771.1	1p21	2013-01-17	2013-01-17		ENSG00000079335	ENSG00000079335		"Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"	1718	protein-coding gene	gene with protein product		603504	"CDC10 (cell division cycle 10, S. cerevisiae, homolog)", "CDC14 cell division cycle 14 homolog A (S. cerevisiae)"			9367992, 10409437	Standard	NM_033312		Approved	Cdc14A1, Cdc14A2, cdc14	uc001dtf.2	Q9UNH5	OTTHUMG00000010987	ENST00000336454.3:c.903T>C	1.37:g.100933576T>C		109	0	0		129	67	0.51938	NM_033313	A6MA65|B1AQ14|B1AQ15|O43171|O60727|O60728|Q52LH9|Q8IXX0	Silent	SNP	ENST00000336454.3	37	CCDS769.1																																																																																			T|0.931;C|0.069	0.069	strong		0.398	CDC14A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000030220.1	NM_033312		C	100933576	T	C	100933576	2	2	22	1	0	0	0	0	0	0	0	1	3058	1461	51	3		3	CDC14A	1	100933576	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	5155	100933576	148317045	191	3092											
S1PR1	1901	hgsc.bcm.edu	37	chr1	101704772	101704772	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaaaaccaagaaattccacCgacccatgtactattttatt	15	11	5	10	1	0	1	0	0	0	1	1	3	1	2	4	1	2	1	4	1	7	6	rs150493209	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:101704772C>A	ENST00000305352.6	+	2	607	c.232C>A	c.(232-234)Cga>Aga	p.R78R	S1PR1_ENST00000475821.1_3'UTR|RP4-575N6.4_ENST00000432195.1_RNA	NM_001400.4	NP_001391.2	P21453	S1PR1_HUMAN	sphingosine-1-phosphate receptor 1	78					actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|angiogenesis (GO:0001525)|blood vessel maturation (GO:0001955)|brain development (GO:0007420)|cardiac muscle tissue growth involved in heart morphogenesis (GO:0003245)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|chemotaxis (GO:0006935)|endothelial cell differentiation (GO:0045446)|G-protein coupled receptor signaling pathway (GO:0007186)|heart trabecula morphogenesis (GO:0061384)|lamellipodium assembly (GO:0030032)|negative regulation of stress fiber assembly (GO:0051497)|neuron differentiation (GO:0030182)|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 positive chemotaxis (GO:0050927)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of bone mineralization (GO:0030500)|regulation of bone resorption (GO:0045124)|regulation of cell adhesion (GO:0030155)|sphingosine-1-phosphate signaling pathway (GO:0003376)|T cell migration (GO:0072678)|transmission of nerve impulse (GO:0019226)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|G-protein coupled receptor binding (GO:0001664)|sphingolipid binding (GO:0046625)|sphingosine-1-phosphate receptor activity (GO:0038036)			NS(1)|autonomic_ganglia(1)|breast(1)|large_intestine(7)|lung(23)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	43						GAAATTCCACCGACCCATGTA	0.473											OREG0013620	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	3	0.000599042	0.0023	0.0	5008	,	,		20524	0.0		0.0	False		,,,				2504	0.0				p.R78R		Atlas-SNP	.											.	S1PR1	87	.	0			c.C232A						PASS	.	C		5,4401	9.9+/-24.2	0,5,2198	113	115	114		232	5	1	1	dbSNP_134	114	0,8600		0,0,4300	no	coding-synonymous	S1PR1	NM_001400.4		0,5,6498	AA,AC,CC		0.0,0.1135,0.0384		78/383	101704772	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	1901	exon2			TTCCACCGACCCA	M31210	CCDS777.1	1p21	2012-08-08	2008-04-30	2008-04-30	ENSG00000170989	ENSG00000170989		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate", "CD molecules"	3165	protein-coding gene	gene with protein product		601974	"endothelial differentiation, sphingolipid G-protein-coupled receptor, 1"	EDG1		2160972, 9488656	Standard	NM_001400		Approved	edg-1, D1S3362, CD363	uc001dud.2	P21453	OTTHUMG00000010835	ENST00000305352.6:c.232C>A	1.37:g.101704772C>A		164	0	0	1360	139	62	0.446043	NM_001400	D3DT66|Q9BYY4|Q9NYN8	Silent	SNP	ENST00000305352.6	37	CCDS777.1																																																																																			C|1.000;A|0.000	0.000	strong		0.473	S1PR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029908.1	NM_001400		A	101704772	C	A	101704772	2	1	22	1	0	0	0	0	0	0	0	1	13808	644	23	4		4	S1PR1	1	101704772	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	771196	101704772	147545849	192	3093											
FNDC7	163479	hgsc.bcm.edu	37	chr1	109273351	109273351	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atcacccagtcagtaatcaaCgtgagctggactattgggag	12	9	11	9	1	3	1	3	1	0	0	3	3	3	3	1	2	2	2	1	2	3	3	rs76462144	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:109273351C>A	ENST00000370017.3	+	9	1957	c.1680C>A	c.(1678-1680)aaC>aaA	p.N560K	FNDC7_ENST00000271311.2_Missense_Mutation_p.N561K	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	560	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)		CAGTAATCAACGTGAGCTGGA	0.453													C|||	140	0.0279553	0.1006	0.0086	5008	,	,		19811	0.0		0.001	False		,,,				2504	0.0				p.N560K		Atlas-SNP	.											FNDC7_ENST00000370017,NS,carcinoma,0,2	FNDC7	113	2	0			c.C1680A						PASS	.	C	LYS/ASN	382,4024	193.3+/-218.5	18,346,1839	151	133	139		1680	-0.3	1	1	dbSNP_131	139	4,8596	3.7+/-12.6	0,4,4296	yes	missense	FNDC7	NM_001144937.1	94	18,350,6135	AA,AC,CC		0.0465,8.67,2.9679	probably-damaging	560/734	109273351	386,12620	2203	4300	6503	SO:0001583	missense	163479	exon9			AATCAACGTGAGC		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.1680C>A	1.37:g.109273351C>A	ENSP00000359034:p.Asn560Lys	176	0	0		153	77	0.503268	NM_001144937	A1L468|E9PAZ5|Q6PF16|Q8NA51	Missense_Mutation	SNP	ENST00000370017.3	37	CCDS44185.1	67|67	0.030677655677655676|0.030677655677655676	63|63	0.12804878048780488|0.12804878048780488	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	0|0	0.0|0.0	C|C	19.57|19.57	3.852633|3.852633	0.71719|0.71719	0.0867|0.0867	4.65E-4|4.65E-4	ENSG00000143107|ENSG00000143107	ENST00000370017;ENST00000271311|ENST00000445274	D;D|.	0.99220|.	-5.58;-5.58|.	6.05|6.05	-0.336|-0.336	0.12658|0.12658	Fibronectin, type III (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.58337|0.58337	0.2115|0.2115	M|M	0.72894|0.72894	2.215|2.215	0.48135|0.48135	D|D	0.999597|0.999597	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.999;0.998|.	T|T	0.62300|0.62300	-0.6883|-0.6883	10|5	0.05833|.	T|.	0.94|.	-25.7874|-25.7874	12.6633|12.6633	0.56826|0.56826	0.0:0.563:0.0:0.437|0.0:0.563:0.0:0.437	.|.	561;560|.	Q5VTL7;E9PAZ5|.	FNDC7_HUMAN;.|.	K|S	560;561|336	ENSP00000359034:N560K;ENSP00000271311:N561K|.	ENSP00000271311:N561K|.	N|R	+|+	3|1	2|0	FNDC7|FNDC7	109074874|109074874	0.002000|0.002000	0.14202|0.14202	0.998000|0.998000	0.56505|0.56505	0.989000|0.989000	0.77384|0.77384	-1.351000|-1.351000	0.02622|0.02622	0.023000|0.023000	0.15187|0.15187	0.655000|0.655000	0.94253|0.94253	AAC|CGT	A|0.027;C|0.973;T|0.000	0.027	strong		0.453	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532		A	109273351	C	A	109273351	3	1	22	1	0	0	0	0	1	0	0	0	5981	535	19	4	1714	4	FNDC7	1	109273351	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	7568579	109273351	139977270	193	3094											
AKNAD1	254268	hgsc.bcm.edu	37	chr1	109395230	109395230	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctgagagaggtccccatcAtaaggcaaatcctcctgctt	11	10	8	12	0	2	2	1	1	1	1	5	3	5	2	4	2	1	2	4	2	2	2	rs142279898	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:109395230A>G	ENST00000370001.3	-	2	325	c.57T>C	c.(55-57)taT>taC	p.Y19Y	AKNAD1_ENST00000369995.3_Silent_p.Y19Y|AKNAD1_ENST00000357393.4_Intron|AKNAD1_ENST00000369994.1_Silent_p.Y19Y	NM_152763.4	NP_689976.2	Q5T1N1	AKND1_HUMAN	AKNA domain containing 1	19						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						GGTCCCCATCATAAGGCAAAT	0.438													A|||	15	0.00299521	0.0113	0.0	5008	,	,		19172	0.0		0.0	False		,,,				2504	0.0				p.Y19Y		Atlas-SNP	.											.	AKNAD1	83	.	0			c.T57C						PASS	.	A		29,4377	33.5+/-64.1	0,29,2174	72	72	72		57	-0.7	1	1	dbSNP_134	72	0,8598		0,0,4299	no	coding-synonymous	AKNAD1	NM_152763.3		0,29,6473	GG,GA,AA		0.0,0.6582,0.223		19/837	109395230	29,12975	2203	4299	6502	SO:0001819	synonymous_variant	254268	exon2			CCCATCATAAGGC	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.57T>C	1.37:g.109395230A>G		83	0	0		99	49	0.494949	NM_152763	B9EK62|Q5T1N0|Q8N990|Q8NCN9	Silent	SNP	ENST00000370001.3	37	CCDS791.2																																																																																			A|0.998;G|0.002	0.002	strong		0.438	AKNAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030923.2	NM_152763		G	109395230	A	G	109395230	2	3	22	1	0	0	0	0	0	0	0	1	464	224	8	3		3	AKNAD1	1	109395230	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	121879	109395230	139855391	194	3095											
GPSM2	29899	hgsc.bcm.edu	37	chr1	109465084	109465084	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgaagggttctttgacttaTtaagccgatttcaaagcaat	13	14	8	6	1	2	2	1	2	1	0	2	3	2	2	1	1	2	2	1	1	5	5	rs61758992		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:109465084T>A	ENST00000406462.2	+	14	2259	c.1486T>A	c.(1486-1488)Tta>Ata	p.L496I	GPSM2_ENST00000264126.3_Missense_Mutation_p.L496I|AKNAD1_ENST00000357393.4_Intron			P81274	GPSM2_HUMAN	G-protein signaling modulator 2	496	GoLoco 1. {ECO:0000255|PROSITE- ProRule:PRU00097}.				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)		CTTTGACTTATTAAGCCGATT	0.353													T|||	1	0.000199681	0.0008	0.0	5008	,	,		17405	0.0		0.0	False		,,,				2504	0.0				p.L496I		Atlas-SNP	.											.	GPSM2	56	.	0			c.T1486A						PASS	.	T	ILE/LEU	6,4400	9.9+/-24.2	0,6,2197	124	124	124		1486	-3.6	0	1	dbSNP_129	124	0,8600		0,0,4300	yes	missense	GPSM2	NM_013296.4	5	0,6,6497	AA,AT,TT		0.0,0.1362,0.0461	possibly-damaging	496/685	109465084	6,13000	2203	4300	6503	SO:0001583	missense	29899	exon13			GACTTATTAAGCC	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.1486T>A	1.37:g.109465084T>A	ENSP00000385510:p.Leu496Ile	197	0	0		178	78	0.438202	NM_013296	Q5T1N8|Q6IBL7|Q8N0Z5	Missense_Mutation	SNP	ENST00000406462.2	37	CCDS792.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	21.6|21.6	4.170507|4.170507	0.78452|0.78452	0.001362|0.001362	0.0|0.0	ENSG00000121957|ENSG00000121957	ENST00000406462;ENST00000264126|ENST00000441735	D;D|.	0.97941|.	-4.62;-4.62|.	6.17|6.17	-3.58|-3.58	0.04597|0.04597	GoLoco motif (3);|.	0.076404|.	0.53938|.	D|.	0.000049|.	T|.	0.26846|.	0.0657|.	L|L	0.53249|0.53249	1.67|1.67	0.25458|0.25458	N|N	0.987941|0.987941	B|.	0.22276|.	0.067|.	B|.	0.25291|.	0.059|.	T|.	0.40794|.	-0.9544|.	10|.	0.54805|.	T|.	0.06|.	-5.8623|-5.8623	11.0483|11.0483	0.47872|0.47872	0.0:0.5338:0.1124:0.3538|0.0:0.5338:0.1124:0.3538	rs61758992|rs61758992	496|.	P81274|.	GPSM2_HUMAN|.	I|X	496|85	ENSP00000385510:L496I;ENSP00000264126:L496I|.	ENSP00000264126:L496I|.	L|Y	+|+	1|3	2|2	GPSM2|GPSM2	109266607|109266607	0.073000|0.073000	0.21202|0.21202	0.000000|0.000000	0.03702|0.03702	0.983000|0.983000	0.72400|0.72400	0.418000|0.418000	0.21230|0.21230	-0.938000|-0.938000	0.03714|0.03714	0.533000|0.533000	0.62120|0.62120	TTA|TAT	T|1.000;A|0.000	0.000	weak		0.353	GPSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032400.3	NM_013296		A	109465084	T	A	109465084	3	1	22	1	0	0	0	0	1	0	0	0	6744	1490	52	5	1532	5	GPSM2	1	109465084	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	69854	109465084	139785537	195	3096											
CLCC1	23155	hgsc.bcm.edu	37	chr1	109479953	109479953	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcctgccgtcttctatcccGtggccgaagtgcctggggag	4	10	13	14	3	2	0	0	0	2	0	4	2	4	1	5	3	2	0	5	3	2	2	rs150665002		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:109479953G>A	ENST00000369971.2	-	10	1258	c.1129C>T	c.(1129-1131)Cgg>Tgg	p.R377W	CLCC1_ENST00000482889.1_Intron|CLCC1_ENST00000369970.3_Missense_Mutation_p.R327W|AKNAD1_ENST00000357393.4_Intron|CLCC1_ENST00000369976.1_Intron|CLCC1_ENST00000302500.4_Missense_Mutation_p.R256W|CLCC1_ENST00000415331.1_Missense_Mutation_p.R327W|CLCC1_ENST00000369968.2_Missense_Mutation_p.R192W|CLCC1_ENST00000356970.2_Missense_Mutation_p.R377W|CLCC1_ENST00000348264.2_Missense_Mutation_p.R192W|CLCC1_ENST00000369969.2_Missense_Mutation_p.R256W	NM_001048210.1	NP_001041675.1	Q96S66	CLCC1_HUMAN	chloride channel CLIC-like 1	377						chloride channel complex (GO:0034707)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	chloride channel activity (GO:0005254)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|liver(1)|skin(1)	14		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.231)		CTTCTATCCCGTGGCCGAAGT	0.517													g|||	1	0.000199681	0.0008	0.0	5008	,	,		15244	0.0		0.0	False		,,,				2504	0.0				p.R377W		Atlas-SNP	.											.	CLCC1	55	.	0			c.C1129T						PASS	.	A	TRP/ARG,TRP/ARG	7,4399	11.4+/-27.6	0,7,2196	67	69	68		1129,979	2.7	0	1	dbSNP_134	68	0,8600		0,0,4300	yes	missense,missense	CLCC1	NM_001048210.1,NM_015127.3	101,101	0,7,6496	AA,AG,GG		0.0,0.1589,0.0538	probably-damaging,probably-damaging	377/552,327/502	109479953	7,12999	2203	4300	6503	SO:0001583	missense	23155	exon10			TATCCCGTGGCCG	AB018304	CCDS793.1, CCDS41362.1, CCDS60214.1, CCDS60215.1	1p13.3	2008-02-05			ENSG00000121940	ENSG00000121940			29675	protein-coding gene	gene with protein product	"Mid1-related chloride channel (yeast)"					9872452, 11279057	Standard	NM_001048210		Approved	MCLC	uc001dwf.2	Q96S66	OTTHUMG00000011732	ENST00000369971.2:c.1129C>T	1.37:g.109479953G>A	ENSP00000358988:p.Arg377Trp	97	0	0		106	54	0.509434	NM_001048210	O94861|Q8WYP8|Q8WYP9|Q9BU25	Missense_Mutation	SNP	ENST00000369971.2	37	CCDS41362.1	.	.	.	.	.	.	.	.	.	.	g	6.512	0.462630	0.12402	0.001589	0.0	ENSG00000121940	ENST00000356970;ENST00000369971;ENST00000415331;ENST00000369969;ENST00000369968;ENST00000369970;ENST00000348264;ENST00000302500	T;T;T;T;T;T;T;T	0.49720	0.77;0.77;0.77;0.77;0.77;0.77;0.77;0.77	5.57	2.72	0.32119	.	0.690178	0.15514	N	0.258371	T	0.08670	0.0215	N	0.08118	0	0.09310	N	1	B;B;B;B	0.22851	0.008;0.076;0.008;0.0	B;B;B;B	0.17433	0.006;0.018;0.006;0.001	T	0.24261	-1.0165	10	0.36615	T	0.2	-3.3681	4.209	0.10502	0.2394:0.4109:0.2766:0.0731	.	192;256;327;377	Q96S66-4;Q96S66-3;Q96S66-2;Q96S66	.;.;.;CLCC1_HUMAN	W	377;377;327;256;192;327;192;256	ENSP00000349456:R377W;ENSP00000358988:R377W;ENSP00000411591:R327W;ENSP00000358986:R256W;ENSP00000358985:R192W;ENSP00000358987:R327W;ENSP00000337243:R192W;ENSP00000306552:R256W	ENSP00000306552:R256W	R	-	1	2	CLCC1	109281476	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	0.037000	0.13840	0.422000	0.26005	-0.820000	0.03113	CGG	G|1.000;A|0.000	0.000	strong		0.517	CLCC1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032405.1	NM_015127		A	109479953	G	A	109479953	3	1	22	1	0	0	0	0	1	0	0	0	3462	1144	40	1	534	1	CLCC1	1	109479953	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	14869	109479953	139770668	196	3097											
PSRC1	84722	hgsc.bcm.edu	37	chr1	109824361	109824361	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagggggtgctccgcgtcaaAgagttcacagtgggcagcag	9	6	17	9	2	2	1	2	0	0	1	3	2	3	1	1	3	2	4	1	3	1	1	rs11800211	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:109824361A>C	ENST00000438534.2	-	4	537	c.399T>G	c.(397-399)tcT>tcG	p.S133S	PSRC1_ENST00000369907.3_Silent_p.S133S|PSRC1_ENST00000369904.3_Silent_p.S133S|PSRC1_ENST00000409138.2_Silent_p.S133S|PSRC1_ENST00000369903.2_Silent_p.S133S|PSRC1_ENST00000409267.1_Silent_p.S133S|PSRC1_ENST00000369909.2_Silent_p.S133S	NM_001005290.3	NP_001005290.1	Q6PGN9	PSRC1_HUMAN	proline/serine-rich coiled-coil 1	133	4 X 4 AA repeats of P-X-X-P.				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)		TCCGCGTCAAAGAGTTCACAG	0.627													A|||	250	0.0499201	0.1831	0.0101	5008	,	,		18059	0.0		0.001	False		,,,				2504	0.0				p.S133S		Atlas-SNP	.											.	PSRC1	12	.	0			c.T399G						PASS	.	A	,,	768,3638	311.9+/-292.3	61,646,1496	59	62	61		399,399,399	0.7	0.9	1	dbSNP_120	61	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous,coding-synonymous,coding-synonymous	PSRC1	NM_001005290.3,NM_001032291.2,NM_032636.7	,,	61,654,5788	CC,CA,AA		0.093,17.4308,5.9665	,,	133/311,133/334,133/334	109824361	776,12230	2203	4300	6503	SO:0001819	synonymous_variant	84722	exon4			CGTCAAAGAGTTC		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.399T>G	1.37:g.109824361A>C		126	0	0		146	83	0.568493	NM_001032291	Q5T2Z3|Q6ZTI8|Q71MG3|Q9BV77	Silent	SNP	ENST00000438534.2	37																																																																																				A|0.938;C|0.062	0.062	strong		0.627	PSRC1-202	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000335567.3	NM_032636		C	109824361	A	C	109824361	2	2	22	1	0	0	0	0	0	0	0	1	12731	59	3	5		5	PSRC1	1	109824361	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	344408	109824361	139426260	197	3098											
CSF1	1435	hgsc.bcm.edu	37	chr1	110466776	110466776	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcatcctggtcttgctggcCgtcggaggcctcttgttcta	3	14	12	12	2	4	0	1	0	3	0	6	1	5	1	3	4	1	2	3	4	1	4	rs3208449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:110466776C>T	ENST00000329608.6	+	6	1924	c.1533C>T	c.(1531-1533)gcC>gcT	p.A511A	CSF1_ENST00000369802.3_Silent_p.A511A|CSF1_ENST00000420111.2_Silent_p.A213A|CSF1_ENST00000369801.1_Silent_p.A395A|CSF1_ENST00000344188.5_Silent_p.A395A	NM_000757.5|NM_172211.3	NP_000748|NP_757350.1	P09603	CSF1_HUMAN	colony stimulating factor 1 (macrophage)	511					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)		TCTTGCTGGCCGTCGGAGGCC	0.637													C|||	14	0.00279553	0.0106	0.0	5008	,	,		16807	0.0		0.0	False		,,,				2504	0.0				p.A511A		Atlas-SNP	.											.	CSF1	40	.	0			c.C1533T						PASS	.	C	,,,	28,4376		0,28,2174	34	34	34		1533,1185,639,1533	-8.4	0.1	1	dbSNP_105	34	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CSF1	NM_000757.5,NM_172210.2,NM_172211.2,NM_172212.2	,,,	0,29,6473	TT,TC,CC		0.0116,0.6358,0.223	,,,	511/555,395/439,213/257,511/555	110466776	29,12975	2202	4300	6502	SO:0001819	synonymous_variant	1435	exon6			GCTGGCCGTCGGA	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.1533C>T	1.37:g.110466776C>T		69	0	0		96	51	0.53125	NM_000757	A8K6J5|Q13130|Q14086|Q14806|Q5VVF3|Q5VVF4|Q9UQR8	Silent	SNP	ENST00000329608.6	37	CCDS816.1																																																																																			C|0.996;T|0.004	0.004	strong		0.637	CSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032208.1	NM_000757		T	110466776	C	T	110466776	2	4	22	1	0	0	0	0	0	0	0	1	3933	639	23	1		1	CSF1	1	110466776	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	642415	110466776	138783845	198	3099											
RBM15	64783	hgsc.bcm.edu	37	chr1	110884493	110884493	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcttgtggagggttcaacTggaggcaaagtggcccagct	8	10	14	9	0	2	0	1	0	1	0	2	2	2	2	1	5	2	3	1	5	2	3	rs61745292	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:110884493T>C	ENST00000369784.3	+	1	3366	c.2466T>C	c.(2464-2466)acT>acC	p.T822T	RBM15_ENST00000487146.2_Silent_p.T822T|RBM15_ENST00000602849.1_Silent_p.T822T|RP5-1074L1.1_ENST00000449169.1_RNA	NM_022768.4	NP_073605.4	Q96T37	RBM15_HUMAN	RNA binding motif protein 15	822	SPOC. {ECO:0000255|PROSITE- ProRule:PRU00249}.				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)		AGGGTTCAACTGGAGGCAAAG	0.517			T	MKL1	acute megakaryocytic leukemia								T|||	146	0.0291534	0.1051	0.0086	5008	,	,		19970	0.0		0.001	False		,,,				2504	0.0				p.T822T		Atlas-SNP	.		Dom	yes		1	1p13	64783	RNA binding motif protein 15		L	.	RBM15	93	.	0			c.T2466C						PASS	.	T	,	324,4082	171.2+/-201.5	12,300,1891	79	77	78		2466,2466	-0.2	1	1	dbSNP_129	78	9,8591	5.7+/-21.5	0,9,4291	no	coding-synonymous,coding-synonymous	RBM15	NM_001201545.1,NM_022768.4	,	12,309,6182	CC,CT,TT		0.1047,7.3536,2.5604	,	822/970,822/978	110884493	333,12673	2203	4300	6503	SO:0001819	synonymous_variant	64783	exon1			TTCAACTGGAGGC	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.2466T>C	1.37:g.110884493T>C		120	0	0		140	60	0.428571	NM_022768	A1A693|Q3ZB86|Q4V760|Q5D058|Q5T613|Q86VW9|Q96PE4|Q96SC5|Q96SC6|Q96SC9|Q96SD0|Q96T38|Q9BRA5|Q9H6R8|Q9H9Y0	Silent	SNP	ENST00000369784.3	37	CCDS822.1																																																																																			T|0.974;C|0.026	0.026	strong		0.517	RBM15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000031114.2	NM_022768		C	110884493	T	C	110884493	2	2	22	1	0	0	0	0	0	0	0	1	13131	1567	55	3		3	RBM15	1	110884493	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	417717	110884493	138366128	199	3100											
DENND2D	79961	hgsc.bcm.edu	37	chr1	111738589	111738589	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagtgacagtcttcccaggAgcagggaaggctgcctctcg	9	7	14	11	1	2	2	0	1	2	1	4	4	3	4	2	3	2	2	2	3	1	1	rs34558744	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:111738589A>T	ENST00000357640.4	-	6	823	c.594T>A	c.(592-594)gcT>gcA	p.A198A	DENND2D_ENST00000473682.1_5'UTR|DENND2D_ENST00000369752.5_Silent_p.A195A	NM_024901.3	NP_079177.2	Q9H6A0	DEN2D_HUMAN	DENN/MADD domain containing 2D	198	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				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)		TCTTCCCAGGAGCAGGGAAGG	0.557													A|||	56	0.0111821	0.0401	0.0043	5008	,	,		18465	0.0		0.0	False		,,,				2504	0.0				p.A198A		Atlas-SNP	.											.	DENND2D	50	.	0			c.T594A						PASS	.	A		190,4216	121.7+/-159.2	6,178,2019	106	100	102		594	-0.2	1	1	dbSNP_126	102	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DENND2D	NM_024901.3		6,179,6318	TT,TA,AA		0.0116,4.3123,1.4686		198/472	111738589	191,12815	2203	4300	6503	SO:0001819	synonymous_variant	79961	exon6			CCCAGGAGCAGGG		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.594T>A	1.37:g.111738589A>T		49	0	0		70	33	0.471429	NM_024901	Q5T5V6|Q9BSU0	Silent	SNP	ENST00000357640.4	37	CCDS831.1																																																																																			A|0.988;T|0.012	0.012	strong		0.557	DENND2D-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000034456.1	NM_024901		T	111738589	A	T	111738589	2	4	22	1	0	0	0	0	0	0	0	1	4433	291	11	5		5	DENND2D	1	111738589	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	854096	111738589	137512032	200	3101											
CHIA	27159	hgsc.bcm.edu	37	chr1	111854859	111854859	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaccaactgggcccagtacCggccaggcctggggcgcttc	6	6	13	16	2	1	0	1	0	0	0	2	0	1	0	5	5	2	2	5	5	2	2	rs61752461	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:111854859C>T	ENST00000369740.1	+	4	206	c.103C>T	c.(103-105)Cgg>Tgg	p.R35W	CHIA_ENST00000430615.1_Intron|CHIA_ENST00000483391.1_Intron|CHIA_ENST00000451398.2_Intron|CHIA_ENST00000343320.6_Missense_Mutation_p.R35W|CHIA_ENST00000353665.6_Intron	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	35					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)		GGCCCAGTACCGGCCAGGCCT	0.582													C|||	58	0.0115815	0.0393	0.0086	5008	,	,		18399	0.0		0.0	False		,,,				2504	0.0				p.R35W		Atlas-SNP	.											CHIA_ENST00000369740,NS,carcinoma,-2,1	CHIA	115	1	0			c.C103T						PASS	.	C	,TRP/ARG	170,4018		2,166,1926	70	74	73		,103	-0.2	0.2	1	dbSNP_129	73	0,8432		0,0,4216	yes	intron,missense	CHIA	NM_021797.2,NM_201653.2	,101	2,166,6142	TT,TC,CC		0.0,4.0592,1.3471	,probably-damaging	,35/477	111854859	170,12450	2094	4216	6310	SO:0001583	missense	27159	exon4			CAGTACCGGCCAG	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.103C>T	1.37:g.111854859C>T	ENSP00000358755:p.Arg35Trp	188	0	0		197	92	0.467005	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Missense_Mutation	SNP	ENST00000369740.1	37	CCDS41368.1	26	0.011904761904761904	23	0.046747967479674794	3	0.008287292817679558	0	0.0	0	0.0	C	17.72	3.459828	0.63401	0.040592	0.0	ENSG00000134216	ENST00000369740;ENST00000343320	T;T	0.06933	3.24;3.24	5.08	-0.166	0.13351	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.47852	U	0.000201	T	0.17874	0.0429	H	0.95294	3.65	0.80722	D	1	P	0.47484	0.896	P	0.51453	0.67	T	0.41998	-0.9477	10	0.66056	D	0.02	-8.6166	13.0776	0.59095	0.7282:0.2718:0.0:0.0	rs61752461	35	Q9BZP6	CHIA_HUMAN	W	35	ENSP00000358755:R35W;ENSP00000341828:R35W	ENSP00000341828:R35W	R	+	1	2	CHIA	111656382	0.000000	0.05858	0.241000	0.24154	0.789000	0.44602	-0.273000	0.08548	0.179000	0.19938	0.655000	0.94253	CGG	C|0.988;T|0.012	0.012	strong		0.582	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1			T	111854859	C	T	111854859	3	4	22	1	0	0	0	0	1	0	0	0	3344	643	23	1	113	1	CHIA	1	111854859	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	116270	111854859	137395762	201	3102											
OVGP1	5016	hgsc.bcm.edu	37	chr1	111957721	111957721	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgatctcagtcttctctcCtagagctacagtgtgctttc	7	15	8	11	0	3	2	1	1	3	1	7	2	4	2	1	0	3	2	1	0	2	4	rs115512535	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:111957721C>T	ENST00000369732.3	-	11	1457	c.1402G>A	c.(1402-1404)Gga>Aga	p.G468R		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	468					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)		GTCTTCTCTCCTAGAGCTACA	0.498													C|||	11	0.00219649	0.0083	0.0	5008	,	,		20915	0.0		0.0	False		,,,				2504	0.0				p.G468R		Atlas-SNP	.											.	OVGP1	177	.	0			c.G1402A						PASS	.	C	ARG/GLY	57,4349	55.5+/-91.7	0,57,2146	121	104	110		1402	-0.9	0	1	dbSNP_132	110	1,8599	1.2+/-3.3	0,1,4299	yes	missense	OVGP1	NM_002557.3	125	0,58,6445	TT,TC,CC		0.0116,1.2937,0.4459	possibly-damaging	468/679	111957721	58,12948	2203	4300	6503	SO:0001583	missense	5016	exon11			TCTCTCCTAGAGC	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.1402G>A	1.37:g.111957721C>T	ENSP00000358747:p.Gly468Arg	298	0	0		300	134	0.446667	NM_002557	A0AV19|B9EGE1|Q15841	Missense_Mutation	SNP	ENST00000369732.3	37	CCDS834.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	17.36	3.368778	0.61624	0.012937	1.16E-4	ENSG00000085465	ENST00000369732;ENST00000369728;ENST00000434331	T	0.04317	3.65	4.86	-0.95	0.10372	.	0.931884	0.09108	N	0.847418	T	0.01489	0.0048	L	0.39898	1.24	0.09310	N	1	P;P	0.48764	0.675;0.915	B;B	0.41946	0.131;0.371	T	0.45977	-0.9224	10	0.40728	T	0.16	-0.097	5.5535	0.17103	0.0:0.5337:0.1411:0.3252	.	468;532	Q12889;Q59HH5	OVGP1_HUMAN;.	R	468;532;276	ENSP00000358747:G468R	ENSP00000358743:G532R	G	-	1	0	OVGP1	111759244	0.000000	0.05858	0.000000	0.03702	0.895000	0.52256	0.199000	0.17237	-0.209000	0.10156	0.585000	0.79938	GGA	C|0.997;T|0.003	0.003	strong		0.498	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557		T	111957721	C	T	111957721	3	4	22	1	0	0	0	0	1	0	0	0	11334	690	24	2	638	2	OVGP1	1	111957721	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	102862	111957721	137292900	202	3103											
ADORA3	140	hgsc.bcm.edu	37	chr1	112045709	112045709	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcgtgggtaaagataagcaGtaggcaagtcataaaaaggc	16	6	14	5	1	1	1	1	0	0	1	1	1	1	1	0	4	1	4	0	4	8	4	rs77883500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:112045709G>C	ENST00000241356.4	-	1	673	c.268C>G	c.(268-270)Ctg>Gtg	p.L90V	ADORA3_ENST00000369716.4_Missense_Mutation_p.L90V|ADORA3_ENST00000486342.1_5'UTR|ADORA3_ENST00000369717.4_Intron	NM_000677.3	NP_000668.1	P33765	AA3R_HUMAN	adenosine A3 receptor	90					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)	AAGATAAGCAGTAGGCAAGTC	0.552													G|||	86	0.0171725	0.0613	0.0058	5008	,	,		21547	0.0		0.001	False		,,,				2504	0.0				p.L90V		Atlas-SNP	.											.	ADORA3	104	.	0			c.C268G						PASS	.	G	VAL/LEU,,VAL/LEU	184,4222	117.5+/-155.4	2,180,2021	84	64	70		268,,268	1.1	0.7	1	dbSNP_131	70	1,8599		0,1,4299	yes	missense,intron,missense	ADORA3	NM_000677.3,NM_001081976.1,NM_020683.6	32,,32	2,181,6320	CC,CG,GG		0.0116,4.1761,1.4224	benign,,benign	90/319,,90/348	112045709	185,12821	2203	4300	6503	SO:0001583	missense	140	exon1			TAAGCAGTAGGCA	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.268C>G	1.37:g.112045709G>C	ENSP00000241356:p.Leu90Val	262	0	0		291	135	0.463918	NM_020683	A2A3P4|Q6UWU0|Q9BYZ1	Missense_Mutation	SNP	ENST00000241356.4	37	CCDS839.1	33	0.01510989010989011	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	0	0.0	G	4.114	0.019297	0.08006	0.041761	1.16E-4	ENSG00000121933	ENST00000369716;ENST00000241356	T;T	0.37235	1.21;1.21	5.26	1.07	0.20283	GPCR, rhodopsin-like superfamily (1);	0.645763	0.12883	N	0.431230	T	0.05777	0.0151	N	0.05510	-0.035	0.22292	N	0.999222	B;B	0.21381	0.055;0.004	B;B	0.24394	0.053;0.012	T	0.45101	-0.9284	10	0.10377	T	0.69	-1.0214	11.5274	0.50588	0.0:0.1113:0.3199:0.5688	.	90;90	P33765;P33765-2	AA3R_HUMAN;.	V	90	ENSP00000358730:L90V;ENSP00000241356:L90V	ENSP00000241356:L90V	L	-	1	2	ADORA3	111847232	0.001000	0.12720	0.667000	0.29798	0.701000	0.40568	-0.483000	0.06536	0.013000	0.14918	0.561000	0.74099	CTG	G|0.985;C|0.015	0.015	strong		0.552	ADORA3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033065.1	NM_000677, NM_020683		C	112045709	G	C	112045709	3	2	22	1	0	0	0	0	1	0	0	0	329	1020	36	4	1410	4	ADORA3	1	112045709	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	87988	112045709	137204912	203	3104											
ST7L	54879	hgsc.bcm.edu	37	chr1	113068651	113068651	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tggctcagccagaactcaaaCctaggtcttctgacttcaaa	12	10	7	12	0	5	2	3	1	2	1	5	2	5	2	2	2	3	1	2	2	4	3	rs12069022	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:113068651C>T	ENST00000358039.4	-	15	2016	c.1712G>A	c.(1711-1713)gGt>gAt	p.G571D	WNT2B_ENST00000369686.5_3'UTR|ST7L_ENST00000369669.1_Missense_Mutation_p.G388D|ST7L_ENST00000490067.1_Missense_Mutation_p.G554D|ST7L_ENST00000360743.4_Missense_Mutation_p.G540D|ST7L_ENST00000544629.1_Missense_Mutation_p.G506D	NM_017744.4|NM_138727.3	NP_060214.2|NP_620055.1	Q8TDW4	ST7L_HUMAN	suppression of tumorigenicity 7 like	571			G -> D (in dbSNP:rs12069022).		negative regulation of cell growth (GO:0030308)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(4)|large_intestine(3)|lung(1)|prostate(2)|stomach(1)|urinary_tract(3)	15	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)		agaactcaaacctaggtcttc	0.478													C|||	174	0.0347444	0.1263	0.0101	5008	,	,		18280	0.0		0.0	False		,,,				2504	0.0				p.G571D		Atlas-SNP	.											.	ST7L	31	.	0			c.G1712A						PASS	.	C	ASP/GLY,ASP/GLY,ASP/GLY	441,3965	212.5+/-232.4	23,395,1785	114	113	113		1712,1661,1619	1.9	0.1	1	dbSNP_120	113	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense	ST7L	NM_017744.4,NM_138727.3,NM_138728.2	94,94,94	23,398,6082	TT,TC,CC		0.0349,10.0091,3.4138	probably-damaging,probably-damaging,probably-damaging	571/576,554/559,540/545	113068651	444,12562	2203	4300	6503	SO:0001583	missense	54879	exon15			CTCAAACCTAGGT	AB081317	CCDS848.1, CCDS849.1, CCDS850.1, CCDS852.1	1p13.1	2008-06-06			ENSG00000007341	ENSG00000007341			18441	protein-coding gene	gene with protein product						12012006	Standard	NM_138729		Approved	FLJ20284, STLR, ST7R, FAM4B	uc001ecd.3	Q8TDW4	OTTHUMG00000011753	ENST00000358039.4:c.1712G>A	1.37:g.113068651C>T	ENSP00000350734:p.Gly571Asp	61	0	0		73	38	0.520548	NM_017744	A8K4S7|Q49AH6|Q5TEI4|Q5U5K6|Q6N067|Q7Z2Z0|Q7Z3C2|Q8N7P8|Q8TDW1|Q8TDW2|Q8TDW3|Q9NXF3	Missense_Mutation	SNP	ENST00000358039.4	37	CCDS848.1	44	0.020146520146520148	42	0.08536585365853659	2	0.0055248618784530384	0	0.0	0	0.0	C	15.95	2.984826	0.53934	0.100091	3.49E-4	ENSG00000007341	ENST00000358039;ENST00000360743;ENST00000369673;ENST00000544629;ENST00000369669;ENST00000490067	T;T;T;T;T	0.19394	2.43;2.24;2.15;2.39;2.43	3.81	1.87	0.25490	.	1.917730	0.02054	N	0.050248	T	0.04003	0.0112	N	0.08118	0	0.20563	N	0.999889	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;0.001;0.001;0.0;0.0	T	0.32052	-0.9921	10	0.87932	D	0	.	5.8421	0.18639	0.0:0.7468:0.0:0.2532	rs12069022;rs12069022	506;506;554;540;571	B7Z3J2;F5H2P3;Q8TDW4-3;Q8TDW4-2;Q8TDW4	.;.;.;.;ST7L_HUMAN	D	571;540;321;506;388;554	ENSP00000350734:G571D;ENSP00000353972:G540D;ENSP00000445499:G506D;ENSP00000358683:G388D;ENSP00000417140:G554D	ENSP00000350734:G571D	G	-	2	0	ST7L	112870174	0.000000	0.05858	0.071000	0.20095	0.353000	0.29299	0.130000	0.15850	0.558000	0.29135	-0.119000	0.15052	GGT	C|0.963;T|0.037	0.037	strong		0.478	ST7L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032504.3			T	113068651	C	T	113068651	3	4	22	1	0	0	0	0	1	0	0	0	15245	507	18	2	19	2	ST7L	1	113068651	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1022942	113068651	136181970	204	3105											
ST7L	54879	hgsc.bcm.edu	37	chr1	113153536	113153536	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttctgaaatgctgctctcTgttcctcccatcagtggttg	5	15	10	11	0	3	1	1	1	2	0	6	1	5	1	2	2	2	5	2	2	1	3	rs35364712	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:113153536T>C	ENST00000358039.4	-	3	682	c.378A>G	c.(376-378)acA>acG	p.T126T	ST7L_ENST00000543570.1_Silent_p.T109T|ST7L_ENST00000343210.7_Silent_p.T126T|ST7L_ENST00000369668.2_Silent_p.T126T|ST7L_ENST00000369666.1_Silent_p.T109T|ST7L_ENST00000369669.1_5'UTR|ST7L_ENST00000490067.1_Silent_p.T109T|ST7L_ENST00000538187.1_Silent_p.T70T|ST7L_ENST00000360743.4_Silent_p.T126T|ST7L_ENST00000463235.1_5'UTR|ST7L_ENST00000544629.1_Silent_p.T126T	NM_017744.4|NM_138727.3	NP_060214.2|NP_620055.1	Q8TDW4	ST7L_HUMAN	suppression of tumorigenicity 7 like	126					negative regulation of cell growth (GO:0030308)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(4)|large_intestine(3)|lung(1)|prostate(2)|stomach(1)|urinary_tract(3)	15	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)		TGCTGCTCTCTGTTCCTCCCA	0.408													T|||	59	0.0117812	0.0431	0.0029	5008	,	,		21004	0.0		0.0	False		,,,				2504	0.0				p.T126T		Atlas-SNP	.											.	ST7L	31	.	0			c.A378G						PASS	.	T	,,,	197,4209	124.5+/-161.8	5,187,2011	156	150	152		378,327,378,378	4.9	1	1	dbSNP_126	152	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ST7L	NM_017744.4,NM_138727.3,NM_138728.2,NM_138729.3	,,,	5,188,6310	CC,CT,TT		0.0116,4.4712,1.5224	,,,	126/576,109/559,126/545,126/556	113153536	198,12808	2203	4300	6503	SO:0001819	synonymous_variant	54879	exon3			GCTCTCTGTTCCT	AB081317	CCDS848.1, CCDS849.1, CCDS850.1, CCDS852.1	1p13.1	2008-06-06			ENSG00000007341	ENSG00000007341			18441	protein-coding gene	gene with protein product						12012006	Standard	NM_138729		Approved	FLJ20284, STLR, ST7R, FAM4B	uc001ecd.3	Q8TDW4	OTTHUMG00000011753	ENST00000358039.4:c.378A>G	1.37:g.113153536T>C		254	0	0		268	134	0.5	NM_138729	A8K4S7|Q49AH6|Q5TEI4|Q5U5K6|Q6N067|Q7Z2Z0|Q7Z3C2|Q8N7P8|Q8TDW1|Q8TDW2|Q8TDW3|Q9NXF3	Silent	SNP	ENST00000358039.4	37	CCDS848.1																																																																																			T|0.984;C|0.016	0.016	strong		0.408	ST7L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032504.3			C	113153536	T	C	113153536	2	2	22	1	0	0	0	0	0	0	0	1	15245	1567	55	3		3	ST7L	1	113153536	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	84885	113153536	136097085	205	3106											
CAPZA1	829	hgsc.bcm.edu	37	chr1	113202386	113202386	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctacagcccaggtggttggCgtgcttaagattcaggtgag	8	10	14	9	1	1	2	1	1	0	1	1	2	1	2	2	4	3	2	2	4	2	4	rs12074157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:113202386C>T	ENST00000263168.3	+	7	1242	c.570C>T	c.(568-570)ggC>ggT	p.G190G	CAPZA1_ENST00000476936.1_3'UTR	NM_006135.2	NP_006126.1	P52907	CAZA1_HUMAN	capping protein (actin filament) muscle Z-line, alpha 1	190					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)		AGGTGGTTGGCGTGCTTAAGA	0.403													c|||	179	0.0357428	0.1301	0.0101	5008	,	,		16515	0.0		0.0	False		,,,				2504	0.0				p.G190G		Atlas-SNP	.											CAPZA1,colon,carcinoma,0,1	CAPZA1	16	1	0			c.C570T						PASS	.	C		459,3947	217.1+/-235.6	24,411,1768	94	89	91		570	4.4	1	1	dbSNP_120	91	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	CAPZA1	NM_006135.2		24,414,6065	TT,TC,CC		0.0349,10.4176,3.5522		190/287	113202386	462,12544	2203	4300	6503	SO:0001819	synonymous_variant	829	exon7			GGTTGGCGTGCTT	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.570C>T	1.37:g.113202386C>T		77	0	0		86	35	0.406977	NM_006135	Q53FQ6|Q6FHD5	Silent	SNP	ENST00000263168.3	37	CCDS30805.1																																																																																			C|0.968;T|0.032	0.032	strong		0.403	CAPZA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032567.2	NM_006135		T	113202386	C	T	113202386	2	4	22	1	0	0	0	0	0	0	0	1	2642	755	27	1		1	CAPZA1	1	113202386	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	48850	113202386	136048235	206	3107											
MAGI3	260425	hgsc.bcm.edu	37	chr1	113933814	113933814	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggctccgcgaggagcccggCgggggcacctgctgcgtcgt	3	5	18	15	7	0	0	0	0	0	0	2	2	1	1	3	5	3	3	3	5	0	0	rs182574963	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:113933814C>T	ENST00000307546.9	+	1	234	c.159C>T	c.(157-159)ggC>ggT	p.G53G	MAGI3_ENST00000369615.1_Silent_p.G53G|MAGI3_ENST00000369611.4_Silent_p.G53G|MAGI3_ENST00000486456.1_3'UTR|MAGI3_ENST00000369617.4_Silent_p.G53G	NM_001142782.1	NP_001136254.1	Q5TCQ9	MAGI3_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 3	53	Interaction with ADRB1 and TGFA. {ECO:0000250}.|PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)		AGGAGCCCGGCGGGGGCACCT	0.746													C|||	31	0.0061901	0.0204	0.0058	5008	,	,		9388	0.0		0.0	False		,,,				2504	0.0				p.G53G		Atlas-SNP	.											.	MAGI3	181	.	0			c.C159T						PASS	.	C	,	45,4037		0,45,1996	5	7	6		159,159	2.9	1	1		6	2,8118		0,2,4058	no	coding-synonymous,coding-synonymous	MAGI3	NM_001142782.1,NM_152900.2	,	0,47,6054	TT,TC,CC		0.0246,1.1024,0.3852	,	53/1482,53/1126	113933814	47,12155	2041	4060	6101	SO:0001819	synonymous_variant	260425	exon1			GCCCGGCGGGGGC	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.159C>T	1.37:g.113933814C>T		26	0	0		35	26	0.742857	NM_152900	Q5TCQ8|Q5TCR0|Q9H2V6|Q9H5Y8|Q9HBC4|Q9HCD8	Silent	SNP	ENST00000307546.9	37	CCDS44196.1																																																																																			C|0.994;T|0.006	0.006	strong		0.746	MAGI3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000032429.1	NM_152900		T	113933814	C	T	113933814	2	4	22	1	0	0	0	0	0	0	0	1	9201	755	27	1		1	MAGI3	1	113933814	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	731428	113933814	135316807	207	3108											
SYCP1	6847	hgsc.bcm.edu	37	chr1	115537343	115537343	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggtttcagaagaagagacaTtgaaaacactgtataggaac	17	9	10	5	0	1	4	1	1	0	3	1	6	1	5	0	2	2	2	0	2	7	4	rs17033011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:115537343T>C	ENST00000369522.3	+	31	2968	c.2728T>C	c.(2728-2730)Ttg>Ctg	p.L910L	SYCP1_ENST00000477590.1_3'UTR|SYCP1_ENST00000369518.1_Silent_p.L910L	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	910					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)		AGAAGAGACATTGAAAACACT	0.274													T|||	185	0.0369409	0.1354	0.0086	5008	,	,		12816	0.0		0.0	False		,,,				2504	0.0				p.L910L		Atlas-SNP	.											.	SYCP1	149	.	0			c.T2728C						PASS	.			470,3920	196.0+/-220.5	22,426,1747	32	35	34		2728	-1.8	0	1	dbSNP_123	34	6,8570	4.3+/-15.6	0,6,4282	no	coding-synonymous	SYCP1	NM_003176.2		22,432,6029	CC,CT,TT		0.07,10.7062,3.6711		910/977	115537343	476,12490	2195	4288	6483	SO:0001819	synonymous_variant	6847	exon31			GAGACATTGAAAA	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.2728T>C	1.37:g.115537343T>C		93	0	0		108	53	0.490741	NM_003176	O14963|Q5VXJ6	Silent	SNP	ENST00000369522.3	37	CCDS879.1																																																																																			T|0.954;C|0.046	0.046	strong		0.274	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176		C	115537343	T	C	115537343	2	2	22	1	0	0	0	0	0	0	0	1	15446	1490	52	3		3	SYCP1	1	115537343	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1603529	115537343	133713278	208	3109											
PTGFRN	5738	hgsc.bcm.edu	37	chr1	117452869	117452869	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gctgctgctggcgctcctgtCgttgggtgagtgtgcgcggg	1	11	19	10	4	0	1	0	1	0	0	2	1	1	1	1	3	3	5	1	3	0	1	rs77292583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:117452869C>G	ENST00000393203.2	+	1	191	c.44C>G	c.(43-45)tCg>tGg	p.S15W	RP4-753F5.1_ENST00000610171.1_lincRNA	NM_020440.2	NP_065173.2	Q9P2B2	FPRP_HUMAN	prostaglandin F2 receptor inhibitor	15					lipid particle organization (GO:0034389)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)	46	Lung SC(450;0.225)	all_cancers(81;0.00104)|all_lung(203;8.97e-05)|all_epithelial(167;0.000139)|Lung NSC(69;0.000446)		Lung(183;0.0704)|LUSC - Lung squamous cell carcinoma(189;0.227)|Colorectal(144;0.248)		GCGCTCCTGTCGTTGGGTGAG	0.786													C|||	146	0.0291534	0.1074	0.0058	5008	,	,		7813	0.0		0.0	False		,,,				2504	0.0				p.S15W		Atlas-SNP	.											PTGFRN,NS,carcinoma,0,1	PTGFRN	91	1	0			c.C44G						PASS	.	C	TRP/SER	237,3861		2,233,1814	4	6	5		44	0.3	0.1	1	dbSNP_132	5	3,8095		0,3,4046	no	missense	PTGFRN	NM_020440.2	177	2,236,5860	GG,GC,CC		0.037,5.7833,1.9679	benign	15/880	117452869	240,11956	2049	4049	6098	SO:0001583	missense	5738	exon1			TCCTGTCGTTGGG	AB014734	CCDS890.1	1p13.1	2013-01-29	2013-01-25		ENSG00000134247	ENSG00000134247		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9601	protein-coding gene	gene with protein product		601204	"prostaglandin F2 receptor negative regulator"			8655148	Standard	NM_020440		Approved	FPRP, EWI-F, CD9P-1, FLJ11001, KIAA1436, SMAP-6, CD315	uc001egv.1	Q9P2B2	OTTHUMG00000012028	ENST00000393203.2:c.44C>G	1.37:g.117452869C>G	ENSP00000376899:p.Ser15Trp	16	0	0		8	4	0.5	NM_020440	Q5VVU9|Q8N2K6	Missense_Mutation	SNP	ENST00000393203.2	37	CCDS890.1	47	0.02152014652014652	45	0.09146341463414634	2	0.0055248618784530384	0	0.0	0	0.0	C	5.911	0.352168	0.11182	0.057833	3.7E-4	ENSG00000134247	ENST00000393203	T	0.03982	3.74	3.41	0.296	0.15757	Immunoglobulin-like (1);	6.098340	0.00166	N	0.000011	T	0.01156	0.0038	N	0.14661	0.345	0.44214	D	0.997042	B	0.02656	0.0	B	0.01281	0.0	T	0.33394	-0.9870	10	0.66056	D	0.02	0.1948	3.6279	0.08120	0.0:0.498:0.2382:0.2638	.	15	Q9P2B2	FPRP_HUMAN	W	15	ENSP00000376899:S15W	ENSP00000376899:S15W	S	+	2	0	PTGFRN	117254392	0.444000	0.25649	0.089000	0.20774	0.001000	0.01503	-0.612000	0.05616	-0.140000	0.11394	-0.481000	0.04817	TCG	C|0.978;G|0.022	0.022	strong		0.786	PTGFRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033271.1	NM_020440		G	117452869	C	G	117452869	3	3	22	1	0	0	0	0	1	0	0	0	12763	893	31	4	46	4	PTGFRN	1	117452869	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1915526	117452869	131797752	209	3110											
PTGFRN	5738	hgsc.bcm.edu	37	chr1	117484581	117484581	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atcctgttaaggcggactgcCaacgacgccgtggagctcca	9	7	12	13	4	0	0	0	0	0	0	2	3	2	2	4	3	3	2	4	3	2	1	rs77895792	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:117484581C>T	ENST00000393203.2	+	2	441	c.294C>T	c.(292-294)gcC>gcT	p.A98A		NM_020440.2	NP_065173.2	Q9P2B2	FPRP_HUMAN	prostaglandin F2 receptor inhibitor	98	Ig-like C2-type 1.				lipid particle organization (GO:0034389)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)	46	Lung SC(450;0.225)	all_cancers(81;0.00104)|all_lung(203;8.97e-05)|all_epithelial(167;0.000139)|Lung NSC(69;0.000446)		Lung(183;0.0704)|LUSC - Lung squamous cell carcinoma(189;0.227)|Colorectal(144;0.248)		GGCGGACTGCCAACGACGCCG	0.592													C|||	23	0.00459265	0.0166	0.0014	5008	,	,		17326	0.0		0.0	False		,,,				2504	0.0				p.A98A		Atlas-SNP	.											.	PTGFRN	91	.	0			c.C294T						PASS	.	C		46,4360	46.7+/-81.2	0,46,2157	85	79	81		294	4.2	1	1	dbSNP_131	81	0,8600		0,0,4300	no	coding-synonymous	PTGFRN	NM_020440.2		0,46,6457	TT,TC,CC		0.0,1.044,0.3537		98/880	117484581	46,12960	2203	4300	6503	SO:0001819	synonymous_variant	5738	exon2			GACTGCCAACGAC	AB014734	CCDS890.1	1p13.1	2013-01-29	2013-01-25		ENSG00000134247	ENSG00000134247		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9601	protein-coding gene	gene with protein product		601204	"prostaglandin F2 receptor negative regulator"			8655148	Standard	NM_020440		Approved	FPRP, EWI-F, CD9P-1, FLJ11001, KIAA1436, SMAP-6, CD315	uc001egv.1	Q9P2B2	OTTHUMG00000012028	ENST00000393203.2:c.294C>T	1.37:g.117484581C>T		205	0	0		199	100	0.502513	NM_020440	Q5VVU9|Q8N2K6	Silent	SNP	ENST00000393203.2	37	CCDS890.1																																																																																			C|0.995;T|0.005	0.005	strong		0.592	PTGFRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033271.1	NM_020440		T	117484581	C	T	117484581	2	4	22	1	0	0	0	0	0	0	0	1	12763	581	21	2		2	PTGFRN	1	117484581	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	31712	117484581	131766040	210	3111											
PTGFRN	5738	hgsc.bcm.edu	37	chr1	117527444	117527444	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcgacctcagcctggagcgCgtgagtgtgctggaattctt	7	10	14	10	3	2	1	1	1	1	0	2	4	2	3	2	2	4	1	2	2	1	2	rs17036676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:117527444C>T	ENST00000393203.2	+	8	2457	c.2310C>T	c.(2308-2310)cgC>cgT	p.R770R		NM_020440.2	NP_065173.2	Q9P2B2	FPRP_HUMAN	prostaglandin F2 receptor inhibitor	770	Ig-like C2-type 6.				lipid particle organization (GO:0034389)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)	46	Lung SC(450;0.225)	all_cancers(81;0.00104)|all_lung(203;8.97e-05)|all_epithelial(167;0.000139)|Lung NSC(69;0.000446)		Lung(183;0.0704)|LUSC - Lung squamous cell carcinoma(189;0.227)|Colorectal(144;0.248)		GCCTGGAGCGCGTGAGTGTGC	0.587													C|||	23	0.00459265	0.0166	0.0014	5008	,	,		21854	0.0		0.0	False		,,,				2504	0.0				p.R770R		Atlas-SNP	.											PTGFRN,NS,chondrosarcoma,+1,1	PTGFRN	91	1	0			c.C2310T						PASS	.	C		60,4346	56.2+/-92.4	1,58,2144	219	170	187		2310	-11.2	0	1	dbSNP_123	187	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	PTGFRN	NM_020440.2		1,60,6442	TT,TC,CC		0.0233,1.3618,0.4767		770/880	117527444	62,12944	2203	4300	6503	SO:0001819	synonymous_variant	5738	exon8			GGAGCGCGTGAGT	AB014734	CCDS890.1	1p13.1	2013-01-29	2013-01-25		ENSG00000134247	ENSG00000134247		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9601	protein-coding gene	gene with protein product		601204	"prostaglandin F2 receptor negative regulator"			8655148	Standard	NM_020440		Approved	FPRP, EWI-F, CD9P-1, FLJ11001, KIAA1436, SMAP-6, CD315	uc001egv.1	Q9P2B2	OTTHUMG00000012028	ENST00000393203.2:c.2310C>T	1.37:g.117527444C>T		149	0	0		193	94	0.487047	NM_020440	Q5VVU9|Q8N2K6	Silent	SNP	ENST00000393203.2	37	CCDS890.1																																																																																			C|0.994;T|0.006	0.006	strong		0.587	PTGFRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033271.1	NM_020440		T	117527444	C	T	117527444	2	4	22	1	0	0	0	0	0	0	0	1	12763	755	27	1		1	PTGFRN	1	117527444	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	42863	117527444	131723177	211	3112											
CD101	9398	hgsc.bcm.edu	37	chr1	117576631	117576631	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacactgcgttccaacacaCggaaagaaaaagctctctgg	15	6	8	12	2	1	1	0	0	1	1	3	2	2	2	1	2	4	2	1	2	5	1	rs34248572	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:117576631C>T	ENST00000256652.4	+	9	3032	c.2974C>T	c.(2974-2976)Cgg>Tgg	p.R992W	CD101_ENST00000369470.1_Missense_Mutation_p.R992W|RP11-27K13.3_ENST00000445523.1_RNA|RP11-27K13.3_ENST00000421254.1_RNA|CD101_ENST00000467588.1_3'UTR	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	992			R -> W (in dbSNP:rs34248572).		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						TTCCAACACACGGAAAGAAAA	0.517													C|||	117	0.0233626	0.0817	0.0115	5008	,	,		19361	0.001		0.0	False		,,,				2504	0.0				p.R992W		Atlas-SNP	.											CD101,NS,carcinoma,-1,1	CD101	95	1	0			c.C2974T						PASS	.	C	TRP/ARG	286,4120	157.0+/-190.0	13,260,1930	123	112	116		2974	-0.3	0	1	dbSNP_126	116	5,8595	3.0+/-9.4	0,5,4295	yes	missense	CD101	NM_004258.3	101	13,265,6225	TT,TC,CC		0.0581,6.4911,2.2374	probably-damaging	992/1022	117576631	291,12715	2203	4300	6503	SO:0001583	missense	9398	exon9			AACACACGGAAAG	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.2974C>T	1.37:g.117576631C>T	ENSP00000256652:p.Arg992Trp	138	0	0		112	53	0.473214	NM_001256109	Q15856	Missense_Mutation	SNP	ENST00000256652.4	37	CCDS891.1	48	0.02197802197802198	45	0.09146341463414634	3	0.008287292817679558	0	0.0	0	0.0	C	14.76	2.631571	0.46944	0.064911	5.81E-4	ENSG00000134256	ENST00000256652;ENST00000369470	T;T	0.03772	3.81;3.81	5.83	-0.273	0.12915	.	1.475580	0.04746	N	0.423700	T	0.01523	0.0049	N	0.14661	0.345	0.09310	N	1	D	0.63880	0.993	B	0.44315	0.446	T	0.49234	-0.8961	10	0.72032	D	0.01	-0.5271	9.27	0.37666	0.5351:0.3393:0.1256:0.0	rs34248572	992	Q93033	IGSF2_HUMAN	W	992	ENSP00000256652:R992W;ENSP00000358482:R992W	ENSP00000256652:R992W	R	+	1	2	CD101	117378154	0.000000	0.05858	0.000000	0.03702	0.250000	0.25880	-0.056000	0.11787	0.306000	0.22856	0.563000	0.77884	CGG	C|0.972;T|0.028	0.028	strong		0.517	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258		T	117576631	C	T	117576631	3	4	22	1	0	0	0	0	1	0	0	0	2964	527	19	1	3008	1	CD101	1	117576631	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	49187	117576631	131673990	212	3113											
TTF2	8458	hgsc.bcm.edu	37	chr1	117618024	117618024	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcacagtcacaactcaataaGcaagccccagaaagggggac	16	4	9	12	0	3	1	3	0	0	1	3	2	3	2	2	2	3	1	2	2	5	1	rs17036832	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:117618024G>C	ENST00000369466.4	+	5	862	c.818G>C	c.(817-819)aGc>aCc	p.S273T		NM_003594.3	NP_003585.3	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase II	273					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)		AACTCAATAAGCAAGCCCCAG	0.473													G|||	125	0.0249601	0.09	0.0072	5008	,	,		19352	0.0		0.001	False		,,,				2504	0.0				p.S273T		Atlas-SNP	.											.	TTF2	92	.	0			c.G818C						PASS	.	G	THR/SER	262,4144	143.8+/-178.8	17,228,1958	98	109	105		818	-1.2	0	1	dbSNP_123	105	5,8595	4.3+/-15.6	0,5,4295	yes	missense	TTF2	NM_003594.3	58	17,233,6253	CC,CG,GG		0.0581,5.9464,2.0529	benign	273/1163	117618024	267,12739	2203	4300	6503	SO:0001583	missense	8458	exon5			CAATAAGCAAGCC	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.818G>C	1.37:g.117618024G>C	ENSP00000358478:p.Ser273Thr	120	0	0		118	58	0.491525	NM_003594	A8K4Q2|O75921|Q5T2K7|Q5VVU8|Q8N6I8	Missense_Mutation	SNP	ENST00000369466.4	37	CCDS892.1	49	0.022435897435897436	45	0.09146341463414634	4	0.011049723756906077	0	0.0	0	0.0	G	10.55	1.380822	0.24944	0.059464	5.81E-4	ENSG00000116830	ENST00000369466	D	0.86956	-2.19	5.13	-1.21	0.09524	.	0.471757	0.18081	N	0.152313	T	0.61974	0.2390	L	0.56769	1.78	0.09310	N	1	B;B	0.20052	0.002;0.041	B;B	0.14578	0.003;0.011	T	0.48502	-0.9030	10	0.24483	T	0.36	-0.004	1.0168	0.01509	0.3182:0.2659:0.2795:0.1364	rs17036832;rs52826473;rs17036832	273;273	Q9UNY4;Q9UNY4-2	TTF2_HUMAN;.	T	273	ENSP00000358478:S273T	ENSP00000358478:S273T	S	+	2	0	TTF2	117419547	0.000000	0.05858	0.005000	0.12908	0.093000	0.18481	-0.924000	0.03996	-0.081000	0.12662	0.655000	0.94253	AGC	A|0.000;C|0.019;G|0.980	0.019	strong		0.473	TTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033277.3			C	117618024	G	C	117618024	3	2	22	1	0	0	0	0	1	0	0	0	16734	971	34	4	836	4	TTF2	1	117618024	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	41393	117618024	131632597	213	3114											
TTF2	8458	hgsc.bcm.edu	37	chr1	117637966	117637966	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcagaattggaggcaattcaAagaaattcagcatcccaaaa	18	7	8	8	0	2	2	2	0	0	2	3	3	3	3	1	2	1	3	1	2	6	3	rs34079217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:117637966A>G	ENST00000369466.4	+	19	3056	c.3012A>G	c.(3010-3012)caA>caG	p.Q1004Q	MIR942_ENST00000401111.1_RNA	NM_003594.3	NP_003585.3	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase II	1004	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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)		AGGCAATTCAAAGAAATTCAG	0.358													A|||	171	0.0341454	0.1263	0.0058	5008	,	,		22139	0.0		0.0	False		,,,				2504	0.0				p.Q1004Q		Atlas-SNP	.											.	TTF2	92	.	0			c.A3012G						PASS	.	A		535,3871	240.9+/-251.5	30,475,1698	133	136	135		3012	2.4	0.5	1	dbSNP_126	135	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	TTF2	NM_003594.3		30,481,5992	GG,GA,AA		0.0698,12.1425,4.1596		1004/1163	117637966	541,12465	2203	4300	6503	SO:0001819	synonymous_variant	8458	exon19			AATTCAAAGAAAT	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.3012A>G	1.37:g.117637966A>G		96	0	0		107	43	0.401869	NM_003594	A8K4Q2|O75921|Q5T2K7|Q5VVU8|Q8N6I8	Silent	SNP	ENST00000369466.4	37	CCDS892.1																																																																																			A|0.964;G|0.036	0.036	strong		0.358	TTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033277.3			G	117637966	A	G	117637966	2	3	22	1	0	0	0	0	0	0	0	1	16734	11	1	3		3	TTF2	1	117637966	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	19942	117637966	131612655	214	3115											
FAM46C	54855	hgsc.bcm.edu	37	chr1	118166195	118166195	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agactgatcgccaccaagaaCccagaagaaatcagaggcgg	16	3	11	11	2	1	6	1	1	0	5	2	6	1	6	3	2	1	0	3	2	4	0	rs10923359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:118166195C>T	ENST00000369448.3	+	2	952	c.705C>T	c.(703-705)aaC>aaT	p.N235N		NM_017709.3	NP_060179.2	Q5VWP2	FA46C_HUMAN	family with sequence similarity 46, member C	235										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	15	Lung SC(450;0.225)	all_cancers(81;0.000101)|all_lung(203;3.4e-06)|all_epithelial(167;4.98e-06)|Lung NSC(69;2.33e-05)		Lung(183;0.0576)|LUSC - Lung squamous cell carcinoma(189;0.192)|Colorectal(144;0.247)		CCACCAAGAACCCAGAAGAAA	0.527			"Mis, F, O"		MM					Multiple Myeloma(3;1.13e-06)			C|||	85	0.0169728	0.0613	0.0058	5008	,	,		18879	0.0		0.0	False		,,,				2504	0.0				p.N235N		Atlas-SNP	.		Rec	yes		1	1p12	54855	"family with sequence similarity 46, member C"		L	.	FAM46C	25	.	0			c.C705T						PASS	.	C		207,4199	127.4+/-164.3	6,195,2002	69	74	72		705	4.8	1	1	dbSNP_120	72	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	FAM46C	NM_017709.3		6,197,6300	TT,TC,CC		0.0233,4.6981,1.607		235/392	118166195	209,12797	2203	4300	6503	SO:0001819	synonymous_variant	54855	exon2			CAAGAACCCAGAA	BC036516	CCDS896.1	1p12	2008-02-05			ENSG00000183508	ENSG00000183508			24712	protein-coding gene	gene with protein product		613952				12477932	Standard	NM_017709		Approved	FLJ20202	uc001ehe.3	Q5VWP2	OTTHUMG00000013703	ENST00000369448.3:c.705C>T	1.37:g.118166195C>T		135	0	0		128	56	0.4375	NM_017709	A3KMG2|Q8NE25|Q9NXK0	Silent	SNP	ENST00000369448.3	37	CCDS896.1																																																																																			C|0.979;T|0.021	0.021	strong		0.527	FAM46C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038424.1	NM_017709		T	118166195	C	T	118166195	2	4	22	1	0	0	0	0	0	0	0	1	5575	506	18	2		2	FAM46C	1	118166195	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	528229	118166195	131084426	215	3116											
SPAG17	200162	hgsc.bcm.edu	37	chr1	118512719	118512719	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctttcagtcctgtgctgggtGggggctgctttactttaaac	5	15	12	9	0	1	0	1	0	0	0	2	0	2	0	1	3	4	3	1	3	3	5	rs140504036	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:118512719G>T	ENST00000336338.5	-	46	6412	c.6347C>A	c.(6346-6348)cCa>cAa	p.P2116Q	SPAG17_ENST00000492438.1_5'Flank	NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	2116						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)		TGTGCTGGGTGGGGGCTGCTT	0.393													G|||	3	0.000599042	0.0023	0.0	5008	,	,		18332	0.0		0.0	False		,,,				2504	0.0				p.P2116Q		Atlas-SNP	.											.	SPAG17	263	.	0			c.C6347A						PASS	.	G	GLN/PRO	8,4398	14.3+/-33.2	0,8,2195	141	139	140		6347	5.3	1	1	dbSNP_134	140	0,8600		0,0,4300	yes	missense	SPAG17	NM_206996.2	76	0,8,6495	TT,TG,GG		0.0,0.1816,0.0615	probably-damaging	2116/2224	118512719	8,12998	2203	4300	6503	SO:0001583	missense	200162	exon46			CTGGGTGGGGGCT		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.6347C>A	1.37:g.118512719G>T	ENSP00000337804:p.Pro2116Gln	59	0	0		49	49	1	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.974497	0.74246	0.001816	0.0	ENSG00000155761	ENST00000336338;ENST00000437255	T	0.21031	2.03	5.3	5.3	0.74995	.	0.067501	0.64402	D	0.000011	T	0.37732	0.1014	M	0.78049	2.395	0.32515	N	0.536992	D	0.67145	0.996	D	0.65573	0.936	T	0.30909	-0.9962	10	0.87932	D	0	.	15.9899	0.80197	0.0:0.0:1.0:0.0	.	2116	Q6Q759	SPG17_HUMAN	Q	2116;596	ENSP00000337804:P2116Q	ENSP00000337804:P2116Q	P	-	2	0	SPAG17	118314242	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.801000	0.69115	2.775000	0.95449	0.650000	0.86243	CCA	G|0.999;T|0.001	0.001	strong		0.393	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		T	118512719	G	T	118512719	3	4	22	1	0	0	0	0	1	0	0	0	14994	1348	47	4	336	4	SPAG17	1	118512719	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	346524	118512719	130737902	216	3117											
SPAG17	200162	hgsc.bcm.edu	37	chr1	118598362	118598362	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aactggttacttacttttagAttctttaatggaaaaaattt	14	18	5	4	0	1	1	0	0	1	1	1	2	1	2	0	2	3	1	0	2	8	8	rs138706127	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:118598362A>G	ENST00000336338.5	-	19	2781	c.2716T>C	c.(2716-2718)Tct>Cct	p.S906P		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	906						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)		TTACTTTTAGATTCTTTAATG	0.303													A|||	23	0.00459265	0.0174	0.0	5008	,	,		16823	0.0		0.0	False		,,,				2504	0.0				p.S906P		Atlas-SNP	.											SPAG17,NS,haematopoietic_neoplasm,0,1	SPAG17	263	1	0			c.T2716C						scavenged	.	A	PRO/SER	93,4307	73.6+/-111.7	1,91,2108	67	68	68		2716	4.4	1	1	dbSNP_134	68	1,8595	1.2+/-3.3	0,1,4297	yes	missense	SPAG17	NM_206996.2	74	1,92,6405	GG,GA,AA		0.0116,2.1136,0.7233	possibly-damaging	906/2224	118598362	94,12902	2200	4298	6498	SO:0001583	missense	200162	exon19			TTTTAGATTCTTT		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.2716T>C	1.37:g.118598362A>G	ENSP00000337804:p.Ser906Pro	64	1	0.015625		60	38	0.633333	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	A	13.34	2.206952	0.39003	0.021136	1.16E-4	ENSG00000155761	ENST00000336338	T	0.30981	1.51	5.55	4.42	0.53409	.	0.557030	0.19693	N	0.108216	T	0.14787	0.0357	L	0.59436	1.845	0.27117	N	0.962222	B	0.18166	0.026	B	0.19391	0.025	T	0.18304	-1.0341	10	0.72032	D	0.01	.	9.3895	0.38363	0.9185:0.0:0.0815:0.0	.	906	Q6Q759	SPG17_HUMAN	P	906	ENSP00000337804:S906P	ENSP00000337804:S906P	S	-	1	0	SPAG17	118399885	1.000000	0.71417	0.999000	0.59377	0.166000	0.22503	2.832000	0.48152	1.112000	0.41740	0.477000	0.44152	TCT	A|0.993;G|0.007	0.007	strong		0.303	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		G	118598362	A	G	118598362	3	3	22	1	0	0	0	0	1	0	0	0	14994	333	12	3	4075	3	SPAG17	1	118598362	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	85643	118598362	130652259	217	3118											
SPAG17	200162	hgsc.bcm.edu	37	chr1	118634297	118634297	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcgaattggattcagcaaatAattgtaatatctcatgtcta	14	15	6	6	1	3	0	2	0	2	0	5	2	3	1	0	1	1	2	0	1	6	7	rs150596428	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:118634297A>C	ENST00000336338.5	-	10	1356	c.1291T>G	c.(1291-1293)Tat>Gat	p.Y431D		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	431						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)		TTCAGCAAATAATTGTAATAT	0.383													C|||	6	0.00119808	0.0045	0.0	5008	,	,		18256	0.0		0.0	False		,,,				2504	0.0				p.Y431D		Atlas-SNP	.											.	SPAG17	263	.	0			c.T1291G						PASS	.	C	ASP/TYR	28,4376	822.7+/-416.5	1,26,2175	89	85	86		1291	5.6	1	1	dbSNP_134	86	0,8600		0,0,4300	yes	missense	SPAG17	NM_206996.2	160	1,26,6475	CC,CA,AA		0.0,0.6358,0.2153	benign	431/2224	118634297	28,12976	2202	4300	6502	SO:0001583	missense	200162	exon10			GCAAATAATTGTA		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.1291T>G	1.37:g.118634297A>C	ENSP00000337804:p.Tyr431Asp	145	0	0		145	59	0.406897	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	.	.	.	.	.	.	.	.	.	.	C	7.275	0.607874	0.14002	0.006358	0.0	ENSG00000155761	ENST00000336338	T	0.67171	-0.25	5.59	5.59	0.84812	.	0.259606	0.43747	N	0.000525	T	0.07863	0.0197	N	0.00043	-2.47	0.26007	N	0.982046	B	0.02656	0.0	B	0.01281	0.0	T	0.33317	-0.9873	10	0.02654	T	1	.	16.0877	0.81070	0.1351:0.8649:0.0:0.0	.	431	Q6Q759	SPG17_HUMAN	D	431	ENSP00000337804:Y431D	ENSP00000337804:Y431D	Y	-	1	0	SPAG17	118435820	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.779000	0.47734	1.387000	0.46486	-0.127000	0.14921	TAT	A|0.997;C|0.003	0.003	strong		0.383	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		C	118634297	A	C	118634297	3	2	22	1	0	0	0	0	1	0	0	0	14994	362	13	5	5536	5	SPAG17	1	118634297	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	35935	118634297	130616324	218	3119											
TBX15	6913	hgsc.bcm.edu	37	chr1	119427937	119427937	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agccctgggtagctctgcaaGgcagccatgttgcttcgggc	6	9	14	12	1	1	0	0	0	1	0	2	0	1	0	2	3	5	6	2	3	2	3	rs145938710	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:119427937G>A	ENST00000369429.3	-	8	1236	c.1227C>T	c.(1225-1227)gcC>gcT	p.A409A	TBX15_ENST00000207157.3_Silent_p.A303A			Q96SF7	TBX15_HUMAN	T-box 15	409					embryonic cranial skeleton morphogenesis (GO:0048701)	Tle3-Aes complex (GO:0070722)	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)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(19)|ovary(1)|pancreas(1)|skin(5)	37	all_neural(166;0.117)	all_cancers(81;0.000692)|all_lung(203;3.05e-06)|Lung NSC(69;2.13e-05)|all_epithelial(167;0.000237)		Lung(183;0.044)|LUSC - Lung squamous cell carcinoma(189;0.141)		AGCTCTGCAAGGCAGCCATGT	0.542													G|||	8	0.00159744	0.0061	0.0	5008	,	,		20115	0.0		0.0	False		,,,				2504	0.0				p.A303A		Atlas-SNP	.											.	TBX15	95	.	0			c.C909T						PASS	.	G		18,4388	23.3+/-48.9	0,18,2185	47	45	46		909	2.3	1	1	dbSNP_134	46	0,8600		0,0,4300	no	coding-synonymous	TBX15	NM_152380.2		0,18,6485	AA,AG,GG		0.0,0.4085,0.1384		303/497	119427937	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	6913	exon8			CTGCAAGGCAGCC	AK127536	CCDS30816.1	1p11.1	2008-02-05	2004-10-05		ENSG00000092607	ENSG00000092607		"T-boxes"	11594	protein-coding gene	gene with protein product		604127	"T-box 14"	TBX14		9693034	Standard	XM_005271162		Approved		uc001ehl.1	Q96SF7	OTTHUMG00000012263	ENST00000369429.3:c.1227C>T	1.37:g.119427937G>A		67	0	0		70	36	0.514286	NM_152380	Q08E76|Q5JT54|Q5T9S7	Silent	SNP	ENST00000369429.3	37																																																																																				G|0.998;A|0.002	0.002	strong		0.542	TBX15-002	PUTATIVE	not_organism_supported|upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000034351.1	NM_152380		A	119427937	G	A	119427937	2	1	22	1	0	0	0	0	0	0	0	1	15667	987	35	2		2	TBX15	1	119427937	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	793640	119427937	129822684	219	3120											
HSD3B2	3284	hgsc.bcm.edu	37	chr1	119962118	119962118	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tcctgaaaagagcctgccagGacgtctcggtcgtcatccac	9	8	10	14	3	2	2	1	1	1	1	6	3	4	3	4	2	2	0	4	2	2	0	rs4986954	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:119962118G>A	ENST00000543831.1	+	3	469	c.220G>A	c.(220-222)Gac>Aac	p.D74N	HSD3B2_ENST00000471656.1_3'UTR|HSD3B2_ENST00000369416.3_Missense_Mutation_p.D74N	NM_001166120.1	NP_001159592.1	P26439	3BHS2_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2	74			D -> N (in dbSNP:rs4986954).		androgen biosynthetic process (GO:0006702)|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 (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial membrane (GO:0031966)|smooth endoplasmic reticulum membrane (GO:0030868)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|steroid delta-isomerase activity (GO:0004769)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(19)|ovary(2)|skin(1)	27	all_neural(166;0.187)	all_lung(203;1.06e-06)|Lung NSC(69;7.5e-06)|all_epithelial(167;0.000284)		Lung(183;0.015)|LUSC - Lung squamous cell carcinoma(189;0.0836)	Corticotropin(DB01285)|Medroxyprogesterone Acetate(DB00603)|Trilostane(DB01108)	AGCCTGCCAGGACGTCTCGGT	0.498													G|||	15	0.00299521	0.0113	0.0	5008	,	,		20071	0.0		0.0	False		,,,				2504	0.0				p.D74N		Atlas-SNP	.											.	HSD3B2	48	.	0			c.G220A						PASS	.	G	ASN/ASP,ASN/ASP	39,4367		1,37,2165	112	89	97		220,220	3.9	0.9	1	dbSNP_111	97	0,8600		0,0,4300	no	missense,missense	HSD3B2	NM_000198.3,NM_001166120.1	23,23	1,37,6465	AA,AG,GG		0.0,0.8852,0.2999	benign,benign	74/373,74/373	119962118	39,12967	2203	4300	6503	SO:0001583	missense	3284	exon3			TGCCAGGACGTCT	BC038419	CCDS902.1	1p12	2014-06-03			ENSG00000203859	ENSG00000203859	1.1.1.145, 5.3.3.1	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	5218	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 11E, member 2"	613890				1363812, 19027726	Standard	NM_000198		Approved	SDR11E2	uc001eht.3	P26439	OTTHUMG00000012526	ENST00000543831.1:c.220G>A	1.37:g.119962118G>A	ENSP00000445122:p.Asp74Asn	161	0	0		196	88	0.44898	NM_001166120	A2RRA5|Q16010|Q53GD4|Q6AI10|Q6LDB9|Q99890|Q9UD08	Missense_Mutation	SNP	ENST00000543831.1	37	CCDS902.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	-	14.37	2.514988	0.44763	0.008852	0.0	ENSG00000203859	ENST00000543831;ENST00000433745;ENST00000369416	D;D;D	0.88509	-2.39;-2.39;-2.39	3.93	3.93	0.45458	3-beta hydroxysteroid dehydrogenase/isomerase (1);NAD(P)-binding domain (1);	0.054278	0.64402	D	0.000001	T	0.81969	0.4935	L	0.41906	1.305	0.30554	N	0.765177	P;P	0.36874	0.572;0.464	B;P	0.45913	0.173;0.497	T	0.77305	-0.2637	9	.	.	.	-17.182	13.5239	0.61584	0.0:0.0:1.0:0.0	rs4986954;rs52821087;rs4986954	74;74	P26439-2;P26439	.;3BHS2_HUMAN	N	74	ENSP00000445122:D74N;ENSP00000388292:D74N;ENSP00000358424:D74N	.	D	+	1	0	HSD3B2	119763641	1.000000	0.71417	0.934000	0.37439	0.009000	0.06853	7.003000	0.76310	1.943000	0.56356	0.298000	0.19748	GAC	G|0.996;A|0.004	0.004	strong		0.498	HSD3B2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034994.1	NM_000198		A	119962118	G	A	119962118	3	1	22	1	0	0	0	0	1	0	0	0	7400	1174	41	2	226	2	HSD3B2	1	119962118	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	534181	119962118	129288503	220	3121											
HSD3B1	3283	hgsc.bcm.edu	37	chr1	120057163	120057163	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaggctcagcgagatctggcGtataagccactctacagctg	11	8	11	11	2	3	1	1	0	2	1	3	2	3	1	1	2	4	3	1	2	4	3	rs33913717	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120057163G>A	ENST00000369413.3	+	4	1162	c.1017G>A	c.(1015-1017)gcG>gcA	p.A339A	HSD3B1_ENST00000235547.6_Silent_p.A341A|HSD3B1_ENST00000528909.1_Silent_p.A339A			P14060	3BHS1_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	339					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)	GAGATCTGGCGTATAAGCCAC	0.517													g|||	37	0.00738818	0.0272	0.0014	5008	,	,		21238	0.0		0.0	False		,,,				2504	0.0				p.A339A		Atlas-SNP	.											HSD3B1,caecum,carcinoma,+1,1	HSD3B1	53	1	0			c.G1017A						PASS	.	A		118,4288	89.2+/-127.9	7,104,2092	83	73	76		1017	-6.5	0	1	dbSNP_126	76	0,8600		0,0,4300	yes	coding-synonymous	HSD3B1	NM_000862.2		7,104,6392	AA,AG,GG		0.0,2.6782,0.9073		339/374	120057163	118,12888	2203	4300	6503	SO:0001819	synonymous_variant	3283	exon4			TCTGGCGTATAAG	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.1017G>A	1.37:g.120057163G>A		233	0	0		250	127	0.508	NM_000862	A8K691|Q14545|Q8IV65	Silent	SNP	ENST00000369413.3	37	CCDS903.1																																																																																			G|0.990;A|0.010	0.010	strong		0.517	HSD3B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034993.3	NM_000862		A	120057163	G	A	120057163	2	1	22	1	0	0	0	0	0	0	0	1	7399	1132	40	1		1	HSD3B1	1	120057163	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	95045	120057163	129193458	221	3122											
ZNF697	90874	hgsc.bcm.edu	37	chr1	120165412	120165412	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccgcacacttgtgcggcttGttgcccgtgtggatgcggcg	3	10	15	13	5	0	0	0	0	0	0	0	1	0	1	2	3	3	3	2	3	0	3	rs61734323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120165412G>A	ENST00000421812.2	-	3	1673	c.1554C>T	c.(1552-1554)aaC>aaT	p.N518N		NM_001080470.1	NP_001073939.1	Q5TEC3	ZN697_HUMAN	zinc finger protein 697	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)			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)		TGTGCGGCTTGTTGCCCGTGT	0.642													G|||	60	0.0119808	0.0431	0.0029	5008	,	,		16736	0.0		0.001	False		,,,				2504	0.0				p.N518N		Atlas-SNP	.											.	ZNF697	26	.	0			c.C1554T						PASS	.	G		129,4179		2,125,2027	12	17	15		1554	4.1	1	1	dbSNP_129	15	1,8545		0,1,4272	no	coding-synonymous	ZNF697	NM_001080470.1		2,126,6299	AA,AG,GG		0.0117,2.9944,1.0114		518/546	120165412	130,12724	2154	4273	6427	SO:0001819	synonymous_variant	90874	exon3			CGGCTTGTTGCCC	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.1554C>T	1.37:g.120165412G>A		154	0	0		153	72	0.470588	NM_001080470	Q96IT2	Silent	SNP	ENST00000421812.2	37	CCDS44202.1																																																																																			G|0.994;A|0.006	0.006	strong		0.642	ZNF697-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036349.3	XM_371286		A	120165412	G	A	120165412	2	1	22	1	0	0	0	0	0	0	0	1	18115	1368	48	2		2	ZNF697	1	120165412	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	108249	120165412	129085209	222	3123											
REG4	83998	hgsc.bcm.edu	37	chr1	120341193	120341193	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaccaggatctgtacagataCatggccccatcaatccactg	12	8	8	13	0	2	1	1	0	1	1	3	3	3	2	4	2	2	1	4	2	3	2	rs75358916	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120341193C>T	ENST00000354219.1	-	6	775	c.336G>A	c.(334-336)atG>atA	p.M112I	REG4_ENST00000530654.1_Intron|REG4_ENST00000256585.5_Missense_Mutation_p.M112I	NM_001159352.1	NP_001152824.1	Q9BYZ8	REG4_HUMAN	regenerating islet-derived family, member 4	112	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)	heparin binding (GO:0008201)|mannan binding (GO:2001065)			central_nervous_system(1)|large_intestine(1)|lung(8)|ovary(2)|prostate(1)|skin(2)	15	all_cancers(5;4.81e-10)|all_epithelial(5;7.98e-11)|Melanoma(3;1.93e-05)|Breast(55;0.218)|all_neural(166;0.219)	all_lung(203;8.1e-07)|Lung NSC(69;5.89e-06)|all_epithelial(167;0.000959)		Lung(183;0.011)|LUSC - Lung squamous cell carcinoma(189;0.0588)		TGTACAGATACATGGCCCCAT	0.532													C|||	42	0.00838658	0.031	0.0014	5008	,	,		17162	0.0		0.0	False		,,,				2504	0.0				p.M112I		Atlas-SNP	.											.	REG4	36	.	0			c.G336A						PASS	.	C	ILE/MET,ILE/MET	128,4278	93.4+/-132.2	2,124,2077	201	185	190		336,336	-7.1	0	1	dbSNP_131	190	0,8600		0,0,4300	yes	missense,missense	REG4	NM_001159352.1,NM_032044.3	10,10	2,124,6377	TT,TC,CC		0.0,2.9051,0.9842	benign,benign	112/159,112/159	120341193	128,12878	2203	4300	6503	SO:0001583	missense	83998	exon5			CAGATACATGGCC	AY007243	CCDS906.1, CCDS53354.1	1p13.1-p12	2008-02-05			ENSG00000134193	ENSG00000134193			22977	protein-coding gene	gene with protein product	"regenerating gene type IV", " gastrointestinal secretory protein"	609846				11311942, 12455032	Standard	NM_032044		Approved	REG-IV, RELP, GISP	uc001eif.3	Q9BYZ8	OTTHUMG00000012175	ENST00000354219.1:c.336G>A	1.37:g.120341193C>T	ENSP00000346158:p.Met112Ile	203	1	0.00492611		225	120	0.533333	NM_032044	Q8NER6|Q8NER7	Missense_Mutation	SNP	ENST00000354219.1	37	CCDS906.1	16	0.007326007326007326	15	0.03048780487804878	1	0.0027624309392265192	0	0.0	0	0.0	C	9.514	1.106451	0.20632	0.029051	0.0	ENSG00000134193	ENST00000354219;ENST00000256585	T;T	0.07216	3.21;3.21	5.02	-7.05	0.01573	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	1.458410	0.04405	N	0.364865	T	0.01156	0.0038	N	0.11756	0.17	0.09310	N	1	B	0.02656	0.0	B	0.11329	0.006	T	0.43523	-0.9386	10	0.32370	T	0.25	0.8924	7.2514	0.26152	0.0:0.1828:0.4589:0.3583	.	112	Q9BYZ8	REG4_HUMAN	I	112	ENSP00000346158:M112I;ENSP00000256585:M112I	ENSP00000256585:M112I	M	-	3	0	REG4	120142716	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.742000	0.01835	-1.675000	0.01459	-0.893000	0.02921	ATG	C|0.991;T|0.009	0.009	strong		0.532	REG4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033675.1	NM_032044		T	120341193	C	T	120341193	3	4	22	1	0	0	0	0	1	0	0	0	13229	478	17	2	148	2	REG4	1	120341193	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	175781	120341193	128909428	223	3124											
NBPF7	343505	hgsc.bcm.edu	37	chr1	120378657	120378657	+	IGR	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtttcttcccctttggaattGgagtgttcgctggctacatc	5	16	10	10	1	1	0	0	0	1	0	4	2	2	2	2	3	1	4	2	3	2	6	rs6684816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120378657G>A								REG4 (24374 upstream) : ADAM30 (57498 downstream)																							CTTTGGAATTGGAGTGTTCGC	0.443													g|||	111	0.0221645	0.0756	0.0086	5008	,	,		21408	0.0		0.004	False		,,,				2504	0.001				p.S363S		Atlas-SNP	.											.	NBPF7	46	.	0			c.C1089T						PASS	.	G		224,3620		5,214,1703	107	105	105		1089	-1	0	1	dbSNP_116	105	45,8253		1,43,4105	no	coding-synonymous	NBPF7	NM_001047980.1		6,257,5808	AA,AG,GG		0.5423,5.8273,2.2155		363/422	120378657	269,11873	1922	4149	6071	SO:0001628	intergenic_variant	343505	exon7			GGAATTGGAGTGT																													1.37:g.120378657G>A		164	0	0		202	96	0.475248	NM_001047980		Silent	SNP		37																																																																																				A|0.016;G|0.984	0.016	strong	0	0.443									A	120378657	G	A	120378657	1	1	22	0	1	0	0	0	0	0	0	0	10207	1335	47	2		2	NBPF7	1	120378657	IGR	SNP	G	TCGA-G8-6324-01A-11D-2210-10	37464	120378657	128871964	224	3125											
NBPF7	343505	hgsc.bcm.edu	37	chr1	120378702	120378702	+	IGR	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagagcaaactttctgttcAactagtgccaagaaagtgcc	13	9	9	10	0	2	2	1	0	1	2	2	2	2	2	2	0	5	3	2	0	5	3	rs10158823	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120378702A>G								REG4 (24419 upstream) : ADAM30 (57453 downstream)																							CTTTCTGTTCAACTAGTGCCA	0.488													a|||	405	0.0808706	0.295	0.0216	5008	,	,		21265	0.0		0.0	False		,,,				2504	0.0				p.V348V		Atlas-SNP	.											.	NBPF7	46	.	0			c.T1044C						PASS	.	A		848,3086		97,654,1216	107	106	107		1044	-0.1	0	1	dbSNP_119	107	21,8319		0,21,4149	no	coding-synonymous	NBPF7	NM_001047980.1		97,675,5365	GG,GA,AA		0.2518,21.5557,7.08		348/422	120378702	869,11405	1967	4170	6137	SO:0001628	intergenic_variant	343505	exon7			CTGTTCAACTAGT																													1.37:g.120378702A>G		152	0	0		203	105	0.517241	NM_001047980		Silent	SNP		37																																																																																				A|0.919;G|0.081	0.081	strong	0	0.488									G	120378702	A	G	120378702	1	3	22	0	1	0	0	0	0	0	0	0	10207	117	5	3		3	NBPF7	1	120378702	IGR	SNP	A	TCGA-G8-6324-01A-11D-2210-10	45	120378702	128871919	225	3126											
NBPF7	343505	hgsc.bcm.edu	37	chr1	120384162	120384162	+	IGR	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggaggcatctctcccttcccGtaacttctcccttaactgga	7	12	7	15	1	2	0	0	0	2	0	6	2	4	2	3	3	2	2	3	3	2	4	rs78204967	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120384162G>A								REG4 (29879 upstream) : ADAM30 (51993 downstream)																							CTCCCTTCCCGTAACTTCTCC	0.493													g|||	119	0.023762	0.0802	0.0115	5008	,	,		21233	0.0		0.004	False		,,,				2504	0.001				p.R134W		Atlas-SNP	.											NBPF7,NS,carcinoma,0,1	NBPF7	46	1	0			c.C400T						scavenged	.	G	TRP/ARG	282,4124	147.6+/-182.1	8,266,1929	137	154	148		400	-0.1	0	1	dbSNP_131	148	49,8551	29.6+/-80.5	1,47,4252	no	missense	NBPF7	NM_001047980.1	101	9,313,6181	AA,AG,GG		0.5698,6.4004,2.545	probably-damaging	134/422	120384162	331,12675	2203	4300	6503	SO:0001628	intergenic_variant	343505	exon3			CTTCCCGTAACTT																													1.37:g.120384162G>A		245	2	0.00816326		204	99	0.485294	NM_001047980		Missense_Mutation	SNP		37																																																																																				G|0.983;A|0.017	0.017	strong	0	0.493									A	120384162	G	A	120384162	1	1	22	0	1	0	0	0	0	0	0	0	10207	1144	40	1		1	NBPF7	1	120384162	IGR	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5460	120384162	128866459	226	3127											
NBPF7	343505	hgsc.bcm.edu	37	chr1	120386922	120386922	+	IGR	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atggtgagcctatagatcttActgtatttgttctgctggtt	7	18	10	6	0	2	2	0	1	2	1	2	2	2	2	1	2	3	4	1	2	4	7	rs12068863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120386922A>T								REG4 (32639 upstream) : ADAM30 (49233 downstream)																							TATAGATCTTACTGTATTTGT	0.428											OREG0013730	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	a|||	371	0.0740815	0.27	0.0202	5008	,	,		20192	0.0		0.0	False		,,,				2504	0.0				.		Atlas-SNP	.											.	NBPF7	46	.	0			c.235+2T>A						PASS	.	A		829,3303		91,647,1328	78	86	83			0.7	0	1	dbSNP_120	83	22,8414		0,22,4196	no	splice-5	NBPF7	NM_001047980.1		91,669,5524	TT,TA,AA		0.2608,20.0629,6.7712			120386922	851,11717	2066	4218	6284	SO:0001628	intergenic_variant	343505	exon2			GATCTTACTGTAT																													1.37:g.120386922A>T		83	0	0	1503	109	40	0.366972	NM_001047980		Splice_Site	SNP		37																																																																																				A|0.957;T|0.043	0.043	strong	0	0.428									T	120386922	A	T	120386922	1	4	22	0	1	0	0	0	0	0	0	0	10207	405	14	5		5	NBPF7	1	120386922	IGR	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2760	120386922	128863699	227	3128											
NOTCH2	4853	hgsc.bcm.edu	37	chr1	120480583	120480583	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gactctgcttttttctgaacGcaagtacctttgtttttaca	8	18	6	9	1	2	1	0	1	2	0	2	2	2	1	1	0	4	4	1	0	4	8	rs7543643	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120480583G>A	ENST00000256646.2	-	20	3453	c.3234C>T	c.(3232-3234)tgC>tgT	p.C1078C		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	1078	EGF-like 28. {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)		TTTTCTGAACGCAAGTACCTT	0.468			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome				G|||	356	0.0710863	0.2458	0.0202	5008	,	,		18636	0.002		0.001	False		,,,				2504	0.0143				p.C1078C		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.C3234T						PASS	.	G	,	906,3500	350.5+/-310.9	88,730,1385	133	122	125		3234,3234	-1.8	0	1	dbSNP_116	125	24,8576	16.6+/-54.9	0,24,4276	yes	coding-synonymous,coding-synonymous	NOTCH2	NM_001200001.1,NM_024408.3	,	88,754,5661	AA,AG,GG		0.2791,20.5629,7.1505	,	1078/1236,1078/2472	120480583	930,12076	2203	4300	6503	SO:0001819	synonymous_variant	4853	exon20	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	CTGAACGCAAGTA	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.3234C>T	1.37:g.120480583G>A		135	0	0		123	62	0.504065	NM_001200001	Q5T3X7|Q99734|Q9H240	Silent	SNP	ENST00000256646.2	37	CCDS908.1																																																																																			G|0.925;A|0.075	0.075	strong		0.468	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		A	120480583	G	A	120480583	2	1	22	1	0	0	0	0	0	0	0	1	10557	1079	38	1		1	NOTCH2	1	120480583	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	93661	120480583	128770038	228	3129											
PPIAL4G	644591	hgsc.bcm.edu	37	chr1	143767730	143767730	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaaatcctttctctccagtgCtcagagcacgaaagttttct	10	13	7	11	1	3	1	1	0	2	1	6	3	5	1	2	0	2	3	2	0	2	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:143767730C>T	ENST00000419275.1	-	1	151	c.119G>A	c.(118-120)aGc>aAc	p.S40N		NM_001123068.1	NP_001116540.1	A2BFH1	PAL4G_HUMAN	peptidylprolyl isomerase A (cyclophilin A)-like 4G	40	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				protein folding (GO:0006457)	cytoplasm (GO:0005737)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|endometrium(2)|kidney(1)|lung(8)|ovary(1)|skin(1)	14						CTCTCCAGTGCTCAGAGCACG	0.473																																					p.S40N		Atlas-SNP	.											.	PPIAL4G	22	.	0			c.G119A						PASS	.						84	81	82					1																	143767730		1568	3562	5130	SO:0001583	missense	644591	exon1			CCAGTGCTCAGAG		CCDS41375.1, CCDS41375.2	1q21.1	2010-06-03			ENSG00000236334	ENSG00000236334			33996	protein-coding gene	gene with protein product							Standard	NM_001123068		Approved		uc001ejt.3	A2BFH1	OTTHUMG00000013629	ENST00000419275.1:c.119G>A	1.37:g.143767730C>T	ENSP00000393845:p.Ser40Asn	1116	0	0		1225	155	0.126531	NM_001123068	A1L431	Missense_Mutation	SNP	ENST00000419275.1	37	CCDS41375.1	.	.	.	.	.	.	.	.	.	.	.	14.94	2.685463	0.47991	.	.	ENSG00000236334	ENST00000419275	T	0.44482	0.92	0.523	-0.795	0.10915	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (3);Cyclophilin-like (1);	0.235838	0.42682	U	0.000663	T	0.16342	0.0393	L	0.49571	1.57	0.23010	N	0.99844	B	0.22480	0.07	B	0.35114	0.196	T	0.35475	-0.9787	10	0.35671	T	0.21	.	4.7838	0.13215	0.0:0.7163:0.0:0.2837	.	40	A2BFH1	PAL4G_HUMAN	N	40	ENSP00000393845:S40N	ENSP00000393845:S40N	S	-	2	0	PPIAL4G	142559253	1.000000	0.71417	0.814000	0.32528	0.857000	0.48899	2.074000	0.41529	-0.252000	0.09528	0.403000	0.27427	AGC	.	.	none		0.473	PPIAL4G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037969.1	NM_001123068		T	143767730	C	T	143767730	3	4	22	1	0	0	0	0	1	0	0	0	12330	797	28	2	379	2	PPIAL4G	1	143767730	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	23287147	143767730	105482891	229	3130											
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144852477	144852477	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtcacaaggctggagtacatGgcagagcccttagggatttc	10	9	13	9	0	1	1	1	0	0	1	2	3	1	3	1	4	2	3	1	4	3	3	rs148370554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:144852477G>A	ENST00000369354.3	-	44	7211	c.7022C>T	c.(7021-7023)cCa>cTa	p.P2341L	PDE4DIP_ENST00000313382.9_Missense_Mutation_p.P2235L|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.P2477L|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.P2426L|PDE4DIP_ENST00000369356.4_Intron|PDE4DIP_ENST00000524974.1_5'UTR			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2341					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)		TGGAGTACATGGCAGAGCCCT	0.512			T	PDGFRB	MPD								.|||	165	0.0329473	0.1203	0.0072	5008	,	,		45392	0.0		0.001	False		,,,				2504	0.0				p.P2341L		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C7022T						PASS	.						50	49	49					1																	144852477		2203	4293	6496	SO:0001583	missense	9659	exon44			GTACATGGCAGAG	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.7022C>T	1.37:g.144852477G>A	ENSP00000358360:p.Pro2341Leu	83	0	0		118	6	0.0508475	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	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	.	4.717	0.133299	0.09032	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000530740;ENST00000369359	T;T;T;T	0.01787	4.64;4.74;4.74;4.75	4.47	0.476	0.16779	.	.	.	.	.	T	0.00845	0.0028	M	0.64404	1.975	0.09310	N	1	B;B	0.12630	0.0;0.006	B;B	0.08055	0.0;0.003	T	0.40961	-0.9535	9	0.54805	T	0.06	.	7.4413	0.27185	0.3516:0.0:0.6483:0.0	.	2235;2341	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	L	2235;2341;2426;2477	ENSP00000327209:P2235L;ENSP00000358360:P2341L;ENSP00000435654:P2426L;ENSP00000358366:P2477L	ENSP00000327209:P2235L	P	-	2	0	PDE4DIP	143563834	0.000000	0.05858	0.001000	0.08648	0.174000	0.22865	0.216000	0.17585	-0.094000	0.12374	-0.274000	0.10170	CCA	.	.	weak		0.512	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		A	144852477	G	A	144852477	3	1	22	1	0	0	0	0	1	0	0	0	11652	1348	47	2	22	2	PDE4DIP	1	144852477	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1084747	144852477	104398144	230	3131											
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144873983	144873983	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagatgcactggttgatgaTggtttagaagacaacacagc	13	10	12	6	0	0	5	0	3	0	3	0	6	0	5	0	2	3	3	0	2	3	3	rs148165371	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:144873983T>C	ENST00000369354.3	-	31	5163	c.4974A>G	c.(4972-4974)ccA>ccG	p.P1658P	PDE4DIP_ENST00000313382.9_Silent_p.P1614P|PDE4DIP_ENST00000369359.4_Silent_p.P1794P|PDE4DIP_ENST00000530740.1_Intron|PDE4DIP_ENST00000369356.4_Silent_p.P1658P|PDE4DIP_ENST00000524974.1_5'UTR|RP4-791M13.5_ENST00000531288.1_RNA			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1658					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)		TGGTTGATGATGGTTTAGAAG	0.473			T	PDGFRB	MPD								.|||	3	0.000599042	0.0023	0.0	5008	,	,		42684	0.0		0.0	False		,,,				2504	0.0				p.P1658P		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A4974G						PASS	.	T	,,	11,4395	17.9+/-39.9	0,11,2192	417	423	421		4842,4974,4974	5.3	1	1	dbSNP_134	421	0,8594		0,0,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	PDE4DIP	NM_001198832.1,NM_001198834.2,NM_014644.4	,,	0,11,6489	CC,CT,TT		0.0,0.2497,0.0846	,,	1614/2241,1658/2363,1658/2347	144873983	11,12989	2203	4297	6500	SO:0001819	synonymous_variant	9659	exon31			TGATGATGGTTTA	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.4974A>G	1.37:g.144873983T>C		355	0	0		418	111	0.26555	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	37	CCDS30824.1																																																																																			T|0.999;C|0.001	0.001	strong		0.473	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		C	144873983	T	C	144873983	2	2	22	1	0	0	0	0	0	0	0	1	11652	1451	51	3		3	PDE4DIP	1	144873983	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	21506	144873983	104376638	231	3132											
NOTCH2NL	388677	hgsc.bcm.edu	37	chr1	145281413	145281413	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctgcctgtctcatccctgtGcaaatggaagtacctgtacc	8	11	8	14	0	1	0	1	0	1	0	3	1	2	1	5	1	4	3	5	1	4	2	rs76765512	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:145281413G>A	ENST00000369340.3	+	5	787	c.343G>A	c.(343-345)Gca>Aca	p.A115T	NOTCH2NL_ENST00000362074.6_Missense_Mutation_p.A115T|RP11-458D21.5_ENST00000468030.1_Missense_Mutation_p.A115T|NOTCH2NL_ENST00000344859.3_Missense_Mutation_p.A115T			Q7Z3S9	NT2NL_HUMAN	notch 2 N-terminal like	115	EGF-like 4. {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						TCATCCCTGTGCAAATGGAAG	0.502																																					p.A115T		Atlas-SNP	.											.	NOTCH2NL	100	.	0			c.G343A						PASS	.	G	THR/ALA	228,4178	115.4+/-153.4	0,228,1975	339	343	342		343	2.9	1	1	dbSNP_131	342	2,8596	1.2+/-3.3	0,2,4297	no	missense	NOTCH2NL	NM_203458.3	58	0,230,6272	AA,AG,GG		0.0233,5.1748,1.7687	possibly-damaging	115/237	145281413	230,12774	2203	4299	6502	SO:0001583	missense	388677	exon4			CCCTGTGCAAATG		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.343G>A	1.37:g.145281413G>A	ENSP00000358346:p.Ala115Thr	1344	2	0.0014881		1480	388	0.262162	NM_203458	Q5BKT8|Q5VTG9|Q5XG84|Q6P192|Q8NC23|Q8WUQ9|Q96FY1	Missense_Mutation	SNP	ENST00000369340.3	37	CCDS909.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.233634	0.79688	0.051748	2.33E-4	ENSG00000213240	ENST00000362074;ENST00000344859;ENST00000369340	D;D;D	0.87491	-2.26;-2.26;-2.26	2.87	2.87	0.33458	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.76835	0.4043	L	0.37507	1.11	0.32769	N	0.504048	P;P	0.49783	0.825;0.928	B;P	0.48571	0.342;0.582	T	0.70378	-0.4888	9	0.29301	T	0.29	.	11.5361	0.50639	0.0:0.0:1.0:0.0	.	115;115	Q7Z3S9-2;Q7Z3S9	.;NT2NL_HUMAN	T	115	ENSP00000354929:A115T;ENSP00000344557:A115T;ENSP00000358346:A115T	ENSP00000344557:A115T	A	+	1	0	NOTCH2NL	143992770	1.000000	0.71417	0.999000	0.59377	0.982000	0.71751	7.645000	0.83430	1.601000	0.50113	0.400000	0.26472	GCA	G|0.980;A|0.020	0.020	strong		0.502	NOTCH2NL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038546.1	NM_203458		A	145281413	G	A	145281413	3	1	22	1	0	0	0	0	1	0	0	0	10558	1319	46	2	353	2	NOTCH2NL	1	145281413	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	407430	145281413	103969208	232	3133											
CHD1L	9557	hgsc.bcm.edu	37	chr1	146757092	146757092	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagacagaagaaaagacaagAagcagctgccaagagaagga	21	1	12	7	0	0	6	0	0	0	6	0	8	0	7	1	1	3	2	1	1	7	0	rs13374920	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:146757092A>C	ENST00000369258.4	+	17	1966	c.1946A>C	c.(1945-1947)gAa>gCa	p.E649A	CHD1L_ENST00000467213.1_3'UTR|CHD1L_ENST00000369259.3_Missense_Mutation_p.E445A|CHD1L_ENST00000361293.5_Missense_Mutation_p.E368A|CHD1L_ENST00000431239.1_Missense_Mutation_p.E555A	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	649			E -> A (in dbSNP:rs13374920).		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)					AAAAGACAAGAAGCAGCTGCC	0.493													A|||	114	0.0227636	0.0825	0.0058	5008	,	,		19571	0.0		0.0	False		,,,				2504	0.001				p.E649A		Atlas-SNP	.											CHD1L,right_upper_lobe,carcinoma,+1,1	CHD1L	72	1	0			c.A1946C						PASS	.	A	ALA/GLU	307,4099	165.8+/-197.2	8,291,1904	148	146	147		1946	3.4	1	1	dbSNP_121	147	5,8595	4.3+/-15.6	0,5,4295	yes	missense	CHD1L	NM_004284.3	107	8,296,6199	CC,CA,AA		0.0581,6.9678,2.3989	possibly-damaging	649/898	146757092	312,12694	2203	4300	6503	SO:0001583	missense	9557	exon17			GACAAGAAGCAGC	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.1946A>C	1.37:g.146757092A>C	ENSP00000358262:p.Glu649Ala	176	0	0		183	95	0.519126	NM_004284	A5YM64|B4DDE1|B5MDZ7|Q53EZ3|Q5VXX7|Q6DD94|Q6PK83|Q86XH3|Q96HF7|Q96SP3|Q9BVJ1|Q9NVV8	Missense_Mutation	SNP	ENST00000369258.4	37	CCDS927.1	47	0.02152014652014652	46	0.09349593495934959	1	0.0027624309392265192	0	0.0	0	0.0	A	8.801	0.932825	0.18131	0.069678	5.81E-4	ENSG00000131778	ENST00000431239;ENST00000369259;ENST00000369258;ENST00000361293	D;T;D;D	0.89810	-2.57;-1.43;-2.45;-1.55	5.78	3.4	0.38934	.	0.337634	0.31809	N	0.007040	T	0.76765	0.4033	L	0.43152	1.355	0.44098	D	0.996861	P;B;B	0.39181	0.663;0.419;0.339	B;B;B	0.38921	0.285;0.151;0.04	T	0.74481	-0.3651	10	0.49607	T	0.09	.	10.1412	0.42736	0.6754:0.3246:0.0:0.0	rs13374920;rs52828089;rs13374920	555;445;649	Q86WJ1-2;Q86WJ1-3;Q86WJ1	.;.;CHD1L_HUMAN	A	555;445;649;368	ENSP00000389031:E555A;ENSP00000358263:E445A;ENSP00000358262:E649A;ENSP00000355100:E368A	ENSP00000355100:E368A	E	+	2	0	CHD1L	145223716	1.000000	0.71417	0.989000	0.46669	0.006000	0.05464	2.163000	0.42377	0.418000	0.25898	-0.446000	0.05623	GAA	A|0.976;C|0.024	0.024	strong		0.493	CHD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040377.1	NM_004284		C	146757092	A	C	146757092	3	2	22	1	0	0	0	0	1	0	0	0	3326	246	9	5	2012	5	CHD1L	1	146757092	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1475679	146757092	102493529	233	3134											
CHD1L	9557	hgsc.bcm.edu	37	chr1	146763171	146763171	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgttttacctcagacctgagTttgggaggtgtccttttatt	6	18	10	7	0	1	2	1	1	0	1	2	3	2	3	3	2	1	2	3	2	2	6	rs61756300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:146763171T>A	ENST00000369258.4	+	20	2348	c.2328T>A	c.(2326-2328)agT>agA	p.S776R	CHD1L_ENST00000467213.1_3'UTR|CHD1L_ENST00000369259.3_Missense_Mutation_p.S572R|CHD1L_ENST00000361293.5_Missense_Mutation_p.S495R|CHD1L_ENST00000431239.1_Missense_Mutation_p.S682R	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	776	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				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)					CAGACCTGAGTTTGGGAGGTG	0.403													T|||	101	0.0201677	0.0749	0.0029	5008	,	,		20473	0.0		0.0	False		,,,				2504	0.0				p.S776R		Atlas-SNP	.											.	CHD1L	72	.	0			c.T2328A						PASS	.	T	ARG/SER	265,4141	152.5+/-186.2	6,253,1944	196	162	173		2328	4.6	1	1	dbSNP_129	173	6,8594	4.3+/-15.6	0,6,4294	yes	missense	CHD1L	NM_004284.3	110	6,259,6238	AA,AT,TT		0.0698,6.0145,2.0837	benign	776/898	146763171	271,12735	2203	4300	6503	SO:0001583	missense	9557	exon20			CCTGAGTTTGGGA	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.2328T>A	1.37:g.146763171T>A	ENSP00000358262:p.Ser776Arg	383	0	0		378	182	0.481481	NM_004284	A5YM64|B4DDE1|B5MDZ7|Q53EZ3|Q5VXX7|Q6DD94|Q6PK83|Q86XH3|Q96HF7|Q96SP3|Q9BVJ1|Q9NVV8	Missense_Mutation	SNP	ENST00000369258.4	37	CCDS927.1	30	0.013736263736263736	28	0.056910569105691054	2	0.0055248618784530384	0	0.0	0	0.0	T	12.55	1.970529	0.34754	0.060145	6.98E-4	ENSG00000131778	ENST00000431239;ENST00000369259;ENST00000369258;ENST00000361293	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	5.82	4.63	0.57726	Appr-1-p processing (1);	0.600804	0.20767	N	0.086044	T	0.11836	0.0288	N	0.25647	0.755	0.26362	N	0.977023	P;B;B	0.40476	0.718;0.063;0.032	B;B;B	0.35470	0.203;0.055;0.021	T	0.04650	-1.0936	10	0.23302	T	0.38	.	9.3476	0.38118	0.0:0.0:0.1803:0.8197	rs61756300	682;572;776	Q86WJ1-2;Q86WJ1-3;Q86WJ1	.;.;CHD1L_HUMAN	R	682;572;776;495	ENSP00000389031:S682R;ENSP00000358263:S572R;ENSP00000358262:S776R;ENSP00000355100:S495R	ENSP00000355100:S495R	S	+	3	2	CHD1L	145229795	0.305000	0.24481	1.000000	0.80357	0.902000	0.53008	0.451000	0.21779	2.223000	0.72356	0.454000	0.30748	AGT	T|0.984;A|0.016	0.016	strong		0.403	CHD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040377.1	NM_004284		A	146763171	T	A	146763171	3	1	22	1	0	0	0	0	1	0	0	0	3326	1722	60	5	2406	5	CHD1L	1	146763171	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	6079	146763171	102487450	234	3135											
OTUD7B	56957	hgsc.bcm.edu	37	chr1	149916584	149916584	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ttctcagacacaggcccatcCccagctgcctcctccttgcc	6	9	6	20	0	1	1	1	0	1	1	5	1	4	1	7	1	3	1	7	1	0	2	rs200362140	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:149916584C>G	ENST00000369135.4	-	12	1998	c.1704G>C	c.(1702-1704)ggG>ggC	p.G568G		NM_020205.2	NP_064590.2	Q6GQQ9	OTU7B_HUMAN	OTU deubiquitinase 7B	568					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)			CAGGCCCATCCCCAGCTGCCT	0.572													C|||	10	0.00199681	0.0076	0.0	5008	,	,		16047	0.0		0.0	False		,,,				2504	0.0				p.G568G		Atlas-SNP	.											.	OTUD7B	76	.	0			c.G1704C						PASS	.	C		16,4136		0,16,2060	73	82	79		1704	0.7	1	1		79	0,8438		0,0,4219	no	coding-synonymous	OTUD7B	NM_020205.2		0,16,6279	GG,GC,CC		0.0,0.3854,0.1271		568/844	149916584	16,12574	2076	4219	6295	SO:0001819	synonymous_variant	56957	exon12			CCCATCCCCAGCT	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.1704G>C	1.37:g.149916584C>G		63	0	0		70	39	0.557143	NM_020205	B7Z643|D3DUZ8|Q5SZ60|Q8WWA7|Q9NQ53|Q9UFF4	Silent	SNP	ENST00000369135.4	37	CCDS41389.1																																																																																			C|0.999;G|0.001	0.001	strong		0.572	OTUD7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034146.3	NM_020205		G	149916584	C	G	149916584	2	3	22	1	0	0	0	0	0	0	0	1	11328	610	22	4		4	OTUD7B	1	149916584	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3153413	149916584	99334037	235	3136											
TARS2	80222	hgsc.bcm.edu	37	chr1	150470182	150470182	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gattctaccaggcatatcacAgatacactcgccctcaagcc	12	8	6	15	1	3	1	2	0	1	1	4	2	3	1	3	1	3	1	3	1	4	4	rs115388015	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:150470182A>G	ENST00000369064.3	+	10	1231	c.1197A>G	c.(1195-1197)acA>acG	p.T399T	TARS2_ENST00000463555.1_3'UTR|TARS2_ENST00000606933.1_Silent_p.T317T|TARS2_ENST00000438568.2_3'UTR|TARS2_ENST00000369054.2_Silent_p.T269T	NM_025150.3	NP_079426.2	Q9BW92	SYTM_HUMAN	threonyl-tRNA synthetase 2, mitochondrial (putative)	399					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)	GGCATATCACAGATACACTCG	0.512													A|||	83	0.0165735	0.059	0.0072	5008	,	,		16357	0.0		0.0	False		,,,				2504	0.0				p.T399T		Atlas-SNP	.											.	TARS2	91	.	0			c.A1197G						PASS	.	A		210,4196	128.6+/-165.4	9,192,2002	56	49	51		1197	-0.3	0	1	dbSNP_132	51	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	TARS2	NM_025150.3		9,195,6299	GG,GA,AA		0.0349,4.7662,1.6377		399/719	150470182	213,12793	2203	4300	6503	SO:0001819	synonymous_variant	80222	exon10			TATCACAGATACA	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.1197A>G	1.37:g.150470182A>G		67	0	0		60	28	0.466667	NM_025150	Q53GW7|Q96I50|Q9H9V2	Silent	SNP	ENST00000369064.3	37	CCDS952.1																																																																																			A|0.981;G|0.019	0.019	strong		0.512	TARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035847.1	NM_025150		G	150470182	A	G	150470182	2	3	22	1	0	0	0	0	0	0	0	1	15575	175	7	3		3	TARS2	1	150470182	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	553598	150470182	98780439	236	3137											
ECM1	1893	hgsc.bcm.edu	37	chr1	150482639	150482639	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gagctgccctctctccagcaCcccaatgaacagaaggaagg	12	5	10	14	0	1	2	0	1	1	1	3	4	2	3	4	2	4	2	4	2	4	0	rs74352693	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:150482639C>T	ENST00000369047.4	+	5	491	c.366C>T	c.(364-366)caC>caT	p.H122H	ECM1_ENST00000470432.1_3'UTR|ECM1_ENST00000346569.6_Silent_p.H122H|ECM1_ENST00000369049.4_Silent_p.H149H	NM_004425.3	NP_004416.2	Q16610	ECM1_HUMAN	extracellular matrix protein 1	122					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)			CTCTCCAGCACCCCAATGAAC	0.587													C|||	81	0.0161741	0.0575	0.0072	5008	,	,		18178	0.0		0.0	False		,,,				2504	0.0				p.H149H	Melanoma(156;1696 2560 11093 19685)	Atlas-SNP	.											.	ECM1	96	.	0			c.C447T						PASS	.	C	,,	203,4203	126.1+/-163.2	7,189,2007	138	139	139		447,366,366	-1.3	0	1	dbSNP_132	139	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	ECM1	NM_001202858.1,NM_004425.3,NM_022664.2	,,	7,192,6304	TT,TC,CC		0.0349,4.6074,1.5839	,,	149/568,122/541,122/416	150482639	206,12800	2203	4300	6503	SO:0001819	synonymous_variant	1893	exon5			CCAGCACCCCAAT	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.366C>T	1.37:g.150482639C>T		101	0	0		110	51	0.463636	NM_001202858	A8K8S0|B4DW49|B4DY60|O43266|Q5T5G4|Q5T5G5|Q5T5G6|Q8IZ60	Silent	SNP	ENST00000369047.4	37	CCDS953.1																																																																																			C|0.982;T|0.018	0.018	strong		0.587	ECM1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035832.2	NM_004425		T	150482639	C	T	150482639	2	4	22	1	0	0	0	0	0	0	0	1	4899	506	18	2		2	ECM1	1	150482639	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	12457	150482639	98767982	237	3138											
ECM1	1893	hgsc.bcm.edu	37	chr1	150484016	150484016	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgctgcacgcggcagggggaGgctcggttctcctgcttcca	4	9	15	13	3	1	0	0	0	1	0	4	1	2	1	2	5	3	6	2	5	0	2	rs78194273	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:150484016G>A	ENST00000369047.4	+	7	917	c.792G>A	c.(790-792)gaG>gaA	p.E264E	ECM1_ENST00000470432.1_3'UTR|ECM1_ENST00000346569.6_Intron|ECM1_ENST00000369049.4_Silent_p.E291E	NM_004425.3	NP_004416.2	Q16610	ECM1_HUMAN	extracellular matrix protein 1	264	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)			GGCAGGGGGAGGCTCGGTTCT	0.632													G|||	82	0.0163738	0.0582	0.0072	5008	,	,		16846	0.0		0.0	False		,,,				2504	0.0				p.E291E	Melanoma(156;1696 2560 11093 19685)	Atlas-SNP	.											.	ECM1	96	.	0			c.G873A						PASS	.	G	,,	207,4199	127.4+/-164.3	7,193,2003	52	50	51		873,792,	4.5	1	1	dbSNP_132	51	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous,intron	ECM1	NM_001202858.1,NM_004425.3,NM_022664.2	,,	7,196,6300	AA,AG,GG		0.0349,4.6981,1.6146	,,	291/568,264/541,	150484016	210,12796	2203	4300	6503	SO:0001819	synonymous_variant	1893	exon7			GGGGGAGGCTCGG	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.792G>A	1.37:g.150484016G>A		88	0	0		99	54	0.545455	NM_001202858	A8K8S0|B4DW49|B4DY60|O43266|Q5T5G4|Q5T5G5|Q5T5G6|Q8IZ60	Silent	SNP	ENST00000369047.4	37	CCDS953.1																																																																																			G|0.984;A|0.016	0.016	strong		0.632	ECM1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035832.2	NM_004425		A	150484016	G	A	150484016	2	1	22	1	0	0	0	0	0	0	0	1	4899	991	35	2		2	ECM1	1	150484016	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1377	150484016	98766605	238	3139											
PRUNE	58497	hgsc.bcm.edu	37	chr1	150997155	150997155	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccatcgagccgaaacactGccctccctgccatgtttcag	9	8	7	17	2	1	0	1	0	0	0	3	2	2	0	5	0	4	1	5	0	1	1	rs56805474	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:150997155G>A	ENST00000271620.3	+	4	560	c.404G>A	c.(403-405)tGc>tAc	p.C135Y	PRUNE_ENST00000368936.1_5'UTR|PRUNE_ENST00000368935.1_Intron|PRUNE_ENST00000467771.1_3'UTR|RNU6-884P_ENST00000363889.1_RNA|PRUNE_ENST00000368937.1_Intron|PRUNE_ENST00000271619.8_Intron|PRUNE_ENST00000368934.1_5'Flank	NM_021222.1	NP_067045.1	Q86TP1	PRUNE_HUMAN	prune exopolyphosphatase	135						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)			CCGAAACACTGCCCTCCCTGC	0.577											OREG0013792	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	g|||	156	0.0311502	0.1142	0.0043	5008	,	,		17672	0.0		0.002	False		,,,				2504	0.0				p.C135Y		Atlas-SNP	.											.	PRUNE	40	.	0			c.G404A						PASS	.	G	TYR/CYS	427,3979	208.8+/-229.8	19,389,1795	103	89	94		404	3.8	1	1	dbSNP_129	94	2,8598	2.2+/-6.3	0,2,4298	yes	missense	PRUNE	NM_021222.1	194	19,391,6093	AA,AG,GG		0.0233,9.6913,3.2985	possibly-damaging	135/454	150997155	429,12577	2203	4300	6503	SO:0001583	missense	58497	exon4			AACACTGCCCTCC	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.404G>A	1.37:g.150997155G>A	ENSP00000271620:p.Cys135Tyr	106	0	0	1737	100	33	0.33	NM_021222	B2RCH8|B4DFL7|Q5SZF9|Q659E5|Q6P4E0|Q8N654|Q96JU5|Q9C071|Q9C072|Q9UIV0	Missense_Mutation	SNP	ENST00000271620.3	37	CCDS977.1	58	0.026556776556776556	57	0.11585365853658537	1	0.0027624309392265192	0	0.0	0	0.0	g	8.084	0.773045	0.16051	0.096913	2.33E-4	ENSG00000143363	ENST00000271620;ENST00000302413	T	0.30182	1.54	5.76	3.84	0.44239	Phosphoesterase, RecJ-like (1);	0.361754	0.29362	N	0.012374	T	0.09247	0.0228	N	0.22421	0.69	0.80722	D	1	D	0.53151	0.958	P	0.48334	0.574	T	0.06250	-1.0837	10	0.02654	T	1	.	9.1856	0.37168	0.0892:0.1831:0.7278:0.0	rs56805474	135	Q86TP1	PRUNE_HUMAN	Y	135;68	ENSP00000271620:C135Y	ENSP00000271620:C135Y	C	+	2	0	PRUNE	149263779	0.975000	0.34042	0.998000	0.56505	0.961000	0.63080	2.512000	0.45485	1.436000	0.47453	0.645000	0.84053	TGC	G|0.965;A|0.035	0.035	strong		0.577	PRUNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084885.1	NM_021222		A	150997155	G	A	150997155	3	1	22	1	0	0	0	0	1	0	0	0	12652	1319	46	2	418	2	PRUNE	1	150997155	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	513139	150997155	98253466	239	3140											
SEMA6C	10500	hgsc.bcm.edu	37	chr1	151107277	151107277	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aaggacccatcacttacccaCcagatcccctgatatccaca	13	7	4	17	0	1	2	1	1	0	1	3	3	3	3	6	1	1	0	6	1	3	2	rs149398166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:151107277C>T	ENST00000341697.3	-	16	3346	c.1655G>A	c.(1654-1656)gGt>gAt	p.G552D	SEMA6C_ENST00000479820.1_5'Flank			Q9H3T2	SEM6C_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	552					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)			CACTTACCCACCAGATCCCCT	0.527													C|||	19	0.00379393	0.0144	0.0	5008	,	,		19859	0.0		0.0	False		,,,				2504	0.0				p.G552D		Atlas-SNP	.											.	SEMA6C	70	.	0			c.G1655A						PASS	.	C	ASP/GLY,ASP/GLY,ASP/GLY	40,4366	43.8+/-77.6	2,36,2165	134	121	125		1655,1535,1655	3.2	1	1	dbSNP_134	125	0,8600		0,0,4300	yes	missense,missense,missense	SEMA6C	NM_001178061.1,NM_001178062.1,NM_030913.4	94,94,94	2,36,6465	TT,TC,CC		0.0,0.9079,0.3076	possibly-damaging,possibly-damaging,possibly-damaging	552/963,512/923,552/931	151107277	40,12966	2203	4300	6503	SO:0001583	missense	10500	exon16			TACCCACCAGATC	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.1655G>A	1.37:g.151107277C>T	ENSP00000344148:p.Gly552Asp	178	0	0		206	107	0.519417	NM_001178061	D3DV15|Q5JR71|Q5JR72|Q5JR73|Q8WXT8|Q8WXT9|Q8WXU0|Q96JF8	Missense_Mutation	SNP	ENST00000341697.3	37	CCDS984.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	11.28	1.593364	0.28357	0.009079	0.0	ENSG00000143434	ENST00000368914;ENST00000368912;ENST00000368913;ENST00000341697	T;T;T;T	0.46063	0.88;0.88;0.88;0.88	5.25	3.22	0.36961	.	3.389920	0.00550	N	0.000248	T	0.33498	0.0865	L	0.44542	1.39	0.32800	D	0.500067	B;D;B;D	0.54772	0.002;0.96;0.1;0.968	B;P;B;P	0.50934	0.01;0.523;0.257;0.654	T	0.06232	-1.0838	10	0.37606	T	0.19	.	11.5843	0.50910	0.0:0.527:0.473:0.0	.	552;512;552;552	B4DZD4;Q9H3T2-2;Q9H3T2-3;Q9H3T2	.;.;.;SEM6C_HUMAN	D	552;512;552;552	ENSP00000357910:G552D;ENSP00000357908:G512D;ENSP00000357909:G552D;ENSP00000344148:G552D	ENSP00000344148:G552D	G	-	2	0	SEMA6C	149373901	0.981000	0.34729	1.000000	0.80357	0.599000	0.36880	1.049000	0.30392	1.349000	0.45751	0.561000	0.74099	GGT	C|0.995;T|0.005	0.005	strong		0.527	SEMA6C-004	KNOWN	alternative_5_UTR|mRNA_start_NF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034074.1	NM_030913		T	151107277	C	T	151107277	3	4	22	1	0	0	0	0	1	0	0	0	14056	507	18	2	1253	2	SEMA6C	1	151107277	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	110122	151107277	98143344	240	3141											
LYSMD1	388695	hgsc.bcm.edu	37	chr1	151138250	151138250	+	5'UTR	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcagagatcctcaaaggtccGctccgcataagataggtcac	12	8	9	12	2	3	2	3	0	0	2	6	3	6	2	3	2	0	2	3	2	3	2	rs113805704	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:151138250G>T	ENST00000368908.5	-	0	145				SCNM1_ENST00000368905.4_5'Flank|LYSMD1_ENST00000440902.2_Missense_Mutation_p.S3R	NM_212551.4	NP_997716.1	Q96S90	LYSM1_HUMAN	LysM, putative peptidoglycan-binding, domain containing 1											endometrium(2)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7	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)			TCAAAGGTCCGCTCCGCATAA	0.537													G|||	38	0.00758786	0.0287	0.0	5008	,	,		18656	0.0		0.0	False		,,,				2504	0.0				p.S3R		Atlas-SNP	.											.	LYSMD1	23	.	0			c.C9A						PASS	.	G	ARG/SER,,	33,1351		1,31,660	142	137	138		9,,	-8.1	0	1	dbSNP_132	138	1,3181		0,1,1590	yes	missense,intron,utr-5	LYSMD1,TNFAIP8L2-SCNM1	NM_001136543.1,NM_001204848.1,NM_212551.4	110,,	1,32,2250	TT,TG,GG		0.0314,2.3844,0.7446	,,	3/180,,	151138250	34,4532	692	1591	2283	SO:0001623	5_prime_UTR_variant	388695	exon1			AGGTCCGCTCCGC	BX647911	CCDS986.1, CCDS44218.1	1q21.2	2008-02-05			ENSG00000163155	ENSG00000163155			32070	protein-coding gene	gene with protein product						12477932	Standard	NM_212551		Approved	SB145, MGC35223, RP11-68I18.5	uc001ewy.3	Q96S90	OTTHUMG00000012260	ENST00000368908.5:c.-516C>A	1.37:g.151138250G>T		121	0	0		98	52	0.530612	NM_001136543	B4DQA1|Q69YX9	Missense_Mutation	SNP	ENST00000368908.5	37	CCDS986.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	16.76	3.211662	0.58452	0.023844	3.14E-4	ENSG00000163155	ENST00000440902	T	0.32988	1.43	4.06	-8.13	0.01073	.	.	.	.	.	T	0.05090	0.0136	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.27606	-1.0069	8	0.87932	D	0	.	0.7224	0.00943	0.307:0.2957:0.1987:0.1986	.	3	Q96S90-2	.	R	3	ENSP00000404059:S3R	ENSP00000404059:S3R	S	-	3	2	LYSMD1	149404874	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.795000	0.01752	-2.291000	0.00666	0.603000	0.83216	AGC	G|0.994;T|0.006	0.006	strong		0.537	LYSMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034070.3	NM_212551		T	151138250	G	T	151138250	1	4	22	0	1	0	0	0	0	0	0	0	9133	1078	38	4		4	LYSMD1	1	151138250	5'UTR	SNP	G	TCGA-G8-6324-01A-11D-2210-10	30973	151138250	98112371	241	3142											
CGN	57530	hgsc.bcm.edu	37	chr1	151493098	151493098	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttctggttctactaaggcCgtggcagggcagggtgagct	6	11	15	9	1	3	1	0	1	3	0	3	1	3	1	1	5	2	4	1	5	2	4	rs141884525	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:151493098C>T	ENST00000271636.7	+	5	1204	c.1071C>T	c.(1069-1071)gcC>gcT	p.A357A		NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	351	Interacts with ZO-2.				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)			CTACTAAGGCCGTGGCAGGGC	0.557													C|||	28	0.00559105	0.0106	0.0	5008	,	,		19386	0.0129		0.0	False		,,,				2504	0.001				p.A357A		Atlas-SNP	.											.	CGN	106	.	0			c.C1071T						PASS	.	C		31,4375	36.8+/-68.6	0,31,2172	76	68	71		1071	3	0	1	dbSNP_134	71	0,8600		0,0,4300	no	coding-synonymous	CGN	NM_020770.2		0,31,6472	TT,TC,CC		0.0,0.7036,0.2384		357/1204	151493098	31,12975	2203	4300	6503	SO:0001819	synonymous_variant	57530	exon5			TAAGGCCGTGGCA	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.1071C>T	1.37:g.151493098C>T		192	0	0		196	101	0.515306	NM_020770	A6H8L3|A7MD22|Q5T386|Q9NR25	Silent	SNP	ENST00000271636.7	37	CCDS999.1	5	0.0022893772893772895	2	0.0040650406504065045	0	0.0	3	0.005244755244755245	0	0.0	C	1.548	-0.540081	0.04053	0.007036	0.0	ENSG00000143375	ENST00000416743	.	.	.	4.97	3.02	0.34903	.	.	.	.	.	T	0.20495	0.0493	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.18461	-1.0336	4	.	.	.	0.3924	10.9367	0.47249	0.0:0.6821:0.2427:0.0752	.	.	.	.	L	66	.	.	P	+	2	0	CGN	149759722	0.026000	0.19158	0.030000	0.17652	0.001000	0.01503	0.384000	0.20668	0.266000	0.21894	-0.797000	0.03246	CCG	C|0.997;T|0.003	0.003	strong		0.557	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770		T	151493098	C	T	151493098	2	4	22	1	0	0	0	0	0	0	0	1	3305	639	23	1		1	CGN	1	151493098	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	354848	151493098	97757523	242	3143											
CGN	57530	hgsc.bcm.edu	37	chr1	151496718	151496718	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttaggctccagaacatgaagCgcctcttggaccagggtgaa	11	8	12	10	1	1	3	0	2	1	1	2	4	2	4	3	3	2	1	3	3	4	2	rs16833336	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:151496718C>T	ENST00000271636.7	+	7	1418	c.1285C>T	c.(1285-1287)Cgc>Tgc	p.R429C		NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	423	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)			GAACATGAAGCGCCTCTTGGA	0.433													C|||	189	0.0377396	0.1377	0.0058	5008	,	,		20806	0.0		0.003	False		,,,				2504	0.0				p.R429C		Atlas-SNP	.											CGN,colon,carcinoma,-1,2	CGN	106	2	0			c.C1285T						PASS	.	C	CYS/ARG	482,3924	225.6+/-241.4	29,424,1750	72	67	69		1285	4	1	1	dbSNP_123	69	6,8594	4.3+/-15.6	0,6,4294	yes	missense	CGN	NM_020770.2	180	29,430,6044	TT,TC,CC		0.0698,10.9396,3.7521	benign	429/1204	151496718	488,12518	2203	4300	6503	SO:0001583	missense	57530	exon7			ATGAAGCGCCTCT	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.1285C>T	1.37:g.151496718C>T	ENSP00000271636:p.Arg429Cys	67	0	0		85	34	0.4	NM_020770	A6H8L3|A7MD22|Q5T386|Q9NR25	Missense_Mutation	SNP	ENST00000271636.7	37	CCDS999.1	79	0.036172161172161175	77	0.1565040650406504	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	15.65	2.896561	0.52121	0.109396	6.98E-4	ENSG00000143375	ENST00000271636	T	0.63417	-0.04	4.95	4.02	0.46733	.	0.429980	0.25004	N	0.033881	T	0.19248	0.0462	N	0.08118	0	0.26850	N	0.96819	P	0.46327	0.876	B	0.34452	0.183	T	0.04781	-1.0927	10	0.72032	D	0.01	0.3796	10.5107	0.44860	0.1942:0.8058:0.0:0.0	rs16833336;rs16833336	423	Q9P2M7	CING_HUMAN	C	429	ENSP00000271636:R429C	ENSP00000271636:R429C	R	+	1	0	CGN	149763342	0.706000	0.27856	0.997000	0.53966	0.893000	0.52053	0.899000	0.28417	1.041000	0.40125	0.491000	0.48974	CGC	C|0.961;T|0.039	0.039	strong		0.433	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770		T	151496718	C	T	151496718	3	4	22	1	0	0	0	0	1	0	0	0	3305	768	27	1	1307	1	CGN	1	151496718	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3620	151496718	97753903	243	3144											
SNX27	81609	hgsc.bcm.edu	37	chr1	151638486	151638486	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagtgatcagtcactccttTggtaagtaccagtggctgat	10	12	11	8	0	2	2	2	2	0	0	3	3	3	2	2	2	1	3	2	2	3	3	rs150091333	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:151638486T>C	ENST00000458013.2	+	6	1104	c.984T>C	c.(982-984)ttT>ttC	p.F328F	SNX27_ENST00000368838.1_Splice_Site_p.F235F|SNX27_ENST00000482791.1_3'UTR|SNX27_ENST00000368843.3_Splice_Site_p.F328F			Q96L92	SNX27_HUMAN	sorting nexin family member 27	328	FERM-like region F1.|Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				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)			GTCACTCCTTTGGTAAGTACC	0.403													T|||	19	0.00379393	0.0144	0.0	5008	,	,		21524	0.0		0.0	False		,,,				2504	0.0				p.F328F	Colon(46;291 966 40145 41237 41888)	Atlas-SNP	.											.	SNX27	44	.	0			c.T984C						PASS	.	T		62,4344	58.1+/-94.6	0,62,2141	169	146	154		984	3.9	1	1	dbSNP_134	154	6,8594	5.0+/-18.6	0,6,4294	yes	coding-synonymous-near-splice	SNX27	NM_030918.5		0,68,6435	CC,CT,TT		0.0698,1.4072,0.5228		328/529	151638486	68,12938	2203	4300	6503	SO:0001630	splice_region_variant	81609	exon6			CTCCTTTGGTAAG	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.985+1T>C	1.37:g.151638486T>C		95	0	0		110	50	0.454545	NM_030918	Q32Q36|Q4AEJ5|Q5VWB0|Q5VWB1|Q5VWB2|Q6IPP6|Q86UB1|Q96D79|Q9H3K8	Silent	SNP	ENST00000458013.2	37																																																																																				T|0.994;C|0.006	0.006	strong		0.403	SNX27-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000036624.3	NM_030918	Silent	C	151638486	T	C	151638486	5	2	22	1	0	0	0	0	0	0	1	0	14912	1826	63	3	1006	3	SNX27	1	151638486	Splice_Site	SNP	T	TCGA-G8-6324-01A-11D-2210-10	141768	151638486	97612135	244	3145											
TCHHL1	126637	hgsc.bcm.edu	37	chr1	152060495	152060495	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	agctcacctgaaaaaagtccCcaaactcgccctggatgagt	13	7	8	13	1	1	2	1	2	0	0	3	3	2	3	4	1	2	1	4	1	4	0	rs76137589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152060495C>T	ENST00000368806.1	-	2	189	c.125G>A	c.(124-126)gGg>gAg	p.G42E		NM_001008536.1	NP_001008536.1	Q5QJ38	TCHL1_HUMAN	trichohyalin-like 1	42							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)			AAAAAAGTCCCCAAACTCGCC	0.458													c|||	59	0.0117812	0.0431	0.0029	5008	,	,		19439	0.0		0.0	False		,,,				2504	0.0				p.G42E		Atlas-SNP	.											.	TCHHL1	132	.	0			c.G125A						PASS	.	C	GLU/GLY	196,4210		8,180,2015	183	181	182		125	-0.3	0.9	1	dbSNP_131	182	0,8600		0,0,4300	yes	missense	TCHHL1	NM_001008536.1	98	8,180,6315	TT,TC,CC		0.0,4.4485,1.507	possibly-damaging	42/905	152060495	196,12810	2203	4300	6503	SO:0001583	missense	126637	exon2			AAGTCCCCAAACT		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.125G>A	1.37:g.152060495C>T	ENSP00000357796:p.Gly42Glu	127	0	0		120	51	0.425	NM_001008536	B2RPK8|Q5VTJ9	Missense_Mutation	SNP	ENST00000368806.1	37	CCDS30857.1	21	0.009615384615384616	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	0	0.0	.	11.72	1.721614	0.30503	0.044485	0.0	ENSG00000182898	ENST00000368806	T	0.10573	2.86	6.0	-0.34	0.12643	S100/CaBP-9k-type, calcium binding, subdomain (1);EF-hand-like domain (1);	0.624434	0.13321	N	0.396729	T	0.05593	0.0147	L	0.58969	1.84	0.29774	N	0.834538	D	0.56746	0.977	P	0.51324	0.666	T	0.28004	-1.0057	10	0.20519	T	0.43	-1.2812	5.8572	0.18727	0.0:0.5081:0.1244:0.3675	.	42	Q5QJ38	TCHL1_HUMAN	E	42	ENSP00000357796:G42E	ENSP00000357796:G42E	G	-	2	0	TCHHL1	150327119	0.666000	0.27475	0.918000	0.36340	0.264000	0.26372	-0.095000	0.11077	-0.059000	0.13154	-0.136000	0.14681	GGG	C|0.985;T|0.015	0.015	strong		0.458	TCHHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036638.2	XM_060104		T	152060495	C	T	152060495	3	4	22	1	0	0	0	0	1	0	0	0	15716	623	22	2	2597	2	TCHHL1	1	152060495	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	422009	152060495	97190126	245	3146											
HRNR	388697	hgsc.bcm.edu	37	chr1	152191052	152191052	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	catagctggaagactgcccgGaaccagacccatgtcggcca	11	5	11	14	2	0	2	0	0	0	2	1	4	0	4	4	3	3	1	4	3	3	1	rs115232928	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152191052G>T	ENST00000368801.2	-	3	3128	c.3053C>A	c.(3052-3054)tCc>tAc	p.S1018Y	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1018					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)			AGACTGCCCGGAACCAGACCC	0.607													G|||	95	0.0189696	0.0696	0.0043	5008	,	,		21165	0.0		0.0	False		,,,				2504	0.0				p.S1018Y		Atlas-SNP	.											.	HRNR	403	.	0			c.C3053A						PASS	.	G	TYR/SER	190,4216	121.3+/-158.8	4,182,2017	135	149	145		3053	-0.1	0	1	dbSNP_132	145	0,8600		0,0,4300	no	missense	HRNR	NM_001009931.1	144	4,182,6317	TT,TG,GG		0.0,4.3123,1.4609	probably-damaging	1018/2851	152191052	190,12816	2203	4300	6503	SO:0001583	missense	388697	exon3			TGCCCGGAACCAG	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.3053C>A	1.37:g.152191052G>T	ENSP00000357791:p.Ser1018Tyr	224	0	0		264	122	0.462121	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	25	0.011446886446886446	22	0.044715447154471545	3	0.008287292817679558	0	0.0	0	0.0	G	4.651	0.121012	0.08881	0.043123	0.0	ENSG00000197915	ENST00000368801	T	0.02472	4.28	3.24	-0.0513	0.13827	.	.	.	.	.	T	0.01695	0.0054	L	0.29908	0.895	0.09310	N	1	D	0.69078	0.997	D	0.65987	0.94	T	0.44832	-0.9302	9	0.28530	T	0.3	.	3.0366	0.06124	0.2539:0.0:0.536:0.21	.	1018	Q86YZ3	HORN_HUMAN	Y	1018	ENSP00000357791:S1018Y	ENSP00000357791:S1018Y	S	-	2	0	HRNR	150457676	0.008000	0.16893	0.000000	0.03702	0.002000	0.02628	0.817000	0.27281	-0.110000	0.12022	0.558000	0.71614	TCC	G|0.985;T|0.015	0.015	strong		0.607	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		T	152191052	G	T	152191052	3	4	22	1	0	0	0	0	1	0	0	0	7368	1174	41	4	5503	4	HRNR	1	152191052	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	130557	152191052	97059569	246	3147											
HRNR	388697	hgsc.bcm.edu	37	chr1	152191116	152191116	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agatccagacccatgttggcCgtggcccaaagactgacggg	10	6	13	12	2	0	4	0	1	0	3	1	4	1	4	4	3	0	1	4	3	1	1	rs138107632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152191116C>T	ENST00000368801.2	-	3	3064	c.2989G>A	c.(2989-2991)Ggc>Agc	p.G997S	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	997					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)			CCATGTTGGCCGTGGCCCAAA	0.582													C|||	96	0.0191693	0.0696	0.0043	5008	,	,		24162	0.001		0.0	False		,,,				2504	0.0				p.G997S		Atlas-SNP	.											.	HRNR	403	.	0			c.G2989A						PASS	.	C	SER/GLY	190,4216	121.3+/-158.8	4,182,2017	136	140	139		2989	-1.5	0	1	dbSNP_134	139	0,8594		0,0,4297	no	missense	HRNR	NM_001009931.1	56	4,182,6314	TT,TC,CC		0.0,4.3123,1.4615	probably-damaging	997/2851	152191116	190,12810	2203	4297	6500	SO:0001583	missense	388697	exon3			GTTGGCCGTGGCC	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.2989G>A	1.37:g.152191116C>T	ENSP00000357791:p.Gly997Ser	221	1	0.00452489		266	124	0.466165	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	26	0.011904761904761904	22	0.044715447154471545	3	0.008287292817679558	1	0.0017482517482517483	0	0.0	C	9.275	1.046626	0.19748	0.043123	0.0	ENSG00000197915	ENST00000368801	T	0.01705	4.68	3.65	-1.49	0.08718	.	.	.	.	.	T	0.00271	0.0008	N	0.04297	-0.235	0.09310	N	1	D	0.57899	0.981	B	0.37943	0.261	T	0.37934	-0.9684	9	0.12430	T	0.62	.	7.1807	0.25770	0.0:0.4928:0.0:0.5072	.	997	Q86YZ3	HORN_HUMAN	S	997	ENSP00000357791:G997S	ENSP00000357791:G997S	G	-	1	0	HRNR	150457740	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.954000	0.03873	-0.422000	0.07405	0.556000	0.70494	GGC	C|0.985;T|0.015	0.015	strong		0.582	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		T	152191116	C	T	152191116	3	4	22	1	0	0	0	0	1	0	0	0	7368	652	23	1	5567	1	HRNR	1	152191116	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	64	152191116	97059505	247	3148											
HRNR	388697	hgsc.bcm.edu	37	chr1	152193049	152193049	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggactgtcctgagccagaCtcatgttgcccaaagccaga	11	7	11	12	0	1	3	1	1	0	2	2	5	2	4	4	1	3	1	4	1	1	1	rs114845154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152193049C>T	ENST00000368801.2	-	3	1131	c.1056G>A	c.(1054-1056)gaG>gaA	p.E352E	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	352					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)			CTGAGCCAGACTCATGTTGCC	0.557													C|||	95	0.0189696	0.0696	0.0043	5008	,	,		22156	0.0		0.0	False		,,,				2504	0.0				p.E352E		Atlas-SNP	.											HRNR,NS,carcinoma,-2,1	HRNR	403	1	0			c.G1056A						PASS	.	C		188,4218	120.8+/-158.4	2,184,2017	118	121	120		1056	-8.3	0	1	dbSNP_132	120	0,8600		0,0,4300	no	coding-synonymous	HRNR	NM_001009931.1		2,184,6317	TT,TC,CC		0.0,4.2669,1.4455		352/2851	152193049	188,12818	2203	4300	6503	SO:0001819	synonymous_variant	388697	exon3			GCCAGACTCATGT	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.1056G>A	1.37:g.152193049C>T		114	0	0		123	54	0.439024	NM_001009931	Q5DT20|Q5U1F4	Silent	SNP	ENST00000368801.2	37	CCDS30859.1																																																																																			C|0.985;T|0.015	0.015	strong		0.557	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868		T	152193049	C	T	152193049	2	4	22	1	0	0	0	0	0	0	0	1	7368	564	20	2		2	HRNR	1	152193049	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1933	152193049	97057572	248	3149											
FLG	2312	hgsc.bcm.edu	37	chr1	152275559	152275559	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgatacgcagaatcttgtgAaagactactaaagtgaccat	15	10	9	7	1	1	5	0	3	1	2	1	5	1	5	1	0	2	1	1	0	6	4	rs3126065	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152275559A>G	ENST00000368799.1	-	3	11838	c.11803T>C	c.(11803-11805)Tca>Cca	p.S3935P	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3935	Ser-rich.		S -> P (in dbSNP:rs3126065).		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)			GAATCTTGTGAAAGACTACTA	0.468									Ichthyosis				A|||	548	0.109425	0.3979	0.0303	5008	,	,		22781	0.0		0.001	False		,,,				2504	0.0				p.S3935P		Atlas-SNP	.											.	FLG	900	.	0			c.T11803C						PASS	.	A	PRO/SER	1446,2960	468.3+/-355.1	228,990,985	138	133	135		11803	-0.9	0	1	dbSNP_103	135	14,8586	9.8+/-36.6	0,14,4286	yes	missense	FLG	NM_002016.1	74	228,1004,5271	GG,GA,AA		0.1628,32.8189,11.2256	probably-damaging	3935/4062	152275559	1460,11546	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTTGTGAAAGACT	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.11803T>C	1.37:g.152275559A>G	ENSP00000357789:p.Ser3935Pro	177	1	0.00564972		178	178	1	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	185	0.08470695970695971	174	0.35365853658536583	11	0.03038674033149171	0	0.0	0	0.0	A	4.914	0.169897	0.09339	0.328189	0.001628	ENSG00000143631	ENST00000368799	T	0.03772	3.81	2.35	-0.929	0.10444	.	.	.	.	.	T	0.01661	0.0053	L	0.52573	1.65	0.80722	P	0.0	D	0.53885	0.963	B	0.44108	0.441	T	0.39461	-0.9613	8	0.46703	T	0.11	.	1.6209	0.02713	0.4417:0.0:0.2748:0.2835	rs3126065;rs3126065	3935	P20930	FILA_HUMAN	P	3935	ENSP00000357789:S3935P	ENSP00000357789:S3935P	S	-	1	0	FLG	150542183	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.627000	0.05521	-0.321000	0.08627	0.533000	0.62120	TCA	A|0.871;G|0.129	0.129	strong		0.468	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		G	152275559	A	G	152275559	3	3	22	1	0	0	0	0	1	0	0	0	5930	246	9	3	386	3	FLG	1	152275559	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	82510	152275559	96975062	249	3150			1	24		12	12	9983	N	T_G_C_A	3.860175e-07
FLG	2312	hgsc.bcm.edu	37	chr1	152276474	152276474	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgtctgctgactgctggtGgtgggatccatgtctctctc	3	14	13	11	0	3	1	0	1	3	0	6	2	4	2	1	3	2	3	1	3	0	0	rs76019722		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152276474G>A	ENST00000368799.1	-	3	10923	c.10888C>T	c.(10888-10890)Cac>Tac	p.H3630Y	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3630	Ser-rich.		H -> Y (in dbSNP:rs9436065).		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)			GACTGCTGGTGGTGGGATCCA	0.542									Ichthyosis																												p.H3630Y		Atlas-SNP	.											.	FLG	900	.	0			c.C10888T						PASS	.	G	TYR/HIS	1203,3199		0,1203,998	203	163	176		10888	2.2	0	1	dbSNP_131	176	14,8576		0,14,4281	no	missense	FLG	NM_002016.1	83	0,1217,5279	AA,AG,GG		0.163,27.3285,9.3673	probably-damaging	3630/4062	152276474	1217,11775	2201	4295	6496	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GCTGGTGGTGGGA	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.10888C>T	1.37:g.152276474G>A	ENSP00000357789:p.His3630Tyr	367	0	0		572	364	0.636364	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	157	0.07188644688644688	146	0.2967479674796748	11	0.03038674033149171	0	0.0	0	0.0	G	9.840	1.190882	0.21954	0.273285	0.00163	ENSG00000143631	ENST00000368799	T	0.01665	4.7	4.11	2.18	0.27775	.	.	.	.	.	T	0.01627	0.0052	M	0.63428	1.95	0.09310	N	1	D	0.67145	0.996	D	0.75020	0.985	T	0.24728	-1.0152	9	0.02654	T	1	.	6.2399	0.20785	0.2304:0.0:0.7696:0.0	rs9436065;rs52822444;rs9436065	3630	P20930	FILA_HUMAN	Y	3630	ENSP00000357789:H3630Y	ENSP00000357789:H3630Y	H	-	1	0	FLG	150543098	0.000000	0.05858	0.001000	0.08648	0.027000	0.11550	0.464000	0.21988	1.051000	0.40369	0.502000	0.49764	CAC	G|0.997;A|0.003	0.003	weak		0.542	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152276474	G	A	152276474	3	1	22	1	0	0	0	0	1	0	0	0	5930	1348	47	2	1301	2	FLG	1	152276474	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	915	152276474	96974147	250	3151			1	24		12	12	9983	N	T_G_C_A	3.860175e-07
FLG	2312	hgsc.bcm.edu	37	chr1	152276603	152276603	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctgcagagtgcccgtgacCggctctgtcttcgtgatggg	4	11	14	12	3	3	3	0	2	3	1	4	3	3	3	2	2	2	2	2	2	0	1	rs111939167		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152276603C>T	ENST00000368799.1	-	3	10794	c.10759G>A	c.(10759-10761)Ggt>Agt	p.G3587S	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3587	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)			TGCCCGTGACCGGCTCTGTCT	0.562									Ichthyosis																												p.G3587S		Atlas-SNP	.											FLG,NS,carcinoma,0,1	FLG	900	1	0			c.G10759A						PASS	.						176	237	216					1																	152276603		2200	4294	6494	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CGTGACCGGCTCT	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.10759G>A	1.37:g.152276603C>T	ENSP00000357789:p.Gly3587Ser	609	0	0		581	297	0.511188	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	3.513	-0.099425	0.07010	.	.	ENSG00000143631	ENST00000368799	T	0.00902	5.56	3.24	-6.48	0.01896	.	.	.	.	.	T	0.00144	0.0004	N	0.25890	0.77	0.09310	N	1	P	0.47106	0.89	B	0.41646	0.362	T	0.48790	-0.9004	9	0.05436	T	0.98	.	1.8762	0.03219	0.2398:0.387:0.2291:0.1442	.	3587	P20930	FILA_HUMAN	S	3587	ENSP00000357789:G3587S	ENSP00000357789:G3587S	G	-	1	0	FLG	150543227	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.237000	0.00545	-3.276000	0.00198	-0.507000	0.04495	GGT	T|1.000;|0.000	1.000	weak		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152276603	C	T	152276603	3	4	22	1	0	0	0	0	1	0	0	0	5930	652	23	1	1430	1	FLG	1	152276603	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	129	152276603	96974018	251	3152			1	24		12	12	9983	N	T_G_C_A	3.860175e-07
FLG	2312	hgsc.bcm.edu	37	chr1	152277239	152277239	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccagaccttccccctgaccGgtcacgtgcggactcttggt	5	10	10	16	3	2	2	1	1	1	1	4	3	4	3	5	3	1	0	5	3	0	2	rs111486002	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152277239G>A	ENST00000368799.1	-	3	10158	c.10123C>T	c.(10123-10125)Cgg>Tgg	p.R3375W	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3375	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)			CCCCCTGACCGGTCACGTGCG	0.587									Ichthyosis				G|||	106	0.0211661	0.0756	0.0072	5008	,	,		19341	0.001		0.0	False		,,,				2504	0.0				p.R3375W		Atlas-SNP	.											.	FLG	900	.	0			c.C10123T						PASS	.	G	TRP/ARG	153,4253	93.4+/-132.2	4,145,2054	286	306	299		10123	1.8	0	1	dbSNP_132	299	2,8598	2.2+/-6.3	0,2,4298	no	missense	FLG	NM_002016.1	101	4,147,6352	AA,AG,GG		0.0233,3.4725,1.1918	probably-damaging	3375/4062	152277239	155,12851	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTGACCGGTCACG	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.10123C>T	1.37:g.152277239G>A	ENSP00000357789:p.Arg3375Trp	443	1	0.00225734		385	185	0.480519	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	23	0.010531135531135532	21	0.042682926829268296	2	0.0055248618784530384	0	0.0	0	0.0	G	9.323	1.058443	0.19987	0.034725	2.33E-4	ENSG00000143631	ENST00000368799;ENST00000368796	T	0.00966	5.49	1.82	1.82	0.25136	.	.	.	.	.	T	0.01454	0.0047	M	0.63428	1.95	0.09310	N	1	D	0.89917	1.0	D	0.71414	0.973	T	0.51529	-0.8694	9	0.72032	D	0.01	.	7.1799	0.25765	0.0:0.0:1.0:0.0	.	3375	P20930	FILA_HUMAN	W	3375;313	ENSP00000357789:R3375W	ENSP00000357786:R313W	R	-	1	2	FLG	150543863	.	.	0.001000	0.08648	0.001000	0.01503	.	.	1.327000	0.45338	0.454000	0.30748	CGG	G|0.986;A|0.014	0.014	strong		0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152277239	G	A	152277239	3	1	22	1	0	0	0	0	1	0	0	0	5930	1115	39	1	2066	1	FLG	1	152277239	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	636	152277239	96973382	252	3153			1	24		12	12	9983	N	T_G_C_A	3.860175e-07
FLG	2312	hgsc.bcm.edu	37	chr1	152281136	152281136	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcccctgactggccacgtgCggactctttgtggctctgct	3	13	11	14	2	2	1	0	1	2	0	3	2	3	2	3	3	2	2	3	3	0	2	rs78125326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152281136C>T	ENST00000368799.1	-	3	6261	c.6226G>A	c.(6226-6228)Gca>Aca	p.A2076T	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2076	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)			TGGCCACGTGCGGACTCTTTG	0.567									Ichthyosis				-|||	353	0.0704872	0.2496	0.0245	5008	,	,		29453	0.003		0.003	False		,,,				2504	0.0				p.A2076T		Atlas-SNP	.											.	FLG	900	.	0			c.G6226A						PASS	.	C	THR/ALA	898,3508		0,898,1305	315	259	278		6226	-4.7	0	1	dbSNP_131	278	11,8589		0,11,4289	no	missense	FLG	NM_002016.1	58	0,909,5594	TT,TC,CC		0.1279,20.3813,6.9891	benign	2076/4062	152281136	909,12097	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CACGTGCGGACTC	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.6226G>A	1.37:g.152281136C>T	ENSP00000357789:p.Ala2076Thr	482	0	0		915	460	0.502732	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	125	0.05723443223443223	114	0.23170731707317074	9	0.024861878453038673	1	0.0017482517482517483	1	0.0013192612137203166	c	4.927	0.172270	0.09391	0.203813	0.001279	ENSG00000143631	ENST00000368799	T	0.01705	4.68	2.33	-4.66	0.03329	.	.	.	.	.	T	0.00241	0.0007	N	0.11064	0.09	0.09310	N	1	B	0.14438	0.01	B	0.12156	0.007	T	0.44360	-0.9333	9	0.13108	T	0.6	.	1.7607	0.02992	0.1438:0.1924:0.1433:0.5205	.	2076	P20930	FILA_HUMAN	T	2076	ENSP00000357789:A2076T	ENSP00000357789:A2076T	A	-	1	0	FLG	150547760	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.201000	0.01236	-2.043000	0.00913	-0.330000	0.08379	GCA	C|0.942;T|0.058	0.058	strong		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152281136	C	T	152281136	3	4	22	1	0	0	0	0	1	0	0	0	5930	768	27	1	5963	1	FLG	1	152281136	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3897	152281136	96969485	253	3154			1	24		12	12	9983	N	T_G_C_A	3.860175e-07
FLG	2312	hgsc.bcm.edu	37	chr1	152282899	152282899	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	accccgggtgtccacgaatgGtgtcctgaccgtcttgggat	6	10	13	12	3	1	1	0	1	1	0	3	3	3	2	5	3	0	0	5	3	1	1	rs3120648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152282899G>T	ENST00000368799.1	-	3	4498	c.4463C>A	c.(4462-4464)aCc>aAc	p.T1488N	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1488	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)			TCCACGAATGGTGTCCTGACC	0.582									Ichthyosis				G|||	402	0.0802716	0.2905	0.0245	5008	,	,		21397	0.0		0.001	False		,,,				2504	0.0				p.T1488N		Atlas-SNP	.											.	FLG	900	.	0			c.C4463A						PASS	.	G	ASN/THR	1035,3371	381.1+/-324.0	111,813,1279	386	372	377		4463	-2.2	0	1	dbSNP_103	377	10,8590	7.7+/-29.5	0,10,4290	no	missense	FLG	NM_002016.1	65	111,823,5569	TT,TG,GG		0.1163,23.4907,8.0348	benign	1488/4062	152282899	1045,11961	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CGAATGGTGTCCT	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.4463C>A	1.37:g.152282899G>T	ENSP00000357789:p.Thr1488Asn	461	0	0		424	423	0.997642	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	141	0.06456043956043957	132	0.2682926829268293	9	0.024861878453038673	0	0.0	0	0.0	G	9.042	0.989984	0.18966	0.234907	0.001163	ENSG00000143631	ENST00000368799	T	0.01725	4.67	3.12	-2.23	0.06930	.	.	.	.	.	T	0.00666	0.0022	M	0.78223	2.4	0.80722	P	0.0	B	0.20052	0.041	B	0.13407	0.009	T	0.46679	-0.9174	8	0.13470	T	0.59	.	2.2485	0.04037	0.1236:0.3919:0.3103:0.1742	rs3120648;rs58109062	1488	P20930	FILA_HUMAN	N	1488	ENSP00000357789:T1488N	ENSP00000357789:T1488N	T	-	2	0	FLG	150549523	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.592000	0.05747	-0.155000	0.11098	-0.321000	0.08615	ACC	G|0.915;T|0.085	0.085	strong		0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152282899	G	T	152282899	3	4	22	1	0	0	0	0	1	0	0	0	5930	1261	44	4	7726	4	FLG	1	152282899	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1763	152282899	96967722	254	3155			1	24		12	12	9983	N	T_G_C_A	3.860175e-07
FLG	2312	hgsc.bcm.edu	37	chr1	152283367	152283367	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagaggaagactctgtgtgaTgagtgcctgattgtctggag	9	11	16	5	0	2	5	0	3	2	2	2	8	2	7	1	2	1	0	1	2	1	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152283367T>C	ENST00000368799.1	-	3	4030	c.3995A>G	c.(3994-3996)cAt>cGt	p.H1332R	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	1332	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)			CTCTGTGTGATGAGTGCCTGA	0.552									Ichthyosis																												p.H1332R		Atlas-SNP	.											.	FLG	900	.	0			c.A3995G						PASS	.						304	292	296					1																	152283367		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GTGTGATGAGTGC	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.3995A>G	1.37:g.152283367T>C	ENSP00000357789:p.His1332Arg	509	0	0		622	48	0.0771704	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	2.821	-0.244841	0.05906	.	.	ENSG00000143631	ENST00000368799	T	0.03951	3.75	2.24	-3.75	0.04372	.	.	.	.	.	T	0.00580	0.0019	N	0.05383	-0.06	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45673	-0.9245	9	0.11182	T	0.66	.	8.4062	0.32616	0.0:0.3846:0.0:0.6154	.	1332	P20930	FILA_HUMAN	R	1332	ENSP00000357789:H1332R	ENSP00000357789:H1332R	H	-	2	0	FLG	150549991	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-3.669000	0.00398	-1.560000	0.01686	-1.470000	0.01010	CAT	.	.	none		0.552	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		C	152283367	T	C	152283367	3	2	22	1	0	0	0	0	1	0	0	0	5930	1464	51	3	8194	3	FLG	1	152283367	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	468	152283367	96967254	255	3156			1	24		12	12	9983	N	T_G_C_A	3.860175e-07
FLG	2312	hgsc.bcm.edu	37	chr1	152284382	152284382	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctgcagagtgcccgtgacCggctctgtcttcgtgatggg	4	11	15	11	3	3	3	0	2	3	1	4	3	3	3	2	2	2	2	2	2	0	1	rs149595328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152284382C>T	ENST00000368799.1	-	3	3015	c.2980G>A	c.(2980-2982)Ggt>Agt	p.G994S	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	994	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.G994C(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)			TGCCCGTGACCGGCTCTGTCT	0.577									Ichthyosis				T|||	23	0.00459265	0.0166	0.0014	5008	,	,		20620	0.0		0.0	False		,,,				2504	0.0				p.G994S		Atlas-SNP	.											FLG,NS,carcinoma,+1,2	FLG	900	2	1	Substitution - Missense(1)	lung(1)	c.G2980A						PASS	.	C	SER/GLY	62,4344	820.7+/-416.4	0,62,2141	242	245	244		2980	-0.6	0	1	dbSNP_134	244	0,8600		0,0,4300	no	missense	FLG	NM_002016.1	56	0,62,6441	TT,TC,CC		0.0,1.4072,0.4767	benign	994/4062	152284382	62,12944	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CGTGACCGGCTCT	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.2980G>A	1.37:g.152284382C>T	ENSP00000357789:p.Gly994Ser	581	0	0		674	50	0.074184	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	t	7.940	0.742605	0.15642	0.014072	0.0	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.00649	5.98	2.34	-0.615	0.11587	.	.	.	.	.	T	0.00144	0.0004	L	0.32530	0.975	0.09310	N	1	B	0.29232	0.238	B	0.12156	0.007	T	0.28713	-1.0035	9	0.06625	T	0.88	.	5.25	0.15517	0.0:0.5849:0.0:0.4151	.	994	P20930	FILA_HUMAN	S	994;201	ENSP00000357789:G994S	ENSP00000357789:G994S	G	-	1	0	FLG	150551006	0.000000	0.05858	0.001000	0.08648	0.126000	0.20510	-0.003000	0.12901	0.047000	0.15862	0.291000	0.19559	GGT	C|0.995;T|0.005	0.005	strong		0.577	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152284382	C	T	152284382	3	4	22	1	0	0	0	0	1	0	0	0	5930	652	23	1	9209	1	FLG	1	152284382	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1015	152284382	96966239	256	3157			1	24		12	12	9983	N	T_G_C_A	3.860175e-07
FLG	2312	hgsc.bcm.edu	37	chr1	152284457	152284457	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgagcagatccacgatggtTtctggaagcagacccagacc	11	7	11	12	1	1	4	0	1	1	3	2	6	2	5	3	2	2	3	3	2	1	1	rs376429887|rs3120652	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152284457T>A	ENST00000368799.1	-	3	2940	c.2905A>T	c.(2905-2907)Aac>Tac	p.N969Y	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	969	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)			CCACGATGGTTTCTGGAAGCA	0.582									Ichthyosis				T|||	297	0.0593051	0.2141	0.0187	5008	,	,		21442	0.0		0.001	False		,,,				2504	0.0				p.N969Y		Atlas-SNP	.											.	FLG	900	.	0			c.A2905T						PASS	.	T	TYR/ASN	721,3685	260.4+/-263.7	46,629,1528	236	238	237		2905	-6	0	1	dbSNP_103	237	9,8591	7.1+/-27.0	0,9,4291	no	missense	FLG	NM_002016.1	143	46,638,5819	AA,AT,TT		0.1047,16.364,5.6128	possibly-damaging	969/4062	152284457	730,12276	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GATGGTTTCTGGA	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.2905A>T	1.37:g.152284457T>A	ENSP00000357789:p.Asn969Tyr	446	0	0		538	214	0.39777	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	83	0.038003663003663	78	0.15853658536585366	5	0.013812154696132596	0	0.0	0	0.0	t	2.680	-0.275489	0.05679	0.16364	0.001047	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.01647	4.71	3.01	-6.01	0.02199	.	.	.	.	.	T	0.00724	0.0024	M	0.68317	2.08	0.80722	P	0.0	P	0.39831	0.69	B	0.34093	0.175	T	0.03433	-1.1037	8	0.59425	D	0.04	.	8.703	0.34338	0.0:0.0998:0.6558:0.2444	.	969	P20930	FILA_HUMAN	Y	969;176	ENSP00000357789:N969Y	ENSP00000357789:N969Y	N	-	1	0	FLG	150551081	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-1.749000	0.01824	-1.940000	0.01043	-0.641000	0.03968	AAC	T|0.942;A|0.058	0.058	strong		0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152284457	T	A	152284457	3	1	22	1	0	0	0	0	1	0	0	0	5930	1841	64	5	9284	5	FLG	1	152284457	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	75	152284457	96966164	257	3158			1	24		12	12	9983	N	T_G_C_A	3.860175e-07
FLG	2312	hgsc.bcm.edu	37	chr1	152284576	152284576	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	acccctctgattgtccctggCctgcctgtgagtgtctagag	5	12	11	13	0	2	3	0	2	2	1	3	3	3	3	5	1	1	0	5	1	1	2	rs143382793	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152284576C>A	ENST00000368799.1	-	3	2821	c.2786G>T	c.(2785-2787)gGc>gTc	p.G929V	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	929	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)			TTGTCCCTGGCCTGCCTGTGA	0.557									Ichthyosis																												p.G929V		Atlas-SNP	.											.	FLG	900	.	0			c.G2786T						PASS	.						327	313	318					1																	152284576		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CCCTGGCCTGCCT	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.2786G>T	1.37:g.152284576C>A	ENSP00000357789:p.Gly929Val	591	1	0.00169205		745	145	0.194631	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	-	1.719	-0.497190	0.04291	.	.	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.06528	3.29	1.17	0.0422	0.14216	.	.	.	.	.	T	0.06142	0.0159	M	0.77820	2.39	0.09310	N	1	D	0.67145	0.996	P	0.58970	0.849	T	0.24977	-1.0145	9	0.21014	T	0.42	.	4.8967	0.13753	0.0:0.6064:0.3936:0.0	.	929	P20930	FILA_HUMAN	V	929;136	ENSP00000357789:G929V	ENSP00000357789:G929V	G	-	2	0	FLG	150551200	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.167000	0.09940	0.033000	0.15463	0.479000	0.44913	GGC	C|0.993;A|0.007	0.007	strong		0.557	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152284576	C	A	152284576	3	1	22	1	0	0	0	0	1	0	0	0	5930	739	26	4	9403	4	FLG	1	152284576	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	119	152284576	96966045	258	3159			1	24		12	12	9983	N	T_G_C_A	3.860175e-07
FLG	2312	hgsc.bcm.edu	37	chr1	152285188	152285188	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgaagcttgtccgtgcccaGtgcctgagtgtctggagctg	6	11	14	10	1	1	2	0	2	1	0	2	3	2	3	3	1	4	2	3	1	1	1	rs3120655	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152285188G>A	ENST00000368799.1	-	3	2209	c.2174C>T	c.(2173-2175)aCt>aTt	p.T725I	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	725	Ser-rich.		T -> I (in dbSNP:rs3120655).		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)			TCCGTGCCCAGTGCCTGAGTG	0.567									Ichthyosis				-|||	562	0.11222	0.407	0.0331	5008	,	,		21307	0.0		0.001	False		,,,				2504	0.0				p.T725I		Atlas-SNP	.											.	FLG	900	.	0			c.C2174T						PASS	.	G	ILE/THR	1483,2923		249,985,969	379	400	393		2174	3	0	1	dbSNP_103	393	19,8581		0,19,4281	no	missense	FLG	NM_002016.1	89	249,1004,5250	AA,AG,GG		0.2209,33.6586,11.5485	possibly-damaging	725/4062	152285188	1502,11504	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGCCCAGTGCCTG	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.2174C>T	1.37:g.152285188G>A	ENSP00000357789:p.Thr725Ile	243	1	0.00411523		274	272	0.992701	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	165	0.07554945054945054	152	0.3089430894308943	12	0.03314917127071823	1	0.0017482517482517483	0	0.0	-	6.095	0.385885	0.11524	0.336586	0.002209	ENSG00000143631	ENST00000368799	T	0.03358	3.96	3.89	2.97	0.34412	.	.	.	.	.	T	0.00580	0.0019	N	0.03281	-0.365	0.80722	P	0.0	B	0.14805	0.011	B	0.17979	0.02	T	0.46317	-0.9200	8	0.16896	T	0.51	1.9131	8.0676	0.30669	0.1154:0.0:0.8846:0.0	.	725	P20930	FILA_HUMAN	I	725	ENSP00000357789:T725I	ENSP00000357789:T725I	T	-	2	0	FLG	150551812	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.408000	0.07169	0.832000	0.34804	-0.663000	0.03849	ACT	.	.	weak		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152285188	G	A	152285188	3	1	22	1	0	0	0	0	1	0	0	0	5930	1029	36	2	10015	2	FLG	1	152285188	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	612	152285188	96965433	259	3160			1	24		12	12	9983	N	T_G_C_A	3.860175e-07
FLG	2312	hgsc.bcm.edu	37	chr1	152285541	152285541	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttgtcctgggccccgatgaTtgtccctggcccacctgtga	4	11	11	15	1	0	2	0	2	0	0	2	3	2	2	6	2	0	0	6	2	0	2	rs116417983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152285541T>C	ENST00000368799.1	-	3	1856	c.1821A>G	c.(1819-1821)caA>caG	p.Q607Q	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	607	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)			GCCCCGATGATTGTCCCTGGC	0.567									Ichthyosis				T|||	94	0.01877	0.0688	0.0043	5008	,	,		18467	0.0		0.0	False		,,,				2504	0.0				p.Q607Q		Atlas-SNP	.											.	FLG	900	.	0			c.A1821G						PASS	.	T		186,4220	120.0+/-157.7	5,176,2022	287	283	284		1821	-1.6	0	1	dbSNP_132	284	0,8600		0,0,4300	no	coding-synonymous	FLG	NM_002016.1		5,176,6322	CC,CT,TT		0.0,4.2215,1.4301		607/4062	152285541	186,12820	2203	4300	6503	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CGATGATTGTCCC	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.1821A>G	1.37:g.152285541T>C		535	0	0		542	253	0.46679	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			T|0.986;C|0.014	0.014	strong		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		C	152285541	T	C	152285541	2	2	22	1	0	0	0	0	0	0	0	1	5930	1490	52	3		3	FLG	1	152285541	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	353	152285541	96965080	260	3161			1	24		12	12	9983	N	T_G_C_A	3.860175e-07
FLG2	388698	hgsc.bcm.edu	37	chr1	152324397	152324397	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcactgtcactgtactcactGtggccagatccccttcttcc	6	13	6	16	0	4	1	3	0	1	1	6	1	6	1	4	1	1	1	4	1	1	3	rs79983774	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152324397G>A	ENST00000388718.5	-	3	5937	c.5865C>T	c.(5863-5865)caC>caT	p.H1955H	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1955					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)			TGTACTCACTGTGGCCAGATC	0.532													g|||	341	0.0680911	0.2421	0.0231	5008	,	,		27530	0.0		0.005	False		,,,				2504	0.0				p.H1955H		Atlas-SNP	.											.	FLG2	431	.	0			c.C5865T						PASS	.	G		841,3565	331.8+/-302.1	70,701,1432	329	310	316		5865	-2.1	0	1	dbSNP_131	316	25,8575	17.9+/-57.8	0,25,4275	no	coding-synonymous	FLG2	NM_001014342.2		70,726,5707	AA,AG,GG		0.2907,19.0876,6.6585		1955/2392	152324397	866,12140	2203	4300	6503	SO:0001819	synonymous_variant	388698	exon3			CTCACTGTGGCCA	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.5865C>T	1.37:g.152324397G>A		383	0	0		426	211	0.495305	NM_001014342	Q9H4U1	Silent	SNP	ENST00000388718.5	37	CCDS30861.1																																																																																			G|0.940;A|0.060	0.060	strong		0.532	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		A	152324397	G	A	152324397	2	1	22	1	0	0	0	0	0	0	0	1	5931	1368	48	2		2	FLG2	1	152324397	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	38856	152324397	96926224	261	3162											
FLG2	388698	hgsc.bcm.edu	37	chr1	152325456	152325456	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggctcttcatgttgagatccGgcttggccgtaagtgtgttc	5	14	13	9	2	2	1	1	1	1	1	4	2	3	1	2	3	0	5	2	3	1	5	rs73007787	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152325456G>A	ENST00000388718.5	-	3	4878	c.4806C>T	c.(4804-4806)gcC>gcT	p.A1602A	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1602					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)			GTTGAGATCCGGCTTGGCCGT	0.512													g|||	341	0.0680911	0.2421	0.0231	5008	,	,		26525	0.0		0.005	False		,,,				2504	0.0				p.A1602A		Atlas-SNP	.											.	FLG2	431	.	0			c.C4806T						PASS	.	G		841,3565	331.8+/-302.1	70,701,1432	353	305	321		4806	-7.5	0	1	dbSNP_130	321	25,8575	17.9+/-57.8	0,25,4275	no	coding-synonymous	FLG2	NM_001014342.2		70,726,5707	AA,AG,GG		0.2907,19.0876,6.6585		1602/2392	152325456	866,12140	2203	4300	6503	SO:0001819	synonymous_variant	388698	exon3			AGATCCGGCTTGG	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.4806C>T	1.37:g.152325456G>A		404	1	0.00247525		399	226	0.566416	NM_001014342	Q9H4U1	Silent	SNP	ENST00000388718.5	37	CCDS30861.1																																																																																			G|0.940;A|0.060	0.060	strong		0.512	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		A	152325456	G	A	152325456	2	1	22	1	0	0	0	0	0	0	0	1	5931	1103	39	1		1	FLG2	1	152325456	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1059	152325456	96925165	262	3163											
FLG2	388698	hgsc.bcm.edu	37	chr1	152326516	152326516	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccttgaccagactggctaTgtctagtggtatttattgtc	7	16	10	8	0	1	2	0	1	1	1	3	2	2	2	2	2	0	2	2	2	4	7	rs16833974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152326516T>C	ENST00000388718.5	-	3	3818	c.3746A>G	c.(3745-3747)cAt>cGt	p.H1249R	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1249	Ser-rich.		H -> R (in dbSNP:rs16833974).		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)			AGACTGGCTATGTCTAGTGGT	0.478													T|||	341	0.0680911	0.2421	0.0231	5008	,	,		25196	0.0		0.005	False		,,,				2504	0.0				p.H1249R		Atlas-SNP	.											.	FLG2	431	.	0			c.A3746G						PASS	.	T	ARG/HIS	842,3564	332.0+/-302.3	71,700,1432	263	245	251		3746	2.5	0	1	dbSNP_123	251	25,8575	17.9+/-57.8	0,25,4275	yes	missense	FLG2	NM_001014342.2	29	71,725,5707	CC,CT,TT		0.2907,19.1103,6.6662	possibly-damaging	1249/2392	152326516	867,12139	2203	4300	6503	SO:0001583	missense	388698	exon3			TGGCTATGTCTAG	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.3746A>G	1.37:g.152326516T>C	ENSP00000373370:p.His1249Arg	271	0	0		349	175	0.501433	NM_001014342	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	118	0.05402930402930403	112	0.22764227642276422	4	0.011049723756906077	0	0.0	2	0.002638522427440633	T	9.679	1.148853	0.21288	0.191103	0.002907	ENSG00000143520	ENST00000388718	T	0.37752	1.18	3.64	2.47	0.30058	.	.	.	.	.	T	0.09468	0.0233	L	0.52266	1.64	0.80722	P	0.0	P	0.39480	0.675	B	0.28638	0.092	T	0.17410	-1.0370	8	0.16420	T	0.52	-0.2453	7.1344	0.25521	0.0:0.0:0.2304:0.7696	rs16833974;rs16833974	1249	Q5D862	FILA2_HUMAN	R	1249	ENSP00000373370:H1249R	ENSP00000373370:H1249R	H	-	2	0	FLG2	150593140	0.000000	0.05858	0.001000	0.08648	0.076000	0.17211	-0.219000	0.09228	0.384000	0.24942	0.254000	0.18369	CAT	T|0.932;C|0.068	0.068	strong		0.478	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342		C	152326516	T	C	152326516	3	2	22	1	0	0	0	0	1	0	0	0	5931	1464	51	3	3433	3	FLG2	1	152326516	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1060	152326516	96924105	263	3164											
CRNN	49860	hgsc.bcm.edu	37	chr1	152382436	152382436	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgcgtctgggtctgtccCtgttctctagcccctccgtg	1	13	12	15	2	3	0	0	0	3	0	6	0	5	0	4	2	2	2	4	2	1	2	rs6695830	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152382436C>G	ENST00000271835.3	-	3	1184	c.1122G>C	c.(1120-1122)caG>caC	p.Q374H	RP1-91G5.3_ENST00000411804.1_RNA	NM_016190.2	NP_057274.1	Q9UBG3	CRNN_HUMAN	cornulin	374	Gln-rich.		Q -> H (in dbSNP:rs6695830).		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)			GGGTCTGTCCCTGTTCTCTAG	0.592													C|||	366	0.0730831	0.261	0.0231	5008	,	,		25184	0.0		0.005	False		,,,				2504	0.0				p.Q374H		Atlas-SNP	.											CRNN,NS,carcinoma,-2,1	CRNN	78	1	0			c.G1122C						PASS	.	C	HIS/GLN	855,3551	336.0+/-304.2	78,699,1426	171	145	154		1122	1	0	1	dbSNP_116	154	23,8577	16.6+/-54.9	0,23,4277	yes	missense	CRNN	NM_016190.2	24	78,722,5703	GG,GC,CC		0.2674,19.4054,6.7507	possibly-damaging	374/496	152382436	878,12128	2203	4300	6503	SO:0001583	missense	49860	exon3			CTGTCCCTGTTCT	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.1122G>C	1.37:g.152382436C>G	ENSP00000271835:p.Gln374His	361	0	0		341	340	0.997067	NM_016190	B2RE60|Q8N613	Missense_Mutation	SNP	ENST00000271835.3	37	CCDS1010.1	120	0.054945054945054944	114	0.23170731707317074	4	0.011049723756906077	0	0.0	2	0.002638522427440633	C	14.19	2.462134	0.43736	0.194054	0.002674	ENSG00000143536	ENST00000271835	T	0.05139	3.49	4.86	0.955	0.19602	.	0.889113	0.09605	N	0.779761	T	0.04182	0.0116	L	0.54323	1.7	0.80722	P	0.0	D	0.56035	0.974	P	0.49012	0.598	T	0.36286	-0.9754	9	0.62326	D	0.03	.	6.7488	0.23475	0.0:0.6177:0.0:0.3823	rs6695830;rs6695830	374	Q9UBG3	CRNN_HUMAN	H	374	ENSP00000271835:Q374H	ENSP00000271835:Q374H	Q	-	3	2	CRNN	150649060	0.361000	0.24972	0.006000	0.13384	0.150000	0.21749	0.677000	0.25262	0.018000	0.15052	-0.225000	0.12378	CAG	C|0.939;G|0.061	0.061	strong		0.592	CRNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034503.1	NM_016190		G	152382436	C	G	152382436	3	3	22	1	0	0	0	0	1	0	0	0	3894	680	24	4	369	4	CRNN	1	152382436	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	55920	152382436	96868185	264	3165											
LCE3D	84648	hgsc.bcm.edu	37	chr1	152552311	152552311	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagcttggggcacagccagaGgaagctggaggcagacactg	11	4	17	9	0	0	2	0	0	0	2	0	5	0	4	1	5	3	4	1	5	1	1	rs149516289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152552311G>A	ENST00000368787.3	-	2	158	c.102C>T	c.(100-102)tcC>tcT	p.S34S		NM_032563.1	NP_115952.1	Q9BYE3	LCE3D_HUMAN	late cornified envelope 3D	34					keratinization (GO:0031424)					breast(1)|endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)|stomach(2)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)	UCEC - Uterine corpus endometrioid carcinoma (5;0.153)|KIRC - Kidney renal clear cell carcinoma(4;0.0323)|Kidney(5;0.0378)		CACAGCCAGAGGAAGCTGGAG	0.662													G|||	43	0.00858626	0.0325	0.0	5008	,	,		16707	0.0		0.0	False		,,,				2504	0.0				p.S34S		Atlas-SNP	.											.	LCE3D	28	.	0			c.C102T						PASS	.	G		102,4304	81.4+/-119.9	2,98,2103	75	83	81		102	-1.4	0.1	1	dbSNP_134	81	0,8600		0,0,4300	no	coding-synonymous	LCE3D	NM_032563.1		2,98,6403	AA,AG,GG		0.0,2.315,0.7843		34/93	152552311	102,12904	2203	4300	6503	SO:0001819	synonymous_variant	84648	exon2			GCCAGAGGAAGCT	BI670519	CCDS1014.1	1q21	2008-02-05	2004-05-21	2004-10-15	ENSG00000163202	ENSG00000163202		"Late cornified envelopes"	16615	protein-coding gene	gene with protein product		612616	"small proline rich-like (epidermal differentiation complex) 6B"	SPRL6B, SPRL6A		11698679	Standard	NM_032563		Approved	LEP16	uc001fab.3	Q9BYE3	OTTHUMG00000012384	ENST00000368787.3:c.102C>T	1.37:g.152552311G>A		271	0	0		263	137	0.520913	NM_032563	Q3MIL1	Silent	SNP	ENST00000368787.3	37	CCDS1014.1																																																																																			G|0.992;A|0.008	0.008	strong		0.662	LCE3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034504.1	NM_032563		A	152552311	G	A	152552311	2	1	22	1	0	0	0	0	0	0	0	1	8681	987	35	2		2	LCE3D	1	152552311	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	169875	152552311	96698310	265	3166											
LCE3C	353144	hgsc.bcm.edu	37	chr1	152573464	152573464	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaaggcgggggctcctgccGtggccatggctctgggggct	3	7	19	12	2	1	0	0	0	1	0	2	0	2	0	3	7	1	4	3	7	1	0	rs148755167	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152573464G>A	ENST00000333881.3	+	1	327	c.257G>A	c.(256-258)cGt>cAt	p.R86H		NM_178434.2	NP_848521.1	Q5T5A8	LCE3C_HUMAN	late cornified envelope 3C	86					keratinization (GO:0031424)					lung(1)	1	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)	UCEC - Uterine corpus endometrioid carcinoma (5;0.153)|KIRC - Kidney renal clear cell carcinoma(4;0.0313)|Kidney(5;0.0367)		GGCTCCTGCCGTGGCCATGGC	0.597													G|||	62	0.0123802	0.0469	0.0	5008	,	,		6910	0.0		0.0	False		,,,				2504	0.0				p.R86H		Atlas-SNP	.											.	LCE3C	3	.	0			c.G257A						PASS	.	G	HIS/ARG	128,3478		23,82,1698	32	32	32		257	3.1	0.5	1	dbSNP_134	32	2,5326		0,2,2662	no	missense	LCE3C	NM_178434.2	29	23,84,4360	AA,AG,GG		0.0375,3.5496,1.4551	benign	86/95	152573464	130,8804	1803	2664	4467	SO:0001583	missense	353144	exon1			CCTGCCGTGGCCA	BI670516	CCDS1015.1	1q21.3	2008-02-05		2004-10-15	ENSG00000244057	ENSG00000244057		"Late cornified envelopes"	16612	protein-coding gene	gene with protein product		612615	"small proline rich-like (epidermal differentiation complex) 3A"	SPRL3A		11698679	Standard	NM_178434		Approved	LEP15	uc001fac.2	Q5T5A8	OTTHUMG00000014403	ENST00000333881.3:c.257G>A	1.37:g.152573464G>A	ENSP00000334644:p.Arg86His	62	0	0		161	79	0.490683	NM_178434	A1L420	Missense_Mutation	SNP	ENST00000333881.3	37	CCDS1015.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	G	3.891	-0.024030	0.07634	0.035496	3.75E-4	ENSG00000244057	ENST00000333881	T	0.03524	3.9	4.01	3.08	0.35506	.	.	.	.	.	T	0.00967	0.0032	.	.	.	0.09310	N	1	B	0.18741	0.03	B	0.06405	0.002	T	0.47156	-0.9139	8	0.29301	T	0.29	.	9.3733	0.38268	0.0:0.2192:0.7808:0.0	.	86	Q5T5A8	LCE3C_HUMAN	H	86	ENSP00000334644:R86H	ENSP00000334644:R86H	R	+	2	0	LCE3C	150840088	0.520000	0.26250	0.478000	0.27316	0.166000	0.22503	1.037000	0.30241	0.858000	0.35431	0.313000	0.20887	CGT	G|0.988;A|0.012	0.012	strong		0.597	LCE3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040061.2	NM_178434		A	152573464	G	A	152573464	3	1	22	1	0	0	0	0	1	0	0	0	8680	1145	40	1	259	1	LCE3C	1	152573464	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	21153	152573464	96677157	266	3167											
LCE2B	26239	hgsc.bcm.edu	37	chr1	152659392	152659392	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ccaagtgtaccccaaaatgtCcacctaagtgtccccctaaa	13	8	5	15	0	0	0	0	0	0	0	2	0	2	0	7	0	1	1	7	0	7	3	rs61730791	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152659392C>T	ENST00000368780.3	+	2	127	c.73C>T	c.(73-75)Cca>Tca	p.P25S	LCE2B_ENST00000417924.2_Missense_Mutation_p.P25S	NM_014357.4	NP_055172.1	O14633	LCE2B_HUMAN	late cornified envelope 2B	25	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)			CCCAAAATGTCCACCTAAGTG	0.572													C|||	65	0.0129792	0.0461	0.0043	5008	,	,		15748	0.0		0.001	False		,,,				2504	0.0				p.P25S		Atlas-SNP	.											.	LCE2B	40	.	0			c.C73T						PASS	.	C	SER/PRO	146,4260	102.5+/-141.1	4,138,2061	123	122	123		73	1.5	0	1	dbSNP_129	123	1,8599		0,1,4299	yes	missense	LCE2B	NM_014357.4	74	4,139,6360	TT,TC,CC		0.0116,3.3137,1.1302	benign	25/111	152659392	147,12859	2203	4300	6503	SO:0001583	missense	26239	exon2			AAATGTCCACCTA	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.73C>T	1.37:g.152659392C>T	ENSP00000357769:p.Pro25Ser	237	0	0		240	124	0.516667	NM_014357	Q5TA80	Missense_Mutation	SNP	ENST00000368780.3	37	CCDS1020.1	24	0.01098901098901099	21	0.042682926829268296	3	0.008287292817679558	0	0.0	0	0.0	C	1.661	-0.511564	0.04200	0.033137	1.16E-4	ENSG00000159455	ENST00000417924;ENST00000368780	T;T	0.03607	3.87;3.87	2.46	1.45	0.22620	.	.	.	.	.	T	0.01940	0.0061	M	0.77820	2.39	0.09310	N	1	B	0.14012	0.009	B	0.17722	0.019	T	0.40213	-0.9575	9	0.87932	D	0	.	4.1955	0.10441	0.0:0.7428:0.0:0.2572	rs61730791	25	O14633	LCE2B_HUMAN	S	25	ENSP00000414043:P25S;ENSP00000357769:P25S	ENSP00000357769:P25S	P	+	1	0	LCE2B	150926016	0.000000	0.05858	0.001000	0.08648	0.514000	0.34195	-0.555000	0.05999	0.257000	0.21650	0.313000	0.20887	CCA	C|0.986;T|0.014	0.014	strong		0.572	LCE2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034524.1	NM_014357		T	152659392	C	T	152659392	3	4	22	1	0	0	0	0	1	0	0	0	8675	855	30	2	75	2	LCE2B	1	152659392	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	85928	152659392	96591229	267	3168											
KPRP	448834	hgsc.bcm.edu	37	chr1	152732998	152732998	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ataacagtcgctgtcctcgcCgccccatttcaagctgctct	7	11	7	16	3	2	0	1	0	1	0	5	0	3	0	4	0	3	3	4	0	2	2	rs140912923	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152732998C>T	ENST00000606109.1	+	1	962	c.934C>T	c.(934-936)Cgc>Tgc	p.R312C	KPRP_ENST00000368773.1_Missense_Mutation_p.R312C			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	312	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)			CTGTCCTCGCCGCCCCATTTC	0.597													C|||	24	0.00479233	0.0174	0.0014	5008	,	,		16798	0.0		0.0	False		,,,				2504	0.0				p.R312C		Atlas-SNP	.											KPRP,NS,carcinoma,0,3	KPRP	152	3	0			c.C934T						PASS	.	C	CYS/ARG	69,4337	62.9+/-100.1	2,65,2136	48	47	48		934	-8.3	0	1	dbSNP_134	48	0,8600		0,0,4300	no	missense	KPRP	NM_001025231.1	180	2,65,6436	TT,TC,CC		0.0,1.566,0.5305	possibly-damaging	312/580	152732998	69,12937	2203	4300	6503	SO:0001583	missense	448834	exon2			CCTCGCCGCCCCA	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.934C>T	1.37:g.152732998C>T	ENSP00000475216:p.Arg312Cys	72	0	0		110	55	0.5	NM_001025231		Missense_Mutation	SNP	ENST00000606109.1	37	CCDS30862.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	C	9.290	1.050327	0.19827	0.01566	0.0	ENSG00000203786	ENST00000368773	T	0.16196	2.36	5.3	-8.26	0.01021	.	1.822830	0.02592	N	0.100084	T	0.03305	0.0096	N	0.19112	0.55	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.43909	-0.9362	10	0.72032	D	0.01	-0.013	9.3493	0.38129	0.1476:0.6376:0.1235:0.0913	.	312	Q5T749	KPRP_HUMAN	C	312	ENSP00000357762:R312C	ENSP00000357762:R312C	R	+	1	0	KPRP	150999622	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.771000	0.04699	-1.006000	0.03412	-0.502000	0.04539	CGC	C|0.994;T|0.006	0.006	strong		0.597	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231		T	152732998	C	T	152732998	3	4	22	1	0	0	0	0	1	0	0	0	8445	652	23	1	936	1	KPRP	1	152732998	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	73606	152732998	96517623	268	3169											
LCE1C	353133	hgsc.bcm.edu	37	chr1	152777874	152777874	+	Silent	SNP	T	T	A																															ggacactttgggggacacttTggggtggggcacttgggagg																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152777874T>A	ENST00000607093.1	-	1	80	c.81A>T	c.(79-81)ccA>ccT	p.P27P	LCE1C_ENST00000368768.1_Silent_p.P27P			Q5T751	LCE1C_HUMAN	late cornified envelope 1C	27	Pro-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)			ggggacactttggggTGgggc	0.647																																					p.P27P		Atlas-SNP	.											.	LCE1C	40	.	0			c.A81T						PASS	.						46	47	46					1																	152777874		2203	4300	6503	SO:0001819	synonymous_variant	353133	exon2			ACACTTTGGGGTG		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.81A>T	1.37:g.152777874T>A		282	0	0		403	21	0.0521092	NM_178351		Silent	SNP	ENST00000607093.1	37	CCDS1026.1																																																																																			.	.	none		0.647	LCE1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034658.2	NM_178351		A	152777874	T	A	152777874	2	1	22	1	0	0	0	0	0	0	0	1	8670	1799	63	5		5	LCE1C	1	152777874	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	44876	152777874	96472747	269	3170	45	2									
LCE1C	353133	hgsc.bcm.edu	37	chr1	152777877	152777877	+	Silent	SNP	G	G	A																															cactttgggggacactttggGgtggggcacttgggagggca																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152777877G>A	ENST00000607093.1	-	1	77	c.78C>T	c.(76-78)acC>acT	p.T26T	LCE1C_ENST00000368768.1_Silent_p.T26T			Q5T751	LCE1C_HUMAN	late cornified envelope 1C	26	Pro-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)			gacactttggggTGgggcact	0.647																																					p.T26T		Atlas-SNP	.											.	LCE1C	40	.	0			c.C78T						PASS	.						45	46	46					1																	152777877		2203	4300	6503	SO:0001819	synonymous_variant	353133	exon2			CTTTGGGGTGGGG		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.78C>T	1.37:g.152777877G>A		279	0	0		409	29	0.0709046	NM_178351		Silent	SNP	ENST00000607093.1	37	CCDS1026.1																																																																																			.	.	none		0.647	LCE1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034658.2	NM_178351		A	152777877	G	A	152777877	2	1	22	1	0	0	0	0	0	0	0	1	8670	1219	43	2		2	LCE1C	1	152777877	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3	152777877	96472744	270	3171	45	2									
IVL	3713	hgsc.bcm.edu	37	chr1	152882811	152882811	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgaagcacccggagcagcagGaggggcagctggagctccca	10	3	16	12	1	0	1	0	1	0	0	1	4	1	4	2	5	5	6	2	5	1	0	rs75111974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152882811G>A	ENST00000368764.3	+	2	602	c.538G>A	c.(538-540)Gag>Aag	p.E180K	IVL_ENST00000392667.2_Missense_Mutation_p.E34K			P07476	INVO_HUMAN	involucrin	180	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)			ggagcagcaggaggggcagct	0.647													G|||	107	0.0213658	0.0779	0.0058	5008	,	,		15888	0.0		0.0	False		,,,				2504	0.0				p.E180K		Atlas-SNP	.											.	IVL	100	.	0			c.G538A						PASS	.	G	LYS/GLU	255,4147		3,249,1949	13	15	14		538	0.1	0	1	dbSNP_131	14	2,8584		0,2,4291	no	missense	IVL	NM_005547.2	56	3,251,6240	AA,AG,GG		0.0233,5.7928,1.9787	possibly-damaging	180/586	152882811	257,12731	2201	4293	6494	SO:0001583	missense	3713	exon2			CAGCAGGAGGGGC	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.538G>A	1.37:g.152882811G>A	ENSP00000357753:p.Glu180Lys	126	0	0		205	112	0.546341	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	37	CCDS1030.1	31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	G	9.931	1.214712	0.22289	0.057928	2.33E-4	ENSG00000163207	ENST00000368764;ENST00000392667	T;T	0.11495	3.0;2.77	3.55	0.138	0.14793	.	.	.	.	.	T	0.03520	0.0101	L	0.38531	1.155	0.09310	N	1	P	0.38280	0.625	B	0.39738	0.308	T	0.39761	-0.9598	9	0.25106	T	0.35	.	12.3464	0.55124	0.0:0.5062:0.4938:0.0	rs62641593	180	P07476	INVO_HUMAN	K	180;34	ENSP00000357753:E180K;ENSP00000376435:E34K	ENSP00000357753:E180K	E	+	1	0	IVL	151149435	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	0.353000	0.20130	0.285000	0.22329	-0.662000	0.03851	GAG	G|0.980;A|0.020	0.020	strong		0.647	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547		A	152882811	G	A	152882811	3	1	22	1	0	0	0	0	1	0	0	0	7938	1175	41	2	540	2	IVL	1	152882811	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	104934	152882811	96367810	271	3172											
IVL	3713	hgsc.bcm.edu	37	chr1	152883036	152883036	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcaggaggggcagctggagCtctctgagcagcaggaggga	10	4	19	8	0	1	1	0	1	1	0	2	5	1	5	0	6	5	6	0	6	0	0	rs4459054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152883036C>T	ENST00000368764.3	+	2	827	c.763C>T	c.(763-765)Ctc>Ttc	p.L255F	IVL_ENST00000392667.2_Missense_Mutation_p.L109F			P07476	INVO_HUMAN	involucrin	255	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)			gcagctggagctctctgagca	0.657													C|||	107	0.0213658	0.0779	0.0058	5008	,	,		19088	0.0		0.0	False		,,,				2504	0.0				p.L255F		Atlas-SNP	.											IVL,NS,carcinoma,-2,1	IVL	100	1	0			c.C763T						PASS	.		PHE/LEU	213,3727		5,203,1762	10	10	10		763	-0.7	0	1	dbSNP_111	10	3,7787		0,3,3892	no	missense	IVL	NM_005547.2	22	5,206,5654	TT,TC,CC		0.0385,5.4061,1.8414	benign	255/586	152883036	216,11514	1970	3895	5865	SO:0001583	missense	3713	exon2			CTGGAGCTCTCTG	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.763C>T	1.37:g.152883036C>T	ENSP00000357753:p.Leu255Phe	169	0	0		208	88	0.423077	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	37	CCDS1030.1	31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	C	0.147	-1.096036	0.01843	0.054061	3.85E-4	ENSG00000163207	ENST00000368764;ENST00000392667	T;T	0.11821	2.96;2.74	0.329	-0.658	0.11428	.	.	.	.	.	T	0.01835	0.0058	L	0.29908	0.895	0.09310	N	1	B	0.32245	0.361	B	0.28305	0.088	T	0.47328	-0.9126	9	0.11794	T	0.64	.	4.7855	0.13223	0.3488:0.6511:0.0:1.0E-4	rs4459054;rs7413034	255	P07476	INVO_HUMAN	F	255;109	ENSP00000357753:L255F;ENSP00000376435:L109F	ENSP00000357753:L255F	L	+	1	0	IVL	151149660	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.401000	0.07232	-0.793000	0.04475	0.123000	0.15791	CTC	C|0.986;T|0.014	0.014	strong		0.657	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547		T	152883036	C	T	152883036	3	4	22	1	0	0	0	0	1	0	0	0	7938	797	28	2	765	2	IVL	1	152883036	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	225	152883036	96367585	272	3173											
SPRR1A	6698	hgsc.bcm.edu	37	chr1	152957856	152957856	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aaggtgcctgagccctgccaCcccaaagtgcctgagccctg	8	6	11	16	0	0	2	0	2	0	0	0	2	0	2	7	1	5	0	7	1	2	0	rs143282605		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152957856C>G	ENST00000368762.1	+	1	150	c.150C>G	c.(148-150)caC>caG	p.H50Q	SPRR1A_ENST00000307122.2_Missense_Mutation_p.H50Q			P35321	SPR1A_HUMAN	small proline-rich protein 1A	50	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)			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)			AGCCCTGCCACCCCAAAGTGC	0.647																																					p.H50Q		Atlas-SNP	.											.	SPRR1A	17	.	0			c.C150G						PASS	.																																			SO:0001583	missense	6698	exon2			CTGCCACCCCAAA	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.150C>G	1.37:g.152957856C>G	ENSP00000357751:p.His50Gln	158	0	0		125	24	0.192	NM_001199828	B1AN47|D3DV31|Q2M303|Q9UDG4	Missense_Mutation	SNP	ENST00000368762.1	37	CCDS1032.1	.	.	.	.	.	.	.	.	.	.	C	3.605	-0.080674	0.07141	.	.	ENSG00000169474	ENST00000307122;ENST00000368762	T;T	0.11169	2.8;2.8	5.64	-8.48	0.00935	.	0.637243	0.13026	N	0.419668	T	0.01222	0.0040	.	.	.	0.09310	N	0.999997	B	0.30326	0.276	B	0.32393	0.145	T	0.37009	-0.9724	9	0.29301	T	0.29	-0.4448	1.0644	0.01608	0.3555:0.2828:0.17:0.1916	.	50	P35321	SPR1A_HUMAN	Q	50	ENSP00000307340:H50Q;ENSP00000357751:H50Q	ENSP00000307340:H50Q	H	+	3	2	SPRR1A	151224480	0.020000	0.18652	0.125000	0.21846	0.298000	0.27526	-1.221000	0.02968	-1.749000	0.01330	-0.300000	0.09419	CAC	.	.	weak		0.647	SPRR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040062.1	NM_005987		G	152957856	C	G	152957856	3	3	22	1	0	0	0	0	1	0	0	0	15110	506	18	4	152	4	SPRR1A	1	152957856	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	74820	152957856	96292765	273	3174											
S100A3	6274	hgsc.bcm.edu	37	chr1	153520203	153520203	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcagtccttgaagtactcGtggcagtagagacagaggca	11	7	15	8	1	0	3	0	1	0	2	2	4	1	3	1	3	1	5	1	3	3	3	rs41265164	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153520203G>A	ENST00000368713.3	-	3	457	c.261C>T	c.(259-261)caC>caT	p.H87H	S100A4_ENST00000368715.1_5'Flank|S100A4_ENST00000368716.4_5'Flank|S100A4_ENST00000354332.4_5'Flank|S100A4_ENST00000481009.1_5'Flank|S100A4_ENST00000368714.1_Intron|S100A3_ENST00000368712.1_Silent_p.H87H	NM_002960.1	NP_002951.1	P33764	S10A3_HUMAN	S100 calcium binding protein A3	87						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)			TGAAGTACTCGTGGCAGTAGA	0.592													G|||	760	0.151757	0.4228	0.1037	5008	,	,		19755	0.0149		0.0517	False		,,,				2504	0.0634				p.H87H		Atlas-SNP	.											.	S100A3	7	.	0			c.C261T						PASS	.	G		1633,2773	502.5+/-365.3	318,997,888	157	139	145		261	-2.6	1	1	dbSNP_127	145	466,8134	137.9+/-194.8	16,434,3850	no	coding-synonymous	S100A3	NM_002960.1		334,1431,4738	AA,AG,GG		5.4186,37.0631,16.1387		87/102	153520203	2099,10907	2203	4300	6503	SO:0001819	synonymous_variant	6274	exon3			GTACTCGTGGCAG	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.261C>T	1.37:g.153520203G>A		156	0	0		146	74	0.506849	NM_002960	D3DV51|Q6FGE4	Silent	SNP	ENST00000368713.3	37	CCDS1043.1																																																																																			A|0.147;C|0.000;G|0.853;T|0.000	0.147	strong		0.592	S100A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037726.1	NM_002960		A	153520203	G	A	153520203	2	1	22	1	0	0	0	0	0	0	0	1	13794	1136	40	1		1	S100A3	1	153520203	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	562347	153520203	95730418	274	3175											
S100A3	6274	hgsc.bcm.edu	37	chr1	153520898	153520898	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgtatttgtccccacagcGccctgcgtattcctggaagg	6	12	10	13	2	0	0	0	0	0	0	2	1	2	1	4	2	2	2	4	2	3	5	rs61731550	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153520898G>A	ENST00000368713.3	-	2	260	c.64C>T	c.(64-66)Cgc>Tgc	p.R22C	S100A4_ENST00000368716.4_5'Flank|S100A4_ENST00000354332.4_5'Flank|S100A4_ENST00000368714.1_Intron|S100A3_ENST00000368712.1_Missense_Mutation_p.R22C	NM_002960.1	NP_002951.1	P33764	S10A3_HUMAN	S100 calcium binding protein A3	22	EF-hand 1.					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)			TCCCCACAGCGCCCTGCGTAT	0.622													G|||	51	0.0101837	0.0363	0.0043	5008	,	,		17589	0.0		0.0	False		,,,				2504	0.0				p.R22C		Atlas-SNP	.											.	S100A3	7	.	0			c.C64T						PASS	.	G	CYS/ARG	128,4278	94.4+/-133.1	2,124,2077	153	147	149		64	3.4	0	1	dbSNP_129	149	0,8600		0,0,4300	yes	missense	S100A3	NM_002960.1	180	2,124,6377	AA,AG,GG		0.0,2.9051,0.9842	probably-damaging	22/102	153520898	128,12878	2203	4300	6503	SO:0001583	missense	6274	exon2			CACAGCGCCCTGC	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.64C>T	1.37:g.153520898G>A	ENSP00000357702:p.Arg22Cys	58	0	0		51	28	0.54902	NM_002960	D3DV51|Q6FGE4	Missense_Mutation	SNP	ENST00000368713.3	37	CCDS1043.1	17	0.007783882783882784	14	0.028455284552845527	3	0.008287292817679558	0	0.0	0	0.0	G	12.38	1.921365	0.33908	0.029051	0.0	ENSG00000188015	ENST00000368713;ENST00000368712	T;T	0.12039	2.72;2.72	5.42	3.43	0.39272	S100/CaBP-9k-type, calcium binding, subdomain (1);EF-hand-like domain (1);	0.495237	0.19790	N	0.106001	T	0.09512	0.0234	M	0.67569	2.06	0.18873	N	0.999985	D	0.64830	0.994	P	0.48770	0.589	T	0.09751	-1.0660	10	0.87932	D	0	.	6.1806	0.20470	0.094:0.0:0.7225:0.1835	.	22	P33764	S10A3_HUMAN	C	22	ENSP00000357702:R22C;ENSP00000357701:R22C	ENSP00000357701:R22C	R	-	1	0	S100A3	151787522	0.002000	0.14202	0.002000	0.10522	0.003000	0.03518	1.236000	0.32683	1.295000	0.44724	0.643000	0.83706	CGC	G|0.991;A|0.009	0.009	strong		0.622	S100A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037726.1	NM_002960		A	153520898	G	A	153520898	3	1	22	1	0	0	0	0	1	0	0	0	13794	1087	38	1	249	1	S100A3	1	153520898	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	695	153520898	95729723	275	3176											
S100A3	6274	hgsc.bcm.edu	37	chr1	153520954	153520954	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctaccgcctgctccagaggcCtggccatcctcactgtcaca	7	8	8	18	1	2	1	2	0	0	1	4	1	4	1	6	2	2	1	6	2	1	1	rs36022742	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153520954C>T	ENST00000368713.3	-	2	204	c.8G>A	c.(7-9)aGg>aAg	p.R3K	S100A4_ENST00000368716.4_5'Flank|S100A4_ENST00000354332.4_5'Flank|S100A4_ENST00000368714.1_Intron|S100A3_ENST00000368712.1_Missense_Mutation_p.R3K	NM_002960.1	NP_002951.1	P33764	S10A3_HUMAN	S100 calcium binding protein A3	3			R -> K (in dbSNP:rs36022742).			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)			CTCCAGAGGCCTGGCCATCCT	0.602													C|||	713	0.142372	0.3896	0.0994	5008	,	,		17421	0.0149		0.0517	False		,,,				2504	0.0634				p.R3K		Atlas-SNP	.											.	S100A3	7	.	0			c.G8A						PASS	.	C	LYS/ARG	1514,2892	471.8+/-356.2	272,970,961	105	105	105		8	0.8	0	1	dbSNP_126	105	465,8135	135.4+/-192.6	16,433,3851	yes	missense	S100A3	NM_002960.1	26	288,1403,4812	TT,TC,CC		5.407,34.3622,15.2161	benign	3/102	153520954	1979,11027	2203	4300	6503	SO:0001583	missense	6274	exon2			AGAGGCCTGGCCA	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.8G>A	1.37:g.153520954C>T	ENSP00000357702:p.Arg3Lys	45	0	0		48	22	0.458333	NM_002960	D3DV51|Q6FGE4	Missense_Mutation	SNP	ENST00000368713.3	37	CCDS1043.1	255	0.11675824175824176	180	0.36585365853658536	33	0.09116022099447514	9	0.015734265734265736	33	0.04353562005277045	C	7.322	0.617075	0.14129	0.343622	0.05407	ENSG00000188015	ENST00000368713;ENST00000368712	T;T	0.13538	2.58;2.58	5.05	0.817	0.18773	EF-hand-like domain (1);	0.427486	0.25430	N	0.030730	T	0.02418	0.0074	N	0.14661	0.345	0.80722	P	0.0	B	0.22276	0.067	B	0.15052	0.012	T	0.40739	-0.9547	9	0.56958	D	0.05	.	8.5814	0.33630	0.0:0.4703:0.4447:0.085	rs36022742;rs59565142;rs61732314	3	P33764	S10A3_HUMAN	K	3	ENSP00000357702:R3K;ENSP00000357701:R3K	ENSP00000357701:R3K	R	-	2	0	S100A3	151787578	0.000000	0.05858	0.002000	0.10522	0.038000	0.13279	-0.160000	0.10041	-0.025000	0.13918	-0.163000	0.13421	AGG	C|0.861;T|0.139	0.139	strong		0.602	S100A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037726.1	NM_002960		T	153520954	C	T	153520954	3	4	22	1	0	0	0	0	1	0	0	0	13794	681	24	2	305	2	S100A3	1	153520954	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	56	153520954	95729667	276	3177											
S100A2	6273	hgsc.bcm.edu	37	chr1	153534027	153534027	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtcactgttctcatccaggCtgcccatcagcttcttcagc	6	12	8	15	0	5	0	4	0	2	0	7	0	6	0	2	2	3	3	2	2	0	3	rs1047325	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153534027C>T	ENST00000368708.3	-	3	554	c.182G>A	c.(181-183)aGc>aAc	p.S61N	S100A2_ENST00000368707.4_3'UTR|S100A2_ENST00000368710.1_Missense_Mutation_p.S61N|S100A2_ENST00000497140.1_Missense_Mutation_p.S28N|S100A2_ENST00000368709.1_Missense_Mutation_p.S61N|S100A2_ENST00000487430.2_Missense_Mutation_p.S61N	NM_005978.3	NP_005969.1	P29034	S10A2_HUMAN	S100 calcium binding protein A2	62	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				endothelial cell migration (GO:0043542)		calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)			endometrium(1)|large_intestine(2)|lung(1)|ovary(1)	5	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)		Olopatadine(DB00768)	CTCATCCAGGCTGCCCATCAG	0.537													T|||	757	0.151158	0.4463	0.0821	5008	,	,		21128	0.0109		0.0527	False		,,,				2504	0.047				p.S61N		Atlas-SNP	.											.	S100A2	14	.	0			c.G182A						PASS	.	T	ASN/SER	1775,2631	643.4+/-397.8	363,1049,791	235	219	224		182	-4.6	0	1	dbSNP_86	224	441,8159	799.7+/-407.4	15,411,3874	yes	missense	S100A2	NM_005978.3	46	378,1460,4665	TT,TC,CC		5.1279,40.286,17.0383	benign	61/98	153534027	2216,10790	2203	4300	6503	SO:0001583	missense	6273	exon3			TCCAGGCTGCCCA	BC002829	CCDS1044.1	1q21	2013-01-10	2001-11-28		ENSG00000196754	ENSG00000196754		"S100 calcium binding proteins", "EF-hand domain containing"	10492	protein-coding gene	gene with protein product		176993	"S100 calcium-binding protein A2"	S100L		8341667	Standard	NM_005978		Approved	CAN19	uc001fcb.3	P29034	OTTHUMG00000035031	ENST00000368708.3:c.182G>A	1.37:g.153534027C>T	ENSP00000357697:p.Ser61Asn	253	0	0		250	248	0.992	NM_005978	O00266|Q3KRB9|Q5RHS8|Q9BU83	Missense_Mutation	SNP	ENST00000368708.3	37	CCDS1044.1	274	0.12545787545787546	208	0.42276422764227645	30	0.08287292817679558	4	0.006993006993006993	32	0.04221635883905013	T	5.767	0.325859	0.10900	0.40286	0.051279	ENSG00000196754	ENST00000368708;ENST00000368710;ENST00000368709;ENST00000368707	T;T;T	0.14266	2.52;2.52;2.52	4.77	-4.58	0.03410	S100/Calbindin-D9k, conserved site (1);EF-hand-like domain (1);	0.948424	0.08683	N	0.909215	T	0.01940	0.0061	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43940	-0.9360	8	0.44086	T	0.13	.	1.7661	0.03002	0.1195:0.308:0.2454:0.3271	rs1047325;rs3174843;rs52793522;rs56586255;rs60177723;rs1047325	62	P29034	S10A2_HUMAN	N	61;61;61;102	ENSP00000357697:S61N;ENSP00000357699:S61N;ENSP00000357698:S61N	ENSP00000357696:S102N	S	-	2	0	S100A2	151800651	0.019000	0.18553	0.000000	0.03702	0.286000	0.27126	0.583000	0.23849	-1.416000	0.02019	-0.254000	0.11334	AGC	C|0.841;T|0.159	0.159	strong		0.537	S100A2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084789.1	NM_005978		T	153534027	C	T	153534027	3	4	22	1	0	0	0	0	1	0	0	0	13793	797	28	2	115	2	S100A2	1	153534027	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	13073	153534027	95716594	277	3178											
INTS3	65123	hgsc.bcm.edu	37	chr1	153740285	153740285	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggctcctgtgccacctcacGccctccatctacacagaggt	7	8	8	18	2	2	1	1	0	1	1	4	1	4	1	5	2	2	1	5	2	1	1	rs61736048	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153740285G>A	ENST00000318967.2	+	21	2794	c.2226G>A	c.(2224-2226)acG>acA	p.T742T	INTS3_ENST00000456435.1_Silent_p.T536T|INTS3_ENST00000435409.2_Silent_p.T742T|INTS3_ENST00000512605.1_Silent_p.T536T|INTS3_ENST00000476843.1_3'UTR	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	743					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)			GCCACCTCACGCCCTCCATCT	0.592													G|||	61	0.0121805	0.0446	0.0029	5008	,	,		18290	0.0		0.0	False		,,,				2504	0.0				p.T742T		Atlas-SNP	.											.	INTS3	83	.	0			c.G2226A						PASS	.	G		170,4236	112.9+/-151.0	2,166,2035	91	75	81		2226	-11.7	0.1	1	dbSNP_129	81	0,8600		0,0,4300	no	coding-synonymous	INTS3	NM_023015.3		2,166,6335	AA,AG,GG		0.0,3.8584,1.3071		742/1043	153740285	170,12836	2203	4300	6503	SO:0001819	synonymous_variant	65123	exon21			CCTCACGCCCTCC	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.2226G>A	1.37:g.153740285G>A		74	0	0		76	38	0.5	NM_023015	A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Silent	SNP	ENST00000318967.2	37	CCDS1052.1																																																																																			G|0.983;A|0.017	0.017	strong		0.592	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015		A	153740285	G	A	153740285	2	1	22	1	0	0	0	0	0	0	0	1	7788	1074	38	1		1	INTS3	1	153740285	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	206258	153740285	95510336	278	3179											
SLC27A3	11000	hgsc.bcm.edu	37	chr1	153750650	153750650	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctcagagcaaggcagaacGtggccataaggtccggctgg	11	6	14	10	2	1	2	1	0	1	2	3	2	2	2	2	5	2	3	2	5	3	1	rs35102232	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153750650G>A	ENST00000368661.3	+	5	1381	c.1316G>A	c.(1315-1317)cGt>cAt	p.R439H	SLC27A3_ENST00000271857.2_Missense_Mutation_p.R520H|SLC27A3_ENST00000484014.1_3'UTR	NM_024330.1	NP_077306.1	Q5K4L6	S27A3_HUMAN	solute carrier family 27 (fatty acid transporter), member 3	439			R -> H (in dbSNP:rs35102232).		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)			AAGGCAGAACGTGGCCATAAG	0.627													G|||	89	0.0177716	0.0628	0.0072	5008	,	,		17430	0.0		0.001	False		,,,				2504	0.0				p.R439H		Atlas-SNP	.											.	SLC27A3	42	.	0			c.G1316A						PASS	.	G	HIS/ARG	257,4147		5,247,1950	32	38	36		1316	-2.7	0	1	dbSNP_126	36	2,8598		0,2,4298	yes	missense	SLC27A3	NM_024330.1	29	5,249,6248	AA,AG,GG		0.0233,5.8356,1.9917	possibly-damaging	439/731	153750650	259,12745	2202	4300	6502	SO:0001583	missense	11000	exon5			CAGAACGTGGCCA	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.1316G>A	1.37:g.153750650G>A	ENSP00000357650:p.Arg439His	37	0	0		36	16	0.444444	NM_024330	Q5VUQ7|Q5VUQ8|Q5VUR3|Q6ZV16|Q8N2X7|Q8TEJ0|Q96SW5|Q9BTJ5|Q9BTY5	Missense_Mutation	SNP	ENST00000368661.3	37	CCDS1053.1	39|39	0.017857142857142856|0.017857142857142856	34|34	0.06910569105691057|0.06910569105691057	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	G|G	13.72|13.72	2.320062|2.320062	0.41096|0.41096	0.058356|0.058356	2.33E-4|2.33E-4	ENSG00000143554|ENSG00000143554	ENST00000271857;ENST00000368661|ENST00000458027	T;T|.	0.41758|.	0.99;0.99|.	5.03|5.03	-2.66|-2.66	0.06077|0.06077	AMP-dependent synthetase/ligase (1);|.	0.933680|.	0.09084|.	N|.	0.850843|.	T|T	0.37812|0.37812	0.1017|0.1017	M|M	0.83312|0.83312	2.635|2.635	0.09310|0.09310	N|N	1|1	B|.	0.19073|.	0.033|.	B|.	0.21546|.	0.035|.	T|T	0.49303|0.49303	-0.8954|-0.8954	10|5	0.42905|.	T|.	0.14|.	1.8444|1.8444	7.2084|7.2084	0.25919|0.25919	0.4489:0.1139:0.4372:0.0|0.4489:0.1139:0.4372:0.0	rs35102232|rs35102232	439|.	Q5K4L6|.	S27A3_HUMAN|.	H|M	520;439|144	ENSP00000271857:R520H;ENSP00000357650:R439H|.	ENSP00000271857:R520H|.	R|V	+|+	2|1	0|0	SLC27A3|SLC27A3	152017274|152017274	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.193000|0.193000	0.23685|0.23685	-1.444000|-1.444000	0.02403|0.02403	-0.720000|-0.720000	0.04935|0.04935	-0.605000|-0.605000	0.04089|0.04089	CGT|GTG	G|0.979;A|0.021	0.021	strong		0.627	SLC27A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_024330		A	153750650	G	A	153750650	3	1	22	1	0	0	0	0	1	0	0	0	14542	1145	40	1	1334	1	SLC27A3	1	153750650	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	10365	153750650	95499971	279	3180											
GATAD2B	57459	hgsc.bcm.edu	37	chr1	153788927	153788927	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttggctgcagcctgtgagttGgcagcatcagtcatggcgct	6	11	14	10	1	2	1	2	1	0	0	2	1	2	1	1	3	3	6	1	3	0	2	rs114813239	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153788927G>A	ENST00000368655.4	-	7	1281	c.1038C>T	c.(1036-1038)gcC>gcT	p.A346A		NM_020699.2	NP_065750.1	Q8WXI9	P66B_HUMAN	GATA zinc finger domain containing 2B	346	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)			CCTGTGAGTTGGCAGCATCAG	0.537													G|||	51	0.0101837	0.0371	0.0029	5008	,	,		19938	0.0		0.0	False		,,,				2504	0.0				p.A346A		Atlas-SNP	.											.	GATAD2B	62	.	0			c.C1038T						PASS	.	G		139,4267	99.4+/-138.0	2,135,2066	105	83	90		1038	4.2	1	1	dbSNP_132	90	0,8600		0,0,4300	no	coding-synonymous	GATAD2B	NM_020699.2		2,135,6366	AA,AG,GG		0.0,3.1548,1.0687		346/594	153788927	139,12867	2203	4300	6503	SO:0001819	synonymous_variant	57459	exon7			TGAGTTGGCAGCA	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.1038C>T	1.37:g.153788927G>A		289	0	0		307	144	0.469055	NM_020699	D3DUZ2|Q5VUR2|Q7LG68|Q9ULS0	Silent	SNP	ENST00000368655.4	37	CCDS1054.1																																																																																			G|0.987;A|0.013	0.013	strong		0.537	GATAD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090305.1	NM_020699		A	153788927	G	A	153788927	2	1	22	1	0	0	0	0	0	0	0	1	6269	1335	47	2		2	GATAD2B	1	153788927	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	38277	153788927	95461694	280	3181											
GBA	2629	hgsc.bcm.edu	37	chr1	155210498	155210498	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgcttaccctactcaaaggcTtgggacattcctgaggacag	10	10	10	11	0	1	1	1	1	0	0	2	3	2	3	2	3	3	2	2	3	3	4	rs150466109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155210498T>C	ENST00000327247.5	-	3	270	c.38A>G	c.(37-39)aAg>aGg	p.K13R	GBA_ENST00000368373.3_Missense_Mutation_p.K13R|GBA_ENST00000428024.3_Intron|GBA_ENST00000427500.3_Missense_Mutation_p.K13R|GBA_ENST00000493842.1_5'UTR|GBA_ENST00000536770.1_Missense_Mutation_p.K13R	NM_001005741.2|NM_001005742.2	NP_001005741.1|NP_001005742.1	P04062	GLCM_HUMAN	glucosidase, beta, acid	13					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)	ACTCAAAGGCTTGGGACATTC	0.557									Gaucher disease type I				t|||	118	0.0235623	0.084	0.0072	5008	,	,		19504	0.002		0.0	False		,,,				2504	0.0				p.K13R		Atlas-SNP	.											.	GBA	46	.	0			c.A38G	GRCh37	CM065215	GBA	M	rs150466109	PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS,,ARG/LYS	312,4094	166.9+/-198.0	11,290,1902	154	142	146		38,38,38,,38	-0.4	0	1	dbSNP_134	146	3,8597	2.2+/-6.3	0,3,4297	no	missense,missense,missense,intron,missense	GBA	NM_000157.3,NM_001005741.2,NM_001005742.2,NM_001171811.1,NM_001171812.1	26,26,26,,26	11,293,6199	CC,CT,TT		0.0349,7.0813,2.422	benign,benign,benign,,benign	13/537,13/537,13/537,,13/488	155210498	315,12691	2203	4300	6503	SO:0001583	missense	2629	exon3	Familial Cancer Database	glucocerebrosidase insufficiency	AAAGGCTTGGGAC	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.38A>G	1.37:g.155210498T>C	ENSP00000314508:p.Lys13Arg	53	0	0		60	31	0.516667	NM_001005742	A8K796|B7Z5G2|B7Z6S1|J3KQG4|J3KQK9|Q16545|Q4VX22|Q6I9R6|Q9UMJ8	Missense_Mutation	SNP	ENST00000327247.5	37	CCDS1102.1	44	0.020146520146520148	43	0.08739837398373984	1	0.0027624309392265192	0	0.0	0	0.0	T	5.065	0.197635	0.09652	0.070813	3.49E-4	ENSG00000177628	ENST00000427500;ENST00000368373;ENST00000327247;ENST00000536770;ENST00000402928	D;D;D;D	0.99474	-5.59;-5.62;-5.62;-5.97	3.32	-0.397	0.12423	.	1.116300	0.07210	U	0.859048	D	0.90789	0.7108	N	0.03608	-0.345	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	D	0.91133	0.4939	10	0.24483	T	0.36	.	2.0673	0.03605	0.2405:0.2836:0.0:0.4759	.	13;13;13	B7Z5G2;F5H241;P04062	.;.;GLCM_HUMAN	R	13	ENSP00000402577:K13R;ENSP00000357357:K13R;ENSP00000314508:K13R;ENSP00000445560:K13R	ENSP00000314508:K13R	K	-	2	0	GBA	153477122	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.370000	0.07523	0.052000	0.16007	0.482000	0.46254	AAG	T|0.979;C|0.021	0.021	strong		0.557	GBA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087204.1	NM_000157		C	155210498	T	C	155210498	3	2	22	1	0	0	0	0	1	0	0	0	6274	1609	56	3	1612	3	GBA	1	155210498	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1421571	155210498	94040123	281	3182											
HCN3	57657	hgsc.bcm.edu	37	chr1	155247408	155247408	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcagagcagcggccggcggcGggggccagcgaaggggcgac	7	0	22	12	6	0	1	0	0	0	1	0	3	0	1	2	7	3	2	2	7	1	0	rs184885598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155247408G>T	ENST00000368358.3	+	1	35	c.27G>T	c.(25-27)gcG>gcT	p.A9A	CLK2_ENST00000536801.1_5'UTR	NM_020897.2	NP_065948.1	Q9P1Z3	HCN3_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 3	9					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)			GGCCGGCGGCGGGGGCCAGCG	0.726													G|||	109	0.0217652	0.0794	0.0058	5008	,	,		10168	0.0		0.0	False		,,,				2504	0.0				p.A9A		Atlas-SNP	.											.	HCN3	74	.	0			c.G27T						PASS	.			200,3496		3,194,1651	3	5	4		27	-1.1	0	1		4	0,7522		0,0,3761	no	coding-synonymous	HCN3	NM_020897.1		3,194,5412	TT,TG,GG		0.0,5.4113,1.7828		9/775	155247408	200,11018	1848	3761	5609	SO:0001819	synonymous_variant	57657	exon1			GGCGGCGGGGGCC	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.27G>T	1.37:g.155247408G>T		2	0	0		13	8	0.615385	NM_020897	D3DV90|Q4VX12|Q8N6W6|Q9BWQ2	Silent	SNP	ENST00000368358.3	37	CCDS1108.1																																																																																			G|0.983;T|0.017	0.017	strong		0.726	HCN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087388.1	NM_020897		T	155247408	G	T	155247408	2	4	22	1	0	0	0	0	0	0	0	1	7007	1103	39	4		4	HCN3	1	155247408	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	36910	155247408	94003213	282	3183											
ASH1L	55870	hgsc.bcm.edu	37	chr1	155451343	155451343	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attattgatgtttgtactacAagaagccttaagcggttcct	11	15	8	7	1	0	2	0	1	0	1	1	2	1	2	2	1	4	3	2	1	6	7	rs114218266	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155451343A>C	ENST00000368346.3	-	3	1957	c.1318T>G	c.(1318-1320)Tgt>Ggt	p.C440G	ASH1L_ENST00000392403.3_Missense_Mutation_p.C440G|ASH1L_ENST00000548830.1_3'UTR			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	440					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)			TTTGTACTACAAGAAGCCTTA	0.423													A|||	103	0.0205671	0.0734	0.0058	5008	,	,		19464	0.002		0.0	False		,,,				2504	0.0				p.C440G		Atlas-SNP	.											.	ASH1L	279	.	0			c.T1318G						PASS	.	A	GLY/CYS	299,4107	155.5+/-188.7	12,275,1916	61	60	60		1318	3.6	1	1	dbSNP_132	60	2,8598	1.2+/-3.3	0,2,4298	yes	missense	ASH1L	NM_018489.2	159	12,277,6214	CC,CA,AA		0.0233,6.7862,2.3143	possibly-damaging	440/2965	155451343	301,12705	2203	4300	6503	SO:0001583	missense	55870	exon3			TACTACAAGAAGC	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.1318T>G	1.37:g.155451343A>C	ENSP00000357330:p.Cys440Gly	137	0	0		179	77	0.430168	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	37		35	0.016025641025641024	34	0.06910569105691057	1	0.0027624309392265192	0	0.0	0	0.0	A	15.65	2.897292	0.52121	0.067862	2.33E-4	ENSG00000116539	ENST00000368346;ENST00000392403	D;D	0.91407	-2.84;-2.83	4.73	3.6	0.41247	.	0.327762	0.30538	N	0.009409	T	0.74772	0.3760	N	0.14661	0.345	0.80722	D	1	P;P	0.50528	0.895;0.936	B;P	0.44477	0.264;0.451	T	0.78445	-0.2201	10	0.72032	D	0.01	.	7.8358	0.29369	0.8353:0.0:0.1647:0.0	.	440;440	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	G	440	ENSP00000357330:C440G;ENSP00000376204:C440G	ENSP00000357330:C440G	C	-	1	0	ASH1L	153717967	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.294000	0.59043	0.936000	0.37367	0.460000	0.39030	TGT	A|0.981;C|0.019	0.019	strong		0.423	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489		C	155451343	A	C	155451343	3	2	22	1	0	0	0	0	1	0	0	0	1041	130	5	5	7680	5	ASH1L	1	155451343	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	203935	155451343	93799278	283	3184											
YY1AP1	55249	hgsc.bcm.edu	37	chr1	155629982	155629982	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gccgcattgacaggctggatCatgttacagccaccgccaag	10	7	11	13	2	1	1	1	1	0	0	1	2	1	2	4	2	2	3	4	2	2	2	rs145852062	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155629982C>T	ENST00000295566.4	-	11	1880	c.1857G>A	c.(1855-1857)atG>atA	p.M619I	YY1AP1_ENST00000368340.5_Missense_Mutation_p.M691I|YY1AP1_ENST00000359205.5_Missense_Mutation_p.M562I|MSTO1_ENST00000538143.1_Intron|YY1AP1_ENST00000404643.1_Missense_Mutation_p.M553I|YY1AP1_ENST00000347088.5_Missense_Mutation_p.M573I|YY1AP1_ENST00000407221.1_Missense_Mutation_p.M542I|YY1AP1_ENST00000368330.2_Missense_Mutation_p.M573I|YY1AP1_ENST00000355499.4_Missense_Mutation_p.M573I|YY1AP1_ENST00000368339.5_Missense_Mutation_p.M711I|YY1AP1_ENST00000361831.5_Missense_Mutation_p.M562I|MSTO1_ENST00000452804.2_Intron|YY1AP1_ENST00000535662.1_Missense_Mutation_p.M419I|YY1AP1_ENST00000311573.5_Missense_Mutation_p.M542I	NM_001198906.1|NM_139118.2	NP_001185835.1|NP_620829.1	Q9H869	YYAP1_HUMAN	YY1 associated protein 1	619					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)					CAGGCTGGATCATGTTACAGC	0.537													C|||	100	0.0199681	0.0719	0.0072	5008	,	,		19458	0.0		0.0	False		,,,				2504	0.0				p.M711I		Atlas-SNP	.											.	YY1AP1	104	.	0			c.G2133A						PASS	.	C	,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET	286,4120	156.6+/-189.7	10,266,1927	87	80	83		,1521,1719,1857,1686,1659,2073,2133,1719,1719,1686,1686	2.5	1	1	dbSNP_134	83	2,8592	1.2+/-3.3	0,2,4295	no	utr-3,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	YY1AP1	NM_001198906.1,NM_139121.2,NM_139119.2,NM_139118.2,NM_018253.3,NM_001198905.1,NM_001198904.1,NM_001198903.1,NM_001198902.1,NM_001198901.1,NM_001198900.1,NM_001198899.1	,10,10,10,10,10,10,10,10,10,10,10	10,268,6222	TT,TC,CC		0.0233,6.4911,2.2154	,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	,507/685,573/751,619/797,562/740,553/731,691/869,711/889,573/751,573/751,562/740,562/740	155629982	288,12712	2203	4297	6500	SO:0001583	missense	55249	exon10			CTGGATCATGTTA	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.1857G>A	1.37:g.155629982C>T	ENSP00000295566:p.Met619Ile	291	1	0.00343643		320	162	0.50625	NM_001198903	B0QZ54|B4DMP2|B4E0I0|D3DV96|D3DV98|H7BY62|Q5VYZ1|Q5VYZ4|Q5VYZ7|Q7L4C3|Q7L5E2|Q8IXA6|Q8TEW5|Q8TF04|Q96HB6|Q9BQ64|Q9NV84	Missense_Mutation	SNP	ENST00000295566.4	37	CCDS1115.1	34	0.015567765567765568	31	0.06300813008130081	3	0.008287292817679558	0	0.0	0	0.0	c	13.31	2.198345	0.38806	0.064911	2.33E-4	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	0.23552	1.96;1.96;1.97;1.96;1.96;1.92;1.95;1.96;1.97;1.98;1.9;1.97	2.53	2.53	0.30540	.	0.744128	0.12619	N	0.453204	T	0.13457	0.0326	L	0.47716	1.5	0.80722	D	1	B;B;B;B;B	0.21905	0.009;0.013;0.031;0.062;0.053	B;B;B;B;B	0.34652	0.015;0.02;0.187;0.068;0.013	T	0.08207	-1.0733	10	0.16896	T	0.51	.	13.0809	0.59114	0.0:1.0:0.0:0.0	.	711;553;619;573;691	B4DMP2;Q9H869-4;Q9H869;Q9H869-2;Q5VYZ1	.;.;YYAP1_HUMAN;.;.	I	562;573;542;573;562;691;619;573;542;553;711;419	ENSP00000352134:M562I;ENSP00000347686:M573I;ENSP00000311138:M542I;ENSP00000316079:M573I;ENSP00000355298:M562I;ENSP00000357324:M691I;ENSP00000295566:M619I;ENSP00000357314:M573I;ENSP00000385791:M542I;ENSP00000385390:M553I;ENSP00000357323:M711I;ENSP00000437926:M419I	ENSP00000295566:M619I	M	-	3	0	YY1AP1	153896606	1.000000	0.71417	0.995000	0.50966	0.972000	0.66771	2.589000	0.46145	1.419000	0.47118	0.306000	0.20318	ATG	C|0.981;T|0.019	0.019	strong		0.537	YY1AP1-043	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000086027.1	NM_139118		T	155629982	C	T	155629982	3	4	22	1	0	0	0	0	1	0	0	0	17523	826	29	2	537	2	YY1AP1	1	155629982	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	178639	155629982	93620639	284	3185											
ARHGEF2	9181	hgsc.bcm.edu	37	chr1	155931630	155931630	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagctgataaataccctcGtccacattggacagcagctc	11	9	7	14	1	0	1	0	1	0	0	4	2	2	2	3	1	4	3	3	1	3	3	rs143812169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155931630G>A	ENST00000361247.4	-	11	1389	c.1290C>T	c.(1288-1290)gaC>gaT	p.D430D	ARHGEF2_ENST00000313695.7_Silent_p.D402D|ARHGEF2_ENST00000462460.2_Silent_p.D475D|ARHGEF2_ENST00000368315.4_Silent_p.D431D|ARHGEF2_ENST00000368316.1_Silent_p.D402D|ARHGEF2_ENST00000313667.4_Silent_p.D429D|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	430	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)					AAATACCCTCGTCCACATTGG	0.632													G|||	21	0.00419329	0.0136	0.0	5008	,	,		17097	0.0		0.0	False		,,,				2504	0.0031				p.D430D	Melanoma(178;35 2768 6610 28839)	Atlas-SNP	.											.	ARHGEF2	81	.	0			c.C1290T						PASS	.	G	,,	90,4316	73.6+/-111.7	1,88,2114	74	73	73		1290,1287,1206	4	1	1	dbSNP_134	73	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	ARHGEF2	NM_001162383.1,NM_001162384.1,NM_004723.3	,,	1,89,6413	AA,AG,GG		0.0116,2.0427,0.6997	,,	430/987,429/986,402/959	155931630	91,12915	2203	4300	6503	SO:0001819	synonymous_variant	9181	exon11			ACCCTCGTCCACA	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.1290C>T	1.37:g.155931630G>A		201	0	0		189	95	0.502645	NM_001162383	D3DVA6|O75142|Q15079|Q5VY92|Q8TDA3|Q8WUG4|Q9H023	Silent	SNP	ENST00000361247.4	37	CCDS53376.1																																																																																			G|0.995;A|0.005	0.005	strong		0.632	ARHGEF2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046204.2	NM_004723		A	155931630	G	A	155931630	2	1	22	1	0	0	0	0	0	0	0	1	903	1136	40	1		1	ARHGEF2	1	155931630	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	301648	155931630	93318991	285	3186											
ARHGEF2	9181	hgsc.bcm.edu	37	chr1	155935158	155935158	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgagggagtctgtggactgTgagaggatccggcgcagccc	7	8	17	9	2	1	2	0	2	1	1	2	6	2	5	2	4	1	1	2	4	0	1	rs149517516	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155935158T>C	ENST00000361247.4	-	6	615	c.516A>G	c.(514-516)tcA>tcG	p.S172S	ARHGEF2_ENST00000313695.7_Silent_p.S145S|ARHGEF2_ENST00000462460.2_Silent_p.S217S|ARHGEF2_ENST00000368315.4_Silent_p.S173S|ARHGEF2_ENST00000368316.1_Silent_p.S145S|ARHGEF2_ENST00000313667.4_Silent_p.S172S|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	172					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)					CTGTGGACTGTGAGAGGATCC	0.587													T|||	17	0.00339457	0.0129	0.0	5008	,	,		19917	0.0		0.0	False		,,,				2504	0.0				p.S172S	Melanoma(178;35 2768 6610 28839)	Atlas-SNP	.											.	ARHGEF2	81	.	0			c.A516G						PASS	.	T	,,	90,4316	73.6+/-111.7	1,88,2114	72	72	72		516,516,435	-11.3	0.3	1	dbSNP_134	72	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	ARHGEF2	NM_001162383.1,NM_001162384.1,NM_004723.3	,,	1,88,6414	CC,CT,TT		0.0,2.0427,0.692	,,	172/987,172/986,145/959	155935158	90,12916	2203	4300	6503	SO:0001819	synonymous_variant	9181	exon6			GGACTGTGAGAGG	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.516A>G	1.37:g.155935158T>C		158	0	0		170	87	0.511765	NM_001162383	D3DVA6|O75142|Q15079|Q5VY92|Q8TDA3|Q8WUG4|Q9H023	Silent	SNP	ENST00000361247.4	37	CCDS53376.1																																																																																			T|0.995;C|0.005	0.005	strong		0.587	ARHGEF2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046204.2	NM_004723		C	155935158	T	C	155935158	2	2	22	1	0	0	0	0	0	0	0	1	903	1683	59	3		3	ARHGEF2	1	155935158	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	3528	155935158	93315463	286	3187											
SSR2	6746	hgsc.bcm.edu	37	chr1	155988108	155988108	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcattccagacacaatgccAaagtcttctggagggaagga	14	7	11	9	0	2	1	0	0	2	1	3	4	3	4	2	3	2	1	2	3	3	2	rs34428308	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155988108A>G	ENST00000295702.4	-	3	278	c.207T>C	c.(205-207)ttT>ttC	p.F69F	SSR2_ENST00000480567.1_Silent_p.F69F|SSR2_ENST00000496742.1_Intron|SSR2_ENST00000529008.1_Silent_p.F69F	NM_003145.3	NP_003136.1	P43308	SSRB_HUMAN	signal sequence receptor, beta (translocon-associated protein beta)	69					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)					ACACAATGCCAAAGTCTTCTG	0.468													A|||	43	0.00858626	0.0318	0.0014	5008	,	,		20208	0.0		0.0	False		,,,				2504	0.0				p.F69F		Atlas-SNP	.											.	SSR2	20	.	0			c.T207C						PASS	.	A		164,4242	108.2+/-146.6	4,156,2043	114	105	108		207	1.1	1	1	dbSNP_126	108	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SSR2	NM_003145.3		4,157,6342	GG,GA,AA		0.0116,3.7222,1.2686		69/184	155988108	165,12841	2203	4300	6503	SO:0001819	synonymous_variant	6746	exon3			AATGCCAAAGTCT	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.207T>C	1.37:g.155988108A>G		61	0	0		66	37	0.560606	NM_003145	B2R9K9|D3DVA7|Q53HI0|Q5VY95|Q5VY96|Q6IB31|Q9BWE4	Silent	SNP	ENST00000295702.4	37	CCDS1126.1																																																																																			A|0.990;G|0.010	0.010	strong		0.468	SSR2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046172.2	NM_003145		G	155988108	A	G	155988108	2	3	22	1	0	0	0	0	0	0	0	1	15206	127	5	3		3	SSR2	1	155988108	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	52950	155988108	93262513	287	3188											
RAB25	57111	hgsc.bcm.edu	37	chr1	156039960	156039960	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgccctcccagaaatctttgCgaaggtgtccaagcagagac	11	8	10	12	1	1	2	0	0	1	2	3	4	3	2	3	1	3	1	3	1	3	1	rs115837676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156039960C>T	ENST00000361084.5	+	5	765	c.524C>T	c.(523-525)gCg>gTg	p.A175V		NM_020387.2	NP_065120.2	P57735	RAB25_HUMAN	RAB25, member RAS oncogene family	175					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)					GAAATCTTTGCGAAGGTGTCC	0.597													C|||	29	0.00579073	0.0212	0.0014	5008	,	,		18839	0.0		0.0	False		,,,				2504	0.0				p.A175V		Atlas-SNP	.											RAB25,NS,carcinoma,-1,1	RAB25	18	1	0			c.C524T						PASS	.	C	VAL/ALA	100,3904		2,96,1904	65	69	68		524	4.9	0.1	1	dbSNP_132	68	0,8350		0,0,4175	no	missense	RAB25	NM_020387.2	64	2,96,6079	TT,TC,CC		0.0,2.4975,0.8095	benign	175/214	156039960	100,12254	2002	4175	6177	SO:0001583	missense	57111	exon5			TCTTTGCGAAGGT	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.524C>T	1.37:g.156039960C>T	ENSP00000354376:p.Ala175Val	331	1	0.00302115		317	157	0.495268	NM_020387	Q5VYA2|Q8NG24|Q96GB1|Q9BT12	Missense_Mutation	SNP	ENST00000361084.5	37	CCDS41413.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	C	13.90	2.375470	0.42105	0.024975	0.0	ENSG00000132698	ENST00000361084	T	0.80033	-1.33	5.85	4.94	0.65067	.	0.395029	0.26800	N	0.022433	T	0.48370	0.1496	N	0.11560	0.145	0.09310	N	1	B	0.17465	0.022	B	0.09377	0.004	T	0.50533	-0.8817	10	0.87932	D	0	.	12.4852	0.55868	0.1671:0.8329:0.0:0.0	.	175	P57735	RAB25_HUMAN	V	175	ENSP00000354376:A175V	ENSP00000354376:A175V	A	+	2	0	RAB25	154306584	0.001000	0.12720	0.130000	0.21974	0.895000	0.52256	0.961000	0.29267	1.475000	0.48197	-0.152000	0.13540	GCG	C|0.996;T|0.004	0.004	strong		0.597	RAB25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046185.1			T	156039960	C	T	156039960	3	4	22	1	0	0	0	0	1	0	0	0	12927	768	27	1	542	1	RAB25	1	156039960	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	51852	156039960	93210661	288	3189											
CCT3	7203	hgsc.bcm.edu	37	chr1	156281999	156281999	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctctggtcggctgactatccGggccccacaggctctaatgg	6	9	12	14	2	2	1	0	1	2	0	4	1	3	1	3	5	0	2	3	5	2	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156281999G>A	ENST00000295688.3	-	11	1268	c.988C>T	c.(988-990)Cgg>Tgg	p.R330W	CCT3_ENST00000368261.3_Missense_Mutation_p.R285W|CCT3_ENST00000472765.2_Missense_Mutation_p.R285W|CCT3_ENST00000368259.2_Missense_Mutation_p.R292W	NM_005998.4	NP_005989.3	P49368	TCPG_HUMAN	chaperonin containing TCP1, subunit 3 (gamma)	330					'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)					CTGACTATCCGGGCCCCACAG	0.468																																					p.R330W		Atlas-SNP	.											.	CCT3	61	.	0			c.C988T						PASS	.						57	61	60					1																	156281999		2203	4300	6503	SO:0001583	missense	7203	exon11			CTATCCGGGCCCC	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.988C>T	1.37:g.156281999G>A	ENSP00000295688:p.Arg330Trp	86	0	0		92	48	0.521739	NM_005998	A6NE14|Q5SZY1|Q9BR64	Missense_Mutation	SNP	ENST00000295688.3	37	CCDS1140.2	.	.	.	.	.	.	.	.	.	.	G	27.7	4.856417	0.91355	.	.	ENSG00000163468	ENST00000295688;ENST00000368259;ENST00000368261;ENST00000472765	T;T;T;T	0.80214	-1.35;-1.35;-1.35;-1.35	6.15	5.24	0.73138	.	0.000000	0.85682	D	0.000000	D	0.88822	0.6541	M	0.88512	2.96	0.58432	D	0.999999	D;D;D	0.76494	0.999;0.997;0.997	D;D;D	0.69307	0.963;0.949;0.949	D	0.91190	0.4983	10	0.72032	D	0.01	-15.521	14.8519	0.70303	0.0:0.0:0.8555:0.1445	.	292;329;330	P49368-2;E9PAQ6;P49368	.;.;TCPG_HUMAN	W	330;292;285;285	ENSP00000295688:R330W;ENSP00000357242:R292W;ENSP00000357244:R285W;ENSP00000431543:R285W	ENSP00000295688:R330W	R	-	1	2	CCT3	154548623	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.908000	0.87438	1.610000	0.50200	0.643000	0.83706	CGG	.	.	none		0.468	CCT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060602.3	NM_005998		A	156281999	G	A	156281999	3	1	22	1	0	0	0	0	1	0	0	0	2956	1115	39	1	665	1	CCT3	1	156281999	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	242039	156281999	92968622	289	3190											
C1orf61	10485	hgsc.bcm.edu	37	chr1	156377720	156377720	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caccgttctgtacacctggtGgagattccacaatggcttgt	8	12	10	11	1	1	1	0	0	1	1	2	2	2	1	3	3	1	3	3	3	2	4	rs141938076	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156377720G>A	ENST00000368243.1	-	5	335	c.219C>T	c.(217-219)tcC>tcT	p.S73S	C1orf61_ENST00000488498.2_5'UTR	NM_006365.1	NP_006356.1	Q13536	CROC4_HUMAN	chromosome 1 open reading frame 61	73						nucleus (GO:0005634)				large_intestine(2)|lung(2)|skin(1)	5	Hepatocellular(266;0.158)					TACACCTGGTGGAGATTCCAC	0.582													G|||	12	0.00239617	0.0083	0.0014	5008	,	,		19992	0.0		0.0	False		,,,				2504	0.0				p.S73S		Atlas-SNP	.											.	C1orf61	15	.	0			c.C219T						PASS	.	G		24,4382		0,24,2179	114	86	96		219	-0.4	0	1	dbSNP_134	96	0,8594		0,0,4297	no	coding-synonymous	C1orf61	NM_006365.1		0,24,6476	AA,AG,GG		0.0,0.5447,0.1846		73/157	156377720	24,12976	2203	4297	6500	SO:0001819	synonymous_variant	10485	exon5			CCTGGTGGAGATT		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.219C>T	1.37:g.156377720G>A		106	0	0		124	53	0.427419	NM_006365	B1ALL5|B1ALL8	Silent	SNP	ENST00000368243.1	37	CCDS1142.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	3.575	-0.086754	0.07097	0.005447	0.0	ENSG00000125462	ENST00000368242	.	.	.	3.36	-0.454	0.12197	.	.	.	.	.	T	0.12305	0.0299	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.32719	-0.9896	4	.	.	.	.	5.8054	0.18438	0.5029:0.0:0.4971:0.0	.	.	.	.	L	105	.	.	P	-	2	0	C1orf61	154644344	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.003000	0.13083	-0.069000	0.12931	0.542000	0.68232	CCA	G|0.998;A|0.002	0.002	strong		0.582	C1orf61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075988.1	NM_006365		A	156377720	G	A	156377720	2	1	22	1	0	0	0	0	0	0	0	1	2054	1335	47	2		2	C1orf61	1	156377720	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	95721	156377720	92872901	290	3191											
IQGAP3	128239	hgsc.bcm.edu	37	chr1	156539169	156539169	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttcctggactccgctcaccGcttggcctcctccagccggc	3	9	9	20	3	1	0	1	0	0	0	5	1	5	1	7	3	1	2	7	3	0	2	rs370931618		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156539169G>A	ENST00000361170.2	-	2	134	c.124C>T	c.(124-126)Cgc>Tgc	p.R42C		NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	42	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				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)					TCCGCTCACCGCTTGGCCTCC	0.557													G|||	1	0.000199681	0.0008	0.0	5008	,	,		13122	0.0		0.0	False		,,,				2504	0.0				p.R42C		Atlas-SNP	.											.	IQGAP3	146	.	0			c.C124T						PASS	.	G	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	43	36	39		124	5	1	1		39	0,8600		0,0,4300	no	missense-near-splice	IQGAP3	NM_178229.4	180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	42/1632	156539169	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	128239	exon2			CTCACCGCTTGGC	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.125+1C>T	1.37:g.156539169G>A		153	0	0		107	43	0.401869	NM_178229	Q5T3H8	Missense_Mutation	SNP	ENST00000361170.2	37	CCDS1144.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.053545	0.75960	2.27E-4	0.0	ENSG00000183856	ENST00000361170	D	0.95554	-3.74	4.97	4.97	0.65823	Calponin homology domain (5);	0.000000	0.85682	D	0.000000	D	0.97139	0.9065	M	0.72353	2.195	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97567	1.0102	10	0.72032	D	0.01	-13.4997	16.978	0.86319	0.0:0.0:1.0:0.0	.	42	Q86VI3	IQGA3_HUMAN	C	42	ENSP00000354451:R42C	ENSP00000354451:R42C	R	-	1	0	IQGAP3	154805793	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	2.887000	0.48586	2.592000	0.87571	0.467000	0.42956	CGC	.	.	none		0.557	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229	Missense_Mutation	A	156539169	G	A	156539169	5	1	22	1	0	0	0	0	0	0	1	0	7825	1101	38	1	4919	1	IQGAP3	1	156539169	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	161449	156539169	92711452	291	3192											
TTC24	164118	hgsc.bcm.edu	37	chr1	156555577	156555577	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccacgtttaccaagcacaCgccctgcagagggacagtcc	10	5	9	17	2	0	1	0	0	0	1	1	2	1	2	5	1	3	3	5	1	2	2	rs147693801	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156555577C>T	ENST00000368237.3	+	8	1529	c.1529C>T	c.(1528-1530)aCg>aTg	p.T510M	TTC24_ENST00000368236.3_Missense_Mutation_p.T510M|TTC24_ENST00000478081.1_3'UTR|AL365181.1_ENST00000581084.1_RNA			A2A3L6	TTC24_HUMAN	tetratricopeptide repeat domain 24	510										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)					ACCAAGCACACGCCCTGCAGA	0.517													C|||	55	0.0109824	0.0393	0.0029	5008	,	,		20692	0.0		0.001	False		,,,				2504	0.0				p.T510M		Atlas-SNP	.											TTC24,right_upper_lobe,carcinoma,-1,1	TTC24	46	1	0			c.C1529T						PASS	.	C	MET/THR	122,4138		3,116,2011	117	119	118		1529	-0.6	0	1	dbSNP_134	118	0,8462		0,0,4231	yes	missense	TTC24	NM_001105669.2	81	3,116,6242	TT,TC,CC		0.0,2.8638,0.959	benign	510/583	156555577	122,12600	2130	4231	6361	SO:0001583	missense	164118	exon9			AGCACACGCCCTG		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.1529C>T	1.37:g.156555577C>T	ENSP00000357220:p.Thr510Met	123	0	0		155	65	0.419355	NM_001105669	Q5T3H7	Missense_Mutation	SNP	ENST00000368237.3	37	CCDS53379.1	13|13	0.005952380952380952|0.005952380952380952	12|12	0.024390243902439025|0.024390243902439025	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	C|C	4.199|4.199	0.035700|0.035700	0.08148|0.08148	0.028638|0.028638	0.0|0.0	ENSG00000187862|ENSG00000187862	ENST00000340086|ENST00000368236;ENST00000368237	.|T;T	.|0.26223	.|1.75;1.75	3.22|3.22	-0.612|-0.612	0.11597|0.11597	.|.	.|17.220800	.|0.00397	.|N	.|0.000056	T|T	0.03915|0.03915	0.0110|0.0110	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|T	0.29971|0.29971	-0.9994|-0.9994	5|10	.|0.48119	.|T	.|0.1	.|.	3.0131|3.0131	0.06051|0.06051	0.0:0.2819:0.2328:0.4852|0.0:0.2819:0.2328:0.4852	.|.	.|510	.|A2A3L6	.|TTC24_HUMAN	C|M	283|510	.|ENSP00000357219:T510M;ENSP00000357220:T510M	.|ENSP00000357219:T510M	R|T	+|+	1|2	0|0	TTC24|TTC24	154822201|154822201	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.015000|0.015000	0.08874|0.08874	0.040000|0.040000	0.13905|0.13905	-0.118000|-0.118000	0.11851|0.11851	-0.379000|-0.379000	0.06801|0.06801	CGC|ACG	C|0.994;T|0.006	0.006	strong		0.517	TTC24-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158547.1	XM_089384		T	156555577	C	T	156555577	3	4	22	1	0	0	0	0	1	0	0	0	16707	536	19	1	1559	1	TTC24	1	156555577	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	16408	156555577	92695044	292	3193											
GPATCH4	54865	hgsc.bcm.edu	37	chr1	156565389	156565389	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccttcttgatgtcgccttttCttcttcttgctttttctgat	2	23	5	11	1	5	2	0	2	5	0	6	2	5	2	2	0	1	1	2	0	0	9	rs145851878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156565389C>T	ENST00000438976.2	-	8	774	c.744G>A	c.(742-744)aaG>aaA	p.K248K	GPATCH4_ENST00000368232.4_Silent_p.K243K|GPATCH4_ENST00000497287.1_5'Flank			Q5T3I0	GPTC4_HUMAN	G patch domain containing 4	243							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)					GTCGCCTTTTCTTCTTCTTGC	0.468													C|||	68	0.0135783	0.0499	0.0029	5008	,	,		22178	0.0		0.0	False		,,,				2504	0.0				p.K248K		Atlas-SNP	.											.	GPATCH4	34	.	0			c.G744A						PASS	.	C	,	172,4234	115.4+/-153.4	4,164,2035	332	314	320		744,729	1	0.4	1	dbSNP_134	320	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	GPATCH4	NM_015590.3,NM_182679.2	,	4,164,6335	TT,TC,CC		0.0,3.9038,1.3225	,	248/376,243/371	156565389	172,12834	2203	4300	6503	SO:0001819	synonymous_variant	54865	exon8			CCTTTTCTTCTTC	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.744G>A	1.37:g.156565389C>T		237	0	0		284	130	0.457746	NM_015590	Q5T3I1|Q6ZUE7|Q8IWG8|Q9NXH4	Silent	SNP	ENST00000438976.2	37	CCDS44245.1																																																																																			C|0.988;T|0.012	0.012	strong		0.468	GPATCH4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386947.1	NM_017725		T	156565389	C	T	156565389	2	4	22	1	0	0	0	0	0	0	0	1	6601	912	32	2		2	GPATCH4	1	156565389	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	9812	156565389	92685232	293	3194											
GPATCH4	54865	hgsc.bcm.edu	37	chr1	156567847	156567847	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttcacaaacttctgatacaGcaagttgggcttgggatgat	11	12	10	8	0	2	2	1	2	1	0	2	3	2	3	0	2	3	3	0	2	3	5	rs141345590	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156567847G>C	ENST00000438976.2	-	5	358	c.328C>G	c.(328-330)Ctg>Gtg	p.L110V	GPATCH4_ENST00000368232.4_Missense_Mutation_p.L105V|GPATCH4_ENST00000334588.7_Missense_Mutation_p.L59V|GPATCH4_ENST00000497287.1_5'UTR			Q5T3I0	GPTC4_HUMAN	G patch domain containing 4	105							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)					TTCTGATACAGCAAGTTGGGC	0.463													G|||	68	0.0135783	0.0499	0.0029	5008	,	,		21358	0.0		0.0	False		,,,				2504	0.0				p.L110V		Atlas-SNP	.											.	GPATCH4	34	.	0			c.C328G						PASS	.	G	VAL/LEU,VAL/LEU	171,4235	115.0+/-153.0	4,163,2036	145	141	142		328,313	2.3	1	1	dbSNP_134	142	0,8600		0,0,4300	yes	missense,missense	GPATCH4	NM_015590.3,NM_182679.2	32,32	4,163,6336	CC,CG,GG		0.0,3.8811,1.3148	probably-damaging,probably-damaging	110/376,105/371	156567847	171,12835	2203	4300	6503	SO:0001583	missense	54865	exon5			GATACAGCAAGTT	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.328C>G	1.37:g.156567847G>C	ENSP00000396441:p.Leu110Val	175	0	0		182	91	0.5	NM_015590	Q5T3I1|Q6ZUE7|Q8IWG8|Q9NXH4	Missense_Mutation	SNP	ENST00000438976.2	37	CCDS44245.1	15	0.006868131868131868	14	0.028455284552845527	1	0.0027624309392265192	0	0.0	0	0.0	G	16.61	3.172437	0.57584	0.038811	0.0	ENSG00000160818	ENST00000368232;ENST00000368229;ENST00000438976;ENST00000334588	.	.	.	5.47	2.33	0.28932	.	0.073719	0.53938	D	0.000052	T	0.36496	0.0969	L	0.57130	1.785	0.41650	D	0.989123	D;D	0.58268	0.982;0.982	P;P	0.51266	0.664;0.664	T	0.31696	-0.9934	9	0.42905	T	0.14	-1.1016	3.0104	0.06043	0.2718:0.0:0.5275:0.2007	.	110;105	E9PAV9;Q5T3I0	.;GPTC4_HUMAN	V	105;105;110;59	.	ENSP00000334793:L59V	L	-	1	2	GPATCH4	154834471	1.000000	0.71417	0.994000	0.49952	0.998000	0.95712	1.145000	0.31577	0.837000	0.34925	0.655000	0.94253	CTG	G|0.988;C|0.012	0.012	strong		0.463	GPATCH4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386947.1	NM_017725		C	156567847	G	C	156567847	3	2	22	1	0	0	0	0	1	0	0	0	6601	962	34	4	815	4	GPATCH4	1	156567847	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2458	156567847	92682774	294	3195											
HAPLN2	60484	hgsc.bcm.edu	37	chr1	156593928	156593928	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acggcatcgaggacgagagcGtggcgctgaccttgagcttg	8	7	16	10	5	0	3	0	2	0	1	1	6	0	4	1	3	2	3	1	3	0	2	rs149573918	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156593928G>T	ENST00000255039.1	+	4	822	c.415G>T	c.(415-417)Gtg>Ttg	p.V139L	HAPLN2_ENST00000494218.1_3'UTR	NM_021817.2	NP_068589.1	Q9GZV7	HPLN2_HUMAN	hyaluronan and proteoglycan link protein 2	139	Ig-like V-type.				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)					GGACGAGAGCGTGGCGCTGAC	0.692													G|||	68	0.0135783	0.0499	0.0029	5008	,	,		14129	0.0		0.0	False		,,,				2504	0.0				p.V139L		Atlas-SNP	.											.	HAPLN2	20	.	0			c.G415T						PASS	.	G	LEU/VAL	162,4192		4,154,2019	42	36	38		415	1.9	1	1	dbSNP_134	38	2,8482		0,2,4240	yes	missense	HAPLN2	NM_021817.2	32	4,156,6259	TT,TG,GG		0.0236,3.7207,1.2775	benign	139/341	156593928	164,12674	2177	4242	6419	SO:0001583	missense	60484	exon4			GAGAGCGTGGCGC	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.415G>T	1.37:g.156593928G>T	ENSP00000255039:p.Val139Leu	170	0	0		213	99	0.464789	NM_021817	Q5T3J0	Missense_Mutation	SNP	ENST00000255039.1	37	CCDS1148.1	16	0.007326007326007326	15	0.03048780487804878	1	0.0027624309392265192	0	0.0	0	0.0	G	13.59	2.283640	0.40394	0.037207	2.36E-4	ENSG00000132702	ENST00000255039;ENST00000544775;ENST00000456112	T;T	0.26957	1.7;1.7	4.04	1.89	0.25635	Immunoglobulin subtype (1);Immunoglobulin-like (1);	0.225805	0.35838	N	0.002959	T	0.05090	0.0136	N	0.17379	0.485	0.32704	N	0.512539	B	0.10296	0.003	B	0.18871	0.023	T	0.29731	-1.0002	10	0.27082	T	0.32	-15.0291	7.6488	0.28336	0.0:0.1512:0.5635:0.2853	.	139	Q9GZV7	HPLN2_HUMAN	L	139;112;139	ENSP00000255039:V139L;ENSP00000388835:V139L	ENSP00000255039:V139L	V	+	1	0	HAPLN2	154860552	0.867000	0.29959	1.000000	0.80357	0.971000	0.66376	0.920000	0.28705	0.995000	0.38917	0.655000	0.94253	GTG	G|0.986;T|0.014	0.014	strong		0.692	HAPLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081039.1	NM_021817		T	156593928	G	T	156593928	3	4	22	1	0	0	0	0	1	0	0	0	6964	1145	40	4	421	4	HAPLN2	1	156593928	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	26081	156593928	92656693	295	3196											
BCAN	63827	hgsc.bcm.edu	37	chr1	156621251	156621251	+	Missense_Mutation	SNP	C	C	T																															ctttcctcctgccacagactCggcccagccttctgccatcc																								rs12065791	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156621251C>T	ENST00000329117.5	+	7	1403	c.1067C>T	c.(1066-1068)tCg>tTg	p.S356L	BCAN_ENST00000361588.5_Missense_Mutation_p.S356L|RP11-284F21.7_ENST00000448869.1_RNA	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	356			S -> L (in dbSNP:rs12065791).		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)					GCCACAGACTCGGCCCAGCCT	0.557													C|||	237	0.0473243	0.1687	0.0173	5008	,	,		18259	0.0		0.002	False		,,,				2504	0.0				p.S356L		Atlas-SNP	.											.	BCAN	174	.	0			c.C1067T						PASS	.	C	LEU/SER,LEU/SER	656,3750	268.0+/-268.2	43,570,1590	47	44	45		1067,1067	5.2	1	1	dbSNP_120	45	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	BCAN	NM_021948.4,NM_198427.1	145,145	43,574,5886	TT,TC,CC		0.0465,14.8888,5.0746	benign,benign	356/912,356/672	156621251	660,12346	2203	4300	6503	SO:0001583	missense	63827	exon7			CAGACTCGGCCCA	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.1067C>T	1.37:g.156621251C>T	ENSP00000331210:p.Ser356Leu	35	0	0		50	26	0.52	NM_198427	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Missense_Mutation	SNP	ENST00000329117.5	37	CCDS1149.1	88	0.040293040293040296	79	0.16056910569105692	7	0.019337016574585635	0	0.0	2	0.002638522427440633	C	9.099	1.003544	0.19121	0.148888	4.65E-4	ENSG00000132692	ENST00000329117;ENST00000361588	T;T	0.11495	2.77;2.77	5.17	5.17	0.71159	C-type lectin fold (1);C-type lectin-like (1);	0.474289	0.19636	N	0.109545	T	0.02533	0.0077	L	0.27053	0.805	0.32632	N	0.521804	P;B	0.42518	0.782;0.145	B;B	0.29077	0.098;0.041	T	0.45190	-0.9278	10	0.33141	T	0.24	-10.544	11.8228	0.52250	0.0:0.8238:0.1762:0.0	rs12065791;rs12065791	356;356	Q96GW7;Q96GW7-2	PGCB_HUMAN;.	L	356	ENSP00000331210:S356L;ENSP00000354925:S356L	ENSP00000331210:S356L	S	+	2	0	BCAN	154887875	0.998000	0.40836	0.995000	0.50966	0.125000	0.20455	3.340000	0.52143	2.692000	0.91855	0.655000	0.94253	TCG	C|0.949;T|0.051	0.051	strong		0.557	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948		T	156621251	C	T	156621251	3	4	22	1	0	0	0	0	1	0	0	0	1345	893	31	1	1089	1	BCAN	1	156621251	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	27323	156621251	92629370	296	3197	46	2									
BCAN	63827	hgsc.bcm.edu	37	chr1	156621252	156621252	+	Silent	SNP	G	G	A																															tttcctcctgccacagactcGgcccagccttctgccatccc																								rs146863260	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156621252G>A	ENST00000329117.5	+	7	1404	c.1068G>A	c.(1066-1068)tcG>tcA	p.S356S	BCAN_ENST00000361588.5_Silent_p.S356S|RP11-284F21.7_ENST00000448869.1_RNA	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	356			S -> L (in dbSNP:rs12065791).		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)					CCACAGACTCGGCCCAGCCTT	0.562													G|||	19	0.00379393	0.0144	0.0	5008	,	,		18343	0.0		0.0	False		,,,				2504	0.0				p.S356S		Atlas-SNP	.											.	BCAN	174	.	0			c.G1068A						PASS	.	G	,	62,4344	58.7+/-95.3	0,62,2141	47	44	45		1068,1068	1.5	0.9	1	dbSNP_134	45	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	BCAN	NM_021948.4,NM_198427.1	,	0,62,6441	AA,AG,GG		0.0,1.4072,0.4767	,	356/912,356/672	156621252	62,12944	2203	4300	6503	SO:0001819	synonymous_variant	63827	exon7			AGACTCGGCCCAG	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.1068G>A	1.37:g.156621252G>A		35	0	0		51	24	0.470588	NM_198427	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Silent	SNP	ENST00000329117.5	37	CCDS1149.1																																																																																			G|0.994;A|0.006	0.006	strong		0.562	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948		A	156621252	G	A	156621252	2	1	22	1	0	0	0	0	0	0	0	1	1345	1103	39	1		1	BCAN	1	156621252	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1	156621252	92629369	297	3198	46	2									
INSRR	3645	hgsc.bcm.edu	37	chr1	156814884	156814884	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctactgtggggcatggtgcgCgcaaagacgaaggtggcggc	8	6	18	9	4	0	1	0	0	0	1	0	2	0	1	0	6	2	2	0	6	3	1	rs149474857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156814884C>T	ENST00000368195.3	-	12	2817	c.2421G>A	c.(2419-2421)gcG>gcA	p.A807A	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	807					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)					GCATGGTGCGCGCAAAGACGA	0.617													C|||	36	0.0071885	0.0272	0.0	5008	,	,		16306	0.0		0.0	False		,,,				2504	0.0				p.A807A		Atlas-SNP	.											.	INSRR	309	.	0			c.G2421A						PASS	.	C	,	104,4302	78.3+/-116.7	0,104,2099	23	22	22		,2421	-4.1	0.9	1	dbSNP_134	22	1,8599		0,1,4299	no	intron,coding-synonymous	INSRR,NTRK1	NM_001007792.1,NM_014215.2	,	0,105,6398	TT,TC,CC		0.0116,2.3604,0.8073	,	,807/1298	156814884	105,12901	2203	4300	6503	SO:0001819	synonymous_variant	3645	exon12			GGTGCGCGCAAAG	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.2421G>A	1.37:g.156814884C>T		83	0	0		115	56	0.486957	NM_014215	O60724|Q5VZS3	Silent	SNP	ENST00000368195.3	37	CCDS1160.1																																																																																			C|0.991;T|0.009	0.009	strong		0.617	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215		T	156814884	C	T	156814884	2	4	22	1	0	0	0	0	0	0	0	1	7783	755	27	1		1	INSRR	1	156814884	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	193632	156814884	92435737	298	3199											
NTRK1	4914	hgsc.bcm.edu	37	chr1	156838432	156838432	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagctggagcagtcagccaCggtgatggtgagaagacctt	11	7	15	8	1	1	4	1	2	0	3	1	6	1	5	2	3	3	2	2	3	1	1	rs55909005	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156838432C>T	ENST00000524377.1	+	6	751	c.710C>T	c.(709-711)aCg>aTg	p.T237M	NTRK1_ENST00000392302.2_Missense_Mutation_p.T207M|NTRK1_ENST00000368196.3_Missense_Mutation_p.T237M|NTRK1_ENST00000358660.3_Missense_Mutation_p.T237M	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	237	Ig-like C2-type 1.		T -> M (in dbSNP:rs55909005). {ECO:0000269|PubMed:17344846}.		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)	CAGTCAGCCACGGTGATGGTG	0.637			T	"TPM3, TPR, TFG"	papillary thyroid					TSP Lung(10;0.080)			C|||	87	0.0173722	0.0598	0.0115	5008	,	,		15696	0.0		0.0	False		,,,				2504	0.0				p.T237M		Atlas-SNP	.		Dom	yes		1	1q21-q22	4914	"neurotrophic tyrosine kinase, receptor, type 1"		E	.	NTRK1	287	.	0			c.C710T						PASS	.	C	MET/THR,MET/THR,MET/THR	196,3896		4,188,1854	14	14	14		620,710,710	2.5	0.5	1	dbSNP_129	14	5,8021		0,5,4008	yes	missense,missense,missense	NTRK1	NM_001007792.1,NM_001012331.1,NM_002529.3	81,81,81	4,193,5862	TT,TC,CC		0.0623,4.7898,1.6587	probably-damaging,probably-damaging,probably-damaging	207/761,237/791,237/797	156838432	201,11917	2046	4013	6059	SO:0001583	missense	4914	exon6			CAGCCACGGTGAT	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.710C>T	1.37:g.156838432C>T	ENSP00000431418:p.Thr237Met	93	0	0		103	53	0.514563	NM_001012331	B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Missense_Mutation	SNP	ENST00000524377.1	37	CCDS1161.1	27	0.012362637362637362	22	0.044715447154471545	5	0.013812154696132596	0	0.0	0	0.0	C	13.13	2.144047	0.37825	0.047898	6.23E-4	ENSG00000198400	ENST00000392302;ENST00000368196;ENST00000524377;ENST00000358660	T;T;T;T	0.16073	2.37;2.37;2.37;2.37	4.38	2.47	0.30058	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.432209	0.19724	N	0.107503	T	0.16514	0.0397	L	0.52573	1.65	0.32458	N	0.544507	P;D;D;D	0.89917	0.791;1.0;1.0;0.998	B;P;D;P	0.85130	0.248;0.806;0.997;0.886	T	0.03354	-1.1045	10	0.35671	T	0.21	.	6.7504	0.23483	0.0:0.782:0.0:0.218	rs55909005	237;237;237;207	A8K3Z4;P04629-2;P04629;A6NF12	.;.;NTRK1_HUMAN;.	M	207;237;237;237	ENSP00000376120:T207M;ENSP00000357179:T237M;ENSP00000431418:T237M;ENSP00000351486:T237M	ENSP00000351486:T237M	T	+	2	0	NTRK1	155105056	0.172000	0.23043	0.531000	0.27976	0.749000	0.42624	0.489000	0.22387	0.577000	0.29470	0.462000	0.41574	ACG	C|0.987;T|0.013	0.013	strong		0.637	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392279.1	NM_002529		T	156838432	C	T	156838432	3	4	22	1	0	0	0	0	1	0	0	0	10715	536	19	1	862	1	NTRK1	1	156838432	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	23548	156838432	92412189	299	3200											
C1orf92	149499	hgsc.bcm.edu	37	chr1	156902678	156902678	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccacaatgtcctgcgtacGccataatccaggagctgatg	10	8	9	14	2	0	1	0	1	0	0	2	2	2	2	5	1	3	2	5	1	3	2	rs11264585	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156902678G>A	ENST00000337428.7	+	15	1751	c.1597G>A	c.(1597-1599)Gcc>Acc	p.A533T	ARHGEF11_ENST00000487682.1_5'Flank|LRRC71_ENST00000490146.1_3'UTR	NM_144702.2	NP_653303.2	Q8N4P6	LRC71_HUMAN	leucine rich repeat containing 71	533			A -> T (in dbSNP:rs11264585).							endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|stomach(1)	12						TCCTGCGTACGCCATAATCCA	0.498													G|||	121	0.0241613	0.0862	0.0101	5008	,	,		18240	0.0		0.0	False		,,,				2504	0.0				p.A533T		Atlas-SNP	.											.	LRRC71	33	.	0			c.G1597A						PASS	.	G	THR/ALA	265,3689		9,247,1721	48	46	47		1597	-11	0	1	dbSNP_120	47	3,8317		0,3,4157	yes	missense	LRRC71	NM_144702.2	58	9,250,5878	AA,AG,GG		0.0361,6.7021,2.1835	benign	533/560	156902678	268,12006	1977	4160	6137	SO:0001583	missense	149499	exon15			GCGTACGCCATAA	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.1597G>A	1.37:g.156902678G>A	ENSP00000336661:p.Ala533Thr	98	0	0		115	57	0.495652	NM_144702	Q96M24	Missense_Mutation	SNP	ENST00000337428.7	37	CCDS44249.1	34	0.015567765567765568	28	0.056910569105691054	6	0.016574585635359115	0	0.0	0	0.0	G	1.828	-0.470466	0.04445	0.067021	3.61E-4	ENSG00000160838	ENST00000337428	T	0.18810	2.19	5.48	-11.0	0.00169	.	1.768440	0.02711	N	0.112830	T	0.01695	0.0054	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22417	-1.0217	10	0.12766	T	0.61	-0.0908	4.8021	0.13301	0.2877:0.1877:0.4323:0.0923	rs11264585;rs52828876;rs11264585	533	Q8N4P6	LRC71_HUMAN	T	533	ENSP00000336661:A533T	ENSP00000336661:A533T	A	+	1	0	LRRC71	155169302	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.651000	0.05372	-2.183000	0.00763	-1.149000	0.01842	GCC	G|0.981;A|0.019	0.019	strong		0.498	LRRC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098961.1	NM_144702		A	156902678	G	A	156902678	3	1	22	1	0	0	0	0	1	0	0	0	2071	1087	38	1	1655	1	C1orf92	1	156902678	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	64246	156902678	92347943	300	3201											
FCRL5	83416	hgsc.bcm.edu	37	chr1	157514685	157514685	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttccttatatccagtacaGcgatatgcaccattgtcctt	9	15	5	12	1	0	0	0	0	0	0	3	1	3	0	4	0	3	2	4	0	4	7	rs11803066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:157514685G>A	ENST00000361835.3	-	4	652	c.495C>T	c.(493-495)cgC>cgT	p.R165R	FCRL5_ENST00000368190.3_Silent_p.R165R|FCRL5_ENST00000368189.3_Silent_p.R165R|FCRL5_ENST00000368191.3_Silent_p.R80R|FCRL5_ENST00000356953.4_Silent_p.R165R	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	165					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)				ATCCAGTACAGCGATATGCAC	0.368													G|||	72	0.014377	0.053	0.0029	5008	,	,		21706	0.0		0.0	False		,,,				2504	0.0				p.R165R		Atlas-SNP	.											.	FCRL5	177	.	0			c.C495T						PASS	.	G	,	233,4173	138.8+/-174.5	5,223,1975	153	142	146		495,495	-3.5	0	1	dbSNP_120	146	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	FCRL5	NM_001195388.1,NM_031281.2	,	5,223,6275	AA,AG,GG		0.0,5.2882,1.7915	,	165/999,165/978	157514685	233,12773	2203	4300	6503	SO:0001819	synonymous_variant	83416	exon4			AGTACAGCGATAT	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.495C>T	1.37:g.157514685G>A		155	0	0		190	103	0.542105	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Silent	SNP	ENST00000361835.3	37	CCDS1165.1																																																																																			G|0.982;A|0.018	0.018	strong		0.368	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281		A	157514685	G	A	157514685	2	1	22	1	0	0	0	0	0	0	0	1	5806	958	34	2		2	FCRL5	1	157514685	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	612007	157514685	91735936	301	3202											
FCRL2	79368	hgsc.bcm.edu	37	chr1	157736673	157736673	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgtggaacaaggcatacaaCagcaaagcaacaccagtgaa	18	5	9	9	0	0	1	0	1	0	0	0	2	0	2	1	2	6	3	1	2	7	2	rs34445670	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:157736673C>T	ENST00000361516.3	-	7	1299	c.1251G>A	c.(1249-1251)ctG>ctA	p.L417L	FCRL2_ENST00000469986.1_Silent_p.L164L|FCRL2_ENST00000368181.4_Silent_p.L133L|FCRL2_ENST00000392274.3_Silent_p.L417L	NM_030764.3	NP_110391.2	Q96LA5	FCRL2_HUMAN	Fc receptor-like 2	417					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)			AGGCATACAACAGCAAAGCAA	0.418													C|||	92	0.0183706	0.0643	0.0086	5008	,	,		19517	0.0		0.001	False		,,,				2504	0.0				p.L417L		Atlas-SNP	.											.	FCRL2	104	.	0			c.G1251A						PASS	.	C		271,4135	152.5+/-186.2	9,253,1941	135	126	129		1251	-0.2	0	1	dbSNP_126	129	0,8600		0,0,4300	no	coding-synonymous	FCRL2	NM_030764.3		9,253,6241	TT,TC,CC		0.0,6.1507,2.0837		417/509	157736673	271,12735	2203	4300	6503	SO:0001819	synonymous_variant	79368	exon7			ATACAACAGCAAA	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.1251G>A	1.37:g.157736673C>T		325	0	0		336	150	0.446429	NM_030764	A0N0M5|A1L307|A6NMS0|Q6NTA1|Q9BZI4|Q9BZI5|Q9BZI6	Silent	SNP	ENST00000361516.3	37	CCDS1168.1																																																																																			C|0.983;T|0.017	0.017	strong		0.418	FCRL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051408.2	NM_030764		T	157736673	C	T	157736673	2	4	22	1	0	0	0	0	0	0	0	1	5803	465	17	2		2	FCRL2	1	157736673	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	221988	157736673	91513948	302	3203											
FCRL1	115350	hgsc.bcm.edu	37	chr1	157771979	157771979	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgaggattgggcgagacacCgggactgagggagacagtag	12	5	18	6	2	0	4	0	2	0	2	0	8	0	6	1	4	0	1	1	4	1	2	rs12035302	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:157771979C>T	ENST00000368176.3	-	5	679	c.612G>A	c.(610-612)ccG>ccA	p.P204P	FCRL1_ENST00000489998.1_5'UTR|FCRL1_ENST00000491942.1_Silent_p.P204P|FCRL1_ENST00000358292.3_Silent_p.P204P	NM_001159398.1|NM_052938.4	NP_001152870.1|NP_443170.1	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1	204						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)			GGCGAGACACCGGGACTGAGG	0.582													C|||	122	0.024361	0.0832	0.0058	5008	,	,		19850	0.006		0.001	False		,,,				2504	0.001				p.P204P	GBM(54;482 1003 11223 30131 35730)	Atlas-SNP	.											.	FCRL1	164	.	0			c.G612A						PASS	.	C	,,	291,4115	141.5+/-176.9	15,261,1927	34	36	35		612,612,612	1.2	1	1	dbSNP_120	35	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	FCRL1	NM_001159397.1,NM_001159398.1,NM_052938.4	,,	15,266,6222	TT,TC,CC		0.0581,6.6046,2.2759	,,	204/367,204/429,204/430	157771979	296,12710	2203	4300	6503	SO:0001819	synonymous_variant	115350	exon5			AGACACCGGGACT	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.612G>A	1.37:g.157771979C>T		134	0	0		136	65	0.477941	NM_001159397	B2RE05|Q8N759|Q8NDI0|Q96PJ6	Silent	SNP	ENST00000368176.3	37	CCDS1170.1																																																																																			C|0.978;T|0.022	0.022	strong		0.582	FCRL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051401.1	NM_052938		T	157771979	C	T	157771979	2	4	22	1	0	0	0	0	0	0	0	1	5802	639	23	1		1	FCRL1	1	157771979	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	35306	157771979	91478642	303	3204											
CD1B	910	hgsc.bcm.edu	37	chr1	158299299	158299299	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgggcaggatgtcccctagCtgagtgccctgctgctcctg	4	11	13	13	0	0	1	0	1	0	0	2	2	2	2	4	2	4	4	4	2	1	2	rs11806249	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158299299C>T	ENST00000368168.3	-	4	854	c.747G>A	c.(745-747)caG>caA	p.Q249Q		NM_001764.2	NP_001755.1	P29016	CD1B_HUMAN	CD1b molecule	249	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)					TGTCCCCTAGCTGAGTGCCCT	0.612													.|||	67	0.0133786	0.0499	0.0014	5008	,	,		18986	0.0		0.0	False		,,,				2504	0.0				p.Q249Q		Atlas-SNP	.											.	CD1B	78	.	0			c.G747A						PASS	.	C		188,4218	120.0+/-157.7	5,178,2020	140	124	129		747	2.3	0	1	dbSNP_120	129	0,8600		0,0,4300	no	coding-synonymous	CD1B	NM_001764.2		5,178,6320	TT,TC,CC		0.0,4.2669,1.4455		249/334	158299299	188,12818	2203	4300	6503	SO:0001819	synonymous_variant	910	exon4			CCCTAGCTGAGTG	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.747G>A	1.37:g.158299299C>T		286	0	0		325	151	0.464615	NM_001764	Q5TDK9|Q5TDL0|Q9UMM2	Silent	SNP	ENST00000368168.3	37	CCDS1176.1																																																																																			C|0.984;T|0.016	0.016	strong		0.612	CD1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046350.2	NM_001764		T	158299299	C	T	158299299	2	4	22	1	0	0	0	0	0	0	0	1	2977	796	28	2		2	CD1B	1	158299299	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	527320	158299299	90951322	304	3205											
CD1E	913	hgsc.bcm.edu	37	chr1	158325765	158325765	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggggcactcagcgaggggaCgtcctgcctaatgctgacga	8	6	15	12	4	1	1	1	1	0	0	2	4	2	2	2	4	3	2	2	4	1	1	rs61734677	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158325765C>T	ENST00000368167.3	+	4	1013	c.774C>T	c.(772-774)gaC>gaT	p.D258D	CD1E_ENST00000368160.3_Silent_p.D258D|CD1E_ENST00000368157.1_Intron|CD1E_ENST00000452291.2_Silent_p.D69D|CD1E_ENST00000368165.3_Silent_p.D168D|CD1E_ENST00000368164.3_Silent_p.D69D|CD1E_ENST00000368163.3_Intron|CD1E_ENST00000368156.1_Silent_p.D168D|CD1E_ENST00000368166.3_Silent_p.D69D|CD1E_ENST00000368155.3_Intron|CD1E_ENST00000368154.1_Intron|CD1E_ENST00000444681.2_Silent_p.D159D|CD1E_ENST00000434258.1_Silent_p.D256D|CD1E_ENST00000368161.3_Silent_p.D258D	NM_030893.3	NP_112155.2	P15812	CD1E_HUMAN	CD1e molecule	258	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)					AGCGAGGGGACGTCCTGCCTA	0.617													C|||	198	0.0395367	0.1483	0.0029	5008	,	,		15430	0.0		0.0	False		,,,				2504	0.0				p.D258D		Atlas-SNP	.											.	CD1E	129	.	0			c.C774T						PASS	.	C	,,,,,,,,,,,,	609,3797	265.9+/-266.9	48,513,1642	115	111	112		774,774,,207,207,504,,,207,,477,504,774	-5.1	0	1	dbSNP_129	112	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous,intron,intron,coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous	CD1E	NM_001042583.2,NM_001042584.2,NM_001042585.2,NM_001042586.2,NM_001042587.2,NM_001185107.1,NM_001185108.1,NM_001185110.1,NM_001185112.1,NM_001185113.1,NM_001185114.1,NM_001185115.1,NM_030893.3	,,,,,,,,,,,,	48,519,5936	TT,TC,CC		0.0698,13.8221,4.7286	,,,,,,,,,,,,	258/377,258/291,,69/188,69/102,168/299,,,69/200,,159/290,168/287,258/389	158325765	615,12391	2203	4300	6503	SO:0001819	synonymous_variant	913	exon4			AGGGGACGTCCTG	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.774C>T	1.37:g.158325765C>T		296	0	0		313	162	0.517572	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	37	CCDS41417.1	66	0.03021978021978022	65	0.13211382113821138	1	0.0027624309392265192	0	0.0	0	0.0	C	0.065	-1.215843	0.01542	0.138221	6.98E-4	ENSG00000158488	ENST00000368162	.	.	.	4.6	-5.12	0.02893	.	.	.	.	.	T	0.10551	0.0258	.	.	.	0.20074	N	0.999933	.	.	.	.	.	.	T	0.29701	-1.0003	4	.	.	.	-27.8278	6.6347	0.22877	0.1308:0.2718:0.0:0.5974	rs61734677	.	.	.	C	28	.	.	R	+	1	0	CD1E	156592389	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-4.235000	0.00269	-1.234000	0.02548	-1.008000	0.02478	CGT	C|0.978;T|0.022	0.022	strong		0.617	CD1E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046353.3	NM_030893		T	158325765	C	T	158325765	2	4	22	1	0	0	0	0	0	0	0	1	2980	535	19	1		1	CD1E	1	158325765	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	26466	158325765	90924856	305	3206											
CD1E	913	hgsc.bcm.edu	37	chr1	158325819	158325819	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgagcaaccctggatgtggcGgctggggaggcagctggcct	6	6	18	11	2	0	0	0	0	0	0	0	3	0	2	2	7	3	4	2	7	1	0	rs61734678	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158325819G>A	ENST00000368167.3	+	4	1067	c.828G>A	c.(826-828)gcG>gcA	p.A276A	CD1E_ENST00000368160.3_Silent_p.A276A|CD1E_ENST00000368157.1_Intron|CD1E_ENST00000452291.2_Silent_p.A87A|CD1E_ENST00000368165.3_Silent_p.A186A|CD1E_ENST00000368164.3_Intron|CD1E_ENST00000368163.3_Intron|CD1E_ENST00000368156.1_Silent_p.A186A|CD1E_ENST00000368166.3_Silent_p.A87A|CD1E_ENST00000368155.3_Intron|CD1E_ENST00000368154.1_Intron|CD1E_ENST00000444681.2_Silent_p.A177A|CD1E_ENST00000434258.1_Silent_p.A274A|CD1E_ENST00000368161.3_Intron	NM_030893.3	NP_112155.2	P15812	CD1E_HUMAN	CD1e molecule	276	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)					TGGATGTGGCGGCTGGGGAGG	0.607													G|||	70	0.0139776	0.0507	0.0043	5008	,	,		15775	0.0		0.0	False		,,,				2504	0.0				p.A276A		Atlas-SNP	.											CD1E,colon,carcinoma,+1,2	CD1E	129	2	0			c.G828A						PASS	.	G	,,,,,,,,,,,,	153,4253	104.3+/-142.8	6,141,2056	85	86	86		828,,,261,,558,,,261,,531,558,828	-8.6	0	1	dbSNP_129	86	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,intron,intron,coding-synonymous,intron,coding-synonymous,intron,intron,coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous	CD1E	NM_001042583.2,NM_001042584.2,NM_001042585.2,NM_001042586.2,NM_001042587.2,NM_001185107.1,NM_001185108.1,NM_001185110.1,NM_001185112.1,NM_001185113.1,NM_001185114.1,NM_001185115.1,NM_030893.3	,,,,,,,,,,,,	6,142,6355	AA,AG,GG		0.0116,3.4725,1.1841	,,,,,,,,,,,,	276/377,,,87/188,,186/299,,,87/200,,177/290,186/287,276/389	158325819	154,12852	2203	4300	6503	SO:0001819	synonymous_variant	913	exon4			TGTGGCGGCTGGG	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.828G>A	1.37:g.158325819G>A		219	0	0		249	114	0.457831	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	Silent	SNP	ENST00000368167.3	37	CCDS41417.1																																																																																			G|0.988;A|0.012	0.012	strong		0.607	CD1E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046353.3	NM_030893		A	158325819	G	A	158325819	2	1	22	1	0	0	0	0	0	0	0	1	2980	1103	39	1		1	CD1E	1	158325819	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	54	158325819	90924802	306	3207											
CD1E	913	hgsc.bcm.edu	37	chr1	158326645	158326645	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tatcgtggatcaaaaacagaGtattgaagaagtggaagaca	18	8	11	4	1	1	4	1	1	0	3	2	6	1	6	0	2	1	1	0	2	7	3	rs61734680	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158326645G>A	ENST00000368167.3	+	6	1365	c.1126G>A	c.(1126-1128)Gta>Ata	p.V376I	CD1E_ENST00000368160.3_Missense_Mutation_p.V364I|CD1E_ENST00000368157.1_Missense_Mutation_p.V120I|CD1E_ENST00000452291.2_Missense_Mutation_p.V187I|CD1E_ENST00000368165.3_Missense_Mutation_p.V286I|CD1E_ENST00000368164.3_3'UTR|CD1E_ENST00000368163.3_Missense_Mutation_p.V309I|CD1E_ENST00000368156.1_Missense_Mutation_p.V274I|CD1E_ENST00000368166.3_Missense_Mutation_p.V175I|CD1E_ENST00000368155.3_Missense_Mutation_p.V219I|CD1E_ENST00000368154.1_Missense_Mutation_p.V132I|CD1E_ENST00000444681.2_Missense_Mutation_p.V277I|CD1E_ENST00000368161.3_3'UTR	NM_030893.3	NP_112155.2	P15812	CD1E_HUMAN	CD1e molecule	376					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)					CAAAAACAGAGTATTGAAGAA	0.438													G|||	198	0.0395367	0.1483	0.0029	5008	,	,		17554	0.0		0.0	False		,,,				2504	0.0				p.V376I		Atlas-SNP	.											.	CD1E	129	.	0			c.G1126A						PASS	.	G	ILE/VAL,,ILE/VAL,ILE/VAL,,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	507,3337		39,429,1454	111	108	109		1090,,925,523,,856,655,358,559,394,829,820,1126	-7.8	0	1	dbSNP_129	109	6,8242		0,6,4118	yes	missense,utr-3,missense,missense,utr-3,missense,missense,missense,missense,missense,missense,missense,missense	CD1E	NM_001042583.2,NM_001042584.2,NM_001042585.2,NM_001042586.2,NM_001042587.2,NM_001185107.1,NM_001185108.1,NM_001185110.1,NM_001185112.1,NM_001185113.1,NM_001185114.1,NM_001185115.1,NM_030893.3	29,,29,29,,29,29,29,29,29,29,29,29	39,435,5572	AA,AG,GG		0.0727,13.1894,4.2425	benign,,benign,benign,,benign,benign,benign,benign,benign,benign,benign,benign	364/377,,309/322,175/188,,286/299,219/232,120/133,187/200,132/145,277/290,274/287,376/389	158326645	513,11579	1922	4124	6046	SO:0001583	missense	913	exon6			AACAGAGTATTGA	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.1126G>A	1.37:g.158326645G>A	ENSP00000357149:p.Val376Ile	97	0	0		99	48	0.484848	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	Missense_Mutation	SNP	ENST00000368167.3	37	CCDS41417.1	66	0.03021978021978022	65	0.13211382113821138	1	0.0027624309392265192	0	0.0	0	0.0	G	7.949	0.744370	0.15710	0.131894	7.27E-4	ENSG00000158488	ENST00000444681;ENST00000368167;ENST00000452291;ENST00000368165;ENST00000368166;ENST00000368163;ENST00000368157;ENST00000368160;ENST00000368156;ENST00000368155;ENST00000368154	T;T;T;T;T;T;T;T;T;T;T	0.48522	5.17;4.63;3.37;3.4;3.55;3.38;0.81;4.72;3.58;3.47;0.81	3.9	-7.8	0.01214	.	1.447200	0.04683	N	0.412624	T	0.05686	0.0149	N	0.03608	-0.345	0.09310	N	1	B;B;B;B;B;B;B;P;B;B	0.42078	0.002;0.009;0.0;0.001;0.001;0.001;0.003;0.77;0.003;0.0	B;B;B;B;B;B;B;B;B;B	0.38712	0.0;0.004;0.0;0.001;0.001;0.0;0.001;0.28;0.002;0.0	T	0.14476	-1.0471	10	0.30078	T	0.28	-0.168	2.001	0.03467	0.2855:0.3958:0.1205:0.1982	rs61734680	277;286;219;175;364;376;187;132;274;309	E7EP01;P15812-5;P15812-7;P15812-9;P15812-2;P15812;P15812-8;P15812-11;P15812-6;P15812-4	.;.;.;.;.;CD1E_HUMAN;.;.;.;.	I	277;376;187;286;175;309;120;364;274;219;132	ENSP00000402906:V277I;ENSP00000357149:V376I;ENSP00000416228:V187I;ENSP00000357147:V286I;ENSP00000357148:V175I;ENSP00000357145:V309I;ENSP00000357139:V120I;ENSP00000357142:V364I;ENSP00000357138:V274I;ENSP00000357137:V219I;ENSP00000357136:V132I	ENSP00000357136:V132I	V	+	1	0	CD1E	156593269	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	-0.133000	0.10451	-1.713000	0.01392	-2.501000	0.00191	GTA	G|0.978;A|0.022	0.022	strong		0.438	CD1E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046353.3	NM_030893		A	158326645	G	A	158326645	3	1	22	1	0	0	0	0	1	0	0	0	2980	1029	36	2	1148	2	CD1E	1	158326645	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	826	158326645	90923976	307	3208											
OR10T2	128360	hgsc.bcm.edu	37	chr1	158368915	158368915	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tatcccatcacagcaatgagGaggcagttggtgcaagcaaa	14	7	11	9	0	1	1	1	1	0	0	2	2	2	2	1	3	3	5	1	3	4	2	rs56704148	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158368915G>T	ENST00000334438.1	-	1	341	c.342C>A	c.(340-342)ctC>ctA	p.L114L		NM_001004475.1	NP_001004475.1	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T, member 2	114						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)					CAGCAATGAGGAGGCAGTTGG	0.498													G|||	46	0.0091853	0.034	0.0014	5008	,	,		21129	0.0		0.0	False		,,,				2504	0.0				p.L114L		Atlas-SNP	.											.	OR10T2	76	.	0			c.C342A						PASS	.	G		139,4267	98.0+/-136.7	5,129,2069	122	121	121		342	-1	1	1	dbSNP_129	121	0,8600		0,0,4300	no	coding-synonymous	OR10T2	NM_001004475.1		5,129,6369	TT,TG,GG		0.0,3.1548,1.0687		114/315	158368915	139,12867	2203	4300	6503	SO:0001819	synonymous_variant	128360	exon1			AATGAGGAGGCAG	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.342C>A	1.37:g.158368915G>T		134	0	0		147	74	0.503401	NM_001004475	Q6IF98	Silent	SNP	ENST00000334438.1	37	CCDS30895.1																																																																																			G|0.989;T|0.011	0.011	strong		0.498	OR10T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046371.1	NM_001004475		T	158368915	G	T	158368915	2	4	22	1	0	0	0	0	0	0	0	1	10928	1161	41	4		4	OR10T2	1	158368915	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	42270	158368915	90881706	308	3209											
OR10T2	128360	hgsc.bcm.edu	37	chr1	158369025	158369025	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccagcagctgagggatgaTgacaaaagtgtagcaggact	14	6	14	7	0	0	3	0	3	0	0	0	6	0	5	1	2	3	4	1	2	3	1	rs6662597	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158369025T>C	ENST00000334438.1	-	1	231	c.232A>G	c.(232-234)Atc>Gtc	p.I78V		NM_001004475.1	NP_001004475.1	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T, member 2	78			I -> V (in dbSNP:rs6662597).			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)					TGAGGGATGATGACAAAAGTG	0.502													T|||	63	0.0125799	0.0477	0.0	5008	,	,		20910	0.0		0.0	False		,,,				2504	0.0				p.I78V		Atlas-SNP	.											.	OR10T2	76	.	0			c.A232G						PASS	.	T	VAL/ILE	143,4263	99.4+/-138.0	3,137,2063	96	95	96		232	4.7	1	1	dbSNP_116	96	0,8600		0,0,4300	yes	missense	OR10T2	NM_001004475.1	29	3,137,6363	CC,CT,TT		0.0,3.2456,1.0995	possibly-damaging	78/315	158369025	143,12863	2203	4300	6503	SO:0001583	missense	128360	exon1			GGATGATGACAAA	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.232A>G	1.37:g.158369025T>C	ENSP00000334115:p.Ile78Val	96	0	0		91	53	0.582418	NM_001004475	Q6IF98	Missense_Mutation	SNP	ENST00000334438.1	37	CCDS30895.1	21	0.009615384615384616	21	0.042682926829268296	0	0.0	0	0.0	0	0.0	T	16.66	3.184032	0.57800	0.032456	0.0	ENSG00000186306	ENST00000334438	T	0.00611	6.23	4.73	4.73	0.59995	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39759	U	0.001269	T	0.00271	0.0008	L	0.41573	1.285	0.09310	N	0.999995	P	0.36282	0.546	B	0.31442	0.13	T	0.50668	-0.8801	10	0.37606	T	0.19	.	13.3352	0.60515	0.0:0.0:0.0:1.0	rs6662597;rs52820437;rs56418545;rs6662597	78	Q8NGX3	O10T2_HUMAN	V	78	ENSP00000334115:I78V	ENSP00000334115:I78V	I	-	1	0	OR10T2	156635649	0.969000	0.33509	1.000000	0.80357	0.999000	0.98932	2.867000	0.48428	1.973000	0.57446	0.528000	0.53228	ATC	T|0.985;C|0.015	0.015	strong		0.502	OR10T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046371.1	NM_001004475		C	158369025	T	C	158369025	3	2	22	1	0	0	0	0	1	0	0	0	10928	1464	51	3	714	3	OR10T2	1	158369025	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	110	158369025	90881596	309	3210											
OR10T2	128360	hgsc.bcm.edu	37	chr1	158369210	158369210	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccccaggctggagaaacccAccaggatgaactgtgtaacc	12	5	10	14	0	0	2	0	1	0	1	0	4	0	3	5	3	3	2	5	3	3	1	rs6660222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158369210A>G	ENST00000334438.1	-	1	46	c.47T>C	c.(46-48)gTg>gCg	p.V16A		NM_001004475.1	NP_001004475.1	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T, member 2	16			V -> A (in dbSNP:rs6660222).			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)					GGAGAAACCCACCAGGATGAA	0.448													A|||	103	0.0205671	0.0772	0.0	5008	,	,		18704	0.0		0.0	False		,,,				2504	0.001				p.V16A		Atlas-SNP	.											.	OR10T2	76	.	0			c.T47C						PASS	.	A	ALA/VAL	237,4169	128.2+/-165.1	5,227,1971	35	39	37		47	4.7	0.9	1	dbSNP_116	37	0,8600		0,0,4300	yes	missense	OR10T2	NM_001004475.1	64	5,227,6271	GG,GA,AA		0.0,5.379,1.8222	benign	16/315	158369210	237,12769	2203	4300	6503	SO:0001583	missense	128360	exon1			AAACCCACCAGGA	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.47T>C	1.37:g.158369210A>G	ENSP00000334115:p.Val16Ala	96	0	0		111	53	0.477477	NM_001004475	Q6IF98	Missense_Mutation	SNP	ENST00000334438.1	37	CCDS30895.1	38	0.0173992673992674	38	0.07723577235772358	0	0.0	0	0.0	0	0.0	A	10.40	1.341006	0.24339	0.05379	0.0	ENSG00000186306	ENST00000334438	T	0.01406	4.93	4.65	4.65	0.58169	.	0.000000	0.34411	U	0.003988	T	0.00637	0.0021	L	0.41710	1.295	0.20764	N	0.99986	B	0.34161	0.439	B	0.36666	0.23	T	0.48658	-0.9016	10	0.87932	D	0	.	4.0026	0.09587	0.7202:0.0:0.0962:0.1837	rs6660222;rs52824469;rs56643236;rs6660222	16	Q8NGX3	O10T2_HUMAN	A	16	ENSP00000334115:V16A	ENSP00000334115:V16A	V	-	2	0	OR10T2	156635834	0.176000	0.23096	0.922000	0.36590	0.528000	0.34623	1.079000	0.30766	1.939000	0.56221	0.482000	0.46254	GTG	A|0.976;G|0.024	0.024	strong		0.448	OR10T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046371.1	NM_001004475		G	158369210	A	G	158369210	3	3	22	1	0	0	0	0	1	0	0	0	10928	159	6	3	899	3	OR10T2	1	158369210	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	185	158369210	90881411	310	3211											
OR10K1	391109	hgsc.bcm.edu	37	chr1	158435572	158435572	+	Missense_Mutation	SNP	C	C	T																															ttgctctgagatttgctataCctttgtcattgtacccaaga																								rs78779179|rs386635902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158435572C>T	ENST00000289451.2	+	1	301	c.221C>T	c.(220-222)aCc>aTc	p.T74I		NM_001004473.1	NP_001004473.1	Q8NGX5	O10K1_HUMAN	olfactory receptor, family 10, subfamily K, 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)			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)					ATTTGCTATACCTTTGTCATT	0.453													C|||	189	0.0377396	0.1354	0.013	5008	,	,		24656	0.0		0.001	False		,,,				2504	0.0				p.T74I		Atlas-SNP	.											.	OR10K1	80	.	0			c.C221T						PASS	.	C	ILE/THR	501,3905	216.4+/-235.1	27,447,1729	209	190	197		221	4.5	1	1	dbSNP_131	197	8,8592	6.4+/-24.3	0,8,4292	yes	missense	OR10K1	NM_001004473.1	89	27,455,6021	TT,TC,CC		0.093,11.3709,3.9136	probably-damaging	74/314	158435572	509,12497	2203	4300	6503	SO:0001583	missense	391109	exon1			GCTATACCTTTGT	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.221C>T	1.37:g.158435572C>T	ENSP00000289451:p.Thr74Ile	490	0	0		474	204	0.43038	NM_001004473	Q6IFS2	Missense_Mutation	SNP	ENST00000289451.2	37	CCDS30897.1	55	0.025183150183150184	49	0.09959349593495935	6	0.016574585635359115	0	0.0	0	0.0	c	13.70	2.316088	0.40996	0.113709	9.3E-4	ENSG00000173285	ENST00000289451	T	0.00444	7.4	4.5	4.5	0.54988	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44285	D	0.000467	T	0.00384	0.0012	L	0.49778	1.585	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.53173	-0.8476	10	0.62326	D	0.03	.	10.4216	0.44354	0.0:0.9045:0.0:0.0955	.	74	Q8NGX5	O10K1_HUMAN	I	74	ENSP00000289451:T74I	ENSP00000289451:T74I	T	+	2	0	OR10K1	156702196	0.000000	0.05858	0.999000	0.59377	0.887000	0.51463	0.237000	0.17985	2.311000	0.77944	0.557000	0.71058	ACC	C|0.966;T|0.034	0.034	strong		0.453	OR10K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046367.1			T	158435572	C	T	158435572	3	4	22	1	0	0	0	0	1	0	0	0	10922	507	18	2	223	2	OR10K1	1	158435572	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	66362	158435572	90815049	311	3212	47	2									
OR10K1	391109	hgsc.bcm.edu	37	chr1	158435573	158435573	+	Silent	SNP	C	C	G																															tgctctgagatttgctatacCtttgtcattgtacccaagat																								rs76205582|rs386635902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158435573C>G	ENST00000289451.2	+	1	302	c.222C>G	c.(220-222)acC>acG	p.T74T		NM_001004473.1	NP_001004473.1	Q8NGX5	O10K1_HUMAN	olfactory receptor, family 10, subfamily K, 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)			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)					TTTGCTATACCTTTGTCATTG	0.458													C|||	189	0.0377396	0.1354	0.013	5008	,	,		24689	0.0		0.001	False		,,,				2504	0.0				p.T74T		Atlas-SNP	.											.	OR10K1	80	.	0			c.C222G						PASS	.	C		503,3903	214.8+/-234.0	27,449,1727	209	190	196		222	-0.3	1	1	dbSNP_131	196	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	OR10K1	NM_001004473.1		27,457,6019	GG,GC,CC		0.093,11.4163,3.929		74/314	158435573	511,12495	2203	4300	6503	SO:0001819	synonymous_variant	391109	exon1			CTATACCTTTGTC	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.222C>G	1.37:g.158435573C>G		489	1	0.00204499		474	205	0.432489	NM_001004473	Q6IFS2	Silent	SNP	ENST00000289451.2	37	CCDS30897.1																																																																																			C|0.966;G|0.034	0.034	strong		0.458	OR10K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046367.1			G	158435573	C	G	158435573	2	3	22	1	0	0	0	0	0	0	0	1	10922	668	24	4		4	OR10K1	1	158435573	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1	158435573	90815048	312	3213	47	2									
OR10K1	391109	hgsc.bcm.edu	37	chr1	158436201	158436201	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catacaccatccttaccccaTtgttcaatccaatgatttat	12	14	2	13	0	1	1	1	1	0	0	3	1	3	1	5	0	2	1	5	0	5	6	rs76117330	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158436201T>C	ENST00000289451.2	+	1	930	c.850T>C	c.(850-852)Ttg>Ctg	p.L284L		NM_001004473.1	NP_001004473.1	Q8NGX5	O10K1_HUMAN	olfactory receptor, family 10, subfamily K, 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)			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)					CCTTACCCCATTGTTCAATCC	0.388													T|||	189	0.0377396	0.1354	0.013	5008	,	,		21238	0.0		0.001	False		,,,				2504	0.0				p.L284L		Atlas-SNP	.											.	OR10K1	80	.	0			c.T850C						PASS	.	T		513,3893	235.2+/-247.8	29,455,1719	146	140	142		850	-7	0	1	dbSNP_131	142	8,8592	7.1+/-27.0	0,8,4292	no	coding-synonymous	OR10K1	NM_001004473.1		29,463,6011	CC,CT,TT		0.093,11.6432,4.0058		284/314	158436201	521,12485	2203	4300	6503	SO:0001819	synonymous_variant	391109	exon1			ACCCCATTGTTCA	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.850T>C	1.37:g.158436201T>C		131	0	0		139	62	0.446043	NM_001004473	Q6IFS2	Silent	SNP	ENST00000289451.2	37	CCDS30897.1																																																																																			T|0.963;C|0.037	0.037	strong		0.388	OR10K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046367.1			C	158436201	T	C	158436201	2	2	22	1	0	0	0	0	0	0	0	1	10922	1490	52	3		3	OR10K1	1	158436201	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	628	158436201	90814420	313	3214											
OR6Y1	391112	hgsc.bcm.edu	37	chr1	158517099	158517099	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcatacatgagtttgggaCgggcataggtgaaaagtgtc	12	9	15	5	1	0	2	0	2	0	0	1	3	0	3	0	4	1	3	0	4	4	3	rs113154921	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158517099C>A	ENST00000302617.3	-	1	796	c.797G>T	c.(796-798)cGt>cTt	p.R266L		NM_001005189.1	NP_001005189.1	Q8NGX8	OR6Y1_HUMAN	olfactory receptor, family 6, subfamily Y, member 1	266						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)					GAGTTTGGGACGGGCATAGGT	0.483													C|||	99	0.0197684	0.0719	0.0043	5008	,	,		24161	0.0		0.001	False		,,,				2504	0.0				p.R266L		Atlas-SNP	.											.	OR6Y1	73	.	0			c.G797T						PASS	.	C	LEU/ARG	264,4142	148.4+/-182.8	11,242,1950	208	195	200		797	3.5	1	1	dbSNP_132	200	5,8595	5.0+/-18.6	0,5,4295	yes	missense	OR6Y1	NM_001005189.1	102	11,247,6245	AA,AC,CC		0.0581,5.9918,2.0683	probably-damaging	266/326	158517099	269,12737	2203	4300	6503	SO:0001583	missense	391112	exon1			TTGGGACGGGCAT	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.797G>T	1.37:g.158517099C>A	ENSP00000304807:p.Arg266Leu	152	0	0		142	68	0.478873	NM_001005189	Q6IFS0	Missense_Mutation	SNP	ENST00000302617.3	37	CCDS30899.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	C	18.23	3.577221	0.65878	0.059918	5.81E-4	ENSG00000197532	ENST00000302617	T	0.36699	1.24	5.34	3.49	0.39957	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42172	D	0.000750	T	0.35740	0.0942	M	0.73319	2.225	0.09310	N	1	D	0.64830	0.994	P	0.58660	0.843	T	0.18681	-1.0329	10	0.87932	D	0	.	8.5271	0.33311	0.0:0.7603:0.0:0.2397	.	266	Q8NGX8	OR6Y1_HUMAN	L	266	ENSP00000304807:R266L	ENSP00000304807:R266L	R	-	2	0	OR6Y1	156783723	0.000000	0.05858	0.983000	0.44433	0.927000	0.56198	-0.100000	0.10990	0.822000	0.34565	0.655000	0.94253	CGT	A|0.018;C|0.982;G|0.000	0.018	strong		0.483	OR6Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051844.1	NM_001005189		A	158517099	C	A	158517099	3	1	22	1	0	0	0	0	1	0	0	0	11222	536	19	4	182	4	OR6Y1	1	158517099	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	80898	158517099	90733522	314	3215											
OR10X1	128367	hgsc.bcm.edu	37	chr1	158549082	158549082	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttactgtctatacaagacAgcctaataactgccagcata	14	10	7	10	0	1	1	0	0	1	1	1	1	1	1	2	1	6	2	2	1	7	6	rs61755876	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158549082A>T	ENST00000368150.1	-	1	607	c.608T>A	c.(607-609)cTg>cAg	p.L203Q		NM_001004477.1	NP_001004477.1	Q8NGY0	O10X1_HUMAN	olfactory receptor, family 10, subfamily X, member 1 (gene/pseudogene)	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)|cervix(1)|endometrium(2)|large_intestine(6)|lung(22)|ovary(2)|skin(2)|urinary_tract(1)	37	all_hematologic(112;0.0378)					TATACAAGACAGCCTAATAAC	0.433													A|||	79	0.0157748	0.0582	0.0029	5008	,	,		22248	0.0		0.0	False		,,,				2504	0.0				p.L203Q		Atlas-SNP	.											.	OR10X1	96	.	0			c.T608A						PASS	.	A	GLN/LEU	227,4179	134.9+/-171.1	6,215,1982	85	85	85		608	4.8	0	1	dbSNP_129	85	3,8597	2.2+/-6.3	0,3,4297	yes	missense	OR10X1	NM_001004477.1	113	6,218,6279	TT,TA,AA		0.0349,5.1521,1.7684	probably-damaging	203/327	158549082	230,12776	2203	4300	6503	SO:0001583	missense	128367	exon1			CAAGACAGCCTAA	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.608T>A	1.37:g.158549082A>T	ENSP00000357132:p.Leu203Gln	185	0	0		207	100	0.483092	NM_001004477	Q6IFR8	Missense_Mutation	SNP	ENST00000368150.1	37	CCDS30900.1	26	0.011904761904761904	26	0.052845528455284556	0	0.0	0	0.0	0	0.0	A	13.52	2.261476	0.39995	0.051521	3.49E-4	ENSG00000186400	ENST00000368150	T	0.00411	7.53	4.8	4.8	0.61643	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37393	N	0.002120	T	0.01124	0.0037	H	0.97390	3.995	0.22684	N	0.998857	D	0.89917	1.0	D	0.97110	1.0	T	0.29701	-1.0003	10	0.87932	D	0	.	13.4538	0.61187	1.0:0.0:0.0:0.0	rs61755876	203	Q8NGY0	O10X1_HUMAN	Q	203	ENSP00000357132:L203Q	ENSP00000357132:L203Q	L	-	2	0	OR10X1	156815706	0.944000	0.32072	0.042000	0.18584	0.176000	0.22953	8.331000	0.90022	1.998000	0.58463	0.455000	0.32223	CTG	A|0.972;T|0.028	0.028	strong		0.433	OR10X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051850.2	NM_001004477		T	158549082	A	T	158549082	3	4	22	1	0	0	0	0	1	0	0	0	10931	188	7	5	367	5	OR10X1	1	158549082	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	31983	158549082	90701539	315	3216											
OR10Z1	128368	hgsc.bcm.edu	37	chr1	158576394	158576394	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcaggctggatagccatctgCacacccccatgtacctcttc	8	10	7	16	0	3	0	1	0	2	0	4	1	3	1	4	2	3	3	4	2	2	3	rs116792162	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158576394C>A	ENST00000361284.1	+	1	166	c.166C>A	c.(166-168)Cac>Aac	p.H56N		NM_001004478.1	NP_001004478.1	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z, member 1	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(6)|lung(21)|pancreas(1)|prostate(3)|skin(4)	37	all_hematologic(112;0.0378)					TAGCCATCTGCACACCCCCAT	0.512													C|||	36	0.0071885	0.0265	0.0014	5008	,	,		20596	0.0		0.0	False		,,,				2504	0.0				p.H56N		Atlas-SNP	.											OR10Z1,right_upper_lobe,carcinoma,-1,1	OR10Z1	99	1	0			c.C166A						PASS	.	C	ASN/HIS	101,4305	79.9+/-118.3	1,99,2103	257	247	251		166	5.4	0.9	1	dbSNP_132	251	1,8599	1.2+/-3.3	0,1,4299	yes	missense	OR10Z1	NM_001004478.1	68	1,100,6402	AA,AC,CC		0.0116,2.2923,0.7843	probably-damaging	56/314	158576394	102,12904	2203	4300	6503	SO:0001583	missense	128368	exon1			CATCTGCACACCC	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.166C>A	1.37:g.158576394C>A	ENSP00000354707:p.His56Asn	316	0	0		368	182	0.494565	NM_001004478	Q5VYL0|Q6IFR7	Missense_Mutation	SNP	ENST00000361284.1	37	CCDS30901.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	16.63	3.176489	0.57692	0.022923	1.16E-4	ENSG00000198967	ENST00000361284	T	0.15952	2.38	5.36	5.36	0.76844	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43579	D	0.000544	T	0.42449	0.1203	M	0.92268	3.29	0.34002	D	0.650477	D	0.76494	0.999	D	0.79108	0.992	T	0.56312	-0.8000	10	0.66056	D	0.02	.	13.5532	0.61745	0.1563:0.8437:0.0:0.0	.	56	Q8NGY1	O10Z1_HUMAN	N	56	ENSP00000354707:H56N	ENSP00000354707:H56N	H	+	1	0	OR10Z1	156843018	0.443000	0.25641	0.927000	0.36925	0.716000	0.41182	1.115000	0.31209	2.783000	0.95769	0.655000	0.94253	CAC	C|0.992;A|0.008	0.008	strong		0.512	OR10Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051853.1	NM_001004478		A	158576394	C	A	158576394	3	1	22	1	0	0	0	0	1	0	0	0	10932	710	25	4	168	4	OR10Z1	1	158576394	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	27312	158576394	90674227	316	3217											
OR10Z1	128368	hgsc.bcm.edu	37	chr1	158576472	158576472	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgggcatcatccctagaatgCtctctggcctggctgggggg	5	10	15	11	0	2	1	1	0	1	1	4	1	3	1	2	6	1	3	2	6	2	1	rs76424590	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158576472C>T	ENST00000361284.1	+	1	244	c.244C>T	c.(244-246)Ctc>Ttc	p.L82F		NM_001004478.1	NP_001004478.1	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z, member 1	82						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)					CCCTAGAATGCTCTCTGGCCT	0.542													C|||	190	0.0379393	0.1377	0.0086	5008	,	,		20262	0.0		0.002	False		,,,				2504	0.0				p.L82F		Atlas-SNP	.											OR10Z1,NS,carcinoma,-2,1	OR10Z1	99	1	0			c.C244T						PASS	.	C	PHE/LEU	525,3881	238.7+/-250.0	33,459,1711	203	209	207		244	5.4	1	1	dbSNP_131	207	12,8588	9.1+/-34.3	0,12,4288	yes	missense	OR10Z1	NM_001004478.1	22	33,471,5999	TT,TC,CC		0.1395,11.9156,4.1289	probably-damaging	82/314	158576472	537,12469	2203	4300	6503	SO:0001583	missense	128368	exon1			AGAATGCTCTCTG	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.244C>T	1.37:g.158576472C>T	ENSP00000354707:p.Leu82Phe	211	0	0		210	93	0.442857	NM_001004478	Q5VYL0|Q6IFR7	Missense_Mutation	SNP	ENST00000361284.1	37	CCDS30901.1	68	0.031135531135531136	66	0.13414634146341464	2	0.0055248618784530384	0	0.0	0	0.0	C	17.17	3.321840	0.60634	0.119156	0.001395	ENSG00000198967	ENST00000361284	T	0.00419	7.48	5.36	5.36	0.76844	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36778	N	0.002405	T	0.01222	0.0040	H	0.97077	3.935	0.26251	P	0.97873	D	0.89917	1.0	D	0.80764	0.994	T	0.03296	-1.1051	9	0.87932	D	0	.	13.5532	0.61745	0.1563:0.8437:0.0:0.0	.	82	Q8NGY1	O10Z1_HUMAN	F	82	ENSP00000354707:L82F	ENSP00000354707:L82F	L	+	1	0	OR10Z1	156843096	0.996000	0.38824	0.997000	0.53966	0.647000	0.38526	1.184000	0.32053	2.783000	0.95769	0.655000	0.94253	CTC	C|0.962;T|0.038	0.038	strong		0.542	OR10Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051853.1	NM_001004478		T	158576472	C	T	158576472	3	4	22	1	0	0	0	0	1	0	0	0	10932	797	28	2	246	2	OR10Z1	1	158576472	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	78	158576472	90674149	317	3218											
SPTA1	6708	hgsc.bcm.edu	37	chr1	158587368	158587368	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccagagttcctgtttcttTgagcaatgatctagttaaga	10	16	8	7	0	2	4	0	2	2	2	4	4	4	4	2	0	1	4	2	0	3	6	rs111980420	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158587368T>C	ENST00000368147.4	-	47	6739	c.6559A>G	c.(6559-6561)Aaa>Gaa	p.K2187E		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2187					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)					CCTGTTTCTTTGAGCAATGAT	0.343													T|||	50	0.00998403	0.0363	0.0029	5008	,	,		21215	0.0		0.0	False		,,,				2504	0.0				p.K2187E		Atlas-SNP	.											.	SPTA1	720	.	0			c.A6559G						PASS	.	T	GLU/LYS	109,3607		1,107,1750	110	101	104		6559	4	1	1	dbSNP_132	104	1,8199		0,1,4099	yes	missense	SPTA1	NM_003126.2	56	1,108,5849	CC,CT,TT		0.0122,2.9333,0.9231	benign	2187/2420	158587368	110,11806	1858	4100	5958	SO:0001583	missense	6708	exon47			TTTCTTTGAGCAA	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.6559A>G	1.37:g.158587368T>C	ENSP00000357129:p.Lys2187Glu	231	0	0		190	112	0.589474	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	T	5.051	0.195152	0.09599	0.029333	1.22E-4	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.53423	0.62;0.62	5.15	4.01	0.46588	.	0.000000	0.33792	N	0.004556	T	0.07728	0.0194	N	0.12182	0.205	0.34813	D	0.737938	B	0.10296	0.003	B	0.09377	0.004	T	0.27262	-1.0079	10	0.02654	T	1	.	5.5016	0.16831	0.0:0.0873:0.1765:0.7361	.	2187	P02549	SPTA1_HUMAN	E	2187;2184	ENSP00000357130:K2187E;ENSP00000357129:K2184E	ENSP00000357129:K2184E	K	-	1	0	SPTA1	156853992	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.835000	0.48175	1.068000	0.40764	0.533000	0.62120	AAA	T|0.994;C|0.006	0.006	strong		0.343	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		C	158587368	T	C	158587368	3	2	22	1	0	0	0	0	1	0	0	0	15131	1821	63	3	724	3	SPTA1	1	158587368	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	10896	158587368	90663253	318	3219											
SPTA1	6708	hgsc.bcm.edu	37	chr1	158618320	158618320	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ttatctcccaggggtacgagGtccctttcaaagccctcatg	8	11	9	13	1	3	0	2	0	1	0	5	1	4	0	3	3	2	1	3	3	3	3	rs34773716	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158618320G>A	ENST00000368147.4	-	26	3873	c.3693C>T	c.(3691-3693)gaC>gaT	p.D1231D		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1231					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)					GGGGTACGAGGTCCCTTTCAA	0.498													G|||	134	0.0267572	0.0938	0.013	5008	,	,		14013	0.0		0.001	False		,,,				2504	0.0				p.D1231D		Atlas-SNP	.											SPTA1,NS,carcinoma,-2,1	SPTA1	720	1	0			c.C3693T						PASS	.	G		250,3612		10,230,1691	115	116	115		3693	-0.7	0.4	1	dbSNP_126	115	5,8249		0,5,4122	yes	coding-synonymous	SPTA1	NM_003126.2		10,235,5813	AA,AG,GG		0.0606,6.4733,2.1047		1231/2420	158618320	255,11861	1931	4127	6058	SO:0001819	synonymous_variant	6708	exon26			TACGAGGTCCCTT	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.3693C>T	1.37:g.158618320G>A		82	0	0		80	53	0.6625	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	37	CCDS41423.1																																																																																			G|0.988;A|0.012	0.012	strong		0.498	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		A	158618320	G	A	158618320	2	1	22	1	0	0	0	0	0	0	0	1	15131	1252	44	2		2	SPTA1	1	158618320	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	30952	158618320	90632301	319	3220											
SPTA1	6708	hgsc.bcm.edu	37	chr1	158623092	158623092	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatctgctcctggcgctgggTgatgtttcctggctcttctc	3	15	11	12	1	3	1	0	1	3	0	6	1	5	1	2	3	1	4	2	3	1	2	rs145054175	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158623092T>A	ENST00000368147.4	-	22	3340	c.3160A>T	c.(3160-3162)Acc>Tcc	p.T1054S		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1054					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)					TGGCGCTGGGTGATGTTTCCT	0.517													T|||	25	0.00499201	0.0182	0.0014	5008	,	,		15465	0.0		0.0	False		,,,				2504	0.0				p.T1054S		Atlas-SNP	.											SPTA1,NS,carcinoma,+1,1	SPTA1	720	1	0			c.A3160T						scavenged	.	T	SER/THR	56,3900		0,56,1922	118	122	120		3160	-1.3	0.2	1	dbSNP_134	120	0,8344		0,0,4172	yes	missense	SPTA1	NM_003126.2	58	0,56,6094	AA,AT,TT		0.0,1.4156,0.4553	benign	1054/2420	158623092	56,12244	1978	4172	6150	SO:0001583	missense	6708	exon22			GCTGGGTGATGTT	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.3160A>T	1.37:g.158623092T>A	ENSP00000357129:p.Thr1054Ser	137	2	0.0145985		124	62	0.5	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	T	12.06	1.823290	0.32237	0.014156	0.0	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.65916	-0.18;-0.18	5.15	-1.33	0.09172	Src homology-3 domain (1);	2.011270	0.03053	N	0.154860	T	0.13457	0.0326	N	0.03608	-0.345	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.07790	-1.0754	10	0.10636	T	0.68	.	8.2403	0.31656	0.0:0.5787:0.1365:0.2848	.	1054	P02549	SPTA1_HUMAN	S	1054	ENSP00000357130:T1054S;ENSP00000357129:T1054S	ENSP00000357129:T1054S	T	-	1	0	SPTA1	156889716	0.008000	0.16893	0.150000	0.22450	0.671000	0.39405	0.091000	0.15046	-0.379000	0.07906	-1.139000	0.01908	ACC	T|0.996;A|0.004	0.004	strong		0.517	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		A	158623092	T	A	158623092	3	1	22	1	0	0	0	0	1	0	0	0	15131	1696	59	5	4223	5	SPTA1	1	158623092	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	4772	158623092	90627529	320	3221											
SPTA1	6708	hgsc.bcm.edu	37	chr1	158623103	158623103	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcgctgggtgatgtttcctGgctcttctcgtcgccgctgt	1	14	14	12	4	2	1	0	1	2	0	5	1	3	1	2	3	0	4	2	3	0	2	rs116297260	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158623103G>A	ENST00000368147.4	-	22	3329	c.3149C>T	c.(3148-3150)cCa>cTa	p.P1050L		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1050					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)					GATGTTTCCTGGCTCTTCTCG	0.532													G|||	40	0.00798722	0.0295	0.0014	5008	,	,		15095	0.0		0.0	False		,,,				2504	0.0				p.P1050L		Atlas-SNP	.											.	SPTA1	720	.	0			c.C3149T						PASS	.	G	LEU/PRO	81,3859		0,81,1889	116	119	118		3149	3.3	0.9	1	dbSNP_132	118	0,8370		0,0,4185	yes	missense	SPTA1	NM_003126.2	98	0,81,6074	AA,AG,GG		0.0,2.0558,0.658	benign	1050/2420	158623103	81,12229	1970	4185	6155	SO:0001583	missense	6708	exon22			TTTCCTGGCTCTT	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.3149C>T	1.37:g.158623103G>A	ENSP00000357129:p.Pro1050Leu	134	0	0		130	65	0.5	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	G	11.31	1.600501	0.28534	0.020558	0.0	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.31510	1.49;1.49	5.15	3.28	0.37604	Src homology-3 domain (1);	0.273133	0.19703	N	0.107990	T	0.06962	0.0177	N	0.22421	0.69	0.47123	D	0.999327	B	0.11235	0.004	B	0.10450	0.005	T	0.12863	-1.0531	10	0.28530	T	0.3	.	4.5022	0.11869	0.1722:0.0:0.5672:0.2606	.	1050	P02549	SPTA1_HUMAN	L	1050	ENSP00000357130:P1050L;ENSP00000357129:P1050L	ENSP00000357129:P1050L	P	-	2	0	SPTA1	156889727	1.000000	0.71417	0.878000	0.34440	0.726000	0.41606	4.176000	0.58269	0.762000	0.33152	0.655000	0.94253	CCA	G|0.995;A|0.005	0.005	strong		0.532	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		A	158623103	G	A	158623103	3	1	22	1	0	0	0	0	1	0	0	0	15131	1348	47	2	4234	2	SPTA1	1	158623103	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	11	158623103	90627518	321	3222											
SPTA1	6708	hgsc.bcm.edu	37	chr1	158626382	158626382	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgtttgcctgattccgcagaGctttcatactgtctccaaat	8	14	7	12	2	2	2	1	1	1	1	4	2	3	2	3	0	3	3	3	0	2	4	rs34706737	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158626382G>A	ENST00000368147.4	-	20	3050	c.2870C>T	c.(2869-2871)gCt>gTt	p.A957V		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	957			A -> V (in dbSNP:rs34706737).		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)					ATTCCGCAGAGCTTTCATACT	0.398													G|||	173	0.0345447	0.1248	0.0101	5008	,	,		16513	0.0		0.001	False		,,,				2504	0.0				p.A957V		Atlas-SNP	.											.	SPTA1	720	.	0			c.C2870T						PASS	.	G	VAL/ALA	340,3368		17,306,1531	170	174	173		2870	2.5	0	1	dbSNP_126	173	11,8171		0,11,4080	yes	missense	SPTA1	NM_003126.2	64	17,317,5611	AA,AG,GG		0.1344,9.1694,2.9521	possibly-damaging	957/2420	158626382	351,11539	1854	4091	5945	SO:0001583	missense	6708	exon20			CGCAGAGCTTTCA	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.2870C>T	1.37:g.158626382G>A	ENSP00000357129:p.Ala957Val	83	0	0		72	30	0.416667	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	73	0.033424908424908424	69	0.1402439024390244	4	0.011049723756906077	0	0.0	0	0.0	G	16.62	3.174122	0.57692	0.091694	0.001344	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.52295	0.67;0.67	5.5	2.53	0.30540	.	0.000000	0.32120	N	0.006555	T	0.42154	0.1190	M	0.66297	2.02	0.40998	D	0.9849	P	0.46952	0.887	P	0.53722	0.733	T	0.31943	-0.9925	10	0.39692	T	0.17	.	9.6117	0.39668	0.0:0.1322:0.4583:0.4095	rs34706737	957	P02549	SPTA1_HUMAN	V	957	ENSP00000357130:A957V;ENSP00000357129:A957V	ENSP00000357129:A957V	A	-	2	0	SPTA1	156893006	0.999000	0.42202	0.038000	0.18304	0.494000	0.33585	2.748000	0.47483	0.395000	0.25257	0.655000	0.94253	GCT	G|0.976;A|0.024	0.024	strong		0.398	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		A	158626382	G	A	158626382	3	1	22	1	0	0	0	0	1	0	0	0	15131	971	34	2	4521	2	SPTA1	1	158626382	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3279	158626382	90624239	322	3223											
SPTA1	6708	hgsc.bcm.edu	37	chr1	158631106	158631106	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccattttgtttcccctttctGttatctcttgaatgcgtggt	4	20	7	10	1	2	1	0	1	2	0	4	1	3	1	3	1	1	2	3	1	2	6	rs35121052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158631106G>C	ENST00000368147.4	-	18	2738	c.2558C>G	c.(2557-2559)aCa>aGa	p.T853R		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	853			T -> R (in dbSNP:rs35121052).		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)					TCCCCTTTCTGTTATCTCTTG	0.438													G|||	531	0.10603	0.382	0.0331	5008	,	,		17472	0.0		0.003	False		,,,				2504	0.0				p.T853R		Atlas-SNP	.											.	SPTA1	720	.	0			c.C2558G						PASS	.	G	ARG/THR	1121,2763		177,767,998	266	264	265		2558	3.9	1	1	dbSNP_126	265	21,8275		0,21,4127	yes	missense	SPTA1	NM_003126.2	71	177,788,5125	CC,CG,GG		0.2531,28.862,9.376	benign	853/2420	158631106	1142,11038	1942	4148	6090	SO:0001583	missense	6708	exon18			CTTTCTGTTATCT	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.2558C>G	1.37:g.158631106G>C	ENSP00000357129:p.Thr853Arg	311	0	0		338	165	0.488166	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	192	0.08791208791208792	181	0.3678861788617886	11	0.03038674033149171	0	0.0	0	0.0	G	16.67	3.187725	0.57909	0.28862	0.002531	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.52057	0.68;0.68	4.81	3.9	0.45041	.	.	.	.	.	T	0.39145	0.1067	M	0.64997	1.995	0.23076	P	0.99833702	P	0.44659	0.84	P	0.51550	0.673	T	0.29243	-1.0018	8	0.18710	T	0.47	.	11.9273	0.52827	0.0851:0.0:0.9149:0.0	rs35121052;rs61126478	853	P02549	SPTA1_HUMAN	R	853	ENSP00000357130:T853R;ENSP00000357129:T853R	ENSP00000357129:T853R	T	-	2	0	SPTA1	156897730	1.000000	0.71417	1.000000	0.80357	0.643000	0.38383	5.076000	0.64413	1.249000	0.43950	0.650000	0.86243	ACA	G|0.933;C|0.067	0.067	strong		0.438	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		C	158631106	G	C	158631106	3	2	22	1	0	0	0	0	1	0	0	0	15131	1377	48	4	4841	4	SPTA1	1	158631106	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4724	158631106	90619515	323	3224											
SPTA1	6708	hgsc.bcm.edu	37	chr1	158632531	158632531	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagggttcagtctcttggaTccaggcctcctcatcctctg	5	13	10	13	0	4	1	2	1	2	0	8	2	7	2	4	3	0	1	4	3	0	2	rs7547313	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158632531T>C	ENST00000368147.4	-	17	2605	c.2425A>G	c.(2425-2427)Atc>Gtc	p.I809V		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	809			I -> V (in dbSNP:rs7547313).		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)					GTCTCTTGGATCCAGGCCTCC	0.502													T|||	516	0.103035	0.3707	0.0331	5008	,	,		16779	0.0		0.003	False		,,,				2504	0.0				p.I809V		Atlas-SNP	.											SPTA1,NS,carcinoma,+2,1	SPTA1	720	1	0			c.A2425G						PASS	.	T	VAL/ILE	1083,2813		165,753,1030	100	103	102		2425	4.3	1	1	dbSNP_116	102	19,8255		0,19,4118	yes	missense	SPTA1	NM_003126.2	29	165,772,5148	CC,CT,TT		0.2296,27.7977,9.0551	possibly-damaging	809/2420	158632531	1102,11068	1948	4137	6085	SO:0001583	missense	6708	exon17			CTTGGATCCAGGC	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.2425A>G	1.37:g.158632531T>C	ENSP00000357129:p.Ile809Val	179	0	0		205	104	0.507317	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	183	0.08379120879120878	172	0.34959349593495936	11	0.03038674033149171	0	0.0	0	0.0	T	21.0	4.080651	0.76528	0.277977	0.002296	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.39787	1.06;1.06	4.28	4.28	0.50868	.	0.000000	0.32852	N	0.005568	T	0.40196	0.1107	L	0.37466	1.105	0.22531	P	0.999012003	D	0.76494	0.999	D	0.91635	0.999	T	0.38824	-0.9643	9	0.44086	T	0.13	.	10.915	0.47131	0.0:0.0:0.0:1.0	rs7547313;rs7547313	809	P02549	SPTA1_HUMAN	V	809	ENSP00000357130:I809V;ENSP00000357129:I809V	ENSP00000357129:I809V	I	-	1	0	SPTA1	156899155	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.011000	0.76359	1.786000	0.52430	0.460000	0.39030	ATC	T|0.946;C|0.054	0.054	strong		0.502	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		C	158632531	T	C	158632531	3	2	22	1	0	0	0	0	1	0	0	0	15131	1435	50	3	4978	3	SPTA1	1	158632531	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1425	158632531	90618090	324	3225											
OR6K2	81448	hgsc.bcm.edu	37	chr1	158669980	158669980	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccaggcaatctcaggaagggGtgtgataaagccacaaacac	15	5	11	10	0	1	1	1	1	1	0	2	2	1	2	2	4	2	1	2	4	5	1	rs111363268	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158669980G>A	ENST00000359610.2	-	1	506	c.463C>T	c.(463-465)Ccc>Tcc	p.P155S		NM_001005279.1	NP_001005279.1	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K, 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(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)					TCAGGAAGGGGTGTGATAAAG	0.488													G|||	119	0.023762	0.0847	0.0086	5008	,	,		23707	0.0		0.001	False		,,,				2504	0.0				p.P155S		Atlas-SNP	.											OR6K2,right_upper_lobe,carcinoma,+2,1	OR6K2	104	1	0			c.C463T						PASS	.	G	SER/PRO	340,4066	178.7+/-207.4	12,316,1875	123	107	113		463	3.9	0.1	1	dbSNP_132	113	2,8598	1.2+/-3.3	0,2,4298	yes	missense	OR6K2	NM_001005279.1	74	12,318,6173	AA,AG,GG		0.0233,7.7167,2.6296	possibly-damaging	155/325	158669980	342,12664	2203	4300	6503	SO:0001583	missense	81448	exon1			GAAGGGGTGTGAT	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.463C>T	1.37:g.158669980G>A	ENSP00000352626:p.Pro155Ser	73	0	0		85	42	0.494118	NM_001005279	B9EH33|Q6IFR6	Missense_Mutation	SNP	ENST00000359610.2	37	CCDS30902.1	37	0.01694139194139194	36	0.07317073170731707	1	0.0027624309392265192	0	0.0	0	0.0	G	10.46	1.356369	0.24598	0.077167	2.33E-4	ENSG00000196171	ENST00000359610	T	0.29142	1.58	4.84	3.92	0.45320	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37955	N	0.001874	T	0.06050	0.0157	N	0.00879	-1.12	0.09310	N	1	D	0.56035	0.974	P	0.60236	0.871	T	0.03807	-1.1002	10	0.18710	T	0.47	-12.7456	3.6905	0.08344	0.0886:0.1687:0.5679:0.1749	.	155	Q8NGY2	OR6K2_HUMAN	S	155	ENSP00000352626:P155S	ENSP00000352626:P155S	P	-	1	0	OR6K2	156936604	0.000000	0.05858	0.145000	0.22337	0.977000	0.68977	-0.103000	0.10940	1.232000	0.43678	0.650000	0.86243	CCC	G|0.977;A|0.023	0.023	strong		0.488	OR6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059061.1	NM_001005279		A	158669980	G	A	158669980	3	1	22	1	0	0	0	0	1	0	0	0	11211	1261	44	2	515	2	OR6K2	1	158669980	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	37449	158669980	90580641	325	3226											
IGSF9	57549	hgsc.bcm.edu	37	chr1	159898437	159898437	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	caggacctggcaagggactgGgtggggctgctggagggggt	6	6	22	7	0	0	0	0	0	0	0	0	3	0	3	1	9	1	3	1	9	1	0	rs35574000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:159898437G>A	ENST00000368094.1	-	19	2938	c.2741C>T	c.(2740-2742)cCc>cTc	p.P914L	TAGLN2_ENST00000368097.4_5'Flank|IGSF9_ENST00000361509.3_Missense_Mutation_p.P898L|IGSF9_ENST00000493195.1_5'UTR	NM_001135050.1	NP_001128522.1	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9	914	Pro-rich.		P -> L (in dbSNP:rs35574000).		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)			CAAGGGACTGGGTGGGGCTGC	0.657													G|||	74	0.0147764	0.0522	0.0072	5008	,	,		14684	0.0		0.0	False		,,,				2504	0.0				p.P914L		Atlas-SNP	.											.	IGSF9	123	.	0			c.C2741T						PASS	.	G	LEU/PRO,LEU/PRO	267,4113		7,253,1930	9	9	9		2741,2693	4.6	0.1	1	dbSNP_126	9	4,8536		0,4,4266	yes	missense,missense	IGSF9	NM_001135050.1,NM_020789.3	98,98	7,257,6196	AA,AG,GG		0.0468,6.0959,2.0975	probably-damaging,probably-damaging	914/1180,898/1164	159898437	271,12649	2190	4270	6460	SO:0001583	missense	57549	exon19			GGACTGGGTGGGG	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.2741C>T	1.37:g.159898437G>A	ENSP00000357073:p.Pro914Leu	96	0	0		104	56	0.538462	NM_001135050		Missense_Mutation	SNP	ENST00000368094.1	37	CCDS44254.1	27	0.012362637362637362	26	0.052845528455284556	1	0.0027624309392265192	0	0.0	0	0.0	G	14.74	2.625456	0.46840	0.060959	4.68E-4	ENSG00000085552	ENST00000361509;ENST00000368094;ENST00000198587	T;T	0.66815	-0.23;-0.14	4.63	4.63	0.57726	.	0.000000	0.37906	N	0.001887	T	0.58694	0.2140	N	0.24115	0.695	0.21697	N	0.999586	D;B	0.89917	1.0;0.19	D;B	0.83275	0.996;0.081	T	0.53704	-0.8401	9	.	.	.	-10.2414	12.8357	0.57771	0.0:0.0:1.0:0.0	rs35574000	914;452	Q9P2J2;C9JI81	TUTLA_HUMAN;.	L	898;914;452	ENSP00000355049:P898L;ENSP00000357073:P914L	.	P	-	2	0	IGSF9	158165061	0.579000	0.26725	0.117000	0.21633	0.543000	0.35085	4.142000	0.58044	2.378000	0.81104	0.655000	0.94253	CCC	G|0.987;A|0.013	0.013	strong		0.657	IGSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059115.1	NM_020789		A	159898437	G	A	159898437	3	1	22	1	0	0	0	0	1	0	0	0	7614	1232	43	2	810	2	IGSF9	1	159898437	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1228457	159898437	89352184	326	3227											
IGSF9	57549	hgsc.bcm.edu	37	chr1	159900655	159900655	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gcattcggtcaggacgcttgGccctgggagacatgaggaca	9	7	15	10	2	1	2	1	1	0	1	2	5	1	4	1	5	0	2	1	5	0	2	rs140306211	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:159900655G>A	ENST00000368094.1	-	14	1837	c.1640C>T	c.(1639-1641)gCc>gTc	p.A547V	IGSF9_ENST00000361509.3_Missense_Mutation_p.A531V|IGSF9_ENST00000493195.1_5'UTR	NM_001135050.1	NP_001128522.1	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9	547	Fibronectin type-III 1. {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)			AGGACGCTTGGCCCTGGGAGA	0.617													G|||	17	0.00339457	0.0129	0.0	5008	,	,		19874	0.0		0.0	False		,,,				2504	0.0				p.A547V		Atlas-SNP	.											.	IGSF9	123	.	0			c.C1640T						PASS	.	G	VAL/ALA,VAL/ALA	78,4328	67.0+/-104.6	0,78,2125	34	35	35		1640,1592	4.7	1	1	dbSNP_134	35	0,8600		0,0,4300	yes	missense,missense	IGSF9	NM_001135050.1,NM_020789.3	64,64	0,78,6425	AA,AG,GG		0.0,1.7703,0.5997	benign,benign	547/1180,531/1164	159900655	78,12928	2203	4300	6503	SO:0001583	missense	57549	exon14			CGCTTGGCCCTGG	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.1640C>T	1.37:g.159900655G>A	ENSP00000357073:p.Ala547Val	152	0	0		146	71	0.486301	NM_001135050		Missense_Mutation	SNP	ENST00000368094.1	37	CCDS44254.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	G	8.888	0.953376	0.18431	0.017703	0.0	ENSG00000085552	ENST00000361509;ENST00000368094	T;T	0.56776	0.44;0.44	4.65	4.65	0.58169	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.165414	0.28700	N	0.014421	T	0.13670	0.0331	N	0.05510	-0.035	0.33488	D	0.588349	B	0.13145	0.007	B	0.20384	0.029	T	0.10337	-1.0634	9	.	.	.	-14.7856	8.6122	0.33808	0.1024:0.0:0.8976:0.0	.	547	Q9P2J2	TUTLA_HUMAN	V	531;547	ENSP00000355049:A531V;ENSP00000357073:A547V	.	A	-	2	0	IGSF9	158167279	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	3.744000	0.55112	2.400000	0.81607	0.462000	0.41574	GCC	G|0.994;A|0.006	0.006	strong		0.617	IGSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059115.1	NM_020789		A	159900655	G	A	159900655	3	1	22	1	0	0	0	0	1	0	0	0	7614	1203	42	2	1931	2	IGSF9	1	159900655	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2218	159900655	89349966	327	3228											
ATP1A2	477	hgsc.bcm.edu	37	chr1	160090993	160090993	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttccccaggatgaccacaaGctgtccttggatgagctggg	8	9	12	12	0	0	2	0	2	0	0	2	4	2	4	4	3	2	2	4	3	1	2	rs61734527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:160090993G>A	ENST00000361216.3	+	3	218	c.129G>A	c.(127-129)aaG>aaA	p.K43K	ATP1A2_ENST00000392233.3_Silent_p.K43K	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	43					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)			ATGACCACAAGCTGTCCTTGG	0.537													G|||	33	0.00658946	0.0242	0.0014	5008	,	,		21718	0.0		0.0	False		,,,				2504	0.0				p.K43K		Atlas-SNP	.											.	ATP1A2	167	.	0			c.G129A						PASS	.	G		122,4284	90.2+/-128.9	2,118,2083	229	232	231		129	3.7	1	1	dbSNP_129	231	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ATP1A2	NM_000702.3		2,119,6382	AA,AG,GG		0.0116,2.769,0.9457		43/1021	160090993	123,12883	2203	4300	6503	SO:0001819	synonymous_variant	477	exon3			CCACAAGCTGTCC	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.129G>A	1.37:g.160090993G>A		85	0	0		77	29	0.376623	NM_000702	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Silent	SNP	ENST00000361216.3	37	CCDS1196.1																																																																																			G|0.991;A|0.009	0.009	strong		0.537	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702		A	160090993	G	A	160090993	2	1	22	1	0	0	0	0	0	0	0	1	1129	962	34	2		2	ATP1A2	1	160090993	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	190338	160090993	89159628	328	3229											
ATP1A2	477	hgsc.bcm.edu	37	chr1	160104950	160104950	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tccagagaagccaaggcatgCgtggtgcacggctctgacct	9	7	13	12	2	1	2	0	1	1	1	2	3	2	2	3	3	3	3	3	3	2	0	rs61734529	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:160104950C>T	ENST00000361216.3	+	15	2069	c.1980C>T	c.(1978-1980)tgC>tgT	p.C660C	ATP1A2_ENST00000392233.3_Silent_p.C660C	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	660					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)			CCAAGGCATGCGTGGTGCACG	0.612													C|||	104	0.0207668	0.0779	0.0014	5008	,	,		22206	0.0		0.0	False		,,,				2504	0.0				p.C660C		Atlas-SNP	.											.	ATP1A2	167	.	0			c.C1980T						PASS	.	C		301,4105	164.0+/-195.7	10,281,1912	99	72	81		1980	-6.2	0.4	1	dbSNP_129	81	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ATP1A2	NM_000702.3		10,283,6210	TT,TC,CC		0.0233,6.8316,2.3297		660/1021	160104950	303,12703	2203	4300	6503	SO:0001819	synonymous_variant	477	exon15			GGCATGCGTGGTG	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.1980C>T	1.37:g.160104950C>T		356	0	0		414	216	0.521739	NM_000702	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Silent	SNP	ENST00000361216.3	37	CCDS1196.1	34	0.015567765567765568	34	0.06910569105691057	0	0.0	0	0.0	0	0.0	C	9.163	1.019313	0.19355	0.068316	2.33E-4	ENSG00000018625	ENST00000447527	.	.	.	4.44	-6.19	0.02078	.	.	.	.	.	T	0.47173	0.1431	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60662	-0.7219	4	.	.	.	.	13.6226	0.62146	0.0:0.609:0.0:0.391	rs61734529	.	.	.	V	371	.	.	A	+	2	0	ATP1A2	158371574	0.002000	0.14202	0.400000	0.26346	0.942000	0.58702	-1.400000	0.02504	-1.346000	0.02211	0.511000	0.50034	GCG	C|0.978;T|0.022	0.022	strong		0.612	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702		T	160104950	C	T	160104950	2	4	22	1	0	0	0	0	0	0	0	1	1129	776	27	1		1	ATP1A2	1	160104950	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	13957	160104950	89145671	329	3230											
ATP1A4	480	hgsc.bcm.edu	37	chr1	160129273	160129273	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcacccatgagaaccctctGgagacccgaaacatctgctt	11	9	7	14	1	3	2	1	1	2	2	3	5	3	2	3	1	3	1	3	1	2	2	rs61734686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:160129273G>A	ENST00000368081.4	+	6	1206	c.735G>A	c.(733-735)ctG>ctA	p.L245L		NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	245					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)			AGAACCCTCTGGAGACCCGAA	0.507													G|||	53	0.0105831	0.0401	0.0	5008	,	,		17615	0.0		0.0	False		,,,				2504	0.0				p.L245L		Atlas-SNP	.											.	ATP1A4	167	.	0			c.G735A						PASS	.	G		96,4310	77.3+/-115.6	3,90,2110	97	100	99		735	2.6	1	1	dbSNP_129	99	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ATP1A4	NM_144699.3		3,91,6409	AA,AG,GG		0.0116,2.1788,0.7458		245/1030	160129273	97,12909	2203	4300	6503	SO:0001819	synonymous_variant	480	exon6			CCCTCTGGAGACC	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.735G>A	1.37:g.160129273G>A		176	0	0		150	72	0.48	NM_144699	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Silent	SNP	ENST00000368081.4	37	CCDS1197.1																																																																																			G|0.992;A|0.008	0.008	strong		0.507	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699		A	160129273	G	A	160129273	2	1	22	1	0	0	0	0	0	0	0	1	1131	1335	47	2		2	ATP1A4	1	160129273	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	24323	160129273	89121348	330	3231											
PEX19	5824	hgsc.bcm.edu	37	chr1	160253413	160253413	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggggagggtttggctttatcGaaatcatcaagagcaccttc	10	11	12	8	1	2	1	2	0	0	1	4	3	2	2	1	4	1	3	1	4	3	4	rs141911166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:160253413G>A	ENST00000368072.5	-	2	108	c.87C>T	c.(85-87)ttC>ttT	p.F29F	PEX19_ENST00000440949.3_5'UTR|PEX19_ENST00000532508.1_5'UTR|DCAF8_ENST00000556710.1_Intron|DCAF8_ENST00000608310.1_Intron	NM_001193644.1|NM_002857.3	NP_001180573.1|NP_002848.1	P40855	PEX19_HUMAN	peroxisomal biogenesis factor 19	29	Docking to the peroxisome membrane and binding to PEX3.|Necessary for PEX19 function on peroxisome biogenesis.				chaperone-mediated protein folding (GO:0061077)|chaperone-mediated protein transport (GO:0072321)|establishment of protein localization to peroxisome (GO:0072663)|negative regulation of lipid binding (GO:1900131)|peroxisome fission (GO:0016559)|peroxisome membrane biogenesis (GO:0016557)|peroxisome organization (GO:0007031)|protein import into peroxisome membrane (GO:0045046)|protein stabilization (GO:0050821)|protein targeting to peroxisome (GO:0006625)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	ATPase binding (GO:0051117)|peroxisome membrane class-1 targeting sequence binding (GO:0036105)|protein N-terminus binding (GO:0047485)			cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(2)	11	all_cancers(52;1.27e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TGGCTTTATCGAAATCATCAA	0.532													G|||	2	0.000399361	0.0015	0.0	5008	,	,		18595	0.0		0.0	False		,,,				2504	0.0				p.F29F		Atlas-SNP	.											PEX19,NS,carcinoma,0,3	PEX19	34	3	0			c.C87T						PASS	.	G	,	5,4401	9.9+/-24.2	0,5,2198	81	75	77		87,87	1.1	1	1	dbSNP_134	77	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PEX19	NM_001193644.1,NM_002857.3	,	0,5,6498	AA,AG,GG		0.0,0.1135,0.0384	,	29/280,29/300	160253413	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	5824	exon2			TTTATCGAAATCA	Y09048	CCDS1201.1	1q22	2008-07-18	2004-03-17	2004-03-19	ENSG00000162735	ENSG00000162735			9713	protein-coding gene	gene with protein product	"housekeeping gene, 33kD"	600279	"peroxisomal farnesylated protein"	PXF		9339377, 10051604	Standard	NM_002857		Approved	HK33, D1S2223E, PMP1, PMPI, PXMP1		P40855	OTTHUMG00000033112	ENST00000368072.5:c.87C>T	1.37:g.160253413G>A		81	0	0		103	53	0.514563	NM_002857	D3DVE7|Q5QNY4|Q8NI97	Silent	SNP	ENST00000368072.5	37	CCDS1201.1																																																																																			G|1.000;A|0.000	0.000	strong		0.532	PEX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080642.2	NM_002857		A	160253413	G	A	160253413	2	1	22	1	0	0	0	0	0	0	0	1	11753	1049	37	1		1	PEX19	1	160253413	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	124140	160253413	88997208	331	3232											
COPA	1314	hgsc.bcm.edu	37	chr1	160302298	160302298	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatactaccaagtcttctgTggggtggaactgagcacaca	11	10	11	9	0	2	2	0	2	2	0	2	3	2	3	1	3	4	1	1	3	4	3	rs57425682	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:160302298T>C	ENST00000241704.7	-	6	665	c.436A>G	c.(436-438)Aca>Gca	p.T146A	COPA_ENST00000368069.3_Missense_Mutation_p.T146A	NM_001098398.1|NM_004371.3	NP_001091868.1|NP_004362.2	P53621	COPA_HUMAN	coatomer protein complex, subunit alpha	146					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)			AAGTCTTCTGTGGGGTGGAAC	0.473													C|||	275	0.0549121	0.177	0.0202	5008	,	,		16356	0.0238		0.0	False		,,,				2504	0.0031				p.T146A		Atlas-SNP	.											.	COPA	181	.	0			c.A436G						PASS	.	C	ALA/THR,ALA/THR	633,3773	767.1+/-413.5	60,513,1630	132	118	123		436,436	3.9	1	1	dbSNP_129	123	8,8592	818.9+/-406.8	0,8,4292	yes	missense,missense	COPA	NM_001098398.1,NM_004371.3	58,58	60,521,5922	CC,CT,TT		0.093,14.3668,4.9285	benign,benign	146/1234,146/1225	160302298	641,12365	2203	4300	6503	SO:0001583	missense	1314	exon6			CTTCTGTGGGGTG	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.436A>G	1.37:g.160302298T>C	ENSP00000241704:p.Thr146Ala	52	0	0		50	29	0.58	NM_001098398	Q5T201|Q8IXZ9	Missense_Mutation	SNP	ENST00000241704.7	37	CCDS1202.1	95	0.043498168498168496	66	0.13414634146341464	9	0.024861878453038673	20	0.03496503496503497	0	0.0	C	13.43	2.233892	0.39498	0.143668	9.3E-4	ENSG00000122218	ENST00000368069;ENST00000241704	T;T	0.59906	0.23;0.23	5.05	3.92	0.45320	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.119729	0.64402	N	0.000017	T	0.26340	0.0643	L	0.39020	1.185	0.42906	P	0.005758999999999959	B;B	0.06786	0.001;0.001	B;B	0.16289	0.012;0.015	T	0.05517	-1.0880	9	0.54805	T	0.06	-2.4504	7.7922	0.29127	0.7177:0.1453:0.0:0.137	rs57425682;rs61739741	146;146	P53621;P53621-2	COPA_HUMAN;.	A	146	ENSP00000357048:T146A;ENSP00000241704:T146A	ENSP00000241704:T146A	T	-	1	0	COPA	158568922	1.000000	0.71417	0.999000	0.59377	0.678000	0.39670	4.802000	0.62539	0.403000	0.25479	-1.641000	0.00772	ACA	T|0.956;C|0.044	0.044	strong		0.473	COPA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080638.1	NM_004371		C	160302298	T	C	160302298	3	2	22	1	0	0	0	0	1	0	0	0	3729	1696	59	3	3377	3	COPA	1	160302298	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	48885	160302298	88948323	332	3233											
ITLN1	55600	hgsc.bcm.edu	37	chr1	160853312	160853312	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccttgaagtaagtattagcCtcatctagggaatacacagg	13	11	9	8	0	2	1	1	1	1	0	3	2	3	2	2	2	2	2	2	2	7	6	rs79969862	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:160853312C>T	ENST00000326245.3	-	3	178	c.63G>A	c.(61-63)gaG>gaA	p.E21E	ITLN1_ENST00000487531.1_5'Flank	NM_017625.2	NP_060095.2	Q8WWA0	ITLN1_HUMAN	intelectin 1 (galactofuranose binding)	21					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)			AAGTATTAGCCTCATCTAGGG	0.463													C|||	89	0.0177716	0.0461	0.0043	5008	,	,		18185	0.0		0.0	False		,,,				2504	0.0256				p.E21E		Atlas-SNP	.											.	ITLN1	45	.	0			c.G63A						PASS	.	C		182,4224	117.1+/-155.0	5,172,2026	159	145	150		63	-3	0	1	dbSNP_132	150	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ITLN1	NM_017625.2		5,173,6325	TT,TC,CC		0.0116,4.1307,1.407		21/314	160853312	183,12823	2203	4300	6503	SO:0001819	synonymous_variant	55600	exon3			ATTAGCCTCATCT	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.63G>A	1.37:g.160853312C>T		154	0	0		149	61	0.409396	NM_017625	Q5IWS4|Q5VYI4|Q6YDJ3|Q9NP67	Silent	SNP	ENST00000326245.3	37	CCDS1211.1																																																																																			C|0.984;T|0.016	0.016	strong		0.463	ITLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071462.1	NM_017625		T	160853312	C	T	160853312	2	4	22	1	0	0	0	0	0	0	0	1	7919	680	24	2		2	ITLN1	1	160853312	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	551014	160853312	88397309	333	3234											
ARHGAP30	257106	hgsc.bcm.edu	37	chr1	161022247	161022247	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tacccctgtcctcagcccccCgtggaagtttacgcttagtc	6	11	8	16	2	1	0	1	0	0	0	3	1	2	1	6	1	3	2	6	1	4	4	rs149524176	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:161022247C>T	ENST00000368013.3	-	8	1243	c.923G>A	c.(922-924)cGg>cAg	p.R308Q	ARHGAP30_ENST00000368016.3_Missense_Mutation_p.R308Q|ARHGAP30_ENST00000368015.1_Missense_Mutation_p.R131Q	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	308					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)			CTCAGCCCCCCGTGGAAGTTT	0.537													C|||	4	0.000798722	0.003	0.0	5008	,	,		16986	0.0		0.0	False		,,,				2504	0.0				p.R308Q		Atlas-SNP	.											LOC257106,NS,carcinoma,-1,2	ARHGAP30	105	2	0			c.G923A						PASS	.	C	GLN/ARG,GLN/ARG	5,4401	9.9+/-24.2	0,5,2198	198	211	207		923,923	3.8	0.5	1	dbSNP_134	207	0,8600		0,0,4300	no	missense,missense	ARHGAP30	NM_001025598.1,NM_181720.2	43,43	0,5,6498	TT,TC,CC		0.0,0.1135,0.0384	possibly-damaging,possibly-damaging	308/1102,308/891	161022247	5,13001	2203	4300	6503	SO:0001583	missense	257106	exon8			GCCCCCCGTGGAA	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.923G>A	1.37:g.161022247C>T	ENSP00000356992:p.Arg308Gln	87	0	0		89	35	0.393258	NM_001025598	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Missense_Mutation	SNP	ENST00000368013.3	37	CCDS30918.1	.	.	.	.	.	.	.	.	.	.	C	14.08	2.429037	0.43122	0.001135	0.0	ENSG00000186517	ENST00000368016;ENST00000368013;ENST00000368017;ENST00000368015	T;T;T	0.38401	2.84;2.76;1.14	4.72	3.77	0.43336	.	0.396100	0.21881	N	0.067728	T	0.28333	0.0700	L	0.56199	1.76	0.09310	N	1	D;D	0.65815	0.995;0.989	P;P	0.56788	0.716;0.806	T	0.11665	-1.0578	10	0.66056	D	0.02	.	5.6555	0.17640	0.2053:0.6933:0.0:0.1014	.	308;308	Q7Z6I6;Q7Z6I6-2	RHG30_HUMAN;.	Q	308;308;160;131	ENSP00000356995:R308Q;ENSP00000356992:R308Q;ENSP00000356994:R131Q	ENSP00000356992:R308Q	R	-	2	0	ARHGAP30	159288871	0.000000	0.05858	0.542000	0.28115	0.981000	0.71138	0.424000	0.21330	0.924000	0.37069	0.549000	0.68633	CGG	C|0.999;T|0.001	0.001	strong		0.537	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720		T	161022247	C	T	161022247	3	4	22	1	0	0	0	0	1	0	0	0	879	652	23	1	2402	1	ARHGAP30	1	161022247	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	168935	161022247	88228374	334	3235											
B4GALT3	8703	hgsc.bcm.edu	37	chr1	161141862	161141862	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcgtccaggaattctgggtaCggaccaggaggtcaaatctg	10	8	14	9	2	3	0	1	0	2	0	4	3	4	3	2	5	1	1	2	5	3	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:161141862C>T	ENST00000319769.5	-	8	1148	c.926G>A	c.(925-927)cGt>cAt	p.R309H	PPOX_ENST00000495483.1_Intron|PPOX_ENST00000432542.2_Intron|PPOX_ENST00000535223.1_Intron|B4GALT3_ENST00000367998.1_Missense_Mutation_p.R309H|B4GALT3_ENST00000470882.1_5'UTR	NM_001199873.1|NM_003779.3	NP_001186802.1|NP_003770.1	O60512	B4GT3_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 3	309					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)	ATTCTGGGTACGGACCAGGAG	0.502																																					p.R309H		Atlas-SNP	.											.	B4GALT3	39	.	0			c.G926A						PASS	.						73	77	76					1																	161141862		2203	4300	6503	SO:0001583	missense	8703	exon8			TGGGTACGGACCA	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.926G>A	1.37:g.161141862C>T	ENSP00000320965:p.Arg309His	73	0	0		89	43	0.483146	NM_003779	D3DVG3|O60910|Q9BPZ4|Q9H8T2	Missense_Mutation	SNP	ENST00000319769.5	37	CCDS1222.1	.	.	.	.	.	.	.	.	.	.	C	12.45	1.940163	0.34283	.	.	ENSG00000158850	ENST00000319769;ENST00000407555;ENST00000367998;ENST00000367997	T;T	0.35421	1.31;1.31	5.28	4.35	0.52113	.	0.213738	0.49305	D	0.000153	T	0.09730	0.0239	N	0.13235	0.315	0.45307	D	0.998302	P	0.38167	0.621	B	0.34722	0.188	T	0.08146	-1.0736	10	0.13470	T	0.59	.	13.4642	0.61243	0.0:0.9213:0.0:0.0787	.	309	O60512	B4GT3_HUMAN	H	309;286;309;309	ENSP00000320965:R309H;ENSP00000356977:R309H	ENSP00000320965:R309H	R	-	2	0	B4GALT3	159408486	0.954000	0.32549	0.999000	0.59377	0.999000	0.98932	2.130000	0.42064	2.746000	0.94184	0.655000	0.94253	CGT	.	.	none		0.502	B4GALT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083054.1	NM_003779		T	161141862	C	T	161141862	3	4	22	1	0	0	0	0	1	0	0	0	1272	536	19	1	259	1	B4GALT3	1	161141862	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	119615	161141862	88108759	335	3236											
FCGR3A	2214	hgsc.bcm.edu	37	chr1	161518233	161518233	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atatggacttctagctgcacCgggtcactgagggtggagag	9	9	15	8	1	2	2	1	1	1	1	2	4	2	3	1	4	2	2	1	4	2	3	rs139622799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:161518233C>A	ENST00000436743.1	-	4	451	c.297G>T	c.(295-297)ccG>ccT	p.P99P	FCGR3A_ENST00000367969.3_Silent_p.P135P|RP11-25K21.6_ENST00000537821.2_RNA|FCGR3A_ENST00000476031.1_5'UTR|FCGR3A_ENST00000443193.1_Silent_p.P134P|FCGR3A_ENST00000540048.1_Silent_p.P99P	NM_001127593.1|NM_001127595.1|NM_001127596.1	NP_001121065.1|NP_001121067.1|NP_001121068.1	P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)	99	Ig-like C2-type 1.				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)	CTAGCTGCACCGGGTCACTGA	0.512																																					p.P135P		Atlas-SNP	.											FCGR3A,lower_third,carcinoma,-2,1	FCGR3A	38	1	0			c.G405T						scavenged	.	C	,,,,	144,4262	81.4+/-119.9	0,144,2059	114	112	113		405,402,297,297,294	-8.9	0	1	dbSNP_134	113	7,8587	5.0+/-18.6	0,7,4290	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FCGR3A	NM_000569.6,NM_001127592.1,NM_001127593.1,NM_001127595.1,NM_001127596.1	,,,,	0,151,6349	AA,AC,CC		0.0815,3.2683,1.1615	,,,,	135/291,134/290,99/255,99/255,98/254	161518233	151,12849	2203	4297	6500	SO:0001819	synonymous_variant	2214	exon3			CTGCACCGGGTCA	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	ENST00000436743.1:c.297G>T	1.37:g.161518233C>A		488	2	0.00409836		585	181	0.309402	NM_000569	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Silent	SNP	ENST00000436743.1	37	CCDS44266.1	32	0.014652014652014652	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	C	11.25	1.583746	0.28268	0.032683	8.15E-4	ENSG00000203747	ENST00000426740	.	.	.	4.43	-8.86	0.00795	.	.	.	.	.	T	0.26011	0.0634	.	.	.	0.38428	D	0.94635	.	.	.	.	.	.	T	0.47873	-0.9083	4	.	.	.	.	7.0855	0.25255	0.2513:0.1676:0.0:0.5811	.	.	.	.	L	116	.	.	R	-	2	0	FCGR3A	159784857	0.000000	0.05858	0.029000	0.17559	0.763000	0.43281	-5.433000	0.00123	-3.094000	0.00246	-0.218000	0.12543	CGG	C|0.985;A|0.015	0.015	strong		0.512	FCGR3A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102169.2	NM_000569		A	161518233	C	A	161518233	2	1	22	1	0	0	0	0	0	0	0	1	5792	639	23	4		4	FCGR3A	1	161518233	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	376371	161518233	87732388	336	3237											
FCGR2B	2213	hgsc.bcm.edu	37	chr1	161645058	161645058	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccctcccagctctcccaggaTaccctgagtgcagggaaatg	9	7	10	15	0	1	1	0	1	1	0	3	3	2	3	4	2	3	2	4	2	2	1	rs148534844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:161645058T>G	ENST00000358671.5	+	6	853	c.772T>G	c.(772-774)Tac>Gac	p.Y258D	FCGR2B_ENST00000367960.5_Missense_Mutation_p.Y251D|FCGR2B_ENST00000367962.4_Missense_Mutation_p.Y258D|FCGR2B_ENST00000236937.9_Intron|FCGR2B_ENST00000403078.3_Intron|RP11-25K21.1_ENST00000453111.1_RNA|FCGR2B_ENST00000367961.4_Missense_Mutation_p.Y251D	NM_001002275.2|NM_004001.4	NP_001002275.1|NP_003992.3	P31994	FCG2B_HUMAN	Fc fragment of IgG, low affinity IIb, receptor (CD32)	258			Y -> D (in dbSNP:rs148534844). {ECO:0000269|PubMed:8466861}.		immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)						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)|Antithymocyte globulin(DB00098)|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)	TCTCCCAGGATACCCTGAGTG	0.612			T	?	ALL																																p.Y258D		Atlas-SNP	.		Dom	yes		1	1q23	2213	"Fc fragment of IgG, low affinity IIb, receptor for (CD32)"		L	.	FCGR2B	33	.	0			c.T772G						PASS	.	T	,,ASP/TYR,ASP/TYR,ASP/TYR	54,4350		0,54,2148	31	29	29		,,769,751,772	-1.8	0.6	1	dbSNP_134	29	1,8599		0,1,4299	no	intron,intron,missense,missense,missense	FCGR2B	NM_001002273.2,NM_001002274.2,NM_001002275.2,NM_001190828.1,NM_004001.4	,,160,160,160	0,55,6447	GG,GT,TT		0.0116,1.2262,0.4229	,,benign,benign,benign	,,257/310,251/304,258/311	161645058	55,12949	2202	4300	6502	SO:0001583	missense	2213	exon6			CCAGGATACCCTG	BC031992	CCDS30924.1, CCDS30925.1, CCDS53414.1	1q23	2013-01-11	2005-02-02		ENSG00000072694	ENSG00000072694		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	3618	protein-coding gene	gene with protein product		604590	"Fc fragment of IgG, low affinity IIb, receptor for (CD32)"	FCG2, FCGR2		2139735	Standard	NM_004001		Approved	CD32, CD32B	uc001gaz.2	P31994	OTTHUMG00000034470	ENST00000358671.5:c.772T>G	1.37:g.161645058T>G	ENSP00000351497:p.Tyr258Asp	324	0	0		331	141	0.425982	NM_004001	A6H8N3|O95649|Q53X85|Q5VXA9|Q8NIA1	Missense_Mutation	SNP	ENST00000358671.5	37	CCDS30924.1	23	0.010531135531135532	19	0.03861788617886179	4	0.011049723756906077	0	0.0	0	0.0	A	9.704	1.155245	0.21454	0.012262	1.16E-4	ENSG00000072694	ENST00000367962;ENST00000367960;ENST00000367961;ENST00000358671	T;T;T;T	0.27557	4.78;1.66;1.66;4.78	5.06	-1.78	0.07957	.	1.572250	0.03874	N	0.276032	T	0.04318	0.0119	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.11329	0.006;0.002	T	0.27806	-1.0063	10	0.31617	T	0.26	.	3.8406	0.08912	0.4674:0.0:0.1509:0.3817	.	251;258	P31994-3;P31994	.;FCG2B_HUMAN	D	258;251;251;258	ENSP00000356939:Y258D;ENSP00000356937:Y251D;ENSP00000356938:Y251D;ENSP00000351497:Y258D	ENSP00000351497:Y258D	Y	+	1	0	FCGR2B	159911682	0.585000	0.26774	0.642000	0.29436	0.834000	0.47266	0.095000	0.15127	-0.667000	0.05303	-0.384000	0.06662	TAC	T|0.992;G|0.008	0.008	strong		0.612	FCGR2B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000083337.4	NM_004001		G	161645058	T	G	161645058	3	3	22	1	0	0	0	0	1	0	0	0	5790	1406	49	5	794	5	FCGR2B	1	161645058	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	126825	161645058	87605563	337	3238											
UHMK1	127933	hgsc.bcm.edu	37	chr1	162467927	162467927	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttcgctgctgcggcaaccCtggctcgccccccggcgccc	2	6	13	20	5	0	0	0	0	0	0	2	0	0	0	5	4	3	5	5	4	1	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:162467927C>G	ENST00000489294.1	+	1	295	c.137C>G	c.(136-138)cCt>cGt	p.P46R	UHMK1_ENST00000538489.1_Missense_Mutation_p.P46R|UHMK1_ENST00000545294.1_Intron|UHMK1_ENST00000282169.8_3'UTR	NM_175866.4	NP_787062.1	Q8TAS1	UHMK1_HUMAN	U2AF homology motif (UHM) kinase 1	46	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)			TGCGGCAACCCTGGCTCGCCC	0.697																																					p.P46R		Atlas-SNP	.											UHMK1_ENST00000489294,NS,carcinoma,0,2	UHMK1	65	2	0			c.C137G						PASS	.						11	14	13					1																	162467927		2186	4284	6470	SO:0001583	missense	127933	exon1			GCAACCCTGGCTC	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.137C>G	1.37:g.162467927C>G	ENSP00000420270:p.Pro46Arg	115	0	0		122	57	0.467213	NM_175866	A8K8K4|G3V1M1|Q96C22	Missense_Mutation	SNP	ENST00000489294.1	37	CCDS1239.1	.	.	.	.	.	.	.	.	.	.	C	13.90	2.374293	0.42105	.	.	ENSG00000152332	ENST00000538489;ENST00000489294	T;T	0.19669	2.13;2.13	4.94	4.94	0.65067	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.064455	0.64402	D	0.000006	T	0.05044	0.0135	N	0.16166	0.38	.	.	.	P;B	0.35821	0.523;0.324	B;B	0.24541	0.054;0.053	T	0.23332	-1.0191	9	0.39692	T	0.17	-9.9211	13.8569	0.63534	0.0:1.0:0.0:0.0	.	46;46	Q8TAS1-2;Q8TAS1	.;UHMK1_HUMAN	R	46	ENSP00000446416:P46R;ENSP00000420270:P46R	ENSP00000420270:P46R	P	+	2	0	UHMK1	160734551	0.781000	0.28676	0.811000	0.32455	0.991000	0.79684	3.781000	0.55394	2.715000	0.92844	0.655000	0.94253	CCT	.	.	none		0.697	UHMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076788.1	NM_175866		G	162467927	C	G	162467927	3	3	22	1	0	0	0	0	1	0	0	0	16981	681	24	4	189	4	UHMK1	1	162467927	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	822869	162467927	86782694	338	3239											
UAP1	6675	hgsc.bcm.edu	37	chr1	162560209	162560209	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gacaaccctactactgcaagGcatgctttgatgtcccttca	10	11	7	13	0	1	1	1	1	0	0	2	2	2	1	2	1	5	3	2	1	4	4	rs61743694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:162560209G>A	ENST00000367925.1	+	7	1298	c.1266G>A	c.(1264-1266)agG>agA	p.R422R	UAP1_ENST00000367926.4_Silent_p.R422R|UAP1_ENST00000367924.1_Silent_p.R422R|UAP1_ENST00000271469.3_Silent_p.R422R|RP11-359K18.4_ENST00000609669.1_RNA			Q16222	UAP1_HUMAN	UDP-N-acetylglucosamine pyrophosphorylase 1	422					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)			CTACTGCAAGGCATGCTTTGA	0.458													G|||	119	0.023762	0.0877	0.0043	5008	,	,		19084	0.0		0.0	False		,,,				2504	0.0				p.R422R		Atlas-SNP	.											.	UAP1	47	.	0			c.G1266A						PASS	.	G		377,4029	191.2+/-216.9	15,347,1841	174	159	164		1266	1	0.6	1	dbSNP_129	164	8,8592	5.0+/-18.6	0,8,4292	no	coding-synonymous	UAP1	NM_003115.4		15,355,6133	AA,AG,GG		0.093,8.5565,2.9602		422/506	162560209	385,12621	2203	4300	6503	SO:0001819	synonymous_variant	6675	exon8			TGCAAGGCATGCT	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.1266G>A	1.37:g.162560209G>A		167	0	0		162	88	0.54321	NM_003115	B2R6R8|Q5VTA9|Q5VTB0|Q5VTB1|Q96GM2	Silent	SNP	ENST00000367925.1	37																																																																																				G|0.969;A|0.031	0.031	strong		0.458	UAP1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000083203.1	NM_003115		A	162560209	G	A	162560209	2	1	22	1	0	0	0	0	0	0	0	1	16840	1194	42	2		2	UAP1	1	162560209	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	92282	162560209	86690412	339	3240											
UCK2	7371	hgsc.bcm.edu	37	chr1	165859482	165859482	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcagctcctggggcagaaTgaggtggactatcgccagaa	10	7	15	9	1	0	3	0	1	0	2	2	4	1	4	2	4	2	3	2	4	3	1	rs145654595		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:165859482T>C	ENST00000367879.4	+	2	444	c.141T>C	c.(139-141)aaT>aaC	p.N47N	UCK2_ENST00000372212.4_Silent_p.N47N	NM_012474.4	NP_036606.2	Q9BZX2	UCK2_HUMAN	uridine-cytidine kinase 2	47					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)					TGGGGCAGAATGAGGTGGACT	0.557																																					p.N47N		Atlas-SNP	.											.	UCK2	31	.	0			c.T141C						PASS	.	T		2,4404	4.2+/-10.8	0,2,2201	138	120	126		141	-3.1	1	1	dbSNP_134	126	0,8600		0,0,4300	no	coding-synonymous	UCK2	NM_012474.4		0,2,6501	CC,CT,TT		0.0,0.0454,0.0154		47/262	165859482	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	7371	exon2			GCAGAATGAGGTG	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.141T>C	1.37:g.165859482T>C		207	0	0		243	118	0.485597	NM_012474	Q5VV91|Q7KZV3|Q92528|Q96KG5|Q9BU42	Silent	SNP	ENST00000367879.4	37	CCDS1252.1																																																																																			T|1.000;C|0.000	0.000	weak		0.557	UCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096753.1	NM_012474		C	165859482	T	C	165859482	2	2	22	1	0	0	0	0	0	0	0	1	16939	1461	51	3		3	UCK2	1	165859482	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	3299273	165859482	83391139	340	3241											
DUSP27	92235	hgsc.bcm.edu	37	chr1	167095768	167095768	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaccacggcaggaggcgccGcgcagactcgatgtcctcgg	7	4	16	14	6	0	1	0	0	0	1	3	4	1	3	3	5	0	2	3	5	0	0			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:167095768G>A	ENST00000361200.2	+	6	1566	c.1400G>A	c.(1399-1401)cGc>cAc	p.R467H	DUSP27_ENST00000443333.1_Missense_Mutation_p.R467H|DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000271385.5_Missense_Mutation_p.R467H			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	467					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.R467H(1)		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						AGGAGGCGCCGCGCAGACTCG	0.652																																					p.R467H		Atlas-SNP	.											DUSP27,NS,carcinoma,0,2	DUSP27	235	2	1	Substitution - Missense(1)	lung(1)	c.G1400A						PASS	.						21	21	21					1																	167095768		2202	4300	6502	SO:0001583	missense	92235	exon5			GGCGCCGCGCAGA	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.1400G>A	1.37:g.167095768G>A	ENSP00000354483:p.Arg467His	83	0	0		98	13	0.132653	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	37	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	G	13.16	2.155451	0.38021	.	.	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.03607	3.87;3.87;3.87	5.02	4.1	0.47936	.	0.086313	0.49305	D	0.000150	T	0.02649	0.0080	M	0.67953	2.075	0.30396	N	0.780517	B	0.19817	0.039	B	0.12156	0.007	T	0.12268	-1.0554	10	0.87932	D	0	-16.6929	13.7869	0.63115	0.076:0.0:0.924:0.0	.	467	Q5VZP5	DUS27_HUMAN	H	467	ENSP00000354483:R467H;ENSP00000271385:R467H;ENSP00000404874:R467H	ENSP00000271385:R467H	R	+	2	0	DUSP27	165362392	0.650000	0.27331	0.790000	0.31976	0.263000	0.26337	2.340000	0.43974	2.291000	0.77112	0.643000	0.83706	CGC	.	.	none		0.652	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		A	167095768	G	A	167095768	3	1	22	1	0	0	0	0	1	0	0	0	4826	1087	38	1	1418	1	DUSP27	1	167095768	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1236286	167095768	82154853	341	3242											
DUSP27	92235	hgsc.bcm.edu	37	chr1	167096770	167096770	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catgcagtctgtgctgtcctGcaacaccacactgagctcac	9	9	8	15	0	2	1	1	1	1	0	3	1	3	1	2	0	5	4	2	0	1	0	rs371850525		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:167096770G>C	ENST00000361200.2	+	6	2568	c.2402G>C	c.(2401-2403)tGc>tCc	p.C801S	DUSP27_ENST00000443333.1_Missense_Mutation_p.C801S|DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000271385.5_Missense_Mutation_p.C801S			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	801					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						GTGCTGTCCTGCAACACCACA	0.567																																					p.C801S		Atlas-SNP	.											.	DUSP27	235	.	0			c.G2402C						PASS	.	G	SER/CYS	1,4405	2.1+/-5.4	0,1,2202	83	74	77		2402	3.2	0.9	1		77	0,8600		0,0,4300	no	missense	DUSP27	NM_001080426.1	112	0,1,6502	CC,CG,GG		0.0,0.0227,0.0077	benign	801/1159	167096770	1,13005	2203	4300	6503	SO:0001583	missense	92235	exon5			TGTCCTGCAACAC	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.2402G>C	1.37:g.167096770G>C	ENSP00000354483:p.Cys801Ser	96	0	0		94	41	0.43617	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	37	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.752901	0.00085	2.27E-4	0.0	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.03035	4.07;4.07;4.07	5.17	3.24	0.37175	.	1.061880	0.07353	N	0.882768	T	0.00412	0.0013	N	0.01352	-0.895	0.18873	N	0.999988	B	0.02656	0.0	B	0.04013	0.001	T	0.33033	-0.9884	10	0.05721	T	0.95	-3.5335	9.1613	0.37023	0.1176:0.3669:0.5156:0.0	.	801	Q5VZP5	DUS27_HUMAN	S	801	ENSP00000354483:C801S;ENSP00000271385:C801S;ENSP00000404874:C801S	ENSP00000271385:C801S	C	+	2	0	DUSP27	165363394	0.260000	0.24053	0.904000	0.35570	0.039000	0.13416	0.246000	0.18160	1.143000	0.42306	-0.371000	0.07208	TGC	.	.	none		0.567	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		C	167096770	G	C	167096770	3	2	22	1	0	0	0	0	1	0	0	0	4826	1319	46	4	2420	4	DUSP27	1	167096770	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1002	167096770	82153851	342	3243											
XCL1	6375	hgsc.bcm.edu	37	chr1	168549321	168549321	+	Missense_Mutation	SNP	G	G	C																															gtgtagggagtgaagtctcaGataagaggacctgtgtgagc																								rs56148248	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:168549321G>C	ENST00000367818.3	+	2	247	c.82G>C	c.(82-84)Gat>Cat	p.D28H		NM_002995.2	NP_002986.1	P47992	XCL1_HUMAN	chemokine (C motif) ligand 1	28					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)					TGAAGTCTCAGATAAGAGGAC	0.433													G|||	160	0.0319489	0.115	0.0029	5008	,	,		19069	0.001		0.005	False		,,,				2504	0.0				p.D28H		Atlas-SNP	.											.	XCL1	16	.	0			c.G82C						PASS	.	G	HIS/ASP	274,4132		34,206,1963	129	132	131		82	0.2	0	1	dbSNP_129	131	4,8596		0,4,4296	no	missense	XCL1	NM_002995.2	81	34,210,6259	CC,CG,GG		0.0465,6.2188,2.1375	benign	28/115	168549321	278,12728	2203	4300	6503	SO:0001583	missense	6375	exon2			GTCTCAGATAAGA	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.82G>C	1.37:g.168549321G>C	ENSP00000356792:p.Asp28His	281	0	0		161	68	0.42236	NM_002995	Q52MA8	Missense_Mutation	SNP	ENST00000367818.3	37	CCDS1274.1	44	0.020146520146520148	37	0.07520325203252033	2	0.0055248618784530384	1	0.0017482517482517483	4	0.005277044854881266	G	11.98	1.801914	0.31869	0.062188	4.65E-4	ENSG00000143184	ENST00000367818	T	0.03982	3.74	4.36	0.171	0.15026	Chemokine interleukin-8-like domain (2);	1.336140	0.04578	N	0.394548	T	0.02193	0.0068	L	0.29908	0.895	0.25228	N	0.98985	P	0.44309	0.832	P	0.49085	0.6	T	0.37009	-0.9724	9	0.62326	D	0.03	-0.0463	3.0265	0.06092	0.0977:0.3375:0.3913:0.1734	rs56148248	28	P47992	XCL1_HUMAN	H	28	ENSP00000356792:D28H	ENSP00000356792:D28H	D	+	1	0	XCL1	166815945	0.001000	0.12720	0.006000	0.13384	0.548000	0.35241	0.157000	0.16402	0.172000	0.19760	0.655000	0.94253	GAT	G|0.982;C|0.018	0.018	strong		0.433	XCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083612.1	NM_002995		C	168549321	G	C	168549321	3	2	22	1	0	0	0	0	1	0	0	0	17438	942	33	4	88	4	XCL1	1	168549321	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1452551	168549321	80701300	343	3244	48	2									
XCL1	6375	hgsc.bcm.edu	37	chr1	168549325	168549325	+	Missense_Mutation	SNP	A	A	G																															agggagtgaagtctcagataAgaggacctgtgtgagcctca																								rs61546281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:168549325A>G	ENST00000367818.3	+	2	251	c.86A>G	c.(85-87)aAg>aGg	p.K29R		NM_002995.2	NP_002986.1	P47992	XCL1_HUMAN	chemokine (C motif) ligand 1	29					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)					GTCTCAGATAAGAGGACCTGT	0.443													A|||	162	0.0323482	0.1165	0.0029	5008	,	,		19121	0.001		0.005	False		,,,				2504	0.0				p.K29R		Atlas-SNP	.											.	XCL1	16	.	0			c.A86G						PASS	.	A	ARG/LYS	158,4248		35,88,2080	131	134	133		86	-0.5	0	1	dbSNP_129	133	2,8598		0,2,4298	no	missense	XCL1	NM_002995.2	26	35,90,6378	GG,GA,AA		0.0233,3.586,1.2302	benign	29/115	168549325	160,12846	2203	4300	6503	SO:0001583	missense	6375	exon2			CAGATAAGAGGAC	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.86A>G	1.37:g.168549325A>G	ENSP00000356792:p.Lys29Arg	292	0	0		170	68	0.4	NM_002995	Q52MA8	Missense_Mutation	SNP	ENST00000367818.3	37	CCDS1274.1	41	0.018772893772893772	35	0.07113821138211382	1	0.0027624309392265192	1	0.0017482517482517483	4	0.005277044854881266	A	4.417	0.077069	0.08485	0.03586	2.33E-4	ENSG00000143184	ENST00000367818	T	0.04809	3.55	4.36	-0.539	0.11865	Chemokine interleukin-8-like domain (3);	0.562682	0.17985	N	0.155390	T	0.00936	0.0031	N	0.26162	0.8	0.25269	N	0.989532	B	0.10296	0.003	B	0.08055	0.003	T	0.48317	-0.9046	9	0.16896	T	0.51	-0.7914	7.4105	0.27016	0.483:0.0:0.517:0.0	rs61546281	29	P47992	XCL1_HUMAN	R	29	ENSP00000356792:K29R	ENSP00000356792:K29R	K	+	2	0	XCL1	166815949	0.000000	0.05858	0.002000	0.10522	0.518000	0.34316	-0.858000	0.04281	0.011000	0.14865	0.533000	0.62120	AAG	A|0.981;G|0.019	0.019	strong		0.443	XCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083612.1	NM_002995		G	168549325	A	G	168549325	3	3	22	1	0	0	0	0	1	0	0	0	17438	72	3	3	92	3	XCL1	1	168549325	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	4	168549325	80701296	344	3245	48	2									
BLZF1	8548	hgsc.bcm.edu	37	chr1	169345883	169345883	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtccaatctagaaagcatcAtagtcttcagagtccatgga	14	10	8	9	0	4	2	2	0	2	2	6	3	6	3	2	1	1	1	2	1	4	3	rs112226207	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:169345883A>G	ENST00000367808.3	+	3	557	c.134A>G	c.(133-135)cAt>cGt	p.H45R	BLZF1_ENST00000329281.2_Missense_Mutation_p.H45R|BLZF1_ENST00000367807.3_Missense_Mutation_p.H45R			Q9H2G9	GO45_HUMAN	basic leucine zipper nuclear factor 1	45					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)					AGAAAGCATCATAGTCTTCAG	0.453													A|||	8	0.00159744	0.0053	0.0014	5008	,	,		18203	0.0		0.0	False		,,,				2504	0.0				p.H45R		Atlas-SNP	.											.	BLZF1	57	.	0			c.A134G						PASS	.	A	ARG/HIS	30,4376	36.0+/-67.5	0,30,2173	95	95	95		134	-1.9	0	1	dbSNP_132	95	0,8600		0,0,4300	yes	missense	BLZF1	NM_003666.2	29	0,30,6473	GG,GA,AA		0.0,0.6809,0.2307	benign	45/401	169345883	30,12976	2203	4300	6503	SO:0001583	missense	8548	exon3			AGCATCATAGTCT	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.134A>G	1.37:g.169345883A>G	ENSP00000356782:p.His45Arg	143	0	0		144	71	0.493056	NM_003666	O15298|Q5T531|Q5T533|Q9GZX4	Missense_Mutation	SNP	ENST00000367808.3	37	CCDS1278.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	A	4.096	0.015897	0.07959	0.006809	0.0	ENSG00000117475	ENST00000367808;ENST00000329281;ENST00000367807;ENST00000420531;ENST00000426663	T;T;T;T;T	0.42513	1.57;1.57;0.97;0.97;1.57	5.27	-1.89	0.07689	.	0.566329	0.20243	N	0.096258	T	0.07234	0.0183	N	0.22421	0.69	0.26193	N	0.979556	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.001;0.001;0.003	T	0.34279	-0.9835	9	0.09590	T	0.72	-2.9441	6.7849	0.23668	0.5046:0.3627:0.1328:0.0	.	45;45;45	A8K6R0;Q9H2G9;Q9H2G9-2	.;GO45_HUMAN;.	R	45	ENSP00000356782:H45R;ENSP00000327541:H45R;ENSP00000356781:H45R;ENSP00000414668:H45R;ENSP00000404408:H45R	ENSP00000327541:H45R	H	+	2	0	BLZF1	167612507	0.001000	0.12720	0.000000	0.03702	0.695000	0.40330	0.633000	0.24598	-0.247000	0.09597	-0.389000	0.06534	CAT	A|0.997;G|0.003	0.003	strong		0.453	BLZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086109.1	NM_003666		G	169345883	A	G	169345883	3	3	22	1	0	0	0	0	1	0	0	0	1453	217	8	3	140	3	BLZF1	1	169345883	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	796558	169345883	79904738	345	3246											
SLC19A2	10560	hgsc.bcm.edu	37	chr1	169446639	169446639	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagatgacattcaggctgaaCagcgaccagcctgccactga	12	6	11	12	1	1	4	1	3	0	1	1	6	1	4	3	1	4	1	3	1	1	1	rs150548640	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:169446639C>A	ENST00000236137.5	-	2	797	c.561G>T	c.(559-561)ctG>ctT	p.L187L	SLC19A2_ENST00000367804.4_Intron	NM_006996.2	NP_008927.1	O60779	S19A2_HUMAN	solute carrier family 19 (thiamine transporter), member 2	187					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)	TCAGGCTGAACAGCGACCAGC	0.498													C|||	17	0.00339457	0.0106	0.0043	5008	,	,		19254	0.0		0.0	False		,,,				2504	0.0				p.L187L		Atlas-SNP	.											.	SLC19A2	35	.	0			c.G561T						PASS	.	C		48,4358	49.6+/-84.7	1,46,2156	57	59	58		561	-1.5	1	1	dbSNP_134	58	0,8600		0,0,4300	no	coding-synonymous	SLC19A2	NM_006996.2		1,46,6456	AA,AC,CC		0.0,1.0894,0.3691		187/498	169446639	48,12958	2203	4300	6503	SO:0001819	synonymous_variant	10560	exon2			GCTGAACAGCGAC	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.561G>T	1.37:g.169446639C>A		76	0	0		82	50	0.609756	NM_006996	B2R9H0|B4E1X4|Q8WV87|Q9UBL7|Q9UKJ2|Q9UN31|Q9UN43	Silent	SNP	ENST00000236137.5	37	CCDS1280.1																																																																																			C|0.996;A|0.004	0.004	strong		0.498	SLC19A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086106.1	NM_006996		A	169446639	C	A	169446639	2	1	22	1	0	0	0	0	0	0	0	1	14444	465	17	4		4	SLC19A2	1	169446639	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	100756	169446639	79803982	346	3247											
SELE	6401	hgsc.bcm.edu	37	chr1	169697218	169697218	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccttcacatgtgggcttctcGttgtcccactcccctgtggg	3	13	10	15	1	2	0	1	0	1	0	5	0	4	0	4	2	0	2	4	2	0	3	rs5365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:169697218G>A	ENST00000333360.7	-	8	1399	c.1260C>T	c.(1258-1260)aaC>aaT	p.N420N	SELE_ENST00000367777.1_Silent_p.N420N|SELE_ENST00000367774.1_Intron|C1orf112_ENST00000498289.1_Intron|SELE_ENST00000367776.1_Intron|SELE_ENST00000367780.4_Intron|SELE_ENST00000367781.4_Intron|SELE_ENST00000367779.4_Intron|SELE_ENST00000367782.4_Silent_p.N420N|SELE_ENST00000367775.1_Intron	NM_000450.2	NP_000441.2	P16581	LYAM2_HUMAN	selectin E	420	Sushi 4. {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)	TGGGCTTCTCGTTGTCCCACT	0.448													G|||	101	0.0201677	0.0756	0.0014	5008	,	,		19018	0.0		0.0	False		,,,				2504	0.0				p.N420N		Atlas-SNP	.											.	SELE	84	.	0			c.C1260T						PASS	.	G		284,4122	157.0+/-190.0	5,274,1924	96	109	104		1260	-10.5	0	1	dbSNP_52	104	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SELE	NM_000450.2		5,276,6222	AA,AG,GG		0.0233,6.4458,2.199		420/611	169697218	286,12720	2203	4300	6503	SO:0001819	synonymous_variant	6401	exon8			CTTCTCGTTGTCC	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.1260C>T	1.37:g.169697218G>A		67	0	0		60	27	0.45	NM_000450	A2RRD6|P16111	Silent	SNP	ENST00000333360.7	37	CCDS1283.1																																																																																			G|0.982;A|0.018	0.018	strong		0.448	SELE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084333.1	NM_000450		A	169697218	G	A	169697218	2	1	22	1	0	0	0	0	0	0	0	1	14028	1136	40	1		1	SELE	1	169697218	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	250579	169697218	79553403	347	3248											
C1orf112	55732	hgsc.bcm.edu	37	chr1	169796197	169796197	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctctcccttcccagcaagtTtcctccaagcctttatgcta	7	14	4	16	0	1	0	0	0	1	0	6	0	5	0	5	0	3	3	5	0	4	5	rs142988055	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:169796197T>C	ENST00000286031.6	+	11	1554	c.854T>C	c.(853-855)tTt>tCt	p.F285S	C1orf112_ENST00000413811.2_Missense_Mutation_p.F256S|C1orf112_ENST00000498289.1_3'UTR|C1orf112_ENST00000359326.4_Missense_Mutation_p.F285S	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	285										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)					CCCAGCAAGTTTCCTCCAAGC	0.388													T|||	89	0.0177716	0.0658	0.0029	5008	,	,		14059	0.0		0.0	False		,,,				2504	0.0				p.F285S		Atlas-SNP	.											.	C1orf112	74	.	0			c.T854C						PASS	.	T	SER/PHE	258,4148	144.2+/-179.2	8,242,1953	87	87	87		854	5	1	1	dbSNP_134	87	0,8600		0,0,4300	yes	missense	C1orf112	NM_018186.2	155	8,242,6253	CC,CT,TT		0.0,5.8557,1.9837	probably-damaging	285/854	169796197	258,12748	2203	4300	6503	SO:0001583	missense	55732	exon11			GCAAGTTTCCTCC	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.854T>C	1.37:g.169796197T>C	ENSP00000286031:p.Phe285Ser	242	0	0		242	125	0.516529	NM_018186	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Missense_Mutation	SNP	ENST00000286031.6	37	CCDS1285.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	T	18.57	3.652833	0.67472	0.058557	0.0	ENSG00000000460	ENST00000413811;ENST00000359326;ENST00000286031	T;T;T	0.58210	0.35;0.35;0.35	5.04	5.04	0.67666	.	0.088478	0.85682	D	0.000000	T	0.64034	0.2562	M	0.78637	2.42	0.46011	D	0.998815	D;P;D	0.61080	0.979;0.91;0.989	P;P;D	0.66084	0.776;0.821;0.941	T	0.70317	-0.4905	10	0.72032	D	0.01	-12.7977	13.0228	0.58799	0.0:0.0:0.0:1.0	.	256;227;285	B4E0A9;B4DGF2;Q9NSG2	.;.;CA112_HUMAN	S	256;285;285	ENSP00000389257:F256S;ENSP00000352276:F285S;ENSP00000286031:F285S	ENSP00000286031:F285S	F	+	2	0	C1orf112	168062821	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	3.338000	0.52128	2.002000	0.58637	0.528000	0.53228	TTT	T|0.984;C|0.016	0.016	strong		0.388	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186		C	169796197	T	C	169796197	3	2	22	1	0	0	0	0	1	0	0	0	1987	1841	64	3	888	3	C1orf112	1	169796197	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	98979	169796197	79454424	348	3249											
C1orf112	55732	hgsc.bcm.edu	37	chr1	169796859	169796859	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tattacatgtaagacctgccAtgtgaactgcagtttccaca	12	12	7	10	0	0	2	0	1	0	1	1	2	1	2	3	0	4	3	3	0	4	4	rs149832132	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:169796859A>C	ENST00000286031.6	+	12	1705	c.1005A>C	c.(1003-1005)ccA>ccC	p.P335P	C1orf112_ENST00000413811.2_Intron|C1orf112_ENST00000498289.1_3'UTR|C1orf112_ENST00000359326.4_Silent_p.P335P	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	335										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)					AAGACCTGCCATGTGAACTGC	0.398													A|||	14	0.00279553	0.0106	0.0	5008	,	,		19847	0.0		0.0	False		,,,				2504	0.0				p.P335P		Atlas-SNP	.											.	C1orf112	74	.	0			c.A1005C						PASS	.	A		42,4364	45.3+/-79.5	0,42,2161	348	345	346		1005	-10.8	0	1	dbSNP_134	346	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	C1orf112	NM_018186.2		0,43,6460	CC,CA,AA		0.0116,0.9532,0.3306		335/854	169796859	43,12963	2203	4300	6503	SO:0001819	synonymous_variant	55732	exon12			CCTGCCATGTGAA	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.1005A>C	1.37:g.169796859A>C		67	0	0		76	26	0.342105	NM_018186	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Silent	SNP	ENST00000286031.6	37	CCDS1285.1																																																																																			A|0.997;C|0.003	0.003	strong		0.398	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186		C	169796859	A	C	169796859	2	2	22	1	0	0	0	0	0	0	0	1	1987	204	8	5		5	C1orf112	1	169796859	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	662	169796859	79453762	349	3250											
FMO3	2328	hgsc.bcm.edu	37	chr1	171076888	171076888	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gggatgttaccactgaaaggGatggtaaaaaagaatcggct	15	8	13	5	1	0	2	0	1	0	1	1	4	0	4	1	4	1	3	1	4	6	2	rs12072582	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:171076888G>C	ENST00000367755.4	+	4	505	c.394G>C	c.(394-396)Gat>Cat	p.D132H	FMO3_ENST00000542847.1_Missense_Mutation_p.D112H|FMO3_ENST00000538429.1_Missense_Mutation_p.D69H|FMO3_ENST00000392085.2_Missense_Mutation_p.D132H	NM_001002294.2	NP_001002294.1	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	132			D -> H (in dbSNP:rs12072582). {ECO:0000269|PubMed:12527699, ECO:0000269|Ref.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)	CACTGAAAGGGATGGTAAAAA	0.413													G|||	73	0.0145767	0.0522	0.0058	5008	,	,		15662	0.0		0.0	False		,,,				2504	0.0				p.D132H		Atlas-SNP	.											.	FMO3	73	.	0			c.G394C	GRCh37	CM033905	FMO3	M	rs12072582	PASS	.	G	HIS/ASP,HIS/ASP	176,4230	113.8+/-151.8	2,172,2029	132	133	133		394,394	-2.1	0	1	dbSNP_120	133	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	FMO3	NM_001002294.2,NM_006894.5	81,81	2,173,6328	CC,CG,GG		0.0116,3.9946,1.3609	benign,benign	132/533,132/533	171076888	177,12829	2203	4300	6503	SO:0001583	missense	2328	exon4			GAAAGGGATGGTA	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.394G>C	1.37:g.171076888G>C	ENSP00000356729:p.Asp132His	176	0	0		189	73	0.386243	NM_006894	B2R816|Q14854|Q8N5N5	Missense_Mutation	SNP	ENST00000367755.4	37	CCDS1292.1	23	0.010531135531135532	20	0.04065040650406504	3	0.008287292817679558	0	0.0	0	0.0	G	8.560	0.877541	0.17395	0.039946	1.16E-4	ENSG00000007933	ENST00000367755;ENST00000392085;ENST00000542847;ENST00000538429	T;T;T;T	0.57436	0.4;0.4;0.4;0.4	4.84	-2.13	0.07144	.	0.100095	0.64402	N	0.000003	T	0.26085	0.0636	M	0.65677	2.01	0.34737	D	0.730401	B;B;B	0.26512	0.151;0.09;0.036	B;B;B	0.31245	0.126;0.069;0.078	T	0.02588	-1.1137	10	0.49607	T	0.09	-2.9075	3.4783	0.07593	0.1388:0.3402:0.4052:0.1158	rs12072582;rs52790216;rs58199544;rs12072582	69;112;132	F5H261;F5GZZ8;P31513	.;.;FMO3_HUMAN	H	132;132;112;69	ENSP00000356729:D132H;ENSP00000375935:D132H;ENSP00000444073:D112H;ENSP00000439500:D69H	ENSP00000356729:D132H	D	+	1	0	FMO3	169343512	0.005000	0.15991	0.035000	0.18076	0.054000	0.15201	0.421000	0.21280	-0.407000	0.07576	0.591000	0.81541	GAT	G|0.983;C|0.017	0.017	strong		0.413	FMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086219.1	NM_006894		C	171076888	G	C	171076888	3	2	22	1	0	0	0	0	1	0	0	0	5964	1174	41	4	404	4	FMO3	1	171076888	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1280029	171076888	78173733	350	3251											
FMO2	2327	hgsc.bcm.edu	37	chr1	171162551	171162552	+	In_Frame_Ins	INS	-	-	GAC																															aagaaatgtcctgtttcagtINSgactttccaatgcctgaaga																								rs2020868|rs397844260	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:171162551_171162552insGAC	ENST00000209929.7	+	3	368_369	c.210_211insGAC	c.(211-213)gac>GACgac	p.71_71D>DD	FMO2_ENST00000529935.1_3'UTR|FMO2_ENST00000441535.1_In_Frame_Ins_p.71_71D>DD			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	71					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)					CCTGTTTCAGTGACTTTCCAAT	0.342														516	0.103035	0.298	0.0476	5008	,	,		17166	0.002		0.0447	False		,,,				2504	0.0429				p.S70delinsSD		Pindel,Atlas-Indel	.											.	FMO2	66	.	0			c.210_211insGAC						PASS	.			1054,3212		148,758,1227						4.3	1		dbSNP_98	103	398,7856		12,374,3741	no	coding	FMO2	NM_001460.2		160,1132,4968	A1A1,A1R,RR		4.8219,24.707,11.5974				1452,11068				SO:0001652	inframe_insertion	2327	exon3			.	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.211_213dupGAC	1.37:g.171162552_171162554dupGAC	ENSP00000209929:p.Asp71dup	76	0	.		58	19	0.328	NM_001460	Q53XR0	In_Frame_Ins	INS	ENST00000209929.7	37	CCDS1293.1																																																																																			-|0.904;GAC|0.096	0.096	strong		0.342	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460		GAC	171162552	-	GAC	171162551	7	5	22	1	0	1	1	0	0	0	0	0	5963	1693	59	0	216	0	FMO2	1	171162551	In_Frame_Ins	INS	-	TCGA-G8-6324-01A-11D-2210-10	85663	171162551	78088070	351	3252											
FMO2	2327	hgsc.bcm.edu	37	chr1	171162583	171162583	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctgaagattttccaaactTcctgcataattctaaacttc	12	14	4	11	0	1	2	0	1	1	1	4	2	3	2	3	0	3	1	3	0	5	7	rs2020860	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:171162583T>C	ENST00000209929.7	+	3	400	c.242T>C	c.(241-243)tTc>tCc	p.F81S	FMO2_ENST00000529935.1_3'UTR|FMO2_ENST00000441535.1_Missense_Mutation_p.F81S			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	81					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)					TTTCCAAACTTCCTGCATAAT	0.353													T|||	516	0.103035	0.298	0.0476	5008	,	,		16096	0.002		0.0447	False		,,,				2504	0.0429				p.F81S		Atlas-SNP	.											FMO2,colon,carcinoma,+1,1	FMO2	66	1	0			c.T242C						PASS	.	T	SER/PHE	1075,3331	373.0+/-320.6	151,773,1279	75	76	75		242	5.4	1	1	dbSNP_98	75	409,8191	123.1+/-182.0	13,383,3904	yes	missense	FMO2	NM_001460.2	155	164,1156,5183	CC,CT,TT		4.7558,24.3985,11.4101	probably-damaging	81/472	171162583	1484,11522	2203	4300	6503	SO:0001583	missense	2327	exon3			CAAACTTCCTGCA	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.242T>C	1.37:g.171162583T>C	ENSP00000209929:p.Phe81Ser	66	0	0		55	24	0.436364	NM_001460	Q53XR0	Missense_Mutation	SNP	ENST00000209929.7	37	CCDS1293.1	205	0.09386446886446886	156	0.3170731707317073	18	0.049723756906077346	0	0.0	31	0.040897097625329816	T	22.7	4.324261	0.81580	0.243985	0.047558	ENSG00000094963	ENST00000209929;ENST00000441535	T;T	0.60920	0.15;0.15	5.44	5.44	0.79542	.	0.172296	0.53938	D	0.000041	T	0.81754	0.4889	H	0.97265	3.97	0.23834	P	0.99671674	D	0.76494	0.999	D	0.78314	0.991	D	0.88765	0.3260	9	0.87932	D	0	-14.2724	15.165	0.72818	0.0:0.0:0.0:1.0	rs2020860;rs2266704;rs56518508;rs57046818;rs2020860	81	Q99518	FMO2_HUMAN	S	81	ENSP00000209929:F81S;ENSP00000405905:F81S	ENSP00000209929:F81S	F	+	2	0	FMO2	169429207	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.960000	0.49161	2.062000	0.61559	0.533000	0.62120	TTC	T|0.895;C|0.105	0.105	strong		0.353	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460		C	171162583	T	C	171162583	3	2	22	1	0	0	0	0	1	0	0	0	5963	1783	62	3	248	3	FMO2	1	171162583	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	32	171162583	78088038	352	3253											
FMO2	2327	hgsc.bcm.edu	37	chr1	171165803	171165803	+	Frame_Shift_Del	DEL	G	G	-																															tcaagacaactgtccttagtGtgagaaaatgtccagatttc																								rs28369860	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:171165803delG	ENST00000209929.7	+	4	495	c.337delG	c.(337-339)gtgfs	p.V113fs	RP1-127D3.4_ENST00000422841.1_RNA|RP1-127D3.4_ENST00000445290.1_RNA|RP1-127D3.4_ENST00000445909.1_RNA|FMO2_ENST00000529935.1_3'UTR|FMO2_ENST00000441535.1_Frame_Shift_Del_p.V113fs			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	113					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)					TGTCCTTAGTGTGAGAAAATG	0.453													G|G|-|deletion	515	0.102835	0.2973	0.0476	5008	,	,		22626	0.002		0.0447	False		,,,				2504	0.0429				p.S112fs		Pindel,Atlas-Indel	.											.	FMO2	66	.	0			c.336delT	GRCh37	CD033950	FMO2	D	rs28369860	PASS	.			1055,3211		149,757,1227	106	106	106			2.2	1	1	dbSNP_125	115	398,7856		12,374,3741	no	frameshift	FMO2	NM_001460.2		161,1131,4968	A1A1,A1R,RR		4.8219,24.7304,11.6054			171165803	1453,11067	2093	4290	6383	SO:0001589	frameshift_variant	2327	exon4			.	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.337delG	1.37:g.171165803delG	ENSP00000209929:p.Val113fs	184	0	.		155	43	0.277	NM_001460	Q53XR0	Frame_Shift_Del	DEL	ENST00000209929.7	37	CCDS1293.1																																																																																			.	.	weak		0.453	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460		-	171165803	G	-	171165803	7	5	22	1	0	1	0	1	0	0	0	0	5963	1377	48	0	347	0	FMO2	1	171165803	Frame_Shift_Del	DEL	G	TCGA-G8-6324-01A-11D-2210-10	3220	171165803	78084818	353	3254											
FMO2	2327	hgsc.bcm.edu	37	chr1	171176879	171176879	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttgtgtagcctgccctcagaGagaactatgatgatggacat	11	11	11	8	0	1	4	1	2	0	2	1	6	1	5	2	1	3	1	2	1	3	3	rs6671692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:171176879G>A	ENST00000209929.7	+	8	1364	c.1206G>A	c.(1204-1206)gaG>gaA	p.E402E	RP1-127D3.4_ENST00000422841.1_RNA|RP1-127D3.4_ENST00000445290.1_RNA|RP1-127D3.4_ENST00000445909.1_RNA|FMO2_ENST00000529935.1_3'UTR|FMO2_ENST00000441535.1_Silent_p.E402E			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	401					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)					TGCCCTCAGAGAGAACTATGA	0.313													G|||	232	0.0463259	0.1573	0.0115	5008	,	,		19971	0.0		0.001	False		,,,				2504	0.0153				p.E402E		Atlas-SNP	.											.	FMO2	66	.	0			c.G1206A						PASS	.	G		502,3904	229.4+/-244.0	26,450,1727	100	106	104		1206	5.8	0.5	1	dbSNP_116	104	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	FMO2	NM_001460.2		26,456,6021	AA,AG,GG		0.0698,11.3936,3.9059		402/472	171176879	508,12498	2203	4300	6503	SO:0001819	synonymous_variant	2327	exon8			CTCAGAGAGAACT	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.1206G>A	1.37:g.171176879G>A		206	0	0		196	86	0.438776	NM_001460	Q53XR0	Silent	SNP	ENST00000209929.7	37	CCDS1293.1																																																																																			G|0.953;A|0.047	0.047	strong		0.313	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460		A	171176879	G	A	171176879	2	1	22	1	0	0	0	0	0	0	0	1	5963	933	33	2		2	FMO2	1	171176879	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	11076	171176879	78073742	354	3255											
BAT2L2	23215	hgsc.bcm.edu	37	chr1	171553209	171553209	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaacttgccaaggcacaatcCggtcttgcctttcagcaaac	11	9	8	13	1	2	0	1	0	1	0	3	1	3	0	3	2	5	2	3	2	4	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:171553209C>T	ENST00000338920.4	+	29	7755	c.7518C>T	c.(7516-7518)tcC>tcT	p.S2506S	PRRC2C_ENST00000392078.3_Silent_p.S2508S|PRRC2C_ENST00000367742.3_Silent_p.S2508S|PRRC2C_ENST00000426496.2_Silent_p.S2441S	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	2506	Gln-rich.				hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										AGGCACAATCCGGTCTTGCCT	0.463																																					p.S2506S		Atlas-SNP	.											.	.	.	.	0			c.C7518T						PASS	.						181	172	175					1																	171553209		2203	4300	6503	SO:0001819	synonymous_variant	23215	exon29			ACAATCCGGTCTT	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.7518C>T	1.37:g.171553209C>T		254	0	0		272	133	0.488971	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Silent	SNP	ENST00000338920.4	37	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	C	5.989	0.366324	0.11352	.	.	ENSG00000117523	ENST00000495585	.	.	.	5.98	-12.0	0.00017	.	.	.	.	.	T	0.19805	0.0476	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54702	-0.8254	4	.	.	.	.	4.6701	0.12685	0.2829:0.418:0.1692:0.1299	.	.	.	.	L	989	.	.	P	+	2	0	PRRC2C	169819833	0.000000	0.05858	0.002000	0.10522	0.916000	0.54674	-2.380000	0.01066	-4.069000	0.00076	-2.084000	0.00378	CCG	.	.	none		0.463	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		T	171553209	C	T	171553209	2	4	22	1	0	0	0	0	0	0	0	1	1321	639	23	1		1	BAT2L2	1	171553209	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	376330	171553209	77697412	355	3256											
FASLG	356	hgsc.bcm.edu	37	chr1	172628488	172628488	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaggccaccaccaccaccGccaccgccaccactaccacc	11	1	6	23	2	0	0	0	0	0	0	0	1	0	1	11	2	1	0	11	2	1	1	rs61756244	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:172628488G>A	ENST00000367721.2	+	1	331	c.147G>A	c.(145-147)ccG>ccA	p.P49P	FASLG_ENST00000340030.3_Silent_p.P49P	NM_000639.1	NP_000630.1	P48023	TNFL6_HUMAN	Fas ligand (TNF superfamily, member 6)	49	Poly-Pro.|Pro-rich.				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)|cellular chloride ion homeostasis (GO:0030644)|endosomal lumen acidification (GO:0048388)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|immune response (GO:0006955)|inflammatory cell apoptotic process (GO:0006925)|necroptotic process (GO:0070266)|necroptotic signaling pathway (GO:0097527)|negative regulation of angiogenesis (GO:0016525)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|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 neuron apoptotic process (GO:0043525)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to growth factor (GO:0070848)|response to lipopolysaccharide (GO:0032496)|retinal cell programmed cell death (GO:0046666)|signal transduction (GO:0007165)|T cell apoptotic process (GO:0070231)|transcription, DNA-templated (GO:0006351)	caveola (GO:0005901)|cytoplasmic membrane-bounded vesicle (GO:0016023)|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)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	receptor binding (GO:0005102)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(12)|prostate(1)|skin(1)	19						caccaccaccgccaccgccac	0.662													G|||	242	0.0483227	0.1717	0.0216	5008	,	,		10744	0.0		0.0	False		,,,				2504	0.0				p.P49P	Ovarian(28;486 876 30334 44033)	Atlas-SNP	.											.	FASLG	44	.	0			c.G147A						PASS	.	G		714,3692	267.4+/-267.8	68,578,1557	56	57	57		147	-8.6	0	1	dbSNP_129	57	7,8593	3.7+/-12.6	0,7,4293	no	coding-synonymous	FASLG	NM_000639.1		68,585,5850	AA,AG,GG		0.0814,16.2052,5.5436		49/282	172628488	721,12285	2203	4300	6503	SO:0001819	synonymous_variant	356	exon1			ACCACCGCCACCG	U11821	CCDS1304.1	1q23	2014-09-17	2005-01-07	2005-01-07	ENSG00000117560	ENSG00000117560		"Tumor necrosis factor (ligand) superfamily", "CD molecules", "Endogenous ligands"	11936	protein-coding gene	gene with protein product		134638	"tumor necrosis factor (ligand) superfamily, member 6"	APT1LG1, TNFSF6		7826947, 9022072	Standard	NM_000639		Approved	FasL, CD178	uc001gis.3	P48023	OTTHUMG00000034841	ENST00000367721.2:c.147G>A	1.37:g.172628488G>A		139	0	0		136	60	0.441176	NM_000639	Q9BZP9	Silent	SNP	ENST00000367721.2	37	CCDS1304.1																																																																																			G|0.944;A|0.056	0.056	strong		0.662	FASLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084276.1			A	172628488	G	A	172628488	2	1	22	1	0	0	0	0	0	0	0	1	5690	1074	38	1		1	FASLG	1	172628488	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1075279	172628488	76622133	356	3257											
SLC9A11	284525	hgsc.bcm.edu	37	chr1	173516915	173516915	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcatatcattatgtgaaacGtgggaaaactgaaccgtatc	14	12	8	7	2	2	2	2	2	0	0	3	3	2	3	1	1	3	1	1	1	7	4	rs114115413	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173516915G>A	ENST00000367714.3	-	13	1892	c.1470C>T	c.(1468-1470)caC>caT	p.H490H	SLC9C2_ENST00000536496.1_Silent_p.H388H|SLC9C2_ENST00000466087.1_5'UTR	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	490					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										TATGTGAAACGTGGGAAAACT	0.353													G|||	61	0.0121805	0.0454	0.0014	5008	,	,		18017	0.0		0.0	False		,,,				2504	0.0				p.H490H		Atlas-SNP	.											.	.	.	.	0			c.C1470T						PASS	.	G		125,4281	92.0+/-130.7	3,119,2081	134	119	124		1470	-8.2	0	1	dbSNP_132	124	0,8600		0,0,4300	no	coding-synonymous	SLC9A11	NM_178527.3		3,119,6381	AA,AG,GG		0.0,2.837,0.9611		490/1125	173516915	125,12881	2203	4300	6503	SO:0001819	synonymous_variant	284525	exon13			TGAAACGTGGGAA	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.1470C>T	1.37:g.173516915G>A		114	0	0		92	37	0.402174	NM_178527	Q86UF3	Silent	SNP	ENST00000367714.3	37	CCDS1308.1																																																																																			G|0.989;A|0.011	0.011	strong		0.353	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527		A	173516915	G	A	173516915	2	1	22	1	0	0	0	0	0	0	0	1	14726	1136	40	1		1	SLC9A11	1	173516915	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	888427	173516915	75733706	357	3258											
SLC9A11	284525	hgsc.bcm.edu	37	chr1	173526520	173526520	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcgttcagcgagattataaaCatcaggagcccagagtaaat	15	9	9	8	2	2	2	2	0	0	2	3	4	2	3	1	1	3	2	1	1	5	4	rs116588526	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173526520C>T	ENST00000367714.3	-	10	1596	c.1174G>A	c.(1174-1176)Gtt>Att	p.V392I	SLC9C2_ENST00000536496.1_Missense_Mutation_p.V290I|SLC9C2_ENST00000466087.1_5'UTR|RP3-436N22.3_ENST00000431459.1_RNA	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	392					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										AGATTATAAACATCAGGAGCC	0.343													C|||	61	0.0121805	0.0454	0.0014	5008	,	,		17169	0.0		0.0	False		,,,				2504	0.0				p.V392I		Atlas-SNP	.											.	.	.	.	0			c.G1174A						PASS	.	C	ILE/VAL	125,4281	89.7+/-128.4	3,119,2081	112	124	120		1174	-9.1	0.1	1	dbSNP_132	120	0,8600		0,0,4300	yes	missense	SLC9A11	NM_178527.3	29	3,119,6381	TT,TC,CC		0.0,2.837,0.9611	benign	392/1125	173526520	125,12881	2203	4300	6503	SO:0001583	missense	284525	exon10			TATAAACATCAGG	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.1174G>A	1.37:g.173526520C>T	ENSP00000356687:p.Val392Ile	238	0	0		223	118	0.529148	NM_178527	Q86UF3	Missense_Mutation	SNP	ENST00000367714.3	37	CCDS1308.1	21	0.009615384615384616	20	0.04065040650406504	1	0.0027624309392265192	0	0.0	0	0.0	C	0.013	-1.635886	0.00806	0.02837	0.0	ENSG00000162753	ENST00000367714;ENST00000536496	T;T	0.22945	1.93;1.93	5.57	-9.13	0.00704	Cation/H+ exchanger (1);	1.176240	0.06215	N	0.685727	T	0.02342	0.0072	N	0.02539	-0.55	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.39440	-0.9614	10	0.21014	T	0.42	-6.9326	11.2419	0.48974	0.1172:0.6529:0.0:0.2299	.	392	Q5TAH2	S9A11_HUMAN	I	392;290	ENSP00000356687:V392I;ENSP00000445437:V290I	ENSP00000356687:V392I	V	-	1	0	SLC9A11	171793143	0.001000	0.12720	0.050000	0.19076	0.051000	0.14879	-1.894000	0.01607	-1.269000	0.02436	-1.130000	0.01982	GTT	C|0.989;T|0.011	0.011	strong		0.343	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527		T	173526520	C	T	173526520	3	4	22	1	0	0	0	0	1	0	0	0	14726	478	17	2	2276	2	SLC9A11	1	173526520	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	9605	173526520	75724101	358	3259											
SLC9A11	284525	hgsc.bcm.edu	37	chr1	173552703	173552703	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tttccaaaaaaaattgatgcGatgctacaaatgatcaatga	18	11	6	6	1	1	3	1	3	0	0	2	4	2	3	1	0	3	1	1	0	7	3	rs16828416	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173552703G>A	ENST00000367714.3	-	6	1004	c.582C>T	c.(580-582)atC>atT	p.I194I	SLC9C2_ENST00000536496.1_Silent_p.I92I|RP3-436N22.3_ENST00000431459.1_RNA	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	194					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										AAATTGATGCGATGCTACAAA	0.303													G|||	344	0.0686901	0.2466	0.0245	5008	,	,		16936	0.0		0.0	False		,,,				2504	0.001				p.I194I		Atlas-SNP	.											.	.	.	.	0			c.C582T						PASS	.	G		996,3410	357.6+/-314.0	113,770,1320	55	60	58		582	0.1	0	1	dbSNP_123	58	6,8590	5.0+/-18.6	0,6,4292	yes	coding-synonymous	SLC9A11	NM_178527.3		113,776,5612	AA,AG,GG		0.0698,22.6055,7.7065		194/1125	173552703	1002,12000	2203	4298	6501	SO:0001819	synonymous_variant	284525	exon6			TGATGCGATGCTA	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.582C>T	1.37:g.173552703G>A		212	0	0		202	98	0.485149	NM_178527	Q86UF3	Silent	SNP	ENST00000367714.3	37	CCDS1308.1																																																																																			G|0.910;A|0.090	0.090	strong		0.303	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527		A	173552703	G	A	173552703	2	1	22	1	0	0	0	0	0	0	0	1	14726	1048	37	1		1	SLC9A11	1	173552703	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	26183	173552703	75697918	359	3260											
ANKRD45	339416	hgsc.bcm.edu	37	chr1	173596257	173596257	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttctgtgtcagtaacagctaAagagacttttgcaatatatt	13	15	7	6	0	2	1	1	0	1	1	2	2	2	1	0	0	3	3	0	0	6	8	rs12059066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173596257A>T	ENST00000333279.2	-	4	598	c.538T>A	c.(538-540)Tta>Ata	p.L180I		NM_198493.2	NP_940895.1	Q5TZF3	ANR45_HUMAN	ankyrin repeat domain 45	196										NS(2)|endometrium(2)|large_intestine(4)|lung(3)|skin(1)	12						GTAACAGCTAAAGAGACTTTT	0.373													A|||	965	0.192692	0.6989	0.0504	5008	,	,		20198	0.0		0.005	False		,,,				2504	0.001				p.L180I		Atlas-SNP	.											.	ANKRD45	36	.	0			c.T538A						PASS	.	A	ILE/LEU	2539,1867	632.6+/-395.9	756,1027,420	145	150	148		538	-3.8	0	1	dbSNP_120	148	32,8568	19.8+/-62.0	0,32,4268	yes	missense	ANKRD45	NM_198493.2	5	756,1059,4688	TT,TA,AA		0.3721,42.374,19.7678	benign	180/267	173596257	2571,10435	2203	4300	6503	SO:0001583	missense	339416	exon4			CAGCTAAAGAGAC		CCDS1309.1	1q25.1	2013-01-10			ENSG00000183831	ENSG00000183831		"Ankyrin repeat domain containing"	24786	protein-coding gene	gene with protein product	"cancer/testis antigen 117"						Standard	NM_198493		Approved	FLJ45235, CT117	uc001gja.1	Q5TZF3	OTTHUMG00000040546	ENST00000333279.2:c.538T>A	1.37:g.173596257A>T	ENSP00000331268:p.Leu180Ile	67	0	0		54	53	0.981481	NM_198493	A1A4G2|Q6ZST1	Missense_Mutation	SNP	ENST00000333279.2	37	CCDS1309.1	377	0.17261904761904762	353	0.717479674796748	20	0.055248618784530384	0	0.0	4	0.005277044854881266	A	11.25	1.583800	0.28268	0.57626	0.003721	ENSG00000183831	ENST00000333279	T	0.13778	2.56	5.35	-3.79	0.04320	.	1.555310	0.03916	N	0.282716	T	0.01870	0.0059	N	0.22421	0.69	0.80722	P	0.0	B	0.27068	0.167	B	0.19148	0.024	T	0.35895	-0.9770	9	0.36615	T	0.2	-17.7491	1.2921	0.02062	0.1379:0.3633:0.2467:0.2521	rs12059066;rs52822128;rs12059066	196	Q5TZF3	ANR45_HUMAN	I	180	ENSP00000331268:L180I	ENSP00000331268:L180I	L	-	1	2	ANKRD45	171862880	0.000000	0.05858	0.000000	0.03702	0.656000	0.38851	-0.559000	0.05971	-1.213000	0.02617	0.455000	0.32223	TTA	A|0.814;T|0.186	0.186	strong		0.373	ANKRD45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097580.2	NM_198493		T	173596257	A	T	173596257	3	4	22	1	0	0	0	0	1	0	0	0	673	11	1	5	274	5	ANKRD45	1	173596257	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	43554	173596257	75654364	360	3261											
ANKRD45	339416	hgsc.bcm.edu	37	chr1	173596273	173596273	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctaaagagacttttgcaatAtattttttcagagtcagcct	12	15	7	7	0	2	2	2	0	0	2	2	3	2	2	1	0	2	2	1	0	5	8	rs12059068	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173596273A>G	ENST00000333279.2	-	4	582	c.522T>C	c.(520-522)taT>taC	p.Y174Y		NM_198493.2	NP_940895.1	Q5TZF3	ANR45_HUMAN	ankyrin repeat domain 45	190										NS(2)|endometrium(2)|large_intestine(4)|lung(3)|skin(1)	12						CTTTTGCAATATATTTTTTCA	0.388													A|||	965	0.192692	0.6989	0.0504	5008	,	,		19880	0.0		0.005	False		,,,				2504	0.001				p.Y174Y		Atlas-SNP	.											.	ANKRD45	36	.	0			c.T522C						PASS	.	A		2539,1867	632.6+/-395.9	756,1027,420	124	128	127		522	-0.2	0.9	1	dbSNP_120	127	32,8568	19.2+/-60.6	0,32,4268	no	coding-synonymous	ANKRD45	NM_198493.2		756,1059,4688	GG,GA,AA		0.3721,42.374,19.7678		174/267	173596273	2571,10435	2203	4300	6503	SO:0001819	synonymous_variant	339416	exon4			TGCAATATATTTT		CCDS1309.1	1q25.1	2013-01-10			ENSG00000183831	ENSG00000183831		"Ankyrin repeat domain containing"	24786	protein-coding gene	gene with protein product	"cancer/testis antigen 117"						Standard	NM_198493		Approved	FLJ45235, CT117	uc001gja.1	Q5TZF3	OTTHUMG00000040546	ENST00000333279.2:c.522T>C	1.37:g.173596273A>G		58	0	0		56	56	1	NM_198493	A1A4G2|Q6ZST1	Silent	SNP	ENST00000333279.2	37	CCDS1309.1																																																																																			A|0.781;G|0.219	0.219	strong		0.388	ANKRD45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097580.2	NM_198493		G	173596273	A	G	173596273	2	3	22	1	0	0	0	0	0	0	0	1	673	456	16	3		3	ANKRD45	1	173596273	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	16	173596273	75654348	361	3262											
KLHL20	27252	hgsc.bcm.edu	37	chr1	173725101	173725101	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaaaactacctcctattgccGcaagaacgaccactaatgca	16	7	5	13	2	0	1	0	0	0	1	1	2	1	1	4	0	5	2	4	0	7	4	rs16846395	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173725101G>A	ENST00000209884.4	+	6	1027	c.891G>A	c.(889-891)ccG>ccA	p.P297P	KLHL20_ENST00000546011.1_Silent_p.P108P	NM_014458.3	NP_055273.2	Q9Y2M5	KLH20_HUMAN	kelch-like family member 20	297					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						TCCTATTGCCGCAAGAACGAC	0.403													G|||	472	0.0942492	0.3404	0.0274	5008	,	,		18997	0.0		0.003	False		,,,				2504	0.0				p.P297P	GBM(159;862 2695 6559 23041)	Atlas-SNP	.											.	KLHL20	54	.	0			c.G891A						PASS	.	G		1110,3296	397.2+/-330.3	139,832,1232	108	99	102		891	1.2	1	1	dbSNP_123	102	23,8577	15.3+/-51.7	0,23,4277	no	coding-synonymous	KLHL20	NM_014458.3		139,855,5509	AA,AG,GG		0.2674,25.1929,8.7114		297/610	173725101	1133,11873	2203	4300	6503	SO:0001819	synonymous_variant	27252	exon6			ATTGCCGCAAGAA	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.891G>A	1.37:g.173725101G>A		125	0	0		119	60	0.504202	NM_014458	B3KMA0|B4DUR0|Q5TZF2|Q5ZF45|Q9H457	Silent	SNP	ENST00000209884.4	37	CCDS1310.1																																																																																			G|0.899;A|0.101	0.101	strong		0.403	KLHL20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097582.1	NM_014458		A	173725101	G	A	173725101	2	1	22	1	0	0	0	0	0	0	0	1	8384	1074	38	1		1	KLHL20	1	173725101	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	128828	173725101	75525520	362	3263											
KLHL20	27252	hgsc.bcm.edu	37	chr1	173735378	173735378	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcagtacttggaggctttctTtatgctgtgggtggccagga	6	13	15	7	0	1	0	0	0	1	0	1	2	1	2	1	5	2	4	1	5	2	5	rs7536773	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173735378T>C	ENST00000209884.4	+	8	1381	c.1245T>C	c.(1243-1245)ctT>ctC	p.L415L	KLHL20_ENST00000546011.1_Silent_p.L226L	NM_014458.3	NP_055273.2	Q9Y2M5	KLH20_HUMAN	kelch-like family member 20	415					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						GAGGCTTTCTTTATGCTGTGG	0.433													C|||	555	0.110823	0.3971	0.0346	5008	,	,		15265	0.0		0.006	False		,,,				2504	0.0				p.L415L	GBM(159;862 2695 6559 23041)	Atlas-SNP	.											.	KLHL20	54	.	0			c.T1245C						PASS	.	C		1333,3073	695.2+/-405.9	197,939,1067	285	261	269		1245	0.1	1	1	dbSNP_116	269	31,8569	818.0+/-406.9	0,31,4269	no	coding-synonymous	KLHL20	NM_014458.3		197,970,5336	CC,CT,TT		0.3605,30.2542,10.4875		415/610	173735378	1364,11642	2203	4300	6503	SO:0001819	synonymous_variant	27252	exon8			CTTTCTTTATGCT	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.1245T>C	1.37:g.173735378T>C		303	0	0		330	135	0.409091	NM_014458	B3KMA0|B4DUR0|Q5TZF2|Q5ZF45|Q9H457	Silent	SNP	ENST00000209884.4	37	CCDS1310.1																																																																																			T|0.875;C|0.125	0.125	strong		0.433	KLHL20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097582.1	NM_014458		C	173735378	T	C	173735378	2	2	22	1	0	0	0	0	0	0	0	1	8384	1828	64	3		3	KLHL20	1	173735378	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	10277	173735378	75515243	363	3264											
CENPL	91687	hgsc.bcm.edu	37	chr1	173772506	173772506	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgttagactctgctccattTgcaaggaataagggcagaca	12	10	11	8	0	1	2	0	0	1	2	2	3	2	3	1	2	2	4	1	2	4	3	rs16846420	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173772506T>G	ENST00000345664.6	-	4	771	c.558A>C	c.(556-558)gcA>gcC	p.A186A	CENPL_ENST00000367710.3_Silent_p.A186A|CENPL_ENST00000356198.2_Silent_p.A232A	NM_001171182.1	NP_001164653.1	Q8N0S6	CENPL_HUMAN	centromere protein L	186					mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(3)	11						CTGCTCCATTTGCAAGGAATA	0.408													T|||	564	0.11262	0.4032	0.0346	5008	,	,		19168	0.0		0.007	False		,,,				2504	0.0				p.A232A		Atlas-SNP	.											.	CENPL	26	.	0			c.A696C						PASS	.	T	,,	1339,3067	438.4+/-345.3	198,943,1062	104	114	111		696,558,558	5	1	1	dbSNP_123	111	31,8569	18.5+/-59.3	0,31,4269	no	coding-synonymous,coding-synonymous,coding-synonymous	CENPL	NM_001127181.2,NM_001171182.1,NM_033319.3	,,	198,974,5331	GG,GT,TT		0.3605,30.3904,10.5336	,,	232/391,186/345,186/345	173772506	1370,11636	2203	4300	6503	SO:0001819	synonymous_variant	91687	exon6			TCCATTTGCAAGG	BC033154, BC019022, AK055606	CCDS30938.1, CCDS44277.1	1q25.1	2013-11-05	2006-06-15	2006-06-15	ENSG00000120334	ENSG00000120334			17879	protein-coding gene	gene with protein product		611503	"chromosome 1 open reading frame 155"	C1orf155		16622420, 16622419	Standard	NM_033319		Approved	dJ383J4.3, FLJ31044	uc001gje.4	Q8N0S6	OTTHUMG00000034802	ENST00000345664.6:c.558A>C	1.37:g.173772506T>G		176	0	0		171	85	0.497076	NM_001127181	Q5TEL5|Q96ND4	Silent	SNP	ENST00000345664.6	37	CCDS30938.1																																																																																			T|0.876;G|0.124	0.124	strong		0.408	CENPL-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084213.1	NM_033319		G	173772506	T	G	173772506	2	3	22	1	0	0	0	0	0	0	0	1	3238	1799	63	5		5	CENPL	1	173772506	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	37128	173772506	75478115	364	3265											
ZBTB37	84614	hgsc.bcm.edu	37	chr1	173839435	173839435	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcctgagccatctaaaccaGttgcgcatgcagggccgtct	8	9	11	13	2	2	1	0	1	2	0	3	1	3	1	4	1	4	3	4	1	2	2	rs9425761	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173839435G>A	ENST00000367701.5	+	2	263	c.72G>A	c.(70-72)caG>caA	p.Q24Q	ZBTB37_ENST00000367704.1_Silent_p.Q24Q|ZBTB37_ENST00000427304.1_Silent_p.Q24Q|GAS5_ENST00000364084.1_RNA|ZBTB37_ENST00000432989.1_Silent_p.Q24Q|ZBTB37_ENST00000367702.1_Silent_p.Q24Q			Q5TC79	ZBT37_HUMAN	zinc finger and BTB domain containing 37	24					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						ATCTAAACCAGTTGCGCATGC	0.527													G|||	560	0.111821	0.4009	0.0346	5008	,	,		17279	0.0		0.006	False		,,,				2504	0.0				p.Q24Q		Atlas-SNP	.											.	ZBTB37	38	.	0			c.G72A						PASS	.	G	,	1333,3073	446.1+/-347.9	199,935,1069	79	73	75		72,72	3.8	1	1	dbSNP_119	75	31,8569	20.4+/-63.3	0,31,4269	no	coding-synonymous,coding-synonymous	ZBTB37	NM_001122770.1,NM_032522.3	,	199,966,5338	AA,AG,GG		0.3605,30.2542,10.4875	,	24/504,24/362	173839435	1364,11642	2203	4300	6503	SO:0001819	synonymous_variant	84614	exon3			AAACCAGTTGCGC	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.72G>A	1.37:g.173839435G>A		170	0	0		192	89	0.463542	NM_032522	Q5TC80|Q96M87|Q9BQ88	Silent	SNP	ENST00000367701.5	37	CCDS44278.1																																																																																			G|0.875;A|0.125	0.125	strong		0.527	ZBTB37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090729.2	NM_032522		A	173839435	G	A	173839435	2	1	22	1	0	0	0	0	0	0	0	1	17553	1020	36	2		2	ZBTB37	1	173839435	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	66929	173839435	75411186	365	3266											
RABGAP1L	9910	hgsc.bcm.edu	37	chr1	174219724	174219724	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagtgatgtgtttaccttcAgtgtctccttggaggtaaaa	10	14	10	7	0	2	1	1	1	1	0	3	2	2	2	2	2	1	2	2	2	3	5	rs7339904	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:174219724A>G	ENST00000251507.4	+	6	1003	c.829A>G	c.(829-831)Agt>Ggt	p.S277G	RABGAP1L_ENST00000367689.3_5'UTR|RABGAP1L_ENST00000357444.6_Missense_Mutation_p.S240G	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						GTTTACCTTCAGTGTCTCCTT	0.388													A|||	328	0.0654952	0.2405	0.0144	5008	,	,		16084	0.0		0.0	False		,,,				2504	0.0				p.S277G		Atlas-SNP	.											.	RABGAP1L	103	.	0			c.A829G						PASS	.	A	GLY/SER	917,3489	353.1+/-312.0	107,703,1393	141	138	139		829	4.7	1	1	dbSNP_116	139	6,8594	5.0+/-18.6	0,6,4294	yes	missense	RABGAP1L	NM_014857.4	56	107,709,5687	GG,GA,AA		0.0698,20.8125,7.0967	benign	277/816	174219724	923,12083	2203	4300	6503	SO:0001583	missense	9910	exon6			ACCTTCAGTGTCT	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.829A>G	1.37:g.174219724A>G	ENSP00000251507:p.Ser277Gly	97	0	0		104	56	0.538462	NM_014857	B7ZAA4	Missense_Mutation	SNP	ENST00000251507.4	37	CCDS1314.1	137	0.06272893772893773	132	0.2682926829268293	5	0.013812154696132596	0	0.0	0	0.0	A	15.94	2.982019	0.53827	0.208125	6.98E-4	ENSG00000152061	ENST00000357444;ENST00000251507;ENST00000457696;ENST00000367692	T;T;T	0.47528	0.87;3.46;0.84	5.8	4.68	0.58851	.	0.235735	0.48767	N	0.000180	T	0.00012	0.0000	L	0.38531	1.155	0.09310	P	1.0	P;B;B	0.35328	0.495;0.017;0.372	B;B;B	0.30401	0.115;0.066;0.083	T	0.27571	-1.0070	9	0.23891	T	0.37	.	11.7008	0.51569	0.9314:0.0:0.0686:0.0	rs7339904;rs52822913;rs7339904	277;277;240	B7WPG6;Q5R372;Q5R372-2	.;RBG1L_HUMAN;.	G	240;277;277;277	ENSP00000350027:S240G;ENSP00000251507:S277G;ENSP00000403136:S277G	ENSP00000251507:S277G	S	+	1	0	RABGAP1L	172486347	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.023000	0.64084	1.044000	0.40200	0.459000	0.35465	AGT	A|0.914;G|0.086	0.086	strong		0.388	RABGAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084497.1	NM_001243765		G	174219724	A	G	174219724	3	3	22	1	0	0	0	0	1	0	0	0	12980	188	7	3	847	3	RABGAP1L	1	174219724	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	380289	174219724	75030897	366	3267											
TNR	7143	hgsc.bcm.edu	37	chr1	175306758	175306758	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggtaaaccccactcaaaGtgtctccattcatcaaatgc	12	10	7	12	0	4	0	3	0	1	0	5	0	4	0	3	2	2	1	3	2	4	2	rs61731114	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:175306758G>A	ENST00000367674.2	-	19	4148	c.3440C>T	c.(3439-3441)aCt>aTt	p.T1147I	RP3-518E13.2_ENST00000569593.1_RNA|TNR_ENST00000263525.2_Missense_Mutation_p.T1147I			Q92752	TENR_HUMAN	tenascin R	1147	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)					CCCACTCAAAGTGTCTCCATT	0.502													G|||	49	0.00978435	0.0303	0.013	5008	,	,		21455	0.0		0.0	False		,,,				2504	0.0				p.T1147I		Atlas-SNP	.											.	TNR	399	.	0			c.C3440T						PASS	.	G	ILE/THR	137,4269	96.7+/-135.4	4,129,2070	58	54	55		3440	5.4	1	1	dbSNP_129	55	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TNR	NM_003285.2	89	4,130,6369	AA,AG,GG		0.0116,3.1094,1.061	benign	1147/1359	175306758	138,12868	2203	4300	6503	SO:0001583	missense	7143	exon19			CTCAAAGTGTCTC	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.3440C>T	1.37:g.175306758G>A	ENSP00000356646:p.Thr1147Ile	143	0	0		131	71	0.541985	NM_003285	C9J563|Q15568|Q5R3G0	Missense_Mutation	SNP	ENST00000367674.2	37	CCDS1318.1	24	0.01098901098901099	20	0.04065040650406504	4	0.011049723756906077	0	0.0	0	0.0	G	22.4	4.278785	0.80692	0.031094	1.16E-4	ENSG00000116147	ENST00000367674;ENST00000263525;ENST00000367673	T;T	0.77229	-1.08;-1.08	5.37	5.37	0.77165	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.055231	0.64402	D	0.000001	T	0.47340	0.1440	M	0.62088	1.915	0.58432	D	0.999995	P	0.49253	0.921	B	0.43301	0.415	T	0.69997	-0.4993	10	0.59425	D	0.04	.	13.659	0.62354	0.0:0.0:0.8453:0.1547	.	1147	Q92752	TENR_HUMAN	I	1147;1147;1057	ENSP00000356646:T1147I;ENSP00000263525:T1147I	ENSP00000263525:T1147I	T	-	2	0	TNR	173573381	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	5.037000	0.64170	2.500000	0.84329	0.655000	0.94253	ACT	G|0.989;A|0.011	0.011	strong		0.502	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285		A	175306758	G	A	175306758	3	1	22	1	0	0	0	0	1	0	0	0	16353	1029	36	2	656	2	TNR	1	175306758	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1087034	175306758	73943863	367	3268											
TNR	7143	hgsc.bcm.edu	37	chr1	175335162	175335162	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgaggcaatcccagaggaTggggtaaaggtaattcggta	12	9	14	6	1	1	2	0	1	1	1	3	3	2	3	1	6	0	4	1	6	5	4	rs7516376	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:175335162T>C	ENST00000367674.2	-	11	2874	c.2166A>G	c.(2164-2166)ccA>ccG	p.P722P	TNR_ENST00000263525.2_Silent_p.P722P			Q92752	TENR_HUMAN	tenascin R	722	Fibronectin type-III 5. {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)					TCCCAGAGGATGGGGTAAAGG	0.552													T|||	277	0.0553115	0.1989	0.0202	5008	,	,		21185	0.0		0.0	False		,,,				2504	0.0				p.P722P		Atlas-SNP	.											TNR,NS,carcinoma,-1,2	TNR	399	2	0			c.A2166G						PASS	.	T		774,3632	314.1+/-293.5	71,632,1500	169	158	162		2166	-11.8	0.2	1	dbSNP_116	162	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	TNR	NM_003285.2		71,637,5795	CC,CT,TT		0.0581,17.567,5.9895		722/1359	175335162	779,12227	2203	4300	6503	SO:0001819	synonymous_variant	7143	exon11			AGAGGATGGGGTA	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.2166A>G	1.37:g.175335162T>C		228	0	0		241	114	0.473029	NM_003285	C9J563|Q15568|Q5R3G0	Silent	SNP	ENST00000367674.2	37	CCDS1318.1																																																																																			T|0.929;C|0.071	0.071	strong		0.552	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285		C	175335162	T	C	175335162	2	2	22	1	0	0	0	0	0	0	0	1	16353	1451	51	3		3	TNR	1	175335162	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	28404	175335162	73915459	368	3269											
PAPPA2	60676	hgsc.bcm.edu	37	chr1	176564092	176564092	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcaagtggggaggaggaagCgactgacttggtcctgacag	10	8	16	7	1	1	2	1	2	0	0	2	6	2	5	1	5	1	0	1	5	2	2	rs34698817	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:176564092C>T	ENST00000367662.3	+	3	2516	c.1352C>T	c.(1351-1353)gCg>gTg	p.A451V	PAPPA2_ENST00000367661.3_Missense_Mutation_p.A451V	NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	451	Metalloprotease.				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						GAGGAGGAAGCGACTGACTTG	0.532													C|||	17	0.00339457	0.0113	0.0029	5008	,	,		21732	0.0		0.0	False		,,,				2504	0.0				p.A451V		Atlas-SNP	.											PAPPA2_ENST00000367661,NS,carcinoma,-1,1	PAPPA2	665	1	0			c.C1352T						PASS	.	C	VAL/ALA,VAL/ALA	29,4195		0,29,2083	99	105	103		1352,1352	2.4	0	1	dbSNP_126	103	0,8456		0,0,4228	yes	missense,missense	PAPPA2	NM_020318.2,NM_021936.2	64,64	0,29,6311	TT,TC,CC		0.0,0.6866,0.2287	benign,benign	451/1792,451/828	176564092	29,12651	2112	4228	6340	SO:0001583	missense	60676	exon3			AGGAAGCGACTGA	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.1352C>T	1.37:g.176564092C>T	ENSP00000356634:p.Ala451Val	91	0	0		76	34	0.447368	NM_021936	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	ENST00000367662.3	37	CCDS41438.1	6	0.0027472527472527475	4	0.008130081300813009	2	0.0055248618784530384	0	0.0	0	0.0	C	0.118	-1.128701	0.01756	0.006866	0.0	ENSG00000116183	ENST00000367662;ENST00000367661	T;T	0.30448	4.78;1.53	4.87	2.4	0.29515	.	1.625110	0.03455	N	0.211229	T	0.12732	0.0309	N	0.14661	0.345	0.09310	N	1	B;B	0.15473	0.008;0.013	B;B	0.08055	0.003;0.001	T	0.18871	-1.0323	10	0.18276	T	0.48	0.1753	3.9845	0.09509	0.1568:0.3405:0.0:0.5026	rs34698817	451;451	Q9BXP8;A9Z1Y8	PAPP2_HUMAN;.	V	451	ENSP00000356634:A451V;ENSP00000356633:A451V	ENSP00000356633:A451V	A	+	2	0	PAPPA2	174830715	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.277000	0.18734	0.230000	0.21059	-0.300000	0.09419	GCG	C|0.997;T|0.003	0.003	strong		0.532	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			T	176564092	C	T	176564092	3	4	22	1	0	0	0	0	1	0	0	0	11442	768	27	1	1358	1	PAPPA2	1	176564092	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1228930	176564092	72686529	369	3270											
ASTN1	460	hgsc.bcm.edu	37	chr1	176915087	176915087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttcctttcagcacctgtcCggcagccacttccttggaat	6	13	8	14	1	1	0	1	0	0	0	4	1	4	1	5	2	2	3	5	2	1	4	rs138686233	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:176915087C>T	ENST00000367654.3	-	13	2459	c.2248G>A	c.(2248-2250)Gga>Aga	p.G750R	ASTN1_ENST00000367657.3_Missense_Mutation_p.G742R|ASTN1_ENST00000424564.2_Missense_Mutation_p.G742R|ASTN1_ENST00000361833.2_Missense_Mutation_p.G742R|ASTN1_ENST00000281881.3_5'UTR	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	750					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)		p.G742*(1)		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						AGCACCTGTCCGGCAGCCACT	0.463													C|||	8	0.00159744	0.0061	0.0	5008	,	,		19496	0.0		0.0	False		,,,				2504	0.0				p.G742R		Atlas-SNP	.											ASTN1,NS,carcinoma,0,1	ASTN1	314	1	1	Substitution - Nonsense(1)	lung(1)	c.G2224A						PASS	.	C	ARG/GLY,ARG/GLY	37,4369	41.6+/-74.8	0,37,2166	110	118	115		2224,2224	5.2	1	1	dbSNP_134	115	0,8600		0,0,4300	yes	missense,missense	ASTN1	NM_004319.1,NM_207108.1	125,125	0,37,6466	TT,TC,CC		0.0,0.8398,0.2845	possibly-damaging,possibly-damaging	742/1295,742/1217	176915087	37,12969	2203	4300	6503	SO:0001583	missense	460	exon13			CCTGTCCGGCAGC	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.2248G>A	1.37:g.176915087C>T	ENSP00000356626:p.Gly750Arg	94	0	0		82	49	0.597561	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	ENST00000367654.3	37		0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	25.9	4.687682	0.88639	0.008398	0.0	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	T;T;T;T	0.17370	2.28;2.7;2.7;2.29	5.25	5.25	0.73442	.	0.107853	0.64402	D	0.000004	T	0.15478	0.0373	L	0.27053	0.805	0.58432	D	0.999998	D;D;D	0.67145	0.996;0.993;0.993	P;P;P	0.54856	0.762;0.762;0.762	T	0.00555	-1.1673	10	0.87932	D	0	-17.5766	11.9089	0.52727	0.0:0.9195:0.0:0.0805	.	750;742;742	O14525;O14525-2;B1AJS1	ASTN1_HUMAN;.;.	R	742;742;750;742;742	ENSP00000356629:G742R;ENSP00000354536:G742R;ENSP00000356626:G750R;ENSP00000395041:G742R	ENSP00000354536:G742R	G	-	1	0	ASTN1	175181710	1.000000	0.71417	0.951000	0.38953	0.992000	0.81027	5.539000	0.67199	2.467000	0.83353	0.655000	0.94253	GGA	C|0.998;T|0.002	0.002	strong		0.463	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319		T	176915087	C	T	176915087	3	4	22	1	0	0	0	0	1	0	0	0	1064	661	23	1	1708	1	ASTN1	1	176915087	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	350995	176915087	72335534	370	3271											
ANGPTL1	9068	hgsc.bcm.edu	37	chr1	178834231	178834231	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcagaccaggagtatactgTtggctgttaggaatatgttg	11	12	13	5	0	0	1	0	0	0	1	0	3	0	3	1	3	2	6	1	3	5	6	rs6689778	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:178834231T>C	ENST00000234816.2	-	3	1128	c.681A>G	c.(679-681)caA>caG	p.Q227Q	ANGPTL1_ENST00000367629.1_Silent_p.Q227Q|RALGPS2_ENST00000367635.3_Intron|RALGPS2_ENST00000367634.2_Intron	NM_004673.3	NP_004664.1	O95841	ANGL1_HUMAN	angiopoietin-like 1	227					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						GAGTATACTGTTGGCTGTTAG	0.498													A|||	283	0.0565096	0.2035	0.0202	5008	,	,		18124	0.0		0.0	False		,,,				2504	0.0				p.Q227Q		Atlas-SNP	.											.	ANGPTL1	41	.	0			c.A681G						PASS	.	A	,	822,3584		80,662,1461	118	108	111		681,	-8.9	0.1	1	dbSNP_116	111	4,8596		0,4,4296	no	coding-synonymous,intron	ANGPTL1,RALGPS2	NM_004673.3,NM_152663.3	,	80,666,5757	CC,CT,TT		0.0465,18.6564,6.3509	,	227/492,	178834231	826,12180	2203	4300	6503	SO:0001819	synonymous_variant	9068	exon3			ATACTGTTGGCTG	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.681A>G	1.37:g.178834231T>C		110	0	0		128	48	0.375	NM_004673	Q5T5Z5	Silent	SNP	ENST00000234816.2	37	CCDS1327.1																																																																																			T|0.939;C|0.061	0.061	strong		0.498	ANGPTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084924.1	NM_004673		C	178834231	T	C	178834231	2	2	22	1	0	0	0	0	0	0	0	1	613	1722	60	3		3	ANGPTL1	1	178834231	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1919144	178834231	70416390	371	3272											
C1orf125	126859	hgsc.bcm.edu	37	chr1	179363114	179363114	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagacttggtaactcagcgaGtgatggaccagcgcatttta	12	10	11	8	2	1	2	1	1	0	1	1	4	1	3	1	2	3	2	1	2	3	4	rs139341288	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:179363114G>C	ENST00000367618.3	+	10	1327	c.940G>C	c.(940-942)Gtg>Ctg	p.V314L	AXDND1_ENST00000461179.2_3'UTR|AXDND1_ENST00000457238.2_Missense_Mutation_p.V314L	NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	314										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						AACTCAGCGAGTGATGGACCA	0.378													G|||	21	0.00419329	0.0159	0.0	5008	,	,		17593	0.0		0.0	False		,,,				2504	0.0				p.V314L		Atlas-SNP	.											.	AXDND1	142	.	0			c.G940C						PASS	.	G	LEU/VAL	55,4351	55.5+/-91.7	1,53,2149	153	150	151		940	-8.5	0.4	1	dbSNP_134	151	0,8600		0,0,4300	yes	missense	AXDND1	NM_144696.4	32	1,53,6449	CC,CG,GG		0.0,1.2483,0.4229	benign	314/1013	179363114	55,12951	2203	4300	6503	SO:0001583	missense	126859	exon10			CAGCGAGTGATGG	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.940G>C	1.37:g.179363114G>C	ENSP00000356590:p.Val314Leu	75	0	0		79	33	0.417722	NM_144696	Q6AWB2|Q96LJ3|Q96M01	Missense_Mutation	SNP	ENST00000367618.3	37	CCDS30948.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	11.60	1.686179	0.29962	0.012483	0.0	ENSG00000162779	ENST00000367618;ENST00000360322;ENST00000457238;ENST00000434088	T;T;T	0.44083	2.23;0.93;2.25	5.33	-8.49	0.00931	.	1.179580	0.05606	N	0.577214	T	0.15609	0.0376	N	0.17474	0.49	0.09310	N	0.999999	B;B;B	0.11235	0.001;0.002;0.004	B;B;B	0.11329	0.005;0.005;0.006	T	0.16748	-1.0392	10	0.24483	T	0.36	-0.2882	8.4441	0.32833	0.3562:0.1866:0.4572:0.0	.	272;314;314	E9PCJ4;Q5T1B0;F5GWM2	.;AXDN1_HUMAN;.	L	314;272;314;248	ENSP00000356590:V314L;ENSP00000416712:V314L;ENSP00000391716:V248L	ENSP00000353471:V272L	V	+	1	0	AXDND1	177629737	0.041000	0.20044	0.412000	0.26496	0.994000	0.84299	-1.684000	0.01932	-1.766000	0.01302	-0.152000	0.13540	GTG	G|0.997;C|0.003	0.003	strong		0.378	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696		C	179363114	G	C	179363114	3	2	22	1	0	0	0	0	1	0	0	0	1995	1029	36	4	974	4	C1orf125	1	179363114	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	528883	179363114	69887507	372	3273											
TDRD5	163589	hgsc.bcm.edu	37	chr1	179564885	179564885	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccgaagcaaataatgagcAtggaaaagacttccaagtta	18	7	8	8	1	0	2	0	1	0	1	1	4	1	3	2	1	2	3	2	1	7	3	rs147268063	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:179564885A>G	ENST00000367614.1	+	4	1122	c.763A>G	c.(763-765)Atg>Gtg	p.M255V	TDRD5_ENST00000294848.8_Missense_Mutation_p.M255V|TDRD5_ENST00000444136.1_Missense_Mutation_p.M255V	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	255					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						AATAATGAGCATGGAAAAGAC	0.383													A|||	16	0.00319489	0.0121	0.0	5008	,	,		17514	0.0		0.0	False		,,,				2504	0.0				p.M255V		Atlas-SNP	.											.	TDRD5	149	.	0			c.A763G						PASS	.	A	VAL/MET,VAL/MET,VAL/MET,VAL/MET	39,4367	44.6+/-78.6	0,39,2164	88	89	89		763,763,763,763	-11.4	0	1	dbSNP_134	89	0,8600		0,0,4300	yes	missense,missense,missense,missense	TDRD5	NM_001199085.1,NM_001199089.1,NM_001199091.1,NM_173533.3	21,21,21,21	0,39,6464	GG,GA,AA		0.0,0.8852,0.2999	benign,benign,benign,benign	255/1036,255/1036,255/982,255/982	179564885	39,12967	2203	4300	6503	SO:0001583	missense	163589	exon4			ATGAGCATGGAAA	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.763A>G	1.37:g.179564885A>G	ENSP00000356586:p.Met255Val	113	0	0		149	72	0.483221	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	37	CCDS1332.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	3.552	-0.091465	0.07053	0.008852	0.0	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136	T;T;T	0.10960	2.82;2.82;3.01	5.69	-11.4	0.00090	.	1.295340	0.05464	N	0.551832	T	0.02455	0.0075	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	0.29792	-1.0000	10	0.16896	T	0.51	-18.0062	3.1803	0.06582	0.3073:0.3169:0.2888:0.0871	.	255;255	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	V	255	ENSP00000356586:M255V;ENSP00000294848:M255V;ENSP00000406052:M255V	ENSP00000294848:M255V	M	+	1	0	TDRD5	177831508	0.000000	0.05858	0.000000	0.03702	0.648000	0.38561	-0.275000	0.08525	-1.928000	0.01059	0.477000	0.44152	ATG	A|0.997;G|0.003	0.003	strong		0.383	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		G	179564885	A	G	179564885	3	3	22	1	0	0	0	0	1	0	0	0	15748	217	8	3	773	3	TDRD5	1	179564885	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	201771	179564885	69685736	373	3274											
TDRD5	163589	hgsc.bcm.edu	37	chr1	179621253	179621253	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cattgtcttgacagaactggGttatccttcccagcagcact	9	12	8	12	0	1	2	0	1	1	1	3	2	3	2	2	1	3	3	2	1	2	4	rs147309264	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:179621253G>T	ENST00000367614.1	+	13	2440	c.2081G>T	c.(2080-2082)gGt>gTt	p.G694V	TDRD5_ENST00000294848.8_Missense_Mutation_p.G694V|TDRD5_ENST00000444136.1_Missense_Mutation_p.G694V	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	694					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						ACAGAACTGGGTTATCCTTCC	0.403													G|||	16	0.00319489	0.0121	0.0	5008	,	,		16263	0.0		0.0	False		,,,				2504	0.0				p.G694V		Atlas-SNP	.											.	TDRD5	149	.	0			c.G2081T						PASS	.	G	VAL/GLY,VAL/GLY,VAL/GLY,VAL/GLY,VAL/GLY	39,4367	44.6+/-78.6	0,39,2164	103	97	99		2081,2081,2081,746,2081	2.4	0	1	dbSNP_134	99	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense	TDRD5	NM_001199085.1,NM_001199089.1,NM_001199091.1,NM_001199092.1,NM_173533.3	109,109,109,109,109	0,39,6464	TT,TG,GG		0.0,0.8852,0.2999	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	694/1036,694/1036,694/982,249/537,694/982	179621253	39,12967	2203	4300	6503	SO:0001583	missense	163589	exon13			AACTGGGTTATCC	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.2081G>T	1.37:g.179621253G>T	ENSP00000356586:p.Gly694Val	164	0	0		215	107	0.497674	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	37	CCDS1332.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	10.14	1.269759	0.23221	0.008852	0.0	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136;ENST00000417329	T;T;T;T	0.34859	2.61;2.61;2.85;1.34	5.28	2.41	0.29592	.	1.593960	0.03140	N	0.166439	T	0.28433	0.0703	L	0.44542	1.39	0.19775	N	0.999957	P;B	0.35872	0.525;0.265	B;B	0.39971	0.315;0.167	T	0.19257	-1.0311	10	0.26408	T	0.33	-22.1301	7.4534	0.27252	0.3467:0.0:0.6533:0.0	.	694;694	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	V	694;694;694;150	ENSP00000356586:G694V;ENSP00000294848:G694V;ENSP00000406052:G694V;ENSP00000410744:G150V	ENSP00000294848:G694V	G	+	2	0	TDRD5	177887876	0.005000	0.15991	0.016000	0.15963	0.936000	0.57629	0.997000	0.29731	0.244000	0.21351	-0.259000	0.10710	GGT	G|0.997;T|0.003	0.003	strong		0.403	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533		T	179621253	G	T	179621253	3	4	22	1	0	0	0	0	1	0	0	0	15748	1261	44	4	2127	4	TDRD5	1	179621253	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	56368	179621253	69629368	374	3275											
CEP350	9857	hgsc.bcm.edu	37	chr1	179983153	179983153	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaatactgccttaaataaggActttttacctattgaaattc	15	15	4	7	0	0	1	0	1	0	0	1	2	0	2	2	1	3	0	2	1	8	9	rs111349041	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:179983153A>G	ENST00000367607.3	+	10	1983	c.1565A>G	c.(1564-1566)gAc>gGc	p.D522G		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	522					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						TTAAATAAGGACTTTTTACCT	0.378													A|||	63	0.0125799	0.0461	0.0029	5008	,	,		19374	0.0		0.0	False		,,,				2504	0.0				p.D522G		Atlas-SNP	.											.	CEP350	418	.	0			c.A1565G						PASS	.	A	GLY/ASP	160,4246	106.0+/-144.5	4,152,2047	43	43	43		1565	5.6	1	1	dbSNP_132	43	2,8598	1.2+/-3.3	0,2,4298	yes	missense	CEP350	NM_014810.4	94	4,154,6345	GG,GA,AA		0.0233,3.6314,1.2456	possibly-damaging	522/3118	179983153	162,12844	2203	4300	6503	SO:0001583	missense	9857	exon10			ATAAGGACTTTTT	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.1565A>G	1.37:g.179983153A>G	ENSP00000356579:p.Asp522Gly	75	0	0		75	46	0.613333	NM_014810	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	37	CCDS1336.1	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	A	19.07	3.755539	0.69648	0.036314	2.33E-4	ENSG00000135837	ENST00000367607	D	0.89485	-2.52	5.6	5.6	0.85130	.	0.122043	0.36555	N	0.002523	T	0.73345	0.3575	M	0.65975	2.015	0.46901	D	0.999242	P;P	0.49635	0.78;0.926	B;P	0.47673	0.265;0.554	T	0.81703	-0.0812	9	.	.	.	.	15.7476	0.77958	1.0:0.0:0.0:0.0	.	522;522	E7EU22;Q5VT06	.;CE350_HUMAN	G	522	ENSP00000356579:D522G	.	D	+	2	0	CEP350	178249776	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.597000	0.74118	2.251000	0.74343	0.528000	0.53228	GAC	A|0.986;G|0.014	0.014	strong		0.378	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810		G	179983153	A	G	179983153	3	3	22	1	0	0	0	0	1	0	0	0	3256	275	10	3	1599	3	CEP350	1	179983153	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	361900	179983153	69267468	375	3276											
XPR1	9213	hgsc.bcm.edu	37	chr1	180772708	180772708	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccttaaactggccttcagTgagttctacctcagtctaat	10	13	7	11	0	4	1	2	1	2	0	4	2	4	1	3	1	2	1	3	1	4	5	rs12078050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:180772708T>C	ENST00000367590.4	+	4	606	c.408T>C	c.(406-408)agT>agC	p.S136S	XPR1_ENST00000367589.3_Silent_p.S136S	NM_004736.3	NP_004727.2	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor 1	136	SPX. {ECO:0000255|PROSITE- ProRule:PRU00714}.				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						TGGCCTTCAGTGAGTTCTACC	0.408													C|||	258	0.0515176	0.1808	0.0259	5008	,	,		19232	0.0		0.001	False		,,,				2504	0.0				p.S136S		Atlas-SNP	.											.	XPR1	76	.	0			c.T408C						PASS	.	C	,	636,3770	767.9+/-413.5	45,546,1612	119	123	121		408,408	0.9	1	1	dbSNP_120	121	4,8596	819.1+/-406.8	0,4,4296	no	coding-synonymous,coding-synonymous	XPR1	NM_001135669.1,NM_004736.3	,	45,550,5908	CC,CT,TT		0.0465,14.4349,4.9208	,	136/632,136/697	180772708	640,12366	2203	4300	6503	SO:0001819	synonymous_variant	9213	exon4			CTTCAGTGAGTTC	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.408T>C	1.37:g.180772708T>C		70	0	0		68	36	0.529412	NM_004736	O95719|Q7L8K9|Q8IW20|Q9NT19|Q9UFB9	Silent	SNP	ENST00000367590.4	37	CCDS1340.1																																																																																			T|0.942;C|0.058	0.058	strong		0.408	XPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084996.2	NM_004736		C	180772708	T	C	180772708	2	2	22	1	0	0	0	0	0	0	0	1	17466	1693	59	3		3	XPR1	1	180772708	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	789555	180772708	68477913	376	3277											
XPR1	9213	hgsc.bcm.edu	37	chr1	180804033	180804033	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cgagtatttacagcccccttCcataaggtaggctttgctga	9	12	9	11	1	0	1	0	1	0	0	1	2	1	1	3	2	3	4	3	2	4	7	rs61742073	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:180804033C>T	ENST00000367590.4	+	10	1356	c.1158C>T	c.(1156-1158)ttC>ttT	p.F386F	XPR1_ENST00000367589.3_Silent_p.F386F	NM_004736.3	NP_004727.2	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor 1	386					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						CAGCCCCCTTCCATAAGGTAG	0.403													C|||	258	0.0515176	0.1808	0.0259	5008	,	,		19539	0.0		0.001	False		,,,				2504	0.0				p.F386F		Atlas-SNP	.											.	XPR1	76	.	0			c.C1158T						PASS	.	C	,	636,3770	267.1+/-267.6	45,546,1612	64	65	64		1158,1158	4.3	1	1	dbSNP_129	64	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous	XPR1	NM_001135669.1,NM_004736.3	,	45,550,5908	TT,TC,CC		0.0465,14.4349,4.9208	,	386/632,386/697	180804033	640,12366	2203	4300	6503	SO:0001819	synonymous_variant	9213	exon10			CCCCTTCCATAAG	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.1158C>T	1.37:g.180804033C>T		71	0	0		67	30	0.447761	NM_004736	O95719|Q7L8K9|Q8IW20|Q9NT19|Q9UFB9	Silent	SNP	ENST00000367590.4	37	CCDS1340.1																																																																																			C|0.949;T|0.051	0.051	strong		0.403	XPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084996.2	NM_004736		T	180804033	C	T	180804033	2	4	22	1	0	0	0	0	0	0	0	1	17466	854	30	2		2	XPR1	1	180804033	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	31325	180804033	68446588	377	3278											
XPR1	9213	hgsc.bcm.edu	37	chr1	180849394	180849394	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaatcggtcatggaagtacaAccagagcatatccctgcgcc	12	7	10	12	2	1	1	1	0	0	1	3	3	2	2	3	2	4	2	3	2	5	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:180849394A>G	ENST00000367590.4	+	14	2189	c.1991A>G	c.(1990-1992)aAc>aGc	p.N664S	XPR1_ENST00000367589.3_Missense_Mutation_p.N599S	NM_004736.3	NP_004727.2	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor 1	664					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						TGGAAGTACAACCAGAGCATA	0.512																																					p.N664S		Atlas-SNP	.											.	XPR1	76	.	0			c.A1991G						PASS	.						155	146	149					1																	180849394		2203	4300	6503	SO:0001583	missense	9213	exon14			AGTACAACCAGAG	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.1991A>G	1.37:g.180849394A>G	ENSP00000356562:p.Asn664Ser	111	0	0		130	66	0.507692	NM_004736	O95719|Q7L8K9|Q8IW20|Q9NT19|Q9UFB9	Missense_Mutation	SNP	ENST00000367590.4	37	CCDS1340.1	.	.	.	.	.	.	.	.	.	.	A	8.539	0.872854	0.17322	.	.	ENSG00000143324	ENST00000367590;ENST00000367589	T	0.40476	1.03	5.56	1.18	0.20946	.	0.390605	0.32002	N	0.006729	T	0.10852	0.0265	N	0.00823	-1.155	0.20821	N	0.999847	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.35649	-0.9780	10	0.06891	T	0.86	-0.9318	7.5346	0.27702	0.4444:0.0:0.5556:0.0	.	599;664	Q9UBH6-2;Q9UBH6	.;XPR1_HUMAN	S	664;599	ENSP00000356562:N664S	ENSP00000356561:N599S	N	+	2	0	XPR1	179116017	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	1.285000	0.33261	0.243000	0.21327	-0.462000	0.05337	AAC	.	.	none		0.512	XPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084996.2	NM_004736		G	180849394	A	G	180849394	3	3	22	1	0	0	0	0	1	0	0	0	17466	43	2	3	2045	3	XPR1	1	180849394	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	45361	180849394	68401227	378	3279											
RGS8	85397	hgsc.bcm.edu	37	chr1	182640848	182640848	+	5'UTR	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ccaactggatggtcagagagGcttcgggttaaggtgttctg	8	11	15	7	1	2	1	1	0	1	1	3	3	2	2	1	5	1	3	1	5	2	3	rs115960776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:182640848G>A	ENST00000483095.2	-	0	98				RGS8_ENST00000491420.2_5'UTR|RGS8_ENST00000367556.1_5'UTR|RGS8_ENST00000367557.4_5'UTR|RGS8_ENST00000258302.4_Silent_p.S8S			P57771	RGS8_HUMAN	regulator of G-protein signaling 8						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						GGTCAGAGAGGCTTCGGGTTA	0.502													G|||	104	0.0207668	0.0749	0.0072	5008	,	,		20143	0.0		0.0	False		,,,				2504	0.0				p.S8S	Ovarian(189;1262 3804 41973)	Atlas-SNP	.											.	RGS8	51	.	0			c.C24T						PASS	.	G	,	243,4163	142.3+/-177.5	10,223,1970	173	176	175		,24	4.4	1	1	dbSNP_132	175	5,8595	3.7+/-12.6	0,5,4295	no	utr-5,coding-synonymous	RGS8	NM_001102450.1,NM_033345.2	,	10,228,6265	AA,AG,GG		0.0581,5.5152,1.9068	,	,8/199	182640848	248,12758	2203	4300	6503	SO:0001623	5_prime_UTR_variant	85397	exon2			AGAGAGGCTTCGG	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.-160C>T	1.37:g.182640848G>A		286	0	0		215	80	0.372093	NM_033345	B4DGL9|Q3SYD2	Silent	SNP	ENST00000483095.2	37	CCDS41443.1																																																																																			G|0.981;A|0.019	0.019	strong		0.502	RGS8-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358979.1	NM_033345		A	182640848	G	A	182640848	1	1	22	0	1	0	0	0	0	0	0	0	13327	1194	42	2		2	RGS8	1	182640848	5'UTR	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1791454	182640848	66609773	379	3280											
NPL	80896	hgsc.bcm.edu	37	chr1	182787797	182787797	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gatcagaatcgccagcaacaGtttgctttcctttttggggt	8	14	10	9	1	1	1	1	0	0	1	3	2	2	1	2	2	3	3	2	2	2	4	rs58343016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:182787797G>A	ENST00000367553.1	+	8	623	c.579G>A	c.(577-579)caG>caA	p.Q193Q	NPL_ENST00000367554.3_Silent_p.Q174Q|NPL_ENST00000367555.1_Silent_p.Q193Q|NPL_ENST00000258317.2_Silent_p.Q193Q|NPL_ENST00000367552.2_Silent_p.Q193Q|NPL_ENST00000463899.1_3'UTR	NM_001200056.1|NM_030769.2	NP_001186985.1|NP_110396.1	Q9BXD5	NPL_HUMAN	N-acetylneuraminate pyruvate lyase (dihydrodipicolinate synthase)	193					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						GCCAGCAACAGTTTGCTTTCC	0.458													G|||	83	0.0165735	0.0605	0.0043	5008	,	,		20020	0.0		0.0	False		,,,				2504	0.0				p.Q193Q		Atlas-SNP	.											.	NPL	55	.	0			c.G579A						PASS	.	G	,,,,	222,4184	133.7+/-170.0	5,212,1986	73	73	73		522,579,579,579,579	-0.5	1	1	dbSNP_129	73	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NPL	NM_001200050.1,NM_001200051.1,NM_001200052.1,NM_001200056.1,NM_030769.2	,,,,	5,212,6286	AA,AG,GG		0.0,5.0386,1.7069	,,,,	174/302,193/241,193/231,193/285,193/321	182787797	222,12784	2203	4300	6503	SO:0001819	synonymous_variant	80896	exon9			GCAACAGTTTGCT	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.579G>A	1.37:g.182787797G>A		59	0	0		60	30	0.5	NM_001200052	B2R839|Q4G0Q8|Q4G0Z2|Q64L88|Q6PEL0	Silent	SNP	ENST00000367553.1	37	CCDS1350.1																																																																																			G|0.983;A|0.017	0.017	strong		0.458	NPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085463.1	NM_030769		A	182787797	G	A	182787797	2	1	22	1	0	0	0	0	0	0	0	1	10594	1020	36	2		2	NPL	1	182787797	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	146949	182787797	66462824	380	3281											
DHX9	1660	hgsc.bcm.edu	37	chr1	182827297	182827297	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcacagtcctgtgccctGtcacttgtcagacaactgta	9	10	9	13	0	2	1	2	0	0	1	3	1	3	1	2	0	3	3	2	0	2	2	rs73063095	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:182827297G>A	ENST00000367549.3	+	8	842	c.732G>A	c.(730-732)ctG>ctA	p.L244L		NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	244	DRBM 2. {ECO:0000255|PROSITE- ProRule:PRU00266}.|Interaction with BRCA1.|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						CCTGTGCCCTGTCACTTGTCA	0.408													G|||	104	0.0207668	0.0741	0.0072	5008	,	,		20027	0.001		0.0	False		,,,				2504	0.0				p.L244L	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.G732A						PASS	.	G		243,3731		8,227,1752	100	95	97		732	1.1	1	1	dbSNP_130	97	0,8354		0,0,4177	no	coding-synonymous	DHX9	NM_001357.4		8,227,5929	AA,AG,GG		0.0,6.1147,1.9711		244/1271	182827297	243,12085	1987	4177	6164	SO:0001819	synonymous_variant	1660	exon8			TGCCCTGTCACTT	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.732G>A	1.37:g.182827297G>A		178	0	0		173	76	0.439306	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Silent	SNP	ENST00000367549.3	37	CCDS41444.1																																																																																			G|0.986;A|0.014	0.014	strong		0.408	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		A	182827297	G	A	182827297	2	1	22	1	0	0	0	0	0	0	0	1	4518	1364	48	2		2	DHX9	1	182827297	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	39500	182827297	66423324	381	3282											
C1orf14	81626	hgsc.bcm.edu	37	chr1	182922003	182922003	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggcagcaggggctcctccGccgccgccgccgccgcctct	2	5	13	21	6	1	0	0	0	1	0	3	0	3	0	8	3	1	3	8	3	0	0	rs13373887	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:182922003G>T	ENST00000367547.3	-	1	502	c.266C>A	c.(265-267)gCg>gAg	p.A89E	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	161										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|pancreas(1)|prostate(1)|skin(2)	15						GGGCTCCTccgccgccgccgc	0.741													T|||	190	0.0379393	0.1293	0.0159	5008	,	,		11211	0.0		0.005	False		,,,				2504	0.0031				p.A89E		Atlas-SNP	.											.	SHCBP1L	64	.	0			c.C266A						PASS	.	T	GLU/ALA	443,3869		18,407,1731	6	7	7		266	0	0	1	dbSNP_121	7	23,8443		0,23,4210	yes	missense	SHCBP1L	NM_030933.2	107	18,430,5941	TT,TG,GG		0.2717,10.2737,3.6469	benign	89/654	182922003	466,12312	2156	4233	6389	SO:0001583	missense	81626	exon1			TCCTCCGCCGCCG	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.266C>A	1.37:g.182922003G>T	ENSP00000356518:p.Ala89Glu	33	0	0		37	28	0.756757	NM_030933	Q4G195|Q9BZQ3|Q9H2B6	Missense_Mutation	SNP	ENST00000367547.3	37	CCDS30955.1	66	0.03021978021978022	60	0.12195121951219512	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	T	0.005	-2.169349	0.00315	0.102737	0.002717	ENSG00000157060	ENST00000367547;ENST00000287709	T	0.39229	1.09	3.96	0.04	0.14207	.	1.066270	0.07492	N	0.905864	T	0.00178	0.0005	N	0.01874	-0.695	0.21499	N	0.999663	B	0.02656	0.0	B	0.04013	0.001	T	0.09930	-1.0652	10	0.02654	T	1	.	4.0773	0.09911	0.0:0.2058:0.3591:0.4351	rs13373887	89	Q9BZQ2-3	.	E	89;158	ENSP00000356518:A89E	ENSP00000287709:A158E	A	-	2	0	SHCBP1L	181188626	.	.	0.003000	0.11579	0.009000	0.06853	.	.	-0.560000	0.06102	-0.865000	0.03005	GCG	G|0.965;T|0.035	0.035	strong		0.741	SHCBP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085956.1	NM_030933		T	182922003	G	T	182922003	3	4	22	1	0	0	0	0	1	0	0	0	2002	1087	38	4	1735	4	C1orf14	1	182922003	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	94706	182922003	66328618	382	3283											
LAMC2	3918	hgsc.bcm.edu	37	chr1	183184650	183184650	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaaaccaggtgtgacaggaGccagatgcgaccgatgtctg	11	7	14	9	2	1	2	0	1	1	1	1	5	1	3	3	2	3	1	3	2	2	1	rs12065473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:183184650G>C	ENST00000264144.4	+	3	396	c.331G>C	c.(331-333)Gcc>Ccc	p.A111P	LAMC2_ENST00000493293.1_Missense_Mutation_p.A111P	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	111	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.		A -> P (in dbSNP:rs12065473).		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						TGTGACAGGAGCCAGATGCGA	0.547													G|||	160	0.0319489	0.1135	0.013	5008	,	,		19074	0.0		0.001	False		,,,				2504	0.0				p.A111P		Atlas-SNP	.											.	LAMC2	113	.	0			c.G331C						PASS	.	G	PRO/ALA,PRO/ALA	484,3922	226.9+/-242.2	23,438,1742	124	110	115		331,331	2	0.7	1	dbSNP_120	115	7,8593	5.0+/-18.6	0,7,4293	yes	missense,missense	LAMC2	NM_005562.2,NM_018891.2	27,27	23,445,6035	CC,CG,GG		0.0814,10.985,3.7752	benign,benign	111/1194,111/1112	183184650	491,12515	2203	4300	6503	SO:0001583	missense	3918	exon3			ACAGGAGCCAGAT	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.331G>C	1.37:g.183184650G>C	ENSP00000264144:p.Ala111Pro	150	0	0		173	77	0.445087	NM_005562	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Missense_Mutation	SNP	ENST00000264144.4	37	CCDS1352.1	51	0.023351648351648352	46	0.09349593495934959	5	0.013812154696132596	0	0.0	0	0.0	G	16.35	3.099112	0.56183	0.10985	8.14E-4	ENSG00000058085	ENST00000493293;ENST00000537180;ENST00000264144	T;T	0.61392	0.11;0.11	4.97	2.0	0.26442	EGF-like, laminin (4);Growth factor, receptor (1);	0.621389	0.16329	N	0.219195	T	0.00637	0.0021	N	0.05230	-0.09	0.27001	N	0.964914	B;B	0.26041	0.14;0.034	B;B	0.31495	0.131;0.039	T	0.04678	-1.0934	10	0.30854	T	0.27	.	5.6168	0.17436	0.2342:0.148:0.6178:0.0	rs12065473;rs52806764;rs12065473	111;111	Q13753;Q13753-2	LAMC2_HUMAN;.	P	111	ENSP00000432063:A111P;ENSP00000264144:A111P	ENSP00000264144:A111P	A	+	1	0	LAMC2	181451273	0.946000	0.32159	0.668000	0.29813	0.953000	0.61014	1.823000	0.39062	0.139000	0.18822	-0.137000	0.14449	GCC	G|0.963;C|0.037	0.037	strong		0.547	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562		C	183184650	G	C	183184650	3	2	22	1	0	0	0	0	1	0	0	0	8624	971	34	4	341	4	LAMC2	1	183184650	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	262647	183184650	66065971	383	3284											
HMCN1	83872	hgsc.bcm.edu	37	chr1	186026366	186026366	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgttttattttgtcttacagCtcctccaagcatcataggaa	10	16	6	9	0	2	0	1	0	1	0	4	1	4	1	2	1	3	3	2	1	5	6	rs140744695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:186026366C>T	ENST00000271588.4	+	46	7374	c.7145C>T	c.(7144-7146)gCt>gTt	p.A2382V	HMCN1_ENST00000367492.2_Splice_Site_p.A2382V	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2382					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						TGTCTTACAGCTCCTCCAAGC	0.363													C|||	2	0.000399361	0.0015	0.0	5008	,	,		17150	0.0		0.0	False		,,,				2504	0.0				p.A2382V		Atlas-SNP	.											.	HMCN1	797	.	0			c.C7145T						PASS	.	C	VAL/ALA	5,4401	9.9+/-24.2	0,5,2198	77	77	77		7145	-2.6	0.7	1	dbSNP_134	77	0,8598		0,0,4299	yes	missense-near-splice	HMCN1	NM_031935.2	64	0,5,6497	TT,TC,CC		0.0,0.1135,0.0384	benign	2382/5636	186026366	5,12999	2203	4299	6502	SO:0001630	splice_region_variant	83872	exon46			TTACAGCTCCTCC	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.7145-1C>T	1.37:g.186026366C>T		74	0	0		91	41	0.450549	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	1.308	-0.602865	0.03744	0.001135	0.0	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.72167	-0.63;-0.63	5.8	-2.64	0.06114	Immunoglobulin-like fold (1);	0.288142	0.38058	N	0.001832	T	0.32285	0.0824	N	0.00746	-1.225	0.34659	D	0.722457	B	0.09022	0.002	B	0.06405	0.002	T	0.31024	-0.9958	9	.	.	.	.	12.1208	0.53889	0.0:0.2184:0.0:0.7816	.	2382	Q96RW7	HMCN1_HUMAN	V	2382	ENSP00000271588:A2382V;ENSP00000356462:A2382V	.	A	+	2	0	HMCN1	184292989	0.973000	0.33851	0.699000	0.30290	0.417000	0.31264	1.939000	0.40213	-0.338000	0.08413	-0.142000	0.14014	GCT	C|0.999;T|0.001	0.001	strong		0.363	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	Missense_Mutation	T	186026366	C	T	186026366	5	4	22	1	0	0	0	0	0	0	1	0	7229	811	28	2	7327	2	HMCN1	1	186026366	Splice_Site	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2841716	186026366	63224255	384	3285											
HMCN1	83872	hgsc.bcm.edu	37	chr1	186043899	186043899	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaatccgatgatcatgttaaTattgctgcgaatggacacac	14	11	8	8	2	1	1	1	1	0	0	2	4	2	2	1	1	2	2	1	1	4	3	rs77026548	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:186043899T>C	ENST00000271588.4	+	53	8395	c.8166T>C	c.(8164-8166)aaT>aaC	p.N2722N	HMCN1_ENST00000367492.2_Silent_p.N2722N	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2722	Ig-like C2-type 25.				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						ATCATGTTAATATTGCTGCGA	0.383													T|||	153	0.0305511	0.1104	0.0086	5008	,	,		14973	0.0		0.001	False		,,,				2504	0.0				p.N2722N		Atlas-SNP	.											.	HMCN1	797	.	0			c.T8166C						PASS	.	T		425,3981	208.2+/-229.3	24,377,1802	113	109	110		8166	-2	0.1	1	dbSNP_131	110	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	HMCN1	NM_031935.2		24,383,6096	CC,CT,TT		0.0698,9.6459,3.3139		2722/5636	186043899	431,12575	2203	4300	6503	SO:0001819	synonymous_variant	83872	exon53			TGTTAATATTGCT	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.8166T>C	1.37:g.186043899T>C		119	0	0		126	61	0.484127	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	37	CCDS30956.1																																																																																			T|0.967;C|0.033	0.033	strong		0.383	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		C	186043899	T	C	186043899	2	2	22	1	0	0	0	0	0	0	0	1	7229	1403	49	3		3	HMCN1	1	186043899	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	17533	186043899	63206722	385	3286											
HMCN1	83872	hgsc.bcm.edu	37	chr1	186057347	186057347	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaatcctgtgacattaacAtgtgatgccactgggatccc	11	10	9	11	0	0	2	0	2	0	0	2	3	2	3	3	1	3	1	3	1	2	1	rs61745374	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:186057347A>T	ENST00000271588.4	+	62	9745	c.9516A>T	c.(9514-9516)acA>acT	p.T3172T	HMCN1_ENST00000367492.2_Silent_p.T3172T	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3172	Ig-like C2-type 30.				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						TGACATTAACATGTGATGCCA	0.428													A|||	206	0.0411342	0.1498	0.0101	5008	,	,		17561	0.0		0.001	False		,,,				2504	0.0				p.T3172T		Atlas-SNP	.											.	HMCN1	797	.	0			c.A9516T						PASS	.	A		558,3848	250.9+/-257.8	49,460,1694	98	87	91		9516	-11.3	0	1	dbSNP_129	91	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	HMCN1	NM_031935.2		49,466,5988	TT,TA,AA		0.0698,12.6645,4.3365		3172/5636	186057347	564,12442	2203	4300	6503	SO:0001819	synonymous_variant	83872	exon62			ATTAACATGTGAT	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.9516A>T	1.37:g.186057347A>T		71	0	0		73	50	0.684932	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	37	CCDS30956.1																																																																																			A|0.953;T|0.047	0.047	strong		0.428	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		T	186057347	A	T	186057347	2	4	22	1	0	0	0	0	0	0	0	1	7229	204	8	5		5	HMCN1	1	186057347	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	13448	186057347	63193274	386	3287											
C1orf27	54953	hgsc.bcm.edu	37	chr1	186355168	186355168	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tagttcttggagtatttattAttactactttagaactggca	11	18	7	5	0	1	1	0	0	1	1	1	2	1	2	0	2	3	3	0	2	8	11	rs115570554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:186355168A>G	ENST00000287859.6	+	4	408	c.283A>G	c.(283-285)Att>Gtt	p.I95V	C1orf27_ENST00000432021.3_Missense_Mutation_p.I95V|C1orf27_ENST00000367470.3_Missense_Mutation_p.I95V|C1orf27_ENST00000419367.3_Intron	NM_017847.5	NP_060317.3	Q5SWX8	ODR4_HUMAN	chromosome 1 open reading frame 27	95						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						AGTATTTATTATTACTACTTT	0.289													A|||	21	0.00419329	0.0151	0.0014	5008	,	,		15027	0.0		0.0	False		,,,				2504	0.0				p.I95V		Atlas-SNP	.											.	C1orf27	41	.	0			c.A283G						PASS	.	A	VAL/ILE,,VAL/ILE	36,3532		0,36,1748	54	51	52		283,,283	2.5	1	1	dbSNP_132	52	0,8118		0,0,4059	yes	missense,intron,missense	C1orf27	NM_001164245.1,NM_001164246.1,NM_017847.5	29,,29	0,36,5807	GG,GA,AA		0.0,1.009,0.3081	benign,,benign	95/432,,95/455	186355168	36,11650	1784	4059	5843	SO:0001583	missense	54953	exon4			TTTATTATTACTA	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.283A>G	1.37:g.186355168A>G	ENSP00000287859:p.Ile95Val	41	0	0		56	24	0.428571	NM_001164245	B4DNY0|E9PFR7|Q19CC6|Q8WYB6|Q9BTS2|Q9H6A6|Q9NX06	Missense_Mutation	SNP	ENST00000287859.6	37	CCDS53448.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	A	1.145	-0.648372	0.03506	0.01009	0.0	ENSG00000157181	ENST00000367470;ENST00000432021;ENST00000287859	T;T;T	0.38401	1.14;1.14;1.14	4.97	2.47	0.30058	.	0.271361	0.41500	N	0.000862	T	0.12860	0.0312	L	0.29908	0.895	0.33076	D	0.535996	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.22382	-1.0218	10	0.05833	T	0.94	-21.9948	4.69	0.12776	0.6635:0.1637:0.1728:0.0	.	95;95	Q5SWX8-2;Q5SWX8	.;ODR4_HUMAN	V	95	ENSP00000356440:I95V;ENSP00000402029:I95V;ENSP00000287859:I95V	ENSP00000287859:I95V	I	+	1	0	C1orf27	184621791	0.727000	0.28069	0.998000	0.56505	0.985000	0.73830	0.258000	0.18387	0.851000	0.35264	-0.263000	0.10527	ATT	A|0.997;G|0.003	0.003	strong		0.289	C1orf27-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086352.2	NM_017847		G	186355168	A	G	186355168	3	3	22	1	0	0	0	0	1	0	0	0	2038	449	16	3	293	3	C1orf27	1	186355168	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	297821	186355168	62895453	387	3288											
RGS13	6003	hgsc.bcm.edu	37	chr1	192613522	192613522	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gagatgaatctaagaggcccCcttcaaagtaagtagcattt	14	10	9	8	0	2	3	1	1	1	2	2	4	2	3	2	1	1	3	2	1	5	5	rs146420296		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:192613522C>T	ENST00000391995.2	+	4	346	c.58C>T	c.(58-60)Cct>Tct	p.P20S	RGS13_ENST00000543215.1_Missense_Mutation_p.P20S	NM_002927.4	NP_002918.1	O14921	RGS13_HUMAN	regulator of G-protein signaling 13	20					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of GTPase activity (GO:0043547)|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)			endometrium(1)|kidney(1)|large_intestine(4)|lung(12)|skin(1)	19						TAAGAGGCCCCCTTCAAAGTA	0.289																																					p.P20S		Atlas-SNP	.											.	RGS13	31	.	0			c.C58T						PASS	.	C	SER/PRO,SER/PRO	1,4405	2.1+/-5.4	0,1,2202	122	135	131		58,58	3.7	0.5	1	dbSNP_134	131	0,8598		0,0,4299	no	missense,missense	RGS13	NM_002927.4,NM_144766.2	74,74	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	20/160,20/160	192613522	1,13003	2203	4299	6502	SO:0001583	missense	6003	exon4			AGGCCCCCTTCAA	AF030107	CCDS1376.1	1q31.2	2008-02-05	2007-08-14		ENSG00000127074	ENSG00000127074		"Regulators of G-protein signaling"	9995	protein-coding gene	gene with protein product		607190	"regulator of G-protein signalling 13"			11875076	Standard	NM_144766		Approved		uc001gsk.3	O14921	OTTHUMG00000035601	ENST00000391995.2:c.58C>T	1.37:g.192613522C>T	ENSP00000375853:p.Pro20Ser	235	0	0		214	96	0.448598	NM_002927	Q6PGR2|Q8TD63|Q9BX45	Missense_Mutation	SNP	ENST00000391995.2	37	CCDS1376.1	.	.	.	.	.	.	.	.	.	.	C	4.758	0.140916	0.09083	2.27E-4	0.0	ENSG00000127074	ENST00000391995;ENST00000543215	T;T	0.29655	1.56;1.56	5.62	3.67	0.42095	.	0.906400	0.09503	N	0.793331	T	0.18130	0.0435	N	0.24115	0.695	0.23653	N	0.997194	B	0.06786	0.001	B	0.06405	0.002	T	0.28073	-1.0055	10	0.07175	T	0.84	.	8.174	0.31270	0.0:0.7495:0.1625:0.0881	.	20	O14921	RGS13_HUMAN	S	20	ENSP00000375853:P20S;ENSP00000442837:P20S	ENSP00000375853:P20S	P	+	1	0	RGS13	190880145	0.086000	0.21541	0.478000	0.27316	0.701000	0.40568	1.077000	0.30741	1.460000	0.47911	0.655000	0.94253	CCT	C|1.000;T|0.000	0.000	weak		0.289	RGS13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086400.1	NM_002927		T	192613522	C	T	192613522	3	4	22	1	0	0	0	0	1	0	0	0	13311	623	22	2	60	2	RGS13	1	192613522	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6258354	192613522	56637099	388	3289											
RGS13	6003	hgsc.bcm.edu	37	chr1	192628623	192628623	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gaaatgtaccaaaaacttttGaaaactatgcagtccaacaa	19	9	5	8	0	0	1	0	1	0	0	1	2	1	1	2	0	5	2	2	0	9	4	rs16834603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:192628623G>C	ENST00000391995.2	+	7	738	c.450G>C	c.(448-450)ttG>ttC	p.L150F	RGS13_ENST00000543215.1_Missense_Mutation_p.L150F|RGS13_ENST00000482095.1_3'UTR	NM_002927.4	NP_002918.1	O14921	RGS13_HUMAN	regulator of G-protein signaling 13	150	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.		L -> F (in dbSNP:rs16834603). {ECO:0000269|Ref.2}.		G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of GTPase activity (GO:0043547)|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)			endometrium(1)|kidney(1)|large_intestine(4)|lung(12)|skin(1)	19						AAAAACTTTTGAAAACTATGC	0.323													G|||	207	0.0413339	0.1513	0.0101	5008	,	,		16977	0.0		0.0	False		,,,				2504	0.0				p.L150F		Atlas-SNP	.											.	RGS13	31	.	0			c.G450C						PASS	.	G	PHE/LEU,PHE/LEU	577,3829	246.2+/-254.9	48,481,1674	46	45	45		450,450	2.7	1	1	dbSNP_123	45	4,8596	3.0+/-9.4	0,4,4296	yes	missense,missense	RGS13	NM_002927.4,NM_144766.2	22,22	48,485,5970	CC,CG,GG		0.0465,13.0958,4.4672	benign,benign	150/160,150/160	192628623	581,12425	2203	4300	6503	SO:0001583	missense	6003	exon7			ACTTTTGAAAACT	AF030107	CCDS1376.1	1q31.2	2008-02-05	2007-08-14		ENSG00000127074	ENSG00000127074		"Regulators of G-protein signaling"	9995	protein-coding gene	gene with protein product		607190	"regulator of G-protein signalling 13"			11875076	Standard	NM_144766		Approved		uc001gsk.3	O14921	OTTHUMG00000035601	ENST00000391995.2:c.450G>C	1.37:g.192628623G>C	ENSP00000375853:p.Leu150Phe	156	0	0		181	94	0.519337	NM_002927	Q6PGR2|Q8TD63|Q9BX45	Missense_Mutation	SNP	ENST00000391995.2	37	CCDS1376.1	71	0.03250915750915751	70	0.14227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	G	13.88	2.368730	0.42003	0.130958	4.65E-4	ENSG00000127074	ENST00000391995;ENST00000543215	T;T	0.36157	1.27;1.27	5.89	2.73	0.32206	Regulator of G protein signalling (2);Regulator of G protein signalling superfamily (1);	0.277274	0.34725	N	0.003740	T	0.00300	0.0009	M	0.75085	2.285	0.31991	P	0.6046279999999999	B	0.29531	0.247	B	0.35470	0.203	T	0.11743	-1.0575	9	0.62326	D	0.03	.	5.6215	0.17459	0.0815:0.1835:0.6077:0.1273	rs16834603;rs52813648;rs16834603	150	O14921	RGS13_HUMAN	F	150	ENSP00000375853:L150F;ENSP00000442837:L150F	ENSP00000375853:L150F	L	+	3	2	RGS13	190895246	0.082000	0.21442	1.000000	0.80357	0.888000	0.51559	0.259000	0.18405	1.497000	0.48584	0.591000	0.81541	TTG	G|0.955;C|0.045	0.045	strong		0.323	RGS13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086400.1	NM_002927		C	192628623	G	C	192628623	3	2	22	1	0	0	0	0	1	0	0	0	13311	1281	45	4	464	4	RGS13	1	192628623	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	15101	192628623	56621998	389	3290											
KCNT2	343450	hgsc.bcm.edu	37	chr1	196303117	196303117	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcttatttctttgcttccCtctgtaggaagagacagggt	7	16	9	9	0	3	1	0	0	3	1	4	3	4	2	1	2	1	2	1	2	3	6	rs116401401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:196303117C>T	ENST00000294725.9	-	17	2772	c.1857G>A	c.(1855-1857)gaG>gaA	p.E619E	KCNT2_ENST00000498426.1_5'UTR|KCNT2_ENST00000367431.4_Silent_p.E569E|KCNT2_ENST00000609185.1_Silent_p.E569E|KCNT2_ENST00000451324.2_Silent_p.E230E|KCNT2_ENST00000367433.5_Silent_p.E619E			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	619					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						CTTTGCTTCCCTCTGTAGGAA	0.393													C|||	25	0.00499201	0.0166	0.0043	5008	,	,		16218	0.0		0.0	False		,,,				2504	0.0				p.E619E		Atlas-SNP	.											.	KCNT2	243	.	0			c.G1857A						PASS	.	C		52,4354	52.3+/-87.9	0,52,2151	126	115	118		1857	0.6	1	1	dbSNP_132	118	0,8600		0,0,4300	no	coding-synonymous	KCNT2	NM_198503.2		0,52,6451	TT,TC,CC		0.0,1.1802,0.3998		619/1136	196303117	52,12954	2203	4300	6503	SO:0001819	synonymous_variant	343450	exon17			GCTTCCCTCTGTA	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.1857G>A	1.37:g.196303117C>T		122	0	0		147	72	0.489796	NM_198503	Q3SY59|Q5VTN1|Q6ZMT3	Silent	SNP	ENST00000294725.9	37	CCDS1384.1																																																																																			C|0.995;T|0.005	0.005	strong		0.393	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503		T	196303117	C	T	196303117	2	4	22	1	0	0	0	0	0	0	0	1	8101	680	24	2		2	KCNT2	1	196303117	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3674494	196303117	52947504	390	3291											
CFH	3075	hgsc.bcm.edu	37	chr1	196706659	196706659	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	acacggaaccattaattcatCcaggtcttcacaagaaagtt	15	10	6	10	1	3	1	2	0	1	1	4	2	4	2	2	2	1	1	2	2	4	4	rs114743644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:196706659C>A	ENST00000367429.4	+	17	2891	c.2651C>A	c.(2650-2652)tCc>tAc	p.S884Y		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	884	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						ATTAATTCATCCAGGTCTTCA	0.338													C|||	4	0.000798722	0.0023	0.0014	5008	,	,		13290	0.0		0.0	False		,,,				2504	0.0				p.S884Y		Atlas-SNP	.											.	CFH	251	.	0			c.C2651A						PASS	.	C	TYR/SER	13,4393		0,13,2190	72	68	70		2651	3.6	0	1	dbSNP_133	70	0,8600		0,0,4300	yes	missense	CFH	NM_000186.3	144	0,13,6490	AA,AC,CC		0.0,0.2951,0.1	probably-damaging	884/1232	196706659	13,12993	2203	4300	6503	SO:0001583	missense	3075	exon17			ATTCATCCAGGTC	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.2651C>A	1.37:g.196706659C>A	ENSP00000356399:p.Ser884Tyr	103	0	0		92	46	0.5	NM_000186	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Missense_Mutation	SNP	ENST00000367429.4	37	CCDS1385.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	.	13.20	2.165002	0.38217	0.002951	0.0	ENSG00000000971	ENST00000367429	T	0.64438	-0.1	5.52	3.61	0.41365	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.50837	0.1639	M	0.67625	2.065	0.09310	N	0.999999	P	0.39250	0.665	B	0.35727	0.209	T	0.42032	-0.9475	9	0.07482	T	0.82	.	6.1966	0.20553	0.1744:0.6935:0.0:0.1321	.	884	P08603	CFAH_HUMAN	Y	884	ENSP00000356399:S884Y	ENSP00000356399:S884Y	S	+	2	0	CFH	194973282	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	0.262000	0.18460	1.455000	0.47813	0.650000	0.86243	TCC	C|0.999;A|0.001	0.001	strong		0.338	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186		A	196706659	C	A	196706659	3	1	22	1	0	0	0	0	1	0	0	0	3285	855	30	4	2735	4	CFH	1	196706659	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	403542	196706659	52543962	391	3292											
CFHR4	3080	hgsc.bcm.edu	37	chr1	196887411	196887411	+	Intron	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaggaaaaagtgacataaaaTattatgcaaaaacaggggat	22	7	9	3	0	0	1	0	1	0	0	0	3	0	3	0	3	2	1	0	3	9	3	rs200907976		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:196887411T>C	ENST00000367421.3	+	2	135				CFHR4_ENST00000251424.4_Missense_Mutation_p.Y291H|CFHR4_ENST00000367418.2_Missense_Mutation_p.Y291H|CFHR4_ENST00000608469.1_Missense_Mutation_p.Y161H|CFHR4_ENST00000367416.2_Missense_Mutation_p.Y537H			P36980	FHR2_HUMAN	complement factor H-related 2							extracellular region (GO:0005576)				large_intestine(2)|ovary(1)|skin(3)	6						TGACATAAAATATTATGCAAA	0.294													T|||	1	0.000199681	0.0	0.0014	5008	,	,		15761	0.0		0.0	False		,,,				2504	0.0				p.Y538H		Atlas-SNP	.											.	CFHR4	141	.	0			c.T1612C						PASS	.	T	HIS/TYR,HIS/TYR,HIS/TYR	6,4396	11.4+/-27.6	1,4,2196	112	122	119		1612,1609,871	-6.5	0	1		119	0,8598		0,0,4299	yes	missense,missense,missense	CFHR4	NM_001201550.2,NM_001201551.1,NM_006684.4	83,83,83	1,4,6495	CC,CT,TT		0.0,0.1363,0.0462	benign,benign,benign	538/579,537/578,291/332	196887411	6,12994	2201	4299	6500	SO:0001627	intron_variant	10877	exon10			ATAAAATATTATG	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.59-31174T>C	1.37:g.196887411T>C		354	1	0.00282486		393	216	0.549618	NM_001201550	Q14310|Q5T9T1	Missense_Mutation	SNP	ENST00000367421.3	37		.	.	.	.	.	.	.	.	.	.	T	10.95	1.496577	0.26861	0.001363	0.0	ENSG00000134365	ENST00000367416;ENST00000367418;ENST00000251424;ENST00000538553	D;D;D	0.82984	-1.67;-1.67;-1.67	3.24	-6.48	0.01896	Complement control module (1);	.	.	.	.	T	0.60130	0.2245	N	0.08118	0	0.09310	N	1	B;D;P	0.58970	0.069;0.984;0.826	B;P;B	0.46796	0.032;0.527;0.188	T	0.58901	-0.7554	9	0.23302	T	0.38	.	0.0302	0.00005	0.2859:0.209:0.2273:0.2777	.	537;538;291	C9J7J7;Q5DVJ7;Q92496	.;.;FHR4_HUMAN	H	537;291;291;291	ENSP00000356386:Y537H;ENSP00000356388:Y291H;ENSP00000251424:Y291H	ENSP00000251424:Y291H	Y	+	1	0	CFHR4	195154034	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-3.116000	0.00597	-2.574000	0.00466	-0.483000	0.04790	TAT	.	.	weak		0.294	CFHR2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005666		C	196887411	T	C	196887411	1	2	22	0	1	0	0	0	0	0	0	0	3289	1406	49	3		3	CFHR4	1	196887411	Intron	SNP	T	TCGA-G8-6324-01A-11D-2210-10	180752	196887411	52363210	392	3293											
C1orf53	388722	hgsc.bcm.edu	37	chr1	197872001	197872001	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgagcgaagagttaaccgcGgcggagcgacagatcgcgga	11	4	17	9	7	0	3	0	1	0	2	1	7	0	5	1	3	3	1	1	3	2	1	rs73083807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:197872001G>A	ENST00000367393.3	+	1	225	c.222G>A	c.(220-222)gcG>gcA	p.A74A		NM_001024594.2	NP_001019765.1	Q5VUE5	CA053_HUMAN	chromosome 1 open reading frame 53	74										endometrium(1)|lung(1)	2						AGTTAACCGCGGCGGAGCGAC	0.756													G|||	123	0.0245607	0.0877	0.0101	5008	,	,		10681	0.0		0.0	False		,,,				2504	0.0				p.A74A		Atlas-SNP	.											.	C1orf53	18	.	0			c.G222A						PASS	.	G		263,3423		4,255,1584	7	8	8		222	0.1	0	1	dbSNP_130	8	3,8019		0,3,4008	no	coding-synonymous	C1orf53	NM_001024594.2		4,258,5592	AA,AG,GG		0.0374,7.1351,2.272		74/146	197872001	266,11442	1843	4011	5854	SO:0001819	synonymous_variant	388722	exon1			AACCGCGGCGGAG	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.222G>A	1.37:g.197872001G>A		20	0	0		15	7	0.466667	NM_001024594	A1L4N2|Q5VUE4	Silent	SNP	ENST00000367393.3	37	CCDS44290.1																																																																																			G|0.972;A|0.028	0.028	strong		0.756	C1orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086555.1	NM_001024594		A	197872001	G	A	197872001	2	1	22	1	0	0	0	0	0	0	0	1	2047	1103	39	1		1	C1orf53	1	197872001	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	984590	197872001	51378620	393	3294											
ATP6V1G3	127124	hgsc.bcm.edu	37	chr1	198498234	198498234	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agattgttttagtcgaaactCtttatctctctgcattctgt	8	19	6	8	1	4	1	0	0	4	1	6	2	4	1	0	0	2	2	0	0	3	6	rs16843254	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:198498234C>G	ENST00000367382.1	-	2	244	c.160G>C	c.(160-162)Gag>Cag	p.E54Q	ATP6V1G3_ENST00000367381.1_Missense_Mutation_p.E60Q|ATP6V1G3_ENST00000309309.7_3'UTR|ATP6V1G3_ENST00000489986.1_Missense_Mutation_p.E60Q|ATP6V1G3_ENST00000281087.2_Missense_Mutation_p.E54Q			Q96LB4	VATG3_HUMAN	ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G3	54			E -> Q (in dbSNP:rs16843254).		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)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	ATPase binding (GO:0051117)|hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)	7						AGTCGAAACTCTTTATCTCTC	0.323													C|||	155	0.0309505	0.1142	0.0058	5008	,	,		9490	0.0		0.0	False		,,,				2504	0.0				p.E54Q		Atlas-SNP	.											.	ATP6V1G3	26	.	0			c.G160C						PASS	.	C	GLN/GLU,	460,3944	219.4+/-237.2	26,408,1768	148	140	143		160,	3.3	0	1	dbSNP_123	143	5,8593	3.7+/-12.6	0,5,4294	yes	missense,utr-3	ATP6V1G3	NM_133262.2,NM_133326.1	29,	26,413,6062	GG,GC,CC		0.0582,10.445,3.5764	possibly-damaging,	54/119,	198498234	465,12537	2202	4299	6501	SO:0001583	missense	127124	exon3			GAAACTCTTTATC	AY039760	CCDS1395.1, CCDS1396.1	1q32.2	2010-04-21	2006-01-13		ENSG00000151418	ENSG00000151418		"ATPases / V-type"	18265	protein-coding gene	gene with protein product			"ATPase, H+ transporting, lysosomal 13kD, V1 subunit G isoform 3", "ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G isoform 3"			9442887	Standard	NM_133262		Approved	ATP6G3, Vma10	uc001gup.3	Q96LB4	OTTHUMG00000035661	ENST00000367382.1:c.160G>C	1.37:g.198498234C>G	ENSP00000356352:p.Glu54Gln	66	0	0		100	58	0.58	NM_133262	Q495K2|Q495K4|Q5T9L6	Missense_Mutation	SNP	ENST00000367382.1	37	CCDS1395.1	62	0.028388278388278388	61	0.12398373983739837	1	0.0027624309392265192	0	0.0	0	0.0	C	8.216	0.801462	0.16397	0.10445	5.82E-4	ENSG00000151418	ENST00000367382;ENST00000367381;ENST00000281087;ENST00000489986	T;T;T;T	0.50548	0.74;0.79;0.74;0.79	5.19	3.31	0.37934	.	0.194878	0.53938	N	0.000054	T	0.01254	0.0041	L	0.53729	1.69	0.31164	N	0.704056	D;D	0.67145	0.996;0.989	P;P	0.60473	0.801;0.875	T	0.15780	-1.0425	10	0.15499	T	0.54	-20.9559	15.1522	0.72709	0.0:0.732:0.268:0.0	rs16843254;rs16843254	60;54	Q96LB4-4;Q96LB4	.;VATG3_HUMAN	Q	54;60;54;60	ENSP00000356352:E54Q;ENSP00000356351:E60Q;ENSP00000281087:E54Q;ENSP00000417171:E60Q	ENSP00000281087:E54Q	E	-	1	0	ATP6V1G3	196764857	1.000000	0.71417	0.044000	0.18714	0.074000	0.17049	3.337000	0.52120	0.682000	0.31407	-0.127000	0.14921	GAG	C|0.959;G|0.041	0.041	strong		0.323	ATP6V1G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086559.1	NM_133326		G	198498234	C	G	198498234	3	3	22	1	0	0	0	0	1	0	0	0	1188	922	32	4	204	4	ATP6V1G3	1	198498234	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	626233	198498234	50752387	394	3295											
C1orf106	55765	hgsc.bcm.edu	37	chr1	200860731	200860731	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gcaggccgcagggaggctcgGggggagggaagatggcctgg	7	3	23	8	2	0	1	0	0	0	1	1	4	0	4	2	9	0	3	2	9	1	0	rs141245080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:200860731G>A	ENST00000367342.4	+	1	263	c.63G>A	c.(61-63)cgG>cgA	p.R21R		NM_018265.3	NP_060735.3	Q3KP66	CA106_HUMAN	chromosome 1 open reading frame 106	21										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(2)	21						GGGAGGCTCGGGGGGAGGGAA	0.622													G|||	43	0.00858626	0.0303	0.0029	5008	,	,		15948	0.0		0.001	False		,,,				2504	0.0				p.R35R		Atlas-SNP	.											.	C1orf106	59	.	0			c.G105A						PASS	.	G		142,4264	94.8+/-133.5	3,136,2064	25	29	27		63	1.5	0	1	dbSNP_134	27	1,8599		0,1,4299	no	coding-synonymous	C1orf106	NM_018265.3		3,137,6363	AA,AG,GG		0.0116,3.2229,1.0995		21/664	200860731	143,12863	2203	4300	6503	SO:0001819	synonymous_variant	55765	exon1			GGCTCGGGGGGAG	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.63G>A	1.37:g.200860731G>A		182	0	0		188	106	0.56383	NM_018265	B4E1K9|E9PFY0|Q9NV65|Q9NVI0	Silent	SNP	ENST00000367342.4	37																																																																																				A|0.008;C|0.001;G|0.991	0.008	strong		0.622	C1orf106-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000087057.2	NM_018265		A	200860731	G	A	200860731	2	1	22	1	0	0	0	0	0	0	0	1	1982	1219	43	2		2	C1orf106	1	200860731	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2362497	200860731	48389890	395	3296											
CACNA1S	779	hgsc.bcm.edu	37	chr1	201046164	201046164	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccaggagggcgaagatgaCgatgaagaggaagagcagca	15	2	17	7	2	0	5	0	2	0	3	0	9	0	7	1	3	2	2	1	3	3	0	rs114191482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:201046164C>T	ENST00000362061.3	-	12	1937	c.1711G>A	c.(1711-1713)Gtc>Atc	p.V571I	CACNA1S_ENST00000367338.3_Missense_Mutation_p.V571I	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	571					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)	GCGAAGATGACGATGAAGAGG	0.557													C|||	8	0.00159744	0.0053	0.0	5008	,	,		23357	0.001		0.0	False		,,,				2504	0.0				p.V571I		Atlas-SNP	.											.	CACNA1S	249	.	0			c.G1711A						PASS	.	C	ILE/VAL	29,4377	37.6+/-69.7	0,29,2174	152	135	141		1711	-2.8	1	1	dbSNP_132	141	0,8600		0,0,4300	yes	missense	CACNA1S	NM_000069.2	29	0,29,6474	TT,TC,CC		0.0,0.6582,0.223	benign	571/1874	201046164	29,12977	2203	4300	6503	SO:0001583	missense	779	exon12			AGATGACGATGAA	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.1711G>A	1.37:g.201046164C>T	ENSP00000355192:p.Val571Ile	311	0	0		368	187	0.508152	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	37	CCDS1407.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	C	4.708	0.131666	0.08981	0.006582	0.0	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.98381	-4.9;-4.9	4.45	-2.76	0.05896	Ion transport (1);	0.302241	0.36034	N	0.002837	D	0.87888	0.6291	N	0.11201	0.11	0.24428	N	0.994582	B	0.06786	0.001	B	0.08055	0.003	T	0.82733	-0.0311	10	0.02654	T	1	.	8.3162	0.32102	0.1089:0.1105:0.0:0.7805	.	571	Q13698	CAC1S_HUMAN	I	571	ENSP00000355192:V571I;ENSP00000356307:V571I	ENSP00000355192:V571I	V	-	1	0	CACNA1S	199312787	0.896000	0.30565	0.989000	0.46669	0.995000	0.86356	-0.005000	0.12855	-0.570000	0.06022	0.549000	0.68633	GTC	C|0.997;T|0.003	0.003	strong		0.557	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		T	201046164	C	T	201046164	3	4	22	1	0	0	0	0	1	0	0	0	2549	536	19	1	4042	1	CACNA1S	1	201046164	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	185433	201046164	48204457	396	3297											
CACNA1S	779	hgsc.bcm.edu	37	chr1	201058428	201058428	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ccctccatggtaatgcactgGtacacggtgagcatggagaa	11	8	12	10	1	0	2	0	1	0	1	1	3	1	2	2	4	3	4	2	4	3	2	rs61734621	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:201058428G>A	ENST00000362061.3	-	6	1084	c.858C>T	c.(856-858)taC>taT	p.Y286Y	CACNA1S_ENST00000367338.3_Silent_p.Y286Y	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	286					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)	TAATGCACTGGTACACGGTGA	0.607													G|||	79	0.0157748	0.056	0.0058	5008	,	,		19962	0.0		0.0	False		,,,				2504	0.001				p.Y286Y		Atlas-SNP	.											.	CACNA1S	249	.	0			c.C858T						PASS	.	G		217,4189	134.9+/-171.1	6,205,1992	104	83	90		858	3.9	1	1	dbSNP_129	90	15,8585	11.2+/-40.8	0,15,4285	no	coding-synonymous	CACNA1S	NM_000069.2		6,220,6277	AA,AG,GG		0.1744,4.9251,1.7838		286/1874	201058428	232,12774	2203	4300	6503	SO:0001819	synonymous_variant	779	exon6			GCACTGGTACACG	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.858C>T	1.37:g.201058428G>A		220	1	0.00454545		261	125	0.478927	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Silent	SNP	ENST00000362061.3	37	CCDS1407.1																																																																																			G|0.984;A|0.016	0.016	strong		0.607	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		A	201058428	G	A	201058428	2	1	22	1	0	0	0	0	0	0	0	1	2549	1256	44	2		2	CACNA1S	1	201058428	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	12264	201058428	48192193	397	3298											
PKP1	5317	hgsc.bcm.edu	37	chr1	201282334	201282334	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcgggagcctgacaacaggcGcttcagctcctacagccaga	10	5	12	14	2	1	2	1	1	0	1	2	3	2	3	3	2	5	2	3	2	2	2	rs34626929	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:201282334G>A	ENST00000352845.3	+	3	347	c.347G>A	c.(346-348)cGc>cAc	p.R116H	PKP1_ENST00000367324.3_Missense_Mutation_p.R116H|PKP1_ENST00000263946.3_Missense_Mutation_p.R116H			Q13835	PKP1_HUMAN	plakophilin 1	116			R -> H (in dbSNP:rs34626929).		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						GACAACAGGCGCTTCAGCTCC	0.582													G|||	125	0.0249601	0.093	0.0014	5008	,	,		15377	0.0		0.001	False		,,,				2504	0.0				p.R116H		Atlas-SNP	.											.	PKP1	127	.	0			c.G347A						PASS	.	G	HIS/ARG,HIS/ARG	335,4069		12,311,1879	12	14	13		347,347	4.2	1	1	dbSNP_126	13	5,8591		0,5,4293	yes	missense,missense	PKP1	NM_000299.3,NM_001005337.2	29,29	12,316,6172	AA,AG,GG		0.0582,7.6067,2.6154	probably-damaging,probably-damaging	116/748,116/727	201282334	340,12660	2202	4298	6500	SO:0001583	missense	5317	exon3			ACAGGCGCTTCAG	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.347G>A	1.37:g.201282334G>A	ENSP00000295597:p.Arg116His	223	0	0		226	126	0.557522	NM_001005337	O00645|Q14CA0|Q15152	Missense_Mutation	SNP	ENST00000352845.3	37	CCDS30966.1	39	0.017857142857142856	39	0.07926829268292683	0	0.0	0	0.0	0	0.0	G	19.95	3.921490	0.73213	0.076067	5.82E-4	ENSG00000081277	ENST00000367324;ENST00000263946;ENST00000352845	T;T;T	0.77750	-1.12;-1.05;-1.05	4.25	4.25	0.50352	.	0.085098	0.50627	D	0.000107	T	0.22085	0.0532	L	0.29908	0.895	0.50467	D	0.999874	D;D	0.89917	0.999;1.0	P;D	0.68621	0.904;0.959	T	0.62553	-0.6830	10	0.46703	T	0.11	-3.6844	15.3441	0.74320	0.0:0.0:1.0:0.0	rs34626929	116;116	Q13835-2;Q13835	.;PKP1_HUMAN	H	116	ENSP00000356293:R116H;ENSP00000263946:R116H;ENSP00000295597:R116H	ENSP00000263946:R116H	R	+	2	0	PKP1	199548957	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.051000	0.71072	2.373000	0.80994	0.491000	0.48974	CGC	G|0.974;A|0.026	0.026	strong		0.582	PKP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086897.1	NM_000299		A	201282334	G	A	201282334	3	1	22	1	0	0	0	0	1	0	0	0	11993	1087	38	1	357	1	PKP1	1	201282334	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	223906	201282334	47968287	398	3299											
SYT2	127833	hgsc.bcm.edu	37	chr1	202569555	202569555	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagacagtgagcttcccggcCgtgggcacatagcgcaggga	9	5	15	12	3	0	2	0	1	0	1	1	3	1	3	2	3	2	3	2	3	1	2	rs907699	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:202569555C>T	ENST00000367267.1	-	7	1041	c.849G>A	c.(847-849)acG>acA	p.T283T	SYT2_ENST00000367268.4_Silent_p.T283T	NM_001136504.1	NP_001129976.1	Q8N9I0	SYT2_HUMAN	synaptotagmin II	283	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)	GCTTCCCGGCCGTGGGCACAT	0.607											OREG0014101	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	419	0.0836661	0.3011	0.0245	5008	,	,		20029	0.0		0.003	False		,,,				2504	0.001				p.T283T		Atlas-SNP	.											.	SYT2	51	.	0			c.G849A						PASS	.	C	,	1168,3238	411.7+/-335.8	150,868,1185	86	83	84		849,849	-4.4	0.7	1	dbSNP_86	84	45,8555	30.1+/-81.4	0,45,4255	no	coding-synonymous,coding-synonymous	SYT2	NM_001136504.1,NM_177402.4	,	150,913,5440	TT,TC,CC		0.5233,26.5093,9.3265	,	283/420,283/420	202569555	1213,11793	2203	4300	6503	SO:0001819	synonymous_variant	127833	exon7			CCCGGCCGTGGGC	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.849G>A	1.37:g.202569555C>T		87	0	0	2130	106	55	0.518868	NM_177402	Q496K5|Q8NBE5	Silent	SNP	ENST00000367267.1	37	CCDS1427.1																																																																																			C|0.917;T|0.083	0.083	strong		0.607	SYT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099157.1	NM_177402		T	202569555	C	T	202569555	2	4	22	1	0	0	0	0	0	0	0	1	15489	639	23	1		1	SYT2	1	202569555	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1287221	202569555	46681066	399	3300											
CHI3L1	1116	hgsc.bcm.edu	37	chr1	203152851	203152851	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcccatcaaagccatgggtgCgcagaaatggcggtactgac	11	6	13	11	2	1	2	1	1	0	1	1	2	1	2	2	3	3	2	2	3	3	1	rs147131854	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:203152851C>T	ENST00000255409.3	-	5	508	c.383G>A	c.(382-384)cGc>cAc	p.R128H		NM_001276.2	NP_001267.2	P36222	CH3L1_HUMAN	chitinase 3-like 1 (cartilage glycoprotein-39)	128					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cellular response to tumor necrosis factor (GO:0071356)|chitin catabolic process (GO:0006032)|inflammatory response (GO:0006954)|interleukin-8 secretion (GO:0072606)|lung development (GO:0030324)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase B signaling (GO:0051897)|response to interleukin-1 (GO:0070555)|response to interleukin-6 (GO:0070741)|response to mechanical stimulus (GO:0009612)|response to tumor necrosis factor (GO:0034612)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|extracellular matrix structural constituent (GO:0005201)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)	p.R128H(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|skin(1)	18						GCCATGGGTGCGCAGAAATGG	0.532													C|||	2	0.000399361	0.0	0.0	5008	,	,		22573	0.0		0.0	False		,,,				2504	0.002				p.R128H		Atlas-SNP	.											CHI3L1,colon,carcinoma,0,1	CHI3L1	51	1	1	Substitution - Missense(1)	large_intestine(1)	c.G383A						PASS	.	C	HIS/ARG	5,4401	9.9+/-24.2	0,5,2198	136	109	118		383	5.7	0.9	1	dbSNP_134	118	5,8595	4.3+/-15.6	0,5,4295	yes	missense	CHI3L1	NM_001276.2	29	0,10,6493	TT,TC,CC		0.0581,0.1135,0.0769	probably-damaging	128/384	203152851	10,12996	2203	4300	6503	SO:0001583	missense	1116	exon5			TGGGTGCGCAGAA	BC008568	CCDS1435.1	1q32.1	2008-02-05			ENSG00000133048	ENSG00000133048			1932	protein-coding gene	gene with protein product		601525				8245017, 9244440	Standard	NM_001276		Approved	GP39, YKL40	uc001gzi.2	P36222	OTTHUMG00000042122	ENST00000255409.3:c.383G>A	1.37:g.203152851C>T	ENSP00000255409:p.Arg128His	101	0	0		103	50	0.485437	NM_001276	B2R7B0|P30923|Q8IVA4|Q96HI7	Missense_Mutation	SNP	ENST00000255409.3	37	CCDS1435.1	.	.	.	.	.	.	.	.	.	.	C	19.23	3.787628	0.70337	0.001135	5.81E-4	ENSG00000133048	ENST00000255409	T	0.07114	3.22	5.69	5.69	0.88448	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.50627	D	0.000104	T	0.35799	0.0944	M	0.87456	2.885	0.54753	D	0.999988	D	0.89917	1.0	D	0.97110	1.0	T	0.15407	-1.0438	10	0.62326	D	0.03	-35.3845	17.3057	0.87194	0.0:1.0:0.0:0.0	.	128	P36222	CH3L1_HUMAN	H	128	ENSP00000255409:R128H	ENSP00000255409:R128H	R	-	2	0	CHI3L1	201419474	1.000000	0.71417	0.910000	0.35882	0.095000	0.18619	7.061000	0.76699	2.664000	0.90586	0.655000	0.94253	CGC	C|0.999;T|0.001	0.001	strong		0.532	CHI3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100265.1	NM_001276		T	203152851	C	T	203152851	3	4	22	1	0	0	0	0	1	0	0	0	3342	768	27	1	792	1	CHI3L1	1	203152851	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	583296	203152851	46097770	400	3301											
ETNK2	55224	hgsc.bcm.edu	37	chr1	204109238	204109238	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atattcatagtcaatgaaccGcacgtgacctatgaagtaga	15	10	8	8	2	2	4	2	3	0	1	2	4	2	4	2	0	1	2	2	0	7	5	rs565275436		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:204109238G>A	ENST00000367202.4	-	5	943	c.793C>T	c.(793-795)Cgg>Tgg	p.R265W	ETNK2_ENST00000367198.2_Missense_Mutation_p.R87W|ETNK2_ENST00000477125.1_5'UTR|ETNK2_ENST00000367197.1_5'UTR|ETNK2_ENST00000367199.2_Missense_Mutation_p.R196W|ETNK2_ENST00000367201.3_Missense_Mutation_p.R265W|RP11-74C13.3_ENST00000433869.1_RNA	NM_018208.2	NP_060678.2	Q9NVF9	EKI2_HUMAN	ethanolamine kinase 2	265					glycerophospholipid biosynthetic process (GO:0046474)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|placenta development (GO:0001890)|post-embryonic development (GO:0009791)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ethanolamine kinase activity (GO:0004305)			breast(1)|central_nervous_system(1)|large_intestine(4)|ovary(1)	7	all_cancers(21;0.032)|Breast(84;0.116)|all_epithelial(62;0.196)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)			TCAATGAACCGCACGTGACCT	0.488													G|||	1	0.000199681	0.0008	0.0	5008	,	,		22874	0.0		0.0	False		,,,				2504	0.0				p.R265W		Atlas-SNP	.											ETNK2_ENST00000367202,NS,carcinoma,0,2	ETNK2	48	2	0			c.C793T						PASS	.						152	134	140					1																	204109238		2203	4300	6503	SO:0001583	missense	55224	exon5			TGAACCGCACGTG	AK001623	CCDS1442.2, CCDS73006.1	1q32.1	2008-02-05			ENSG00000143845	ENSG00000143845			25575	protein-coding gene	gene with protein product		609859				12477932	Standard	XM_005245302		Approved	FLJ10761, EKI2	uc001hao.4	Q9NVF9	OTTHUMG00000036061	ENST00000367202.4:c.793C>T	1.37:g.204109238G>A	ENSP00000356170:p.Arg265Trp	100	0	0		111	53	0.477477	NM_018208	B7Z7K1|Q5SXX5|Q68CK3|Q96G05	Missense_Mutation	SNP	ENST00000367202.4	37	CCDS1442.2	.	.	.	.	.	.	.	.	.	.	G	15.70	2.910054	0.52439	.	.	ENSG00000143845	ENST00000367201;ENST00000367202;ENST00000367199;ENST00000455266;ENST00000367198;ENST00000422699;ENST00000452983;ENST00000444817	T;T;T;T;T;T;T	0.58652	0.32;0.32;0.32;0.32;0.32;0.32;0.32	5.4	1.99	0.26369	Protein kinase-like domain (1);Choline/ethanolamine kinase (1);	0.207171	0.44097	D	0.000494	T	0.71281	0.3321	M	0.82323	2.585	0.40505	D	0.98068	D;D;D	0.89917	0.995;0.996;1.0	P;P;P	0.62014	0.663;0.773;0.897	T	0.73398	-0.3995	10	0.62326	D	0.03	-8.4891	9.3644	0.38215	0.0756:0.0:0.6588:0.2656	.	224;265;265	Q9NVF9-3;Q9NVF9;Q9NVF9-2	.;EKI2_HUMAN;.	W	265;265;196;131;87;131;122;111	ENSP00000356169:R265W;ENSP00000356170:R265W;ENSP00000356167:R196W;ENSP00000356166:R87W;ENSP00000405497:R131W;ENSP00000398091:R122W;ENSP00000406241:R111W	ENSP00000356166:R87W	R	-	1	2	ETNK2	202375861	0.148000	0.22702	0.308000	0.25141	0.327000	0.28475	2.116000	0.41930	0.590000	0.29694	0.650000	0.86243	CGG	.	.	none		0.488	ETNK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087893.1	NM_018208		A	204109238	G	A	204109238	3	1	22	1	0	0	0	0	1	0	0	0	5276	1086	38	1	383	1	ETNK2	1	204109238	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	956387	204109238	45141383	401	3302											
NFASC	23114	hgsc.bcm.edu	37	chr1	204939763	204939763	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgctccctactggctggaCgaacccaagaaccttattct	9	10	8	14	1	1	1	0	0	1	1	2	3	2	2	3	2	4	3	3	2	5	3	rs6690894	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:204939763C>T	ENST00000401399.1	+	10	1222	c.1023C>T	c.(1021-1023)gaC>gaT	p.D341D	NFASC_ENST00000404907.1_Silent_p.D352D|NFASC_ENST00000539706.1_Silent_p.D352D|NFASC_ENST00000339876.6_Silent_p.D341D|NFASC_ENST00000360049.4_Silent_p.D352D|NFASC_ENST00000338586.6_Silent_p.D341D|NFASC_ENST00000404076.1_Silent_p.D335D|NFASC_ENST00000367169.4_Silent_p.D341D|NFASC_ENST00000338515.6_Silent_p.D341D|NFASC_ENST00000403080.1_Silent_p.D341D|NFASC_ENST00000367172.4_Silent_p.D341D|NFASC_ENST00000367171.4_Silent_p.D341D|NFASC_ENST00000367170.4_Silent_p.D341D|NFASC_ENST00000513543.1_Silent_p.D352D			O94856	NFASC_HUMAN	neurofascin	341	Ig-like C2-type 4.				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)			ACTGGCTGGACGAACCCAAGA	0.552													C|||	104	0.0207668	0.0764	0.0029	5008	,	,		18345	0.0		0.0	False		,,,				2504	0.001				p.D352D		Atlas-SNP	.											.	NFASC	396	.	0			c.C1056T						PASS	.	C	,,,,,	288,4118	158.9+/-191.5	13,262,1928	87	76	80		1023,1023,1056,1056,1005,1056	-8.8	0.4	1	dbSNP_116	80	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NFASC	NM_001005388.2,NM_001005389.1,NM_001160331.1,NM_001160332.1,NM_001160333.1,NM_015090.3	,,,,,	13,263,6227	TT,TC,CC		0.0116,6.5365,2.2221	,,,,,	341/1241,341/620,352/1190,352/1175,335/614,352/1170	204939763	289,12717	2203	4300	6503	SO:0001819	synonymous_variant	23114	exon11			GCTGGACGAACCC	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.1023C>T	1.37:g.204939763C>T		101	0	0		131	60	0.458015	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	37	CCDS53460.1	30	0.013736263736263736	29	0.05894308943089431	1	0.0027624309392265192	0	0.0	0	0.0	C	8.636	0.894786	0.17613	0.065365	1.16E-4	ENSG00000163531	ENST00000367173	.	.	.	5.64	-8.77	0.00827	.	.	.	.	.	T	0.12475	0.0303	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68655	-0.5351	4	.	.	.	.	17.7033	0.88301	0.0:0.1936:0.0:0.8064	rs6690894;rs6690894	.	.	.	M	311	.	.	T	+	2	0	NFASC	203206386	0.189000	0.23263	0.369000	0.25952	0.985000	0.73830	-0.441000	0.06879	-2.495000	0.00514	-0.797000	0.03246	ACG	C|0.974;T|0.026	0.026	strong		0.552	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388		T	204939763	C	T	204939763	2	4	22	1	0	0	0	0	0	0	0	1	10368	535	19	1		1	NFASC	1	204939763	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	830525	204939763	44310858	402	3303											
CNTN2	6900	hgsc.bcm.edu	37	chr1	205033518	205033518	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcccgcgggggagagatcCttatcccctgccagccccgg	5	5	14	17	4	0	1	0	0	0	1	2	3	2	2	7	4	2	0	7	4	1	1	rs79431021	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:205033518C>G	ENST00000331830.4	+	11	1593	c.1309C>G	c.(1309-1311)Ctt>Gtt	p.L437V	AL583832.1_ENST00000515887.1_RNA	NM_005076.3	NP_005067.1	Q02246	CNTN2_HUMAN	contactin 2 (axonal)	437	Ig-like C2-type 5.				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)			GGGAGAGATCCTTATCCCCTG	0.627													G|||	176	0.0351438	0.1112	0.0202	5008	,	,		13924	0.0		0.0129	False		,,,				2504	0.002				p.L437V	Melanoma(183;2548 2817 37099 41192)	Atlas-SNP	.											.	CNTN2	116	.	0			c.C1309G						PASS	.	G	VAL/LEU	380,4026	787.3+/-414.9	19,342,1842	91	107	101		1309	-7	0	1	dbSNP_132	101	148,8452	809.3+/-407.2	1,146,4153	yes	missense	CNTN2	NM_005076.3	32	20,488,5995	GG,GC,CC		1.7209,8.6246,4.0597	benign	437/1041	205033518	528,12478	2203	4300	6503	SO:0001583	missense	6900	exon11			GAGATCCTTATCC	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.1309C>G	1.37:g.205033518C>G	ENSP00000330633:p.Leu437Val	175	0	0		161	82	0.509317	NM_005076	P78432|Q5T054	Missense_Mutation	SNP	ENST00000331830.4	37	CCDS1449.1	76	0.0347985347985348	59	0.11991869918699187	7	0.019337016574585635	0	0.0	10	0.013192612137203167	G	0.460	-0.889703	0.02511	0.086246	0.017209	ENSG00000184144	ENST00000331830	T	0.66460	-0.21	5.33	-6.97	0.01616	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.302220	0.05908	N	0.631129	T	0.00496	0.0016	N	0.02985	-0.445	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.05241	-1.0897	10	0.15952	T	0.53	.	8.1491	0.31130	0.7102:0.0949:0.1004:0.0945	.	437;328	Q02246;Q68DA2	CNTN2_HUMAN;.	V	437	ENSP00000330633:L437V	ENSP00000330633:L437V	L	+	1	0	CNTN2	203300141	0.000000	0.05858	0.000000	0.03702	0.366000	0.29705	0.009000	0.13219	-1.704000	0.01407	-0.978000	0.02582	CTT	C|0.962;G|0.038	0.038	strong		0.627	CNTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090080.3	NM_005076		G	205033518	C	G	205033518	3	3	22	1	0	0	0	0	1	0	0	0	3643	681	24	4	1347	4	CNTN2	1	205033518	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	93755	205033518	44217103	403	3304											
SRGAP2	23380	hgsc.bcm.edu	37	chr1	206566947	206566947	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgaaggccatcaaagccCggaatgagtacttgctggct	11	8	12	10	1	1	2	1	2	0	0	1	3	1	3	2	3	4	4	2	3	4	2	rs375845037		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:206566947C>T	ENST00000414007.1	+	3	328	c.328C>T	c.(328-330)Cgg>Tgg	p.R110W	SRGAP2_ENST00000419187.2_5'UTR			O75044	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2	250	F-BAR domain.				actin filament severing (GO:0051014)|axon guidance (GO:0007411)|dendritic spine development (GO:0060996)|extension of a leading process involved in cell motility in cerebral cortex radial glia guided migration (GO:0021816)|filopodium assembly (GO:0046847)|lamellipodium assembly involved in ameboidal cell migration (GO:0003363)|negative regulation of neuron migration (GO:2001223)|neuron projection morphogenesis (GO:0048812)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic spine head (GO:0044327)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	protein homodimerization activity (GO:0042803)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)			NS(1)|breast(1)|kidney(1)|lung(1)	4	Breast(84;0.137)					CATCAAAGCCCGGAATGAGTA	0.428																																					p.Q97X		Atlas-SNP	.											.	.	.	.	0			c.C289T						PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG	13,3921		0,13,1954	127	110	115		491,491,491	5.7	1	1		115	0,8334		0,0,4167	yes	missense,missense,missense	SRGAP2	NM_001042758.1,NM_001170637.1,NM_015326.2	101,101,101	0,13,6121	TT,TC,CC		0.0,0.3305,0.106	probably-damaging,probably-damaging,probably-damaging	250/837,250/1071,250/1072	206566947	13,12255	1967	4167	6134	SO:0001583	missense	100996712	exon3			AAAGCCCGGAATG	AB007925	CCDS73017.1	1q32.1	2014-08-13	2004-11-12	2004-11-12	ENSG00000163486	ENSG00000266028		"Rho GTPase activating proteins"	19751	protein-coding gene	gene with protein product		606524	"formin binding protein 2"	FNBP2		15046868, 11672528	Standard	XM_005277510		Approved	KIAA0456, ARHGAP34, SRGAP2A	uc001hdy.3	O75044	OTTHUMG00000184381	ENST00000414007.1:c.328C>T	1.37:g.206566947C>T	ENSP00000390898:p.Arg110Trp	553	0	0		647	99	0.153014	NM_001271887		Nonsense_Mutation	SNP	ENST00000414007.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.4|21.4	4.139626|4.139626	0.77775|0.77775	0.003305|0.003305	0.0|0.0	ENSG00000163486|ENSG00000163486	ENST00000295713|ENST00000414359;ENST00000414007	.|T	.|0.16457	.|2.34	5.73|5.73	5.73|5.73	0.89815|0.89815	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.42899|0.42899	0.1223|0.1223	.|.	.|.	.|.	.|0.30974	.|N	.|0.7227589999999999	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.91635	.|0.998;0.999;0.999	T|T	0.48927|0.48927	-0.8991|-0.8991	3|8	.|0.87932	.|D	.|0	.|.	14.6067|14.6067	0.68483|0.68483	0.1807:0.8193:0.0:0.0|0.1807:0.8193:0.0:0.0	.|.	.|97;250;250	.|B4DDU0;O75044;B7Z3G4	.|.;FNBP2_HUMAN;.	L|W	163|164;110	.|ENSP00000390898:R110W	.|ENSP00000390898:R110W	P|R	+|+	2|1	0|2	SRGAP2|SRGAP2	204633570|204633570	0.998000|0.998000	0.40836|0.40836	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	2.909000|2.909000	0.48758|0.48758	2.705000|2.705000	0.92388|0.92388	0.555000|0.555000	0.69702|0.69702	CCG|CGG	.	.	none		0.428	SRGAP2-201	KNOWN	basic	protein_coding	protein_coding		NM_015326		T	206566947	C	T	206566947	3	4	22	1	0	0	0	0	1	0	0	0	15161	643	23	1	502	1	SRGAP2	1	206566947	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1533429	206566947	42683674	404	3305											
SRGAP2	23380	hgsc.bcm.edu	37	chr1	206574931	206574931	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccaccagtgacaagcagcGcctcatggagatgtacaaca	13	6	10	12	1	1	2	1	1	0	1	1	3	1	2	3	1	5	2	3	1	3	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:206574931G>A	ENST00000414007.1	+	4	563	c.563G>A	c.(562-564)cGc>cAc	p.R188H	SRGAP2_ENST00000419187.2_5'UTR			O75044	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2	328	F-BAR domain.				actin filament severing (GO:0051014)|axon guidance (GO:0007411)|dendritic spine development (GO:0060996)|extension of a leading process involved in cell motility in cerebral cortex radial glia guided migration (GO:0021816)|filopodium assembly (GO:0046847)|lamellipodium assembly involved in ameboidal cell migration (GO:0003363)|negative regulation of neuron migration (GO:2001223)|neuron projection morphogenesis (GO:0048812)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic spine head (GO:0044327)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	protein homodimerization activity (GO:0042803)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)			NS(1)|breast(1)|kidney(1)|lung(1)	4	Breast(84;0.137)					GACAAGCAGCGCCTCATGGAG	0.527																																					p.R174H		Atlas-SNP	.											SRGAP2_ENST00000414007,NS,carcinoma,0,3	.	.	3	0			c.G521A						scavenged	.						16	14	14					1																	206574931		1795	4026	5821	SO:0001583	missense	100996712	exon4			AGCAGCGCCTCAT	AB007925	CCDS73017.1	1q32.1	2014-08-13	2004-11-12	2004-11-12	ENSG00000163486	ENSG00000266028		"Rho GTPase activating proteins"	19751	protein-coding gene	gene with protein product		606524	"formin binding protein 2"	FNBP2		15046868, 11672528	Standard	XM_005277510		Approved	KIAA0456, ARHGAP34, SRGAP2A	uc001hdy.3	O75044	OTTHUMG00000184381	ENST00000414007.1:c.563G>A	1.37:g.206574931G>A	ENSP00000390898:p.Arg188His	1644	1	0.000608273		1642	188	0.114495	NM_001271887		Missense_Mutation	SNP	ENST00000414007.1	37		.	.	.	.	.	.	.	.	.	.	G	28.8	4.949468	0.92660	.	.	ENSG00000163486	ENST00000414359;ENST00000414007	T	0.13778	2.56	6.02	6.02	0.97574	.	0.054744	0.64402	D	0.000001	T	0.21881	0.0527	.	.	.	0.80722	D	1.000000	D;P;B	0.60160	0.987;0.602;0.174	P;B;B	0.45474	0.482;0.107;0.02	T	0.00601	-1.1650	8	0.49607	T	0.09	.	20.5373	0.99239	0.0:0.0:1.0:0.0	.	175;328;327	B4DDU0;O75044;B7Z3G4	.;FNBP2_HUMAN;.	H	241;188	ENSP00000390898:R188H	ENSP00000390898:R188H	R	+	2	0	SRGAP2	204641554	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.558000	0.73942	2.857000	0.98124	0.650000	0.86243	CGC	.	.	none		0.527	SRGAP2-201	KNOWN	basic	protein_coding	protein_coding		NM_015326		A	206574931	G	A	206574931	3	1	22	1	0	0	0	0	1	0	0	0	15161	1087	38	1	741	1	SRGAP2	1	206574931	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	7984	206574931	42675690	405	3306											
IKBKE	9641	hgsc.bcm.edu	37	chr1	206658404	206658404	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagaactgaggtccaggctgCggactgtgagtgaggctgga	9	7	17	8	1	0	4	0	3	0	1	1	6	1	6	1	5	2	2	1	5	1	0			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:206658404C>T	ENST00000367120.3	+	14	1871	c.1498C>T	c.(1498-1500)Cgg>Tgg	p.R500W	IKBKE_ENST00000537984.1_Missense_Mutation_p.R415W	NM_001193322.1|NM_014002.3	NP_001180251.1|NP_054721.1	Q14164	IKKE_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase epsilon	500	Interaction with DDX3X.				immune response (GO:0006955)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of type I interferon production (GO:0032480)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein phosphorylation (GO:0006468)|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)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|NF-kappaB-inducing kinase activity (GO:0004704)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|ovary(3)|skin(2)	32	Breast(84;0.137)					GTCCAGGCTGCGGACTGTGAG	0.617																																					p.R500W		Atlas-SNP	.											.	IKBKE	77	.	0			c.C1498T						PASS	.						47	42	44					1																	206658404		2203	4300	6503	SO:0001583	missense	9641	exon14			AGGCTGCGGACTG	AB016590	CCDS30996.1, CCDS53464.1, CCDS73019.1	1q31	2014-05-06			ENSG00000143466				14552	protein-coding gene	gene with protein product		605048				10421793, 10882136	Standard	NM_001193321		Approved	IKKE, IKK-i, KIAA0151	uc001hdz.2	Q14164	OTTHUMG00000184613	ENST00000367120.3:c.1498C>T	1.37:g.206658404C>T	ENSP00000356087:p.Arg500Trp	162	0	0		122	56	0.459016	NM_001193322	D3DT78|Q3B754|Q3KR43|Q5JTS6	Missense_Mutation	SNP	ENST00000367120.3	37	CCDS30996.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.070122	0.76301	.	.	ENSG00000143466	ENST00000367120;ENST00000537984	T;T	0.64085	-0.08;0.08	5.24	4.32	0.51571	.	0.527792	0.20321	N	0.094636	T	0.60274	0.2256	L	0.36672	1.1	0.22961	N	0.998503	D;D	0.69078	0.991;0.997	P;P	0.50192	0.549;0.634	T	0.55611	-0.8114	10	0.66056	D	0.02	2.2858	12.7736	0.57436	0.1634:0.8366:0.0:0.0	.	415;500	Q3B754;Q14164	.;IKKE_HUMAN	W	500;415	ENSP00000356087:R500W;ENSP00000444529:R415W	ENSP00000356087:R500W	R	+	1	2	IKBKE	204725027	0.993000	0.37304	1.000000	0.80357	0.994000	0.84299	1.450000	0.35134	1.204000	0.43247	0.563000	0.77884	CGG	.	.	none		0.617	IKBKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088484.1			T	206658404	C	T	206658404	3	4	22	1	0	0	0	0	1	0	0	0	7621	759	27	1	1544	1	IKBKE	1	206658404	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	83473	206658404	42592217	406	3307											
IKBKE	9641	hgsc.bcm.edu	37	chr1	206666601	206666601	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	agtatggcttccctgcagctCctggaagagctatctcacca	9	10	9	13	0	1	1	1	0	1	1	4	2	3	2	3	2	3	5	3	2	3	3	rs144382861	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:206666601C>A	ENST00000367120.3	+	20	2308	c.1935C>A	c.(1933-1935)ctC>ctA	p.L645L	IKBKE_ENST00000537984.1_Silent_p.L560L|C1orf147_ENST00000367119.1_Intron	NM_001193322.1|NM_014002.3	NP_001180251.1|NP_054721.1	Q14164	IKKE_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase epsilon	645	Interaction with DDX3X.				immune response (GO:0006955)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of type I interferon production (GO:0032480)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein phosphorylation (GO:0006468)|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)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|IkappaB kinase activity (GO:0008384)|NF-kappaB-inducing kinase activity (GO:0004704)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|ovary(3)|skin(2)	32	Breast(84;0.137)					CCCTGCAGCTCCTGGAAGAGC	0.587													C|||	5	0.000998403	0.0038	0.0	5008	,	,		17760	0.0		0.0	False		,,,				2504	0.0				p.L645L		Atlas-SNP	.											.	IKBKE	77	.	0			c.C1935A						PASS	.	C	,,	21,4385	28.1+/-56.4	0,21,2182	61	68	65		1680,,1935	2	1	1	dbSNP_134	65	0,8600		0,0,4300	no	coding-synonymous,intron,coding-synonymous	IKBKE	NM_001193321.1,NM_001193322.1,NM_014002.3	,,	0,21,6482	AA,AC,CC		0.0,0.4766,0.1615	,,	560/632,,645/717	206666601	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	9641	exon20			GCAGCTCCTGGAA	AB016590	CCDS30996.1, CCDS53464.1, CCDS73019.1	1q31	2014-05-06			ENSG00000143466				14552	protein-coding gene	gene with protein product		605048				10421793, 10882136	Standard	NM_001193321		Approved	IKKE, IKK-i, KIAA0151	uc001hdz.2	Q14164	OTTHUMG00000184613	ENST00000367120.3:c.1935C>A	1.37:g.206666601C>A		93	0	0		95	47	0.494737	NM_014002	D3DT78|Q3B754|Q3KR43|Q5JTS6	Silent	SNP	ENST00000367120.3	37	CCDS30996.1																																																																																			C|0.999;A|0.001	0.001	strong		0.587	IKBKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088484.1			A	206666601	C	A	206666601	2	1	22	1	0	0	0	0	0	0	0	1	7621	842	30	4		4	IKBKE	1	206666601	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	8197	206666601	42584020	407	3308											
C4BPA	722	hgsc.bcm.edu	37	chr1	207305069	207305069	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaaatttgagatggaccccAtaccaaggatgtgagggtga	15	8	12	6	0	0	3	0	3	0	1	0	6	0	5	3	3	1	0	3	3	4	2	rs6663608	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:207305069A>C	ENST00000367070.3	+	8	1262	c.1068A>C	c.(1066-1068)ccA>ccC	p.P356P		NM_000715.3	NP_000706.1	P04003	C4BPA_HUMAN	complement component 4 binding protein, alpha	356	Sushi 5. {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						GATGGACCCCATACCAAGGAT	0.368													A|||	276	0.0551118	0.1967	0.0187	5008	,	,		20256	0.0		0.001	False		,,,				2504	0.002				p.P356P		Atlas-SNP	.											.	C4BPA	70	.	0			c.A1068C						PASS	.	A		733,3673	284.3+/-277.5	69,595,1539	117	101	106		1068	-8.7	0	1	dbSNP_116	106	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	C4BPA	NM_000715.3		69,601,5833	CC,CA,AA		0.0698,16.6364,5.682		356/598	207305069	739,12267	2203	4300	6503	SO:0001819	synonymous_variant	722	exon8			GACCCCATACCAA	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.1068A>C	1.37:g.207305069A>C		87	0	0		117	52	0.444444	NM_000715	Q5VVQ8	Silent	SNP	ENST00000367070.3	37	CCDS1477.1																																																																																			A|0.930;C|0.070	0.070	strong		0.368	C4BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088089.3			C	207305069	A	C	207305069	2	2	22	1	0	0	0	0	0	0	0	1	2251	204	8	5		5	C4BPA	1	207305069	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	638468	207305069	41945552	408	3309											
CR1	1378	hgsc.bcm.edu	37	chr1	207782889	207782889	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagaagttgaaaatgcaattAgagtaccaggaaacaggagt	18	7	11	5	0	0	3	0	1	0	2	0	5	0	5	1	2	3	3	1	2	7	3	rs17047661	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:207782889A>G	ENST00000367049.4	+	37	6151	c.6151A>G	c.(6151-6153)Aga>Gga	p.R2051G	RP11-78B10.2_ENST00000596003.1_RNA|CR1_ENST00000367051.1_Missense_Mutation_p.R1601G|CR1_ENST00000400960.2_Missense_Mutation_p.R1601G|CR1_ENST00000367052.1_Missense_Mutation_p.R1601G|RP11-78B10.2_ENST00000597497.1_RNA|CR1_ENST00000367053.1_Missense_Mutation_p.R1601G	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1601					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						AAATGCAATTAGAGTACCAGG	0.468													a|||	984	0.196486	0.7103	0.0519	5008	,	,		19576	0.0		0.0089	False		,,,				2504	0.0				p.R2051G		Atlas-SNP	.											.	CR1	354	.	0			c.A6151G	GRCh37	CM015242	CR1	M	rs17047661	PASS	.	C	GLY/ARG,GLY/ARG	2160,1626		630,900,363	59	58	58		4801,6151	-2	0	1	dbSNP_123	58	27,8203		0,27,4088	yes	missense,missense	CR1	NM_000573.3,NM_000651.4	125,125	630,927,4451	GG,GA,AA		0.3281,42.9477,18.2007	probably-damaging,probably-damaging	1601/2040,2051/2490	207782889	2187,9829	1893	4115	6008	SO:0001583	missense	1378	exon37			GCAATTAGAGTAC	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.6151A>G	1.37:g.207782889A>G	ENSP00000356016:p.Arg2051Gly	131	0	0		152	77	0.506579	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	333	0.15247252747252749	314	0.6382113821138211	17	0.04696132596685083	0	0.0	2	0.002638522427440633	a	8.718	0.913598	0.17907	0.570523	0.003281	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000534202;ENST00000367049	T;T;T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11;1.62;-0.11	2.54	-2.03	0.07365	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.00012	0.0000	M	0.80422	2.495	0.80722	P	0.0	B;D;D	0.59767	0.257;0.982;0.986	B;D;P	0.69479	0.069;0.964;0.79	T	0.47222	-0.9134	8	0.23891	T	0.37	.	4.646	0.12572	0.3825:0.4843:0.1331:0.0	rs17047661;rs52836690;rs17047661	1601;1601;2051	Q5SR44;P17927;E9PDY4	.;CR1_HUMAN;.	G	1601;1601;1601;1601;1151;2051	ENSP00000356019:R1601G;ENSP00000356018:R1601G;ENSP00000356020:R1601G;ENSP00000383744:R1601G;ENSP00000436139:R1151G;ENSP00000356016:R2051G	ENSP00000356016:R2051G	R	+	1	2	CR1	205849512	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.157000	0.10085	-0.445000	0.07159	-0.525000	0.04345	AGA	A|0.769;G|0.231	0.231	strong		0.468	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573		G	207782889	A	G	207782889	3	3	22	1	0	0	0	0	1	0	0	0	3842	412	15	3	6297	3	CR1	1	207782889	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	477820	207782889	41467732	409	3310											
CR1L	1379	hgsc.bcm.edu	37	chr1	207890818	207890818	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctttctagaaatcttttGtccaaatcctccagctatcc	9	17	3	12	0	3	1	0	0	3	1	7	1	7	1	4	0	1	1	4	0	4	6	rs113806677	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:207890818G>A	ENST00000508064.2	+	11	1484	c.1424G>A	c.(1423-1425)tGt>tAt	p.C475Y		NM_175710.1	NP_783641.1	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	475	Sushi 8. {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						GAAATCTTTTGTCCAAATCCT	0.388													g|||	139	0.0277556	0.1014	0.0072	5008	,	,		18100	0.0		0.0	False		,,,				2504	0.0				p.C475Y		Atlas-SNP	.											CR1L_ENST00000508064,NS,carcinoma,-1,1	CR1L	97	1	0			c.G1424A						PASS	.	G	TYR/CYS	344,3278		18,308,1485	80	74	76		1424	3	0.1	1	dbSNP_132	76	1,8137		0,1,4068	yes	missense	CR1L	NM_175710.1	194	18,309,5553	AA,AG,GG		0.0123,9.4975,2.9337	probably-damaging	475/570	207890818	345,11415	1811	4069	5880	SO:0001583	missense	1379	exon11			TCTTTTGTCCAAA	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.1424G>A	1.37:g.207890818G>A	ENSP00000421736:p.Cys475Tyr	262	0	0		210	112	0.533333	NM_175710	Q32MC9|Q8NEU7	Missense_Mutation	SNP	ENST00000508064.2	37	CCDS44310.1	52	0.023809523809523808	50	0.1016260162601626	2	0.0055248618784530384	0	0.0	0	0.0	.	14.21	2.467416	0.43839	0.094975	1.23E-4	ENSG00000197721	ENST00000508064	D	0.99784	-6.74	3.01	3.01	0.34805	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	D	0.95401	0.8507	H	0.99719	4.725	0.25098	N	0.99081	D	0.89917	1.0	D	0.97110	1.0	T	0.80630	-0.1297	9	0.87932	D	0	.	10.1225	0.42630	0.0:0.0:1.0:0.0	.	475	Q2VPA4	CR1L_HUMAN	Y	475	ENSP00000421736:C475Y	ENSP00000421736:C475Y	C	+	2	0	CR1L	205957441	0.981000	0.34729	0.142000	0.22268	0.288000	0.27193	4.125000	0.57931	1.639000	0.50556	0.305000	0.20034	TGT	G|0.976;A|0.024	0.024	strong		0.388	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735		A	207890818	G	A	207890818	3	1	22	1	0	0	0	0	1	0	0	0	3843	1377	48	2	1466	2	CR1L	1	207890818	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	107929	207890818	41359803	410	3311											
LAMB3	3914	hgsc.bcm.edu	37	chr1	209797061	209797061	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtaggctgtgctcagcatcCggaaggctcctgtggcgaga	7	8	15	11	3	1	1	1	0	0	1	3	3	3	2	2	4	2	5	2	4	2	1	rs114174766	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:209797061C>T	ENST00000356082.4	-	16	2281	c.2147G>A	c.(2146-2148)cGg>cAg	p.R716Q	MIR4260_ENST00000583107.1_RNA|LAMB3_ENST00000367030.3_Missense_Mutation_p.R716Q|LAMB3_ENST00000391911.1_Missense_Mutation_p.R716Q	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	716	Domain II.				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)		GCTCAGCATCCGGAAGGCTCC	0.652													c|||	9	0.00179712	0.0061	0.0014	5008	,	,		19113	0.0		0.0	False		,,,				2504	0.0				p.R716Q		Atlas-SNP	.											.	LAMB3	136	.	0			c.G2147A						PASS	.	T	GLN/ARG,GLN/ARG,GLN/ARG	23,4383	29.0+/-57.7	0,23,2180	31	31	31		2147,2147,2147	1.2	0.7	1	dbSNP_132	31	0,8600		0,0,4300	yes	missense,missense,missense	LAMB3	NM_000228.2,NM_001017402.1,NM_001127641.1	43,43,43	0,23,6480	TT,TC,CC		0.0,0.522,0.1768	benign,benign,benign	716/1173,716/1173,716/1173	209797061	23,12983	2203	4300	6503	SO:0001583	missense	3914	exon16			AGCATCCGGAAGG	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.2147G>A	1.37:g.209797061C>T	ENSP00000348384:p.Arg716Gln	101	0	0		75	37	0.493333	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Missense_Mutation	SNP	ENST00000356082.4	37	CCDS1487.1	4	0.0018315018315018315	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	c	6.857	0.527355	0.13066	0.00522	0.0	ENSG00000196878	ENST00000391911;ENST00000356082;ENST00000367030	T;T;T	0.35789	1.29;1.29;1.29	5.15	1.19	0.21007	.	0.666644	0.15639	N	0.251967	T	0.15435	0.0372	L	0.35723	1.085	0.18873	N	0.999981	B	0.16802	0.019	B	0.06405	0.002	T	0.23904	-1.0175	10	0.14252	T	0.57	.	4.7578	0.13093	0.1382:0.5549:0.0:0.3069	.	716	Q13751	LAMB3_HUMAN	Q	716	ENSP00000375778:R716Q;ENSP00000348384:R716Q;ENSP00000355997:R716Q	ENSP00000348384:R716Q	R	-	2	0	LAMB3	207863684	0.020000	0.18652	0.733000	0.30861	0.335000	0.28730	-0.012000	0.12699	0.043000	0.15746	-0.365000	0.07479	CGG	C|0.998;T|0.002	0.002	strong		0.652	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228		T	209797061	C	T	209797061	3	4	22	1	0	0	0	0	1	0	0	0	8621	652	23	1	1403	1	LAMB3	1	209797061	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1906243	209797061	39453560	411	3312											
TRAF3IP3	80342	hgsc.bcm.edu	37	chr1	209933659	209933659	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggagcaagggccctccaggcGgccaggacaggtgactgtcc	8	4	16	13	1	0	1	0	1	0	0	2	3	2	3	4	6	1	1	4	6	1	0	rs78296889	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:209933659G>A	ENST00000367024.1	+	3	791	c.275G>A	c.(274-276)cGg>cAg	p.R92Q	TRAF3IP3_ENST00000367025.3_Missense_Mutation_p.R92Q|TRAF3IP3_ENST00000367026.3_Missense_Mutation_p.R92Q|TRAF3IP3_ENST00000400959.3_Missense_Mutation_p.R92Q|TRAF3IP3_ENST00000010338.4_Missense_Mutation_p.R92Q			Q9Y228	T3JAM_HUMAN	TRAF3 interacting protein 3	92						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)		CCCTCCAGGCGGCCAGGACAG	0.597													G|||	87	0.0173722	0.0628	0.0058	5008	,	,		17422	0.0		0.0	False		,,,				2504	0.0				p.R92Q		Atlas-SNP	.											.	TRAF3IP3	68	.	0			c.G275A						PASS	.	G	GLN/ARG	220,4186	125.7+/-162.9	4,212,1987	25	26	25		275	1.8	0	1	dbSNP_132	25	3,8597	3.0+/-9.4	0,3,4297	yes	missense	TRAF3IP3	NM_025228.2	43	4,215,6284	AA,AG,GG		0.0349,4.9932,1.7146	possibly-damaging	92/552	209933659	223,12783	2203	4300	6503	SO:0001583	missense	80342	exon3			CCAGGCGGCCAGG		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.275G>A	1.37:g.209933659G>A	ENSP00000355991:p.Arg92Gln	150	0	0		158	65	0.411392	NM_025228	A1L464|A6NIU9|Q2YDB5|Q4VY06|Q7Z706	Missense_Mutation	SNP	ENST00000367024.1	37	CCDS1490.2	38	0.0173992673992674	36	0.07317073170731707	2	0.0055248618784530384	0	0.0	0	0.0	G	11.69	1.712561	0.30322	0.049932	3.49E-4	ENSG00000009790	ENST00000400959;ENST00000367025;ENST00000458110;ENST00000367026;ENST00000367024;ENST00000010338	T;T;T;T;T	0.46819	0.86;0.87;0.91;0.87;0.91	4.69	1.75	0.24633	.	2.341960	0.02012	N	0.047071	T	0.05044	0.0135	L	0.44542	1.39	0.09310	N	1	B;D;B;P	0.56746	0.003;0.977;0.007;0.938	B;P;B;B	0.46718	0.003;0.525;0.007;0.308	T	0.12682	-1.0538	10	0.13108	T	0.6	-7.597	7.4585	0.27280	0.2986:0.0:0.7014:0.0	.	92;92;92;92	Q9Y228;Q9Y228-2;Q9Y228-3;E2QRE5	T3JAM_HUMAN;.;.;.	Q	92;92;75;92;92;92	ENSP00000383743:R92Q;ENSP00000355992:R92Q;ENSP00000355993:R92Q;ENSP00000355991:R92Q;ENSP00000010338:R92Q	ENSP00000010338:R92Q	R	+	2	0	TRAF3IP3	208000282	0.000000	0.05858	0.008000	0.14137	0.006000	0.05464	-0.029000	0.12329	0.523000	0.28482	-0.448000	0.05591	CGG	G|0.984;A|0.016	0.016	strong		0.597	TRAF3IP3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088734.2			A	209933659	G	A	209933659	3	1	22	1	0	0	0	0	1	0	0	0	16457	1116	39	1	277	1	TRAF3IP3	1	209933659	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	136598	209933659	39316962	412	3313											
KCNH1	3756	hgsc.bcm.edu	37	chr1	210857145	210857145	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaggcactcggaccctggCgcctgtagctttgcgtggtc	4	9	13	15	3	0	0	0	0	0	0	2	1	0	1	3	4	2	3	3	4	1	2	rs112047226	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:210857145C>T	ENST00000271751.4	-	11	2475	c.2448G>A	c.(2446-2448)gcG>gcA	p.A816A	KCNH1_ENST00000367007.4_Silent_p.A789A			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	816					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)		CGGACCCTGGCGCCTGTAGCT	0.662													C|||	50	0.00998403	0.034	0.0072	5008	,	,		16634	0.0		0.0	False		,,,				2504	0.0				p.A816A		Atlas-SNP	.											KCNH1,colon,carcinoma,-1,1	KCNH1	199	1	0			c.G2448A						PASS	.	C	,	127,4279	89.7+/-128.4	3,121,2079	44	50	48		2367,2448	-9.5	0	1	dbSNP_132	48	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	KCNH1	NM_002238.3,NM_172362.2	,	3,121,6379	TT,TC,CC		0.0,2.8824,0.9765	,	789/963,816/990	210857145	127,12879	2203	4300	6503	SO:0001819	synonymous_variant	3756	exon11			CCCTGGCGCCTGT	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.2448G>A	1.37:g.210857145C>T		56	0	0		74	32	0.432432	NM_172362	B1AQ26|O76035|Q14CL3	Silent	SNP	ENST00000271751.4	37	CCDS1496.1																																																																																			C|0.987;T|0.013	0.013	strong		0.662	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238		T	210857145	C	T	210857145	2	4	22	1	0	0	0	0	0	0	0	1	8040	755	27	1		1	KCNH1	1	210857145	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	923486	210857145	38393476	413	3314											
TATDN3	128387	hgsc.bcm.edu	37	chr1	212969889	212969889	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tggcccttgtggcagttgccGaacattcaggagaatttgaa	10	11	12	8	1	1	2	1	1	0	1	1	4	1	2	2	3	2	2	2	3	3	4	rs55709122	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:212969889G>A	ENST00000366974.4	+	3	224	c.130G>A	c.(130-132)Gaa>Aaa	p.E44K	TATDN3_ENST00000525569.1_3'UTR|TATDN3_ENST00000531963.1_Missense_Mutation_p.E44K|TATDN3_ENST00000366973.4_Missense_Mutation_p.E44K|TATDN3_ENST00000532324.1_Missense_Mutation_p.E44K|TATDN3_ENST00000530441.1_Missense_Mutation_p.E44K|TATDN3_ENST00000526641.1_Missense_Mutation_p.E44K|TATDN3_ENST00000526997.1_Missense_Mutation_p.E44K	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	44					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)		GGCAGTTGCCGAACATTCAGG	0.289													G|||	8	0.00159744	0.0061	0.0	5008	,	,		13128	0.0		0.0	False		,,,				2504	0.0				p.E44K		Atlas-SNP	.											.	TATDN3	23	.	0			c.G130A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	43,4363	41.6+/-74.8	0,43,2160	38	41	40		130,130,130,130,130	5.8	1	1	dbSNP_129	40	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense	TATDN3	NM_001042552.2,NM_001042553.2,NM_001146169.1,NM_001146170.1,NM_001146171.1	56,56,56,56,56	0,43,6460	AA,AG,GG		0.0,0.9759,0.3306	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	44/275,44/274,44/241,44/254,44/282	212969889	43,12963	2203	4300	6503	SO:0001583	missense	128387	exon3			GTTGCCGAACATT	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.130G>A	1.37:g.212969889G>A	ENSP00000355941:p.Glu44Lys	78	0	0		99	52	0.525253	NM_001146170	A6NGS3|B7Z1C1|B7Z978|B7ZLQ6|E9PJE5|E9PNH3|G3V151|Q4G0L1	Missense_Mutation	SNP	ENST00000366974.4	37	CCDS31019.1	5|5	0.0022893772893772895|0.0022893772893772895	5|5	0.01016260162601626|0.01016260162601626	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	29.3|29.3	4.990408|4.990408	0.93106|0.93106	0.009759|0.009759	0.0|0.0	ENSG00000203705|ENSG00000203705	ENST00000532324;ENST00000366974;ENST00000530441;ENST00000526641;ENST00000531963;ENST00000366973;ENST00000526997;ENST00000530399|ENST00000488246	.|.	.|.	.|.	5.75|5.75	5.75|5.75	0.90469|0.90469	.|.	0.046199|.	0.85682|.	D|.	0.000000|.	T|T	0.69904|0.69904	0.3163|0.3163	M|M	0.72118|0.72118	2.19|2.19	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.67145|.	0.995;0.996;0.995;0.989;0.992|.	P;P;P;P;P|.	0.61275|.	0.836;0.836;0.886;0.658;0.769|.	T|T	0.71938|0.71938	-0.4441|-0.4441	9|5	0.29301|.	T|.	0.29|.	-8.3766|-8.3766	18.7217|18.7217	0.91697|0.91697	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs55709122|rs55709122	44;44;44;44;44|.	E9PNH3;G3V151;E9PJE5;Q17R31-2;Q17R31|.	.;.;.;.;TATD3_HUMAN|.	K|Q	44;44;44;44;44;44;44;43|43	.|.	ENSP00000355940:E44K|.	E|R	+|+	1|2	0|0	TATDN3|TATDN3	211036512|211036512	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.952000|0.952000	0.60782|0.60782	4.428000|4.428000	0.59894|0.59894	2.731000|2.731000	0.93534|0.93534	0.555000|0.555000	0.69702|0.69702	GAA|CGA	G|0.997;A|0.003	0.003	strong		0.289	TATDN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089396.2	XM_375838		A	212969889	G	A	212969889	3	1	22	1	0	0	0	0	1	0	0	0	15608	1059	37	1	140	1	TATDN3	1	212969889	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2112744	212969889	36280732	414	3315											
SMYD2	56950	hgsc.bcm.edu	37	chr1	214507580	214507580	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actccctcaacgtggcctccAtgtggttgaagctagggaga	9	9	12	11	1	1	2	1	1	0	1	3	3	3	2	3	3	2	2	3	3	3	2	rs34259050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:214507580A>G	ENST00000366957.5	+	11	1172	c.1150A>G	c.(1150-1152)Atg>Gtg	p.M384V	SMYD2_ENST00000491455.1_3'UTR|SMYD2_ENST00000415093.2_3'UTR	NM_020197.2	NP_064582.2	Q9NRG4	SMYD2_HUMAN	SET and MYND domain containing 2	384					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)		CGTGGCCTCCATGTGGTTGAA	0.542													A|||	54	0.0107827	0.0098	0.0115	5008	,	,		20709	0.001		0.0209	False		,,,				2504	0.0112				p.M384V		Atlas-SNP	.											.	SMYD2	40	.	0			c.A1150G						PASS	.	A	VAL/MET	31,4375	36.0+/-67.5	0,31,2172	241	230	234		1150	5.1	1	1	dbSNP_126	234	199,8401	87.1+/-149.5	2,195,4103	yes	missense	SMYD2	NM_020197.2	21	2,226,6275	GG,GA,AA		2.314,0.7036,1.7684	benign	384/434	214507580	230,12776	2203	4300	6503	SO:0001583	missense	56950	exon11			GCCTCCATGTGGT	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.1150A>G	1.37:g.214507580A>G	ENSP00000355924:p.Met384Val	133	0	0		179	86	0.480447	NM_020197	B2R9P9|I6L9H7|Q4V765|Q5VSH9|Q96AI4	Missense_Mutation	SNP	ENST00000366957.5	37	CCDS31022.1	22	0.010073260073260074	4	0.008130081300813009	5	0.013812154696132596	1	0.0017482517482517483	12	0.0158311345646438	A	14.03	2.413182	0.42817	0.007036	0.02314	ENSG00000143499	ENST00000366957	T	0.61392	0.11	6.17	5.05	0.67936	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.30572	0.0769	L	0.48362	1.52	0.80722	D	1	B	0.26512	0.151	B	0.17979	0.02	T	0.21143	-1.0254	10	0.14656	T	0.56	-5.5028	12.297	0.54854	0.9345:0.0:0.0655:0.0	rs34259050	384	Q9NRG4	SMYD2_HUMAN	V	384	ENSP00000355924:M384V	ENSP00000355924:M384V	M	+	1	0	SMYD2	212574203	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.874000	0.48483	1.158000	0.42547	0.533000	0.62120	ATG	A|0.983;G|0.017	0.017	strong		0.542	SMYD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089998.1	NM_020197		G	214507580	A	G	214507580	3	3	22	1	0	0	0	0	1	0	0	0	14837	217	8	3	1192	3	SMYD2	1	214507580	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1537691	214507580	34743041	415	3316											
GPATCH2	55105	hgsc.bcm.edu	37	chr1	217793718	217793718	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccttgcctggcgtttcagAgggcaagatatacttcgaga	9	12	11	9	2	1	3	1	0	0	3	3	4	2	3	2	2	2	2	2	2	3	6	rs34839777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:217793718A>G	ENST00000366935.3	-	2	290	c.180T>C	c.(178-180)ccT>ccC	p.P60P	GPATCH2_ENST00000366934.3_Silent_p.P60P	NM_018040.2	NP_060510.1	Q9NW75	GPTC2_HUMAN	G patch domain containing 2	60					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)		GGCGTTTCAGAGGGCAAGATA	0.498													A|||	38	0.00758786	0.0265	0.0043	5008	,	,		17711	0.0		0.0	False		,,,				2504	0.0				p.P60P		Atlas-SNP	.											.	GPATCH2	53	.	0			c.T180C						PASS	.	A		114,4292	85.3+/-124.0	3,108,2092	136	123	128		180	-4	1	1	dbSNP_126	128	0,8600		0,0,4300	no	coding-synonymous	GPATCH2	NM_018040.2		3,108,6392	GG,GA,AA		0.0,2.5874,0.8765		60/529	217793718	114,12892	2203	4300	6503	SO:0001819	synonymous_variant	55105	exon2			TTTCAGAGGGCAA	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.180T>C	1.37:g.217793718A>G		51	0	0		51	22	0.431373	NM_018040	Q5VYK7|Q5VYK8|Q86YE7	Silent	SNP	ENST00000366935.3	37	CCDS1518.1																																																																																			A|0.990;G|0.010	0.010	strong		0.498	GPATCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001272.1	NM_018040		G	217793718	A	G	217793718	2	3	22	1	0	0	0	0	0	0	0	1	6599	291	11	3		3	GPATCH2	1	217793718	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	3286138	217793718	31456903	416	3317											
SPATA17	128153	hgsc.bcm.edu	37	chr1	217824488	217824488	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaaaatggtggagaagtttcTtaggcagaaagcaatatcaa	18	9	10	4	0	2	2	1	0	1	2	2	3	2	2	0	3	1	3	0	3	8	3	rs143446051		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:217824488T>C	ENST00000366933.4	+	3	263	c.208T>C	c.(208-210)Tta>Cta	p.L70L		NM_138796.2	NP_620151.1	Q96L03	SPT17_HUMAN	spermatogenesis associated 17	70	IQ 2. {ECO:0000255|PROSITE- ProRule:PRU00116}.					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)		GAGAAGTTTCTTAGGCAGAAA	0.299													T|||	1	0.000199681	0.0	0.0	5008	,	,		18465	0.0		0.001	False		,,,				2504	0.0				p.L70L		Atlas-SNP	.											.	SPATA17	59	.	0			c.T208C						PASS	.	T		1,4405	2.1+/-5.4	0,1,2202	84	94	91		208	2.5	1	1	dbSNP_134	91	15,8569	10.5+/-38.8	0,15,4277	no	coding-synonymous	SPATA17	NM_138796.2		0,16,6479	CC,CT,TT		0.1747,0.0227,0.1232		70/362	217824488	16,12974	2203	4292	6495	SO:0001819	synonymous_variant	128153	exon3			AGTTTCTTAGGCA	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.208T>C	1.37:g.217824488T>C		191	0	0		217	104	0.479263	NM_138796	A5D6N2	Silent	SNP	ENST00000366933.4	37	CCDS1519.1																																																																																			T|0.998;C|0.002	0.002	strong		0.299	SPATA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092433.2	NM_138796		C	217824488	T	C	217824488	2	2	22	1	0	0	0	0	0	0	0	1	15017	1606	56	3		3	SPATA17	1	217824488	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	30770	217824488	31426133	417	3318											
DISP1	84976	hgsc.bcm.edu	37	chr1	223178226	223178226	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgccttgtctacaagtcccAgtgacaagggacaaagcaaa	15	7	9	10	0	1	1	0	1	1	0	2	2	2	2	2	1	3	1	2	1	5	2	rs61743732	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:223178226A>G	ENST00000284476.6	+	8	3651	c.3487A>G	c.(3487-3489)Agt>Ggt	p.S1163G		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	1163					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)		TACAAGTCCCAGTGACAAGGG	0.453													A|||	129	0.0257588	0.093	0.0058	5008	,	,		23051	0.0		0.002	False		,,,				2504	0.0				p.S1163G		Atlas-SNP	.											.	DISP1	145	.	0			c.A3487G						PASS	.	A	GLY/SER	372,4034	188.8+/-215.1	12,348,1843	85	89	88		3487	1.6	0	1	dbSNP_129	88	3,8597	3.0+/-9.4	0,3,4297	yes	missense	DISP1	NM_032890.3	56	12,351,6140	GG,GA,AA		0.0349,8.443,2.8833	benign	1163/1525	223178226	375,12631	2203	4300	6503	SO:0001583	missense	84976	exon10			AGTCCCAGTGACA	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.3487A>G	1.37:g.223178226A>G	ENSP00000284476:p.Ser1163Gly	27	0	0		28	12	0.428571	NM_032890	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Missense_Mutation	SNP	ENST00000284476.6	37	CCDS1536.1	56	0.02564102564102564	53	0.10772357723577236	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	A	0.004	-2.279509	0.00254	0.08443	3.49E-4	ENSG00000154309	ENST00000284476	D	0.91351	-2.83	5.66	1.56	0.23342	.	0.630262	0.17522	N	0.171240	T	0.03477	0.0100	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30880	-0.9963	10	0.05436	T	0.98	-4.8804	7.9026	0.29744	0.1384:0.2477:0.6138:0.0	rs61743732	1163	Q96F81	DISP1_HUMAN	G	1163	ENSP00000284476:S1163G	ENSP00000284476:S1163G	S	+	1	0	DISP1	221244849	0.084000	0.21492	0.004000	0.12327	0.204000	0.24138	2.705000	0.47127	0.030000	0.15379	-0.415000	0.06103	AGT	A|0.971;G|0.029	0.029	strong		0.453	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890		G	223178226	A	G	223178226	3	3	22	1	0	0	0	0	1	0	0	0	4541	188	7	3	3513	3	DISP1	1	223178226	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	5353738	223178226	26072395	418	3319											
TLR5	7100	hgsc.bcm.edu	37	chr1	223285042	223285042	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tggagatgaggtacccgtagGagaaagtagagaatatctag	15	8	14	4	1	1	4	0	1	1	3	1	7	1	4	1	3	1	3	1	3	7	5	rs5744169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:223285042G>A	ENST00000540964.1	-	4	1793	c.1332C>T	c.(1330-1332)ctC>ctT	p.L444L	TLR5_ENST00000342210.6_Silent_p.L444L			O60602	TLR5_HUMAN	toll-like receptor 5	444			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)		GTACCCGTAGGAGAAAGTAGA	0.418													G|||	101	0.0201677	0.0734	0.0029	5008	,	,		19084	0.0		0.002	False		,,,				2504	0.0				p.L444L		Atlas-SNP	.											.	TLR5	86	.	0			c.C1332T						PASS	.	G		315,4091	163.3+/-195.1	11,293,1899	82	85	84		1332	-2.9	0.9	1	dbSNP_114	84	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	TLR5	NM_003268.5		11,296,6196	AA,AG,GG		0.0349,7.1493,2.445		444/859	223285042	318,12688	2203	4300	6503	SO:0001819	synonymous_variant	7100	exon6			CCGTAGGAGAAAG		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.1332C>T	1.37:g.223285042G>A		136	0	0		143	63	0.440559	NM_003268	B1AZ05|B3Y633|B9VJ63|D1CS80|D3DTB8|O15456|Q32MI2|Q32MI3	Silent	SNP	ENST00000540964.1	37	CCDS31033.1																																																																																			G|0.976;A|0.024	0.024	strong		0.418	TLR5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003268		A	223285042	G	A	223285042	2	1	22	1	0	0	0	0	0	0	0	1	15969	1161	41	2		2	TLR5	1	223285042	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	106816	223285042	25965579	419	3320											
TP53BP2	7159	hgsc.bcm.edu	37	chr1	223984072	223984072	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ttctttcgtaaggcttctagGtcagcatcactctggtttcg	6	16	9	10	2	5	0	2	0	3	0	7	0	5	0	0	3	1	4	0	3	2	6	rs141654811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:223984072G>A	ENST00000343537.7	-	13	2460	c.2169C>T	c.(2167-2169)gaC>gaT	p.D723D	TP53BP2_ENST00000391879.2_5'UTR|TP53BP2_ENST00000498843.1_5'UTR|TP53BP2_ENST00000391878.2_Silent_p.D594D	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	717					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)		AGGCTTCTAGGTCAGCATCAC	0.438																																					p.D723D		Atlas-SNP	.											.	TP53BP2	144	.	0			c.C2169T						PASS	.	G	,	0,4406		0,0,2203	142	137	139		2169,1782	2.8	0.8	1	dbSNP_134	139	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	TP53BP2	NM_001031685.2,NM_005426.2	,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,	723/1135,594/1006	223984072	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	7159	exon13			TTCTAGGTCAGCA	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.2169C>T	1.37:g.223984072G>A		283	0	0		247	112	0.453441	NM_001031685	B4DG66|Q12892|Q86X75|Q96KQ3	Silent	SNP	ENST00000343537.7	37	CCDS44319.1																																																																																			G|1.000;A|0.000	0.000	strong		0.438	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3	NM_001031685, NM_005426		A	223984072	G	A	223984072	2	1	22	1	0	0	0	0	0	0	0	1	16399	1252	44	2		2	TP53BP2	1	223984072	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	699030	223984072	25266549	420	3321											
WDR26	80232	hgsc.bcm.edu	37	chr1	224607296	224607296	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttttgcacgtaggtcttcTgcatggctacacatcagata	9	13	9	10	1	3	1	1	0	2	1	3	1	3	1	0	2	3	5	0	2	3	6	rs142827296	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:224607296T>C	ENST00000414423.2	-	5	979	c.786A>G	c.(784-786)gcA>gcG	p.A262A	WDR26_ENST00000295024.6_Silent_p.A115A|WDR26_ENST00000366852.2_3'UTR	NM_001115113.2|NM_025160.6	NP_001108585.2|NP_079436.4	Q9H7D7	WDR26_HUMAN	WD repeat domain 26	262						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)		GTAGGTCTTCTGCATGGCTAC	0.353													T|||	6	0.00119808	0.0038	0.0	5008	,	,		17617	0.001		0.0	False		,,,				2504	0.0				p.A262A		Atlas-SNP	.											WDR26_ENST00000414423,NS,carcinoma,0,2	WDR26	104	2	0			c.A786G						PASS	.	T	,	8,4398	14.3+/-33.2	0,8,2195	126	112	117		738,786	-1	1	1	dbSNP_134	117	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	WDR26	NM_001115113.2,NM_025160.6	,	0,8,6495	CC,CT,TT		0.0,0.1816,0.0615	,	246/646,262/662	224607296	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	80232	exon5			GTCTTCTGCATGG	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.786A>G	1.37:g.224607296T>C		77	0	0		100	46	0.46	NM_025160	A0MNN3|Q4G100|Q59EC4|Q5GLZ9|Q86UY4|Q9H3C2	Silent	SNP	ENST00000414423.2	37	CCDS31037.2																																																																																			T|0.999;C|0.001	0.001	strong		0.353	WDR26-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091760.2	NM_025160		C	224607296	T	C	224607296	2	2	22	1	0	0	0	0	0	0	0	1	17298	1567	55	3		3	WDR26	1	224607296	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	623224	224607296	24643325	421	3322											
EPHX1	2052	hgsc.bcm.edu	37	chr1	226032896	226032896	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgccttcccttttgagctaTtgcacacgcctgaaaagtgg	8	12	9	12	1	0	2	0	2	0	0	1	2	1	2	3	1	3	2	3	1	3	5	rs2234700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:226032896T>C	ENST00000366837.4	+	9	1412	c.1216T>C	c.(1216-1218)Ttg>Ctg	p.L406L	RP11-285F7.2_ENST00000424332.1_RNA|EPHX1_ENST00000272167.5_Silent_p.L406L	NM_000120.3	NP_000111.1	P07099	HYEP_HUMAN	epoxide hydrolase 1, microsomal (xenobiotic)	406				L -> F (in Ref. 3; CAA68486). {ECO:0000305}.	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)					TTTTGAGCTATTGCACACGCC	0.572													t|||	106	0.0211661	0.0741	0.0043	5008	,	,		13351	0.001		0.0	False		,,,				2504	0.0041				p.L406L		Atlas-SNP	.											.	EPHX1	57	.	0			c.T1216C						PASS	.	C	,	208,4198	127.8+/-164.7	7,194,2002	102	93	96		1216,1216	-10	0	1	dbSNP_98	96	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	EPHX1	NM_000120.3,NM_001136018.2	,	7,194,6302	CC,CT,TT		0.0,4.7208,1.5993	,	406/456,406/456	226032896	208,12798	2203	4300	6503	SO:0001819	synonymous_variant	2052	exon9			GAGCTATTGCACA	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.1216T>C	1.37:g.226032896T>C		143	0	0		147	78	0.530612	NM_001136018	B2R8N0|Q5VTJ6|Q9NP75|Q9NPE7|Q9NQU6|Q9NQU7|Q9NQU8|Q9NQU9|Q9NQV0|Q9NQV1|Q9NQV2	Silent	SNP	ENST00000366837.4	37	CCDS1547.1																																																																																			T|0.980;C|0.020	0.020	strong		0.572	EPHX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092064.1	NM_000120		C	226032896	T	C	226032896	2	2	22	1	0	0	0	0	0	0	0	1	5181	1490	52	3		3	EPHX1	1	226032896	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1425600	226032896	23217725	422	3323											
TMEM63A	9725	hgsc.bcm.edu	37	chr1	226034913	226034913	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tcagaatccgaggcacgtagGgctgtcagcaaatggatttg	11	9	13	8	2	2	1	2	0	0	1	3	3	3	2	1	3	1	4	1	3	3	2	rs58852301	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:226034913G>A	ENST00000366835.3	-	24	2522	c.2252C>T	c.(2251-2253)cCc>cTc	p.P751L	RP11-285F7.2_ENST00000424332.1_RNA	NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	751					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)					AGGCACGTAGGGCTGTCAGCA	0.592													G|||	193	0.0385383	0.1346	0.0202	5008	,	,		20323	0.0		0.0	False		,,,				2504	0.001				p.P751L		Atlas-SNP	.											TMEM63A,colon,carcinoma,+1,1	TMEM63A	75	1	0			c.C2252T						PASS	.	G	LEU/PRO	562,3838	234.2+/-247.1	35,492,1673	65	56	59		2252	3.1	1	1	dbSNP_129	59	0,8598		0,0,4299	yes	missense-near-splice	TMEM63A	NM_014698.2	98	35,492,5972	AA,AG,GG		0.0,12.7727,4.3237	benign	751/808	226034913	562,12436	2200	4299	6499	SO:0001630	splice_region_variant	9725	exon24			ACGTAGGGCTGTC		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.2251-1C>T	1.37:g.226034913G>A		104	0	0		98	46	0.469388	NM_014698	Q53GI7|Q5TE96|Q8N2U2	Missense_Mutation	SNP	ENST00000366835.3	37	CCDS31042.1	78	0.03571428571428571	70	0.14227642276422764	8	0.022099447513812154	0	0.0	0	0.0	G	10.91	1.484973	0.26598	0.127727	0.0	ENSG00000196187	ENST00000366835	T	0.16597	2.33	4.11	3.1	0.35709	.	0.162225	0.53938	D	0.000053	T	0.00109	0.0003	L	0.57536	1.79	0.09310	P	0.99999999815609	B	0.06786	0.001	B	0.08055	0.003	T	0.05989	-1.0852	9	0.33940	T	0.23	-22.7721	5.9809	0.19407	0.1448:0.0:0.8552:0.0	rs58852301	751	O94886	TM63A_HUMAN	L	751	ENSP00000355800:P751L	ENSP00000355800:P751L	P	-	2	0	TMEM63A	224101536	1.000000	0.71417	0.999000	0.59377	0.909000	0.53808	1.585000	0.36600	2.146000	0.66826	0.448000	0.29417	CCC	G|0.956;A|0.044	0.044	strong		0.592	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698	Missense_Mutation	A	226034913	G	A	226034913	5	1	22	1	0	0	0	0	0	0	1	0	16205	1246	43	2	175	2	TMEM63A	1	226034913	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2017	226034913	23215708	423	3324											
TMEM63A	9725	hgsc.bcm.edu	37	chr1	226050503	226050503	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggtagatcagtttggccacGttgtagcacagctgcacatc	10	10	11	10	1	1	1	1	0	0	1	2	1	1	1	1	2	3	7	1	2	2	4	rs10915888	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:226050503G>A	ENST00000366835.3	-	11	1065	c.795C>T	c.(793-795)aaC>aaT	p.N265N	TMEM63A_ENST00000537914.1_De_novo_Start_OutOfFrame|TMEM63A_ENST00000474478.1_5'UTR	NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	265					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)					GTTTGGCCACGTTGTAGCACA	0.572													G|||	199	0.0397364	0.1392	0.0202	5008	,	,		18776	0.0		0.0	False		,,,				2504	0.001				p.N265N		Atlas-SNP	.											.	TMEM63A	75	.	0			c.C795T						PASS	.	G		574,3832	255.8+/-260.9	35,504,1664	114	81	92		795	-1	0.8	1	dbSNP_120	92	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TMEM63A	NM_014698.2		35,506,5962	AA,AG,GG		0.0233,13.0277,4.4287		265/808	226050503	576,12430	2203	4300	6503	SO:0001819	synonymous_variant	9725	exon11			GGCCACGTTGTAG		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.795C>T	1.37:g.226050503G>A		170	0	0		203	108	0.53202	NM_014698	Q53GI7|Q5TE96|Q8N2U2	Silent	SNP	ENST00000366835.3	37	CCDS31042.1																																																																																			G|0.956;A|0.044	0.044	strong		0.572	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698		A	226050503	G	A	226050503	2	1	22	1	0	0	0	0	0	0	0	1	16205	1136	40	1		1	TMEM63A	1	226050503	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	15590	226050503	23200118	424	3325											
LEFTY1	10637	hgsc.bcm.edu	37	chr1	226074436	226074436	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	acactaggcgcctatggctgGagcctccttggcacgagcgc	7	7	13	14	3	0	0	0	0	0	0	1	2	1	1	3	4	2	2	3	4	2	3	rs35684337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:226074436G>C	ENST00000272134.5	-	4	1171	c.1092C>G	c.(1090-1092)ctC>ctG	p.L364L	RP4-559A3.7_ENST00000432920.2_3'UTR|LEFTY1_ENST00000492457.1_5'Flank	NM_020997.3	NP_066277.1	O75610	LFTY1_HUMAN	left-right determination factor 1	364					cell growth (GO:0016049)|determination of left/right symmetry (GO:0007368)|heart morphogenesis (GO:0003007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)				cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	10	Breast(184;0.197)					CCTATGGCTGGAGCCTCCTTG	0.602													G|||	195	0.0389377	0.1354	0.0216	5008	,	,		18096	0.0		0.0	False		,,,				2504	0.001				p.L364L		Atlas-SNP	.											.	LEFTY1	30	.	0			c.C1092G						PASS	.	G		556,3840		26,504,1668	60	62	61		1092	1.1	0.8	1	dbSNP_126	61	0,8598		0,0,4299	no	coding-synonymous	LEFTY1	NM_020997.3		26,504,5967	CC,CG,GG		0.0,12.6479,4.2789		364/367	226074436	556,12438	2198	4299	6497	SO:0001819	synonymous_variant	10637	exon4			TGGCTGGAGCCTC	AF081507	CCDS1548.1	1q42.1	2008-02-05	2004-11-17	2004-11-17	ENSG00000243709	ENSG00000243709			6552	protein-coding gene	gene with protein product		603037	"left-right determination, factor B"	LEFTB		10053005, 10886363	Standard	NM_020997		Approved	LEFTYB	uc001hpo.3	O75610	OTTHUMG00000037443	ENST00000272134.5:c.1092C>G	1.37:g.226074436G>C		182	0	0		198	109	0.550505	NM_020997	B2R7U0|Q53H67|Q5TE94	Silent	SNP	ENST00000272134.5	37	CCDS1548.1																																																																																			G|0.963;C|0.037	0.037	strong		0.602	LEFTY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091155.1	NM_020997		C	226074436	G	C	226074436	2	2	22	1	0	0	0	0	0	0	0	1	8724	1161	41	4		4	LEFTY1	1	226074436	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	23933	226074436	23176185	425	3326											
LEFTY1	10637	hgsc.bcm.edu	37	chr1	226074635	226074635	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagggcctccgggggctgcCggcaggtgcccacacactca	6	4	14	17	2	1	0	1	0	0	0	2	0	2	0	5	5	2	2	5	5	0	0	rs61739581	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:226074635C>T	ENST00000272134.5	-	4	972	c.893G>A	c.(892-894)cGg>cAg	p.R298Q	RP4-559A3.7_ENST00000432920.2_3'UTR|LEFTY1_ENST00000492457.1_5'Flank	NM_020997.3	NP_066277.1	O75610	LFTY1_HUMAN	left-right determination factor 1	298					cell growth (GO:0016049)|determination of left/right symmetry (GO:0007368)|heart morphogenesis (GO:0003007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)				cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	10	Breast(184;0.197)					CGGGGGCTGCCGGCAGGTGCC	0.642													c|||	331	0.0660942	0.236	0.0245	5008	,	,		16397	0.0		0.002	False		,,,				2504	0.0				p.R298Q		Atlas-SNP	.											.	LEFTY1	30	.	0			c.G893A						PASS	.	C	GLN/ARG	866,3536		78,710,1413	16	20	19		893	-8	0.7	1	dbSNP_129	19	12,8578		0,12,4283	no	missense	LEFTY1	NM_020997.3	43	78,722,5696	TT,TC,CC		0.1397,19.6729,6.758	benign	298/367	226074635	878,12114	2201	4295	6496	SO:0001583	missense	10637	exon4			GGCTGCCGGCAGG	AF081507	CCDS1548.1	1q42.1	2008-02-05	2004-11-17	2004-11-17	ENSG00000243709	ENSG00000243709			6552	protein-coding gene	gene with protein product		603037	"left-right determination, factor B"	LEFTB		10053005, 10886363	Standard	NM_020997		Approved	LEFTYB	uc001hpo.3	O75610	OTTHUMG00000037443	ENST00000272134.5:c.893G>A	1.37:g.226074635C>T	ENSP00000272134:p.Arg298Gln	293	0	0		285	134	0.470175	NM_020997	B2R7U0|Q53H67|Q5TE94	Missense_Mutation	SNP	ENST00000272134.5	37	CCDS1548.1	124	0.056776556776556776	114	0.23170731707317074	10	0.027624309392265192	0	0.0	0	0.0	c	6.256	0.415350	0.11870	0.196729	0.001397	ENSG00000243709	ENST00000272134	D	0.83506	-1.73	4.0	-7.99	0.01131	Transforming growth factor-beta, C-terminal (3);	0.426594	0.27613	N	0.018587	T	0.00039	0.0001	N	0.11131	0.1	0.53688	P	2.6999999999999247E-5	B	0.02656	0.0	B	0.06405	0.002	T	0.23261	-1.0193	9	0.12430	T	0.62	.	3.7673	0.08627	0.2397:0.4502:0.0985:0.2116	.	298	O75610	LFTY1_HUMAN	Q	298	ENSP00000272134:R298Q	ENSP00000272134:R298Q	R	-	2	0	LEFTY1	224141258	0.810000	0.29049	0.721000	0.30653	0.735000	0.41995	-0.153000	0.10144	-2.307000	0.00653	-0.993000	0.02533	CGG	C|0.939;T|0.061	0.061	strong		0.642	LEFTY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091155.1	NM_020997		T	226074635	C	T	226074635	3	4	22	1	0	0	0	0	1	0	0	0	8724	652	23	1	211	1	LEFTY1	1	226074635	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	199	226074635	23175986	426	3327											
LEFTY1	10637	hgsc.bcm.edu	37	chr1	226076598	226076598	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccacgtactgggccctcaCgtgggtggggatgaccagct	6	7	16	12	2	1	1	1	1	0	0	1	2	1	2	3	5	2	2	3	5	1	1	rs35273824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:226076598C>T	ENST00000272134.5	-	1	248	c.169G>A	c.(169-171)Gtg>Atg	p.V57M	RP4-559A3.7_ENST00000432920.2_Intron|LEFTY1_ENST00000492457.1_Intron	NM_020997.3	NP_066277.1	O75610	LFTY1_HUMAN	left-right determination factor 1	57			V -> M (in dbSNP:rs35273824).		cell growth (GO:0016049)|determination of left/right symmetry (GO:0007368)|heart morphogenesis (GO:0003007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)				cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	10	Breast(184;0.197)					TGGGCCCTCACGTGGGTGGGG	0.697													C|||	194	0.038738	0.1346	0.0216	5008	,	,		17711	0.0		0.0	False		,,,				2504	0.001				p.V57M		Atlas-SNP	.											.	LEFTY1	30	.	0			c.G169A						PASS	.	C	MET/VAL	581,3825	246.8+/-255.3	33,515,1655	30	32	31		169	1	0.1	1	dbSNP_126	31	0,8598		0,0,4299	yes	missense	LEFTY1	NM_020997.3	21	33,515,5954	TT,TC,CC		0.0,13.1866,4.4679	probably-damaging	57/367	226076598	581,12423	2203	4299	6502	SO:0001583	missense	10637	exon1			CCCTCACGTGGGT	AF081507	CCDS1548.1	1q42.1	2008-02-05	2004-11-17	2004-11-17	ENSG00000243709	ENSG00000243709			6552	protein-coding gene	gene with protein product		603037	"left-right determination, factor B"	LEFTB		10053005, 10886363	Standard	NM_020997		Approved	LEFTYB	uc001hpo.3	O75610	OTTHUMG00000037443	ENST00000272134.5:c.169G>A	1.37:g.226076598C>T	ENSP00000272134:p.Val57Met	187	0	0		194	103	0.530928	NM_020997	B2R7U0|Q53H67|Q5TE94	Missense_Mutation	SNP	ENST00000272134.5	37	CCDS1548.1	78	0.03571428571428571	70	0.14227642276422764	8	0.022099447513812154	0	0.0	0	0.0	c	11.47	1.647249	0.29246	0.131866	0.0	ENSG00000243709	ENST00000272134	T	0.58940	0.3	4.18	0.96	0.19631	Transforming growth factor-beta, N-terminal (1);	0.188005	0.47093	D	0.000242	T	0.00967	0.0032	M	0.74881	2.28	0.44789	P	0.0022060000000000413	D;D	0.89917	1.0;1.0	D;D	0.75020	0.985;0.985	T	0.29305	-1.0016	9	0.34782	T	0.22	.	4.8349	0.13460	0.0:0.613:0.177:0.21	rs35273824	57;57	B2R7U0;O75610	.;LFTY1_HUMAN	M	57	ENSP00000272134:V57M	ENSP00000272134:V57M	V	-	1	0	LEFTY1	224143221	0.997000	0.39634	0.125000	0.21846	0.032000	0.12392	2.679000	0.46909	0.249000	0.21456	0.313000	0.20887	GTG	C|0.956;T|0.044	0.044	strong		0.697	LEFTY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091155.1	NM_020997		T	226076598	C	T	226076598	3	4	22	1	0	0	0	0	1	0	0	0	8724	536	19	1	947	1	LEFTY1	1	226076598	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1963	226076598	23174023	427	3328											
C1orf95	375057	hgsc.bcm.edu	37	chr1	226785102	226785102	+	Intron	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccaccatccacgttccctgtAttttcccacgcccatctaca	8	11	3	19	2	1	0	0	0	1	0	4	0	4	0	6	0	1	2	6	0	2	5	rs73098850	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:226785102A>G	ENST00000366788.3	+	2	487				C1orf95_ENST00000366789.4_Intron	NM_001003665.3	NP_001003665.1	Q69YW2	STUM_HUMAN	chromosome 1 open reading frame 95							integral component of membrane (GO:0016021)				large_intestine(1)|lung(4)|ovary(3)	8	Breast(184;0.133)	Prostate(94;0.0885)		GBM - Glioblastoma multiforme(131;0.113)		CGTTCCCTGTATTTTCCCACG	0.468													A|||	272	0.0543131	0.1914	0.0245	5008	,	,		21325	0.0		0.001	False		,,,				2504	0.001				.		Atlas-SNP	.											.	C1orf95	16	.	0			c.383-2A>G						PASS	.	A		248,1136		22,204,466	354	286	306			-2.8	0	1	dbSNP_130	306	0,3182		0,0,1591	yes	intron	C1orf95	NM_001003665.3		22,204,2057	GG,GA,AA		0.0,17.9191,5.4314			226785102	248,4318	692	1591	2283	SO:0001627	intron_variant	375057	exon3			CCCTGTATTTTCC	AF035308	CCDS31044.1	1q42.12	2012-06-26			ENSG00000203685	ENSG00000203685			30491	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_001003665		Approved	DKFZp761P211	uc021pjw.1	Q69YW2	OTTHUMG00000037583	ENST00000366788.3:c.382+420A>G	1.37:g.226785102A>G		171	0	0		205	101	0.492683	NM_001003665	A6NGL2	Splice_Site	SNP	ENST00000366788.3	37	CCDS31044.1																																																																																			A|0.961;G|0.039	0.039	strong		0.468	C1orf95-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091634.1	NM_001003665		G	226785102	A	G	226785102	1	3	22	0	1	0	0	0	0	0	0	0	2074	463	16	3		3	C1orf95	1	226785102	Intron	SNP	A	TCGA-G8-6324-01A-11D-2210-10	708504	226785102	22465519	428	3329											
CDC42BPA	8476	hgsc.bcm.edu	37	chr1	227348245	227348245	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggatttatctttatttaccGttccatcttccatcagcttc	8	18	4	11	1	3	0	1	0	2	0	6	1	5	1	3	1	2	2	3	1	3	9	rs34614709	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:227348245G>A	ENST00000366769.3	-	6	1983	c.692C>T	c.(691-693)aCg>aTg	p.T231M	CDC42BPA_ENST00000535525.1_Splice_Site_p.T231M|CDC42BPA_ENST00000334218.5_Splice_Site_p.T231M|CDC42BPA_ENST00000366764.2_Splice_Site_p.T231M|CDC42BPA_ENST00000366767.3_Splice_Site_p.T231M|CDC42BPA_ENST00000366765.3_Splice_Site_p.T231M|CDC42BPA_ENST00000366766.2_Splice_Site_p.T231M	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)				TTTATTTACCGTTCCATCTTC	0.318													G|||	29	0.00579073	0.0219	0.0	5008	,	,		16832	0.0		0.0	False		,,,				2504	0.0				p.T231M		Atlas-SNP	.											.	CDC42BPA	528	.	0			c.C692T						PASS	.	G	MET/THR,MET/THR	77,4329	68.7+/-106.4	1,75,2127	130	139	136		692,692	5.2	1	1	dbSNP_126	136	1,8599	1.2+/-3.3	0,1,4299	yes	missense-near-splice,missense-near-splice	CDC42BPA	NM_003607.3,NM_014826.4	81,81	1,76,6426	AA,AG,GG		0.0116,1.7476,0.5997	probably-damaging,probably-damaging	231/1720,231/1639	227348245	78,12928	2203	4300	6503	SO:0001630	splice_region_variant	8476	exon6			TTTACCGTTCCAT	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.693+1C>T	1.37:g.227348245G>A		311	0	0		305	136	0.445902	NM_003607		Missense_Mutation	SNP	ENST00000366769.3	37	CCDS1558.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	25.7	4.667652	0.88348	0.017476	1.16E-4	ENSG00000143776	ENST00000366769;ENST00000366767;ENST00000334218;ENST00000366766;ENST00000366764;ENST00000535525;ENST00000366765	T;T;T;T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19;-0.19;-0.19;-0.19	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.60741	0.2292	L	0.55743	1.74	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	0.65084	-0.6254	10	0.22109	T	0.4	.	17.4674	0.87637	0.0:0.0:1.0:0.0	rs34614709	231;231;231;231	F5H5N0;Q5VT25-4;Q5VT25-3;Q5VT25-5	.;.;.;.	M	231	ENSP00000355731:T231M;ENSP00000355729:T231M;ENSP00000335341:T231M;ENSP00000355728:T231M;ENSP00000355726:T231M;ENSP00000443275:T231M;ENSP00000355727:T231M	ENSP00000335341:T231M	T	-	2	0	CDC42BPA	225414868	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.035000	0.93752	2.394000	0.81467	0.585000	0.79938	ACG	G|0.995;A|0.005	0.005	strong		0.318	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826	Missense_Mutation	A	227348245	G	A	227348245	5	1	22	1	0	0	0	0	0	0	1	0	3074	1159	40	1	4591	1	CDC42BPA	1	227348245	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	563143	227348245	21902376	429	3330											
CDC42BPA	8476	hgsc.bcm.edu	37	chr1	227504745	227504745	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatgttcttctctcttctcaAtggagaattattgcattcat	10	18	5	8	0	5	1	2	0	4	1	7	2	5	1	0	1	1	2	0	1	4	6	rs144296174		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:227504745A>G	ENST00000366769.3	-	1	1430	c.139T>C	c.(139-141)Ttg>Ctg	p.L47L	CDC42BPA_ENST00000535525.1_Silent_p.L47L|CDC42BPA_ENST00000334218.5_Silent_p.L47L|CDC42BPA_ENST00000366764.2_Silent_p.L47L|CDC42BPA_ENST00000366767.3_Silent_p.L47L|CDC42BPA_ENST00000366765.3_Silent_p.L47L|CDC42BPA_ENST00000366766.2_Silent_p.L47L	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)				TCTCTTCTCAATGGAGAATTA	0.378													a|||	1	0.000199681	0.0008	0.0	5008	,	,		18255	0.0		0.0	False		,,,				2504	0.0				p.L47L		Atlas-SNP	.											.	CDC42BPA	528	.	0			c.T139C						PASS	.	A	,	5,4401	9.9+/-24.2	0,5,2198	102	96	98		139,139	-1.5	0.8	1	dbSNP_134	98	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CDC42BPA	NM_003607.3,NM_014826.4	,	0,5,6498	GG,GA,AA		0.0,0.1135,0.0384	,	47/1720,47/1639	227504745	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	8476	exon1			TTCTCAATGGAGA	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.139T>C	1.37:g.227504745A>G		129	0	0		167	84	0.502994	NM_003607		Silent	SNP	ENST00000366769.3	37	CCDS1558.1																																																																																			A|1.000;G|0.000	0.000	strong		0.378	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826		G	227504745	A	G	227504745	2	3	22	1	0	0	0	0	0	0	0	1	3074	98	4	3		3	CDC42BPA	1	227504745	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	156500	227504745	21745876	430	3331											
ZNF678	339500	hgsc.bcm.edu	37	chr1	227842405	227842405	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gaattcatactggagagaaaCcctacaaatgtgacgaatgt	16	9	9	7	1	1	2	1	1	0	1	1	6	1	3	1	1	3	0	1	1	6	3	rs61283390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:227842405C>A	ENST00000343776.5	+	4	799	c.454C>A	c.(454-456)Ccc>Acc	p.P152T	ZNF678_ENST00000608949.1_Intron|ZNF678_ENST00000397097.3_Missense_Mutation_p.P207T	NM_178549.3	NP_848644.2	Q5SXM1	ZN678_HUMAN	zinc finger protein 678	152			P -> T (in dbSNP:rs61283390).		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)				TGGAGAGAAACCCTACAAATG	0.353													C|||	51	0.0101837	0.0371	0.0029	5008	,	,		20735	0.0		0.0	False		,,,				2504	0.0				p.P207T		Atlas-SNP	.											.	ZNF678	137	.	0			c.C619A						PASS	.	C	THR/PRO	173,4229	104.7+/-143.2	5,163,2033	56	65	62		619	-3.1	0	1	dbSNP_129	62	0,8598		0,0,4299	no	missense	ZNF678	NM_178549.3	38	5,163,6332	AA,AC,CC		0.0,3.93,1.3308	possibly-damaging	207/581	227842405	173,12827	2201	4299	6500	SO:0001583	missense	339500	exon4			GAGAAACCCTACA	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.454C>A	1.37:g.227842405C>A	ENSP00000344828:p.Pro152Thr	62	0	0		90	52	0.577778	NM_178549	Q8IVQ9	Missense_Mutation	SNP	ENST00000343776.5	37		23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	C	10.34	1.322066	0.23994	0.0393	0.0	ENSG00000181450	ENST00000343776;ENST00000397097;ENST00000440339	T;T;T	0.28895	2.31;2.31;1.59	1.55	-3.11	0.05299	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.16642	0.0400	M	0.78637	2.42	0.24660	N	0.993474	D	0.54964	0.969	P	0.61275	0.886	T	0.25433	-1.0132	9	0.66056	D	0.02	.	7.8273	0.29322	0.0:0.7281:0.0:0.2719	rs61283390;rs61739464	152	Q5SXM1	ZN678_HUMAN	T	152;207;207	ENSP00000344828:P152T;ENSP00000440403:P207T;ENSP00000394651:P207T	ENSP00000344828:P152T	P	+	1	0	ZNF678	225909028	0.030000	0.19436	0.000000	0.03702	0.000000	0.00434	0.807000	0.27140	-0.880000	0.03997	-0.924000	0.02725	CCC	C|0.987;A|0.013	0.013	strong		0.353	ZNF678-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000091976.2	NM_178549		A	227842405	C	A	227842405	3	1	22	1	0	0	0	0	1	0	0	0	18100	507	18	4	633	4	ZNF678	1	227842405	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	337660	227842405	21408216	431	3332											
ZNF678	339500	hgsc.bcm.edu	37	chr1	227842516	227842516	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aatgtgatgaatgtgacaaaGtttttaattggtggtcacaa	14	14	10	3	0	1	3	1	3	0	0	1	3	1	3	0	2	0	1	0	2	5	4	rs61744724	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:227842516G>C	ENST00000343776.5	+	4	910	c.565G>C	c.(565-567)Gtt>Ctt	p.V189L	ZNF678_ENST00000608949.1_Intron|ZNF678_ENST00000397097.3_Missense_Mutation_p.V244L	NM_178549.3	NP_848644.2	Q5SXM1	ZN678_HUMAN	zinc finger protein 678	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)			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)				ATGTGACAAAGTTTTTAATTG	0.373													G|||	82	0.0163738	0.059	0.0043	5008	,	,		18566	0.0		0.001	False		,,,				2504	0.0				p.V244L		Atlas-SNP	.											.	ZNF678	137	.	0			c.G730C						PASS	.	G	LEU/VAL	213,4193	124.5+/-161.8	3,207,1993	88	103	98		730	1.2	0.1	1	dbSNP_129	98	1,8597	1.2+/-3.3	0,1,4298	no	missense	ZNF678	NM_178549.3	32	3,208,6291	CC,CG,GG		0.0116,4.8343,1.6456	benign	244/581	227842516	214,12790	2203	4299	6502	SO:0001583	missense	339500	exon4			GACAAAGTTTTTA	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.565G>C	1.37:g.227842516G>C	ENSP00000344828:p.Val189Leu	56	0	0		60	30	0.5	NM_178549	Q8IVQ9	Missense_Mutation	SNP	ENST00000343776.5	37		27	0.012362637362637362	22	0.044715447154471545	1	0.0027624309392265192	4	0.006993006993006993	0	0.0	G	10.75	1.437218	0.25900	0.048343	1.16E-4	ENSG00000181450	ENST00000343776;ENST00000397097	T;T	0.35605	1.3;1.3	1.21	1.21	0.21127	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04724	0.0128	L	0.41415	1.275	0.19945	N	0.999946	P	0.36171	0.541	B	0.36608	0.229	T	0.09100	-1.0690	9	0.72032	D	0.01	.	5.6119	0.17410	0.0:0.3493:0.6507:0.0	rs61744724	189	Q5SXM1	ZN678_HUMAN	L	189;244	ENSP00000344828:V189L;ENSP00000440403:V244L	ENSP00000344828:V189L	V	+	1	0	ZNF678	225909139	0.001000	0.12720	0.092000	0.20876	0.083000	0.17756	-0.016000	0.12613	0.502000	0.28037	0.505000	0.49811	GTT	G|0.987;C|0.013	0.013	strong		0.373	ZNF678-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000091976.2	NM_178549		C	227842516	G	C	227842516	3	2	22	1	0	0	0	0	1	0	0	0	18100	1029	36	4	744	4	ZNF678	1	227842516	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	111	227842516	21408105	432	3333											
ZNF678	339500	hgsc.bcm.edu	37	chr1	227842561	227842561	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctagccataagaaaattcatAgtggagagaaaccataccca	18	7	7	9	0	1	2	1	0	0	2	1	4	1	3	3	1	3	0	3	1	7	5	rs116552491	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:227842561A>G	ENST00000343776.5	+	4	955	c.610A>G	c.(610-612)Agt>Ggt	p.S204G	ZNF678_ENST00000608949.1_Intron|ZNF678_ENST00000397097.3_Missense_Mutation_p.S259G	NM_178549.3	NP_848644.2	Q5SXM1	ZN678_HUMAN	zinc finger protein 678	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)			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)				GAAAATTCATAGTGGAGAGAA	0.373													A|||	30	0.00599042	0.0212	0.0014	5008	,	,		19312	0.0		0.001	False		,,,				2504	0.0				p.S259G		Atlas-SNP	.											.	ZNF678	137	.	0			c.A775G						PASS	.	A	GLY/SER	77,4327	64.1+/-101.4	0,77,2125	100	115	110		775	0.3	0	1	dbSNP_132	110	0,8594		0,0,4297	no	missense	ZNF678	NM_178549.3	56	0,77,6422	GG,GA,AA		0.0,1.7484,0.5924	possibly-damaging	259/581	227842561	77,12921	2202	4297	6499	SO:0001583	missense	339500	exon4			ATTCATAGTGGAG	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.610A>G	1.37:g.227842561A>G	ENSP00000344828:p.Ser204Gly	49	0	0		46	23	0.5	NM_178549	Q8IVQ9	Missense_Mutation	SNP	ENST00000343776.5	37		10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	A	13.99	2.401576	0.42613	0.017484	0.0	ENSG00000181450	ENST00000343776;ENST00000397097	T;T	0.19669	2.13;2.13	1.49	0.308	0.15815	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10937	0.0267	L	0.58354	1.805	0.24788	N	0.992776	P	0.43938	0.822	B	0.44044	0.439	T	0.13926	-1.0491	9	0.87932	D	0	.	4.1011	0.10014	0.7609:0.0:0.2391:0.0	.	204	Q5SXM1	ZN678_HUMAN	G	204;259	ENSP00000344828:S204G;ENSP00000440403:S259G	ENSP00000344828:S204G	S	+	1	0	ZNF678	225909184	0.232000	0.23762	0.004000	0.12327	0.027000	0.11550	1.213000	0.32407	0.587000	0.29643	0.413000	0.27773	AGT	A|0.996;G|0.004	0.004	strong		0.373	ZNF678-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000091976.2	NM_178549		G	227842561	A	G	227842561	3	3	22	1	0	0	0	0	1	0	0	0	18100	420	15	3	789	3	ZNF678	1	227842561	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	45	227842561	21408060	433	3334											
PRSS38	339501	hgsc.bcm.edu	37	chr1	228003843	228003843	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggcggcgtccctgcgccCgagaggaagtggccgtggca	5	5	18	13	5	0	1	0	0	0	1	1	3	1	2	3	5	1	1	3	5	1	0	rs113353225	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228003843C>T	ENST00000366757.3	+	2	225	c.201C>T	c.(199-201)ccC>ccT	p.P67P		NM_183062.2	NP_898885.1	A1L453	PRS38_HUMAN	protease, serine, 38	67	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					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						TCCCTGCGCCCGAGAGGAAGT	0.672													C|||	73	0.0145767	0.0537	0.0029	5008	,	,		14096	0.0		0.0	False		,,,				2504	0.0				p.P67P		Atlas-SNP	.											.	PRSS38	55	.	0			c.C201T						PASS	.	C		279,4127	151.8+/-185.6	4,271,1928	67	75	73		201	-8.3	0	1	dbSNP_132	73	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	PRSS38	NM_183062.2		4,272,6226	TT,TC,CC		0.0116,6.3323,2.1532		67/327	228003843	280,12724	2203	4299	6502	SO:0001819	synonymous_variant	339501	exon2			TGCGCCCGAGAGG		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.201C>T	1.37:g.228003843C>T		195	1	0.00512821		246	139	0.565041	NM_183062	Q7RTY6	Silent	SNP	ENST00000366757.3	37	CCDS1563.1																																																																																			C|0.982;T|0.018	0.018	strong		0.672	PRSS38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091981.1	NM_183062		T	228003843	C	T	228003843	2	4	22	1	0	0	0	0	0	0	0	1	12639	639	23	1		1	PRSS38	1	228003843	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	161282	228003843	21246778	434	3335											
PRSS38	339501	hgsc.bcm.edu	37	chr1	228003879	228003879	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggcaggtcagcgtgcactaCgcaggcctccacgtctgcgg	6	7	14	14	4	2	0	1	0	1	0	3	0	3	0	2	4	4	3	2	4	1	1	rs112241411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228003879C>T	ENST00000366757.3	+	2	261	c.237C>T	c.(235-237)taC>taT	p.Y79Y		NM_183062.2	NP_898885.1	A1L453	PRS38_HUMAN	protease, serine, 38	79	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					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						GCGTGCACTACGCAGGCCTCC	0.662													C|||	73	0.0145767	0.0537	0.0029	5008	,	,		13078	0.0		0.0	False		,,,				2504	0.0				p.Y79Y		Atlas-SNP	.											PRSS38,colon,carcinoma,0,1	PRSS38	55	1	0			c.C237T						PASS	.	C		279,4127	150.3+/-184.3	4,271,1928	60	68	65		237	-0.7	0	1	dbSNP_132	65	1,8597		0,1,4298	no	coding-synonymous	PRSS38	NM_183062.2		4,272,6226	TT,TC,CC		0.0116,6.3323,2.1532		79/327	228003879	280,12724	2203	4299	6502	SO:0001819	synonymous_variant	339501	exon2			GCACTACGCAGGC		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.237C>T	1.37:g.228003879C>T		190	0	0		254	131	0.515748	NM_183062	Q7RTY6	Silent	SNP	ENST00000366757.3	37	CCDS1563.1																																																																																			C|0.982;T|0.018	0.018	strong		0.662	PRSS38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091981.1	NM_183062		T	228003879	C	T	228003879	2	4	22	1	0	0	0	0	0	0	0	1	12639	547	19	1		1	PRSS38	1	228003879	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	36	228003879	21246742	435	3336											
WNT9A	7483	hgsc.bcm.edu	37	chr1	228109696	228109696	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtggtctccaccccagccttGatcacctggcagaagggtgc	7	8	12	14	0	2	2	1	1	1	1	3	2	2	2	5	3	2	1	5	3	1	1	rs112703157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228109696G>A	ENST00000272164.5	-	4	631	c.621C>T	c.(619-621)atC>atT	p.I207I		NM_003395.2	NP_003386.1	O14904	WNT9A_HUMAN	wingless-type MMTV integration site family, member 9A	207					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)				CCCCAGCCTTGATCACCTGGC	0.677													G|||	122	0.024361	0.0862	0.0115	5008	,	,		17033	0.0		0.0	False		,,,				2504	0.0				p.I207I		Atlas-SNP	.											.	WNT9A	39	.	0			c.C621T						PASS	.	G		318,4080		6,306,1887	34	35	34		621	3.4	1	1	dbSNP_132	34	2,8592		0,2,4295	no	coding-synonymous	WNT9A	NM_003395.2		6,308,6182	AA,AG,GG		0.0233,7.2306,2.4631		207/366	228109696	320,12672	2199	4297	6496	SO:0001819	synonymous_variant	7483	exon4			AGCCTTGATCACC	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.621C>T	1.37:g.228109696G>A		69	0	0		84	30	0.357143	NM_003395	A6NLW2|Q2M2J3|Q5VWU0|Q96S50	Silent	SNP	ENST00000272164.5	37	CCDS31045.1																																																																																			G|0.977;A|0.023	0.023	strong		0.677	WNT9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091646.1	NM_003395		A	228109696	G	A	228109696	2	1	22	1	0	0	0	0	0	0	0	1	17413	1280	45	2		2	WNT9A	1	228109696	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	105817	228109696	21140925	436	3337											
WNT3A	89780	hgsc.bcm.edu	37	chr1	228238443	228238443	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgtgcagaaggcacggccGccatctgtggctgcagcagc	8	6	14	13	2	1	1	0	0	1	1	1	1	1	1	2	3	4	5	2	3	1	0	rs61743220	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228238443G>A	ENST00000284523.1	+	3	478	c.400G>A	c.(400-402)Gcc>Acc	p.A134T	WNT3A_ENST00000366753.2_Missense_Mutation_p.A134T	NM_033131.3	NP_149122.1	P56704	WNT3A_HUMAN	wingless-type MMTV integration site family, member 3A	134					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)				AGGCACGGCCGCCATCTGTGG	0.627													G|||	31	0.0061901	0.0234	0.0	5008	,	,		17447	0.0		0.0	False		,,,				2504	0.0				p.A134T		Atlas-SNP	.											.	WNT3A	40	.	0			c.G400A						PASS	.	G	THR/ALA	115,4291	86.3+/-125.0	1,113,2089	80	72	75		400	-2	0	1	dbSNP_129	75	0,8600		0,0,4300	yes	missense	WNT3A	NM_033131.3	58	1,113,6389	AA,AG,GG		0.0,2.6101,0.8842	benign	134/353	228238443	115,12891	2203	4300	6503	SO:0001583	missense	89780	exon3			ACGGCCGCCATCT	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.400G>A	1.37:g.228238443G>A	ENSP00000284523:p.Ala134Thr	189	0	0		167	79	0.473054	NM_033131	Q3SY79|Q3SY80|Q969P2	Missense_Mutation	SNP	ENST00000284523.1	37	CCDS1564.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	G	0.524	-0.860772	0.02610	0.026101	0.0	ENSG00000154342	ENST00000284523;ENST00000366753	T;T	0.75367	-0.93;-0.93	4.78	-1.98	0.07480	.	0.443415	0.23894	N	0.043517	T	0.15782	0.0380	N	0.00771	-1.2	0.24533	N	0.994101	B;B	0.06786	0.0;0.001	B;B	0.09377	0.002;0.004	T	0.25984	-1.0116	10	0.10377	T	0.69	.	12.1436	0.54012	0.6823:0.0:0.3177:0.0	rs61743220	134;134	P56704;Q3SY79	WNT3A_HUMAN;.	T	134	ENSP00000284523:A134T;ENSP00000355715:A134T	ENSP00000284523:A134T	A	+	1	0	WNT3A	226305066	0.916000	0.31088	0.005000	0.12908	0.134000	0.20937	1.632000	0.37102	-0.810000	0.04375	-1.094000	0.02160	GCC	G|0.992;A|0.008	0.008	strong		0.627	WNT3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091648.1	NM_033131		A	228238443	G	A	228238443	3	1	22	1	0	0	0	0	1	0	0	0	17404	1087	38	1	410	1	WNT3A	1	228238443	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	128747	228238443	21012178	437	3338											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228399628	228399628	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgggagaaggaccagcaGccggtggcggccggcgcgcg	7	2	20	12	6	0	1	0	0	0	1	0	3	0	2	3	6	3	2	3	6	1	0	rs114375717	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228399628G>A	ENST00000422127.1	+	2	188	c.144G>A	c.(142-144)caG>caA	p.Q48Q	C1orf145_ENST00000295012.5_Intron|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000570156.2_Silent_p.Q48Q|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000284548.11_Silent_p.Q48Q	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	48	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)				AGGACCAGCAGCCGGTGGCGG	0.682													G|||	39	0.00778754	0.0287	0.0014	5008	,	,		11232	0.0		0.0	False		,,,				2504	0.0				p.Q48Q		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G144A						PASS	.	G	,	120,3834		0,120,1857	8	10	10		144,144	1.5	0.9	1	dbSNP_132	10	0,8146		0,0,4073	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	0,120,5930	AA,AG,GG		0.0,3.0349,0.9917	,	48/7969,48/6621	228399628	120,11980	1977	4073	6050	SO:0001819	synonymous_variant	84033	exon2			CCAGCAGCCGGTG	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.144G>A	1.37:g.228399628G>A		62	0	0		71	42	0.591549	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			G|0.992;A|0.008	0.008	strong		0.682	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228399628	G	A	228399628	2	1	22	1	0	0	0	0	0	0	0	1	10821	962	34	2		2	OBSCN	1	228399628	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	161185	228399628	20850993	438	3339											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228404864	228404864	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctgggccactccggtgagcGcttcttgcaggaggatgtgg	5	9	17	10	2	1	1	0	1	1	0	2	3	2	3	2	5	2	3	2	5	0	2	rs141921462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228404864G>A	ENST00000422127.1	+	8	2572	c.2528G>A	c.(2527-2529)cGc>cAc	p.R843H	OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000570156.2_Missense_Mutation_p.R843H|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000284548.11_Missense_Mutation_p.R843H	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	843	Ig-like 8.				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)				TCCGGTGAGCGCTTCTTGCAG	0.662													G|||	36	0.0071885	0.0272	0.0	5008	,	,		16092	0.0		0.0	False		,,,				2504	0.0				p.R843H		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G2528A						PASS	.	G	HIS/ARG,HIS/ARG	124,4184		1,122,2031	64	72	69		2528,2528	-2.1	0	1	dbSNP_134	69	1,8503		0,1,4251	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	29,29	1,123,6282	AA,AG,GG		0.0118,2.8784,0.9756	probably-damaging,probably-damaging	843/7969,843/6621	228404864	125,12687	2154	4252	6406	SO:0001583	missense	84033	exon8			GTGAGCGCTTCTT	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.2528G>A	1.37:g.228404864G>A	ENSP00000409493:p.Arg843His	94	0	0		91	57	0.626374	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	37	CCDS58065.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	.	8.071	0.770330	0.15983	0.028784	1.18E-4	ENSG00000154358	ENST00000284548;ENST00000422127	T;T	0.52057	0.68;0.68	4.79	-2.11	0.07187	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.987508	0.08243	N	0.975792	T	0.20659	0.0497	L	0.58101	1.795	0.09310	N	0.999998	B;D	0.64830	0.008;0.994	B;P	0.48454	0.003;0.578	T	0.31110	-0.9955	10	0.14656	T	0.56	.	7.3341	0.26599	0.6513:0.0:0.2172:0.1315	.	843;843	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	H	843	ENSP00000284548:R843H;ENSP00000409493:R843H	ENSP00000284548:R843H	R	+	2	0	OBSCN	226471487	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.113000	0.03296	-0.663000	0.05331	-0.768000	0.03414	CGC	G|0.996;A|0.004	0.004	strong		0.662	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228404864	G	A	228404864	3	1	22	1	0	0	0	0	1	0	0	0	10821	1087	38	1	2554	1	OBSCN	1	228404864	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5236	228404864	20845757	439	3340											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228461655	228461655	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagccagggggacacccaCaccctgaccgtgcatggcgc	8	3	13	17	2	0	1	0	1	0	0	0	2	0	2	5	3	2	1	5	3	0	0	rs138055037	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228461655C>T	ENST00000422127.1	+	18	5366	c.5322C>T	c.(5320-5322)caC>caT	p.H1774H	RP5-1139B12.3_ENST00000602947.1_RNA|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000570156.2_Silent_p.H2149H|RP5-1139B12.2_ENST00000602517.1_RNA|OBSCN_ENST00000359599.6_Silent_p.H621H|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Silent_p.H1774H|RP5-1139B12.3_ENST00000602529.1_RNA	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1774	Fibronectin type-III 2. {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)				GGGACACCCACACCCTGACCG	0.662													C|||	35	0.00698882	0.0265	0.0	5008	,	,		17285	0.0		0.0	False		,,,				2504	0.0				p.H2149H		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C6447T						PASS	.	C	,	115,4115		1,113,2001	19	23	22		5322,5322	1.3	1	1	dbSNP_134	22	0,8446		0,0,4223	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	1,113,6224	TT,TC,CC		0.0,2.7187,0.9072	,	1774/7969,1774/6621	228461655	115,12561	2115	4223	6338	SO:0001819	synonymous_variant	84033	exon22			CACCCACACCCTG	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.5322C>T	1.37:g.228461655C>T		185	0	0		184	103	0.559783	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			C|0.996;T|0.004	0.004	strong		0.662	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228461655	C	T	228461655	2	4	22	1	0	0	0	0	0	0	0	1	10821	477	17	2		2	OBSCN	1	228461655	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	56791	228461655	20788966	440	3341											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228473959	228473959	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagcccgggggctaccacgTgctgaccctgcggcagctgg	5	5	15	16	3	0	1	0	1	0	0	0	1	0	1	4	4	5	4	4	4	1	1	rs202022683	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228473959T>G	ENST00000422127.1	+	34	9229	c.9185T>G	c.(9184-9186)gTg>gGg	p.V3062G	OBSCN_ENST00000366707.4_Missense_Mutation_p.V181G|OBSCN_ENST00000570156.2_Missense_Mutation_p.V3491G|OBSCN_ENST00000359599.6_Missense_Mutation_p.V1909G|OBSCN_ENST00000366709.4_Missense_Mutation_p.V181G|OBSCN_ENST00000284548.11_Missense_Mutation_p.V3062G	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3062	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)				GGCTACCACGTGCTGACCCTG	0.662													T|||	36	0.0071885	0.0272	0.0	5008	,	,		17519	0.0		0.0	False		,,,				2504	0.0				p.V3491G		Atlas-SNP	.											OBSCN_ENST00000570156,NS,haematopoietic_neoplasm,0,4	OBSCN	2142	4	0			c.T10472G						scavenged	.	T	GLY/VAL,GLY/VAL	98,4070		1,96,1987	26	33	31		9185,9185	4.5	1	1	dbSNP_134	31	0,8434		0,0,4217	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	109,109	1,96,6204	GG,GT,TT		0.0,2.3512,0.7777	possibly-damaging,possibly-damaging	3062/7969,3062/6621	228473959	98,12504	2084	4217	6301	SO:0001583	missense	84033	exon39			ACCACGTGCTGAC	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.9185T>G	1.37:g.228473959T>G	ENSP00000409493:p.Val3062Gly	192	2	0.0104167		204	101	0.495098	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	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.084154	0.76642	0.023512	0.0	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	T;T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23;-0.23	5.67	4.49	0.54785	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.638941	0.14451	N	0.318802	T	0.59555	0.2202	M	0.66939	2.045	0.39455	D	0.967471	P;D	0.54207	0.877;0.965	P;P	0.62435	0.818;0.902	T	0.66208	-0.5981	10	0.23891	T	0.37	.	6.0668	0.19868	0.1444:0.0756:0.0:0.7801	.	3062;3062	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	G	3062;3062;181;181;1909	ENSP00000284548:V3062G;ENSP00000409493:V3062G;ENSP00000355668:V181G;ENSP00000355670:V181G;ENSP00000352613:V1909G	ENSP00000284548:V3062G	V	+	2	0	OBSCN	226540582	0.533000	0.26354	0.959000	0.39883	0.795000	0.44927	1.070000	0.30653	2.155000	0.67459	0.459000	0.35465	GTG	.	.	weak		0.662	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		G	228473959	T	G	228473959	3	3	22	1	0	0	0	0	1	0	0	0	10821	1696	59	5	9315	5	OBSCN	1	228473959	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	12304	228473959	20776662	441	3342											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228504486	228504486	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caggcatgcttcacctgcacGctcagcgaggcggtgcccgt	6	7	13	15	4	2	0	2	0	0	0	2	1	2	0	2	3	4	4	2	3	0	1	rs372827129	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228504486G>A	ENST00000422127.1	+	51	13406	c.13362G>A	c.(13360-13362)acG>acA	p.T4454T	OBSCN_ENST00000366707.4_Silent_p.T2088T|OBSCN_ENST00000570156.2_Silent_p.T5411T|OBSCN_ENST00000366709.4_Silent_p.T1573T|OBSCN_ENST00000284548.11_Silent_p.T4454T	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4454	Ig-like 46.				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)				TCACCTGCACGCTCAGCGAGG	0.672													g|||	36	0.0071885	0.0272	0.0	5008	,	,		15193	0.0		0.0	False		,,,				2504	0.0				p.T5411T		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G16233A						PASS	.		,	111,4087		0,111,1988	16	21	19		13362,13362	-0.1	0.1	1		19	0,8410		0,0,4205	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	0,111,6193	AA,AG,GG		0.0,2.6441,0.8804	,	4454/7969,4454/6621	228504486	111,12497	2099	4205	6304	SO:0001819	synonymous_variant	84033	exon62			CTGCACGCTCAGC	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.13362G>A	1.37:g.228504486G>A		65	0	0		99	60	0.606061	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			.	.	none		0.672	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228504486	G	A	228504486	2	1	22	1	0	0	0	0	0	0	0	1	10821	1074	38	1		1	OBSCN	1	228504486	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	30527	228504486	20746135	442	3343											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228547691	228547691	+	Intron	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acactgcccggtgcgaccccCggaggggaccccaattccaa	9	4	11	17	3	0	0	0	0	0	0	1	3	1	2	6	4	2	0	6	4	2	1	rs367920745	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228547691C>T	ENST00000422127.1	+	80	18705				OBSCN_ENST00000366707.4_Intron|OBSCN_ENST00000570156.2_Intron|OBSCN_ENST00000366709.4_Silent_p.P3485P|OBSCN_ENST00000284548.11_Silent_p.P6366P	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)				GTGCGACCCCCGGAGGGGACC	0.647													C|||	36	0.0071885	0.0272	0.0	5008	,	,		17215	0.0		0.0	False		,,,				2504	0.0				p.P6366P		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C19098T						PASS	.	C	,	82,3694		1,80,1807	17	20	19		,19098	-8.8	0	1		19	0,8218		0,0,4109	no	intron,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	1,80,5916	TT,TC,CC		0.0,2.1716,0.6837	,	,6366/6621	228547691	82,11912	1888	4109	5997	SO:0001627	intron_variant	84033	exon81			GACCCCCGGAGGG	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.18662-2586C>T	1.37:g.228547691C>T		128	0	0		164	83	0.506098	NM_052843	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			.	.	none		0.647	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228547691	C	T	228547691	1	4	22	0	1	0	0	0	0	0	0	0	10821	639	23	1		1	OBSCN	1	228547691	Intron	SNP	C	TCGA-G8-6324-01A-11D-2210-10	43205	228547691	20702930	443	3344											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228559225	228559225	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gggcgctgccaggcctgcgcGagccactgatggagcaccgc	6	4	16	15	4	0	1	0	1	0	0	0	3	0	2	4	3	4	2	4	3	0	0	rs200269110	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228559225G>A	ENST00000422127.1	+	94	20790	c.20746G>A	c.(20746-20748)Gag>Aag	p.E6916K	OBSCN_ENST00000366707.4_Missense_Mutation_p.E4550K|OBSCN_ENST00000570156.2_Missense_Mutation_p.E7873K	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	6916					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)				AGGCCTGCGCGAGCCACTGAT	0.746													G|||	34	0.00678914	0.0257	0.0	5008	,	,		12917	0.0		0.0	False		,,,				2504	0.0				p.E7873K		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G23617A						PASS	.	G	LYS/GLU	70,3774		0,70,1852	5	9	8		20746	4.4	0.9	1		8	0,8116		0,0,4058	yes	missense	OBSCN	NM_001098623.1	56	0,70,5910	AA,AG,GG		0.0,1.821,0.5853	benign	6916/7969	228559225	70,11890	1922	4058	5980	SO:0001583	missense	84033	exon105			CTGCGCGAGCCAC	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.20746G>A	1.37:g.228559225G>A	ENSP00000409493:p.Glu6916Lys	12	0	0		20	8	0.4	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	37	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.35|17.35	3.368034|3.368034	0.61513|0.61513	0.01821|0.01821	0.0|0.0	ENSG00000154358|ENSG00000154358	ENST00000422127;ENST00000366707|ENST00000441106	T;T|T	0.65549|0.72394	-0.16;-0.1|-0.65	4.41|4.41	4.41|4.41	0.53225|0.53225	.|.	.|.	.|.	.|.	.|.	T|T	0.64068|0.64068	0.2565|0.2565	L|L	0.53249|0.53249	1.67|1.67	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.83275|.	0.996|.	T|T	0.72301|0.72301	-0.4334|-0.4334	9|7	0.40728|0.41790	T|T	0.16|0.15	.|.	17.2084|17.2084	0.86924|0.86924	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	6916|.	Q5VST9|.	OBSCN_HUMAN|.	K|Q	6916;4550|1532	ENSP00000409493:E6916K;ENSP00000355668:E4550K|ENSP00000388554:R1532Q	ENSP00000355668:E4550K|ENSP00000388554:R1532Q	E|R	+|+	1|2	0|0	OBSCN|OBSCN	226625848|226625848	0.999000|0.999000	0.42202|0.42202	0.931000|0.931000	0.37212|0.37212	0.040000|0.040000	0.13550|0.13550	2.926000|2.926000	0.48892|0.48892	2.300000|2.300000	0.77407|0.77407	0.555000|0.555000	0.69702|0.69702	GAG|CGA	.	.	weak		0.746	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228559225	G	A	228559225	3	1	22	1	0	0	0	0	1	0	0	0	10821	1059	37	1	22326	1	OBSCN	1	228559225	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	11534	228559225	20691396	444	3345											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228560181	228560181	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccagggctgagtcccagtcGgaggagcagcaggaggccag	9	3	18	11	1	0	1	0	1	0	0	2	4	1	4	3	5	2	3	3	5	0	0	rs62640372	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228560181G>A	ENST00000422127.1	+	94	21746	c.21702G>A	c.(21700-21702)tcG>tcA	p.S7234S	OBSCN_ENST00000366707.4_Silent_p.S4868S|OBSCN_ENST00000570156.2_Silent_p.S8191S	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	7234					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)				AGTCCCAGTCGGAGGAGCAGC	0.692													G|||	32	0.00638978	0.0227	0.0014	5008	,	,		15712	0.001		0.0	False		,,,				2504	0.0				p.S8191S		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G24573A						PASS	.	G		93,4067		0,93,1987	13	16	15		21702	-2.1	0.6	1	dbSNP_129	15	0,8404		0,0,4202	no	coding-synonymous	OBSCN	NM_001098623.1		0,93,6189	AA,AG,GG		0.0,2.2356,0.7402		7234/7969	228560181	93,12471	2080	4202	6282	SO:0001819	synonymous_variant	84033	exon105			CCAGTCGGAGGAG	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.21702G>A	1.37:g.228560181G>A		94	0	0		92	44	0.478261	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1	7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	G	6.630	0.484618	0.12641	0.022356	0.0	ENSG00000154358	ENST00000441106	.	.	.	1.05	-2.1	0.07210	.	.	.	.	.	T	0.09774	0.0240	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.24835	-1.0149	4	.	.	.	.	2.4475	0.04509	0.0:0.253:0.2936:0.4534	rs62640372	.	.	.	R	1851	.	.	G	+	1	0	OBSCN	226626804	0.013000	0.17824	0.600000	0.28864	0.363000	0.29612	-0.971000	0.03806	0.119000	0.18210	0.121000	0.15741	GGA	G|0.996;A|0.004	0.004	strong		0.692	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228560181	G	A	228560181	2	1	22	1	0	0	0	0	0	0	0	1	10821	1103	39	1		1	OBSCN	1	228560181	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	956	228560181	20690440	445	3346											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228565325	228565325	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atcaccgaatacaacctgctCaaggtcgtggacctgggcaa	12	7	10	12	2	2	0	2	0	0	0	3	2	2	1	3	3	3	2	3	3	5	1	rs61743077	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228565325C>T	ENST00000422127.1	+	102	23459	c.23415C>T	c.(23413-23415)ctC>ctT	p.L7805L	OBSCN_ENST00000366707.4_Silent_p.L5439L|OBSCN_ENST00000570156.2_Silent_p.L8762L	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	7805	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)				ACAACCTGCTCAAGGTCGTGG	0.562													C|||	54	0.0107827	0.0386	0.0029	5008	,	,		21756	0.0		0.001	False		,,,				2504	0.0				p.L8762L		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C26286T						PASS	.	C		187,4189		1,185,2002	95	97	96		23415	-2.4	0.9	1	dbSNP_129	96	0,8542		0,0,4271	no	coding-synonymous	OBSCN	NM_001098623.1		1,185,6273	TT,TC,CC		0.0,4.2733,1.4476		7805/7969	228565325	187,12731	2188	4271	6459	SO:0001819	synonymous_variant	84033	exon113			CCTGCTCAAGGTC	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.23415C>T	1.37:g.228565325C>T		142	0	0		170	94	0.552941	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1	17	0.007783882783882784	15	0.03048780487804878	2	0.0055248618784530384	0	0.0	0	0.0	C	15.09	2.729743	0.48833	0.042733	0.0	ENSG00000154358	ENST00000441106	.	.	.	5.14	-2.38	0.06622	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.2	0.31419	0.0:0.1855:0.4897:0.3248	rs61743077	.	.	.	X	2422	.	.	Q	+	1	0	OBSCN	226631948	0.995000	0.38212	0.873000	0.34254	0.884000	0.51177	0.219000	0.17641	-0.368000	0.08040	0.313000	0.20887	CAA	C|0.992;T|0.008	0.008	strong		0.562	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228565325	C	T	228565325	2	4	22	1	0	0	0	0	0	0	0	1	10821	813	29	2		2	OBSCN	1	228565325	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	5144	228565325	20685296	446	3347											
TRIM17	51127	hgsc.bcm.edu	37	chr1	228601506	228601506	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgggcacccacctgccactCggctaagctctgctcctccc	5	8	8	20	1	1	0	0	0	1	0	4	0	3	0	5	2	3	4	5	2	1	1	rs116188608	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228601506C>T	ENST00000366697.2	-	2	1473	c.517G>A	c.(517-519)Gag>Aag	p.E173K	TRIM17_ENST00000366698.2_Missense_Mutation_p.E173K|TRIM17_ENST00000295033.3_Missense_Mutation_p.E173K|TRIM17_ENST00000456946.2_Missense_Mutation_p.E173K			Q9Y577	TRI17_HUMAN	tripartite motif containing 17	173					protein autoubiquitination (GO:0051865)	intracellular (GO:0005622)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)	10		Prostate(94;0.0724)				ACCTGCCACTCGGCTAAGCTC	0.607													C|||	54	0.0107827	0.0378	0.0043	5008	,	,		16452	0.0		0.001	False		,,,				2504	0.0				p.E173K		Atlas-SNP	.											.	TRIM17	66	.	0			c.G517A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU	193,4213	121.3+/-158.8	1,191,2011	120	90	100		517,517,517	1.6	0.1	1	dbSNP_132	100	0,8600		0,0,4300	yes	missense,missense,missense	TRIM17	NM_001024940.2,NM_001134855.1,NM_016102.3	56,56,56	1,191,6311	TT,TC,CC		0.0,4.3804,1.4839	benign,benign,benign	173/478,173/344,173/478	228601506	193,12813	2203	4300	6503	SO:0001583	missense	51127	exon3			GCCACTCGGCTAA	AF156271	CCDS1571.1, CCDS44327.1	1q42	2013-01-09	2011-01-25	2001-11-30	ENSG00000162931	ENSG00000162931		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	13430	protein-coding gene	gene with protein product	"ring finger protein 16", "RING finger protein terf", "testis RING finger protein"	606123	"tripartite motif-containing 17"	RNF16		9792805, 10894938	Standard	NM_016102		Approved	terf, RBCC	uc001hsv.3	Q9Y577	OTTHUMG00000039974	ENST00000366697.2:c.517G>A	1.37:g.228601506C>T	ENSP00000355658:p.Glu173Lys	93	0	0		109	44	0.40367	NM_001024940	B4DVJ2|Q5VST8	Missense_Mutation	SNP	ENST00000366697.2	37	CCDS1571.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	C	0.010	-1.780416	0.00634	0.043804	0.0	ENSG00000162931	ENST00000366697;ENST00000366698;ENST00000295033;ENST00000456946;ENST00000479800;ENST00000355586	T;T;T;T;T;T	0.18810	3.58;3.58;3.58;3.58;3.58;2.19	3.5	1.56	0.23342	.	0.000000	0.38663	N	0.001611	T	0.03520	0.0101	M	0.66939	2.045	0.09310	N	1	B;B	0.20550	0.046;0.004	B;B	0.17433	0.018;0.002	T	0.30149	-0.9988	10	0.08599	T	0.76	.	4.9406	0.13963	0.0:0.6631:0.2166:0.1203	.	173;173	Q9Y577-2;Q9Y577	.;TRI17_HUMAN	K	173;173;173;173;146;173	ENSP00000355658:E173K;ENSP00000355659:E173K;ENSP00000295033:E173K;ENSP00000403312:E173K;ENSP00000430468:E146K;ENSP00000347794:E173K	ENSP00000295033:E173K	E	-	1	0	TRIM17	226668129	0.008000	0.16893	0.143000	0.22291	0.036000	0.12997	0.247000	0.18179	0.452000	0.26830	-0.254000	0.11334	GAG	C|0.986;T|0.014	0.014	strong		0.607	TRIM17-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096439.2	NM_016102		T	228601506	C	T	228601506	3	4	22	1	0	0	0	0	1	0	0	0	16508	893	31	1	1085	1	TRIM17	1	228601506	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	36181	228601506	20649115	447	3348											
HIST3H3	8290	hgsc.bcm.edu	37	chr1	228612934	228612934	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcttcacgccgccagtggcAggtgcgctcttgcgagccac	5	9	12	15	4	3	0	1	0	2	0	3	1	3	0	3	2	3	2	3	2	0	3	rs61740979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228612934A>G	ENST00000366696.1	-	1	92	c.93T>C	c.(91-93)ccT>ccC	p.P31P		NM_003493.2	NP_003484.1	Q16695	H31T_HUMAN	histone cluster 3, H3	31					telomere maintenance (GO:0000723)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(1)|lung(2)|prostate(2)|skin(1)	6		Prostate(94;0.0724)				CGCCAGTGGCAGGTGCGCTCT	0.667													g|||	80	0.0159744	0.0567	0.0058	5008	,	,		13386	0.0		0.001	False		,,,				2504	0.0				p.P31P		Atlas-SNP	.											.	HIST3H3	20	.	0			c.T93C						PASS	.	C		240,4162		1,238,1962	36	43	41		93	-6.5	0	1	dbSNP_129	41	0,8594		0,0,4297	no	coding-synonymous	HIST3H3	NM_003493.2		1,238,6259	GG,GA,AA		0.0,5.4521,1.8467		31/137	228612934	240,12756	2201	4297	6498	SO:0001819	synonymous_variant	8290	exon1			AGTGGCAGGTGCG	Z49861	CCDS1572.1	1q42.13	2012-09-19	2006-10-11	2003-02-21	ENSG00000168148	ENSG00000168148		"Histones / Replication-dependent"	4778	protein-coding gene	gene with protein product		602820	"H3 histone family, member T", "histone 3, H3"	H3FT		8834248, 12408966	Standard	NM_003493		Approved	H3t, H3/g, H3.4	uc001hsx.1	Q16695	OTTHUMG00000040044	ENST00000366696.1:c.93T>C	1.37:g.228612934A>G		93	0	0		64	24	0.375	NM_003493	B2R5K3|Q6FGU4	Silent	SNP	ENST00000366696.1	37	CCDS1572.1																																																																																			A|0.981;G|0.019	0.019	strong		0.667	HIST3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096595.2	NM_003493		G	228612934	A	G	228612934	2	3	22	1	0	0	0	0	0	0	0	1	7193	175	7	3		3	HIST3H3	1	228612934	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	11428	228612934	20637687	448	3349											
HIST3H3	8290	hgsc.bcm.edu	37	chr1	228612994	228612994	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcggcgccttgccacccgtTgacttgcgcgcagtctgctt	3	10	12	16	6	1	1	0	1	1	0	1	1	1	1	3	1	3	3	3	1	0	4	rs61741017	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228612994T>C	ENST00000366696.1	-	1	32	c.33A>G	c.(31-33)tcA>tcG	p.S11S		NM_003493.2	NP_003484.1	Q16695	H31T_HUMAN	histone cluster 3, H3	11					telomere maintenance (GO:0000723)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(1)|lung(2)|prostate(2)|skin(1)	6		Prostate(94;0.0724)				TGCCACCCGTTGACTTGCGCG	0.652													c|||	80	0.0159744	0.0567	0.0058	5008	,	,		14474	0.0		0.001	False		,,,				2504	0.0				p.S11S		Atlas-SNP	.											.	HIST3H3	20	.	0			c.A33G						PASS	.	C		249,4147	735.3+/-410.7	1,247,1950	42	50	47		33	-7.2	0	1	dbSNP_129	47	0,8592		0,0,4296	no	coding-synonymous	HIST3H3	NM_003493.2		1,247,6246	CC,CT,TT		0.0,5.6642,1.9172		11/137	228612994	249,12739	2198	4296	6494	SO:0001819	synonymous_variant	8290	exon1			ACCCGTTGACTTG	Z49861	CCDS1572.1	1q42.13	2012-09-19	2006-10-11	2003-02-21	ENSG00000168148	ENSG00000168148		"Histones / Replication-dependent"	4778	protein-coding gene	gene with protein product		602820	"H3 histone family, member T", "histone 3, H3"	H3FT		8834248, 12408966	Standard	NM_003493		Approved	H3t, H3/g, H3.4	uc001hsx.1	Q16695	OTTHUMG00000040044	ENST00000366696.1:c.33A>G	1.37:g.228612994T>C		160	0	0		143	64	0.447552	NM_003493	B2R5K3|Q6FGU4	Silent	SNP	ENST00000366696.1	37	CCDS1572.1																																																																																			T|0.984;C|0.016	0.016	strong		0.652	HIST3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096595.2	NM_003493		C	228612994	T	C	228612994	2	2	22	1	0	0	0	0	0	0	0	1	7193	1799	63	3		3	HIST3H3	1	228612994	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	60	228612994	20637627	449	3350											
RAB4A	5867	hgsc.bcm.edu	37	chr1	229431613	229431613	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggtccgtgacgagaagttaTtaccgaggcgcggccggggc	8	6	17	10	6	0	2	0	1	0	1	1	4	1	2	3	5	1	1	3	5	3	2	rs114366150	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229431613T>C	ENST00000366690.4	+	4	454	c.246T>C	c.(244-246)taT>taC	p.Y82Y	RAB4A_ENST00000473894.1_3'UTR	NM_004578.2	NP_004569.2	P20338	RAB4A_HUMAN	RAB4A, member RAS oncogene family	82					antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|regulation of endocytosis (GO:0030100)|small GTPase mediated signal transduction (GO:0007264)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|protein transporter activity (GO:0008565)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|skin(1)	11	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.178)				CGAGAAGTTATTACCGAGGCG	0.522													T|||	9	0.00179712	0.0053	0.0029	5008	,	,		18011	0.0		0.0	False		,,,				2504	0.0				p.Y82Y	Esophageal Squamous(11;250 603 9619 16563)	Atlas-SNP	.											.	RAB4A	29	.	0			c.T246C						PASS	.	T		34,4372	39.2+/-71.8	0,34,2169	76	78	77		246	-5.4	0.8	1	dbSNP_132	77	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RAB4A	NM_004578.2		0,35,6468	CC,CT,TT		0.0116,0.7717,0.2691		82/219	229431613	35,12971	2203	4300	6503	SO:0001819	synonymous_variant	5867	exon4			AAGTTATTACCGA	BC004309	CCDS31050.1, CCDS73046.1	1q42-q43	2014-04-03		2002-02-28	ENSG00000168118	ENSG00000168118		"RAB, member RAS oncogene"	9781	protein-coding gene	gene with protein product		179511		RAB4			Standard	NM_004578		Approved	HRES-1/RAB4	uc001hth.4	P20338	OTTHUMG00000037627	ENST00000366690.4:c.246T>C	1.37:g.229431613T>C		68	0	0		96	41	0.427083	NM_004578	Q5T7P7|Q9BQ44	Silent	SNP	ENST00000366690.4	37	CCDS31050.1																																																																																			T|0.998;C|0.002	0.002	strong		0.522	RAB4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091727.3	NM_004578		C	229431613	T	C	229431613	2	2	22	1	0	0	0	0	0	0	0	1	12961	1500	52	3		3	RAB4A	1	229431613	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	818619	229431613	19819008	450	3351											
ACTA1	58	hgsc.bcm.edu	37	chr1	229567384	229567384	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatttgcgctccggcggggcGatgatctgcaagacagcgcg	7	8	15	11	6	1	2	0	1	1	1	2	3	2	2	1	3	3	2	1	3	2	2	rs74897770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229567384G>T	ENST00000366684.3	-	7	1098	c.996C>A	c.(994-996)atC>atA	p.I332I	ACTA1_ENST00000366683.2_Silent_p.I244I	NM_001100.3	NP_001091.1	P68133	ACTS_HUMAN	actin, alpha 1, skeletal muscle	332					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)				CCGGCGGGGCGATGATCTGCA	0.652													G|||	99	0.0197684	0.0734	0.0014	5008	,	,		13992	0.0		0.001	False		,,,				2504	0.0				p.I332I		Atlas-SNP	.											.	ACTA1	65	.	0			c.C996A						PASS	.	G		253,4153	146.5+/-181.1	10,233,1960	85	86	86		996	0.8	1	1	dbSNP_131	86	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ACTA1	NM_001100.3		10,235,6258	TT,TG,GG		0.0233,5.7422,1.9606		332/378	229567384	255,12751	2203	4300	6503	SO:0001819	synonymous_variant	58	exon7			CGGGGCGATGATC	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.996C>A	1.37:g.229567384G>T		119	0	0		99	43	0.434343	NM_001100	P02568|P99020|Q5T8M9	Silent	SNP	ENST00000366684.3	37	CCDS1578.1																																																																																			G|0.982;T|0.018	0.018	strong		0.652	ACTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092781.1	NM_001100		T	229567384	G	T	229567384	2	4	22	1	0	0	0	0	0	0	0	1	191	1048	37	4		4	ACTA1	1	229567384	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	135771	229567384	19683237	451	3352											
NUP133	55746	hgsc.bcm.edu	37	chr1	229622236	229622236	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtttctagaaaaaatgataGgaacaccaccacaggcacca	17	7	7	10	0	1	2	0	1	1	1	1	3	1	3	3	2	1	2	3	2	6	3	rs35442997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229622236G>A	ENST00000261396.3	-	11	1473	c.1382C>T	c.(1381-1383)cCt>cTt	p.P461L	NUP133_ENST00000537506.1_Missense_Mutation_p.P445L	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	461					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)				AAAAATGATAGGAACACCACC	0.368													G|||	50	0.00998403	0.0325	0.0043	5008	,	,		17685	0.0		0.002	False		,,,				2504	0.002				p.P461L		Atlas-SNP	.											.	NUP133	111	.	0			c.C1382T						PASS	.	G	LEU/PRO	141,4265	99.8+/-138.5	4,133,2066	92	93	93		1382	4.3	0.5	1	dbSNP_126	93	4,8596	4.3+/-15.6	0,4,4296	yes	missense	NUP133	NM_018230.2	98	4,137,6362	AA,AG,GG		0.0465,3.2002,1.1149	benign	461/1157	229622236	145,12861	2203	4300	6503	SO:0001583	missense	55746	exon11			ATGATAGGAACAC		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.1382C>T	1.37:g.229622236G>A	ENSP00000261396:p.Pro461Leu	146	0	0		176	74	0.420455	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Missense_Mutation	SNP	ENST00000261396.3	37	CCDS1579.1	23	0.010531135531135532	22	0.044715447154471545	0	0.0	0	0.0	1	0.0013192612137203166	G	18.11	3.549917	0.65311	0.032002	4.65E-4	ENSG00000069248	ENST00000366681;ENST00000261396;ENST00000366679;ENST00000537506	T;T;T	0.40225	1.04;1.04;1.04	5.21	4.3	0.51218	WD40/YVTN repeat-like-containing domain (1);	0.251116	0.47093	N	0.000247	T	0.14442	0.0349	M	0.65975	2.015	0.80722	D	1	P	0.47841	0.901	P	0.45276	0.475	T	0.15435	-1.0437	10	0.11485	T	0.65	-6.4934	13.9867	0.64339	0.0737:0.0:0.9263:0.0	rs35442997	461	Q8WUM0	NU133_HUMAN	L	461;461;461;445	ENSP00000261396:P461L;ENSP00000355640:P461L;ENSP00000443496:P445L	ENSP00000261396:P461L	P	-	2	0	NUP133	227688859	1.000000	0.71417	0.535000	0.28026	0.989000	0.77384	6.520000	0.73773	1.321000	0.45227	0.467000	0.42956	CCT	G|0.990;A|0.010	0.010	strong		0.368	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230		A	229622236	G	A	229622236	3	1	22	1	0	0	0	0	1	0	0	0	10763	1000	35	2	2152	2	NUP133	1	229622236	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	54852	229622236	19628385	452	3353											
NUP133	55746	hgsc.bcm.edu	37	chr1	229636561	229636561	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagagccactaagtcggcaCtccagtggaaatcactaggt	14	7	10	10	1	1	1	1	0	0	1	3	2	2	2	2	3	1	1	2	3	4	2	rs75411588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229636561C>T	ENST00000261396.3	-	4	546	c.455G>A	c.(454-456)aGt>aAt	p.S152N	NUP133_ENST00000537506.1_Missense_Mutation_p.S136N|NUP133_ENST00000366678.3_Missense_Mutation_p.S152N	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	152					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)				TAAGTCGGCACTCCAGTGGAA	0.388													C|||	163	0.0325479	0.1135	0.0115	5008	,	,		19355	0.0		0.003	False		,,,				2504	0.002				p.S152N		Atlas-SNP	.											.	NUP133	111	.	0			c.G455A						PASS	.	C	ASN/SER	400,4006	198.4+/-222.2	12,376,1815	59	58	58		455	2	0.7	1	dbSNP_131	58	7,8593	6.4+/-24.3	0,7,4293	yes	missense	NUP133	NM_018230.2	46	12,383,6108	TT,TC,CC		0.0814,9.0785,3.1293	benign	152/1157	229636561	407,12599	2203	4300	6503	SO:0001583	missense	55746	exon4			TCGGCACTCCAGT		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.455G>A	1.37:g.229636561C>T	ENSP00000261396:p.Ser152Asn	55	0	0		77	38	0.493506	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Missense_Mutation	SNP	ENST00000261396.3	37	CCDS1579.1	46	0.021062271062271064	42	0.08536585365853659	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	C	9.530	1.110704	0.20714	0.090785	8.14E-4	ENSG00000069248	ENST00000366681;ENST00000261396;ENST00000366679;ENST00000537506;ENST00000366678	T;T;T;T	0.23754	1.89;1.89;1.89;1.89	5.93	1.98	0.26296	WD40/YVTN repeat-like-containing domain (1);Nucleoporin, Nup133/Nup155-like, N-terminal (1);	0.372720	0.33813	N	0.004533	T	0.00524	0.0017	L	0.32530	0.975	0.47214	D	0.999358	B	0.09022	0.002	B	0.08055	0.003	T	0.21042	-1.0257	10	0.16420	T	0.52	-7.1368	6.2296	0.20728	0.0:0.558:0.1243:0.3178	.	152	Q8WUM0	NU133_HUMAN	N	152;152;152;136;152	ENSP00000261396:S152N;ENSP00000355640:S152N;ENSP00000443496:S136N;ENSP00000355639:S152N	ENSP00000261396:S152N	S	-	2	0	NUP133	227703184	0.996000	0.38824	0.673000	0.29887	0.384000	0.30261	0.731000	0.26058	0.845000	0.35118	0.557000	0.71058	AGT	C|0.972;T|0.028	0.028	strong		0.388	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230		T	229636561	C	T	229636561	3	4	22	1	0	0	0	0	1	0	0	0	10763	565	20	2	3107	2	NUP133	1	229636561	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	14325	229636561	19614060	453	3354											
TAF5L	27097	hgsc.bcm.edu	37	chr1	229750089	229750089	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacgagcccccaccattaccTgttagattggccgccatctc	8	9	8	16	2	1	1	0	0	1	1	2	3	1	1	6	1	2	1	6	1	2	3	rs144626601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229750089T>C	ENST00000366676.1	-	1	140	c.141A>G	c.(139-141)acA>acG	p.T47T	TAF5L_ENST00000477957.1_5'UTR|TAF5L_ENST00000258281.2_Splice_Site_p.T47T|TAF5L_ENST00000366675.3_Splice_Site_p.T47T|TAF5L_ENST00000366674.1_Silent_p.T47T			O75529	TAF5L_HUMAN	TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa	47					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|transcription from RNA polymerase II promoter (GO:0006366)	STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)	11	Breast(184;0.193)|Ovarian(103;0.249)	Prostate(94;0.167)				CACCATTACCTGTTAGATTGG	0.557													T|||	17	0.00339457	0.0129	0.0	5008	,	,		20513	0.0		0.0	False		,,,				2504	0.0				p.T47T		Atlas-SNP	.											.	TAF5L	76	.	0			c.A141G						PASS	.	T	,	51,4355	53.6+/-89.4	0,51,2152	105	95	99		141,141	3.5	1	1	dbSNP_134	99	0,8600		0,0,4300	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	TAF5L	NM_001025247.1,NM_014409.3	,	0,51,6452	CC,CT,TT		0.0,1.1575,0.3921	,	47/326,47/590	229750089	51,12955	2203	4300	6503	SO:0001630	splice_region_variant	27097	exon2			ATTACCTGTTAGA	AF069736	CCDS1581.1, CCDS31051.1	1q42.11-q42.3	2013-01-10	2002-08-29		ENSG00000135801	ENSG00000135801		"WD repeat domain containing"	17304	protein-coding gene	gene with protein product	"PCAF associated factor 65 beta"		"TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65 kD"			9674425, 11124703	Standard	XM_005273100		Approved	PAF65B	uc001htq.3	O75529	OTTHUMG00000039463	ENST00000366676.1:c.142+1A>G	1.37:g.229750089T>C		136	0	0		156	65	0.416667	NM_001025247	Q5TDI5|Q5TDI6|Q8IW31	Silent	SNP	ENST00000366676.1	37	CCDS1581.1																																																																																			T|0.997;C|0.003	0.003	strong		0.557	TAF5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095229.1	NM_014409	Silent	C	229750089	T	C	229750089	5	2	22	1	0	0	0	0	0	0	1	0	15544	1594	55	3	1650	3	TAF5L	1	229750089	Splice_Site	SNP	T	TCGA-G8-6324-01A-11D-2210-10	113528	229750089	19500532	454	3355											
URB2	9816	hgsc.bcm.edu	37	chr1	229770827	229770827	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctgagccagctttgctggtCggcctgcaggcagcccgaag	6	7	15	13	2	0	1	0	1	0	0	1	2	0	1	3	3	5	5	3	3	1	1	rs115641620	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229770827C>T	ENST00000258243.2	+	4	603	c.467C>T	c.(466-468)tCg>tTg	p.S156L		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	156						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						CTTTGCTGGTCGGCCTGCAGG	0.587													C|||	43	0.00858626	0.0318	0.0014	5008	,	,		21011	0.0		0.0	False		,,,				2504	0.0				p.S156L		Atlas-SNP	.											.	URB2	152	.	0			c.C467T						PASS	.	C	LEU/SER	113,4293	87.8+/-126.4	1,111,2091	62	53	56		467	-7.6	0	1	dbSNP_132	56	1,8599		0,1,4299	no	missense	URB2	NM_014777.2	145	1,112,6390	TT,TC,CC		0.0116,2.5647,0.8765	benign	156/1525	229770827	114,12892	2203	4300	6503	SO:0001583	missense	9816	exon4			GCTGGTCGGCCTG	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.467C>T	1.37:g.229770827C>T	ENSP00000258243:p.Ser156Leu	108	0	0		117	62	0.529915	NM_014777	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	C	0.017	-1.506370	0.00992	0.025647	1.16E-4	ENSG00000135763	ENST00000258243	T	0.09911	2.93	5.68	-7.55	0.01327	.	0.884065	0.09779	N	0.756927	T	0.01558	0.0050	N	0.04994	-0.135	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40251	-0.9573	9	.	.	.	-0.0083	19.9267	0.97106	0.0:0.1135:0.0:0.8865	.	156	Q14146	URB2_HUMAN	L	156	ENSP00000258243:S156L	.	S	+	2	0	URB2	227837450	0.045000	0.20229	0.000000	0.03702	0.006000	0.05464	0.359000	0.20233	-1.352000	0.02194	-1.684000	0.00734	TCG	C|0.992;T|0.008	0.008	strong		0.587	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777		T	229770827	C	T	229770827	3	4	22	1	0	0	0	0	1	0	0	0	17040	893	31	1	477	1	URB2	1	229770827	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	20738	229770827	19479794	455	3356											
URB2	9816	hgsc.bcm.edu	37	chr1	229772285	229772285	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aggtgttgctctggagatctCgaacctcccttcgttgctcc	5	13	10	13	2	2	1	0	0	2	1	6	3	4	1	3	2	3	4	3	2	1	3	rs115230066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229772285C>T	ENST00000258243.2	+	4	2061	c.1925C>T	c.(1924-1926)tCg>tTg	p.S642L		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	642						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						CTGGAGATCTCGAACCTCCCT	0.468													C|||	6	0.00119808	0.0045	0.0	5008	,	,		21056	0.0		0.0	False		,,,				2504	0.0				p.S642L		Atlas-SNP	.											.	URB2	152	.	0			c.C1925T						PASS	.	C	LEU/SER	10,4396	16.8+/-37.8	0,10,2193	206	212	210		1925	2.9	0	1	dbSNP_132	210	0,8600		0,0,4300	yes	missense	URB2	NM_014777.2	145	0,10,6493	TT,TC,CC		0.0,0.227,0.0769	possibly-damaging	642/1525	229772285	10,12996	2203	4300	6503	SO:0001583	missense	9816	exon4			AGATCTCGAACCT	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.1925C>T	1.37:g.229772285C>T	ENSP00000258243:p.Ser642Leu	215	0	0		253	130	0.513834	NM_014777	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	6.986	0.551949	0.13374	0.00227	0.0	ENSG00000135763	ENST00000258243	T	0.31769	1.48	4.79	2.91	0.33838	.	1.112010	0.06634	N	0.759866	T	0.26593	0.0650	L	0.51422	1.61	0.09310	N	1	B	0.18968	0.032	B	0.08055	0.003	T	0.21895	-1.0232	9	.	.	.	-2.6001	4.7928	0.13257	0.0:0.4546:0.297:0.2483	.	642	Q14146	URB2_HUMAN	L	642	ENSP00000258243:S642L	.	S	+	2	0	URB2	227838908	0.001000	0.12720	0.002000	0.10522	0.001000	0.01503	1.070000	0.30653	1.391000	0.46566	-0.157000	0.13467	TCG	C|0.999;T|0.001	0.001	strong		0.468	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777		T	229772285	C	T	229772285	3	4	22	1	0	0	0	0	1	0	0	0	17040	893	31	1	1935	1	URB2	1	229772285	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1458	229772285	19478336	456	3357											
URB2	9816	hgsc.bcm.edu	37	chr1	229783328	229783328	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggcctgtcttagatgtcctGgctgcactgctgcggcaggg	4	10	16	11	1	1	1	0	0	1	1	2	1	2	1	2	4	3	4	2	4	1	1	rs115914317	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229783328G>C	ENST00000258243.2	+	7	4114	c.3978G>C	c.(3976-3978)ctG>ctC	p.L1326L		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	1326						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						TAGATGTCCTGGCTGCACTGC	0.552													G|||	17	0.00339457	0.0129	0.0	5008	,	,		17934	0.0		0.0	False		,,,				2504	0.0				p.L1326L		Atlas-SNP	.											.	URB2	152	.	0			c.G3978C						PASS	.	G		51,4355	53.6+/-89.4	0,51,2152	78	71	73		3978	4.7	1	1	dbSNP_132	73	0,8600		0,0,4300	no	coding-synonymous	URB2	NM_014777.2		0,51,6452	CC,CG,GG		0.0,1.1575,0.3921		1326/1525	229783328	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	9816	exon7			TGTCCTGGCTGCA	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.3978G>C	1.37:g.229783328G>C		163	0	0		147	76	0.517007	NM_014777	Q5VYC9	Silent	SNP	ENST00000258243.2	37	CCDS31052.1																																																																																			G|0.997;C|0.003	0.003	strong		0.552	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777		C	229783328	G	C	229783328	2	2	22	1	0	0	0	0	0	0	0	1	17040	1335	47	4		4	URB2	1	229783328	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	11043	229783328	19467293	457	3358											
URB2	9816	hgsc.bcm.edu	37	chr1	229783361	229783361	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cggcagggggaggaggccatCggcaacccccaccacgtcag	9	2	15	15	3	1	0	1	0	0	0	2	2	1	2	4	6	1	2	4	6	1	0	rs137900306	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229783361C>T	ENST00000258243.2	+	7	4147	c.4011C>T	c.(4009-4011)atC>atT	p.I1337I		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	1337						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						AGGAGGCCATCGGCAACCCCC	0.612													C|||	5	0.000998403	0.0038	0.0	5008	,	,		14676	0.0		0.0	False		,,,				2504	0.0				p.I1337I		Atlas-SNP	.											.	URB2	152	.	0			c.C4011T						PASS	.	C		11,4395	17.9+/-39.9	0,11,2192	90	74	79		4011	-0.1	0.1	1	dbSNP_134	79	0,8600		0,0,4300	no	coding-synonymous	URB2	NM_014777.2		0,11,6492	TT,TC,CC		0.0,0.2497,0.0846		1337/1525	229783361	11,12995	2203	4300	6503	SO:0001819	synonymous_variant	9816	exon7			GGCCATCGGCAAC	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.4011C>T	1.37:g.229783361C>T		168	0	0		142	74	0.521127	NM_014777	Q5VYC9	Silent	SNP	ENST00000258243.2	37	CCDS31052.1																																																																																			C|0.999;T|0.001	0.001	strong		0.612	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777		T	229783361	C	T	229783361	2	4	22	1	0	0	0	0	0	0	0	1	17040	874	31	1		1	URB2	1	229783361	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	33	229783361	19467260	458	3359											
URB2	9816	hgsc.bcm.edu	37	chr1	229787055	229787055	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcagttatgcgggaagggcGgcagaaggacaaaggtaatt	13	8	15	5	2	1	1	1	0	0	1	1	3	1	3	0	5	1	3	0	5	5	4	rs41310553	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229787055G>A	ENST00000258243.2	+	8	4359	c.4223G>A	c.(4222-4224)cGg>cAg	p.R1408Q		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	1408						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						CGGGAAGGGCGGCAGAAGGAC	0.388													G|||	41	0.0081869	0.0083	0.0159	5008	,	,		17462	0.0		0.0139	False		,,,				2504	0.0051				p.R1408Q		Atlas-SNP	.											.	URB2	152	.	0			c.G4223A						PASS	.	G	GLN/ARG	58,4348	56.8+/-93.2	0,58,2145	87	84	85		4223	4.9	1	1	dbSNP_127	85	149,8451	72.9+/-135.5	1,147,4152	yes	missense	URB2	NM_014777.2	43	1,205,6297	AA,AG,GG		1.7326,1.3164,1.5916	probably-damaging	1408/1525	229787055	207,12799	2203	4300	6503	SO:0001583	missense	9816	exon8			AAGGGCGGCAGAA	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.4223G>A	1.37:g.229787055G>A	ENSP00000258243:p.Arg1408Gln	121	0	0		115	63	0.547826	NM_014777	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	20	0.009157509157509158	3	0.006097560975609756	7	0.019337016574585635	0	0.0	10	0.013192612137203167	G	25.7	4.661699	0.88154	0.013164	0.017326	ENSG00000135763	ENST00000258243;ENST00000434387	T;T	0.45668	0.89;0.89	5.78	4.86	0.63082	Nucleolar 27S pre-rRNA processing, Urb2/Npa2, C-terminal (1);	0.116848	0.53938	D	0.000042	T	0.46210	0.1381	M	0.69823	2.125	0.40363	D	0.97926	D	0.89917	1.0	D	0.69824	0.966	T	0.59968	-0.7354	9	.	.	.	-18.2991	14.7398	0.69445	0.0695:0.0:0.9305:0.0	rs41310553	1408	Q14146	URB2_HUMAN	Q	1408;24	ENSP00000258243:R1408Q;ENSP00000395107:R24Q	.	R	+	2	0	URB2	227853678	0.967000	0.33354	0.971000	0.41717	0.989000	0.77384	5.262000	0.65501	1.435000	0.47434	0.655000	0.94253	CGG	G|0.986;A|0.014	0.014	strong		0.388	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777		A	229787055	G	A	229787055	3	1	22	1	0	0	0	0	1	0	0	0	17040	1116	39	1	4249	1	URB2	1	229787055	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3694	229787055	19463566	459	3360											
GALNT2	2590	hgsc.bcm.edu	37	chr1	230391058	230391058	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cggaagcagcacccctacacGttcccgggtggcagtggcac	8	5	13	15	3	0	0	0	0	0	0	1	1	1	1	3	4	3	5	3	4	2	2	rs75919037	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:230391058G>A	ENST00000366672.4	+	11	1176	c.1104G>A	c.(1102-1104)acG>acA	p.T368T	GALNT2_ENST00000541865.1_Missense_Mutation_p.V244I|GALNT2_ENST00000543760.1_Silent_p.T330T	NM_004481.3	NP_004472.1	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2	368					cellular protein metabolic process (GO:0044267)|immunoglobulin biosynthetic process (GO:0002378)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(5)|skin(2)	32	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				ACCCCTACACGTTCCCGGGTG	0.587													G|||	10	0.00199681	0.0076	0.0	5008	,	,		19672	0.0		0.0	False		,,,				2504	0.0				p.T368T		Atlas-SNP	.											GALNT2,ear,carcinoma,+1,1	GALNT2	83	1	0			c.G1104A						PASS	.	G		42,4364	45.3+/-79.5	0,42,2161	173	129	144		1104	-8.4	0.7	1	dbSNP_132	144	0,8600		0,0,4300	no	coding-synonymous	GALNT2	NM_004481.3		0,42,6461	AA,AG,GG		0.0,0.9532,0.3229		368/572	230391058	42,12964	2203	4300	6503	SO:0001819	synonymous_variant	2590	exon11			CTACACGTTCCCG	BC041120	CCDS1582.1	1q41-q42	2014-03-13	2014-03-13		ENSG00000143641	ENSG00000143641	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4124	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 2"	602274	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)"			9592121, 7592619	Standard	NM_004481		Approved	GalNAc-T2	uc010pwa.1	Q10471	OTTHUMG00000037771	ENST00000366672.4:c.1104G>A	1.37:g.230391058G>A		133	0	0		115	69	0.6	NM_004481	A8K1Y3|B7Z8V8|C5HU00|Q9NPY4	Silent	SNP	ENST00000366672.4	37	CCDS1582.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	2.687	-0.274072	0.05679	0.009532	0.0	ENSG00000143641	ENST00000541865	T	0.41065	1.01	4.97	-8.41	0.00961	.	.	.	.	.	T	0.19525	0.0469	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.35847	-0.9772	6	0.59425	D	0.04	.	1.101	0.01683	0.1909:0.2919:0.1871:0.3301	.	.	.	.	I	244	ENSP00000444346:V244I	ENSP00000444346:V244I	V	+	1	0	GALNT2	228457681	0.000000	0.05858	0.694000	0.30210	0.977000	0.68977	-2.466000	0.00994	-1.729000	0.01364	-0.244000	0.11960	GTT	G|0.996;A|0.004	0.004	strong		0.587	GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092158.1	NM_004481		A	230391058	G	A	230391058	2	1	22	1	0	0	0	0	0	0	0	1	6221	1132	40	1		1	GALNT2	1	230391058	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	604003	230391058	18859563	460	3361											
COG2	22796	hgsc.bcm.edu	37	chr1	230796533	230796533	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gacaaagccctcaaccagctTtctgtgcctttgggacaatt	10	11	8	12	0	2	0	1	0	1	0	2	2	2	1	3	1	4	1	3	1	3	3	rs16852160	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:230796533T>G	ENST00000366669.4	+	3	379	c.264T>G	c.(262-264)ctT>ctG	p.L88L	COG2_ENST00000535166.1_5'UTR|COG2_ENST00000534989.1_Silent_p.L29L|COG2_ENST00000366668.3_Silent_p.L88L	NM_001145036.1|NM_007357.2	NP_001138508.1|NP_031383.1	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2	88					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)				TCAACCAGCTTTCTGTGCCTT	0.423													T|||	161	0.0321486	0.1127	0.0115	5008	,	,		16141	0.001		0.001	False		,,,				2504	0.002				p.L88L		Atlas-SNP	.											.	COG2	61	.	0			c.T264G						PASS	.	T	,	436,3970	208.8+/-229.8	20,396,1787	221	178	193		264,264	-0.9	1	1	dbSNP_123	193	13,8587	9.1+/-34.3	0,13,4287	no	coding-synonymous,coding-synonymous	COG2	NM_001145036.1,NM_007357.2	,	20,409,6074	GG,GT,TT		0.1512,9.8956,3.4523	,	88/738,88/739	230796533	449,12557	2203	4300	6503	SO:0001819	synonymous_variant	22796	exon3			CCAGCTTTCTGTG	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.264T>G	1.37:g.230796533T>G		232	0	0		245	105	0.428571	NM_007357	Q86U99	Silent	SNP	ENST00000366669.4	37	CCDS1584.1																																																																																			T|0.962;G|0.038	0.038	strong		0.423	COG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092087.1	NM_007357		G	230796533	T	G	230796533	2	3	22	1	0	0	0	0	0	0	0	1	3660	1828	64	5		5	COG2	1	230796533	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	405475	230796533	18454088	461	3362											
COG2	22796	hgsc.bcm.edu	37	chr1	230810756	230810756	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttacagtgaaaaaggcaaTactgttcctggatatgactt	13	14	8	6	0	0	2	0	2	0	0	1	3	1	3	1	2	2	2	1	2	6	6	rs6681346	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:230810756T>A	ENST00000366669.4	+	9	1027	c.912T>A	c.(910-912)aaT>aaA	p.N304K	COG2_ENST00000535166.1_Missense_Mutation_p.N188K|COG2_ENST00000534989.1_Missense_Mutation_p.N245K|COG2_ENST00000366668.3_Missense_Mutation_p.N304K	NM_001145036.1|NM_007357.2	NP_001138508.1|NP_031383.1	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2	304			N -> K (in dbSNP:rs6681346).		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)				AAAAAGGCAATACTGTTCCTG	0.368													T|||	475	0.0948482	0.2156	0.0231	5008	,	,		16747	0.0625		0.0159	False		,,,				2504	0.0971				p.N304K		Atlas-SNP	.											.	COG2	61	.	0			c.T912A						PASS	.	T	LYS/ASN,LYS/ASN	793,3613	316.9+/-294.8	78,637,1488	127	136	133		912,912	-2.2	0.3	1	dbSNP_116	133	90,8510	51.1+/-111.2	1,88,4211	yes	missense,missense	COG2	NM_001145036.1,NM_007357.2	94,94	79,725,5699	AA,AT,TT		1.0465,17.9982,6.7892	benign,benign	304/738,304/739	230810756	883,12123	2203	4300	6503	SO:0001583	missense	22796	exon9			AGGCAATACTGTT	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.912T>A	1.37:g.230810756T>A	ENSP00000355629:p.Asn304Lys	104	0	0		101	49	0.485149	NM_007357	Q86U99	Missense_Mutation	SNP	ENST00000366669.4	37	CCDS1584.1	154	0.07051282051282051	104	0.21138211382113822	8	0.022099447513812154	34	0.05944055944055944	8	0.010554089709762533	T	11.50	1.658121	0.29425	0.179982	0.010465	ENSG00000135775	ENST00000366669;ENST00000535166;ENST00000366668;ENST00000534989	T;T;T;T	0.27256	1.68;1.68;1.68;1.68	5.92	-2.23	0.06930	.	0.182059	0.56097	D	0.000023	T	0.00012	0.0000	L	0.47716	1.5	0.21355	P	0.999712339	B;B	0.26195	0.144;0.045	B;B	0.18263	0.021;0.021	T	0.40021	-0.9585	9	0.07990	T	0.79	-16.6064	11.4718	0.50272	0.0:0.3913:0.0:0.6087	rs6681346;rs17848117;rs52807515;rs6681346	304;304	Q86U99;Q14746	.;COG2_HUMAN	K	304;188;304;245	ENSP00000355629:N304K;ENSP00000445724:N188K;ENSP00000355628:N304K;ENSP00000440349:N245K	ENSP00000355628:N304K	N	+	3	2	COG2	228877379	0.753000	0.28349	0.277000	0.24703	0.994000	0.84299	0.099000	0.15210	-0.398000	0.07679	0.533000	0.62120	AAT	T|0.922;A|0.078	0.078	strong		0.368	COG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092087.1	NM_007357		A	230810756	T	A	230810756	3	1	22	1	0	0	0	0	1	0	0	0	3660	1403	49	5	946	5	COG2	1	230810756	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	14223	230810756	18439865	462	3363											
AGT	183	hgsc.bcm.edu	37	chr1	230846305	230846305	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgcggccctcaacttgtcttCggtgtcaagttttgcagcga	6	13	11	11	3	3	0	2	0	1	0	4	1	3	0	1	2	4	2	1	2	2	4	rs11568032	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:230846305C>T	ENST00000366667.4	-	2	506	c.292G>A	c.(292-294)Gaa>Aaa	p.E98K	RP11-99J16__A.2_ENST00000412344.1_RNA	NM_000029.3	NP_000020.1	P01019	ANGT_HUMAN	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	98			E -> K (in dbSNP:rs11568032).		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)		AACTTGTCTTCGGTGTCAAGT	0.562													C|||	17	0.00339457	0.0113	0.0029	5008	,	,		21719	0.0		0.0	False		,,,				2504	0.0				p.E98K		Atlas-SNP	.											.	AGT	62	.	0			c.G292A						PASS	.	C	LYS/GLU	62,4344	58.1+/-94.6	0,62,2141	90	88	89		292	4.2	0	1	dbSNP_120	89	0,8600		0,0,4300	yes	missense	AGT	NM_000029.3	56	0,62,6441	TT,TC,CC		0.0,1.4072,0.4767	benign	98/486	230846305	62,12944	2203	4300	6503	SO:0001583	missense	183	exon2			TGTCTTCGGTGTC	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.292G>A	1.37:g.230846305C>T	ENSP00000355627:p.Glu98Lys	193	0	0		183	86	0.469945	NM_000029	Q16358|Q16359|Q96F91	Missense_Mutation	SNP	ENST00000366667.4	37	CCDS1585.1	9	0.004120879120879121	7	0.014227642276422764	2	0.0055248618784530384	0	0.0	0	0.0	C	8.409	0.843741	0.16963	0.014072	0.0	ENSG00000135744	ENST00000366667;ENST00000430091	D	0.87412	-2.25	5.09	4.18	0.49190	Serpin domain (1);	0.637587	0.16103	N	0.229456	T	0.73621	0.3610	M	0.62723	1.935	0.09310	N	1	P;P;P	0.40794	0.685;0.729;0.685	B;B;B	0.29785	0.107;0.101;0.107	T	0.66135	-0.5999	10	0.23302	T	0.38	.	5.7631	0.18211	0.1411:0.6438:0.1367:0.0785	rs11568032;rs52801258;rs59896600;rs11568032	98;98;98	B0ZBE2;B2R5S1;P01019	.;.;ANGT_HUMAN	K	98	ENSP00000355627:E98K	ENSP00000355627:E98K	E	-	1	0	AGT	228912928	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	0.721000	0.25911	1.276000	0.44395	0.491000	0.48974	GAA	C|0.994;T|0.006	0.006	strong		0.562	AGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092102.1	NM_000029		T	230846305	C	T	230846305	3	4	22	1	0	0	0	0	1	0	0	0	399	893	31	1	1181	1	AGT	1	230846305	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	35549	230846305	18404316	463	3364											
CAPN9	10753	hgsc.bcm.edu	37	chr1	230916057	230916057	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagatttggtgccaatgtgcTgacaatcggctatgccattt	9	13	11	8	1	0	2	0	1	0	1	1	3	0	2	2	2	3	2	2	2	3	3	rs79844715	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:230916057T>G	ENST00000271971.2	+	10	1360	c.1247T>G	c.(1246-1248)cTg>cGg	p.L416R	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.L353R|CAPN9_ENST00000354537.1_Missense_Mutation_p.L390R	NM_006615.2	NP_006606.1	O14815	CAN9_HUMAN	calpain 9	416	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)				GCCAATGTGCTGACAATCGGC	0.483													T|||	7	0.00139776	0.0045	0.0014	5008	,	,		17721	0.0		0.0	False		,,,				2504	0.0				p.L416R		Atlas-SNP	.											.	CAPN9	116	.	0			c.T1247G						PASS	.	T	ARG/LEU,ARG/LEU	23,4383	29.9+/-59.1	0,23,2180	124	112	116		1247,1169	5.5	1	1	dbSNP_131	116	0,8600		0,0,4300	yes	missense,missense	CAPN9	NM_006615.2,NM_016452.1	102,102	0,23,6480	GG,GT,TT		0.0,0.522,0.1768	probably-damaging,probably-damaging	416/691,390/665	230916057	23,12983	2203	4300	6503	SO:0001583	missense	10753	exon10			ATGTGCTGACAAT	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.1247T>G	1.37:g.230916057T>G	ENSP00000271971:p.Leu416Arg	136	0	0		148	71	0.47973	NM_006615	B1APS1|B1AQI0|Q9NS74	Missense_Mutation	SNP	ENST00000271971.2	37	CCDS1586.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	T	10.03	1.239188	0.22711	0.00522	0.0	ENSG00000135773	ENST00000271971;ENST00000354537;ENST00000366666	D;D;D	0.88586	-2.4;-2.4;-2.4	5.54	5.54	0.83059	Peptidase C2, calpain, large subunit, domain III (2);Peptidase C2, calpain, domain III (1);	0.197529	0.44483	D	0.000444	D	0.92691	0.7677	M	0.88241	2.94	0.58432	D	0.999996	D;D;D	0.67145	0.996;0.991;0.993	D;P;P	0.64410	0.925;0.793;0.869	D	0.92319	0.5864	10	0.31617	T	0.26	.	15.3798	0.74645	0.0:0.0:0.0:1.0	.	353;390;416	E7ESS6;O14815-2;O14815	.;.;CAN9_HUMAN	R	416;390;353	ENSP00000271971:L416R;ENSP00000346538:L390R;ENSP00000355626:L353R	ENSP00000271971:L416R	L	+	2	0	CAPN9	228982680	1.000000	0.71417	0.998000	0.56505	0.017000	0.09413	3.833000	0.55790	2.112000	0.64535	0.524000	0.50904	CTG	T|0.998;G|0.002	0.002	strong		0.483	CAPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092179.1	NM_006615		G	230916057	T	G	230916057	3	3	22	1	0	0	0	0	1	0	0	0	2634	1580	55	5	1285	5	CAPN9	1	230916057	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	69752	230916057	18334564	464	3365											
TRIM67	440730	hgsc.bcm.edu	37	chr1	231298970	231298970	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgcaggcgggagtgcagcTggcggcctcggcggcggtgc	3	5	22	11	5	0	0	0	0	0	0	1	1	0	1	1	8	4	3	1	8	0	0	rs372035563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:231298970T>C	ENST00000366653.5	+	1	255	c.255T>C	c.(253-255)gcT>gcC	p.A85A	TRIM67_ENST00000366652.2_Silent_p.A85A|TRIM67_ENST00000444294.3_Silent_p.A85A|TRIM67_ENST00000449018.3_Silent_p.A45A			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67	85	Gly-rich.				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)				GGAGTGCAGCTGGCGGCCTCG	0.756													T|||	20	0.00399361	0.0151	0.0	5008	,	,		9536	0.0		0.0	False		,,,				2504	0.0				p.A85A		Atlas-SNP	.											.	TRIM67	160	.	0			c.T255C						PASS	.	T		1,2915		0,1,1457	2	2	2		255	-8.1	0	1		2	0,6030		0,0,3015	no	coding-synonymous	TRIM67	NM_001004342.3		0,1,4472	CC,CT,TT		0.0,0.0343,0.0112		85/784	231298970	1,8945	1458	3015	4473	SO:0001819	synonymous_variant	440730	exon1			TGCAGCTGGCGGC	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.255T>C	1.37:g.231298970T>C		11	0	0		17	5	0.294118	NM_001004342	Q5TER7|Q5TER8|Q7Z4K7	Silent	SNP	ENST00000366653.5	37	CCDS44333.1																																																																																			.	.	none		0.756	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	NM_001004342		C	231298970	T	C	231298970	2	2	22	1	0	0	0	0	0	0	0	1	16555	1567	55	3		3	TRIM67	1	231298970	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	382913	231298970	17951651	465	3366											
EXOC8	149371	hgsc.bcm.edu	37	chr1	231472916	231472916	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgggccatgtggtccgcatcGtattccactaggtccccatt	6	12	10	13	2	0	0	0	0	0	0	4	0	3	0	5	3	0	2	5	3	2	4	rs73116365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:231472916G>A	ENST00000360394.2	-	1	662	c.576C>T	c.(574-576)taC>taT	p.Y192Y	SPRTN_ENST00000391858.4_5'UTR|SPRTN_ENST00000008440.9_5'Flank|EXOC8_ENST00000366645.1_Silent_p.Y188Y|SPRTN_ENST00000295050.7_5'Flank	NM_175876.3	NP_787072.2	Q8IYI6	EXOC8_HUMAN	exocyst complex component 8	192	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)				GGTCCGCATCGTATTCCACTA	0.587													G|||	77	0.0153754	0.0537	0.0072	5008	,	,		17457	0.0		0.001	False		,,,				2504	0.0				p.Y192Y		Atlas-SNP	.											.	EXOC8	42	.	0			c.C576T						PASS	.	G		215,4191	130.2+/-166.9	7,201,1995	77	66	70		576	1.2	1	1	dbSNP_130	70	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	EXOC8	NM_175876.3		7,203,6293	AA,AG,GG		0.0233,4.8797,1.6685		192/726	231472916	217,12789	2203	4300	6503	SO:0001819	synonymous_variant	149371	exon1			CGCATCGTATTCC	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.576C>T	1.37:g.231472916G>A		95	0	0		108	53	0.490741	NM_175876	B3KU33|Q5TE82	Silent	SNP	ENST00000360394.2	37	CCDS1593.1																																																																																			G|0.983;A|0.017	0.017	strong		0.587	EXOC8-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_175876		A	231472916	G	A	231472916	2	1	22	1	0	0	0	0	0	0	0	1	5313	1140	40	1		1	EXOC8	1	231472916	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	173946	231472916	17777705	466	3367											
C1orf124	83932	hgsc.bcm.edu	37	chr1	231487133	231487133	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccgtgccagcacaggccaccGtattacggctatgtcaaacg	10	7	10	14	4	1	0	1	0	0	0	1	0	1	0	4	2	4	3	4	2	4	3	rs73116379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:231487133G>A	ENST00000295050.7	+	4	870	c.534G>A	c.(532-534)ccG>ccA	p.P178P	SPRTN_ENST00000391858.4_Silent_p.P178P|SPRTN_ENST00000008440.9_Silent_p.P135P|SPRTN_ENST00000469904.1_3'UTR	NM_001010984.2|NM_032018.5	NP_001010984.1|NP_114407.3	Q9H040	SPRTN_HUMAN	SprT-like N-terminal domain	178	SprT-like.				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)										ACAGGCCACCGTATTACGGCT	0.512													G|||	76	0.0151757	0.053	0.0072	5008	,	,		14878	0.0		0.001	False		,,,				2504	0.0				p.P178P		Atlas-SNP	.											.	.	.	.	0			c.G534A						PASS	.	G	,	218,4188	131.4+/-167.9	7,204,1992	68	67	68		534,534	-11.5	0	1	dbSNP_130	68	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	C1orf124	NM_001010984.1,NM_032018.4	,	7,207,6289	AA,AG,GG		0.0349,4.9478,1.6992	,	178/251,178/490	231487133	221,12785	2203	4300	6503	SO:0001819	synonymous_variant	83932	exon4			GCCACCGTATTAC	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.534G>A	1.37:g.231487133G>A		95	0	0		104	48	0.461538	NM_032018	B1AKT0|B5MEF7|Q5TE78|Q6UWW6|Q96BC5|Q96KA0	Silent	SNP	ENST00000295050.7	37	CCDS1594.1																																																																																			G|0.983;A|0.017	0.017	strong		0.512	SPRTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092858.1	NM_032018		A	231487133	G	A	231487133	2	1	22	1	0	0	0	0	0	0	0	1	1994	1132	40	1		1	C1orf124	1	231487133	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	14217	231487133	17763488	467	3368											
SIPA1L2	57568	hgsc.bcm.edu	37	chr1	232575051	232575051	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cctgccaggtgcacagggccGaggatggtggcaggcatgca	8	5	17	11	1	0	0	0	0	0	0	0	2	0	1	3	6	3	4	3	6	0	0	rs189356281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:232575051G>A	ENST00000366630.1	-	14	4192	c.3834C>T	c.(3832-3834)ctC>ctT	p.L1278L	SIPA1L2_ENST00000308942.4_Silent_p.L352L|SIPA1L2_ENST00000262861.4_Silent_p.L1278L			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	1278					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)				GCACAGGGCCGAGGATGGTGG	0.667													G|||	21	0.00419329	0.0144	0.0	5008	,	,		18627	0.0		0.002	False		,,,				2504	0.0				p.L1278L		Atlas-SNP	.											SIPA1L2,colon,carcinoma,-2,1	SIPA1L2	218	1	0			c.C3834T						scavenged	.	G		77,3971		0,77,1947	37	41	40		3834	-10.3	0	1		40	3,8363		0,3,4180	no	coding-synonymous	SIPA1L2	NM_020808.3		0,80,6127	AA,AG,GG		0.0359,1.9022,0.6444		1278/1723	232575051	80,12334	2024	4183	6207	SO:0001819	synonymous_variant	57568	exon13			AGGGCCGAGGATG	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.3834C>T	1.37:g.232575051G>A		106	1	0.00943396		123	61	0.495935	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Silent	SNP	ENST00000366630.1	37	CCDS41474.1																																																																																			G|0.996;A|0.004	0.004	strong		0.667	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		A	232575051	G	A	232575051	2	1	22	1	0	0	0	0	0	0	0	1	14345	1045	37	1		1	SIPA1L2	1	232575051	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1087918	232575051	16675570	468	3369											
KIAA1383	54627	hgsc.bcm.edu	37	chr1	232942276	232942276	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atccaagttctgcagcacacGaacatcctccaatgcttgta	12	10	6	13	1	1	0	0	0	1	0	4	1	4	0	3	0	4	5	3	0	4	3	rs61735495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:232942276G>A	ENST00000418460.1	+	1	1634	c.1507G>A	c.(1507-1509)Gaa>Aaa	p.E503K		NM_019090.2	NP_061963.2	Q9P2G4	MAP10_HUMAN	microtubule-associated protein 10	361					cytoplasmic microtubule organization (GO:0031122)|positive regulation of cytokinesis (GO:0032467)|regulation of microtubule-based process (GO:0032886)|spindle midzone assembly involved in mitosis (GO:0051256)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)	microtubule binding (GO:0008017)										TGCAGCACACGAACATCCTCC	0.403													G|||	107	0.0213658	0.0794	0.0029	5008	,	,		20484	0.0		0.0	False		,,,				2504	0.0				p.E503K		Atlas-SNP	.											.	.	.	.	0			c.G1507A						PASS	.	G	LYS/GLU	242,3624		6,230,1697	71	69	70		1507	2.5	0	1	dbSNP_129	70	0,8278		0,0,4139	yes	missense	KIAA1383	NM_019090.2	56	6,230,5836	AA,AG,GG		0.0,6.2597,1.9928	possibly-damaging	503/1048	232942276	242,11902	1933	4139	6072	SO:0001583	missense	54627	exon1			GCACACGAACATC	AB037804	CCDS44334.1	1q42.2	2013-02-12	2013-02-12	2013-02-12	ENSG00000212916	ENSG00000212916			29265	protein-coding gene	gene with protein product	"microtubule regulator 120 KDa"		"KIAA1383"	KIAA1383		23264731	Standard	NM_019090		Approved	MTR120	uc001hvh.2	Q9P2G4	OTTHUMG00000037819	ENST00000418460.1:c.1507G>A	1.37:g.232942276G>A	ENSP00000403208:p.Glu503Lys	67	0	0		90	50	0.555556	NM_019090	A8K2F1|Q32MI1|Q58EZ9|Q5VV83	Missense_Mutation	SNP	ENST00000418460.1	37	CCDS44334.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	G	17.33	3.362324	0.61403	0.062597	0.0	ENSG00000212916	ENST00000418460	.	.	.	4.69	2.48	0.30137	.	.	.	.	.	T	0.04679	0.0127	M	0.67953	2.075	0.09310	N	1	P	0.49559	0.925	B	0.43052	0.406	T	0.02774	-1.1112	8	0.37606	T	0.19	-11.7864	6.2799	0.21001	0.1287:0.1763:0.695:0.0	rs61735495	361	Q9P2G4	K1383_HUMAN	K	503	.	ENSP00000403208:E503K	E	+	1	0	KIAA1383	231008899	0.003000	0.15002	0.008000	0.14137	0.002000	0.02628	0.383000	0.20651	0.673000	0.31224	0.655000	0.94253	GAA	G|0.988;A|0.012	0.012	strong		0.403	MAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092317.3	NM_019090		A	232942276	G	A	232942276	3	1	22	1	0	0	0	0	1	0	0	0	8237	1059	37	1	1509	1	KIAA1383	1	232942276	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	367225	232942276	16308345	469	3370											
KIAA1383	54627	hgsc.bcm.edu	37	chr1	232943513	232943513	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcagccgggtcacctgtacActcatacagaaaatttcata	13	11	6	11	1	4	1	4	0	0	1	4	1	4	1	2	1	3	1	2	1	5	5	rs61735509	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:232943513A>T	ENST00000418460.1	+	1	2871	c.2744A>T	c.(2743-2745)cAc>cTc	p.H915L		NM_019090.2	NP_061963.2	Q9P2G4	MAP10_HUMAN	microtubule-associated protein 10	773					cytoplasmic microtubule organization (GO:0031122)|positive regulation of cytokinesis (GO:0032467)|regulation of microtubule-based process (GO:0032886)|spindle midzone assembly involved in mitosis (GO:0051256)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)	microtubule binding (GO:0008017)										TCACCTGTACACTCATACAGA	0.388													A|||	96	0.0191693	0.0696	0.0058	5008	,	,		19105	0.0		0.0	False		,,,				2504	0.0				p.H915L		Atlas-SNP	.											.	.	.	.	0			c.A2744T						PASS	.	A	LEU/HIS	220,3454		5,210,1622	47	47	47		2744	-4.8	0	1	dbSNP_129	47	6,8134		0,6,4064	yes	missense	KIAA1383	NM_019090.2	99	5,216,5686	TT,TA,AA		0.0737,5.988,1.913	benign	915/1048	232943513	226,11588	1837	4070	5907	SO:0001583	missense	54627	exon1			CTGTACACTCATA	AB037804	CCDS44334.1	1q42.2	2013-02-12	2013-02-12	2013-02-12	ENSG00000212916	ENSG00000212916			29265	protein-coding gene	gene with protein product	"microtubule regulator 120 KDa"		"KIAA1383"	KIAA1383		23264731	Standard	NM_019090		Approved	MTR120	uc001hvh.2	Q9P2G4	OTTHUMG00000037819	ENST00000418460.1:c.2744A>T	1.37:g.232943513A>T	ENSP00000403208:p.His915Leu	89	0	0		106	55	0.518868	NM_019090	A8K2F1|Q32MI1|Q58EZ9|Q5VV83	Missense_Mutation	SNP	ENST00000418460.1	37	CCDS44334.1	26	0.011904761904761904	24	0.04878048780487805	2	0.0055248618784530384	0	0.0	0	0.0	A	0.104	-1.148237	0.01714	0.05988	7.37E-4	ENSG00000212916	ENST00000418460	.	.	.	5.94	-4.76	0.03229	.	1.184600	0.06521	N	0.739754	T	0.01489	0.0048	N	0.16307	0.4	0.09310	N	1	B	0.15141	0.012	B	0.14578	0.011	T	0.20207	-1.0282	9	0.11485	T	0.65	0.0447	0.8514	0.01173	0.2763:0.1074:0.2072:0.409	rs61735509	773	Q9P2G4	K1383_HUMAN	L	915	.	ENSP00000403208:H915L	H	+	2	0	KIAA1383	231010136	0.000000	0.05858	0.012000	0.15200	0.035000	0.12851	0.776000	0.26704	-0.904000	0.03876	0.482000	0.46254	CAC	A|0.989;T|0.011	0.011	strong		0.388	MAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092317.3	NM_019090		T	232943513	A	T	232943513	3	4	22	1	0	0	0	0	1	0	0	0	8237	159	6	5	2746	5	KIAA1383	1	232943513	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1237	232943513	16307108	470	3371											
KIAA1804	84451	hgsc.bcm.edu	37	chr1	233489682	233489682	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccatccacctgccctgagccGtttgccaagctcatgaaagg	9	8	9	15	1	1	2	1	2	0	0	2	2	2	2	6	1	4	2	6	1	2	1	rs56268427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:233489682G>A	ENST00000366624.3	+	3	1377	c.1116G>A	c.(1114-1116)ccG>ccA	p.P372P	MLK4_ENST00000366623.3_Silent_p.P372P	NM_032435.2	NP_115811.2																					GCCCTGAGCCGTTTGCCAAGC	0.468													G|||	255	0.0509185	0.1823	0.0173	5008	,	,		18556	0.0		0.002	False		,,,				2504	0.0				p.P372P		Atlas-SNP	.											.	KIAA1804	129	.	0			c.G1116A						PASS	.	G		698,3708	291.0+/-281.2	53,592,1558	126	110	116		1116	-9.8	0.1	1	dbSNP_129	116	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	KIAA1804	NM_032435.2		53,599,5851	AA,AG,GG		0.0814,15.842,5.4206		372/1037	233489682	705,12301	2203	4300	6503	SO:0001819	synonymous_variant	0	exon3			TGAGCCGTTTGCC																												ENST00000366624.3:c.1116G>A	1.37:g.233489682G>A		200	0	0		212	107	0.504717	NM_032435		Silent	SNP	ENST00000366624.3	37	CCDS1598.1																																																																																			G|0.951;A|0.049	0.049	strong		0.468	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1			A	233489682	G	A	233489682	2	1	22	1	0	0	0	0	0	0	0	1	8268	1132	40	1		1	KIAA1804	1	233489682	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	546169	233489682	15760939	471	3372											
ARID4B	51742	hgsc.bcm.edu	37	chr1	235357460	235357460	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgaaatggtggtttggacaAgcgccgaagtttacagtttt	10	13	12	6	2	0	1	0	1	0	0	0	3	0	2	1	3	2	3	1	3	4	5	rs62000435	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:235357460A>G	ENST00000264183.3	-	19	2490	c.1993T>C	c.(1993-1995)Ttg>Ctg	p.L665L	ARID4B_ENST00000349213.3_Silent_p.L579L|ARID4B_ENST00000366603.2_Silent_p.L665L	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	665					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)			GGTTTGGACAAGCGCCGAAGT	0.343													A|||	25	0.00499201	0.0174	0.0029	5008	,	,		16650	0.0		0.0	False		,,,				2504	0.0				p.L665L		Atlas-SNP	.											.	ARID4B	142	.	0			c.T1993C						PASS	.	A	,,	112,4294	82.4+/-120.9	1,110,2092	144	135	138		1993,1993,1735	3.9	1	1	dbSNP_129	138	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	ARID4B	NM_001206794.1,NM_016374.5,NM_031371.3	,,	1,112,6390	GG,GA,AA		0.0233,2.542,0.8765	,,	665/1313,665/1313,579/1227	235357460	114,12892	2203	4300	6503	SO:0001819	synonymous_variant	51742	exon19			TGGACAAGCGCCG	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.1993T>C	1.37:g.235357460A>G		181	0	0		191	100	0.52356	NM_016374	A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	Silent	SNP	ENST00000264183.3	37	CCDS31061.1																																																																																			A|0.992;G|0.008	0.008	strong		0.343	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374		G	235357460	A	G	235357460	2	3	22	1	0	0	0	0	0	0	0	1	920	69	3	3		3	ARID4B	1	235357460	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1867778	235357460	13893161	472	3373											
ARID4B	51742	hgsc.bcm.edu	37	chr1	235377279	235377281	+	In_Frame_Del	DEL	TCC	TCC	-																															cttcatcctcttcttcttctTcctcctcctcctcctcttct																								rs113894806|rs10588817|rs113458177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:235377279_235377281delTCC	ENST00000264183.3	-	17	2141_2143	c.1644_1646delGGA	c.(1642-1647)gaggaa>gaa	p.548_549EE>E	ARID4B_ENST00000349213.3_Intron|ARID4B_ENST00000366603.2_In_Frame_Del_p.548_549EE>E	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	548	Glu-rich.				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)	p.E548E(2)		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)			ttcttcttcttcctcctcctcct	0.414														183	0.0365415	0.1203	0.0144	5008	,	,		17403	0.001		0.008	False		,,,				2504	0.0051				p.549_549del		Pindel,Atlas-Indel	.											.	ARID4B	142	.	2	Substitution - coding silent(2)	endometrium(1)|kidney(1)	c.1645_1647del						PASS	.																																			SO:0001651	inframe_deletion	51742	exon17			.	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.1644_1646delGGA	1.37:g.235377288_235377290delTCC	ENSP00000264183:p.Glu553del	137	0	.		176	28	0.159	NM_016374	A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	In_Frame_Del	DEL	ENST00000264183.3	37	CCDS31061.1																																																																																			TCC|0.967;-|0.033	0.033	strong		0.414	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374		-	235377281	TCC	-	235377279	7	5	22	1	0	1	0	1	0	0	0	0	920	1783	62	0	2324	0	ARID4B	1	235377279	In_Frame_Del	DEL	TCC	TCGA-G8-6324-01A-11D-2210-10	19819	235377279	13873342	473	3374											
LYST	1130	hgsc.bcm.edu	37	chr1	235933535	235933535	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgcttaatattaaacatctgCtggtggtgatctgctctgat	9	16	9	7	0	3	2	0	2	3	0	3	2	3	2	0	2	4	3	0	2	4	3	rs6665568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:235933535C>G	ENST00000389794.3	-	20	6021	c.5847G>C	c.(5845-5847)caG>caC	p.Q1949H	LYST_ENST00000536965.1_3'UTR|LYST_ENST00000389793.2_Missense_Mutation_p.Q1949H			Q99698	LYST_HUMAN	lysosomal trafficking regulator	1949			Q -> H (in dbSNP:rs6665568).		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)			TAAACATCTGCTGGTGGTGAT	0.388													C|||	308	0.0615016	0.2194	0.0245	5008	,	,		17686	0.0		0.001	False		,,,				2504	0.0				p.Q1949H		Atlas-SNP	.											.	LYST	370	.	0			c.G5847C						PASS	.	C	HIS/GLN	828,3578	327.5+/-300.1	76,676,1451	128	132	131		5847	0.8	0.7	1	dbSNP_116	131	10,8590	6.4+/-24.3	0,10,4290	yes	missense	LYST	NM_000081.2	24	76,686,5741	GG,GC,CC		0.1163,18.7926,6.4432	benign	1949/3802	235933535	838,12168	2203	4300	6503	SO:0001583	missense	1130	exon20			CATCTGCTGGTGG	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.5847G>C	1.37:g.235933535C>G	ENSP00000374444:p.Gln1949His	172	0	0		154	74	0.480519	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	37	CCDS31062.1	115	0.052655677655677656	108	0.21951219512195122	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	C	8.986	0.976514	0.18736	0.187926	0.001163	ENSG00000143669	ENST00000389794;ENST00000389793	T;T	0.61158	0.13;0.13	5.48	0.809	0.18725	.	0.630262	0.18067	N	0.152750	T	0.00012	0.0000	N	0.17082	0.46	0.09310	P	1.0	B	0.02656	0.0	B	0.04013	0.001	T	0.11966	-1.0566	9	0.13853	T	0.58	.	2.9878	0.05973	0.217:0.4875:0.1067:0.1888	rs6665568;rs52790740;rs6665568	1949	Q99698	LYST_HUMAN	H	1949	ENSP00000374444:Q1949H;ENSP00000374443:Q1949H	ENSP00000374443:Q1949H	Q	-	3	2	LYST	234000158	0.152000	0.22762	0.656000	0.29637	0.957000	0.61999	-0.438000	0.06905	0.266000	0.21894	0.650000	0.86243	CAG	C|0.943;G|0.057	0.057	strong		0.388	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			G	235933535	C	G	235933535	3	3	22	1	0	0	0	0	1	0	0	0	9137	796	28	4	5694	4	LYST	1	235933535	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	556256	235933535	13317086	474	3375											
LYST	1130	hgsc.bcm.edu	37	chr1	235971802	235971802	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttacataaatctgaagcacGtcctgaggcaagcactggtt	12	11	9	9	1	1	2	0	2	1	0	2	2	2	2	1	2	3	4	1	2	5	4	rs16832868	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:235971802G>A	ENST00000389794.3	-	5	2490	c.2316C>T	c.(2314-2316)gaC>gaT	p.D772D	LYST_ENST00000536965.1_Silent_p.D772D|LYST_ENST00000389793.2_Silent_p.D772D			Q99698	LYST_HUMAN	lysosomal trafficking regulator	772					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)			TCTGAAGCACGTCCTGAGGCA	0.468													G|||	309	0.0617013	0.2201	0.0245	5008	,	,		17331	0.0		0.001	False		,,,				2504	0.0				p.D772D		Atlas-SNP	.											.	LYST	370	.	0			c.C2316T						PASS	.	G		827,3579	328.3+/-300.5	75,677,1451	88	86	87		2316	3.5	1	1	dbSNP_123	87	10,8590	6.4+/-24.3	0,10,4290	no	coding-synonymous	LYST	NM_000081.2		75,687,5741	AA,AG,GG		0.1163,18.7699,6.4355		772/3802	235971802	837,12169	2203	4300	6503	SO:0001819	synonymous_variant	1130	exon5			AAGCACGTCCTGA	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.2316C>T	1.37:g.235971802G>A		189	0	0		173	90	0.520231	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	37	CCDS31062.1																																																																																			G|0.934;A|0.066	0.066	strong		0.468	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			A	235971802	G	A	235971802	2	1	22	1	0	0	0	0	0	0	0	1	9137	1136	40	1		1	LYST	1	235971802	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	38267	235971802	13278819	475	3376											
ERO1LB	56605	hgsc.bcm.edu	37	chr1	236381833	236381833	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttattacctactgtgttgtaAtaagactttaaaattctgta	13	18	5	5	0	1	1	0	0	1	1	1	1	1	1	1	0	2	3	1	0	8	10	rs11811758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:236381833A>G	ENST00000354619.5	-	16	1588	c.1387T>C	c.(1387-1389)Tta>Cta	p.L463L	GPR137B_ENST00000477559.1_Intron	NM_019891.3	NP_063944.3	Q86YB8	ERO1B_HUMAN	ERO1-like beta (S. cerevisiae)	463					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)	CTGTGTTGTAATAAGACTTTA	0.318													A|||	231	0.0461262	0.1626	0.0216	5008	,	,		15266	0.0		0.001	False		,,,				2504	0.0				p.L463L		Atlas-SNP	.											.	ERO1LB	48	.	0			c.T1387C						PASS	.	A		620,3778	261.0+/-264.0	45,530,1624	57	63	61		1387	-4.8	0.8	1	dbSNP_120	61	8,8554	6.4+/-24.3	0,8,4273	no	coding-synonymous	ERO1LB	NM_019891.3		45,538,5897	GG,GA,AA		0.0934,14.0973,4.8457		463/468	236381833	628,12332	2199	4281	6480	SO:0001819	synonymous_variant	56605	exon16			GTTGTAATAAGAC	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.1387T>C	1.37:g.236381833A>G		244	0	0		216	121	0.560185	NM_019891	B4DF57|Q5T1H4|Q8IZ11|Q9NR62	Silent	SNP	ENST00000354619.5	37	CCDS31064.1																																																																																			A|0.961;G|0.039	0.039	strong		0.318	ERO1LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096371.1	NM_019891		G	236381833	A	G	236381833	2	3	22	1	0	0	0	0	0	0	0	1	5242	98	4	3		3	ERO1LB	1	236381833	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	410031	236381833	12868788	476	3377											
RYR2	6262	hgsc.bcm.edu	37	chr1	237620034	237620034	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aattctctgtatgagttgctGggtaagaagcatgattgggt	10	14	13	4	0	1	3	0	2	1	1	2	3	1	3	0	2	2	5	0	2	4	5	rs78281932	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:237620034G>A	ENST00000366574.2	+	16	1928	c.1611G>A	c.(1609-1611)ctG>ctA	p.L537L	RYR2_ENST00000360064.6_Splice_Site_p.L535L|RYR2_ENST00000542537.1_Splice_Site_p.L521L	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	537					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)			ATGAGTTGCTGGGTAAGAAGC	0.433													G|||	300	0.0599042	0.2148	0.0202	5008	,	,		18734	0.0		0.001	False		,,,				2504	0.001				p.L537L		Atlas-SNP	.											.	RYR2	1273	.	0			c.G1611A						PASS	.	G		683,3123		48,587,1268	158	154	155		1611	-3	1	1	dbSNP_131	155	10,8242		0,10,4116	yes	coding-synonymous-near-splice	RYR2	NM_001035.2		48,597,5384	AA,AG,GG		0.1212,17.9453,5.7472		537/4968	237620034	693,11365	1903	4126	6029	SO:0001630	splice_region_variant	6262	exon16			GTTGCTGGGTAAG	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.1612+1G>A	1.37:g.237620034G>A		105	0	0		107	54	0.504673	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	37	CCDS55691.1																																																																																			G|0.960;A|0.040	0.040	strong		0.433	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	Silent	A	237620034	G	A	237620034	5	1	22	1	0	0	0	0	0	0	1	0	13784	1362	47	2	1673	2	RYR2	1	237620034	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1238201	237620034	11630587	477	3378											
ZP4	57829	hgsc.bcm.edu	37	chr1	238046056	238046056	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acttacggagcttttctggaGggtccttagtggcttggagt	6	14	14	7	1	1	0	0	0	1	0	2	3	2	3	1	5	2	2	1	5	2	5	rs35187146	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:238046056G>A	ENST00000366570.4	-	11	1639	c.1481C>T	c.(1480-1482)cCt>cTt	p.P494L	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	494					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)			CTTTTCTGGAGGGTCCTTAGT	0.418													G|||	98	0.0195687	0.0681	0.0101	5008	,	,		18510	0.0		0.001	False		,,,				2504	0.0				p.P494L	NSCLC(166;160 2029 11600 18754 19936)	Atlas-SNP	.											.	ZP4	161	.	0			c.C1481T						PASS	.	G	LEU/PRO	232,4174	136.1+/-172.1	4,224,1975	113	113	113		1481	3.3	0	1	dbSNP_126	113	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ZP4	NM_021186.3	98	4,225,6274	AA,AG,GG		0.0116,5.2655,1.7915	benign	494/541	238046056	233,12773	2203	4300	6503	SO:0001583	missense	57829	exon11			TCTGGAGGGTCCT	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.1481C>T	1.37:g.238046056G>A	ENSP00000355529:p.Pro494Leu	103	0	0		107	44	0.411215	NM_021186	B2RAE1	Missense_Mutation	SNP	ENST00000366570.4	37	CCDS1615.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	G	13.86	2.362971	0.41902	0.052655	1.16E-4	ENSG00000116996	ENST00000366570	T	0.75154	-0.91	4.2	3.29	0.37713	.	1.113200	0.06962	N	0.816574	T	0.11750	0.0286	L	0.38175	1.15	0.09310	N	1	B	0.18741	0.03	B	0.12837	0.008	T	0.13737	-1.0498	10	0.11485	T	0.65	-6.9559	8.323	0.32140	0.1076:0.0:0.8924:0.0	rs35187146	494	Q12836	ZP4_HUMAN	L	494	ENSP00000355529:P494L	ENSP00000355529:P494L	P	-	2	0	ZP4	236112679	0.088000	0.21588	0.002000	0.10522	0.836000	0.47400	2.346000	0.44027	1.146000	0.42352	-0.126000	0.14955	CCT	G|0.985;A|0.015	0.015	strong		0.418	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1			A	238046056	G	A	238046056	3	1	22	1	0	0	0	0	1	0	0	0	18233	1000	35	2	149	2	ZP4	1	238046056	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	426022	238046056	11204565	478	3379											
ZP4	57829	hgsc.bcm.edu	37	chr1	238049143	238049143	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gaaaacctggacattgattgGgagagagttgctacttactg	12	11	12	6	0	0	2	0	1	0	1	0	6	0	4	1	2	4	2	1	2	4	5	rs34811980	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:238049143G>A	ENST00000366570.4	-	7	1041	c.883C>T	c.(883-885)Cca>Tca	p.P295S	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	295	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.		P -> S (in dbSNP:rs34811980).		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)			ACATTGATTGGGAGAGAGTTG	0.502													G|||	157	0.0313498	0.1112	0.013	5008	,	,		18469	0.0		0.001	False		,,,				2504	0.0				p.P295S	NSCLC(166;160 2029 11600 18754 19936)	Atlas-SNP	.											.	ZP4	161	.	0			c.C883T						PASS	.	G	SER/PRO	393,4013	196.4+/-220.7	14,365,1824	167	161	163		883	4.8	0.1	1	dbSNP_126	163	6,8594	4.3+/-15.6	0,6,4294	yes	missense	ZP4	NM_021186.3	74	14,371,6118	AA,AG,GG		0.0698,8.9197,3.0678	probably-damaging	295/541	238049143	399,12607	2203	4300	6503	SO:0001583	missense	57829	exon7			TGATTGGGAGAGA	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.883C>T	1.37:g.238049143G>A	ENSP00000355529:p.Pro295Ser	73	0	0		94	51	0.542553	NM_021186	B2RAE1	Missense_Mutation	SNP	ENST00000366570.4	37	CCDS1615.1	56	0.02564102564102564	52	0.10569105691056911	4	0.011049723756906077	0	0.0	0	0.0	G	18.15	3.560913	0.65538	0.089197	6.98E-4	ENSG00000116996	ENST00000366570	T	0.81163	-1.46	4.85	4.85	0.62838	Zona pellucida sperm-binding protein (3);	0.124427	0.53938	D	0.000041	T	0.13841	0.0335	M	0.70275	2.135	0.09310	N	1	D	0.76494	0.999	D	0.74023	0.982	T	0.48514	-0.9029	10	0.34782	T	0.22	-14.4465	10.7036	0.45942	0.0:0.0:0.8094:0.1905	rs34811980	295	Q12836	ZP4_HUMAN	S	295	ENSP00000355529:P295S	ENSP00000355529:P295S	P	-	1	0	ZP4	236115766	0.999000	0.42202	0.076000	0.20297	0.635000	0.38103	3.598000	0.54038	2.242000	0.73789	0.650000	0.86243	CCA	G|0.973;A|0.027	0.027	strong		0.502	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1			A	238049143	G	A	238049143	3	1	22	1	0	0	0	0	1	0	0	0	18233	1232	43	2	763	2	ZP4	1	238049143	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3087	238049143	11201478	479	3380											
ZP4	57829	hgsc.bcm.edu	37	chr1	238053226	238053226	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaccaccttgtgttcagccGcgcctgctccttcaactcca	7	11	6	17	2	2	0	2	0	0	0	4	0	4	0	6	0	4	2	6	0	2	4	rs34370253	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:238053226G>A	ENST00000366570.4	-	3	499	c.341C>T	c.(340-342)gCg>gTg	p.A114V	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	114			A -> V (in dbSNP:rs34370253).		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)			GTGTTCAGCCGCGCCTGCTCC	0.567													G|||	154	0.0307508	0.1089	0.013	5008	,	,		19719	0.0		0.001	False		,,,				2504	0.0				p.A114V	NSCLC(166;160 2029 11600 18754 19936)	Atlas-SNP	.											ZP4,caecum,carcinoma,0,1	ZP4	161	1	0			c.C341T						PASS	.	G	VAL/ALA	386,4020	194.0+/-219.0	14,358,1831	199	206	203		341	-6.6	0	1	dbSNP_126	203	6,8594	4.3+/-15.6	0,6,4294	yes	missense	ZP4	NM_021186.3	64	14,364,6125	AA,AG,GG		0.0698,8.7608,3.014	benign	114/541	238053226	392,12614	2203	4300	6503	SO:0001583	missense	57829	exon3			TCAGCCGCGCCTG	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.341C>T	1.37:g.238053226G>A	ENSP00000355529:p.Ala114Val	210	1	0.0047619		172	84	0.488372	NM_021186	B2RAE1	Missense_Mutation	SNP	ENST00000366570.4	37	CCDS1615.1	56	0.02564102564102564	52	0.10569105691056911	4	0.011049723756906077	0	0.0	0	0.0	G	0.052	-1.248697	0.01469	0.087608	6.98E-4	ENSG00000116996	ENST00000366570	T	0.74632	-0.86	4.37	-6.58	0.01836	.	0.845246	0.10705	N	0.643569	T	0.00875	0.0029	N	0.11201	0.11	0.09310	N	1	B	0.17667	0.023	B	0.10450	0.005	T	0.13522	-1.0506	10	0.02654	T	1	0.4495	3.7495	0.08561	0.5715:0.1196:0.1878:0.1212	rs34370253	114	Q12836	ZP4_HUMAN	V	114	ENSP00000355529:A114V	ENSP00000355529:A114V	A	-	2	0	ZP4	236119849	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.059000	0.11731	-2.021000	0.00939	-2.828000	0.00107	GCG	G|0.972;A|0.028	0.028	strong		0.567	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1			A	238053226	G	A	238053226	3	1	22	1	0	0	0	0	1	0	0	0	18233	1087	38	1	1321	1	ZP4	1	238053226	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4083	238053226	11197395	480	3381											
FMN2	56776	hgsc.bcm.edu	37	chr1	240371409	240371409	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagcgggcataccccctccGccccctctacccggagtggg	5	5	13	18	3	1	0	0	0	1	0	2	2	2	2	6	4	3	1	6	4	2	2	rs373533409	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:240371409G>T	ENST00000319653.9	+	5	3527	c.3297G>T	c.(3295-3297)ccG>ccT	p.P1099P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1099	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)			TACCCCCTCCGCCCCCTCTAC	0.731																																					p.P1099P		Atlas-SNP	.											FMN2,NS,neuroblastoma,0,1	FMN2	451	1	0			c.G3297T						scavenged	.						6	8	8					1																	240371409		2016	4072	6088	SO:0001819	synonymous_variant	56776	exon5			CCCTCCGCCCCCT	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.3297G>T	1.37:g.240371409G>T		142	0	0		149	7	0.0469799	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			.	.	none		0.731	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		T	240371409	G	T	240371409	2	4	22	1	0	0	0	0	0	0	0	1	5958	1074	38	4		4	FMN2	1	240371409	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2318183	240371409	8879212	481	3382											
FH	2271	hgsc.bcm.edu	37	chr1	241663825	241663825	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttggcctggattcccaccacGcagttttctgtaaaggaaac	10	11	9	11	1	1	0	0	0	1	0	2	2	2	2	3	3	1	3	3	3	3	5	rs2070080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:241663825G>A	ENST00000366560.3	-	9	1340	c.1302C>T	c.(1300-1302)tgC>tgT	p.C434C		NM_000143.3	NP_000134.2	P07954	FUMH_HUMAN	fumarate hydratase	434					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)		TTCCCACCACGCAGTTTTCTG	0.438			"Mis, N, F"			"lieomyomatosis, renal"			Hereditary Leiomyomatosis and Renal Cell Cancer				G|||	183	0.0365415	0.1346	0.0072	5008	,	,		15620	0.0		0.0	False		,,,				2504	0.0				p.C434C	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,NS,carcinoma,0,1	FH	64	1	0			c.C1302T						PASS	.	G		428,3978	207.2+/-228.6	19,390,1794	135	129	131		1302	-10.7	0.7	1	dbSNP_96	131	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous	FH	NM_000143.3		19,395,6089	AA,AG,GG		0.0581,9.714,3.3292		434/511	241663825	433,12573	2203	4300	6503	SO:0001819	synonymous_variant	2271	exon9	Familial Cancer Database	HLRCC, Reed syndrome, Hereditary Multiple Leiomyomata of Skin and Uterus	CACCACGCAGTTT	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.1302C>T	1.37:g.241663825G>A		149	0	0		142	68	0.478873	NM_000143	B1ANK7	Silent	SNP	ENST00000366560.3	37	CCDS1617.1																																																																																			G|0.972;A|0.028	0.028	strong		0.438	FH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095490.1	NM_000143		A	241663825	G	A	241663825	2	1	22	1	0	0	0	0	0	0	0	1	5883	1079	38	1		1	FH	1	241663825	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1292416	241663825	7586796	482	3383											
FH	2271	hgsc.bcm.edu	37	chr1	241676972	241676972	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	taatcctggtttacttcagcGgccgctcgcttcaagatgcc	7	12	9	13	3	2	1	2	0	0	1	4	1	3	1	3	2	3	3	3	2	3	5	rs10926501	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:241676972G>A	ENST00000366560.3	-	3	347	c.309C>T	c.(307-309)gcC>gcT	p.A103A	FH_ENST00000493477.1_5'Flank	NM_000143.3	NP_000134.2	P07954	FUMH_HUMAN	fumarate hydratase	103					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)		TTACTTCAGCGGCCGCTCGCT	0.353			"Mis, N, F"			"lieomyomatosis, renal"			Hereditary Leiomyomatosis and Renal Cell Cancer				G|||	169	0.033746	0.1241	0.0072	5008	,	,		16468	0.0		0.0	False		,,,				2504	0.0				p.A103A	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,NS,carcinoma,0,2	FH	64	2	0			c.C309T						PASS	.	G		386,4020	191.6+/-217.2	18,350,1835	121	123	122		309	0.9	1	1	dbSNP_120	122	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	FH	NM_000143.3		18,353,6132	AA,AG,GG		0.0349,8.7608,2.9909		103/511	241676972	389,12617	2203	4300	6503	SO:0001819	synonymous_variant	2271	exon3	Familial Cancer Database	HLRCC, Reed syndrome, Hereditary Multiple Leiomyomata of Skin and Uterus	TTCAGCGGCCGCT	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.309C>T	1.37:g.241676972G>A		282	0	0		273	141	0.516484	NM_000143	B1ANK7	Silent	SNP	ENST00000366560.3	37	CCDS1617.1																																																																																			G|0.975;A|0.025	0.025	strong		0.353	FH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095490.1	NM_000143		A	241676972	G	A	241676972	2	1	22	1	0	0	0	0	0	0	0	1	5883	1103	39	1		1	FH	1	241676972	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	13147	241676972	7573649	483	3384											
CEP170	9859	hgsc.bcm.edu	37	chr1	243328226	243328226	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagggctgtcttattctcccActggactgaacaaatttacg	10	12	9	10	1	2	1	0	1	2	0	3	3	2	2	1	2	2	1	1	2	4	4			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:243328226A>G	ENST00000366542.1	-	13	3087	c.3036T>C	c.(3034-3036)agT>agC	p.S1012S	CEP170_ENST00000366543.1_Silent_p.S914S|RP11-261C10.4_ENST00000437499.1_RNA|CEP170_ENST00000366544.1_Silent_p.S914S|RP11-261C10.4_ENST00000422938.1_RNA|CEP170_ENST00000490813.1_5'Flank	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	1012	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)			TTATTCTCCCACTGGACTGAA	0.408																																					p.S1012S		Atlas-SNP	.											.	CEP170	153	.	0			c.T3036C						PASS	.						157	139	145					1																	243328226		1909	4120	6029	SO:0001819	synonymous_variant	9859	exon13			TCTCCCACTGGAC	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.3036T>C	1.37:g.243328226A>G		527	0	0		616	236	0.383117	NM_014812	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Silent	SNP	ENST00000366542.1	37	CCDS44339.1	.	.	.	.	.	.	.	.	.	.	A	1.317	-0.600452	0.03744	.	.	ENSG00000143702	ENST00000336415	.	.	.	4.37	4.37	0.52481	.	.	.	.	.	T	0.64125	0.2570	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63567	-0.6608	4	.	.	.	-11.7439	12.8963	0.58101	1.0:0.0:0.0:0.0	.	.	.	.	A	976	.	.	V	-	2	0	CEP170	241394849	1.000000	0.71417	1.000000	0.80357	0.588000	0.36517	1.938000	0.40203	1.823000	0.53134	0.454000	0.30748	GTG	.	.	none		0.408	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812		G	243328226	A	G	243328226	2	3	22	1	0	0	0	0	0	0	0	1	3252	156	6	3		3	CEP170	1	243328226	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1651254	243328226	5922395	484	3385											
CEP170	9859	hgsc.bcm.edu	37	chr1	243329093	243329093	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttttccaggagcagagctGcctaagtgaagtagggtttt	9	13	12	7	0	1	2	0	1	1	1	2	3	2	3	2	2	3	4	2	2	3	6	rs2789194	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:243329093G>C	ENST00000366542.1	-	13	2220	c.2169C>G	c.(2167-2169)ggC>ggG	p.G723G	CEP170_ENST00000366543.1_Silent_p.G625G|RP11-261C10.4_ENST00000437499.1_RNA|CEP170_ENST00000366544.1_Silent_p.G625G|RP11-261C10.4_ENST00000422938.1_RNA|CEP170_ENST00000490813.1_5'Flank	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	723						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)			GAGCAGAGCTGCCTAAGTGAA	0.398													G|||	192	0.0383387	0.143	0.0043	5008	,	,		20676	0.0		0.0	False		,,,				2504	0.0				p.G723G		Atlas-SNP	.											.	CEP170	153	.	0			c.C2169G						PASS	.	G	,,	483,3189		39,405,1392	163	150	154		1875,1875,2169	1	0	1	dbSNP_100	154	3,8169		0,3,4083	no	coding-synonymous,coding-synonymous,coding-synonymous	CEP170	NM_001042404.1,NM_001042405.1,NM_014812.2	,,	39,408,5475	CC,CG,GG		0.0367,13.1536,4.1033	,,	625/1487,625/1461,723/1585	243329093	486,11358	1836	4086	5922	SO:0001819	synonymous_variant	9859	exon13			AGAGCTGCCTAAG	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.2169C>G	1.37:g.243329093G>C		222	0	0		217	108	0.497696	NM_014812	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Silent	SNP	ENST00000366542.1	37	CCDS44339.1	64	0.029304029304029304	61	0.12398373983739837	3	0.008287292817679558	0	0.0	0	0.0	G	0.006	-2.025614	0.00414	0.131536	3.67E-4	ENSG00000143702	ENST00000336415	.	.	.	5.25	1.02	0.19986	.	.	.	.	.	T	0.00241	0.0007	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.15407	-1.0438	4	.	.	.	-3.8866	4.2033	0.10476	0.1806:0.0:0.4641:0.3553	rs2789194;rs2789194	.	.	.	G	687	.	.	A	-	2	0	CEP170	241395716	0.104000	0.21937	0.003000	0.11579	0.284000	0.27059	0.869000	0.27996	-0.080000	0.12685	-0.439000	0.05793	GCA	G|0.978;C|0.022	0.022	strong		0.398	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812		C	243329093	G	C	243329093	2	2	22	1	0	0	0	0	0	0	0	1	3252	1306	46	4		4	CEP170	1	243329093	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	867	243329093	5921528	485	3386											
ZNF238	10472	hgsc.bcm.edu	37	chr1	244217662	244217662	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgggaacatgtggatgcgaTtgccctcagactcagcaggc	9	8	13	11	1	2	1	2	0	0	1	2	4	2	3	1	3	4	1	1	3	1	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:244217662T>C	ENST00000358704.4	+	2	735	c.586T>C	c.(586-588)Ttg>Ctg	p.L196L		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	187				KLNILPSKRDLAAEPGNMWMRLPSDSAGIPQAGGEAEPHAT AAGKTVASPCSSTESLSQRSVTSVRDSADVDCVLDLSVKSS LSGVENLNSSYFSSQ -> IEHPAQQKGLGGRAWEHVDAIA LRLSRHPPGWRRGRATRHSSWKNSSQPLQLNRVFVPE (in Ref. 1; AAA81368). {ECO:0000305}.	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)										GTGGATGCGATTGCCCTCAGA	0.567																																					p.L196L		Atlas-SNP	.											.	.	.	.	0			c.T586C						PASS	.						51	57	55					1																	244217662		2203	4300	6503	SO:0001819	synonymous_variant	10472	exon2			ATGCGATTGCCCT	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.586T>C	1.37:g.244217662T>C		169	0	0		167	91	0.54491	NM_205768	A8K5U3|Q13397|Q5VU40|Q8N463|Q9UD99	Silent	SNP	ENST00000358704.4	37	CCDS1622.1																																																																																			.	.	none		0.567	ZBTB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096513.2	NM_205768		C	244217662	T	C	244217662	2	2	22	1	0	0	0	0	0	0	0	1	17805	1490	52	3		3	ZNF238	1	244217662	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	888569	244217662	5032959	486	3387											
KIF26B	55083	hgsc.bcm.edu	37	chr1	245775265	245775265	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagtaccggatggagaagagCgggaaagggggaagtaagtc	14	4	18	5	2	0	2	0	0	0	2	1	6	0	5	1	5	2	2	1	5	5	2	rs61741293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:245775265C>T	ENST00000407071.2	+	9	2525	c.2085C>T	c.(2083-2085)agC>agT	p.S695S	RP11-522M21.2_ENST00000418402.1_RNA|KIF26B_ENST00000366518.4_Silent_p.S314S	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	695	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)			TGGAGAAGAGCGGGAAAGGGG	0.587													C|||	71	0.0141773	0.0514	0.0029	5008	,	,		17393	0.0		0.001	False		,,,				2504	0.0				p.S695S		Atlas-SNP	.											.	KIF26B	343	.	0			c.C2085T						PASS	.	C		149,3979		1,147,1916	55	62	60		2085	0.9	1	1	dbSNP_129	60	4,8378		0,4,4187	no	coding-synonymous	KIF26B	NM_018012.3		1,151,6103	TT,TC,CC		0.0477,3.6095,1.223		695/2109	245775265	153,12357	2064	4191	6255	SO:0001819	synonymous_variant	55083	exon9			GAAGAGCGGGAAA	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.2085C>T	1.37:g.245775265C>T		94	0	0		111	43	0.387387	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Silent	SNP	ENST00000407071.2	37	CCDS44342.1																																																																																			C|0.989;T|0.011	0.011	strong		0.587	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		T	245775265	C	T	245775265	2	4	22	1	0	0	0	0	0	0	0	1	8304	767	27	1		1	KIF26B	1	245775265	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1557603	245775265	3475356	487	3388											
CNST	163882	hgsc.bcm.edu	37	chr1	246755204	246755204	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	aaattcctggaaaaagaagtCcaagaagcaaaaaagggact	21	5	9	6	0	0	2	0	0	0	2	2	4	2	4	2	2	1	1	2	2	9	1	rs116182112	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:246755204C>T	ENST00000366513.4	+	2	609	c.340C>T	c.(340-342)Cca>Tca	p.P114S	CNST_ENST00000366512.3_Missense_Mutation_p.P114S|CNST_ENST00000483271.1_3'UTR	NM_152609.2	NP_689822.2	Q6PJW8	CNST_HUMAN	consortin, connexin sorting protein	114					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						AAAAAGAAGTCCAAGAAGCAA	0.393													C|||	10	0.00199681	0.0076	0.0	5008	,	,		20543	0.0		0.0	False		,,,				2504	0.0				p.P114S		Atlas-SNP	.											.	CNST	73	.	0			c.C340T						PASS	.	C	SER/PRO,SER/PRO	22,4376		0,22,2177	30	31	31		340,340	-12.3	0	1	dbSNP_132	31	1,8591		0,1,4295	yes	missense,missense	CNST	NM_001139459.1,NM_152609.2	74,74	0,23,6472	TT,TC,CC		0.0116,0.5002,0.1771	benign,benign	114/617,114/726	246755204	23,12967	2199	4296	6495	SO:0001583	missense	163882	exon2			AGAAGTCCAAGAA	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.340C>T	1.37:g.246755204C>T	ENSP00000355470:p.Pro114Ser	54	0	0		45	22	0.488889	NM_152609	Q5VSY9|Q5VTM7|Q8IYA9|Q8N3L5|Q8NB09|Q8TEI2|Q96MR5	Missense_Mutation	SNP	ENST00000366513.4	37	CCDS1628.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	0.124	-1.122387	0.01785	0.005002	1.16E-4	ENSG00000162852	ENST00000366513;ENST00000366512;ENST00000366511	T;T;T	0.21734	1.99;1.99;1.99	6.17	-12.3	0.00002	.	1.657020	0.02939	N	0.140268	T	0.08268	0.0206	L	0.39633	1.23	0.09310	N	0.999998	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.14559	-1.0468	10	0.25751	T	0.34	-0.1849	3.0934	0.06301	0.2575:0.3466:0.279:0.1169	.	114;114	Q6PJW8;Q6PJW8-2	CNST_HUMAN;.	S	114	ENSP00000355470:P114S;ENSP00000355469:P114S;ENSP00000355468:P114S	ENSP00000355468:P114S	P	+	1	0	CNST	244821827	0.031000	0.19500	0.002000	0.10522	0.852000	0.48524	-1.106000	0.03319	-4.388000	0.00052	-1.094000	0.02160	CCA	C|0.998;T|0.002	0.002	strong		0.393	CNST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096780.1	NM_152609		T	246755204	C	T	246755204	3	4	22	1	0	0	0	0	1	0	0	0	3636	855	30	2	342	2	CNST	1	246755204	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	979939	246755204	2495417	488	3389											
AHCTF1	25909	hgsc.bcm.edu	37	chr1	247013203	247013203	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcaccatcgaaagttcctcGtttggcactaaaatggattt	12	13	7	9	2	1	0	1	0	0	0	4	2	2	1	2	2	0	3	2	2	3	4	rs41308156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:247013203G>A	ENST00000391829.2	-	33	6228	c.6105C>T	c.(6103-6105)aaC>aaT	p.N2035N	AHCTF1_ENST00000470300.1_5'UTR|AHCTF1_ENST00000366508.1_Silent_p.N2070N|AHCTF1_ENST00000326225.3_Silent_p.N2044N			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	2035	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)			AAAGTTCCTCGTTTGGCACTA	0.383													G|||	221	0.0441294	0.1641	0.0058	5008	,	,		19777	0.0		0.0	False		,,,				2504	0.0				p.N2044N	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.C6132T						PASS	.	G		555,3851	241.8+/-252.1	29,497,1677	59	60	60		6132	0.8	0.9	1	dbSNP_127	60	5,8589	4.3+/-15.6	0,5,4292	no	coding-synonymous	AHCTF1	NM_015446.4		29,502,5969	AA,AG,GG		0.0582,12.5965,4.3077		2044/2276	247013203	560,12440	2203	4297	6500	SO:0001819	synonymous_variant	25909	exon33			TTCCTCGTTTGGC		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.6105C>T	1.37:g.247013203G>A		201	0	0		231	101	0.437229	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Silent	SNP	ENST00000391829.2	37																																																																																				.	.	weak		0.383	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446		A	247013203	G	A	247013203	2	1	22	1	0	0	0	0	0	0	0	1	408	1136	40	1		1	AHCTF1	1	247013203	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	257999	247013203	2237418	489	3390											
AHCTF1	25909	hgsc.bcm.edu	37	chr1	247013733	247013733	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgaaaccttaacttctttttTagtagtttcttcaactgctg	9	19	5	8	0	3	1	1	1	2	0	3	1	3	1	1	0	4	3	1	0	5	8	rs139763225	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:247013733T>C	ENST00000391829.2	-	33	5698	c.5575A>G	c.(5575-5577)Aaa>Gaa	p.K1859E	AHCTF1_ENST00000470300.1_5'UTR|AHCTF1_ENST00000366508.1_Missense_Mutation_p.K1894E|AHCTF1_ENST00000326225.3_Missense_Mutation_p.K1868E			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	1859	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)			ACTTCTTTTTTAGTAGTTTCT	0.328													T|||	222	0.0443291	0.1657	0.0043	5008	,	,		19442	0.0		0.0	False		,,,				2504	0.0				p.K1868E	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.A5602G						PASS	.	T	GLU/LYS	482,3810		21,440,1685	23	25	24		5602	5.2	0.4	1	dbSNP_134	24	6,8524		0,6,4259	no	missense	AHCTF1	NM_015446.4	56	21,446,5944	CC,CT,TT		0.0703,11.2302,3.806	benign	1868/2276	247013733	488,12334	2146	4265	6411	SO:0001583	missense	25909	exon33			CTTTTTTAGTAGT		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.5575A>G	1.37:g.247013733T>C	ENSP00000375705:p.Lys1859Glu	406	0	0		408	167	0.409314	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Missense_Mutation	SNP	ENST00000391829.2	37		75	0.034340659340659344	74	0.15040650406504066	1	0.0027624309392265192	0	0.0	0	0.0	T	0	-2.799134	0.00076	0.112302	7.03E-4	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	T;T;T	0.29917	1.55;1.55;1.55	5.15	5.15	0.70609	.	2.053990	0.02125	N	0.055937	T	0.00109	0.0003	N	0.22421	0.69	0.09310	N	1	B;B;B	0.17667	0.014;0.016;0.023	B;B;B	0.14023	0.004;0.01;0.007	T	0.37979	-0.9682	10	0.05959	T	0.93	-0.8216	4.3077	0.10955	0.1767:0.097:0.0:0.7263	.	720;1894;1859	B3KTD2;Q8WYP5-2;Q8WYP5	.;.;ELYS_HUMAN	E	1894;1868;1859	ENSP00000355464:K1894E;ENSP00000355465:K1868E;ENSP00000375705:K1859E	ENSP00000355465:K1868E	K	-	1	0	AHCTF1	245080356	0.010000	0.17322	0.450000	0.26969	0.205000	0.24178	1.124000	0.31320	1.927000	0.55829	0.533000	0.62120	AAA	.	.	weak		0.328	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446		C	247013733	T	C	247013733	3	2	22	1	0	0	0	0	1	0	0	0	408	1763	61	3	1241	3	AHCTF1	1	247013733	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	530	247013733	2236888	490	3391											
ZNF695	57116	hgsc.bcm.edu	37	chr1	247150631	247150631	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgaattctcttatgctgaaTaaggtatgagaaccaggtaa	15	12	9	5	0	1	3	0	3	1	1	2	4	1	3	1	2	2	3	1	2	7	5	rs77178548	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:247150631T>C	ENST00000339986.7	-	4	1333	c.1186A>G	c.(1186-1188)Att>Gtt	p.I396V	ZNF695_ENST00000498046.2_Intron|ZNF695_ENST00000487338.2_Intron	NM_020394.4	NP_065127	Q8IW36	ZN695_HUMAN	zinc finger protein 695	396					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)			TTATGCTGAATAAGGTATGAG	0.398													T|||	157	0.0313498	0.1165	0.0043	5008	,	,		21162	0.0		0.0	False		,,,				2504	0.0				p.I396V		Atlas-SNP	.											.	ZNF695	55	.	0			c.A1186G						PASS	.	T	,VAL/ILE	387,3903		17,353,1775	51	55	53		,1186	0.6	0	1	dbSNP_132	53	3,8535		0,3,4266	no	intron,missense	ZNF695	NM_001204221.1,NM_020394.4	,29	17,356,6041	CC,CT,TT		0.0351,9.021,3.0402	,benign	,396/516	247150631	390,12438	2145	4269	6414	SO:0001583	missense	57116	exon4			GCTGAATAAGGTA		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.1186A>G	1.37:g.247150631T>C	ENSP00000341236:p.Ile396Val	46	0	0		54	24	0.444444	NM_020394	Q5T0N9|Q5T0P1|Q5T0P3|Q7Z2W8|Q7Z648	Missense_Mutation	SNP	ENST00000339986.7	37	CCDS44344.1	54	0.024725274725274724	52	0.10569105691056911	2	0.0055248618784530384	0	0.0	0	0.0	T	11.16	1.556933	0.27827	0.09021	3.51E-4	ENSG00000197472	ENST00000339986	T	0.07216	3.21	0.642	0.642	0.17765	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00073	0.0002	N	0.02111	-0.68	0.09310	N	1	B	0.17465	0.022	B	0.08055	0.003	T	0.44742	-0.9308	9	0.66056	D	0.02	.	5.509	0.16870	0.0:1.0E-4:0.0:0.9999	.	396	Q8IW36	ZN695_HUMAN	V	396	ENSP00000341236:I396V	ENSP00000341236:I396V	I	-	1	0	ZNF695	245217254	0.000000	0.05858	0.009000	0.14445	0.744000	0.42396	-0.039000	0.12124	0.534000	0.28695	0.172000	0.16884	ATT	T|0.968;C|0.032	0.032	strong		0.398	ZNF695-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097823.5	NM_020394		C	247150631	T	C	247150631	3	2	22	1	0	0	0	0	1	0	0	0	18113	1406	49	3	365	3	ZNF695	1	247150631	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	136898	247150631	2099990	491	3392											
OR2G2	81470	hgsc.bcm.edu	37	chr1	247751936	247751936	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtaaacctgtgggaacccaTgaaaactatcgcctatggtg	12	9	11	9	1	0	1	0	1	0	0	1	2	0	2	3	3	3	1	3	3	7	3	rs146039934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:247751936T>G	ENST00000320065.1	+	1	275	c.275T>G	c.(274-276)aTg>aGg	p.M92R	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	92						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)			TGGGAACCCATGAAAACTATC	0.527													t|||	30	0.00599042	0.0219	0.0014	5008	,	,		21752	0.0		0.0	False		,,,				2504	0.0				p.M92R		Atlas-SNP	.											.	OR2G2	88	.	0			c.T275G						PASS	.	C	ARG/MET	98,4308	79.9+/-118.3	1,96,2106	185	152	163		275	-6.5	0	1	dbSNP_134	163	0,8600		0,0,4300	yes	missense	OR2G2	NM_001001915.1	91	1,96,6406	GG,GT,TT		0.0,2.2242,0.7535	benign	92/318	247751936	98,12908	2203	4300	6503	SO:0001583	missense	81470	exon1			AACCCATGAAAAC	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.275T>G	1.37:g.247751936T>G	ENSP00000326349:p.Met92Arg	354	0	0		347	176	0.507205	NM_001001915	Q5JQT2|Q6IEZ0	Missense_Mutation	SNP	ENST00000320065.1	37	CCDS31092.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	t	2.892	-0.229477	0.06022	0.022242	0.0	ENSG00000177489	ENST00000320065	T	0.01347	4.99	4.29	-6.53	0.01866	GPCR, rhodopsin-like superfamily (1);	2.209360	0.02699	U	0.111542	T	0.00271	0.0008	N	0.00408	-1.53	0.09310	N	1	B	0.16396	0.017	B	0.22753	0.041	T	0.49934	-0.8886	10	0.30078	T	0.28	.	1.2983	0.02074	0.4808:0.1651:0.1223:0.2318	.	92	Q8NGZ5	OR2G2_HUMAN	R	92	ENSP00000326349:M92R	ENSP00000326349:M92R	M	+	2	0	OR2G2	245818559	0.000000	0.05858	0.000000	0.03702	0.145000	0.21501	-0.280000	0.08468	-0.902000	0.03886	-0.332000	0.08345	ATG	T|0.994;G|0.006	0.006	strong		0.527	OR2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097623.1			G	247751936	T	G	247751936	3	3	22	1	0	0	0	0	1	0	0	0	11007	1464	51	5	277	5	OR2G2	1	247751936	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	601305	247751936	1498685	492	3393											
OR14A16	284532	hgsc.bcm.edu	37	chr1	247978768	247978768	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagccaaggaatgaaatggaGttgttgtgtatcaaagaatt	15	11	11	4	0	1	2	1	1	0	1	1	4	1	4	1	2	1	3	1	2	6	4	rs61740923	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:247978768G>A	ENST00000357627.1	-	1	263	c.264C>T	c.(262-264)aaC>aaT	p.N88N		NM_001001966.1	NP_001001966.1	Q8NHC5	O14AG_HUMAN	olfactory receptor, family 14, subfamily A, member 16	88						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						ATGAAATGGAGTTGTTGTGTA	0.448													g|||	78	0.0155751	0.053	0.0029	5008	,	,		19549	0.0		0.003	False		,,,				2504	0.0031				p.N88N	Ovarian(112;180 1586 15073 21914 33526)	Atlas-SNP	.											.	OR14A16	90	.	0			c.C264T						PASS	.	T		187,4219	120.4+/-158.0	7,173,2023	91	91	91		264	-0.9	0	1	dbSNP_129	91	19,8581	14.0+/-48.4	0,19,4281	no	coding-synonymous	OR14A16	NM_001001966.1		7,192,6304	AA,AG,GG		0.2209,4.2442,1.5839		88/310	247978768	206,12800	2203	4300	6503	SO:0001819	synonymous_variant	284532	exon1			AATGGAGTTGTTG	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.264C>T	1.37:g.247978768G>A		191	0	0		203	84	0.413793	NM_001001966	Q6IF96	Silent	SNP	ENST00000357627.1	37	CCDS31097.1																																																																																			G|0.986;A|0.014	0.014	strong		0.448	OR14A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096856.1	NM_001001966		A	247978768	G	A	247978768	2	1	22	1	0	0	0	0	0	0	0	1	10954	1020	36	2		2	OR14A16	1	247978768	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	226832	247978768	1271853	493	3394											
OR2T12	127064	hgsc.bcm.edu	37	chr1	248458718	248458718	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggaggaagtacatgggccTgtggagccggtggtcccagt	8	7	17	9	1	0	0	0	0	0	0	1	3	1	3	3	6	2	1	3	6	2	1	rs79635253	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248458718T>C	ENST00000317996.1	-	1	162	c.163A>G	c.(163-165)Agg>Ggg	p.R55G		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, 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)			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)			TACATGGGCCTGTGGAGCCGG	0.527													-|||	151	0.0301518	0.0915	0.0144	5008	,	,		12875	0.001		0.0169	False		,,,				2504	0.002				p.R55G		Atlas-SNP	.											.	OR2T12	113	.	0			c.A163G						PASS	.	T	GLY/ARG	443,3963	195.7+/-220.2	54,335,1814	81	65	70		163	1.5	0.2	1	dbSNP_131	70	170,8426	69.0+/-131.5	10,150,4138	no	missense	OR2T12	NM_001004692.1	125	64,485,5952	CC,CT,TT		1.9777,10.0545,4.7147	benign	55/321	248458718	613,12389	2203	4298	6501	SO:0001583	missense	127064	exon1			TGGGCCTGTGGAG	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.163A>G	1.37:g.248458718T>C	ENSP00000324583:p.Arg55Gly	491	1	0.00203666		530	345	0.650943	NM_001004692		Missense_Mutation	SNP	ENST00000317996.1	37	CCDS31110.1	82	0.037545787545787544	51	0.10365853658536585	8	0.022099447513812154	0	0.0	23	0.030343007915567283	t	9.783	1.175918	0.21704	0.100545	0.019777	ENSG00000177201	ENST00000317996	T	0.00384	7.6	1.55	1.55	0.23275	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36303	U	0.002679	T	0.00012	0.0000	L	0.52011	1.625	0.09310	N	0.999998	B	0.12013	0.005	B	0.14023	0.01	T	0.51371	-0.8714	10	0.87932	D	0	.	4.983	0.14176	0.2683:0.0:0.0:0.7317	.	55	Q8NG77	O2T12_HUMAN	G	55	ENSP00000324583:R55G	ENSP00000324583:R55G	R	-	1	2	OR2T12	246525341	0.001000	0.12720	0.159000	0.22649	0.174000	0.22865	-0.039000	0.12124	0.540000	0.28808	0.147000	0.16070	AGG	T|0.961;C|0.039	0.039	strong		0.527	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692		C	248458718	T	C	248458718	3	2	22	1	0	0	0	0	1	0	0	0	11028	1579	55	3	802	3	OR2T12	1	248458718	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	479950	248458718	791903	494	3395											
OR2T4	127074	hgsc.bcm.edu	37	chr1	248524974	248524974	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atccaaacatccaatggccaAtatcacctggatggccaacc	14	7	6	14	0	1	0	1	0	0	0	3	1	3	1	6	3	2	0	6	3	5	1	rs57795102	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248524974A>G	ENST00000366475.1	+	1	92	c.92A>G	c.(91-93)aAt>aGt	p.N31S		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	31			N -> S (in dbSNP:rs57795102).			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)			CCAATGGCCAATATCACCTGG	0.478													a|||	348	0.0694888	0.2337	0.0331	5008	,	,		15454	0.002		0.0109	False		,,,				2504	0.0031				p.N31S		Atlas-SNP	.											OR2T4,NS,adenocarcinoma,-1,1	OR2T4	126	1	0			c.A92G						PASS	.	A	SER/ASN	939,3461		137,665,1398	112	96	102		92	0.2	0.1	1	dbSNP_129	102	98,8342		12,74,4134	yes	missense	OR2T4	NM_001004696.1	46	149,739,5532	GG,GA,AA		1.1611,21.3409,8.0763	benign	31/349	248524974	1037,11803	2200	4220	6420	SO:0001583	missense	127074	exon1			TGGCCAATATCAC	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.92A>G	1.37:g.248524974A>G	ENSP00000355431:p.Asn31Ser	775	1	0.00129032		800	387	0.48375	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	37	CCDS31113.1	149	0.06822344322344322	130	0.26422764227642276	10	0.027624309392265192	0	0.0	9	0.011873350923482849	A	3.277	-0.147841	0.06627	0.213409	0.011611	ENSG00000196944	ENST00000366475	T	0.36340	1.26	0.189	0.189	0.15119	.	1.272670	0.05590	N	0.574537	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.11235	0.004	B	0.09377	0.004	T	0.34428	-0.9829	8	0.25751	T	0.34	.	.	.	.	rs57795102	31	Q8NH00	OR2T4_HUMAN	S	31	ENSP00000355431:N31S	ENSP00000355431:N31S	N	+	2	0	OR2T4	246591597	0.000000	0.05858	0.062000	0.19696	0.036000	0.12997	-0.514000	0.06298	0.250000	0.21479	0.248000	0.18094	AAT	A|0.925;G|0.075	0.075	strong		0.478	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696		G	248524974	A	G	248524974	3	3	22	1	0	0	0	0	1	0	0	0	11036	101	4	3	94	3	OR2T4	1	248524974	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	66256	248524974	725647	495	3396											
OR2T3	343173	hgsc.bcm.edu	37	chr1	248636934	248636934	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggccaggtcactggagatGataccatttccccgtcaggc	8	9	12	12	1	2	2	2	1	0	1	3	3	3	2	4	4	1	0	4	4	1	2	rs148766825	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248636934G>T	ENST00000359594.2	+	1	308	c.283G>T	c.(283-285)Gat>Tat	p.D95Y		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	95						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)			CACTGGAGATGATACCATTTC	0.552													.|||	287	0.0573083	0.2065	0.0173	5008	,	,		20624	0.0		0.001	False		,,,				2504	0.001				p.D95Y		Atlas-SNP	.											.	OR2T3	79	.	0			c.G283T						PASS	.	T	TYR/ASP	740,3640	744.5+/-411.6	104,532,1554	59	51	54		283	-3.5	0	1	dbSNP_134	54	11,8581	817.4+/-406.9	0,11,4285	no	missense	OR2T3	NM_001005495.1	160	104,543,5839	TT,TG,GG		0.128,16.895,5.7894	benign	95/319	248636934	751,12221	2190	4296	6486	SO:0001583	missense	343173	exon1			GGAGATGATACCA		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.283G>T	1.37:g.248636934G>T	ENSP00000352604:p.Asp95Tyr	635	2	0.00314961		441	278	0.630385	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	37	CCDS31117.1	101	0.04624542124542125	96	0.1951219512195122	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	t	5.919	0.353667	0.11182	0.16895	0.00128	ENSG00000196539	ENST00000359594	T	0.36340	1.26	2.65	-3.45	0.04781	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22034	-1.0228	9	0.72032	D	0.01	.	1.1933	0.01869	0.4366:0.2119:0.224:0.1274	.	95	Q8NH03	OR2T3_HUMAN	Y	95	ENSP00000352604:D95Y	ENSP00000352604:D95Y	D	+	1	0	OR2T3	246703557	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.501000	0.22578	-2.758000	0.00371	-3.175000	0.00056	GAT	G|1.000;|0.000	.	weak		0.552	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495		T	248636934	G	T	248636934	3	4	22	1	0	0	0	0	1	0	0	0	11032	1290	45	4	285	4	OR2T3	1	248636934	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	111960	248636934	613687	496	3397											
OR2T34	127068	hgsc.bcm.edu	37	chr1	248737419	248737419	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagatgaccatgatgggggTgagaagcatgaggatgcagc	12	6	18	5	0	0	5	0	4	0	2	0	8	0	6	1	4	3	2	1	4	1	0	rs145854970		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248737419T>C	ENST00000328782.2	-	1	661	c.640A>G	c.(640-642)Acc>Gcc	p.T214A		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	214						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)			ATGATGGGGGTGAGAAGCATG	0.557																																					p.T214A		Atlas-SNP	.											OR2T34,NS,carcinoma,+1,2	OR2T34	72	2	0			c.A640G						scavenged	.						196	210	206					1																	248737419		2114	4300	6414	SO:0001583	missense	127068	exon1			TGGGGGTGAGAAG	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.640A>G	1.37:g.248737419T>C	ENSP00000330904:p.Thr214Ala	307	0	0		206	17	0.0825243	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Missense_Mutation	SNP	ENST00000328782.2	37	CCDS31120.1	.	.	.	.	.	.	.	.	.	.	.	8.088	0.773777	0.16051	.	.	ENSG00000183310	ENST00000328782	T	0.36520	1.25	2.37	-2.05	0.07321	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.15609	0.0376	N	0.11818	0.18	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22208	-1.0223	9	0.59425	D	0.04	.	0.341	0.00334	0.2537:0.2468:0.1387:0.3608	.	214	Q8NGX1	O2T34_HUMAN	A	214	ENSP00000330904:T214A	ENSP00000330904:T214A	T	-	1	0	OR2T34	246804042	0.000000	0.05858	0.035000	0.18076	0.091000	0.18340	-0.914000	0.04038	-0.298000	0.08921	-1.680000	0.00737	ACC	.	.	weak		0.557	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821		C	248737419	T	C	248737419	3	2	22	1	0	0	0	0	1	0	0	0	11034	1696	59	3	320	3	OR2T34	1	248737419	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	100485	248737419	513202	497	3398											
OR2T27	403239	hgsc.bcm.edu	37	chr1	248813309	248813310	+	Frame_Shift_Ins	INS	-	-	A																															cctgtgacatccttgttcctINSaaggctgtaaatgagtggat																								rs141113411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248813309_248813310insA	ENST00000344889.3	-	1	875_876	c.876_877insT	c.(874-879)cttaggfs	p.R293fs		NM_001001824.1	NP_001001824.1	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T, member 27	293						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)			TCCTTGTTCCTAAGGCTGTAAA	0.485													AA|AA|AAA|insertion	231	0.0461262	0.1664	0.013	5008	,	,		19512	0.0		0.0	False		,,,				2504	0.002				p.R293_N294delinsX		Atlas-Indel	.											.	OR2T27	52	.	0			c.877_878insT						PASS	.			510,3700		101,308,1696						0.7	0.2		dbSNP_134	74	5,8185		0,5,4090	no	frameshift	OR2T27	NM_001001824.1		101,313,5786	A1A1,A1R,RR		0.0611,12.114,4.1532				515,11885				SO:0001589	frameshift_variant	403239	exon1			.		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.877dupT	1.37:g.248813311_248813311dupA	ENSP00000342008:p.Arg293fs	280	0	0		251	39	0.155378	NM_001001824		Frame_Shift_Ins	INS	ENST00000344889.3	37	CCDS31124.1																																																																																			-|0.960;A|0.040	0.040	strong		0.485	OR2T27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097124.1	NM_001001824		A	248813310	-	A	248813309	7	5	22	1	0	1	1	0	0	0	0	0	11030	1521	53	0	79	0	OR2T27	1	248813309	Frame_Shift_Ins	INS	-	TCGA-G8-6324-01A-11D-2210-10	75890	248813309	437312	498	3399			2	25	96527768	4	4	165	N	G_A_-	2.156859e-06
OR2T27	403239	hgsc.bcm.edu	37	chr1	248813352	248813352	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agcatgggagtaaggatggtGtagaaggcagatacagcttt	13	9	15	4	0	0	2	0	0	0	2	0	4	0	4	0	4	3	5	0	4	4	4	rs147773385	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248813352G>A	ENST00000344889.3	-	1	833	c.834C>T	c.(832-834)taC>taT	p.Y278Y		NM_001001824.1	NP_001001824.1	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T, member 27	278						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Y278*(1)		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)			TAAGGATGGTGTAGAAGGCAG	0.522													G|||	106	0.0211661	0.0772	0.0058	5008	,	,		16990	0.0		0.0	False		,,,				2504	0.0				p.Y278Y		Atlas-SNP	.											OR2T27,colon,carcinoma,0,1	OR2T27	52	1	1	Substitution - Nonsense(1)	large_intestine(1)	c.C834T						scavenged	.	G		158,4196		8,142,2027	78	73	74		834	0.4	1	1	dbSNP_134	74	0,8548		0,0,4274	no	coding-synonymous	OR2T27	NM_001001824.1		8,142,6301	AA,AG,GG		0.0,3.6288,1.2246		278/318	248813352	158,12744	2177	4274	6451	SO:0001819	synonymous_variant	403239	exon1			GATGGTGTAGAAG		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.834C>T	1.37:g.248813352G>A		246	0	0		166	26	0.156627	NM_001001824		Silent	SNP	ENST00000344889.3	37	CCDS31124.1																																																																																			G|0.986;A|0.014	0.014	strong		0.522	OR2T27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097124.1	NM_001001824		A	248813352	G	A	248813352	2	1	22	1	0	0	0	0	0	0	0	1	11030	1372	48	2		2	OR2T27	1	248813352	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	43	248813352	437269	499	3400			2	25	96527768	4	4	165	N	G_A_-	2.156859e-06
OR2T27	403239	hgsc.bcm.edu	37	chr1	248813421	248813421	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcagcacgtatgtgtacatGgcagccccatagaagaggct	11	7	13	10	1	0	2	0	0	0	2	0	2	0	2	2	3	3	6	2	3	4	3	rs200410497	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248813421G>A	ENST00000344889.3	-	1	764	c.765C>T	c.(763-765)gcC>gcT	p.A255A		NM_001001824.1	NP_001001824.1	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T, member 27	255						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)			ATGTGTACATGGCAGCCCCAT	0.527													G|||	320	0.0638978	0.2292	0.0231	5008	,	,		17935	0.0		0.001	False		,,,				2504	0.0				p.A255A		Atlas-SNP	.											.	OR2T27	52	.	0			c.C765T						PASS	.	G		669,3711		76,517,1597	39	30	33		765	0.1	0	1	dbSNP_134	33	6,8522		0,6,4258	no	coding-synonymous	OR2T27	NM_001001824.1		76,523,5855	AA,AG,GG		0.0704,15.274,5.2293		255/318	248813421	675,12233	2190	4264	6454	SO:0001819	synonymous_variant	403239	exon1			GTACATGGCAGCC		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.765C>T	1.37:g.248813421G>A		163	0	0		154	69	0.448052	NM_001001824		Silent	SNP	ENST00000344889.3	37	CCDS31124.1																																																																																			G|0.969;A|0.031	0.031	strong		0.527	OR2T27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097124.1	NM_001001824		A	248813421	G	A	248813421	2	1	22	1	0	0	0	0	0	0	0	1	11030	1335	47	2		2	OR2T27	1	248813421	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	69	248813421	437200	500	3401			2	25	96527768	4	4	165	N	G_A_-	2.156859e-06
OR2T27	403239	hgsc.bcm.edu	37	chr1	248813473	248813473	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgtgaggagcaggtggccAcagcctttcccctcccctct	5	10	11	15	0	1	1	0	1	1	0	3	2	3	2	6	3	2	1	6	3	0	1	rs78776291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248813473A>C	ENST00000344889.3	-	1	712	c.713T>G	c.(712-714)gTg>gGg	p.V238G		NM_001001824.1	NP_001001824.1	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T, member 27	238						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)			GCAGGTGGCCACAGCCTTTCC	0.527													A|||	333	0.0664936	0.2375	0.0245	5008	,	,		19295	0.0		0.002	False		,,,				2504	0.0				p.V238G		Atlas-SNP	.											.	OR2T27	52	.	0			c.T713G						PASS	.	A	GLY/VAL	869,3497		137,595,1451	49	32	38		713	2.3	0.6	1	dbSNP_131	38	8,8502		0,8,4247	no	missense	OR2T27	NM_001001824.1	109	137,603,5698	CC,CA,AA		0.094,19.9038,6.8111	possibly-damaging	238/318	248813473	877,11999	2183	4255	6438	SO:0001583	missense	403239	exon1			GTGGCCACAGCCT		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.713T>G	1.37:g.248813473A>C	ENSP00000342008:p.Val238Gly	110	0	0		193	108	0.559586	NM_001001824		Missense_Mutation	SNP	ENST00000344889.3	37	CCDS31124.1	119	0.05448717948717949	116	0.23577235772357724	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	.	9.994	1.231495	0.22626	0.199038	9.4E-4	ENSG00000187701	ENST00000344889	T	0.00158	8.65	3.42	2.28	0.28536	GPCR, rhodopsin-like superfamily (1);	0.212577	0.23378	N	0.048838	T	0.00012	0.0000	L	0.33339	1.005	0.34364	P	0.308697	P	0.37038	0.579	B	0.43623	0.425	T	0.27400	-1.0075	9	0.87932	D	0	.	7.831	0.29342	0.8936:0.0:0.1064:0.0	.	238	Q8NH04	O2T27_HUMAN	G	238	ENSP00000342008:V238G	ENSP00000342008:V238G	V	-	2	0	OR2T27	246880096	0.031000	0.19500	0.564000	0.28396	0.057000	0.15508	3.181000	0.50903	0.513000	0.28278	-0.548000	0.04221	GTG	A|0.941;C|0.059	0.059	strong		0.527	OR2T27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097124.1	NM_001001824		C	248813473	A	C	248813473	3	2	22	1	0	0	0	0	1	0	0	0	11030	159	6	5	243	5	OR2T27	1	248813473	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	52	248813473	437148	501	3402			2	25	96527768	4	4	165	N	G_A_-	2.156859e-06
OR14I1	401994	hgsc.bcm.edu	37	chr1	248844695	248844695	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgcagaaaatatatcttcAcaaagagtctccacatggct	14	12	6	9	0	3	2	1	0	2	2	4	2	3	2	1	1	1	2	1	1	5	4	rs114135727	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248844695A>T	ENST00000342623.3	-	1	934	c.911T>A	c.(910-912)gTg>gAg	p.V304E		NM_001004734.1	NP_001004734.1	A6ND48	O14I1_HUMAN	olfactory receptor, family 14, subfamily I, member 1	304						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						ATATATCTTCACAAAGAGTCT	0.353													A|||	95	0.0189696	0.0703	0.0029	5008	,	,		17508	0.0		0.0	False		,,,				2504	0.0				p.V304E		Atlas-SNP	.											.	OR14I1	64	.	0			c.T911A						PASS	.	A	GLU/VAL	283,4123		10,263,1930	51	54	53		911	-2.2	0	1	dbSNP_132	53	0,8600		0,0,4300	yes	missense	OR14I1	NM_001004734.1	121	10,263,6230	TT,TA,AA		0.0,6.4231,2.1759	benign	304/312	248844695	283,12723	2203	4300	6503	SO:0001583	missense	401994	exon1			ATCTTCACAAAGA		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.911T>A	1.37:g.248844695A>T	ENSP00000339726:p.Val304Glu	43	0	0		51	24	0.470588	NM_001004734		Missense_Mutation	SNP	ENST00000342623.3	37	CCDS31125.1	39	0.017857142857142856	39	0.07926829268292683	0	0.0	0	0.0	0	0.0	.	0.008	-1.879400	0.00537	0.064231	0.0	ENSG00000189181	ENST00000342623	T	0.37235	1.21	2.84	-2.22	0.06952	.	2.383690	0.01770	N	0.031135	T	0.00637	0.0021	N	0.04373	-0.215	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.11084	-1.0602	10	0.06236	T	0.91	.	0.9342	0.01341	0.3966:0.2734:0.1869:0.1431	.	304	A6ND48	O14I1_HUMAN	E	304	ENSP00000339726:V304E	ENSP00000339726:V304E	V	-	2	0	OR14I1	246911318	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-1.457000	0.02374	-0.041000	0.13558	-0.505000	0.04504	GTG	A|0.982;T|0.018	0.018	strong		0.353	OR14I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097128.1	NM_001004734		T	248844695	A	T	248844695	3	4	22	1	0	0	0	0	1	0	0	0	10956	159	6	5	28	5	OR14I1	1	248844695	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	31222	248844695	405926	502	3403											
TPO	7173	hgsc.bcm.edu	37	chr2	1418188	1418188	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgttaattttagaatgagagCgctcgctgtgctgtctgtca	8	14	11	8	3	2	2	1	1	1	2	3	3	2	2	0	0	2	4	0	0	3	3	rs151268825	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:1418188C>T	ENST00000345913.4	+	2	99	c.8C>T	c.(7-9)gCg>gTg	p.A3V	TPO_ENST00000382198.1_Missense_Mutation_p.A3V|TPO_ENST00000539820.1_Missense_Mutation_p.A3V|TPO_ENST00000349624.3_Missense_Mutation_p.A3V|TPO_ENST00000497517.2_Intron|TPO_ENST00000382269.3_Missense_Mutation_p.A3V|TPO_ENST00000337415.3_Missense_Mutation_p.A3V|TPO_ENST00000346956.3_Missense_Mutation_p.A3V|TPO_ENST00000329066.4_Missense_Mutation_p.A3V|TPO_ENST00000382201.3_Missense_Mutation_p.A3V	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	3					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)	AGAATGAGAGCGCTCGCTGTG	0.522													C|||	16	0.00319489	0.0106	0.0014	5008	,	,		16782	0.0		0.0	False		,,,				2504	0.001				p.A3V		Atlas-SNP	.											TPO,NS,carcinoma,-1,1	TPO	224	1	0			c.C8T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	16,4390	22.3+/-47.3	0,16,2187	71	69	70		8,8,8,8,8,8	-5.3	0	2	dbSNP_134	70	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense	TPO	NM_000547.5,NM_001206744.1,NM_001206745.1,NM_175719.3,NM_175721.3,NM_175722.3	64,64,64,64,64,64	0,16,6487	TT,TC,CC		0.0,0.3631,0.123	benign,benign,benign,benign,benign,benign	3/934,3/934,3/877,3/877,3/890,3/761	1418188	16,12990	2203	4300	6503	SO:0001583	missense	7173	exon2			TGAGAGCGCTCGC		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.8C>T	2.37:g.1418188C>T	ENSP00000318820:p.Ala3Val	144	0	0		128	65	0.507812	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	37	CCDS1643.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	10.67	1.414818	0.25465	0.003631	0.0	ENSG00000115705	ENST00000382269;ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000539820;ENST00000329066;ENST00000382201;ENST00000423320;ENST00000382198	T;T;T;T;T;T;T;T;T;T	0.65732	0.31;-0.17;-0.17;-0.11;0.15;0.31;-0.17;-0.06;0.34;0.15	5.39	-5.3	0.02738	.	1.351910	0.04684	N	0.412836	T	0.41903	0.1179	N	0.13043	0.29	0.09310	N	1	B;B;B;B;B	0.17852	0.003;0.012;0.024;0.014;0.004	B;B;B;B;B	0.10450	0.005;0.003;0.003;0.001;0.002	T	0.32161	-0.9917	10	0.41790	T	0.15	-1.8566	9.1002	0.36664	0.0:0.1854:0.127:0.6876	.	3;3;3;3;3	P07202-4;P07202-5;E9PFM6;P07202-2;P07202	.;.;.;.;PERT_HUMAN	V	3	ENSP00000371704:A3V;ENSP00000337263:A3V;ENSP00000318820:A3V;ENSP00000263886:A3V;ENSP00000332044:A3V;ENSP00000444840:A3V;ENSP00000329869:A3V;ENSP00000371636:A3V;ENSP00000390994:A3V;ENSP00000371633:A3V	ENSP00000329869:A3V	A	+	2	0	TPO	1397195	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.480000	0.00983	-0.936000	0.03723	-0.768000	0.03414	GCG	C|0.999;T|0.001	0.001	strong		0.522	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		T	1418188	C	T	1418188	3	4	22	1	0	0	0	0	1	0	0	0	16425	768	27	1	10	1	TPO	2	1418188	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10		1418188	241781185	503	3404											
PXDN	7837	hgsc.bcm.edu	37	chr2	1642700	1642700	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccagatgcatctgagcgtGtgctgaaggctgaggtgctg	7	10	15	9	1	1	4	0	3	1	1	2	4	2	4	1	2	4	4	1	2	1	0	rs61747875	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:1642700G>A	ENST00000252804.4	-	21	4174	c.4124C>T	c.(4123-4125)aCa>aTa	p.T1375I		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	1375					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)		ATCTGAGCGTGTGCTGAAGGC	0.537													G|||	52	0.0103834	0.0363	0.0043	5008	,	,		20910	0.0		0.001	False		,,,				2504	0.0				p.T1375I		Atlas-SNP	.											.	PXDN	255	.	0			c.C4124T						PASS	.	G	ILE/THR	103,4175		1,101,2037	127	133	131		4124	3	0.1	2	dbSNP_129	131	5,8483		0,5,4239	yes	missense	PXDN	NM_012293.1	89	1,106,6276	AA,AG,GG		0.0589,2.4077,0.846	benign	1375/1480	1642700	108,12658	2139	4244	6383	SO:0001583	missense	7837	exon21			GAGCGTGTGCTGA	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.4124C>T	2.37:g.1642700G>A	ENSP00000252804:p.Thr1375Ile	130	0	0		131	53	0.40458	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	37	CCDS46221.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	G	10.13	1.265304	0.23136	0.024077	5.89E-4	ENSG00000130508	ENST00000252804	T	0.61040	0.14	5.43	3.05	0.35203	.	0.558829	0.19914	N	0.103226	T	0.08268	0.0206	N	0.03608	-0.345	0.20074	N	0.999932	B	0.16603	0.018	B	0.15484	0.013	T	0.07693	-1.0759	10	0.41790	T	0.15	-30.0156	7.522	0.27633	0.1358:0.0:0.1542:0.71	.	1375	Q92626	PXDN_HUMAN	I	1375	ENSP00000252804:T1375I	ENSP00000252804:T1375I	T	-	2	0	PXDN	1621707	0.735000	0.28153	0.080000	0.20451	0.000000	0.00434	3.286000	0.51724	0.446000	0.26666	-1.114000	0.02060	ACA	G|0.990;A|0.010	0.010	strong		0.537	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		A	1642700	G	A	1642700	3	1	22	1	0	0	0	0	1	0	0	0	12862	1377	48	2	327	2	PXDN	2	1642700	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	224512	1642700	241556673	504	3405											
PXDN	7837	hgsc.bcm.edu	37	chr2	1642736	1642736	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgctgttgctgagatgttccCcctgtctcccaacactgtgg	5	13	10	13	0	1	1	0	1	1	1	3	2	2	1	3	1	3	4	3	1	1	2	rs61747868	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:1642736C>T	ENST00000252804.4	-	21	4138	c.4088G>A	c.(4087-4089)gGg>gAg	p.G1363E		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	1363					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)		GAGATGTTCCCCCTGTCTCCC	0.527													C|||	49	0.00978435	0.034	0.0043	5008	,	,		20724	0.0		0.001	False		,,,				2504	0.0				p.G1363E		Atlas-SNP	.											.	PXDN	255	.	0			c.G4088A						PASS	.	C	GLU/GLY	96,4162		1,94,2034	103	106	105		4088	3.2	0	2	dbSNP_129	105	5,8489		0,5,4242	yes	missense	PXDN	NM_012293.1	98	1,99,6276	TT,TC,CC		0.0589,2.2546,0.792	benign	1363/1480	1642736	101,12651	2129	4247	6376	SO:0001583	missense	7837	exon21			TGTTCCCCCTGTC	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.4088G>A	2.37:g.1642736C>T	ENSP00000252804:p.Gly1363Glu	105	0	0		107	47	0.439252	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	37	CCDS46221.1	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	C	0.157	-1.085078	0.01888	0.022546	5.89E-4	ENSG00000130508	ENST00000252804	T	0.58652	0.32	5.07	3.21	0.36854	.	1.792660	0.02747	N	0.116942	T	0.22205	0.0535	L	0.36672	1.1	0.09310	N	1	B	0.16603	0.018	B	0.18263	0.021	T	0.24728	-1.0152	10	0.02654	T	1	-1.7644	7.7153	0.28700	0.0:0.7222:0.0:0.2778	.	1363	Q92626	PXDN_HUMAN	E	1363	ENSP00000252804:G1363E	ENSP00000252804:G1363E	G	-	2	0	PXDN	1621743	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.343000	0.19944	0.604000	0.29930	0.563000	0.77884	GGG	C|0.992;T|0.008	0.008	strong		0.527	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		T	1642736	C	T	1642736	3	4	22	1	0	0	0	0	1	0	0	0	12862	623	22	2	363	2	PXDN	2	1642736	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	36	1642736	241556637	505	3406											
PXDN	7837	hgsc.bcm.edu	37	chr2	1647186	1647186	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtctaccctggggatctcGtcacagctgccgtagccgtg	6	9	13	13	3	3	0	1	0	2	0	4	1	3	1	3	3	4	2	3	3	2	2	rs111450110	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:1647186G>A	ENST00000252804.4	-	19	3956	c.3906C>T	c.(3904-3906)gaC>gaT	p.D1302D		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	1302					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)		TGGGGATCTCGTCACAGCTGC	0.612													G|||	57	0.0113818	0.0393	0.0072	5008	,	,		16011	0.0		0.0	False		,,,				2504	0.0				p.D1302D		Atlas-SNP	.											.	PXDN	255	.	0			c.C3906T						PASS	.	G		167,4063		5,157,1953	65	76	72		3906	-9	0	2	dbSNP_132	72	1,8443		0,1,4221	yes	coding-synonymous	PXDN	NM_012293.1		5,158,6174	AA,AG,GG		0.0118,3.948,1.3255		1302/1480	1647186	168,12506	2115	4222	6337	SO:0001819	synonymous_variant	7837	exon19			GATCTCGTCACAG	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.3906C>T	2.37:g.1647186G>A		65	0	0		71	31	0.43662	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Silent	SNP	ENST00000252804.4	37	CCDS46221.1																																																																																			G|0.992;A|0.008	0.008	strong		0.612	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		A	1647186	G	A	1647186	2	1	22	1	0	0	0	0	0	0	0	1	12862	1136	40	1		1	PXDN	2	1647186	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4450	1647186	241552187	506	3407											
TTC15	51112	hgsc.bcm.edu	37	chr2	3425731	3425731	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ccagggctacggcaagagcgGgctgctcaccagccacacga	10	3	13	15	3	1	1	1	0	0	1	1	2	1	1	3	3	4	4	3	3	2	1	rs35775829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:3425731G>A	ENST00000324266.5	+	4	1439	c.1244G>A	c.(1243-1245)gGg>gAg	p.G415E	TRAPPC12_ENST00000382110.2_Missense_Mutation_p.G415E	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	415					vesicle-mediated transport (GO:0016192)												GGCAAGAGCGGGCTGCTCACC	0.587													G|||	30	0.00599042	0.0227	0.0	5008	,	,		18288	0.0		0.0	False		,,,				2504	0.0				p.G415E		Atlas-SNP	.											.	.	.	.	0			c.G1244A						PASS	.	G	GLU/GLY	107,4299	82.4+/-120.9	0,107,2096	32	31	31		1244	4.7	1	2	dbSNP_126	31	2,8598	2.2+/-6.3	0,2,4298	yes	missense	TTC15	NM_016030.5	98	0,109,6394	AA,AG,GG		0.0233,2.4285,0.8381	probably-damaging	415/736	3425731	109,12897	2203	4300	6503	SO:0001583	missense	51112	exon4			AGAGCGGGCTGCT	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.1244G>A	2.37:g.3425731G>A	ENSP00000324318:p.Gly415Glu	133	0	0		176	87	0.494318	NM_016030	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Missense_Mutation	SNP	ENST00000324266.5	37	CCDS1652.1	10|10	0.004578754578754579|0.004578754578754579	10|10	0.02032520325203252|0.02032520325203252	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	28.0|28.0	4.879029|4.879029	0.91740|0.91740	0.024285|0.024285	2.33E-4|2.33E-4	ENSG00000171853|ENSG00000171853	ENST00000382110;ENST00000304601;ENST00000324266|ENST00000441983	T;T|.	0.53206|.	0.63;0.63|.	4.72|4.72	4.72|4.72	0.59763|0.59763	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.61924|0.61924	0.2386|0.2386	M|M	0.82323|0.82323	2.585|2.585	0.80722|0.80722	D|D	1|1	D;P|.	0.53312|.	0.959;0.93|.	P;P|.	0.52881|.	0.712;0.712|.	T|T	0.68462|0.68462	-0.5402|-0.5402	10|7	0.44086|0.18710	T|T	0.13|0.47	.|.	16.8604|16.8604	0.86016|0.86016	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs35775829|rs35775829	398;415|.	E7ENL7;Q8WVT3|.	.;TPC12_HUMAN|.	E|S	415;398;415|95	ENSP00000371544:G415E;ENSP00000324318:G415E|.	ENSP00000303612:G398E|ENSP00000409960:G95S	G|G	+|+	2|1	0|0	TTC15|TTC15	3404738|3404738	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	7.184000|7.184000	0.77705|0.77705	2.439000|2.439000	0.82584|0.82584	0.563000|0.563000	0.77884|0.77884	GGG|GGC	G|0.992;A|0.008	0.008	strong		0.587	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030		A	3425731	G	A	3425731	3	1	22	1	0	0	0	0	1	0	0	0	16697	1232	43	2	1254	2	TTC15	2	3425731	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1778545	3425731	239773642	507	3408											
CMPK2	129607	hgsc.bcm.edu	37	chr2	7005236	7005236	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	caccaccgggtgcagcggggGctccgggacgggcacgacct	6	3	17	15	5	0	0	0	0	0	0	1	2	1	1	4	5	2	3	4	5	0	0	rs575313172		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:7005236G>T	ENST00000256722.5	-	1	591	c.592C>A	c.(592-594)Ccc>Acc	p.P198T	CMPK2_ENST00000404168.1_Missense_Mutation_p.P198T|CMPK2_ENST00000458098.1_Missense_Mutation_p.P198T|CMPK2_ENST00000478738.1_Intron	NM_207315.3	NP_997198.2	Q5EBM0	CMPK2_HUMAN	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	198					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)					TGCAGCGGGGGCTCCGGGACG	0.721													G|||	1	0.000199681	0.0008	0.0	5008	,	,		11581	0.0		0.0	False		,,,				2504	0.0				p.P198T		Atlas-SNP	.											.	CMPK2	30	.	0			c.C592A						PASS	.						3	5	4					2																	7005236		1735	3836	5571	SO:0001583	missense	129607	exon1			GCGGGGGCTCCGG		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.592C>A	2.37:g.7005236G>T	ENSP00000256722:p.Pro198Thr	6	0	0		12	6	0.5	NM_001256478	A2RUB0|A5D8T2|B7ZM18|Q6ZRU2|Q96AL8	Missense_Mutation	SNP	ENST00000256722.5	37	CCDS42648.1	.	.	.	.	.	.	.	.	.	.	G	18.09	3.547309	0.65311	.	.	ENSG00000134326	ENST00000458098;ENST00000256722;ENST00000404168	T	0.57436	0.4	4.43	3.55	0.40652	.	0.061334	0.64402	D	0.000003	T	0.55065	0.1897	L	0.29908	0.895	0.38526	D	0.948847	D;D	0.67145	0.996;0.994	P;P	0.62014	0.897;0.663	T	0.60311	-0.7288	10	0.66056	D	0.02	-21.992	10.2012	0.43084	0.0989:0.0:0.9011:0.0	.	198;198	Q5EBM0-3;Q5EBM0	.;CMPK2_HUMAN	T	198	ENSP00000256722:P198T	ENSP00000256722:P198T	P	-	1	0	CMPK2	6922687	1.000000	0.71417	0.566000	0.28421	0.894000	0.52154	2.696000	0.47052	1.069000	0.40788	0.563000	0.77884	CCC	.	.	none		0.721	CMPK2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323339.2	NM_207315		T	7005236	G	T	7005236	3	4	22	1	0	0	0	0	1	0	0	0	3583	1203	42	4	777	4	CMPK2	2	7005236	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3579505	7005236	236194137	508	3409											
MBOAT2	129642	hgsc.bcm.edu	37	chr2	8998971	8998971	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtattctttcttctttgagtTtttttcactggcaacaacaa	9	19	5	8	0	4	1	1	1	3	0	4	1	4	1	0	1	2	3	0	1	4	8	rs35943010	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:8998971T>C	ENST00000305997.3	-	13	1599	c.1401A>G	c.(1399-1401)aaA>aaG	p.K467K	MBOAT2_ENST00000486484.1_5'Flank	NM_138799.2	NP_620154.2	Q6ZWT7	MBOA2_HUMAN	membrane bound O-acyltransferase domain containing 2	467					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)					TTCTTTGAGTTTTTTTCACTG	0.318													T|||	74	0.0147764	0.0227	0.0086	5008	,	,		17674	0.003		0.004	False		,,,				2504	0.0317				p.K467K	Ovarian(194;1699 3813 22401)	Atlas-SNP	.											.	MBOAT2	36	.	0			c.A1401G						PASS	.	T		69,4337	61.7+/-98.7	1,67,2135	77	79	78		1401	1.2	0.8	2	dbSNP_126	78	14,8586	9.8+/-36.6	0,14,4286	no	coding-synonymous	MBOAT2	NM_138799.2		1,81,6421	CC,CT,TT		0.1628,1.566,0.6382		467/521	8998971	83,12923	2203	4300	6503	SO:0001819	synonymous_variant	129642	exon13			TTGAGTTTTTTTC	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.1401A>G	2.37:g.8998971T>C		130	0	0		106	45	0.424528	NM_138799	A9EDR2|Q8NCE7|Q96KY4	Silent	SNP	ENST00000305997.3	37	CCDS1660.1																																																																																			T|0.994;C|0.006	0.006	strong		0.318	MBOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206735.1	NM_138799		C	8998971	T	C	8998971	2	2	22	1	0	0	0	0	0	0	0	1	9366	1838	64	3		3	MBOAT2	2	8998971	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1993735	8998971	234200402	509	3410											
MBOAT2	129642	hgsc.bcm.edu	37	chr2	9013424	9013424	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aactaagagcttctgaacaaCcgcagtctgaaaagcgcaag	16	6	9	10	2	2	3	0	2	2	1	2	3	2	3	1	0	5	3	1	0	7	2	rs34573615	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:9013424C>T	ENST00000305997.3	-	8	895	c.697G>A	c.(697-699)Gtt>Att	p.V233I	MBOAT2_ENST00000486484.1_5'UTR	NM_138799.2	NP_620154.2	Q6ZWT7	MBOA2_HUMAN	membrane bound O-acyltransferase domain containing 2	233					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)					TTCTGAACAACCGCAGTCTGA	0.398													C|||	71	0.0141773	0.0212	0.0086	5008	,	,		19264	0.003		0.004	False		,,,				2504	0.0307				p.V233I	Ovarian(194;1699 3813 22401)	Atlas-SNP	.											.	MBOAT2	36	.	0			c.G697A						PASS	.	C	ILE/VAL	69,4337	62.3+/-99.4	1,67,2135	83	81	82		697	5.2	0.1	2	dbSNP_126	82	13,8587	9.8+/-36.6	0,13,4287	yes	missense	MBOAT2	NM_138799.2	29	1,80,6422	TT,TC,CC		0.1512,1.566,0.6305	probably-damaging	233/521	9013424	82,12924	2203	4300	6503	SO:0001583	missense	129642	exon8			GAACAACCGCAGT	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.697G>A	2.37:g.9013424C>T	ENSP00000302177:p.Val233Ile	97	0	0		95	61	0.642105	NM_138799	A9EDR2|Q8NCE7|Q96KY4	Missense_Mutation	SNP	ENST00000305997.3	37	CCDS1660.1	20	0.009157509157509158	14	0.028455284552845527	4	0.011049723756906077	0	0.0	2	0.002638522427440633	C	26.8	4.769230	0.90020	0.01566	0.001512	ENSG00000143797	ENST00000305997	T	0.72615	-0.67	5.22	5.22	0.72569	.	0.173169	0.50627	D	0.000119	T	0.71888	0.3393	M	0.88775	2.98	0.80722	D	1	D;D	0.61697	0.99;0.99	D;D	0.64506	0.92;0.926	D	0.83693	0.0178	10	0.72032	D	0.01	-23.1005	18.7799	0.91928	0.0:1.0:0.0:0.0	rs34573615	233;233	B7Z3I3;Q6ZWT7	.;MBOA2_HUMAN	I	233	ENSP00000302177:V233I	ENSP00000302177:V233I	V	-	1	0	MBOAT2	8930875	1.000000	0.71417	0.062000	0.19696	0.024000	0.10985	7.292000	0.78731	2.418000	0.82041	0.460000	0.39030	GTT	C|0.994;T|0.006	0.006	strong		0.398	MBOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206735.1	NM_138799		T	9013424	C	T	9013424	3	4	22	1	0	0	0	0	1	0	0	0	9366	507	18	2	889	2	MBOAT2	2	9013424	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	14453	9013424	234185949	510	3411											
GRHL1	29841	hgsc.bcm.edu	37	chr2	10101289	10101289	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccatggcaaccagctgggCattgataagagaggccatct	11	7	11	12	0	1	2	0	1	1	1	1	3	1	2	4	3	2	3	4	3	2	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:10101289C>T	ENST00000324907.9	+	4	529	c.393C>T	c.(391-393)ggC>ggT	p.G131G	GRHL1_ENST00000405379.2_Silent_p.G131G|GRHL1_ENST00000324883.5_5'UTR	NM_198182.2	NP_937825.2	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1 (Drosophila)	131					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)		ACCAGCTGGGCATTGATAAGA	0.498																																					p.G131G		Atlas-SNP	.											.	GRHL1	95	.	0			c.C393T						PASS	.						77	84	81					2																	10101289		1327	2309	3636	SO:0001819	synonymous_variant	29841	exon4			GCTGGGCATTGAT	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.393C>T	2.37:g.10101289C>T		177	0	0		181	80	0.441989	NM_198182	A6NLA4|B2R7E4|B5MEC2|Q53T93|Q6NWN7|Q6NWN8|Q6NWN9|Q8NI33	Silent	SNP	ENST00000324907.9	37	CCDS33144.2																																																																																			.	.	none		0.498	GRHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323543.2	NM_014552		T	10101289	C	T	10101289	2	4	22	1	0	0	0	0	0	0	0	1	6772	697	25	2		2	GRHL1	2	10101289	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1087865	10101289	233098084	511	3412											
NOL10	79954	hgsc.bcm.edu	37	chr2	10729257	10729257	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaactggggctttaggactgTctgctggtcctccttgagtc	6	13	12	10	0	1	1	0	1	1	0	4	2	3	2	2	4	2	2	2	4	2	3	rs34359340	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:10729257T>C	ENST00000381685.5	-	19	1861	c.1756A>G	c.(1756-1758)Aca>Gca	p.T586A	NOL10_ENST00000542668.1_Missense_Mutation_p.T536A|NOL10_ENST00000345985.3_Missense_Mutation_p.T536A|NOL10_ENST00000538384.1_Missense_Mutation_p.T560A|AC092687.5_ENST00000414538.1_RNA	NM_024894.3	NP_079170.2	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	586						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)		TTTAGGACTGTCTGCTGGTCC	0.473													T|||	179	0.0357428	0.1301	0.0101	5008	,	,		18410	0.0		0.0	False		,,,				2504	0.0				p.T586A		Atlas-SNP	.											.	NOL10	22	.	0			c.A1756G						PASS	.	T	ALA/THR	471,3935	223.0+/-239.6	22,427,1754	167	172	170		1756	2.9	1	2	dbSNP_126	170	0,8600		0,0,4300	yes	missense	NOL10	NM_024894.2	58	22,427,6054	CC,CT,TT		0.0,10.69,3.6214	probably-damaging	586/689	10729257	471,12535	2203	4300	6503	SO:0001583	missense	79954	exon19			GGACTGTCTGCTG	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.1756A>G	2.37:g.10729257T>C	ENSP00000371101:p.Thr586Ala	239	0	0		247	116	0.469636	NM_024894	A8K3R5|B4DLV0|Q53RC9|Q96TA5|Q9H7Y7|Q9H855	Missense_Mutation	SNP	ENST00000381685.5	37	CCDS1673.2	59	0.027014652014652016	57	0.11585365853658537	2	0.0055248618784530384	0	0.0	0	0.0	T	4.966	0.179358	0.09443	0.1069	0.0	ENSG00000115761	ENST00000345985;ENST00000381685;ENST00000542668;ENST00000538384	T;T;T;T	0.40756	1.02;2.21;1.61;2.21	5.35	2.93	0.34026	.	0.131457	0.64402	N	0.000001	T	0.00496	0.0016	M	0.65975	2.015	0.58432	D	0.999992	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.06405	0.001;0.001;0.002	T	0.04737	-1.0930	10	0.07644	T	0.81	-16.2693	8.127	0.31005	0.0:0.0702:0.1358:0.794	rs34359340	560;586;536	B4DLV0;Q9BSC4;Q9BSC4-2	.;NOL10_HUMAN;.	A	536;586;536;560	ENSP00000263837:T536A;ENSP00000371101:T586A;ENSP00000437625:T536A;ENSP00000439663:T560A	ENSP00000263837:T536A	T	-	1	0	NOL10	10646708	1.000000	0.71417	0.966000	0.40874	0.758000	0.43043	2.567000	0.45956	0.415000	0.25817	-0.435000	0.05868	ACA	T|0.964;C|0.036	0.036	strong		0.473	NOL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239227.1	NM_024894		C	10729257	T	C	10729257	3	2	22	1	0	0	0	0	1	0	0	0	10529	1667	58	3	322	3	NOL10	2	10729257	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	627968	10729257	232470116	512	3413											
NOL10	79954	hgsc.bcm.edu	37	chr2	10797952	10797952	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggaaatgaacggacttaatGggcagcccatactggtgatc	12	9	12	8	1	0	2	0	2	0	0	1	4	0	4	1	4	3	1	1	4	4	2	rs61737663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:10797952G>A	ENST00000381685.5	-	11	927	c.822C>T	c.(820-822)ccC>ccT	p.P274P	NOL10_ENST00000542668.1_Silent_p.P224P|NOL10_ENST00000345985.3_Intron|NOL10_ENST00000538384.1_Silent_p.P248P	NM_024894.3	NP_079170.2	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	274						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)		CGGACTTAATGGGCAGCCCAT	0.348													G|||	83	0.0165735	0.0582	0.0086	5008	,	,		18192	0.0		0.0	False		,,,				2504	0.0				p.P274P		Atlas-SNP	.											.	NOL10	22	.	0			c.C822T						PASS	.	G		67,1317		0,67,625	131	122	124		822	3.5	1	2	dbSNP_129	124	0,3182		0,0,1591	no	coding-synonymous	NOL10	NM_024894.2		0,67,2216	AA,AG,GG		0.0,4.841,1.4674		274/689	10797952	67,4499	692	1591	2283	SO:0001819	synonymous_variant	79954	exon11			CTTAATGGGCAGC	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.822C>T	2.37:g.10797952G>A		199	0	0		192	92	0.479167	NM_024894	A8K3R5|B4DLV0|Q53RC9|Q96TA5|Q9H7Y7|Q9H855	Silent	SNP	ENST00000381685.5	37	CCDS1673.2																																																																																			G|0.988;A|0.012	0.012	strong		0.348	NOL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239227.1	NM_024894		A	10797952	G	A	10797952	2	1	22	1	0	0	0	0	0	0	0	1	10529	1335	47	2		2	NOL10	2	10797952	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	68695	10797952	232401421	513	3414											
ROCK2	9475	hgsc.bcm.edu	37	chr2	11484212	11484212	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgcctgccccgtcccccggCgcggtctcgggggcgccggg	0	4	18	19	8	1	0	0	0	1	0	3	0	2	0	6	5	1	0	6	5	0	0	rs368832806	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:11484212C>A	ENST00000315872.6	-	1	499	c.51G>T	c.(49-51)gcG>gcT	p.A17A	ROCK2_ENST00000462366.1_Intron	NM_004850.3	NP_004841.2	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein kinase 2	17					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)		CGTCCCCCGGCGCGGTCTCGG	0.741													C|||	9	0.00179712	0.0061	0.0	5008	,	,		9307	0.001		0.0	False		,,,				2504	0.0				p.A17A		Atlas-SNP	.											ROCK2_ENST00000315872,NS,carcinoma,-2,2	ROCK2	224	2	0			c.G51T						PASS	.	C		7,3463		0,7,1728	10	12	11		51	-1.3	0	2		11	0,7918		0,0,3959	no	coding-synonymous	ROCK2	NM_004850.3		0,7,5687	AA,AC,CC		0.0,0.2017,0.0615		17/1389	11484212	7,11381	1735	3959	5694	SO:0001819	synonymous_variant	9475	exon1			CCCCGGCGCGGTC	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.51G>T	2.37:g.11484212C>A		28	0	0		53	35	0.660377	NM_004850	Q53QZ0|Q53SJ7|Q9UQN5	Silent	SNP	ENST00000315872.6	37	CCDS42654.1																																																																																			.	.	weak		0.741	ROCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313886.3			A	11484212	C	A	11484212	2	1	22	1	0	0	0	0	0	0	0	1	13533	755	27	4		4	ROCK2	2	11484212	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	686260	11484212	231715161	514	3415											
NTSR2	23620	hgsc.bcm.edu	37	chr2	11800180	11800180	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacactcactcagtccacgcGtcatcaggtacgtagcagta	11	8	8	14	3	4	0	4	0	0	0	5	0	5	0	1	1	2	4	1	1	3	3	rs35653499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:11800180G>A	ENST00000306928.5	-	3	1012	c.978C>T	c.(976-978)gaC>gaT	p.D326D		NM_012344.3	NP_036476	O95665	NTR2_HUMAN	neurotensin receptor 2	326					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)	CAGTCCACGCGTCATCAGGTA	0.602													G|||	81	0.0161741	0.0446	0.0086	5008	,	,		21158	0.0159		0.0	False		,,,				2504	0.0				p.D326D		Atlas-SNP	.											.	NTSR2	36	.	0			c.C978T						PASS	.	G		196,4210	122.1+/-159.5	7,182,2014	105	89	95		978	-1.8	0	2	dbSNP_126	95	0,8600		0,0,4300	no	coding-synonymous	NTSR2	NM_012344.3		7,182,6314	AA,AG,GG		0.0,4.4485,1.507		326/411	11800180	196,12810	2203	4300	6503	SO:0001819	synonymous_variant	23620	exon3			CCACGCGTCATCA	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.978C>T	2.37:g.11800180G>A		93	0	0		105	55	0.52381	NM_012344	Q53QQ5|Q57Z87|Q8IY58|Q8TBH6	Silent	SNP	ENST00000306928.5	37	CCDS1681.1																																																																																			G|0.982;A|0.018	0.018	strong		0.602	NTSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239297.1			A	11800180	G	A	11800180	2	1	22	1	0	0	0	0	0	0	0	1	10720	1136	40	1		1	NTSR2	2	11800180	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	315968	11800180	231399193	515	3416											
NBAS	51594	hgsc.bcm.edu	37	chr2	15358939	15358939	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgagaatggcttcagttctAaagaacacgaggagcttgct	12	11	11	7	1	2	2	1	1	1	2	2	5	2	3	0	2	3	4	0	2	4	5	rs114448506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:15358939A>C	ENST00000281513.5	-	48	6415	c.6390T>G	c.(6388-6390)ttT>ttG	p.F2130L	NBAS_ENST00000441750.1_Missense_Mutation_p.F2010L	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	2130					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						CTTCAGTTCTAAAGAACACGA	0.517													A|||	12	0.00239617	0.0091	0.0	5008	,	,		19280	0.0		0.0	False		,,,				2504	0.0				p.F2130L		Atlas-SNP	.											.	NBAS	246	.	0			c.T6390G						PASS	.	A	LEU/PHE	37,4369	42.3+/-75.8	0,37,2166	68	73	71		6390	-4.2	0	2	dbSNP_132	71	1,8599	1.2+/-3.3	0,1,4299	yes	missense	NBAS	NM_015909.2	22	0,38,6465	CC,CA,AA		0.0116,0.8398,0.2922	possibly-damaging	2130/2372	15358939	38,12968	2203	4300	6503	SO:0001583	missense	51594	exon48			AGTTCTAAAGAAC	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.6390T>G	2.37:g.15358939A>C	ENSP00000281513:p.Phe2130Leu	221	0	0		238	127	0.533613	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	37	CCDS1685.1	5|5	0.0022893772893772895|0.0022893772893772895	5|5	0.01016260162601626|0.01016260162601626	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	A|A	14.99|14.99	2.699080|2.699080	0.48307|0.48307	0.008398|0.008398	1.16E-4|1.16E-4	ENSG00000151779|ENSG00000151779	ENST00000441750;ENST00000281513|ENST00000442506	T;T|.	0.09255|.	3.0;3.17|.	5.63|5.63	-4.15|-4.15	0.03881|0.03881	.|.	0.248251|.	0.47455|.	D|.	0.000222|.	T|.	0.55752|.	0.1940|.	M|M	0.65498|0.65498	2.005|2.005	0.32809|0.32809	D|D	0.501197|0.501197	P;B|.	0.43231|.	0.801;0.397|.	P;B|.	0.44811|.	0.461;0.176|.	T|.	0.65405|.	-0.6176|.	10|.	0.87932|.	D|.	0|.	.|.	16.982|16.982	0.86331|0.86331	0.1405:0.0:0.8595:0.0|0.1405:0.0:0.8595:0.0	.|.	2010;2130|.	A2RRP1-2;A2RRP1|.	.;NBAS_HUMAN|.	L|X	2010;2130|1178	ENSP00000413201:F2010L;ENSP00000281513:F2130L|.	ENSP00000281513:F2130L|.	F|L	-|-	3|2	2|0	NBAS|NBAS	15276390|15276390	0.998000|0.998000	0.40836|0.40836	0.001000|0.001000	0.08648|0.08648	0.824000|0.824000	0.46624|0.46624	1.102000|1.102000	0.31050|0.31050	-1.413000|-1.413000	0.02027|0.02027	-0.326000|-0.326000	0.08463|0.08463	TTT|TTA	A|0.997;C|0.003	0.003	strong		0.517	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		C	15358939	A	C	15358939	3	2	22	1	0	0	0	0	1	0	0	0	10195	359	13	5	745	5	NBAS	2	15358939	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	3558759	15358939	227840434	516	3417											
GEN1	348654	hgsc.bcm.edu	37	chr2	17961321	17961321	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagaatcattgtttgaagcAgcatatcctgagatcgttgc	12	12	10	7	1	1	3	1	2	0	2	3	5	2	3	1	0	3	4	1	0	4	4	rs16983864	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:17961321A>G	ENST00000381254.2	+	13	1555	c.1341A>G	c.(1339-1341)gcA>gcG	p.A447A	GEN1_ENST00000317402.7_Silent_p.A447A|SMC6_ENST00000402989.1_Intron	NM_001130009.1	NP_001123481.1	Q17RS7	GEN_HUMAN	GEN1 Holliday junction 5' flap endonuclease	447					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)					TGTTTGAAGCAGCATATCCTG	0.308								Homologous recombination					A|||	236	0.0471246	0.1377	0.0072	5008	,	,		18870	0.0308		0.005	False		,,,				2504	0.0133				p.A447A		Atlas-SNP	.											.	GEN1	79	.	0			c.A1341G						PASS	.	A	,	466,3940	216.4+/-235.1	23,420,1760	62	64	64		1341,1341	-0.6	1	2	dbSNP_123	64	34,8566	22.8+/-68.1	0,34,4266	no	coding-synonymous,coding-synonymous	GEN1	NM_001130009.1,NM_182625.3	,	23,454,6026	GG,GA,AA		0.3953,10.5765,3.8444	,	447/909,447/909	17961321	500,12506	2203	4300	6503	SO:0001819	synonymous_variant	348654	exon13			TGAAGCAGCATAT	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.1341A>G	2.37:g.17961321A>G		52	0	0		53	26	0.490566	NM_182625	Q17RS9|Q6ZN37	Silent	SNP	ENST00000381254.2	37	CCDS1691.1																																																																																			A|0.963;G|0.037	0.037	strong		0.308	GEN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241661.2	NM_182625		G	17961321	A	G	17961321	2	3	22	1	0	0	0	0	0	0	0	1	6343	175	7	3		3	GEN1	2	17961321	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2602382	17961321	225238052	517	3418											
GEN1	348654	hgsc.bcm.edu	37	chr2	17962117	17962117	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcacaagaacagttcatgtcTtctctaagacctttggctat	11	13	7	10	0	3	2	1	0	2	2	4	2	3	2	1	1	1	3	1	1	4	5	rs61762986	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:17962117T>A	ENST00000381254.2	+	14	1852	c.1638T>A	c.(1636-1638)tcT>tcA	p.S546S	GEN1_ENST00000317402.7_Silent_p.S546S|SMC6_ENST00000402989.1_Intron	NM_001130009.1	NP_001123481.1	Q17RS7	GEN_HUMAN	GEN1 Holliday junction 5' flap endonuclease	546					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)					AGTTCATGTCTTCTCTAAGAC	0.363								Homologous recombination					T|||	50	0.00998403	0.0121	0.0216	5008	,	,		18882	0.0		0.0189	False		,,,				2504	0.0				p.S546S		Atlas-SNP	.											.	GEN1	79	.	0			c.T1638A						PASS	.	T	,	64,4342	61.1+/-98.1	1,62,2140	82	77	79		1638,1638	0	0.7	2	dbSNP_129	79	126,8474	64.2+/-126.4	4,118,4178	no	coding-synonymous,coding-synonymous	GEN1	NM_001130009.1,NM_182625.3	,	5,180,6318	AA,AT,TT		1.4651,1.4526,1.4609	,	546/909,546/909	17962117	190,12816	2203	4300	6503	SO:0001819	synonymous_variant	348654	exon14			CATGTCTTCTCTA	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.1638T>A	2.37:g.17962117T>A		109	0	0		116	57	0.491379	NM_182625	Q17RS9|Q6ZN37	Silent	SNP	ENST00000381254.2	37	CCDS1691.1																																																																																			T|0.987;A|0.013	0.013	strong		0.363	GEN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241661.2	NM_182625		A	17962117	T	A	17962117	2	1	22	1	0	0	0	0	0	0	0	1	6343	1596	56	5		5	GEN1	2	17962117	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	796	17962117	225237256	518	3419											
PUM2	23369	hgsc.bcm.edu	37	chr2	20508156	20508156	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgattaccaggatagtcaaaCtgtaaggattccagaccaac	15	9	8	9	0	1	2	1	1	0	1	2	4	2	4	3	2	3	1	3	2	5	4	rs34057700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:20508156C>T	ENST00000361078.2	-	5	730	c.708G>A	c.(706-708)caG>caA	p.Q236Q	PUM2_ENST00000536417.1_Silent_p.Q180Q|PUM2_ENST00000420234.1_5'Flank|PUM2_ENST00000338086.5_Silent_p.Q236Q|PUM2_ENST00000403432.1_Silent_p.Q236Q|PUM2_ENST00000319801.5_Silent_p.Q236Q			Q8TB72	PUM2_HUMAN	pumilio RNA-binding family member 2	236	Interaction with SNAPIN.				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)					GATAGTCAAACTGTAAGGATT	0.408													C|||	145	0.0289537	0.1021	0.013	5008	,	,		17612	0.0		0.001	False		,,,				2504	0.0				p.Q236Q		Atlas-SNP	.											.	PUM2	91	.	0			c.G708A						PASS	.	C		404,4002	200.8+/-224.0	18,368,1817	83	81	81		708	5.2	1	2	dbSNP_126	81	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	PUM2	NM_015317.1		18,370,6115	TT,TC,CC		0.0233,9.1693,3.1216		236/1065	20508156	406,12600	2203	4300	6503	SO:0001819	synonymous_variant	23369	exon5			GTCAAACTGTAAG	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.708G>A	2.37:g.20508156C>T		177	0	0		180	85	0.472222	NM_015317	B3KSL0|B4E2B6|D6W527|O00234|Q53TV7|Q8WY43|Q9HAN2	Silent	SNP	ENST00000361078.2	37																																																																																				C|0.974;T|0.026	0.026	strong		0.408	PUM2-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015317		T	20508156	C	T	20508156	2	4	22	1	0	0	0	0	0	0	0	1	12841	564	20	2		2	PUM2	2	20508156	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2546039	20508156	222691217	519	3420											
C2orf43	60526	hgsc.bcm.edu	37	chr2	20886706	20886706	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttagggagtcagcaatcatgTctgccatttcctggttaaaa	11	13	9	8	0	3	0	2	0	1	0	4	1	4	1	2	2	2	2	2	2	4	3	rs147773589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:20886706T>C	ENST00000237822.3	-	7	1014	c.935A>G	c.(934-936)gAc>gGc	p.D312G	C2orf43_ENST00000435420.2_Missense_Mutation_p.D264G|C2orf43_ENST00000403006.2_Missense_Mutation_p.D182G|C2orf43_ENST00000440866.2_3'UTR|C2orf43_ENST00000541941.1_Missense_Mutation_p.D182G|C2orf43_ENST00000381090.3_Missense_Mutation_p.D312G	NM_001282721.1|NM_021925.2	NP_001269650.1|NP_068744.1	Q9H6V9	CB043_HUMAN	chromosome 2 open reading frame 43	312										endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGCAATCATGTCTGCCATTTC	0.433													T|||	7	0.00139776	0.0053	0.0	5008	,	,		18458	0.0		0.0	False		,,,				2504	0.0				p.D312G		Atlas-SNP	.											.	C2orf43	28	.	0			c.A935G						PASS	.	T	GLY/ASP	30,4376	37.6+/-69.7	0,30,2173	159	141	147		935	-4	0	2	dbSNP_134	147	0,8600		0,0,4300	yes	missense	C2orf43	NM_021925.2	94	0,30,6473	CC,CT,TT		0.0,0.6809,0.2307	benign	312/326	20886706	30,12976	2203	4300	6503	SO:0001583	missense	60526	exon7			ATCATGTCTGCCA	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.935A>G	2.37:g.20886706T>C	ENSP00000237822:p.Asp312Gly	191	0	0		167	89	0.532934	NM_021925	B7ZA47|B7ZAJ5|D6W530|E7ESN0|Q53T37|Q53T58	Missense_Mutation	SNP	ENST00000237822.3	37	CCDS1702.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	4.392	0.072364	0.08436	0.006809	0.0	ENSG00000118961	ENST00000403006;ENST00000381090;ENST00000237822;ENST00000435420;ENST00000541941	T;T;T	0.46063	0.88;1.49;0.88	5.93	-4.01	0.04045	.	2.110680	0.01630	N	0.023469	T	0.20740	0.0499	L	0.28274	0.84	0.09310	N	1	B;B;B;B	0.11235	0.001;0.001;0.002;0.004	B;B;B;B	0.09377	0.001;0.001;0.003;0.004	T	0.12451	-1.0547	10	0.24483	T	0.36	0.2807	7.2059	0.25907	0.0808:0.0673:0.4763:0.3756	.	270;264;312;312	B4DS38;B7ZAJ5;Q9H6V9;B5MDU6	.;.;CB043_HUMAN;.	G	182;312;312;264;182	ENSP00000384267:D182G;ENSP00000388635:D264G;ENSP00000440570:D182G	ENSP00000237822:D312G	D	-	2	0	C2orf43	20750187	0.000000	0.05858	0.000000	0.03702	0.088000	0.18126	-0.087000	0.11215	-0.401000	0.07644	0.533000	0.62120	GAC	T|0.998;C|0.002	0.002	strong		0.433	C2orf43-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242861.1	NM_021925		C	20886706	T	C	20886706	3	2	22	1	0	0	0	0	1	0	0	0	2169	1667	58	3	46	3	C2orf43	2	20886706	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	378550	20886706	222312667	520	3421											
C2orf43	60526	hgsc.bcm.edu	37	chr2	21001192	21001192	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaaaatgaattcctcatgcAcaggaatttcttccttgagt	13	13	6	9	0	2	2	1	2	1	0	4	3	4	3	2	1	1	1	2	1	4	4	rs139472393	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:21001192A>G	ENST00000237822.3	-	2	111	c.32T>C	c.(31-33)gTg>gCg	p.V11A	C2orf43_ENST00000435420.2_Missense_Mutation_p.V11A|C2orf43_ENST00000403006.2_Intron|C2orf43_ENST00000419825.2_Missense_Mutation_p.V11A|C2orf43_ENST00000440866.2_Missense_Mutation_p.V11A|C2orf43_ENST00000541941.1_Intron|C2orf43_ENST00000381090.3_Missense_Mutation_p.V11A	NM_001282721.1|NM_021925.2	NP_001269650.1|NP_068744.1	Q9H6V9	CB043_HUMAN	chromosome 2 open reading frame 43	11										endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTCCTCATGCACAGGAATTTC	0.408													A|||	7	0.00139776	0.0053	0.0	5008	,	,		17655	0.0		0.0	False		,,,				2504	0.0				p.V11A		Atlas-SNP	.											.	C2orf43	28	.	0			c.T32C						PASS	.	A	ALA/VAL	21,4385	29.0+/-57.7	0,21,2182	82	84	84		32	5.9	1	2	dbSNP_134	84	0,8600		0,0,4300	yes	missense	C2orf43	NM_021925.2	64	0,21,6482	GG,GA,AA		0.0,0.4766,0.1615	possibly-damaging	11/326	21001192	21,12985	2203	4300	6503	SO:0001583	missense	60526	exon2			TCATGCACAGGAA	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.32T>C	2.37:g.21001192A>G	ENSP00000237822:p.Val11Ala	112	0	0		91	34	0.373626	NM_021925	B7ZA47|B7ZAJ5|D6W530|E7ESN0|Q53T37|Q53T58	Missense_Mutation	SNP	ENST00000237822.3	37	CCDS1702.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	A	16.00	2.998870	0.54147	0.004766	0.0	ENSG00000118961	ENST00000381090;ENST00000237822;ENST00000435420;ENST00000440866;ENST00000412261;ENST00000402479;ENST00000419825	.	.	.	5.94	5.94	0.96194	.	0.514514	0.19627	N	0.109780	T	0.50497	0.1619	L	0.44542	1.39	0.32473	N	0.54249	B;P;P;D;P;P	0.60575	0.349;0.852;0.952;0.988;0.852;0.852	B;B;P;P;B;B	0.49085	0.091;0.177;0.452;0.6;0.177;0.177	T	0.63567	-0.6608	9	0.62326	D	0.03	-8.1279	15.3805	0.74651	1.0:0.0:0.0:0.0	.	11;11;11;11;11;11	B4DS38;B4DRG3;B7ZAJ5;B4DWE2;Q9H6V9;B5MDU6	.;.;.;.;CB043_HUMAN;.	A	11	.	ENSP00000237822:V11A	V	-	2	0	C2orf43	20864673	0.996000	0.38824	0.992000	0.48379	0.114000	0.19823	5.670000	0.68088	2.279000	0.76181	0.459000	0.35465	GTG	A|0.999;G|0.001	0.001	strong		0.408	C2orf43-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242861.1	NM_021925		G	21001192	A	G	21001192	3	3	22	1	0	0	0	0	1	0	0	0	2169	159	6	3	969	3	C2orf43	2	21001192	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	114486	21001192	222198181	521	3422											
APOB	338	hgsc.bcm.edu	37	chr2	21224843	21224843	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatcagaaattattttcttcGtcgcaatggcctggctttta	10	16	7	8	2	2	1	1	0	1	1	4	1	2	1	1	2	0	2	1	2	5	6	rs12713450	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:21224843G>A	ENST00000233242.1	-	29	13578	c.13451C>T	c.(13450-13452)aCg>aTg	p.T4484M	RP11-116D2.1_ENST00000567376.2_lincRNA	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	4484			T -> M (in dbSNP:rs12713450).		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)					TATTTTCTTCGTCGCAATGGC	0.378													G|||	192	0.0383387	0.1263	0.0259	5008	,	,		18757	0.0		0.006	False		,,,				2504	0.001				p.T4484M		Atlas-SNP	.											APOB,NS,carcinoma,+1,1	APOB	761	1	0			c.C13451T						scavenged	.	G	MET/THR	444,3962	204.8+/-226.9	20,404,1779	85	91	89		13451	2.2	0	2	dbSNP_126	89	43,8557	28.5+/-78.6	0,43,4257	yes	missense	APOB	NM_000384.2	81	20,447,6036	AA,AG,GG		0.5,10.0772,3.7444	benign	4484/4564	21224843	487,12519	2203	4300	6503	SO:0001583	missense	338	exon29			TTCTTCGTCGCAA	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.13451C>T	2.37:g.21224843G>A	ENSP00000233242:p.Thr4484Met	100	1	0.01		118	60	0.508475	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	72	0.03296703296703297	60	0.12195121951219512	8	0.022099447513812154	0	0.0	4	0.005277044854881266	G	0.008	-1.930298	0.00488	0.100772	0.005	ENSG00000084674	ENST00000233242	T	0.37915	1.17	5.9	2.22	0.28083	.	0.646971	0.15282	N	0.270656	T	0.00109	0.0003	N	0.00095	-2.16	0.22552	N	0.998995	B	0.06786	0.001	B	0.04013	0.001	T	0.33085	-0.9882	10	0.28530	T	0.3	.	6.3395	0.21314	0.4718:0.0:0.5282:0.0	rs12713450;rs17240965;rs52805962;rs60161843;rs12713450	4484	P04114	APOB_HUMAN	M	4484	ENSP00000233242:T4484M	ENSP00000233242:T4484M	T	-	2	0	APOB	21078348	0.907000	0.30839	0.005000	0.12908	0.008000	0.06430	1.767000	0.38501	0.490000	0.27771	-0.312000	0.09012	ACG	G|0.968;A|0.032	0.032	strong		0.378	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			A	21224843	G	A	21224843	3	1	22	1	0	0	0	0	1	0	0	0	785	1145	40	1	244	1	APOB	2	21224843	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	223651	21224843	221974530	522	3423											
APOB	338	hgsc.bcm.edu	37	chr2	21258523	21258523	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgccacatgcttcctcttagCgtccagtgtgtactgacagg	7	12	10	12	1	1	1	0	1	1	0	3	1	3	1	3	1	4	2	3	1	2	3	rs61741625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:21258523C>T	ENST00000233242.1	-	7	878	c.751G>A	c.(751-753)Gct>Act	p.A251T	APOB_ENST00000399256.4_Missense_Mutation_p.A251T	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	251	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)					TTCCTCTTAGCGTCCAGTGTG	0.502													C|||	13	0.00259585	0.0098	0.0	5008	,	,		21477	0.0		0.0	False		,,,				2504	0.0				p.A251T		Atlas-SNP	.											.	APOB	761	.	0			c.G751A						PASS	.	C	THR/ALA	34,4372	38.4+/-70.7	0,34,2169	130	105	114		751	-8.5	0	2	dbSNP_129	114	0,8600		0,0,4300	yes	missense	APOB	NM_000384.2	58	0,34,6469	TT,TC,CC		0.0,0.7717,0.2614	benign	251/4564	21258523	34,12972	2203	4300	6503	SO:0001583	missense	338	exon7			TCTTAGCGTCCAG	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.751G>A	2.37:g.21258523C>T	ENSP00000233242:p.Ala251Thr	120	0	0		106	58	0.54717	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	C	13.65	2.299459	0.40694	0.007717	0.0	ENSG00000084674	ENST00000233242;ENST00000535079;ENST00000399256	T;T	0.04809	3.55;3.55	5.73	-8.49	0.00931	Lipid transport protein, beta-sheet shell (1);Lipid transport protein, N-terminal (3);Vitellinogen, beta-sheet N-terminal (1);	1.266020	0.05424	N	0.544746	T	0.01029	0.0034	N	0.22421	0.69	0.09310	N	1	P	0.39520	0.676	B	0.32289	0.143	T	0.38628	-0.9652	10	0.21014	T	0.42	.	4.2167	0.10539	0.3063:0.3153:0.3062:0.0722	.	251	P04114	APOB_HUMAN	T	251	ENSP00000233242:A251T;ENSP00000382200:A251T	ENSP00000233242:A251T	A	-	1	0	APOB	21112028	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.261000	0.02855	-1.679000	0.01452	-1.193000	0.01689	GCT	C|0.997;T|0.003	0.003	strong		0.502	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			T	21258523	C	T	21258523	3	4	22	1	0	0	0	0	1	0	0	0	785	768	27	1	13032	1	APOB	2	21258523	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	33680	21258523	221940850	523	3424											
C2orf44	80304	hgsc.bcm.edu	37	chr2	24260862	24260862	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacagatactagacagaggActctggatttctttaataag	14	12	8	7	0	3	3	1	0	2	3	3	5	3	5	0	2	1	0	0	2	4	6	rs115270382	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:24260862A>G	ENST00000295148.4	-	2	1560	c.1503T>C	c.(1501-1503)agT>agC	p.S501S	C2orf44_ENST00000406895.3_Silent_p.S501S	NM_025203.2	NP_079479.1	Q9H6R7	CB044_HUMAN	chromosome 2 open reading frame 44	501									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)					TAGACAGAGGACTCTGGATTT	0.488			T	ALK	NSCLC								A|||	27	0.00539137	0.0204	0.0	5008	,	,		17626	0.0		0.0	False		,,,				2504	0.0				p.S501S		Atlas-SNP	.		Dom	yes		2	2p23.3	80304	chromosome 2 open reading frame 44		E	.	C2orf44	56	.	0			c.T1503C						PASS	.	A	,	136,4270	94.4+/-133.1	2,132,2069	65	69	68		1503,1503	-3.5	0.1	2	dbSNP_132	68	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	C2orf44	NM_001142319.1,NM_025203.2	,	2,133,6368	GG,GA,AA		0.0116,3.0867,1.0534	,	501/623,501/722	24260862	137,12869	2203	4300	6503	SO:0001819	synonymous_variant	80304	exon2			CAGAGGACTCTGG	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.1503T>C	2.37:g.24260862A>G		126	0	0		156	72	0.461538	NM_025203	D6W532|Q8IYK0|Q9HBP5	Silent	SNP	ENST00000295148.4	37	CCDS1705.1																																																																																			A|0.992;G|0.008	0.008	strong		0.488	C2orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246825.1	NM_025203		G	24260862	A	G	24260862	2	3	22	1	0	0	0	0	0	0	0	1	2170	272	10	3		3	C2orf44	2	24260862	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	3002339	24260862	218938511	524	3425											
ITSN2	50618	hgsc.bcm.edu	37	chr2	24498674	24498674	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcacgtttgatcttataaagCtgttcaagggctaactgctg	10	14	9	8	1	3	1	2	1	1	0	3	1	3	1	0	1	3	5	0	1	5	5	rs77507357	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:24498674C>T	ENST00000355123.4	-	18	2432	c.1989G>A	c.(1987-1989)caG>caA	p.Q663Q	SCARNA21_ENST00000515996.1_RNA|ITSN2_ENST00000361999.3_Silent_p.Q636Q|ITSN2_ENST00000406921.3_Silent_p.Q663Q	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	663					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)					TCTTATAAAGCTGTTCAAGGG	0.338													T|||	40	0.00798722	0.0303	0.0	5008	,	,		17795	0.0		0.0	False		,,,				2504	0.0				p.Q663Q		Atlas-SNP	.											.	ITSN2	224	.	0			c.G1989A						PASS	.	T	,,	143,4263	812.9+/-416.1	4,135,2064	147	140	142		1989,1908,1989	-4.5	0.9	2	dbSNP_132	142	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	ITSN2	NM_006277.2,NM_019595.3,NM_147152.2	,,	4,135,6364	TT,TC,CC		0.0,3.2456,1.0995	,,	663/1698,636/1671,663/1250	24498674	143,12863	2203	4300	6503	SO:0001819	synonymous_variant	50618	exon18			ATAAAGCTGTTCA	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.1989G>A	2.37:g.24498674C>T		172	0	0		201	104	0.517413	NM_147152	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Silent	SNP	ENST00000355123.4	37	CCDS1710.2																																																																																			C|0.989;T|0.011	0.011	strong		0.338	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277		T	24498674	C	T	24498674	2	4	22	1	0	0	0	0	0	0	0	1	7936	796	28	2		2	ITSN2	2	24498674	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	237812	24498674	218700699	525	3426											
HADHB	3032	hgsc.bcm.edu	37	chr2	26505745	26505745	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctgcaatgttaatcatggcGgaggaaaaggctctggccat	11	10	12	8	1	3	0	1	0	2	0	3	2	3	2	1	5	1	3	1	5	4	1	rs7572240	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:26505745G>A	ENST00000317799.5	+	11	1070	c.966G>A	c.(964-966)gcG>gcA	p.A322A	HADHB_ENST00000494615.1_3'UTR|HADHB_ENST00000405867.3_Silent_p.A199A|HADHB_ENST00000537713.1_Silent_p.A307A|HADHB_ENST00000545822.1_Silent_p.A300A	NM_000183.2	NP_000174.1	P55084	ECHB_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), beta subunit	322					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)					TAATCATGGCGGAGGAAAAGG	0.388													g|||	101	0.0201677	0.0726	0.0043	5008	,	,		18252	0.0		0.002	False		,,,				2504	0.0				p.A322A		Atlas-SNP	.											.	HADHB	50	.	0			c.G966A						PASS	.	G		268,4138	151.0+/-185.0	6,256,1941	91	87	89		966	-8.4	0.7	2	dbSNP_116	89	4,8596	2.2+/-6.3	0,4,4296	no	coding-synonymous	HADHB	NM_000183.2		6,260,6237	AA,AG,GG		0.0465,6.0826,2.0913		322/475	26505745	272,12734	2203	4300	6503	SO:0001819	synonymous_variant	3032	exon11			CATGGCGGAGGAA		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.966G>A	2.37:g.26505745G>A		71	0	0		53	26	0.490566	NM_000183	B2RB16|B4E2W0|O14969|Q53TA6|Q96C77|Q9H3F5|Q9T2V8	Silent	SNP	ENST00000317799.5	37	CCDS1722.1																																																																																			G|0.982;A|0.018	0.018	strong		0.388	HADHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214050.2	NM_000183		A	26505745	G	A	26505745	2	1	22	1	0	0	0	0	0	0	0	1	6953	1103	39	1		1	HADHB	2	26505745	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2007071	26505745	216693628	526	3427											
GPR113	165082	hgsc.bcm.edu	37	chr2	26540951	26540951	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccttgggccatcggccaaaGctagaagatagggggatggg	10	6	16	9	1	0	2	0	0	0	2	1	3	0	3	3	5	1	1	3	5	4	3	rs116141676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:26540951G>A	ENST00000311519.1	-	2	218	c.219C>T	c.(217-219)agC>agT	p.S73S	GPR113_ENST00000421160.2_Intron|GPR113_ENST00000333478.6_Intron|GPR113_ENST00000459892.1_Intron|GPR113_ENST00000541401.1_Intron	NM_001145168.1	NP_001138640.1	Q8IZF5	GP113_HUMAN	G protein-coupled receptor 113	73					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)					ATCGGCCAAAGCTAGAAGATA	0.582													G|||	83	0.0165735	0.0605	0.0043	5008	,	,		19300	0.0		0.0	False		,,,				2504	0.0				p.S73S		Atlas-SNP	.											.	GPR113	134	.	0			c.C219T						PASS	.	G	,,	66,1318		3,60,629	58	64	62		219,,	0	0	2	dbSNP_132	62	0,3182		0,0,1591	no	coding-synonymous,intron,intron	GPR113	NM_001145168.1,NM_001145169.1,NM_153835.3	,,	3,60,2220	AA,AG,GG		0.0,4.7688,1.4455	,,	73/1080,,	26540951	66,4500	692	1591	2283	SO:0001819	synonymous_variant	165082	exon2			GCCAAAGCTAGAA	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.219C>T	2.37:g.26540951G>A		125	0	0		145	59	0.406897	NM_001145168	B4DF15|E9PEV1|Q53TA5|Q6UXT7|Q6UXX3|Q86SL7|Q8IXD8|Q8TDT3	Silent	SNP	ENST00000311519.1	37	CCDS46239.1																																																																																			G|0.986;A|0.014	0.014	strong		0.582	GPR113-004	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316892.1	NM_153835		A	26540951	G	A	26540951	2	1	22	1	0	0	0	0	0	0	0	1	6638	962	34	2		2	GPR113	2	26540951	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	35206	26540951	216658422	527	3428											
OTOF	9381	hgsc.bcm.edu	37	chr2	26699033	26699033	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	acgggtgggaaggcatgcagGcccaggccctgggctgcctt	6	6	17	12	1	0	0	0	0	0	0	0	1	0	1	3	6	2	3	3	6	1	1	rs73920285	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:26699033G>A	ENST00000272371.2	-	23	2955	c.2829C>T	c.(2827-2829)ggC>ggT	p.G943G	OTOF_ENST00000403946.3_Silent_p.G943G|OTOF_ENST00000402415.3_Silent_p.G253G|OTOF_ENST00000338581.6_Silent_p.G196G|OTOF_ENST00000339598.3_Silent_p.G196G	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	943					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)					AGGCATGCAGGCCCAGGCCCT	0.667													G|||	218	0.0435304	0.1566	0.013	5008	,	,		13310	0.0		0.002	False		,,,				2504	0.0				p.G943G	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											OTOF_ENST00000402415,NS,carcinoma,0,3	OTOF	524	3	0			c.C2829T						PASS	.	G	,,,	542,3860	235.2+/-247.8	27,488,1686	34	35	35	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	588,2829,759,588	3.6	1	2	dbSNP_130	35	3,8593	2.2+/-6.3	0,3,4295	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OTOF	NM_004802.3,NM_194248.2,NM_194322.2,NM_194323.2	,,,	27,491,5981	AA,AG,GG		0.0349,12.3126,4.193	,,,	196/1231,943/1998,253/1308,196/1231	26699033	545,12453	2201	4298	6499	SO:0001819	synonymous_variant	9381	exon23			ATGCAGGCCCAGG	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.2829C>T	2.37:g.26699033G>A		85	0	0		91	38	0.417582	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Silent	SNP	ENST00000272371.2	37	CCDS1725.1																																																																																			G|0.953;A|0.047	0.047	strong		0.667	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3			A	26699033	G	A	26699033	2	1	22	1	0	0	0	0	0	0	0	1	11312	1190	42	2		2	OTOF	2	26699033	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	158082	26699033	216500340	528	3429											
PREB	10113	hgsc.bcm.edu	37	chr2	27354306	27354306	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggaaacctggaaaggcactCtggagcagcaggatggtcac	13	5	14	9	0	2	0	1	0	1	0	2	4	2	4	1	6	3	3	1	6	2	0	rs61276776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27354306C>T	ENST00000260643.2	-	9	1483	c.1230G>A	c.(1228-1230)caG>caA	p.Q410Q	PREB_ENST00000406567.3_Silent_p.Q352Q|PREB_ENST00000416802.1_5'Flank	NM_013388.4	NP_037520.1	Q9HCU5	PREB_HUMAN	prolactin regulatory element binding	410					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)					GAAAGGCACTCTGGAGCAGCA	0.577													C|||	48	0.00958466	0.0325	0.0072	5008	,	,		19726	0.0		0.0	False		,,,				2504	0.0				p.Q410Q		Atlas-SNP	.											.	PREB	37	.	0			c.G1230A						PASS	.	C		113,4285		3,107,2089	61	57	58		1230	5.1	1	2	dbSNP_129	58	1,8563		0,1,4281	no	coding-synonymous	PREB	NM_013388.4		3,108,6370	TT,TC,CC		0.0117,2.5693,0.8795		410/418	27354306	114,12848	2199	4282	6481	SO:0001819	synonymous_variant	10113	exon9			GGCACTCTGGAGC		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.1230G>A	2.37:g.27354306C>T		96	0	0		87	38	0.436782	NM_013388	Q53SZ8|Q9UH94	Silent	SNP	ENST00000260643.2	37	CCDS1738.1	17	0.007783882783882784	13	0.026422764227642278	4	0.011049723756906077	0	0.0	0	0.0	C	14.76	2.630999	0.46944	0.025693	1.17E-4	ENSG00000138073	ENST00000456259	.	.	.	5.05	5.05	0.67936	.	.	.	.	.	T	0.45796	0.1360	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58521	-0.7622	4	.	.	.	-19.6044	13.7879	0.63121	0.0:1.0:0.0:0.0	rs61276776	.	.	.	K	153	.	.	R	-	2	0	PREB	27207810	0.977000	0.34250	1.000000	0.80357	0.997000	0.91878	1.333000	0.33816	2.611000	0.88343	0.655000	0.94253	AGA	C|0.989;T|0.011	0.011	strong		0.577	PREB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214195.1	NM_013388		T	27354306	C	T	27354306	2	4	22	1	0	0	0	0	0	0	0	1	12482	912	32	2		2	PREB	2	27354306	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	655273	27354306	215845067	529	3430											
C2orf53	339779	hgsc.bcm.edu	37	chr2	27361049	27361049	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggactgagtggaagagaacGgtggttgagagggagggagg	11	5	23	2	1	0	3	0	2	0	2	0	9	0	7	0	7	1	1	0	7	2	1	rs61739485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27361049G>C	ENST00000335524.3	-	3	674	c.149C>G	c.(148-150)cCg>cGg	p.P50R		NM_178553.3	NP_848648.2	Q53SZ7	PRR30_HUMAN		50	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)					GGAAGAGAACGGTGGTTGAGA	0.592													G|||	118	0.0235623	0.0817	0.0115	5008	,	,		18470	0.0		0.002	False		,,,				2504	0.0				p.P50R		Atlas-SNP	.											.	C2orf53	45	.	0			c.C149G						PASS	.	G	ARG/PRO	269,4137	150.3+/-184.3	10,249,1944	99	90	93		149	0.8	0	2	dbSNP_129	93	3,8597	3.0+/-9.4	0,3,4297	yes	missense	C2orf53	NM_178553.3	103	10,252,6241	CC,CG,GG		0.0349,6.1053,2.0913	benign	50/413	27361049	272,12734	2203	4300	6503	SO:0001583	missense	339779	exon3			GAGAACGGTGGTT																												ENST00000335524.3:c.149C>G	2.37:g.27361049G>C	ENSP00000335017:p.Pro50Arg	144	0	0		144	50	0.347222	NM_178553	Q86UE2	Missense_Mutation	SNP	ENST00000335524.3	37	CCDS1739.1	29	0.013278388278388278	26	0.052845528455284556	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	8.058	0.767521	0.15983	0.061053	3.49E-4	ENSG00000186143	ENST00000335524	T	0.48522	0.81	3.88	0.835	0.18886	.	.	.	.	.	T	0.04227	0.0117	L	0.27053	0.805	0.09310	N	1	B	0.14438	0.01	B	0.12837	0.008	T	0.09015	-1.0694	9	0.56958	D	0.05	-0.0394	8.7685	0.34717	0.0:0.256:0.5932:0.1508	rs61739485	50	Q53SZ7	CB053_HUMAN	R	50	ENSP00000335017:P50R	ENSP00000335017:P50R	P	-	2	0	C2orf53	27214553	0.014000	0.17966	0.000000	0.03702	0.002000	0.02628	1.283000	0.33237	-0.082000	0.12640	0.561000	0.74099	CCG	G|0.972;C|0.028	0.028	strong		0.592	C2orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250188.1			C	27361049	G	C	27361049	3	2	22	1	0	0	0	0	1	0	0	0	2176	1116	39	4	1093	4	C2orf53	2	27361049	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6743	27361049	215838324	530	3431											
C2orf16	84226	hgsc.bcm.edu	37	chr2	27801739	27801739	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtatccagagctttggataTaaaaaaccctgggacagata	16	9	9	7	0	0	2	0	0	0	2	1	4	1	4	2	2	2	2	2	2	6	5	rs13416968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27801739T>C	ENST00000408964.2	+	1	2351	c.2300T>C	c.(2299-2301)aTa>aCa	p.I767T		NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	767			I -> T (in dbSNP:rs13416968).			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)					GCTTTGGATATAAAAAACCCT	0.408													T|||	55	0.0109824	0.0378	0.0043	5008	,	,		19518	0.0		0.002	False		,,,				2504	0.0				p.I767T		Atlas-SNP	.											.	C2orf16	357	.	0			c.T2300C						PASS	.	T	THR/ILE	113,3507		3,107,1700	138	136	137		2300	2.4	0.6	2	dbSNP_121	137	2,8150		0,2,4074	yes	missense	C2orf16	NM_032266.3	89	3,109,5774	CC,CT,TT		0.0245,3.1215,0.9769	probably-damaging	767/1985	27801739	115,11657	1810	4076	5886	SO:0001583	missense	84226	exon1			TGGATATAAAAAA	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.2300T>C	2.37:g.27801739T>C	ENSP00000386190:p.Ile767Thr	156	0	0		219	104	0.474886	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	21	0.009615384615384616	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	3.675	-0.066708	0.07273	0.031215	2.45E-4	ENSG00000221843	ENST00000408964	T	0.09723	2.95	4.83	2.41	0.29592	.	.	.	.	.	T	0.01353	0.0044	N	0.24115	0.695	0.09310	N	1	B	0.24368	0.102	B	0.18561	0.022	T	0.38802	-0.9644	9	0.37606	T	0.19	.	4.9147	0.13840	0.0:0.0967:0.1882:0.7151	rs13416968;rs13416968	767	Q68DN1	CB016_HUMAN	T	767	ENSP00000386190:I767T	ENSP00000386190:I767T	I	+	2	0	C2orf16	27655243	0.169000	0.23002	0.607000	0.28956	0.030000	0.12068	0.133000	0.15912	0.420000	0.25954	-0.488000	0.04728	ATA	T|0.986;C|0.014	0.014	strong		0.408	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		C	27801739	T	C	27801739	3	2	22	1	0	0	0	0	1	0	0	0	2159	1406	49	3	2302	3	C2orf16	2	27801739	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	440690	27801739	215397634	531	3432											
C2orf16	84226	hgsc.bcm.edu	37	chr2	27802457	27802457	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acaaactcaacgttcaatggTatatcccaagaagtcattca	16	10	5	10	1	4	1	4	0	0	1	5	1	5	1	1	1	2	2	1	1	7	4	rs12329054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27802457T>C	ENST00000408964.2	+	1	3069	c.3018T>C	c.(3016-3018)ggT>ggC	p.G1006G	AC074091.1_ENST00000408604.1_RNA	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1006						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)					CGTTCAATGGTATATCCCAAG	0.443													T|||	55	0.0109824	0.0378	0.0043	5008	,	,		20778	0.0		0.002	False		,,,				2504	0.0				p.G1006G		Atlas-SNP	.											.	C2orf16	357	.	0			c.T3018C						PASS	.	T		122,3976		3,116,1930	101	100	100		3018	-0.3	0.1	2	dbSNP_120	100	3,8421		0,3,4209	no	coding-synonymous	C2orf16	NM_032266.3		3,119,6139	CC,CT,TT		0.0356,2.9771,0.9982		1006/1985	27802457	125,12397	2049	4212	6261	SO:0001819	synonymous_variant	84226	exon1			CAATGGTATATCC	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.3018T>C	2.37:g.27802457T>C		96	0	0		102	59	0.578431	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Silent	SNP	ENST00000408964.2	37	CCDS42666.1																																																																																			T|0.986;C|0.014	0.014	strong		0.443	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		C	27802457	T	C	27802457	2	2	22	1	0	0	0	0	0	0	0	1	2159	1625	57	3		3	C2orf16	2	27802457	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	718	27802457	215396916	532	3433											
C2orf16	84226	hgsc.bcm.edu	37	chr2	27803810	27803810	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcttcgactgcccaagccCacagattcccaaagtggtat	10	9	7	15	1	1	1	0	0	1	1	3	2	2	1	4	1	2	1	4	1	3	3	rs13408423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27803810C>T	ENST00000408964.2	+	1	4422	c.4371C>T	c.(4369-4371)ccC>ccT	p.P1457P	ZNF512_ENST00000413371.2_5'Flank|ZNF512_ENST00000379717.1_5'Flank|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000416005.2_5'Flank|ZNF512_ENST00000556601.1_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000355467.4_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1457						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)					TGCCCAAGCCCACAGATTCCC	0.493													C|||	55	0.0109824	0.0378	0.0043	5008	,	,		18436	0.0		0.002	False		,,,				2504	0.0				p.P1457P		Atlas-SNP	.											.	C2orf16	357	.	0			c.C4371T						PASS	.	C		118,3726		3,112,1807	97	100	99		4371	2.5	0	2	dbSNP_121	99	2,8260		0,2,4129	no	coding-synonymous	C2orf16	NM_032266.3		3,114,5936	TT,TC,CC		0.0242,3.0697,0.9912		1457/1985	27803810	120,11986	1922	4131	6053	SO:0001819	synonymous_variant	84226	exon1			CAAGCCCACAGAT	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.4371C>T	2.37:g.27803810C>T		62	0	0		68	42	0.617647	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Silent	SNP	ENST00000408964.2	37	CCDS42666.1																																																																																			C|0.986;T|0.014	0.014	strong		0.493	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		T	27803810	C	T	27803810	2	4	22	1	0	0	0	0	0	0	0	1	2159	581	21	2		2	C2orf16	2	27803810	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1353	27803810	215395563	533	3434											
C2orf16	84226	hgsc.bcm.edu	37	chr2	27804114	27804114	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtccttctgagagaacccgtCataacccctcttggagaaac	11	9	8	13	1	3	3	1	1	2	2	4	5	4	3	4	1	3	0	4	1	3	3	rs13392197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27804114C>T	ENST00000408964.2	+	1	4726	c.4675C>T	c.(4675-4677)Cat>Tat	p.H1559Y	ZNF512_ENST00000413371.2_5'Flank|ZNF512_ENST00000379717.1_5'Flank|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000416005.2_5'Flank|ZNF512_ENST00000556601.1_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000355467.4_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1559	Arg-rich.		H -> Y (in dbSNP:rs13392197).			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)					GAGAACCCGTCATAACCCCTC	0.537													C|||	59	0.0117812	0.0408	0.0043	5008	,	,		18030	0.0		0.002	False		,,,				2504	0.0				p.H1559Y		Atlas-SNP	.											.	C2orf16	357	.	0			c.C4675T						PASS	.	C	TYR/HIS	130,3650		3,124,1763	118	118	118		4675	-5.8	0	2	dbSNP_121	118	3,8217		0,3,4107	yes	missense	C2orf16	NM_032266.3	83	3,127,5870	TT,TC,CC		0.0365,3.4392,1.1083	benign	1559/1985	27804114	133,11867	1890	4110	6000	SO:0001583	missense	84226	exon1			ACCCGTCATAACC	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.4675C>T	2.37:g.27804114C>T	ENSP00000386190:p.His1559Tyr	90	0	0		81	44	0.54321	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	24	0.01098901098901099	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	5.555	0.287230	0.10513	0.034392	3.65E-4	ENSG00000221843	ENST00000408964	T	0.04809	3.55	4.05	-5.76	0.02376	.	.	.	.	.	T	0.00552	0.0018	N	0.25647	0.755	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.47699	-0.9097	9	0.08381	T	0.77	.	2.2504	0.04042	0.1341:0.3469:0.1054:0.4136	rs13392197;rs52835437;rs13392197	1559	Q68DN1	CB016_HUMAN	Y	1559	ENSP00000386190:H1559Y	ENSP00000386190:H1559Y	H	+	1	0	C2orf16	27657618	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.314000	0.01125	-1.329000	0.02258	-0.379000	0.06801	CAT	C|0.983;T|0.017	0.017	strong		0.537	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		T	27804114	C	T	27804114	3	4	22	1	0	0	0	0	1	0	0	0	2159	826	29	2	4677	2	C2orf16	2	27804114	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	304	27804114	215395259	534	3435											
C2orf16	84226	hgsc.bcm.edu	37	chr2	27804690	27804690	+	Missense_Mutation	SNP	C	C	T																															gtccctctgagagaagacatCacagtccctctgagagaagc																								rs555322236	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27804690C>T	ENST00000408964.2	+	1	5302	c.5251C>T	c.(5251-5253)Cac>Tac	p.H1751Y	ZNF512_ENST00000413371.2_5'Flank|ZNF512_ENST00000379717.1_5'Flank|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000416005.2_5'Flank|ZNF512_ENST00000556601.1_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000355467.4_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1751	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)					GAGAAGACATCACAGTCCCTC	0.557													C|||	6	0.00119808	0.0038	0.0	5008	,	,		20958	0.001		0.0	False		,,,				2504	0.0				p.H1751Y		Atlas-SNP	.											.	C2orf16	357	.	0			c.C5251T						PASS	.						192	196	195					2																	27804690		1920	4145	6065	SO:0001583	missense	84226	exon1			AGACATCACAGTC	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.5251C>T	2.37:g.27804690C>T	ENSP00000386190:p.His1751Tyr	171	0	0		158	13	0.0822785	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	C	14.08	2.428580	0.43122	.	.	ENSG00000221843	ENST00000408964	T	0.05199	3.48	3.97	2.1	0.27182	.	.	.	.	.	T	0.04770	0.0129	L	0.34521	1.04	0.09310	N	1	P	0.47604	0.898	B	0.37550	0.253	T	0.41520	-0.9504	9	0.30078	T	0.28	.	8.7197	0.34434	0.1703:0.6649:0.1648:0.0	.	1751	Q68DN1	CB016_HUMAN	Y	1751	ENSP00000386190:H1751Y	ENSP00000386190:H1751Y	H	+	1	0	C2orf16	27658194	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.020000	0.13466	0.607000	0.29982	0.456000	0.33151	CAC	.	.	none		0.557	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		T	27804690	C	T	27804690	3	4	22	1	0	0	0	0	1	0	0	0	2159	826	29	2	5253	2	C2orf16	2	27804690	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	576	27804690	215394683	535	3436	49	2									
C2orf16	84226	hgsc.bcm.edu	37	chr2	27804691	27804691	+	Missense_Mutation	SNP	A	A	G																															tccctctgagagaagacatcAcagtccctctgagagaagcc																								rs573591891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27804691A>G	ENST00000408964.2	+	1	5303	c.5252A>G	c.(5251-5253)cAc>cGc	p.H1751R	ZNF512_ENST00000413371.2_5'Flank|ZNF512_ENST00000379717.1_5'Flank|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000416005.2_5'Flank|ZNF512_ENST00000556601.1_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000355467.4_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1751	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)					AGAAGACATCACAGTCCCTCT	0.552													A|||	8	0.00159744	0.0053	0.0	5008	,	,		20961	0.001		0.0	False		,,,				2504	0.0				p.H1751R		Atlas-SNP	.											.	C2orf16	357	.	0			c.A5252G						PASS	.						192	196	195					2																	27804691		1917	4144	6061	SO:0001583	missense	84226	exon1			GACATCACAGTCC	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.5252A>G	2.37:g.27804691A>G	ENSP00000386190:p.His1751Arg	169	0	0		157	13	0.0828025	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	A	0.005	-2.199397	0.00299	.	.	ENSG00000221843	ENST00000408964	T	0.04706	3.57	3.97	-7.95	0.01148	.	.	.	.	.	T	0.01592	0.0051	N	0.01729	-0.75	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.42682	-0.9437	9	0.02654	T	1	.	14.4295	0.67240	0.7984:0.0:0.1133:0.0882	.	1751	Q68DN1	CB016_HUMAN	R	1751	ENSP00000386190:H1751R	ENSP00000386190:H1751R	H	+	2	0	C2orf16	27658195	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-11.276000	0.00004	-2.917000	0.00306	-1.919000	0.00516	CAC	.	.	none		0.552	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		G	27804691	A	G	27804691	3	3	22	1	0	0	0	0	1	0	0	0	2159	159	6	3	5254	3	C2orf16	2	27804691	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1	27804691	215394682	536	3437	49	2									
SUPT7L	9913	hgsc.bcm.edu	37	chr2	27883958	27883958	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaggaggtgacccagggcaCgagggaagaggttcactctc	11	5	16	9	1	2	3	1	1	1	2	3	6	2	5	1	5	0	2	1	5	1	1	rs6756254	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27883958C>T	ENST00000337768.5	-	3	881	c.312G>A	c.(310-312)tcG>tcA	p.S104S	SUPT7L_ENST00000404798.2_Intron|SUPT7L_ENST00000464789.2_Silent_p.S102S|SUPT7L_ENST00000405491.1_Silent_p.S102S|SUPT7L_ENST00000406540.1_Silent_p.S102S|SLC4A1AP_ENST00000326019.6_5'Flank	NM_001282729.1|NM_014860.1	NP_001269658.1|NP_055675.1	O94864	ST65G_HUMAN	suppressor of Ty 7 (S. cerevisiae)-like	104					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)					ACCCAGGGCACGAGGGAAGAG	0.527													C|||	333	0.0664936	0.2307	0.0187	5008	,	,		20175	0.0		0.0129	False		,,,				2504	0.002				p.S104S		Atlas-SNP	.											.	SUPT7L	36	.	0			c.G312A						PASS	.	C		690,3508		61,568,1470	117	123	121		312	-2.7	0.3	2	dbSNP_116	121	65,8345		0,65,4140	no	coding-synonymous	SUPT7L	NM_014860.1		61,633,5610	TT,TC,CC		0.7729,16.4364,5.9883		104/415	27883958	755,11853	2099	4205	6304	SO:0001819	synonymous_variant	9913	exon3			AGGGCACGAGGGA	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.312G>A	2.37:g.27883958C>T		358	0	0		440	194	0.440909	NM_014860	B4E3W3|Q6IB21|Q9H2T6	Silent	SNP	ENST00000337768.5	37	CCDS42667.1																																																																																			C|0.940;T|0.060	0.060	strong		0.527	SUPT7L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324568.1	NM_014860		T	27883958	C	T	27883958	2	4	22	1	0	0	0	0	0	0	0	1	15416	523	19	1		1	SUPT7L	2	27883958	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	79267	27883958	215315415	537	3438											
SLC4A1AP	22950	hgsc.bcm.edu	37	chr2	27886820	27886820	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagtcagagaccctggcgtcGcaagacctcagtggggactt	9	7	13	12	2	2	2	2	0	0	2	3	4	2	3	2	3	0	1	2	3	1	1	rs58106741	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27886820G>T	ENST00000326019.6	+	1	483	c.201G>T	c.(199-201)tcG>tcT	p.S67S	SUPT7L_ENST00000404798.2_5'Flank|SUPT7L_ENST00000464789.2_5'Flank|SUPT7L_ENST00000405491.1_5'Flank|SUPT7L_ENST00000406540.1_5'Flank|SUPT7L_ENST00000337768.5_5'Flank	NM_018158.2	NP_060628.2	Q9BWU0	NADAP_HUMAN	solute carrier family 4 (anion exchanger), member 1, adaptor protein	67						cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(172;0.155)					CCCTGGCGTCGCAAGACCTCA	0.592													G|||	334	0.0666933	0.2315	0.0187	5008	,	,		16985	0.0		0.0129	False		,,,				2504	0.002				p.S67S		Atlas-SNP	.											.	SLC4A1AP	63	.	0			c.G201T						PASS	.	G		771,3635	315.5+/-294.2	77,617,1509	77	76	76		201	-2.8	0	2	dbSNP_129	76	68,8532	40.3+/-97.0	0,68,4232	no	coding-synonymous	SLC4A1AP	NM_018158.2		77,685,5741	TT,TG,GG		0.7907,17.4989,6.4509		67/797	27886820	839,12167	2203	4300	6503	SO:0001819	synonymous_variant	22950	exon1			GGCGTCGCAAGAC		CCDS33166.1	2p23.3	2010-03-11	2001-11-28		ENSG00000163798	ENSG00000163798			13813	protein-coding gene	gene with protein product	"lung cancer oncogene 3"	602655	"solute carrier family 4 (anion exchanger), member 1, adapter protein"			9422766	Standard	NM_018158		Approved	kanadaptin, HLC3	uc002rlk.4	Q9BWU0	OTTHUMG00000151944	ENST00000326019.6:c.201G>T	2.37:g.27886820G>T		66	0	0		57	26	0.45614	NM_018158	A6NJ39|Q4KMT1|Q4KMX0|Q7Z5Q9|Q9NVN2	Silent	SNP	ENST00000326019.6	37	CCDS33166.1																																																																																			G|0.940;T|0.060	0.060	strong		0.592	SLC4A1AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324550.1	NM_018158		T	27886820	G	T	27886820	2	4	22	1	0	0	0	0	0	0	0	1	14668	1074	38	4		4	SLC4A1AP	2	27886820	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2862	27886820	215312553	538	3439											
SPDYA	245711	hgsc.bcm.edu	37	chr2	29063342	29063342	+	3'UTR	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tactggttctgaaggtatgaTttagtaatatgccagaatta	13	15	9	4	0	1	3	0	2	1	1	1	3	1	3	1	2	2	3	1	2	8	8	rs6747208	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:29063342T>C	ENST00000462832.1	+	0	1756				SPDYA_ENST00000379579.4_Intron|SPDYA_ENST00000334056.5_Intron					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)					GAAGGTATGATTTAGTAATAT	0.373													T|||	36	0.0071885	0.0272	0.0	5008	,	,		19472	0.0		0.0	False		,,,				2504	0.0				p.I286T		Atlas-SNP	.											.	SPDYA	41	.	0			c.T857C						PASS	.	T	THR/ILE,,	85,4321	68.7+/-106.4	0,85,2118	69	68	69		857,,	1.7	0.9	2	dbSNP_116	69	1,8599	1.2+/-3.3	0,1,4299	yes	missense,intron,intron	SPDYA	NM_001008779.1,NM_001142634.1,NM_182756.3	89,,	0,86,6417	CC,CT,TT		0.0116,1.9292,0.6612	,,	286/287,,	29063342	86,12920	2203	4300	6503	SO:0001624	3_prime_UTR_variant	245711	exon5			GTATGATTTAGTA	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	ENST00000462832.1:c.*1753T>C	2.37:g.29063342T>C		110	0	0		109	56	0.513761	NM_001008779		Missense_Mutation	SNP	ENST00000462832.1	37																																																																																				T|0.993;C|0.007	0.007	strong		0.373	SPDYA-003	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000157172.2	NM_182756		C	29063342	T	C	29063342	1	2	22	0	1	0	0	0	0	0	0	0	15042	1493	52	3		3	SPDYA	2	29063342	3'UTR	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1176522	29063342	214136031	539	3440											
ALK	238	hgsc.bcm.edu	37	chr2	29416750	29416750	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcttccacaagtggaccAtattctatcggcaaagcggt	10	11	8	12	2	2	0	0	0	2	0	5	1	4	1	3	3	1	1	3	3	4	4	rs55772745	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:29416750A>G	ENST00000389048.3	-	29	5109	c.4203T>C	c.(4201-4203)taT>taC	p.Y1401Y	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1401					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)	CAAGTGGACCATATTCTATCG	0.488			"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				A|||	114	0.0227636	0.0847	0.0029	5008	,	,		17238	0.0		0.0	False		,,,				2504	0.0				p.Y1401Y		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	.	ALK	533	.	0			c.T4203C						PASS	.			255,4149		7,241,1954	43	47	45		4203	-10.6	0	2	dbSNP_129	45	1,8599		0,1,4299	no	coding-synonymous	ALK	NM_004304.4		7,242,6253	GG,GA,AA		0.0116,5.7902,1.9686		1401/1621	29416750	256,12748	2202	4300	6502	SO:0001819	synonymous_variant	238	exon29	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	TGGACCATATTCT	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.4203T>C	2.37:g.29416750A>G		146	0	0		133	78	0.586466	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			A|0.979;G|0.021	0.021	strong		0.488	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		G	29416750	A	G	29416750	2	3	22	1	0	0	0	0	0	0	0	1	525	224	8	3		3	ALK	2	29416750	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	353408	29416750	213782623	540	3441											
ALK	238	hgsc.bcm.edu	37	chr2	29445425	29445425	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttgggtcgttgggcattccGgacacctggccttcatacac	6	11	11	13	2	1	0	1	0	0	0	3	1	2	1	3	4	1	2	3	4	1	5	rs56146053	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:29445425G>A	ENST00000389048.3	-	21	4314	c.3408C>T	c.(3406-3408)tcC>tcT	p.S1136S	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1136	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)	TGGGCATTCCGGACACCTGGC	0.572			"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				G|||	167	0.0333466	0.1225	0.0072	5008	,	,		16613	0.0		0.0	False		,,,				2504	0.0				p.S1136S		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	ALK,colon,carcinoma,0,1	ALK	533	1	0			c.C3408T						PASS	.	G		379,4027	193.0+/-218.2	13,353,1837	57	55	56		3408	-5.2	0.9	2	dbSNP_129	56	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ALK	NM_004304.4		13,354,6136	AA,AG,GG		0.0116,8.6019,2.9217		1136/1621	29445425	380,12626	2203	4300	6503	SO:0001819	synonymous_variant	238	exon21	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	CATTCCGGACACC	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.3408C>T	2.37:g.29445425G>A		125	0	0		138	57	0.413043	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			G|0.970;A|0.030	0.030	strong		0.572	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		A	29445425	G	A	29445425	2	1	22	1	0	0	0	0	0	0	0	1	525	1103	39	1		1	ALK	2	29445425	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	28675	29445425	213753948	541	3442											
ALK	238	hgsc.bcm.edu	37	chr2	30143259	30143259	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgcagtccagagctagcgaGccgcgggcctcgggcctgcc	5	4	16	16	5	0	1	0	0	0	1	2	2	1	1	5	2	4	2	5	2	1	1	rs192127241	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:30143259G>T	ENST00000389048.3	-	1	1173	c.267C>A	c.(265-267)ggC>ggA	p.G89G	ALK_ENST00000431873.1_Silent_p.G89G	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	89					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)	GAGCTAGCGAGCCGCGGGCCT	0.721			"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				G|||	16	0.00319489	0.0113	0.0014	5008	,	,		11936	0.0		0.0	False		,,,				2504	0.0				p.G89G		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	.	ALK	533	.	0			c.C267A						PASS	.	G		73,4275		0,73,2101	12	14	13		267	2.2	0.3	2		13	0,8484		0,0,4242	no	coding-synonymous	ALK	NM_004304.4		0,73,6343	TT,TG,GG		0.0,1.6789,0.5689		89/1621	30143259	73,12759	2174	4242	6416	SO:0001819	synonymous_variant	238	exon1	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	TAGCGAGCCGCGG	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.267C>A	2.37:g.30143259G>T		15	0	0		20	9	0.45	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			G|0.998;T|0.002	0.002	strong		0.721	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		T	30143259	G	T	30143259	2	4	22	1	0	0	0	0	0	0	0	1	525	958	34	4		4	ALK	2	30143259	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	697834	30143259	213056114	542	3443											
LBH	81606	hgsc.bcm.edu	37	chr2	30457288	30457288	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cagccccgactatctgagatCggccaagatgactgaggtga	11	7	12	11	2	1	5	0	4	1	2	2	7	1	5	3	2	1	0	3	2	2	1	rs144194149	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:30457288C>T	ENST00000395323.3	+	2	252	c.44C>T	c.(43-45)tCg>tTg	p.S15L	LBH_ENST00000406087.1_Missense_Mutation_p.S15L|LBH_ENST00000401506.1_Missense_Mutation_p.S21L|LBH_ENST00000467242.1_3'UTR|LBH_ENST00000404397.1_Missense_Mutation_p.S15L|LBH_ENST00000407930.2_5'UTR	NM_030915.3	NP_112177.2	Q53QV2	LBH_HUMAN	limb bud and heart development	15					multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|large_intestine(1)|lung(2)	5	Acute lymphoblastic leukemia(172;0.155)					TATCTGAGATCGGCCAAGATG	0.537													C|||	12	0.00239617	0.0076	0.0029	5008	,	,		20573	0.0		0.0	False		,,,				2504	0.0				p.S15L		Atlas-SNP	.											.	LBH	14	.	0			c.C44T						PASS	.	C	LEU/SER	58,4348	56.8+/-93.2	1,56,2146	138	116	124		44	4.5	1	2	dbSNP_134	124	0,8600		0,0,4300	yes	missense	LBH	NM_030915.3	145	1,56,6446	TT,TC,CC		0.0,1.3164,0.4459	possibly-damaging	15/106	30457288	58,12948	2203	4300	6503	SO:0001583	missense	81606	exon2			TGAGATCGGCCAA	AF110224	CCDS33173.1	2p23.1	2012-12-07	2012-12-07		ENSG00000213626	ENSG00000213626			29532	protein-coding gene	gene with protein product		611763	"limb bud and heart development homolog (mouse)"			11230166, 11336496	Standard	NM_030915		Approved		uc002rne.2	Q53QV2	OTTHUMG00000152051	ENST00000395323.3:c.44C>T	2.37:g.30457288C>T	ENSP00000378733:p.Ser15Leu	171	0	0		186	98	0.526882	NM_030915	B2RBC2|Q9H0Q1	Missense_Mutation	SNP	ENST00000395323.3	37	CCDS33173.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	21.8	4.205678	0.79127	0.013164	0.0	ENSG00000213626	ENST00000395323;ENST00000406087;ENST00000404397;ENST00000401506	.	.	.	4.47	4.47	0.54385	.	0.250189	0.33895	N	0.004451	T	0.51126	0.1656	L	0.56769	1.78	0.80722	D	1	D	0.62365	0.991	P	0.47134	0.539	T	0.60915	-0.7168	9	0.46703	T	0.11	-7.442	14.6316	0.68660	0.0:1.0:0.0:0.0	.	15	Q53QV2	LBH_HUMAN	L	15;15;15;21	.	ENSP00000378733:S15L	S	+	2	0	LBH	30310792	0.992000	0.36948	0.990000	0.47175	0.952000	0.60782	3.080000	0.50112	2.028000	0.59812	0.455000	0.32223	TCG	C|0.996;T|0.004	0.004	strong		0.537	LBH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325091.1	NM_030915		T	30457288	C	T	30457288	3	4	22	1	0	0	0	0	1	0	0	0	8659	893	31	1	50	1	LBH	2	30457288	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	314029	30457288	212742085	543	3444											
XDH	7498	hgsc.bcm.edu	37	chr2	31598339	31598339	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcaccggaagtccaccatGccaccaggggcatcgggagg	9	4	15	13	2	0	0	0	0	0	0	2	2	1	2	5	5	2	2	5	5	1	0	rs45612839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:31598339G>C	ENST00000379416.3	-	15	1557	c.1509C>G	c.(1507-1509)ggC>ggG	p.G503G		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	503					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)	AGTCCACCATGCCACCAGGGG	0.602													G|||	314	0.0626997	0.2277	0.0159	5008	,	,		17654	0.0		0.002	False		,,,				2504	0.0				p.G503G	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.C1509G						PASS	.	G		857,3549	338.1+/-305.1	72,713,1418	86	80	82		1509	2.4	1	2	dbSNP_127	82	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	XDH	NM_000379.3		72,720,5711	CC,CG,GG		0.0814,19.4507,6.6431		503/1334	31598339	864,12142	2203	4300	6503	SO:0001819	synonymous_variant	7498	exon15			CACCATGCCACCA	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.1509C>G	2.37:g.31598339G>C		130	0	0		118	55	0.466102	NM_000379	Q16681|Q16712|Q4PJ16	Silent	SNP	ENST00000379416.3	37	CCDS1775.1																																																																																			G|0.936;C|0.064	0.064	strong		0.602	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379		C	31598339	G	C	31598339	2	2	22	1	0	0	0	0	0	0	0	1	17441	1306	46	4		4	XDH	2	31598339	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1141051	31598339	211601034	544	3445											
NLRC4	58484	hgsc.bcm.edu	37	chr2	32463353	32463353	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaataaacacatcttcttcAggtttttcaggccttcagct	11	14	6	10	0	5	0	3	0	2	0	5	1	5	0	1	2	2	2	1	2	3	6	rs202095832		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:32463353A>G	ENST00000404025.2	-	7	2857	c.2369T>C	c.(2368-2370)cTg>cCg	p.L790P	NLRC4_ENST00000342905.6_Missense_Mutation_p.L125P|NLRC4_ENST00000402280.1_Missense_Mutation_p.L790P|NLRC4_ENST00000360906.5_Missense_Mutation_p.L790P			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	790					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)					CATCTTCTTCAGGTTTTTCAG	0.368													A|||	1	0.000199681	0.0008	0.0	5008	,	,		19319	0.0		0.0	False		,,,				2504	0.0				p.L790P		Atlas-SNP	.											.	NLRC4	165	.	0			c.T2369C						PASS	.	A	PRO/LEU,PRO/LEU,PRO/LEU	3,4403	6.2+/-15.9	0,3,2200	101	101	101		2369,2369,2369	4.6	0.9	2		101	0,8600		0,0,4300	no	missense,missense,missense	NLRC4	NM_001199138.1,NM_001199139.1,NM_021209.4	98,98,98	0,3,6500	GG,GA,AA		0.0,0.0681,0.0231	probably-damaging,probably-damaging,probably-damaging	790/1025,790/1025,790/1025	32463353	3,13003	2203	4300	6503	SO:0001583	missense	58484	exon6			TTCTTCAGGTTTT	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.2369T>C	2.37:g.32463353A>G	ENSP00000385090:p.Leu790Pro	91	0	0		113	61	0.539823	NM_001199138	A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	Missense_Mutation	SNP	ENST00000404025.2	37	CCDS33174.1	.	.	.	.	.	.	.	.	.	.	A	12.13	1.846213	0.32606	6.81E-4	0.0	ENSG00000091106	ENST00000360906;ENST00000402280;ENST00000342905;ENST00000404025	T;T;T;T	0.57752	0.38;0.38;0.38;0.38	4.63	4.63	0.57726	.	0.000000	0.31949	N	0.006818	T	0.64527	0.2606	M	0.63843	1.955	0.34053	D	0.656327	D;D	0.71674	0.998;0.994	D;P	0.65874	0.939;0.879	T	0.71251	-0.4648	9	0.34782	T	0.22	-3.8349	10.6228	0.45489	1.0:0.0:0.0:0.0	.	125;790	Q9NPP4-2;Q9NPP4	.;NLRC4_HUMAN	P	790;790;125;790	ENSP00000354159:L790P;ENSP00000385428:L790P;ENSP00000339666:L125P;ENSP00000385090:L790P	ENSP00000339666:L125P	L	-	2	0	NLRC4	32316857	0.984000	0.35163	0.947000	0.38551	0.111000	0.19643	1.992000	0.40737	2.088000	0.63022	0.533000	0.62120	CTG	.	.	weak		0.368	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325222.2	NM_021209		G	32463353	A	G	32463353	3	3	22	1	0	0	0	0	1	0	0	0	10478	188	7	3	721	3	NLRC4	2	32463353	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	865014	32463353	210736020	545	3446											
BIRC6	57448	hgsc.bcm.edu	37	chr2	32673884	32673884	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatggattatatagctcaccAtttgatccagtcctctttga	10	16	6	9	0	2	2	1	2	1	0	4	3	4	3	3	1	1	1	3	1	4	6	rs150651833	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:32673884A>G	ENST00000421745.2	+	22	4640	c.4506A>G	c.(4504-4506)ccA>ccG	p.P1502P		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	1502					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)					ATAGCTCACCATTTGATCCAG	0.318													A|||	9	0.00179712	0.0061	0.0014	5008	,	,		14704	0.0		0.0	False		,,,				2504	0.0				p.P1502P	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.A4506G						PASS	.	A		24,4382	30.8+/-60.4	0,24,2179	120	123	122		4506	-3.2	1	2	dbSNP_134	122	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	BIRC6	NM_016252.3		0,28,6475	GG,GA,AA		0.0465,0.5447,0.2153		1502/4858	32673884	28,12978	2203	4300	6503	SO:0001819	synonymous_variant	57448	exon22			CTCACCATTTGAT	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.4506A>G	2.37:g.32673884A>G		155	0	0		136	57	0.419118	NM_016252	Q9ULD1	Silent	SNP	ENST00000421745.2	37	CCDS33175.2																																																																																			A|0.998;G|0.002	0.002	strong		0.318	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		G	32673884	A	G	32673884	2	3	22	1	0	0	0	0	0	0	0	1	1438	204	8	3		3	BIRC6	2	32673884	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	210531	32673884	210525489	546	3447											
HEATR5B	54497	hgsc.bcm.edu	37	chr2	37280711	37280711	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgctggcggacacctttagcTtgtttaacacattcagcaaa	11	12	8	10	1	1	0	1	0	0	0	1	1	1	1	1	2	4	4	1	2	3	6	rs10202107	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:37280711T>C	ENST00000233099.5	-	17	2534	c.2439A>G	c.(2437-2439)caA>caG	p.Q813Q	HEATR5B_ENST00000354531.2_Silent_p.Q813Q	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	813						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)				CACCTTTAGCTTGTTTAACAC	0.313													T|||	56	0.0111821	0.0416	0.0014	5008	,	,		17495	0.0		0.0	False		,,,				2504	0.0				p.Q813Q		Atlas-SNP	.											.	HEATR5B	185	.	0			c.A2439G						PASS	.	T		121,4285	91.1+/-129.8	2,117,2084	56	57	57		2439	2.3	1	2	dbSNP_119	57	0,8600		0,0,4300	no	coding-synonymous	HEATR5B	NM_019024.1		2,117,6384	CC,CT,TT		0.0,2.7463,0.9303		813/2072	37280711	121,12885	2203	4300	6503	SO:0001819	synonymous_variant	54497	exon17			TTTAGCTTGTTTA	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.2439A>G	2.37:g.37280711T>C		221	0	0		196	101	0.515306	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Silent	SNP	ENST00000233099.5	37	CCDS33181.1																																																																																			T|0.989;C|0.011	0.011	strong		0.313	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		C	37280711	T	C	37280711	2	2	22	1	0	0	0	0	0	0	0	1	7041	1606	56	3		3	HEATR5B	2	37280711	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	4606827	37280711	205918662	547	3448											
EIF2AK2	5610	hgsc.bcm.edu	37	chr2	37353464	37353464	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttaacacgtttaataacgtaAgtctttccgtcaattctgtg	11	16	6	8	3	3	0	1	0	2	0	4	0	4	0	1	0	2	2	1	0	5	7	rs2307478	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:37353464A>G	ENST00000233057.4	-	11	1198	c.876T>C	c.(874-876)acT>acC	p.T292T	EIF2AK2_ENST00000395127.2_Silent_p.T292T|EIF2AK2_ENST00000405334.1_Intron	NM_001135651.2	NP_001129123.1	P19525	E2AK2_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 2	292	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)				TAATAACGTAAGTCTTTCCGT	0.313													A|||	82	0.0163738	0.0613	0.0014	5008	,	,		17810	0.0		0.0	False		,,,				2504	0.0				p.T292T		Atlas-SNP	.											.	EIF2AK2	54	.	0			c.T876C						PASS	.	A	,,	237,4169	141.1+/-176.5	6,225,1972	95	93	93		876,,876	-2.7	0	2	dbSNP_100	93	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous,intron,coding-synonymous	EIF2AK2	NM_001135651.1,NM_001135652.1,NM_002759.2	,,	6,226,6270	GG,GA,AA		0.0116,5.379,1.8302	,,	292/552,,292/552	37353464	238,12766	2203	4299	6502	SO:0001819	synonymous_variant	5610	exon11			AACGTAAGTCTTT	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.876T>C	2.37:g.37353464A>G		196	0	0		152	79	0.519737	NM_001135651	A8K3P0|D6W584|E9PC80|Q52M43|Q7Z6F6|Q9UIR4	Silent	SNP	ENST00000233057.4	37	CCDS1786.1																																																																																			A|0.985;G|0.015	0.015	strong		0.313	EIF2AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218571.2	NM_002759		G	37353464	A	G	37353464	2	3	22	1	0	0	0	0	0	0	0	1	4999	59	3	3		3	EIF2AK2	2	37353464	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	72753	37353464	205845909	548	3449											
SULT6B1	391365	hgsc.bcm.edu	37	chr2	37406645	37406645	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaattcatcccaagagccaTagcttggaatatcggggaca	14	8	10	9	1	1	2	1	0	0	2	3	4	2	4	2	3	2	1	2	3	5	4	rs61737618	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:37406645T>C	ENST00000535679.1	-	4	484	c.485A>G	c.(484-486)tAt>tGt	p.Y162C	SULT6B1_ENST00000260637.3_Missense_Mutation_p.Y124C|SULT6B1_ENST00000407963.1_Missense_Mutation_p.Y124C|SULT6B1_ENST00000379149.2_Intron			Q6IMI4	ST6B1_HUMAN	sulfotransferase family, cytosolic, 6B, member 1	162						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)				CCAAGAGCCATAGCTTGGAAT	0.378													T|||	9	0.00179712	0.0068	0.0	5008	,	,		19591	0.0		0.0	False		,,,				2504	0.0				p.Y124C		Atlas-SNP	.											.	SULT6B1	46	.	0			c.A371G						PASS	.	T	CYS/TYR	33,4373	38.4+/-70.7	0,33,2170	161	151	154		371	3	1	2	dbSNP_129	154	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SULT6B1	NM_001032377.1	194	0,34,6469	CC,CT,TT		0.0116,0.749,0.2614	probably-damaging	124/266	37406645	34,12972	2203	4300	6503	SO:0001583	missense	391365	exon4			GAGCCATAGCTTG	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.485A>G	2.37:g.37406645T>C	ENSP00000444081:p.Tyr162Cys	60	0	0		60	33	0.55	NM_001032377	B2RTS7	Missense_Mutation	SNP	ENST00000535679.1	37		3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	T	15.08	2.726804	0.48833	0.00749	1.16E-4	ENSG00000138068	ENST00000535679;ENST00000260637;ENST00000407963	D;D;D	0.82167	-1.58;-1.58;-1.58	4.27	3.02	0.34903	Sulfotransferase domain (1);	1.254540	0.05257	N	0.515113	D	0.86522	0.5953	M	0.73372	2.23	0.40291	D	0.9785	D	0.71674	0.998	D	0.65443	0.935	T	0.81870	-0.0734	10	0.40728	T	0.16	.	9.6717	0.40017	0.1561:0.0:0.0:0.8439	.	162	Q6IMI4	ST6B1_HUMAN	C	162;124;124	ENSP00000444081:Y162C;ENSP00000260637:Y124C;ENSP00000384950:Y124C	ENSP00000260637:Y124C	Y	-	2	0	SULT6B1	37260149	0.715000	0.27946	0.981000	0.43875	0.855000	0.48748	0.833000	0.27504	1.928000	0.55862	0.459000	0.35465	TAT	T|0.997;C|0.003	0.003	strong		0.378	SULT6B1-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001032377		C	37406645	T	C	37406645	3	2	22	1	0	0	0	0	1	0	0	0	15399	1406	49	3	442	3	SULT6B1	2	37406645	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	53181	37406645	205792728	549	3450											
CEBPZ	10153	hgsc.bcm.edu	37	chr2	37454998	37454998	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatgggacagagccatttgAtttaaaaagcaaattgcata	16	11	8	6	0	1	2	1	1	0	1	1	3	1	3	1	1	3	2	1	1	5	5	rs1803251	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:37454998A>G	ENST00000234170.5	-	2	1483	c.1338T>C	c.(1336-1338)aaT>aaC	p.N446N		NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	446					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)				GAGCCATTTGATTTAAAAAGC	0.343													A|||	451	0.0900559	0.32	0.0389	5008	,	,		21260	0.0		0.001	False		,,,				2504	0.0				p.N446N		Atlas-SNP	.											.	CEBPZ	68	.	0			c.T1338C						PASS	.	A		1241,3163	393.3+/-328.8	184,873,1145	69	70	70		1338	3	1	2	dbSNP_89	70	15,8585	8.4+/-32.0	0,15,4285	no	coding-synonymous	CEBPZ	NM_005760.2		184,888,5430	GG,GA,AA		0.1744,28.1789,9.6586		446/1055	37454998	1256,11748	2202	4300	6502	SO:0001819	synonymous_variant	10153	exon2			CATTTGATTTAAA	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.1338T>C	2.37:g.37454998A>G		61	0	0		68	36	0.529412	NM_005760	Q8NE75	Silent	SNP	ENST00000234170.5	37	CCDS1787.1																																																																																			A|0.912;G|0.088	0.088	strong		0.343	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760		G	37454998	A	G	37454998	2	3	22	1	0	0	0	0	0	0	0	1	3206	330	12	3		3	CEBPZ	2	37454998	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	48353	37454998	205744375	550	3451											
C2orf56	55471	hgsc.bcm.edu	37	chr2	37459308	37459308	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggaatgagcctgcagaaaacCcggtgacgccgatgctgcgg	10	5	15	11	4	0	3	0	2	0	1	0	5	0	4	3	3	5	2	3	3	3	0	rs2714473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:37459308C>G	ENST00000002125.4	+	2	155	c.115C>G	c.(115-117)Ccg>Gcg	p.P39A	NDUFAF7_ENST00000336237.6_Missense_Mutation_p.P39A|CEBPZ_ENST00000234170.5_5'Flank|NDUFAF7_ENST00000483999.1_Intron	NM_144736.4	NP_653337.1	Q7L592	NDUF7_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 7	39			P -> A (in dbSNP:rs2714473).		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)										TGCAGAAAACCCGGTGACGCC	0.463													C|||	361	0.0720847	0.2564	0.0303	5008	,	,		19737	0.0		0.001	False		,,,				2504	0.0				p.P39A		Atlas-SNP	.											.	.	.	.	0			c.C115G						PASS	.	C	ALA/PRO,ALA/PRO	982,3424	366.1+/-317.7	113,756,1334	110	105	107		115,115	2.7	0	2	dbSNP_100	107	14,8586	8.4+/-32.0	0,14,4286	yes	missense,missense	C2orf56	NM_001083946.1,NM_144736.4	27,27	113,770,5620	GG,GC,CC		0.1628,22.2878,7.658	benign,benign	39/344,39/442	37459308	996,12010	2203	4300	6503	SO:0001583	missense	55471	exon2			GAAAACCCGGTGA		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.115C>G	2.37:g.37459308C>G	ENSP00000002125:p.Pro39Ala	123	0	0		133	64	0.481203	NM_001083946	Q7Z399|Q9P1G3	Missense_Mutation	SNP	ENST00000002125.4	37	CCDS1788.1	107	0.04899267399267399	98	0.1991869918699187	9	0.024861878453038673	0	0.0	0	0.0	C	7.698	0.692572	0.15039	0.222878	0.001628	ENSG00000003509	ENST00000002125;ENST00000336237	T;T	0.40225	1.05;1.04	5.51	2.68	0.31781	.	1.761130	0.02616	N	0.102632	T	0.00012	0.0000	N	0.05467	-0.045	0.80722	P	0.0	B;B;B;B	0.15930	0.001;0.009;0.015;0.0	B;B;B;B	0.12837	0.003;0.004;0.008;0.004	T	0.17745	-1.0359	9	0.08599	T	0.76	0.7393	3.0899	0.06290	0.2362:0.4978:0.1281:0.1379	rs2714473;rs52835713;rs2714473	39;39;39;39	E7EUC2;B4DQY3;Q7L592-2;Q7L592	.;.;.;MIDA_HUMAN	A	39	ENSP00000002125:P39A;ENSP00000337431:P39A	ENSP00000002125:P39A	P	+	1	0	C2orf56	37312812	0.000000	0.05858	0.006000	0.13384	0.962000	0.63368	0.599000	0.24089	0.268000	0.21939	-0.319000	0.08680	CCG	C|0.931;G|0.069	0.069	strong		0.463	NDUFAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250267.1	NM_144736		G	37459308	C	G	37459308	3	3	22	1	0	0	0	0	1	0	0	0	2179	623	22	4	121	4	C2orf56	2	37459308	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4310	37459308	205740065	551	3452											
CYP1B1	1545	hgsc.bcm.edu	37	chr2	38301803	38301803	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aagtactgcagccagggcatCacgtccaccaggctgcccgc	9	5	11	16	2	1	0	1	0	0	0	2	0	2	0	4	2	4	4	4	2	2	1	rs9341249	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:38301803C>G	ENST00000260630.3	-	2	1130	c.729G>C	c.(727-729)gtG>gtC	p.V243V	CYP1B1-AS1_ENST00000589303.1_RNA|CYP1B1_ENST00000494864.1_Intron|CYP1B1_ENST00000407341.1_Silent_p.V243V|CYP1B1-AS1_ENST00000431999.1_RNA	NM_000104.3	NP_000095	Q16678	CP1B1_HUMAN	cytochrome P450, family 1, subfamily B, polypeptide 1	243					angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|blood vessel morphogenesis (GO:0048514)|cell adhesion (GO:0007155)|cellular aromatic compound metabolic process (GO:0006725)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to organic cyclic compound (GO:0071407)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell-cell adhesion (GO:0071603)|epoxygenase P450 pathway (GO:0019373)|estrogen metabolic process (GO:0008210)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|membrane lipid catabolic process (GO:0046466)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nitric oxide biosynthetic process (GO:0006809)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to toxic substance (GO:0009636)|retinal blood vessel morphogenesis (GO:0061304)|retinal metabolic process (GO:0042574)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|toxin metabolic process (GO:0009404)|trabecular meshwork development (GO:0002930)|visual perception (GO:0007601)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	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)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)	13		all_hematologic(82;0.21)			Amodiaquine(DB00613)|Arsenic trioxide(DB01169)|Biotin(DB00121)|Caffeine(DB00201)|Clozapine(DB00363)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Flutamide(DB00499)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Melatonin(DB01065)|Mitoxantrone(DB01204)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Primaquine(DB01087)|Procarbazine(DB01168)|Progesterone(DB00396)|Propofol(DB00818)|Tamoxifen(DB00675)|Testosterone(DB00624)|Theophylline(DB00277)	GCCAGGGCATCACGTCCACCA	0.627													c|||	383	0.0764776	0.2678	0.0159	5008	,	,		16495	0.0129		0.003	False		,,,				2504	0.002				p.V243V		Atlas-SNP	.											.	CYP1B1	39	.	0			c.G729C						PASS	.	A		917,3489	333.9+/-303.2	93,731,1379	43	41	42		729	1.5	1	2	dbSNP_119	42	21,8579	12.6+/-44.7	0,21,4279	yes	coding-synonymous	CYP1B1	NM_000104.3		93,752,5658	GG,GC,CC		0.2442,20.8125,7.2121		243/544	38301803	938,12068	2203	4300	6503	SO:0001819	synonymous_variant	1545	exon2			GGGCATCACGTCC	U56438	CCDS1793.1	2p22.2	2008-02-05	2003-01-14		ENSG00000138061	ENSG00000138061		"Cytochrome P450s"	2597	protein-coding gene	gene with protein product		601771	"cytochrome P450, subfamily I (dioxin-inducible), polypeptide 1 (glaucoma 3, primary infantile)"	GLC3A		8175734, 15128046	Standard	NM_000104		Approved	CP1B	uc002rqo.2	Q16678	OTTHUMG00000100970	ENST00000260630.3:c.729G>C	2.37:g.38301803C>G		107	0	0		148	148	1	NM_000104	Q5TZW8|Q93089|Q9H316	Silent	SNP	ENST00000260630.3	37	CCDS1793.1																																																																																			C|0.934;G|0.066	0.066	strong		0.627	CYP1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218580.3	NM_000104		G	38301803	C	G	38301803	2	3	22	1	0	0	0	0	0	0	0	1	4153	813	29	4		4	CYP1B1	2	38301803	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	842495	38301803	204897570	552	3453											
THADA	63892	hgsc.bcm.edu	37	chr2	43518843	43518843	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaccagccttacctccacacAtgtctgcatgtggtgggaaa	11	9	9	12	0	1	0	0	0	1	0	2	1	2	1	4	2	4	1	4	2	3	1	rs17030648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:43518843A>G	ENST00000405006.4	-	34	5353	c.5002T>C	c.(5002-5004)Tgt>Cgt	p.C1668R	THADA_ENST00000330266.7_Intron|THADA_ENST00000405975.2_Missense_Mutation_p.C1668R|THADA_ENST00000415080.2_Missense_Mutation_p.C1349R	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	1668			C -> R (in dbSNP:rs17030648).							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)				ACCTCCACACATGTCTGCATG	0.393													A|||	159	0.0317492	0.1157	0.0086	5008	,	,		16790	0.0		0.0	False		,,,				2504	0.0				p.C1668R		Atlas-SNP	.											.	THADA	131	.	0			c.T5002C						PASS	.	A	ARG/CYS,ARG/CYS	351,3379		16,319,1530	62	58	59		5002,5002	-5.8	0	2	dbSNP_123	59	7,8131		0,7,4062	yes	missense,missense	THADA	NM_001083953.1,NM_022065.4	180,180	16,326,5592	GG,GA,AA		0.086,9.4102,3.0165	benign,benign	1668/1954,1668/1954	43518843	358,11510	1865	4069	5934	SO:0001583	missense	63892	exon34			CCACACATGTCTG	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.5002T>C	2.37:g.43518843A>G	ENSP00000385995:p.Cys1668Arg	204	1	0.00490196		213	118	0.553991	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Missense_Mutation	SNP	ENST00000405006.4	37	CCDS46268.1	62	0.028388278388278388	61	0.12398373983739837	1	0.0027624309392265192	0	0.0	0	0.0	A	0.081	-1.182910	0.01620	0.094102	8.6E-4	ENSG00000115970	ENST00000405975;ENST00000356975;ENST00000415080;ENST00000405006	T;T;T	0.67698	-0.28;-0.28;-0.28	4.52	-5.84	0.02318	.	1.778280	0.02439	N	0.084348	T	0.01092	0.0036	L	0.35723	1.085	0.58432	P	9.99999999995449E-6	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.15292	-1.0442	9	0.13108	T	0.6	-12.3615	13.0032	0.58687	0.3567:0.0:0.6433:0.0	rs17030648;rs52831994;rs17030648	1595;1668	B6ZDQ0;Q6YHU6	.;THADA_HUMAN	R	1668;1595;1349;1668	ENSP00000386088:C1668R;ENSP00000416048:C1349R;ENSP00000385995:C1668R	ENSP00000349464:C1595R	C	-	1	0	THADA	43372347	0.000000	0.05858	0.000000	0.03702	0.183000	0.23260	-2.041000	0.01415	-1.081000	0.03105	-0.384000	0.06662	TGT	A|0.958;G|0.042	0.042	strong		0.393	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065		G	43518843	A	G	43518843	3	3	22	1	0	0	0	0	1	0	0	0	15855	217	8	3	879	3	THADA	2	43518843	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	5217040	43518843	199680530	553	3454											
LRPPRC	10128	hgsc.bcm.edu	37	chr2	44172496	44172496	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcttgccatgctttgccaaTactcttacaaggcctacata	11	12	6	12	0	1	0	0	0	1	0	1	0	1	0	3	1	7	2	3	1	6	6	rs145963884	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:44172496T>C	ENST00000260665.7	-	22	2328	c.2271A>G	c.(2269-2271)gtA>gtG	p.V757V		NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	757					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)				GCTTTGCCAATACTCTTACAA	0.378													T|||	5	0.000998403	0.0038	0.0	5008	,	,		22524	0.0		0.0	False		,,,				2504	0.0				p.V757V		Atlas-SNP	.											.	LRPPRC	105	.	0			c.A2271G						PASS	.	T		7,4399	12.9+/-30.5	0,7,2196	137	122	127		2271	-0.7	1	2	dbSNP_134	127	0,8598		0,0,4299	no	coding-synonymous	LRPPRC	NM_133259.3		0,7,6495	CC,CT,TT		0.0,0.1589,0.0538		757/1395	44172496	7,12997	2203	4299	6502	SO:0001819	synonymous_variant	10128	exon22			TGCCAATACTCTT	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.2271A>G	2.37:g.44172496T>C		96	0	0		130	54	0.415385	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Silent	SNP	ENST00000260665.7	37	CCDS33189.1																																																																																			T|0.999;C|0.001	0.001	strong		0.378	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259		C	44172496	T	C	44172496	2	2	22	1	0	0	0	0	0	0	0	1	8974	1393	49	3		3	LRPPRC	2	44172496	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	653653	44172496	199026877	554	3455											
LRPPRC	10128	hgsc.bcm.edu	37	chr2	44175293	44175293	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggaacatggtagctttccaGgagattacgaatgcctctgt	11	11	11	8	1	1	1	0	0	1	1	2	4	2	2	2	3	4	2	2	3	4	3	rs35881858	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:44175293G>A	ENST00000260665.7	-	18	1945	c.1888C>T	c.(1888-1890)Ctg>Ttg	p.L630L		NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	630					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)				TAGCTTTCCAGGAGATTACGA	0.358													G|||	126	0.0251597	0.0923	0.0043	5008	,	,		15884	0.0		0.001	False		,,,				2504	0.0				p.L630L		Atlas-SNP	.											.	LRPPRC	105	.	0			c.C1888T						PASS	.	G		269,4135	149.2+/-183.4	6,257,1939	94	99	97		1888	3.8	0.8	2	dbSNP_126	97	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	LRPPRC	NM_133259.3		6,260,6236	AA,AG,GG		0.0349,6.1081,2.0917		630/1395	44175293	272,12732	2202	4300	6502	SO:0001819	synonymous_variant	10128	exon18			TTTCCAGGAGATT	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.1888C>T	2.37:g.44175293G>A		32	0	0		53	19	0.358491	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Silent	SNP	ENST00000260665.7	37	CCDS33189.1																																																																																			G|0.983;A|0.017	0.017	strong		0.358	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259		A	44175293	G	A	44175293	2	1	22	1	0	0	0	0	0	0	0	1	8974	991	35	2		2	LRPPRC	2	44175293	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2797	44175293	199024080	555	3456											
PREPL	9581	hgsc.bcm.edu	37	chr2	44550528	44550528	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgtagtgtccatcatggtgTtgagaacatccaagaaaggt	12	11	12	6	0	1	2	1	1	0	2	3	3	3	2	2	2	1	2	2	2	4	2	rs75128515	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:44550528T>C	ENST00000409936.1	-	12	2206	c.1769A>G	c.(1768-1770)aAc>aGc	p.N590S	PREPL_ENST00000260648.6_Missense_Mutation_p.N590S|PREPL_ENST00000409957.1_Missense_Mutation_p.N501S|PREPL_ENST00000409411.1_Missense_Mutation_p.N501S|PREPL_ENST00000378520.3_Missense_Mutation_p.N524S|PREPL_ENST00000378511.3_Missense_Mutation_p.N528S|PREPL_ENST00000541738.1_Missense_Mutation_p.N501S|PREPL_ENST00000409272.1_Missense_Mutation_p.N590S|PREPL_ENST00000410081.1_Missense_Mutation_p.N590S	NM_001171606.1	NP_001165077.1	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like	590						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)				CATCATGGTGTTGAGAACATC	0.348													T|||	50	0.00998403	0.0363	0.0029	5008	,	,		17612	0.0		0.0	False		,,,				2504	0.0				p.N590S		Atlas-SNP	.											.	PREPL	69	.	0			c.A1769G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN	146,4260	103.0+/-141.5	2,142,2059	115	103	107		1583,1571,1769,1769,1502,1502,1769	4.2	1	2	dbSNP_131	107	2,8598	1.2+/-3.3	0,2,4298	yes	missense,missense,missense,missense,missense,missense,missense	PREPL	NM_001042385.2,NM_001042386.2,NM_001171603.1,NM_001171606.1,NM_001171613.1,NM_001171617.1,NM_006036.4	46,46,46,46,46,46,46	2,144,6357	CC,CT,TT		0.0233,3.3137,1.1379	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	528/666,524/662,590/728,590/728,501/639,501/639,590/728	44550528	148,12858	2203	4300	6503	SO:0001583	missense	9581	exon12			ATGGTGTTGAGAA	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.1769A>G	2.37:g.44550528T>C	ENSP00000386543:p.Asn590Ser	89	0	0		136	68	0.5	NM_001171603	A7E2X6|D6W5A3|O43163|Q4J6C3|Q4J6C4|Q4ZG39|Q6ZMW7|Q96DW7	Missense_Mutation	SNP	ENST00000409936.1	37	CCDS33190.1	22	0.010073260073260074	22	0.044715447154471545	0	0.0	0	0.0	0	0.0	T	17.70	3.454601	0.63290	0.033137	2.33E-4	ENSG00000138078	ENST00000541738;ENST00000409411;ENST00000409957;ENST00000409936;ENST00000260648;ENST00000409272;ENST00000410081;ENST00000378520;ENST00000378511	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	5.3	4.15	0.48705	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.105776	0.64402	D	0.000005	T	0.16342	0.0393	L	0.49778	1.585	0.40476	D	0.980399	D;B;B	0.61697	0.99;0.302;0.374	D;B;B	0.72982	0.979;0.162;0.383	T	0.05699	-1.0869	10	0.52906	T	0.07	-17.8051	10.6101	0.45417	0.0:0.0754:0.0:0.9246	.	528;524;590	Q4J6C6-3;Q4J6C6-2;Q4J6C6	.;.;PPCEL_HUMAN	S	501;501;501;590;590;590;590;524;528	ENSP00000439626:N501S;ENSP00000387095:N501S;ENSP00000387241:N501S;ENSP00000386543:N590S;ENSP00000260648:N590S;ENSP00000386909:N590S;ENSP00000386509:N590S;ENSP00000367781:N524S;ENSP00000367772:N528S	ENSP00000260648:N590S	N	-	2	0	PREPL	44404032	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.187000	0.58344	0.864000	0.35578	0.533000	0.62120	AAC	T|0.987;C|0.013	0.013	strong		0.348	PREPL-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327900.1	NM_006036		C	44550528	T	C	44550528	3	2	22	1	0	0	0	0	1	0	0	0	12487	1725	60	3	430	3	PREPL	2	44550528	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	375235	44550528	198648845	556	3457											
PREPL	9581	hgsc.bcm.edu	37	chr2	44571008	44571008	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccacatatttttcatctggAgcaactctgatacaatcaat	13	13	5	10	0	4	1	2	1	2	0	4	2	4	2	1	1	3	1	1	1	5	4	rs72875319	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:44571008A>T	ENST00000409936.1	-	5	929	c.492T>A	c.(490-492)gcT>gcA	p.A164A	PREPL_ENST00000260648.6_Silent_p.A164A|PREPL_ENST00000409957.1_Silent_p.A75A|PREPL_ENST00000409411.1_Silent_p.A75A|PREPL_ENST00000378520.3_Silent_p.A164A|PREPL_ENST00000378511.3_Silent_p.A164A|PREPL_ENST00000541738.1_Silent_p.A75A|PREPL_ENST00000409272.1_Silent_p.A164A|PREPL_ENST00000540817.1_5'UTR|PREPL_ENST00000410081.1_Silent_p.A164A	NM_001171606.1	NP_001165077.1	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like	164						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)				TTTCATCTGGAGCAACTCTGA	0.363													A|||	190	0.0379393	0.1309	0.0231	5008	,	,		16552	0.0		0.001	False		,,,				2504	0.0				p.A164A		Atlas-SNP	.											.	PREPL	69	.	0			c.T492A						PASS	.	A	,,,,,,	487,3919	228.8+/-243.5	28,431,1744	110	113	112		492,492,492,492,225,225,492	4.5	1	2	dbSNP_130	112	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PREPL	NM_001042385.2,NM_001042386.2,NM_001171603.1,NM_001171606.1,NM_001171613.1,NM_001171617.1,NM_006036.4	,,,,,,	28,433,6042	TT,TA,AA		0.0233,11.0531,3.7598	,,,,,,	164/666,164/662,164/728,164/728,75/639,75/639,164/728	44571008	489,12517	2203	4300	6503	SO:0001819	synonymous_variant	9581	exon5			ATCTGGAGCAACT	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.492T>A	2.37:g.44571008A>T		116	0	0		114	50	0.438596	NM_001171603	A7E2X6|D6W5A3|O43163|Q4J6C3|Q4J6C4|Q4ZG39|Q6ZMW7|Q96DW7	Silent	SNP	ENST00000409936.1	37	CCDS33190.1																																																																																			A|0.966;T|0.034	0.034	strong		0.363	PREPL-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327900.1	NM_006036		T	44571008	A	T	44571008	2	4	22	1	0	0	0	0	0	0	0	1	12487	291	11	5		5	PREPL	2	44571008	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	20480	44571008	198628365	557	3458											
MSH2	4436	hgsc.bcm.edu	37	chr2	47637246	47637246	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tacttaggcttctcctggcaAtctctctcagtttgaagaca	9	14	7	11	0	3	2	1	1	3	1	6	2	3	2	1	2	1	3	1	2	4	4	rs17217772|rs63751227|rs63750924	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:47637246A>G	ENST00000233146.2	+	3	603	c.380A>G	c.(379-381)aAt>aGt	p.N127S	MSH2_ENST00000406134.1_Missense_Mutation_p.N127S|MSH2_ENST00000543555.1_Missense_Mutation_p.N61S	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	127			N -> S (in HNPCC1; shows significantly decreased repair efficiency when associated with variant Pro-328; presumed to enhance cancer risk considerably when associated with Pro-328; this concomitant defect with another variant could explain its recurrent occurrence in CRC patients; dbSNP:rs17217772). {ECO:0000269|PubMed:12655564, ECO:0000269|Ref.9}.		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)			TCTCCTGGCAATctctctcag	0.333			"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				A|||	124	0.0247604	0.087	0.0115	5008	,	,		17721	0.0		0.001	False		,,,				2504	0.0				p.N127S		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.A380G	GRCh37	CD982801|CM011415|CM081337	MSH2	D|M	rs17217772	PASS	.	A	SER/ASN	339,4067	176.2+/-205.4	17,305,1881	178	180	180	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	380	4.6	1	2	dbSNP_123	180	4,8596	3.7+/-12.6	0,4,4296	no	missense	MSH2	NM_000251.1	46	17,309,6177	GG,GA,AA		0.0465,7.6941,2.6372	possibly-damaging	127/935	47637246	343,12663	2203	4300	6503	SO:0001583	missense	4436	exon3	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	CTGGCAATCTCTC	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.380A>G	2.37:g.47637246A>G	ENSP00000233146:p.Asn127Ser	103	0	0		88	44	0.5	NM_000251	B4E2Z2|O75488	Missense_Mutation	SNP	ENST00000233146.2	37	CCDS1834.1	41|41	0.018772893772893772|0.018772893772893772	36|36	0.07317073170731707|0.07317073170731707	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	A|A	15.07|15.07	2.724903|2.724903	0.48833|0.48833	0.076941|0.076941	4.65E-4|4.65E-4	ENSG00000095002|ENSG00000095002	ENST00000413880|ENST00000233146;ENST00000454849;ENST00000543555;ENST00000406134;ENST00000419559;ENST00000432737;ENST00000453755;ENST00000448533;ENST00000394792	.|D;D;D;D	.|0.89485	.|-2.52;-2.52;-2.52;-2.52	5.73|5.73	4.59|4.59	0.56863|0.56863	.|DNA mismatch repair protein MutS-like, N-terminal (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.62551|0.62551	0.2437|0.2437	M|M	0.93150|0.93150	3.385|3.385	0.80722|0.80722	D|D	1|1	.|P;P	.|0.51057	.|0.941;0.912	.|P;P	.|0.60068	.|0.812;0.868	T|T	0.77913|0.77913	-0.2410|-0.2410	6|10	0.18276|0.87932	T|D	0.48|0	-16.5115|-16.5115	11.6216|11.6216	0.51121|0.51121	0.9307:0.0:0.0693:0.0|0.9307:0.0:0.0693:0.0	rs17217772;rs60111901|rs17217772;rs60111901	.|127;127	.|E9PHA6;P43246	.|.;MSH2_HUMAN	V|S	13|127;61;61;127;127;127;127;127;127	.|ENSP00000233146:N127S;ENSP00000411482:N61S;ENSP00000442697:N61S;ENSP00000384199:N127S	ENSP00000402969:I13V|ENSP00000233146:N127S	I|N	+|+	1|2	0|0	MSH2|MSH2	47490750|47490750	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.064000|0.064000	0.16182|0.16182	9.227000|9.227000	0.95236|0.95236	1.008000|1.008000	0.39264|0.39264	-0.322000|-0.322000	0.08575|0.08575	ATC|AAT	A|0.965;G|0.035	0.035	strong		0.333	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3			G	47637246	A	G	47637246	3	3	22	1	0	0	0	0	1	0	0	0	9879	101	4	3	390	3	MSH2	2	47637246	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	3066238	47637246	195562127	558	3459											
MSH2	4436	hgsc.bcm.edu	37	chr2	47637439	47637439	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tccaatcttgaggctctcctCatccagattggaccaaagga	11	10	8	12	0	3	2	1	1	2	1	6	4	5	4	4	3	0	1	4	3	2	2	rs1800151	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:47637439C>T	ENST00000233146.2	+	3	796	c.573C>T	c.(571-573)ctC>ctT	p.L191L	MSH2_ENST00000406134.1_Silent_p.L191L|MSH2_ENST00000543555.1_Silent_p.L125L	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	191					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)			AGGCTCTCCTCATCCAGATTG	0.463			"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				C|||	97	0.019369	0.0696	0.0072	5008	,	,		15087	0.0		0.0	False		,,,				2504	0.0				p.L191L		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.C573T						PASS	.	C		254,4152	146.9+/-181.5	4,246,1953	182	176	178	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	573	1.6	1	2	dbSNP_89	178	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	MSH2	NM_000251.1		4,250,6249	TT,TC,CC		0.0465,5.7649,1.9837		191/935	47637439	258,12748	2203	4300	6503	SO:0001819	synonymous_variant	4436	exon3	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	TCTCCTCATCCAG	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.573C>T	2.37:g.47637439C>T		106	0	0		129	55	0.426357	NM_000251	B4E2Z2|O75488	Silent	SNP	ENST00000233146.2	37	CCDS1834.1																																																																																			C|0.977;T|0.023	0.023	strong		0.463	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3			T	47637439	C	T	47637439	2	4	22	1	0	0	0	0	0	0	0	1	9879	813	29	2		2	MSH2	2	47637439	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	193	47637439	195561934	559	3460											
KCNK12	56660	hgsc.bcm.edu	37	chr2	47748487	47748487	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	atgcagcacacgccgagcagGatgaagaggaagttgcccag	13	4	14	10	2	0	2	0	1	0	1	0	5	0	4	2	2	4	4	2	2	2	1	rs77883212	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:47748487G>A	ENST00000327876.4	-	2	1459	c.852C>T	c.(850-852)atC>atT	p.I284I	MSH2_ENST00000461394.1_Intron	NM_022055.1	NP_071338.1	Q9HB15	KCNKC_HUMAN	potassium channel, subfamily K, member 12	284						integral component of membrane (GO:0016021)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.0?(2)|p.?(2)		NS(1)|endometrium(1)|lung(3)|ovary(1)	6		all_hematologic(82;0.0495)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CGCCGAGCAGGATGAAGAGGA	0.607													G|||	48	0.00958466	0.0333	0.0058	5008	,	,		13662	0.0		0.0	False		,,,				2504	0.0				p.I284I		Atlas-SNP	.											.	KCNK12	11	.	4	Whole gene deletion(2)|Unknown(2)	haematopoietic_and_lymphoid_tissue(3)|prostate(1)	c.C852T						PASS	.	G		151,4255	103.0+/-141.5	2,147,2054	57	54	55		852	1.5	1	2	dbSNP_132	55	4,8594	3.0+/-9.4	0,4,4295	no	coding-synonymous	KCNK12	NM_022055.1		2,151,6349	AA,AG,GG		0.0465,3.4271,1.1919		284/431	47748487	155,12849	2203	4299	6502	SO:0001819	synonymous_variant	56660	exon2			GAGCAGGATGAAG	AF287302	CCDS1835.1	2p16.3	2012-03-07			ENSG00000184261	ENSG00000184261		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6274	protein-coding gene	gene with protein product		607366				11060316	Standard	NM_022055		Approved	THIK-2, THIK2, K2p12.1	uc002rwb.3	Q9HB15	OTTHUMG00000129131	ENST00000327876.4:c.852C>T	2.37:g.47748487G>A		86	0	0		81	35	0.432099	NM_022055		Silent	SNP	ENST00000327876.4	37	CCDS1835.1																																																																																			G|0.986;A|0.014	0.014	strong		0.607	KCNK12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251182.2	NM_022055		A	47748487	G	A	47748487	2	1	22	1	0	0	0	0	0	0	0	1	8069	1164	41	2		2	KCNK12	2	47748487	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	111048	47748487	195450886	560	3461											
NRXN1	9378	hgsc.bcm.edu	37	chr2	50280469	50280469	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctgtgctagtagccagggtCgtggtagtctccataattga	8	12	13	8	1	1	1	0	1	1	0	3	1	1	1	2	2	2	4	2	2	4	5	rs74714098	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:50280469C>T	ENST00000406316.2	-	20	5454	c.3978G>A	c.(3976-3978)acG>acA	p.T1326T	NRXN1_ENST00000401710.1_Silent_p.T344T|NRXN1_ENST00000401669.2_Silent_p.T1356T|NRXN1_ENST00000402717.3_Silent_p.T1348T|NRXN1_ENST00000404971.1_Silent_p.T1396T|NRXN1_ENST00000342183.5_Silent_p.T291T|NRXN1_ENST00000405472.3_Silent_p.T1348T|NRXN1_ENST00000406859.3_Silent_p.T1326T	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	1326	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)			TAGCCAGGGTCGTGGTAGTCT	0.473													C|||	82	0.0163738	0.0575	0.0043	5008	,	,		16560	0.0		0.001	False		,,,				2504	0.002				p.T1396T		Atlas-SNP	.											.	NRXN1	1118	.	0			c.G4188A						PASS	.	C	,,	186,4220	119.2+/-156.9	6,174,2023	135	131	132		4188,3978,873	-7.8	0.8	2	dbSNP_131	132	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	NRXN1	NM_001135659.1,NM_004801.4,NM_138735.2	,,	6,175,6322	TT,TC,CC		0.0116,4.2215,1.4378	,,	1396/1548,1326/1478,291/443	50280469	187,12819	2203	4300	6503	SO:0001819	synonymous_variant	9378	exon22			CAGGGTCGTGGTA	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.3978G>A	2.37:g.50280469C>T		198	0	0		204	104	0.509804	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	37	CCDS54360.1																																																																																			C|0.983;T|0.017	0.017	strong		0.473	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			T	50280469	C	T	50280469	2	4	22	1	0	0	0	0	0	0	0	1	10674	871	31	1		1	NRXN1	2	50280469	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2531982	50280469	192918904	561	3462											
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54895682	54895682	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaagacaaagagaagcggttCagcctttttggcaaaaagaa	18	7	10	6	1	1	3	1	0	0	3	1	4	1	3	1	2	2	2	1	2	6	3	rs2229505	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:54895682C>T	ENST00000356805.4	+	36	7352	c.7071C>T	c.(7069-7071)ttC>ttT	p.F2357F		NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	2357					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)			AGAAGCGGTTCAGCCTTTTTG	0.522													C|||	178	0.0355431	0.1165	0.0245	5008	,	,		17151	0.001		0.005	False		,,,				2504	0.001				p.F2357F		Atlas-SNP	.											.	SPTBN1	378	.	0			c.C7071T						PASS	.	C		429,3977		18,393,1792	25	23	24		7071	3.7	1	2	dbSNP_98	24	14,8584		0,14,4285	no	coding-synonymous	SPTBN1	NM_003128.2		18,407,6077	TT,TC,CC		0.1628,9.7367,3.4066		2357/2365	54895682	443,12561	2203	4299	6502	SO:0001819	synonymous_variant	6711	exon36			GCGGTTCAGCCTT		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.7071C>T	2.37:g.54895682C>T		94	0	0		97	43	0.443299	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Silent	SNP	ENST00000356805.4	37	CCDS33198.1																																																																																			C|0.962;T|0.038	0.038	strong		0.522	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			T	54895682	C	T	54895682	2	4	22	1	0	0	0	0	0	0	0	1	15134	825	29	2		2	SPTBN1	2	54895682	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4615213	54895682	188303691	562	3463											
EFEMP1	2202	hgsc.bcm.edu	37	chr2	56145110	56145110	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggctgttttcggaaggcaGaggtatcctccatagtggtt	7	13	14	7	1	0	1	0	0	0	1	3	2	2	2	2	5	0	5	2	5	3	5	rs12292	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:56145110G>T	ENST00000394555.2	-	4	642	c.207C>A	c.(205-207)ctC>ctA	p.L69L	EFEMP1_ENST00000355426.3_Silent_p.L69L|EFEMP1_ENST00000424836.2_Silent_p.L11L|EFEMP1_ENST00000394554.1_Silent_p.L69L	NM_001039348.2|NM_001039349.2	NP_001034437.1|NP_001034438.1	Q12805	FBLN3_HUMAN	EGF containing fibulin-like extracellular matrix protein 1	69	EGF-like 1; atypical. {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)			TCGGAAGGCAGAGGTATCCTC	0.458													G|||	193	0.0385383	0.1369	0.0159	5008	,	,		21544	0.0		0.001	False		,,,				2504	0.0				p.L69L	GBM(92;934 1319 7714 28760 40110)	Atlas-SNP	.											.	EFEMP1	81	.	0			c.C207A						PASS	.	G	,	526,3880	239.6+/-250.7	28,470,1705	111	112	112		207,207	1.7	1	2	dbSNP_52	112	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	EFEMP1	NM_001039348.2,NM_001039349.2	,	28,473,6002	TT,TG,GG		0.0349,11.9383,4.0674	,	69/494,69/494	56145110	529,12477	2203	4300	6503	SO:0001819	synonymous_variant	2202	exon4			AAGGCAGAGGTAT	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.207C>A	2.37:g.56145110G>T		248	0	0		229	122	0.532751	NM_001039349	A8K3I4|B4DW75|D6W5D2|Q541U7	Silent	SNP	ENST00000394555.2	37	CCDS1857.1	58	0.026556776556776556	53	0.10772357723577236	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	9.474	1.096510	0.20552	0.119383	3.49E-4	ENSG00000115380	ENST00000405693	.	.	.	5.68	1.67	0.24075	.	.	.	.	.	T	0.00695	0.0023	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.01600	-1.1315	5	0.27785	T	0.31	.	3.1782	0.06576	0.1297:0.1199:0.5058:0.2445	rs12292;rs12292	.	.	.	Y	5	.	ENSP00000384951:S5Y	S	-	2	0	EFEMP1	55998614	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.101000	0.31037	0.288000	0.22398	0.650000	0.86243	TCT	G|0.951;T|0.049	0.049	strong		0.458	EFEMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251491.2			T	56145110	G	T	56145110	2	4	22	1	0	0	0	0	0	0	0	1	4943	929	33	4		4	EFEMP1	2	56145110	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1249428	56145110	187054263	563	3464											
VRK2	7444	hgsc.bcm.edu	37	chr2	58350340	58350340	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cataatgggacaatagagttTaccagcttggatgcccacaa	14	9	9	9	0	0	1	0	0	0	1	0	3	0	3	2	2	3	2	2	2	5	5	rs17049354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:58350340T>C	ENST00000435505.2	+	11	1393	c.648T>C	c.(646-648)ttT>ttC	p.F216F	VRK2_ENST00000417641.2_Silent_p.F216F|VRK2_ENST00000340157.4_Silent_p.F216F|VRK2_ENST00000412104.2_Silent_p.F216F|VRK2_ENST00000440705.2_Silent_p.F193F			Q86Y07	VRK2_HUMAN	vaccinia related kinase 2	216	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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						CAATAGAGTTTACCAGCTTGG	0.388													T|||	210	0.0419329	0.152	0.0115	5008	,	,		18926	0.0		0.001	False		,,,				2504	0.0				p.F216F		Atlas-SNP	.											.	VRK2	46	.	0			c.T648C						PASS	.	T	,,,,	501,3905	232.3+/-245.9	34,433,1736	108	105	106		648,648,579,648,648	1.8	1	2	dbSNP_123	106	8,8592	4.3+/-15.6	0,8,4292	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	VRK2	NM_001130480.2,NM_001130481.2,NM_001130482.2,NM_001130483.2,NM_006296.5	,,,,	34,441,6028	CC,CT,TT		0.093,11.3709,3.9136	,,,,	216/509,216/509,193/486,216/397,216/509	58350340	509,12497	2203	4300	6503	SO:0001819	synonymous_variant	7444	exon8			AGAGTTTACCAGC	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.648T>C	2.37:g.58350340T>C		76	0	0		72	38	0.527778	NM_001130480	B4DKL0|D6W5D4|D6W5D6|Q49AK9|Q53EU9|Q53S39|Q53S77|Q53TU1|Q86Y08|Q86Y09|Q86Y10|Q86Y11|Q86Y12|Q8IXI5|Q99987	Silent	SNP	ENST00000435505.2	37	CCDS1859.1																																																																																			T|0.962;C|0.038	0.038	strong		0.388	VRK2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325304.2	NM_006296		C	58350340	T	C	58350340	2	2	22	1	0	0	0	0	0	0	0	1	17235	1751	61	3		3	VRK2	2	58350340	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2205230	58350340	184849033	564	3465											
REL	5966	hgsc.bcm.edu	37	chr2	61148988	61148988	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctactatccctcacctgggcCcatctcaagtggattgtcac	8	11	7	15	0	3	0	3	0	1	0	5	1	4	1	3	2	1	0	3	2	3	3	rs34661029	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:61148988C>G	ENST00000295025.8	+	11	1498	c.1178C>G	c.(1177-1179)cCc>cGc	p.P393R	REL_ENST00000394479.3_Missense_Mutation_p.P361R	NM_002908.2	NP_002899.1	Q04864	REL_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog	393					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)			TCACCTGGGCCCATCTCAAGT	0.512			A		Hodgkin Lymphoma								C|||	34	0.00678914	0.025	0.0014	5008	,	,		16212	0.0		0.0	False		,,,				2504	0.0				p.P393R		Atlas-SNP	.		Dom	yes		2	2p13-p12	5966	v-rel reticuloendotheliosis viral oncogene homolog (avian)		L	.	REL	48	.	0			c.C1178G						PASS	.	C	ARG/PRO	93,4313	74.1+/-112.3	0,93,2110	100	98	99		1178	3.6	0.9	2	dbSNP_126	99	1,8599	1.2+/-3.3	0,1,4299	yes	missense	REL	NM_002908.2	103	0,94,6409	GG,GC,CC		0.0116,2.1108,0.7227	benign	393/620	61148988	94,12912	2203	4300	6503	SO:0001583	missense	5966	exon11			CTGGGCCCATCTC	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.1178C>G	2.37:g.61148988C>G	ENSP00000295025:p.Pro393Arg	105	0	0		132	132	1	NM_002908	Q17RU2|Q2PNZ7|Q6LDY0	Missense_Mutation	SNP	ENST00000295025.8	37	CCDS1864.1	7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	C	10.88	1.476325	0.26511	0.021108	1.16E-4	ENSG00000162924	ENST00000295025;ENST00000394479	T;T	0.42131	0.98;0.98	5.54	3.63	0.41609	.	0.859295	0.10279	N	0.693783	T	0.12135	0.0295	N	0.08118	0	0.09310	N	1	B;B	0.28128	0.201;0.181	B;B	0.20577	0.014;0.03	T	0.09314	-1.0680	10	0.52906	T	0.07	-22.6802	9.6826	0.40078	0.159:0.6877:0.1533:0.0	rs34661029	361;393	Q17RU2;Q04864	.;REL_HUMAN	R	393;361	ENSP00000295025:P393R;ENSP00000377989:P361R	ENSP00000295025:P393R	P	+	2	0	REL	61002492	0.771000	0.28555	0.926000	0.36857	0.866000	0.49608	1.214000	0.32419	1.345000	0.45676	-0.158000	0.13435	CCC	C|0.993;G|0.007	0.007	strong		0.512	REL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251576.3	NM_002908		G	61148988	C	G	61148988	3	3	22	1	0	0	0	0	1	0	0	0	13230	623	22	4	1220	4	REL	2	61148988	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2798648	61148988	182050385	565	3466											
PUS10	150962	hgsc.bcm.edu	37	chr2	61188643	61188643	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acattcaatttcaagaacagCgcatacagcctttggtgagt	13	11	8	9	1	2	2	2	1	0	1	2	2	2	2	1	1	4	1	1	1	4	4	rs113622721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:61188643C>T	ENST00000316752.6	-	10	1090	c.829G>A	c.(829-831)Gct>Act	p.A277T	PUS10_ENST00000407787.1_Missense_Mutation_p.A277T	NM_144709.2	NP_653310.2	Q3MIT2	PUS10_HUMAN	pseudouridylate synthase 10	277					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)			TCAAGAACAGCGCATACAGCC	0.348													C|||	87	0.0173722	0.0658	0.0	5008	,	,		19044	0.0		0.0	False		,,,				2504	0.0				p.A277T		Atlas-SNP	.											.	PUS10	49	.	0			c.G829A						PASS	.	C	THR/ALA	177,4229	114.6+/-152.6	4,169,2030	222	236	232		829	-2.4	1	2	dbSNP_132	232	4,8596	3.0+/-9.4	0,4,4296	yes	missense	PUS10	NM_144709.2	58	4,173,6326	TT,TC,CC		0.0465,4.0172,1.3917	benign	277/530	61188643	181,12825	2203	4300	6503	SO:0001583	missense	150962	exon10			GAACAGCGCATAC	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.829G>A	2.37:g.61188643C>T	ENSP00000326003:p.Ala277Thr	211	0	0		235	112	0.476596	NM_144709	Q5JPJ5|Q96MI8	Missense_Mutation	SNP	ENST00000316752.6	37	CCDS1865.1	47	0.02152014652014652	47	0.09552845528455285	0	0.0	0	0.0	0	0.0	C	4.727	0.135097	0.09032	0.040172	4.65E-4	ENSG00000162927	ENST00000316752;ENST00000407787	T;T	0.38722	1.12;1.12	5.91	-2.41	0.06562	.	0.476386	0.23506	N	0.047441	T	0.00241	0.0007	N	0.00583	-1.355	0.31617	N	0.650811	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27806	-1.0063	10	0.10902	T	0.67	-7.5462	4.7823	0.13208	0.4331:0.1848:0.0:0.3822	.	277;277	A8K6R4;Q3MIT2	.;PUS10_HUMAN	T	277	ENSP00000326003:A277T;ENSP00000386074:A277T	ENSP00000326003:A277T	A	-	1	0	PUS10	61042147	0.997000	0.39634	0.991000	0.47740	0.993000	0.82548	0.379000	0.20585	-0.138000	0.11434	-0.247000	0.11927	GCT	C|0.985;T|0.015	0.015	strong		0.348	PUS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251582.2	NM_144709		T	61188643	C	T	61188643	3	4	22	1	0	0	0	0	1	0	0	0	12846	768	27	1	796	1	PUS10	2	61188643	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	39655	61188643	182010730	566	3467											
USP34	9736	hgsc.bcm.edu	37	chr2	61433919	61433919	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctctgaagataagggcgtgTagacttcaaaaccgaaagaa	16	8	10	7	2	2	4	1	1	1	3	3	5	2	4	1	1	1	1	1	1	7	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:61433919T>C	ENST00000398571.2	-	71	9098	c.9022A>G	c.(9022-9024)Aca>Gca	p.T3008A	USP34_ENST00000472689.1_5'Flank	NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	3008					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)			TAAGGGCGTGTAGACTTCAAA	0.388																																					p.T3008A		Atlas-SNP	.											.	USP34	334	.	0			c.A9022G						PASS	.						69	64	66					2																	61433919		1842	4099	5941	SO:0001583	missense	9736	exon71			GGCGTGTAGACTT	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.9022A>G	2.37:g.61433919T>C	ENSP00000381577:p.Thr3008Ala	101	0	0		89	40	0.449438	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	37	CCDS42686.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.32|16.32	3.090012|3.090012	0.55968|0.55968	.|.	.|.	ENSG00000115464|ENSG00000115464	ENST00000263989;ENST00000398571|ENST00000411912	T|.	0.64438|.	-0.1|.	5.82|5.82	5.82|5.82	0.92795|0.92795	Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.53351|0.53351	0.1791|0.1791	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	0.50074|0.50074	-0.8870|-0.8870	10|5	0.19590|.	T|.	0.45|.	.|.	16.19|16.19	0.81981|0.81981	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	3008|.	Q70CQ2|.	UBP34_HUMAN|.	A|C	2856;3008|767	ENSP00000381577:T3008A|.	ENSP00000263989:T2856A|.	T|Y	-|-	1|2	0|0	USP34|USP34	61287423|61287423	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	6.295000|6.295000	0.72744|0.72744	2.225000|2.225000	0.72522|0.72522	0.460000|0.460000	0.39030|0.39030	ACA|TAC	.	.	none		0.388	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			C	61433919	T	C	61433919	3	2	22	1	0	0	0	0	1	0	0	0	17080	1638	57	3	1658	3	USP34	2	61433919	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	245276	61433919	181765454	567	3468											
USP34	9736	hgsc.bcm.edu	37	chr2	61575022	61575023	+	In_Frame_Ins	INS	-	-	TGG																															acccatcgtggtggtggtgaINStggtggtggtggtggtggtg																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:61575022_61575023insTGG	ENST00000398571.2	-	15	2343_2344	c.2267_2268insCCA	c.(2266-2268)cat>caCCAt	p.756_756H>HH		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	756					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)			ggtggtggtgatggtggtggtg	0.386																																					p.H756delinsHH		Pindel,Atlas-Indel	.											.	USP34	334	.	0			c.2268_2269insCCA						PASS	.																																			SO:0001652	inframe_insertion	9736	exon15			.	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.2265_2267dupCCA	2.37:g.61575029_61575031dupTGG	ENSP00000381577:p.His760dup	41	0	.		54	17	0.315	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	In_Frame_Ins	INS	ENST00000398571.2	37	CCDS42686.1																																																																																			.	.	none		0.386	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			TGG	61575023	-	TGG	61575022	7	5	22	1	0	1	1	0	0	0	0	0	17080	330	12	0	8636	0	USP34	2	61575022	In_Frame_Ins	INS	-	TCGA-G8-6324-01A-11D-2210-10	141103	61575022	181624351	568	3469											
B3GNT2	10678	hgsc.bcm.edu	37	chr2	62449664	62449664	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaacctgacctgagggtcacGtcggtggttacgggttttaa	8	11	14	8	3	1	2	1	2	0	0	2	3	1	2	2	4	2	2	2	4	3	3	rs72893877	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:62449664G>A	ENST00000301998.4	+	2	561	c.309G>A	c.(307-309)acG>acA	p.T103T	B3GNT2_ENST00000405767.1_Silent_p.T103T	NM_006577.5	NP_006568.2	Q9NY97	B3GN2_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	103					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)			TGAGGGTCACGTCGGTGGTTA	0.502													G|||	22	0.00439297	0.0151	0.0029	5008	,	,		18758	0.0		0.0	False		,,,				2504	0.0				p.T103T		Atlas-SNP	.											.	B3GNT2	34	.	0			c.G309A						PASS	.	G		63,4343	56.2+/-92.4	0,63,2140	216	242	233		309	-11.5	0	2	dbSNP_130	233	0,8600		0,0,4300	no	coding-synonymous	B3GNT2	NM_006577.5		0,63,6440	AA,AG,GG		0.0,1.4299,0.4844		103/398	62449664	63,12943	2203	4300	6503	SO:0001819	synonymous_variant	10678	exon2			GGTCACGTCGGTG	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.309G>A	2.37:g.62449664G>A		106	0	0		132	76	0.575758	NM_006577	Q54AC1|Q9NQQ9|Q9NQR0|Q9NUT9	Silent	SNP	ENST00000301998.4	37	CCDS1870.1																																																																																			G|0.996;A|0.004	0.004	strong		0.502	B3GNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251606.2	NM_006577		A	62449664	G	A	62449664	2	1	22	1	0	0	0	0	0	0	0	1	1257	1132	40	1		1	B3GNT2	2	62449664	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	874642	62449664	180749709	569	3470											
VPS54	51542	hgsc.bcm.edu	37	chr2	64160864	64160864	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgtgctctttgctggatgaaGaatcagtagtacattctggc	9	14	11	7	0	3	2	1	1	2	1	3	3	3	3	0	2	3	4	0	2	4	4	rs34015596	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:64160864G>C	ENST00000272322.4	-	12	1836	c.1682C>G	c.(1681-1683)tCt>tGt	p.S561C	VPS54_ENST00000354504.3_Missense_Mutation_p.S408C|VPS54_ENST00000409558.4_Missense_Mutation_p.S549C			Q9P1Q0	VPS54_HUMAN	vacuolar protein sorting 54 homolog (S. cerevisiae)	561			S -> C (in dbSNP:rs34015596).		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						GCTGGATGAAGAATCAGTAGT	0.428													G|||	139	0.0277556	0.0998	0.0101	5008	,	,		17370	0.0		0.0	False		,,,				2504	0.0				p.S561C		Atlas-SNP	.											.	VPS54	57	.	0			c.C1682G						PASS	.	G	CYS/SER,CYS/SER	358,4048	185.0+/-212.2	14,330,1859	123	119	120		1646,1682	5.5	1	2	dbSNP_126	120	0,8600		0,0,4300	yes	missense,missense	VPS54	NM_001005739.1,NM_016516.2	112,112	14,330,6159	CC,CG,GG		0.0,8.1253,2.7526	probably-damaging,probably-damaging	549/966,561/978	64160864	358,12648	2203	4300	6503	SO:0001583	missense	51542	exon12			GATGAAGAATCAG	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.1682C>G	2.37:g.64160864G>C	ENSP00000272322:p.Ser561Cys	88	0	0		88	50	0.568182	NM_016516	Q5VIR5|Q86YF7|Q8N6G3|Q9NPV0|Q9NT07|Q9NUJ0	Missense_Mutation	SNP	ENST00000272322.4	37	CCDS33208.1	38	0.0173992673992674	34	0.06910569105691057	4	0.011049723756906077	0	0.0	0	0.0	G	22.3	4.266853	0.80469	0.081253	0.0	ENSG00000143952	ENST00000354504;ENST00000272322;ENST00000409558;ENST00000483277;ENST00000394400	T;T;T	0.34859	1.34;1.37;1.37	5.47	5.47	0.80525	.	0.218968	0.49305	D	0.000159	T	0.03220	0.0094	N	0.22421	0.69	0.80722	D	1	D;D;D	0.63880	0.992;0.989;0.993	P;P;P	0.58660	0.794;0.701;0.843	T	0.01182	-1.1426	10	0.48119	T	0.1	.	19.3282	0.94273	0.0:0.0:1.0:0.0	rs34015596	408;561;549	Q9P1Q0-3;Q9P1Q0;Q9P1Q0-4	.;VPS54_HUMAN;.	C	408;561;549;549;561	ENSP00000346499:S408C;ENSP00000272322:S561C;ENSP00000386980:S549C	ENSP00000272322:S561C	S	-	2	0	VPS54	64014368	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.562000	0.82300	2.566000	0.86566	0.563000	0.77884	TCT	G|0.970;C|0.030	0.030	strong		0.428	VPS54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327062.2	NM_016516		C	64160864	G	C	64160864	3	2	22	1	0	0	0	0	1	0	0	0	17231	942	33	4	1299	4	VPS54	2	64160864	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1711200	64160864	179038509	570	3471											
CEP68	23177	hgsc.bcm.edu	37	chr2	65298657	65298657	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gccttcccagaacaacaactAtttgctcaggacatgatgct	12	10	7	12	0	1	2	1	1	0	1	2	3	2	3	2	1	5	2	2	1	4	3	rs13389745	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:65298657A>G	ENST00000377990.2	+	3	630	c.427A>G	c.(427-429)Att>Gtt	p.I143V	CEP68_ENST00000537589.1_5'UTR|CEP68_ENST00000260569.4_Missense_Mutation_p.I143V|CEP68_ENST00000497039.1_3'UTR|CEP68_ENST00000546106.1_Missense_Mutation_p.I143V|RAB1A_ENST00000494188.1_Intron	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	143					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						AACAACAACTATTTGCTCAGG	0.517													A|||	358	0.0714856	0.261	0.0187	5008	,	,		22452	0.0		0.0	False		,,,				2504	0.0				p.I143V		Atlas-SNP	.											.	CEP68	69	.	0			c.A427G						PASS	.	A	VAL/ILE	853,3553	336.3+/-304.3	84,685,1434	104	99	101		427	-0.6	0	2	dbSNP_121	101	3,8597	3.7+/-12.6	0,3,4297	yes	missense	CEP68	NM_015147.2	29	84,688,5731	GG,GA,AA		0.0349,19.36,6.5816	benign	143/758	65298657	856,12150	2203	4300	6503	SO:0001583	missense	23177	exon3			ACAACTATTTGCT	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.427A>G	2.37:g.65298657A>G	ENSP00000367229:p.Ile143Val	163	0	0		202	101	0.5	NM_015147	B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	Missense_Mutation	SNP	ENST00000377990.2	37	CCDS1880.2	148	0.06776556776556776	143	0.29065040650406504	5	0.013812154696132596	0	0.0	0	0.0	A	5.245	0.230663	0.09969	0.1936	3.49E-4	ENSG00000011523	ENST00000377990;ENST00000546106;ENST00000260569;ENST00000545501	T;T;T	0.28255	1.62;1.62;1.62	6.07	-0.64	0.11493	.	0.631703	0.14683	N	0.304637	T	0.00012	0.0000	N	0.04508	-0.205	0.58432	P	1.0000000000287557E-6	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	0.42015	-0.9476	9	0.02654	T	1	-1.7066	11.1914	0.48687	0.317:0.2513:0.4316:0.0	rs13389745;rs52830313;rs57922580;rs13389745	131;143;143;143;143	F5H3N9;F5H2Y2;Q76N32;Q76N32-2;Q05C09	.;.;CEP68_HUMAN;.;.	V	143;143;143;131	ENSP00000367229:I143V;ENSP00000438306:I143V;ENSP00000260569:I143V	ENSP00000260569:I143V	I	+	1	0	CEP68	65152161	0.000000	0.05858	0.001000	0.08648	0.027000	0.11550	-0.938000	0.03938	-0.309000	0.08779	-1.959000	0.00480	ATT	A|0.929;G|0.071	0.071	strong		0.517	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2	NM_015147		G	65298657	A	G	65298657	3	3	22	1	0	0	0	0	1	0	0	0	3260	449	16	3	433	3	CEP68	2	65298657	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1137793	65298657	177900716	571	3472											
ETAA1	54465	hgsc.bcm.edu	37	chr2	67624739	67624739	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggctagagaggggcctccCgggccagtgcggcagcgaga	7	3	20	11	3	0	2	0	0	0	2	1	4	1	2	3	6	2	2	3	6	1	1	rs182131786	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:67624739C>A	ENST00000272342.5	+	1	289	c.159C>A	c.(157-159)ccC>ccA	p.P53P		NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	53						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						AGGGGCCTCCCGGGCCAGTGC	0.721													C|||	5	0.000998403	0.0038	0.0	5008	,	,		11612	0.0		0.0	False		,,,				2504	0.0				p.P53P		Atlas-SNP	.											ETAA1,colon,carcinoma,+2,1	ETAA1	88	1	0			c.C159A						PASS	.	C		10,4090		0,10,2040	5	7	6		159	-0.4	0	2		6	1,8047		0,1,4023	no	coding-synonymous	ETAA1	NM_019002.3		0,11,6063	AA,AC,CC		0.0124,0.2439,0.0905		53/927	67624739	11,12137	2050	4024	6074	SO:0001819	synonymous_variant	54465	exon1			GCCTCCCGGGCCA	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.159C>A	2.37:g.67624739C>A		12	0	0		33	23	0.69697	NM_019002	Q05BT7|Q53SC4	Silent	SNP	ENST00000272342.5	37	CCDS1882.1																																																																																			C|0.999;A|0.001	0.001	strong		0.721	ETAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251735.1	NM_019002		A	67624739	C	A	67624739	2	1	22	1	0	0	0	0	0	0	0	1	5269	639	23	4		4	ETAA1	2	67624739	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2326082	67624739	175574634	572	3473											
ETAA1	54465	hgsc.bcm.edu	37	chr2	67631541	67631541	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcatcaaaagtaggttcttTctttgatgattggaatgatc	11	16	9	5	0	3	3	1	3	2	0	4	4	3	4	0	2	1	3	0	2	4	5	rs145096592	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:67631541T>C	ENST00000272342.5	+	5	1857	c.1727T>C	c.(1726-1728)tTc>tCc	p.F576S	ETAA1_ENST00000462772.1_Intron	NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	576						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						GTAGGTTCTTTCTTTGATGAT	0.363													T|||	4	0.000798722	0.003	0.0	5008	,	,		20046	0.0		0.0	False		,,,				2504	0.0				p.F576S		Atlas-SNP	.											.	ETAA1	88	.	0			c.T1727C						PASS	.	T	SER/PHE	14,4392	20.2+/-43.8	0,14,2189	80	84	83		1727	2.9	1	2	dbSNP_134	83	1,8597	1.2+/-3.3	0,1,4298	yes	missense	ETAA1	NM_019002.3	155	0,15,6487	CC,CT,TT		0.0116,0.3177,0.1153	benign	576/927	67631541	15,12989	2203	4299	6502	SO:0001583	missense	54465	exon5			GTTCTTTCTTTGA	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.1727T>C	2.37:g.67631541T>C	ENSP00000272342:p.Phe576Ser	106	0	0		108	56	0.518519	NM_019002	Q05BT7|Q53SC4	Missense_Mutation	SNP	ENST00000272342.5	37	CCDS1882.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	T	9.471	1.095577	0.20471	0.003177	1.16E-4	ENSG00000143971	ENST00000272342	T	0.19669	2.13	5.3	2.91	0.33838	.	0.634419	0.15834	N	0.242376	T	0.09686	0.0238	L	0.39898	1.24	0.26563	N	0.973703	P	0.42518	0.782	B	0.37650	0.255	T	0.07809	-1.0753	10	0.10902	T	0.67	-36.4777	8.156	0.31169	0.0:0.1631:0.0:0.8369	.	576	Q9NY74	ETAA1_HUMAN	S	576	ENSP00000272342:F576S	ENSP00000272342:F576S	F	+	2	0	ETAA1	67485045	0.146000	0.22672	0.998000	0.56505	0.629000	0.37895	1.768000	0.38511	1.046000	0.40249	0.533000	0.62120	TTC	T|0.999;C|0.001	0.001	strong		0.363	ETAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251735.1	NM_019002		C	67631541	T	C	67631541	3	2	22	1	0	0	0	0	1	0	0	0	5269	1783	62	3	1745	3	ETAA1	2	67631541	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	6802	67631541	175567832	573	3474											
PNO1	56902	hgsc.bcm.edu	37	chr2	68385240	68385240	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaggccggcgaagaggccCgtcttcccacccctctgtgg	5	6	13	17	3	2	1	0	0	2	1	3	2	3	1	6	4	0	0	6	4	1	1	rs61735657	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:68385240C>G	ENST00000263657.2	+	1	265	c.174C>G	c.(172-174)ccC>ccG	p.P58P	WDR92_ENST00000409164.1_5'Flank|WDR92_ENST00000492039.2_5'Flank|WDR92_ENST00000295121.6_5'Flank|RP11-474G23.1_ENST00000406334.3_Silent_p.T150T|WDR92_ENST00000406245.2_5'Flank	NM_020143.2	NP_064528.1	Q9NRX1	PNO1_HUMAN	partner of NOB1 homolog (S. cerevisiae)	58						nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(2)	4						CGAAGAGGCCCGTCTTCCCAC	0.672													C|||	109	0.0217652	0.0779	0.0	5008	,	,		15102	0.0		0.001	False		,,,				2504	0.0051				p.P58P	NSCLC(83;642 1410 13044 32832 40058)	Atlas-SNP	.											.	PNO1	17	.	0			c.C174G						PASS	.	C		289,4109		7,275,1917	13	19	17		174	-4.9	0.9	2	dbSNP_129	17	17,8575		0,17,4279	no	coding-synonymous	PNO1	NM_020143.2		7,292,6196	GG,GC,CC		0.1979,6.5712,2.3557		58/253	68385240	306,12684	2199	4296	6495	SO:0001819	synonymous_variant	56902	exon1			GAGGCCCGTCTTC	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.174C>G	2.37:g.68385240C>G		56	0	0		78	39	0.5	NM_020143	A8K6Q0|Q53G13|Q8WVB8	Silent	SNP	ENST00000263657.2	37	CCDS1885.1																																																																																			C|0.979;G|0.021	0.021	strong		0.672	PNO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251756.1	NM_020143		G	68385240	C	G	68385240	2	3	22	1	0	0	0	0	0	0	0	1	12170	639	23	4		4	PNO1	2	68385240	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	753699	68385240	174814133	574	3475											
ARHGAP25	9938	hgsc.bcm.edu	37	chr2	69049916	69049916	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaaaaaagaactctggagaaGaggaaattgattctttgcag	17	9	11	4	0	2	4	0	1	2	3	2	7	2	5	0	2	2	1	0	2	6	3	rs61734450	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:69049916G>A	ENST00000295381.3	+	10	2061	c.1642G>A	c.(1642-1644)Gag>Aag	p.E548K	ARHGAP25_ENST00000409030.3_Missense_Mutation_p.E541K|ARHGAP25_ENST00000409220.1_Missense_Mutation_p.E542K|ARHGAP25_ENST00000467265.1_Missense_Mutation_p.E509K|ARHGAP25_ENST00000409202.3_Missense_Mutation_p.E549K|ARHGAP25_ENST00000479844.1_Missense_Mutation_p.E242K	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25	548					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						CTCTGGAGAAGAGGAAATTGA	0.443													G|||	9	0.00179712	0.0068	0.0	5008	,	,		20738	0.0		0.0	False		,,,				2504	0.0				p.E549K		Atlas-SNP	.											ARHGAP25,NS,carcinoma,0,1	ARHGAP25	175	1	0			c.G1645A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	15,4389	21.2+/-45.6	0,15,2187	70	79	76		1645,1624,1525,1621	4.5	1	2	dbSNP_129	76	0,8598		0,0,4299	yes	missense,missense,missense,missense	ARHGAP25	NM_001007231.2,NM_001166276.1,NM_001166277.1,NM_014882.2	56,56,56,56	0,15,6486	AA,AG,GG		0.0,0.3406,0.1154	benign,benign,benign,benign	549/647,542/640,509/607,541/639	69049916	15,12987	2202	4299	6501	SO:0001583	missense	9938	exon10			GGAGAAGAGGAAA	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.1642G>A	2.37:g.69049916G>A	ENSP00000295381:p.Glu548Lys	69	0	0		68	31	0.455882	NM_001007231	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Missense_Mutation	SNP	ENST00000295381.3	37		2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	11.43	1.637568	0.29157	0.003406	0.0	ENSG00000163219	ENST00000295381;ENST00000409202;ENST00000467265;ENST00000409030;ENST00000409220;ENST00000482106;ENST00000543533;ENST00000479844	T;T;T;T;T;T	0.41400	2.82;2.82;2.56;1.0;1.0;1.0	5.42	4.53	0.55603	.	0.709828	0.14852	N	0.294619	T	0.26412	0.0645	N	0.19112	0.55	0.80722	D	1	B;P;P;B;B	0.39480	0.361;0.675;0.675;0.355;0.015	B;B;B;B;B	0.36666	0.054;0.154;0.23;0.165;0.011	T	0.02728	-1.1118	10	0.08381	T	0.77	.	13.8458	0.63466	0.0:0.153:0.847:0.0	rs61734450	509;549;542;541;548	E9PFQ7;P42331-4;G5E9G2;P42331-3;P42331	.;.;.;.;RHG25_HUMAN	K	548;549;509;541;542;542;533;242	ENSP00000295381:E548K;ENSP00000386911:E549K;ENSP00000420583:E509K;ENSP00000386863:E541K;ENSP00000386241:E542K;ENSP00000417467:E242K	ENSP00000295381:E548K	E	+	1	0	ARHGAP25	68903420	0.641000	0.27251	0.975000	0.42487	0.790000	0.44656	1.904000	0.39868	1.399000	0.46721	0.557000	0.71058	GAG	G|0.998;A|0.002	0.002	strong		0.443	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882		A	69049916	G	A	69049916	3	1	22	1	0	0	0	0	1	0	0	0	874	943	33	2	1723	2	ARHGAP25	2	69049916	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	664676	69049916	174149457	575	3476											
BMP10	27302	hgsc.bcm.edu	37	chr2	69093288	69093288	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gaaaacacgatgagcaaaggGttatgcttattctgggcact	13	10	11	7	1	1	1	0	1	1	0	1	3	1	1	0	2	3	4	0	2	5	3	rs2231345	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:69093288G>T	ENST00000295379.1	-	2	908	c.750C>A	c.(748-750)aaC>aaA	p.N250K		NM_014482.1	NP_055297.1	O95393	BMP10_HUMAN	bone morphogenetic protein 10	250			N -> K (in dbSNP:rs2231345).		activin receptor signaling pathway (GO:0032924)|adult heart development (GO:0007512)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heart trabecula formation (GO:0060347)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell migration (GO:0010596)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction (GO:0055117)|sarcomere organization (GO:0045214)|ventricular cardiac muscle cell development (GO:0055015)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Z disc (GO:0030018)	hormone activity (GO:0005179)|receptor serine/threonine kinase binding (GO:0033612)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(15)|ovary(2)	27						TGAGCAAAGGGTTATGCTTAT	0.488													G|||	78	0.0155751	0.0537	0.0101	5008	,	,		22010	0.0		0.0	False		,,,				2504	0.0				p.N250K		Atlas-SNP	.											.	BMP10	70	.	0			c.C750A						PASS	.	G	LYS/ASN	212,4194	129.4+/-166.1	8,196,1999	106	94	98		750	-0.1	0.6	2	dbSNP_98	98	0,8600		0,0,4300	yes	missense	BMP10	NM_014482.1	94	8,196,6299	TT,TG,GG		0.0,4.8116,1.63	benign	250/425	69093288	212,12794	2203	4300	6503	SO:0001583	missense	27302	exon2			CAAAGGGTTATGC	AF101441	CCDS1890.1	2p13.2	2014-09-17			ENSG00000163217	ENSG00000163217		"Bone morphogenetic proteins", "Endogenous ligands"	20869	protein-coding gene	gene with protein product		608748				10072785	Standard	NM_014482		Approved		uc002sez.1	O95393	OTTHUMG00000129573	ENST00000295379.1:c.750C>A	2.37:g.69093288G>T	ENSP00000295379:p.Asn250Lys	346	0	0		349	168	0.481375	NM_014482	Q53R17|Q6NTE0	Missense_Mutation	SNP	ENST00000295379.1	37	CCDS1890.1	34	0.015567765567765568	29	0.05894308943089431	5	0.013812154696132596	0	0.0	0	0.0	G	0.876	-0.730477	0.03135	0.048116	0.0	ENSG00000163217	ENST00000295379	T	0.63417	-0.04	5.44	-0.119	0.13543	Transforming growth factor-beta, N-terminal (1);	0.340366	0.33457	N	0.004893	T	0.02193	0.0068	N	0.01705	-0.755	0.26995	N	0.965051	B	0.09022	0.002	B	0.06405	0.002	T	0.07501	-1.0769	10	0.05620	T	0.96	.	0.5561	0.00671	0.2685:0.2748:0.2527:0.204	rs2231345;rs52835894;rs2231345	250	O95393	BMP10_HUMAN	K	250	ENSP00000295379:N250K	ENSP00000295379:N250K	N	-	3	2	BMP10	68946792	0.130000	0.22417	0.596000	0.28811	0.989000	0.77384	-0.205000	0.09411	-0.164000	0.10927	0.655000	0.94253	AAC	G|0.979;T|0.021	0.021	strong		0.488	BMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251768.1	NM_014482		T	69093288	G	T	69093288	3	4	22	1	0	0	0	0	1	0	0	0	1457	1252	44	4	528	4	BMP10	2	69093288	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	43372	69093288	174106085	576	3477											
GKN2	200504	hgsc.bcm.edu	37	chr2	69172570	69172570	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagcctttgcacagcctccaGcaccgacattatctggaaaa	12	8	7	14	1	1	0	0	0	1	0	2	2	2	1	4	1	4	2	4	1	3	2	rs73935451	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:69172570G>A	ENST00000328895.4	-	6	593	c.485C>T	c.(484-486)gCt>gTt	p.A162V	GKN2_ENST00000481498.1_3'UTR	NM_182536.2	NP_872342.2	Q86XP6	GKN2_HUMAN	gastrokine 2	162						extracellular region (GO:0005576)				autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|urinary_tract(1)	15						ACAGCCTCCAGCACCGACATT	0.343													G|||	95	0.0189696	0.0703	0.0029	5008	,	,		14842	0.0		0.0	False		,,,				2504	0.0				p.A162V		Atlas-SNP	.											.	GKN2	28	.	0			c.C485T						PASS	.	G	VAL/ALA	192,4214	117.5+/-155.4	5,182,2016	86	98	94		485	4.6	0	2	dbSNP_130	94	3,8597	3.0+/-9.4	0,3,4297	yes	missense	GKN2	NM_182536.2	64	5,185,6313	AA,AG,GG		0.0349,4.3577,1.4993	benign	162/185	69172570	195,12811	2203	4300	6503	SO:0001583	missense	200504	exon6			CCTCCAGCACCGA	AF494509	CCDS33215.1	2p14	2012-10-10			ENSG00000183607	ENSG00000183607		"BRICHOS domain containing"	24588	protein-coding gene	gene with protein product	"down regulated in gastric cancer GDDR", "BRICHOS domain containing 1B"					15774165, 15924415, 16888721	Standard	NM_182536		Approved	TFIZ1, PRO813, VLTI465, blottin, GDDR, BRICD1B	uc002sfa.3	Q86XP6	OTTHUMG00000152655	ENST00000328895.4:c.485C>T	2.37:g.69172570G>A	ENSP00000329292:p.Ala162Val	138	0	0		152	85	0.559211	NM_182536	Q6UWS6	Missense_Mutation	SNP	ENST00000328895.4	37	CCDS33215.1	36	0.016483516483516484	35	0.07113821138211382	1	0.0027624309392265192	0	0.0	0	0.0	G	16.09	3.023294	0.54683	0.043577	3.49E-4	ENSG00000183607	ENST00000328895	T	0.45668	0.89	5.48	4.61	0.57282	.	0.626420	0.16479	N	0.212605	T	0.02688	0.0081	L	0.50333	1.59	0.25024	N	0.991315	P	0.48294	0.908	B	0.34138	0.176	T	0.06075	-1.0847	10	0.66056	D	0.02	-5.4299	9.8712	0.41175	0.0908:0.0:0.9092:0.0	.	162	Q86XP6	GKN2_HUMAN	V	162	ENSP00000329292:A162V	ENSP00000329292:A162V	A	-	2	0	GKN2	69026074	0.014000	0.17966	0.006000	0.13384	0.410000	0.31052	1.135000	0.31454	1.562000	0.49601	0.650000	0.86243	GCT	G|0.983;A|0.017	0.017	strong		0.343	GKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327191.1	NM_182536		A	69172570	G	A	69172570	3	1	22	1	0	0	0	0	1	0	0	0	6433	971	34	2	73	2	GKN2	2	69172570	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	79282	69172570	174026803	577	3478											
PCYOX1	51449	hgsc.bcm.edu	37	chr2	70485332	70485332	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcggagctcgtctcctcgctGctggggttgtggctgttgct	1	13	16	11	3	1	0	0	0	1	0	4	1	1	1	1	4	3	7	1	4	0	2	rs114523411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:70485332G>A	ENST00000433351.2	+	1	64	c.36G>A	c.(34-36)ctG>ctA	p.L12L	PCYOX1_ENST00000505044.2_Intron|PCYOX1_ENST00000545138.1_5'Flank|PCYOX1_ENST00000264441.5_Silent_p.L12L	NM_016297.3	NP_057381.3	Q9UHG3	PCYOX_HUMAN	prenylcysteine oxidase 1	12					prenylated protein catabolic process (GO:0030327)|prenylcysteine catabolic process (GO:0030328)|prenylcysteine metabolic process (GO:0030329)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	chloride-transporting ATPase activity (GO:0008555)|prenylcysteine oxidase activity (GO:0001735)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)	15						TCTCCTCGCTGCTGGGGTTGT	0.706													G|||	23	0.00459265	0.0174	0.0	5008	,	,		9844	0.0		0.0	False		,,,				2504	0.0				p.L12L		Atlas-SNP	.											.	PCYOX1	34	.	0			c.G36A						PASS	.	G		49,4355	50.9+/-86.3	0,49,2153	38	39	39		36	-3.9	0	2	dbSNP_132	39	0,8600		0,0,4300	no	coding-synonymous	PCYOX1	NM_016297.3		0,49,6453	AA,AG,GG		0.0,1.1126,0.3768		12/506	70485332	49,12955	2202	4300	6502	SO:0001819	synonymous_variant	51449	exon1			CTCGCTGCTGGGG	AB020715	CCDS1902.1	2p13.3	2008-02-05			ENSG00000116005	ENSG00000116005	1.8.3.5		20588	protein-coding gene	gene with protein product		610995				10585463, 12186880	Standard	NM_016297		Approved	KIAA0908, PCL1	uc002sgn.4	Q9UHG3	OTTHUMG00000129671	ENST00000433351.2:c.36G>A	2.37:g.70485332G>A		137	0	0		111	40	0.36036	NM_016297	B2RB14|B7Z9P8|O94982|Q8N4N5|Q96QM8	Silent	SNP	ENST00000433351.2	37	CCDS1902.1																																																																																			G|0.995;A|0.005	0.005	strong		0.706	PCYOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251872.3	NM_016297		A	70485332	G	A	70485332	2	1	22	1	0	0	0	0	0	0	0	1	11617	1306	46	2		2	PCYOX1	2	70485332	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1312762	70485332	172714041	578	3479											
PCYOX1	51449	hgsc.bcm.edu	37	chr2	70503954	70503954	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcgtcttggtggccactccGttgaatcgaaaaatgtcgaa	11	11	10	9	4	1	1	0	1	1	0	5	3	2	1	2	2	0	1	2	2	4	2	rs36012096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:70503954G>T	ENST00000433351.2	+	6	976	c.948G>T	c.(946-948)ccG>ccT	p.P316P	PCYOX1_ENST00000505044.2_Silent_p.P239P|PCYOX1_ENST00000545138.1_Silent_p.P238P|PCYOX1_ENST00000264441.5_Intron	NM_016297.3	NP_057381.3	Q9UHG3	PCYOX_HUMAN	prenylcysteine oxidase 1	316					prenylated protein catabolic process (GO:0030327)|prenylcysteine catabolic process (GO:0030328)|prenylcysteine metabolic process (GO:0030329)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	chloride-transporting ATPase activity (GO:0008555)|prenylcysteine oxidase activity (GO:0001735)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)	15						TGGCCACTCCGTTGAATCGAA	0.368													G|||	464	0.0926518	0.3048	0.0187	5008	,	,		18461	0.001		0.003	False		,,,				2504	0.045				p.P316P		Atlas-SNP	.											.	PCYOX1	34	.	0			c.G948T						PASS	.	G		987,3419	365.1+/-317.3	112,763,1328	54	57	56		948	-5.4	0.9	2	dbSNP_126	56	25,8575	17.3+/-56.4	0,25,4275	no	coding-synonymous	PCYOX1	NM_016297.3		112,788,5603	TT,TG,GG		0.2907,22.4013,7.781		316/506	70503954	1012,11994	2203	4300	6503	SO:0001819	synonymous_variant	51449	exon6			CACTCCGTTGAAT	AB020715	CCDS1902.1	2p13.3	2008-02-05			ENSG00000116005	ENSG00000116005	1.8.3.5		20588	protein-coding gene	gene with protein product		610995				10585463, 12186880	Standard	NM_016297		Approved	KIAA0908, PCL1	uc002sgn.4	Q9UHG3	OTTHUMG00000129671	ENST00000433351.2:c.948G>T	2.37:g.70503954G>T		197	0	0		199	89	0.447236	NM_016297	B2RB14|B7Z9P8|O94982|Q8N4N5|Q96QM8	Silent	SNP	ENST00000433351.2	37	CCDS1902.1																																																																																			G|0.926;T|0.074	0.074	strong		0.368	PCYOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251872.3	NM_016297		T	70503954	G	T	70503954	2	4	22	1	0	0	0	0	0	0	0	1	11617	1132	40	4		4	PCYOX1	2	70503954	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	18622	70503954	172695419	579	3480											
FAM136A	84908	hgsc.bcm.edu	37	chr2	70528092	70528092	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgtcctcacaacagctggcGctgcaccggaacatgagacc	10	6	10	15	2	1	1	1	1	0	1	2	3	2	2	3	2	4	3	3	2	2	0	rs72904358	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:70528092G>A	ENST00000037869.3	-	2	186	c.108C>T	c.(106-108)agC>agT	p.S36S	FAM136A_ENST00000430566.1_Silent_p.S143S|FAM136A_ENST00000450256.1_Missense_Mutation_p.R102C|AC022201.5_ENST00000445084.1_RNA	NM_032822.2	NP_116211.2	Q96C01	F136A_HUMAN	family with sequence similarity 136, member A	36						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				breast(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	6						AACAGCTGGCGCTGCACCGGA	0.577													G|||	492	0.0982428	0.3124	0.0202	5008	,	,		19465	0.001		0.003	False		,,,				2504	0.0624				p.S36S		Atlas-SNP	.											FAM136A,caecum,carcinoma,0,1	FAM136A	14	1	0			c.C108T						scavenged	.	G		1006,3400	373.9+/-321.0	116,774,1313	75	76	76		108	-1.5	1	2	dbSNP_130	76	25,8575	17.3+/-56.4	0,25,4275	no	coding-synonymous	FAM136A	NM_032822.2		116,799,5588	AA,AG,GG		0.2907,22.8325,7.9271		36/139	70528092	1031,11975	2203	4300	6503	SO:0001819	synonymous_variant	84908	exon2			GCTGGCGCTGCAC	BC014975	CCDS1904.1	2p14	2014-02-12	2007-07-10		ENSG00000035141	ENSG00000035141			25911	protein-coding gene	gene with protein product	"hypothetical protein FLJ14668"					12477932	Standard	NM_032822		Approved	FLJ14668	uc002sgq.4	Q96C01	OTTHUMG00000129668	ENST00000037869.3:c.108C>T	2.37:g.70528092G>A		217	2	0.00921659		225	113	0.502222	NM_032822	Q96SS3	Silent	SNP	ENST00000037869.3	37	CCDS1904.1	165	0.07554945054945054	151	0.30691056910569103	9	0.024861878453038673	1	0.0017482517482517483	4	0.005277044854881266	G	13.18	2.160192	0.38119	0.228325	0.002907	ENSG00000035141	ENST00000450256	.	.	.	5.01	-1.49	0.08718	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.34030	-0.9845	4	0.87932	D	0	.	10.957	0.47364	0.4179:0.0:0.5821:0.0	.	.	.	.	C	102	.	ENSP00000391468:R102C	R	-	1	0	FAM136A	70381596	0.992000	0.36948	0.966000	0.40874	0.969000	0.65631	0.199000	0.17237	-0.250000	0.09555	-0.263000	0.10527	CGC	G|0.921;A|0.079	0.079	strong		0.577	FAM136A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251869.2	NM_032822		A	70528092	G	A	70528092	2	1	22	1	0	0	0	0	0	0	0	1	5455	1078	38	1		1	FAM136A	2	70528092	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	24138	70528092	172671281	580	3481											
ADD2	119	hgsc.bcm.edu	37	chr2	70933494	70933494	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtcaaagtaaggctgccccTgcgggggcggcggcgaggca	7	4	19	11	4	1	0	1	0	0	0	1	1	1	0	2	7	2	3	2	7	2	1	rs201443444	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:70933494T>C	ENST00000264436.4	-	3	491	c.47A>G	c.(46-48)cAg>cGg	p.Q16R	ADD2_ENST00000413157.2_Missense_Mutation_p.Q16R|ADD2_ENST00000355733.3_Missense_Mutation_p.Q16R|ADD2_ENST00000473232.1_5'Flank|ADD2_ENST00000430656.1_Missense_Mutation_p.Q32R|ADD2_ENST00000407644.2_Missense_Mutation_p.Q16R	NM_001617.3	NP_001608.1	P35612	ADDB_HUMAN	adducin 2 (beta)	16					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						AGGCTGCCCCTGCGGGGGCGG	0.642													T|||	73	0.0145767	0.0204	0.0144	5008	,	,		17067	0.0169		0.0189	False		,,,				2504	0.0				p.Q32R		Atlas-SNP	.											.	ADD2	261	.	0			c.A95G						PASS	.	T	ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN	67,4337	58.1+/-94.6	1,65,2136	43	48	46		47,95,47,47,47	5.1	1	2	dbSNP_134	46	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense	ADD2	NM_001185054.1,NM_001185055.1,NM_001617.3,NM_017482.3,NM_017488.3	43,43,43,43,43	1,65,6436	CC,CT,TT		0.0,1.5213,0.5152	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	16/727,32/576,16/727,16/560,16/644	70933494	67,12937	2202	4300	6502	SO:0001583	missense	119	exon2			TGCCCCTGCGGGG	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.47A>G	2.37:g.70933494T>C	ENSP00000264436:p.Gln16Arg	111	0	0		111	54	0.486486	NM_001185055	A8K4P2|B4DM17|D6W5G7|D6W5G8|Q13482|Q16412|Q59G82|Q5U5P4|Q6P0P2|Q6PGQ4|Q7Z688|Q7Z689|Q7Z690|Q7Z691	Missense_Mutation	SNP	ENST00000264436.4	37	CCDS1906.1	48	0.02197802197802198	27	0.054878048780487805	6	0.016574585635359115	6	0.01048951048951049	9	0.011873350923482849	T	13.89	2.372523	0.42003	0.015213	0.0	ENSG00000075340	ENST00000264436;ENST00000407644;ENST00000456320;ENST00000355733;ENST00000522886;ENST00000264439;ENST00000356565;ENST00000517596;ENST00000413157;ENST00000430656;ENST00000415348;ENST00000425976;ENST00000447731	T;T;T;T;T;T;T;T	0.30448	1.58;1.58;1.58;1.58;1.58;1.53;1.58;1.58	5.11	5.11	0.69529	.	0.367672	0.26875	N	0.022043	T	0.03520	0.0101	L	0.29908	0.895	0.32494	N	0.539867	B;B;D;B;B;P	0.55385	0.138;0.058;0.971;0.215;0.18;0.867	B;B;B;B;B;B	0.39217	0.065;0.098;0.294;0.065;0.109;0.269	T	0.09400	-1.0676	10	0.52906	T	0.07	-11.8187	13.1749	0.59621	0.0:0.0:0.0:1.0	.	32;16;16;16;16;16	B4DM17;P35612-4;E9PAN1;Q05DK5;P35612;P35612-3	.;.;.;.;ADDB_HUMAN;.	R	16;16;16;16;16;16;16;16;16;32;16;16;16	ENSP00000264436:Q16R;ENSP00000384677:Q16R;ENSP00000347972:Q16R;ENSP00000430243:Q16R;ENSP00000388072:Q16R;ENSP00000398112:Q32R;ENSP00000412357:Q16R;ENSP00000412681:Q16R	ENSP00000264436:Q16R	Q	-	2	0	ADD2	70787002	0.024000	0.19004	0.998000	0.56505	0.919000	0.55068	0.633000	0.24598	2.265000	0.75225	0.482000	0.46254	CAG	T|0.978;C|0.022	0.022	strong		0.642	ADD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251918.4	NM_001617		C	70933494	T	C	70933494	3	2	22	1	0	0	0	0	1	0	0	0	305	1580	55	3	2370	3	ADD2	2	70933494	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	405402	70933494	172265879	581	3482											
CLEC4F	165530	hgsc.bcm.edu	37	chr2	71043607	71043607	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctgctttttataaaggcctgGgtctgggagtttaaagcatt	9	15	11	6	0	1	0	0	0	1	0	1	1	1	1	1	3	2	3	1	3	5	7	rs114209954	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71043607G>C	ENST00000272367.2	-	4	982	c.906C>G	c.(904-906)acC>acG	p.T302T	CLEC4F_ENST00000426626.1_Silent_p.T302T	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	302					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						TAAAGGCCTGGGTCTGGGAGT	0.403													G|||	63	0.0125799	0.0461	0.0029	5008	,	,		19886	0.0		0.0	False		,,,				2504	0.0				p.T302T	Colon(107;10 2157 6841 26035)	Atlas-SNP	.											.	CLEC4F	95	.	0			c.C906G						PASS	.	G		214,4192	126.1+/-163.2	4,206,1993	89	95	93		906	-0.9	0.3	2	dbSNP_132	93	1,8599		0,1,4299	no	coding-synonymous	CLEC4F	NM_173535.2		4,207,6292	CC,CG,GG		0.0116,4.857,1.6531		302/590	71043607	215,12791	2203	4300	6503	SO:0001819	synonymous_variant	165530	exon4			GGCCTGGGTCTGG	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.906C>G	2.37:g.71043607G>C		186	0	0		171	82	0.479532	NM_173535	A4QPA5	Silent	SNP	ENST00000272367.2	37	CCDS1910.1																																																																																			G|0.985;C|0.015	0.015	strong		0.403	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535		C	71043607	G	C	71043607	2	2	22	1	0	0	0	0	0	0	0	1	3518	1219	43	4		4	CLEC4F	2	71043607	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	110113	71043607	172155766	582	3483											
CLEC4F	165530	hgsc.bcm.edu	37	chr2	71044076	71044076	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttaccatctggatgtcagcaTtggtgtttcccagatgatca	9	14	9	9	0	3	2	2	1	1	1	4	3	4	3	2	2	2	2	2	2	1	3	rs61754946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71044076T>C	ENST00000272367.2	-	4	513	c.437A>G	c.(436-438)aAt>aGt	p.N146S	CLEC4F_ENST00000426626.1_Missense_Mutation_p.N146S	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	146					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						GATGTCAGCATTGGTGTTTCC	0.473													C|||	95	0.0189696	0.0703	0.0029	5008	,	,		20407	0.0		0.0	False		,,,				2504	0.0				p.N146S	Colon(107;10 2157 6841 26035)	Atlas-SNP	.											.	CLEC4F	95	.	0			c.A437G						PASS	.	C	SER/ASN	282,4124	800.8+/-415.6	6,270,1927	142	120	127		437	-2.8	0	2	dbSNP_129	127	1,8599		0,1,4299	yes	missense	CLEC4F	NM_173535.2	46	6,271,6226	CC,CT,TT		0.0116,6.4004,2.1759	benign	146/590	71044076	283,12723	2203	4300	6503	SO:0001583	missense	165530	exon4			TCAGCATTGGTGT	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.437A>G	2.37:g.71044076T>C	ENSP00000272367:p.Asn146Ser	199	0	0		254	112	0.440945	NM_173535	A4QPA5	Missense_Mutation	SNP	ENST00000272367.2	37	CCDS1910.1	27	0.012362637362637362	27	0.054878048780487805	0	0.0	0	0.0	0	0.0	C	0.067	-1.210900	0.01555	0.064004	1.16E-4	ENSG00000152672	ENST00000272367;ENST00000426626	T;T	0.01854	4.6;4.63	5.15	-2.79	0.05841	.	0.560537	0.16319	N	0.219645	T	0.00109	0.0003	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	0.40346	-0.9568	10	0.02654	T	1	.	6.1052	0.20069	0.0:0.2149:0.2644:0.5207	.	146;146	B7ZMM1;Q8N1N0	.;CLC4F_HUMAN	S	146	ENSP00000272367:N146S;ENSP00000390581:N146S	ENSP00000272367:N146S	N	-	2	0	CLEC4F	70897584	0.066000	0.20996	0.001000	0.08648	0.003000	0.03518	0.005000	0.13129	-0.464000	0.06963	-1.201000	0.01664	AAT	T|0.979;C|0.021	0.021	strong		0.473	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535		C	71044076	T	C	71044076	3	2	22	1	0	0	0	0	1	0	0	0	3518	1493	52	3	1348	3	CLEC4F	2	71044076	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	469	71044076	172155297	583	3484											
CLEC4F	165530	hgsc.bcm.edu	37	chr2	71046536	71046536	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgttgtctcccagaattacGgcttgcacaggcttcggaac	9	11	10	11	2	1	1	0	0	1	1	3	2	1	2	1	3	3	4	1	3	3	4	rs17006361	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71046536G>A	ENST00000272367.2	-	3	295	c.219C>T	c.(217-219)gcC>gcT	p.A73A	CLEC4F_ENST00000426626.1_Silent_p.A73A	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	73					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						CCAGAATTACGGCTTGCACAG	0.532													A|||	198	0.0395367	0.143	0.013	5008	,	,		18946	0.0		0.0	False		,,,				2504	0.0				p.A73A	Colon(107;10 2157 6841 26035)	Atlas-SNP	.											CLEC4F,NS,carcinoma,0,3	CLEC4F	95	3	0			c.C219T						PASS	.	A		584,3822	259.8+/-263.3	32,520,1651	124	107	112		219	0	0	2	dbSNP_123	112	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	CLEC4F	NM_173535.2		32,523,5948	AA,AG,GG		0.0349,13.2547,4.5133		73/590	71046536	587,12419	2203	4300	6503	SO:0001819	synonymous_variant	165530	exon3			AATTACGGCTTGC	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.219C>T	2.37:g.71046536G>A		180	0	0		167	85	0.508982	NM_173535	A4QPA5	Silent	SNP	ENST00000272367.2	37	CCDS1910.1																																																																																			G|0.948;A|0.052	0.052	strong		0.532	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535		A	71046536	G	A	71046536	2	1	22	1	0	0	0	0	0	0	0	1	3518	1103	39	1		1	CLEC4F	2	71046536	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2460	71046536	172152837	584	3485											
ANKRD53	79998	hgsc.bcm.edu	37	chr2	71212380	71212380	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagccttcctggcagctgtgCgatctcatcaaggactcccc	8	9	9	15	1	2	0	2	0	1	0	5	2	4	1	4	2	3	2	4	2	2	1	rs61732288	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71212380C>A	ENST00000360589.3	+	6	1577	c.1543C>A	c.(1543-1545)Cga>Aga	p.R515R	ANKRD53_ENST00000272421.6_3'UTR|ANKRD53_ENST00000441349.1_3'UTR|AC007040.11_ENST00000606025.1_Intron|ANKRD53_ENST00000457410.1_Silent_p.R481R	NM_001115116.1	NP_001108588.1	Q8N9V6	ANR53_HUMAN	ankyrin repeat domain 53	515										endometrium(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	11						GGCAGCTGTGCGATCTCATCA	0.572											OREG0014687	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	184	0.0367412	0.1331	0.0101	5008	,	,		13411	0.0		0.001	False		,,,				2504	0.0				p.R515R		Atlas-SNP	.											.	ANKRD53	55	.	0			c.C1543A						PASS	.	C	,	182,1202		12,158,522	31	32	31		1543,	-0.8	0.1	2	dbSNP_129	31	2,3180		0,2,1589	no	coding-synonymous,utr-3	ANKRD53	NM_001115116.1,NM_024933.3	,	12,160,2111	AA,AC,CC		0.0629,13.1503,4.0298	,	515/531,	71212380	184,4382	692	1591	2283	SO:0001819	synonymous_variant	79998	exon6			GCTGTGCGATCTC	BC035234	CCDS1913.1, CCDS46321.1	2p13.3	2013-01-10			ENSG00000144031	ENSG00000144031		"Ankyrin repeat domain containing"	25691	protein-coding gene	gene with protein product							Standard	NM_024933		Approved	FLJ12056, FLJ36160	uc002shl.4	Q8N9V6	OTTHUMG00000129712	ENST00000360589.3:c.1543C>A	2.37:g.71212380C>A		134	0	0	1128	135	56	0.414815	NM_001115116	Q8IYP8	Silent	SNP	ENST00000360589.3	37	CCDS46321.1																																																																																			C|0.968;A|0.032	0.032	strong		0.572	ANKRD53-004	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330275.2	NM_024933		A	71212380	C	A	71212380	2	1	22	1	0	0	0	0	0	0	0	1	679	760	27	4		4	ANKRD53	2	71212380	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	165844	71212380	171986993	585	3486											
MCEE	84693	hgsc.bcm.edu	37	chr2	71351641	71351641	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtggaagaagctcttactgTtggaatgggagcttgaagtc	10	12	14	5	0	1	2	0	1	1	1	2	5	1	5	0	3	3	3	0	3	5	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71351641T>C	ENST00000244217.5	-	2	90	c.73A>G	c.(73-75)Aca>Gca	p.T25A	AC007881.1_ENST00000578636.1_RNA	NM_032601.3	NP_115990.3	Q96PE7	MCEE_HUMAN	methylmalonyl CoA epimerase	25					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|L-methylmalonyl-CoA metabolic process (GO:0046491)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	metal ion binding (GO:0046872)|methylmalonyl-CoA epimerase activity (GO:0004493)			kidney(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9						GCTCTTACTGTTGGAATGGGA	0.418																																					p.T25A		Atlas-SNP	.											.	MCEE	19	.	0			c.A73G						PASS	.						87	95	92					2																	71351641		2203	4300	6503	SO:0001583	missense	84693	exon2			TTACTGTTGGAAT	AF364547	CCDS1915.1	2p13.3	2011-05-12			ENSG00000124370	ENSG00000124370	5.1.99.1		16732	protein-coding gene	gene with protein product	"glyoxalase domain containing 2"	608419				16697227, 16752391, 16843692	Standard	NM_032601		Approved	GLOD2	uc002shs.2	Q96PE7	OTTHUMG00000129709	ENST00000244217.5:c.73A>G	2.37:g.71351641T>C	ENSP00000244217:p.Thr25Ala	55	0	0		51	25	0.490196	NM_032601	Q53TP1|Q8WW63	Missense_Mutation	SNP	ENST00000244217.5	37	CCDS1915.1	.	.	.	.	.	.	.	.	.	.	T	11.40	1.627801	0.28978	.	.	ENSG00000124370	ENST00000244217	T	0.62941	-0.01	5.33	-5.38	0.02673	.	0.745129	0.13573	N	0.377891	T	0.42494	0.1205	L	0.35723	1.085	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.26849	-1.0091	10	0.20519	T	0.43	-5.2959	9.1858	0.37170	0.1202:0.5708:0.0:0.3089	.	25	Q96PE7	MCEE_HUMAN	A	25	ENSP00000244217:T25A	ENSP00000244217:T25A	T	-	1	0	MCEE	71205149	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.466000	0.06672	-0.914000	0.03827	0.528000	0.53228	ACA	.	.	none		0.418	MCEE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251917.3	NM_032601		C	71351641	T	C	71351641	3	2	22	1	0	0	0	0	1	0	0	0	9386	1725	60	3	465	3	MCEE	2	71351641	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	139261	71351641	171847732	586	3487											
DYSF	8291	hgsc.bcm.edu	37	chr2	71838661	71838661	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatctcctcccccagcctcGtggtagagtgtgggggccag	6	8	13	14	1	1	1	0	0	1	1	4	1	2	1	5	3	1	1	5	3	1	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71838661G>A	ENST00000258104.3	+	38	4349	c.4072G>A	c.(4072-4074)Gtg>Atg	p.V1358M	DYSF_ENST00000409651.1_Missense_Mutation_p.V1390M|DYSF_ENST00000410020.3_Missense_Mutation_p.V1376M|DYSF_ENST00000429174.2_Missense_Mutation_p.V1358M|DYSF_ENST00000410041.1_Missense_Mutation_p.V1376M|DYSF_ENST00000409744.1_Missense_Mutation_p.V1345M|DYSF_ENST00000409366.1_Missense_Mutation_p.V1359M|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000394120.2_Missense_Mutation_p.V1359M|DYSF_ENST00000409582.3_Missense_Mutation_p.V1375M|DYSF_ENST00000413539.2_Missense_Mutation_p.V1389M|DYSF_ENST00000409762.1_Missense_Mutation_p.V1375M	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1358	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)			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						CCCCAGCCTCGTGGTAGAGTG	0.567																																					p.V1390M		Atlas-SNP	.											DYSF_ENST00000410020,NS,carcinoma,0,2	DYSF	536	2	0			c.G4168A						PASS	.						58	57	57					2																	71838661		2203	4300	6503	SO:0001583	missense	8291	exon39			AGCCTCGTGGTAG	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.4072G>A	2.37:g.71838661G>A	ENSP00000258104:p.Val1358Met	79	0	0		66	31	0.469697	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	37	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	G	16.19	3.054472	0.55218	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	D;D;D;D;D;D;D;D;D;D;D	0.82711	-1.64;-1.64;-1.64;-1.64;-1.64;-1.64;-1.64;-1.64;-1.64;-1.64;-1.64	5.54	4.65	0.58169	C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.213647	0.42548	D	0.000687	D	0.86053	0.5841	L	0.54323	1.7	0.32057	N	0.596244	D;D;D;D;D;D;P;P;B;P;B;P;P;D;P	0.71674	0.984;0.998;0.998;0.995;0.995;0.995;0.851;0.773;0.415;0.769;0.077;0.46;0.769;0.995;0.807	P;P;P;P;P;D;P;P;B;B;B;B;B;P;P	0.66497	0.843;0.855;0.9;0.9;0.9;0.944;0.554;0.684;0.433;0.433;0.087;0.238;0.433;0.855;0.569	D	0.85452	0.1161	10	0.40728	T	0.16	-21.6668	8.921	0.35612	0.1689:0.0:0.8311:0.0	.	101;1390;1376;1359;1345;1376;1345;1375;1344;1389;1375;1358;1344;1359;1358	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	M	1389;1375;1375;1358;1358;1390;1359;1345;1359;1376;1376	ENSP00000407046:V1389M;ENSP00000387137:V1375M;ENSP00000386547:V1375M;ENSP00000398305:V1358M;ENSP00000258104:V1358M;ENSP00000386683:V1390M;ENSP00000377678:V1359M;ENSP00000386285:V1345M;ENSP00000386512:V1359M;ENSP00000386881:V1376M;ENSP00000386617:V1376M	ENSP00000258104:V1358M	V	+	1	0	DYSF	71692169	0.054000	0.20591	0.944000	0.38274	0.395000	0.30598	0.451000	0.21779	2.623000	0.88846	0.561000	0.74099	GTG	.	.	none		0.567	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		A	71838661	G	A	71838661	3	1	22	1	0	0	0	0	1	0	0	0	4861	1145	40	1	4414	1	DYSF	2	71838661	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	487020	71838661	171360712	587	3488											
RAB11FIP5	26056	hgsc.bcm.edu	37	chr2	73339675	73339675	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatccagggcccccggcggCagctcgaaggagcactcctc	7	4	12	18	3	0	0	0	0	0	0	4	2	2	1	5	4	2	3	5	4	1	0	rs143108301	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:73339675C>T	ENST00000258098.6	-	1	471	c.231G>A	c.(229-231)ctG>ctA	p.L77L	RP11-44N22.3_ENST00000608612.1_RNA	NM_015470.2	NP_056285.1	Q9BXF6	RFIP5_HUMAN	RAB11 family interacting protein 5 (class I)	77	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				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						CCCCCGGCGGCAGCTCGAAGG	0.736													C|||	2	0.000399361	0.0008	0.0	5008	,	,		10052	0.001		0.0	False		,,,				2504	0.0				p.L77L		Atlas-SNP	.											.	RAB11FIP5	66	.	0			c.G231A						PASS	.	C		4,4354		0,4,2175	11	10	10		231	1.9	1	2	dbSNP_134	10	0,8504		0,0,4252	no	coding-synonymous	RAB11FIP5	NM_015470.2		0,4,6427	TT,TC,CC		0.0,0.0918,0.0311		77/654	73339675	4,12858	2179	4252	6431	SO:0001819	synonymous_variant	26056	exon1			CGGCGGCAGCTCG	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.231G>A	2.37:g.73339675C>T		44	0	0		69	30	0.434783	NM_015470	O94939|Q9P0M1	Silent	SNP	ENST00000258098.6	37	CCDS1923.1																																																																																			C|1.000;T|0.000	0.000	weak		0.736	RAB11FIP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251995.1	NM_015470		T	73339675	C	T	73339675	2	4	22	1	0	0	0	0	0	0	0	1	12912	697	25	2		2	RAB11FIP5	2	73339675	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1501014	73339675	169859698	588	3489											
EGR4	1961	hgsc.bcm.edu	37	chr2	73518716	73518716	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcgcgcgaagcggcggcCgcacacgtcgcaagcaaaag	10	2	15	14	8	0	0	0	0	0	0	1	1	0	0	1	2	3	4	1	2	4	0	rs141733943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:73518716C>T	ENST00000545030.1	-	2	1713	c.1639G>A	c.(1639-1641)Ggc>Agc	p.G547S	EGR4_ENST00000436467.2_Missense_Mutation_p.G444S	NM_001965.3	NP_001956.3	Q05215	EGR4_HUMAN	early growth response 4	547					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						AAGCGGCGGCCGCACACGTCG	0.662													C|||	2	0.000399361	0.0015	0.0	5008	,	,		12645	0.0		0.0	False		,,,				2504	0.0				p.G547S		Atlas-SNP	.											.	EGR4	52	.	0			c.G1639A						PASS	.	C	SER/GLY	2,4404		0,2,2201	24	28	27		1639	4.8	1	2	dbSNP_134	27	0,8596		0,0,4298	no	missense	EGR4	NM_001965.3	56	0,2,6499	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging	547/590	73518716	2,13000	2203	4298	6501	SO:0001583	missense	1961	exon2			GGCGGCCGCACAC		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.1639G>A	2.37:g.73518716C>T	ENSP00000445626:p.Gly547Ser	146	0	0		176	99	0.5625	NM_001965	B2RAE3|G3V1T5|Q2Z1P5	Missense_Mutation	SNP	ENST00000545030.1	37	CCDS1925.2	.	.	.	.	.	.	.	.	.	.	C	31	5.103602	0.94245	4.54E-4	0.0	ENSG00000135625	ENST00000545030;ENST00000436467	T;T	0.07216	3.21;3.21	4.79	4.79	0.61399	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000005	T	0.20780	0.0500	L	0.37897	1.145	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.77557	0.989;0.99	T	0.00715	-1.1597	10	0.87932	D	0	-21.0702	16.5595	0.84535	0.0:1.0:0.0:0.0	.	444;547	Q05215;G3V1T5	EGR4_HUMAN;.	S	547;444	ENSP00000445626:G547S;ENSP00000419687:G444S	ENSP00000419687:G444S	G	-	1	0	EGR4	73372224	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.631000	0.83237	2.478000	0.83669	0.655000	0.94253	GGC	C|1.000;T|0.000	0.000	weak		0.662	EGR4-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001965		T	73518716	C	T	73518716	3	4	22	1	0	0	0	0	1	0	0	0	4976	652	23	1	134	1	EGR4	2	73518716	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	179041	73518716	169680657	589	3490											
ALMS1	7840	hgsc.bcm.edu	37	chr2	73676189	73676189	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgtttctggaccagctgaCggaaagactgggacaccagc	10	7	13	11	1	1	2	0	1	1	1	1	5	1	5	2	3	2	3	2	3	1	1	rs77517267	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:73676189C>T	ENST00000264448.6	+	8	2643	c.2532C>T	c.(2530-2532)gaC>gaT	p.D844D	ALMS1_ENST00000409009.1_Silent_p.D802D|ALMS1_ENST00000377715.1_Silent_p.D844D	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	844	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						GACCAGCTGACGGAAAGACTG	0.507													C|||	183	0.0365415	0.1324	0.0115	5008	,	,		19422	0.0		0.0	False		,,,				2504	0.0				p.D844D		Atlas-SNP	.											ALMS1,NS,carcinoma,+2,1	ALMS1	384	1	0			c.C2532T						PASS	.	C		414,3376		30,354,1511	76	79	78		2532	-6.5	0	2	dbSNP_132	78	3,8219		0,3,4108	no	coding-synonymous	ALMS1	NM_015120.4		30,357,5619	TT,TC,CC		0.0365,10.9235,3.4715		844/4168	73676189	417,11595	1895	4111	6006	SO:0001819	synonymous_variant	7840	exon8			AGCTGACGGAAAG	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.2532C>T	2.37:g.73676189C>T		141	0	0		157	79	0.503185	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	37	CCDS42697.1																																																																																			C|0.976;T|0.024	0.024	strong		0.507	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		T	73676189	C	T	73676189	2	4	22	1	0	0	0	0	0	0	0	1	535	535	19	1		1	ALMS1	2	73676189	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	157473	73676189	169523184	590	3491											
ALMS1	7840	hgsc.bcm.edu	37	chr2	73676315	73676315	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actgaagaggctctgaaagtAtcaattgttcctggaccagg	12	10	11	8	0	2	3	1	2	1	1	3	4	3	4	2	3	0	3	2	3	4	3	rs76266696	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:73676315A>G	ENST00000264448.6	+	8	2769	c.2658A>G	c.(2656-2658)gtA>gtG	p.V886V	ALMS1_ENST00000409009.1_Silent_p.V844V|ALMS1_ENST00000377715.1_Silent_p.V886V	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	886	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						CTCTGAAAGTATCAATTGTTC	0.463													A|||	39	0.00778754	0.028	0.0029	5008	,	,		20537	0.0		0.0	False		,,,				2504	0.0				p.V886V		Atlas-SNP	.											.	ALMS1	384	.	0			c.A2658G						PASS	.	A		90,3660		1,88,1786	98	102	101		2658	-0.3	0	2	dbSNP_132	101	2,8196		0,2,4097	no	coding-synonymous	ALMS1	NM_015120.4		1,90,5883	GG,GA,AA		0.0244,2.4,0.77		886/4168	73676315	92,11856	1875	4099	5974	SO:0001819	synonymous_variant	7840	exon8			GAAAGTATCAATT	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.2658A>G	2.37:g.73676315A>G		260	0	0		264	128	0.484848	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	37	CCDS42697.1																																																																																			A|0.994;G|0.006	0.006	strong		0.463	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		G	73676315	A	G	73676315	2	3	22	1	0	0	0	0	0	0	0	1	535	436	16	3		3	ALMS1	2	73676315	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	126	73676315	169523058	591	3492											
ALMS1	7840	hgsc.bcm.edu	37	chr2	73786188	73786188	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acactaaagccattacacagAaagaggagatccataggaag	19	5	9	8	0	0	3	0	0	0	3	1	5	1	4	2	2	2	0	2	2	6	3	rs34071195	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:73786188A>G	ENST00000264448.6	+	15	10411	c.10300A>G	c.(10300-10302)Aaa>Gaa	p.K3434E	ALMS1_ENST00000409009.1_Missense_Mutation_p.K3392E	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	3434			K -> E (in dbSNP:rs34071195).		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						CATTACACAGAAAGAGGAGAT	0.468													A|||	92	0.0183706	0.0658	0.0072	5008	,	,		16247	0.0		0.0	False		,,,				2504	0.0				p.K3434E		Atlas-SNP	.											.	ALMS1	384	.	0			c.A10300G						PASS	.	A	GLU/LYS	195,3577		8,179,1699	101	101	101		10300	3.8	1	2	dbSNP_126	101	2,8234		0,2,4116	yes	missense	ALMS1	NM_015120.4	56	8,181,5815	GG,GA,AA		0.0243,5.1697,1.6406	probably-damaging	3434/4168	73786188	197,11811	1886	4118	6004	SO:0001583	missense	7840	exon15			ACACAGAAAGAGG	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.10300A>G	2.37:g.73786188A>G	ENSP00000264448:p.Lys3434Glu	131	0	0		143	70	0.48951	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	29	0.013278388278388278	26	0.052845528455284556	3	0.008287292817679558	0	0.0	0	0.0	A	18.42	3.620149	0.66787	0.051697	2.43E-4	ENSG00000116127	ENST00000409009;ENST00000264448	T;T	0.07327	3.2;3.2	3.75	3.75	0.43078	.	0.162704	0.29239	N	0.012727	T	0.02848	0.0085	L	0.48642	1.525	0.80722	D	1	P;D;P	0.64830	0.886;0.994;0.932	P;D;P	0.72982	0.55;0.979;0.546	T	0.00158	-1.1976	10	0.72032	D	0.01	.	9.1435	0.36919	1.0:0.0:0.0:0.0	rs34071195	3434;3392;3434	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	E	3392;3434	ENSP00000386627:K3392E;ENSP00000264448:K3434E	ENSP00000264448:K3434E	K	+	1	0	ALMS1	73639696	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	2.265000	0.43311	1.946000	0.56461	0.377000	0.23210	AAA	A|0.991;G|0.009	0.009	strong		0.468	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		G	73786188	A	G	73786188	3	3	22	1	0	0	0	0	1	0	0	0	535	247	9	3	10358	3	ALMS1	2	73786188	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	109873	73786188	169413185	592	3493											
NAT8	9027	hgsc.bcm.edu	37	chr2	73868446	73868446	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccagaagcaggagccacgctCactcaggtaggatttggtaa	12	7	12	10	1	2	1	2	0	0	1	2	3	2	3	2	4	2	4	2	4	3	3	rs13424561	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:73868446C>T	ENST00000272425.3	-	2	459	c.310G>A	c.(310-312)Gag>Aag	p.E104K		NM_003960.3|NM_016347.2	NP_003951.3|NP_057431.2			N-acetyltransferase 8 (GCN5-related, putative)											breast(1)|endometrium(2)|kidney(2)|lung(2)|ovary(1)|prostate(1)	9						GAGCCACGCTCACTCAGGTAG	0.537													.|||	179	0.0357428	0.1286	0.013	5008	,	,		22094	0.0		0.0	False		,,,				2504	0.0				p.E104K		Atlas-SNP	.											.	NAT8	26	.	0			c.G310A						PASS	.	C	LYS/GLU	505,3901	235.2+/-247.8	38,429,1736	118	112	114		310	-0.2	0	2	dbSNP_121	114	3,8597	3.7+/-12.6	0,3,4297	yes	missense	NAT8	NM_003960.3	56	38,432,6033	TT,TC,CC		0.0349,11.4616,3.9059	possibly-damaging	104/228	73868446	508,12498	2203	4300	6503	SO:0001583	missense	9027	exon2			CACGCTCACTCAG	AB013094	CCDS1926.1	2p13.2	2012-03-20	2008-09-24		ENSG00000144035	ENSG00000144035			18069	protein-coding gene	gene with protein product		606716	"N-acetyltransferase 8"			11397015, 9852678, 19011241	Standard	NM_003960		Approved	Hcml1, TSC501, GLA, ATase2	uc002sji.1	Q9UHE5	OTTHUMG00000129818	ENST00000272425.3:c.310G>A	2.37:g.73868446C>T	ENSP00000272425:p.Glu104Lys	139	0	0		164	83	0.506098	NM_003960		Missense_Mutation	SNP	ENST00000272425.3	37	CCDS1926.1	75	0.034340659340659344	71	0.1443089430894309	4	0.011049723756906077	0	0.0	0	0.0	C	2.671	-0.277447	0.05679	0.114616	3.49E-4	ENSG00000144035	ENST00000272425	T	0.29397	1.57	3.86	-0.22	0.13130	GCN5-related N-acetyltransferase (GNAT) domain (1);Acyl-CoA N-acyltransferase (2);	1.343440	0.05236	N	0.511242	T	0.00144	0.0004	L	0.31752	0.955	0.80722	P	0.0	B	0.24426	0.103	B	0.17722	0.019	T	0.20739	-1.0266	9	0.08179	T	0.78	-1.1728	7.9371	0.29935	0.0:0.5069:0.0:0.4931	rs13424561;rs13424561	104	Q9UHE5	NAT8_HUMAN	K	104	ENSP00000272425:E104K	ENSP00000272425:E104K	E	-	1	0	NAT8	73721954	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	-0.648000	0.05391	-0.174000	0.10743	-0.151000	0.13558	GAG	C|0.956;T|0.044	0.044	strong		0.537	NAT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327854.1	NM_003960		T	73868446	C	T	73868446	3	4	22	1	0	0	0	0	1	0	0	0	10188	835	29	2	377	2	NAT8	2	73868446	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	82258	73868446	169330927	593	3494											
ACTG2	72	hgsc.bcm.edu	37	chr2	74140616	74140616	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcctctctgtccacaggcatCgtcctggattcaggtgatgg	6	12	11	12	1	2	1	1	1	1	0	7	2	5	2	3	4	0	1	3	4	0	1	rs34286914	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74140616C>T	ENST00000409624.1	+	7	1099	c.456C>T	c.(454-456)atC>atT	p.I152I	ACTG2_ENST00000409731.3_Silent_p.I109I|ACTG2_ENST00000345517.3_Silent_p.I152I			P63267	ACTH_HUMAN	actin, gamma 2, smooth muscle, enteric	152					muscle contraction (GO:0006936)	blood microparticle (GO:0072562)|cell periphery (GO:0071944)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			large_intestine(3)|lung(14)|skin(1)	18						CCACAGGCATCGTCCTGGATT	0.507													C|||	124	0.0247604	0.0908	0.0043	5008	,	,		20140	0.0		0.001	False		,,,				2504	0.0				p.I152I		Atlas-SNP	.											.	ACTG2	37	.	0			c.C456T						PASS	.	C	,	388,4018	193.6+/-218.7	20,348,1835	106	98	101		327,456	-9.2	0.3	2	dbSNP_126	101	2,8598		0,2,4298	no	coding-synonymous,coding-synonymous	ACTG2	NM_001199893.1,NM_001615.3	,	20,350,6133	TT,TC,CC		0.0233,8.8062,2.9986	,	109/334,152/377	74140616	390,12616	2203	4300	6503	SO:0001819	synonymous_variant	72	exon6			AGGCATCGTCCTG		CCDS1930.1, CCDS56124.1	2p13.1	2008-05-20			ENSG00000163017	ENSG00000163017			145	protein-coding gene	gene with protein product		102545		ACTL3, ACTA3		1710027, 1673027	Standard	NM_001199893		Approved	ACTSG	uc002sjw.3	P63267	OTTHUMG00000129813	ENST00000409624.1:c.456C>T	2.37:g.74140616C>T		144	0	0		137	66	0.481752	NM_001615	B2R7E7|B4E315|D6W5H8|E9PG30|P12718|Q504R1|Q6FI22	Silent	SNP	ENST00000409624.1	37	CCDS1930.1																																																																																			C|0.976;T|0.024	0.024	strong		0.507	ACTG2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328086.1	NM_001615		T	74140616	C	T	74140616	2	4	22	1	0	0	0	0	0	0	0	1	197	874	31	1		1	ACTG2	2	74140616	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	272170	74140616	169058757	594	3495											
DGUOK	1716	hgsc.bcm.edu	37	chr2	74174013	74174013	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aagccagtacagatctttgaGaggtctgtgtacagtgacag	12	10	12	7	0	2	3	0	2	2	2	2	4	2	3	1	1	3	2	1	1	3	3	rs1804599	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74174013G>A	ENST00000264093.4	+	3	508	c.423G>A	c.(421-423)gaG>gaA	p.E141E	DGUOK_ENST00000462685.1_3'UTR|DGUOK_ENST00000348222.1_Silent_p.E141E|DGUOK_ENST00000356837.6_Silent_p.E119E|DGUOK-AS1_ENST00000453103.1_RNA	NM_080916.2	NP_550438.1	Q16854	DGUOK_HUMAN	deoxyguanosine kinase	141					deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|dGTP metabolic process (GO:0046070)|guanosine metabolic process (GO:0008617)|negative regulation of neuron projection development (GO:0010977)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|protein phosphorylation (GO:0006468)|purine deoxyribonucleoside metabolic process (GO:0046122)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|deoxyguanosine kinase activity (GO:0004138)|nucleoside kinase activity (GO:0019206)			endometrium(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	8					Nelarabine(DB01280)	AGATCTTTGAGAGGTCTGTGT	0.507													G|||	89	0.0177716	0.0613	0.0115	5008	,	,		17020	0.0		0.0	False		,,,				2504	0.0				p.E141E		Atlas-SNP	.											.	DGUOK	16	.	0			c.G423A						PASS	.	G	,	197,4209	124.1+/-161.4	6,185,2012	49	43	45		423,423	4.8	1	2	dbSNP_89	45	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	DGUOK	NM_080916.1,NM_080918.1	,	6,187,6310	AA,AG,GG		0.0233,4.4712,1.5301	,	141/278,141/190	74174013	199,12807	2203	4300	6503	SO:0001819	synonymous_variant	1716	exon3			CTTTGAGAGGTCT	U41668	CCDS1931.1, CCDS1932.1	2p13	2008-02-05			ENSG00000114956	ENSG00000114956	2.7.1.113		2858	protein-coding gene	gene with protein product		601465					Standard	NM_080916		Approved	dGK	uc002sjx.3	Q16854	OTTHUMG00000129819	ENST00000264093.4:c.423G>A	2.37:g.74174013G>A		64	0	0		70	38	0.542857	NM_080918	P78532|Q16759|Q4ZG09|Q7L1W9|Q96BC1	Silent	SNP	ENST00000264093.4	37	CCDS1931.1																																																																																			G|0.986;A|0.014	0.014	strong		0.507	DGUOK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252050.1			A	74174013	G	A	74174013	2	1	22	1	0	0	0	0	0	0	0	1	4477	933	33	2		2	DGUOK	2	74174013	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	33397	74174013	169025360	595	3496											
TET3	200424	hgsc.bcm.edu	37	chr2	74275174	74275174	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gatgacaagctggaagagctCatccggcagtttgaggctga	11	8	14	8	1	1	4	1	3	0	1	2	6	2	5	1	3	2	5	1	3	2	1	rs73951129	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74275174C>T	ENST00000409262.3	+	1	1725	c.1725C>T	c.(1723-1725)ctC>ctT	p.L575L		NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3	575					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						TGGAAGAGCTCATCCGGCAGT	0.602													C|||	79	0.0157748	0.0582	0.0	5008	,	,		17465	0.001		0.001	False		,,,				2504	0.0				p.L575L		Atlas-SNP	.											.	TET3	101	.	0			c.C1725T						PASS	.	C		157,3687		4,149,1769	41	45	43		1725	4.5	1	2	dbSNP_130	43	1,8255		0,1,4127	no	coding-synonymous	TET3	NM_144993.1		4,150,5896	TT,TC,CC		0.0121,4.0843,1.3058		575/1661	74275174	158,11942	1922	4128	6050	SO:0001819	synonymous_variant	200424	exon1			AGAGCTCATCCGG		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.1725C>T	2.37:g.74275174C>T		121	0	0		121	65	0.53719	NM_144993	A6NEI3|Q86Z24|Q8TBM9	Silent	SNP	ENST00000409262.3	37	CCDS46339.1																																																																																			C|0.984;T|0.016	0.016	strong		0.602	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328141.4			T	74275174	C	T	74275174	2	4	22	1	0	0	0	0	0	0	0	1	15786	813	29	2		2	TET3	2	74275174	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	101161	74275174	168924199	596	3497											
DCTN1	1639	hgsc.bcm.edu	37	chr2	74593482	74593482	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgcagacactcataggggctGctggagggggtcccatagat	9	7	15	10	1	1	2	1	0	0	2	2	3	2	3	1	5	1	3	1	5	2	2	rs140986485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74593482G>A	ENST00000361874.3	-	23	2966	c.2649C>T	c.(2647-2649)agC>agT	p.S883S	DCTN1_ENST00000409240.1_Silent_p.S846S|DCTN1_ENST00000407639.2_Silent_p.S749S|DCTN1_ENST00000409567.3_Silent_p.S863S|DCTN1_ENST00000409438.1_Silent_p.S749S|DCTN1_ENST00000495643.1_5'UTR|DCTN1_ENST00000409868.1_Silent_p.S866S|DCTN1_ENST00000394003.3_Silent_p.S876S|RP11-287D1.3_ENST00000451608.2_5'Flank	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	883					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						CATAGGGGCTGCTGGAGGGGG	0.582													G|||	13	0.00259585	0.0098	0.0	5008	,	,		18862	0.0		0.0	False		,,,				2504	0.0				p.S883S		Atlas-SNP	.											.	DCTN1	110	.	0			c.C2649T						PASS	.	G	,,,,,	26,4380	32.6+/-62.9	0,26,2177	50	54	53		2589,2247,2538,2628,2649,2247	5.4	1	2	dbSNP_134	53	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DCTN1	NM_001135040.2,NM_001135041.2,NM_001190836.1,NM_001190837.1,NM_004082.4,NM_023019.3	,,,,,	0,26,6477	AA,AG,GG		0.0,0.5901,0.1999	,,,,,	863/1254,749/1140,846/1237,876/1272,883/1279,749/1145	74593482	26,12980	2203	4300	6503	SO:0001819	synonymous_variant	1639	exon23			GGGGCTGCTGGAG		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.2649C>T	2.37:g.74593482G>A		140	0	0		138	64	0.463768	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Silent	SNP	ENST00000361874.3	37	CCDS1939.1																																																																																			G|0.997;A|0.003	0.003	strong		0.582	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082		A	74593482	G	A	74593482	2	1	22	1	0	0	0	0	0	0	0	1	4308	1310	46	2		2	DCTN1	2	74593482	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	318308	74593482	168605891	597	3498											
DCTN1	1639	hgsc.bcm.edu	37	chr2	74596321	74596321	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagatgcttcctgctggttTgtcagttcccgattcacatc	7	14	8	12	1	2	1	2	0	0	1	5	2	4	1	2	1	2	4	2	1	0	4	rs13429423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74596321T>C	ENST00000361874.3	-	15	1922	c.1605A>G	c.(1603-1605)acA>acG	p.T535T	DCTN1_ENST00000409240.1_Silent_p.T498T|DCTN1_ENST00000407639.2_Silent_p.T401T|DCTN1_ENST00000409567.3_Silent_p.T515T|DCTN1_ENST00000409438.1_Silent_p.T401T|DCTN1_ENST00000495643.1_5'Flank|DCTN1_ENST00000409868.1_Silent_p.T518T|DCTN1_ENST00000394003.3_Silent_p.T528T	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	535					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						CCTGCTGGTTTGTCAGTTCCC	0.532													T|||	222	0.0443291	0.1611	0.013	5008	,	,		20259	0.0		0.0	False		,,,				2504	0.0				p.T535T		Atlas-SNP	.											.	DCTN1	110	.	0			c.A1605G						PASS	.	T	,,,,,	590,3816	259.5+/-263.1	37,516,1650	137	126	130		1545,1203,1494,1584,1605,1203	-3.8	1	2	dbSNP_121	130	6,8594	3.7+/-12.6	0,6,4294	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DCTN1	NM_001135040.2,NM_001135041.2,NM_001190836.1,NM_001190837.1,NM_004082.4,NM_023019.3	,,,,,	37,522,5944	CC,CT,TT		0.0698,13.3908,4.5825	,,,,,	515/1254,401/1140,498/1237,528/1272,535/1279,401/1145	74596321	596,12410	2203	4300	6503	SO:0001819	synonymous_variant	1639	exon15			CTGGTTTGTCAGT		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.1605A>G	2.37:g.74596321T>C		252	0	0		305	151	0.495082	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Silent	SNP	ENST00000361874.3	37	CCDS1939.1																																																																																			T|0.956;C|0.044	0.044	strong		0.532	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082		C	74596321	T	C	74596321	2	2	22	1	0	0	0	0	0	0	0	1	4308	1799	63	3		3	DCTN1	2	74596321	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2839	74596321	168603052	598	3499											
DCTN1	1639	hgsc.bcm.edu	37	chr2	74597937	74597937	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atagcgttcctttgcctccaGcgcctccttggcttcctgag	4	13	9	15	2	0	1	0	1	0	0	4	1	4	1	6	1	3	2	6	1	1	5	rs13420401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74597937G>T	ENST00000361874.3	-	10	1176	c.859C>A	c.(859-861)Ctg>Atg	p.L287M	DCTN1_ENST00000409240.1_Missense_Mutation_p.L250M|DCTN1_ENST00000407639.2_Missense_Mutation_p.L153M|DCTN1_ENST00000409567.3_Missense_Mutation_p.L267M|DCTN1_ENST00000409438.1_Missense_Mutation_p.L153M|DCTN1_ENST00000495643.1_5'Flank|DCTN1_ENST00000409868.1_Missense_Mutation_p.L270M|DCTN1_ENST00000394003.3_Missense_Mutation_p.L280M	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	287			L -> M (in dbSNP:rs13420401).		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						TTTGCCTCCAGCGCCTCCTTG	0.567													G|||	229	0.0457268	0.1649	0.0159	5008	,	,		21252	0.0		0.0	False		,,,				2504	0.0				p.L287M		Atlas-SNP	.											.	DCTN1	110	.	0			c.C859A						PASS	.	G	MET/LEU,MET/LEU,MET/LEU,MET/LEU,MET/LEU,MET/LEU	604,3802	264.1+/-265.8	38,528,1637	99	96	97		799,457,748,838,859,457	3.5	0.7	2	dbSNP_121	97	6,8594	3.7+/-12.6	0,6,4294	yes	missense,missense,missense,missense,missense,missense	DCTN1	NM_001135040.2,NM_001135041.2,NM_001190836.1,NM_001190837.1,NM_004082.4,NM_023019.3	15,15,15,15,15,15	38,534,5931	TT,TG,GG		0.0698,13.7086,4.6901	benign,benign,benign,benign,benign,benign	267/1254,153/1140,250/1237,280/1272,287/1279,153/1145	74597937	610,12396	2203	4300	6503	SO:0001583	missense	1639	exon10			CCTCCAGCGCCTC		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.859C>A	2.37:g.74597937G>T	ENSP00000354791:p.Leu287Met	113	0	0		138	73	0.528986	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Missense_Mutation	SNP	ENST00000361874.3	37	CCDS1939.1	85	0.03891941391941392	79	0.16056910569105692	6	0.016574585635359115	0	0.0	0	0.0	G	10.70	1.423353	0.25639	0.137086	6.98E-4	ENSG00000204843	ENST00000361874;ENST00000394003;ENST00000393999;ENST00000407639;ENST00000409438;ENST00000409240;ENST00000409868;ENST00000409567	T;T;T;T;T;T;T	0.79845	-0.86;-1.08;-0.79;-0.79;-1.31;-1.04;-1.09	5.66	3.48	0.39840	.	0.000000	0.33792	N	0.004541	T	0.00784	0.0026	M	0.75264	2.295	0.30403	P	0.7798160000000001	B;B;B;B;P;B	0.35575	0.204;0.245;0.034;0.129;0.51;0.057	B;B;B;B;B;B	0.32624	0.049;0.049;0.007;0.043;0.149;0.015	T	0.37798	-0.9690	9	0.33940	T	0.23	-5.9903	8.5044	0.33179	0.0832:0.0:0.6425:0.2743	rs13420401;rs58339203	267;250;287;280;153;153	E9PGE1;E9PFS5;Q14203;A8MY36;Q14203-2;G5E9H4	.;.;DCTN1_HUMAN;.;.;.	M	287;280;270;153;153;250;270;267	ENSP00000354791:L287M;ENSP00000377571:L280M;ENSP00000384844:L153M;ENSP00000387270:L153M;ENSP00000386406:L250M;ENSP00000387327:L270M;ENSP00000386843:L267M	ENSP00000354791:L287M	L	-	1	2	DCTN1	74451445	0.680000	0.27605	0.708000	0.30435	0.947000	0.59692	0.896000	0.28377	1.345000	0.45676	0.655000	0.94253	CTG	G|0.954;T|0.046	0.046	strong		0.567	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082		T	74597937	G	T	74597937	3	4	22	1	0	0	0	0	1	0	0	0	4308	962	34	4	3069	4	DCTN1	2	74597937	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1616	74597937	168601436	599	3500											
MOGS	7841	hgsc.bcm.edu	37	chr2	74688884	74688884	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgcagttgaggttggggccGacccaccacccgaacgagcc	8	5	13	15	3	0	1	0	1	0	0	0	4	0	1	5	3	3	3	5	3	1	2	rs13405869	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74688884G>A	ENST00000233616.4	-	4	2194	c.2032C>T	c.(2032-2034)Cgg>Tgg	p.R678W	MOGS_ENST00000452063.2_Missense_Mutation_p.R572W|MOGS_ENST00000462443.1_5'Flank|MOGS_ENST00000409065.1_3'UTR	NM_006302.2	NP_006293.2	Q13724	MOGS_HUMAN	mannosyl-oligosaccharide glucosidase	678					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						GGTTGGGGCCGACCCACCACC	0.597													G|||	133	0.0265575	0.0961	0.0086	5008	,	,		18324	0.0		0.0	False		,,,				2504	0.0				p.R678W		Atlas-SNP	.											.	MOGS	58	.	0			c.C2032T						PASS	.	G	TRP/ARG,TRP/ARG	309,3659		17,275,1692	64	76	72		1714,2032	-0.3	0.9	2	dbSNP_121	72	3,8293		0,3,4145	yes	missense,missense	MOGS	NM_001146158.1,NM_006302.2	101,101	17,278,5837	AA,AG,GG		0.0362,7.7873,2.544	probably-damaging,probably-damaging	572/732,678/838	74688884	312,11952	1984	4148	6132	SO:0001583	missense	7841	exon4			GGGGCCGACCCAC	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.2032C>T	2.37:g.74688884G>A	ENSP00000233616:p.Arg678Trp	126	0	0		118	47	0.398305	NM_006302	A8K938|F5H6D0|Q17RN9|Q8TCT5	Missense_Mutation	SNP	ENST00000233616.4	37	CCDS42700.1	63	0.028846153846153848	59	0.11991869918699187	4	0.011049723756906077	0	0.0	0	0.0	G	8.207	0.799569	0.16397	0.077873	3.62E-4	ENSG00000115275	ENST00000233616;ENST00000452063	T;T	0.39406	1.08;1.08	5.01	-0.259	0.12971	Six-hairpin glycosidase-like (1);	0.118143	0.52532	N	0.000072	T	0.01124	0.0037	M	0.61703	1.905	0.09310	P	0.999999999995561	D	0.89917	1.0	D	0.81914	0.995	T	0.21621	-1.0240	9	0.52906	T	0.07	-11.998	8.8519	0.35206	0.0776:0.0:0.271:0.6514	rs13405869	678	Q13724	MOGS_HUMAN	W	678;572	ENSP00000233616:R678W;ENSP00000388201:R572W	ENSP00000233616:R678W	R	-	1	2	MOGS	74542392	0.955000	0.32602	0.865000	0.33974	0.148000	0.21650	0.271000	0.18626	-0.231000	0.09825	-2.140000	0.00339	CGG	G|0.980;A|0.020	0.020	strong		0.597	MOGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328382.1	NM_006302		A	74688884	G	A	74688884	3	1	22	1	0	0	0	0	1	0	0	0	9706	1057	37	1	485	1	MOGS	2	74688884	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	90947	74688884	168510489	600	3501											
CCDC142	84865	hgsc.bcm.edu	37	chr2	74708453	74708453	+	Silent	SNP	A	A	T																															gcagtgccagaggatgtgggAaggctgctctgacccccaag																								rs115125840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74708453A>T	ENST00000393965.3	-	3	1551	c.1155T>A	c.(1153-1155)ctT>ctA	p.L385L	TTC31_ENST00000442235.2_5'Flank|CCDC142_ENST00000290418.4_Silent_p.L385L|TTC31_ENST00000410003.1_5'Flank|TTC31_ENST00000233623.5_5'Flank|CCDC142_ENST00000471713.1_5'UTR	NM_032779.3	NP_116168.3	Q17RM4	CC142_HUMAN	coiled-coil domain containing 142	385										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	16						AGGATGTGGGAAGGCTGCTCT	0.557													A|||	19	0.00379393	0.0144	0.0	5008	,	,		19536	0.0		0.0	False		,,,				2504	0.0				p.L385L		Atlas-SNP	.											.	CCDC142	40	.	0			c.T1155A						PASS	.	A		32,4374	37.6+/-69.7	0,32,2171	111	126	121		1155	-2.6	0	2	dbSNP_132	121	0,8600		0,0,4300	no	coding-synonymous	CCDC142	NM_032779.3		0,32,6471	TT,TA,AA		0.0,0.7263,0.246		385/744	74708453	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	84865	exon3			TGTGGGAAGGCTG	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.1155T>A	2.37:g.74708453A>T		173	0	0		144	56	0.388889	NM_032779	B7ZKV5|Q8NBJ3|Q8NBV2|Q96KA7	Silent	SNP	ENST00000393965.3	37																																																																																				A|0.997;T|0.003	0.003	strong		0.557	CCDC142-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000328391.1	NM_032779		T	74708453	A	T	74708453	2	4	22	1	0	0	0	0	0	0	0	1	2778	233	9	5		5	CCDC142	2	74708453	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	19569	74708453	168490920	601	3502	50	2									
CCDC142	84865	hgsc.bcm.edu	37	chr2	74708454	74708454	+	Missense_Mutation	SNP	A	A	C																															cagtgccagaggatgtgggaAggctgctctgacccccaaga																								rs142978072	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74708454A>C	ENST00000393965.3	-	3	1550	c.1154T>G	c.(1153-1155)cTt>cGt	p.L385R	TTC31_ENST00000442235.2_5'Flank|CCDC142_ENST00000290418.4_Missense_Mutation_p.L385R|TTC31_ENST00000410003.1_5'Flank|TTC31_ENST00000233623.5_5'Flank|CCDC142_ENST00000471713.1_5'UTR	NM_032779.3	NP_116168.3	Q17RM4	CC142_HUMAN	coiled-coil domain containing 142	385										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	16						GGATGTGGGAAGGCTGCTCTG	0.552													A|||	19	0.00379393	0.0144	0.0	5008	,	,		19474	0.0		0.0	False		,,,				2504	0.0				p.L385R		Atlas-SNP	.											.	CCDC142	40	.	0			c.T1154G						PASS	.	A	ARG/LEU	32,4374	37.6+/-69.7	0,32,2171	111	127	121		1154	-2	0.1	2	dbSNP_134	121	0,8600		0,0,4300	yes	missense	CCDC142	NM_032779.3	102	0,32,6471	CC,CA,AA		0.0,0.7263,0.246	possibly-damaging	385/744	74708454	32,12974	2203	4300	6503	SO:0001583	missense	84865	exon3			GTGGGAAGGCTGC	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.1154T>G	2.37:g.74708454A>C	ENSP00000377537:p.Leu385Arg	175	0	0		145	56	0.386207	NM_032779	B7ZKV5|Q8NBJ3|Q8NBV2|Q96KA7	Missense_Mutation	SNP	ENST00000393965.3	37		6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	A	2.527	-0.309466	0.05458	0.007263	0.0	ENSG00000135637	ENST00000393965;ENST00000290418	T;T	0.43688	0.94;0.94	4.74	-2.0	0.07433	.	1.069320	0.07370	N	0.885599	T	0.32376	0.0827	L	0.41236	1.265	0.09310	N	1	P;P;P	0.47677	0.899;0.899;0.899	P;P;P	0.51355	0.466;0.466;0.667	T	0.36578	-0.9742	10	0.52906	T	0.07	0.0723	5.5768	0.17228	0.3761:0.1645:0.4594:0.0	.	385;385;385	Q17RM4;Q17RM4-2;Q17RM4-3	CC142_HUMAN;.;.	R	385	ENSP00000377537:L385R;ENSP00000290418:L385R	ENSP00000290418:L385R	L	-	2	0	CCDC142	74561962	0.003000	0.15002	0.052000	0.19188	0.399000	0.30720	0.052000	0.14163	-0.208000	0.10171	0.460000	0.39030	CTT	A|0.997;C|0.003	0.003	strong		0.552	CCDC142-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000328391.1	NM_032779		C	74708454	A	C	74708454	3	2	22	1	0	0	0	0	1	0	0	0	2778	72	3	5	1105	5	CCDC142	2	74708454	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1	74708454	168490919	602	3503	50	2									
HK2	3099	hgsc.bcm.edu	37	chr2	75107671	75107671	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtcaagatgctgcccacctaCgtgtgtgctaccccggacgg	7	8	12	14	3	1	1	1	0	0	1	1	2	1	2	4	2	5	2	4	2	3	2	rs28363033	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:75107671C>T	ENST00000290573.2	+	10	2145	c.1545C>T	c.(1543-1545)taC>taT	p.Y515Y	HK2_ENST00000409174.1_Silent_p.Y487Y	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	515	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						TGCCCACCTACGTGTGTGCTA	0.597													C|||	56	0.0111821	0.0393	0.0043	5008	,	,		19072	0.0		0.001	False		,,,				2504	0.0				p.Y515Y		Atlas-SNP	.											.	HK2	85	.	0			c.C1545T						PASS	.	C		155,4251	107.3+/-145.7	4,147,2052	64	63	63		1545	-4	0.9	2	dbSNP_125	63	0,8600		0,0,4300	no	coding-synonymous	HK2	NM_000189.4		4,147,6352	TT,TC,CC		0.0,3.5179,1.1918		515/918	75107671	155,12851	2203	4300	6503	SO:0001819	synonymous_variant	3099	exon10			CACCTACGTGTGT		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.1545C>T	2.37:g.75107671C>T		129	0	0		163	62	0.380368	NM_000189	D6W5J2|Q8WU87|Q9UN82	Silent	SNP	ENST00000290573.2	37	CCDS1956.1																																																																																			C|0.988;T|0.012	0.012	strong		0.597	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2	NM_000189		T	75107671	C	T	75107671	2	4	22	1	0	0	0	0	0	0	0	1	7200	547	19	1		1	HK2	2	75107671	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	399217	75107671	168091702	603	3504											
LRRTM1	347730	hgsc.bcm.edu	37	chr2	80529706	80529706	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcggcgtgctcgccgcctggAagagccacggtggcaggctc	5	6	16	14	5	0	1	0	0	0	1	3	2	0	2	3	5	2	3	3	5	1	0	rs35054232	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:80529706A>G	ENST00000295057.3	-	2	1895	c.1239T>C	c.(1237-1239)ctT>ctC	p.L413L	CTNNA2_ENST00000540488.1_Intron|CTNNA2_ENST00000466387.1_Intron|CTNNA2_ENST00000541047.1_Intron|CTNNA2_ENST00000402739.4_Intron|LRRTM1_ENST00000409148.1_Silent_p.L413L|CTNNA2_ENST00000361291.4_Intron|CTNNA2_ENST00000496558.1_Intron	NM_178839.4	NP_849161.2	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	413					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						CGCCGCCTGGAAGAGCCACGG	0.682										HNSCC(69;0.2)			G|||	228	0.0455272	0.1604	0.0115	5008	,	,		16729	0.004		0.001	False		,,,				2504	0.0031				p.L413L		Atlas-SNP	.											.	LRRTM1	251	.	0			c.T1239C						PASS	.	G	,,	569,3833	754.3+/-412.4	41,487,1673	49	45	47		,,1239	2	1	2	dbSNP_126	47	37,8557	806.0+/-407.3	0,37,4260	no	intron,intron,coding-synonymous	CTNNA2,LRRTM1	NM_001164883.1,NM_004389.3,NM_178839.4	,,	41,524,5933	GG,GA,AA		0.4305,12.9259,4.663	,,	,,413/523	80529706	606,12390	2201	4297	6498	SO:0001819	synonymous_variant	347730	exon2			GCCTGGAAGAGCC	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.1239T>C	2.37:g.80529706A>G		33	0	0		37	13	0.351351	NM_178839	A8K397|D6W5K1|Q96DN1	Silent	SNP	ENST00000295057.3	37	CCDS1966.1																																																																																			A|0.958;G|0.042	0.042	strong		0.682	LRRTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313614.1	NM_178839		G	80529706	A	G	80529706	2	3	22	1	0	0	0	0	0	0	0	1	9048	233	9	3		3	LRRTM1	2	80529706	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	5422035	80529706	162669667	604	3505											
CTNNA2	1496	hgsc.bcm.edu	37	chr2	80620370	80620370	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaaaggagatcctctcaacaTtgcgattgataagatgacta	16	10	8	7	1	1	4	1	2	1	2	3	6	2	4	1	1	2	0	1	1	5	4	rs61754542	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:80620370T>C	ENST00000402739.4	+	7	1096	c.1091T>C	c.(1090-1092)aTt>aCt	p.I364T	CTNNA2_ENST00000540488.1_Missense_Mutation_p.I364T|CTNNA2_ENST00000466387.1_Missense_Mutation_p.I364T|CTNNA2_ENST00000343114.3_Missense_Mutation_p.I43T|CTNNA2_ENST00000541047.1_Missense_Mutation_p.I364T|CTNNA2_ENST00000361291.4_Missense_Mutation_p.I398T|CTNNA2_ENST00000496558.1_Missense_Mutation_p.I364T	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	364					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						CCTCTCAACATTGCGATTGAT	0.294													T|||	69	0.013778	0.0499	0.0014	5008	,	,		16684	0.0		0.001	False		,,,				2504	0.001				p.I364T		Atlas-SNP	.											.	CTNNA2	462	.	0			c.T1091C						PASS	.	T	THR/ILE,THR/ILE	161,3487		4,153,1667	99	93	95		1091,1091	5.9	1	2	dbSNP_129	95	4,8156		0,4,4076	yes	missense,missense	CTNNA2	NM_001164883.1,NM_004389.3	89,89	4,157,5743	CC,CT,TT		0.049,4.4134,1.3974	benign,benign	364/861,364/906	80620370	165,11643	1824	4080	5904	SO:0001583	missense	1496	exon8			TCAACATTGCGAT		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.1091T>C	2.37:g.80620370T>C	ENSP00000384638:p.Ile364Thr	237	0	0		227	93	0.409692	NM_001164883	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Missense_Mutation	SNP	ENST00000402739.4	37		24	0.01098901098901099	23	0.046747967479674794	0	0.0	0	0.0	1	0.0013192612137203166	T	8.517	0.867937	0.17250	0.044134	4.9E-4	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488;ENST00000343114;ENST00000409550	T;T;T;T;T;T;T;T	0.35789	1.29;1.29;1.29;1.29;1.29;1.29;2.59;1.3	5.88	5.88	0.94601	.	0.135082	0.52532	D	0.000073	T	0.02342	0.0072	N	0.02142	-0.665	0.37091	D	0.89945	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.16808	-1.0390	9	.	.	.	.	15.9407	0.79750	0.0:0.0:0.0:1.0	rs61754542	364;364;364	P26232;P26232-3;P26232-2	CTNA2_HUMAN;.;.	T	364;364;398;364;364;364;43;29	ENSP00000418191:I364T;ENSP00000419295:I364T;ENSP00000355398:I398T;ENSP00000384638:I364T;ENSP00000444675:I364T;ENSP00000441705:I364T;ENSP00000341500:I43T;ENSP00000386587:I29T	.	I	+	2	0	CTNNA2	80473881	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	2.197000	0.42696	2.243000	0.73865	0.533000	0.62120	ATT	T|0.992;C|0.008	0.008	strong		0.294	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389		C	80620370	T	C	80620370	3	2	22	1	0	0	0	0	1	0	0	0	4015	1493	52	3	909	3	CTNNA2	2	80620370	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	90664	80620370	162579003	605	3506											
DNAH6	1768	hgsc.bcm.edu	37	chr2	84752784	84752784	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaggaatcattaaacgtccAgtaagcatagcaaaaaaaag	20	6	8	7	1	1	0	1	0	0	0	2	1	2	1	1	1	3	4	1	1	9	3	rs73945104	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:84752784A>C	ENST00000237449.6	+	2	329	c.321A>C	c.(319-321)ccA>ccC	p.P107P	DNAH6_ENST00000468661.1_3'UTR|DNAH6_ENST00000389394.3_Silent_p.P107P|DNAH6_ENST00000398278.2_Silent_p.P107P			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	107	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						TTAAACGTCCAGTAAGCATAG	0.348													A|||	65	0.0129792	0.0477	0.0029	5008	,	,		16979	0.0		0.0	False		,,,				2504	0.0				p.P107P		Atlas-SNP	.											.	DNAH6	194	.	0			c.A321C						PASS	.						114	92	98					2																	84752784		692	1591	2283	SO:0001819	synonymous_variant	1768	exon3			ACGTCCAGTAAGC	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.321A>C	2.37:g.84752784A>C		277	0	0		261	130	0.498084	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	37	CCDS46348.1																																																																																			A|0.989;C|0.011	0.011	strong		0.348	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		C	84752784	A	C	84752784	2	2	22	1	0	0	0	0	0	0	0	1	4607	175	7	5		5	DNAH6	2	84752784	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	4132414	84752784	158446589	606	3507											
DNAH6	1768	hgsc.bcm.edu	37	chr2	84924783	84924783	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tatttgaaaaggatgaactgGagcaggttttagcggccacc	12	10	12	7	1	0	2	0	2	0	0	0	4	0	4	2	4	3	2	2	4	5	4	rs73943384	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:84924783G>C	ENST00000237449.6	+	46	7617	c.7609G>C	c.(7609-7611)Gag>Cag	p.E2537Q	DNAH6_ENST00000389394.3_Missense_Mutation_p.E2537Q|DNAH6_ENST00000398278.2_Missense_Mutation_p.E2488Q|DNAH6_ENST00000602588.1_Missense_Mutation_p.E509Q			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	2537	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						GGATGAACTGGAGCAGGTTTT	0.428													G|||	68	0.0135783	0.0499	0.0029	5008	,	,		16198	0.0		0.0	False		,,,				2504	0.0				p.E2537Q		Atlas-SNP	.											.	DNAH6	194	.	0			c.G7609C						PASS	.	G	GLN/GLU	42,1342		0,42,650	138	126	130		7609	5.7	1	2	dbSNP_130	130	1,3181		0,1,1590	yes	missense	DNAH6	NM_001370.1	29	0,43,2240	CC,CG,GG		0.0314,3.0347,0.9417	probably-damaging	2537/4159	84924783	43,4523	692	1591	2283	SO:0001583	missense	1768	exon47			GAACTGGAGCAGG	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.7609G>C	2.37:g.84924783G>C	ENSP00000237449:p.Glu2537Gln	77	0	0		75	37	0.493333	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	37	CCDS46348.1	23	0.010531135531135532	21	0.042682926829268296	2	0.0055248618784530384	0	0.0	0	0.0	G	25.4	4.630590	0.87660	0.030347	3.14E-4	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.56103	0.73;0.48;0.73	5.67	5.67	0.87782	Dynein heavy chain, P-loop containing D4 domain (1);ATPase, AAA+ type, core (1);	.	.	.	.	T	0.38401	0.1039	L	0.57130	1.785	0.47949	D	0.999553	D;D	0.67145	0.996;0.99	D;D	0.70716	0.97;0.962	T	0.57751	-0.7757	9	0.49607	T	0.09	.	18.5426	0.91035	0.0:0.0:1.0:0.0	.	2537;2488	Q9C0G6;Q9C0G6-4	DYH6_HUMAN;.	Q	2537;2488;2537	ENSP00000374045:E2537Q;ENSP00000381326:E2488Q;ENSP00000237449:E2537Q	ENSP00000237449:E2537Q	E	+	1	0	DNAH6	84778294	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	4.379000	0.59575	2.682000	0.91365	0.484000	0.47621	GAG	G|0.989;C|0.011	0.011	strong		0.428	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		C	84924783	G	C	84924783	3	2	22	1	0	0	0	0	1	0	0	0	4607	1175	41	4	7791	4	DNAH6	2	84924783	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	171999	84924783	158274590	607	3508											
TCF7L1	83439	hgsc.bcm.edu	37	chr2	85510654	85510654	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcccctcctcgatgtccccTccagcgccacagtcaaggac	7	6	9	19	2	1	0	1	0	0	0	5	2	4	1	7	2	1	0	7	2	1	0	rs115942112	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:85510654T>A	ENST00000282111.3	+	4	753	c.478T>A	c.(478-480)Tcc>Acc	p.S160T		NM_031283.2	NP_112573.1	Q9HCS4	TF7L1_HUMAN	transcription factor 7-like 1 (T-cell specific, HMG-box)	160	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(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|skin(4)|upper_aerodigestive_tract(1)	18						CGATGTCCCCTCCAGCGCCAC	0.507													T|||	60	0.0119808	0.0393	0.0	5008	,	,		20302	0.005		0.0	False		,,,				2504	0.0031				p.S160T		Atlas-SNP	.											.	TCF7L1	44	.	0			c.T478A						PASS	.	T	THR/SER	134,4272	97.1+/-135.8	1,132,2070	257	224	235		478	3.1	1	2	dbSNP_132	235	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TCF7L1	NM_031283.2	58	1,133,6369	AA,AT,TT		0.0116,3.0413,1.038	benign	160/589	85510654	135,12871	2203	4300	6503	SO:0001583	missense	83439	exon4			GTCCCCTCCAGCG	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.478T>A	2.37:g.85510654T>A	ENSP00000282111:p.Ser160Thr	106	0	0		131	57	0.435115	NM_031283	Q53R97|Q6PD70|Q9NP00	Missense_Mutation	SNP	ENST00000282111.3	37	CCDS1971.1	21	0.009615384615384616	21	0.042682926829268296	0	0.0	0	0.0	0	0.0	T	12.34	1.910078	0.33721	0.030413	1.16E-4	ENSG00000152284	ENST00000282111;ENST00000442813	D	0.98550	-4.99	5.44	3.08	0.35506	CTNNB1 binding, N-teminal (1);	0.586502	0.18208	N	0.148291	D	0.83608	0.5291	N	0.22421	0.69	0.26675	N	0.971648	B	0.33000	0.393	B	0.34536	0.185	D	0.84356	0.0535	10	0.56958	D	0.05	.	5.5742	0.17215	0.0:0.09:0.1841:0.7258	.	160	Q9HCS4	TF7L1_HUMAN	T	160;10	ENSP00000282111:S160T	ENSP00000282111:S160T	S	+	1	0	TCF7L1	85364165	0.989000	0.36119	0.998000	0.56505	0.988000	0.76386	0.065000	0.14466	0.382000	0.24878	0.533000	0.62120	TCC	T|0.989;A|0.011	0.011	strong		0.507	TCF7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252301.2	NM_031283		A	85510654	T	A	85510654	3	1	22	1	0	0	0	0	1	0	0	0	15712	1551	54	5	492	5	TCF7L1	2	85510654	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	585871	85510654	157688719	608	3509											
RETSAT	54884	hgsc.bcm.edu	37	chr2	85570440	85570440	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tacaagttccgcttcaggatGgcgctgctgcacagcagggc	8	8	13	12	2	1	0	1	0	0	0	2	1	2	1	1	3	4	6	1	3	2	3	rs150706527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:85570440G>A	ENST00000295802.4	-	11	1870	c.1758C>T	c.(1756-1758)gcC>gcT	p.A586A	RETSAT_ENST00000457495.2_Silent_p.A525A|RETSAT_ENST00000263854.6_3'UTR|RETSAT_ENST00000475624.2_5'Flank	NM_017750.3	NP_060220.3	Q6NUM9	RETST_HUMAN	retinol saturase (all-trans-retinol 13,14-reductase)	586					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)	GCTTCAGGATGGCGCTGCTGC	0.552													G|||	17	0.00339457	0.0129	0.0	5008	,	,		32923	0.0		0.0	False		,,,				2504	0.0				p.A586A		Atlas-SNP	.											RETSAT,NS,carcinoma,-2,1	RETSAT	56	1	0			c.C1758T						PASS	.	G		51,4355	50.9+/-86.3	0,51,2152	81	84	83		1758	1.9	1	2	dbSNP_134	83	0,8600		0,0,4300	no	coding-synonymous	RETSAT	NM_017750.3		0,51,6452	AA,AG,GG		0.0,1.1575,0.3921		586/611	85570440	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	54884	exon11			CAGGATGGCGCTG	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.1758C>T	2.37:g.85570440G>A		299	0	0		328	73	0.222561	NM_017750	A6NIK3|Q53R95|Q53SA9|Q6UX05|Q8N2H5|Q96FA4|Q9NXE5	Silent	SNP	ENST00000295802.4	37	CCDS1972.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	7.937	0.741884	0.15642	0.011575	0.0	ENSG00000042445	ENST00000449375	.	.	.	4.89	1.86	0.25419	.	.	.	.	.	T	0.38134	0.1029	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21655	-1.0239	4	.	.	.	-15.1159	4.0777	0.09912	0.1989:0.0:0.6169:0.1842	.	.	.	.	L	375	.	.	P	-	2	0	RETSAT	85423951	0.882000	0.30256	0.993000	0.49108	0.657000	0.38888	0.224000	0.17738	0.579000	0.29504	0.462000	0.41574	CCA	G|0.996;A|0.004	0.004	strong		0.552	RETSAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252489.1	NM_017750		A	85570440	G	A	85570440	2	1	22	1	0	0	0	0	0	0	0	1	13253	1335	47	2		2	RETSAT	2	85570440	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	59786	85570440	157628933	609	3510											
POLR1A	25885	hgsc.bcm.edu	37	chr2	86305404	86305404	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatagcaatcaaagagtcttTttcctggaagatgaaaccaa	17	10	7	7	0	2	3	1	1	1	2	3	4	3	4	2	1	2	1	2	1	7	3	rs35239368	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:86305404T>C	ENST00000263857.6	-	10	1468	c.1090A>G	c.(1090-1092)Aaa>Gaa	p.K364E	POLR1A_ENST00000409681.1_Missense_Mutation_p.K364E			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	364			K -> E (in dbSNP:rs35239368).		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						AAAGAGTCTTTTTCCTGGAAG	0.408													T|||	658	0.13139	0.447	0.036	5008	,	,		19186	0.0		0.003	False		,,,				2504	0.0399				p.K364E		Atlas-SNP	.											.	POLR1A	137	.	0			c.A1090G						PASS	.	T	GLU/LYS	1319,2381		256,807,787	94	84	87		1090	1.3	1	2	dbSNP_126	87	12,8170		0,12,4079	yes	missense	POLR1A	NM_015425.3	56	256,819,4866	CC,CT,TT		0.1467,35.6486,11.2018	benign	364/1721	86305404	1331,10551	1850	4091	5941	SO:0001583	missense	25885	exon10			AGTCTTTTTCCTG	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.1090A>G	2.37:g.86305404T>C	ENSP00000263857:p.Lys364Glu	111	0	0		128	64	0.5	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	ENST00000263857.6	37	CCDS42706.1	212	0.09706959706959707	200	0.4065040650406504	10	0.027624309392265192	0	0.0	2	0.002638522427440633	T	6.764	0.509783	0.12883	0.356486	0.001467	ENSG00000068654	ENST00000263857;ENST00000409681	T;T	0.66280	-0.2;-0.2	5.22	1.33	0.21861	RNA polymerase, N-terminal (1);	1.947470	0.02022	N	0.047881	T	0.00012	0.0000	N	0.02011	-0.69	0.52501	P	4.700000000001925E-5	B;B	0.11235	0.0;0.004	B;B	0.08055	0.001;0.003	T	0.32719	-0.9896	9	0.02654	T	1	-9.8026	6.3055	0.21137	0.1469:0.0:0.4215:0.4317	rs35239368	364;364	B9ZVN9;O95602	.;RPA1_HUMAN	E	364	ENSP00000263857:K364E;ENSP00000386300:K364E	ENSP00000263857:K364E	K	-	1	0	POLR1A	86158915	0.098000	0.21812	0.985000	0.45067	0.766000	0.43426	0.898000	0.28404	0.901000	0.36495	0.459000	0.35465	AAA	T|0.930;C|0.070	0.070	strong		0.408	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425		C	86305404	T	C	86305404	3	2	22	1	0	0	0	0	1	0	0	0	12218	1850	64	3	4172	3	POLR1A	2	86305404	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	734964	86305404	156893969	610	3511											
PTCD3	55037	hgsc.bcm.edu	37	chr2	86358214	86358214	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttcagataagttttttcaGtcagccatgagcatagtaag	12	15	8	6	0	3	2	3	1	0	1	3	2	3	2	1	0	2	3	1	0	3	8	rs146203968		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:86358214G>C	ENST00000254630.7	+	16	1317	c.1251G>C	c.(1249-1251)caG>caC	p.Q417H		NM_017952.5	NP_060422.4	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3	417					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						AGTTTTTTCAGTCAGCCATGA	0.318													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16645	0.0		0.0	False		,,,				2504	0.0				p.Q417H		Atlas-SNP	.											.	PTCD3	51	.	0			c.G1251C						PASS	.	G	HIS/GLN	1,4405	2.1+/-5.4	0,1,2202	78	78	78		1251	1.9	1	2	dbSNP_134	78	0,8592		0,0,4296	no	missense	PTCD3	NM_017952.5	24	0,1,6498	CC,CG,GG		0.0,0.0227,0.0077	benign	417/690	86358214	1,12997	2203	4296	6499	SO:0001583	missense	55037	exon16			TTTTCAGTCAGCC		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.1251G>C	2.37:g.86358214G>C	ENSP00000254630:p.Gln417His	154	0	0		142	65	0.457746	NM_017952	A6NHD2|D6W5M1|Q597H0|Q658Y9|Q9BUZ8|Q9NWL0	Missense_Mutation	SNP	ENST00000254630.7	37	CCDS33235.1	.	.	.	.	.	.	.	.	.	.	G	9.979	1.227623	0.22542	2.27E-4	0.0	ENSG00000132300	ENST00000254630	T	0.31769	1.48	6.16	1.9	0.25705	.	0.469117	0.24400	N	0.038860	T	0.22704	0.0548	L	0.44542	1.39	0.58432	D	0.999994	B;B	0.09022	0.002;0.001	B;B	0.11329	0.006;0.003	T	0.06481	-1.0824	10	0.56958	D	0.05	-1.4753	5.8329	0.18590	0.2275:0.0:0.6349:0.1376	.	8;417	Q96EY7-2;Q96EY7	.;PTCD3_HUMAN	H	417	ENSP00000254630:Q417H	ENSP00000254630:Q417H	Q	+	3	2	PTCD3	86211725	0.976000	0.34144	0.999000	0.59377	0.903000	0.53119	0.568000	0.23623	0.488000	0.27723	-0.158000	0.13435	CAG	G|1.000;C|0.000	0.000	weak		0.318	PTCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329854.1	NM_017952		C	86358214	G	C	86358214	3	2	22	1	0	0	0	0	1	0	0	0	12741	1020	36	4	1313	4	PTCD3	2	86358214	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	52810	86358214	156841159	611	3512											
IMMT	10989	hgsc.bcm.edu	37	chr2	86385812	86385812	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accagctcatgatactgagaTacaaccttagcctcagactg	13	9	7	12	0	2	3	2	2	0	2	2	4	2	3	3	0	5	1	3	0	4	3	rs2228352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:86385812T>C	ENST00000410111.3	-	10	1452	c.1065A>G	c.(1063-1065)gtA>gtG	p.V355V	Y_RNA_ENST00000363371.1_RNA|IMMT_ENST00000490238.1_5'UTR|IMMT_ENST00000409051.2_Silent_p.V308V|IMMT_ENST00000449247.2_Silent_p.V344V|IMMT_ENST00000254636.5_Silent_p.V256V|IMMT_ENST00000442664.2_Silent_p.V354V	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	355					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						GATACTGAGATACAACCTTAG	0.433													T|||	224	0.0447284	0.1331	0.0115	5008	,	,		20269	0.0		0.001	False		,,,				2504	0.0399				p.V355V		Atlas-SNP	.											.	IMMT	65	.	0			c.A1065G						PASS	.	T	,,	366,3392		15,336,1528	60	55	56		1062,1032,1065	-7.7	0.7	2	dbSNP_98	56	3,8249		0,3,4123	no	coding-synonymous,coding-synonymous,coding-synonymous	IMMT	NM_001100169.1,NM_001100170.1,NM_006839.2	,,	15,339,5651	CC,CT,TT		0.0364,9.7392,3.0724	,,	354/758,344/748,355/759	86385812	369,11641	1879	4126	6005	SO:0001819	synonymous_variant	10989	exon10			CTGAGATACAACC	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.1065A>G	2.37:g.86385812T>C		109	0	0		117	50	0.42735	NM_006839	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Silent	SNP	ENST00000410111.3	37	CCDS46355.1	56	0.02564102564102564	51	0.10365853658536585	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	T	9.781	1.175415	0.21704	0.097392	3.64E-4	ENSG00000132305	ENST00000419070	.	.	.	5.76	-7.73	0.01245	.	.	.	.	.	T	0.01940	0.0061	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49011	-0.8983	4	.	.	.	-18.6743	10.0221	0.42048	0.0:0.2774:0.1707:0.5519	rs2228352;rs2228352	.	.	.	V	210	.	.	I	-	1	0	IMMT	86239323	0.003000	0.15002	0.651000	0.29564	0.993000	0.82548	-1.546000	0.02188	-1.085000	0.03088	-0.256000	0.11100	ATC	T|0.968;C|0.032	0.032	strong		0.433	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839		C	86385812	T	C	86385812	2	2	22	1	0	0	0	0	0	0	0	1	7727	1393	49	3		3	IMMT	2	86385812	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	27598	86385812	156813561	612	3513											
KDM3A	55818	hgsc.bcm.edu	37	chr2	86709704	86709704	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	taaccatcaagcccagcattCtgggctttgacactcctcac	10	10	6	15	0	3	1	2	1	1	0	4	1	4	1	3	1	3	2	3	1	2	3	rs34673273	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:86709704C>T	ENST00000409556.1	+	19	3174	c.2809C>T	c.(2809-2811)Ctg>Ttg	p.L937L	KDM3A_ENST00000409064.1_Silent_p.L937L|KDM3A_ENST00000542128.1_Silent_p.L885L|KDM3A_ENST00000312912.5_Silent_p.L937L			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	937					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						gcccagcattctgggctttga	0.443													C|||	122	0.024361	0.09	0.0043	5008	,	,		19735	0.0		0.0	False		,,,				2504	0.0				p.L937L	NSCLC(96;1150 1523 6936 46253 49736)	Atlas-SNP	.											.	KDM3A	179	.	0			c.C2809T						PASS	.	C	,	377,4029	193.3+/-218.5	18,341,1844	126	119	121		2809,2809	3.7	1	2	dbSNP_126	121	1,8599	3.0+/-9.4	0,1,4299	no	coding-synonymous,coding-synonymous	KDM3A	NM_001146688.1,NM_018433.5	,	18,342,6143	TT,TC,CC		0.0116,8.5565,2.9064	,	937/1322,937/1322	86709704	378,12628	2203	4300	6503	SO:0001819	synonymous_variant	55818	exon18			AGCATTCTGGGCT	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.2809C>T	2.37:g.86709704C>T		144	0	0		185	96	0.518919	NM_001146688	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Silent	SNP	ENST00000409556.1	37	CCDS1990.1																																																																																			C|0.969;T|0.031	0.031	strong		0.443	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433		T	86709704	C	T	86709704	2	4	22	1	0	0	0	0	0	0	0	1	8135	912	32	2		2	KDM3A	2	86709704	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	323892	86709704	156489669	613	3514											
CD8B	926	hgsc.bcm.edu	37	chr2	87073817	87073817	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gacaactcacagcacaggtgGatggccactcccagggaaac	13	4	11	13	0	1	0	1	0	0	0	2	3	2	2	2	4	3	1	2	4	2	0	rs1126874		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:87073817G>C	ENST00000390655.6	-	4	631	c.573C>G	c.(571-573)atC>atG	p.I191M	CD8B_ENST00000393761.2_Intron|CD8B_ENST00000331469.2_Missense_Mutation_p.I191M|CD8B_ENST00000393759.2_Missense_Mutation_p.I191M|CD8B_ENST00000349455.3_Intron|CD8B_ENST00000431506.2_Intron	NM_004931.4	NP_004922.1	P10966	CD8B_HUMAN	CD8b molecule	191					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)	p.I191M(2)		NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	13						AGCACAGGTGGATGGCCACTC	0.552																																					p.I191M		Atlas-SNP	.											CD8B_ENST00000393759,NS,carcinoma,0,2	CD8B	37	2	2	Substitution - Missense(2)	kidney(2)	c.C573G						scavenged	.																																			SO:0001583	missense	926	exon4			CAGGTGGATGGCC		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.573C>G	2.37:g.87073817G>C	ENSP00000375070:p.Ile191Met	402	0	0		413	29	0.0702179	NM_004931	P14860|P14861|Q15980|Q496E0|Q496E1|Q496E2|Q9UDB4|Q9UDB5|Q9UDB6|Q9UDB7|Q9UDB8|Q9UDB9|Q9UDC0|Q9UQ55	Missense_Mutation	SNP	ENST00000390655.6	37	CCDS1997.1	.	.	.	.	.	.	.	.	.	.	g	11.44	1.639958	0.29157	.	.	ENSG00000172116	ENST00000393759;ENST00000331469;ENST00000390655;ENST00000445248	.	.	.	4.91	0.92	0.19397	.	0.581228	0.17685	N	0.165462	T	0.30386	0.0763	.	.	.	0.09310	N	0.999999	B;B;B;B	0.33807	0.3;0.3;0.426;0.426	B;B;B;B	0.35278	0.098;0.098;0.199;0.199	T	0.17745	-1.0359	8	0.59425	D	0.04	-3.6541	5.5609	0.17144	0.1776:0.2773:0.545:0.0	.	191;191;191;191	Q53QL8;P10966;P10966-2;P10966-6	.;CD8B_HUMAN;.;.	M	191	.	ENSP00000331172:I191M	I	-	3	3	CD8B	86927328	0.916000	0.31088	0.002000	0.10522	0.678000	0.39670	0.548000	0.23314	0.063000	0.16370	0.655000	0.94253	ATC	.	.	weak		0.552	CD8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330402.1	NM_172099		C	87073817	G	C	87073817	3	2	22	1	0	0	0	0	1	0	0	0	3047	1164	41	4	345	4	CD8B	2	87073817	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	364113	87073817	156125556	614	3515											
SMYD1	150572	hgsc.bcm.edu	37	chr2	88396213	88396213	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaagaacgcaagaggcagctGaagaagcagtactactttga	16	6	12	7	1	0	5	0	2	0	3	0	6	0	5	0	1	5	5	0	1	7	3	rs13403507	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:88396213G>A	ENST00000419482.2	+	6	883	c.798G>A	c.(796-798)ctG>ctA	p.L266L	SMYD1_ENST00000438570.1_Intron|SMYD1_ENST00000444564.2_Silent_p.L253L	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	266					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						AGAGGCAGCTGAAGAAGCAGT	0.493													G|||	44	0.00878594	0.0333	0.0	5008	,	,		22022	0.0		0.0	False		,,,				2504	0.0				p.L266L		Atlas-SNP	.											.	SMYD1	95	.	0			c.G798A						PASS	.	G		105,4301	84.4+/-122.9	0,105,2098	106	98	101		798	-0.6	1	2	dbSNP_121	101	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SMYD1	NM_198274.3		0,106,6397	AA,AG,GG		0.0116,2.3831,0.815		266/491	88396213	106,12900	2203	4300	6503	SO:0001819	synonymous_variant	150572	exon6			GCAGCTGAAGAAG	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.798G>A	2.37:g.88396213G>A		156	0	0		115	58	0.504348	NM_198274	A0AV30|A6NE13	Silent	SNP	ENST00000419482.2	37	CCDS33240.1																																																																																			G|0.992;A|0.008	0.008	strong		0.493	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915		A	88396213	G	A	88396213	2	1	22	1	0	0	0	0	0	0	0	1	14836	1277	45	2		2	SMYD1	2	88396213	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1322396	88396213	154803160	615	3516											
THNSL2	55258	hgsc.bcm.edu	37	chr2	88478341	88478341	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcgatgagccgatcaagaCtgtgtttgccgatgtggctt	7	12	13	9	3	1	2	1	1	0	1	2	5	1	2	2	1	2	3	2	1	1	2	rs34136143	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:88478341C>A	ENST00000324166.5	+	4	2302	c.611C>A	c.(610-612)aCt>aAt	p.T204N	THNSL2_ENST00000496844.1_3'UTR|THNSL2_ENST00000377254.3_Missense_Mutation_p.T204N|THNSL2_ENST00000402102.1_Missense_Mutation_p.T204N|THNSL2_ENST00000358591.2_Missense_Mutation_p.T204N|THNSL2_ENST00000343544.4_Missense_Mutation_p.T204N|THNSL2_ENST00000449349.1_Missense_Mutation_p.T172N	NM_018271.4	NP_060741.3	Q86YJ6	THNS2_HUMAN	threonine synthase-like 2 (S. cerevisiae)	204			T -> N (in dbSNP:rs34136143).		2-oxobutyrate biosynthetic process (GO:0046360)|dephosphorylation (GO:0016311)|serine family amino acid catabolic process (GO:0009071)	extracellular space (GO:0005615)	lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)|serine binding (GO:0070905)			breast(4)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	27						CCGATCAAGACTGTGTTTGCC	0.552													C|||	221	0.0441294	0.0779	0.0144	5008	,	,		18531	0.005		0.0109	False		,,,				2504	0.0941				p.T204N		Atlas-SNP	.											.	THNSL2	66	.	0			c.C611A						PASS	.	C	ASN/THR	309,4097	166.2+/-197.5	9,291,1903	194	174	180		611	4.1	1	2	dbSNP_126	180	82,8518	48.9+/-108.6	0,82,4218	yes	missense	THNSL2	NM_018271.4	65	9,373,6121	AA,AC,CC		0.9535,7.0132,3.0063	benign	204/485	88478341	391,12615	2203	4300	6503	SO:0001583	missense	55258	exon4			TCAAGACTGTGTT		CCDS2002.2, CCDS58718.1, CCDS74539.1	2p11.2	2007-06-20			ENSG00000144115	ENSG00000144115			25602	protein-coding gene	gene with protein product		611261				17034760	Standard	NM_018271		Approved	FLJ10916	uc021vkr.1	Q86YJ6	OTTHUMG00000130314	ENST00000324166.5:c.611C>A	2.37:g.88478341C>A	ENSP00000327323:p.Thr204Asn	188	0	0		204	204	1	NM_018271	B3KTB1|B5MDX8|B7WPF8|D9ZZB8|Q6P2M7|Q6PI27|Q9NV54	Missense_Mutation	SNP	ENST00000324166.5	37	CCDS2002.2	54	0.024725274725274724	38	0.07723577235772358	7	0.019337016574585635	0	0.0	9	0.011873350923482849	C	9.986	1.229403	0.22542	0.070132	0.009535	ENSG00000144115	ENST00000358591;ENST00000377254;ENST00000402102;ENST00000449349;ENST00000544063;ENST00000343544;ENST00000324166	T;T;T;T;T;T	0.10860	2.83;2.83;2.83;2.83;2.83;2.83	5.08	4.07	0.47477	Threonine synthase (1);Pyridoxal phosphate-dependent enzyme, beta subunit (2);	0.601847	0.16677	N	0.204129	T	0.00300	0.0009	N	0.03016	-0.435	0.22880	N	0.998614	B;B;B;B	0.11235	0.001;0.0;0.004;0.001	B;B;B;B	0.09377	0.003;0.001;0.001;0.004	T	0.32161	-0.9917	10	0.59425	D	0.04	.	10.4043	0.44248	0.3747:0.6253:0.0:0.0	rs34136143	46;204;172;204	A8K0C1;Q86YJ6;C9JU10;Q86YJ6-2	.;THNS2_HUMAN;.;.	N	204;204;204;172;46;204;204	ENSP00000351402:T204N;ENSP00000366464:T204N;ENSP00000384475:T204N;ENSP00000407553:T172N;ENSP00000339563:T204N;ENSP00000327323:T204N	ENSP00000327323:T204N	T	+	2	0	THNSL2	88259456	0.998000	0.40836	0.951000	0.38953	0.214000	0.24535	4.088000	0.57678	2.553000	0.86117	0.561000	0.74099	ACT	C|0.974;A|0.026	0.026	strong		0.552	THNSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252662.1	NM_018271		A	88478341	C	A	88478341	3	1	22	1	0	0	0	0	1	0	0	0	15878	565	20	4	625	4	THNSL2	2	88478341	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	82128	88478341	154721032	616	3517											
FAM178B	51252	hgsc.bcm.edu	37	chr2	97543701	97543701	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caggtccttgagcatggtgcGgtgcatggcctgggggctct	4	10	17	10	1	1	1	0	1	1	0	2	1	2	1	2	6	3	3	2	6	0	1	rs34013660	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:97543701G>A	ENST00000417561.3	-	20	2376	c.2377C>T	c.(2377-2379)Cgc>Tgc	p.R793C	FAM178B_ENST00000470789.1_5'UTR|FAM178B_ENST00000393526.2_Missense_Mutation_p.R85C|FAM178B_ENST00000327896.3_Missense_Mutation_p.R613C|FAM178B_ENST00000490605.2_Missense_Mutation_p.R645C			Q8IXR5	F178B_HUMAN	family with sequence similarity 178, member B	793			R -> C (in dbSNP:rs34013660).							large_intestine(1)|ovary(1)	2						AGCATGGTGCGGTGCATGGCC	0.672													G|||	86	0.0171725	0.0635	0.0014	5008	,	,		16465	0.0		0.001	False		,,,				2504	0.0				p.R645C		Atlas-SNP	.											FAM178B_ENST00000417561,colon,carcinoma,+1,2	FAM178B	35	2	0			c.C1933T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG	256,4150	147.3+/-181.8	8,240,1955	77	64	68		1933,310,253	2.3	1	2	dbSNP_126	68	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense	FAM178B	NM_001122646.2,NM_001172667.1,NM_016490.4	180,180,180	8,242,6253	AA,AG,GG		0.0233,5.8103,1.9837	probably-damaging,probably-damaging,probably-damaging	645/680,104/139,85/120	97543701	258,12748	2203	4300	6503	SO:0001583	missense	51252	exon16			TGGTGCGGTGCAT	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.2377C>T	2.37:g.97543701G>A	ENSP00000413245:p.Arg793Cys	120	0	0		84	44	0.52381	NM_001122646	A8MXN2|E9PD86|Q8IUY0|Q9P0P4	Missense_Mutation	SNP	ENST00000417561.3	37		30	0.013736263736263736	29	0.05894308943089431	0	0.0	0	0.0	1	0.0013192612137203166	G	16.16	3.045853	0.55110	0.058103	2.33E-4	ENSG00000168754	ENST00000417561;ENST00000327896;ENST00000393526;ENST00000490605	T;T;T;T	0.60797	0.18;0.2;0.16;0.18	5.2	2.31	0.28768	.	.	.	.	.	T	0.14830	0.0358	M	0.62723	1.935	0.41162	D	0.986107	D	0.71674	0.998	P	0.53861	0.736	T	0.33369	-0.9871	9	0.87932	D	0	-4.1547	4.8677	0.13616	0.1825:0.0:0.636:0.1815	rs34013660	793	Q8IXR5	F178B_HUMAN	C	793;613;85;645	ENSP00000413245:R793C;ENSP00000333553:R613C;ENSP00000377160:R85C;ENSP00000429896:R645C	ENSP00000333553:R613C	R	-	1	0	FAM178B	96907428	0.594000	0.26849	0.988000	0.46212	0.405000	0.30901	0.542000	0.23222	0.161000	0.19458	0.455000	0.32223	CGC	G|0.979;A|0.021	0.021	strong		0.672	FAM178B-202	KNOWN	basic	protein_coding	protein_coding		NM_016490		A	97543701	G	A	97543701	3	1	22	1	0	0	0	0	1	0	0	0	5509	1116	39	1	114	1	FAM178B	2	97543701	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	9065360	97543701	145655672	617	3518											
ANKRD36B	0	hgsc.bcm.edu	37	chr2	98129757	98129758	+	IGR	INS	-	-	T																															gctcttctgttattcttaacINSttttccctaactttttggtg																								rs367988895|rs567331785	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:98129757_98129758insT								AC159540.1 (38708 upstream) : ANKRD36B (34269 downstream)																							TTATTCTTAACTTTTCCCTAAC	0.337																																					p.K897fs		Atlas-Indel	.											.	.	.	.	0			c.2691_2692insA						PASS	.																																			SO:0001628	intergenic_variant	57730	exon38			.																													2.37:g.98129761_98129761dupT		1139	0	0		678	61	0.0899705	NM_025190		Frame_Shift_Ins	INS		37																																																																																				.	.	weak	0	0.337									T	98129758	-	T	98129757	6	5	22	0	1	1	1	0	0	0	0	0	666	564	20	0		0	ANKRD36B	2	98129757	IGR	INS	-	TCGA-G8-6324-01A-11D-2210-10	586056	98129757	145069616	618	3519											
ANKRD36B	57730	hgsc.bcm.edu	37	chr2	98197010	98197010	+	RNA	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttttcttcgactcacagcaaGtaacagtggctgatattcat	11	14	7	9	1	3	1	2	1	1	0	4	2	3	1	0	1	2	3	0	1	3	6	rs2922614	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:98197010G>A	ENST00000443455.1	-	0	650							Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B																		CTCACAGCAAGTAACAGTGGC	0.303													.|||	57	0.0113818	0.0401	0.0043	5008	,	,		20283	0.001		0.0	False		,,,				2504	0.0				p.L158F		Atlas-SNP	.											.	.	.	.	0			c.C472T						PASS	.	G	PHE/LEU	51,1333		1,49,642	161	125	136		472	-0.4	0	2	dbSNP_101	136	0,3182		0,0,1591	no	missense	ANKRD36B	NM_025190.3	22	1,49,2233	AA,AG,GG		0.0,3.685,1.117	benign	158/1354	98197010	51,4515	692	1591	2283			57730	exon4			CAGCAAGTAACAG	AK024934	CCDS74543.1	2q11.2	2013-01-11	2008-03-25	2008-03-25	ENSG00000196912	ENSG00000196912		"Ankyrin repeat domain containing"	29333	protein-coding gene	gene with protein product	"melanoma-associated antigen", "CLL-associated antigen KW-1"		"KIAA1641"	KIAA1641		10997877	Standard	NM_025190		Approved	FLJ21281	uc010yvc.1	Q8N2N9	OTTHUMG00000130547		2.37:g.98197010G>A		533	0	0		517	223	0.431335	NM_025190	Q08AK5|Q6IPR0|Q6PI49|Q8IZM7|Q8TDH6|Q96N30|Q9H759	Missense_Mutation	SNP	ENST00000443455.1	37																																																																																				G|0.984;A|0.016	0.016	strong		0.303	ANKRD36B-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000328967.2	NM_025190		A	98197010	G	A	98197010	1	1	22	0	1	0	0	0	0	0	0	0	666	1029	36	2		2	ANKRD36B	2	98197010	RNA	SNP	G	TCGA-G8-6324-01A-11D-2210-10	67253	98197010	145002363	619	3520											
ANKRD36B	57730	hgsc.bcm.edu	37	chr2	98201527	98201527	+	RNA	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acatccgtaatatttggatcGgcgccattttgcagcagaag	11	11	10	9	3	0	1	0	0	0	1	2	2	1	2	2	2	2	3	2	2	3	5			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:98201527G>A	ENST00000443455.1	-	0	508							Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B																		TATTTGGATCGGCGCCATTTT	0.413																																					p.A110A		Atlas-SNP	.											.	.	.	.	0			c.C330T						PASS	.						22	18	19					2																	98201527		692	1578	2270			57730	exon3			TGGATCGGCGCCA	AK024934	CCDS74543.1	2q11.2	2013-01-11	2008-03-25	2008-03-25	ENSG00000196912	ENSG00000196912		"Ankyrin repeat domain containing"	29333	protein-coding gene	gene with protein product	"melanoma-associated antigen", "CLL-associated antigen KW-1"		"KIAA1641"	KIAA1641		10997877	Standard	NM_025190		Approved	FLJ21281	uc010yvc.1	Q8N2N9	OTTHUMG00000130547		2.37:g.98201527G>A		1252	1	0.000798722		1172	406	0.346416	NM_025190	Q08AK5|Q6IPR0|Q6PI49|Q8IZM7|Q8TDH6|Q96N30|Q9H759	Silent	SNP	ENST00000443455.1	37																																																																																				.	.	none		0.413	ANKRD36B-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000328967.2	NM_025190		A	98201527	G	A	98201527	1	1	22	0	1	0	0	0	0	0	0	0	666	1103	39	1		1	ANKRD36B	2	98201527	RNA	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4517	98201527	144997846	620	3521											
ANKRD36B	57730	hgsc.bcm.edu	37	chr2	98206012	98206012	+	RNA	SNP	G	G	A																															ccttcctgtctctcttattgGcgtcataatacgtgagcaga																								rs185401750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:98206012G>A	ENST00000443455.1	-	0	315							Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B																		TCTCTTATTGGCGTCATAATA	0.522													.|||	73	0.0145767	0.0469	0.0043	5008	,	,		11591	0.006		0.001	False		,,,				2504	0.001				p.A46V		Atlas-SNP	.											.	.	.	.	0			c.C137T						PASS	.	G	VAL/ALA	41,1343		2,37,653	106	82	89		137	0.8	0	2		89	0,3182		0,0,1591	no	missense	ANKRD36B	NM_025190.3	64	2,37,2244	AA,AG,GG		0.0,2.9624,0.8979	benign	46/1354	98206012	41,4525	692	1591	2283			57730	exon1			TTATTGGCGTCAT	AK024934	CCDS74543.1	2q11.2	2013-01-11	2008-03-25	2008-03-25	ENSG00000196912	ENSG00000196912		"Ankyrin repeat domain containing"	29333	protein-coding gene	gene with protein product	"melanoma-associated antigen", "CLL-associated antigen KW-1"		"KIAA1641"	KIAA1641		10997877	Standard	NM_025190		Approved	FLJ21281	uc010yvc.1	Q8N2N9	OTTHUMG00000130547		2.37:g.98206012G>A		292	1	0.00342466		259	124	0.478764	NM_025190	Q08AK5|Q6IPR0|Q6PI49|Q8IZM7|Q8TDH6|Q96N30|Q9H759	Missense_Mutation	SNP	ENST00000443455.1	37																																																																																				G|0.989;A|0.011	0.011	strong		0.522	ANKRD36B-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000328967.2	NM_025190		A	98206012	G	A	98206012	1	1	22	0	1	0	0	0	0	0	0	0	666	1203	42	2		2	ANKRD36B	2	98206012	RNA	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4485	98206012	144993361	621	3522	51	2									
ANKRD36B	57730	hgsc.bcm.edu	37	chr2	98206013	98206013	+	RNA	SNP	C	C	T																															cttcctgtctctcttattggCgtcataatacgtgagcagaa																								rs188661236	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:98206013C>T	ENST00000443455.1	-	0	314							Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B																		CTCTTATTGGCGTCATAATAC	0.522													.|||	73	0.0145767	0.0469	0.0043	5008	,	,		11667	0.006		0.001	False		,,,				2504	0.001				p.A46T		Atlas-SNP	.											.	.	.	.	0			c.G136A						PASS	.	C	THR/ALA	41,1343		2,37,653	107	83	90		136	-1.5	0	2		90	0,3182		0,0,1591	no	missense	ANKRD36B	NM_025190.3	58	2,37,2244	TT,TC,CC		0.0,2.9624,0.8979	benign	46/1354	98206013	41,4525	692	1591	2283			57730	exon1			TATTGGCGTCATA	AK024934	CCDS74543.1	2q11.2	2013-01-11	2008-03-25	2008-03-25	ENSG00000196912	ENSG00000196912		"Ankyrin repeat domain containing"	29333	protein-coding gene	gene with protein product	"melanoma-associated antigen", "CLL-associated antigen KW-1"		"KIAA1641"	KIAA1641		10997877	Standard	NM_025190		Approved	FLJ21281	uc010yvc.1	Q8N2N9	OTTHUMG00000130547		2.37:g.98206013C>T		295	1	0.00338983		262	127	0.484733	NM_025190	Q08AK5|Q6IPR0|Q6PI49|Q8IZM7|Q8TDH6|Q96N30|Q9H759	Missense_Mutation	SNP	ENST00000443455.1	37																																																																																				C|0.989;T|0.011	0.011	strong		0.522	ANKRD36B-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000328967.2	NM_025190		T	98206013	C	T	98206013	1	4	22	0	1	0	0	0	0	0	0	0	666	768	27	1		1	ANKRD36B	2	98206013	RNA	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1	98206013	144993360	622	3523	51	2									
VWA3B	200403	hgsc.bcm.edu	37	chr2	98779418	98779418	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tggccgagcctcccaagcccGacgtggccactgtggactgc	6	6	13	16	3	0	0	0	0	0	0	1	3	1	1	5	3	3	0	5	3	1	0	rs77092382	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:98779418G>A	ENST00000477737.1	+	8	1297	c.1093G>A	c.(1093-1095)Gac>Aac	p.D365N	VWA3B_ENST00000435344.1_Missense_Mutation_p.D365N|VWA3B_ENST00000451075.2_Missense_Mutation_p.D215N	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	365										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						TCCCAAGCCCGACGTGGCCAC	0.567													G|||	132	0.0263578	0.0946	0.0101	5008	,	,		16753	0.0		0.0	False		,,,				2504	0.0				p.D365N		Atlas-SNP	.											.	VWA3B	138	.	0			c.G1093A						PASS	.	G	ASN/ASP	319,3775		17,285,1745	56	64	62		1093	-9.4	0	2	dbSNP_131	62	4,8420		0,4,4208	no	missense	VWA3B	NM_144992.4	23	17,289,5953	AA,AG,GG		0.0475,7.7919,2.5803	benign	365/1295	98779418	323,12195	2047	4212	6259	SO:0001583	missense	200403	exon8			AAGCCCGACGTGG	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.1093G>A	2.37:g.98779418G>A	ENSP00000417955:p.Asp365Asn	133	0	0		139	60	0.431655	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	37	CCDS42718.1	35	0.016025641025641024	33	0.06707317073170732	2	0.0055248618784530384	0	0.0	0	0.0	G	10.25	1.297516	0.23650	0.077919	4.75E-4	ENSG00000168658	ENST00000435344;ENST00000477737;ENST00000451075	T;T;T	0.23147	1.92;3.36;2.47	4.68	-9.37	0.00626	.	2.270810	0.02023	N	0.047965	T	0.00496	0.0016	N	0.04959	-0.14	0.09310	N	1	B;B;B	0.12630	0.006;0.001;0.002	B;B;B	0.04013	0.001;0.001;0.001	T	0.11179	-1.0598	10	0.34782	T	0.22	.	4.1345	0.10164	0.5431:0.1901:0.1706:0.0961	.	215;365;365	B7Z7Q7;Q502W6;Q502W6-8	.;VWA3B_HUMAN;.	N	365;365;215	ENSP00000401959:D365N;ENSP00000417955:D365N;ENSP00000389463:D215N	ENSP00000411168:D365N	D	+	1	0	VWA3B	98145850	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.018000	0.01444	-2.385000	0.00590	-0.781000	0.03364	GAC	G|0.981;A|0.019	0.019	strong		0.567	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992		A	98779418	G	A	98779418	3	1	22	1	0	0	0	0	1	0	0	0	17256	1058	37	1	1119	1	VWA3B	2	98779418	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	573405	98779418	144419955	623	3524											
MGAT4A	11320	hgsc.bcm.edu	37	chr2	99256447	99256447	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggattttaagaagtaatggTttcatataatctttatcctg	12	18	7	4	0	2	1	1	0	1	1	3	2	3	2	1	2	0	2	1	2	6	8			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:99256447T>A	ENST00000264968.3	-	11	1509	c.1146A>T	c.(1144-1146)aaA>aaT	p.K382N	MGAT4A_ENST00000414521.2_Missense_Mutation_p.K254N|MGAT4A_ENST00000409391.1_Missense_Mutation_p.K382N|MGAT4A_ENST00000393487.1_Missense_Mutation_p.K382N			Q9UM21	MGT4A_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme A	382					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						GAAGTAATGGTTTCATATAAT	0.343																																					p.K382N		Atlas-SNP	.											.	MGAT4A	51	.	0			c.A1146T						PASS	.						63	67	66					2																	99256447		2203	4300	6503	SO:0001583	missense	11320	exon12			TAATGGTTTCATA	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.1146A>T	2.37:g.99256447T>A	ENSP00000264968:p.Lys382Asn	78	0	0		82	42	0.512195	NM_012214	B4E2R6|D3DVH6|E9PEN2|Q53S97|Q86Z15	Missense_Mutation	SNP	ENST00000264968.3	37	CCDS2036.1	.	.	.	.	.	.	.	.	.	.	T	17.73	3.462708	0.63513	.	.	ENSG00000071073	ENST00000393487;ENST00000414521;ENST00000264968;ENST00000409391	T;T;T;T	0.26957	1.7;1.75;1.7;1.7	5.64	1.45	0.22620	.	0.000000	0.85682	D	0.000000	T	0.49762	0.1576	M	0.85777	2.775	0.54753	D	0.999987	D;D	0.76494	0.988;0.999	P;D	0.78314	0.815;0.991	T	0.50792	-0.8786	10	0.52906	T	0.07	-5.7696	10.1002	0.42499	0.0:0.2309:0.0:0.7691	.	254;382	E9PEN2;Q9UM21	.;MGT4A_HUMAN	N	382;254;382;382	ENSP00000377127:K382N;ENSP00000404889:K254N;ENSP00000264968:K382N;ENSP00000386841:K382N	ENSP00000264968:K382N	K	-	3	2	MGAT4A	98622879	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	0.644000	0.24766	0.394000	0.25230	0.455000	0.32223	AAA	.	.	none		0.343	MGAT4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252988.2	NM_012214		A	99256447	T	A	99256447	3	1	22	1	0	0	0	0	1	0	0	0	9554	1722	60	5	560	5	MGAT4A	2	99256447	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	477029	99256447	143942926	624	3525											
C2orf55	343990	hgsc.bcm.edu	37	chr2	99412654	99412654	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagctttgccccctgcttcCggtccacagcgggcttcaca	5	10	10	16	2	1	1	1	1	0	0	3	1	3	1	4	2	4	3	4	2	0	3	rs73962467	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:99412654C>T	ENST00000397899.2	-	9	3009	c.2678G>A	c.(2677-2679)cGg>cAg	p.R893Q		NM_207362.2	NP_997245.2	Q6NV74	K121L_HUMAN	KIAA1211-like	893																	CCCCTGCTTCCGGTCCACAGC	0.507													C|||	33	0.00658946	0.0219	0.0058	5008	,	,		19267	0.0		0.0	False		,,,				2504	0.0				p.R893Q		Atlas-SNP	.											.	.	.	.	0			c.G2678A						PASS	.	C	GLN/ARG	69,3687		3,63,1812	145	141	143		2678	0.3	0.2	2	dbSNP_130	143	1,8221		0,1,4110	yes	missense	C2orf55	NM_207362.2	43	3,64,5922	TT,TC,CC		0.0122,1.8371,0.5844	benign	893/963	99412654	70,11908	1878	4111	5989	SO:0001583	missense	343990	exon9			TGCTTCCGGTCCA	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.2678G>A	2.37:g.99412654C>T	ENSP00000380996:p.Arg893Gln	119	0	0		112	54	0.482143	NM_207362		Missense_Mutation	SNP	ENST00000397899.2	37	CCDS42720.1	19	0.0086996336996337	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	C	5.887	0.347744	0.11126	0.018371	1.22E-4	ENSG00000196872	ENST00000397899	T	0.39592	1.07	5.17	0.328	0.15918	.	1.201180	0.05934	N	0.635672	T	0.06188	0.0160	N	0.11427	0.14	0.09310	N	1	B	0.19706	0.038	B	0.15870	0.014	T	0.14755	-1.0461	10	0.02654	T	1	-0.9202	3.636	0.08148	0.0:0.3473:0.1965:0.4562	.	893	Q6NV74	CB055_HUMAN	Q	893	ENSP00000380996:R893Q	ENSP00000380996:R893Q	R	-	2	0	C2orf55	98779086	0.996000	0.38824	0.172000	0.22920	0.097000	0.18754	0.215000	0.17562	0.182000	0.20032	0.563000	0.77884	CGG	C|0.991;T|0.009	0.009	strong		0.507	KIAA1211L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329933.1	NM_207362		T	99412654	C	T	99412654	3	4	22	1	0	0	0	0	1	0	0	0	2178	652	23	1	218	1	C2orf55	2	99412654	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	156207	99412654	143786719	625	3526											
TSGA10	80705	hgsc.bcm.edu	37	chr2	99722135	99722135	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agcttttcatcatttctcgtCgaagtcgggtaatttcttcc	7	17	7	10	3	4	0	2	0	2	0	8	1	5	0	1	1	1	2	1	1	2	6	rs146207401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:99722135C>T	ENST00000393483.3	-	8	1080	c.236G>A	c.(235-237)cGa>cAa	p.R79Q	TSGA10_ENST00000478090.1_5'UTR|TSGA10_ENST00000539964.1_Missense_Mutation_p.R79Q|TSGA10_ENST00000410001.1_Missense_Mutation_p.R79Q|TSGA10_ENST00000355053.4_Missense_Mutation_p.R79Q|TSGA10_ENST00000542655.1_Missense_Mutation_p.R79Q	NM_025244.2	NP_079520.1	Q9BZW7	TSG10_HUMAN	testis specific, 10	79					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						CATTTCTCGTCGAAGTCGGGT	0.368																																					p.R79Q		Atlas-SNP	.											.	TSGA10	81	.	0			c.G236A						PASS	.	C	GLN/ARG,GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	203	195	198		236,236	5	1	2	dbSNP_134	198	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	TSGA10	NM_025244.2,NM_182911.3	43,43	0,4,6499	TT,TC,CC		0.0233,0.0454,0.0308	probably-damaging,probably-damaging	79/699,79/699	99722135	4,13002	2203	4300	6503	SO:0001583	missense	80705	exon7			TCTCGTCGAAGTC	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.236G>A	2.37:g.99722135C>T	ENSP00000377123:p.Arg79Gln	73	0	0		66	30	0.454545	NM_182911	B7Z925|D3DVH7|Q8NEP0|Q9BWX0	Missense_Mutation	SNP	ENST00000393483.3	37	CCDS2037.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.031503	0.93575	4.54E-4	2.33E-4	ENSG00000135951	ENST00000393483;ENST00000410001;ENST00000355053;ENST00000539964;ENST00000409564;ENST00000393482;ENST00000542655	T;T;T;T;T;T;T	0.54675	0.56;0.56;0.56;0.56;0.56;0.56;0.56	4.99	4.99	0.66335	.	0.158903	0.29853	N	0.011034	T	0.64746	0.2626	L	0.59436	1.845	0.34409	D	0.696207	D;D	0.71674	0.998;0.998	P;P	0.59889	0.865;0.865	T	0.69423	-0.5149	10	0.28530	T	0.3	-6.6381	17.049	0.86513	0.0:1.0:0.0:0.0	.	79;79	B7Z925;Q9BZW7	.;TSG10_HUMAN	Q	79	ENSP00000377123:R79Q;ENSP00000386956:R79Q;ENSP00000347161:R79Q;ENSP00000444419:R79Q;ENSP00000386508:R79Q;ENSP00000377122:R79Q;ENSP00000445623:R79Q	ENSP00000347161:R79Q	R	-	2	0	TSGA10	99088567	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	4.326000	0.59241	2.601000	0.87937	0.650000	0.86243	CGA	C|0.999;T|0.001	0.001	strong		0.368	TSGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253125.1	NM_182911		T	99722135	C	T	99722135	3	4	22	1	0	0	0	0	1	0	0	0	16632	884	31	1	1916	1	TSGA10	2	99722135	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	309481	99722135	143477238	626	3527											
LONRF2	164832	hgsc.bcm.edu	37	chr2	100911980	100911980	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaaatattaattcttcggcCagaacagttatgttaaagtt	14	14	7	6	2	1	1	0	0	1	1	2	2	1	1	1	1	1	3	1	1	7	7	rs116227203	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:100911980C>T	ENST00000393437.3	-	8	2151	c.1512G>A	c.(1510-1512)ctG>ctA	p.L504L	LONRF2_ENST00000409647.1_Silent_p.L261L	NM_198461.3	NP_940863.3	Q1L5Z9	LONF2_HUMAN	LON peptidase N-terminal domain and ring finger 2	504							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						ATTCTTCGGCCAGAACAGTTA	0.343													C|||	73	0.0145767	0.0522	0.0043	5008	,	,		19323	0.0		0.001	False		,,,				2504	0.0				p.L504L		Atlas-SNP	.											.	LONRF2	62	.	0			c.G1512A						PASS	.	C		200,4206	124.5+/-161.8	1,198,2004	95	93	94		1512	3.3	0.2	2	dbSNP_132	94	0,8600		0,0,4300	no	coding-synonymous	LONRF2	NM_198461.3		1,198,6304	TT,TC,CC		0.0,4.5393,1.5378		504/755	100911980	200,12806	2203	4300	6503	SO:0001819	synonymous_variant	164832	exon8			TTCGGCCAGAACA	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.1512G>A	2.37:g.100911980C>T		80	0	0		90	41	0.455556	NM_198461	B9A006|Q6ZSR4	Silent	SNP	ENST00000393437.3	37	CCDS2046.2																																																																																			C|0.986;T|0.014	0.014	strong		0.343	LONRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253161.2	NM_198461		T	100911980	C	T	100911980	2	4	22	1	0	0	0	0	0	0	0	1	8904	581	21	2		2	LONRF2	2	100911980	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1189845	100911980	142287393	627	3528											
RPL31	6160	hgsc.bcm.edu	37	chr2	101619211	101619211	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaaaaagggccgttctgcCatcaacgaagtggtaacccg	14	6	11	10	3	2	1	1	0	1	1	2	2	2	1	3	2	3	2	3	2	6	2	rs141007382	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:101619211C>T	ENST00000264258.3	+	2	649	c.48C>T	c.(46-48)gcC>gcT	p.A16A	RPL31_ENST00000409038.1_Silent_p.A16A|RPL31_ENST00000409000.1_Silent_p.A16A|RPL31_ENST00000409733.1_Silent_p.A16A|RPL31_ENST00000409320.3_Silent_p.A16A|RPL31_ENST00000409650.1_Silent_p.A16A|RPL31_ENST00000409028.4_Silent_p.A16A|RPL31_ENST00000409711.1_Silent_p.A16A|AC016738.4_ENST00000452364.1_RNA	NM_000993.4	NP_000984.1	P62899	RL31_HUMAN	ribosomal protein L31	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)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			kidney(1)|large_intestine(2)|lung(1)|prostate(1)|urinary_tract(3)	8						GCCGTTCTGCCATCAACGAAG	0.532													C|||	5	0.000998403	0.0038	0.0	5008	,	,		19707	0.0		0.0	False		,,,				2504	0.0				p.A16A		Atlas-SNP	.											.	RPL31	12	.	0			c.C48T						PASS	.	C	,,	13,4393	19.1+/-41.9	0,13,2190	71	66	68		48,48,48	2.5	1	2	dbSNP_134	68	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	RPL31	NM_000993.4,NM_001098577.2,NM_001099693.1	,,	0,13,6490	TT,TC,CC		0.0,0.2951,0.1	,,	16/126,16/129,16/122	101619211	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	6160	exon2			TTCTGCCATCAAC	X15940	CCDS2049.1, CCDS46373.1, CCDS46374.1	2q11.2	2011-04-06			ENSG00000071082	ENSG00000071082		"L ribosomal proteins"	10334	protein-coding gene	gene with protein product						2780320, 11875025	Standard	NM_000993		Approved	L31	uc010fiu.1	P62899	OTTHUMG00000130687	ENST00000264258.3:c.48C>T	2.37:g.101619211C>T		183	0	0		219	114	0.520548	NM_001098577	B7Z4K2|D3DVJ4|P12947|Q53SQ5|Q6IRZ0|Q6LBJ6	Silent	SNP	ENST00000264258.3	37	CCDS2049.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	13.12	2.141667	0.37825	0.002951	0.0	ENSG00000071082	ENST00000441435	.	.	.	5.38	2.51	0.30379	.	.	.	.	.	T	0.56587	0.1995	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50939	-0.8768	4	.	.	.	.	8.4008	0.32586	0.1258:0.7401:0.0:0.1341	.	.	.	.	L	4	.	.	P	+	2	0	RPL31	100985643	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.039000	0.49791	0.839000	0.34971	-0.150000	0.13652	CCA	C|0.999;T|0.001	0.001	strong		0.532	RPL31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253182.3	NM_001098577		T	101619211	C	T	101619211	2	4	22	1	0	0	0	0	0	0	0	1	13596	581	21	2		2	RPL31	2	101619211	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	707231	101619211	141580162	628	3529											
IL1R2	7850	hgsc.bcm.edu	37	chr2	102626187	102626187	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaaaatgactctgctaggacGgtcccaggagaagaagagac	16	5	12	8	1	1	4	0	1	1	3	2	7	2	5	1	3	1	1	1	3	5	1	rs2230401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:102626187G>A	ENST00000332549.3	+	3	460	c.231G>A	c.(229-231)acG>acA	p.T77T	IL1R2_ENST00000441002.1_Silent_p.T77T|IL1R2_ENST00000393414.2_Silent_p.T77T	NM_004633.3	NP_004624.1	P27930	IL1R2_HUMAN	interleukin 1 receptor, type II	77	Ig-like C2-type 1.				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						CTGCTAGGACGGTCCCAGGAG	0.597													G|||	215	0.0429313	0.1551	0.013	5008	,	,		18355	0.0		0.001	False		,,,				2504	0.0				p.T77T	Pancreas(106;189 1628 2302 5133 12295)	Atlas-SNP	.											.	IL1R2	58	.	0			c.G231A						PASS	.	G	,	507,3899	234.6+/-247.4	31,445,1727	157	164	161		231,231	-3.7	0	2	dbSNP_98	161	12,8588	9.1+/-34.3	0,12,4288	no	coding-synonymous,coding-synonymous	IL1R2	NM_004633.3,NM_173343.1	,	31,457,6015	AA,AG,GG		0.1395,11.507,3.9905	,	77/399,77/399	102626187	519,12487	2203	4300	6503	SO:0001819	synonymous_variant	7850	exon3			TAGGACGGTCCCA	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.231G>A	2.37:g.102626187G>A		81	0	0		81	34	0.419753	NM_001261419	D3DVJ5|Q6LCE6|Q9UE68	Silent	SNP	ENST00000332549.3	37	CCDS2054.1																																																																																			G|0.958;A|0.042	0.042	strong		0.597	IL1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253191.1	NM_004633		A	102626187	G	A	102626187	2	1	22	1	0	0	0	0	0	0	0	1	7668	1103	39	1		1	IL1R2	2	102626187	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1006976	102626187	140573186	629	3530											
IL1R1	3554	hgsc.bcm.edu	37	chr2	102781466	102781466	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggacattactattgcgtggtAaggtaagagaggaattagta	14	11	13	3	1	0	1	0	0	0	1	0	4	0	3	0	4	2	3	0	4	7	7	rs144946641	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:102781466A>G	ENST00000410023.1	+	4	612	c.294A>G	c.(292-294)gtA>gtG	p.V98V	IL1R1_ENST00000409329.1_Silent_p.V98V|IL1R1_ENST00000233946.3_Silent_p.V98V|IL1R1_ENST00000424272.1_Silent_p.V98V|IL1R1_ENST00000409929.1_Silent_p.V98V|IL1R1_ENST00000409589.1_Silent_p.V98V|IL1R1_ENST00000409288.1_Silent_p.V98V			P14778	IL1R1_HUMAN	interleukin 1 receptor, type I	98	Ig-like C2-type 1.				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)	p.V98V(1)		breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|prostate(2)|skin(3)	19					Anakinra(DB00026)	ATTGCGTGGTAAGGTAAGAGA	0.358													A|||	16	0.00319489	0.0121	0.0	5008	,	,		18836	0.0		0.0	False		,,,				2504	0.0				p.V98V		Atlas-SNP	.											IL1R1,NS,carcinoma,0,1	IL1R1	52	1	1	Substitution - coding silent(1)	lung(1)	c.A294G						PASS	.	A		24,4382	30.8+/-60.4	0,24,2179	99	90	93		294	-5	0.3	2	dbSNP_134	93	0,8600		0,0,4300	no	coding-synonymous	IL1R1	NM_000877.2		0,24,6479	GG,GA,AA		0.0,0.5447,0.1845		98/570	102781466	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	3554	exon3			CGTGGTAAGGTAA	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.294A>G	2.37:g.102781466A>G		81	0	0		93	44	0.473118	NM_000877	Q587I7	Silent	SNP	ENST00000410023.1	37	CCDS2055.1																																																																																			A|0.998;G|0.002	0.002	strong		0.358	IL1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253299.1			G	102781466	A	G	102781466	2	3	22	1	0	0	0	0	0	0	0	1	7667	349	13	3		3	IL1R1	2	102781466	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	155279	102781466	140417907	630	3531											
IL1RL1	9173	hgsc.bcm.edu	37	chr2	102957136	102957136	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttatttcagaattgtcaggCtcttcaaggatcaaggtaca	12	13	8	8	0	5	1	4	0	1	1	5	2	5	2	0	3	1	2	0	3	5	5	rs114797672	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:102957136C>T	ENST00000233954.1	+	5	729	c.458C>T	c.(457-459)gCt>gTt	p.A153V	IL1RL1_ENST00000311734.2_Missense_Mutation_p.A153V|IL1RL1_ENST00000404917.2_Missense_Mutation_p.A36V|IL1RL1_ENST00000393393.3_Missense_Mutation_p.A153V|IL1RL1_ENST00000409584.1_Missense_Mutation_p.A153V	NM_016232.4	NP_057316.3	Q01638	ILRL1_HUMAN	interleukin 1 receptor-like 1	153	Ig-like C2-type 2.				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						AATTGTCAGGCTCTTCAAGGA	0.373													c|||	20	0.00399361	0.0136	0.0029	5008	,	,		17359	0.0		0.0	False		,,,				2504	0.0				p.A153V		Atlas-SNP	.											.	IL1RL1	114	.	0			c.C458T						PASS	.	C	VAL/ALA,VAL/ALA	92,4314	75.7+/-113.9	1,90,2112	125	121	122		458,458	1.9	0.4	2	dbSNP_132	122	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	IL1RL1	NM_003856.2,NM_016232.4	64,64	1,91,6411	TT,TC,CC		0.0116,2.0881,0.7151	benign,benign	153/329,153/557	102957136	93,12913	2203	4300	6503	SO:0001583	missense	9173	exon5			GTCAGGCTCTTCA	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.458C>T	2.37:g.102957136C>T	ENSP00000233954:p.Ala153Val	301	0	0		268	128	0.477612	NM_016232	A8K6B3|B4E0I3|Q53TU7|Q8NEJ3|Q9ULV7|Q9UQ44	Missense_Mutation	SNP	ENST00000233954.1	37	CCDS2057.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	C	10.58	1.390800	0.25118	0.020881	1.16E-4	ENSG00000115602	ENST00000233954;ENST00000393393;ENST00000404917;ENST00000311734;ENST00000409584	T;T;T;T;T	0.12774	2.65;2.65;2.65;2.65;2.65	5.07	1.88	0.25563	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.784816	0.11927	N	0.516068	T	0.03136	0.0092	N	0.11560	0.145	0.29045	N	0.884885	B;B;B	0.22480	0.07;0.056;0.034	B;B;B	0.27262	0.078;0.046;0.034	T	0.40117	-0.9580	10	0.28530	T	0.3	.	5.6013	0.17355	0.1466:0.6513:0.0:0.2021	.	36;153;153	B4E0I3;Q01638-2;Q01638	.;.;ILRL1_HUMAN	V	153;153;36;153;153	ENSP00000233954:A153V;ENSP00000377052:A153V;ENSP00000384822:A36V;ENSP00000310371:A153V;ENSP00000386618:A153V	ENSP00000233954:A153V	A	+	2	0	IL1RL1	102323568	0.043000	0.20138	0.398000	0.26321	0.905000	0.53344	0.083000	0.14871	0.044000	0.15775	0.563000	0.77884	GCT	C|0.992;T|0.008	0.008	strong		0.373	IL1RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253296.1	NM_016232		T	102957136	C	T	102957136	3	4	22	1	0	0	0	0	1	0	0	0	7672	797	28	2	472	2	IL1RL1	2	102957136	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	175670	102957136	140242237	631	3532											
SLC9A4	389015	hgsc.bcm.edu	37	chr2	103142761	103142761	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctctcctacccctacgggaAtcctcagtctgcaggaagag	9	8	9	15	1	3	1	1	0	2	1	5	3	4	3	5	2	3	1	5	2	4	2	rs115217520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:103142761A>T	ENST00000295269.4	+	11	2451	c.1994A>T	c.(1993-1995)aAt>aTt	p.N665I		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	665					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						CCCTACGGGAATCCTCAGTCT	0.498													A|||	11	0.00219649	0.0083	0.0	5008	,	,		15709	0.0		0.0	False		,,,				2504	0.0				p.N665I		Atlas-SNP	.											.	SLC9A4	115	.	0			c.A1994T						PASS	.	A	ILE/ASN	27,4379	33.5+/-64.1	0,27,2176	126	118	121		1994	3.4	0	2	dbSNP_133	121	2,8598	2.2+/-6.3	0,2,4298	yes	missense	SLC9A4	NM_001011552.3	149	0,29,6474	TT,TA,AA		0.0233,0.6128,0.223	benign	665/799	103142761	29,12977	2203	4300	6503	SO:0001583	missense	389015	exon11			ACGGGAATCCTCA		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.1994A>T	2.37:g.103142761A>T	ENSP00000295269:p.Asn665Ile	123	0	0		131	59	0.450382	NM_001011552	Q69YK0	Missense_Mutation	SNP	ENST00000295269.4	37	CCDS33264.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	12.38	1.919817	0.33908	0.006128	2.33E-4	ENSG00000180251	ENST00000295269	T	0.46451	0.87	5.8	3.38	0.38709	.	2.143600	0.02112	N	0.054895	T	0.33294	0.0858	L	0.44542	1.39	0.09310	N	1	B	0.22604	0.072	B	0.26517	0.07	T	0.26292	-1.0107	10	0.42905	T	0.14	.	8.6644	0.34112	0.8465:0.0:0.1535:0.0	.	665	Q6AI14	SL9A4_HUMAN	I	665	ENSP00000295269:N665I	ENSP00000295269:N665I	N	+	2	0	SLC9A4	102509193	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.084000	0.14891	0.438000	0.26450	0.533000	0.62120	AAT	A|0.997;T|0.003	0.003	strong		0.498	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3		T	103142761	A	T	103142761	3	4	22	1	0	0	0	0	1	0	0	0	14731	101	4	5	2036	5	SLC9A4	2	103142761	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	185625	103142761	140056612	632	3533											
SLC9A4	389015	hgsc.bcm.edu	37	chr2	103148868	103148868	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggtcacttcagaagcaagaGgcacaagaaataataccaat	18	6	9	8	0	2	3	2	0	0	3	2	3	2	3	1	2	2	2	1	2	7	3	rs59687519	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:103148868G>A	ENST00000295269.4	+	12	2575	c.2118G>A	c.(2116-2118)gaG>gaA	p.E706E		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	706					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						AGAAGCAAGAGGCACAAGAAA	0.468													G|||	88	0.0175719	0.062	0.0086	5008	,	,		21876	0.0		0.0	False		,,,				2504	0.0				p.E706E		Atlas-SNP	.											.	SLC9A4	115	.	0			c.G2118A						PASS	.	G		265,4141	150.3+/-184.3	9,247,1947	93	90	91		2118	0.7	0	2	dbSNP_129	91	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SLC9A4	NM_001011552.3		9,249,6245	AA,AG,GG		0.0233,6.0145,2.0529		706/799	103148868	267,12739	2203	4300	6503	SO:0001819	synonymous_variant	389015	exon12			GCAAGAGGCACAA		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.2118G>A	2.37:g.103148868G>A		80	0	0		102	59	0.578431	NM_001011552	Q69YK0	Silent	SNP	ENST00000295269.4	37	CCDS33264.1																																																																																			G|0.981;A|0.019	0.019	strong		0.468	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3		A	103148868	G	A	103148868	2	1	22	1	0	0	0	0	0	0	0	1	14731	991	35	2		2	SLC9A4	2	103148868	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6107	103148868	140050505	633	3534											
MRPS9	64965	hgsc.bcm.edu	37	chr2	105708936	105708936	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gaggaagaatttgtgcagagGtttcgaagaagtgtaactct	13	11	13	4	1	1	3	0	0	1	3	2	6	1	4	0	2	2	3	0	2	5	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:105708936G>C	ENST00000258455.3	+	8	839	c.729G>C	c.(727-729)agG>agC	p.R243S		NM_182640.2	NP_872578.1	P82933	RT09_HUMAN	mitochondrial ribosomal protein S9	243					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						TTGTGCAGAGGTTTCGAAGAA	0.388																																					p.R243S		Atlas-SNP	.											.	MRPS9	32	.	0			c.G729C						PASS	.						140	143	142					2																	105708936		2203	4300	6503	SO:0001583	missense	64965	exon8			GCAGAGGTTTCGA		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.729G>C	2.37:g.105708936G>C	ENSP00000258455:p.Arg243Ser	81	0	0		90	46	0.511111	NM_182640	Q6PG40	Missense_Mutation	SNP	ENST00000258455.3	37	CCDS2065.1	.	.	.	.	.	.	.	.	.	.	G	11.24	1.580061	0.28180	.	.	ENSG00000135972	ENST00000258455	D	0.92099	-2.97	5.61	1.81	0.25067	.	0.318283	0.38111	N	0.001806	D	0.86896	0.6043	M	0.61703	1.905	0.42674	D	0.993529	B	0.16396	0.017	B	0.10450	0.005	T	0.76602	-0.2899	10	0.39692	T	0.17	-24.4138	2.1982	0.03916	0.2617:0.1209:0.4925:0.1249	.	243	P82933	RT09_HUMAN	S	243	ENSP00000258455:R243S	ENSP00000258455:R243S	R	+	3	2	MRPS9	105075368	0.997000	0.39634	0.988000	0.46212	0.789000	0.44602	0.322000	0.19576	0.115000	0.18071	0.655000	0.94253	AGG	.	.	none		0.388	MRPS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253352.1	NM_182640		C	105708936	G	C	105708936	3	2	22	1	0	0	0	0	1	0	0	0	9858	1252	44	4	759	4	MRPS9	2	105708936	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2560068	105708936	137490437	634	3535											
TGFBRAP1	9392	hgsc.bcm.edu	37	chr2	105924699	105924699	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgttgacgcgctccttgtcGcccatcagcagctcccgctc	5	10	9	17	4	1	1	1	1	0	0	5	1	3	1	3	0	2	5	3	0	0	2	rs115690647	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:105924699G>A	ENST00000393359.2	-	2	486	c.60C>T	c.(58-60)ggC>ggT	p.G20G	TGFBRAP1_ENST00000258449.1_Silent_p.G20G			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	20					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						GCTCCTTGTCGCCCATCAGCA	0.547													G|||	39	0.00778754	0.0295	0.0	5008	,	,		18930	0.0		0.0	False		,,,				2504	0.0				p.G20G	Esophageal Squamous(183;794 2019 9730 21801 48859)	Atlas-SNP	.											.	TGFBRAP1	70	.	0			c.C60T						PASS	.	G	,	101,4305	80.4+/-118.8	0,101,2102	42	41	42		60,60	-3.4	0.2	2	dbSNP_132	42	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	TGFBRAP1	NM_001142621.1,NM_004257.4	,	0,101,6402	AA,AG,GG		0.0,2.2923,0.7766	,	20/861,20/861	105924699	101,12905	2203	4300	6503	SO:0001819	synonymous_variant	9392	exon2			CTTGTCGCCCATC	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.60C>T	2.37:g.105924699G>A		76	0	0		88	50	0.568182	NM_004257	A8K5R7|D3DVJ8|O60466	Silent	SNP	ENST00000393359.2	37	CCDS2067.1																																																																																			G|0.990;A|0.010	0.010	strong		0.547	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257		A	105924699	G	A	105924699	2	1	22	1	0	0	0	0	0	0	0	1	15839	1074	38	1		1	TGFBRAP1	2	105924699	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	215763	105924699	137274674	635	3536											
FHL2	2274	hgsc.bcm.edu	37	chr2	106002854	106002854	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgggcttcccacactcctcGcaggtgttggcgaacagggt	7	9	13	12	2	0	0	0	0	0	0	3	1	2	0	2	4	1	3	2	4	1	2	rs11537578	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:106002854G>A	ENST00000409807.1	-	2	454	c.120C>T	c.(118-120)tgC>tgT	p.C40C	FHL2_ENST00000408995.1_Silent_p.C40C|FHL2_ENST00000344213.4_Silent_p.C150C|FHL2_ENST00000358129.4_Silent_p.C40C|FHL2_ENST00000336660.5_Silent_p.C40C|FHL2_ENST00000393353.3_Silent_p.C40C|FHL2_ENST00000322142.8_Silent_p.C40C|FHL2_ENST00000393352.3_Silent_p.C40C|FHL2_ENST00000607522.1_Silent_p.C40C|FHL2_ENST00000409177.1_Silent_p.C156C			Q14192	FHL2_HUMAN	four and a half LIM domains 2	40	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				androgen receptor signaling pathway (GO:0030521)|atrial cardiac muscle cell development (GO:0055014)|cellular lipid metabolic process (GO:0044255)|heart trabecula formation (GO:0060347)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|ventricular cardiac muscle cell development (GO:0055015)	actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|M band (GO:0031430)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Z disc (GO:0030018)	androgen receptor binding (GO:0050681)|identical protein binding (GO:0042802)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	9						CACACTCCTCGCAGGTGTTGG	0.607													G|||	58	0.0115815	0.0416	0.0043	5008	,	,		16948	0.0		0.0	False		,,,				2504	0.0				p.C40C		Atlas-SNP	.											.	FHL2	18	.	0			c.C120T						PASS	.	G	,,,	166,4240	111.2+/-149.4	4,158,2041	71	66	68		120,120,120,120	-5.8	0.6	2	dbSNP_120	68	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FHL2	NM_001039492.2,NM_001450.3,NM_201555.1,NM_201557.3	,,,	4,159,6340	AA,AG,GG		0.0116,3.7676,1.284	,,,	40/280,40/280,40/280,40/280	106002854	167,12839	2203	4300	6503	SO:0001819	synonymous_variant	2274	exon3			CTCCTCGCAGGTG		CCDS2070.1	2q12.2	2014-09-17			ENSG00000115641	ENSG00000115641			3703	protein-coding gene	gene with protein product		602633				8753811	Standard	NM_201557		Approved	SLIM3, DRAL	uc002tcy.3	Q14192	OTTHUMG00000153120	ENST00000409807.1:c.120C>T	2.37:g.106002854G>A		116	0	0		138	72	0.521739	NM_001039492	Q13229|Q13644|Q2I5I4|Q5TM15|Q9P294	Silent	SNP	ENST00000409807.1	37	CCDS2070.1																																																																																			G|0.989;A|0.011	0.011	strong		0.607	FHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329654.1			A	106002854	G	A	106002854	2	1	22	1	0	0	0	0	0	0	0	1	5887	1079	38	1		1	FHL2	2	106002854	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	78155	106002854	137196519	636	3537											
RGPD3	653489	hgsc.bcm.edu	37	chr2	107084716	107084716	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcaccgaggcgacgtacCgctccccgtaggccttgctg	5	7	12	17	5	0	0	0	0	0	0	1	2	1	0	6	2	3	5	6	2	2	3	rs190902687	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:107084716C>T	ENST00000409886.3	-	1	116	c.29G>A	c.(28-30)cGg>cAg	p.R10Q	RGPD3_ENST00000304514.7_Missense_Mutation_p.R10Q	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	10					protein targeting to Golgi (GO:0000042)					breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						GGCGACGTACCGCTCCCCGTA	0.692													.|||	45	0.00898562	0.0318	0.0043	5008	,	,		11990	0.0		0.0	False		,,,				2504	0.0				p.R10Q		Atlas-SNP	.											.	RGPD3	316	.	0			c.G29A						PASS	.	C	GLN/ARG	26,1358		0,26,666	63	92	84		29	1.8	1	2		84	0,3182		0,0,1591	no	missense	RGPD3	NM_001144013.1	43	0,26,2257	TT,TC,CC		0.0,1.8786,0.5694	probably-damaging	10/1759	107084716	26,4540	692	1591	2283	SO:0001583	missense	653489	exon1			ACGTACCGCTCCC		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.29G>A	2.37:g.107084716C>T	ENSP00000386588:p.Arg10Gln	341	0	0		437	193	0.441648	NM_001144013	B8ZZM4	Missense_Mutation	SNP	ENST00000409886.3	37	CCDS46379.1	18	0.008241758241758242	16	0.032520325203252036	2	0.0055248618784530384	0	0.0	0	0.0	.	12.78	2.039118	0.35989	0.018786	0.0	ENSG00000153165	ENST00000409886;ENST00000304514	T;T	0.53857	0.6;0.6	1.8	1.8	0.24995	.	.	.	.	.	T	0.27313	0.0670	L	0.54323	1.7	0.23685	N	0.997116	D	0.58620	0.983	P	0.49192	0.602	T	0.18429	-1.0337	9	0.59425	D	0.04	-11.0149	7.0248	0.24934	0.0:1.0:0.0:0.0	.	10	A6NKT7	RGPD3_HUMAN	Q	10	ENSP00000386588:R10Q;ENSP00000303659:R10Q	ENSP00000303659:R10Q	R	-	2	0	RGPD3	106451148	1.000000	0.71417	0.989000	0.46669	0.038000	0.13279	3.375000	0.52410	0.984000	0.38629	0.186000	0.17326	CGG	C|0.992;T|0.008	0.008	strong		0.692	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931		T	107084716	C	T	107084716	3	4	22	1	0	0	0	0	1	0	0	0	13302	652	23	1	5339	1	RGPD3	2	107084716	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1081862	107084716	136114657	637	3538											
RANBP2	5903	hgsc.bcm.edu	37	chr2	109347314	109347314	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctttatgaattggaagaaaaCacagacaaagccgttgaatg	17	9	9	6	1	0	4	0	2	0	2	0	5	0	5	1	1	2	1	1	1	7	4	rs144278795	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:109347314C>G	ENST00000283195.6	+	3	351	c.225C>G	c.(223-225)aaC>aaG	p.N75K		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	75					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						TGGAAGAAAACACAGACAAAG	0.353													C|||	16	0.00319489	0.0083	0.0058	5008	,	,		16939	0.0		0.001	False		,,,				2504	0.0				p.N75K		Atlas-SNP	.											.	RANBP2	488	.	0			c.C225G						PASS	.	C	LYS/ASN	19,2931		0,19,1456	102	123	115		225	-0.8	0.8	2	dbSNP_134	115	0,5138		0,0,2569	no	missense	RANBP2	NM_006267.4	94	0,19,4025	GG,GC,CC		0.0,0.6441,0.2349	probably-damaging	75/3225	109347314	19,8069	1475	2569	4044	SO:0001583	missense	5903	exon3			AGAAAACACAGAC	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.225C>G	2.37:g.109347314C>G	ENSP00000283195:p.Asn75Lys	250	0	0		296	142	0.47973	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	C	15.44	2.833077	0.50951	0.006441	0.0	ENSG00000153201	ENST00000409491;ENST00000283195;ENST00000456637	T	0.61392	0.11	4.24	-0.825	0.10809	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	.	.	.	.	T	0.56645	0.1999	L	0.55103	1.725	0.27121	N	0.962148	D	0.61080	0.989	P	0.62435	0.902	T	0.55854	-0.8075	9	0.45353	T	0.12	-19.048	9.7309	0.40361	0.0:0.4107:0.0:0.5893	.	75	P49792	RBP2_HUMAN	K	75;75;49	ENSP00000283195:N75K	ENSP00000283195:N75K	N	+	3	2	RANBP2	108713746	0.342000	0.24809	0.759000	0.31340	0.848000	0.48234	-0.351000	0.07711	-0.299000	0.08909	-0.237000	0.12165	AAC	C|0.996;G|0.004	0.004	strong		0.353	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		G	109347314	C	G	109347314	3	3	22	1	0	0	0	0	1	0	0	0	13043	477	17	4	235	4	RANBP2	2	109347314	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2262598	109347314	133852059	638	3539											
RANBP2	5903	hgsc.bcm.edu	37	chr2	109384665	109384665	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgcacctttgaaaagtaacaAtagtgaaactagttcagtag	16	11	8	6	0	1	2	1	2	0	0	1	2	1	2	1	0	3	4	1	0	8	6	rs145613015	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:109384665A>G	ENST00000283195.6	+	20	7796	c.7670A>G	c.(7669-7671)aAt>aGt	p.N2557S		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	2557					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						AAAAGTAACAATAGTGAAACT	0.363													A|||	10	0.00199681	0.0068	0.0014	5008	,	,		20419	0.0		0.0	False		,,,				2504	0.0				p.N2557S		Atlas-SNP	.											.	RANBP2	488	.	0			c.A7670G						PASS	.	A	SER/ASN	27,4379	30.8+/-60.4	1,25,2177	84	98	93		7670	-1	0	2	dbSNP_134	93	0,8594		0,0,4297	no	missense	RANBP2	NM_006267.4	46	1,25,6474	GG,GA,AA		0.0,0.6128,0.2077	benign	2557/3225	109384665	27,12973	2203	4297	6500	SO:0001583	missense	5903	exon20			GTAACAATAGTGA	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.7670A>G	2.37:g.109384665A>G	ENSP00000283195:p.Asn2557Ser	369	0	0		378	186	0.492063	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	A	0.024	-1.385684	0.01194	0.006128	0.0	ENSG00000153201	ENST00000409491;ENST00000283195	T	0.25250	1.81	5.31	-1.03	0.10102	.	.	.	.	.	T	0.04679	0.0127	N	0.00926	-1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39292	-0.9621	9	0.07644	T	0.81	-6.4079	10.0576	0.42255	0.5205:0.0:0.4795:0.0	.	2557	P49792	RBP2_HUMAN	S	1581;2557	ENSP00000283195:N2557S	ENSP00000283195:N2557S	N	+	2	0	RANBP2	108751097	0.000000	0.05858	0.007000	0.13788	0.682000	0.39822	-0.668000	0.05268	-0.097000	0.12307	0.377000	0.23210	AAT	.	.	weak		0.363	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		G	109384665	A	G	109384665	3	3	22	1	0	0	0	0	1	0	0	0	13043	101	4	3	7748	3	RANBP2	2	109384665	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	37351	109384665	133814708	639	3540											
CCDC138	165055	hgsc.bcm.edu	37	chr2	109429277	109429277	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgcatatatactgttgcagaGgaagtacgagtttatgacaa	14	11	10	6	2	0	2	0	1	0	1	0	4	0	3	0	1	3	5	0	1	7	7	rs58170568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:109429277G>C	ENST00000295124.4	+	9	995	c.935G>C	c.(934-936)aGg>aCg	p.R312T	CCDC138_ENST00000412964.2_Splice_Site_p.R312T	NM_144978.1	NP_659415.1	Q96M89	CC138_HUMAN	coiled-coil domain containing 138	312										endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	14						CTGTTGCAGAGGAAGTACGAG	0.318													G|||	31	0.0061901	0.0212	0.0043	5008	,	,		19524	0.0		0.0	False		,,,				2504	0.0				p.R312T		Atlas-SNP	.											.	CCDC138	49	.	0			c.G935C						PASS	.	G	THR/ARG	77,4329	68.1+/-105.8	1,75,2127	88	90	89		935	5.5	1	2	dbSNP_129	89	0,8598		0,0,4299	yes	missense-near-splice	CCDC138	NM_144978.1	71	1,75,6426	CC,CG,GG		0.0,1.7476,0.5921	benign	312/666	109429277	77,12927	2203	4299	6502	SO:0001630	splice_region_variant	165055	exon9			TGCAGAGGAAGTA	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.934-1G>C	2.37:g.109429277G>C		165	0	0		163	76	0.466258	NM_144978	Q05DF1|Q4ZG07|Q53TE1|Q6ZUY5|Q86VL7	Missense_Mutation	SNP	ENST00000295124.4	37	CCDS2080.1	14|14	0.00641025641025641|0.00641025641025641	11|11	0.022357723577235773|0.022357723577235773	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	G|G	13.96|13.96	2.393929|2.393929	0.42410|0.42410	0.017476|0.017476	0.0|0.0	ENSG00000163006|ENSG00000163006	ENST00000456512|ENST00000412964;ENST00000295124	.|D;D	.|0.89681	.|-2.55;-2.55	5.49|5.49	5.49|5.49	0.81192|0.81192	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.89670|0.89670	0.6782|0.6782	M|M	0.72894|0.72894	2.215|2.215	0.44798|0.44798	D|D	0.997805|0.997805	.|D;B	.|0.76494	.|0.999;0.441	.|D;B	.|0.83275	.|0.996;0.2	D|D	0.89997|0.89997	0.4112|0.4112	5|10	.|0.45353	.|T	.|0.12	.|.	18.1478|18.1478	0.89663|0.89663	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs58170568|rs58170568	.|312;312	.|Q96M89-2;Q96M89	.|.;CC138_HUMAN	R|T	209|312	.|ENSP00000411800:R312T;ENSP00000295124:R312T	.|ENSP00000295124:R312T	G|R	+|+	1|2	0|0	CCDC138|CCDC138	108795709|108795709	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.398000|0.398000	0.30690|0.30690	5.570000|5.570000	0.67398|0.67398	2.572000|2.572000	0.86782|0.86782	0.655000|0.655000	0.94253|0.94253	GGA|AGG	G|0.993;C|0.007	0.007	strong		0.318	CCDC138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253593.1	NM_144978	Missense_Mutation	C	109429277	G	C	109429277	5	2	22	1	0	0	0	0	0	0	1	0	2774	1014	35	4	969	4	CCDC138	2	109429277	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	44612	109429277	133770096	640	3541											
ANKRD57	65124	hgsc.bcm.edu	37	chr2	110372688	110372688	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgccagaacctccgtgacCtggtgatgggcagctccccg	6	6	12	17	3	0	3	0	2	0	1	2	3	2	3	7	2	2	2	7	2	1	0	rs72938294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:110372688C>G	ENST00000356454.3	+	1	778	c.622C>G	c.(622-624)Ctg>Gtg	p.L208V	SEPT10_ENST00000356688.4_5'Flank|SEPT10_ENST00000397714.2_5'Flank|SEPT10_ENST00000334001.6_5'Flank|SEPT10_ENST00000397712.2_5'Flank|SEPT10_ENST00000545389.1_5'Flank|SEPT10_ENST00000437928.1_5'Flank|SEPT10_ENST00000415095.1_5'Flank	NM_023016.3	NP_075392.2	Q53LP3	SWAHC_HUMAN	sosondowah ankyrin repeat domain family member C	208																	CCTCCGTGACCTGGTGATGGG	0.736													C|||	95	0.0189696	0.0688	0.0058	5008	,	,		11693	0.0		0.0	False		,,,				2504	0.0				p.L208V		Atlas-SNP	.											.	.	.	.	0			c.C622G						PASS	.	C	VAL/LEU	168,3274		1,166,1554	8	9	9		622	1.7	0	2	dbSNP_130	9	3,6469		0,3,3233	yes	missense	ANKRD57	NM_023016.3	32	1,169,4787	GG,GC,CC		0.0464,4.8809,1.7248	possibly-damaging	208/526	110372688	171,9743	1721	3236	4957	SO:0001583	missense	65124	exon1			CGTGACCTGGTGA	AK023346	CCDS33270.1	2q13	2013-01-10	2012-01-12	2012-01-12	ENSG00000198142	ENSG00000198142		"Ankyrin repeat domain containing"	26149	protein-coding gene	gene with protein product			"ankyrin repeat domain 57"	C2orf26, ANKRD57		22234889	Standard	NM_023016		Approved	FLJ21870	uc002tfb.3	Q53LP3	OTTHUMG00000153219	ENST00000356454.3:c.622C>G	2.37:g.110372688C>G	ENSP00000365830:p.Leu208Val	68	0	0		83	40	0.481928	NM_023016	Q8NE15|Q9H6U1	Missense_Mutation	SNP	ENST00000356454.3	37	CCDS33270.1	36	0.016483516483516484	31	0.06300813008130081	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	0.725	-0.782051	0.02907	0.048809	4.64E-4	ENSG00000198142	ENST00000356454	T	0.26373	1.74	3.58	1.66	0.24008	.	1.034310	0.07796	N	0.955796	T	0.01661	0.0053	N	0.22421	0.69	0.09310	N	1	B	0.22003	0.063	B	0.22386	0.039	T	0.27971	-1.0058	10	0.38643	T	0.18	-1.0053	4.8489	0.13528	0.1515:0.615:0.147:0.0865	.	208	Q53LP3	ANR57_HUMAN	V	208	ENSP00000365830:L208V	ENSP00000365830:L208V	L	+	1	2	ANKRD57	109729977	0.000000	0.05858	0.037000	0.18230	0.225000	0.24961	0.616000	0.24344	0.273000	0.22049	0.462000	0.41574	CTG	C|0.983;G|0.017	0.017	strong		0.736	SOWAHC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330168.1	NM_023016		G	110372688	C	G	110372688	3	3	22	1	0	0	0	0	1	0	0	0	683	680	24	4	624	4	ANKRD57	2	110372688	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	943411	110372688	132826685	641	3542											
MERTK	10461	hgsc.bcm.edu	37	chr2	112722854	112722854	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagtgcagatcaacatcaaaGgtaagcagcaaggctaggct	15	6	12	8	0	2	1	2	0	0	1	2	2	2	1	0	3	4	6	0	3	5	2	rs7588635	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:112722854G>A	ENST00000295408.4	+	5	1101	c.844G>A	c.(844-846)Gca>Aca	p.A282T	MERTK_ENST00000421804.2_Splice_Site_p.A282T|MERTK_ENST00000409780.1_Splice_Site_p.A106T			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	282			A -> T (in dbSNP:rs7588635). {ECO:0000269|PubMed:11062461, ECO:0000269|PubMed:17344846}.		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						CAACATCAAAGGTAAGCAGCA	0.567													G|||	233	0.0465256	0.171	0.0086	5008	,	,		19523	0.0		0.001	False		,,,				2504	0.0				p.A282T		Atlas-SNP	.											.	MERTK	112	.	0			c.G844A						PASS	.	G	THR/ALA	598,3808	255.2+/-260.5	47,504,1652	102	80	88		844	5.8	1	2	dbSNP_116	88	6,8594	4.3+/-15.6	0,6,4294	yes	missense-near-splice	MERTK	NM_006343.2	58	47,510,5946	AA,AG,GG		0.0698,13.5724,4.644	benign	282/1000	112722854	604,12402	2203	4300	6503	SO:0001630	splice_region_variant	10461	exon5			ATCAAAGGTAAGC	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.844+1G>A	2.37:g.112722854G>A		219	1	0.00456621		201	94	0.467662	NM_006343	Q9HBB4	Missense_Mutation	SNP	ENST00000295408.4	37	CCDS2094.1	90	0.04120879120879121	87	0.17682926829268292	3	0.008287292817679558	0	0.0	0	0.0	G	17.78	3.474628	0.63737	0.135724	6.98E-4	ENSG00000153208	ENST00000295408;ENST00000421804;ENST00000409780	T;T;T	0.36520	1.25;1.25;1.25	5.75	5.75	0.90469	Immunoglobulin-like fold (1);	0.534882	0.13857	U	0.357982	T	0.00109	0.0003	L	0.58101	1.795	0.30039	P	0.8128029999999999	B	0.32245	0.361	B	0.25140	0.058	T	0.05084	-1.0907	9	0.72032	D	0.01	-0.4319	19.5333	0.95239	0.0:0.0:1.0:0.0	rs7588635;rs17838486;rs7588635	282	Q12866	MERTK_HUMAN	T	282;282;106	ENSP00000295408:A282T;ENSP00000389152:A282T;ENSP00000387277:A106T	ENSP00000295408:A282T	A	+	1	0	MERTK	112439325	1.000000	0.71417	1.000000	0.80357	0.579000	0.36224	4.652000	0.61454	2.720000	0.93068	0.563000	0.77884	GCA	G|0.947;A|0.053	0.053	strong		0.567	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2		Missense_Mutation	A	112722854	G	A	112722854	5	1	22	1	0	0	0	0	0	0	1	0	9488	1014	35	2	862	2	MERTK	2	112722854	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2350166	112722854	130476519	642	3543											
MERTK	10461	hgsc.bcm.edu	37	chr2	112740561	112740561	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccacgtgtggcagagtgcAgggatttccgtaagtctaaa	10	10	12	9	2	1	1	0	0	1	1	3	2	3	2	2	2	1	3	2	2	3	3	rs115203717	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:112740561A>G	ENST00000295408.4	+	8	1544	c.1287A>G	c.(1285-1287)gcA>gcG	p.A429A	MERTK_ENST00000421804.2_Silent_p.A429A|MERTK_ENST00000409780.1_Silent_p.A253A			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	429	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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						GGCAGAGTGCAGGGATTTCCG	0.448													A|||	28	0.00559105	0.0197	0.0029	5008	,	,		19646	0.0		0.0	False		,,,				2504	0.0				p.A429A		Atlas-SNP	.											.	MERTK	112	.	0			c.A1287G						PASS	.	A		48,4358	50.9+/-86.3	1,46,2156	111	106	108		1287	-9.6	0	2	dbSNP_132	108	0,8600		0,0,4300	no	coding-synonymous	MERTK	NM_006343.2		1,46,6456	GG,GA,AA		0.0,1.0894,0.3691		429/1000	112740561	48,12958	2203	4300	6503	SO:0001819	synonymous_variant	10461	exon8			GAGTGCAGGGATT	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.1287A>G	2.37:g.112740561A>G		151	0	0		123	54	0.439024	NM_006343	Q9HBB4	Silent	SNP	ENST00000295408.4	37	CCDS2094.1																																																																																			A|0.995;G|0.005	0.005	strong		0.448	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2			G	112740561	A	G	112740561	2	3	22	1	0	0	0	0	0	0	0	1	9488	175	7	3		3	MERTK	2	112740561	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	17707	112740561	130458812	643	3544											
RGPD5	727851	hgsc.bcm.edu	37	chr2	113147751	113147751	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcctggttccgaaatgccaAatttaaatccatcagcagac	13	11	6	11	1	1	1	1	0	0	1	4	2	4	1	4	1	2	2	4	1	4	4	rs561418400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:113147751A>C	ENST00000302558.3	-	20	2962	c.2771T>G	c.(2770-2772)tTt>tGt	p.F924C	RGPD8_ENST00000409750.1_Missense_Mutation_p.F784C	NM_001164463.1	NP_001157935.1	O14715	RGPD8_HUMAN	RANBP2-like and GRIP domain containing 8	924					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						CGAAATGCCAAATTTAAATCC	0.398													.|||	287	0.0573083	0.2126	0.0086	5008	,	,		19416	0.0		0.0	False		,,,				2504	0.0				p.F924C		Atlas-SNP	.											.	RGPD8	81	.	0			c.T2771G						PASS	.						6	9	8					2																	113147751		655	1498	2153	SO:0001583	missense	727851	exon20			ATGCCAAATTTAA	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.2771T>G	2.37:g.113147751A>C	ENSP00000306637:p.Phe924Cys	627	0	0		720	230	0.319444	NM_001164463	Q5CZA8	Missense_Mutation	SNP	ENST00000302558.3	37	CCDS46394.1	.	.	.	.	.	.	.	.	.	.	-	11.55	1.670972	0.29693	.	.	ENSG00000169629	ENST00000302558;ENST00000409750	T;T	0.52983	0.65;0.64	2.33	2.33	0.28932	.	.	.	.	.	T	0.61223	0.2330	M	0.73598	2.24	0.80722	D	1	D	0.76494	0.999	D	0.66979	0.948	T	0.59359	-0.7469	9	0.37606	T	0.19	-28.0606	8.2389	0.31645	1.0:0.0:0.0:0.0	.	924	O14715	RGPD8_HUMAN	C	924;784	ENSP00000306637:F924C;ENSP00000386511:F784C	ENSP00000306637:F924C	F	-	2	0	RGPD8	112864222	1.000000	0.71417	0.998000	0.56505	0.288000	0.27193	8.054000	0.89451	1.076000	0.40961	0.147000	0.16070	TTT	.	.	none		0.398	RGPD8-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375951.1	XM_001722279		C	113147751	A	C	113147751	3	2	22	1	0	0	0	0	1	0	0	0	13304	14	1	5	13556	5	RGPD5	2	113147751	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	407190	113147751	130051622	644	3545											
CKAP2L	150468	hgsc.bcm.edu	37	chr2	113509891	113509891	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagtgttgttaattttacTggacagttcgagttgtgctt	8	17	11	5	1	0	1	0	0	0	1	1	3	0	2	0	1	2	5	0	1	2	7	rs36046436	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:113509891T>C	ENST00000302450.6	-	5	1633	c.1555A>G	c.(1555-1557)Agt>Ggt	p.S519G	CKAP2L_ENST00000541405.1_Missense_Mutation_p.S354G	NM_152515.3	NP_689728.3	Q8IYA6	CKP2L_HUMAN	cytoskeleton associated protein 2-like	519			S -> G (in dbSNP:rs36046436).			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						TTAATTTTACTGGACAGTTCG	0.348													T|||	66	0.0131789	0.0492	0.0014	5008	,	,		17493	0.0		0.0	False		,,,				2504	0.0				p.S519G		Atlas-SNP	.											.	CKAP2L	54	.	0			c.A1555G						PASS	.	T	GLY/SER	207,4199	127.8+/-164.7	5,197,2001	253	252	252		1555	0.2	0	2	dbSNP_126	252	0,8600		0,0,4300	yes	missense	CKAP2L	NM_152515.3	56	5,197,6301	CC,CT,TT		0.0,4.6981,1.5916	benign	519/746	113509891	207,12799	2203	4300	6503	SO:0001583	missense	150468	exon5			TTTTACTGGACAG	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.1555A>G	2.37:g.113509891T>C	ENSP00000305204:p.Ser519Gly	396	0	0		382	184	0.481675	NM_152515	A8K915|B4DZE3|B7ZAC6|F5H0M5|Q53QF8|Q53RS8|Q8N1J8	Missense_Mutation	SNP	ENST00000302450.6	37	CCDS2100.1	20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	T	5.135	0.210489	0.09757	0.046981	0.0	ENSG00000169607	ENST00000541405;ENST00000302450	T;T	0.22945	1.93;1.93	5.61	0.251	0.15540	.	0.735060	0.14028	N	0.346338	T	0.01730	0.0055	N	0.22421	0.69	0.09310	N	1	B;B	0.24426	0.034;0.103	B;B	0.25140	0.04;0.058	T	0.23583	-1.0184	10	0.21014	T	0.42	0.2974	1.8328	0.03133	0.1345:0.1548:0.1396:0.5711	rs36046436	108;519	Q8IYA6-2;Q8IYA6	.;CKP2L_HUMAN	G	354;519	ENSP00000438763:S354G;ENSP00000305204:S519G	ENSP00000305204:S519G	S	-	1	0	CKAP2L	113226362	0.001000	0.12720	0.041000	0.18516	0.163000	0.22366	0.999000	0.29757	0.391000	0.25143	-0.481000	0.04817	AGT	T|0.983;C|0.017	0.017	strong		0.348	CKAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254082.2	NM_152515		C	113509891	T	C	113509891	3	2	22	1	0	0	0	0	1	0	0	0	3445	1580	55	3	702	3	CKAP2L	2	113509891	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	362140	113509891	129689482	645	3546											
IL1A	3552	hgsc.bcm.edu	37	chr2	113539224	113539224	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcctccaggtcatcatcagtGatggattggcttaaactcaa	11	11	9	10	0	4	1	4	1	0	0	5	2	5	2	2	3	1	1	2	3	3	2	rs20540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:113539224G>A	ENST00000263339.3	-	4	431	c.276C>T	c.(274-276)atC>atT	p.I92I		NM_000575.3	NP_000566.3	P01583	IL1A_HUMAN	interleukin 1, alpha	92					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|cytokine-mediated signaling pathway (GO:0019221)|ectopic germ cell programmed cell death (GO:0035234)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fever generation (GO:0001660)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell division (GO:0051781)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of mitosis (GO:0045840)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation vascular endothelial growth factor production (GO:0010575)|response to copper ion (GO:0046688)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	copper ion binding (GO:0005507)|cytokine activity (GO:0005125)			breast(2)|large_intestine(1)|lung(9)	12					Rilonacept(DB06372)	CATCATCAGTGATGGATTGGC	0.453													G|||	96	0.0191693	0.0719	0.0014	5008	,	,		23080	0.0		0.0	False		,,,				2504	0.0				p.I92I		Atlas-SNP	.											.	IL1A	19	.	0			c.C276T						PASS	.	G		263,4143	149.9+/-184.0	9,245,1949	218	203	208		276	0	0	2	dbSNP_67	208	0,8600		0,0,4300	no	coding-synonymous	IL1A	NM_000575.3		9,245,6249	AA,AG,GG		0.0,5.9691,2.0221		92/272	113539224	263,12743	2203	4300	6503	SO:0001819	synonymous_variant	3552	exon4			ATCAGTGATGGAT	M28983	CCDS2101.1	2q14	2014-01-30			ENSG00000115008	ENSG00000115008		"Interleukins and interleukin receptors", "Endogenous ligands"	5991	protein-coding gene	gene with protein product	"preinterleukin 1 alpha", "hematopoietin-1", "pro-interleukin-1-alpha"	147760		IL1		8188271, 2989698	Standard	NM_000575		Approved	IL1F1, IL-1A, IL1-ALPHA	uc002tig.3	P01583	OTTHUMG00000131315	ENST00000263339.3:c.276C>T	2.37:g.113539224G>A		243	1	0.00411523		242	112	0.46281	NM_000575	Q53QF9|Q7RU02	Silent	SNP	ENST00000263339.3	37	CCDS2101.1																																																																																			G|0.980;A|0.020	0.020	strong		0.453	IL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254084.1	NM_000575		A	113539224	G	A	113539224	2	1	22	1	0	0	0	0	0	0	0	1	7659	1280	45	2		2	IL1A	2	113539224	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	29333	113539224	129660149	646	3547											
FOXD4L1	200350	hgsc.bcm.edu	37	chr2	114257381	114257381	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagggcacctactggagccTggaccccgcctcccaggaca	9	4	11	17	1	0	0	0	0	0	0	1	3	1	3	6	4	2	1	6	4	2	1	rs13428956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:114257381T>G	ENST00000306507.5	+	1	721	c.548T>G	c.(547-549)cTg>cGg	p.L183R		NM_012184.4	NP_036316.1	Q9NU39	FX4L1_HUMAN	forkhead box D4-like 1	183					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						TACTGGAGCCTGGACCCCGCC	0.652													.|||	306	0.0611022	0.2216	0.0159	5008	,	,		10688	0.0		0.0	False		,,,				2504	0.002				p.L183R		Atlas-SNP	.											.	FOXD4L1	48	.	0			c.T548G						PASS	.	T	ARG/LEU	727,3503		131,465,1519	54	72	66		548	2.6	1	2	dbSNP_121	66	3,8201		0,3,4099	no	missense	FOXD4L1	NM_012184.4	102	131,468,5618	GG,GT,TT		0.0366,17.1868,5.871	probably-damaging	183/409	114257381	730,11704	2115	4102	6217	SO:0001583	missense	200350	exon1			GGAGCCTGGACCC	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.548T>G	2.37:g.114257381T>G	ENSP00000302756:p.Leu183Arg	148	0	0		174	82	0.471264	NM_012184	B3KWN1|B9EGF3	Missense_Mutation	SNP	ENST00000306507.5	37	CCDS2117.1	91	0.041666666666666664	90	0.18292682926829268	1	0.0027624309392265192	0	0.0	0	0.0	.	17.71	3.456701	0.63401	0.171868	3.66E-4	ENSG00000184492	ENST00000306507	D	0.97041	-4.22	2.57	2.57	0.30868	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.27841	U	0.017640	T	0.15219	0.0367	M	0.93854	3.465	0.09310	P	0.99999539299	D	0.76494	0.999	D	0.81914	0.995	T	0.05886	-1.0858	9	0.87932	D	0	.	8.6531	0.34046	0.0:0.0:0.0:1.0	rs13428956	183	Q9NU39	FX4L1_HUMAN	R	183	ENSP00000302756:L183R	ENSP00000302756:L183R	L	+	2	0	FOXD4L1	113973851	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	7.431000	0.80335	1.190000	0.43042	0.155000	0.16302	CTG	T|0.973;G|0.027	0.027	strong		0.652	FOXD4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254148.1	NM_012184		G	114257381	T	G	114257381	3	3	22	1	0	0	0	0	1	0	0	0	6008	1580	55	5	550	5	FOXD4L1	2	114257381	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	718157	114257381	128941992	647	3548											
C1QL2	165257	hgsc.bcm.edu	37	chr2	119915750	119915750	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggcagtgtaagggtcgcaGatcatgcggcaggtgcccat	8	7	16	10	3	1	1	1	0	0	1	2	1	1	1	1	4	2	4	1	4	1	1	rs113019193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:119915750G>T	ENST00000272520.3	-	1	715	c.96C>A	c.(94-96)atC>atA	p.I32I		NM_182528.3	NP_872334.2	Q7Z5L3	C1QL2_HUMAN	complement component 1, q subcomponent-like 2	32					protein oligomerization (GO:0051259)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)				NS(1)|endometrium(1)|large_intestine(3)|pancreas(1)|prostate(1)	7						AAGGGTCGCAGATCATGCGGC	0.721										HNSCC(49;0.14)			G|||	87	0.0173722	0.0628	0.0043	5008	,	,		7998	0.0		0.001	False		,,,				2504	0.0				p.I32I		Atlas-SNP	.											.	C1QL2	25	.	0			c.C96A						PASS	.	G		134,3240		1,132,1554	6	7	7		96	3.3	1	2	dbSNP_132	7	8,7550		0,8,3771	no	coding-synonymous	C1QL2	NM_182528.3		1,140,5325	TT,TG,GG		0.1058,3.9715,1.2989		32/288	119915750	142,10790	1687	3779	5466	SO:0001819	synonymous_variant	165257	exon1			GTCGCAGATCATG	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.96C>A	2.37:g.119915750G>T		7	0	0		7	4	0.571429	NM_182528		Silent	SNP	ENST00000272520.3	37	CCDS42737.1																																																																																			G|0.981;T|0.019	0.019	strong		0.721	C1QL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330527.2	NM_182528		T	119915750	G	T	119915750	2	4	22	1	0	0	0	0	0	0	0	1	1961	932	33	4		4	C1QL2	2	119915750	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5658369	119915750	123283623	648	3549											
TMEM37	6344	hgsc.bcm.edu	37	chr2	120194673	120194673	+	IGR	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gatctgcttcagagacctggGccaggcccatgtgcccgggc	6	7	14	14	1	2	1	1	0	1	1	2	3	2	1	4	3	2	1	4	3	0	1	rs114197773	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:120194673G>A	ENST00000019103.5	-	0	1865				TMEM37_ENST00000465296.1_3'UTR|TMEM37_ENST00000409826.1_Missense_Mutation_p.G89D|TMEM37_ENST00000306406.4_Missense_Mutation_p.G77D	NM_002980.2	NP_002971.2	P47872	SCTR_HUMAN	secretin receptor						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)	AGAGACCTGGGCCAGGCCCAT	0.652													G|||	140	0.0279553	0.0976	0.0101	5008	,	,		14451	0.0		0.004	False		,,,				2504	0.0				p.G77D		Atlas-SNP	.											.	TMEM37	40	.	0			c.G230A						PASS	.	G	ASP/GLY	327,4077	168.3+/-199.2	12,303,1887	51	54	53		230	2.8	0.8	2	dbSNP_132	53	8,8590	6.4+/-24.3	0,8,4291	yes	missense	TMEM37	NM_183240.2	94	12,311,6178	AA,AG,GG		0.093,7.4251,2.5765	benign	77/191	120194673	335,12667	2202	4299	6501	SO:0001628	intergenic_variant	140738	exon2			ACCTGGGCCAGGC		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		2.37:g.120194673G>A		38	0	0		54	25	0.462963	NM_183240	Q12961|Q13213|Q53T00	Missense_Mutation	SNP	ENST00000019103.5	37	CCDS2127.1	47	0.02152014652014652	41	0.08333333333333333	3	0.008287292817679558	0	0.0	3	0.00395778364116095	G	5.612	0.297674	0.10622	0.074251	9.3E-4	ENSG00000171227	ENST00000409826;ENST00000306406	.	.	.	4.74	2.78	0.32641	.	0.572504	0.18041	N	0.153613	T	0.01387	0.0045	L	0.29908	0.895	0.09310	N	0.99999	B	0.21606	0.058	B	0.22601	0.04	T	0.06698	-1.0812	9	0.15499	T	0.54	-3.9992	8.7558	0.34645	0.2022:0.0:0.7978:0.0	.	77	Q8WXS4	CCGL_HUMAN	D	89;77	.	ENSP00000303148:G77D	G	+	2	0	TMEM37	119911143	0.094000	0.21725	0.818000	0.32626	0.630000	0.37929	0.340000	0.19892	1.234000	0.43709	0.561000	0.74099	GGC	G|0.973;A|0.027	0.027	strong		0.652	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2			A	120194673	G	A	120194673	1	1	22	0	1	0	0	0	0	0	0	0	16173	1203	42	2		2	TMEM37	2	120194673	IGR	SNP	G	TCGA-G8-6324-01A-11D-2210-10	278923	120194673	123004700	649	3550											
BIN1	274	hgsc.bcm.edu	37	chr2	127827598	127827598	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcggggaactggcccaggtaCgtgtccatggtcagcagcgc	7	7	15	12	3	1	0	1	0	0	0	3	1	2	1	2	5	4	2	2	5	2	1	rs61748158	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:127827598C>T	ENST00000316724.5	-	5	795	c.384G>A	c.(382-384)acG>acA	p.T128T	BIN1_ENST00000259238.4_Silent_p.T128T|BIN1_ENST00000393040.3_Silent_p.T128T|BIN1_ENST00000348750.4_Silent_p.T128T|BIN1_ENST00000357970.3_Silent_p.T128T|BIN1_ENST00000409400.1_Silent_p.T128T|BIN1_ENST00000393041.3_Silent_p.T128T|BIN1_ENST00000376113.2_Silent_p.T128T|BIN1_ENST00000346226.3_Silent_p.T128T|BIN1_ENST00000351659.3_Silent_p.T128T|BIN1_ENST00000352848.3_Silent_p.T128T	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	128	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)		GGCCCAGGTACGTGTCCATGG	0.597													C|||	18	0.00359425	0.0106	0.0014	5008	,	,		19793	0.003		0.0	False		,,,				2504	0.0				p.T128T		Atlas-SNP	.											.	BIN1	85	.	0			c.G384A						PASS	.	C	,,,,,,,,,	24,4382		0,24,2179	138	108	118		384,384,384,384,384,384,384,384,384,384	-9.6	0.6	2	dbSNP_129	118	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BIN1	NM_004305.3,NM_139343.2,NM_139344.2,NM_139345.2,NM_139346.2,NM_139347.2,NM_139348.2,NM_139349.2,NM_139350.2,NM_139351.2	,,,,,,,,,	0,24,6479	TT,TC,CC		0.0,0.5447,0.1845	,,,,,,,,,	128/455,128/594,128/551,128/507,128/498,128/519,128/483,128/476,128/440,128/410	127827598	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	274	exon5			CAGGTACGTGTCC	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.384G>A	2.37:g.127827598C>T		67	0	0		64	32	0.5	NM_139346	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Silent	SNP	ENST00000316724.5	37	CCDS2138.1																																																																																			C|0.998;T|0.002	0.002	strong		0.597	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343		T	127827598	C	T	127827598	2	4	22	1	0	0	0	0	0	0	0	1	1432	523	19	1		1	BIN1	2	127827598	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	7632925	127827598	115371775	650	3551											
IWS1	55677	hgsc.bcm.edu	37	chr2	128261099	128261099	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttgcctgacttgtctgataCagcatcactgtcagagtcat	9	14	8	10	0	4	3	3	2	1	1	4	3	4	3	1	0	3	1	1	0	1	3	rs34785867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128261099C>T	ENST00000295321.4	-	4	1532	c.1273G>A	c.(1273-1275)Gta>Ata	p.V425I	AC010976.2_ENST00000599001.1_RNA|IWS1_ENST00000455721.2_Missense_Mutation_p.V432I|IWS1_ENST00000486662.1_5'Flank	NM_017969.2	NP_060439.2	Q96ST2	IWS1_HUMAN	IWS1 homolog (S. cerevisiae)	425	Glu-rich.		V -> I (in dbSNP:rs34785867).		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)		TTGTCTGATACAGCATCACTG	0.383													C|||	98	0.0195687	0.0711	0.0058	5008	,	,		15170	0.0		0.0	False		,,,				2504	0.0				p.V425I		Atlas-SNP	.											.	IWS1	61	.	0			c.G1273A						PASS	.	C	ILE/VAL	309,4097	167.3+/-198.3	10,289,1904	128	111	117		1273	-6.2	0	2	dbSNP_126	117	2,8598	1.2+/-3.3	0,2,4298	yes	missense	IWS1	NM_017969.2	29	10,291,6202	TT,TC,CC		0.0233,7.0132,2.3912	benign	425/820	128261099	311,12695	2203	4300	6503	SO:0001583	missense	55677	exon4			CTGATACAGCATC	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.1273G>A	2.37:g.128261099C>T	ENSP00000295321:p.Val425Ile	176	0	0		185	184	0.994595	NM_017969	Q2TB65|Q6P157|Q8N3E8|Q96MI7|Q9NV97|Q9NWH8	Missense_Mutation	SNP	ENST00000295321.4	37	CCDS2146.1	27	0.012362637362637362	25	0.0508130081300813	2	0.0055248618784530384	0	0.0	0	0.0	C	10.39	1.337907	0.24253	0.070132	2.33E-4	ENSG00000163166	ENST00000295321;ENST00000433551;ENST00000455721	T;T	0.31247	2.33;1.5	5.67	-6.15	0.02105	.	1.260290	0.05632	N	0.581936	T	0.01124	0.0037	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24440	-1.0160	10	0.37606	T	0.19	0.5854	9.4352	0.38635	0.1086:0.6567:0.1211:0.1136	rs34785867	425	Q96ST2	IWS1_HUMAN	I	425;378;432	ENSP00000295321:V425I;ENSP00000399245:V432I	ENSP00000295321:V425I	V	-	1	0	IWS1	127977569	0.000000	0.05858	0.003000	0.11579	0.981000	0.71138	-0.215000	0.09279	-1.101000	0.03027	-0.793000	0.03317	GTA	C|0.977;T|0.023	0.023	strong		0.383	IWS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254384.2	NM_017969		T	128261099	C	T	128261099	3	4	22	1	0	0	0	0	1	0	0	0	7940	478	17	2	1230	2	IWS1	2	128261099	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	433501	128261099	114938274	651	3552											
MYO7B	4648	hgsc.bcm.edu	37	chr2	128341904	128341904	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gacgaagaaagccgcttcccGcaggtgtgtgttcgggcctg	7	8	15	11	4	0	1	0	0	0	1	2	3	1	1	3	2	1	3	3	2	2	2	rs61743462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128341904G>A	ENST00000409816.2	+	12	1583	c.1551G>A	c.(1549-1551)ccG>ccA	p.P517P	MYO7B_ENST00000389524.4_Silent_p.P517P|MYO7B_ENST00000428314.1_Silent_p.P517P			Q6PIF6	MYO7B_HUMAN	myosin VIIB	517	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)		GCCGCTTCCCGCAGGTGTGTG	0.602													G|||	54	0.0107827	0.0393	0.0029	5008	,	,		18661	0.0		0.0	False		,,,				2504	0.0				p.P517P		Atlas-SNP	.											.	MYO7B	359	.	0			c.G1551A						PASS	.	G		144,3842		1,142,1850	55	59	57		1551	-6.6	0.9	2	dbSNP_129	57	1,8289		0,1,4144	no	coding-synonymous	MYO7B	NM_001080527.1		1,143,5994	AA,AG,GG		0.0121,3.6126,1.1812		517/2117	128341904	145,12131	1993	4145	6138	SO:0001819	synonymous_variant	4648	exon13			CTTCCCGCAGGTG		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.1551G>A	2.37:g.128341904G>A		92	0	0		119	53	0.445378	NM_001080527	Q14786|Q8TEE1	Silent	SNP	ENST00000409816.2	37	CCDS46405.1																																																																																			G|0.993;A|0.007	0.007	strong		0.602	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001		A	128341904	G	A	128341904	2	1	22	1	0	0	0	0	0	0	0	1	10092	1074	38	1		1	MYO7B	2	128341904	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	80805	128341904	114857469	652	3553											
MYO7B	4648	hgsc.bcm.edu	37	chr2	128364787	128364787	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttgcctccgcagatcctcGtgggctttgagcgcctgcag	4	11	12	14	3	1	2	0	1	1	1	4	2	3	2	4	1	3	3	4	1	0	2	rs201386852	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128364787G>C	ENST00000409816.2	+	20	2463	c.2431G>C	c.(2431-2433)Gtg>Ctg	p.V811L	MYO7B_ENST00000389524.4_Missense_Mutation_p.V811L|MYO7B_ENST00000428314.1_Missense_Mutation_p.V811L			Q6PIF6	MYO7B_HUMAN	myosin VIIB	811	IQ 3. {ECO:0000255|PROSITE- ProRule:PRU00116}.					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)		GCAGATCCTCGTGGGCTTTGA	0.632													G|||	2	0.000399361	0.0015	0.0	5008	,	,		17201	0.0		0.0	False		,,,				2504	0.0				p.V811L		Atlas-SNP	.											.	MYO7B	359	.	0			c.G2431C						PASS	.	G	LEU/VAL	8,3810		0,8,1901	7	9	8		2431	-6.2	0.1	2		8	0,7854		0,0,3927	yes	missense	MYO7B	NM_001080527.1	32	0,8,5828	CC,CG,GG		0.0,0.2095,0.0685	benign	811/2117	128364787	8,11664	1909	3927	5836	SO:0001583	missense	4648	exon21			ATCCTCGTGGGCT		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.2431G>C	2.37:g.128364787G>C	ENSP00000386461:p.Val811Leu	192	0	0		180	93	0.516667	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	.	.	.	.	.	.	.	.	.	.	G	4.550	0.102047	0.08731	0.002095	0.0	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	D;D;D	0.86627	-2.15;-2.15;-2.15	5.6	-6.22	0.02058	.	0.757314	0.11581	N	0.549776	T	0.52901	0.1763	N	0.01352	-0.895	0.09310	N	0.999991	B	0.02656	0.0	B	0.04013	0.001	T	0.59177	-0.7503	10	0.07990	T	0.79	.	1.1174	0.01717	0.1671:0.2857:0.2377:0.3095	.	811	Q6PIF6	MYO7B_HUMAN	L	811	ENSP00000374175:V811L;ENSP00000415090:V811L;ENSP00000386461:V811L	ENSP00000374175:V811L	V	+	1	0	MYO7B	128081257	0.000000	0.05858	0.057000	0.19452	0.727000	0.41649	-0.731000	0.04909	-1.131000	0.02910	-0.344000	0.07964	GTG	.	.	weak		0.632	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001		C	128364787	G	C	128364787	3	2	22	1	0	0	0	0	1	0	0	0	10092	1145	40	4	2509	4	MYO7B	2	128364787	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	22883	128364787	114834586	653	3554											
MYO7B	4648	hgsc.bcm.edu	37	chr2	128367433	128367433	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgtttccccaggccgccctgGtcatatggaacgtcatcctg	6	11	10	14	2	2	0	2	0	0	0	4	1	4	1	5	3	1	1	5	3	2	2	rs61741454	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128367433G>A	ENST00000409816.2	+	23	3066	c.3034G>A	c.(3034-3036)Gtc>Atc	p.V1012I	MYO7B_ENST00000389524.4_Missense_Mutation_p.V1012I|MYO7B_ENST00000428314.1_Missense_Mutation_p.V1012I			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1012	MyTH4 1. {ECO:0000255|PROSITE- ProRule:PRU00359}.					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)		GGCCGCCCTGGTCATATGGAA	0.592													G|||	36	0.0071885	0.0234	0.0072	5008	,	,		18749	0.0		0.0	False		,,,				2504	0.0				p.V1012I		Atlas-SNP	.											.	MYO7B	359	.	0			c.G3034A						PASS	.	G	ILE/VAL	91,4015		2,87,1964	48	52	51		3034	2.6	0	2	dbSNP_129	51	2,8426		0,2,4212	yes	missense	MYO7B	NM_001080527.1	29	2,89,6176	AA,AG,GG		0.0237,2.2163,0.742	benign	1012/2117	128367433	93,12441	2053	4214	6267	SO:0001583	missense	4648	exon24			GCCCTGGTCATAT		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.3034G>A	2.37:g.128367433G>A	ENSP00000386461:p.Val1012Ile	207	1	0.00483092		203	105	0.517241	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	12	0.005494505494505495	9	0.018292682926829267	3	0.008287292817679558	0	0.0	0	0.0	G	8.417	0.845525	0.16963	0.022163	2.37E-4	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	D;D;D	0.87103	-2.21;-2.21;-2.21	5.47	2.57	0.30868	MyTH4 domain (2);	0.485163	0.20625	N	0.088698	T	0.62122	0.2402	N	0.17474	0.49	0.09310	N	1	B	0.12630	0.006	B	0.08055	0.003	T	0.63328	-0.6662	10	0.72032	D	0.01	.	8.5581	0.33494	0.1397:0.1265:0.7338:0.0	rs61741454	1012	Q6PIF6	MYO7B_HUMAN	I	1012	ENSP00000374175:V1012I;ENSP00000415090:V1012I;ENSP00000386461:V1012I	ENSP00000374175:V1012I	V	+	1	0	MYO7B	128083903	0.888000	0.30383	0.039000	0.18376	0.011000	0.07611	2.293000	0.43558	0.678000	0.31325	0.655000	0.94253	GTC	G|0.993;A|0.007	0.007	strong		0.592	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001		A	128367433	G	A	128367433	3	1	22	1	0	0	0	0	1	0	0	0	10092	1261	44	2	3124	2	MYO7B	2	128367433	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2646	128367433	114831940	654	3555											
MYO7B	4648	hgsc.bcm.edu	37	chr2	128367556	128367556	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acacgctgggcagggagcacGgtgcccaggttccacagcac	9	4	14	14	2	0	0	0	0	0	0	1	1	1	1	2	4	3	5	2	4	0	1	rs199654311	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128367556G>A	ENST00000409816.2	+	23	3189	c.3157G>A	c.(3157-3159)Ggt>Agt	p.G1053S	MYO7B_ENST00000389524.4_Missense_Mutation_p.G1053S|MYO7B_ENST00000428314.1_Missense_Mutation_p.G1053S			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1053	MyTH4 1. {ECO:0000255|PROSITE- ProRule:PRU00359}.					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)		CAGGGAGCACGGTGCCCAGGT	0.642													G|||	13	0.00259585	0.0098	0.0	5008	,	,		17986	0.0		0.0	False		,,,				2504	0.0				p.G1053S		Atlas-SNP	.											.	MYO7B	359	.	0			c.G3157A						PASS	.	G	SER/GLY	32,4284		0,32,2126	29	33	32		3157	-6.9	0	2		32	0,8518		0,0,4259	yes	missense	MYO7B	NM_001080527.1	56	0,32,6385	AA,AG,GG		0.0,0.7414,0.2493	benign	1053/2117	128367556	32,12802	2158	4259	6417	SO:0001583	missense	4648	exon24			GAGCACGGTGCCC		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.3157G>A	2.37:g.128367556G>A	ENSP00000386461:p.Gly1053Ser	100	0	0		108	58	0.537037	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	8.095	0.775454	0.16051	0.007414	0.0	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	D;D;D	0.86164	-2.08;-2.08;-2.08	5.17	-6.92	0.01644	MyTH4 domain (2);	1.887620	0.02507	N	0.091055	T	0.52885	0.1762	N	0.00841	-1.15	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.64101	-0.6486	10	0.07030	T	0.85	.	10.025	0.42066	0.4891:0.1097:0.4012:0.0	.	1053	Q6PIF6	MYO7B_HUMAN	S	1053	ENSP00000374175:G1053S;ENSP00000415090:G1053S;ENSP00000386461:G1053S	ENSP00000374175:G1053S	G	+	1	0	MYO7B	128084026	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.438000	0.06905	-1.703000	0.01409	-0.140000	0.14226	GGT	G|0.999;A|0.001	0.001	strong		0.642	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001		A	128367556	G	A	128367556	3	1	22	1	0	0	0	0	1	0	0	0	10092	1116	39	1	3247	1	MYO7B	2	128367556	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	123	128367556	114831817	655	3556											
MYO7B	4648	hgsc.bcm.edu	37	chr2	128378009	128378009	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcctgctcagcctctgcctcGgctgcttcccaccctcagag	4	10	8	19	1	3	1	2	0	1	1	6	1	5	1	5	1	4	3	5	1	0	1	rs199900811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128378009G>A	ENST00000409816.2	+	25	3447	c.3415G>A	c.(3415-3417)Ggc>Agc	p.G1139S	MYO7B_ENST00000389524.4_Missense_Mutation_p.G1139S|MYO7B_ENST00000409090.1_5'UTR|MYO7B_ENST00000428314.1_Missense_Mutation_p.G1139S			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1139	MyTH4 1. {ECO:0000255|PROSITE- ProRule:PRU00359}.					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)		CCTCTGCCTCGGCTGCTTCCC	0.607													G|||	13	0.00259585	0.0098	0.0	5008	,	,		14187	0.0		0.0	False		,,,				2504	0.0				p.G1139S		Atlas-SNP	.											.	MYO7B	359	.	0			c.G3415A						PASS	.	G	SER/GLY	30,3642		0,30,1806	33	36	35		3415	4.2	1	2		35	0,8174		0,0,4087	yes	missense	MYO7B	NM_001080527.1	56	0,30,5893	AA,AG,GG		0.0,0.817,0.2533	probably-damaging	1139/2117	128378009	30,11816	1836	4087	5923	SO:0001583	missense	4648	exon26			TGCCTCGGCTGCT		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.3415G>A	2.37:g.128378009G>A	ENSP00000386461:p.Gly1139Ser	205	0	0		236	120	0.508475	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	6	0.0027472527472527475	2	0.0040650406504065045	0	0.0	3	0.005244755244755245	1	0.0013192612137203166	.	26.3	4.726017	0.89298	0.00817	0.0	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	D;D;D	0.91407	-2.84;-2.84;-2.84	4.16	4.16	0.48862	MyTH4 domain (3);	0.000000	0.85682	D	0.000000	D	0.91074	0.7191	L	0.48986	1.54	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.89742	0.3934	10	0.25106	T	0.35	.	17.0488	0.86513	0.0:0.0:1.0:0.0	.	1139	Q6PIF6	MYO7B_HUMAN	S	1139	ENSP00000374175:G1139S;ENSP00000415090:G1139S;ENSP00000386461:G1139S	ENSP00000374175:G1139S	G	+	1	0	MYO7B	128094479	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	8.993000	0.93524	2.318000	0.78349	0.456000	0.33151	GGC	G|0.997;A|0.003	0.003	strong		0.607	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001		A	128378009	G	A	128378009	3	1	22	1	0	0	0	0	1	0	0	0	10092	1116	39	1	3513	1	MYO7B	2	128378009	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	10453	128378009	114821364	656	3557											
MYO7B	4648	hgsc.bcm.edu	37	chr2	128381717	128381717	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	catgatggatgccatcgcccGgtgtgagcagatggcccagg	8	7	15	11	2	0	3	0	2	0	1	1	4	0	4	3	4	2	1	3	4	0	0	rs2245408	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128381717G>A	ENST00000409816.2	+	28	3823	c.3791G>A	c.(3790-3792)cGg>cAg	p.R1264Q	RP11-286H15.1_ENST00000609697.1_RNA|MYO7B_ENST00000389524.4_Missense_Mutation_p.R1264Q|MYO7B_ENST00000409090.1_Missense_Mutation_p.R117Q|MYO7B_ENST00000428314.1_Missense_Mutation_p.R1264Q			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1264	FERM 1. {ECO:0000255|PROSITE- ProRule:PRU00084}.		R -> Q (in dbSNP:rs2245408).			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)		GCCATCGCCCGGTGTGAGCAG	0.667													A|||	64	0.0127796	0.0439	0.0086	5008	,	,		17463	0.0		0.0	False		,,,				2504	0.0				p.R1264Q		Atlas-SNP	.											.	MYO7B	359	.	0			c.G3791A						PASS	.	A	GLN/ARG	141,3873		2,137,1868	21	26	25		3791	3.8	1	2	dbSNP_100	25	2,8324		0,2,4161	yes	missense	MYO7B	NM_001080527.1	43	2,139,6029	AA,AG,GG		0.024,3.5127,1.1588	benign	1264/2117	128381717	143,12197	2007	4163	6170	SO:0001583	missense	4648	exon29			TCGCCCGGTGTGA		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.3791G>A	2.37:g.128381717G>A	ENSP00000386461:p.Arg1264Gln	78	0	0		90	51	0.566667	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	22	0.010073260073260074	19	0.03861788617886179	3	0.008287292817679558	0	0.0	0	0.0	.	9.528	1.110073	0.20714	0.035127	2.4E-4	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000272666;ENST00000409816;ENST00000437387;ENST00000409090	T;T;T;T;T	0.77229	-1.08;-1.08;-1.08;-1.08;-1.08	3.76	3.76	0.43208	Band 4.1 domain (1);FERM domain (1);	0.000000	0.85682	N	0.000000	T	0.09247	0.0228	N	0.00084	-2.21	0.22562	N	0.998982	B	0.02656	0.0	B	0.01281	0.0	T	0.38308	-0.9667	10	0.02654	T	1	.	9.5173	0.39113	0.9119:0.0:0.0881:0.0	rs2245408;rs2245408	1264	Q6PIF6	MYO7B_HUMAN	Q	1264;1264;117;1264;117;117	ENSP00000374175:R1264Q;ENSP00000415090:R1264Q;ENSP00000386461:R1264Q;ENSP00000404927:R117Q;ENSP00000386850:R117Q	ENSP00000272666:R117Q	R	+	2	0	MYO7B	128098187	1.000000	0.71417	0.998000	0.56505	0.832000	0.47134	4.758000	0.62220	0.809000	0.34255	-0.490000	0.04691	CGG	G|0.990;A|0.010	0.010	strong		0.667	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001		A	128381717	G	A	128381717	3	1	22	1	0	0	0	0	1	0	0	0	10092	1116	39	1	3901	1	MYO7B	2	128381717	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3708	128381717	114817656	657	3558											
MYO7B	4648	hgsc.bcm.edu	37	chr2	128381861	128381861	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tatttaccgccaagtcctccGaggagtctggtctggcgagt	7	11	12	11	3	2	0	0	0	2	0	4	3	4	1	4	3	1	0	4	3	3	3	rs61743523	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128381861G>A	ENST00000409816.2	+	28	3967	c.3935G>A	c.(3934-3936)cGa>cAa	p.R1312Q	RP11-286H15.1_ENST00000609697.1_RNA|MYO7B_ENST00000389524.4_Missense_Mutation_p.R1312Q|MYO7B_ENST00000409090.1_Missense_Mutation_p.R165Q|MYO7B_ENST00000428314.1_Missense_Mutation_p.R1312Q			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1312	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)		CAAGTCCTCCGAGGAGTCTGG	0.592													A|||	36	0.0071885	0.0234	0.0072	5008	,	,		19505	0.0		0.0	False		,,,				2504	0.0				p.R1312Q		Atlas-SNP	.											.	MYO7B	359	.	0			c.G3935A						PASS	.	A	GLN/ARG	82,3886		2,78,1904	15	16	16		3935	-0.1	0.1	2	dbSNP_129	16	2,8290		0,2,4144	yes	missense	MYO7B	NM_001080527.1	43	2,80,6048	AA,AG,GG		0.0241,2.0665,0.6852	benign	1312/2117	128381861	84,12176	1984	4146	6130	SO:0001583	missense	4648	exon29			TCCTCCGAGGAGT		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.3935G>A	2.37:g.128381861G>A	ENSP00000386461:p.Arg1312Gln	69	0	0		74	40	0.540541	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	12	0.005494505494505495	9	0.018292682926829267	3	0.008287292817679558	0	0.0	0	0.0	.	13.32	2.200829	0.38905	0.020665	2.41E-4	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000272666;ENST00000409816;ENST00000437387;ENST00000409090	T;T;T;T;T	0.74947	-0.89;-0.89;-0.89;-0.6;-0.89	3.68	-0.0642	0.13773	FERM central domain (1);Band 4.1 domain (1);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.715826	0.13724	N	0.367181	T	0.49236	0.1545	M	0.79258	2.445	0.21579	N	0.999633	P	0.42337	0.776	B	0.32465	0.146	T	0.49995	-0.8879	10	0.38643	T	0.18	.	5.7748	0.18273	0.2859:0.0:0.5394:0.1747	rs61743523	1312	Q6PIF6	MYO7B_HUMAN	Q	1312;1312;165;1312;165;165	ENSP00000374175:R1312Q;ENSP00000415090:R1312Q;ENSP00000386461:R1312Q;ENSP00000404927:R165Q;ENSP00000386850:R165Q	ENSP00000272666:R165Q	R	+	2	0	MYO7B	128098331	0.985000	0.35326	0.083000	0.20561	0.098000	0.18820	2.232000	0.43018	-0.259000	0.09432	-0.361000	0.07541	CGA	G|0.993;A|0.007	0.007	strong		0.592	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001		A	128381861	G	A	128381861	3	1	22	1	0	0	0	0	1	0	0	0	10092	1058	37	1	4045	1	MYO7B	2	128381861	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	144	128381861	114817512	658	3559											
GPR17	2840	hgsc.bcm.edu	37	chr2	128408747	128408747	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcaagctccgcaggcccctCtacgcacacctggcctgtgc	6	7	9	19	2	2	0	1	0	1	0	3	0	3	0	5	2	3	3	5	2	2	1	rs34722685	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128408747C>A	ENST00000272644.3	+	3	596	c.522C>A	c.(520-522)ctC>ctA	p.L174L	LIMS2_ENST00000410038.1_5'Flank|LIMS2_ENST00000545738.2_Intron|GPR17_ENST00000544369.1_Silent_p.L174L|LIMS2_ENST00000410011.1_Intron|LIMS2_ENST00000324938.5_Intron|LIMS2_ENST00000409254.1_5'Flank|LIMS2_ENST00000409455.1_Intron|LIMS2_ENST00000355119.4_Intron|LIMS2_ENST00000409808.2_Intron|GPR17_ENST00000393018.3_Silent_p.L174L|GPR17_ENST00000486700.1_3'UTR	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	174					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)		GCAGGCCCCTCTACGCACACC	0.637													C|||	70	0.0139776	0.0499	0.0058	5008	,	,		18872	0.0		0.0	False		,,,				2504	0.0				p.L174L		Atlas-SNP	.											.	GPR17	56	.	0			c.C522A						PASS	.	C	,,,,,,,	158,4248	106.5+/-144.9	2,154,2047	112	99	103		,,,522,438,438,522,	3.6	1	2	dbSNP_126	103	1,8599		0,1,4299	no	intron,intron,intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron	GPR17,LIMS2	NM_001136037.2,NM_001161403.1,NM_001161404.1,NM_001161415.1,NM_001161416.1,NM_001161417.1,NM_005291.2,NM_017980.4	,,,,,,,	2,155,6346	AA,AC,CC		0.0116,3.586,1.2225	,,,,,,,	,,,174/368,146/340,146/340,174/368,	128408747	159,12847	2203	4300	6503	SO:0001819	synonymous_variant	2840	exon3			GCCCCTCTACGCA		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.522C>A	2.37:g.128408747C>A		84	0	0		88	44	0.5	NM_005291	A8K9L0|B2R9X0|Q8N5S7|Q9UDZ6|Q9UE21	Silent	SNP	ENST00000272644.3	37	CCDS2148.1																																																																																			C|0.985;A|0.015	0.015	strong		0.637	GPR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254390.1			A	128408747	C	A	128408747	2	1	22	1	0	0	0	0	0	0	0	1	6675	900	32	4		4	GPR17	2	128408747	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	26886	128408747	114790626	659	3560											
UGGT1	56886	hgsc.bcm.edu	37	chr2	128870784	128870784	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcaccgccagcttatatcAaaaagcaatgcaggcaaaat	16	9	6	10	1	2	0	2	0	0	0	2	0	2	0	2	1	3	4	2	1	7	3	rs149605444	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128870784A>G	ENST00000259253.6	+	6	695	c.648A>G	c.(646-648)tcA>tcG	p.S216S	UGGT1_ENST00000375990.3_Silent_p.S192S	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	216					'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						AGCTTATATCAAAAAGCAATG	0.353													A|||	25	0.00499201	0.0189	0.0	5008	,	,		15033	0.0		0.0	False		,,,				2504	0.0				p.S216S		Atlas-SNP	.											.	UGGT1	126	.	0			c.A648G						PASS	.	A		64,4342	58.1+/-94.6	1,62,2140	71	74	73		648	-1.1	0.1	2	dbSNP_134	73	0,8598		0,0,4299	no	coding-synonymous	UGGT1	NM_020120.3		1,62,6439	GG,GA,AA		0.0,1.4526,0.4922		216/1556	128870784	64,12940	2203	4299	6502	SO:0001819	synonymous_variant	56886	exon6			TATATCAAAAAGC	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.648A>G	2.37:g.128870784A>G		243	0	0		290	132	0.455172	NM_020120	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Silent	SNP	ENST00000259253.6	37	CCDS2154.1																																																																																			A|0.995;G|0.005	0.005	strong		0.353	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120		G	128870784	A	G	128870784	2	3	22	1	0	0	0	0	0	0	0	1	16956	117	5	3		3	UGGT1	2	128870784	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	462037	128870784	114328589	660	3561											
CFC1	55997	hgsc.bcm.edu	37	chr2	131356322	131356322	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tccagttgagcggtgactgtCggtgcttctgagtggcaacc	6	11	14	10	2	1	3	0	3	1	0	3	3	2	3	2	3	3	3	2	3	1	2	rs201431919	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:131356322C>T	ENST00000259216.4	-	3	402	c.140G>A	c.(139-141)cGa>cAa	p.R47Q		NM_032545.3	NP_115934.1	P0CG37	CFC1_HUMAN	cripto, FRL-1, cryptic family 1	47					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)					CGGTGACTGTCGGTGCTTCTG	0.537													c|||	372	0.0742812	0.2663	0.0259	5008	,	,		16561	0.0		0.002	False		,,,				2504	0.0				p.R47Q		Atlas-SNP	.											CFC1,fourth_ventricle,glioma,0,1	.	.	1	0			c.G140A	GRCh37	CM023185	CFC1	M		PASS	.						15	23	21					2																	131356322		2174	4254	6428	SO:0001583	missense	653275	exon3			GACTGTCGGTGCT	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.140G>A	2.37:g.131356322C>T	ENSP00000259216:p.Arg47Gln	1076	0	0		797	540	0.677541	NM_001079530	B2RCY0|B9EJD3|Q53T05|Q9GZR3	Missense_Mutation	SNP	ENST00000259216.4	37	CCDS2162.1	101	0.04624542124542125	92	0.18699186991869918	9	0.024861878453038673	0	0.0	0	0.0	.	0.054	-1.241061	0.01493	.	.	ENSG00000136698	ENST00000259216	D	0.88818	-2.43	1.91	0.598	0.17512	.	0.638739	0.14771	N	0.299398	T	0.00109	0.0003	N	0.00197	-1.87	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22836	-1.0205	10	0.07030	T	0.85	-32.4582	1.7088	0.02888	0.2856:0.1859:0.0:0.5285	.	47	P0CG37	CFC1_HUMAN	Q	47	ENSP00000259216:R47Q	ENSP00000259216:R47Q	R	-	2	0	CFC1	131072792	0.006000	0.16342	0.003000	0.11579	0.092000	0.18411	0.487000	0.22356	-0.207000	0.10187	-0.665000	0.03846	CGA	C|0.969;T|0.031	0.031	strong		0.537	CFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333367.1	NM_032545		T	131356322	C	T	131356322	3	4	22	1	0	0	0	0	1	0	0	0	3281	884	31	1	1243	1	CFC1	2	131356322	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2485538	131356322	111843051	661	3562											
GPR148	344561	hgsc.bcm.edu	37	chr2	131487691	131487691	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacatacctgtacctgctcCgctaccggcagctgttgggc	6	10	10	15	2	1	0	1	0	0	0	2	0	2	0	4	2	5	6	4	2	3	4	rs143265147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:131487691C>T	ENST00000309926.4	+	1	1049	c.967C>T	c.(967-969)Cgc>Tgc	p.R323C		NM_207364.2	NP_997247.2	Q8TDV2	GP148_HUMAN	G protein-coupled receptor 148	323						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)					GTACCTGCTCCGCTACCGGCA	0.577													.|||	23	0.00459265	0.0144	0.0043	5008	,	,		20324	0.0		0.001	False		,,,				2504	0.0				p.R323C		Atlas-SNP	.											GPR148,NS,carcinoma,0,1	GPR148	54	1	0			c.C967T						PASS	.	C	CYS/ARG	56,4350		1,54,2148	60	51	54		967	-4.1	0	2	dbSNP_134	54	1,8599		0,1,4299	yes	missense	GPR148	NM_207364.2	180	1,55,6447	TT,TC,CC		0.0116,1.271,0.4383	benign	323/348	131487691	57,12949	2203	4300	6503	SO:0001583	missense	344561	exon1			CTGCTCCGCTACC	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.967C>T	2.37:g.131487691C>T	ENSP00000308908:p.Arg323Cys	78	0	0		114	58	0.508772	NM_207364	Q2M369|Q86SP7|Q86U87	Missense_Mutation	SNP	ENST00000309926.4	37	CCDS2163.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	.	8.765	0.924629	0.18056	0.01271	1.16E-4	ENSG00000173302	ENST00000309926	T	0.40476	1.03	3.49	-4.14	0.03892	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46442	U	0.000284	T	0.13586	0.0329	L	0.27053	0.805	0.32198	N	0.578142	B	0.18741	0.03	B	0.13407	0.009	T	0.01810	-1.1269	10	0.52906	T	0.07	-10.4178	0.3322	0.00320	0.2767:0.2483:0.1305:0.3444	.	323	Q8TDV2	GP148_HUMAN	C	323	ENSP00000308908:R323C	ENSP00000308908:R323C	R	+	1	0	GPR148	131204161	0.959000	0.32827	0.000000	0.03702	0.359000	0.29487	-0.164000	0.09983	-0.512000	0.06505	-0.261000	0.10672	CGC	C|0.996;T|0.004	0.004	strong		0.577	GPR148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254552.3	XM_293092		T	131487691	C	T	131487691	3	4	22	1	0	0	0	0	1	0	0	0	6661	652	23	1	969	1	GPR148	2	131487691	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	131369	131487691	111711682	662	3563											
ARHGEF4	50649	hgsc.bcm.edu	37	chr2	131803624	131803624	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttcagctgttggccggccCtgctacctgacgcgccagaa	6	9	12	14	3	1	2	1	1	0	1	1	2	1	2	4	2	3	4	4	2	2	3	rs114004756	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:131803624C>T	ENST00000326016.5	+	14	2454	c.1935C>T	c.(1933-1935)ccC>ccT	p.P645P	ARHGEF4_ENST00000525839.1_3'UTR|ARHGEF4_ENST00000428230.2_Silent_p.P147P|ARHGEF4_ENST00000392953.3_3'UTR|ARHGEF4_ENST00000355771.3_Silent_p.P574P|ARHGEF4_ENST00000409303.1_Silent_p.P585P	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	645					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)		TTGGCCGGCCCTGCTACCTGA	0.677													C|||	20	0.00399361	0.0151	0.0	5008	,	,		16752	0.0		0.0	False		,,,				2504	0.0				p.P645P		Atlas-SNP	.											.	ARHGEF4	89	.	0			c.C1935T						PASS	.	C	,	66,4340	61.1+/-98.1	3,60,2140	61	72	68		1935,	-1.7	1	2	dbSNP_132	68	0,8600		0,0,4300	no	coding-synonymous,utr-3	ARHGEF4	NM_015320.2,NM_032995.1	,	3,60,6440	TT,TC,CC		0.0,1.498,0.5075	,	645/691,	131803624	66,12940	2203	4300	6503	SO:0001819	synonymous_variant	50649	exon14			CCGGCCCTGCTAC	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.1935C>T	2.37:g.131803624C>T		166	0	0		180	73	0.405556	NM_015320	Q9HDC6|Q9UPP0	Silent	SNP	ENST00000326016.5	37	CCDS2165.1																																																																																			C|0.996;T|0.004	0.004	strong		0.677	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254554.4			T	131803624	C	T	131803624	2	4	22	1	0	0	0	0	0	0	0	1	908	668	24	2		2	ARHGEF4	2	131803624	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	315933	131803624	111395749	663	3564											
GPR39	2863	hgsc.bcm.edu	37	chr2	133403034	133403036	+	In_Frame_Del	DEL	AGA	AGA	-																															gtcctctgcaaggagaactgAgaagattttcttaagcactt																								rs557760477|rs113224054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:133403034_133403036delAGA	ENST00000329321.3	+	2	1686_1688	c.1217_1219delAGA	c.(1216-1221)gagaag>gag	p.K407del	GPR39_ENST00000470071.1_3'UTR|LYPD1_ENST00000397463.2_3'UTR	NM_001508.2	NP_001499.1	O43194	GPR39_HUMAN	G protein-coupled receptor 39	407					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)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						AGGAGAACTGAGAAGATTTTCTT	0.601														13	0.00259585	0.0098	0.0	5008	,	,		18521	0.0		0.0	False		,,,				2504	0.0				p.406_406del		Pindel	.											.	GPR39	60	.	0			c.1216_1218del						PASS	.		,,	25,4241		2,21,2110					,,	-1.8	0		dbSNP_132	52	2,8252		1,0,4126	no	utr-3,coding,utr-3	GPR39,LYPD1	NM_144586.5,NM_001508.2,NM_001077427.2	,,	3,21,6236	A1A1,A1R,RR		0.0242,0.586,0.2157	,,	,,		27,12493				SO:0001651	inframe_deletion	2863	exon2			.	AF034633	CCDS2170.1	2q21-q22	2012-08-21			ENSG00000183840	ENSG00000183840		"GPCR / Class A : Orphans"	4496	protein-coding gene	gene with protein product		602886				9441746	Standard	NM_001508		Approved		uc002ttl.3	O43194	OTTHUMG00000131679	ENST00000329321.3:c.1217_1219delAGA	2.37:g.133403037_133403039delAGA	ENSP00000327417:p.Lys407del	26	0	.		23	10	0.435	NM_001508	B2RC12|B6V9G4|Q08AS2|Q53R01	In_Frame_Del	DEL	ENST00000329321.3	37	CCDS2170.1																																																																																			AGA|0.500;-|0.500	0.500	weak		0.601	GPR39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254582.1			-	133403036	AGA	-	133403034	7	5	22	1	0	1	0	1	0	0	0	0	6701	304	11	0	1223	0	GPR39	2	133403034	In_Frame_Del	DEL	AGA	TCGA-G8-6324-01A-11D-2210-10	1599410	133403034	109796339	664	3565											
LYPD1	116372	hgsc.bcm.edu	37	chr2	133403647	133403647	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccgagaagagggctaattTgaggaacaggatggtggtgc	11	8	17	5	1	0	3	0	1	0	2	0	6	0	5	1	5	3	1	1	5	3	2	rs139508764	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:133403647T>C	ENST00000397463.2	-	3	669	c.397A>G	c.(397-399)Aaa>Gaa	p.K133E	LYPD1_ENST00000345008.6_Missense_Mutation_p.K81E|GPR39_ENST00000470071.1_3'UTR|GPR39_ENST00000329321.3_3'UTR	NM_144586.5	NP_653187.3	Q8N2G4	LYPD1_HUMAN	LY6/PLAUR domain containing 1	133				K -> R (in Ref. 2; BAC85518). {ECO:0000305}.		anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				lung(2)	2						AGGGCTAATTTGAGGAACAGG	0.612													T|||	16	0.00319489	0.0113	0.0014	5008	,	,		16585	0.0		0.0	False		,,,				2504	0.0				p.K133E		Atlas-SNP	.											.	LYPD1	11	.	0			c.A397G						PASS	.	T	GLU/LYS,,GLU/LYS	34,3886		1,32,1927	66	73	71		241,,397	-1.4	0	2	dbSNP_134	71	0,8316		0,0,4158	yes	missense,utr-3,missense	GPR39,LYPD1	NM_001077427.2,NM_001508.2,NM_144586.5	56,,56	1,32,6085	CC,CT,TT		0.0,0.8673,0.2779	benign,,benign	81/90,,133/142	133403647	34,12202	1960	4158	6118	SO:0001583	missense	116372	exon3			CTAATTTGAGGAA	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.397A>G	2.37:g.133403647T>C	ENSP00000380605:p.Lys133Glu	180	0	0		158	85	0.537975	NM_144586	H7BXW6|Q6ZP52|Q6ZWI4|Q96AC2	Missense_Mutation	SNP	ENST00000397463.2	37	CCDS42759.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	T	8.848	0.943963	0.18281	0.008673	0.0	ENSG00000150551	ENST00000409034;ENST00000397463;ENST00000345008	D;D	0.82526	-1.62;-1.62	5.55	-1.42	0.08913	.	1.164150	0.06065	N	0.658974	T	0.58680	0.2139	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.50833	-0.8781	10	0.42905	T	0.14	-15.7811	8.1786	0.31296	0.0:0.1191:0.444:0.4369	.	133;149	Q8N2G4;Q8N2G4-3	LYPD1_HUMAN;.	E	156;133;81	ENSP00000380605:K133E;ENSP00000340563:K81E	ENSP00000340563:K81E	K	-	1	0	LYPD1	133120117	0.001000	0.12720	0.021000	0.16686	0.724000	0.41520	-0.106000	0.10890	-0.206000	0.10203	0.529000	0.55759	AAA	T|0.998;C|0.002	0.002	strong		0.612	LYPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331821.1	NM_144586		C	133403647	T	C	133403647	3	2	22	1	0	0	0	0	1	0	0	0	9118	1821	63	3	32	3	LYPD1	2	133403647	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	613	133403647	109795726	665	3566											
NCKAP5	344148	hgsc.bcm.edu	37	chr2	133887676	133887676	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttccagttcatgtatcagcTtctcatgctataaaagacac	12	13	5	11	0	3	1	3	0	1	1	5	1	4	1	1	0	2	4	1	0	4	6	rs35356262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:133887676T>C	ENST00000409261.1	-	6	588	c.215A>G	c.(214-216)aAg>aGg	p.K72R	NCKAP5_ENST00000405974.3_Missense_Mutation_p.K72R|NCKAP5_ENST00000409213.1_Missense_Mutation_p.K72R|NCKAP5_ENST00000317721.6_Missense_Mutation_p.K72R	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	72										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						ATGTATCAGCTTCTCATGCTA	0.403													T|||	6	0.00119808	0.0045	0.0	5008	,	,		20515	0.0		0.0	False		,,,				2504	0.0				p.K72R		Atlas-SNP	.											.	NCKAP5	322	.	0			c.A215G						PASS	.	T	ARG/LYS,ARG/LYS	25,3761		0,25,1868	69	65	66		215,215	3.8	1	2	dbSNP_126	66	0,8236		0,0,4118	yes	missense,missense	NCKAP5	NM_207363.2,NM_207481.3	26,26	0,25,5986	CC,CT,TT		0.0,0.6603,0.208	probably-damaging,probably-damaging	72/1910,72/591	133887676	25,11997	1893	4118	6011	SO:0001583	missense	344148	exon6			ATCAGCTTCTCAT	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.215A>G	2.37:g.133887676T>C	ENSP00000387128:p.Lys72Arg	99	0	0		81	37	0.45679	NM_207481	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	2|2	9.157509157509158E-4|9.157509157509158E-4	2|2	0.0040650406504065045|0.0040650406504065045	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	T|T	22.4|22.4	4.279946|4.279946	0.80692|0.80692	0.006603|0.006603	0.0|0.0	ENSG00000176771|ENSG00000176771	ENST00000409261;ENST00000409213;ENST00000317721;ENST00000405974;ENST00000537661;ENST00000542834|ENST00000427594	T;T;T;T|.	0.51817|.	2.68;0.69;2.68;0.69|.	6.17|6.17	3.85|3.85	0.44370|0.44370	.|.	.|.	.|.	.|.	.|.	T|T	0.19765|0.19765	0.0475|0.0475	L|L	0.27053|0.27053	0.805|0.805	0.24242|0.24242	N|N	0.995352|0.995352	B;B;B;D|.	0.58620|.	0.006;0.063;0.126;0.983|.	B;B;B;P|.	0.56865|.	0.005;0.033;0.074;0.808|.	T|T	0.14952|0.14952	-1.0454|-1.0454	9|5	0.66056|.	D|.	0.02|.	.|.	7.094|7.094	0.25299|0.25299	0.0:0.1686:0.0:0.8314|0.0:0.1686:0.0:0.8314	rs35356262|rs35356262	72;47;72;72|.	F5GYX5;O14513-3;O14513-2;O14513|.	.;.;.;NCKP5_HUMAN|.	R|G	72;72;72;72;72;47|68	ENSP00000387128:K72R;ENSP00000386952:K72R;ENSP00000380603:K72R;ENSP00000385692:K72R|.	ENSP00000380603:K72R|.	K|S	-|-	2|1	0|0	NCKAP5|NCKAP5	133604146|133604146	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	3.758000|3.758000	0.55220|0.55220	1.163000|1.163000	0.42636|0.42636	0.533000|0.533000	0.62120|0.62120	AAG|AGC	T|0.999;C|0.001	0.001	strong		0.403	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481		C	133887676	T	C	133887676	3	2	22	1	0	0	0	0	1	0	0	0	10232	1609	56	3	5574	3	NCKAP5	2	133887676	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	484029	133887676	109311697	666	3567											
YSK4	80122	hgsc.bcm.edu	37	chr2	135745648	135745648	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acgacttaactagggctcccGgaggctcgtttgatgggctg	7	10	14	10	3	0	1	0	1	0	0	2	3	1	2	1	4	1	4	1	4	2	3	rs113683052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:135745648G>A	ENST00000375845.3	-	7	824	c.794C>T	c.(793-795)cCg>cTg	p.P265L	MAP3K19_ENST00000392918.3_Intron|MAP3K19_ENST00000375844.3_Intron|MAP3K19_ENST00000392915.1_Missense_Mutation_p.P282L|MAP3K19_ENST00000315513.3_5'UTR|MAP3K19_ENST00000392917.3_Intron|MAP3K19_ENST00000358371.4_Missense_Mutation_p.P152L	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	265							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)										TAGGGCTCCCGGAGGCTCGTT	0.448													G|||	44	0.00878594	0.031	0.0043	5008	,	,		19304	0.0		0.0	False		,,,				2504	0.0				p.P265L		Atlas-SNP	.											.	.	.	.	0			c.C794T						PASS	.	G	,LEU/PRO	119,4287	89.7+/-128.4	0,119,2084	78	83	81		,794	1	0	2	dbSNP_132	81	2,8598	2.2+/-6.3	0,2,4298	yes	intron,missense	YSK4	NM_001018046.1,NM_025052.3	,98	0,121,6382	AA,AG,GG		0.0233,2.7009,0.9303	,benign	,265/1329	135745648	121,12885	2203	4300	6503	SO:0001583	missense	80122	exon7			GCTCCCGGAGGCT	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.794C>T	2.37:g.135745648G>A	ENSP00000365005:p.Pro265Leu	119	0	0		106	45	0.424528	NM_025052	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	37	CCDS2176.2	9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	G	2.128	-0.399907	0.04865	0.027009	2.33E-4	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000392915	T;T;T	0.69306	-0.39;-0.39;1.98	4.72	1.02	0.19986	.	0.637582	0.12907	N	0.429241	T	0.22205	0.0535	N	0.22421	0.69	0.09310	N	0.999997	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.19386	-1.0307	10	0.52906	T	0.07	.	2.7976	0.05405	0.1402:0.0796:0.1588:0.6214	.	152;282;265	Q56UN5-3;A8MWG7;Q56UN5	.;.;YSK4_HUMAN	L	265;152;282	ENSP00000365005:P265L;ENSP00000351140:P152L;ENSP00000376647:P282L	ENSP00000351140:P152L	P	-	2	0	YSK4	135462118	0.000000	0.05858	0.004000	0.12327	0.000000	0.00434	-0.057000	0.11768	0.020000	0.15106	-0.271000	0.10264	CCG	G|0.989;A|0.011	0.011	strong		0.448	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052		A	135745648	G	A	135745648	3	1	22	1	0	0	0	0	1	0	0	0	17510	1116	39	1	3208	1	YSK4	2	135745648	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1857972	135745648	107453725	667	3568											
ZRANB3	84083	hgsc.bcm.edu	37	chr2	135988236	135988236	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	actttccacgagtggagttcGgatttgcttggactgggatg	7	13	14	7	2	0	0	0	0	0	0	2	5	1	4	1	4	1	2	1	4	0	4	rs200823309	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:135988236G>A	ENST00000264159.6	-	13	1917	c.1801C>T	c.(1801-1803)Cga>Tga	p.R601*	ZRANB3_ENST00000401392.1_Nonsense_Mutation_p.R601*|ZRANB3_ENST00000412849.1_5'UTR|ZRANB3_ENST00000536680.1_Nonsense_Mutation_p.R601*	NM_032143.2	NP_115519.2	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	601					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)		AGTGGAGTTCGGATTTGCTTG	0.507													G|||	2	0.000399361	0.0015	0.0	5008	,	,		19706	0.0		0.0	False		,,,				2504	0.0				p.R601X		Atlas-SNP	.											.	ZRANB3	109	.	0			c.C1801T						PASS	.	G	stop/ARG	10,3932		0,10,1961	158	155	156		1801	-0.6	0	2		156	1,8297		0,1,4148	yes	stop-gained	ZRANB3	NM_032143.2		0,11,6109	AA,AG,GG		0.0121,0.2537,0.0899		601/1080	135988236	11,12229	1971	4149	6120	SO:0001587	stop_gained	84083	exon13			GAGTTCGGATTTG	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.1801C>T	2.37:g.135988236G>A	ENSP00000264159:p.Arg601*	349	0	0		323	145	0.448916	NM_032143	B3KYA1|B4E375|B5MDI3|D3DP76|E9PBP0|Q53SM1|Q6P2C4|Q8N1P4|Q9H0E8	Nonsense_Mutation	SNP	ENST00000264159.6	37	CCDS46419.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	36	5.734207	0.96865	0.002537	1.21E-4	ENSG00000121988	ENST00000538542;ENST00000283060;ENST00000401392;ENST00000264159;ENST00000536680	.	.	.	4.8	-0.643	0.11482	.	1.959680	0.01762	N	0.030630	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.5281	2.7512	0.05281	0.137:0.0772:0.2876:0.4982	.	.	.	.	X	66;66;601;601;601	.	ENSP00000264159:R601X	R	-	1	2	ZRANB3	135704706	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.257000	0.18369	-0.270000	0.09285	-0.375000	0.07067	CGA	G|1.000;A|0.000	0.000	strong		0.507	ZRANB3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318254.1	NM_032143		A	135988236	G	A	135988236	4	1	22	1	0	0	0	0	0	1	0	0	18239	1124	39	1	1474	1	ZRANB3	2	135988236	Nonsense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	242588	135988236	107211137	668	3569											
LRP1B	53353	hgsc.bcm.edu	37	chr2	141274456	141274456	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taagctaaatacaatgtctcAccacagtggaattcatcacg	15	10	6	10	1	3	0	3	0	1	0	4	1	3	1	1	1	2	1	1	1	6	4			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:141274456A>G	ENST00000389484.3	-	50	9121		c.e50+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)		ACAATGTCTCACCACAGTGGA	0.328										TSP Lung(27;0.18)																											.	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.8149+2T>C						PASS	.						146	134	138					2																	141274456		2203	4300	6503	SO:0001630	splice_region_variant	53353	exon51			TGTCTCACCACAG	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.8149+1T>C	2.37:g.141274456A>G		80	0	0		66	12	0.181818	NM_018557	Q8WY29|Q8WY30|Q8WY31	Splice_Site	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	A	18.09	3.546269	0.65198	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	.	.	.	4.92	4.92	0.64577	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5612	0.68136	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	LRP1B	140990926	1.000000	0.71417	0.994000	0.49952	0.576000	0.36127	9.278000	0.95766	1.815000	0.52974	0.460000	0.39030	.	.	.	none		0.328	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	Intron	G	141274456	A	G	141274456	5	3	22	1	0	0	0	0	0	0	1	0	8964	173	6	3	5816	3	LRP1B	2	141274456	Splice_Site	SNP	A	TCGA-G8-6324-01A-11D-2210-10	5286220	141274456	101924917	669	3570											
GTDC1	79712	hgsc.bcm.edu	37	chr2	144966208	144966208	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggaatggtctgagagaaataTaaagcagatgtccgggctct	13	9	13	6	1	2	3	0	1	2	2	3	5	3	4	1	3	1	2	1	3	5	2	rs16823579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:144966208T>C	ENST00000392869.2	-	3	293	c.141A>G	c.(139-141)ttA>ttG	p.L47L	GTDC1_ENST00000467352.1_5'Flank|GTDC1_ENST00000409298.1_Silent_p.L47L|GTDC1_ENST00000392867.3_Silent_p.L47L|GTDC1_ENST00000344850.4_Silent_p.L47L|GTDC1_ENST00000409214.1_Silent_p.L47L|GTDC1_ENST00000241391.5_Silent_p.L47L|GTDC1_ENST00000542155.1_Silent_p.L47L|GTDC1_ENST00000463875.2_Intron	NM_001284234.1	NP_001271163.1	Q4AE62	GTDC1_HUMAN	glycosyltransferase-like domain containing 1	47					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)		GAGAGAAATATAAAGCAGATG	0.413													T|||	190	0.0379393	0.1384	0.0101	5008	,	,		16667	0.0		0.0	False		,,,				2504	0.0				p.L47L		Atlas-SNP	.											.	GTDC1	61	.	0			c.A141G						PASS	.	T	,,	568,3838	252.1+/-258.6	34,500,1669	81	82	82		141,141,141	-12.2	0	2	dbSNP_123	82	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	GTDC1	NM_001006636.3,NM_001164629.2,NM_024659.4	,,	34,502,5967	CC,CT,TT		0.0233,12.8915,4.3826	,,	47/459,47/459,47/374	144966208	570,12436	2203	4300	6503	SO:0001819	synonymous_variant	79712	exon4			GAAATATAAAGCA	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.141A>G	2.37:g.144966208T>C		94	0	0		64	41	0.640625	NM_001006636	A8K5P2|D3DP81|Q53SM7|Q53TC5|Q6P7E7|Q6PJB6|Q6WKW6|Q9HAE5	Silent	SNP	ENST00000392869.2	37	CCDS33300.1																																																																																			T|0.957;C|0.043	0.043	strong		0.413	GTDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254779.2	NM_024659		C	144966208	T	C	144966208	2	2	22	1	0	0	0	0	0	0	0	1	6860	1403	49	3		3	GTDC1	2	144966208	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	3691752	144966208	98233165	670	3571											
EPC2	26122	hgsc.bcm.edu	37	chr2	149528738	149528738	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttctaatttctctcggaccaAtgcttccagtaaacattgtg	10	15	6	10	1	2	0	0	0	2	0	5	1	3	1	2	1	2	2	2	1	4	6	rs34444151	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:149528738A>G	ENST00000258484.6	+	10	1536	c.1502A>G	c.(1501-1503)aAt>aGt	p.N501S		NM_015630.3	NP_056445.3	Q52LR7	EPC2_HUMAN	enhancer of polycomb homolog 2 (Drosophila)	501					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)		TCTCGGACCAATGCTTCCAGT	0.378													A|||	43	0.00858626	0.0265	0.0029	5008	,	,		19522	0.0		0.0	False		,,,				2504	0.0061				p.N501S		Atlas-SNP	.											.	EPC2	57	.	0			c.A1502G						PASS	.	A	SER/ASN	71,3607		1,69,1769	55	54	54		1502	5.4	1	2	dbSNP_126	54	4,8166		0,4,4081	yes	missense	EPC2	NM_015630.3	46	1,73,5850	GG,GA,AA		0.049,1.9304,0.633	benign	501/808	149528738	75,11773	1839	4085	5924	SO:0001583	missense	26122	exon10			GGACCAATGCTTC	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.1502A>G	2.37:g.149528738A>G	ENSP00000258484:p.Asn501Ser	216	0	0		181	96	0.530387	NM_015630	B3KWT7|D3DP89|Q7L9J1|Q96RR7|Q9NUT8|Q9NVR1|Q9UFM9	Missense_Mutation	SNP	ENST00000258484.6	37	CCDS46422.1	18	0.008241758241758242	17	0.034552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	A	14.04	2.415328	0.42817	0.019304	4.9E-4	ENSG00000135999	ENST00000258484	T	0.16324	2.35	5.36	5.36	0.76844	.	0.097920	0.64402	D	0.000002	T	0.05777	0.0151	L	0.40543	1.245	0.80722	D	1	B	0.25521	0.128	B	0.23018	0.043	T	0.01863	-1.1258	10	0.54805	T	0.06	-4.6206	15.6403	0.76993	1.0:0.0:0.0:0.0	rs34444151	501	Q52LR7	EPC2_HUMAN	S	501	ENSP00000258484:N501S	ENSP00000258484:N501S	N	+	2	0	EPC2	149245208	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.325000	0.59234	2.140000	0.66376	0.460000	0.39030	AAT	A|0.992;G|0.008	0.008	strong		0.378	EPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332278.1	NM_015630		G	149528738	A	G	149528738	3	3	22	1	0	0	0	0	1	0	0	0	5163	101	4	3	1540	3	EPC2	2	149528738	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	4562530	149528738	93670635	671	3572											
KIF5C	3800	hgsc.bcm.edu	37	chr2	149861927	149861927	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tctagagaattgcagacactGcacaaccttcggaaactctt	13	10	7	11	1	2	2	0	0	2	2	3	4	2	3	1	1	4	2	1	1	4	4	rs184488465	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:149861927G>A	ENST00000435030.1	+	22	2762	c.2394G>A	c.(2392-2394)ctG>ctA	p.L798L	KIF5C_ENST00000397413.1_Silent_p.L566L|KIF5C_ENST00000414838.2_Silent_p.L703L|KIF5C_ENST00000464066.1_3'UTR			O60282	KIF5C_HUMAN	kinesin family member 5C	798					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)		TGCAGACACTGCACAACCTTC	0.428													G|||	12	0.00239617	0.0091	0.0	5008	,	,		16356	0.0		0.0	False		,,,				2504	0.0				p.L798L		Atlas-SNP	.											.	KIF5C	166	.	0			c.G2394A						PASS	.	G		16,3708		0,16,1846	73	71	72		2105	-0.9	1	2		72	0,8218		0,0,4109	no	coding-synonymous	KIF5C	NM_004522.1		0,16,5955	AA,AG,GG		0.0,0.4296,0.134		798/958	149861927	16,11926	1862	4109	5971	SO:0001819	synonymous_variant	3800	exon22			GACACTGCACAAC	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.2394G>A	2.37:g.149861927G>A		69	0	0		66	44	0.666667	NM_004522	O95079|Q2YDC5	Silent	SNP	ENST00000435030.1	37																																																																																				G|0.999;A|0.001	0.001	strong		0.428	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522		A	149861927	G	A	149861927	2	1	22	1	0	0	0	0	0	0	0	1	8316	1306	46	2		2	KIF5C	2	149861927	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	333189	149861927	93337446	672	3573											
RIF1	55183	hgsc.bcm.edu	37	chr2	152320501	152320501	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtaatttacatgagaagacTcttggggaaactagtgctaa	15	11	10	5	0	1	2	0	1	1	2	1	4	1	3	0	2	3	2	0	2	6	6	rs7566841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:152320501T>C	ENST00000243326.5	+	29	4950	c.4467T>C	c.(4465-4467)acT>acC	p.T1489T	RIF1_ENST00000430328.2_Silent_p.T1489T|RIF1_ENST00000453091.2_Silent_p.T1489T|RIF1_ENST00000428287.2_Silent_p.T1489T|RIF1_ENST00000444746.2_Silent_p.T1489T			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)		ATGAGAAGACTCTTGGGGAAA	0.368													T|||	101	0.0201677	0.0734	0.0043	5008	,	,		19435	0.0		0.001	False		,,,				2504	0.0				p.T1489T		Atlas-SNP	.											.	RIF1	244	.	0			c.T4467C						PASS	.	T	,,,	213,4191		4,205,1993	57	65	62		4467,4467,4467,4467	1.7	0.1	2	dbSNP_116	62	1,8589		0,1,4294	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RIF1	NM_001177663.1,NM_001177664.1,NM_001177665.1,NM_018151.4	,,,	4,206,6287	CC,CT,TT		0.0116,4.8365,1.6469	,,,	1489/2447,1489/2447,1489/2447,1489/2473	152320501	214,12780	2202	4295	6497	SO:0001819	synonymous_variant	55183	exon30			GAAGACTCTTGGG	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.4467T>C	2.37:g.152320501T>C		113	0	0		80	50	0.625	NM_018151	A0AVS0|Q9NS16	Silent	SNP	ENST00000243326.5	37	CCDS2194.1																																																																																			T|0.981;C|0.019	0.019	strong		0.368	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3			C	152320501	T	C	152320501	2	2	22	1	0	0	0	0	0	0	0	1	13374	1538	54	3		3	RIF1	2	152320501	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2458574	152320501	90878872	673	3574											
RIF1	55183	hgsc.bcm.edu	37	chr2	152321618	152321618	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctaatgaaaattttaaaactGttggcccgtgtttaggagac	13	13	9	6	1	0	2	0	1	0	1	0	3	0	2	1	2	1	2	1	2	6	6	rs2444258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:152321618G>A	ENST00000243326.5	+	29	6067	c.5584G>A	c.(5584-5586)Gtt>Att	p.V1862I	RIF1_ENST00000430328.2_Missense_Mutation_p.V1862I|RIF1_ENST00000453091.2_Missense_Mutation_p.V1862I|RIF1_ENST00000428287.2_Missense_Mutation_p.V1862I|RIF1_ENST00000444746.2_Missense_Mutation_p.V1862I			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)		TTTTAAAACTGTTGGCCCGTG	0.368													G|||	370	0.0738818	0.2617	0.0317	5008	,	,		17559	0.0		0.002	False		,,,				2504	0.0				p.V1862I		Atlas-SNP	.											.	RIF1	244	.	0			c.G5584A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	986,3420	359.6+/-314.9	101,784,1318	57	63	61		5584,5584,5584,5584	-4	0	2	dbSNP_100	61	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense,missense,missense	RIF1	NM_001177663.1,NM_001177664.1,NM_001177665.1,NM_018151.4	29,29,29,29	101,789,5613	AA,AG,GG		0.0581,22.3786,7.6196	benign,benign,benign,benign	1862/2447,1862/2447,1862/2447,1862/2473	152321618	991,12015	2203	4300	6503	SO:0001583	missense	55183	exon30			AAAACTGTTGGCC	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.5584G>A	2.37:g.152321618G>A	ENSP00000243326:p.Val1862Ile	84	0	0		97	29	0.298969	NM_018151	A0AVS0|Q9NS16	Missense_Mutation	SNP	ENST00000243326.5	37	CCDS2194.1	146	0.06684981684981685	137	0.2784552845528455	9	0.024861878453038673	0	0.0	0	0.0	G	10.51	1.369197	0.24771	0.223786	5.81E-4	ENSG00000080345	ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000430328	T;T;T;T;T	0.09723	2.96;2.95;2.95;2.96;2.95	5.68	-3.96	0.04106	.	1.726510	0.02579	N	0.098634	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B	0.29988	0.172;0.264	B;B	0.24269	0.023;0.052	T	0.41342	-0.9514	9	0.31617	T	0.26	0.8111	4.8656	0.13607	0.4276:0.089:0.3932:0.0902	rs2444258;rs52808590;rs60545876;rs2444258	1862;1862	Q5UIP0;Q5UIP0-2	RIF1_HUMAN;.	I	1862	ENSP00000390181:V1862I;ENSP00000414615:V1862I;ENSP00000415691:V1862I;ENSP00000243326:V1862I;ENSP00000416123:V1862I	ENSP00000243326:V1862I	V	+	1	0	RIF1	152029864	0.000000	0.05858	0.000000	0.03702	0.068000	0.16541	0.006000	0.13152	-0.725000	0.04901	0.650000	0.86243	GTT	G|0.918;A|0.082	0.082	strong		0.368	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3			A	152321618	G	A	152321618	3	1	22	1	0	0	0	0	1	0	0	0	13374	1377	48	2	5698	2	RIF1	2	152321618	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1117	152321618	90877755	674	3575											
NEB	4703	hgsc.bcm.edu	37	chr2	152547268	152547268	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	agctgtttcgtgttgagctgGgcttgcaacagtacaggaga	9	11	14	7	1	0	2	0	1	0	1	1	3	0	2	0	2	5	7	0	2	2	4	rs373946448	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:152547268G>A	ENST00000172853.10	-	24	2430	c.2283C>T	c.(2281-2283)gcC>gcT	p.A761A	NEB_ENST00000427231.2_Silent_p.A761A|NEB_ENST00000397345.3_Silent_p.A761A|NEB_ENST00000604864.1_Silent_p.A761A|NEB_ENST00000603639.1_Silent_p.A761A|NEB_ENST00000409198.1_Silent_p.A761A			P20929	NEBU_HUMAN	nebulin	761					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)		TGTTGAGCTGGGCTTGCAACA	0.398													G|||	3	0.000599042	0.0023	0.0	5008	,	,		18181	0.0		0.0	False		,,,				2504	0.0				p.A761A		Atlas-SNP	.											.	NEB	1697	.	0			c.C2283T						PASS	.	G	,,	11,3913		0,11,1951	112	112	112		2283,2283,2283	0.6	1	2		112	0,8302		0,0,4151	no	coding-synonymous,coding-synonymous,coding-synonymous	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	,,	0,11,6102	AA,AG,GG		0.0,0.2803,0.09	,,	761/8526,761/8526,761/6670	152547268	11,12215	1962	4151	6113	SO:0001819	synonymous_variant	4703	exon24			GAGCTGGGCTTGC	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.2283C>T	2.37:g.152547268G>A		164	0	0		170	91	0.535294	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				.	.	weak		0.398	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		A	152547268	G	A	152547268	2	1	22	1	0	0	0	0	0	0	0	1	10311	1219	43	2		2	NEB	2	152547268	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	225650	152547268	90652105	675	3576											
FMNL2	114793	hgsc.bcm.edu	37	chr2	153475556	153475556	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcttctggcacattgtccaTggggtcagaagtggtagcag	8	10	15	8	0	2	1	1	0	1	1	3	1	3	1	1	5	1	4	1	5	2	3	rs11897929	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:153475556T>C	ENST00000288670.9	+	14	1878	c.1511T>C	c.(1510-1512)aTg>aCg	p.M504T	FMNL2_ENST00000475377.2_5'Flank	NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	504			M -> T (in dbSNP:rs11897929).		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						ACATTGTCCATGGGGTCAGAA	0.537													T|||	386	0.0770767	0.2769	0.0259	5008	,	,		16892	0.0		0.002	False		,,,				2504	0.0				p.M504T		Atlas-SNP	.											.	FMNL2	75	.	0			c.T1511C						PASS	.	T	THR/MET	828,3056		87,654,1201	67	70	69		1511	-2.1	0	2	dbSNP_120	69	3,8279		0,3,4138	yes	missense	FMNL2	NM_052905.3	81	87,657,5339	CC,CT,TT		0.0362,21.3182,6.8305	benign	504/1093	153475556	831,11335	1942	4141	6083	SO:0001583	missense	114793	exon14			TGTCCATGGGGTC	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.1511T>C	2.37:g.153475556T>C	ENSP00000288670:p.Met504Thr	181	0	0		172	93	0.540698	NM_052905	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Missense_Mutation	SNP	ENST00000288670.9	37	CCDS46429.1	136	0.06227106227106227	128	0.2601626016260163	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	T	0.957	-0.704556	0.03255	0.213182	3.62E-4	ENSG00000157827	ENST00000288670;ENST00000421344	D	0.90004	-2.6	5.57	-2.14	0.07123	.	0.947878	0.08957	N	0.869194	T	0.00039	0.0001	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.01520	-1.1334	9	0.13108	T	0.6	.	11.4827	0.50335	0.0:0.5749:0.0:0.4251	rs11897929;rs11897929	504	Q96PY5-3	.	T	504;1	ENSP00000288670:M504T	ENSP00000288670:M504T	M	+	2	0	FMNL2	153183802	0.000000	0.05858	0.000000	0.03702	0.103000	0.19146	-0.531000	0.06171	-0.792000	0.04480	-0.973000	0.02599	ATG	T|0.920;C|0.080	0.080	strong		0.537	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905		C	153475556	T	C	153475556	3	2	22	1	0	0	0	0	1	0	0	0	5960	1464	51	3	1565	3	FMNL2	2	153475556	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	928288	153475556	89723817	676	3577											
GPD2	2820	hgsc.bcm.edu	37	chr2	157425931	157425931	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataccataaatgctgctgtcAaaactcataatttaaaagca	18	11	4	8	0	2	0	2	0	0	0	2	0	2	0	1	0	5	3	1	0	8	5	rs35096779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:157425931A>C	ENST00000310454.6	+	11	1729	c.1357A>C	c.(1357-1359)Aaa>Caa	p.K453Q	GPD2_ENST00000540309.1_Intron|GPD2_ENST00000438166.2_Missense_Mutation_p.K453Q|GPD2_ENST00000409125.4_Missense_Mutation_p.K226Q|GPD2_ENST00000409674.1_Missense_Mutation_p.K453Q	NM_001083112.2	NP_001076581.2	P43304	GPDM_HUMAN	glycerol-3-phosphate dehydrogenase 2 (mitochondrial)	453			K -> Q (in dbSNP:rs35096779).		camera-type eye development (GO:0043010)|cellular lipid metabolic process (GO:0044255)|gluconeogenesis (GO:0006094)|glycerol catabolic process (GO:0019563)|glycerol-3-phosphate metabolic process (GO:0006072)|multicellular organism growth (GO:0035264)|small molecule metabolic process (GO:0044281)	glycerol-3-phosphate dehydrogenase complex (GO:0009331)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|glycerol-3-phosphate dehydrogenase activity (GO:0004368)|sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity (GO:0052591)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(1)|stomach(1)	22						TGCTGCTGTCAAAACTCATAA	0.423													A|||	166	0.033147	0.1165	0.0159	5008	,	,		17986	0.0		0.001	False		,,,				2504	0.0				p.K453Q		Atlas-SNP	.											.	GPD2	59	.	0			c.A1357C						PASS	.	A	GLN/LYS,GLN/LYS	527,3879	239.6+/-250.7	30,467,1706	79	78	78		1357,1357	3.3	0.8	2	dbSNP_126	78	6,8594	3.7+/-12.6	0,6,4294	yes	missense,missense	GPD2	NM_000408.4,NM_001083112.2	53,53	30,473,6000	CC,CA,AA		0.0698,11.961,4.0981	benign,benign	453/728,453/728	157425931	533,12473	2203	4300	6503	SO:0001583	missense	2820	exon11			GCTGTCAAAACTC		CCDS2202.1	2q24.1	2013-01-10			ENSG00000115159	ENSG00000115159	1.1.1.8	"EF-hand domain containing"	4456	protein-coding gene	gene with protein product		138430					Standard	NM_001083112		Approved		uc002tzd.4	P43304	OTTHUMG00000131951	ENST00000310454.6:c.1357A>C	2.37:g.157425931A>C	ENSP00000308610:p.Lys453Gln	85	0	0		120	55	0.458333	NM_001083112	A8K4V0|B3KSA9|Q59FR1|Q9HAP9	Missense_Mutation	SNP	ENST00000310454.6	37	CCDS2202.1	63	0.028846153846153848	56	0.11382113821138211	7	0.019337016574585635	0	0.0	0	0.0	A	14.01	2.408743	0.42715	0.11961	6.98E-4	ENSG00000115159	ENST00000310454;ENST00000409125;ENST00000438166;ENST00000409674	T;T;T;T	0.60171	0.21;0.42;0.21;0.21	5.78	3.34	0.38264	.	0.179590	0.56097	N	0.000021	T	0.00967	0.0032	L	0.48877	1.53	0.39253	D	0.96407	B	0.06786	0.001	B	0.13407	0.009	T	0.02288	-1.1182	10	0.52906	T	0.07	.	13.5438	0.61690	0.6092:0.3908:0.0:0.0	rs35096779	453	P43304	GPDM_HUMAN	Q	453;226;453;453	ENSP00000308610:K453Q;ENSP00000386484:K226Q;ENSP00000409708:K453Q;ENSP00000386425:K453Q	ENSP00000308610:K453Q	K	+	1	0	GPD2	157134177	0.997000	0.39634	0.775000	0.31657	0.987000	0.75469	2.271000	0.43364	0.427000	0.26145	0.528000	0.53228	AAA	A|0.963;C|0.037	0.037	strong		0.423	GPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254910.3			C	157425931	A	C	157425931	3	2	22	1	0	0	0	0	1	0	0	0	6614	131	5	5	1395	5	GPD2	2	157425931	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	3950375	157425931	85773442	677	3578											
UPP2	151531	hgsc.bcm.edu	37	chr2	158971664	158971664	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgaaagcatttgcactgtttAtgcacaaggagctcgggttt	10	13	11	7	1	0	1	0	1	0	0	1	2	0	2	0	2	4	6	0	2	3	4	rs7561584	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:158971664A>C	ENST00000005756.4	+	3	426	c.232A>C	c.(232-234)Atg>Ctg	p.M78L	UPP2_ENST00000460456.1_Intron|UPP2_ENST00000605860.1_Missense_Mutation_p.M135L|UPP2_ENST00000409859.4_Missense_Mutation_p.M135L	NM_173355.3	NP_775491.1	O95045	UPP2_HUMAN	uridine phosphorylase 2	78			M -> L (in dbSNP:rs7561584).		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)	TGCACTGTTTATGCACAAGGA	0.458													A|||	24	0.00479233	0.0166	0.0029	5008	,	,		14199	0.0		0.0	False		,,,				2504	0.0				p.M135L		Atlas-SNP	.											.	UPP2	60	.	0			c.A403C						PASS	.	A	LEU/MET,LEU/MET	83,4323	70.9+/-108.8	2,79,2122	104	104	104		232,403	4.5	0.9	2	dbSNP_116	104	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	UPP2	NM_173355.3,NM_001135098.1	15,15	2,82,6419	CC,CA,AA		0.0349,1.8838,0.6612	benign,benign	78/318,135/375	158971664	86,12920	2203	4300	6503	SO:0001583	missense	151531	exon5			CTGTTTATGCACA	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.232A>C	2.37:g.158971664A>C	ENSP00000005756:p.Met78Leu	118	0	0		88	35	0.397727	NM_001135098	B3KV87	Missense_Mutation	SNP	ENST00000005756.4	37	CCDS2207.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	A	6.495	0.459468	0.12342	0.018838	3.49E-4	ENSG00000007001	ENST00000409859;ENST00000005756	T;T	0.35421	1.31;1.31	5.7	4.53	0.55603	Nucleoside phosphorylase domain (1);	0.153191	0.64402	D	0.000007	T	0.10294	0.0252	N	0.12961	0.28	0.46317	D	0.998983	B	0.06786	0.001	B	0.08055	0.003	T	0.04128	-1.0975	10	0.11794	T	0.64	.	11.9742	0.53081	0.8546:0.1454:0.0:0.0	rs7561584;rs7561584	78	O95045	UPP2_HUMAN	L	135;78	ENSP00000387230:M135L;ENSP00000005756:M78L	ENSP00000005756:M78L	M	+	1	0	UPP2	158679910	1.000000	0.71417	0.940000	0.37924	0.318000	0.28184	5.969000	0.70422	0.974000	0.38366	0.533000	0.62120	ATG	A|0.994;C|0.006	0.006	strong		0.458	UPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254929.2	NM_173355		C	158971664	A	C	158971664	3	2	22	1	0	0	0	0	1	0	0	0	17028	449	16	5	421	5	UPP2	2	158971664	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1545733	158971664	84227709	678	3579											
UPP2	151531	hgsc.bcm.edu	37	chr2	158977928	158977928	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccacattgcagggattgcAccagggactgttgtaataac	11	10	10	10	0	0	0	0	0	0	0	1	2	1	2	2	2	3	4	2	2	2	5	rs10186677	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:158977928A>C	ENST00000005756.4	+	5	656	c.462A>C	c.(460-462)gcA>gcC	p.A154A	UPP2_ENST00000460456.1_Intron|UPP2_ENST00000605860.1_Silent_p.A211A|UPP2_ENST00000409859.4_Silent_p.A211A	NM_173355.3	NP_775491.1	O95045	UPP2_HUMAN	uridine phosphorylase 2	154					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)	CAGGGATTGCACCAGGGACTG	0.383													A|||	84	0.0167732	0.0605	0.0058	5008	,	,		18783	0.0		0.0	False		,,,				2504	0.0				p.A211A		Atlas-SNP	.											.	UPP2	60	.	0			c.A633C						PASS	.	A	,	210,4196	129.0+/-165.8	5,200,1998	201	207	205		633,462	-4.8	0	2	dbSNP_119	205	4,8594	3.7+/-12.6	0,4,4295	no	coding-synonymous,coding-synonymous	UPP2	NM_001135098.1,NM_173355.3	,	5,204,6293	CC,CA,AA		0.0465,4.7662,1.6456	,	211/375,154/318	158977928	214,12790	2203	4299	6502	SO:0001819	synonymous_variant	151531	exon7			GATTGCACCAGGG	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.462A>C	2.37:g.158977928A>C		382	0	0		303	185	0.610561	NM_001135098	B3KV87	Silent	SNP	ENST00000005756.4	37	CCDS2207.1																																																																																			A|0.980;C|0.020	0.020	strong		0.383	UPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254929.2	NM_173355		C	158977928	A	C	158977928	2	2	22	1	0	0	0	0	0	0	0	1	17028	146	6	5		5	UPP2	2	158977928	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	6264	158977928	84221445	679	3580											
TANC1	85461	hgsc.bcm.edu	37	chr2	160019901	160019901	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agaagggagtgcttcatgacCgcagggcagataactgctcc	11	7	13	10	1	1	3	1	1	0	2	2	4	2	4	2	2	3	4	2	2	2	2	rs55929944	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160019901C>T	ENST00000263635.6	+	8	1027	c.790C>T	c.(790-792)Cgc>Tgc	p.R264C	TANC1_ENST00000454300.1_Missense_Mutation_p.R158C	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	264					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						GCTTCATGACCGCAGGGCAGA	0.522													C|||	163	0.0325479	0.1172	0.0086	5008	,	,		19708	0.0		0.002	False		,,,				2504	0.0				p.R264C		Atlas-SNP	.											.	TANC1	157	.	0			c.C790T						PASS	.	C	CYS/ARG,CYS/ARG	436,3492		33,370,1561	74	79	77		787,790	6	1	2	dbSNP_129	77	2,8292		0,2,4145	yes	missense,missense	TANC1	NM_001145909.1,NM_033394.2	180,180	33,372,5706	TT,TC,CC		0.0241,11.0998,3.5837	probably-damaging,probably-damaging	263/1391,264/1862	160019901	438,11784	1964	4147	6111	SO:0001583	missense	85461	exon8			CATGACCGCAGGG	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.790C>T	2.37:g.160019901C>T	ENSP00000263635:p.Arg264Cys	280	0	0		278	165	0.593525	NM_033394	C9JD88|Q49AI8	Missense_Mutation	SNP	ENST00000263635.6	37	CCDS42766.1	62	0.028388278388278388	57	0.11585365853658537	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	C	15.63	2.890072	0.52014	0.110998	2.41E-4	ENSG00000115183	ENST00000454300;ENST00000263635	T;T	0.70869	-0.51;-0.52	6.04	6.04	0.98038	.	0.113037	0.64402	D	0.000007	T	0.02455	0.0075	L	0.54323	1.7	0.80722	D	1	B;B	0.24721	0.066;0.11	B;B	0.17722	0.01;0.019	T	0.25710	-1.0124	10	0.66056	D	0.02	.	20.5948	0.99439	0.0:1.0:0.0:0.0	rs55929944	263;264	B9EK39;Q9C0D5	.;TANC1_HUMAN	C	158;264	ENSP00000396339:R158C;ENSP00000263635:R264C	ENSP00000263635:R264C	R	+	1	0	TANC1	159728147	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.696000	0.54757	2.873000	0.98535	0.563000	0.77884	CGC	C|0.971;T|0.029	0.029	strong		0.522	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1			T	160019901	C	T	160019901	3	4	22	1	0	0	0	0	1	0	0	0	15559	652	23	1	812	1	TANC1	2	160019901	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1041973	160019901	83179472	680	3581											
TANC1	85461	hgsc.bcm.edu	37	chr2	160087410	160087410	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggataactaagactgtttctCatctgtaccaggaaagtatc	13	12	8	8	0	2	1	1	0	2	1	4	3	2	3	1	2	2	3	1	2	5	5	rs77049231	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160087410C>T	ENST00000263635.6	+	27	5710	c.5473C>T	c.(5473-5475)Cat>Tat	p.H1825Y	TANC1_ENST00000454300.1_Missense_Mutation_p.H1719Y	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	1825					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						GACTGTTTCTCATCTGTACCA	0.453													C|||	220	0.0439297	0.1611	0.0086	5008	,	,		18665	0.0		0.001	False		,,,				2504	0.0				p.H1825Y		Atlas-SNP	.											.	TANC1	157	.	0			c.C5473T						PASS	.	C	,TYR/HIS	476,3394		31,414,1490	76	77	77		,5473	5.2	0	2	dbSNP_131	77	2,8310		0,2,4154	yes	utr-3,missense	TANC1	NM_001145909.1,NM_033394.2	,83	31,416,5644	TT,TC,CC		0.0241,12.2997,3.9238	,possibly-damaging	,1825/1862	160087410	478,11704	1935	4156	6091	SO:0001583	missense	85461	exon27			GTTTCTCATCTGT	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.5473C>T	2.37:g.160087410C>T	ENSP00000263635:p.His1825Tyr	193	0	0		165	94	0.569697	NM_033394	C9JD88|Q49AI8	Missense_Mutation	SNP	ENST00000263635.6	37	CCDS42766.1	66	0.03021978021978022	64	0.13008130081300814	2	0.0055248618784530384	0	0.0	0	0.0	C	13.58	2.280696	0.40294	0.122997	2.41E-4	ENSG00000115183	ENST00000454300;ENST00000263635	T;T	0.71817	-0.59;-0.6	6.06	5.18	0.71444	.	0.096342	0.64402	D	0.000001	T	0.01489	0.0048	L	0.56769	1.78	0.23003	P	0.99844134	D	0.56521	0.976	B	0.40636	0.335	T	0.33675	-0.9859	8	.	.	.	.	17.4939	0.87712	0.0:0.876:0.124:0.0	.	1825	Q9C0D5	TANC1_HUMAN	Y	1719;1825	ENSP00000396339:H1719Y;ENSP00000263635:H1825Y	.	H	+	1	0	TANC1	159795656	1.000000	0.71417	0.030000	0.17652	0.010000	0.07245	5.453000	0.66645	1.559000	0.49555	0.655000	0.94253	CAT	C|0.980;T|0.020	0.020	strong		0.453	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1			T	160087410	C	T	160087410	3	4	22	1	0	0	0	0	1	0	0	0	15559	826	29	2	5576	2	TANC1	2	160087410	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	67509	160087410	83111963	681	3582											
WDSUB1	151525	hgsc.bcm.edu	37	chr2	160104988	160104988	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttggtcctgagctcttcaaTtttcctcagcactttactac	7	16	5	13	0	3	1	2	1	1	0	5	1	5	1	2	1	4	2	2	1	3	7	rs74475652	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160104988T>C	ENST00000409990.3	-	10	1424	c.1168A>G	c.(1168-1170)Att>Gtt	p.I390V	WDSUB1_ENST00000392796.3_Missense_Mutation_p.I390V|WDSUB1_ENST00000358147.4_Missense_Mutation_p.I298V|WDSUB1_ENST00000359774.4_Missense_Mutation_p.I390V|WDSUB1_ENST00000409124.1_Intron	NM_001128213.1	NP_001121685	Q8N9V3	WSDU1_HUMAN	WD repeat, sterile alpha motif and U-box domain containing 1	390	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.						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						AGCTCTTCAATTTTCCTCAGC	0.388													T|||	219	0.04373	0.1604	0.0086	5008	,	,		19089	0.0		0.001	False		,,,				2504	0.0				p.I390V		Atlas-SNP	.											.	WDSUB1	39	.	0			c.A1168G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE	583,3823	258.3+/-262.4	45,493,1665	100	101	101		1168,1168,1168	3.5	1	2	dbSNP_131	101	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense	WDSUB1	NM_001128212.1,NM_001128213.1,NM_152528.2	29,29,29	45,495,5963	CC,CT,TT		0.0233,13.232,4.4979	benign,benign,benign	390/477,390/477,390/477	160104988	585,12421	2203	4300	6503	SO:0001583	missense	151525	exon10			CTTCAATTTTCCT	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.1168A>G	2.37:g.160104988T>C	ENSP00000387078:p.Ile390Val	101	0	0		91	44	0.483516	NM_152528	Q53TI9|Q8N6N8	Missense_Mutation	SNP	ENST00000409990.3	37	CCDS2208.1	64	0.029304029304029304	62	0.12601626016260162	2	0.0055248618784530384	0	0.0	0	0.0	T	11.96	1.793785	0.31685	0.13232	2.33E-4	ENSG00000196151	ENST00000359774;ENST00000358147;ENST00000392796;ENST00000409990	T;T;T;T	0.51325	0.71;0.71;0.71;0.71	5.97	3.55	0.40652	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.114020	0.64402	N	0.000011	T	0.00552	0.0018	M	0.64997	1.995	0.09310	P	1.0	B;B	0.24258	0.009;0.1	B;B	0.28465	0.007;0.09	T	0.08785	-1.0705	9	0.38643	T	0.18	.	10.5342	0.44994	0.0:0.132:0.0:0.868	.	298;390	Q8N9V3-2;Q8N9V3	.;WSDU1_HUMAN	V	390;298;390;390	ENSP00000352820:I390V;ENSP00000350866:I298V;ENSP00000376545:I390V;ENSP00000387078:I390V	ENSP00000350866:I298V	I	-	1	0	WDSUB1	159813234	1.000000	0.71417	0.993000	0.49108	0.992000	0.81027	3.080000	0.50112	0.486000	0.27676	0.528000	0.53228	ATT	T|0.958;C|0.042	0.042	strong		0.388	WDSUB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333339.1	NM_152528		C	160104988	T	C	160104988	3	2	22	1	0	0	0	0	1	0	0	0	17356	1493	52	3	270	3	WDSUB1	2	160104988	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	17578	160104988	83094385	682	3583											
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160287443	160287443	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtgactgggattcagaacAtaaggcagcaggagcagagc	14	5	15	7	0	1	3	1	1	0	2	1	5	1	5	0	4	4	3	0	4	2	2	rs200904019	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160287443A>C	ENST00000392783.2	-	10	2620	c.2125T>G	c.(2125-2127)Tgt>Ggt	p.C709G	BAZ2B_ENST00000355831.2_Missense_Mutation_p.C709G|BAZ2B_ENST00000343439.5_Intron|BAZ2B_ENST00000392782.1_Missense_Mutation_p.C707G	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	709					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						GATTCAGAACATAAGGCAGCA	0.453													A|||	6	0.00119808	0.0045	0.0	5008	,	,		18357	0.0		0.0	False		,,,				2504	0.0				p.C709G		Atlas-SNP	.											.	BAZ2B	196	.	0			c.T2125G						PASS	.	A	GLY/CYS	20,3846		0,20,1913	145	144	144		2125	5.7	1	2		144	0,8272		0,0,4136	yes	missense	BAZ2B	NM_013450.2	159	0,20,6049	CC,CA,AA		0.0,0.5173,0.1648	probably-damaging	709/2169	160287443	20,12118	1933	4136	6069	SO:0001583	missense	29994	exon10			CAGAACATAAGGC	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.2125T>G	2.37:g.160287443A>C	ENSP00000376534:p.Cys709Gly	172	0	0		162	70	0.432099	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	37	CCDS2209.2	4	0.0018315018315018315	1	0.0020325203252032522	0	0.0	3	0.005244755244755245	0	0.0	A	14.89	2.670797	0.47781	0.005173	0.0	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831	T;T;T	0.21191	2.02;2.02;2.02	5.71	5.71	0.89125	.	0.000000	0.40222	U	0.001146	T	0.27063	0.0663	L	0.32530	0.975	0.80722	D	1	D;D;D	0.71674	0.996;0.978;0.998	P;D;D	0.75484	0.889;0.922;0.986	T	0.02398	-1.1165	10	0.25751	T	0.34	-8.1218	15.968	0.79987	1.0:0.0:0.0:0.0	.	513;707;709	Q9UIF8-4;Q9UIF8-5;Q9UIF8	.;.;BAZ2B_HUMAN	G	707;709;709	ENSP00000376533:C707G;ENSP00000376534:C709G;ENSP00000348087:C709G	ENSP00000348087:C709G	C	-	1	0	BAZ2B	159995689	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.327000	0.52045	2.175000	0.68902	0.523000	0.50628	TGT	A|0.998;C|0.002	0.002	strong		0.453	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			C	160287443	A	C	160287443	3	2	22	1	0	0	0	0	1	0	0	0	1332	217	8	5	4493	5	BAZ2B	2	160287443	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	182455	160287443	82911930	683	3584											
LY75	4065	hgsc.bcm.edu	37	chr2	160690646	160690646	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtagcaacagttctgaaaTggtatccacggagtatttag	12	13	10	6	1	1	1	0	1	1	0	2	2	2	2	1	2	2	5	1	2	6	7	rs6722188	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160690646T>C	ENST00000263636.4	-	27	3777	c.3750A>G	c.(3748-3750)ccA>ccG	p.P1250P	LY75_ENST00000554112.1_Silent_p.P1250P|LY75-CD302_ENST00000505052.1_Silent_p.P1250P|LY75_ENST00000553424.1_Silent_p.P1250P|LY75-CD302_ENST00000504764.1_Silent_p.P1250P	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1250					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)		AGTTCTGAAATGGTATCCACG	0.353													T|||	553	0.110423	0.4024	0.0288	5008	,	,		20151	0.0		0.001	False		,,,				2504	0.0				p.P1250P		Atlas-SNP	.											.	LY75	151	.	0			c.A3750G						PASS	.	T	,,	1532,2874	485.3+/-360.3	266,1000,937	145	134	138		3750,3750,3750	-4.4	1	2	dbSNP_116	138	18,8582	11.9+/-42.8	0,18,4282	no	coding-synonymous,coding-synonymous,coding-synonymous	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	,,	266,1018,5219	CC,CT,TT		0.2093,34.7708,11.9176	,,	1250/1874,1250/1818,1250/1723	160690646	1550,11456	2203	4300	6503	SO:0001819	synonymous_variant	4065	exon27			CTGAAATGGTATC	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.3750A>G	2.37:g.160690646T>C		182	0	0		150	86	0.573333	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Silent	SNP	ENST00000263636.4	37	CCDS2211.1																																																																																			T|0.880;C|0.120	0.120	strong		0.353	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1			C	160690646	T	C	160690646	2	2	22	1	0	0	0	0	0	0	0	1	9108	1451	51	3		3	LY75	2	160690646	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	403203	160690646	82508727	684	3585											
LY75	4065	hgsc.bcm.edu	37	chr2	160735775	160735775	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agggattttacctacctcatCtggaggacacatcttatcag	11	12	8	10	0	4	0	2	0	2	0	4	3	4	3	2	3	2	0	2	3	3	4	rs77761086	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160735775C>T	ENST00000263636.4	-	9	1537	c.1510G>A	c.(1510-1512)Gat>Aat	p.D504N	LY75_ENST00000554112.1_Missense_Mutation_p.D504N|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.D504N|LY75_ENST00000553424.1_Missense_Mutation_p.D504N|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.D504N	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	504	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)		CCTACCTCATCTGGAGGACAC	0.353													C|||	26	0.00519169	0.0197	0.0	5008	,	,		19467	0.0		0.0	False		,,,				2504	0.0				p.D504N		Atlas-SNP	.											.	LY75	151	.	0			c.G1510A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP	59,4345	58.1+/-94.6	0,59,2143	199	183	189		1510,1510,1510	2.4	0.4	2	dbSNP_131	189	0,8598		0,0,4299	yes	missense,missense,missense	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	23,23,23	0,59,6442	TT,TC,CC		0.0,1.3397,0.4538	benign,benign,benign	504/1874,504/1818,504/1723	160735775	59,12943	2202	4299	6501	SO:0001583	missense	4065	exon9			CCTCATCTGGAGG	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.1510G>A	2.37:g.160735775C>T	ENSP00000263636:p.Asp504Asn	117	0	0		92	35	0.380435	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	C	4.816	0.151794	0.09185	0.013397	0.0	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.55413	0.52;3.0;2.98;0.52;3.0	5.4	2.44	0.29823	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (1);	1.063440	0.07525	N	0.911197	T	0.41096	0.1144	M	0.82056	2.57	0.09310	N	1	B;B;B;B	0.16603	0.001;0.018;0.018;0.007	B;B;B;B	0.22386	0.005;0.039;0.017;0.009	T	0.44221	-0.9342	10	0.34782	T	0.22	-1.7808	11.0531	0.47903	0.0:0.6813:0.0:0.3187	.	122;504;504;504	Q59H44;O60449-3;O60449;O60449-2	.;.;LY75_HUMAN;.	N	504	ENSP00000451511:D504N;ENSP00000451446:D504N;ENSP00000263636:D504N;ENSP00000423463:D504N;ENSP00000421035:D504N	ENSP00000423463:D504N	D	-	1	0	LY75;LY75-CD302	160444021	0.095000	0.21747	0.411000	0.26484	0.053000	0.15095	0.244000	0.18124	0.025000	0.15241	-1.595000	0.00837	GAT	C|0.994;T|0.006	0.006	strong		0.353	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1			T	160735775	C	T	160735775	3	4	22	1	0	0	0	0	1	0	0	0	9108	913	32	2	3766	2	LY75	2	160735775	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	45129	160735775	82463598	685	3586											
LY75	4065	hgsc.bcm.edu	37	chr2	160737717	160737717	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aataaagttggtatgtttatGttcttaaggcctatccacac	12	15	7	7	0	1	0	0	0	1	0	2	0	2	0	2	2	0	4	2	2	7	8	rs79199281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160737717G>A	ENST00000263636.4	-	8	1308	c.1281C>T	c.(1279-1281)aaC>aaT	p.N427N	LY75_ENST00000554112.1_Silent_p.N427N|LY75-CD302_ENST00000505052.1_Silent_p.N427N|LY75_ENST00000553424.1_Silent_p.N427N|LY75-CD302_ENST00000504764.1_Silent_p.N427N	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	427	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)		GTATGTTTATGTTCTTAAGGC	0.323													G|||	26	0.00519169	0.0197	0.0	5008	,	,		19352	0.0		0.0	False		,,,				2504	0.0				p.N427N		Atlas-SNP	.											.	LY75	151	.	0			c.C1281T						PASS	.	G	,,	59,4347	58.1+/-94.6	0,59,2144	177	164	168		1281,1281,1281	1.9	1	2	dbSNP_131	168	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	,,	0,59,6444	AA,AG,GG		0.0,1.3391,0.4536	,,	427/1874,427/1818,427/1723	160737717	59,12947	2203	4300	6503	SO:0001819	synonymous_variant	4065	exon8			GTTTATGTTCTTA	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.1281C>T	2.37:g.160737717G>A		88	0	0		89	23	0.258427	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Silent	SNP	ENST00000263636.4	37	CCDS2211.1																																																																																			G|0.994;A|0.006	0.006	strong		0.323	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1			A	160737717	G	A	160737717	2	1	22	1	0	0	0	0	0	0	0	1	9108	1368	48	2		2	LY75	2	160737717	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1942	160737717	82461656	686	3587											
LY75	4065	hgsc.bcm.edu	37	chr2	160738803	160738803	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagccagcctgcatcacagcGggtatctgagtatgtccaga	10	8	11	12	1	2	2	1	1	1	1	3	2	3	2	3	1	4	3	3	1	2	2	rs35675007	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160738803G>A	ENST00000263636.4	-	7	1105	c.1078C>T	c.(1078-1080)Cgc>Tgc	p.R360C	LY75_ENST00000554112.1_Missense_Mutation_p.R360C|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.R360C|LY75_ENST00000553424.1_Missense_Mutation_p.R360C|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.R360C	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	360					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)		GCATCACAGCGGGTATCTGAG	0.398													G|||	19	0.00379393	0.0121	0.0	5008	,	,		22106	0.001		0.0	False		,,,				2504	0.002				p.R360C		Atlas-SNP	.											LY75,NS,carcinoma,+1,1	LY75	151	1	0			c.C1078T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG	44,4362	48.2+/-83.0	0,44,2159	114	111	112		1078,1078,1078	5.6	0.9	2	dbSNP_126	112	16,8584	11.9+/-42.8	0,16,4284	yes	missense,missense,missense	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	180,180,180	0,60,6443	AA,AG,GG		0.186,0.9986,0.4613	possibly-damaging,possibly-damaging,possibly-damaging	360/1874,360/1818,360/1723	160738803	60,12946	2203	4300	6503	SO:0001583	missense	4065	exon7			CACAGCGGGTATC	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.1078C>T	2.37:g.160738803G>A	ENSP00000263636:p.Arg360Cys	77	0	0		77	27	0.350649	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	17.54	3.416115	0.62511	0.009986	0.00186	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.07444	3.19;3.19;3.19;3.19;3.19	5.57	5.57	0.84162	C-type lectin-like (1);	1.087950	0.07314	U	0.876324	T	0.14399	0.0348	L	0.43152	1.355	0.19300	N	0.99998	B;D;D	0.76494	0.272;0.999;0.999	B;P;P	0.56278	0.072;0.724;0.795	T	0.29912	-0.9996	10	0.54805	T	0.06	0.0491	14.2185	0.65809	0.0:0.2692:0.7308:0.0	rs35675007	360;360;360	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	C	360	ENSP00000451511:R360C;ENSP00000451446:R360C;ENSP00000263636:R360C;ENSP00000423463:R360C;ENSP00000421035:R360C	ENSP00000423463:R360C	R	-	1	0	LY75;LY75-CD302	160447049	0.995000	0.38212	0.857000	0.33713	0.986000	0.74619	2.505000	0.45424	2.632000	0.89209	0.650000	0.86243	CGC	G|0.996;A|0.004	0.004	strong		0.398	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1			A	160738803	G	A	160738803	3	1	22	1	0	0	0	0	1	0	0	0	9108	1116	39	1	4206	1	LY75	2	160738803	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1086	160738803	82460570	687	3588											
PLA2R1	22925	hgsc.bcm.edu	37	chr2	160901403	160901403	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acctggacagagtactgcagCgggcctgtgatcatcttcct	8	10	11	12	1	2	2	1	1	1	1	3	3	3	3	3	2	3	2	3	2	1	2	rs35005192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160901403C>T	ENST00000283243.7	-	2	581	c.375G>A	c.(373-375)ccG>ccA	p.P125P	PLA2R1_ENST00000392771.1_Silent_p.P125P	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	125	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						AGTACTGCAGCGGGCCTGTGA	0.502													C|||	27	0.00539137	0.0204	0.0	5008	,	,		17735	0.0		0.0	False		,,,				2504	0.0				p.P125P		Atlas-SNP	.											.	PLA2R1	153	.	0			c.G375A						PASS	.	C	,,	59,4347	56.8+/-93.2	0,59,2144	82	82	82		375,375,375	-12.1	0	2	dbSNP_126	82	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	PLA2R1	NM_001007267.2,NM_001195641.1,NM_007366.4	,,	0,59,6444	TT,TC,CC		0.0,1.3391,0.4536	,,	125/1325,125/1462,125/1464	160901403	59,12947	2203	4300	6503	SO:0001819	synonymous_variant	22925	exon2			CTGCAGCGGGCCT	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.375G>A	2.37:g.160901403C>T		132	0	0		137	58	0.423358	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Silent	SNP	ENST00000283243.7	37	CCDS33309.1																																																																																			C|0.994;T|0.006	0.006	strong		0.502	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1			T	160901403	C	T	160901403	2	4	22	1	0	0	0	0	0	0	0	1	12019	755	27	1		1	PLA2R1	2	160901403	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	162600	160901403	82297970	688	3589											
TANK	10010	hgsc.bcm.edu	37	chr2	162088034	162088034	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttccctcactcgattcccCgggaaaagcaatccgaggac	10	9	8	14	3	1	0	1	0	0	0	5	4	4	2	4	2	1	1	4	2	3	3	rs2229759	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:162088034C>T	ENST00000392749.2	+	7	1312	c.1073C>T	c.(1072-1074)cCg>cTg	p.P358L	TANK_ENST00000259075.2_Missense_Mutation_p.P358L|AC009299.2_ENST00000421122.2_RNA|TANK_ENST00000405852.1_Missense_Mutation_p.P358L|TANK_ENST00000406287.1_Intron|TANK_ENST00000402568.1_Intron|AC009299.2_ENST00000445372.1_RNA	NM_001199135.1	NP_001186064.1	Q92844	TANK_HUMAN	TRAF family member-associated NFKB activator	358			P -> L (in dbSNP:rs2229759).		I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)	21						CTCGATTCCCCGGGAAAAGCA	0.433													C|||	128	0.0255591	0.0938	0.0058	5008	,	,		19086	0.0		0.0	False		,,,				2504	0.0				p.P358L		Atlas-SNP	.											TANK,NS,carcinoma,-1,1	TANK	35	1	0			c.C1073T						PASS	.	C	LEU/PRO,LEU/PRO	230,4176	129.8+/-166.5	4,222,1977	45	45	45		1073,1073	5.6	1	2	dbSNP_98	45	3,8595	3.0+/-9.4	0,3,4296	yes	missense,missense	TANK	NM_001199135.1,NM_004180.2	98,98	4,225,6273	TT,TC,CC		0.0349,5.2202,1.7918	probably-damaging,probably-damaging	358/426,358/426	162088034	233,12771	2203	4299	6502	SO:0001583	missense	10010	exon7			ATTCCCCGGGAAA	U59863	CCDS2215.1, CCDS46436.1	2q24-q31	2008-02-05			ENSG00000136560	ENSG00000136560			11562	protein-coding gene	gene with protein product		603893		TRAF2		8710854, 8855313	Standard	NM_004180		Approved	I-TRAF	uc002ubr.2	Q92844	OTTHUMG00000132037	ENST00000392749.2:c.1073C>T	2.37:g.162088034C>T	ENSP00000376505:p.Pro358Leu	39	0	0		24	12	0.5	NM_004180	D3DPB5|Q7Z4J6|Q92885	Missense_Mutation	SNP	ENST00000392749.2	37	CCDS2215.1	49	0.022435897435897436	47	0.09552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	C	16.38	3.106713	0.56291	0.052202	3.49E-4	ENSG00000136560	ENST00000259075;ENST00000392749;ENST00000405852;ENST00000437623;ENST00000439442	T;T;T;T;T	0.35973	1.68;1.68;1.29;1.28;1.61	5.57	5.57	0.84162	.	0.280521	0.34460	N	0.003944	T	0.01489	0.0048	L	0.59436	1.845	0.80722	D	1	D	0.63046	0.992	P	0.48454	0.578	T	0.00126	-1.2021	10	0.87932	D	0	-5.8187	15.5156	0.75822	0.1389:0.8611:0.0:0.0	rs2229759;rs35125118	358	Q92844	TANK_HUMAN	L	358;358;358;249;113	ENSP00000259075:P358L;ENSP00000376505:P358L;ENSP00000385487:P358L;ENSP00000412556:P249L;ENSP00000387439:P113L	ENSP00000259075:P358L	P	+	2	0	TANK	161796280	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	3.944000	0.56629	2.784000	0.95788	0.585000	0.79938	CCG	C|0.977;T|0.023	0.023	strong		0.433	TANK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324232.1	NM_133484		T	162088034	C	T	162088034	3	4	22	1	0	0	0	0	1	0	0	0	15561	652	23	1	1128	1	TANK	2	162088034	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1186631	162088034	81111339	689	3590											
IFIH1	64135	hgsc.bcm.edu	37	chr2	163128883	163128883	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	taggtgctctcatcagctctGgctcgaccacgggcctgaaa	8	9	11	13	2	3	1	2	1	2	0	5	2	3	1	2	3	2	3	2	3	2	1	rs13418718	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:163128883G>A	ENST00000263642.2	-	13	2864	c.2469C>T	c.(2467-2469)gcC>gcT	p.A823A		NM_022168.3	NP_071451.2	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	823	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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						CATCAGCTCTGGCTCGACCAC	0.428													G|||	473	0.0944489	0.3374	0.0389	5008	,	,		19695	0.0		0.0	False		,,,				2504	0.0				p.A823A		Atlas-SNP	.											.	IFIH1	102	.	0			c.C2469T						PASS	.	G		1416,2990	462.1+/-353.1	226,964,1013	80	70	74		2469	1.3	1	2	dbSNP_121	74	7,8593	3.7+/-12.6	0,7,4293	no	coding-synonymous	IFIH1	NM_022168.2		226,971,5306	AA,AG,GG		0.0814,32.138,10.9411		823/1026	163128883	1423,11583	2203	4300	6503	SO:0001819	synonymous_variant	64135	exon13			AGCTCTGGCTCGA	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.2469C>T	2.37:g.163128883G>A		248	0	0		188	106	0.56383	NM_022168	Q2NKL6|Q6DC96|Q86X56|Q96MX8|Q9H3G6	Silent	SNP	ENST00000263642.2	37	CCDS2217.1																																																																																			G|0.888;A|0.112	0.112	strong		0.428	IFIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255078.2	NM_022168		A	163128883	G	A	163128883	2	1	22	1	0	0	0	0	0	0	0	1	7529	1335	47	2		2	IFIH1	2	163128883	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1040849	163128883	80070490	690	3591											
TTC21B	79809	hgsc.bcm.edu	37	chr2	166758389	166758389	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggctgttccatctgaacaCgttttagtacccgagcttgt	7	14	9	11	2	1	1	0	1	1	0	2	2	2	1	2	1	3	5	2	1	3	5	rs76726265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:166758389C>T	ENST00000243344.7	-	20	2737	c.2600G>A	c.(2599-2601)cGt>cAt	p.R867H		NM_024753.4	NP_079029.3	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	867			R -> C (in JBTS11; functionally null mutation in vitro). {ECO:0000269|PubMed:21258341}.|R -> H (found in a patient with Meckel- Gruber syndrome also carrying a homozygous variant in CC2D2A; functionally null mutation in vitro; dbSNP:rs76726265). {ECO:0000269|PubMed:21258341}.		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						CATCTGAACACGTTTTAGTAC	0.378													C|||	6	0.00119808	0.0038	0.0014	5008	,	,		14632	0.0		0.0	False		,,,				2504	0.0				p.R867H		Atlas-SNP	.											TTC21B,NS,carcinoma,-1,1	TTC21B	130	1	0			c.G2600A						PASS	.	C	HIS/ARG	25,4381	31.7+/-61.6	0,25,2178	59	55	56		2600	5.7	1	2	dbSNP_131	56	0,8600		0,0,4300	yes	missense	TTC21B	NM_024753.3	29	0,25,6478	TT,TC,CC		0.0,0.5674,0.1922	probably-damaging	867/1317	166758389	25,12981	2203	4300	6503	SO:0001583	missense	79809	exon20			TGAACACGTTTTA	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.2600G>A	2.37:g.166758389C>T	ENSP00000243344:p.Arg867His	178	0	0		181	80	0.441989	NM_024753	A8MUZ3|Q3LIE4|Q53T84|Q6P4A1|Q6PIF5|Q8NCN3|Q96MA4|Q9HAK8	Missense_Mutation	SNP	ENST00000243344.7	37	CCDS33315.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	34	5.320668	0.95682	0.005674	0.0	ENSG00000123607	ENST00000243344	T	0.55234	0.53	5.7	5.7	0.88788	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.68054	0.2959	M	0.75884	2.315	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.73297	-0.4027	10	0.62326	D	0.03	-13.8163	19.8381	0.96666	0.0:1.0:0.0:0.0	.	867	Q7Z4L5	TT21B_HUMAN	H	867	ENSP00000243344:R867H	ENSP00000243344:R867H	R	-	2	0	TTC21B	166466635	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.061000	0.71148	2.692000	0.91855	0.650000	0.86243	CGT	C|0.998;T|0.002	0.002	strong		0.378	TTC21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333770.1	NM_024753		T	166758389	C	T	166758389	3	4	22	1	0	0	0	0	1	0	0	0	16703	536	19	1	1390	1	TTC21B	2	166758389	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3629506	166758389	76440984	691	3592											
TTC21B	79809	hgsc.bcm.edu	37	chr2	166781188	166781188	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aggttgcccaggacttgcagGctaaacaaaacaaatcagca	16	6	9	10	0	1	0	1	0	0	0	1	1	1	1	1	3	5	4	1	3	5	3	rs16851307	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:166781188G>A	ENST00000243344.7	-	12	1524	c.1387C>T	c.(1387-1389)Cct>Tct	p.P463S		NM_024753.4	NP_079029.3	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	463			P -> S (in dbSNP:rs16851307).		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						GGACTTGCAGGCTAAACAAAA	0.353													G|||	55	0.0109824	0.0386	0.0058	5008	,	,		13522	0.0		0.0	False		,,,				2504	0.0				p.P463S		Atlas-SNP	.											.	TTC21B	130	.	0			c.C1387T						PASS	.	G	SER/PRO	192,4214	119.2+/-156.9	6,180,2017	46	46	46		1387	5.8	1	2	dbSNP_123	46	0,8600		0,0,4300	yes	missense-near-splice	TTC21B	NM_024753.3	74	6,180,6317	AA,AG,GG		0.0,4.3577,1.4762	benign	463/1317	166781188	192,12814	2203	4300	6503	SO:0001630	splice_region_variant	79809	exon12			TTGCAGGCTAAAC	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.1387-1C>T	2.37:g.166781188G>A		121	0	0		115	44	0.382609	NM_024753	A8MUZ3|Q3LIE4|Q53T84|Q6P4A1|Q6PIF5|Q8NCN3|Q96MA4|Q9HAK8	Missense_Mutation	SNP	ENST00000243344.7	37	CCDS33315.1	27	0.012362637362637362	25	0.0508130081300813	2	0.0055248618784530384	0	0.0	0	0.0	G	19.77	3.889969	0.72524	0.043577	0.0	ENSG00000123607	ENST00000243344	T	0.63417	-0.04	5.76	5.76	0.90799	.	0.049003	0.85682	D	0.000000	T	0.26195	0.0639	M	0.74389	2.26	0.80722	D	1	P	0.39748	0.686	B	0.38156	0.266	T	0.53927	-0.8369	10	0.36615	T	0.2	-18.9007	19.9766	0.97312	0.0:0.0:1.0:0.0	rs16851307;rs52837751;rs58123452;rs16851307	463	Q7Z4L5	TT21B_HUMAN	S	463	ENSP00000243344:P463S	ENSP00000243344:P463S	P	-	1	0	TTC21B	166489434	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	6.194000	0.72082	2.728000	0.93425	0.561000	0.74099	CCT	G|0.983;A|0.017	0.017	strong		0.353	TTC21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333770.1	NM_024753	Missense_Mutation	A	166781188	G	A	166781188	5	1	22	1	0	0	0	0	0	0	1	0	16703	1217	42	2	2635	2	TTC21B	2	166781188	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	22799	166781188	76418185	692	3593											
SCN1A	6323	hgsc.bcm.edu	37	chr2	166868775	166868775	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atcgtctttcgctgatcaatAtatatatcttcaaatgccta	12	16	4	9	2	4	1	2	1	2	0	6	1	4	1	1	0	1	1	1	0	7	7	rs36031496	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:166868775A>G	ENST00000303395.4	-	19	3722	c.3723T>C	c.(3721-3723)taT>taC	p.Y1241Y	AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000597623.1_RNA|SCN1A_ENST00000423058.2_Silent_p.Y1241Y|SCN1A_ENST00000409050.1_Silent_p.Y1213Y|SCN1A_ENST00000375405.3_Silent_p.Y1230Y			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1241					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)	GCTGATCAATATATATATCTT	0.284													A|||	179	0.0357428	0.1316	0.0072	5008	,	,		18217	0.0		0.0	False		,,,				2504	0.0				p.Y1241Y		Atlas-SNP	.											.	SCN1A	641	.	0			c.T3723C						PASS	.	A	,,,	554,3852	240.3+/-251.1	48,458,1697	51	49	50		3723,3639,3723,3690	3.2	1	2	dbSNP_126	50	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SCN1A	NM_001165963.1,NM_001165964.1,NM_001202435.1,NM_006920.4	,,,	48,458,5995	GG,GA,AA		0.0,12.5738,4.2609	,,,	1241/2010,1213/1982,1241/2010,1230/1999	166868775	554,12448	2203	4298	6501	SO:0001819	synonymous_variant	6323	exon19			ATCAATATATATA	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.3723T>C	2.37:g.166868775A>G		179	0	0		190	119	0.626316	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Silent	SNP	ENST00000303395.4	37	CCDS54413.1																																																																																			.	.	none		0.284	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		G	166868775	A	G	166868775	2	3	22	1	0	0	0	0	0	0	0	1	13929	456	16	3		3	SCN1A	2	166868775	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	87587	166868775	76330598	693	3594											
SCN1A	6323	hgsc.bcm.edu	37	chr2	166900425	166900425	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctctacggctctcgttatcCtcaaaggtgctgtgctcatc	6	14	8	13	2	4	0	2	0	2	0	8	0	5	0	1	2	3	4	1	2	3	2	rs145035963		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:166900425C>T	ENST00000303395.4	-	11	1796	c.1797G>A	c.(1795-1797)gaG>gaA	p.E599E	AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000595268.1_RNA|SCN1A_ENST00000423058.2_Silent_p.E599E|SCN1A_ENST00000409050.1_Silent_p.E599E|AC010127.3_ENST00000599041.1_RNA|SCN1A_ENST00000375405.3_Silent_p.E599E			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	599					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)	TCTCGTTATCCTCAAAGGTGC	0.527													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20315	0.0		0.0	False		,,,				2504	0.0				p.E599E		Atlas-SNP	.											.	SCN1A	641	.	0			c.G1797A						PASS	.	C	,,,	4,4402	8.1+/-20.4	0,4,2199	168	148	155		1797,1797,1797,1797	3.3	1	2	dbSNP_134	155	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SCN1A	NM_001165963.1,NM_001165964.1,NM_001202435.1,NM_006920.4	,,,	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	,,,	599/2010,599/1982,599/2010,599/1999	166900425	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	6323	exon11			GTTATCCTCAAAG	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.1797G>A	2.37:g.166900425C>T		213	0	0		195	111	0.569231	NM_001165964	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Silent	SNP	ENST00000303395.4	37	CCDS54413.1																																																																																			C|1.000;T|0.000	0.000	strong		0.527	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		T	166900425	C	T	166900425	2	4	22	1	0	0	0	0	0	0	0	1	13929	680	24	2		2	SCN1A	2	166900425	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	31650	166900425	76298948	694	3595											
SCN9A	6335	hgsc.bcm.edu	37	chr2	167142979	167142979	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catctcccttttcctctccaCtggagagcttcttttgattc	5	17	5	14	0	3	2	0	1	3	1	7	3	4	2	3	1	1	1	3	1	0	6	rs58022607	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:167142979C>T	ENST00000409435.1	-	10	1468	c.1469G>A	c.(1468-1470)aGt>aAt	p.S490N	AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Missense_Mutation_p.S491N|SCN9A_ENST00000409672.1_Missense_Mutation_p.S490N|SCN9A_ENST00000375387.4_Missense_Mutation_p.S491N			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	490			S -> N (in dbSNP:rs58022607). {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)	TTCCTCTCCACTGGAGAGCTT	0.423													C|||	230	0.0459265	0.1551	0.0187	5008	,	,		19535	0.0		0.004	False		,,,				2504	0.0082				p.S490N		Atlas-SNP	.											.	SCN9A	296	.	0			c.G1469A						PASS	.	C	ASN/SER	464,3260		28,408,1426	111	104	106		1469	4	1	2	dbSNP_129	106	44,8140		3,38,4051	yes	missense	SCN9A	NM_002977.3	46	31,446,5477	TT,TC,CC		0.5376,12.4597,4.266	benign	490/1978	167142979	508,11400	1862	4092	5954	SO:0001583	missense	6335	exon11			TCTCCACTGGAGA	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.1469G>A	2.37:g.167142979C>T	ENSP00000386330:p.Ser490Asn	168	0	0		181	181	1	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Missense_Mutation	SNP	ENST00000409435.1	37	CCDS46441.1	95	0.043498168498168496	85	0.17276422764227642	8	0.022099447513812154	0	0.0	2	0.002638522427440633	C	11.89	1.773085	0.31411	0.124597	0.005376	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435;ENST00000454569;ENST00000452182	D;D;D;D;D;D	0.90900	-2.75;-2.75;-2.75;-2.75;-2.75;-2.75	5.82	4.01	0.46588	Domain of unknown function DUF3451 (1);	0.994312	0.08172	N	0.986830	T	0.01592	0.0051	M	0.66939	2.045	0.40162	P	0.022926000000000002	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.003;0.003	T	0.53599	-0.8416	9	0.31617	T	0.26	.	6.4457	0.21875	0.2587:0.6092:0.0:0.1321	rs58022607	490;490;491	E7EUN6;Q15858;E9PF08	.;SCN9A_HUMAN;.	N	490;491;491;490;355;355	ENSP00000386306:S490N;ENSP00000364536:S491N;ENSP00000304748:S491N;ENSP00000386330:S490N;ENSP00000413212:S355N;ENSP00000393141:S355N	ENSP00000304748:S491N	S	-	2	0	SCN9A	166851225	0.956000	0.32656	1.000000	0.80357	0.897000	0.52465	0.338000	0.19858	1.468000	0.48064	0.484000	0.47621	AGT	C|0.964;T|0.036	0.036	strong		0.423	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		T	167142979	C	T	167142979	3	4	22	1	0	0	0	0	1	0	0	0	13940	565	20	2	4532	2	SCN9A	2	167142979	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	242554	167142979	76056394	695	3596											
SCN9A	6335	hgsc.bcm.edu	37	chr2	167145106	167145106	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaaaggagcccaggaaaatCactacgacaaagaagatcat	20	5	8	8	1	2	2	2	0	0	2	2	5	2	4	1	2	2	0	1	2	7	2	rs58465962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:167145106C>A	ENST00000409435.1	-	9	1154	c.1155G>T	c.(1153-1155)gtG>gtT	p.V385V	AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Silent_p.V386V|SCN9A_ENST00000409672.1_Silent_p.V385V|SCN9A_ENST00000375387.4_Silent_p.V386V			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	385					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)	CCAGGAAAATCACTACGACAA	0.383													C|||	229	0.0457268	0.1551	0.0187	5008	,	,		15943	0.0		0.003	False		,,,				2504	0.0082				p.V385V		Atlas-SNP	.											.	SCN9A	296	.	0			c.G1155T						PASS	.	C		457,3229		28,401,1414	79	76	77		1155	1.8	1	2	dbSNP_129	77	45,8183		3,39,4072	no	coding-synonymous	SCN9A	NM_002977.3		31,440,5486	AA,AC,CC		0.5469,12.3983,4.2135		385/1978	167145106	502,11412	1843	4114	5957	SO:0001819	synonymous_variant	6335	exon10			GAAAATCACTACG	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.1155G>T	2.37:g.167145106C>A		89	0	0		50	50	1	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Silent	SNP	ENST00000409435.1	37	CCDS46441.1																																																																																			C|0.964;A|0.036	0.036	strong		0.383	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		A	167145106	C	A	167145106	2	1	22	1	0	0	0	0	0	0	0	1	13940	813	29	4		4	SCN9A	2	167145106	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2127	167145106	76054267	696	3597											
XIRP2	129446	hgsc.bcm.edu	37	chr2	168100280	168100280	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cacagaaattaaagttgtccGaggaatatccatggaagaaa	18	8	9	6	1	0	2	0	0	0	2	2	5	2	4	2	2	0	1	2	2	7	3	rs201184820		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:168100280G>A	ENST00000409195.1	+	9	2467	c.2378G>A	c.(2377-2379)cGa>cAa	p.R793Q	XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.R793Q|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.R571Q|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	618					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						AAAGTTGTCCGAGGAATATCC	0.408													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18882	0.0		0.0	False		,,,				2504	0.0				p.R793Q		Atlas-SNP	.											XIRP2,larynx,carcinoma,+1,2	XIRP2	914	2	0			c.G2378A						PASS	.	G	GLN/ARG,GLN/ARG,,,	4,3694		0,4,1845	72	70	70		1712,2378,,,	5.9	1	2		70	0,8182		0,0,4091	yes	missense,missense,intron,intron,intron	XIRP2	NM_001199144.1,NM_152381.5,NM_001079810.3,NM_001199143.1,NM_001199145.1	43,43,,,	0,4,5936	AA,AG,GG		0.0,0.1082,0.0337	probably-damaging,probably-damaging,,,	571/3328,793/3550,,,	168100280	4,11876	1849	4091	5940	SO:0001583	missense	129446	exon9			TTGTCCGAGGAAT	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.2378G>A	2.37:g.168100280G>A	ENSP00000386840:p.Arg793Gln	199	0	0		140	83	0.592857	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	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	G	19.05	3.752177	0.69533	0.001082	0.0	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.04234	3.68;3.68;3.67	5.92	5.92	0.95590	.	0.058183	0.64402	D	0.000001	T	0.24851	0.0603	M	0.80422	2.495	0.39027	D	0.959861	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.69479	0.92;0.964;0.964	T	0.00270	-1.1860	10	0.49607	T	0.09	-12.8648	20.3213	0.98679	0.0:0.0:1.0:0.0	.	618;618;571	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	Q	793;793;571	ENSP00000386840:R793Q;ENSP00000295237:R793Q;ENSP00000387255:R571Q	ENSP00000295237:R793Q	R	+	2	0	XIRP2	167808526	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.728000	0.54991	2.810000	0.96702	0.650000	0.86243	CGA	.	.	weak		0.408	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		A	168100280	G	A	168100280	3	1	22	1	0	0	0	0	1	0	0	0	17445	1058	37	1	2408	1	XIRP2	2	168100280	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	955174	168100280	75099093	697	3598											
ABCB11	8647	hgsc.bcm.edu	37	chr2	169853220	169853220	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aatttgatcatttcgctctcGatgttcagcaaccttcaaaa	12	14	5	10	2	4	1	3	1	1	0	6	2	4	1	1	0	2	3	1	0	4	4	rs11568377	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:169853220G>A	ENST00000263817.6	-	6	526	c.402C>T	c.(400-402)atC>atT	p.I134I		NM_003742.2	NP_003733.2	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 11	134	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				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)	TTTCGCTCTCGATGTTCAGCA	0.378													A|||	331	0.0660942	0.2179	0.0202	5008	,	,		13403	0.001		0.001	False		,,,				2504	0.0276				p.I134I		Atlas-SNP	.											.	ABCB11	136	.	0			c.C402T						PASS	.	A		590,3158		41,508,1325	60	57	58		402	2.8	0.9	2	dbSNP_121	58	3,8211		0,3,4104	no	coding-synonymous	ABCB11	NM_003742.2		41,511,5429	AA,AG,GG		0.0365,15.7417,4.9574		134/1322	169853220	593,11369	1874	4107	5981	SO:0001819	synonymous_variant	8647	exon6			GCTCTCGATGTTC	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.402C>T	2.37:g.169853220G>A		84	0	0		59	59	1	NM_003742	Q53TL2|Q9UNB2	Silent	SNP	ENST00000263817.6	37	CCDS46444.1																																																																																			G|0.935;A|0.065	0.065	strong		0.378	ABCB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333616.2	NM_003742		A	169853220	G	A	169853220	2	1	22	1	0	0	0	0	0	0	0	1	42	1048	37	1		1	ABCB11	2	169853220	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1752940	169853220	73346153	698	3599											
LRP2	4036	hgsc.bcm.edu	37	chr2	169993977	169993977	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tcaaatattatgggctgcttCcccatttccatgacaaagtc	11	13	6	11	0	1	1	1	1	0	0	4	1	3	1	3	1	1	2	3	1	4	4	rs34029982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:169993977C>T	ENST00000263816.3	-	76	13830	c.13545G>A	c.(13543-13545)ggG>ggA	p.G4515G		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	4515					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)"	TGGGCTGCTTCCCCATTTCCA	0.438													C|||	26	0.00519169	0.0197	0.0	5008	,	,		18764	0.0		0.0	False		,,,				2504	0.0				p.G4515G		Atlas-SNP	.											.	LRP2	751	.	0			c.G13545A						PASS	.	C		95,4311	69.2+/-107.0	0,95,2108	151	144	146		13545	3.6	1	2	dbSNP_126	146	0,8600		0,0,4300	no	coding-synonymous	LRP2	NM_004525.2		0,95,6408	TT,TC,CC		0.0,2.1562,0.7304		4515/4656	169993977	95,12911	2203	4300	6503	SO:0001819	synonymous_variant	4036	exon76			CTGCTTCCCCATT		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.13545G>A	2.37:g.169993977C>T		113	0	0		96	46	0.479167	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			C|0.992;T|0.008	0.008	strong		0.438	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		T	169993977	C	T	169993977	2	4	22	1	0	0	0	0	0	0	0	1	8965	842	30	2		2	LRP2	2	169993977	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	140757	169993977	73205396	699	3600											
LRP2	4036	hgsc.bcm.edu	37	chr2	170034473	170034473	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcttcaaaaatggtaatagcGaaagggtgaggcagtgcccc	13	8	12	8	1	2	1	1	1	1	0	2	2	2	1	2	3	2	2	2	3	5	3	rs139363553	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170034473G>A	ENST00000263816.3	-	53	10518	c.10233C>T	c.(10231-10233)ttC>ttT	p.F3411F	LRP2_ENST00000461418.1_5'UTR	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3411					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)"	TGGTAATAGCGAAAGGGTGAG	0.433													G|||	7	0.00139776	0.0053	0.0	5008	,	,		20637	0.0		0.0	False		,,,				2504	0.0				p.F3411F		Atlas-SNP	.											.	LRP2	751	.	0			c.C10233T						PASS	.	G		25,4381	31.7+/-61.6	0,25,2178	169	146	154		10233	2	1	2	dbSNP_134	154	0,8600		0,0,4300	no	coding-synonymous	LRP2	NM_004525.2		0,25,6478	AA,AG,GG		0.0,0.5674,0.1922		3411/4656	170034473	25,12981	2203	4300	6503	SO:0001819	synonymous_variant	4036	exon53			AATAGCGAAAGGG		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.10233C>T	2.37:g.170034473G>A		346	1	0.00289017		268	116	0.432836	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			G|0.999;A|0.001	0.001	strong		0.433	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		A	170034473	G	A	170034473	2	1	22	1	0	0	0	0	0	0	0	1	8965	1049	37	1		1	LRP2	2	170034473	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	40496	170034473	73164900	700	3601											
LRP2	4036	hgsc.bcm.edu	37	chr2	170038097	170038097	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcctactctcccaatgtatgCgcggtgaccccagtctgccc	6	9	9	17	2	2	1	0	1	2	0	3	1	2	1	5	1	3	1	5	1	3	2	rs137983840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170038097C>T	ENST00000263816.3	-	52	10315	c.10030G>A	c.(10030-10032)Gca>Aca	p.A3344T	LRP2_ENST00000461418.1_5'UTR	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3344					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)"	CCAATGTATGCGCGGTGACCC	0.483													C|||	8	0.00159744	0.0053	0.0014	5008	,	,		18886	0.0		0.0	False		,,,				2504	0.0				p.A3344T		Atlas-SNP	.											LRP2,NS,carcinoma,0,1	LRP2	751	1	0			c.G10030A						PASS	.	C	THR/ALA	23,4383	29.9+/-59.1	0,23,2180	151	123	132		10030	4.8	0.8	2	dbSNP_134	132	1,8599	1.2+/-3.3	0,1,4299	yes	missense	LRP2	NM_004525.2	58	0,24,6479	TT,TC,CC		0.0116,0.522,0.1845	probably-damaging	3344/4656	170038097	24,12982	2203	4300	6503	SO:0001583	missense	4036	exon52			TGTATGCGCGGTG		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.10030G>A	2.37:g.170038097C>T	ENSP00000263816:p.Ala3344Thr	197	0	0		183	82	0.448087	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	2	9.157509157509158E-4	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	C	17.25	3.341348	0.60963	0.00522	1.16E-4	ENSG00000081479	ENST00000263816;ENST00000536293	D	0.97811	-4.55	5.66	4.76	0.60689	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.170562	0.52532	D	0.000080	D	0.98327	0.9445	M	0.92169	3.28	0.80722	D	1	D	0.76494	0.999	P	0.62184	0.899	D	0.96079	0.9052	10	0.59425	D	0.04	.	16.2936	0.82761	0.0:0.7787:0.2213:0.0	.	3344	P98164	LRP2_HUMAN	T	3344;39	ENSP00000263816:A3344T	ENSP00000263816:A3344T	A	-	1	0	LRP2	169746343	0.991000	0.36638	0.788000	0.31933	0.219000	0.24729	2.604000	0.46274	2.661000	0.90470	0.655000	0.94253	GCA	C|0.999;T|0.001	0.001	strong		0.483	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		T	170038097	C	T	170038097	3	4	22	1	0	0	0	0	1	0	0	0	8965	768	27	1	4049	1	LRP2	2	170038097	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3624	170038097	73161276	701	3602											
BBS5	129880	hgsc.bcm.edu	37	chr2	170336102	170336102	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	ctttgggaggatcgggatgtCcgtttcgacctgtccgcgca	5	11	14	11	5	0	0	0	0	0	0	4	4	2	3	3	3	0	2	3	3	0	2	rs10188609	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170336102C>G	ENST00000295240.3	+	1	415	c.39C>G	c.(37-39)gtC>gtG	p.V13V	BBS5_ENST00000392663.2_Silent_p.V13V|RP11-724O16.1_ENST00000513963.1_Silent_p.V13V|BBS5_ENST00000554017.1_Silent_p.V13V	NM_152384.2	NP_689597.1	Q8N3I7	BBS5_HUMAN	Bardet-Biedl syndrome 5	13					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						ATCGGGATGTCCGTTTCGACC	0.637									Bardet-Biedl syndrome				C|||	233	0.0465256	0.1702	0.0115	5008	,	,		17042	0.0		0.0	False		,,,				2504	0.0				p.V13V		Atlas-SNP	.											.	BBS5	27	.	0			c.C39G						PASS	.	C		613,3793	265.3+/-266.6	56,501,1646	134	121	125		39	5.1	1	2	dbSNP_119	125	0,8600		0,0,4300	no	coding-synonymous	BBS5	NM_152384.2		56,501,5946	GG,GC,CC		0.0,13.9128,4.7132		13/342	170336102	613,12393	2203	4300	6503	SO:0001819	synonymous_variant	129880	exon1	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	GGATGTCCGTTTC	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.39C>G	2.37:g.170336102C>G		104	0	0		81	33	0.407407	NM_152384	D3DPC3|Q6PKN0	Silent	SNP	ENST00000295240.3	37	CCDS2233.1																																																																																			C|0.954;G|0.046	0.046	strong		0.637	BBS5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255265.2	NM_152384		G	170336102	C	G	170336102	2	3	22	1	0	0	0	0	0	0	0	1	1340	842	30	4		4	BBS5	2	170336102	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	298005	170336102	72863271	702	3603											
FASTKD1	79675	hgsc.bcm.edu	37	chr2	170403106	170403106	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggtcacactgtggtaaaacGgcttcaattcgggatatccc	11	10	10	10	2	2	0	2	0	0	0	4	1	3	1	1	4	1	2	1	4	4	4	rs16857030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170403106G>A	ENST00000453153.2	-	8	1669	c.1323C>T	c.(1321-1323)gcC>gcT	p.A441A	FASTKD1_ENST00000453929.2_Silent_p.A441A	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	441					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						GTGGTAAAACGGCTTCAATTC	0.428													G|||	494	0.0986422	0.2496	0.0764	5008	,	,		19180	0.003		0.0636	False		,,,				2504	0.045				p.A441A		Atlas-SNP	.											.	FASTKD1	86	.	0			c.C1323T						PASS	.	G		878,3528	338.9+/-305.5	90,698,1415	70	72	72		1323	-1.6	0.9	2	dbSNP_123	72	483,8117	139.5+/-196.2	10,463,3827	no	coding-synonymous	FASTKD1	NM_024622.3		100,1161,5242	AA,AG,GG		5.6163,19.9274,10.4644		441/848	170403106	1361,11645	2203	4300	6503	SO:0001819	synonymous_variant	79675	exon8			TAAAACGGCTTCA	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.1323C>T	2.37:g.170403106G>A		228	0	0		173	70	0.404624	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Silent	SNP	ENST00000453153.2	37	CCDS33318.1																																																																																			G|0.902;A|0.098	0.098	strong		0.428	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622		A	170403106	G	A	170403106	2	1	22	1	0	0	0	0	0	0	0	1	5693	1103	39	1		1	FASTKD1	2	170403106	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	67004	170403106	72796267	703	3604											
FASTKD1	79675	hgsc.bcm.edu	37	chr2	170413700	170413700	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatttcagaaaagataccttTtaatcagacatgagtttctg	15	14	6	6	0	3	4	2	1	1	3	3	4	3	4	1	0	1	1	1	0	5	5			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170413700T>C	ENST00000453153.2	-	6	1425	c.1079A>G	c.(1078-1080)aAa>aGa	p.K360R	FASTKD1_ENST00000453929.2_Missense_Mutation_p.K360R	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	360					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						AAGATACCTTTTAATCAGACA	0.378																																					p.K360R		Atlas-SNP	.											.	FASTKD1	86	.	0			c.A1079G						PASS	.						140	133	135					2																	170413700		2203	4300	6503	SO:0001583	missense	79675	exon6			TACCTTTTAATCA	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.1079A>G	2.37:g.170413700T>C	ENSP00000400513:p.Lys360Arg	107	0	0		83	46	0.554217	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Missense_Mutation	SNP	ENST00000453153.2	37	CCDS33318.1	.	.	.	.	.	.	.	.	.	.	T	14.27	2.486556	0.44249	.	.	ENSG00000138399	ENST00000453153;ENST00000453929	T;T	0.18810	2.19;2.19	5.02	5.02	0.67125	.	0.200255	0.52532	D	0.000064	T	0.25901	0.0631	M	0.74881	2.28	0.33094	D	0.538328	P;B	0.48350	0.909;0.053	B;B	0.43623	0.425;0.039	T	0.42396	-0.9454	10	0.25751	T	0.34	.	10.0946	0.42466	0.0:0.0:0.1684:0.8316	.	360;360	Q53R41-2;Q53R41	.;FAKD1_HUMAN	R	360	ENSP00000400513:K360R;ENSP00000403229:K360R	ENSP00000400513:K360R	K	-	2	0	FASTKD1	170121946	1.000000	0.71417	1.000000	0.80357	0.848000	0.48234	3.291000	0.51764	2.006000	0.58801	0.533000	0.62120	AAA	.	.	none		0.378	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622		C	170413700	T	C	170413700	3	2	22	1	0	0	0	0	1	0	0	0	5693	1841	64	3	1504	3	FASTKD1	2	170413700	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	10594	170413700	72785673	704	3605											
FASTKD1	79675	hgsc.bcm.edu	37	chr2	170428198	170428198	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacacattcaccagggtatcGtcattcattaatttgaattt	13	15	5	8	1	3	1	3	1	0	0	4	1	3	1	1	1	1	1	1	1	4	6	rs113959605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170428198G>A	ENST00000453153.2	-	2	688	c.342C>T	c.(340-342)gaC>gaT	p.D114D	FASTKD1_ENST00000453929.2_Silent_p.D114D	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	114					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						CCAGGGTATCGTCATTCATTA	0.279													G|||	37	0.00738818	0.0265	0.0014	5008	,	,		17370	0.0		0.001	False		,,,				2504	0.0				p.D114D		Atlas-SNP	.											.	FASTKD1	86	.	0			c.C342T						PASS	.	G		89,4315	68.7+/-106.4	2,85,2115	46	45	45		342	-5.3	0	2	dbSNP_132	45	1,8599		0,1,4299	no	coding-synonymous	FASTKD1	NM_024622.3		2,86,6414	AA,AG,GG		0.0116,2.0209,0.6921		114/848	170428198	90,12914	2202	4300	6502	SO:0001819	synonymous_variant	79675	exon2			GGTATCGTCATTC	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.342C>T	2.37:g.170428198G>A		157	0	0		106	45	0.424528	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Silent	SNP	ENST00000453153.2	37	CCDS33318.1																																																																																			G|0.993;A|0.007	0.007	strong		0.279	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622		A	170428198	G	A	170428198	2	1	22	1	0	0	0	0	0	0	0	1	5693	1136	40	1		1	FASTKD1	2	170428198	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	14498	170428198	72771175	705	3606											
PPIG	9360	hgsc.bcm.edu	37	chr2	170493784	170493784	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctaaaagtcgtgatcataaTagctcaaataacagcaggga	17	9	8	7	1	3	1	2	1	1	0	4	2	3	2	0	1	3	2	0	1	6	4	rs114584157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170493784T>C	ENST00000260970.3	+	14	2236	c.2016T>C	c.(2014-2016)aaT>aaC	p.N672N	PPIG_ENST00000448752.2_Silent_p.N672N|PPIG_ENST00000409714.3_Silent_p.N657N	NM_004792.2	NP_004783.2	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G (cyclophilin G)	672					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)	GTGATCATAATAGCTCAAATA	0.353													T|||	8	0.00159744	0.0061	0.0	5008	,	,		19790	0.0		0.0	False		,,,				2504	0.0				p.N672N		Atlas-SNP	.											.	PPIG	100	.	0			c.T2016C						PASS	.	T		42,4364	43.1+/-76.7	1,40,2162	70	74	73		2016	2.2	1	2	dbSNP_132	73	0,8600		0,0,4300	no	coding-synonymous	PPIG	NM_004792.2		1,40,6462	CC,CT,TT		0.0,0.9532,0.3229		672/755	170493784	42,12964	2203	4300	6503	SO:0001819	synonymous_variant	9360	exon14			TCATAATAGCTCA	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.2016T>C	2.37:g.170493784T>C		137	0	0		123	44	0.357724	NM_004792	D3DPC5|D3DPC6|O00706|Q53R40|Q53SN4|Q96DG9	Silent	SNP	ENST00000260970.3	37	CCDS2235.1																																																																																			T|0.997;C|0.003	0.003	strong		0.353	PPIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255264.2			C	170493784	T	C	170493784	2	2	22	1	0	0	0	0	0	0	0	1	12336	1403	49	3		3	PPIG	2	170493784	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	65586	170493784	72705589	706	3607											
C2orf77	129881	hgsc.bcm.edu	37	chr2	170502509	170502509	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tggtccacggccacctccagGtccttcctgtacagctttta	6	12	8	15	1	0	0	0	0	0	0	4	0	4	0	6	3	2	2	6	3	2	4	rs112720712	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170502509G>A	ENST00000447353.1	-	9	1606	c.1501C>T	c.(1501-1503)Cct>Tct	p.P501S		NM_001085447.1	NP_001078916.1	Q0VFZ6	CC173_HUMAN	coiled-coil domain containing 173	501																	CCACCTCCAGGTCCTTCCTGT	0.433													G|||	49	0.00978435	0.034	0.0043	5008	,	,		17210	0.0		0.001	False		,,,				2504	0.0				p.P501S		Atlas-SNP	.											.	.	.	.	0			c.C1501T						PASS	.	G	SER/PRO	119,3659		2,115,1772	169	173	171		1501	2	1	2	dbSNP_132	171	0,8212		0,0,4106	yes	missense	C2orf77	NM_001085447.1	74	2,115,5878	AA,AG,GG		0.0,3.1498,0.9925	benign	501/553	170502509	119,11871	1889	4106	5995	SO:0001583	missense	129881	exon9			CTCCAGGTCCTTC	BC015980, BC117445	CCDS46445.1	2q31.1	2012-08-07	2012-08-07	2012-08-07	ENSG00000154479	ENSG00000154479			25064	protein-coding gene	gene with protein product	"hypothetical LOC129881"		"chromosome 2 open reading frame 77"	C2orf77		12477932	Standard	NM_001085447		Approved	LOC129881	uc002ufe.2	Q0VFZ6	OTTHUMG00000154116	ENST00000447353.1:c.1501C>T	2.37:g.170502509G>A	ENSP00000391504:p.Pro501Ser	122	0	0		109	49	0.449541	NM_001085447	Q6PJF6	Missense_Mutation	SNP	ENST00000447353.1	37	CCDS46445.1	20	0.009157509157509158	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	13.71	2.319074	0.41096	0.031498	0.0	ENSG00000154479	ENST00000447353	.	.	.	5.87	2.01	0.26516	.	0.916393	0.09355	N	0.813572	T	0.06462	0.0166	L	0.40543	1.245	0.20074	N	0.999938	B	0.09022	0.002	B	0.08055	0.003	T	0.24657	-1.0154	9	0.07482	T	0.82	.	1.5507	0.02574	0.229:0.2733:0.3648:0.1329	.	501	Q0VFZ6	CB077_HUMAN	S	501	.	ENSP00000391504:P501S	P	-	1	0	C2orf77	170210755	0.219000	0.23619	0.992000	0.48379	0.992000	0.81027	0.199000	0.17237	0.467000	0.27218	0.655000	0.94253	CCT	G|0.990;A|0.010	0.010	strong		0.433	CCDC173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333954.2	NM_001085447		A	170502509	G	A	170502509	3	1	22	1	0	0	0	0	1	0	0	0	2196	1261	44	2	161	2	C2orf77	2	170502509	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	8725	170502509	72696864	707	3608											
C2orf77	129881	hgsc.bcm.edu	37	chr2	170537661	170537661	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttttccactcatcgtgtggAattatggtgacctgctggag	7	14	11	9	1	1	1	1	1	0	0	3	3	2	3	2	3	1	1	2	3	2	3	rs145389999	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170537661A>G	ENST00000447353.1	-	2	255	c.150T>C	c.(148-150)atT>atC	p.I50I		NM_001085447.1	NP_001078916.1	Q0VFZ6	CC173_HUMAN	coiled-coil domain containing 173	50																	CATCGTGTGGAATTATGGTGA	0.393													A|||	52	0.0103834	0.0356	0.0072	5008	,	,		17148	0.0		0.0	False		,,,				2504	0.0				p.I50I		Atlas-SNP	.											.	.	.	.	0			c.T150C						PASS	.	A		89,3817		1,87,1865	161	153	156		150	3.2	1	2	dbSNP_134	156	0,8292		0,0,4146	no	coding-synonymous	C2orf77	NM_001085447.1		1,87,6011	GG,GA,AA		0.0,2.2785,0.7296		50/553	170537661	89,12109	1953	4146	6099	SO:0001819	synonymous_variant	129881	exon2			GTGTGGAATTATG	BC015980, BC117445	CCDS46445.1	2q31.1	2012-08-07	2012-08-07	2012-08-07	ENSG00000154479	ENSG00000154479			25064	protein-coding gene	gene with protein product	"hypothetical LOC129881"		"chromosome 2 open reading frame 77"	C2orf77		12477932	Standard	NM_001085447		Approved	LOC129881	uc002ufe.2	Q0VFZ6	OTTHUMG00000154116	ENST00000447353.1:c.150T>C	2.37:g.170537661A>G		203	1	0.00492611		202	108	0.534653	NM_001085447	Q6PJF6	Silent	SNP	ENST00000447353.1	37	CCDS46445.1																																																																																			A|0.993;G|0.007	0.007	strong		0.393	CCDC173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333954.2	NM_001085447		G	170537661	A	G	170537661	2	3	22	1	0	0	0	0	0	0	0	1	2196	242	9	3		3	C2orf77	2	170537661	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	35152	170537661	72661712	708	3609											
UBR3	130507	hgsc.bcm.edu	37	chr2	170684548	170684548	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gactgcggggacagcaacgtGatgcgggagagcgggtgagt	9	5	20	7	4	0	3	0	2	0	1	0	6	0	4	0	4	5	1	0	4	1	0	rs79036304	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170684548G>A	ENST00000272793.5	+	1	581	c.531G>A	c.(529-531)gtG>gtA	p.V177V	UBR3_ENST00000418381.1_Silent_p.V177V			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	177					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						ACAGCAACGTGATGCGGGAGA	0.726													g|||	320	0.0638978	0.174	0.0461	5008	,	,		9387	0.0109		0.0258	False		,,,				2504	0.0215				p.V177V		Atlas-SNP	.											.	UBR3	182	.	0			c.G531A						PASS	.						6	6	6					2																	170684548		685	1551	2236	SO:0001819	synonymous_variant	130507	exon1			CAACGTGATGCGG	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.531G>A	2.37:g.170684548G>A		26	0	0		16	9	0.5625	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Silent	SNP	ENST00000272793.5	37																																																																																				G|0.940;A|0.060	0.060	strong		0.726	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070		A	170684548	G	A	170684548	2	1	22	1	0	0	0	0	0	0	0	1	16918	1277	45	2		2	UBR3	2	170684548	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	146887	170684548	72514825	709	3610											
MYO3B	140469	hgsc.bcm.edu	37	chr2	171256771	171256771	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgagttcgcagctatttcctCtcaacatcagactgataaaa	13	12	6	10	1	2	3	2	2	1	1	5	3	3	3	1	0	2	3	1	0	4	4	rs148136770|rs552913139	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:171256771C>T	ENST00000408978.4	+	17	2008	c.1865C>T	c.(1864-1866)tCt>tTt	p.S622F	MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000334231.6_Missense_Mutation_p.S631F|MYO3B_ENST00000409044.3_Missense_Mutation_p.S622F	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	622	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						GCTATTTCCTCTCAACATCAG	0.408																																					p.S622F		Atlas-SNP	.											.	MYO3B	320	.	0			c.C1865T						PASS	.	C	PHE/SER,PHE/SER,PHE/SER	5,3711		0,5,1853	199	181	187		1865,1865,1865	6	1	2	dbSNP_134	187	0,8214		0,0,4107	yes	missense,missense,missense	MYO3B	NM_001083615.2,NM_001171642.1,NM_138995.3	155,155,155	0,5,5960	TT,TC,CC		0.0,0.1346,0.0419	possibly-damaging,possibly-damaging,possibly-damaging	622/1315,622/1276,622/1342	171256771	5,11925	1858	4107	5965	SO:0001583	missense	140469	exon17			TTTCCTCTCAACA		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.1865C>T	2.37:g.171256771C>T	ENSP00000386213:p.Ser622Phe	166	0	0		129	56	0.434109	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Missense_Mutation	SNP	ENST00000408978.4	37	CCDS42773.1	3	0.0013736263736263737	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	C	32	5.164240	0.94727	0.001346	0.0	ENSG00000071909	ENST00000409044;ENST00000408978;ENST00000317915;ENST00000484338;ENST00000334231	T;T;T;T	0.79454	-1.27;-1.27;-1.25;-1.27	6.03	6.03	0.97812	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.89047	0.6604	M	0.86268	2.805	0.80722	D	1	D;P;P	0.58268	0.982;0.539;0.885	P;B;P	0.61132	0.884;0.281;0.688	D	0.89522	0.3779	10	0.87932	D	0	.	20.5568	0.99304	0.0:1.0:0.0:0.0	.	622;622;622	Q8WXR4-5;Q8WXR4-4;Q8WXR4	.;.;MYO3B_HUMAN	F	622;622;621;631;631	ENSP00000386497:S622F;ENSP00000386213:S622F;ENSP00000446237:S631F;ENSP00000335100:S631F	ENSP00000314213:S621F	S	+	2	0	MYO3B	170965017	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.818000	0.86416	2.861000	0.98227	0.655000	0.94253	TCT	C|0.999;T|0.001	0.001	strong		0.408	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1			T	171256771	C	T	171256771	3	4	22	1	0	0	0	0	1	0	0	0	10086	913	32	2	1931	2	MYO3B	2	171256771	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	572223	171256771	71942602	710	3611											
GAD1	2571	hgsc.bcm.edu	37	chr2	171713564	171713564	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaaccagatcaacaaatgcCtggaactggctgaatacctc	16	7	7	11	0	1	2	1	1	0	1	2	3	1	3	3	2	5	1	3	2	7	1	rs769392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:171713564C>T	ENST00000358196.3	+	15	2000	c.1450C>T	c.(1450-1452)Ctg>Ttg	p.L484L		NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	484					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						CAACAAATGCCTGGAACTGGC	0.418													C|||	213	0.0425319	0.1505	0.0202	5008	,	,		19163	0.0		0.0	False		,,,				2504	0.0				p.L484L		Atlas-SNP	.											.	GAD1	79	.	0			c.C1450T						PASS	.	C		566,3840	254.3+/-259.9	31,504,1668	162	175	171		1450	1.6	1	2	dbSNP_98	171	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	GAD1	NM_000817.2		31,507,5965	TT,TC,CC		0.0349,12.8461,4.3749		484/595	171713564	569,12437	2203	4300	6503	SO:0001819	synonymous_variant	2571	exon15			AAATGCCTGGAAC		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.1450C>T	2.37:g.171713564C>T		65	0	0		73	27	0.369863	NM_000817	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Silent	SNP	ENST00000358196.3	37	CCDS2239.1																																																																																			C|0.959;T|0.041	0.041	strong		0.418	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2			T	171713564	C	T	171713564	2	4	22	1	0	0	0	0	0	0	0	1	6187	680	24	2		2	GAD1	2	171713564	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	456793	171713564	71485809	711	3612											
GAD1	2571	hgsc.bcm.edu	37	chr2	171715387	171715387	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccagacagccctcaacgacGggaaaagctacacaaggtat	15	4	10	12	2	1	1	1	0	0	1	1	3	1	2	2	2	4	2	2	2	6	2	rs769402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:171715387G>A	ENST00000358196.3	+	16	2145	c.1595G>A	c.(1594-1596)cGg>cAg	p.R532Q		NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	532			R -> Q (in dbSNP:rs769402). {ECO:0000269|Ref.9}.		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						CCTCAACGACGGGAAAAGCTA	0.453													G|||	305	0.0609026	0.2216	0.0159	5008	,	,		20178	0.0		0.001	False		,,,				2504	0.0				p.R532Q		Atlas-SNP	.											.	GAD1	79	.	0			c.G1595A						PASS	.	G	GLN/ARG	807,3599	321.3+/-297.0	68,671,1464	82	83	83		1595	3.8	1	2	dbSNP_98	83	13,8587	9.1+/-34.3	0,13,4287	yes	missense	GAD1	NM_000817.2	43	68,684,5751	AA,AG,GG		0.1512,18.3159,6.3048	benign	532/595	171715387	820,12186	2203	4300	6503	SO:0001583	missense	2571	exon16			AACGACGGGAAAA		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.1595G>A	2.37:g.171715387G>A	ENSP00000350928:p.Arg532Gln	111	0	0		118	61	0.516949	NM_000817	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Missense_Mutation	SNP	ENST00000358196.3	37	CCDS2239.1	105	0.04807692307692308	96	0.1951219512195122	9	0.024861878453038673	0	0.0	0	0.0	G	13.06	2.125053	0.37533	0.183159	0.001512	ENSG00000128683	ENST00000358196	T	0.16597	2.33	5.63	3.84	0.44239	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.174131	0.50627	N	0.000104	T	0.00012	0.0000	L	0.31526	0.94	0.09310	P	1.0	B	0.14012	0.009	B	0.04013	0.001	T	0.39440	-0.9614	9	0.12430	T	0.62	-7.3586	9.081	0.36552	0.2195:0.0:0.7805:0.0	rs769402;rs2229844;rs2266645;rs10209273;rs52821361;rs769402	532	Q99259	DCE1_HUMAN	Q	532	ENSP00000350928:R532Q	ENSP00000350928:R532Q	R	+	2	0	GAD1	171423633	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.305000	0.59110	0.736000	0.32559	0.655000	0.94253	CGG	G|0.935;A|0.065	0.065	strong		0.453	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2			A	171715387	G	A	171715387	3	1	22	1	0	0	0	0	1	0	0	0	6187	1116	39	1	1694	1	GAD1	2	171715387	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1823	171715387	71483986	712	3613											
CHRNA1	1134	hgsc.bcm.edu	37	chr2	175613477	175613477	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttctgtaaaaatctttttgTcttgcttttctctggatggt	6	21	7	7	0	4	0	0	0	4	0	5	1	4	1	0	2	1	2	0	2	3	7	rs6739001	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:175613477T>A	ENST00000261007.5	-	9	1214	c.1148A>T	c.(1147-1149)gAc>gTc	p.D383V	CHRNA1_ENST00000348749.5_Missense_Mutation_p.D358V|CHRNA1_ENST00000409542.1_Missense_Mutation_p.D276V|CHRNA1_ENST00000409219.1_Intron|AC018890.6_ENST00000442996.1_RNA	NM_001039523.2	NP_001034612.1	P02708	ACHA_HUMAN	cholinergic receptor, nicotinic, alpha 1 (muscle)	383			D -> V (in dbSNP:rs6739001).		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)	AATCTTTTTGTCTTGCTTTTC	0.408											OREG0015079	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	94	0.01877	0.0703	0.0014	5008	,	,		19250	0.0		0.0	False		,,,				2504	0.0				p.D383V		Atlas-SNP	.											.	CHRNA1	92	.	0			c.A1148T						PASS	.	T	VAL/ASP,VAL/ASP	251,4155	144.6+/-179.5	5,241,1957	137	130	133		1073,1148	5.5	1	2	dbSNP_116	133	1,8599		0,1,4299	yes	missense,missense	CHRNA1	NM_000079.3,NM_001039523.2	152,152	5,242,6256	AA,AT,TT		0.0116,5.6968,1.9376	benign,benign	358/458,383/483	175613477	252,12754	2203	4300	6503	SO:0001583	missense	1134	exon9			TTTTTGTCTTGCT	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.1148A>T	2.37:g.175613477T>A	ENSP00000261007:p.Asp383Val	175	0	0	1924	134	59	0.440298	NM_001039523	B4DRV6|D3DPE8	Missense_Mutation	SNP	ENST00000261007.5	37	CCDS33331.1	37	0.01694139194139194	37	0.07520325203252033	0	0.0	0	0.0	0	0.0	T	14.25	2.478393	0.44044	0.056968	1.16E-4	ENSG00000138435	ENST00000348749;ENST00000261007;ENST00000409542	D;D;D	0.85773	-2.03;-2.03;-2.03	5.51	5.51	0.81932	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.943943	0.09150	N	0.841683	T	0.19967	0.0480	L	0.27053	0.805	0.80722	D	1	B;B	0.23540	0.003;0.087	B;B	0.25759	0.007;0.063	T	0.48559	-0.9025	10	0.40728	T	0.16	.	11.8621	0.52471	0.0:0.0:0.1458:0.8542	rs6739001;rs52820919;rs6739001	358;383	Q53SH4;P02708	.;ACHA_HUMAN	V	358;383;276	ENSP00000261008:D358V;ENSP00000261007:D383V;ENSP00000387026:D276V	ENSP00000261007:D383V	D	-	2	0	CHRNA1	175321723	0.997000	0.39634	0.998000	0.56505	0.992000	0.81027	2.634000	0.46528	2.217000	0.71921	0.533000	0.62120	GAC	T|0.971;A|0.029	0.029	strong		0.408	CHRNA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334116.1			A	175613477	T	A	175613477	3	1	22	1	0	0	0	0	1	0	0	0	3383	1667	58	5	308	5	CHRNA1	2	175613477	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	3898090	175613477	67585896	713	3614											
EVX2	344191	hgsc.bcm.edu	37	chr2	176948445	176948445	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggagaatctcttgcccgcCgtagggctgtgcagccctct	5	11	12	13	2	2	1	0	0	2	1	3	2	2	1	3	2	3	3	3	2	2	3	rs61731351	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:176948445C>G	ENST00000308618.4	-	1	196	c.60G>C	c.(58-60)acG>acC	p.T20T		NM_001080458.1	NP_001073927.1	Q03828	EVX2_HUMAN	even-skipped homeobox 2	20					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)		TCTTGCCCGCCGTAGGGCTGT	0.547													C|||	188	0.0375399	0.1369	0.0086	5008	,	,		16189	0.0		0.001	False		,,,				2504	0.0				p.T20T		Atlas-SNP	.											EVX2,NS,carcinoma,0,1	EVX2	51	1	0			c.G60C						PASS	.	C		572,3834	242.8+/-252.7	42,488,1673	68	79	75		60	0	1	2	dbSNP_129	75	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	EVX2	NM_001080458.1		42,489,5972	GG,GC,CC		0.0116,12.9823,4.4057		20/477	176948445	573,12433	2203	4300	6503	SO:0001819	synonymous_variant	344191	exon1			GCCCGCCGTAGGG		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.60G>C	2.37:g.176948445C>G		72	0	0		104	54	0.519231	NM_001080458		Silent	SNP	ENST00000308618.4	37	CCDS33333.1																																																																																			C|0.930;G|0.070	0.070	strong		0.547	EVX2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359252.1			G	176948445	C	G	176948445	2	3	22	1	0	0	0	0	0	0	0	1	5297	639	23	4		4	EVX2	2	176948445	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1334968	176948445	66250928	714	3615											
HOXD9	3235	hgsc.bcm.edu	37	chr2	176988765	176988765	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagaaagaattcctcttcaaCatgtacctcacccgggaccg	12	8	8	13	2	3	2	2	0	1	2	4	4	4	3	4	1	2	1	4	1	4	3	rs35649704	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:176988765C>T	ENST00000249499.6	+	2	1330	c.921C>T	c.(919-921)aaC>aaT	p.N307N	HOXD-AS2_ENST00000440016.2_RNA	NM_014213.3	NP_055028.3	P28356	HXD9_HUMAN	homeobox D9	307					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)		TCCTCTTCAACATGTACCTCA	0.537													C|||	83	0.0165735	0.0613	0.0029	5008	,	,		17944	0.0		0.0	False		,,,				2504	0.0				p.N307N	GBM(47;924 952 7959 9248 12176)	Atlas-SNP	.											.	HOXD9	49	.	0			c.C921T						PASS	.	C		186,4220	118.8+/-156.5	4,178,2021	94	105	101		921	3.9	1	2	dbSNP_126	101	0,8600		0,0,4300	no	coding-synonymous	HOXD9	NM_014213.3		4,178,6321	TT,TC,CC		0.0,4.2215,1.4301		307/353	176988765	186,12820	2203	4300	6503	SO:0001819	synonymous_variant	3235	exon2			CTTCAACATGTAC		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.921C>T	2.37:g.176988765C>T		162	0	0		170	86	0.505882	NM_014213	Q86ST1	Silent	SNP	ENST00000249499.6	37	CCDS2267.2																																																																																			C|0.987;T|0.013	0.013	strong		0.537	HOXD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255698.4			T	176988765	C	T	176988765	2	4	22	1	0	0	0	0	0	0	0	1	7335	477	17	2		2	HOXD9	2	176988765	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	40320	176988765	66210608	715	3616											
HOXD8	3234	hgsc.bcm.edu	37	chr2	176995146	176995146	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaagtacaaggcggcggctGcggcggcggcggcggcgggc	5	2	21	13	8	0	0	0	0	0	0	0	0	0	0	1	9	2	2	1	9	3	1	rs192755857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:176995146G>A	ENST00000313173.4	+	1	679	c.52G>A	c.(52-54)Gcg>Acg	p.A18T	HOXD-AS2_ENST00000440016.2_RNA|HOXD8_ENST00000548663.1_Missense_Mutation_p.A18T|HOXD8_ENST00000429017.1_Intron|HOXD8_ENST00000544999.1_Missense_Mutation_p.A18T|HOXD8_ENST00000450510.2_Missense_Mutation_p.A18T	NM_001199746.1|NM_019558.3	NP_001186675.1|NP_062458.1	P13378	HXD8_HUMAN	homeobox D8	18	Poly-Ala.				anterior/posterior axis specification, embryo (GO:0008595)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system morphogenesis (GO:0048705)|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(2)|lung(5)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.195)	Colorectal(32;0.0224)|READ - Rectum adenocarcinoma(9;0.0556)		ggcggcggctgcggcggcggc	0.726													G|||	92	0.0183706	0.0681	0.0029	5008	,	,		5924	0.0		0.0	False		,,,				2504	0.0				p.A18T		Atlas-SNP	.											.	HOXD8	24	.	0			c.G52A						PASS	.						1	1	1					2																	176995146		405	891	1296	SO:0001583	missense	3234	exon1			GCGGCTGCGGCGG		CCDS2268.1, CCDS56148.1, CCDS56149.1	2q31.1	2011-06-20	2005-12-22		ENSG00000175879	ENSG00000175879		"Homeoboxes / ANTP class : HOXL subclass"	5139	protein-coding gene	gene with protein product		142985	"homeo box D8"	HOX4, HOX4E		1973146, 1358459	Standard	NM_001199747		Approved		uc002uko.3	P13378	OTTHUMG00000132513	ENST00000313173.4:c.52G>A	2.37:g.176995146G>A	ENSP00000315949:p.Ala18Thr	2	0	0		9	7	0.777778	NM_001199746	F8WBG7|Q5BL00|Q8IXZ1	Missense_Mutation	SNP	ENST00000313173.4	37	CCDS2268.1	76	0.0347985347985348	32	0.06504065040650407	8	0.022099447513812154	29	0.050699300699300696	7	0.009234828496042216	G	15.69	2.907048	0.52333	.	.	ENSG00000175879	ENST00000313173;ENST00000544999;ENST00000548663;ENST00000450510	D;D;D;D	0.93763	-3.28;-3.25;-3.0;-3.25	2.06	1.06	0.20224	.	.	.	.	.	T	0.30230	0.0758	N	0.08118	0	0.22968	N	0.998491	B;B	0.26081	0.124;0.141	B;B	0.17722	0.014;0.019	T	0.54036	-0.8353	9	0.14656	T	0.56	.	5.7146	0.17952	0.0:0.0:0.6812:0.3188	.	18;18	Q8IXZ1;P13378	.;HXD8_HUMAN	T	18	ENSP00000315949:A18T;ENSP00000437431:A18T;ENSP00000448196:A18T;ENSP00000409026:A18T	ENSP00000315949:A18T	A	+	1	0	HOXD8	176703392	0.986000	0.35501	0.504000	0.27639	0.610000	0.37248	0.000000	0.12993	-0.051000	0.13334	0.186000	0.17326	GCG	G|0.966;A|0.034	0.034	strong		0.726	HOXD8-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255694.1			A	176995146	G	A	176995146	3	1	22	1	0	0	0	0	1	0	0	0	7334	1319	46	2	54	2	HOXD8	2	176995146	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6381	176995146	66204227	716	3617											
HOXD3	3232	hgsc.bcm.edu	37	chr2	177034130	177034130	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgcatgcggccgggcactggGaacagccagggtgggggtgg	6	5	21	9	2	0	0	0	0	0	0	0	1	0	1	2	7	4	2	2	7	1	0	rs77818566	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:177034130G>A	ENST00000468418.3	+	3	2378	c.288G>A	c.(286-288)ggG>ggA	p.G96G	HOXD3_ENST00000249440.3_Silent_p.G96G|HOXD3_ENST00000410016.1_Silent_p.G96G			P31249	HXD3_HUMAN	homeobox D3	96					anterior/posterior pattern specification (GO:0009952)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|embryonic skeletal system morphogenesis (GO:0048704)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron differentiation (GO:0045666)|thyroid gland development (GO:0030878)|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)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(11)|prostate(1)|upper_aerodigestive_tract(2)	23			OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226)	Colorectal(32;0.247)		CGGGCACTGGGAACAGCCAGG	0.647													G|||	289	0.0577077	0.2133	0.0101	5008	,	,		14552	0.0		0.0	False		,,,				2504	0.0				p.G96G		Atlas-SNP	.											.	HOXD3	65	.	0			c.G288A						PASS	.	G		749,3657	262.5+/-264.9	73,603,1527	24	26	25		288	3.6	1	2	dbSNP_131	25	18,8582	9.8+/-36.6	0,18,4282	no	coding-synonymous	HOXD3	NM_006898.4		73,621,5809	AA,AG,GG		0.2093,16.9995,5.8973		96/433	177034130	767,12239	2203	4300	6503	SO:0001819	synonymous_variant	3232	exon2			CACTGGGAACAGC		CCDS2270.1	2q31.1	2011-06-20	2005-12-22		ENSG00000128652	ENSG00000128652		"Homeoboxes / ANTP class : HOXL subclass"	5137	protein-coding gene	gene with protein product		142980	"homeo box D3"	HOX4A, HOX4, HOX1D		1973146, 1358459	Standard	NM_006898		Approved		uc002ukt.1	P31249	OTTHUMG00000132517	ENST00000468418.3:c.288G>A	2.37:g.177034130G>A		141	0	0		116	56	0.482759	NM_006898	Q99955|Q9BSC5	Silent	SNP	ENST00000468418.3	37	CCDS2270.1																																																																																			G|0.949;A|0.051	0.051	strong		0.647	HOXD3-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334246.4			A	177034130	G	A	177034130	2	1	22	1	0	0	0	0	0	0	0	1	7332	1161	41	2		2	HOXD3	2	177034130	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	38984	177034130	66165243	717	3618											
PDE11A	50940	hgsc.bcm.edu	37	chr2	178592452	178592452	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cagttgtggtatagaaccatCcgatagtttttcctcactgt	9	15	8	9	1	1	1	1	0	0	1	3	2	3	1	3	1	1	3	3	1	4	6	rs77341035	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:178592452C>A	ENST00000286063.6	-	12	2294	c.1977G>T	c.(1975-1977)cgG>cgT	p.R659R	PDE11A_ENST00000358450.4_Silent_p.R409R|PDE11A_ENST00000449286.2_Silent_p.R301R|PDE11A_ENST00000409504.1_Silent_p.R301R|PDE11A_ENST00000389683.3_Silent_p.R215R|PDE11A_ENST00000497003.1_5'UTR	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	659	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)	ATAGAACCATCCGATAGTTTT	0.468									Primary Pigmented Nodular Adrenocortical Disease, Familial				C|||	54	0.0107827	0.0393	0.0029	5008	,	,		22848	0.0		0.0	False		,,,				2504	0.0				p.R659R		Atlas-SNP	.											.	PDE11A	283	.	0			c.G1977T						PASS	.	C	,,,	96,4310	77.8+/-116.1	0,96,2107	185	153	164		645,1227,903,1977	-7.6	0.9	2	dbSNP_131	164	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDE11A	NM_001077196.1,NM_001077197.1,NM_001077358.1,NM_016953.3	,,,	0,97,6406	AA,AC,CC		0.0116,2.1788,0.7458	,,,	215/490,409/684,301/576,659/934	178592452	97,12909	2203	4300	6503	SO:0001819	synonymous_variant	50940	exon12	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	AACCATCCGATAG	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.1977G>T	2.37:g.178592452C>A		105	0	0		112	54	0.482143	NM_016953	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Silent	SNP	ENST00000286063.6	37	CCDS33334.1	24	0.01098901098901099	22	0.044715447154471545	2	0.0055248618784530384	0	0.0	0	0.0	C	11.02	1.515710	0.27123	0.021788	1.16E-4	ENSG00000128655	ENST00000433879	.	.	.	5.67	-7.56	0.01322	.	.	.	.	.	T	0.10252	0.0251	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39014	-0.9634	4	.	.	.	.	2.2102	0.03945	0.1021:0.2177:0.3161:0.3641	.	.	.	.	V	267	.	.	G	-	2	0	PDE11A	178300698	0.947000	0.32204	0.922000	0.36590	0.991000	0.79684	-0.087000	0.11215	-0.991000	0.03476	-0.290000	0.09829	GGA	C|0.989;A|0.011	0.011	strong		0.468	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2			A	178592452	C	A	178592452	2	1	22	1	0	0	0	0	0	0	0	1	11640	842	30	4		4	PDE11A	2	178592452	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1558322	178592452	64606921	718	3619											
OSBPL6	114880	hgsc.bcm.edu	37	chr2	179226431	179226431	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattctcttttgaagtctgcAtttaatagcatagctataga	12	16	6	7	0	2	2	0	1	2	1	3	2	2	2	0	0	3	3	0	0	6	9	rs145291582	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179226431A>G	ENST00000190611.4	+	13	1552	c.1176A>G	c.(1174-1176)gcA>gcG	p.A392A	OSBPL6_ENST00000315022.2_Silent_p.A396A|OSBPL6_ENST00000357080.4_Silent_p.A361A|OSBPL6_ENST00000409631.1_Silent_p.A392A|OSBPL6_ENST00000392505.2_Silent_p.A417A|OSBPL6_ENST00000409045.3_Silent_p.A361A|OSBPL6_ENST00000359685.3_Silent_p.A392A	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	392					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)			TGAAGTCTGCATTTAATAGCA	0.438													a|||	19	0.00379393	0.0136	0.0014	5008	,	,		20040	0.0		0.0	False		,,,				2504	0.0				p.A417A		Atlas-SNP	.											OSBPL6,NS,carcinoma,+1,1	OSBPL6	178	1	0			c.A1251G						PASS	.	A	,,,,	58,4348	55.5+/-91.7	0,58,2145	104	98	100		1251,1083,1176,1176,1188	-11.1	0.2	2	dbSNP_134	100	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OSBPL6	NM_001201480.1,NM_001201481.1,NM_001201482.1,NM_032523.3,NM_145739.2	,,,,	0,58,6445	GG,GA,AA		0.0,1.3164,0.4459	,,,,	417/960,361/904,392/899,392/935,396/939	179226431	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	114880	exon14			GTCTGCATTTAAT	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.1176A>G	2.37:g.179226431A>G		290	0	0		289	144	0.49827	NM_001201480	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Silent	SNP	ENST00000190611.4	37	CCDS2277.1																																																																																			A|0.995;G|0.005	0.005	strong		0.438	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523		G	179226431	A	G	179226431	2	3	22	1	0	0	0	0	0	0	0	1	11290	204	8	3		3	OSBPL6	2	179226431	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	633979	179226431	63972942	719	3620											
TTN	7273	hgsc.bcm.edu	37	chr2	179401015	179401015	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aattgggacatcagatttggGagtgatgggttctgatattt	10	15	13	3	0	2	3	1	2	1	1	2	5	2	5	0	3	0	1	0	3	2	5	rs72629779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179401015G>A	ENST00000591111.1	-	307	95760	c.95536C>T	c.(95536-95538)Ccc>Tcc	p.P31846S	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.P24614S|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.P30919S|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P24547S|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.P24422S|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.P33487S			Q8WZ42	TITIN_HUMAN	titin	31846	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)			TCAGATTTGGGAGTGATGGGT	0.403													G|||	69	0.013778	0.0499	0.0043	5008	,	,		21952	0.0		0.0	False		,,,				2504	0.0				p.P33487S		Atlas-SNP	.											.	TTN	18412	.	0			c.C100459T						PASS	.	G	SER/PRO,SER/PRO,SER/PRO,SER/PRO	127,3629		1,125,1752	87	80	83		73264,92755,73639,73840	5.8	1	2	dbSNP_130	83	2,8222		0,2,4110	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	74,74,74,74	1,127,5862	AA,AG,GG		0.0243,3.3813,1.0768	probably-damaging,probably-damaging,probably-damaging,probably-damaging	24422/26927,30919/33424,24547/27052,24614/27119	179401015	129,11851	1878	4112	5990	SO:0001583	missense	7273	exon357			ATTTGGGAGTGAT	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.95536C>T	2.37:g.179401015G>A	ENSP00000465570:p.Pro31846Ser	178	0	0		179	85	0.47486	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	37		22	0.010073260073260074	20	0.04065040650406504	2	0.0055248618784530384	0	0.0	0	0.0	G	20.0	3.930466	0.73327	0.033813	2.43E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.54675	0.56;0.56;0.56;0.56	5.76	5.76	0.90799	Fibronectin, type III (2);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.46927	0.1418	M	0.80183	2.485	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	0.69327	-0.5174	9	0.87932	D	0	.	19.9595	0.97236	0.0:0.0:1.0:0.0	.	24422;24547;24614;31846	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	S	30919;24422;24614;24547;24419	ENSP00000343764:P30919S;ENSP00000434586:P24422S;ENSP00000340554:P24614S;ENSP00000352154:P24547S	ENSP00000340554:P24614S	P	-	1	0	TTN	179109261	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.997000	0.88414	2.706000	0.92434	0.563000	0.77884	CCC	G|0.990;A|0.010	0.010	strong		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179401015	G	A	179401015	3	1	22	1	0	0	0	0	1	0	0	0	16750	1174	41	2	7544	2	TTN	2	179401015	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	174584	179401015	63798358	720	3621											
TTN	7273	hgsc.bcm.edu	37	chr2	179412452	179412452	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaatgaccacaactgtgaCgctaaatgttttaacaccag	14	10	6	11	1	0	2	0	2	0	0	1	2	1	2	3	0	2	2	3	0	5	3	rs67665715	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179412452C>T	ENST00000591111.1	-	289	89202	c.88978G>A	c.(88978-88980)Gtc>Atc	p.V29660I	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V22428I|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V28733I|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V22361I|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.V22236I|TTN_ENST00000589042.1_Missense_Mutation_p.V31301I			Q8WZ42	TITIN_HUMAN	titin	29660	Ig-like 135.				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)			ACAACTGTGACGCTAAATGTT	0.478													C|||	180	0.0359425	0.1271	0.0159	5008	,	,		20351	0.0		0.001	False		,,,				2504	0.0				p.V31301I		Atlas-SNP	.											.	TTN	18412	.	0			c.G93901A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	395,3517		24,347,1585	139	130	133		67282,67081,86197,66706	-2.3	0.9	2	dbSNP_130	133	8,8316		0,8,4154	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	29,29,29,29	24,355,5739	TT,TC,CC		0.0961,10.0971,3.2936	benign,benign,benign,benign	22428/27119,22361/27052,28733/33424,22236/26927	179412452	403,11833	1956	4162	6118	SO:0001583	missense	7273	exon339			CTGTGACGCTAAA	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.88978G>A	2.37:g.179412452C>T	ENSP00000465570:p.Val29660Ile	387	0	0		438	243	0.554795	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	37		86	0.039377289377289376	78	0.15853658536585366	8	0.022099447513812154	0	0.0	0	0.0	C	6.281	0.420045	0.11928	0.100971	9.61E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	5.92	-2.32	0.06745	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Fibronectin, type III (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00271	0.0008	N	0.17631	0.505	0.30962	P	0.723517	B;B;B;B	0.09022	0.002;0.002;0.002;0.002	B;B;B;B	0.08055	0.002;0.002;0.003;0.003	T	0.09618	-1.0666	8	0.87932	D	0	.	13.3122	0.60386	0.0:0.727:0.0:0.273	.	22236;22361;22428;29660	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	28733;22236;22428;22361;22233	ENSP00000343764:V28733I;ENSP00000434586:V22236I;ENSP00000340554:V22428I;ENSP00000352154:V22361I	ENSP00000340554:V22428I	V	-	1	0	TTN	179120698	0.965000	0.33210	0.865000	0.33974	0.314000	0.28054	0.991000	0.29654	-0.306000	0.08818	-1.934000	0.00508	GTC	C|0.967;T|0.033	0.033	strong		0.478	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179412452	C	T	179412452	3	4	22	1	0	0	0	0	1	0	0	0	16750	536	19	1	14174	1	TTN	2	179412452	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	11437	179412452	63786921	721	3622											
TTN	7273	hgsc.bcm.edu	37	chr2	179416659	179416659	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcctgggggaccaggaatcCtgaactggtgttttgccaca	8	11	12	10	0	0	1	0	1	0	0	2	3	2	3	4	4	2	1	4	4	2	3	rs11887722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179416659C>T	ENST00000591111.1	-	285	86269	c.86045G>A	c.(86044-86046)aGg>aAg	p.R28682K	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R21450K|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R27755K|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R21383K|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R21258K|TTN_ENST00000589042.1_Missense_Mutation_p.R30323K			Q8WZ42	TITIN_HUMAN	titin	28682					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)			ACCAGGAATCCTGAACTGGTG	0.448													C|||	180	0.0359425	0.1271	0.0159	5008	,	,		22703	0.0		0.001	False		,,,				2504	0.0				p.R30323K		Atlas-SNP	.											.	TTN	18412	.	0			c.G90968A						PASS	.	C	LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG	418,3824		24,370,1727	132	141	138		64349,64148,83264,63773	5.8	1	2	dbSNP_120	138	8,8456		0,8,4224	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	26,26,26,26	24,378,5951	TT,TC,CC		0.0945,9.8538,3.3527	benign,benign,benign,benign	21450/27119,21383/27052,27755/33424,21258/26927	179416659	426,12280	2121	4232	6353	SO:0001583	missense	7273	exon335			GGAATCCTGAACT	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.86045G>A	2.37:g.179416659C>T	ENSP00000465570:p.Arg28682Lys	84	0	0		109	56	0.513761	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	37		86	0.039377289377289376	78	0.15853658536585366	8	0.022099447513812154	0	0.0	0	0.0	C	13.17	2.157290	0.38119	0.098538	9.45E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.62105	0.05;0.29;0.27;0.26	5.76	5.76	0.90799	Fibronectin, type III (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00178	0.0005	N	0.03608	-0.345	0.21933	P	0.999463905	B;B;B;B	0.06786	0.001;0.001;0.001;0.001	B;B;B;B	0.06405	0.002;0.002;0.002;0.002	T	0.03184	-1.1063	8	0.87932	D	0	.	12.6943	0.56994	0.0:0.8821:0.0:0.1179	rs11887722;rs52822649;rs11887722	21258;21383;21450;28682	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	K	27755;21258;21450;21383;21255	ENSP00000343764:R27755K;ENSP00000434586:R21258K;ENSP00000340554:R21450K;ENSP00000352154:R21383K	ENSP00000340554:R21450K	R	-	2	0	TTN	179124905	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	1.947000	0.40293	2.719000	0.93026	0.655000	0.94253	AGG	C|0.949;T|0.051	0.051	strong		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179416659	C	T	179416659	3	4	22	1	0	0	0	0	1	0	0	0	16750	681	24	2	17123	2	TTN	2	179416659	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4207	179416659	63782714	722	3623											
TTN	7273	hgsc.bcm.edu	37	chr2	179428061	179428061	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aacatagcctttaacaggtgCgccaccatcataaattggct	13	10	7	11	1	1	0	1	0	0	0	1	0	1	0	3	2	4	1	3	2	5	5	rs11896637	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179428061C>T	ENST00000591111.1	-	276	78099	c.77875G>A	c.(77875-77877)Gca>Aca	p.A25959T	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.A18727T|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A25032T|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.A18660T|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.A18535T|TTN_ENST00000589042.1_Missense_Mutation_p.A27600T			Q8WZ42	TITIN_HUMAN	titin	25959	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)			TTAACAGGTGCGCCACCATCA	0.493													C|||	178	0.0355431	0.1256	0.0159	5008	,	,		21438	0.0		0.001	False		,,,				2504	0.0				p.A27600T		Atlas-SNP	.											.	TTN	18412	.	0			c.G82798A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA	398,3684		21,356,1664	72	71	71		56179,55978,75094,55603	3.9	0.3	2	dbSNP_120	71	8,8402		0,8,4197	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	58,58,58,58	21,364,5861	TT,TC,CC		0.0951,9.7501,3.2501	benign,benign,benign,benign	18727/27119,18660/27052,25032/33424,18535/26927	179428061	406,12086	2041	4205	6246	SO:0001583	missense	7273	exon326			CAGGTGCGCCACC	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.77875G>A	2.37:g.179428061C>T	ENSP00000465570:p.Ala25959Thr	198	0	0		238	115	0.483193	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	37		85	0.03891941391941392	77	0.1565040650406504	8	0.022099447513812154	0	0.0	0	0.0	C	18.20	3.570710	0.65765	0.097501	9.51E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	5.74	3.93	0.45458	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00241	0.0007	L	0.47190	1.495	0.19300	P	0.9999757677	B;B;B;B	0.22414	0.069;0.069;0.069;0.02	B;B;B;B	0.17433	0.018;0.018;0.018;0.018	T	0.06481	-1.0824	8	0.87932	D	0	.	12.9829	0.58575	0.0:0.8666:0.0:0.1334	rs11896637;rs52798942;rs11896637	18535;18660;18727;25959	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	25032;18535;18727;18660;18533	ENSP00000343764:A25032T;ENSP00000434586:A18535T;ENSP00000340554:A18727T;ENSP00000352154:A18660T	ENSP00000340554:A18727T	A	-	1	0	TTN	179136307	0.999000	0.42202	0.344000	0.25628	0.992000	0.81027	4.111000	0.57838	0.755000	0.32990	0.563000	0.77884	GCA	C|0.965;T|0.035	0.035	strong		0.493	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179428061	C	T	179428061	3	4	22	1	0	0	0	0	1	0	0	0	16750	768	27	1	25329	1	TTN	2	179428061	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	11402	179428061	63771312	723	3624											
TTN	7273	hgsc.bcm.edu	37	chr2	179430224	179430224	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggtaactttaaactaggctGtatagtcaagtccttggcta	11	14	9	7	0	1	0	1	0	0	0	2	0	2	0	1	3	2	4	1	3	8	8	rs79926414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179430224G>T	ENST00000591111.1	-	276	75936	c.75712C>A	c.(75712-75714)Cag>Aag	p.Q25238K	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.Q18006K|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.Q24311K|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.Q17939K|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.Q17814K|TTN_ENST00000589042.1_Missense_Mutation_p.Q26879K			Q8WZ42	TITIN_HUMAN	titin	25238					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)			AAACTAGGCTGTATAGTCAAG	0.388													G|||	79	0.0157748	0.0567	0.0058	5008	,	,		22772	0.0		0.0	False		,,,				2504	0.0				p.Q26879K		Atlas-SNP	.											.	TTN	18412	.	0			c.C80635A						PASS	.	G	LYS/GLN,LYS/GLN,LYS/GLN,LYS/GLN	176,3544		5,166,1689	130	127	128		54016,53815,72931,53440	5.5	1	2	dbSNP_131	128	1,8199		0,1,4099	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	53,53,53,53	5,167,5788	TT,TG,GG		0.0122,4.7312,1.4849	benign,benign,benign,benign	18006/27119,17939/27052,24311/33424,17814/26927	179430224	177,11743	1860	4100	5960	SO:0001583	missense	7273	exon326			TAGGCTGTATAGT	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.75712C>A	2.37:g.179430224G>T	ENSP00000465570:p.Gln25238Lys	199	1	0.00502513		151	90	0.596026	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	37		42	0.019230769230769232	39	0.07926829268292683	3	0.008287292817679558	0	0.0	0	0.0	G	9.263	1.043608	0.19748	0.047312	1.22E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.61980	0.06;0.33;0.3;0.3	5.49	5.49	0.81192	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.01835	0.0058	N	0.00465	-1.465	0.26115	N	0.980629	B;B;B;B	0.09022	0.001;0.002;0.002;0.001	B;B;B;B	0.04013	0.0;0.001;0.001;0.0	T	0.07028	-1.0794	9	0.87932	D	0	.	14.8449	0.70254	0.0:0.2548:0.7452:0.0	.	17814;17939;18006;25238	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	K	24311;17814;18006;17939;17812	ENSP00000343764:Q24311K;ENSP00000434586:Q17814K;ENSP00000340554:Q18006K;ENSP00000352154:Q17939K	ENSP00000340554:Q18006K	Q	-	1	0	TTN	179138470	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.169000	0.50809	2.595000	0.87683	0.484000	0.47621	CAG	G|0.976;T|0.024	0.024	strong		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179430224	G	T	179430224	3	4	22	1	0	0	0	0	1	0	0	0	16750	1386	48	4	27492	4	TTN	2	179430224	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2163	179430224	63769149	724	3625											
TTN	7273	hgsc.bcm.edu	37	chr2	179435887	179435887	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atactttactcggcttgccaAtgcccacgatgttctctgca	8	13	7	13	2	1	0	0	0	1	0	3	1	1	0	2	1	5	3	2	1	3	5	rs744427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179435887A>G	ENST00000591111.1	-	276	70273	c.70049T>C	c.(70048-70050)aTt>aCt	p.I23350T	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I16118T|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.I22423T|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.I16051T|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.I15926T|TTN_ENST00000589042.1_Missense_Mutation_p.I24991T			Q8WZ42	TITIN_HUMAN	titin	23350	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)			CGGCTTGCCAATGCCCACGAT	0.438													A|||	82	0.0163738	0.0582	0.0072	5008	,	,		22831	0.0		0.0	False		,,,				2504	0.0				p.I24991T		Atlas-SNP	.											.	TTN	18412	.	0			c.T74972C						PASS	.	A	THR/ILE,THR/ILE,THR/ILE,THR/ILE	193,3777		5,183,1797	107	108	107		48353,48152,67268,47777	4.1	0.9	2	dbSNP_86	107	1,8337		0,1,4168	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	89,89,89,89	5,184,5965	GG,GA,AA		0.012,4.8615,1.5762	benign,benign,benign,benign	16118/27119,16051/27052,22423/33424,15926/26927	179435887	194,12114	1985	4169	6154	SO:0001583	missense	7273	exon326			TTGCCAATGCCCA	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.70049T>C	2.37:g.179435887A>G	ENSP00000465570:p.Ile23350Thr	53	0	0		70	37	0.528571	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	37		42	0.019230769230769232	39	0.07926829268292683	3	0.008287292817679558	0	0.0	0	0.0	A	9.233	1.036446	0.19669	0.048615	1.2E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.53206	0.63;0.63;0.63;0.63	5.28	4.13	0.48395	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.02418	0.0074	L	0.33093	0.98	0.25488	N	0.987672	B;B;B;B	0.09022	0.0;0.0;0.002;0.002	B;B;B;B	0.09377	0.001;0.001;0.004;0.004	T	0.05419	-1.0886	9	0.87932	D	0	.	11.1794	0.48618	0.9275:0.0:0.0725:0.0	rs744427;rs52837048;rs744427	15926;16051;16118;23350	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	22423;15926;16118;16051;15924	ENSP00000343764:I22423T;ENSP00000434586:I15926T;ENSP00000340554:I16118T;ENSP00000352154:I16051T	ENSP00000340554:I16118T	I	-	2	0	TTN	179144133	1.000000	0.71417	0.915000	0.36163	0.984000	0.73092	6.333000	0.72939	0.959000	0.37980	-0.256000	0.11100	ATT	A|0.984;G|0.016	0.016	strong		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179435887	A	G	179435887	3	3	22	1	0	0	0	0	1	0	0	0	16750	101	4	3	33155	3	TTN	2	179435887	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	5663	179435887	63763486	725	3626											
TTN	7273	hgsc.bcm.edu	37	chr2	179441917	179441917	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcagcagaaacattactgaTttcaacaggacctgggggac	13	9	10	9	0	2	2	2	1	0	1	2	4	2	4	1	3	4	1	1	3	3	3	rs72646881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179441917T>C	ENST00000591111.1	-	274	64446	c.64222A>G	c.(64222-64224)Atc>Gtc	p.I21408V	RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I14176V|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.I20481V|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.I14109V|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|RP11-171I2.5_ENST00000604215.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.I13984V|TTN_ENST00000589042.1_Missense_Mutation_p.I23049V			Q8WZ42	TITIN_HUMAN	titin	21408	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)			ACATTACTGATTTCAACAGGA	0.448													T|||	182	0.0363419	0.1278	0.0173	5008	,	,		21850	0.0		0.001	False		,,,				2504	0.0				p.I23049V		Atlas-SNP	.											TTN_ENST00000359218,NS,carcinoma,+2,5	TTN	18412	5	0			c.A69145G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	402,3490		24,354,1568	60	59	59		42526,42325,61441,41950	3.2	1	2	dbSNP_130	59	8,8272		0,8,4132	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	29,29,29,29	24,362,5700	CC,CT,TT		0.0966,10.3289,3.3684	benign,benign,benign,benign	14176/27119,14109/27052,20481/33424,13984/26927	179441917	410,11762	1946	4140	6086	SO:0001583	missense	7273	exon324			TACTGATTTCAAC	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.64222A>G	2.37:g.179441917T>C	ENSP00000465570:p.Ile21408Val	112	0	0		116	56	0.482759	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	37		86	0.039377289377289376	78	0.15853658536585366	8	0.022099447513812154	0	0.0	0	0.0	T	10.04	1.241565	0.22711	0.103289	9.66E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.53423	0.62;0.62;0.62;0.62	5.62	3.18	0.36537	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00073	0.0002	N	0.02368	-0.58	0.40312	P	0.02127100000000004	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	0.07616	-1.0763	8	0.87932	D	0	.	4.7345	0.12981	0.129:0.2044:0.0:0.6665	.	13984;14109;14176;21408	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	V	20481;13984;14176;14109;13982	ENSP00000343764:I20481V;ENSP00000434586:I13984V;ENSP00000340554:I14176V;ENSP00000352154:I14109V	ENSP00000340554:I14176V	I	-	1	0	TTN	179150163	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.225000	0.32551	0.466000	0.27193	0.533000	0.62120	ATC	T|0.967;C|0.033	0.033	strong		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179441917	T	C	179441917	3	2	22	1	0	0	0	0	1	0	0	0	16750	1493	52	3	38990	3	TTN	2	179441917	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	6030	179441917	63757456	726	3627											
TTN	7273	hgsc.bcm.edu	37	chr2	179447787	179447787	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caaggtgcacagattccgctGcatggccatctttatgcctt	8	12	9	12	1	1	1	0	0	1	1	2	1	2	1	3	2	3	3	3	2	2	4	rs62618736	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179447787G>T	ENST00000591111.1	-	263	61044	c.60820C>A	c.(60820-60822)Cag>Aag	p.Q20274K	TTN-AS1_ENST00000590743.1_RNA|RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.Q13042K|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.Q19347K|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.Q12975K|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.Q12850K|TTN_ENST00000589042.1_Missense_Mutation_p.Q21915K			Q8WZ42	TITIN_HUMAN	titin	20274	Ig-like 111.				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)			AGATTCCGCTGCATGGCCATC	0.458													G|||	80	0.0159744	0.0575	0.0058	5008	,	,		18275	0.0		0.0	False		,,,				2504	0.0				p.Q21915K		Atlas-SNP	.											.	TTN	18412	.	0			c.C65743A						PASS	.	G	LYS/GLN,LYS/GLN,LYS/GLN,LYS/GLN	187,3793		5,177,1808	81	78	79		39124,38923,58039,38548	-1.6	1	2	dbSNP_129	79	1,8339		0,1,4169	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	53,53,53,53	5,178,5977	TT,TG,GG		0.012,4.6985,1.526	benign,benign,benign,benign	13042/27119,12975/27052,19347/33424,12850/26927	179447787	188,12132	1990	4170	6160	SO:0001583	missense	7273	exon313			TCCGCTGCATGGC	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.60820C>A	2.37:g.179447787G>T	ENSP00000465570:p.Gln20274Lys	182	0	0		228	122	0.535088	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	37		42	0.019230769230769232	39	0.07926829268292683	3	0.008287292817679558	0	0.0	0	0.0	G	14.68	2.608015	0.46527	0.046985	1.2E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14	5.82	-1.62	0.08372	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	0.02970	0.0088	N	0.04132	-0.27	0.23946	N	0.99638	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	0.03898	-1.0994	9	0.87932	D	0	.	18.5575	0.91090	0.0:0.0:0.6894:0.3106	rs62618736	12850;12975;13042;20274	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	K	19347;12850;13042;12975;12848	ENSP00000343764:Q19347K;ENSP00000434586:Q12850K;ENSP00000340554:Q13042K;ENSP00000352154:Q12975K	ENSP00000340554:Q13042K	Q	-	1	0	TTN	179156033	0.009000	0.17119	0.957000	0.39632	0.907000	0.53573	0.075000	0.14686	-0.544000	0.06232	-0.274000	0.10170	CAG	G|0.985;T|0.015	0.015	strong		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179447787	G	T	179447787	3	4	22	1	0	0	0	0	1	0	0	0	16750	1328	46	4	42436	4	TTN	2	179447787	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5870	179447787	63751586	727	3628											
TTN	7273	hgsc.bcm.edu	37	chr2	179552895	179552895	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tctttcttcttctctataaaCtgaaatggacacaccttcct	10	16	3	12	0	4	1	0	1	4	0	6	2	5	2	2	1	1	0	2	1	4	6	rs72650028	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179552895C>T	ENST00000591111.1	-	125	31527	c.31303G>A	c.(31303-31305)Gtt>Att	p.V10435I	TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V9508I|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.V10752I			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)			TCTCTATAAACTGAAATGGAC	0.393													C|||	66	0.0131789	0.0477	0.0043	5008	,	,		19860	0.0		0.0	False		,,,				2504	0.0				p.V10752I		Atlas-SNP	.											.	TTN	18412	.	0			c.G32254A						PASS	.	C	ILE/VAL,,,	126,3626		1,124,1751	168	169	168		28522,,,	4.9	1	2	dbSNP_130	168	2,8194		0,2,4096	yes	missense,intron,intron,intron	TTN	NM_133378.4,NM_003319.4,NM_133432.3,NM_133437.3	29,,,	1,126,5847	TT,TC,CC		0.0244,3.3582,1.0713	possibly-damaging,,,	9508/33424,,,	179552895	128,11820	1876	4098	5974	SO:0001583	missense	7273	exon127			TATAAACTGAAAT	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.31303G>A	2.37:g.179552895C>T	ENSP00000465570:p.Val10435Ile	157	0	0		147	78	0.530612	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	37		22	0.010073260073260074	20	0.04065040650406504	2	0.0055248618784530384	0	0.0	0	0.0	C	14.87	2.665728	0.47677	0.033582	2.44E-4	ENSG00000155657	ENST00000342992	T	0.71222	-0.55	4.94	4.94	0.65067	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.47985	0.1475	L	0.49778	1.585	0.80722	D	1	P	0.44690	0.841	P	0.55824	0.785	T	0.69355	-0.5167	9	0.87932	D	0	.	14.0185	0.64539	0.0:1.0:0.0:0.0	.	10435	Q8WZ42	TITIN_HUMAN	I	9508	ENSP00000343764:V9508I	ENSP00000343764:V9508I	V	-	1	0	TTN	179261140	0.996000	0.38824	1.000000	0.80357	0.951000	0.60555	2.506000	0.45433	2.460000	0.83146	0.467000	0.42956	GTT	C|0.991;T|0.009	0.009	strong		0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179552895	C	T	179552895	3	4	22	1	0	0	0	0	1	0	0	0	16750	565	20	2	72219	2	TTN	2	179552895	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	105108	179552895	63646478	728	3629											
TTN	7273	hgsc.bcm.edu	37	chr2	179560847	179560847	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cagttcgtcataaggttcttCgaaagattcaatgaagactc	13	12	8	8	2	3	3	2	1	1	2	6	4	3	3	0	1	0	2	0	1	4	5	rs73038324	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179560847C>T	ENST00000591111.1	-	112	30225	c.30001G>A	c.(30001-30003)Gaa>Aaa	p.E10001K	TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E9074K|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.E10318K			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)			TAAGGTTCTTCGAAAGATTCA	0.383													C|||	194	0.038738	0.1377	0.0159	5008	,	,		19287	0.0		0.001	False		,,,				2504	0.0				p.E10318K		Atlas-SNP	.											.	TTN	18412	.	0			c.G30952A						PASS	.	C	,,,LYS/GLU	347,3211		17,313,1449	126	105	111		,,,27220	5.8	0.9	2	dbSNP_130	111	9,7899		0,9,3945	yes	intron,intron,intron,missense	TTN	NM_003319.4,NM_133432.3,NM_133437.3,NM_133378.4	,,,56	17,322,5394	TT,TC,CC		0.1138,9.7527,3.1048	,,,benign	,,,9074/33424	179560847	356,11110	1779	3954	5733	SO:0001583	missense	7273	exon114			GTTCTTCGAAAGA	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.30001G>A	2.37:g.179560847C>T	ENSP00000465570:p.Glu10001Lys	242	0	0		234	119	0.508547	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	37		84	0.038461538461538464	77	0.1565040650406504	7	0.019337016574585635	0	0.0	0	0.0	C	18.27	3.586510	0.66105	0.097527	0.001138	ENSG00000155657	ENST00000342992;ENST00000414766	T	0.64260	-0.09	5.78	5.78	0.91487	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.00356	0.0011	M	0.66939	2.045	0.09310	P	1.0	B;P	0.50710	0.327;0.938	B;B	0.36845	0.026;0.234	T	0.36915	-0.9728	8	0.87932	D	0	.	15.5205	0.75862	0.0:1.0:0.0:0.0	.	10001;10001	Q8WZ42;Q8WZ42-5	TITIN_HUMAN;.	K	9074;196	ENSP00000343764:E9074K	ENSP00000343764:E9074K	E	-	1	0	TTN	179269092	0.966000	0.33281	0.949000	0.38748	0.899000	0.52679	2.415000	0.44635	2.729000	0.93468	0.650000	0.86243	GAA	C|0.968;T|0.032	0.032	strong		0.383	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179560847	C	T	179560847	3	4	22	1	0	0	0	0	1	0	0	0	16750	893	31	1	73573	1	TTN	2	179560847	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	7952	179560847	63638526	729	3630											
TTN	7273	hgsc.bcm.edu	37	chr2	179577870	179577870	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccatattagtagctatacaTgtgtagtcaccactgtctga	11	13	8	9	0	2	1	1	1	1	0	2	1	2	1	2	0	2	3	2	0	6	6	rs61232800	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179577870T>C	ENST00000591111.1	-	91	26264	c.26040A>G	c.(26038-26040)acA>acG	p.T8680T	TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Silent_p.T7753T|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Silent_p.T8997T			Q8WZ42	TITIN_HUMAN	titin	12837	Ig-like 69.				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)			TAGCTATACATGTGTAGTCAC	0.388													T|||	122	0.024361	0.0893	0.0058	5008	,	,		22217	0.0		0.0	False		,,,				2504	0.0				p.T8997T		Atlas-SNP	.											.	TTN	18412	.	0			c.A26991G						PASS	.	T	,,,	265,3699		10,245,1727	90	90	90		,23259,,	-11.7	0.5	2	dbSNP_129	90	13,8331		0,13,4159	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	10,258,5886	CC,CT,TT		0.1558,6.6852,2.2587	,,,	,7753/33424,,	179577870	278,12030	1982	4172	6154	SO:0001819	synonymous_variant	7273	exon93			TATACATGTGTAG	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.26040A>G	2.37:g.179577870T>C		285	0	0		288	134	0.465278	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	37																																																																																				T|0.981;C|0.019	0.019	strong		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179577870	T	C	179577870	2	2	22	1	0	0	0	0	0	0	0	1	16750	1451	51	3		3	TTN	2	179577870	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	17023	179577870	63621503	730	3631											
TTN	7273	hgsc.bcm.edu	37	chr2	179586779	179586779	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcggttgagcaccagtaacAtgacactcaaaatcagcact	15	8	7	11	1	2	2	2	2	0	0	3	2	2	2	1	1	3	4	1	1	3	2	rs16866469	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179586779A>G	ENST00000591111.1	-	76	21884	c.21660T>C	c.(21658-21660)caT>caC	p.H7220H	TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Silent_p.H6293H|RP11-171I2.1_ENST00000590024.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Silent_p.H7537H			Q8WZ42	TITIN_HUMAN	titin	12789	Ig-like 54.				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)			CACCAGTAACATGACACTCAA	0.428													A|||	101	0.0201677	0.0749	0.0029	5008	,	,		21079	0.0		0.0	False		,,,				2504	0.0				p.H7537H		Atlas-SNP	.											.	TTN	18412	.	0			c.T22611C						PASS	.	A	,,,	195,3703		6,183,1760	229	217	221		,18879,,	-2.7	1	2	dbSNP_123	221	6,8288		0,6,4141	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	6,189,5901	GG,GA,AA		0.0723,5.0026,1.6486	,,,	,6293/33424,,	179586779	201,11991	1949	4147	6096	SO:0001819	synonymous_variant	7273	exon78			AGTAACATGACAC	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.21660T>C	2.37:g.179586779A>G		123	0	0		120	58	0.483333	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	37																																																																																				A|0.982;G|0.018	0.018	strong		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179586779	A	G	179586779	2	3	22	1	0	0	0	0	0	0	0	1	16750	214	8	3		3	TTN	2	179586779	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	8909	179586779	63612594	731	3632											
TTN	7273	hgsc.bcm.edu	37	chr2	179594590	179594590	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcggattttaggagtgccTgttatttggcattcaaatgt	9	16	10	6	1	1	0	1	0	0	0	2	2	1	2	1	3	1	2	1	3	3	5	rs66523653	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179594590T>A	ENST00000591111.1	-	61	17663	c.17439A>T	c.(17437-17439)acA>acT	p.T5813T	TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Silent_p.T4886T|RP11-171I2.1_ENST00000590024.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Silent_p.T6130T			Q8WZ42	TITIN_HUMAN	titin	12614	Ig-like 39.				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)			TAGGAGTGCCTGTTATTTGGC	0.408													T|||	78	0.0155751	0.0537	0.0101	5008	,	,		18115	0.0		0.0	False		,,,				2504	0.0				p.T6130T		Atlas-SNP	.											.	TTN	18412	.	0			c.A18390T						PASS	.	T	,,,	168,3604		3,162,1721	58	56	57		,14658,,	2.1	1	2	dbSNP_130	57	1,8225		0,1,4112	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	3,163,5833	AA,AT,TT		0.0122,4.4539,1.4086	,,,	,4886/33424,,	179594590	169,11829	1886	4113	5999	SO:0001819	synonymous_variant	7273	exon63			AGTGCCTGTTATT	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.17439A>T	2.37:g.179594590T>A		253	0	0		237	118	0.49789	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	37																																																																																				T|0.984;A|0.016	0.016	strong		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179594590	T	A	179594590	2	1	22	1	0	0	0	0	0	0	0	1	16750	1567	55	5		5	TTN	2	179594590	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	7811	179594590	63604783	732	3633											
TTN	7273	hgsc.bcm.edu	37	chr2	179598399	179598399	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttcattttcagccaggcaCgtgtatttgcctccaaaact	9	13	7	12	1	2	0	2	0	0	0	3	0	3	0	3	1	3	3	3	1	3	5	rs72648932	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179598399C>T	ENST00000591111.1	-	51	14990	c.14766G>A	c.(14764-14766)acG>acA	p.T4922T	TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Silent_p.T3995T|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Silent_p.T5239T			Q8WZ42	TITIN_HUMAN	titin	12314	Ig-like 29.				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)			CAGCCAGGCACGTGTATTTGC	0.378													C|||	120	0.0239617	0.0877	0.0058	5008	,	,		20602	0.0		0.0	False		,,,				2504	0.0				p.T5239T		Atlas-SNP	.											.	TTN	18412	.	0			c.G15717A						PASS	.	C	,,,	223,3501		8,207,1647	136	130	132		,11985,,	-7.5	1	2	dbSNP_130	132	7,8189		0,7,4091	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	8,214,5738	TT,TC,CC		0.0854,5.9882,1.9295	,,,	,3995/33424,,	179598399	230,11690	1862	4098	5960	SO:0001819	synonymous_variant	7273	exon53			CAGGCACGTGTAT	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.14766G>A	2.37:g.179598399C>T		125	0	0		153	82	0.535948	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	37																																																																																				C|0.980;T|0.020	0.020	strong		0.378	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179598399	C	T	179598399	2	4	22	1	0	0	0	0	0	0	0	1	16750	523	19	1		1	TTN	2	179598399	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3809	179598399	63600974	733	3634											
TTN	7273	hgsc.bcm.edu	37	chr2	179610477	179610477	+	Intron	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttccttggactaattttccAtctttgtaccagtaaaccgt	9	16	5	11	1	1	0	0	0	1	0	3	1	3	1	4	1	2	2	4	1	4	8	rs16866488	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179610477A>G	ENST00000591111.1	-	46	10585				TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron|TTN_ENST00000360870.5_Silent_p.D5550D|TTN-AS1_ENST00000578746.1_RNA|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_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)			CTAATTTTCCATCTTTGTACC	0.418													A|||	51	0.0101837	0.0371	0.0029	5008	,	,		20781	0.0		0.0	False		,,,				2504	0.0				p.D5550D		Atlas-SNP	.											.	TTN	18412	.	0			c.T16650C						PASS	.	A	,,,,	123,4283	93.0+/-131.7	2,119,2082	118	118	118		,,16650,,	-0.3	1	2	dbSNP_123	118	4,8594	3.0+/-9.4	0,4,4295	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	2,123,6377	GG,GA,AA		0.0465,2.7916,0.9766	,,,,	,,5550/5605,,	179610477	127,12877	2203	4299	6502	SO:0001627	intron_variant	7273	exon46			TTTTCCATCTTTG	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.10361-3829T>C	2.37:g.179610477A>G		163	0	0		168	88	0.52381	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	Silent	SNP	ENST00000591111.1	37																																																																																				A|0.987;G|0.013	0.013	strong		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179610477	A	G	179610477	1	3	22	0	1	0	0	0	0	0	0	0	16750	214	8	3		3	TTN	2	179610477	Intron	SNP	A	TCGA-G8-6324-01A-11D-2210-10	12078	179610477	63588896	734	3635											
TTN	7273	hgsc.bcm.edu	37	chr2	179610619	179610619	+	Intron	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccacctgaaattcaaaaaaaCtgtctgtgtagttgctcttt	12	14	6	9	0	3	1	1	1	2	0	3	1	3	1	2	0	2	3	2	0	5	4	rs16866489	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179610619C>G	ENST00000591111.1	-	46	10585				TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron|TTN_ENST00000360870.5_Missense_Mutation_p.S5503T|TTN-AS1_ENST00000578746.1_RNA|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_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)			TTCAAAAAAACTGTCTGTGTA	0.378													C|||	29	0.00579073	0.0204	0.0029	5008	,	,		21580	0.0		0.0	False		,,,				2504	0.0				p.S5503T		Atlas-SNP	.											.	TTN	18412	.	0			c.G16508C						PASS	.	C	,,THR/SER,,	80,4326	70.9+/-108.8	0,80,2123	114	111	112		,,16508,,	5.1	1	2	dbSNP_123	112	2,8596	1.2+/-3.3	0,2,4297	yes	intron,intron,missense,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,58,,	0,82,6420	GG,GC,CC		0.0233,1.8157,0.6306	,,,,	,,5503/5605,,	179610619	82,12922	2203	4299	6502	SO:0001627	intron_variant	7273	exon46			AAAAAACTGTCTG	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.10361-3971G>C	2.37:g.179610619C>G		91	0	0		118	66	0.559322	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	37		13	0.005952380952380952	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	0	0.0	C	12.68	2.011534	0.35511	0.018157	2.33E-4	ENSG00000155657	ENST00000360870;ENST00000306136	T	0.58210	0.35	5.94	5.06	0.68205	.	.	.	.	.	T	0.22704	0.0548	L	0.27053	0.805	0.80722	D	1	P	0.35272	0.493	B	0.33620	0.167	T	0.06770	-1.0808	9	0.30078	T	0.28	.	12.1518	0.54053	0.0:0.9185:0.0:0.0815	rs16866489;rs16866489	5503	Q8WZ42-6	.	T	5503;784	ENSP00000354117:S5503T	ENSP00000304714:S784T	S	-	2	0	TTN	179318864	1.000000	0.71417	1.000000	0.80357	0.591000	0.36615	2.864000	0.48404	2.816000	0.96949	0.563000	0.77884	AGT	C|0.992;G|0.008	0.008	strong		0.378	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179610619	C	G	179610619	1	3	22	0	1	0	0	0	0	0	0	0	16750	565	20	4		4	TTN	2	179610619	Intron	SNP	C	TCGA-G8-6324-01A-11D-2210-10	142	179610619	63588754	735	3636											
TTN	7273	hgsc.bcm.edu	37	chr2	179610695	179610695	+	Intron	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgcttttctttgctatcaCagcaaatatttcagaatctc	10	18	4	9	0	4	1	2	0	2	1	5	1	4	1	0	0	3	3	0	0	4	7	rs72648915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179610695C>T	ENST00000591111.1	-	46	10585				TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron|TTN_ENST00000360870.5_Missense_Mutation_p.V5478M|TTN-AS1_ENST00000578746.1_RNA|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_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)			TTTGCTATCACAGCAAATATT	0.403													T|||	192	0.0383387	0.1399	0.0101	5008	,	,		20502	0.0		0.0	False		,,,				2504	0.0				p.V5478M		Atlas-SNP	.											.	TTN	18412	.	0			c.G16432A						PASS	.	T	,,MET/VAL,,	529,3877	774.4+/-414.0	33,463,1707	108	105	106		,,16432,,	-6.2	0	2	dbSNP_130	106	7,8593	817.5+/-406.9	0,7,4293	no	intron,intron,missense,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,21,,	33,470,6000	TT,TC,CC		0.0814,12.0064,4.1212	,,,,	,,5478/5605,,	179610695	536,12470	2203	4300	6503	SO:0001627	intron_variant	7273	exon46			CTATCACAGCAAA	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.10361-4047G>A	2.37:g.179610695C>T		97	0	0		100	47	0.47	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	37		68	0.031135531135531136	63	0.12804878048780488	5	0.013812154696132596	0	0.0	0	0.0	T	0.009	-1.801722	0.00611	0.120064	8.14E-4	ENSG00000155657	ENST00000360870;ENST00000306136	T	0.59083	0.29	6.07	-6.15	0.02105	.	.	.	.	.	T	0.00300	0.0009	N	0.12182	0.205	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.05550	-1.0878	8	0.25106	T	0.35	.	5.6092	0.17396	0.098:0.3526:0.417:0.1325	.	5478	Q8WZ42-6	.	M	5478;759	ENSP00000354117:V5478M	ENSP00000304714:V759M	V	-	1	0	TTN	179318940	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-0.290000	0.08354	-1.567000	0.01671	-1.170000	0.01741	GTG	C|0.961;T|0.039	0.039	strong		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179610695	C	T	179610695	1	4	22	0	1	0	0	0	0	0	0	0	16750	478	17	2		2	TTN	2	179610695	Intron	SNP	C	TCGA-G8-6324-01A-11D-2210-10	76	179610695	63588678	736	3637											
TTN	7273	hgsc.bcm.edu	37	chr2	179611680	179611680	+	Intron	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccctctcttctgtaggtgtGtagaaatgctcatttggtgt	6	16	10	9	0	3	1	1	0	2	1	4	1	3	1	2	2	1	3	2	2	3	4	rs72648911	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179611680G>A	ENST00000591111.1	-	46	10585				TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron|TTN_ENST00000360870.5_Silent_p.Y5149Y|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_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)			CTGTAGGTGTGTAGAAATGCT	0.413													A|||	235	0.0469249	0.1725	0.0101	5008	,	,		19409	0.0		0.0	False		,,,				2504	0.0				p.Y5149Y		Atlas-SNP	.											.	TTN	18412	.	0			c.C15447T						PASS	.	A	,,,,	667,3739	763.1+/-413.2	50,567,1586	138	134	135		,,15447,,	-2.6	0.9	2	dbSNP_130	135	8,8590	818.5+/-406.9	0,8,4291	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	50,575,5877	AA,AG,GG		0.093,15.1384,5.1907	,,,,	,,5149/5605,,	179611680	675,12329	2203	4299	6502	SO:0001627	intron_variant	7273	exon46			AGGTGTGTAGAAA	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.10361-5032C>T	2.37:g.179611680G>A		181	0	0		190	99	0.521053	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	Silent	SNP	ENST00000591111.1	37																																																																																				G|0.954;A|0.046	0.046	strong		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179611680	G	A	179611680	1	1	22	0	1	0	0	0	0	0	0	0	16750	1372	48	2		2	TTN	2	179611680	Intron	SNP	G	TCGA-G8-6324-01A-11D-2210-10	985	179611680	63587693	737	3638											
TTN	7273	hgsc.bcm.edu	37	chr2	179613147	179613147	+	Intron	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcacacttttagagatattGtgtgtgtcaggttgtaacgt	9	16	11	5	1	1	1	1	0	0	1	1	2	1	1	0	1	2	3	0	1	3	6	rs75785339	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179613147G>C	ENST00000591111.1	-	45	10585				TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron|TTN_ENST00000360870.5_Missense_Mutation_p.H4660Q|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_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)			TAGAGATATTGTGTGTGTCAG	0.373													C|||	193	0.0385383	0.1407	0.0101	5008	,	,		18083	0.0		0.0	False		,,,				2504	0.0				p.H4660Q		Atlas-SNP	.											.	TTN	18412	.	0			c.C13980G						PASS	.	C	,,GLN/HIS,,	523,3883	761.1+/-413.0	31,461,1711	88	98	95		,,13980,,	0.5	0	2	dbSNP_131	95	8,8588	808.7+/-407.2	0,8,4290	yes	intron,intron,missense,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,24,,	31,469,6001	CC,CG,GG		0.0931,11.8702,4.084	,,,,	,,4660/5605,,	179613147	531,12471	2203	4298	6501	SO:0001627	intron_variant	7273	exon46			GATATTGTGTGTG	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+4703C>G	2.37:g.179613147G>C		282	0	0		317	147	0.463722	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	37		68	0.031135531135531136	63	0.12804878048780488	5	0.013812154696132596	0	0.0	0	0.0	C	6.309	0.425027	0.11987	0.118702	9.31E-4	ENSG00000155657	ENST00000360870	T	0.54479	0.57	5.05	0.501	0.16925	.	.	.	.	.	T	0.00210	0.0006	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.14952	-1.0454	8	0.16896	T	0.51	.	0.9872	0.01449	0.2832:0.2095:0.3228:0.1845	.	4660	Q8WZ42-6	.	Q	4660	ENSP00000354117:H4660Q	ENSP00000354117:H4660Q	H	-	3	2	TTN	179321392	0.000000	0.05858	0.002000	0.10522	0.016000	0.09150	-1.023000	0.03607	0.113000	0.18004	-0.127000	0.14921	CAC	G|0.964;C|0.036	0.036	strong		0.373	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179613147	G	C	179613147	1	2	22	0	1	0	0	0	0	0	0	0	16750	1368	48	4		4	TTN	2	179613147	Intron	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1467	179613147	63586226	738	3639											
TTN	7273	hgsc.bcm.edu	37	chr2	179613258	179613258	+	Intron	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagctggatctcctatatgAgaatacatttgttttagatc	12	15	8	6	0	1	3	0	1	1	3	3	5	1	4	1	1	2	2	1	1	5	6	rs72648906	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179613258A>C	ENST00000591111.1	-	45	10585				TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron|TTN_ENST00000360870.5_Silent_p.S4623S|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_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)			CTCCTATATGAGAATACATTT	0.368													A|||	104	0.0207668	0.0764	0.0043	5008	,	,		18443	0.0		0.0	False		,,,				2504	0.0				p.S4623S		Atlas-SNP	.											.	TTN	18412	.	0			c.T13869G						PASS	.	A	,,,,	244,4160	139.2+/-174.8	7,230,1965	99	109	106		,,13869,,	3.5	1	2	dbSNP_130	106	6,8590	3.7+/-12.6	0,6,4292	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	7,236,6257	CC,CA,AA		0.0698,5.5404,1.9231	,,,,	,,4623/5605,,	179613258	250,12750	2202	4298	6500	SO:0001627	intron_variant	7273	exon46			TATATGAGAATAC	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+4592T>G	2.37:g.179613258A>C		190	0	0		202	97	0.480198	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	Silent	SNP	ENST00000591111.1	37																																																																																				A|0.977;C|0.023	0.023	strong		0.368	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179613258	A	C	179613258	1	2	22	0	1	0	0	0	0	0	0	0	16750	291	11	5		5	TTN	2	179613258	Intron	SNP	A	TCGA-G8-6324-01A-11D-2210-10	111	179613258	63586115	739	3640											
TTN	7273	hgsc.bcm.edu	37	chr2	179613962	179613962	+	Intron	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatttctttcttaatagtgaCatcactgaaatcatcaacaa	15	15	3	8	0	5	2	3	2	2	0	5	2	5	2	0	0	1	0	0	0	6	5	rs72648903	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179613962C>T	ENST00000591111.1	-	45	10585				TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron|TTN_ENST00000360870.5_Missense_Mutation_p.V4389I|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_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)			TTAATAGTGACATCACTGAAA	0.343													C|||	95	0.0189696	0.0703	0.0029	5008	,	,		19175	0.0		0.0	False		,,,				2504	0.0				p.V4389I		Atlas-SNP	.											TTN_ENST00000360870,rectum,carcinoma,+1,1	TTN	18412	1	0			c.G13165A						PASS	.	C	,,ILE/VAL,,	221,4179	123.7+/-161.0	6,209,1985	57	62	60		,,13165,,	3.4	0	2	dbSNP_130	60	6,8586	3.7+/-12.6	0,6,4290	yes	intron,intron,missense,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,29,,	6,215,6275	TT,TC,CC		0.0698,5.0227,1.7472	,,,,	,,4389/5605,,	179613962	227,12765	2200	4296	6496	SO:0001627	intron_variant	7273	exon46			TAGTGACATCACT	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+3888G>A	2.37:g.179613962C>T		74	0	0		83	28	0.337349	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	37		35	0.016025641025641024	34	0.06910569105691057	1	0.0027624309392265192	0	0.0	0	0.0	C	10.23	1.293061	0.23564	0.050227	6.98E-4	ENSG00000155657	ENST00000360870	T	0.60672	0.17	5.23	3.42	0.39159	.	.	.	.	.	T	0.04452	0.0122	N	0.24115	0.695	0.09310	N	0.999999	B	0.06786	0.001	B	0.06405	0.002	T	0.02126	-1.1209	9	0.16420	T	0.52	.	13.5505	0.61730	0.0:0.8613:0.0:0.1387	.	4389	Q8WZ42-6	.	I	4389	ENSP00000354117:V4389I	ENSP00000354117:V4389I	V	-	1	0	TTN	179322207	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	1.120000	0.31271	0.434000	0.26340	-2.010000	0.00438	GTC	C|0.980;T|0.020	0.020	strong		0.343	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179613962	C	T	179613962	1	4	22	0	1	0	0	0	0	0	0	0	16750	478	17	2		2	TTN	2	179613962	Intron	SNP	C	TCGA-G8-6324-01A-11D-2210-10	704	179613962	63585411	740	3641											
TTN	7273	hgsc.bcm.edu	37	chr2	179614059	179614059	+	Intron	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctttcccttcagcctgacaTtgtatgaattcagccctgat	8	15	6	12	0	3	3	2	3	1	0	4	3	4	3	3	0	2	1	3	0	2	5	rs16866490	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179614059T>C	ENST00000591111.1	-	45	10585				TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron|TTN_ENST00000360870.5_Silent_p.Q4356Q|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_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)			CAGCCTGACATTGTATGAATT	0.413													T|||	29	0.00579073	0.0204	0.0029	5008	,	,		18368	0.0		0.0	False		,,,				2504	0.0				p.Q4356Q		Atlas-SNP	.											.	TTN	18412	.	0			c.A13068G						PASS	.	T	,,,,	78,4328	62.9+/-100.1	0,78,2125	87	93	91		,,13068,,	-3.6	0	2	dbSNP_123	91	2,8594	1.2+/-3.3	0,2,4296	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	0,80,6421	CC,CT,TT		0.0233,1.7703,0.6153	,,,,	,,4356/5605,,	179614059	80,12922	2203	4298	6501	SO:0001627	intron_variant	7273	exon46			CTGACATTGTATG	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+3791A>G	2.37:g.179614059T>C		74	0	0		58	29	0.5	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	Silent	SNP	ENST00000591111.1	37																																																																																				T|0.991;C|0.009	0.009	strong		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179614059	T	C	179614059	1	2	22	0	1	0	0	0	0	0	0	0	16750	1490	52	3		3	TTN	2	179614059	Intron	SNP	T	TCGA-G8-6324-01A-11D-2210-10	97	179614059	63585314	741	3642											
TTN	7273	hgsc.bcm.edu	37	chr2	179621353	179621353	+	Intron	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgtgtggatggaactttgaGatacactttcaaaaacctgc	12	12	9	8	0	1	1	1	1	0	1	1	4	1	3	1	2	4	0	1	2	4	3	rs57389274	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179621353G>A	ENST00000591111.1	-	44	10528				TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.S3446F|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron|TTN_ENST00000360870.5_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.S3617F			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)			GGAACTTTGAGATACACTTTC	0.383													G|||	98	0.0195687	0.0726	0.0029	5008	,	,		22444	0.0		0.0	False		,,,				2504	0.0				p.S3617F		Atlas-SNP	.											.	TTN	18412	.	0			c.C10850T						PASS	.	G	,,,,PHE/SER	191,3647		6,179,1734	112	113	113		,,,,10337	3.3	0.8	2	dbSNP_129	113	6,8254		0,6,4124	yes	intron,intron,intron,intron,missense	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,155	6,185,5858	AA,AG,GG		0.0726,4.9766,1.6284	,,,,	,,,,3446/27119	179621353	197,11901	1919	4130	6049	SO:0001627	intron_variant	7273	exon46			CTTTGAGATACAC	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.10303+2357C>T	2.37:g.179621353G>A		122	0	0		135	58	0.42963	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	37		36	0.016483516483516484	35	0.07113821138211382	1	0.0027624309392265192	0	0.0	0	0.0	G	12.02	1.813296	0.32053	0.049766	7.26E-4	ENSG00000155657	ENST00000342175	T	0.60672	0.17	6.17	3.3	0.37823	.	.	.	.	.	T	0.06735	0.0172	.	.	.	0.80722	D	1	B	0.24092	0.097	B	0.23150	0.044	T	0.08249	-1.0731	8	0.87932	D	0	.	12.2661	0.54679	0.0:0.1167:0.6404:0.2429	rs57389274	3446	E7ET18	.	F	3446	ENSP00000340554:S3446F	ENSP00000340554:S3446F	S	-	2	0	TTN	179329598	1.000000	0.71417	0.783000	0.31826	0.997000	0.91878	2.776000	0.47709	0.422000	0.26005	0.655000	0.94253	TCT	G|0.982;A|0.018	0.018	strong		0.383	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179621353	G	A	179621353	1	1	22	0	1	0	0	0	0	0	0	0	16750	942	33	2		2	TTN	2	179621353	Intron	SNP	G	TCGA-G8-6324-01A-11D-2210-10	7294	179621353	63578020	742	3643											
ITGA4	3676	hgsc.bcm.edu	37	chr2	182376480	182376480	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttctgctgatttacaggttTctgcaaagattgggtttttg	7	18	11	5	0	2	2	0	1	2	1	2	2	2	2	0	2	3	5	0	2	2	7	rs35322532	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:182376480T>A	ENST00000397033.2	+	17	2330	c.1900T>A	c.(1900-1902)Tct>Act	p.S634T		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	634			S -> T (in dbSNP:rs35322532).		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)	TTTACAGGTTTCTGCAAAGAT	0.338													T|||	86	0.0171725	0.0605	0.0072	5008	,	,		16437	0.0		0.001	False		,,,				2504	0.0				p.S634T		Atlas-SNP	.											.	ITGA4	142	.	0			c.T1900A						PASS	.	T	THR/SER	206,3446		6,194,1626	148	144	145		1900	4.7	1	2	dbSNP_126	145	9,8139		0,9,4065	yes	missense	ITGA4	NM_000885.4	58	6,203,5691	AA,AT,TT		0.1105,5.6407,1.822	possibly-damaging	634/1033	182376480	215,11585	1826	4074	5900	SO:0001583	missense	3676	exon17			CAGGTTTCTGCAA		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.1900T>A	2.37:g.182376480T>A	ENSP00000380227:p.Ser634Thr	192	0	0		149	149	1	NM_000885	D3DPG4|Q7Z4L6	Missense_Mutation	SNP	ENST00000397033.2	37	CCDS42788.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	T	18.59	3.657151	0.67586	0.056407	0.001105	ENSG00000115232	ENST00000397033	T	0.50001	0.76	5.87	4.68	0.58851	Integrin alpha-2 (1);	0.170160	0.53938	D	0.000050	T	0.09949	0.0244	L	0.41710	1.295	0.48185	D	0.999603	D;P	0.54397	0.966;0.906	P;P	0.55999	0.646;0.789	T	0.02385	-1.1167	10	0.42905	T	0.14	.	10.2631	0.43438	0.2642:0.0:0.0:0.7358	rs35322532	456;634	Q59H74;P13612	.;ITA4_HUMAN	T	634	ENSP00000380227:S634T	ENSP00000380227:S634T	S	+	1	0	ITGA4	182084725	1.000000	0.71417	0.989000	0.46669	0.992000	0.81027	2.791000	0.47829	1.004000	0.39156	0.529000	0.55759	TCT	T|0.987;A|0.013	0.013	strong		0.338	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1			A	182376480	T	A	182376480	3	1	22	1	0	0	0	0	1	0	0	0	7887	1783	62	5	1966	5	ITGA4	2	182376480	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2755127	182376480	60822893	743	3644											
SSFA2	6744	hgsc.bcm.edu	37	chr2	182780817	182780817	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaagccccccagagtgaggCgccgcgggtggaggaatgcc	9	3	17	12	3	0	3	0	1	0	2	0	5	0	5	5	4	2	0	5	4	2	0	rs16867510	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:182780817C>T	ENST00000431877.2	+	11	2629	c.2450C>T	c.(2449-2451)gCg>gTg	p.A817V	SSFA2_ENST00000409001.1_Missense_Mutation_p.A817V|SSFA2_ENST00000428267.2_Missense_Mutation_p.A664V|SSFA2_ENST00000320370.7_Missense_Mutation_p.A817V|SSFA2_ENST00000409136.1_Missense_Mutation_p.A326V	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	817			A -> V (in dbSNP:rs16867510).			cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(18)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	38			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			CAGAGTGAGGCGCCGCGGGTG	0.507													C|||	172	0.034345	0.1263	0.0072	5008	,	,		20029	0.0		0.0	False		,,,				2504	0.0				p.A817V		Atlas-SNP	.											SSFA2,colon,carcinoma,0,1	SSFA2	130	1	0			c.C2450T						scavenged	.	C	VAL/ALA,VAL/ALA	438,3968	210.2+/-230.7	29,380,1794	66	73	71		2450,2450	-9.2	0	2	dbSNP_123	71	7,8593	5.7+/-21.5	0,7,4293	yes	missense,missense	SSFA2	NM_001130445.1,NM_006751.5	64,64	29,387,6087	TT,TC,CC		0.0814,9.941,3.4215	benign,benign	817/1260,817/1257	182780817	445,12561	2203	4300	6503	SO:0001583	missense	6744	exon11			GTGAGGCGCCGCG	M61199	CCDS2284.1, CCDS46467.1, CCDS74611.1	2q32.1	2012-02-01			ENSG00000138434	ENSG00000138434			11319	protein-coding gene	gene with protein product	"cleavage signal-1 protein", "KRAS-induced actin-interacting protein", "sperm associated antigen 13"	118990				1555770	Standard	XM_005246812		Approved	CS-1, SPAG13, KRAP, KIAA1927	uc002uoh.3	P28290	OTTHUMG00000132584	ENST00000431877.2:c.2450C>T	2.37:g.182780817C>T	ENSP00000388731:p.Ala817Val	191	1	0.0052356		188	92	0.489362	NM_001130445	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Missense_Mutation	SNP	ENST00000431877.2	37	CCDS46467.1	52	0.023809523809523808	51	0.10365853658536585	1	0.0027624309392265192	0	0.0	0	0.0	C	2.957	-0.215497	0.06101	0.09941	8.14E-4	ENSG00000138434	ENST00000431877;ENST00000320370;ENST00000409001;ENST00000428267;ENST00000409136	T;T;T;T;T	0.14391	2.74;2.51;2.74;2.73;2.52	5.95	-9.19	0.00685	.	1.558920	0.02820	N	0.125417	T	0.00144	0.0004	N	0.03115	-0.41	0.80722	P	0.0	B;B;B;B;B	0.13594	0.003;0.008;0.002;0.002;0.002	B;B;B;B;B	0.06405	0.002;0.001;0.0;0.0;0.0	T	0.27123	-1.0083	9	0.20046	T	0.44	3.6137	7.4998	0.27511	0.0819:0.4875:0.2579:0.1727	rs16867510	664;326;817;817;817	E7END2;E7EUL7;E9PHV5;P28290;P28290-3	.;.;.;SSFA2_HUMAN;.	V	817;817;817;664;326	ENSP00000388731:A817V;ENSP00000314669:A817V;ENSP00000387319:A817V;ENSP00000409867:A664V;ENSP00000386916:A326V	ENSP00000314669:A817V	A	+	2	0	SSFA2	182489062	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.387000	0.02535	-1.938000	0.01046	-0.793000	0.03317	GCG	C|0.965;T|0.035	0.035	strong		0.507	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255793.2	NM_006751		T	182780817	C	T	182780817	3	4	22	1	0	0	0	0	1	0	0	0	15198	768	27	1	2492	1	SSFA2	2	182780817	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	404337	182780817	60418556	744	3645											
NCKAP1	10787	hgsc.bcm.edu	37	chr2	183817154	183817154	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaagttcagcaacttgtgaTgaaatatgccacataaggct	14	12	8	7	0	1	2	1	2	0	0	1	2	1	2	1	1	3	3	1	1	5	5	rs111993802	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:183817154T>C	ENST00000361354.4	-	23	2952	c.2580A>G	c.(2578-2580)tcA>tcG	p.S860S	NCKAP1_ENST00000360982.2_Silent_p.S866S	NM_013436.3	NP_038464.1	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1	860					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)			CAACTTGTGATGAAATATGCC	0.313													t|||	50	0.00998403	0.0356	0.0043	5008	,	,		17373	0.0		0.0	False		,,,				2504	0.0				p.S866S		Atlas-SNP	.											.	NCKAP1	105	.	0			c.A2598G						PASS	.	C	,	133,4273	92.5+/-131.2	2,129,2072	68	73	71		2580,2598	3.2	1	2	dbSNP_132	71	6,8580	4.3+/-15.6	0,6,4287	no	coding-synonymous,coding-synonymous	NCKAP1	NM_013436.3,NM_205842.1	,	2,135,6359	CC,CT,TT		0.0699,3.0186,1.0699	,	860/1129,866/1135	183817154	139,12853	2203	4293	6496	SO:0001819	synonymous_variant	10787	exon24			TTGTGATGAAATA	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.2580A>G	2.37:g.183817154T>C		193	0	0		188	97	0.515957	NM_205842	O60329|Q53QN5|Q53S94|Q53Y35	Silent	SNP	ENST00000361354.4	37	CCDS2287.1																																																																																			T|0.987;C|0.013	0.013	strong		0.313	NCKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255867.2	NM_205842		C	183817154	T	C	183817154	2	2	22	1	0	0	0	0	0	0	0	1	10230	1451	51	3		3	NCKAP1	2	183817154	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1036337	183817154	59382219	745	3646											
NUP35	129401	hgsc.bcm.edu	37	chr2	183993085	183993085	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgcccagttcttacctggAtttttaatgggggatttgcc	8	15	10	8	0	1	0	0	0	1	0	1	2	1	2	3	3	3	1	3	3	3	6	rs61743390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:183993085A>G	ENST00000295119.4	+	2	214	c.111A>G	c.(109-111)ggA>ggG	p.G37G	NUP35_ENST00000497330.1_3'UTR|NUP35_ENST00000409798.1_Silent_p.G20G|NUP35_ENST00000541912.1_5'UTR	NM_138285.3	NP_612142.2	Q8NFH5	NUP53_HUMAN	nucleoporin 35kDa	37					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						TCTTACCTGGATTTTTAATGG	0.438													A|||	44	0.00878594	0.0333	0.0	5008	,	,		14995	0.0		0.0	False		,,,				2504	0.0				p.G37G		Atlas-SNP	.											.	NUP35	28	.	0			c.A111G						PASS	.	A		148,4258	101.6+/-140.2	0,148,2055	80	78	79		111	2.7	1	2	dbSNP_129	79	2,8598		0,2,4298	no	coding-synonymous	NUP35	NM_138285.3		0,150,6353	GG,GA,AA		0.0233,3.3591,1.1533		37/327	183993085	150,12856	2203	4300	6503	SO:0001819	synonymous_variant	129401	exon2			ACCTGGATTTTTA	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.111A>G	2.37:g.183993085A>G		90	0	0		99	44	0.444444	NM_138285	B4DP57|B4DYB4|Q4ZFZ9|Q53S95|Q8TDJ1	Silent	SNP	ENST00000295119.4	37	CCDS2290.1																																																																																			A|0.989;G|0.011	0.011	strong		0.438	NUP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255865.1	NM_138285		G	183993085	A	G	183993085	2	3	22	1	0	0	0	0	0	0	0	1	10772	320	12	3		3	NUP35	2	183993085	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	175931	183993085	59206288	746	3647											
ITGAV	3685	hgsc.bcm.edu	37	chr2	187490232	187490232	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttgtaccattggagaactgaGatgaaacaggagcgagagcc	14	7	13	7	1	0	4	0	2	0	3	0	8	0	5	2	2	5	1	2	2	3	3	rs114767222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:187490232G>A	ENST00000261023.3	+	4	715	c.441G>A	c.(439-441)gaG>gaA	p.E147E	ITGAV_ENST00000374907.3_Silent_p.E147E|ITGAV_ENST00000433736.2_Silent_p.E101E	NM_002210.3	NP_002201	P06756	ITAV_HUMAN	integrin, alpha V	147					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)	GGAGAACTGAGATGAAACAGG	0.403													G|||	50	0.00998403	0.034	0.0072	5008	,	,		17909	0.0		0.0	False		,,,				2504	0.0				p.E147E	Melanoma(58;108 1995 6081)	Atlas-SNP	.											.	ITGAV	124	.	0			c.G441A						PASS	.	G	,,	118,4288	88.7+/-127.4	2,114,2087	126	115	118		303,441,441	0.5	0.3	2	dbSNP_132	118	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	ITGAV	NM_001144999.1,NM_001145000.1,NM_002210.3	,,	2,114,6387	AA,AG,GG		0.0,2.6782,0.9073	,,	101/1003,147/1013,147/1049	187490232	118,12888	2203	4300	6503	SO:0001819	synonymous_variant	3685	exon4			AACTGAGATGAAA		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.441G>A	2.37:g.187490232G>A		95	0	0		85	33	0.388235	NM_001145000	A0AV67|B0LPF4|B7Z883|B7ZLX0|D3DPG8|E7EWZ6|Q53SK4|Q59EB7|Q6LD15	Silent	SNP	ENST00000261023.3	37	CCDS2292.1																																																																																			G|0.992;A|0.008	0.008	strong		0.403	ITGAV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255882.2	NM_002210		A	187490232	G	A	187490232	2	1	22	1	0	0	0	0	0	0	0	1	7897	933	33	2		2	ITGAV	2	187490232	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3497147	187490232	55709141	747	3648											
CALCRL	10203	hgsc.bcm.edu	37	chr2	188250275	188250275	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tatatttttatgcttaccatAaaaaaaggcaagagaaccag	18	11	6	6	0	0	1	0	0	0	1	0	2	0	1	2	1	3	2	2	1	10	7	rs13391909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:188250275A>T	ENST00000409998.1	-	5	829	c.48T>A	c.(46-48)ttT>ttA	p.F16L	CALCRL_ENST00000392370.3_Missense_Mutation_p.F16L|CALCRL_ENST00000410068.1_Missense_Mutation_p.F16L|AC007319.1_ENST00000453517.1_RNA|AC007319.1_ENST00000412276.1_RNA			Q16602	CALRL_HUMAN	calcitonin receptor-like	16			F -> L (in dbSNP:rs13391909).		adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|angiogenesis (GO:0001525)|calcium ion transport (GO:0006816)|cAMP biosynthetic process (GO:0006171)|cellular response to sucrose stimulus (GO:0071329)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|heart development (GO:0007507)|negative regulation of inflammatory response (GO:0050728)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|regulation of muscle contraction (GO:0006937)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	adrenomedullin receptor activity (GO:0001605)|calcitonin gene-related polypeptide receptor activity (GO:0001635)|calcitonin receptor activity (GO:0004948)|G-protein coupled receptor activity (GO:0004930)|protein transporter activity (GO:0008565)			endometrium(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227)			TGCTTACCATAAAAAAAGGCA	0.274													A|||	207	0.0413339	0.1483	0.0159	5008	,	,		15603	0.0		0.0	False		,,,				2504	0.0				p.F16L		Atlas-SNP	.											.	CALCRL	73	.	0			c.T48A						PASS	.	A	LEU/PHE	527,3865		26,475,1695	30	33	32		48	-3.4	0	2	dbSNP_121	32	8,8520		0,8,4256	yes	missense	CALCRL	NM_005795.4	22	26,483,5951	TT,TA,AA		0.0938,11.9991,4.1409	benign	16/462	188250275	535,12385	2196	4264	6460	SO:0001583	missense	10203	exon3			TACCATAAAAAAA	U17473	CCDS2293.1	2q21.1-q21.3	2012-08-10			ENSG00000064989	ENSG00000064989		"GPCR / Class B : Calcitonin receptors"	16709	protein-coding gene	gene with protein product		114190				7818539, 8626685	Standard	NM_005795		Approved	CGRPR, CRLR	uc010frt.4	Q16602	OTTHUMG00000132636	ENST00000409998.1:c.48T>A	2.37:g.188250275A>T	ENSP00000386972:p.Phe16Leu	112	0	0		104	53	0.509615	NM_001271751	A8K6G5|A8KAD3|Q53S02|Q53TS5	Missense_Mutation	SNP	ENST00000409998.1	37	CCDS2293.1	96	0.04395604395604396	92	0.18699186991869918	4	0.011049723756906077	0	0.0	0	0.0	A	0.734	-0.779016	0.02929	0.119991	9.38E-4	ENSG00000064989	ENST00000392370;ENST00000409998;ENST00000410068;ENST00000447403;ENST00000410102	T;T;T;T;T	0.59906	1.04;1.04;1.04;1.57;0.23	5.81	-3.39	0.04868	.	1.007640	0.07990	N	0.986908	T	0.00039	0.0001	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.07501	-1.0769	9	0.09843	T	0.71	.	4.5787	0.12248	0.3334:0.0:0.1511:0.5155	rs13391909;rs52830213;rs13391909	16	Q16602	CALRL_HUMAN	L	16	ENSP00000376177:F16L;ENSP00000386972:F16L;ENSP00000387190:F16L;ENSP00000415626:F16L;ENSP00000386599:F16L	ENSP00000376177:F16L	F	-	3	2	CALCRL	187958520	0.102000	0.21896	0.017000	0.16124	0.202000	0.24057	0.018000	0.13422	-0.859000	0.04105	-0.468000	0.05107	TTT	A|0.954;T|0.046	0.046	strong		0.274	CALCRL-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334648.1	NM_005795		T	188250275	A	T	188250275	3	4	22	1	0	0	0	0	1	0	0	0	2582	359	13	5	1385	5	CALCRL	2	188250275	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	760043	188250275	54949098	748	3649											
DIRC1	116093	hgsc.bcm.edu	37	chr2	189599373	189599373	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaatattttccaccccctcAatgagttaagacactttagc	12	14	4	11	0	1	2	1	1	0	1	2	2	2	2	3	0	1	1	3	0	5	7	rs58846152	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:189599373A>G	ENST00000308100.4	-	2	545	c.275T>C	c.(274-276)tTg>tCg	p.L92S	AC079613.1_ENST00000431708.1_RNA	NM_052952.2	NP_443184.1	Q969H9	DIRC1_HUMAN	disrupted in renal carcinoma 1	92			L -> S (in dbSNP:rs58846152).							large_intestine(1)|lung(6)	7			OV - Ovarian serous cystadenocarcinoma(117;0.00842)|Epithelial(96;0.102)			CCACCCCCTCAATGAGTTAAG	0.383													A|||	167	0.0333466	0.121	0.0086	5008	,	,		18397	0.0		0.001	False		,,,				2504	0.0				p.L92S		Atlas-SNP	.											.	DIRC1	13	.	0			c.T275C						PASS	.	A	SER/LEU	350,4056	180.8+/-209.0	13,324,1866	155	160	158		275	1.2	0	2	dbSNP_129	158	2,8598	1.2+/-3.3	0,2,4298	yes	missense	DIRC1	NM_052952.2	145	13,326,6164	GG,GA,AA		0.0233,7.9437,2.7064	benign	92/105	189599373	352,12654	2203	4300	6503	SO:0001583	missense	116093	exon2			CCCCTCAATGAGT	AY039011	CCDS2296.1	2q33	2008-05-22			ENSG00000174325	ENSG00000174325			15760	protein-coding gene	gene with protein product		606423				11587072	Standard	NM_052952		Approved		uc002uqi.1	Q969H9	OTTHUMG00000132646	ENST00000308100.4:c.275T>C	2.37:g.189599373A>G	ENSP00000307860:p.Leu92Ser	214	0	0		186	79	0.424731	NM_052952	Q08AK1	Missense_Mutation	SNP	ENST00000308100.4	37	CCDS2296.1	53	0.024267399267399268	49	0.09959349593495935	4	0.011049723756906077	0	0.0	0	0.0	A	1.548	-0.540046	0.04053	0.079437	2.33E-4	ENSG00000174325	ENST00000308100	T	0.42131	0.98	2.38	1.21	0.21127	.	.	.	.	.	T	0.00524	0.0017	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.11251	-1.0595	9	0.87932	D	0	.	4.1545	0.10254	0.8279:0.0:0.1721:0.0	rs58846152	92	Q969H9	DIRC1_HUMAN	S	92	ENSP00000307860:L92S	ENSP00000307860:L92S	L	-	2	0	DIRC1	189307618	0.031000	0.19500	0.003000	0.11579	0.015000	0.08874	0.917000	0.28665	0.329000	0.23460	0.533000	0.62120	TTG	A|0.976;G|0.024	0.024	strong		0.383	DIRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255897.2	NM_052952		G	189599373	A	G	189599373	3	3	22	1	0	0	0	0	1	0	0	0	4535	131	5	3	43	3	DIRC1	2	189599373	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1349098	189599373	53600000	749	3650											
SLC40A1	30061	hgsc.bcm.edu	37	chr2	190437572	190437572	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaatctcattgagaacttacGagaacccatccatggtacat	14	10	7	10	1	1	2	1	1	1	2	3	5	2	2	2	1	4	1	2	1	5	3	rs11568344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:190437572G>A	ENST00000261024.2	-	4	813	c.387C>T	c.(385-387)ctC>ctT	p.L129L	SLC40A1_ENST00000418714.1_5'Flank	NM_014585.5	NP_055400.1	Q9NP59	S40A1_HUMAN	solute carrier family 40 (iron-regulated transporter), member 1	129					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)			GAGAACTTACGAGAACCCATC	0.383													G|||	164	0.0327476	0.118	0.0115	5008	,	,		19151	0.0		0.0	False		,,,				2504	0.0				p.L129L		Atlas-SNP	.											.	SLC40A1	51	.	0			c.C387T						PASS	.	G		492,3914	228.5+/-243.3	22,448,1733	77	73	74		387	0.8	1	2	dbSNP_121	74	4,8596	2.2+/-6.3	0,4,4296	yes	coding-synonymous-near-splice	SLC40A1	NM_014585.5		22,452,6029	AA,AG,GG		0.0465,11.1666,3.8136		129/572	190437572	496,12510	2203	4300	6503	SO:0001630	splice_region_variant	30061	exon4			ACTTACGAGAACC	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.387+1C>T	2.37:g.190437572G>A		186	0	0		196	98	0.5	NM_014585	Q6FI62|Q7Z4F8|Q8IVB2|Q9NRL0	Silent	SNP	ENST00000261024.2	37	CCDS2299.1																																																																																			G|0.960;A|0.040	0.040	strong		0.383	SLC40A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255916.2		Silent	A	190437572	G	A	190437572	5	1	22	1	0	0	0	0	0	0	1	0	14643	1072	37	1	1348	1	SLC40A1	2	190437572	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	838199	190437572	52761801	750	3651											
TMEFF2	23671	hgsc.bcm.edu	37	chr2	192922499	192922499	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agtttctccagagccttcatGgactgtaggacagaaaaaca	14	9	9	9	0	2	2	1	0	1	2	3	4	2	4	2	2	2	2	2	2	3	3	rs61744272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:192922499G>A	ENST00000272771.5	-	5	1626	c.442C>T	c.(442-444)Cat>Tat	p.H148Y	TMEFF2_ENST00000392314.1_Missense_Mutation_p.H148Y	NM_016192.2	NP_057276.2	Q9UIK5	TEFF2_HUMAN	transmembrane protein with EGF-like and two follistatin-like domains 2	148						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)			GAGCCTTCATGGACTGTAGGA	0.403													G|||	92	0.0183706	0.0635	0.0086	5008	,	,		18753	0.0		0.002	False		,,,				2504	0.0				p.H148Y	Pancreas(50;1277 1381 28487 47072)	Atlas-SNP	.											.	TMEFF2	54	.	0			c.C442T						PASS	.	G	TYR/HIS	282,4124	158.5+/-191.2	10,262,1931	95	86	89		442	4	0.9	2	dbSNP_129	89	2,8598	2.2+/-6.3	0,2,4298	yes	missense	TMEFF2	NM_016192.2	83	10,264,6229	AA,AG,GG		0.0233,6.4004,2.1836	possibly-damaging	148/375	192922499	284,12722	2203	4300	6503	SO:0001583	missense	23671	exon5			CTTCATGGACTGT	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.442C>T	2.37:g.192922499G>A	ENSP00000272771:p.His148Tyr	130	0	0		128	68	0.53125	NM_016192	Q2FA44|Q4ZFW4|Q53H90|Q53RE1|Q8N2R5|Q9NR15|Q9NSS5|Q9P2Y9|Q9UK65	Missense_Mutation	SNP	ENST00000272771.5	37	CCDS2314.1	31	0.014194139194139194	27	0.054878048780487805	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	G	1.594	-0.528334	0.04112	0.064004	2.33E-4	ENSG00000144339	ENST00000392314;ENST00000272771	T;T	0.58797	0.31;0.31	4.93	3.99	0.46301	.	0.338199	0.31335	N	0.007834	T	0.03827	0.0108	N	0.03608	-0.345	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.03043	-1.1079	10	0.15499	T	0.54	-18.1134	13.1246	0.59346	0.0:0.0:0.78:0.2199	.	148	Q9UIK5	TEFF2_HUMAN	Y	148	ENSP00000376128:H148Y;ENSP00000272771:H148Y	ENSP00000272771:H148Y	H	-	1	0	TMEFF2	192630744	1.000000	0.71417	0.949000	0.38748	0.824000	0.46624	3.823000	0.55715	2.713000	0.92767	0.655000	0.94253	CAT	G|0.982;A|0.018	0.018	strong		0.403	TMEFF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256065.2	NM_016192		A	192922499	G	A	192922499	3	1	22	1	0	0	0	0	1	0	0	0	16029	1348	47	2	706	2	TMEFF2	2	192922499	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2484927	192922499	50276874	751	3652											
HECW2	57520	hgsc.bcm.edu	37	chr2	197087061	197087061	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctaggtcactcaggtcacaTagactaagatgacaaacaga	16	8	8	9	0	4	4	3	1	1	3	4	4	4	4	0	2	1	0	0	2	4	3	rs16847486	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:197087061T>C	ENST00000260983.3	-	24	4202	c.4020A>G	c.(4018-4020)ctA>ctG	p.L1340L	HECW2_ENST00000409111.1_Silent_p.L984L	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	1340	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						TCAGGTCACATAGACTAAGAT	0.388													T|||	140	0.0279553	0.0976	0.0159	5008	,	,		21341	0.0		0.0	False		,,,				2504	0.0				p.L1340L		Atlas-SNP	.											.	HECW2	239	.	0			c.A4020G						PASS	.	T		443,3963	214.8+/-234.0	23,397,1783	120	104	110		4020	-1.3	0.8	2	dbSNP_123	110	10,8590	7.1+/-27.0	0,10,4290	no	coding-synonymous	HECW2	NM_020760.1		23,407,6073	CC,CT,TT		0.1163,10.0545,3.483		1340/1573	197087061	453,12553	2203	4300	6503	SO:0001819	synonymous_variant	57520	exon24			GTCACATAGACTA	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.4020A>G	2.37:g.197087061T>C		79	0	0		93	55	0.591398	NM_020760	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Silent	SNP	ENST00000260983.3	37	CCDS33354.1																																																																																			T|0.965;C|0.035	0.035	strong		0.388	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760		C	197087061	T	C	197087061	2	2	22	1	0	0	0	0	0	0	0	1	7052	1393	49	3		3	HECW2	2	197087061	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	4164562	197087061	46112312	752	3653											
SF3B1	23451	hgsc.bcm.edu	37	chr2	198266834	198266834	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcactgatggtccgaacttTctgctgctcatccacaagac	10	10	8	13	1	2	2	1	1	1	1	4	3	4	2	2	1	4	3	2	1	2	1	rs559063155		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:198266834T>C	ENST00000335508.6	-	15	2189	c.2098A>G	c.(2098-2100)Aaa>Gaa	p.K700E	SNORA4_ENST00000365564.1_RNA|SF3B1_ENST00000462613.1_5'UTR	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	700					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.K700E(179)|p.Q699_K700del(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)			GTCCGAACTTTCTGCTGCTCA	0.408			Mis		myelodysplastic syndrome								T|||	1	0.000199681	0.0	0.0	5008	,	,		17946	0.0		0.0	False		,,,				2504	0.001				p.K700E		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	SF3B1,NS,haematopoietic_neoplasm,0,263	SF3B1	1038	263	181	Substitution - Missense(179)|Deletion - In frame(2)	haematopoietic_and_lymphoid_tissue(153)|NS(20)|breast(5)|pancreas(2)|central_nervous_system(1)	c.A2098G						PASS	.																																			SO:0001583	missense	23451	exon15			GAACTTTCTGCTG	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.2098A>G	2.37:g.198266834T>C	ENSP00000335321:p.Lys700Glu	173	0	0		214	70	0.327103	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	37	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	T	33	5.243295	0.95272	.	.	ENSG00000115524	ENST00000335508	T	0.63580	-0.05	6.02	6.02	0.97574	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.85609	0.5736	H	0.95504	3.68	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89820	0.3988	10	0.87932	D	0	.	16.542	0.84395	0.0:0.0:0.0:1.0	.	700	O75533	SF3B1_HUMAN	E	700	ENSP00000335321:K700E	ENSP00000335321:K700E	K	-	1	0	SF3B1	197975079	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.555000	0.82223	2.304000	0.77564	0.528000	0.53228	AAA	.	.	none		0.408	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			C	198266834	T	C	198266834	3	2	22	1	0	0	0	0	1	0	0	0	14164	1792	62	3	1860	3	SF3B1	2	198266834	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1179773	198266834	44932539	753	3654											
SMARCAL1	50485	hgsc.bcm.edu	37	chr2	217285104	217285104	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcgagtcaccctccaccagCagtgagggacaggccggcct	9	4	13	15	2	1	1	1	1	0	0	2	3	2	2	5	3	2	1	5	3	0	0	rs2066522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:217285104C>G	ENST00000357276.4	+	5	1275	c.945C>G	c.(943-945)agC>agG	p.S315R	SMARCAL1_ENST00000358207.5_Missense_Mutation_p.S315R	NM_014140.3	NP_054859.2	Q9NZC9	SMAL1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	315			S -> R (in dbSNP:rs2066522).		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)		CCTCCACCAGCAGTGAGGGAC	0.572									Schimke Immuno-Osseous Dysplasia				C|||	170	0.0339457	0.0809	0.0331	5008	,	,		17373	0.0		0.0338	False		,,,				2504	0.0061				p.S315R		Atlas-SNP	.											SMARCAL1,right_upper_lobe,carcinoma,+1,1	SMARCAL1	93	1	0			c.C945G						scavenged	.	C	ARG/SER,ARG/SER	353,4053	181.9+/-209.8	17,319,1867	90	73	79		945,945	-0.2	0	2	dbSNP_98	79	249,8351	99.3+/-160.8	2,245,4053	yes	missense,missense	SMARCAL1	NM_001127207.1,NM_014140.3	110,110	19,564,5920	GG,GC,CC		2.8953,8.0118,4.6286	possibly-damaging,possibly-damaging	315/955,315/955	217285104	602,12404	2203	4300	6503	SO:0001583	missense	50485	exon5	Familial Cancer Database	SIOD	CACCAGCAGTGAG	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.945C>G	2.37:g.217285104C>G	ENSP00000349823:p.Ser315Arg	164	1	0.00609756		160	76	0.475	NM_014140	A6NEH0|Q53R00|Q96AY1|Q9NXQ5|Q9UFH3|Q9UI93	Missense_Mutation	SNP	ENST00000357276.4	37	CCDS2403.1	65	0.02976190476190476	36	0.07317073170731707	9	0.024861878453038673	0	0.0	20	0.026385224274406333	C	19.69	3.875544	0.72180	0.080118	0.028953	ENSG00000138375	ENST00000357276;ENST00000358207;ENST00000427645;ENST00000392128;ENST00000412913	D;D;T;D;T	0.85955	-2.04;-2.04;1.51;-2.05;0.68	3.96	-0.186	0.13272	.	1.145540	0.06356	N	0.710693	T	0.14614	0.0353	L	0.36672	1.1	0.09310	N	1	P	0.43287	0.802	B	0.31614	0.133	T	0.38436	-0.9661	10	0.38643	T	0.18	.	7.9086	0.29776	0.0:0.6035:0.0:0.3965	rs2066522;rs2266768;rs52816735;rs2066522	315	Q9NZC9	SMAL1_HUMAN	R	315;315;214;179;35	ENSP00000349823:S315R;ENSP00000350940:S315R;ENSP00000392997:S214R;ENSP00000375974:S179R;ENSP00000390248:S35R	ENSP00000349823:S315R	S	+	3	2	SMARCAL1	216993349	0.000000	0.05858	0.001000	0.08648	0.897000	0.52465	0.450000	0.21762	0.000000	0.14550	0.561000	0.74099	AGC	C|0.957;G|0.043	0.043	strong		0.572	SMARCAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256671.2			G	217285104	C	G	217285104	3	3	22	1	0	0	0	0	1	0	0	0	14788	709	25	4	955	4	SMARCAL1	2	217285104	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	19018270	217285104	25914269	754	3655											
RUFY4	285180	hgsc.bcm.edu	37	chr2	218953991	218953991	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagagagaaggaccgcctgTggcagaggctccagcatctc	10	6	13	12	1	2	3	1	0	1	3	4	5	3	4	3	3	1	3	3	3	1	0	rs201137688	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:218953991T>G	ENST00000344321.7	+	12	2037	c.1519T>G	c.(1519-1521)Tgg>Ggg	p.W507G	RUFY4_ENST00000374155.3_Missense_Mutation_p.W527G|RUFY4_ENST00000441828.2_3'UTR	NM_198483.3	NP_940885.2	Q6ZNE9	RUFY4_HUMAN	RUN and FYVE domain containing 4	507							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)		GGACCGCCTGTGGCAGAGGCT	0.527													T|||	2	0.000399361	0.0	0.0	5008	,	,		19104	0.0		0.001	False		,,,				2504	0.001				p.W507G		Atlas-SNP	.											.	RUFY4	59	.	0			c.T1519G						PASS	.	T	GLY/TRP	3,3833		0,3,1915	48	50	49		1519	4.9	1	2		49	14,8270		0,14,4128	yes	missense	RUFY4	NM_198483.3	184	0,17,6043	GG,GT,TT		0.169,0.0782,0.1403	probably-damaging	507/572	218953991	17,12103	1918	4142	6060	SO:0001583	missense	285180	exon12			CGCCTGTGGCAGA	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.1519T>G	2.37:g.218953991T>G	ENSP00000345900:p.Trp507Gly	141	0	0		183	74	0.404372	NM_198483	Q6ZR96	Missense_Mutation	SNP	ENST00000344321.7	37		.	.	.	.	.	.	.	.	.	.	T	16.23	3.064752	0.55432	7.82E-4	0.00169	ENSG00000188282	ENST00000344321;ENST00000374155	T;T	0.66280	1.15;-0.2	4.92	4.92	0.64577	Zinc finger, FYVE/PHD-type (1);	0.000000	0.49305	D	0.000154	T	0.76842	0.4044	M	0.80616	2.505	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.75545	-0.3280	10	0.27082	T	0.32	-16.7446	10.8813	0.46939	0.0:0.0:0.0:1.0	.	507	Q6ZNE9	RUFY4_HUMAN	G	507;527	ENSP00000345900:W507G;ENSP00000363270:W527G	ENSP00000345900:W507G	W	+	1	0	RUFY4	218662236	1.000000	0.71417	0.962000	0.40283	0.771000	0.43674	3.616000	0.54174	2.079000	0.62486	0.454000	0.30748	TGG	T|0.999;G|0.001	0.001	weak		0.527	RUFY4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198483		G	218953991	T	G	218953991	3	3	22	1	0	0	0	0	1	0	0	0	13756	1696	59	5	1557	5	RUFY4	2	218953991	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1668887	218953991	24245382	755	3656											
RUFY4	285180	hgsc.bcm.edu	37	chr2	218954716	218954716	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccatgcttgctccatggattAcaagaagagagaccgctgct	11	9	10	11	1	0	3	0	0	0	3	1	5	1	4	3	1	4	4	3	1	3	2	rs116710266	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:218954716A>G	ENST00000344321.7	+	13	2173	c.1655A>G	c.(1654-1656)tAc>tGc	p.Y552C	RUFY4_ENST00000374155.3_3'UTR|RUFY4_ENST00000441828.2_3'UTR	NM_198483.3	NP_940885.2	Q6ZNE9	RUFY4_HUMAN	RUN and FYVE domain containing 4	552							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)		TCCATGGATTACAAGAAGAGA	0.632													A|||	70	0.0139776	0.0499	0.0058	5008	,	,		17641	0.0		0.0	False		,,,				2504	0.0				p.Y552C		Atlas-SNP	.											.	RUFY4	59	.	0			c.A1655G						PASS	.	A	CYS/TYR	158,3840		3,152,1844	37	44	42		1655	0.7	0.7	2	dbSNP_132	42	0,8322		0,0,4161	yes	missense	RUFY4	NM_198483.3	194	3,152,6005	GG,GA,AA		0.0,3.952,1.2825	probably-damaging	552/572	218954716	158,12162	1999	4161	6160	SO:0001583	missense	285180	exon13			TGGATTACAAGAA	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.1655A>G	2.37:g.218954716A>G	ENSP00000345900:p.Tyr552Cys	214	0	0		280	153	0.546429	NM_198483	Q6ZR96	Missense_Mutation	SNP	ENST00000344321.7	37		35	0.016025641025641024	31	0.06300813008130081	4	0.011049723756906077	0	0.0	0	0.0	A	11.43	1.636570	0.29068	0.03952	0.0	ENSG00000188282	ENST00000344321	T	0.76709	-1.04	4.6	0.663	0.17885	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE-related (1);Zinc finger, FYVE/PHD-type (1);	.	.	.	.	T	0.17238	0.0414	M	0.68952	2.095	0.80722	D	1	P	0.46784	0.884	B	0.32342	0.144	T	0.47182	-0.9137	9	0.59425	D	0.04	.	1.8069	0.03082	0.5702:0.1707:0.0947:0.1644	.	552	Q6ZNE9	RUFY4_HUMAN	C	552	ENSP00000345900:Y552C	ENSP00000345900:Y552C	Y	+	2	0	RUFY4	218662961	0.997000	0.39634	0.740000	0.30986	0.070000	0.16714	0.369000	0.20416	0.249000	0.21456	-0.488000	0.04728	TAC	A|0.982;G|0.018	0.018	strong		0.632	RUFY4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198483		G	218954716	A	G	218954716	3	3	22	1	0	0	0	0	1	0	0	0	13756	391	14	3	1697	3	RUFY4	2	218954716	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	725	218954716	24244657	756	3657											
CXCR2	3579	hgsc.bcm.edu	37	chr2	218999798	218999798	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctacctgctgaacctagccTtggccgacctactctttgcc	6	12	7	16	1	2	1	0	1	2	0	2	2	2	1	6	1	6	1	6	1	4	5	rs142747099	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:218999798T>C	ENST00000318507.2	+	3	701	c.274T>C	c.(274-276)Ttg>Ctg	p.L92L		NM_001557.3	NP_001548.1	P25025	CXCR2_HUMAN	chemokine (C-X-C motif) receptor 2	92					cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|inflammatory response (GO:0006954)|interleukin-8-mediated signaling pathway (GO:0038112)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|interleukin-8 binding (GO:0019959)|interleukin-8 receptor activity (GO:0004918)|signal transducer activity (GO:0004871)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(11)|skin(1)|stomach(1)	22						GAACCTAGCCTTGGCCGACCT	0.567																																					p.L92L		Atlas-SNP	.											.	CXCR2	54	.	0			c.T274C						PASS	.	T	,	6,4400	11.4+/-27.6	0,6,2197	144	136	138		274,274	-0.1	0.8	2	dbSNP_134	138	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CXCR2	NM_001168298.1,NM_001557.3	,	0,6,6497	CC,CT,TT		0.0,0.1362,0.0461	,	92/361,92/361	218999798	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	3579	exon4			CTAGCCTTGGCCG	U11869	CCDS2408.1	2q35	2012-08-08	2009-11-25	2009-11-25	ENSG00000180871	ENSG00000180871		"CD molecules", "GPCR / Class A : Chemokine receptors : C-X-C motif", "Interleukins and interleukin receptors"	6027	protein-coding gene	gene with protein product		146928	"interleukin 8 receptor, beta"	IL8RB		1427896	Standard	NM_001557		Approved	CMKAR2, CD182	uc002vha.2	P25025	OTTHUMG00000133107	ENST00000318507.2:c.274T>C	2.37:g.218999798T>C		249	1	0.00401606		238	109	0.457983	NM_001168298	Q8IUZ1|Q9P2T6|Q9P2T7	Silent	SNP	ENST00000318507.2	37	CCDS2408.1																																																																																			T|0.999;C|0.001	0.001	strong		0.567	CXCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256772.2	NM_001557		C	218999798	T	C	218999798	2	2	22	1	0	0	0	0	0	0	0	1	4093	1606	56	3		3	CXCR2	2	218999798	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	45082	218999798	24199575	757	3658											
CXCR2	3579	hgsc.bcm.edu	37	chr2	219000193	219000193	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctttggcttcatcgtgccActgctgatcatgctgttctg	4	16	9	12	1	3	1	2	1	1	0	5	1	4	1	2	1	3	4	2	1	0	3	rs2228414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:219000193A>G	ENST00000318507.2	+	3	1096	c.669A>G	c.(667-669)ccA>ccG	p.P223P		NM_001557.3	NP_001548.1	P25025	CXCR2_HUMAN	chemokine (C-X-C motif) receptor 2	223					cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|inflammatory response (GO:0006954)|interleukin-8-mediated signaling pathway (GO:0038112)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|interleukin-8 binding (GO:0019959)|interleukin-8 receptor activity (GO:0004918)|signal transducer activity (GO:0004871)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(11)|skin(1)|stomach(1)	22						TCATCGTGCCACTGCTGATCA	0.562													G|||	66	0.0131789	0.0469	0.0058	5008	,	,		21834	0.0		0.0	False		,,,				2504	0.0				p.P223P		Atlas-SNP	.											.	CXCR2	54	.	0			c.A669G						PASS	.	G	,	167,4239	111.2+/-149.4	3,161,2039	174	159	164		669,669	-10.8	0	2	dbSNP_98	164	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CXCR2	NM_001168298.1,NM_001557.3	,	3,161,6339	GG,GA,AA		0.0,3.7903,1.284	,	223/361,223/361	219000193	167,12839	2203	4300	6503	SO:0001819	synonymous_variant	3579	exon4			CGTGCCACTGCTG	U11869	CCDS2408.1	2q35	2012-08-08	2009-11-25	2009-11-25	ENSG00000180871	ENSG00000180871		"CD molecules", "GPCR / Class A : Chemokine receptors : C-X-C motif", "Interleukins and interleukin receptors"	6027	protein-coding gene	gene with protein product		146928	"interleukin 8 receptor, beta"	IL8RB		1427896	Standard	NM_001557		Approved	CMKAR2, CD182	uc002vha.2	P25025	OTTHUMG00000133107	ENST00000318507.2:c.669A>G	2.37:g.219000193A>G		253	0	0		214	124	0.579439	NM_001168298	Q8IUZ1|Q9P2T6|Q9P2T7	Silent	SNP	ENST00000318507.2	37	CCDS2408.1																																																																																			A|0.985;G|0.015	0.015	strong		0.562	CXCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256772.2	NM_001557		G	219000193	A	G	219000193	2	3	22	1	0	0	0	0	0	0	0	1	4093	146	6	3		3	CXCR2	2	219000193	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	395	219000193	24199180	758	3659											
PLCD4	84812	hgsc.bcm.edu	37	chr2	219483526	219483526	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tggaccatcaggagcgcctgGaccagtatcggcaggatgga	10	6	15	10	2	1	0	1	0	0	0	2	5	1	5	3	6	1	2	3	6	1	1	rs200863393		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:219483526G>C	ENST00000450993.2	+	4	745	c.406G>C	c.(406-408)Gac>Cac	p.D136H	PLCD4_ENST00000432688.1_Missense_Mutation_p.D136H|PLCD4_ENST00000417849.1_Missense_Mutation_p.D136H|U3_ENST00000516996.1_RNA	NM_032726.3	NP_116115.1	Q9BRC7	PLCD4_HUMAN	phospholipase C, delta 4	136	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				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)		GGAGCGCCTGGACCAGTATCG	0.582													G|||	1	0.000199681	0.0	0.0	5008	,	,		20288	0.0		0.001	False		,,,				2504	0.0				p.D136H		Atlas-SNP	.											.	PLCD4	51	.	0			c.G406C						PASS	.	G	HIS/ASP	0,4162		0,0,2081	18	18	18		406	4.9	1	2		18	2,8408		0,2,4203	yes	missense	PLCD4	NM_032726.3	81	0,2,6284	CC,CG,GG		0.0238,0.0,0.0159	probably-damaging	136/763	219483526	2,12570	2081	4205	6286	SO:0001583	missense	84812	exon4			CGCCTGGACCAGT	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.406G>C	2.37:g.219483526G>C	ENSP00000388631:p.Asp136His	88	0	0		101	48	0.475248	NM_032726	Q53FS8	Missense_Mutation	SNP	ENST00000450993.2	37	CCDS46516.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	18.34	3.603570	0.66445	0.0	2.38E-4	ENSG00000115556	ENST00000450993;ENST00000251959;ENST00000457426;ENST00000417849;ENST00000432688	T;T;T	0.43688	0.94;0.94;0.94	4.89	4.89	0.63831	.	1.041430	0.07513	N	0.909165	T	0.69441	0.3111	M	0.76838	2.35	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.61063	-0.7138	10	0.51188	T	0.08	.	16.8055	0.85626	0.0:0.0:1.0:0.0	.	83;136	B4DN84;Q9BRC7	.;PLCD4_HUMAN	H	136	ENSP00000388631:D136H;ENSP00000396942:D136H;ENSP00000396185:D136H	ENSP00000251959:D136H	D	+	1	0	PLCD4	219191770	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.473000	0.97714	2.553000	0.86117	0.655000	0.94253	GAC	G|1.000;C|0.000	0.000	strong		0.582	PLCD4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336876.1			C	219483526	G	C	219483526	3	2	22	1	0	0	0	0	1	0	0	0	12042	1174	41	4	416	4	PLCD4	2	219483526	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	483333	219483526	23715847	759	3660											
ZNF142	7701	hgsc.bcm.edu	37	chr2	219515109	219515109	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccgctgagccccttggccttTatccacagccttttgggagt	5	12	10	14	1	0	1	0	1	0	0	1	2	1	2	6	2	2	1	6	2	1	5	rs61733648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:219515109T>G	ENST00000449707.1	-	5	842	c.421A>C	c.(421-423)Aaa>Caa	p.K141Q	ZNF142_ENST00000411696.2_Missense_Mutation_p.K141Q	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	141					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)		CCTTGGCCTTTATCCACAGCC	0.527													T|||	67	0.0133786	0.0492	0.0029	5008	,	,		19332	0.0		0.0	False		,,,				2504	0.0				p.K141Q	Colon(170;867 1942 8995 15834 18053)	Atlas-SNP	.											.	ZNF142	190	.	0			c.A421C						PASS	.	T	GLN/LYS	162,3762		0,162,1800	230	233	232		421	4.1	0	2	dbSNP_129	232	1,8297		0,1,4148	yes	missense	ZNF142	NM_001105537.1	53	0,163,5948	GG,GT,TT		0.0121,4.1284,1.3337	possibly-damaging	141/1688	219515109	163,12059	1962	4149	6111	SO:0001583	missense	7701	exon5			GGCCTTTATCCAC	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.421A>C	2.37:g.219515109T>G	ENSP00000408643:p.Lys141Gln	175	0	0		191	96	0.502618	NM_001105537	Q92510	Missense_Mutation	SNP	ENST00000449707.1	37	CCDS42817.1	22	0.010073260073260074	22	0.044715447154471545	0	0.0	0	0.0	0	0.0	T	8.836	0.941010	0.18281	0.041284	1.21E-4	ENSG00000115568	ENST00000449707;ENST00000411696	T;T	0.12984	2.63;2.63	5.2	4.05	0.47172	.	0.711144	0.13741	N	0.365968	T	0.02193	0.0068	L	0.44542	1.39	0.09310	N	1	P	0.39282	0.666	B	0.35859	0.212	T	0.21999	-1.0229	10	0.21014	T	0.42	-0.251	7.4012	0.26965	0.0:0.0962:0.0:0.9038	.	141	P52746	ZN142_HUMAN	Q	141	ENSP00000408643:K141Q;ENSP00000398798:K141Q	ENSP00000398798:K141Q	K	-	1	0	ZNF142	219223353	0.172000	0.23043	0.048000	0.18961	0.098000	0.18820	1.797000	0.38804	1.011000	0.39340	0.533000	0.62120	AAA	T|0.990;G|0.010	0.010	strong		0.527	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081		G	219515109	T	G	219515109	3	3	22	1	0	0	0	0	1	0	0	0	17746	1763	61	5	4666	5	ZNF142	2	219515109	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	31583	219515109	23684264	760	3661											
CYP27A1	1593	hgsc.bcm.edu	37	chr2	219674482	219674482	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacgacctgacctatgggccGttcaccacgtgagctggggc	7	7	13	14	3	1	2	1	2	0	0	1	3	1	2	4	3	1	2	4	3	1	2	rs692003	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:219674482G>A	ENST00000258415.4	+	2	865	c.438G>A	c.(436-438)ccG>ccA	p.P146P		NM_000784.3	NP_000775.1	Q02318	CP27A_HUMAN	cytochrome P450, family 27, subfamily A, polypeptide 1	146					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)	CCTATGGGCCGTTCACCACGT	0.622													G|||	366	0.0730831	0.2632	0.0259	5008	,	,		16942	0.0		0.0	False		,,,				2504	0.0				p.P146P		Atlas-SNP	.											.	CYP27A1	52	.	0			c.G438A						PASS	.	G		877,3529	341.2+/-306.6	84,709,1410	90	78	82		438	2.9	0.9	2	dbSNP_83	82	8,8592	5.0+/-18.6	0,8,4292	no	coding-synonymous	CYP27A1	NM_000784.3		84,717,5702	AA,AG,GG		0.093,19.9047,6.8046		146/532	219674482	885,12121	2203	4300	6503	SO:0001819	synonymous_variant	1593	exon2			TGGGCCGTTCACC	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.438G>A	2.37:g.219674482G>A		82	0	0		73	32	0.438356	NM_000784	A8K303|Q6LDB4|Q86YQ6	Silent	SNP	ENST00000258415.4	37	CCDS2423.1																																																																																			G|0.935;A|0.065	0.065	strong		0.622	CYP27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109734.4			A	219674482	G	A	219674482	2	1	22	1	0	0	0	0	0	0	0	1	4160	1132	40	1		1	CYP27A1	2	219674482	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	159373	219674482	23524891	761	3662											
PTPRN	5798	hgsc.bcm.edu	37	chr2	220164886	220164886	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttggcacctgctggacttcActggaggtagggctggcagt	6	10	15	10	0	1	0	1	0	0	0	1	2	1	2	1	6	1	5	1	6	1	3	rs35314717	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220164886A>C	ENST00000295718.2	-	9	1497	c.1257T>G	c.(1255-1257)agT>agG	p.S419R	AC114803.3_ENST00000417355.1_RNA|PTPRN_ENST00000409251.3_Missense_Mutation_p.S419R|PTPRN_ENST00000423636.2_Missense_Mutation_p.S329R	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	419			S -> R (in dbSNP:rs35314717).		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)		GCTGGACTTCACTGGAGGTAG	0.627													A|||	162	0.0323482	0.1172	0.0101	5008	,	,		16965	0.0		0.0	False		,,,				2504	0.0				p.S419R		Atlas-SNP	.											.	PTPRN	138	.	0			c.T1257G						PASS	.	A	ARG/SER,ARG/SER,ARG/SER	475,3931	223.9+/-240.3	29,417,1757	67	76	73		1257,987,1257	-2.4	0	2	dbSNP_126	73	6,8594	4.3+/-15.6	0,6,4294	yes	missense,missense,missense	PTPRN	NM_001199763.1,NM_001199764.1,NM_002846.3	110,110,110	29,423,6051	CC,CA,AA		0.0698,10.7808,3.6983	benign,benign,benign	419/951,329/890,419/980	220164886	481,12525	2203	4300	6503	SO:0001583	missense	5798	exon9			GACTTCACTGGAG		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.1257T>G	2.37:g.220164886A>C	ENSP00000295718:p.Ser419Arg	73	0	0		89	53	0.595506	NM_002846	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Missense_Mutation	SNP	ENST00000295718.2	37	CCDS2440.1	63	0.028846153846153848	61	0.12398373983739837	2	0.0055248618784530384	0	0.0	0	0.0	A	4.756	0.140493	0.09083	0.107808	6.98E-4	ENSG00000054356	ENST00000409251;ENST00000295718;ENST00000539342;ENST00000537666	T;T;T	0.27104	1.69;1.69;1.69	4.27	-2.38	0.06622	.	1.386960	0.04458	N	0.373874	T	0.00210	0.0006	N	0.24115	0.695	0.80722	P	0.0	B;B	0.23735	0.09;0.09	B;B	0.21360	0.034;0.015	T	0.23619	-1.0183	9	0.16420	T	0.52	.	7.6045	0.28095	0.276:0.1662:0.5578:0.0	rs35314717;rs60827710	419;419	Q6NSL1;Q16849	.;PTPRN_HUMAN	R	419;419;419;329	ENSP00000386638:S419R;ENSP00000295718:S419R;ENSP00000444244:S329R	ENSP00000295718:S419R	S	-	3	2	PTPRN	219873130	0.000000	0.05858	0.001000	0.08648	0.379000	0.30106	-0.764000	0.04735	-0.686000	0.05170	0.459000	0.35465	AGT	A|0.966;C|0.034	0.034	strong		0.627	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2			C	220164886	A	C	220164886	3	2	22	1	0	0	0	0	1	0	0	0	12822	156	6	5	1742	5	PTPRN	2	220164886	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	490404	220164886	23034487	762	3663											
DNPEP	23549	hgsc.bcm.edu	37	chr2	220250769	220250769	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggtgtgggatgcgaagaaTgggccgctccacgtgcacca	9	6	15	11	3	0	1	0	0	0	1	1	3	1	2	3	3	2	2	3	3	2	0	rs6742404	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220250769T>C	ENST00000273075.4	-	6	731	c.511A>G	c.(511-513)Att>Gtt	p.I171V	AC053503.4_ENST00000420563.1_RNA|DNPEP_ENST00000373972.1_Missense_Mutation_p.I96V|DNPEP_ENST00000523282.1_Missense_Mutation_p.I179V	NM_012100.2	NP_036232	Q9ULA0	DNPEP_HUMAN	aspartyl aminopeptidase	161					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)		ATGCGAAGAATGGGCCGCTCC	0.627													T|||	134	0.0267572	0.0961	0.0101	5008	,	,		19551	0.0		0.0	False		,,,				2504	0.0				p.I171V		Atlas-SNP	.											.	DNPEP	40	.	0			c.A511G						PASS	.	T	VAL/ILE	385,3907		26,333,1787	83	94	90		511	3.7	1	2	dbSNP_116	90	1,8519		0,1,4259	yes	missense	DNPEP	NM_012100.2	29	26,334,6046	CC,CT,TT		0.0117,8.9702,3.0128	benign	171/486	220250769	386,12426	2146	4260	6406	SO:0001583	missense	23549	exon6			GAAGAATGGGCCG		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.511A>G	2.37:g.220250769T>C	ENSP00000273075:p.Ile171Val	182	0	0		210	111	0.528571	NM_012100	Q9BW44|Q9NUV5	Missense_Mutation	SNP	ENST00000273075.4	37	CCDS42823.1	43	0.019688644688644688	41	0.08333333333333333	2	0.0055248618784530384	0	0.0	0	0.0	T	12.99	2.104829	0.37145	0.089702	1.17E-4	ENSG00000123992	ENST00000273075;ENST00000337010;ENST00000373972;ENST00000523282;ENST00000535056;ENST00000457935;ENST00000429013;ENST00000521459;ENST00000322176;ENST00000434339;ENST00000430206	.	.	.	4.87	3.71	0.42584	Peptidase M18, domain 2 (1);	0.138463	0.51477	D	0.000095	T	0.03477	0.0100	L	0.46614	1.455	0.49798	D	0.999821	B;B;B;B;B	0.21606	0.005;0.058;0.033;0.005;0.002	B;B;B;B;B	0.24269	0.033;0.052;0.052;0.015;0.02	T	0.04017	-1.0984	9	0.49607	T	0.09	-6.0541	10.134	0.42695	0.0:0.0791:0.0:0.9209	rs6742404	179;171;179;161;171	E7ETB3;B7Z822;B7Z7F0;Q9ULA0;Q53SB6	.;.;.;DNPEP_HUMAN;.	V	171;171;96;179;64;179;157;171;171;96;96	.	ENSP00000273075:I171V	I	-	1	0	DNPEP	219959013	0.580000	0.26733	0.998000	0.56505	0.850000	0.48378	0.182000	0.16900	0.718000	0.32166	0.459000	0.35465	ATT	T|0.962;C|0.038	0.038	strong		0.627	DNPEP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000130212.1	NM_012100		C	220250769	T	C	220250769	3	2	22	1	0	0	0	0	1	0	0	0	4681	1464	51	3	986	3	DNPEP	2	220250769	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	85883	220250769	22948604	763	3664											
DES	1674	hgsc.bcm.edu	37	chr2	220290674	220290674	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttctcttcctccccaggtcGtcagtgaggccacacagcag	7	9	9	16	1	2	1	1	1	1	0	6	1	4	1	4	2	1	1	4	2	0	2	rs73991549	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220290674G>A	ENST00000373960.3	+	9	1461	c.1375G>A	c.(1375-1377)Gtc>Atc	p.V459I	AC053503.6_ENST00000431827.1_RNA	NM_001927.3	NP_001918.3	P17661	DESM_HUMAN	desmin	459	Tail.				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)	p.V459I(1)		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)		TCCCCAGGTCGTCAGTGAGGC	0.607													G|||	49	0.00978435	0.0325	0.0072	5008	,	,		19604	0.0		0.001	False		,,,				2504	0.0				p.V459I		Atlas-SNP	.											DES,brain,glioma,0,2	DES	53	2	1	Substitution - Missense(1)	central_nervous_system(1)	c.G1375A	GRCh37	CM070889	DES	M	rs73991549	PASS	.	G	ILE/VAL	157,4249	107.3+/-145.7	2,153,2048	173	151	158		1375	4.2	1	2	dbSNP_130	158	1,8599	1.2+/-3.3	0,1,4299	yes	missense	DES	NM_001927.3	29	2,154,6347	AA,AG,GG		0.0116,3.5633,1.2148	benign	459/471	220290674	158,12848	2203	4300	6503	SO:0001583	missense	1674	exon9			CAGGTCGTCAGTG	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.1375G>A	2.37:g.220290674G>A	ENSP00000363071:p.Val459Ile	54	0	0		51	26	0.509804	NM_001927	Q15787|Q549R7|Q549R8|Q549R9|Q8IZR1|Q8IZR6|Q8NES2|Q8NEU6|Q8TAC4|Q8TCX2|Q8TD99|Q9UHN5|Q9UJ80	Missense_Mutation	SNP	ENST00000373960.3	37	CCDS33383.1	14	0.00641025641025641	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	8.078	0.771762	0.16051	0.035633	1.16E-4	ENSG00000175084	ENST00000373960	D	0.96913	-4.17	5.17	4.23	0.50019	.	0.000000	0.35207	N	0.003373	T	0.77572	0.4150	L	0.41961	1.31	0.39176	D	0.962688	P	0.36587	0.559	B	0.31547	0.132	D	0.86120	0.1568	10	0.06891	T	0.86	.	13.8879	0.63719	0.0:0.1537:0.8463:0.0	.	459	P17661	DESM_HUMAN	I	459	ENSP00000363071:V459I	ENSP00000363071:V459I	V	+	1	0	DES	219998918	1.000000	0.71417	0.999000	0.59377	0.834000	0.47266	7.003000	0.76310	2.409000	0.81822	0.655000	0.94253	GTC	G|0.989;A|0.011	0.011	strong		0.607	DES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130240.1	NM_001927		A	220290674	G	A	220290674	3	1	22	1	0	0	0	0	1	0	0	0	4451	1145	40	1	1409	1	DES	2	220290674	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	39905	220290674	22908699	764	3665											
SPEG	10290	hgsc.bcm.edu	37	chr2	220347907	220347907	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagcgggtgtgggtgaccAtgcccagaaggccacccccc	8	4	14	15	1	0	3	0	1	0	2	0	3	0	3	6	3	2	0	6	3	1	0	rs200747365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220347907A>G	ENST00000312358.7	+	30	5854	c.5722A>G	c.(5722-5724)Atg>Gtg	p.M1908V	SPEG_ENST00000485813.1_3'UTR|AC053503.11_ENST00000429882.1_RNA	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1908					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)		GTGGGTGACCATGCCCAGAAG	0.672													A|||	9	0.00179712	0.0053	0.0029	5008	,	,		14834	0.0		0.0	False		,,,				2504	0.0				p.M1908V		Atlas-SNP	.											.	SPEG	272	.	0			c.A5722G						PASS	.	A	VAL/MET	26,3634		0,26,1804	8	10	9		5722	2.7	1	2		9	0,8058		0,0,4029	no	missense	SPEG	NM_005876.4	21	0,26,5833	GG,GA,AA		0.0,0.7104,0.2219	benign	1908/3268	220347907	26,11692	1830	4029	5859	SO:0001583	missense	10290	exon30			GTGACCATGCCCA	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.5722A>G	2.37:g.220347907A>G	ENSP00000311684:p.Met1908Val	88	0	0		84	42	0.5	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	37	CCDS42824.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	A	8.935	0.964345	0.18583	0.007104	0.0	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.59772	0.24	4.75	2.74	0.32292	Protein kinase-like domain (1);	0.410582	0.17489	N	0.172415	T	0.11367	0.0277	N	0.00377	-1.585	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.26018	-1.0115	10	0.02654	T	1	.	5.4349	0.16476	0.3428:0.0:0.6572:0.0	.	1908	Q15772	SPEG_HUMAN	V	1908	ENSP00000311684:M1908V	ENSP00000265327:M1908V	M	+	1	0	SPEG	220056151	0.991000	0.36638	0.999000	0.59377	0.966000	0.64601	2.141000	0.42168	0.456000	0.26937	0.374000	0.22700	ATG	A|1.000;G|0.000	0.000	strong		0.672	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		G	220347907	A	G	220347907	3	3	22	1	0	0	0	0	1	0	0	0	15051	217	8	3	5852	3	SPEG	2	220347907	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	57233	220347907	22851466	765	3666											
GMPPA	29926	hgsc.bcm.edu	37	chr2	220370746	220370746	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagggggtgaccgtgggtgaGggtgtgcggctccgggagag	6	6	23	6	3	0	3	0	2	0	1	1	4	1	3	2	6	1	1	2	6	1	0	rs13428617	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220370746G>A	ENST00000358215.3	+	11	1314	c.945G>A	c.(943-945)gaG>gaA	p.E315E	GMPPA_ENST00000341142.3_Silent_p.E315E|GMPPA_ENST00000373917.3_Silent_p.E368E|GMPPA_ENST00000313597.5_Silent_p.E315E|AC053503.11_ENST00000429882.1_RNA|GMPPA_ENST00000373908.1_Silent_p.E315E	NM_205847.2	NP_995319.1	Q96IJ6	GMPPA_HUMAN	GDP-mannose pyrophosphorylase A	315					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)		CCGTGGGTGAGGGTGTGCGGC	0.622													G|||	101	0.0201677	0.0726	0.0058	5008	,	,		17609	0.001		0.0	False		,,,				2504	0.0				p.E315E		Atlas-SNP	.											.	GMPPA	50	.	0			c.G945A						PASS	.	G	,	286,4116		10,266,1925	40	33	36		945,945	3	1	2	dbSNP_121	36	3,8591		0,3,4294	no	coding-synonymous,coding-synonymous	GMPPA	NM_013335.3,NM_205847.2	,	10,269,6219	AA,AG,GG		0.0349,6.497,2.2238	,	315/421,315/421	220370746	289,12707	2201	4297	6498	SO:0001819	synonymous_variant	29926	exon11			GGGTGAGGGTGTG	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.945G>A	2.37:g.220370746G>A		57	0	0		72	32	0.444444	NM_205847	A6NJ74|A8K3Q6|B3KMT4|Q53GI0|Q9NWC3|Q9Y5P5	Silent	SNP	ENST00000358215.3	37	CCDS2441.1																																																																																			G|0.979;A|0.021	0.021	strong		0.622	GMPPA-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130230.1	NM_013335		A	220370746	G	A	220370746	2	1	22	1	0	0	0	0	0	0	0	1	6502	991	35	2		2	GMPPA	2	220370746	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	22839	220370746	22828627	766	3667											
INHA	3623	hgsc.bcm.edu	37	chr2	220439826	220439826	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggaccagaccacccagtggaGgggagagagcccgacgctca	11	2	15	13	2	1	2	1	0	0	2	1	7	1	5	4	4	1	1	4	4	0	0	rs12720061	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220439826G>A	ENST00000243786.2	+	2	859	c.679G>A	c.(679-681)Ggg>Agg	p.G227R		NM_002191.3	NP_002182.1	P05111	INHA_HUMAN	inhibin, alpha	227			G -> R (in dbSNP:rs12720061).		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)		ACCCAGTGGAGGGGAGAGAGC	0.687													G|||	165	0.0329473	0.1225	0.0043	5008	,	,		18962	0.0		0.0	False		,,,				2504	0.0				p.G227R		Atlas-SNP	.											.	INHA	30	.	0			c.G679A	GRCh37	CM041026	INHA	M	rs12720061	PASS	.	G	ARG/GLY	400,4006	195.7+/-220.2	17,366,1820	38	41	40		679	5.5	0.9	2	dbSNP_121	40	4,8596	3.7+/-12.6	0,4,4296	yes	missense	INHA	NM_002191.3	125	17,370,6116	AA,AG,GG		0.0465,9.0785,3.1063	benign	227/367	220439826	404,12602	2203	4300	6503	SO:0001583	missense	3623	exon2			AGTGGAGGGGAGA		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.679G>A	2.37:g.220439826G>A	ENSP00000243786:p.Gly227Arg	121	0	0		139	75	0.539568	NM_002191	A8K8H5	Missense_Mutation	SNP	ENST00000243786.2	37	CCDS2444.1	52	0.023809523809523808	50	0.1016260162601626	2	0.0055248618784530384	0	0.0	0	0.0	G	13.05	2.120959	0.37436	0.090785	4.65E-4	ENSG00000123999	ENST00000243786	D	0.84944	-1.92	5.48	5.48	0.80851	.	0.394385	0.24085	N	0.041686	T	0.08935	0.0221	L	0.41079	1.255	0.25639	N	0.986228	B	0.21905	0.062	B	0.17722	0.019	T	0.16424	-1.0403	9	.	.	.	-13.0624	9.3942	0.38392	0.0778:0.145:0.7772:0.0	rs12720061;rs57625669	227	P05111	INHA_HUMAN	R	227	ENSP00000243786:G227R	.	G	+	1	0	INHA	220148070	0.002000	0.14202	0.937000	0.37676	0.995000	0.86356	1.128000	0.31369	2.564000	0.86499	0.561000	0.74099	GGG	G|0.973;A|0.027	0.027	strong		0.687	INHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131425.1			A	220439826	G	A	220439826	3	1	22	1	0	0	0	0	1	0	0	0	7749	1000	35	2	685	2	INHA	2	220439826	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	69080	220439826	22759547	767	3668											
SCG2	7857	hgsc.bcm.edu	37	chr2	224462714	224462714	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atatcctcaacactgagcccGtctggtagggcctcagtccc	8	9	9	15	1	3	1	2	1	1	0	5	1	5	1	4	2	2	1	4	2	3	2	rs721233	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:224462714G>A	ENST00000305409.2	-	2	1519	c.1287C>T	c.(1285-1287)gaC>gaT	p.D429D		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)		CACTGAGCCCGTCTGGTAGGG	0.468													G|||	277	0.0553115	0.1604	0.0346	5008	,	,		19418	0.001		0.0189	False		,,,				2504	0.0215				p.D429D		Atlas-SNP	.											.	SCG2	99	.	0			c.C1287T						PASS	.	G		663,3743	279.3+/-274.7	49,565,1589	78	78	78		1287	-3.1	0.2	2	dbSNP_86	78	173,8427	78.6+/-141.3	3,167,4130	no	coding-synonymous	SCG2	NM_003469.4		52,732,5719	AA,AG,GG		2.0116,15.0477,6.4278		429/618	224462714	836,12170	2203	4300	6503	SO:0001819	synonymous_variant	7857	exon2			GAGCCCGTCTGGT	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.1287C>T	2.37:g.224462714G>A		86	0	0		79	44	0.556962	NM_003469	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Silent	SNP	ENST00000305409.2	37	CCDS2457.1																																																																																			G|0.932;A|0.068	0.068	strong		0.468	SCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256870.2	NM_003469		A	224462714	G	A	224462714	2	1	22	1	0	0	0	0	0	0	0	1	13906	1136	40	1		1	SCG2	2	224462714	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4022888	224462714	18736659	768	3669											
RHBDD1	84236	hgsc.bcm.edu	37	chr2	227860232	227860232	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cggcttcacagattcgatagCcagtgaggtggcatcttggg	8	10	14	9	2	2	2	1	1	1	1	3	3	2	2	1	4	1	2	1	4	1	4	rs61745917	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:227860232C>T	ENST00000341329.3	+	7	1184	c.942C>T	c.(940-942)agC>agT	p.S314S	RHBDD1_ENST00000392062.2_Silent_p.S314S|RHBDD1_ENST00000493526.1_3'UTR	NM_032276.3	NP_115652.2	Q8TEB9	RHBL4_HUMAN	rhomboid domain containing 1	314	VCP/p97-interacting motif (VIM). {ECO:0000250}.				apoptotic process (GO:0006915)|cellular response to unfolded protein (GO:0034620)|cellular response to UV (GO:0034644)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|membrane protein intracellular domain proteolysis (GO:0031293)|membrane protein proteolysis (GO:0033619)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein processing (GO:0010954)|positive regulation of secretion (GO:0051047)|post-translational protein modification (GO:0043687)|spermatid differentiation (GO:0048515)	endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum quality control compartment (GO:0044322)|integral component of endoplasmic reticulum membrane (GO:0030176)|mitochondrion (GO:0005739)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)			breast(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19		Renal(207;0.023)|all_lung(227;0.13)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;1.47e-11)|all cancers(144;1.52e-08)|Lung(261;0.0128)|LUSC - Lung squamous cell carcinoma(224;0.0175)		GATTCGATAGCCAGTGAGGTG	0.448													C|||	29	0.00579073	0.0212	0.0014	5008	,	,		18839	0.0		0.0	False		,,,				2504	0.0				p.S314S		Atlas-SNP	.											.	RHBDD1	34	.	0			c.C942T						PASS	.	C	,	58,4348	57.4+/-93.9	0,58,2145	67	61	63		942,942	2.4	0.8	2	dbSNP_129	63	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	RHBDD1	NM_001167608.1,NM_032276.3	,	0,58,6445	TT,TC,CC		0.0,1.3164,0.4459	,	314/316,314/316	227860232	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	84236	exon9			CGATAGCCAGTGA	AK074258	CCDS2464.1	2q36.3	2012-07-09			ENSG00000144468	ENSG00000144468			23081	protein-coding gene	gene with protein product						12838346	Standard	NM_032276		Approved	DKFZp547E052	uc002voi.3	Q8TEB9	OTTHUMG00000133178	ENST00000341329.3:c.942C>T	2.37:g.227860232C>T		179	0	0		188	95	0.505319	NM_001167608	Q495B9|Q53S43|Q5EBM8|Q6P5V8|Q8IV60|Q9H057	Silent	SNP	ENST00000341329.3	37	CCDS2464.1																																																																																			C|0.996;T|0.004	0.004	strong		0.448	RHBDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256885.2			T	227860232	C	T	227860232	2	4	22	1	0	0	0	0	0	0	0	1	13331	738	26	2		2	RHBDD1	2	227860232	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3397518	227860232	15339141	769	3670											
SLC19A3	80704	hgsc.bcm.edu	37	chr2	228566993	228566993	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aagcagaggatcacagtgggGtaaatccaggaactgcttag	14	7	13	7	0	1	1	1	0	0	1	2	3	2	3	1	4	3	3	1	4	5	2	rs34080459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:228566993G>A	ENST00000258403.3	-	2	113	c.42C>T	c.(40-42)taC>taT	p.Y14Y	SLC19A3_ENST00000409287.1_Silent_p.Y14Y|SLC19A3_ENST00000541617.1_5'UTR	NM_025243.3	NP_079519.1	Q9BZV2	S19A3_HUMAN	solute carrier family 19 (thiamine transporter), member 3	14					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)	TCACAGTGGGGTAAATCCAGG	0.383													G|||	79	0.0157748	0.0537	0.0086	5008	,	,		19039	0.001		0.001	False		,,,				2504	0.0				p.Y14Y		Atlas-SNP	.											.	SLC19A3	62	.	0			c.C42T						PASS	.	G		221,4185	134.9+/-171.1	6,209,1988	108	115	113		42	1.7	1	2	dbSNP_126	113	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SLC19A3	NM_025243.3		6,210,6287	AA,AG,GG		0.0116,5.0159,1.7069		14/497	228566993	222,12784	2203	4300	6503	SO:0001819	synonymous_variant	80704	exon2			AGTGGGGTAAATC	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.42C>T	2.37:g.228566993G>A		78	0	0		71	34	0.478873	NM_025243		Silent	SNP	ENST00000258403.3	37	CCDS2468.1																																																																																			G|0.982;A|0.018	0.018	strong		0.383	SLC19A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256894.1			A	228566993	G	A	228566993	2	1	22	1	0	0	0	0	0	0	0	1	14445	1256	44	2		2	SLC19A3	2	228566993	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	706761	228566993	14632380	770	3671											
WDR69	164781	hgsc.bcm.edu	37	chr2	228750106	228750106	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaacatggagaattaaagaCtaagtccatagatttgcttg	17	11	8	5	0	0	3	0	0	0	3	1	4	1	3	1	1	2	1	1	1	7	5	rs11894733	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:228750106C>T	ENST00000309931.2	+	2	163	c.80C>T	c.(79-81)aCt>aTt	p.T27I	DAW1_ENST00000373666.2_Missense_Mutation_p.T27I|DAW1_ENST00000545118.1_Missense_Mutation_p.T12I|SNORA25_ENST00000607153.1_RNA	NM_178821.1	NP_849143.1	Q8N136	DAW1_HUMAN	dynein assembly factor with WDR repeat domains 1	27			T -> I (in dbSNP:rs11894733).			cilium (GO:0005929)											GAATTAAAGACTAAGTCCATA	0.343													C|||	299	0.0597045	0.2179	0.0159	5008	,	,		14283	0.0		0.0	False		,,,				2504	0.0				p.T27I		Atlas-SNP	.											.	.	.	.	0			c.C80T						PASS	.	C	ILE/THR	760,3646	307.2+/-289.9	67,626,1510	113	118	116		80	4.6	1	2	dbSNP_120	116	9,8591	7.1+/-27.0	0,9,4291	yes	missense	WDR69	NM_178821.1	89	67,635,5801	TT,TC,CC		0.1047,17.2492,5.9127	possibly-damaging	27/416	228750106	769,12237	2203	4300	6503	SO:0001583	missense	164781	exon2			TAAAGACTAAGTC		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.80C>T	2.37:g.228750106C>T	ENSP00000311899:p.Thr27Ile	70	0	0		67	28	0.41791	NM_178821	Q6ZRY1|Q8N776	Missense_Mutation	SNP	ENST00000309931.2	37	CCDS2470.1	109	0.04990842490842491	102	0.2073170731707317	7	0.019337016574585635	0	0.0	0	0.0	C	12.91	2.079117	0.36662	0.172492	0.001047	ENSG00000123977	ENST00000373666;ENST00000309931;ENST00000440997;ENST00000545118	T;T;T;T	0.53423	0.69;0.64;0.71;0.62	5.52	4.61	0.57282	.	0.172732	0.50627	D	0.000108	T	0.00073	0.0002	M	0.81341	2.54	0.19575	P	0.9999648258	P	0.52170	0.951	P	0.44394	0.448	T	0.08638	-1.0712	9	0.41790	T	0.15	.	10.7579	0.46247	0.0:0.9014:0.0:0.0986	rs11894733;rs52813204;rs56552186;rs58221385;rs11894733	27	Q8N136	WDR69_HUMAN	I	27;27;12;12	ENSP00000362770:T27I;ENSP00000311899:T27I;ENSP00000394853:T12I;ENSP00000437887:T12I	ENSP00000311899:T27I	T	+	2	0	WDR69	228458350	1.000000	0.71417	0.995000	0.50966	0.330000	0.28571	4.893000	0.63199	1.234000	0.43709	0.655000	0.94253	ACT	C|0.939;T|0.061	0.061	strong		0.343	DAW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331745.1	NM_178821		T	228750106	C	T	228750106	3	4	22	1	0	0	0	0	1	0	0	0	17334	565	20	2	86	2	WDR69	2	228750106	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	183113	228750106	14449267	771	3672											
SPHKAP	80309	hgsc.bcm.edu	37	chr2	228882588	228882588	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgagccggggaggcttgtgTttcctcacagcggtcccgct	4	10	14	13	3	1	1	1	1	0	0	3	2	3	2	3	4	2	3	3	4	0	2	rs73994847	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:228882588T>C	ENST00000392056.3	-	7	3028	c.2982A>G	c.(2980-2982)aaA>aaG	p.K994K	SPHKAP_ENST00000344657.5_Silent_p.K994K	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	994						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)		GAGGCTTGTGTTTCCTCACAG	0.537													T|||	177	0.0353435	0.1301	0.0072	5008	,	,		20344	0.0		0.0	False		,,,				2504	0.0				p.K994K		Atlas-SNP	.											.	SPHKAP	750	.	0			c.A2982G						PASS	.	T	,	552,3854	246.8+/-255.3	32,488,1683	83	74	77		2982,2982	-4	1	2	dbSNP_130	77	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	SPHKAP	NM_001142644.1,NM_030623.3	,	32,493,5978	CC,CT,TT		0.0581,12.5284,4.2826	,	994/1701,994/1672	228882588	557,12449	2203	4300	6503	SO:0001819	synonymous_variant	80309	exon7			CTTGTGTTTCCTC		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.2982A>G	2.37:g.228882588T>C		85	0	0		101	53	0.524752	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Silent	SNP	ENST00000392056.3	37	CCDS46537.1																																																																																			T|0.953;C|0.047	0.047	strong		0.537	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		C	228882588	T	C	228882588	2	2	22	1	0	0	0	0	0	0	0	1	15063	1722	60	3		3	SPHKAP	2	228882588	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	132482	228882588	14316785	772	3673											
SP110	3431	hgsc.bcm.edu	37	chr2	231065630	231065630	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccttcgtggtgtactaggcGtcttctgggacctctttcct	3	15	10	13	2	3	0	0	0	3	0	5	1	4	1	3	3	1	1	3	3	2	5	rs59573011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:231065630G>A	ENST00000358662.4	-	10	1178	c.1100C>T	c.(1099-1101)aCg>aTg	p.T367M	SP110_ENST00000540870.1_Missense_Mutation_p.T373M|SP110_ENST00000258381.6_Missense_Mutation_p.T367M|SP110_ENST00000486146.2_5'Flank|SP110_ENST00000392048.3_Missense_Mutation_p.T365M|SP110_ENST00000338556.3_Missense_Mutation_p.T69M|SP110_ENST00000258382.5_Missense_Mutation_p.T367M	NM_004509.3	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein	367			T -> M (in dbSNP:rs59573011). {ECO:0000269|PubMed:16816019}.		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)		TGTACTAGGCGTCTTCTGGGA	0.443													G|||	83	0.0165735	0.0598	0.0058	5008	,	,		18713	0.0		0.0	False		,,,				2504	0.0				p.T373M		Atlas-SNP	.											.	SP110	105	.	0			c.C1118T						PASS	.	G	MET/THR,MET/THR,MET/THR,MET/THR	231,4175	137.7+/-173.5	9,213,1981	228	200	210		1118,1100,1100,1100	-0.6	0	2	dbSNP_129	210	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense,missense	SP110	NM_001185015.1,NM_004509.3,NM_004510.3,NM_080424.2	81,81,81,81	9,215,6279	AA,AG,GG		0.0233,5.2429,1.7915	probably-damaging,probably-damaging,probably-damaging,probably-damaging	373/556,367/690,367/550,367/714	231065630	233,12773	2203	4300	6503	SO:0001583	missense	3431	exon11			CTAGGCGTCTTCT	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.1100C>T	2.37:g.231065630G>A	ENSP00000351488:p.Thr367Met	167	0	0		196	86	0.438776	NM_001185015	B4DVI4|F5H1M1|Q14976|Q14977|Q53TG2|Q8WUZ6|Q9HCT8	Missense_Mutation	SNP	ENST00000358662.4	37	CCDS2474.1	29	0.013278388278388278	26	0.052845528455284556	3	0.008287292817679558	0	0.0	0	0.0	G	12.50	1.957341	0.34565	0.052429	2.33E-4	ENSG00000135899	ENST00000258381;ENST00000358662;ENST00000392048;ENST00000258382;ENST00000540870;ENST00000338556	T;T;T;T;T;T	0.65364	1.07;0.92;-0.15;-0.15;-0.15;2.46	2.49	-0.633	0.11519	.	.	.	.	.	T	0.11580	0.0282	N	0.22421	0.69	0.09310	N	1	D;D;D;D;P	0.67145	0.985;0.996;0.985;0.994;0.512	P;P;P;B;B	0.48030	0.541;0.564;0.541;0.389;0.047	T	0.10730	-1.0617	9	0.51188	T	0.08	.	2.8987	0.05699	0.3085:0.2426:0.4489:0.0	rs59573011	365;69;373;367;367	G5E9C0;E7ER70;F5H1M1;Q9HB58;Q9HB58-6	.;.;.;SP110_HUMAN;.	M	367;367;365;367;373;69	ENSP00000258381:T367M;ENSP00000351488:T367M;ENSP00000375902:T365M;ENSP00000258382:T367M;ENSP00000439558:T373M;ENSP00000344049:T69M	ENSP00000258381:T367M	T	-	2	0	SP110	230773874	0.014000	0.17966	0.025000	0.17156	0.009000	0.06853	-0.059000	0.11731	-0.148000	0.11234	0.557000	0.71058	ACG	G|0.980;A|0.020	0.020	strong		0.443	SP110-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000332414.1	NM_080424		A	231065630	G	A	231065630	3	1	22	1	0	0	0	0	1	0	0	0	14976	1145	40	1	1145	1	SP110	2	231065630	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2183042	231065630	12133743	773	3674											
SP100	6672	hgsc.bcm.edu	37	chr2	231380146	231380146	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagggatgtggaataacaccGctgcagctgacaagcagttt	12	8	12	9	1	0	1	0	1	0	0	0	3	0	3	1	2	4	5	1	2	3	2	rs61733089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:231380146G>A	ENST00000264052.5	+	25	2786	c.2431G>A	c.(2431-2433)Gct>Act	p.A811T	SP100_ENST00000340126.4_Intron	NM_003113.3	NP_003104.2	P23497	SP100_HUMAN	SP100 nuclear antigen	811					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)		GAATAACACCGCTGCAGCTGA	0.433													G|||	41	0.0081869	0.0287	0.0043	5008	,	,		19980	0.0		0.0	False		,,,				2504	0.0				p.A811T		Atlas-SNP	.											.	SP100	167	.	0			c.G2431A						PASS	.	G	,THR/ALA	125,4281	89.2+/-127.9	1,123,2079	47	49	49		,2431	0.2	0.1	2	dbSNP_129	49	0,8600		0,0,4300	yes	intron,missense	SP100	NM_001080391.1,NM_003113.3	,58	1,123,6379	AA,AG,GG		0.0,2.837,0.9611	,	,811/880	231380146	125,12881	2203	4300	6503	SO:0001583	missense	6672	exon25			AACACCGCTGCAG	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.2431G>A	2.37:g.231380146G>A	ENSP00000264052:p.Ala811Thr	80	0	0		78	40	0.512821	NM_003113	B4DDX5|B8ZZD8|E7EUA7|E9PH61|F8WFE2|O75450|Q13343|Q8TE34|Q96F70|Q96T24|Q96T95|Q9NP33|Q9UE32	Missense_Mutation	SNP	ENST00000264052.5	37	CCDS2477.1	13	0.005952380952380952	11	0.022357723577235773	2	0.0055248618784530384	0	0.0	0	0.0	G	9.783	1.175944	0.21704	0.02837	0.0	ENSG00000067066	ENST00000264052	D	0.93189	-3.18	0.158	0.158	0.14942	High mobility group, HMG1/HMG2, subgroup (1);High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	.	.	.	.	T	0.69949	0.3168	L	0.33485	1.01	0.43347	D	0.995409	P	0.42078	0.77	B	0.34346	0.18	T	0.73636	-0.3920	9	0.87932	D	0	.	6.0348	0.19702	5.0E-4:0.0:0.9995:0.0	rs61733089	811	P23497	SP100_HUMAN	T	811	ENSP00000264052:A811T	ENSP00000264052:A811T	A	+	1	0	SP100	231088390	0.000000	0.05858	0.057000	0.19452	0.058000	0.15608	-0.122000	0.10627	0.202000	0.20498	0.205000	0.17691	GCT	G|0.991;A|0.009	0.009	strong		0.433	SP100-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256914.2	NM_003113		A	231380146	G	A	231380146	3	1	22	1	0	0	0	0	1	0	0	0	14975	1087	38	1	2529	1	SP100	2	231380146	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	314516	231380146	11819227	774	3675											
GPR55	9290	hgsc.bcm.edu	37	chr2	231775371	231775371	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacgcttccgtacatgctgaCgaagtaaaggcactccacca	12	7	9	13	3	0	1	0	1	0	0	2	3	2	1	3	1	2	5	3	1	4	3	rs80290067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:231775371C>T	ENST00000392040.1	-	2	499	c.307G>A	c.(307-309)Gtc>Atc	p.V103I	GPR55_ENST00000392039.2_Missense_Mutation_p.V103I|AC012507.4_ENST00000454890.1_RNA	NM_005683.3	NP_005674.2	Q9Y2T6	GPR55_HUMAN	G protein-coupled receptor 55	103					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)		TACATGCTGACGAAGTAAAGG	0.597													c|||	144	0.028754	0.1051	0.0072	5008	,	,		21034	0.0		0.0	False		,,,				2504	0.0				p.V103I		Atlas-SNP	.											.	GPR55	46	.	0			c.G307A						PASS	.	C	ILE/VAL	423,3983	197.1+/-221.3	26,371,1806	66	44	52		307	-5.3	0.7	2	dbSNP_131	52	5,8595	4.3+/-15.6	0,5,4295	yes	missense	GPR55	NM_005683.3	29	26,376,6101	TT,TC,CC		0.0581,9.6005,3.2908	benign	103/320	231775371	428,12578	2203	4300	6503	SO:0001583	missense	9290	exon2			TGCTGACGAAGTA	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.307G>A	2.37:g.231775371C>T	ENSP00000375894:p.Val103Ile	43	0	0		47	20	0.425532	NM_005683	Q8N580	Missense_Mutation	SNP	ENST00000392040.1	37	CCDS2480.1	53	0.024267399267399268	49	0.09959349593495935	4	0.011049723756906077	0	0.0	0	0.0	c	0.687	-0.795929	0.02862	0.096005	5.81E-4	ENSG00000135898	ENST00000392040;ENST00000392039;ENST00000438398	T;T;T	0.72835	-0.69;-0.69;-0.69	5.38	-5.31	0.02730	GPCR, rhodopsin-like superfamily (1);	0.408961	0.25774	N	0.028383	T	0.01254	0.0041	N	0.12569	0.235	0.24899	N	0.992118	B	0.17465	0.022	B	0.15870	0.014	T	0.13442	-1.0509	10	0.02654	T	1	-33.6109	12.2542	0.54615	0.0:0.5177:0.0:0.4823	.	103	Q9Y2T6	GPR55_HUMAN	I	103	ENSP00000375894:V103I;ENSP00000375893:V103I;ENSP00000412768:V103I	ENSP00000375893:V103I	V	-	1	0	GPR55	231483615	0.000000	0.05858	0.728000	0.30774	0.241000	0.25554	-0.686000	0.05161	-0.943000	0.03691	-1.598000	0.00824	GTC	C|0.971;T|0.029	0.029	strong		0.597	GPR55-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332618.1	NM_005683		T	231775371	C	T	231775371	3	4	22	1	0	0	0	0	1	0	0	0	6707	536	19	1	656	1	GPR55	2	231775371	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	395225	231775371	11424002	775	3676											
NCL	4691	hgsc.bcm.edu	37	chr2	232320281	232320281	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcaatttcaccgtcttccatGgcctccttggcagctttggc	5	14	8	14	1	3	0	2	0	1	0	5	0	5	0	4	3	1	2	4	3	1	4	rs78372304	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:232320281G>A	ENST00000322723.4	-	13	2127	c.1887C>T	c.(1885-1887)gcC>gcT	p.A629A	SNORA75_ENST00000384158.1_RNA|SNORD20_ENST00000384550.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	629	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				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)		CGTCTTCCATGGCCTCCTTGG	0.488													.|||	26	0.00519169	0.0189	0.0014	5008	,	,		21137	0.0		0.0	False		,,,				2504	0.0				p.A629A		Atlas-SNP	.											.	NCL	80	.	0			c.C1887T						PASS	.	G		73,4333	65.3+/-102.7	2,69,2132	209	222	218		1887	2.1	1	2	dbSNP_131	218	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	NCL	NM_005381.2		2,71,6430	AA,AG,GG		0.0233,1.6568,0.5767		629/711	232320281	75,12931	2203	4300	6503	SO:0001819	synonymous_variant	4691	exon13			TTCCATGGCCTCC		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.1887C>T	2.37:g.232320281G>A		259	0	0		210	109	0.519048	NM_005381	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	Silent	SNP	ENST00000322723.4	37	CCDS33397.1																																																																																			G|0.994;A|0.006	0.006	strong		0.488	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381		A	232320281	G	A	232320281	2	1	22	1	0	0	0	0	0	0	0	1	10235	1335	47	2		2	NCL	2	232320281	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	544910	232320281	10879092	776	3677											
ALPPL2	251	hgsc.bcm.edu	37	chr2	233271852	233271852	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcagcctgcacagacagcCgccaagaacctcatcatctt	11	7	7	16	1	3	2	2	0	1	2	3	2	3	2	4	0	5	2	4	0	2	1	rs61730280	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:233271852C>T	ENST00000295453.3	+	2	205	c.153C>T	c.(151-153)gcC>gcT	p.A51A		NM_031313.2	NP_112603.2	P10696	PPBN_HUMAN	alkaline phosphatase, placental-like 2	51					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(1)	13		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)	Amifostine(DB01143)	CACAGACAGCCGCCAAGAACC	0.672													c|||	45	0.00898562	0.034	0.0	5008	,	,		15470	0.0		0.0	False		,,,				2504	0.0				p.A51A		Atlas-SNP	.											.	ALPPL2	36	.	0			c.C153T						PASS	.	C		143,4263	100.7+/-139.4	0,143,2060	67	81	76		153	-2.5	0.2	2	dbSNP_129	76	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ALPPL2	NM_031313.2		0,145,6358	TT,TC,CC		0.0233,3.2456,1.1149		51/533	233271852	145,12861	2203	4300	6503	SO:0001819	synonymous_variant	251	exon2			GACAGCCGCCAAG	J04948	CCDS2491.1	2q37	2008-05-20			ENSG00000163286	ENSG00000163286			441	protein-coding gene	gene with protein product		171810					Standard	NM_031313		Approved		uc002vss.4	P10696	OTTHUMG00000133257	ENST00000295453.3:c.153C>T	2.37:g.233271852C>T		93	0	0		116	54	0.465517	NM_031313	A8KAF2|Q16727|Q53S81|Q96CM1	Silent	SNP	ENST00000295453.3	37	CCDS2491.1																																																																																			C|0.990;T|0.010	0.010	strong		0.672	ALPPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257034.2	NM_031313		T	233271852	C	T	233271852	2	4	22	1	0	0	0	0	0	0	0	1	549	639	23	1		1	ALPPL2	2	233271852	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	951571	233271852	9927521	777	3678											
ALPI	248	hgsc.bcm.edu	37	chr2	233323000	233323000	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggcggtcatgttcgacgaCgccattgagagggcgggcca	8	6	17	10	5	1	1	1	1	0	1	2	5	1	1	2	4	0	1	2	4	0	2	rs10195208	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:233323000C>T	ENST00000295463.3	+	9	1142	c.1065C>T	c.(1063-1065)gaC>gaT	p.D355D		NM_001631.3	NP_001622.2	P09923	PPBI_HUMAN	alkaline phosphatase, intestinal	355					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)		TGTTCGACGACGCCATTGAGA	0.627													C|||	253	0.0505192	0.1884	0.0058	5008	,	,		17694	0.0		0.0	False		,,,				2504	0.0				p.D355D		Atlas-SNP	.											ALPI,NS,carcinoma,+2,1	ALPI	64	1	0			c.C1065T						PASS	.	C		624,3782	271.6+/-270.3	39,546,1618	86	76	79		1065	-8.9	0	2	dbSNP_119	79	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	ALPI	NM_001631.3		39,554,5910	TT,TC,CC		0.093,14.1625,4.8593		355/529	233323000	632,12374	2203	4300	6503	SO:0001819	synonymous_variant	248	exon9			CGACGACGCCATT	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.1065C>T	2.37:g.233323000C>T		240	1	0.00416667		266	128	0.481203	NM_001631	B2R7Y4|Q53S80|Q9UBV5|Q9UCL2	Silent	SNP	ENST00000295463.3	37	CCDS2492.1																																																																																			C|0.950;T|0.050	0.050	strong		0.627	ALPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257035.2	NM_001631		T	233323000	C	T	233323000	2	4	22	1	0	0	0	0	0	0	0	1	543	535	19	1		1	ALPI	2	233323000	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	51148	233323000	9876373	778	3679											
NEU2	4759	hgsc.bcm.edu	37	chr2	233899148	233899148	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgacagggcccggagcctggTggtgcccgcctacgcctacc	5	5	14	17	4	0	0	0	0	0	0	0	2	0	1	6	4	4	0	6	4	2	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:233899148T>C	ENST00000233840.3	+	2	524	c.524T>C	c.(523-525)gTg>gCg	p.V175A		NM_005383.2	NP_005374.2	Q9Y3R4	NEUR2_HUMAN	sialidase 2 (cytosolic sialidase)	175					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)	CGGAGCCTGGTGGTGCCCGCC	0.657																																					p.V175A		Atlas-SNP	.											.	NEU2	42	.	0			c.T524C						PASS	.																																			SO:0001583	missense	4759	exon2			GCCTGGTGGTGCC	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.524T>C	2.37:g.233899148T>C	ENSP00000233840:p.Val175Ala	98	0	0		104	48	0.461538	NM_005383	Q3KNW4|Q6NTB4	Missense_Mutation	SNP	ENST00000233840.3	37	CCDS2501.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.120495	0.77323	.	.	ENSG00000115488	ENST00000233840	D	0.85955	-2.05	4.88	4.88	0.63580	Neuraminidase (2);	0.234313	0.29707	N	0.011404	D	0.90113	0.6911	L	0.60455	1.87	0.38849	D	0.956227	D	0.65815	0.995	D	0.70487	0.969	D	0.91831	0.5475	10	0.87932	D	0	-13.5728	13.6972	0.62587	0.0:0.0:0.0:1.0	.	175	Q9Y3R4	NEUR2_HUMAN	A	175	ENSP00000233840:V175A	ENSP00000233840:V175A	V	+	2	0	NEU2	233607392	1.000000	0.71417	0.994000	0.49952	0.610000	0.37248	7.783000	0.85696	1.821000	0.53095	0.459000	0.35465	GTG	.	.	none		0.657	NEU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257053.2	NM_005383		C	233899148	T	C	233899148	3	2	22	1	0	0	0	0	1	0	0	0	10351	1696	59	3	530	3	NEU2	2	233899148	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	576148	233899148	9300225	779	3680											
USP40	55230	hgsc.bcm.edu	37	chr2	234398065	234398065	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggcgcttcctctccaccGtccaggctctgaggtgggct	3	10	13	15	2	2	1	0	1	2	0	5	1	4	1	4	4	0	3	4	4	0	1	rs34026756	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:234398065G>A	ENST00000427112.2	-	26	3109	c.3074C>T	c.(3073-3075)aCg>aTg	p.T1025M	USP40_ENST00000496298.1_5'UTR|USP40_ENST00000450966.1_Missense_Mutation_p.T1037M|USP40_ENST00000251722.6_Missense_Mutation_p.T1025M			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	1025			T -> M (in dbSNP:rs34026756).		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)		CCTCTCCACCGTCCAGGCTCT	0.572													G|||	90	0.0179712	0.0658	0.0043	5008	,	,		17455	0.0		0.0	False		,,,				2504	0.0				p.T1037M		Atlas-SNP	.											USP40_ENST00000450966,NS,carcinoma,+1,2	USP40	174	2	0			c.C3110T						PASS	.	G	MET/THR	242,3748		6,230,1759	34	38	36		3110	4.6	0.9	2	dbSNP_126	36	2,8304		0,2,4151	yes	missense	USP40	NM_018218.2	81	6,232,5910	AA,AG,GG		0.0241,6.0652,1.9844	probably-damaging	1037/1248	234398065	244,12052	1995	4153	6148	SO:0001583	missense	55230	exon26			TCCACCGTCCAGG	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.3074C>T	2.37:g.234398065G>A	ENSP00000387898:p.Thr1025Met	218	1	0.00458716		200	102	0.51	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	37	CCDS46547.1	35|35	0.016025641025641024|0.016025641025641024	34|34	0.06910569105691057|0.06910569105691057	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	G|G	19.02|19.02	3.746166|3.746166	0.69418|0.69418	0.060652|0.060652	2.41E-4|2.41E-4	ENSG00000085982|ENSG00000085982	ENST00000454354;ENST00000430158|ENST00000450966;ENST00000251722;ENST00000427112	.|T;T;T	.|0.05580	.|3.42;3.42;3.42	5.5|5.5	4.57|4.57	0.56435|0.56435	.|.	.|0.947819	.|0.08861	.|N	.|0.883028	T|T	0.01730|0.01730	0.0055|0.0055	M|M	0.66939|0.66939	2.045|2.045	0.32511|0.32511	N|N	0.537508|0.537508	.|D;D	.|0.89917	.|1.0;0.999	.|D;P	.|0.63957	.|0.92;0.878	T|T	0.00967|0.00967	-1.1497|-1.1497	5|10	.|0.59425	.|D	.|0.04	.|.	15.0977|15.0977	0.72247|0.72247	0.0:0.0:0.8577:0.1423|0.0:0.0:0.8577:0.1423	rs34026756|rs34026756	.|1037;685	.|Q9NVE5-3;B4DN96	.|.;.	W|M	15;201|1037;1025;1025	.|ENSP00000415434:T1037M;ENSP00000251722:T1025M;ENSP00000387898:T1025M	.|ENSP00000251722:T1025M	R|T	-|-	1|2	2|0	USP40|USP40	234062804|234062804	1.000000|1.000000	0.71417|0.71417	0.945000|0.945000	0.38365|0.38365	0.606000|0.606000	0.37113|0.37113	3.308000|3.308000	0.51896|0.51896	2.571000|2.571000	0.86741|0.86741	0.650000|0.650000	0.86243|0.86243	CGG|ACG	G|0.985;A|0.015	0.015	strong		0.572	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294		A	234398065	G	A	234398065	3	1	22	1	0	0	0	0	1	0	0	0	17087	1145	40	1	657	1	USP40	2	234398065	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	498917	234398065	8801308	780	3681											
CXCR7	57007	hgsc.bcm.edu	37	chr2	237489796	237489796	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcccttctccattatcgctGtcttctacttcctgctggcc	3	17	5	16	1	3	0	0	0	3	0	7	0	5	0	4	1	2	2	4	1	2	6	rs35095494	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:237489796G>A	ENST00000272928.3	+	2	998	c.688G>A	c.(688-690)Gtc>Atc	p.V230I		NM_020311.2	NP_064707.1	P25106	ACKR3_HUMAN	atypical chemokine receptor 3	230					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)										CATTATCGCTGTCTTCTACTT	0.572													G|||	59	0.0117812	0.0431	0.0029	5008	,	,		21400	0.0		0.0	False		,,,				2504	0.0				p.V230I		Atlas-SNP	.											.	CXCR7	72	.	0			c.G688A						PASS	.	G	ILE/VAL	212,4194	128.6+/-165.4	5,202,1996	103	88	93		688	0.6	0.3	2	dbSNP_126	93	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CXCR7	NM_020311.2	29	5,204,6294	AA,AG,GG		0.0233,4.8116,1.6454	benign	230/363	237489796	214,12792	2203	4300	6503	SO:0001583	missense	57007	exon2			ATCGCTGTCTTCT	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.688G>A	2.37:g.237489796G>A	ENSP00000272928:p.Val230Ile	136	0	0		172	90	0.523256	NM_020311	A8K6J4|Q53RV4|Q8NE10|Q92938|Q92986	Missense_Mutation	SNP	ENST00000272928.3	37	CCDS2516.1	21	0.009615384615384616	20	0.04065040650406504	1	0.0027624309392265192	0	0.0	0	0.0	G	6.438	0.448991	0.12223	0.048116	2.33E-4	ENSG00000144476	ENST00000272928	T	0.37235	1.21	5.7	0.629	0.17687	GPCR, rhodopsin-like superfamily (1);	0.285365	0.33346	N	0.005017	T	0.02807	0.0084	N	0.25245	0.725	0.26027	N	0.981791	B	0.09022	0.002	B	0.14023	0.01	T	0.12142	-1.0559	9	.	.	.	.	5.5847	0.17267	0.3325:0.2292:0.4382:0.0	rs35095494	230	P25106	CXCR7_HUMAN	I	230	ENSP00000272928:V230I	.	V	+	1	0	CXCR7	237154535	0.001000	0.12720	0.276000	0.24689	0.421000	0.31385	-0.112000	0.10791	0.052000	0.16007	-0.140000	0.14226	GTC	G|0.984;A|0.016	0.016	strong		0.572	ACKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257079.2	NM_020311		A	237489796	G	A	237489796	3	1	22	1	0	0	0	0	1	0	0	0	4098	1377	48	2	690	2	CXCR7	2	237489796	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3091731	237489796	5709577	781	3682											
COL6A3	1293	hgsc.bcm.edu	37	chr2	238253332	238253332	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	taggtgaccacagccacccgGgccccccgtgggcagttgct	6	6	13	16	2	0	1	0	1	0	0	0	1	0	1	6	3	2	3	6	3	1	2	rs10084221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:238253332G>A	ENST00000295550.4	-	36	7781	c.7329C>T	c.(7327-7329)gcC>gcT	p.A2443A	COL6A3_ENST00000346358.4_Silent_p.A2243A|COL6A3_ENST00000353578.4_Silent_p.A2237A|COL6A3_ENST00000347401.3_Silent_p.A2242A|COL6A3_ENST00000472056.1_Silent_p.A1836A|COL6A3_ENST00000409809.1_Silent_p.A2237A	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2443	Nonhelical region.|VWFA 11. {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)		CAGCCACCCGGGCCCCCCGTG	0.557													G|||	355	0.0708866	0.2171	0.0375	5008	,	,		19167	0.005		0.0189	False		,,,				2504	0.0184				p.A2443A		Atlas-SNP	.											.	COL6A3	608	.	0			c.C7329T						PASS	.	G	,,	801,3605	296.7+/-284.4	54,693,1456	55	61	59		7329,5508,6711	3.4	1	2	dbSNP_119	59	177,8423	78.6+/-141.3	1,175,4124	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	55,868,5580	AA,AG,GG		2.0581,18.1798,7.5196	,,	2443/3178,1836/2571,2237/2972	238253332	978,12028	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon36			CACCCGGGCCCCC	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.7329C>T	2.37:g.238253332G>A		54	0	0		77	34	0.441558	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			G|0.935;A|0.065	0.065	strong		0.557	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		A	238253332	G	A	238253332	2	1	22	1	0	0	0	0	0	0	0	1	3703	1219	43	2		2	COL6A3	2	238253332	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	763536	238253332	4946041	782	3683											
COL6A3	1293	hgsc.bcm.edu	37	chr2	238289842	238289842	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccggtagccggctgaactcGtgaataggttgttacgaaca	10	9	12	10	4	0	2	0	2	0	0	1	3	0	2	2	3	4	4	2	3	6	4	rs34741387	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:238289842G>A	ENST00000295550.4	-	5	2065	c.1613C>T	c.(1612-1614)aCg>aTg	p.T538M	COL6A3_ENST00000346358.4_Missense_Mutation_p.T538M|COL6A3_ENST00000353578.4_Missense_Mutation_p.T332M|COL6A3_ENST00000347401.3_Missense_Mutation_p.T337M|COL6A3_ENST00000392004.3_Missense_Mutation_p.T332M|COL6A3_ENST00000392003.2_Missense_Mutation_p.T131M|COL6A3_ENST00000472056.1_Missense_Mutation_p.T131M|COL6A3_ENST00000409809.1_Missense_Mutation_p.T332M	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	538	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.		T -> M (in dbSNP:rs34741387).		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.T538K(1)|p.T332K(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)		GGCTGAACTCGTGAATAGGTT	0.552													G|||	44	0.00878594	0.031	0.0043	5008	,	,		18735	0.0		0.0	False		,,,				2504	0.0				p.T538M		Atlas-SNP	.											.	COL6A3	608	.	2	Substitution - Missense(2)	lung(2)	c.C1613T						PASS	.	G	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	115,4291	85.3+/-124.0	1,113,2089	69	80	76		1613,392,995,392,995	3.6	0.5	2	dbSNP_126	76	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense,missense	COL6A3	NM_004369.3,NM_057164.4,NM_057165.4,NM_057166.4,NM_057167.3	81,81,81,81,81	1,114,6388	AA,AG,GG		0.0116,2.6101,0.8919	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	538/3178,131/1037,332/1238,131/2571,332/2972	238289842	116,12890	2203	4300	6503	SO:0001583	missense	1293	exon5			GAACTCGTGAATA	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.1613C>T	2.37:g.238289842G>A	ENSP00000295550:p.Thr538Met	50	0	0		58	33	0.568965	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	G	11.65	1.702027	0.30232	0.026101	1.16E-4	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358;ENST00000392004;ENST00000392003;ENST00000433762	D;D;D;D;D;D;D;D;D	0.84070	-1.8;-1.8;-1.8;-1.8;-1.8;-1.8;-1.8;-1.8;-1.8	5.6	3.62	0.41486	von Willebrand factor, type A (3);	0.360229	0.23277	N	0.049959	T	0.80964	0.4725	M	0.87547	2.89	0.24906	N	0.992072	D;D;D;D;D;D	0.89917	0.999;1.0;0.984;0.998;1.0;0.994	D;D;P;D;D;P	0.79784	0.916;0.993;0.87;0.964;0.99;0.88	T	0.77525	-0.2555	10	0.51188	T	0.08	.	12.068	0.53598	0.0695:0.0:0.8014:0.129	rs34741387	538;131;131;332;332;538	E9PCV6;E9PFQ6;A8MT30;E9PGQ9;P12111-2;P12111	.;.;.;.;.;CO6A3_HUMAN	M	538;337;332;131;332;538;332;131;538	ENSP00000295550:T538M;ENSP00000315609:T337M;ENSP00000315873:T332M;ENSP00000418285:T131M;ENSP00000386844:T332M;ENSP00000295546:T538M;ENSP00000375861:T332M;ENSP00000375860:T131M;ENSP00000389539:T538M	ENSP00000295550:T538M	T	-	2	0	COL6A3	237954581	0.193000	0.23313	0.484000	0.27391	0.010000	0.07245	0.549000	0.23329	1.366000	0.46076	0.655000	0.94253	ACG	G|0.991;A|0.009	0.009	strong		0.552	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		A	238289842	G	A	238289842	3	1	22	1	0	0	0	0	1	0	0	0	3703	1145	40	1	8127	1	COL6A3	2	238289842	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	36510	238289842	4909531	783	3684											
RBM44	375316	hgsc.bcm.edu	37	chr2	238725833	238725833	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcaagatactaacacagagAgtactcagtttcagtcaagt	15	10	8	8	0	4	2	4	0	0	2	4	3	4	2	0	0	3	2	0	0	5	4	rs73086770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:238725833A>G	ENST00000409864.1	+	3	528	c.274A>G	c.(274-276)Agt>Ggt	p.S92G	RBM44_ENST00000444524.2_Intron|RBM44_ENST00000316997.4_Missense_Mutation_p.S92G			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	91						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)		TAACACAGAGAGTACTCAGTT	0.323													A|||	182	0.0363419	0.1286	0.0144	5008	,	,		19482	0.0		0.002	False		,,,				2504	0.0				p.S92G		Atlas-SNP	.											.	RBM44	167	.	0			c.A274G						PASS	.	A	GLY/SER	365,3309		23,319,1495	60	60	60		274	3.2	0	2	dbSNP_130	60	19,8129		0,19,4055	yes	missense	RBM44	NM_001080504.2	56	23,338,5550	GG,GA,AA		0.2332,9.9347,3.2482	possibly-damaging	92/1053	238725833	384,11438	1837	4074	5911	SO:0001583	missense	375316	exon3			ACAGAGAGTACTC	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.274A>G	2.37:g.238725833A>G	ENSP00000386727:p.Ser92Gly	185	0	0		213	85	0.399061	NM_001080504	A0AUW3	Missense_Mutation	SNP	ENST00000409864.1	37	CCDS46554.1	88	0.040293040293040296	79	0.16056910569105692	8	0.022099447513812154	0	0.0	1	0.0013192612137203166	A	9.408	1.079719	0.20309	0.099347	0.002332	ENSG00000177483	ENST00000316997;ENST00000409864	T;T	0.33216	1.42;1.42	5.62	3.15	0.36227	.	0.588960	0.17242	N	0.181502	T	0.00073	0.0002	L	0.39898	1.24	0.80722	P	0.0	P	0.49090	0.919	B	0.39339	0.297	T	0.11941	-1.0567	9	0.32370	T	0.25	-3.005	9.875	0.41197	0.6671:0.3329:0.0:0.0	.	91	Q6ZP01	RBM44_HUMAN	G	92	ENSP00000321179:S92G;ENSP00000386727:S92G	ENSP00000321179:S92G	S	+	1	0	RBM44	238390572	0.000000	0.05858	0.000000	0.03702	0.785000	0.44390	0.011000	0.13264	0.374000	0.24650	0.460000	0.39030	AGT	A|0.967;G|0.033	0.033	strong		0.323	RBM44-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328733.2	NM_001080504		G	238725833	A	G	238725833	3	3	22	1	0	0	0	0	1	0	0	0	13153	304	11	3	280	3	RBM44	2	238725833	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	435991	238725833	4473540	784	3685											
TRAF3IP1	26146	hgsc.bcm.edu	37	chr2	239237783	239237783	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagacagaggcaacagggagCgggacagagactccgagcgc	14	1	16	10	3	0	3	0	0	0	3	1	7	1	5	1	3	3	1	1	3	2	0	rs34723381	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:239237783C>T	ENST00000373327.4	+	5	937	c.715C>T	c.(715-717)Cgg>Tgg	p.R239W	TRAF3IP1_ENST00000391994.2_Missense_Mutation_p.R239W|TRAF3IP1_ENST00000391993.3_Missense_Mutation_p.R239W	NM_015650.3	NP_056465.2	Q8TDR0	MIPT3_HUMAN	TNF receptor-associated factor 3 interacting protein 1	239	Abolishes microtubules-binding when missing.|Arg-rich.|DISC1-interaction domain.		R -> W (in dbSNP:rs34723381).		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)		caacagggagcgggacagaga	0.597													C|||	228	0.0455272	0.1611	0.0216	5008	,	,		16990	0.0		0.0	False		,,,				2504	0.0				p.R239W		Atlas-SNP	.											.	TRAF3IP1	58	.	0			c.C715T						PASS	.	C	TRP/ARG,TRP/ARG	516,3828		27,462,1683	71	72	72		715,715	3.2	0.1	2	dbSNP_126	72	8,8478		0,8,4235	yes	missense,missense	TRAF3IP1	NM_001139490.1,NM_015650.3	101,101	27,470,5918	TT,TC,CC		0.0943,11.8785,4.0842	probably-damaging,probably-damaging	239/626,239/692	239237783	524,12306	2172	4243	6415	SO:0001583	missense	26146	exon5			AGGGAGCGGGACA	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.715C>T	2.37:g.239237783C>T	ENSP00000362424:p.Arg239Trp	142	0	0		132	55	0.416667	NM_015650	Q6PCT1|Q7L8N9|Q9NRD6|Q9Y4Q1	Missense_Mutation	SNP	ENST00000373327.4	37	CCDS33415.1	101	0.04624542124542125	91	0.18495934959349594	10	0.027624309392265192	0	0.0	0	0.0	C	15.99	2.996440	0.54147	0.118785	9.43E-4	ENSG00000204104	ENST00000391993;ENST00000373327;ENST00000391994;ENST00000440998	T;T;T	0.15372	2.43;2.43;2.43	4.12	3.17	0.36434	.	0.811391	0.10616	N	0.653948	T	0.00073	0.0002	M	0.61703	1.905	0.46096	P	0.0011360000000000259	D;D	0.69078	0.997;0.997	P;P	0.55055	0.656;0.767	T	0.10847	-1.0612	9	0.72032	D	0.01	-4.3779	12.5493	0.56218	0.0:0.7311:0.2689:0.0	rs34723381	239;239	Q8TDR0-2;Q8TDR0	.;MIPT3_HUMAN	W	239	ENSP00000375851:R239W;ENSP00000362424:R239W;ENSP00000375852:R239W	ENSP00000362424:R239W	R	+	1	2	TRAF3IP1	238902522	0.112000	0.22096	0.055000	0.19348	0.014000	0.08584	0.585000	0.23879	2.023000	0.59567	0.467000	0.42956	CGG	C|0.950;T|0.050	0.050	strong		0.597	TRAF3IP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328312.1	NM_015650		T	239237783	C	T	239237783	3	4	22	1	0	0	0	0	1	0	0	0	16455	759	27	1	733	1	TRAF3IP1	2	239237783	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	511950	239237783	3961590	785	3686											
HDAC4	9759	hgsc.bcm.edu	37	chr2	240003873	240003873	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gacatgtacaggacgctgggGtcgctgtagaaagcctgctg	9	8	15	9	2	0	1	0	0	0	1	1	3	0	2	1	3	3	5	1	3	3	2	rs10168964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:240003873G>A	ENST00000345617.3	-	21	3353	c.2562C>T	c.(2560-2562)gaC>gaT	p.D854D	HDAC4_ENST00000543185.1_Silent_p.D438D	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	854	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)		GGACGCTGGGGTCGCTGTAGA	0.587													G|||	381	0.0760783	0.2799	0.0159	5008	,	,		15695	0.0		0.0	False		,,,				2504	0.0				p.D854D		Atlas-SNP	.											.	HDAC4	127	.	0			c.C2562T						PASS	.	G		1088,3318	396.7+/-330.2	134,820,1249	172	156	161		2562	3	1	2	dbSNP_119	161	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	HDAC4	NM_006037.3		134,826,5543	AA,AG,GG		0.0698,24.6936,8.4115		854/1085	240003873	1094,11912	2203	4300	6503	SO:0001819	synonymous_variant	9759	exon21			GCTGGGGTCGCTG	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.2562C>T	2.37:g.240003873G>A		243	0	0		326	324	0.993865	NM_006037	Q9UND6	Silent	SNP	ENST00000345617.3	37	CCDS2529.1																																																																																			G|0.924;A|0.076	0.076	strong		0.587	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037		A	240003873	G	A	240003873	2	1	22	1	0	0	0	0	0	0	0	1	7018	1252	44	2		2	HDAC4	2	240003873	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	766090	240003873	3195500	786	3687											
HDAC4	9759	hgsc.bcm.edu	37	chr2	240111556	240111556	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctcgtggagctgcgcctcGtgctgccgggagagctgctc	3	9	16	13	4	0	1	0	0	0	1	3	3	0	2	2	2	7	5	2	2	0	0	rs6740794	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:240111556G>A	ENST00000345617.3	-	4	1103	c.312C>T	c.(310-312)caC>caT	p.H104H	HDAC4_ENST00000541256.1_Silent_p.H73H	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	104					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)		GCTGCGCCTCGTGCTGCCGGG	0.677													g|||	239	0.0477236	0.171	0.0173	5008	,	,		14486	0.0		0.001	False		,,,				2504	0.0				p.H104H		Atlas-SNP	.											HDAC4,colon,carcinoma,0,1	HDAC4	127	1	0			c.C312T						PASS	.	A		671,3735	265.6+/-266.7	50,571,1582	30	27	28		312	-0.9	1	2	dbSNP_116	28	12,8588	7.1+/-27.0	0,12,4288	no	coding-synonymous	HDAC4	NM_006037.3		50,583,5870	AA,AG,GG		0.1395,15.2292,5.2514		104/1085	240111556	683,12323	2203	4300	6503	SO:0001819	synonymous_variant	9759	exon4			CGCCTCGTGCTGC	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.312C>T	2.37:g.240111556G>A		83	0	0		115	54	0.469565	NM_006037	Q9UND6	Silent	SNP	ENST00000345617.3	37	CCDS2529.1																																																																																			G|0.938;A|0.062	0.062	strong		0.677	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037		A	240111556	G	A	240111556	2	1	22	1	0	0	0	0	0	0	0	1	7018	1136	40	1		1	HDAC4	2	240111556	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	107683	240111556	3087817	787	3688											
PRR21	643905	hgsc.bcm.edu	37	chr2	240981362	240981362	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagctgtggctgaagaggcgTagatgaagagacttggatga	12	8	17	4	1	0	6	0	3	0	3	0	9	0	7	0	3	1	3	0	3	3	2	rs115420937	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:240981362T>C	ENST00000408934.1	-	1	1037	c.1038A>G	c.(1036-1038)ctA>ctG	p.L346L		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	346										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						TGAAGAGGCGTAGATGAAGAG	0.562													t|||	43	0.00858626	0.031	0.0029	5008	,	,		22045	0.0		0.0	False		,,,				2504	0.0				p.L346L		Atlas-SNP	.											.	PRR21	53	.	0			c.A1038G						PASS	.	T		100,4306	80.4+/-118.8	3,94,2106	145	128	134		1038	-1	0	2	dbSNP_132	134	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	PRR21	NM_001080835.1		3,98,6402	CC,CT,TT		0.0465,2.2696,0.7996		346/390	240981362	104,12902	2203	4300	6503	SO:0001819	synonymous_variant	643905	exon1			GAGGCGTAGATGA	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.1038A>G	2.37:g.240981362T>C		144	0	0		133	57	0.428571	NM_001080835		Silent	SNP	ENST00000408934.1	37	CCDS33417.1																																																																																			T|0.992;C|0.008	0.008	strong		0.562	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835		C	240981362	T	C	240981362	2	2	22	1	0	0	0	0	0	0	0	1	12604	1625	57	3		3	PRR21	2	240981362	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	869806	240981362	2218011	788	3689											
PRR21	643905	hgsc.bcm.edu	37	chr2	240982009	240982009	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gcatggaggaagggccgtggGtgaagaggcatggacgaagg	11	4	21	5	2	0	2	0	1	0	1	0	6	0	5	1	7	0	2	1	7	3	0	rs202192655		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:240982009G>A	ENST00000408934.1	-	1	390	c.391C>T	c.(391-393)Ccc>Tcc	p.P131S		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	131	Pro-rich.							p.P131S(2)		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						AGGGCCGTGGGTGAAGAGGCA	0.647																																					p.P131S		Atlas-SNP	.											PRR21,NS,malignant_melanoma,0,2	PRR21	53	2	2	Substitution - Missense(2)	NS(2)	c.C391T						scavenged	.						4	3	3					2																	240982009		1301	2740	4041	SO:0001583	missense	643905	exon1			CCGTGGGTGAAGA	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.391C>T	2.37:g.240982009G>A	ENSP00000386166:p.Pro131Ser	35	0	0		12	2	0.166667	NM_001080835		Missense_Mutation	SNP	ENST00000408934.1	37	CCDS33417.1	.	.	.	.	.	.	.	.	.	.	-	0.018	-1.469388	0.01044	.	.	ENSG00000221961	ENST00000408934;ENST00000486799	T;T	0.13307	2.6;2.6	1.73	-3.03	0.05429	.	.	.	.	.	T	0.10766	0.0263	N	0.08118	0	0.09310	N	1	D	0.63880	0.993	P	0.61940	0.896	T	0.12993	-1.0526	9	0.10111	T	0.7	.	7.6745	0.28478	0.3709:0.0:0.6291:0.0	.	131	Q8WXC7	PRR21_HUMAN	S	131	ENSP00000386166:P131S;ENSP00000418240:P131S	ENSP00000386166:P131S	P	-	1	0	PRR21	240630682	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.053000	0.03500	-0.874000	0.04027	-0.481000	0.04817	CCC	.	.	weak		0.647	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835		A	240982009	G	A	240982009	3	1	22	1	0	0	0	0	1	0	0	0	12604	1261	44	2	781	2	PRR21	2	240982009	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	647	240982009	2217364	789	3690											
PRR21	643905	hgsc.bcm.edu	37	chr2	240982200	240982200	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagagccgtgggtgaagggaCatgggtgaagagccgtggat	11	6	19	5	2	0	4	0	2	0	2	0	6	0	6	2	4	2	0	2	4	3	0	rs114958540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:240982200C>T	ENST00000408934.1	-	1	199	c.200G>A	c.(199-201)tGt>tAt	p.C67Y		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	67	Pro-rich.									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						GGTGAAGGGACATGGGTGAAG	0.607													N|||	410	0.081869	0.0651	0.0605	5008	,	,		14426	0.1677		0.0666	False		,,,				2504	0.047				p.C67Y		Atlas-SNP	.											PRR21,NS,carcinoma,+1,2	PRR21	53	2	0			c.G200A						scavenged	.						136	123	127					2																	240982200		2202	4300	6502	SO:0001583	missense	643905	exon1			AAGGGACATGGGT	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.200G>A	2.37:g.240982200C>T	ENSP00000386166:p.Cys67Tyr	147	2	0.0136054		170	10	0.0588235	NM_001080835		Missense_Mutation	SNP	ENST00000408934.1	37	CCDS33417.1	.	.	.	.	.	.	.	.	.	.	N	2.358	-0.347289	0.05208	.	.	ENSG00000221961	ENST00000408934;ENST00000486799	T;T	0.13420	2.59;2.59	1.46	-2.3	0.06785	.	.	.	.	.	T	0.05731	0.0150	N	0.08118	0	0.09310	N	1	B	0.21071	0.051	B	0.15870	0.014	T	0.43637	-0.9379	9	0.19590	T	0.45	.	8.228	0.31582	0.0:0.7349:0.0:0.2651	.	67	Q8WXC7	PRR21_HUMAN	Y	67	ENSP00000386166:C67Y;ENSP00000418240:C67Y	ENSP00000386166:C67Y	C	-	2	0	PRR21	240630873	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.852000	0.04308	-0.717000	0.04955	-1.756000	0.00673	TGT	C|0.980;T|0.019	0.019	strong		0.607	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835		T	240982200	C	T	240982200	3	4	22	1	0	0	0	0	1	0	0	0	12604	478	17	2	972	2	PRR21	2	240982200	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	191	240982200	2217173	790	3691											
GPC1	2817	hgsc.bcm.edu	37	chr2	241404914	241404914	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccccgaggtcatgggtgaCggcctggccaaccagatcaa	9	6	12	14	2	2	2	2	1	0	1	3	3	3	2	5	4	1	0	5	4	2	0	rs2228329	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:241404914C>T	ENST00000264039.2	+	8	1541	c.1293C>T	c.(1291-1293)gaC>gaT	p.D431D		NM_002081.2	NP_002072.2	P35052	GPC1_HUMAN	glypican 1	431					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)		TCATGGGTGACGGCCTGGCCA	0.612													C|||	59	0.0117812	0.0416	0.0058	5008	,	,		19053	0.0		0.0	False		,,,				2504	0.0				p.D431D		Atlas-SNP	.											.	GPC1	32	.	0			c.C1293T						PASS	.	C		128,4278	93.0+/-131.7	2,124,2077	92	77	82		1293	-2.5	1	2	dbSNP_98	82	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GPC1	NM_002081.2		2,125,6376	TT,TC,CC		0.0116,2.9051,0.9918		431/559	241404914	129,12877	2203	4300	6503	SO:0001819	synonymous_variant	2817	exon8			GGGTGACGGCCTG	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.1293C>T	2.37:g.241404914C>T		117	0	0		115	54	0.469565	NM_002081	B3KTD1|Q53QM4	Silent	SNP	ENST00000264039.2	37	CCDS2534.1	17	0.007783882783882784	15	0.03048780487804878	2	0.0055248618784530384	0	0.0	0	0.0	C	2.512	-0.312638	0.05422	0.029051	1.16E-4	ENSG00000063660	ENST00000420138;ENST00000455111	.	.	.	3.56	-2.52	0.06346	.	.	.	.	.	T	0.29389	0.0732	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40459	-0.9562	4	.	.	.	-27.9108	9.046	0.36347	0.0:0.2401:0.0:0.7599	rs2228329;rs2228329	.	.	.	W	471;183	.	.	R	+	1	2	GPC1	241053587	0.000000	0.05858	0.965000	0.40720	0.315000	0.28087	-3.267000	0.00533	-0.465000	0.06953	-0.269000	0.10298	CGG	C|0.991;T|0.009	0.009	strong		0.612	GPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257179.3	NM_002081		T	241404914	C	T	241404914	2	4	22	1	0	0	0	0	0	0	0	1	6605	535	19	1		1	GPC1	2	241404914	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	422714	241404914	1794459	791	3692											
GPR35	2859	hgsc.bcm.edu	37	chr2	241569535	241569535	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagcagtggacggagaccCgcatctacatgaccaacctg	11	6	11	13	2	1	2	0	1	1	1	1	4	1	3	3	2	4	3	3	2	2	1	rs115880579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:241569535C>T	ENST00000319838.5	+	6	1108	c.166C>T	c.(166-168)Cgc>Tgc	p.R56C	GPR35_ENST00000407714.1_Missense_Mutation_p.R56C|GPR35_ENST00000430267.1_Missense_Mutation_p.R56C|GPR35_ENST00000403859.1_Missense_Mutation_p.R56C|GPR35_ENST00000438013.2_Missense_Mutation_p.R87C	NM_001195381.1	NP_001182310.1	Q9HC97	GPR35_HUMAN	G protein-coupled receptor 35	56					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)		GACGGAGACCCGCATCTACAT	0.642													C|||	29	0.00579073	0.0204	0.0029	5008	,	,		18411	0.0		0.0	False		,,,				2504	0.0				p.R87C		Atlas-SNP	.											GPR35,NS,malignant_melanoma,-1,1	GPR35	43	1	0			c.C259T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG	72,4334	65.3+/-102.7	1,70,2132	103	89	94		259,259,166	3.1	0.2	2	dbSNP_132	94	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense,missense	GPR35	NM_001195381.1,NM_001195382.1,NM_005301.3	180,180,180	1,74,6428	TT,TC,CC		0.0465,1.6341,0.5843	probably-damaging,probably-damaging,probably-damaging	87/341,87/341,56/310	241569535	76,12930	2203	4300	6503	SO:0001583	missense	2859	exon6			GAGACCCGCATCT		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.166C>T	2.37:g.241569535C>T	ENSP00000322731:p.Arg56Cys	94	0	0		60	27	0.45	NM_001195382	J3KR30|O43495|Q17R58|Q4VBN5|Q4ZFV2|Q6FHI8|Q86UH4	Missense_Mutation	SNP	ENST00000319838.5	37	CCDS2541.1	16	0.007326007326007326	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	0	0.0	C	15.47	2.843986	0.51164	0.016341	4.65E-4	ENSG00000178623	ENST00000319838;ENST00000403859;ENST00000438013;ENST00000407714;ENST00000430267	T;T;T;T;T	0.37915	1.17;1.17;1.17;1.17;1.17	4.02	3.06	0.35304	GPCR, rhodopsin-like superfamily (1);	0.640810	0.14659	N	0.306078	T	0.33614	0.0869	M	0.79693	2.465	0.09310	N	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.992;0.991;0.991	T	0.14980	-1.0453	10	0.54805	T	0.06	-20.0686	9.7984	0.40748	0.0:0.6693:0.3307:0.0	.	141;87;56	Q6ZMP9;A8K2J1;Q9HC97	.;.;GPR35_HUMAN	C	56;56;87;56;56	ENSP00000322731:R56C;ENSP00000385140:R56C;ENSP00000415890:R87C;ENSP00000384263:R56C;ENSP00000411788:R56C	ENSP00000322731:R56C	R	+	1	0	GPR35	241218208	0.000000	0.05858	0.235000	0.24058	0.783000	0.44284	-0.829000	0.04415	2.250000	0.74265	0.462000	0.41574	CGC	C|0.993;T|0.007	0.007	strong		0.642	GPR35-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325631.1	NM_001195382		T	241569535	C	T	241569535	3	4	22	1	0	0	0	0	1	0	0	0	6698	652	23	1	168	1	GPR35	2	241569535	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	164621	241569535	1629838	792	3693											
AQP12B	653437	hgsc.bcm.edu	37	chr2	241622008	241622008	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgtccaaggtgaccccgtGcgccaggaagagcaggaaga	11	3	14	13	3	0	3	0	1	0	2	1	5	1	5	5	3	2	1	5	3	3	0	rs187845451	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:241622008G>A	ENST00000407834.3	-	1	309	c.247C>T	c.(247-249)Cac>Tac	p.H83Y		NM_001102467.1	NP_001095937.1	A6NM10	AQ12B_HUMAN	aquaporin 12B	71						integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|lung(8)|ovary(1)	13		all_epithelial(40;1.71e-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;2.2e-31)|all cancers(36;1.08e-28)|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;7.52e-06)|Lung(119;0.00163)|LUSC - Lung squamous cell carcinoma(224;0.008)|Colorectal(34;0.0124)|COAD - Colon adenocarcinoma(134;0.0757)		GTGACCCCGTGCGCCAGGAAG	0.672													N|||	54	0.0107827	0.0408	0.0	5008	,	,		18265	0.0		0.0	False		,,,				2504	0.0				p.H83Y		Atlas-SNP	.											AQP12B,colon,carcinoma,+2,1	AQP12B	33	1	0			c.C247T						PASS	.		TYR/HIS	141,4265		1,139,2063	50	51	50		247	2.5	0.5	2		50	0,8598		0,0,4299	no	missense	AQP12B	NM_001102467.1	83	1,139,6362	AA,AG,GG		0.0,3.2002,1.0843	probably-damaging	83/308	241622008	141,12863	2203	4299	6502	SO:0001583	missense	653437	exon1			CCCCGTGCGCCAG	BC041460	CCDS46560.1	2q37.3	2007-12-14	2005-05-26	2005-05-26	ENSG00000185176	ENSG00000185176		"Ion channels / Aquaporins"	6096	protein-coding gene	gene with protein product			"insulin synthesis associated 3"	INSSA3			Standard	NM_001102467		Approved		uc010fzj.3	A6NM10	OTTHUMG00000152263	ENST00000407834.3:c.247C>T	2.37:g.241622008G>A	ENSP00000384894:p.His83Tyr	165	0	0		245	98	0.4	NM_001102467	A4QPB9	Missense_Mutation	SNP	ENST00000407834.3	37	CCDS46560.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	.	13.39	2.223741	0.39300	0.032002	0.0	ENSG00000185176	ENST00000407834	T	0.14516	2.5	2.53	2.53	0.30540	.	0.000000	0.85682	D	0.000000	T	0.10380	0.0254	M	0.80982	2.52	0.44547	D	0.997501	D	0.89917	1.0	D	0.87578	0.998	T	0.02053	-1.1222	9	.	.	.	-1.4545	11.1973	0.48719	0.0:0.0:1.0:0.0	.	83	A6NM10-2	.	Y	83	ENSP00000384894:H83Y	.	H	-	1	0	AQP12B	241270681	1.000000	0.71417	0.528000	0.27938	0.035000	0.12851	8.195000	0.89723	1.720000	0.51447	0.479000	0.44913	CAC	G|0.991;A|0.009	0.009	strong		0.672	AQP12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325625.1			A	241622008	G	A	241622008	3	1	22	1	0	0	0	0	1	0	0	0	825	1319	46	2	688	2	AQP12B	2	241622008	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	52473	241622008	1577365	793	3694											
C2orf54	79919	hgsc.bcm.edu	37	chr2	241835110	241835110	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ataattcaaggccatcctccGgctgggtggcctctggttcc	6	11	11	13	1	2	0	1	0	1	0	5	0	5	0	5	5	0	2	5	5	2	3	rs146162100	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:241835110G>A	ENST00000388934.4	-	1	463	c.305C>T	c.(304-306)cCg>cTg	p.P102L		NM_001085437.1	NP_001078906	Q08AI8	CB054_HUMAN	chromosome 2 open reading frame 54	102										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)		GCCATCCTCCGGCTGGGTGGC	0.637													G|||	47	0.00938498	0.0348	0.0	5008	,	,		21036	0.0		0.0	False		,,,				2504	0.001				p.P102L		Atlas-SNP	.											.	C2orf54	14	.	0			c.C305T						PASS	.	G	LEU/PRO	108,3930		1,106,1912	39	43	42		305	2	0	2	dbSNP_134	42	0,8320		0,0,4160	yes	missense	C2orf54	NM_001085437.1	98	1,106,6072	AA,AG,GG		0.0,2.6746,0.8739	benign	102/448	241835110	108,12250	2019	4160	6179	SO:0001583	missense	79919	exon1			TCCTCCGGCTGGG	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.305C>T	2.37:g.241835110G>A	ENSP00000373586:p.Pro102Leu	143	0	0		142	68	0.478873	NM_001085437	B3KPP9|H7BXM3|Q08AI9|Q53QU5|Q9H622	Missense_Mutation	SNP	ENST00000388934.4	37	CCDS42839.1	21	0.009615384615384616	21	0.042682926829268296	0	0.0	0	0.0	0	0.0	G	4.191	0.034120	0.08101	0.026746	0.0	ENSG00000172478	ENST00000388934;ENST00000414499;ENST00000454476	T;T;T	0.11495	2.77;2.77;2.77	4.87	2.03	0.26663	.	0.889113	0.09556	N	0.786255	T	0.01730	0.0055	L	0.40543	1.245	0.09310	N	1	B	0.18461	0.028	B	0.13407	0.009	T	0.40021	-0.9585	10	0.27082	T	0.32	4.8878	4.8735	0.13644	0.2407:0.0:0.558:0.2014	.	102	Q08AI8	CB054_HUMAN	L	102;102;92	ENSP00000373586:P102L;ENSP00000390935:P102L;ENSP00000394874:P92L	ENSP00000373586:P102L	P	-	2	0	C2orf54	241483783	0.000000	0.05858	0.001000	0.08648	0.047000	0.14425	-0.397000	0.07269	0.474000	0.27392	0.561000	0.74099	CCG	G|0.990;A|0.010	0.010	strong		0.637	C2orf54-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324353.1	NM_024861, NM_001085437		A	241835110	G	A	241835110	3	1	22	1	0	0	0	0	1	0	0	0	2177	1116	39	1	1072	1	C2orf54	2	241835110	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	213102	241835110	1364263	794	3695											
SNED1	25992	hgsc.bcm.edu	37	chr2	242012729	242012729	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	catggaggaagcccccaagcGggtcagcctggccctccagc	8	4	13	16	1	1	0	1	0	0	0	2	2	2	2	5	4	4	0	5	4	2	0	rs6721345	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242012729G>A	ENST00000310397.8	+	27	3866	c.3866G>A	c.(3865-3867)cGg>cAg	p.R1289Q	MTERFD2_ENST00000464344.2_5'UTR|SNED1_ENST00000401884.1_Missense_Mutation_p.R1289Q|SNED1_ENST00000405547.3_Intron|SNED1_ENST00000342631.6_Intron	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	1289			R -> Q (in dbSNP:rs6721345).		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)		GCCCCCAAGCGGGTCAGCCTG	0.637													A|||	170	0.0339457	0.1218	0.013	5008	,	,		18018	0.0		0.0	False		,,,				2504	0.0				p.R1289Q		Atlas-SNP	.											.	SNED1	76	.	0			c.G3866A						PASS	.	A	GLN/ARG	389,3689		21,347,1671	23	30	27		3866	-1.4	0	2	dbSNP_116	27	1,8307		0,1,4153	yes	missense	SNED1	NM_001080437.1	43	21,348,5824	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	0.012,9.539,3.1487	benign	1289/1414	242012729	390,11996	2039	4154	6193	SO:0001583	missense	25992	exon27			CCAAGCGGGTCAG	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.3866G>A	2.37:g.242012729G>A	ENSP00000308893:p.Arg1289Gln	150	0	0		161	72	0.447205	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Missense_Mutation	SNP	ENST00000310397.8	37	CCDS46562.1	55	0.025183150183150184	50	0.1016260162601626	5	0.013812154696132596	0	0.0	0	0.0	A	1.776	-0.483082	0.04383	0.09539	1.2E-4	ENSG00000162804	ENST00000401884;ENST00000310397	D;D	0.82433	-1.61;-1.58	4.46	-1.35	0.09114	.	0.544077	0.15478	N	0.260251	T	0.01627	0.0052	N	0.00583	-1.355	0.09310	N	1	B;B	0.12630	0.006;0.002	B;B	0.06405	0.002;0.001	T	0.20207	-1.0282	10	0.10111	T	0.7	.	6.6262	0.22830	0.1901:0.5219:0.288:0.0	rs6721345;rs6721345	1289;1289	Q8TER0-5;Q8TER0	.;SNED1_HUMAN	Q	1289	ENSP00000384871:R1289Q;ENSP00000308893:R1289Q	ENSP00000308893:R1289Q	R	+	2	0	SNED1	241661402	0.000000	0.05858	0.018000	0.16275	0.715000	0.41141	0.261000	0.18442	-0.370000	0.08016	-0.381000	0.06696	CGG	G|0.966;A|0.034	0.034	strong		0.637	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482		A	242012729	G	A	242012729	3	1	22	1	0	0	0	0	1	0	0	0	14860	1116	39	1	3972	1	SNED1	2	242012729	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	177619	242012729	1186644	795	3696											
MTERFD2	130916	hgsc.bcm.edu	37	chr2	242036769	242036769	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cacttctccttgagaagcctGacagtgtcgttaatgtcctg	8	13	9	11	1	1	2	0	2	1	1	4	3	2	2	3	0	1	1	3	0	2	3	rs10171090	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242036769G>A	ENST00000391980.2	-	3	652	c.594C>T	c.(592-594)gtC>gtT	p.V198V	MTERFD2_ENST00000464344.2_Intron|MTERFD2_ENST00000495694.1_Intron|MTERFD2_ENST00000406593.1_Silent_p.V10V|MTERFD2_ENST00000407095.3_Silent_p.V198V	NM_182501.3	NP_872307.2	Q7Z6M4	MTEF4_HUMAN		198					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)		TGAGAAGCCTGACAGTGTCGT	0.473													G|||	111	0.0221645	0.0772	0.013	5008	,	,		21463	0.0		0.0	False		,,,				2504	0.0				p.V198V		Atlas-SNP	.											.	MTERFD2	33	.	0			c.C594T						PASS	.	G		262,4144	148.8+/-183.1	9,244,1950	101	87	92		594	-1.5	0	2	dbSNP_119	92	0,8600		0,0,4300	no	coding-synonymous	MTERFD2	NM_182501.3		9,244,6250	AA,AG,GG		0.0,5.9464,2.0145		198/382	242036769	262,12744	2203	4300	6503	SO:0001819	synonymous_variant	130916	exon3			AAGCCTGACAGTG																												ENST00000391980.2:c.594C>T	2.37:g.242036769G>A		129	0	0		118	52	0.440678	NM_182501	A8K6K0|Q9P0E0	Silent	SNP	ENST00000391980.2	37	CCDS2544.1																																																																																			G|0.978;A|0.022	0.022	strong		0.473	MTERFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323798.4			A	242036769	G	A	242036769	2	1	22	1	0	0	0	0	0	0	0	1	9929	1277	45	2		2	MTERFD2	2	242036769	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	24040	242036769	1162604	796	3697											
PASK	23178	hgsc.bcm.edu	37	chr2	242065635	242065635	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccgtaagccatctcgatggtAgcagctcccggagtaggcac	9	7	12	13	3	1	0	0	0	1	0	3	2	2	1	3	3	3	6	3	3	3	3	rs77674262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242065635A>G	ENST00000405260.1	-	10	3393	c.2695T>C	c.(2695-2697)Tac>Cac	p.Y899H	PASK_ENST00000539818.1_Missense_Mutation_p.Y683H|PASK_ENST00000544142.1_Missense_Mutation_p.Y713H|PASK_ENST00000234040.4_Missense_Mutation_p.Y899H|PASK_ENST00000403638.3_Missense_Mutation_p.Y899H|PASK_ENST00000358649.4_Missense_Mutation_p.Y899H	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	899				Y -> H (in Ref. 1; AAK69752). {ECO:0000305}.	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)		TCTCGATGGTAGCAGCTCCCG	0.637													A|||	109	0.0217652	0.0764	0.0115	5008	,	,		17584	0.0		0.0	False		,,,				2504	0.0				p.Y899H		Atlas-SNP	.											.	PASK	230	.	0			c.T2695C						PASS	.	A	HIS/TYR	255,4151	142.3+/-177.5	10,235,1958	70	56	61		2695	2.4	0.9	2	dbSNP_131	61	0,8600		0,0,4300	yes	missense	PASK	NM_015148.2	83	10,235,6258	GG,GA,AA		0.0,5.7876,1.9606	benign	899/1324	242065635	255,12751	2203	4300	6503	SO:0001583	missense	23178	exon10			GATGGTAGCAGCT	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.2695T>C	2.37:g.242065635A>G	ENSP00000384016:p.Tyr899His	126	0	0		143	74	0.517483	NM_015148	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Missense_Mutation	SNP	ENST00000405260.1	37	CCDS2545.1	42	0.019230769230769232	38	0.07723577235772358	4	0.011049723756906077	0	0.0	0	0.0	A	6.136	0.393272	0.11638	0.057876	0.0	ENSG00000115687	ENST00000234040;ENST00000544142;ENST00000405260;ENST00000358649;ENST00000539818;ENST00000403638	T;T;T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.33;-0.37;0.57	4.94	2.43	0.29744	.	0.703722	0.12909	N	0.429094	T	0.06872	0.0175	M	0.62723	1.935	0.28200	N	0.927392	B;B;B;B;B	0.18013	0.014;0.025;0.025;0.015;0.014	B;B;B;B;B	0.18561	0.01;0.022;0.022;0.022;0.01	T	0.24440	-1.0160	10	0.45353	T	0.12	.	5.2611	0.15573	0.758:0.0:0.0873:0.1548	.	864;713;899;899;899	B7Z7R6;F5GYW7;Q96RG2-2;G5E9F1;Q96RG2	.;.;.;.;PASK_HUMAN	H	899;713;899;899;683;899	ENSP00000234040:Y899H;ENSP00000441374:Y713H;ENSP00000384016:Y899H;ENSP00000351475:Y899H;ENSP00000443083:Y683H;ENSP00000384438:Y899H	ENSP00000234040:Y899H	Y	-	1	0	PASK	241714308	1.000000	0.71417	0.911000	0.35937	0.022000	0.10575	2.054000	0.41335	0.734000	0.32515	-0.411000	0.06167	TAC	A|0.979;G|0.021	0.021	strong		0.637	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148		G	242065635	A	G	242065635	3	3	22	1	0	0	0	0	1	0	0	0	11481	420	15	3	1312	3	PASK	2	242065635	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	28866	242065635	1133738	797	3698											
FARP2	9855	hgsc.bcm.edu	37	chr2	242352768	242352768	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctggaccgagagcacctcaaAgtgaacgagtatttgcctgg	11	8	12	10	2	1	2	1	1	0	1	1	5	1	3	3	2	3	2	3	2	3	2	rs16843643	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242352768A>C	ENST00000264042.3	+	7	725	c.555A>C	c.(553-555)aaA>aaC	p.K185N	FARP2_ENST00000373287.4_Missense_Mutation_p.K185N|FARP2_ENST00000545004.1_Missense_Mutation_p.K185N	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	185	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.		K -> N (in dbSNP:rs16843643).		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)		AGCACCTCAAAGTGAACGAGT	0.403													A|||	203	0.0405351	0.146	0.013	5008	,	,		20493	0.001		0.0	False		,,,				2504	0.0				p.K185N		Atlas-SNP	.											.	FARP2	92	.	0			c.A555C						PASS	.	A	ASN/LYS	514,3892	231.7+/-245.5	32,450,1721	104	82	90		555	-5.4	0	2	dbSNP_123	90	10,8590	7.7+/-29.5	0,10,4290	yes	missense	FARP2	NM_014808.2	94	32,460,6011	CC,CA,AA		0.1163,11.6659,4.0289	probably-damaging	185/1055	242352768	524,12482	2203	4300	6503	SO:0001583	missense	9855	exon7			CCTCAAAGTGAAC	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.555A>C	2.37:g.242352768A>C	ENSP00000264042:p.Lys185Asn	50	0	0		58	32	0.551724	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Missense_Mutation	SNP	ENST00000264042.3	37	CCDS33424.1	69	0.03159340659340659	64	0.13008130081300814	5	0.013812154696132596	0	0.0	0	0.0	A	8.513	0.866895	0.17250	0.116659	0.001163	ENSG00000006607	ENST00000264042;ENST00000545004;ENST00000373287	T;T;T	0.30714	1.52;1.52;1.52	5.34	-5.39	0.02664	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.312765	0.32533	N	0.005966	T	0.00241	0.0007	L	0.41124	1.26	0.09310	N	1	D;B;P	0.54772	0.968;0.116;0.947	P;B;P	0.50791	0.598;0.078;0.65	T	0.03034	-1.1080	10	0.59425	D	0.04	.	3.6724	0.08279	0.3864:0.1157:0.3863:0.1116	rs16843643;rs52827477;rs59890453;rs16843643	185;185;185	O94887-2;F5GZ84;O94887	.;.;FARP2_HUMAN	N	185	ENSP00000264042:K185N;ENSP00000443876:K185N;ENSP00000362384:K185N	ENSP00000264042:K185N	K	+	3	2	FARP2	242001441	0.001000	0.12720	0.000000	0.03702	0.336000	0.28762	0.092000	0.15066	-1.367000	0.02152	0.528000	0.53228	AAA	A|0.960;C|0.040	0.040	strong		0.403	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1			C	242352768	A	C	242352768	3	2	22	1	0	0	0	0	1	0	0	0	5685	69	3	5	577	5	FARP2	2	242352768	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	287133	242352768	846605	798	3699											
THAP4	51078	hgsc.bcm.edu	37	chr2	242572693	242572693	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggctctgggaaggcttctgCggtgtcgcggtaagtgatga	6	10	18	7	3	2	2	0	2	2	0	3	3	2	3	0	5	1	3	0	5	2	2	rs147500721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242572693C>T	ENST00000407315.1	-	2	1310	c.879G>A	c.(877-879)ccG>ccA	p.P293P		NM_015963.5	NP_057047.4	Q8WY91	THAP4_HUMAN	THAP domain containing 4	293							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	9		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;2.3e-33)|all cancers(36;8.99e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.68e-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;0.0844)		AAGGCTTCTGCGGTGTCGCGG	0.657													C|||	46	0.0091853	0.0325	0.0029	5008	,	,		15917	0.0		0.001	False		,,,				2504	0.0				p.P293P		Atlas-SNP	.											.	THAP4	27	.	0			c.G879A						PASS	.	C		190,4216	121.7+/-159.2	5,180,2018	74	80	78		879	-11	0.2	2	dbSNP_134	78	0,8592		0,0,4296	no	coding-synonymous	THAP4	NM_015963.5		5,180,6314	TT,TC,CC		0.0,4.3123,1.4618		293/578	242572693	190,12808	2203	4296	6499	SO:0001819	synonymous_variant	51078	exon2			CTTCTGCGGTGTC	AF258556	CCDS2551.1, CCDS54440.1	2q37.3	2013-01-25			ENSG00000176946	ENSG00000176946		"THAP (C2CH-type zinc finger) domain containing"	23187	protein-coding gene	gene with protein product		612533				12575992, 10810093	Standard	NM_015963		Approved	CGI-36	uc002wbt.3	Q8WY91	OTTHUMG00000133410	ENST00000407315.1:c.879G>A	2.37:g.242572693C>T		69	0	0		76	44	0.578947	NM_015963	Q53NU7|Q6GRN0|Q6IPJ3|Q9NW26|Q9Y325	Silent	SNP	ENST00000407315.1	37	CCDS2551.1																																																																																			C|0.985;T|0.015	0.015	strong		0.657	THAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257267.3	NM_015963		T	242572693	C	T	242572693	2	4	22	1	0	0	0	0	0	0	0	1	15861	755	27	1		1	THAP4	2	242572693	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	219925	242572693	626680	799	3700											
C2orf85	285093	hgsc.bcm.edu	37	chr2	242814604	242814604	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggggctccctctgcagcccGgttggcgtggcccagggctg	2	7	17	15	3	1	0	0	0	1	0	2	0	2	0	3	6	2	4	3	6	0	1	rs78628254	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242814604G>C	ENST00000343216.3	+	2	925	c.897G>C	c.(895-897)ccG>ccC	p.P299P		NM_173821.2	NP_776182.2																					TCTGCAGCCCGGTTGGCGTGG	0.667													G|||	228	0.0455272	0.1664	0.0086	5008	,	,		18709	0.0		0.002	False		,,,				2504	0.0				p.P299P		Atlas-SNP	.											.	.	.	.	0			c.G897C						PASS	.			556,3250		37,482,1384	36	41	39		897	-5.6	0	2	dbSNP_131	39	3,8227		0,3,4112	no	coding-synonymous	C2orf85	NM_173821.2		37,485,5496	CC,CG,GG		0.0365,14.6085,4.6444		299/573	242814604	559,11477	1903	4115	6018	SO:0001819	synonymous_variant	285093	exon2			CAGCCCGGTTGGC																												ENST00000343216.3:c.897G>C	2.37:g.242814604G>C		56	0	0		73	40	0.547945	NM_173821		Silent	SNP	ENST00000343216.3	37	CCDS42843.1																																																																																			G|0.967;C|0.033	0.033	strong		0.667	CXXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322310.1			C	242814604	G	C	242814604	2	2	22	1	0	0	0	0	0	0	0	1	2202	1103	39	4		4	C2orf85	2	242814604	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	241911	242814604	384769	800	3701											
C2orf85	285093	hgsc.bcm.edu	37	chr2	242814778	242814778	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aacaccctctcggagcccacCgatggccctgtggccactaa	9	6	9	17	2	1	0	0	0	1	0	2	2	1	1	5	3	2	0	5	3	2	1	rs7597435	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242814778C>T	ENST00000343216.3	+	2	1099	c.1071C>T	c.(1069-1071)acC>acT	p.T357T		NM_173821.2	NP_776182.2																					CGGAGCCCACCGATGGCCCTG	0.612													C|||	204	0.0407348	0.1475	0.0101	5008	,	,		19528	0.0		0.002	False		,,,				2504	0.0				p.T357T		Atlas-SNP	.											.	.	.	.	0			c.C1071T						PASS	.	C		534,3442		35,464,1489	29	34	32		1071	-4.3	0	2	dbSNP_116	32	3,8279		0,3,4138	no	coding-synonymous	C2orf85	NM_173821.2		35,467,5627	TT,TC,CC		0.0362,13.4306,4.3808		357/573	242814778	537,11721	1988	4141	6129	SO:0001819	synonymous_variant	285093	exon2			GCCCACCGATGGC																												ENST00000343216.3:c.1071C>T	2.37:g.242814778C>T		182	0	0		198	88	0.444444	NM_173821		Silent	SNP	ENST00000343216.3	37	CCDS42843.1																																																																																			C|0.963;T|0.037	0.037	strong		0.612	CXXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322310.1			T	242814778	C	T	242814778	2	4	22	1	0	0	0	0	0	0	0	1	2202	639	23	1		1	C2orf85	2	242814778	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	174	242814778	384595	801	3702											
C2orf85	285093	hgsc.bcm.edu	37	chr2	242815157	242815157	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagtcttcgatgtcataaagCgcaagggcggtggccacgtt	9	9	13	10	4	2	0	1	0	1	0	3	1	2	0	1	3	1	2	1	3	3	3	rs77317868	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242815157C>T	ENST00000343216.3	+	2	1478	c.1450C>T	c.(1450-1452)Cgc>Tgc	p.R484C		NM_173821.2	NP_776182.2																					TGTCATAAAGCGCAAGGGCGG	0.627													C|||	168	0.0335463	0.121	0.0086	5008	,	,		15580	0.0		0.002	False		,,,				2504	0.0				p.R484C		Atlas-SNP	.											.	.	.	.	0			c.C1450T						PASS	.	C	CYS/ARG	469,3695		27,415,1640	69	80	76		1450	-3.6	0	2	dbSNP_131	76	4,8400		0,4,4198	yes	missense	C2orf85	NM_173821.2	180	27,419,5838	TT,TC,CC		0.0476,11.2632,3.7635	benign	484/573	242815157	473,12095	2082	4202	6284	SO:0001583	missense	285093	exon2			ATAAAGCGCAAGG																												ENST00000343216.3:c.1450C>T	2.37:g.242815157C>T	ENSP00000345374:p.Arg484Cys	76	0	0		73	36	0.493151	NM_173821		Missense_Mutation	SNP	ENST00000343216.3	37	CCDS42843.1	49	0.022435897435897436	44	0.08943089430894309	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	.	7.258	0.604519	0.14002	0.112632	4.76E-4	ENSG00000188011	ENST00000343216	T	0.22539	1.95	2.14	-3.6	0.04570	.	.	.	.	.	T	0.00144	0.0004	N	0.03608	-0.345	0.09310	N	1	B	0.21225	0.053	B	0.06405	0.002	T	0.32322	-0.9911	9	0.87932	D	0	-7.0233	0.6619	0.00844	0.4047:0.248:0.1829:0.1644	.	484	Q14D33	CB085_HUMAN	C	484	ENSP00000345374:R484C	ENSP00000345374:R484C	R	+	1	0	C2orf85	242463830	0.000000	0.05858	0.000000	0.03702	0.242000	0.25591	-1.257000	0.02866	-0.945000	0.03681	0.196000	0.17591	CGC	C|0.973;T|0.027	0.027	strong		0.627	CXXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322310.1			T	242815157	C	T	242815157	3	4	22	1	0	0	0	0	1	0	0	0	2202	768	27	1	1456	1	C2orf85	2	242815157	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	379	242815157	384216	802	3703											
CNTN4	152330	hgsc.bcm.edu	37	chr3	2787338	2787338	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagtgcacagcgacaaactcGtttggaacaattgttagcag	13	9	10	9	2	0	0	0	0	0	0	1	2	0	1	0	1	5	4	0	1	4	3	rs116041691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:2787338G>A	ENST00000397461.1	+	5	699	c.315G>A	c.(313-315)tcG>tcA	p.S105S	CNTN4_ENST00000427331.1_Silent_p.S105S|CNTN4_ENST00000418658.1_Silent_p.S105S	NM_001206955.1	NP_001193884.1	Q8IWV2	CNTN4_HUMAN	contactin 4	105	Ig-like C2-type 1.				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)		CGACAAACTCGTTTGGAACAA	0.408													G|||	28	0.00559105	0.0212	0.0	5008	,	,		17052	0.0		0.0	False		,,,				2504	0.0				p.S105S		Atlas-SNP	.											CNTN4_ENST00000418658,NS,carcinoma,0,1	CNTN4	335	1	0			c.G315A						PASS	.	G	,	64,3818		1,62,1878	146	137	140		315,315	-7.4	0.7	3	dbSNP_132	140	1,8275		0,1,4137	no	coding-synonymous,coding-synonymous	CNTN4	NM_001206955.1,NM_175607.2	,	1,63,6015	AA,AG,GG		0.0121,1.6486,0.5346	,	105/1027,105/1027	2787338	65,12093	1941	4138	6079	SO:0001819	synonymous_variant	152330	exon6			AAACTCGTTTGGA	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.315G>A	3.37:g.2787338G>A		105	0	0		78	48	0.615385	NM_175607	B2RAX3|Q8IX14|Q8TC35	Silent	SNP	ENST00000397461.1	37	CCDS43041.1																																																																																			G|0.996;A|0.004	0.004	strong		0.408	CNTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239236.2			A	2787338	G	A	2787338	2	1	22	1	0	0	0	0	0	0	0	1	3645	1132	40	1		1	CNTN4	3	2787338	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10		2787338	195235092	803	3704											
SRGAP3	9901	hgsc.bcm.edu	37	chr3	9034605	9034605	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cctaccggcccatcacccccCcaaagccgtaatccgagatg	10	5	7	19	3	1	1	1	0	0	1	2	2	2	1	8	1	2	1	8	1	3	2	rs150617309	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:9034605C>G	ENST00000383836.3	-	20	2970	c.2543G>C	c.(2542-2544)gGg>gCg	p.G848A	SRGAP3_ENST00000360413.3_Missense_Mutation_p.G824A	NM_014850.3	NP_055665.1	O43295	SRGP3_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	848					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)		CATCACCCCCCCAAAGCCGTA	0.557			T	RAF1	pilocytic astrocytoma																																p.G848A		Atlas-SNP	.		Dom	yes		3	3p25.3	9901	SLIT-ROBO Rho GTPase activating protein 3		M	.	SRGAP3	146	.	0			c.G2543C						PASS	.						83	79	81					3																	9034605		2203	4300	6503	SO:0001583	missense	9901	exon20			ACCCCCCCAAAGC	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.2543G>C	3.37:g.9034605C>G	ENSP00000373347:p.Gly848Ala	70	0	0		69	36	0.521739	NM_014850	Q8IX13|Q8IZV8	Missense_Mutation	SNP	ENST00000383836.3	37	CCDS2572.1	.	.	.	.	.	.	.	.	.	.	C	5.202	0.222874	0.09863	.	.	ENSG00000196220	ENST00000383836;ENST00000360413	T;T	0.22134	1.97;2.37	5.17	5.17	0.71159	.	0.270733	0.35708	N	0.003023	T	0.12860	0.0312	N	0.22421	0.69	0.47621	D	0.999477	B;B	0.09022	0.002;0.001	B;B	0.10450	0.005;0.002	T	0.04551	-1.0943	10	0.02654	T	1	.	13.9514	0.64118	0.0:0.8479:0.1521:0.0	.	824;848	O43295-2;O43295	.;SRGP2_HUMAN	A	848;824	ENSP00000373347:G848A;ENSP00000353587:G824A	ENSP00000353587:G824A	G	-	2	0	SRGAP3	9009605	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.779000	0.55379	2.410000	0.81850	0.591000	0.81541	GGG	C|1.000;G|0.000	0.000	alt		0.557	SRGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207137.3			G	9034605	C	G	9034605	3	3	22	1	0	0	0	0	1	0	0	0	15162	623	22	4	768	4	SRGAP3	3	9034605	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6247267	9034605	188987825	804	3705											
OGG1	4968	hgsc.bcm.edu	37	chr3	9796508	9796508	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agcctggctgcagcagctacGagagtcctcatatgaggagg	10	7	14	10	1	1	2	1	1	0	1	2	4	2	3	2	3	5	4	2	3	2	2	rs1805373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:9796508G>A	ENST00000344629.7	+	4	1029	c.686G>A	c.(685-687)cGa>cAa	p.R229Q	OGG1_ENST00000302008.8_Missense_Mutation_p.R229Q|OGG1_ENST00000339511.5_Missense_Mutation_p.R229Q|OGG1_ENST00000302003.7_Missense_Mutation_p.R229Q|OGG1_ENST00000449570.2_Missense_Mutation_p.R229Q|OGG1_ENST00000383826.5_Intron|OGG1_ENST00000302036.7_Missense_Mutation_p.R229Q|OGG1_ENST00000349503.5_Missense_Mutation_p.R229Q			O15527	OGG1_HUMAN	8-oxoguanine DNA glycosylase	229			R -> Q (in dbSNP:rs1805373). {ECO:0000269|Ref.13}.		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)					CAGCAGCTACGAGAGTCCTCA	0.642								Base excision repair (BER), DNA glycosylases					G|||	141	0.028155	0.1029	0.0072	5008	,	,		19186	0.0		0.0	False		,,,				2504	0.0				p.R229Q		Atlas-SNP	.											.	OGG1	57	.	0			c.G686A	GRCh37	CM074394	OGG1	M	rs1805373	PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,,GLN/ARG,GLN/ARG	384,4022	185.7+/-212.7	11,362,1830	33	28	30		686,686,686,686,686,,686,686	3.1	0.8	3	dbSNP_98	30	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense,missense,missense,missense,intron,missense,missense	OGG1	NM_002542.5,NM_016819.3,NM_016820.3,NM_016821.2,NM_016826.2,NM_016827.2,NM_016828.2,NM_016829.2	43,43,43,43,43,,43,43	11,365,6127	AA,AG,GG		0.0349,8.7154,2.9755	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,,possibly-damaging,possibly-damaging	229/346,229/325,229/411,229/425,229/358,,229/357,229/323	9796508	387,12619	2203	4300	6503	SO:0001583	missense	4968	exon4			AGCTACGAGAGTC	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.686G>A	3.37:g.9796508G>A	ENSP00000342851:p.Arg229Gln	137	0	0		146	59	0.40411	NM_016819	A8K1E3|O00390|O00670|O00705|O14876|O95488|P78554|Q9BW42|Q9UIK0|Q9UIK1|Q9UIK2|Q9UL34|Q9Y2C0|Q9Y2C1|Q9Y6C3|Q9Y6C4	Missense_Mutation	SNP	ENST00000344629.7	37	CCDS2581.1	43|43	0.019688644688644688|0.019688644688644688	39|39	0.07926829268292683|0.07926829268292683	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	0|0	0.0|0.0	G|G	16.07|16.07	3.017581|3.017581	0.54576|0.54576	0.087154|0.087154	3.49E-4|3.49E-4	ENSG00000114026|ENSG00000114026	ENST00000441094|ENST00000302003;ENST00000344629;ENST00000302036;ENST00000349503;ENST00000339511;ENST00000449570;ENST00000302008;ENST00000339542	.|T;T;T;T;T;T;T	.|0.56275	.|0.47;0.47;0.47;0.47;0.47;0.47;0.47	5.78|5.78	3.07|3.07	0.35406|0.35406	.|HhH-GPD domain (2);DNA glycosylase (2);	.|0.261230	.|0.45361	.|N	.|0.000369	T|T	0.03520|0.03520	0.0101|0.0101	M|M	0.76938|0.76938	2.355|2.355	0.53005|0.53005	D|D	0.999968|0.999968	.|D;D;P;P;D;P;B;P	.|0.61697	.|0.982;0.99;0.954;0.907;0.977;0.954;0.312;0.933	.|B;B;B;B;B;B;B;B	.|0.43331	.|0.345;0.416;0.299;0.133;0.133;0.299;0.019;0.082	T|T	0.02320|0.02320	-1.1177|-1.1177	5|10	.|0.54805	.|T	.|0.06	-3.3716|-3.3716	11.2674|11.2674	0.49118|0.49118	0.1972:0.0:0.8028:0.0|0.1972:0.0:0.8028:0.0	rs1805373;rs2266693;rs52816862;rs56468739;rs1805373|rs1805373;rs2266693;rs52816862;rs56468739;rs1805373	.|72;229;229;229;229;229;229;229	.|F8WA07;E5KPM6;E5KPM5;E5KPM7;E5KPM9;E5KPN0;O15527;O15527-2	.|.;.;.;.;.;.;OGG1_HUMAN;.	K|Q	127|229;229;229;229;229;229;229;72	.|ENSP00000305584:R229Q;ENSP00000342851:R229Q;ENSP00000306561:R229Q;ENSP00000303132:R229Q;ENSP00000345520:R229Q;ENSP00000403598:R229Q;ENSP00000305527:R229Q	.|ENSP00000305584:R229Q	E|R	+|+	1|2	0|0	OGG1|OGG1	9771508|9771508	0.813000|0.813000	0.29090|0.29090	0.768000|0.768000	0.31515|0.31515	0.370000|0.370000	0.29829|0.29829	2.465000|2.465000	0.45075|0.45075	0.384000|0.384000	0.24942|0.24942	-0.203000|-0.203000	0.12734|0.12734	GAG|CGA	G|0.969;A|0.031	0.031	strong		0.642	OGG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214223.2	NM_016821		A	9796508	G	A	9796508	3	1	22	1	0	0	0	0	1	0	0	0	10854	1058	37	1	700	1	OGG1	3	9796508	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	761903	9796508	188225922	805	3706											
CAMK1	8536	hgsc.bcm.edu	37	chr3	9804658	9804658	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ttcacagcatccagcacctgGaagatgaggcggctggcgtc	9	7	13	12	2	1	2	1	1	0	1	3	3	2	3	2	4	2	3	2	4	1	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:9804658G>A	ENST00000256460.3	-	5	546	c.369C>T	c.(367-369)ttC>ttT	p.F123F	OGG1_ENST00000302008.8_Intron|OGG1_ENST00000449570.2_Intron|OGG1_ENST00000383826.5_Intron|OGG1_ENST00000302036.7_Intron|OGG1_ENST00000349503.5_Intron	NM_003656.4	NP_003647.1	Q14012	KCC1A_HUMAN	calcium/calmodulin-dependent protein kinase I	123	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)		CCAGCACCTGGAAGATGAGGC	0.597																																					p.F123F		Atlas-SNP	.											.	CAMK1	32	.	0			c.C369T						PASS	.						71	63	66					3																	9804658		2203	4300	6503	SO:0001819	synonymous_variant	8536	exon5			CACCTGGAAGATG	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.369C>T	3.37:g.9804658G>A		127	0	0		121	70	0.578512	NM_003656	Q3KPF6	Silent	SNP	ENST00000256460.3	37	CCDS2582.1																																																																																			.	.	none		0.597	CAMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250206.1	NM_003656		A	9804658	G	A	9804658	2	1	22	1	0	0	0	0	0	0	0	1	2598	1165	41	2		2	CAMK1	3	9804658	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	8150	9804658	188217772	806	3707											
CRELD1	78987	hgsc.bcm.edu	37	chr3	9984855	9984855	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caggtgggctccaagtgtctCggtgagtctcctgctgatgg	5	11	15	10	1	2	2	0	2	2	0	5	2	3	2	2	4	1	2	2	4	1	0	rs79223485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:9984855C>T	ENST00000383811.3	+	8	1511	c.912C>T	c.(910-912)ctC>ctT	p.L304L	CRELD1_ENST00000326434.5_Splice_Site_p.L304L|CRELD1_ENST00000397170.3_Splice_Site_p.L304L|CRELD1_ENST00000452070.1_Splice_Site_p.L304L|CRELD1_ENST00000489674.1_3'UTR	NM_015513.4	NP_056328	Q96HD1	CREL1_HUMAN	cysteine-rich with EGF-like domains 1	304					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						CCAAGTGTCTCGGTGAGTCTC	0.612													C|||	106	0.0211661	0.0772	0.0058	5008	,	,		19596	0.0		0.0	False		,,,				2504	0.0				p.L304L		Atlas-SNP	.											.	CRELD1	48	.	0			c.C912T						PASS	.	C	,,	289,4117	156.6+/-189.7	12,265,1926	45	47	46		912,912,912	-1.4	1	3	dbSNP_132	46	3,8597	3.0+/-9.4	0,3,4297	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	CRELD1	NM_001031717.3,NM_001077415.2,NM_015513.4	,,	12,268,6223	TT,TC,CC		0.0349,6.5592,2.2451	,,	304/423,304/421,304/421	9984855	292,12714	2203	4300	6503	SO:0001630	splice_region_variant	78987	exon9			GTGTCTCGGTGAG	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.913+1C>T	3.37:g.9984855C>T		107	0	0		102	43	0.421569	NM_001077415	A8MX90|B2RAA9|Q6I9X5|Q8NFT4|Q9Y409	Silent	SNP	ENST00000383811.3	37	CCDS2593.1																																																																																			C|0.975;T|0.025	0.025	strong		0.612	CRELD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250533.1	NM_015513	Silent	T	9984855	C	T	9984855	5	4	22	1	0	0	0	0	0	0	1	0	3868	898	31	1	942	1	CRELD1	3	9984855	Splice_Site	SNP	C	TCGA-G8-6324-01A-11D-2210-10	180197	9984855	188037575	807	3708											
TATDN2	9797	hgsc.bcm.edu	37	chr3	10311949	10311949	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcagccgttccggagccttcTtccttcaccaccgactatgt	6	12	7	16	3	3	0	2	0	1	0	5	2	5	1	6	1	2	1	6	1	1	5	rs145595744	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:10311949T>C	ENST00000287652.4	+	4	2134	c.1083T>C	c.(1081-1083)tcT>tcC	p.S361S	RP11-438J1.1_ENST00000450534.1_3'UTR|TATDN2_ENST00000448281.2_Silent_p.S361S	NM_014760.3	NP_055575.3	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	361					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						CGGAGCCTTCTTCCTTCACCA	0.522													T|||	18	0.00359425	0.0136	0.0	5008	,	,		20081	0.0		0.0	False		,,,				2504	0.0				p.S361S		Atlas-SNP	.											.	TATDN2	59	.	0			c.T1083C						PASS	.	T		28,4378	34.3+/-65.2	1,26,2176	168	162	164		1083	-5.2	0	3	dbSNP_134	164	0,8600		0,0,4300	no	coding-synonymous	TATDN2	NM_014760.3		1,26,6476	CC,CT,TT		0.0,0.6355,0.2153		361/762	10311949	28,12978	2203	4300	6503	SO:0001819	synonymous_variant	9797	exon4			GCCTTCTTCCTTC	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.1083T>C	3.37:g.10311949T>C		83	0	0		131	80	0.610687	NM_014760	Q3MIL9|Q5BKU0	Silent	SNP	ENST00000287652.4	37	CCDS33698.1																																																																																			T|0.997;C|0.003	0.003	strong		0.522	TATDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339641.1	XM_376203		C	10311949	T	C	10311949	2	2	22	1	0	0	0	0	0	0	0	1	15607	1596	56	3		3	TATDN2	3	10311949	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	327094	10311949	187710481	808	3709											
TBC1D5	9779	hgsc.bcm.edu	37	chr3	17208285	17208286	+	Frame_Shift_Del	DEL	CG	CG	-																															aatggcccctgacatttgaaCgctctggccttggcctcggc																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CG	CG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:17208285_17208286delCG	ENST00000253692.7	-	21	3731_3732	c.2067_2068delCG	c.(2065-2070)agcgttfs	p.V690fs	TBC1D5_ENST00000429383.4_Frame_Shift_Del_p.V690fs|TBC1D5_ENST00000414318.2_5'UTR|TBC1D5_ENST00000446818.2_Frame_Shift_Del_p.V712fs	NM_014744.2	NP_055559.1	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5	690						retromer complex (GO:0030904)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	36						GACATTTGAACGCTCTGGCCTT	0.51																																					p.712_712del		Pindel,Atlas-Indel	.											.	TBC1D5	69	.	0			c.2134_2135del						PASS	.																																			SO:0001589	frameshift_variant	9779	exon23			.	D86965	CCDS33714.1, CCDS46770.1	3p24.3	2013-07-09			ENSG00000131374	ENSG00000131374			19166	protein-coding gene	gene with protein product		615740				19531583	Standard	NM_014744		Approved	KIAA0210	uc003cbe.3	Q92609	OTTHUMG00000155488	ENST00000253692.7:c.2067_2068delCG	3.37:g.17208285_17208286delCG	ENSP00000253692:p.Val690fs	165	0	.		180	46	0.256	NM_001134381	A6NP25|C9JP52	Frame_Shift_Del	DEL	ENST00000253692.7	37	CCDS33714.1																																																																																			.	.	none		0.51	TBC1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340301.3	NM_014744		-	17208286	CG	-	17208285	7	5	22	1	0	1	0	1	0	0	0	0	15638	536	19	0	327	0	TBC1D5	3	17208285	Frame_Shift_Del	DEL	CG	TCGA-G8-6324-01A-11D-2210-10	6896336	17208285	180814145	809	3710											
SLC4A7	9497	hgsc.bcm.edu	37	chr3	27436247	27436247	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccatgagcaaatcaaggtgaTagccagctcctttctgaaaa	14	9	8	10	0	2	3	1	3	1	0	3	3	3	3	3	1	3	2	3	1	5	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:27436247T>C	ENST00000295736.5	-	20	2922	c.2852A>G	c.(2851-2853)tAt>tGt	p.Y951C	SLC4A7_ENST00000446700.1_Missense_Mutation_p.Y943C|SLC4A7_ENST00000454389.1_Missense_Mutation_p.Y960C|SLC4A7_ENST00000388777.4_Missense_Mutation_p.Y501C|SLC4A7_ENST00000435667.2_Missense_Mutation_p.Y836C|SLC4A7_ENST00000428386.1_Missense_Mutation_p.Y827C|SLC4A7_ENST00000445684.1_Missense_Mutation_p.Y947C|SLC4A7_ENST00000425128.2_3'UTR|SLC4A7_ENST00000440156.1_Missense_Mutation_p.Y947C|SLC4A7_ENST00000437179.1_Missense_Mutation_p.Y832C|SLC4A7_ENST00000455077.1_Missense_Mutation_p.Y832C	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	951					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)	ATCAAGGTGATAGCCAGCTCC	0.393																																					p.Y951C		Atlas-SNP	.											.	SLC4A7	119	.	0			c.A2852G						PASS	.						101	93	96					3																	27436247		2203	4300	6503	SO:0001583	missense	9497	exon20			AGGTGATAGCCAG	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.2852A>G	3.37:g.27436247T>C	ENSP00000295736:p.Tyr951Cys	80	0	0		85	47	0.552941	NM_003615	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Missense_Mutation	SNP	ENST00000295736.5	37	CCDS33721.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.526853	0.85706	.	.	ENSG00000033867	ENST00000419036;ENST00000295736;ENST00000428386;ENST00000454389;ENST00000440156;ENST00000437179;ENST00000446700;ENST00000455077;ENST00000445684;ENST00000435667;ENST00000388777;ENST00000428179	D;D;D;D;D;D;D;D;D;D;D;D	0.82167	-1.58;-1.58;-1.58;-1.58;-1.58;-1.58;-1.58;-1.58;-1.58;-1.58;-1.58;-1.58	5.84	5.84	0.93424	Bicarbonate transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.94095	0.8107	H	0.96365	3.81	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	D	0.95792	0.8825	10	0.87932	D	0	.	16.2194	0.82247	0.0:0.0:0.0:1.0	.	947;832;943;947;960;501;827;951;832	E9PFN4;B5M452;E9PGC1;B5M453;E9PDL9;F8W7E6;Q9Y6M7-2;Q9Y6M7;B2CI53	.;.;.;.;.;.;.;S4A7_HUMAN;.	C	502;951;827;960;947;832;943;832;947;836;501;847	ENSP00000411031:Y502C;ENSP00000295736:Y951C;ENSP00000416368:Y827C;ENSP00000390394:Y960C;ENSP00000414797:Y947C;ENSP00000394252:Y832C;ENSP00000406605:Y943C;ENSP00000407382:Y832C;ENSP00000406804:Y947C;ENSP00000395336:Y836C;ENSP00000373429:Y501C;ENSP00000388703:Y847C	ENSP00000295736:Y951C	Y	-	2	0	SLC4A7	27411251	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.234000	0.73211	0.528000	0.53228	TAT	.	.	none		0.393	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615		C	27436247	T	C	27436247	3	2	22	1	0	0	0	0	1	0	0	0	14673	1406	49	3	816	3	SLC4A7	3	27436247	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	10227962	27436247	170586183	810	3711											
EOMES	8320	hgsc.bcm.edu	37	chr3	27758756	27758756	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tctagagatttgatggaaggGggtgtctctatccaagaaga	12	11	13	5	0	2	4	0	1	2	3	4	6	3	5	1	3	0	0	1	3	5	3	rs6783101	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:27758756G>A	ENST00000295743.4	-	6	2069	c.1866C>T	c.(1864-1866)ccC>ccT	p.P622P	EOMES_ENST00000449599.1_Silent_p.P641P|EOMES_ENST00000537516.1_Silent_p.P346P|EOMES_ENST00000461503.1_5'Flank			O95936	EOMES_HUMAN	eomesodermin	622	Required for transcription activation. {ECO:0000250}.				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						TGATGGAAGGGGGTGTCTCTA	0.463													G|||	182	0.0363419	0.1316	0.0115	5008	,	,		18478	0.0		0.0	False		,,,				2504	0.0				p.P622P		Atlas-SNP	.											.	EOMES	65	.	0			c.C1866T						PASS	.	G		548,3858	247.5+/-255.7	26,496,1681	118	122	121		1866	-1.7	1	3	dbSNP_116	121	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	EOMES	NM_005442.2		26,503,5974	AA,AG,GG		0.0814,12.4376,4.2673		622/687	27758756	555,12451	2203	4300	6503	SO:0001819	synonymous_variant	8320	exon6			GGAAGGGGGTGTC	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.1866C>T	3.37:g.27758756G>A		197	0	0		212	99	0.466981	NM_005442	B7Z4I2|B7ZA51|G3XAI5|Q8TAZ2|Q9UPM7	Silent	SNP	ENST00000295743.4	37	CCDS2646.1																																																																																			G|0.963;A|0.037	0.037	strong		0.463	EOMES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252995.1	NM_005442		A	27758756	G	A	27758756	2	1	22	1	0	0	0	0	0	0	0	1	5149	1219	43	2		2	EOMES	3	27758756	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	322509	27758756	170263674	811	3712											
GADL1	339896	hgsc.bcm.edu	37	chr3	30842517	30842517	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctgtgtcatagctcacatCatagaatttatcctgctgga	10	14	7	10	0	3	1	3	0	0	1	5	2	5	2	2	1	2	2	2	1	4	4	rs61738477	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:30842517C>A	ENST00000282538.5	-	12	1264	c.1114G>T	c.(1114-1116)Gat>Tat	p.D372Y	GADL1_ENST00000454381.3_Missense_Mutation_p.D372Y	NM_207359.2	NP_997242.2	Q6ZQY3	GADL1_HUMAN	glutamate decarboxylase-like 1	372					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						TAGCTCACATCATAGAATTTA	0.418													C|||	22	0.00439297	0.0144	0.0043	5008	,	,		19418	0.0		0.0	False		,,,				2504	0.0				p.D372Y		Atlas-SNP	.											.	GADL1	91	.	0			c.G1114T						PASS	.	C	TYR/ASP	66,4340	60.5+/-97.4	1,64,2138	132	117	122		1114	5.5	1	3	dbSNP_129	122	1,8599	1.2+/-3.3	0,1,4299	yes	missense	GADL1	NM_207359.2	160	1,65,6437	AA,AC,CC		0.0116,1.498,0.5151	probably-damaging	372/522	30842517	67,12939	2203	4300	6503	SO:0001583	missense	339896	exon12			TCACATCATAGAA	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.1114G>T	3.37:g.30842517C>A	ENSP00000282538:p.Asp372Tyr	99	0	0		122	46	0.377049	NM_207359		Missense_Mutation	SNP	ENST00000282538.5	37	CCDS2649.2	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	C	26.6	4.752769	0.89753	0.01498	1.16E-4	ENSG00000144644	ENST00000282538;ENST00000454381	T;T	0.43688	0.94;0.94	5.47	5.47	0.80525	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.052957	0.64402	D	0.000001	T	0.68696	0.3029	M	0.93375	3.41	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.80311	-0.1436	10	0.87932	D	0	.	19.3171	0.94218	0.0:1.0:0.0:0.0	.	372	Q6ZQY3	GADL1_HUMAN	Y	372	ENSP00000282538:D372Y;ENSP00000427059:D372Y	ENSP00000282538:D372Y	D	-	1	0	GADL1	30817521	1.000000	0.71417	0.998000	0.56505	0.976000	0.68499	7.487000	0.81328	2.571000	0.86741	0.585000	0.79938	GAT	C|0.996;A|0.004	0.004	strong		0.418	GADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253106.2	NM_207359		A	30842517	C	A	30842517	3	1	22	1	0	0	0	0	1	0	0	0	6193	826	29	4	467	4	GADL1	3	30842517	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3083761	30842517	167179913	812	3713											
CLASP2	23122	hgsc.bcm.edu	37	chr3	33759474	33759474	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgcacctgggcgcagaagtaCtccatgctgcggggctccat	7	8	13	13	2	0	1	0	0	0	1	2	1	2	1	3	3	4	5	3	3	2	1	rs112019256	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:33759474C>T	ENST00000468888.2	-	1	67	c.21G>A	c.(19-21)gaG>gaA	p.E7E	CLASP2_ENST00000307312.7_5'UTR|CLASP2_ENST00000399362.4_Silent_p.E7E|CLASP2_ENST00000359576.5_Silent_p.E7E			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						CGCAGAAGTACTCCATGCTGC	0.726													C|||	37	0.00738818	0.025	0.0014	5008	,	,		9762	0.002		0.0	False		,,,				2504	0.001				p.E7E		Atlas-SNP	.											.	CLASP2	138	.	0			c.G21A						PASS	.	C		54,3038		0,54,1492	3	4	3		21	1	1	3	dbSNP_132	3	2,7002		0,2,3500	no	coding-synonymous	CLASP2	NM_015097.2		0,56,4992	TT,TC,CC		0.0286,1.7464,0.5547		7/1516	33759474	56,10040	1546	3502	5048	SO:0001819	synonymous_variant	23122	exon1			GAAGTACTCCATG	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.21G>A	3.37:g.33759474C>T		23	0	0		14	5	0.357143	NM_015097	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Silent	SNP	ENST00000468888.2	37																																																																																				C|0.333;T|0.667	0.667	weak		0.726	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044		T	33759474	C	T	33759474	2	4	22	1	0	0	0	0	0	0	0	1	3457	564	20	2		2	CLASP2	3	33759474	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2916957	33759474	164262956	813	3714											
TRANK1	9881	hgsc.bcm.edu	37	chr3	36887863	36887863	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acccgagcccgtgtgatggcGgtgtacagctgcttcagctc	6	9	13	13	3	1	1	1	1	0	0	2	2	1	1	2	2	5	4	2	2	1	2	rs142584752	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:36887863G>A	ENST00000429976.2	-	16	5182	c.4935C>T	c.(4933-4935)acC>acT	p.T1645T	TRANK1_ENST00000301807.6_Silent_p.T1095T|TRANK1_ENST00000428977.2_Silent_p.T1095T|TRANK1_ENST00000463984.1_5'UTR	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	1645							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						GTGTGATGGCGGTGTACAGCT	0.448													G|||	14	0.00279553	0.0106	0.0	5008	,	,		18174	0.0		0.0	False		,,,				2504	0.0				p.T1645T		Atlas-SNP	.											.	TRANK1	398	.	0			c.C4935T						PASS	.	G		30,3826		1,28,1899	56	54	55		4935	-10.3	0.4	3	dbSNP_134	55	1,8267		0,1,4133	no	coding-synonymous	TRANK1	NM_014831.2		1,29,6032	AA,AG,GG		0.0121,0.778,0.2557		1645/2926	36887863	31,12093	1928	4134	6062	SO:0001819	synonymous_variant	9881	exon16			GATGGCGGTGTAC	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.4935C>T	3.37:g.36887863G>A		175	0	0		224	92	0.410714	NM_014831	Q8N8K0	Silent	SNP	ENST00000429976.2	37	CCDS46789.2																																																																																			G|0.998;A|0.002	0.002	strong		0.448	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		A	36887863	G	A	36887863	2	1	22	1	0	0	0	0	0	0	0	1	16469	1103	39	1		1	TRANK1	3	36887863	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3128389	36887863	161134567	814	3715											
TRANK1	9881	hgsc.bcm.edu	37	chr3	36898699	36898699	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttcttcagcatttctgaagtGcactcgatctcccaggtcat	8	14	7	12	1	5	1	2	1	3	0	7	2	5	1	1	1	2	2	1	1	1	3	rs187740236	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:36898699G>A	ENST00000429976.2	-	12	2629	c.2382C>T	c.(2380-2382)tgC>tgT	p.C794C	TRANK1_ENST00000301807.6_Silent_p.C244C|TRANK1_ENST00000428977.2_Silent_p.C244C	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	794							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						TTTCTGAAGTGCACTCGATCT	0.502													G|||	14	0.00279553	0.0106	0.0	5008	,	,		20254	0.0		0.0	False		,,,				2504	0.0				p.C794C		Atlas-SNP	.											.	TRANK1	398	.	0			c.C2382T						PASS	.	G		34,4008		1,32,1988	243	235	238		2382	-3.4	0.7	3		238	0,8392		0,0,4196	yes	coding-synonymous	TRANK1	NM_014831.2		1,32,6184	AA,AG,GG		0.0,0.8412,0.2734		794/2926	36898699	34,12400	2021	4196	6217	SO:0001819	synonymous_variant	9881	exon12			TGAAGTGCACTCG	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.2382C>T	3.37:g.36898699G>A		54	0	0		74	35	0.472973	NM_014831	Q8N8K0	Silent	SNP	ENST00000429976.2	37	CCDS46789.2																																																																																			G|0.998;A|0.002	0.002	strong		0.502	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		A	36898699	G	A	36898699	2	1	22	1	0	0	0	0	0	0	0	1	16469	1311	46	2		2	TRANK1	3	36898699	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	10836	36898699	161123731	815	3716											
EPM2AIP1	9852	hgsc.bcm.edu	37	chr3	37033348	37033348	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtacaaatatggtcaaaggcAgcagcagcaaagactttact	16	8	9	8	0	1	1	1	0	0	1	1	1	1	1	0	2	5	5	0	2	6	4	rs200289425	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:37033348A>G	ENST00000322716.5	-	1	1447	c.1221T>C	c.(1219-1221)gcT>gcC	p.A407A	MLH1_ENST00000458205.2_5'Flank|MLH1_ENST00000539477.1_5'Flank|MLH1_ENST00000435176.1_5'Flank|MLH1_ENST00000455445.2_5'Flank|MLH1_ENST00000231790.2_5'Flank|MLH1_ENST00000536378.1_5'Flank	NM_014805.3	NP_055620.1	Q7L775	EPMIP_HUMAN	EPM2A (laforin) interacting protein 1	407					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						GGTCAAAGGCAGCAGCAGCAA	0.383													A|||	4	0.000798722	0.003	0.0	5008	,	,		19336	0.0		0.0	False		,,,				2504	0.0				p.A407A		Atlas-SNP	.											.	EPM2AIP1	47	.	0			c.T1221C						PASS	.	A		4,3784		0,4,1890	93	95	95		1221	-2.3	1	3		95	0,8210		0,0,4105	no	coding-synonymous	EPM2AIP1	NM_014805.3		0,4,5995	GG,GA,AA		0.0,0.1056,0.0333		407/608	37033348	4,11994	1894	4105	5999	SO:0001819	synonymous_variant	9852	exon1			AAAGGCAGCAGCA	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.1221T>C	3.37:g.37033348A>G		144	0	0		135	65	0.481481	NM_014805	O94866|Q9H3L3	Silent	SNP	ENST00000322716.5	37	CCDS46790.1																																																																																			A|0.999;G|0.001	0.001	strong		0.383	EPM2AIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470593.1	NM_014805		G	37033348	A	G	37033348	2	3	22	1	0	0	0	0	0	0	0	1	5186	175	7	3		3	EPM2AIP1	3	37033348	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	134649	37033348	160989082	816	3717											
LRRFIP2	9209	hgsc.bcm.edu	37	chr3	37144480	37144480	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acttcccctacgattggagcGactgaaataatcagcggcag	12	8	10	11	3	1	1	1	1	0	0	2	4	2	2	2	2	3	1	2	2	3	4	rs143314448	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:37144480G>A	ENST00000336686.4	-	15	888	c.808C>T	c.(808-810)Cgc>Tgc	p.R270C	LRRFIP2_ENST00000354379.4_Intron|LRRFIP2_ENST00000421307.1_Missense_Mutation_p.R270C|LRRFIP2_ENST00000440230.1_Intron|LRRFIP2_ENST00000421276.2_Intron|LRRFIP2_ENST00000396428.2_Intron			Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting protein 2	270	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						CGATTGGAGCGACTGAAATAA	0.403													G|||	5	0.000998403	0.0038	0.0	5008	,	,		15844	0.0		0.0	False		,,,				2504	0.0				p.R270C		Atlas-SNP	.											.	LRRFIP2	71	.	1	Whole gene deletion(1)	ovary(1)	c.C808T						PASS	.	G	,CYS/ARG,	12,4386		0,12,2187	79	61	67		,808,	6.2	1	3	dbSNP_134	67	0,8592		0,0,4296	yes	intron,missense,intron	LRRFIP2	NM_001134369.1,NM_006309.2,NM_017724.2	,180,	0,12,6483	AA,AG,GG		0.0,0.2729,0.0924	,probably-damaging,	,270/722,	37144480	12,12978	2199	4296	6495	SO:0001583	missense	9209	exon16			TGGAGCGACTGAA	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.808C>T	3.37:g.37144480G>A	ENSP00000338727:p.Arg270Cys	102	0	0		81	39	0.481481	NM_006309	A8K649|A8MXR0|B4DY63|Q68CV3|Q9NXH5	Missense_Mutation	SNP	ENST00000336686.4	37	CCDS2664.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	33	5.265897	0.95399	0.002729	0.0	ENSG00000093167	ENST00000421307;ENST00000336686	T;T	0.56275	0.47;0.47	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.63628	0.2527	N	0.22421	0.69	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.64859	-0.6308	10	0.66056	D	0.02	-8.9955	20.4549	0.99139	0.0:0.0:1.0:0.0	.	270	Q9Y608	LRRF2_HUMAN	C	270	ENSP00000392217:R270C;ENSP00000338727:R270C	ENSP00000338727:R270C	R	-	1	0	LRRFIP2	37119484	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	6.226000	0.72277	2.937000	0.99478	0.650000	0.86243	CGC	G|0.999;A|0.001	0.001	strong		0.403	LRRFIP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253335.3	NM_006309		A	37144480	G	A	37144480	3	1	22	1	0	0	0	0	1	0	0	0	9037	1058	37	1	1413	1	LRRFIP2	3	37144480	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	111132	37144480	160877950	817	3718											
LRRFIP2	9209	hgsc.bcm.edu	37	chr3	37154417	37154417	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaactaaccagtaggtcttTatgagaatcagaagacctct	15	10	8	8	0	3	4	1	1	2	4	3	5	3	4	2	1	2	1	2	1	6	4	rs34902788	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:37154417T>C	ENST00000336686.4	-	8	507	c.427A>G	c.(427-429)Aaa>Gaa	p.K143E	LRRFIP2_ENST00000354379.4_Intron|LRRFIP2_ENST00000421307.1_Missense_Mutation_p.K143E|LRRFIP2_ENST00000440230.1_Intron|LRRFIP2_ENST00000421276.2_Intron|LRRFIP2_ENST00000396428.2_Missense_Mutation_p.K112E			Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting protein 2	143	DVL3-binding.|Ser-rich.		K -> E (in dbSNP:rs34902788).		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						AGTAGGTCTTTATGAGAATCA	0.368													T|||	72	0.014377	0.0514	0.0058	5008	,	,		18111	0.0		0.0	False		,,,				2504	0.0				p.K143E		Atlas-SNP	.											.	LRRFIP2	71	.	1	Whole gene deletion(1)	ovary(1)	c.A427G						PASS	.	T	,GLU/LYS,	190,4216	120.4+/-158.0	7,176,2020	128	128	128		,427,	4.3	1	3	dbSNP_126	128	2,8598	1.2+/-3.3	0,2,4298	yes	intron,missense,intron	LRRFIP2	NM_001134369.1,NM_006309.2,NM_017724.2	,56,	7,178,6318	CC,CT,TT		0.0233,4.3123,1.4762	,possibly-damaging,	,143/722,	37154417	192,12814	2203	4300	6503	SO:0001583	missense	9209	exon9			GGTCTTTATGAGA	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.427A>G	3.37:g.37154417T>C	ENSP00000338727:p.Lys143Glu	43	0	0		46	16	0.347826	NM_006309	A8K649|A8MXR0|B4DY63|Q68CV3|Q9NXH5	Missense_Mutation	SNP	ENST00000336686.4	37	CCDS2664.1	17	0.007783882783882784	15	0.03048780487804878	2	0.0055248618784530384	0	0.0	0	0.0	T	10.81	1.454776	0.26161	0.043123	2.33E-4	ENSG00000093167	ENST00000421307;ENST00000336686;ENST00000396428	T;T;T	0.48201	0.82;0.82;0.87	5.52	4.29	0.51040	.	0.266541	0.34959	N	0.003544	T	0.06554	0.0168	N	0.08118	0	0.29065	N	0.883669	B;B	0.27853	0.076;0.191	B;B	0.28465	0.077;0.09	T	0.04153	-1.0973	10	0.12766	T	0.61	-16.635	12.8465	0.57833	0.0:0.0:0.1352:0.8648	rs34902788	112;143	A8MXR0;Q9Y608	.;LRRF2_HUMAN	E	143;143;112	ENSP00000392217:K143E;ENSP00000338727:K143E;ENSP00000379705:K112E	ENSP00000338727:K143E	K	-	1	0	LRRFIP2	37129421	1.000000	0.71417	0.981000	0.43875	0.935000	0.57460	3.954000	0.56708	2.232000	0.73038	0.482000	0.46254	AAA	T|0.987;C|0.013	0.013	strong		0.368	LRRFIP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253335.3	NM_006309		C	37154417	T	C	37154417	3	2	22	1	0	0	0	0	1	0	0	0	9037	1763	61	3	1822	3	LRRFIP2	3	37154417	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	9937	37154417	160868013	818	3719											
ITGA9	3680	hgsc.bcm.edu	37	chr3	37536020	37536020	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaagtacggagaggaacaCggctcctgccaggctgggat	12	5	15	9	2	0	2	0	0	0	2	1	5	1	4	2	5	3	3	2	5	4	1	rs62001860	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:37536020C>T	ENST00000264741.5	+	5	829	c.573C>T	c.(571-573)caC>caT	p.H191H	ITGA9_ENST00000422441.1_Silent_p.H191H	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	191					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)		GAGAGGAACACGGCTCCTGCC	0.532													C|||	36	0.0071885	0.0272	0.0	5008	,	,		20312	0.0		0.0	False		,,,				2504	0.0				p.H191H		Atlas-SNP	.											.	ITGA9	98	.	0			c.C573T						PASS	.	C		68,4338	64.1+/-101.4	0,68,2135	152	152	152		573	-0.1	1	3	dbSNP_129	152	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ITGA9	NM_002207.2		0,69,6434	TT,TC,CC		0.0116,1.5433,0.5305		191/1036	37536020	69,12937	2203	4300	6503	SO:0001819	synonymous_variant	3680	exon5			GGAACACGGCTCC	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.573C>T	3.37:g.37536020C>T		326	1	0.00306748		312	150	0.480769	NM_002207	Q14638	Silent	SNP	ENST00000264741.5	37	CCDS2669.1																																																																																			C|0.994;T|0.006	0.006	strong		0.532	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207		T	37536020	C	T	37536020	2	4	22	1	0	0	0	0	0	0	0	1	7892	535	19	1		1	ITGA9	3	37536020	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	381603	37536020	160486410	819	3720											
ACVR2B	93	hgsc.bcm.edu	37	chr3	38523754	38523754	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atcaacttccagagagatgcCttcctgcgcattgacatgta	11	11	8	11	1	1	3	1	1	0	2	3	4	3	3	3	0	3	2	3	0	2	4	rs149695736	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:38523754C>T	ENST00000352511.4	+	9	1612	c.1140C>T	c.(1138-1140)gcC>gcT	p.A380A		NM_001106.3	NP_001097.2	Q13705	AVR2B_HUMAN	activin A receptor, type IIB	380	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)		AGAGAGATGCCTTCCTGCGCA	0.572													C|||	8	0.00159744	0.0061	0.0	5008	,	,		21138	0.0		0.0	False		,,,				2504	0.0				p.A380A		Atlas-SNP	.											ACVR2B_ENST00000352511,caecum,carcinoma,0,2	ACVR2B	88	2	0			c.C1140T						PASS	.	C		10,4396	16.8+/-37.8	0,10,2193	128	96	107		1140	3.5	1	3	dbSNP_134	107	0,8600		0,0,4300	yes	coding-synonymous	ACVR2B	NM_001106.3		0,10,6493	TT,TC,CC		0.0,0.227,0.0769		380/513	38523754	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	93	exon9			AGATGCCTTCCTG	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.1140C>T	3.37:g.38523754C>T		218	1	0.00458716		277	141	0.509025	NM_001106	Q4VAV0	Silent	SNP	ENST00000352511.4	37	CCDS2679.1																																																																																			C|0.999;T|0.001	0.001	strong		0.572	ACVR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254059.3	NM_001106		T	38523754	C	T	38523754	2	4	22	1	0	0	0	0	0	0	0	1	224	668	24	2		2	ACVR2B	3	38523754	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	987734	38523754	159498676	820	3721											
SCN5A	6331	hgsc.bcm.edu	37	chr3	38592356	38592356	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatgggcaggtccatgttgAtgaggcttatctggttgggc	6	12	15	8	0	1	2	0	2	1	0	2	2	2	2	2	5	0	4	2	5	1	3	rs45563942	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:38592356A>G	ENST00000333535.4	-	28	5656	c.5507T>C	c.(5506-5508)aTc>aCc	p.I1836T	SCN5A_ENST00000450102.2_Missense_Mutation_p.I1782T|SCN5A_ENST00000414099.2_Missense_Mutation_p.I1818T|SCN5A_ENST00000443581.1_Missense_Mutation_p.I1835T|SCN5A_ENST00000425664.1_Missense_Mutation_p.I1818T|SCN5A_ENST00000455624.2_Missense_Mutation_p.I1803T|SCN5A_ENST00000413689.1_Missense_Mutation_p.I1836T|SCN5A_ENST00000423572.2_Missense_Mutation_p.I1835T|SCN5A_ENST00000464652.1_5'Flank|SCN5A_ENST00000451551.2_Missense_Mutation_p.I1782T|SCN5A_ENST00000449557.2_Missense_Mutation_p.I1782T			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	1836					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)	GTCCATGTTGATGAGGCTTAT	0.552													A|||	8	0.00159744	0.0061	0.0	5008	,	,		21013	0.0		0.0	False		,,,				2504	0.0				p.I1836T		Atlas-SNP	.											.	SCN5A	634	.	0			c.T5507C						PASS	.	A	THR/ILE,THR/ILE,THR/ILE,THR/ILE,THR/ILE,THR/ILE	11,4249		0,11,2119	85	92	90		5504,5507,5453,5408,5345,5507	4.8	1	3	dbSNP_127	90	0,8484		0,0,4242	yes	missense,missense,missense,missense,missense,missense	SCN5A	NM_000335.4,NM_001099404.1,NM_001099405.1,NM_001160160.1,NM_001160161.1,NM_198056.2	89,89,89,89,89,89	0,11,6361	GG,GA,AA		0.0,0.2582,0.0863	benign,benign,benign,benign,benign,benign	1835/2016,1836/2017,1818/1999,1803/1984,1782/1963,1836/2017	38592356	11,12733	2130	4242	6372	SO:0001583	missense	6331	exon28			ATGTTGATGAGGC	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.5507T>C	3.37:g.38592356A>G	ENSP00000328968:p.Ile1836Thr	72	0	0		72	37	0.513889	NM_198056	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Missense_Mutation	SNP	ENST00000333535.4	37	CCDS46796.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	16.43	3.122483	0.56613	0.002582	0.0	ENSG00000183873	ENST00000414099;ENST00000423572;ENST00000413689;ENST00000451551;ENST00000443581;ENST00000425664;ENST00000333535;ENST00000455624;ENST00000450102;ENST00000449557	D;D;D;D;D;D;D;D;D;D	0.96427	-3.92;-3.93;-3.93;-4.0;-3.93;-3.92;-3.93;-4.01;-4.0;-4.0	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	D	0.97539	0.9194	M	0.89095	3.005	0.49213	D	0.999767	B;P;B;B;B;B	0.50710	0.146;0.938;0.07;0.17;0.065;0.261	B;D;B;P;B;P	0.73380	0.379;0.98;0.265;0.547;0.351;0.734	D	0.96083	0.9055	10	0.66056	D	0.02	.	14.5421	0.68002	1.0:0.0:0.0:0.0	rs45563942	1782;1803;1818;1836;1835;1836	E9PEF3;E9PHB6;E9PG18;Q14524;Q14524-2;E9PEK2	.;.;.;SCN5A_HUMAN;.;.	T	1818;1835;1836;1782;1835;1818;1836;1803;1782;1782	ENSP00000398962:I1818T;ENSP00000398266:I1835T;ENSP00000410257:I1836T;ENSP00000388797:I1782T;ENSP00000397915:I1835T;ENSP00000416634:I1818T;ENSP00000328968:I1836T;ENSP00000399524:I1803T;ENSP00000403355:I1782T;ENSP00000413996:I1782T	ENSP00000328968:I1836T	I	-	2	0	SCN5A	38567360	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.133000	0.94460	2.025000	0.59659	0.460000	0.39030	ATC	A|0.999;G|0.001	0.001	strong		0.552	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056		G	38592356	A	G	38592356	3	3	22	1	0	0	0	0	1	0	0	0	13937	333	12	3	547	3	SCN5A	3	38592356	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	68602	38592356	159430074	821	3722											
SCN10A	6336	hgsc.bcm.edu	37	chr3	38770198	38770198	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgtgccagcggggccagtcTtcatggggcgcggagatatt	7	9	16	9	3	2	1	1	0	1	1	2	2	2	1	2	5	2	0	2	5	1	3	rs146028829		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:38770198T>G	ENST00000449082.2	-	15	2474	c.2475A>C	c.(2473-2475)gaA>gaC	p.E825D		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	825					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)	p.E825D(1)		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)	GGGGCCAGTCTTCATGGGGCG	0.517													T|||	1	0.000199681	0.0	0.0	5008	,	,		18556	0.0		0.001	False		,,,				2504	0.0				p.E825D		Atlas-SNP	.											SCN10A,NS,carcinoma,0,2	SCN10A	359	2	1	Substitution - Missense(1)	kidney(1)	c.A2475C						PASS	.	T	ASP/GLU	2,4404	4.2+/-10.8	0,2,2201	121	117	118		2475	-9.4	0	3	dbSNP_134	118	19,8581	14.6+/-50.1	0,19,4281	yes	missense	SCN10A	NM_006514.2	45	0,21,6482	GG,GT,TT		0.2209,0.0454,0.1615	benign	825/1957	38770198	21,12985	2203	4300	6503	SO:0001583	missense	6336	exon15			CCAGTCTTCATGG	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.2475A>C	3.37:g.38770198T>G	ENSP00000390600:p.Glu825Asp	324	0	0		347	160	0.461095	NM_006514	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	37	CCDS33736.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	3.068	-0.191656	0.06299	4.54E-4	0.002209	ENSG00000185313	ENST00000449082	D	0.98531	-4.98	4.73	-9.45	0.00600	Ion transport (1);	1.276660	0.04859	N	0.443792	D	0.93058	0.7790	N	0.16478	0.41	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	D	0.86553	0.1836	10	0.45353	T	0.12	.	6.9757	0.24674	0.0871:0.3789:0.4161:0.1179	.	825	Q9Y5Y9	SCNAA_HUMAN	D	825	ENSP00000390600:E825D	ENSP00000390600:E825D	E	-	3	2	SCN10A	38745202	0.000000	0.05858	0.000000	0.03702	0.069000	0.16628	-1.935000	0.01550	-2.903000	0.00311	0.533000	0.62120	GAA	T|0.999;G|0.001	0.001	strong		0.517	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		G	38770198	T	G	38770198	3	3	22	1	0	0	0	0	1	0	0	0	13927	1606	56	5	3447	5	SCN10A	3	38770198	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	177842	38770198	159252232	822	3723											
TTC21A	199223	hgsc.bcm.edu	37	chr3	39166887	39166887	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggggaggaagagaccacagCgctcctgaaggaggcagtgg	11	3	19	8	1	0	2	0	1	0	1	1	6	1	5	2	6	1	2	2	6	2	0	rs74824603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:39166887C>T	ENST00000431162.2	+	11	1414	c.1280C>T	c.(1279-1281)gCg>gTg	p.A427V	TTC21A_ENST00000301819.6_Missense_Mutation_p.A427V|TTC21A_ENST00000440121.1_Missense_Mutation_p.A378V			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	427										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)		GAGACCACAGCGCTCCTGAAG	0.552											OREG0015487	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	12	0.00239617	0.0083	0.0014	5008	,	,		22490	0.0		0.0	False		,,,				2504	0.0				p.A427V		Atlas-SNP	.											.	TTC21A	96	.	0			c.C1280T						PASS	.						74	74	74					3																	39166887		2029	4198	6227	SO:0001583	missense	199223	exon11			CCACAGCGCTCCT	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.1280C>T	3.37:g.39166887C>T	ENSP00000398211:p.Ala427Val	129	0	0	883	130	61	0.469231	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	37	CCDS46800.1	.	.	.	.	.	.	.	.	.	.	C	5.561	0.288299	0.10513	.	.	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.36157	1.27;1.27;1.27	5.73	0.827	0.18835	.	0.834776	0.10720	N	0.641804	T	0.21022	0.0506	L	0.34521	1.04	0.09310	N	1	B;B;B	0.21309	0.031;0.054;0.032	B;B;B	0.12156	0.007;0.004;0.005	T	0.24657	-1.0154	10	0.27785	T	0.31	-0.2644	1.2509	0.01982	0.2566:0.4043:0.1248:0.2143	.	378;427;427	Q8NDW8-6;Q8NDW8-7;Q8NDW8	.;.;TT21A_HUMAN	V	427;409;427;378	ENSP00000301819:A427V;ENSP00000398211:A427V;ENSP00000410882:A378V	ENSP00000301819:A427V	A	+	2	0	TTC21A	39141891	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	0.215000	0.17562	0.074000	0.16767	0.609000	0.83330	GCG	A|0.004;C|0.994;T|0.001	0.001	strong		0.552	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755		T	39166887	C	T	39166887	3	4	22	1	0	0	0	0	1	0	0	0	16702	768	27	1	1322	1	TTC21A	3	39166887	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	396689	39166887	158855543	823	3724											
TTC21A	199223	hgsc.bcm.edu	37	chr3	39180100	39180100	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agaaatttgtggaggccattGaaatctgcaacgatgtaagc	14	10	11	6	1	1	2	0	1	1	1	1	4	1	3	1	2	3	2	1	2	4	3	rs80238762	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:39180100G>A	ENST00000431162.2	+	28	4005	c.3871G>A	c.(3871-3873)Gaa>Aaa	p.E1291K	TTC21A_ENST00000493856.1_3'UTR|TTC21A_ENST00000301819.6_Missense_Mutation_p.E1292K|TTC21A_ENST00000440121.1_Missense_Mutation_p.E1243K			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	1291				E -> K (in Ref. 2; BAG63755). {ECO:0000305}.						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)		GGAGGCCATTGAAATCTGCAA	0.522													G|||	29	0.00579073	0.0008	0.0173	5008	,	,		20962	0.0		0.0159	False		,,,				2504	0.0				p.E1291K		Atlas-SNP	.											.	TTC21A	96	.	0			c.G3871A						PASS	.	G	LYS/GLU,LYS/GLU	8,3990		0,8,1991	113	110	111		3727,3871	5.1	0.9	3	dbSNP_132	111	91,8241		1,89,4076	yes	missense,missense	TTC21A	NM_001105513.2,NM_145755.2	56,56	1,97,6067	AA,AG,GG		1.0922,0.2001,0.8029	possibly-damaging,possibly-damaging	1243/1273,1291/1321	39180100	99,12231	1999	4166	6165	SO:0001583	missense	199223	exon28			GCCATTGAAATCT	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.3871G>A	3.37:g.39180100G>A	ENSP00000398211:p.Glu1291Lys	236	1	0.00423729		236	111	0.470339	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	37	CCDS46800.1	15	0.006868131868131868	0	0.0	7	0.019337016574585635	0	0.0	8	0.010554089709762533	G	22.7	4.325101	0.81580	0.002001	0.010922	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.78481	-1.18;-1.18;-1.18	5.14	5.14	0.70334	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.151938	0.42682	D	0.000679	T	0.72486	0.3466	M	0.64170	1.965	0.58432	D	0.999999	P;D;P	0.55605	0.921;0.972;0.953	P;P;P	0.53912	0.497;0.737;0.551	T	0.78620	-0.2133	10	0.41790	T	0.15	-2.9838	17.3579	0.87342	0.0:0.0:1.0:0.0	.	1243;1292;1291	Q8NDW8-6;Q8NDW8-7;Q8NDW8	.;.;TT21A_HUMAN	K	1292;1274;1291;1243	ENSP00000301819:E1292K;ENSP00000398211:E1291K;ENSP00000410882:E1243K	ENSP00000301819:E1292K	E	+	1	0	TTC21A	39155104	1.000000	0.71417	0.918000	0.36340	0.278000	0.26855	7.431000	0.80335	2.377000	0.81083	0.561000	0.74099	GAA	G|0.989;A|0.011	0.011	strong		0.522	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755		A	39180100	G	A	39180100	3	1	22	1	0	0	0	0	1	0	0	0	16702	1291	45	2	3984	2	TTC21A	3	39180100	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	13213	39180100	158842330	824	3725											
XIRP1	165904	hgsc.bcm.edu	37	chr3	39225549	39225549	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggtgggagcctgggttcctGggtggctctgcctgctcggt	2	11	18	10	1	1	0	0	0	1	0	3	1	2	1	3	6	3	3	3	6	0	1	rs36091974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:39225549G>C	ENST00000340369.3	-	2	5616	c.5388C>G	c.(5386-5388)ccC>ccG	p.P1796P	XIRP1_ENST00000396251.1_3'UTR|XIRP1_ENST00000421646.1_Silent_p.P479P	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	1796	Interaction with FLNC.				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)		CTGGGTTCCTGGGTGGCTCTG	0.602													G|||	121	0.0241613	0.0862	0.0086	5008	,	,		20643	0.0		0.001	False		,,,				2504	0.0				p.P1796P		Atlas-SNP	.											.	XIRP1	173	.	0			c.C5388G						PASS	.	G	,	362,4044	186.4+/-213.3	17,328,1858	126	132	130		,5388	2.4	0	3	dbSNP_126	130	3,8597	3.0+/-9.4	0,3,4297	yes	utr-3,coding-synonymous	XIRP1	NM_001198621.1,NM_194293.2	,	17,331,6155	CC,CG,GG		0.0349,8.2161,2.8064	,	,1796/1844	39225549	365,12641	2203	4300	6503	SO:0001819	synonymous_variant	165904	exon2			GTTCCTGGGTGGC	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.5388C>G	3.37:g.39225549G>C		187	0	0		214	107	0.5	NM_194293	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Silent	SNP	ENST00000340369.3	37	CCDS2683.1																																																																																			G|0.973;C|0.027	0.027	strong		0.602	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522		C	39225549	G	C	39225549	2	2	22	1	0	0	0	0	0	0	0	1	17444	1335	47	4		4	XIRP1	3	39225549	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	45449	39225549	158796881	825	3726											
XIRP1	165904	hgsc.bcm.edu	37	chr3	39228514	39228514	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggtgcccctgccctgtgcccGagagcacatacttggcaaga	8	7	12	14	1	0	2	0	0	0	2	0	3	0	2	4	2	5	2	4	2	2	2	rs61736154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:39228514G>A	ENST00000340369.3	-	2	2651	c.2423C>T	c.(2422-2424)tCg>tTg	p.S808L	XIRP1_ENST00000396251.1_Missense_Mutation_p.S808L|XIRP1_ENST00000421646.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	808					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)		CCCTGTGCCCGAGAGCACATA	0.612													G|||	103	0.0205671	0.0719	0.0058	5008	,	,		19504	0.0		0.0	False		,,,				2504	0.0041				p.S808L		Atlas-SNP	.											.	XIRP1	173	.	0			c.C2423T						PASS	.	G	LEU/SER,LEU/SER	316,4090	169.1+/-199.8	13,290,1900	64	65	65		2423,2423	3.2	0.6	3	dbSNP_129	65	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	XIRP1	NM_001198621.1,NM_194293.2	145,145	13,293,6197	AA,AG,GG		0.0349,7.172,2.4527	benign,benign	808/1122,808/1844	39228514	319,12687	2203	4300	6503	SO:0001583	missense	165904	exon2			GTGCCCGAGAGCA	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.2423C>T	3.37:g.39228514G>A	ENSP00000343140:p.Ser808Leu	149	0	0		158	73	0.462025	NM_001198621	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	37	CCDS2683.1	38	0.0173992673992674	36	0.07317073170731707	2	0.0055248618784530384	0	0.0	0	0.0	G	3.312	-0.140545	0.06669	0.07172	3.49E-4	ENSG00000168334	ENST00000396251;ENST00000340369	T;T	0.04862	3.54;3.95	4.11	3.23	0.37069	.	0.252041	0.37178	N	0.002208	T	0.00356	0.0011	N	0.14661	0.345	0.09310	N	0.999996	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41034	-0.9531	10	0.56958	D	0.05	.	10.0728	0.42343	0.1005:0.0:0.8995:0.0	.	808;808	Q702N8;Q702N8-2	XIRP1_HUMAN;.	L	808	ENSP00000379550:S808L;ENSP00000343140:S808L	ENSP00000343140:S808L	S	-	2	0	XIRP1	39203518	0.352000	0.24895	0.624000	0.29186	0.033000	0.12548	1.016000	0.29976	1.099000	0.41499	-0.244000	0.11960	TCG	G|0.977;A|0.023	0.023	strong		0.612	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522		A	39228514	G	A	39228514	3	1	22	1	0	0	0	0	1	0	0	0	17444	1059	37	1	3112	1	XIRP1	3	39228514	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2965	39228514	158793916	826	3727											
MYRIP	25924	hgsc.bcm.edu	37	chr3	40223771	40223771	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgaagacccctccagtggagGctccatcgaggcagccaagg	10	5	13	13	1	0	2	0	1	0	1	3	4	2	3	5	4	1	2	5	4	2	0	rs59923220	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:40223771G>A	ENST00000302541.6	+	9	1276	c.934G>A	c.(934-936)Gct>Act	p.A312T	MYRIP_ENST00000539167.1_Missense_Mutation_p.A125T|MYRIP_ENST00000444716.1_Missense_Mutation_p.A312T|MYRIP_ENST00000459828.1_3'UTR|MYRIP_ENST00000396217.3_Missense_Mutation_p.A223T|MYRIP_ENST00000425621.1_Missense_Mutation_p.A312T	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	312	Myosin-binding.		A -> T (in dbSNP:rs59923220). {ECO:0000269|PubMed:15489334}.		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)		TCCAGTGGAGGCTCCATCGAG	0.567													G|||	391	0.0780751	0.2746	0.0346	5008	,	,		17481	0.0		0.004	False		,,,				2504	0.0				p.A312T		Atlas-SNP	.											.	MYRIP	98	.	0			c.G934A						PASS	.	G	THR/ALA	1037,3369	382.8+/-324.6	108,821,1274	76	77	77		934	0.8	0.1	3	dbSNP_129	77	13,8587	9.8+/-36.6	0,13,4287	yes	missense	MYRIP	NM_015460.2	58	108,834,5561	AA,AG,GG		0.1512,23.5361,8.0732	benign	312/860	40223771	1050,11956	2203	4300	6503	SO:0001583	missense	25924	exon9			GTGGAGGCTCCAT	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.934G>A	3.37:g.40223771G>A	ENSP00000301972:p.Ala312Thr	124	0	0		140	62	0.442857	NM_015460	B3KWM3|B3KWW4|B7Z2H1|B7Z9V3|G3XAI8|Q32M41|Q32M42|Q569F7|Q8IUF5|Q9Y3V4	Missense_Mutation	SNP	ENST00000302541.6	37	CCDS2689.1	161	0.07371794871794872	150	0.3048780487804878	10	0.027624309392265192	0	0.0	1	0.0013192612137203166	G	9.859	1.195685	0.22037	0.235361	0.001512	ENSG00000170011	ENST00000444716;ENST00000302541;ENST00000425621;ENST00000396217;ENST00000539167	T;T;T;T;T	0.25250	1.81;1.81;1.81;1.81;1.81	5.27	0.792	0.18625	Myelin-associated oligodendrocytic basic protein (MOBP) (1);	0.590955	0.16727	N	0.202020	T	0.00012	0.0000	L	0.40543	1.245	0.54753	P	1.799999999996249E-5	B;B;B	0.22080	0.064;0.001;0.003	B;B;B	0.22152	0.038;0.006;0.009	T	0.43032	-0.9416	8	.	.	.	.	6.3243	0.21234	0.2573:0.0:0.6071:0.1356	rs59923220	223;312;312	Q32M42;G3XAI8;Q8NFW9	.;.;MYRIP_HUMAN	T	312;312;312;223;125	ENSP00000398665:A312T;ENSP00000301972:A312T;ENSP00000389323:A312T;ENSP00000379519:A223T;ENSP00000438297:A125T	.	A	+	1	0	MYRIP	40198775	0.997000	0.39634	0.096000	0.21009	0.003000	0.03518	0.665000	0.25083	0.211000	0.20683	-0.136000	0.14681	GCT	G|0.927;A|0.073	0.073	strong		0.567	MYRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254181.2	NM_015460		A	40223771	G	A	40223771	3	1	22	1	0	0	0	0	1	0	0	0	10109	1203	42	2	964	2	MYRIP	3	40223771	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	995257	40223771	157798659	827	3728											
CYP8B1	1582	hgsc.bcm.edu	37	chr3	42916596	42916596	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtggctcacggagagcatcTtgtgaaagagacgctggagt	10	9	15	7	2	2	3	1	1	1	2	2	6	2	4	0	3	1	3	0	3	1	1	rs35764459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:42916596T>C	ENST00000316161.4	-	1	1037	c.713A>G	c.(712-714)aAg>aGg	p.K238R	KRBOX1_ENST00000426937.1_Intron|RP11-141M3.5_ENST00000471537.1_RNA|CYP8B1_ENST00000437102.1_Missense_Mutation_p.K238R	NM_004391.2	NP_004382.2	Q9UNU6	CP8B1_HUMAN	cytochrome P450, family 8, subfamily B, polypeptide 1	238			K -> R (in dbSNP:rs35764459).		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)		GGAGAGCATCTTGTGAAAGAG	0.572													T|||	108	0.0215655	0.0779	0.0072	5008	,	,		18049	0.0		0.0	False		,,,				2504	0.0				p.K238R		Atlas-SNP	.											.	CYP8B1	59	.	0			c.A713G						PASS	.	T	ARG/LYS	305,4099		8,289,1905	25	27	26		713	4.2	0	3	dbSNP_126	26	7,8589		0,7,4291	yes	missense	CYP8B1	NM_004391.2	26	8,296,6196	CC,CT,TT		0.0814,6.9255,2.4	benign	238/502	42916596	312,12688	2202	4298	6500	SO:0001583	missense	1582	exon1			AGCATCTTGTGAA	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.713A>G	3.37:g.42916596T>C	ENSP00000318867:p.Lys238Arg	98	0	0		98	46	0.469388	NM_004391	B2RCY3|O75958|Q6NWT2|Q6NWT3	Missense_Mutation	SNP	ENST00000316161.4	37	CCDS2707.1	40	0.018315018315018316	38	0.07723577235772358	2	0.0055248618784530384	0	0.0	0	0.0	T	10.40	1.340138	0.24339	0.069255	8.14E-4	ENSG00000180432	ENST00000437102;ENST00000316161	T;T	0.69685	-0.42;-0.42	5.34	4.18	0.49190	.	0.469912	0.21438	N	0.074528	T	0.05410	0.0143	L	0.38838	1.175	0.09310	N	1	B;B	0.28258	0.205;0.205	B;B	0.29077	0.098;0.098	T	0.05566	-1.0877	10	0.42905	T	0.14	-8.3878	8.1412	0.31084	0.0:0.1655:0.0:0.8345	rs35764459;rs56678767	238;238	C9JFR9;Q9UNU6	.;CP8B1_HUMAN	R	238	ENSP00000404499:K238R;ENSP00000318867:K238R	ENSP00000318867:K238R	K	-	2	0	CYP8B1	42891600	0.004000	0.15560	0.011000	0.14972	0.684000	0.39900	1.063000	0.30567	0.885000	0.36088	0.449000	0.29647	AAG	T|0.977;C|0.023	0.023	strong		0.572	CYP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256653.1	NM_004391		C	42916596	T	C	42916596	3	2	22	1	0	0	0	0	1	0	0	0	4200	1609	56	3	796	3	CYP8B1	3	42916596	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2692825	42916596	155105834	828	3729											
LARS2	23395	hgsc.bcm.edu	37	chr3	45459030	45459030	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cctgctgaaaatgccgcagtCgagaggaatctacatccaca	13	7	9	12	2	1	2	0	1	1	1	3	4	2	3	3	1	3	2	3	1	4	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:45459030C>T	ENST00000415258.1	+	4	561	c.420C>T	c.(418-420)gtC>gtT	p.V140V	LARS2_ENST00000265537.3_Silent_p.V140V|LARS2_ENST00000414984.1_Silent_p.V97V			Q15031	SYLM_HUMAN	leucyl-tRNA synthetase 2, mitochondrial	140					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)	ATGCCGCAGTCGAGAGGAATC	0.398																																					p.V140V		Atlas-SNP	.											.	LARS2	48	.	0			c.C420T						PASS	.						123	116	118					3																	45459030		2203	4300	6503	SO:0001819	synonymous_variant	23395	exon5			CGCAGTCGAGAGG	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.420C>T	3.37:g.45459030C>T		143	0	0		100	29	0.29	NM_015340		Silent	SNP	ENST00000415258.1	37	CCDS2728.1																																																																																			.	.	none		0.398	LARS2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345001.1	NM_015340		T	45459030	C	T	45459030	2	4	22	1	0	0	0	0	0	0	0	1	8644	871	31	1		1	LARS2	3	45459030	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2542434	45459030	152563400	829	3730											
CXCR6	10663	hgsc.bcm.edu	37	chr3	45987980	45987980	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcagaacagacaccatggcaGagcatgattaccatgaagac	16	6	9	10	0	1	6	1	2	0	4	1	6	1	6	2	1	3	2	2	1	3	1	rs2234355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:45987980G>A	ENST00000458629.1	+	1	1470	c.7G>A	c.(7-9)Gag>Aag	p.E3K	FYCO1_ENST00000535325.1_Intron|FYCO1_ENST00000438446.1_Intron|CXCR6_ENST00000304552.4_Missense_Mutation_p.E3K|CXCR6_ENST00000457814.1_Missense_Mutation_p.E3K|FYCO1_ENST00000296137.2_Intron|CXCR6_ENST00000438735.1_Missense_Mutation_p.E3K			O00574	CXCR6_HUMAN	chemokine (C-X-C motif) receptor 6	3			E -> K (in dbSNP:rs2234355). {ECO:0000269|Ref.4}.		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)		CACCATGGCAGAGCATGATTA	0.483													G|||	702	0.140176	0.4909	0.0677	5008	,	,		22359	0.0		0.005	False		,,,				2504	0.001				p.E3K	Esophageal Squamous(63;1005 1117 15521 45762 47089)	Atlas-SNP	.											.	CXCR6	17	.	0			c.G7A						PASS	.	G	LYS/GLU,	1842,2564	534.4+/-373.9	402,1038,763	139	141	140		7,	3.8	0.2	3	dbSNP_98	140	23,8577	16.0+/-53.3	0,23,4277	yes	missense,intron	CXCR6,FYCO1	NM_006564.1,NM_024513.2	56,	402,1061,5040	AA,AG,GG		0.2674,41.8066,14.3395	benign,	3/343,	45987980	1865,11141	2203	4300	6503	SO:0001583	missense	10663	exon2			ATGGCAGAGCATG	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.7G>A	3.37:g.45987980G>A	ENSP00000395704:p.Glu3Lys	171	0	0		137	67	0.489051	NM_006564	O00575|Q9HCA5	Missense_Mutation	SNP	ENST00000458629.1	37	CCDS2735.1	255	0.11675824175824176	230	0.46747967479674796	24	0.06629834254143646	0	0.0	1	0.0013192612137203166	G	17.55	3.418151	0.62622	0.418066	0.002674	ENSG00000172215	ENST00000438735;ENST00000304552;ENST00000458629;ENST00000457814	T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21	5.57	3.8	0.43715	.	3.673050	0.00622	N	0.000453	T	0.00012	0.0000	N	0.19112	0.55	0.35184	P	0.227213	P	0.39665	0.682	B	0.30401	0.115	T	0.29882	-0.9997	9	0.46703	T	0.11	.	9.5395	0.39242	0.1649:0.0:0.8351:0.0	rs2234355;rs52808267;rs56447809;rs2234355	3	O00574	CXCR6_HUMAN	K	3	ENSP00000396218:E3K;ENSP00000304414:E3K;ENSP00000395704:E3K;ENSP00000396886:E3K	ENSP00000304414:E3K	E	+	1	0	CXCR6	45962984	0.000000	0.05858	0.206000	0.23566	0.198000	0.23893	0.391000	0.20784	0.729000	0.32403	0.655000	0.94253	GAG	G|0.857;A|0.143	0.143	strong		0.483	CXCR6-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344395.1			A	45987980	G	A	45987980	3	1	22	1	0	0	0	0	1	0	0	0	4097	943	33	2	9	2	CXCR6	3	45987980	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	528950	45987980	152034450	830	3731											
FYCO1	79443	hgsc.bcm.edu	37	chr3	46009620	46009620	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcttgaagcttctcccctagCtcctgcatctcctgggccgc	4	11	9	17	1	2	1	0	1	2	0	5	1	3	1	5	1	3	4	5	1	2	3	rs34147726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:46009620C>T	ENST00000296137.2	-	8	1411	c.1206G>A	c.(1204-1206)gaG>gaA	p.E402E	FYCO1_ENST00000535325.1_Silent_p.E402E	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	402					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)		TCTCCCCTAGCTCCTGCATCT	0.572													C|||	489	0.0976438	0.354	0.0303	5008	,	,		19633	0.0		0.0	False		,,,				2504	0.0				p.E402E		Atlas-SNP	.											.	FYCO1	115	.	0			c.G1206A						PASS	.	C		1328,3078	445.1+/-347.6	201,926,1076	195	195	195		1206	2.8	0.9	3	dbSNP_126	195	13,8587	9.1+/-34.3	0,13,4287	no	coding-synonymous	FYCO1	NM_024513.2		201,939,5363	TT,TC,CC		0.1512,30.1407,10.3106		402/1479	46009620	1341,11665	2203	4300	6503	SO:0001819	synonymous_variant	79443	exon8			CCCTAGCTCCTGC	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.1206G>A	3.37:g.46009620C>T		149	0	0		139	59	0.42446	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Silent	SNP	ENST00000296137.2	37	CCDS2734.1																																																																																			C|0.907;T|0.093	0.093	strong		0.572	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513		T	46009620	C	T	46009620	2	4	22	1	0	0	0	0	0	0	0	1	6133	796	28	2		2	FYCO1	3	46009620	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	21640	46009620	152012810	831	3732											
CCR2	729230	hgsc.bcm.edu	37	chr3	46401243	46401243	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggtccaggagtgagaccAggaaagaatgtgaaagtgac	15	5	16	5	0	0	4	0	3	0	2	1	8	1	7	2	4	0	0	2	4	3	0	rs3918386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:46401243A>G	ENST00000400888.2	+	2	1056	c.1017A>G	c.(1015-1017)ccA>ccG	p.P339P	CCR2_ENST00000292301.4_Silent_p.P339P			P41597	CCR2_HUMAN	chemokine (C-C motif) receptor 2	339					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)		GAGTGAGACCAGGAAAGAATG	0.498													A|||	356	0.0710863	0.2595	0.0187	5008	,	,		19407	0.0		0.0	False		,,,				2504	0.0				p.P339P		Atlas-SNP	.											.	CCR2	103	.	0			c.A1017G						PASS	.	A		597,2539		60,477,1031	119	108	111		1017	-4.7	0	3	dbSNP_108	111	7,7157		0,7,3575	no	coding-synonymous	CCR2	NM_001123041.2		60,484,4606	GG,GA,AA		0.0977,19.037,5.8641		339/375	46401243	604,9696	1568	3582	5150	SO:0001819	synonymous_variant	729230	exon3			GAGACCAGGAAAG		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.1017A>G	3.37:g.46401243A>G		87	0	0		74	32	0.432432	NM_001123041	A0AVQ3|B2RMT0|Q4VBL2	Silent	SNP	ENST00000400888.2	37	CCDS43078.1																																																																																			A|0.940;G|0.060	0.060	strong		0.498	CCR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344292.1	NM_000647		G	46401243	A	G	46401243	2	3	22	1	0	0	0	0	0	0	0	1	2943	175	7	3		3	CCR2	3	46401243	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	391623	46401243	151621187	832	3733											
LTF	4057	hgsc.bcm.edu	37	chr3	46496843	46496843	+	Frame_Shift_Del	DEL	C	C	-																															ggagaaggcacatttgttttCccctgtccccgcacacaggc																								rs571988865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:46496843delC	ENST00000231751.4	-	5	884	c.589delG	c.(589-591)gaafs	p.E197fs	LTF_ENST00000417439.1_Frame_Shift_Del_p.E197fs|LTF_ENST00000426532.2_Frame_Shift_Del_p.E153fs	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	197	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)		CATTTGTTTTCCCCTGTCCCC	0.562													CCCC|CCCC|CCC|deletion	12	0.00239617	0.0091	0.0	5008	,	,		22260	0.0		0.0	False		,,,				2504	0.0				p.E197fs		Pindel,Atlas-Indel	.											.	LTF	98	.	0			c.590delA						PASS	.		,	55,4211		13,29,2091	144	122	129		,	-9.6	0	3		130	74,8180		37,0,4090	no	frameshift,frameshift	LTF	NM_002343.3,NM_001199149.1	,	50,29,6181	A1A1,A1R,RR		0.8965,1.2893,1.0304	,	,	46496843	129,12391	2203	4300	6503	SO:0001589	frameshift_variant	4057	exon5			.		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.589delG	3.37:g.46496843delC	ENSP00000231751:p.Glu197fs	128	0	.		143	43	0.301	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	37	CCDS33747.1																																																																																			.	.	none		0.562	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343		-	46496843	C	-	46496843	7	5	22	1	0	1	0	1	0	0	0	0	9088	864	30	0	1595	0	LTF	3	46496843	Frame_Shift_Del	DEL	C	TCGA-G8-6324-01A-11D-2210-10	95600	46496843	151525587	833	3734											
LTF	4057	hgsc.bcm.edu	37	chr3	46496854	46496854	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atttgttttcccctgtccccGcacacaggcgacacaggttg	7	11	9	14	2	0	0	0	0	0	0	2	1	2	0	4	2	0	3	4	2	0	4	rs60938611	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:46496854G>A	ENST00000231751.4	-	5	873	c.578C>T	c.(577-579)gCg>gTg	p.A193V	LTF_ENST00000417439.1_Missense_Mutation_p.A193V|LTF_ENST00000426532.2_Missense_Mutation_p.A149V	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	193	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)		CCCTGTCCCCGCACACAGGCG	0.552													G|||	324	0.0646965	0.2337	0.0216	5008	,	,		22455	0.0		0.0	False		,,,				2504	0.0				p.A193V		Atlas-SNP	.											.	LTF	98	.	0			c.C578T						PASS	.	G	VAL/ALA,VAL/ALA	726,3680	299.6+/-285.9	64,598,1541	140	115	124		446,578	-5.2	0	3	dbSNP_129	124	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	LTF	NM_001199149.1,NM_002343.3	64,64	64,603,5836	AA,AG,GG		0.0581,16.4775,5.6205	benign,benign	149/667,193/711	46496854	731,12275	2203	4300	6503	SO:0001583	missense	4057	exon5			GTCCCCGCACACA		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.578C>T	3.37:g.46496854G>A	ENSP00000231751:p.Ala193Val	132	0	0		141	68	0.482269	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Missense_Mutation	SNP	ENST00000231751.4	37	CCDS33747.1	102|102	0.046703296703296704|0.046703296703296704	92|92	0.18699186991869918|0.18699186991869918	7|7	0.019337016574585635|0.019337016574585635	0|0	0.0|0.0	3|3	0.00395778364116095|0.00395778364116095	G|G	7.510|7.510	0.654550|0.654550	0.14580|0.14580	0.164775|0.164775	5.81E-4|5.81E-4	ENSG00000012223|ENSG00000012223	ENST00000231751;ENST00000426532;ENST00000417439;ENST00000443496|ENST00000443743	T;T;T;T|.	0.34667|.	1.35;1.35;1.35;1.35|.	4.79|4.79	-5.21|-5.21	0.02815|0.02815	.|.	1.046820|.	0.07391|.	N|.	0.889107|.	T|T	0.00039|0.00039	0.0001|0.0001	N|N	0.25245|0.25245	0.725|0.725	0.80722|0.80722	P|P	0.0|0.0	B;B;B|.	0.15473|.	0.013;0.011;0.013|.	B;B;B|.	0.08055|.	0.002;0.003;0.002|.	T|T	0.29761|0.29761	-1.0001|-1.0001	9|5	0.10377|0.87932	T|D	0.69|0	0.3304|0.3304	5.6254|5.6254	0.17480|0.17480	0.3945:0.0:0.398:0.2075|0.3945:0.0:0.398:0.2075	rs60938611;rs61740469|rs60938611;rs61740469	193;180;193|.	E7ER44;E7EQB2;P02788|.	.;.;TRFL_HUMAN|.	V|W	193;149;193;180|126	ENSP00000231751:A193V;ENSP00000405719:A149V;ENSP00000405546:A193V;ENSP00000397427:A180V|.	ENSP00000231751:A193V|ENSP00000393737:R126W	A|R	-|-	2|1	0|2	LTF|LTF	46471858|46471858	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.023000|0.023000	0.10783|0.10783	-0.754000|-0.754000	0.04787|0.04787	-0.692000|-0.692000	0.05128|0.05128	-1.728000|-1.728000	0.00702|0.00702	GCG|CGG	G|0.949;A|0.051	0.051	strong		0.552	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343		A	46496854	G	A	46496854	3	1	22	1	0	0	0	0	1	0	0	0	9088	1087	38	1	1606	1	LTF	3	46496854	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	11	46496854	151525576	834	3735											
LTF	4057	hgsc.bcm.edu	37	chr3	46501308	46501308	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctacggccagccagacacagTcctgggagagaggggccaag	11	3	15	12	1	0	2	0	0	0	2	1	4	1	3	4	4	2	0	4	4	2	1	rs61740461	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:46501308T>C	ENST00000231751.4	-	2	340	c.45A>G	c.(43-45)ggA>ggG	p.G15G	LTF_ENST00000417439.1_Splice_Site_p.G15G|LTF_ENST00000426532.2_5'UTR	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	15					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)		CCAGACACAGTCCTGGGAGAG	0.562													T|||	351	0.0700879	0.2549	0.0202	5008	,	,		17512	0.0		0.0	False		,,,				2504	0.0				p.G15G		Atlas-SNP	.											.	LTF	98	.	0			c.A45G						PASS	.	T	,	855,3551	318.8+/-295.8	83,689,1431	58	50	52		,45	0.4	1	3	dbSNP_129	52	6,8594	3.7+/-12.6	0,6,4294	yes	utr-5,coding-synonymous-near-splice	LTF	NM_001199149.1,NM_002343.3	,	83,695,5725	CC,CT,TT		0.0698,19.4054,6.62	,	,15/711	46501308	861,12145	2203	4300	6503	SO:0001630	splice_region_variant	4057	exon2			ACACAGTCCTGGG		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.44-1A>G	3.37:g.46501308T>C		135	0	0		120	65	0.541667	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Silent	SNP	ENST00000231751.4	37	CCDS33747.1																																																																																			T|0.931;C|0.069	0.069	strong		0.562	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343	Silent	C	46501308	T	C	46501308	5	2	22	1	0	0	0	0	0	0	1	0	9088	1681	58	3	2151	3	LTF	3	46501308	Splice_Site	SNP	T	TCGA-G8-6324-01A-11D-2210-10	4454	46501308	151521122	835	3736											
KIF9	64147	hgsc.bcm.edu	37	chr3	47286320	47286320	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttcttggacttggctttcTtcccaggtttggtagagaaa	7	16	10	8	0	3	1	0	0	3	1	4	3	4	2	1	4	0	3	1	4	2	7	rs115610071	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:47286320T>C	ENST00000265529.3	-	16	2155	c.1475A>G	c.(1474-1476)aAg>aGg	p.K492R	KIF9_ENST00000452770.2_Missense_Mutation_p.K492R|KIF9_ENST00000335044.2_Missense_Mutation_p.K492R|KIF9-AS1_ENST00000429315.3_RNA|KIF9_ENST00000487440.1_5'UTR|KIF9_ENST00000352910.4_Missense_Mutation_p.K399R|KIF9_ENST00000444589.2_Missense_Mutation_p.K492R			Q9HAQ2	KIF9_HUMAN	kinesin family member 9	492					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)		CTTGGCTTTCTTCCCAGGTTT	0.567													T|||	19	0.00379393	0.0	0.0086	5008	,	,		19521	0.001		0.008	False		,,,				2504	0.0041				p.K492R	Colon(44;962 1147 15977 24541)	Atlas-SNP	.											.	KIF9	59	.	0			c.A1475G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS	7,4399	12.9+/-30.5	0,7,2196	177	149	158		1475,1475,1475	4.7	1	3	dbSNP_132	158	103,8497	56.4+/-117.6	2,99,4199	yes	missense,missense,missense	KIF9	NM_001134878.1,NM_022342.4,NM_182902.3	26,26,26	2,106,6395	CC,CT,TT		1.1977,0.1589,0.8458	benign,benign,benign	492/791,492/726,492/791	47286320	110,12896	2203	4300	6503	SO:0001583	missense	64147	exon15			GCTTTCTTCCCAG	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.1475A>G	3.37:g.47286320T>C	ENSP00000265529:p.Lys492Arg	216	0	0		175	84	0.48	NM_182902	Q86Z28|Q9H8A4	Missense_Mutation	SNP	ENST00000265529.3	37	CCDS2752.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	T	8.708	0.911321	0.17833	0.001589	0.011977	ENSG00000088727	ENST00000335044;ENST00000265529;ENST00000444589;ENST00000452770;ENST00000352910	T;T;T;T;T	0.51574	0.7;0.7;0.7;0.7;0.7	4.65	4.65	0.58169	.	0.263417	0.32372	N	0.006192	T	0.19208	0.0461	N	0.16478	0.41	0.24963	N	0.991717	P;B	0.38020	0.615;0.373	B;B	0.34779	0.189;0.051	T	0.07849	-1.0751	10	0.23302	T	0.38	.	7.0449	0.25040	0.0:0.0998:0.0:0.9002	.	492;492	Q9HAQ2-2;Q9HAQ2	.;KIF9_HUMAN	R	492;492;492;492;399	ENSP00000333942:K492R;ENSP00000265529:K492R;ENSP00000414987:K492R;ENSP00000391100:K492R;ENSP00000292334:K399R	ENSP00000265529:K492R	K	-	2	0	KIF9	47261324	1.000000	0.71417	1.000000	0.80357	0.030000	0.12068	2.914000	0.48797	2.095000	0.63458	0.528000	0.53228	AAG	T|0.992;C|0.008	0.008	strong		0.567	KIF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257475.2			C	47286320	T	C	47286320	3	2	22	1	0	0	0	0	1	0	0	0	8319	1609	56	3	925	3	KIF9	3	47286320	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	785012	47286320	150736110	836	3737											
PTPN23	25930	hgsc.bcm.edu	37	chr3	47454398	47454398	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaatcccatcttcctcccCgccccccctttcctccccac	4	9	1	27	1	1	0	0	0	1	0	6	0	6	0	11	0	0	0	11	0	1	2	rs140165828	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:47454398C>T	ENST00000265562.4	+	25	4711	c.4634C>T	c.(4633-4635)cCg>cTg	p.P1545L	PTPN23_ENST00000431726.1_Missense_Mutation_p.P1419L	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	1545	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)		TCTTCCTCCCCGCCCCCCCTT	0.701													C|||	9	0.00179712	0.0068	0.0	5008	,	,		11435	0.0		0.0	False		,,,				2504	0.0				p.P1545L		Atlas-SNP	.											PTPN23,NS,carcinoma,-1,1	PTPN23	85	1	0			c.C4634T						PASS	.	C	LEU/PRO	19,4375		0,19,2178	21	24	23		4634	3.9	0.8	3	dbSNP_134	23	0,8586		0,0,4293	yes	missense	PTPN23	NM_015466.2	98	0,19,6471	TT,TC,CC		0.0,0.4324,0.1464	probably-damaging	1545/1637	47454398	19,12961	2197	4293	6490	SO:0001583	missense	25930	exon25			CCTCCCCGCCCCC	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.4634C>T	3.37:g.47454398C>T	ENSP00000265562:p.Pro1545Leu	237	0	0		247	116	0.469636	NM_015466	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Missense_Mutation	SNP	ENST00000265562.4	37	CCDS2754.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	13.75	2.328844	0.41197	0.004324	0.0	ENSG00000076201	ENST00000265562	T	0.02916	4.11	3.9	3.9	0.45041	.	0.171581	0.36932	N	0.002332	T	0.02929	0.0087	L	0.27053	0.805	0.50171	D	0.999851	D	0.64830	0.994	P	0.51453	0.67	T	0.50825	-0.8782	10	0.72032	D	0.01	-10.0851	11.2398	0.48962	0.0:0.8134:0.1866:0.0	.	1545	Q9H3S7	PTN23_HUMAN	L	1545	ENSP00000265562:P1545L	ENSP00000265562:P1545L	P	+	2	0	PTPN23	47429402	0.499000	0.26083	0.835000	0.33067	0.668000	0.39293	2.241000	0.43097	2.146000	0.66826	0.563000	0.77884	CCG	C|0.998;T|0.002	0.002	strong		0.701	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	NM_015466		T	47454398	C	T	47454398	3	4	22	1	0	0	0	0	1	0	0	0	12803	652	23	1	4732	1	PTPN23	3	47454398	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	168078	47454398	150568032	837	3738											
CSPG5	10675	hgsc.bcm.edu	37	chr3	47619025	47619025	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tctccttggggagttcagaaGctgggctcagcttgtcgccg	5	11	14	11	2	3	1	2	0	1	1	5	2	3	2	2	3	2	4	2	3	1	3	rs35863063	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:47619025G>C	ENST00000383738.2	-	2	2589	c.491C>G	c.(490-492)gCt>gGt	p.A164G	CSPG5_ENST00000264723.4_Missense_Mutation_p.A164G|CSPG5_ENST00000465441.1_5'Flank|CSPG5_ENST00000456150.1_Missense_Mutation_p.A26G	NM_001206943.1|NM_001206945.1	NP_001193872.1|NP_001193874.1	O95196	CSPG5_HUMAN	chondroitin sulfate proteoglycan 5 (neuroglycan C)	164					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)		GAGTTCAGAAGCTGGGCTCAG	0.652													G|||	97	0.019369	0.0696	0.0072	5008	,	,		14217	0.0		0.0	False		,,,				2504	0.0				p.A164G		Atlas-SNP	.											.	CSPG5	46	.	0			c.C491G						PASS	.	G	GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA	266,4134		10,246,1944	27	34	32		77,491,491,77,491	-4.3	0	3	dbSNP_126	32	1,8597		0,1,4298	yes	missense,missense,missense,missense,missense	CSPG5	NM_001206942.1,NM_001206943.1,NM_001206944.1,NM_001206945.1,NM_006574.3	60,60,60,60,60	10,247,6242	CC,CG,GG		0.0116,6.0455,2.0542	benign,benign,benign,benign,benign	26/402,164/567,164/478,26/429,164/540	47619025	267,12731	2200	4299	6499	SO:0001583	missense	10675	exon2			TCAGAAGCTGGGC	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.491C>G	3.37:g.47619025G>C	ENSP00000373244:p.Ala164Gly	60	0	0		57	26	0.45614	NM_006574	Q71M39|Q71M40	Missense_Mutation	SNP	ENST00000383738.2	37	CCDS56253.1	38	0.0173992673992674	34	0.06910569105691057	4	0.011049723756906077	0	0.0	0	0.0	G	0.369	-0.934853	0.02340	0.060455	1.16E-4	ENSG00000114646	ENST00000456150;ENST00000383738;ENST00000264723	T;T;T	0.41400	1.0;1.0;1.0	3.92	-4.28	0.03732	Chondroitin sulphate attachment (1);	0.534137	0.14716	N	0.302660	T	0.00815	0.0027	N	0.04508	-0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.17289	-1.0374	10	0.09590	T	0.72	-0.5678	0.8637	0.01198	0.2327:0.2926:0.2766:0.1981	rs35863063	164;164	O95196;O95196-2	CSPG5_HUMAN;.	G	26;164;164	ENSP00000392096:A26G;ENSP00000373244:A164G;ENSP00000264723:A164G	ENSP00000264723:A164G	A	-	2	0	CSPG5	47594029	0.002000	0.14202	0.001000	0.08648	0.453000	0.32348	-1.165000	0.03132	-0.599000	0.05798	0.579000	0.79373	GCT	G|0.981;C|0.019	0.019	strong		0.652	CSPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257489.1	NM_006574		C	47619025	G	C	47619025	3	2	22	1	0	0	0	0	1	0	0	0	3963	971	34	4	1144	4	CSPG5	3	47619025	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	164627	47619025	150403405	838	3739											
FBXW12	285231	hgsc.bcm.edu	37	chr3	48420987	48420987	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atatggtattgtacttctacActgctctcctgacaagaaat	12	14	6	9	0	2	2	0	1	2	1	3	2	2	2	1	1	3	3	1	1	6	6	rs77256337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:48420987A>G	ENST00000296438.5	+	7	899	c.713A>G	c.(712-714)cAc>cGc	p.H238R	RN7SL321P_ENST00000581742.1_RNA|FBXW12_ENST00000436231.1_Missense_Mutation_p.H81R|FBXW12_ENST00000445170.1_Missense_Mutation_p.H219R|FBXW12_ENST00000415155.1_Missense_Mutation_p.H168R	NM_207102.2	NP_996985.2	Q6X9E4	FBW12_HUMAN	F-box and WD repeat domain containing 12	238										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GTACTTCTACACTGCTCTCCT	0.428													A|||	33	0.00658946	0.0234	0.0029	5008	,	,		24553	0.0		0.0	False		,,,				2504	0.0				p.H238R		Atlas-SNP	.											.	FBXW12	44	.	0			c.A713G						PASS	.	A	ARG/HIS,ARG/HIS,ARG/HIS	77,4329	67.6+/-105.2	1,75,2127	301	269	280		503,656,713	-7.2	0	3	dbSNP_131	280	0,8600		0,0,4300	yes	missense,missense,missense	FBXW12	NM_001159927.1,NM_001159929.1,NM_207102.2	29,29,29	1,75,6427	GG,GA,AA		0.0,1.7476,0.592	benign,benign,benign	168/395,219/446,238/465	48420987	77,12929	2203	4300	6503	SO:0001583	missense	285231	exon7			TTCTACACTGCTC	AK097594, AY247969	CCDS2764.1, CCDS54577.1, CCDS54578.1	3p21.31	2011-07-01	2007-02-08	2004-07-21	ENSG00000164049	ENSG00000164049		"F-boxes / WD-40 domains", "WD repeat domain containing"	20729	protein-coding gene	gene with protein product		609075	"F-box only protein 35", "F-box and WD-40 domain protein 12"	FBXO35		15040455	Standard	NM_207102		Approved	Fbw12	uc010hjv.3	Q6X9E4	OTTHUMG00000133530	ENST00000296438.5:c.713A>G	3.37:g.48420987A>G	ENSP00000296438:p.His238Arg	214	1	0.0046729		220	119	0.540909	NM_207102	E9PG36|Q494Y9|Q494Z0	Missense_Mutation	SNP	ENST00000296438.5	37	CCDS2764.1	8	0.003663003663003663	6	0.012195121951219513	2	0.0055248618784530384	0	0.0	0	0.0	A	1.575	-0.533025	0.04112	0.017476	0.0	ENSG00000164049	ENST00000458736;ENST00000296438;ENST00000436231;ENST00000445170;ENST00000415155	T;T;T;T	0.62232	1.62;0.04;1.62;3.52	4.03	-7.21	0.01490	WD40/YVTN repeat-like-containing domain (1);Quinoprotein amine dehydrogenase, beta chain-like (1);	1.379180	0.04600	N	0.398402	T	0.20414	0.0491	N	0.19112	0.55	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;0.0	T	0.10870	-1.0611	10	0.16420	T	0.52	-12.9603	1.3588	0.02187	0.1804:0.1139:0.2788:0.4269	.	137;219;168;238	E9PCA2;E9PG36;Q494Z0;Q6X9E4	.;.;.;FBW12_HUMAN	R	137;238;81;219;168	ENSP00000296438:H238R;ENSP00000413866:H81R;ENSP00000406139:H219R;ENSP00000414683:H168R	ENSP00000296438:H238R	H	+	2	0	FBXW12	48395991	0.005000	0.15991	0.000000	0.03702	0.020000	0.10135	-0.149000	0.10204	-1.503000	0.01812	-1.253000	0.01494	CAC	A|0.994;G|0.006	0.006	strong		0.428	FBXW12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257505.1	NM_207102		G	48420987	A	G	48420987	3	3	22	1	0	0	0	0	1	0	0	0	5773	159	6	3	772	3	FBXW12	3	48420987	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	801962	48420987	149601443	839	3740											
SLC26A6	65010	hgsc.bcm.edu	37	chr3	48664473	48664473	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgttgcatcttccatcttatCtcctgagctcacctgctggg	5	15	8	13	0	4	1	1	1	3	0	6	1	5	1	3	1	3	4	3	1	1	3	rs59643945	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:48664473C>T	ENST00000395550.2	-	18	1956	c.1909G>A	c.(1909-1911)Gat>Aat	p.D637N	SLC26A6_ENST00000383733.3_Missense_Mutation_p.D618N|SLC26A6_ENST00000358747.6_Missense_Mutation_p.D616N|SLC26A6_ENST00000337000.8_Missense_Mutation_p.D529N|SLC26A6_ENST00000420764.2_Missense_Mutation_p.D636N|SLC26A6_ENST00000455886.2_Missense_Mutation_p.D601N			Q9BXS9	S26A6_HUMAN	solute carrier family 26 (anion exchanger), member 6	637	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				angiotensin-activated signaling pathway (GO:0038166)|anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular response to cAMP (GO:0071320)|cellular response to fructose stimulus (GO:0071332)|cellular response to interferon-gamma (GO:0071346)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|epithelial fluid transport (GO:0042045)|formate transport (GO:0015724)|intestinal absorption (GO:0050892)|intracellular pH elevation (GO:0051454)|ion transport (GO:0006811)|mannitol transport (GO:0015797)|oxalate transport (GO:0019532)|oxalic acid secretion (GO:0046724)|positive regulation of dipeptide transmembrane transport (GO:2001150)|protein kinase C signaling (GO:0070528)|regulation of intracellular pH (GO:0051453)|sperm capacitation (GO:0048240)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transepithelial chloride transport (GO:0030321)|transepithelial transport (GO:0070633)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|chloride channel complex (GO:0034707)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane-bounded vesicle (GO:0031988)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)|vesicle membrane (GO:0012506)	anion:anion antiporter activity (GO:0015301)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride channel activity (GO:0005254)|chloride transmembrane transporter activity (GO:0015108)|efflux transmembrane transporter activity (GO:0015562)|formate efflux transmembrane transporter activity (GO:0015660)|formate transmembrane transporter activity (GO:0015499)|formate uptake transmembrane transporter activity (GO:0015659)|oxalate transmembrane transporter activity (GO:0019531)|PDZ domain binding (GO:0030165)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)		SLC26A6/PRKAR2A(2)	NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(1)|lung(11)|ovary(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00609)		TCCATCTTATCTCCTGAGCTC	0.597													C|||	329	0.0656949	0.2231	0.0346	5008	,	,		18821	0.0		0.008	False		,,,				2504	0.002				p.D637N	NSCLC(13;369 479 28271 30152 44026)	Atlas-SNP	.											.	SLC26A6	45	.	0			c.G1909A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	695,3405		68,559,1423	92	98	96		1846,1909,1906,1852	-0.5	0	3	dbSNP_129	96	49,8343		0,49,4147	yes	missense,missense,missense,missense	SLC26A6	NM_001040454.1,NM_022911.2,NM_134263.2,NM_134426.2	23,23,23,23	68,608,5570	TT,TC,CC		0.5839,16.9512,5.9558	benign,benign,benign,benign	616/739,637/760,636/759,618/741	48664473	744,11748	2050	4196	6246	SO:0001583	missense	65010	exon18			TCTTATCTCCTGA	AF279265	CCDS43087.1, CCDS46824.1, CCDS46825.1, CCDS46826.1, CCDS63627.1, CCDS63628.1	3p21.31	2013-08-05	2013-07-18		ENSG00000225697	ENSG00000225697		"Solute carriers"	14472	protein-coding gene	gene with protein product	"pendrin-like protein 1", "pendrin L1", "sulfate anion transporter", "anion transporter 1"	610068	"solute carrier family 26, member 6"			11087667, 11247665	Standard	NM_022911		Approved	DKFZp586E1422		Q9BXS9	OTTHUMG00000186381	ENST00000395550.2:c.1909G>A	3.37:g.48664473C>T	ENSP00000378920:p.Asp637Asn	208	1	0.00480769		175	96	0.548571	NM_022911	B4DMZ1|Q548A7|Q96Q90|Q9NQU1	Missense_Mutation	SNP	ENST00000395550.2	37	CCDS43087.1	116	0.05311355311355311	101	0.20528455284552846	11	0.03038674033149171	0	0.0	4	0.005277044854881266	C	9.598	1.128019	0.20959	0.169512	0.005839	ENSG00000225697	ENST00000420764;ENST00000395550;ENST00000383733;ENST00000337000;ENST00000447978;ENST00000358747;ENST00000455886	D;D;D;D;D;D	0.92545	-2.95;-2.93;-3.05;-2.96;-2.93;-3.06	3.63	-0.494	0.12034	Sulphate transporter/antisigma-factor antagonist STAS (3);	.	.	.	.	T	0.00241	0.0007	N	0.10972	0.075	0.80722	P	0.0	B;B;B;B;B;B;B	0.21905	0.004;0.0;0.005;0.0;0.001;0.0;0.062	B;B;B;B;B;B;B	0.28638	0.013;0.001;0.009;0.002;0.006;0.003;0.092	T	0.24548	-1.0157	8	0.51188	T	0.08	.	3.7251	0.08472	0.0:0.4123:0.1909:0.3969	rs59643945	601;631;529;618;636;637;4023	B4DMZ1;Q86YZ4;G3XAC1;Q9BXS9-2;Q548A7;Q9BXS9;Q5Y190	.;.;.;.;.;S26A6_HUMAN;.	N	636;637;618;529;631;616;601	ENSP00000404684:D636N;ENSP00000378920:D637N;ENSP00000373239:D618N;ENSP00000337648:D529N;ENSP00000351597:D616N;ENSP00000401066:D601N	ENSP00000337648:D529N	D	-	1	0	SLC26A6	48639477	0.001000	0.12720	0.000000	0.03702	0.151000	0.21798	0.206000	0.17375	-0.112000	0.11979	-0.339000	0.08088	GAT	C|0.962;T|0.038	0.038	strong		0.597	SLC26A6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345040.1	NM_022911		T	48664473	C	T	48664473	3	4	22	1	0	0	0	0	1	0	0	0	14536	913	32	2	386	2	SLC26A6	3	48664473	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	243486	48664473	149357957	840	3741											
CELSR3	1951	hgsc.bcm.edu	37	chr3	48699134	48699134	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcgcgacgaaagcgtgcccGgttcgccgaggttactttcc	6	8	14	13	7	0	0	0	0	0	0	2	3	1	0	3	3	3	2	3	3	2	3	rs76423828	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:48699134G>T	ENST00000164024.4	-	1	1214	c.934C>A	c.(934-936)Cgg>Agg	p.R312R	RP11-148G20.1_ENST00000421275.1_RNA|CELSR3_ENST00000544264.1_Silent_p.R312R	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	312					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)		AAGCGTGCCCGGTTCGCCGAG	0.701													G|||	29	0.00579073	0.0212	0.0014	5008	,	,		14032	0.0		0.0	False		,,,				2504	0.0				p.R312R		Atlas-SNP	.											.	CELSR3	237	.	0			c.C934A						PASS	.	G		51,4315		0,51,2132	39	43	42		934	1.4	0	3	dbSNP_131	42	1,8499		0,1,4249	no	coding-synonymous	CELSR3	NM_001407.2		0,52,6381	TT,TG,GG		0.0118,1.1681,0.4042		312/3313	48699134	52,12814	2183	4250	6433	SO:0001819	synonymous_variant	1951	exon1			GTGCCCGGTTCGC	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.934C>A	3.37:g.48699134G>T		46	0	0		68	33	0.485294	NM_001407	O75092	Silent	SNP	ENST00000164024.4	37	CCDS2775.1																																																																																			G|0.995;T|0.005	0.005	strong		0.701	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		T	48699134	G	T	48699134	2	4	22	1	0	0	0	0	0	0	0	1	3225	1115	39	4		4	CELSR3	3	48699134	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	34661	48699134	149323296	841	3742											
USP19	10869	hgsc.bcm.edu	37	chr3	49149020	49149020	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcagaagaaattccactggTgctgggcacaggaccccggt	10	7	12	12	1	1	2	1	0	0	2	2	3	2	3	3	4	1	2	3	4	2	1	rs13321689	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:49149020T>C	ENST00000398888.2	-	20	3139	c.2821A>G	c.(2821-2823)Acc>Gcc	p.T941A	USP19_ENST00000453664.1_Missense_Mutation_p.T1032A|USP19_ENST00000398896.1_Missense_Mutation_p.T749A|USP19_ENST00000398892.3_Missense_Mutation_p.T981A|USP19_ENST00000417901.1_Missense_Mutation_p.T1044A|USP19_ENST00000434032.2_Missense_Mutation_p.T1042A|USP19_ENST00000398898.2_Missense_Mutation_p.T981A	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	941	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)		ATTCCACTGGTGCTGGGCACA	0.637													T|||	96	0.0191693	0.0688	0.0072	5008	,	,		17360	0.0		0.0	False		,,,				2504	0.0				p.T1044A		Atlas-SNP	.											.	USP19	158	.	0			c.A3130G						PASS	.	T	ALA/THR,ALA/THR,ALA/THR,ALA/THR	283,3485		9,265,1610	27	29	29		3124,3130,3094,2821	4.9	1	3	dbSNP_121	29	6,8216		0,6,4105	yes	missense,missense,missense,missense	USP19	NM_001199160.1,NM_001199161.1,NM_001199162.1,NM_006677.2	58,58,58,58	9,271,5715	CC,CT,TT		0.073,7.5106,2.4103	benign,benign,benign,benign	1042/1420,1044/1385,1032/1373,941/1319	49149020	289,11701	1884	4111	5995	SO:0001583	missense	10869	exon21			CACTGGTGCTGGG	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.2821A>G	3.37:g.49149020T>C	ENSP00000381863:p.Thr941Ala	65	0	0		64	39	0.609375	NM_001199161	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Missense_Mutation	SNP	ENST00000398888.2	37	CCDS43090.1	42	0.019230769230769232	37	0.07520325203252033	5	0.013812154696132596	0	0.0	0	0.0	T	2.392	-0.339698	0.05243	0.075106	7.3E-4	ENSG00000172046	ENST00000398896;ENST00000398898;ENST00000417901;ENST00000453664;ENST00000398892;ENST00000398888;ENST00000434032	T;T;T;T;T;T;T	0.18657	2.2;2.21;2.3;2.3;2.2;2.3;2.29	6.04	4.93	0.64822	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.787862	0.12324	N	0.478992	T	0.00384	0.0012	N	0.02213	-0.635	0.09310	N	1	B;B;B;B;B	0.10296	0.003;0.003;0.001;0.0;0.001	B;B;B;B;B	0.14578	0.011;0.011;0.005;0.005;0.005	T	0.38001	-0.9681	10	0.14252	T	0.57	-11.953	5.3341	0.15947	0.0:0.0978:0.2401:0.6621	rs13321689	1042;1032;941;981;749	E9PEG8;E7EN22;O94966;B5MEG5;E7ESU0	.;.;UBP19_HUMAN;.;.	A	749;981;1044;1032;981;941;1042	ENSP00000381870:T749A;ENSP00000381872:T981A;ENSP00000395260:T1044A;ENSP00000400090:T1032A;ENSP00000381867:T981A;ENSP00000381863:T941A;ENSP00000401197:T1042A	ENSP00000381863:T941A	T	-	1	0	USP19	49124024	0.999000	0.42202	1.000000	0.80357	0.996000	0.88848	0.989000	0.29629	2.330000	0.79161	0.529000	0.55759	ACC	T|0.972;C|0.028	0.028	strong		0.637	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677		C	49149020	T	C	49149020	3	2	22	1	0	0	0	0	1	0	0	0	17065	1696	59	3	1163	3	USP19	3	49149020	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	449886	49149020	148873410	842	3743											
BSN	8927	hgsc.bcm.edu	37	chr3	49698695	49698695	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagtccccgctgatagccgTgccccactgcagaagccacg	8	5	10	18	3	0	2	0	1	0	1	1	2	1	2	7	0	4	2	7	0	2	1	rs149210839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:49698695T>C	ENST00000296452.4	+	6	9531	c.9417T>C	c.(9415-9417)cgT>cgC	p.R3139R		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	3139					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)		CTGATAGCCGTGCCCCACTGC	0.602													T|||	14	0.00279553	0.0098	0.0014	5008	,	,		16801	0.0		0.0	False		,,,				2504	0.0				p.R3139R		Atlas-SNP	.											.	BSN	272	.	0			c.T9417C						PASS	.	T		26,4380	32.6+/-62.9	0,26,2177	67	53	58		9417	-2.3	0	3	dbSNP_134	58	0,8600		0,0,4300	no	coding-synonymous	BSN	NM_003458.3		0,26,6477	CC,CT,TT		0.0,0.5901,0.1999		3139/3927	49698695	26,12980	2203	4300	6503	SO:0001819	synonymous_variant	8927	exon6			TAGCCGTGCCCCA	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.9417T>C	3.37:g.49698695T>C		163	0	0		154	70	0.454545	NM_003458	O43161|Q7LGH3	Silent	SNP	ENST00000296452.4	37	CCDS2800.1																																																																																			T|0.998;C|0.002	0.002	strong		0.602	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		C	49698695	T	C	49698695	2	2	22	1	0	0	0	0	0	0	0	1	1532	1683	59	3		3	BSN	3	49698695	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	549675	49698695	148323735	843	3744											
UBA7	7318	hgsc.bcm.edu	37	chr3	49845526	49845526	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgctaccacaaagtccacaTggaagttgctgtcatcatcc	11	9	7	14	1	2	0	2	0	0	0	4	1	4	1	4	1	2	3	4	1	3	2	rs2230149	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:49845526T>C	ENST00000333486.3	-	20	2608	c.2450A>G	c.(2449-2451)cAt>cGt	p.H817R	MIR5193_ENST00000584510.1_RNA	NM_003335.2	NP_003326.2	P41226	UBA7_HUMAN	ubiquitin-like modifier activating enzyme 7	817			H -> R (in dbSNP:rs2230149).		cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|modification-dependent protein catabolic process (GO:0019941)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ISG15 activating enzyme activity (GO:0019782)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(15)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;3.58e-06)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		AAAGTCCACATGGAAGTTGCT	0.567													T|||	138	0.0275559	0.0983	0.0072	5008	,	,		22642	0.0		0.003	False		,,,				2504	0.0				p.H817R		Atlas-SNP	.											.	UBA7	64	.	0			c.A2450G						PASS	.	T	ARG/HIS	325,4081	171.6+/-201.8	20,285,1898	94	87	89		2450	5.3	0.9	3	dbSNP_98	89	1,8599	1.2+/-3.3	0,1,4299	yes	missense	UBA7	NM_003335.2	29	20,286,6197	CC,CT,TT		0.0116,7.3763,2.5065	probably-damaging	817/1013	49845526	326,12680	2203	4300	6503	SO:0001583	missense	7318	exon20			TCCACATGGAAGT	BC006378	CCDS2805.1	3p21	2007-11-30	2007-11-30	2007-11-30	ENSG00000182179	ENSG00000182179		"Ubiquitin-like modifier activating enzymes"	12471	protein-coding gene	gene with protein product	"UBA1, ubiquitin-activating enzyme E1 homolog B (yeast)", "UBA7, ubiquitin-activating enzyme E1"	191325	"ubiquitin-activating enzyme E1-like"	UBE1L		8327486	Standard	NM_003335		Approved	D8, UBE2, UBA1B	uc003cxr.3	P41226	OTTHUMG00000158267	ENST00000333486.3:c.2450A>G	3.37:g.49845526T>C	ENSP00000333266:p.His817Arg	90	0	0		84	38	0.452381	NM_003335	Q9BRB2	Missense_Mutation	SNP	ENST00000333486.3	37	CCDS2805.1	46	0.021062271062271064	41	0.08333333333333333	3	0.008287292817679558	0	0.0	2	0.002638522427440633	T	22.6	4.310618	0.81358	0.073763	1.16E-4	ENSG00000182179	ENST00000333486	T	0.47177	0.85	5.34	5.34	0.76211	Molybdenum cofactor biosynthesis, MoeB (1);Ubiquitin-like 1 activating enzyme, catalytic cysteine domain (1);	0.177580	0.53938	D	0.000047	T	0.19446	0.0467	H	0.96398	3.815	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.70263	-0.4920	10	0.87932	D	0	-17.9904	15.6299	0.76899	0.0:0.0:0.0:1.0	rs2230149;rs2234387;rs2230149	817	P41226	UBA7_HUMAN	R	817	ENSP00000333266:H817R	ENSP00000333266:H817R	H	-	2	0	UBA7	49820530	1.000000	0.71417	0.902000	0.35471	0.771000	0.43674	5.762000	0.68809	2.169000	0.68431	0.459000	0.35465	CAT	T|0.973;C|0.027	0.027	strong		0.567	UBA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350503.1	NM_003335		C	49845526	T	C	49845526	3	2	22	1	0	0	0	0	1	0	0	0	16848	1464	51	3	608	3	UBA7	3	49845526	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	146831	49845526	148176904	844	3745											
DNAH1	25981	hgsc.bcm.edu	37	chr3	52365223	52365223	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aggtcggcgtcctggactacGacgaggagaagaagctatac	12	6	14	9	4	0	2	0	0	0	2	2	6	1	3	1	4	3	1	1	4	5	3	rs55931436	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:52365223G>A	ENST00000420323.2	+	7	1192	c.931G>A	c.(931-933)Gac>Aac	p.D311N		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	311	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)		CCTGGACTACGACGAGGAGAA	0.567													G|||	89	0.0177716	0.0643	0.0058	5008	,	,		20717	0.0		0.0	False		,,,				2504	0.0				p.D311N		Atlas-SNP	.											.	DNAH1	534	.	0			c.G931A						PASS	.	G	ASN/ASP	167,3917		5,157,1880	56	59	58		931	3.6	0	3	dbSNP_129	58	1,8383		0,1,4191	yes	missense	DNAH1	NM_015512.4	23	5,158,6071	AA,AG,GG		0.0119,4.0891,1.3474	benign	311/4266	52365223	168,12300	2042	4192	6234	SO:0001583	missense	25981	exon7			GACTACGACGAGG	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.931G>A	3.37:g.52365223G>A	ENSP00000401514:p.Asp311Asn	150	0	0		194	91	0.469072	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	33	0.01510989010989011	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	0	0.0	G	10.94	1.491737	0.26774	0.040891	1.19E-4	ENSG00000114841	ENST00000420323	T	0.23348	1.91	5.38	3.58	0.41010	.	0.000000	0.53938	D	0.000051	T	0.01627	0.0052	L	0.46885	1.475	0.26172	N	0.979848	B;P	0.39326	0.07;0.668	B;B	0.36186	0.022;0.219	T	0.01452	-1.1351	10	0.52906	T	0.07	.	11.8483	0.52397	0.1429:0.0:0.8571:0.0	rs55931436;rs61734655	311;311	C9JXH6;Q9P2D7-3	.;.	N	311	ENSP00000401514:D311N	ENSP00000401514:D311N	D	+	1	0	DNAH1	52340263	0.986000	0.35501	0.008000	0.14137	0.151000	0.21798	2.173000	0.42472	0.643000	0.30638	0.462000	0.41574	GAC	G|0.984;A|0.016	0.016	strong		0.567	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512		A	52365223	G	A	52365223	3	1	22	1	0	0	0	0	1	0	0	0	4599	1058	37	1	953	1	DNAH1	3	52365223	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2519697	52365223	145657207	845	3746											
ITIH1	3697	hgsc.bcm.edu	37	chr3	52823864	52823864	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaccaagctgtgctgcggcAggacgggtaacctgccaggg	8	5	17	11	2	0	0	0	0	0	0	0	2	0	2	3	5	5	4	3	5	2	1	rs61730358	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:52823864A>T	ENST00000273283.2	+	19	2339	c.2315A>T	c.(2314-2316)cAg>cTg	p.Q772L	ITIH1_ENST00000405128.3_Missense_Mutation_p.Q138L|ITIH1_ENST00000537050.1_Missense_Mutation_p.Q484L|ITIH1_ENST00000540715.1_Missense_Mutation_p.Q630L|ITIH1_ENST00000542827.1_3'UTR	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	772	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)		GTGCTGCGGCAGGACGGGTAA	0.627													A|||	96	0.0191693	0.0681	0.0086	5008	,	,		20037	0.0		0.0	False		,,,				2504	0.0				p.Q772L		Atlas-SNP	.											.	ITIH1	108	.	0			c.A2315T						PASS	.	A	LEU/GLN,LEU/GLN,LEU/GLN,LEU/GLN	272,4134	152.9+/-186.6	11,250,1942	55	54	54		1889,1451,1451,2315	5.4	1	3	dbSNP_129	54	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense,missense	ITIH1	NM_001166434.1,NM_001166435.1,NM_001166436.1,NM_002215.2	113,113,113,113	11,252,6240	TT,TA,AA		0.0233,6.1734,2.1067	benign,benign,benign,benign	630/770,484/624,484/624,772/912	52823864	274,12732	2203	4300	6503	SO:0001583	missense	3697	exon19			TGCGGCAGGACGG		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.2315A>T	3.37:g.52823864A>T	ENSP00000273283:p.Gln772Leu	56	0	0		62	29	0.467742	NM_002215	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Missense_Mutation	SNP	ENST00000273283.2	37	CCDS2864.1	36	0.016483516483516484	35	0.07113821138211382	1	0.0027624309392265192	0	0.0	0	0.0	A	15.98	2.991954	0.54041	0.061734	2.33E-4	ENSG00000055957	ENST00000273283;ENST00000540715;ENST00000537050;ENST00000428133;ENST00000405128	T;T;T;T;T	0.11712	2.75;2.75;2.75;2.75;2.75	5.42	5.42	0.78866	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);	0.203207	0.43919	D	0.000515	T	0.01254	0.0041	L	0.49350	1.555	0.33937	D	0.642752	B;P;B;P	0.42337	0.006;0.776;0.425;0.661	B;B;B;P	0.48982	0.015;0.41;0.182;0.597	T	0.06534	-1.0821	10	0.40728	T	0.16	-18.8137	12.9885	0.58606	1.0:0.0:0.0:0.0	rs61730358	630;138;373;772	F5H165;B5MCP1;Q9P1C5;P19827	.;.;.;ITIH1_HUMAN	L	772;630;484;325;138	ENSP00000273283:Q772L;ENSP00000443973:Q630L;ENSP00000443847:Q484L;ENSP00000395836:Q325L;ENSP00000384589:Q138L	ENSP00000273283:Q772L	Q	+	2	0	ITIH1	52798904	1.000000	0.71417	0.993000	0.49108	0.101000	0.19017	5.862000	0.69560	2.043000	0.60533	0.460000	0.39030	CAG	A|0.981;T|0.019	0.019	strong		0.627	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215		T	52823864	A	T	52823864	3	4	22	1	0	0	0	0	1	0	0	0	7912	188	7	5	2389	5	ITIH1	3	52823864	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	458641	52823864	145198566	846	3747											
ITIH3	3699	hgsc.bcm.edu	37	chr3	52840325	52840325	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagtggacggggatccccaCttcatcatccaaattccgga	10	8	9	14	2	2	0	2	0	0	0	5	3	5	3	5	4	0	0	5	4	1	2	rs34397833	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:52840325C>T	ENST00000449956.2	+	18	1965	c.1959C>T	c.(1957-1959)caC>caT	p.H653H	ITIH3_ENST00000416872.2_Intron	NM_002217.3	NP_002208.3	Q06033	ITIH3_HUMAN	inter-alpha-trypsin inhibitor heavy chain 3	653					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)		GGGATCCCCACTTCATCATCC	0.582													C|||	219	0.04373	0.1581	0.013	5008	,	,		15639	0.0		0.0	False		,,,				2504	0.001				p.H653H		Atlas-SNP	.											.	ITIH3	132	.	0			c.C1959T						PASS	.	C		412,3666		24,364,1651	53	55	55		1959	4.6	1	3	dbSNP_126	55	1,8389		0,1,4194	no	coding-synonymous	ITIH3	NM_002217.3		24,365,5845	TT,TC,CC		0.0119,10.103,3.3125		653/891	52840325	413,12055	2039	4195	6234	SO:0001819	synonymous_variant	3699	exon18			TCCCCACTTCATC		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.1959C>T	3.37:g.52840325C>T		125	0	0		123	64	0.520325	NM_002217	Q3B7H5|Q53F06|Q6LAM2|Q99085	Silent	SNP	ENST00000449956.2	37	CCDS46845.1	75	0.034340659340659344	71	0.1443089430894309	4	0.011049723756906077	0	0.0	0	0.0	C	3.086	-0.187992	0.06299	0.10103	1.19E-4	ENSG00000162267	ENST00000398670;ENST00000536431	.	.	.	5.48	4.61	0.57282	.	.	.	.	.	T	0.00580	0.0019	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.00478	-1.1715	5	0.15952	T	0.53	-32.6536	13.5864	0.61933	0.0:0.9234:0.0:0.0766	rs34397833;rs61654726	.	.	.	F	654;642	.	ENSP00000381662:L654F	L	+	1	0	ITIH3	52815365	1.000000	0.71417	1.000000	0.80357	0.441000	0.31987	1.124000	0.31320	1.457000	0.47850	0.561000	0.74099	CTT	C|0.971;T|0.029	0.029	strong		0.582	ITIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352668.2	NM_002217		T	52840325	C	T	52840325	2	4	22	1	0	0	0	0	0	0	0	1	7914	564	20	2		2	ITIH3	3	52840325	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	16461	52840325	145182105	847	3748											
LRTM1	57408	hgsc.bcm.edu	37	chr3	54958884	54958884	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaatcaagctccctcagctgAgggagggaatggaaaagtct	14	7	12	8	0	3	1	2	1	1	0	4	4	4	4	1	3	2	2	1	3	5	0	rs35757787	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:54958884A>G	ENST00000273286.5	-	2	528	c.366T>C	c.(364-366)ccT>ccC	p.P122P	CACNA2D3_ENST00000490478.1_Intron|CACNA2D3_ENST00000474759.1_Intron|LRTM1_ENST00000493075.1_Silent_p.P46P|CACNA2D3_ENST00000415676.2_Intron|CACNA2D3_ENST00000288197.5_Intron	NM_020678.2	NP_065729.1	Q9HBL6	LRTM1_HUMAN	leucine-rich repeats and transmembrane domains 1	122						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)		CCCTCAGCTGAGGGAGGGAAT	0.478													A|||	154	0.0307508	0.1127	0.0058	5008	,	,		20302	0.0		0.001	False		,,,				2504	0.0				p.P122P		Atlas-SNP	.											.	LRTM1	52	.	0			c.T366C						PASS	.	A	,	420,3986	205.8+/-227.6	14,392,1797	76	75	75		,366	-11.5	0	3	dbSNP_126	75	2,8598	2.2+/-6.3	0,2,4298	no	intron,coding-synonymous	CACNA2D3,LRTM1	NM_018398.2,NM_020678.2	,	14,394,6095	GG,GA,AA		0.0233,9.5325,3.2447	,	,122/346	54958884	422,12584	2203	4300	6503	SO:0001819	synonymous_variant	57408	exon2			CAGCTGAGGGAGG	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.366T>C	3.37:g.54958884A>G		122	0	0		124	67	0.540323	NM_020678	Q8IUU2	Silent	SNP	ENST00000273286.5	37	CCDS2876.1																																																																																			A|0.971;G|0.029	0.029	strong		0.478	LRTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351399.1	NM_020678		G	54958884	A	G	54958884	2	3	22	1	0	0	0	0	0	0	0	1	9053	291	11	3		3	LRTM1	3	54958884	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2118559	54958884	143063546	848	3749											
ERC2	26059	hgsc.bcm.edu	37	chr3	56026204	56026204	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactcgtcgcggtagtaagaCgcctctttatcgagctgttt	7	13	10	11	5	1	1	0	0	1	1	4	2	1	1	1	1	1	4	1	1	3	5	rs61732592	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:56026204C>T	ENST00000288221.6	-	11	2391	c.2136G>A	c.(2134-2136)gcG>gcA	p.A712A		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	712						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)		GGTAGTAAGACGCCTCTTTAT	0.458													C|||	44	0.00878594	0.0325	0.0014	5008	,	,		19132	0.0		0.0	False		,,,				2504	0.0				p.A712A		Atlas-SNP	.											ERC2_ENST00000288221,caecum,carcinoma,-1,2	ERC2	221	2	0			c.G2136A						PASS	.	C		77,3739		2,73,1833	195	189	191		2136	1.6	1	3	dbSNP_129	191	1,8253		0,1,4126	no	coding-synonymous	ERC2	NM_015576.1		2,74,5959	TT,TC,CC		0.0121,2.0178,0.6462		712/958	56026204	78,11992	1908	4127	6035	SO:0001819	synonymous_variant	26059	exon11			GTAAGACGCCTCT	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.2136G>A	3.37:g.56026204C>T		217	0	0		231	118	0.510823	NM_015576	Q2T9F6|Q86TK4	Silent	SNP	ENST00000288221.6	37	CCDS46851.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	C	6.971	0.549089	0.13312	0.020178	1.21E-4	ENSG00000187672	ENST00000492584	.	.	.	5.47	1.64	0.23874	.	.	.	.	.	T	0.15652	0.0377	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.06144	-1.0843	4	.	.	.	-11.4437	5.8817	0.18858	0.0:0.2089:0.3824:0.4087	.	.	.	.	H	363	.	.	R	-	2	0	ERC2	56001244	0.126000	0.22350	1.000000	0.80357	0.978000	0.69477	-0.482000	0.06544	0.039000	0.15632	-0.469000	0.05056	CGT	C|0.988;T|0.012	0.012	strong		0.458	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576		T	56026204	C	T	56026204	2	4	22	1	0	0	0	0	0	0	0	1	5213	523	19	1		1	ERC2	3	56026204	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1067320	56026204	141996226	849	3750											
C3orf63	23272	hgsc.bcm.edu	37	chr3	56667213	56667213	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ataaaatttgaaagagctggTtgagcagaaatgtttacatc	16	12	9	4	0	0	4	0	2	0	2	1	4	0	4	0	1	3	4	0	1	5	5	rs34828128	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:56667213T>C	ENST00000493960.2	-	18	3616	c.3606A>G	c.(3604-3606)caA>caG	p.Q1202Q	FAM208A_ENST00000431842.2_Silent_p.Q765Q|FAM208A_ENST00000355628.5_Silent_p.Q1141Q	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	1202							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						AAAGAGCTGGTTGAGCAGAAA	0.353													T|||	31	0.0061901	0.0	0.0101	5008	,	,		18670	0.0		0.0149	False		,,,				2504	0.0092				p.Q1202Q		Atlas-SNP	.											.	FAM208A	113	.	0			c.A3606G						PASS	.	T	,	17,4389	24.3+/-50.5	0,17,2186	114	116	115		3606,2295	-1.5	1	3	dbSNP_126	115	154,8446	73.8+/-136.5	3,148,4149	no	coding-synonymous,coding-synonymous	FAM208A	NM_001112736.1,NM_015224.3	,	3,165,6335	CC,CT,TT		1.7907,0.3858,1.3148	,	1202/1513,765/1234	56667213	171,12835	2203	4300	6503	SO:0001819	synonymous_variant	23272	exon18			AGCTGGTTGAGCA	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.3606A>G	3.37:g.56667213T>C		179	0	0		156	68	0.435897	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Silent	SNP	ENST00000493960.2	37	CCDS46853.1																																																																																			T|0.987;C|0.013	0.013	strong		0.353	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224		C	56667213	T	C	56667213	2	2	22	1	0	0	0	0	0	0	0	1	2241	1722	60	3		3	C3orf63	3	56667213	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	641009	56667213	141355217	850	3751											
DNAH12	201625	hgsc.bcm.edu	37	chr3	57469151	57469151	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctacagtccgggctttttcTacataagatatcagatccat	11	13	6	11	1	2	2	1	0	1	2	4	2	4	2	3	1	2	1	3	1	4	6			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:57469151T>C	ENST00000351747.2	-	13	1782	c.1602A>G	c.(1600-1602)gtA>gtG	p.V534V	DNAH12_ENST00000389536.4_Silent_p.V534V	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	534	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						GGGCTTTTTCTACATAAGATA	0.318																																					p.V534V		Atlas-SNP	.											.	DNAH12	182	.	0			c.A1602G						PASS	.						269	210	228					3																	57469151		692	1591	2283	SO:0001819	synonymous_variant	201625	exon13			TTTTTCTACATAA	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.1602A>G	3.37:g.57469151T>C		169	0	0		155	79	0.509677	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Silent	SNP	ENST00000351747.2	37																																																																																				.	.	none		0.318	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504		C	57469151	T	C	57469151	2	2	22	1	0	0	0	0	0	0	0	1	4602	1509	53	3		3	DNAH12	3	57469151	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	801938	57469151	140553279	851	3752											
SLMAP	7871	hgsc.bcm.edu	37	chr3	57743531	57743531	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acttttgattgcaaagtgctAtcaaggaaccacgctctcgt	11	12	8	10	2	2	1	1	1	1	0	3	2	2	2	1	1	3	3	1	1	4	4	rs147270008		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:57743531A>G	ENST00000428312.1	+	1	247	c.153A>G	c.(151-153)ctA>ctG	p.L51L	SLMAP_ENST00000416870.1_5'UTR|SLMAP_ENST00000449503.2_Silent_p.L51L|SLMAP_ENST00000383718.3_Silent_p.L51L|SLMAP_ENST00000295952.3_Silent_p.L51L|SLMAP_ENST00000295951.3_Silent_p.L51L			Q14BN4	SLMAP_HUMAN	sarcolemma associated protein	51	FHA. {ECO:0000255|PROSITE- ProRule:PRU00086}.|Necessary for targeting to centrosomes. {ECO:0000250}.				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)		GCAAAGTGCTATCAAGGAACC	0.498																																					p.L51L		Atlas-SNP	.											.	SLMAP	46	.	0			c.A153G						PASS	.	A		1,4405		0,1,2202	78	70	73		153	1.8	1	3	dbSNP_134	73	0,8600		0,0,4300	no	coding-synonymous	SLMAP	NM_007159.2		0,1,6502	GG,GA,AA		0.0,0.0227,0.0077		51/812	57743531	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	7871	exon1			AGTGCTATCAAGG	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.153A>G	3.37:g.57743531A>G		224	0	0		223	106	0.475336	NM_007159	Q14C95|Q6AI54|Q6UXC9|Q6ZVQ8|Q8NCW9|Q9H297|Q9HCH1|Q9Y681	Silent	SNP	ENST00000428312.1	37																																																																																				A|1.000;G|0.000	0.000	weak		0.498	SLMAP-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351584.1	NM_007159		G	57743531	A	G	57743531	2	3	22	1	0	0	0	0	0	0	0	1	14764	436	16	3		3	SLMAP	3	57743531	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	274380	57743531	140278899	852	3753											
LRIG1	26018	hgsc.bcm.edu	37	chr3	66431280	66431280	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actgcatacgacccggccacCgtgttctgaaggacagcgcc	9	6	11	15	4	1	1	0	1	1	0	1	3	1	2	4	2	3	2	4	2	2	2	rs9877201	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:66431280C>T	ENST00000273261.3	-	18	3300	c.2776G>A	c.(2776-2778)Ggt>Agt	p.G926S	SLC25A26_ENST00000536651.1_3'UTR|LRIG1_ENST00000496559.2_5'UTR|LRIG1_ENST00000383703.3_Missense_Mutation_p.G903S	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	926			G -> S (in dbSNP:rs9877201).		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)		ACCCGGCCACCGTGTTCTGAA	0.597													C|||	554	0.110623	0.3873	0.0346	5008	,	,		18811	0.0		0.0179	False		,,,				2504	0.0				p.G926S		Atlas-SNP	.											LRIG1,NS,carcinoma,0,1	LRIG1	138	1	0			c.G2776A						PASS	.	C	SER/GLY	1492,2914	473.5+/-356.7	259,974,970	49	52	51		2776	-3.4	0	3	dbSNP_119	51	84,8516	48.9+/-108.6	1,82,4217	yes	missense	LRIG1	NM_015541.2	56	260,1056,5187	TT,TC,CC		0.9767,33.8629,12.1175	benign	926/1094	66431280	1576,11430	2203	4300	6503	SO:0001583	missense	26018	exon18			GGCCACCGTGTTC	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.2776G>A	3.37:g.66431280C>T	ENSP00000273261:p.Gly926Ser	73	0	0		85	36	0.423529	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Missense_Mutation	SNP	ENST00000273261.3	37	CCDS33783.1	210	0.09615384615384616	187	0.3800813008130081	8	0.022099447513812154	0	0.0	15	0.01978891820580475	C	10.82	1.457361	0.26161	0.338629	0.009767	ENSG00000144749	ENST00000273261;ENST00000383703;ENST00000383702	T;T	0.69040	-0.18;-0.37	5.34	-3.41	0.04839	.	0.402609	0.28016	N	0.016939	T	0.00012	0.0000	N	0.02315	-0.6	0.80722	P	0.0	B;B;B	0.24651	0.012;0.108;0.007	B;B;B	0.15870	0.014;0.014;0.002	T	0.38908	-0.9639	9	0.18710	T	0.47	.	8.9885	0.36008	0.145:0.5962:0.0:0.2587	rs9877201;rs52813156;rs59347115;rs9877201	903;926;926	Q96JA1-2;Q5XWD3;Q96JA1	.;.;LRIG1_HUMAN	S	926;903;829	ENSP00000273261:G926S;ENSP00000373208:G903S	ENSP00000273261:G926S	G	-	1	0	LRIG1	66513970	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	-0.284000	0.08422	-0.442000	0.07190	-0.794000	0.03295	GGT	C|0.879;T|0.121	0.121	strong		0.597	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541		T	66431280	C	T	66431280	3	4	22	1	0	0	0	0	1	0	0	0	8953	652	23	1	513	1	LRIG1	3	66431280	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	8687749	66431280	131591150	853	3754											
LRIG1	26018	hgsc.bcm.edu	37	chr3	66433458	66433458	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttcctggtctggtagatgatGcacacccagaccagtgacgt	9	10	11	11	1	1	4	0	2	1	2	2	4	2	4	3	2	1	2	3	2	1	2	rs34042409	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:66433458G>A	ENST00000273261.3	-	15	2963	c.2439C>T	c.(2437-2439)tgC>tgT	p.C813C	SLC25A26_ENST00000536651.1_Intron|LRIG1_ENST00000496559.2_5'UTR|LRIG1_ENST00000383703.3_Silent_p.C790C	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	813					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)		GGTAGATGATGCACACCCAGA	0.577													G|||	261	0.0521166	0.1906	0.013	5008	,	,		19695	0.0		0.0	False		,,,				2504	0.0				p.C813C		Atlas-SNP	.											.	LRIG1	138	.	0			c.C2439T						PASS	.	G		705,3701	294.7+/-283.3	56,593,1554	115	90	99		2439	5.9	1	3	dbSNP_126	99	7,8593	5.7+/-21.5	0,7,4293	yes	coding-synonymous	LRIG1	NM_015541.2		56,600,5847	AA,AG,GG		0.0814,16.0009,5.4744		813/1094	66433458	712,12294	2203	4300	6503	SO:0001819	synonymous_variant	26018	exon15			GATGATGCACACC	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.2439C>T	3.37:g.66433458G>A		95	0	0		89	41	0.460674	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Silent	SNP	ENST00000273261.3	37	CCDS33783.1																																																																																			G|0.941;A|0.059	0.059	strong		0.577	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541		A	66433458	G	A	66433458	2	1	22	1	0	0	0	0	0	0	0	1	8953	1311	46	2		2	LRIG1	3	66433458	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2178	66433458	131588972	854	3755											
PROK2	60675	hgsc.bcm.edu	37	chr3	71821933	71821933	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccgtaaacaggccaagcctGgcagacatgggcaagtgtga	12	6	13	10	1	0	2	0	1	0	1	1	2	1	2	3	3	2	3	3	3	4	1	rs60239864	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:71821933G>T	ENST00000295619.3	-	4	340	c.332C>A	c.(331-333)cCa>cAa	p.P111Q	PROK2_ENST00000353065.3_Missense_Mutation_p.P90Q	NM_001126128.1	NP_001119600.1	Q9HC23	PROK2_HUMAN	prokineticin 2	111					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)		GGCCAAGCCTGGCAGACATGG	0.408													G|||	33	0.00658946	0.0242	0.0014	5008	,	,		16471	0.0		0.0	False		,,,				2504	0.0				p.P111Q		Atlas-SNP	.											.	PROK2	13	.	0			c.C332A						PASS	.	G	GLN/PRO,GLN/PRO	86,4320	73.1+/-111.1	1,84,2118	79	85	83		332,269	5.8	1	3	dbSNP_129	83	0,8600		0,0,4300	yes	missense,missense	PROK2	NM_001126128.1,NM_021935.3	76,76	1,84,6418	TT,TG,GG		0.0,1.9519,0.6612	probably-damaging,probably-damaging	111/130,90/109	71821933	86,12920	2203	4300	6503	SO:0001583	missense	60675	exon4			AAGCCTGGCAGAC	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.332C>A	3.37:g.71821933G>T	ENSP00000295619:p.Pro111Gln	121	0	0		152	94	0.618421	NM_001126128	Q53Z79|Q6ISR0	Missense_Mutation	SNP	ENST00000295619.3	37	CCDS46868.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	27.9	4.873120	0.91664	0.019519	0.0	ENSG00000163421	ENST00000353065;ENST00000295619	T;T	0.72725	-0.68;-0.68	5.85	5.85	0.93711	Prokineticin domain (2);	0.000000	0.85682	D	0.000000	T	0.72020	0.3409	L	0.59436	1.845	0.58432	D	0.999998	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.974	T	0.77600	-0.2527	10	0.51188	T	0.08	-11.9075	18.9291	0.92558	0.0:0.0:1.0:0.0	rs60239864	111;90	Q9HC23;Q6ISR0	PROK2_HUMAN;.	Q	90;111	ENSP00000295618:P90Q;ENSP00000295619:P111Q	ENSP00000295619:P111Q	P	-	2	0	PROK2	71904623	1.000000	0.71417	0.980000	0.43619	0.999000	0.98932	8.067000	0.89488	2.773000	0.95371	0.650000	0.86243	CCA	G|0.994;T|0.006	0.006	strong		0.408	PROK2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352302.1	NM_001126128		T	71821933	G	T	71821933	3	4	22	1	0	0	0	0	1	0	0	0	12563	1348	47	4	61	4	PROK2	3	71821933	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5388475	71821933	126200497	855	3756											
GXYLT2	727936	hgsc.bcm.edu	37	chr3	72971414	72971414	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacagaatctaccccatcacAttttctgttggaaaccctca	12	11	4	14	0	4	1	2	0	2	1	4	2	4	2	3	1	2	1	3	1	3	4	rs61741329	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:72971414A>G	ENST00000389617.4	+	3	689	c.528A>G	c.(526-528)acA>acG	p.T176T		NM_001080393.1	NP_001073862.1	A0PJZ3	GXLT2_HUMAN	glucoside xylosyltransferase 2	176					O-glycan processing (GO:0016266)	integral component of membrane (GO:0016021)	UDP-xylosyltransferase activity (GO:0035252)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	18						ACCCCATCACATTTTCTGTTG	0.448													A|||	177	0.0353435	0.1256	0.0159	5008	,	,		18993	0.0		0.0	False		,,,				2504	0.0				p.T176T		Atlas-SNP	.											.	GXYLT2	43	.	0			c.A528G						PASS	.	A		362,3352		19,324,1514	210	215	213		528	-2.9	1	3	dbSNP_129	213	4,8206		0,4,4101	no	coding-synonymous	GXYLT2	NM_001080393.1		19,328,5615	GG,GA,AA		0.0487,9.7469,3.0694		176/444	72971414	366,11558	1857	4105	5962	SO:0001819	synonymous_variant	727936	exon3			CATCACATTTTCT	AC098481	CCDS46870.1	3p13	2013-02-22	2009-11-17	2009-11-17	ENSG00000172986	ENSG00000172986		"Glycosyltransferase family 8 domain containing"	33383	protein-coding gene	gene with protein product		613322	"glycosyltransferase 8 domain containing 4"	GLT8D4		19940119	Standard	NM_001080393		Approved		uc003dpg.3	A0PJZ3	OTTHUMG00000158815	ENST00000389617.4:c.528A>G	3.37:g.72971414A>G		148	0	0		131	60	0.458015	NM_001080393		Silent	SNP	ENST00000389617.4	37	CCDS46870.1																																																																																			A|0.976;G|0.024	0.024	strong		0.448	GXYLT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352318.1	NM_001080393		G	72971414	A	G	72971414	2	3	22	1	0	0	0	0	0	0	0	1	6913	204	8	3		3	GXYLT2	3	72971414	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1149481	72971414	125051016	856	3757											
ROBO2	6092	hgsc.bcm.edu	37	chr3	77614215	77614215	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttattcatggtcagagcgaTcaacccccaaggtctcagtg	10	10	9	12	1	4	1	4	0	1	1	5	2	4	1	2	2	2	0	2	2	3	2	rs185792666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:77614215T>C	ENST00000461745.1	+	12	2693	c.1793T>C	c.(1792-1794)aTc>aCc	p.I598T	ROBO2_ENST00000487694.3_Missense_Mutation_p.I614T|ROBO2_ENST00000332191.8_Missense_Mutation_p.I598T	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	598	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)		GTCAGAGCGATCAACCCCCAA	0.498													T|||	10	0.00199681	0.0	0.0086	5008	,	,		17327	0.0		0.004	False		,,,				2504	0.0				p.I598T		Atlas-SNP	.											.	ROBO2	527	.	0			c.T1793C						PASS	.	T	THR/ILE,THR/ILE	2,3978		0,2,1988	131	129	130		1841,1793	6	1	3		130	43,8283		0,43,4120	yes	missense,missense	ROBO2	NM_001128929.2,NM_002942.4	89,89	0,45,6108	CC,CT,TT		0.5165,0.0503,0.3657	possibly-damaging,possibly-damaging	614/1395,598/1379	77614215	45,12261	1990	4163	6153	SO:0001583	missense	6092	exon12			GAGCGATCAACCC	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.1793T>C	3.37:g.77614215T>C	ENSP00000417164:p.Ile598Thr	61	0	0		82	44	0.536585	NM_002942	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	37	CCDS43109.1	5	0.0022893772893772895	0	0.0	5	0.013812154696132596	0	0.0	0	0.0	T	17.82	3.482426	0.63962	5.03E-4	0.005165	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191;ENST00000398467	T;T;T	0.57595	0.39;0.39;0.39	6.02	6.02	0.97574	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.46758	D	0.000269	T	0.47135	0.1429	N	0.25890	0.77	0.39849	D	0.973215	P;P;B	0.35411	0.486;0.5;0.296	P;P;P	0.50825	0.651;0.588;0.651	T	0.51340	-0.8718	9	0.20519	T	0.43	.	16.542	0.84395	0.0:0.0:0.0:1.0	.	614;598;598	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	T	614;614;618;598;598;319	ENSP00000417335:I614T;ENSP00000417164:I598T;ENSP00000327536:I598T	ENSP00000327536:I598T	I	+	2	0	ROBO2	77696905	1.000000	0.71417	0.995000	0.50966	0.962000	0.63368	5.141000	0.64814	2.304000	0.77564	0.528000	0.53228	ATC	T|0.996;C|0.004	0.004	strong		0.498	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		C	77614215	T	C	77614215	3	2	22	1	0	0	0	0	1	0	0	0	13529	1435	50	3	1841	3	ROBO2	3	77614215	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	4642801	77614215	120408215	857	3758											
ROBO1	6091	hgsc.bcm.edu	37	chr3	78676701	78676701	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgctggtggcacgggacaTggcatttcttggtcatagct	6	13	13	9	1	2	0	1	0	1	0	2	1	2	1	0	5	2	4	0	5	1	4	rs116125749	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:78676701T>C	ENST00000464233.1	-	26	3758	c.3645A>G	c.(3643-3645)ccA>ccG	p.P1215P	ROBO1_ENST00000495273.1_Silent_p.P1170P|ROBO1_ENST00000436010.2_Silent_p.P1176P|ROBO1_ENST00000467549.1_Silent_p.P1115P	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	1215					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)		GCACGGGACATGGCATTTCTT	0.413													T|||	52	0.0103834	0.0371	0.0043	5008	,	,		19868	0.0		0.0	False		,,,				2504	0.0				p.P1215P		Atlas-SNP	.											.	ROBO1	833	.	0			c.A3645G						PASS	.	T	,,	114,3892		1,112,1890	59	70	67		3345,3645,3510	-1.6	1	3	dbSNP_132	67	1,8321		0,1,4160	no	coding-synonymous,coding-synonymous,coding-synonymous	ROBO1	NM_001145845.1,NM_002941.3,NM_133631.3	,,	1,113,6050	CC,CT,TT		0.012,2.8457,0.9328	,,	1115/1552,1215/1652,1170/1607	78676701	115,12213	2003	4161	6164	SO:0001819	synonymous_variant	6091	exon26			GGGACATGGCATT	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.3645A>G	3.37:g.78676701T>C		268	0	0		244	120	0.491803	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Silent	SNP	ENST00000464233.1	37	CCDS54611.1	17	0.007783882783882784	17	0.034552845528455285	0	0.0	0	0.0	0	0.0	T	5.980	0.364753	0.11296	0.028457	1.2E-4	ENSG00000169855	ENST00000472273	.	.	.	5.29	-1.6	0.08426	.	.	.	.	.	T	0.17152	0.0412	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.17137	-1.0379	4	.	.	.	.	1.2302	0.01942	0.174:0.1782:0.1809:0.4669	.	.	.	.	R	142	.	.	H	-	2	0	ROBO1	78759391	0.944000	0.32072	0.963000	0.40424	0.670000	0.39368	0.033000	0.13754	-0.468000	0.06922	-1.447000	0.01057	CAT	T|0.991;C|0.009	0.009	strong		0.413	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		C	78676701	T	C	78676701	2	2	22	1	0	0	0	0	0	0	0	1	13528	1451	51	3		3	ROBO1	3	78676701	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1062486	78676701	119345729	858	3759											
ROBO1	6091	hgsc.bcm.edu	37	chr3	79174619	79174619	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	actctacctgtatagcccagCgaattgtcatcgttatcaga	11	12	7	11	2	3	1	2	0	1	1	4	2	3	1	2	0	3	2	2	0	5	5	rs139237706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:79174619C>T	ENST00000464233.1	-	3	272	c.159G>A	c.(157-159)tcG>tcA	p.S53S		NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	53					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)		TATAGCCCAGCGAATTGTCAT	0.488													C|||	6	0.00119808	0.003	0.0014	5008	,	,		17914	0.0		0.0	False		,,,				2504	0.001				p.S53S		Atlas-SNP	.											.	ROBO1	833	.	0			c.G159A						PASS	.	C		11,3935		0,11,1962	139	134	135		159	5.4	1	3	dbSNP_134	135	0,8292		0,0,4146	no	coding-synonymous	ROBO1	NM_002941.3		0,11,6108	TT,TC,CC		0.0,0.2788,0.0899		53/1652	79174619	11,12227	1973	4146	6119	SO:0001819	synonymous_variant	6091	exon3			GCCCAGCGAATTG	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.159G>A	3.37:g.79174619C>T		192	0	0		195	94	0.482051	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Silent	SNP	ENST00000464233.1	37	CCDS54611.1																																																																																			C|0.998;T|0.002	0.002	strong		0.488	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		T	79174619	C	T	79174619	2	4	22	1	0	0	0	0	0	0	0	1	13528	755	27	1		1	ROBO1	3	79174619	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	497918	79174619	118847811	859	3760											
GBE1	2632	hgsc.bcm.edu	37	chr3	81586149	81586149	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacttgtagcgaagaaggtcGtcgtcagttaaatgaaactg	14	10	11	6	3	1	2	1	1	0	1	3	3	1	2	0	1	3	2	0	1	7	3	rs2229520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:81586149G>A	ENST00000429644.2	-	13	2359	c.1716C>T	c.(1714-1716)gaC>gaT	p.D572D	GBE1_ENST00000489715.1_Silent_p.D531D	NM_000158.3	NP_000149	Q04446	GLGB_HUMAN	glucan (1,4-alpha-), branching enzyme 1	572					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)		GAAGAAGGTCGTCGTCAGTTA	0.413									Glycogen Storage Disease, type IV				A|||	77	0.0153754	0.0552	0.0058	5008	,	,		16494	0.0		0.0	False		,,,				2504	0.0				p.D572D		Atlas-SNP	.											.	GBE1	111	.	0			c.C1716T						PASS	.	A		195,3489		3,189,1650	114	110	111		1716	0.1	1	3	dbSNP_98	111	2,8168		0,2,4083	no	coding-synonymous	GBE1	NM_000158.3		3,191,5733	AA,AG,GG		0.0245,5.2932,1.6619		572/703	81586149	197,11657	1842	4085	5927	SO:0001819	synonymous_variant	2632	exon13	Familial Cancer Database	Andersen Disease, Brancher deficiency	AAGGTCGTCGTCA		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.1716C>T	3.37:g.81586149G>A		107	0	0		127	49	0.385827	NM_000158	B3KWV3|Q96EN0	Silent	SNP	ENST00000429644.2	37	CCDS54612.1																																																																																			G|0.987;A|0.013	0.013	strong		0.413	GBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352760.2			A	81586149	G	A	81586149	2	1	22	1	0	0	0	0	0	0	0	1	6278	1136	40	1		1	GBE1	3	81586149	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2411530	81586149	116436281	860	3761											
NSUN3	63899	hgsc.bcm.edu	37	chr3	93845062	93845062	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgattgcacacaggtctgcaAttaaggccttacgtcctgga	10	11	10	10	1	1	1	0	1	1	0	2	2	2	2	2	3	3	2	2	3	3	3	rs61730354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:93845062A>G	ENST00000314622.4	+	6	962	c.751A>G	c.(751-753)Att>Gtt	p.I251V		NM_022072.3	NP_071355.1	Q9H649	NSUN3_HUMAN	NOP2/Sun domain family, member 3	251							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|skin(1)	18						CAGGTCTGCAATTAAGGCCTT	0.388													A|||	89	0.0177716	0.0537	0.0115	5008	,	,		18150	0.0		0.007	False		,,,				2504	0.0031				p.I251V		Atlas-SNP	.											.	NSUN3	33	.	0			c.A751G						PASS	.	A	VAL/ILE	193,4213	120.4+/-158.0	6,181,2016	52	49	50		751	3.3	1	3	dbSNP_129	50	93,8507	51.9+/-112.3	0,93,4207	yes	missense	NSUN3	NM_022072.3	29	6,274,6223	GG,GA,AA		1.0814,4.3804,2.199	benign	251/341	93845062	286,12720	2203	4300	6503	SO:0001583	missense	63899	exon6			TCTGCAATTAAGG	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.751A>G	3.37:g.93845062A>G	ENSP00000318986:p.Ile251Val	124	0	0		150	82	0.546667	NM_022072	Q6PG41|Q8IXG9|Q9H6M2	Missense_Mutation	SNP	ENST00000314622.4	37	CCDS2927.1	25	0.011446886446886446	18	0.036585365853658534	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	A	9.012	0.982684	0.18889	0.043804	0.010814	ENSG00000178694	ENST00000314622	T	0.25579	1.79	5.64	3.29	0.37713	Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p (1);	0.121362	0.64402	D	0.000015	T	0.03136	0.0092	N	0.17723	0.515	0.35580	D	0.806204	B	0.21821	0.061	B	0.23574	0.047	T	0.16453	-1.0402	10	0.25751	T	0.34	-12.7984	7.4732	0.27361	0.6633:0.0:0.3367:0.0	rs61730354	251	Q9H649	NSUN3_HUMAN	V	251	ENSP00000318986:I251V	ENSP00000318986:I251V	I	+	1	0	NSUN3	95327752	0.993000	0.37304	1.000000	0.80357	0.720000	0.41350	0.754000	0.26390	0.964000	0.38108	0.377000	0.23210	ATT	A|0.982;G|0.018	0.018	strong		0.388	NSUN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352934.1	NM_022072		G	93845062	A	G	93845062	3	3	22	1	0	0	0	0	1	0	0	0	10688	101	4	3	773	3	NSUN3	3	93845062	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	12258913	93845062	104177368	861	3762											
SENP7	57337	hgsc.bcm.edu	37	chr3	101090924	101090924	+	Missense_Mutation	SNP	T	T	A																															tttttctttattgtgcgcagTctgctttgcagaattgtcat																								rs116197973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:101090924T>A	ENST00000394095.2	-	7	777	c.724A>T	c.(724-726)Act>Tct	p.T242S	SENP7_ENST00000394091.1_Missense_Mutation_p.T78S|SENP7_ENST00000314261.7_Missense_Mutation_p.T176S|SENP7_ENST00000348610.3_Missense_Mutation_p.T209S|SENP7_ENST00000394094.2_Missense_Mutation_p.T177S|SENP7_ENST00000358203.3_Missense_Mutation_p.T78S	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	242						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						TTGTGCGCAGTCTGCTTTGCA	0.368													C|||	50	0.00998403	0.0371	0.0014	5008	,	,		13274	0.0		0.0	False		,,,				2504	0.0				p.T242S		Atlas-SNP	.											.	SENP7	170	.	0			c.A724T						PASS	.	C	SER/THR,SER/THR	156,4250		4,148,2051	135	126	129		529,724	1.3	0	3	dbSNP_132	129	0,8600		0,0,4300	yes	missense,missense	SENP7	NM_001077203.1,NM_020654.3	58,58	4,148,6351	AA,AT,TT		0.0,3.5406,1.1994	benign,benign	177/986,242/1051	101090924	156,12850	2203	4300	6503	SO:0001583	missense	57337	exon7			GCGCAGTCTGCTT		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.724A>T	3.37:g.101090924T>A	ENSP00000377655:p.Thr242Ser	145	0	0		158	73	0.462025	NM_020654	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Missense_Mutation	SNP	ENST00000394095.2	37	CCDS2941.2	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	3.708	-0.060054	0.07317	0.035406	0.0	ENSG00000138468	ENST00000394095;ENST00000394094;ENST00000314261;ENST00000394091;ENST00000358203;ENST00000348610	T;T;T;T;T;T	0.16743	2.32;2.33;2.32;2.32;2.32;2.32	5.1	1.33	0.21861	.	1.879190	0.02560	N	0.096662	T	0.01940	0.0061	N	0.04508	-0.205	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;0.001;0.0	T	0.29792	-1.0000	10	0.32370	T	0.25	-0.178	7.9128	0.29800	0.0:0.565:0.0:0.435	.	78;176;209;242	Q9BQF6-4;Q9BQF6-5;Q9BQF6-2;Q9BQF6	.;.;.;SENP7_HUMAN	S	242;177;176;78;78;209	ENSP00000377655:T242S;ENSP00000377654:T177S;ENSP00000313624:T176S;ENSP00000377651:T78S;ENSP00000350936:T78S;ENSP00000342159:T209S	ENSP00000313624:T176S	T	-	1	0	SENP7	102573614	0.029000	0.19370	0.027000	0.17364	0.001000	0.01503	-0.162000	0.10012	-0.170000	0.10816	-0.927000	0.02713	ACT	T|0.988;A|0.012	0.012	strong		0.368	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654		A	101090924	T	A	101090924	3	1	22	1	0	0	0	0	1	0	0	0	14066	1667	58	5	2500	5	SENP7	3	101090924	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	7245862	101090924	96931506	862	3763	52	2									
SENP7	57337	hgsc.bcm.edu	37	chr3	101090925	101090925	+	Missense_Mutation	SNP	C	C	A																															ttttctttattgtgcgcagtCtgctttgcagaattgtcatc																								rs115061809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:101090925C>A	ENST00000394095.2	-	7	776	c.723G>T	c.(721-723)caG>caT	p.Q241H	SENP7_ENST00000394091.1_Missense_Mutation_p.Q77H|SENP7_ENST00000314261.7_Missense_Mutation_p.Q175H|SENP7_ENST00000348610.3_Missense_Mutation_p.Q208H|SENP7_ENST00000394094.2_Missense_Mutation_p.Q176H|SENP7_ENST00000358203.3_Missense_Mutation_p.Q77H	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	241						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						TGTGCGCAGTCTGCTTTGCAG	0.368													C|||	50	0.00998403	0.0371	0.0014	5008	,	,		13309	0.0		0.0	False		,,,				2504	0.0				p.Q241H		Atlas-SNP	.											.	SENP7	170	.	0			c.G723T						PASS	.	C	HIS/GLN,HIS/GLN	156,4250	103.8+/-142.4	4,148,2051	135	127	129		528,723	1.7	0.2	3	dbSNP_132	129	0,8600		0,0,4300	yes	missense,missense	SENP7	NM_001077203.1,NM_020654.3	24,24	4,148,6351	AA,AC,CC		0.0,3.5406,1.1994	possibly-damaging,possibly-damaging	176/986,241/1051	101090925	156,12850	2203	4300	6503	SO:0001583	missense	57337	exon7			CGCAGTCTGCTTT		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.723G>T	3.37:g.101090925C>A	ENSP00000377655:p.Gln241His	145	0	0		156	72	0.461538	NM_020654	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Missense_Mutation	SNP	ENST00000394095.2	37	CCDS2941.2	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	10.27	1.303827	0.23736	0.035406	0.0	ENSG00000138468	ENST00000394095;ENST00000394094;ENST00000314261;ENST00000394091;ENST00000358203;ENST00000348610	T;T;T;T;T;T	0.20069	2.12;2.1;2.15;2.11;2.11;2.13	5.1	1.66	0.24008	.	0.601428	0.14885	N	0.292719	T	0.05273	0.0140	L	0.54323	1.7	0.09310	N	1	P;P;P;P	0.48503	0.911;0.846;0.797;0.694	P;P;P;B	0.47470	0.465;0.465;0.548;0.346	T	0.08743	-1.0707	10	0.87932	D	0	-0.6991	2.926	0.05784	0.2106:0.529:0.0:0.2604	.	77;175;208;241	Q9BQF6-4;Q9BQF6-5;Q9BQF6-2;Q9BQF6	.;.;.;SENP7_HUMAN	H	241;176;175;77;77;208	ENSP00000377655:Q241H;ENSP00000377654:Q176H;ENSP00000313624:Q175H;ENSP00000377651:Q77H;ENSP00000350936:Q77H;ENSP00000342159:Q208H	ENSP00000313624:Q175H	Q	-	3	2	SENP7	102573615	0.220000	0.23631	0.175000	0.22980	0.007000	0.05969	0.278000	0.18753	0.606000	0.29965	0.585000	0.79938	CAG	C|0.988;A|0.012	0.012	strong		0.368	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654		A	101090925	C	A	101090925	3	1	22	1	0	0	0	0	1	0	0	0	14066	912	32	4	2501	4	SENP7	3	101090925	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1	101090925	96931505	863	3764	52	2									
PCNP	57092	hgsc.bcm.edu	37	chr3	101293097	101293097	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggagacgagaagcctgaaaAgtcgcagcgagctggagccg	12	3	17	9	4	0	3	0	1	0	2	1	7	0	4	2	2	4	2	2	2	3	0	rs116752753	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:101293097A>G	ENST00000265260.3	+	1	159	c.38A>G	c.(37-39)aAg>aGg	p.K13R	PCNP_ENST00000469941.1_5'UTR|PCNP_ENST00000486406.1_3'UTR|PCNP_ENST00000296024.5_Missense_Mutation_p.K13R	NM_020357.1	NP_065090.1	Q8WW12	PCNP_HUMAN	PEST proteolytic signal containing nuclear protein	13					cell cycle (GO:0007049)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)	nucleus (GO:0005634)				large_intestine(1)|lung(1)	2						AAGCCTGAAAAGTCGCAGCGA	0.677													A|||	49	0.00978435	0.0363	0.0014	5008	,	,		12760	0.0		0.0	False		,,,				2504	0.0				p.K13R		Atlas-SNP	.											.	PCNP	8	.	0			c.A38G						PASS	.	A	ARG/LYS	87,3257		0,87,1585	23	27	26		38	2.6	0.9	3	dbSNP_132	26	1,6167		0,1,3083	yes	missense	PCNP	NM_020357.1	26	0,88,4668	GG,GA,AA		0.0162,2.6017,0.9251	benign	13/179	101293097	88,9424	1672	3084	4756	SO:0001583	missense	57092	exon1			CTGAAAAGTCGCA		CCDS2942.1	3q12.3	2006-03-09			ENSG00000081154	ENSG00000081154			30023	protein-coding gene	gene with protein product		615210				12176013	Standard	NM_020357		Approved		uc003dva.3	Q8WW12	OTTHUMG00000159108	ENST00000265260.3:c.38A>G	3.37:g.101293097A>G	ENSP00000265260:p.Lys13Arg	161	0	0		210	114	0.542857	NM_020357	B2RBE7|D3DN52|Q53GF3|Q6AI44|Q96CU3|Q9NS81	Missense_Mutation	SNP	ENST00000265260.3	37	CCDS2942.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	A	15.73	2.921230	0.52653	0.026017	1.62E-4	ENSG00000081154	ENST00000265260;ENST00000296024	.	.	.	5.08	2.59	0.31030	.	2.264980	0.01941	N	0.041900	T	0.06735	0.0172	N	0.08118	0	0.27175	N	0.960801	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.14868	-1.0457	9	0.27785	T	0.31	.	1.8535	0.03174	0.5685:0.1752:0.0887:0.1676	.	13;13	Q8WW12-2;Q8WW12	.;PCNP_HUMAN	R	13	.	ENSP00000265260:K13R	K	+	2	0	PCNP	102775787	1.000000	0.71417	0.891000	0.34965	0.933000	0.57130	1.646000	0.37249	0.366000	0.24427	-0.336000	0.08194	AAG	A|0.993;G|0.007	0.007	strong		0.677	PCNP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353338.2	NM_020357		G	101293097	A	G	101293097	3	3	22	1	0	0	0	0	1	0	0	0	11598	72	3	3	40	3	PCNP	3	101293097	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	202172	101293097	96729333	864	3765											
ZBTB11	27107	hgsc.bcm.edu	37	chr3	101370091	101370091	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcagatagcttctgtccttgCtgttgtgctaatacataatt	9	17	7	8	0	2	1	1	0	1	1	3	1	3	1	1	0	4	4	1	0	4	8	rs34525894	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:101370091C>T	ENST00000312938.4	-	11	3661	c.3081G>A	c.(3079-3081)caG>caA	p.Q1027Q		NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	1027					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						TCTGTCCTTGCTGTTGTGCTA	0.378													C|||	258	0.0515176	0.1891	0.0115	5008	,	,		24052	0.0		0.0	False		,,,				2504	0.0				p.Q1027Q		Atlas-SNP	.											.	ZBTB11	77	.	0			c.G3081A						PASS	.	C		757,3649	309.7+/-291.2	72,613,1518	132	129	130		3081	5.4	1	3	dbSNP_126	130	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ZBTB11	NM_014415.3		72,615,5816	TT,TC,CC		0.0233,17.1811,5.8358		1027/1054	101370091	759,12247	2203	4300	6503	SO:0001819	synonymous_variant	27107	exon11			TCCTTGCTGTTGT	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.3081G>A	3.37:g.101370091C>T		209	0	0		221	95	0.429864	NM_014415	Q2NKP9	Silent	SNP	ENST00000312938.4	37	CCDS2943.1																																																																																			C|0.948;T|0.052	0.052	strong		0.378	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353441.2	NM_014415		T	101370091	C	T	101370091	2	4	22	1	0	0	0	0	0	0	0	1	17539	796	28	2		2	ZBTB11	3	101370091	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	76994	101370091	96652339	865	3766											
GUCA1C	9626	hgsc.bcm.edu	37	chr3	108627024	108627024	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagatcctgatcttttgccaTgccattgataaattcttcta	10	16	6	9	0	3	3	0	2	3	1	4	4	4	3	3	0	2	0	3	0	3	7	rs16854916	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:108627024T>C	ENST00000261047.3	-	4	607	c.475A>G	c.(475-477)Atg>Gtg	p.M159V	GUCA1C_ENST00000393963.3_Missense_Mutation_p.H172R	NM_005459.3	NP_005450.3	O95843	GUC1C_HUMAN	guanylate cyclase activator 1C	159	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.		M -> V (in dbSNP:rs16854916).		phototransduction, visible light (GO:0007603)|positive regulation of guanylate cyclase activity (GO:0031284)|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)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)			endometrium(2)|large_intestine(1)|liver(1)|lung(8)|pancreas(1)|skin(1)	14						TCTTTTGCCATGCCATTGATA	0.398													T|||	76	0.0151757	0.056	0.0029	5008	,	,		17705	0.0		0.0	False		,,,				2504	0.0				p.M159V	NSCLC(157;1360 1999 30631 40189 44208)	Atlas-SNP	.											.	GUCA1C	39	.	0			c.A475G						PASS	.	T	VAL/MET	184,4222	119.6+/-157.3	3,178,2022	84	82	83		475	-0.5	0	3	dbSNP_123	83	1,8599	1.2+/-3.3	0,1,4299	yes	missense	GUCA1C	NM_005459.3	21	3,179,6321	CC,CT,TT		0.0116,4.1761,1.4224	benign	159/210	108627024	185,12821	2203	4300	6503	SO:0001583	missense	9626	exon4			TTGCCATGCCATT	AF110002	CCDS2954.1	3q13.1	2013-01-10			ENSG00000138472	ENSG00000138472		"EF-hand domain containing"	4680	protein-coding gene	gene with protein product	"guanylyl cyclase-activating protein 3"	605128				10037746, 11860507	Standard	NM_005459		Approved	GCAP3	uc003dxj.2	O95843	OTTHUMG00000159204	ENST00000261047.3:c.475A>G	3.37:g.108627024T>C	ENSP00000261047:p.Met159Val	101	0	0		115	52	0.452174	NM_005459	O95844|Q9UNM0	Missense_Mutation	SNP	ENST00000261047.3	37	CCDS2954.1	29|29	0.013278388278388278|0.013278388278388278	28|28	0.056910569105691054|0.056910569105691054	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	T|T	0.866|0.866	-0.733700|-0.733700	0.03111|0.03111	0.041761|0.041761	1.16E-4|1.16E-4	ENSG00000138472|ENSG00000138472	ENST00000393963|ENST00000261047	T|T	0.66638|0.71817	-0.22|-0.6	5.67|5.67	-0.534|-0.534	0.11883|0.11883	.|EF-hand-like domain (1);	.|1.183010	.|0.05826	.|N	.|0.616757	T|T	0.06508|0.06508	0.0167|0.0167	N|N	0.05280|0.05280	-0.08|-0.08	0.09310|0.09310	N|N	1|1	B|B	0.13145|0.02656	0.007|0.0	B|B	0.10450|0.01281	0.005|0.0	T|T	0.08597|0.08597	-1.0714|-1.0714	9|10	0.41790|0.07175	T|T	0.15|0.84	.|.	3.7193|3.7193	0.08450|0.08450	0.1218:0.0744:0.2242:0.5796|0.1218:0.0744:0.2242:0.5796	rs16854916;rs52837740;rs56517263;rs16854916|rs16854916;rs52837740;rs56517263;rs16854916	172|159	C9JNI2|O95843	.|GUC1C_HUMAN	R|V	172|159	ENSP00000377535:H172R|ENSP00000261047:M159V	ENSP00000377535:H172R|ENSP00000261047:M159V	H|M	-|-	2|1	0|0	GUCA1C|GUCA1C	110109714|110109714	0.002000|0.002000	0.14202|0.14202	0.000000|0.000000	0.03702|0.03702	0.322000|0.322000	0.28314|0.28314	0.442000|0.442000	0.21628|0.21628	0.073000|0.073000	0.16731|0.16731	-0.461000|-0.461000	0.05368|0.05368	CAT|ATG	T|0.982;C|0.018	0.018	strong		0.398	GUCA1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353819.1	NM_005459		C	108627024	T	C	108627024	3	2	22	1	0	0	0	0	1	0	0	0	6899	1464	51	3	158	3	GUCA1C	3	108627024	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	7256933	108627024	89395406	866	3767											
MORC1	27136	hgsc.bcm.edu	37	chr3	108780895	108780895	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgatttgtgcttctttcaaTatggattcagctggaagtag	9	17	10	5	0	3	1	2	1	1	0	3	3	3	3	0	2	2	3	0	2	4	7	rs79817474	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:108780895T>A	ENST00000483760.1	-	11	949	c.906A>T	c.(904-906)atA>atT	p.I302I	MORC1_ENST00000232603.5_Silent_p.I302I					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						CTTCTTTCAATATGGATTCAG	0.343													T|||	38	0.00758786	0.0265	0.0043	5008	,	,		19655	0.0		0.0	False		,,,				2504	0.0				p.I302I		Atlas-SNP	.											.	MORC1	211	.	0			c.A906T						PASS	.	T		125,4281	92.0+/-130.7	2,121,2080	191	175	181		906	-8.9	0	3	dbSNP_132	181	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	MORC1	NM_014429.3		2,123,6378	AA,AT,TT		0.0233,2.837,0.9765		302/985	108780895	127,12879	2203	4300	6503	SO:0001819	synonymous_variant	27136	exon11			TTTCAATATGGAT	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.906A>T	3.37:g.108780895T>A		128	0	0		121	68	0.561983	NM_014429		Silent	SNP	ENST00000483760.1	37																																																																																				T|0.989;A|0.011	0.011	strong		0.343	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1			A	108780895	T	A	108780895	2	1	22	1	0	0	0	0	0	0	0	1	9710	1396	49	5		5	MORC1	3	108780895	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	153871	108780895	89241535	867	3768											
DPPA4	55211	hgsc.bcm.edu	37	chr3	109049507	109049507	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccctcaaggagagcagtggaAttttccagggcaggcggctc	9	7	14	11	1	1	1	1	0	0	1	3	3	2	2	2	5	1	3	2	5	2	2	rs16834356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:109049507A>G	ENST00000335658.6	-	5	597	c.543T>C	c.(541-543)aaT>aaC	p.N181N	DPPA4_ENST00000478791.1_5'UTR	NM_018189.3	NP_060659.3	Q7L190	DPPA4_HUMAN	developmental pluripotency associated 4	181					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						GAGCAGTGGAATTTTCCAGGG	0.547													A|||	41	0.0081869	0.028	0.0043	5008	,	,		15162	0.0		0.001	False		,,,				2504	0.0				p.N181N		Atlas-SNP	.											.	DPPA4	56	.	0			c.T543C						PASS	.	A		122,4284	93.0+/-131.7	3,116,2084	71	77	75		543	-8.2	0	3	dbSNP_123	75	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DPPA4	NM_018189.3		3,117,6383	GG,GA,AA		0.0116,2.769,0.9457		181/305	109049507	123,12883	2203	4300	6503	SO:0001819	synonymous_variant	55211	exon5			AGTGGAATTTTCC	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.543T>C	3.37:g.109049507A>G		207	1	0.00483092		204	204	1	NM_018189	A8K4M7|Q9H9N5|Q9NVI6	Silent	SNP	ENST00000335658.6	37	CCDS33814.1																																																																																			A|0.991;G|0.009	0.009	strong		0.547	DPPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353897.1	NM_018189		G	109049507	A	G	109049507	2	3	22	1	0	0	0	0	0	0	0	1	4738	98	4	3		3	DPPA4	3	109049507	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	268612	109049507	88972923	868	3769											
ZBED2	79413	hgsc.bcm.edu	37	chr3	111312965	111312965	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	accagttctcctgtctcactAatctcttcctcctccttcat	6	16	2	17	0	4	0	2	0	3	0	10	0	7	0	5	0	0	1	5	0	1	4	rs34083626	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:111312965A>T	ENST00000317012.4	-	2	1092	c.84T>A	c.(82-84)atT>atA	p.I28I	CD96_ENST00000283285.5_Intron|CD96_ENST00000352690.4_Intron|CD96_ENST00000438817.2_Intron	NM_024508.4	NP_078784.2	Q9BTP6	ZBED2_HUMAN	zinc finger, BED-type containing 2	28							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|lung(1)|skin(2)	6						CTGTCTCACTAATCTCTTCCT	0.517													A|||	266	0.053115	0.1891	0.0187	5008	,	,		14454	0.0		0.003	False		,,,				2504	0.0				p.I28I		Atlas-SNP	.											.	ZBED2	22	.	0			c.T84A						PASS	.	A	,,	642,3764	274.6+/-272.0	38,566,1599	268	221	237		,84,	0.4	0	3	dbSNP_126	237	9,8591	5.7+/-21.5	0,9,4291	no	intron,coding-synonymous,intron	CD96,ZBED2	NM_005816.4,NM_024508.4,NM_198196.2	,,	38,575,5890	TT,TA,AA		0.1047,14.571,5.0054	,,	,28/219,	111312965	651,12355	2203	4300	6503	SO:0001819	synonymous_variant	79413	exon2			CTCACTAATCTCT	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.84T>A	3.37:g.111312965A>T		265	1	0.00377358		304	136	0.447368	NM_024508	D3DN62	Silent	SNP	ENST00000317012.4	37	CCDS2960.2																																																																																			A|0.950;T|0.050	0.050	strong		0.517	ZBED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157228.2	NM_024508		T	111312965	A	T	111312965	2	4	22	1	0	0	0	0	0	0	0	1	17533	358	13	5		5	ZBED2	3	111312965	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2263458	111312965	86709465	869	3770											
SLC35A5	55032	hgsc.bcm.edu	37	chr3	112292765	112292765	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gttatcttctcaaattttagCattataacaacagctcttct	12	17	3	9	0	4	0	1	0	4	0	5	0	4	0	0	0	4	3	0	0	6	7	rs61732187	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:112292765C>T	ENST00000492406.1	+	5	673	c.390C>T	c.(388-390)agC>agT	p.S130S	SLC35A5_ENST00000460713.1_3'UTR	NM_017945.2	NP_060415.1	Q9BS91	S35A5_HUMAN	solute carrier family 35, member A5	130					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						CAAATTTTAGCATTATAACAA	0.353													C|||	119	0.023762	0.0832	0.013	5008	,	,		18592	0.0		0.0	False		,,,				2504	0.0				p.S130S		Atlas-SNP	.											.	SLC35A5	40	.	0			c.C390T						PASS	.	C		278,4128	156.6+/-189.7	8,262,1933	191	205	200		390	5.9	1	3	dbSNP_129	200	0,8600		0,0,4300	no	coding-synonymous	SLC35A5	NM_017945.2		8,262,6233	TT,TC,CC		0.0,6.3096,2.1375		130/425	112292765	278,12728	2203	4300	6503	SO:0001819	synonymous_variant	55032	exon5			TTTTAGCATTATA	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.390C>T	3.37:g.112292765C>T		168	0	0		183	183	1	NM_017945	D3DN66|Q69YY6|Q6ZMD6|Q9NWM9	Silent	SNP	ENST00000492406.1	37	CCDS2967.1																																																																																			C|0.976;T|0.024	0.024	strong		0.353	SLC35A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354184.1	NM_017945		T	112292765	C	T	112292765	2	4	22	1	0	0	0	0	0	0	0	1	14589	709	25	2		2	SLC35A5	3	112292765	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	979800	112292765	85729665	870	3771											
CD200R1L	344807	hgsc.bcm.edu	37	chr3	112545875	112545875	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggacagactcttgttgccaGtcaaatgggagacatggcag	11	8	13	9	1	2	2	1	0	1	2	2	4	2	3	1	3	1	2	1	3	1	2	rs61740125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:112545875G>A	ENST00000398214.1	-	4	869	c.644C>T	c.(643-645)aCt>aTt	p.T215I	CD200R1L_ENST00000448932.1_Missense_Mutation_p.T194I|CD200R1L_ENST00000488794.1_Missense_Mutation_p.T194I	NM_001008784.2	NP_001008784.2	Q6Q8B3	MO2R2_HUMAN	CD200 receptor 1-like	215	Ig-like C2-type.					integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|urinary_tract(2)	19						CTTGTTGCCAGTCAAATGGGA	0.453													G|||	201	0.0401358	0.0968	0.0115	5008	,	,		19144	0.002		0.001	False		,,,				2504	0.0634				p.T215I		Atlas-SNP	.											.	CD200R1L	47	.	0			c.C644T						PASS	.	G	ILE/THR,ILE/THR	351,4045	164.4+/-196.0	7,337,1854	66	70	68		644,581	3.5	0.3	3	dbSNP_129	68	6,8592	5.0+/-18.6	0,6,4293	yes	missense,missense	CD200R1L	NM_001008784.2,NM_001199215.1	89,89	7,343,6147	AA,AG,GG		0.0698,7.9845,2.7474	probably-damaging,probably-damaging	215/272,194/251	112545875	357,12637	2198	4299	6497	SO:0001583	missense	344807	exon4			TTGCCAGTCAAAT	AY284976	CCDS43131.1, CCDS56267.1	3q13.2	2014-05-15	2008-10-08		ENSG00000206531	ENSG00000206531		"Immunoglobulin superfamily / C2-set domain containing"	24665	protein-coding gene	gene with protein product	"CD200 receptor 2"						Standard	NM_001008784		Approved	CD200RLa, CD200R2	uc003dzi.1	Q6Q8B3	OTTHUMG00000159283	ENST00000398214.1:c.644C>T	3.37:g.112545875G>A	ENSP00000381272:p.Thr215Ile	130	0	0		141	141	1	NM_001008784	Q6WHB7	Missense_Mutation	SNP	ENST00000398214.1	37	CCDS43131.1	71	0.03250915750915751	65	0.13211382113821138	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	G	16.52	3.146835	0.57151	0.079845	6.98E-4	ENSG00000206531	ENST00000398214;ENST00000488794;ENST00000448932	T;T;T	0.76578	-1.03;-1.03;-1.03	4.35	3.45	0.39498	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.276049	0.31279	N	0.007923	T	0.07324	0.0185	M	0.87547	2.89	0.34063	P	0.342499	D	0.76494	0.999	D	0.72982	0.979	T	0.63220	-0.6686	9	0.72032	D	0.01	.	10.1628	0.42862	0.0:0.2033:0.7967:0.0	.	215	Q6Q8B3	MO2R2_HUMAN	I	215;194;194	ENSP00000381272:T215I;ENSP00000418413:T194I;ENSP00000415132:T194I	ENSP00000381272:T215I	T	-	2	0	CD200R1L	114028565	0.138000	0.22547	0.331000	0.25455	0.900000	0.52787	2.570000	0.45981	1.126000	0.42016	0.655000	0.94253	ACT	G|0.979;A|0.021	0.021	strong		0.453	CD200R1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354365.1	NM_001008784		A	112545875	G	A	112545875	3	1	22	1	0	0	0	0	1	0	0	0	2984	1029	36	2	183	2	CD200R1L	3	112545875	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	253110	112545875	85476555	871	3772											
BOC	91653	hgsc.bcm.edu	37	chr3	112993412	112993412	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggctcccgccgaggctccCatcatcctcagctcgccccg	4	6	11	20	4	2	0	2	0	0	0	6	1	5	0	6	3	1	3	6	3	0	0	rs7615578	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:112993412C>T	ENST00000495514.1	+	9	2129	c.1425C>T	c.(1423-1425)ccC>ccT	p.P475P	BOC_ENST00000273395.4_Silent_p.P475P|BOC_ENST00000355385.3_Silent_p.P475P|BOC_ENST00000497495.1_3'UTR			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	475	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)			CCGAGGCTCCCATCATCCTCA	0.672													C|||	55	0.0109824	0.0401	0.0029	5008	,	,		17614	0.0		0.0	False		,,,				2504	0.0				p.P475P		Atlas-SNP	.											.	BOC	139	.	0			c.C1425T						PASS	.	C		178,4226		3,172,2027	29	34	32		1425	-2.2	0.3	3	dbSNP_116	32	2,8596		0,2,4297	no	coding-synonymous	BOC	NM_033254.2		3,174,6324	TT,TC,CC		0.0233,4.0418,1.3844		475/1115	112993412	180,12822	2202	4299	6501	SO:0001819	synonymous_variant	91653	exon9			GGCTCCCATCATC	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.1425C>T	3.37:g.112993412C>T		169	0	0		215	104	0.483721	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Silent	SNP	ENST00000495514.1	37	CCDS2971.1																																																																																			C|0.985;T|0.015	0.015	strong		0.672	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254		T	112993412	C	T	112993412	2	4	22	1	0	0	0	0	0	0	0	1	1481	581	21	2		2	BOC	3	112993412	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	447537	112993412	85029018	872	3773											
SIDT1	54847	hgsc.bcm.edu	37	chr3	113285272	113285272	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taccctgccatgcaggtgacAgccgtgagggtgtatgtgaa	9	9	14	9	1	0	3	0	3	0	0	0	3	0	3	3	2	4	2	3	2	3	2	rs61734094	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:113285272A>C	ENST00000264852.4	+	2	954	c.228A>C	c.(226-228)acA>acC	p.T76T	SIDT1_ENST00000393830.3_Silent_p.T76T	NM_017699.2	NP_060169.2	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1	76					dsRNA transport (GO:0033227)	integral component of membrane (GO:0016021)	RNA transmembrane transporter activity (GO:0051033)			breast(1)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|liver(2)|lung(15)|ovary(3)|pancreas(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50						TGCAGGTGACAGCCGTGAGGG	0.507													C|||	101	0.0201677	0.0545	0.0086	5008	,	,		19117	0.0079		0.0099	False		,,,				2504	0.0051				p.T76T		Atlas-SNP	.											.	SIDT1	99	.	0			c.A228C						PASS	.	C		265,4141	802.1+/-415.6	10,245,1948	246	191	210		228	-11.2	0	3	dbSNP_129	210	60,8540	816.6+/-406.9	2,56,4242	no	coding-synonymous	SIDT1	NM_017699.2		12,301,6190	CC,CA,AA		0.6977,6.0145,2.4988		76/828	113285272	325,12681	2203	4300	6503	SO:0001819	synonymous_variant	54847	exon2			GGTGACAGCCGTG	AK000181	CCDS2974.1	3q13.31	2009-11-26			ENSG00000072858	ENSG00000072858			25967	protein-coding gene	gene with protein product		606816					Standard	NM_017699		Approved	FLJ20174, SID-1	uc003eak.3	Q9NXL6	OTTHUMG00000159299	ENST00000264852.4:c.228A>C	3.37:g.113285272A>C		133	0	0		139	72	0.517986	NM_017699	Q17RR4	Silent	SNP	ENST00000264852.4	37	CCDS2974.1																																																																																			A|0.978;C|0.022	0.022	strong		0.507	SIDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317564.1	NM_017699		C	113285272	A	C	113285272	2	2	22	1	0	0	0	0	0	0	0	1	14317	175	7	5		5	SIDT1	3	113285272	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	291860	113285272	84737158	873	3774											
SIDT1	54847	hgsc.bcm.edu	37	chr3	113323785	113323785	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaccattgctgtgttttacGcgctgcccgtgatccagctg	5	13	10	13	3	1	1	1	1	0	0	2	1	2	1	3	0	4	4	3	0	1	3	rs61732220	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:113323785G>T	ENST00000264852.4	+	14	2092	c.1366G>T	c.(1366-1368)Gcg>Tcg	p.A456S	SIDT1_ENST00000463226.1_3'UTR|SIDT1_ENST00000393830.3_Missense_Mutation_p.A456S	NM_017699.2	NP_060169.2	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1	456					dsRNA transport (GO:0033227)	integral component of membrane (GO:0016021)	RNA transmembrane transporter activity (GO:0051033)			breast(1)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|liver(2)|lung(15)|ovary(3)|pancreas(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50						TGTGTTTTACGCGCTGCCCGT	0.468													G|||	91	0.0181709	0.0666	0.0043	5008	,	,		15956	0.0		0.0	False		,,,				2504	0.0				p.A456S		Atlas-SNP	.											.	SIDT1	99	.	0			c.G1366T						PASS	.	G	SER/ALA	281,4125	155.2+/-188.4	10,261,1932	129	119	122		1366	5.9	1	3	dbSNP_129	122	2,8598	2.2+/-6.3	0,2,4298	yes	missense	SIDT1	NM_017699.2	99	10,263,6230	TT,TG,GG		0.0233,6.3777,2.1759	benign	456/828	113323785	283,12723	2203	4300	6503	SO:0001583	missense	54847	exon14			TTTTACGCGCTGC	AK000181	CCDS2974.1	3q13.31	2009-11-26			ENSG00000072858	ENSG00000072858			25967	protein-coding gene	gene with protein product		606816					Standard	NM_017699		Approved	FLJ20174, SID-1	uc003eak.3	Q9NXL6	OTTHUMG00000159299	ENST00000264852.4:c.1366G>T	3.37:g.113323785G>T	ENSP00000264852:p.Ala456Ser	75	0	0		78	41	0.525641	NM_017699	Q17RR4	Missense_Mutation	SNP	ENST00000264852.4	37	CCDS2974.1	34	0.015567765567765568	33	0.06707317073170732	1	0.0027624309392265192	0	0.0	0	0.0	G	15.33	2.801458	0.50315	0.063777	2.33E-4	ENSG00000072858	ENST00000264852;ENST00000393830	T;T	0.21361	2.01;2.01	5.88	5.88	0.94601	.	0.090977	0.47852	D	0.000207	T	0.02193	0.0068	L	0.51914	1.62	0.80722	D	1	B;B	0.29766	0.215;0.256	B;B	0.37047	0.154;0.24	T	0.01460	-1.1349	10	0.26408	T	0.33	-3.7185	20.2441	0.98394	0.0:0.0:1.0:0.0	rs61732220	456;456	Q9NXL6-2;Q9NXL6	.;SIDT1_HUMAN	S	456	ENSP00000264852:A456S;ENSP00000377416:A456S	ENSP00000264852:A456S	A	+	1	0	SIDT1	114806475	1.000000	0.71417	1.000000	0.80357	0.066000	0.16364	9.697000	0.98697	2.774000	0.95407	0.655000	0.94253	GCG	G|0.981;T|0.019	0.019	strong		0.468	SIDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317564.1	NM_017699		T	113323785	G	T	113323785	3	4	22	1	0	0	0	0	1	0	0	0	14317	1087	38	4	1420	4	SIDT1	3	113323785	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	38513	113323785	84698645	874	3775											
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113379720	113379720	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	catttaggcatgtgtgcaaaGaatgatgttggtgaggctca	11	12	13	5	0	1	3	1	2	0	1	1	3	1	3	0	3	1	4	0	3	3	3	rs114838141	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:113379720G>A	ENST00000478658.1	-	5	826	c.809C>T	c.(808-810)tCt>tTt	p.S270F	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Missense_Mutation_p.S270F			Q68DE3	K2018_HUMAN	KIAA2018	270						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						TGTGTGCAAAGAATGATGTTG	0.413													G|||	22	0.00439297	0.0166	0.0	5008	,	,		22506	0.0		0.0	False		,,,				2504	0.0				p.S270F		Atlas-SNP	.											.	KIAA2018	180	.	0			c.C809T						PASS	.	G	PHE/SER	49,3769		0,49,1860	60	57	58		809	5.4	0.1	3	dbSNP_132	58	0,8260		0,0,4130	yes	missense	KIAA2018	NM_001009899.2	155	0,49,5990	AA,AG,GG		0.0,1.2834,0.4057	possibly-damaging	270/2246	113379720	49,12029	1909	4130	6039	SO:0001583	missense	205717	exon7			TGCAAAGAATGAT	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.809C>T	3.37:g.113379720G>A	ENSP00000420721:p.Ser270Phe	173	0	0		200	78	0.39	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Missense_Mutation	SNP	ENST00000478658.1	37	CCDS43133.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	12.32	1.903297	0.33628	0.012834	0.0	ENSG00000176542	ENST00000316407;ENST00000478658	T;T	0.17691	2.26;2.26	5.36	5.36	0.76844	.	0.360582	0.24061	N	0.041908	T	0.11281	0.0275	N	0.08118	0	0.30845	N	0.735209	D	0.76494	0.999	D	0.67231	0.95	T	0.04333	-1.0959	10	0.72032	D	0.01	-4.2876	14.9458	0.71029	0.0:0.0:0.8566:0.1433	.	270	Q68DE3	K2018_HUMAN	F	270	ENSP00000320794:S270F;ENSP00000420721:S270F	ENSP00000320794:S270F	S	-	2	0	KIAA2018	114862410	0.990000	0.36364	0.073000	0.20177	0.608000	0.37181	4.214000	0.58527	2.789000	0.95967	0.655000	0.94253	TCT	G|0.996;A|0.004	0.004	strong		0.413	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		A	113379720	G	A	113379720	3	1	22	1	0	0	0	0	1	0	0	0	8277	942	33	2	5932	2	KIAA2018	3	113379720	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	55935	113379720	84642710	875	3776											
ZDHHC23	254887	hgsc.bcm.edu	37	chr3	113673098	113673098	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagtctcaacaatcgcacaaCaaaggatgaccccaagggct	15	5	8	13	1	1	1	1	1	1	0	3	2	1	2	2	2	2	2	2	2	5	0	rs149202494		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:113673098C>T	ENST00000330212.3	+	3	1012	c.713C>T	c.(712-714)aCa>aTa	p.T238I	ZDHHC23_ENST00000498275.1_Missense_Mutation_p.T232I	NM_173570.3	NP_775841.2	Q8IYP9	ZDH23_HUMAN	zinc finger, DHHC-type containing 23	238					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						AATCGCACAACAAAGGATGAC	0.597													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18066	0.0		0.0	False		,,,				2504	0.0				p.T238I		Atlas-SNP	.											.	ZDHHC23	38	.	0			c.C713T						PASS	.	C	ILE/THR	2,4404	4.2+/-10.8	0,2,2201	81	79	80		713	-1.8	0	3	dbSNP_134	80	0,8600		0,0,4300	no	missense	ZDHHC23	NM_173570.3	89	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign	238/410	113673098	2,13004	2203	4300	6503	SO:0001583	missense	254887	exon3			GCACAACAAAGGA	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.713C>T	3.37:g.113673098C>T	ENSP00000330485:p.Thr238Ile	151	0	0		168	84	0.5	NM_173570	D3DN76	Missense_Mutation	SNP	ENST00000330212.3	37	CCDS33827.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	0.022	-1.410585	0.01145	4.54E-4	0.0	ENSG00000184307	ENST00000330212;ENST00000498275	T;T	0.24723	1.84;1.84	5.11	-1.77	0.07982	.	1.393810	0.04616	N	0.401098	T	0.09555	0.0235	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25363	-1.0134	10	0.20519	T	0.43	-12.359	5.4023	0.16303	0.0:0.3117:0.1628:0.5255	.	238	Q8IYP9	ZDH23_HUMAN	I	238;232	ENSP00000330485:T238I;ENSP00000417840:T232I	ENSP00000330485:T238I	T	+	2	0	ZDHHC23	115155788	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-0.478000	0.06575	-0.376000	0.07943	-0.459000	0.05422	ACA	C|1.000;T|0.000	0.000	strong		0.597	ZDHHC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354702.1	NM_173570		T	113673098	C	T	113673098	3	4	22	1	0	0	0	0	1	0	0	0	17629	478	17	2	719	2	ZDHHC23	3	113673098	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	293378	113673098	84349332	876	3777											
KIAA1407	57577	hgsc.bcm.edu	37	chr3	113699599	113699599	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tctttggctattgcttccagCtgctggttcctcttaattct	4	19	7	11	0	3	0	0	0	3	0	5	0	5	0	2	2	3	5	2	2	2	7	rs35546981	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:113699599C>G	ENST00000295878.3	-	14	2351	c.2205G>C	c.(2203-2205)caG>caC	p.Q735H	KIAA1407_ENST00000545063.1_3'UTR	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	735										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						TTGCTTCCAGCTGCTGGTTCC	0.363													C|||	5	0.000998403	0.003	0.0014	5008	,	,		18688	0.0		0.0	False		,,,				2504	0.0				p.Q735H		Atlas-SNP	.											.	KIAA1407	80	.	0			c.G2205C						PASS	.	C	HIS/GLN	32,4374	37.6+/-69.7	0,32,2171	170	161	164		2205	3.8	1	3	dbSNP_126	164	0,8600		0,0,4300	yes	missense	KIAA1407	NM_020817.1	24	0,32,6471	GG,GC,CC		0.0,0.7263,0.246	probably-damaging	735/937	113699599	32,12974	2203	4300	6503	SO:0001583	missense	57577	exon14			TTCCAGCTGCTGG	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.2205G>C	3.37:g.113699599C>G	ENSP00000295878:p.Gln735His	223	1	0.00448431		266	121	0.454887	NM_020817	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	37	CCDS2977.1	3	0.0013736263736263737	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	C	17.30	3.354777	0.61293	0.007263	0.0	ENSG00000163617	ENST00000295878	T	0.33216	1.42	5.57	3.75	0.43078	.	0.298923	0.36932	N	0.002326	T	0.24160	0.0585	L	0.59436	1.845	0.80722	D	1	B	0.21071	0.051	B	0.21917	0.037	T	0.07693	-1.0759	10	0.56958	D	0.05	.	12.7141	0.57105	0.2994:0.7006:0.0:0.0	rs35546981	735	Q8NCU4	K1407_HUMAN	H	735	ENSP00000295878:Q735H	ENSP00000295878:Q735H	Q	-	3	2	KIAA1407	115182289	0.988000	0.35896	1.000000	0.80357	0.940000	0.58332	0.569000	0.23638	0.797000	0.33971	0.591000	0.81541	CAG	C|0.997;G|0.003	0.003	strong		0.363	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817		G	113699599	C	G	113699599	3	3	22	1	0	0	0	0	1	0	0	0	8238	796	28	4	621	4	KIAA1407	3	113699599	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	26501	113699599	84322831	877	3778											
ZNF80	7634	hgsc.bcm.edu	37	chr3	113955726	113955726	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agtgtgaatctgctgatgtcGaacaaggaggctgtttttgt	9	14	13	5	1	1	2	0	2	1	0	2	4	1	3	0	2	2	3	0	2	3	2	rs79892855	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:113955726G>A	ENST00000482457.2	-	1	699	c.196C>T	c.(196-198)Cga>Tga	p.R66*	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	66					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)				TGCTGATGTCGAACAAGGAGG	0.483													G|||	74	0.0147764	0.053	0.0043	5008	,	,		24200	0.0		0.0	False		,,,				2504	0.001				p.R66X	GBM(23;986 1114 21716)	Atlas-SNP	.											.	ZNF80	75	.	0			c.C196T						PASS	.	G	stop/ARG	188,4218	120.4+/-158.0	5,178,2020	105	90	95		196	-1.3	0	3	dbSNP_131	95	0,8600		0,0,4300	yes	stop-gained	ZNF80	NM_007136.3		5,178,6320	AA,AG,GG		0.0,4.2669,1.4455		66/274	113955726	188,12818	2203	4300	6503	SO:0001587	stop_gained	7634	exon1			GATGTCGAACAAG	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.196C>T	3.37:g.113955726G>A	ENSP00000417192:p.Arg66*	88	0	0		89	40	0.449438	NM_007136	Q6NSW4|Q6NT14	Nonsense_Mutation	SNP	ENST00000482457.2	37	CCDS2979.1	28	0.01282051282051282	26	0.052845528455284556	2	0.0055248618784530384	0	0.0	0	0.0	G	33	5.211008	0.95069	0.042669	0.0	ENSG00000174255	ENST00000482457	.	.	.	3.01	-1.33	0.09172	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	.	0.2983	0.00269	0.2292:0.1648:0.2619:0.3441	.	.	.	.	X	66	.	ENSP00000309812:R66X	R	-	1	2	ZNF80	115438416	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.585000	0.00423	-0.318000	0.08665	-0.136000	0.14681	CGA	G|0.987;A|0.013	0.013	strong		0.483	ZNF80-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354696.2	NM_007136		A	113955726	G	A	113955726	4	1	22	1	0	0	0	0	0	1	0	0	18183	1066	37	1	629	1	ZNF80	3	113955726	Nonsense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	256127	113955726	84066704	878	3779											
ZNF80	7634	hgsc.bcm.edu	37	chr3	113955890	113955890	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cctgtgagtgcagaccatcaCctgtccccaacccatcgcgt	8	8	8	17	2	1	2	1	1	0	1	3	2	2	2	6	0	2	1	6	0	1	0	rs112412956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:113955890C>T	ENST00000482457.2	-	1	535	c.32G>A	c.(31-33)gGt>gAt	p.G11D	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	11					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)				CAGACCATCACCTGTCCCCAA	0.522													c|||	73	0.0145767	0.053	0.0043	5008	,	,		21555	0.0		0.0	False		,,,				2504	0.0				p.G11D	GBM(23;986 1114 21716)	Atlas-SNP	.											.	ZNF80	75	.	0			c.G32A						PASS	.	T	ASP/GLY	188,4218	120.8+/-158.4	5,178,2020	111	111	111		32	-0.9	0	3	dbSNP_132	111	0,8600		0,0,4300	yes	missense	ZNF80	NM_007136.3	94	5,178,6320	TT,TC,CC		0.0,4.2669,1.4455	benign	11/274	113955890	188,12818	2203	4300	6503	SO:0001583	missense	7634	exon1			CCATCACCTGTCC	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.32G>A	3.37:g.113955890C>T	ENSP00000417192:p.Gly11Asp	131	0	0		153	78	0.509804	NM_007136	Q6NSW4|Q6NT14	Missense_Mutation	SNP	ENST00000482457.2	37	CCDS2979.1	28	0.01282051282051282	26	0.052845528455284556	2	0.0055248618784530384	0	0.0	0	0.0	c	0.052	-1.246531	0.01481	0.042669	0.0	ENSG00000174255	ENST00000482457	T	0.20463	2.07	2.88	-0.868	0.10652	.	.	.	.	.	T	0.01254	0.0041	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29119	-1.0022	9	0.87932	D	0	.	3.3265	0.07068	0.1783:0.2377:0.0:0.5841	.	11	P51504	ZNF80_HUMAN	D	11	ENSP00000417192:G11D	ENSP00000309812:G11D	G	-	2	0	ZNF80	115438580	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.250000	0.02885	-0.172000	0.10779	-2.079000	0.00380	GGT	C|0.987;T|0.013	0.013	strong		0.522	ZNF80-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354696.2	NM_007136		T	113955890	C	T	113955890	3	4	22	1	0	0	0	0	1	0	0	0	18183	507	18	2	793	2	ZNF80	3	113955890	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	164	113955890	84066540	879	3780											
C3orf30	152405	hgsc.bcm.edu	37	chr3	118865615	118865615	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gagagaagagcttccgagcaGatggaccgcagaatgtctgg	12	6	15	8	2	1	4	0	0	1	4	2	8	2	5	2	2	2	3	2	2	2	1	rs9859242	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:118865615G>C	ENST00000295622.1	+	1	619	c.579G>C	c.(577-579)caG>caC	p.Q193H	IGSF11_ENST00000441144.2_5'Flank|IGSF11_ENST00000354673.2_5'Flank|IGSF11_ENST00000425327.2_5'Flank|RP11-484M3.5_ENST00000490594.1_5'Flank	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	193			Q -> H (in dbSNP:rs9859242).							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)		CTTCCGAGCAGATGGACCGCA	0.512													G|||	113	0.0225639	0.084	0.0029	5008	,	,		22926	0.0		0.0	False		,,,				2504	0.0				p.Q193H		Atlas-SNP	.											.	C3orf30	64	.	0			c.G579C						PASS	.	G	HIS/GLN	361,4045	184.3+/-211.7	17,327,1859	97	100	99		579	2.2	0	3	dbSNP_119	99	2,8598	2.2+/-6.3	0,2,4298	yes	missense	C3orf30	NM_152539.2	24	17,329,6157	CC,CG,GG		0.0233,8.1934,2.791	possibly-damaging	193/537	118865615	363,12643	2203	4300	6503	SO:0001583	missense	152405	exon1			CGAGCAGATGGAC	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.579G>C	3.37:g.118865615G>C	ENSP00000295622:p.Gln193His	78	0	0		112	48	0.428571	NM_152539	A1L4B7	Missense_Mutation	SNP	ENST00000295622.1	37	CCDS2984.1	29|29	0.013278388278388278|0.013278388278388278	28|28	0.056910569105691054|0.056910569105691054	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	G|G	13.18|13.18	2.160413|2.160413	0.38119|0.38119	0.081934|0.081934	2.33E-4|2.33E-4	ENSG00000163424|ENSG00000163424	ENST00000460150|ENST00000295622;ENST00000470341	.|T	.|0.26223	.|1.75	4.09|4.09	2.24|2.24	0.28232|0.28232	.|.	.|1.043520	.|0.07559	.|N	.|0.916758	T|T	0.02767|0.02767	0.0083|0.0083	L|L	0.52573|0.52573	1.65|1.65	0.09310|0.09310	N|N	1|1	.|D;D	.|0.89917	.|1.0;0.999	.|D;D	.|0.74023	.|0.982;0.971	T|T	0.04128|0.04128	-1.0975|-1.0975	5|10	.|0.41790	.|T	.|0.15	0.0286|0.0286	6.1512|6.1512	0.20313|0.20313	0.1027:0.3712:0.5262:0.0|0.1027:0.3712:0.5262:0.0	rs9859242;rs9859242|rs9859242;rs9859242	.|193;193	.|E9PFE5;Q96M34	.|.;CC030_HUMAN	H|H	157|193	.|ENSP00000295622:Q193H	.|ENSP00000295622:Q193H	D|Q	+|+	1|3	0|2	C3orf30|C3orf30	120348305|120348305	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.003000|0.003000	0.03518|0.03518	-0.341000|-0.341000	0.07811|0.07811	0.661000|0.661000	0.30985|0.30985	0.514000|0.514000	0.50259|0.50259	GAT|CAG	G|0.977;C|0.023	0.023	strong		0.512	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539		C	118865615	G	C	118865615	3	2	22	1	0	0	0	0	1	0	0	0	2222	933	33	4	581	4	C3orf30	3	118865615	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4909725	118865615	79156815	880	3781											
PLA1A	51365	hgsc.bcm.edu	37	chr3	119336962	119336962	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gatggcctttccctgtgccaGctacaaggccttccttgctg	5	12	10	14	0	0	0	0	0	0	0	2	1	2	0	5	2	4	2	5	2	2	4	rs2692622	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119336962G>A	ENST00000273371.4	+	7	923	c.851G>A	c.(850-852)aGc>aAc	p.S284N	PLA1A_ENST00000494440.1_Missense_Mutation_p.S268N|PLA1A_ENST00000495992.1_Missense_Mutation_p.S268N|PLA1A_ENST00000488919.1_Missense_Mutation_p.S111N	NM_015900.3	NP_056984.1	Q53H76	PLA1A_HUMAN	phospholipase A1 member A	284			S -> N (in dbSNP:rs2692622).		lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|phosphatidylserine metabolic process (GO:0006658)	extracellular vesicular exosome (GO:0070062)	phosphatidylcholine 1-acylhydrolase activity (GO:0008970)			NS(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CCCTGTGCCAGCTACAAGGCC	0.502													G|||	238	0.047524	0.1725	0.0144	5008	,	,		20613	0.0		0.0	False		,,,				2504	0.0				p.S284N		Atlas-SNP	.											.	PLA1A	65	.	0			c.G851A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER	611,3795	267.1+/-267.6	36,539,1628	323	307	313		803,332,851	0.3	0.7	3	dbSNP_100	313	6,8594	4.3+/-15.6	0,6,4294	yes	missense,missense,missense	PLA1A	NM_001206960.1,NM_001206961.1,NM_015900.3	46,46,46	36,545,5922	AA,AG,GG		0.0698,13.8675,4.744	benign,benign,benign	268/441,111/284,284/457	119336962	617,12389	2203	4300	6503	SO:0001583	missense	51365	exon7			GTGCCAGCTACAA	AF035268	CCDS2991.1, CCDS56268.1, CCDS56269.1	3q13.13-q13.2	2002-11-28			ENSG00000144837	ENSG00000144837			17661	protein-coding gene	gene with protein product		607460				10196188	Standard	NM_015900		Approved	ps-PLA1	uc003ecu.3	Q53H76	OTTHUMG00000159425	ENST00000273371.4:c.851G>A	3.37:g.119336962G>A	ENSP00000273371:p.Ser284Asn	177	0	0		239	132	0.552301	NM_015900	B2R8V2|B4DXA2|O95991|Q86WX6|Q9UPD2	Missense_Mutation	SNP	ENST00000273371.4	37	CCDS2991.1	71	0.03250915750915751	68	0.13821138211382114	3	0.008287292817679558	0	0.0	0	0.0	G	11.49	1.653192	0.29425	0.138675	6.98E-4	ENSG00000144837	ENST00000273371;ENST00000488919;ENST00000495992;ENST00000494440;ENST00000475963	D;D;D;D;D	0.93247	-3.19;-3.19;-3.19;-3.19;-3.19	5.26	0.275	0.15659	Lipase, N-terminal (1);	0.427416	0.31268	N	0.007943	T	0.04679	0.0127	L	0.41492	1.28	0.46011	P	0.0011889999999999956	B;B	0.18013	0.005;0.025	B;B	0.20184	0.009;0.028	T	0.55611	-0.8114	9	0.56958	D	0.05	-5.9575	5.7584	0.18186	0.2197:0.2586:0.5217:0.0	rs2692622;rs52825291;rs2692622	268;284	Q53H76-3;Q53H76	.;PLA1A_HUMAN	N	284;111;268;268;150	ENSP00000273371:S284N;ENSP00000420625:S111N;ENSP00000417326:S268N;ENSP00000418793:S268N;ENSP00000417295:S150N	ENSP00000273371:S284N	S	+	2	0	PLA1A	120819652	0.995000	0.38212	0.688000	0.30117	0.454000	0.32378	0.833000	0.27504	-0.255000	0.09486	0.555000	0.69702	AGC	G|0.946;A|0.054	0.054	strong		0.502	PLA1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355252.2			A	119336962	G	A	119336962	3	1	22	1	0	0	0	0	1	0	0	0	11997	971	34	2	877	2	PLA1A	3	119336962	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	471347	119336962	78685468	881	3782											
PLA1A	51365	hgsc.bcm.edu	37	chr3	119347623	119347623	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagataaaccaagtgaaattCaagtttcagtcttccaaccg	15	10	6	10	1	3	2	2	1	1	1	4	2	4	2	3	0	2	1	3	0	6	4	rs115172544	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119347623C>A	ENST00000273371.4	+	10	1269	c.1197C>A	c.(1195-1197)ttC>ttA	p.F399L	PLA1A_ENST00000494440.1_Missense_Mutation_p.F383L|PLA1A_ENST00000495992.1_Missense_Mutation_p.F383L|PLA1A_ENST00000488919.1_Missense_Mutation_p.F226L	NM_015900.3	NP_056984.1	Q53H76	PLA1A_HUMAN	phospholipase A1 member A	399	Involved in the recognition of diacyl- phospholipids.				lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|phosphatidylserine metabolic process (GO:0006658)	extracellular vesicular exosome (GO:0070062)	phosphatidylcholine 1-acylhydrolase activity (GO:0008970)			NS(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						AAGTGAAATTCAAGTTTCAGT	0.468													C|||	78	0.0155751	0.0545	0.0086	5008	,	,		21512	0.0		0.0	False		,,,				2504	0.0				p.F399L		Atlas-SNP	.											.	PLA1A	65	.	0			c.C1197A						PASS	.	C	LEU/PHE,LEU/PHE,LEU/PHE	161,4245	108.2+/-146.6	4,153,2046	141	134	136		1149,678,1197	2.2	0.9	3	dbSNP_132	136	0,8600		0,0,4300	yes	missense,missense,missense	PLA1A	NM_001206960.1,NM_001206961.1,NM_015900.3	22,22,22	4,153,6346	AA,AC,CC		0.0,3.6541,1.2379	benign,benign,benign	383/441,226/284,399/457	119347623	161,12845	2203	4300	6503	SO:0001583	missense	51365	exon10			GAAATTCAAGTTT	AF035268	CCDS2991.1, CCDS56268.1, CCDS56269.1	3q13.13-q13.2	2002-11-28			ENSG00000144837	ENSG00000144837			17661	protein-coding gene	gene with protein product		607460				10196188	Standard	NM_015900		Approved	ps-PLA1	uc003ecu.3	Q53H76	OTTHUMG00000159425	ENST00000273371.4:c.1197C>A	3.37:g.119347623C>A	ENSP00000273371:p.Phe399Leu	156	0	0		141	65	0.460993	NM_015900	B2R8V2|B4DXA2|O95991|Q86WX6|Q9UPD2	Missense_Mutation	SNP	ENST00000273371.4	37	CCDS2991.1	26	0.011904761904761904	24	0.04878048780487805	2	0.0055248618784530384	0	0.0	0	0.0	C	0.008	-1.883913	0.00532	0.036541	0.0	ENSG00000144837	ENST00000273371;ENST00000488919;ENST00000495992;ENST00000494440	D;D;D;D	0.90004	-2.0;-2.6;-2.04;-2.12	5.29	2.23	0.28157	.	1.028510	0.07692	N	0.938840	T	0.34687	0.0906	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	0.45234	-0.9275	10	0.02654	T	1	-0.7164	9.9541	0.41655	0.1251:0.5238:0.3511:0.0	.	383;399	Q53H76-3;Q53H76	.;PLA1A_HUMAN	L	399;226;383;383	ENSP00000273371:F399L;ENSP00000420625:F226L;ENSP00000417326:F383L;ENSP00000418793:F383L	ENSP00000273371:F399L	F	+	3	2	PLA1A	120830313	0.945000	0.32115	0.862000	0.33874	0.035000	0.12851	0.606000	0.24194	0.590000	0.29694	-0.304000	0.09214	TTC	C|0.984;A|0.016	0.016	strong		0.468	PLA1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355252.2			A	119347623	C	A	119347623	3	1	22	1	0	0	0	0	1	0	0	0	11997	825	29	4	1235	4	PLA1A	3	119347623	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	10661	119347623	78674807	882	3783											
C3orf15	89876	hgsc.bcm.edu	37	chr3	119445092	119445092	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaagcgtgcttgggaagccTctctccccgctctgagtgac	7	9	12	13	2	2	3	0	2	2	1	4	4	3	4	3	1	3	2	3	1	2	1	rs9817771	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119445092T>A	ENST00000273390.5	+	7	834	c.757T>A	c.(757-759)Tct>Act	p.S253T		NM_033364.3	NP_203528	Q7Z4T9	MAAT1_HUMAN	MYCBP-associated, testis expressed 1	253			S -> T (in dbSNP:rs9817771).			mitochondrion (GO:0005739)											TTGGGAAGCCTCTCTCCCCGC	0.542													A|||	70	0.0139776	0.0514	0.0014	5008	,	,		19226	0.0		0.0	False		,,,				2504	0.001				p.S253T		Atlas-SNP	.											.	.	.	.	0			c.T757A						PASS	.	A	THR/SER	209,4197	807.3+/-415.9	3,203,1997	57	55	56		757	4.4	0.8	3	dbSNP_119	56	4,8596	819.2+/-406.8	1,2,4297	yes	missense	C3orf15	NM_033364.3	58	4,205,6294	AA,AT,TT		0.0465,4.7435,1.6377	benign	253/768	119445092	213,12793	2203	4300	6503	SO:0001583	missense	89876	exon7			GAAGCCTCTCTCC	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.757T>A	3.37:g.119445092T>A	ENSP00000273390:p.Ser253Thr	98	0	0		111	56	0.504505	NM_033364	A0AVK2|A8K1J9|B3KP23|B4DG52|B4DZ14|C9JUG4|Q68DX2|Q8TD41|Q96A45|Q96JE8	Missense_Mutation	SNP	ENST00000273390.5	37	CCDS2994.1	20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	A	1.705	-0.500484	0.04291	0.047435	4.65E-4	ENSG00000183833	ENST00000273390	T	0.23147	1.92	5.62	4.44	0.53790	.	0.293168	0.41938	N	0.000789	T	0.00815	0.0027	N	0.00630	-1.315	0.80722	D	1	B;B;B;B;B	0.06786	0.0;0.001;0.0;0.0;0.0	B;B;B;B;B	0.06405	0.002;0.001;0.001;0.0;0.0	T	0.26430	-1.0103	10	0.02654	T	1	-7.7599	5.0067	0.14291	0.6979:0.1217:0.0641:0.1163	rs9817771;rs52835037;rs9817771	253;14;191;253;253	Q7Z4T9;Q9UFB4;Q7Z4T9-3;Q4G0Y0;Q7Z4T9-7	AAT1_HUMAN;.;.;.;.	T	253	ENSP00000273390:S253T	ENSP00000273390:S253T	S	+	1	0	C3orf15	120927782	1.000000	0.71417	0.839000	0.33178	0.385000	0.30292	3.898000	0.56281	0.484000	0.27630	-0.265000	0.10407	TCT	T|0.984;A|0.016	0.016	strong		0.542	MAATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355222.1	NM_033364		A	119445092	T	A	119445092	3	1	22	1	0	0	0	0	1	0	0	0	2211	1551	54	5	783	5	C3orf15	3	119445092	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	97469	119445092	78577338	883	3784											
C3orf15	89876	hgsc.bcm.edu	37	chr3	119445139	119445139	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagtttgagaagaggaggaaAatgatgaatgaaatggagag	18	7	15	1	0	0	6	0	4	0	3	0	10	0	8	0	3	0	1	0	3	5	1	rs9835381	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119445139A>G	ENST00000273390.5	+	7	881	c.804A>G	c.(802-804)aaA>aaG	p.K268K		NM_033364.3	NP_203528	Q7Z4T9	MAAT1_HUMAN	MYCBP-associated, testis expressed 1	268						mitochondrion (GO:0005739)											AGAGGAGGAAAATGATGAATG	0.517													G|||	70	0.0139776	0.0514	0.0014	5008	,	,		19708	0.0		0.0	False		,,,				2504	0.001				p.K268K		Atlas-SNP	.											.	.	.	.	0			c.A804G						PASS	.	G		209,4197	807.1+/-415.9	3,203,1997	69	67	67		804	4.6	1	3	dbSNP_119	67	4,8596	819.0+/-406.8	1,2,4297	no	coding-synonymous	C3orf15	NM_033364.3		4,205,6294	GG,GA,AA		0.0465,4.7435,1.6377		268/768	119445139	213,12793	2203	4300	6503	SO:0001819	synonymous_variant	89876	exon7			GAGGAAAATGATG	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.804A>G	3.37:g.119445139A>G		153	0	0		131	62	0.473282	NM_033364	A0AVK2|A8K1J9|B3KP23|B4DG52|B4DZ14|C9JUG4|Q68DX2|Q8TD41|Q96A45|Q96JE8	Silent	SNP	ENST00000273390.5	37	CCDS2994.1																																																																																			A|0.983;G|0.017	0.017	strong		0.517	MAATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355222.1	NM_033364		G	119445139	A	G	119445139	2	3	22	1	0	0	0	0	0	0	0	1	2211	11	1	3		3	C3orf15	3	119445139	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	47	119445139	78577291	884	3785											
C3orf15	89876	hgsc.bcm.edu	37	chr3	119449159	119449159	+	Missense_Mutation	SNP	G	G	A																															tatgaagcacttgaatgcccGgtggtctaaactgcaggagg																								rs61742290	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119449159G>A	ENST00000273390.5	+	8	1030	c.953G>A	c.(952-954)cGg>cAg	p.R318Q		NM_033364.3	NP_203528	Q7Z4T9	MAAT1_HUMAN	MYCBP-associated, testis expressed 1	318						mitochondrion (GO:0005739)											TTGAATGCCCGGTGGTCTAAA	0.438													G|||	23	0.00459265	0.0151	0.0043	5008	,	,		19286	0.0		0.0	False		,,,				2504	0.0				p.R318Q		Atlas-SNP	.											C3orf15,NS,carcinoma,+1,2	.	.	2	0			c.G953A						PASS	.	G	GLN/ARG	62,4344	58.7+/-95.3	0,62,2141	193	196	195		953	1.5	1	3	dbSNP_129	195	0,8600		0,0,4300	yes	missense	C3orf15	NM_033364.3	43	0,62,6441	AA,AG,GG		0.0,1.4072,0.4767	benign	318/768	119449159	62,12944	2203	4300	6503	SO:0001583	missense	89876	exon8			ATGCCCGGTGGTC	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.953G>A	3.37:g.119449159G>A	ENSP00000273390:p.Arg318Gln	108	0	0		131	69	0.526718	NM_033364	A0AVK2|A8K1J9|B3KP23|B4DG52|B4DZ14|C9JUG4|Q68DX2|Q8TD41|Q96A45|Q96JE8	Missense_Mutation	SNP	ENST00000273390.5	37	CCDS2994.1	8	0.003663003663003663	6	0.012195121951219513	2	0.0055248618784530384	0	0.0	0	0.0	G	6.250	0.414169	0.11870	0.014072	0.0	ENSG00000183833	ENST00000273390	T	0.21734	1.99	5.2	1.55	0.23275	.	0.711873	0.14769	N	0.299528	T	0.05410	0.0143	N	0.04636	-0.2	0.80722	D	1	B;B;B;B;B	0.19935	0.008;0.04;0.012;0.019;0.005	B;B;B;B;B	0.12156	0.004;0.003;0.007;0.005;0.003	T	0.27297	-1.0078	10	0.12430	T	0.62	-20.1193	8.0697	0.30682	0.6841:0.0:0.3159:0.0	rs61742290	318;79;256;318;318	Q7Z4T9;Q9UFB4;Q7Z4T9-3;Q4G0Y0;Q7Z4T9-7	AAT1_HUMAN;.;.;.;.	Q	318	ENSP00000273390:R318Q	ENSP00000273390:R318Q	R	+	2	0	C3orf15	120931849	0.005000	0.15991	0.967000	0.41034	0.762000	0.43233	0.707000	0.25704	0.382000	0.24878	-0.484000	0.04775	CGG	G|0.995;A|0.005	0.005	strong		0.438	MAATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355222.1	NM_033364		A	119449159	G	A	119449159	3	1	22	1	0	0	0	0	1	0	0	0	2211	1116	39	1	983	1	C3orf15	3	119449159	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4020	119449159	78573271	885	3786	53	2									
C3orf15	89876	hgsc.bcm.edu	37	chr3	119449165	119449165	+	Missense_Mutation	SNP	C	C	G																															gcacttgaatgcccggtggtCtaaactgcaggagggaaaag																								rs9819218	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119449165C>G	ENST00000273390.5	+	8	1036	c.959C>G	c.(958-960)tCt>tGt	p.S320C		NM_033364.3	NP_203528	Q7Z4T9	MAAT1_HUMAN	MYCBP-associated, testis expressed 1	320			S -> C (in dbSNP:rs9819218).			mitochondrion (GO:0005739)											GCCCGGTGGTCTAAACTGCAG	0.443													C|||	68	0.0135783	0.0507	0.0014	5008	,	,		19022	0.0		0.0	False		,,,				2504	0.0				p.S320C		Atlas-SNP	.											.	.	.	.	0			c.C959G						PASS	.	C	CYS/SER	201,4205	126.1+/-163.2	3,195,2005	197	200	199		959	0	0.7	3	dbSNP_119	199	4,8596	1.2+/-3.3	1,2,4297	yes	missense	C3orf15	NM_033364.3	112	4,197,6302	GG,GC,CC		0.0465,4.562,1.5762	benign	320/768	119449165	205,12801	2203	4300	6503	SO:0001583	missense	89876	exon8			GGTGGTCTAAACT	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.959C>G	3.37:g.119449165C>G	ENSP00000273390:p.Ser320Cys	108	0	0		127	63	0.496063	NM_033364	A0AVK2|A8K1J9|B3KP23|B4DG52|B4DZ14|C9JUG4|Q68DX2|Q8TD41|Q96A45|Q96JE8	Missense_Mutation	SNP	ENST00000273390.5	37	CCDS2994.1	20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	C	10.39	1.336987	0.24253	0.04562	4.65E-4	ENSG00000183833	ENST00000273390	T	0.24723	1.84	5.2	0.0316	0.14171	.	0.702681	0.14937	N	0.289762	T	0.02649	0.0080	L	0.43152	1.355	0.09310	N	1	B;B;B;B;B	0.20887	0.049;0.016;0.02;0.006;0.005	B;B;B;B;B	0.28232	0.087;0.032;0.036;0.009;0.004	T	0.21552	-1.0242	10	0.45353	T	0.12	-11.3776	1.5557	0.02584	0.26:0.3334:0.2513:0.1553	rs9819218;rs56635541;rs9819218	320;81;258;320;320	Q7Z4T9;Q9UFB4;Q7Z4T9-3;Q4G0Y0;Q7Z4T9-7	AAT1_HUMAN;.;.;.;.	C	320	ENSP00000273390:S320C	ENSP00000273390:S320C	S	+	2	0	C3orf15	120931855	0.002000	0.14202	0.668000	0.29813	0.882000	0.50991	0.021000	0.13489	0.001000	0.14605	-0.259000	0.10710	TCT	C|0.982;G|0.018	0.018	strong		0.443	MAATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355222.1	NM_033364		G	119449165	C	G	119449165	3	3	22	1	0	0	0	0	1	0	0	0	2211	913	32	4	989	4	C3orf15	3	119449165	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6	119449165	78573265	886	3787	53	2									
C3orf15	89876	hgsc.bcm.edu	37	chr3	119466025	119466025	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acataatactgaataccgaaGcgaatactgcagaagaacaa	20	6	7	8	2	0	3	0	1	0	2	0	5	0	3	1	0	6	1	1	0	10	4	rs9853426	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119466025G>A	ENST00000273390.5	+	15	2043	c.1966G>A	c.(1966-1968)Gcg>Acg	p.A656T	RP11-169N13.4_ENST00000489428.2_RNA	NM_033364.3	NP_203528	Q7Z4T9	MAAT1_HUMAN	MYCBP-associated, testis expressed 1	492						mitochondrion (GO:0005739)											GAATACCGAAGCGAATACTGC	0.388													G|||	71	0.0141773	0.0522	0.0014	5008	,	,		20049	0.0		0.0	False		,,,				2504	0.001				p.A656T		Atlas-SNP	.											.	.	.	.	0			c.G1966A						PASS	.	G	THR/ALA	210,4196	129.8+/-166.5	3,204,1996	112	105	107		1966	5.5	1	3	dbSNP_119	107	4,8596	1.2+/-3.3	1,2,4297	yes	missense	C3orf15	NM_033364.3	58	4,206,6293	AA,AG,GG		0.0465,4.7662,1.6454	benign	656/768	119466025	214,12792	2203	4300	6503	SO:0001583	missense	89876	exon15			ACCGAAGCGAATA	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.1966G>A	3.37:g.119466025G>A	ENSP00000273390:p.Ala656Thr	134	0	0		146	75	0.513699	NM_033364	A0AVK2|A8K1J9|B3KP23|B4DG52|B4DZ14|C9JUG4|Q68DX2|Q8TD41|Q96A45|Q96JE8	Missense_Mutation	SNP	ENST00000273390.5	37	CCDS2994.1	20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	G	14.23	2.472805	0.43942	0.047662	4.65E-4	ENSG00000183833	ENST00000273390	T	0.22743	1.94	5.47	5.47	0.80525	.	0.170071	0.51477	D	0.000100	T	0.03136	0.0092	L	0.29908	0.895	0.80722	D	1	B;B;B	0.23990	0.095;0.055;0.095	B;B;B	0.26416	0.051;0.048;0.069	T	0.02519	-1.1147	10	0.42905	T	0.14	-11.3258	19.3267	0.94265	0.0:0.0:1.0:0.0	rs9853426;rs52829415;rs9853426	492;594;656	Q7Z4T9;Q7Z4T9-3;Q7Z4T9-7	AAT1_HUMAN;.;.	T	656	ENSP00000273390:A656T	ENSP00000273390:A656T	A	+	1	0	C3orf15	120948715	1.000000	0.71417	0.999000	0.59377	0.271000	0.26615	7.014000	0.76380	2.565000	0.86533	0.591000	0.81541	GCG	G|0.983;A|0.017	0.017	strong		0.388	MAATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355222.1	NM_033364		A	119466025	G	A	119466025	3	1	22	1	0	0	0	0	1	0	0	0	2211	971	34	2	2024	2	C3orf15	3	119466025	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	16860	119466025	78556405	887	3788											
NR1I2	8856	hgsc.bcm.edu	37	chr3	119530546	119530546	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagatgaaaacctttgacacTaccttctcccatttcaagaa	14	11	4	12	0	2	4	1	2	1	2	3	4	2	4	3	0	2	0	3	0	5	4	rs12721611	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119530546T>C	ENST00000337940.4	+	4	657	c.609T>C	c.(607-609)acT>acC	p.T203T	NR1I2_ENST00000466380.1_Silent_p.T164T|NR1I2_ENST00000393716.2_Silent_p.T164T	NM_022002.2	NP_071285.1	O75469	NR1I2_HUMAN	nuclear receptor subfamily 1, group I, member 2	164	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)	CCTTTGACACTACCTTCTCCC	0.527													T|||	76	0.0151757	0.0545	0.0058	5008	,	,		20683	0.0		0.0	False		,,,				2504	0.0				p.T203T		Atlas-SNP	.											.	NR1I2	44	.	0			c.T609C						PASS	.	T	,,	232,4174	136.5+/-172.5	3,226,1974	110	97	101		492,609,492	3	1	3	dbSNP_126	101	6,8594	2.2+/-6.3	1,4,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	NR1I2	NM_003889.3,NM_022002.2,NM_033013.2	,,	4,230,6269	CC,CT,TT		0.0698,5.2655,1.8299	,,	164/435,203/474,164/398	119530546	238,12768	2203	4300	6503	SO:0001819	synonymous_variant	8856	exon4			TGACACTACCTTC	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	ENST00000337940.4:c.609T>C	3.37:g.119530546T>C		83	0	0		89	48	0.539326	NM_022002	Q006P5|Q008C8|Q96AC7|Q9UJ22|Q9UJ23|Q9UJ24|Q9UJ25|Q9UJ26|Q9UJ27|Q9UNW4	Silent	SNP	ENST00000337940.4	37	CCDS2995.1																																																																																			T|0.981;C|0.019	0.019	strong		0.527	NR1I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355126.1			C	119530546	T	C	119530546	2	2	22	1	0	0	0	0	0	0	0	1	10629	1509	53	3		3	NR1I2	3	119530546	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	64521	119530546	78491884	888	3789											
POLQ	10721	hgsc.bcm.edu	37	chr3	121207083	121207083	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtccaaagcttcaaccatCtgaacagaatccatttctga	13	12	5	11	0	3	3	1	2	2	1	5	3	5	3	3	0	3	1	3	0	4	3	rs3218639	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:121207083C>A	ENST00000264233.5	-	16	4823	c.4695G>T	c.(4693-4695)caG>caT	p.Q1565H		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1565					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)		CTTCAACCATCTGAACAGAAT	0.338								DNA polymerases (catalytic subunits)					C|||	23	0.00459265	0.0159	0.0029	5008	,	,		20878	0.0		0.0	False		,,,				2504	0.0				p.Q1565H	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.G4695T						PASS	.	C	HIS/GLN	75,4331	65.8+/-103.3	1,73,2129	73	72	73		4695	5.3	1	3	dbSNP_106	73	0,8600		0,0,4300	yes	missense	POLQ	NM_199420.3	24	1,73,6429	AA,AC,CC		0.0,1.7022,0.5767	probably-damaging	1565/2591	121207083	75,12931	2203	4300	6503	SO:0001583	missense	10721	exon16			AACCATCTGAACA	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.4695G>T	3.37:g.121207083C>A	ENSP00000264233:p.Gln1565His	78	0	0		57	24	0.421053	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	14.28	2.488609	0.44249	0.017022	0.0	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.57436	0.4	6.17	5.3	0.74995	.	0.354292	0.29205	N	0.012838	T	0.41880	0.1178	L	0.36672	1.1	0.26824	N	0.968735	D;P	0.71674	0.998;0.865	D;B	0.66084	0.941;0.391	T	0.46190	-0.9209	10	0.48119	T	0.1	.	8.7602	0.34669	0.0:0.6832:0.1822:0.1345	rs3218639;rs52804917;rs3218639	1565;737	O75417;O75417-2	DPOLQ_HUMAN;.	H	1188;1565;1701	ENSP00000264233:Q1565H	ENSP00000264233:Q1565H	Q	-	3	2	POLQ	122689773	1.000000	0.71417	1.000000	0.80357	0.578000	0.36192	1.322000	0.33689	1.632000	0.50472	-0.140000	0.14226	CAG	C|0.993;A|0.007	0.007	strong		0.338	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		A	121207083	C	A	121207083	3	1	22	1	0	0	0	0	1	0	0	0	12217	912	32	4	3137	4	POLQ	3	121207083	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1676537	121207083	76815347	889	3790											
POLQ	10721	hgsc.bcm.edu	37	chr3	121251924	121251924	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acttttactgactccaaaagCggtacagggcgaaagtcggt	12	9	11	9	3	0	1	0	1	0	0	2	2	1	1	1	3	3	1	1	3	5	3	rs41390550	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:121251924C>T	ENST00000264233.5	-	6	1001	c.873G>A	c.(871-873)ccG>ccA	p.P291P	POLQ_ENST00000488282.1_5'UTR	NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	291					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)		ACTCCAAAAGCGGTACAGGGC	0.428								DNA polymerases (catalytic subunits)					C|||	107	0.0213658	0.0749	0.0115	5008	,	,		17115	0.0		0.0	False		,,,				2504	0.0				p.P291P	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.G873A						PASS	.	C		267,4139	152.5+/-186.2	7,253,1943	94	93	93		873	0.1	1	3	dbSNP_127	93	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	POLQ	NM_199420.3		7,257,6239	TT,TC,CC		0.0465,6.0599,2.0837		291/2591	121251924	271,12735	2203	4300	6503	SO:0001819	synonymous_variant	10721	exon6			CAAAAGCGGTACA	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.873G>A	3.37:g.121251924C>T		317	0	0		260	117	0.45	NM_199420	O95160|Q6VMB5	Silent	SNP	ENST00000264233.5	37	CCDS33833.1																																																																																			C|0.982;T|0.018	0.018	strong		0.428	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		T	121251924	C	T	121251924	2	4	22	1	0	0	0	0	0	0	0	1	12217	755	27	1		1	POLQ	3	121251924	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	44841	121251924	76770506	890	3791											
ILDR1	286676	hgsc.bcm.edu	37	chr3	121712098	121712098	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcgggccagtgtggggagtGcgagccgcggcggtgggccc	3	5	21	12	5	0	0	0	0	0	0	1	2	0	1	3	6	2	0	3	6	0	0	rs34284625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:121712098G>A	ENST00000344209.5	-	7	1624	c.1498C>T	c.(1498-1500)Cac>Tac	p.H500Y	ILDR1_ENST00000273691.3_Missense_Mutation_p.H456Y|ILDR1_ENST00000460554.1_5'UTR|ILDR1_ENST00000393631.1_Missense_Mutation_p.H411Y|ILDR1_ENST00000462014.1_Missense_Mutation_p.H468Y	NM_001199799.1	NP_001186728.1	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor 1	500					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)		TGTGGGGAGTGCGAGCCGCGG	0.632													G|||	201	0.0401358	0.1445	0.0144	5008	,	,		15335	0.0		0.0	False		,,,				2504	0.0				p.H500Y		Atlas-SNP	.											.	ILDR1	120	.	0			c.C1498T						PASS	.	G	TYR/HIS,TYR/HIS,TYR/HIS	520,3882		26,468,1707	23	24	24		1498,1231,1366	4	0	3	dbSNP_126	24	8,8590		0,8,4291	yes	missense,missense,missense	ILDR1	NM_001199799.1,NM_001199800.1,NM_175924.3	83,83,83	26,476,5998	AA,AG,GG		0.093,11.8128,4.0615	benign,benign,benign	500/547,411/458,456/503	121712098	528,12472	2201	4299	6500	SO:0001583	missense	286676	exon7			GGGAGTGCGAGCC	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.1498C>T	3.37:g.121712098G>A	ENSP00000345667:p.His500Tyr	152	0	0		173	81	0.468208	NM_001199799	Q6ZP61|Q7Z578	Missense_Mutation	SNP	ENST00000344209.5	37	CCDS56271.1	78	0.03571428571428571	74	0.15040650406504066	4	0.011049723756906077	0	0.0	0	0.0	G	11.04	1.522102	0.27211	0.118128	9.3E-4	ENSG00000145103	ENST00000273691;ENST00000344209;ENST00000393631;ENST00000462014	T;T;T;T	0.76709	-0.44;-0.44;-1.04;-0.04	5.76	3.99	0.46301	.	1.592350	0.03082	N	0.158662	T	0.00784	0.0026	N	0.22421	0.69	0.80722	P	0.0	B;B;B;B	0.32620	0.378;0.165;0.378;0.378	B;B;B;B	0.28849	0.095;0.044;0.095;0.095	T	0.22661	-1.0210	9	0.56958	D	0.05	-1.8466	11.555	0.50741	0.1185:0.0:0.8815:0.0	rs34284625	411;500;456;468	Q86SU0-5;Q86SU0;Q86SU0-2;Q86SU0-6	.;ILDR1_HUMAN;.;.	Y	456;500;411;468	ENSP00000273691:H456Y;ENSP00000345667:H500Y;ENSP00000377251:H411Y;ENSP00000419414:H468Y	ENSP00000273691:H456Y	H	-	1	0	ILDR1	123194788	0.109000	0.22037	0.001000	0.08648	0.252000	0.25951	2.180000	0.42537	0.802000	0.34089	0.563000	0.77884	CAC	G|0.956;A|0.044	0.044	strong		0.632	ILDR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355666.1	NM_175924		A	121712098	G	A	121712098	3	1	22	1	0	0	0	0	1	0	0	0	7718	1319	46	2	150	2	ILDR1	3	121712098	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	460174	121712098	76310332	891	3792											
ILDR1	286676	hgsc.bcm.edu	37	chr3	121712271	121712271	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgcggggcctctcctgacagCggctcctgaaaggagggtgg	6	7	17	11	2	1	2	0	2	1	0	3	3	2	3	3	6	2	1	3	6	1	0	rs34883204	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:121712271C>T	ENST00000344209.5	-	7	1451	c.1325G>A	c.(1324-1326)cGc>cAc	p.R442H	ILDR1_ENST00000273691.3_Missense_Mutation_p.R398H|ILDR1_ENST00000460554.1_5'UTR|ILDR1_ENST00000393631.1_Missense_Mutation_p.R353H|ILDR1_ENST00000462014.1_Missense_Mutation_p.R410H	NM_001199799.1	NP_001186728.1	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor 1	442	Arg-rich.				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)		CTCCTGACAGCGGCTCCTGAA	0.672													C|||	202	0.0403355	0.1452	0.0144	5008	,	,		16784	0.0		0.0	False		,,,				2504	0.0				p.R442H		Atlas-SNP	.											ILDR1_ENST00000344209,colon,carcinoma,-1,2	ILDR1	120	2	0			c.G1325A						scavenged	.	C	HIS/ARG,HIS/ARG,HIS/ARG	528,3878		24,480,1699	22	24	23		1325,1058,1193	-0.6	0.2	3	dbSNP_126	23	8,8592		0,8,4292	yes	missense,missense,missense	ILDR1	NM_001199799.1,NM_001199800.1,NM_175924.3	29,29,29	24,488,5991	TT,TC,CC		0.093,11.9837,4.1212	probably-damaging,probably-damaging,probably-damaging	442/547,353/458,398/503	121712271	536,12470	2203	4300	6503	SO:0001583	missense	286676	exon7			TGACAGCGGCTCC	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.1325G>A	3.37:g.121712271C>T	ENSP00000345667:p.Arg442His	85	1	0.0117647		102	56	0.54902	NM_001199799	Q6ZP61|Q7Z578	Missense_Mutation	SNP	ENST00000344209.5	37	CCDS56271.1	78	0.03571428571428571	74	0.15040650406504066	4	0.011049723756906077	0	0.0	0	0.0	C	7.187	0.590696	0.13812	0.119837	9.3E-4	ENSG00000145103	ENST00000273691;ENST00000344209;ENST00000393631;ENST00000462014	T;T;D;T	0.82984	-1.18;-0.64;-1.67;-0.71	4.69	-0.554	0.11811	.	0.768774	0.12399	N	0.472300	T	0.01287	0.0042	M	0.61703	1.905	0.38075	P	0.06350900000000004	B;B;B;B	0.10296	0.003;0.001;0.003;0.003	B;B;B;B	0.06405	0.001;0.0;0.001;0.002	T	0.38156	-0.9674	9	0.45353	T	0.12	-5.2038	8.9045	0.35515	0.0:0.3969:0.0:0.6031	rs34883204	353;442;398;410	Q86SU0-5;Q86SU0;Q86SU0-2;Q86SU0-6	.;ILDR1_HUMAN;.;.	H	398;442;353;410	ENSP00000273691:R398H;ENSP00000345667:R442H;ENSP00000377251:R353H;ENSP00000419414:R410H	ENSP00000273691:R398H	R	-	2	0	ILDR1	123194961	0.000000	0.05858	0.161000	0.22692	0.133000	0.20885	-0.271000	0.08572	-0.338000	0.08413	-0.345000	0.07892	CGC	C|0.960;T|0.040	0.040	strong		0.672	ILDR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355666.1	NM_175924		T	121712271	C	T	121712271	3	4	22	1	0	0	0	0	1	0	0	0	7718	768	27	1	323	1	ILDR1	3	121712271	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	173	121712271	76310159	892	3793											
CSTA	1475	hgsc.bcm.edu	37	chr3	122060390	122060390	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	taccaggttgacaaaaacaaGgatgacgagctgacgggctt	14	7	12	8	2	0	3	0	3	0	0	0	5	0	4	1	3	3	3	1	3	4	3	rs34021626	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122060390G>T	ENST00000264474.3	+	3	322	c.273G>T	c.(271-273)aaG>aaT	p.K91N		NM_005213.3	NP_005204.1	P01040	CYTA_HUMAN	cystatin A (stefin A)	91					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)		ACAAAAACAAGGATGACGAGC	0.408													G|||	96	0.0191693	0.0688	0.0072	5008	,	,		18439	0.0		0.0	False		,,,				2504	0.0				p.K91N	Pancreas(26;157 1503 12440)	Atlas-SNP	.											.	CSTA	11	.	0			c.G273T						PASS	.	G	ASN/LYS	255,4151	147.6+/-182.1	8,239,1956	122	120	120		273	3.6	0	3	dbSNP_126	120	1,8599	1.2+/-3.3	0,1,4299	yes	missense	CSTA	NM_005213.3	94	8,240,6255	TT,TG,GG		0.0116,5.7876,1.9683	benign	91/99	122060390	256,12750	2203	4300	6503	SO:0001583	missense	1475	exon3			AAACAAGGATGAC		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.273G>T	3.37:g.122060390G>T	ENSP00000264474:p.Lys91Asn	83	0	0		86	48	0.55814	NM_005213	Q6IB90	Missense_Mutation	SNP	ENST00000264474.3	37	CCDS3011.1	33	0.01510989010989011	29	0.05894308943089431	4	0.011049723756906077	0	0.0	0	0.0	G	16.40	3.111876	0.56398	0.057876	1.16E-4	ENSG00000121552	ENST00000264474	T	0.77098	-1.07	5.34	3.56	0.40772	Proteinase inhibitor I25, cystatin (2);	0.284783	0.37053	N	0.002270	T	0.37945	0.1022	.	.	.	0.18873	N	0.999989	P	0.52577	0.954	P	0.57057	0.812	T	0.55541	-0.8125	9	0.49607	T	0.09	-9.3656	7.8305	0.29340	0.1844:0.0:0.8156:0.0	rs34021626	91	P01040	CYTA_HUMAN	N	91	ENSP00000264474:K91N	ENSP00000264474:K91N	K	+	3	2	CSTA	123543080	0.006000	0.16342	0.013000	0.15412	0.046000	0.14306	0.259000	0.18405	0.824000	0.34613	0.655000	0.94253	AAG	G|0.984;T|0.016	0.016	strong		0.408	CSTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355751.1	NM_005213		T	122060390	G	T	122060390	3	4	22	1	0	0	0	0	1	0	0	0	3983	991	35	4	283	4	CSTA	3	122060390	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	348119	122060390	75962040	893	3794											
PARP15	165631	hgsc.bcm.edu	37	chr3	122351055	122351055	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccgaacttgttcttcctacGcaatagagaaggtaatactg	12	11	8	10	2	1	1	0	0	1	1	2	3	2	1	2	1	3	3	2	1	7	7	rs34383355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122351055G>A	ENST00000464300.2	+	10	1627	c.1561G>A	c.(1561-1563)Gca>Aca	p.A521T	PARP15_ENST00000483793.1_Missense_Mutation_p.A326T|PARP15_ENST00000493645.1_Missense_Mutation_p.A218T|PARP15_ENST00000465304.1_3'UTR|PARP15_ENST00000310366.4_Missense_Mutation_p.A287T	NM_001113523.1	NP_001106995.1	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15	521	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.		A -> T (in dbSNP:rs34383355).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0531)		TTCTTCCTACGCAATAGAGAA	0.358													G|||	100	0.0199681	0.0734	0.0029	5008	,	,		22011	0.0		0.001	False		,,,				2504	0.0				p.A521T		Atlas-SNP	.											PARP15_ENST00000464300,NS,carcinoma,0,2	PARP15	115	2	0			c.G1561A						PASS	.	G	THR/ALA,THR/ALA	252,4154	145.7+/-180.5	6,240,1957	64	63	63		859,1561	-7.6	0	3	dbSNP_126	63	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense	PARP15	NM_152615.1,NM_001113523.1	58,58	6,243,6254	AA,AG,GG		0.0349,5.7195,1.9606	benign,benign	287/445,521/679	122351055	255,12751	2203	4300	6503	SO:0001583	missense	165631	exon10			TCCTACGCAATAG	AK097916	CCDS3016.1, CCDS46893.1	3q21	2010-02-16			ENSG00000173200	ENSG00000173200		"Poly (ADP-ribose) polymerases"	26876	protein-coding gene	gene with protein product		612066				15273990	Standard	NM_001113523		Approved	FLJ40597, pART7	uc003efm.2	Q460N3	OTTHUMG00000159523	ENST00000464300.2:c.1561G>A	3.37:g.122351055G>A	ENSP00000417214:p.Ala521Thr	47	0	0		23	15	0.652174	NM_001113523	J3KR47|Q8N1K3	Missense_Mutation	SNP	ENST00000464300.2	37	CCDS46893.1	32	0.014652014652014652	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	1.319	-0.600018	0.03744	0.057195	3.49E-4	ENSG00000173200	ENST00000464300;ENST00000483793;ENST00000542823;ENST00000310366;ENST00000493645	T;T;T;T	0.12984	2.63;2.63;2.63;2.63	3.77	-7.55	0.01327	Poly(ADP-ribose) polymerase, catalytic domain (2);	.	.	.	.	T	0.00384	0.0012	N	0.01576	-0.805	0.09310	N	1	B;B;B;B;B	0.17465	0.0;0.0;0.0;0.022;0.0	B;B;B;B;B	0.10450	0.002;0.0;0.0;0.005;0.002	T	0.43376	-0.9395	9	0.13470	T	0.59	.	6.614	0.22766	0.2724:0.3821:0.3455:0.0	rs34383355;rs56885169	218;287;268;326;499	B7ZL48;Q460N3-2;F5H8I1;C9J7L3;Q460N3	.;.;.;.;PAR15_HUMAN	T	521;326;268;287;218	ENSP00000417214:A521T;ENSP00000417785:A326T;ENSP00000308436:A287T;ENSP00000419488:A218T	ENSP00000308436:A287T	A	+	1	0	PARP15	123833745	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	0.060000	0.14342	-1.640000	0.01525	-1.085000	0.02201	GCA	G|0.981;A|0.019	0.019	strong		0.358	PARP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355964.2	NM_152615		A	122351055	G	A	122351055	3	1	22	1	0	0	0	0	1	0	0	0	11468	1087	38	1	1668	1	PARP15	3	122351055	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	290665	122351055	75671375	894	3795											
PARP15	165631	hgsc.bcm.edu	37	chr3	122354796	122354796	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggagtcttcacaaagggacGtgcaggattagtcacccctc	10	9	11	11	1	3	0	2	0	1	0	4	3	3	3	2	3	1	1	2	3	2	2	rs145474072	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122354796G>C	ENST00000464300.2	+	12	1952	c.1886G>C	c.(1885-1887)cGt>cCt	p.R629P	PARP15_ENST00000483793.1_Missense_Mutation_p.R434P|PARP15_ENST00000493645.1_Missense_Mutation_p.R326P|PARP15_ENST00000465304.1_3'UTR|PARP15_ENST00000310366.4_Missense_Mutation_p.R395P	NM_001113523.1	NP_001106995.1	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15	629	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0531)		ACAAAGGGACGTGCAGGATTA	0.478													G|||	29	0.00579073	0.0219	0.0	5008	,	,		19916	0.0		0.0	False		,,,				2504	0.0				p.R629P		Atlas-SNP	.											.	PARP15	115	.	0			c.G1886C						PASS	.	G	PRO/ARG,PRO/ARG	66,4340	62.3+/-99.4	2,62,2139	162	132	142		1184,1886	-4.6	0	3	dbSNP_134	142	0,8600		0,0,4300	yes	missense,missense	PARP15	NM_152615.1,NM_001113523.1	103,103	2,62,6439	CC,CG,GG		0.0,1.498,0.5075	benign,benign	395/445,629/679	122354796	66,12940	2203	4300	6503	SO:0001583	missense	165631	exon12			AGGGACGTGCAGG	AK097916	CCDS3016.1, CCDS46893.1	3q21	2010-02-16			ENSG00000173200	ENSG00000173200		"Poly (ADP-ribose) polymerases"	26876	protein-coding gene	gene with protein product		612066				15273990	Standard	NM_001113523		Approved	FLJ40597, pART7	uc003efm.2	Q460N3	OTTHUMG00000159523	ENST00000464300.2:c.1886G>C	3.37:g.122354796G>C	ENSP00000417214:p.Arg629Pro	127	0	0		115	58	0.504348	NM_001113523	J3KR47|Q8N1K3	Missense_Mutation	SNP	ENST00000464300.2	37	CCDS46893.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	G	8.506	0.865423	0.17250	0.01498	0.0	ENSG00000173200	ENST00000464300;ENST00000483793;ENST00000542823;ENST00000310366;ENST00000493645	T;T;T;T	0.13657	2.57;2.57;2.57;2.57	3.99	-4.55	0.03441	Poly(ADP-ribose) polymerase, catalytic domain (2);	.	.	.	.	T	0.05686	0.0149	N	0.26162	0.8	0.09310	N	1	P;B;B;D;B	0.56521	0.566;0.246;0.427;0.976;0.124	B;B;B;B;B	0.43386	0.348;0.222;0.119;0.418;0.162	T	0.14504	-1.0470	9	0.45353	T	0.12	.	5.9187	0.19070	0.3756:0.2583:0.3661:0.0	.	326;395;376;434;607	B7ZL48;Q460N3-2;F5H8I1;C9J7L3;Q460N3	.;.;.;.;PAR15_HUMAN	P	629;434;376;395;326	ENSP00000417214:R629P;ENSP00000417785:R434P;ENSP00000308436:R395P;ENSP00000419488:R326P	ENSP00000308436:R395P	R	+	2	0	PARP15	123837486	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.511000	0.06321	-1.056000	0.03205	-1.043000	0.02367	CGT	G|0.995;C|0.005	0.005	strong		0.478	PARP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355964.2	NM_152615		C	122354796	G	C	122354796	3	2	22	1	0	0	0	0	1	0	0	0	11468	1145	40	4	2001	4	PARP15	3	122354796	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3741	122354796	75667634	895	3796											
PARP14	54625	hgsc.bcm.edu	37	chr3	122419151	122419151	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaccagctgttcttctgaaGccctgttagaagcagaaaag	13	10	9	9	0	2	3	0	1	2	2	2	3	2	3	2	0	4	4	2	0	6	4	rs201474464		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122419151G>A	ENST00000474629.2	+	6	2016	c.1750G>A	c.(1750-1752)Gcc>Acc	p.A584T		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	584					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)		TTCTTCTGAAGCCCTGTTAGA	0.398													G|||	1	0.000199681	0.0008	0.0	5008	,	,		21056	0.0		0.0	False		,,,				2504	0.0				p.A584T		Atlas-SNP	.											PARP14_ENST00000474629,caecum,carcinoma,-2,2	PARP14	242	2	0			c.G1750A						PASS	.	G	THR/ALA	10,3702		0,10,1846	38	35	36		1750	3.5	0	3		36	0,8178		0,0,4089	yes	missense	PARP14	NM_017554.2	58	0,10,5935	AA,AG,GG		0.0,0.2694,0.0841	benign	584/1802	122419151	10,11880	1856	4089	5945	SO:0001583	missense	54625	exon6			TCTGAAGCCCTGT	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.1750G>A	3.37:g.122419151G>A	ENSP00000418194:p.Ala584Thr	79	0	0		77	32	0.415584	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	37	CCDS46894.1	.	.	.	.	.	.	.	.	.	.	G	8.583	0.882878	0.17467	0.002694	0.0	ENSG00000173193	ENST00000474629;ENST00000398162	T	0.09817	2.94	5.34	3.52	0.40303	.	0.755868	0.11822	N	0.526062	T	0.06690	0.0171	N	0.22421	0.69	0.09310	N	1	B;B	0.15473	0.005;0.013	B;B	0.09377	0.002;0.004	T	0.33343	-0.9872	10	0.02654	T	1	.	11.1929	0.48696	0.1539:0.0:0.8461:0.0	.	584;584	Q460N5-4;Q460N5	.;PAR14_HUMAN	T	584;503	ENSP00000418194:A584T	ENSP00000381228:A503T	A	+	1	0	PARP14	123901841	0.558000	0.26554	0.005000	0.12908	0.634000	0.38068	2.752000	0.47516	1.494000	0.48533	-0.142000	0.14014	GCC	.	.	weak		0.398	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		A	122419151	G	A	122419151	3	1	22	1	0	0	0	0	1	0	0	0	11467	971	34	2	1772	2	PARP14	3	122419151	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	64355	122419151	75603279	896	3797											
PARP14	54625	hgsc.bcm.edu	37	chr3	122419292	122419292	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacaaaattcctccccaaacActgtaatcatcaatgagtta	17	10	3	11	0	2	1	2	1	0	0	4	1	4	1	3	0	2	2	3	0	7	3	rs7632072	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122419292A>G	ENST00000474629.2	+	6	2157	c.1891A>G	c.(1891-1893)Act>Gct	p.T631A		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	631					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)		CTCCCCAAACACTGTAATCAT	0.348													A|||	278	0.0555112	0.1218	0.0576	5008	,	,		21423	0.001		0.0487	False		,,,				2504	0.0276				p.T631A		Atlas-SNP	.											.	PARP14	242	.	0			c.A1891G						PASS	.	A	ALA/THR	342,3342		18,306,1518	31	30	31		1891	2.1	0	3	dbSNP_116	31	361,7841		5,351,3745	yes	missense	PARP14	NM_017554.2	58	23,657,5263	GG,GA,AA		4.4014,9.2834,5.9145	probably-damaging	631/1802	122419292	703,11183	1842	4101	5943	SO:0001583	missense	54625	exon6			CCAAACACTGTAA	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.1891A>G	3.37:g.122419292A>G	ENSP00000418194:p.Thr631Ala	65	0	0		87	42	0.482759	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	37	CCDS46894.1	111	0.050824175824175824	49	0.09959349593495935	22	0.06077348066298342	1	0.0017482517482517483	39	0.051451187335092345	A	13.04	2.119612	0.37436	0.092834	0.044014	ENSG00000173193	ENST00000474629;ENST00000398162	T	0.10099	2.91	6.06	2.12	0.27331	.	0.174182	0.39759	N	0.001269	T	0.00271	0.0008	M	0.66939	2.045	0.09310	N	1	P;B	0.38827	0.649;0.376	B;B	0.33690	0.168;0.055	T	0.30268	-0.9984	10	0.36615	T	0.2	.	3.82	0.08832	0.663:0.1354:0.0717:0.1299	rs7632072;rs52827643;rs7632072	631;631	Q460N5-4;Q460N5	.;PAR14_HUMAN	A	631;550	ENSP00000418194:T631A	ENSP00000381228:T550A	T	+	1	0	PARP14	123901982	0.014000	0.17966	0.001000	0.08648	0.003000	0.03518	1.250000	0.32850	0.497000	0.27926	0.533000	0.62120	ACT	A|0.950;G|0.050	0.050	strong		0.348	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		G	122419292	A	G	122419292	3	3	22	1	0	0	0	0	1	0	0	0	11467	159	6	3	1913	3	PARP14	3	122419292	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	141	122419292	75603138	897	3798											
PARP14	54625	hgsc.bcm.edu	37	chr3	122419993	122419993	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agactcctaccgggcaatgcCaccatctccaaggcaggaaa	13	5	9	14	1	1	1	0	0	1	1	3	2	2	2	5	3	2	2	5	3	4	1	rs16833421	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122419993C>T	ENST00000474629.2	+	6	2858	c.2592C>T	c.(2590-2592)gcC>gcT	p.A864A		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	864	Macro 1. {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)		CGGGCAATGCCACCATCTCCA	0.612													C|||	169	0.033746	0.1188	0.0173	5008	,	,		19518	0.0		0.0	False		,,,				2504	0.0				p.A864A		Atlas-SNP	.											.	PARP14	242	.	0			c.C2592T						PASS	.	C		326,3758		15,296,1731	33	35	34		2592	-0.9	0	3	dbSNP_123	34	3,8335		0,3,4166	yes	coding-synonymous	PARP14	NM_017554.2		15,299,5897	TT,TC,CC		0.036,7.9824,2.6485		864/1802	122419993	329,12093	2042	4169	6211	SO:0001819	synonymous_variant	54625	exon6			CAATGCCACCATC	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.2592C>T	3.37:g.122419993C>T		56	0	0		75	37	0.493333	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Silent	SNP	ENST00000474629.2	37	CCDS46894.1																																																																																			C|0.965;T|0.035	0.035	strong		0.612	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		T	122419993	C	T	122419993	2	4	22	1	0	0	0	0	0	0	0	1	11467	581	21	2		2	PARP14	3	122419993	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	701	122419993	75602437	898	3799											
PARP14	54625	hgsc.bcm.edu	37	chr3	122437536	122437536	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctagagatgaaattgaggCgatgatcaagagagttcgat	14	9	14	4	2	1	5	1	3	0	2	2	9	1	5	0	2	0	2	0	2	3	3	rs61732767	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122437536C>T	ENST00000474629.2	+	14	4804	c.4538C>T	c.(4537-4539)gCg>gTg	p.A1513V	PARP14_ENST00000475640.1_3'UTR	NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1513					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)		GAAATTGAGGCGATGATCAAG	0.388													C|||	54	0.0107827	0.0363	0.0086	5008	,	,		21623	0.0		0.0	False		,,,				2504	0.0				p.A1513V		Atlas-SNP	.											.	PARP14	242	.	0			c.C4538T						PASS	.	C	VAL/ALA	89,3737		3,83,1827	209	205	206		4538	-3.8	0	3	dbSNP_129	206	1,8273		0,1,4136	yes	missense	PARP14	NM_017554.2	64	3,84,5963	TT,TC,CC		0.0121,2.3262,0.7438	benign	1513/1802	122437536	90,12010	1913	4137	6050	SO:0001583	missense	54625	exon14			TTGAGGCGATGAT	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.4538C>T	3.37:g.122437536C>T	ENSP00000418194:p.Ala1513Val	164	0	0		138	51	0.369565	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	37	CCDS46894.1	20	0.009157509157509158	16	0.032520325203252036	4	0.011049723756906077	0	0.0	0	0.0	C	12.90	2.075995	0.36662	0.023262	1.21E-4	ENSG00000173193	ENST00000474629;ENST00000398162;ENST00000310290;ENST00000398157	T	0.31510	1.49	5.05	-3.77	0.04346	.	1.394450	0.04317	N	0.350052	T	0.04815	0.0130	L	0.29908	0.895	0.09310	N	1	B;P	0.37330	0.166;0.59	B;B	0.26094	0.035;0.066	T	0.11324	-1.0592	10	0.30078	T	0.28	.	1.8967	0.03259	0.3644:0.238:0.2884:0.1093	rs61732767	1513;1513	Q460N5-4;Q460N5	.;PAR14_HUMAN	V	1513;1432;116;509	ENSP00000418194:A1513V	ENSP00000310633:A116V	A	+	2	0	PARP14	123920226	0.000000	0.05858	0.005000	0.12908	0.945000	0.59286	0.740000	0.26188	-0.515000	0.06479	-0.271000	0.10264	GCG	C|0.990;T|0.010	0.010	strong		0.388	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		T	122437536	C	T	122437536	3	4	22	1	0	0	0	0	1	0	0	0	11467	768	27	1	4592	1	PARP14	3	122437536	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	17543	122437536	75584894	899	3800											
HSPBAP1	79663	hgsc.bcm.edu	37	chr3	122496628	122496628	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgccatgaaggacctgcgAaaggtatttagcattccagt	11	11	10	9	1	0	1	0	1	0	0	1	3	1	2	3	2	3	2	3	2	4	5	rs16833517	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122496628A>C	ENST00000306103.2	-	2	333	c.190T>G	c.(190-192)Tcg>Gcg	p.S64A	HSPBAP1_ENST00000465044.1_5'UTR|HSPBAP1_ENST00000383659.1_Missense_Mutation_p.S64A	NM_024610.5	NP_078886.2	Q96EW2	HBAP1_HUMAN	HSPB (heat shock 27kDa) associated protein 1	64			S -> A (in dbSNP:rs16833517).			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)		AGGACCTGCGAAAGGTATTTA	0.413													A|||	256	0.0511182	0.1831	0.0202	5008	,	,		20190	0.0		0.0	False		,,,				2504	0.0				p.S64A		Atlas-SNP	.											HSPBAP1,NS,carcinoma,+1,1	HSPBAP1	32	1	0			c.T190G						PASS	.	A	ALA/SER	634,3772	274.0+/-271.7	39,556,1608	188	169	175		190	2.8	0.9	3	dbSNP_123	175	3,8597	3.0+/-9.4	0,3,4297	yes	missense	HSPBAP1	NM_024610.5	99	39,559,5905	CC,CA,AA		0.0349,14.3895,4.8977	benign	64/489	122496628	637,12369	2203	4300	6503	SO:0001583	missense	79663	exon2			CCTGCGAAAGGTA	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.190T>G	3.37:g.122496628A>C	ENSP00000302562:p.Ser64Ala	275	0	0		346	191	0.552023	NM_024610	Q6P476|Q8N8J4|Q8NHH6|Q8WWF0	Missense_Mutation	SNP	ENST00000306103.2	37	CCDS3017.1	75	0.034340659340659344	67	0.13617886178861788	8	0.022099447513812154	0	0.0	0	0.0	A	9.139	1.013317	0.19277	0.143895	3.49E-4	ENSG00000169087	ENST00000383659;ENST00000306103	T;T	0.69040	-0.37;3.02	5.32	2.8	0.32819	.	0.105878	0.64402	N	0.000002	T	0.00496	0.0016	L	0.43757	1.38	0.37348	D	0.910665	B;B	0.28324	0.124;0.207	B;B	0.29353	0.057;0.101	T	0.02093	-1.1215	10	0.11485	T	0.65	.	6.8743	0.24139	0.6936:0.1567:0.0:0.1497	rs16833517;rs57105676;rs16833517	64;64	Q96EW2-2;Q96EW2	.;HBAP1_HUMAN	A	64	ENSP00000373155:S64A;ENSP00000302562:S64A	ENSP00000302562:S64A	S	-	1	0	HSPBAP1	123979318	1.000000	0.71417	0.943000	0.38184	0.390000	0.30446	2.466000	0.45084	0.405000	0.25532	0.528000	0.53228	TCG	A|0.951;C|0.049	0.049	strong		0.413	HSPBAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356161.1	NM_024610		C	122496628	A	C	122496628	3	2	22	1	0	0	0	0	1	0	0	0	7434	246	9	5	1304	5	HSPBAP1	3	122496628	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	59092	122496628	75525802	900	3801											
SEMA5B	54437	hgsc.bcm.edu	37	chr3	122634665	122634665	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaggctcatgttggagctGtcctcgagtgtgctgcaacg	7	10	14	10	2	1	1	1	0	0	1	3	3	2	2	1	2	4	5	1	2	1	1	rs34037493	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122634665G>C	ENST00000357599.3	-	13	2147	c.1761C>G	c.(1759-1761)gaC>gaG	p.D587E	SEMA5B_ENST00000195173.4_Missense_Mutation_p.D587E|SEMA5B_ENST00000451055.2_Missense_Mutation_p.D641E	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	587					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)		TGTTGGAGCTGTCCTCGAGTG	0.597													G|||	161	0.0321486	0.1089	0.0216	5008	,	,		18045	0.0		0.002	False		,,,				2504	0.0				p.D641E		Atlas-SNP	.											.	SEMA5B	303	.	0			c.C1923G						PASS	.	G	GLU/ASP	369,4037	187.4+/-214.1	18,333,1852	142	134	137		1761	4.6	1	3	dbSNP_126	137	4,8596	3.7+/-12.6	0,4,4296	yes	missense	SEMA5B	NM_001031702.2	45	18,337,6148	CC,CG,GG		0.0465,8.3749,2.8679	benign	587/1152	122634665	373,12633	2203	4300	6503	SO:0001583	missense	54437	exon13			GGAGCTGTCCTCG	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.1761C>G	3.37:g.122634665G>C	ENSP00000350215:p.Asp587Glu	255	0	0		280	144	0.514286	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Missense_Mutation	SNP	ENST00000357599.3	37	CCDS35491.1	62	0.028388278388278388	51	0.10365853658536585	9	0.024861878453038673	0	0.0	2	0.002638522427440633	G	12.03	1.817110	0.32145	0.083749	4.65E-4	ENSG00000082684	ENST00000357599;ENST00000195173;ENST00000418793;ENST00000451055;ENST00000393583	T;T;T;T	0.21361	2.01;2.01;2.01;2.01	4.64	4.64	0.57946	.	0.000000	0.85682	D	0.000000	T	0.00271	0.0008	N	0.11284	0.12	0.54753	D	0.999981	B;B;B	0.27559	0.086;0.181;0.181	B;B;B	0.27500	0.048;0.08;0.08	T	0.11108	-1.0601	10	0.05525	T	0.97	.	14.3689	0.66826	0.0:0.0:1.0:0.0	rs34037493;rs59368219	529;587;587	D3YTI7;B5ME80;Q9P283	.;.;SEM5B_HUMAN	E	587;587;529;641;587	ENSP00000350215:D587E;ENSP00000195173:D587E;ENSP00000389588:D641E;ENSP00000377208:D587E	ENSP00000195173:D587E	D	-	3	2	SEMA5B	124117355	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.083000	0.41615	2.404000	0.81709	0.561000	0.74099	GAC	G|0.970;C|0.030	0.030	strong		0.597	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702		C	122634665	G	C	122634665	3	2	22	1	0	0	0	0	1	0	0	0	14053	1368	48	4	1738	4	SEMA5B	3	122634665	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	138037	122634665	75387765	901	3802											
CCDC14	64770	hgsc.bcm.edu	37	chr3	123633665	123633665	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccttaaagacttctggagTctagctatgttggcatctaa	10	14	9	8	0	3	1	0	0	3	1	4	2	4	2	1	2	1	3	1	2	5	6	rs13319634	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:123633665T>C	ENST00000488653.2	-	13	2913	c.2823A>G	c.(2821-2823)agA>agG	p.R941R	CCDC14_ENST00000485727.1_Silent_p.R741R|CCDC14_ENST00000433542.2_Silent_p.R900R|CCDC14_ENST00000489746.1_Silent_p.R741R|CCDC14_ENST00000483247.1_5'UTR|CCDC14_ENST00000310351.4_Silent_p.R781R			Q49A88	CCD14_HUMAN	coiled-coil domain containing 14	941					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)		ACTTCTGGAGTCTAGCTATGT	0.403													T|||	124	0.0247604	0.09	0.0072	5008	,	,		477	0.0		0.0	False		,,,				2504	0.0				p.R900R		Atlas-SNP	.											.	CCDC14	97	.	0			c.A2700G						PASS	.	T		317,4089		15,287,1901	20	20	20		2700	-3.3	0.8	3	dbSNP_121	20	7,8589		0,7,4291	no	coding-synonymous	CCDC14	NM_022757.4		15,294,6192	CC,CT,TT		0.0814,7.1947,2.4919		900/913	123633665	324,12678	2203	4298	6501	SO:0001819	synonymous_variant	64770	exon12			CTGGAGTCTAGCT	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.2823A>G	3.37:g.123633665T>C		167	0	0		197	82	0.416244	NM_022757	B7Z2T2|B8ZZ41|B8ZZ58|D3DN98|Q7Z3N3|Q86T30|Q8IWF8|Q8WUJ8|Q96K47|Q9H9A3|Q9UFH0	Silent	SNP	ENST00000488653.2	37																																																																																				T|0.970;C|0.030	0.030	strong		0.403	CCDC14-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_022757		C	123633665	T	C	123633665	2	2	22	1	0	0	0	0	0	0	0	1	2775	1664	58	3		3	CCDC14	3	123633665	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	999000	123633665	74388765	902	3803											
KALRN	8997	hgsc.bcm.edu	37	chr3	124174062	124174062	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcttctgattcagctggcCgatagctttgtggaaaaagg	11	11	12	7	1	2	1	1	1	1	0	2	3	2	2	1	3	3	3	1	3	4	4	rs61747979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:124174062C>T	ENST00000240874.3	+	22	3742	c.3585C>T	c.(3583-3585)gcC>gcT	p.A1195A	KALRN_ENST00000460856.1_Silent_p.A1186A|KALRN_ENST00000360013.3_Silent_p.A1195A	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1195					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)	p.A1195A(2)		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						TTCAGCTGGCCGATAGCTTTG	0.483													C|||	160	0.0319489	0.1172	0.0072	5008	,	,		21547	0.0		0.0	False		,,,				2504	0.0				p.A1195A		Atlas-SNP	.											.	KALRN	556	.	2	Substitution - coding silent(2)	lung(2)	c.C3585T						PASS	.	C	,	413,3993	203.5+/-225.9	25,363,1815	118	109	112		3585,3585	-9.4	0	3	dbSNP_129	112	3,8597	1.2+/-3.3	0,3,4297	no	coding-synonymous,coding-synonymous	KALRN	NM_001024660.3,NM_003947.4	,	25,366,6112	TT,TC,CC		0.0349,9.3736,3.1985	,	1195/2987,1195/1664	124174062	416,12590	2203	4300	6503	SO:0001819	synonymous_variant	8997	exon22			GCTGGCCGATAGC	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.3585C>T	3.37:g.124174062C>T		108	0	0		104	51	0.490385	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	37	CCDS3027.1	68	0.031135531135531136	66	0.13414634146341464	2	0.0055248618784530384	0	0.0	0	0.0	C	6.766	0.510205	0.12883	0.093736	3.49E-4	ENSG00000160145	ENST00000354186	.	.	.	4.71	-9.42	0.00610	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.09310	P	0.9999999999999124	.	.	.	.	.	.	T	0.01925	-1.1246	3	.	.	.	.	3.8289	0.08865	0.2842:0.1245:0.0655:0.5257	rs61747979	.	.	.	L	1164	.	.	P	+	2	0	KALRN	125656752	0.000000	0.05858	0.027000	0.17364	0.936000	0.57629	-4.076000	0.00300	-4.614000	0.00039	-1.741000	0.00685	CCG	C|0.969;T|0.031	0.031	strong		0.483	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		T	124174062	C	T	124174062	2	4	22	1	0	0	0	0	0	0	0	1	7984	639	23	1		1	KALRN	3	124174062	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	540397	124174062	73848368	903	3804											
KALRN	8997	hgsc.bcm.edu	37	chr3	124374487	124374487	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtacagacagagaaagactaTgtcaaggatctgggcattgt	14	9	12	6	0	2	3	1	0	1	3	2	5	2	4	0	2	1	2	0	2	4	3	rs55750661	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:124374487T>C	ENST00000291478.5	+	6	904	c.741T>C	c.(739-741)taT>taC	p.Y247Y	KALRN_ENST00000459915.1_Silent_p.Y36Y|KALRN_ENST00000428018.2_Silent_p.Y215Y|KALRN_ENST00000360013.3_Silent_p.Y1944Y|KALRN_ENST00000393496.1_Silent_p.Y285Y	NM_007064.3	NP_008995.2	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1943					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						AGAAAGACTATGTCAAGGATC	0.493													t|||	8	0.00159744	0.0038	0.0029	5008	,	,		20398	0.0		0.001	False		,,,				2504	0.0				p.Y1944Y		Atlas-SNP	.											.	KALRN	556	.	0			c.T5832C						PASS	.	C	,	22,4384	29.0+/-57.7	0,22,2181	203	186	191		5832,741	-2.5	1	3	dbSNP_129	191	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	KALRN	NM_001024660.3,NM_007064.3	,	0,24,6479	CC,CT,TT		0.0233,0.4993,0.1845	,	1944/2987,247/1290	124374487	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	8997	exon39			AGACTATGTCAAG	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.741T>C	3.37:g.124374487T>C		138	0	0		140	67	0.478571	NM_001024660	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000291478.5	37	CCDS3028.1	3	0.0013736263736263737	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	0	0.0	t	10.36	1.329889	0.24167	0.004993	2.33E-4	ENSG00000160145	ENST00000354186	.	.	.	5.42	-2.53	0.06326	.	.	.	.	.	T	0.55465	0.1922	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59112	-0.7515	4	.	.	.	.	13.5294	0.61613	0.0:0.5623:0.0:0.4377	rs55750661	.	.	.	T	1913	.	.	M	+	2	0	KALRN	125857177	0.434000	0.25570	0.977000	0.42913	0.995000	0.86356	-0.455000	0.06762	-0.595000	0.05828	-0.253000	0.11424	ATG	T|0.998;C|0.002	0.002	strong		0.493	KALRN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000246891.5	NM_003947		C	124374487	T	C	124374487	2	2	22	1	0	0	0	0	0	0	0	1	7984	1471	51	3		3	KALRN	3	124374487	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	200425	124374487	73647943	904	3805											
HEG1	57493	hgsc.bcm.edu	37	chr3	124732426	124732426	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ctgaagaagaagaagaggagGaggaggaagaggaggaggag	18	1	21	1	0	0	6	0	1	0	5	0	13	0	13	0	7	0	0	0	7	5	0	rs113838848	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:124732426G>A	ENST00000311127.4	-	6	2064	c.1997C>T	c.(1996-1998)tCc>tTc	p.S666F	HEG1_ENST00000477536.1_5'UTR	NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	666	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						agaagaggaggaggaggaaga	0.493													G|||	86	0.0171725	0.0598	0.0101	5008	,	,		20835	0.0		0.0	False		,,,				2504	0.0				p.S666F		Atlas-SNP	.											.	HEG1	109	.	0			c.C1997T						PASS	.	G	PHE/SER	183,4127		5,173,1977	55	61	59		1997	0.6	0	3	dbSNP_132	59	1,8509		0,1,4254	yes	missense	HEG1	NM_020733.1	155	5,174,6231	AA,AG,GG		0.0118,4.2459,1.4353	probably-damaging	666/1382	124732426	184,12636	2155	4255	6410	SO:0001583	missense	57493	exon6			GAGGAGGAGGAGG	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.1997C>T	3.37:g.124732426G>A	ENSP00000311502:p.Ser666Phe	123	0	0		130	72	0.553846	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Missense_Mutation	SNP	ENST00000311127.4	37	CCDS46898.1	28	0.01282051282051282	24	0.04878048780487805	4	0.011049723756906077	0	0.0	0	0.0	G	6.371	0.436495	0.12104	0.042459	1.18E-4	ENSG00000173706	ENST00000311127	D	0.89617	-2.54	0.635	0.635	0.17723	.	22.921900	0.01454	U	0.015599	T	0.57359	0.2048	N	0.08118	0	0.09310	N	1	D;D	0.58268	0.982;0.972	P;P	0.58013	0.452;0.831	T	0.72865	-0.4163	9	0.66056	D	0.02	.	.	.	.	.	666;666	Q9ULI3-2;Q9ULI3	.;HEG1_HUMAN	F	666	ENSP00000311502:S666F	ENSP00000311502:S666F	S	-	2	0	HEG1	126215116	0.001000	0.12720	0.004000	0.12327	0.003000	0.03518	0.345000	0.19979	0.619000	0.30197	0.313000	0.20887	TCC	G|0.986;A|0.014	0.014	strong		0.493	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386		A	124732426	G	A	124732426	3	1	22	1	0	0	0	0	1	0	0	0	7053	1174	41	2	2196	2	HEG1	3	124732426	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	357939	124732426	73290004	905	3806											
SNX4	8723	hgsc.bcm.edu	37	chr3	125179676	125179676	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tgcataatgttcttcatcttCcaaaatatcatcaatagaag	15	14	4	8	0	5	1	3	0	2	1	6	1	6	1	1	0	1	2	1	0	7	6			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:125179676C>T	ENST00000251775.4	-	10	907	c.883G>A	c.(883-885)Gaa>Aaa	p.E295K	SNX4_ENST00000536067.1_Missense_Mutation_p.E150K	NM_003794.2	NP_003785.1	O95219	SNX4_HUMAN	sorting nexin 4	295					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						TCTTCATCTTCCAAAATATCA	0.333																																					p.E295K		Atlas-SNP	.											.	SNX4	29	.	0			c.G883A						PASS	.						85	82	83					3																	125179676		2202	4298	6500	SO:0001583	missense	8723	exon10			CATCTTCCAAAAT	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.883G>A	3.37:g.125179676C>T	ENSP00000251775:p.Glu295Lys	203	0	0		196	94	0.479592	NM_003794	B3KMH0|B4DQV4|D3DNA3	Missense_Mutation	SNP	ENST00000251775.4	37	CCDS3032.1	.	.	.	.	.	.	.	.	.	.	C	30	5.053128	0.93793	.	.	ENSG00000114520	ENST00000251775;ENST00000536067	T;T	0.76578	-1.03;-1.03	5.34	5.34	0.76211	.	0.513245	0.21868	N	0.067933	D	0.86451	0.5936	M	0.72894	2.215	0.80722	D	1	D	0.76494	0.999	D	0.68353	0.957	D	0.83631	0.0145	10	0.29301	T	0.29	-16.9581	17.4034	0.87467	0.0:1.0:0.0:0.0	.	295	O95219	SNX4_HUMAN	K	295;150	ENSP00000251775:E295K;ENSP00000440824:E150K	ENSP00000251775:E295K	E	-	1	0	SNX4	126662366	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.541000	0.73865	2.776000	0.95493	0.650000	0.86243	GAA	.	.	none		0.333	SNX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356299.1	NM_003794		T	125179676	C	T	125179676	3	4	22	1	0	0	0	0	1	0	0	0	14919	864	30	2	489	2	SNX4	3	125179676	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	447250	125179676	72842754	906	3807											
ALDH1L1	10840	hgsc.bcm.edu	37	chr3	125854404	125854404	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcagccggccccggtcccgCgcactgatcttcccccaccg	5	6	9	21	5	2	1	1	1	1	0	4	1	4	1	7	2	1	1	7	2	0	1	rs114109734	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:125854404C>T	ENST00000393434.2	-	12	1795	c.1446G>A	c.(1444-1446)gcG>gcA	p.A482A	ALDH1L1_ENST00000452905.2_Silent_p.A381A|ALDH1L1_ENST00000472186.1_Silent_p.A482A|ALDH1L1_ENST00000273450.3_Silent_p.A492A|ALDH1L1_ENST00000393431.2_Silent_p.A482A	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	482	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)	CCCGGTCCCGCGCACTGATCT	0.632													C|||	15	0.00299521	0.0106	0.0014	5008	,	,		15773	0.0		0.0	False		,,,				2504	0.0				p.A492A		Atlas-SNP	.											.	ALDH1L1	138	.	0			c.G1476A						PASS	.	C		49,4357	50.9+/-86.3	0,49,2154	136	102	114		1446	-7.5	0	3	dbSNP_133	114	0,8600		0,0,4300	no	coding-synonymous	ALDH1L1	NM_012190.2		0,49,6454	TT,TC,CC		0.0,1.1121,0.3767		482/903	125854404	49,12957	2203	4300	6503	SO:0001819	synonymous_variant	10840	exon12			GTCCCGCGCACTG	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.1446G>A	3.37:g.125854404C>T		75	0	0		79	35	0.443038	NM_001270364	B4DG36|E9PBX3|Q68CS1	Silent	SNP	ENST00000393434.2	37	CCDS3034.1																																																																																			C|0.996;T|0.004	0.004	strong		0.632	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190		T	125854404	C	T	125854404	2	4	22	1	0	0	0	0	0	0	0	1	494	755	27	1		1	ALDH1L1	3	125854404	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	674728	125854404	72168026	907	3808											
ALDH1L1	10840	hgsc.bcm.edu	37	chr3	125855665	125855665	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccctcggcatccacgaacTcccccccaatgaagagctgg	9	5	9	18	3	0	2	0	1	0	1	3	3	2	2	5	2	2	2	5	2	3	0	rs9282691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:125855665T>G	ENST00000393434.2	-	11	1635	c.1286A>C	c.(1285-1287)gAg>gCg	p.E429A	ALDH1L1_ENST00000452905.2_Missense_Mutation_p.E328A|ALDH1L1_ENST00000472186.1_Missense_Mutation_p.E429A|ALDH1L1_ENST00000273450.3_Missense_Mutation_p.E439A|ALDH1L1_ENST00000393431.2_Missense_Mutation_p.E429A	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	429	Aldehyde dehydrogenase.		E -> A (in dbSNP:rs9282691).		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)	ATCCACGAACTCCCCCCCAAT	0.587													T|||	348	0.0694888	0.2368	0.0331	5008	,	,		19282	0.0		0.0	False		,,,				2504	0.0123				p.E439A		Atlas-SNP	.											.	ALDH1L1	138	.	0			c.A1316C						PASS	.	T	ALA/GLU	884,3522	318.8+/-295.8	95,694,1414	99	89	92		1286	-6.2	0	3	dbSNP_126	92	5,8595	3.0+/-9.4	0,5,4295	yes	missense	ALDH1L1	NM_012190.2	107	95,699,5709	GG,GT,TT		0.0581,20.0635,6.8353	benign	429/903	125855665	889,12117	2203	4300	6503	SO:0001583	missense	10840	exon11			ACGAACTCCCCCC	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.1286A>C	3.37:g.125855665T>G	ENSP00000377083:p.Glu429Ala	79	0	0		93	49	0.526882	NM_001270364	B4DG36|E9PBX3|Q68CS1	Missense_Mutation	SNP	ENST00000393434.2	37	CCDS3034.1	118	0.05402930402930403	104	0.21138211382113822	14	0.03867403314917127	0	0.0	0	0.0	T	4.666	0.123895	0.08931	0.200635	5.81E-4	ENSG00000144908	ENST00000273450;ENST00000472186;ENST00000452905;ENST00000393434;ENST00000393431	T;T;T;T;T	0.09445	2.98;2.98;2.98;2.98;3.08	3.67	-6.25	0.02039	Acyl carrier protein-like (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	2.485370	0.02081	N	0.052371	T	0.00012	0.0000	L	0.49126	1.545	0.80722	P	0.0	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.35724	-0.9777	9	0.51188	T	0.08	.	3.3174	0.07038	0.1797:0.0968:0.1379:0.5855	rs9282691;rs52830184;rs60301528;rs9282691	328;481;429	E9PBX3;Q59G10;O75891	.;.;AL1L1_HUMAN	A	439;429;328;429;429	ENSP00000273450:E439A;ENSP00000420293:E429A;ENSP00000395881:E328A;ENSP00000377083:E429A;ENSP00000377081:E429A	ENSP00000273450:E439A	E	-	2	0	ALDH1L1	127338355	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.150000	0.16263	-1.451000	0.01933	-0.402000	0.06365	GAG	T|0.935;G|0.065	0.065	strong		0.587	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190		G	125855665	T	G	125855665	3	3	22	1	0	0	0	0	1	0	0	0	494	1551	54	5	1474	5	ALDH1L1	3	125855665	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1261	125855665	72166765	908	3809											
CCDC37	348807	hgsc.bcm.edu	37	chr3	126137456	126137456	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactctgctggcccccagtaTgccctggatgtcaagcggag	7	8	12	14	1	2	0	1	0	1	0	2	2	2	2	3	3	3	2	3	3	2	1	rs76764772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:126137456T>C	ENST00000352312.1	+	7	588	c.489T>C	c.(487-489)taT>taC	p.Y163Y	CCDC37_ENST00000505024.1_Silent_p.Y164Y|CCDC37_ENST00000393425.1_Silent_p.Y164Y	NM_182628.2	NP_872434.2	Q494V2	CCD37_HUMAN	coiled-coil domain containing 37	163										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)		GCCCCCAGTATGCCCTGGATG	0.667													T|||	283	0.0565096	0.2057	0.0159	5008	,	,		14709	0.0		0.0	False		,,,				2504	0.0				p.Y163Y		Atlas-SNP	.											.	CCDC37	69	.	0			c.T489C						PASS	.	T		794,3608		80,634,1487	34	36	35		489	-6.4	0	3	dbSNP_131	35	10,8588		0,10,4289	no	coding-synonymous	CCDC37	NM_182628.2		80,644,5776	CC,CT,TT		0.1163,18.0373,6.1846		163/612	126137456	804,12196	2201	4299	6500	SO:0001819	synonymous_variant	348807	exon7			CCAGTATGCCCTG	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.489T>C	3.37:g.126137456T>C		67	0	0		66	29	0.439394	NM_182628	D3DNA8|Q494V1|Q494V4|Q8N838	Silent	SNP	ENST00000352312.1	37	CCDS3037.1																																																																																			T|0.941;C|0.059	0.059	strong		0.667	CCDC37-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000370099.4	NM_182628		C	126137456	T	C	126137456	2	2	22	1	0	0	0	0	0	0	0	1	2811	1471	51	3		3	CCDC37	3	126137456	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	281791	126137456	71884974	909	3810											
CCDC37	348807	hgsc.bcm.edu	37	chr3	126142189	126142189	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgaactctcccatccccccCacgcaggaggacaccgacag	10	4	8	19	3	1	0	0	0	1	0	4	4	2	2	5	2	1	1	5	2	1	0	rs78360289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:126142189C>A	ENST00000352312.1	+	12	1203	c.1104C>A	c.(1102-1104)ccC>ccA	p.P368P	CCDC37_ENST00000505024.1_Silent_p.P369P|CCDC37_ENST00000393425.1_Silent_p.P369P	NM_182628.2	NP_872434.2	Q494V2	CCD37_HUMAN	coiled-coil domain containing 37	368										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)		CCATCCCCCCCACGCAGGAGG	0.662																																					p.P368P		Atlas-SNP	.											.	CCDC37	69	.	0			c.C1104A						PASS	.						41	36	38					3																	126142189		2203	4300	6503	SO:0001819	synonymous_variant	348807	exon12			CCCCCCCACGCAG	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.1104C>A	3.37:g.126142189C>A		128	0	0		148	79	0.533784	NM_182628	D3DNA8|Q494V1|Q494V4|Q8N838	Silent	SNP	ENST00000352312.1	37	CCDS3037.1																																																																																			C|0.992;T|0.008	.	alt		0.662	CCDC37-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000370099.4	NM_182628		A	126142189	C	A	126142189	2	1	22	1	0	0	0	0	0	0	0	1	2811	581	21	4		4	CCDC37	3	126142189	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4733	126142189	71880241	910	3811											
C3orf22	152065	hgsc.bcm.edu	37	chr3	126270923	126270923	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagtcgtttgtgacctcccaGggctgcaggggctcagggtc	5	9	16	11	1	1	1	1	1	0	0	4	2	2	1	2	4	1	4	2	4	0	1	rs34760151	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:126270923G>C	ENST00000318225.2	-	3	510	c.132C>G	c.(130-132)ccC>ccG	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													G|||	481	0.0960463	0.2685	0.0403	5008	,	,		18751	0.002		0.0288	False		,,,				2504	0.0685				p.P44P		Atlas-SNP	.											.	C3orf22	17	.	0			c.C132G						PASS	.	G		894,3512	348.0+/-309.7	98,698,1407	83	77	79		132	0	0	3	dbSNP_126	79	294,8306	108.0+/-168.7	6,282,4012	no	coding-synonymous	C3orf22	NM_152533.1		104,980,5419	CC,CG,GG		3.4186,20.2905,9.1342		44/142	126270923	1188,11818	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>G	3.37:g.126270923G>C		83	0	0		106	50	0.471698	NM_152533	B3KUS9	Silent	SNP	ENST00000318225.2	37	CCDS3040.1																																																																																			G|0.912;C|0.088	0.088	strong		0.602	C3orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370231.2	NM_152533		C	126270923	G	C	126270923	2	2	22	1	0	0	0	0	0	0	0	1	2217	987	35	4		4	C3orf22	3	126270923	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	128734	126270923	71751507	911	3812											
C3orf22	152065	hgsc.bcm.edu	37	chr3	126272160	126272160	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgcacctgtacggaaacttcTtggcaaaattctcctgggcc	9	10	9	13	2	2	0	0	0	2	0	3	1	2	1	3	3	2	3	3	3	4	4	rs146981008	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:126272160T>C	ENST00000318225.2	-	2	452	c.74A>G	c.(73-75)aAg>aGg	p.K25R		NM_152533.1	NP_689746.1	Q8N5N4	CC022_HUMAN	chromosome 3 open reading frame 22	25										large_intestine(1)|lung(3)|ovary(2)|prostate(1)	7				GBM - Glioblastoma multiforme(114;0.147)		CGGAAACTTCTTGGCAAAATT	0.562													T|||	5	0.000998403	0.0008	0.0058	5008	,	,		17166	0.0		0.0	False		,,,				2504	0.0				p.K25R		Atlas-SNP	.											.	C3orf22	17	.	0			c.A74G						PASS	.	T	ARG/LYS	5,4401	9.9+/-24.2	0,5,2198	242	246	245		74	1.9	0.5	3	dbSNP_134	245	0,8600		0,0,4300	yes	missense	C3orf22	NM_152533.1	26	0,5,6498	CC,CT,TT		0.0,0.1135,0.0384	possibly-damaging	25/142	126272160	5,13001	2203	4300	6503	SO:0001583	missense	152065	exon2			AACTTCTTGGCAA		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.74A>G	3.37:g.126272160T>C	ENSP00000316644:p.Lys25Arg	114	0	0		75	34	0.453333	NM_152533	B3KUS9	Missense_Mutation	SNP	ENST00000318225.2	37	CCDS3040.1	3	0.0013736263736263737	0	0.0	3	0.008287292817679558	0	0.0	0	0.0	T	9.445	1.088997	0.20390	0.001135	0.0	ENSG00000180697	ENST00000318225	.	.	.	2.96	1.87	0.25490	.	0.557035	0.13645	N	0.372704	T	0.11750	0.0286	N	0.12746	0.255	0.21604	N	0.999627	B	0.17667	0.023	B	0.17433	0.018	T	0.19877	-1.0292	9	0.22109	T	0.4	.	3.4088	0.07351	0.0:0.2278:0.0:0.7722	.	25	Q8N5N4	CC022_HUMAN	R	25	.	ENSP00000316644:K25R	K	-	2	0	C3orf22	127754850	0.013000	0.17824	0.465000	0.27155	0.240000	0.25518	0.519000	0.22862	0.602000	0.29896	0.402000	0.26972	AAG	T|0.999;C|0.001	0.001	strong		0.562	C3orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370231.2	NM_152533		C	126272160	T	C	126272160	3	2	22	1	0	0	0	0	1	0	0	0	2217	1609	56	3	363	3	C3orf22	3	126272160	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1237	126272160	71750270	912	3813											
MCM2	4171	hgsc.bcm.edu	37	chr3	127340583	127340583	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	atgaacaagttcagccacgaCctgaaaaggaaaatgatcct	17	7	8	9	1	1	3	1	3	0	0	2	5	2	4	3	1	2	1	3	1	6	1	rs6794323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:127340583C>T	ENST00000265056.7	+	16	2926	c.2682C>T	c.(2680-2682)gaC>gaT	p.D894D	MCM2_ENST00000468414.1_3'UTR	NM_004526.2	NP_004517.2	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	894					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						TCAGCCACGACCTGAAAAGGA	0.498													C|||	319	0.0636981	0.2269	0.0231	5008	,	,		22127	0.0		0.003	False		,,,				2504	0.0				p.D894D		Atlas-SNP	.											.	MCM2	79	.	0			c.C2682T						PASS	.	C		764,3642	311.1+/-291.9	56,652,1495	99	93	95		2682	4.5	1	3	dbSNP_116	95	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	MCM2	NM_004526.2		56,660,5787	TT,TC,CC		0.093,17.34,5.9357		894/905	127340583	772,12234	2203	4300	6503	SO:0001819	synonymous_variant	4171	exon16			CCACGACCTGAAA	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.2682C>T	3.37:g.127340583C>T		81	0	0		90	41	0.455556	NM_004526	Q14577|Q15023|Q8N2V1|Q969W7|Q96AE1|Q9BRM7	Silent	SNP	ENST00000265056.7	37	CCDS3043.1	133	0.060897435897435896	124	0.25203252032520324	9	0.024861878453038673	0	0.0	0	0.0	C	2.284	-0.364112	0.05103	0.1734	9.3E-4	ENSG00000073111	ENST00000491422	.	.	.	5.38	4.5	0.54988	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.23013	-1.0200	3	.	.	.	-47.6264	6.5614	0.22489	0.0:0.6888:0.0:0.3112	rs6794323;rs17538760;rs56589702;rs6794323	.	.	.	I	826	.	.	T	+	2	0	MCM2	128823273	1.000000	0.71417	0.993000	0.49108	0.308000	0.27856	1.539000	0.36104	1.263000	0.44181	0.313000	0.20887	ACC	C|0.930;T|0.070	0.070	strong		0.498	MCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356612.1			T	127340583	C	T	127340583	2	4	22	1	0	0	0	0	0	0	0	1	9395	506	18	2		2	MCM2	3	127340583	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1068423	127340583	70681847	913	3814											
PODXL2	50512	hgsc.bcm.edu	37	chr3	127379364	127379369	+	In_Frame_Del	DEL	GAAGAG	GAAGAG	-																															tgcctcccagagaggaggaaGaagaggaagaggaagaggag																								rs200281996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAAGAG	GAAGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:127379364_127379369delGAAGAG	ENST00000342480.6	+	3	532_537	c.493_498delGAAGAG	c.(493-498)gaagagdel	p.EE171del		NM_015720.2	NP_056535.1	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2	171	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						agaggaggaagaagaggaagaggaag	0.553														37	0.00738818	0.0212	0.0014	5008	,	,		22508	0.005		0.0	False		,,,				2504	0.0031				p.164_166del		Pindel,Atlas-Indel	.											.	PODXL2	53	.	0			c.492_497del						PASS	.			61,4203		1,59,2072						-4.8	0.4			53	3,8251		1,1,4125	no	coding	PODXL2	NM_015720.2		2,60,6197	A1A1,A1R,RR		0.0363,1.4306,0.5113				64,12454				SO:0001651	inframe_deletion	50512	exon3			.	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.493_498delGAAGAG	3.37:g.127379370_127379375delGAAGAG	ENSP00000345359:p.Glu171_Glu172del	95	0	.		79	29	0.367	NM_015720	Q6UVY4|Q8WUV6	In_Frame_Del	DEL	ENST00000342480.6	37	CCDS3044.1																																																																																			GAAGAG|0.992;-|0.008	0.008	strong		0.553	PODXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356638.1	NM_015720		-	127379369	GAAGAG	-	127379364	7	5	22	1	0	1	0	1	0	0	0	0	12190	943	33	0	503	0	PODXL2	3	127379364	In_Frame_Del	DEL	GAAGAG	TCGA-G8-6324-01A-11D-2210-10	38781	127379364	70643066	914	3815											
PODXL2	50512	hgsc.bcm.edu	37	chr3	127387388	127387388	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcctggcacatctctctgagCaagcccagcgagaaggagca	11	5	12	13	1	2	2	0	1	2	1	3	4	2	3	2	2	4	3	2	2	2	0	rs34716022	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:127387388C>T	ENST00000342480.6	+	5	1350	c.1311C>T	c.(1309-1311)agC>agT	p.S437S		NM_015720.2	NP_056535.1	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2	437					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						TCTCTCTGAGCAAGCCCAGCG	0.682													C|||	315	0.0628994	0.2239	0.0231	5008	,	,		17746	0.0		0.003	False		,,,				2504	0.0				p.S437S		Atlas-SNP	.											.	PODXL2	53	.	0			c.C1311T						PASS	.	C		750,3654		52,646,1504	22	19	20		1311	4.3	1	3	dbSNP_126	20	8,8586		0,8,4289	no	coding-synonymous	PODXL2	NM_015720.2		52,654,5793	TT,TC,CC		0.0931,17.03,5.8317		437/606	127387388	758,12240	2202	4297	6499	SO:0001819	synonymous_variant	50512	exon5			TCTGAGCAAGCCC	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.1311C>T	3.37:g.127387388C>T		230	0	0		253	133	0.525692	NM_015720	Q6UVY4|Q8WUV6	Silent	SNP	ENST00000342480.6	37	CCDS3044.1																																																																																			C|0.938;T|0.062	0.062	strong		0.682	PODXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356638.1	NM_015720		T	127387388	C	T	127387388	2	4	22	1	0	0	0	0	0	0	0	1	12190	709	25	2		2	PODXL2	3	127387388	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	8024	127387388	70635042	915	3816											
COPG	22820	hgsc.bcm.edu	37	chr3	128984409	128984409	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagggtggctttgagtataaGcgcgctatcgtggactgcat	8	11	14	8	3	0	1	0	1	0	0	1	2	0	2	0	3	2	4	0	3	3	4	rs78889622	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:128984409G>A	ENST00000314797.6	+	14	1346	c.1242G>A	c.(1240-1242)aaG>aaA	p.K414K		NM_016128.3	NP_057212.1	Q9Y678	COPG1_HUMAN	coatomer protein complex, subunit gamma 1	414					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)										TTGAGTATAAGCGCGCTATCG	0.517													G|||	150	0.0299521	0.1036	0.0173	5008	,	,		21492	0.0		0.001	False		,,,				2504	0.0				p.K414K		Atlas-SNP	.											.	.	.	.	0			c.G1242A						PASS	.	G		378,4028	191.9+/-217.4	11,356,1836	175	158	164		1242	4.1	1	3	dbSNP_131	164	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	COPG	NM_016128.3		11,363,6129	AA,AG,GG		0.0814,8.5792,2.9602		414/875	128984409	385,12621	2203	4300	6503	SO:0001819	synonymous_variant	22820	exon14			GTATAAGCGCGCT	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.1242G>A	3.37:g.128984409G>A		126	0	0		140	63	0.45	NM_016128	A8K6M8|B3KMF6|Q54AC4	Silent	SNP	ENST00000314797.6	37	CCDS33851.1																																																																																			G|0.973;A|0.027	0.027	strong		0.517	COPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355456.1	NM_016128		A	128984409	G	A	128984409	2	1	22	1	0	0	0	0	0	0	0	1	3733	962	34	2		2	COPG	3	128984409	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1597021	128984409	69038021	916	3817											
H1FOO	132243	hgsc.bcm.edu	37	chr3	129267915	129267915	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acggctcccaggagagcgggTgaggccaaggggaagggccc	9	2	19	11	2	0	2	0	1	0	1	1	4	1	3	3	7	1	1	3	7	2	0	rs60616647	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:129267915T>C	ENST00000324382.2	+	3	455	c.450T>C	c.(448-450)ggT>ggC	p.G150G	H1FOO_ENST00000503977.1_Silent_p.G11G	NM_153833.1	NP_722575.1	Q8IZA3	H1FOO_HUMAN	H1 histone family, member O, oocyte-specific	150					meiotic nuclear division (GO:0007126)|negative regulation of stem cell differentiation (GO:2000737)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of DNA methylation (GO:0044030)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|female germ cell nucleus (GO:0001674)|nucleosome (GO:0000786)|nucleus (GO:0005634)	nucleosomal DNA binding (GO:0031492)			endometrium(1)|lung(4)|skin(1)	6						GGAGAGCGGGTGAGGCCAAGG	0.607													C|||	315	0.0628994	0.2277	0.0202	5008	,	,		16740	0.0		0.0	False		,,,				2504	0.0				p.G150G		Atlas-SNP	.											.	H1FOO	20	.	0			c.T450C						PASS	.	C		795,3611	723.7+/-409.4	75,645,1483	30	30	30		450	-5.2	0	3	dbSNP_129	30	10,8590	800.0+/-407.4	0,10,4290	no	coding-synonymous	H1FOO	NM_153833.1		75,655,5773	CC,CT,TT		0.1163,18.0436,6.1895		150/347	129267915	805,12201	2203	4300	6503	SO:0001819	synonymous_variant	132243	exon3			AGCGGGTGAGGCC	AY158091	CCDS3064.1	3q21.3	2011-01-27			ENSG00000178804	ENSG00000178804		"Histones / Replication-independent"	18463	protein-coding gene	gene with protein product						12408966	Standard	NM_153833		Approved		uc003emu.3	Q8IZA3	OTTHUMG00000159541	ENST00000324382.2:c.450T>C	3.37:g.129267915T>C		127	0	0		134	134	1	NM_153833	Q86WT7	Silent	SNP	ENST00000324382.2	37	CCDS3064.1																																																																																			T|0.938;C|0.062	0.062	strong		0.607	H1FOO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356100.3	NM_153833		C	129267915	T	C	129267915	2	2	22	1	0	0	0	0	0	0	0	1	6931	1683	59	3		3	H1FOO	3	129267915	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	283506	129267915	68754515	917	3818											
COL6A5	256076	hgsc.bcm.edu	37	chr3	130095598	130095598	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcggacaatcagagacctcAgcacattttcccaaaacatg	14	9	6	12	1	2	1	2	0	0	1	4	3	3	2	2	1	2	1	2	1	3	3	rs115250607	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:130095598A>G	ENST00000432398.2	+	3	1080	c.586A>G	c.(586-588)Agc>Ggc	p.S196G	COL6A5_ENST00000265379.6_Missense_Mutation_p.S196G	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	196	Nonhelical region.|VWFA 1. {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						CAGAGACCTCAGCACATTTTC	0.463													A|||	97	0.019369	0.0703	0.0058	5008	,	,		20670	0.0		0.0	False		,,,				2504	0.0				p.S196G		Atlas-SNP	.											.	COL6A5	205	.	0			c.A586G						PASS	.	A	GLY/SER	75,1309		0,75,617	92	79	83		586	0.6	0.9	3	dbSNP_132	83	0,3182		0,0,1591	yes	missense	COL6A5	NM_153264.5	56	0,75,2208	GG,GA,AA		0.0,5.4191,1.6426	benign	196/2527	130095598	75,4491	692	1591	2283	SO:0001583	missense	256076	exon3			GACCTCAGCACAT	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.586A>G	3.37:g.130095598A>G	ENSP00000390895:p.Ser196Gly	165	0	0		175	73	0.417143	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		30	0.013736263736263736	28	0.056910569105691054	2	0.0055248618784530384	0	0.0	0	0.0	A	7.887	0.731439	0.15507	0.054191	0.0	ENSG00000172752	ENST00000432398;ENST00000265379	T;T	0.77877	-1.13;-1.13	4.91	0.623	0.17654	.	.	.	.	.	T	0.12689	0.0308	N	0.11313	0.125	0.09310	N	0.999998	B	0.13145	0.007	B	0.19666	0.026	T	0.07731	-1.0757	9	0.20046	T	0.44	.	8.6998	0.34318	0.6916:0.0:0.3084:0.0	.	196	A8TX70-2	.	G	196	ENSP00000390895:S196G;ENSP00000265379:S196G	ENSP00000265379:S196G	S	+	1	0	COL6A5	131578288	0.000000	0.05858	0.929000	0.37066	0.781000	0.44180	-0.161000	0.10026	0.278000	0.22164	0.374000	0.22700	AGC	A|0.983;G|0.017	0.017	strong		0.463	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		G	130095598	A	G	130095598	3	3	22	1	0	0	0	0	1	0	0	0	3704	188	7	3	592	3	COL6A5	3	130095598	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	827683	130095598	67926832	918	3819											
COL6A5	256076	hgsc.bcm.edu	37	chr3	130150704	130150704	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaacagccagtaggtcatccAtcatcacggccaccatggag	13	6	9	13	1	3	0	3	0	0	0	4	1	4	1	4	3	2	1	4	3	2	1	rs61750883	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:130150704A>G	ENST00000432398.2	+	33	6138	c.5644A>G	c.(5644-5646)Atc>Gtc	p.I1882V	COL6A5_ENST00000265379.6_Missense_Mutation_p.I1882V	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1882	Nonhelical region.|VWFA 8. {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						TAGGTCATCCATCATCACGGC	0.473													A|||	60	0.0119808	0.0431	0.0043	5008	,	,		20100	0.0		0.0	False		,,,				2504	0.0				p.I1882V		Atlas-SNP	.											.	COL6A5	205	.	0			c.A5644G						PASS	.	A	VAL/ILE	68,1316		3,62,627	197	163	173		5644	-2.3	0.4	3	dbSNP_129	173	0,3182		0,0,1591	yes	missense	COL6A5	NM_153264.5	29	3,62,2218	GG,GA,AA		0.0,4.9133,1.4893	benign	1882/2527	130150704	68,4498	692	1591	2283	SO:0001583	missense	256076	exon33			TCATCCATCATCA	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.5644A>G	3.37:g.130150704A>G	ENSP00000390895:p.Ile1882Val	68	0	0		68	33	0.485294	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		14|14	0.00641025641025641|0.00641025641025641	14|14	0.028455284552845527|0.028455284552845527	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	A|A	1.127|1.127	-0.653563|-0.653563	0.03480|0.03480	0.049133|0.049133	0.0|0.0	ENSG00000172752|ENSG00000172752	ENST00000512836|ENST00000432398;ENST00000265379	.|T;T	.|0.13196	.|2.61;2.61	5.64|5.64	-2.28|-2.28	0.06826|0.06826	.|.	.|.	.|.	.|.	.|.	T|T	0.02193|0.02193	0.0068|0.0068	L|L	0.52266|0.52266	1.64|1.64	0.09310|0.09310	N|N	1|1	.|P	.|0.40083	.|0.702	.|P	.|0.45449	.|0.481	T|T	0.22730|0.22730	-1.0208|-1.0208	5|9	.|0.16420	.|T	.|0.52	.|.	11.0646|11.0646	0.47968|0.47968	0.5749:0.0:0.4251:0.0|0.5749:0.0:0.4251:0.0	rs61750883|rs61750883	.|1882	.|A8TX70-2	.|.	R|V	133|1882	.|ENSP00000390895:I1882V;ENSP00000265379:I1882V	.|ENSP00000265379:I1882V	H|I	+|+	2|1	0|0	COL6A5|COL6A5	131633394|131633394	0.004000|0.004000	0.15560|0.15560	0.400000|0.400000	0.26346|0.26346	0.036000|0.036000	0.12997|0.12997	0.173000|0.173000	0.16724|0.16724	-0.386000|-0.386000	0.07821|0.07821	-0.379000|-0.379000	0.06801|0.06801	CAT|ATC	A|0.993;G|0.007	0.007	strong		0.473	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		G	130150704	A	G	130150704	3	3	22	1	0	0	0	0	1	0	0	0	3704	217	8	3	5770	3	COL6A5	3	130150704	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	55106	130150704	67871726	919	3820											
COL6A5	256076	hgsc.bcm.edu	37	chr3	130188009	130188009	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aatggagatgtttttattggCcatgccttgcagtggacaat	10	14	11	6	0	0	1	0	0	0	1	0	3	0	2	2	3	2	2	2	3	3	5	rs59160673	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:130188009C>T	ENST00000432398.2	+	38	7655	c.7161C>T	c.(7159-7161)ggC>ggT	p.G2387G	COL6A5_ENST00000265379.6_Silent_p.G2387G	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	2387	Nonhelical region.|VWFA 10. {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						TTTTTATTGGCCATGCCTTGC	0.388													C|||	67	0.0133786	0.0499	0.0014	5008	,	,		23052	0.0		0.0	False		,,,				2504	0.0				p.G2387G		Atlas-SNP	.											.	COL6A5	205	.	0			c.C7161T						PASS	.	C		164,3580		2,160,1710	118	106	110		7161	1.4	0.9	3	dbSNP_129	110	0,8222		0,0,4111	no	coding-synonymous	COL6A5	NM_153264.5		2,160,5821	TT,TC,CC		0.0,4.3803,1.3705		2387/2527	130188009	164,11802	1872	4111	5983	SO:0001819	synonymous_variant	256076	exon38			TATTGGCCATGCC	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.7161C>T	3.37:g.130188009C>T		103	0	0		108	49	0.453704	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Silent	SNP	ENST00000432398.2	37		19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	C	4.754	0.140218	0.09083	0.043803	0.0	ENSG00000172752	ENST00000512836	.	.	.	5.35	1.44	0.22558	.	.	.	.	.	T	0.22126	0.0533	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.10382	-1.0632	4	.	.	.	.	6.4978	0.22152	0.0:0.6424:0.1312:0.2264	rs59160673	.	.	.	S	639	.	.	P	+	1	0	COL6A5	131670699	0.738000	0.28186	0.950000	0.38849	0.667000	0.39255	-0.305000	0.08188	-0.018000	0.14079	-0.137000	0.14449	CCA	C|0.989;T|0.011	0.011	strong		0.388	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		T	130188009	C	T	130188009	2	4	22	1	0	0	0	0	0	0	0	1	3704	726	26	2		2	COL6A5	3	130188009	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	37305	130188009	67834421	920	3821											
COL6A6	131873	hgsc.bcm.edu	37	chr3	130287096	130287096	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aacagattcatgtcccaaagCgacatttcaaatgcaataga	17	9	6	9	1	2	2	2	0	0	2	3	3	3	2	1	0	3	1	1	0	5	3	rs61730501	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:130287096C>T	ENST00000358511.6	+	5	2080	c.2049C>T	c.(2047-2049)agC>agT	p.S683S	COL6A6_ENST00000453409.2_Silent_p.S683S	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	683	Nonhelical region.|VWFA 4. {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						TGTCCCAAAGCGACATTTCAA	0.478													C|||	67	0.0133786	0.0477	0.0029	5008	,	,		20256	0.0		0.001	False		,,,				2504	0.001				p.S683S		Atlas-SNP	.											.	COL6A6	497	.	0			c.C2049T						PASS	.	C		128,3762		1,126,1818	153	152	152		2049	-11.5	0	3	dbSNP_129	152	1,8267		0,1,4133	no	coding-synonymous	COL6A6	NM_001102608.1		1,127,5951	TT,TC,CC		0.0121,3.2905,1.061		683/2264	130287096	129,12029	1945	4134	6079	SO:0001819	synonymous_variant	131873	exon5			CCAAAGCGACATT	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.2049C>T	3.37:g.130287096C>T		243	0	0		247	126	0.510121	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Silent	SNP	ENST00000358511.6	37	CCDS46911.1																																																																																			C|0.993;T|0.007	0.007	strong		0.478	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		T	130287096	C	T	130287096	2	4	22	1	0	0	0	0	0	0	0	1	3705	767	27	1		1	COL6A6	3	130287096	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	99087	130287096	67735334	921	3822											
COL6A6	131873	hgsc.bcm.edu	37	chr3	130289687	130289687	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcggattgaagttttagaCgttgtgtttgtcattgatag	10	16	12	3	2	1	3	1	2	0	1	1	4	1	4	0	1	1	3	0	1	4	7	rs59562634	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:130289687C>T	ENST00000358511.6	+	6	2458	c.2427C>T	c.(2425-2427)gaC>gaT	p.D809D	COL6A6_ENST00000453409.2_Silent_p.D809D	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	809	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						AAGTTTTAGACGTTGTGTTTG	0.388													T|||	352	0.0702875	0.2526	0.0245	5008	,	,		20800	0.0		0.001	False		,,,				2504	0.0				p.D809D		Atlas-SNP	.											.	COL6A6	497	.	0			c.C2427T						PASS	.	T		838,2942		86,666,1138	85	88	87		2427	-7.7	0	3	dbSNP_129	87	16,8238		0,16,4111	no	coding-synonymous	COL6A6	NM_001102608.1		86,682,5249	TT,TC,CC		0.1938,22.1693,7.0966		809/2264	130289687	854,11180	1890	4127	6017	SO:0001819	synonymous_variant	131873	exon6			TTTAGACGTTGTG	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.2427C>T	3.37:g.130289687C>T		76	0	0		75	74	0.986667	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Silent	SNP	ENST00000358511.6	37	CCDS46911.1																																																																																			C|0.945;T|0.055	0.055	strong		0.388	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		T	130289687	C	T	130289687	2	4	22	1	0	0	0	0	0	0	0	1	3705	535	19	1		1	COL6A6	3	130289687	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2591	130289687	67732743	922	3823											
ATP2C1	27032	hgsc.bcm.edu	37	chr3	130698205	130698205	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgttacaacactcattgcCtcaggagtatcaataaaaat	15	11	6	9	0	3	0	3	0	0	0	3	1	3	1	1	1	3	3	1	1	7	4	rs114319700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:130698205C>T	ENST00000510168.1	+	19	2233	c.1683C>T	c.(1681-1683)gcC>gcT	p.A561A	ATP2C1_ENST00000328560.8_Silent_p.A561A|ATP2C1_ENST00000507488.2_Silent_p.A545A|ATP2C1_ENST00000422190.2_Silent_p.A561A|ATP2C1_ENST00000504381.1_Silent_p.A506A|ATP2C1_ENST00000508532.1_Silent_p.A561A|ATP2C1_ENST00000393221.4_Silent_p.A595A|ATP2C1_ENST00000428331.2_Silent_p.A561A|ATP2C1_ENST00000505330.1_Silent_p.A545A|ATP2C1_ENST00000533801.2_Silent_p.A556A|ATP2C1_ENST00000513801.1_Silent_p.A545A|ATP2C1_ENST00000359644.3_Silent_p.A561A|ATP2C1_ENST00000504948.1_Silent_p.A545A			P98194	AT2C1_HUMAN	ATPase, Ca++ transporting, type 2C, member 1	561					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)	CACTCATTGCCTCAGGAGTAT	0.413									Hailey-Hailey disease				C|||	19	0.00379393	0.0129	0.0014	5008	,	,		17464	0.001		0.0	False		,,,				2504	0.0				p.A595A	Esophageal Squamous(99;456 1443 27647 34099 42636)	Atlas-SNP	.											.	ATP2C1	94	.	0			c.C1785T						PASS	.	C	,,,,,,,,,,	60,4346	57.4+/-93.9	0,60,2143	121	118	119		1683,1683,1683,1683,1785,1785,1668,1635,1635,1683,1683	4.8	1	3	dbSNP_132	119	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ATP2C1	NM_001001485.2,NM_001001486.1,NM_001001487.1,NM_001199179.1,NM_001199180.1,NM_001199181.1,NM_001199182.1,NM_001199183.1,NM_001199184.1,NM_001199185.1,NM_014382.3	,,,,,,,,,,	0,60,6443	TT,TC,CC		0.0,1.3618,0.4613	,,,,,,,,,,	561/889,561/950,561/940,561/920,595/974,595/954,556/945,545/924,545/904,561/889,561/920	130698205	60,12946	2203	4300	6503	SO:0001819	synonymous_variant	27032	exon18	Familial Cancer Database	HHD, Familial Benign Chronic Pemphigus, Benign Familial Pemphigus	CATTGCCTCAGGA	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.1683C>T	3.37:g.130698205C>T		122	0	0		146	87	0.59589	NM_001199181	B2RAT7|B4DSW3|B7Z3X9|G3XAH8|G8JLN9|O76005|Q86V72|Q86V73|Q8N6V1|Q8NCJ7	Silent	SNP	ENST00000510168.1	37	CCDS46914.1	8	0.003663003663003663	7	0.014227642276422764	0	0.0	1	0.0017482517482517483	0	0.0	C	10.04	1.240288	0.22711	0.013618	0.0	ENSG00000017260	ENST00000504612	.	.	.	5.68	4.8	0.61643	.	.	.	.	.	T	0.49847	0.1581	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53549	-0.8423	4	.	.	.	.	7.3917	0.26913	0.1283:0.6805:0.1237:0.0676	.	.	.	.	L	515	.	.	P	+	2	0	ATP2C1	132180895	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.225000	0.32551	1.386000	0.46466	0.655000	0.94253	CCT	C|0.995;T|0.005	0.005	strong		0.413	ATP2C1-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356648.2	NM_001001486		T	130698205	C	T	130698205	2	4	22	1	0	0	0	0	0	0	0	1	1143	668	24	2		2	ATP2C1	3	130698205	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	408518	130698205	67324225	923	3824											
DNAJC13	23317	hgsc.bcm.edu	37	chr3	132218075	132218075	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agaatcaccattgttgcctgCggctacagagctagctttcc	9	11	9	12	1	1	2	1	0	0	2	2	2	2	2	3	1	5	4	3	1	3	5	rs61748102	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:132218075C>T	ENST00000260818.6	+	37	4510	c.4262C>T	c.(4261-4263)gCg>gTg	p.A1421V		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	1421					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						TTGTTGCCTGCGGCTACAGAG	0.438													C|||	64	0.0127796	0.0242	0.0101	5008	,	,		18844	0.0		0.0209	False		,,,				2504	0.0041				p.A1421V		Atlas-SNP	.											.	DNAJC13	253	.	0			c.C4262T						PASS	.	C	VAL/ALA	112,4294	88.7+/-127.4	0,112,2091	93	93	93		4262	5.4	1	3	dbSNP_129	93	162,8438	76.0+/-138.7	1,160,4139	yes	missense	DNAJC13	NM_015268.3	64	1,272,6230	TT,TC,CC		1.8837,2.542,2.1067	probably-damaging	1421/2244	132218075	274,12732	2203	4300	6503	SO:0001583	missense	23317	exon37			TGCCTGCGGCTAC	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.4262C>T	3.37:g.132218075C>T	ENSP00000260818:p.Ala1421Val	142	0	0		148	66	0.445946	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	37	CCDS33857.1	36	0.016483516483516484	13	0.026422764227642278	6	0.016574585635359115	0	0.0	17	0.022427440633245383	C	34	5.360586	0.95877	0.02542	0.018837	ENSG00000138246	ENST00000260818;ENST00000538066	T	0.52754	0.65	5.42	5.42	0.78866	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.44030	0.1274	M	0.81802	2.56	0.80722	D	1	D	0.71674	0.998	P	0.56648	0.803	T	0.64698	-0.6346	10	0.72032	D	0.01	.	19.5793	0.95459	0.0:1.0:0.0:0.0	rs61748102	1421	O75165	DJC13_HUMAN	V	1421;68	ENSP00000260818:A1421V	ENSP00000260818:A1421V	A	+	2	0	DNAJC13	133700765	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	7.535000	0.82014	2.706000	0.92434	0.555000	0.69702	GCG	C|0.981;T|0.019	0.019	strong		0.438	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268		T	132218075	C	T	132218075	3	4	22	1	0	0	0	0	1	0	0	0	4634	768	27	1	4404	1	DNAJC13	3	132218075	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1519870	132218075	65804355	924	3825											
UBA5	79876	hgsc.bcm.edu	37	chr3	132384704	132384704	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aacgaatgggaattgtaagcGactatgaggtatgataaacc	16	9	11	5	2	0	2	0	2	0	0	0	5	0	3	1	2	3	2	1	2	8	5	rs61748106	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:132384704G>A	ENST00000356232.4	+	2	1271	c.199G>A	c.(199-201)Gac>Aac	p.D67N	UBA5_ENST00000493720.2_Missense_Mutation_p.D67N|UBA5_ENST00000473651.1_Missense_Mutation_p.D67N|UBA5_ENST00000494238.2_Missense_Mutation_p.D11N|UBA5_ENST00000264991.4_Missense_Mutation_p.D11N	NM_024818.3	NP_079094.1	Q9GZZ9	UBA5_HUMAN	ubiquitin-like modifier activating enzyme 5	67					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						AATTGTAAGCGACTATGAGGT	0.303													G|||	2	0.000399361	0.0015	0.0	5008	,	,		18495	0.0		0.0	False		,,,				2504	0.0				p.D67N		Atlas-SNP	.											UBA5,colon,carcinoma,0,1	UBA5	33	1	0			c.G199A						PASS	.	G	ASN/ASP,ASN/ASP	7,4399	12.9+/-30.5	0,7,2196	90	98	96		199,31	4.3	0.7	3	dbSNP_129	96	0,8600		0,0,4300	yes	missense,missense	UBA5	NM_024818.3,NM_198329.2	23,23	0,7,6496	AA,AG,GG		0.0,0.1589,0.0538	benign,benign	67/405,11/349	132384704	7,12999	2203	4300	6503	SO:0001583	missense	79876	exon2			GTAAGCGACTATG	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.199G>A	3.37:g.132384704G>A	ENSP00000348565:p.Asp67Asn	102	0	0		99	44	0.444444	NM_024818	A6NJL3|D3DNC8|Q96ST1	Missense_Mutation	SNP	ENST00000356232.4	37	CCDS3076.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	4.515	0.095620	0.08681	0.001589	0.0	ENSG00000081307	ENST00000264991;ENST00000356232;ENST00000493720;ENST00000468022;ENST00000473651;ENST00000494238;ENST00000489361	T;T;T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58;1.58;1.58	6.03	4.26	0.50523	Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.14056	0.0340	N	0.04959	-0.14	0.80722	D	1	B;B	0.11235	0.004;0.002	B;B	0.09377	0.004;0.002	T	0.07616	-1.0763	10	0.12103	T	0.63	-19.1821	11.318	0.49403	0.1873:0.0:0.8127:0.0	rs61748106	67;67	E7EWE1;Q9GZZ9	.;UBA5_HUMAN	N	11;67;67;11;67;11;11	ENSP00000264991:D11N;ENSP00000348565:D67N;ENSP00000417879:D67N;ENSP00000418569:D11N;ENSP00000424984:D67N;ENSP00000418807:D11N;ENSP00000417905:D11N	ENSP00000264991:D11N	D	+	1	0	UBA5	133867394	1.000000	0.71417	0.700000	0.30305	0.868000	0.49771	4.654000	0.61469	0.898000	0.36418	-0.794000	0.03295	GAC	G|0.999;A|0.001	0.001	strong		0.303	UBA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357187.2	NM_024818		A	132384704	G	A	132384704	3	1	22	1	0	0	0	0	1	0	0	0	16845	1058	37	1	205	1	UBA5	3	132384704	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	166629	132384704	65637726	925	3826											
TF	7018	hgsc.bcm.edu	37	chr3	133486988	133486988	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aacaacaaagagggatactaCggctacacaggcgctttcag	15	6	10	10	2	1	1	1	0	0	1	1	2	1	2	0	3	5	2	0	3	6	4	rs7845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:133486988C>T	ENST00000402696.3	+	13	2087	c.1602C>T	c.(1600-1602)taC>taT	p.Y534Y	TF_ENST00000264998.3_Silent_p.Y407Y	NM_001063.3	NP_001054	P02787	TRFE_HUMAN	transferrin	534	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)	AGGGATACTACGGCTACACAG	0.448													C|||	71	0.0141773	0.0522	0.0029	5008	,	,		19620	0.0		0.0	False		,,,				2504	0.0				p.Y534Y		Atlas-SNP	.											.	TF	116	.	0			c.C1602T						PASS	.	C		174,4232	113.3+/-151.4	5,164,2034	81	83	82		1602	-2.4	1	3	dbSNP_52	82	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TF	NM_001063.3		5,166,6332	TT,TC,CC		0.0233,3.9492,1.3532		534/699	133486988	176,12830	2203	4300	6503	SO:0001819	synonymous_variant	7018	exon13			ATACTACGGCTAC		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.1602C>T	3.37:g.133486988C>T		78	0	0		81	36	0.444444	NM_001063	O43890|Q1HBA5|Q9NQB8|Q9UHV0	Silent	SNP	ENST00000402696.3	37	CCDS3080.1																																																																																			C|0.985;G|0.000;T|0.015	0.015	strong		0.448	TF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317775.1	NM_001063		T	133486988	C	T	133486988	2	4	22	1	0	0	0	0	0	0	0	1	15800	547	19	1		1	TF	3	133486988	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1102284	133486988	64535442	926	3827											
SLCO2A1	6578	hgsc.bcm.edu	37	chr3	133653566	133653566	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccagggtggggtcagatgagGcctgccgccttctgcacgtt	5	9	15	12	2	2	2	1	1	1	1	2	2	2	2	4	4	2	2	4	4	0	2	rs72978391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:133653566G>A	ENST00000310926.4	-	14	2196	c.1923C>T	c.(1921-1923)ggC>ggT	p.G641G	SLCO2A1_ENST00000493729.1_Silent_p.G565G	NM_005630.2	NP_005621.2	Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family, member 2A1	641					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)	GTCAGATGAGGCCTGCCGCCT	0.557													G|||	160	0.0319489	0.112	0.0144	5008	,	,		18588	0.0		0.002	False		,,,				2504	0.0				p.G641G		Atlas-SNP	.											.	SLCO2A1	72	.	0			c.C1923T						PASS	.	G		407,3999	201.8+/-224.7	15,377,1811	121	103	109		1923	2.6	0.7	3	dbSNP_130	109	7,8593	4.3+/-15.6	0,7,4293	no	coding-synonymous	SLCO2A1	NM_005630.2		15,384,6104	AA,AG,GG		0.0814,9.2374,3.1831		641/644	133653566	414,12592	2203	4300	6503	SO:0001819	synonymous_variant	6578	exon14			GATGAGGCCTGCC		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.1923C>T	3.37:g.133653566G>A		49	0	0		74	32	0.432432	NM_005630	Q86V98|Q8IUN2	Silent	SNP	ENST00000310926.4	37	CCDS3084.1																																																																																			G|0.970;A|0.030	0.030	strong		0.557	SLCO2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357131.1	NM_005630		A	133653566	G	A	133653566	2	1	22	1	0	0	0	0	0	0	0	1	14741	1190	42	2		2	SLCO2A1	3	133653566	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	166578	133653566	64368864	927	3828											
STAG1	10274	hgsc.bcm.edu	37	chr3	136062724	136062724	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcagactcaggttcttgaatCtggtctcccatgggccgact	7	12	10	12	1	5	2	2	1	3	1	6	3	5	2	2	3	0	1	2	3	1	2	rs34149860	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:136062724C>G	ENST00000383202.2	-	30	3652	c.3396G>C	c.(3394-3396)caG>caC	p.Q1132H	STAG1_ENST00000236698.5_Missense_Mutation_p.Q1132H|STAG1_ENST00000536929.1_Missense_Mutation_p.Q716H|STAG1_ENST00000434713.2_Missense_Mutation_p.Q872H	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	1132			Q -> H (in dbSNP:rs34149860).		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						GTTCTTGAATCTGGTCTCCCA	0.448													C|||	436	0.0870607	0.3124	0.0303	5008	,	,		20341	0.0		0.002	False		,,,				2504	0.0				p.Q1132H		Atlas-SNP	.											.	STAG1	135	.	0			c.G3396C						PASS	.	C	HIS/GLN	1218,3188	421.7+/-339.5	170,878,1155	100	99	99		3396	3.5	1	3	dbSNP_126	99	12,8588	8.4+/-32.0	0,12,4288	yes	missense	STAG1	NM_005862.2	24	170,890,5443	GG,GC,CC		0.1395,27.6441,9.4572	benign	1132/1259	136062724	1230,11776	2203	4300	6503	SO:0001583	missense	10274	exon30			TTGAATCTGGTCT	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.3396G>C	3.37:g.136062724C>G	ENSP00000372689:p.Gln1132His	136	0	0		160	87	0.54375	NM_005862	O00539|Q6P275	Missense_Mutation	SNP	ENST00000383202.2	37	CCDS3090.1	157	0.07188644688644688	145	0.29471544715447157	11	0.03038674033149171	0	0.0	1	0.0013192612137203166	C	8.880	0.951348	0.18431	0.276441	0.001395	ENSG00000118007	ENST00000383202;ENST00000236698;ENST00000434713;ENST00000536929	T;T;T;T	0.32272	1.87;1.9;1.85;1.46	5.48	3.45	0.39498	.	0.196262	0.47455	D	0.000221	T	0.00012	0.0000	N	0.11201	0.11	0.26204	P	0.9793941	B;B	0.06786	0.001;0.001	B;B	0.10450	0.005;0.002	T	0.34725	-0.9817	9	0.41790	T	0.15	.	9.8937	0.41304	0.0:0.7454:0.0:0.2546	rs34149860	1132;1132	Q6P275;Q8WVM7	.;STAG1_HUMAN	H	1132;1132;872;716	ENSP00000372689:Q1132H;ENSP00000236698:Q1132H;ENSP00000404396:Q872H;ENSP00000445787:Q716H	ENSP00000236698:Q1132H	Q	-	3	2	STAG1	137545414	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.602000	0.36783	1.316000	0.45131	-0.137000	0.14449	CAG	C|0.914;G|0.086	0.086	strong		0.448	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862		G	136062724	C	G	136062724	3	3	22	1	0	0	0	0	1	0	0	0	15257	912	32	4	400	4	STAG1	3	136062724	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2409158	136062724	61959706	928	3829											
DZIP1L	199221	hgsc.bcm.edu	37	chr3	137787173	137787173	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gggtcctggtctttggctggGcctctctggtgaccagtgtg	2	13	16	10	0	2	1	0	1	2	0	4	1	3	1	3	5	0	1	3	5	0	1	rs11917468	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:137787173G>A	ENST00000327532.2	-	13	2014	c.1652C>T	c.(1651-1653)gCc>gTc	p.A551V	DZIP1L_ENST00000488595.1_5'UTR	NM_173543.2	NP_775814.2	Q8IYY4	DZI1L_HUMAN	DAZ interacting zinc finger protein 1-like	551			A -> V (in dbSNP:rs11917468).		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						CTTTGGCTGGGCCTCTCTGGT	0.577											OREG0015830	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	262	0.0523163	0.1868	0.0202	5008	,	,		16312	0.0		0.001	False		,,,				2504	0.0				p.A551V		Atlas-SNP	.											.	DZIP1L	88	.	0			c.C1652T						PASS	.	G	VAL/ALA	707,3699	290.1+/-280.8	50,607,1546	71	78	75		1652	-2.2	0	3	dbSNP_120	75	12,8588	9.1+/-34.3	0,12,4288	yes	missense	DZIP1L	NM_173543.2	64	50,619,5834	AA,AG,GG		0.1395,16.0463,5.5282	benign	551/768	137787173	719,12287	2203	4300	6503	SO:0001583	missense	199221	exon13			GGCTGGGCCTCTC	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.1652C>T	3.37:g.137787173G>A	ENSP00000332148:p.Ala551Val	209	0	0	1636	166	77	0.463855	NM_173543	C9JUG5|Q96M38	Missense_Mutation	SNP	ENST00000327532.2	37	CCDS3096.1	72	0.03296703296703297	66	0.13414634146341464	6	0.016574585635359115	0	0.0	0	0.0	G	3.102	-0.184558	0.06340	0.160463	0.001395	ENSG00000158163	ENST00000327532	T	0.39056	1.1	4.91	-2.15	0.07102	.	1.124280	0.06592	N	0.752174	T	0.00073	0.0002	N	0.02011	-0.69	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.17379	-1.0371	10	0.20046	T	0.44	0.1447	9.7913	0.40708	0.6267:0.0:0.3733:0.0	rs11917468;rs52808108;rs11917468	551	Q8IYY4	DZI1L_HUMAN	V	551	ENSP00000332148:A551V	ENSP00000332148:A551V	A	-	2	0	DZIP1L	139269863	0.000000	0.05858	0.000000	0.03702	0.128000	0.20619	-0.062000	0.11674	-0.389000	0.07786	0.650000	0.86243	GCC	G|0.948;A|0.052	0.052	strong		0.577	DZIP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357548.1	NM_173543		A	137787173	G	A	137787173	3	1	22	1	0	0	0	0	1	0	0	0	4866	1203	42	2	667	2	DZIP1L	3	137787173	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1724449	137787173	60235257	929	3830											
ESYT3	83850	hgsc.bcm.edu	37	chr3	138176436	138176436	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggtcaacggtgtcaaggcAcacactaatacgtgcaaccg	13	6	11	11	3	2	0	2	0	0	0	2	0	2	0	1	3	4	2	1	3	5	2	rs35605373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:138176436A>G	ENST00000389567.4	+	4	717	c.531A>G	c.(529-531)gcA>gcG	p.A177A	ESYT3_ENST00000289135.4_Silent_p.A177A	NM_031913.3	NP_114119.2	A0FGR9	ESYT3_HUMAN	extended synaptotagmin-like protein 3	177	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						GTGTCAAGGCACACACTAATA	0.587													A|||	118	0.0235623	0.0825	0.013	5008	,	,		20302	0.0		0.0	False		,,,				2504	0.0				p.A177A		Atlas-SNP	.											.	ESYT3	64	.	0			c.A531G						PASS	.	A		310,4096	166.5+/-197.7	5,300,1898	182	160	168		531	-10.9	0	3	dbSNP_126	168	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	ESYT3	NM_031913.3		5,304,6194	GG,GA,AA		0.0465,7.0359,2.4143		177/887	138176436	314,12692	2203	4300	6503	SO:0001819	synonymous_variant	83850	exon4			CAAGGCACACACT	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.531A>G	3.37:g.138176436A>G		130	0	0		154	75	0.487013	NM_031913	A8K0G5|Q6ZV21|Q8NDZ5|Q9BQR9	Silent	SNP	ENST00000389567.4	37	CCDS3101.2																																																																																			A|0.975;G|0.025	0.025	strong		0.587	ESYT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303993.1	NM_031913		G	138176436	A	G	138176436	2	3	22	1	0	0	0	0	0	0	0	1	5268	146	6	3		3	ESYT3	3	138176436	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	389263	138176436	59845994	930	3831											
RBP1	5947	hgsc.bcm.edu	37	chr3	139257727	139257727	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctcagcgtgcggatgatcaTatggtcaccgtcctgcacga	8	9	12	12	4	3	1	3	1	0	0	4	3	4	2	2	2	3	2	2	2	1	1	rs34674353	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:139257727T>C	ENST00000483943.2	-	2	334	c.334A>G	c.(334-336)Atg>Gtg	p.M112V	RBP1_ENST00000492918.1_Missense_Mutation_p.M112V|RP11-319G6.1_ENST00000381790.3_RNA|RBP1_ENST00000232219.2_Missense_Mutation_p.M112V|RP11-319G6.1_ENST00000515247.1_RNA	NM_001130993.1	NP_001124465.1	P09455	RET1_HUMAN	retinol binding protein 1, cellular	50					phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|vitamin A metabolic process (GO:0006776)	cytosol (GO:0005829)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			endometrium(1)|large_intestine(2)|lung(1)|prostate(1)	5					Acitretin(DB00459)|Vitamin A(DB00162)	CGGATGATCATATGGTCACCG	0.532													T|||	48	0.00958466	0.034	0.0043	5008	,	,		19972	0.0		0.0	False		,,,				2504	0.0				p.M112V		Atlas-SNP	.											.	RBP1	39	.	0			c.A334G						PASS	.	T	VAL/MET,VAL/MET,VAL/MET	98,4308	79.3+/-117.8	0,98,2105	242	194	210		334,334,334	5.3	1	3	dbSNP_126	210	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense	RBP1	NM_002899.3,NM_001130993.1,NM_001130992.1	21,21,21	0,100,6403	CC,CT,TT		0.0233,2.2242,0.7689	benign,benign,benign	112/198,112/154,112/158	139257727	100,12906	2203	4300	6503	SO:0001583	missense	5947	exon2			TGATCATATGGTC		CCDS3110.2, CCDS46925.1, CCDS46926.1	3q21-q23	2013-03-01	2001-11-28		ENSG00000114115	ENSG00000114115		"Fatty acid binding protein family"	9919	protein-coding gene	gene with protein product		180260	"retinol-binding protein 1, cellular"			1654334, 9858824	Standard	NM_002899		Approved	CRABP-I, CRBP1, CRBP, RBPC, CRBPI	uc003eti.2	P09455	OTTHUMG00000155751	ENST00000483943.2:c.334A>G	3.37:g.139257727T>C	ENSP00000424813:p.Met112Val	260	0	0		274	141	0.514599	NM_002899	A8K2Q0|B7Z7A0|E7EWV0|F2Z2F2|Q6FGX8	Missense_Mutation	SNP	ENST00000483943.2	37	CCDS46925.1	13	0.005952380952380952	11	0.022357723577235773	2	0.0055248618784530384	0	0.0	0	0.0	T	14.91	2.676656	0.47886	0.022242	2.33E-4	ENSG00000114115	ENST00000232219;ENST00000483943;ENST00000492918	T;T;T	0.21031	2.03;2.03;2.03	5.28	5.28	0.74379	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.057277	0.64402	D	0.000002	T	0.12050	0.0293	L	0.33485	1.01	0.45979	D	0.998796	P;P;B	0.37548	0.599;0.543;0.04	P;B;B	0.45167	0.472;0.243;0.072	T	0.02484	-1.1152	10	0.28530	T	0.3	.	14.3982	0.67025	0.0:0.0:0.0:1.0	rs34674353	112;112;50	F2Z2F2;E7EWV0;P09455	.;.;RET1_HUMAN	V	112	ENSP00000232219:M112V;ENSP00000424813:M112V;ENSP00000429166:M112V	ENSP00000232219:M112V	M	-	1	0	RBP1	140740417	1.000000	0.71417	0.999000	0.59377	0.834000	0.47266	4.774000	0.62339	1.988000	0.58038	0.455000	0.32223	ATG	T|0.992;C|0.008	0.008	strong		0.532	RBP1-003	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000341497.2	NM_002899		C	139257727	T	C	139257727	3	2	22	1	0	0	0	0	1	0	0	0	13170	1406	49	3	339	3	RBP1	3	139257727	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1081291	139257727	58764703	931	3832											
CLSTN2	64084	hgsc.bcm.edu	37	chr3	140281768	140281768	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aagtgctcagaactcaatggGcgctacactagcaatgagtt	13	9	10	9	1	2	2	2	1	0	1	2	2	2	2	0	1	4	4	0	1	6	3	rs35951028	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:140281768G>A	ENST00000458420.3	+	14	2518	c.2328G>A	c.(2326-2328)ggG>ggA	p.G776G		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	776					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						AACTCAATGGGCGCTACACTA	0.542										HNSCC(16;0.037)			G|||	111	0.0221645	0.0779	0.0115	5008	,	,		21673	0.0		0.0	False		,,,				2504	0.0				p.G776G	GBM(45;858 913 3709 36904 37282)	Atlas-SNP	.											.	CLSTN2	190	.	0			c.G2328A						PASS	.	G		331,4075	175.5+/-204.9	8,315,1880	60	58	59		2328	3.8	1	3	dbSNP_126	59	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	CLSTN2	NM_022131.2		8,319,6176	AA,AG,GG		0.0465,7.5125,2.5757		776/956	140281768	335,12671	2203	4300	6503	SO:0001819	synonymous_variant	64084	exon14			CAATGGGCGCTAC	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.2328G>A	3.37:g.140281768G>A		114	0	0		128	127	0.992188	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Silent	SNP	ENST00000458420.3	37	CCDS3112.1																																																																																			G|0.973;A|0.027	0.027	strong		0.542	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131		A	140281768	G	A	140281768	2	1	22	1	0	0	0	0	0	0	0	1	3564	1190	42	2		2	CLSTN2	3	140281768	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1024041	140281768	57740662	932	3833											
ACPL2	92370	hgsc.bcm.edu	37	chr3	141006162	141006162	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tatcatctctctaggaaaccGtatcacccaaaactggaagc	14	9	6	12	1	4	0	2	0	2	0	5	2	4	2	2	2	3	1	2	2	7	3	rs34601454	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:141006162G>A	ENST00000286353.4	+	5	509	c.372G>A	c.(370-372)ccG>ccA	p.P124P	ACPL2_ENST00000393007.1_Silent_p.P108P|ACPL2_ENST00000393010.2_Silent_p.P124P|ACPL2_ENST00000502783.1_Silent_p.P86P|ACPL2_ENST00000508812.1_Silent_p.P115P|ACPL2_ENST00000504264.1_Silent_p.P107P|RP11-438D8.2_ENST00000507698.1_RNA	NM_001037172.1|NM_001282728.1	NP_001032249.1|NP_001269657.1	Q8TE99	PXYP1_HUMAN		124						extracellular region (GO:0005576)	acid phosphatase activity (GO:0003993)			endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|prostate(2)|skin(2)	23						CTAGGAAACCGTATCACCCAA	0.473													G|||	162	0.0323482	0.1157	0.013	5008	,	,		20337	0.0		0.0	False		,,,				2504	0.0				p.P124P		Atlas-SNP	.											.	ACPL2	50	.	0			c.G372A						PASS	.	G	,	377,4029	189.9+/-215.9	16,345,1842	151	158	155		372,372	-11.3	0	3	dbSNP_126	155	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	ACPL2	NM_001037172.1,NM_152282.3	,	16,348,6139	AA,AG,GG		0.0349,8.5565,2.9217	,	124/481,124/481	141006162	380,12626	2203	4300	6503	SO:0001819	synonymous_variant	92370	exon7			GAAACCGTATCAC																												ENST00000286353.4:c.372G>A	3.37:g.141006162G>A		115	0	0		97	41	0.42268	NM_152282	D3DNF5|Q49AJ2|W0TR04	Silent	SNP	ENST00000286353.4	37	CCDS3116.1																																																																																			G|0.969;A|0.031	0.031	strong		0.473	ACPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359533.2			A	141006162	G	A	141006162	2	1	22	1	0	0	0	0	0	0	0	1	166	1132	40	1		1	ACPL2	3	141006162	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	724394	141006162	57016268	933	3834											
RASA2	5922	hgsc.bcm.edu	37	chr3	141248572	141248572	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaagtagccatcaaaaaagaAgacttgtgtaatcacagtgg	18	8	9	6	0	2	2	2	0	0	2	2	2	2	2	1	1	1	2	1	1	7	3	rs144759014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:141248572A>C	ENST00000452898.1	+	4	413	c.378A>C	c.(376-378)gaA>gaC	p.E126D	RASA2_ENST00000286364.3_Missense_Mutation_p.E126D	NM_006506.2	NP_006497.2	Q15283	RASA2_HUMAN	RAS p21 protein activator 2	126					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						TCAAAAAAGAAGACTTGTGTA	0.318													A|||	3	0.000599042	0.0023	0.0	5008	,	,		15787	0.0		0.0	False		,,,				2504	0.0				p.E126D		Atlas-SNP	.											RASA2_ENST00000286364,temporal_lobe,glioma,+2,2	RASA2	169	2	0			c.A378C						PASS	.	A	ASP/GLU	7,4399	12.9+/-30.5	0,7,2196	72	74	74		378	4.7	1	3	dbSNP_134	74	0,8598		0,0,4299	yes	missense	RASA2	NM_006506.2	45	0,7,6495	CC,CA,AA		0.0,0.1589,0.0538	possibly-damaging	126/850	141248572	7,12997	2203	4299	6502	SO:0001583	missense	5922	exon4			AAAAGAAGACTTG	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.378A>C	3.37:g.141248572A>C	ENSP00000391677:p.Glu126Asp	35	0	0		42	17	0.404762	NM_006506	A8K7K1|G3V0F9|O00695|Q15284|Q92594|Q99577|Q9UEQ2	Missense_Mutation	SNP	ENST00000452898.1	37		.	.	.	.	.	.	.	.	.	.	A	16.18	3.051372	0.55218	0.001589	0.0	ENSG00000155903	ENST00000286364;ENST00000452898	T;T	0.70869	-0.52;-0.52	5.84	4.68	0.58851	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.055137	0.64402	D	0.000001	T	0.70064	0.3181	M	0.80183	2.485	0.46356	D	0.999007	B;B;B	0.23490	0.051;0.086;0.051	B;B;B	0.31686	0.063;0.134;0.063	T	0.63060	-0.6721	10	0.21014	T	0.42	.	8.3803	0.32468	0.8469:0.0:0.1531:0.0	.	126;126;126	A8K7K1;G3V0F9;Q15283	.;.;RASA2_HUMAN	D	126	ENSP00000286364:E126D;ENSP00000391677:E126D	ENSP00000286364:E126D	E	+	3	2	RASA2	142731262	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.541000	0.36126	1.030000	0.39839	0.533000	0.62120	GAA	A|1.000;C|0.000	0.000	strong		0.318	RASA2-201	KNOWN	basic	protein_coding	protein_coding		NM_006506		C	141248572	A	C	141248572	3	2	22	1	0	0	0	0	1	0	0	0	13076	69	3	5	392	5	RASA2	3	141248572	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	242410	141248572	56773858	934	3835											
SR140	23350	hgsc.bcm.edu	37	chr3	142747230	142747230	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catgtttactataggtggaaGctttattctattctgcaggc	9	16	9	7	0	2	0	0	0	2	0	2	1	2	1	0	3	3	3	0	3	6	9	rs80238215	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:142747230G>A	ENST00000473835.2	+	15	1518	c.1428G>A	c.(1426-1428)aaG>aaA	p.K476K	U2SURP_ENST00000397933.2_Silent_p.K67K|U2SURP_ENST00000493598.2_Silent_p.K475K	NM_001080415.1	NP_001073884.1	O15042	SR140_HUMAN	U2 snRNP-associated SURP domain containing	476					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						ATAGGTGGAAGCTTTATTCTA	0.313													G|||	35	0.00698882	0.0234	0.0058	5008	,	,		15948	0.0		0.0	False		,,,				2504	0.0				p.K476K		Atlas-SNP	.											.	U2SURP	66	.	0			c.G1428A						PASS	.	G		61,3529		1,59,1735	74	70	71		1428	2	1	3	dbSNP_132	71	0,8136		0,0,4068	no	coding-synonymous	U2SURP	NM_001080415.1		1,59,5803	AA,AG,GG		0.0,1.6992,0.5202		476/1030	142747230	61,11665	1795	4068	5863	SO:0001819	synonymous_variant	23350	exon15			GTGGAAGCTTTAT	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.1428G>A	3.37:g.142747230G>A		232	0	0		184	85	0.461957	NM_001080415	A0PJ60|Q0D2M1|Q2NKQ7|Q9BR70	Silent	SNP	ENST00000473835.2	37	CCDS46928.1																																																																																			G|0.991;A|0.009	0.009	strong		0.313	U2SURP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354603.2	NM_001080415		A	142747230	G	A	142747230	2	1	22	1	0	0	0	0	0	0	0	1	15146	962	34	2		2	SR140	3	142747230	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1498658	142747230	55275200	935	3836											
SLC9A9	285195	hgsc.bcm.edu	37	chr3	143185920	143185920	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgggggttgttcctcctccAaatacccagacagtgaagaa	12	9	10	10	0	0	3	0	1	0	2	3	3	3	3	4	2	1	2	4	2	4	3	rs61734421	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:143185920A>G	ENST00000316549.6	-	12	1636	c.1428T>C	c.(1426-1428)ttT>ttC	p.F476F		NM_173653.3	NP_775924.1	Q8IVB4	SL9A9_HUMAN	solute carrier family 9, subfamily A (NHE9, cation proton antiporter 9), member 9	476					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						TTCCTCCTCCAAATACCCAGA	0.473													A|||	23	0.00459265	0.0166	0.0014	5008	,	,		19226	0.0		0.0	False		,,,				2504	0.0				p.F476F		Atlas-SNP	.											.	SLC9A9	117	.	0			c.T1428C						PASS	.	A		91,4315	75.2+/-113.4	1,89,2113	141	116	124		1428	-3	0.9	3	dbSNP_129	124	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SLC9A9	NM_173653.3		1,91,6411	GG,GA,AA		0.0233,2.0654,0.7151		476/646	143185920	93,12913	2203	4300	6503	SO:0001819	synonymous_variant	285195	exon12			TCCTCCAAATACC	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.1428T>C	3.37:g.143185920A>G		311	0	0		314	151	0.480892	NM_173653	A6NMQ9|Q3LIC2|Q5JPI6|Q5WA58|Q8NAB9	Silent	SNP	ENST00000316549.6	37	CCDS33872.1																																																																																			A|0.993;G|0.007	0.007	strong		0.473	SLC9A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354994.1	NM_173653		G	143185920	A	G	143185920	2	3	22	1	0	0	0	0	0	0	0	1	14736	127	5	3		3	SLC9A9	3	143185920	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	438690	143185920	54836510	936	3837											
PLOD2	5352	hgsc.bcm.edu	37	chr3	145794607	145794607	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgccagaggtcattgttatAatgggaagtattgtaattag	12	14	11	4	0	1	1	1	0	0	1	1	2	1	2	1	2	1	3	1	2	6	7	rs115199093	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:145794607A>G	ENST00000360060.3	-	14	1753	c.1576T>C	c.(1576-1578)Tat>Cat	p.Y526H	PLOD2_ENST00000461497.1_Missense_Mutation_p.Y207H|PLOD2_ENST00000282903.5_Missense_Mutation_p.Y547H|PLOD2_ENST00000494950.1_Missense_Mutation_p.Y492H|RP11-274H2.2_ENST00000480247.1_RNA	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	526					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)	TCATTGTTATAATGGGAAGTA	0.299													A|||	8	0.00159744	0.0053	0.0014	5008	,	,		15142	0.0		0.0	False		,,,				2504	0.0				p.Y547H		Atlas-SNP	.											.	PLOD2	81	.	0			c.T1639C						PASS	.	A	HIS/TYR,HIS/TYR	26,4380	32.6+/-62.9	0,26,2177	90	98	96		1576,1639	3.7	1	3	dbSNP_132	96	1,8573	1.2+/-3.3	0,1,4286	yes	missense,missense	PLOD2	NM_000935.2,NM_182943.2	83,83	0,27,6463	GG,GA,AA		0.0117,0.5901,0.208	benign,benign	526/738,547/759	145794607	27,12953	2203	4287	6490	SO:0001583	missense	5352	exon15			TGTTATAATGGGA	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.1576T>C	3.37:g.145794607A>G	ENSP00000353170:p.Tyr526His	154	0	0		156	78	0.5	NM_182943	B3KWS3|Q59ED2|Q8N170	Missense_Mutation	SNP	ENST00000360060.3	37	CCDS3131.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	A	17.15	3.315084	0.60524	0.005901	1.17E-4	ENSG00000152952	ENST00000461497;ENST00000282903;ENST00000360060;ENST00000494950	D;D;D;D	0.85484	-1.99;-1.99;-1.99;-1.99	5.12	3.72	0.42706	.	0.178784	0.50627	D	0.000101	T	0.80834	0.4699	L	0.51422	1.61	0.45183	D	0.99819	P;P;P;P	0.47545	0.865;0.773;0.738;0.897	P;P;P;P	0.52109	0.628;0.492;0.69;0.497	T	0.79610	-0.1732	10	0.42905	T	0.14	-10.2013	8.8487	0.35186	0.8839:0.0:0.1161:0.0	.	492;526;547;207	E7ETU9;O00469;O00469-2;B3KWS3	.;PLOD2_HUMAN;.;.	H	207;547;526;492	ENSP00000419354:Y207H;ENSP00000282903:Y547H;ENSP00000353170:Y526H;ENSP00000420094:Y492H	ENSP00000282903:Y547H	Y	-	1	0	PLOD2	147277297	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	3.164000	0.50770	0.604000	0.29930	0.529000	0.55759	TAT	A|0.998;G|0.002	0.002	strong		0.299	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935		G	145794607	A	G	145794607	3	3	22	1	0	0	0	0	1	0	0	0	12111	362	13	3	661	3	PLOD2	3	145794607	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2608687	145794607	52227823	937	3838											
PLOD2	5352	hgsc.bcm.edu	37	chr3	145809622	145809622	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcgactgtatcgaattcacAaagagtgcagccattatcct	12	11	8	10	2	1	1	1	0	0	1	4	3	2	1	2	0	2	2	2	0	4	3	rs138948307	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:145809622A>G	ENST00000360060.3	-	8	1021	c.844T>C	c.(844-846)Tgt>Cgt	p.C282R	PLOD2_ENST00000282903.5_Missense_Mutation_p.C282R|PLOD2_ENST00000494950.1_Missense_Mutation_p.C227R|RP11-274H2.2_ENST00000480247.1_RNA	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	282					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)	TCGAATTCACAAAGAGTGCAG	0.343													A|||	3	0.000599042	0.0015	0.0014	5008	,	,		17493	0.0		0.0	False		,,,				2504	0.0				p.C282R		Atlas-SNP	.											.	PLOD2	81	.	0			c.T844C						PASS	.	A	ARG/CYS,ARG/CYS	9,4397	15.5+/-35.6	0,9,2194	104	92	96		844,844	6.1	0.7	3	dbSNP_134	96	0,8600		0,0,4300	yes	missense,missense	PLOD2	NM_000935.2,NM_182943.2	180,180	0,9,6494	GG,GA,AA		0.0,0.2043,0.0692	probably-damaging,probably-damaging	282/738,282/759	145809622	9,12997	2203	4300	6503	SO:0001583	missense	5352	exon8			ATTCACAAAGAGT	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.844T>C	3.37:g.145809622A>G	ENSP00000353170:p.Cys282Arg	115	0	0		136	53	0.389706	NM_182943	B3KWS3|Q59ED2|Q8N170	Missense_Mutation	SNP	ENST00000360060.3	37	CCDS3131.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.172440	0.78452	0.002043	0.0	ENSG00000152952	ENST00000282903;ENST00000360060;ENST00000494950	T;T;T	0.69306	-0.39;-0.37;-0.35	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	D	0.84651	0.5519	M	0.89353	3.025	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.996	D;D;P	0.91635	0.997;0.999;0.903	D	0.87463	0.2409	10	0.87932	D	0	-32.5497	15.6071	0.76682	1.0:0.0:0.0:0.0	.	227;282;282	E7ETU9;O00469;O00469-2	.;PLOD2_HUMAN;.	R	282;282;227	ENSP00000282903:C282R;ENSP00000353170:C282R;ENSP00000420094:C227R	ENSP00000282903:C282R	C	-	1	0	PLOD2	147292312	1.000000	0.71417	0.726000	0.30738	0.917000	0.54804	7.900000	0.87376	2.323000	0.78572	0.528000	0.53228	TGT	A|0.999;G|0.001	0.001	strong		0.343	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935		G	145809622	A	G	145809622	3	3	22	1	0	0	0	0	1	0	0	0	12111	130	5	3	1484	3	PLOD2	3	145809622	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	15015	145809622	52212808	938	3839											
PLSCR5	389158	hgsc.bcm.edu	37	chr3	146311832	146311832	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagtggaacagaaagtacGattgaagcagatgctttcct	14	9	11	7	1	0	4	0	1	0	3	1	6	1	5	1	1	4	3	1	1	4	3	rs12107687	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:146311832G>T	ENST00000443512.1	-	4	1331	c.328C>A	c.(328-330)Cgt>Agt	p.R110S	PLSCR5_ENST00000492200.1_Missense_Mutation_p.R110S|PLSCR5_ENST00000482567.1_Missense_Mutation_p.R98S	NM_001085420.1	NP_001078889.1	A0PG75	PLS5_HUMAN	phospholipid scramblase family, member 5	110			R -> S (in dbSNP:rs12107687).							endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|urinary_tract(1)	12						CAGAAAGTACGATTGAAGCAG	0.433													G|||	76	0.0151757	0.0545	0.0058	5008	,	,		14788	0.0		0.0	False		,,,				2504	0.0				p.R110S		Atlas-SNP	.											.	PLSCR5	35	.	0			c.C328A						PASS	.	G	SER/ARG	192,3650		3,186,1732	141	139	139		328	5.7	1	3	dbSNP_120	139	2,8270		0,2,4134	yes	missense	PLSCR5	NM_001085420.1	110	3,188,5866	TT,TG,GG		0.0242,4.9974,1.6015	probably-damaging	110/272	146311832	194,11920	1921	4136	6057	SO:0001583	missense	389158	exon4			AAGTACGATTGAA	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.328C>A	3.37:g.146311832G>T	ENSP00000390111:p.Arg110Ser	141	0	0		142	72	0.507042	NM_001085420	B2RXK5	Missense_Mutation	SNP	ENST00000443512.1	37	CCDS46931.1	20	0.009157509157509158	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	0	0.0	G	19.70	3.876593	0.72180	0.049974	2.42E-4	ENSG00000231213	ENST00000492200;ENST00000482567;ENST00000443512	T;T;T	0.56103	0.48;0.48;0.48	5.69	5.69	0.88448	Tubby, C-terminal (1);	.	.	.	.	T	0.44456	0.1294	H	0.94222	3.51	0.39506	D	0.968276	D;D	0.89917	0.984;1.0	P;D	0.83275	0.871;0.996	T	0.76570	-0.2911	9	0.87932	D	0	-22.5708	14.6371	0.68696	0.0:0.0:0.8546:0.1454	rs12107687;rs52836343;rs12107687	98;110	B2RXK5;A0PG75	.;PLS5_HUMAN	S	110;98;110	ENSP00000417184:R110S;ENSP00000418626:R98S;ENSP00000390111:R110S	ENSP00000390111:R110S	R	-	1	0	PLSCR5	147794522	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.190000	0.58365	2.679000	0.91253	0.650000	0.86243	CGT	G|0.987;T|0.013	0.013	strong		0.433	PLSCR5-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355365.1	XM_371670		T	146311832	G	T	146311832	3	4	22	1	0	0	0	0	1	0	0	0	12122	1058	37	4	503	4	PLSCR5	3	146311832	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	502210	146311832	51710598	939	3840											
CPB1	1360	hgsc.bcm.edu	37	chr3	148545789	148545789	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tctattatctcattattcagCgagaaggtgttccgtgttaa	10	16	8	7	2	3	1	2	0	2	1	5	2	4	1	1	1	1	2	1	1	5	6	rs80013498	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:148545789C>T	ENST00000491148.1	+	3	406	c.72C>T	c.(70-72)ggC>ggT	p.G24G	CPB1_ENST00000282957.4_Splice_Site_p.G24G			P15086	CBPB1_HUMAN	carboxypeptidase B1 (tissue)	24						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)			CATTATTCAGCGAGAAGGTGT	0.408													C|||	50	0.00998403	0.0356	0.0029	5008	,	,		21398	0.001		0.0	False		,,,				2504	0.0				p.G24G		Atlas-SNP	.											.	CPB1	74	.	0			c.C72T						PASS	.	C		163,4243	110.4+/-148.6	2,159,2042	101	103	102		72	-7.2	0.1	3	dbSNP_131	102	0,8600		0,0,4300	yes	coding-synonymous-near-splice	CPB1	NM_001871.2		2,159,6342	TT,TC,CC		0.0,3.6995,1.2533		24/418	148545789	163,12843	2203	4300	6503	SO:0001630	splice_region_variant	1360	exon2			ATTCAGCGAGAAG	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.72-1C>T	3.37:g.148545789C>T		111	0	0		146	71	0.486301	NM_001871	O60834|Q53XJ0|Q96BQ8	Silent	SNP	ENST00000491148.1	37	CCDS33874.1																																																																																			C|0.986;T|0.014	0.014	strong		0.408	CPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355928.1	NM_001871	Silent	T	148545789	C	T	148545789	5	4	22	1	0	0	0	0	0	0	1	0	3798	782	27	1	78	1	CPB1	3	148545789	Splice_Site	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2233957	148545789	49476641	940	3841											
CPA3	1359	hgsc.bcm.edu	37	chr3	148601596	148601596	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaactgccacctaaccatgaGgacttggtacgtagacaaaa	16	7	8	10	1	0	2	0	1	0	1	0	3	0	3	3	2	4	2	3	2	6	4	rs140411214	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:148601596G>A	ENST00000296046.3	+	9	1027	c.975G>A	c.(973-975)gaG>gaA	p.E325E	RP11-680B3.2_ENST00000488190.1_RNA	NM_001870.2	NP_001861.2	P15088	CBPA3_HUMAN	carboxypeptidase A3 (mast cell)	325					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)			CTAACCATGAGGACTTGGTAC	0.398													G|||	21	0.00419329	0.0151	0.0014	5008	,	,		20428	0.0		0.0	False		,,,				2504	0.0				p.E325E		Atlas-SNP	.											.	CPA3	75	.	0			c.G975A						PASS	.	G		66,4340	62.3+/-99.4	0,66,2137	96	80	86		975	0.8	0.1	3	dbSNP_134	86	0,8600		0,0,4300	no	coding-synonymous	CPA3	NM_001870.2		0,66,6437	AA,AG,GG		0.0,1.498,0.5075		325/418	148601596	66,12940	2203	4300	6503	SO:0001819	synonymous_variant	1359	exon9			CCATGAGGACTTG		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.975G>A	3.37:g.148601596G>A		136	0	0		143	67	0.468531	NM_001870	Q96E94	Silent	SNP	ENST00000296046.3	37	CCDS3138.1																																																																																			G|0.995;A|0.005	0.005	strong		0.398	CPA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355974.1	NM_001870		A	148601596	G	A	148601596	2	1	22	1	0	0	0	0	0	0	0	1	3793	991	35	2		2	CPA3	3	148601596	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	55807	148601596	49420834	941	3842											
GYG1	2992	hgsc.bcm.edu	37	chr3	148714662	148714662	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacatacaatcagctgttgcAtcttgcttctgagcaaggta	12	12	8	9	0	3	1	1	1	2	0	3	1	3	1	0	1	6	6	0	1	5	5	rs35054019	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:148714662A>T	ENST00000345003.4	+	4	752	c.452A>T	c.(451-453)cAt>cTt	p.H151L	GYG1_ENST00000296048.6_Missense_Mutation_p.H151L|GYG1_ENST00000484197.1_Missense_Mutation_p.H151L|GYG1_ENST00000483267.1_Missense_Mutation_p.H151L	NM_004130.3	NP_004121.2	P46976	GLYG_HUMAN	glycogenin 1	151					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)			CAGCTGTTGCATCTTGCTTCT	0.433													A|||	46	0.0091853	0.0348	0.0	5008	,	,		19931	0.0		0.0	False		,,,				2504	0.0				p.H151L		Atlas-SNP	.											.	GYG1	29	.	0			c.A452T						PASS	.	A	LEU/HIS,LEU/HIS,LEU/HIS	137,4269	98.5+/-137.1	1,135,2067	76	70	72		452,452,452	1.1	0.1	3	dbSNP_126	72	0,8600		0,0,4300	yes	missense,missense,missense	GYG1	NM_001184720.1,NM_001184721.1,NM_004130.3	99,99,99	1,135,6367	TT,TA,AA		0.0,3.1094,1.0534	benign,benign,benign	151/334,151/280,151/351	148714662	137,12869	2203	4300	6503	SO:0001583	missense	2992	exon4			TGTTGCATCTTGC	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.452A>T	3.37:g.148714662A>T	ENSP00000340736:p.His151Leu	154	0	0		179	85	0.47486	NM_004130	D3DNH0|D3DNH1|D3DNH2|Q6FHZ1|Q9UNV0	Missense_Mutation	SNP	ENST00000345003.4	37	CCDS3139.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	A	11.23	1.576606	0.28092	0.031094	0.0	ENSG00000163754	ENST00000345003;ENST00000296048;ENST00000483267;ENST00000484197;ENST00000492285;ENST00000461191	T;T;T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02;-0.02;-0.02	6.11	1.11	0.20524	.	0.519143	0.23943	N	0.043027	T	0.24431	0.0592	L	0.33339	1.005	0.20873	N	0.999833	B;B;B;B	0.13145	0.001;0.007;0.001;0.0	B;B;B;B	0.20184	0.004;0.028;0.01;0.005	T	0.31861	-0.9928	10	0.59425	D	0.04	-35.2266	9.9467	0.41613	0.7509:0.0:0.2491:0.0	rs35054019	151;151;151;151	G5E9W8;D3DNH0;P46976-2;P46976	.;.;.;GLYG_HUMAN	L	151;151;151;151;105;151	ENSP00000340736:H151L;ENSP00000296048:H151L;ENSP00000419499:H151L;ENSP00000420683:H151L;ENSP00000418297:H105L;ENSP00000420247:H151L	ENSP00000296048:H151L	H	+	2	0	GYG1	150197352	0.258000	0.24033	0.099000	0.21106	0.896000	0.52359	1.243000	0.32767	-0.028000	0.13850	-0.261000	0.10672	CAT	A|0.990;T|0.010	0.010	strong		0.433	GYG1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356046.1	NM_004130		T	148714662	A	T	148714662	3	4	22	1	0	0	0	0	1	0	0	0	6914	217	8	5	466	5	GYG1	3	148714662	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	113066	148714662	49307768	942	3843											
HLTF	6596	hgsc.bcm.edu	37	chr3	148768130	148768130	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taaacataaaaattcaagtgTacatctgattttatatgttg	16	16	5	4	0	2	1	1	1	1	0	2	1	2	1	0	0	2	2	0	0	9	8	rs16861365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:148768130T>C	ENST00000310053.5	-	15	1699	c.1506A>G	c.(1504-1506)gtA>gtG	p.V502V	HLTF_ENST00000392912.2_Silent_p.V502V|HLTF_ENST00000494055.1_Silent_p.V502V|HLTF_ENST00000465259.1_Silent_p.V501V	NM_003071.3|NM_139048.2	NP_003062.2|NP_620636.1	Q14527	HLTF_HUMAN	helicase-like transcription factor	502	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				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)			AATTCAAGTGTACATCTGATT	0.289													T|||	149	0.0297524	0.1097	0.0043	5008	,	,		15001	0.0		0.001	False		,,,				2504	0.0				p.V502V		Atlas-SNP	.											.	HLTF	87	.	0			c.A1506G						PASS	.	T	,	443,3959	207.5+/-228.8	25,393,1783	64	66	65		1506,1506	1.6	1	3	dbSNP_123	65	6,8578	4.3+/-15.6	0,6,4286	no	coding-synonymous,coding-synonymous	HLTF	NM_003071.3,NM_139048.2	,	25,399,6069	CC,CT,TT		0.0699,10.0636,3.4576	,	502/1010,502/1010	148768130	449,12537	2201	4292	6493	SO:0001819	synonymous_variant	6596	exon15			CAAGTGTACATCT	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.1506A>G	3.37:g.148768130T>C		157	0	0		161	84	0.521739	NM_139048	D3DNH3|Q14536|Q16051|Q7KYJ6|Q86YA5|Q92652|Q96KM9	Silent	SNP	ENST00000310053.5	37	CCDS33875.1																																																																																			T|0.956;C|0.044	0.044	strong		0.289	HLTF-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356064.1			C	148768130	T	C	148768130	2	2	22	1	0	0	0	0	0	0	0	1	7224	1625	57	3		3	HLTF	3	148768130	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	53468	148768130	49254300	943	3844											
CP	1356	hgsc.bcm.edu	37	chr3	148901300	148901300	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttttctctccactggaacaCggaatgtgctatcagtatac	10	13	7	11	1	2	0	1	0	1	0	4	2	3	2	1	2	3	2	1	2	5	5	rs115552500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:148901300C>T	ENST00000264613.6	-	13	2640	c.2378G>A	c.(2377-2379)cGt>cAt	p.R793H	CP_ENST00000462336.1_5'Flank	NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	793	F5/8 type A 3.|Plastocyanin-like 5.		R -> H. {ECO:0000269|PubMed:15557511}.		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)	CACTGGAACACGGAATGTGCT	0.373													C|||	61	0.0121805	0.0234	0.013	5008	,	,		13349	0.001		0.0169	False		,,,				2504	0.0031				p.R793H		Atlas-SNP	.											.	CP	112	.	0			c.G2378A	GRCh37	CM045287	CP	M	rs115552500	PASS	.	C	HIS/ARG	89,4317	74.1+/-112.3	1,87,2115	133	118	123		2378	-1.8	0	3	dbSNP_132	123	79,8521	46.3+/-105.2	0,79,4221	yes	missense	CP	NM_000096.3	29	1,166,6336	TT,TC,CC		0.9186,2.02,1.2917	possibly-damaging	793/1066	148901300	168,12838	2203	4300	6503	SO:0001583	missense	1356	exon13			GGAACACGGAATG	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.2378G>A	3.37:g.148901300C>T	ENSP00000264613:p.Arg793His	83	0	0		67	35	0.522388	NM_000096	Q14063|Q2PP18|Q9UKS4	Missense_Mutation	SNP	ENST00000264613.6	37	CCDS3141.1	25	0.011446886446886446	4	0.008130081300813009	8	0.022099447513812154	1	0.0017482517482517483	12	0.0158311345646438	C	14.94	2.684284	0.47991	0.0202	0.009186	ENSG00000047457	ENST00000264613;ENST00000494544	D;D	0.98937	-5.25;-5.25	5.39	-1.8	0.07907	Cupredoxin (2);	1.207680	0.05806	N	0.613068	D	0.93877	0.8041	L	0.49350	1.555	0.09310	N	1	P;P;P	0.47350	0.528;0.802;0.894	B;B;B	0.42653	0.279;0.394;0.394	D	0.90687	0.4610	10	0.42905	T	0.14	0.5473	6.2989	0.21101	0.0:0.338:0.3602:0.3019	.	793;793;793	A8K5A4;P00450;Q1L857	.;CERU_HUMAN;.	H	793;576	ENSP00000264613:R793H;ENSP00000420545:R576H	ENSP00000264613:R793H	R	-	2	0	CP	150383990	0.000000	0.05858	0.000000	0.03702	0.304000	0.27724	-0.336000	0.07863	-0.782000	0.04541	0.555000	0.69702	CGT	C|0.987;T|0.013	0.013	strong		0.373	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096		T	148901300	C	T	148901300	3	4	22	1	0	0	0	0	1	0	0	0	3789	536	19	1	847	1	CP	3	148901300	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	133170	148901300	49121130	944	3845											
TSC22D2	9819	hgsc.bcm.edu	37	chr3	150176316	150176316	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	atgatcaattatcccaactcCcaacccaacaggccaatcct	14	8	3	16	0	1	1	1	1	0	0	4	1	4	1	5	1	3	0	5	1	6	1	rs149526922	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:150176316C>A	ENST00000361875.3	+	4	3252	c.2236C>A	c.(2236-2238)Cca>Aca	p.P746T	TSC22D2_ENST00000361136.2_Missense_Mutation_p.P722T	NM_014779.2	NP_055594.1	O75157	T22D2_HUMAN	TSC22 domain family, member 2	746					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)			ATCCCAACTCCCAACCCAACA	0.438													C|||	2	0.000399361	0.0015	0.0	5008	,	,		19128	0.0		0.0	False		,,,				2504	0.0				p.P746T		Atlas-SNP	.											.	TSC22D2	42	.	0			c.C2236A						PASS	.	C	THR/PRO	9,4397	15.5+/-35.6	0,9,2194	117	113	115		2236	4.3	1	3	dbSNP_134	115	0,8600		0,0,4300	yes	missense	TSC22D2	NM_014779.2	38	0,9,6494	AA,AC,CC		0.0,0.2043,0.0692	possibly-damaging	746/781	150176316	9,12997	2203	4300	6503	SO:0001583	missense	9819	exon4			CAACTCCCAACCC	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.2236C>A	3.37:g.150176316C>A	ENSP00000354543:p.Pro746Thr	272	0	0		275	129	0.469091	NM_014779	D3DNI5|Q6PI50|Q9H2Z6|Q9H2Z7|Q9H2Z8	Missense_Mutation	SNP	ENST00000361875.3	37	CCDS3149.1	1|1	4.578754578754579E-4|4.578754578754579E-4	1|1	0.0020325203252032522|0.0020325203252032522	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	0.007|0.007	-1.972930|-1.972930	0.00452|0.00452	0.002043|0.002043	0.0|0.0	ENSG00000196428|ENSG00000196428	ENST00000466814|ENST00000543241;ENST00000361875;ENST00000361136	.|T;T	.|0.29917	.|1.55;1.56	5.38|5.38	4.27|4.27	0.50696|0.50696	.|.	0.273316|0.273316	0.25256|0.25256	N|N	0.031991|0.031991	T|T	0.09949|0.09949	0.0244|0.0244	N|N	0.04508|0.04508	-0.205|-0.205	0.28151|0.28151	N|N	0.92938|0.92938	.|B;B	.|0.33919	.|0.037;0.432	.|B;B	.|0.33196	.|0.023;0.159	T|T	0.35871|0.35871	-0.9771|-0.9771	6|10	.|0.02654	.|T	.|1	.|.	4.617|4.617	0.12432|0.12432	0.0:0.765:0.0:0.235|0.0:0.765:0.0:0.235	.|.	.|722;746	.|O75157-2;O75157	.|.;T22D2_HUMAN	H|T	169|195;746;722	.|ENSP00000354543:P746T;ENSP00000354893:P722T	.|ENSP00000354893:P722T	P|P	+|+	2|1	0|0	TSC22D2|TSC22D2	151659006|151659006	0.996000|0.996000	0.38824|0.38824	1.000000|1.000000	0.80357|0.80357	0.032000|0.032000	0.12392|0.12392	0.943000|0.943000	0.29030|0.29030	2.693000|2.693000	0.91896|0.91896	0.655000|0.655000	0.94253|0.94253	CCC|CCA	C|0.999;A|0.001	0.001	strong		0.438	TSC22D2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357123.2	NM_014779		A	150176316	C	A	150176316	3	1	22	1	0	0	0	0	1	0	0	0	16623	623	22	4	2250	4	TSC22D2	3	150176316	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1275016	150176316	47846114	945	3846											
EIF2A	83939	hgsc.bcm.edu	37	chr3	150285535	150285535	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgattttgtattatcaccTggaccccaaccatacaaggt	13	12	6	10	0	1	1	1	1	0	0	1	2	1	2	4	2	2	1	4	2	6	5	rs376872417	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:150285535T>C	ENST00000460851.1	+	7	640	c.531T>C	c.(529-531)ccT>ccC	p.P177P	EIF2A_ENST00000273435.5_Silent_p.P172P|EIF2A_ENST00000487799.1_Silent_p.P152P|SERP1_ENST00000490945.1_Intron|EIF2A_ENST00000406576.3_Silent_p.P116P|EIF2A_ENST00000383043.3_5'Flank|SERP1_ENST00000479209.1_Intron			Q9BY44	EIF2A_HUMAN	eukaryotic translation initiation factor 2A, 65kDa	177					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)			TATTATCACCTGGACCCCAAC	0.279													T|||	3	0.000599042	0.0023	0.0	5008	,	,		19889	0.0		0.0	False		,,,				2504	0.0				p.P177P		Atlas-SNP	.											.	EIF2A	59	.	0			c.T531C						PASS	.	T		3,3595		0,3,1796	77	67	70		531	2.2	1	3		70	0,8122		0,0,4061	no	coding-synonymous	EIF2A	NM_032025.3		0,3,5857	CC,CT,TT		0.0,0.0834,0.0256		177/586	150285535	3,11717	1799	4061	5860	SO:0001819	synonymous_variant	83939	exon7			ATCACCTGGACCC	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.531T>C	3.37:g.150285535T>C		174	0	0		187	95	0.508021	NM_032025	A8MPS6|B4DF96|B4DQ14|D3DNI9|Q5QTR2|Q7Z4E9|Q8NFM1|Q96EW9|Q96K81	Silent	SNP	ENST00000460851.1	37	CCDS46935.1																																																																																			.	.	weak		0.279	EIF2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357259.2	NM_032025		C	150285535	T	C	150285535	2	2	22	1	0	0	0	0	0	0	0	1	4997	1567	55	3		3	EIF2A	3	150285535	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	109219	150285535	47736895	946	3847											
FAM194A	131831	hgsc.bcm.edu	37	chr3	150391789	150391789	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagtcagaaacttgctccCatgtttgtagtgcttctcta	9	15	8	9	0	2	2	1	1	1	1	4	2	3	2	1	0	3	4	1	0	4	5	rs11919896	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:150391789C>T	ENST00000295910.6	-	11	1349	c.1297G>A	c.(1297-1299)Ggg>Agg	p.G433R	FAM194A_ENST00000491361.1_Missense_Mutation_p.G287R	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						AACTTGCTCCCATGTTTGTAG	0.338													C|||	120	0.0239617	0.084	0.0101	5008	,	,		20313	0.0		0.002	False		,,,				2504	0.0				p.G433R		Atlas-SNP	.											.	FAM194A	91	.	0			c.G1297A						PASS	.	C	ARG/GLY	318,4088	171.2+/-201.5	8,302,1893	153	148	149		1297	4.9	0.5	3	dbSNP_120	149	2,8598	1.2+/-3.3	0,2,4298	yes	missense	FAM194A	NM_152394.3	125	8,304,6191	TT,TC,CC		0.0233,7.2174,2.4604	probably-damaging	433/664	150391789	320,12686	2203	4300	6503	SO:0001583	missense	131831	exon11			TGCTCCCATGTTT																												ENST00000295910.6:c.1297G>A	3.37:g.150391789C>T	ENSP00000295910:p.Gly433Arg	78	0	0		62	30	0.483871	NM_152394		Missense_Mutation	SNP	ENST00000295910.6	37	CCDS3151.2	48	0.02197802197802198	42	0.08536585365853659	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	C	19.68	3.873229	0.72180	0.072174	2.33E-4	ENSG00000163645	ENST00000295910;ENST00000491361;ENST00000313811	T;T	0.14893	2.47;2.47	4.94	4.94	0.65067	.	0.238409	0.29307	N	0.012528	T	0.01905	0.0060	M	0.68593	2.085	0.39844	D	0.973152	D	0.89917	1.0	D	0.97110	1.0	T	0.00144	-1.1994	10	0.54805	T	0.06	-12.8489	17.0788	0.86593	0.0:1.0:0.0:0.0	rs11919896;rs52830969;rs11919896	433	Q7L0X2	F194A_HUMAN	R	433;287;391	ENSP00000295910:G433R;ENSP00000419366:G287R	ENSP00000295910:G433R	G	-	1	0	FAM194A	151874479	0.965000	0.33210	0.523000	0.27875	0.854000	0.48673	3.537000	0.53590	2.540000	0.85666	0.655000	0.94253	GGG	C|0.970;T|0.030	0.030	strong		0.338	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1			T	150391789	C	T	150391789	3	4	22	1	0	0	0	0	1	0	0	0	5531	594	21	2	710	2	FAM194A	3	150391789	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	106254	150391789	47630641	947	3848											
MED12L	116931	hgsc.bcm.edu	37	chr3	150874033	150874033	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atggcctccagcacgggcgaTggccctgtccctgtgccacc	5	7	12	17	2	0	0	0	0	0	0	2	1	2	0	6	3	2	1	6	3	0	0	rs61734152	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:150874033T>C	ENST00000474524.1	+	5	680	c.642T>C	c.(640-642)gaT>gaC	p.D214D	MED12L_ENST00000273432.4_Silent_p.D214D|MED12L_ENST00000422248.2_Silent_p.D214D|MED12L_ENST00000309237.4_Silent_p.D214D	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	214						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)			GCACGGGCGATGGCCCTGTCC	0.473													T|||	81	0.0161741	0.059	0.0029	5008	,	,		19291	0.0		0.001	False		,,,				2504	0.0				p.D214D		Atlas-SNP	.											MED12L,NS,carcinoma,+2,1	MED12L	271	1	0			c.T642C						PASS	.	T		264,4142	150.3+/-184.3	8,248,1947	113	106	109		642	-8.9	0	3	dbSNP_129	109	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	MED12L	NM_053002.4		8,252,6243	CC,CT,TT		0.0465,5.9918,2.0606		214/2146	150874033	268,12738	2203	4300	6503	SO:0001819	synonymous_variant	116931	exon5			GGGCGATGGCCCT	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.642T>C	3.37:g.150874033T>C		66	0	0		75	27	0.36	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Silent	SNP	ENST00000474524.1	37	CCDS33876.1																																																																																			T|0.983;C|0.017	0.017	strong		0.473	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		C	150874033	T	C	150874033	2	2	22	1	0	0	0	0	0	0	0	1	9438	1461	51	3		3	MED12L	3	150874033	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	482244	150874033	47148397	948	3849											
GPR87	53836	hgsc.bcm.edu	37	chr3	151017855	151017855	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatctcttacgacggcttacTtggtaattttgcaagcgtca	9	15	8	9	3	2	0	1	0	1	0	3	1	2	0	0	2	4	3	0	2	5	7	rs141290943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:151017855T>G	ENST00000260843.4	-	2	498	c.34A>C	c.(34-36)Aat>Cat	p.N12H	MED12L_ENST00000273432.4_Intron|MED12L_ENST00000474524.1_Intron|MED12L_ENST00000491549.1_Intron	NM_023915.3	NP_076404.3	Q9BY21	GPR87_HUMAN	G protein-coupled receptor 87	12					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)			GACGGCTTACTTGGTAATTTT	0.413													T|||	4	0.000798722	0.003	0.0	5008	,	,		18522	0.0		0.0	False		,,,				2504	0.0				p.N12H		Atlas-SNP	.											.	GPR87	52	.	0			c.A34C						PASS	.	T	HIS/ASN,	32,4374	37.6+/-69.7	0,32,2171	102	94	97		34,	1.4	1	3	dbSNP_134	97	1,8599	1.2+/-3.3	0,1,4299	yes	missense-near-splice,intron	GPR87,MED12L	NM_023915.3,NM_053002.4	68,	0,33,6470	GG,GT,TT		0.0116,0.7263,0.2537	benign,	12/359,	151017855	33,12973	2203	4300	6503	SO:0001630	splice_region_variant	53836	exon2			GCTTACTTGGTAA	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.34+1A>C	3.37:g.151017855T>G		76	0	0		73	44	0.60274	NM_023915	Q5KU35|Q96JZ8|Q9BXC2	Missense_Mutation	SNP	ENST00000260843.4	37	CCDS3157.1	.	.	.	.	.	.	.	.	.	.	T	9.296	1.051901	0.19827	0.007263	1.16E-4	ENSG00000138271	ENST00000260843	T	0.62232	0.04	4.49	1.38	0.22167	.	0.688041	0.13625	N	0.374112	T	0.28067	0.0692	N	0.08118	0	0.80722	D	1	B	0.17268	0.021	B	0.13407	0.009	T	0.04855	-1.0922	9	.	.	.	-0.5324	7.7237	0.28746	0.0:0.8001:0.0:0.1999	.	12	Q9BY21	GPR87_HUMAN	H	12	ENSP00000260843:N12H	.	N	-	1	0	GPR87	152500545	1.000000	0.71417	1.000000	0.80357	0.606000	0.37113	1.189000	0.32114	0.152000	0.19188	0.533000	0.62120	AAT	T|0.998;G|0.002	0.002	strong		0.413	GPR87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357788.1		Missense_Mutation	G	151017855	T	G	151017855	5	3	22	1	0	0	0	0	0	0	1	0	6724	1623	56	5	1050	5	GPR87	3	151017855	Splice_Site	SNP	T	TCGA-G8-6324-01A-11D-2210-10	143822	151017855	47004575	949	3850											
MED12L	116931	hgsc.bcm.edu	37	chr3	151127074	151127074	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctctttgctgcgcaagcacGgccctcccctcagctccctc	4	10	7	20	2	2	0	1	0	1	0	6	0	4	0	4	1	4	4	4	1	1	1	rs78970280	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:151127074G>A	ENST00000474524.1	+	38	5797	c.5759G>A	c.(5758-5760)cGg>cAg	p.R1920Q	MED12L_ENST00000273432.4_Intron	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	1920	Gln-rich.					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)			GCGCAAGCACGGCCCTCCCCT	0.527													G|||	36	0.0071885	0.0265	0.0014	5008	,	,		14258	0.0		0.0	False		,,,				2504	0.0				p.R1920Q		Atlas-SNP	.											MED12L,colon,carcinoma,-1,1	MED12L	271	1	0			c.G5759A						PASS	.	G	GLN/ARG	74,4332	66.4+/-103.9	1,72,2130	74	76	76		5759	5.8	1	3	dbSNP_132	76	0,8600		0,0,4300	yes	missense	MED12L	NM_053002.4	43	1,72,6430	AA,AG,GG		0.0,1.6795,0.569	probably-damaging	1920/2146	151127074	74,12932	2203	4300	6503	SO:0001583	missense	116931	exon38			AAGCACGGCCCTC	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.5759G>A	3.37:g.151127074G>A	ENSP00000417235:p.Arg1920Gln	81	0	0		71	32	0.450704	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	37	CCDS33876.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	G	15.65	2.896847	0.52121	0.016795	0.0	ENSG00000144893	ENST00000474524	T	0.55588	0.51	5.75	5.75	0.90469	Mediator complex, subunit Med12, catenin-binding (1);	0.133081	0.51477	D	0.000099	T	0.44582	0.1300	L	0.57536	1.79	0.80722	D	1	D	0.69078	0.997	D	0.70227	0.968	T	0.52734	-0.8536	10	0.23891	T	0.37	-27.2348	17.7294	0.88373	0.0:0.0:1.0:0.0	.	1920	Q86YW9	MD12L_HUMAN	Q	1920	ENSP00000417235:R1920Q	ENSP00000417235:R1920Q	R	+	2	0	MED12L	152609764	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.424000	0.52764	2.708000	0.92522	0.650000	0.86243	CGG	G|0.993;A|0.007	0.007	strong		0.527	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		A	151127074	G	A	151127074	3	1	22	1	0	0	0	0	1	0	0	0	9438	1116	39	1	5909	1	MED12L	3	151127074	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	109219	151127074	46895356	950	3851											
IGSF10	285313	hgsc.bcm.edu	37	chr3	151155197	151155197	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctatcagatactgataactTtgtggtccattggaaaatcg	12	13	9	7	1	1	2	1	1	0	1	3	3	2	3	1	2	2	1	1	2	5	5	rs141741834	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:151155197T>C	ENST00000282466.3	-	6	7151	c.7152A>G	c.(7150-7152)caA>caG	p.Q2384Q	IGSF10_ENST00000495443.1_5'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	2384	Ig-like C2-type 10.				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)			ACTGATAACTTTGTGGTCCAT	0.403													T|||	44	0.00878594	0.0333	0.0	5008	,	,		21182	0.0		0.0	False		,,,				2504	0.0				p.Q2384Q		Atlas-SNP	.											.	IGSF10	279	.	0			c.A7152G						PASS	.	T	,,	84,4322	70.9+/-108.8	0,84,2119	124	124	124		1233,1089,7152	-11.2	0	3	dbSNP_134	124	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	IGSF10	NM_001178145.1,NM_001178146.1,NM_178822.4	,,	0,84,6419	CC,CT,TT		0.0,1.9065,0.6459	,,	411/651,363/603,2384/2624	151155197	84,12922	2203	4300	6503	SO:0001819	synonymous_variant	285313	exon6			ATAACTTTGTGGT	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.7152A>G	3.37:g.151155197T>C		130	0	0		129	71	0.550388	NM_178822	Q86YJ9|Q8N772|Q8NA84	Silent	SNP	ENST00000282466.3	37	CCDS3160.1																																																																																			T|0.993;C|0.007	0.007	strong		0.403	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		C	151155197	T	C	151155197	2	2	22	1	0	0	0	0	0	0	0	1	7606	1838	64	3		3	IGSF10	3	151155197	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	28123	151155197	46867233	951	3852											
IGSF10	285313	hgsc.bcm.edu	37	chr3	151165106	151165106	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaagacagtggatgaatgtTgattggttgtgccttgtatt	10	15	13	3	0	0	3	0	2	0	1	0	5	0	4	1	2	1	3	1	2	3	6	rs35491609	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:151165106T>G	ENST00000282466.3	-	4	2662	c.2663A>C	c.(2662-2664)cAa>cCa	p.Q888P		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	888					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)			GGATGAATGTTGATTGGTTGT	0.428													T|||	37	0.00738818	0.0272	0.0014	5008	,	,		22524	0.0		0.0	False		,,,				2504	0.0				p.Q888P		Atlas-SNP	.											IGSF10,NS,carcinoma,-1,1	IGSF10	279	1	0			c.A2663C						PASS	.	T	PRO/GLN	99,4307	79.3+/-117.8	0,99,2104	356	355	355		2663	-5	0	3	dbSNP_126	355	0,8600		0,0,4300	yes	missense	IGSF10	NM_178822.4	76	0,99,6404	GG,GT,TT		0.0,2.2469,0.7612	benign	888/2624	151165106	99,12907	2203	4300	6503	SO:0001583	missense	285313	exon4			GAATGTTGATTGG	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.2663A>C	3.37:g.151165106T>G	ENSP00000282466:p.Gln888Pro	324	0	0		348	156	0.448276	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	37	CCDS3160.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	T	10.97	1.500447	0.26861	0.022469	0.0	ENSG00000152580	ENST00000282466	T	0.68903	-0.36	5.41	-5.03	0.02973	.	0.536026	0.15865	N	0.240805	T	0.20333	0.0489	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.08055	0.003	T	0.16541	-1.0399	10	0.20519	T	0.43	.	7.7274	0.28767	0.0:0.217:0.3727:0.4103	rs35491609	888	Q6WRI0	IGS10_HUMAN	P	888	ENSP00000282466:Q888P	ENSP00000282466:Q888P	Q	-	2	0	IGSF10	152647796	0.000000	0.05858	0.000000	0.03702	0.347000	0.29111	-0.226000	0.09139	-0.598000	0.05806	0.482000	0.46254	CAA	T|0.992;G|0.008	0.008	strong		0.428	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		G	151165106	T	G	151165106	3	3	22	1	0	0	0	0	1	0	0	0	7606	1812	63	5	5268	5	IGSF10	3	151165106	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	9909	151165106	46857324	952	3853											
DHX36	170506	hgsc.bcm.edu	37	chr3	154002774	154002774	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcttcttgtttatccaaagcGttctgtaaaggaagagtgtg	10	15	10	6	1	3	1	0	0	3	1	4	2	4	2	1	1	1	3	1	1	5	6	rs114098462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:154002774G>A	ENST00000496811.1	-	18	2114	c.2034C>T	c.(2032-2034)aaC>aaT	p.N678N	DHX36_ENST00000308361.6_Silent_p.N678N|DHX36_ENST00000329463.5_Silent_p.N664N|DHX36_ENST00000544526.1_Silent_p.N664N	NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	678					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)			TATCCAAAGCGTTCTGTAAAG	0.373													G|||	46	0.0091853	0.0325	0.0029	5008	,	,		19458	0.0		0.001	False		,,,				2504	0.0				p.N678N		Atlas-SNP	.											.	DHX36	98	.	0			c.C2034T						PASS	.	G	,	114,4292	87.8+/-126.4	1,112,2090	102	101	101		1992,2034	-4.6	0.8	3	dbSNP_132	101	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	DHX36	NM_001114397.1,NM_020865.2	,	1,112,6390	AA,AG,GG		0.0,2.5874,0.8765	,	664/995,678/1009	154002774	114,12892	2203	4300	6503	SO:0001819	synonymous_variant	170506	exon18			CAAAGCGTTCTGT	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.2034C>T	3.37:g.154002774G>A		155	0	0		172	75	0.436047	NM_020865	B2RB00|Q70JU3|Q8IYE5|Q9P240	Silent	SNP	ENST00000496811.1	37	CCDS3171.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	G	9.279	1.047589	0.19827	0.025874	0.0	ENSG00000174953	ENST00000469977	.	.	.	5.6	-4.64	0.03349	.	.	.	.	.	T	0.41096	0.1144	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61113	-0.7128	4	.	.	.	.	15.9172	0.79531	0.4712:0.0:0.5288:0.0	.	.	.	.	M	125	.	.	T	-	2	0	DHX36	155485468	0.990000	0.36364	0.828000	0.32881	0.775000	0.43874	0.509000	0.22707	-1.147000	0.02851	-0.880000	0.02959	ACG	G|0.992;A|0.008	0.008	strong		0.373	DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353349.1	NM_020865		A	154002774	G	A	154002774	2	1	22	1	0	0	0	0	0	0	0	1	4511	1136	40	1		1	DHX36	3	154002774	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2837668	154002774	44019656	953	3854											
C3orf33	285315	hgsc.bcm.edu	37	chr3	155493497	155493497	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaccttacttacttctcaaTgaagctataataggtaaagt	14	14	6	7	0	1	1	1	1	1	0	2	1	1	1	1	1	4	3	1	1	10	8	rs377018605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:155493497T>C	ENST00000340171.2	-	3	413	c.315A>G	c.(313-315)tcA>tcG	p.S105S	C3orf33_ENST00000534941.1_Silent_p.S62S			Q6P1S2	CC033_HUMAN	chromosome 3 open reading frame 33	105					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)			TACTTCTCAATGAAGCTATAA	0.269													T|||	6	0.00119808	0.0038	0.0014	5008	,	,		15710	0.0		0.0	False		,,,				2504	0.0				p.S62S		Atlas-SNP	.											.	C3orf33	18	.	0			c.A186G						PASS	.	T		16,3586		0,16,1785	67	70	69		186	-4.1	0.7	3		69	1,8111		0,1,4055	no	coding-synonymous	C3orf33	NM_173657.1		0,17,5840	CC,CT,TT		0.0123,0.4442,0.1451		62/252	155493497	17,11697	1801	4056	5857	SO:0001819	synonymous_variant	285315	exon4			TCTCAATGAAGCT	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.315A>G	3.37:g.155493497T>C		111	0	0		100	55	0.55	NM_173657	A8K1H5|Q86YE6|Q8IXA7|Q96NB5	Silent	SNP	ENST00000340171.2	37																																																																																				.	.	weak		0.269	C3orf33-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351167.1	NM_173657		C	155493497	T	C	155493497	2	2	22	1	0	0	0	0	0	0	0	1	2225	1451	51	3		3	C3orf33	3	155493497	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1490723	155493497	42528933	954	3855											
KCNAB1	7881	hgsc.bcm.edu	37	chr3	155838488	155838488	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agtctgggttttctgtagcaGggaaagacaaatctcccaag	12	10	11	8	0	3	1	0	0	3	1	4	2	3	2	1	2	1	3	1	2	4	3	rs67167156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:155838488G>C	ENST00000490337.1	+	1	152	c.88G>C	c.(88-90)Ggg>Cgg	p.G30R	KCNAB1_ENST00000389636.5_Missense_Mutation_p.G30R	NM_172160.2	NP_751892.1	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 1	30					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)			TTCTGTAGCAGGGAAAGACAA	0.547													G|||	90	0.0179712	0.0666	0.0029	5008	,	,		19474	0.0		0.0	False		,,,				2504	0.0				p.G30R		Atlas-SNP	.											.	KCNAB1	176	.	0			c.G88C						PASS	.	G	ARG/GLY	235,4171	139.6+/-175.2	6,223,1974	86	94	92		88	-2	0	3	dbSNP_130	92	2,8598	1.2+/-3.3	0,2,4298	yes	missense	KCNAB1	NM_172160.2	125	6,225,6272	CC,CG,GG		0.0233,5.3336,1.8222	benign	30/420	155838488	237,12769	2203	4300	6503	SO:0001583	missense	7881	exon1			GTAGCAGGGAAAG	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.88G>C	3.37:g.155838488G>C	ENSP00000419952:p.Gly30Arg	110	0	0		99	61	0.616162	NM_172160	A8K9H8|A8KAD4|B3KPZ4|Q13031|Q13302|Q16547|Q6PI60|Q99869	Missense_Mutation	SNP	ENST00000490337.1	37	CCDS3174.1	32	0.014652014652014652	31	0.06300813008130081	1	0.0027624309392265192	0	0.0	0	0.0	G	11.35	1.613207	0.28712	0.053336	2.33E-4	ENSG00000169282	ENST00000490337;ENST00000389636	T;T	0.10960	3.21;2.82	5.47	-1.96	0.07525	.	.	.	.	.	T	0.00608	0.0020	N	0.08118	0	0.09310	N	0.999998	B;B	0.19583	0.037;0.01	B;B	0.15870	0.014;0.014	T	0.37731	-0.9693	9	0.59425	D	0.04	-10.322	11.9133	0.52751	0.8314:0.0:0.1686:0.0	.	30;30	B7Z8E5;Q14722	.;KCAB1_HUMAN	R	30	ENSP00000419952:G30R;ENSP00000374287:G30R	ENSP00000374287:G30R	G	+	1	0	KCNAB1	157321182	0.884000	0.30299	0.000000	0.03702	0.802000	0.45316	0.538000	0.23160	-0.249000	0.09569	0.557000	0.71058	GGG	G|0.981;C|0.019	0.019	strong		0.547	KCNAB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351411.1	NM_003471		C	155838488	G	C	155838488	3	2	22	1	0	0	0	0	1	0	0	0	8018	1000	35	4	90	4	KCNAB1	3	155838488	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	344991	155838488	42183942	955	3856											
GFM1	85476	hgsc.bcm.edu	37	chr3	158372389	158372389	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccagtagagacaattcccAcccatttgtaggcctggctt	9	11	8	13	0	0	1	0	0	0	1	2	2	2	1	4	2	0	3	4	2	3	5			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:158372389A>C	ENST00000486715.1	+	8	1409	c.1052A>C	c.(1051-1053)cAc>cCc	p.H351P	GFM1_ENST00000478576.1_Missense_Mutation_p.H351P|GFM1_ENST00000264263.5_Missense_Mutation_p.H370P	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)			GACAATTCCCACCCATTTGTA	0.308																																					p.H351P		Atlas-SNP	.											.	GFM1	83	.	0			c.A1052C						PASS	.																																			SO:0001583	missense	85476	exon8			ATTCCCACCCATT	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.1052A>C	3.37:g.158372389A>C	ENSP00000419038:p.His351Pro	110	0	0		127	62	0.488189	NM_024996		Missense_Mutation	SNP	ENST00000486715.1	37	CCDS33885.1	.	.	.	.	.	.	.	.	.	.	A	13.40	2.225950	0.39300	.	.	ENSG00000168827	ENST00000486715;ENST00000478576;ENST00000264263;ENST00000312756	T;T;T	0.79845	-1.31;-1.31;-1.31	5.66	5.66	0.87406	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.216872	0.49305	D	0.000147	T	0.72930	0.3522	N	0.22421	0.69	0.80722	D	1	B;B;B	0.34161	0.439;0.203;0.047	B;B;B	0.39660	0.306;0.162;0.112	T	0.75445	-0.3315	10	0.72032	D	0.01	-10.9205	11.6275	0.51153	0.867:0.0:0.0:0.133	.	370;351;351	Q96RP9-2;Q96RP9;C9IZ01	.;EFGM_HUMAN;.	P	351;351;370;85	ENSP00000419038:H351P;ENSP00000418755:H351P;ENSP00000264263:H370P	ENSP00000264263:H370P	H	+	2	0	GFM1	159855083	0.996000	0.38824	0.988000	0.46212	0.739000	0.42172	5.152000	0.64882	2.140000	0.66376	0.533000	0.62120	CAC	.	.	none		0.308	GFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352271.1	NM_024996		C	158372389	A	C	158372389	3	2	22	1	0	0	0	0	1	0	0	0	6349	159	6	5	1082	5	GFM1	3	158372389	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2533901	158372389	39650041	956	3857											
ARL14	80117	hgsc.bcm.edu	37	chr3	160395483	160395483	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	atgaacacattaaaaatgtgCctgttgttctattagccaac	14	13	6	8	0	1	1	0	1	1	0	1	1	1	1	2	0	4	2	2	0	7	5	rs35633732	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:160395483C>A	ENST00000320767.2	+	1	536	c.349C>A	c.(349-351)Cct>Act	p.P117T		NM_025047.2	NP_079323.1	Q8N4G2	ARL14_HUMAN	ADP-ribosylation factor-like 14	117			P -> T (in dbSNP:rs35633732).		small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)	GTP binding (GO:0005525)			lung(6)	6			Lung(72;7.02e-05)|LUSC - Lung squamous cell carcinoma(72;7.23e-05)			TAAAAATGTGCCTGTTGTTCT	0.443													C|||	224	0.0447284	0.1641	0.0086	5008	,	,		21657	0.0		0.001	False		,,,				2504	0.0				p.P117T		Atlas-SNP	.											.	ARL14	16	.	0			c.C349A						PASS	.	C	THR/PRO	635,3771	273.1+/-271.2	46,543,1614	75	69	71		349	5.9	0.8	3	dbSNP_126	71	7,8593	5.0+/-18.6	0,7,4293	yes	missense	ARL14	NM_025047.2	38	46,550,5907	AA,AC,CC		0.0814,14.4122,4.9362	probably-damaging	117/193	160395483	642,12364	2203	4300	6503	SO:0001583	missense	80117	exon1			AATGTGCCTGTTG	AK026248	CCDS3192.1	3q25.33	2014-05-09	2005-11-03	2005-11-03	ENSG00000179674	ENSG00000179674		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	22974	protein-coding gene	gene with protein product		614439	"ADP-ribosylation factor 7"	ARF7		15367757	Standard	NM_025047		Approved	FLJ22595	uc003fdq.3	Q8N4G2	OTTHUMG00000159031	ENST00000320767.2:c.349C>A	3.37:g.160395483C>A	ENSP00000323847:p.Pro117Thr	118	0	0		123	122	0.99187	NM_025047	Q9H655	Missense_Mutation	SNP	ENST00000320767.2	37	CCDS3192.1	122	0.055860805860805864	100	0.2032520325203252	5	0.013812154696132596	4	0.006993006993006993	13	0.017150395778364115	C	16.30	3.085550	0.55861	0.144122	8.14E-4	ENSG00000179674	ENST00000320767	T	0.74315	-0.83	5.95	5.95	0.96441	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.00496	0.0016	M	0.75150	2.29	0.09310	P	0.99999024684	D	0.89917	1.0	D	0.97110	1.0	T	0.02539	-1.1144	9	0.54805	T	0.06	-21.0946	19.3683	0.94473	0.0:1.0:0.0:0.0	rs35633732;rs35633732	117	Q8N4G2	ARL14_HUMAN	T	117	ENSP00000323847:P117T	ENSP00000323847:P117T	P	+	1	0	ARL14	161878177	0.994000	0.37717	0.842000	0.33263	0.656000	0.38851	3.803000	0.55560	2.822000	0.97130	0.563000	0.77884	CCT	C|0.942;A|0.058	0.058	strong		0.443	ARL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352958.1	NM_025047		A	160395483	C	A	160395483	3	1	22	1	0	0	0	0	1	0	0	0	930	739	26	4	351	4	ARL14	3	160395483	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2023094	160395483	37626947	957	3858											
OTOL1	131149	hgsc.bcm.edu	37	chr3	161221262	161221262	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaggggtccgaggccccacTgggaagaagggctctcgggg	9	4	18	10	2	1	1	0	0	1	1	3	3	2	2	3	7	0	1	3	7	3	0	rs113998122	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:161221262T>A	ENST00000327928.4	+	4	966	c.966T>A	c.(964-966)acT>acA	p.T322T		NM_001080440.1	NP_001073909.1	A6NHN0	OTOL1_HUMAN	otolin 1	322	Collagen-like 3.					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						GAGGCCCCACTGGGAAGAAGG	0.572													T|||	50	0.00998403	0.0378	0.0	5008	,	,		13649	0.0		0.0	False		,,,				2504	0.0				p.T322T		Atlas-SNP	.											.	OTOL1	63	.	0			c.T966A						PASS	.	T		116,3608		0,116,1746	30	30	30		966	-7.4	0	3	dbSNP_132	30	2,8184		0,2,4091	no	coding-synonymous	OTOL1	NM_001080440.1		0,118,5837	AA,AT,TT		0.0244,3.1149,0.9908		322/478	161221262	118,11792	1862	4093	5955	SO:0001819	synonymous_variant	131149	exon4			CCCCACTGGGAAG		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.966T>A	3.37:g.161221262T>A		108	0	0		107	60	0.560748	NM_001080440		Silent	SNP	ENST00000327928.4	37	CCDS46948.1																																																																																			T|0.990;A|0.010	0.010	strong		0.572	OTOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353184.1	NM_001080440		A	161221262	T	A	161221262	2	1	22	1	0	0	0	0	0	0	0	1	11313	1567	55	5		5	OTOL1	3	161221262	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	825779	161221262	36801168	958	3859											
SI	6476	hgsc.bcm.edu	37	chr3	164750325	164750325	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attacctggttagaagcatcAtaagtgaaattggaatgagc	15	11	10	5	0	1	3	1	2	0	1	1	4	1	4	1	2	3	2	1	2	6	4	rs140829463	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:164750325A>G	ENST00000264382.3	-	24	2783	c.2721T>C	c.(2719-2721)taT>taC	p.Y907Y		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	907	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)	TAGAAGCATCATAAGTGAAAT	0.313										HNSCC(35;0.089)			A|||	2	0.000399361	0.0015	0.0	5008	,	,		14779	0.0		0.0	False		,,,				2504	0.0				p.Y907Y		Atlas-SNP	.											.	SI	500	.	0			c.T2721C						PASS	.	A		10,4394	16.8+/-37.8	0,10,2192	133	128	130		2721	1.2	0.3	3	dbSNP_134	130	0,8600		0,0,4300	no	coding-synonymous	SI	NM_001041.3		0,10,6492	GG,GA,AA		0.0,0.2271,0.0769		907/1828	164750325	10,12994	2202	4300	6502	SO:0001819	synonymous_variant	6476	exon24			AGCATCATAAGTG	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.2721T>C	3.37:g.164750325A>G		65	0	0		57	24	0.421053	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Silent	SNP	ENST00000264382.3	37	CCDS3196.1																																																																																			A|0.999;G|0.001	0.001	strong		0.313	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		G	164750325	A	G	164750325	2	3	22	1	0	0	0	0	0	0	0	1	14312	224	8	3		3	SI	3	164750325	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	3529063	164750325	33272105	959	3860											
MECOM	2122	hgsc.bcm.edu	37	chr3	168833976	168833976	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cctctcttcagaggacctctCgggctggagctccactggct	5	10	11	15	1	3	1	1	0	2	1	6	3	4	3	3	4	1	3	3	4	0	1	rs149928659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:168833976C>T	ENST00000464456.1	-	7	2320	c.1120G>A	c.(1120-1122)Gag>Aag	p.E374K	MECOM_ENST00000494292.1_Missense_Mutation_p.E562K|MECOM_ENST00000433243.2_Missense_Mutation_p.E375K|MECOM_ENST00000264674.3_Missense_Mutation_p.E439K|MECOM_ENST00000472280.1_Missense_Mutation_p.E375K|MECOM_ENST00000468789.1_Missense_Mutation_p.E374K|MECOM_ENST00000460814.1_Missense_Mutation_p.E374K|MECOM_ENST00000392736.3_Missense_Mutation_p.E374K	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						GAGGACCTCTCGGGCTGGAGC	0.493													C|||	2	0.000399361	0.0015	0.0	5008	,	,		17401	0.0		0.0	False		,,,				2504	0.0				p.E562K		Atlas-SNP	.											.	MECOM	216	.	0			c.G1684A						PASS	.						360	301	321					3																	168833976		2203	4300	6503	SO:0001583	missense	2122	exon8			ACCTCTCGGGCTG	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.1120G>A	3.37:g.168833976C>T	ENSP00000419770:p.Glu374Lys	240	0	0		187	90	0.481283	NM_004991	Q13466|Q6FH90	Missense_Mutation	SNP	ENST00000464456.1	37	CCDS54669.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	13.87	2.365132	0.41902	.	.	ENSG00000085276	ENST00000264674;ENST00000392736;ENST00000464456;ENST00000472280;ENST00000494292;ENST00000468789;ENST00000460814;ENST00000433243	T;T;T;T;T;T;T;T	0.07021	3.29;3.28;3.25;3.38;3.23;3.28;3.24;3.38	6.03	6.03	0.97812	.	0.000000	0.53938	D	0.000059	T	0.11495	0.0280	L	0.54323	1.7	0.51482	D	0.999928	P;P;P;P;P	0.45569	0.826;0.789;0.861;0.789;0.491	B;B;B;B;B	0.35510	0.204;0.128;0.101;0.182;0.06	T	0.01608	-1.1313	10	0.59425	D	0.04	-16.0383	20.5568	0.99304	0.0:1.0:0.0:0.0	.	562;375;562;439;374	Q03112-3;Q03112-6;E7EQ57;Q03112-4;Q03112	.;.;.;.;EVI1_HUMAN	K	439;374;374;375;562;374;374;375	ENSP00000264674:E439K;ENSP00000376493:E374K;ENSP00000419770:E374K;ENSP00000420048:E375K;ENSP00000417899:E562K;ENSP00000419995:E374K;ENSP00000420466:E374K;ENSP00000394302:E375K	ENSP00000264674:E439K	E	-	1	0	MECOM	170316670	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.830000	0.69324	2.861000	0.98227	0.655000	0.94253	GAG	C|0.999;T|0.001	0.001	strong		0.493	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351519.1	NM_005241, NM_004991		T	168833976	C	T	168833976	3	4	22	1	0	0	0	0	1	0	0	0	9431	893	31	1	2075	1	MECOM	3	168833976	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4083651	168833976	29188454	960	3861											
SEC62	7095	hgsc.bcm.edu	37	chr3	169700525	169700525	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aagcagttttttcaccgagcCctaaaagtaatgaaaatgaa	17	10	7	7	1	1	2	1	2	0	0	1	3	1	2	2	0	2	3	2	0	7	5	rs35176867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:169700525C>G	ENST00000337002.4	+	4	340	c.282C>G	c.(280-282)gcC>gcG	p.A94A	SEC62-AS1_ENST00000479626.1_RNA|SEC62_ENST00000480708.1_Silent_p.A94A	NM_003262.3	NP_003253.1	Q99442	SEC62_HUMAN	SEC62 homolog (S. cerevisiae)	94					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)			NS(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	9						TTCACCGAGCCCTAAAAGTAA	0.323													C|||	102	0.0203674	0.0749	0.0043	5008	,	,		16024	0.0		0.0	False		,,,				2504	0.0				p.A94A		Atlas-SNP	.											.	SEC62	27	.	0			c.C282G						PASS	.	C		246,4122	129.0+/-165.8	11,224,1949	63	75	71		282	-2.3	0.9	3	dbSNP_126	71	0,8592		0,0,4296	no	coding-synonymous	SEC62	NM_003262.3		11,224,6245	GG,GC,CC		0.0,5.6319,1.8981		94/400	169700525	246,12714	2184	4296	6480	SO:0001819	synonymous_variant	7095	exon4			CCGAGCCCTAAAA	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.282C>G	3.37:g.169700525C>G		176	0	0		195	98	0.502564	NM_003262	D3DNQ0|O00682|O00729	Silent	SNP	ENST00000337002.4	37	CCDS3210.1																																																																																			C|0.983;G|0.017	0.017	strong		0.323	SEC62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352043.1			G	169700525	C	G	169700525	2	3	22	1	0	0	0	0	0	0	0	1	14019	610	22	4		4	SEC62	3	169700525	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	866549	169700525	28321905	961	3862											
FNDC3B	64778	hgsc.bcm.edu	37	chr3	171969312	171969312	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gcaagaagcagcccaaagtcGaatgattcagacttgcaagg	15	6	11	9	1	1	3	1	1	0	2	2	4	1	3	1	1	3	3	1	1	5	2	rs34553291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:171969312G>C	ENST00000336824.4	+	6	870	c.771G>C	c.(769-771)tcG>tcC	p.S257S	FNDC3B_ENST00000415807.2_Silent_p.S257S|FNDC3B_ENST00000416957.1_Silent_p.S257S	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	257					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)		GCCCAAAGTCGAATGATTCAG	0.468													G|||	28	0.00559105	0.0212	0.0	5008	,	,		17937	0.0		0.0	False		,,,				2504	0.0				p.S257S		Atlas-SNP	.											FNDC3B,rectum,carcinoma,+1,1	FNDC3B	118	1	0			c.G771C						PASS	.	G	,	92,4314	75.7+/-113.9	0,92,2111	69	71	70		771,771	-7.6	0.1	3	dbSNP_126	70	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	FNDC3B	NM_001135095.1,NM_022763.3	,	0,92,6411	CC,CG,GG		0.0,2.0881,0.7074	,	257/1205,257/1205	171969312	92,12914	2203	4300	6503	SO:0001819	synonymous_variant	64778	exon6			AAAGTCGAATGAT	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.771G>C	3.37:g.171969312G>C		29	0	0		39	17	0.435897	NM_001135095	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Silent	SNP	ENST00000336824.4	37	CCDS3217.1																																																																																			G|0.993;C|0.007	0.007	strong		0.468	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763		C	171969312	G	C	171969312	2	2	22	1	0	0	0	0	0	0	0	1	5978	1045	37	4		4	FNDC3B	3	171969312	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2268787	171969312	26053118	962	3863											
ECT2	1894	hgsc.bcm.edu	37	chr3	172480580	172480580	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgaaccttcaaagaaactttAtgttgtcaagcaagaggcaa	16	10	8	7	0	2	3	2	1	0	2	2	3	2	3	1	1	3	3	1	1	7	4	rs138074177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:172480580A>G	ENST00000392692.3	+	10	1165	c.989A>G	c.(988-990)tAt>tGt	p.Y330C	ECT2_ENST00000232458.5_Missense_Mutation_p.Y299C|ECT2_ENST00000427830.1_Missense_Mutation_p.Y299C|ECT2_ENST00000540509.1_Missense_Mutation_p.Y330C|ECT2_ENST00000417960.1_Missense_Mutation_p.Y298C|ECT2_ENST00000441497.2_Missense_Mutation_p.Y299C	NM_001258315.1	NP_001245244.1	Q9H8V3	ECT2_HUMAN	epithelial cell transforming 2	330	BRCT 2. {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)			AAGAAACTTTATGTTGTCAAG	0.313													A|||	2	0.000399361	0.0008	0.0	5008	,	,		17827	0.0		0.001	False		,,,				2504	0.0				p.Y330C		Atlas-SNP	.											.	ECT2	79	.	0			c.A989G						PASS	.	A	CYS/TYR	3,4403	6.2+/-15.9	0,3,2200	89	90	90		896	4.7	1	3	dbSNP_134	90	2,8596	2.2+/-6.3	0,2,4297	yes	missense	ECT2	NM_018098.4	194	0,5,6497	GG,GA,AA		0.0233,0.0681,0.0384	probably-damaging	299/884	172480580	5,12999	2203	4299	6502	SO:0001583	missense	1894	exon10			AACTTTATGTTGT	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.989A>G	3.37:g.172480580A>G	ENSP00000376457:p.Tyr330Cys	163	0	0		144	74	0.513889	NM_001258315	Q0MT80|Q2M269|Q6U836|Q9NSV8|Q9NVW9	Missense_Mutation	SNP	ENST00000392692.3	37	CCDS58860.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	A|A	16.30|16.30	3.083153|3.083153	0.55861|0.55861	6.81E-4|6.81E-4	2.33E-4|2.33E-4	ENSG00000114346|ENSG00000114346	ENST00000444250|ENST00000232458;ENST00000392692;ENST00000427830;ENST00000417960;ENST00000441497;ENST00000540509	.|T;T;T;T;T;T	.|0.79141	.|-1.24;-1.24;-1.24;-1.24;-1.24;-1.24	5.84|5.84	4.65|4.65	0.58169|0.58169	.|.	.|0.105654	.|0.64402	.|D	.|0.000003	D|D	0.85106|0.85106	0.5621|0.5621	M|M	0.73598|0.73598	2.24|2.24	0.53688|0.53688	D|D	0.999974|0.999974	.|P;D;P;P	.|0.58620	.|0.783;0.983;0.941;0.929	.|B;P;P;P	.|0.61003	.|0.325;0.882;0.753;0.525	D|D	0.85632|0.85632	0.1271|0.1271	5|10	.|0.62326	.|D	.|0.03	-13.9317|-13.9317	11.9979|11.9979	0.53214|0.53214	0.8666:0.0:0.0:0.1334|0.8666:0.0:0.0:0.1334	.|.	.|330;330;299;298	.|Q9H8V3;Q9H8V3-3;G5E9L8;Q9H8V3-2	.|ECT2_HUMAN;.;.;.	V|C	2|299;330;299;298;299;330	.|ENSP00000232458:Y299C;ENSP00000376457:Y330C;ENSP00000401910:Y299C;ENSP00000415876:Y298C;ENSP00000412259:Y299C;ENSP00000443160:Y330C	.|ENSP00000232458:Y299C	M|Y	+|+	1|2	0|0	ECT2|ECT2	173963274|173963274	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	4.323000|4.323000	0.59221|0.59221	0.990000|0.990000	0.38787|0.38787	0.482000|0.482000	0.46254|0.46254	ATG|TAT	A|0.999;G|0.001	0.001	strong		0.313	ECT2-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345994.2	NM_018098		G	172480580	A	G	172480580	3	3	22	1	0	0	0	0	1	0	0	0	4903	449	16	3	926	3	ECT2	3	172480580	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	511268	172480580	25541850	963	3864											
FXR1	8087	hgsc.bcm.edu	37	chr3	180630500	180630500	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagctgacggtggaggttcgCggctctaacggggctttcta	6	10	16	9	4	2	1	0	1	2	0	3	3	2	2	0	6	2	4	0	6	2	4	rs1805578	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:180630500C>T	ENST00000357559.4	+	1	411	c.27C>T	c.(25-27)cgC>cgT	p.R9R	FXR1_ENST00000305586.7_5'UTR|FXR1_ENST00000468861.1_5'UTR|FXR1_ENST00000491674.1_Silent_p.R9R|FXR1_ENST00000480918.1_5'Flank|FXR1_ENST00000491062.1_Silent_p.R9R|FXR1_ENST00000445140.2_Silent_p.R9R	NM_001013438.2|NM_005087.3	NP_001013456.1|NP_005078.2	P51114	FXR1_HUMAN	fragile X mental retardation, autosomal homolog 1	9	Agenet-like 1.				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)			TGGAGGTTCGCGGCTCTAACG	0.592											OREG0015934	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	179	0.0357428	0.1263	0.0159	5008	,	,		11846	0.0		0.001	False		,,,				2504	0.0				p.R9R		Atlas-SNP	.											.	FXR1	75	.	0			c.C27T						PASS	.	C	,,	444,3962	214.1+/-233.5	22,400,1781	146	145	145		27,,27	0.7	1	3	dbSNP_92	145	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,utr-5,coding-synonymous	FXR1	NM_001013438.2,NM_001013439.2,NM_005087.3	,,	22,405,6076	TT,TC,CC		0.0581,10.0772,3.4523	,,	9/540,,9/622	180630500	449,12557	2203	4300	6503	SO:0001819	synonymous_variant	8087	exon1			GGTTCGCGGCTCT	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.27C>T	3.37:g.180630500C>T		312	1	0.00320513	1963	304	168	0.552632	NM_001013438	A8K9B8|Q7Z450|Q8N6R8	Silent	SNP	ENST00000357559.4	37	CCDS3238.1																																																																																			C|0.961;T|0.039	0.039	strong		0.592	FXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350265.5			T	180630500	C	T	180630500	2	4	22	1	0	0	0	0	0	0	0	1	6123	755	27	1		1	FXR1	3	180630500	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	8149920	180630500	17391930	964	3865											
MCF2L2	23101	hgsc.bcm.edu	37	chr3	182994744	182994744	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctttcaaagatttcttcaCtctgaagtgaaagaaatttt	13	15	7	6	0	4	4	2	2	2	2	4	4	4	4	0	1	0	1	0	1	4	5	rs61731401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:182994744C>T	ENST00000328913.3	-	15	2075	c.1778G>A	c.(1777-1779)aGt>aAt	p.S593N	MCF2L2_ENST00000473233.1_Splice_Site_p.S593N|MCF2L2_ENST00000447025.2_Splice_Site_p.S593N|MCF2L2_ENST00000414362.2_Splice_Site_p.S593N	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	593							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)			GATTTCTTCACTCTGAAGTGA	0.443													T|||	136	0.0271565	0.0983	0.0072	5008	,	,		13396	0.0		0.001	False		,,,				2504	0.0				p.S593N		Atlas-SNP	.											MCF2L2,brain,glioma,0,1	MCF2L2	164	1	0			c.G1778A						PASS	.	T	ASN/SER	379,4027	769.4+/-413.7	24,331,1848	23	23	23		1778	3.7	1	3	dbSNP_129	23	2,8598	800.0+/-407.4	0,2,4298	yes	missense-near-splice	MCF2L2	NM_015078.2	46	24,333,6146	TT,TC,CC		0.0233,8.6019,2.9294	benign	593/1115	182994744	381,12625	2203	4300	6503	SO:0001630	splice_region_variant	23101	exon15			TCTTCACTCTGAA	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.1777-1G>A	3.37:g.182994744C>T		131	0	0		104	47	0.451923	NM_015078	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Missense_Mutation	SNP	ENST00000328913.3	37	CCDS3243.1	46	0.021062271062271064	43	0.08739837398373984	3	0.008287292817679558	0	0.0	0	0.0	T	0.017	-1.489466	0.01018	0.086019	2.33E-4	ENSG00000053524	ENST00000328913;ENST00000473233;ENST00000447025;ENST00000437431;ENST00000414362	T;T;T;T	0.04603	4.59;4.6;3.71;3.59	4.9	3.66	0.41972	.	0.531863	0.17868	N	0.159298	T	0.00109	0.0003	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	0.57394	-0.7819	10	0.31617	T	0.26	.	4.0278	0.09695	0.1805:0.097:0.0:0.7224	.	593;593	Q86YR7-2;Q86YR7	.;MF2L2_HUMAN	N	593;593;593;129;593	ENSP00000328118:S593N;ENSP00000420070:S593N;ENSP00000388190:S593N;ENSP00000414131:S593N	ENSP00000328118:S593N	S	-	2	0	MCF2L2	184477438	1.000000	0.71417	1.000000	0.80357	0.162000	0.22319	1.042000	0.30303	1.010000	0.39314	-0.360000	0.07572	AGT	C|0.975;T|0.025	0.025	strong		0.443	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078	Missense_Mutation	T	182994744	C	T	182994744	5	4	22	1	0	0	0	0	0	0	1	0	9389	579	20	2	1630	2	MCF2L2	3	182994744	Splice_Site	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2364244	182994744	15027686	965	3866											
ABCC5	10057	hgsc.bcm.edu	37	chr3	183696387	183696387	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggagccacacccacagtgatGctctggaagtacccagcttt	10	8	10	13	0	1	1	0	1	1	0	1	3	1	3	3	2	4	3	3	2	2	2	rs1053386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:183696387G>A	ENST00000334444.6	-	9	1440	c.1200C>T	c.(1198-1200)agC>agT	p.S400S	ABCC5_ENST00000265586.6_Silent_p.S400S|ABCC5_ENST00000492216.1_5'UTR	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	400	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.			S -> G (in Ref. 1; AAD04169). {ECO:0000305}.	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)	CCACAGTGATGCTCTGGAAGT	0.488													G|||	455	0.0908546	0.3321	0.0216	5008	,	,		19202	0.0		0.001	False		,,,				2504	0.0				p.S400S		Atlas-SNP	.											.	ABCC5	142	.	0			c.C1200T						PASS	.	G		1053,3073		142,769,1152	91	108	103		1200	2.9	1	3	dbSNP_86	103	6,8404		0,6,4199	no	coding-synonymous	ABCC5	NM_005688.2		142,775,5351	AA,AG,GG		0.0713,25.5211,8.4477		400/1438	183696387	1059,11477	2063	4205	6268	SO:0001819	synonymous_variant	10057	exon9			AGTGATGCTCTGG	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.1200C>T	3.37:g.183696387G>A		46	0	0		49	49	1	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Silent	SNP	ENST00000334444.6	37	CCDS43176.1																																																																																			G|0.913;A|0.087	0.087	strong		0.488	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688		A	183696387	G	A	183696387	2	1	22	1	0	0	0	0	0	0	0	1	56	1310	46	2		2	ABCC5	3	183696387	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	701643	183696387	14326043	966	3867											
HTR3E	285242	hgsc.bcm.edu	37	chr3	183824398	183824398	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtggttgcagttcagccacGcgatggacgccatgctcttc	6	11	12	12	3	2	0	1	0	1	0	3	2	2	1	2	2	3	4	2	2	0	3	rs13324468	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:183824398G>A	ENST00000415389.2	+	9	1754	c.1288G>A	c.(1288-1290)Gcg>Acg	p.A430T	HTR3E_ENST00000440596.2_Missense_Mutation_p.A456T|HTR3E_ENST00000335304.2_Missense_Mutation_p.A445T|HTR3E_ENST00000436361.2_Missense_Mutation_p.A430T|HTR3E-AS1_ENST00000431427.1_RNA|HTR3E_ENST00000425359.2_Missense_Mutation_p.A415T	NM_001256613.1|NM_198313.2	NP_001243542.1|NP_938055.1	A5X5Y0	5HT3E_HUMAN	5-hydroxytryptamine (serotonin) receptor 3E, ionotropic	430			A -> T (in dbSNP:rs13324468).		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)	GTTCAGCCACGCGATGGACGC	0.607													G|||	210	0.0419329	0.1543	0.0086	5008	,	,		18903	0.0		0.0	False		,,,				2504	0.0				p.A456T	Melanoma(7;227 727 6634 44770)	Atlas-SNP	.											.	HTR3E	65	.	0			c.G1366A						PASS	.	G	THR/ALA	520,3886	239.0+/-250.2	27,466,1710	171	152	158		1333	-5.5	0	3	dbSNP_121	158	5,8595	4.3+/-15.6	0,5,4295	no	missense	HTR3E	NM_182589.2	58	27,471,6005	AA,AG,GG		0.0581,11.8021,4.0366	benign	445/472	183824398	525,12481	2203	4300	6503	SO:0001583	missense	285242	exon7			AGCCACGCGATGG	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.1288G>A	3.37:g.183824398G>A	ENSP00000401444:p.Ala430Thr	328	0	0		283	146	0.515901	NM_001256614	A8IKD7|E9PGF1|Q495G1|Q495G3|Q6V706|Q6V707|Q7Z6B2	Missense_Mutation	SNP	ENST00000415389.2	37	CCDS58868.1	109	0.04990842490842491	104	0.21138211382113822	5	0.013812154696132596	0	0.0	0	0.0	g	4.180	0.031992	0.08101	0.118021	5.81E-4	ENSG00000186038	ENST00000415389;ENST00000425359;ENST00000335304;ENST00000436361;ENST00000440596	D;D;D;D;D	0.81908	-1.55;-1.55;-1.55;-1.55;-1.55	4.07	-5.5	0.02576	Neurotransmitter-gated ion-channel transmembrane domain (1);	2.871980	0.03018	N	0.150396	T	0.00109	0.0003	N	0.04043	-0.29	0.80722	P	0.0	B;B;B;B;B	0.12013	0.001;0.0;0.005;0.001;0.001	B;B;B;B;B	0.11329	0.005;0.004;0.006;0.002;0.002	T	0.10019	-1.0648	9	0.49607	T	0.09	.	7.9969	0.30273	0.2122:0.3113:0.4765:0.0	rs13324468;rs56491361;rs13324468	456;430;430;445;415	E9PGF1;A5X5Y0;A5X5Y0-4;A5X5Y0-3;A5X5Y0-2	.;5HT3E_HUMAN;.;.;.	T	430;415;445;430;456	ENSP00000401444:A430T;ENSP00000401900:A415T;ENSP00000335511:A445T;ENSP00000395833:A430T;ENSP00000406050:A456T	ENSP00000335511:A445T	A	+	1	0	HTR3E	185307092	0.000000	0.05858	0.038000	0.18304	0.020000	0.10135	0.081000	0.14823	-1.048000	0.03238	-2.223000	0.00295	GCG	G|0.941;A|0.059	0.059	strong		0.607	HTR3E-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346284.1	NM_182589		A	183824398	G	A	183824398	3	1	22	1	0	0	0	0	1	0	0	0	7457	1087	38	1	1363	1	HTR3E	3	183824398	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	128011	183824398	14198032	967	3868											
ALG3	10195	hgsc.bcm.edu	37	chr3	183963000	183963000	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttgacctgaaaaagcagcaAccccagccccagcgctgggc	11	4	11	15	1	0	2	0	2	0	0	0	2	0	2	5	1	5	4	5	1	3	1	rs2233464	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:183963000A>G	ENST00000397676.3	-	4	621	c.591T>C	c.(589-591)ggT>ggC	p.G197G	ALG3_ENST00000445626.2_Silent_p.G149G|ALG3_ENST00000463495.1_5'Flank|ALG3_ENST00000455059.1_Silent_p.G157G|ALG3_ENST00000418734.2_Silent_p.G141G|EIF2B5_ENST00000444495.1_Intron	NM_005787.5	NP_005778.1	Q92685	ALG3_HUMAN	ALG3, alpha-1,3- mannosyltransferase	197					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|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)	alpha-1,3-mannosyltransferase activity (GO:0000033)|dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity (GO:0052925)			kidney(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	9	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			AAAAGCAGCAACCCCAGCCCC	0.542													G|||	247	0.0493211	0.1808	0.0115	5008	,	,		20053	0.0		0.0	False		,,,				2504	0.0				p.G197G		Atlas-SNP	.											.	ALG3	48	.	0			c.T591C						PASS	.	G	,	483,3459		24,435,1512	36	42	40		447,591	2	1	3	dbSNP_98	40	4,8306		0,4,4151	no	coding-synonymous,coding-synonymous	ALG3	NM_001006941.2,NM_005787.5	,	24,439,5663	GG,GA,AA		0.0481,12.2527,3.9749	,	149/391,197/439	183963000	487,11765	1971	4155	6126	SO:0001819	synonymous_variant	10195	exon4			GCAGCAACCCCAG	BC002839	CCDS46967.1, CCDS46968.1	3q27.3	2013-02-26	2013-02-26		ENSG00000214160	ENSG00000214160	2.4.1.258	"Dolichyl D-mannosyl phosphate dependent mannosyltransferases"	23056	protein-coding gene	gene with protein product	"carbohydrate deficient glycoprotein syndrome type IV", "dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase", "dol-P-Man dependent alpha-1,3- mannosyltransferase"	608750	"asparagine-linked glycosylation 3 homolog (yeast, alpha-1,3-mannosyltransferase)", "asparagine-linked glycosylation 3, alpha-1,3- mannosyltransferase homolog (S. cerevisiae)"			1058125	Standard	NM_005787		Approved	NOT56L, Not56, CDGS4, D16Ertd36e	uc003fne.2	Q92685	OTTHUMG00000156823	ENST00000397676.3:c.591T>C	3.37:g.183963000A>G		128	0	0		136	67	0.492647	NM_005787	A8JZZ6|Q9BT71	Silent	SNP	ENST00000397676.3	37	CCDS46968.1																																																																																			A|0.962;G|0.038	0.038	strong		0.542	ALG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346033.1	NM_005787		G	183963000	A	G	183963000	2	3	22	1	0	0	0	0	0	0	0	1	520	30	2	3		3	ALG3	3	183963000	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	138602	183963000	14059430	968	3869											
ECE2	9718	hgsc.bcm.edu	37	chr3	183967500	183967500	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcatggcctctccaggggcAggtagggcgcctccggagtt	6	7	16	12	2	1	0	0	0	1	0	3	1	2	1	4	6	1	4	4	6	1	2	rs2233461	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:183967500A>C	ENST00000402825.3	+	1	18	c.18A>C	c.(16-18)gcA>gcC	p.A6A	ALG3_ENST00000397676.3_5'Flank|ALG3_ENST00000445626.2_5'Flank|ALG3_ENST00000455059.1_5'Flank|ALG3_ENST00000418734.2_5'Flank|ECE2_ENST00000324557.4_Silent_p.A6A|EIF2B5_ENST00000444495.1_Intron	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2	6	Methyltransferase-like 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)			CTCCAGGGGCAGGTAGGGCGC	0.672											OREG0015944	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	246	0.0491214	0.1793	0.013	5008	,	,		15078	0.0		0.0	False		,,,				2504	0.0				p.A6A		Atlas-SNP	.											.	ECE2	303	.	0			c.A18C						PASS	.	C	,	533,3863		28,477,1693	18	21	20		18,18	-10.9	0	3	dbSNP_98	20	4,8584		0,4,4290	no	coding-synonymous,coding-synonymous	ECE2	NM_014693.3,NM_032331.3	,	28,481,5983	CC,CA,AA		0.0466,12.1247,4.1359	,	6/884,6/256	183967500	537,12447	2198	4294	6492	SO:0001819	synonymous_variant	9718	exon1			AGGGGCAGGTAGG	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.18A>C	3.37:g.183967500A>C		51	0	0	1988	58	34	0.586207	NM_014693	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Silent	SNP	ENST00000402825.3	37	CCDS3256.2																																																																																			A|0.943;C|0.057	0.057	strong		0.672	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693		C	183967500	A	C	183967500	2	2	22	1	0	0	0	0	0	0	0	1	4892	175	7	5		5	ECE2	3	183967500	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	4500	183967500	14054930	969	3870											
CAMK2N2	94032	hgsc.bcm.edu	37	chr3	183978936	183978936	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggccgatctggcccagcttGgggggtcgcttggcctggtt	2	10	17	12	3	1	0	0	0	1	0	2	1	1	0	3	7	1	3	3	7	0	3	rs75699255	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:183978936G>A	ENST00000296238.3	-	1	315	c.138C>T	c.(136-138)ccC>ccT	p.P46P	ECE2_ENST00000402825.3_Intron|EIF2B5_ENST00000444495.1_Intron	NM_033259.2	NP_150284.1	Q96S95	CK2N2_HUMAN	calcium/calmodulin-dependent protein kinase II inhibitor 2	46	Inhibitory domain. {ECO:0000250}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium-dependent protein kinase inhibitor activity (GO:0008427)					all_cancers(143;1.09e-10)|Ovarian(172;0.0339)		Epithelial(37;2.51e-33)|OV - Ovarian serous cystadenocarcinoma(80;5.69e-22)			GGCCCAGCTTGGGGGGTCGCT	0.736													G|||	200	0.0399361	0.146	0.0101	5008	,	,		8663	0.0		0.0	False		,,,				2504	0.0				p.P46P		Atlas-SNP	.											.	CAMK2N2	2	.	0			c.C138T						PASS	.	G	,	416,3990		19,378,1806	18	21	20		,138	-0.8	1	3	dbSNP_132	20	3,8597		0,3,4297	no	intron,coding-synonymous	ECE2,CAMK2N2	NM_014693.3,NM_033259.2	,	19,381,6103	AA,AG,GG		0.0349,9.4417,3.2216	,	,46/80	183978936	419,12587	2203	4300	6503	SO:0001819	synonymous_variant	94032	exon1			CAGCTTGGGGGGT	AY037149	CCDS3257.1	3q27.1	2006-03-27			ENSG00000163888	ENSG00000163888			24197	protein-coding gene	gene with protein product		608721				11444830, 9724800	Standard	NM_033259		Approved	CaM-KIIN	uc003fnj.1	Q96S95	OTTHUMG00000156821	ENST00000296238.3:c.138C>T	3.37:g.183978936G>A		42	0	0		50	31	0.62	NM_033259		Silent	SNP	ENST00000296238.3	37	CCDS3257.1																																																																																			G|0.962;A|0.038	0.038	strong		0.736	CAMK2N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346010.1	NM_033259		A	183978936	G	A	183978936	2	1	22	1	0	0	0	0	0	0	0	1	2606	1335	47	2		2	CAMK2N2	3	183978936	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	11436	183978936	14043494	970	3871											
ECE2	9718	hgsc.bcm.edu	37	chr3	184005719	184005719	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgtgaaggccacgtttgaccGgcaaagcaaagaaattgtga	14	7	12	8	3	0	4	0	3	0	1	0	4	0	4	2	2	1	3	2	2	4	2	rs35875049	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184005719G>A	ENST00000402825.3	+	11	1712	c.1712G>A	c.(1711-1713)cGg>cAg	p.R571Q	ECE2_ENST00000404464.3_Missense_Mutation_p.R453Q|ECE2_ENST00000357474.5_Missense_Mutation_p.R499Q|EIF2B5_ENST00000444495.1_Intron|ECE2_ENST00000359140.4_Missense_Mutation_p.R424Q	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2	571	Endothelin-converting enzyme 2 region.		R -> Q (in dbSNP:rs35875049).		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)			ACGTTTGACCGGCAAAGCAAA	0.483													G|||	185	0.0369409	0.1346	0.0101	5008	,	,		19271	0.0		0.0	False		,,,				2504	0.0				p.R571Q		Atlas-SNP	.											ECE2_ENST00000402825,colon,carcinoma,0,3	ECE2	303	3	0			c.G1712A						scavenged	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	421,3985	206.5+/-228.1	19,383,1801	78	70	73		1271,1496,1358,1712	4.1	1	3	dbSNP_126	73	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense	ECE2	NM_001037324.2,NM_001100120.1,NM_001100121.1,NM_014693.3	43,43,43,43	19,386,6098	AA,AG,GG		0.0349,9.5552,3.26	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	424/737,499/812,453/766,571/884	184005719	424,12582	2203	4300	6503	SO:0001583	missense	9718	exon11			TTGACCGGCAAAG	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.1712G>A	3.37:g.184005719G>A	ENSP00000384223:p.Arg571Gln	65	1	0.0153846		64	30	0.46875	NM_014693	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Missense_Mutation	SNP	ENST00000402825.3	37	CCDS3256.2	76	0.0347985347985348	73	0.1483739837398374	3	0.008287292817679558	0	0.0	0	0.0	G	10.80	1.452917	0.26161	0.095552	3.49E-4	ENSG00000145194	ENST00000402825;ENST00000359140;ENST00000404464;ENST00000357474;ENST00000430587	T;T;T;T;T	0.73897	-0.79;-0.79;-0.79;-0.79;-0.79	4.95	4.07	0.47477	Peptidase M13 (1);Metallopeptidase, catalytic domain (1);	0.167177	0.42682	N	0.000677	T	0.00300	0.0009	N	0.04203	-0.255	0.31828	P	0.62512	B;B;B;B;B;B;B	0.32829	0.028;0.134;0.386;0.009;0.334;0.11;0.307	B;B;B;B;B;B;B	0.26416	0.028;0.041;0.064;0.003;0.038;0.024;0.069	T	0.08330	-1.0727	9	0.18276	T	0.48	-16.4724	8.5975	0.33725	0.1774:0.0:0.8226:0.0	rs35875049	173;424;442;453;499;424;571	B4DHU4;B4DKF3;B4DF19;O60344-2;O60344-5;O60344-3;O60344	.;.;.;.;.;.;ECE2_HUMAN	Q	571;424;453;499;445	ENSP00000384223:R571Q;ENSP00000352052:R424Q;ENSP00000385846:R453Q;ENSP00000350066:R499Q;ENSP00000398444:R445Q	ENSP00000350066:R499Q	R	+	2	0	ECE2	185488413	0.996000	0.38824	1.000000	0.80357	0.786000	0.44442	2.550000	0.45811	1.078000	0.41014	-0.140000	0.14226	CGG	G|0.967;A|0.033	0.033	strong		0.483	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693		A	184005719	G	A	184005719	3	1	22	1	0	0	0	0	1	0	0	0	4892	1116	39	1	2318	1	ECE2	3	184005719	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	26783	184005719	14016711	971	3872											
PSMD2	5708	hgsc.bcm.edu	37	chr3	184023918	184023918	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccgcagttttgccaacacActggtggatgtgtgtgcata	8	13	11	9	1	0	0	0	0	0	0	1	1	1	1	2	2	3	3	2	2	2	4	rs34477849	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184023918A>G	ENST00000310118.4	+	14	2337	c.1779A>G	c.(1777-1779)acA>acG	p.T593T	PSMD2_ENST00000435761.1_Silent_p.T434T|PSMD2_ENST00000439383.1_Silent_p.T463T|EIF2B5_ENST00000444495.1_Intron	NM_002808.3	NP_002799.3	Q13200	PSMD2_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 2	593					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)	TTGCCAACACACTGGTGGATG	0.507											OREG0015947	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	103	0.0205671	0.0741	0.0072	5008	,	,		22790	0.0		0.0	False		,,,				2504	0.0				p.T593T	Colon(24;313 636 6917 9932 15554)	Atlas-SNP	.											.	PSMD2	56	.	0			c.A1779G						PASS	.	A		261,4145	150.3+/-184.3	8,245,1950	150	112	125		1779	-12	0	3	dbSNP_126	125	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	PSMD2	NM_002808.3		8,247,6248	GG,GA,AA		0.0233,5.9237,2.0221		593/909	184023918	263,12743	2203	4300	6503	SO:0001819	synonymous_variant	5708	exon14			CAACACACTGGTG	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.1779A>G	3.37:g.184023918A>G		284	1	0.00352113	1988	362	189	0.522099	NM_002808	B4DX07|B4DXY1|E7EW34|E9PCS3|Q12932|Q15321|Q53XQ4|Q96I12	Silent	SNP	ENST00000310118.4	37	CCDS3258.1	35	0.016025641025641024	33	0.06707317073170732	2	0.0055248618784530384	0	0.0	0	0.0	A	9.215	1.031899	0.19590	0.059237	2.33E-4	ENSG00000175166	ENST00000432855	.	.	.	6.0	-12.0	0.00017	.	.	.	.	.	T	0.04907	0.0132	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54077	-0.8347	4	.	.	.	-13.3765	7.9576	0.30051	0.2487:0.1375:0.4867:0.1271	rs34477849;rs34477849	.	.	.	R	54	.	.	H	+	2	0	PSMD2	185506612	0.000000	0.05858	0.009000	0.14445	0.973000	0.67179	-2.546000	0.00932	-2.989000	0.00280	-1.179000	0.01719	CAC	A|0.976;G|0.024	0.024	strong		0.507	PSMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345843.1	NM_002808		G	184023918	A	G	184023918	2	3	22	1	0	0	0	0	0	0	0	1	12710	146	6	3		3	PSMD2	3	184023918	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	18199	184023918	13998512	972	3873											
EIF4G1	1981	hgsc.bcm.edu	37	chr3	184039304	184039304	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccgtgaaactggggagccatAtcgcctctctccagaaccca	10	7	9	15	2	1	2	0	1	1	1	4	3	2	3	5	2	3	0	5	2	3	1	rs16858632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184039304A>G	ENST00000346169.2	+	10	1203	c.932A>G	c.(931-933)tAt>tGt	p.Y311C	EIF4G1_ENST00000382330.3_Missense_Mutation_p.Y318C|EIF4G1_ENST00000434061.2_Missense_Mutation_p.Y115C|EIF4G1_ENST00000342981.4_Missense_Mutation_p.Y311C|EIF4G1_ENST00000352767.3_Missense_Mutation_p.Y318C|EIF4G1_ENST00000441154.1_Missense_Mutation_p.Y147C|EIF4G1_ENST00000350481.5_Missense_Mutation_p.Y147C|EIF4G1_ENST00000427845.1_Missense_Mutation_p.Y224C|EIF4G1_ENST00000414031.1_Missense_Mutation_p.Y271C|EIF4G1_ENST00000424196.1_Missense_Mutation_p.Y318C|EIF4G1_ENST00000435046.2_Missense_Mutation_p.Y115C|EIF4G1_ENST00000392537.2_Missense_Mutation_p.Y224C|EIF4G1_ENST00000319274.6_Missense_Mutation_p.Y311C|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000411531.1_Missense_Mutation_p.Y271C	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	311			Y -> C (in dbSNP:rs16858632). {ECO:0000269|PubMed:21907011}.		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)			GGGGAGCCATATCGCCTCTCT	0.493													A|||	104	0.0207668	0.0749	0.0072	5008	,	,		19071	0.0		0.0	False		,,,				2504	0.0				p.Y318C		Atlas-SNP	.											.	EIF4G1	151	.	0			c.A953G						PASS	.	A	CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR	263,4143	151.0+/-185.0	8,247,1948	61	61	61		953,953,344,932,932,440,671	3.1	1	3	dbSNP_123	61	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense,missense,missense,missense	EIF4G1	NM_001194946.1,NM_001194947.1,NM_004953.4,NM_182917.4,NM_198241.2,NM_198242.2,NM_198244.2	194,194,194,194,194,194,194	8,250,6245	GG,GA,AA		0.0349,5.9691,2.0452	benign,benign,benign,benign,benign,benign,benign	318/1607,318/1607,115/1405,311/1601,311/1600,147/1436,224/1513	184039304	266,12740	2203	4300	6503	SO:0001583	missense	1981	exon11			AGCCATATCGCCT	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.932A>G	3.37:g.184039304A>G	ENSP00000316879:p.Tyr311Cys	157	0	0		137	64	0.467153	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Missense_Mutation	SNP	ENST00000346169.2	37	CCDS3259.1	36	0.016483516483516484	34	0.06910569105691057	2	0.0055248618784530384	0	0.0	0	0.0	A	11.01	1.512111	0.27036	0.059691	3.49E-4	ENSG00000114867	ENST00000346169;ENST00000414031;ENST00000392537;ENST00000444134;ENST00000450424;ENST00000421110;ENST00000382330;ENST00000426123;ENST00000350481;ENST00000352767;ENST00000427845;ENST00000342981;ENST00000319274;ENST00000424196;ENST00000411531;ENST00000444861;ENST00000441154;ENST00000428387;ENST00000434061;ENST00000427607;ENST00000457456;ENST00000435046	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.52526	4.06;4.06;3.96;0.66;2.96;2.96;4.06;3.13;3.87;4.06;3.97;4.06;4.06;4.06;4.06;2.54;3.87;0.81;3.87;0.84;1.32;3.87	5.5	3.12	0.35913	.	0.732877	0.13056	N	0.417280	T	0.02418	0.0074	N	0.19112	0.55	0.29831	N	0.830056	B;B;B;B	0.26081	0.0;0.0;0.141;0.001	B;B;B;B	0.22753	0.001;0.001;0.041;0.001	T	0.05468	-1.0883	10	0.54805	T	0.06	-0.6548	6.9547	0.24563	0.755:0.1607:0.0843:0.0	rs16858632;rs16858632	318;311;311;318	E9PFM1;D3DNT2;Q04637;B2RU10	.;.;IF4G1_HUMAN;.	C	311;271;224;115;311;318;318;252;147;318;224;311;311;318;271;147;147;115;115;115;115;115	ENSP00000316879:Y311C;ENSP00000391935:Y271C;ENSP00000376320:Y224C;ENSP00000407244:Y115C;ENSP00000391412:Y311C;ENSP00000413159:Y318C;ENSP00000371767:Y318C;ENSP00000403269:Y252C;ENSP00000317600:Y147C;ENSP00000338020:Y318C;ENSP00000407682:Y224C;ENSP00000343450:Y311C;ENSP00000323737:Y311C;ENSP00000416255:Y318C;ENSP00000395974:Y271C;ENSP00000398145:Y147C;ENSP00000399858:Y147C;ENSP00000411707:Y115C;ENSP00000411826:Y115C;ENSP00000409545:Y115C;ENSP00000399969:Y115C;ENSP00000404754:Y115C	ENSP00000323737:Y311C	Y	+	2	0	EIF4G1	185521998	0.889000	0.30405	0.999000	0.59377	0.971000	0.66376	1.202000	0.32271	1.106000	0.41623	0.533000	0.62120	TAT	A|0.976;G|0.024	0.024	strong		0.493	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917		G	184039304	A	G	184039304	3	3	22	1	0	0	0	0	1	0	0	0	5038	449	16	3	962	3	EIF4G1	3	184039304	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	15386	184039304	13983126	973	3874											
CHRD	8646	hgsc.bcm.edu	37	chr3	184099050	184099050	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggggtcgccgtaccaggggcCctggcagggtcagctgcaag	6	5	18	12	2	1	0	1	0	0	0	2	0	1	0	3	6	3	4	3	6	2	1	rs34095724	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184099050C>T	ENST00000204604.1	+	3	526	c.280C>T	c.(280-282)Cct>Tct	p.P94S	CHRD_ENST00000348986.3_Missense_Mutation_p.P94S|CHRD_ENST00000482805.1_3'UTR|CHRD_ENST00000545352.1_5'Flank|EIF2B5_ENST00000444495.1_Intron|CHRD_ENST00000450923.1_Missense_Mutation_p.P94S	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	94	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.		P -> S (in dbSNP:rs34095724).		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)			TACCAGGGGCCCTGGCAGGGT	0.657													C|||	195	0.0389377	0.093	0.0173	5008	,	,		14626	0.002		0.0378	False		,,,				2504	0.0204				p.P94S		Atlas-SNP	.											.	CHRD	149	.	0			c.C280T						PASS	.	C	SER/PRO	410,3994		18,374,1810	21	26	24		280	4.3	1	3	dbSNP_126	24	292,8302		2,288,4007	yes	missense	CHRD	NM_003741.2	74	20,662,5817	TT,TC,CC		3.3977,9.3097,5.4008	benign	94/956	184099050	702,12296	2202	4297	6499	SO:0001583	missense	8646	exon3			AGGGGCCCTGGCA	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.280C>T	3.37:g.184099050C>T	ENSP00000204604:p.Pro94Ser	232	0	0		259	135	0.521236	NM_003741	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Missense_Mutation	SNP	ENST00000204604.1	37	CCDS3266.1	92	0.04212454212454213	53	0.10772357723577236	9	0.024861878453038673	1	0.0017482517482517483	29	0.03825857519788918	C	3.315	-0.140029	0.06669	0.093097	0.033977	ENSG00000090539	ENST00000204604;ENST00000450923;ENST00000348986	T;T;T	0.13307	2.83;2.6;2.61	5.18	4.3	0.51218	von Willebrand factor, type C (3);	0.242099	0.43110	D	0.000610	T	0.00144	0.0004	N	0.12182	0.205	0.80722	D	1	B;B	0.11235	0.0;0.004	B;B	0.15870	0.007;0.014	T	0.49960	-0.8883	10	0.20519	T	0.43	-8.4545	7.7367	0.28819	0.0:0.5773:0.3366:0.0861	rs34095724	94;94	E7ESX1;Q9H2X0	.;CHRD_HUMAN	S	94	ENSP00000204604:P94S;ENSP00000408972:P94S;ENSP00000334036:P94S	ENSP00000204604:P94S	P	+	1	0	CHRD	185581744	0.001000	0.12720	1.000000	0.80357	0.678000	0.39670	0.462000	0.21956	1.169000	0.42739	0.561000	0.74099	CCT	C|0.949;T|0.051	0.051	strong		0.657	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741		T	184099050	C	T	184099050	3	4	22	1	0	0	0	0	1	0	0	0	3374	623	22	2	290	2	CHRD	3	184099050	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	59746	184099050	13923380	974	3875											
EHHADH	1962	hgsc.bcm.edu	37	chr3	184910042	184910042	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tactgctaggggagcctgccAagctttgccattctttcagg	7	12	11	11	0	2	0	1	0	1	0	2	1	2	1	3	3	6	2	3	3	3	5	rs11927618	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184910042A>G	ENST00000231887.3	-	7	2219	c.2144T>C	c.(2143-2145)tTg>tCg	p.L715S	EHHADH_ENST00000456310.1_Missense_Mutation_p.L619S|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	715			L -> S (in dbSNP:rs11927618).		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)			GGAGCCTGCCAAGCTTTGCCA	0.438													A|||	136	0.0271565	0.0976	0.0086	5008	,	,		19259	0.0		0.001	False		,,,				2504	0.0				p.L715S		Atlas-SNP	.											.	EHHADH	73	.	0			c.T2144C						PASS	.	A	SER/LEU,SER/LEU	328,4078	169.1+/-199.8	18,292,1893	71	77	75		1856,2144	5.9	1	3	dbSNP_120	75	2,8598		0,2,4298	yes	missense,missense	EHHADH	NM_001166415.1,NM_001966.3	145,145	18,294,6191	GG,GA,AA		0.0233,7.4444,2.5373	possibly-damaging,possibly-damaging	619/628,715/724	184910042	330,12676	2203	4300	6503	SO:0001583	missense	1962	exon7			CCTGCCAAGCTTT	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.2144T>C	3.37:g.184910042A>G	ENSP00000231887:p.Leu715Ser	126	0	0		128	67	0.523438	NM_001966	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Missense_Mutation	SNP	ENST00000231887.3	37	CCDS33901.1	42	0.019230769230769232	38	0.07723577235772358	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	A	14.60	2.584965	0.46110	0.074444	2.33E-4	ENSG00000113790	ENST00000231887;ENST00000456310	T;T	0.75050	-0.49;-0.9	5.91	5.91	0.95273	.	0.563402	0.17628	N	0.167493	T	0.06690	0.0171	N	0.14661	0.345	0.80722	D	1	P	0.48834	0.916	B	0.41988	0.372	T	0.16571	-1.0398	10	0.33940	T	0.23	-11.2071	11.1978	0.48724	0.8307:0.0:0.0:0.1693	rs11927618;rs11927618	715	Q08426	ECHP_HUMAN	S	715;619	ENSP00000231887:L715S;ENSP00000387746:L619S	ENSP00000231887:L715S	L	-	2	0	EHHADH	186392736	0.991000	0.36638	0.998000	0.56505	0.771000	0.43674	2.683000	0.46943	2.254000	0.74563	0.533000	0.62120	TTG	A|0.975;G|0.025	0.025	strong		0.438	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1			G	184910042	A	G	184910042	3	3	22	1	0	0	0	0	1	0	0	0	4984	131	5	3	31	3	EHHADH	3	184910042	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	810992	184910042	13112388	975	3876											
EHHADH	1962	hgsc.bcm.edu	37	chr3	184922267	184922267	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccacgatgctccggagggagTtgaccacttatttgctttcc	7	12	10	12	2	0	1	0	1	0	0	2	4	2	3	4	2	2	3	4	2	1	4	rs115754857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184922267T>C	ENST00000231887.3	-	6	922	c.847A>G	c.(847-849)Act>Gct	p.T283A	EHHADH_ENST00000456310.1_Missense_Mutation_p.T187A	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	283	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)			CCGGAGGGAGTTGACCACTTA	0.488													T|||	82	0.0163738	0.0605	0.0029	5008	,	,		21681	0.0		0.0	False		,,,				2504	0.0				p.T283A		Atlas-SNP	.											.	EHHADH	73	.	0			c.A847G						PASS	.	T	ALA/THR,ALA/THR	170,4236	112.1+/-150.2	3,164,2036	121	118	119		559,847	1.6	0.4	3	dbSNP_132	119	0,8600		0,0,4300	yes	missense,missense	EHHADH	NM_001166415.1,NM_001966.3	58,58	3,164,6336	CC,CT,TT		0.0,3.8584,1.3071	benign,benign	187/628,283/724	184922267	170,12836	2203	4300	6503	SO:0001583	missense	1962	exon6			AGGGAGTTGACCA	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.847A>G	3.37:g.184922267T>C	ENSP00000231887:p.Thr283Ala	61	0	0		56	21	0.375	NM_001966	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Missense_Mutation	SNP	ENST00000231887.3	37	CCDS33901.1	18	0.008241758241758242	17	0.034552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	T	7.470	0.646535	0.14451	0.038584	0.0	ENSG00000113790	ENST00000537544;ENST00000231887;ENST00000456310	T;T	0.74526	-0.44;-0.85	5.53	1.61	0.23674	.	0.442567	0.26761	N	0.022621	T	0.21674	0.0522	L	0.27053	0.805	0.09310	N	1	B	0.09022	0.002	B	0.11329	0.006	T	0.15492	-1.0435	10	0.35671	T	0.21	-3.3999	1.5805	0.02633	0.1344:0.1596:0.1395:0.5665	.	283	Q08426	ECHP_HUMAN	A	283;283;187	ENSP00000231887:T283A;ENSP00000387746:T187A	ENSP00000231887:T283A	T	-	1	0	EHHADH	186404961	0.100000	0.21855	0.382000	0.26119	0.937000	0.57800	1.287000	0.33284	0.035000	0.15519	-0.309000	0.09137	ACT	T|0.986;C|0.014	0.014	strong		0.488	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1			C	184922267	T	C	184922267	3	2	22	1	0	0	0	0	1	0	0	0	4984	1725	60	3	1332	3	EHHADH	3	184922267	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	12225	184922267	13100163	976	3877											
AHSG	197	hgsc.bcm.edu	37	chr3	186338634	186338634	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcgcacccccggaaaacacGcacagtggtgcagcctagtg	10	5	12	14	3	0	0	0	0	0	0	1	1	0	1	3	2	3	3	3	2	3	1	rs77385737	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:186338634G>A	ENST00000273784.5	+	7	1098	c.1022G>A	c.(1021-1023)cGc>cAc	p.R341H	AHSG_ENST00000411641.2_Missense_Mutation_p.R340H	NM_001622.2	NP_001613.2	P02765	FETUA_HUMAN	alpha-2-HS-glycoprotein	340					acute-phase response (GO:0006953)|negative regulation of bone mineralization (GO:0030502)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of phosphorylation (GO:0042326)|ossification (GO:0001503)|pinocytosis (GO:0006907)|positive regulation of phagocytosis (GO:0050766)|regulation of bone mineralization (GO:0030500)|regulation of inflammatory response (GO:0050727)|skeletal system development (GO:0001501)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|kinase inhibitor activity (GO:0019210)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(2)|stomach(1)	22	all_cancers(143;3.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.27e-20)	GBM - Glioblastoma multiforme(93;0.0463)		CGGAAAACACGCACAGTGGTG	0.602													.|||	17	0.00339457	0.0121	0.0	5008	,	,		21835	0.0		0.001	False		,,,				2504	0.0				p.R340H		Atlas-SNP	.											AHSG,NS,carcinoma,+1,1	AHSG	40	1	0			c.G1019A						scavenged	.	G	HIS/ARG	59,4347	58.1+/-94.6	1,57,2145	81	77	79		1019	1.7	0	3	dbSNP_132	79	2,8598	2.2+/-6.3	0,2,4298	yes	missense	AHSG	NM_001622.2	29	1,59,6443	AA,AG,GG		0.0233,1.3391,0.469	probably-damaging	340/368	186338634	61,12945	2203	4300	6503	SO:0001583	missense	197	exon7			AAACACGCACAGT	D67013, M16961	CCDS3278.1	3q27.3	2006-02-22			ENSG00000145192	ENSG00000145192			349	protein-coding gene	gene with protein product		138680				9322749, 7736783	Standard	NM_001622		Approved	FETUA, A2HS, HSGA	uc003fqk.4	P02765	OTTHUMG00000156605	ENST00000273784.5:c.1022G>A	3.37:g.186338634G>A	ENSP00000273784:p.Arg341His	124	1	0.00806452		169	86	0.508876	NM_001622	A8K9N6|B2R7G1|O14961|O14962|Q9P152	Missense_Mutation	SNP	ENST00000273784.5	37		5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	g	9.995	1.232001	0.22626	0.013391	2.33E-4	ENSG00000145192	ENST00000411641;ENST00000541510;ENST00000273784	T;T	0.05258	3.47;3.47	4.63	1.7	0.24286	.	0.972799	0.08447	N	0.944617	T	0.04634	0.0126	L	0.44542	1.39	0.09310	N	1	B;B;B	0.10296	0.003;0.002;0.001	B;B;B	0.06405	0.002;0.0;0.0	T	0.38436	-0.9661	10	0.44086	T	0.13	-0.6739	7.4138	0.27032	0.3211:0.508:0.1709:0.0	.	406;340;341	F5H0Q5;P02765;C9JV77	.;FETUA_HUMAN;.	H	340;406;341	ENSP00000393887:R340H;ENSP00000273784:R341H	ENSP00000273784:R341H	R	+	2	0	AHSG	187821328	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.305000	0.08188	0.216000	0.20781	-0.344000	0.07964	CGC	G|0.996;A|0.004	0.004	strong		0.602	AHSG-002	NOVEL	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000344762.1	NM_001622		A	186338634	G	A	186338634	3	1	22	1	0	0	0	0	1	0	0	0	420	1087	38	1	1045	1	AHSG	3	186338634	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1416367	186338634	11683796	977	3878											
ADIPOQ	9370	hgsc.bcm.edu	37	chr3	186570951	186570951	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gcttcccctgcccaagggggCctgcacaggttggatggcgg	5	7	16	13	1	0	0	0	0	0	0	1	1	1	1	4	6	2	3	4	6	1	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:186570951C>T	ENST00000412955.2	+	2	245	c.104C>T	c.(103-105)gCc>gTc	p.A35V	ADIPOQ-AS1_ENST00000422718.1_RNA|ADIPOQ_ENST00000444204.2_Missense_Mutation_p.A35V|ADIPOQ_ENST00000320741.2_Missense_Mutation_p.A35V			Q15848	ADIPO_HUMAN	adiponectin, C1Q and collagen domain containing	35					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)		CCCAAGGGGGCCTGCACAGGT	0.627																																					p.A35V		Atlas-SNP	.											.	ADIPOQ	35	.	0			c.C104T						PASS	.						51	52	51					3																	186570951		2203	4300	6503	SO:0001583	missense	9370	exon3			AGGGGGCCTGCAC	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.104C>T	3.37:g.186570951C>T	ENSP00000405611:p.Ala35Val	235	1	0.00425532		241	128	0.53112	NM_001177800	Q58EX9	Missense_Mutation	SNP	ENST00000412955.2	37	CCDS3284.1	.	.	.	.	.	.	.	.	.	.	C	14.75	2.627218	0.46944	.	.	ENSG00000181092	ENST00000412955;ENST00000320741;ENST00000444204	D;D;D	0.90676	-2.71;-2.71;-2.71	5.21	0.744	0.18353	.	0.825880	0.10698	N	0.644378	T	0.80396	0.4615	N	0.24115	0.695	0.19300	N	0.999976	B	0.06786	0.001	B	0.08055	0.003	T	0.64326	-0.6434	10	0.27082	T	0.32	.	4.1548	0.10256	0.139:0.4701:0.2975:0.0934	.	35	Q15848	ADIPO_HUMAN	V	35	ENSP00000405611:A35V;ENSP00000320709:A35V;ENSP00000389814:A35V	ENSP00000320709:A35V	A	+	2	0	ADIPOQ	188053645	0.068000	0.21057	0.807000	0.32361	0.936000	0.57629	1.784000	0.38674	0.213000	0.20722	0.655000	0.94253	GCC	.	.	none		0.627	ADIPOQ-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344490.2	NM_004797		T	186570951	C	T	186570951	3	4	22	1	0	0	0	0	1	0	0	0	317	739	26	2	106	2	ADIPOQ	3	186570951	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	232317	186570951	11451479	978	3879											
LPP	4026	hgsc.bcm.edu	37	chr3	188326955	188326955	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctattctttttagagctccActggttcaacagcctctcct	7	15	5	14	0	3	1	1	0	2	1	5	1	4	1	4	1	3	2	4	1	3	6	rs35417432	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:188326955A>G	ENST00000312675.4	+	6	682	c.436A>G	c.(436-438)Act>Gct	p.T146A	LPP_ENST00000448637.1_Missense_Mutation_p.T146A|LPP_ENST00000543006.1_Missense_Mutation_p.T146A|LPP_ENST00000471917.1_3'UTR	NM_001167672.1|NM_005578.3	NP_001161144.1|NP_005569.1	Q93052	LPP_HUMAN	LIM domain containing preferred translocation partner in lipoma	146	Pro-rich.		T -> A (in dbSNP:rs35417432).		cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)		HMGA2/LPP(161)	NS(1)|breast(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		TTAGAGCTCCACTGGTTCAAC	0.388			T	"HMGA2, MLL, C12orf9"	"lipoma, leukemia"								A|||	270	0.0539137	0.1899	0.0231	5008	,	,		16335	0.0		0.003	False		,,,				2504	0.0				p.T146A		Atlas-SNP	.		Dom	yes		3	3q28	4026	LIM domain containing preferred translocation partner in lipoma		"L, M"	.	LPP	72	.	0			c.A436G						PASS	.	A	ALA/THR,ALA/THR,ALA/THR	779,3627	315.2+/-294.0	66,647,1490	96	96	96		436,436,436	-2.5	0.2	3	dbSNP_126	96	10,8590	5.0+/-18.6	0,10,4290	yes	missense,missense,missense	LPP	NM_001167671.1,NM_001167672.1,NM_005578.3	58,58,58	66,657,5780	GG,GA,AA		0.1163,17.6804,6.0664	benign,benign,benign	146/613,146/466,146/613	188326955	789,12217	2203	4300	6503	SO:0001583	missense	4026	exon6			AGCTCCACTGGTT	AL833171	CCDS3291.1	3q27-q28	2004-03-02	2002-01-14		ENSG00000145012	ENSG00000145012			6679	protein-coding gene	gene with protein product		600700	"LIM domain-containing preferred translocation partner in lipoma"			8812423	Standard	XM_005247453		Approved		uc003frs.2	Q93052	OTTHUMG00000156387	ENST00000312675.4:c.436A>G	3.37:g.188326955A>G	ENSP00000318089:p.Thr146Ala	86	0	0		109	46	0.422018	NM_005578	A1L4L6|D3DNV6|Q8NFX5	Missense_Mutation	SNP	ENST00000312675.4	37	CCDS3291.1	99	0.04532967032967033	89	0.18089430894308944	9	0.024861878453038673	0	0.0	1	0.0013192612137203166	A	3.408	-0.120818	0.06838	0.176804	0.001163	ENSG00000145012	ENST00000448637;ENST00000416784;ENST00000312675;ENST00000543006	T;T;T;T	0.52057	2.06;1.09;0.68;0.68	5.64	-2.45	0.06481	.	0.868823	0.09583	N	0.782522	T	0.00039	0.0001	N	0.11560	0.145	0.80722	P	0.0	B;B;B	0.15930	0.015;0.0;0.0	B;B;B	0.10450	0.005;0.002;0.0	T	0.35001	-0.9806	9	0.07482	T	0.82	.	15.6517	0.77099	0.2645:0.0:0.7355:0.0	rs35417432	146;146;146	B7Z8W0;C9JUT4;Q93052	.;.;LPP_HUMAN	A	146	ENSP00000393602:T146A;ENSP00000410340:T146A;ENSP00000318089:T146A;ENSP00000438891:T146A	ENSP00000318089:T146A	T	+	1	0	LPP	189809649	0.000000	0.05858	0.211000	0.23655	0.179000	0.23085	-0.288000	0.08377	-0.925000	0.03775	0.533000	0.62120	ACT	A|0.939;G|0.061	0.061	strong		0.388	LPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344030.1	NM_005578		G	188326955	A	G	188326955	3	3	22	1	0	0	0	0	1	0	0	0	8932	159	6	3	450	3	LPP	3	188326955	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1756004	188326955	9695475	979	3880											
LPP	4026	hgsc.bcm.edu	37	chr3	188327555	188327555	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accagaaccctcctgggatgTatccagtcactggtcccaag	10	8	9	14	0	1	1	1	0	0	1	4	2	4	2	5	2	1	1	5	2	3	1	rs7645635	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:188327555T>C	ENST00000312675.4	+	6	1282	c.1036T>C	c.(1036-1038)Tat>Cat	p.Y346H	LPP_ENST00000448637.1_Missense_Mutation_p.Y346H|LPP_ENST00000543006.1_Missense_Mutation_p.Y346H|LPP_ENST00000471917.1_3'UTR	NM_001167672.1|NM_005578.3	NP_001161144.1|NP_005569.1	Q93052	LPP_HUMAN	LIM domain containing preferred translocation partner in lipoma	346	Pro-rich.		Y -> H (in dbSNP:rs7645635).		cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)		HMGA2/LPP(161)	NS(1)|breast(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		TCCTGGGATGTATCCAGTCAC	0.522			T	"HMGA2, MLL, C12orf9"	"lipoma, leukemia"								T|||	1002	0.20008	0.7126	0.0764	5008	,	,		18753	0.0		0.005	False		,,,				2504	0.002				p.Y346H		Atlas-SNP	.		Dom	yes		3	3q28	4026	LIM domain containing preferred translocation partner in lipoma		"L, M"	.	LPP	72	.	0			c.T1036C						PASS	.	T	HIS/TYR,,HIS/TYR	2581,1825		769,1043,391	42	42	42		1036,,1036	6.2	0.9	3	dbSNP_116	42	34,8564		0,34,4265	yes	missense,intron,missense	LPP	NM_001167671.1,NM_001167672.1,NM_005578.3	83,,83	769,1077,4656	CC,CT,TT		0.3954,41.4208,20.1092	probably-damaging,,probably-damaging	346/613,,346/613	188327555	2615,10389	2203	4299	6502	SO:0001583	missense	4026	exon6			GGGATGTATCCAG	AL833171	CCDS3291.1	3q27-q28	2004-03-02	2002-01-14		ENSG00000145012	ENSG00000145012			6679	protein-coding gene	gene with protein product		600700	"LIM domain-containing preferred translocation partner in lipoma"			8812423	Standard	XM_005247453		Approved		uc003frs.2	Q93052	OTTHUMG00000156387	ENST00000312675.4:c.1036T>C	3.37:g.188327555T>C	ENSP00000318089:p.Tyr346His	116	0	0		111	52	0.468468	NM_005578	A1L4L6|D3DNV6|Q8NFX5	Missense_Mutation	SNP	ENST00000312675.4	37	CCDS3291.1	360	0.16483516483516483	328	0.6666666666666666	28	0.07734806629834254	0	0.0	4	0.005277044854881266	T	16.16	3.043406	0.55003	0.585792	0.003954	ENSG00000145012	ENST00000448637;ENST00000312675;ENST00000543006;ENST00000415906	T;T;T;T	0.54866	1.79;0.55;0.55;1.41	6.17	6.17	0.99709	.	0.188754	0.37348	N	0.002140	T	0.00012	0.0000	M	0.66939	2.045	0.22050	P	0.999392708	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.965	T	0.47611	-0.9104	9	0.15499	T	0.54	.	16.0034	0.80327	0.0:0.0:0.0:1.0	rs7645635;rs52823079;rs57290235;rs7645635	346;346	C9JUT4;Q93052	.;LPP_HUMAN	H	346;346;346;183	ENSP00000393602:Y346H;ENSP00000318089:Y346H;ENSP00000438891:Y346H;ENSP00000393008:Y183H	ENSP00000318089:Y346H	Y	+	1	0	LPP	189810249	1.000000	0.71417	0.850000	0.33497	0.194000	0.23727	5.358000	0.66064	2.371000	0.80710	0.533000	0.62120	TAT	T|0.786;C|0.214	0.214	strong		0.522	LPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344030.1	NM_005578		C	188327555	T	C	188327555	3	2	22	1	0	0	0	0	1	0	0	0	8932	1638	57	3	1050	3	LPP	3	188327555	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	600	188327555	9694875	980	3881											
FGF12	2257	hgsc.bcm.edu	37	chr3	192078253	192078253	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtccttggtcccatcaatggTaccatctgggtgcatctgca	7	12	10	12	0	3	0	1	0	2	0	5	0	5	0	3	3	3	3	3	3	2	2	rs142373936		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:192078253T>C	ENST00000454309.2	-	2	1099	c.274A>G	c.(274-276)Acc>Gcc	p.T92A	FGF12_ENST00000430714.1_Intron|FGF12_ENST00000450716.1_Missense_Mutation_p.T30A|FGF12_ENST00000264730.3_Missense_Mutation_p.T30A|FGF12_ENST00000445105.2_Missense_Mutation_p.T30A	NM_021032.4	NP_066360.1	P61328	FGF12_HUMAN	fibroblast growth factor 12	92					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)		CCATCAATGGTACCATCTGGG	0.408													T|||	1	0.000199681	0.0008	0.0	5008	,	,		19416	0.0		0.0	False		,,,				2504	0.0				p.T92A		Atlas-SNP	.											.	FGF12	88	.	0			c.A274G						PASS	.	T	ALA/THR,ALA/THR	1,4405	2.1+/-5.4	0,1,2202	176	150	159		88,274	3	1	3	dbSNP_134	159	0,8600		0,0,4300	no	missense,missense	FGF12	NM_004113.5,NM_021032.4	58,58	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign,benign	30/182,92/244	192078253	1,13005	2203	4300	6503	SO:0001583	missense	2257	exon2			CAATGGTACCATC	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.274A>G	3.37:g.192078253T>C	ENSP00000413496:p.Thr92Ala	214	0	0		213	92	0.431925	NM_021032	B2R6B7|B2R976|O35339|P70376|Q8TBG5|Q92912|Q93001	Missense_Mutation	SNP	ENST00000454309.2	37	CCDS3301.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	13.05	2.121112	0.37436	2.27E-4	0.0	ENSG00000114279	ENST00000264730;ENST00000392454;ENST00000445105;ENST00000454309;ENST00000450716;ENST00000448795;ENST00000418610	D;D;D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53;-1.53;-1.53	5.53	3.03	0.35002	.	0.136032	0.64402	N	0.000002	T	0.70657	0.3249	L	0.48935	1.535	0.47441	D	0.999428	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.64846	-0.6311	10	0.42905	T	0.14	.	6.4797	0.22055	0.1389:0.0758:0.0:0.7853	.	30;92	P61328-2;P61328	.;FGF12_HUMAN	A	30;30;30;92;30;6;30	ENSP00000264730:T30A;ENSP00000393686:T30A;ENSP00000413496:T92A;ENSP00000397635:T30A;ENSP00000412904:T6A;ENSP00000395517:T30A	ENSP00000264730:T30A	T	-	1	0	FGF12	193560947	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.860000	0.39428	0.953000	0.37825	0.482000	0.46254	ACC	T|1.000;C|0.000	0.000	strong		0.408	FGF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343160.1	NM_021032		C	192078253	T	C	192078253	3	2	22	1	0	0	0	0	1	0	0	0	5849	1638	57	3	473	3	FGF12	3	192078253	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	3750698	192078253	5944177	981	3882											
ATP13A4	84239	hgsc.bcm.edu	37	chr3	193120459	193120459	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttcagagttgttcttcattGctctcaaatactggattgct	8	17	7	9	0	4	1	3	0	2	1	5	2	4	2	0	1	3	4	0	1	2	7	rs9863164	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:193120459G>A	ENST00000342695.4	-	30	3895	c.3573C>T	c.(3571-3573)agC>agT	p.S1191S	ATP13A4_ENST00000392443.3_Silent_p.S1172S|ATP13A4_ENST00000482964.1_5'UTR|ATP13A4_ENST00000400270.2_Silent_p.S207S	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	1191						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)		GTTCTTCATTGCTCTCAAATA	0.438													G|||	110	0.0219649	0.0802	0.0058	5008	,	,		18998	0.0		0.0	False		,,,				2504	0.0				p.S1191S		Atlas-SNP	.											.	ATP13A4	154	.	0			c.C3573T						PASS	.	G		302,4104	165.1+/-196.6	13,276,1914	91	89	90		3573	4.1	1	3	dbSNP_119	90	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	ATP13A4	NM_032279.2		13,280,6210	AA,AG,GG		0.0465,6.8543,2.3528		1191/1197	193120459	306,12700	2203	4300	6503	SO:0001819	synonymous_variant	84239	exon30			TTCATTGCTCTCA	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.3573C>T	3.37:g.193120459G>A		99	0	0		108	49	0.453704	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Silent	SNP	ENST00000342695.4	37	CCDS3304.2																																																																																			G|0.974;A|0.026	0.026	strong		0.438	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279		A	193120459	G	A	193120459	2	1	22	1	0	0	0	0	0	0	0	1	1126	1310	46	2		2	ATP13A4	3	193120459	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1042206	193120459	4901971	982	3883											
ATP13A4	84239	hgsc.bcm.edu	37	chr3	193120627	193120627	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcttttaatcatcatccaCagggctcgattttcaataac	12	14	4	11	1	4	0	3	0	1	0	6	1	5	0	1	1	1	1	1	1	3	5	rs61733355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:193120627C>T	ENST00000342695.4	-	30	3727	c.3405G>A	c.(3403-3405)ctG>ctA	p.L1135L	ATP13A4_ENST00000392443.3_Silent_p.L1116L|ATP13A4_ENST00000482964.1_5'UTR|ATP13A4_ENST00000400270.2_Silent_p.L151L	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	1135						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)		TCATCATCCACAGGGCTCGAT	0.448													C|||	72	0.014377	0.0522	0.0043	5008	,	,		18910	0.0		0.0	False		,,,				2504	0.0				p.L1135L		Atlas-SNP	.											.	ATP13A4	154	.	0			c.G3405A						PASS	.	C		237,4169	139.2+/-174.8	10,217,1976	74	71	72		3405	0	1	3	dbSNP_129	72	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	ATP13A4	NM_032279.2		10,220,6273	TT,TC,CC		0.0349,5.379,1.8453		1135/1197	193120627	240,12766	2203	4300	6503	SO:0001819	synonymous_variant	84239	exon30			CATCCACAGGGCT	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.3405G>A	3.37:g.193120627C>T		128	0	0		146	63	0.431507	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Silent	SNP	ENST00000342695.4	37	CCDS3304.2																																																																																			C|0.982;T|0.018	0.018	strong		0.448	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279		T	193120627	C	T	193120627	2	4	22	1	0	0	0	0	0	0	0	1	1126	465	17	2		2	ATP13A4	3	193120627	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	168	193120627	4901803	983	3884											
CPN2	1370	hgsc.bcm.edu	37	chr3	194062821	194062821	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgggggagaccagagagcGcgttgttgctcagcttcagg	7	8	16	10	2	2	2	2	0	0	2	2	4	2	2	2	3	3	4	2	3	0	3	rs146126834	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:194062821G>A	ENST00000323830.3	-	2	700	c.611C>T	c.(610-612)gCg>gTg	p.A204V	CPN2_ENST00000429275.1_Missense_Mutation_p.A204V	NM_001080513.2	NP_001073982	P22792	CPN2_HUMAN	carboxypeptidase N, polypeptide 2	204					protein stabilization (GO:0050821)|regulation of catalytic activity (GO:0050790)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	enzyme regulator activity (GO:0030234)	p.A204V(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|ovary(5)|prostate(1)	27	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.65e-05)		ACCAGAGAGCGCGTTGTTGCT	0.617													G|||	13	0.00259585	0.0083	0.0014	5008	,	,		20075	0.0		0.001	False		,,,				2504	0.0				p.A204V		Atlas-SNP	.											CPN2,NS,carcinoma,0,1	CPN2	56	1	1	Substitution - Missense(1)	endometrium(1)	c.C611T						PASS	.	G	VAL/ALA	46,4360	48.2+/-83.0	0,46,2157	47	52	50		611	-3.7	0	3	dbSNP_134	50	1,8599	1.2+/-3.3	0,1,4299	yes	missense	CPN2	NM_001080513.2	64	0,47,6456	AA,AG,GG		0.0116,1.044,0.3614	benign	204/546	194062821	47,12959	2203	4300	6503	SO:0001583	missense	1370	exon2			GAGAGCGCGTTGT	J05158	CCDS33920.1	3q29	2012-02-10	2007-02-23		ENSG00000178772	ENSG00000178772	3.4.17.3		2313	protein-coding gene	gene with protein product		603104	"carboxypeptidase N, polypeptide 2, 83kD"	ACBP		2378615, 9628828	Standard	XM_005269280		Approved		uc003fts.3	P22792	OTTHUMG00000156047	ENST00000323830.3:c.611C>T	3.37:g.194062821G>A	ENSP00000319464:p.Ala204Val	124	0	0		142	77	0.542253	NM_001080513	B2RPE7|Q86SU4|Q8N5V4	Missense_Mutation	SNP	ENST00000323830.3	37	CCDS33920.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	5.618	0.298668	0.10622	0.01044	1.16E-4	ENSG00000178772	ENST00000323830;ENST00000429275	T;T	0.57907	0.37;0.37	4.77	-3.7	0.04437	.	1.593460	0.04366	N	0.358343	T	0.19127	0.0459	N	0.25031	0.7	0.09310	N	1	P	0.39520	0.676	B	0.25759	0.063	T	0.14531	-1.0469	10	0.29301	T	0.29	.	1.8943	0.03254	0.2691:0.1002:0.1357:0.495	.	204	P22792	CPN2_HUMAN	V	204	ENSP00000319464:A204V;ENSP00000402232:A204V	ENSP00000319464:A204V	A	-	2	0	CPN2	195544516	0.000000	0.05858	0.000000	0.03702	0.297000	0.27493	-2.161000	0.01278	-0.371000	0.08004	-0.305000	0.09177	GCG	G|0.996;A|0.004	0.004	strong		0.617	CPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342856.2	NM_001080513		A	194062821	G	A	194062821	3	1	22	1	0	0	0	0	1	0	0	0	3812	1087	38	1	1030	1	CPN2	3	194062821	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	942194	194062821	3959609	984	3885											
TMEM44	93109	hgsc.bcm.edu	37	chr3	194325103	194325103	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgaacgggagggtacgacggGgggtcctgcagggacgcatc	8	5	19	9	4	0	1	0	1	0	0	2	4	1	3	1	6	3	3	1	6	2	1	rs745169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:194325103G>A	ENST00000392432.2	-	10	1435	c.1230C>T	c.(1228-1230)ccC>ccT	p.P410P	TMEM44_ENST00000473092.1_Silent_p.P363P|TMEM44_ENST00000347147.4_Silent_p.P363P|TMEM44_ENST00000381975.3_Missense_Mutation_p.P362L|TMEM44_ENST00000273580.7_Silent_p.P363P	NM_001166305.1	NP_001159777.1	Q2T9K0	TMM44_HUMAN	transmembrane protein 44	410						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)		GGTACGACGGGGGGTCCTGCA	0.657													G|||	314	0.0626997	0.2277	0.0101	5008	,	,		15940	0.002		0.001	False		,,,				2504	0.0031				p.P362L		Atlas-SNP	.											.	TMEM44	42	.	0			c.C1085T						PASS	.	G	,,LEU/PRO,	772,3568		78,616,1476	29	26	27		1089,1230,1085,1089	-5.4	0.4	3	dbSNP_86	27	9,8525		0,9,4258	yes	coding-synonymous,coding-synonymous,missense,coding-synonymous	TMEM44	NM_001011655.2,NM_001166305.1,NM_001166306.1,NM_138399.4	,,98,	78,625,5734	AA,AG,GG		0.1055,17.788,6.0665	,,,	363/429,410/476,362/397,363/439	194325103	781,12093	2170	4267	6437	SO:0001819	synonymous_variant	93109	exon9			CGACGGGGGGTCC	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.1230C>T	3.37:g.194325103G>A		104	0	0		131	65	0.496183	NM_001166306	A1L3V7|B7ZLZ5|B7ZLZ6|C9JJ62|E9PGA9|Q0P6F7|Q6ZT47|Q8IXR1|Q8N4G3	Missense_Mutation	SNP	ENST00000392432.2	37	CCDS54699.1	106	0.048534798534798536	102	0.2073170731707317	4	0.011049723756906077	0	0.0	0	0.0	G	11.04	1.523178	0.27211	0.17788	0.001055	ENSG00000145014	ENST00000381975;ENST00000429560	T	0.35789	1.29	5.23	-5.43	0.02632	.	0.095734	0.42964	D	0.000626	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999837588	B;B	0.09022	0.002;0.0	B;B	0.08055	0.003;0.002	T	0.09552	-1.0669	8	0.66056	D	0.02	-23.756	7.3059	0.26447	0.3646:0.466:0.1694:0.0	rs745169;rs745169	94;362	Q6PL43;Q2T9K0-4	.;.	L	362;94	ENSP00000371402:P362L	ENSP00000371402:P362L	P	-	2	0	TMEM44	195806392	0.819000	0.29175	0.431000	0.26735	0.097000	0.18754	-0.564000	0.05936	-1.360000	0.02172	0.447000	0.29281	CCC	G|0.930;A|0.070	0.070	strong		0.657	TMEM44-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000342750.1	NM_138399		A	194325103	G	A	194325103	2	1	22	1	0	0	0	0	0	0	0	1	16183	1232	43	2		2	TMEM44	3	194325103	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	262282	194325103	3697327	985	3886											
LSG1	55341	hgsc.bcm.edu	37	chr3	194371925	194371925	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtgttgattgttgaactcttAccaacattagggtagcccac	10	13	9	9	0	1	2	0	2	1	0	1	2	1	2	2	1	4	3	2	1	5	6	rs35636619	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:194371925A>G	ENST00000265245.5	-	9	1508	c.1194T>C	c.(1192-1194)ggT>ggC	p.G398G	AC046143.2_ENST00000582474.1_RNA	NM_018385.2	NP_060855.2	Q9H089	LSG1_HUMAN	large 60S subunit nuclear export GTPase 1	398	CP-type G. {ECO:0000255|PROSITE- ProRule:PRU01058}.				GTP catabolic process (GO:0006184)|nuclear export (GO:0051168)|protein transport (GO:0015031)|ribosome biogenesis (GO:0042254)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|large_intestine(2)|lung(9)	16	all_cancers(143;1.68e-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;7.55e-06)		TTGAACTCTTACCAACATTAG	0.418													A|||	13	0.00259585	0.0083	0.0014	5008	,	,		21914	0.0		0.001	False		,,,				2504	0.0				p.G398G		Atlas-SNP	.											.	LSG1	38	.	0			c.T1194C						PASS	.	A		13,4393	20.2+/-43.8	0,13,2190	162	146	151		1194	0.8	1	3	dbSNP_126	151	0,8600		0,0,4300	no	coding-synonymous	LSG1	NM_018385.2		0,13,6490	GG,GA,AA		0.0,0.2951,0.1		398/659	194371925	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	55341	exon9			ACTCTTACCAACA		CCDS33922.1	3q29	2013-08-21	2013-08-21		ENSG00000041802	ENSG00000041802			25652	protein-coding gene	gene with protein product		610780	"large subunit GTPase 1 homolog (S. cerevisiae)"			11230166	Standard	NM_018385		Approved	FLJ11301	uc003fui.3	Q9H089	OTTHUMG00000156021	ENST00000265245.5:c.1194T>C	3.37:g.194371925A>G		182	0	0		184	83	0.451087	NM_018385	A0JLT4|A0PJK3|A6NI18|Q7L9H8|Q9NUK8	Silent	SNP	ENST00000265245.5	37	CCDS33922.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	A	10.82	1.457387	0.26161	0.002951	0.0	ENSG00000041802	ENST00000437613	.	.	.	6.06	0.824	0.18818	.	.	.	.	.	T	0.40322	0.1112	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.28073	-1.0055	4	.	.	.	.	0.5788	0.00708	0.4085:0.17:0.2244:0.1971	rs35636619	.	.	.	A	132	.	.	V	-	2	0	LSG1	195853214	0.841000	0.29509	1.000000	0.80357	0.996000	0.88848	-0.065000	0.11617	0.549000	0.28973	0.533000	0.62120	GTA	A|0.999;G|0.001	0.001	strong		0.418	LSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342740.1	NM_018385		G	194371925	A	G	194371925	2	3	22	1	0	0	0	0	0	0	0	1	9058	378	14	3		3	LSG1	3	194371925	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	46822	194371925	3650505	986	3887											
MUC20	200958	hgsc.bcm.edu	37	chr3	195452679	195452679	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	catcaccccctcatggtcccCgggatctgacgtcactctcc	6	9	7	19	2	5	1	3	1	2	0	7	2	6	2	5	2	0	0	5	2	0	0			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195452679C>T	ENST00000447234.2	+	2	1331	c.1205C>T	c.(1204-1206)cCg>cTg	p.P402L	MUC20_ENST00000436408.1_Missense_Mutation_p.P402L|MUC20_ENST00000445522.2_Missense_Mutation_p.P367L|MUC20_ENST00000320736.6_Missense_Mutation_p.P231L	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	402					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)		TCATGGTCCCCGGGATCTGAC	0.577																																					p.P231L		Atlas-SNP	.											.	MUC20	84	.	0			c.C692T						PASS	.						4	3	4					3																	195452679		1669	3676	5345	SO:0001583	missense	200958	exon3			GGTCCCCGGGATC	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.1205C>T	3.37:g.195452679C>T	ENSP00000414350:p.Pro402Leu	609	0	0		990	191	0.192929	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	37		.	.	.	.	.	.	.	.	.	.	c	0.869	-0.732706	0.03135	.	.	ENSG00000176945	ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	T;T;T;T	0.11169	3.13;3.17;3.42;2.8	3.26	-6.52	0.01872	.	0.588934	0.14297	N	0.328508	T	0.02848	0.0085	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30995	-0.9959	10	0.87932	D	0	10.2224	0.1188	0.00063	0.242:0.2215:0.2078:0.3286	.	231	E9PH32	.	L	402;231;402;367	ENSP00000414350:P402L;ENSP00000325431:P231L;ENSP00000396774:P402L;ENSP00000405629:P367L	ENSP00000325431:P231L	P	+	2	0	MUC20	196938350	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.247000	0.02893	-2.014000	0.00948	-0.972000	0.02603	CCG	.	.	none		0.577	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673		T	195452679	C	T	195452679	3	4	22	1	0	0	0	0	1	0	0	0	9985	652	23	1	702	1	MUC20	3	195452679	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1080754	195452679	2569751	987	3888											
MUC4	4585	hgsc.bcm.edu	37	chr3	195481111	195481111	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgccgcccatccccagtcaGgtttggagggcaggcctcgc	5	7	14	15	2	1	0	1	0	0	0	3	1	2	1	5	4	1	2	5	4	0	1	rs73079395	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195481111G>T	ENST00000346145.4	-	18	2632	c.2593C>A	c.(2593-2595)Ctg>Atg	p.L865M	MUC4_ENST00000463781.3_Missense_Mutation_p.L5101M|MUC4_ENST00000349607.4_Missense_Mutation_p.L814M|MUC4_ENST00000475231.1_Missense_Mutation_p.L5049M	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	1858	Ser-rich.				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)		TCCCCAGTCAGGTTTGGAGGG	0.662													.|||	325	0.0648962	0.2322	0.0245	5008	,	,		15840	0.0		0.001	False		,,,				2504	0.0				p.L5101M		Atlas-SNP	.											.	MUC4	1505	.	0			c.C15301A						PASS	.	G	MET/LEU,MET/LEU,MET/LEU	900,3506		99,702,1402	63	67	65		2593,15301,2440	1.3	0.6	3	dbSNP_130	65	6,8594		0,6,4294	yes	missense,missense,missense	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	15,15,15	99,708,5696	TT,TG,GG		0.0698,20.4267,6.966	possibly-damaging,possibly-damaging,possibly-damaging	865/1177,5101/5413,814/1126	195481111	906,12100	2203	4300	6503	SO:0001583	missense	4585	exon19			CAGTCAGGTTTGG	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.2593C>A	3.37:g.195481111G>T	ENSP00000304207:p.Leu865Met	232	0	0		307	155	0.504886	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	37	CCDS3310.1	113	0.051739926739926737	106	0.21544715447154472	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	.	8.877	0.950622	0.18431	0.204267	6.98E-4	ENSG00000145113	ENST00000349607;ENST00000346145;ENST00000463781;ENST00000475231;ENST00000392409	T;T;T;T	0.46451	0.87;1.23;1.21;1.16	4.96	1.32	0.21799	.	0.408184	0.20459	N	0.091933	T	0.00039	0.0001	L	0.43757	1.38	0.80722	P	0.0	P;B;P;B;B;P	0.39352	0.554;0.254;0.494;0.057;0.057;0.669	B;B;B;B;B;B	0.42112	0.078;0.118;0.19;0.015;0.015;0.376	T	0.15292	-1.0442	9	0.32370	T	0.25	-1.7434	12.0729	0.53626	0.0:0.0:0.611:0.389	.	4973;814;865;5101;5049;1806	E7ESK3;Q99102-12;Q99102-13;E9PDY6;E7ENC5;Q99102-10	.;.;.;.;.;.	M	814;865;5101;5049;1601	ENSP00000338109:L814M;ENSP00000304207:L865M;ENSP00000417498:L5101M;ENSP00000420243:L5049M	ENSP00000304207:L865M	L	-	1	2	MUC4	196966782	0.986000	0.35501	0.621000	0.29145	0.157000	0.22087	0.811000	0.27198	0.329000	0.23460	0.436000	0.28706	CTG	G|0.924;T|0.076	0.076	strong		0.662	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406		T	195481111	G	T	195481111	3	4	22	1	0	0	0	0	1	0	0	0	9987	991	35	4	965	4	MUC4	3	195481111	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	28432	195481111	2541319	988	3889											
TFRC	7037	hgsc.bcm.edu	37	chr3	195787102	195787102	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aacagtgggctggcagaaacCttgaagttgctggtacctga	11	9	13	8	0	0	3	0	2	0	1	0	3	0	3	2	3	4	5	2	3	4	3	rs111276121	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195787102C>T	ENST00000360110.4	-	14	1654	c.1485G>A	c.(1483-1485)aaG>aaA	p.K495K	TFRC_ENST00000420415.1_Silent_p.K414K|TFRC_ENST00000465288.1_5'UTR|TFRC_ENST00000535031.1_Silent_p.K213K|TFRC_ENST00000540528.1_3'UTR|TFRC_ENST00000392396.3_Silent_p.K495K	NM_001128148.1	NP_001121620.1	P02786	TFR1_HUMAN	transferrin receptor	495					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)	TGGCAGAAACCTTGAAGTTGC	0.338			T	BCL6	NHL								C|||	9	0.00179712	0.0068	0.0	5008	,	,		19006	0.0		0.0	False		,,,				2504	0.0				p.K495K		Atlas-SNP	.		Dom	yes		3	3q29	7037	"transferrin receptor (p90, CD71)"		L	.	TFRC	54	.	0			c.G1485A						PASS	.	C	,	27,4379	33.5+/-64.1	0,27,2176	158	144	148		1485,1485	-0.4	1	3	dbSNP_132	148	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	TFRC	NM_001128148.1,NM_003234.2	,	0,27,6476	TT,TC,CC		0.0,0.6128,0.2076	,	495/761,495/761	195787102	27,12979	2203	4300	6503	SO:0001819	synonymous_variant	7037	exon14			AGAAACCTTGAAG	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.1485G>A	3.37:g.195787102C>T		177	0	0		164	86	0.52439	NM_001128148	D3DXB0|Q1HE24|Q59G55|Q9UCN0|Q9UCU5|Q9UDF9|Q9UK21	Silent	SNP	ENST00000360110.4	37	CCDS3312.1																																																																																			C|0.997;T|0.003	0.003	strong		0.338	TFRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341346.1			T	195787102	C	T	195787102	2	4	22	1	0	0	0	0	0	0	0	1	15827	680	24	2		2	TFRC	3	195787102	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	305991	195787102	2235328	989	3890											
ZDHHC19	131540	hgsc.bcm.edu	37	chr3	195935346	195935346	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatggcgcccgagtagaggCacagggacaggacaagcagc	12	2	16	11	2	0	1	0	0	0	1	0	4	0	3	1	4	2	4	1	4	2	1	rs75505676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195935346C>T	ENST00000296326.3	-	4	573	c.494G>A	c.(493-495)tGc>tAc	p.C165Y	ZDHHC19_ENST00000488508.1_5'UTR	NM_001039617.1	NP_001034706.1	Q8WVZ1	ZDH19_HUMAN	zinc finger, DHHC-type containing 19	165						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)		CGAGTAGAGGCACAGGGACAG	0.602													C|||	15	0.00299521	0.0098	0.0029	5008	,	,		16054	0.0		0.0	False		,,,				2504	0.0				p.C165Y		Atlas-SNP	.											.	ZDHHC19	25	.	0			c.G494A						PASS	.	C	TYR/CYS	41,4341		0,41,2150	117	137	130		494	4.7	1	3	dbSNP_131	130	0,8560		0,0,4280	yes	missense	ZDHHC19	NM_001039617.1	194	0,41,6430	TT,TC,CC		0.0,0.9356,0.3168	probably-damaging	165/310	195935346	41,12901	2191	4280	6471	SO:0001583	missense	131540	exon4			TAGAGGCACAGGG	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.494G>A	3.37:g.195935346C>T	ENSP00000296326:p.Cys165Tyr	242	0	0		244	116	0.47541	NM_001039617	A8MSY6|B3KVI1	Missense_Mutation	SNP	ENST00000296326.3	37	CCDS43190.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	C	19.39	3.817947	0.71028	0.009356	0.0	ENSG00000163958	ENST00000296326	T	0.24350	1.86	5.61	4.72	0.59763	Zinc finger, DHHC-type, palmitoyltransferase (1);	0.000000	0.64402	D	0.000008	T	0.44912	0.1316	M	0.93328	3.405	0.36364	D	0.860879	P	0.52463	0.953	P	0.54544	0.755	T	0.69262	-0.5191	10	0.66056	D	0.02	-33.5711	11.8273	0.52275	0.1753:0.8247:0.0:0.0	.	165	Q8WVZ1	ZDH19_HUMAN	Y	165	ENSP00000296326:C165Y	ENSP00000296326:C165Y	C	-	2	0	ZDHHC19	197419743	0.937000	0.31787	0.983000	0.44433	0.650000	0.38633	0.889000	0.28282	1.342000	0.45619	0.561000	0.74099	TGC	C|0.996;T|0.004	0.004	strong		0.602	ZDHHC19-007	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341533.1	NM_144637		T	195935346	C	T	195935346	3	4	22	1	0	0	0	0	1	0	0	0	17624	710	25	2	451	2	ZDHHC19	3	195935346	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	148244	195935346	2087084	990	3891											
C3orf43	255798	hgsc.bcm.edu	37	chr3	196234777	196234777	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttagtttttgacagatggtAtcaactcttcgagggatgac	10	14	11	6	1	2	3	1	2	1	1	3	5	2	4	0	2	1	3	0	2	3	5	rs187809363	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:196234777A>G	ENST00000397537.2	-	3	782	c.626T>C	c.(625-627)aTa>aCa	p.I209T		NM_001077657.1	NP_001071125.1	Q147U7	SMCO1_HUMAN	single-pass membrane protein with coiled-coil domains 1	209						integral component of membrane (GO:0016021)											gacagatggtatcaaCTCTTC	0.428													A|||	7	0.00139776	0.0053	0.0	5008	,	,		17582	0.0		0.0	False		,,,				2504	0.0				p.I209T		Atlas-SNP	.											C3orf43,NS,malignant_melanoma,+1,1	C3orf43	25	1	0			c.T626C						PASS	.	A	THR/ILE	15,3743		0,15,1864	111	102	105		626	4	0	3		105	0,8236		0,0,4118	yes	missense	C3orf43	NM_001077657.1	89	0,15,5982	GG,GA,AA		0.0,0.3991,0.1251	benign	209/215	196234777	15,11979	1879	4118	5997	SO:0001583	missense	255798	exon3			GATGGTATCAACT	AK123917	CCDS43192.1	3q29	2013-03-08	2013-03-08	2013-03-08	ENSG00000214097	ENSG00000214097			27407	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 43"	C3orf43			Standard	NM_001077657		Approved	FLJ41923, DKFZp313B0440		Q147U7	OTTHUMG00000155581	ENST00000397537.2:c.626T>C	3.37:g.196234777A>G	ENSP00000380671:p.Ile209Thr	187	0	0		208	97	0.466346	NM_001077657	B3KW20	Missense_Mutation	SNP	ENST00000397537.2	37	CCDS43192.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	A	11.14	1.550303	0.27739	0.003991	0.0	ENSG00000214097	ENST00000397537	T	0.36340	1.26	5.39	4.03	0.46877	.	.	.	.	.	T	0.28067	0.0692	L	0.29908	0.895	0.09310	N	1	B;B	0.26195	0.144;0.144	B;B	0.27715	0.051;0.082	T	0.18999	-1.0319	9	0.72032	D	0.01	-4.7237	9.3415	0.38082	0.9032:0.0:0.0968:0.0	.	209;201	Q147U7;E9PGG7	CC043_HUMAN;.	T	209	ENSP00000380671:I209T	ENSP00000380671:I209T	I	-	2	0	C3orf43	197719174	0.957000	0.32711	0.010000	0.14722	0.013000	0.08279	2.479000	0.45197	2.054000	0.61138	0.533000	0.62120	ATA	A|0.999;G|0.001	0.001	strong		0.428	SMCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340776.1	NM_001006109		G	196234777	A	G	196234777	3	3	22	1	0	0	0	0	1	0	0	0	2232	449	16	3	22	3	C3orf43	3	196234777	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	299431	196234777	1787653	991	3892											
C3orf43	255798	hgsc.bcm.edu	37	chr3	196235191	196235191	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtataaaatattcaattccAttgaagtgagcctacaaaaa	18	12	5	6	0	1	2	1	2	0	0	2	2	2	2	2	0	2	1	2	0	9	7	rs73891273	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:196235191A>G	ENST00000397537.2	-	3	368	c.212T>C	c.(211-213)aTg>aCg	p.M71T		NM_001077657.1	NP_001071125.1	Q147U7	SMCO1_HUMAN	single-pass membrane protein with coiled-coil domains 1	71						integral component of membrane (GO:0016021)											ATTCAATTCCATTGAAGTGAG	0.358													.|||	265	0.0529153	0.1876	0.0231	5008	,	,		16968	0.0		0.001	False		,,,				2504	0.0				p.M71T		Atlas-SNP	.											C3orf43,NS,carcinoma,+1,1	C3orf43	25	1	0			c.T212C						PASS	.	A	THR/MET	559,3137		45,469,1334	62	60	60		212	5.5	1	3	dbSNP_130	60	5,8181		0,5,4088	yes	missense	C3orf43	NM_001077657.1	81	45,474,5422	GG,GA,AA		0.0611,15.1245,4.7467	possibly-damaging	71/215	196235191	564,11318	1848	4093	5941	SO:0001583	missense	255798	exon3			AATTCCATTGAAG	AK123917	CCDS43192.1	3q29	2013-03-08	2013-03-08	2013-03-08	ENSG00000214097	ENSG00000214097			27407	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 43"	C3orf43			Standard	NM_001077657		Approved	FLJ41923, DKFZp313B0440		Q147U7	OTTHUMG00000155581	ENST00000397537.2:c.212T>C	3.37:g.196235191A>G	ENSP00000380671:p.Met71Thr	37	0	0		54	22	0.407407	NM_001077657	B3KW20	Missense_Mutation	SNP	ENST00000397537.2	37	CCDS43192.1	97	0.044413919413919416	90	0.18292682926829268	7	0.019337016574585635	0	0.0	0	0.0	A	14.07	2.425685	0.43020	0.151245	6.11E-4	ENSG00000214097	ENST00000397537	T	0.36699	1.24	5.46	5.46	0.80206	.	.	.	.	.	T	0.00073	0.0002	L	0.34521	1.04	0.30114	P	0.806335	B;B	0.32160	0.358;0.358	B;B	0.32762	0.152;0.152	T	0.11179	-1.0598	8	0.59425	D	0.04	-16.9577	13.0552	0.58975	1.0:0.0:0.0:0.0	.	71;63	Q147U7;E9PGG7	CC043_HUMAN;.	T	71	ENSP00000380671:M71T	ENSP00000380671:M71T	M	-	2	0	C3orf43	197719588	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	4.753000	0.62183	2.062000	0.61559	0.533000	0.62120	ATG	A|0.971;G|0.029	0.029	strong		0.358	SMCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340776.1	NM_001006109		G	196235191	A	G	196235191	3	3	22	1	0	0	0	0	1	0	0	0	2232	217	8	3	436	3	C3orf43	3	196235191	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	414	196235191	1787239	992	3893											
WDR53	348793	hgsc.bcm.edu	37	chr3	196281263	196281263	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgaagcgttagtatttccaCcctgcttggtgcaagttcct	7	14	9	11	1	0	1	0	1	0	0	2	1	2	1	3	1	3	5	3	1	4	5	rs61730533	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:196281263C>T	ENST00000332629.5	-	4	1463	c.896G>A	c.(895-897)gGt>gAt	p.G299D	WDR53_ENST00000433160.1_Missense_Mutation_p.G140D|WDR53_ENST00000429115.1_Missense_Mutation_p.G138D	NM_182627.1	NP_872433.1	Q7Z5U6	WDR53_HUMAN	WD repeat domain 53	299										breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)	13	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.6e-23)|all cancers(36;1.54e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.29e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00326)		AGTATTTCCACCCTGCTTGGT	0.418													C|||	283	0.0565096	0.1997	0.0245	5008	,	,		18151	0.0		0.002	False		,,,				2504	0.0				p.G299D		Atlas-SNP	.											.	WDR53	26	.	0			c.G896A						PASS	.	C	ASP/GLY	759,3647	310.0+/-291.3	63,633,1507	290	249	263		896	-3.3	0	3	dbSNP_129	263	11,8589	8.4+/-32.0	0,11,4289	yes	missense	WDR53	NM_182627.1	94	63,644,5796	TT,TC,CC		0.1279,17.2265,5.9203	benign	299/359	196281263	770,12236	2203	4300	6503	SO:0001583	missense	348793	exon4			TTTCCACCCTGCT	BC054030	CCDS3318.1	3q29	2013-01-09			ENSG00000185798	ENSG00000185798		"WD repeat domain containing"	28786	protein-coding gene	gene with protein product		615110				12477932	Standard	NM_182627		Approved	MGC64882, MGC12928	uc003fwt.3	Q7Z5U6	OTTHUMG00000155572	ENST00000332629.5:c.896G>A	3.37:g.196281263C>T	ENSP00000328079:p.Gly299Asp	523	1	0.00191205		549	259	0.471767	NM_182627	A0MNP1	Missense_Mutation	SNP	ENST00000332629.5	37	CCDS3318.1	113	0.051739926739926737	104	0.21138211382113822	8	0.022099447513812154	0	0.0	1	0.0013192612137203166	C	0.015	-1.543285	0.00934	0.172265	0.001279	ENSG00000185798	ENST00000332629;ENST00000429115;ENST00000433160	T;T;T	0.72282	-0.64;1.94;1.94	5.67	-3.35	0.04928	.	1.642950	0.02577	N	0.098418	T	0.00039	0.0001	N	0.12182	0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.11966	-1.0566	9	0.02654	T	1	-15.4206	0.1558	0.00098	0.3118:0.235:0.2066:0.2466	.	299	Q7Z5U6	WDR53_HUMAN	D	299;138;140	ENSP00000328079:G299D;ENSP00000396668:G138D;ENSP00000410677:G140D	ENSP00000328079:G299D	G	-	2	0	WDR53	197765660	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-0.565000	0.05929	-0.487000	0.06735	-1.036000	0.02392	GGT	C|0.942;T|0.058	0.058	strong		0.418	WDR53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340689.1	NM_182627		T	196281263	C	T	196281263	3	4	22	1	0	0	0	0	1	0	0	0	17320	507	18	2	184	2	WDR53	3	196281263	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	46072	196281263	1741167	993	3894											
DLG1	1739	hgsc.bcm.edu	37	chr3	196842831	196842831	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctccttttctgagctctccActtagatcagcaggtcctcc	6	14	6	15	0	4	2	1	1	3	1	8	2	6	2	4	1	2	2	4	1	1	3	rs79212676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:196842831A>G	ENST00000419354.1	-	14	1795	c.1509T>C	c.(1507-1509)agT>agC	p.S503S	DLG1_ENST00000357674.4_Silent_p.S470S|DLG1_ENST00000443183.1_Silent_p.S387S|DLG1_ENST00000346964.2_Silent_p.S503S|DLG1_ENST00000452595.1_Silent_p.S387S|DLG1_ENST00000314062.3_Silent_p.S452S|DLG1_ENST00000450955.1_Silent_p.S470S|DLG1_ENST00000392382.2_Silent_p.S470S|DLG1_ENST00000422288.1_Silent_p.S452S|DLG1_ENST00000448528.2_Silent_p.S503S			Q12959	DLG1_HUMAN	discs, large homolog 1 (Drosophila)	503	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)		TGAGCTCTCCACTTAGATCAG	0.408													A|||	40	0.00798722	0.0265	0.0072	5008	,	,		16788	0.0		0.0	False		,,,				2504	0.0				p.S503S		Atlas-SNP	.											.	DLG1	120	.	0			c.T1509C						PASS	.	A	,,,,	118,4288	88.7+/-127.4	1,116,2086	119	114	116		1509,1410,1161,1161,1509	3.2	1	3	dbSNP_131	116	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DLG1	NM_001098424.1,NM_001204386.1,NM_001204387.1,NM_001204388.1,NM_004087.2	,,,,	1,116,6386	GG,GA,AA		0.0,2.6782,0.9073	,,,,	503/905,470/893,387/801,387/789,503/927	196842831	118,12888	2203	4300	6503	SO:0001819	synonymous_variant	1739	exon14			CTCTCCACTTAGA	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.1509T>C	3.37:g.196842831A>G		170	0	0		195	88	0.451282	NM_001098424	A5YKK7|B4DGU1|B4DGZ8|B7ZMM0|B9EIQ5|D3DXB8|D3DXB9|E7EWL7|E9PG21|Q12958	Silent	SNP	ENST00000419354.1	37	CCDS43194.1																																																																																			A|0.990;G|0.010	0.010	strong		0.408	DLG1-008	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258170.2	NM_004087		G	196842831	A	G	196842831	2	3	22	1	0	0	0	0	0	0	0	1	4556	156	6	3		3	DLG1	3	196842831	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	561568	196842831	1179599	994	3895											
ZNF141	7700	hgsc.bcm.edu	37	chr4	367290	367290	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tagacagtcctcaaaactgaAtgaacataagaaagttcata	19	9	6	7	0	2	4	2	2	0	2	3	4	3	4	1	0	2	1	1	0	8	4	rs61733102	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:367290A>G	ENST00000240499.7	+	4	1213	c.1064A>G	c.(1063-1065)aAt>aGt	p.N355S	ZNF141_ENST00000505939.1_Intron|ZNF141_ENST00000512994.1_Intron	NM_003441.2	NP_003432.1	Q15928	ZN141_HUMAN	zinc finger protein 141	355					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						TCAAAACTGAATGAACATAAG	0.408													a|||	13	0.00259585	0.0098	0.0	5008	,	,		20026	0.0		0.0	False		,,,				2504	0.0				p.N355S		Atlas-SNP	.											.	ZNF141	48	.	0			c.A1064G						PASS	.	A	SER/ASN	33,4373	36.8+/-68.6	0,33,2170	37	40	39		1064	-2.5	0	4	dbSNP_129	39	0,8596		0,0,4298	no	missense	ZNF141	NM_003441.2	46	0,33,6468	GG,GA,AA		0.0,0.749,0.2538	benign	355/475	367290	33,12969	2203	4298	6501	SO:0001583	missense	7700	exon4			AACTGAATGAACA	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.1064A>G	4.37:g.367290A>G	ENSP00000240499:p.Asn355Ser	35	0	0		61	31	0.508197	NM_003441	Q6DK07	Missense_Mutation	SNP	ENST00000240499.7	37	CCDS33931.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	10.25	1.299693	0.23650	0.00749	0.0	ENSG00000131127	ENST00000240499	T	0.03272	3.99	1.24	-2.48	0.06423	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01558	0.0050	N	0.25992	0.78	0.09310	N	1	B	0.12013	0.005	B	0.11329	0.006	T	0.46762	-0.9168	8	.	.	.	.	2.176	0.03862	0.556:0.0:0.1963:0.2477	rs61733102	355	Q15928	ZN141_HUMAN	S	355	ENSP00000240499:N355S	.	N	+	2	0	ZNF141	357290	0.000000	0.05858	0.001000	0.08648	0.756000	0.42949	-0.780000	0.04654	-1.529000	0.01754	-0.856000	0.03024	AAT	A|0.998;G|0.002	0.002	strong		0.408	ZNF141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357710.1	NM_003441		G	367290	A	G	367290	3	3	22	1	0	0	0	0	1	0	0	0	17745	101	4	3	1078	3	ZNF141	4	367290	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10		367290	190786986	995	3896											
PDE6B	5158	hgsc.bcm.edu	37	chr4	660340	660340	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctatgatggaccggaacaaGgcggccgagctccccaagct	10	5	12	14	3	0	1	0	1	0	0	1	4	1	3	5	4	3	2	5	4	4	1	rs61739716	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:660340G>A	ENST00000496514.1	+	20	2310	c.2289G>A	c.(2287-2289)aaG>aaA	p.K763K	PDE6B_ENST00000255622.6_Silent_p.K763K|PDE6B_ENST00000429163.2_Silent_p.K484K			P35913	PDE6B_HUMAN	phosphodiesterase 6B, cGMP-specific, rod, beta	763					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)	ACCGGAACAAGGCGGCCGAGC	0.652													.|||	53	0.0105831	0.0378	0.0014	5008	,	,		15996	0.0		0.001	False		,,,				2504	0.001				p.K763K	GBM(71;463 1194 9848 25922 46834)	Atlas-SNP	.											.	PDE6B	80	.	0			c.G2289A						PASS	.	G	,,	159,4247	108.2+/-146.6	2,155,2046	96	78	84		2289,2289,1452	1	1	4	dbSNP_129	84	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	PDE6B	NM_000283.3,NM_001145291.1,NM_001145292.1	,,	2,155,6346	AA,AG,GG		0.0,3.6087,1.2225	,,	763/855,763/854,484/576	660340	159,12847	2203	4300	6503	SO:0001819	synonymous_variant	5158	exon20			GAACAAGGCGGCC	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.2289G>A	4.37:g.660340G>A		79	0	0		85	34	0.4	NM_001145291	B7Z9T9|E7ETT3|Q53XN5|Q9BWH5|Q9UD49	Silent	SNP	ENST00000496514.1	37	CCDS33932.1	18	0.008241758241758242	18	0.036585365853658534	0	0.0	0	0.0	0	0.0	G	9.994	1.231604	0.22626	0.036087	0.0	ENSG00000133256	ENST00000461490	.	.	.	4.26	0.984	0.19773	.	.	.	.	.	T	0.22282	0.0537	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.13150	-1.0520	4	.	.	.	.	6.8943	0.24247	0.5241:0.0:0.4759:0.0	rs61739716	.	.	.	K	44	.	.	R	+	2	0	PDE6B	650340	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	1.242000	0.32755	0.120000	0.18254	0.650000	0.86243	AGG	G|0.990;A|0.010	0.010	strong		0.652	PDE6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358109.1	NM_000283		A	660340	G	A	660340	2	1	22	1	0	0	0	0	0	0	0	1	11655	991	35	2		2	PDE6B	4	660340	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	293050	660340	190493936	996	3897											
KIAA1530	57654	hgsc.bcm.edu	37	chr4	1374769	1374769	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcagctgcagaagcaggaGcgcccgggtaggtctgggca	8	4	18	11	3	1	1	0	0	1	1	1	2	1	2	1	5	4	6	1	5	2	1	rs115722661	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:1374769G>A	ENST00000389851.4	+	12	2301	c.1854G>A	c.(1852-1854)gaG>gaA	p.E618E	UVSSA_ENST00000511216.1_Silent_p.E618E|UVSSA_ENST00000507531.1_Silent_p.E618E|UVSSA_ENST00000512728.1_Silent_p.E169E|UVSSA_ENST00000511563.1_Silent_p.E169E	NM_020894.2	NP_065945.2	Q2YD98	UVSSA_HUMAN	UV-stimulated scaffold protein A	618					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)										AGAAGCAGGAGCGCCCGGGTA	0.667													G|||	14	0.00279553	0.0098	0.0014	5008	,	,		15251	0.0		0.0	False		,,,				2504	0.0				p.E618E		Atlas-SNP	.											.	.	.	.	0			c.G1854A						PASS	.	G		67,4331	61.1+/-98.1	0,67,2132	30	34	33		1854	-3.4	0	4	dbSNP_133	33	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	KIAA1530	NM_020894.2		0,68,6430	AA,AG,GG		0.0116,1.5234,0.5232		618/710	1374769	68,12928	2199	4299	6498	SO:0001819	synonymous_variant	57654	exon12			GCAGGAGCGCCCG	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.1854G>A	4.37:g.1374769G>A		213	0	0		202	97	0.480198	NM_020894	A8K9E6|B2RU11|Q8WTX4|Q9P1Z8	Silent	SNP	ENST00000389851.4	37	CCDS33938.1																																																																																			G|0.995;A|0.005	0.005	strong		0.667	UVSSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359480.1	NM_020894		A	1374769	G	A	1374769	2	1	22	1	0	0	0	0	0	0	0	1	8250	962	34	2		2	KIAA1530	4	1374769	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	714429	1374769	189779507	997	3898											
FGFR3	2261	hgsc.bcm.edu	37	chr4	1803251	1803251	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccgcggcgagcaccgcatTggaggcatcaaggtgggcgc	7	6	16	12	5	1	0	1	0	0	0	2	2	2	1	2	5	1	3	2	5	1	2	rs2305181	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:1803251T>C	ENST00000260795.2	+	4	705	c.603T>C	c.(601-603)atT>atC	p.I201I	FGFR3_ENST00000481110.2_Silent_p.I201I|FGFR3_ENST00000440486.2_Silent_p.I201I|FGFR3_ENST00000352904.1_Silent_p.I201I|FGFR3_ENST00000412135.2_Silent_p.I201I|FGFR3_ENST00000340107.4_Silent_p.I201I			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	201	Ig-like C2-type 2.				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)	AGCACCGCATTGGAGGCATCA	0.721		1	"Mis, T"	"IGH@, ETV6"	"bladder, MM, T-cell lymphoma"		"Hypochondroplasia, Thanatophoric dysplasia"		Saethre-Chotzen syndrome;Muenke syndrome				N|||	527	0.105232	0.3359	0.0461	5008	,	,		10686	0.0298		0.0119	False		,,,				2504	0.0092				p.I201I		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"L, E"	.	FGFR3	3320	.	0			c.T603C						PASS	.	C	,,	1007,3249		98,811,1219	7	7	7		603,603,603	-6.3	0.9	4	dbSNP_100	7	68,8282		1,66,4108	no	coding-synonymous,coding-synonymous,coding-synonymous	FGFR3	NM_000142.4,NM_001163213.1,NM_022965.3	,,	99,877,5327	CC,CT,TT		0.8144,23.6607,8.5277	,,	201/807,201/809,201/695	1803251	1075,11531	2128	4175	6303	SO:0001819	synonymous_variant	2261	exon5	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	CCGCATTGGAGGC	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.603T>C	4.37:g.1803251T>C		29	0	0		36	15	0.416667	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Silent	SNP	ENST00000260795.2	37	CCDS3353.1																																																																																			T|0.879;C|0.121	0.121	strong		0.721	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142		C	1803251	T	C	1803251	2	2	22	1	0	0	0	0	0	0	0	1	5875	1800	63	3		3	FGFR3	4	1803251	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	428482	1803251	189351025	998	3899											
WHSC2	7469	hgsc.bcm.edu	37	chr4	1985668	1985668	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggtgtctgagtggtaggggcGacagccggaggtgtggtggg	5	8	23	5	2	1	1	0	1	1	0	1	3	1	2	1	8	1	1	1	8	1	1	rs2234574	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:1985668G>A	ENST00000411638.2	-	9	1224	c.1209C>T	c.(1207-1209)gtC>gtT	p.V403V	NELFA_ENST00000542778.1_Silent_p.V268V|MIR943_ENST00000401286.1_RNA|NELFA_ENST00000382882.3_Silent_p.V414V	NM_005663.4	NP_005654.3	Q9H3P2	NELFA_HUMAN	negative elongation factor complex member A	403					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)										TGGTAGGGGCGACAGCCGGAG	0.682													G|||	137	0.0273562	0.0825	0.013	5008	,	,		13899	0.0129		0.002	False		,,,				2504	0.0041				p.V414V		Atlas-SNP	.											.	.	.	.	0			c.C1242T						PASS	.	G		286,4120	156.6+/-189.7	5,276,1922	42	45	44		1242	-2	0	4	dbSNP_98	44	13,8585	9.1+/-34.3	0,13,4286	no	coding-synonymous	WHSC2	NM_005663.4		5,289,6208	AA,AG,GG		0.1512,6.4911,2.2993		414/540	1985668	299,12705	2203	4299	6502	SO:0001819	synonymous_variant	7469	exon9			AGGGGCGACAGCC	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.1209C>T	4.37:g.1985668G>A		70	0	0		126	66	0.52381	NM_005663	A2A2T1|O95392	Silent	SNP	ENST00000411638.2	37																																																																																				G|0.977;A|0.023	0.023	strong		0.682	NELFA-015	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000473007.1	NM_005663		A	1985668	G	A	1985668	2	1	22	1	0	0	0	0	0	0	0	1	17379	1045	37	1		1	WHSC2	4	1985668	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	182417	1985668	189168608	999	3900											
FAM193A	8603	hgsc.bcm.edu	37	chr4	2661342	2661342	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacagacaccatgaggcacAtgttatcgtcccggctgagc	10	8	10	13	2	1	3	1	2	0	1	3	3	2	3	2	2	1	3	2	2	1	1	rs17164077	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:2661342A>G	ENST00000324666.5	+	7	925	c.574A>G	c.(574-576)Atg>Gtg	p.M192V	FAM193A_ENST00000505311.1_Missense_Mutation_p.M192V|FAM193A_ENST00000382839.3_Missense_Mutation_p.M192V|FAM193A_ENST00000545951.1_Missense_Mutation_p.M192V|FAM193A_ENST00000502458.1_Missense_Mutation_p.M216V	NM_001256666.1	NP_001243595.1	P78312	F193A_HUMAN	family with sequence similarity 193, member A	192			M -> V (in dbSNP:rs17164077). {ECO:0000269|PubMed:9734812}.							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						CATGAGGCACATGTTATCGTC	0.488													A|||	339	0.0676917	0.2443	0.0202	5008	,	,		20584	0.0		0.002	False		,,,				2504	0.0				p.M216V		Atlas-SNP	.											FAM193A,colon,carcinoma,0,1	FAM193A	103	1	0			c.A646G						PASS	.	A	VAL/MET	918,3488	354.9+/-312.8	96,726,1381	97	91	93		574	-2.5	0	4	dbSNP_123	93	7,8593	4.3+/-15.6	0,7,4293	yes	missense	FAM193A	NM_003704.3	21	96,733,5674	GG,GA,AA		0.0814,20.8352,7.1121	benign	192/1225	2661342	925,12081	2203	4300	6503	SO:0001583	missense	8603	exon8			AGGCACATGTTAT	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.574A>G	4.37:g.2661342A>G	ENSP00000324587:p.Met192Val	98	0	0		89	42	0.47191	NM_001256667	B7ZM85|B9EGR0|E9PFA1|O43607|P78311|P78313|Q9UEG8	Missense_Mutation	SNP	ENST00000324666.5	37	CCDS58875.1	109	0.04990842490842491	101	0.20528455284552846	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	A	12.59	1.983129	0.34942	0.208352	8.14E-4	ENSG00000125386	ENST00000382839;ENST00000324666;ENST00000545951;ENST00000502458;ENST00000513350	T;T;T;T;T	0.35048	1.41;1.82;1.4;1.43;1.33	5.82	-2.52	0.06346	.	0.074856	0.85682	N	0.000000	T	0.00039	0.0001	L	0.56769	1.78	0.23314	P	0.99792346	B;B;B;B;B	0.09022	0.001;0.001;0.002;0.001;0.001	B;B;B;B;B	0.06405	0.002;0.002;0.002;0.002;0.002	T	0.12863	-1.0531	9	0.56958	D	0.05	-7.4139	11.1394	0.48394	0.5558:0.0:0.4442:0.0	rs17164077	192;216;192;216;192	B9EGR0;E9PFA1;P78312;B7ZM85;P78312-2	.;.;F193A_HUMAN;.;.	V	192;192;192;216;46	ENSP00000372290:M192V;ENSP00000324587:M192V;ENSP00000443617:M192V;ENSP00000427505:M216V;ENSP00000427260:M46V	ENSP00000324587:M192V	M	+	1	0	FAM193A	2631140	0.995000	0.38212	0.043000	0.18650	0.738000	0.42128	2.222000	0.42926	-0.672000	0.05266	0.459000	0.35465	ATG	A|0.937;G|0.063	0.063	strong		0.488	FAM193A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360903.1	NM_003704		G	2661342	A	G	2661342	3	3	22	1	0	0	0	0	1	0	0	0	5529	217	8	3	592	3	FAM193A	4	2661342	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	675674	2661342	188492934	1000	3901											
ADD1	118	hgsc.bcm.edu	37	chr4	2896419	2896419	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tatgctgcacgcccggacgtGaagtgcgtcgtgcacattca	8	9	12	12	5	1	1	1	1	0	0	2	2	1	2	1	1	4	3	1	1	2	2	rs112813723	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:2896419G>A	ENST00000398129.1	+	5	722	c.702G>A	c.(700-702)gtG>gtA	p.V234V	ADD1_ENST00000264758.7_Silent_p.V234V|ADD1_ENST00000513328.2_Silent_p.V234V|ADD1_ENST00000503455.2_Silent_p.V234V|ADD1_ENST00000355842.3_Silent_p.V234V|ADD1_ENST00000446856.1_Silent_p.V234V|ADD1_ENST00000398125.1_Silent_p.V234V|ADD1_ENST00000398123.2_Silent_p.V234V			P35611	ADDA_HUMAN	adducin 1 (alpha)	234					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cell morphogenesis (GO:0000902)|cell volume homeostasis (GO:0006884)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to retinoic acid (GO:0071300)|endoplasmic reticulum unfolded protein response (GO:0030968)|erythrocyte differentiation (GO:0030218)|hemoglobin metabolic process (GO:0020027)|homeostasis of number of cells within a tissue (GO:0048873)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endocytosis (GO:0045807)|positive regulation of protein binding (GO:0032092)	cytosol (GO:0005829)|dendritic spine (GO:0043197)|F-actin capping protein complex (GO:0008290)|focal adhesion (GO:0005925)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)|transcription factor binding (GO:0008134)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)	22				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GCCCGGACGTGAAGTGCGTCG	0.542													G|||	49	0.00978435	0.0356	0.0014	5008	,	,		14014	0.0		0.001	False		,,,				2504	0.0				p.V234V	Esophageal Squamous(71;505 1201 20414 34538 37449)	Atlas-SNP	.											.	ADD1	56	.	0			c.G702A						PASS	.	G	,,,	140,4266	98.9+/-137.6	3,134,2066	63	54	57		702,702,702,702	-4.3	0.1	4	dbSNP_132	57	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ADD1	NM_001119.4,NM_014189.3,NM_014190.3,NM_176801.2	,,,	3,136,6364	AA,AG,GG		0.0233,3.1775,1.0918	,,,	234/738,234/769,234/632,234/663	2896419	142,12864	2203	4300	6503	SO:0001819	synonymous_variant	118	exon6			GGACGTGAAGTGC	L07261	CCDS3363.1, CCDS3364.1, CCDS43205.1, CCDS75094.1	4p16.3	2009-04-22			ENSG00000087274	ENSG00000087274			243	protein-coding gene	gene with protein product		102680				1840603	Standard	NM_001119		Approved		uc003gfq.3	P35611	OTTHUMG00000122080	ENST00000398129.1:c.702G>A	4.37:g.2896419G>A		240	0	0		294	148	0.503401	NM_014190	A2A3N8|A2A3P0|B4DI79|D3DVR3|D3DVR4|D3DVR5|Q13734|Q14729|Q16156|Q86XM2|Q9UJB6	Silent	SNP	ENST00000398129.1	37	CCDS43205.1																																																																																			G|0.988;A|0.012	0.012	strong		0.542	ADD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242840.1	NM_014189		A	2896419	G	A	2896419	2	1	22	1	0	0	0	0	0	0	0	1	304	1277	45	2		2	ADD1	4	2896419	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	235077	2896419	188257857	1001	3902											
NOP14	8602	hgsc.bcm.edu	37	chr4	2955361	2955361	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agggcatcttctcgttgagcTtgtctctccctctggggaaa	6	13	11	11	1	4	1	0	1	4	0	7	2	5	2	1	3	1	3	1	3	1	3	rs111987238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:2955361T>G	ENST00000314262.6	-	5	672	c.624A>C	c.(622-624)caA>caC	p.Q208H	NOP14_ENST00000416614.2_Missense_Mutation_p.Q208H|NOP14-AS1_ENST00000515194.1_RNA|NOP14_ENST00000502735.1_Missense_Mutation_p.Q208H|NOP14_ENST00000398071.4_Missense_Mutation_p.Q208H|NOP14-AS1_ENST00000503709.1_RNA	NM_003703.1	NP_003694.1	P78316	NOP14_HUMAN	NOP14 nucleolar protein	208					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						CTCGTTGAGCTTGTCTCTCCC	0.498													T|||	15	0.00299521	0.0106	0.0014	5008	,	,		19504	0.0		0.0	False		,,,				2504	0.0				p.Q208H		Atlas-SNP	.											.	NOP14	69	.	0			c.A624C						PASS	.	T	HIS/GLN	58,4348	56.8+/-93.2	0,58,2145	229	213	219		624	-1.6	0.2	4	dbSNP_132	219	0,8600		0,0,4300	yes	missense	NOP14	NM_003703.1	24	0,58,6445	GG,GT,TT		0.0,1.3164,0.4459	probably-damaging	208/858	2955361	58,12948	2203	4300	6503	SO:0001583	missense	8602	exon5			TTGAGCTTGTCTC	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.624A>C	4.37:g.2955361T>G	ENSP00000315674:p.Gln208His	117	0	0		115	55	0.478261	NM_003703	D3DVR6|Q7LGI5|Q7Z6K0|Q8TBR6	Missense_Mutation	SNP	ENST00000314262.6	37	CCDS33945.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	T	12.38	1.921617	0.33908	0.013164	0.0	ENSG00000087269	ENST00000416614;ENST00000314262;ENST00000502735;ENST00000398071;ENST00000546137	T;T;T;T	0.50277	0.75;0.75;0.75;0.75	4.64	-1.62	0.08372	.	0.000000	0.85682	D	0.000000	T	0.54935	0.1889	M	0.91818	3.245	0.48762	D	0.999708	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.69953	-0.5005	10	0.87932	D	0	-37.2025	11.6825	0.51466	0.0:0.4263:0.0:0.5737	.	208;208	E9PFK5;P78316	.;NOP14_HUMAN	H	208;208;208;208;107	ENSP00000405068:Q208H;ENSP00000315674:Q208H;ENSP00000427415:Q208H;ENSP00000381146:Q208H	ENSP00000315674:Q208H	Q	-	3	2	NOP14	2925159	0.987000	0.35691	0.169000	0.22859	0.121000	0.20230	0.274000	0.18680	-0.361000	0.08125	-0.415000	0.06103	CAA	T|0.995;G|0.005	0.005	strong		0.498	NOP14-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358135.2	NM_003703		G	2955361	T	G	2955361	3	3	22	1	0	0	0	0	1	0	0	0	10545	1606	56	5	2005	5	NOP14	4	2955361	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	58942	2955361	188198915	1002	3903											
MAN2B2	23324	hgsc.bcm.edu	37	chr4	6602378	6602378	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctgcaggacattttgcctcGgtctacaacccgctggcctg	6	10	10	15	2	1	0	0	0	1	0	2	1	1	1	4	3	4	2	4	3	2	3	rs73796294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:6602378G>A	ENST00000285599.3	+	10	1470	c.1434G>A	c.(1432-1434)tcG>tcA	p.S478S	MAN2B2_ENST00000504248.1_Silent_p.S427S	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	478					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						ATTTTGCCTCGGTCTACAACC	0.597													G|||	186	0.0371406	0.1331	0.013	5008	,	,		19561	0.0		0.001	False		,,,				2504	0.0				p.S478S		Atlas-SNP	.											.	MAN2B2	80	.	0			c.G1434A						PASS	.	G		515,3891	236.8+/-248.8	34,447,1722	155	122	133		1434	-7.5	0	4	dbSNP_130	133	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	MAN2B2	NM_015274.1		34,453,6016	AA,AG,GG		0.0698,11.6886,4.0058		478/1010	6602378	521,12485	2203	4300	6503	SO:0001819	synonymous_variant	23324	exon10			TGCCTCGGTCTAC	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.1434G>A	4.37:g.6602378G>A		80	0	0		79	40	0.506329	NM_015274	Q66MP2|Q86T67	Silent	SNP	ENST00000285599.3	37	CCDS33951.1	65	0.02976190476190476	62	0.12601626016260162	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	4.539	0.100114	0.08731	0.116886	6.98E-4	ENSG00000013288	ENST00000505907	.	.	.	4.67	-7.52	0.01341	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.42109	P	0.008626000000000023	.	.	.	.	.	.	T	0.26744	-1.0094	3	.	.	.	-3.5583	0.9855	0.01445	0.1784:0.1741:0.2587:0.3887	.	.	.	.	Q	477	.	.	R	+	2	0	MAN2B2	6653279	0.014000	0.17966	0.003000	0.11579	0.008000	0.06430	-0.480000	0.06559	-1.075000	0.03129	-1.224000	0.01588	CGG	G|0.959;A|0.041	0.041	strong		0.597	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274		A	6602378	G	A	6602378	2	1	22	1	0	0	0	0	0	0	0	1	9226	1103	39	1		1	MAN2B2	4	6602378	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3647017	6602378	184551898	1003	3904											
MAN2B2	23324	hgsc.bcm.edu	37	chr4	6611560	6611560	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaattacacgtatgcaatccGctcccggctcacccatgtgc	9	9	8	15	3	1	0	1	0	0	0	3	1	3	0	3	1	3	4	3	1	4	2	rs61733399	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:6611560G>A	ENST00000285599.3	+	13	2078	c.2042G>A	c.(2041-2043)cGc>cAc	p.R681H	MAN2B2_ENST00000504248.1_Missense_Mutation_p.R630H|MAN2B2_ENST00000504960.1_3'UTR	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	681					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						TATGCAATCCGCTCCCGGCTC	0.572													G|||	86	0.0171725	0.0613	0.0072	5008	,	,		18387	0.0		0.0	False		,,,				2504	0.0				p.R681H		Atlas-SNP	.											.	MAN2B2	80	.	0			c.G2042A						PASS	.		HIS/ARG	207,4199	128.6+/-165.4	4,199,2000	76	78	78		2042	0.2	0	4	dbSNP_129	78	3,8597	3.0+/-9.4	0,3,4297	yes	missense	MAN2B2	NM_015274.1	29	4,202,6297	AA,AG,GG		0.0349,4.6981,1.6146	benign	681/1010	6611560	210,12796	2203	4300	6503	SO:0001583	missense	23324	exon13			CAATCCGCTCCCG	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.2042G>A	4.37:g.6611560G>A	ENSP00000285599:p.Arg681His	103	0	0		100	55	0.55	NM_015274	Q66MP2|Q86T67	Missense_Mutation	SNP	ENST00000285599.3	37	CCDS33951.1	30|30	0.013736263736263736|0.013736263736263736	25|25	0.0508130081300813|0.0508130081300813	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	0|0	0.0|0.0	g|g	0.366|0.366	-0.936607|-0.936607	0.02340|0.02340	0.046981|0.046981	3.49E-4|3.49E-4	ENSG00000013288|ENSG00000013288	ENST00000505907|ENST00000285599;ENST00000504248	.|T;T	.|0.78364	.|-1.17;-1.17	4.28|4.28	0.172|0.172	0.15031|0.15031	.|Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	.|0.616553	.|0.17323	.|N	.|0.178421	T|T	0.10465|0.10465	0.0256|0.0256	N|N	0.01705|0.01705	-0.755|-0.755	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.09022	.|0.002;0.001;0.002	.|B;B;B	.|0.08055	.|0.003;0.003;0.003	T|T	0.11348|0.11348	-1.0591|-1.0591	5|10	.|0.14656	.|T	.|0.56	-9.5755|-9.5755	4.7133|4.7133	0.12882|0.12882	0.4981:0.0:0.0855:0.4164|0.4981:0.0:0.0855:0.4164	rs61733399|rs61733399	.|630;681;681	.|E9PCD7;Q9Y2E5;Q9Y2E5-2	.|.;MA2B2_HUMAN;.	T|H	680|681;630	.|ENSP00000285599:R681H;ENSP00000423129:R630H	.|ENSP00000285599:R681H	A|R	+|+	1|2	0|0	MAN2B2|MAN2B2	6662461|6662461	0.000000|0.000000	0.05858|0.05858	0.015000|0.015000	0.15790|0.15790	0.083000|0.083000	0.17756|0.17756	0.078000|0.078000	0.14761|0.14761	-0.229000|-0.229000	0.09854|0.09854	-0.482000|-0.482000	0.04802|0.04802	GCT|CGC	G|0.981;A|0.019	0.019	strong		0.572	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274		A	6611560	G	A	6611560	3	1	22	1	0	0	0	0	1	0	0	0	9226	1087	38	1	2092	1	MAN2B2	4	6611560	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	9182	6611560	184542716	1004	3905											
MAN2B2	23324	hgsc.bcm.edu	37	chr4	6621677	6621677	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgctgcaggcgctggggtcCgtggtggcagtggaggagcg	4	7	22	8	3	0	0	0	0	0	0	1	2	1	2	1	7	3	4	1	7	0	0	rs147252633	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:6621677C>G	ENST00000285599.3	+	18	2874	c.2838C>G	c.(2836-2838)tcC>tcG	p.S946S	MAN2B2_ENST00000504248.1_Silent_p.S895S	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	946					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						CGCTGGGGTCCGTGGTGGCAG	0.652													C|||	15	0.00299521	0.0106	0.0014	5008	,	,		17764	0.0		0.0	False		,,,				2504	0.0				p.S946S		Atlas-SNP	.											.	MAN2B2	80	.	0			c.C2838G						PASS	.	C		58,4348	53.6+/-89.4	0,58,2145	50	55	53		2838	-0.9	0	4	dbSNP_134	53	0,8600		0,0,4300	no	coding-synonymous	MAN2B2	NM_015274.1		0,58,6445	GG,GC,CC		0.0,1.3164,0.4459		946/1010	6621677	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	23324	exon18			GGGGTCCGTGGTG	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.2838C>G	4.37:g.6621677C>G		204	0	0		181	88	0.486188	NM_015274	Q66MP2|Q86T67	Silent	SNP	ENST00000285599.3	37	CCDS33951.1																																																																																			C|0.994;G|0.006	0.006	strong		0.652	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274		G	6621677	C	G	6621677	2	3	22	1	0	0	0	0	0	0	0	1	9226	639	23	4		4	MAN2B2	4	6621677	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	10117	6621677	184532599	1005	3906											
SORCS2	57537	hgsc.bcm.edu	37	chr4	7741941	7741941	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctaggcaaccactcaggcGtggtcctgagcatcaactcc	9	8	9	15	1	2	1	2	1	0	0	5	1	5	1	4	3	3	2	4	3	3	1	rs189272447		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:7741941G>A	ENST00000507866.2	+	27	3539	c.3430G>A	c.(3430-3432)Gtg>Atg	p.V1144M	SORCS2_ENST00000329016.9_Missense_Mutation_p.V987M	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	1144					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						CCACTCAGGCGTGGTCCTGAG	0.617													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16669	0.0		0.0	False		,,,				2504	0.0				p.V1144M		Atlas-SNP	.											.	SORCS2	98	.	0			c.G3430A						PASS	.	G	MET/VAL	4,4138		0,4,2067	44	48	47		3430	3.8	0.9	4		47	1,8397		0,1,4198	yes	missense	SORCS2	NM_020777.2	21	0,5,6265	AA,AG,GG		0.0119,0.0966,0.0399	probably-damaging	1144/1160	7741941	5,12535	2071	4199	6270	SO:0001583	missense	57537	exon27			TCAGGCGTGGTCC	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.3430G>A	4.37:g.7741941G>A	ENSP00000422185:p.Val1144Met	20	0	0		19	8	0.421053	NM_020777	Q9P2L7	Missense_Mutation	SNP	ENST00000507866.2	37	CCDS47008.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	21.3	4.122447	0.77436	9.66E-4	1.19E-4	ENSG00000184985	ENST00000507866;ENST00000329016;ENST00000505529	T;T	0.19394	2.17;2.15	3.78	3.78	0.43462	.	0.167836	0.25948	U	0.027280	T	0.38295	0.1035	L	0.60455	1.87	0.58432	D	0.999996	D;D	0.76494	0.999;0.958	P;B	0.58970	0.849;0.13	T	0.39375	-0.9617	10	0.87932	D	0	.	15.8127	0.78576	0.0:0.0:1.0:0.0	.	987;1144	B5MED8;Q96PQ0	.;SORC2_HUMAN	M	1144;987;86	ENSP00000422185:V1144M;ENSP00000329124:V987M	ENSP00000329124:V987M	V	+	1	0	SORCS2	7792841	1.000000	0.71417	0.893000	0.35052	0.845000	0.48019	7.974000	0.88039	1.935000	0.56089	0.561000	0.74099	GTG	G|0.999;A|0.001	0.001	strong		0.617	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777		A	7741941	G	A	7741941	3	1	22	1	0	0	0	0	1	0	0	0	14946	1145	40	1	3536	1	SORCS2	4	7741941	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1120264	7741941	183412335	1006	3907											
NKX3-2	579	hgsc.bcm.edu	37	chr4	13545610	13545610	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atctcgctgtcgctccggccCgcggcttcctcctctaggtc	2	11	10	18	5	2	0	0	0	2	0	8	0	5	0	4	3	0	3	4	3	1	2	rs10032202	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:13545610C>T	ENST00000382438.5	-	1	1064	c.429G>A	c.(427-429)gcG>gcA	p.A143A	AC006445.8_ENST00000501050.1_lincRNA	NM_001189.3	NP_001180.1	P78367	NKX32_HUMAN	NK3 homeobox 2	143					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						CGCTCCGGCCCGCGGCTTCCT	0.731													C|||	196	0.0391374	0.1437	0.0058	5008	,	,		11648	0.0		0.002	False		,,,				2504	0.0				p.A143A		Atlas-SNP	.											.	NKX3-2	15	.	0			c.G429A						PASS	.	C		260,3434		1,258,1588	3	4	4		429	3.1	1	4	dbSNP_119	4	10,7596		0,10,3793	no	coding-synonymous	NKX3-2	NM_001189.3		1,268,5381	TT,TC,CC		0.1315,7.0384,2.3894		143/334	13545610	270,11030	1847	3803	5650	SO:0001819	synonymous_variant	579	exon1			CCGGCCCGCGGCT	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.429G>A	4.37:g.13545610C>T		24	0	0		26	13	0.5	NM_001189	Q2M2I7	Silent	SNP	ENST00000382438.5	37	CCDS3410.1																																																																																			C|0.964;T|0.036	0.036	strong		0.731	NKX3-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207317.3			T	13545610	C	T	13545610	2	4	22	1	0	0	0	0	0	0	0	1	10465	639	23	1		1	NKX3-2	4	13545610	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	5803669	13545610	177608666	1007	3908											
FBXL5	26234	hgsc.bcm.edu	37	chr4	15627092	15627092	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acaaaatgagtgaccacaatAcgcaaaggctggagaagcac	18	4	10	9	1	0	3	0	2	0	1	0	4	0	3	1	2	2	3	1	2	6	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:15627092A>G	ENST00000341285.3	-	9	1757	c.1633T>C	c.(1633-1635)Tat>Cat	p.Y545H	FBXL5_ENST00000412094.2_Missense_Mutation_p.Y528H|FBXL5_ENST00000382358.4_Missense_Mutation_p.Y419H	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	545					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						TGACCACAATACGCAAAGGCT	0.423																																					p.Y545H		Atlas-SNP	.											.	FBXL5	52	.	0			c.T1633C						PASS	.						71	58	62					4																	15627092		2203	4300	6503	SO:0001583	missense	26234	exon9			CACAATACGCAAA	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.1633T>C	4.37:g.15627092A>G	ENSP00000344866:p.Tyr545His	131	0	0		134	6	0.0447761	NM_012161	A8MSK4|B4DIB5|Q4W5A8|Q8NHP3|Q9NXN2|Q9P0I0|Q9P0X5|Q9UJT7|Q9UKC8	Missense_Mutation	SNP	ENST00000341285.3	37	CCDS3415.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.7|21.7	4.187808|4.187808	0.78789|0.78789	.|.	.|.	ENSG00000118564|ENSG00000118564	ENST00000513163|ENST00000341285;ENST00000412094;ENST00000382358	.|T;T;T	.|0.38401	.|1.17;1.19;1.14	5.72|5.72	5.72|5.72	0.89469|0.89469	.|.	.|0.108992	.|0.64402	.|D	.|0.000005	T|T	0.48095|0.48095	0.1481|0.1481	L|L	0.29908|0.29908	0.895|0.895	0.50467|0.50467	D|D	0.999876|0.999876	.|D;D	.|0.89917	.|1.0;0.999	.|D;D	.|0.85130	.|0.997;0.994	T|T	0.36601|0.36601	-0.9741|-0.9741	5|10	.|0.30078	.|T	.|0.28	-20.3568|-20.3568	16.0006|16.0006	0.80290|0.80290	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|528;545	.|Q9UKA1-2;Q9UKA1	.|.;FBXL5_HUMAN	A|H	465|545;528;419	.|ENSP00000344866:Y545H;ENSP00000408679:Y528H;ENSP00000371795:Y419H	.|ENSP00000344866:Y545H	V|Y	-|-	2|1	0|0	FBXL5|FBXL5	15236190|15236190	0.997000|0.997000	0.39634|0.39634	0.864000|0.864000	0.33941|0.33941	0.943000|0.943000	0.58893|0.58893	3.468000|3.468000	0.53086|0.53086	2.180000|2.180000	0.69256|0.69256	0.460000|0.460000	0.39030|0.39030	GTA|TAT	.	.	none		0.423	FBXL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214235.2			G	15627092	A	G	15627092	3	3	22	1	0	0	0	0	1	0	0	0	5730	391	14	3	454	3	FBXL5	4	15627092	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2081482	15627092	175527184	1008	3909											
CLRN2	645104	hgsc.bcm.edu	37	chr4	17517141	17517141	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggccgccaatcccaattcacGagtgagtatattgggagcat	11	9	11	10	2	1	1	1	1	0	0	2	3	2	2	3	2	1	2	3	2	4	4	rs201838208	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:17517141G>A	ENST00000511148.2	+	1	354	c.252G>A	c.(250-252)acG>acA	p.T84T		NM_001079827.2	NP_001073296.1	A0PK11	CLRN2_HUMAN	clarin 2	84						integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|upper_aerodigestive_tract(1)	15						CCCAATTCACGAGTGAGTATA	0.483													G|||	3	0.000599042	0.0023	0.0	5008	,	,		18289	0.0		0.0	False		,,,				2504	0.0				p.T84T		Atlas-SNP	.											.	CLRN2	40	.	0			c.G252A						PASS	.	G		5,3809		0,5,1902	46	45	45		252	-10.8	0.1	4		45	0,8216		0,0,4108	yes	coding-synonymous-near-splice	CLRN2	NM_001079827.2		0,5,6010	AA,AG,GG		0.0,0.1311,0.0416		84/233	17517141	5,12025	1907	4108	6015	SO:0001630	splice_region_variant	645104	exon1			ATTCACGAGTGAG		CCDS47032.1	4p15.32	2008-01-17			ENSG00000249581	ENSG00000249581			33939	protein-coding gene	gene with protein product						12080385	Standard	NM_001079827		Approved		uc003gpg.1	A0PK11	OTTHUMG00000160273	ENST00000511148.2:c.253+1G>A	4.37:g.17517141G>A		164	0	0		148	80	0.540541	NM_001079827		Silent	SNP	ENST00000511148.2	37	CCDS47032.1																																																																																			.	.	weak		0.483	CLRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359990.2	NM_001079827	Silent	A	17517141	G	A	17517141	5	1	22	1	0	0	0	0	0	0	1	0	3560	1072	37	1	254	1	CLRN2	4	17517141	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1890049	17517141	173637135	1009	3910											
MED28	80306	hgsc.bcm.edu	37	chr4	17616349	17616349	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caggccccgccgggccttccGggccaagcttcgcttcttca	4	8	11	18	4	2	0	1	0	1	0	4	0	3	0	6	3	1	2	6	3	1	4	rs146036794	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:17616349G>A	ENST00000237380.7	+	1	96	c.72G>A	c.(70-72)ccG>ccA	p.P24P	AC006160.5_ENST00000511010.1_RNA	NM_025205.3	NP_079481.2	Q9H204	MED28_HUMAN	mediator complex subunit 28	24					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						CGGGCCTTCCGGGCCAAGCTT	0.587													G|||	27	0.00539137	0.0204	0.0	5008	,	,		14224	0.0		0.0	False		,,,				2504	0.0				p.P24P		Atlas-SNP	.											.	MED28	16	.	0			c.G72A						PASS	.	G		68,4338	54.9+/-90.9	1,66,2136	51	60	57		72	2.6	1	4	dbSNP_134	57	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	MED28	NM_025205.3		1,68,6434	AA,AG,GG		0.0233,1.5433,0.5382		24/179	17616349	70,12936	2203	4300	6503	SO:0001819	synonymous_variant	80306	exon1			CCTTCCGGGCCAA	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.72G>A	4.37:g.17616349G>A		101	0	0		156	72	0.461538	NM_025205	Q9BZJ5	Silent	SNP	ENST00000237380.7	37	CCDS33963.1																																																																																			G|0.996;A|0.004	0.004	strong		0.587	MED28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360055.3	NM_025205		A	17616349	G	A	17616349	2	1	22	1	0	0	0	0	0	0	0	1	9455	1103	39	1		1	MED28	4	17616349	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	99208	17616349	173537927	1010	3911											
SEL1L3	23231	hgsc.bcm.edu	37	chr4	25806279	25806279	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaaggggacgatagagctaaTttggtgaagaccatcaatgc	15	8	12	6	1	1	3	1	1	0	2	1	5	1	4	1	3	2	1	1	3	5	3	rs16877591	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:25806279T>C	ENST00000399878.3	-	10	1782	c.1660A>G	c.(1660-1662)Att>Gtt	p.I554V	SEL1L3_ENST00000502949.1_Missense_Mutation_p.I401V|SEL1L3_ENST00000264868.5_Missense_Mutation_p.I519V	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	554			I -> V (in dbSNP:rs16877591).			integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						ATAGAGCTAATTTGGTGAAGA	0.423													T|||	315	0.0628994	0.2307	0.013	5008	,	,		19704	0.001		0.0	False		,,,				2504	0.0				p.I554V		Atlas-SNP	.											.	SEL1L3	62	.	0			c.A1660G						PASS	.	T	VAL/ILE	657,3117		65,527,1295	105	101	102		1660	4.8	1	4	dbSNP_123	102	5,8259		0,5,4127	yes	missense	SEL1L3	NM_015187.3	29	65,532,5422	CC,CT,TT		0.0605,17.4086,5.4993	benign	554/1133	25806279	662,11376	1887	4132	6019	SO:0001583	missense	23231	exon10			AGCTAATTTGGTG	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.1660A>G	4.37:g.25806279T>C	ENSP00000382767:p.Ile554Val	237	0	0		237	120	0.506329	NM_015187	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Missense_Mutation	SNP	ENST00000399878.3	37	CCDS47037.1	103	0.04716117216117216	98	0.1991869918699187	5	0.013812154696132596	0	0.0	0	0.0	T	2.128	-0.399879	0.04865	0.174086	6.05E-4	ENSG00000091490	ENST00000399878;ENST00000264868;ENST00000502949	T;T;T	0.15139	2.64;2.67;2.45	6.02	4.84	0.62591	Tetratricopeptide-like helical (1);	0.609972	0.19314	N	0.117326	T	0.00012	0.0000	L	0.46157	1.445	0.35888	P	0.17056099999999996	B	0.09022	0.002	B	0.04013	0.001	T	0.35251	-0.9796	9	0.22706	T	0.39	-16.5487	1.9195	0.03304	0.1312:0.1514:0.1366:0.5808	rs16877591;rs56773321;rs16877591	554	Q68CR1	SE1L3_HUMAN	V	554;519;401	ENSP00000382767:I554V;ENSP00000264868:I519V;ENSP00000425438:I401V	ENSP00000264868:I519V	I	-	1	0	SEL1L3	25415377	0.939000	0.31865	1.000000	0.80357	0.338000	0.28826	0.314000	0.19432	1.093000	0.41377	0.533000	0.62120	ATT	T|0.933;C|0.067	0.067	strong		0.423	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187		C	25806279	T	C	25806279	3	2	22	1	0	0	0	0	1	0	0	0	14027	1493	52	3	1798	3	SEL1L3	4	25806279	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	8189930	25806279	165347997	1011	3912											
SEL1L3	23231	hgsc.bcm.edu	37	chr4	25849329	25849329	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaaattgacaacacaaggcTgagagcataaatactcaacc	18	6	6	11	0	1	2	1	2	0	1	1	3	1	2	2	1	4	2	2	1	7	3	rs16877661	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:25849329T>C	ENST00000399878.3	-	2	442	c.320A>G	c.(319-321)cAg>cGg	p.Q107R	SEL1L3_ENST00000502949.1_5'UTR|SEL1L3_ENST00000513364.1_Intron|SEL1L3_ENST00000264868.5_Missense_Mutation_p.Q72R	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	107			Q -> R (in dbSNP:rs16877661).			integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						AACACAAGGCTGAGAGCATAA	0.408													T|||	106	0.0211661	0.0779	0.0043	5008	,	,		20619	0.0		0.0	False		,,,				2504	0.0				p.Q107R		Atlas-SNP	.											.	SEL1L3	62	.	0			c.A320G						PASS	.	T	ARG/GLN	216,3516		6,204,1656	116	105	108		320	5.2	1	4	dbSNP_123	108	2,8224		0,2,4111	yes	missense	SEL1L3	NM_015187.3	43	6,206,5767	CC,CT,TT		0.0243,5.7878,1.823	benign	107/1133	25849329	218,11740	1866	4113	5979	SO:0001583	missense	23231	exon2			CAAGGCTGAGAGC	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.320A>G	4.37:g.25849329T>C	ENSP00000382767:p.Gln107Arg	107	0	0		103	52	0.504854	NM_015187	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Missense_Mutation	SNP	ENST00000399878.3	37	CCDS47037.1	35	0.016025641025641024	32	0.06504065040650407	3	0.008287292817679558	0	0.0	0	0.0	T	12.92	2.082924	0.36758	0.057878	2.43E-4	ENSG00000091490	ENST00000399878;ENST00000264868	T;T	0.11712	2.75;2.76	5.25	5.25	0.73442	.	0.355245	0.29980	N	0.010710	T	0.00666	0.0022	L	0.38531	1.155	0.80722	D	1	B	0.16396	0.017	B	0.15870	0.014	T	0.18745	-1.0327	10	0.59425	D	0.04	-16.01	9.7021	0.40194	0.0:0.0776:0.0:0.9224	rs16877661;rs52796481;rs16877661	107	Q68CR1	SE1L3_HUMAN	R	107;72	ENSP00000382767:Q107R;ENSP00000264868:Q72R	ENSP00000264868:Q72R	Q	-	2	0	SEL1L3	25458427	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.246000	0.51414	1.995000	0.58328	0.449000	0.29647	CAG	T|0.984;C|0.016	0.016	strong		0.408	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187		C	25849329	T	C	25849329	3	2	22	1	0	0	0	0	1	0	0	0	14027	1580	55	3	3170	3	SEL1L3	4	25849329	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	43050	25849329	165304947	1012	3913											
PCDH7	5099	hgsc.bcm.edu	37	chr4	31144189	31144189	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctgctggatgccggtccgCacttctccggagaggaagaa	8	8	13	12	3	1	2	0	0	1	2	4	5	3	4	4	4	2	2	4	4	2	1	rs148629328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:31144189C>T	ENST00000543491.1	+	3	3486	c.3486C>T	c.(3484-3486)cgC>cgT	p.R1162R				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						TGCCGGTCCGCACTTCTCCGG	0.552													C|||	19	0.00379393	0.0144	0.0	5008	,	,		15274	0.0		0.0	False		,,,				2504	0.0				p.R1162R		Atlas-SNP	.											.	PCDH7	215	.	0			c.C3486T						PASS	.	C	,	56,3986		0,56,1965	91	91	91		3486,3462	2.1	1	4	dbSNP_134	91	2,8402		0,2,4200	no	coding-synonymous,coding-synonymous	PCDH7	NM_001173523.1,NM_032457.3	,	0,58,6165	TT,TC,CC		0.0238,1.3855,0.466	,	1162/1256,1154/1248	31144189	58,12388	2021	4202	6223	SO:0001819	synonymous_variant	5099	exon3			GGTCCGCACTTCT	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.3486C>T	4.37:g.31144189C>T		102	0	0		114	54	0.473684	NM_001173523	O60246|O60247|Q4W5C4	Silent	SNP	ENST00000543491.1	37	CCDS54753.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	5.456	0.269217	0.10349	0.013855	2.38E-4	ENSG00000169851	ENST00000511884	.	.	.	5.86	2.14	0.27477	.	.	.	.	.	T	0.51109	0.1655	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48364	-0.9042	4	.	.	.	.	10.4605	0.44577	0.0:0.731:0.0:0.269	.	.	.	.	Y	844	.	.	H	+	1	0	PCDH7	30753287	0.983000	0.35010	0.999000	0.59377	0.829000	0.46940	0.584000	0.23864	0.146000	0.19002	0.650000	0.86243	CAC	C|0.997;T|0.003	0.003	strong		0.552	PCDH7-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_032457, NM_002589		T	31144189	C	T	31144189	2	4	22	1	0	0	0	0	0	0	0	1	11525	697	25	2		2	PCDH7	4	31144189	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	5294860	31144189	160010087	1013	3914											
TLR6	10333	hgsc.bcm.edu	37	chr4	38829702	38829702	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttttacgacttgtttaggaaCgctctttattttattgctgt	7	21	7	6	2	1	0	0	0	1	0	1	2	1	1	0	1	3	3	0	1	5	10	rs5743816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:38829702C>T	ENST00000381950.1	-	1	1458	c.1393G>A	c.(1393-1395)Gtt>Att	p.V465I	TLR6_ENST00000436693.2_Missense_Mutation_p.V465I			Q9Y2C9	TLR6_HUMAN	toll-like receptor 6	465			V -> I (in dbSNP:rs5743816). {ECO:0000269|PubMed:21618349}.		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						TGTTTAGGAACGCTCTTTATT	0.388													c|||	159	0.0317492	0.1006	0.0029	5008	,	,		20792	0.0069		0.001	False		,,,				2504	0.0164				p.V465I		Atlas-SNP	.											.	TLR6	67	.	0			c.G1393A						PASS	.						133	145	141					4																	38829702		2203	4300	6503	SO:0001583	missense	10333	exon2			TAGGAACGCTCTT		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.1393G>A	4.37:g.38829702C>T	ENSP00000371376:p.Val465Ile	207	0	0		211	80	0.379147	NM_006068	B3Y640|B6CH35|B6RFS4|B6RFS5|Q2NKL3	Missense_Mutation	SNP	ENST00000381950.1	37	CCDS3446.1	49	0.022435897435897436	45	0.09146341463414634	3	0.008287292817679558	1	0.0017482517482517483	0	0.0	c	0	-2.849326	0.00066	.	.	ENSG00000174130	ENST00000436693;ENST00000381950	T;T	0.48522	0.81;0.81	5.14	2.63	0.31362	.	0.182497	0.38326	N	0.001737	T	0.00875	0.0029	N	0.16201	0.385	0.45554	P	0.0014960000000000528	B	0.02656	0.0	B	0.10450	0.005	T	0.11567	-1.0582	9	0.07325	T	0.83	.	9.4019	0.38437	0.0:0.2162:0.0:0.7838	rs5743816	465	Q9Y2C9	TLR6_HUMAN	I	465	ENSP00000389600:V465I;ENSP00000371376:V465I	ENSP00000371376:V465I	V	-	1	0	TLR6	38506097	0.066000	0.20996	0.500000	0.27589	0.056000	0.15407	0.404000	0.20999	0.787000	0.33731	-0.578000	0.04140	GTT	C|0.931;T|0.069	0.069	strong		0.388	TLR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250431.1			T	38829702	C	T	38829702	3	4	22	1	0	0	0	0	1	0	0	0	15970	536	19	1	1001	1	TLR6	4	38829702	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	7685513	38829702	152324574	1014	3915											
FAM114A1	92689	hgsc.bcm.edu	37	chr4	38907222	38907222	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aattctggatcttctgaaggAgcccaaccaaatactgaaaa	16	9	7	9	0	3	2	0	2	3	0	3	4	3	4	2	2	3	0	2	2	7	3	rs17501308	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:38907222A>G	ENST00000358869.2	+	5	692	c.516A>G	c.(514-516)ggA>ggG	p.G172G	FAM114A1_ENST00000515037.1_5'UTR	NM_138389.2	NP_612398.2	Q8IWE2	NXP20_HUMAN	family with sequence similarity 114, member A1	172						cytoplasm (GO:0005737)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	20						CTTCTGAAGGAGCCCAACCAA	0.433													G|||	37	0.00738818	0.0257	0.0014	5008	,	,		17480	0.0		0.0	False		,,,				2504	0.002				p.G172G		Atlas-SNP	.											.	FAM114A1	42	.	0			c.A516G						PASS	.	G		110,4296	816.0+/-416.2	1,108,2094	100	102	101		516	2	0.2	4	dbSNP_123	101	1,8599	819.2+/-406.8	0,1,4299	no	coding-synonymous	FAM114A1	NM_138389.2		1,109,6393	GG,GA,AA		0.0116,2.4966,0.8535		172/564	38907222	111,12895	2203	4300	6503	SO:0001819	synonymous_variant	92689	exon5			TGAAGGAGCCCAA		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.516A>G	4.37:g.38907222A>G		206	1	0.00485437		171	96	0.561404	NM_138389	A8K9W6|Q6MZV4|Q9BVL6	Silent	SNP	ENST00000358869.2	37	CCDS3447.1																																																																																			A|0.990;G|0.010	0.010	strong		0.433	FAM114A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250436.1	NM_138389		G	38907222	A	G	38907222	2	3	22	1	0	0	0	0	0	0	0	1	5408	291	11	3		3	FAM114A1	4	38907222	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	77520	38907222	152247054	1015	3916											
FAM114A1	92689	hgsc.bcm.edu	37	chr4	38933869	38933869	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atttcaggaagtatacatgtCgtccattgaaagtctggcgg	11	12	11	7	2	2	1	1	1	1	0	4	2	3	2	1	3	1	1	1	3	4	4	rs36058104	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:38933869C>T	ENST00000358869.2	+	12	1513	c.1337C>T	c.(1336-1338)tCg>tTg	p.S446L	FAM114A1_ENST00000515037.1_Missense_Mutation_p.S239L	NM_138389.2	NP_612398.2	Q8IWE2	NXP20_HUMAN	family with sequence similarity 114, member A1	446			S -> L (in dbSNP:rs36058104).			cytoplasm (GO:0005737)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	20						GTATACATGTCGTCCATTGAA	0.368													T|||	146	0.0291534	0.0734	0.0058	5008	,	,		17511	0.005		0.002	False		,,,				2504	0.0389				p.S446L		Atlas-SNP	.											.	FAM114A1	42	.	0			c.C1337T						PASS	.	T	LEU/SER	267,4139	799.7+/-415.5	6,255,1942	63	62	62		1337	4.4	0.7	4	dbSNP_126	62	53,8547	816.7+/-406.9	2,49,4249	yes	missense	FAM114A1	NM_138389.2	145	8,304,6191	TT,TC,CC		0.6163,6.0599,2.4604	benign	446/564	38933869	320,12686	2203	4300	6503	SO:0001583	missense	92689	exon12			ACATGTCGTCCAT		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.1337C>T	4.37:g.38933869C>T	ENSP00000351740:p.Ser446Leu	257	0	0		261	106	0.40613	NM_138389	A8K9W6|Q6MZV4|Q9BVL6	Missense_Mutation	SNP	ENST00000358869.2	37	CCDS3447.1	27	0.012362637362637362	22	0.044715447154471545	2	0.0055248618784530384	2	0.0034965034965034965	1	0.0013192612137203166	T	0.057	-1.233148	0.01505	0.060599	0.006163	ENSG00000197712	ENST00000515037;ENST00000358869;ENST00000355404	T;T	0.22539	1.95;2.98	5.62	4.43	0.53597	.	0.312620	0.32231	N	0.006386	T	0.00468	0.0015	N	0.00446	-1.495	0.09310	N	0.999992	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36841	-0.9731	10	0.12103	T	0.63	-1.327	4.0001	0.09576	0.1273:0.068:0.1332:0.6715	rs36058104	239;446	Q6MZV4;Q8IWE2	.;NXP20_HUMAN	L	239;446;239	ENSP00000424115:S239L;ENSP00000351740:S446L	ENSP00000347569:S239L	S	+	2	0	FAM114A1	38610264	1.000000	0.71417	0.736000	0.30914	0.196000	0.23810	3.031000	0.49728	0.411000	0.25702	-0.516000	0.04426	TCG	C|0.979;T|0.021	0.021	strong		0.368	FAM114A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250436.1	NM_138389		T	38933869	C	T	38933869	3	4	22	1	0	0	0	0	1	0	0	0	5408	893	31	1	1375	1	FAM114A1	4	38933869	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	26647	38933869	152220407	1016	3917											
TMEM156	80008	hgsc.bcm.edu	37	chr4	39033851	39033851	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caattatatactcacctttcGgtgtcttgaaatattccggc	10	15	6	10	2	2	1	1	1	1	0	4	1	3	1	2	2	1	0	2	2	6	7	rs61732938	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:39033851G>A	ENST00000381938.3	-	1	190	c.83C>T	c.(82-84)cCg>cTg	p.P28L	TMEM156_ENST00000372489.2_5'UTR	NM_024943.1	NP_079219.1	Q8N614	TM156_HUMAN	transmembrane protein 156	28						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|stomach(1)	10						CTCACCTTTCGGTGTCTTGAA	0.333													G|||	9	0.00179712	0.0061	0.0014	5008	,	,		16764	0.0		0.0	False		,,,				2504	0.0				p.P28L		Atlas-SNP	.											.	TMEM156	31	.	0			c.C83T						PASS	.	G	LEU/PRO	28,4376	31.7+/-61.6	0,28,2174	50	47	48		83	3.7	1	4	dbSNP_129	48	0,8600		0,0,4300	yes	missense	TMEM156	NM_024943.1	98	0,28,6474	AA,AG,GG		0.0,0.6358,0.2153	benign	28/297	39033851	28,12976	2202	4300	6502	SO:0001583	missense	80008	exon1			CCTTTCGGTGTCT	AK026888	CCDS3448.1	4p14	2008-02-05			ENSG00000121895	ENSG00000121895			26260	protein-coding gene	gene with protein product						12477932	Standard	NM_024943		Approved	FLJ23235	uc003gto.3	Q8N614	OTTHUMG00000128582	ENST00000381938.3:c.83C>T	4.37:g.39033851G>A	ENSP00000371364:p.Pro28Leu	79	0	0		75	37	0.493333	NM_024943	Q9H5N9	Missense_Mutation	SNP	ENST00000381938.3	37	CCDS3448.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	0.012	-1.665798	0.00765	0.006358	0.0	ENSG00000121895	ENST00000381938;ENST00000344606	T;T	0.42513	1.98;0.97	5.39	3.65	0.41850	.	0.637311	0.14864	N	0.293940	T	0.19485	0.0468	L	0.34521	1.04	0.40731	D	0.982742	B	0.26902	0.163	B	0.22880	0.042	T	0.03384	-1.1042	10	0.09590	T	0.72	-3.7493	7.8212	0.29288	0.1868:0.0:0.8132:0.0	.	28	Q8N614	TM156_HUMAN	L	28	ENSP00000371364:P28L;ENSP00000343758:P28L	ENSP00000343758:P28L	P	-	2	0	TMEM156	38710246	0.962000	0.33011	0.992000	0.48379	0.081000	0.17604	1.670000	0.37502	1.404000	0.46819	-0.216000	0.12614	CCG	G|0.998;A|0.002	0.002	strong		0.333	TMEM156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250435.3	NM_024943		A	39033851	G	A	39033851	3	1	22	1	0	0	0	0	1	0	0	0	16088	1116	39	1	831	1	TMEM156	4	39033851	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	99982	39033851	152120425	1017	3918											
WDR19	57728	hgsc.bcm.edu	37	chr4	39267749	39267749	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atctcctgggggagaacgatGgcatgcctaaggtactgaac	11	8	13	9	1	1	2	0	1	1	1	2	4	1	2	2	4	4	2	2	4	4	2	rs16995209	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:39267749G>A	ENST00000399820.3	+	29	3404	c.3250G>A	c.(3250-3252)Ggc>Agc	p.G1084S	WDR19_ENST00000288634.7_Missense_Mutation_p.G924S	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	1084			G -> S (in dbSNP:rs16995209).		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						GGAGAACGATGGCATGCCTAA	0.453													G|||	185	0.0369409	0.1301	0.0173	5008	,	,		15274	0.0		0.001	False		,,,				2504	0.0				p.G1084S		Atlas-SNP	.											.	WDR19	96	.	0			c.G3250A						PASS	.	G	SER/GLY	417,3589		21,375,1607	68	72	71		3250	5.4	1	4	dbSNP_123	71	3,8325		0,3,4161	yes	missense	WDR19	NM_025132.3	56	21,378,5768	AA,AG,GG		0.036,10.4094,3.4052	probably-damaging	1084/1343	39267749	420,11914	2003	4164	6167	SO:0001583	missense	57728	exon29			AACGATGGCATGC	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.3250G>A	4.37:g.39267749G>A	ENSP00000382717:p.Gly1084Ser	141	0	0		161	66	0.409938	NM_025132	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Missense_Mutation	SNP	ENST00000399820.3	37	CCDS47042.1	54	0.024725274725274724	49	0.09959349593495935	5	0.013812154696132596	0	0.0	0	0.0	G	18.81	3.703584	0.68501	0.104094	3.6E-4	ENSG00000157796	ENST00000399820;ENST00000288634	T;T	0.68624	-0.34;-0.34	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.11324	0.0276	M	0.91090	3.175	0.80722	D	1	P	0.41947	0.766	P	0.47162	0.54	T	0.60662	-0.7219	10	0.52906	T	0.07	-18.5327	19.2559	0.93945	0.0:0.0:1.0:0.0	rs16995209;rs52802549;rs16995209	1084	Q8NEZ3	WDR19_HUMAN	S	1084;924	ENSP00000382717:G1084S;ENSP00000288634:G924S	ENSP00000288634:G924S	G	+	1	0	WDR19	38944144	1.000000	0.71417	0.983000	0.44433	0.048000	0.14542	9.108000	0.94275	2.539000	0.85634	0.455000	0.32223	GGC	G|0.962;A|0.038	0.038	strong		0.453	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1			A	39267749	G	A	39267749	3	1	22	1	0	0	0	0	1	0	0	0	17294	1348	47	2	3364	2	WDR19	4	39267749	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	233898	39267749	151886527	1018	3919											
RFC1	5981	hgsc.bcm.edu	37	chr4	39306504	39306504	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	gccttcaaactgctcttactCcgggtgtcacttgcattcag	7	13	8	13	1	4	0	3	0	1	0	5	0	5	0	2	1	4	2	2	1	2	4	rs2066792	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:39306504C>G	ENST00000381897.1	-	15	2176	c.2043G>C	c.(2041-2043)cgG>cgC	p.R681R	RFC1_ENST00000349703.2_Silent_p.R680R	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	681					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						TGCTCTTACTCCGGGTGTCAC	0.433													C|||	397	0.0792732	0.2821	0.0346	5008	,	,		17846	0.0		0.0	False		,,,				2504	0.0				p.R681R	Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)	Atlas-SNP	.											.	RFC1	114	.	0			c.G2043C						PASS	.	C	,	1058,3348	387.9+/-326.7	128,802,1273	261	268	266		2043,2040	1.7	1	4	dbSNP_94	266	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous,coding-synonymous	RFC1	NM_001204747.1,NM_002913.4	,	128,807,5568	GG,GC,CC		0.0581,24.0127,8.1732	,	681/1149,680/1148	39306504	1063,11943	2203	4300	6503	SO:0001819	synonymous_variant	5981	exon15			CTTACTCCGGGTG	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.2043G>C	4.37:g.39306504C>G		143	0	0		161	77	0.478261	NM_001204747	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Silent	SNP	ENST00000381897.1	37	CCDS56329.1																																																																																			C|0.922;G|0.078	0.078	strong		0.433	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1	NM_002913		G	39306504	C	G	39306504	2	3	22	1	0	0	0	0	0	0	0	1	13259	842	30	4		4	RFC1	4	39306504	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	38755	39306504	151847772	1019	3920											
N4BP2	55728	hgsc.bcm.edu	37	chr4	40122377	40122377	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaaaactcattcaacattatGggtgactggccttcatctga	13	12	7	9	0	4	2	3	2	1	0	4	2	4	2	1	2	2	0	1	2	4	3	rs78767806	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:40122377G>A	ENST00000261435.6	+	9	3062	c.2646G>A	c.(2644-2646)atG>atA	p.M882I		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	882					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						TCAACATTATGGGTGACTGGC	0.388													G|||	127	0.0253594	0.0938	0.0043	5008	,	,		21899	0.0		0.0	False		,,,				2504	0.0				p.M882I		Atlas-SNP	.											.	N4BP2	166	.	0			c.G2646A						PASS	.	G	ILE/MET	297,4109	155.5+/-188.7	7,283,1913	55	56	55		2646	3.7	0.2	4	dbSNP_131	55	3,8595	2.2+/-6.3	0,3,4296	yes	missense	N4BP2	NM_018177.4	10	7,286,6209	AA,AG,GG		0.0349,6.7408,2.307	benign	882/1771	40122377	300,12704	2203	4299	6502	SO:0001583	missense	55728	exon9			CATTATGGGTGAC	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.2646G>A	4.37:g.40122377G>A	ENSP00000261435:p.Met882Ile	250	0	0		240	104	0.433333	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	37	CCDS3457.1	44|44	0.020146520146520148|0.020146520146520148	42|42	0.08536585365853659|0.08536585365853659	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	G|G	6.953|6.953	0.545704|0.545704	0.13312|0.13312	0.067408|0.067408	3.49E-4|3.49E-4	ENSG00000078177|ENSG00000078177	ENST00000513269|ENST00000261435;ENST00000381804	.|T	.|0.16073	.|2.37	5.48|5.48	3.72|3.72	0.42706|0.42706	.|.	.|0.426709	.|0.19802	.|N	.|0.105727	T|T	0.00300|0.00300	0.0009|0.0009	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.06405	.|0.002;0.001	T|T	0.34502|0.34502	-0.9826|-0.9826	5|10	.|0.35671	.|T	.|0.21	-1.4935|-1.4935	5.7473|5.7473	0.18128|0.18128	0.1425:0.0:0.5811:0.2764|0.1425:0.0:0.5811:0.2764	.|.	.|882;882	.|Q86UW6-2;Q86UW6	.|.;N4BP2_HUMAN	R|I	529|882;802	.|ENSP00000261435:M882I	.|ENSP00000261435:M882I	G|M	+|+	1|3	0|0	N4BP2|N4BP2	39798772|39798772	0.070000|0.070000	0.21116|0.21116	0.168000|0.168000	0.22838|0.22838	0.735000|0.735000	0.41995|0.41995	0.254000|0.254000	0.18314|0.18314	0.778000|0.778000	0.33520|0.33520	0.655000|0.655000	0.94253|0.94253	GGG|ATG	G|0.975;A|0.025	0.025	strong		0.388	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177		A	40122377	G	A	40122377	3	1	22	1	0	0	0	0	1	0	0	0	10119	1348	47	2	2672	2	N4BP2	4	40122377	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	815873	40122377	151031899	1020	3921											
ATP8A1	10396	hgsc.bcm.edu	37	chr4	42576646	42576646	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaaaactcacccataagcaaCtcccgctatggtgcacttct	13	9	5	14	1	2	0	1	0	1	0	3	0	3	0	2	1	4	3	2	1	5	3	rs61755862	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:42576646C>T	ENST00000381668.5	-	14	1516	c.1285G>A	c.(1285-1287)Gtt>Att	p.V429I	ATP8A1_ENST00000264449.10_Missense_Mutation_p.V429I	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	429					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)	CCATAAGCAACTCCCGCTATG	0.343													C|||	126	0.0251597	0.0923	0.0058	5008	,	,		17551	0.0		0.0	False		,,,				2504	0.0				p.V429I		Atlas-SNP	.											ATP8A1_ENST00000264449,NS,carcinoma,+1,2	ATP8A1	206	2	0			c.G1285A						PASS	.	C	ILE/VAL,ILE/VAL	297,4109	159.6+/-192.1	13,271,1919	55	56	56		1285,1285	3.4	1	4	dbSNP_129	56	2,8596	1.2+/-3.3	0,2,4297	yes	missense,missense	ATP8A1	NM_001105529.1,NM_006095.2	29,29	13,273,6216	TT,TC,CC		0.0233,6.7408,2.2993	benign,benign	429/1150,429/1165	42576646	299,12705	2203	4299	6502	SO:0001583	missense	10396	exon14			AAGCAACTCCCGC	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.1285G>A	4.37:g.42576646C>T	ENSP00000371084:p.Val429Ile	206	0	0		190	84	0.442105	NM_001105529	Q32M35|Q32M36|Q4W5J7|Q4W5P2	Missense_Mutation	SNP	ENST00000381668.5	37	CCDS3466.1	40	0.018315018315018316	38	0.07723577235772358	2	0.0055248618784530384	0	0.0	0	0.0	C	4.770	0.143139	0.09083	0.067408	2.33E-4	ENSG00000124406	ENST00000381668;ENST00000264449	T;T	0.74947	-0.89;-0.89	5.27	3.4	0.38934	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.068109	0.64402	D	0.000017	T	0.04137	0.0115	N	0.11845	0.185	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.001;0.003;0.001	T	0.03325	-1.1048	10	0.09338	T	0.73	.	6.9831	0.24713	0.0:0.6446:0.0:0.3554	.	429;429;429	B4DII6;Q32M35;Q9Y2Q0	.;.;AT8A1_HUMAN	I	429	ENSP00000371084:V429I;ENSP00000264449:V429I	ENSP00000264449:V429I	V	-	1	0	ATP8A1	42271403	0.999000	0.42202	1.000000	0.80357	0.986000	0.74619	0.657000	0.24963	1.459000	0.47892	0.591000	0.81541	GTT	C|0.975;T|0.025	0.025	strong		0.343	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	NM_006095		T	42576646	C	T	42576646	3	4	22	1	0	0	0	0	1	0	0	0	1192	565	20	2	2305	2	ATP8A1	4	42576646	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2454269	42576646	148577630	1021	3922											
GABRA4	2557	hgsc.bcm.edu	37	chr4	46995387	46995387	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacaggaagcgcaggagggCgaaactgaccccggcggaca	12	1	16	12	4	0	1	0	1	0	0	0	5	0	4	2	5	2	2	2	5	2	0	rs16859837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:46995387C>T	ENST00000264318.3	-	1	1037	c.55G>A	c.(55-57)Gcc>Acc	p.A19T	GABRA4_ENST00000509316.1_5'UTR	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	19			A -> T (in dbSNP:rs16859837).		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)	CGCAGGAGGGCGAAACTGACC	0.582													C|||	59	0.0117812	0.0439	0.0014	5008	,	,		16882	0.0		0.0	False		,,,				2504	0.0				p.A19T	Ovarian(6;283 369 8234 12290 33402)	Atlas-SNP	.											.	GABRA4	129	.	0			c.G55A						PASS	.	C	THR/ALA,,	164,4242	109.9+/-148.2	5,154,2044	115	109	111		55,,	1.8	1	4	dbSNP_123	111	2,8598	1.2+/-3.3	0,2,4298	yes	missense,intron,intron	GABRA4	NM_000809.3,NM_001204266.1,NM_001204267.1	58,,	5,156,6342	TT,TC,CC		0.0233,3.7222,1.2763	benign,,	19/555,,	46995387	166,12840	2203	4300	6503	SO:0001583	missense	2557	exon1			GGAGGGCGAAACT		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.55G>A	4.37:g.46995387C>T	ENSP00000264318:p.Ala19Thr	185	0	0		194	192	0.989691	NM_000809	Q8IYR7	Missense_Mutation	SNP	ENST00000264318.3	37	CCDS3473.1	27	0.012362637362637362	27	0.054878048780487805	0	0.0	0	0.0	0	0.0	C	15.70	2.911015	0.52439	0.037222	2.33E-4	ENSG00000109158	ENST00000264318	T	0.79845	-1.31	4.72	1.79	0.24919	.	0.494117	0.20686	N	0.087559	T	0.17789	0.0427	N	0.08118	0	0.28598	N	0.909322	B	0.06786	0.001	B	0.04013	0.001	T	0.13980	-1.0489	10	0.20519	T	0.43	.	5.9264	0.19114	0.0:0.6558:0.0:0.3442	rs16859837;rs52821342;rs16859837	19	P48169	GBRA4_HUMAN	T	19	ENSP00000264318:A19T	ENSP00000264318:A19T	A	-	1	0	GABRA4	46690144	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	1.961000	0.40432	0.595000	0.29777	-0.237000	0.12165	GCC	C|0.984;T|0.016	0.016	strong		0.582	GABRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216893.1			T	46995387	C	T	46995387	3	4	22	1	0	0	0	0	1	0	0	0	6171	768	27	1	1645	1	GABRA4	4	46995387	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4418741	46995387	144158889	1022	3923											
GABRB1	2560	hgsc.bcm.edu	37	chr4	47408850	47408850	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagtatgcctttgtaaattaCatcttctttgggaaaggccc	10	14	9	8	0	2	0	0	0	2	0	2	2	2	1	2	2	2	2	2	2	5	6	rs115114447	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:47408850C>T	ENST00000295454.3	+	8	1279	c.987C>T	c.(985-987)taC>taT	p.Y329Y	GABRB1_ENST00000538619.1_Silent_p.Y259Y	NM_000812.3	NP_000803.2	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 1	329					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)	TTGTAAATTACATCTTCTTTG	0.423													C|||	77	0.0153754	0.056	0.0043	5008	,	,		19488	0.0		0.0	False		,,,				2504	0.0				p.Y329Y		Atlas-SNP	.											GABRB1,colon,carcinoma,+1,1	GABRB1	107	1	0			c.C987T						PASS	.	C		236,4170	138.4+/-174.2	4,228,1971	167	161	163		987	1.1	1	4	dbSNP_132	163	4,8596	1.2+/-3.3	0,4,4296	no	coding-synonymous	GABRB1	NM_000812.3		4,232,6267	TT,TC,CC		0.0465,5.3563,1.8453		329/475	47408850	240,12766	2203	4300	6503	SO:0001819	synonymous_variant	2560	exon8			AAATTACATCTTC		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.987C>T	4.37:g.47408850C>T		222	0	0		235	235	1	NM_000812	B2R6U7|D6REL3|Q16166|Q8TBK3	Silent	SNP	ENST00000295454.3	37	CCDS3474.1																																																																																			C|0.982;T|0.018	0.018	strong		0.423	GABRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216896.1			T	47408850	C	T	47408850	2	4	22	1	0	0	0	0	0	0	0	1	6174	489	17	2		2	GABRB1	4	47408850	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	413463	47408850	143745426	1023	3924											
COMMD8	54951	hgsc.bcm.edu	37	chr4	47462210	47462210	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggctttgaaaaatttggcaAtatcttctaaaacgtgcatc	13	14	7	7	1	2	1	0	1	2	0	3	1	2	1	0	2	2	3	0	2	6	5	rs114141818	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:47462210A>C	ENST00000381571.4	-	2	240	c.173T>G	c.(172-174)aTt>aGt	p.I58S		NM_017845.3	NP_060315.1	Q9NX08	COMD8_HUMAN	COMM domain containing 8	58										large_intestine(2)|lung(5)|prostate(1)	8						AAATTTGGCAATATCTTCTAA	0.353													a|||	64	0.0127796	0.0469	0.0029	5008	,	,		16655	0.0		0.0	False		,,,				2504	0.0				p.I58S		Atlas-SNP	.											.	COMMD8	15	.	0			c.T173G						PASS	.	G	SER/ILE	201,4205	126.1+/-163.2	3,195,2005	104	106	106		173	1.7	0	4	dbSNP_132	106	2,8598		0,2,4298	yes	missense	COMMD8	NM_017845.3	142	3,197,6303	CC,CA,AA		0.0233,4.562,1.5608	benign	58/184	47462210	203,12803	2203	4300	6503	SO:0001583	missense	54951	exon2			TTGGCAATATCTT	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.173T>G	4.37:g.47462210A>C	ENSP00000370984:p.Ile58Ser	119	0	0		108	108	1	NM_017845	Q8WUR4|Q9HC15	Missense_Mutation	SNP	ENST00000381571.4	37	CCDS3475.1	20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	a	1.694	-0.503300	0.04261	0.04562	2.33E-4	ENSG00000169019	ENST00000381571	T	0.11277	2.79	5.57	1.71	0.24356	.	0.431904	0.26832	N	0.022272	T	0.01189	0.0039	L	0.35723	1.085	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.28933	-1.0028	10	0.44086	T	0.13	-30.318	8.7378	0.34539	0.6292:0.0:0.3708:0.0	.	58	Q9NX08	COMD8_HUMAN	S	58	ENSP00000370984:I58S	ENSP00000370984:I58S	I	-	2	0	COMMD8	47156967	0.102000	0.21896	0.018000	0.16275	0.009000	0.06853	1.363000	0.34159	0.090000	0.17273	-0.253000	0.11424	ATT	A|0.985;C|0.015	0.015	strong		0.353	COMMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216898.2	NM_017845		C	47462210	A	C	47462210	3	2	22	1	0	0	0	0	1	0	0	0	3724	101	4	5	394	5	COMMD8	4	47462210	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	53360	47462210	143692066	1024	3925											
TXK	7294	hgsc.bcm.edu	37	chr4	48096101	48096101	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcccctcttaccggctgcAttgtgctggtgataccagat	6	13	10	12	1	1	2	0	1	1	1	2	2	2	2	4	2	4	4	4	2	2	4	rs73151620	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:48096101A>G	ENST00000264316.4	-	8	787	c.702T>C	c.(700-702)aaT>aaC	p.N234N	TXK_ENST00000510457.1_5'UTR	NM_003328.2	NP_003319.2	P42681	TXK_HUMAN	TXK tyrosine kinase	234	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						TACCGGCTGCATTGTGCTGGT	0.473													A|||	174	0.0347444	0.1263	0.0101	5008	,	,		17952	0.0		0.0	False		,,,				2504	0.0				p.N234N		Atlas-SNP	.											.	TXK	58	.	0			c.T702C						PASS	.	A		544,3862	245.6+/-254.5	32,480,1691	131	130	130		702	-9.1	0.2	4	dbSNP_130	130	3,8597	1.2+/-3.3	0,3,4297	no	coding-synonymous	TXK	NM_003328.2		32,483,5988	GG,GA,AA		0.0349,12.3468,4.2058		234/528	48096101	547,12459	2203	4300	6503	SO:0001819	synonymous_variant	7294	exon8			GGCTGCATTGTGC	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.702T>C	4.37:g.48096101A>G		87	0	0		92	92	1	NM_003328	Q14220	Silent	SNP	ENST00000264316.4	37	CCDS3480.1																																																																																			A|0.959;G|0.041	0.041	strong		0.473	TXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219869.7	NM_003328		G	48096101	A	G	48096101	2	3	22	1	0	0	0	0	0	0	0	1	16801	214	8	3		3	TXK	4	48096101	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	633891	48096101	143058175	1025	3926											
USP46	64854	hgsc.bcm.edu	37	chr4	53494283	53494283	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttctcccggaatggacggcaGaagtacaatgcctgaagcac	12	7	11	11	2	1	2	0	1	1	1	2	4	1	4	2	3	3	3	2	3	5	2	rs115007179	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:53494283G>A	ENST00000441222.3	-	3	349	c.165C>T	c.(163-165)ttC>ttT	p.F55F	USP46_ENST00000504078.1_5'Flank|USP46_ENST00000508499.1_Silent_p.F48F|USP46_ENST00000451218.2_Silent_p.F28F	NM_022832.3	NP_073743.2	P62068	UBP46_HUMAN	ubiquitin specific peptidase 46	55	USP.				adult feeding behavior (GO:0008343)|behavioral fear response (GO:0001662)|behavioral response to ethanol (GO:0048149)|protein deubiquitination (GO:0016579)|regulation of synaptic transmission, GABAergic (GO:0032228)|righting reflex (GO:0060013)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(2)	12			LUSC - Lung squamous cell carcinoma(32;0.0295)			ATGGACGGCAGAAGTACAATG	0.522													G|||	43	0.00858626	0.031	0.0029	5008	,	,		21730	0.0		0.0	False		,,,				2504	0.0				p.F55F		Atlas-SNP	.											.	USP46	38	.	0			c.C165T						PASS	.	G	,	110,3966		2,106,1930	90	85	86		144,165	5.2	1	4	dbSNP_132	86	3,8385		0,3,4191	no	coding-synonymous,coding-synonymous	USP46	NM_001134223.1,NM_022832.3	,	2,109,6121	AA,AG,GG		0.0358,2.6987,0.9066	,	48/360,55/367	53494283	113,12351	2038	4194	6232	SO:0001819	synonymous_variant	64854	exon3			ACGGCAGAAGTAC	AK022614	CCDS47053.1, CCDS47054.1	4q12	2008-02-05	2005-08-08		ENSG00000109189	ENSG00000109189		"Ubiquitin-specific peptidases"	20075	protein-coding gene	gene with protein product		612849	"ubiquitin specific protease 46"			12838346	Standard	NM_022832		Approved	FLJ12552	uc003gzn.3	P62068	OTTHUMG00000160640	ENST00000441222.3:c.165C>T	4.37:g.53494283G>A		102	0	0		102	101	0.990196	NM_022832	B7Z3Y7|B7Z675|B7Z7S3|G8ACC7|Q80V95|Q9H7U4|Q9H9T8	Silent	SNP	ENST00000441222.3	37	CCDS47053.1																																																																																			G|0.997;A|0.003	0.003	strong		0.522	USP46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361516.2	NM_022832		A	53494283	G	A	53494283	2	1	22	1	0	0	0	0	0	0	0	1	17092	933	33	2		2	USP46	4	53494283	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5398182	53494283	137659993	1026	3927											
KIT	3815	hgsc.bcm.edu	37	chr4	55561862	55561862	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagcagaatgaatggatcacGgaaaaggcagaagccaccaa	19	3	11	8	1	1	3	1	1	0	2	1	5	1	5	2	3	2	2	2	3	7	0	rs56411694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:55561862G>T	ENST00000288135.5	+	2	349	c.252G>T	c.(250-252)acG>acT	p.T84T		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	84	Ig-like C2-type 1.				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)	AATGGATCACGGAAAAGGCAG	0.443		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				G|||	99	0.0197684	0.0696	0.0101	5008	,	,		19742	0.0		0.0	False		,,,				2504	0.0				p.T84T		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.G252T						PASS	.	G	,	273,4133	155.5+/-188.7	9,255,1939	96	89	92		252,252	-10.4	0	4	dbSNP_129	92	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	KIT	NM_000222.2,NM_001093772.1	,	9,260,6234	TT,TG,GG		0.0581,6.1961,2.1375	,	84/977,84/973	55561862	278,12728	2203	4300	6503	SO:0001819	synonymous_variant	3815	exon2	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	GATCACGGAAAAG	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.252G>T	4.37:g.55561862G>T		112	0	0		98	46	0.469388	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Silent	SNP	ENST00000288135.5	37	CCDS3496.1																																																																																			G|0.981;T|0.019	0.019	strong		0.443	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			T	55561862	G	T	55561862	2	4	22	1	0	0	0	0	0	0	0	1	8338	1103	39	4		4	KIT	4	55561862	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2067579	55561862	135592414	1027	3928											
KDR	3791	hgsc.bcm.edu	37	chr4	55956183	55956183	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggccaagccaaagtcacaGattttaaccacgttcttctc	11	10	7	13	2	3	1	1	0	2	1	4	1	3	1	3	1	2	1	3	1	3	4	rs145298133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:55956183G>T	ENST00000263923.4	-	23	3427	c.3132C>A	c.(3130-3132)atC>atA	p.I1044I	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)	1044	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)	CAAAGTCACAGATTTTAACCA	0.428			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)			G|||	3	0.000599042	0.0023	0.0	5008	,	,		18361	0.0		0.0	False		,,,				2504	0.0				p.I1044I		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	.	KDR	307	.	0			c.C3132A						PASS	.	G		10,4396	16.8+/-37.8	0,10,2193	94	93	94		3132	5.7	1	4	dbSNP_134	94	0,8600		0,0,4300	no	coding-synonymous	KDR	NM_002253.2		0,10,6493	TT,TG,GG		0.0,0.227,0.0769		1044/1357	55956183	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	3791	exon23			GTCACAGATTTTA	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.3132C>A	4.37:g.55956183G>T		68	0	0		80	28	0.35	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Silent	SNP	ENST00000263923.4	37	CCDS3497.1																																																																																			G|0.999;T|0.001	0.001	strong		0.428	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			T	55956183	G	T	55956183	2	4	22	1	0	0	0	0	0	0	0	1	8148	932	33	4		4	KDR	4	55956183	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	394321	55956183	135198093	1028	3929											
NMU	10874	hgsc.bcm.edu	37	chr4	56466734	56466734	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgacttgcaaagggactttgGaattcttcctagaagagaaa	14	11	10	6	0	1	3	0	1	1	2	2	6	2	5	1	2	1	1	1	2	5	5	rs12108463	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:56466734G>T	ENST00000264218.3	-	8	549	c.444C>A	c.(442-444)ttC>ttA	p.F148L	NMU_ENST00000507338.1_Missense_Mutation_p.F123L|NMU_ENST00000511469.1_Missense_Mutation_p.F132L|NMU_ENST00000515325.1_5'UTR|NMU_ENST00000505262.1_Missense_Mutation_p.F121L	NM_006681.2	NP_006672.1	P48645	NMU_HUMAN	neuromedin U	148			F -> L (in dbSNP:rs12108463).		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)		AGGGACTTTGGAATTCTTCCT	0.299													G|||	209	0.0417332	0.1543	0.0072	5008	,	,		17523	0.0		0.0	False		,,,				2504	0.0				p.F148L		Atlas-SNP	.											.	NMU	17	.	0			c.C444A						PASS	.	G	LEU/PHE	585,3821	251.8+/-258.4	41,503,1659	54	59	57		444	-3	0.2	4	dbSNP_120	57	5,8585	3.7+/-12.6	0,5,4290	yes	missense	NMU	NM_006681.2	22	41,508,5949	TT,TG,GG		0.0582,13.2773,4.5399	benign	148/175	56466734	590,12406	2203	4295	6498	SO:0001583	missense	10874	exon8			ACTTTGGAATTCT	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.444C>A	4.37:g.56466734G>T	ENSP00000264218:p.Phe148Leu	230	0	0		213	91	0.42723	NM_006681		Missense_Mutation	SNP	ENST00000264218.3	37	CCDS3501.1	64	0.029304029304029304	62	0.12601626016260162	2	0.0055248618784530384	0	0.0	0	0.0	G	4.096	0.015910	0.07959	0.132773	5.82E-4	ENSG00000109255	ENST00000511469;ENST00000264218;ENST00000505262;ENST00000541393;ENST00000507338	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	4.72	-2.96	0.05547	.	0.703326	0.13471	N	0.385414	T	0.00144	0.0004	N	0.11064	0.09	0.09310	N	0.999996	B	0.09022	0.002	B	0.08055	0.003	T	0.13019	-1.0525	10	0.07813	T	0.8	-6.4377	2.1008	0.03679	0.3758:0.1231:0.3762:0.1249	rs12108463;rs52827993;rs12108463	148	P48645	NMU_HUMAN	L	132;148;121;131;123	ENSP00000422399:F132L;ENSP00000264218:F148L;ENSP00000424246:F121L;ENSP00000422870:F123L	ENSP00000264218:F148L	F	-	3	2	NMU	56161491	0.165000	0.22948	0.173000	0.22940	0.971000	0.66376	-1.188000	0.03064	-0.684000	0.05183	0.585000	0.79938	TTC	G|0.960;T|0.040	0.040	strong		0.299	NMU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220006.2			T	56466734	G	T	56466734	3	4	22	1	0	0	0	0	1	0	0	0	10514	1165	41	4	88	4	NMU	4	56466734	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	510551	56466734	134687542	1029	3930											
NMU	10874	hgsc.bcm.edu	37	chr4	56475330	56475330	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taatcataaagcaaagctccTccagtgcgttggatgcctaa	13	10	8	10	1	1	0	1	0	0	0	3	1	3	1	3	1	4	3	3	1	5	4	rs35892915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:56475330T>C	ENST00000264218.3	-	4	341	c.236A>G	c.(235-237)gAg>gGg	p.E79G	NMU_ENST00000507338.1_Missense_Mutation_p.E79G|NMU_ENST00000511469.1_Missense_Mutation_p.E63G|NMU_ENST00000515325.1_5'UTR|NMU_ENST00000505262.1_Missense_Mutation_p.E79G	NM_006681.2	NP_006672.1	P48645	NMU_HUMAN	neuromedin U	79			E -> G (in dbSNP:rs35892915).		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)		GCAAAGCTCCTCCAGTGCGTT	0.363													T|||	114	0.0227636	0.0847	0.0029	5008	,	,		19593	0.0		0.0	False		,,,				2504	0.0				p.E79G		Atlas-SNP	.											.	NMU	17	.	0			c.A236G						PASS	.	T	GLY/GLU	312,4094	168.0+/-198.9	9,294,1900	111	111	111		236	1.7	0.9	4	dbSNP_126	111	5,8595	3.0+/-9.4	0,5,4295	yes	missense	NMU	NM_006681.2	98	9,299,6195	CC,CT,TT		0.0581,7.0813,2.4373	possibly-damaging	79/175	56475330	317,12689	2203	4300	6503	SO:0001583	missense	10874	exon4			AGCTCCTCCAGTG	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.236A>G	4.37:g.56475330T>C	ENSP00000264218:p.Glu79Gly	71	0	0		87	43	0.494253	NM_006681		Missense_Mutation	SNP	ENST00000264218.3	37	CCDS3501.1	32	0.014652014652014652	31	0.06300813008130081	1	0.0027624309392265192	0	0.0	0	0.0	T	13.36	2.215110	0.39102	0.070813	5.81E-4	ENSG00000109255	ENST00000511469;ENST00000264218;ENST00000505262;ENST00000541393;ENST00000507338	T;T;T;T	0.51574	0.7;0.7;1.31;0.7	5.51	1.72	0.24424	.	0.342720	0.28778	N	0.014164	T	0.04363	0.0120	M	0.65498	2.005	0.34244	D	0.67794	P	0.38922	0.651	B	0.35859	0.212	T	0.26538	-1.0100	10	0.66056	D	0.02	-11.2	8.6898	0.34260	0.0:0.2134:0.0:0.7866	rs35892915	79	P48645	NMU_HUMAN	G	63;79;79;79;79	ENSP00000422399:E63G;ENSP00000264218:E79G;ENSP00000424246:E79G;ENSP00000422870:E79G	ENSP00000264218:E79G	E	-	2	0	NMU	56170087	1.000000	0.71417	0.873000	0.34254	0.350000	0.29205	2.040000	0.41203	0.073000	0.16731	0.533000	0.62120	GAG	T|0.978;C|0.022	0.022	strong		0.363	NMU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220006.2			C	56475330	T	C	56475330	3	2	22	1	0	0	0	0	1	0	0	0	10514	1551	54	3	312	3	NMU	4	56475330	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	8596	56475330	134678946	1030	3931											
CEP135	9662	hgsc.bcm.edu	37	chr4	56837458	56837458	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgaacttatgccagaaagAaaaggagagactgagtgatg	17	8	12	4	0	0	6	0	3	0	3	0	8	0	7	1	1	2	0	1	1	5	2	rs141602415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:56837458A>G	ENST00000257287.4	+	10	1257	c.1133A>G	c.(1132-1134)gAa>gGa	p.E378G		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	378					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)					TGCCAGAAAGAAAAGGAGAGA	0.294													A|||	4	0.000798722	0.003	0.0	5008	,	,		15338	0.0		0.0	False		,,,				2504	0.0				p.E378G		Atlas-SNP	.											CEP135,NS,carcinoma,+1,1	CEP135	115	1	0			c.A1133G						PASS	.	A	GLY/GLU	25,4381	26.2+/-53.5	0,25,2178	42	43	43		1133	6	1	4	dbSNP_134	43	0,8600		0,0,4300	yes	missense	CEP135	NM_025009.3	98	0,25,6478	GG,GA,AA		0.0,0.5674,0.1922	probably-damaging	378/1141	56837458	25,12981	2203	4300	6503	SO:0001583	missense	9662	exon10			AGAAAGAAAAGGA	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.1133A>G	4.37:g.56837458A>G	ENSP00000257287:p.Glu378Gly	141	0	0		122	57	0.467213	NM_025009	B2RMY0|O75130|Q58F25|Q9H8H7	Missense_Mutation	SNP	ENST00000257287.4	37	CCDS33986.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	A	25.9	4.681724	0.88542	0.005674	0.0	ENSG00000174799	ENST00000257287	T	0.53640	0.61	6.04	6.04	0.98038	.	0.091491	0.64402	D	0.000001	T	0.56920	0.2018	M	0.63428	1.95	0.42620	D	0.993343	D	0.69078	0.997	P	0.62885	0.908	T	0.63404	-0.6645	10	0.52906	T	0.07	.	16.5763	0.84648	1.0:0.0:0.0:0.0	.	378	Q66GS9	CP135_HUMAN	G	378	ENSP00000257287:E378G	ENSP00000257287:E378G	E	+	2	0	CEP135	56532215	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.387000	0.73191	2.317000	0.78254	0.459000	0.35465	GAA	A|0.998;G|0.002	0.002	strong		0.294	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009		G	56837458	A	G	56837458	3	3	22	1	0	0	0	0	1	0	0	0	3249	246	9	3	1167	3	CEP135	4	56837458	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	362128	56837458	134316818	1031	3932											
KIAA1211	57482	hgsc.bcm.edu	37	chr4	57180546	57180546	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccgcgggaagagcagcagcGgagcctggaagcgccaggtt	9	3	18	11	4	0	1	0	0	0	1	0	4	0	4	3	4	5	3	3	4	2	1	rs145781098	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:57180546G>A	ENST00000504228.1	+	6	983	c.878G>A	c.(877-879)cGg>cAg	p.R293Q	KIAA1211_ENST00000541073.1_Missense_Mutation_p.R286Q|KIAA1211_ENST00000264229.6_Missense_Mutation_p.R293Q			Q6ZU35	K1211_HUMAN	KIAA1211	293	Glu-rich.									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)					GAGCAGCAGCGGAGCCTGGAA	0.697													G|||	27	0.00539137	0.0197	0.0014	5008	,	,		13712	0.0		0.0	False		,,,				2504	0.0				p.R293Q		Atlas-SNP	.											.	KIAA1211	178	.	0			c.G878A						PASS	.	G	GLN/ARG	46,3696		0,46,1825	5	8	7		878	-2.7	0	4	dbSNP_134	7	6,7630		0,6,3812	no	missense	KIAA1211	NM_020722.1	43	0,52,5637	AA,AG,GG		0.0786,1.2293,0.457	benign	293/1234	57180546	52,11326	1871	3818	5689	SO:0001583	missense	57482	exon8			AGCAGCGGAGCCT	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.878G>A	4.37:g.57180546G>A	ENSP00000423366:p.Arg293Gln	39	0	0		49	24	0.489796	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	37	CCDS43230.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	G	12.98	2.100302	0.37048	0.012293	7.86E-4	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073;ENST00000546221	T;T;T	0.14391	2.51;2.51;2.52	4.88	-2.66	0.06077	.	.	.	.	.	T	0.00815	0.0027	N	0.00246	-1.78	0.09310	N	1	B;B;B	0.15930	0.015;0.015;0.015	B;B;B	0.11329	0.006;0.003;0.003	T	0.44159	-0.9346	9	0.11485	T	0.65	-0.6858	6.6117	0.22755	0.3545:0.2188:0.4268:0.0	.	286;286;293	B7ZVZ4;F5H1N7;Q6ZU35	.;.;K1211_HUMAN	Q	293;293;286;203	ENSP00000264229:R293Q;ENSP00000423366:R293Q;ENSP00000444006:R286Q	ENSP00000264229:R293Q	R	+	2	0	KIAA1211	56875303	0.000000	0.05858	0.000000	0.03702	0.143000	0.21401	-0.656000	0.05342	-0.778000	0.04566	0.462000	0.41574	CGG	G|0.994;A|0.006	0.006	strong		0.697	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722		A	57180546	G	A	57180546	3	1	22	1	0	0	0	0	1	0	0	0	8224	1116	39	1	896	1	KIAA1211	4	57180546	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	343088	57180546	133973730	1032	3933											
TMPRSS11F	389208	hgsc.bcm.edu	37	chr4	68934515	68934515	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctggtaatggcatgtttgaAgatgtcatccttattccaca	10	14	9	8	0	1	2	1	1	0	1	3	2	3	2	2	2	0	4	2	2	3	4	rs35687346	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:68934515A>G	ENST00000356291.2	-	7	635	c.576T>C	c.(574-576)tcT>tcC	p.S192S	UBA6-AS1_ENST00000500538.2_RNA|UBA6-AS1_ENST00000511571.1_RNA|UBA6-AS1_ENST00000499180.2_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	192						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						GCATGTTTGAAGATGTCATCC	0.423													A|||	232	0.0463259	0.1619	0.0216	5008	,	,		21406	0.0		0.003	False		,,,				2504	0.0				p.S192S		Atlas-SNP	.											.	TMPRSS11F	79	.	0			c.T576C						PASS	.	A		551,3855	245.3+/-254.3	37,477,1689	88	83	85		576	-1.1	1	4	dbSNP_126	85	39,8561	25.1+/-72.6	0,39,4261	no	coding-synonymous	TMPRSS11F	NM_207407.2		37,516,5950	GG,GA,AA		0.4535,12.5057,4.5364		192/439	68934515	590,12416	2203	4300	6503	SO:0001819	synonymous_variant	389208	exon7			GTTTGAAGATGTC	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.576T>C	4.37:g.68934515A>G		129	0	0		132	61	0.462121	NM_207407	A8MXX2	Silent	SNP	ENST00000356291.2	37	CCDS3520.1																																																																																			A|0.955;G|0.045	0.045	strong		0.423	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407		G	68934515	A	G	68934515	2	3	22	1	0	0	0	0	0	0	0	1	16258	59	3	3		3	TMPRSS11F	4	68934515	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	11753969	68934515	122219761	1033	3934											
TMPRSS11F	389208	hgsc.bcm.edu	37	chr4	68938185	68938185	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tatgagcactataagaatatCcacaccttgttcatctggac	13	12	6	10	0	2	2	1	1	1	1	3	3	3	3	2	1	1	2	2	1	5	6	rs1438391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:68938185C>T	ENST00000356291.2	-	5	429	c.370G>A	c.(370-372)Gat>Aat	p.D124N	UBA6-AS1_ENST00000500538.2_RNA|UBA6-AS1_ENST00000511571.1_RNA|UBA6-AS1_ENST00000499180.2_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	124	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.		D -> N (in dbSNP:rs1438391).			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						ATAAGAATATCCACACCTTGT	0.303													C|||	190	0.0379393	0.1301	0.0216	5008	,	,		12334	0.0		0.003	False		,,,				2504	0.0				p.D124N		Atlas-SNP	.											.	TMPRSS11F	79	.	0			c.G370A						PASS	.	C	ASN/ASP	471,3935	220.0+/-237.6	24,423,1756	89	89	89		370	3.6	0	4	dbSNP_88	89	35,8565	22.8+/-68.1	0,35,4265	yes	missense	TMPRSS11F	NM_207407.2	23	24,458,6021	TT,TC,CC		0.407,10.69,3.8905	benign	124/439	68938185	506,12500	2203	4300	6503	SO:0001583	missense	389208	exon5			GAATATCCACACC	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.370G>A	4.37:g.68938185C>T	ENSP00000348639:p.Asp124Asn	54	0	0		58	28	0.482759	NM_207407	A8MXX2	Missense_Mutation	SNP	ENST00000356291.2	37	CCDS3520.1	70	0.03205128205128205	61	0.12398373983739837	9	0.024861878453038673	0	0.0	0	0.0	C	1.216	-0.628370	0.03610	0.1069	0.00407	ENSG00000198092	ENST00000356291	T	0.37235	1.21	6.07	3.63	0.41609	SEA (3);	0.702903	0.13299	N	0.398399	T	0.00144	0.0004	N	0.01048	-1.04	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.26292	-1.0107	9	0.12103	T	0.63	.	5.8211	0.18528	0.0:0.0872:0.1681:0.7447	rs1438391;rs1438391	124	Q6ZWK6	TM11F_HUMAN	N	124	ENSP00000348639:D124N	ENSP00000348639:D124N	D	-	1	0	TMPRSS11F	68620780	0.556000	0.26538	0.016000	0.15963	0.005000	0.04900	1.049000	0.30392	0.514000	0.28300	-0.302000	0.09304	GAT	C|0.960;T|0.040	0.040	strong		0.303	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407		T	68938185	C	T	68938185	3	4	22	1	0	0	0	0	1	0	0	0	16258	855	30	2	970	2	TMPRSS11F	4	68938185	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3670	68938185	122216091	1034	3935											
TMPRSS11B	132724	hgsc.bcm.edu	37	chr4	69094472	69094472	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agacatacctgacatgcatcAgcttctcctgacataaatcc	13	10	5	13	0	2	3	1	2	1	1	4	3	3	3	3	0	3	2	3	0	3	3	rs34044450	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:69094472A>T	ENST00000332644.5	-	9	1238	c.1077T>A	c.(1075-1077)gcT>gcA	p.A359A		NM_182502.3	NP_872308.2	Q86T26	TM11B_HUMAN	transmembrane protease, serine 11B	359	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.A359A(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)	27						GACATGCATCAGCTTCTCCTG	0.323													A|||	48	0.00958466	0.0356	0.0014	5008	,	,		19437	0.0		0.0	False		,,,				2504	0.0				p.A359A		Atlas-SNP	.											TMPRSS11B,NS,carcinoma,0,1	TMPRSS11B	66	1	1	Substitution - coding silent(1)	lung(1)	c.T1077A						PASS	.	A		116,4290	88.2+/-126.9	2,112,2089	131	120	124		1077	-5.8	0	4	dbSNP_126	124	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	TMPRSS11B	NM_182502.3		2,120,6381	TT,TA,AA		0.093,2.6328,0.9534		359/417	69094472	124,12882	2203	4300	6503	SO:0001819	synonymous_variant	132724	exon9			TGCATCAGCTTCT	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.1077T>A	4.37:g.69094472A>T		234	0	0		252	114	0.452381	NM_182502	A8K4D9	Silent	SNP	ENST00000332644.5	37	CCDS3521.1																																																																																			A|0.990;T|0.010	0.010	strong		0.323	TMPRSS11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251431.2	NM_182502		T	69094472	A	T	69094472	2	4	22	1	0	0	0	0	0	0	0	1	16255	175	7	5		5	TMPRSS11B	4	69094472	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	156287	69094472	122059804	1035	3936											
TMPRSS11B	132724	hgsc.bcm.edu	37	chr4	69098115	69098115	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagttgttggtaagcatttcAgaagcagccttgctgatttc	9	14	10	8	0	1	2	1	1	0	1	2	2	1	2	1	1	4	6	1	1	2	6	rs10018067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:69098115A>G	ENST00000332644.5	-	6	650	c.489T>C	c.(487-489)tcT>tcC	p.S163S		NM_182502.3	NP_872308.2	Q86T26	TM11B_HUMAN	transmembrane protease, serine 11B	163						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						TAAGCATTTCAGAAGCAGCCT	0.289													a|||	141	0.028155	0.1006	0.0086	5008	,	,		13924	0.0		0.0	False		,,,				2504	0.002				p.S163S		Atlas-SNP	.											.	TMPRSS11B	66	.	0			c.T489C						PASS	.	G		346,4054	754.8+/-412.5	17,312,1871	49	56	53		489	1.9	0	4	dbSNP_119	53	14,8572	810.0+/-407.1	0,14,4279	no	coding-synonymous	TMPRSS11B	NM_182502.3		17,326,6150	GG,GA,AA		0.1631,7.8636,2.7722		163/417	69098115	360,12626	2200	4293	6493	SO:0001819	synonymous_variant	132724	exon6			CATTTCAGAAGCA	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.489T>C	4.37:g.69098115A>G		114	0	0		158	80	0.506329	NM_182502	A8K4D9	Silent	SNP	ENST00000332644.5	37	CCDS3521.1																																																																																			A|0.973;G|0.027	0.027	strong		0.289	TMPRSS11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251431.2	NM_182502		G	69098115	A	G	69098115	2	3	22	1	0	0	0	0	0	0	0	1	16255	175	7	3		3	TMPRSS11B	4	69098115	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	3643	69098115	122056161	1036	3937											
TMPRSS11B	132724	hgsc.bcm.edu	37	chr4	69100200	69100200	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccatgagtttaatggaagcAggaactgcattccaggatgc	12	9	11	9	0	0	1	0	1	0	0	1	4	1	4	2	3	4	3	2	3	3	3	rs4431295	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:69100200A>G	ENST00000332644.5	-	5	611	c.450T>C	c.(448-450)ccT>ccC	p.P150P		NM_182502.3	NP_872308.2	Q86T26	TM11B_HUMAN	transmembrane protease, serine 11B	150	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						TAATGGAAGCAGGAACTGCAT	0.328													G|||	141	0.028155	0.1006	0.0086	5008	,	,		17100	0.0		0.0	False		,,,				2504	0.002				p.P150P		Atlas-SNP	.											.	TMPRSS11B	66	.	0			c.T450C						PASS	.	G		351,4055	794.2+/-415.3	20,311,1872	108	104	106		450	-8.9	0	4	dbSNP_111	106	14,8586	818.7+/-406.8	0,14,4286	no	coding-synonymous	TMPRSS11B	NM_182502.3		20,325,6158	GG,GA,AA		0.1628,7.9664,2.8064		150/417	69100200	365,12641	2203	4300	6503	SO:0001819	synonymous_variant	132724	exon5			GGAAGCAGGAACT	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.450T>C	4.37:g.69100200A>G		83	0	0		108	56	0.518519	NM_182502	A8K4D9	Silent	SNP	ENST00000332644.5	37	CCDS3521.1																																																																																			A|0.970;G|0.030	0.030	strong		0.328	TMPRSS11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251431.2	NM_182502		G	69100200	A	G	69100200	2	3	22	1	0	0	0	0	0	0	0	1	16255	175	7	3		3	TMPRSS11B	4	69100200	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2085	69100200	122054076	1037	3938											
UGT2B11	10720	hgsc.bcm.edu	37	chr4	70078393	70078393	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctccaggagtttcgcataagCcatatgtcagcttttcccat	9	13	7	12	1	1	0	1	0	0	0	4	1	3	1	3	1	2	3	3	1	2	5	rs138593124	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:70078393C>T	ENST00000446444.1	-	2	776	c.768G>A	c.(766-768)tgG>tgA	p.W256*	RP11-704M14.1_ENST00000504301.1_RNA|RP11-704M14.1_ENST00000505646.1_RNA	NM_001073.1	NP_001064.1	O75310	UDB11_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B11	256					estrogen metabolic process (GO:0008210)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			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						TTCGCATAAGCCATATGTCAG	0.388													.|||	22	0.00439297	0.0159	0.0014	5008	,	,		14009	0.0		0.0	False		,,,				2504	0.0				p.W256X		Atlas-SNP	.											.	UGT2B11	92	.	0			c.G768A						PASS	.	C	stop/TRP	83,4323		1,81,2121	141	147	145		768	2	0.2	4	dbSNP_134	145	0,8598		0,0,4299	no	stop-gained	UGT2B11	NM_001073.1		1,81,6420	TT,TC,CC		0.0,1.8838,0.6383		256/530	70078393	83,12921	2203	4299	6502	SO:0001587	stop_gained	10720	exon2			CATAAGCCATATG	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.768G>A	4.37:g.70078393C>T	ENSP00000387683:p.Trp256*	312	0	0		336	151	0.449405	NM_001073	Q3KNV9	Nonsense_Mutation	SNP	ENST00000446444.1	37	CCDS3527.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	-	12.43	1.936842	0.34189	0.018838	0.0	ENSG00000213759	ENST00000446444	.	.	.	1.96	1.96	0.26148	.	0.000000	0.64402	U	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.5515	0.39313	0.0:1.0:0.0:0.0	.	.	.	.	X	256	.	ENSP00000387683:W256X	W	-	3	0	UGT2B11	70112982	1.000000	0.71417	0.183000	0.23137	0.044000	0.14063	4.939000	0.63526	1.087000	0.41251	0.184000	0.17185	TGG	C|0.993;T|0.007	0.007	strong		0.388	UGT2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251551.2	NM_001073		T	70078393	C	T	70078393	4	4	22	1	0	0	0	0	0	1	0	0	16972	740	26	2	841	2	UGT2B11	4	70078393	Nonsense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	978193	70078393	121075883	1038	3939											
C4orf40	401137	hgsc.bcm.edu	37	chr4	71024268	71024268	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcccttagctactcagttgaAtgttcctcctctccctccta	6	15	4	16	0	2	1	1	1	1	0	7	1	6	1	5	0	2	3	5	0	4	5	rs116632053	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:71024268A>G	ENST00000344526.5	+	3	488	c.299A>G	c.(298-300)aAt>aGt	p.N100S	C4orf40_ENST00000502441.2_Intron|C4orf40_ENST00000502294.1_Missense_Mutation_p.N100S	NM_214711.3	NP_999876.2	Q6MZM9	PRR27_HUMAN		100	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						ACTCAGTTGAATGTTCCTCCT	0.512													A|||	48	0.00958466	0.0348	0.0029	5008	,	,		20664	0.0		0.0	False		,,,				2504	0.0				p.N100S		Atlas-SNP	.											.	C4orf40	19	.	0			c.A299G						PASS	.	A	SER/ASN	178,4228	115.4+/-153.4	1,176,2026	264	254	257		299	-7.7	0	4	dbSNP_132	257	1,8599	1.2+/-3.3	0,1,4299	yes	missense	C4orf40	NM_214711.3	46	1,177,6325	GG,GA,AA		0.0116,4.0399,1.3763	benign	100/220	71024268	179,12827	2203	4300	6503	SO:0001583	missense	401137	exon3			AGTTGAATGTTCC																												ENST00000344526.5:c.299A>G	4.37:g.71024268A>G	ENSP00000343172:p.Asn100Ser	209	0	0		213	100	0.469484	NM_214711	A8MXP0|Q6MZR6	Missense_Mutation	SNP	ENST00000344526.5	37	CCDS3535.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	A	10.53	1.375740	0.24857	0.040399	1.16E-4	ENSG00000187533	ENST00000502294;ENST00000344526	T;T	0.34859	1.34;1.34	3.84	-7.67	0.01272	.	.	.	.	.	T	0.02767	0.0083	N	0.14661	0.345	0.09310	N	1	B	0.14438	0.01	B	0.13407	0.009	T	0.17992	-1.0351	9	0.13853	T	0.58	0.3329	1.6043	0.02681	0.3253:0.1509:0.0919:0.4319	.	100	Q6MZM9	CD040_HUMAN	S	100	ENSP00000426249:N100S;ENSP00000343172:N100S	ENSP00000343172:N100S	N	+	2	0	C4orf40	71058857	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.709000	0.00819	-2.592000	0.00456	-0.842000	0.03052	AAT	A|0.986;G|0.014	0.014	strong		0.512	C4orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251558.1			G	71024268	A	G	71024268	3	3	22	1	0	0	0	0	1	0	0	0	2271	101	4	3	309	3	C4orf40	4	71024268	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	945875	71024268	120130008	1039	3940											
C4orf40	401137	hgsc.bcm.edu	37	chr4	71024552	71024552	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cagctgcagaggaaccttcaCcagctgagcctgctacagcc	10	6	10	15	0	1	2	1	1	0	1	1	3	1	3	4	1	8	4	4	1	2	2	rs143985138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:71024552C>G	ENST00000344526.5	+	3	772	c.583C>G	c.(583-585)Cca>Gca	p.P195A	C4orf40_ENST00000502294.1_Missense_Mutation_p.P195A	NM_214711.3	NP_999876.2	Q6MZM9	PRR27_HUMAN		195	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						GGAACCTTCACCAGCTGAGCC	0.557													C|||	48	0.00958466	0.0348	0.0029	5008	,	,		16492	0.0		0.0	False		,,,				2504	0.0				p.P195A		Atlas-SNP	.											.	C4orf40	19	.	0			c.C583G						PASS	.	C	ALA/PRO	172,4234		1,170,2032	57	52	54		583	-7.9	0	4	dbSNP_134	54	1,8599		0,1,4299	yes	missense	C4orf40	NM_214711.3	27	1,171,6331	GG,GC,CC		0.0116,3.9038,1.3302	benign	195/220	71024552	173,12833	2203	4300	6503	SO:0001583	missense	401137	exon3			CCTTCACCAGCTG																												ENST00000344526.5:c.583C>G	4.37:g.71024552C>G	ENSP00000343172:p.Pro195Ala	325	0	0		303	136	0.448845	NM_214711	A8MXP0|Q6MZR6	Missense_Mutation	SNP	ENST00000344526.5	37	CCDS3535.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	C	5.440	0.266257	0.10294	0.039038	1.16E-4	ENSG00000187533	ENST00000502294;ENST00000344526	T;T	0.28454	1.61;1.61	3.97	-7.94	0.01152	.	.	.	.	.	T	0.02047	0.0064	N	0.14661	0.345	0.09310	N	1	B	0.14438	0.01	B	0.12837	0.008	T	0.26538	-1.0100	9	0.02654	T	1	5.212	3.7914	0.08722	0.2107:0.3878:0.3086:0.0929	.	195	Q6MZM9	CD040_HUMAN	A	195	ENSP00000426249:P195A;ENSP00000343172:P195A	ENSP00000343172:P195A	P	+	1	0	C4orf40	71059141	0.001000	0.12720	0.000000	0.03702	0.012000	0.07955	0.133000	0.15912	-1.914000	0.01078	0.411000	0.27672	CCA	C|0.987;G|0.013	0.013	strong		0.557	C4orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251558.1			G	71024552	C	G	71024552	3	3	22	1	0	0	0	0	1	0	0	0	2271	507	18	4	593	4	C4orf40	4	71024552	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	284	71024552	120129724	1040	3941											
PROL1	58503	hgsc.bcm.edu	37	chr4	71275631	71275632	+	Frame_Shift_Ins	INS	-	-	C																															cacctccatatcagcagcaaINScccccgcagcatctactgaa																								rs573505950|rs201259916	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:71275631_71275632insC	ENST00000399575.2	+	3	760_761	c.586_587insC	c.(586-588)accfs	p.T196fs		NM_021225.4	NP_067048.4	Q99935	PROL1_HUMAN	proline rich, lacrimal 1	196	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)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)	15		all_hematologic(202;0.196)				ATCAGCAGCAACCCCCGCAGCA	0.49													CCCCC|CCCCC|CCCCCC|insertion	10	0.00199681	0.0068	0.0014	5008	,	,		19421	0.0		0.0	False		,,,				2504	0.0				p.T196fs		Pindel,Atlas-Indel	.											.	PROL1	46	.	0			c.586_587insC						PASS	.			26,3928		2,22,1953						0.2	0			139	0,8034		0,0,4017	no	frameshift	PROL1	NM_021225.4		2,22,5970	A1A1,A1R,RR		0.0,0.6576,0.2169				26,11962				SO:0001589	frameshift_variant	58503	exon3			.	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.591dupC	4.37:g.71275636_71275636dupC	ENSP00000382485:p.Thr196fs	167	0	.		197	65	0.33	NM_021225	A8MZ07|P85047	Frame_Shift_Ins	INS	ENST00000399575.2	37	CCDS43235.1																																																																																			.	.	none		0.49	PROL1-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000362639.1	NM_021225		C	71275632	-	C	71275631	7	5	22	1	0	1	1	0	0	0	0	0	12566	43	2	0	592	0	PROL1	4	71275631	Frame_Shift_Ins	INS	-	TCGA-G8-6324-01A-11D-2210-10	251079	71275631	119878645	1041	3942											
ENAM	10117	hgsc.bcm.edu	37	chr4	71508869	71508869	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accaagaaatctctccacctTttaaggaagatccagggagg	14	8	9	10	0	1	2	0	0	1	2	4	4	3	4	4	3	0	0	4	3	4	2	rs2609428	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:71508869T>C	ENST00000396073.3	+	9	2007	c.1726T>C	c.(1726-1728)Ttt>Ctt	p.F576L	ENAM_ENST00000472903.1_Intron	NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	576			F -> L (in dbSNP:rs2609428).		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)			CTCTCCACCTTTTAAGGAAGA	0.443													T|||	197	0.0393371	0.1346	0.0144	5008	,	,		20189	0.0		0.0089	False		,,,				2504	0.0				p.F576L		Atlas-SNP	.											.	ENAM	140	.	0			c.T1726C						PASS	.	T	LEU/PHE	528,3878	231.7+/-245.5	27,474,1702	161	168	166		1726	3.5	0.9	4	dbSNP_100	166	29,8571	18.5+/-59.3	0,29,4271	yes	missense	ENAM	NM_031889.2	22	27,503,5973	CC,CT,TT		0.3372,11.9837,4.2826	benign	576/1143	71508869	557,12449	2203	4300	6503	SO:0001583	missense	10117	exon9			CCACCTTTTAAGG	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.1726T>C	4.37:g.71508869T>C	ENSP00000379383:p.Phe576Leu	125	0	0		137	62	0.452555	NM_031889	Q17RI5|Q9H3D1	Missense_Mutation	SNP	ENST00000396073.3	37	CCDS3544.2	80	0.03663003663003663	72	0.14634146341463414	5	0.013812154696132596	0	0.0	3	0.00395778364116095	T	12.85	2.062285	0.36373	0.119837	0.003372	ENSG00000132464	ENST00000396073	T	0.40756	1.02	5.83	3.45	0.39498	.	0.216214	0.33438	N	0.004920	T	0.00109	0.0003	N	0.20574	0.59	0.41757	P	0.010307999999999984	B	0.23735	0.09	B	0.26969	0.075	T	0.14008	-1.0488	9	0.05620	T	0.96	-5.2885	6.2822	0.21013	0.0:0.1986:0.0:0.8014	rs2609428;rs2609428	576	Q9NRM1	ENAM_HUMAN	L	576	ENSP00000379383:F576L	ENSP00000379383:F576L	F	+	1	0	ENAM	71727733	0.757000	0.28394	0.948000	0.38648	0.909000	0.53808	0.881000	0.28173	1.034000	0.39945	0.533000	0.62120	TTT	T|0.952;C|0.048	0.048	strong		0.443	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3	NM_031889		C	71508869	T	C	71508869	3	2	22	1	0	0	0	0	1	0	0	0	5114	1841	64	3	1756	3	ENAM	4	71508869	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	233238	71508869	119645407	1042	3943											
ENAM	10117	hgsc.bcm.edu	37	chr4	71510368	71510368	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accaccggaactccatctagCgatggaaggcaaagcccatt	13	6	9	13	2	1	0	0	0	1	0	2	3	2	2	4	3	3	1	4	3	4	2	rs61737041	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:71510368C>T	ENST00000396073.3	+	9	3506	c.3225C>T	c.(3223-3225)agC>agT	p.S1075S	ENAM_ENST00000472903.1_Intron	NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	1075					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)			CTCCATCTAGCGATGGAAGGC	0.433													C|||	40	0.00798722	0.0295	0.0014	5008	,	,		24126	0.0		0.0	False		,,,				2504	0.0				p.S1075S		Atlas-SNP	.											.	ENAM	140	.	0			c.C3225T						PASS	.	C		106,4300	82.4+/-120.9	2,102,2099	96	93	94		3225	4.2	1	4	dbSNP_129	94	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ENAM	NM_031889.2		2,103,6398	TT,TC,CC		0.0116,2.4058,0.8227		1075/1143	71510368	107,12899	2203	4300	6503	SO:0001819	synonymous_variant	10117	exon9			ATCTAGCGATGGA	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.3225C>T	4.37:g.71510368C>T		254	0	0		266	127	0.477444	NM_031889	Q17RI5|Q9H3D1	Silent	SNP	ENST00000396073.3	37	CCDS3544.2																																																																																			C|0.993;T|0.007	0.007	strong		0.433	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3	NM_031889		T	71510368	C	T	71510368	2	4	22	1	0	0	0	0	0	0	0	1	5114	767	27	1		1	ENAM	4	71510368	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1499	71510368	119643908	1043	3944											
IGJ	3512	hgsc.bcm.edu	37	chr4	71522999	71522999	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gagatattctccctgttgttCagaggaacactaaaagaaaa	16	10	8	7	0	2	3	1	0	1	3	3	5	2	4	1	1	1	2	1	1	6	5	rs75928327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:71522999C>T	ENST00000254801.4	-	3	367	c.198G>A	c.(196-198)ctG>ctA	p.L66L	IGJ_ENST00000543780.1_Silent_p.L82L|ENAM_ENST00000472903.1_Intron	NM_144646.3	NP_653247.1	P01591	IGJ_HUMAN	immunoglobulin J polypeptide, linker protein for immunoglobulin alpha and mu polypeptides	66					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)			CCCTGTTGTTCAGAGGAACAC	0.328													C|||	45	0.00898562	0.034	0.0	5008	,	,		16873	0.0		0.0	False		,,,				2504	0.0				p.L66L		Atlas-SNP	.											.	IGJ	13	.	0			c.G198A						PASS	.	C		103,4303	82.9+/-121.4	0,103,2100	81	77	78		198	4.7	1	4	dbSNP_132	78	2,8594	2.2+/-6.3	0,2,4296	no	coding-synonymous	IGJ	NM_144646.3		0,105,6396	TT,TC,CC		0.0233,2.3377,0.8076		66/160	71522999	105,12897	2203	4298	6501	SO:0001819	synonymous_variant	3512	exon3			GTTGTTCAGAGGA	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.198G>A	4.37:g.71522999C>T		46	0	0		51	22	0.431373	NM_144646		Silent	SNP	ENST00000254801.4	37	CCDS3545.1																																																																																			C|0.990;T|0.010	0.010	strong		0.328	IGJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252160.1	NM_144646		T	71522999	C	T	71522999	2	4	22	1	0	0	0	0	0	0	0	1	7601	813	29	2		2	IGJ	4	71522999	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	12631	71522999	119631277	1044	3945											
UTP3	57050	hgsc.bcm.edu	37	chr4	71555656	71555656	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aattgctaaaaataggggacTtactcctaggagaaagaaga	18	8	10	5	0	0	3	0	0	0	3	1	5	1	4	1	3	2	1	1	3	9	5	rs111975570	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:71555656T>G	ENST00000254803.2	+	1	1461	c.1262T>G	c.(1261-1263)cTt>cGt	p.L421R		NM_020368.2	NP_065101.1	Q9NQZ2	SAS10_HUMAN	UTP3, small subunit (SSU) processome component, homolog (S. cerevisiae)	421					brain development (GO:0007420)|chromatin modification (GO:0016568)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(4)	18			Lung(101;0.235)			AATAGGGGACTTACTCCTAGG	0.388													T|||	36	0.0071885	0.0272	0.0	5008	,	,		17360	0.0		0.0	False		,,,				2504	0.0				p.L421R		Atlas-SNP	.											.	UTP3	40	.	0			c.T1262G						PASS	.	T	ARG/LEU	64,4342	61.1+/-98.1	0,64,2139	89	95	93		1262	5.5	1	4	dbSNP_132	93	0,8600		0,0,4300	yes	missense	UTP3	NM_020368.2	102	0,64,6439	GG,GT,TT		0.0,1.4526,0.4921	probably-damaging	421/480	71555656	64,12942	2203	4300	6503	SO:0001583	missense	57050	exon1			GGGGACTTACTCC	AL136590	CCDS3546.1	4q13.3	2008-02-05			ENSG00000132467	ENSG00000132467			24477	protein-coding gene	gene with protein product	"disrupter of silencing 10"	611614				12477932	Standard	NM_020368		Approved	FLJ23256, DKFZp761F222, SAS10, CRLZ1	uc003hfo.3	Q9NQZ2	OTTHUMG00000129911	ENST00000254803.2:c.1262T>G	4.37:g.71555656T>G	ENSP00000254803:p.Leu421Arg	71	0	0		76	37	0.486842	NM_020368	Q6FI82	Missense_Mutation	SNP	ENST00000254803.2	37	CCDS3546.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	T	20.6	4.011830	0.75046	0.014526	0.0	ENSG00000132467	ENST00000254803	T	0.62788	-0.0	5.46	5.46	0.80206	Something about silencing protein 10 (Sas10), C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.70710	0.3255	H	0.96111	3.77	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85360	0.1107	10	0.72032	D	0.01	-6.9132	15.8384	0.78818	0.0:0.0:0.0:1.0	.	421	Q9NQZ2	SAS10_HUMAN	R	421	ENSP00000254803:L421R	ENSP00000254803:L421R	L	+	2	0	UTP3	71774520	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.366000	0.79548	2.191000	0.70037	0.533000	0.62120	CTT	T|0.994;G|0.006	0.006	strong		0.388	UTP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252163.2	NM_020368		G	71555656	T	G	71555656	3	3	22	1	0	0	0	0	1	0	0	0	17116	1609	56	5	1264	5	UTP3	4	71555656	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	32657	71555656	119598620	1045	3946											
SLC4A4	8671	hgsc.bcm.edu	37	chr4	72338467	72338467	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttggattggcctgtggtcCgccttcctatgtctcatttt	3	18	9	11	1	1	0	1	0	1	0	4	1	3	1	4	3	0	0	4	3	1	6	rs35169468	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:72338467C>T	ENST00000264485.5	+	14	1800	c.1683C>T	c.(1681-1683)tcC>tcT	p.S561S	SLC4A4_ENST00000425175.1_Silent_p.S561S|SLC4A4_ENST00000351898.6_Silent_p.S561S|SLC4A4_ENST00000514331.1_3'UTR|SLC4A4_ENST00000512686.1_Silent_p.S517S|SLC4A4_ENST00000340595.3_Silent_p.S517S	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	561					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)	GCCTGTGGTCCGCCTTCCTAT	0.433													C|||	81	0.0161741	0.0446	0.0072	5008	,	,		17363	0.0		0.0	False		,,,				2504	0.0174				p.S561S		Atlas-SNP	.											.	SLC4A4	269	.	0			c.C1683T						PASS	.	C	,,	161,4245	110.8+/-149.0	2,157,2044	175	173	174		1683,1683,1551	-3.7	1	4	dbSNP_126	174	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC4A4	NM_001098484.2,NM_001134742.1,NM_003759.3	,,	2,159,6342	TT,TC,CC		0.0233,3.6541,1.2533	,,	561/1080,561/1095,517/1036	72338467	163,12843	2203	4300	6503	SO:0001819	synonymous_variant	8671	exon14			GTGGTCCGCCTTC	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.1683C>T	4.37:g.72338467C>T		117	0	0		124	52	0.419355	NM_001098484	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Silent	SNP	ENST00000264485.5	37	CCDS43236.1																																																																																			C|0.988;T|0.012	0.012	strong		0.433	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759		T	72338467	C	T	72338467	2	4	22	1	0	0	0	0	0	0	0	1	14671	639	23	1		1	SLC4A4	4	72338467	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	782811	72338467	118815809	1046	3947											
NPFFR2	10886	hgsc.bcm.edu	37	chr4	73012709	73012709	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgcaggttccagtgtgtggTctacccttttaaaccaaagc	9	13	9	10	0	1	0	0	0	1	0	2	0	2	0	3	2	4	2	3	2	4	5	rs61733659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:73012709T>C	ENST00000308744.6	+	4	847	c.749T>C	c.(748-750)gTc>gCc	p.V250A	NPFFR2_ENST00000395999.1_Missense_Mutation_p.V151A|NPFFR2_ENST00000506359.1_3'UTR|NPFFR2_ENST00000344413.5_3'UTR|NPFFR2_ENST00000358749.3_Missense_Mutation_p.V148A	NM_004885.2	NP_004876.2	Q9Y5X5	NPFF2_HUMAN	neuropeptide FF receptor 2	250					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)			CAGTGTGTGGTCTACCCTTTT	0.393													T|||	47	0.00938498	0.0348	0.0014	5008	,	,		18136	0.0		0.0	False		,,,				2504	0.0				p.V250A		Atlas-SNP	.											.	NPFFR2	98	.	0			c.T749C						PASS	.	T	ALA/VAL,ALA/VAL,ALA/VAL	122,4284	91.6+/-130.3	5,112,2086	189	190	190		452,749,443	5.8	1	4	dbSNP_129	190	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense	NPFFR2	NM_001144756.1,NM_004885.2,NM_053036.2	64,64,64	5,114,6384	CC,CT,TT		0.0233,2.769,0.9534	possibly-damaging,possibly-damaging,possibly-damaging	151/424,250/523,148/421	73012709	124,12882	2203	4300	6503	SO:0001583	missense	10886	exon4			GTGTGGTCTACCC	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.749T>C	4.37:g.73012709T>C	ENSP00000307822:p.Val250Ala	84	0	0		86	42	0.488372	NM_004885	Q96RV1|Q9NR49	Missense_Mutation	SNP	ENST00000308744.6	37	CCDS3551.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	T	17.37	3.371957	0.61624	0.02769	2.33E-4	ENSG00000056291	ENST00000308744;ENST00000395999;ENST00000358749	T;T;T	0.38887	1.11;1.11;1.11	5.81	5.81	0.92471	GPCR, rhodopsin-like superfamily (1);	0.256399	0.27725	N	0.018102	T	0.32133	0.0819	M	0.85299	2.745	0.80722	D	1	P;D	0.55385	0.772;0.971	P;P	0.57057	0.628;0.812	T	0.60662	-0.7219	10	0.87932	D	0	.	15.8328	0.78769	0.0:0.0:0.0:1.0	rs61733659	151;250	Q9Y5X5-3;Q9Y5X5	.;NPFF2_HUMAN	A	250;151;148	ENSP00000307822:V250A;ENSP00000379321:V151A;ENSP00000351599:V148A	ENSP00000307822:V250A	V	+	2	0	NPFFR2	73231573	1.000000	0.71417	0.974000	0.42286	0.178000	0.23041	7.911000	0.87458	2.221000	0.72209	0.528000	0.53228	GTC	T|0.990;C|0.010	0.010	strong		0.393	NPFFR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252170.2	NM_004885		C	73012709	T	C	73012709	3	2	22	1	0	0	0	0	1	0	0	0	10587	1667	58	3	769	3	NPFFR2	4	73012709	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	674242	73012709	118141567	1047	3948											
AFP	174	hgsc.bcm.edu	37	chr4	74316461	74316461	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacaaactattggcctgtggCgagggagcggtgagtgtctg	8	9	17	7	2	1	1	0	1	1	0	1	4	1	2	1	4	2	0	1	4	2	2	rs115622472	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:74316461C>T	ENST00000395792.2	+	11	1519	c.1419C>T	c.(1417-1419)ggC>ggT	p.G473G	AFP_ENST00000226359.2_Silent_p.G473G	NM_001134.1	NP_001125.1	P02771	FETA_HUMAN	alpha-fetoprotein	473	Albumin 3. {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)			TGGCCTGTGGCGAGGGAGCGG	0.522									Alpha-Fetoprotein, Hereditary Persistence of				C|||	22	0.00439297	0.0159	0.0014	5008	,	,		18710	0.0		0.0	False		,,,				2504	0.0				p.G473G		Atlas-SNP	.											.	AFP	60	.	0			c.C1419T						PASS	.	C		76,4330	67.6+/-105.2	0,76,2127	156	134	142		1419	-9.9	0.1	4	dbSNP_132	142	3,8597		0,3,4297	no	coding-synonymous	AFP	NM_001134.1		0,79,6424	TT,TC,CC		0.0349,1.7249,0.6074		473/610	74316461	79,12927	2203	4300	6503	SO:0001819	synonymous_variant	174	exon11	Familial Cancer Database	HPAFP	CTGTGGCGAGGGA	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.1419C>T	4.37:g.74316461C>T		145	0	0		161	70	0.434783	NM_001134	B2RBU3	Silent	SNP	ENST00000395792.2	37	CCDS3556.1																																																																																			C|0.994;T|0.006	0.006	strong		0.522	AFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252284.3			T	74316461	C	T	74316461	2	4	22	1	0	0	0	0	0	0	0	1	363	755	27	1		1	AFP	4	74316461	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1303752	74316461	116837815	1048	3949											
PPEF2	5470	hgsc.bcm.edu	37	chr4	76788564	76788564	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcagagccgactcctccactCtgctaatcctgggacaggag	9	8	10	14	1	2	1	1	0	1	1	5	4	5	3	4	2	2	1	4	2	1	1	rs34155925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:76788564C>T	ENST00000286719.7	-	14	2014	c.1658G>A	c.(1657-1659)aGa>aAa	p.R553K		NM_006239.2	NP_006230.2	O14830	PPE2_HUMAN	protein phosphatase, EF-hand calcium binding domain 2	553			R -> K (in dbSNP:rs34155925).		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)			CTCCTCCACTCTGCTAATCCT	0.403													C|||	639	0.127596	0.4531	0.0346	5008	,	,		19539	0.0079		0.002	False		,,,				2504	0.0061				p.R553K	NSCLC(105;1359 1603 15961 44567 47947)	Atlas-SNP	.											.	PPEF2	108	.	0			c.G1658A						PASS	.	C	LYS/ARG	1783,2623	524.1+/-371.2	357,1069,777	55	57	57		1658	4.3	1	4	dbSNP_126	57	21,8579	14.0+/-48.4	0,21,4279	yes	missense	PPEF2	NM_006239.2	26	357,1090,5056	TT,TC,CC		0.2442,40.4675,13.8705	benign	553/754	76788564	1804,11202	2203	4300	6503	SO:0001583	missense	5470	exon14			TCCACTCTGCTAA	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.1658G>A	4.37:g.76788564C>T	ENSP00000286719:p.Arg553Lys	127	0	0		136	66	0.485294	NM_006239	O14831	Missense_Mutation	SNP	ENST00000286719.7	37	CCDS34013.1	251	0.11492673992673992	239	0.48577235772357724	9	0.024861878453038673	2	0.0034965034965034965	1	0.0013192612137203166	C	12.33	1.906038	0.33628	0.404675	0.002442	ENSG00000156194	ENST00000286719;ENST00000337500	T	0.05081	3.5	6.04	4.31	0.51392	.	4.318100	0.00508	N	0.000165	T	0.00012	0.0000	L	0.55990	1.75	0.21627	P	0.999610337	B;B	0.30146	0.27;0.031	B;B	0.41946	0.371;0.015	T	0.47611	-0.9104	9	0.46703	T	0.11	1.3252	5.7123	0.17941	0.0:0.6724:0.1619:0.1657	rs34155925;rs57342715	553;553	O14830-2;O14830	.;PPE2_HUMAN	K	553	ENSP00000286719:R553K	ENSP00000286719:R553K	R	-	2	0	PPEF2	77007588	0.978000	0.34361	1.000000	0.80357	0.979000	0.70002	1.205000	0.32308	1.571000	0.49722	0.561000	0.74099	AGA	C|0.877;T|0.123	0.123	strong		0.403	PPEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362929.1	NM_006239		T	76788564	C	T	76788564	3	4	22	1	0	0	0	0	1	0	0	0	12317	913	32	2	619	2	PPEF2	4	76788564	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2472103	76788564	114365712	1049	3950											
PPEF2	5470	hgsc.bcm.edu	37	chr4	76797551	76797551	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtcaccaggaggcctgcttgCtgccggcaccgctctagctc	5	8	12	16	2	2	0	1	0	1	0	3	1	2	1	4	3	4	5	4	3	1	2	rs370312706		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:76797551C>G	ENST00000286719.7	-	11	1565	c.1209G>C	c.(1207-1209)caG>caC	p.Q403H		NM_006239.2	NP_006230.2	O14830	PPE2_HUMAN	protein phosphatase, EF-hand calcium binding domain 2	403	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)			GGCCTGCTTGCTGCCGGCACC	0.677																																					p.Q403H	NSCLC(105;1359 1603 15961 44567 47947)	Atlas-SNP	.											.	PPEF2	108	.	0			c.G1209C						PASS	.						29	32	31					4																	76797551		2203	4300	6503	SO:0001583	missense	5470	exon11			TGCTTGCTGCCGG	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.1209G>C	4.37:g.76797551C>G	ENSP00000286719:p.Gln403His	98	0	0		86	40	0.465116	NM_006239	O14831	Missense_Mutation	SNP	ENST00000286719.7	37	CCDS34013.1	.	.	.	.	.	.	.	.	.	.	C	11.77	1.738539	0.30774	.	.	ENSG00000156194	ENST00000286719;ENST00000337500	T	0.41758	0.99	4.94	3.21	0.36854	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (1);Metallophosphoesterase domain (1);	1.466720	0.04609	N	0.399943	T	0.43100	0.1232	L	0.41236	1.265	0.25277	N	0.989465	P;P	0.41569	0.755;0.6	P;B	0.44946	0.465;0.382	T	0.29640	-1.0005	10	0.33940	T	0.23	0.0283	9.0738	0.36508	0.0:0.8174:0.0:0.1826	.	403;403	O14830-2;O14830	.;PPE2_HUMAN	H	403	ENSP00000286719:Q403H	ENSP00000286719:Q403H	Q	-	3	2	PPEF2	77016575	0.764000	0.28473	0.014000	0.15608	0.095000	0.18619	2.772000	0.47678	0.510000	0.28216	-0.339000	0.08088	CAG	.	.	alt		0.677	PPEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362929.1	NM_006239		G	76797551	C	G	76797551	3	3	22	1	0	0	0	0	1	0	0	0	12317	796	28	4	1080	4	PPEF2	4	76797551	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	8987	76797551	114356725	1050	3951											
SCARB2	950	hgsc.bcm.edu	37	chr4	77102148	77102148	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tctaattaagtcaattttagGgtctccaacagattggtctc	11	15	7	8	0	4	1	1	0	3	1	6	1	4	1	1	2	1	0	1	2	5	5	rs143558324	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:77102148G>C	ENST00000264896.2	-	3	731	c.382C>G	c.(382-384)Cct>Gct	p.P128A	SCARB2_ENST00000452464.2_Intron	NM_005506.3	NP_005497.1	Q14108	SCRB2_HUMAN	scavenger receptor class B, member 2	128					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)			TCAATTTTAGGGTCTCCAACA	0.323													G|||	6	0.00119808	0.0045	0.0	5008	,	,		15540	0.0		0.0	False		,,,				2504	0.0				p.P128A		Atlas-SNP	.											.	SCARB2	47	.	0			c.C382G						PASS	.	G	,ALA/PRO	19,4383	26.2+/-53.5	0,19,2182	103	104	104		,382	3.2	0.9	4	dbSNP_134	104	0,8598		0,0,4299	yes	intron,missense	SCARB2	NM_001204255.1,NM_005506.3	,27	0,19,6481	CC,CG,GG		0.0,0.4316,0.1462	,benign	,128/479	77102148	19,12981	2201	4299	6500	SO:0001583	missense	950	exon3			TTTTAGGGTCTCC	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.382C>G	4.37:g.77102148G>C	ENSP00000264896:p.Pro128Ala	61	0	0		61	33	0.540984	NM_005506	B4DKD8|E7EM68|Q53Y63	Missense_Mutation	SNP	ENST00000264896.2	37	CCDS3577.1	.	.	.	.	.	.	.	.	.	.	G	12.17	1.857612	0.32791	0.004316	0.0	ENSG00000138760	ENST00000264896	T	0.72282	-0.64	5.87	3.17	0.36434	.	0.189182	0.64402	N	0.000018	T	0.75034	0.3795	M	0.71206	2.165	0.80722	D	1	B	0.29481	0.245	B	0.43575	0.424	T	0.66697	-0.5858	10	0.09590	T	0.72	.	16.5946	0.84792	0.0:0.3673:0.6327:0.0	.	128	Q14108	SCRB2_HUMAN	A	128	ENSP00000264896:P128A	ENSP00000264896:P128A	P	-	1	0	SCARB2	77321172	1.000000	0.71417	0.946000	0.38457	0.282000	0.26991	3.001000	0.49488	0.452000	0.26830	-0.176000	0.13171	CCT	G|0.999;C|0.001	0.001	strong		0.323	SCARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252403.1	NM_005506		C	77102148	G	C	77102148	3	2	22	1	0	0	0	0	1	0	0	0	13897	1232	43	4	1094	4	SCARB2	4	77102148	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	304597	77102148	114052128	1051	3952											
CCDC158	339965	hgsc.bcm.edu	37	chr4	77288833	77288833	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tttcttggctgtcaactcttCtactactttgcgcagcatct	6	17	6	12	1	5	0	1	0	4	0	5	0	5	0	0	1	5	3	0	1	3	6	rs17001824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:77288833C>T	ENST00000388914.3	-	11	1596	c.1444G>A	c.(1444-1446)Gaa>Aaa	p.E482K		NM_001042784.1	NP_001036249.1	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	482										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						GTCAACTCTTCTACTACTTTG	0.453													C|||	103	0.0205671	0.0734	0.0086	5008	,	,		19288	0.0		0.0	False		,,,				2504	0.0				p.E482K		Atlas-SNP	.											.	CCDC158	114	.	0			c.G1444A						PASS	.	C	LYS/GLU	235,3573		12,211,1681	72	70	70		1444	5.7	1	4	dbSNP_123	70	8,8232		1,6,4113	yes	missense	CCDC158	NM_001042784.1	56	13,217,5794	TT,TC,CC		0.0971,6.1712,2.0169	possibly-damaging	482/1114	77288833	243,11805	1904	4120	6024	SO:0001583	missense	339965	exon11			ACTCTTCTACTAC	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.1444G>A	4.37:g.77288833C>T	ENSP00000373566:p.Glu482Lys	98	0	0		127	58	0.456693	NM_001042784	Q8IYQ1|Q8N7D4|Q8N7E3	Missense_Mutation	SNP	ENST00000388914.3	37	CCDS43242.1	32	0.014652014652014652	29	0.05894308943089431	3	0.008287292817679558	0	0.0	0	0.0	C	26.5	4.747697	0.89663	0.061712	9.71E-4	ENSG00000163749	ENST00000388914	T	0.78364	-1.17	5.71	5.71	0.89125	.	0.000000	0.64402	D	0.000019	T	0.36826	0.0981	N	0.19112	0.55	0.80722	D	1	D	0.71674	0.998	D	0.78314	0.991	T	0.66077	-0.6013	9	.	.	.	.	17.6416	0.88138	0.0:1.0:0.0:0.0	rs17001824;rs17001824	482	Q5M9N0	CD158_HUMAN	K	482	ENSP00000373566:E482K	.	E	-	1	0	CCDC158	77507857	0.999000	0.42202	0.963000	0.40424	0.995000	0.86356	5.178000	0.65037	2.711000	0.92665	0.563000	0.77884	GAA	C|0.981;T|0.019	0.019	strong		0.453	CCDC158-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362694.2	NM_001042784		T	77288833	C	T	77288833	3	4	22	1	0	0	0	0	1	0	0	0	2792	922	32	2	1953	2	CCDC158	4	77288833	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	186685	77288833	113865443	1052	3953											
SHROOM3	57619	hgsc.bcm.edu	37	chr4	77476809	77476809	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgagctccaaactgcaggcTggggatgaggttgtgcacat	9	9	14	9	0	0	2	0	2	0	0	1	3	1	3	1	4	4	5	1	4	1	1	rs75039400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:77476809T>C	ENST00000296043.6	+	2	1169	c.216T>C	c.(214-216)gcT>gcC	p.A72A		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	72	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)			AACTGCAGGCTGGGGATGAGG	0.577													C|||	84	0.0167732	0.0628	0.0014	5008	,	,		18555	0.0		0.0	False		,,,				2504	0.0				p.A72A		Atlas-SNP	.											.	SHROOM3	134	.	0			c.T216C						PASS	.	C		219,4187	806.1+/-415.8	4,211,1988	110	105	107		216	-7.1	0	4	dbSNP_131	107	3,8597	819.2+/-406.8	0,3,4297	no	coding-synonymous	SHROOM3	NM_020859.3		4,214,6285	CC,CT,TT		0.0349,4.9705,1.7069		72/1997	77476809	222,12784	2203	4300	6503	SO:0001819	synonymous_variant	57619	exon2			GCAGGCTGGGGAT	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.216T>C	4.37:g.77476809T>C		64	0	0		95	40	0.421053	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Silent	SNP	ENST00000296043.6	37	CCDS3579.2																																																																																			T|0.980;C|0.020	0.020	strong		0.577	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859		C	77476809	T	C	77476809	2	2	22	1	0	0	0	0	0	0	0	1	14310	1567	55	3		3	SHROOM3	4	77476809	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	187976	77476809	113677467	1053	3954											
SHROOM3	57619	hgsc.bcm.edu	37	chr4	77660550	77660550	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctcctggtctagccttgaTcagaaacggctctgccggcc	7	9	11	14	2	3	2	1	1	2	1	4	2	4	2	4	3	4	2	4	3	2	2	rs61745983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:77660550T>C	ENST00000296043.6	+	5	2177	c.1224T>C	c.(1222-1224)gaT>gaC	p.D408D		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	408					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)			CTAGCCTTGATCAGAAACGGC	0.577													T|||	94	0.01877	0.0681	0.0058	5008	,	,		19865	0.0		0.0	False		,,,				2504	0.0				p.D408D		Atlas-SNP	.											.	SHROOM3	134	.	0			c.T1224C						PASS	.	T		262,4144	146.1+/-180.8	7,248,1948	45	45	45		1224	-1.7	1	4	dbSNP_129	45	1,8599	2.2+/-6.3	0,1,4299	no	coding-synonymous	SHROOM3	NM_020859.3		7,249,6247	CC,CT,TT		0.0116,5.9464,2.0221		408/1997	77660550	263,12743	2203	4300	6503	SO:0001819	synonymous_variant	57619	exon5			CCTTGATCAGAAA	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.1224T>C	4.37:g.77660550T>C		136	0	0		132	58	0.439394	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Silent	SNP	ENST00000296043.6	37	CCDS3579.2																																																																																			T|0.978;C|0.022	0.022	strong		0.577	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859		C	77660550	T	C	77660550	2	2	22	1	0	0	0	0	0	0	0	1	14310	1432	50	3		3	SHROOM3	4	77660550	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	183741	77660550	113493726	1054	3955											
CCNI	10983	hgsc.bcm.edu	37	chr4	77976374	77976374	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tttctccatttccagactaaCcatggccagagcaagcatgg	11	10	8	12	0	1	2	0	0	1	2	3	2	2	2	4	2	3	2	4	2	2	3	rs4252903	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:77976374C>T	ENST00000237654.4	-	6	1195	c.619G>A	c.(619-621)Gtt>Att	p.V207I	CCNI_ENST00000537948.1_Missense_Mutation_p.V193I|CCNI_ENST00000504697.1_5'Flank	NM_006835.2	NP_006826.1	Q14094	CCNI_HUMAN	cyclin I	207			V -> I (in dbSNP:rs4252903). {ECO:0000269|Ref.4}.		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						TCCAGACTAACCATGGCCAGA	0.438													C|||	38	0.00758786	0.0287	0.0	5008	,	,		16139	0.0		0.0	False		,,,				2504	0.0				p.V207I		Atlas-SNP	.											.	CCNI	22	.	0			c.G619A						PASS	.	C	ILE/VAL	99,4307	79.3+/-117.8	2,95,2106	113	101	105		619	2.2	1	4	dbSNP_111	105	1,8599		0,1,4299	yes	missense	CCNI	NM_006835.2	29	2,96,6405	TT,TC,CC		0.0116,2.2469,0.7689	benign	207/378	77976374	100,12906	2203	4300	6503	SO:0001583	missense	10983	exon6			GACTAACCATGGC	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.619G>A	4.37:g.77976374C>T	ENSP00000237654:p.Val207Ile	171	0	0		220	102	0.463636	NM_006835	B2R6M0|B7Z6X4	Missense_Mutation	SNP	ENST00000237654.4	37	CCDS3580.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	5.722	0.317763	0.10845	0.022469	1.16E-4	ENSG00000118816	ENST00000237654;ENST00000537948	T;T	0.13657	2.57;2.57	5.87	2.22	0.28083	Cyclin-like (1);	0.328648	0.36268	N	0.002681	T	0.02083	0.0065	N	0.04959	-0.14	0.37675	D	0.92327	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.36335	-0.9752	10	0.07030	T	0.85	-3.5062	6.2538	0.20861	0.0:0.6096:0.1228:0.2676	rs4252903;rs52822018;rs4252903	193;207	B7Z6X4;Q14094	.;CCNI_HUMAN	I	207;193	ENSP00000237654:V207I;ENSP00000441001:V193I	ENSP00000237654:V207I	V	-	1	0	CCNI	78195398	0.993000	0.37304	1.000000	0.80357	0.993000	0.82548	0.319000	0.19522	0.484000	0.27630	0.655000	0.94253	GTT	C|0.992;T|0.008	0.008	strong		0.438	CCNI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252412.2	NM_006835		T	77976374	C	T	77976374	3	4	22	1	0	0	0	0	1	0	0	0	2928	507	18	2	522	2	CCNI	4	77976374	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	315824	77976374	113177902	1055	3956											
CCNG2	901	hgsc.bcm.edu	37	chr4	78079768	78079768	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaacgtctacctggaacaagAagagagattccaacctcgag	15	6	10	10	2	1	3	0	0	1	3	3	7	2	4	3	1	4	0	3	1	6	2	rs4150051	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:78079768A>G	ENST00000316355.5	+	2	439	c.83A>G	c.(82-84)gAa>gGa	p.E28G	CCNG2_ENST00000502280.1_Missense_Mutation_p.E28G|CCNG2_ENST00000395640.1_Missense_Mutation_p.E28G|CCNG2_ENST00000509972.1_Missense_Mutation_p.E28G|CCNG2_ENST00000497512.1_3'UTR|CCNG2_ENST00000354403.5_Missense_Mutation_p.E28G	NM_004354.2	NP_004345.1	Q16589	CCNG2_HUMAN	cyclin G2	28			E -> G (in dbSNP:rs4150051). {ECO:0000269|Ref.3}.		cell cycle checkpoint (GO:0000075)|mitotic nuclear division (GO:0007067)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)				breast(1)|kidney(2)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	10						CTGGAACAAGAAGAGAGATTC	0.502													A|||	22	0.00439297	0.0144	0.0043	5008	,	,		16831	0.0		0.0	False		,,,				2504	0.0				p.E28G		Atlas-SNP	.											.	CCNG2	27	.	0			c.A83G						PASS	.	A	GLY/GLU	67,4339	62.3+/-99.4	2,63,2138	112	112	112		83	5.6	1	4	dbSNP_110	112	1,8599		0,1,4299	yes	missense	CCNG2	NM_004354.2	98	2,64,6437	GG,GA,AA		0.0116,1.5207,0.5228	probably-damaging	28/345	78079768	68,12938	2203	4300	6503	SO:0001583	missense	901	exon2			AACAAGAAGAGAG	BC032518	CCDS3581.1	4q21.22	2009-05-07			ENSG00000138764	ENSG00000138764			1593	protein-coding gene	gene with protein product		603203				8806701	Standard	NM_004354		Approved		uc003hkq.4	Q16589	OTTHUMG00000130100	ENST00000316355.5:c.83A>G	4.37:g.78079768A>G	ENSP00000315743:p.Glu28Gly	132	0	0		125	61	0.488	NM_004354	B4DF25|Q6FGA7|Q6FGC6	Missense_Mutation	SNP	ENST00000316355.5	37	CCDS3581.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	24.2	4.508863	0.85282	0.015207	1.16E-4	ENSG00000138764	ENST00000316355;ENST00000354403;ENST00000502280;ENST00000395640;ENST00000512918;ENST00000509972	T;T;T;T;T;T	0.57436	0.4;0.4;0.4;0.4;1.69;1.69	5.57	5.57	0.84162	Cyclin-like (1);	0.000000	0.85682	D	0.000000	T	0.64125	0.2570	M	0.88979	2.995	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.78046	-0.2357	10	0.87932	D	0	-16.452	15.3858	0.74699	1.0:0.0:0.0:0.0	rs4150051	28;28	B4DF25;Q16589	.;CCNG2_HUMAN	G	28	ENSP00000315743:E28G;ENSP00000346379:E28G;ENSP00000424665:E28G;ENSP00000379002:E28G;ENSP00000426085:E28G;ENSP00000426476:E28G	ENSP00000315743:E28G	E	+	2	0	CCNG2	78298792	1.000000	0.71417	1.000000	0.80357	0.550000	0.35303	7.252000	0.78309	2.126000	0.65437	0.459000	0.35465	GAA	A|0.996;G|0.004	0.004	strong		0.502	CCNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252404.3	NM_004354		G	78079768	A	G	78079768	3	3	22	1	0	0	0	0	1	0	0	0	2926	246	9	3	85	3	CCNG2	4	78079768	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	103394	78079768	113074508	1056	3957											
FRAS1	80144	hgsc.bcm.edu	37	chr4	79351542	79351542	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggtgtgcttcttaagcataCagctgagttccgaaggccga	9	11	12	9	2	1	1	0	1	1	0	2	3	2	1	2	2	4	4	2	2	3	4	rs34271211	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:79351542C>T	ENST00000325942.6	+	37	5380	c.4940C>T	c.(4939-4941)aCa>aTa	p.T1647I	FRAS1_ENST00000264895.6_Missense_Mutation_p.T1647I	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	1647					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						CTTAAGCATACAGCTGAGTTC	0.498													C|||	41	0.0081869	0.031	0.0	5008	,	,		19131	0.0		0.0	False		,,,				2504	0.0				p.T1647I		Atlas-SNP	.											.	FRAS1	779	.	0			c.C4940T						PASS	.	C	ILE/THR,ILE/THR	123,3785		2,119,1833	59	61	61		4940,4940	4	0	4	dbSNP_126	61	0,8324		0,0,4162	yes	missense,missense	FRAS1	NM_001166133.1,NM_025074.6	89,89	2,119,5995	TT,TC,CC		0.0,3.1474,1.0056	possibly-damaging,possibly-damaging	1647/1977,1647/4013	79351542	123,12109	1954	4162	6116	SO:0001583	missense	80144	exon37			AGCATACAGCTGA	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.4940C>T	4.37:g.79351542C>T	ENSP00000326330:p.Thr1647Ile	100	0	0		86	38	0.44186	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	37	CCDS54772.1	18	0.008241758241758242	18	0.036585365853658534	0	0.0	0	0.0	0	0.0	C	13.88	2.368547	0.42003	0.031474	0.0	ENSG00000138759	ENST00000325942;ENST00000264895;ENST00000545316	T;T	0.26810	1.71;1.71	5.68	3.98	0.46160	.	0.367128	0.29307	N	0.012540	T	0.04272	0.0118	L	0.57536	1.79	0.09310	N	1	P;P	0.47302	0.565;0.893	B;B	0.39876	0.205;0.312	T	0.10613	-1.0622	10	0.20046	T	0.44	.	2.3609	0.04307	0.2218:0.458:0.1775:0.1427	rs34271211	1647;1647	E9PHH6;A2RRR8	.;.	I	1647;1647;67	ENSP00000326330:T1647I;ENSP00000264895:T1647I	ENSP00000264895:T1647I	T	+	2	0	FRAS1	79570566	0.019000	0.18553	0.003000	0.11579	0.001000	0.01503	2.837000	0.48191	0.883000	0.36040	-0.229000	0.12294	ACA	C|0.992;T|0.008	0.008	strong		0.498	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			T	79351542	C	T	79351542	3	4	22	1	0	0	0	0	1	0	0	0	6050	478	17	2	5086	2	FRAS1	4	79351542	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1271774	79351542	111802734	1057	3958											
FRAS1	80144	hgsc.bcm.edu	37	chr4	79396610	79396610	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agctacaatgtcagtgagaaGgcagggtctgtcagtgtcac	11	9	13	8	0	4	1	3	1	1	1	4	2	4	1	0	2	2	2	0	2	3	1	rs79849142	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:79396610G>A	ENST00000264895.6	+	54	8141	c.7701G>A	c.(7699-7701)aaG>aaA	p.K2567K		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	2567	Calx-beta 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						TCAGTGAGAAGGCAGGGTCTG	0.502													G|||	149	0.0297524	0.1074	0.0101	5008	,	,		22558	0.0		0.0	False		,,,				2504	0.0				p.K2567K		Atlas-SNP	.											.	FRAS1	779	.	0			c.G7701A						PASS	.	G		324,3850		17,290,1780	117	129	125		7701	1.3	1	4	dbSNP_132	125	3,8441		0,3,4219	no	coding-synonymous	FRAS1	NM_025074.6		17,293,5999	AA,AG,GG		0.0355,7.7623,2.5915		2567/4013	79396610	327,12291	2087	4222	6309	SO:0001819	synonymous_variant	80144	exon54			TGAGAAGGCAGGG	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.7701G>A	4.37:g.79396610G>A		220	1	0.00454545		220	110	0.5	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	44	0.020146520146520148	41	0.08333333333333333	3	0.008287292817679558	0	0.0	0	0.0	G	9.007	0.981435	0.18812	0.077623	3.55E-4	ENSG00000138759	ENST00000512123	.	.	.	5.44	1.34	0.21922	.	.	.	.	.	T	0.02970	0.0088	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.03761	-1.1006	4	.	.	.	.	1.7426	0.02955	0.3312:0.1357:0.4093:0.1237	.	.	.	.	S	796	.	.	G	+	1	0	FRAS1	79615634	0.990000	0.36364	0.999000	0.59377	0.994000	0.84299	0.287000	0.18920	0.212000	0.20703	0.591000	0.81541	GGC	G|0.984;A|0.016	0.016	strong		0.502	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	79396610	G	A	79396610	2	1	22	1	0	0	0	0	0	0	0	1	6050	991	35	2		2	FRAS1	4	79396610	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	45068	79396610	111757666	1058	3959											
PRDM8	56978	hgsc.bcm.edu	37	chr4	81124299	81124299	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgaacggaggttgcgggtcCctgccgagcggcggcggcgg	4	5	20	12	7	0	1	0	1	0	0	1	3	1	2	2	7	4	1	2	7	1	1	rs150632206	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:81124299C>T	ENST00000504452.1	+	8	2522	c.1683C>T	c.(1681-1683)tcC>tcT	p.S561S	PRDM8_ENST00000339711.4_Silent_p.S561S|PRDM8_ENST00000415738.2_Silent_p.S561S			Q9NQV8	PRDM8_HUMAN	PR domain containing 8	561					corpus callosum morphogenesis (GO:0021540)|corticospinal tract morphogenesis (GO:0021957)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(2)	10						GTTGCGGGTCCCTGCCGAGCG	0.746													C|||	105	0.0209665	0.0764	0.0058	5008	,	,		7601	0.0		0.0	False		,,,				2504	0.0				p.S561S		Atlas-SNP	.											.	PRDM8	44	.	0			c.C1683T						PASS	.	C	,	100,2254		0,100,1077	2	3	3		1683,1683	-2.1	1	4	dbSNP_134	3	1,5715		0,1,2857	no	coding-synonymous,coding-synonymous	PRDM8	NM_001099403.1,NM_020226.3	,	0,101,3934	TT,TC,CC		0.0175,4.2481,1.2515	,	561/690,561/690	81124299	101,7969	1177	2858	4035	SO:0001819	synonymous_variant	56978	exon4			CGGGTCCCTGCCG	AF275815	CCDS43243.1	4q21	2008-08-21				ENSG00000152784			13993	protein-coding gene	gene with protein product							Standard	NM_020226		Approved		uc003hmc.4	Q9NQV8		ENST00000504452.1:c.1683C>T	4.37:g.81124299C>T		2	0	0		4	4	1	NM_001099403	A8K7X2|Q6IQ36	Silent	SNP	ENST00000504452.1	37	CCDS43243.1																																																																																			C|0.982;T|0.018	0.018	strong		0.746	PRDM8-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362793.1			T	81124299	C	T	81124299	2	4	22	1	0	0	0	0	0	0	0	1	12474	610	22	2		2	PRDM8	4	81124299	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1727689	81124299	110029977	1059	3960											
C4orf22	255119	hgsc.bcm.edu	37	chr4	81866010	81866010	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgttagtaattcaagtcccAactatcaagtgattgccgat	12	13	7	9	1	2	1	2	1	0	0	3	2	3	1	2	0	2	2	2	0	6	5	rs201959026		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:81866010A>C	ENST00000358105.3	+	5	572	c.523A>C	c.(523-525)Aac>Cac	p.N175H	C4orf22_ENST00000508675.1_Missense_Mutation_p.N192H	NM_152770.2	NP_689983.2	Q6V702	CD022_HUMAN	chromosome 4 open reading frame 22	175										NS(1)|large_intestine(3)|lung(5)|prostate(1)|skin(5)	15						TTCAAGTCCCAACTATCAAGT	0.313													A|||	1	0.000199681	0.0008	0.0	5008	,	,		16588	0.0		0.0	False		,,,				2504	0.0				p.N192H		Atlas-SNP	.											.	C4orf22	35	.	0			c.A574C						PASS	.	A	HIS/ASN,HIS/ASN	8,4396	12.9+/-30.5	0,8,2194	70	71	71		574,523	5.8	1	4		71	0,8594		0,0,4297	yes	missense,missense	C4orf22	NM_001206997.1,NM_152770.2	68,68	0,8,6491	CC,CA,AA		0.0,0.1817,0.0615	possibly-damaging,possibly-damaging	192/251,175/234	81866010	8,12990	2202	4297	6499	SO:0001583	missense	255119	exon6			AGTCCCAACTATC	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.523A>C	4.37:g.81866010A>C	ENSP00000350818:p.Asn175His	282	1	0.0035461		328	148	0.451219	NM_001206997	E7EQ13|Q6ZQY4|Q8N4G9	Missense_Mutation	SNP	ENST00000358105.3	37	CCDS3587.1	.	.	.	.	.	.	.	.	.	.	A	17.34	3.364872	0.61513	0.001817	0.0	ENSG00000197826	ENST00000358105;ENST00000508675	T;T	0.36878	1.23;1.23	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.55609	0.1931	M	0.77616	2.38	0.46203	D	0.998921	P;D	0.54397	0.956;0.966	P;P	0.55667	0.73;0.781	T	0.60010	-0.7346	10	0.56958	D	0.05	.	15.1462	0.72653	1.0:0.0:0.0:0.0	.	192;175	E7EQ13;Q6V702	.;CD022_HUMAN	H	175;192	ENSP00000350818:N175H;ENSP00000425786:N192H	ENSP00000350818:N175H	N	+	1	0	C4orf22	82085034	1.000000	0.71417	1.000000	0.80357	0.650000	0.38633	6.456000	0.73501	2.216000	0.71823	0.533000	0.62120	AAC	.	.	weak		0.313	C4orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252629.2	NM_152770		C	81866010	A	C	81866010	3	2	22	1	0	0	0	0	1	0	0	0	2257	130	5	5	541	5	C4orf22	4	81866010	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	741711	81866010	109288266	1060	3961											
BMP3	651	hgsc.bcm.edu	37	chr4	81952658	81952658	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acagcacggtccaggcggccCggacaccgggctccctggag	7	3	15	16	4	0	0	0	0	0	0	2	2	2	2	4	6	1	2	4	6	0	0	rs61729824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:81952658C>G	ENST00000282701.2	+	1	540	c.220C>G	c.(220-222)Cgg>Ggg	p.R74G		NM_001201.2	NP_001192.2	P12645	BMP3_HUMAN	bone morphogenetic protein 3	74					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						CCAGGCGGCCCGGACACCGGG	0.687													c|||	28	0.00559105	0.0197	0.0029	5008	,	,		13952	0.0		0.0	False		,,,				2504	0.0				p.R74G		Atlas-SNP	.											.	BMP3	59	.	0			c.C220G						PASS	.						18	21	20					4																	81952658		2199	4298	6497	SO:0001583	missense	651	exon1			GCGGCCCGGACAC	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.220C>G	4.37:g.81952658C>G	ENSP00000282701:p.Arg74Gly	78	0	0		103	47	0.456311	NM_001201	Q4VAS5	Missense_Mutation	SNP	ENST00000282701.2	37	CCDS3588.1	.	.	.	.	.	.	.	.	.	.	c	7.074	0.568893	0.13560	.	.	ENSG00000152785	ENST00000282701	T	0.64803	-0.12	3.44	2.6	0.31112	Transforming growth factor-beta, N-terminal (1);	1.192490	0.06406	N	0.719754	T	0.41880	0.1178	N	0.08118	0	0.09310	N	1	B	0.25007	0.116	B	0.28849	0.095	T	0.35649	-0.9780	10	0.22109	T	0.4	.	7.0017	0.24813	0.0:0.875:0.0:0.125	.	74	P12645	BMP3_HUMAN	G	74	ENSP00000282701:R74G	ENSP00000282701:R74G	R	+	1	2	BMP3	82171682	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.383000	0.07398	1.034000	0.39945	-0.215000	0.12644	CGG	C|0.988;T|0.012	.	alt		0.687	BMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252634.1			G	81952658	C	G	81952658	3	3	22	1	0	0	0	0	1	0	0	0	1461	643	23	4	222	4	BMP3	4	81952658	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	86648	81952658	109201618	1061	3962											
HPSE	10855	hgsc.bcm.edu	37	chr4	84222208	84222208	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaccgcaagtacttggtgacAttatggaggtttatggcata	12	12	11	6	1	0	1	0	1	0	0	0	2	0	2	1	4	2	4	1	4	6	6	rs11031	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:84222208A>G	ENST00000405413.2	-	12	1513	c.1377T>C	c.(1375-1377)aaT>aaC	p.N459N	HPSE_ENST00000512196.1_Silent_p.N385N|HPSE_ENST00000311412.5_Silent_p.N459N|HPSE_ENST00000513463.1_Silent_p.N401N	NM_006665.5	NP_006656.2	Q9Y251	HPSE_HUMAN	heparanase	459					carbohydrate metabolic process (GO:0005975)|cell-matrix adhesion (GO:0007160)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|positive regulation of blood coagulation (GO:0030194)|positive regulation of hair follicle development (GO:0051798)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation vascular endothelial growth factor production (GO:0010575)|proteoglycan metabolic process (GO:0006029)|regulation of hair follicle development (GO:0051797)|small molecule metabolic process (GO:0044281)|vascular wound healing (GO:0061042)	extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)	beta-glucuronidase activity (GO:0004566)|heparanase activity (GO:0030305)|protein dimerization activity (GO:0046983)|syndecan binding (GO:0045545)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	20		Hepatocellular(203;0.114)		COAD - Colon adenocarcinoma(81;0.141)	Dalteparin(DB06779)|Heparin(DB01109)	ACTTGGTGACATTATGGAGGT	0.353													A|||	426	0.0850639	0.3064	0.0259	5008	,	,		18825	0.0		0.003	False		,,,				2504	0.0				p.N459N		Atlas-SNP	.											.	HPSE	55	.	0			c.T1377C						PASS	.	A	,,,	1123,3283	402.2+/-332.3	156,811,1236	119	126	123		1377,1155,1203,1377	-3.8	1	4	dbSNP_52	123	18,8582	11.9+/-42.8	0,18,4282	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HPSE	NM_001098540.2,NM_001166498.2,NM_001199830.1,NM_006665.5	,,,	156,829,5518	GG,GA,AA		0.2093,25.488,8.7729	,,,	459/544,385/470,401/486,459/544	84222208	1141,11865	2203	4300	6503	SO:0001819	synonymous_variant	10855	exon11			GGTGACATTATGG	AF144325	CCDS3602.1, CCDS54774.1, CCDS56337.1	4q21.3	2008-02-05			ENSG00000173083	ENSG00000173083			5164	protein-coding gene	gene with protein product		604724				10395325, 10395326	Standard	NM_006665		Approved	HPA, HSE1, HPSE1	uc003hoj.4	Q9Y251	OTTHUMG00000130425	ENST00000405413.2:c.1377T>C	4.37:g.84222208A>G		121	0	0		134	66	0.492537	NM_001098540	A9JIG7|C7F7I3|C7F7I4|E9PCA9|E9PGR1|Q53GE5|Q9UL39	Silent	SNP	ENST00000405413.2	37	CCDS3602.1																																																																																			A|0.911;G|0.089	0.089	strong		0.353	HPSE-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252812.2	NM_006665		G	84222208	A	G	84222208	2	3	22	1	0	0	0	0	0	0	0	1	7353	214	8	3		3	HPSE	4	84222208	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2269550	84222208	106932068	1062	3963											
HELQ	113510	hgsc.bcm.edu	37	chr4	84350870	84350870	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaaatgtaccattcatgaaAtgatagatgtcatcaagatt	18	12	6	5	0	3	4	3	2	0	2	3	4	3	4	1	0	1	1	1	0	6	4	rs59255439	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:84350870A>G	ENST00000295488.3	-	12	2487	c.2325T>C	c.(2323-2325)caT>caC	p.H775H	HELQ_ENST00000510985.1_Silent_p.H708H	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	775					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						CATTCATGAAATGATAGATGT	0.328								Other identified genes with known or suspected DNA repair function					G|||	497	0.0992412	0.3563	0.036	5008	,	,		15251	0.0		0.001	False		,,,				2504	0.0				p.H775H		Atlas-SNP	.											.	HELQ	95	.	0			c.T2325C						PASS	.	G		1348,3052	683.1+/-404.2	191,966,1043	43	39	40		2325	1.2	1	4	dbSNP_129	40	18,8578	810.1+/-407.1	0,18,4280	no	coding-synonymous	HELQ	NM_133636.2		191,984,5323	GG,GA,AA		0.2094,30.6364,10.5109		775/1102	84350870	1366,11630	2200	4298	6498	SO:0001819	synonymous_variant	113510	exon12			CATGAAATGATAG	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.2325T>C	4.37:g.84350870A>G		84	0	0		82	42	0.512195	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Silent	SNP	ENST00000295488.3	37	CCDS3603.1																																																																																			A|0.908;G|0.092	0.092	strong		0.328	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636		G	84350870	A	G	84350870	2	3	22	1	0	0	0	0	0	0	0	1	7056	98	4	3		3	HELQ	4	84350870	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	128662	84350870	106803406	1063	3964											
HELQ	113510	hgsc.bcm.edu	37	chr4	84361071	84361071	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ttcacagttcttcttactagGacaaaaaactaagcaggaat	16	11	6	8	0	3	0	1	0	2	0	3	2	3	2	0	2	3	2	0	2	7	6	rs6817280	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:84361071G>A	ENST00000295488.3	-	8	1915	c.1753C>T	c.(1753-1755)Cct>Tct	p.P585S	HELQ_ENST00000510985.1_Missense_Mutation_p.P518S	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	585	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.		P -> S (in dbSNP:rs6817280).		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						TTCTTACTAGGACAAAAAACT	0.303								Other identified genes with known or suspected DNA repair function					G|||	422	0.0842652	0.3026	0.0303	5008	,	,		16565	0.0		0.001	False		,,,				2504	0.0				p.P585S		Atlas-SNP	.											.	HELQ	95	.	0			c.C1753T						PASS	.	G	SER/PRO	1127,3279	391.0+/-327.9	138,851,1214	64	67	66		1753	5.7	1	4	dbSNP_116	66	14,8584	9.1+/-34.3	0,14,4285	yes	missense	HELQ	NM_133636.2	74	138,865,5499	AA,AG,GG		0.1628,25.5788,8.7742	possibly-damaging	585/1102	84361071	1141,11863	2203	4299	6502	SO:0001583	missense	113510	exon8			TACTAGGACAAAA	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.1753C>T	4.37:g.84361071G>A	ENSP00000295488:p.Pro585Ser	335	1	0.00298507		376	192	0.510638	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Missense_Mutation	SNP	ENST00000295488.3	37	CCDS3603.1	134	0.06135531135531135	122	0.24796747967479674	11	0.03038674033149171	0	0.0	1	0.0013192612137203166	G	21.9	4.217196	0.79352	0.255788	0.001628	ENSG00000163312	ENST00000295488;ENST00000510985	T;D	0.91686	-0.57;-2.89	5.68	5.68	0.88126	Helicase, C-terminal (1);	0.051961	0.85682	D	0.000000	T	0.00144	0.0004	L	0.28694	0.88	0.09310	P	0.99999999573404	D;P	0.71674	0.998;0.855	D;P	0.64687	0.928;0.474	T	0.42361	-0.9456	9	0.11485	T	0.65	.	19.7785	0.96405	0.0:0.0:1.0:0.0	rs6817280;rs6817280	518;585	E3W980;Q8TDG4	.;HELQ_HUMAN	S	585;518	ENSP00000295488:P585S;ENSP00000424539:P518S	ENSP00000295488:P585S	P	-	1	0	HELQ	84580095	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.458000	0.66679	2.675000	0.91044	0.655000	0.94253	CCT	G|0.916;A|0.084	0.084	strong		0.303	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636		A	84361071	G	A	84361071	3	1	22	1	0	0	0	0	1	0	0	0	7056	1174	41	2	1596	2	HELQ	4	84361071	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	10201	84361071	106793205	1064	3965											
HELQ	113510	hgsc.bcm.edu	37	chr4	84374692	84374692	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctctatgcaattatggggcAgttcctcattcacagtgttg	8	14	10	9	0	3	0	2	0	1	0	4	0	4	0	1	2	1	5	1	2	3	5	rs17006837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:84374692A>G	ENST00000295488.3	-	2	866	c.704T>C	c.(703-705)cTg>cCg	p.L235P	HELQ_ENST00000440639.2_5'Flank|MRPS18C_ENST00000295491.4_5'Flank|MRPS18C_ENST00000507019.1_5'Flank|HELQ_ENST00000510985.1_Missense_Mutation_p.L235P|MRPS18C_ENST00000507349.1_5'Flank	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	235			L -> P (in dbSNP:rs17006837).		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						ATTATGGGGCAGTTCCTCATT	0.378								Other identified genes with known or suspected DNA repair function					a|||	675	0.134784	0.4894	0.0331	5008	,	,		20460	0.0		0.004	False		,,,				2504	0.001				p.L235P		Atlas-SNP	.											.	HELQ	95	.	0			c.T704C						PASS	.	G	PRO/LEU	1835,2571	527.1+/-372.1	367,1101,735	132	138	136		704	-1.4	0	4	dbSNP_123	136	27,8573	16.0+/-53.3	0,27,4273	yes	missense	HELQ	NM_133636.2	98	367,1128,5008	GG,GA,AA		0.314,41.6478,14.3165	benign	235/1102	84374692	1862,11144	2203	4300	6503	SO:0001583	missense	113510	exon2			TGGGGCAGTTCCT	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.704T>C	4.37:g.84374692A>G	ENSP00000295488:p.Leu235Pro	124	0	0		123	64	0.520325	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Missense_Mutation	SNP	ENST00000295488.3	37	CCDS3603.1	202	0.0924908424908425	187	0.3800813008130081	12	0.03314917127071823	0	0.0	3	0.00395778364116095	a	9.849	1.193106	0.21954	0.416478	0.00314	ENSG00000163312	ENST00000295488;ENST00000510985	T;T	0.69926	0.03;-0.44	5.43	-1.43	0.08884	.	0.989793	0.08215	N	0.980008	T	0.00012	0.0000	L	0.59436	1.845	0.80722	P	0.0	P;B;D;B	0.57571	0.8;0.06;0.98;0.006	B;B;P;B	0.56700	0.278;0.018;0.804;0.003	T	0.20840	-1.0263	9	0.32370	T	0.25	-34.7802	6.3635	0.21441	0.6213:0.1187:0.2599:0.0	rs17006837;rs61470575;rs17006837	235;235;198;235	E3W980;E3W982;Q8TDG4-2;Q8TDG4	.;.;.;HELQ_HUMAN	P	235	ENSP00000295488:L235P;ENSP00000424539:L235P	ENSP00000295488:L235P	L	-	2	0	HELQ	84593716	0.000000	0.05858	0.006000	0.13384	0.002000	0.02628	0.386000	0.20702	-0.126000	0.11682	-1.060000	0.02296	CTG	A|0.864;G|0.136	0.136	strong		0.378	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636		G	84374692	A	G	84374692	3	3	22	1	0	0	0	0	1	0	0	0	7056	188	7	3	2669	3	HELQ	4	84374692	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	13621	84374692	106779584	1065	3966											
MAPK10	5602	hgsc.bcm.edu	37	chr4	86950354	86950354	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacggagagtgagtacctgaAggagaaggctgtccttttac	11	9	13	8	1	0	4	0	2	0	2	1	6	1	4	2	3	2	2	2	3	4	3	rs148438622	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:86950354A>G	ENST00000359221.3	-	13	1774	c.1248T>C	c.(1246-1248)ccT>ccC	p.P416P	MAPK10_ENST00000395157.3_Silent_p.P271P|MAPK10_ENST00000395166.1_Silent_p.P378P|MAPK10_ENST00000395161.2_Silent_p.P416P|MAPK10_ENST00000395169.3_Silent_p.P378P|MAPK10_ENST00000395160.3_Silent_p.P271P|MAPK10_ENST00000361569.2_Silent_p.P416P|MAPK10_ENST00000449047.2_Silent_p.P271P			P53779	MK10_HUMAN	mitogen-activated protein kinase 10	416					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)		GAGTACCTGAAGGAGAAGGCT	0.353																																					p.P416P		Atlas-SNP	.											MAPK10_ENST00000449047,colon,carcinoma,-2,2	MAPK10	106	2	0			c.T1248C						PASS	.	A	,,,	5,4401	11.4+/-27.6	0,5,2198	215	200	205		1248,1134,813,1248	6	1	4	dbSNP_134	205	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MAPK10	NM_002753.3,NM_138980.2,NM_138981.2,NM_138982.2	,,,	0,5,6498	GG,GA,AA		0.0,0.1135,0.0384	,,,	416/423,378/427,271/278,416/465	86950354	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	5602	exon13			ACCTGAAGGAGAA	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.1248T>C	4.37:g.86950354A>G		103	0	0		100	45	0.45	NM_002753	A6NFS3|A6NG28|B3KQ94|Q15707|Q49AP1	Silent	SNP	ENST00000359221.3	37	CCDS34026.1	.	.	.	.	.	.	.	.	.	.	A	10.37	1.331983	0.24167	0.001135	0.0	ENSG00000109339	ENST00000515400	.	.	.	5.96	5.96	0.96718	.	.	.	.	.	T	0.63850	0.2546	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62955	-0.6744	4	.	.	.	-10.1507	11.1954	0.48709	0.9281:0.0:0.0718:0.0	.	.	.	.	L	329	.	.	F	-	1	0	MAPK10	87169378	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.314000	0.51943	2.278000	0.76064	0.533000	0.62120	TTC	A|1.000;G|0.000	0.000	strong		0.353	MAPK10-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000361363.2			G	86950354	A	G	86950354	2	3	22	1	0	0	0	0	0	0	0	1	9281	59	3	3		3	MAPK10	4	86950354	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2575662	86950354	104203922	1066	3967											
PTPN13	5783	hgsc.bcm.edu	37	chr4	87653594	87653594	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgaaaatgacaattgaaccAtttatatctttggatttgcc	13	15	7	6	0	1	3	0	3	1	0	1	4	1	4	2	1	2	0	2	1	6	6	rs201078979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:87653594A>G	ENST00000411767.2	+	11	1713	c.1650A>G	c.(1648-1650)ccA>ccG	p.P550P	PTPN13_ENST00000436978.1_Silent_p.P550P|PTPN13_ENST00000511467.1_Silent_p.P550P|PTPN13_ENST00000316707.6_Silent_p.P550P|PTPN13_ENST00000427191.2_Silent_p.P550P			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	550					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)		CAATTGAACCATTTATATCTT	0.289													A|||	8	0.00159744	0.0061	0.0	5008	,	,		17350	0.0		0.0	False		,,,				2504	0.0				p.P550P		Atlas-SNP	.											.	PTPN13	203	.	0			c.A1650G						PASS	.	A	,,,	19,3581		0,19,1781	57	53	54		1650,1650,1650,1650	3.2	1	4		54	1,8119		0,1,4059	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPN13	NM_006264.2,NM_080683.2,NM_080684.2,NM_080685.2	,,,	0,20,5840	GG,GA,AA		0.0123,0.5278,0.1706	,,,	550/2467,550/2486,550/2295,550/2491	87653594	20,11700	1800	4060	5860	SO:0001819	synonymous_variant	5783	exon11			TGAACCATTTATA		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.1650A>G	4.37:g.87653594A>G		87	0	0		77	31	0.402597	NM_006264	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Silent	SNP	ENST00000411767.2	37	CCDS47094.1																																																																																			A|0.999;G|0.001	0.001	strong		0.289	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			G	87653594	A	G	87653594	2	3	22	1	0	0	0	0	0	0	0	1	12795	204	8	3		3	PTPN13	4	87653594	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	703240	87653594	103500682	1067	3968											
PTPN13	5783	hgsc.bcm.edu	37	chr4	87696623	87696623	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttatgtggaggtcatgacagCctttatcaagtggtatatat	11	15	10	5	0	2	1	2	1	0	0	2	2	2	2	1	3	1	1	1	3	6	6	rs148059206	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:87696623C>T	ENST00000411767.2	+	35	5772	c.5709C>T	c.(5707-5709)agC>agT	p.S1903S	PTPN13_ENST00000436978.1_Silent_p.S1908S|PTPN13_ENST00000511467.1_Silent_p.S1908S|PTPN13_ENST00000316707.6_Silent_p.S1712S|PTPN13_ENST00000427191.2_Silent_p.S1884S			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1903	PDZ 5. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)		GTCATGACAGCCTTTATCAAG	0.353													C|||	9	0.00179712	0.0068	0.0	5008	,	,		20073	0.0		0.0	False		,,,				2504	0.0				p.S1908S		Atlas-SNP	.											.	PTPN13	203	.	0			c.C5724T						PASS	.	C	,,,	20,3920		0,20,1950	94	89	90		5652,5709,5136,5724	1	0.3	4	dbSNP_134	90	1,8343		0,1,4171	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPN13	NM_006264.2,NM_080683.2,NM_080684.2,NM_080685.2	,,,	0,21,6121	TT,TC,CC		0.012,0.5076,0.171	,,,	1884/2467,1903/2486,1712/2295,1908/2491	87696623	21,12263	1970	4172	6142	SO:0001819	synonymous_variant	5783	exon35			TGACAGCCTTTAT		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.5709C>T	4.37:g.87696623C>T		141	0	0		143	69	0.482517	NM_080685	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Silent	SNP	ENST00000411767.2	37	CCDS47094.1																																																																																			C|0.999;T|0.001	0.001	strong		0.353	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			T	87696623	C	T	87696623	2	4	22	1	0	0	0	0	0	0	0	1	12795	738	26	2		2	PTPN13	4	87696623	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	43029	87696623	103457653	1068	3969											
HSD17B13	345275	hgsc.bcm.edu	37	chr4	88243832	88243832	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctgtcgttttgcaaattcAtaagtagtctgcctgcctat	8	16	7	10	1	3	0	1	0	2	0	4	0	3	0	2	0	3	3	2	0	4	6	rs137887488	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88243832A>G	ENST00000328546.4	-	1	226	c.162T>C	c.(160-162)taT>taC	p.Y54Y	HSD17B13_ENST00000302219.6_Silent_p.Y54Y|RP11-529H2.2_ENST00000508163.1_RNA	NM_178135.3	NP_835236.2	Q7Z5P4	DHB13_HUMAN	hydroxysteroid (17-beta) dehydrogenase 13	54						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)		TTGCAAATTCATAAGTAGTCT	0.388													A|||	10	0.00199681	0.0068	0.0014	5008	,	,		20127	0.0		0.0	False		,,,				2504	0.0				p.Y54Y		Atlas-SNP	.											.	HSD17B13	27	.	0			c.T162C						PASS	.	A	,	39,4367	43.1+/-76.7	0,39,2164	109	110	110		162,162	-0.3	1	4	dbSNP_134	110	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	HSD17B13	NM_001136230.1,NM_178135.3	,	0,39,6464	GG,GA,AA		0.0,0.8852,0.2999	,	54/265,54/301	88243832	39,12967	2203	4300	6503	SO:0001819	synonymous_variant	345275	exon1			AAATTCATAAGTA		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.162T>C	4.37:g.88243832A>G		173	0	0		186	89	0.478495	NM_178135	A8K9R9|Q2M1L5|Q86W22|Q86W23	Silent	SNP	ENST00000328546.4	37	CCDS3618.1																																																																																			A|0.996;G|0.004	0.004	strong		0.388	HSD17B13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253052.1	NM_178135		G	88243832	A	G	88243832	2	3	22	1	0	0	0	0	0	0	0	1	7391	224	8	3		3	HSD17B13	4	88243832	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	547209	88243832	102910444	1069	3970											
HSD17B11	51170	hgsc.bcm.edu	37	chr4	88278484	88278484	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgaaattaggacacagacaTgttgttttgactccagttat	13	13	8	7	1	0	2	0	1	0	1	1	4	1	3	1	1	0	3	1	1	3	5	rs34025653	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88278484T>G	ENST00000358290.4	-	5	957	c.642A>C	c.(640-642)acA>acC	p.T214T	HSD17B11_ENST00000507286.1_Silent_p.T170T|HSD17B11_ENST00000507518.1_5'UTR	NM_016245.3	NP_057329.2	Q8NBQ5	DHB11_HUMAN	hydroxysteroid (17-beta) dehydrogenase 11	214					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)		GACACAGACATGTTGTTTTGA	0.368													T|||	288	0.057508	0.2095	0.0159	5008	,	,		19416	0.0		0.0	False		,,,				2504	0.0				p.T214T		Atlas-SNP	.											.	HSD17B11	28	.	0			c.A642C						PASS	.	T		732,3672	301.5+/-286.9	69,594,1539	134	115	122		642	-11.3	0.6	4	dbSNP_126	122	7,8593	4.3+/-15.6	0,7,4293	no	coding-synonymous	HSD17B11	NM_016245.3		69,601,5832	GG,GT,TT		0.0814,16.6213,5.6829		214/301	88278484	739,12265	2202	4300	6502	SO:0001819	synonymous_variant	51170	exon5			CAGACATGTTGTT	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.642A>C	4.37:g.88278484T>G		179	0	0		176	68	0.386364	NM_016245	Q96HF6|Q9UKU4	Silent	SNP	ENST00000358290.4	37	CCDS3619.1																																																																																			T|0.938;G|0.062	0.062	strong		0.368	HSD17B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253041.1	NM_016245		G	88278484	T	G	88278484	2	3	22	1	0	0	0	0	0	0	0	1	7389	1451	51	5		5	HSD17B11	4	88278484	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	34652	88278484	102875792	1070	3971											
NUDT9	53343	hgsc.bcm.edu	37	chr4	88344063	88344063	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccctcggggcgctcatggcGggacgcctcctgggaaaggc	5	5	17	14	4	1	0	1	0	0	0	3	2	2	2	3	6	0	1	3	6	1	0	rs11937770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88344063G>C	ENST00000302174.4	+	1	330	c.6G>C	c.(4-6)gcG>gcC	p.A2A	NUDT9_ENST00000473942.1_Intron	NM_024047.4	NP_076952.1	Q9BW91	NUDT9_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 9	2					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)			endometrium(1)|large_intestine(4)|lung(6)	11		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000937)		CGCTCATGGCGGGACGCCTCC	0.667													C|||	539	0.107628	0.3865	0.0187	5008	,	,		15327	0.001		0.003	False		,,,				2504	0.0112				p.A2A		Atlas-SNP	.											.	NUDT9	21	.	0			c.G6C						PASS	.	C	,	1471,2935	670.9+/-402.4	263,945,995	59	65	63		6,	1.3	0.7	4	dbSNP_120	63	20,8580	809.7+/-407.1	0,20,4280	no	coding-synonymous,intron	NUDT9	NM_024047.3,NM_198038.1	,	263,965,5275	CC,CG,GG		0.2326,33.3863,11.4639	,	2/351,	88344063	1491,11515	2203	4300	6503	SO:0001819	synonymous_variant	53343	exon1			CATGGCGGGACGC	AY026252	CCDS3620.1, CCDS3621.1	4q22.1	2008-08-29			ENSG00000170502	ENSG00000170502		"Nudix motif containing"	8056	protein-coding gene	gene with protein product		606022				11385575, 12427752	Standard	NM_024047		Approved	MGC3037	uc003hqq.3	Q9BW91	OTTHUMG00000130591	ENST00000302174.4:c.6G>C	4.37:g.88344063G>C		37	0	0		21	20	0.952381	NM_001248011	Q8NBN1|Q8NCB9|Q8NG25	Silent	SNP	ENST00000302174.4	37	CCDS3620.1																																																																																			G|0.895;C|0.105	0.105	strong		0.667	NUDT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253035.2			C	88344063	G	C	88344063	2	2	22	1	0	0	0	0	0	0	0	1	10755	1103	39	4		4	NUDT9	4	88344063	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	65579	88344063	102810213	1071	3972											
SPP1	6696	hgsc.bcm.edu	37	chr4	88903774	88903774	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggacagccgtgggaaggacaGttatgaaacgagtcagctgg	12	6	16	7	2	1	1	1	1	0	0	1	5	1	4	1	4	3	2	1	4	3	1	rs7435825	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88903774G>A	ENST00000395080.3	+	7	798	c.671G>A	c.(670-672)aGt>aAt	p.S224N	SPP1_ENST00000360804.4_Missense_Mutation_p.S197N|SPP1_ENST00000509659.1_3'UTR|SPP1_ENST00000237623.7_Missense_Mutation_p.S210N	NM_001040058.1|NM_001251830.1	NP_001035147.1|NP_001238759.1	P10451	OSTP_HUMAN	secreted phosphoprotein 1	224			S -> N (in dbSNP:rs7435825).		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)		GGGAAGGACAGTTATGAAACG	0.517													G|||	253	0.0505192	0.1861	0.0101	5008	,	,		19566	0.0		0.0	False		,,,				2504	0.0				p.S237N		Atlas-SNP	.											.	SPP1	35	.	0			c.G710A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER	628,3778	269.2+/-268.9	47,534,1622	158	145	149		629,671,590	4	0.6	4	dbSNP_116	149	4,8596	3.0+/-9.4	0,4,4296	yes	missense,missense,missense	SPP1	NM_000582.2,NM_001040058.1,NM_001040060.1	46,46,46	47,538,5918	AA,AG,GG		0.0465,14.2533,4.8593	probably-damaging,probably-damaging,probably-damaging	210/301,224/315,197/288	88903774	632,12374	2203	4300	6503	SO:0001583	missense	6696	exon8			AGGACAGTTATGA		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.671G>A	4.37:g.88903774G>A	ENSP00000378517:p.Ser224Asn	186	0	0		182	85	0.467033	NM_001251830	B2RDA1|Q15681|Q15682|Q15683|Q4W597|Q567T5|Q8NBK2|Q96IZ1	Missense_Mutation	SNP	ENST00000395080.3	37	CCDS43250.1	94	0.04304029304029304	92	0.18699186991869918	2	0.0055248618784530384	0	0.0	0	0.0	G	15.46	2.840614	0.51057	0.142533	4.65E-4	ENSG00000118785	ENST00000359072;ENST00000535912;ENST00000237623;ENST00000395080;ENST00000360804;ENST00000508233	T;T;T;T	0.47869	0.83;0.83;0.83;0.83	4.84	3.99	0.46301	.	0.332965	0.27563	N	0.018811	T	0.00073	0.0002	L	0.61218	1.895	0.33157	P	0.453592	P;B;P;B;P	0.41366	0.747;0.003;0.594;0.006;0.594	B;B;B;B;B	0.42771	0.397;0.011;0.261;0.028;0.261	T	0.08066	-1.0740	9	0.72032	D	0.01	.	9.3187	0.37950	0.1012:0.0:0.8988:0.0	rs7435825;rs52832944;rs7435825	237;183;210;197;224	B7Z351;Q3LGB0;B2RDA1;Q567T5;P10451	.;.;.;.;OSTP_HUMAN	N	202;183;210;224;197;183	ENSP00000237623:S210N;ENSP00000378517:S224N;ENSP00000354042:S197N;ENSP00000422973:S183N	ENSP00000237623:S210N	S	+	2	0	SPP1	89122798	0.999000	0.42202	0.648000	0.29521	0.342000	0.28953	1.862000	0.39448	1.159000	0.42565	0.453000	0.30009	AGT	G|0.958;A|0.042	0.042	strong		0.517	SPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253048.3			A	88903774	G	A	88903774	3	1	22	1	0	0	0	0	1	0	0	0	15101	1029	36	2	693	2	SPP1	4	88903774	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	559711	88903774	102250502	1072	3973											
HERC6	55008	hgsc.bcm.edu	37	chr4	89338691	89338691	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaccgaacaggatcactgtaAtgttaaagctcttttaggaa	15	11	8	7	1	2	0	1	0	1	0	2	3	2	2	1	2	3	3	1	2	7	4	rs190243300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:89338691A>G	ENST00000264346.7	+	13	1732	c.1673A>G	c.(1672-1674)aAt>aGt	p.N558S	HERC6_ENST00000380265.5_Missense_Mutation_p.N558S	NM_017912.3	NP_060382.3	Q8IVU3	HERC6_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 6	558					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)		GATCACTGTAATGTTAAAGCT	0.373													A|||	17	0.00339457	0.0083	0.0043	5008	,	,		17266	0.0		0.003	False		,,,				2504	0.0				p.N558S		Atlas-SNP	.											.	HERC6	104	.	0			c.A1673G						PASS	.	A	SER/ASN,SER/ASN	17,3737		0,17,1860	65	61	62		1673,1673	0.7	0	4		62	5,8207		0,5,4101	yes	missense,missense	HERC6	NM_001165136.1,NM_017912.3	46,46	0,22,5961	GG,GA,AA		0.0609,0.4529,0.1839	benign,benign	558/987,558/1023	89338691	22,11944	1877	4106	5983	SO:0001583	missense	55008	exon13			ACTGTAATGTTAA	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.1673A>G	4.37:g.89338691A>G	ENSP00000264346:p.Asn558Ser	53	0	0		59	24	0.40678	NM_017912	B4DIY5|Q5GC90|Q5GRH3|Q5HYM6|Q5JPB6|Q6PIF4|Q8NAN3|Q9NWS4	Missense_Mutation	SNP	ENST00000264346.7	37	CCDS47098.1	5	0.0022893772893772895	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	A	6.688	0.495465	0.12762	0.004529	6.09E-4	ENSG00000138642	ENST00000380265;ENST00000264346	T;T	0.38240	1.15;1.17	4.79	0.721	0.18219	.	0.377680	0.25885	N	0.027670	T	0.12220	0.0297	N	0.19112	0.55	0.09310	N	0.999999	B;B	0.20052	0.041;0.024	B;B	0.14578	0.011;0.005	T	0.18999	-1.0319	10	0.14252	T	0.57	.	6.1186	0.20139	0.6064:0.3068:0.0867:0.0	.	558;558	Q8IVU3-2;Q8IVU3	.;HERC6_HUMAN	S	558	ENSP00000369617:N558S;ENSP00000264346:N558S	ENSP00000264346:N558S	N	+	2	0	HERC6	89557714	0.001000	0.12720	0.002000	0.10522	0.001000	0.01503	0.982000	0.29539	0.414000	0.25790	-0.438000	0.05819	AAT	A|0.998;G|0.002	0.002	strong		0.373	HERC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363259.2			G	89338691	A	G	89338691	3	3	22	1	0	0	0	0	1	0	0	0	7071	101	4	3	1520	3	HERC6	4	89338691	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	434917	89338691	101815585	1073	3974											
NAP1L5	266812	hgsc.bcm.edu	37	chr4	89618415	89618426	+	In_Frame_Del	DEL	GCAGCCTCTGCC	GCAGCCTCTGCC	-																															cgtcatgtttggcccccgcgGcagcctctgccgcagcctcc																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GCAGCCTCTGCC	GCAGCCTCTGCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:89618415_89618426delGCAGCCTCTGCC	ENST00000323061.5	-	1	960_971	c.480_491delGGCAGAGGCTGC	c.(478-492)gcggcagaggctgcc>gcc	p.160_164AAEAA>A	HERC3_ENST00000543130.1_Intron|HERC3_ENST00000264345.3_Intron|HERC3_ENST00000402738.1_Intron	NM_153757.2	NP_715638.1	Q96NT1	NP1L5_HUMAN	nucleosome assembly protein 1-like 5	160	Glu-rich.				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)		GGCCCCCGCGGCAGCCTCTGCCGCAGcctcct	0.608																																					p.161_164del		Pindel,Atlas-Indel	.											.	NAP1L5	23	.	0			c.481_492del						PASS	.		,	4,4262		1,2,2130					,	-3.3	0			93	0,8252		0,0,4126	no	coding,intron	HERC3,NAP1L5	NM_153757.2,NM_014606.1	,	1,2,6256	A1A1,A1R,RR		0.0,0.0938,0.032	,	,		4,12514				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.480_491delGGCAGAGGCTGC	4.37:g.89618415_89618426delGCAGCCTCTGCC	ENSP00000320488:p.Ala160_Ala163del	279	0	.		285	66	0.232	NM_153757		In_Frame_Del	DEL	ENST00000323061.5	37	CCDS3632.1																																																																																			.	.	none		0.608	NAP1L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253551.1	NM_153757		-	89618426	GCAGCCTCTGCC	-	89618415	7	5	22	1	0	1	0	1	0	0	0	0	10169	1203	42	0	61	0	NAP1L5	4	89618415	In_Frame_Del	DEL	GCAGCCTCTGCC	TCGA-G8-6324-01A-11D-2210-10	279724	89618415	101535861	1074	3975											
GPRIN3	285513	hgsc.bcm.edu	37	chr4	90168945	90168945	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccctttcaatctaacacagAagacggggcaggacggacgc	12	6	11	12	3	2	2	1	0	1	2	3	4	3	4	1	4	1	1	1	4	3	2	rs34322172	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:90168945A>C	ENST00000609438.1	-	2	2835	c.2317T>G	c.(2317-2319)Tct>Gct	p.S773A	GPRIN3_ENST00000333209.4_Missense_Mutation_p.S773A	NM_198281.2	NP_938022.2	Q6ZVF9	GRIN3_HUMAN	GPRIN family member 3	773										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)		TCTAACACAGAAGACGGGGCA	0.463													A|||	34	0.00678914	0.025	0.0014	5008	,	,		17083	0.0		0.0	False		,,,				2504	0.0				p.S773A		Atlas-SNP	.											.	GPRIN3	90	.	0			c.T2317G						PASS	.	A	ALA/SER	121,4285	90.2+/-128.9	3,115,2085	91	97	95		2317	4.2	0	4	dbSNP_126	95	0,8600		0,0,4300	yes	missense	GPRIN3	NM_198281.2	99	3,115,6385	CC,CA,AA		0.0,2.7463,0.9303	probably-damaging	773/777	90168945	121,12885	2203	4300	6503	SO:0001583	missense	285513	exon2			ACACAGAAGACGG	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.2317T>G	4.37:g.90168945A>C	ENSP00000476603:p.Ser773Ala	173	0	0		183	93	0.508197	NM_198281	Q8IVE4	Missense_Mutation	SNP	ENST00000609438.1	37	CCDS34030.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	A	7.014	0.557400	0.13436	0.027463	0.0	ENSG00000185477	ENST00000333209	T	0.15256	2.44	5.45	4.24	0.50183	.	0.261257	0.20448	N	0.092147	T	0.04543	0.0124	N	0.22421	0.69	0.31631	N	0.649051	B	0.27997	0.197	B	0.31812	0.136	T	0.05616	-1.0874	10	0.87932	D	0	-8.6401	11.9204	0.52789	0.7247:0.2753:0.0:0.0	rs34322172	773	Q6ZVF9	GRIN3_HUMAN	A	773	ENSP00000328672:S773A	ENSP00000328672:S773A	S	-	1	0	GPRIN3	90387968	1.000000	0.71417	0.032000	0.17829	0.031000	0.12232	4.535000	0.60629	1.051000	0.40369	0.533000	0.62120	TCT	A|0.992;C|0.008	0.008	strong		0.463	GPRIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363540.2	NM_198281		C	90168945	A	C	90168945	3	2	22	1	0	0	0	0	1	0	0	0	6740	246	9	5	17	5	GPRIN3	4	90168945	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	550530	90168945	100985331	1075	3976											
GPRIN3	285513	hgsc.bcm.edu	37	chr4	90169025	90169025	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaacactgtgctgccttcctCtgagcttcttatttgaagaa	10	14	7	10	0	2	3	0	2	2	1	3	3	3	3	2	0	4	2	2	0	4	4	rs17015286	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:90169025C>T	ENST00000609438.1	-	2	2755	c.2237G>A	c.(2236-2238)aGa>aAa	p.R746K	GPRIN3_ENST00000333209.4_Missense_Mutation_p.R746K	NM_198281.2	NP_938022.2	Q6ZVF9	GRIN3_HUMAN	GPRIN family member 3	746			R -> K (in dbSNP:rs17015286).							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)		CTGCCTTCCTCTGAGCTTCTT	0.468													T|||	299	0.0597045	0.2163	0.0173	5008	,	,		17742	0.0		0.0	False		,,,				2504	0.001				p.R746K		Atlas-SNP	.											.	GPRIN3	90	.	0			c.G2237A						PASS	.	T	LYS/ARG	800,3606	751.2+/-412.2	79,642,1482	108	110	109		2237	5.3	1	4	dbSNP_123	109	16,8584	818.7+/-406.8	0,16,4284	yes	missense	GPRIN3	NM_198281.2	26	79,658,5766	TT,TC,CC		0.186,18.1571,6.274	benign	746/777	90169025	816,12190	2203	4300	6503	SO:0001583	missense	285513	exon2			CTTCCTCTGAGCT	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.2237G>A	4.37:g.90169025C>T	ENSP00000476603:p.Arg746Lys	169	0	0		176	92	0.522727	NM_198281	Q8IVE4	Missense_Mutation	SNP	ENST00000609438.1	37	CCDS34030.1	112	0.05128205128205128	107	0.21747967479674796	5	0.013812154696132596	0	0.0	0	0.0	T	9.991	1.230900	0.22542	0.181571	0.00186	ENSG00000185477	ENST00000333209	T	0.19394	2.15	5.26	5.26	0.73747	.	0.000000	0.36234	N	0.002708	T	0.00012	0.0000	N	0.01228	-0.945	0.49130	P	2.4299999999999322E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.33420	-0.9869	9	0.02654	T	1	-13.2449	11.2596	0.49074	0.0:0.0711:0.0:0.9289	rs17015286;rs52823204;rs56606122;rs61213802;rs17015286	746	Q6ZVF9	GRIN3_HUMAN	K	746	ENSP00000328672:R746K	ENSP00000328672:R746K	R	-	2	0	GPRIN3	90388048	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.662000	0.61525	1.023000	0.39654	-0.254000	0.11334	AGA	C|0.933;T|0.067	0.067	strong		0.468	GPRIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363540.2	NM_198281		T	90169025	C	T	90169025	3	4	22	1	0	0	0	0	1	0	0	0	6740	913	32	2	97	2	GPRIN3	4	90169025	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	80	90169025	100985251	1076	3977											
GPRIN3	285513	hgsc.bcm.edu	37	chr4	90170015	90170015	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ttgatgaggttttaaggaccCcacctggtaggctcgcaagt	9	11	12	9	1	0	2	0	2	0	0	1	3	0	3	3	4	0	4	3	4	3	4	rs114960901	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:90170015C>A	ENST00000609438.1	-	2	1765	c.1247G>T	c.(1246-1248)gGg>gTg	p.G416V	GPRIN3_ENST00000333209.4_Missense_Mutation_p.G416V	NM_198281.2	NP_938022.2	Q6ZVF9	GRIN3_HUMAN	GPRIN family member 3	416										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)		TTTAAGGACCCCACCTGGTAG	0.507													C|||	41	0.0081869	0.0295	0.0029	5008	,	,		19599	0.0		0.0	False		,,,				2504	0.0				p.G416V		Atlas-SNP	.											GPRIN3,colon,carcinoma,+1,1	GPRIN3	90	1	0			c.G1247T						PASS	.	C	VAL/GLY	114,4292	85.8+/-124.5	1,112,2090	108	112	110		1247	2.8	0	4	dbSNP_132	110	1,8599		0,1,4299	yes	missense	GPRIN3	NM_198281.2	109	1,113,6389	AA,AC,CC		0.0116,2.5874,0.8842	benign	416/777	90170015	115,12891	2203	4300	6503	SO:0001583	missense	285513	exon2			AGGACCCCACCTG	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.1247G>T	4.37:g.90170015C>A	ENSP00000476603:p.Gly416Val	172	0	0		190	95	0.5	NM_198281	Q8IVE4	Missense_Mutation	SNP	ENST00000609438.1	37	CCDS34030.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	C	10.41	1.341579	0.24339	0.025874	1.16E-4	ENSG00000185477	ENST00000333209	T	0.11385	2.78	5.38	2.81	0.32909	.	0.502634	0.14825	N	0.296209	T	0.01592	0.0051	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.34129	-0.9841	10	0.45353	T	0.12	-1.3894	1.9135	0.03292	0.1497:0.0899:0.2415:0.5188	.	416	Q6ZVF9	GRIN3_HUMAN	V	416	ENSP00000328672:G416V	ENSP00000328672:G416V	G	-	2	0	GPRIN3	90389038	0.000000	0.05858	0.014000	0.15608	0.026000	0.11368	-0.091000	0.11146	1.050000	0.40346	-0.290000	0.09829	GGG	C|0.991;A|0.009	0.009	strong		0.507	GPRIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363540.2	NM_198281		A	90170015	C	A	90170015	3	1	22	1	0	0	0	0	1	0	0	0	6740	623	22	4	1087	4	GPRIN3	4	90170015	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	990	90170015	100984261	1077	3978											
FAM190A	401145	hgsc.bcm.edu	37	chr4	91230407	91230407	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attatgtctcctgggaaataTaggttagagggtcaatgtag	12	13	12	4	0	2	1	1	0	1	1	3	2	2	2	1	3	0	2	1	3	7	5	rs34445159	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:91230407T>C	ENST00000509176.1	+	2	1260	c.972T>C	c.(970-972)taT>taC	p.Y324Y	CCSER1_ENST00000432775.2_Silent_p.Y324Y|CCSER1_ENST00000333691.8_Silent_p.Y324Y	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	324																	CTGGGAAATATAGGTTAGAGG	0.413													T|||	23	0.00459265	0.0166	0.0014	5008	,	,		20571	0.0		0.0	False		,,,				2504	0.0				p.Y324Y		Atlas-SNP	.											.	.	.	.	0			c.T972C						PASS	.	T	,	68,3690		1,66,1812	124	117	119		972,972	1.3	1	4	dbSNP_126	119	1,8211		0,1,4105	no	coding-synonymous,coding-synonymous	FAM190A	NM_001145065.1,NM_207491.2	,	1,67,5917	CC,CT,TT		0.0122,1.8095,0.5764	,	324/901,324/678	91230407	69,11901	1879	4106	5985	SO:0001819	synonymous_variant	401145	exon2			GAAATATAGGTTA		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.972T>C	4.37:g.91230407T>C		178	0	0		218	92	0.422018	NM_001145065	Q4W5M0|Q86V57	Silent	SNP	ENST00000509176.1	37	CCDS47099.1																																																																																			T|0.995;C|0.005	0.005	strong		0.413	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065		C	91230407	T	C	91230407	2	2	22	1	0	0	0	0	0	0	0	1	5526	1413	49	3		3	FAM190A	4	91230407	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1060392	91230407	99923869	1078	3979											
ATOH1	474	hgsc.bcm.edu	37	chr4	94750227	94750227	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagagcatcccgtctacccGcctgagctgtccctcctgga	7	8	10	16	2	1	2	0	1	1	1	4	4	4	3	5	1	3	2	5	1	1	1	rs138388359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:94750227G>A	ENST00000306011.3	+	1	186	c.150G>A	c.(148-150)ccG>ccA	p.P50P		NM_005172.1	NP_005163.1	Q92858	ATOH1_HUMAN	atonal homolog 1 (Drosophila)	50					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)		CCGTCTACCCGCCTGAGCTGT	0.672													G|||	8	0.00159744	0.0061	0.0	5008	,	,		13999	0.0		0.0	False		,,,				2504	0.0				p.P50P		Atlas-SNP	.											.	ATOH1	40	.	0			c.G150A						PASS	.	G		30,4376	32.6+/-62.9	0,30,2173	34	36	35		150	-6.8	0.4	4	dbSNP_134	35	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous	ATOH1	NM_005172.1		0,31,6470	AA,AG,GG		0.0116,0.6809,0.2384		50/355	94750227	31,12971	2203	4298	6501	SO:0001819	synonymous_variant	474	exon1			CTACCCGCCTGAG	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.150G>A	4.37:g.94750227G>A		133	0	0		115	52	0.452174	NM_005172	Q14CT9	Silent	SNP	ENST00000306011.3	37	CCDS3638.1																																																																																			A|0.001;G|0.999;T|0.000	0.001	strong		0.672	ATOH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253585.1	NM_005172		A	94750227	G	A	94750227	2	1	22	1	0	0	0	0	0	0	0	1	1112	1074	38	1		1	ATOH1	4	94750227	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3519820	94750227	96404049	1079	3980											
ATOH1	474	hgsc.bcm.edu	37	chr4	94750650	94750650	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gttatcccgtcgttcaacaaCgacaagaagctgtccaaata	14	9	7	11	3	1	1	1	0	0	1	4	2	3	1	2	0	3	3	2	0	7	3	rs34543561	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:94750650C>T	ENST00000306011.3	+	1	609	c.573C>T	c.(571-573)aaC>aaT	p.N191N		NM_005172.1	NP_005163.1	Q92858	ATOH1_HUMAN	atonal homolog 1 (Drosophila)	191	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				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)		CGTTCAACAACGACAAGAAGC	0.582													C|||	29	0.00579073	0.0219	0.0	5008	,	,		17596	0.0		0.0	False		,,,				2504	0.0				p.N191N		Atlas-SNP	.											ATOH1,NS,carcinoma,+2,1	ATOH1	40	1	0			c.C573T						PASS	.	C		97,4309	77.8+/-116.1	2,93,2108	53	54	53		573	4.4	1	4	dbSNP_126	53	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ATOH1	NM_005172.1		2,95,6406	TT,TC,CC		0.0233,2.2015,0.7612		191/355	94750650	99,12907	2203	4300	6503	SO:0001819	synonymous_variant	474	exon1			CAACAACGACAAG	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.573C>T	4.37:g.94750650C>T		139	0	0		192	98	0.510417	NM_005172	Q14CT9	Silent	SNP	ENST00000306011.3	37	CCDS3638.1																																																																																			C|0.992;T|0.008	0.008	strong		0.582	ATOH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253585.1	NM_005172		T	94750650	C	T	94750650	2	4	22	1	0	0	0	0	0	0	0	1	1112	535	19	1		1	ATOH1	4	94750650	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	423	94750650	96403626	1080	3981											
PDLIM5	10611	hgsc.bcm.edu	37	chr4	95539204	95539204	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcctcggtagcttccacaCggagcatgcccgagagcctg	7	8	11	15	3	0	1	0	0	0	1	3	3	2	2	4	2	4	3	4	2	1	3	rs141653509	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:95539204C>T	ENST00000317968.4	+	8	1106	c.970C>T	c.(970-972)Cgg>Tgg	p.R324W	PDLIM5_ENST00000542407.1_Missense_Mutation_p.R202W|PDLIM5_ENST00000514743.1_Missense_Mutation_p.R353W|PDLIM5_ENST00000380176.3_3'UTR|PDLIM5_ENST00000437932.1_Missense_Mutation_p.R215W	NM_001256428.1|NM_006457.4	NP_001243357.1|NP_006448	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5	324					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)		AGCTTCCACACGGAGCATGCC	0.547													C|||	7	0.00139776	0.0045	0.0	5008	,	,		15988	0.001		0.0	False		,,,				2504	0.0				p.R353W		Atlas-SNP	.											PDLIM5,NS,carcinoma,-1,1	PDLIM5	76	1	0			c.C1057T						PASS	.	C	TRP/ARG,TRP/ARG	25,4381	30.8+/-60.4	0,25,2178	48	48	48		643,970	0.8	0	4	dbSNP_134	48	0,8600		0,0,4300	yes	missense,missense	PDLIM5	NM_001011513.2,NM_006457.3	101,101	0,25,6478	TT,TC,CC		0.0,0.5674,0.1922	probably-damaging,probably-damaging	215/488,324/597	95539204	25,12981	2203	4300	6503	SO:0001583	missense	10611	exon12			TCCACACGGAGCA	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.970C>T	4.37:g.95539204C>T	ENSP00000321746:p.Arg324Trp	83	0	0		115	64	0.556522	NM_001256426	A8K6F9|D6RB78|E9PBF5|O60705|Q56VN4|Q5UW38|Q8WVK0	Missense_Mutation	SNP	ENST00000317968.4	37	CCDS3641.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	10.95	1.494439	0.26774	0.005674	0.0	ENSG00000163110	ENST00000437932;ENST00000317968;ENST00000503974;ENST00000542407;ENST00000514743	T;T;T;T;T	0.59364	0.48;0.67;0.48;0.27;0.46	5.14	0.821	0.18799	.	0.458336	0.23654	N	0.045883	T	0.33323	0.0859	L	0.47716	1.5	0.09310	N	1	B;B;B;B	0.23490	0.009;0.086;0.005;0.006	B;B;B;B	0.10450	0.002;0.004;0.003;0.005	T	0.29671	-1.0004	10	0.59425	D	0.04	.	2.7512	0.05281	0.4316:0.3432:0.1293:0.0959	.	221;353;324;215	E9PBF5;D6RB78;Q96HC4;Q96HC4-4	.;.;PDLI5_HUMAN;.	W	215;324;221;202;353	ENSP00000398469:R215W;ENSP00000321746:R324W;ENSP00000424297:R221W;ENSP00000442187:R202W;ENSP00000424360:R353W	ENSP00000321746:R324W	R	+	1	2	PDLIM5	95758227	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-0.059000	0.11731	0.187000	0.20147	0.585000	0.79938	CGG	C|0.999;T|0.001	0.001	strong		0.547	PDLIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253586.1			T	95539204	C	T	95539204	3	4	22	1	0	0	0	0	1	0	0	0	11692	527	19	1	1156	1	PDLIM5	4	95539204	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	788554	95539204	95615072	1081	3982											
ADH1B	125	hgsc.bcm.edu	37	chr4	100237169	100237169	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actgcattctcatccaccacCgtgtactgggagaaggtgct	9	10	10	12	1	1	1	1	0	1	1	3	2	2	1	3	2	3	3	3	2	2	2	rs139645116	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:100237169C>T	ENST00000305046.8	-	5	520	c.453G>A	c.(451-453)acG>acA	p.T151T	ADH1B_ENST00000394887.3_Silent_p.T111T|ADH1B_ENST00000504498.1_5'Flank			P00325	ADH1B_HUMAN	alcohol dehydrogenase 1B (class I), beta polypeptide	151					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)	CATCCACCACCGTGTACTGGG	0.582													.|||	13	0.00259585	0.0098	0.0	5008	,	,		18733	0.0		0.0	False		,,,				2504	0.0				p.T151T		Atlas-SNP	.											.	ADH1B	68	.	0			c.G453A						PASS	.	C		31,4375	36.0+/-67.5	0,31,2172	131	118	122		453	-7.9	0.1	4	dbSNP_134	122	0,8600		0,0,4300	no	coding-synonymous	ADH1B	NM_000668.4		0,31,6472	TT,TC,CC		0.0,0.7036,0.2384		151/376	100237169	31,12975	2203	4300	6503	SO:0001819	synonymous_variant	125	exon5			CACCACCGTGTAC	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.453G>A	4.37:g.100237169C>T		317	1	0.00315457		286	137	0.479021	NM_000668	A8MYN5|B4DRS9|B4DVC3|Q13711|Q4ZGI9|Q96KI7	Silent	SNP	ENST00000305046.8	37	CCDS34033.1																																																																																			C|0.998;T|0.002	0.002	strong		0.582	ADH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364853.1	NM_000668		T	100237169	C	T	100237169	2	4	22	1	0	0	0	0	0	0	0	1	308	639	23	1		1	ADH1B	4	100237169	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4697965	100237169	90917107	1082	3983											
MTTP	4547	hgsc.bcm.edu	37	chr4	100512919	100512919	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	attttggactgaatttcctaCaaaccattaaggggaaaata	16	12	7	6	0	0	1	0	1	0	0	1	3	1	3	2	3	2	0	2	3	7	6	rs17599091	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:100512919C>G	ENST00000265517.5	+	6	933	c.730C>G	c.(730-732)Caa>Gaa	p.Q244E	MTTP_ENST00000511045.1_Missense_Mutation_p.Q271E|MTTP_ENST00000457717.1_Missense_Mutation_p.Q244E			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	244	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.		Q -> E (in dbSNP:rs17599091). {ECO:0000269|PubMed:11792722}.		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)	GAATTTCCTACAAACCATTAA	0.303													C|||	103	0.0205671	0.0477	0.0086	5008	,	,		18429	0.0		0.0239	False		,,,				2504	0.0102				p.Q244E		Atlas-SNP	.											.	MTTP	127	.	0			c.C730G						PASS	.	C	GLU/GLN	240,4166	137.7+/-173.5	7,226,1970	65	64	64		730	3.5	0.6	4	dbSNP_123	64	289,8311	107.0+/-167.8	4,281,4015	yes	missense	MTTP	NM_000253.2	29	11,507,5985	GG,GC,CC		3.3605,5.4471,4.0674	benign	244/895	100512919	529,12477	2203	4300	6503	SO:0001583	missense	4547	exon7			TTCCTACAAACCA		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.730C>G	4.37:g.100512919C>G	ENSP00000265517:p.Gln244Glu	117	0	0		150	60	0.4	NM_000253	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	49	0.022435897435897436	25	0.0508130081300813	3	0.008287292817679558	0	0.0	21	0.027704485488126648	C	0.588	-0.834158	0.02713	0.054471	0.033605	ENSG00000138823	ENST00000511045;ENST00000457717;ENST00000265517;ENST00000538053	T;T;T	0.40225	1.04;1.04;1.04	5.53	3.47	0.39725	Lipid transport protein, beta-sheet shell (1);Lipid transport protein, N-terminal (3);Vitellinogen, beta-sheet N-terminal (1);	0.964707	0.08632	N	0.916909	T	0.05135	0.0137	L	0.38531	1.155	0.09310	N	1	B;B	0.14805	0.003;0.011	B;B	0.19148	0.008;0.024	T	0.25502	-1.0130	10	0.02654	T	1	-25.7225	7.9279	0.29885	0.3471:0.5753:0.0:0.0775	rs17599091;rs52789259	271;244	E9PBP6;P55157	.;MTP_HUMAN	E	271;244;244;244	ENSP00000427679:Q271E;ENSP00000400821:Q244E;ENSP00000265517:Q244E	ENSP00000265517:Q244E	Q	+	1	0	MTTP	100731942	0.044000	0.20184	0.609000	0.28983	0.195000	0.23768	0.419000	0.21247	1.429000	0.47314	0.650000	0.86243	CAA	C|0.964;G|0.036	0.036	strong		0.303	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3			G	100512919	C	G	100512919	3	3	22	1	0	0	0	0	1	0	0	0	9973	479	17	4	752	4	MTTP	4	100512919	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	275750	100512919	90641357	1083	3984											
EMCN	51705	hgsc.bcm.edu	37	chr4	101386643	101386643	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgtaacacttgttactgttaCgtttgaaatgatggagtcat	11	16	9	5	1	1	2	1	2	0	0	1	3	1	3	0	1	3	4	0	1	4	5	rs78403369	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:101386643C>T	ENST00000296420.4	-	4	491	c.313G>A	c.(313-315)Gta>Ata	p.V105I	EMCN_ENST00000511970.1_Missense_Mutation_p.V105I|EMCN_ENST00000305864.3_Missense_Mutation_p.V105I|EMCN_ENST00000502327.1_5'UTR	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)		GTTACTGTTACGTTTGAAATG	0.363													C|||	82	0.0163738	0.0582	0.0043	5008	,	,		18744	0.0		0.002	False		,,,				2504	0.0				p.V105I		Atlas-SNP	.											.	EMCN	37	.	0			c.G313A						PASS	.	C	ILE/VAL,ILE/VAL	256,4150	146.1+/-180.8	8,240,1955	193	169	177		313,313	-5.4	0	4	dbSNP_132	177	32,8568	21.0+/-64.5	0,32,4268	yes	missense,missense	EMCN	NM_001159694.1,NM_016242.3	29,29	8,272,6223	TT,TC,CC		0.3721,5.8103,2.2144	possibly-damaging,possibly-damaging	105/249,105/262	101386643	288,12718	2203	4300	6503	SO:0001583	missense	51705	exon4			CTGTTACGTTTGA	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.313G>A	4.37:g.101386643C>T	ENSP00000296420:p.Val105Ile	127	0	0		132	65	0.492424	NM_001159694	A8K716|B4E347|Q8NEY5|Q8WWE7|Q9NRM8	Missense_Mutation	SNP	ENST00000296420.4	37	CCDS3655.1	37	0.01694139194139194	33	0.06707317073170732	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	5.591	0.293797	0.10567	0.058103	0.003721	ENSG00000164035	ENST00000296420;ENST00000305864;ENST00000506300;ENST00000511970;ENST00000502569	.	.	.	3.93	-5.39	0.02664	.	5.984870	0.00541	N	0.000223	T	0.01695	0.0054	N	0.08118	0	0.09310	N	1	B;B;B	0.25667	0.107;0.131;0.131	B;B;B	0.17098	0.01;0.017;0.017	T	0.06481	-1.0824	9	0.19590	T	0.45	0.1434	13.3485	0.60589	0.0:0.2287:0.0:0.7713	.	105;105;105	Q9ULC0-2;B4E347;Q9ULC0	.;.;MUCEN_HUMAN	I	105;105;32;105;105	.	ENSP00000296420:V105I	V	-	1	0	EMCN	101605666	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.676000	0.00840	-1.586000	0.01632	-0.150000	0.13652	GTA	C|0.980;T|0.020	0.020	strong		0.363	EMCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253699.2	NM_016242		T	101386643	C	T	101386643	3	4	22	1	0	0	0	0	1	0	0	0	5088	536	19	1	504	1	EMCN	4	101386643	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	873724	101386643	89767633	1084	3985											
BANK1	55024	hgsc.bcm.edu	37	chr4	102965016	102965016	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtttcaacaaaagacagccAgaagacaatctgatgatgac	17	8	8	8	0	2	6	1	3	1	3	2	6	2	6	1	0	2	1	1	0	5	1	rs140337324		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:102965016A>G	ENST00000322953.4	+	11	2195	c.1921A>G	c.(1921-1923)Aga>Gga	p.R641G	BANK1_ENST00000444316.2_Missense_Mutation_p.R611G|BANK1_ENST00000508653.1_Missense_Mutation_p.R508G|BANK1_ENST00000504592.1_Missense_Mutation_p.R626G|BANK1_ENST00000428908.1_Missense_Mutation_p.R508G	NM_017935.4	NP_060405	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	641					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)		AAAGACAGCCAGAAGACAATC	0.333													A|||	1	0.000199681	0.0008	0.0	5008	,	,		16410	0.0		0.0	False		,,,				2504	0.0				p.R641G		Atlas-SNP	.											.	BANK1	95	.	0			c.A1921G						PASS	.	A	GLY/ARG,GLY/ARG,GLY/ARG	7,4399	12.9+/-30.5	0,7,2196	130	137	135		1831,1522,1921	2.8	1	4	dbSNP_134	135	0,8598		0,0,4299	yes	missense,missense,missense	BANK1	NM_001083907.2,NM_001127507.2,NM_017935.4	125,125,125	0,7,6495	GG,GA,AA		0.0,0.1589,0.0538	probably-damaging,probably-damaging,probably-damaging	611/756,508/653,641/786	102965016	7,12997	2203	4299	6502	SO:0001583	missense	55024	exon11			ACAGCCAGAAGAC	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.1921A>G	4.37:g.102965016A>G	ENSP00000320509:p.Arg641Gly	56	0	0		60	26	0.433333	NM_017935	A8K7W8|B0F3S2|Q8N5K8|Q8NB56|Q8WYN5|Q9NWP2	Missense_Mutation	SNP	ENST00000322953.4	37	CCDS34038.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	15.88	2.962531	0.53400	0.001589	0.0	ENSG00000153064	ENST00000504592;ENST00000322953;ENST00000428908;ENST00000508653;ENST00000444316	T;T;T;T;T	0.56103	0.48;0.48;0.48;0.48;0.48	5.4	2.84	0.33178	.	0.152125	0.42172	D	0.000760	T	0.61739	0.2371	L	0.47716	1.5	0.27143	N	0.961604	P;D;D	0.89917	0.951;1.0;1.0	P;D;D	0.87578	0.631;0.998;0.998	T	0.53865	-0.8378	10	0.44086	T	0.13	.	9.7001	0.40180	0.6632:0.3368:0.0:0.0	.	508;641;626	Q8NDB2-4;Q8NDB2;Q8NDB2-2	.;BANK1_HUMAN;.	G	626;641;508;508;611	ENSP00000421443:R626G;ENSP00000320509:R641G;ENSP00000412748:R508G;ENSP00000422314:R508G;ENSP00000388817:R611G	ENSP00000320509:R641G	R	+	1	2	BANK1	103184039	0.998000	0.40836	0.999000	0.59377	0.930000	0.56654	0.952000	0.29149	0.311000	0.23014	0.402000	0.26972	AGA	A|0.999;G|0.001	0.001	strong		0.333	BANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363161.1	NM_017935		G	102965016	A	G	102965016	3	3	22	1	0	0	0	0	1	0	0	0	1309	180	7	3	1963	3	BANK1	4	102965016	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1578373	102965016	88189260	1085	3986											
CENPE	1062	hgsc.bcm.edu	37	chr4	104070041	104070041	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggatttttctaagtcctgaGtatttattatttgagctgtc	8	19	9	5	0	1	2	0	2	1	0	3	3	2	3	1	1	1	2	1	1	4	8	rs79431579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:104070041G>A	ENST00000265148.3	-	28	3892	c.3803C>T	c.(3802-3804)aCt>aTt	p.T1268I	CENPE_ENST00000380026.3_Missense_Mutation_p.T1243I	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	1268					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)		TAAGTCCTGAGTATTTATTAT	0.338													G|||	53	0.0105831	0.0318	0.0101	5008	,	,		19012	0.0		0.001	False		,,,				2504	0.0031				p.T1268I		Atlas-SNP	.											.	CENPE	253	.	0			c.C3803T						PASS	.	G	ILE/THR	160,4246	106.9+/-145.3	4,152,2047	138	143	141		3803	-6.5	0	4	dbSNP_131	141	15,8585	10.5+/-38.8	0,15,4285	yes	missense	CENPE	NM_001813.2	89	4,167,6332	AA,AG,GG		0.1744,3.6314,1.3455	benign	1268/2702	104070041	175,12831	2203	4300	6503	SO:0001583	missense	1062	exon28			TCCTGAGTATTTA	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.3803C>T	4.37:g.104070041G>A	ENSP00000265148:p.Thr1268Ile	203	0	0		185	92	0.497297	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	24	0.01098901098901099	20	0.04065040650406504	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	G	11.01	1.512446	0.27123	0.036314	0.001744	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026	T;T	0.71341	-0.56;-0.56	4.06	-6.52	0.01872	.	.	.	.	.	T	0.11239	0.0274	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	0.14364	-1.0475	9	0.16896	T	0.51	.	6.5259	0.22301	0.2333:0.0:0.5348:0.232	.	1243;1268	Q02224-3;Q02224	.;CENPE_HUMAN	I	1268;1268;1243	ENSP00000265148:T1268I;ENSP00000369365:T1243I	ENSP00000265148:T1268I	T	-	2	0	CENPE	104289490	0.000000	0.05858	0.000000	0.03702	0.537000	0.34900	-1.463000	0.02361	-1.120000	0.02953	-1.155000	0.01812	ACT	G|0.985;A|0.015	0.015	strong		0.338	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	104070041	G	A	104070041	3	1	22	1	0	0	0	0	1	0	0	0	3232	1029	36	2	4390	2	CENPE	4	104070041	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1105025	104070041	87084235	1086	3987											
CENPE	1062	hgsc.bcm.edu	37	chr4	104080217	104080217	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaatttttgggcttctttagAgagattaactatttcctgat	11	18	7	5	0	1	3	0	1	1	2	2	4	2	3	1	1	1	1	1	1	4	8	rs75568479	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:104080217A>C	ENST00000265148.3	-	22	2640	c.2551T>G	c.(2551-2553)Tct>Gct	p.S851A	CENPE_ENST00000380026.3_Missense_Mutation_p.S826A	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	851					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)		GCTTCTTTAGAGAGATTAACT	0.373													A|||	53	0.0105831	0.0318	0.0101	5008	,	,		17002	0.0		0.001	False		,,,				2504	0.0031				p.S851A		Atlas-SNP	.											.	CENPE	253	.	0			c.T2551G						PASS	.	A	ALA/SER	160,4246	105.6+/-144.1	4,152,2047	77	74	75		2551	4.9	0.1	4	dbSNP_131	75	15,8585	9.8+/-36.6	0,15,4285	yes	missense	CENPE	NM_001813.2	99	4,167,6332	CC,CA,AA		0.1744,3.6314,1.3455	probably-damaging	851/2702	104080217	175,12831	2203	4300	6503	SO:0001583	missense	1062	exon22			CTTTAGAGAGATT	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.2551T>G	4.37:g.104080217A>C	ENSP00000265148:p.Ser851Ala	174	0	0		204	107	0.52451	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	24	0.01098901098901099	20	0.04065040650406504	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	A	11.57	1.679425	0.29783	0.036314	0.001744	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026;ENST00000503705	T;T;T	0.81163	-1.46;-1.46;-1.46	4.94	4.94	0.65067	.	.	.	.	.	T	0.51024	0.1650	M	0.62723	1.935	0.18873	N	0.999984	P;P	0.48089	0.732;0.905	B;B	0.41988	0.372;0.369	T	0.61471	-0.7056	9	0.32370	T	0.25	.	14.9037	0.70699	1.0:0.0:0.0:0.0	.	826;851	Q02224-3;Q02224	.;CENPE_HUMAN	A	851;851;826;851	ENSP00000265148:S851A;ENSP00000369365:S826A;ENSP00000423981:S851A	ENSP00000265148:S851A	S	-	1	0	CENPE	104299666	0.997000	0.39634	0.084000	0.20598	0.866000	0.49608	2.194000	0.42668	1.971000	0.57363	0.477000	0.44152	TCT	A|0.985;C|0.015	0.015	strong		0.373	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	104080217	A	C	104080217	3	2	22	1	0	0	0	0	1	0	0	0	3232	304	11	5	5666	5	CENPE	4	104080217	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	10176	104080217	87074059	1087	3988											
TET2	54790	hgsc.bcm.edu	37	chr4	106156983	106156983	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagaaaacaacacagctggaGcacaagtcacaaatgtacca	19	4	7	11	0	1	1	1	0	0	1	1	2	1	2	1	1	5	3	1	1	6	1	rs35695427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:106156983G>A	ENST00000540549.1	+	3	2744	c.1884G>A	c.(1882-1884)gaG>gaA	p.E628E	TET2_ENST00000513237.1_Silent_p.E649E|TET2_ENST00000413648.2_Silent_p.E628E|TET2_ENST00000380013.4_Silent_p.E628E|TET2_ENST00000394764.1_Silent_p.E628E|TET2_ENST00000305737.2_Silent_p.E628E|TET2_ENST00000545826.1_Silent_p.E628E			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	628	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)		CACAGCTGGAGCACAAGTCAC	0.478			"Mis N, F"		MDS								G|||	65	0.0129792	0.0484	0.0014	5008	,	,		20615	0.0		0.0	False		,,,				2504	0.0				p.E628E		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	TET2_ENST00000305737,bladder,carcinoma,+2,2	TET2	1762	2	0			c.G1884A						PASS	.	G	,	225,4181	136.1+/-172.1	11,203,1989	70	71	71		1884,1884	0	0.1	4	dbSNP_126	71	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	TET2	NM_001127208.2,NM_017628.4	,	11,205,6287	AA,AG,GG		0.0233,5.1067,1.7453	,	628/2003,628/1166	106156983	227,12779	2203	4300	6503	SO:0001819	synonymous_variant	54790	exon3			GCTGGAGCACAAG	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.1884G>A	4.37:g.106156983G>A		132	0	0		136	71	0.522059	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Silent	SNP	ENST00000540549.1	37	CCDS47120.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	G	0.008	-1.911390	0.00508	0.051067	2.33E-4	ENSG00000168769	ENST00000535110	.	.	.	5.59	-0.00446	0.14022	.	.	.	.	.	T	0.02380	0.0073	.	.	.	0.48341	D	0.999636	.	.	.	.	.	.	T	0.27157	-1.0082	5	0.02654	T	1	.	1.5409	0.02555	0.3344:0.1288:0.389:0.1477	rs35695427	.	.	.	N	628	.	ENSP00000438851:S628N	S	+	2	0	TET2	106376432	0.996000	0.38824	0.083000	0.20561	0.103000	0.19146	0.236000	0.17967	0.243000	0.21327	-0.143000	0.13931	AGC	G|0.982;A|0.018	0.018	strong		0.478	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		A	106156983	G	A	106156983	2	1	22	1	0	0	0	0	0	0	0	1	15785	962	34	2		2	TET2	4	106156983	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2076766	106156983	84997293	1088	3989											
NPNT	255743	hgsc.bcm.edu	37	chr4	106819089	106819089	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaatagtgtcatcgattggcCtatgtcgttatggtgggagg	9	13	14	5	2	1	0	1	0	0	0	3	2	1	1	1	4	0	1	1	4	4	4	rs147630398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:106819089C>T	ENST00000379987.2	+	2	319	c.103C>T	c.(103-105)Cta>Tta	p.L35L	NPNT_ENST00000514622.1_Silent_p.L35L|NPNT_ENST00000427316.2_Silent_p.L35L|NPNT_ENST00000305572.8_Silent_p.L35L|NPNT_ENST00000453617.2_Silent_p.L35L|NPNT_ENST00000506666.1_Silent_p.L35L	NM_001033047.2	NP_001028219.1	Q6UXI9	NPNT_HUMAN	nephronectin	35					branching involved in ureteric bud morphogenesis (GO:0001658)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to tumor necrosis factor (GO:0071356)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|pilomotor reflex (GO:0097195)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of smooth muscle contraction (GO:0045987)|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)|ureteric bud development (GO:0001657)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integrin alpha8-beta1 complex (GO:0034678)|proteinaceous extracellular matrix (GO:0005578)|smooth muscle contractile fiber (GO:0030485)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			kidney(5)|large_intestine(2)|lung(10)|prostate(2)|skin(1)|urinary_tract(1)	21		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.41e-07)		ATCGATTGGCCTATGTCGTTA	0.468													C|||	7	0.00139776	0.0	0.0029	5008	,	,		18023	0.0		0.002	False		,,,				2504	0.0031				p.L35L		Atlas-SNP	.											.	NPNT	69	.	0			c.C103T						PASS	.	C	,,,,	2,4404	4.2+/-10.8	0,2,2201	135	123	127		103,103,103,103,103	5.8	1	4	dbSNP_134	127	13,8587	9.8+/-36.6	0,13,4287	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NPNT	NM_001033047.2,NM_001184690.1,NM_001184691.1,NM_001184692.1,NM_001184693.1	,,,,	0,15,6488	TT,TC,CC		0.1512,0.0454,0.1153	,,,,	35/566,35/583,35/596,35/537,35/567	106819089	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	255743	exon2			ATTGGCCTATGTC		CCDS34046.1, CCDS54784.1, CCDS54785.1, CCDS54786.1, CCDS54787.1	4q25	2005-10-07							27405	protein-coding gene	gene with protein product		610306				15754038	Standard	NM_001033047		Approved	EGFL6L, POEM	uc011cfd.2	Q6UXI9		ENST00000379987.2:c.103C>T	4.37:g.106819089C>T		191	0	0		205	113	0.55122	NM_001184692	A6NFT9|A8K1W4|B4DIT4|B4DYK3|B4E2H7|B4E3H2|D6RCA1|E9PCK8|E9PCQ1|E9PE64|E9PF04	Silent	SNP	ENST00000379987.2	37	CCDS34046.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	C	6.225	0.409722	0.11812	4.54E-4	0.001512	ENSG00000168743	ENST00000514837	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	T	0.57592	0.2064	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59700	-0.7405	4	.	.	.	.	12.8916	0.58073	0.0:0.9222:0.0:0.0778	.	.	.	.	L	11	.	.	P	+	2	0	NPNT	107038538	1.000000	0.71417	1.000000	0.80357	0.488000	0.33401	1.277000	0.33167	2.746000	0.94184	0.655000	0.94253	CCT	C|0.999;T|0.001	0.001	strong		0.468	NPNT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364083.1	NM_198278		T	106819089	C	T	106819089	2	4	22	1	0	0	0	0	0	0	0	1	10599	680	24	2		2	NPNT	4	106819089	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	662106	106819089	84335187	1089	3990											
PAPSS1	9061	hgsc.bcm.edu	37	chr4	108552787	108552787	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagagaatgtaagacttacTgttcagagtcatagtagtcc	14	11	9	7	0	2	3	2	0	0	3	3	4	3	3	1	0	1	3	1	0	5	5			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:108552787T>C	ENST00000265174.4	-	11	2008	c.1736A>G	c.(1735-1737)cAc>cGc	p.H579R		NM_005443.4	NP_005434.4	O43252	PAPS1_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 1	579					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)		TAAGACTTACTGTTCAGAGTC	0.403																																					p.H579R		Atlas-SNP	.											.	PAPSS1	57	.	0			c.A1736G						PASS	.						113	111	112					4																	108552787		2203	4300	6503	SO:0001630	splice_region_variant	9061	exon11			ACTTACTGTTCAG	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.1736+1A>G	4.37:g.108552787T>C		100	0	0		112	45	0.401786	NM_005443	O43841|O75332|Q96FB1|Q96TF4|Q9P1P9|Q9UE98	Missense_Mutation	SNP	ENST00000265174.4	37	CCDS3676.1	.	.	.	.	.	.	.	.	.	.	T	4.243	0.044005	0.08196	.	.	ENSG00000138801	ENST00000265174	T	0.26957	1.7	5.62	5.62	0.85841	Sulphate adenylyltransferase (2);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.188956	0.56097	D	0.000029	T	0.06096	0.0158	N	0.00125	-2.05	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.37267	-0.9713	9	.	.	.	-22.1456	15.8538	0.78960	0.0:0.0:0.0:1.0	.	579	O43252	PAPS1_HUMAN	R	579	ENSP00000265174:H579R	.	H	-	2	0	PAPSS1	108772236	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.979000	0.40608	2.141000	0.66446	0.528000	0.53228	CAC	.	.	none		0.403	PAPSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253946.2		Missense_Mutation	C	108552787	T	C	108552787	5	2	22	1	0	0	0	0	0	0	1	0	11443	1594	55	3	146	3	PAPSS1	4	108552787	Splice_Site	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1733698	108552787	82601489	1090	3991											
SGMS2	166929	hgsc.bcm.edu	37	chr4	108816880	108816880	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaaggcaccaaaaagtacccGgactatatccaaattgctat	17	8	6	10	1	0	0	0	0	0	0	1	1	1	1	3	2	2	3	3	2	8	5	rs150784082	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:108816880G>A	ENST00000394684.4	+	3	728	c.171G>A	c.(169-171)ccG>ccA	p.P57P	SGMS2_ENST00000359079.4_Silent_p.P57P|RP11-286E11.1_ENST00000499098.1_RNA|RP11-286E11.1_ENST00000513071.1_RNA|SGMS2_ENST00000394686.3_Silent_p.P57P	NM_001136258.1	NP_001129730.1	Q8NHU3	SMS2_HUMAN	sphingomyelin synthase 2	57					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)		AAAAGTACCCGGACTATATCC	0.443													G|||	22	0.00439297	0.0159	0.0014	5008	,	,		20353	0.0		0.0	False		,,,				2504	0.0				p.P57P		Atlas-SNP	.											.	SGMS2	39	.	0			c.G171A						PASS	.	G	,,	56,4350	55.5+/-91.7	0,56,2147	98	94	95		171,171,171	-5.7	0.7	4	dbSNP_134	95	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	SGMS2	NM_001136257.1,NM_001136258.1,NM_152621.5	,,	0,57,6446	AA,AG,GG		0.0116,1.271,0.4383	,,	57/366,57/366,57/366	108816880	57,12949	2203	4300	6503	SO:0001819	synonymous_variant	166929	exon2			GTACCCGGACTAT	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.171G>A	4.37:g.108816880G>A		101	0	0		98	52	0.530612	NM_001136257	A8K2S9|B2RA61	Silent	SNP	ENST00000394684.4	37	CCDS3677.1																																																																																			G|0.996;A|0.004	0.004	strong		0.443	SGMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254752.1	NM_152621		A	108816880	G	A	108816880	2	1	22	1	0	0	0	0	0	0	0	1	14230	1103	39	1		1	SGMS2	4	108816880	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	264093	108816880	82337396	1091	3992											
CFI	3426	hgsc.bcm.edu	37	chr4	110681527	110681527	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	atttgcaatggaagcctttgCcttggcatgctgtgcaaaca	10	12	10	9	0	0	0	0	0	0	0	0	1	0	1	2	2	6	4	2	2	3	3	rs112534524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:110681527C>T	ENST00000394634.2	-	6	989	c.782G>A	c.(781-783)gGc>gAc	p.G261D	CFI_ENST00000512148.1_Missense_Mutation_p.G261D|CFI_ENST00000394635.3_Missense_Mutation_p.G261D	NM_000204.3	NP_000195	P05156	CFAI_HUMAN	complement factor I	261	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.				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)		GAAGCCTTTGCCTTGGCATGC	0.413													C|||	2	0.000399361	0.0	0.0	5008	,	,		19374	0.0		0.002	False		,,,				2504	0.0				p.G261D		Atlas-SNP	.											.	CFI	59	.	0			c.G782A	GRCh37	CM071595	CFI	M	rs112534524	PASS	.	C	ASP/GLY	5,4401	9.9+/-24.2	0,5,2198	127	113	117		782	2.2	0	4	dbSNP_132	117	17,8583	12.6+/-44.7	0,17,4283	yes	missense	CFI	NM_000204.3	94	0,22,6481	TT,TC,CC		0.1977,0.1135,0.1692	possibly-damaging	261/584	110681527	22,12984	2203	4300	6503	SO:0001583	missense	3426	exon6			CCTTTGCCTTGGC	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.782G>A	4.37:g.110681527C>T	ENSP00000378130:p.Gly261Asp	157	0	0		134	49	0.365672	NM_000204	O60442	Missense_Mutation	SNP	ENST00000394634.2	37	CCDS34049.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	10.82	1.457707	0.26161	0.001135	0.001977	ENSG00000205403	ENST00000394635;ENST00000394634;ENST00000540104;ENST00000512148;ENST00000536228	D;D;D	0.95272	-3.66;-3.66;-3.66	5.92	2.15	0.27550	.	0.579484	0.20634	N	0.088529	D	0.86251	0.5888	N	0.12471	0.22	0.09310	N	1	B;B;B	0.22800	0.074;0.036;0.075	B;B;B	0.28465	0.09;0.029;0.081	T	0.76713	-0.2858	10	0.44086	T	0.13	-6.4257	5.5586	0.17131	0.0:0.5559:0.1361:0.3081	.	261;261;261	E7ETH0;G3XAM2;P05156	.;.;CFAI_HUMAN	D	261;261;261;261;243	ENSP00000378131:G261D;ENSP00000378130:G261D;ENSP00000427438:G261D	ENSP00000378130:G261D	G	-	2	0	CFI	110900976	0.000000	0.05858	0.002000	0.10522	0.008000	0.06430	-0.052000	0.11865	0.424000	0.26061	0.655000	0.94253	GGC	C|0.998;G|0.000;T|0.002	0.002	strong		0.413	CFI-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_000204		T	110681527	C	T	110681527	3	4	22	1	0	0	0	0	1	0	0	0	3291	739	26	2	1001	2	CFI	4	110681527	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1864647	110681527	80472749	1092	3993											
LRIT3	345193	hgsc.bcm.edu	37	chr4	110791453	110791453	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acacataactctgcagtgacTgtgttgtattccaagtatgg	11	13	9	8	0	1	1	0	1	1	0	2	1	2	1	1	1	2	4	1	1	4	5	rs9994891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:110791453T>C	ENST00000594814.1	+	4	1548	c.1548T>C	c.(1546-1548)acT>acC	p.T516T	LRIT3_ENST00000327908.3_Silent_p.T333T|LRIT3_ENST00000379920.3_Silent_p.T471T|LRIT3_ENST00000409621.2_Silent_p.T333T	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	516	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)		CTGCAGTGACTGTGTTGTATT	0.473													T|||	588	0.117412	0.4228	0.0346	5008	,	,		22015	0.001		0.004	False		,,,				2504	0.0				p.T516T		Atlas-SNP	.											.	LRIT3	107	.	0			c.T1548C						PASS	.	T		1599,2807	496.0+/-363.4	295,1009,899	152	139	144		1413	-6	0	4	dbSNP_119	144	61,8539	36.4+/-91.3	1,59,4240	no	coding-synonymous	LRIT3	NM_198506.2		296,1068,5139	CC,CT,TT		0.7093,36.2914,12.7633		471/635	110791453	1660,11346	2203	4300	6503	SO:0001819	synonymous_variant	345193	exon4			AGTGACTGTGTTG	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.1548T>C	4.37:g.110791453T>C		128	0	0		151	148	0.980132	NM_198506	C9J1C2|Q6ZTG1	Silent	SNP	ENST00000594814.1	37	CCDS3688.3																																																																																			T|0.866;C|0.134	0.134	strong		0.473	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506		C	110791453	T	C	110791453	2	2	22	1	0	0	0	0	0	0	0	1	8958	1567	55	3		3	LRIT3	4	110791453	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	109926	110791453	80362823	1093	3994											
ANK2	287	hgsc.bcm.edu	37	chr4	114279770	114279770	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgaagattttctatccagTgtagatgaggaaaataaggc	14	12	10	5	0	2	4	0	2	2	2	3	5	3	5	1	2	0	1	1	2	6	5	rs145557320	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:114279770T>C	ENST00000357077.4	+	38	10049	c.9996T>C	c.(9994-9996)agT>agC	p.S3332S	ANK2_ENST00000510275.2_Intron|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000264366.6_Silent_p.S3299S|ANK2_ENST00000509550.1_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	3332					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)		TTCTATCCAGTGTAGATGAGG	0.443													T|||	39	0.00778754	0.0272	0.0029	5008	,	,		18580	0.0		0.001	False		,,,				2504	0.0				p.S3332S		Atlas-SNP	.											.	ANK2	576	.	0			c.T9996C						PASS	.	T	,,	114,4292	85.8+/-124.5	0,114,2089	110	113	112		,9996,	-2.8	0.2	4	dbSNP_134	112	1,8599	1.2+/-3.3	0,1,4299	no	intron,coding-synonymous,intron	ANK2	NM_001127493.1,NM_001148.4,NM_020977.3	,,	0,115,6388	CC,CT,TT		0.0116,2.5874,0.8842	,,	,3332/3958,	114279770	115,12891	2203	4300	6503	SO:0001819	synonymous_variant	287	exon38			ATCCAGTGTAGAT	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.9996T>C	4.37:g.114279770T>C		74	0	0		93	45	0.483871	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Silent	SNP	ENST00000357077.4	37	CCDS3702.1																																																																																			T|0.992;C|0.008	0.008	strong		0.443	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		C	114279770	T	C	114279770	2	2	22	1	0	0	0	0	0	0	0	1	621	1693	59	3		3	ANK2	4	114279770	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	3488317	114279770	76874506	1094	3995											
CAMK2D	817	hgsc.bcm.edu	37	chr4	114438740	114438740	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcataagctccagccttgatCtgctgatagagtctgtgttg	8	14	10	9	0	3	3	1	2	2	1	4	3	4	3	2	0	3	3	2	0	2	4			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:114438740C>T	ENST00000342666.5	-	9	674	c.675G>A	c.(673-675)caG>caA	p.Q225Q	CAMK2D_ENST00000296402.5_Silent_p.Q225Q|CAMK2D_ENST00000394526.2_Silent_p.Q225Q|CAMK2D_ENST00000394524.3_Silent_p.Q225Q|CAMK2D_ENST00000429180.1_Silent_p.Q225Q|CAMK2D_ENST00000505990.1_Silent_p.Q225Q|CAMK2D_ENST00000508738.1_Silent_p.Q225Q|CAMK2D_ENST00000515496.1_Silent_p.Q225Q|CAMK2D_ENST00000511664.1_Silent_p.Q225Q|CAMK2D_ENST00000379773.2_Silent_p.Q225Q|CAMK2D_ENST00000394522.3_Silent_p.Q225Q|CAMK2D_ENST00000454265.2_Silent_p.Q225Q|CAMK2D_ENST00000418639.2_Silent_p.Q225Q|CAMK2D_ENST00000514328.1_Silent_p.Q225Q			Q13557	KCC2D_HUMAN	calcium/calmodulin-dependent protein kinase II delta	225	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				calcium ion transport (GO:0006816)|cardiac muscle cell contraction (GO:0086003)|cellular response to calcium ion (GO:0071277)|cytokine-mediated signaling pathway (GO:0019221)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|G1/S transition of mitotic cell cycle (GO:0000082)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle cell action potential (GO:0098901)|regulation of cardiac muscle cell action potential involved in regulation of contraction (GO:0098909)|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 cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of cell growth (GO:0001558)|regulation of cellular localization (GO:0060341)|regulation of generation of L-type calcium current (GO:1902514)|regulation of heart contraction (GO:0008016)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of histone deacetylase activity (GO:1901725)|regulation of membrane depolarization (GO:0003254)|regulation of relaxation of cardiac muscle (GO:1901897)|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 the force of heart contraction (GO:0002026)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|relaxation of cardiac muscle (GO:0055119)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|calcium channel complex (GO:0034704)|calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intercalated disc (GO:0014704)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|ion channel binding (GO:0044325)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|sodium channel inhibitor activity (GO:0019871)|titin binding (GO:0031432)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	13		Ovarian(17;0.00369)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000271)		CAGCCTTGATCTGCTGATAGA	0.383																																					p.Q225Q		Atlas-SNP	.											.	CAMK2D	55	.	0			c.G675A						PASS	.						129	131	130					4																	114438740		2203	4300	6503	SO:0001819	synonymous_variant	817	exon9			CTTGATCTGCTGA	U50361	CCDS3703.1, CCDS3704.1, CCDS43263.1, CCDS47127.1, CCDS54797.1	4q26	2008-10-30	2008-10-30		ENSG00000145349	ENSG00000145349			1462	protein-coding gene	gene with protein product		607708	"calcium/calmodulin-dependent protein kinase (CaM kinase) II delta"	CAMKD			Standard	NM_001221		Approved		uc003ibi.3	Q13557	OTTHUMG00000132910	ENST00000342666.5:c.675G>A	4.37:g.114438740C>T		66	0	0		85	4	0.0470588	NM_172128	A8MVS8|Q52PK4|Q59G21|Q8N553|Q9UGH6|Q9UQE9	Silent	SNP	ENST00000342666.5	37	CCDS3703.1																																																																																			.	.	none		0.383	CAMK2D-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256420.2			T	114438740	C	T	114438740	2	4	22	1	0	0	0	0	0	0	0	1	2603	912	32	2		2	CAMK2D	4	114438740	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	158970	114438740	76715536	1095	3996											
TRAM1L1	133022	hgsc.bcm.edu	37	chr4	118005458	118005458	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gattatgaagatttctctttCctctttggcggacagtctac	8	16	8	9	1	3	2	0	1	3	1	5	4	4	3	1	2	1	0	1	2	3	5	rs35809332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:118005458C>T	ENST00000310754.4	-	1	1278	c.1092G>A	c.(1090-1092)agG>agA	p.R364R		NM_152402.2	NP_689615.2	Q8N609	TR1L1_HUMAN	translocation associated membrane protein 1-like 1	364					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						ATTTCTCTTTCCTCTTTGGCG	0.378													C|||	56	0.0111821	0.0401	0.0043	5008	,	,		18119	0.0		0.0	False		,,,				2504	0.0				p.R364R		Atlas-SNP	.											.	TRAM1L1	55	.	0			c.G1092A						PASS	.	C		161,4245	94.8+/-133.5	4,153,2046	135	140	138		1092	2.9	1	4	dbSNP_126	138	0,8600		0,0,4300	no	coding-synonymous	TRAM1L1	NM_152402.2		4,153,6346	TT,TC,CC		0.0,3.6541,1.2379		364/370	118005458	161,12845	2203	4300	6503	SO:0001819	synonymous_variant	133022	exon1			CTCTTTCCTCTTT	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.1092G>A	4.37:g.118005458C>T		205	0	0		199	94	0.472362	NM_152402	Q8N2L7	Silent	SNP	ENST00000310754.4	37	CCDS3707.1																																																																																			C|0.987;T|0.013	0.013	strong		0.378	TRAM1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256513.1	NM_152402		T	118005458	C	T	118005458	2	4	22	1	0	0	0	0	0	0	0	1	16467	854	30	2		2	TRAM1L1	4	118005458	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3566718	118005458	73148818	1096	3997											
SEC24D	9871	hgsc.bcm.edu	37	chr4	119659518	119659518	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	atgaccttcaaaggctggtgGagaactgctttaaaagctac	13	10	10	8	0	1	2	1	1	0	1	1	3	1	2	1	3	4	3	1	3	5	4	rs1128403	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:119659518G>A	ENST00000280551.6	-	19	2632	c.2394C>T	c.(2392-2394)ctC>ctT	p.L798L	SEC24D_ENST00000419654.2_Silent_p.L354L|SEC24D_ENST00000505134.1_5'UTR|SEC24D_ENST00000379735.5_Silent_p.L799L|SEC24D_ENST00000511481.1_Silent_p.L429L|SEC24D_ENST00000429811.2_Silent_p.L354L			O94855	SC24D_HUMAN	SEC24 family member D	798					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						AAGGCTGGTGGAGAACTGCTT	0.403													G|||	197	0.0393371	0.1309	0.0202	5008	,	,		19037	0.0		0.008	False		,,,				2504	0.002				p.L798L		Atlas-SNP	.											.	SEC24D	96	.	0			c.C2394T						PASS	.	G		499,3907	234.6+/-247.4	25,449,1729	100	89	93		2394	-10.1	0.1	4	dbSNP_86	93	28,8572	19.8+/-62.0	0,28,4272	no	coding-synonymous	SEC24D	NM_014822.2		25,477,6001	AA,AG,GG		0.3256,11.3255,4.052		798/1033	119659518	527,12479	2203	4300	6503	SO:0001819	synonymous_variant	9871	exon19			CTGGTGGAGAACT	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.2394C>T	4.37:g.119659518G>A		170	0	0		178	75	0.421348	NM_014822	Q8IYI7	Silent	SNP	ENST00000280551.6	37	CCDS3710.1																																																																																			G|0.956;A|0.044	0.044	strong		0.403	SEC24D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256514.4			A	119659518	G	A	119659518	2	1	22	1	0	0	0	0	0	0	0	1	14012	1161	41	2		2	SEC24D	4	119659518	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1654060	119659518	71494758	1097	3998											
SYNPO2	171024	hgsc.bcm.edu	37	chr4	119952589	119952589	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtcgagaatggagaagtatGtggtcgattcagacacggtg	12	9	15	5	3	1	3	1	0	0	3	3	6	1	3	0	3	0	1	0	3	3	2	rs115012720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:119952589G>A	ENST00000429713.2	+	4	2841	c.2659G>A	c.(2659-2661)Gtg>Atg	p.V887M	SYNPO2_ENST00000307142.4_Missense_Mutation_p.V887M|SYNPO2_ENST00000434046.2_Missense_Mutation_p.V887M|SYNPO2_ENST00000448416.2_Intron	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	887						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						GGAGAAGTATGTGGTCGATTC	0.562													G|||	28	0.00559105	0.0212	0.0	5008	,	,		20471	0.0		0.0	False		,,,				2504	0.0				p.V887M		Atlas-SNP	.											.	SYNPO2	353	.	0			c.G2659A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL	100,4306	80.4+/-118.8	1,98,2104	126	118	121		2659,2659,2659	5.8	1	4	dbSNP_132	121	3,8597	1.2+/-3.3	0,3,4297	yes	missense,missense,missense	SYNPO2	NM_001128933.1,NM_001128934.1,NM_133477.2	21,21,21	1,101,6401	AA,AG,GG		0.0349,2.2696,0.7919	probably-damaging,probably-damaging,probably-damaging	887/1094,887/1110,887/1262	119952589	103,12903	2203	4300	6503	SO:0001583	missense	171024	exon4			AAGTATGTGGTCG	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.2659G>A	4.37:g.119952589G>A	ENSP00000395143:p.Val887Met	53	0	0		83	42	0.506024	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	37	CCDS47129.1	8|8	0.003663003663003663|0.003663003663003663	8|8	0.016260162601626018|0.016260162601626018	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	18.38|18.38	3.611213|3.611213	0.66558|0.66558	0.022696|0.022696	3.49E-4|3.49E-4	ENSG00000172403|ENSG00000172403	ENST00000504178|ENST00000307142;ENST00000429713;ENST00000434046	.|T;T;T	.|0.25085	.|1.82;1.87;1.88	5.76|5.76	5.76|5.76	0.90799|0.90799	.|.	.|0.000000	.|0.56097	.|D	.|0.000026	T|T	0.39200|0.39200	0.1069|0.1069	M|M	0.79258|0.79258	2.445|2.445	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;0.999	.|D;D;D;D	.|0.87578	.|0.998;0.994;0.986;0.99	T|T	0.43972|0.43972	-0.9358|-0.9358	5|9	.|.	.|.	.|.	-20.0199|-20.0199	19.9596|19.9596	0.97236|0.97236	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|887;887;887;887	.|B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6	.|.;.;.;SYNP2_HUMAN	Y|M	838|887	.|ENSP00000306015:V887M;ENSP00000395143:V887M;ENSP00000390965:V887M	.|.	C|V	+|+	2|1	0|0	SYNPO2|SYNPO2	120172037|120172037	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.948000|0.948000	0.59901|0.59901	5.790000|5.790000	0.69038|0.69038	2.726000|2.726000	0.93360|0.93360	0.655000|0.655000	0.94253|0.94253	TGT|GTG	G|0.993;A|0.007	0.007	strong		0.562	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1			A	119952589	G	A	119952589	3	1	22	1	0	0	0	0	1	0	0	0	15472	1377	48	2	2673	2	SYNPO2	4	119952589	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	293071	119952589	71201687	1098	3999											
PDE5A	8654	hgsc.bcm.edu	37	chr4	120440278	120440278	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagcaatgcaagtatctccAggtcagtcagcttgttctgc	9	12	9	11	0	5	0	3	0	2	0	6	0	5	0	1	1	4	5	1	1	3	3	rs116396619	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:120440278A>G	ENST00000354960.3	-	14	2241	c.1922T>C	c.(1921-1923)cTg>cCg	p.L641P	PDE5A_ENST00000512739.1_5'Flank|PDE5A_ENST00000394439.1_Missense_Mutation_p.L589P|RP11-33B1.1_ENST00000498873.1_RNA|PDE5A_ENST00000264805.5_Missense_Mutation_p.L599P	NM_001083.3	NP_001074.2	O76074	PDE5A_HUMAN	phosphodiesterase 5A, cGMP-specific	641	Catalytic. {ECO:0000250}.				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)	AAGTATCTCCAGGTCAGTCAG	0.408													A|||	26	0.00519169	0.0174	0.0029	5008	,	,		18416	0.0		0.001	False		,,,				2504	0.0				p.L641P		Atlas-SNP	.											.	PDE5A	83	.	0			c.T1922C						PASS	.	A	PRO/LEU,PRO/LEU,PRO/LEU	58,4348	56.8+/-93.2	0,58,2145	125	104	111		1922,1796,1766	5.5	1	4	dbSNP_132	111	0,8600		0,0,4300	yes	missense,missense,missense	PDE5A	NM_001083.3,NM_033430.2,NM_033437.3	98,98,98	0,58,6445	GG,GA,AA		0.0,1.3164,0.4459	probably-damaging,probably-damaging,probably-damaging	641/876,599/834,589/824	120440278	58,12948	2203	4300	6503	SO:0001583	missense	8654	exon14			ATCTCCAGGTCAG	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.1922T>C	4.37:g.120440278A>G	ENSP00000347046:p.Leu641Pro	241	1	0.00414938		261	129	0.494253	NM_001083	A0AV69|A8K2C4|O75026|O75887|Q86UI0|Q86V66|Q9Y6Z6	Missense_Mutation	SNP	ENST00000354960.3	37	CCDS3713.1	7	0.003205128205128205	6	0.012195121951219513	0	0.0	0	0.0	1	0.0013192612137203166	A	20.9	4.064397	0.76187	0.013164	0.0	ENSG00000138735	ENST00000354960;ENST00000394439;ENST00000264805	D;D;D	0.85702	-2.02;-2.02;-2.02	5.46	5.46	0.80206	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	D	0.91520	0.7322	H	0.94964	3.605	0.80722	D	1	D;D	0.63046	0.992;0.989	D;D	0.72982	0.979;0.916	D	0.92792	0.6249	10	0.87932	D	0	.	9.4099	0.38485	0.9202:0.0:0.0798:0.0	.	641;599	O76074;O76074-2	PDE5A_HUMAN;.	P	641;589;599	ENSP00000347046:L641P;ENSP00000377957:L589P;ENSP00000264805:L599P	ENSP00000264805:L599P	L	-	2	0	PDE5A	120659726	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.113000	0.77095	2.081000	0.62600	0.533000	0.62120	CTG	A|0.996;G|0.004	0.004	strong		0.408	PDE5A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256529.1	NM_001083		G	120440278	A	G	120440278	3	3	22	1	0	0	0	0	1	0	0	0	11653	188	7	3	737	3	PDE5A	4	120440278	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	487689	120440278	70713998	1099	4000											
BBS12	166379	hgsc.bcm.edu	37	chr4	123664333	123664333	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aattgaaaaatgtataaacaGtaagcggttggtaatcggct	16	11	10	4	2	0	1	0	1	0	0	1	1	0	1	0	3	2	5	0	3	8	6	rs7665271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:123664333G>C	ENST00000314218.3	+	2	1479	c.1286G>C	c.(1285-1287)aGt>aCt	p.S429T	BBS12_ENST00000542236.1_Missense_Mutation_p.S429T	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	429			S -> T (in dbSNP:rs7665271).		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						TGTATAAACAGTAAGCGGTTG	0.453									Bardet-Biedl syndrome				G|||	186	0.0371406	0.1301	0.0173	5008	,	,		20575	0.0		0.002	False		,,,				2504	0.0				p.S429T		Atlas-SNP	.											.	BBS12	63	.	0			c.G1286C						PASS	.	G	THR/SER,THR/SER	451,3955	215.5+/-234.4	21,409,1773	75	79	78		1286,1286	-0.6	0	4	dbSNP_116	78	12,8588	9.1+/-34.3	0,12,4288	yes	missense,missense	BBS12	NM_001178007.1,NM_152618.2	58,58	21,421,6061	CC,CG,GG		0.1395,10.236,3.5599	possibly-damaging,possibly-damaging	429/711,429/711	123664333	463,12543	2203	4300	6503	SO:0001583	missense	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	TAAACAGTAAGCG	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.1286G>C	4.37:g.123664333G>C	ENSP00000319062:p.Ser429Thr	78	0	0		105	43	0.409524	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Missense_Mutation	SNP	ENST00000314218.3	37	CCDS3728.1	75	0.034340659340659344	65	0.13211382113821138	9	0.024861878453038673	0	0.0	1	0.0013192612137203166	G	0.004	-2.356069	0.00217	0.10236	0.001395	ENSG00000181004	ENST00000314218;ENST00000542236	T;T	0.79033	-1.23;-1.23	5.58	-0.599	0.11645	.	0.533090	0.21899	N	0.067461	T	0.01627	0.0052	M	0.67953	2.075	0.80722	P	0.0	B	0.18461	0.028	B	0.15052	0.012	T	0.21177	-1.0253	9	0.38643	T	0.18	-14.2272	7.1191	0.25433	0.2915:0.3132:0.3953:0.0	rs7665271;rs7665271	429	Q6ZW61	BBS12_HUMAN	T	429	ENSP00000319062:S429T;ENSP00000438273:S429T	ENSP00000319062:S429T	S	+	2	0	BBS12	123883783	0.005000	0.15991	0.000000	0.03702	0.013000	0.08279	0.239000	0.18023	-0.537000	0.06290	-0.157000	0.13467	AGT	G|0.959;C|0.041	0.041	strong		0.453	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618		C	123664333	G	C	123664333	3	2	22	1	0	0	0	0	1	0	0	0	1337	1029	36	4	1288	4	BBS12	4	123664333	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3224055	123664333	67489943	1100	4001											
NUDT6	11162	hgsc.bcm.edu	37	chr4	123814170	123814170	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagttgtattttcagtcttcGccaggtcattgagatccatc	8	15	9	9	1	3	1	2	1	1	1	6	3	4	1	2	1	0	2	2	1	1	6	rs138619142		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:123814170G>A	ENST00000304430.5	-	5	797	c.764C>T	c.(763-765)gCg>gTg	p.A255V	FGF2_ENST00000264498.3_3'UTR|NUDT6_ENST00000339154.2_Missense_Mutation_p.A86V|FGF2_ENST00000608478.1_3'UTR|NUDT6_ENST00000608639.1_5'Flank|NUDT6_ENST00000502270.1_Missense_Mutation_p.A86V	NM_007083.4	NP_009014.2	P53370	NUDT6_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 6	255	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						TTCAGTCTTCGCCAGGTCATT	0.433													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18368	0.0		0.0	False		,,,				2504	0.0				p.A255V		Atlas-SNP	.											.	NUDT6	50	.	0			c.C764T						PASS	.	G	,VAL/ALA,VAL/ALA	15,4391	22.3+/-47.3	0,15,2188	134	125	128		,764,257	-3.6	0	4	dbSNP_134	128	0,8600		0,0,4300	yes	utr-3,missense,missense	FGF2,NUDT6	NM_002006.4,NM_007083.3,NM_198041.1	,64,64	0,15,6488	AA,AG,GG		0.0,0.3404,0.1153	,benign,benign	,255/317,86/148	123814170	15,12991	2203	4300	6503	SO:0001583	missense	11162	exon5			GTCTTCGCCAGGT	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.764C>T	4.37:g.123814170G>A	ENSP00000306070:p.Ala255Val	212	0	0		231	114	0.493506	NM_007083	A8K756|O95097|Q9UQD9	Missense_Mutation	SNP	ENST00000304430.5	37	CCDS43268.1	.	.	.	.	.	.	.	.	.	.	G	0.014	-1.606796	0.00842	0.003404	0.0	ENSG00000170917	ENST00000304430;ENST00000339154;ENST00000502270	T;T;T	0.29397	1.57;1.57;1.57	5.11	-3.64	0.04515	NUDIX hydrolase domain (3);NUDIX hydrolase domain-like (1);	0.356862	0.31312	N	0.007867	T	0.14960	0.0361	L	0.41124	1.26	0.38646	D	0.951723	B	0.31241	0.315	B	0.24006	0.05	T	0.43410	-0.9393	10	0.02654	T	1	-8.3014	10.6191	0.45470	0.2019:0.0:0.6699:0.1282	.	255	P53370	NUDT6_HUMAN	V	255;86;86	ENSP00000306070:A255V;ENSP00000344011:A86V;ENSP00000424117:A86V	ENSP00000306070:A255V	A	-	2	0	NUDT6	124033620	0.857000	0.29778	0.016000	0.15963	0.203000	0.24098	1.354000	0.34056	-0.254000	0.09500	-0.312000	0.09012	GCG	G|0.998;A|0.002	0.002	strong		0.433	NUDT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095331.3	NM_007083		A	123814170	G	A	123814170	3	1	22	1	0	0	0	0	1	0	0	0	10752	1087	38	1	190	1	NUDT6	4	123814170	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	149837	123814170	67340106	1101	4002											
PLK4	10733	hgsc.bcm.edu	37	chr4	128808620	128808620	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acacctcagactgaaaccgtAcaacagtggtttgggaatct	13	9	9	10	1	2	2	1	1	1	1	2	3	2	3	2	2	3	2	2	2	4	2	rs112831813	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:128808620A>T	ENST00000270861.5	+	6	1702	c.1428A>T	c.(1426-1428)gtA>gtT	p.V476V	PLK4_ENST00000513090.1_Silent_p.V444V|PLK4_ENST00000514379.1_Silent_p.V435V|PLK4_ENST00000515069.1_Silent_p.V476V|PLK4_ENST00000507249.1_Silent_p.V442V	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	476					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						CTGAAACCGTACAACAGTGGT	0.363													A|||	26	0.00519169	0.0182	0.0029	5008	,	,		16496	0.0		0.0	False		,,,				2504	0.0				p.V476V	Colon(135;508 1718 19061 31832 42879)	Atlas-SNP	.											.	PLK4	65	.	0			c.A1428T						PASS	.	A	,,	76,4330	65.8+/-103.3	0,76,2127	65	66	65		1332,1305,1428	-5.6	0.9	4	dbSNP_132	65	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	PLK4	NM_001190799.1,NM_001190801.1,NM_014264.4	,,	0,77,6426	TT,TA,AA		0.0116,1.7249,0.592	,,	444/939,435/930,476/971	128808620	77,12929	2203	4300	6503	SO:0001819	synonymous_variant	10733	exon6			AACCGTACAACAG	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.1428A>T	4.37:g.128808620A>T		406	0	0		482	238	0.493776	NM_014264	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Silent	SNP	ENST00000270861.5	37	CCDS3735.1																																																																																			A|0.993;T|0.007	0.007	strong		0.363	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257095.3			T	128808620	A	T	128808620	2	4	22	1	0	0	0	0	0	0	0	1	12107	378	14	5		5	PLK4	4	128808620	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	4994450	128808620	62345656	1102	4003											
MAML3	55534	hgsc.bcm.edu	37	chr4	140811131	140811131	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgctgctgctgttgctgttGctgtttctgctgcatgagtt	2	18	12	9	0	1	1	0	1	1	0	1	1	1	1	0	0	7	11	0	0	0	4			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:140811131G>T	ENST00000509479.2	-	2	2315	c.1459C>A	c.(1459-1461)Caa>Aaa	p.Q487K	MAML3_ENST00000398940.1_Missense_Mutation_p.Q26K|MAML3_ENST00000327122.5_Missense_Mutation_p.Q331K	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)					tgttgctgttgctgtttctgc	0.557																																					p.Q487K		Atlas-SNP	.											.	MAML3	192	.	0			c.C1459A						PASS	.						19	21	20					4																	140811131		2198	4294	6492	SO:0001583	missense	55534	exon2			GCTGTTGCTGTTT	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.1459C>A	4.37:g.140811131G>T	ENSP00000421180:p.Gln487Lys	74	0	0		93	7	0.0752688	NM_018717		Missense_Mutation	SNP	ENST00000509479.2	37	CCDS54805.1	.	.	.	.	.	.	.	.	.	.	G	1.344	-0.593356	0.03771	.	.	ENSG00000196782	ENST00000509479;ENST00000327122;ENST00000398940	T;T	0.66460	0.85;-0.21	4.28	4.28	0.50868	.	0.000000	0.85682	D	0.000000	T	0.40570	0.1122	N	0.08118	0	0.46499	D	0.999073	B	0.19200	0.034	B	0.18871	0.023	T	0.36359	-0.9751	10	0.02654	T	1	.	12.5248	0.56079	0.0:0.0:1.0:0.0	.	487	Q96JK9	MAML3_HUMAN	K	487;331;26	ENSP00000421180:Q487K;ENSP00000313316:Q331K	ENSP00000313316:Q331K	Q	-	1	0	MAML3	141030581	1.000000	0.71417	1.000000	0.80357	0.599000	0.36880	6.453000	0.73488	2.671000	0.90904	0.650000	0.86243	CAA	.	.	none		0.557	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			T	140811131	G	T	140811131	3	4	22	1	0	0	0	0	1	0	0	0	9216	1328	46	4	1965	4	MAML3	4	140811131	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	12002511	140811131	50343145	1103	4004											
ZNF330	27309	hgsc.bcm.edu	37	chr4	142155072	142155072	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagatactgagtcatcagatTtgtttactaatttgaattta	13	17	6	5	0	2	4	2	2	0	2	2	4	2	4	0	0	2	1	0	0	5	8	rs34631212	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:142155072T>A	ENST00000262990.4	+	10	1120	c.892T>A	c.(892-894)Ttg>Atg	p.L298M	ZNF330_ENST00000421169.2_Missense_Mutation_p.L238M	NM_014487.4	NP_055302.1	Q9Y3S2	ZN330_HUMAN	zinc finger protein 330	298			L -> M (in dbSNP:rs34631212).			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)					GTCATCAGATTTGTTTACTAA	0.453													T|||	199	0.0397364	0.1437	0.0115	5008	,	,		20408	0.0		0.001	False		,,,				2504	0.0				p.L298M		Atlas-SNP	.											.	ZNF330	31	.	0			c.T892A						PASS	.	T	MET/LEU	459,3947	218.4+/-236.5	16,427,1760	127	133	131		892	2.1	1	4	dbSNP_126	131	3,8597	3.0+/-9.4	0,3,4297	yes	missense	ZNF330	NM_014487.4	15	16,430,6057	AA,AT,TT		0.0349,10.4176,3.5522	benign	298/321	142155072	462,12544	2203	4300	6503	SO:0001583	missense	27309	exon10			TCAGATTTGTTTA	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.892T>A	4.37:g.142155072T>A	ENSP00000262990:p.Leu298Met	131	0	0		164	74	0.451219	NM_014487	B2RDA3	Missense_Mutation	SNP	ENST00000262990.4	37	CCDS3754.1	73	0.033424908424908424	68	0.13821138211382114	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	T	13.71	2.318489	0.40996	0.104176	3.49E-4	ENSG00000109445	ENST00000262990;ENST00000421169	T;T	0.31510	1.49;1.49	6.17	2.08	0.27032	.	0.358122	0.29212	N	0.012804	T	0.00144	0.0004	N	0.14661	0.345	0.28660	N	0.906172	B;B	0.29716	0.255;0.225	B;B	0.39771	0.146;0.309	T	0.15378	-1.0439	10	0.36615	T	0.2	-31.7734	6.1183	0.20139	0.0:0.456:0.2274:0.3166	rs34631212;rs57194793	238;298	E9PDK6;Q9Y3S2	.;ZN330_HUMAN	M	298;238	ENSP00000262990:L298M;ENSP00000397397:L238M	ENSP00000262990:L298M	L	+	1	2	ZNF330	142374522	0.504000	0.26123	1.000000	0.80357	0.990000	0.78478	0.442000	0.21628	0.416000	0.25844	0.533000	0.62120	TTG	T|0.968;A|0.032	0.032	strong		0.453	ZNF330-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257271.2	NM_014487		A	142155072	T	A	142155072	3	1	22	1	0	0	0	0	1	0	0	0	17863	1838	64	5	926	5	ZNF330	4	142155072	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1343941	142155072	48999204	1104	4005											
PRMT10	90826	hgsc.bcm.edu	37	chr4	148575601	148575601	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtctttattctgggtaaaacTttttgcaacatccatttcac	10	17	5	9	0	3	0	1	0	2	0	4	0	4	0	1	1	3	2	1	1	4	7	rs17023638	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:148575601T>C	ENST00000322396.6	-	9	1689	c.1447A>G	c.(1447-1449)Agt>Ggt	p.S483G	PRMT10_ENST00000541232.1_Missense_Mutation_p.S370G|TMEM184C_ENST00000508208.1_Intron	NM_138364.2	NP_612373.2	Q6P2P2	ANM9_HUMAN		483			S -> G (in dbSNP:rs17023638).			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						TGGGTAAAACTTTTTGCAACA	0.403													T|||	127	0.0253594	0.0938	0.0043	5008	,	,		19860	0.0		0.0	False		,,,				2504	0.0				p.S483G		Atlas-SNP	.											.	PRMT10	68	.	0			c.A1447G						PASS	.	T	GLY/SER	301,4105	161.8+/-193.9	10,281,1912	108	108	108		1447	0.4	0.4	4	dbSNP_123	108	1,8599	1.2+/-3.3	0,1,4299	yes	missense	PRMT10	NM_138364.2	56	10,282,6211	CC,CT,TT		0.0116,6.8316,2.322	benign	483/846	148575601	302,12704	2203	4300	6503	SO:0001583	missense	90826	exon9			TAAAACTTTTTGC																												ENST00000322396.6:c.1447A>G	4.37:g.148575601T>C	ENSP00000314396:p.Ser483Gly	68	0	0		102	43	0.421569	NM_138364	A8KA39|B3KU92|Q6ZR58|Q8N383|Q9BT55|Q9NT98	Missense_Mutation	SNP	ENST00000322396.6	37	CCDS3771.1	64	0.029304029304029304	64	0.13008130081300814	0	0.0	0	0.0	0	0.0	T	10.31	1.315040	0.23908	0.068316	1.16E-4	ENSG00000164169	ENST00000322396;ENST00000541232	T;T	0.45668	0.89;0.89	6.04	0.437	0.16555	.	0.391208	0.33792	N	0.004547	T	0.00241	0.0007	L	0.31294	0.92	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.15150	-1.0447	9	0.13853	T	0.58	-20.9041	5.4198	0.16394	0.1195:0.2119:0.0:0.6686	rs17023638;rs17023638	483	Q6P2P2	ANM10_HUMAN	G	483;370	ENSP00000314396:S483G;ENSP00000439508:S370G	ENSP00000314396:S483G	S	-	1	0	PRMT10	148795051	0.002000	0.14202	0.389000	0.26208	0.971000	0.66376	0.093000	0.15086	0.116000	0.18110	0.459000	0.35465	AGT	T|0.963;C|0.037	0.037	strong		0.403	PRMT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364650.1			C	148575601	T	C	148575601	3	2	22	1	0	0	0	0	1	0	0	0	12548	1609	56	3	1106	3	PRMT10	4	148575601	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	6420529	148575601	42578675	1105	4006											
PRMT10	90826	hgsc.bcm.edu	37	chr4	148594177	148594177	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	taagagtttgatccctgcttCcatcttgtttgctgccacga	7	15	8	11	1	1	2	0	1	1	1	3	3	3	2	3	0	3	4	3	0	1	5	rs73853975	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:148594177C>T	ENST00000322396.6	-	4	918	c.676G>A	c.(676-678)Gaa>Aaa	p.E226K	PRMT10_ENST00000541232.1_Missense_Mutation_p.E113K	NM_138364.2	NP_612373.2	Q6P2P2	ANM9_HUMAN		226	SAM-dependent MTase PRMT-type 1. {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						ATCCCTGCTTCCATCTTGTTT	0.388													C|||	229	0.0457268	0.1702	0.0058	5008	,	,		14532	0.0		0.0	False		,,,				2504	0.0				p.E226K		Atlas-SNP	.											.	PRMT10	68	.	0			c.G676A						PASS	.	C	LYS/GLU	610,3796	267.1+/-267.6	41,528,1634	160	150	154		676	4.6	1	4	dbSNP_130	154	3,8597	3.0+/-9.4	0,3,4297	yes	missense	PRMT10	NM_138364.2	56	41,531,5931	TT,TC,CC		0.0349,13.8448,4.7132	benign	226/846	148594177	613,12393	2203	4300	6503	SO:0001583	missense	90826	exon4			CTGCTTCCATCTT																												ENST00000322396.6:c.676G>A	4.37:g.148594177C>T	ENSP00000314396:p.Glu226Lys	114	0	0		151	77	0.509934	NM_138364	A8KA39|B3KU92|Q6ZR58|Q8N383|Q9BT55|Q9NT98	Missense_Mutation	SNP	ENST00000322396.6	37	CCDS3771.1	106	0.048534798534798536	105	0.21341463414634146	1	0.0027624309392265192	0	0.0	0	0.0	C	18.24	3.579466	0.65878	0.138448	3.49E-4	ENSG00000164169	ENST00000322396;ENST00000541232	T;T	0.23348	1.91;1.91	5.44	4.58	0.56647	.	0.210963	0.49305	D	0.000159	T	0.00012	0.0000	L	0.38733	1.17	0.24656	P	0.99349699	B	0.24675	0.109	B	0.30943	0.122	T	0.21211	-1.0252	9	0.41790	T	0.15	-7.5111	10.3867	0.44145	0.0:0.791:0.1363:0.0727	.	226	Q6P2P2	ANM10_HUMAN	K	226;113	ENSP00000314396:E226K;ENSP00000439508:E113K	ENSP00000314396:E226K	E	-	1	0	PRMT10	148813627	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	3.053000	0.49901	1.242000	0.43836	0.655000	0.94253	GAA	C|0.946;T|0.054	0.054	strong		0.388	PRMT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364650.1			T	148594177	C	T	148594177	3	4	22	1	0	0	0	0	1	0	0	0	12548	864	30	2	1897	2	PRMT10	4	148594177	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	18576	148594177	42560099	1106	4007											
KIAA0922	23240	hgsc.bcm.edu	37	chr4	154525446	154525446	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaactgacattaaaacttcAgagaacacagccgagttcaa	18	7	7	9	1	2	2	2	1	0	1	2	5	2	2	1	0	4	1	1	0	5	3	rs17030219	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:154525446A>C	ENST00000409663.3	+	25	3331	c.3279A>C	c.(3277-3279)tcA>tcC	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													A|||	52	0.0103834	0.0378	0.0014	5008	,	,		19441	0.0		0.001	False		,,,				2504	0.0				p.S1094S		Atlas-SNP	.											.	KIAA0922	214	.	0			c.A3282C						PASS	.	A	,	171,4235	111.6+/-149.8	2,167,2034	51	52	52		3282,3279	1.9	0.5	4	dbSNP_123	52	1,8599		0,1,4299	yes	coding-synonymous,coding-synonymous	KIAA0922	NM_001131007.1,NM_015196.3	,	2,168,6333	CC,CA,AA		0.0116,3.8811,1.3225	,	1094/1611,1093/1610	154525446	172,12834	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>C	4.37:g.154525446A>C		135	0	0		134	75	0.559702	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Silent	SNP	ENST00000409663.3	37	CCDS3783.2																																																																																			A|0.987;C|0.013	0.013	strong		0.408	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196		C	154525446	A	C	154525446	2	2	22	1	0	0	0	0	0	0	0	1	8210	175	7	5		5	KIAA0922	4	154525446	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	5931269	154525446	36628830	1107	4008											
DCHS2	54798	hgsc.bcm.edu	37	chr4	155156875	155156875	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcagaggagaaagacacatTcacaaaaacagtgcaagatg	19	6	9	7	0	2	4	2	0	0	4	2	5	2	4	0	1	2	1	0	1	4	2	rs61746101	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:155156875T>G	ENST00000357232.4	-	25	7563	c.7564A>C	c.(7564-7566)Aat>Cat	p.N2522H		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2522	Cadherin 22. {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)		AAAGACACATTCACAAAAACA	0.408													T|||	214	0.0427316	0.1558	0.0086	5008	,	,		18956	0.0		0.002	False		,,,				2504	0.0				p.N2522H		Atlas-SNP	.											.	DCHS2	594	.	0			c.A7564C						PASS	.	T	HIS/ASN	567,3839	253.0+/-259.1	26,515,1662	81	82	82		7564	5.7	1	4	dbSNP_129	82	9,8591	6.4+/-24.3	0,9,4291	yes	missense	DCHS2	NM_017639.3	68	26,524,5953	GG,GT,TT		0.1047,12.8688,4.4287	probably-damaging	2522/2917	155156875	576,12430	2203	4300	6503	SO:0001583	missense	54798	exon25			ACACATTCACAAA	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.7564A>C	4.37:g.155156875T>G	ENSP00000349768:p.Asn2522His	74	0	0		97	48	0.494845	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	72	0.03296703296703297	71	0.1443089430894309	1	0.0027624309392265192	0	0.0	0	0.0	T	18.70	3.680330	0.68042	0.128688	0.001047	ENSG00000197410	ENST00000357232	T	0.60672	0.17	5.71	5.71	0.89125	Cadherin (3);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.01320	0.0043	L	0.58669	1.825	0.80722	D	1	D	0.89917	1.0	D	0.73708	0.981	T	0.04495	-1.0947	10	0.56958	D	0.05	.	15.9843	0.80138	0.0:0.0:0.0:1.0	.	2522	Q6V1P9	PCD23_HUMAN	H	2522	ENSP00000349768:N2522H	ENSP00000349768:N2522H	N	-	1	0	DCHS2	155376325	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.229000	0.58625	2.176000	0.68965	0.383000	0.25322	AAT	T|0.959;G|0.041	0.041	strong		0.408	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		G	155156875	T	G	155156875	3	3	22	1	0	0	0	0	1	0	0	0	4290	1783	62	5	1190	5	DCHS2	4	155156875	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	631429	155156875	35997401	1108	4009											
DCHS2	54798	hgsc.bcm.edu	37	chr4	155158104	155158104	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtttgaaaatgtaacaagcGtgcttccaaccagagcatcc	13	10	8	10	1	0	2	0	1	0	1	2	2	2	2	3	0	5	4	3	0	5	3	rs17031279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:155158104G>A	ENST00000357232.4	-	25	6334	c.6335C>T	c.(6334-6336)aCg>aTg	p.T2112M		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2112	Cadherin 19. {ECO:0000255|PROSITE- ProRule:PRU00043}.		T -> M (in dbSNP:rs17031279).		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)		TGTAACAAGCGTGCTTCCAAC	0.383													G|||	106	0.0211661	0.0749	0.0058	5008	,	,		22095	0.0		0.002	False		,,,				2504	0.001				p.T2112M		Atlas-SNP	.											.	DCHS2	594	.	0			c.C6335T						PASS	.	G	MET/THR	258,4148	149.2+/-183.4	6,246,1951	158	152	154		6335	4.1	0.1	4	dbSNP_123	154	5,8595	4.3+/-15.6	0,5,4295	yes	missense	DCHS2	NM_017639.3	81	6,251,6246	AA,AG,GG		0.0581,5.8557,2.0221	probably-damaging	2112/2917	155158104	263,12743	2203	4300	6503	SO:0001583	missense	54798	exon25			ACAAGCGTGCTTC	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.6335C>T	4.37:g.155158104G>A	ENSP00000349768:p.Thr2112Met	162	0	0		178	90	0.505618	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	26	0.011904761904761904	26	0.052845528455284556	0	0.0	0	0.0	0	0.0	G	10.93	1.488688	0.26686	0.058557	5.81E-4	ENSG00000197410	ENST00000357232	T	0.52754	0.65	5.82	4.09	0.47781	Cadherin (3);Cadherin-like (1);	0.347781	0.26669	N	0.023120	T	0.14614	0.0353	M	0.76002	2.32	0.30495	N	0.770966	D	0.89917	1.0	D	0.66847	0.947	T	0.47995	-0.9073	10	0.42905	T	0.14	.	4.1039	0.10028	0.147:0.1359:0.5918:0.1253	rs17031279;rs52827899;rs17031279	2112	Q6V1P9	PCD23_HUMAN	M	2112	ENSP00000349768:T2112M	ENSP00000349768:T2112M	T	-	2	0	DCHS2	155377554	0.994000	0.37717	0.138000	0.22173	0.167000	0.22549	2.937000	0.48979	1.459000	0.47892	0.557000	0.71058	ACG	G|0.979;A|0.021	0.021	strong		0.383	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		A	155158104	G	A	155158104	3	1	22	1	0	0	0	0	1	0	0	0	4290	1145	40	1	2419	1	DCHS2	4	155158104	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1229	155158104	35996172	1109	4010											
DCHS2	54798	hgsc.bcm.edu	37	chr4	155158259	155158260	+	In_Frame_Ins	INS	-	-	GTT																															tggcttccacaagaaattgaINSgttgttgatattgtatccag																								rs138652483|rs376550327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:155158259_155158260insGTT	ENST00000357232.4	-	25	6178_6179	c.6179_6180insAAC	c.(6178-6180)act>acAACt	p.2060_2060T>TT		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2060	Cadherin 18. {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)		CAAGAAATTGAGTTGTTGATAT	0.376														103	0.0205671	0.0734	0.0058	5008	,	,		19389	0.0		0.002	False		,,,				2504	0.0				p.T2060delinsTT		Pindel,Atlas-Indel	.											.	DCHS2	594	.	0			c.6180_6181insAAC						PASS	.			254,4010		7,240,1885						3.4	0.1		dbSNP_134	82	6,8246		0,6,4120	no	coding	DCHS2	NM_017639.3		7,246,6005	A1A1,A1R,RR		0.0727,5.9568,2.0773				260,12256				SO:0001652	inframe_insertion	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.6177_6179dupAAC	4.37:g.155158263_155158265dupGTT	ENSP00000349768:p.Thr2060dup	140	0	.		126	40	0.317	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	In_Frame_Ins	INS	ENST00000357232.4	37	CCDS3785.1																																																																																			-|0.988;GTT|0.012	0.012	strong		0.376	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		GTT	155158260	-	GTT	155158259	7	5	22	1	0	1	1	0	0	0	0	0	4290	291	11	0	2574	0	DCHS2	4	155158259	In_Frame_Ins	INS	-	TCGA-G8-6324-01A-11D-2210-10	155	155158259	35996017	1110	4011											
DCHS2	54798	hgsc.bcm.edu	37	chr4	155219318	155219318	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	tgtctggtttgtaggcgactCgggggaaagaaacacatcaa	12	9	13	7	2	2	1	1	0	1	1	3	3	2	2	0	4	1	2	0	4	4	2	rs28561984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:155219318C>G	ENST00000357232.4	-	18	4782	c.4783G>C	c.(4783-4785)Gag>Cag	p.E1595Q		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1595	Cadherin 14. {ECO:0000255|PROSITE- ProRule:PRU00043}.		E -> Q (in dbSNP:rs28561984).		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)		GTAGGCGACTCGGGGGAAAGA	0.428													G|||	406	0.0810703	0.261	0.0418	5008	,	,		19868	0.0109		0.0179	False		,,,				2504	0.0031				p.E1595Q		Atlas-SNP	.											.	DCHS2	594	.	0			c.G4783C						PASS	.						89	90	89					4																	155219318		2203	4300	6503	SO:0001583	missense	54798	exon18			GCGACTCGGGGGA	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.4783G>C	4.37:g.155219318C>G	ENSP00000349768:p.Glu1595Gln	212	0	0		206	94	0.456311	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	173	0.07921245421245421	142	0.2886178861788618	11	0.03038674033149171	6	0.01048951048951049	14	0.018469656992084433	G	0.003	-2.426918	0.00186	.	.	ENSG00000197410	ENST00000357232	T	0.61627	0.09	5.66	0.139	0.14798	Cadherin (2);Cadherin-like (1);	0.917277	0.09327	N	0.817476	T	0.00012	0.0000	N	0.02916	-0.46	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.25916	-1.0118	9	0.10377	T	0.69	.	3.0954	0.06308	0.1424:0.376:0.2865:0.1951	rs28561984	1595	Q6V1P9	PCD23_HUMAN	Q	1595	ENSP00000349768:E1595Q	ENSP00000349768:E1595Q	E	-	1	0	DCHS2	155438768	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	0.438000	0.21559	-0.142000	0.11354	-0.127000	0.14921	GAG	C|0.867;G|0.027;T|0.106	0.027	strong		0.428	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		G	155219318	C	G	155219318	3	3	22	1	0	0	0	0	1	0	0	0	4290	893	31	4	3999	4	DCHS2	4	155219318	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	61059	155219318	35934958	1111	4012											
DCHS2	54798	hgsc.bcm.edu	37	chr4	155219373	155219373	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaactggatcattgtcattAacatcagtgacatatacttt	15	14	5	7	0	3	1	3	1	0	0	3	2	3	2	0	1	3	0	0	1	5	5	rs17031391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:155219373A>G	ENST00000357232.4	-	18	4727	c.4728T>C	c.(4726-4728)gtT>gtC	p.V1576V		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1576	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)		CATTGTCATTAACATCAGTGA	0.438													A|||	405	0.0808706	0.2602	0.0418	5008	,	,		19929	0.0109		0.0179	False		,,,				2504	0.0031				p.V1576V		Atlas-SNP	.											.	DCHS2	594	.	0			c.T4728C						PASS	.	A		945,3461	361.4+/-315.7	116,713,1374	103	102	102		4728	-1.4	1	4	dbSNP_123	102	148,8452	72.6+/-135.2	3,142,4155	no	coding-synonymous	DCHS2	NM_017639.3		119,855,5529	GG,GA,AA		1.7209,21.448,8.4038		1576/2917	155219373	1093,11913	2203	4300	6503	SO:0001819	synonymous_variant	54798	exon18			GTCATTAACATCA	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.4728T>C	4.37:g.155219373A>G		199	0	0		214	98	0.457944	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	37	CCDS3785.1																																																																																			A|0.913;G|0.087	0.087	strong		0.438	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		G	155219373	A	G	155219373	2	3	22	1	0	0	0	0	0	0	0	1	4290	349	13	3		3	DCHS2	4	155219373	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	55	155219373	35934903	1112	4013											
DCHS2	54798	hgsc.bcm.edu	37	chr4	155407595	155407595	+	Nonstop_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtattatcttacaggaaatCtaggcaagattttgtttttc	11	17	8	5	0	2	1	0	0	2	1	3	2	2	2	0	3	1	3	0	3	6	8	rs140554741	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:155407595C>A	ENST00000456341.2	-	2	2108	c.2109G>T	c.(2107-2109)taG>taT	p.*703Y	DCHS2_ENST00000443500.1_Nonstop_Mutation_p.*710Y|DCHS2_ENST00000339452.1_Intron			Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	0	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.*710Y(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)		TACAGGAAATCTAGGCAAGAT	0.353													C|||	93	0.0185703	0.0008	0.0086	5008	,	,		21542	0.001		0.0298	False		,,,				2504	0.0562				p.X710Y		Atlas-SNP	.											DCHS2_ENST00000443500,NS,carcinoma,0,1	DCHS2	594	1	1	Nonstop extension(1)	kidney(1)	c.G2130T						PASS	.						268	215	231					4																	155407595		692	1591	2283	SO:0001578	stop_lost	54798	exon2			GGAAATCTAGGCA	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		ENST00000456341.2:c.2109G>T	4.37:g.155407595C>A		113	0	0		97	36	0.371134	NM_001142553	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000456341.2	37		24	0.01098901098901099	0	0.0	3	0.008287292817679558	0	0.0	21	0.027704485488126648	C	13.13	2.144810	0.37825	.	.	ENSG00000197410	ENST00000456341;ENST00000443500	.	.	.	2.87	-2.53	0.06326	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.6935	0.05127	0.3797:0.2807:0.0:0.3396	.	.	.	.	Y	703;710	.	.	X	-	3	2	DCHS2	155627045	0.000000	0.05858	0.000000	0.03702	0.592000	0.36648	-0.749000	0.04813	-0.726000	0.04895	0.561000	0.74099	TAG	C|0.989;A|0.011	0.011	strong		0.353	DCHS2-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000365285.1	NM_001142552		A	155407595	C	A	155407595	4	1	22	1	0	0	0	0	0	0	0	0	4290	927	32	4	8950	4	DCHS2	4	155407595	Nonstop_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	188222	155407595	35746681	1113	4014											
NPY2R	4887	hgsc.bcm.edu	37	chr4	156135250	156135250	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	attgaggtacaagttgttctCatattggcctactgctccat	9	15	8	9	0	1	1	1	1	1	0	3	1	2	1	2	2	3	4	2	2	4	7	rs2342674	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:156135250C>T	ENST00000329476.3	+	2	648	c.159C>T	c.(157-159)ctC>ctT	p.L53L	NPY2R_ENST00000506608.1_Silent_p.L53L	NM_000910.2	NP_000901.1	P49146	NPY2R_HUMAN	neuropeptide Y receptor Y2	53					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)	AAGTTGTTCTCATATTGGCCT	0.468													C|||	144	0.028754	0.1067	0.0043	5008	,	,		21334	0.0		0.0	False		,,,				2504	0.0				p.L53L		Atlas-SNP	.											.	NPY2R	87	.	0			c.C159T						PASS	.	C		400,4006	199.1+/-222.7	17,366,1820	213	198	203		159	1.6	0.9	4	dbSNP_100	203	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	NPY2R	NM_000910.2		17,368,6118	TT,TC,CC		0.0233,9.0785,3.0909		53/382	156135250	402,12604	2203	4300	6503	SO:0001819	synonymous_variant	4887	exon2			TGTTCTCATATTG	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.159C>T	4.37:g.156135250C>T		262	0	0		272	133	0.488971	NM_000910	Q13281|Q13457|Q4W5G7|Q6AZZ6|Q9UE67	Silent	SNP	ENST00000329476.3	37	CCDS3791.1																																																																																			C|0.967;T|0.033	0.033	strong		0.468	NPY2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365128.1	NM_000910		T	156135250	C	T	156135250	2	4	22	1	0	0	0	0	0	0	0	1	10618	813	29	2		2	NPY2R	4	156135250	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	727655	156135250	35019026	1114	4015											
NAF1	92345	hgsc.bcm.edu	37	chr4	164087753	164087753	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cccctcaaacgactgtagcgGcggctgtgtccctggcacag	7	7	12	15	3	1	0	1	0	0	0	2	1	2	0	3	3	2	3	3	3	2	1	rs12331663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:164087753G>A	ENST00000274054.2	-	1	320	c.127C>T	c.(127-129)Ccg>Tcg	p.P43S	NAF1_ENST00000422287.2_Missense_Mutation_p.P43S	NM_138386.2	NP_612395.2	Q96HR8	NAF1_HUMAN	nuclear assembly factor 1 ribonucleoprotein	43			P -> S (in dbSNP:rs12331663).		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)				GACTGTAGCGGCGGCTGTGTC	0.657													G|||	148	0.0295527	0.1104	0.0029	5008	,	,		11685	0.0		0.0	False		,,,				2504	0.0				p.P43S		Atlas-SNP	.											.	NAF1	69	.	0			c.C127T						PASS	.	G	SER/PRO,SER/PRO	409,3655		27,355,1650	8	12	11		127,127	0.6	0	4	dbSNP_120	11	7,8217		0,7,4105	yes	missense,missense	NAF1	NM_001128931.1,NM_138386.2	74,74	27,362,5755	AA,AG,GG		0.0851,10.064,3.3854	benign,benign	43/390,43/495	164087753	416,11872	2032	4112	6144	SO:0001583	missense	92345	exon1			GTAGCGGCGGCTG		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.127C>T	4.37:g.164087753G>A	ENSP00000274054:p.Pro43Ser	94	0	0		90	49	0.544444	NM_138386	D3DP28|E9PAZ2	Missense_Mutation	SNP	ENST00000274054.2	37	CCDS3803.1	58	0.026556776556776556	56	0.11382113821138211	2	0.0055248618784530384	0	0.0	0	0.0	G	9.310	1.055342	0.19907	0.10064	8.51E-4	ENSG00000145414	ENST00000422287;ENST00000274054	T;T	0.31510	1.49;1.51	2.42	0.648	0.17801	.	0.570177	0.14188	N	0.335578	T	0.00210	0.0006	N	0.08118	0	0.09310	N	1	B;B	0.31655	0.0;0.334	B;B	0.18561	0.0;0.022	T	0.21484	-1.0244	10	0.07644	T	0.81	-0.4303	4.7772	0.13185	0.3241:0.0:0.6759:0.0	rs12331663;rs52833318;rs12331663	43;43	E9PAZ2;Q96HR8	.;NAF1_HUMAN	S	43	ENSP00000408963:P43S;ENSP00000274054:P43S	ENSP00000274054:P43S	P	-	1	0	NAF1	164307203	0.000000	0.05858	0.010000	0.14722	0.377000	0.30045	-0.380000	0.07427	0.135000	0.18707	-0.680000	0.03767	CCG	G|0.963;A|0.037	0.037	strong		0.657	NAF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364684.2	NM_138386		A	164087753	G	A	164087753	3	1	22	1	0	0	0	0	1	0	0	0	10149	1203	42	2	1530	2	NAF1	4	164087753	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	7952503	164087753	27066523	1115	4016											
KLHL2	11275	hgsc.bcm.edu	37	chr4	166149999	166149999	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacaattgtggcagaagacAtggaaatttctgctcataga	14	11	9	7	0	3	3	2	0	1	3	3	4	3	4	0	2	1	2	0	2	4	3	rs80341433	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:166149999A>G	ENST00000226725.6	+	3	452	c.193A>G	c.(193-195)Atg>Gtg	p.M65V	KLHL2_ENST00000538127.1_Intron|KLHL2_ENST00000421009.2_Silent_p.T8T|KLHL2_ENST00000514860.1_Missense_Mutation_p.M69V	NM_007246.3	NP_009177.3	O95198	KLHL2_HUMAN	kelch-like family member 2	65	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				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)		GGCAGAAGACATGGAAATTTC	0.348													A|||	32	0.00638978	0.0234	0.0014	5008	,	,		20934	0.0		0.0	False		,,,				2504	0.0				p.M69V		Atlas-SNP	.											.	KLHL2	42	.	0			c.A205G						PASS	.	A	VAL/MET,,VAL/MET	77,4329	65.3+/-102.7	1,75,2127	68	65	66		205,,193	4.2	1	4	dbSNP_131	66	1,8599		0,1,4299	no	missense,intron,missense	KLHL2	NM_001161521.1,NM_001161522.1,NM_007246.3	21,,21	1,76,6426	GG,GA,AA		0.0116,1.7476,0.5997	benign,,benign	69/598,,65/594	166149999	78,12928	2203	4300	6503	SO:0001583	missense	11275	exon3			GAAGACATGGAAA	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.193A>G	4.37:g.166149999A>G	ENSP00000226725:p.Met65Val	736	0	0		576	285	0.494792	NM_001161521	A6NCM7|B2RD18|B4DFH7|F5H6M3|Q8N484|Q8TBH5	Missense_Mutation	SNP	ENST00000226725.6	37	CCDS34094.1	.	.	.	.	.	.	.	.	.	.	A	8.320	0.824018	0.16678	0.017476	1.16E-4	ENSG00000109466	ENST00000226725;ENST00000511305;ENST00000509704;ENST00000514860	T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19	4.16	4.16	0.48862	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.104953	0.64402	D	0.000003	T	0.10121	0.0248	N	0.00157	-1.96	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.10847	-1.0612	10	0.13470	T	0.59	.	8.1516	0.31143	0.9087:0.0:0.0913:0.0	.	69;65	B4DFH7;O95198	.;KLHL2_HUMAN	V	65;105;27;69	ENSP00000226725:M65V;ENSP00000422113:M105V;ENSP00000421324:M27V;ENSP00000424198:M69V	ENSP00000226725:M65V	M	+	1	0	KLHL2	166369449	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	4.885000	0.63142	1.750000	0.51863	0.383000	0.25322	ATG	A|0.994;G|0.006	0.006	strong		0.348	KLHL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364439.1			G	166149999	A	G	166149999	3	3	22	1	0	0	0	0	1	0	0	0	8383	217	8	3	245	3	KLHL2	4	166149999	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2062246	166149999	25004277	1116	4017											
DDX60L	91351	hgsc.bcm.edu	37	chr4	169342926	169342926	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	actacctttgcgggtgcaacGtacacaaccaccccgacatc	11	7	7	16	3	0	0	0	0	0	0	1	1	0	0	4	1	6	2	4	1	4	3	rs73863330	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:169342926G>A	ENST00000511577.1	-	17	2626	c.2379C>T	c.(2377-2379)taC>taT	p.Y793Y	DDX60L_ENST00000505890.1_Silent_p.Y793Y|DDX60L_ENST00000260184.7_Silent_p.Y793Y			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	793	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.						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)		CGGGTGCAACGTACACAACCA	0.468													g|||	24	0.00479233	0.0182	0.0	5008	,	,		23719	0.0		0.0	False		,,,				2504	0.0				p.Y793Y		Atlas-SNP	.											DDX60L,NS,carcinoma,-1,1	DDX60L	116	1	0			c.C2379T						PASS	.	A		61,4345	57.4+/-93.9	0,61,2142	225	226	226		2379	1.4	0	4	dbSNP_130	226	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous	DDX60L	NM_001012967.1		0,72,6431	AA,AG,GG		0.1279,1.3845,0.5536		793/1707	169342926	72,12934	2203	4300	6503	SO:0001819	synonymous_variant	91351	exon17			TGCAACGTACACA	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.2379C>T	4.37:g.169342926G>A		110	0	0		106	62	0.584906	NM_001012967	Q96ND6	Silent	SNP	ENST00000511577.1	37																																																																																				G|0.994;A|0.006	0.006	strong		0.468	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		A	169342926	G	A	169342926	2	1	22	1	0	0	0	0	0	0	0	1	4381	1140	40	1		1	DDX60L	4	169342926	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3192927	169342926	21811350	1117	4018											
PALLD	23022	hgsc.bcm.edu	37	chr4	169611765	169611765	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaatttcaggaactgcaaaaCacagccgtggcggaaggcca	14	5	12	10	2	1	0	1	0	0	0	1	3	1	2	2	4	4	1	2	4	5	1	rs17054482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:169611765C>T	ENST00000505667.1	+	7	1520	c.1347C>T	c.(1345-1347)aaC>aaT	p.N449N	PALLD_ENST00000261509.6_Silent_p.N449N|PALLD_ENST00000335742.7_Silent_p.N67N|PALLD_ENST00000512127.1_Silent_p.N67N|PALLD_ENST00000333488.4_Silent_p.N326N			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	449	Ig-like C2-type 2.				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)		AACTGCAAAACACAGCCGTGG	0.498									Pancreatic Cancer, Familial Clustering of				c|||	210	0.0419329	0.1498	0.0159	5008	,	,		17440	0.0		0.001	False		,,,				2504	0.0				p.N449N	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.C1347T						PASS	.	T	,,	570,3836	251.8+/-258.4	41,488,1674	80	94	90		1347,201,1347	3.2	0.9	4	dbSNP_123	90	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous,coding-synonymous,coding-synonymous	PALLD	NM_001166108.1,NM_001166109.1,NM_016081.3	,,	41,496,5966	TT,TC,CC		0.093,12.9369,4.4441	,,	449/1124,67/778,449/1107	169611765	578,12428	2203	4300	6503	SO:0001819	synonymous_variant	23022	exon7	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	GCAAAACACAGCC	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.1347C>T	4.37:g.169611765C>T		156	0	0		128	62	0.484375	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Silent	SNP	ENST00000505667.1	37	CCDS54818.1																																																																																			C|0.962;T|0.038	0.038	strong		0.498	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081		T	169611765	C	T	169611765	2	4	22	1	0	0	0	0	0	0	0	1	11416	477	17	2		2	PALLD	4	169611765	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	268839	169611765	21542511	1118	4019											
MFAP3L	9848	hgsc.bcm.edu	37	chr4	170912685	170912685	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gacgtgacatcggtagaaggTtctgcagtttcgggggaatg	9	10	16	6	3	1	2	0	1	1	1	3	4	1	3	0	4	1	4	0	4	3	3	rs61740817	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:170912685T>C	ENST00000361618.3	-	3	1381	c.1074A>G	c.(1072-1074)gaA>gaG	p.E358E	RP11-6E9.4_ENST00000508955.1_RNA|MFAP3L_ENST00000393704.3_Silent_p.E255E	NM_021647.6	NP_067679.6	O75121	MFA3L_HUMAN	microfibrillar-associated protein 3-like	358						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0201)|LUSC - Lung squamous cell carcinoma(193;0.116)		CGGTAGAAGGTTCTGCAGTTT	0.512													.|||	324	0.0646965	0.239	0.0101	5008	,	,		19333	0.0		0.001	False		,,,				2504	0.0				p.E358E		Atlas-SNP	.											MFAP3L,NS,carcinoma,-2,1	MFAP3L	59	1	0			c.A1074G						PASS	.	C	,	788,3618	751.8+/-412.2	79,630,1494	191	160	170		765,1074	2.5	1	4	dbSNP_129	170	8,8592	818.9+/-406.8	0,8,4292	no	coding-synonymous,coding-synonymous	MFAP3L	NM_001009554.2,NM_021647.6	,	79,638,5786	CC,CT,TT		0.093,17.8847,6.1203	,	255/307,358/410	170912685	796,12210	2203	4300	6503	SO:0001819	synonymous_variant	9848	exon3			AGAAGGTTCTGCA	AB014526	CCDS34103.1, CCDS43281.1	4q33	2014-08-12			ENSG00000198948	ENSG00000198948		"Immunoglobulin superfamily / I-set domain containing"	29083	protein-coding gene	gene with protein product						9734811	Standard	XM_005263366		Approved	KIAA0626, NYD-sp9	uc003isp.4	O75121	OTTHUMG00000160942	ENST00000361618.3:c.1074A>G	4.37:g.170912685T>C		168	0	0		213	105	0.492958	NM_021647	A8K1X6|D3DP35|Q4W5N7|Q4W5N9|Q6TNA8|Q9BVE1|Q9BXK0	Silent	SNP	ENST00000361618.3	37	CCDS34103.1																																																																																			T|0.933;C|0.067	0.067	strong		0.512	MFAP3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363043.2	NM_021647		C	170912685	T	C	170912685	2	2	22	1	0	0	0	0	0	0	0	1	9525	1722	60	3		3	MFAP3L	4	170912685	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1300920	170912685	20241591	1119	4020											
HPGD	3248	hgsc.bcm.edu	37	chr4	175414444	175414444	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcattcagtctcacaccacTgttcataagattagcagcca	12	10	7	12	0	3	1	3	0	1	1	4	1	3	1	2	1	2	3	2	1	2	4	rs200207595		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:175414444T>G	ENST00000296522.6	-	6	966	c.520A>C	c.(520-522)Agt>Cgt	p.S174R	HPGD_ENST00000542498.1_Intron|HPGD_ENST00000510901.1_Missense_Mutation_p.S53R|HPGD_ENST00000296521.7_Intron|HPGD_ENST00000541923.1_Missense_Mutation_p.S53R|HPGD_ENST00000422112.2_Missense_Mutation_p.S106R	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)	174					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)		CTCACACCACTGTTCATAAGA	0.363																																					p.S174R		Atlas-SNP	.											.	HPGD	19	.	0			c.A520C						PASS	.	T	ARG/SER,	4,4402	8.1+/-20.4	0,4,2199	96	91	93		520,	5.6	1	4		93	0,8598		0,0,4299	yes	missense,intron	HPGD	NM_000860.4,NM_001145816.1	110,	0,4,6498	GG,GT,TT		0.0,0.0908,0.0308	possibly-damaging,	174/267,	175414444	4,13000	2203	4299	6502	SO:0001583	missense	3248	exon6			CACCACTGTTCAT		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.520A>C	4.37:g.175414444T>G	ENSP00000296522:p.Ser174Arg	135	0	0		121	53	0.438017	NM_000860	B4DTA4|B4DU74|B4DV57|D3DP43|E7EV11|O00749|Q06F08|Q12998	Missense_Mutation	SNP	ENST00000296522.6	37	CCDS3821.1	.	.	.	.	.	.	.	.	.	.	T	16.52	3.146678	0.57151	9.08E-4	0.0	ENSG00000164120	ENST00000296522;ENST00000510901;ENST00000422112;ENST00000541923;ENST00000506910;ENST00000514584	D;D;T;D;D;D	0.82433	-1.61;-1.61;-1.29;-1.61;-1.61;-1.61	5.58	5.58	0.84498	NAD(P)-binding domain (1);	0.099373	0.64402	D	0.000001	T	0.79816	0.4511	L	0.31371	0.925	0.80722	D	1	P;D;D	0.71674	0.925;0.98;0.998	B;P;P	0.60682	0.446;0.595;0.878	T	0.76613	-0.2895	10	0.02654	T	1	.	9.2337	0.37453	0.2704:0.0:0.0:0.7296	.	106;174;53	E7EV11;P15428;B4DU74	.;PGDH_HUMAN;.	R	174;53;106;53;53;53	ENSP00000296522:S174R;ENSP00000422418:S53R;ENSP00000398720:S106R;ENSP00000438017:S53R;ENSP00000423066:S53R;ENSP00000423110:S53R	ENSP00000296522:S174R	S	-	1	0	HPGD	175651019	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.963000	0.56773	2.119000	0.64992	0.533000	0.62120	AGT	.	.	weak		0.363	HPGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362228.3			G	175414444	T	G	175414444	3	3	22	1	0	0	0	0	1	0	0	0	7343	1580	55	5	288	5	HPGD	4	175414444	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	4501759	175414444	15739832	1120	4021											
NEIL3	55247	hgsc.bcm.edu	37	chr4	178231219	178231219	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctgcggagtctgcagggcCgcgccttgcggctcgcagcc	3	7	15	16	5	2	0	0	0	2	0	3	1	2	1	3	3	4	3	3	3	0	1	rs34007209	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:178231219C>T	ENST00000264596.3	+	1	230	c.112C>T	c.(112-114)Cgc>Tgc	p.R38C		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	38			R -> C (in dbSNP:rs34007209). {ECO:0000269|Ref.3}.		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)		TCTGCAGGGCCGCGCCTTGCG	0.652								Base excision repair (BER), DNA glycosylases					C|||	530	0.105831	0.3623	0.0447	5008	,	,		12349	0.0		0.0149	False		,,,				2504	0.0051				p.R38C		Atlas-SNP	.											NEIL3,NS,carcinoma,0,2	NEIL3	89	2	0			c.C112T						PASS	.	C	CYS/ARG	1374,3022		237,900,1061	14	16	15		112	-0.4	0	4	dbSNP_126	15	159,8417		4,151,4133	no	missense	NEIL3	NM_018248.2	180	241,1051,5194	TT,TC,CC		1.854,31.2557,11.8178	possibly-damaging	38/606	178231219	1533,11439	2198	4288	6486	SO:0001583	missense	55247	exon1			CAGGGCCGCGCCT	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.112C>T	4.37:g.178231219C>T	ENSP00000264596:p.Arg38Cys	32	0	0		57	33	0.578947	NM_018248	Q2PPJ3|Q8NG51|Q9NV95	Missense_Mutation	SNP	ENST00000264596.3	37	CCDS3828.1	198	0.09065934065934066	170	0.34552845528455284	16	0.04419889502762431	0	0.0	12	0.0158311345646438	C	13.86	2.362325	0.41902	0.312557	0.01854	ENSG00000109674	ENST00000264596	T	0.23552	1.9	4.59	-0.355	0.12587	DNA glycosylase/AP lyase, catalytic domain (1);	1.002150	0.08041	N	0.995170	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.48640	0.913	B	0.35312	0.2	T	0.41893	-0.9483	9	0.59425	D	0.04	-0.0398	4.619	0.12440	0.0:0.4873:0.155:0.3576	rs34007209	38	Q8TAT5	NEIL3_HUMAN	C	38	ENSP00000264596:R38C	ENSP00000264596:R38C	R	+	1	0	NEIL3	178468213	0.000000	0.05858	0.000000	0.03702	0.060000	0.15804	-0.600000	0.05693	-0.228000	0.09869	0.561000	0.74099	CGC	C|0.884;T|0.116	0.116	strong		0.652	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248		T	178231219	C	T	178231219	3	4	22	1	0	0	0	0	1	0	0	0	10329	652	23	1	114	1	NEIL3	4	178231219	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2816775	178231219	12923057	1121	4022											
NEIL3	55247	hgsc.bcm.edu	37	chr4	178257364	178257364	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gaaagtgaagttaaaaaacaGaaaggccggatgctaggtga	18	6	13	4	1	0	3	0	2	0	1	0	5	0	4	1	3	2	2	1	3	7	2	rs17064658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:178257364G>C	ENST00000264596.3	+	4	634	c.516G>C	c.(514-516)caG>caC	p.Q172H		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	172			Q -> H (in dbSNP:rs17064658). {ECO:0000269|Ref.3}.		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)		TTAAAAAACAGAAAGGCCGGA	0.398								Base excision repair (BER), DNA glycosylases					G|||	123	0.0245607	0.0741	0.0144	5008	,	,		16964	0.0		0.0099	False		,,,				2504	0.0051				p.Q172H		Atlas-SNP	.											.	NEIL3	89	.	0			c.G516C						PASS	.	G	HIS/GLN	255,4151	147.3+/-181.8	12,231,1960	138	142	141		516	2.3	0.7	4	dbSNP_123	141	99,8501	54.0+/-114.7	1,97,4202	yes	missense	NEIL3	NM_018248.2	24	13,328,6162	CC,CG,GG		1.1512,5.7876,2.7218	possibly-damaging	172/606	178257364	354,12652	2203	4300	6503	SO:0001583	missense	55247	exon4			AAAACAGAAAGGC	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.516G>C	4.37:g.178257364G>C	ENSP00000264596:p.Gln172His	95	0	0		88	41	0.465909	NM_018248	Q2PPJ3|Q8NG51|Q9NV95	Missense_Mutation	SNP	ENST00000264596.3	37	CCDS3828.1	44	0.020146520146520148	29	0.05894308943089431	7	0.019337016574585635	0	0.0	8	0.010554089709762533	G	11.19	1.566029	0.27915	0.057876	0.011512	ENSG00000109674	ENST00000264596	T	0.14516	2.5	4.93	2.28	0.28536	DNA glycosylase/AP lyase, H2TH DNA-binding (1);Ribosomal protein S13-like, H2TH (1);	0.118971	0.64402	D	0.000017	T	0.01454	0.0047	L	0.31207	0.915	0.40999	D	0.984912	D	0.53312	0.959	P	0.53760	0.734	T	0.07195	-1.0785	10	0.37606	T	0.19	-13.2033	7.8072	0.29209	0.3219:0.0:0.6781:0.0	rs17064658;rs52811923;rs17064658	172	Q8TAT5	NEIL3_HUMAN	H	172	ENSP00000264596:Q172H	ENSP00000264596:Q172H	Q	+	3	2	NEIL3	178494358	0.987000	0.35691	0.674000	0.29902	0.558000	0.35554	1.962000	0.40442	0.367000	0.24454	0.655000	0.94253	CAG	G|0.975;C|0.025	0.025	strong		0.398	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248		C	178257364	G	C	178257364	3	2	22	1	0	0	0	0	1	0	0	0	10329	933	33	4	530	4	NEIL3	4	178257364	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	26145	178257364	12896912	1122	4023											
NEIL3	55247	hgsc.bcm.edu	37	chr4	178283474	178283474	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccttcccattctgcaaccAtggcaagcgttccaccatga	9	10	7	15	1	1	1	0	1	1	0	4	1	4	1	5	1	3	3	5	1	2	3	rs35418725	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:178283474A>G	ENST00000264596.3	+	10	1785	c.1667A>G	c.(1666-1668)cAt>cGt	p.H556R		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	556			H -> R (in dbSNP:rs35418725). {ECO:0000269|Ref.3}.		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)		TTCTGCAACCATGGCAAGCGT	0.383								Base excision repair (BER), DNA glycosylases					A|||	24	0.00479233	0.0174	0.0014	5008	,	,		19183	0.0		0.0	False		,,,				2504	0.0				p.H556R		Atlas-SNP	.											.	NEIL3	89	.	0			c.A1667G						PASS	.	A	ARG/HIS	74,4332	60.5+/-97.4	0,74,2129	93	94	94		1667	3.5	1	4	dbSNP_126	94	0,8600		0,0,4300	yes	missense	NEIL3	NM_018248.2	29	0,74,6429	GG,GA,AA		0.0,1.6795,0.569	possibly-damaging	556/606	178283474	74,12932	2203	4300	6503	SO:0001583	missense	55247	exon10			GCAACCATGGCAA	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.1667A>G	4.37:g.178283474A>G	ENSP00000264596:p.His556Arg	146	0	0		124	55	0.443548	NM_018248	Q2PPJ3|Q8NG51|Q9NV95	Missense_Mutation	SNP	ENST00000264596.3	37	CCDS3828.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	A	17.52	3.409952	0.62399	0.016795	0.0	ENSG00000109674	ENST00000264596	T	0.26223	1.75	4.63	3.45	0.39498	Zinc finger, GRF-type (1);	0.000000	0.85682	D	0.000000	T	0.42017	0.1184	H	0.94542	3.55	0.58432	D	0.999995	D	0.64830	0.994	D	0.70487	0.969	T	0.61936	-0.6960	10	0.87932	D	0	-19.9676	10.3252	0.43790	0.9223:0.0:0.0777:0.0	rs35418725	556	Q8TAT5	NEIL3_HUMAN	R	556	ENSP00000264596:H556R	ENSP00000264596:H556R	H	+	2	0	NEIL3	178520468	1.000000	0.71417	0.983000	0.44433	0.753000	0.42808	8.872000	0.92352	0.937000	0.37394	0.402000	0.26972	CAT	A|0.996;G|0.004	0.004	strong		0.383	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248		G	178283474	A	G	178283474	3	3	22	1	0	0	0	0	1	0	0	0	10329	217	8	3	1705	3	NEIL3	4	178283474	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	26110	178283474	12870802	1123	4024											
ODZ3	55714	hgsc.bcm.edu	37	chr4	183594275	183594275	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctggagatcacagctcttcaTtgatcagccacagtttctta	10	13	7	11	0	5	2	3	1	2	1	5	3	5	2	1	1	2	2	1	1	1	4	rs201144002		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:183594275T>C	ENST00000511685.1	+	7	1352	c.1229T>C	c.(1228-1230)aTt>aCt	p.I410T	TENM3_ENST00000406950.2_Missense_Mutation_p.I410T			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	410					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)										CAGCTCTTCATTGATCAGCCA	0.438																																					p.I410T		Atlas-SNP	.											.	.	.	.	0			c.T1229C						PASS	.	T	THR/ILE	0,3630		0,0,1815	63	59	60		1229	4.9	1	4		60	1,8189		0,1,4094	yes	missense	ODZ3	NM_001080477.1	89	0,1,5909	CC,CT,TT		0.0122,0.0,0.0085	possibly-damaging	410/2700	183594275	1,11819	1815	4095	5910	SO:0001583	missense	55714	exon6			TCTTCATTGATCA	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.1229T>C	4.37:g.183594275T>C	ENSP00000424226:p.Ile410Thr	210	1	0.0047619		195	100	0.512821	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	T	17.79	3.476907	0.63849	0.0	1.22E-4	ENSG00000218336	ENST00000511685;ENST00000406950	T;T	0.29397	1.57;1.57	4.91	4.91	0.64330	.	.	.	.	.	T	0.31765	0.0807	M	0.67397	2.05	0.53688	D	0.999978	B	0.33694	0.421	B	0.26864	0.074	T	0.15780	-1.0425	9	0.44086	T	0.13	.	15.0662	0.71996	0.0:0.0:0.0:1.0	.	410	Q9P273	TEN3_HUMAN	T	410	ENSP00000424226:I410T;ENSP00000385276:I410T	ENSP00000385276:I410T	I	+	2	0	ODZ3	183831269	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	7.822000	0.86651	2.197000	0.70478	0.456000	0.33151	ATT	.	.	weak		0.438	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			C	183594275	T	C	183594275	3	2	22	1	0	0	0	0	1	0	0	0	10845	1493	52	3	1251	3	ODZ3	4	183594275	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	5310801	183594275	7560001	1124	4025											
ODZ3	55714	hgsc.bcm.edu	37	chr4	183720831	183720831	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatggccgaggtgcaggtgaGccggcgccgggccggcggcg	4	3	22	12	7	0	1	0	1	0	0	0	3	0	1	4	7	2	1	4	7	0	0			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:183720831G>A	ENST00000511685.1	+	28	7550	c.7427G>A	c.(7426-7428)aGc>aAc	p.S2476N	TENM3_ENST00000406950.2_Missense_Mutation_p.S2476N			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	2476					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)										GTGCAGGTGAgccggcgccgg	0.697																																					p.S2476N		Atlas-SNP	.											.	.	.	.	0			c.G7427A						PASS	.						5	7	7					4																	183720831		1716	3423	5139	SO:0001583	missense	55714	exon27			AGGTGAGCCGGCG	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.7427G>A	4.37:g.183720831G>A	ENSP00000424226:p.Ser2476Asn	3	0	0		10	8	0.8	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	G	12.83	2.054373	0.36277	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.86627	-2.15;-2.15	4.79	3.94	0.45596	.	.	.	.	.	T	0.79505	0.4457	L	0.32530	0.975	0.53005	D	0.999968	B	0.27498	0.18	B	0.18871	0.023	T	0.74352	-0.3693	9	0.18276	T	0.48	.	15.4632	0.75377	0.0:0.1392:0.8608:0.0	.	2476	Q9P273	TEN3_HUMAN	N	2476	ENSP00000424226:S2476N;ENSP00000385276:S2476N	ENSP00000385276:S2476N	S	+	2	0	ODZ3	183957825	1.000000	0.71417	0.997000	0.53966	0.764000	0.43329	6.546000	0.73887	1.357000	0.45904	0.557000	0.71058	AGC	.	.	none		0.697	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			A	183720831	G	A	183720831	3	1	22	1	0	0	0	0	1	0	0	0	10845	971	34	2	7533	2	ODZ3	4	183720831	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	126556	183720831	7433445	1125	4026											
DCTD	1635	hgsc.bcm.edu	37	chr4	183814234	183814234	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcctcgcagcagttgcctcGtcactatcatggtatttatc	8	13	8	12	2	2	0	2	0	0	0	5	0	2	0	2	1	3	4	2	1	3	5	rs369366826		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:183814234G>A	ENST00000438320.2	-	5	698	c.408C>T	c.(406-408)gaC>gaT	p.D136D	DCTD_ENST00000357067.3_Silent_p.D147D|DCTD_ENST00000510370.1_Silent_p.D136D	NM_001921.2	NP_001912.2	P32321	DCTD_HUMAN	dCMP deaminase	136					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)	CAGTTGCCTCGTCACTATCAT	0.507													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17184	0.0		0.0	False		,,,				2504	0.0				p.D147D		Atlas-SNP	.											.	DCTD	30	.	0			c.C441T						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	72	67	69		441,408	-10.8	0	4		69	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	DCTD	NM_001012732.1,NM_001921.2	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	147/190,136/179	183814234	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1635	exon5			TGCCTCGTCACTA	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.408C>T	4.37:g.183814234G>A		215	0	0		233	110	0.472103	NM_001012732	B2R836|D3DP49|D3DP50|Q5M7Z8|Q9BVD8	Silent	SNP	ENST00000438320.2	37	CCDS3831.1																																																																																			.	.	weak		0.507	DCTD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361743.2			A	183814234	G	A	183814234	2	1	22	1	0	0	0	0	0	0	0	1	4307	1136	40	1		1	DCTD	4	183814234	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	93403	183814234	7340042	1126	4027											
CLDN22	53842	hgsc.bcm.edu	37	chr4	184240777	184240777	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgtgtttgtgccactgcgtAgtggcccgaagctaggggag	6	11	16	8	2	0	0	0	0	0	0	0	2	0	1	2	3	3	3	2	3	3	4			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:184240777A>G	ENST00000323319.5	-	1	1150	c.595T>C	c.(595-597)Tac>Cac	p.Y199H	WWC2_ENST00000403733.3_3'UTR	NM_001111319.1	NP_001104789.1	Q8N7P3	CLD22_HUMAN	claudin 22	199					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)			cervix(1)|kidney(1)|lung(3)|prostate(1)|skin(1)	7		all_lung(41;6.9e-12)|Lung NSC(41;1.28e-11)|Colorectal(36;0.0172)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)|Esophageal squamous(56;0.176)		all cancers(43;4.1e-26)|Epithelial(43;6.45e-22)|OV - Ovarian serous cystadenocarcinoma(60;7.64e-10)|Colorectal(24;5.87e-06)|GBM - Glioblastoma multiforme(59;6.5e-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)		GCCACTGCGTAGTGGCCCGAA	0.542																																					p.Y199H		Atlas-SNP	.											CLDN22,NS,carcinoma,+2,1	CLDN22	20	1	0			c.T595C						scavenged	.						232	210	217					4																	184240777		1568	3582	5150	SO:0001583	missense	53842	exon1			CTGCGTAGTGGCC	AK098064	CCDS43286.1	4q35.1	2010-08-05			ENSG00000177300	ENSG00000177300		"Claudins"	2044	protein-coding gene	gene with protein product							Standard	NM_001111319		Approved	CLDN21	uc010isa.1	Q8N7P3	OTTHUMG00000160627	ENST00000323319.5:c.595T>C	4.37:g.184240777A>G	ENSP00000318113:p.Tyr199His	243	2	0.00823045		300	153	0.51	NM_001111319		Missense_Mutation	SNP	ENST00000323319.5	37	CCDS43286.1	.	.	.	.	.	.	.	.	.	.	A	11.23	1.577764	0.28180	.	.	ENSG00000177300	ENST00000323319	D	0.85411	-1.98	6.07	2.4	0.29515	.	0.831349	0.11145	N	0.594777	T	0.80974	0.4727	M	0.63843	1.955	0.09310	N	1	B	0.29508	0.246	B	0.26094	0.066	T	0.69135	-0.5225	10	0.54805	T	0.06	.	6.5842	0.22612	0.7044:0.0:0.1875:0.108	.	199	Q8N7P3	CLD22_HUMAN	H	199	ENSP00000318113:Y199H	ENSP00000318113:Y199H	Y	-	1	0	CLDN22	184477771	0.029000	0.19370	0.651000	0.29564	0.026000	0.11368	0.963000	0.29293	0.176000	0.19873	-1.139000	0.01908	TAC	.	.	none		0.542	CLDN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361493.1			G	184240777	A	G	184240777	3	3	22	1	0	0	0	0	1	0	0	0	3485	420	15	3	71	3	CLDN22	4	184240777	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	426543	184240777	6913499	1127	4028											
HELT	391723	hgsc.bcm.edu	37	chr4	185940196	185940196	+	Intron	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacttgggtggaccgatggcAgggaagtgcccgcacgggac	8	5	17	11	3	0	0	0	0	0	0	0	4	0	3	2	5	1	2	2	5	1	1	rs370662812		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:185940196A>T	ENST00000515777.1	+	1	115				HELT_ENST00000505610.1_Intron|HELT_ENST00000338875.4_Silent_p.A38A			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)		GACCGATGGCAGGGAAGTGCC	0.602																																					p.A38A		Atlas-SNP	.											.	HELT	34	.	0			c.A114T						PASS	.	A		0,4406		0,0,2203	75	70	72		114	-2.8	0	4		72	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	HELT	NM_001029887.1		0,1,6502	TT,TA,AA		0.0116,0.0,0.0077		38/328	185940196	1,13005	2203	4300	6503	SO:0001627	intron_variant	391723	exon1			GATGGCAGGGAAG	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+87A>T	4.37:g.185940196A>T		112	0	0		114	60	0.526316	NM_001029887	B2RTS5|B7ZMI7|B7ZMI8	Silent	SNP	ENST00000515777.1	37																																																																																				.	.	weak		0.602	HELT-002	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000360792.1	NM_001300781		T	185940196	A	T	185940196	1	4	22	0	1	0	0	0	0	0	0	0	7057	175	7	5		5	HELT	4	185940196	Intron	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1699419	185940196	5214080	1128	4029											
SORBS2	8470	hgsc.bcm.edu	37	chr4	186545346	186545346	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttggagtcctcctcacataAcagggagcccatgctttccg	8	10	9	14	1	1	0	1	0	0	0	4	2	4	2	4	2	3	1	4	2	1	3	rs61736043	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:186545346A>T	ENST00000284776.7	-	13	1734	c.1225T>A	c.(1225-1227)Tta>Ata	p.L409I	SORBS2_ENST00000498125.1_Intron|SORBS2_ENST00000431808.1_Missense_Mutation_p.L409I|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000437304.2_Intron|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000449407.2_Intron|SORBS2_ENST00000448662.2_Intron|SORBS2_ENST00000418609.1_Missense_Mutation_p.L313I|SORBS2_ENST00000355634.5_Missense_Mutation_p.L509I	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	409					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)		TCCTCACATAACAGGGAGCCC	0.577													A|||	57	0.0113818	0.0416	0.0029	5008	,	,		18529	0.0		0.0	False		,,,				2504	0.0				p.L509I	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-SNP	.											.	SORBS2	300	.	0			c.T1525A						PASS	.	A	ILE/LEU,ILE/LEU,,,,,,	170,4236	112.5+/-150.6	2,166,2035	63	58	60		937,1225,,,,,,	-10.1	0	4	dbSNP_129	60	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,intron,intron,intron,intron,intron,intron	SORBS2	NM_001145674.1,NM_021069.4,NM_001145670.1,NM_001145671.1,NM_001145672.1,NM_001145673.1,NM_001145675.1,NM_003603.5	5,5,,,,,,	2,167,6334	TT,TA,AA		0.0116,3.8584,1.3148	probably-damaging,probably-damaging,,,,,,	313/1005,409/1101,,,,,,	186545346	171,12835	2203	4300	6503	SO:0001583	missense	8470	exon16			CACATAACAGGGA		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.1225T>A	4.37:g.186545346A>T	ENSP00000284776:p.Leu409Ile	249	1	0.00401606		253	121	0.478261	NM_001270771	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Missense_Mutation	SNP	ENST00000284776.7	37	CCDS3845.1	23	0.010531135531135532	21	0.042682926829268296	2	0.0055248618784530384	0	0.0	0	0.0	A	11.06	1.528292	0.27299	0.038584	1.16E-4	ENSG00000154556	ENST00000284776;ENST00000431808;ENST00000418609;ENST00000355634	T;T;T;T	0.37411	1.31;1.31;1.2;1.29	5.72	-10.1	0.00402	.	0.248771	0.33180	N	0.005188	T	0.14399	0.0348	L	0.42245	1.32	0.09310	N	1	D;D;D	0.71674	0.998;0.998;0.995	D;D;P	0.75020	0.985;0.984;0.792	T	0.63470	-0.6630	10	0.45353	T	0.12	-2.604	18.4155	0.90568	0.2035:0.0853:0.7112:0.0	rs61736043	313;509;409	B7Z3X6;B3KPQ7;O94875	.;.;SRBS2_HUMAN	I	409;409;313;509	ENSP00000284776:L409I;ENSP00000411764:L409I;ENSP00000397482:L313I;ENSP00000347852:L509I	ENSP00000284776:L409I	L	-	1	2	SORBS2	186782340	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.844000	0.04345	-2.307000	0.00653	-0.479000	0.04858	TTA	A|0.977;T|0.023	0.023	strong		0.577	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603		T	186545346	A	T	186545346	3	4	22	1	0	0	0	0	1	0	0	0	14943	40	2	5	2113	5	SORBS2	4	186545346	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	605150	186545346	4608930	1129	4030											
SORBS2	8470	hgsc.bcm.edu	37	chr4	186573817	186573817	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagagcagcagacataccCggcttgtgcaccatgtgaat	12	7	11	11	1	0	3	0	1	0	2	0	3	0	3	2	1	5	5	2	1	2	2	rs61732192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:186573817C>T	ENST00000284776.7	-	7	842	c.333G>A	c.(331-333)ccG>ccA	p.P111P	SORBS2_ENST00000498125.1_5'UTR|SORBS2_ENST00000431808.1_Splice_Site_p.P111P|SORBS2_ENST00000319471.9_Splice_Site_p.P197P|SORBS2_ENST00000437304.2_Splice_Site_p.P290P|SORBS2_ENST00000393528.3_Splice_Site_p.P157P|SORBS2_ENST00000449407.2_Splice_Site_p.P197P|SORBS2_ENST00000448662.2_Splice_Site_p.P180P|SORBS2_ENST00000418609.1_Splice_Site_p.P30P|SORBS2_ENST00000355634.5_Splice_Site_p.P211P	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	111	SoHo. {ECO:0000255|PROSITE- ProRule:PRU00195}.				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)		CAGACATACCCGGCTTGTGCA	0.483													C|||	82	0.0163738	0.0598	0.0043	5008	,	,		22370	0.0		0.0	False		,,,				2504	0.0				p.P290P	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-SNP	.											SORBS2_ENST00000448662,NS,carcinoma,-1,4	SORBS2	300	4	0			c.G870A						scavenged	.	C	,,,,,,,	224,4182	132.9+/-169.3	5,214,1984	247	195	213		591,591,540,870,90,90,471,333	-10.3	0	4	dbSNP_129	213	0,8600		0,0,4300	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	SORBS2	NM_001145670.1,NM_001145671.1,NM_001145672.1,NM_001145673.1,NM_001145674.1,NM_001145675.1,NM_003603.5,NM_021069.4	,,,,,,,	5,214,6284	TT,TC,CC		0.0,5.084,1.7223	,,,,,,,	197/645,197/732,180/662,290/825,30/1005,30/493,157/667,111/1101	186573817	224,12782	2203	4300	6503	SO:0001630	splice_region_variant	8470	exon8			CATACCCGGCTTG		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.334+1G>A	4.37:g.186573817C>T		174	1	0.00574713		149	75	0.503356	NM_001145673	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Silent	SNP	ENST00000284776.7	37	CCDS3845.1	33|33	0.01510989010989011|0.01510989010989011	31|31	0.06300813008130081|0.06300813008130081	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	C|C	4.660|4.660	0.122652|0.122652	0.08931|0.08931	0.05084|0.05084	0.0|0.0	ENSG00000154556|ENSG00000154556	ENST00000438278|ENST00000445625	.|.	.|.	.|.	5.16|5.16	-10.3|-10.3	0.00346|0.00346	.|.	.|.	.|.	.|.	.|.	T|T	0.06050|0.06050	0.0157|0.0157	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.43491|0.43491	-0.9388|-0.9388	4|4	.|.	.|.	.|.	-26.7084|-26.7084	3.9267|3.9267	0.09267|0.09267	0.206:0.1058:0.1231:0.5652|0.206:0.1058:0.1231:0.5652	.|.	.|.	.|.	.|.	R|Q	55|9	.|.	.|.	G|R	-|-	1|2	0|0	SORBS2|SORBS2	186810811|186810811	0.003000|0.003000	0.15002|0.15002	0.047000|0.047000	0.18901|0.18901	0.189000|0.189000	0.23516|0.23516	-1.527000|-1.527000	0.02227|0.02227	-3.174000|-3.174000	0.00224|0.00224	-0.819000|-0.819000	0.03115|0.03115	GGA|CGG	C|0.984;T|0.016	0.016	strong		0.483	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603	Silent	T	186573817	C	T	186573817	5	4	22	1	0	0	0	0	0	0	1	0	14943	666	23	1	3341	1	SORBS2	4	186573817	Splice_Site	SNP	C	TCGA-G8-6324-01A-11D-2210-10	28471	186573817	4580459	1130	4031											
TLR3	7098	hgsc.bcm.edu	37	chr4	187004544	187004544	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tctcacctccacatccttaaCttggagtccaacggctttga	9	12	6	14	1	1	1	1	1	1	0	5	2	4	2	4	2	2	1	4	2	2	3	rs35111588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:187004544C>T	ENST00000296795.3	+	4	1808	c.1704C>T	c.(1702-1704)aaC>aaT	p.N568N	TLR3_ENST00000504367.1_Silent_p.N291N	NM_003265.2	NP_003256.1	O15455	TLR3_HUMAN	toll-like receptor 3	568					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)		ACATCCTTAACTTGGAGTCCA	0.423													C|||	296	0.0591054	0.2156	0.013	5008	,	,		20763	0.0		0.002	False		,,,				2504	0.0				p.N568N		Atlas-SNP	.											.	TLR3	83	.	0			c.C1704T						PASS	.	C		714,3692	297.8+/-285.0	60,594,1549	92	90	91		1704	-2.8	0.9	4	dbSNP_126	91	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	TLR3	NM_003265.2		60,602,5841	TT,TC,CC		0.093,16.2052,5.5513		568/905	187004544	722,12284	2203	4300	6503	SO:0001819	synonymous_variant	7098	exon4			CCTTAACTTGGAG	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.1704C>T	4.37:g.187004544C>T		116	0	0		109	45	0.412844	NM_003265	B2RAI7|B7Z7K0|E6Y0F0|E6Y0F1|E9PGH4|Q4VAL2|Q504W0	Silent	SNP	ENST00000296795.3	37	CCDS3846.1																																																																																			C|0.949;T|0.051	0.051	strong		0.423	TLR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360313.4			T	187004544	C	T	187004544	2	4	22	1	0	0	0	0	0	0	0	1	15967	564	20	2		2	TLR3	4	187004544	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	430727	187004544	4149732	1131	4032											
FAM149A	25854	hgsc.bcm.edu	37	chr4	187088170	187088170	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgttgagtgccatgcctgacGgtacagaacgatcgcgtctt	8	11	12	10	4	1	3	0	2	1	1	2	4	1	3	2	1	4	2	2	1	2	3	rs141044925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:187088170G>A	ENST00000356371.5	+	12	2086	c.2086G>A	c.(2086-2088)Ggt>Agt	p.G696S	FAM149A_ENST00000502970.1_Missense_Mutation_p.G405S|FAM149A_ENST00000503432.1_Missense_Mutation_p.G405S|FAM149A_ENST00000514153.1_Missense_Mutation_p.G405S|FAM149A_ENST00000227065.4_Missense_Mutation_p.G405S|FAM149A_ENST00000389354.5_Missense_Mutation_p.G405S			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	696										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)		CATGCCTGACGGTACAGAACG	0.468													G|||	30	0.00599042	0.0212	0.0029	5008	,	,		17105	0.0		0.0	False		,,,				2504	0.0				p.G405S		Atlas-SNP	.											.	FAM149A	52	.	0			c.G1213A						PASS	.	G	SER/GLY,SER/GLY	64,4342	59.3+/-96.0	0,64,2139	91	85	87		1213,1213	-3.5	0	4	dbSNP_134	87	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	FAM149A	NM_001006655.2,NM_015398.2	56,56	0,66,6437	AA,AG,GG		0.0233,1.4526,0.5075	benign,benign	405/483,405/483	187088170	66,12940	2203	4300	6503	SO:0001583	missense	25854	exon11			CCTGACGGTACAG	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.2086G>A	4.37:g.187088170G>A	ENSP00000348732:p.Gly696Ser	119	0	0		129	51	0.395349	NM_001006655	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	Missense_Mutation	SNP	ENST00000356371.5	37		9|9	0.004120879120879121|0.004120879120879121	8|8	0.016260162601626018|0.016260162601626018	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	G|G	2.916|2.916	-0.224222|-0.224222	0.06061|0.06061	0.014526|0.014526	2.33E-4|2.33E-4	ENSG00000109794|ENSG00000109794	ENST00000503432;ENST00000356371;ENST00000227065;ENST00000502970;ENST00000514153;ENST00000389354|ENST00000512271	T;T;T;T;T;T|.	0.10005|.	2.92;2.94;2.92;2.92;2.92;2.92|.	5.72|5.72	-3.45|-3.45	0.04781|0.04781	.|.	0.347222|.	0.34268|.	N|.	0.004119|.	T|T	0.02047|0.02047	0.0064|0.0064	N|N	0.00500|0.00500	-1.43|-1.43	0.09310|0.09310	N|N	1|1	B;B|.	0.28880|.	0.226;0.085|.	B;B|.	0.16722|.	0.016;0.007|.	T|T	0.35895|0.35895	-0.9770|-0.9770	10|5	0.05620|.	T|.	0.96|.	-2.9758|-2.9758	1.239|1.239	0.01959|0.01959	0.3995:0.2553:0.2218:0.1234|0.3995:0.2553:0.2218:0.1234	.|.	696;696|.	A5PLN7-3;A5PLN7|.	.;F149A_HUMAN|.	S|Q	405;696;405;405;405;405|82	ENSP00000426835:G405S;ENSP00000348732:G696S;ENSP00000227065:G405S;ENSP00000427155:G405S;ENSP00000424380:G405S;ENSP00000374005:G405S|.	ENSP00000227065:G405S|.	G|R	+|+	1|2	0|0	FAM149A|FAM149A	187325164|187325164	0.000000|0.000000	0.05858|0.05858	0.023000|0.023000	0.16930|0.16930	0.003000|0.003000	0.03518|0.03518	0.194000|0.194000	0.17135|0.17135	-0.400000|-0.400000	0.07656|0.07656	-0.469000|-0.469000	0.05056|0.05056	GGT|CGG	G|0.995;A|0.005	0.005	strong		0.468	FAM149A-201	KNOWN	basic	protein_coding	protein_coding		NM_001006655		A	187088170	G	A	187088170	3	1	22	1	0	0	0	0	1	0	0	0	5460	1116	39	1	1247	1	FAM149A	4	187088170	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	83626	187088170	4066106	1132	4033											
FAT1	2195	hgsc.bcm.edu	37	chr4	187524176	187524176	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacagccatggtggacaggtGggcaccttccctcttcattc	7	10	10	14	0	2	0	1	0	1	0	4	1	3	1	3	4	1	1	3	4	0	3	rs200262460	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:187524176G>A	ENST00000441802.2	-	20	11572	c.11363C>T	c.(11362-11364)cCa>cTa	p.P3788L		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	3788					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						GTGGACAGGTGGGCACCTTCC	0.493										HNSCC(5;0.00058)			G|||	4	0.000798722	0.003	0.0	5008	,	,		18565	0.0		0.0	False		,,,				2504	0.0				p.P3788L	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C11363T						PASS	.	G	LEU/PRO	4,3954		0,4,1975	88	88	88		11363	5.3	1	4	dbSNP_134	88	0,8326		0,0,4163	yes	missense	FAT1	NM_005245.3	98	0,4,6138	AA,AG,GG		0.0,0.1011,0.0326	benign	3788/4589	187524176	4,12280	1979	4163	6142	SO:0001583	missense	2195	exon20			ACAGGTGGGCACC	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.11363C>T	4.37:g.187524176G>A	ENSP00000406229:p.Pro3788Leu	122	0	0		123	71	0.577236	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	13.22	2.170718	0.38315	0.001011	0.0	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.32023	1.47	5.26	5.26	0.73747	.	0.056195	0.64402	D	0.000001	T	0.32823	0.0842	L	0.58428	1.81	0.80722	D	1	B	0.30686	0.29	B	0.25759	0.063	T	0.07252	-1.0782	10	0.32370	T	0.25	.	19.2203	0.93793	0.0:0.0:1.0:0.0	.	3788	Q14517	FAT1_HUMAN	L	3788;3790	ENSP00000406229:P3788L	ENSP00000260147:P3790L	P	-	2	0	FAT1	187761170	1.000000	0.71417	0.956000	0.39512	0.080000	0.17528	9.111000	0.94308	2.614000	0.88457	0.557000	0.71058	CCA	G|1.000;A|0.000	0.000	strong		0.493	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		A	187524176	G	A	187524176	3	1	22	1	0	0	0	0	1	0	0	0	5697	1348	47	2	2435	2	FAT1	4	187524176	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	436006	187524176	3630100	1133	4034											
FAT1	2195	hgsc.bcm.edu	37	chr4	187542356	187542356	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctttatcagcatcagctgctCgaatcaccagtgggacattc	10	11	8	12	1	3	0	3	0	0	0	5	2	3	1	1	1	3	3	1	1	2	3	rs56790426	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:187542356C>T	ENST00000441802.2	-	10	5593	c.5384G>A	c.(5383-5385)cGa>cAa	p.R1795Q		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1795	Cadherin 16. {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						ATCAGCTGCTCGAATCACCAG	0.423										HNSCC(5;0.00058)			C|||	44	0.00878594	0.0325	0.0014	5008	,	,		22564	0.0		0.0	False		,,,				2504	0.0				p.R1795Q	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.G5384A						PASS	.	C	GLN/ARG	81,3883		1,79,1902	89	85	87		5384	4.7	1	4	dbSNP_129	87	1,8327		0,1,4163	yes	missense	FAT1	NM_005245.3	43	1,80,6065	TT,TC,CC		0.012,2.0434,0.6671	benign	1795/4589	187542356	82,12210	1982	4164	6146	SO:0001583	missense	2195	exon10			GCTGCTCGAATCA	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.5384G>A	4.37:g.187542356C>T	ENSP00000406229:p.Arg1795Gln	139	0	0		150	71	0.473333	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	C	8.328	0.825754	0.16749	0.020434	1.2E-4	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.01725	4.67	5.5	4.66	0.58398	Cadherin (4);Cadherin-like (1);	0.122272	0.56097	D	0.000036	T	0.00815	0.0027	N	0.25825	0.765	0.53005	D	0.999965	B	0.25007	0.116	B	0.23018	0.043	T	0.62586	-0.6823	10	0.21014	T	0.42	.	11.7859	0.52043	0.0:0.8082:0.1241:0.0676	rs56790426	1795	Q14517	FAT1_HUMAN	Q	1795;1797	ENSP00000406229:R1795Q	ENSP00000260147:R1797Q	R	-	2	0	FAT1	187779350	1.000000	0.71417	1.000000	0.80357	0.050000	0.14768	2.438000	0.44837	1.556000	0.49512	-0.150000	0.13652	CGA	C|0.993;T|0.007	0.007	strong		0.423	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		T	187542356	C	T	187542356	3	4	22	1	0	0	0	0	1	0	0	0	5697	884	31	1	8454	1	FAT1	4	187542356	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	18180	187542356	3611920	1134	4035											
FAT1	2195	hgsc.bcm.edu	37	chr4	187542432	187542432	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcactaatgagtcctgtatAttctgcctgcataaaaactg	12	14	6	9	0	2	1	1	1	1	0	3	1	3	1	2	0	3	2	2	0	6	6			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:187542432A>G	ENST00000441802.2	-	10	5517	c.5308T>C	c.(5308-5310)Tat>Cat	p.Y1770H		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1770	Cadherin 16. {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						AGTCCTGTATATTCTGCCTGC	0.443										HNSCC(5;0.00058)																											p.Y1770H	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T5308C						PASS	.						106	99	101					4																	187542432		1947	4150	6097	SO:0001583	missense	2195	exon10			CTGTATATTCTGC	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.5308T>C	4.37:g.187542432A>G	ENSP00000406229:p.Tyr1770His	244	0	0		264	125	0.473485	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	A	14.22	2.471201	0.43942	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.66638	-0.22	5.5	5.5	0.81552	Cadherin (2);Cadherin-like (1);	0.055265	0.85682	D	0.000000	D	0.85517	0.5715	H	0.94542	3.55	0.58432	D	0.999999	D	0.67145	0.996	D	0.63381	0.914	D	0.89615	0.3844	10	0.72032	D	0.01	.	15.7759	0.78214	1.0:0.0:0.0:0.0	.	1770	Q14517	FAT1_HUMAN	H	1770;1772	ENSP00000406229:Y1770H	ENSP00000260147:Y1772H	Y	-	1	0	FAT1	187779426	1.000000	0.71417	0.279000	0.24732	0.057000	0.15508	9.139000	0.94554	2.308000	0.77769	0.533000	0.62120	TAT	.	.	none		0.443	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		G	187542432	A	G	187542432	3	3	22	1	0	0	0	0	1	0	0	0	5697	449	16	3	8530	3	FAT1	4	187542432	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	76	187542432	3611844	1135	4036											
FAT1	2195	hgsc.bcm.edu	37	chr4	187557863	187557863	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgtaggagatttctgcattgGggccctcatccttgtcggtg	5	14	13	9	1	2	1	1	0	1	1	4	2	3	1	2	4	1	2	2	4	1	4	rs60068521	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:187557863G>A	ENST00000441802.2	-	5	4057	c.3848C>T	c.(3847-3849)cCc>cTc	p.P1283L		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1283	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						TTCTGCATTGGGGCCCTCATC	0.502										HNSCC(5;0.00058)			G|||	6	0.00119808	0.0045	0.0	5008	,	,		15954	0.0		0.0	False		,,,				2504	0.0				p.P1283L	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C3848T						PASS	.	G	LEU/PRO	4,3800		0,4,1898	224	226	225		3848	5	1	4	dbSNP_129	225	0,8238		0,0,4119	yes	missense	FAT1	NM_005245.3	98	0,4,6017	AA,AG,GG		0.0,0.1052,0.0332	benign	1283/4589	187557863	4,12038	1902	4119	6021	SO:0001583	missense	2195	exon5			GCATTGGGGCCCT	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.3848C>T	4.37:g.187557863G>A	ENSP00000406229:p.Pro1283Leu	306	0	0		300	155	0.516667	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	15.34	2.804208	0.50315	0.001052	0.0	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.54071	0.59	4.99	4.99	0.66335	Cadherin (4);Cadherin-like (1);	0.172618	0.52532	D	0.000077	T	0.61999	0.2392	L	0.41415	1.275	0.80722	D	1	D	0.67145	0.996	D	0.63957	0.92	T	0.54906	-0.8223	10	0.22109	T	0.4	.	18.4667	0.90758	0.0:0.0:1.0:0.0	rs60068521	1283	Q14517	FAT1_HUMAN	L	1283	ENSP00000406229:P1283L	ENSP00000260147:P1283L	P	-	2	0	FAT1	187794857	1.000000	0.71417	1.000000	0.80357	0.584000	0.36387	9.657000	0.98554	2.599000	0.87857	0.561000	0.74099	CCC	G|0.999;A|0.001	0.001	strong		0.502	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		A	187557863	G	A	187557863	3	1	22	1	0	0	0	0	1	0	0	0	5697	1232	43	2	10010	2	FAT1	4	187557863	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	15431	187557863	3596413	1136	4037											
ZFP42	132625	hgsc.bcm.edu	37	chr4	188924450	188924450	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atacctggcattgacctatcAgatcctaaacagctcgcaga	13	9	7	12	1	1	3	1	1	0	2	3	3	2	3	3	1	3	3	3	1	4	4	rs61731386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:188924450A>G	ENST00000326866.4	+	4	897	c.489A>G	c.(487-489)tcA>tcG	p.S163S	ZFP42_ENST00000509524.1_Silent_p.S163S	NM_174900.3	NP_777560.2	Q96MM3	ZFP42_HUMAN	ZFP42 zinc finger protein	163					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)		TTGACCTATCAGATCCTAAAC	0.453													A|||	187	0.0373403	0.1362	0.0086	5008	,	,		17571	0.0		0.001	False		,,,				2504	0.0				p.S163S		Atlas-SNP	.											.	ZFP42	87	.	0			c.A489G						PASS	.	A		449,3957	202.5+/-225.2	25,399,1779	103	116	112		489	-1.9	0	4	dbSNP_129	112	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ZFP42	NM_174900.3		25,401,6077	GG,GA,AA		0.0233,10.1906,3.4676		163/311	188924450	451,12555	2203	4300	6503	SO:0001819	synonymous_variant	132625	exon4			CCTATCAGATCCT	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.489A>G	4.37:g.188924450A>G		59	0	0		60	37	0.616667	NM_174900	D3DP65|Q8WXE2	Silent	SNP	ENST00000326866.4	37	CCDS3849.1																																																																																			A|0.972;G|0.028	0.028	strong		0.453	ZFP42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359794.1	NM_174900		G	188924450	A	G	188924450	2	3	22	1	0	0	0	0	0	0	0	1	17665	175	7	3		3	ZFP42	4	188924450	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1366587	188924450	2229826	1137	4038											
TRIML1	339976	hgsc.bcm.edu	37	chr4	189061010	189061010	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagctacgggaggatgcccAccactgccaaggcgctctcc	8	5	12	16	2	1	0	0	0	1	0	2	2	1	2	4	3	4	3	4	3	2	1	rs111308948	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:189061010A>G	ENST00000332517.3	+	1	438	c.298A>G	c.(298-300)Acc>Gcc	p.T100A	RP11-366H4.3_ENST00000501322.2_RNA	NM_178556.3	NP_848651.2	Q8N9V2	TRIML_HUMAN	tripartite motif family-like 1	100					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)		GAGGATGCCCACCACTGCCAA	0.647													G|||	203	0.0405351	0.1445	0.0159	5008	,	,		18008	0.0		0.001	False		,,,				2504	0.0				p.T100A	Melanoma(31;213 1036 16579 23968 32372)	Atlas-SNP	.											.	TRIML1	126	.	0			c.A298G						PASS	.	G	ALA/THR	538,3868	767.9+/-413.5	40,458,1705	41	40	41		298	3.3	0	4	dbSNP_132	41	0,8600		0,0,4300	yes	missense	TRIML1	NM_178556.3	58	40,458,6005	GG,GA,AA		0.0,12.2106,4.1366	benign	100/469	189061010	538,12468	2203	4300	6503	SO:0001583	missense	339976	exon1			ATGCCCACCACTG	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.298A>G	4.37:g.189061010A>G	ENSP00000327738:p.Thr100Ala	134	0	0		156	73	0.467949	NM_178556	Q96BE5	Missense_Mutation	SNP	ENST00000332517.3	37	CCDS3851.1	78	0.03571428571428571	71	0.1443089430894309	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	G	0.714	-0.786047	0.02907	0.122106	0.0	ENSG00000184108	ENST00000332517	T	0.61040	0.14	5.06	3.27	0.37495	.	0.559255	0.16346	N	0.218439	T	0.00144	0.0004	N	0.00347	-1.61	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.05649	-1.0872	9	0.42905	T	0.14	-6.5562	4.0011	0.09580	0.191:0.0:0.6206:0.1884	.	100	Q8N9V2	TRIML_HUMAN	A	100	ENSP00000327738:T100A	ENSP00000327738:T100A	T	+	1	0	TRIML1	189298004	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	0.371000	0.20450	0.776000	0.33473	-0.215000	0.12644	ACC	A|0.962;G|0.038	0.038	strong		0.647	TRIML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359813.1	NM_178556		G	189061010	A	G	189061010	3	3	22	1	0	0	0	0	1	0	0	0	16565	159	6	3	300	3	TRIML1	4	189061010	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	136560	189061010	2093266	1138	4039											
PLEKHG4B	153478	hgsc.bcm.edu	37	chr5	143359	143359	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgctgcagtccggggtcGtcaccctcccaggtgagagc	6	7	14	14	2	1	1	1	1	0	1	4	2	3	1	3	3	4	3	3	3	0	0	rs114876243	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:143359G>A	ENST00000283426.6	+	2	657	c.607G>A	c.(607-609)Gtc>Atc	p.V203I	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	203							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)		GTCCGGGGTCGTCACCCTCCC	0.637													G|||	85	0.0169728	0.0643	0.0	5008	,	,		19147	0.0		0.0	False		,,,				2504	0.0				p.V203I		Atlas-SNP	.											.	PLEKHG4B	167	.	0			c.G607A						PASS	.	G	ILE/VAL	217,4189		9,199,1995	34	39	37		607	-3.8	0	5	dbSNP_132	37	3,8589		0,3,4293	yes	missense	PLEKHG4B	NM_052909.3	29	9,202,6288	AA,AG,GG		0.0349,4.9251,1.6926	benign	203/1272	143359	220,12778	2203	4296	6499	SO:0001583	missense	153478	exon2			GGGGTCGTCACCC	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.607G>A	5.37:g.143359G>A	ENSP00000283426:p.Val203Ile	61	0	0		49	24	0.489796	NM_052909		Missense_Mutation	SNP	ENST00000283426.6	37	CCDS34124.1	22	0.010073260073260074	22	0.044715447154471545	0	0.0	0	0.0	0	0.0	.	0.015	-1.543641	0.00934	0.049251	3.49E-4	ENSG00000153404	ENST00000283426;ENST00000502646	T;T	0.18174	2.23;2.23	2.87	-3.76	0.04359	.	.	.	.	.	T	0.00754	0.0025	N	0.04090	-0.28	0.09310	N	1	B	0.13145	0.007	B	0.04013	0.001	T	0.38308	-0.9667	9	0.05620	T	0.96	.	7.5065	0.27547	0.5943:0.0:0.4057:0.0	.	203	Q96PX9	PKH4B_HUMAN	I	203;117	ENSP00000283426:V203I;ENSP00000422493:V117I	ENSP00000283426:V203I	V	+	1	0	PLEKHG4B	196359	0.000000	0.05858	0.001000	0.08648	0.108000	0.19459	-0.481000	0.06552	-0.665000	0.05317	-0.752000	0.03492	GTC	G|0.985;A|0.015	0.015	strong		0.637	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		A	143359	G	A	143359	3	1	22	1	0	0	0	0	1	0	0	0	12081	1145	40	1	613	1	PLEKHG4B	5	143359	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10		143359	180771901	1139	4040											
PLEKHG4B	153478	hgsc.bcm.edu	37	chr5	155059	155059	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gccagctgaccgcagacctcGacggctcctttccctacagc	7	7	9	18	3	0	2	0	1	0	1	3	3	2	2	5	1	3	3	5	1	1	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:155059G>A	ENST00000283426.6	+	6	1044	c.994G>A	c.(994-996)Gac>Aac	p.D332N		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	332							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)		CGCAGACCTCGACGGCTCCTT	0.577																																					p.D332N		Atlas-SNP	.											PLEKHG4B_ENST00000283426,NS,carcinoma,-2,2	PLEKHG4B	167	2	0			c.G994A						scavenged	.						86	77	80					5																	155059		2203	4300	6503	SO:0001583	missense	153478	exon6			GACCTCGACGGCT	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.994G>A	5.37:g.155059G>A	ENSP00000283426:p.Asp332Asn	54	0	0		71	3	0.0422535	NM_052909		Missense_Mutation	SNP	ENST00000283426.6	37	CCDS34124.1	.	.	.	.	.	.	.	.	.	.	.	10.59	1.394085	0.25205	.	.	ENSG00000153404	ENST00000283426;ENST00000502646	T;T	0.59083	0.29;0.29	3.88	3.01	0.34805	.	.	.	.	.	T	0.66015	0.2747	L	0.60455	1.87	0.09310	N	1	D	0.76494	0.999	P	0.61275	0.886	T	0.53961	-0.8364	9	0.62326	D	0.03	.	7.3764	0.26831	0.126:0.0:0.874:0.0	.	332	Q96PX9	PKH4B_HUMAN	N	332;246	ENSP00000283426:D332N;ENSP00000422493:D246N	ENSP00000283426:D332N	D	+	1	0	PLEKHG4B	208059	1.000000	0.71417	0.000000	0.03702	0.106000	0.19336	4.161000	0.58170	0.623000	0.30267	0.460000	0.39030	GAC	.	.	none		0.577	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		A	155059	G	A	155059	3	1	22	1	0	0	0	0	1	0	0	0	12081	1058	37	1	1016	1	PLEKHG4B	5	155059	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	11700	155059	180760201	1140	4041											
PLEKHG4B	153478	hgsc.bcm.edu	37	chr5	162929	162929	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtcaccaggaggctacctcGgtggctgcagaggccttccc	6	8	13	14	1	1	1	1	0	0	1	3	2	2	2	4	5	2	3	4	5	1	2	rs75342794	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:162929G>C	ENST00000283426.6	+	11	1724	c.1674G>C	c.(1672-1674)tcG>tcC	p.S558S		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	558							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)		AGGCTACCTCGGTGGCTGCAG	0.652													G|||	255	0.0509185	0.1838	0.0159	5008	,	,		15694	0.0		0.001	False		,,,				2504	0.0				p.S558S		Atlas-SNP	.											PLEKHG4B_ENST00000283426,NS,carcinoma,+2,1	PLEKHG4B	167	1	0			c.G1674C						PASS	.	G		691,3685		51,589,1548	25	27	26		1674	-1.1	0	5	dbSNP_131	26	13,8555		0,13,4271	no	coding-synonymous	PLEKHG4B	NM_052909.3		51,602,5819	CC,CG,GG		0.1517,15.7907,5.4388		558/1272	162929	704,12240	2188	4284	6472	SO:0001819	synonymous_variant	153478	exon11			TACCTCGGTGGCT	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.1674G>C	5.37:g.162929G>C		166	0	0		187	99	0.529412	NM_052909		Silent	SNP	ENST00000283426.6	37	CCDS34124.1																																																																																			G|0.941;C|0.059	0.059	strong		0.652	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		C	162929	G	C	162929	2	2	22	1	0	0	0	0	0	0	0	1	12081	1103	39	4		4	PLEKHG4B	5	162929	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	7870	162929	180752331	1141	4042											
SLC9A3	6550	hgsc.bcm.edu	37	chr5	491906	491906	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgagcccactgaggaagacGccgtagagggacagcccggt	11	4	15	11	3	0	4	0	2	0	2	0	6	0	6	3	3	2	1	3	3	2	1	rs6870920	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:491906G>A	ENST00000264938.3	-	2	501	c.492C>T	c.(490-492)ggC>ggT	p.G164G	SLC9A3_ENST00000514375.1_Silent_p.G164G	NM_004174.2	NP_004165.2	P48764	SL9A3_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	164					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)			TGAGGAAGACGCCGTAGAGGG	0.672													G|||	181	0.0361422	0.1301	0.0101	5008	,	,		11795	0.0		0.002	False		,,,				2504	0.0				p.G164G		Atlas-SNP	.											SLC9A3,head_neck,malignant_melanoma,-1,1	SLC9A3	89	1	0			c.C492T						PASS	.	G		407,3969		28,351,1809	27	20	22		492	-8.3	0.5	5	dbSNP_116	22	11,8555		0,11,4272	no	coding-synonymous	SLC9A3	NM_004174.2		28,362,6081	AA,AG,GG		0.1284,9.3007,3.2298		164/835	491906	418,12524	2188	4283	6471	SO:0001819	synonymous_variant	6550	exon2			GAAGACGCCGTAG		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.492C>T	5.37:g.491906G>A		81	0	0		83	43	0.518072	NM_004174	B7ZKR2|E9PF67|Q3MIW3	Silent	SNP	ENST00000264938.3	37	CCDS3855.1																																																																																			G|0.958;A|0.042	0.042	strong		0.672	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174		A	491906	G	A	491906	2	1	22	1	0	0	0	0	0	0	0	1	14728	1074	38	1		1	SLC9A3	5	491906	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	328977	491906	180423354	1142	4043											
NKD2	85409	hgsc.bcm.edu	37	chr5	1036482	1036482	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccgggattgagaactacaCgtccagattcggccctggta	9	8	12	12	4	0	2	0	1	0	2	2	4	1	3	3	3	2	1	3	3	3	4	rs35679233	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:1036482C>A	ENST00000296849.5	+	9	999	c.770C>A	c.(769-771)aCg>aAg	p.T257K	NKD2_ENST00000537972.1_Missense_Mutation_p.T257K|NKD2_ENST00000382730.2_5'Flank|NKD2_ENST00000274150.4_Missense_Mutation_p.T257K	NM_033120.3	NP_149111.1	Q969F2	NKD2_HUMAN	naked cuticle homolog 2 (Drosophila)	257			T -> K (in dbSNP:rs35679233).		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)			GAGAACTACACGTCCAGATTC	0.647													C|||	35	0.00698882	0.0242	0.0043	5008	,	,		10087	0.0		0.0	False		,,,				2504	0.0				p.T257K		Atlas-SNP	.											.	NKD2	39	.	0			c.C770A						PASS	.	C	LYS/THR	64,4342	58.7+/-95.3	0,64,2139	100	78	85		770	2.7	0.2	5	dbSNP_126	85	1,8599	1.2+/-3.3	0,1,4299	yes	missense	NKD2	NM_033120.2	78	0,65,6438	AA,AC,CC		0.0116,1.4526,0.4998	probably-damaging	257/452	1036482	65,12941	2203	4300	6503	SO:0001583	missense	85409	exon9			ACTACACGTCCAG	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.770C>A	5.37:g.1036482C>A	ENSP00000296849:p.Thr257Lys	72	0	0		84	44	0.52381	NM_001271082	Q96EK8|Q9BSN0	Missense_Mutation	SNP	ENST00000296849.5	37	CCDS3859.1	11	0.005036630036630037	8	0.016260162601626018	3	0.008287292817679558	0	0.0	0	0.0	C	14.85	2.658436	0.47467	0.014526	1.16E-4	ENSG00000145506	ENST00000296849;ENST00000274150;ENST00000537972	T;T;T	0.75589	0.25;-0.95;-0.95	4.5	2.69	0.31865	.	0.066054	0.64402	D	0.000014	T	0.71056	0.3295	M	0.76170	2.325	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.68039	0.938;0.955	T	0.76066	-0.3095	10	0.87932	D	0	-4.1939	7.4699	0.27342	0.0:0.7924:0.0:0.2076	rs35679233	257;257	Q969F2-2;Q969F2	.;NKD2_HUMAN	K	257	ENSP00000296849:T257K;ENSP00000274150:T257K;ENSP00000440925:T257K	ENSP00000274150:T257K	T	+	2	0	NKD2	1089482	0.977000	0.34250	0.199000	0.23439	0.223000	0.24884	2.475000	0.45162	0.339000	0.23719	0.491000	0.48974	ACG	C|0.994;A|0.006	0.006	strong		0.647	NKD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206720.2	NM_033120		A	1036482	C	A	1036482	3	1	22	1	0	0	0	0	1	0	0	0	10451	536	19	4	804	4	NKD2	5	1036482	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	544576	1036482	179878778	1143	4044											
SLC6A3	6531	hgsc.bcm.edu	37	chr5	1409226	1409226	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aaatggtccaggagcgtgaaGacgtagatgccaccctggaa	13	6	13	9	2	0	3	0	1	0	2	1	5	1	5	3	3	2	1	3	3	4	1	rs8179035	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:1409226G>C	ENST00000270349.9	-	11	1540	c.1413C>G	c.(1411-1413)gtC>gtG	p.V471V	SLC6A3_ENST00000453492.2_Silent_p.V471V	NM_001044.4	NP_001035.1	Q01959	SC6A3_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 3	471			V -> I (in dbSNP:rs75916702). {ECO:0000269|PubMed:21179162}.		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)	GGAGCGTGAAGACGTAGATGC	0.572													G|||	21	0.00419329	0.0129	0.0029	5008	,	,		17164	0.0		0.002	False		,,,				2504	0.0				p.V471V		Atlas-SNP	.											SLC6A3,NS,carcinoma,-1,1	SLC6A3	102	1	0			c.C1413G						PASS	.	G		59,4343	55.5+/-91.7	0,59,2142	56	49	51		1413	0.7	1	5	dbSNP_125	51	1,8589		0,1,4294	no	coding-synonymous	SLC6A3	NM_001044.4		0,60,6436	CC,CG,GG		0.0116,1.3403,0.4618		471/621	1409226	60,12932	2201	4295	6496	SO:0001819	synonymous_variant	6531	exon11			CGTGAAGACGTAG		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.1413C>G	5.37:g.1409226G>C		44	0	0		63	32	0.507937	NM_001044	A2RUN4|Q14996	Silent	SNP	ENST00000270349.9	37	CCDS3863.1																																																																																			G|0.995;C|0.005	0.005	strong		0.572	SLC6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253650.3	NM_001044		C	1409226	G	C	1409226	2	2	22	1	0	0	0	0	0	0	0	1	14700	929	33	4		4	SLC6A3	5	1409226	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	372744	1409226	179506034	1144	4045											
KIAA0947	23379	hgsc.bcm.edu	37	chr5	5464237	5464237	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaagctaatacaaaaactcAaagaagccaaactcagacca	23	4	4	10	0	2	2	2	0	0	2	2	2	2	2	2	0	5	1	2	0	9	2	rs10065646	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:5464237A>C	ENST00000296564.7	+	13	5012	c.4790A>C	c.(4789-4791)cAa>cCa	p.Q1597P		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		1597			Q -> P (in dbSNP:rs10065646).		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						ACAAAAACTCAAAGAAGCCAA	0.418													A|||	242	0.0483227	0.1725	0.0187	5008	,	,		20166	0.0		0.001	False		,,,				2504	0.0				p.Q1597P		Atlas-SNP	.											.	KIAA0947	301	.	0			c.A4790C						PASS	.	A	PRO/GLN	500,3252		44,412,1420	47	47	47		4790	-0.5	0	5	dbSNP_119	47	9,8207		0,9,4099	yes	missense	KIAA0947	NM_015325.1	76	44,421,5519	CC,CA,AA		0.1095,13.3262,4.253	benign	1597/2267	5464237	509,11459	1876	4108	5984	SO:0001583	missense	23379	exon13			AAACTCAAAGAAG																												ENST00000296564.7:c.4790A>C	5.37:g.5464237A>C	ENSP00000296564:p.Gln1597Pro	43	0	0		43	23	0.534884	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	ENST00000296564.7	37	CCDS47187.1	100	0.045787545787545784	88	0.17886178861788618	12	0.03314917127071823	0	0.0	0	0.0	A	9.076	0.998101	0.19043	0.133262	0.001095	ENSG00000164151	ENST00000296564	T	0.10763	2.84	5.27	-0.478	0.12093	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.15930	0.015	B	0.16722	0.016	T	0.46289	-0.9202	8	0.29301	T	0.29	0.0	7.2058	0.25907	0.3909:0.4671:0.0:0.1421	rs10065646;rs52803291;rs10065646	1597	Q9Y2F5	K0947_HUMAN	P	1597	ENSP00000296564:Q1597P	ENSP00000296564:Q1597P	Q	+	2	0	KIAA0947	5517237	0.000000	0.05858	0.000000	0.03702	0.560000	0.35617	-0.688000	0.05150	-0.319000	0.08652	0.377000	0.23210	CAA	A|0.932;C|0.068	0.068	strong		0.418	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			C	5464237	A	C	5464237	3	2	22	1	0	0	0	0	1	0	0	0	8211	130	5	5	4840	5	KIAA0947	5	5464237	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	4055011	5464237	175451023	1145	4046											
NSUN2	54888	hgsc.bcm.edu	37	chr5	6622139	6622139	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	caatgcatacctggaaagggGacattcatgtcggcatgtag	12	9	12	8	1	1	0	1	0	0	0	2	2	1	2	1	4	2	3	1	4	4	3	rs148924682	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:6622139G>T	ENST00000264670.6	-	6	923	c.612C>A	c.(610-612)gtC>gtA	p.V204V	NSUN2_ENST00000505264.1_Intron|NSUN2_ENST00000539938.1_Intron|NSUN2_ENST00000506139.1_Silent_p.V169V	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	204					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)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	41						CTGGAAAGGGGACATTCATGT	0.408													G|||	51	0.0101837	0.0348	0.0058	5008	,	,		18768	0.0		0.001	False		,,,				2504	0.0				p.V204V		Atlas-SNP	.											NSUN2,NS,carcinoma,-1,1	NSUN2	82	1	0			c.C612A						PASS	.	G	,	150,4256	103.8+/-142.4	3,144,2056	180	150	161		507,612	-1.7	0.3	5	dbSNP_134	161	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	NSUN2	NM_001193455.1,NM_017755.5	,	3,144,6356	TT,TG,GG		0.0,3.4044,1.1533	,	169/733,204/768	6622139	150,12856	2203	4300	6503	SO:0001819	synonymous_variant	54888	exon6			AAAGGGGACATTC	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.612C>A	5.37:g.6622139G>T		118	0	0		109	48	0.440367	NM_017755	A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Silent	SNP	ENST00000264670.6	37	CCDS3869.1																																																																																			G|0.990;T|0.010	0.010	strong		0.408	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1	NM_017755		T	6622139	G	T	6622139	2	4	22	1	0	0	0	0	0	0	0	1	10687	1161	41	4		4	NSUN2	5	6622139	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1157902	6622139	174293121	1146	4047											
ADCY2	108	hgsc.bcm.edu	37	chr5	7690872	7690872	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aaagcggagatcatccagagGctgcagggccccaaggcggg	11	3	16	11	2	1	2	1	0	0	2	2	3	2	2	3	5	2	2	3	5	2	0	rs10079813	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:7690872G>A	ENST00000338316.4	+	5	878	c.789G>A	c.(787-789)agG>agA	p.R263R	ADCY2_ENST00000513693.1_3'UTR|ADCY2_ENST00000537121.1_Silent_p.R83R	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	263					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						TCATCCAGAGGCTGCAGGGCC	0.567													G|||	98	0.0195687	0.0741	0.0	5008	,	,		15611	0.0		0.0	False		,,,				2504	0.0				p.R263R		Atlas-SNP	.											.	ADCY2	337	.	0			c.G789A						PASS	.	G		292,4114	159.6+/-192.1	7,278,1918	70	66	67		789	1.9	1	5	dbSNP_119	67	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	ADCY2	NM_020546.2		7,281,6215	AA,AG,GG		0.0349,6.6273,2.2682		263/1092	7690872	295,12711	2203	4300	6503	SO:0001819	synonymous_variant	108	exon5			CCAGAGGCTGCAG	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.789G>A	5.37:g.7690872G>A		107	0	0		119	53	0.445378	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Silent	SNP	ENST00000338316.4	37	CCDS3872.2																																																																																			G|0.976;A|0.024	0.024	strong		0.567	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		A	7690872	G	A	7690872	2	1	22	1	0	0	0	0	0	0	0	1	294	1194	42	2		2	ADCY2	5	7690872	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1068733	7690872	173224388	1147	4048											
ADCY2	108	hgsc.bcm.edu	37	chr5	7706989	7706989	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	catgatgtgaccttggccaaCcacatggaagctggaggggt	10	8	14	9	0	0	2	0	2	0	0	0	4	0	4	3	5	2	1	3	5	2	1	rs75986905	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:7706989C>T	ENST00000338316.4	+	8	1331	c.1242C>T	c.(1240-1242)aaC>aaT	p.N414N	RP11-711G10.1_ENST00000514105.2_RNA|ADCY2_ENST00000537121.1_Silent_p.N234N	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	414					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						CCTTGGCCAACCACATGGAAG	0.502													C|||	68	0.0135783	0.0484	0.0058	5008	,	,		20791	0.0		0.0	False		,,,				2504	0.0				p.N414N		Atlas-SNP	.											.	ADCY2	337	.	0			c.C1242T						PASS	.	C		199,4207	124.5+/-161.8	4,191,2008	176	155	162		1242	-3.5	1	5	dbSNP_132	162	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ADCY2	NM_020546.2		4,193,6306	TT,TC,CC		0.0233,4.5166,1.5454		414/1092	7706989	201,12805	2203	4300	6503	SO:0001819	synonymous_variant	108	exon8			GGCCAACCACATG	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.1242C>T	5.37:g.7706989C>T		183	0	0		248	123	0.495968	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Silent	SNP	ENST00000338316.4	37	CCDS3872.2																																																																																			C|0.985;T|0.015	0.015	strong		0.502	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		T	7706989	C	T	7706989	2	4	22	1	0	0	0	0	0	0	0	1	294	506	18	2		2	ADCY2	5	7706989	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	16117	7706989	173208271	1148	4049											
MTRR	4552	hgsc.bcm.edu	37	chr5	7885907	7885907	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcctactccaaagactgcagCttgaagataaaagagagcac	16	6	9	10	0	0	4	0	1	0	3	1	5	1	4	2	0	4	3	2	0	5	3	rs10064631	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:7885907C>G	ENST00000264668.2	+	7	1108	c.1078C>G	c.(1078-1080)Ctt>Gtt	p.L360V	MTRR_ENST00000341013.6_3'UTR|MTRR_ENST00000440940.2_Missense_Mutation_p.L333V	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	360	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.		L -> V (in dbSNP:rs10064631). {ECO:0000269|PubMed:10484769}.		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)	AAGACTGCAGCTTGAAGATAA	0.468													C|||	199	0.0397364	0.1445	0.0115	5008	,	,		17404	0.0		0.0	False		,,,				2504	0.0				p.L360V		Atlas-SNP	.											.	MTRR	74	.	0			c.C1078G	GRCh37	CM992646	MTRR	M	rs10064631	PASS	.	C	VAL/LEU,VAL/LEU	639,3767	275.4+/-272.5	46,547,1610	109	109	109		997,1078	5.8	1	5	dbSNP_119	109	8,8592	6.4+/-24.3	0,8,4292	yes	missense,missense	MTRR	NM_002454.2,NM_024010.2	32,32	46,555,5902	GG,GC,CC		0.093,14.503,4.9746	probably-damaging,probably-damaging	333/699,360/726	7885907	647,12359	2203	4300	6503	SO:0001583	missense	4552	exon7			CTGCAGCTTGAAG	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.1078C>G	5.37:g.7885907C>G	ENSP00000264668:p.Leu360Val	176	0	0		197	92	0.467005	NM_024010	O60471|Q32MA9|Q7Z4M8	Missense_Mutation	SNP	ENST00000264668.2	37	CCDS3874.1	75	0.034340659340659344	71	0.1443089430894309	4	0.011049723756906077	0	0.0	0	0.0	C	15.42	2.826850	0.50739	0.14503	9.3E-4	ENSG00000124275	ENST00000264668;ENST00000440940	T;T	0.39406	1.08;1.08	5.83	5.83	0.93111	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	0.00524	0.0017	M	0.66378	2.025	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	T	0.00119	-1.2031	10	0.31617	T	0.26	-27.2783	13.3424	0.60553	0.0:0.9283:0.0:0.0717	rs10064631;rs10064631	360	Q9UBK8	MTRR_HUMAN	V	360;333	ENSP00000264668:L360V;ENSP00000402510:L333V	ENSP00000264668:L360V	L	+	1	0	MTRR	7938907	1.000000	0.71417	0.991000	0.47740	0.034000	0.12701	4.189000	0.58358	2.753000	0.94483	0.650000	0.86243	CTT	C|0.948;G|0.052	0.052	strong		0.468	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1			G	7885907	C	G	7885907	3	3	22	1	0	0	0	0	1	0	0	0	9970	797	28	4	1104	4	MTRR	5	7885907	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	178918	7885907	173029353	1149	4050											
CCT5	22948	hgsc.bcm.edu	37	chr5	10262607	10262607	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccttagatcattgaggaggcGaaacgatcccttcacgatgc	11	9	10	11	3	2	2	2	1	0	1	3	6	3	3	2	2	2	0	2	2	2	3	rs113262482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:10262607G>A	ENST00000280326.4	+	9	1614	c.1194G>A	c.(1192-1194)gcG>gcA	p.A398A	CCT5_ENST00000506600.1_Silent_p.A305A|CTD-2256P15.4_ENST00000606194.1_RNA|CCT5_ENST00000515390.1_Silent_p.A343A|CCT5_ENST00000503026.1_Silent_p.A377A|CCT5_ENST00000515676.1_Silent_p.A360A	NM_012073.3	NP_036205.1	P48643	TCPE_HUMAN	chaperonin containing TCP1, subunit 5 (epsilon)	398					'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						TTGAGGAGGCGAAACGATCCC	0.468													G|||	40	0.00798722	0.0295	0.0	5008	,	,		20572	0.0		0.001	False		,,,				2504	0.0				p.A398A		Atlas-SNP	.											.	CCT5	49	.	0			c.G1194A						PASS	.	G		99,4307	79.3+/-117.8	1,97,2105	160	131	141		1194	-7.7	0.9	5	dbSNP_132	141	3,8597	3.0+/-9.4	0,3,4297	yes	coding-synonymous	CCT5	NM_012073.3		1,100,6402	AA,AG,GG		0.0349,2.2469,0.7843		398/542	10262607	102,12904	2203	4300	6503	SO:0001819	synonymous_variant	22948	exon9			GGAGGCGAAACGA	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.1194G>A	5.37:g.10262607G>A		120	0	0		143	68	0.475524	NM_012073	A8JZY8|A8K2X8|B4DYD8	Silent	SNP	ENST00000280326.4	37	CCDS3877.1																																																																																			G|0.992;A|0.008	0.008	strong		0.468	CCT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253688.2			A	10262607	G	A	10262607	2	1	22	1	0	0	0	0	0	0	0	1	2958	1045	37	1		1	CCT5	5	10262607	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2376700	10262607	170652653	1150	4051											
DNAH5	1767	hgsc.bcm.edu	37	chr5	13701422	13701422	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgcagttaaaaatccctgggGgttaaaaaaacccgtcatcc	14	9	8	10	1	1	0	1	0	0	0	3	0	3	0	3	2	2	3	3	2	7	2	rs113425437	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:13701422G>T	ENST00000265104.4	-	77	13566	c.13462C>A	c.(13462-13464)Ccc>Acc	p.P4488T		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4488					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)					AATCCCTGGGGGTTAAAAAAA	0.418									Kartagener syndrome				G|||	207	0.0413339	0.149	0.0144	5008	,	,		14515	0.0		0.0	False		,,,				2504	0.0				p.P4488T		Atlas-SNP	.											.	DNAH5	868	.	0			c.C13462A						PASS	.	G	THR/PRO	586,3820	256.1+/-261.0	32,522,1649	77	84	82		13462	4.9	1	5	dbSNP_132	82	1,8599	1.2+/-3.3	0,1,4299	yes	missense	DNAH5	NM_001369.2	38	32,523,5948	TT,TG,GG		0.0116,13.3,4.5133	probably-damaging	4488/4625	13701422	587,12419	2203	4300	6503	SO:0001583	missense	1767	exon77	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CCTGGGGGTTAAA	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.13462C>A	5.37:g.13701422G>T	ENSP00000265104:p.Pro4488Thr	80	0	0		73	41	0.561644	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	58	0.026556776556776556	53	0.10772357723577236	5	0.013812154696132596	0	0.0	0	0.0	G	24.4	4.523833	0.85600	0.133	1.16E-4	ENSG00000039139	ENST00000265104	T	0.16196	2.36	5.78	4.91	0.64330	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.00440	0.0014	M	0.67953	2.075	0.80722	D	1	D	0.55385	0.971	D	0.73708	0.981	T	0.00011	-1.2433	10	0.87932	D	0	.	14.6237	0.68605	0.0697:0.0:0.9303:0.0	.	4488	Q8TE73	DYH5_HUMAN	T	4488	ENSP00000265104:P4488T	ENSP00000265104:P4488T	P	-	1	0	DNAH5	13754422	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.987000	0.88182	1.454000	0.47793	0.591000	0.81541	CCC	G|0.961;T|0.039	0.039	strong		0.418	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		T	13701422	G	T	13701422	3	4	22	1	0	0	0	0	1	0	0	0	4606	1232	43	4	424	4	DNAH5	5	13701422	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3438815	13701422	167213838	1151	4052											
DNAH5	1767	hgsc.bcm.edu	37	chr5	13753517	13753517	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagtaggagcatcaatcaacAtctcactgagatttaggttc	13	12	8	8	0	3	1	3	1	1	1	5	3	3	2	0	2	2	3	0	2	5	5			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:13753517A>T	ENST00000265104.4	-	63	10801	c.10697T>A	c.(10696-10698)aTg>aAg	p.M3566K		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3566					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)					ATCAATCAACATCTCACTGAG	0.403									Kartagener syndrome																												p.M3566K		Atlas-SNP	.											DNAH5,NS,carcinoma,+1,1	DNAH5	868	1	0			c.T10697A						PASS	.						136	131	133					5																	13753517		2203	4300	6503	SO:0001583	missense	1767	exon63	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	ATCAACATCTCAC	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.10697T>A	5.37:g.13753517A>T	ENSP00000265104:p.Met3566Lys	218	0	0		216	24	0.111111	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.141563	0.77775	.	.	ENSG00000039139	ENST00000265104	T	0.25250	1.81	5.77	5.77	0.91146	.	0.087828	0.85682	D	0.000000	T	0.48314	0.1493	M	0.89478	3.035	0.80722	D	1	B	0.34290	0.447	B	0.44044	0.439	T	0.54139	-0.8338	10	0.66056	D	0.02	.	16.3948	0.83586	1.0:0.0:0.0:0.0	.	3566	Q8TE73	DYH5_HUMAN	K	3566	ENSP00000265104:M3566K	ENSP00000265104:M3566K	M	-	2	0	DNAH5	13806517	1.000000	0.71417	1.000000	0.80357	0.797000	0.45037	8.851000	0.92205	2.326000	0.78906	0.533000	0.62120	ATG	.	.	none		0.403	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		T	13753517	A	T	13753517	3	4	22	1	0	0	0	0	1	0	0	0	4606	217	8	5	3245	5	DNAH5	5	13753517	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	52095	13753517	167161743	1152	4053											
DNAH5	1767	hgsc.bcm.edu	37	chr5	13841066	13841066	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgaatagtaatcagagtctcGtatttcactcgttccgtgga	10	14	9	8	3	3	2	2	1	1	1	6	3	4	3	1	1	0	3	1	1	4	5	rs6880264	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:13841066G>A	ENST00000265104.4	-	34	5762	c.5658C>T	c.(5656-5658)taC>taT	p.Y1886Y		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1886	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)					TCAGAGTCTCGTATTTCACTC	0.388									Kartagener syndrome				G|||	74	0.0147764	0.0545	0.0029	5008	,	,		19415	0.0		0.0	False		,,,				2504	0.0				p.Y1886Y		Atlas-SNP	.											.	DNAH5	868	.	0			c.C5658T						PASS	.	G		192,4214	122.9+/-160.3	2,188,2013	149	136	141		5658	-2.4	1	5	dbSNP_116	141	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	DNAH5	NM_001369.2		2,191,6310	AA,AG,GG		0.0349,4.3577,1.4993		1886/4625	13841066	195,12811	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon34	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AGTCTCGTATTTC	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.5658C>T	5.37:g.13841066G>A		127	0	0		141	63	0.446809	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			G|0.985;A|0.015	0.015	strong		0.388	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		A	13841066	G	A	13841066	2	1	22	1	0	0	0	0	0	0	0	1	4606	1140	40	1		1	DNAH5	5	13841066	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	87549	13841066	167074194	1153	4054											
TRIO	7204	hgsc.bcm.edu	37	chr5	14291259	14291259	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cactcgacacggcagcatctGcaccagatgtggcatgtgag	10	7	12	12	2	1	2	0	1	1	1	2	3	1	2	1	2	2	4	1	2	0	0	rs61737132	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:14291259G>A	ENST00000344204.4	+	5	999	c.975G>A	c.(973-975)ctG>ctA	p.L325L	TRIO_ENST00000509967.2_Silent_p.L276L|TRIO_ENST00000537187.1_Silent_p.L325L	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	325					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)					GGCAGCATCTGCACCAGATGT	0.562													G|||	213	0.0425319	0.152	0.0173	5008	,	,		19393	0.0		0.0	False		,,,				2504	0.0				p.L325L		Atlas-SNP	.											.	TRIO	305	.	0			c.G975A						PASS	.	G		550,3856	236.8+/-248.8	36,478,1689	54	52	53		975	4.2	1	5	dbSNP_129	53	4,8596	2.2+/-6.3	0,4,4296	no	coding-synonymous	TRIO	NM_007118.2		36,482,5985	AA,AG,GG		0.0465,12.483,4.2596		325/3098	14291259	554,12452	2203	4300	6503	SO:0001819	synonymous_variant	7204	exon5			GCATCTGCACCAG	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.975G>A	5.37:g.14291259G>A		142	0	0		143	63	0.440559	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Silent	SNP	ENST00000344204.4	37	CCDS3883.1																																																																																			G|0.963;A|0.037	0.037	strong		0.562	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		A	14291259	G	A	14291259	2	1	22	1	0	0	0	0	0	0	0	1	16567	1306	46	2		2	TRIO	5	14291259	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	450193	14291259	166624001	1154	4055											
FAM134B	54463	hgsc.bcm.edu	37	chr5	16475209	16475209	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tctgtgaccactgtccaactGttccttctttctcttgagct	5	17	6	13	0	3	2	0	2	3	0	6	2	5	2	3	0	2	2	3	0	1	4	rs34432513	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:16475209G>C	ENST00000306320.9	-	9	1221	c.1135C>G	c.(1135-1137)Cag>Gag	p.Q379E	FAM134B_ENST00000399793.2_Missense_Mutation_p.Q238E	NM_001034850.2	NP_001030022.1	Q9H6L5	F134B_HUMAN	family with sequence similarity 134, member B	379			Q -> E (in dbSNP:rs34432513).		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						CTGTCCAACTGTTCCTTCTTT	0.453													G|||	57	0.0113818	0.0393	0.0058	5008	,	,		20685	0.0		0.001	False		,,,				2504	0.0				p.Q379E		Atlas-SNP	.											.	FAM134B	72	.	0			c.C1135G						PASS	.	G	GLU/GLN,GLU/GLN	137,3809		4,129,1840	165	161	162	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1135,712	3.9	0	5	dbSNP_126	162	2,8320		0,2,4159	yes	missense,missense	FAM134B	NM_001034850.1,NM_019000.3	29,29	4,131,5999	CC,CG,GG		0.024,3.4719,1.133	benign,benign	379/498,238/357	16475209	139,12129	1973	4161	6134	SO:0001583	missense	54463	exon9			CCAACTGTTCCTT	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.1135C>G	5.37:g.16475209G>C	ENSP00000304642:p.Gln379Glu	196	0	0		206	104	0.504854	NM_001034850	Q69YN8|Q9H6K6|Q9H764|Q9NXM8	Missense_Mutation	SNP	ENST00000306320.9	37	CCDS43304.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	G	0.004	-2.276501	0.00254	0.034719	2.4E-4	ENSG00000154153	ENST00000399793;ENST00000306320	T;T	0.43688	0.96;0.94	5.7	3.86	0.44501	.	0.782790	0.11830	N	0.525295	T	0.01976	0.0062	N	0.25647	0.755	0.09310	N	1	B;B	0.23442	0.085;0.034	B;B	0.19666	0.026;0.022	T	0.10823	-1.0613	10	0.02654	T	1	-0.8582	10.5977	0.45347	0.0:0.1293:0.6027:0.2681	rs34432513	379;238	Q9H6L5;Q9H6L5-2	F134B_HUMAN;.	E	238;379	ENSP00000382691:Q238E;ENSP00000304642:Q379E	ENSP00000304642:Q379E	Q	-	1	0	FAM134B	16528209	0.617000	0.27043	0.001000	0.08648	0.391000	0.30476	4.123000	0.57917	0.704000	0.31869	0.655000	0.94253	CAG	G|0.984;C|0.016	0.016	strong		0.453	FAM134B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000366090.1	NM_001034850		C	16475209	G	C	16475209	3	2	22	1	0	0	0	0	1	0	0	0	5451	1386	48	4	362	4	FAM134B	5	16475209	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2183950	16475209	164440051	1155	4056											
MYO10	4651	hgsc.bcm.edu	37	chr5	16673800	16673800	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctctcctcacctccccagcGgtggtgtgggagttgatggt	4	11	13	13	1	2	1	1	1	1	0	4	2	3	2	5	4	1	1	5	4	0	1	rs3188408	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:16673800G>A	ENST00000513610.1	-	36	5617	c.5163C>T	c.(5161-5163)acC>acT	p.T1721T	MYO10_ENST00000515803.1_Silent_p.T1060T|MYO10_ENST00000427430.2_Silent_p.T1078T|MYO10_ENST00000505695.1_Silent_p.T1060T|MYO10_ENST00000274203.9_Silent_p.T1078T	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	1721	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				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						CCTCCCCAGCGGTGGTGTGGG	0.537													G|||	151	0.0301518	0.1074	0.0058	5008	,	,		16446	0.0		0.001	False		,,,				2504	0.0041				p.T1721T		Atlas-SNP	.											.	MYO10	198	.	0			c.C5163T						PASS	.	G		383,3691		24,335,1678	50	52	51		5163	-10.6	0.2	5	dbSNP_105	51	3,8375		0,3,4186	no	coding-synonymous	MYO10	NM_012334.2		24,338,5864	AA,AG,GG		0.0358,9.4011,3.0999		1721/2059	16673800	386,12066	2037	4189	6226	SO:0001819	synonymous_variant	4651	exon36			CCCAGCGGTGGTG	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.5163C>T	5.37:g.16673800G>A		125	0	0		135	65	0.481481	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	37	CCDS54834.1																																																																																			G|0.980;A|0.020	0.020	strong		0.537	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		A	16673800	G	A	16673800	2	1	22	1	0	0	0	0	0	0	0	1	10071	1103	39	1		1	MYO10	5	16673800	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	198591	16673800	164241460	1156	4057											
MYO10	4651	hgsc.bcm.edu	37	chr5	16682062	16682062	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atccagtggtgcatctcctcCggcgtgtcggcgttgcagtg	4	11	14	12	4	1	0	0	0	1	0	5	0	3	0	3	3	2	3	3	3	0	1	rs16868979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:16682062C>T	ENST00000513610.1	-	31	4561	c.4107G>A	c.(4105-4107)ccG>ccA	p.P1369P	MYO10_ENST00000515803.1_Silent_p.P708P|MYO10_ENST00000427430.2_Silent_p.P726P|MYO10_ENST00000505695.1_Silent_p.P708P|MYO10_ENST00000274203.9_Silent_p.P726P	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	1369					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						GCATCTCCTCCGGCGTGTCGG	0.587													C|||	141	0.028155	0.0998	0.0058	5008	,	,		17271	0.0		0.0	False		,,,				2504	0.0051				p.P1369P		Atlas-SNP	.											MYO10,NS,carcinoma,0,1	MYO10	198	1	0			c.G4107A						PASS	.	C		367,3887		21,325,1781	112	113	113		4107	-11.6	0.4	5	dbSNP_123	113	2,8458		0,2,4228	no	coding-synonymous	MYO10	NM_012334.2		21,327,6009	TT,TC,CC		0.0236,8.6272,2.9023		1369/2059	16682062	369,12345	2127	4230	6357	SO:0001819	synonymous_variant	4651	exon31			CTCCTCCGGCGTG	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.4107G>A	5.37:g.16682062C>T		111	0	0		127	64	0.503937	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	37	CCDS54834.1																																																																																			C|0.960;T|0.040	0.040	strong		0.587	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		T	16682062	C	T	16682062	2	4	22	1	0	0	0	0	0	0	0	1	10071	639	23	1		1	MYO10	5	16682062	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	8262	16682062	164233198	1157	4058											
MYO10	4651	hgsc.bcm.edu	37	chr5	16701717	16701717	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctgcacgcttcctcctccagCctgcggagctcctggtcccg	3	9	10	19	3	0	0	0	0	0	0	5	1	5	1	6	2	4	3	6	2	0	1	rs149110	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:16701717C>T	ENST00000513610.1	-	25	3241	c.2787G>A	c.(2785-2787)agG>agA	p.R929R	MYO10_ENST00000515803.1_Silent_p.R268R|MYO10_ENST00000427430.2_Silent_p.R286R|MYO10_ENST00000512061.1_5'Flank|MYO10_ENST00000505695.1_Silent_p.R268R|MYO10_ENST00000274203.9_Silent_p.R286R	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	929	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						CCTCCTCCAGCCTGCGGAGCT	0.637													C|||	327	0.0652955	0.2277	0.0288	5008	,	,		13912	0.0		0.006	False		,,,				2504	0.0				p.R929R		Atlas-SNP	.											.	MYO10	198	.	0			c.G2787A						PASS	.	C		850,3468		77,696,1386	24	29	27		2787	3.2	0.9	5	dbSNP_79	27	49,8505		1,47,4229	no	coding-synonymous	MYO10	NM_012334.2		78,743,5615	TT,TC,CC		0.5728,19.685,6.9842		929/2059	16701717	899,11973	2159	4277	6436	SO:0001819	synonymous_variant	4651	exon25			CTCCAGCCTGCGG	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.2787G>A	5.37:g.16701717C>T		90	0	0		93	46	0.494624	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	37	CCDS54834.1																																																																																			C|0.928;T|0.072	0.072	strong		0.637	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		T	16701717	C	T	16701717	2	4	22	1	0	0	0	0	0	0	0	1	10071	738	26	2		2	MYO10	5	16701717	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	19655	16701717	164213543	1158	4059											
MYO10	4651	hgsc.bcm.edu	37	chr5	16754991	16754991	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaaggattagaggagcttagCgttgccattaaggaatgcag	14	9	13	5	1	0	1	0	0	0	1	0	4	0	4	1	3	4	3	1	3	5	4	rs61736777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:16754991C>T	ENST00000513610.1	-	19	2329	c.1875G>A	c.(1873-1875)acG>acA	p.T625T		NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	625	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						AGGAGCTTAGCGTTGCCATTA	0.398													C|||	153	0.0305511	0.1112	0.0072	5008	,	,		15693	0.0		0.001	False		,,,				2504	0.0				p.T625T		Atlas-SNP	.											.	MYO10	198	.	0			c.G1875A						PASS	.	C		322,3610		11,300,1655	69	66	67		1875	-11.5	0	5	dbSNP_129	67	4,8360		0,4,4178	no	coding-synonymous	MYO10	NM_012334.2		11,304,5833	TT,TC,CC		0.0478,8.1892,2.6513		625/2059	16754991	326,11970	1966	4182	6148	SO:0001819	synonymous_variant	4651	exon19			GCTTAGCGTTGCC	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.1875G>A	5.37:g.16754991C>T		71	0	0		78	33	0.423077	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	37	CCDS54834.1																																																																																			C|0.973;T|0.027	0.027	strong		0.398	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		T	16754991	C	T	16754991	2	4	22	1	0	0	0	0	0	0	0	1	10071	755	27	1		1	MYO10	5	16754991	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	53274	16754991	164160269	1159	4060											
RNASEN	29102	hgsc.bcm.edu	37	chr5	31526531	31526531	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agttgtggtgagaatagcccGgagggtactgataattaacc	12	10	13	6	1	0	2	0	2	0	1	0	4	0	3	2	3	3	2	2	3	5	5	rs77034974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:31526531G>A	ENST00000511367.2	-	4	753	c.509C>T	c.(508-510)cCg>cTg	p.P170L	DROSHA_ENST00000513349.1_Missense_Mutation_p.P170L|DROSHA_ENST00000442743.1_Missense_Mutation_p.P170L|DROSHA_ENST00000504361.1_5'Flank|DROSHA_ENST00000344624.3_Missense_Mutation_p.P170L	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	170	Pro-rich.			YQYPPGYSH -> RERERTSLE (in Ref. 4; CAB45133). {ECO:0000305}.	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						AGAATAGCCCGGAGGGTACTG	0.532													G|||	179	0.0357428	0.1293	0.0115	5008	,	,		13508	0.0		0.0	False		,,,				2504	0.0				p.P170L		Atlas-SNP	.											.	DROSHA	130	.	0			c.C509T						PASS	.	G	LEU/PRO,LEU/PRO	443,3287		29,385,1451	47	47	47		509,509	5.1	0.2	5	dbSNP_131	47	2,8200		0,2,4099	yes	missense,missense	DROSHA	NM_001100412.1,NM_013235.4	98,98	29,387,5550	AA,AG,GG		0.0244,11.8767,3.7295	possibly-damaging,possibly-damaging	170/1338,170/1375	31526531	445,11487	1865	4101	5966	SO:0001583	missense	29102	exon4			TAGCCCGGAGGGT	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.509C>T	5.37:g.31526531G>A	ENSP00000425979:p.Pro170Leu	200	0	0		228	103	0.451754	NM_013235	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Missense_Mutation	SNP	ENST00000511367.2	37	CCDS47195.1	55	0.025183150183150184	51	0.10365853658536585	4	0.011049723756906077	0	0.0	0	0.0	G	10.57	1.386208	0.25031	0.118767	2.44E-4	ENSG00000113360	ENST00000511367;ENST00000344624;ENST00000442743;ENST00000513349;ENST00000265075;ENST00000382188;ENST00000507438	T;T;T;T;T	0.41400	1.56;1.56;1.0;1.0;1.02	5.12	5.12	0.69794	.	0.173463	0.48767	D	0.000168	T	0.00384	0.0012	N	0.14661	0.345	0.22989	N	0.998465	B;B;B	0.28760	0.221;0.033;0.081	B;B;B	0.16722	0.016;0.007;0.007	T	0.00466	-1.1722	10	0.26408	T	0.33	-10.9681	18.5802	0.91168	0.0:0.0:1.0:0.0	.	170;170;170	Q9NRR4-2;E7EMP9;Q9NRR4	.;.;RNC_HUMAN	L	170;170;170;170;163;163;170	ENSP00000425979:P170L;ENSP00000339845:P170L;ENSP00000409335:P170L;ENSP00000424161:P170L;ENSP00000430921:P170L	ENSP00000265075:P163L	P	-	2	0	DROSHA	31562288	0.989000	0.36119	0.199000	0.23439	0.255000	0.26057	4.682000	0.61671	2.366000	0.80165	0.655000	0.94253	CCG	G|0.974;A|0.026	0.026	strong		0.532	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235		A	31526531	G	A	31526531	3	1	22	1	0	0	0	0	1	0	0	0	13432	1116	39	1	3743	1	RNASEN	5	31526531	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	14771540	31526531	149388729	1160	4061											
PDZD2	23037	hgsc.bcm.edu	37	chr5	32077653	32077653	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgtcccatctggatgccaGccacctcacagagaacctgc	9	8	8	16	0	3	1	1	0	2	1	4	3	4	2	5	1	4	0	5	1	1	0	rs61745726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:32077653G>A	ENST00000438447.1	+	19	4011	c.3623G>A	c.(3622-3624)aGc>aAc	p.S1208N	PDZD2_ENST00000282493.3_Missense_Mutation_p.S1208N			O15018	PDZD2_HUMAN	PDZ domain containing 2	1208					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						CTGGATGCCAGCCACCTCACA	0.498													G|||	454	0.090655	0.3298	0.0231	5008	,	,		18720	0.0		0.002	False		,,,				2504	0.0				p.S1208N		Atlas-SNP	.											.	PDZD2	306	.	0			c.G3623A						PASS	.	G	ASN/SER	1252,3154	430.6+/-342.6	174,904,1125	105	101	102		3623	4.1	0	5	dbSNP_129	102	4,8596	3.7+/-12.6	0,4,4296	yes	missense	PDZD2	NM_178140.2	46	174,908,5421	AA,AG,GG		0.0465,28.4158,9.6571	benign	1208/2840	32077653	1256,11750	2203	4300	6503	SO:0001583	missense	23037	exon18			ATGCCAGCCACCT	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.3623G>A	5.37:g.32077653G>A	ENSP00000402033:p.Ser1208Asn	106	0	0		121	121	1	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	178	0.0815018315018315	172	0.34959349593495936	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	G	5.804	0.332658	0.10956	0.284158	4.65E-4	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.06449	3.3;3.3	4.98	4.08	0.47627	.	0.800186	0.10630	N	0.652231	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B;B	0.24823	0.112;0.063	B;B	0.22386	0.026;0.039	T	0.41161	-0.9524	9	0.10636	T	0.68	.	10.343	0.43891	0.1022:0.0:0.8977:0.0	rs61745726	1034;1208	B4E3P2;O15018	.;PDZD2_HUMAN	N	1208;1013;1208	ENSP00000402033:S1208N;ENSP00000282493:S1208N	ENSP00000282493:S1208N	S	+	2	0	PDZD2	32113410	0.543000	0.26434	0.014000	0.15608	0.054000	0.15201	3.444000	0.52914	1.049000	0.40321	0.563000	0.77884	AGC	G|0.913;A|0.087	0.087	strong		0.498	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			A	32077653	G	A	32077653	3	1	22	1	0	0	0	0	1	0	0	0	11710	971	34	2	3693	2	PDZD2	5	32077653	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	551122	32077653	148837607	1161	4062											
PDZD2	23037	hgsc.bcm.edu	37	chr5	32087828	32087828	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtagagagagccctgtgaCggacattgacagcttcatca	12	8	12	9	1	2	4	2	2	0	2	2	7	2	5	1	1	2	2	1	1	1	3	rs36097367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:32087828C>T	ENST00000438447.1	+	20	4662	c.4274C>T	c.(4273-4275)aCg>aTg	p.T1425M	PDZD2_ENST00000282493.3_Missense_Mutation_p.T1425M			O15018	PDZD2_HUMAN	PDZ domain containing 2	1425			T -> M (in dbSNP:rs36097367).		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						AGCCCTGTGACGGACATTGAC	0.607													C|||	183	0.0365415	0.1346	0.0058	5008	,	,		18447	0.0		0.001	False		,,,				2504	0.0				p.T1425M		Atlas-SNP	.											PDZD2,NS,carcinoma,-1,1	PDZD2	306	1	0			c.C4274T						PASS	.	C	MET/THR	527,3879	232.0+/-245.7	27,473,1703	40	41	41		4274	4.7	0.8	5	dbSNP_126	41	5,8595	4.3+/-15.6	0,5,4295	yes	missense	PDZD2	NM_178140.2	81	27,478,5998	TT,TC,CC		0.0581,11.961,4.0904	probably-damaging	1425/2840	32087828	532,12474	2203	4300	6503	SO:0001583	missense	23037	exon19			CTGTGACGGACAT	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.4274C>T	5.37:g.32087828C>T	ENSP00000402033:p.Thr1425Met	95	0	0		149	89	0.597315	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	50	0.022893772893772892	48	0.0975609756097561	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	17.75	3.467294	0.63625	0.11961	5.81E-4	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.09723	2.95;2.95	5.55	4.67	0.58626	.	0.000000	0.45867	D	0.000323	T	0.00384	0.0012	L	0.59436	1.845	0.38283	D	0.942477	D	0.89917	1.0	D	0.71656	0.974	T	0.00203	-1.1924	10	0.87932	D	0	.	13.494	0.61414	0.1575:0.8425:0.0:0.0	rs36097367	1425	O15018	PDZD2_HUMAN	M	1425;1226;1425	ENSP00000402033:T1425M;ENSP00000282493:T1425M	ENSP00000282493:T1425M	T	+	2	0	PDZD2	32123585	0.993000	0.37304	0.800000	0.32199	0.624000	0.37722	3.702000	0.54800	1.331000	0.45412	0.655000	0.94253	ACG	C|0.961;T|0.039	0.039	strong		0.607	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			T	32087828	C	T	32087828	3	4	22	1	0	0	0	0	1	0	0	0	11710	536	19	1	4348	1	PDZD2	5	32087828	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	10175	32087828	148827432	1162	4063											
PDZD2	23037	hgsc.bcm.edu	37	chr5	32093079	32093079	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgttttatcgtcagtgggAtcgaaatctaccatcctaac	10	14	7	10	2	3	0	1	0	2	0	6	2	4	1	2	1	2	1	2	1	4	4	rs16889443	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:32093079A>G	ENST00000438447.1	+	21	8182	c.7794A>G	c.(7792-7794)ggA>ggG	p.G2598G	PDZD2_ENST00000282493.3_Silent_p.G2598G			O15018	PDZD2_HUMAN	PDZ domain containing 2	2598					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						CGTCAGTGGGATCGAAATCTA	0.408													G|||	425	0.0848642	0.3064	0.0259	5008	,	,		18742	0.0		0.002	False		,,,				2504	0.0				p.G2598G		Atlas-SNP	.											.	PDZD2	306	.	0			c.A7794G						PASS	.	G		925,3481	737.3+/-410.9	104,717,1382	83	84	84		7794	1.9	0.1	5	dbSNP_123	84	6,8594	818.6+/-406.8	0,6,4294	no	coding-synonymous	PDZD2	NM_178140.2		104,723,5676	GG,GA,AA		0.0698,20.9941,7.1582		2598/2840	32093079	931,12075	2203	4300	6503	SO:0001819	synonymous_variant	23037	exon20			AGTGGGATCGAAA	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.7794A>G	5.37:g.32093079A>G		144	0	0		194	100	0.515464	NM_178140	Q9BXD4	Silent	SNP	ENST00000438447.1	37	CCDS34137.1																																																																																			A|0.932;G|0.068	0.068	strong		0.408	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1			G	32093079	A	G	32093079	2	3	22	1	0	0	0	0	0	0	0	1	11710	320	12	3		3	PDZD2	5	32093079	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	5251	32093079	148822181	1163	4064											
GOLPH3	64083	hgsc.bcm.edu	37	chr5	32126441	32126441	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagccaaatcatactgctcGtccagaagaggagcaaaagc	15	6	10	10	1	1	2	1	0	0	2	3	3	2	3	2	1	5	3	2	1	6	2	rs34212503	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:32126441G>A	ENST00000265070.6	-	4	1089	c.774C>T	c.(772-774)gaC>gaT	p.D258D	GOLPH3_ENST00000512668.1_5'Flank	NM_022130.3	NP_071413.1	Q9H4A6	GOLP3_HUMAN	golgi phosphoprotein 3 (coat-protein)	258					cell adhesion molecule production (GO:0060352)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|gene expression (GO:0010467)|glycoprotein biosynthetic process (GO:0009101)|Golgi organization (GO:0007030)|Golgi to plasma membrane protein transport (GO:0043001)|Golgi vesicle budding (GO:0048194)|lamellipodium assembly (GO:0030032)|leukocyte tethering or rolling (GO:0050901)|positive regulation of protein secretion (GO:0050714)|positive regulation of TOR signaling (GO:0032008)|protein retention in Golgi apparatus (GO:0045053)|protein secretion (GO:0009306)|regulation of mitochondrion organization (GO:0010821)	cytosol (GO:0005829)|endosome (GO:0005768)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	enzyme binding (GO:0019899)|phosphatidylinositol-4-phosphate binding (GO:0070273)			kidney(2)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	11						CATACTGCTCGTCCAGAAGAG	0.557													G|||	219	0.04373	0.1604	0.0072	5008	,	,		19268	0.0		0.002	False		,,,				2504	0.0				p.D258D		Atlas-SNP	.											.	GOLPH3	25	.	0			c.C774T						PASS	.	G		495,3911	231.7+/-245.5	32,431,1740	103	86	92		774	-7.3	0.7	5	dbSNP_126	92	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	GOLPH3	NM_022130.3		32,439,6032	AA,AG,GG		0.093,11.2347,3.8674		258/299	32126441	503,12503	2203	4300	6503	SO:0001819	synonymous_variant	64083	exon4			CTGCTCGTCCAGA	AK075156	CCDS3896.1	5p13.2	2008-07-18			ENSG00000113384	ENSG00000113384			15452	protein-coding gene	gene with protein product	"golgi peripheral membrane protein 1, 34 kDa", "golgi protein", "coat-protein", "golgi-associated protein"	612207				11042173, 16263763	Standard	NM_022130		Approved	GPP34, GOPP1, MIDAS	uc003jhp.1	Q9H4A6	OTTHUMG00000090679	ENST00000265070.6:c.774C>T	5.37:g.32126441G>A		136	0	0		141	65	0.460993	NM_022130	Q9UIW5	Silent	SNP	ENST00000265070.6	37	CCDS3896.1																																																																																			G|0.966;A|0.034	0.034	strong		0.557	GOLPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207363.2	NM_022130		A	32126441	G	A	32126441	2	1	22	1	0	0	0	0	0	0	0	1	6576	1136	40	1		1	GOLPH3	5	32126441	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	33362	32126441	148788819	1164	4065											
NPR3	4883	hgsc.bcm.edu	37	chr5	32712119	32712119	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggccggccatcgagtatgcTctgcgcagcgtggagggcaa	7	6	16	12	5	1	0	0	0	1	0	2	2	1	1	2	4	3	4	2	4	2	1	rs6859964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:32712119T>C	ENST00000265074.8	+	1	580	c.237T>C	c.(235-237)gcT>gcC	p.A79A	NPR3_ENST00000415685.2_Intron|NPR3_ENST00000434067.2_Intron|NPR3_ENST00000415167.2_Silent_p.A79A	NM_000908.3|NM_001204375.1	NP_000899.1|NP_001191304.1	P17342	ANPRC_HUMAN	natriuretic peptide receptor 3	79					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)	TCGAGTATGCTCTGCGCAGCG	0.642													T|||	226	0.0451278	0.1679	0.0043	5008	,	,		14376	0.0		0.001	False		,,,				2504	0.0				p.A79A		Atlas-SNP	.											.	NPR3	65	.	0			c.T237C						PASS	.	T	,,	522,3402		36,450,1476	25	30	28		237,237,	1.2	1	5	dbSNP_116	28	2,8314		0,2,4156	no	coding-synonymous,coding-synonymous,intron	NPR3	NM_000908.3,NM_001204375.1,NM_001204376.1	,,	36,452,5632	CC,CT,TT		0.0241,13.3028,4.281	,,	79/541,79/542,	32712119	524,11716	1962	4158	6120	SO:0001819	synonymous_variant	4883	exon1			GTATGCTCTGCGC		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.237T>C	5.37:g.32712119T>C		99	0	0		124	61	0.491935	NM_000908	A2RRD1|B4DT84|E7EPG9	Silent	SNP	ENST00000265074.8	37	CCDS56357.1																																																																																			T|0.956;C|0.044	0.044	strong		0.642	NPR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317550.3	NM_000908		C	32712119	T	C	32712119	2	2	22	1	0	0	0	0	0	0	0	1	10605	1538	54	3		3	NPR3	5	32712119	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	585678	32712119	148203141	1165	4066											
ADAMTS12	81792	hgsc.bcm.edu	37	chr5	33881385	33881385	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gctattggaaagaaatccttGattgaccgtcaagttaaaaa	16	11	8	6	1	1	3	1	2	0	1	2	4	2	4	2	1	0	2	2	1	7	5	rs16891862	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:33881385G>C	ENST00000504830.1	-	2	663	c.328C>G	c.(328-330)Caa>Gaa	p.Q110E	ADAMTS12_ENST00000515401.1_Missense_Mutation_p.Q110E|ADAMTS12_ENST00000352040.3_Missense_Mutation_p.Q110E	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	110			Q -> E (in dbSNP:rs16891862).		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						AGAAATCCTTGATTGACCGTC	0.478										HNSCC(64;0.19)			G|||	63	0.0125799	0.0446	0.0058	5008	,	,		20577	0.0		0.0	False		,,,				2504	0.0				p.Q110E		Atlas-SNP	.											.	ADAMTS12	464	.	0			c.C328G						PASS	.	G	GLU/GLN	137,4269	97.1+/-135.8	5,127,2071	118	113	115		328	2.2	0	5	dbSNP_123	115	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ADAMTS12	NM_030955.2	29	5,128,6370	CC,CG,GG		0.0116,3.1094,1.061	benign	110/1595	33881385	138,12868	2203	4300	6503	SO:0001583	missense	81792	exon2			ATCCTTGATTGAC	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.328C>G	5.37:g.33881385G>C	ENSP00000422554:p.Gln110Glu	130	0	0		164	72	0.439024	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	15	0.006868131868131868	12	0.024390243902439025	3	0.008287292817679558	0	0.0	0	0.0	G	5.178	0.218364	0.09810	0.031094	1.16E-4	ENSG00000151388	ENST00000504830;ENST00000352040;ENST00000515401	T;T;T	0.05513	3.43;3.43;3.43	5.65	2.19	0.27852	Peptidase M12B, propeptide (1);	1.682860	0.03218	N	0.177161	T	0.01940	0.0061	L	0.42245	1.32	0.09310	N	1	B;B;B	0.21309	0.0;0.054;0.001	B;B;B	0.19666	0.001;0.026;0.02	T	0.42666	-0.9438	10	0.16420	T	0.52	.	2.8766	0.05632	0.1002:0.3354:0.3077:0.2567	rs16891862;rs52818503;rs16891862	110;110;110	P58397-3;D6REX0;P58397	.;.;ATS12_HUMAN	E	110	ENSP00000422554:Q110E;ENSP00000344847:Q110E;ENSP00000421638:Q110E	ENSP00000344847:Q110E	Q	-	1	0	ADAMTS12	33917142	0.018000	0.18449	0.001000	0.08648	0.807000	0.45602	0.455000	0.21843	0.100000	0.17581	0.467000	0.42956	CAA	C|0.011;G|0.989	0.011	strong		0.478	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		C	33881385	G	C	33881385	3	2	22	1	0	0	0	0	1	0	0	0	257	1299	45	4	4548	4	ADAMTS12	5	33881385	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1169266	33881385	147033875	1166	4067											
RXFP3	51289	hgsc.bcm.edu	37	chr5	33937215	33937215	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaacctcttcgtcaccaacCtggcgctgacggactttcag	8	10	8	15	3	4	1	3	1	1	0	5	2	4	2	3	2	2	1	3	2	2	2	rs78710898	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:33937215C>T	ENST00000330120.3	+	1	725	c.370C>T	c.(370-372)Ctg>Ttg	p.L124L		NM_016568.3	NP_057652.1	Q9NSD7	RL3R1_HUMAN	relaxin/insulin-like family peptide receptor 3	124					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						CGTCACCAACCTGGCGCTGAC	0.582													C|||	66	0.0131789	0.0469	0.0058	5008	,	,		19766	0.0		0.0	False		,,,				2504	0.0				p.L124L		Atlas-SNP	.											.	RXFP3	114	.	0			c.C370T						PASS	.	C		146,4260	101.2+/-139.8	5,136,2062	137	126	129		370	4.8	1	5	dbSNP_132	129	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RXFP3	NM_016568.3		5,137,6361	TT,TC,CC		0.0116,3.3137,1.1302		124/470	33937215	147,12859	2203	4300	6503	SO:0001819	synonymous_variant	51289	exon1			ACCAACCTGGCGC	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.370C>T	5.37:g.33937215C>T		111	0	0		139	76	0.546763	NM_016568	Q14DA5	Silent	SNP	ENST00000330120.3	37	CCDS3900.1																																																																																			C|0.989;T|0.011	0.011	strong		0.582	RXFP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207369.1	NM_016568		T	33937215	C	T	33937215	2	4	22	1	0	0	0	0	0	0	0	1	13776	680	24	2		2	RXFP3	5	33937215	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	55830	33937215	146978045	1167	4068											
RAI14	26064	hgsc.bcm.edu	37	chr5	34687817	34687817	+	Intron	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attaatggaagggaattagaTggaagccaaggtatgtcact	15	10	12	4	0	1	1	1	0	0	1	1	4	1	4	1	4	1	1	1	4	7	3	rs10521016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:34687817T>C	ENST00000265109.3	+	2	323				RAI14_ENST00000512629.1_Intron|RAI14_ENST00000503673.1_Intron|RAI14_ENST00000515799.1_Intron|RAI14_ENST00000506376.1_Start_Codon_SNP_p.M1T|RAI14_ENST00000428746.2_Intron	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14							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)					GGGAATTAGATGGAAGCCAAG	0.413													T|||	143	0.0285543	0.1044	0.0072	5008	,	,		19536	0.0		0.0	False		,,,				2504	0.0				p.M1T		Atlas-SNP	.											.	RAI14	100	.	0			c.T2C						PASS	.						187	157	166					5																	34687817		692	1591	2283	SO:0001627	intron_variant	26064	exon1			ATTAGATGGAAGC	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.36+757T>C	5.37:g.34687817T>C		150	0	0		181	180	0.994475	NM_001145523	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Missense_Mutation	SNP	ENST00000265109.3	37	CCDS34142.1	67	0.030677655677655676	65	0.13211382113821138	2	0.0055248618784530384	0	0.0	0	0.0	T	7.737	0.700548	0.15106	.	.	ENSG00000039560	ENST00000506376	T	0.33654	1.4	5.19	-0.0796	0.13710	.	.	.	.	.	T	0.00210	0.0006	.	.	.	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.21518	-1.0243	8	0.56958	D	0.05	.	0.6567	0.00835	0.1705:0.1874:0.1658:0.4763	rs10521016;rs56487933;rs10521016	1	Q9P0K7-3	.	T	1	ENSP00000423854:M1T	ENSP00000423854:M1T	M	+	2	0	RAI14	34723574	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.023000	0.12456	-0.143000	0.11334	-1.087000	0.02190	ATG	T|0.955;C|0.045	0.045	strong		0.413	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577		C	34687817	T	C	34687817	1	2	22	0	1	0	0	0	0	0	0	0	13023	1464	51	3		3	RAI14	5	34687817	Intron	SNP	T	TCGA-G8-6324-01A-11D-2210-10	750602	34687817	146227443	1168	4069											
RAI14	26064	hgsc.bcm.edu	37	chr5	34814745	34814745	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccactatcgggaaaggaaTcggtattttttgctgaacca	11	12	9	9	2	0	1	0	1	0	0	3	3	1	3	2	3	2	2	2	3	5	5	rs150350937		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:34814745T>C	ENST00000265109.3	+	12	1197	c.910T>C	c.(910-912)Tcg>Ccg	p.S304P	RAI14_ENST00000512629.1_Missense_Mutation_p.S275P|RAI14_ENST00000503673.1_Missense_Mutation_p.S304P|RAI14_ENST00000397449.1_Missense_Mutation_p.S297P|RAI14_ENST00000515799.1_Missense_Mutation_p.S307P|RAI14_ENST00000506376.1_Missense_Mutation_p.S296P|RAI14_ENST00000428746.2_Missense_Mutation_p.S304P	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	304						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)					GGGAAAGGAATCGGTATTTTT	0.318																																					p.S307P		Atlas-SNP	.											RAI14,scalp,malignant_melanoma,-1,1	RAI14	100	1	0			c.T919C						PASS	.	T	PRO/SER,PRO/SER,PRO/SER,PRO/SER,PRO/SER,PRO/SER	8,4398	12.9+/-30.5	0,8,2195	174	155	162		910,910,823,886,919,910	3.4	1	5	dbSNP_134	162	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense	RAI14	NM_001145520.1,NM_001145521.1,NM_001145522.1,NM_001145523.1,NM_001145525.1,NM_015577.2	74,74,74,74,74,74	0,8,6495	CC,CT,TT		0.0,0.1816,0.0615	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	304/981,304/981,275/952,296/973,307/984,304/981	34814745	8,12998	2203	4300	6503	SO:0001583	missense	26064	exon14			AAGGAATCGGTAT	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.910T>C	5.37:g.34814745T>C	ENSP00000265109:p.Ser304Pro	318	0	0		291	150	0.515464	NM_001145525	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Missense_Mutation	SNP	ENST00000265109.3	37	CCDS34142.1	.	.	.	.	.	.	.	.	.	.	T	12.81	2.050617	0.36181	0.001816	0.0	ENSG00000039560	ENST00000265109;ENST00000512629;ENST00000428746;ENST00000503673;ENST00000515799;ENST00000506376;ENST00000397449	T;T;T;T;T;T;T	0.38077	1.21;1.16;1.21;1.21;1.22;1.26;1.25	5.86	3.44	0.39384	.	.	.	.	.	T	0.20007	0.0481	N	0.14661	0.345	0.27353	N	0.956195	B;B;B;B	0.09022	0.001;0.001;0.002;0.001	B;B;B;B	0.09377	0.004;0.001;0.004;0.001	T	0.14309	-1.0477	9	0.31617	T	0.26	-4.3706	6.5518	0.22438	0.0:0.3208:0.0:0.6792	.	296;275;307;304	Q9P0K7-3;E9PED3;Q9P0K7-2;Q9P0K7	.;.;.;RAI14_HUMAN	P	304;275;304;304;307;296;297	ENSP00000265109:S304P;ENSP00000422377:S275P;ENSP00000388725:S304P;ENSP00000422942:S304P;ENSP00000427123:S307P;ENSP00000423854:S296P;ENSP00000380591:S297P	ENSP00000265109:S304P	S	+	1	0	RAI14	34850502	0.963000	0.33076	0.987000	0.45799	0.933000	0.57130	0.571000	0.23669	1.139000	0.42245	0.528000	0.53228	TCG	T|1.000;C|0.000	0.000	weak		0.318	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577		C	34814745	T	C	34814745	3	2	22	1	0	0	0	0	1	0	0	0	13023	1435	50	3	1017	3	RAI14	5	34814745	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	126928	34814745	146100515	1169	4070											
DNAJC21	134218	hgsc.bcm.edu	37	chr5	34937649	34937649	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agagataaaagagtgcaggcGcatcgaaaacttgtggaaga	17	6	13	5	2	0	3	0	0	0	3	1	6	0	4	0	2	2	2	0	2	5	2	rs77480286	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:34937649G>A	ENST00000342382.4	+	5	884	c.657G>A	c.(655-657)gcG>gcA	p.A219A	DNAJC21_ENST00000382021.2_Silent_p.A219A|DNAJC21_ENST00000303525.7_Silent_p.A219A			Q5F1R6	DJC21_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 21	219					protein folding (GO:0006457)	ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.A219A(1)		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)			GAGTGCAGGCGCATCGAAAAC	0.478													G|||	41	0.0081869	0.0303	0.0014	5008	,	,		18843	0.0		0.0	False		,,,				2504	0.0				p.A219A		Atlas-SNP	.											DNAJC21,caecum,carcinoma,0,1	DNAJC21	54	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G657A						PASS	.	G	,	68,4338	61.1+/-98.1	1,66,2136	77	85	82		657,657	-11.1	0	5	dbSNP_132	82	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	DNAJC21	NM_001012339.2,NM_194283.3	,	1,68,6434	AA,AG,GG		0.0233,1.5433,0.5382	,	219/532,219/577	34937649	70,12936	2203	4300	6503	SO:0001819	synonymous_variant	134218	exon5			GCAGGCGCATCGA		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.657G>A	5.37:g.34937649G>A		257	1	0.00389105		228	108	0.473684	NM_001012339	Q3B7J9|Q6P086|Q6ZS43|Q86VC6	Silent	SNP	ENST00000342382.4	37	CCDS34144.1																																																																																			G|0.992;A|0.008	0.008	strong		0.478	DNAJC21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157337.1	NM_194283		A	34937649	G	A	34937649	2	1	22	1	0	0	0	0	0	0	0	1	4642	1074	38	1		1	DNAJC21	5	34937649	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	122904	34937649	145977611	1170	4071											
SPEF2	79925	hgsc.bcm.edu	37	chr5	35694454	35694454	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attaccagaaacagaaggtgAaacaatgcttagtaagatct	18	9	8	6	0	1	4	0	1	1	3	1	4	1	4	1	1	4	2	1	1	7	3	rs12332369	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:35694454A>G	ENST00000356031.3	+	13	2118	c.1964A>G	c.(1963-1965)gAa>gGa	p.E655G	SPEF2_ENST00000509059.1_Intron|SPEF2_ENST00000440995.2_Intron|CTD-2113L7.1_ENST00000510433.1_RNA	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	655			E -> G (in dbSNP:rs12332369).		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)			ACAGAAGGTGAAACAATGCTT	0.368													A|||	114	0.0227636	0.0832	0.0058	5008	,	,		17502	0.0		0.0	False		,,,				2504	0.0				p.E655G		Atlas-SNP	.											.	SPEF2	324	.	0			c.A1964G						PASS	.	A	GLY/GLU	258,3442		10,238,1602	93	86	88		1964	3.7	0.9	5	dbSNP_120	88	1,8215		0,1,4107	yes	missense	SPEF2	NM_024867.3	98	10,239,5709	GG,GA,AA		0.0122,6.973,2.1735	benign	655/1823	35694454	259,11657	1850	4108	5958	SO:0001583	missense	79925	exon13			AAGGTGAAACAAT	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.1964A>G	5.37:g.35694454A>G	ENSP00000348314:p.Glu655Gly	166	0	0		180	89	0.494444	NM_024867	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Missense_Mutation	SNP	ENST00000356031.3	37	CCDS43309.1	39	0.017857142857142856	37	0.07520325203252033	2	0.0055248618784530384	0	0.0	0	0.0	A	11.23	1.576102	0.28092	0.06973	1.22E-4	ENSG00000152582	ENST00000356031	T	0.06449	3.3	3.74	3.74	0.42951	.	0.984296	0.08306	N	0.966202	T	0.00300	0.0009	N	0.22421	0.69	0.80722	D	1	B	0.16166	0.016	B	0.09377	0.004	T	0.46965	-0.9153	10	0.33940	T	0.23	.	9.1268	0.36821	1.0:0.0:0.0:0.0	rs12332369;rs52800439;rs12332369	655	Q9C093	SPEF2_HUMAN	G	655	ENSP00000348314:E655G	ENSP00000348314:E655G	E	+	2	0	SPEF2	35730211	0.746000	0.28272	0.862000	0.33874	0.140000	0.21249	2.047000	0.41269	1.941000	0.56285	0.260000	0.18958	GAA	A|0.973;G|0.027	0.027	strong		0.368	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722		G	35694454	A	G	35694454	3	3	22	1	0	0	0	0	1	0	0	0	15050	246	9	3	2035	3	SPEF2	5	35694454	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	756805	35694454	145220806	1171	4072											
UGT3A1	133688	hgsc.bcm.edu	37	chr5	35957462	35957462	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatgggtgttcaacatggaGccaaaggccacaaggacaaa	15	6	12	8	0	1	1	1	1	0	0	1	3	1	3	2	4	2	1	2	4	4	1	rs10428673	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:35957462G>A	ENST00000274278.3	-	5	1260	c.903C>T	c.(901-903)ggC>ggT	p.G301G	UGT3A1_ENST00000513233.1_5'UTR|UGT3A1_ENST00000507113.1_Silent_p.G267G|UGT3A1_ENST00000503189.1_Silent_p.G301G	NM_152404.3	NP_689617.3	Q6NUS8	UD3A1_HUMAN	UDP glycosyltransferase 3 family, polypeptide A1	301						integral component of membrane (GO:0016021)|UDP-N-acetylglucosamine transferase complex (GO:0043541)	glucuronosyltransferase activity (GO:0015020)|UDP-glycosyltransferase activity (GO:0008194)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|skin(4)	46	all_lung(31;0.000197)		Epithelial(62;0.107)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TCAACATGGAGCCAAAGGCCA	0.488													G|||	40	0.00798722	0.028	0.0043	5008	,	,		20323	0.0		0.0	False		,,,				2504	0.0				p.G301G		Atlas-SNP	.											.	UGT3A1	95	.	0			c.C903T						PASS	.	G		109,4297		1,107,2095	104	90	95		903	1.4	1	5	dbSNP_119	95	2,8598		0,2,4298	no	coding-synonymous	UGT3A1	NM_152404.3		1,109,6393	AA,AG,GG		0.0233,2.4739,0.8535		301/524	35957462	111,12895	2203	4300	6503	SO:0001819	synonymous_variant	133688	exon5			CATGGAGCCAAAG		CCDS3913.1, CCDS54841.1	5p13.2	2014-05-20			ENSG00000145626	ENSG00000145626		"UDP glucuronosyltransferases"	26625	protein-coding gene	gene with protein product							Standard	NM_152404		Approved	FLJ34658	uc003jjv.2	Q6NUS8	OTTHUMG00000131107	ENST00000274278.3:c.903C>T	5.37:g.35957462G>A		110	0	0		135	69	0.511111	NM_152404	G5E961|Q8IYS9|Q8NAW4|Q96DM6	Silent	SNP	ENST00000274278.3	37	CCDS3913.1																																																																																			G|0.991;A|0.009	0.009	strong		0.488	UGT3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253770.2	NM_152404		A	35957462	G	A	35957462	2	1	22	1	0	0	0	0	0	0	0	1	16978	958	34	2		2	UGT3A1	5	35957462	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	263008	35957462	144957798	1172	4073											
UGT3A2	167127	hgsc.bcm.edu	37	chr5	36049324	36049324	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agcccaaattccaaagagccGaatgaagtggaaagaatggc	17	5	11	8	1	0	3	0	1	0	2	1	5	1	4	3	2	2	0	3	2	6	1	rs148290056	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:36049324G>A	ENST00000282507.3	-	4	611	c.510C>T	c.(508-510)ttC>ttT	p.F170F	UGT3A2_ENST00000545528.1_Intron|UGT3A2_ENST00000504954.1_Intron|UGT3A2_ENST00000513300.1_Silent_p.F136F	NM_174914.3	NP_777574.2	Q3SY77	UD3A2_HUMAN	UDP glycosyltransferase 3 family, polypeptide A2	170					cellular response to genistein (GO:0071412)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)|UDP-glycosyltransferase activity (GO:0008194)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	43	all_lung(31;0.000179)		Lung(74;0.111)|Epithelial(62;0.113)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CCAAAGAGCCGAATGAAGTGG	0.453																																					p.F170F		Atlas-SNP	.											.	UGT3A2	117	.	0			c.C510T						PASS	.	G	,	33,4373	39.2+/-71.8	0,33,2170	87	82	84		408,510	-2.3	0	5	dbSNP_134	84	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	UGT3A2	NM_001168316.1,NM_174914.3	,	0,33,6470	AA,AG,GG		0.0,0.749,0.2537	,	136/490,170/524	36049324	33,12973	2203	4300	6503	SO:0001819	synonymous_variant	167127	exon4			AGAGCCGAATGAA		CCDS3914.1, CCDS54842.1	5p13.2	2014-05-20			ENSG00000168671	ENSG00000168671		"UDP glucuronosyltransferases"	27266	protein-coding gene	gene with protein product						12975309	Standard	NM_174914		Approved		uc003jjz.2	Q3SY77	OTTHUMG00000131108	ENST00000282507.3:c.510C>T	5.37:g.36049324G>A		101	0	0		112	46	0.410714	NM_174914	B4DUQ7|E9PFK7|Q6UXC4|Q8NBP2	Silent	SNP	ENST00000282507.3	37	CCDS3914.1																																																																																			G|0.996;A|0.004	0.004	strong		0.453	UGT3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253771.2	NM_174914		A	36049324	G	A	36049324	2	1	22	1	0	0	0	0	0	0	0	1	16979	1049	37	1		1	UGT3A2	5	36049324	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	91862	36049324	144865936	1173	4074											
RANBP3L	202151	hgsc.bcm.edu	37	chr5	36257134	36257134	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gttgggaagagaatgcagcaGctgattcaattagggaagta	14	9	14	4	0	1	2	1	1	0	1	1	5	1	4	0	2	3	5	0	2	6	4	rs16902872	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:36257134G>A	ENST00000296604.3	-	10	1297	c.812C>T	c.(811-813)gCt>gTt	p.A271V	RANBP3L_ENST00000515759.1_Missense_Mutation_p.A271V|RANBP3L_ENST00000502994.1_Missense_Mutation_p.A296V	NM_145000.3	NP_659437.3	Q86VV4	RNB3L_HUMAN	RAN binding protein 3-like	271			A -> V (in dbSNP:rs16902872).		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)			GAATGCAGCAGCTGATTCAAT	0.363													G|||	434	0.0866613	0.3132	0.0245	5008	,	,		15384	0.0		0.003	False		,,,				2504	0.0				p.A296V		Atlas-SNP	.											.	RANBP3L	41	.	0			c.C887T						PASS	.	G	VAL/ALA,VAL/ALA	1170,3236	408.6+/-334.7	146,878,1179	107	99	102		887,812	5.4	1	5	dbSNP_123	102	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	RANBP3L	NM_001161429.1,NM_145000.3	64,64	146,882,5475	AA,AG,GG		0.0465,26.5547,9.0266	probably-damaging,probably-damaging	296/491,271/466	36257134	1174,11832	2203	4300	6503	SO:0001583	missense	202151	exon11			GCAGCAGCTGATT	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.812C>T	5.37:g.36257134G>A	ENSP00000296604:p.Ala271Val	172	0	0		136	75	0.551471	NM_001161429	B7Z866|E9PGP9|Q96LK2	Missense_Mutation	SNP	ENST00000296604.3	37	CCDS3918.1	167	0.07646520146520147	158	0.32113821138211385	7	0.019337016574585635	0	0.0	2	0.002638522427440633	G	29.6	5.023090	0.93462	0.265547	4.65E-4	ENSG00000164188	ENST00000296604;ENST00000502994;ENST00000515759	T;T;T	0.59364	1.43;1.4;0.27	5.41	5.41	0.78517	.	0.000000	0.64402	D	0.000002	T	0.00012	0.0000	M	0.68952	2.095	0.18873	P	0.9999869983	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.00621	-1.1640	9	0.87932	D	0	-18.1197	18.337	0.90291	0.0:0.0:1.0:0.0	rs16902872;rs52805488;rs16902872	296;271	E9PGP9;Q86VV4	.;RNB3L_HUMAN	V	271;296;271	ENSP00000296604:A271V;ENSP00000421853:A296V;ENSP00000421149:A271V	ENSP00000296604:A271V	A	-	2	0	RANBP3L	36292891	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	7.191000	0.77763	2.697000	0.92050	0.591000	0.81541	GCT	G|0.906;A|0.094	0.094	strong		0.363	RANBP3L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253773.2	NM_145000		A	36257134	G	A	36257134	3	1	22	1	0	0	0	0	1	0	0	0	13045	971	34	2	605	2	RANBP3L	5	36257134	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	207810	36257134	144658126	1174	4075											
NIPBL	25836	hgsc.bcm.edu	37	chr5	36985751	36985751	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaccatgataataaacaaaaAtcagatgacaggggtgaatc	19	7	9	6	0	1	4	1	3	0	1	2	5	1	4	1	2	1	0	1	2	6	2	rs293756	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:36985751A>G	ENST00000282516.8	+	10	2968	c.2469A>G	c.(2467-2469)aaA>aaG	p.K823K	NIPBL_ENST00000448238.2_Silent_p.K823K|NIPBL_ENST00000504430.1_3'UTR	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	823					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)			ATAAACAAAAATCAGATGACA	0.443													A|||	183	0.0365415	0.1354	0.0058	5008	,	,		19980	0.0		0.0	False		,,,				2504	0.0				p.K823K		Atlas-SNP	.											.	NIPBL	513	.	0			c.A2469G						PASS	.	A	,	506,3900	231.0+/-245.0	27,452,1724	68	67	67		2469,2469	-0.5	1	5	dbSNP_79	67	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	NIPBL	NM_015384.4,NM_133433.3	,	27,453,6023	GG,GA,AA		0.0116,11.4843,3.8982	,	823/2698,823/2805	36985751	507,12499	2203	4300	6503	SO:0001819	synonymous_variant	25836	exon10			ACAAAAATCAGAT	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.2469A>G	5.37:g.36985751A>G		169	0	0		185	101	0.545946	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Silent	SNP	ENST00000282516.8	37	CCDS3920.1																																																																																			A|0.961;G|0.039	0.039	strong		0.443	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		G	36985751	A	G	36985751	2	3	22	1	0	0	0	0	0	0	0	1	10437	98	4	3		3	NIPBL	5	36985751	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	728617	36985751	143929509	1175	4076											
NIPBL	25836	hgsc.bcm.edu	37	chr5	36986297	36986297	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctaagcctgtagttgtgctAcaaaaactgtctttggatga	11	13	10	7	0	1	1	0	1	1	0	1	2	1	2	1	1	4	4	1	1	5	5	rs1669445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:36986297A>G	ENST00000282516.8	+	10	3514	c.3015A>G	c.(3013-3015)ctA>ctG	p.L1005L	NIPBL_ENST00000448238.2_Silent_p.L1005L|NIPBL_ENST00000504430.1_3'UTR	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	1005					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)			TAGTTGTGCTACAAAAACTGT	0.333													A|||	184	0.0367412	0.1362	0.0058	5008	,	,		17335	0.0		0.0	False		,,,				2504	0.0				p.L1005L		Atlas-SNP	.											.	NIPBL	513	.	0			c.A3015G						PASS	.	A	,	504,3902	228.1+/-243.1	27,450,1726	130	147	141	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3015,3015	1.7	1	5	dbSNP_89	141	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	NIPBL	NM_015384.4,NM_133433.3	,	27,451,6025	GG,GA,AA		0.0116,11.4389,3.8828	,	1005/2698,1005/2805	36986297	505,12501	2203	4300	6503	SO:0001819	synonymous_variant	25836	exon10			TGTGCTACAAAAA	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.3015A>G	5.37:g.36986297A>G		33	0	0		45	22	0.488889	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Silent	SNP	ENST00000282516.8	37	CCDS3920.1																																																																																			A|0.961;G|0.039	0.039	strong		0.333	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		G	36986297	A	G	36986297	2	3	22	1	0	0	0	0	0	0	0	1	10437	378	14	3		3	NIPBL	5	36986297	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	546	36986297	143928963	1176	4077											
C5orf42	65250	hgsc.bcm.edu	37	chr5	37115116	37115116	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttactgctgctttggctcCaccagcttttttctgtatgg	4	18	8	11	0	2	0	0	0	2	0	3	0	3	0	2	2	4	5	2	2	2	6	rs7702892	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37115116C>T	ENST00000508244.1	-	49	9277	c.9184G>A	c.(9184-9186)Gga>Aga	p.G3062R	C5orf42_ENST00000274258.7_Missense_Mutation_p.G1960R|C5orf42_ENST00000425232.2_Missense_Mutation_p.G3062R			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	3062			G -> R (in dbSNP:rs7702892).			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)			GCTTTGGCTCCACCAGCTTTT	0.363													C|||	124	0.0247604	0.0908	0.0058	5008	,	,		18889	0.0		0.0	False		,,,				2504	0.0				p.G3062R		Atlas-SNP	.											C5orf42_ENST00000425232,bladder,carcinoma,+1,2	C5orf42	422	2	0			c.G9184A						PASS	.	C	ARG/GLY	340,4066	175.5+/-204.9	13,314,1876	101	90	93		9184	2	0	5	dbSNP_116	93	2,8598	2.2+/-6.3	0,2,4298	yes	missense	C5orf42	NM_023073.3	125	13,316,6174	TT,TC,CC		0.0233,7.7167,2.6296	benign	3062/3198	37115116	342,12664	2203	4300	6503	SO:0001583	missense	65250	exon50			TGGCTCCACCAGC		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.9184G>A	5.37:g.37115116C>T	ENSP00000421690:p.Gly3062Arg	64	0	0		74	39	0.527027	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	45	0.020604395604395604	43	0.08739837398373984	2	0.0055248618784530384	0	0.0	0	0.0	C	13.98	2.398422	0.42512	0.077167	2.33E-4	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429	T;T;T;T	0.22945	1.94;1.94;1.93;1.93	3.78	1.97	0.26223	.	1.267940	0.05991	U	0.646004	T	0.00608	0.0020	N	0.22421	0.69	0.09310	N	1	B;B	0.12013	0.005;0.005	B;B	0.15052	0.012;0.01	T	0.26224	-1.0109	10	0.25751	T	0.34	.	6.7291	0.23373	0.0:0.7655:0.0:0.2345	rs7702892;rs52808859;rs7702892	3062;1960	E9PH94;Q9H799	.;CE042_HUMAN	R	3062;3062;1960;2128	ENSP00000421690:G3062R;ENSP00000389014:G3062R;ENSP00000274258:G1960R;ENSP00000424223:G2128R	ENSP00000274258:G1960R	G	-	1	0	C5orf42	37150873	0.000000	0.05858	0.013000	0.15412	0.825000	0.46686	0.020000	0.13466	0.353000	0.24079	-0.137000	0.14449	GGA	C|0.970;T|0.030	0.030	strong		0.363	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		T	37115116	C	T	37115116	3	4	22	1	0	0	0	0	1	0	0	0	2303	603	21	2	421	2	C5orf42	5	37115116	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	128819	37115116	143800144	1177	4078											
C5orf42	65250	hgsc.bcm.edu	37	chr5	37158363	37158363	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggtattgagggtgaccaaGgtttctctgacatttcactg	9	13	12	7	0	2	3	1	3	1	0	3	4	2	3	1	3	0	2	1	3	2	4	rs16903518	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37158363G>A	ENST00000508244.1	-	38	7868	c.7775C>T	c.(7774-7776)cCt>cTt	p.P2592L	C5orf42_ENST00000274258.7_Missense_Mutation_p.P1472L|C5orf42_ENST00000425232.2_Missense_Mutation_p.P2592L			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2592			P -> L (in dbSNP:rs16903518).			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)			GGGTGACCAAGGTTTCTCTGA	0.368													G|||	122	0.024361	0.09	0.0043	5008	,	,		17612	0.0		0.0	False		,,,				2504	0.0				p.P2592L		Atlas-SNP	.											.	C5orf42	422	.	0			c.C7775T						PASS	.	G	LEU/PRO	340,4066	177.3+/-206.3	13,314,1876	129	125	127		7775	3	0	5	dbSNP_123	127	2,8598	2.2+/-6.3	0,2,4298	yes	missense	C5orf42	NM_023073.3	98	13,316,6174	AA,AG,GG		0.0233,7.7167,2.6296	benign	2592/3198	37158363	342,12664	2203	4300	6503	SO:0001583	missense	65250	exon39			GACCAAGGTTTCT		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.7775C>T	5.37:g.37158363G>A	ENSP00000421690:p.Pro2592Leu	157	0	0		183	92	0.502732	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	45	0.020604395604395604	43	0.08739837398373984	2	0.0055248618784530384	0	0.0	0	0.0	G	7.667	0.686250	0.14973	0.077167	2.33E-4	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.70631	-0.5;-0.5;1.32;1.35	4.88	3.02	0.34903	.	0.626374	0.14293	N	0.328786	T	0.05410	0.0143	L	0.46157	1.445	0.09310	N	0.999998	B;B	0.06786	0.001;0.001	B;B	0.12156	0.004;0.007	T	0.19257	-1.0311	10	0.62326	D	0.03	.	8.7051	0.34349	0.2574:0.0:0.7426:0.0	rs16903518;rs52830390;rs16903518	2592;1472	E9PH94;Q9H799	.;CE042_HUMAN	L	2592;2592;1472;1640;1472	ENSP00000421690:P2592L;ENSP00000389014:P2592L;ENSP00000274258:P1472L;ENSP00000424223:P1640L	ENSP00000274258:P1472L	P	-	2	0	C5orf42	37194120	0.609000	0.26975	0.007000	0.13788	0.048000	0.14542	1.796000	0.38794	0.704000	0.31869	0.563000	0.77884	CCT	G|0.970;A|0.030	0.030	strong		0.368	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		A	37158363	G	A	37158363	3	1	22	1	0	0	0	0	1	0	0	0	2303	1000	35	2	1874	2	C5orf42	5	37158363	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	43247	37158363	143756897	1178	4079											
C5orf42	65250	hgsc.bcm.edu	37	chr5	37173977	37173977	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttggagcaggtggttgtgaAgcaacattgactccatttga	10	12	13	6	0	0	3	0	3	0	0	1	4	1	4	1	3	3	4	1	3	2	4	rs61746147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37173977A>G	ENST00000508244.1	-	31	6144	c.6051T>C	c.(6049-6051)gcT>gcC	p.A2017A	C5orf42_ENST00000274258.7_Silent_p.A897A|C5orf42_ENST00000425232.2_Silent_p.A2017A			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2017						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)			GTGGTTGTGAAGCAACATTGA	0.418													A|||	122	0.024361	0.09	0.0043	5008	,	,		16616	0.0		0.0	False		,,,				2504	0.0				p.A2017A		Atlas-SNP	.											.	C5orf42	422	.	0			c.T6051C						PASS	.	A		341,4065	178.0+/-206.8	13,315,1875	140	133	135		6051	1.9	0.9	5	dbSNP_129	135	2,8598	2.2+/-6.3	0,2,4298	yes	coding-synonymous	C5orf42	NM_023073.3		13,317,6173	GG,GA,AA		0.0233,7.7394,2.6372		2017/3198	37173977	343,12663	2203	4300	6503	SO:0001819	synonymous_variant	65250	exon32			TTGTGAAGCAACA		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.6051T>C	5.37:g.37173977A>G		85	0	0		90	43	0.477778	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Silent	SNP	ENST00000508244.1	37	CCDS34146.2																																																																																			A|0.974;G|0.026	0.026	strong		0.418	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		G	37173977	A	G	37173977	2	3	22	1	0	0	0	0	0	0	0	1	2303	59	3	3		3	C5orf42	5	37173977	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	15614	37173977	143741283	1179	4080											
C5orf42	65250	hgsc.bcm.edu	37	chr5	37182940	37182940	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgatgtaagaatggcagcTgtagaggtctttacacgaat	14	11	11	5	1	1	3	0	1	1	2	1	4	1	3	0	2	2	4	0	2	6	4	rs73750949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37182940T>A	ENST00000508244.1	-	25	5436	c.5343A>T	c.(5341-5343)acA>acT	p.T1781T	C5orf42_ENST00000274258.7_Silent_p.T662T|C5orf42_ENST00000425232.2_Silent_p.T1781T			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	1781						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)			GAATGGCAGCTGTAGAGGTCT	0.363													T|||	144	0.028754	0.1067	0.0043	5008	,	,		18465	0.0		0.0	False		,,,				2504	0.0				p.T1781T		Atlas-SNP	.											.	C5orf42	422	.	0			c.A5343T						PASS	.	T		416,3990	203.1+/-225.7	20,376,1807	83	77	79		5343	1.2	1	5	dbSNP_130	79	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	C5orf42	NM_023073.3		20,377,6106	AA,AT,TT		0.0116,9.4417,3.2062		1781/3198	37182940	417,12589	2203	4300	6503	SO:0001819	synonymous_variant	65250	exon26			GGCAGCTGTAGAG		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.5343A>T	5.37:g.37182940T>A		79	0	0		78	41	0.525641	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Silent	SNP	ENST00000508244.1	37	CCDS34146.2																																																																																			T|0.973;A|0.027	0.027	strong		0.363	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		A	37182940	T	A	37182940	2	1	22	1	0	0	0	0	0	0	0	1	2303	1567	55	5		5	C5orf42	5	37182940	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	8963	37182940	143732320	1180	4081											
C5orf42	65250	hgsc.bcm.edu	37	chr5	37226888	37226888	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagaatgtaaaaaaaatgAgtgatacaaactactatgta	21	10	7	3	0	0	4	0	3	0	1	0	4	0	4	0	0	3	2	0	0	11	5	rs115435816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37226888A>G	ENST00000508244.1	-	11	1902	c.1809T>C	c.(1807-1809)acT>acC	p.T603T	C5orf42_ENST00000274258.7_5'UTR|C5orf42_ENST00000425232.2_Silent_p.T603T			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	603						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)			AAAAAAAATGAGTGATACAAA	0.284													A|||	92	0.0183706	0.0673	0.0043	5008	,	,		18803	0.0		0.0	False		,,,				2504	0.0				p.T603T		Atlas-SNP	.											.	C5orf42	422	.	0			c.T1809C						PASS	.	A		89,1295		5,79,608	46	38	40		1809	4.1	1	5	dbSNP_132	40	1,3175		0,1,1587	no	coding-synonymous	C5orf42	NM_023073.3		5,80,2195	GG,GA,AA		0.0315,6.4306,1.9737		603/3198	37226888	90,4470	692	1588	2280	SO:0001819	synonymous_variant	65250	exon12			AAAATGAGTGATA		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.1809T>C	5.37:g.37226888A>G		93	0	0		90	51	0.566667	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Silent	SNP	ENST00000508244.1	37	CCDS34146.2																																																																																			A|0.984;G|0.016	0.016	strong		0.284	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		G	37226888	A	G	37226888	2	3	22	1	0	0	0	0	0	0	0	1	2303	291	11	3		3	C5orf42	5	37226888	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	43948	37226888	143688372	1181	4082											
C5orf42	65250	hgsc.bcm.edu	37	chr5	37244669	37244669	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gttatgagcacaattcttttCccatttccagatacatacaa	13	14	4	10	0	1	2	0	1	1	1	3	2	3	2	2	0	3	2	2	0	5	7	rs73750958	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37244669C>T	ENST00000508244.1	-	4	471	c.378G>A	c.(376-378)ggG>ggA	p.G126G	C5orf42_ENST00000274258.7_5'UTR|RN7SL37P_ENST00000490461.2_RNA|C5orf42_ENST00000425232.2_Silent_p.G126G			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	126						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)			CAATTCTTTTCCCATTTCCAG	0.348													C|||	153	0.0305511	0.1127	0.0043	5008	,	,		18071	0.0		0.001	False		,,,				2504	0.0				p.G126G		Atlas-SNP	.											.	C5orf42	422	.	0			c.G378A						PASS	.	C		145,1239		8,129,555	70	61	64		378	1.9	1	5	dbSNP_130	64	0,3182		0,0,1591	no	coding-synonymous	C5orf42	NM_023073.3		8,129,2146	TT,TC,CC		0.0,10.4769,3.1756		126/3198	37244669	145,4421	692	1591	2283	SO:0001819	synonymous_variant	65250	exon5			TCTTTTCCCATTT		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.378G>A	5.37:g.37244669C>T		157	0	0		136	49	0.360294	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Silent	SNP	ENST00000508244.1	37	CCDS34146.2																																																																																			C|0.980;T|0.020	0.020	strong		0.348	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		T	37244669	C	T	37244669	2	4	22	1	0	0	0	0	0	0	0	1	2303	842	30	2		2	C5orf42	5	37244669	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	17781	37244669	143670591	1182	4083											
C5orf42	65250	hgsc.bcm.edu	37	chr5	37245935	37245935	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttatcatccaaaagaaaaaCggcttctttttcctaagaga	15	13	5	8	1	2	2	1	0	1	2	4	3	4	2	2	1	1	1	2	1	6	6	rs73750959	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37245935C>T	ENST00000508244.1	-	2	187	c.94G>A	c.(94-96)Gtt>Att	p.V32I	C5orf42_ENST00000274258.7_5'UTR|RN7SL37P_ENST00000490461.2_RNA|C5orf42_ENST00000425232.2_Missense_Mutation_p.V32I			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	32						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)			AAAAGAAAAACGGCTTCTTTT	0.328													C|||	152	0.0303514	0.1127	0.0043	5008	,	,		15998	0.0		0.0	False		,,,				2504	0.0				p.V32I		Atlas-SNP	.											.	C5orf42	422	.	0			c.G94A						PASS	.	C	ILE/VAL	145,1239		8,129,555	77	69	71		94	4.3	1	5	dbSNP_130	71	0,3176		0,0,1588	yes	missense	C5orf42	NM_023073.3	29	8,129,2143	TT,TC,CC		0.0,10.4769,3.1798	possibly-damaging	32/3198	37245935	145,4415	692	1588	2280	SO:0001583	missense	65250	exon3			GAAAAACGGCTTC		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.94G>A	5.37:g.37245935C>T	ENSP00000421690:p.Val32Ile	87	0	0		74	36	0.486486	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	53	0.024267399267399268	52	0.10569105691056911	1	0.0027624309392265192	0	0.0	0	0.0	C	12.59	1.983446	0.35036	0.104769	0.0	ENSG00000197603	ENST00000508244;ENST00000425232	T;T	0.51817	0.69;0.69	5.34	4.35	0.52113	.	0.391851	0.21991	U	0.066147	T	0.00724	0.0024	L	0.41824	1.3	0.80722	D	1	P	0.51351	0.944	B	0.37198	0.243	T	0.00783	-1.1568	10	0.59425	D	0.04	-10.2005	12.5366	0.56145	0.0:0.8874:0.0:0.1126	.	32	E9PH94	.	I	32	ENSP00000421690:V32I;ENSP00000389014:V32I	ENSP00000389014:V32I	V	-	1	0	C5orf42	37281692	1.000000	0.71417	1.000000	0.80357	0.430000	0.31655	3.683000	0.54663	2.497000	0.84241	0.313000	0.20887	GTT	C|0.980;T|0.020	0.020	strong		0.328	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		T	37245935	C	T	37245935	3	4	22	1	0	0	0	0	1	0	0	0	2303	536	19	1	9699	1	C5orf42	5	37245935	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1266	37245935	143669325	1183	4084											
NUP155	9631	hgsc.bcm.edu	37	chr5	37299007	37299007	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgtgccagcataaattttGccaaggagaacaatcttgag	13	10	11	7	0	1	2	0	1	1	1	1	3	1	2	2	2	4	1	2	2	5	4	rs216400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37299007G>A	ENST00000231498.3	-	32	3959	c.3756C>T	c.(3754-3756)ggC>ggT	p.G1252G	NUP155_ENST00000513532.1_Silent_p.G1188G|NUP155_ENST00000381843.2_Silent_p.G1193G|NUP155_ENST00000502533.1_5'UTR	NM_153485.1	NP_705618.1	O75694	NU155_HUMAN	nucleoporin 155kDa	1252					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)			CATAAATTTTGCCAAGGAGAA	0.408													G|||	150	0.0299521	0.1112	0.0043	5008	,	,		18740	0.0		0.0	False		,,,				2504	0.0				p.G1252G		Atlas-SNP	.											.	NUP155	116	.	0			c.C3756T						PASS	.	G	,	437,3969	210.5+/-231.0	24,389,1790	134	119	124		3579,3756	0.7	1	5	dbSNP_79	124	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	NUP155	NM_004298.2,NM_153485.1	,	24,390,6089	AA,AG,GG		0.0116,9.9183,3.3677	,	1193/1333,1252/1392	37299007	438,12568	2203	4300	6503	SO:0001819	synonymous_variant	9631	exon32			AATTTTGCCAAGG	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.3756C>T	5.37:g.37299007G>A		87	0	0		108	40	0.37037	NM_153485	Q9UBE9|Q9UFL5	Silent	SNP	ENST00000231498.3	37	CCDS3921.1																																																																																			G|0.967;A|0.033	0.033	strong		0.408	NUP155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207593.2	NM_153485, NM_004298		A	37299007	G	A	37299007	2	1	22	1	0	0	0	0	0	0	0	1	10765	1306	46	2		2	NUP155	5	37299007	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	53072	37299007	143616253	1184	4085											
LIFR	3977	hgsc.bcm.edu	37	chr5	38510768	38510768	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caaaatgttatgtctgagccTacaagtatcactttatcttg	12	15	6	8	0	3	1	1	1	2	0	3	1	3	1	1	0	2	2	1	0	7	6	rs141925289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:38510768T>C	ENST00000263409.4	-	7	951	c.789A>G	c.(787-789)gtA>gtG	p.V263V	LIFR_ENST00000453190.2_Silent_p.V263V|LIFR_ENST00000503088.1_5'UTR	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	263					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)					TGTCTGAGCCTACAAGTATCA	0.348			T	PLAG1	salivary adenoma								T|||	21	0.00419329	0.0159	0.0	5008	,	,		17591	0.0		0.0	False		,,,				2504	0.0				p.V263V	Melanoma(13;4 730 6426 9861 34751)	Atlas-SNP	.		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	.	LIFR	348	.	0			c.A789G						PASS	.	T	,	38,4368	40.0+/-72.8	0,38,2165	80	73	76		789,789	-0.2	1	5	dbSNP_134	76	0,8600		0,0,4300	yes	coding-synonymous,coding-synonymous	LIFR	NM_001127671.1,NM_002310.5	,	0,38,6465	CC,CT,TT		0.0,0.8625,0.2922	,	263/1098,263/1098	38510768	38,12968	2203	4300	6503	SO:0001819	synonymous_variant	3977	exon7			TGAGCCTACAAGT	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.789A>G	5.37:g.38510768T>C		118	0	0		123	54	0.439024	NM_002310	Q6LCD9	Silent	SNP	ENST00000263409.4	37	CCDS3927.1																																																																																			T|0.997;C|0.003	0.003	strong		0.348	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310		C	38510768	T	C	38510768	2	2	22	1	0	0	0	0	0	0	0	1	8789	1509	53	3		3	LIFR	5	38510768	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1211761	38510768	142404492	1185	4086											
LIFR	3977	hgsc.bcm.edu	37	chr5	38523529	38523529	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gttcaaacttactaattttaCgagctccatactctctttac	11	16	3	11	1	2	0	1	0	1	0	4	1	3	0	1	0	6	2	1	0	6	8	rs140538535	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:38523529C>T	ENST00000263409.4	-	5	715	c.553G>A	c.(553-555)Gta>Ata	p.V185I	LIFR_ENST00000453190.2_Missense_Mutation_p.V185I|LIFR_ENST00000503088.1_5'UTR	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	185					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)					ACTAATTTTACGAGCTCCATA	0.338			T	PLAG1	salivary adenoma								C|||	11	0.00219649	0.0076	0.0014	5008	,	,		16786	0.0		0.0	False		,,,				2504	0.0				p.V185I	Melanoma(13;4 730 6426 9861 34751)	Atlas-SNP	.		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	LIFR_ENST00000263409,NS,carcinoma,0,2	LIFR	348	2	0			c.G553A						PASS	.	C	ILE/VAL,ILE/VAL	11,4395	15.5+/-35.6	0,11,2192	79	86	84		553,553	1.8	0	5	dbSNP_134	84	0,8600		0,0,4300	yes	missense,missense	LIFR	NM_001127671.1,NM_002310.5	29,29	0,11,6492	TT,TC,CC		0.0,0.2497,0.0846	possibly-damaging,possibly-damaging	185/1098,185/1098	38523529	11,12995	2203	4300	6503	SO:0001583	missense	3977	exon5			ATTTTACGAGCTC	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.553G>A	5.37:g.38523529C>T	ENSP00000263409:p.Val185Ile	280	0	0		267	115	0.430712	NM_002310	Q6LCD9	Missense_Mutation	SNP	ENST00000263409.4	37	CCDS3927.1	.	.	.	.	.	.	.	.	.	.	C	8.760	0.923346	0.18056	0.002497	0.0	ENSG00000113594	ENST00000263409;ENST00000453190	T;T	0.65916	-0.18;-0.18	5.53	1.82	0.25136	Immunoglobulin-like fold (1);	0.720295	0.13949	N	0.351669	T	0.49355	0.1552	L	0.49513	1.565	0.09310	N	1	B	0.25809	0.135	B	0.10450	0.005	T	0.29088	-1.0023	10	0.23302	T	0.38	-9.8342	7.3065	0.26451	0.0:0.6505:0.0:0.3495	.	185	P42702	LIFR_HUMAN	I	185	ENSP00000263409:V185I;ENSP00000398368:V185I	ENSP00000263409:V185I	V	-	1	0	LIFR	38559286	0.000000	0.05858	0.023000	0.16930	0.988000	0.76386	-0.741000	0.04855	0.044000	0.15775	0.655000	0.94253	GTA	C|0.999;T|0.001	0.001	strong		0.338	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310		T	38523529	C	T	38523529	3	4	22	1	0	0	0	0	1	0	0	0	8789	536	19	1	2804	1	LIFR	5	38523529	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	12761	38523529	142391731	1186	4087											
RICTOR	253260	hgsc.bcm.edu	37	chr5	38950761	38950761	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggctctgtatcttcattgatAtcaaggaaaaatgtgctagt	12	14	9	6	0	4	1	2	1	2	0	4	2	4	2	0	2	1	3	0	2	6	5	rs150422546	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:38950761A>G	ENST00000357387.3	-	31	3219	c.3189T>C	c.(3187-3189)gaT>gaC	p.D1063D	RICTOR_ENST00000296782.5_Silent_p.D1063D	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)					CTTCATTGATATCAAGGAAAA	0.348													A|||	6	0.00119808	0.0045	0.0	5008	,	,		17156	0.0		0.0	False		,,,				2504	0.0				p.D1063D		Atlas-SNP	.											.	RICTOR	182	.	0			c.T3189C						PASS	.	A		9,4395	15.5+/-35.6	0,9,2193	98	106	103		3189	0	1	5	dbSNP_134	103	0,8592		0,0,4296	yes	coding-synonymous	RICTOR	NM_152756.3		0,9,6489	GG,GA,AA		0.0,0.2044,0.0693		1063/1709	38950761	9,12987	2202	4296	6498	SO:0001819	synonymous_variant	253260	exon31			ATTGATATCAAGG		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.3189T>C	5.37:g.38950761A>G		207	0	0		210	111	0.528571	NM_152756		Silent	SNP	ENST00000357387.3	37	CCDS34148.1																																																																																			A|0.999;G|0.001	0.001	strong		0.348	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756		G	38950761	A	G	38950761	2	3	22	1	0	0	0	0	0	0	0	1	13373	446	16	3		3	RICTOR	5	38950761	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	427232	38950761	141964499	1187	4088											
RICTOR	253260	hgsc.bcm.edu	37	chr5	38960006	38960006	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttattttgaagacttctttcGggtttcattccagatgaagc	9	17	8	7	1	2	4	1	2	1	2	4	4	3	4	1	1	1	1	1	1	3	7	rs73751814	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:38960006G>A	ENST00000357387.3	-	21	1956	c.1926C>T	c.(1924-1926)ccC>ccT	p.P642P	RICTOR_ENST00000503698.1_5'Flank|RICTOR_ENST00000296782.5_Silent_p.P642P	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)					GACTTCTTTCGGGTTTCATTC	0.363													A|||	36	0.0071885	0.025	0.0043	5008	,	,		18686	0.0		0.0	False		,,,				2504	0.0				p.P642P		Atlas-SNP	.											.	RICTOR	182	.	0			c.C1926T						PASS	.	A		92,4314	817.2+/-416.3	1,90,2112	133	135	134		1926	-3.2	1	5	dbSNP_130	134	0,8600		0,0,4300	no	coding-synonymous	RICTOR	NM_152756.3		1,90,6412	AA,AG,GG		0.0,2.0881,0.7074		642/1709	38960006	92,12914	2203	4300	6503	SO:0001819	synonymous_variant	253260	exon21			TCTTTCGGGTTTC		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.1926C>T	5.37:g.38960006G>A		136	0	0		158	82	0.518987	NM_152756		Silent	SNP	ENST00000357387.3	37	CCDS34148.1																																																																																			G|0.993;A|0.007	0.007	strong		0.363	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756		A	38960006	G	A	38960006	2	1	22	1	0	0	0	0	0	0	0	1	13373	1103	39	1		1	RICTOR	5	38960006	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	9245	38960006	141955254	1188	4089											
FYB	2533	hgsc.bcm.edu	37	chr5	39202911	39202911	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	caaacttaggtacattgctgGgtcctgcaggagggctggca	9	9	14	9	0	0	0	0	0	0	0	1	1	1	1	1	5	4	5	1	5	3	3	rs1642515	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:39202911G>A	ENST00000351578.6	-	2	342	c.152C>T	c.(151-153)cCc>cTc	p.P51L	FYB_ENST00000505428.1_Missense_Mutation_p.P51L|FYB_ENST00000540520.1_Missense_Mutation_p.P61L|FYB_ENST00000515010.1_Missense_Mutation_p.P51L|FYB_ENST00000512982.1_Missense_Mutation_p.P51L	NM_199335.3	NP_955367.1	O15117	FYB_HUMAN	FYN binding protein	51			P -> L (in dbSNP:rs1642515).		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)			TACATTGCTGGGTCCTGCAGG	0.502													G|||	182	0.0363419	0.1331	0.0086	5008	,	,		17552	0.0		0.0	False		,,,				2504	0.0				p.P61L		Atlas-SNP	.											.	FYB	354	.	0			c.C182T						PASS	.	G	LEU/PRO,LEU/PRO	449,3361		21,407,1477	60	58	58		152,152	3.4	0.5	5	dbSNP_89	58	5,8235		0,5,4115	yes	missense,missense	FYB	NM_001465.4,NM_199335.3	98,98	21,412,5592	AA,AG,GG		0.0607,11.7848,3.7676	benign,benign	51/830,51/784	39202911	454,11596	1905	4120	6025	SO:0001583	missense	2533	exon2			TTGCTGGGTCCTG	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.152C>T	5.37:g.39202911G>A	ENSP00000316460:p.Pro51Leu	121	0	0		120	57	0.475	NM_001243093	A8K2Y8|B4DLN2|E9PBV9|O00359|Q9NZI9	Missense_Mutation	SNP	ENST00000351578.6	37	CCDS47200.1	64	0.029304029304029304	60	0.12195121951219512	4	0.011049723756906077	0	0.0	0	0.0	G	12.15	1.852358	0.32699	0.117848	6.07E-4	ENSG00000082074	ENST00000351578;ENST00000515010;ENST00000512982;ENST00000505428;ENST00000540520;ENST00000542542;ENST00000510188;ENST00000512138	T;T;T;T;T;T;T	0.73897	0.51;0.51;0.57;0.57;0.56;-0.79;-0.14	6.17	3.39	0.38822	.	0.680112	0.15332	N	0.267922	T	0.01695	0.0054	L	0.43701	1.375	0.20403	P	0.9999089434	B;B	0.20887	0.049;0.007	B;B	0.15052	0.012;0.006	T	0.30504	-0.9976	9	0.56958	D	0.05	-0.0459	5.9531	0.19259	0.2021:0.0:0.6538:0.1441	rs1642515;rs1642515	61;51	B4DLN2;O15117	.;FYB_HUMAN	L	51;51;51;51;61;51;51;51	ENSP00000316460:P51L;ENSP00000426346:P51L;ENSP00000425845:P51L;ENSP00000427114:P51L;ENSP00000442840:P61L;ENSP00000426597:P51L;ENSP00000424919:P51L	ENSP00000316460:P51L	P	-	2	0	FYB	39238668	0.961000	0.32948	0.518000	0.27811	0.688000	0.40055	1.158000	0.31737	0.444000	0.26612	0.655000	0.94253	CCC	G|0.959;A|0.041	0.041	strong		0.502	FYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367098.1	NM_001465		A	39202911	G	A	39202911	3	1	22	1	0	0	0	0	1	0	0	0	6132	1232	43	2	2409	2	FYB	5	39202911	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	242905	39202911	141712349	1189	4090											
RPL37	6167	hgsc.bcm.edu	37	chr5	40834595	40834595	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tttctcttgcgcttggcaggGtagccacatttgccacaggt	6	13	11	11	1	1	0	0	0	1	0	2	0	1	0	2	3	3	3	2	3	1	5	rs6495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:40834595G>A	ENST00000274242.5	-	2	266	c.117C>T	c.(115-117)taC>taT	p.Y39Y	RPL37_ENST00000504562.1_5'UTR|SNORD72_ENST00000390994.1_RNA|RPL37_ENST00000508493.1_Silent_p.Y39Y|RPL37_ENST00000509877.1_Silent_p.Y39Y	NM_000997.4	NP_000988.1	P61927	RL37_HUMAN	ribosomal protein L37	39					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)				GCTTGGCAGGGTAGCCACATT	0.483													G|||	19	0.00379393	0.0136	0.0014	5008	,	,		19990	0.0		0.0	False		,,,				2504	0.0				p.Y39Y	Colon(188;1411 2035 4978 19588 31462)	Atlas-SNP	.											.	RPL37	7	.	0			c.C117T						PASS	.	G		41,4365	44.6+/-78.6	0,41,2162	58	53	55		117	2.9	1	5	dbSNP_52	55	0,8600		0,0,4300	no	coding-synonymous	RPL37	NM_000997.4		0,41,6462	AA,AG,GG		0.0,0.9305,0.3152		39/98	40834595	41,12965	2203	4300	6503	SO:0001819	synonymous_variant	6167	exon2			GGCAGGGTAGCCA	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.117C>T	5.37:g.40834595G>A		62	0	0		100	44	0.44	NM_000997	B2R4H2|P02403|Q6IBB4|Q99883	Silent	SNP	ENST00000274242.5	37	CCDS3934.1																																																																																			G|0.996;A|0.004	0.004	strong		0.483	RPL37-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000211583.2	NM_000997		A	40834595	G	A	40834595	2	1	22	1	0	0	0	0	0	0	0	1	13604	1256	44	2		2	RPL37	5	40834595	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1631684	40834595	140080665	1190	4091											
PLCXD3	345557	hgsc.bcm.edu	37	chr5	41382536	41382536	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccgcatgagctttttggcCacagttccaaacacagagac	11	10	8	12	1	0	2	0	1	0	1	2	3	2	2	3	1	2	3	3	1	1	4	rs16871312	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:41382536C>T	ENST00000377801.3	-	2	278	c.204G>A	c.(202-204)gtG>gtA	p.V68V	PLCXD3_ENST00000328457.3_Silent_p.V68V			Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 3	68	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						GCTTTTTGGCCACAGTTCCAA	0.448													C|||	356	0.0710863	0.2632	0.0115	5008	,	,		17078	0.0		0.0	False		,,,				2504	0.0				p.V68V		Atlas-SNP	.											.	PLCXD3	86	.	0			c.G204A						PASS	.	C		1023,3383	371.2+/-319.9	129,765,1309	59	65	63		204	-0.2	1	5	dbSNP_123	63	8,8592	4.3+/-15.6	0,8,4292	no	coding-synonymous	PLCXD3	NM_001005473.2		129,773,5601	TT,TC,CC		0.093,23.2183,7.9271		68/322	41382536	1031,11975	2203	4300	6503	SO:0001819	synonymous_variant	345557	exon2			TTTGGCCACAGTT		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.204G>A	5.37:g.41382536C>T		32	0	0		36	36	1	NM_001005473	A6NL04	Silent	SNP	ENST00000377801.3	37	CCDS34150.1																																																																																			C|0.907;T|0.093	0.093	strong		0.448	PLCXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367109.1	XM_293875		T	41382536	C	T	41382536	2	4	22	1	0	0	0	0	0	0	0	1	12052	581	21	2		2	PLCXD3	5	41382536	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	547941	41382536	139532724	1191	4092											
MGC42105	167359	hgsc.bcm.edu	37	chr5	43277283	43277283	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atcatccgcctttacgaagtGgtggagaccctatccaagct	10	10	9	12	2	1	1	1	0	0	1	3	3	3	1	4	2	2	1	4	2	4	3	rs61734291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:43277283G>A	ENST00000512796.1	+	3	1916	c.417G>A	c.(415-417)gtG>gtA	p.V139V	NIM1_ENST00000326035.2_Silent_p.V139V			Q8IY84	NIM1_HUMAN		139	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein phosphorylation (GO:0006468)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)										TTTACGAAGTGGTGGAGACCC	0.507													A|||	201	0.0401358	0.1437	0.0159	5008	,	,		20135	0.0		0.0	False		,,,				2504	0.0				p.V139V		Atlas-SNP	.											.	.	.	.	0			c.G417A						PASS	.	A		468,3938	783.5+/-414.6	26,416,1761	103	98	100		417	-8.7	0.5	5	dbSNP_129	100	4,8596	819.2+/-406.8	0,4,4296	no	coding-synonymous	NIM1	NM_153361.2		26,420,6057	AA,AG,GG		0.0465,10.6219,3.6291		139/437	43277283	472,12534	2203	4300	6503	SO:0001819	synonymous_variant	0	exon3			CGAAGTGGTGGAG																												ENST00000512796.1:c.417G>A	5.37:g.43277283G>A		79	0	0		112	58	0.517857	NM_153361	B3KVM1	Silent	SNP	ENST00000512796.1	37	CCDS3943.1																																																																																			G|0.965;A|0.035	0.035	strong		0.507	NIM1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368017.1			A	43277283	G	A	43277283	2	1	22	1	0	0	0	0	0	0	0	1	9561	1335	47	2		2	MGC42105	5	43277283	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1894747	43277283	137637977	1192	4093											
NDUFS4	4724	hgsc.bcm.edu	37	chr5	52856572	52856572	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggctgtagctgccctttccgTttccagggttccgaccaggt	4	12	12	13	2	0	0	0	0	0	0	3	1	3	0	5	3	2	5	5	3	1	4	rs145347909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:52856572T>A	ENST00000296684.5	+	1	108	c.80T>A	c.(79-81)gTt>gAt	p.V27D		NM_002495.2	NP_002486.1	O43181	NDUS4_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 4, 18kDa (NADH-coenzyme Q reductase)	27					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)			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)				GCCCTTTCCGTTTCCAGGGTT	0.547													T|||	6	0.00119808	0.0038	0.0014	5008	,	,		15687	0.0		0.0	False		,,,				2504	0.0				p.V27D		Atlas-SNP	.											.	NDUFS4	17	.	0			c.T80A						PASS	.	T	ASP/VAL	9,4397	15.5+/-35.6	0,9,2194	108	97	101		80	-0.2	0.1	5	dbSNP_134	101	0,8600		0,0,4300	yes	missense	NDUFS4	NM_002495.2	152	0,9,6494	AA,AT,TT		0.0,0.2043,0.0692	possibly-damaging	27/176	52856572	9,12997	2203	4300	6503	SO:0001583	missense	4724	exon1			TTTCCGTTTCCAG	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.80T>A	5.37:g.52856572T>A	ENSP00000296684:p.Val27Asp	63	0	0		80	39	0.4875	NM_002495	Q9BS69	Missense_Mutation	SNP	ENST00000296684.5	37	CCDS3960.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	T	12.86	2.065131	0.36470	0.002043	0.0	ENSG00000164258	ENST00000296684;ENST00000506765	T	0.69040	-0.37	4.72	-0.216	0.13153	.	1.026790	0.07670	N	0.935325	T	0.49236	0.1545	L	0.54323	1.7	0.19775	N	0.999952	B	0.29085	0.232	B	0.26517	0.07	T	0.38373	-0.9664	10	0.30854	T	0.27	-17.1517	7.242	0.26102	0.0:0.3826:0.0:0.6174	.	27	O43181	NDUS4_HUMAN	D	27;23	ENSP00000296684:V27D	ENSP00000296684:V27D	V	+	2	0	NDUFS4	52892329	0.912000	0.30974	0.063000	0.19743	0.310000	0.27922	0.131000	0.15870	-0.025000	0.13918	0.533000	0.62120	GTT	T|0.999;A|0.001	0.001	strong		0.547	NDUFS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214062.2	NM_002495		A	52856572	T	A	52856572	3	1	22	1	0	0	0	0	1	0	0	0	10303	1725	60	5	82	5	NDUFS4	5	52856572	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	9579289	52856572	128058688	1193	4094											
HSPB3	8988	hgsc.bcm.edu	37	chr5	53751818	53751818	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagagacgccaccccgagaaGgcaaatcccactttcagatc	13	5	8	15	2	1	3	1	0	0	3	3	5	2	3	4	1	0	1	4	1	2	1	rs35258119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:53751818G>A	ENST00000302005.1	+	1	374	c.199G>A	c.(199-201)Ggc>Agc	p.G67S		NM_006308.2	NP_006299.1	Q12988	HSPB3_HUMAN	heat shock 27kDa protein 3	67			G -> S (in dbSNP:rs35258119).		cell death (GO:0008219)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|large_intestine(4)|prostate(3)	8		Lung NSC(810;0.00104)				ACCCCGAGAAGGCAAATCCCA	0.552													G|||	41	0.0081869	0.028	0.0058	5008	,	,		19929	0.0		0.0	False		,,,				2504	0.0				p.G67S		Atlas-SNP	.											.	HSPB3	17	.	0			c.G199A						PASS	.	G	SER/GLY	90,4316	75.7+/-113.9	0,90,2113	84	76	79		199	2.1	0	5	dbSNP_126	79	0,8600		0,0,4300	yes	missense	HSPB3	NM_006308.2	56	0,90,6413	AA,AG,GG		0.0,2.0427,0.692	benign	67/151	53751818	90,12916	2203	4300	6503	SO:0001583	missense	8988	exon1			CGAGAAGGCAAAT	Y17782	CCDS3961.1	5q11.2	2011-09-02	2002-08-29		ENSG00000169271	ENSG00000169271		"Heat shock proteins / HSPB"	5248	protein-coding gene	gene with protein product		604624	"heat shock 27kD protein 3"			8972725, 9858786	Standard	NM_006308		Approved	HSPL27	uc003jph.2	Q12988	OTTHUMG00000096995	ENST00000302005.1:c.199G>A	5.37:g.53751818G>A	ENSP00000303394:p.Gly67Ser	139	0	0		146	144	0.986301	NM_006308		Missense_Mutation	SNP	ENST00000302005.1	37	CCDS3961.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	9.517	1.107277	0.20714	0.020427	0.0	ENSG00000169271	ENST00000302005	D	0.91124	-2.79	5.89	2.12	0.27331	Heat shock protein Hsp20 (2);HSP20-like chaperone (1);	0.364101	0.27415	N	0.019475	T	0.69628	0.3132	N	0.16708	0.43	0.09310	N	1	B	0.19445	0.036	B	0.17722	0.019	T	0.65742	-0.6094	10	0.36615	T	0.2	-30.5173	10.6026	0.45375	0.2571:0.0:0.7429:0.0	rs35258119	67	Q12988	HSPB3_HUMAN	S	67	ENSP00000303394:G67S	ENSP00000303394:G67S	G	+	1	0	HSPB3	53787575	0.686000	0.27661	0.045000	0.18777	0.039000	0.13416	0.902000	0.28459	0.813000	0.34350	0.655000	0.94253	GGC	G|0.992;A|0.008	0.008	strong		0.552	HSPB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214074.2			A	53751818	G	A	53751818	3	1	22	1	0	0	0	0	1	0	0	0	7430	1000	35	2	201	2	HSPB3	5	53751818	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	895246	53751818	127163442	1194	4095											
SNX18	112574	hgsc.bcm.edu	37	chr5	53814736	53814736	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cgctacaagcacttcgactgGctgtacgcgcgcctggcgga	7	7	13	14	6	0	0	0	0	0	0	1	2	0	1	1	3	3	4	1	3	3	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:53814736G>C	ENST00000326277.3	+	1	1144	c.954G>C	c.(952-954)tgG>tgC	p.W318C	SNX18_ENST00000343017.6_Missense_Mutation_p.W318C|SNX18_ENST00000381410.4_Missense_Mutation_p.W318C	NM_052870.2	NP_443102.2	Q96RF0	SNX18_HUMAN	sorting nexin 18	318	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				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)				ACTTCGACTGGCTGTACGCGC	0.622																																					p.W318C		Atlas-SNP	.											.	SNX18	102	.	0			c.G954C						PASS	.						48	45	46					5																	53814736		2203	4300	6503	SO:0001583	missense	112574	exon1			CGACTGGCTGTAC	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.954G>C	5.37:g.53814736G>C	ENSP00000317332:p.Trp318Cys	143	0	0		138	15	0.108696	NM_052870	B4E2B3|H7BXX3|Q05BB3|Q0VG02	Missense_Mutation	SNP	ENST00000326277.3	37	CCDS3962.1	.	.	.	.	.	.	.	.	.	.	G	15.12	2.740451	0.49045	.	.	ENSG00000178996	ENST00000343017;ENST00000381410;ENST00000326277	T;T;T	0.41400	1.0;1.0;1.0	4.8	3.94	0.45596	Phox homologous domain (5);	0.000000	0.85682	D	0.000000	T	0.69993	0.3173	M	0.91612	3.225	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.77598	-0.2528	10	0.87932	D	0	-9.487	13.0976	0.59202	0.0771:0.0:0.9229:0.0	.	318;318	Q96RF0;Q96RF0-2	SNX18_HUMAN;.	C	318	ENSP00000342276:W318C;ENSP00000370817:W318C;ENSP00000317332:W318C	ENSP00000317332:W318C	W	+	3	0	SNX18	53850493	1.000000	0.71417	1.000000	0.80357	0.591000	0.36615	9.638000	0.98445	1.250000	0.43966	-0.259000	0.10710	TGG	.	.	none		0.622	SNX18-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214072.2			C	53814736	G	C	53814736	3	2	22	1	0	0	0	0	1	0	0	0	14904	1212	42	4	956	4	SNX18	5	53814736	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	62918	53814736	127100524	1195	4096											
C5orf35	133383	hgsc.bcm.edu	37	chr5	56205559	56205559	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tggatcgcactgaacctaagCcacaacccgaggtgagaggg	12	5	13	11	2	0	2	0	2	0	1	1	5	0	3	3	3	3	1	3	3	3	1	rs80198735	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:56205559C>T	ENST00000285947.2	+	1	473	c.87C>T	c.(85-87)agC>agT	p.S29S	AC008937.3_ENST00000453721.1_RNA|SETD9_ENST00000475908.1_Intron|SETD9_ENST00000541720.1_Silent_p.S29S	NM_153706.3	NP_714917.2	Q8NE22	SETD9_HUMAN	SET domain containing 9	29							methyltransferase activity (GO:0008168)										TGAACCTAAGCCACAACCCGA	0.687													C|||	53	0.0105831	0.0386	0.0029	5008	,	,		9227	0.0		0.0	False		,,,				2504	0.0				p.S29S		Atlas-SNP	.											.	.	.	.	0			c.C87T						PASS	.	C	,	152,4254	98.9+/-137.6	5,142,2056	49	32	38		87,87	2.4	0.5	5	dbSNP_131	38	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	C5orf35	NM_001171990.1,NM_153706.3	,	5,143,6355	TT,TC,CC		0.0116,3.4498,1.1764	,	29/272,29/300	56205559	153,12853	2203	4300	6503	SO:0001819	synonymous_variant	133383	exon1			CCTAAGCCACAAC	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.87C>T	5.37:g.56205559C>T		75	0	0		98	34	0.346939	NM_153706	F5H713	Silent	SNP	ENST00000285947.2	37	CCDS3972.1																																																																																			C|0.987;T|0.013	0.013	strong		0.687	SETD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132304.2	NM_153706		T	56205559	C	T	56205559	2	4	22	1	0	0	0	0	0	0	0	1	2296	738	26	2		2	C5orf35	5	56205559	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2390823	56205559	124709701	1196	4097											
ACTBL2	345651	hgsc.bcm.edu	37	chr5	56778213	56778213	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cttggggttcaggggtgcctCggtgaggaggatgggatgct	5	10	20	6	1	1	1	1	1	0	0	2	4	1	4	1	8	2	2	1	8	0	2	rs73757391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:56778213C>T	ENST00000423391.1	-	1	423	c.322G>A	c.(322-324)Gag>Aag	p.E108K	CTD-2023N9.1_ENST00000506106.1_RNA|AC025470.1_ENST00000584598.1_RNA	NM_001017992.3	NP_001017992.1	Q562R1	ACTBL_HUMAN	actin, beta-like 2	108						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(3)|pancreas(1)|prostate(2)	28		Lung NSC(810;0.000135)|Prostate(74;0.055)|Breast(144;0.0707)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;4.24e-37)		AGGGGTGCCTCGGTGAGGAGG	0.527													C|||	126	0.0251597	0.0946	0.0014	5008	,	,		23302	0.0		0.0	False		,,,				2504	0.0				p.E108K		Atlas-SNP	.											.	ACTBL2	65	.	0			c.G322A						PASS	.	C	LYS/GLU	340,4066	179.0+/-207.6	20,300,1883	105	89	95		322	4	0.9	5	dbSNP_130	95	2,8598	2.2+/-6.3	0,2,4298	yes	missense	ACTBL2	NM_001017992.2	56	20,302,6181	TT,TC,CC		0.0233,7.7167,2.6296	possibly-damaging	108/377	56778213	342,12664	2203	4300	6503	SO:0001583	missense	345651	exon1			GTGCCTCGGTGAG		CCDS34163.1	5q11.2	2014-08-08			ENSG00000169067	ENSG00000169067			17780	protein-coding gene	gene with protein product		614835					Standard	NM_001017992		Approved	DKFZp686D0972	uc003jrm.3	Q562R1	OTTHUMG00000162330	ENST00000423391.1:c.322G>A	5.37:g.56778213C>T	ENSP00000416706:p.Glu108Lys	169	0	0		187	99	0.529412	NM_001017992	B2RPJ1|Q562R2|Q562S9|Q562X8	Missense_Mutation	SNP	ENST00000423391.1	37	CCDS34163.1	45	0.020604395604395604	44	0.08943089430894309	1	0.0027624309392265192	0	0.0	0	0.0	C	13.74	2.327453	0.41197	0.077167	2.33E-4	ENSG00000169067	ENST00000423391	D	0.96940	-4.18	4.91	4.04	0.47022	Actin/actin-like conserved site (1);	0.000000	0.64402	D	0.000005	D	0.82774	0.5110	H	0.98295	4.195	0.48762	D	0.999703	D	0.89917	1.0	D	0.78314	0.991	T	0.76862	-0.2802	10	0.87932	D	0	.	11.3815	0.49761	0.0:0.9109:0.0:0.0891	.	108	Q562R1	ACTBL_HUMAN	K	108	ENSP00000416706:E108K	ENSP00000416706:E108K	E	-	1	0	ACTBL2	56813970	1.000000	0.71417	0.920000	0.36463	0.468000	0.32798	5.904000	0.69886	1.279000	0.44446	0.655000	0.94253	GAG	C|0.973;T|0.027	0.027	strong		0.527	ACTBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368579.1	NM_001017992		T	56778213	C	T	56778213	3	4	22	1	0	0	0	0	1	0	0	0	194	893	31	1	812	1	ACTBL2	5	56778213	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	572654	56778213	124137047	1197	4098											
NDUFAF2	91942	hgsc.bcm.edu	37	chr5	60448734	60448734	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagcactggtaaaaccttTcagccaggatcctggatgcc	11	8	10	12	0	1	0	1	0	0	0	2	2	2	2	4	3	5	3	4	3	2	2	rs77878573	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:60448734T>C	ENST00000296597.5	+	4	589	c.462T>C	c.(460-462)ttT>ttC	p.F154F	NDUFAF2_ENST00000512623.1_3'UTR|NDUFAF2_ENST00000511107.1_3'UTR	NM_174889.4	NP_777549.1	Q8N183	MIMIT_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 2	154					negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)	mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|ovary(1)	6		Lung NSC(810;3.36e-05)|Prostate(74;0.0225)|Ovarian(174;0.17)|Breast(144;0.237)				GTAAAACCTTTCAGCCAGGAT	0.443													T|||	89	0.0177716	0.0658	0.0029	5008	,	,		13669	0.0		0.0	False		,,,				2504	0.0				p.F154F		Atlas-SNP	.											.	NDUFAF2	10	.	0			c.T462C						PASS	.	T		242,4162	130.2+/-166.9	6,230,1966	33	28	30		462	-4.8	1	5	dbSNP_131	30	4,8592	3.0+/-9.4	0,4,4294	no	coding-synonymous	NDUFAF2	NM_174889.4		6,234,6260	CC,CT,TT		0.0465,5.495,1.8923		154/170	60448734	246,12754	2202	4298	6500	SO:0001819	synonymous_variant	91942	exon4			AACCTTTCAGCCA	AB183433	CCDS3979.1	5q12.1	2012-10-12	2012-05-08	2008-02-15	ENSG00000164182	ENSG00000164182		"Mitochondrial respiratory chain complex assembly factors"	28086	protein-coding gene	gene with protein product	"Myc-induced mitochondrial protein"	609653	"NDUFA12-like", "NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 2"	NDUFA12L		15774466, 16200211, 17383918	Standard	NM_174889		Approved	B17.2L, MMTN, mimitin	uc003jsp.4	Q8N183	OTTHUMG00000131221	ENST00000296597.5:c.462T>C	5.37:g.60448734T>C		147	0	0		143	71	0.496504	NM_174889	A8K5I1	Silent	SNP	ENST00000296597.5	37	CCDS3979.1																																																																																			T|0.981;C|0.019	0.019	strong		0.443	NDUFAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253965.1	NM_174889		C	60448734	T	C	60448734	2	2	22	1	0	0	0	0	0	0	0	1	10284	1780	62	3		3	NDUFAF2	5	60448734	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	3670521	60448734	120466526	1198	4099											
SFRS12IP1	285672	hgsc.bcm.edu	37	chr5	64020241	64020241	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagaattcagaactattaggTgtagaagaatgcttttcctt	13	14	9	5	0	1	4	1	0	0	4	2	5	2	4	1	1	2	2	1	1	7	7	rs16879016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:64020241T>C	ENST00000513458.4	-	5	605	c.438A>G	c.(436-438)acA>acG	p.T146T		NM_173829.3	NP_776190.1	Q8N9Q2	SR1IP_HUMAN	SREK1-interacting protein 1	146					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						AACTATTAGGTGTAGAAGAAT	0.294													C|||	724	0.144569	0.4924	0.0519	5008	,	,		18873	0.0238		0.0109	False		,,,				2504	0.002				p.T146T		Atlas-SNP	.											.	SREK1IP1	28	.	0			c.A438G						PASS	.	C		1770,2634	619.0+/-393.3	360,1050,792	34	34	34		438	-9.1	0	5	dbSNP_123	34	59,8533	801.1+/-407.4	0,59,4237	no	coding-synonymous	SREK1IP1	NM_173829.3		360,1109,5029	CC,CT,TT		0.6867,40.1907,14.0736		146/156	64020241	1829,11167	2202	4296	6498	SO:0001819	synonymous_variant	285672	exon5			ATTAGGTGTAGAA	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.438A>G	5.37:g.64020241T>C		179	0	0		180	90	0.5	NM_173829	Q32NC8	Silent	SNP	ENST00000513458.4	37	CCDS34171.1																																																																																			T|0.886;C|0.114	0.114	strong		0.294	SREK1IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368457.4	NM_173829		C	64020241	T	C	64020241	2	2	22	1	0	0	0	0	0	0	0	1	14183	1683	59	3		3	SFRS12IP1	5	64020241	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	3571507	64020241	116895019	1199	4100											
NLN	57486	hgsc.bcm.edu	37	chr5	65054587	65054587	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acgatgctgttggaatgctcGgtattgaggaagtaacttac	11	12	12	6	2	0	1	0	1	0	0	1	4	0	3	0	3	4	5	0	3	5	5	rs34339013	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:65054587G>A	ENST00000380985.5	+	2	413	c.235G>A	c.(235-237)Ggt>Agt	p.G79S	NLN_ENST00000502464.1_Intron	NM_020726.4	NP_065777.1	Q9BYT8	NEUL_HUMAN	neurolysin (metallopeptidase M3 family)	79			G -> S (in dbSNP:rs34339013).			mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0743)|Lung(70;0.00616)		TGGAATGCTCGGTATTGAGGA	0.423													G|||	132	0.0263578	0.093	0.0115	5008	,	,		16846	0.0		0.001	False		,,,				2504	0.0				p.G79S		Atlas-SNP	.											.	NLN	51	.	0			c.G235A						PASS	.	G	SER/GLY	321,4085	171.9+/-202.1	14,293,1896	138	122	128		235	-1.6	0	5	dbSNP_126	128	0,8600		0,0,4300	yes	missense	NLN	NM_020726.4	56	14,293,6196	AA,AG,GG		0.0,7.2855,2.4681	benign	79/705	65054587	321,12685	2203	4300	6503	SO:0001583	missense	57486	exon2			ATGCTCGGTATTG	AJ300837	CCDS3989.1	5q12.3	2008-02-05	2005-03-31		ENSG00000123213	ENSG00000123213	3.4.24.16		16058	protein-coding gene	gene with protein product		611530	"angiotensin binding protein"	AGTBP		10574462	Standard	NM_020726		Approved	KIAA1226	uc003juf.3	Q9BYT8	OTTHUMG00000097803	ENST00000380985.5:c.235G>A	5.37:g.65054587G>A	ENSP00000370372:p.Gly79Ser	127	0	0		129	70	0.542636	NM_020726	Q9ULJ4	Missense_Mutation	SNP	ENST00000380985.5	37	CCDS3989.1	32	0.014652014652014652	27	0.054878048780487805	5	0.013812154696132596	0	0.0	0	0.0	G	8.053	0.766380	0.15983	0.072855	0.0	ENSG00000123213	ENST00000380985;ENST00000340159	T	0.06933	3.24	5.5	-1.6	0.08426	Neurolysin/Thimet oligopeptidase, N-terminal (1);	0.775582	0.12614	N	0.453646	T	0.00241	0.0007	N	0.01352	-0.895	0.09310	N	0.999999	B;B	0.27679	0.001;0.185	B;B	0.14578	0.001;0.011	T	0.44862	-0.9300	10	0.20519	T	0.43	-0.0913	12.5135	0.56019	0.3907:0.0:0.6093:0.0	rs34339013	79;79	Q9BYT8;Q9BQD0	NEUL_HUMAN;.	S	79	ENSP00000370372:G79S	ENSP00000339283:G79S	G	+	1	0	NLN	65090343	0.024000	0.19004	0.001000	0.08648	0.784000	0.44337	0.931000	0.28871	-0.729000	0.04875	-0.880000	0.02959	GGT	G|0.973;A|0.027	0.027	strong		0.423	NLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215060.1			A	65054587	G	A	65054587	3	1	22	1	0	0	0	0	1	0	0	0	10476	1116	39	1	241	1	NLN	5	65054587	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1034346	65054587	115860673	1200	4101											
NLN	57486	hgsc.bcm.edu	37	chr5	65084101	65084101	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gactcagacagaggaactcaAgtattccatagaccaagagt	16	7	9	9	0	2	4	2	0	0	4	3	6	3	5	2	1	1	1	2	1	5	3	rs6863012	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:65084101A>G	ENST00000380985.5	+	8	1293	c.1115A>G	c.(1114-1116)aAg>aGg	p.K372R	NLN_ENST00000502464.1_Missense_Mutation_p.K268R	NM_020726.4	NP_065777.1	Q9BYT8	NEUL_HUMAN	neurolysin (metallopeptidase M3 family)	372			K -> R (in dbSNP:rs6863012).			mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0743)|Lung(70;0.00616)		GAGGAACTCAAGTATTCCATA	0.408													A|||	276	0.0551118	0.1944	0.0202	5008	,	,		20583	0.0		0.004	False		,,,				2504	0.001				p.K372R		Atlas-SNP	.											.	NLN	51	.	0			c.A1115G						PASS	.	A	ARG/LYS	803,3603	319.3+/-296.1	63,677,1463	131	135	133		1115	6.1	1	5	dbSNP_116	133	32,8568	22.8+/-68.1	0,32,4268	yes	missense	NLN	NM_020726.4	26	63,709,5731	GG,GA,AA		0.3721,18.2251,6.4201	benign	372/705	65084101	835,12171	2203	4300	6503	SO:0001583	missense	57486	exon8			AACTCAAGTATTC	AJ300837	CCDS3989.1	5q12.3	2008-02-05	2005-03-31		ENSG00000123213	ENSG00000123213	3.4.24.16		16058	protein-coding gene	gene with protein product		611530	"angiotensin binding protein"	AGTBP		10574462	Standard	NM_020726		Approved	KIAA1226	uc003juf.3	Q9BYT8	OTTHUMG00000097803	ENST00000380985.5:c.1115A>G	5.37:g.65084101A>G	ENSP00000370372:p.Lys372Arg	175	0	0		170	88	0.517647	NM_020726	Q9ULJ4	Missense_Mutation	SNP	ENST00000380985.5	37	CCDS3989.1	108	0.04945054945054945	101	0.20528455284552846	7	0.019337016574585635	0	0.0	0	0.0	A	10.38	1.333268	0.24167	0.182251	0.003721	ENSG00000123213	ENST00000380985;ENST00000502464;ENST00000340159;ENST00000511299	T;T;T	0.08458	3.09;3.09;3.09	6.07	6.07	0.98685	Neurolysin/Thimet oligopeptidase, domain 2 (1);	0.045838	0.85682	D	0.000000	T	0.00012	0.0000	N	0.12961	0.28	0.19575	P	0.9999611304	B;B;D	0.64830	0.001;0.004;0.994	B;B;D	0.73708	0.001;0.008;0.981	T	0.56366	-0.7991	9	0.12430	T	0.62	-22.309	16.6406	0.85098	1.0:0.0:0.0:0.0	rs6863012;rs6863012	67;372;372	Q96K48;Q9BYT8;Q9BQD0	.;NEUL_HUMAN;.	R	372;268;372;100	ENSP00000370372:K372R;ENSP00000423214:K268R;ENSP00000427417:K100R	ENSP00000339283:K372R	K	+	2	0	NLN	65119857	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.934000	0.70138	2.326000	0.78906	0.533000	0.62120	AAG	A|0.936;G|0.064	0.064	strong		0.408	NLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215060.1			G	65084101	A	G	65084101	3	3	22	1	0	0	0	0	1	0	0	0	10476	72	3	3	1145	3	NLN	5	65084101	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	29514	65084101	115831159	1201	4102											
MAST4	375449	hgsc.bcm.edu	37	chr5	66461583	66461583	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacagtgaaagcagcagccaCaagccccggcctggccctga	11	3	11	16	1	0	2	0	2	0	0	0	2	0	2	5	2	4	2	5	2	2	0	rs56201012	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:66461583C>T	ENST00000403625.2	+	29	6871	c.6576C>T	c.(6574-6576)caC>caT	p.H2192H	MAST4_ENST00000405643.1_Silent_p.H2013H|MAST4_ENST00000404260.3_Silent_p.H2195H|MAST4_ENST00000261569.7_Silent_p.H1998H|MAST4_ENST00000403666.1_Silent_p.H2003H	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	2195	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)		GCAGCAGCCACAAGCCCCGGC	0.667													C|||	92	0.0183706	0.0673	0.0043	5008	,	,		14359	0.0		0.0	False		,,,				2504	0.0				p.H2192H		Atlas-SNP	.											.	MAST4	218	.	0			c.C6576T						PASS	.	C	,	176,3520		6,164,1678	6	10	9		6576,6009	1.2	0	5	dbSNP_129	9	0,8114		0,0,4057	no	coding-synonymous,coding-synonymous	MAST4	NM_001164664.1,NM_015183.2	,	6,164,5735	TT,TC,CC		0.0,4.7619,1.4903	,	2192/2624,2003/2435	66461583	176,11634	1848	4057	5905	SO:0001819	synonymous_variant	375449	exon29			CAGCCACAAGCCC	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.6576C>T	5.37:g.66461583C>T		75	0	0		89	40	0.449438	NM_001164664	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Silent	SNP	ENST00000403625.2	37	CCDS54861.1	21	0.009615384615384616	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	0	0.0	C	0.038	-1.299299	0.01364	0.047619	0.0	ENSG00000069020	ENST00000443808	.	.	.	5.0	1.16	0.20824	.	.	.	.	.	.	.	.	.	.	.	0.22389	N	0.999143	.	.	.	.	.	.	.	.	.	.	.	.	.	-3.25	3.4785	0.07594	0.1768:0.386:0.0:0.4373	rs56201012;rs61910710	.	.	.	X	1249	.	.	Q	+	1	0	MAST4	66497339	0.016000	0.18221	0.007000	0.13788	0.092000	0.18411	-0.102000	0.10956	0.022000	0.15160	-0.140000	0.14226	CAA	C|0.990;T|0.010	0.010	strong		0.667	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			T	66461583	C	T	66461583	2	4	22	1	0	0	0	0	0	0	0	1	9336	477	17	2		2	MAST4	5	66461583	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1377482	66461583	114453677	1202	4103											
CD180	4064	hgsc.bcm.edu	37	chr5	66479383	66479383	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcattaatgtgtaagcgggTaaatgccaaatcgaggagtt	14	10	12	5	2	0	0	0	0	0	0	1	2	0	1	1	2	3	4	1	2	5	4	rs2230523	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:66479383T>C	ENST00000256447.4	-	3	1445	c.1288A>G	c.(1288-1290)Acc>Gcc	p.T430A	CTD-2306M10.1_ENST00000602471.1_lincRNA	NM_005582.2	NP_005573.2	Q99467	CD180_HUMAN	CD180 molecule	430			T -> A (in dbSNP:rs2230523).		B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(2)|kidney(7)|large_intestine(12)|liver(1)|lung(8)|ovary(1)|stomach(2)	34		Lung NSC(167;4.94e-05)|Prostate(74;0.00601)|Ovarian(174;0.0654)|Breast(144;0.198)|Colorectal(97;0.234)		Lung(70;0.0046)		TGTAAGCGGGTAAATGCCAAA	0.458													T|||	93	0.0185703	0.0681	0.0043	5008	,	,		21421	0.0		0.0	False		,,,				2504	0.0				p.T430A		Atlas-SNP	.											CD180,NS,carcinoma,+1,2	CD180	78	2	0			c.A1288G						PASS	.	T	ALA/THR	254,4152	146.1+/-180.8	17,220,1966	175	181	179		1288	4.8	0.6	5	dbSNP_98	179	1,8599	1.2+/-3.3	0,1,4299	yes	missense	CD180	NM_005582.2	58	17,221,6265	CC,CT,TT		0.0116,5.7649,1.9606	probably-damaging	430/662	66479383	255,12751	2203	4300	6503	SO:0001583	missense	4064	exon3			AGCGGGTAAATGC	D83597	CCDS3992.1	5q12	2008-02-05	2006-03-28	2005-06-07	ENSG00000134061	ENSG00000134061		"CD molecules"	6726	protein-coding gene	gene with protein product		602226	"lymphocyte antigen 64 (mouse) homolog, radioprotective, 105kD", "CD180 antigen"	LY64		9763566, 8975706	Standard	NM_005582		Approved	RP105, Ly78	uc003juy.2	Q99467	OTTHUMG00000131229	ENST00000256447.4:c.1288A>G	5.37:g.66479383T>C	ENSP00000256447:p.Thr430Ala	174	0	0		146	66	0.452055	NM_005582	B2R7Z7|Q32MM5	Missense_Mutation	SNP	ENST00000256447.4	37	CCDS3992.1	20	0.009157509157509158	18	0.036585365853658534	2	0.0055248618784530384	0	0.0	0	0.0	T	12.29	1.894010	0.33442	0.057649	1.16E-4	ENSG00000134061	ENST00000256447	T	0.58060	0.36	4.81	4.81	0.61882	.	0.083576	0.50627	D	0.000118	T	0.14270	0.0345	M	0.83223	2.63	0.47441	D	0.99942	D	0.55605	0.972	P	0.46026	0.501	T	0.42599	-0.9442	10	0.33141	T	0.24	.	13.091	0.59167	0.0:0.0:0.0:1.0	rs2230523;rs52799097;rs2230523	430	Q99467	CD180_HUMAN	A	430	ENSP00000256447:T430A	ENSP00000256447:T430A	T	-	1	0	CD180	66515139	0.998000	0.40836	0.627000	0.29227	0.064000	0.16182	2.658000	0.46733	2.020000	0.59435	0.460000	0.39030	ACC	T|0.978;C|0.022	0.022	strong		0.458	CD180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253973.2	NM_005582		C	66479383	T	C	66479383	3	2	22	1	0	0	0	0	1	0	0	0	2974	1638	57	3	701	3	CD180	5	66479383	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	17800	66479383	114435877	1203	4104											
CCNB1	891	hgsc.bcm.edu	37	chr5	68471232	68471232	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gttttgtttcaggttgatgtCgagcaacatactttggccaa	9	15	10	7	1	1	1	1	1	0	0	2	2	1	1	1	2	3	4	1	2	3	6	rs2069439	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:68471232C>T	ENST00000256442.5	+	7	1204	c.951C>T	c.(949-951)gtC>gtT	p.V317V	snoU13_ENST00000459230.1_RNA	NM_031966.3	NP_114172.1	P14635	CCNB1_HUMAN	cyclin B1	317					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)		AGGTTGATGTCGAGCAACATA	0.393													C|||	4	0.000798722	0.003	0.0	5008	,	,		20276	0.0		0.0	False		,,,				2504	0.0				p.V317V		Atlas-SNP	.											CCNB1,NS,carcinoma,+1,1	CCNB1	36	1	0			c.C951T						PASS	.	C		26,4380	33.5+/-64.1	0,26,2177	156	145	149		951	-7.2	0.9	5	dbSNP_96	149	0,8600		0,0,4300	no	coding-synonymous	CCNB1	NM_031966.2		0,26,6477	TT,TC,CC		0.0,0.5901,0.1999		317/434	68471232	26,12980	2203	4300	6503	SO:0001819	synonymous_variant	891	exon7			TGATGTCGAGCAA	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.951C>T	5.37:g.68471232C>T		137	0	0		125	47	0.376	NM_031966	A8K066|Q5TZP9	Silent	SNP	ENST00000256442.5	37	CCDS3997.1																																																																																			C|0.998;T|0.002	0.002	strong		0.393	CCNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215084.1	NM_031966		T	68471232	C	T	68471232	2	4	22	1	0	0	0	0	0	0	0	1	2913	871	31	1		1	CCNB1	5	68471232	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1991849	68471232	112444028	1204	4105											
CCDC125	202243	hgsc.bcm.edu	37	chr5	68588029	68588029	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttaccatcctctttaaggTgcttccaattcatccatttt	9	17	4	11	0	2	0	1	0	1	0	5	0	5	0	4	1	2	2	4	1	3	7	rs112794294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:68588029T>C	ENST00000396496.2	-	10	1192	c.1085A>G	c.(1084-1086)cAc>cGc	p.H362R	CCDC125_ENST00000383374.2_Intron|CCDC125_ENST00000460090.1_Intron|CCDC125_ENST00000511257.1_Missense_Mutation_p.H237R|CCDC125_ENST00000396499.1_Missense_Mutation_p.H362R			Q86Z20	CC125_HUMAN	coiled-coil domain containing 125	362						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)		CTCTTTAAGGTGCTTCCAATT	0.318													T|||	58	0.0115815	0.0408	0.0058	5008	,	,		20797	0.0		0.0	False		,,,				2504	0.0				p.H362R		Atlas-SNP	.											.	CCDC125	41	.	0			c.A1085G						PASS	.	T	ARG/HIS	173,4231	113.3+/-151.4	1,171,2030	273	236	248		1085	-0.1	1	5	dbSNP_132	248	0,8600		0,0,4300	yes	missense	CCDC125	NM_176816.3	29	1,171,6330	CC,CT,TT		0.0,3.9282,1.3304	benign	362/512	68588029	173,12831	2202	4300	6502	SO:0001583	missense	202243	exon9			TTAAGGTGCTTCC	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.1085A>G	5.37:g.68588029T>C	ENSP00000379754:p.His362Arg	240	0	0		180	79	0.438889	NM_176816	Q86Z19	Missense_Mutation	SNP	ENST00000396496.2	37	CCDS4000.1	19	0.0086996336996337	15	0.03048780487804878	4	0.011049723756906077	0	0.0	0	0.0	T	0.922	-0.715564	0.03206	0.039282	0.0	ENSG00000183323	ENST00000396496;ENST00000396499;ENST00000511257	T;T;T	0.44482	0.92;0.92;0.92	4.28	-0.0527	0.13821	.	0.770151	0.12698	N	0.446592	T	0.06325	0.0163	L	0.41710	1.295	0.24112	N	0.995833	B	0.06786	0.001	B	0.09377	0.004	T	0.15206	-1.0445	10	0.17832	T	0.49	0.0174	2.3018	0.04164	0.1438:0.086:0.2964:0.4739	.	362	Q86Z20	CC125_HUMAN	R	362;362;237	ENSP00000379754:H362R;ENSP00000379756:H362R;ENSP00000426795:H237R	ENSP00000379754:H362R	H	-	2	0	CCDC125	68623785	0.832000	0.29368	0.951000	0.38953	0.996000	0.88848	0.157000	0.16402	-0.073000	0.12842	0.459000	0.35465	CAC	T|0.986;C|0.014	0.014	strong		0.318	CCDC125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254027.4	NM_176816		C	68588029	T	C	68588029	3	2	22	1	0	0	0	0	1	0	0	0	2763	1696	59	3	462	3	CCDC125	5	68588029	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	116797	68588029	112327231	1205	4106											
RAD17	5884	hgsc.bcm.edu	37	chr5	68710032	68710032	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaatagtgccagtgaactGcctgctagccagccccagcc	10	6	10	15	0	0	2	0	1	0	1	0	2	0	2	6	0	7	1	6	0	4	2	rs145547419	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:68710032G>A	ENST00000509734.1	+	18	2637	c.1959G>A	c.(1957-1959)ctG>ctA	p.L653L	RAD17_ENST00000354312.3_Silent_p.L642L|RAD17_ENST00000358030.2_Silent_p.L477L|RAD17_ENST00000504177.1_3'UTR|RAD17_ENST00000521422.1_Silent_p.L477L|RAD17_ENST00000361732.2_Silent_p.L642L|RAD17_ENST00000345306.6_Silent_p.L642L|MARVELD2_ENST00000325631.5_5'Flank|RAD17_ENST00000282891.6_Silent_p.L556L|RAD17_ENST00000305138.4_Silent_p.L642L|RAD17_ENST00000380774.3_Silent_p.L653L|RAD17_ENST00000354868.5_Silent_p.L642L			O75943	RAD17_HUMAN	RAD17 homolog (S. pombe)	653	Interaction with MCM7.				cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of DNA replication (GO:0008156)|regulation of phosphorylation (GO:0042325)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)						Lung NSC(167;5.19e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;9.36e-57)|Epithelial(20;1.21e-52)|all cancers(19;3.34e-48)|Lung(70;0.0183)		CCAGTGAACTGCCTGCTAGCC	0.507								Other conserved DNA damage response genes																													p.L653L		Atlas-SNP	.											.	RAD17	49	.	0			c.G1959A						PASS	.	G	,,,,,,,	20,4386	28.1+/-56.4	0,20,2183	94	96	96		1926,1926,1959,1431,1668,1926,1926,1926	2.3	1	5	dbSNP_134	96	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RAD17	NM_002873.1,NM_133338.1,NM_133339.1,NM_133340.1,NM_133341.1,NM_133342.1,NM_133343.1,NM_133344.1	,,,,,,,	0,20,6483	AA,AG,GG		0.0,0.4539,0.1538	,,,,,,,	642/671,642/671,653/682,477/506,556/585,642/671,642/671,642/671	68710032	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	5884	exon16			TGAACTGCCTGCT	AF085736	CCDS4003.1, CCDS4004.1, CCDS4005.1, CCDS47226.1	5q13	2010-09-24	2001-11-28		ENSG00000152942	ENSG00000152942			9807	protein-coding gene	gene with protein product		603139	"RAD1 (S. pombe) homolog"			9869296, 9660800	Standard	NM_133343		Approved	Rad24, RAD17Sp, CCYC	uc003jwo.3	O75943	OTTHUMG00000099357	ENST00000509734.1:c.1959G>A	5.37:g.68710032G>A		113	0	0		118	53	0.449153	NM_133339	A8K8X2|D3DWA5|O75714|Q7Z3S4|Q9UNK7|Q9UNR7|Q9UNR8|Q9UPF5	Silent	SNP	ENST00000509734.1	37	CCDS4003.1																																																																																			G|0.998;A|0.002	0.002	strong		0.507	RAD17-008	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369171.1	NM_133344		A	68710032	G	A	68710032	2	1	22	1	0	0	0	0	0	0	0	1	12994	1306	46	2		2	RAD17	5	68710032	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	122003	68710032	112205228	1206	4107											
MARVELD2	153562	hgsc.bcm.edu	37	chr5	68715576	68715576	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gttcaccaccagcctctccaGcaagaccaaaccaccgttcg	11	6	6	18	2	2	1	1	0	1	1	4	1	2	1	7	0	3	3	7	0	2	2	rs140764671	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:68715576G>A	ENST00000325631.5	+	2	438	c.364G>A	c.(364-366)Gca>Aca	p.A122T	MARVELD2_ENST00000413223.2_Missense_Mutation_p.A122T	NM_001038603.2|NM_001244734.1	NP_001033692.2|NP_001231663.1	Q8N4S9	MALD2_HUMAN	MARVEL domain containing 2	122					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)		AGCCTCTCCAGCAAGACCAAA	0.532													G|||	21	0.00419329	0.0151	0.0014	5008	,	,		18849	0.0		0.0	False		,,,				2504	0.0				p.A122T		Atlas-SNP	.											.	MARVELD2	49	.	0			c.G364A						PASS	.	G	THR/ALA	75,4331	65.3+/-102.7	1,73,2129	53	54	54		364	0	0	5	dbSNP_134	54	0,8600		0,0,4300	yes	missense	MARVELD2	NM_001038603.2	58	1,73,6429	AA,AG,GG		0.0,1.7022,0.5767	benign	122/559	68715576	75,12931	2203	4300	6503	SO:0001583	missense	153562	exon2			TCTCCAGCAAGAC	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.364G>A	5.37:g.68715576G>A	ENSP00000323264:p.Ala122Thr	69	0	0		88	43	0.488636	NM_001244734	A1BQX0|A1BQX1|A8KA97|Q96NM9	Missense_Mutation	SNP	ENST00000325631.5	37	CCDS34175.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	2.825	-0.243931	0.05906	0.017022	0.0	ENSG00000152939	ENST00000325631;ENST00000282886;ENST00000454295;ENST00000515844;ENST00000512803;ENST00000436532;ENST00000413223	T;T;T;T;T;T	0.47869	1.48;0.9;0.83;1.48;1.45;1.45	5.07	-0.0336	0.13900	.	0.712658	0.14187	N	0.335596	T	0.12305	0.0299	N	0.12746	0.255	0.09310	N	1	B;B;B	0.09022	0.001;0.002;0.0	B;B;B	0.11329	0.004;0.006;0.002	T	0.10337	-1.0634	10	0.33940	T	0.23	-24.4939	4.5252	0.11978	0.4245:0.0:0.4294:0.1461	.	122;122;122	Q8N4S9-3;Q8N4S9-2;Q8N4S9	.;.;MALD2_HUMAN	T	122	ENSP00000323264:A122T;ENSP00000396244:A122T;ENSP00000421902:A122T;ENSP00000423490:A122T;ENSP00000414776:A122T;ENSP00000398922:A122T	ENSP00000282886:A122T	A	+	1	0	MARVELD2	68751332	0.000000	0.05858	0.001000	0.08648	0.022000	0.10575	-0.332000	0.07904	-0.087000	0.12528	-0.140000	0.14226	GCA	G|0.995;A|0.005	0.005	strong		0.532	MARVELD2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369583.1	NM_144724		A	68715576	G	A	68715576	3	1	22	1	0	0	0	0	1	0	0	0	9327	971	34	2	366	2	MARVELD2	5	68715576	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5544	68715576	112199684	1207	4108											
NAIP	4671	hgsc.bcm.edu	37	chr5	70281620	70281621	+	Frame_Shift_Del	DEL	AT	AT	-																															aagagatatcaagcaaagacAtgtggcggaaactggcgctg																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:70281620_70281621delAT	ENST00000517649.1	-	12	1545_1546	c.1255_1256delAT	c.(1255-1257)atgfs	p.M419fs	NAIP_ENST00000194097.4_Frame_Shift_Del_p.M419fs|NAIP_ENST00000508426.2_Frame_Shift_Del_p.M419fs|NAIP_ENST00000523981.1_Frame_Shift_Del_p.M257fs|NAIP_ENST00000503719.2_Frame_Shift_Del_p.M257fs	NM_004536.2	NP_004527.2	Q13075	BIRC1_HUMAN	NLR family, apoptosis inhibitory protein	419					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)		AAGCAAAGACATGTGGCGGAAA	0.5																																					p.419_419del		Atlas-Indel	.											.	NAIP	38	.	0			c.1256_1257del						PASS	.																																			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.1255_1256delAT	5.37:g.70281620_70281621delAT	ENSP00000428657:p.Met419fs	214	0	0		205	32	0.156098	NM_004536	B9EG72|E9PHD1|O75857|Q13730|Q59GI6|Q8TDZ4|Q99796	Frame_Shift_Del	DEL	ENST00000517649.1	37	CCDS4009.1																																																																																			.	.	none		0.5	NAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372649.6	NM_004536		-	70281621	AT	-	70281620	7	5	22	1	0	1	0	1	0	0	0	0	10156	217	8	0	2979	0	NAIP	5	70281620	Frame_Shift_Del	DEL	AT	TCGA-G8-6324-01A-11D-2210-10	1566044	70281620	110633640	1208	4109											
BDP1	55814	hgsc.bcm.edu	37	chr5	70818150	70818150	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtatgttcctagttcagcaCaaatgacaagaaggaaattc	15	10	8	8	1	1	2	1	1	0	1	3	3	2	3	1	1	1	4	1	1	6	5	rs12187098	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:70818150C>G	ENST00000358731.4	+	23	5289	c.5026C>G	c.(5026-5028)Caa>Gaa	p.Q1676E	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	1676			Q -> E (in dbSNP:rs12187098).		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)		TAGTTCAGCACAAATGACAAG	0.348													C|||	101	0.0201677	0.0454	0.013	5008	,	,		17087	0.0		0.0298	False		,,,				2504	0.002				p.Q1676E		Atlas-SNP	.											.	BDP1	204	.	0			c.C5026G						PASS	.	C	GLU/GLN	182,3514		3,176,1669	130	127	128		5026	4.5	0.1	5	dbSNP_120	128	196,7988		6,184,3902	yes	missense	BDP1	NM_018429.2	29	9,360,5571	GG,GC,CC		2.3949,4.9242,3.1818	possibly-damaging	1676/2625	70818150	378,11502	1848	4092	5940	SO:0001583	missense	55814	exon23			TCAGCACAAATGA	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.5026C>G	5.37:g.70818150C>G	ENSP00000351575:p.Gln1676Glu	165	0	0		173	76	0.439306	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	37	CCDS43328.1	41	0.018772893772893772	19	0.03861788617886179	5	0.013812154696132596	0	0.0	17	0.022427440633245383	C	8.668	0.902198	0.17760	0.049242	0.023949	ENSG00000145734	ENST00000358731;ENST00000451951	T	0.10477	2.87	5.35	4.48	0.54585	.	1.312210	0.05133	N	0.493011	T	0.01489	0.0048	L	0.47716	1.5	0.49687	D	0.999812	P;P	0.42871	0.557;0.792	B;B	0.37601	0.116;0.254	T	0.48514	-0.9029	10	0.02654	T	1	.	11.1063	0.48205	0.0:0.9126:0.0:0.0874	rs12187098;rs13169583;rs52833258;rs56647603;rs12187098	1676;1676	A6H8Y1;A6H8Y1-2	BDP1_HUMAN;.	E	1676;1256	ENSP00000351575:Q1676E	ENSP00000351575:Q1676E	Q	+	1	0	BDP1	70853906	0.019000	0.18553	0.098000	0.21074	0.052000	0.14988	2.086000	0.41643	1.251000	0.43983	0.555000	0.69702	CAA	C|0.971;G|0.029	0.029	strong		0.348	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429		G	70818150	C	G	70818150	3	3	22	1	0	0	0	0	1	0	0	0	1395	479	17	4	5116	4	BDP1	5	70818150	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	536530	70818150	110097110	1209	4110											
BDP1	55814	hgsc.bcm.edu	37	chr5	70845400	70845400	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gccagctcccatattggtcaAatcagtgaataccgaagaaa	15	8	8	10	1	2	2	2	1	0	1	3	3	3	2	3	1	2	1	3	1	6	3	rs59354595	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:70845400A>G	ENST00000358731.4	+	34	7225	c.6962A>G	c.(6961-6963)aAa>aGa	p.K2321R	BDP1_ENST00000380675.2_Intron	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	2321					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)		ATATTGGTCAAATCAGTGAAT	0.418													A|||	204	0.0407348	0.146	0.013	5008	,	,		18672	0.0		0.002	False		,,,				2504	0.0				p.K2321R		Atlas-SNP	.											.	BDP1	204	.	0			c.A6962G						PASS	.	A	ARG/LYS	479,3309		28,423,1443	93	88	89		6962	2.3	0.8	5	dbSNP_129	89	3,8211		0,3,4104	yes	missense	BDP1	NM_018429.2	26	28,426,5547	GG,GA,AA		0.0365,12.6452,4.016	benign	2321/2625	70845400	482,11520	1894	4107	6001	SO:0001583	missense	55814	exon34			TGGTCAAATCAGT	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.6962A>G	5.37:g.70845400A>G	ENSP00000351575:p.Lys2321Arg	218	0	0		228	103	0.451754	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	37	CCDS43328.1	79	0.036172161172161175	73	0.1483739837398374	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	A	12.53	1.964625	0.34659	0.126452	3.65E-4	ENSG00000145734	ENST00000358731;ENST00000451951	T	0.04551	3.6	5.96	2.27	0.28462	.	0.277827	0.31577	N	0.007413	T	0.00012	0.0000	N	0.21448	0.665	0.80722	D	1	B	0.28178	0.202	B	0.26202	0.067	T	0.61033	-0.7144	10	0.12766	T	0.61	.	4.5339	0.12019	0.6602:0.1661:0.1737:0.0	rs59354595;rs61734266	2321	A6H8Y1	BDP1_HUMAN	R	2321;1869	ENSP00000351575:K2321R	ENSP00000351575:K2321R	K	+	2	0	BDP1	70881156	0.700000	0.27796	0.848000	0.33437	0.954000	0.61252	0.169000	0.16641	0.157000	0.19338	0.533000	0.62120	AAA	A|0.963;G|0.037	0.037	strong		0.418	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429		G	70845400	A	G	70845400	3	3	22	1	0	0	0	0	1	0	0	0	1395	14	1	3	7096	3	BDP1	5	70845400	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	27250	70845400	110069860	1210	4111											
MAP1B	4131	hgsc.bcm.edu	37	chr5	71489695	71489695	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tctttctttaaaacccagatCggggagttactaagcaccac	12	11	7	11	1	2	1	0	0	2	1	3	2	2	2	2	2	3	2	2	2	4	5	rs2227915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:71489695C>T	ENST00000296755.7	+	5	811	c.513C>T	c.(511-513)atC>atT	p.I171I		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	171					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)		AAACCCAGATCGGGGAGTTAC	0.433													C|||	156	0.0311502	0.1135	0.0086	5008	,	,		20619	0.0		0.0	False		,,,				2504	0.0				p.I171I	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.C513T						PASS	.	C		353,4053	182.9+/-210.6	14,325,1864	48	47	48		513	2.3	1	5	dbSNP_123	48	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	MAP1B	NM_005909.3		14,329,6160	TT,TC,CC		0.0465,8.0118,2.7449		171/2469	71489695	357,12649	2203	4300	6503	SO:0001819	synonymous_variant	4131	exon5			CCAGATCGGGGAG	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.513C>T	5.37:g.71489695C>T		52	0	0		49	28	0.571429	NM_005909	A2BDK5	Silent	SNP	ENST00000296755.7	37	CCDS4012.1																																																																																			C|0.968;T|0.032	0.032	strong		0.433	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		T	71489695	C	T	71489695	2	4	22	1	0	0	0	0	0	0	0	1	9237	874	31	1		1	MAP1B	5	71489695	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	644295	71489695	109425565	1211	4112											
MAP1B	4131	hgsc.bcm.edu	37	chr5	71495320	71495320	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tactgttacgagactgcagaGaaaatcactagaacccctca	15	8	7	11	1	2	3	2	0	0	3	2	5	2	3	2	0	4	2	2	0	6	3	rs115914542	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:71495320G>A	ENST00000296755.7	+	5	6436	c.6138G>A	c.(6136-6138)gaG>gaA	p.E2046E		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	2046					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)	p.E2046D(2)		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)		AGACTGCAGAGAAAATCACTA	0.458													G|||	7	0.00139776	0.0053	0.0	5008	,	,		19505	0.0		0.0	False		,,,				2504	0.0				p.E2046E	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											MAP1B,rectum,carcinoma,0,2	MAP1B	243	2	2	Substitution - Missense(2)	large_intestine(2)	c.G6138A						PASS	.	G		10,4396	15.5+/-35.6	0,10,2193	117	129	125		6138	3.9	0.9	5	dbSNP_133	125	0,8600		0,0,4300	no	coding-synonymous	MAP1B	NM_005909.3		0,10,6493	AA,AG,GG		0.0,0.227,0.0769		2046/2469	71495320	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	4131	exon5			TGCAGAGAAAATC	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.6138G>A	5.37:g.71495320G>A		122	0	0		163	87	0.533742	NM_005909	A2BDK5	Silent	SNP	ENST00000296755.7	37	CCDS4012.1																																																																																			G|0.999;A|0.001	0.001	strong		0.458	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		A	71495320	G	A	71495320	2	1	22	1	0	0	0	0	0	0	0	1	9237	933	33	2		2	MAP1B	5	71495320	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5625	71495320	109419940	1212	4113											
PTCD2	79810	hgsc.bcm.edu	37	chr5	71618069	71618069	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaaagaaagtggctgttgcAtgtaatctttctggcactaa	13	12	9	7	0	2	1	0	0	2	1	2	1	2	1	0	2	1	5	0	2	5	4			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:71618069A>G	ENST00000380639.5	+	2	214	c.198A>G	c.(196-198)gcA>gcG	p.A66A	PTCD2_ENST00000543322.1_Silent_p.A66A|MRPS27_ENST00000513900.1_5'Flank|MRPS27_ENST00000522095.1_5'Flank|PTCD2_ENST00000536805.1_5'UTR|PTCD2_ENST00000503868.1_Silent_p.A66A|MRPS27_ENST00000457646.4_5'Flank|MRPS27_ENST00000515404.1_5'Flank|MRPS27_ENST00000261413.5_5'Flank	NM_024754.3	NP_079030.3	Q8WV60	PTCD2_HUMAN	pentatricopeptide repeat domain 2	66					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)		TGGCTGTTGCATGTAATCTTT	0.299																																					p.A66A		Atlas-SNP	.											.	PTCD2	31	.	0			c.A198G						PASS	.						107	119	115					5																	71618069		1815	4077	5892	SO:0001819	synonymous_variant	79810	exon2			TGTTGCATGTAAT	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.198A>G	5.37:g.71618069A>G		86	0	0		75	24	0.32	NM_024754	B7Z5D0|B7Z8L7|E9PFV7|Q6IA65|Q9H9R0	Silent	SNP	ENST00000380639.5	37	CCDS4014.2																																																																																			.	.	none		0.299	PTCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218562.6	NM_024754		G	71618069	A	G	71618069	2	3	22	1	0	0	0	0	0	0	0	1	12740	204	8	3		3	PTCD2	5	71618069	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	122749	71618069	109297191	1213	4114											
ZNF366	167465	hgsc.bcm.edu	37	chr5	71740073	71740073	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcctgctccagactcctcAggacaccggctgtctgtgcc	5	9	9	18	1	2	1	1	0	1	1	5	2	5	2	6	2	2	2	6	2	0	0	rs116305374	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:71740073A>T	ENST00000318442.5	-	5	2235	c.1745T>A	c.(1744-1746)cTg>cAg	p.L582Q	RP11-389C8.2_ENST00000564956.1_RNA	NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	582	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)		CAGACTCCTCAGGACACCGGC	0.607													A|||	9	0.00179712	0.0068	0.0	5008	,	,		15362	0.0		0.0	False		,,,				2504	0.0				p.L582Q		Atlas-SNP	.											.	ZNF366	108	.	0			c.T1745A						PASS	.	A	GLN/LEU	17,4379		0,17,2181	36	44	41		1745	5.9	1	5	dbSNP_133	41	0,8588		0,0,4294	yes	missense	ZNF366	NM_152625.1	113	0,17,6475	TT,TA,AA		0.0,0.3867,0.1309	probably-damaging	582/745	71740073	17,12967	2198	4294	6492	SO:0001583	missense	167465	exon5			CTCCTCAGGACAC	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.1745T>A	5.37:g.71740073A>T	ENSP00000313158:p.Leu582Gln	108	0	0		102	42	0.411765	NM_152625	Q5HYI9|Q7RTV4	Missense_Mutation	SNP	ENST00000318442.5	37	CCDS4015.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	20.9	4.063034	0.76187	0.003867	0.0	ENSG00000178175	ENST00000318442	T	0.09723	2.95	5.87	5.87	0.94306	.	0.000000	0.52532	D	0.000062	T	0.17023	0.0409	L	0.36672	1.1	0.47737	D	0.999503	D	0.63880	0.993	D	0.62955	0.909	T	0.07616	-1.0763	10	0.07482	T	0.82	-37.1713	11.6024	0.51010	0.931:0.0:0.069:0.0	.	582	Q8N895	ZN366_HUMAN	Q	582	ENSP00000313158:L582Q	ENSP00000313158:L582Q	L	-	2	0	ZNF366	71775829	1.000000	0.71417	0.992000	0.48379	0.753000	0.42808	6.038000	0.70964	2.371000	0.80710	0.533000	0.62120	CTG	A|0.999;T|0.001	0.001	strong		0.607	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3			T	71740073	A	T	71740073	3	4	22	1	0	0	0	0	1	0	0	0	17885	188	7	5	493	5	ZNF366	5	71740073	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	122004	71740073	109175187	1214	4115											
GFM2	84340	hgsc.bcm.edu	37	chr5	74037369	74037369	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttaccttttcagctggtaaCaaatcaaaattctcactaaa	15	14	3	9	0	3	0	3	0	1	0	4	0	3	0	1	1	3	2	1	1	7	7	rs35565659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:74037369C>T	ENST00000296805.3	-	11	1372	c.915G>A	c.(913-915)ttG>ttA	p.L305L	GFM2_ENST00000509430.1_Silent_p.L305L|GFM2_ENST00000427854.2_Silent_p.L305L|GFM2_ENST00000345239.2_Silent_p.L305L	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)		CAGCTGGTAACAAATCAAAAT	0.303													C|||	152	0.0303514	0.1097	0.0101	5008	,	,		15822	0.0		0.0	False		,,,				2504	0.0				p.L305L		Atlas-SNP	.											.	GFM2	38	.	0			c.G915A						PASS	.	C	,,	392,4000		12,368,1816	42	44	43		915,915,915	3.1	1	5	dbSNP_126	43	5,8569		0,5,4282	no	coding-synonymous,coding-synonymous,coding-synonymous	GFM2	NM_032380.3,NM_170681.1,NM_170691.1	,,	12,373,6098	TT,TC,CC		0.0583,8.9253,3.0619	,,	305/780,305/514,305/733	74037369	397,12569	2196	4287	6483	SO:0001819	synonymous_variant	84340	exon11			TGGTAACAAATCA	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.915G>A	5.37:g.74037369C>T		279	0	0		247	110	0.445344	NM_032380		Silent	SNP	ENST00000296805.3	37	CCDS4023.1																																																																																			C|0.976;T|0.024	0.024	strong		0.303	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380		T	74037369	C	T	74037369	2	4	22	1	0	0	0	0	0	0	0	1	6350	477	17	2		2	GFM2	5	74037369	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2297296	74037369	106877891	1215	4116											
POC5	134359	hgsc.bcm.edu	37	chr5	75001590	75001590	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttccaacttctattgcagtTtctcttacttcagagttatt	8	20	4	9	0	3	1	1	0	2	1	5	1	4	1	1	0	3	3	1	0	4	9	rs77025299	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:75001590T>A	ENST00000428202.2	-	4	435	c.246A>T	c.(244-246)gaA>gaT	p.E82D	POC5_ENST00000380475.2_5'UTR|POC5_ENST00000446329.2_Missense_Mutation_p.E57D|POC5_ENST00000514838.2_Intron|POC5_ENST00000504862.1_5'UTR|POC5_ENST00000510798.1_5'UTR	NM_001099271.1	NP_001092741.1	Q8NA72	POC5_HUMAN	POC5 centriolar protein	82					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						CTATTGCAGTTTCTCTTACTT	0.284													T|||	295	0.0589058	0.211	0.0202	5008	,	,		16251	0.0		0.002	False		,,,				2504	0.0				p.E82D		Atlas-SNP	.											.	POC5	82	.	0			c.A246T						PASS	.	T	ASP/GLU,ASP/GLU	586,2982		47,492,1245	79	71	74		246,171	2.4	0.4	5	dbSNP_131	74	4,8068		0,4,4032	yes	missense,missense	POC5	NM_001099271.1,NM_152408.2	45,45	47,496,5277	AA,AT,TT		0.0496,16.4238,5.0687	benign,benign	82/576,57/551	75001590	590,11050	1784	4036	5820	SO:0001583	missense	134359	exon4			TGCAGTTTCTCTT	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.246A>T	5.37:g.75001590T>A	ENSP00000410216:p.Glu82Asp	67	0	0		55	19	0.345455	NM_001099271	B4DJG7|Q494X7|Q494X9|Q6P085	Missense_Mutation	SNP	ENST00000428202.2	37	CCDS47236.1	96	0.04395604395604396	88	0.17886178861788618	8	0.022099447513812154	0	0.0	0	0.0	T	7.456	0.643625	0.14451	0.164238	4.96E-4	ENSG00000152359	ENST00000428202;ENST00000446329	T;T	0.25414	1.81;1.8	4.91	2.36	0.29203	.	0.396419	0.27609	N	0.018614	T	0.00039	0.0001	L	0.43701	1.375	0.09310	P	0.9999988642	B;B	0.12630	0.006;0.006	B;B	0.13407	0.009;0.006	T	0.16571	-1.0398	9	0.34782	T	0.22	-13.4474	9.2644	0.37632	0.0:0.0:0.3522:0.6478	.	82;57	Q8NA72;Q8NA72-3	POC5_HUMAN;.	D	82;57	ENSP00000410216:E82D;ENSP00000399481:E57D	ENSP00000410216:E82D	E	-	3	2	POC5	75037346	0.911000	0.30947	0.398000	0.26321	0.137000	0.21094	1.191000	0.32138	0.392000	0.25172	0.528000	0.53228	GAA	T|0.965;A|0.035	0.035	strong		0.284	POC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369124.1	NM_152408		A	75001590	T	A	75001590	3	1	22	1	0	0	0	0	1	0	0	0	12186	1838	64	5	1517	5	POC5	5	75001590	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	964221	75001590	105913670	1216	4117											
LHFPL2	10184	hgsc.bcm.edu	37	chr5	77784810	77784810	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgcttgtgcagagaagacAgcacagatgaaagtgaggac	14	7	13	7	0	1	5	0	2	1	3	1	7	1	6	0	1	3	3	0	1	2	1	rs35110604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:77784810A>C	ENST00000515007.2	-	3	907	c.597T>G	c.(595-597)gcT>gcG	p.A199A	LHFPL2_ENST00000380345.2_Silent_p.A199A			Q6ZUX7	LHPL2_HUMAN	lipoma HMGIC fusion partner-like 2	199						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)		CAGAGAAGACAGCACAGATGA	0.473													A|||	116	0.0231629	0.0825	0.0101	5008	,	,		21336	0.0		0.0	False		,,,				2504	0.0				p.A199A		Atlas-SNP	.											.	LHFPL2	9	.	0			c.T597G						PASS	.	A		282,4124	157.4+/-190.3	7,268,1928	134	131	132		597	-4.5	1	5	dbSNP_126	132	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	LHFPL2	NM_005779.2		7,271,6225	CC,CA,AA		0.0349,6.4004,2.1913		199/229	77784810	285,12721	2203	4300	6503	SO:0001819	synonymous_variant	10184	exon5			GAAGACAGCACAG	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.597T>G	5.37:g.77784810A>C		163	0	0		167	83	0.497006	NM_005779	B2RMQ6|Q7Z5P0|Q92605	Silent	SNP	ENST00000515007.2	37	CCDS4042.1																																																																																			A|0.982;C|0.018	0.018	strong		0.473	LHFPL2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369098.2	NM_005779		C	77784810	A	C	77784810	2	2	22	1	0	0	0	0	0	0	0	1	8774	175	7	5		5	LHFPL2	5	77784810	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2783220	77784810	103130450	1217	4118											
ANKRD34B	340120	hgsc.bcm.edu	37	chr5	79854667	79854667	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaggatctttttctttcctAtaagtgctttgccgtcttct	6	19	7	9	1	4	1	0	0	4	1	5	2	5	2	2	1	2	1	2	1	2	7	rs147745221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:79854667A>G	ENST00000338682.3	-	5	1844	c.1172T>C	c.(1171-1173)aTa>aCa	p.I391T		NM_001004441.2	NP_001004441.2	A5PLL1	AN34B_HUMAN	ankyrin repeat domain 34B	391						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)		TTTCTTTCCTATAAGTGCTTT	0.463													a|||	2	0.000399361	0.0015	0.0	5008	,	,		14523	0.0		0.0	False		,,,				2504	0.0				p.I391T		Atlas-SNP	.											.	ANKRD34B	61	.	0			c.T1172C						PASS	.	G	THR/ILE	12,4394	19.1+/-41.9	0,12,2191	57	62	60		1172	-5.4	0	5	dbSNP_134	60	0,8600		0,0,4300	yes	missense	ANKRD34B	NM_001004441.2	89	0,12,6491	GG,GA,AA		0.0,0.2724,0.0923	benign	391/515	79854667	12,12994	2203	4300	6503	SO:0001583	missense	340120	exon5			TTTCCTATAAGTG		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.1172T>C	5.37:g.79854667A>G	ENSP00000339802:p.Ile391Thr	46	0	0		57	34	0.596491	NM_001004441	B2RPH1|Q68D79	Missense_Mutation	SNP	ENST00000338682.3	37	CCDS34194.1	.	.	.	.	.	.	.	.	.	.	a	4.439	0.081337	0.08533	0.002724	0.0	ENSG00000189127	ENST00000338682	T	0.20738	2.05	5.8	-5.38	0.02673	.	17.413900	0.01263	N	0.009220	T	0.17450	0.0419	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25293	-1.0136	10	0.40728	T	0.16	3.3058	10.1179	0.42603	0.5602:0.0:0.3519:0.0879	.	391	A5PLL1	AN34B_HUMAN	T	391	ENSP00000339802:I391T	ENSP00000339802:I391T	I	-	2	0	ANKRD34B	79890423	0.000000	0.05858	0.000000	0.03702	0.673000	0.39480	-0.530000	0.06179	-1.261000	0.02462	-0.976000	0.02587	ATA	A|0.999;G|0.001	0.001	strong		0.463	ANKRD34B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369475.1	NM_001004441		G	79854667	A	G	79854667	3	3	22	1	0	0	0	0	1	0	0	0	663	449	16	3	376	3	ANKRD34B	5	79854667	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2069857	79854667	101060593	1218	4119											
MSH3	4437	hgsc.bcm.edu	37	chr5	79974885	79974885	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgtccgagcaaacagaggCgctcatccacagagccacat	12	6	9	14	2	1	2	1	0	0	2	3	3	3	2	3	1	3	2	3	1	1	1	rs35121792	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:79974885C>T	ENST00000265081.6	+	8	1393	c.1313C>T	c.(1312-1314)gCg>gTg	p.A438V		NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	438					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)		CAAACAGAGGCGCTCATCCAC	0.473								Mismatch excision repair (MMR)					C|||	5	0.000998403	0.0015	0.0	5008	,	,		15950	0.0		0.0	False		,,,				2504	0.0031				p.A438V	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											.	MSH3	129	.	0			c.C1313T						PASS	.	C	VAL/ALA	14,4392	21.2+/-45.6	0,14,2189	133	129	130		1313	-11	0	5	dbSNP_126	130	0,8600		0,0,4300	yes	missense	MSH3	NM_002439.3	64	0,14,6489	TT,TC,CC		0.0,0.3177,0.1076	benign	438/1138	79974885	14,12992	2203	4300	6503	SO:0001583	missense	4437	exon8			CAGAGGCGCTCAT	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.1313C>T	5.37:g.79974885C>T	ENSP00000265081:p.Ala438Val	62	0	0		56	23	0.410714	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	37	CCDS34195.1	.	.	.	.	.	.	.	.	.	.	C	14.36	2.513487	0.44660	0.003177	0.0	ENSG00000113318	ENST00000265081;ENST00000535995	D	0.86562	-2.14	5.51	-11.0	0.00169	DNA mismatch repair protein MutS, connector (2);	1.009680	0.07961	N	0.982372	T	0.70185	0.3195	N	0.14661	0.345	0.09310	N	1	B	0.22800	0.075	B	0.21546	0.035	T	0.55780	-0.8087	9	.	.	.	4.4871	11.55	0.50715	0.1018:0.6438:0.1479:0.1066	rs35121792	438	P20585	MSH3_HUMAN	V	438;429	ENSP00000265081:A438V	.	A	+	2	0	MSH3	80010641	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.700000	0.01905	-2.495000	0.00514	-1.181000	0.01715	GCG	C|0.999;T|0.001	0.001	strong		0.473	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		T	79974885	C	T	79974885	3	4	22	1	0	0	0	0	1	0	0	0	9880	768	27	1	1343	1	MSH3	5	79974885	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	120218	79974885	100940375	1219	4120											
ZCCHC9	84240	hgsc.bcm.edu	37	chr5	80604427	80604427	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	catggaattgcagattgcccCgccgcccttgaaaatcaaga	12	8	9	12	2	1	3	1	1	0	2	1	4	1	4	4	1	2	1	4	1	4	3	rs149561750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:80604427C>T	ENST00000254037.2	+	2	3587	c.432C>T	c.(430-432)ccC>ccT	p.P144P	ZCCHC9_ENST00000438268.2_Silent_p.P144P|ZCCHC9_ENST00000407610.3_Silent_p.P144P|ZCCHC9_ENST00000506458.1_3'UTR|ZCCHC9_ENST00000380199.5_Silent_p.P144P			Q8N567	ZCHC9_HUMAN	zinc finger, CCHC domain containing 9	144					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)		CAGATTGCCCCGCCGCCCTTG	0.473													C|||	2	0.000399361	0.0015	0.0	5008	,	,		14028	0.0		0.0	False		,,,				2504	0.0				p.P144P		Atlas-SNP	.											ZCCHC9,bladder,carcinoma,0,1	ZCCHC9	26	1	0			c.C432T						scavenged	.	C	,,	20,4386	28.1+/-56.4	1,18,2184	87	88	88		432,432,432	-11.9	0.6	5	dbSNP_134	88	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	ZCCHC9	NM_001131035.1,NM_001131036.1,NM_032280.2	,,	1,18,6484	TT,TC,CC		0.0,0.4539,0.1538	,,	144/272,144/272,144/272	80604427	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	84240	exon3			TTGCCCCGCCGCC	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.432C>T	5.37:g.80604427C>T		187	1	0.00534759		180	78	0.433333	NM_001131036	B2RAE7|Q9H027	Silent	SNP	ENST00000254037.2	37	CCDS4054.1																																																																																			C|0.998;T|0.002	0.002	strong		0.473	ZCCHC9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239213.1	NM_032280		T	80604427	C	T	80604427	2	4	22	1	0	0	0	0	0	0	0	1	17610	639	23	1		1	ZCCHC9	5	80604427	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	629542	80604427	100310833	1220	4121											
ZCCHC9	84240	hgsc.bcm.edu	37	chr5	80608363	80608363	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttttctattcctttacagAgcgaatggtcacagttggtc	9	16	8	8	1	2	1	1	0	1	1	4	2	3	1	1	2	2	1	1	2	3	7	rs144053491	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:80608363A>C	ENST00000254037.2	+	5	3853	c.698A>C	c.(697-699)gAg>gCg	p.E233A	ZCCHC9_ENST00000380199.5_Splice_Site_p.E233A|ZCCHC9_ENST00000506458.1_3'UTR|ZCCHC9_ENST00000438268.2_Splice_Site_p.E233A|ZCCHC9_ENST00000407610.3_Splice_Site_p.E233A			Q8N567	ZCHC9_HUMAN	zinc finger, CCHC domain containing 9	233					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)		TCCTTTACAGAGCGAATGGTC	0.368													A|||	2	0.000399361	0.0015	0.0	5008	,	,		20172	0.0		0.0	False		,,,				2504	0.0				p.E233A		Atlas-SNP	.											.	ZCCHC9	26	.	0			c.A698C						PASS	.	A	ALA/GLU,ALA/GLU,ALA/GLU	19,4387	27.2+/-55.0	1,17,2185	75	73	74		698,698,698	5.9	0.9	5	dbSNP_134	74	0,8600		0,0,4300	yes	missense-near-splice,missense-near-splice,missense-near-splice	ZCCHC9	NM_001131035.1,NM_001131036.1,NM_032280.2	107,107,107	1,17,6485	CC,CA,AA		0.0,0.4312,0.1461	benign,benign,benign	233/272,233/272,233/272	80608363	19,12987	2203	4300	6503	SO:0001630	splice_region_variant	84240	exon6			TTACAGAGCGAAT	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.698-1A>C	5.37:g.80608363A>C		116	0	0		107	54	0.504673	NM_001131036	B2RAE7|Q9H027	Missense_Mutation	SNP	ENST00000254037.2	37	CCDS4054.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	A	10.88	1.474400	0.26423	0.004312	0.0	ENSG00000131732	ENST00000254037;ENST00000407610;ENST00000380199;ENST00000438268	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	5.89	5.89	0.94794	.	0.392038	0.30302	N	0.009933	T	0.20047	0.0482	N	0.03608	-0.345	0.29325	N	0.867064	B	0.06786	0.001	B	0.06405	0.002	T	0.13072	-1.0523	9	.	.	.	.	11.9071	0.52719	0.8547:0.1453:0.0:0.0	.	233	Q8N567	ZCHC9_HUMAN	A	233	ENSP00000254037:E233A;ENSP00000385047:E233A;ENSP00000369546:E233A;ENSP00000412637:E233A	.	E	+	2	0	ZCCHC9	80644119	0.991000	0.36638	0.942000	0.38095	0.749000	0.42624	2.913000	0.48790	2.246000	0.74042	0.533000	0.62120	GAG	A|0.998;C|0.002	0.002	strong		0.368	ZCCHC9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239213.1	NM_032280	Missense_Mutation	C	80608363	A	C	80608363	5	2	22	1	0	0	0	0	0	0	1	0	17610	318	11	5	716	5	ZCCHC9	5	80608363	Splice_Site	SNP	A	TCGA-G8-6324-01A-11D-2210-10	3936	80608363	100306897	1221	4122											
ACOT12	134526	hgsc.bcm.edu	37	chr5	80655766	80655766	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaaattgttaaaggtatctTcatgttgtaatcgaactttc	12	18	6	5	1	2	0	1	0	1	0	4	1	2	0	0	1	1	4	0	1	7	8	rs147339997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:80655766T>G	ENST00000307624.3	-	5	480	c.452A>C	c.(451-453)gAa>gCa	p.E151A	ACOT12_ENST00000513751.1_Missense_Mutation_p.E151A	NM_130767.2	NP_570123.1	Q8WYK0	ACO12_HUMAN	acyl-CoA thioesterase 12	151					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)		AAAGGTATCTTCATGTTGTAA	0.333													T|||	11	0.00219649	0.0083	0.0	5008	,	,		17992	0.0		0.0	False		,,,				2504	0.0				p.E151A		Atlas-SNP	.											.	ACOT12	57	.	0			c.A452C						PASS	.	T	ALA/GLU	45,4361	47.5+/-82.1	0,45,2158	127	124	125		452	5	0.7	5	dbSNP_134	125	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ACOT12	NM_130767.2	107	0,46,6457	GG,GT,TT		0.0116,1.0213,0.3537	possibly-damaging	151/556	80655766	46,12960	2203	4300	6503	SO:0001583	missense	134526	exon5			GTATCTTCATGTT	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.452A>C	5.37:g.80655766T>G	ENSP00000303246:p.Glu151Ala	165	0	0		152	79	0.519737	NM_130767	B3KVK9|Q5FWE9	Missense_Mutation	SNP	ENST00000307624.3	37	CCDS4055.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	T	0.472	-0.883839	0.02530	0.010213	1.16E-4	ENSG00000172497	ENST00000307624;ENST00000513751	T;T	0.30981	1.51;1.51	5.04	5.04	0.67666	.	0.058734	0.64402	D	0.000004	T	0.14570	0.0352	L	0.35249	1.045	0.47094	D	0.999312	B;B	0.13145	0.0;0.007	B;B	0.12156	0.001;0.007	T	0.06734	-1.0810	10	0.11794	T	0.64	-31.4031	9.2551	0.37579	0.0:0.0858:0.0:0.9142	.	151;151	Q5FWE9;Q8WYK0	.;ACO12_HUMAN	A	151	ENSP00000303246:E151A;ENSP00000421628:E151A	ENSP00000303246:E151A	E	-	2	0	ACOT12	80691522	0.996000	0.38824	0.705000	0.30386	0.094000	0.18550	1.765000	0.38481	2.030000	0.59900	0.533000	0.62120	GAA	T|0.996;G|0.004	0.004	strong		0.333	ACOT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254074.1	NM_130767		G	80655766	T	G	80655766	3	3	22	1	0	0	0	0	1	0	0	0	150	1783	62	5	1259	5	ACOT12	5	80655766	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	47403	80655766	100259494	1222	4123											
XRCC4	7518	hgsc.bcm.edu	37	chr5	82400773	82400773	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aagcagaatccaccttgtttCtgaacccagtataactcatt	13	12	5	11	0	2	2	1	1	1	1	3	2	3	2	3	0	3	3	3	0	5	5	rs28383138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:82400773C>G	ENST00000511817.1	+	2	115	c.35C>G	c.(34-36)tCt>tGt	p.S12C	XRCC4_ENST00000509268.1_3'UTR|XRCC4_ENST00000396027.4_Missense_Mutation_p.S12C|XRCC4_ENST00000282268.3_Missense_Mutation_p.S12C|XRCC4_ENST00000338635.6_Missense_Mutation_p.S12C			Q13426	XRCC4_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 4	12			S -> C (in dbSNP:rs28383138). {ECO:0000269|Ref.6}.		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)		CACCTTGTTTCTGAACCCAGT	0.333								Non-homologous end-joining					C|||	39	0.00778754	0.0287	0.0014	5008	,	,		14902	0.0		0.0	False		,,,				2504	0.0				p.S12C		Atlas-SNP	.											.	XRCC4	37	.	0			c.C35G						PASS	.	C	CYS/SER,CYS/SER,CYS/SER	104,4302	81.9+/-120.4	4,96,2103	90	94	93		35,35,35	4.8	1	5	dbSNP_125	93	0,8596		0,0,4298	yes	missense,missense,missense	XRCC4	NM_003401.3,NM_022406.2,NM_022550.2	112,112,112	4,96,6401	GG,GC,CC		0.0,2.3604,0.7999	probably-damaging,probably-damaging,probably-damaging	12/335,12/337,12/335	82400773	104,12898	2203	4298	6501	SO:0001583	missense	7518	exon2			TTGTTTCTGAACC	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.35C>G	5.37:g.82400773C>G	ENSP00000421491:p.Ser12Cys	136	0	0		144	69	0.479167	NM_003401	A8K3X4|Q9BS72|Q9UP94	Missense_Mutation	SNP	ENST00000511817.1	37	CCDS4059.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	C	14.29	2.491902	0.44352	0.023604	0.0	ENSG00000152422	ENST00000282268;ENST00000338635;ENST00000396027;ENST00000511817	T;T;T;T	0.21031	2.03;2.03;2.03;2.03	5.67	4.8	0.61643	DNA double-strand break repair and VJ recombination XRCC4, N-terminal (2);	0.132928	0.51477	D	0.000085	T	0.23330	0.0564	M	0.74258	2.255	0.49687	D	0.99981	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	T	0.34378	-0.9831	10	0.87932	D	0	-5.2753	14.8049	0.69945	0.0:0.9305:0.0:0.0695	rs28383138	12;12;12	Q13426-2;Q13426;Q13426-3	.;XRCC4_HUMAN;.	C	12	ENSP00000282268:S12C;ENSP00000342011:S12C;ENSP00000379344:S12C;ENSP00000421491:S12C	ENSP00000282268:S12C	S	+	2	0	XRCC4	82436529	1.000000	0.71417	0.994000	0.49952	0.199000	0.23934	3.483000	0.53194	1.524000	0.49035	0.591000	0.81541	TCT	C|0.993;G|0.007	0.007	strong		0.333	XRCC4-003	NOVEL	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000369624.1	NM_022550		G	82400773	C	G	82400773	3	3	22	1	0	0	0	0	1	0	0	0	17470	913	32	4	37	4	XRCC4	5	82400773	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1745007	82400773	98514487	1223	4124											
VCAN	1462	hgsc.bcm.edu	37	chr5	82835852	82835852	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gtgacactggagcagaaggaCccacggtggcacctctccct	9	6	12	14	1	1	2	0	1	1	1	2	4	1	4	3	4	1	2	3	4	1	0	rs61733401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:82835852C>T	ENST00000265077.3	+	8	7595	c.7030C>T	c.(7030-7032)Ccc>Tcc	p.P2344S	VCAN_ENST00000513016.1_3'UTR|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000512590.2_Intron|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000343200.5_Missense_Mutation_p.P1357S	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2344	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)	AGCAGAAGGACCCACGGTGGC	0.468													C|||	165	0.0329473	0.1172	0.0101	5008	,	,		19057	0.0		0.003	False		,,,				2504	0.0				p.P2344S		Atlas-SNP	.											.	VCAN	498	.	0			c.C7030T						PASS	.	C	,SER/PRO,,SER/PRO	417,3989	203.8+/-226.2	21,375,1807	90	85	87		,4069,,7030	2	0	5	dbSNP_129	87	4,8596	3.7+/-12.6	0,4,4296	yes	intron,missense,intron,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,74,,74	21,379,6103	TT,TC,CC		0.0465,9.4644,3.237	,benign,,benign	,1357/2410,,2344/3397	82835852	421,12585	2203	4300	6503	SO:0001583	missense	1462	exon8			GAAGGACCCACGG	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.7030C>T	5.37:g.82835852C>T	ENSP00000265077:p.Pro2344Ser	166	0	0		175	80	0.457143	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	64	0.029304029304029304	61	0.12398373983739837	3	0.008287292817679558	0	0.0	0	0.0	C	2.456	-0.325144	0.05350	0.094644	4.65E-4	ENSG00000038427	ENST00000265077;ENST00000343200	T;T	0.37235	1.21;1.21	6.07	2.02	0.26589	.	0.557747	0.17822	N	0.160824	T	0.00271	0.0008	L	0.41824	1.3	0.09310	N	1	P;P	0.38597	0.639;0.506	B;B	0.30029	0.11;0.051	T	0.07539	-1.0767	10	0.09843	T	0.71	.	6.8445	0.23980	0.3387:0.5251:0.0:0.1362	rs61733401	1357;2344	P13611-2;P13611	.;CSPG2_HUMAN	S	2344;1357	ENSP00000265077:P2344S;ENSP00000340062:P1357S	ENSP00000265077:P2344S	P	+	1	0	VCAN	82871608	0.000000	0.05858	0.007000	0.13788	0.153000	0.21895	-0.086000	0.11233	0.839000	0.34971	0.650000	0.86243	CCC	C|0.965;T|0.035	0.035	strong		0.468	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		T	82835852	C	T	82835852	3	4	22	1	0	0	0	0	1	0	0	0	17153	507	18	2	7056	2	VCAN	5	82835852	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	435079	82835852	98079408	1224	4125											
VCAN	1462	hgsc.bcm.edu	37	chr5	82836912	82836912	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aacatccctgccaattcctcGtaagtctgccacagttattc	10	12	5	14	1	1	0	0	0	1	0	5	0	3	0	4	0	3	2	4	0	4	4	rs61733389	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:82836912G>A	ENST00000265077.3	+	8	8655	c.8090G>A	c.(8089-8091)cGt>cAt	p.R2697H	VCAN_ENST00000513016.1_3'UTR|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000512590.2_Intron|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000343200.5_Missense_Mutation_p.R1710H	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2697	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)	CCAATTCCTCGTAAGTCTGCC	0.453													A|||	154	0.0307508	0.1097	0.0086	5008	,	,		22255	0.0		0.003	False		,,,				2504	0.0				p.R2697H		Atlas-SNP	.											.	VCAN	498	.	0			c.G8090A						PASS	.	A	,HIS/ARG,,HIS/ARG	375,4031	781.0+/-414.5	12,351,1840	87	82	84		,5129,,8090	3.4	0	5	dbSNP_129	84	4,8596	806.0+/-407.3	0,4,4296	yes	intron,missense,intron,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,29,,29	12,355,6136	AA,AG,GG		0.0465,8.5111,2.914	,benign,,benign	,1710/2410,,2697/3397	82836912	379,12627	2203	4300	6503	SO:0001583	missense	1462	exon8			TTCCTCGTAAGTC	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.8090G>A	5.37:g.82836912G>A	ENSP00000265077:p.Arg2697His	92	0	0		87	51	0.586207	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	59	0.027014652014652016	57	0.11585365853658537	2	0.0055248618784530384	0	0.0	0	0.0	A	3.518	-0.098356	0.07010	0.085111	4.65E-4	ENSG00000038427	ENST00000265077;ENST00000343200	T;T	0.30714	1.52;1.52	6.17	3.43	0.39272	.	0.411591	0.25929	N	0.027400	T	0.00210	0.0006	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	0.19031	-1.0318	10	0.33940	T	0.23	.	9.0379	0.36300	0.1951:0.1117:0.6933:0.0	rs61733389	1710;2697	P13611-2;P13611	.;CSPG2_HUMAN	H	2697;1710	ENSP00000265077:R2697H;ENSP00000340062:R1710H	ENSP00000265077:R2697H	R	+	2	0	VCAN	82872668	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.225000	0.09151	0.183000	0.20059	-1.569000	0.00873	CGT	G|0.967;A|0.033	0.033	strong		0.453	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		A	82836912	G	A	82836912	3	1	22	1	0	0	0	0	1	0	0	0	17153	1145	40	1	8116	1	VCAN	5	82836912	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1060	82836912	98078348	1225	4126											
EDIL3	10085	hgsc.bcm.edu	37	chr5	83433087	83433087	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caatttcttcccataaattcGcctgggcactcacaggaata	12	11	6	12	1	2	0	1	0	1	0	4	1	3	1	2	2	0	1	2	2	5	5	rs58219060	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:83433087G>A	ENST00000296591.5	-	5	859	c.441C>T	c.(439-441)ggC>ggT	p.G147G	EDIL3_ENST00000380138.3_Silent_p.G137G	NM_005711.3	NP_005702.3	O43854	EDIL3_HUMAN	EGF-like repeats and discoidin I-like domains 3	147	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)		CCATAAATTCGCCTGGGCACT	0.393													G|||	159	0.0317492	0.118	0.0029	5008	,	,		16170	0.0		0.001	False		,,,				2504	0.0				p.G147G		Atlas-SNP	.											.	EDIL3	94	.	0			c.C441T						PASS	.	G		465,3941	220.7+/-238.1	23,419,1761	175	153	160		441	-4	1	5	dbSNP_129	160	4,8596	3.7+/-12.6	0,4,4296	yes	coding-synonymous	EDIL3	NM_005711.3		23,423,6057	AA,AG,GG		0.0465,10.5538,3.606		147/481	83433087	469,12537	2203	4300	6503	SO:0001819	synonymous_variant	10085	exon5			AAATTCGCCTGGG	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.441C>T	5.37:g.83433087G>A		59	0	0		67	35	0.522388	NM_005711	B2R763|O43855|Q5D094|Q8N610	Silent	SNP	ENST00000296591.5	37	CCDS4062.1																																																																																			G|0.965;A|0.035	0.035	strong		0.393	EDIL3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239258.1	NM_005711		A	83433087	G	A	83433087	2	1	22	1	0	0	0	0	0	0	0	1	4917	1074	38	1		1	EDIL3	5	83433087	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	596175	83433087	97482173	1226	4127											
RASA1	5921	hgsc.bcm.edu	37	chr5	86681125	86681125	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aattctgttacagattctccAtctcctattgctgcaagaac	11	14	5	11	0	3	2	0	0	3	2	5	2	3	2	2	0	4	3	2	0	5	5	rs137898246		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:86681125A>T	ENST00000274376.6	+	22	3330	c.2766A>T	c.(2764-2766)ccA>ccT	p.P922P	RASA1_ENST00000456692.2_Silent_p.P745P|RASA1_ENST00000506290.1_Silent_p.P756P|RASA1_ENST00000512763.1_Silent_p.P755P	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	922	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				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)		CAGATTCTCCATCTCCTATTG	0.363																																					p.P922P		Atlas-SNP	.											.	RASA1	213	.	0			c.A2766T						PASS	.	A	,	5,4401	8.1+/-20.4	0,5,2198	124	111	116		2766,2235	-1.5	1	5	dbSNP_134	116	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	RASA1	NM_002890.2,NM_022650.2	,	0,5,6498	TT,TA,AA		0.0,0.1135,0.0384	,	922/1048,745/871	86681125	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	5921	exon22			TTCTCCATCTCCT		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.2766A>T	5.37:g.86681125A>T		115	0	0		122	68	0.557377	NM_002890	B2R6W3|Q9UDI1	Silent	SNP	ENST00000274376.6	37	CCDS34200.1																																																																																			A|1.000;G|0.000;T|0.000	0.000	strong		0.363	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890		T	86681125	A	T	86681125	2	4	22	1	0	0	0	0	0	0	0	1	13075	204	8	5		5	RASA1	5	86681125	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	3248038	86681125	94234135	1227	4128											
CCNH	902	hgsc.bcm.edu	37	chr5	86695228	86695228	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacgtgattacgttaagtgcAagctcagcagaatgacatcg	13	10	10	8	3	1	3	1	2	0	1	2	3	1	3	0	0	5	4	0	0	5	3	rs150856919	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:86695228A>T	ENST00000256897.4	-	7	1079	c.855T>A	c.(853-855)ctT>ctA	p.L285L	CCNH_ENST00000508855.1_Silent_p.L211L|CCNH_ENST00000504878.1_Silent_p.L211L	NM_001239.3	NP_001230.1	P51946	CCNH_HUMAN	cyclin H	285					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)		CGTTAAGTGCAAGCTCAGCAG	0.388								Direct reversal of damage;Direct reversal of damage;Nucleotide excision repair (NER)																													p.L285L		Atlas-SNP	.											.	CCNH	40	.	0			c.T855A						PASS	.	A	,	4,4402	8.1+/-20.4	0,4,2199	221	187	198		696,855	4.5	1	5	dbSNP_134	198	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CCNH	NM_001199189.1,NM_001239.3	,	0,4,6499	TT,TA,AA		0.0,0.0908,0.0308	,	232/271,285/324	86695228	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	902	exon7			AAGTGCAAGCTCA	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.855T>A	5.37:g.86695228A>T		86	0	0		75	33	0.44	NM_001239	Q53X72|Q8TBL9	Silent	SNP	ENST00000256897.4	37	CCDS4064.1																																																																																			A|1.000;T|0.000	0.000	strong		0.388	CCNH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239291.3	NM_001239		T	86695228	A	T	86695228	2	4	22	1	0	0	0	0	0	0	0	1	2927	117	5	5		5	CCNH	5	86695228	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	14103	86695228	94220032	1228	4129											
GPR98	84059	hgsc.bcm.edu	37	chr5	90136732	90136732	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tctcaacagagtgctccataCcatcagcatgaaagtggcca	13	8	8	12	0	2	2	2	1	1	1	4	2	3	2	3	1	4	2	3	1	3	1	rs61748627	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:90136732C>G	ENST00000405460.2	+	78	17045	c.16949C>G	c.(16948-16950)aCc>aGc	p.T5650S	GPR98_ENST00000425867.2_Missense_Mutation_p.T1311S	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	5650					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)		GTGCTCCATACCATCAGCATG	0.408													C|||	28	0.00559105	0.0204	0.0014	5008	,	,		19148	0.0		0.0	False		,,,				2504	0.0				p.T5650S		Atlas-SNP	.											.	GPR98	605	.	0			c.C16949G						PASS	.	C	SER/THR	47,3955		1,45,1955	75	75	75		16949	-6.1	0	5	dbSNP_129	75	1,8377		0,1,4188	yes	missense	GPR98	NM_032119.3	58	1,46,6143	GG,GC,CC		0.0119,1.1744,0.3877	benign	5650/6307	90136732	48,12332	2001	4189	6190	SO:0001583	missense	84059	exon78			TCCATACCATCAG	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.16949C>G	5.37:g.90136732C>G	ENSP00000384582:p.Thr5650Ser	63	0	0		58	30	0.517241	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	25	0.011446886446886446	24	0.04878048780487805	1	0.0027624309392265192	0	0.0	0	0.0	C	1.382	-0.583061	0.03827	0.011744	1.19E-4	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.28069	1.63;1.63	6.16	-6.11	0.02131	.	0.807701	0.12567	N	0.457630	T	0.01454	0.0047	N	0.04508	-0.205	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	0.33111	-0.9881	9	.	.	.	.	9.7985	0.40751	0.4619:0.4027:0.1354:0.0	rs61748627	1311;5650;1311	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	S	5650;5650;1311	ENSP00000384582:T5650S;ENSP00000392618:T1311S	.	T	+	2	0	GPR98	90172488	0.001000	0.12720	0.001000	0.08648	0.233000	0.25261	-0.112000	0.10791	-0.739000	0.04809	-0.885000	0.02943	ACC	C|0.988;G|0.012	0.012	strong		0.408	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		G	90136732	C	G	90136732	3	3	22	1	0	0	0	0	1	0	0	0	6730	507	18	4	17259	4	GPR98	5	90136732	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3441504	90136732	90778528	1229	4130											
ARSK	153642	hgsc.bcm.edu	37	chr5	94936744	94936744	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggaaatatatagcctattcGgatggtgcatcaatattgcc	12	13	9	7	1	1	0	1	0	0	0	2	2	1	2	2	3	3	1	2	3	7	7	rs61733083	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:94936744G>A	ENST00000380009.4	+	7	1495	c.1290G>A	c.(1288-1290)tcG>tcA	p.S430S		NM_198150.2	NP_937793.1	Q6UWY0	ARSK_HUMAN	arylsulfatase family, member K	430					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(2)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(1)	16		all_cancers(142;3.38e-06)|all_epithelial(76;6.57e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)		all cancers(79;6.5e-16)		TAGCCTATTCGGATGGTGCAT	0.383													G|||	47	0.00938498	0.034	0.0029	5008	,	,		20862	0.0		0.0	False		,,,				2504	0.0				p.S430S		Atlas-SNP	.											.	ARSK	29	.	0			c.G1290A						PASS	.	G		120,4286	88.7+/-127.4	0,120,2083	125	119	121		1290	-1.4	0.7	5	dbSNP_129	121	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ARSK	NM_198150.2		0,121,6382	AA,AG,GG		0.0116,2.7236,0.9303		430/537	94936744	121,12885	2203	4300	6503	SO:0001819	synonymous_variant	153642	exon7			CTATTCGGATGGT		CCDS4073.1	5q15	2013-02-14	2006-03-07		ENSG00000164291	ENSG00000164291		"Arylsulfatase family"	25239	protein-coding gene	gene with protein product		610011	"arylsulfatase K"			12975309, 16174644	Standard	NM_198150		Approved	DKFZp313G1735, TSULF	uc003kld.3	Q6UWY0	OTTHUMG00000121166	ENST00000380009.4:c.1290G>A	5.37:g.94936744G>A		112	0	0		130	56	0.430769	NM_198150	A2BDE3|B4E1I4|Q3ZCW3|Q8N3Q8	Silent	SNP	ENST00000380009.4	37	CCDS4073.1																																																																																			G|0.990;A|0.010	0.010	strong		0.383	ARSK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241652.2	NM_198150		A	94936744	G	A	94936744	2	1	22	1	0	0	0	0	0	0	0	1	996	1103	39	1		1	ARSK	5	94936744	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4800012	94936744	85978516	1230	4131											
GPR150	285601	hgsc.bcm.edu	37	chr5	94957071	94957071	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgactgccggctccggcgAcagctgcggaagcggctggg	5	4	19	13	6	0	0	0	0	0	0	1	3	1	1	2	6	4	3	2	6	1	0	rs375018988	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:94957071A>T	ENST00000380007.2	+	1	1290	c.1092A>T	c.(1090-1092)cgA>cgT	p.R364R		NM_199243.1	NP_954713.1	Q8NGU9	GP150_HUMAN	G protein-coupled receptor 150	364						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			lung(2)	2		all_cancers(142;0.000462)|all_epithelial(76;2.44e-06)|all_lung(232;0.0318)|Lung NSC(167;0.041)|Ovarian(225;0.051)		all cancers(79;1.82e-16)		GGCTCCGGCGACAGCTGCGGA	0.726													A|||	3	0.000599042	0.0023	0.0	5008	,	,		12900	0.0		0.0	False		,,,				2504	0.0				p.R364R		Atlas-SNP	.											.	GPR150	7	.	0			c.A1092T						PASS	.	A		12,3928		0,12,1958	4	6	5		1092	2.7	0.3	5		5	0,7982		0,0,3991	no	coding-synonymous	GPR150	NM_199243.1		0,12,5949	TT,TA,AA		0.0,0.3046,0.1007		364/435	94957071	12,11910	1970	3991	5961	SO:0001819	synonymous_variant	285601	exon1			CCGGCGACAGCTG	BC030197	CCDS4074.1	5q15	2012-08-21			ENSG00000178015	ENSG00000178015		"GPCR / Class A : Orphans"	23628	protein-coding gene	gene with protein product						12679517	Standard	NM_199243		Approved	PGR11	uc003kle.1	Q8NGU9	OTTHUMG00000121170	ENST00000380007.2:c.1092A>T	5.37:g.94957071A>T		21	0	0		21	14	0.666667	NM_199243		Silent	SNP	ENST00000380007.2	37	CCDS4074.1																																																																																			.	.	weak		0.726	GPR150-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241657.2			T	94957071	A	T	94957071	2	4	22	1	0	0	0	0	0	0	0	1	6664	262	10	5		5	GPR150	5	94957071	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	20327	94957071	85958189	1231	4132											
SPATA9	83890	hgsc.bcm.edu	37	chr5	95011166	95011166	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	attaacttccctcagcagacGaccagatatgtcccttagct	11	11	6	13	1	1	2	1	0	0	2	3	3	3	2	3	0	3	2	3	0	3	4	rs140676515	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:95011166G>A	ENST00000274432.8	-	3	469	c.328C>T	c.(328-330)Cgt>Tgt	p.R110C	RFESD_ENST00000508206.1_Intron|SPATA9_ENST00000395899.3_Missense_Mutation_p.R110C|SPATA9_ENST00000477047.2_5'UTR	NM_031952.3	NP_114158.2	Q9BWV2	SPAT9_HUMAN	spermatogenesis associated 9	110					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)		CTCAGCAGACGACCAGATATG	0.433													G|||	5	0.000998403	0.0038	0.0	5008	,	,		18649	0.0		0.0	False		,,,				2504	0.0				p.R110C		Atlas-SNP	.											SPATA9,NS,carcinoma,+1,1	SPATA9	17	1	0			c.C328T						scavenged	.	G	CYS/ARG	29,4377	35.2+/-66.4	0,29,2174	133	113	120		328	3.9	0	5	dbSNP_134	120	0,8600		0,0,4300	yes	missense	SPATA9	NM_031952.3	180	0,29,6474	AA,AG,GG		0.0,0.6582,0.223	probably-damaging	110/255	95011166	29,12977	2203	4300	6503	SO:0001583	missense	83890	exon3			GCAGACGACCAGA	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.328C>T	5.37:g.95011166G>A	ENSP00000274432:p.Arg110Cys	120	1	0.00833333		137	63	0.459854	NM_031952	A8K8H3|Q4G122|Q86X33|Q8NA28	Missense_Mutation	SNP	ENST00000274432.8	37	CCDS4076.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	12.73	2.024694	0.35701	0.006582	0.0	ENSG00000145757	ENST00000274432;ENST00000395899	T	0.31510	1.49	4.76	3.88	0.44766	.	0.000000	0.51477	D	0.000082	T	0.26448	0.0646	L	0.27053	0.805	0.19300	N	0.999974	D	0.67145	0.996	P	0.57371	0.819	T	0.05818	-1.0862	10	0.87932	D	0	-8.0846	10.6281	0.45519	0.0:0.0:0.8093:0.1907	.	110	Q9BWV2	SPAT9_HUMAN	C	110	ENSP00000274432:R110C	ENSP00000274432:R110C	R	-	1	0	SPATA9	95036922	0.074000	0.21230	0.029000	0.17559	0.011000	0.07611	1.948000	0.40303	1.329000	0.45376	0.655000	0.94253	CGT	G|0.998;A|0.002	0.002	strong		0.433	SPATA9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304036.1	NM_031952		A	95011166	G	A	95011166	3	1	22	1	0	0	0	0	1	0	0	0	15031	1058	37	1	448	1	SPATA9	5	95011166	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	54095	95011166	85904094	1232	4133											
CAST	831	hgsc.bcm.edu	37	chr5	96082128	96082128	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtacagattaaaaccagccaCggtaaatttttagccacagt	15	10	7	9	1	0	1	0	0	0	1	0	1	0	1	3	1	4	2	3	1	6	6	rs78054235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:96082128C>T	ENST00000341926.3	+	15	1196	c.1034C>T	c.(1033-1035)aCg>aTg	p.T345M	CAST_ENST00000509903.1_Splice_Site_p.T310M|CAST_ENST00000325674.7_Splice_Site_p.T393M|CAST_ENST00000395812.2_Splice_Site_p.T387M|CAST_ENST00000309190.5_Splice_Site_p.T323M|CAST_ENST00000348386.3_3'UTR|CAST_ENST00000508608.1_Splice_Site_p.T391M|CAST_ENST00000515663.1_Splice_Site_p.T68M|CAST_ENST00000338252.3_Splice_Site_p.T332M|CAST_ENST00000508579.1_Splice_Site_p.T60M|CAST_ENST00000359176.4_Splice_Site_p.T409M|CAST_ENST00000510756.1_Splice_Site_p.T406M|CAST_ENST00000395813.1_Splice_Site_p.T428M|CAST_ENST00000504465.1_Splice_Site_p.T273M|CAST_ENST00000508830.1_Splice_Site_p.T428M|CAST_ENST00000511049.1_Splice_Site_p.T331M|CAST_ENST00000511782.1_Splice_Site_p.T331M			P20810	ICAL_HUMAN	calpastatin	345					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)		AAACCAGCCACGGTAAATTTT	0.418													c|||	63	0.0125799	0.0454	0.0014	5008	,	,		20246	0.0		0.0	False		,,,				2504	0.002				p.T387M		Atlas-SNP	.											.	CAST	58	.	0			c.C1160T						PASS	.	T	MET/THR,MET/THR,MET/THR	135,4271	98.0+/-136.7	2,131,2070	121	125	124		1160,995,968	1.3	1	5	dbSNP_131	124	2,8598	2.2+/-6.3	0,2,4298	yes	missense-near-splice,missense-near-splice,missense-near-splice	CAST	NM_001042440.2,NM_001190442.1,NM_173060.3	81,81,81	2,133,6368	TT,TC,CC		0.0233,3.064,1.0534	benign,benign,benign	387/751,332/696,323/687	96082128	137,12869	2203	4300	6503	SO:0001630	splice_region_variant	831	exon15			CAGCCACGGTAAA	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.1035+1C>T	5.37:g.96082128C>T		199	0	0		225	112	0.497778	NM_001042440	B7Z468|G5E946|G5E9D3|O95360|Q05DE8|Q7Z4K0|Q96D08|Q9H1Z5	Missense_Mutation	SNP	ENST00000341926.3	37		21|21	0.009615384615384616|0.009615384615384616	20|20	0.04065040650406504|0.04065040650406504	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	c|c	8.238|8.238	0.806130|0.806130	0.16467|0.16467	0.03064|0.03064	2.33E-4|2.33E-4	ENSG00000153113|ENSG00000153113	ENST00000437034|ENST00000338252;ENST00000508830;ENST00000511097;ENST00000395813;ENST00000359176;ENST00000325674;ENST00000395812;ENST00000510756;ENST00000508608;ENST00000341926;ENST00000511049;ENST00000309190;ENST00000510156;ENST00000504465;ENST00000509903;ENST00000511782;ENST00000508579;ENST00000503828;ENST00000515663	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.22743	.|2.24;2.24;1.94;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24	6.17|6.17	1.3|1.3	0.21679|0.21679	.|.	.|0.548082	.|0.21244	.|N	.|0.077779	T|T	0.05731|0.05731	0.0150|0.0150	L|L	0.36672|0.36672	1.1|1.1	0.24426|0.24426	N|N	0.994593|0.994593	.|P;P;B;D;B;D;B;B;B;B;B;P;B;P;B;B;B	.|0.59767	.|0.867;0.79;0.366;0.962;0.43;0.986;0.132;0.055;0.178;0.284;0.055;0.84;0.245;0.741;0.451;0.378;0.178	.|B;B;B;B;B;P;B;B;B;B;B;B;B;B;B;B;B	.|0.57057	.|0.345;0.199;0.108;0.417;0.21;0.812;0.131;0.021;0.057;0.1;0.061;0.234;0.058;0.287;0.066;0.058;0.197	T|T	0.03043|0.03043	-1.1079|-1.1079	5|10	.|0.46703	.|T	.|0.11	-0.1946|-0.1946	5.1484|5.1484	0.14996|0.14996	0.1336:0.5121:0.0:0.3543|0.1336:0.5121:0.0:0.3543	.|.	.|273;193;391;68;96;68;331;310;323;304;345;393;387;409;406;428;332	.|E9PDE4;B7Z8S8;B7Z468;E7EQA0;Q86YM9;E7EPY6;E7EVY3;E9PCH5;G5E946;P20810-4;P20810;P20810-5;G5E9D3;P20810-7;E7ESM9;P20810-6;P20810-2	.|.;.;.;.;.;.;.;.;.;.;ICAL_HUMAN;.;.;.;.;.;.	W|M	97|332;428;393;428;409;393;387;406;391;345;331;323;345;273;310;331;60;60;68	.|ENSP00000343421:T332M;ENSP00000425721:T428M;ENSP00000422951:T393M;ENSP00000379158:T428M;ENSP00000352098:T409M;ENSP00000320319:T393M;ENSP00000379157:T387M;ENSP00000422176:T406M;ENSP00000422677:T391M;ENSP00000339914:T345M;ENSP00000421130:T331M;ENSP00000312523:T323M;ENSP00000422325:T345M;ENSP00000425670:T273M;ENSP00000426946:T310M;ENSP00000423638:T331M;ENSP00000425787:T60M;ENSP00000422807:T60M;ENSP00000422929:T68M	.|ENSP00000312523:T323M	R|T	+|+	1|2	2|0	CAST|CAST	96107884|96107884	0.001000|0.001000	0.12720|0.12720	0.998000|0.998000	0.56505|0.56505	0.117000|0.117000	0.20001|0.20001	-0.754000|-0.754000	0.04787|0.04787	0.168000|0.168000	0.19655|0.19655	-0.733000|-0.733000	0.03571|0.03571	CGG|ACG	C|0.988;T|0.012	0.012	strong		0.418	CAST-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000250199.2	NM_173062	Missense_Mutation	T	96082128	C	T	96082128	5	4	22	1	0	0	0	0	0	0	1	0	2686	550	19	1	1473	1	CAST	5	96082128	Splice_Site	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1070962	96082128	84833132	1233	4134											
FAM174A	345757	hgsc.bcm.edu	37	chr5	99897880	99897880	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caacacgttgtttgatgccaAtcatcctcgaaggtaagtat	12	12	8	9	2	1	1	1	1	0	0	3	2	2	1	2	1	2	4	2	1	5	4	rs76060686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:99897880A>G	ENST00000312637.4	+	2	783	c.557A>G	c.(556-558)aAt>aGt	p.N186S	FAM174A_ENST00000505792.1_3'UTR	NM_198507.1	NP_940909.1	Q8TBP5	F174A_HUMAN	family with sequence similarity 174, member A	186						integral component of membrane (GO:0016021)				breast(2)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						TTTGATGCCAATCATCCTCGA	0.368													A|||	19	0.00379393	0.0144	0.0	5008	,	,		14171	0.0		0.0	False		,,,				2504	0.0				p.N186S		Atlas-SNP	.											.	FAM174A	13	.	0			c.A557G						PASS	.	A	SER/ASN	98,4308	78.3+/-116.7	1,96,2106	143	131	135		557	2.8	1	5	dbSNP_131	135	0,8600		0,0,4300	yes	missense	FAM174A	NM_198507.1	46	1,96,6406	GG,GA,AA		0.0,2.2242,0.7535	benign	186/191	99897880	98,12908	2203	4300	6503	SO:0001583	missense	345757	exon2			ATGCCAATCATCC	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.557A>G	5.37:g.99897880A>G	ENSP00000307954:p.Asn186Ser	206	0	0		242	117	0.483471	NM_198507	A8K0H4	Missense_Mutation	SNP	ENST00000312637.4	37	CCDS4090.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	A	12.69	2.014664	0.35511	0.022242	0.0	ENSG00000174132	ENST00000312637	T	0.50548	0.74	5.21	2.81	0.32909	.	0.211018	0.31145	N	0.008177	T	0.14700	0.0355	L	0.35644	1.08	0.35327	D	0.785245	B	0.31989	0.35	B	0.35655	0.207	T	0.20974	-1.0259	9	.	.	.	-11.1789	8.0143	0.30372	0.8295:0.0:0.1705:0.0	.	186	Q8TBP5	F174A_HUMAN	S	186	ENSP00000307954:N186S	.	N	+	2	0	FAM174A	99925779	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	1.898000	0.39809	0.319000	0.23209	0.383000	0.25322	AAT	A|0.992;G|0.008	0.008	strong		0.368	FAM174A-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000250631.2	NM_198507		G	99897880	A	G	99897880	3	3	22	1	0	0	0	0	1	0	0	0	5500	101	4	3	563	3	FAM174A	5	99897880	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	3815752	99897880	81017380	1234	4135											
FER	2241	hgsc.bcm.edu	37	chr5	108281862	108281862	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaggctatccaaatttgaatCtattcgtcattcaattgctg	11	15	7	8	1	3	1	2	1	1	0	5	2	4	1	1	1	1	2	1	1	5	6			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:108281862C>T	ENST00000281092.4	+	11	1652	c.1268C>T	c.(1267-1269)tCt>tTt	p.S423F	FER_ENST00000536402.1_Silent_p.L319L|FER_ENST00000438717.2_Missense_Mutation_p.S248F	NM_005246.2	NP_005237.2	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	423					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)		AAATTTGAATCTATTCGTCAT	0.373																																					p.S423F	Colon(146;1051 1799 9836 27344 47401)	Atlas-SNP	.											.	FER	100	.	0			c.C1268T						PASS	.						129	134	132					5																	108281862		2202	4300	6502	SO:0001583	missense	2241	exon11			TTGAATCTATTCG	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.1268C>T	5.37:g.108281862C>T	ENSP00000281092:p.Ser423Phe	77	0	0		70	4	0.0571429	NM_005246	B2RCR4|B4DSQ2|H2FLB8	Missense_Mutation	SNP	ENST00000281092.4	37	CCDS4098.1	.	.	.	.	.	.	.	.	.	.	C	19.61	3.859764	0.71834	.	.	ENSG00000151422	ENST00000281092;ENST00000438717	T;T	0.75367	-0.92;-0.93	5.45	5.45	0.79879	.	0.045955	0.85682	D	0.000000	T	0.68842	0.3045	N	0.22421	0.69	0.49213	D	0.999767	P	0.37955	0.612	B	0.41088	0.347	T	0.72261	-0.4345	10	0.66056	D	0.02	-12.8969	19.6346	0.95724	0.0:1.0:0.0:0.0	.	423	P16591	FER_HUMAN	F	423;248	ENSP00000281092:S423F;ENSP00000394297:S248F	ENSP00000281092:S423F	S	+	2	0	FER	108309761	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.910000	0.75741	2.720000	0.93068	0.491000	0.48974	TCT	.	.	none		0.373	FER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250664.1	NM_005246		T	108281862	C	T	108281862	3	4	22	1	0	0	0	0	1	0	0	0	5821	913	32	2	1302	2	FER	5	108281862	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	8383982	108281862	72633398	1235	4136											
FER	2241	hgsc.bcm.edu	37	chr5	108294979	108294979	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacattcctcaacttatagaTcatcactatacaacaaaaca	19	10	1	11	0	3	1	3	0	0	1	4	1	4	1	1	0	5	0	1	0	9	5	rs34869483	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:108294979T>C	ENST00000281092.4	+	13	1971	c.1587T>C	c.(1585-1587)gaT>gaC	p.D529D	FER_ENST00000536402.1_3'UTR|FER_ENST00000438717.2_Silent_p.D354D	NM_005246.2	NP_005237.2	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	529	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				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)		AACTTATAGATCATCACTATA	0.363													T|||	30	0.00599042	0.0015	0.0043	5008	,	,		15833	0.0		0.0119	False		,,,				2504	0.0133				p.D529D	Colon(146;1051 1799 9836 27344 47401)	Atlas-SNP	.											.	FER	100	.	0			c.T1587C						PASS	.	T		14,4390	21.2+/-45.6	0,14,2188	138	131	133		1587	-7.7	0.9	5	dbSNP_126	133	193,8405	84.8+/-147.2	4,185,4110	no	coding-synonymous	FER	NM_005246.2		4,199,6298	CC,CT,TT		2.2447,0.3179,1.5921		529/823	108294979	207,12795	2202	4299	6501	SO:0001819	synonymous_variant	2241	exon13			TATAGATCATCAC	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.1587T>C	5.37:g.108294979T>C		122	0	0		112	44	0.392857	NM_005246	B2RCR4|B4DSQ2|H2FLB8	Silent	SNP	ENST00000281092.4	37	CCDS4098.1																																																																																			T|0.988;C|0.012	0.012	strong		0.363	FER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250664.1	NM_005246		C	108294979	T	C	108294979	2	2	22	1	0	0	0	0	0	0	0	1	5821	1432	50	3		3	FER	5	108294979	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	13117	108294979	72620281	1236	4137											
WDR36	134430	hgsc.bcm.edu	37	chr5	110432841	110432841	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agattagtctttgctgcttaTggaaatgttttctctgcatt	8	19	8	6	0	2	1	0	0	2	1	3	2	2	2	0	1	3	4	0	1	3	6	rs17132775	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:110432841T>C	ENST00000513710.2	+	3	427	c.423T>C	c.(421-423)taT>taC	p.Y141Y	WDR36_ENST00000506538.2_Silent_p.Y141Y|WDR36_ENST00000505303.1_Silent_p.Y85Y			Q8NI36	WDR36_HUMAN	WD repeat domain 36	141					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)		TTGCTGCTTATGGAAATGTTT	0.388													T|||	212	0.0423323	0.1558	0.0072	5008	,	,		15681	0.0		0.001	False		,,,				2504	0.0				p.Y141Y		Atlas-SNP	.											.	WDR36	111	.	0			c.T423C						PASS	.	T		647,3757	277.5+/-273.7	44,559,1599	179	171	174		423	2	1	5	dbSNP_123	174	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	WDR36	NM_139281.2		44,567,5891	CC,CT,TT		0.093,14.6912,5.0369		141/952	110432841	655,12349	2202	4300	6502	SO:0001819	synonymous_variant	134430	exon3			TGCTTATGGAAAT	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.423T>C	5.37:g.110432841T>C		165	0	0		133	133	1	NM_139281	A2RUS4|Q68E02|Q8N1Q2	Silent	SNP	ENST00000513710.2	37	CCDS4102.1																																																																																			T|0.951;C|0.049	0.049	strong		0.388	WDR36-008	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000373504.3	NM_139281		C	110432841	T	C	110432841	2	2	22	1	0	0	0	0	0	0	0	1	17305	1471	51	3		3	WDR36	5	110432841	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2137862	110432841	70482419	1237	4138											
CAMK4	814	hgsc.bcm.edu	37	chr5	110820116	110820116	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagggcaaggaagctctgcTgtgggttttgaagttccaca	10	10	14	7	0	1	1	0	1	1	0	2	3	2	2	1	3	2	5	1	3	4	3	rs6886469	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:110820116T>G	ENST00000282356.4	+	11	1772	c.1374T>G	c.(1372-1374)gcT>gcG	p.A458A	CAMK4_ENST00000512890.1_3'UTR|CAMK4_ENST00000512453.1_Silent_p.A458A	NM_001744.4	NP_001735.1	Q16566	KCC4_HUMAN	calcium/calmodulin-dependent protein kinase IV	458					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|long-term memory (GO:0007616)|myeloid dendritic cell differentiation (GO:0043011)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleocytoplasmic transport (GO:0006913)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of osteoclast differentiation (GO:0045670)|regulation of T cell differentiation in thymus (GO:0033081)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	30		all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109)		GAAGCTCTGCTGTGGGTTTTG	0.512													T|||	46	0.0091853	0.034	0.0014	5008	,	,		19121	0.0		0.0	False		,,,				2504	0.0				p.A458A		Atlas-SNP	.											.	CAMK4	77	.	0			c.T1374G						PASS	.	T		114,4290	87.3+/-125.9	3,108,2091	47	47	47		1374	-3.5	0	5	dbSNP_116	47	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	CAMK4	NM_001744.4		3,110,6389	GG,GT,TT		0.0233,2.5886,0.892		458/474	110820116	116,12888	2202	4300	6502	SO:0001819	synonymous_variant	814	exon11			CTCTGCTGTGGGT	D30742	CCDS4103.1	5q22.1	2012-09-20			ENSG00000152495	ENSG00000152495	2.7.11.17		1464	protein-coding gene	gene with protein product	"brain Ca++-calmodulin-dependent protein kinase type IV", "calcium/calmodulin-dependent protein kinase type IV catalytic chain", "CAM kinase IV", "CAM kinase- GR"	114080				2536634	Standard	NM_001744		Approved	CaMK-GR	uc003kpf.3	Q16566	OTTHUMG00000128792	ENST00000282356.4:c.1374T>G	5.37:g.110820116T>G		78	0	0		69	40	0.57971	NM_001744	D3DSZ7	Silent	SNP	ENST00000282356.4	37	CCDS4103.1																																																																																			T|0.991;G|0.009	0.009	strong		0.512	CAMK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250719.2	NM_001744		G	110820116	T	G	110820116	2	3	22	1	0	0	0	0	0	0	0	1	2607	1567	55	5		5	CAMK4	5	110820116	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	387275	110820116	70095144	1238	4139											
APC	324	hgsc.bcm.edu	37	chr5	112175240	112175240	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agattggaactaggtcagctGaagatcctgtgagcgaagtt	12	10	13	6	1	1	4	1	2	0	2	2	6	2	5	1	2	3	2	1	2	4	3	rs1801166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:112175240G>C	ENST00000457016.1	+	16	4329	c.3949G>C	c.(3949-3951)Gaa>Caa	p.E1317Q	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.E1317Q|APC_ENST00000508376.2_Missense_Mutation_p.E1317Q			P25054	APC_HUMAN	adenomatous polyposis coli	1317	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.		E -> Q (may contribute to colorectal tumor development; dbSNP:rs1801166). {ECO:0000269|PubMed:9724771}.		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.E1317Q(5)|p.E1317*(3)|p.E1317fs*4(3)|p.?(1)|p.K1192fs*3(1)|p.A1316fs*9(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)		TAGGTCAGCTGAAGATCCTGT	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)			G|||	15	0.00299521	0.003	0.0029	5008	,	,		21730	0.0		0.006	False		,,,				2504	0.0031				p.E1317Q	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,bladder,carcinoma,0,14	APC	4158	14	14	Substitution - Missense(5)|Deletion - Frameshift(5)|Substitution - Nonsense(3)|Unknown(1)	large_intestine(9)|stomach(1)|soft_tissue(1)|urinary_tract(1)|lung(1)|skin(1)	c.G3949C	GRCh37	CM980089	APC	M	rs1801166	PASS	.	G	GLN/GLU,GLN/GLU,GLN/GLU	28,4376	33.5+/-64.1	0,28,2174	60	61	61	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3949,3949,3895	5.2	0.7	5	dbSNP_89	61	80,8520	46.3+/-105.2	1,78,4221	yes	missense,missense,missense	APC	NM_000038.5,NM_001127510.2,NM_001127511.2	29,29,29	1,106,6395	CC,CG,GG		0.9302,0.6358,0.8305	benign,benign,benign	1317/2844,1317/2844,1299/2826	112175240	108,12896	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,	TCAGCTGAAGATC	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.3949G>C	5.37:g.112175240G>C	ENSP00000413133:p.Glu1317Gln	171	0	0		162	54	0.333333	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	8	0.003663003663003663	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	9.512	1.105897	0.20632	0.006358	0.009302	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.90324	-2.65;-2.65;-2.65	6.03	5.15	0.70609	.	0.502603	0.24048	N	0.042028	T	0.80325	0.4602	N	0.24115	0.695	0.37326	A	0.90977	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.003	T	0.79045	-0.1964	8	.	.	.	-16.8737	17.2207	0.86956	0.0:0.1257:0.8742:0.0	rs1801166;rs52811293	1319;1317	Q4LE70;P25054	.;APC_HUMAN	Q	1317	ENSP00000413133:E1317Q;ENSP00000257430:E1317Q;ENSP00000427089:E1317Q	.	E	+	1	0	APC	112203139	1.000000	0.71417	0.685000	0.30070	0.277000	0.26821	6.359000	0.73060	1.533000	0.49186	0.655000	0.94253	GAA	G|0.992;C|0.008	0.008	strong		0.438	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		C	112175240	G	C	112175240	3	2	22	1	0	0	0	0	1	0	0	0	763	1291	45	4	4007	4	APC	5	112175240	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1355124	112175240	68740020	1239	4140											
APC	324	hgsc.bcm.edu	37	chr5	112176556	112176556	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggtccagcaagcatctgcGtcttcttctgcacccaacaa	10	9	7	15	1	4	0	0	0	4	0	5	0	5	0	2	1	5	3	2	1	3	2	rs34506289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:112176556G>A	ENST00000457016.1	+	16	5645	c.5265G>A	c.(5263-5265)gcG>gcA	p.A1755A	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Silent_p.A1755A|APC_ENST00000508376.2_Silent_p.A1755A			P25054	APC_HUMAN	adenomatous polyposis coli	1755	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)		AAGCATCTGCGTCTTCTTCTG	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)			G|||	21	0.00419329	0.0068	0.0029	5008	,	,		19623	0.001		0.006	False		,,,				2504	0.0031				p.A1755A	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	.	2	Unknown(1)|Deletion - Frameshift(1)	soft_tissue(1)|skin(1)	c.G5265A						PASS	.	G	,,	43,4361	44.6+/-78.6	0,43,2159	56	55	56		5265,5265,5211	1.6	0	5	dbSNP_126	56	79,8517	43.6+/-101.6	1,77,4220	no	coding-synonymous,coding-synonymous,coding-synonymous	APC	NM_000038.5,NM_001127510.2,NM_001127511.2	,,	1,120,6379	AA,AG,GG		0.919,0.9764,0.9385	,,	1755/2844,1755/2844,1737/2826	112176556	122,12878	2202	4298	6500	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,	ATCTGCGTCTTCT	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.5265G>A	5.37:g.112176556G>A		114	0	0		109	41	0.376147	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																			G|0.992;A|0.008	0.008	strong		0.398	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112176556	G	A	112176556	2	1	22	1	0	0	0	0	0	0	0	1	763	1132	40	1		1	APC	5	112176556	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1316	112176556	68738704	1240	4141											
TSSK1B	83942	hgsc.bcm.edu	37	chr5	112770054	112770054	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cgaccactgtcatcccgcagGcagcgcttggagaagctgaa	10	6	12	13	3	1	2	1	1	0	1	2	4	2	2	2	2	2	4	2	2	2	1	rs111560230	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:112770054G>A	ENST00000390666.3	-	1	674	c.483C>T	c.(481-483)tgC>tgT	p.C161C	CTD-2201G3.1_ENST00000383058.4_RNA|MCC_ENST00000408903.3_Intron|CTD-2201G3.1_ENST00000416046.2_RNA|CTD-2201G3.1_ENST00000510381.2_RNA	NM_032028.3	NP_114417.1	Q9BXA7	TSSK1_HUMAN	testis-specific serine kinase 1B	161	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)		CATCCCGCAGGCAGCGCTTGG	0.577													G|||	2	0.000399361	0.0015	0.0	5008	,	,		21131	0.0		0.0	False		,,,				2504	0.0				p.C161C		Atlas-SNP	.											.	TSSK1B	89	.	0			c.C483T						PASS	.	G	,	2,4402	4.2+/-10.8	0,2,2200	81	77	78		,483	1.2	1	5	dbSNP_132	78	0,8600		0,0,4300	no	intron,coding-synonymous	MCC,TSSK1B	NM_001085377.1,NM_032028.3	,	0,2,6500	AA,AG,GG		0.0,0.0454,0.0154	,	,161/368	112770054	2,13002	2202	4300	6502	SO:0001819	synonymous_variant	83942	exon1			CCGCAGGCAGCGC	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.483C>T	5.37:g.112770054G>A		81	0	0		80	36	0.45	NM_032028	B2R8D9	Silent	SNP	ENST00000390666.3	37	CCDS4112.1																																																																																			G|0.500;A|0.500	0.500	strong		0.577	TSSK1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250774.2	NM_032028		A	112770054	G	A	112770054	2	1	22	1	0	0	0	0	0	0	0	1	16683	1195	42	2		2	TSSK1B	5	112770054	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	593498	112770054	68145206	1241	4142											
YTHDC2	64848	hgsc.bcm.edu	37	chr5	112871458	112871458	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gctgccttggatgtaaatctCtttataagatattttggaag	11	16	9	5	0	1	1	0	0	1	1	2	3	1	3	1	2	1	2	1	2	6	8	rs77052070	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:112871458C>G	ENST00000161863.4	+	7	1278	c.1065C>G	c.(1063-1065)ctC>ctG	p.L355L	YTHDC2_ENST00000515883.1_Silent_p.L355L	NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	355	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				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)		ATGTAAATCTCTTTATAAGAT	0.279													C|||	63	0.0125799	0.0477	0.0	5008	,	,		17937	0.0		0.0	False		,,,				2504	0.0				p.L355L		Atlas-SNP	.											.	YTHDC2	118	.	0			c.C1065G						PASS	.	C		214,4190	128.6+/-165.4	2,210,1990	49	54	52		1065	-5.6	0.5	5	dbSNP_131	52	0,8594		0,0,4297	no	coding-synonymous	YTHDC2	NM_022828.3		2,210,6287	GG,GC,CC		0.0,4.8592,1.6464		355/1431	112871458	214,12784	2202	4297	6499	SO:0001819	synonymous_variant	64848	exon7			AAATCTCTTTATA	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.1065C>G	5.37:g.112871458C>G		96	0	0		109	41	0.376147	NM_022828	B2RP66	Silent	SNP	ENST00000161863.4	37	CCDS4113.1																																																																																			C|0.984;G|0.016	0.016	strong		0.279	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828		G	112871458	C	G	112871458	2	3	22	1	0	0	0	0	0	0	0	1	17512	900	32	4		4	YTHDC2	5	112871458	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	101404	112871458	68043802	1242	4143											
TRIM36	55521	hgsc.bcm.edu	37	chr5	114482847	114482847	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggtgatgaattttgaagcaTtcattgcagtaacttgcact	11	14	10	6	0	1	3	1	3	0	0	1	3	1	3	0	1	4	4	0	1	3	6	rs12109197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:114482847T>C	ENST00000282369.3	-	3	664	c.543A>G	c.(541-543)gaA>gaG	p.E181E	TRIM36_ENST00000515104.1_5'UTR|TRIM36_ENST00000513154.1_Silent_p.E169E|TRIM36-IT1_ENST00000503723.1_RNA|TRIM36_ENST00000514154.1_Silent_p.E26E	NM_018700.3	NP_061170.2	Q9NQ86	TRI36_HUMAN	tripartite motif containing 36	181					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)		TTTTGAAGCATTCATTGCAGT	0.418													T|||	13	0.00259585	0.0098	0.0	5008	,	,		20229	0.0		0.0	False		,,,				2504	0.0				p.E181E		Atlas-SNP	.											.	TRIM36	126	.	0			c.A543G						PASS	.	T		20,4384	27.2+/-55.0	0,20,2182	144	141	142		543	-5.5	0.5	5	dbSNP_120	142	0,8600		0,0,4300	no	coding-synonymous	TRIM36	NM_018700.3		0,20,6482	CC,CT,TT		0.0,0.4541,0.1538		181/729	114482847	20,12984	2202	4300	6502	SO:0001819	synonymous_variant	55521	exon3			GAAGCATTCATTG	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.543A>G	5.37:g.114482847T>C		466	1	0.00214592		459	209	0.455338	NM_018700	A1L3Z1|A6NDD0|B7Z3V4|B7ZAV7|E9PFI8|Q0P5Z9	Silent	SNP	ENST00000282369.3	37	CCDS4115.1																																																																																			T|0.998;C|0.002	0.002	strong		0.418	TRIM36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250854.2	NM_018700		C	114482847	T	C	114482847	2	2	22	1	0	0	0	0	0	0	0	1	16525	1490	52	3		3	TRIM36	5	114482847	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1611389	114482847	66432413	1243	4144											
SEMA6A	57556	hgsc.bcm.edu	37	chr5	115827506	115827506	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	attccgctgaattcatccccGaatggttccaatgtatccat	10	13	6	12	2	1	1	1	1	0	0	5	2	5	1	5	1	0	3	5	1	4	4	rs34096390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:115827506G>A	ENST00000343348.6	-	7	1252	c.465C>T	c.(463-465)ttC>ttT	p.F155F	CTB-118N6.3_ENST00000510682.1_RNA|CTB-118N6.3_ENST00000508640.1_RNA|SEMA6A_ENST00000503962.1_5'UTR|SEMA6A_ENST00000257414.8_Silent_p.F155F|SEMA6A_ENST00000510263.1_Silent_p.F155F|CTB-118N6.3_ENST00000514214.1_RNA	NM_020796.3	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	155	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)		ATTCATCCCCGAATGGTTCCA	0.418													G|||	155	0.0309505	0.1112	0.0086	5008	,	,		21381	0.0		0.002	False		,,,				2504	0.0				p.F155F		Atlas-SNP	.											SEMA6A,NS,carcinoma,-2,1	SEMA6A	93	1	0			c.C465T						scavenged	.	G		326,3528		20,286,1621	120	118	118		465	-12.2	0	5	dbSNP_126	118	3,8247		0,3,4122	no	coding-synonymous	SEMA6A	NM_020796.3		20,289,5743	AA,AG,GG		0.0364,8.4587,2.7181		155/1031	115827506	329,11775	1927	4125	6052	SO:0001819	synonymous_variant	57556	exon7			ATCCCCGAATGGT	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.465C>T	5.37:g.115827506G>A		153	1	0.00653595		228	91	0.399123	NM_020796	Q9P2H9	Silent	SNP	ENST00000343348.6	37	CCDS47256.1																																																																																			G|0.979;A|0.021	0.021	strong		0.418	SEMA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371270.1	NM_020796		A	115827506	G	A	115827506	2	1	22	1	0	0	0	0	0	0	0	1	14054	1049	37	1		1	SEMA6A	5	115827506	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1344659	115827506	65087754	1244	4145											
DMXL1	1657	hgsc.bcm.edu	37	chr5	118529595	118529597	+	In_Frame_Del	DEL	AAT	AAT	-																															tgggaagtgatgatgatgacAatgatgatgatgatgatgtt																								rs200335120|rs374810198|rs146526208|rs150940354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:118529595_118529597delAAT	ENST00000311085.8	+	30	7467_7469	c.7387_7389delAAT	c.(7387-7389)aatdel	p.N2463del	DMXL1_ENST00000539542.1_In_Frame_Del_p.N2463del	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	2463	Poly-Asp.									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)		tgatgatgacaatgatgatgatg	0.315														32	0.00638978	0.0234	0.0014	5008	,	,		16171	0.0		0.0	False		,,,				2504	0.0				p.2462_2463del		Pindel,Atlas-Indel	.											.	DMXL1	268	.	0			c.7386_7388del						PASS	.			93,4171		1,91,2040						-10.3	0.2			98	1,8253		0,1,4126	no	coding	DMXL1	NM_005509.4		1,92,6166	A1A1,A1R,RR		0.0121,2.1811,0.7509				94,12424				SO:0001651	inframe_deletion	1657	exon30			.	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.7387_7389delAAT	5.37:g.118529595_118529597delAAT	ENSP00000309690:p.Asn2463del	52	0	.		55	10	0.182	NM_005509		In_Frame_Del	DEL	ENST00000311085.8	37	CCDS4125.1																																																																																			.	.	weak		0.315	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		-	118529597	AAT	-	118529595	7	5	22	1	0	1	0	1	0	0	0	0	4596	130	5	0	7505	0	DMXL1	5	118529595	In_Frame_Del	DEL	AAT	TCGA-G8-6324-01A-11D-2210-10	2702089	118529595	62385665	1245	4146											
HSD17B4	3295	hgsc.bcm.edu	37	chr5	118877660	118877660	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctgagccagaaacttcagAtgattcttaaagactacgcc	13	10	8	10	1	2	5	1	2	1	3	2	5	2	5	2	0	4	1	2	0	4	4	rs28943594	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:118877660A>G	ENST00000256216.6	+	24	2315	c.2182A>G	c.(2182-2184)Atg>Gtg	p.M728V	HSD17B4_ENST00000509514.1_Missense_Mutation_p.M466V|HSD17B4_ENST00000414835.2_Missense_Mutation_p.M588V|HSD17B4_ENST00000504811.1_Missense_Mutation_p.M753V|HSD17B4_ENST00000510025.1_Missense_Mutation_p.M704V|HSD17B4_ENST00000515320.1_Missense_Mutation_p.M710V|HSD17B4_ENST00000513628.1_Missense_Mutation_p.M591V|HSD17B4_ENST00000522415.1_3'UTR	NM_000414.3	NP_000405.1	P51659	DHB4_HUMAN	hydroxysteroid (17-beta) dehydrogenase 4	728	SCP2.		M -> V (in dbSNP:rs28943594).		alpha-linolenic acid metabolic process (GO:0036109)|androgen metabolic process (GO:0008209)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|estrogen metabolic process (GO:0008210)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|metabolic process (GO:0008152)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|Sertoli cell development (GO:0060009)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)|very long-chain fatty-acyl-CoA metabolic process (GO:0036111)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	17-beta-hydroxysteroid dehydrogenase (NAD+) activity (GO:0044594)|3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity (GO:0033989)|isomerase activity (GO:0016853)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(2)	25		all_cancers(142;0.0206)|Prostate(80;0.0322)		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)		GAAACTTCAGATGATTCTTAA	0.423													A|||	167	0.0333466	0.1218	0.0043	5008	,	,		15072	0.0		0.001	False		,,,				2504	0.002				p.M753V	Colon(35;490 801 34689 41394 43344)	Atlas-SNP	.											.	HSD17B4	63	.	0			c.A2257G						PASS	.	A	VAL/MET,VAL/MET,VAL/MET	405,3999	198.4+/-222.2	21,363,1818	65	64	64		2182,2257,2128	3.5	1	5	dbSNP_125	64	14,8586	10.5+/-38.8	0,14,4286	yes	missense,missense,missense	HSD17B4	NM_000414.3,NM_001199291.1,NM_001199292.1	21,21,21	21,377,6104	GG,GA,AA		0.1628,9.1962,3.2221	benign,benign,benign	728/737,753/762,710/719	118877660	419,12585	2202	4300	6502	SO:0001583	missense	3295	exon25			CTTCAGATGATTC		CCDS4126.1, CCDS56378.1, CCDS56379.1	5q2	2011-09-20			ENSG00000133835	ENSG00000133835	4.2.1.107, 1.1.1.35	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	5213	protein-coding gene	gene with protein product	"17beta-estradiol dehydrogenase type IV", "peroxisomal multifunctional protein 2", "17-beta-HSD IV", "17-beta-hydroxysteroid dehydrogenase 4", "D-bifunctional protein, peroxisomal", "D-3-hydroxyacyl-CoA dehydratase", "3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholest-24-enoyl-CoA hydratase", "beta-keto-reductase", "beta-hydroxyacyl dehydrogenase", "short chain dehydrogenase/reductase family 8C, member 1"	601860				8938456, 19027726	Standard	NM_000414		Approved	MFE-2, DBP, SDR8C1	uc003ksj.3	P51659	OTTHUMG00000128899	ENST00000256216.6:c.2182A>G	5.37:g.118877660A>G	ENSP00000256216:p.Met728Val	222	0	0		172	87	0.505814	NM_001199291	B4DNV1|B4DVS5|E9PB82|F5HE57	Missense_Mutation	SNP	ENST00000256216.6	37	CCDS4126.1	67	0.030677655677655676	64	0.13008130081300814	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	A	11.01	1.512125	0.27036	0.091962	0.001628	ENSG00000133835	ENST00000256216;ENST00000515320;ENST00000510025;ENST00000504811;ENST00000414835;ENST00000513628;ENST00000509514	T;T;T;T;T;T;T	0.21361	2.01;2.01;2.01;2.01;2.01;2.01;2.01	5.94	3.46	0.39613	SCP2 sterol-binding domain (2);	0.276882	0.46145	D	0.000301	T	0.00144	0.0004	N	0.21282	0.65	0.31931	P	0.612166	B;B;B;B;B	0.11235	0.004;0.0;0.0;0.001;0.0	B;B;B;B;B	0.10450	0.003;0.003;0.005;0.001;0.003	T	0.29671	-1.0004	8	.	.	.	-10.0531	8.5921	0.33693	0.7361:0.1351:0.0:0.1288	rs28943594	753;710;704;466;728	F5HE57;E9PB82;E7EWE5;E7EPL9;P51659	.;.;.;.;DHB4_HUMAN	V	728;710;704;753;588;591;466	ENSP00000256216:M728V;ENSP00000424613:M710V;ENSP00000424940:M704V;ENSP00000420914:M753V;ENSP00000411960:M588V;ENSP00000425993:M591V;ENSP00000426272:M466V	.	M	+	1	0	HSD17B4	118905559	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	4.250000	0.58772	0.446000	0.26666	0.455000	0.32223	ATG	A|0.967;G|0.033	0.033	strong		0.423	HSD17B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250863.3	NM_000414		G	118877660	A	G	118877660	3	3	22	1	0	0	0	0	1	0	0	0	7395	333	12	3	2276	3	HSD17B4	5	118877660	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	348065	118877660	62037600	1246	4147											
HSD17B4	3295	hgsc.bcm.edu	37	chr5	118877677	118877677	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagatgattcttaaagactaCgccaagctctgaagggcaca	14	8	9	10	1	2	4	0	2	2	2	2	4	2	4	1	1	2	2	1	1	5	3	rs12714	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:118877677C>T	ENST00000256216.6	+	24	2332	c.2199C>T	c.(2197-2199)taC>taT	p.Y733Y	HSD17B4_ENST00000509514.1_Silent_p.Y471Y|HSD17B4_ENST00000414835.2_Silent_p.Y593Y|HSD17B4_ENST00000504811.1_Silent_p.Y758Y|HSD17B4_ENST00000510025.1_Silent_p.Y709Y|HSD17B4_ENST00000515320.1_Silent_p.Y715Y|HSD17B4_ENST00000513628.1_Silent_p.Y596Y|HSD17B4_ENST00000522415.1_3'UTR	NM_000414.3	NP_000405.1	P51659	DHB4_HUMAN	hydroxysteroid (17-beta) dehydrogenase 4	733	SCP2.				alpha-linolenic acid metabolic process (GO:0036109)|androgen metabolic process (GO:0008209)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|estrogen metabolic process (GO:0008210)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|metabolic process (GO:0008152)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|Sertoli cell development (GO:0060009)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)|very long-chain fatty-acyl-CoA metabolic process (GO:0036111)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	17-beta-hydroxysteroid dehydrogenase (NAD+) activity (GO:0044594)|3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity (GO:0033989)|isomerase activity (GO:0016853)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(2)	25		all_cancers(142;0.0206)|Prostate(80;0.0322)		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)		TTAAAGACTACGCCAAGCTCT	0.408													T|||	249	0.0497204	0.146	0.0072	5008	,	,		15192	0.001		0.001	False		,,,				2504	0.0501				p.Y758Y	Colon(35;490 801 34689 41394 43344)	Atlas-SNP	.											.	HSD17B4	63	.	0			c.C2274T						PASS	.	T	,,	492,3912	780.4+/-414.4	32,428,1742	58	58	58		2199,2274,2145	-10	0.2	5	dbSNP_52	58	16,8584	818.4+/-406.9	0,16,4284	no	coding-synonymous,coding-synonymous,coding-synonymous	HSD17B4	NM_000414.3,NM_001199291.1,NM_001199292.1	,,	32,444,6026	TT,TC,CC		0.186,11.1717,3.9065	,,	733/737,758/762,715/719	118877677	508,12496	2202	4300	6502	SO:0001819	synonymous_variant	3295	exon25			AGACTACGCCAAG		CCDS4126.1, CCDS56378.1, CCDS56379.1	5q2	2011-09-20			ENSG00000133835	ENSG00000133835	4.2.1.107, 1.1.1.35	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"	5213	protein-coding gene	gene with protein product	"17beta-estradiol dehydrogenase type IV", "peroxisomal multifunctional protein 2", "17-beta-HSD IV", "17-beta-hydroxysteroid dehydrogenase 4", "D-bifunctional protein, peroxisomal", "D-3-hydroxyacyl-CoA dehydratase", "3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholest-24-enoyl-CoA hydratase", "beta-keto-reductase", "beta-hydroxyacyl dehydrogenase", "short chain dehydrogenase/reductase family 8C, member 1"	601860				8938456, 19027726	Standard	NM_000414		Approved	MFE-2, DBP, SDR8C1	uc003ksj.3	P51659	OTTHUMG00000128899	ENST00000256216.6:c.2199C>T	5.37:g.118877677C>T		193	0	0		154	79	0.512987	NM_001199291	B4DNV1|B4DVS5|E9PB82|F5HE57	Silent	SNP	ENST00000256216.6	37	CCDS4126.1																																																																																			C|0.960;T|0.040	0.040	strong		0.408	HSD17B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250863.3	NM_000414		T	118877677	C	T	118877677	2	4	22	1	0	0	0	0	0	0	0	1	7395	547	19	1		1	HSD17B4	5	118877677	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	17	118877677	62037583	1247	4148											
ZNF474	133923	hgsc.bcm.edu	37	chr5	121487954	121487954	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccccctgtgatcccggcccGcaggcctggattccgggtat	4	8	12	17	3	0	1	0	1	0	0	2	2	2	2	7	4	0	2	7	4	1	2	rs116158782	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:121487954G>A	ENST00000296600.4	+	2	652	c.269G>A	c.(268-270)cGc>cAc	p.R90H	CTC-441N14.2_ENST00000504829.1_RNA|CTC-441N14.1_ENST00000505209.1_RNA|ZNF474_ENST00000514925.1_Intron	NM_207317.1	NP_997200.1	Q6S9Z5	ZN474_HUMAN	zinc finger protein 474	90							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)		ATCCCGGCCCGCAGGCCTGGA	0.493													G|||	47	0.00938498	0.0348	0.0014	5008	,	,		17011	0.0		0.0	False		,,,				2504	0.0				p.R90H		Atlas-SNP	.											.	ZNF474	43	.	0			c.G269A						PASS	.	G	HIS/ARG	146,4260	102.1+/-140.7	3,140,2060	76	86	82		269	4.7	1	5	dbSNP_132	82	5,8593	4.3+/-15.6	0,5,4294	yes	missense	ZNF474	NM_207317.1	29	3,145,6354	AA,AG,GG		0.0582,3.3137,1.1612	probably-damaging	90/365	121487954	151,12853	2203	4299	6502	SO:0001583	missense	133923	exon2			CGGCCCGCAGGCC	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.269G>A	5.37:g.121487954G>A	ENSP00000296600:p.Arg90His	131	0	0		128	56	0.4375	NM_207317	A8K4M0|Q96M07	Missense_Mutation	SNP	ENST00000296600.4	37	CCDS4130.1	25	0.011446886446886446	24	0.04878048780487805	1	0.0027624309392265192	0	0.0	0	0.0	G	15.38	2.817454	0.50633	0.033137	5.82E-4	ENSG00000164185	ENST00000296600	T	0.50001	0.76	5.58	4.66	0.58398	.	0.157757	0.33980	N	0.004370	T	0.19525	0.0469	L	0.36672	1.1	0.36400	D	0.863073	D	0.89917	1.0	D	0.73708	0.981	T	0.55010	-0.8207	10	0.62326	D	0.03	-6.5368	15.9342	0.79688	0.0:0.135:0.865:0.0	.	90	Q6S9Z5	ZN474_HUMAN	H	90	ENSP00000296600:R90H	ENSP00000296600:R90H	R	+	2	0	ZNF474	121515853	0.999000	0.42202	1.000000	0.80357	0.102000	0.19082	1.797000	0.38804	2.624000	0.88883	0.655000	0.94253	CGC	G|0.988;A|0.012	0.012	strong		0.493	ZNF474-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250883.2	NM_207317		A	121487954	G	A	121487954	3	1	22	1	0	0	0	0	1	0	0	0	17947	1087	38	1	271	1	ZNF474	5	121487954	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2610277	121487954	59427306	1248	4149											
GRAMD3	65983	hgsc.bcm.edu	37	chr5	125696124	125696124	+	Missense_Mutation	SNP	T	T	A																															tatgttccacgggagagaagTgaagccagtgggtccggacc																								rs79046516	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:125696124T>A	ENST00000513040.1	+	1	301	c.101T>A	c.(100-102)gTg>gAg	p.V34E		NM_001146319.1	NP_001139791.1	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3	0						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)		GGGAGAGAAGTGAAGCCAGTG	0.488													T|||	118	0.0235623	0.087	0.0043	5008	,	,		21249	0.0		0.0	False		,,,				2504	0.0				p.V34E		Atlas-SNP	.											.	GRAMD3	30	.	0			c.T101A						PASS	.						123	116	119					5																	125696124		692	1591	2283	SO:0001583	missense	65983	exon1			GAGAAGTGAAGCC	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	ENST00000513040.1:c.101T>A	5.37:g.125696124T>A	ENSP00000426120:p.Val34Glu	184	0	0		215	82	0.381395	NM_001146319	B7Z1F2|B7Z3R1|B7Z6D8|B7Z8T2|D3DSZ3|Q9H753	Missense_Mutation	SNP	ENST00000513040.1	37	CCDS54891.1	43	0.019688644688644688	41	0.08333333333333333	2	0.0055248618784530384	0	0.0	0	0.0	T	9.413	1.081098	0.20309	.	.	ENSG00000155324	ENST00000513040	T	0.36878	1.23	4.15	-5.51	0.02568	.	.	.	.	.	T	0.00496	0.0016	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.18429	-1.0337	8	0.02654	T	1	.	2.4366	0.04485	0.2542:0.0881:0.4343:0.2234	.	34	B7Z6D8	.	E	34	ENSP00000426120:V34E	ENSP00000426120:V34E	V	+	2	0	GRAMD3	125724023	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.306000	0.08178	-0.956000	0.03631	-1.304000	0.01323	GTG	T|0.975;A|0.025	0.025	strong		0.488	GRAMD3-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000371350.1	NM_023927		A	125696124	T	A	125696124	3	1	22	1	0	0	0	0	1	0	0	0	6760	1696	59	5	103	5	GRAMD3	5	125696124	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	4208170	125696124	55219136	1249	4150	54	2									
GRAMD3	65983	hgsc.bcm.edu	37	chr5	125696127	125696127	+	Missense_Mutation	SNP	A	A	G																															gttccacgggagagaagtgaAgccagtgggtccggacctgg																								rs78682130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:125696127A>G	ENST00000513040.1	+	1	304	c.104A>G	c.(103-105)aAg>aGg	p.K35R		NM_001146319.1	NP_001139791.1	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3	0						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)		AGAGAAGTGAAGCCAGTGGGT	0.488													A|||	118	0.0235623	0.087	0.0043	5008	,	,		21319	0.0		0.0	False		,,,				2504	0.0				p.K35R		Atlas-SNP	.											.	GRAMD3	30	.	0			c.A104G						PASS	.	A	ARG/LYS	87,1297		2,83,607	119	112	114		104	4.2	0	5	dbSNP_132	114	0,3182		0,0,1591	yes	missense	GRAMD3	NM_001146319.1	26	2,83,2198	GG,GA,AA		0.0,6.2861,1.9054	benign	35/448	125696127	87,4479	692	1591	2283	SO:0001583	missense	65983	exon1			AAGTGAAGCCAGT	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	ENST00000513040.1:c.104A>G	5.37:g.125696127A>G	ENSP00000426120:p.Lys35Arg	181	0	0		210	80	0.380952	NM_001146319	B7Z1F2|B7Z3R1|B7Z6D8|B7Z8T2|D3DSZ3|Q9H753	Missense_Mutation	SNP	ENST00000513040.1	37	CCDS54891.1	43	0.019688644688644688	41	0.08333333333333333	2	0.0055248618784530384	0	0.0	0	0.0	A	12.15	1.852185	0.32699	0.062861	0.0	ENSG00000155324	ENST00000513040	T	0.35048	1.33	4.15	4.15	0.48705	.	.	.	.	.	T	0.01061	0.0035	.	.	.	0.34252	D	0.678883	B	0.24186	0.099	B	0.22753	0.041	T	0.12682	-1.0538	8	0.16896	T	0.51	.	9.8683	0.41157	1.0:0.0:0.0:0.0	.	35	B7Z6D8	.	R	35	ENSP00000426120:K35R	ENSP00000426120:K35R	K	+	2	0	GRAMD3	125724026	0.158000	0.22850	0.005000	0.12908	0.006000	0.05464	1.900000	0.39828	2.107000	0.64212	0.460000	0.39030	AAG	A|0.975;G|0.025	0.025	strong		0.488	GRAMD3-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000371350.1	NM_023927		G	125696127	A	G	125696127	3	3	22	1	0	0	0	0	1	0	0	0	6760	72	3	3	106	3	GRAMD3	5	125696127	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	3	125696127	55219133	1250	4151	54	2									
ALDH7A1	501	hgsc.bcm.edu	37	chr5	125928395	125928395	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttctcttgctttctttacAgtttcttcatagtctgccac	5	19	5	12	0	5	0	1	0	4	0	6	0	5	0	1	0	3	3	1	0	2	8	rs60720055	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:125928395A>G	ENST00000409134.3	-	3	492	c.273T>C	c.(271-273)acT>acC	p.T91T	ALDH7A1_ENST00000553117.1_Silent_p.T91T|ALDH7A1_ENST00000413020.1_5'UTR|ALDH7A1_ENST00000447989.2_Silent_p.T118T	NM_001182.4|NM_001201377.1	NP_001173.2|NP_001188306.1	P49419	AL7A1_HUMAN	aldehyde dehydrogenase 7 family, member A1	91					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)		CTTTCTTTACAGTTTCTTCAT	0.368													A|||	302	0.0603035	0.1717	0.0274	5008	,	,		18399	0.0		0.0288	False		,,,				2504	0.0276				p.T118T		Atlas-SNP	.											.	ALDH7A1	57	.	0			c.T354C						PASS	.	A	,,	657,3749	278.1+/-274.1	42,573,1588	111	105	107		273,189,354	-9.2	0.1	5	dbSNP_129	107	214,8386	88.9+/-151.2	2,210,4088	no	coding-synonymous,coding-synonymous,coding-synonymous	ALDH7A1	NM_001182.4,NM_001201377.1,NM_001202404.1	,,	44,783,5676	GG,GA,AA		2.4884,14.9115,6.6969	,,	91/540,63/512,118/503	125928395	871,12135	2203	4300	6503	SO:0001819	synonymous_variant	501	exon3			CTTTACAGTTTCT	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.273T>C	5.37:g.125928395A>G		118	0	0		126	63	0.5	NM_001202404	B2R669|B4DIC7|B4DMA0|E7EPT3|O14619|Q6IPU8|Q9BUL4	Silent	SNP	ENST00000409134.3	37	CCDS4137.2																																																																																			A|0.941;G|0.059	0.059	strong		0.368	ALDH7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250921.2	NM_001182		G	125928395	A	G	125928395	2	3	22	1	0	0	0	0	0	0	0	1	504	175	7	3		3	ALDH7A1	5	125928395	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	232268	125928395	54986865	1251	4152											
PHAX	51808	hgsc.bcm.edu	37	chr5	125944131	125944131	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aaaaaggcaattgaacttctGatggaaaccgctgaagttga	16	9	10	6	1	1	4	0	4	1	0	1	5	1	5	1	2	2	3	1	2	6	3	rs61747690	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:125944131G>C	ENST00000297540.4	+	3	1481	c.786G>C	c.(784-786)ctG>ctC	p.L262L		NM_032177.3	NP_115553.2	Q9H814	PHAX_HUMAN	phosphorylated adaptor for RNA export	262	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						TTGAACTTCTGATGGAAACCG	0.348													G|||	184	0.0367412	0.1324	0.0086	5008	,	,		18871	0.0		0.003	False		,,,				2504	0.0				p.L262L		Atlas-SNP	.											.	PHAX	20	.	0			c.G786C						PASS	.	G		471,3935	222.6+/-239.4	27,417,1759	159	167	164		786	0.7	1	5	dbSNP_129	164	12,8588	8.4+/-32.0	0,12,4288	no	coding-synonymous	PHAX	NM_032177.3		27,429,6047	CC,CG,GG		0.1395,10.69,3.7137		262/395	125944131	483,12523	2203	4300	6503	SO:0001819	synonymous_variant	51808	exon3			ACTTCTGATGGAA	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.786G>C	5.37:g.125944131G>C		122	0	0		94	46	0.489362	NM_032177	Q9H8W1	Silent	SNP	ENST00000297540.4	37	CCDS4138.1																																																																																			G|0.963;C|0.037	0.037	strong		0.348	PHAX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250924.1	NM_032177		C	125944131	G	C	125944131	2	2	22	1	0	0	0	0	0	0	0	1	11822	1277	45	4		4	PHAX	5	125944131	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	15736	125944131	54971129	1252	4153											
CTXN3	613212	hgsc.bcm.edu	37	chr5	126993262	126993262	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccctagtgccccttgggaacGaatcagcagattctagcatg	10	9	10	12	1	2	1	1	0	1	1	2	3	2	2	3	1	4	2	3	1	4	4	rs386692235|rs61743797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:126993262G>A	ENST00000379445.3	+	3	600	c.49G>A	c.(49-51)Gaa>Aaa	p.E17K	CTXN3_ENST00000395322.3_Missense_Mutation_p.E17K|CTC-548H10.2_ENST00000512352.1_RNA	NM_001048252.2	NP_001041717.1	Q4LDR2	CTXN3_HUMAN	cortexin 3	17			E -> V (in dbSNP:rs248709). {ECO:0000269|Ref.2}.			integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(1)	4		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0128)|COAD - Colon adenocarcinoma(49;0.0234)|OV - Ovarian serous cystadenocarcinoma(64;0.038)		CCTTGGGAACGAATCAGCAGA	0.478													G|||	11	0.00219649	0.0076	0.0	5008	,	,		21036	0.0		0.001	False		,,,				2504	0.0				p.E17K		Atlas-SNP	.											.	CTXN3	19	.	0			c.G49A						PASS	.						128	111	117					5																	126993262		2203	4300	6503	SO:0001583	missense	613212	exon3			GGGAACGAATCAG	AB219764	CCDS34221.1	5q23.2	2006-09-21				ENSG00000205279			31110	protein-coding gene	gene with protein product							Standard	NM_001048252		Approved		uc003kum.4	Q4LDR2		ENST00000379445.3:c.49G>A	5.37:g.126993262G>A	ENSP00000368758:p.Glu17Lys	68	0	0		83	49	0.590361	NM_001048252	B2RV32|D3DQ82	Missense_Mutation	SNP	ENST00000379445.3	37	CCDS34221.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	1.635	-0.518074	0.04171	.	.	ENSG00000205279	ENST00000379445;ENST00000395322	T;T	0.30714	1.52;1.52	4.52	-5.44	0.02624	.	1.776230	0.02356	N	0.076391	T	0.08670	0.0215	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.17623	-1.0363	9	0.09084	T	0.74	0.374	4.8394	0.13483	0.4246:0.0873:0.3994:0.0887	rs61743797	17	Q4LDR2	CTXN3_HUMAN	K	17	ENSP00000368758:E17K;ENSP00000378732:E17K	ENSP00000368758:E17K	E	+	1	0	CTXN3	127021161	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-1.490000	0.02304	-1.410000	0.02035	-0.940000	0.02684	GAA	G|0.998;A|0.002	0.002	strong		0.478	CTXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372467.1	XM_932841		A	126993262	G	A	126993262	3	1	22	1	0	0	0	0	1	0	0	0	4052	1059	37	1	51	1	CTXN3	5	126993262	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1049131	126993262	53921998	1253	4154											
FBN2	2201	hgsc.bcm.edu	37	chr5	127624905	127624905	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cggtgttgatacattgaccaTttgaacaaatgcctgggctc	10	12	10	9	1	0	3	0	3	0	0	1	3	0	3	2	2	3	2	2	2	3	4	rs149071226	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:127624905T>A	ENST00000508053.1	-	58	7525	c.6551A>T	c.(6550-6552)aAt>aTt	p.N2184I	FBN2_ENST00000262464.4_Missense_Mutation_p.N2184I			P35556	FBN2_HUMAN	fibrillin 2	2184	EGF-like 36; 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)		ACATTGACCATTTGAACAAAT	0.453													T|||	3	0.000599042	0.0023	0.0	5008	,	,		18157	0.0		0.0	False		,,,				2504	0.0				p.N2184I		Atlas-SNP	.											.	FBN2	858	.	0			c.A6551T						PASS	.	T	ILE/ASN	19,4387	26.2+/-53.5	0,19,2184	161	152	155		6551	5.8	1	5	dbSNP_134	155	0,8600		0,0,4300	yes	missense	FBN2	NM_001999.3	149	0,19,6484	AA,AT,TT		0.0,0.4312,0.1461	possibly-damaging	2184/2913	127624905	19,12987	2203	4300	6503	SO:0001583	missense	2201	exon52			TGACCATTTGAAC	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.6551A>T	5.37:g.127624905T>A	ENSP00000424571:p.Asn2184Ile	82	0	0		110	43	0.390909	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	37	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.385239	0.82792	0.004312	0.0	ENSG00000138829	ENST00000262464;ENST00000508053	D;D	0.92647	-3.08;-3.08	5.76	5.76	0.90799	Matrix fibril-associated (1);EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.64402	D	0.000002	D	0.95768	0.8623	M	0.89030	3	0.58432	D	0.999995	D	0.58620	0.983	P	0.60012	0.867	D	0.96209	0.9151	10	0.87932	D	0	.	12.1851	0.54234	0.0:0.0683:0.0:0.9317	.	2184	P35556	FBN2_HUMAN	I	2184	ENSP00000262464:N2184I;ENSP00000424571:N2184I	ENSP00000262464:N2184I	N	-	2	0	FBN2	127652804	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	3.317000	0.51968	2.324000	0.78689	0.533000	0.62120	AAT	T|0.998;A|0.002	0.002	strong		0.453	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		A	127624905	T	A	127624905	3	1	22	1	0	0	0	0	1	0	0	0	5711	1493	52	5	2243	5	FBN2	5	127624905	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	631643	127624905	53290355	1254	4155											
FBN2	2201	hgsc.bcm.edu	37	chr5	127670412	127670412	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acacaagcttgaaacctaccTgtacatcctgtggtcccctt	10	11	6	14	0	0	1	0	1	0	0	2	1	2	1	5	1	4	2	5	1	4	4	rs28763943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:127670412T>G	ENST00000508053.1	-	37	5072	c.4098A>C	c.(4096-4098)acA>acC	p.T1366T	FBN2_ENST00000508989.1_Splice_Site_p.T1333T|FBN2_ENST00000507835.1_Splice_Site_p.T216T|FBN2_ENST00000262464.4_Splice_Site_p.T1366T			P35556	FBN2_HUMAN	fibrillin 2	1366	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)		GAAACCTACCTGTACATCCTG	0.443													T|||	98	0.0195687	0.0726	0.0029	5008	,	,		21065	0.0		0.0	False		,,,				2504	0.0				p.T1366T		Atlas-SNP	.											.	FBN2	858	.	0			c.A4098C						PASS	.	T		331,4075	174.4+/-204.0	15,301,1887	131	117	122		4098	5	1	5	dbSNP_125	122	3,8597	3.0+/-9.4	0,3,4297	yes	coding-synonymous-near-splice	FBN2	NM_001999.3		15,304,6184	GG,GT,TT		0.0349,7.5125,2.568		1366/2913	127670412	334,12672	2203	4300	6503	SO:0001630	splice_region_variant	2201	exon31			CCTACCTGTACAT	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.4099+1A>C	5.37:g.127670412T>G		62	0	0		68	30	0.441176	NM_001999	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	37	CCDS34222.1																																																																																			T|0.975;G|0.025	0.025	strong		0.443	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	Silent	G	127670412	T	G	127670412	5	3	22	1	0	0	0	0	0	0	1	0	5711	1594	55	5	4780	5	FBN2	5	127670412	Splice_Site	SNP	T	TCGA-G8-6324-01A-11D-2210-10	45507	127670412	53244848	1255	4156											
CHSY3	337876	hgsc.bcm.edu	37	chr5	129520932	129520932	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagagttttccagaggtctTggtcttgaaatggcttctgc	7	14	13	7	0	3	3	0	1	3	2	4	4	4	3	1	4	1	2	1	4	1	5	rs73788438	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:129520932T>G	ENST00000305031.4	+	3	2455	c.2097T>G	c.(2095-2097)ctT>ctG	p.L699L		NM_175856.4	NP_787052.3	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	699					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)		CCAGAGGTCTTGGTCTTGAAA	0.433													T|||	191	0.038139	0.1271	0.0245	5008	,	,		20200	0.0		0.001	False		,,,				2504	0.0051				p.L699L		Atlas-SNP	.											CHSY3,colon,carcinoma,+2,2	CHSY3	92	2	0			c.T2097G						PASS	.	T		466,3940	217.1+/-235.6	21,424,1758	88	83	85		2097	-1.4	1	5	dbSNP_130	85	13,8587	10.5+/-38.8	0,13,4287	no	coding-synonymous	CHSY3	NM_175856.4		21,437,6045	GG,GT,TT		0.1512,10.5765,3.6829		699/883	129520932	479,12527	2203	4300	6503	SO:0001819	synonymous_variant	337876	exon3			AGGTCTTGGTCTT	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.2097T>G	5.37:g.129520932T>G		122	0	0		119	55	0.462185	NM_175856	B2RP97|Q76L22|Q86Y52	Silent	SNP	ENST00000305031.4	37	CCDS34223.1																																																																																			T|0.966;G|0.034	0.034	strong		0.433	CHSY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371453.1	NM_175856		G	129520932	T	G	129520932	2	3	22	1	0	0	0	0	0	0	0	1	3415	1799	63	5		5	CHSY3	5	129520932	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1850520	129520932	51394328	1256	4157											
SLC22A5	6584	hgsc.bcm.edu	37	chr5	131729935	131729935	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	taaaagatggtcaagaaaggCccacaatccttaaaagcaca	19	6	7	9	0	1	2	1	0	0	2	2	2	2	2	2	2	1	1	2	2	7	2	rs11568525	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:131729935C>T	ENST00000245407.3	+	10	1866	c.1645C>T	c.(1645-1647)Ccc>Tcc	p.P549S	SLC22A5_ENST00000435065.2_Missense_Mutation_p.P573S	NM_003060.3	NP_003051.1	O76082	S22A5_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 5	549			P -> S (associated with CDSP; unclassified missense variant; dbSNP:rs11568525). {ECO:0000269|PubMed:16931768, ECO:0000269|PubMed:20574985}.		carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|positive regulation of intestinal epithelial structure maintenance (GO:0060731)|quaternary ammonium group transport (GO:0015697)|quorum sensing involved in interaction with host (GO:0052106)|sodium ion transport (GO:0006814)|sodium-dependent organic cation transport (GO:0070715)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|ATP binding (GO:0005524)|carnitine transmembrane transporter activity (GO:0015226)|drug transmembrane transporter activity (GO:0015238)|PDZ domain binding (GO:0030165)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|symporter activity (GO:0015293)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|stomach(1)	8		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Acetylcarnitine(DB08842)|Aminohippurate(DB00345)|Amphetamine(DB00182)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benzylpenicillin(DB01053)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefradine(DB01333)|Ceftazidime(DB00438)|Cephalexin(DB00567)|Cephaloglycin(DB00689)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Creatine(DB00148)|Cyclacillin(DB01000)|Dactinomycin(DB00970)|Desipramine(DB01151)|Diphenhydramine(DB01075)|Dopamine(DB00988)|Epinephrine(DB00668)|Furosemide(DB00695)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Ipratropium bromide(DB00332)|L-Arginine(DB00125)|L-Carnitine(DB00583)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Mepyramine(DB06691)|Methamphetamine(DB01577)|Niacin(DB00627)|Nicotine(DB00184)|Norepinephrine(DB00368)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Probenecid(DB01032)|Procainamide(DB01035)|Quinidine(DB00908)|Quinine(DB00468)|Sparfloxacin(DB01208)|Thiamine(DB00152)|Tiotropium(DB01409)|Valproic Acid(DB00313)|Verapamil(DB00661)	TCAAGAAAGGCCCACAATCCT	0.388													C|||	110	0.0219649	0.0809	0.0043	5008	,	,		21710	0.0		0.0	False		,,,				2504	0.0				p.P549S		Atlas-SNP	.											.	SLC22A5	34	.	0			c.C1645T						PASS	.	C	SER/PRO	307,4099	166.9+/-198.0	5,297,1901	124	117	119		1645	4.4	1	5	dbSNP_126	119	0,8600		0,0,4300	yes	missense	SLC22A5	NM_003060.3	74	5,297,6201	TT,TC,CC		0.0,6.9678,2.3604	benign	549/558	131729935	307,12699	2203	4300	6503	SO:0001583	missense	6584	exon10			GAAAGGCCCACAA	AF057164	CCDS4154.1	5q23.3	2013-05-22	2008-01-11		ENSG00000197375	ENSG00000197375		"Solute carriers"	10969	protein-coding gene	gene with protein product		603377		CDSP		9618255, 9916797, 9685390	Standard	NM_003060		Approved	OCTN2, SCD	uc003kww.4	O76082	OTTHUMG00000059634	ENST00000245407.3:c.1645C>T	5.37:g.131729935C>T	ENSP00000245407:p.Pro549Ser	168	0	0		139	55	0.395683	NM_003060	A2Q0V1|B2R844|D3DQ87|Q6ZQZ8|Q96EH6	Missense_Mutation	SNP	ENST00000245407.3	37	CCDS4154.1	39	0.017857142857142856	37	0.07520325203252033	2	0.0055248618784530384	0	0.0	0	0.0	C	10.62	1.402298	0.25291	0.069678	0.0	ENSG00000197375	ENST00000245407;ENST00000435065	T;T	0.72725	-0.64;-0.68	5.28	4.38	0.52667	.	0.594079	0.17842	N	0.160148	T	0.04815	0.0130	N	0.24115	0.695	0.29262	N	0.871235	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.002	T	0.04178	-1.0971	10	0.09084	T	0.74	.	10.2464	0.43343	0.0:0.9041:0.0:0.0959	rs11568525;rs45558436;rs52826155;rs57292152;rs11568525	573;549	A2Q0V1;O76082	.;S22A5_HUMAN	S	549;573	ENSP00000245407:P549S;ENSP00000402760:P573S	ENSP00000245407:P549S	P	+	1	0	SLC22A5	131757834	0.935000	0.31712	0.985000	0.45067	0.319000	0.28217	1.735000	0.38176	1.392000	0.46585	0.655000	0.94253	CCC	C|0.972;T|0.028	0.028	strong		0.388	SLC22A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132631.1	NM_003060		T	131729935	C	T	131729935	3	4	22	1	0	0	0	0	1	0	0	0	14472	739	26	2	1683	2	SLC22A5	5	131729935	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2209003	131729935	49185325	1257	4158											
ANKRD43	134548	hgsc.bcm.edu	37	chr5	132149593	132149593	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcccgagcccgcacccttcGgccccccgggggcagcggcc	4	2	14	21	5	0	0	0	0	0	0	1	1	0	0	7	4	3	2	7	4	0	1	rs114865630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:132149593G>A	ENST00000378693.2	+	1	561	c.280G>A	c.(280-282)Ggc>Agc	p.G94S		NM_175873.4	NP_787069.3	Q2M3V2	SWAHA_HUMAN	sosondowah ankyrin repeat domain family member A	94	Pro-rich.																CGCACCCTTCGGCCCCCCGGG	0.726													G|||	151	0.0301518	0.1097	0.0086	5008	,	,		9361	0.0		0.0	False		,,,				2504	0.0				p.G94S		Atlas-SNP	.											.	.	.	.	0			c.G280A						PASS	.	G	SER/GLY	228,2496		11,206,1145	9	13	12		280	-6.5	0	5	dbSNP_132	12	4,6042		0,4,3019	no	missense	ANKRD43	NM_175873.4	56	11,210,4164	AA,AG,GG		0.0662,8.37,2.6454	benign	94/550	132149593	232,8538	1362	3023	4385	SO:0001583	missense	134548	exon1			CCCTTCGGCCCCC	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.280G>A	5.37:g.132149593G>A	ENSP00000367965:p.Gly94Ser	4	0	0		16	12	0.75	NM_175873	Q8NAE7	Missense_Mutation	SNP	ENST00000378693.2	37	CCDS43361.1	68	0.031135531135531136	57	0.11585365853658537	11	0.03038674033149171	0	0.0	0	0.0	g	7.170	0.587390	0.13812	0.0837	6.62E-4	ENSG00000198944	ENST00000378693	T	0.35421	1.31	3.95	-6.54	0.01860	.	.	.	.	.	T	0.00210	0.0006	N	0.14661	0.345	0.80722	P	0.0	B	0.18610	0.029	B	0.08055	0.003	T	0.37753	-0.9692	8	0.06236	T	0.91	7.4965	10.6849	0.45837	0.0:0.0953:0.7015:0.2032	.	94	Q2M3V2	ANR43_HUMAN	S	94	ENSP00000367965:G94S	ENSP00000367965:G94S	G	+	1	0	ANKRD43	132177492	0.000000	0.05858	0.002000	0.10522	0.064000	0.16182	-3.229000	0.00549	-0.876000	0.04017	0.290000	0.19541	GGC	G|0.964;A|0.036	0.036	strong		0.726	SOWAHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133062.1	NM_175873		A	132149593	G	A	132149593	3	1	22	1	0	0	0	0	1	0	0	0	671	1116	39	1	282	1	ANKRD43	5	132149593	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	419658	132149593	48765667	1258	4159											
ANKRD43	134548	hgsc.bcm.edu	37	chr5	132150804	132150804	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gacctggcccgaggcttgaaGaagtcgagctccttcagcaa	10	7	12	12	2	1	2	1	1	0	1	3	5	2	2	3	2	2	3	3	2	3	2	rs7719416	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:132150804G>A	ENST00000378693.2	+	1	1772	c.1491G>A	c.(1489-1491)aaG>aaA	p.K497K	AC004775.5_ENST00000607389.1_lincRNA	NM_175873.4	NP_787069.3	Q2M3V2	SWAHA_HUMAN	sosondowah ankyrin repeat domain family member A	497																	GAGGCTTGAAGAAGTCGAGCT	0.587													G|||	151	0.0301518	0.1097	0.0086	5008	,	,		18235	0.0		0.0	False		,,,				2504	0.0				p.K497K		Atlas-SNP	.											.	.	.	.	0			c.G1491A						PASS	.	G		458,3948	214.5+/-233.7	27,404,1772	47	50	49		1491	4.2	1	5	dbSNP_116	49	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous	ANKRD43	NM_175873.4		27,413,6063	AA,AG,GG		0.1047,10.3949,3.5907		497/550	132150804	467,12539	2203	4300	6503	SO:0001819	synonymous_variant	134548	exon1			CTTGAAGAAGTCG	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.1491G>A	5.37:g.132150804G>A		78	0	0		103	50	0.485437	NM_175873	Q8NAE7	Silent	SNP	ENST00000378693.2	37	CCDS43361.1																																																																																			G|0.965;A|0.035	0.035	strong		0.587	SOWAHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133062.1	NM_175873		A	132150804	G	A	132150804	2	1	22	1	0	0	0	0	0	0	0	1	671	933	33	2		2	ANKRD43	5	132150804	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1211	132150804	48764456	1259	4160											
AFF4	27125	hgsc.bcm.edu	37	chr5	132232148	132232148	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgtaaggctttcctggtattCtagtcaaaagattcaggtca	11	14	9	7	0	4	1	3	0	1	1	5	1	5	1	1	3	0	3	1	3	5	6	rs138811630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:132232148C>G	ENST00000265343.5	-	11	2553	c.2174G>C	c.(2173-2175)aGa>aCa	p.R725T	AFF4_ENST00000378595.3_Missense_Mutation_p.R725T	NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	725					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)			TCCTGGTATTCTAGTCAAAAG	0.453													C|||	2	0.000399361	0.0015	0.0	5008	,	,		18395	0.0		0.0	False		,,,				2504	0.0				p.R725T	Ovarian(126;889 1733 2942 10745 11605)	Atlas-SNP	.											.	AFF4	120	.	0			c.G2174C						PASS	.	C	THR/ARG	8,4398	12.9+/-30.5	0,8,2195	125	125	125		2174	4.9	1	5	dbSNP_134	125	0,8600		0,0,4300	yes	missense	AFF4	NM_014423.3	71	0,8,6495	GG,GC,CC		0.0,0.1816,0.0615	probably-damaging	725/1164	132232148	8,12998	2203	4300	6503	SO:0001583	missense	27125	exon11			GGTATTCTAGTCA	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.2174G>C	5.37:g.132232148C>G	ENSP00000265343:p.Arg725Thr	173	0	0		196	89	0.454082	NM_014423	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	Missense_Mutation	SNP	ENST00000265343.5	37	CCDS4164.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	21.2	4.115328	0.77323	0.001816	0.0	ENSG00000072364	ENST00000265343;ENST00000378595	T;T	0.78481	-1.18;-1.18	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	D	0.89385	0.6700	M	0.85777	2.775	0.58432	D	0.999998	D;D	0.67145	0.996;0.991	D;D	0.77557	0.99;0.987	D	0.91090	0.4906	10	0.72032	D	0.01	-16.5422	18.443	0.90673	0.0:1.0:0.0:0.0	.	725;725	Q9UHB7-2;Q9UHB7	.;AFF4_HUMAN	T	725	ENSP00000265343:R725T;ENSP00000367858:R725T	ENSP00000265343:R725T	R	-	2	0	AFF4	132260047	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.593000	0.82686	2.417000	0.82017	0.563000	0.77884	AGA	C|0.999;G|0.001	0.001	strong		0.453	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133049.1	NM_014423		G	132232148	C	G	132232148	3	3	22	1	0	0	0	0	1	0	0	0	359	913	32	4	1361	4	AFF4	5	132232148	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	81344	132232148	48683112	1260	4161											
FSTL4	23105	hgsc.bcm.edu	37	chr5	132535225	132535225	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcactgactatgaagcgcccGtcgggggatgtgtgtggggt	6	9	18	8	3	0	2	0	2	0	0	1	3	0	3	1	4	1	1	1	4	2	1	rs61740558	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:132535225G>A	ENST00000265342.7	-	16	2340	c.2091C>T	c.(2089-2091)gaC>gaT	p.D697D	CTB-49A3.2_ENST00000509051.1_RNA	NM_015082.1	NP_055897.1	Q6MZW2	FSTL4_HUMAN	follistatin-like 4	697						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.D697D(1)		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)			TGAAGCGCCCGTCGGGGGATG	0.607													G|||	110	0.0219649	0.0772	0.0115	5008	,	,		18282	0.0		0.0	False		,,,				2504	0.0				p.D697D		Atlas-SNP	.											FSTL4,colon,carcinoma,0,2	FSTL4	74	2	1	Substitution - coding silent(1)	large_intestine(1)	c.C2091T						PASS	.	G		270,4136	151.8+/-185.6	9,252,1942	49	52	51		2091	-4.1	0.6	5	dbSNP_129	51	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	FSTL4	NM_015082.1		9,258,6236	AA,AG,GG		0.0698,6.128,2.1221		697/843	132535225	276,12730	2203	4300	6503	SO:0001819	synonymous_variant	23105	exon16			GCGCCCGTCGGGG	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.2091C>T	5.37:g.132535225G>A		113	0	0		118	68	0.576271	NM_015082	Q8TBU0|Q9UPU1	Silent	SNP	ENST00000265342.7	37	CCDS34238.1																																																																																			G|0.980;A|0.020	0.020	strong		0.607	FSTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370212.1	XM_048786		A	132535225	G	A	132535225	2	1	22	1	0	0	0	0	0	0	0	1	6087	1136	40	1		1	FSTL4	5	132535225	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	303077	132535225	48380035	1261	4162											
CATSPER3	347732	hgsc.bcm.edu	37	chr5	134343766	134343766	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtttggatctccagacaaTggtgaccatgataactgggg	10	11	12	8	0	1	3	0	2	1	1	2	4	1	4	2	4	1	1	2	4	2	2	rs3896260	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:134343766T>G	ENST00000282611.6	+	4	698	c.612T>G	c.(610-612)aaT>aaG	p.N204K		NM_178019.2	NP_821138.1	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	204			N -> K (in dbSNP:rs3896260).		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)			CTCCAGACAATGGTGACCATG	0.552													G|||	646	0.128994	0.4584	0.0461	5008	,	,		15472	0.0		0.007	False		,,,				2504	0.001				p.N204K		Atlas-SNP	.											.	CATSPER3	38	.	0			c.T612G						PASS	.	G	LYS/ASN	1758,2648	644.5+/-398.0	347,1064,792	184	145	158		612	-2.1	0	5	dbSNP_108	158	24,8576	818.1+/-406.9	0,24,4276	yes	missense	CATSPER3	NM_178019.2	94	347,1088,5068	GG,GT,TT		0.2791,39.9001,13.7014	benign	204/399	134343766	1782,11224	2203	4300	6503	SO:0001583	missense	347732	exon4			AGACAATGGTGAC	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.612T>G	5.37:g.134343766T>G	ENSP00000282611:p.Asn204Lys	249	0	0		303	145	0.478548	NM_178019	Q86XS6	Missense_Mutation	SNP	ENST00000282611.6	37	CCDS4181.1	241	0.11034798534798534	221	0.4491869918699187	17	0.04696132596685083	0	0.0	3	0.00395778364116095	G	0.003	-2.468589	0.00169	0.399001	0.002791	ENSG00000152705	ENST00000282611	D	0.97553	-4.43	4.33	-2.08	0.07254	Ion transport (1);	1.918400	0.01976	N	0.044466	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.50440	-0.8828	8	.	.	.	1.4415	0.1834	0.00126	0.2523:0.1883:0.202:0.3574	rs3896260;rs52815255;rs60117234;rs3896260	204	Q86XQ3	CTSR3_HUMAN	K	204	ENSP00000282611:N204K	.	N	+	3	2	CATSPER3	134371665	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.154000	0.03166	-0.973000	0.03555	-0.358000	0.07595	AAT	T|0.860;G|0.140	0.140	strong		0.552	CATSPER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251191.2	NM_178019		G	134343766	T	G	134343766	3	3	22	1	0	0	0	0	1	0	0	0	2691	1461	51	5	626	5	CATSPER3	5	134343766	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1808541	134343766	46571494	1262	4163											
CATSPER3	347732	hgsc.bcm.edu	37	chr5	134347241	134347241	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtactatgagatcgtgcaTgtgctgagcctaatgctgga	9	12	12	8	1	0	2	0	2	0	1	1	4	0	3	1	1	5	4	1	1	3	3	rs7719874	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:134347241T>C	ENST00000282611.6	+	8	1211	c.1125T>C	c.(1123-1125)caT>caC	p.H375H		NM_178019.2	NP_821138.1	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	375					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)			AGATCGTGCATGTGCTGAGCC	0.562													T|||	293	0.0585064	0.2126	0.0144	5008	,	,		19649	0.0		0.002	False		,,,				2504	0.0				p.H375H		Atlas-SNP	.											.	CATSPER3	38	.	0			c.T1125C						PASS	.	T		785,3621	317.2+/-295.0	66,653,1484	88	76	80		1125	-5.6	0.1	5	dbSNP_116	80	7,8593	6.4+/-24.3	0,7,4293	no	coding-synonymous	CATSPER3	NM_178019.2		66,660,5777	CC,CT,TT		0.0814,17.8166,6.0895		375/399	134347241	792,12214	2203	4300	6503	SO:0001819	synonymous_variant	347732	exon8			CGTGCATGTGCTG	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.1125T>C	5.37:g.134347241T>C		77	0	0		83	39	0.46988	NM_178019	Q86XS6	Silent	SNP	ENST00000282611.6	37	CCDS4181.1																																																																																			T|0.929;C|0.071	0.071	strong		0.562	CATSPER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251191.2	NM_178019		C	134347241	T	C	134347241	2	2	22	1	0	0	0	0	0	0	0	1	2691	1461	51	3		3	CATSPER3	5	134347241	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	3475	134347241	46568019	1263	4164											
C5orf20	140947	hgsc.bcm.edu	37	chr5	134782396	134782396	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaacgggtagagtctgaaacTacaaaccagatgtttccggg	13	8	12	8	2	1	3	0	1	1	2	2	4	2	3	2	2	4	2	2	2	5	3	rs67187482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:134782396T>A	ENST00000503143.2	-	1	642	c.403A>T	c.(403-405)Agt>Tgt	p.S135C	TIFAB_ENST00000537858.1_3'UTR	NM_130848.2	NP_570900.1	Q8TF63	DCNP1_HUMAN		135						nucleus (GO:0005634)				endometrium(1)|lung(1)|prostate(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGTCTGAAACTACAAACCAGA	0.547													T|||	430	0.0858626	0.2867	0.0418	5008	,	,		19738	0.0		0.0179	False		,,,				2504	0.0041				p.S135C		Atlas-SNP	.											.	C5orf20	16	.	0			c.A403T						PASS	.	T	CYS/SER	1116,3290	402.4+/-332.3	149,818,1236	132	143	139		403	-1.8	0	5	dbSNP_130	139	119,8481	61.7+/-123.6	1,117,4182	yes	missense	C5orf20	NM_130848.2	112	150,935,5418	AA,AT,TT		1.3837,25.3291,9.4956	benign	135/245	134782396	1235,11771	2203	4300	6503	SO:0001583	missense	140947	exon1			TGAAACTACAAAC																												ENST00000503143.2:c.403A>T	5.37:g.134782396T>A	ENSP00000421871:p.Ser135Cys	104	0	0		100	42	0.42	NM_130848		Missense_Mutation	SNP	ENST00000503143.2	37	CCDS4186.1	163	0.07463369963369963	132	0.2682926829268293	14	0.03867403314917127	0	0.0	17	0.022427440633245383	T	4.521	0.096694	0.08681	0.253291	0.013837	ENSG00000251380	ENST00000503143	T	0.39056	1.1	2.85	-1.79	0.07932	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.32508	-0.9904	8	0.87932	D	0	.	4.0496	0.09790	0.3788:0.41:0.0:0.2112	.	135	Q8TF63	DCNP1_HUMAN	C	135	ENSP00000421871:S135C	ENSP00000421871:S135C	S	-	1	0	C5orf20	134810295	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.310000	0.19356	-0.278000	0.09180	-0.892000	0.02923	AGT	T|0.905;A|0.095	0.095	strong		0.547	C5orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372531.1			A	134782396	T	A	134782396	3	1	22	1	0	0	0	0	1	0	0	0	2286	1522	53	5	335	5	C5orf20	5	134782396	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	435155	134782396	46132864	1264	4165											
C5orf20	140947	hgsc.bcm.edu	37	chr5	134782443	134782443	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cccgcctggtctggcctgtcTtccttctgctgctatgcagt	2	14	10	15	1	3	0	0	0	3	0	4	0	4	0	4	2	3	3	4	2	1	3	rs113429044	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:134782443T>C	ENST00000503143.2	-	1	595	c.356A>G	c.(355-357)aAg>aGg	p.K119R	TIFAB_ENST00000537858.1_3'UTR	NM_130848.2	NP_570900.1	Q8TF63	DCNP1_HUMAN		119						nucleus (GO:0005634)				endometrium(1)|lung(1)|prostate(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CTGGCCTGTCTTCCTTCTGCT	0.547													T|||	452	0.0902556	0.3033	0.0418	5008	,	,		19866	0.0		0.0179	False		,,,				2504	0.0041				p.K119R		Atlas-SNP	.											.	C5orf20	16	.	0			c.A356G						PASS	.	T	ARG/LYS	1160,3246	410.9+/-335.5	154,852,1197	112	120	117		356	0.2	0	5	dbSNP_132	117	119,8481	61.7+/-123.6	1,117,4182	yes	missense	C5orf20	NM_130848.2	26	155,969,5379	CC,CT,TT		1.3837,26.3277,9.8339	benign	119/245	134782443	1279,11727	2203	4300	6503	SO:0001583	missense	140947	exon1			CCTGTCTTCCTTC																												ENST00000503143.2:c.356A>G	5.37:g.134782443T>C	ENSP00000421871:p.Lys119Arg	83	0	0		83	37	0.445783	NM_130848		Missense_Mutation	SNP	ENST00000503143.2	37	CCDS4186.1	170	0.07783882783882784	139	0.28252032520325204	14	0.03867403314917127	0	0.0	17	0.022427440633245383	T	5.813	0.334340	0.11013	0.263277	0.013837	ENSG00000251380	ENST00000503143	T	0.37915	1.17	2.78	0.236	0.15471	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	5.000000000032756E-6	B	0.16603	0.018	B	0.08055	0.003	T	0.36089	-0.9762	8	0.87932	D	0	.	3.1238	0.06400	0.5045:0.2511:0.0:0.2444	.	119	Q8TF63	DCNP1_HUMAN	R	119	ENSP00000421871:K119R	ENSP00000421871:K119R	K	-	2	0	C5orf20	134810342	0.000000	0.05858	0.013000	0.15412	0.047000	0.14425	-0.373000	0.07494	0.043000	0.15746	-0.669000	0.03829	AAG	T|0.902;C|0.098	0.098	strong		0.547	C5orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372531.1			C	134782443	T	C	134782443	3	2	22	1	0	0	0	0	1	0	0	0	2286	1609	56	3	382	3	C5orf20	5	134782443	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	47	134782443	46132817	1265	4166											
NEUROG1	4762	hgsc.bcm.edu	37	chr5	134871280	134871280	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cggaggctgcctgttggagtCtggcacagtcttcctcgtcg	4	11	14	12	3	2	0	0	0	2	0	5	2	3	2	2	4	1	3	2	4	0	2	rs34137563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:134871280C>T	ENST00000314744.4	-	1	359	c.101G>A	c.(100-102)aGa>aAa	p.R34K		NM_006161.2	NP_006152.2	Q92886	NGN1_HUMAN	neurogenin 1	34					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)			CTGTTGGAGTCTGGCACAGTC	0.692													C|||	30	0.00599042	0.0212	0.0029	5008	,	,		13642	0.0		0.0	False		,,,				2504	0.0				p.R34K		Atlas-SNP	.											.	NEUROG1	18	.	0			c.G101A						PASS	.	C	LYS/ARG	63,4167		2,59,2054	13	12	12		101	3.8	1	5	dbSNP_126	12	0,8264		0,0,4132	yes	missense	NEUROG1	NM_006161.2	26	2,59,6186	TT,TC,CC		0.0,1.4894,0.5042	possibly-damaging	34/238	134871280	63,12431	2115	4132	6247	SO:0001583	missense	4762	exon1			TGGAGTCTGGCAC	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.101G>A	5.37:g.134871280C>T	ENSP00000317580:p.Arg34Lys	23	0	0		30	13	0.433333	NM_006161	Q5U0Q9|Q96HE1	Missense_Mutation	SNP	ENST00000314744.4	37	CCDS4187.1	19	0.0086996336996337	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	C	12.13	1.847045	0.32606	0.014894	0.0	ENSG00000181965	ENST00000314744	D	0.95103	-3.61	4.7	3.83	0.44106	.	0.656928	0.13766	N	0.364252	T	0.74489	0.3723	N	0.24115	0.695	0.26416	N	0.976176	P	0.37864	0.61	B	0.37989	0.262	T	0.72606	-0.4242	10	0.06099	T	0.92	-0.0177	10.6463	0.45621	0.0:0.904:0.0:0.096	rs34137563	34	Q92886	NGN1_HUMAN	K	34	ENSP00000317580:R34K	ENSP00000317580:R34K	R	-	2	0	NEUROG1	134899179	1.000000	0.71417	0.958000	0.39756	0.312000	0.27988	2.898000	0.48672	0.977000	0.38444	-0.258000	0.10820	AGA	C|0.993;T|0.007	0.007	strong		0.692	NEUROG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251192.1	NM_006161		T	134871280	C	T	134871280	3	4	22	1	0	0	0	0	1	0	0	0	10361	913	32	2	616	2	NEUROG1	5	134871280	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	88837	134871280	46043980	1266	4167											
TGFBI	7045	hgsc.bcm.edu	37	chr5	135392482	135392482	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagagaacggagcagactctTgggtaaagaccaacttaagt	16	7	11	7	1	1	3	0	0	1	3	1	5	1	4	1	2	3	2	1	2	6	3	rs200219644		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:135392482T>G	ENST00000442011.2	+	12	1837	c.1676T>G	c.(1675-1677)tTg>tGg	p.L559W	TGFBI_ENST00000305126.8_Missense_Mutation_p.L559W|TGFBI_ENST00000508076.1_5'Flank	NM_000358.2	NP_000349.1	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	559	FAS1 4. {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)			AGCAGACTCTTGGGTAAAGAC	0.512													T|||	1	0.000199681	0.0	0.0	5008	,	,		19392	0.0		0.001	False		,,,				2504	0.0				p.L559W		Atlas-SNP	.											.	TGFBI	76	.	0			c.T1676G						PASS	.	T	TRP/LEU	3,3871		0,3,1934	43	45	45		1676	5.8	1	5		45	0,8266		0,0,4133	yes	missense	TGFBI	NM_000358.2	61	0,3,6067	GG,GT,TT		0.0,0.0774,0.0247	probably-damaging	559/684	135392482	3,12137	1937	4133	6070	SO:0001583	missense	7045	exon12			GACTCTTGGGTAA	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.1676T>G	5.37:g.135392482T>G	ENSP00000416330:p.Leu559Trp	178	0	0		216	117	0.541667	NM_000358	D3DQB1|O14471|O14472|O14476|O43216|O43217|O43218|O43219|Q53XM1	Missense_Mutation	SNP	ENST00000442011.2	37	CCDS47266.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.344323	0.82022	7.74E-4	0.0	ENSG00000120708	ENST00000442011;ENST00000398813;ENST00000305126	D;D	0.92495	-3.05;-3.05	5.75	5.75	0.90469	FAS1 domain (5);	0.345979	0.31636	N	0.007304	D	0.97012	0.9024	M	0.93854	3.465	0.58432	D	0.999999	D;D	0.67145	0.992;0.996	D;D	0.70487	0.969;0.969	D	0.97996	1.0357	10	0.87932	D	0	-1.0597	16.0502	0.80755	0.0:0.0:0.0:1.0	.	292;559	B9ZVW9;Q15582	.;BGH3_HUMAN	W	559;292;559	ENSP00000416330:L559W;ENSP00000306306:L559W	ENSP00000306306:L559W	L	+	2	0	TGFBI	135420381	1.000000	0.71417	1.000000	0.80357	0.737000	0.42083	5.538000	0.67193	2.201000	0.70794	0.496000	0.49642	TTG	.	.	weak		0.512	TGFBI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372108.1			G	135392482	T	G	135392482	3	3	22	1	0	0	0	0	1	0	0	0	15835	1821	63	5	1722	5	TGFBI	5	135392482	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	521202	135392482	45522778	1267	4168											
SPOCK1	6695	hgsc.bcm.edu	37	chr5	136448208	136448208	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgcacttgaccaaattcgaAggtccaacccagtgtttctg	10	12	8	11	1	1	1	0	1	1	0	3	2	2	1	3	1	2	2	3	1	3	4	rs17170968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:136448208A>G	ENST00000394945.1	-	5	559	c.390T>C	c.(388-390)ccT>ccC	p.P130P	SPOCK1_ENST00000282223.7_Silent_p.P130P	NM_004598.3	NP_004589.1	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1	130	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				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)			CCAAATTCGAAGGTCCAACCC	0.498													A|||	379	0.0756789	0.2769	0.0187	5008	,	,		18879	0.0		0.0	False		,,,				2504	0.0				p.P130P		Atlas-SNP	.											.	SPOCK1	58	.	0			c.T390C						PASS	.	A		1146,3260	407.3+/-334.2	151,844,1208	101	97	98		390	-1	1	5	dbSNP_123	98	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous	SPOCK1	NM_004598.3		151,854,5498	GG,GA,AA		0.1163,26.01,8.8882		130/440	136448208	1156,11850	2203	4300	6503	SO:0001819	synonymous_variant	6695	exon5			ATTCGAAGGTCCA	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.390T>C	5.37:g.136448208A>G		75	0	0		62	25	0.403226	NM_004598	B3KSW3|Q59EW0|Q8N630|Q9UCL8	Silent	SNP	ENST00000394945.1	37	CCDS4191.1																																																																																			A|0.924;G|0.076	0.076	strong		0.498	SPOCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251222.1	NM_004598		G	136448208	A	G	136448208	2	3	22	1	0	0	0	0	0	0	0	1	15094	59	3	3		3	SPOCK1	5	136448208	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1055726	136448208	44467052	1268	4169											
KIF20A	10112	hgsc.bcm.edu	37	chr5	137520025	137520025	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcctgcatgattgtcaatGtgaatccctgtgcatctacc	8	14	8	11	0	2	2	1	2	1	0	4	2	4	2	3	0	3	3	3	0	3	3	rs142495138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:137520025G>A	ENST00000394894.3	+	12	1676	c.1450G>A	c.(1450-1452)Gtg>Atg	p.V484M	KIF20A_ENST00000508792.1_Missense_Mutation_p.V466M	NM_005733.2	NP_005724.1	O95235	KI20A_HUMAN	kinesin family member 20A	484	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)			GATTGTCAATGTGAATCCCTG	0.512																																					p.V484M		Atlas-SNP	.											.	KIF20A	53	.	0			c.G1450A						PASS	.	G	MET/VAL	4,4402	8.1+/-20.4	0,4,2199	170	163	165		1450	3.7	1	5	dbSNP_134	165	0,8600		0,0,4300	no	missense	KIF20A	NM_005733.2	21	0,4,6499	AA,AG,GG		0.0,0.0908,0.0308	probably-damaging	484/891	137520025	4,13002	2203	4300	6503	SO:0001583	missense	10112	exon12			GTCAATGTGAATC	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.1450G>A	5.37:g.137520025G>A	ENSP00000378356:p.Val484Met	217	0	0		208	107	0.514423	NM_005733	B4DL79|D3DQB6	Missense_Mutation	SNP	ENST00000394894.3	37	CCDS4199.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.921838	0.33908	9.08E-4	0.0	ENSG00000112984	ENST00000394894;ENST00000508792	T;T	0.55930	0.49;0.49	5.49	3.72	0.42706	Kinesin, motor domain (3);	0.175916	0.27164	N	0.020639	T	0.46268	0.1384	L	0.50919	1.6	0.40300	D	0.978593	B;B	0.25272	0.122;0.036	B;B	0.32149	0.141;0.051	T	0.47341	-0.9125	10	0.72032	D	0.01	-5.3957	6.3677	0.21463	0.3825:0.0:0.6175:0.0	.	466;484	B4DL79;O95235	.;KI20A_HUMAN	M	484;466	ENSP00000378356:V484M;ENSP00000420880:V466M	ENSP00000378356:V484M	V	+	1	0	KIF20A	137547924	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	3.399000	0.52586	0.874000	0.35823	0.643000	0.83706	GTG	G|1.000;A|0.000	0.000	strong		0.512	KIF20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251272.1	NM_005733		A	137520025	G	A	137520025	3	1	22	1	0	0	0	0	1	0	0	0	8295	1377	48	2	1492	2	KIF20A	5	137520025	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1071817	137520025	43395235	1269	4170											
WDR55	54853	hgsc.bcm.edu	37	chr5	140048792	140048792	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gactgcatggttccagtcacCgagagtctgctgtgtactgg	7	11	13	10	1	2	1	1	0	1	1	3	3	3	1	2	2	3	4	2	2	1	2	rs35080423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140048792C>A	ENST00000358337.5	+	6	1026	c.789C>A	c.(787-789)acC>acA	p.T263T	WDR55_ENST00000520764.1_3'UTR	NM_017706.4	NP_060176	Q9H6Y2	WDR55_HUMAN	WD repeat domain 55	263					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)				NS(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCCAGTCACCGAGAGTCTGC	0.547													C|||	51	0.0101837	0.0378	0.0014	5008	,	,		21176	0.0		0.0	False		,,,				2504	0.0				p.T263T		Atlas-SNP	.											WDR55,NS,carcinoma,+2,1	WDR55	27	1	0			c.C789A						scavenged	.	C		113,4293	88.2+/-126.9	3,107,2093	84	77	79		789	-10.2	0.1	5	dbSNP_126	79	0,8600		0,0,4300	no	coding-synonymous	WDR55	NM_017706.4		3,107,6393	AA,AC,CC		0.0,2.5647,0.8688		263/384	140048792	113,12893	2203	4300	6503	SO:0001819	synonymous_variant	54853	exon6			AGTCACCGAGAGT	AK000202	CCDS4235.1	5q31.3	2013-01-09			ENSG00000120314	ENSG00000120314		"WD repeat domain containing"	25971	protein-coding gene	gene with protein product						12477932	Standard	NM_017706		Approved	FLJ20195, FLJ21702	uc003lgr.4	Q9H6Y2	OTTHUMG00000129506	ENST00000358337.5:c.789C>A	5.37:g.140048792C>A		70	1	0.0142857		61	32	0.52459	NM_017706	Q9NXK4	Silent	SNP	ENST00000358337.5	37	CCDS4235.1																																																																																			C|0.991;A|0.009	0.009	strong		0.547	WDR55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251680.3	NM_017706		A	140048792	C	A	140048792	2	1	22	1	0	0	0	0	0	0	0	1	17322	639	23	4		4	WDR55	5	140048792	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2528767	140048792	40866468	1270	4171											
DND1	373863	hgsc.bcm.edu	37	chr5	140051009	140051009	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgcccatcccggccatctaGggtcagcacaacccagatga	11	6	9	15	1	2	2	1	1	1	1	3	2	3	2	4	2	3	1	4	2	2	1	rs146252353	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140051009G>A	ENST00000542735.1	-	4	974	c.931C>T	c.(931-933)Cta>Tta	p.L311L	WDR55_ENST00000520764.1_3'UTR|WDR55_ENST00000358337.5_3'UTR	NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	311					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)			CGGCCATCTAGGGTCAGCACA	0.622													G|||	28	0.00559105	0.0212	0.0	5008	,	,		20864	0.0		0.0	False		,,,				2504	0.0				p.L311L		Atlas-SNP	.											.	DND1	15	.	0			c.C931T						PASS	.	G		78,4010		0,78,1966	22	23	23		931	-1.9	0	5	dbSNP_134	23	0,8094		0,0,4047	no	coding-synonymous	DND1	NM_194249.2		0,78,6013	AA,AG,GG		0.0,1.908,0.6403		311/354	140051009	78,12104	2044	4047	6091	SO:0001819	synonymous_variant	373863	exon4			CATCTAGGGTCAG	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.931C>T	5.37:g.140051009G>A		407	0	0		406	202	0.497537	NM_194249		Silent	SNP	ENST00000542735.1	37	CCDS4236.1																																																																																			G|0.994;A|0.006	0.006	strong		0.622	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249		A	140051009	G	A	140051009	2	1	22	1	0	0	0	0	0	0	0	1	4668	991	35	2		2	DND1	5	140051009	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2217	140051009	40864251	1271	4172											
PCDHA1	56147	hgsc.bcm.edu	37	chr5	140167175	140167175	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcgggacgggggctcgcctTcgctgtgggccacggccagg	3	5	19	14	6	0	0	0	0	0	0	2	1	0	1	3	6	0	2	3	6	0	1	rs61743801	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140167175T>C	ENST00000504120.2	+	1	1300	c.1300T>C	c.(1300-1302)Tcg>Ccg	p.S434P	PCDHA1_ENST00000394633.3_Missense_Mutation_p.S434P|PCDHA1_ENST00000378133.3_Missense_Mutation_p.S434P	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	434	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)			GGGCTCGCCTTCGCTGTGGGC	0.627													.|||	72	0.014377	0.0537	0.0014	5008	,	,		17483	0.0		0.0	False		,,,				2504	0.0				p.S434P		Atlas-SNP	.											.	PCDHA1	387	.	0			c.T1300C						PASS	.	T	PRO/SER,PRO/SER,PRO/SER	236,4170	135.3+/-171.4	10,216,1977	82	88	86		1300,1300,1300	-3.1	0.7	5	dbSNP_129	86	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense,missense	PCDHA1	NM_018900.2,NM_031410.1,NM_031411.1	74,74,74	10,217,6275	CC,CT,TT		0.0116,5.3563,1.8225	,,	434/951,434/808,434/687	140167175	237,12767	2203	4299	6502	SO:0001583	missense	56147	exon1			TCGCCTTCGCTGT	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.1300T>C	5.37:g.140167175T>C	ENSP00000420840:p.Ser434Pro	159	0	0		166	81	0.487952	NM_031411	O75288|Q9NRT7	Missense_Mutation	SNP	ENST00000504120.2	37	CCDS54913.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	t	4.310	0.056796	0.08339	0.053563	1.16E-4	ENSG00000204970	ENST00000504120;ENST00000394633;ENST00000378133	T;T;T	0.44881	0.91;0.91;0.91	3.89	-3.14	0.05250	Cadherin (5);Cadherin-like (1);	0.679068	0.12024	N	0.506656	T	0.02047	0.0064	N	0.02539	-0.55	0.09310	N	1	B;B;B	0.17852	0.024;0.002;0.023	B;B;B	0.32022	0.139;0.002;0.03	T	0.30563	-0.9974	10	0.13853	T	0.58	.	2.4978	0.04626	0.1149:0.2142:0.4488:0.2221	rs61743801	434;434;434	Q9Y5I3;Q9Y5I3-2;Q9Y5I3-3	PCDA1_HUMAN;.;.	P	434	ENSP00000420840:S434P;ENSP00000378129:S434P;ENSP00000367373:S434P	ENSP00000367373:S434P	S	+	1	0	PCDHA1	140147359	0.000000	0.05858	0.741000	0.31004	0.719000	0.41307	-0.511000	0.06321	-0.192000	0.10432	0.369000	0.22263	TCG	T|0.983;C|0.017	0.017	strong		0.627	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900		C	140167175	T	C	140167175	3	2	22	1	0	0	0	0	1	0	0	0	11528	1783	62	3	1302	3	PCDHA1	5	140167175	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	116166	140167175	40748085	1272	4173											
PCDHA1	56147	hgsc.bcm.edu	37	chr5	140167520	140167520	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccgcctctgggcagcaacGtgacgctgcaggtgttcgtg	5	9	15	12	4	1	1	0	1	1	0	2	1	1	1	2	2	4	5	2	2	1	1	rs150585640	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140167520G>A	ENST00000504120.2	+	1	1645	c.1645G>A	c.(1645-1647)Gtg>Atg	p.V549M	PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000378133.3_Missense_Mutation_p.V549M	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	549	Cadherin 5. {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)			GGGCAGCAACGTGACGCTGCA	0.672													.|||	71	0.0141773	0.053	0.0014	5008	,	,		16239	0.0		0.0	False		,,,				2504	0.0				p.V549M		Atlas-SNP	.											.	PCDHA1	387	.	0			c.G1645A						PASS	.	G	MET/VAL,MET/VAL,	233,4173	136.1+/-172.1	9,215,1979	78	81	80		1645,1645,	2.7	1	5	dbSNP_134	80	1,8589	1.2+/-3.3	0,1,4294	no	missense,missense,intron	PCDHA1	NM_018900.2,NM_031410.1,NM_031411.1	21,21,	9,216,6273	AA,AG,GG		0.0116,5.2882,1.8006	,,	549/951,549/808,	140167520	234,12762	2203	4295	6498	SO:0001583	missense	56147	exon1			AGCAACGTGACGC	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.1645G>A	5.37:g.140167520G>A	ENSP00000420840:p.Val549Met	81	0	0		120	60	0.5	NM_031410	O75288|Q9NRT7	Missense_Mutation	SNP	ENST00000504120.2	37	CCDS54913.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	g	16.14	3.037929	0.54896	0.052882	1.16E-4	ENSG00000204970	ENST00000504120;ENST00000378133	T;T	0.53640	0.61;0.61	3.59	2.71	0.32032	Cadherin (5);Cadherin-like (1);	0.209202	0.23219	N	0.050600	T	0.16896	0.0406	M	0.83384	2.64	0.23997	N	0.996224	D;D	0.65815	0.995;0.988	P;P	0.50192	0.634;0.501	T	0.25847	-1.0120	10	0.66056	D	0.02	.	7.0109	0.24861	0.0968:0.1747:0.7285:0.0	.	549;549	Q9Y5I3;Q9Y5I3-3	PCDA1_HUMAN;.	M	549	ENSP00000420840:V549M;ENSP00000367373:V549M	ENSP00000367373:V549M	V	+	1	0	PCDHA1	140147704	0.967000	0.33354	0.987000	0.45799	0.935000	0.57460	2.495000	0.45337	0.621000	0.30232	0.555000	0.69702	GTG	G|0.961;A|0.039	0.039	strong		0.672	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900		A	140167520	G	A	140167520	3	1	22	1	0	0	0	0	1	0	0	0	11528	1145	40	1	1647	1	PCDHA1	5	140167520	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	345	140167520	40747740	1273	4174											
PCDHA2	56146	hgsc.bcm.edu	37	chr5	140176840	140176840	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggtgtgctctggggaggaccCccccaagacggacctcatgg	7	6	15	13	1	2	1	1	0	1	1	2	4	2	4	4	6	1	1	4	6	1	0	rs6858913	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140176840C>T	ENST00000526136.1	+	1	2291	c.2291C>T	c.(2290-2292)cCc>cTc	p.P764L	PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000520672.2_Missense_Mutation_p.P764L|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000378132.1_Missense_Mutation_p.P764L	NM_018905.2	NP_061728.1	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2	764	5 X 4 AA repeats of P-X-X-P.		P -> L (in dbSNP:rs6858913).		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)			GGGGAGGACCCCCCCAAGACG	0.617													.|||	71	0.0141773	0.053	0.0014	5008	,	,		14850	0.0		0.0	False		,,,				2504	0.0				p.P764L		Atlas-SNP	.											.	PCDHA2	404	.	0			c.C2291T						PASS	.	C	,LEU/PRO,,LEU/PRO	225,4181	134.9+/-171.1	9,207,1987	47	51	49		,2291,,2291	1	0.7	5	dbSNP_116	49	1,8599	1.2+/-3.3	0,1,4299	yes	intron,missense,intron,missense	PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_031411.1,NM_031495.1	,98,,98	9,208,6286	TT,TC,CC		0.0116,5.1067,1.7377	,,,	,764/949,,764/825	140176840	226,12780	2203	4300	6503	SO:0001583	missense	56146	exon1			AGGACCCCCCCAA	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.2291C>T	5.37:g.140176840C>T	ENSP00000431748:p.Pro764Leu	269	0	0		305	143	0.468852	NM_031495	O75287|Q9BTV3	Missense_Mutation	SNP	ENST00000526136.1	37	CCDS54914.1	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	c	5.110	0.205978	0.09704	0.051067	1.16E-4	ENSG00000204969	ENST00000520672;ENST00000378132;ENST00000526136	T;T;T	0.11930	2.73;2.73;2.73	4.0	1.05	0.20165	.	2.011240	0.03846	N	0.271521	T	0.01940	0.0061	L	0.42487	1.325	0.09310	N	1	B;B;B	0.13594	0.008;0.001;0.007	B;B;B	0.15052	0.012;0.003;0.012	T	0.29792	-1.0000	10	0.35671	T	0.21	.	6.6028	0.22710	0.0:0.6237:0.131:0.2453	rs6858913;rs52809059;rs6858913	764;764;764	Q9Y5H9-3;Q9Y5H9;Q9Y5H9-2	.;PCDA2_HUMAN;.	L	764	ENSP00000430584:P764L;ENSP00000367372:P764L;ENSP00000431748:P764L	ENSP00000367372:P764L	P	+	2	0	PCDHA2	140157024	0.000000	0.05858	0.736000	0.30914	0.471000	0.32888	0.336000	0.19823	0.265000	0.21872	-0.225000	0.12378	CCC	C|0.982;T|0.018	0.018	strong		0.617	PCDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372877.3	NM_018905		T	140176840	C	T	140176840	3	4	22	1	0	0	0	0	1	0	0	0	11533	623	22	2	2293	2	PCDHA2	5	140176840	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	9320	140176840	40738420	1274	4175											
PCDHA3	56145	hgsc.bcm.edu	37	chr5	140180964	140180964	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagctggcggagctggtgcCgcgcctgttccgggtggcgt	2	8	20	11	5	0	0	0	0	0	0	1	2	1	2	3	6	3	3	3	6	0	1	rs7731327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140180964C>A	ENST00000522353.2	+	1	182	c.182C>A	c.(181-183)cCg>cAg	p.P61Q	PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000532566.2_Missense_Mutation_p.P61Q|PCDHA2_ENST00000520672.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	61	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		P -> Q (in dbSNP:rs7731327).		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)			GAGCTGGTGCCGCGCCTGTTC	0.612													.|||	285	0.0569089	0.208	0.013	5008	,	,		16771	0.0		0.001	False		,,,				2504	0.0				p.P61Q		Atlas-SNP	.											PCDHA3_ENST00000522353,NS,carcinoma,-1,2	PCDHA3	396	2	0			c.C182A						PASS	.	C	,,GLN/PRO,,GLN/PRO	789,3617		66,657,1480	51	63	59		,,182,,182	3.6	1	5	dbSNP_116	59	5,8583		0,5,4289	no	intron,intron,missense,intron,missense	PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_031411.1,NM_031497.1	,,76,,76	66,662,5769	AA,AC,CC		0.0582,17.9074,6.1105	,,,,	,,61/951,,61/825	140180964	794,12200	2203	4294	6497	SO:0001583	missense	56145	exon1			TGGTGCCGCGCCT	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.182C>A	5.37:g.140180964C>A	ENSP00000429808:p.Pro61Gln	75	0	0		84	32	0.380952	NM_031497	O75286	Missense_Mutation	SNP	ENST00000522353.2	37	CCDS54915.1	88	0.040293040293040296	82	0.16666666666666666	6	0.016574585635359115	0	0.0	0	0.0	c	13.35	2.210033	0.39003	0.179074	5.82E-4	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.26067	1.76;1.76	4.48	3.59	0.41128	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	0.203527	0.23851	U	0.043957	T	0.00039	0.0001	M	0.66297	2.02	0.46798	P	8.000000000000229E-4	P;P	0.42871	0.792;0.48	B;B	0.37508	0.224;0.252	T	0.16158	-1.0412	9	0.62326	D	0.03	.	13.352	0.60607	0.0:0.9179:0.0:0.0821	rs7731327	61;61	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	Q	61	ENSP00000429808:P61Q;ENSP00000434086:P61Q	ENSP00000429808:P61Q	P	+	2	0	PCDHA3	140161148	0.000000	0.05858	1.000000	0.80357	0.984000	0.73092	-0.420000	0.07062	2.228000	0.72767	0.586000	0.80456	CCG	C|0.949;A|0.051	0.051	strong		0.612	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906		A	140180964	C	A	140180964	3	1	22	1	0	0	0	0	1	0	0	0	11534	652	23	4	184	4	PCDHA3	5	140180964	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4124	140180964	40734296	1275	4176											
PCDHA4	56144	hgsc.bcm.edu	37	chr5	140188023	140188023	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtgccctggaccgcgagagCgtgtcagcctatgagctggt	7	8	15	11	3	1	2	1	1	0	1	1	4	1	3	3	2	4	1	3	2	1	1	rs7702779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140188023C>T	ENST00000530339.1	+	1	1251	c.1251C>T	c.(1249-1251)agC>agT	p.S417S	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000356878.4_Silent_p.S417S|PCDHA4_ENST00000512229.2_Silent_p.S417S|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	417	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)			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)			ACCGCGAGAGCGTGTCAGCCT	0.612													.|||	285	0.0569089	0.208	0.013	5008	,	,		19748	0.0		0.001	False		,,,				2504	0.0				p.S417S		Atlas-SNP	.											.	PCDHA4	419	.	0			c.C1251T						PASS	.	C	,,,,,	797,3609	321.8+/-297.3	66,665,1472	155	146	149		,,,1251,,1251	-9	0	5	dbSNP_116	149	2,8598	2.2+/-6.3	0,2,4298	no	intron,intron,intron,coding-synonymous,intron,coding-synonymous	PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_031411.1,NM_031500.1	,,,,,	66,667,5770	TT,TC,CC		0.0233,18.089,6.1433	,,,,,	,,,417/948,,417/799	140188023	799,12207	2203	4300	6503	SO:0001819	synonymous_variant	56144	exon1			CGAGAGCGTGTCA	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.1251C>T	5.37:g.140188023C>T		268	0	0		295	151	0.511864	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			C|0.944;T|0.056	0.056	strong		0.612	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		T	140188023	C	T	140188023	2	4	22	1	0	0	0	0	0	0	0	1	11535	767	27	1		1	PCDHA4	5	140188023	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	7059	140188023	40727237	1276	4177											
PCDHA4	56144	hgsc.bcm.edu	37	chr5	140188392	140188392	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caggtgaccgctcgcgatgcCggcgtgccacctctgggcag	5	6	15	15	5	1	1	0	1	1	0	2	2	1	1	4	3	2	2	4	3	0	0	rs7707144	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140188392C>G	ENST00000530339.1	+	1	1620	c.1620C>G	c.(1618-1620)gcC>gcG	p.A540A	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000356878.4_Silent_p.A540A|PCDHA4_ENST00000512229.2_Silent_p.A540A|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	540	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)			CTCGCGATGCCGGCGTGCCAC	0.657													.|||	286	0.0571086	0.208	0.013	5008	,	,		17478	0.001		0.001	False		,,,				2504	0.0				p.A540A		Atlas-SNP	.											PCDHA4_ENST00000530339,NS,carcinoma,0,2	PCDHA4	419	2	0			c.C1620G						PASS	.	G	,,,,,	748,3658		64,620,1519	60	68	65		,,,1620,,1620	-0.6	1	5	dbSNP_116	65	2,8596		0,2,4297	no	intron,intron,intron,coding-synonymous,intron,coding-synonymous	PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_031411.1,NM_031500.1	,,,,,	64,622,5816	GG,GC,CC		0.0233,16.9768,5.7675	,,,,,	,,,540/948,,540/799	140188392	750,12254	2203	4299	6502	SO:0001819	synonymous_variant	56144	exon1			CGATGCCGGCGTG	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.1620C>G	5.37:g.140188392C>G		83	0	0		92	29	0.315217	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			C|0.937;G|0.063	0.063	strong		0.657	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		G	140188392	C	G	140188392	2	3	22	1	0	0	0	0	0	0	0	1	11535	639	23	4		4	PCDHA4	5	140188392	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	369	140188392	40726868	1277	4178											
PCDHA5	56143	hgsc.bcm.edu	37	chr5	140201418	140201418	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctgctgctctggcttctcCttgcctactggaaggcaggg	4	12	12	13	0	2	0	0	0	2	0	4	1	3	1	3	4	4	4	3	4	2	3	rs386692889|rs56285019	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140201418C>T	ENST00000529859.1	+	1	58	c.58C>T	c.(58-60)Ctt>Ttt	p.L20F	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000378126.3_Missense_Mutation_p.L20F|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Missense_Mutation_p.L20F	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	20					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)			CTGGCTTCTCCTTGCCTACTG	0.567													.|||	264	0.0527157	0.1952	0.0058	5008	,	,		14691	0.001		0.001	False		,,,				2504	0.0				p.L20F		Atlas-SNP	.											.	PCDHA5	361	.	0			c.C58T						PASS	.	C	,,,,PHE/LEU,,PHE/LEU	13,4393		4,5,2194	61	68	66		,,,,58,,58	2	0	5	dbSNP_129	66	0,8600		0,0,4300	yes	intron,intron,intron,intron,missense,intron,missense	PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_031411.1,NM_031501.1	,,,,22,,22	4,5,6494	TT,TC,CC		0.0,0.2951,0.1	,,,,,,	,,,,20/937,,20/817	140201418	13,12993	2203	4300	6503	SO:0001583	missense	56143	exon1			CTTCTCCTTGCCT	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.58C>T	5.37:g.140201418C>T	ENSP00000436557:p.Leu20Phe	95	0	0		92	50	0.543478	NM_018908	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	37	CCDS54917.1	76	0.0347985347985348	73	0.1483739837398374	3	0.008287292817679558	0	0.0	0	0.0	C	2.978	-0.211037	0.06140	0.002951	0.0	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	T;T;T	0.54479	0.6;0.57;0.6	3.81	2.0	0.26442	.	.	.	.	.	T	0.00271	0.0008	L	0.52823	1.66	0.80722	P	0.0	B;B;B	0.09022	0.001;0.001;0.002	B;B;B	0.08055	0.001;0.002;0.003	T	0.12889	-1.0530	8	0.11794	T	0.64	.	7.5552	0.27820	0.0:0.7302:0.0:0.2698	rs56285019;rs61730628	20;20;20	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	F	20	ENSP00000433416:L20F;ENSP00000436557:L20F;ENSP00000367366:L20F	ENSP00000367366:L20F	L	+	1	0	PCDHA5	140181602	0.000000	0.05858	0.012000	0.15200	0.358000	0.29455	-0.212000	0.09319	0.224000	0.20940	0.543000	0.68304	CTT	C|0.952;T|0.048	0.048	strong		0.567	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908		T	140201418	C	T	140201418	3	4	22	1	0	0	0	0	1	0	0	0	11536	681	24	2	60	2	PCDHA5	5	140201418	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	13026	140201418	40713842	1278	4179											
PCDHA5	56143	hgsc.bcm.edu	37	chr5	140202132	140202132	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggaaaatgcaccaagtgggAcattagttattaaactgaac	16	10	9	6	0	0	1	0	1	0	0	0	3	0	3	1	2	3	2	1	2	8	3	rs61730633	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140202132A>G	ENST00000529859.1	+	1	772	c.772A>G	c.(772-774)Aca>Gca	p.T258A	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000378126.3_Missense_Mutation_p.T258A|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Missense_Mutation_p.T258A	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	258	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)|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)			ACCAAGTGGGACATTAGTTAT	0.353													.|||	28	0.00559105	0.0212	0.0	5008	,	,		19252	0.0		0.0	False		,,,				2504	0.0				p.T258A		Atlas-SNP	.											.	PCDHA5	361	.	0			c.A772G						PASS	.	A	,,,,ALA/THR,,ALA/THR	104,4302	76.8+/-115.0	0,104,2099	62	65	64		,,,,772,,772	4.1	0.1	5	dbSNP_129	64	0,8598		0,0,4299	yes	intron,intron,intron,intron,missense,intron,missense	PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_031411.1,NM_031501.1	,,,,58,,58	0,104,6398	GG,GA,AA		0.0,2.3604,0.7998	,,,,,,	,,,,258/937,,258/817	140202132	104,12900	2203	4299	6502	SO:0001583	missense	56143	exon1			AGTGGGACATTAG	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.772A>G	5.37:g.140202132A>G	ENSP00000436557:p.Thr258Ala	130	0	0		126	52	0.412698	NM_018908	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	37	CCDS54917.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	A	15.50	2.851517	0.51270	0.023604	0.0	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	T;T;T	0.57107	0.42;0.42;0.42	4.11	4.11	0.48088	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.46983	0.1421	M	0.82517	2.595	0.29191	N	0.875842	P;P;P	0.49862	0.929;0.913;0.913	P;P;B	0.62382	0.901;0.596;0.444	T	0.58042	-0.7706	9	0.62326	D	0.03	.	8.9776	0.35946	0.9105:0.0:0.0895:0.0	rs61730633	258;258;258	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	A	258	ENSP00000433416:T258A;ENSP00000436557:T258A;ENSP00000367366:T258A	ENSP00000367366:T258A	T	+	1	0	PCDHA5	140182316	0.275000	0.24201	0.125000	0.21846	0.947000	0.59692	2.543000	0.45752	1.624000	0.50355	0.533000	0.62120	ACA	A|0.993;G|0.007	0.007	strong		0.353	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908		G	140202132	A	G	140202132	3	3	22	1	0	0	0	0	1	0	0	0	11536	275	10	3	774	3	PCDHA5	5	140202132	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	714	140202132	40713128	1279	4180											
PCDHA5	56143	hgsc.bcm.edu	37	chr5	140202418	140202418	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cccagagatggccataaccaCccttttcctgcctgtcaaag	10	9	7	15	0	1	1	1	0	0	1	2	2	2	1	6	1	2	0	6	1	2	3	rs61735511	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140202418C>A	ENST00000529859.1	+	1	1058	c.1058C>A	c.(1057-1059)aCc>aAc	p.T353N	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000378126.3_Missense_Mutation_p.T353N|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Missense_Mutation_p.T353N	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	353	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)|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)			GCCATAACCACCCTTTTCCTG	0.502													.|||	317	0.0632987	0.2322	0.013	5008	,	,		19770	0.0		0.001	False		,,,				2504	0.0				p.T353N		Atlas-SNP	.											PCDHA5_ENST00000529859,NS,carcinoma,-1,2	PCDHA5	361	2	0			c.C1058A						PASS	.	C	,,,,ASN/THR,,ASN/THR	861,3545	337.0+/-304.7	78,705,1420	87	80	83		,,,,1058,,1058	4	0.2	5	dbSNP_129	83	2,8598	2.2+/-6.3	0,2,4298	yes	intron,intron,intron,intron,missense,intron,missense	PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_031411.1,NM_031501.1	,,,,65,,65	78,707,5718	AA,AC,CC		0.0233,19.5415,6.6354	,,,,,,	,,,,353/937,,353/817	140202418	863,12143	2203	4300	6503	SO:0001583	missense	56143	exon1			TAACCACCCTTTT	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.1058C>A	5.37:g.140202418C>A	ENSP00000436557:p.Thr353Asn	161	0	0		168	86	0.511905	NM_018908	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	37	CCDS54917.1	96	0.04395604395604396	90	0.18292682926829268	6	0.016574585635359115	0	0.0	0	0.0	C	12.70	2.018078	0.35606	0.195415	2.33E-4	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	T;T;T	0.61510	0.1;0.1;0.24	3.97	3.97	0.46021	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.00073	0.0002	L	0.28400	0.85	0.35989	P	0.16346499999999997	B;B;B	0.25743	0.024;0.133;0.063	B;B;B	0.28709	0.093;0.043;0.042	T	0.16928	-1.0386	8	0.87932	D	0	.	16.4	0.83637	0.0:1.0:0.0:0.0	rs61735511	353;353;353	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	N	353	ENSP00000433416:T353N;ENSP00000436557:T353N;ENSP00000367366:T353N	ENSP00000367366:T353N	T	+	2	0	PCDHA5	140182602	1.000000	0.71417	0.240000	0.24138	0.827000	0.46813	7.800000	0.85949	1.900000	0.55004	0.655000	0.94253	ACC	C|0.940;A|0.060	0.060	strong		0.502	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908		A	140202418	C	A	140202418	3	1	22	1	0	0	0	0	1	0	0	0	11536	507	18	4	1060	4	PCDHA5	5	140202418	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	286	140202418	40712842	1280	4181											
PCDHA5	56143	hgsc.bcm.edu	37	chr5	140202821	140202821	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gcggacgcgcaggagaacgcCctggtgtcctactcgctggt	6	7	15	13	5	0	1	0	0	0	1	2	3	1	2	2	4	2	2	2	4	2	1	rs80008076	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140202821C>G	ENST00000529859.1	+	1	1461	c.1461C>G	c.(1459-1461)gcC>gcG	p.A487A	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000378126.3_Silent_p.A487A|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Silent_p.A487A	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	487	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.A487A(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)			AGGAGAACGCCCTGGTGTCCT	0.667													.|||	72	0.014377	0.0537	0.0014	5008	,	,		18355	0.0		0.0	False		,,,				2504	0.0				p.A487A		Atlas-SNP	.											PCDHA5_ENST00000529859,NS,carcinoma,0,2	PCDHA5	361	2	2	Substitution - coding silent(2)	lung(2)	c.C1461G						PASS	.	G	,,,,,,	227,4179	797.7+/-415.4	9,209,1985	68	73	71		,,,,1461,,1461	2	1	5	dbSNP_131	71	1,8599	814.7+/-407.0	0,1,4299	no	intron,intron,intron,intron,coding-synonymous,intron,coding-synonymous	PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_031411.1,NM_031501.1	,,,,,,	9,210,6284	GG,GC,CC		0.0116,5.1521,1.753	,,,,,,	,,,,487/937,,487/817	140202821	228,12778	2203	4300	6503	SO:0001819	synonymous_variant	56143	exon1			GAACGCCCTGGTG	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.1461C>G	5.37:g.140202821C>G		258	0	0		276	145	0.525362	NM_018908	O75284|Q8N4R3	Silent	SNP	ENST00000529859.1	37	CCDS54917.1																																																																																			C|0.983;G|0.017	0.017	strong		0.667	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908		G	140202821	C	G	140202821	2	3	22	1	0	0	0	0	0	0	0	1	11536	610	22	4		4	PCDHA5	5	140202821	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	403	140202821	40712439	1281	4182											
PCDHA6	56142	hgsc.bcm.edu	37	chr5	140209429	140209429	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgagctggtgccgcggtcaCtgggtgcaggccaagtggtg	5	7	19	10	3	1	0	1	0	0	0	1	1	1	0	2	5	3	2	2	5	1	0	rs60309716	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140209429C>G	ENST00000529310.1	+	1	1867	c.1753C>G	c.(1753-1755)Ctg>Gtg	p.L585V	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_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	585	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.		L -> V (in dbSNP:rs60309716).		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)			GCCGCGGTCACTGGGTGCAGG	0.677													.|||	317	0.0632987	0.2322	0.013	5008	,	,		16721	0.0		0.001	False		,,,				2504	0.0				p.L585V		Atlas-SNP	.											.	PCDHA6	442	.	0			c.C1753G						PASS	.	G	,,,,,VAL/LEU,,VAL/LEU,	863,3543	743.4+/-411.5	78,707,1418	87	87	87		,,,,,1753,,1753,	1	0	5	dbSNP_129	87	2,8596	819.0+/-406.8	0,2,4297	no	intron,intron,intron,intron,intron,missense,intron,missense,intron	PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_031411.1,NM_031848.1,NM_031849.1	,,,,,32,,32,	78,709,5715	GG,GC,CC		0.0233,19.5869,6.6518	,,,,,,,,	,,,,,585/951,,585/804,	140209429	865,12139	2203	4299	6502	SO:0001583	missense	56142	exon1			CGGTCACTGGGTG	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.1753C>G	5.37:g.140209429C>G	ENSP00000433378:p.Leu585Val	210	0	0		274	141	0.514599	NM_018909	O75283|Q9NRT8	Missense_Mutation	SNP	ENST00000529310.1	37	CCDS47281.1	96	0.04395604395604396	90	0.18292682926829268	6	0.016574585635359115	0	0.0	0	0.0	G	0.001	-3.111828	0.00032	0.195869	2.33E-4	ENSG00000081842	ENST00000529310	T	0.50001	0.76	3.87	0.98	0.19750	Cadherin (2);Cadherin-like (1);	0.000000	0.33199	N	0.005169	T	0.00012	0.0000	N	0.00237	-1.79	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.19484	-1.0304	9	0.07482	T	0.82	.	3.3104	0.07015	0.0814:0.2713:0.3691:0.2783	rs60309716;rs61730776	585;585	Q9UN73-3;Q9UN73	.;PCDA6_HUMAN	V	585	ENSP00000433378:L585V	ENSP00000433378:L585V	L	+	1	2	PCDHA6	140189613	0.013000	0.17824	0.005000	0.12908	0.002000	0.02628	1.103000	0.31062	-0.149000	0.11215	-0.671000	0.03813	CTG	C|0.940;G|0.060	0.060	strong		0.677	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909		G	140209429	C	G	140209429	3	3	22	1	0	0	0	0	1	0	0	0	11537	564	20	4	1755	4	PCDHA6	5	140209429	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6608	140209429	40705831	1282	4183											
PCDHA6	56142	hgsc.bcm.edu	37	chr5	140209593	140209593	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	accactcgtgtcctggacgaAgcggactctccgcgccaccg	7	6	11	17	6	1	0	0	0	1	0	4	3	2	2	5	2	1	0	5	2	1	0	rs61730636	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140209593A>G	ENST00000529310.1	+	1	2031	c.1917A>G	c.(1915-1917)gaA>gaG	p.E639E	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_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	639	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)			TCCTGGACGAAGCGGACTCTC	0.667													.|||	317	0.0632987	0.2322	0.013	5008	,	,		16276	0.0		0.001	False		,,,				2504	0.0				p.E639E		Atlas-SNP	.											PCDHA6_ENST00000529310,NS,carcinoma,+2,6	PCDHA6	442	6	0			c.A1917G						scavenged	.	A	,,,,,,,,	857,3549	328.0+/-300.3	78,701,1424	58	66	64		,,,,,1917,,1917,	0.9	0.6	5	dbSNP_129	64	2,8596	2.2+/-6.3	0,2,4297	no	intron,intron,intron,intron,intron,coding-synonymous,intron,coding-synonymous,intron	PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_031411.1,NM_031848.1,NM_031849.1	,,,,,,,,	78,703,5721	GG,GA,AA		0.0233,19.4507,6.6057	,,,,,,,,	,,,,,639/951,,639/804,	140209593	859,12145	2203	4299	6502	SO:0001819	synonymous_variant	56142	exon1			GGACGAAGCGGAC	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.1917A>G	5.37:g.140209593A>G		140	1	0.00714286		147	72	0.489796	NM_018909	O75283|Q9NRT8	Silent	SNP	ENST00000529310.1	37	CCDS47281.1																																																																																			A|0.940;G|0.060	0.060	strong		0.667	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909		G	140209593	A	G	140209593	2	3	22	1	0	0	0	0	0	0	0	1	11537	69	3	3		3	PCDHA6	5	140209593	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	164	140209593	40705667	1283	4184											
PCDHA7	56141	hgsc.bcm.edu	37	chr5	140216125	140216125	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttaccctgctgctgtacacGgcgttgcggtgctcagcgcc	4	10	12	15	4	1	0	1	0	0	0	1	0	1	0	2	2	7	5	2	2	2	3	rs61730621	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140216125G>A	ENST00000525929.1	+	1	2157	c.2157G>A	c.(2155-2157)acG>acA	p.T719T	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA7_ENST00000378125.3_Silent_p.T719T|PCDHA6_ENST00000527624.1_Intron	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7	719					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)			TGCTGTACACGGCGTTGCGGT	0.612													.|||	74	0.0147764	0.0552	0.0014	5008	,	,		18171	0.0		0.0	False		,,,				2504	0.0				p.T719T	NSCLC(160;258 2013 5070 22440 28951)	Atlas-SNP	.											.	PCDHA7	367	.	0			c.G2157A						PASS	.	G	,,,,,,,,,	237,4169	140.8+/-176.2	15,207,1981	103	87	92		,,,,,,2157,,,2157	-3.3	0.4	5	dbSNP_129	92	1,8599	1.2+/-3.3	0,1,4299	no	intron,intron,intron,intron,intron,intron,coding-synonymous,intron,intron,coding-synonymous	PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_031411.1,NM_031849.1,NM_031852.1	,,,,,,,,,	15,208,6280	AA,AG,GG		0.0116,5.379,1.8299	,,,,,,,,,	,,,,,,719/938,,,719/790	140216125	238,12768	2203	4300	6503	SO:0001819	synonymous_variant	56141	exon1			GTACACGGCGTTG	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.2157G>A	5.37:g.140216125G>A		302	1	0.00331126		338	183	0.54142	NM_031852	O75282	Silent	SNP	ENST00000525929.1	37	CCDS54918.1																																																																																			G|0.982;A|0.018	0.018	strong		0.612	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	NM_018910		A	140216125	G	A	140216125	2	1	22	1	0	0	0	0	0	0	0	1	11538	1103	39	1		1	PCDHA7	5	140216125	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6532	140216125	40699135	1284	4185											
PCDHA8	56140	hgsc.bcm.edu	37	chr5	140222430	140222430	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgctcgctgtcgagctacatTtcggtgcacacggagagcgg	7	8	14	12	6	0	1	0	0	0	1	3	3	0	1	0	3	4	4	0	3	1	2	rs6873763	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140222430T>G	ENST00000531613.1	+	1	1524	c.1524T>G	c.(1522-1524)atT>atG	p.I508M	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000378123.3_Missense_Mutation_p.I508M|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	508	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(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)			CGAGCTACATTTCGGTGCACA	0.687													.|||	350	0.0698882	0.2564	0.0144	5008	,	,		12674	0.0		0.001	False		,,,				2504	0.0				p.I508M		Atlas-SNP	.											.	PCDHA8	366	.	0			c.T1524G						PASS	.	T	,,,,,,,MET/ILE,,,MET/ILE	994,3394	710.8+/-407.9	169,656,1369	62	70	67		,,,,,,,1524,,,1524	2.8	1	5	dbSNP_116	67	4,8526	800.3+/-407.4	0,4,4261	no	intron,intron,intron,intron,intron,intron,intron,missense,intron,intron,missense	PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031856.1	,,,,,,,10,,,10	169,660,5630	GG,GT,TT		0.0469,22.6527,7.7257	,,,,,,,,,,	,,,,,,,508/951,,,508/815	140222430	998,11920	2194	4265	6459	SO:0001583	missense	56140	exon1			CTACATTTCGGTG	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.1524T>G	5.37:g.140222430T>G	ENSP00000434655:p.Ile508Met	303	0	0		287	156	0.543554	NM_031856	B9EGT7|O75281	Missense_Mutation	SNP	ENST00000531613.1	37	CCDS54919.1	108	0.04945054945054945	101	0.20528455284552846	7	0.019337016574585635	0	0.0	0	0.0	G	11.04	1.520541	0.27211	0.226527	4.69E-4	ENSG00000204962	ENST00000531613;ENST00000378123	T;T	0.61274	0.12;0.12	3.72	2.85	0.33270	Cadherin (4);Cadherin-like (1);	0.000000	0.33199	U	0.005173	T	0.00073	0.0002	M	0.77486	2.375	0.43122	P	0.005152999999999963	P;P	0.45240	0.473;0.854	P;P	0.60068	0.868;0.729	T	0.06303	-1.0834	9	0.87932	D	0	.	8.018	0.30393	0.0:0.2626:0.4599:0.2775	rs6873763	508;508	Q9Y5H6;Q9Y5H6-2	PCDA8_HUMAN;.	M	508	ENSP00000434655:I508M;ENSP00000367363:I508M	ENSP00000367363:I508M	I	+	3	3	PCDHA8	140202614	0.030000	0.19436	1.000000	0.80357	0.083000	0.17756	-0.581000	0.05820	0.682000	0.31407	-0.741000	0.03529	ATT	T|0.933;G|0.067	0.067	strong		0.687	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911		G	140222430	T	G	140222430	3	3	22	1	0	0	0	0	1	0	0	0	11539	1829	64	5	1526	5	PCDHA8	5	140222430	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	6305	140222430	40692830	1285	4186											
PCDHA8	56140	hgsc.bcm.edu	37	chr5	140222534	140222534	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcgcgcgacgcgggcgtgcCgcctctgggcagcaacgtga	5	4	17	15	9	1	1	0	1	1	0	1	2	1	1	2	2	3	2	2	2	1	0	rs6889154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140222534C>A	ENST00000531613.1	+	1	1628	c.1628C>A	c.(1627-1629)cCg>cAg	p.P543Q	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000378123.3_Missense_Mutation_p.P543Q|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	543	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(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)			GCGGGCGTGCCGCCTCTGGGC	0.687													.|||	85	0.0169728	0.0635	0.0014	5008	,	,		15269	0.0		0.0	False		,,,				2504	0.0				p.P543Q		Atlas-SNP	.											PCDHA8_ENST00000531613,NS,carcinoma,-1,6	PCDHA8	366	6	0			c.C1628A						PASS	.	C	,,,,,,,GLN/PRO,,,GLN/PRO	287,4097		26,235,1931	52	61	58		,,,,,,,1628,,,1628	3.7	0.9	5	dbSNP_116	58	2,8524		0,2,4261	no	intron,intron,intron,intron,intron,intron,intron,missense,intron,intron,missense	PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031856.1	,,,,,,,76,,,76	26,237,6192	AA,AC,CC		0.0235,6.5465,2.2386	,,,,,,,,,,	,,,,,,,543/951,,,543/815	140222534	289,12621	2192	4263	6455	SO:0001583	missense	56140	exon1			GCGTGCCGCCTCT	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.1628C>A	5.37:g.140222534C>A	ENSP00000434655:p.Pro543Gln	55	0	0		57	29	0.508772	NM_031856	B9EGT7|O75281	Missense_Mutation	SNP	ENST00000531613.1	37	CCDS54919.1	31	0.014194139194139194	30	0.06097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	C	17.62	3.434270	0.62955	0.065465	2.35E-4	ENSG00000204962	ENST00000531613;ENST00000378123	T;T	0.55588	0.51;0.51	3.72	3.72	0.42706	Cadherin (4);Cadherin-like (1);	0.000000	0.36555	U	0.002521	T	0.22166	0.0534	M	0.87180	2.865	0.46376	D	0.999014	D;D	0.76494	0.999;0.999	D;D	0.80764	0.991;0.994	T	0.66396	-0.5934	10	0.87932	D	0	.	15.9202	0.79556	0.0:1.0:0.0:0.0	rs6889154	543;543	Q9Y5H6;Q9Y5H6-2	PCDA8_HUMAN;.	Q	543	ENSP00000434655:P543Q;ENSP00000367363:P543Q	ENSP00000367363:P543Q	P	+	2	0	PCDHA8	140202718	1.000000	0.71417	0.869000	0.34112	0.258000	0.26162	7.317000	0.79018	1.790000	0.52503	0.306000	0.20318	CCG	C|0.978;A|0.022	0.022	strong		0.687	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911		A	140222534	C	A	140222534	3	1	22	1	0	0	0	0	1	0	0	0	11539	652	23	4	1630	4	PCDHA8	5	140222534	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	104	140222534	40692726	1286	4187											
PCDHA9	9752	hgsc.bcm.edu	37	chr5	140229581	140229581	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	tggtggagcggcggttgggcGagcgctcgctgtcgagctac	4	8	19	10	6	0	0	0	0	0	0	2	3	0	1	0	5	4	4	0	5	1	2	rs59056023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140229581G>C	ENST00000532602.1	+	1	2534	c.1501G>C	c.(1501-1503)Gag>Cag	p.E501Q	PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA9_ENST00000378122.3_Missense_Mutation_p.E501Q|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	501	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		E -> Q (in dbSNP:rs59056023).		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)			GCGGTTGGGCGAGCGCTCGCT	0.672													.|||	319	0.0636981	0.2307	0.0187	5008	,	,		14972	0.0		0.001	False		,,,				2504	0.0				p.E501Q	Melanoma(55;1800 1972 14909)	Atlas-SNP	.											.	PCDHA9	373	.	0			c.G1501C						PASS	.	G	GLN/GLU,,,,,,,,,,,GLN/GLU	877,3515	327.2+/-299.9	127,623,1446	59	65	63		1501,,,,,,,,,,,1501	3.6	1	5	dbSNP_129	63	7,8531	4.3+/-15.6	1,5,4263	no	missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHA9,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_014005.3,NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1	29,,,,,,,,,,,29	128,628,5709	CC,CG,GG		0.082,19.9681,6.8368	,,,,,,,,,,,	501/843,,,,,,,,,,,501/951	140229581	884,12046	2196	4269	6465	SO:0001583	missense	9752	exon1			TTGGGCGAGCGCT	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.1501G>C	5.37:g.140229581G>C	ENSP00000436042:p.Glu501Gln	300	1	0.00333333		346	173	0.5	NM_031857	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	37	CCDS54920.1	129	0.059065934065934064	109	0.22154471544715448	11	0.03038674033149171	1	0.0017482517482517483	8	0.010554089709762533	G	14.45	2.539010	0.45176	0.199681	8.2E-4	ENSG00000204961	ENST00000532602;ENST00000378122	T;T	0.53640	0.69;0.61	3.56	3.56	0.40772	Cadherin (4);Cadherin-like (1);	0.000000	0.31760	U	0.007116	T	0.00039	0.0001	N	0.25245	0.725	0.49687	P	1.8499999999999073E-4	P;P	0.48834	0.916;0.904	P;P	0.61722	0.893;0.631	T	0.06162	-1.0842	9	0.87932	D	0	.	8.4611	0.32927	0.0:0.1643:0.6673:0.1684	rs59056023	501;501	Q9Y5H5;Q9Y5H5-2	PCDA9_HUMAN;.	Q	501	ENSP00000436042:E501Q;ENSP00000367362:E501Q	ENSP00000367362:E501Q	E	+	1	0	PCDHA9	140209765	0.000000	0.05858	1.000000	0.80357	0.295000	0.27426	-0.372000	0.07504	1.973000	0.57446	0.306000	0.20318	GAG	G|0.939;C|0.061	0.061	strong		0.672	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		C	140229581	G	C	140229581	3	2	22	1	0	0	0	0	1	0	0	0	11540	1059	37	4	1503	4	PCDHA9	5	140229581	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	7047	140229581	40685679	1287	4188											
PCDHA9	9752	hgsc.bcm.edu	37	chr5	140229925	140229925	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tacgagctgcagccagaaacGgccagcgcgagcatcccgtt	10	5	12	14	5	0	1	0	0	0	1	1	3	1	1	3	1	7	4	3	1	2	2	rs58792000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140229925G>C	ENST00000532602.1	+	1	2878	c.1845G>C	c.(1843-1845)acG>acC	p.T615T	PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA9_ENST00000378122.3_Silent_p.T615T|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	615	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(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)			AGCCAGAAACGGCCAGCGCGA	0.687													.|||	325	0.0648962	0.2315	0.0187	5008	,	,		16120	0.0		0.006	False		,,,				2504	0.0				p.T615T	Melanoma(55;1800 1972 14909)	Atlas-SNP	.											.	PCDHA9	373	.	0			c.G1845C						PASS	.	G	,,,,,,,,,,,	892,3500		144,604,1448	61	66	64		1845,,,,,,,,,,,1845	2.4	0	5	dbSNP_129	64	19,8521		1,17,4252	no	coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_014005.3,NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1	,,,,,,,,,,,	145,621,5700	CC,CG,GG		0.2225,20.3097,7.0445	,,,,,,,,,,,	615/843,,,,,,,,,,,615/951	140229925	911,12021	2196	4270	6466	SO:0001819	synonymous_variant	9752	exon1			AGAAACGGCCAGC	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.1845G>C	5.37:g.140229925G>C		220	0	0		211	111	0.526066	NM_031857	O15053|Q2M3S5	Silent	SNP	ENST00000532602.1	37	CCDS54920.1																																																																																			G|0.937;C|0.063	0.063	strong		0.687	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		C	140229925	G	C	140229925	2	2	22	1	0	0	0	0	0	0	0	1	11540	1103	39	4		4	PCDHA9	5	140229925	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	344	140229925	40685335	1288	4189											
PCDHA10	56139	hgsc.bcm.edu	37	chr5	140237094	140237094	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gcggacgcgcaggagaacgcCctggtgtcctactctctggt	6	8	14	13	4	1	1	0	0	1	1	3	3	2	2	2	4	2	1	2	4	2	1	rs60872775	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140237094C>G	ENST00000307360.5	+	1	1461	c.1461C>G	c.(1459-1461)gcC>gcG	p.A487A	PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000506939.2_Silent_p.A487A|PCDHA4_ENST00000512229.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	487	Cadherin 5. {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)			AGGAGAACGCCCTGGTGTCCT	0.662													.|||	56	0.0111821	0.0416	0.0014	5008	,	,		16717	0.0		0.0	False		,,,				2504	0.0				p.A487A		Atlas-SNP	.											.	PCDHA10	358	.	0			c.C1461G						PASS	.	C	,,,,,,,,,,,,,	141,4251	805.5+/-415.8	11,119,2066	76	78	78		,1461,,,,,,,,,,,1461,1461	1.8	1	5	dbSNP_129	78	0,8546		0,0,4273	no	intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,coding-synonymous	PCDHA9,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031859.1,NM_031860.1	,,,,,,,,,,,,,	11,119,6339	GG,GC,CC		0.0,3.2104,1.0898	,,,,,,,,,,,,,	,487/949,,,,,,,,,,,487/845,487/686	140237094	141,12797	2196	4273	6469	SO:0001819	synonymous_variant	56139	exon1			GAACGCCCTGGTG	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.1461C>G	5.37:g.140237094C>G		365	0	0		309	157	0.508091	NM_031859	A1L493|O75280|Q9NRU2	Silent	SNP	ENST00000307360.5	37	CCDS54921.1																																																																																			C|0.989;G|0.011	0.011	strong		0.662	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		G	140237094	C	G	140237094	2	3	22	1	0	0	0	0	0	0	0	1	11529	610	22	4		4	PCDHA10	5	140237094	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	7169	140237094	40678166	1289	4190											
PCDHA10	56139	hgsc.bcm.edu	37	chr5	140237826	140237826	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cccaccgagggcgcatgtggGccggtgaagcccacgctggt	6	5	16	14	4	0	1	0	1	0	0	0	2	0	1	4	4	1	2	4	4	1	0	rs180990865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140237826G>C	ENST00000307360.5	+	1	2193	c.2193G>C	c.(2191-2193)ggG>ggC	p.G731G	PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	731					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)			GCGCATGTGGGCCGGTGAAGC	0.672													.|||	66	0.0131789	0.0492	0.0014	5008	,	,		13681	0.0		0.0	False		,,,				2504	0.0				p.G731G		Atlas-SNP	.											.	PCDHA10	358	.	0			c.G2193C						PASS	.	G	,,,,,,,,,,,,,	90,2554		6,78,1238	32	32	32		,2193,,,,,,,,,,,2193,	-2.2	0	5		32	0,4582		0,0,2291	no	intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,intron	PCDHA9,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031859.1,NM_031860.1	,,,,,,,,,,,,,	6,78,3529	CC,CG,GG		0.0,3.4039,1.2455	,,,,,,,,,,,,,	,731/949,,,,,,,,,,,731/845,	140237826	90,7136	1322	2291	3613	SO:0001819	synonymous_variant	56139	exon1			ATGTGGGCCGGTG	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.2193G>C	5.37:g.140237826G>C		235	0	0		234	108	0.461538	NM_031859	A1L493|O75280|Q9NRU2	Silent	SNP	ENST00000307360.5	37	CCDS54921.1																																																																																			G|0.989;C|0.011	0.011	strong		0.672	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		C	140237826	G	C	140237826	2	2	22	1	0	0	0	0	0	0	0	1	11529	1190	42	4		4	PCDHA10	5	140237826	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	732	140237826	40677434	1290	4191											
PCDHA12	56137	hgsc.bcm.edu	37	chr5	140256275	140256275	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acctacaagaattactactcGttggtgctggacagcgccct	10	10	9	12	2	0	1	0	0	0	1	1	2	0	2	2	2	5	2	2	2	5	4	rs73793508	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140256275G>A	ENST00000398631.2	+	1	1218	c.1218G>A	c.(1216-1218)tcG>tcA	p.S406S	PCDHA11_ENST00000398640.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA3_ENST00000522353.2_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	406	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(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)			ATTACTACTCGTTGGTGCTGG	0.607													.|||	65	0.0129792	0.0484	0.0014	5008	,	,		20801	0.0		0.0	False		,,,				2504	0.0				p.S406S	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											PCDHA12,NS,carcinoma,+1,1	PCDHA12	196	1	0			c.G1218A						PASS	.	G	,,,,,,,,,,,,,,,	143,4263	102.1+/-140.7	3,137,2063	190	183	185		,,,1218,,,,,,,,,,,,1218	-9.9	0	5	dbSNP_130	185	0,8596		0,0,4298	no	intron,intron,intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031864.1	,,,,,,,,,,,,,,,	3,137,6361	AA,AG,GG		0.0,3.2456,1.0998	,,,,,,,,,,,,,,,	,,,406/942,,,,,,,,,,,,406/793	140256275	143,12859	2203	4298	6501	SO:0001819	synonymous_variant	56137	exon1			CTACTCGTTGGTG	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.1218G>A	5.37:g.140256275G>A		307	1	0.00325733		312	151	0.483974	NM_018903	O75278|Q2M1N8	Silent	SNP	ENST00000398631.2	37	CCDS47285.1																																																																																			G|0.990;A|0.010	0.010	strong		0.607	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		A	140256275	G	A	140256275	2	1	22	1	0	0	0	0	0	0	0	1	11531	1132	40	1		1	PCDHA12	5	140256275	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	18449	140256275	40658985	1291	4192											
PCDHA13	56136	hgsc.bcm.edu	37	chr5	140264091	140264091	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gtgtgctccagcgcggcaggGagttggtcgtactcgcagca	6	8	16	11	4	0	0	0	0	0	0	3	1	1	1	1	3	4	6	1	3	1	2	rs10076265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140264091G>C	ENST00000289272.2	+	1	2238	c.2238G>C	c.(2236-2238)ggG>ggC	p.G746G	PCDHA11_ENST00000398640.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA13_ENST00000409494.1_Silent_p.G746G|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA3_ENST00000522353.2_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	746	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)			GCGCGGCAGGGAGTTGGTCGT	0.677													g|||	74	0.0147764	0.053	0.0058	5008	,	,		14743	0.0		0.0	False		,,,				2504	0.0				p.G746G	Melanoma(147;1739 1852 5500 27947 37288)	Atlas-SNP	.											PCDHA13,colon,carcinoma,+2,1	PCDHA13	213	1	0			c.G2238C						PASS	.	G	,,,,,,,,,,,,,,,,	248,4158	136.5+/-172.5	6,236,1961	48	53	52		,,,,2238,,,,,,,,,,,,2238	2.8	1	5	dbSNP_119	52	1,8599	1.2+/-3.3	0,1,4299	no	intron,intron,intron,intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018904.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031865.1	,,,,,,,,,,,,,,,,	6,237,6260	CC,CG,GG		0.0116,5.6287,1.9145	,,,,,,,,,,,,,,,,	,,,,746/951,,,,,,,,,,,,746/808	140264091	249,12757	2203	4300	6503	SO:0001819	synonymous_variant	56136	exon1			GGCAGGGAGTTGG	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.2238G>C	5.37:g.140264091G>C		153	0	0		159	83	0.522013	NM_031865	O75277	Silent	SNP	ENST00000289272.2	37	CCDS4240.1																																																																																			G|0.982;C|0.018	0.018	strong		0.677	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		C	140264091	G	C	140264091	2	2	22	1	0	0	0	0	0	0	0	1	11532	1161	41	4		4	PCDHA13	5	140264091	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	7816	140264091	40651169	1292	4193											
PCDHAC2	56134	hgsc.bcm.edu	37	chr5	140346446	140346451	+	In_Frame_Del	DEL	TGCTGC	TGCTGC	-																															actgcctctcctgctgctgtTgctgctgctgctacctggcc																								rs148181752		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGCTGC	TGCTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140346446_140346451delTGCTGC	ENST00000289269.5	+	1	627_632	c.95_100delTGCTGC	c.(94-102)ttgctgctg>ttg	p.32_34LLL>L	PCDHA11_ENST00000398640.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000506939.2_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	32					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)			ctgctgctgttgctgctgctgctACC	0.704																																					p.32_33del	Melanoma(190;638 2083 3390 11909 52360)	Pindel,Atlas-Indel	.											.	PCDHAC2	142	.	0			c.94_99del						PASS	.		,,,,,,,,,,,,,,,,,,	283,11,3622		45,0,193,0,11,1709					,,,,,,,,,,,,,,,,,,	0.2	0.7		dbSNP_134	8	13,29,7600		3,0,7,1,27,3783	no	codingComplex,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,codingComplex,intron	PCDHA9,PCDHAC2,PCDHAC1,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_031883.2,NM_031860.1,NM_031857.1,NM_031849.1,NM_031411.1,NM_018911.2,NM_018910.2,NM_018909.2,NM_018908.2,NM_018907.2,NM_018906.2,NM_018905.2,NM_018904.2,NM_018903.2,NM_018902.3,NM_018901.2,NM_018900.2,NM_018899.5,NM_018898.3	,,,,,,,,,,,,,,,,,,	48,0,200,1,38,5492	A1A1,A1A2,A1R,A2A2,A2R,RR		0.5496,7.5077,2.9071	,,,,,,,,,,,,,,,,,,	,,,,,,,,,,,,,,,,,,		296,40,11222				SO:0001651	inframe_deletion	56134	exon1			.	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.95_100delTGCTGC	5.37:g.140346452_140346457delTGCTGC	ENSP00000289269:p.Leu34_Leu35del	90	0	.		80	17	0.213	NM_031883	Q2M3V1|Q9Y5F4	In_Frame_Del	DEL	ENST00000289269.5	37	CCDS4242.1																																																																																			TGCTGC|0.974;-|0.026	0.026	strong		0.704	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899		-	140346451	TGCTGC	-	140346446	7	5	22	1	0	1	0	1	0	0	0	0	11542	1821	63	0	97	0	PCDHAC2	5	140346446	In_Frame_Del	DEL	TGCTGC	TCGA-G8-6324-01A-11D-2210-10	82355	140346446	40568814	1293	4194											
PCDHAC2	56134	hgsc.bcm.edu	37	chr5	140346670	140346670	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgtcaacgagcgcattgatCgggaggcgctgtgtgagcag	8	8	16	9	5	1	2	1	2	0	0	3	4	1	3	0	2	3	3	0	2	1	1	rs155809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140346670C>A	ENST00000289269.5	+	1	851	c.319C>A	c.(319-321)Cgg>Agg	p.R107R	PCDHA11_ENST00000398640.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000506939.2_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	107	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(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)			GCGCATTGATCGGGAGGCGCT	0.642													C|||	79	0.0157748	0.0567	0.0058	5008	,	,		18549	0.0		0.0	False		,,,				2504	0.0				p.R107R	Melanoma(190;638 2083 3390 11909 52360)	Atlas-SNP	.											.	PCDHAC2	142	.	0			c.C319A						PASS	.	C	,,,,,,,,,,,,,,,,,,	252,4154	137.7+/-173.5	5,242,1956	34	35	35		,319,,,,,,,,,,,,,,,,,319	5.7	1	5	dbSNP_79	35	1,8599	1.2+/-3.3	0,1,4299	no	intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHAC2,PCDHAC1,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018898.3,NM_018899.5,NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018904.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031883.2	,,,,,,,,,,,,,,,,,,	5,243,6255	AA,AC,CC		0.0116,5.7195,1.9453	,,,,,,,,,,,,,,,,,,	,107/1008,,,,,,,,,,,,,,,,,107/885	140346670	253,12753	2203	4300	6503	SO:0001819	synonymous_variant	56134	exon1			ATTGATCGGGAGG	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.319C>A	5.37:g.140346670C>A		28	0	0		28	11	0.392857	NM_031883	Q2M3V1|Q9Y5F4	Silent	SNP	ENST00000289269.5	37	CCDS4242.1																																																																																			C|0.979;A|0.021	0.021	strong		0.642	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899		A	140346670	C	A	140346670	2	1	22	1	0	0	0	0	0	0	0	1	11542	875	31	4		4	PCDHAC2	5	140346670	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	224	140346670	40568590	1294	4195											
PCDHB2	56133	hgsc.bcm.edu	37	chr5	140475514	140475514	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gatcctgactccggagacaaCggaaggatggtgtgctccat	10	8	13	10	2	0	2	0	1	0	1	3	6	3	4	3	4	2	1	3	4	2	0	rs73793576	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140475514C>A	ENST00000194155.4	+	1	1288	c.1140C>A	c.(1138-1140)aaC>aaA	p.N380K		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	380	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(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)			CCGGAGACAACGGAAGGATGG	0.473													C|||	44	0.00878594	0.0325	0.0014	5008	,	,		19966	0.0		0.0	False		,,,				2504	0.0				p.N380K		Atlas-SNP	.											.	PCDHB2	163	.	0			c.C1140A						PASS	.	C	LYS/ASN	116,4290	90.2+/-128.9	2,112,2089	81	73	76		1140	-1.8	1	5	dbSNP_130	76	0,8600		0,0,4300	yes	missense	PCDHB2	NM_018936.2	94	2,112,6389	AA,AC,CC		0.0,2.6328,0.8919	probably-damaging	380/799	140475514	116,12890	2203	4300	6503	SO:0001583	missense	56133	exon1			AGACAACGGAAGG	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.1140C>A	5.37:g.140475514C>A	ENSP00000194155:p.Asn380Lys	135	0	0		138	72	0.521739	NM_018936	Q4KMU1	Missense_Mutation	SNP	ENST00000194155.4	37	CCDS4244.1	16	0.007326007326007326	15	0.03048780487804878	1	0.0027624309392265192	0	0.0	0	0.0	C	11.52	1.663243	0.29515	0.026328	0.0	ENSG00000112852	ENST00000194155	T	0.59906	0.23	5.15	-1.8	0.07907	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.60945	0.2308	H	0.97390	3.995	0.35381	D	0.789909	D	0.71674	0.998	P	0.62435	0.902	T	0.82259	-0.0546	9	0.72032	D	0.01	.	12.3358	0.55067	0.0:0.4067:0.0:0.5933	.	380	Q9Y5E7	PCDB2_HUMAN	K	380	ENSP00000194155:N380K	ENSP00000194155:N380K	N	+	3	2	PCDHB2	140455698	0.014000	0.17966	0.990000	0.47175	0.260000	0.26232	-0.975000	0.03790	-0.310000	0.08766	0.655000	0.94253	AAC	C|0.991;A|0.009	0.009	strong		0.473	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936		A	140475514	C	A	140475514	3	1	22	1	0	0	0	0	1	0	0	0	11551	535	19	4	1142	4	PCDHB2	5	140475514	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	128844	140475514	40439746	1295	4196											
PCDHB2	56133	hgsc.bcm.edu	37	chr5	140475958	140475958	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gactacgaggccctgcaggcGttcgagttccgcgtgggcgc	5	7	16	13	6	0	0	0	0	0	0	2	3	1	0	2	3	2	3	2	3	1	3	rs371176940	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140475958G>T	ENST00000194155.4	+	1	1732	c.1584G>T	c.(1582-1584)gcG>gcT	p.A528A		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	528	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(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)			CCCTGCAGGCGTTCGAGTTCC	0.706													g|||	5	0.000998403	0.0	0.0	5008	,	,		15707	0.0		0.0	False		,,,				2504	0.0051				p.A528A		Atlas-SNP	.											.	PCDHB2	163	.	0			c.G1584T						PASS	.						68	75	73					5																	140475958		2203	4299	6502	SO:0001819	synonymous_variant	56133	exon1			GCAGGCGTTCGAG	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.1584G>T	5.37:g.140475958G>T		209	0	0		205	10	0.0487805	NM_018936	Q4KMU1	Silent	SNP	ENST00000194155.4	37	CCDS4244.1																																																																																			.	.	alt		0.706	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936		T	140475958	G	T	140475958	2	4	22	1	0	0	0	0	0	0	0	1	11551	1132	40	4		4	PCDHB2	5	140475958	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	444	140475958	40439302	1296	4197											
PCDHB4	56131	hgsc.bcm.edu	37	chr5	140503278	140503278	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgctgtacccgctgcagaaTggctccgcgccctgcaccga	6	7	12	16	4	0	1	0	0	0	1	1	2	1	1	4	1	4	6	4	1	2	1	rs535776973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140503278T>C	ENST00000194152.1	+	1	1698	c.1698T>C	c.(1696-1698)aaT>aaC	p.N566N	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	566					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)			CGCTGCAGAATGGCTCCGCGC	0.701													C|||	29	0.00579073	0.0219	0.0	5008	,	,		15744	0.0		0.0	False		,,,				2504	0.0				p.N566N		Atlas-SNP	.											PCDHB4,NS,carcinoma,+1,1	PCDHB4	177	1	0			c.T1698C						scavenged	.						19	23	22					5																	140503278		2185	4269	6454	SO:0001819	synonymous_variant	56131	exon1			GCAGAATGGCTCC	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.1698T>C	5.37:g.140503278T>C		61	1	0.0163934		65	24	0.369231	NM_018938	Q4V761	Silent	SNP	ENST00000194152.1	37	CCDS4246.1																																																																																			.	.	none		0.701	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938		C	140503278	T	C	140503278	2	2	22	1	0	0	0	0	0	0	0	1	11553	1461	51	3		3	PCDHB4	5	140503278	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	27320	140503278	40411982	1297	4198											
PCDHB6	56130	hgsc.bcm.edu	37	chr5	140530534	140530534	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagattcagatccaggttttGgacatcaatgacaacgtccc	12	10	9	10	1	2	3	2	1	0	2	4	5	4	4	2	2	1	1	2	2	2	3	rs10076554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140530534G>C	ENST00000231136.1	+	1	696	c.696G>C	c.(694-696)ttG>ttC	p.L232F	PCDHB6_ENST00000543635.1_Missense_Mutation_p.L96F	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	232	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.		L -> F (in dbSNP:rs10076554).		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)			TCCAGGTTTTGGACATCAATG	0.587													G|||	73	0.0145767	0.0537	0.0029	5008	,	,		17505	0.0		0.0	False		,,,				2504	0.0				p.L232F		Atlas-SNP	.											.	PCDHB6	161	.	0			c.G696C						PASS	.	G	PHE/LEU	193,4213	121.3+/-158.8	4,185,2014	44	48	47		696	0.6	0.5	5	dbSNP_119	47	0,8600		0,0,4300	yes	missense	PCDHB6	NM_018939.2	22	4,185,6314	CC,CG,GG		0.0,4.3804,1.4839	possibly-damaging	232/795	140530534	193,12813	2203	4300	6503	SO:0001583	missense	56130	exon1			GGTTTTGGACATC	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.696G>C	5.37:g.140530534G>C	ENSP00000231136:p.Leu232Phe	103	0	0		108	53	0.490741	NM_018939	B2R8R9	Missense_Mutation	SNP	ENST00000231136.1	37	CCDS4248.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	G	14.12	2.441466	0.43326	0.043804	0.0	ENSG00000113211	ENST00000543635;ENST00000231136;ENST00000542861	T;T	0.01804	4.63;4.63	4.85	0.653	0.17828	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.01320	0.0043	M	0.93106	3.38	0.26654	N	0.97205	D	0.57571	0.98	D	0.63381	0.914	T	0.08432	-1.0722	9	0.72032	D	0.01	.	3.9631	0.09420	0.3108:0.0:0.4427:0.2466	rs10076554;rs61376880;rs10076554	232	Q9Y5E3	PCDB6_HUMAN	F	96;232;17	ENSP00000438466:L96F;ENSP00000231136:L232F	ENSP00000231136:L232F	L	+	3	2	PCDHB6	140510718	0.118000	0.22208	0.455000	0.27031	0.888000	0.51559	-0.354000	0.07681	0.178000	0.19917	0.561000	0.74099	TTG	G|0.986;C|0.014	0.014	strong		0.587	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939		C	140530534	G	C	140530534	3	2	22	1	0	0	0	0	1	0	0	0	11555	1339	47	4	698	4	PCDHB6	5	140530534	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	27256	140530534	40384726	1298	4199											
PCDHB8	56128	hgsc.bcm.edu	37	chr5	140558384	140558384	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tgcagatctctgaggacagtCcaataagcttcctggttgtg	9	12	11	9	0	1	2	0	1	1	1	4	3	3	3	2	2	2	3	2	2	2	3	rs116452537	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140558384C>T	ENST00000239444.2	+	1	1014	c.769C>T	c.(769-771)Cca>Tca	p.P257S	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	257	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(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)			TGAGGACAGTCCAATAAGCTT	0.458													C|||	27	0.00539137	0.0204	0.0	5008	,	,		15847	0.0		0.0	False		,,,				2504	0.0				p.P257S		Atlas-SNP	.											.	PCDHB8	199	.	0			c.C769T						PASS	.	C	SER/PRO	68,4338	61.7+/-98.7	1,66,2136	209	277	254		769	3.3	0.9	5	dbSNP_132	254	0,8600		0,0,4300	yes	missense	PCDHB8	NM_019120.3	74	1,66,6436	TT,TC,CC		0.0,1.5433,0.5228	benign	257/802	140558384	68,12938	2203	4300	6503	SO:0001583	missense	56128	exon1			GACAGTCCAATAA	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.769C>T	5.37:g.140558384C>T	ENSP00000239444:p.Pro257Ser	469	1	0.0021322		285	140	0.491228	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	37	CCDS4250.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	c	13.53	2.263792	0.39995	0.015433	0.0	ENSG00000120322	ENST00000239444	T	0.54279	0.58	4.25	3.33	0.38152	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.41971	0.1182	M	0.79011	2.435	0.32980	D	0.523474	B	0.26935	0.164	B	0.33690	0.168	T	0.67604	-0.5628	9	0.62326	D	0.03	.	13.5777	0.61883	0.0:0.8433:0.1567:0.0	.	257	Q9UN66	PCDB8_HUMAN	S	257	ENSP00000239444:P257S	ENSP00000239444:P257S	P	+	1	0	PCDHB8	140538568	0.033000	0.19621	0.908000	0.35775	0.609000	0.37215	2.681000	0.46926	1.911000	0.55334	0.585000	0.79938	CCA	C|0.994;T|0.006	0.006	strong		0.458	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120		T	140558384	C	T	140558384	3	4	22	1	0	0	0	0	1	0	0	0	11557	855	30	2	771	2	PCDHB8	5	140558384	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	27850	140558384	40356876	1299	4200											
PCDHB16	57717	hgsc.bcm.edu	37	chr5	140562756	140562756	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atcgggaggaggagcctcaaCtaagattaaccctgacagcg	13	6	12	10	2	1	2	1	1	0	1	2	5	1	5	2	3	4	0	2	3	3	2	rs28398442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140562756C>G	ENST00000361016.2	+	1	1777	c.622C>G	c.(622-624)Cta>Gta	p.L208V		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	208	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)			GGAGCCTCAACTAAGATTAAC	0.502													C|||	58	0.0115815	0.0431	0.0014	5008	,	,		17472	0.0		0.0	False		,,,				2504	0.0				p.L208V		Atlas-SNP	.											.	PCDHB16	159	.	0			c.C622G						PASS	.	C	VAL/LEU	154,4252	107.3+/-145.7	3,148,2052	65	66	65		622	-8.7	0	5	dbSNP_125	65	0,8600		0,0,4300	yes	missense	PCDHB16	NM_020957.1	32	3,148,6352	GG,GC,CC		0.0,3.4952,1.1841	benign	208/777	140562756	154,12852	2203	4300	6503	SO:0001583	missense	57717	exon1			CCTCAACTAAGAT	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.622C>G	5.37:g.140562756C>G	ENSP00000354293:p.Leu208Val	65	0	0		73	39	0.534247	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	37	CCDS4251.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	C	2.179	-0.387934	0.04932	0.034952	0.0	ENSG00000196963	ENST00000361016	T	0.49139	0.79	4.69	-8.68	0.00859	Cadherin (4);Cadherin-like (1);	0.962534	0.08410	N	0.950091	T	0.07098	0.0180	L	0.38531	1.155	0.09310	N	1	B	0.21452	0.056	B	0.27170	0.077	T	0.27606	-1.0069	10	0.41790	T	0.15	.	1.2389	0.01958	0.2632:0.3205:0.2274:0.189	rs28398442	208	Q9NRJ7	PCDBG_HUMAN	V	208	ENSP00000354293:L208V	ENSP00000354293:L208V	L	+	1	2	PCDHB16	140542940	0.000000	0.05858	0.001000	0.08648	0.191000	0.23601	-4.894000	0.00173	-1.135000	0.02895	-0.176000	0.13171	CTA	C|0.991;G|0.009	0.009	strong		0.502	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957		G	140562756	C	G	140562756	3	3	22	1	0	0	0	0	1	0	0	0	11550	564	20	4	624	4	PCDHB16	5	140562756	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4372	140562756	40352504	1300	4201											
PCDHB10	56126	hgsc.bcm.edu	37	chr5	140573655	140573655	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtctccatcaacgcggacaaCggccacctgttcgccctcag	8	7	9	17	4	3	0	2	0	1	0	5	1	3	1	4	2	2	1	4	2	2	1	rs17844572	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140573655C>T	ENST00000239446.4	+	1	1714	c.1530C>T	c.(1528-1530)aaC>aaT	p.N510N		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	510	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)			ACGCGGACAACGGCCACCTGT	0.692													C|||	79	0.0157748	0.0582	0.0029	5008	,	,		18416	0.0		0.0	False		,,,				2504	0.0				p.N510N		Atlas-SNP	.											.	PCDHB10	177	.	0			c.C1530T						PASS	.	C		182,4224	107.8+/-146.2	5,172,2026	102	119	113		1530	1.7	0.9	5	dbSNP_123	113	0,8594		0,0,4297	no	coding-synonymous	PCDHB10	NM_018930.3		5,172,6323	TT,TC,CC		0.0,4.1307,1.4		510/801	140573655	182,12818	2203	4297	6500	SO:0001819	synonymous_variant	56126	exon1			GGACAACGGCCAC	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.1530C>T	5.37:g.140573655C>T		374	0	0		395	107	0.270886	NM_018930	Q96T99	Silent	SNP	ENST00000239446.4	37	CCDS4252.1																																																																																			C|0.986;T|0.014	0.014	strong		0.692	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		T	140573655	C	T	140573655	2	4	22	1	0	0	0	0	0	0	0	1	11544	535	19	1		1	PCDHB10	5	140573655	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	10899	140573655	40341605	1301	4202											
PCDHB10	56126	hgsc.bcm.edu	37	chr5	140573759	140573759	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccgcgctgagcagagaggCgctggtgcgcgtgctggtgc	4	6	18	13	5	0	2	0	1	0	1	0	3	0	2	2	3	4	4	2	3	0	0	rs17844584	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140573759C>T	ENST00000239446.4	+	1	1818	c.1634C>T	c.(1633-1635)gCg>gTg	p.A545V		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	545	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)	p.A545V(1)		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)			AGCAGAGAGGCGCTGGTGCGC	0.706													C|||	27	0.00539137	0.0204	0.0	5008	,	,		16480	0.0		0.0	False		,,,				2504	0.0				p.A545V		Atlas-SNP	.											PCDHB10,colon,carcinoma,0,1	PCDHB10	177	1	1	Substitution - Missense(1)	large_intestine(1)	c.C1634T						scavenged	.	C	VAL/ALA	66,4300		0,66,2117	34	48	43		1634	3.5	1	5	dbSNP_123	43	0,8560		0,0,4280	no	missense	PCDHB10	NM_018930.3	64	0,66,6397	TT,TC,CC		0.0,1.5117,0.5106	benign	545/801	140573759	66,12860	2183	4280	6463	SO:0001583	missense	56126	exon1			GAGAGGCGCTGGT	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.1634C>T	5.37:g.140573759C>T	ENSP00000239446:p.Ala545Val	147	1	0.00680272		145	68	0.468966	NM_018930	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	37	CCDS4252.1	.	.	.	.	.	.	.	.	.	.	c	14.35	2.508907	0.44660	0.015117	0.0	ENSG00000120324	ENST00000239446	T	0.01787	4.64	3.53	3.53	0.40419	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.00875	0.0029	N	0.16266	0.395	0.09310	N	1	D	0.54047	0.964	P	0.48921	0.595	T	0.53136	-0.8481	9	0.14252	T	0.57	.	7.8479	0.29437	0.0:0.8331:0.0:0.1669	rs17844584	545	Q9UN67	PCDBA_HUMAN	V	545	ENSP00000239446:A545V	ENSP00000239446:A545V	A	+	2	0	PCDHB10	140553943	0.000000	0.05858	0.998000	0.56505	0.980000	0.70556	-0.423000	0.07034	1.994000	0.58287	0.549000	0.68633	GCG	C|0.993;T|0.007	0.007	strong		0.706	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		T	140573759	C	T	140573759	3	4	22	1	0	0	0	0	1	0	0	0	11544	768	27	1	1636	1	PCDHB10	5	140573759	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	104	140573759	40341501	1302	4203											
PCDHB11	56125	hgsc.bcm.edu	37	chr5	140580958	140580958	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgggcgccacagaccgcggCtccccggctttgagcagcga	6	5	15	15	5	0	2	0	1	0	1	1	3	1	2	4	3	2	3	4	3	0	1	rs74949746	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140580958C>A	ENST00000354757.3	+	1	1611	c.1611C>A	c.(1609-1611)ggC>ggA	p.G537G	PCDHB11_ENST00000536699.1_Silent_p.G172G	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	537	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)			CAGACCGCGGCTCCCCGGCTT	0.672													C|||	58	0.0115815	0.0431	0.0014	5008	,	,		16231	0.0		0.0	False		,,,				2504	0.0				p.G537G		Atlas-SNP	.											PCDHB11,right_upper_lobe,carcinoma,+2,2	PCDHB11	162	2	0			c.C1611A						PASS	.	C		154,4250	103.4+/-141.9	4,146,2052	38	51	47		1611	-2.2	0	5	dbSNP_131	47	0,8598		0,0,4299	no	coding-synonymous	PCDHB11	NM_018931.2		4,146,6351	AA,AC,CC		0.0,3.4968,1.1844		537/798	140580958	154,12848	2202	4299	6501	SO:0001819	synonymous_variant	56125	exon1			CCGCGGCTCCCCG	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.1611C>A	5.37:g.140580958C>A		284	0	0		433	213	0.491917	NM_018931	B4DSF7|Q2M223	Silent	SNP	ENST00000354757.3	37	CCDS4253.1																																																																																			C|0.991;A|0.009	0.009	strong		0.672	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931		A	140580958	C	A	140580958	2	1	22	1	0	0	0	0	0	0	0	1	11545	784	28	4		4	PCDHB11	5	140580958	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	7199	140580958	40334302	1303	4204											
PCDHB12	56124	hgsc.bcm.edu	37	chr5	140589334	140589334	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tataccttttcccatgcctcAgaagatattcgcaagacatt	12	13	5	11	1	1	3	1	0	0	3	3	3	2	3	3	0	2	1	3	0	5	7	rs149716951	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140589334A>G	ENST00000239450.2	+	1	1044	c.855A>G	c.(853-855)tcA>tcG	p.S285S	PCDHB12_ENST00000541609.1_Intron	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	285	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)			CCCATGCCTCAGAAGATATTC	0.403													A|||	27	0.00539137	0.0204	0.0	5008	,	,		20813	0.0		0.0	False		,,,				2504	0.0				p.S285S		Atlas-SNP	.											.	PCDHB12	179	.	0			c.A855G						PASS	.	A		70,4336	63.5+/-100.7	1,68,2134	99	105	103		855	-4.1	1	5	dbSNP_134	103	0,8600		0,0,4300	no	coding-synonymous	PCDHB12	NM_018932.3		1,68,6434	GG,GA,AA		0.0,1.5887,0.5382		285/796	140589334	70,12936	2203	4300	6503	SO:0001819	synonymous_variant	56124	exon1			TGCCTCAGAAGAT	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.855A>G	5.37:g.140589334A>G		138	0	0		121	64	0.528926	NM_018932	B4DDU1	Silent	SNP	ENST00000239450.2	37	CCDS4254.1																																																																																			A|0.994;G|0.006	0.006	strong		0.403	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932		G	140589334	A	G	140589334	2	3	22	1	0	0	0	0	0	0	0	1	11546	175	7	3		3	PCDHB12	5	140589334	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	8376	140589334	40325926	1304	4205											
PCDHB14	56122	hgsc.bcm.edu	37	chr5	140603248	140603248	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gacctagggctgggggtggaGgagctgtcttcacgtgaagc	7	8	18	8	1	2	1	1	1	1	0	2	4	2	3	1	5	2	2	1	5	2	2	rs7713000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140603248G>A	ENST00000239449.4	+	1	171	c.171G>A	c.(169-171)gaG>gaA	p.E57E	PCDHB14_ENST00000515856.2_Intron	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	57	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)			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)			TGGGGGTGGAGGAGCTGTCTT	0.478													g|||	103	0.0205671	0.0734	0.0072	5008	,	,		17325	0.0		0.001	False		,,,				2504	0.0				p.E57E	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.G171A						PASS	.	G		278,4128		6,266,1931	90	93	92		171	1	0.6	5	dbSNP_116	92	0,8600		0,0,4300	no	coding-synonymous	PCDHB14	NM_018934.2		6,266,6231	AA,AG,GG		0.0,6.3096,2.1375		57/799	140603248	278,12728	2203	4300	6503	SO:0001819	synonymous_variant	56122	exon1			GGTGGAGGAGCTG	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.171G>A	5.37:g.140603248G>A		188	0	0		205	106	0.517073	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Silent	SNP	ENST00000239449.4	37	CCDS4256.1																																																																																			G|0.975;A|0.025	0.025	strong		0.478	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934		A	140603248	G	A	140603248	2	1	22	1	0	0	0	0	0	0	0	1	11548	991	35	2		2	PCDHB14	5	140603248	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	13914	140603248	40312012	1305	4206			3	26		6	6	1845	N	G_C	9.040221e-06
PCDHB14	56122	hgsc.bcm.edu	37	chr5	140603794	140603794	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ttggacatcaatgataatgcCcctgagtttcctcagagtct	10	13	8	10	0	3	3	2	2	1	1	4	4	4	4	3	1	1	1	3	1	2	3	rs59600730	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140603794C>T	ENST00000239449.4	+	1	717	c.717C>T	c.(715-717)gcC>gcT	p.A239A	PCDHB14_ENST00000515856.2_Silent_p.A86A	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	239	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)			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)			ATGATAATGCCCCTGAGTTTC	0.517													t|||	132	0.0263578	0.0946	0.0086	5008	,	,		16922	0.0		0.001	False		,,,				2504	0.0				p.A239A	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.C717T						PASS	.	T		304,4102		8,288,1907	70	72	71		717	-1.6	1	5	dbSNP_129	71	3,8597		0,3,4297	no	coding-synonymous	PCDHB14	NM_018934.2		8,291,6204	TT,TC,CC		0.0349,6.8997,2.3604		239/799	140603794	307,12699	2203	4300	6503	SO:0001819	synonymous_variant	56122	exon1			TAATGCCCCTGAG	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.717C>T	5.37:g.140603794C>T		98	0	0		74	25	0.337838	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Silent	SNP	ENST00000239449.4	37	CCDS4256.1																																																																																			C|0.977;T|0.023	0.023	strong		0.517	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934		T	140603794	C	T	140603794	2	4	22	1	0	0	0	0	0	0	0	1	11548	610	22	2		2	PCDHB14	5	140603794	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	546	140603794	40311466	1306	4207			3	26		6	6	1845	N	G_C	9.040221e-06
PCDHB14	56122	hgsc.bcm.edu	37	chr5	140604419	140604419	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctctgacgtcaatgacaacGcccccaccttcacccaaacc	11	7	4	19	2	3	2	2	2	1	0	4	2	3	2	5	0	2	0	5	0	3	1	rs61731253	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140604419G>A	ENST00000239449.4	+	1	1342	c.1342G>A	c.(1342-1344)Gcc>Acc	p.A448T	PCDHB14_ENST00000515856.2_Missense_Mutation_p.A295T	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	448	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)			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)			CAATGACAACGCCCCCACCTT	0.582													g|||	103	0.0205671	0.0734	0.0072	5008	,	,		17391	0.0		0.001	False		,,,				2504	0.0				p.A448T	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.G1342A						PASS	.	G	THR/ALA	278,4128		6,266,1931	145	140	142		1342	3.5	1	5	dbSNP_129	142	0,8600		0,0,4300	no	missense	PCDHB14	NM_018934.2	58	6,266,6231	AA,AG,GG		0.0,6.3096,2.1375	benign	448/799	140604419	278,12728	2203	4300	6503	SO:0001583	missense	56122	exon1			GACAACGCCCCCA	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.1342G>A	5.37:g.140604419G>A	ENSP00000239449:p.Ala448Thr	161	0	0		200	108	0.54	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Missense_Mutation	SNP	ENST00000239449.4	37	CCDS4256.1	39	0.017857142857142856	37	0.07520325203252033	2	0.0055248618784530384	0	0.0	0	0.0	-	8.743	0.919419	0.17982	0.063096	0.0	ENSG00000120327	ENST00000515856;ENST00000239449	T;T	0.03181	4.02;4.02	4.5	3.55	0.40652	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.00300	0.0009	M	0.75777	2.31	0.30169	N	0.801422	P	0.49559	0.925	B	0.34652	0.187	T	0.21827	-1.0234	9	0.56958	D	0.05	.	9.2019	0.37263	0.0:0.2719:0.6013:0.1268	rs61731253	448	Q9Y5E9	PCDBE_HUMAN	T	295;448	ENSP00000444518:A295T;ENSP00000239449:A448T	ENSP00000239449:A448T	A	+	1	0	PCDHB14	140584603	0.003000	0.15002	1.000000	0.80357	0.089000	0.18198	-0.272000	0.08560	2.235000	0.73313	0.556000	0.70494	GCC	G|0.979;A|0.021	0.021	strong		0.582	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934		A	140604419	G	A	140604419	3	1	22	1	0	0	0	0	1	0	0	0	11548	1087	38	1	1344	1	PCDHB14	5	140604419	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	625	140604419	40310841	1307	4208			3	26		6	6	1845	N	G_C	9.040221e-06
PCDHB14	56122	hgsc.bcm.edu	37	chr5	140604641	140604641	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	ccctcaggtcgctggactacGaggccctacaggagttcgag	8	7	13	13	3	1	0	1	0	0	0	3	4	1	2	2	4	2	2	2	4	2	3	rs142548755	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140604641G>C	ENST00000239449.4	+	1	1564	c.1564G>C	c.(1564-1566)Gag>Cag	p.E522Q	PCDHB14_ENST00000515856.2_Missense_Mutation_p.E369Q	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	522	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)			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)			GCTGGACTACGAGGCCCTACA	0.687													g|||	27	0.00539137	0.0204	0.0	5008	,	,		16691	0.0		0.0	False		,,,				2504	0.0				p.E522Q	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.G1564C						PASS	.	G	GLN/GLU	69,4337		0,69,2134	86	91	90		1564	4.2	1	5	dbSNP_134	90	0,8600		0,0,4300	no	missense	PCDHB14	NM_018934.2	29	0,69,6434	CC,CG,GG		0.0,1.566,0.5305	probably-damaging	522/799	140604641	69,12937	2203	4300	6503	SO:0001583	missense	56122	exon1			GACTACGAGGCCC	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.1564G>C	5.37:g.140604641G>C	ENSP00000239449:p.Glu522Gln	246	0	0		281	137	0.487544	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Missense_Mutation	SNP	ENST00000239449.4	37	CCDS4256.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	-	20.7	4.042145	0.75732	0.01566	0.0	ENSG00000120327	ENST00000515856;ENST00000239449	T;T	0.72942	-0.7;-0.7	4.15	4.15	0.48705	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.81917	0.4924	H	0.96048	3.76	0.45634	D	0.998568	D	0.89917	1.0	D	0.97110	1.0	D	0.89840	0.4002	9	0.87932	D	0	.	16.4819	0.84160	0.0:0.0:1.0:0.0	.	522	Q9Y5E9	PCDBE_HUMAN	Q	369;522	ENSP00000444518:E369Q;ENSP00000239449:E522Q	ENSP00000239449:E522Q	E	+	1	0	PCDHB14	140584825	1.000000	0.71417	1.000000	0.80357	0.755000	0.42902	7.687000	0.84139	2.048000	0.60808	0.556000	0.70494	GAG	G|0.994;C|0.006	0.006	strong		0.687	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934		C	140604641	G	C	140604641	3	2	22	1	0	0	0	0	1	0	0	0	11548	1059	37	4	1566	4	PCDHB14	5	140604641	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	222	140604641	40310619	1308	4209			3	26		6	6	1845	N	G_C	9.040221e-06
PCDHB14	56122	hgsc.bcm.edu	37	chr5	140604694	140604694	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccacagaccgcgggtccccGgcgttgagcagcgaggcgct	6	4	16	15	6	0	2	0	1	0	1	1	3	1	2	4	3	2	3	4	3	0	1	rs76971158	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140604694G>A	ENST00000239449.4	+	1	1617	c.1617G>A	c.(1615-1617)ccG>ccA	p.P539P	PCDHB14_ENST00000515856.2_Silent_p.P386P	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	539	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)			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)			GCGGGTCCCCGGCGTTGAGCA	0.672													g|||	132	0.0263578	0.0946	0.0086	5008	,	,		16525	0.0		0.001	False		,,,				2504	0.0				p.P539P	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											PCDHB14,caecum,carcinoma,0,1	PCDHB14	132	1	0			c.G1617A						PASS	.	G		301,4105		7,287,1909	51	57	55		1617	-4.4	0.6	5	dbSNP_131	55	4,8592		0,4,4294	no	coding-synonymous	PCDHB14	NM_018934.2		7,291,6203	AA,AG,GG		0.0465,6.8316,2.3458		539/799	140604694	305,12697	2203	4298	6501	SO:0001819	synonymous_variant	56122	exon1			GTCCCCGGCGTTG	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.1617G>A	5.37:g.140604694G>A		194	0	0		247	119	0.481781	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Silent	SNP	ENST00000239449.4	37	CCDS4256.1																																																																																			G|0.978;A|0.022	0.022	strong		0.672	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934		A	140604694	G	A	140604694	2	1	22	1	0	0	0	0	0	0	0	1	11548	1103	39	1		1	PCDHB14	5	140604694	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	53	140604694	40310566	1309	4210			3	26		6	6	1845	N	G_C	9.040221e-06
PCDHB14	56122	hgsc.bcm.edu	37	chr5	140605092	140605092	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttctcccagccctacctgcCgctccctgaggcggccccgg	3	7	10	21	3	1	1	0	1	1	0	3	1	2	1	7	3	3	1	7	3	1	2	rs76671799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140605092C>G	ENST00000239449.4	+	1	2015	c.2015C>G	c.(2014-2016)cCg>cGg	p.P672R	PCDHB14_ENST00000515856.2_Missense_Mutation_p.P519R	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	672					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)			CCCTACCTGCCGCTCCCTGAG	0.692													c|||	132	0.0263578	0.0946	0.0086	5008	,	,		14125	0.0		0.001	False		,,,				2504	0.0				p.P672R	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.C2015G						PASS	.	C	ARG/PRO	234,4046		6,222,1912	46	53	51		2015	0.6	0.5	5	dbSNP_131	51	3,8453		0,3,4225	no	missense	PCDHB14	NM_018934.2	103	6,225,6137	GG,GC,CC		0.0355,5.4673,1.8609	benign	672/799	140605092	237,12499	2140	4228	6368	SO:0001583	missense	56122	exon1			ACCTGCCGCTCCC	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.2015C>G	5.37:g.140605092C>G	ENSP00000239449:p.Pro672Arg	40	0	0		66	29	0.439394	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Missense_Mutation	SNP	ENST00000239449.4	37	CCDS4256.1	45	0.020604395604395604	42	0.08536585365853659	3	0.008287292817679558	0	0.0	0	0.0	-	12.23	1.876740	0.33162	0.054673	3.55E-4	ENSG00000120327	ENST00000515856;ENST00000239449	T;T	0.51817	0.7;0.69	3.83	0.644	0.17776	.	.	.	.	.	T	0.02533	0.0077	M	0.82923	2.615	0.19945	N	0.999944	B	0.28378	0.209	B	0.30029	0.11	T	0.10177	-1.0641	9	0.39692	T	0.17	.	6.8594	0.24058	0.5742:0.2934:0.1324:0.0	.	672	Q9Y5E9	PCDBE_HUMAN	R	519;672	ENSP00000444518:P519R;ENSP00000239449:P672R	ENSP00000239449:P672R	P	+	2	0	PCDHB14	140585276	0.000000	0.05858	0.479000	0.27329	0.090000	0.18270	0.062000	0.14389	0.695000	0.31675	-0.251000	0.11542	CCG	C|0.978;G|0.022	0.022	strong		0.692	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934		G	140605092	C	G	140605092	3	3	22	1	0	0	0	0	1	0	0	0	11548	652	23	4	2017	4	PCDHB14	5	140605092	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	398	140605092	40310168	1310	4211			3	26		6	6	1845	N	G_C	9.040221e-06
PCDHB15	56121	hgsc.bcm.edu	37	chr5	140627184	140627184	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccagaggcggccccggccCaagcccaggccgactcgctt	6	4	12	19	4	0	1	0	0	0	1	2	2	1	1	6	4	1	1	6	4	1	1	rs79326925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140627184C>G	ENST00000231173.3	+	1	2038	c.2038C>G	c.(2038-2040)Caa>Gaa	p.Q680E		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	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)	p.Q680K(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)			GGCCCCGGCCCAAGCCCAGGC	0.672													C|||	103	0.0205671	0.0734	0.0072	5008	,	,		16390	0.0		0.001	False		,,,				2504	0.0				p.Q680E		Atlas-SNP	.											.	PCDHB15	138	.	1	Substitution - Missense(1)	lung(1)	c.C2038G						PASS	.	C	GLU/GLN	247,4147		5,237,1955	62	68	66		2038	0.1	0	5	dbSNP_131	66	0,8572		0,0,4286	no	missense	PCDHB15	NM_018935.2	29	5,237,6241	GG,GC,CC		0.0,5.6213,1.905	benign	680/788	140627184	247,12719	2197	4286	6483	SO:0001583	missense	56121	exon1			CCGGCCCAAGCCC	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.2038C>G	5.37:g.140627184C>G	ENSP00000231173:p.Gln680Glu	117	0	0		109	63	0.577982	NM_018935	Q8IUX5	Missense_Mutation	SNP	ENST00000231173.3	37	CCDS4257.1	39	0.017857142857142856	37	0.07520325203252033	2	0.0055248618784530384	0	0.0	0	0.0	C	8.308	0.821498	0.16678	0.056213	0.0	ENSG00000113248	ENST00000231173	T	0.46063	0.88	4.25	0.0585	0.14328	.	.	.	.	.	T	0.01592	0.0051	L	0.31120	0.905	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.09185	-1.0686	9	0.10636	T	0.68	.	15.5586	0.76219	0.0:0.5083:0.4917:0.0	.	680	Q9Y5E8	PCDBF_HUMAN	E	680	ENSP00000231173:Q680E	ENSP00000231173:Q680E	Q	+	1	0	PCDHB15	140607368	0.000000	0.05858	0.000000	0.03702	0.360000	0.29518	-0.150000	0.10189	-0.255000	0.09486	0.549000	0.68633	CAA	C|0.979;G|0.021	0.021	strong		0.672	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935		G	140627184	C	G	140627184	3	3	22	1	0	0	0	0	1	0	0	0	11549	595	21	4	2040	4	PCDHB15	5	140627184	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	22092	140627184	40288076	1311	4212											
PCDHGA2	56113	hgsc.bcm.edu	37	chr5	140719294	140719294	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagtaccgcataagcattccGgagaatacgctcgtgggcac	11	7	12	11	4	0	1	0	0	0	1	2	3	1	1	2	2	3	5	2	2	4	4			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140719294G>A	ENST00000394576.2	+	1	756	c.756G>A	c.(754-756)ccG>ccA	p.P252P	PCDHGA1_ENST00000517417.1_Intron	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	252	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)|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)			TAAGCATTCCGGAGAATACGC	0.552																																					p.P252P		Atlas-SNP	.											.	PCDHGA2	205	.	0			c.G756A						PASS	.						74	77	76					5																	140719294		2203	4300	6503	SO:0001819	synonymous_variant	56113	exon1			CATTCCGGAGAAT	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.756G>A	5.37:g.140719294G>A		64	0	0		48	26	0.541667	NM_018915	Q52LL6|Q9Y5D5	Silent	SNP	ENST00000394576.2	37	CCDS47289.1																																																																																			.	.	none		0.552	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374738.1	NM_018915		A	140719294	G	A	140719294	2	1	22	1	0	0	0	0	0	0	0	1	11563	1103	39	1		1	PCDHGA2	5	140719294	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	92110	140719294	40195966	1312	4213											
PCDHGA4	56111	hgsc.bcm.edu	37	chr5	140736328	140736328	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tatatgctctttgctccttcGactatgagcagtttagagac	9	15	8	9	1	1	2	0	1	1	1	3	4	2	2	1	0	3	4	1	0	4	7			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140736328G>A	ENST00000571252.1	+	1	1561	c.1561G>A	c.(1561-1563)Gac>Aac	p.D521N	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	521	Cadherin 5. {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)			TTGCTCCTTCGACTATGAGCA	0.527																																					p.D521N		Atlas-SNP	.											.	PCDHGA4	150	.	0			c.G1561A						PASS	.						131	140	137					5																	140736328		2131	4270	6401	SO:0001583	missense	56111	exon1			TCCTTCGACTATG	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.1561G>A	5.37:g.140736328G>A	ENSP00000458570:p.Asp521Asn	129	0	0		142	73	0.514085	NM_018917	Q9Y5D3	Missense_Mutation	SNP	ENST00000571252.1	37	CCDS58979.1																																																																																			.	.	none		0.527	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917		A	140736328	G	A	140736328	3	1	22	1	0	0	0	0	1	0	0	0	11565	1058	37	1	1563	1	PCDHGA4	5	140736328	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	17034	140736328	40178932	1313	4214											
KIAA0141	9812	hgsc.bcm.edu	37	chr5	141313888	141313888	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtgcctactacgagacccAgcctcttcgtggaaccctga	9	8	10	14	2	1	2	0	1	1	1	2	4	1	3	4	2	5	0	4	2	3	3	rs115183657	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:141313888A>C	ENST00000432126.2	+	9	1115	c.981A>C	c.(979-981)ccA>ccC	p.P327P	KIAA0141_ENST00000194118.4_Silent_p.P327P	NM_001142603.1|NM_014773.3	NP_001136075.1|NP_055588.3	Q14154	DELE_HUMAN	KIAA0141	327					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)			TACGAGACCCAGCCTCTTCGT	0.597													A|||	44	0.00878594	0.0318	0.0029	5008	,	,		14901	0.0		0.0	False		,,,				2504	0.0				p.P327P		Atlas-SNP	.											.	KIAA0141	44	.	0			c.A981C						PASS	.	A	,	104,4302	79.9+/-118.3	0,104,2099	49	47	48		981,981	-7	0	5	dbSNP_132	48	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	KIAA0141	NM_001142603.1,NM_014773.3	,	0,104,6399	CC,CA,AA		0.0,2.3604,0.7996	,	327/516,327/516	141313888	104,12902	2203	4300	6503	SO:0001819	synonymous_variant	9812	exon9			AGACCCAGCCTCT	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.981A>C	5.37:g.141313888A>C		88	0	0		129	61	0.472868	NM_001142603	Q969R4|Q96EU9	Silent	SNP	ENST00000432126.2	37	CCDS4268.1	16	0.007326007326007326	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	0	0.0	A	0.525	-0.860231	0.02610	0.023604	0.0	ENSG00000081791	ENST00000507481	.	.	.	5.55	-6.96	0.01622	.	.	.	.	.	T	0.06371	0.0164	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.24657	-1.0154	4	.	.	.	-1.6157	4.7459	0.13036	0.1625:0.5451:0.1777:0.1147	.	.	.	.	P	29	.	.	Q	+	2	0	KIAA0141	141294072	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.619000	0.05572	-1.086000	0.03084	-0.290000	0.09829	CAG	A|0.991;C|0.009	0.009	strong		0.597	KIAA0141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251863.2	NM_014773		C	141313888	A	C	141313888	2	2	22	1	0	0	0	0	0	0	0	1	8165	175	7	5		5	KIAA0141	5	141313888	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	577560	141313888	39601372	1314	4215											
PCDH12	51294	hgsc.bcm.edu	37	chr5	141329059	141329059	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgcttcacagagaggtccTcttcaggatccaaaggccct	9	10	10	12	0	3	1	2	0	1	1	5	3	5	2	3	3	1	2	3	3	1	3	rs61737141	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:141329059T>G	ENST00000231484.3	-	3	4278	c.3068A>C	c.(3067-3069)gAg>gCg	p.E1023A	AC005740.6_ENST00000607378.1_RNA	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	1023					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)			AGAGAGGTCCTCTTCAGGATC	0.562													T|||	32	0.00638978	0.0242	0.0	5008	,	,		18789	0.0		0.0	False		,,,				2504	0.0				p.E1023A		Atlas-SNP	.											.	PCDH12	133	.	0			c.A3068C						PASS	.	T	ALA/GLU	125,4281	93.0+/-131.7	3,119,2081	159	152	154		3068	3.3	1	5	dbSNP_129	154	0,8600		0,0,4300	yes	missense	PCDH12	NM_016580.2	107	3,119,6381	GG,GT,TT		0.0,2.837,0.9611	possibly-damaging	1023/1185	141329059	125,12881	2203	4300	6503	SO:0001583	missense	51294	exon3			AGGTCCTCTTCAG	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.3068A>C	5.37:g.141329059T>G	ENSP00000231484:p.Glu1023Ala	93	0	0		94	52	0.553191	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	37	CCDS4269.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	T	14.87	2.663251	0.47572	0.02837	0.0	ENSG00000113555	ENST00000231484	T	0.52754	0.65	5.8	3.34	0.38264	.	0.387701	0.27739	N	0.018060	T	0.15609	0.0376	L	0.57536	1.79	0.26311	N	0.977823	B	0.29716	0.255	B	0.26614	0.071	T	0.06716	-1.0811	10	0.33141	T	0.24	.	5.3998	0.16288	0.1828:0.0:0.1684:0.6488	.	1023	Q9NPG4	PCD12_HUMAN	A	1023	ENSP00000231484:E1023A	ENSP00000231484:E1023A	E	-	2	0	PCDH12	141309243	0.960000	0.32886	1.000000	0.80357	0.985000	0.73830	1.632000	0.37102	2.224000	0.72417	0.533000	0.62120	GAG	T|0.989;G|0.011	0.011	strong		0.562	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		G	141329059	T	G	141329059	3	3	22	1	0	0	0	0	1	0	0	0	11519	1551	54	5	494	5	PCDH12	5	141329059	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	15171	141329059	39586201	1315	4216											
PCDH12	51294	hgsc.bcm.edu	37	chr5	141331098	141331098	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caagtacttatttcctcggtGgtttggtttgggctggaatt	6	17	12	6	1	0	0	0	0	0	0	2	1	1	1	1	5	1	4	1	5	4	6	rs115735066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:141331098G>A	ENST00000231484.3	-	2	4148	c.2938C>T	c.(2938-2940)Cac>Tac	p.H980Y	AC005740.6_ENST00000607378.1_RNA	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	980					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)			TTTCCTCGGTGGTTTGGTTTG	0.547											OREG0016877	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	44	0.00878594	0.0318	0.0029	5008	,	,		20762	0.0		0.0	False		,,,				2504	0.0				p.H980Y		Atlas-SNP	.											.	PCDH12	133	.	0			c.C2938T						PASS	.	G	TYR/HIS	104,4302	81.4+/-119.9	0,104,2099	113	103	106		2938	6.1	1	5	dbSNP_132	106	0,8600		0,0,4300	yes	missense	PCDH12	NM_016580.2	83	0,104,6399	AA,AG,GG		0.0,2.3604,0.7996	probably-damaging	980/1185	141331098	104,12902	2203	4300	6503	SO:0001583	missense	51294	exon2			CTCGGTGGTTTGG	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.2938C>T	5.37:g.141331098G>A	ENSP00000231484:p.His980Tyr	106	0	0	1663	118	45	0.381356	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	37	CCDS4269.1	16	0.007326007326007326	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	0	0.0	G	17.98	3.520092	0.64747	0.023604	0.0	ENSG00000113555	ENST00000231484	T	0.52754	0.65	6.08	6.08	0.98989	.	0.107907	0.64402	D	0.000003	T	0.21022	0.0506	M	0.62723	1.935	0.42331	D	0.992297	P	0.43788	0.817	B	0.39339	0.297	T	0.15809	-1.0424	10	0.36615	T	0.2	.	11.4227	0.49991	0.0811:0.0:0.9189:0.0	.	980	Q9NPG4	PCD12_HUMAN	Y	980	ENSP00000231484:H980Y	ENSP00000231484:H980Y	H	-	1	0	PCDH12	141311282	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.297000	0.65704	2.894000	0.99253	0.655000	0.94253	CAC	G|0.991;A|0.009	0.009	strong		0.547	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		A	141331098	G	A	141331098	3	1	22	1	0	0	0	0	1	0	0	0	11519	1348	47	2	628	2	PCDH12	5	141331098	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2039	141331098	39584162	1316	4217											
PCDH12	51294	hgsc.bcm.edu	37	chr5	141336858	141336858	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	atgtttggtctcatcagggcCcacaatgacatccaaggcaa	12	9	9	11	0	2	1	2	1	1	0	4	1	3	1	2	3	0	2	2	3	3	1	rs140883612	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:141336858C>T	ENST00000231484.3	-	1	1769	c.559G>A	c.(559-561)Ggc>Agc	p.G187S	PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	187	Cadherin 2. {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)			TCATCAGGGCCCACAATGACA	0.507													C|||	42	0.00838658	0.0303	0.0029	5008	,	,		19922	0.0		0.0	False		,,,				2504	0.0				p.G187S		Atlas-SNP	.											.	PCDH12	133	.	0			c.G559A						PASS	.	C	SER/GLY	104,4302	81.4+/-119.9	0,104,2099	102	111	108		559	5	1	5	dbSNP_134	108	0,8600		0,0,4300	yes	missense	PCDH12	NM_016580.2	56	0,104,6399	TT,TC,CC		0.0,2.3604,0.7996	probably-damaging	187/1185	141336858	104,12902	2203	4300	6503	SO:0001583	missense	51294	exon1			CAGGGCCCACAAT	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.559G>A	5.37:g.141336858C>T	ENSP00000231484:p.Gly187Ser	220	0	0		225	106	0.471111	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	37	CCDS4269.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	C	10.27	1.304137	0.23736	0.023604	0.0	ENSG00000113555	ENST00000231484	T	0.19669	2.13	4.98	4.98	0.66077	Cadherin (4);Cadherin-like (1);	0.127172	0.52532	D	0.000076	T	0.10294	0.0252	L	0.39898	1.24	0.35472	D	0.797432	D	0.62365	0.991	P	0.60541	0.876	T	0.06058	-1.0848	10	0.13108	T	0.6	.	9.2129	0.37328	0.0:0.9043:0.0:0.0957	.	187	Q9NPG4	PCD12_HUMAN	S	187	ENSP00000231484:G187S	ENSP00000231484:G187S	G	-	1	0	PCDH12	141317042	0.001000	0.12720	1.000000	0.80357	0.554000	0.35429	0.429000	0.21412	2.605000	0.88082	0.655000	0.94253	GGC	C|0.991;T|0.009	0.009	strong		0.507	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		T	141336858	C	T	141336858	3	4	22	1	0	0	0	0	1	0	0	0	11519	623	22	2	3011	2	PCDH12	5	141336858	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	5760	141336858	39578402	1317	4218											
SPINK1	6690	hgsc.bcm.edu	37	chr5	147207605	147207605	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgattttcaaaacataacacGcattcattgggataagtatt	15	13	6	7	2	2	0	2	0	0	0	2	2	2	1	0	1	2	2	0	1	5	8	rs35737774	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:147207605G>A	ENST00000296695.5	-	3	382	c.174C>T	c.(172-174)tgC>tgT	p.C58C	SPINK1_ENST00000510027.2_Silent_p.C58C	NM_003122.3	NP_003113.2	P00995	ISK1_HUMAN	serine peptidase inhibitor, Kazal type 1	58	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				negative regulation of calcium ion import (GO:0090281)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of serine-type endopeptidase activity (GO:1900004)|regulation of acrosome reaction (GO:0060046)|regulation of store-operated calcium entry (GO:2001256)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AACATAACACGCATTCATTGG	0.323									Hereditary Pancreatitis																												p.C58C		Atlas-SNP	.											.	SPINK1	9	.	0			c.C174T						PASS	.	G		624,3782	272.5+/-270.8	42,540,1621	102	95	97		174	-1	0	5	dbSNP_126	97	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SPINK1	NM_003122.3		42,541,5920	AA,AG,GG		0.0116,14.1625,4.8055		58/80	147207605	625,12381	2203	4300	6503	SO:0001819	synonymous_variant	6690	exon3	Familial Cancer Database		TAACACGCATTCA		CCDS4286.1	5q32	2011-08-31	2005-08-17		ENSG00000164266	ENSG00000164266		"Serine peptidase inhibitors, Kazal type"	11244	protein-coding gene	gene with protein product		167790	"serine protease inhibitor, Kazal type 1"				Standard	XM_005268501		Approved	Spink3, PCTT, PSTI, TATI	uc003los.2	P00995	OTTHUMG00000129730	ENST00000296695.5:c.174C>T	5.37:g.147207605G>A		42	0	0		41	41	1	NM_003122		Silent	SNP	ENST00000296695.5	37	CCDS4286.1																																																																																			G|0.956;A|0.044	0.044	strong		0.323	SPINK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251940.2	NM_003122		A	147207605	G	A	147207605	2	1	22	1	0	0	0	0	0	0	0	1	15072	1079	38	1		1	SPINK1	5	147207605	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5870747	147207605	33707655	1318	4219											
SPINK14	408187	hgsc.bcm.edu	37	chr5	147553829	147553829	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tatgagaaagtaaacttgagCtggtacaatggaacggtcaa	16	9	11	5	1	1	2	1	2	0	1	1	4	1	3	0	3	4	3	0	3	8	4	rs79779038	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:147553829C>T	ENST00000356972.1	+	3	144	c.144C>T	c.(142-144)agC>agT	p.S48S	SPINK14_ENST00000562793.1_Intron	NM_001001325.1	NP_001001325.1	Q6IE38	ISK14_HUMAN	serine peptidase inhibitor, Kazal type 14 (putative)	48	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						TAAACTTGAGCTGGTACAATG	0.413													T|||	536	0.107029	0.388	0.0303	5008	,	,		9611	0.001		0.001	False		,,,				2504	0.0				p.S48S		Atlas-SNP	.											.	SPINK14	9	.	0			c.C144T						PASS	.	T		841,2147		340,161,993	107	107	107		144	0.1	1	5	dbSNP_131	107	13,6231		1,11,3110	no	coding-synonymous	SPINK14	NM_001001325.1		341,172,4103	TT,TC,CC		0.2082,28.1459,9.2504		48/98	147553829	854,8378	1494	3122	4616	SO:0001819	synonymous_variant	408187	exon3			CTTGAGCTGGTAC		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.144C>T	5.37:g.147553829C>T		135	0	0		55	55	1	NM_001001325		Silent	SNP	ENST00000356972.1	37	CCDS4288.1																																																																																			C|0.919;T|0.081	0.081	strong		0.413	SPINK14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251943.2	NM_001001325		T	147553829	C	T	147553829	2	4	22	1	0	0	0	0	0	0	0	1	15074	796	28	2		2	SPINK14	5	147553829	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	346224	147553829	33361431	1319	4220											
HTR4	3360	hgsc.bcm.edu	37	chr5	147845463	147845463	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctattgcagaagagcaggaGgaagctggagacaggggaac	14	5	16	6	0	1	3	0	0	1	3	1	7	1	6	0	5	4	3	0	5	4	2	rs73266449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:147845463G>A	ENST00000314512.6	-	7	1265	c.1102C>T	c.(1102-1104)Ctc>Ttc	p.L368F	HTR4_ENST00000521530.1_Intron|HTR4_ENST00000354217.2_Intron|HTR4_ENST00000521735.1_Missense_Mutation_p.L368F	NM_199453.3	NP_955525.1	Q13639	5HT4R_HUMAN	5-hydroxytryptamine (serotonin) receptor 4, G protein-coupled	0					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)|regulation of appetite (GO:0032098)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)			endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Cinitapride(DB08810)|Cisapride(DB00604)|Ergoloid mesylate(DB01049)|Metoclopramide(DB01233)|Ondansetron(DB00904)	AAGAGCAGGAGGAAGCTGGAG	0.433													G|||	200	0.0399361	0.1437	0.0144	5008	,	,		17221	0.0		0.0	False		,,,				2504	0.0				p.L368F	GBM(120;370 1604 14007 17804 41573)	Atlas-SNP	.											.	HTR4	161	.	0			c.C1102T						PASS	.	G	,PHE/LEU	459,3947	219.4+/-237.2	28,403,1772	150	163	158		,1102	-7.4	0.3	5	dbSNP_130	158	3,8597	3.0+/-9.4	0,3,4297	yes	intron,missense	HTR4	NM_001040169.2,NM_199453.3	,22	28,406,6069	AA,AG,GG		0.0349,10.4176,3.5522	,	,368/379	147845463	462,12544	2203	4300	6503	SO:0001583	missense	3360	exon6			GCAGGAGGAAGCT	Y08756	CCDS4291.1, CCDS34270.1, CCDS34271.1, CCDS34272.1, CCDS34273.1, CCDS34273.2, CCDS75353.1	5q31-q33	2012-08-08	2012-02-03		ENSG00000164270	ENSG00000164270		"5-HT (serotonin) receptors", "GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"	5299	protein-coding gene	gene with protein product		602164	"5-hydroxytryptamine (serotonin) receptor 4"			9371406, 9276448	Standard	NM_199453		Approved	5-HT4	uc021yfj.1	Q13639	OTTHUMG00000129931	ENST00000314512.6:c.1102C>T	5.37:g.147845463G>A	ENSP00000314906:p.Leu368Phe	257	0	0		255	118	0.462745	NM_199453	C4WYH4|Q546Q1|Q684M0|Q712M9|Q96KH9|Q96KI0|Q9H199|Q9NY73|Q9UBM6|Q9UBT4|Q9UE22|Q9UE23|Q9UQR6	Missense_Mutation	SNP	ENST00000314512.6	37	CCDS34271.1	77	0.035256410256410256	72	0.14634146341463414	5	0.013812154696132596	0	0.0	0	0.0	G	9.178	1.022933	0.19433	0.104176	3.49E-4	ENSG00000164270	ENST00000314512;ENST00000521735	T;T	0.71817	-0.6;-0.6	5.06	-7.41	0.01392	.	.	.	.	.	T	0.00356	0.0011	.	.	.	0.31926	P	0.612866	B	0.02656	0.0	B	0.01281	0.0	T	0.18745	-1.0327	7	0.09843	T	0.71	.	16.3003	0.82806	0.6695:0.0:0.3305:0.0	.	368	Q684M0	.	F	368	ENSP00000314906:L368F;ENSP00000430979:L368F	ENSP00000314906:L368F	L	-	1	0	HTR4	147825656	0.873000	0.30073	0.266000	0.24541	0.912000	0.54170	-0.283000	0.08433	-2.141000	0.00805	-2.010000	0.00438	CTC	G|0.967;A|0.033	0.033	strong		0.433	HTR4-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374235.1	NM_000870		A	147845463	G	A	147845463	3	1	22	1	0	0	0	0	1	0	0	0	7458	1000	35	2	130	2	HTR4	5	147845463	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	291634	147845463	33069797	1320	4221											
PPARGC1B	133522	hgsc.bcm.edu	37	chr5	149200008	149200008	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcctcagggtggagggtccGgggaggagcaactctatgct	7	8	16	10	1	2	0	1	0	1	0	4	3	4	3	2	6	3	2	2	6	2	1	rs45518035	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149200008G>A	ENST00000309241.5	+	2	123	c.91G>A	c.(91-93)Ggg>Agg	p.G31R	PPARGC1B_ENST00000394320.3_Missense_Mutation_p.G31R|PPARGC1B_ENST00000360453.4_Missense_Mutation_p.G31R|PPARGC1B_ENST00000403750.1_Missense_Mutation_p.G6R	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	31	Abolishes DNA transcriptional activity when missing.				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)			TGGAGGGTCCGGGGAGGAGCA	0.572													G|||	41	0.0081869	0.0295	0.0029	5008	,	,		17247	0.0		0.0	False		,,,				2504	0.0				p.G31R		Atlas-SNP	.											.	PPARGC1B	74	.	0			c.G91A						PASS	.	G	ARG/GLY,ARG/GLY,ARG/GLY	96,4310	78.3+/-116.7	3,90,2110	83	90	88		91,16,91	5.8	0.9	5	dbSNP_127	88	2,8598	1.2+/-3.3	0,2,4298	yes	missense,missense,missense	PPARGC1B	NM_001172698.1,NM_001172699.1,NM_133263.3	125,125,125	3,92,6408	AA,AG,GG		0.0233,2.1788,0.7535	probably-damaging,probably-damaging,probably-damaging	31/985,6/960,31/1024	149200008	98,12908	2203	4300	6503	SO:0001583	missense	133522	exon2			GGGTCCGGGGAGG	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.91G>A	5.37:g.149200008G>A	ENSP00000312649:p.Gly31Arg	30	0	0		45	28	0.622222	NM_133263	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Missense_Mutation	SNP	ENST00000309241.5	37	CCDS4298.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	g	22.2	4.254416	0.80135	0.021788	2.33E-4	ENSG00000155846	ENST00000360453;ENST00000394320;ENST00000309241;ENST00000403750	T;T;T;T	0.16073	2.37;2.46;2.49;2.75	5.76	5.76	0.90799	.	0.096989	0.64402	D	0.000001	T	0.27594	0.0678	M	0.73217	2.22	0.50632	D	0.999885	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.987;0.999	P;P;P;P;D	0.67548	0.875;0.905;0.875;0.558;0.952	T	0.07888	-1.0749	10	0.87932	D	0	-33.0089	19.9678	0.97275	0.0:0.0:1.0:0.0	rs45518035	10;10;31;31;31	Q86YN6-2;Q86YN6-4;Q86YN6-5;Q86YN6;Q86YN6-3	.;.;.;PRGC2_HUMAN;.	R	31;31;31;6	ENSP00000353638:G31R;ENSP00000377855:G31R;ENSP00000312649:G31R;ENSP00000384403:G6R	ENSP00000312649:G31R	G	+	1	0	PPARGC1B	149180201	1.000000	0.71417	0.930000	0.37139	0.301000	0.27625	7.339000	0.79282	2.724000	0.93272	0.651000	0.88453	GGG	G|0.994;A|0.006	0.006	strong		0.572	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263		A	149200008	G	A	149200008	3	1	22	1	0	0	0	0	1	0	0	0	12310	1116	39	1	104	1	PPARGC1B	5	149200008	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1354545	149200008	31715252	1321	4222											
PDE6A	5145	hgsc.bcm.edu	37	chr5	149323781	149323781	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acctcctctgtgttggggacGttagcaatcttcttagagtg	7	14	11	9	1	3	1	0	0	3	1	4	2	4	2	2	2	1	3	2	2	3	4	rs149256612	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149323781G>A	ENST00000255266.5	-	1	575	c.456C>T	c.(454-456)aaC>aaT	p.N152N		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	152	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)	TGTTGGGGACGTTAGCAATCT	0.562																																					p.N152N		Atlas-SNP	.											.	PDE6A	98	.	0			c.C456T						PASS	.	G		3,4403	6.2+/-15.9	0,3,2200	160	137	144		456	2.4	1	5	dbSNP_134	144	0,8600		0,0,4300	no	coding-synonymous	PDE6A	NM_000440.2		0,3,6500	AA,AG,GG		0.0,0.0681,0.0231		152/861	149323781	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	5145	exon1			GGGGACGTTAGCA		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.456C>T	5.37:g.149323781G>A		67	0	0		66	24	0.363636	NM_000440	Q0P638	Silent	SNP	ENST00000255266.5	37	CCDS4299.1																																																																																			G|1.000;A|0.000	0.000	strong		0.562	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2			A	149323781	G	A	149323781	2	1	22	1	0	0	0	0	0	0	0	1	11654	1136	40	1		1	PDE6A	5	149323781	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	123773	149323781	31591479	1322	4223											
PDE6A	5145	hgsc.bcm.edu	37	chr5	149324153	149324153	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tcggagatgagcttggcccgGtagtggaggttgtagtactg	7	11	17	6	2	0	2	0	1	0	1	1	4	0	3	1	5	2	5	1	5	3	5	rs34230349	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149324153G>A	ENST00000255266.5	-	1	203	c.84C>T	c.(82-84)taC>taT	p.Y28Y		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	28					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)	GCTTGGCCCGGTAGTGGAGGT	0.572													G|||	84	0.0167732	0.0461	0.0058	5008	,	,		18582	0.0099		0.0	False		,,,				2504	0.0092				p.Y28Y		Atlas-SNP	.											.	PDE6A	98	.	0			c.C84T						PASS	.	G		199,4207	124.5+/-161.8	2,195,2006	48	43	45		84	2	1	5	dbSNP_126	45	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PDE6A	NM_000440.2		2,196,6305	AA,AG,GG		0.0116,4.5166,1.5378		28/861	149324153	200,12806	2203	4300	6503	SO:0001819	synonymous_variant	5145	exon1			GGCCCGGTAGTGG		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.84C>T	5.37:g.149324153G>A		97	0	0		75	34	0.453333	NM_000440	Q0P638	Silent	SNP	ENST00000255266.5	37	CCDS4299.1																																																																																			G|0.984;A|0.016	0.016	strong		0.572	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2			A	149324153	G	A	149324153	2	1	22	1	0	0	0	0	0	0	0	1	11654	1256	44	2		2	PDE6A	5	149324153	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	372	149324153	31591107	1323	4224											
TIGD6	81789	hgsc.bcm.edu	37	chr5	149375721	149375721	+	Frame_Shift_Del	DEL	C	C	-																															tcatccttttccgctggggtCccacggatgcctcccgcacc																								rs33910807|rs575130996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149375721delC	ENST00000296736.3	-	2	965	c.191delG	c.(190-192)ggafs	p.G64fs	TIGD6_ENST00000515406.2_Frame_Shift_Del_p.G64fs	NM_030953.3	NP_112215.1	Q17RP2	TIGD6_HUMAN	tigger transposable element derived 6	64						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)			CCGCTGGGGTCCCACGGATGC	0.433													CCC|CCC|CC|deletion	476	0.0950479	0.3449	0.0231	5008	,	,		21862	0.0		0.004	False		,,,				2504	0.0				p.G64fs		Pindel,Atlas-Indel	.											.	TIGD6	29	.	0			c.192delA						PASS	.			1204,3060		171,862,1099	71	98	89			-2.9	0.2	5	dbSNP_126	99	16,8222		2,12,4105	yes	frameshift	TIGD6	NM_030953.3		173,874,5204	A1A1,A1R,RR		0.1942,28.2364,9.7584			149375721	1220,11282	2188	4300	6488	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.191delG	5.37:g.149375721delC	ENSP00000296736:p.Gly64fs	66	0	.		82	32	0.39	NM_030953	B3KTZ8|Q96MQ4|Q9H0X7	Frame_Shift_Del	DEL	ENST00000296736.3	37	CCDS4301.1																																																																																			C|0.913;-|0.087	0.087	strong		0.433	TIGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252324.1	NM_030953		-	149375721	C	-	149375721	7	5	22	1	0	1	0	1	0	0	0	0	15915	855	30	0	1378	0	TIGD6	5	149375721	Frame_Shift_Del	DEL	C	TCGA-G8-6324-01A-11D-2210-10	51568	149375721	31539539	1324	4225											
CSF1R	1436	hgsc.bcm.edu	37	chr5	149460544	149460544	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	accgttgctcctggcttcacGaccagctcagggacactggg	7	8	12	14	2	2	0	2	0	0	0	3	2	3	1	3	3	2	4	3	3	0	2	rs41424646		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149460544G>A	ENST00000286301.3	-	3	384	c.93C>T	c.(91-93)gtC>gtT	p.V31V	CSF1R_ENST00000543093.1_Silent_p.V31V	NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	31	Ig-like C2-type 1.				cell proliferation (GO:0008283)|cell-cell junction maintenance (GO:0045217)|cellular response to cytokine stimulus (GO:0071345)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cytokine-mediated signaling pathway (GO:0019221)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary gland duct morphogenesis (GO:0060603)|monocyte differentiation (GO:0030224)|multicellular organismal development (GO:0007275)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of bone resorption (GO:0045124)|regulation of cell shape (GO:0008360)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|macrophage colony-stimulating factor receptor activity (GO:0005011)|protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(38)|kidney(2)|large_intestine(6)|liver(3)|lung(23)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	93			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	CTGGCTTCACGACCAGCTCAG	0.607																																					p.V31V		Atlas-SNP	.											CSF1R_ENST00000286301,caecum,carcinoma,-1,2	CSF1R	250	2	0			c.C93T						scavenged	.	G		6,4400	11.4+/-27.6	0,6,2197	98	69	78		93	-11.5	0.1	5	dbSNP_127	78	0,8600		0,0,4300	no	coding-synonymous	CSF1R	NM_005211.3		0,6,6497	AA,AG,GG		0.0,0.1362,0.0461		31/973	149460544	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	1436	exon3			CTTCACGACCAGC	U63963	CCDS4302.1	5q32	2013-01-11	2008-08-01		ENSG00000182578	ENSG00000182578		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	2433	protein-coding gene	gene with protein product		164770	"McDonough feline sarcoma viral (v-fms) oncogene homolog"	FMS		1611909	Standard	NM_005211		Approved	C-FMS, CSFR, CD115	uc003lrm.3	P07333	OTTHUMG00000130050	ENST00000286301.3:c.93C>T	5.37:g.149460544G>A		136	1	0.00735294		186	94	0.505376	NM_005211	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Silent	SNP	ENST00000286301.3	37	CCDS4302.1																																																																																			T|0.000;G|0.999;A|0.001	0.001	strong		0.607	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2	NM_005211		A	149460544	G	A	149460544	2	1	22	1	0	0	0	0	0	0	0	1	3934	1045	37	1		1	CSF1R	5	149460544	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	84823	149460544	31454716	1325	4226											
PDGFRB	5159	hgsc.bcm.edu	37	chr5	149509508	149509508	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggaactgttccccagcagcGtgggcggcagctcacgtgga	7	6	15	13	4	1	0	1	0	0	0	2	2	2	2	2	4	4	4	2	4	1	1	rs74943037	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149509508G>A	ENST00000261799.4	-	10	1860	c.1391C>T	c.(1390-1392)aCg>aTg	p.T464M		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	464	Ig-like C2-type 5.				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)	p.T464M(1)		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)	CCCCAGCAGCGTGGGCGGCAG	0.612			T	"ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"	"MPD, AML, CMML, CML"						OREG0016927	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	138	0.0275559	0.0953	0.0115	5008	,	,		20674	0.001		0.003	False		,,,				2504	0.0				p.T464M		Atlas-SNP	.		Dom	yes		5	5q31-q32	5159	"platelet-derived growth factor receptor, beta polypeptide"		L	PDGFRB,NS,carcinoma,0,1	PDGFRB	142	1	1	Substitution - Missense(1)	stomach(1)	c.C1391T						scavenged	.	G	MET/THR	393,4013	195.3+/-220.0	26,341,1836	102	74	84		1391	3.8	0.8	5	dbSNP_131	84	3,8597	3.0+/-9.4	0,3,4297	yes	missense	PDGFRB	NM_002609.3	81	26,344,6133	AA,AG,GG		0.0349,8.9197,3.0447	probably-damaging	464/1107	149509508	396,12610	2203	4300	6503	SO:0001583	missense	5159	exon10			AGCAGCGTGGGCG	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.1391C>T	5.37:g.149509508G>A	ENSP00000261799:p.Thr464Met	100	1	0.01	1725	133	58	0.43609	NM_002609	B5A957|Q8N5L4	Missense_Mutation	SNP	ENST00000261799.4	37	CCDS4303.1	56	0.02564102564102564	51	0.10365853658536585	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	6.709	0.499568	0.12762	0.089197	3.49E-4	ENSG00000113721	ENST00000261799;ENST00000544453	T	0.76316	-1.01	4.64	3.76	0.43208	.	0.276731	0.27821	N	0.017704	T	0.06462	0.0166	L	0.59436	1.845	0.27164	N	0.961099	P;B	0.45634	0.863;0.122	B;B	0.39531	0.302;0.022	T	0.04140	-1.0974	10	0.33940	T	0.23	.	12.9704	0.58510	0.0865:0.0:0.9135:0.0	.	464;464	A8KAM8;P09619	.;PGFRB_HUMAN	M	464;134	ENSP00000261799:T464M	ENSP00000261799:T464M	T	-	2	0	PDGFRB	149489701	0.297000	0.24408	0.838000	0.33150	0.007000	0.05969	0.467000	0.22035	0.583000	0.29574	-1.598000	0.00824	ACG	G|0.972;A|0.028	0.028	strong		0.612	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609		A	149509508	G	A	149509508	3	1	22	1	0	0	0	0	1	0	0	0	11671	1145	40	1	1985	1	PDGFRB	5	149509508	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	48964	149509508	31405752	1326	4227											
CDX1	1044	hgsc.bcm.edu	37	chr5	149562398	149562398	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caacgcctggagctggagaaGgagtttcattacagccgtta	11	9	12	9	2	1	1	1	0	0	1	1	4	1	3	2	3	4	3	2	3	4	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149562398G>T	ENST00000231656.8	+	2	595	c.513G>T	c.(511-513)aaG>aaT	p.K171N		NM_001804.2	NP_001795.2	P47902	CDX1_HUMAN	caudal type homeobox 1	171					anterior/posterior pattern specification (GO:0009952)|bone morphogenesis (GO:0060349)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	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)			central_nervous_system(1)|kidney(2)|lung(1)|ovary(1)	5		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGCTGGAGAAGGAGTTTCATT	0.552																																					p.K171N		Atlas-SNP	.											.	CDX1	11	.	0			c.G513T						PASS	.						139	140	140					5																	149562398		2203	4300	6503	SO:0001583	missense	1044	exon2			GGAGAAGGAGTTT	U51095	CCDS4304.1	5q32	2012-03-09	2007-07-09		ENSG00000113722	ENSG00000113722		"Homeoboxes / ANTP class : HOXL subclass"	1805	protein-coding gene	gene with protein product		600746	"caudal type homeo box transcription factor 1"			8530027	Standard	NM_001804		Approved		uc003lrq.3	P47902	OTTHUMG00000169772	ENST00000231656.8:c.513G>T	5.37:g.149562398G>T	ENSP00000231656:p.Lys171Asn	124	0	0		160	71	0.44375	NM_001804	Q4VAU4|Q9NYK8	Missense_Mutation	SNP	ENST00000231656.8	37	CCDS4304.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.156375	0.78114	.	.	ENSG00000113722	ENST00000231656;ENST00000377812	D	0.96491	-4.03	5.87	3.03	0.35002	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.110690	0.64402	D	0.000012	D	0.97170	0.9075	M	0.65677	2.01	0.80722	D	1	D	0.56287	0.975	D	0.67900	0.954	D	0.96399	0.9295	10	0.87932	D	0	-13.0587	11.532	0.50616	0.1832:0.0:0.8168:0.0	.	171	P47902	CDX1_HUMAN	N	171;60	ENSP00000231656:K171N	ENSP00000231656:K171N	K	+	3	2	CDX1	149542591	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.447000	0.52936	0.342000	0.23796	-0.345000	0.07892	AAG	.	.	none		0.552	CDX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252328.7	NM_001804		T	149562398	G	T	149562398	3	4	22	1	0	0	0	0	1	0	0	0	3184	991	35	4	519	4	CDX1	5	149562398	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	52890	149562398	31352862	1327	4228											
TCOF1	6949	hgsc.bcm.edu	37	chr5	149755845	149755845	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gattcttcaagcagtgaggaAtcagatagtgaggaagagaa	16	8	13	4	0	3	4	2	2	1	2	3	8	3	6	0	2	1	1	0	2	5	3	rs34796297	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149755845A>G	ENST00000504761.2	+	13	2094	c.2094A>G	c.(2092-2094)gaA>gaG	p.E698E	TCOF1_ENST00000323668.7_Silent_p.E621E|TCOF1_ENST00000439160.2_Silent_p.E698E|TCOF1_ENST00000513346.1_Silent_p.E698E|TCOF1_ENST00000445265.2_Silent_p.E621E|TCOF1_ENST00000451292.1_Silent_p.E698E|TCOF1_ENST00000377797.3_Silent_p.E698E|TCOF1_ENST00000394269.3_Silent_p.E698E			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	698					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)			GCAGTGAGGAATCAGATAGTG	0.602													A|||	111	0.0221645	0.0787	0.0086	5008	,	,		18022	0.0		0.001	False		,,,				2504	0.0				p.E698E		Atlas-SNP	.											.	TCOF1	154	.	0			c.A2094G						PASS	.	A	,,,,,	268,4128		13,242,1943	119	142	134		1863,2094,2094,2094,1863,2094	1.1	0.3	5	dbSNP_126	134	0,8590		0,0,4295	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TCOF1	NM_000356.3,NM_001008657.2,NM_001135243.1,NM_001135244.1,NM_001135245.1,NM_001195141.1	,,,,,	13,242,6238	GG,GA,AA		0.0,6.0965,2.0638	,,,,,	621/1412,698/959,698/1489,698/1452,621/1413,698/1451	149755845	268,12718	2198	4295	6493	SO:0001819	synonymous_variant	6949	exon13			TGAGGAATCAGAT		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.2094A>G	5.37:g.149755845A>G		42	0	0		54	23	0.425926	NM_001135243	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Silent	SNP	ENST00000504761.2	37	CCDS54936.1																																																																																			A|0.984;G|0.016	0.016	strong		0.602	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656		G	149755845	A	G	149755845	2	3	22	1	0	0	0	0	0	0	0	1	15723	98	4	3		3	TCOF1	5	149755845	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	193447	149755845	31159415	1328	4229											
TCOF1	6949	hgsc.bcm.edu	37	chr5	149759201	149759201	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcctgggaagacagggccttCggctgcccaggcagggaagc	8	5	16	12	1	0	1	0	0	0	1	2	3	1	3	3	5	2	2	3	5	2	1	rs114689020	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149759201C>T	ENST00000504761.2	+	17	2765	c.2765C>T	c.(2764-2766)tCg>tTg	p.S922L	TCOF1_ENST00000323668.7_Missense_Mutation_p.S845L|TCOF1_ENST00000439160.2_Missense_Mutation_p.S922L|TCOF1_ENST00000513346.1_Missense_Mutation_p.S922L|TCOF1_ENST00000445265.2_Missense_Mutation_p.S845L|TCOF1_ENST00000451292.1_Missense_Mutation_p.S922L|TCOF1_ENST00000506063.1_3'UTR|TCOF1_ENST00000377797.3_Missense_Mutation_p.S922L|TCOF1_ENST00000394269.3_Missense_Mutation_p.S922L			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	922					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)			ACAGGGCCTTCGGCTGCCCAG	0.632													C|||	114	0.0227636	0.0787	0.0101	5008	,	,		19801	0.0		0.003	False		,,,				2504	0.0				p.S922L		Atlas-SNP	.											.	TCOF1	154	.	0			c.C2765T						PASS	.	C	LEU/SER,LEU/SER,LEU/SER,LEU/SER,LEU/SER,LEU/SER	281,4125	157.4+/-190.3	14,253,1936	54	60	58		2534,2765,2765,2765,2534,2765	0.4	0	5	dbSNP_132	58	11,8589	8.4+/-32.0	0,11,4289	yes	missense,missense,missense,missense,missense,missense	TCOF1	NM_000356.3,NM_001008657.2,NM_001135243.1,NM_001135244.1,NM_001135245.1,NM_001195141.1	145,145,145,145,145,145	14,264,6225	TT,TC,CC		0.1279,6.3777,2.2451	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	845/1412,922/959,922/1489,922/1452,845/1413,922/1451	149759201	292,12714	2203	4300	6503	SO:0001583	missense	6949	exon17			GGCCTTCGGCTGC		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.2765C>T	5.37:g.149759201C>T	ENSP00000421655:p.Ser922Leu	170	0	0		142	75	0.528169	NM_001135243	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Missense_Mutation	SNP	ENST00000504761.2	37	CCDS54936.1	43	0.019688644688644688	39	0.07926829268292683	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	13.10	2.136775	0.37728	0.063777	0.001279	ENSG00000070814	ENST00000451292;ENST00000377797;ENST00000445265;ENST00000323668;ENST00000439160;ENST00000394269;ENST00000427724;ENST00000504761;ENST00000513346	T;T;T;T;T;T;T;T;T	0.74947	-0.01;-0.01;-0.01;-0.01;-0.02;-0.01;-0.89;-0.01;-0.87	5.63	0.389	0.16269	Treacher Collins syndrome, treacle (1);	1.572510	0.03797	N	0.263889	T	0.05823	0.0152	N	0.11560	0.145	0.09310	N	1	B;B;B;B;B;B;B	0.06786	0.0;0.001;0.001;0.001;0.001;0.001;0.001	B;B;B;B;B;B;B	0.04013	0.0;0.001;0.001;0.001;0.001;0.001;0.001	T	0.25293	-1.0136	10	0.66056	D	0.02	1.7592	4.6859	0.12757	0.1423:0.5093:0.0:0.3484	.	431;922;845;922;922;845;922	B4DRA2;Q13428-7;Q13428-2;Q13428-6;Q13428;Q13428-8;Q13428-5	.;.;.;.;TCOF_HUMAN;.;.	L	922;922;845;845;922;922;922;922;922	ENSP00000400939:S922L;ENSP00000367028:S922L;ENSP00000409944:S845L;ENSP00000325223:S845L;ENSP00000406888:S922L;ENSP00000377811:S922L;ENSP00000390717:S922L;ENSP00000421655:S922L;ENSP00000427484:S922L	ENSP00000325223:S845L	S	+	2	0	TCOF1	149739394	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.568000	0.05909	0.103000	0.17682	-0.254000	0.11334	TCG	C|0.979;T|0.021	0.021	strong		0.632	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656		T	149759201	C	T	149759201	3	4	22	1	0	0	0	0	1	0	0	0	15723	893	31	1	2831	1	TCOF1	5	149759201	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3356	149759201	31156059	1329	4230											
FAT2	2196	hgsc.bcm.edu	37	chr5	150946444	150946444	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgaagcccaataaagtggagGatagtctttgtgaattgtgt	12	13	12	4	0	1	2	0	2	1	0	1	4	1	4	1	2	1	0	1	2	6	4	rs142348925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:150946444G>A	ENST00000261800.5	-	1	2061	c.2049C>T	c.(2047-2049)atC>atT	p.I683I		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	683					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)			TAAAGTGGAGGATAGTCTTTG	0.408													G|||	2	0.000399361	0.0015	0.0	5008	,	,		22771	0.0		0.0	False		,,,				2504	0.0				p.I683I		Atlas-SNP	.											.	FAT2	465	.	0			c.C2049T						PASS	.	G		6,4400	11.4+/-27.6	0,6,2197	117	110	112		2049	2.8	1	5	dbSNP_134	112	0,8600		0,0,4300	no	coding-synonymous	FAT2	NM_001447.2		0,6,6497	AA,AG,GG		0.0,0.1362,0.0461		683/4350	150946444	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon1			GTGGAGGATAGTC	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.2049C>T	5.37:g.150946444G>A		132	0	0		220	98	0.445455	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																			G|0.999;A|0.001	0.001	strong		0.408	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		A	150946444	G	A	150946444	2	1	22	1	0	0	0	0	0	0	0	1	5698	1164	41	2		2	FAT2	5	150946444	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1187243	150946444	29968816	1330	4231											
GLRA1	2741	hgsc.bcm.edu	37	chr5	151231140	151231140	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	atctgccgctccaggtggaaCcgggcctcaatgcaggtgaa	9	7	13	12	2	2	1	1	1	1	0	3	2	3	2	4	4	3	2	4	4	3	0	rs76872663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:151231140C>G	ENST00000455880.2	-	7	1009	c.723G>C	c.(721-723)cgG>cgC	p.R241R	GLRA1_ENST00000274576.4_Silent_p.R241R|GLRA1_ENST00000471351.2_5'UTR|GLRA1_ENST00000545569.1_Silent_p.R158R			P23415	GLRA1_HUMAN	glycine receptor, alpha 1	241					acrosome reaction (GO:0007340)|action potential (GO:0001508)|adult walking behavior (GO:0007628)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|muscle contraction (GO:0006936)|negative regulation of transmission of nerve impulse (GO:0051970)|neuromuscular process controlling posture (GO:0050884)|neuropeptide signaling pathway (GO:0007218)|positive regulation of acrosome reaction (GO:2000344)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|righting reflex (GO:0060013)|startle response (GO:0001964)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|external side of plasma membrane (GO:0009897)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|glycine binding (GO:0016594)|taurine binding (GO:0030977)|transmitter-gated ion channel activity (GO:0022824)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	23		all_hematologic(541;0.0341)|Medulloblastoma(196;0.0912)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Ethanol(DB00898)|Ginkgo biloba(DB01381)|Glycine(DB00145)|Halothane(DB01159)|Isoflurane(DB00753)|Lindane(DB00431)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	CCAGGTGGAACCGGGCCTCAA	0.483													C|||	25	0.00499201	0.0189	0.0	5008	,	,		22610	0.0		0.0	False		,,,				2504	0.0				p.R241R		Atlas-SNP	.											GLRA1,NS,carcinoma,-2,1	GLRA1	61	1	0			c.G723C						PASS	.	C	,	68,4338	60.5+/-97.4	0,68,2135	92	89	90		723,723	-1	1	5	dbSNP_132	90	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	GLRA1	NM_000171.3,NM_001146040.1	,	0,68,6435	GG,GC,CC		0.0,1.5433,0.5228	,	241/450,241/458	151231140	68,12938	2203	4300	6503	SO:0001819	synonymous_variant	2741	exon7			GTGGAACCGGGCC		CCDS4320.1, CCDS54942.1	5q33.1	2012-02-07	2008-01-24		ENSG00000145888	ENSG00000145888		"Ligand-gated ion channels / Glycine receptors"	4326	protein-coding gene	gene with protein product	"startle disease/hyperekplexia", "stiff person syndrome"	138491	"glycine receptor, alpha 1 (startle disease/hyperekplexia)"	STHE		1355335, 8298642	Standard	NM_000171		Approved		uc003lut.3	P23415	OTTHUMG00000130121	ENST00000455880.2:c.723G>C	5.37:g.151231140C>G		109	0	0		145	76	0.524138	NM_000171	B2R6T3|Q14C77|Q6DJV9	Silent	SNP	ENST00000455880.2	37	CCDS54942.1																																																																																			C|0.994;G|0.006	0.006	strong		0.483	GLRA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373959.1			G	151231140	C	G	151231140	2	3	22	1	0	0	0	0	0	0	0	1	6462	494	18	4		4	GLRA1	5	151231140	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	284696	151231140	29684120	1331	4232											
GALNT10	55568	hgsc.bcm.edu	37	chr5	153792453	153792453	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cctctttccctttcagatccGaaatgtgggcacagggctgt	7	12	10	12	1	2	1	1	0	1	1	4	2	4	1	3	2	0	2	3	2	1	2	rs142635658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:153792453G>A	ENST00000297107.6	+	10	1528	c.1391G>A	c.(1390-1392)cGa>cAa	p.R464Q	GALNT10_ENST00000377657.3_Missense_Mutation_p.R137Q|SAP30L-AS1_ENST00000519727.1_RNA|GALNT10_ENST00000377661.2_Missense_Mutation_p.R402Q|SAP30L-AS1_ENST00000524264.1_RNA	NM_198321.3	NP_938080.1	Q86SR1	GLT10_HUMAN	polypeptide N-acetylgalactosaminyltransferase 10	464	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)			TTTCAGATCCGAAATGTGGGC	0.612													G|||	14	0.00279553	0.0106	0.0	5008	,	,		18983	0.0		0.0	False		,,,				2504	0.0				p.R464Q		Atlas-SNP	.											.	GALNT10	70	.	0			c.G1391A						PASS	.	G	GLN/ARG	41,4365	44.6+/-78.6	0,41,2162	85	84	85		1391	3.8	0.4	5	dbSNP_134	85	0,8600		0,0,4300	yes	missense	GALNT10	NM_198321.3	43	0,41,6462	AA,AG,GG		0.0,0.9305,0.3152	benign	464/604	153792453	41,12965	2203	4300	6503	SO:0001583	missense	55568	exon10			AGATCCGAAATGT	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.1391G>A	5.37:g.153792453G>A	ENSP00000297107:p.Arg464Gln	41	0	0		31	17	0.548387	NM_198321	B3KXC9|Q6IN56|Q86VP8|Q8IXJ2|Q8TEJ2|Q96IV2|Q9H8E1|Q9Y4M4	Missense_Mutation	SNP	ENST00000297107.6	37	CCDS4325.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	12.24	1.879954	0.33162	0.009305	0.0	ENSG00000164574	ENST00000297107;ENST00000377661;ENST00000377657	T;T;T	0.28666	1.6;1.6;1.6	5.56	3.77	0.43336	Ricin B-related lectin (1);Ricin B lectin (2);	0.091610	0.85682	D	0.000000	T	0.17492	0.0420	L	0.49256	1.55	0.48571	D	0.99967	B;B;B	0.31752	0.054;0.338;0.04	B;B;B	0.22152	0.013;0.038;0.005	T	0.02736	-1.1117	10	0.26408	T	0.33	.	10.6774	0.45794	0.2076:0.0:0.7924:0.0	.	402;135;464	Q86SR1-2;D6R8Y1;Q86SR1	.;.;GLT10_HUMAN	Q	464;402;137	ENSP00000297107:R464Q;ENSP00000366889:R402Q;ENSP00000366885:R137Q	ENSP00000297107:R464Q	R	+	2	0	GALNT10	153772646	1.000000	0.71417	0.392000	0.26245	0.899000	0.52679	2.936000	0.48971	0.706000	0.31912	0.655000	0.94253	CGA	G|0.997;A|0.003	0.003	strong		0.612	GALNT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252453.1	NM_198321		A	153792453	G	A	153792453	3	1	22	1	0	0	0	0	1	0	0	0	6216	1058	37	1	1429	1	GALNT10	5	153792453	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2561313	153792453	27122807	1332	4233											
SGCD	6444	hgsc.bcm.edu	37	chr5	156184786	156184786	+	Intron	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aacccttcccataactggttGacctcggagttggatcctac	9	11	8	13	1	0	1	0	1	0	0	3	3	2	3	4	3	3	2	4	3	3	5	rs187204080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:156184786G>A	ENST00000435422.3	+	7	1183				SGCD_ENST00000447401.1_Silent_p.*257*|SGCD_ENST00000517913.1_Silent_p.*257*|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)			ATAACTGGTTGACCTCGGAGT	0.448													G|||	14	0.00279553	0.0106	0.0	5008	,	,		17960	0.0		0.0	False		,,,				2504	0.0				p.X257X		Atlas-SNP	.											.	SGCD	52	.	0			c.G770A						PASS	.	G	,,	33,3799		0,33,1883	64	63	63		,,770	0	0	5		63	0,8268		0,0,4134	no	intron,intron,coding-synonymous	SGCD	NM_000337.5,NM_001128209.1,NM_172244.2	,,	0,33,6017	AA,AG,GG		0.0,0.8612,0.2727	,,	,,257/257	156184786	33,12067	1916	4134	6050	SO:0001627	intron_variant	6444	exon8			CTGGTTGACCTCG	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+71G>A	5.37:g.156184786G>A		201	0	0		217	98	0.451613	NM_172244	A8K9S9|Q53XA5|Q99644	Silent	SNP	ENST00000435422.3	37	CCDS47327.1																																																																																			G|0.998;A|0.002	0.002	strong		0.448	SGCD-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000373469.3			A	156184786	G	A	156184786	1	1	22	0	1	0	0	0	0	0	0	0	14216	1285	45	2		2	SGCD	5	156184786	Intron	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2392333	156184786	24730474	1333	4234											
MED7	9443	hgsc.bcm.edu	37	chr5	156565839	156565839	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgaattttctctttgatgttCattctgtccagtacaattgt	8	20	6	7	0	3	2	1	2	2	0	5	2	4	2	1	0	1	2	1	0	3	7	rs151231455	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:156565839C>T	ENST00000286317.5	-	2	985	c.604G>A	c.(604-606)Gaa>Aaa	p.E202K	MED7_ENST00000420343.1_Missense_Mutation_p.E202K	NM_004270.4	NP_004261.1	O43513	MED7_HUMAN	mediator complex subunit 7	202					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)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II transcription cofactor activity (GO:0001104)|transcription coactivator activity (GO:0003713)			kidney(1)|large_intestine(1)|lung(3)|urinary_tract(2)	7	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CTTTGATGTTCATTCTGTCCA	0.388													C|||	37	0.00738818	0.0272	0.0014	5008	,	,		20059	0.0		0.0	False		,,,				2504	0.0				p.E202K		Atlas-SNP	.											.	MED7	18	.	0			c.G604A						PASS	.	C	LYS/GLU,LYS/GLU	127,4279	93.0+/-131.7	4,119,2080	178	165	170		604,604	4	1	5	dbSNP_134	170	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	MED7	NM_001100816.1,NM_004270.4	56,56	4,120,6379	TT,TC,CC		0.0116,2.8824,0.9842	benign,benign	202/234,202/234	156565839	128,12878	2203	4300	6503	SO:0001583	missense	9443	exon2			GATGTTCATTCTG	AF104251	CCDS4334.1	5q33.3	2008-02-05	2007-07-30	2007-07-30	ENSG00000155868	ENSG00000155868			2378	protein-coding gene	gene with protein product		605045	"cofactor required for Sp1 transcriptional activation, subunit 9, 33kDa"	CRSP9		9989412	Standard	NM_004270		Approved	CRSP33	uc003lwm.4	O43513	OTTHUMG00000130243	ENST00000286317.5:c.604G>A	5.37:g.156565839C>T	ENSP00000286317:p.Glu202Lys	348	1	0.00287356		319	149	0.467085	NM_001100816		Missense_Mutation	SNP	ENST00000286317.5	37	CCDS4334.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	C	8.966	0.971874	0.18736	0.028824	1.16E-4	ENSG00000155868	ENST00000286317;ENST00000420343	.	.	.	5.81	4.04	0.47022	.	0.530450	0.21352	N	0.075941	T	0.19005	0.0456	N	0.25647	0.755	0.35254	D	0.778968	B	0.06786	0.001	B	0.04013	0.001	T	0.29397	-1.0013	9	0.18710	T	0.47	-16.0444	11.7459	0.51819	0.0:0.8027:0.1305:0.0668	.	202	O43513	MED7_HUMAN	K	202	.	ENSP00000286317:E202K	E	-	1	0	MED7	156498417	0.986000	0.35501	0.999000	0.59377	0.951000	0.60555	1.750000	0.38329	0.791000	0.33826	-0.137000	0.14449	GAA	C|0.991;T|0.009	0.009	strong		0.388	MED7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252567.2	NM_004270		T	156565839	C	T	156565839	3	4	22	1	0	0	0	0	1	0	0	0	9461	835	29	2	101	2	MED7	5	156565839	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	381053	156565839	24349421	1334	4235											
FAM71B	153745	hgsc.bcm.edu	37	chr5	156589937	156589937	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgactttcacctgccttgcGgtgatgagaacttttcctac	7	14	9	11	1	1	3	1	3	0	1	2	4	2	3	3	1	4	0	3	1	2	5	rs115938677	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:156589937G>A	ENST00000302938.4	-	2	1434	c.1339C>T	c.(1339-1341)Cgc>Tgc	p.R447C		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	447						nucleus (GO:0005634)		p.R447G(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)			CCTGCCTTGCGGTGATGAGAA	0.498													G|||	32	0.00638978	0.0182	0.0014	5008	,	,		20598	0.0		0.0	False		,,,				2504	0.0072				p.R447C		Atlas-SNP	.											FAM71B,NS,carcinoma,0,1	FAM71B	145	1	1	Substitution - Missense(1)	lung(1)	c.C1339T						PASS	.	G	CYS/ARG	87,4319	72.5+/-110.5	2,83,2118	171	162	165		1339	3.8	0.6	5	dbSNP_132	165	1,8599	1.2+/-3.3	0,1,4299	yes	missense	FAM71B	NM_130899.2	180	2,84,6417	AA,AG,GG		0.0116,1.9746,0.6766	probably-damaging	447/606	156589937	88,12918	2203	4300	6503	SO:0001583	missense	153745	exon2			CCTTGCGGTGATG		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.1339C>T	5.37:g.156589937G>A	ENSP00000305596:p.Arg447Cys	78	0	0		64	24	0.375	NM_130899	Q1EDD9|Q8TC64|Q96LY8	Missense_Mutation	SNP	ENST00000302938.4	37	CCDS4335.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	16.74	3.208131	0.58343	0.019746	1.16E-4	ENSG00000170613	ENST00000302938	T	0.19394	2.15	4.64	3.76	0.43208	.	1.354870	0.05270	N	0.517312	T	0.21387	0.0515	M	0.65498	2.005	0.37788	D	0.927243	D	0.69078	0.997	P	0.50490	0.642	T	0.08743	-1.0707	10	0.87932	D	0	-0.0752	10.7971	0.46466	0.0:0.0:0.8103:0.1897	.	447	Q8TC56	FA71B_HUMAN	C	447	ENSP00000305596:R447C	ENSP00000305596:R447C	R	-	1	0	FAM71B	156522515	0.960000	0.32886	0.566000	0.28421	0.204000	0.24138	1.831000	0.39141	1.241000	0.43820	0.655000	0.94253	CGC	G|0.995;A|0.005	0.005	strong		0.498	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899		A	156589937	G	A	156589937	3	1	22	1	0	0	0	0	1	0	0	0	5616	1116	39	1	482	1	FAM71B	5	156589937	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	24098	156589937	24325323	1335	4236											
CYFIP2	26999	hgsc.bcm.edu	37	chr5	156742033	156742033	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcaacaaggactgtcctggCaccgcggaggaatatgagag	12	6	14	9	2	0	1	0	1	0	1	1	5	1	4	2	4	2	2	2	4	4	1	rs17054446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:156742033C>T	ENST00000521420.1	+	12	1300	c.1209C>T	c.(1207-1209)ggC>ggT	p.G403G	CYFIP2_ENST00000541131.1_Silent_p.G354G|CYFIP2_ENST00000377576.3_Silent_p.G429G|CYFIP2_ENST00000522463.1_Silent_p.G233G|CYFIP2_ENST00000435847.2_Silent_p.G103G|CYFIP2_ENST00000347377.6_Silent_p.G429G|CYFIP2_ENST00000318218.6_Silent_p.G429G|CYFIP2_ENST00000442283.2_5'UTR					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)			ACTGTCCTGGCACCGCGGAGG	0.512													C|||	33	0.00658946	0.0234	0.0029	5008	,	,		19474	0.0		0.0	False		,,,				2504	0.0				p.G429G		Atlas-SNP	.											.	CYFIP2	354	.	0			c.C1287T						PASS	.	C	,,	65,4037		0,65,1986	64	64	64		1287,1287,1287	4.6	1	5	dbSNP_123	64	0,8400		0,0,4200	no	coding-synonymous,coding-synonymous,coding-synonymous	CYFIP2	NM_001037332.2,NM_001037333.1,NM_014376.2	,,	0,65,6186	TT,TC,CC		0.0,1.5846,0.5199	,,	429/1254,429/1254,429/1254	156742033	65,12437	2051	4200	6251	SO:0001819	synonymous_variant	26999	exon13			TCCTGGCACCGCG	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.1209C>T	5.37:g.156742033C>T		116	0	0		104	49	0.471154	NM_001037332		Silent	SNP	ENST00000521420.1	37																																																																																				C|0.993;T|0.007	0.007	strong		0.512	CYFIP2-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000373710.1	NM_001037332		T	156742033	C	T	156742033	2	4	22	1	0	0	0	0	0	0	0	1	4140	697	25	2		2	CYFIP2	5	156742033	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	152096	156742033	24173227	1336	4237											
ADAM19	8728	hgsc.bcm.edu	37	chr5	156964944	156964944	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	caatttccgtgtggtggtttGagggttaccacttgaagtat	8	15	12	6	1	0	2	0	2	0	0	1	2	1	2	2	3	1	3	2	3	4	5	rs11134804	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:156964944G>C	ENST00000517905.1	-	4	351	c.307C>G	c.(307-309)Caa>Gaa	p.Q103E	ADAM19_ENST00000430702.2_5'UTR|ADAM19_ENST00000257527.4_Missense_Mutation_p.Q103E|ADAM19_ENST00000394020.1_Missense_Mutation_p.Q105E			Q9H013	ADA19_HUMAN	ADAM metallopeptidase domain 19	103					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)			GTGGTGGTTTGAGGGTTACCA	0.443													G|||	136	0.0271565	0.0968	0.0086	5008	,	,		18034	0.0		0.0	False		,,,				2504	0.002				p.Q103E		Atlas-SNP	.											.	ADAM19	216	.	0			c.C307G						PASS	.	G	GLU/GLN	377,4029	191.9+/-217.4	13,351,1839	207	192	197		307	5.2	1	5	dbSNP_120	197	4,8596	3.0+/-9.4	0,4,4296	yes	missense	ADAM19	NM_033274.3	29	13,355,6135	CC,CG,GG		0.0465,8.5565,2.9294	benign	103/919	156964944	381,12625	2203	4300	6503	SO:0001583	missense	8728	exon4			TGGTTTGAGGGTT	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.307C>G	5.37:g.156964944G>C	ENSP00000428654:p.Gln103Glu	91	0	0		91	44	0.483516	NM_033274	Q9BZL5|Q9UHP2	Missense_Mutation	SNP	ENST00000517905.1	37		51	0.023351648351648352	47	0.09552845528455285	4	0.011049723756906077	0	0.0	0	0.0	G	14.59	2.579496	0.46006	0.085565	4.65E-4	ENSG00000135074	ENST00000257527;ENST00000394020;ENST00000517905	T;T;T	0.05199	3.48;3.48;3.48	5.17	5.17	0.71159	.	0.462253	0.20288	N	0.095302	T	0.00241	0.0007	L	0.41906	1.305	0.80722	D	1	B	0.23249	0.082	B	0.24394	0.053	T	0.39941	-0.9589	10	0.72032	D	0.01	.	14.5834	0.68308	0.0:0.0:1.0:0.0	rs11134804;rs56446321;rs11134804	103	Q9H013-2	.	E	103;105;103	ENSP00000257527:Q103E;ENSP00000377588:Q105E;ENSP00000428654:Q103E	ENSP00000257527:Q103E	Q	-	1	0	ADAM19	156897522	1.000000	0.71417	0.979000	0.43373	0.883000	0.51084	3.257000	0.51500	2.584000	0.87258	0.563000	0.77884	CAA	G|0.965;C|0.035	0.035	strong		0.443	ADAM19-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000373918.1	NM_033274		C	156964944	G	C	156964944	3	2	22	1	0	0	0	0	1	0	0	0	240	1299	45	4	2529	4	ADAM19	5	156964944	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	222911	156964944	23950316	1337	4238											
SOX30	11063	hgsc.bcm.edu	37	chr5	157053365	157053365	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaattataaatccctgagcaCtttttcttcttcctcctcat	10	17	2	12	0	3	1	1	1	2	0	6	1	6	1	3	0	1	1	3	0	4	6	rs889057	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:157053365C>T	ENST00000265007.6	-	5	2586	c.2245G>A	c.(2245-2247)Gtg>Atg	p.V749M	SOX30_ENST00000519442.1_Missense_Mutation_p.V444M|SOX30_ENST00000311371.5_3'UTR	NM_178424.1	NP_848511.1	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30	749			V -> M (in dbSNP:rs889057).		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)			TCCCTGAGCACTTTTTCTTCT	0.373													C|||	5	0.000998403	0.0038	0.0	5008	,	,		17935	0.0		0.0	False		,,,				2504	0.0				p.V749M	Esophageal Squamous(31;525 799 19355 21125 41744)	Atlas-SNP	.											.	SOX30	67	.	0			c.G2245A						PASS	.	C	,MET/VAL	17,4389	11.4+/-27.6	0,17,2186	57	61	60		,2245	5.4	1	5	dbSNP_86	60	0,8600		0,0,4300	yes	utr-3,missense	SOX30	NM_007017.2,NM_178424.1	,21	0,17,6486	TT,TC,CC		0.0,0.3858,0.1307	,probably-damaging	,749/754	157053365	17,12989	2203	4300	6503	SO:0001583	missense	11063	exon5			TGAGCACTTTTTC	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.2245G>A	5.37:g.157053365C>T	ENSP00000265007:p.Val749Met	97	0	0		78	38	0.487179	NM_178424	O94995|Q8IYX6	Missense_Mutation	SNP	ENST00000265007.6	37	CCDS4339.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	17.31	3.357836	0.61403	0.003858	0.0	ENSG00000039600	ENST00000265007;ENST00000519442	D;D	0.98567	-4.82;-5.0	5.44	5.44	0.79542	.	0.000000	0.52532	D	0.000071	D	0.97676	0.9238	L	0.27053	0.805	0.37021	D	0.89618	D;D	0.76494	0.998;0.999	D;D	0.68765	0.915;0.96	D	0.99894	1.1141	10	0.87932	D	0	.	14.3095	0.66407	0.1478:0.8522:0.0:0.0	rs889057;rs52805214;rs889057	444;749	B4DXW7;O94993	.;SOX30_HUMAN	M	749;444	ENSP00000265007:V749M;ENSP00000427984:V444M	ENSP00000265007:V749M	V	-	1	0	SOX30	156985943	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.502000	0.53332	2.712000	0.92718	0.650000	0.86243	GTG	C|0.998;T|0.002	0.002	strong		0.373	SOX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252571.2	NM_007017		T	157053365	C	T	157053365	3	4	22	1	0	0	0	0	1	0	0	0	14967	565	20	2	20	2	SOX30	5	157053365	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	88421	157053365	23861895	1338	4239											
RNF145	153830	hgsc.bcm.edu	37	chr5	158596032	158596032	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagcccagtctgcactgccaGgattaacagcgttactcctt	9	10	8	14	1	1	0	0	0	1	0	2	1	2	1	3	1	6	2	3	1	2	3	rs61732785	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:158596032G>A	ENST00000424310.2	-	8	1329	c.970C>T	c.(970-972)Ctg>Ttg	p.L324L	RNF145_ENST00000521606.2_Silent_p.L341L|RNF145_ENST00000519865.1_Silent_p.L324L|RNF145_ENST00000518802.1_Silent_p.L354L|RNF145_ENST00000520638.1_Silent_p.L338L|RNF145_ENST00000274542.2_Silent_p.L352L	NM_001199383.1	NP_001186312.1	Q96MT1	RN145_HUMAN	ring finger protein 145	324						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)			TGCACTGCCAGGATTAACAGC	0.373													G|||	71	0.0141773	0.053	0.0014	5008	,	,		17610	0.0		0.0	False		,,,				2504	0.0				p.L354L		Atlas-SNP	.											RNF145,right_upper_lobe,carcinoma,+2,1	RNF145	110	1	0			c.C1060T						PASS	.	G	,,,,	200,4206	124.1+/-161.4	2,196,2005	116	119	118		1060,1021,1012,970,1054	4.2	1	5	dbSNP_129	118	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RNF145	NM_001199380.1,NM_001199381.1,NM_001199382.1,NM_001199383.1,NM_144726.2	,,,,	2,199,6302	AA,AG,GG		0.0349,4.5393,1.5608	,,,,	354/694,341/681,338/678,324/664,352/692	158596032	203,12803	2203	4300	6503	SO:0001819	synonymous_variant	153830	exon8			CTGCCAGGATTAA	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.970C>T	5.37:g.158596032G>A		334	1	0.00299401		353	167	0.473088	NM_001199380	B7Z903|B7Z949|E7EVI7|Q8IVP7	Silent	SNP	ENST00000424310.2	37	CCDS56390.1																																																																																			G|0.985;A|0.015	0.015	strong		0.373	RNF145-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374048.1	NM_144726		A	158596032	G	A	158596032	2	1	22	1	0	0	0	0	0	0	0	1	13462	991	35	2		2	RNF145	5	158596032	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1542667	158596032	22319228	1339	4240											
ATP10B	23120	hgsc.bcm.edu	37	chr5	160047491	160047491	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaagcccagggtgcagaggAggctgaaggtgaggcaggtg	11	4	19	7	0	0	3	0	2	0	1	0	4	0	4	1	6	2	3	1	6	2	0	rs375262733		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:160047491A>C	ENST00000327245.5	-	15	3125	c.2279T>G	c.(2278-2280)cTc>cGc	p.L760R	CTC-348L5.1_ENST00000523598.1_RNA	NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	760					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)			GGTGCAGAGGAGGCTGAAGGT	0.597																																					p.L760R		Atlas-SNP	.											.	ATP10B	201	.	0			c.T2279G						PASS	.	A	ARG/LEU	1,4181		0,1,2090	38	40	39		2279	5.4	0.9	5		39	0,8452		0,0,4226	no	missense	ATP10B	NM_025153.2	102	0,1,6316	CC,CA,AA		0.0,0.0239,0.0079	probably-damaging	760/1462	160047491	1,12633	2091	4226	6317	SO:0001583	missense	23120	exon15			CAGAGGAGGCTGA	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.2279T>G	5.37:g.160047491A>C	ENSP00000313600:p.Leu760Arg	199	0	0		241	100	0.414938	NM_025153	Q9H725	Missense_Mutation	SNP	ENST00000327245.5	37	CCDS43394.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.448539	0.84101	2.39E-4	0.0	ENSG00000118322	ENST00000327245;ENST00000520108	T;T	0.79033	-1.23;-1.23	5.36	5.36	0.76844	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.403835	0.25230	N	0.032170	T	0.82144	0.4973	L	0.49455	1.56	0.38198	D	0.940098	P;P	0.51933	0.949;0.949	P;P	0.57846	0.745;0.828	T	0.83105	-0.0126	9	.	.	.	.	14.5725	0.68220	1.0:0.0:0.0:0.0	.	368;760	Q2YDW8;O94823	.;AT10B_HUMAN	R	760;368	ENSP00000313600:L760R;ENSP00000431081:L368R	.	L	-	2	0	ATP10B	159980069	1.000000	0.71417	0.919000	0.36401	0.912000	0.54170	9.159000	0.94728	2.042000	0.60477	0.533000	0.62120	CTC	.	.	weak		0.597	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153		C	160047491	A	C	160047491	3	2	22	1	0	0	0	0	1	0	0	0	1117	304	11	5	2154	5	ATP10B	5	160047491	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1451459	160047491	20867769	1340	4241											
HMMR	3161	hgsc.bcm.edu	37	chr5	162910136	162910136	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagaaccaactcaagcaacAggaggaagactttagaaaac	19	4	9	9	0	1	3	1	0	0	3	1	5	1	5	1	2	5	2	1	2	8	2	rs112257004	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:162910136A>G	ENST00000358715.3	+	14	1676	c.1640A>G	c.(1639-1641)cAg>cGg	p.Q547R	HMMR_ENST00000353866.3_Missense_Mutation_p.Q532R|RP11-80G7.1_ENST00000514724.2_RNA|RP11-80G7.1_ENST00000521666.1_RNA|HMMR_ENST00000393915.4_Missense_Mutation_p.Q548R|HMMR_ENST00000432118.2_Missense_Mutation_p.Q461R			O75330	HMMR_HUMAN	hyaluronan-mediated motility receptor (RHAMM)	547				Q -> R (in Ref. 3; BAF83266). {ECO:0000305}.	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)	CTCAAGCAACAGGAGGAAGAC	0.358													A|||	46	0.0091853	0.0287	0.0115	5008	,	,		17094	0.0		0.0	False		,,,				2504	0.0				p.Q548R		Atlas-SNP	.											.	HMMR	64	.	0			c.A1643G						PASS	.	A	ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN	101,4305		1,99,2103	55	57	57		1643,1382,1640,1595	5.3	0.9	5	dbSNP_132	57	0,8594		0,0,4297	yes	missense,missense,missense,missense	HMMR	NM_001142556.1,NM_001142557.1,NM_012484.2,NM_012485.2	43,43,43,43	1,99,6400	GG,GA,AA		0.0,2.2923,0.7769	benign,benign,benign,benign	548/726,461/639,547/725,532/710	162910136	101,12899	2203	4297	6500	SO:0001583	missense	3161	exon14			AGCAACAGGAGGA	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.1640A>G	5.37:g.162910136A>G	ENSP00000351554:p.Gln547Arg	121	0	0		128	53	0.414062	NM_001142556	A8K3G2|B4E114|D3DQK9|D3DQL0|E9PCS0|Q32N02|Q92767	Missense_Mutation	SNP	ENST00000358715.3	37	CCDS4362.1	17	0.007783882783882784	12	0.024390243902439025	5	0.013812154696132596	0	0.0	0	0.0	A	13.18	2.159585	0.38119	0.022923	0.0	ENSG00000072571	ENST00000416990;ENST00000353866;ENST00000393915;ENST00000426586;ENST00000432118;ENST00000358715	T;T;T;T;T	0.08282	3.11;3.11;3.11;3.11;3.11	5.33	5.33	0.75918	.	0.292472	0.38326	N	0.001730	T	0.06050	0.0157	L	0.60455	1.87	0.27255	N	0.958781	B;P;P;P	0.36959	0.383;0.51;0.575;0.575	B;B;B;P	0.45232	0.165;0.273;0.394;0.474	T	0.12319	-1.0552	10	0.14656	T	0.56	-11.8252	9.8283	0.40925	0.8474:0.0:0.0:0.1526	.	461;548;532;547	O75330-4;O75330-3;O75330-2;O75330	.;.;.;HMMR_HUMAN	R	433;532;548;524;461;547	ENSP00000400527:Q433R;ENSP00000185942:Q532R;ENSP00000377492:Q548R;ENSP00000402673:Q461R;ENSP00000351554:Q547R	ENSP00000185942:Q532R	Q	+	2	0	HMMR	162842714	0.998000	0.40836	0.903000	0.35520	0.684000	0.39900	2.194000	0.42668	2.234000	0.73211	0.533000	0.62120	CAG	A|0.990;G|0.010	0.010	strong		0.358	HMMR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252752.1	NM_012484		G	162910136	A	G	162910136	3	3	22	1	0	0	0	0	1	0	0	0	7251	188	7	3	1697	3	HMMR	5	162910136	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2862645	162910136	18005124	1341	4242											
HMMR	3161	hgsc.bcm.edu	37	chr5	162910165	162910165	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	actttagaaaacagctggaaGatgaagaaggaaggtaatct	18	8	11	4	0	1	4	0	1	1	3	1	6	1	6	0	3	2	2	0	3	8	3	rs2230362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:162910165G>C	ENST00000358715.3	+	14	1705	c.1669G>C	c.(1669-1671)Gat>Cat	p.D557H	HMMR_ENST00000353866.3_Missense_Mutation_p.D542H|RP11-80G7.1_ENST00000514724.2_RNA|RP11-80G7.1_ENST00000521666.1_RNA|HMMR_ENST00000393915.4_Missense_Mutation_p.D558H|HMMR_ENST00000432118.2_Missense_Mutation_p.D471H			O75330	HMMR_HUMAN	hyaluronan-mediated motility receptor (RHAMM)	557			D -> H (in dbSNP:rs2230362).		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)	ACAGCTGGAAGATGAAGAAGG	0.313													G|||	46	0.0091853	0.0287	0.0115	5008	,	,		17759	0.0		0.0	False		,,,				2504	0.0				p.D558H		Atlas-SNP	.											.	HMMR	64	.	0			c.G1672C						PASS	.	G	HIS/ASP,HIS/ASP,HIS/ASP,HIS/ASP	103,4303		1,101,2101	53	54	53		1672,1411,1669,1624	3.2	0.9	5	dbSNP_98	53	0,8598		0,0,4299	yes	missense,missense,missense,missense	HMMR	NM_001142556.1,NM_001142557.1,NM_012484.2,NM_012485.2	81,81,81,81	1,101,6400	CC,CG,GG		0.0,2.3377,0.7921	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	558/726,471/639,557/725,542/710	162910165	103,12901	2203	4299	6502	SO:0001583	missense	3161	exon14			CTGGAAGATGAAG	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.1669G>C	5.37:g.162910165G>C	ENSP00000351554:p.Asp557His	104	0	0		119	48	0.403361	NM_001142556	A8K3G2|B4E114|D3DQK9|D3DQL0|E9PCS0|Q32N02|Q92767	Missense_Mutation	SNP	ENST00000358715.3	37	CCDS4362.1	17	0.007783882783882784	12	0.024390243902439025	5	0.013812154696132596	0	0.0	0	0.0	G	9.635	1.137453	0.21123	0.023377	0.0	ENSG00000072571	ENST00000416990;ENST00000353866;ENST00000393915;ENST00000426586;ENST00000432118;ENST00000358715	T;T;T;T;T	0.07800	3.16;3.16;3.16;3.16;3.16	5.03	3.24	0.37175	.	0.678925	0.15280	N	0.270748	T	0.02304	0.0071	N	0.08118	0	0.09310	N	1	P;P;P;P	0.44380	0.697;0.755;0.834;0.834	B;B;B;B	0.41036	0.332;0.346;0.319;0.319	T	0.36553	-0.9743	10	0.49607	T	0.09	-4.1167	11.5254	0.50576	0.1543:0.0:0.8457:0.0	rs2230362;rs2230362	471;558;542;557	O75330-4;O75330-3;O75330-2;O75330	.;.;.;HMMR_HUMAN	H	443;542;558;534;471;557	ENSP00000400527:D443H;ENSP00000185942:D542H;ENSP00000377492:D558H;ENSP00000402673:D471H;ENSP00000351554:D557H	ENSP00000185942:D542H	D	+	1	0	HMMR	162842743	0.991000	0.36638	0.881000	0.34555	0.305000	0.27757	1.054000	0.30455	1.482000	0.48325	0.655000	0.94253	GAT	G|0.990;C|0.010	0.010	strong		0.313	HMMR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252752.1	NM_012484		C	162910165	G	C	162910165	3	2	22	1	0	0	0	0	1	0	0	0	7251	942	33	4	1726	4	HMMR	5	162910165	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	29	162910165	18005095	1342	4243											
DOCK2	1794	hgsc.bcm.edu	37	chr5	169116304	169116304	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggggcttccctaaggagatTgagatgctcaacaatctgaa	12	9	11	9	1	2	3	1	2	1	2	3	5	3	3	1	3	2	2	1	3	4	3	rs189140579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:169116304T>A	ENST00000256935.8	+	9	890	c.810T>A	c.(808-810)atT>atA	p.I270I		NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	270					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)			CTAAGGAGATTGAGATGCTCA	0.537																																					p.I270I		Atlas-SNP	.											DOCK2,caecum,carcinoma,+2,1	DOCK2	389	1	0			c.T810A						PASS	.						147	125	133					5																	169116304		2203	4300	6503	SO:0001819	synonymous_variant	1794	exon9			GGAGATTGAGATG	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.810T>A	5.37:g.169116304T>A		132	0	0		155	70	0.451613	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	37	CCDS4371.1																																																																																			T|1.000;C|0.000	.	alt		0.537	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		A	169116304	T	A	169116304	2	1	22	1	0	0	0	0	0	0	0	1	4689	1800	63	5		5	DOCK2	5	169116304	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	6206139	169116304	11798956	1343	4244											
DOCK2	1794	hgsc.bcm.edu	37	chr5	169469088	169469088	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ccccagacacaccggcagctGaaggagacgctctacgagac	12	3	11	15	3	1	4	0	1	1	3	1	6	1	4	3	2	2	3	3	2	2	1	rs6555882	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:169469088G>C	ENST00000256935.8	+	38	3908	c.3828G>C	c.(3826-3828)ctG>ctC	p.L1276L	DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000540750.1_Silent_p.L337L|DOCK2_ENST00000520908.1_Silent_p.L768L	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1276	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)			ACCGGCAGCTGAAGGAGACGC	0.577													C|||	461	0.0920527	0.2837	0.0317	5008	,	,		19097	0.0		0.0189	False		,,,				2504	0.046				p.L1276L		Atlas-SNP	.											.	DOCK2	389	.	0			c.G3828C						PASS	.	C		1166,3240	713.1+/-408.2	139,888,1176	61	54	57		3828	3.4	1	5	dbSNP_116	57	164,8436	811.3+/-407.1	3,158,4139	no	coding-synonymous	DOCK2	NM_004946.2		142,1046,5315	CC,CG,GG		1.907,26.4639,10.226		1276/1831	169469088	1330,11676	2203	4300	6503	SO:0001819	synonymous_variant	1794	exon38			GCAGCTGAAGGAG	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.3828G>C	5.37:g.169469088G>C		225	0	0		242	242	1	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	37	CCDS4371.1																																																																																			G|0.867;C|0.133	0.133	strong		0.577	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		C	169469088	G	C	169469088	2	2	22	1	0	0	0	0	0	0	0	1	4689	1277	45	4		4	DOCK2	5	169469088	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	352784	169469088	11446172	1344	4245											
NKX2-5	1482	hgsc.bcm.edu	37	chr5	172662014	172662014	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tccggcggcagccaggctgcGctgctgctgttccaggttta	4	10	14	13	3	0	0	0	0	0	0	2	0	2	0	3	4	4	7	3	4	1	3	rs28936670	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:172662014G>A	ENST00000329198.4	-	1	346	c.73C>T	c.(73-75)Cgc>Tgc	p.R25C	NKX2-5_ENST00000521848.1_Missense_Mutation_p.R25C|NKX2-5_ENST00000424406.2_Missense_Mutation_p.R25C	NM_001166175.1|NM_001166176.1|NM_004387.3	NP_001159647.1|NP_001159648.1|NP_004378.1	P52952	NKX25_HUMAN	NK2 homeobox 5	25			R -> C (in ASD7, TOF, CHNG5 and HLHS2; exhibits significant functional impairment with reduction of transactivation properties and dominant- negative effect; the mutant protein activity on the DIO2, TG and TPO promoters is significantly impaired; dbSNP:rs28936670). {ECO:0000269|PubMed:10587520, ECO:0000269|PubMed:11714651, ECO:0000269|PubMed:14607454, ECO:0000269|PubMed:15342699, ECO:0000269|PubMed:15810002, ECO:0000269|PubMed:16418214}.		adult heart development (GO:0007512)|apoptotic process involved in heart morphogenesis (GO:0003278)|atrial cardiac muscle cell development (GO:0055014)|atrial septum morphogenesis (GO:0060413)|atrioventricular node cell development (GO:0060928)|atrioventricular node cell fate commitment (GO:0060929)|BMP signaling pathway (GO:0030509)|bundle of His development (GO:0003166)|canonical Wnt signaling pathway (GO:0060070)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac ventricle formation (GO:0003211)|cell differentiation (GO:0030154)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|hemopoiesis (GO:0030097)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of myotube differentiation (GO:0010832)|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)|pharyngeal system development (GO:0060037)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart contraction (GO:0045823)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sodium ion transport (GO:0010765)|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 via serum response element binding (GO:0010735)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of voltage-gated calcium channel activity (GO:1901387)|proepicardium development (GO:0003342)|pulmonary myocardium development (GO:0003350)|Purkinje myocyte differentiation (GO:0003168)|regulation of cardiac muscle cell proliferation (GO:0060043)|regulation of cardiac muscle contraction (GO:0055117)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|sarcomere organization (GO:0045214)|septum secundum development (GO:0003285)|spleen development (GO:0048536)|thyroid gland development (GO:0030878)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	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 distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|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)|serum response element binding (GO:0010736)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(7)|prostate(1)	12	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GCCAGGCTGCGCTGCTGCTGT	0.672													G|||	51	0.0101837	0.0363	0.0029	5008	,	,		12104	0.0		0.001	False		,,,				2504	0.0				p.R25C	Esophageal Squamous(72;810 1219 2387 13420 44943)	Atlas-SNP	.											.	NKX2-5	42	.	0			c.C73T	GRCh37	CM993125	NKX2-5	M	rs28936670	PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG	115,4231		0,115,2058	20	25	23	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	73,73,73	3.9	1	5	dbSNP_125	23	8,8528		0,8,4260	yes	missense,missense,missense	NKX2-5	NM_001166175.1,NM_001166176.1,NM_004387.3	180,180,180	0,123,6318	AA,AG,GG		0.0937,2.6461,0.9548	probably-damaging,probably-damaging,probably-damaging	25/113,25/152,25/325	172662014	123,12759	2173	4268	6441	SO:0001583	missense	1482	exon1			GGCTGCGCTGCTG	AB021133	CCDS4387.1, CCDS54949.1, CCDS54950.1	5q34	2014-09-17	2011-06-01	2002-10-04	ENSG00000183072	ENSG00000183072		"Homeoboxes / ANTP class : NKL subclass"	2488	protein-coding gene	gene with protein product	"tinman paralog (Drosophila)"	600584	"cardiac-specific homeo box", "NK2 transcription factor related, locus 5 (Drosophila)"	CSX, NKX2E		7665173, 8900537	Standard	NM_004387		Approved	CSX1, NKX2.5, NKX4-1	uc003mcm.2	P52952	OTTHUMG00000130522	ENST00000329198.4:c.73C>T	5.37:g.172662014G>A	ENSP00000327758:p.Arg25Cys	181	0	0		157	77	0.490446	NM_004387	A8K3K0|B4DNB6|E9PBU6	Missense_Mutation	SNP	ENST00000329198.4	37	CCDS4387.1	10	0.004578754578754579	7	0.014227642276422764	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	17.06	3.293107	0.60086	0.026461	9.37E-4	ENSG00000183072	ENST00000329198;ENST00000424406;ENST00000521848;ENST00000517440	D;D;D;D	0.90385	-2.66;-2.53;-2.6;-2.55	4.76	3.89	0.44902	.	0.491101	0.15624	N	0.252757	T	0.66157	0.2761	L	0.40543	1.245	0.38768	A	0.954489	B;B;B	0.29646	0.253;0.089;0.002	B;B;B	0.21546	0.035;0.008;0.001	T	0.76594	-0.2902	9	0.56958	D	0.05	.	3.5512	0.07847	0.0824:0.2014:0.467:0.2492	rs28936670	25;25;25	B4DNB6;E5RH49;P52952	.;.;NKX25_HUMAN	C	25	ENSP00000327758:R25C;ENSP00000395378:R25C;ENSP00000427906:R25C;ENSP00000429905:R25C	ENSP00000327758:R25C	R	-	1	0	NKX2-5	172594620	0.992000	0.36948	0.993000	0.49108	0.842000	0.47809	1.185000	0.32065	1.118000	0.41863	0.462000	0.41574	CGC	G|0.993;A|0.007	0.007	strong		0.672	NKX2-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252942.2			A	172662014	G	A	172662014	3	1	22	1	0	0	0	0	1	0	0	0	10462	1087	38	1	1044	1	NKX2-5	5	172662014	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3192926	172662014	8253246	1345	4246											
C5orf25	375484	hgsc.bcm.edu	37	chr5	175722243	175722243	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtcctaaaggaggcctacAtgcttctcatgaaaattcaa	14	11	7	9	0	2	1	2	1	1	0	4	2	3	2	2	2	2	1	2	2	6	4	rs7736723	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:175722243A>G	ENST00000443967.1	+	5	1992	c.1585A>G	c.(1585-1587)Atg>Gtg	p.M529V	SIMC1_ENST00000341199.6_Missense_Mutation_p.M114V|SIMC1_ENST00000429602.2_Missense_Mutation_p.M548V|SIMC1_ENST00000430704.2_Missense_Mutation_p.M114V			Q8NDZ2	SIMC1_HUMAN	SUMO-interacting motifs containing 1	529							SUMO polymer binding (GO:0032184)										GGAGGCCTACATGCTTCTCAT	0.483													A|||	81	0.0161741	0.059	0.0043	5008	,	,		16361	0.0		0.0	False		,,,				2504	0.0				p.M114V		Atlas-SNP	.											.	.	.	.	0			c.A340G						PASS	.	A	VAL/MET	276,4128	150.7+/-184.7	3,270,1929	39	32	34		340	4.2	1	5	dbSNP_129	34	1,8595	1.2+/-3.3	0,1,4297	no	missense	C5orf25	NM_198567.4	21	3,271,6226	GG,GA,AA		0.0116,6.267,2.1308	possibly-damaging	114/458	175722243	277,12723	2202	4298	6500	SO:0001583	missense	375484	exon2			GCCTACATGCTTC	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.1585A>G	5.37:g.175722243A>G	ENSP00000406571:p.Met529Val	321	0	0		323	134	0.414861	NM_198567	J3KQQ8|Q6NXN8|Q6ZTU4|Q8IZ15	Missense_Mutation	SNP	ENST00000443967.1	37		32	0.014652014652014652	32	0.06504065040650407	0	0.0	0	0.0	0	0.0	A	16.45	3.127921	0.56721	0.06267	1.16E-4	ENSG00000170085	ENST00000341199;ENST00000430704;ENST00000443967;ENST00000429602	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	4.24	4.24	0.50183	.	0.174470	0.43747	D	0.000531	T	0.05686	0.0149	L	0.48642	1.525	0.25231	N	0.989824	P;P;D	0.57257	0.865;0.782;0.979	B;B;P	0.53401	0.391;0.327;0.725	T	0.01238	-1.1409	10	0.51188	T	0.08	-16.7421	12.4812	0.55844	1.0:0.0:0.0:0.0	rs55844480	548;114;529	B4DRM7;Q8NDZ2-3;Q8NDZ2	.;.;CE025_HUMAN	V	114;114;529;548	ENSP00000342075:M114V;ENSP00000409287:M114V;ENSP00000406571:M529V;ENSP00000410552:M548V	ENSP00000342075:M114V	M	+	1	0	C5orf25	175654849	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.371000	0.59523	1.775000	0.52247	0.496000	0.49642	ATG	A|1.000;|0.000	.	weak		0.483	SIMC1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000253155.2	NM_198567		G	175722243	A	G	175722243	3	3	22	1	0	0	0	0	1	0	0	0	2290	217	8	3	346	3	C5orf25	5	175722243	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	3060229	175722243	5193017	1346	4247											
CDHR2	54825	hgsc.bcm.edu	37	chr5	176011968	176011968	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tggtcacgctggttgtgcggGcctgtgacctagccacggac	5	9	15	12	3	1	1	1	1	0	0	1	2	1	2	3	4	2	2	3	4	1	2	rs114527399	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:176011968G>A	ENST00000510636.1	+	19	2960	c.2686G>A	c.(2686-2688)Gcc>Acc	p.A896T	CDHR2_ENST00000261944.5_Missense_Mutation_p.A896T|CDHR2_ENST00000506348.1_Missense_Mutation_p.A896T	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	896	Cadherin 8. {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						GGTTGTGCGGGCCTGTGACCT	0.627													G|||	9	0.00179712	0.0068	0.0	5008	,	,		19273	0.0		0.0	False		,,,				2504	0.0				p.A896T		Atlas-SNP	.											.	CDHR2	152	.	0			c.G2686A						PASS	.	G	THR/ALA,THR/ALA	29,4319		0,29,2145	29	25	26		2686,2686	5.4	1	5	dbSNP_132	26	0,8520		0,0,4260	yes	missense,missense	CDHR2	NM_001171976.1,NM_017675.4	58,58	0,29,6405	AA,AG,GG		0.0,0.667,0.2254	probably-damaging,probably-damaging	896/1311,896/1311	176011968	29,12839	2174	4260	6434	SO:0001583	missense	54825	exon19			GTGCGGGCCTGTG	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.2686G>A	5.37:g.176011968G>A	ENSP00000424565:p.Ala896Thr	80	0	0		79	37	0.468354	NM_017675	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	37	CCDS34297.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	21.9	4.219121	0.79464	0.00667	0.0	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.75589	-0.95;-0.95;-0.95	5.42	5.42	0.78866	Cadherin (4);Cadherin-like (1);	.	.	.	.	D	0.86493	0.5946	H	0.95611	3.695	0.42064	D	0.991178	D	0.62365	0.991	P	0.59595	0.86	D	0.90838	0.4721	9	0.62326	D	0.03	-45.3354	19.2279	0.93824	0.0:0.0:1.0:0.0	.	896	Q9BYE9	CDHR2_HUMAN	T	896	ENSP00000424565:A896T;ENSP00000261944:A896T;ENSP00000421078:A896T	ENSP00000261944:A896T	A	+	1	0	CDHR2	175944574	1.000000	0.71417	0.999000	0.59377	0.304000	0.27724	7.214000	0.77958	2.547000	0.85894	0.549000	0.68633	GCC	G|0.996;A|0.004	0.004	strong		0.627	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675		A	176011968	G	A	176011968	3	1	22	1	0	0	0	0	1	0	0	0	3121	1203	42	2	2756	2	CDHR2	5	176011968	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	289725	176011968	4903292	1347	4248											
UNC5A	90249	hgsc.bcm.edu	37	chr5	176305523	176305523	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcacgcagcggtacttgcaCtgcaccttcaccctggagcg	7	7	12	15	3	1	0	1	0	0	0	1	1	1	1	2	3	5	5	2	3	1	3	rs146460064	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:176305523C>T	ENST00000329542.4	+	13	2341	c.2067C>T	c.(2065-2067)caC>caT	p.H689H	UNC5A_ENST00000261961.3_Silent_p.H649H	NM_133369.2	NP_588610.2	Q6ZN44	UNC5A_HUMAN	unc-5 homolog A (C. elegans)	689					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)			GGTACTTGCACTGCACCTTCA	0.602													C|||	8	0.00159744	0.0061	0.0	5008	,	,		20146	0.0		0.0	False		,,,				2504	0.0				p.H689H		Atlas-SNP	.											.	UNC5A	76	.	0			c.C2067T						PASS	.	C		41,4365	44.6+/-78.6	0,41,2162	107	83	91		2067	3.8	1	5	dbSNP_134	91	0,8600		0,0,4300	no	coding-synonymous	UNC5A	NM_133369.2		0,41,6462	TT,TC,CC		0.0,0.9305,0.3152		689/843	176305523	41,12965	2203	4300	6503	SO:0001819	synonymous_variant	90249	exon13			CTTGCACTGCACC	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.2067C>T	5.37:g.176305523C>T		223	1	0.00448431		222	116	0.522523	NM_133369	B2RXE6|Q8TF26|Q96GP4	Silent	SNP	ENST00000329542.4	37	CCDS34299.1																																																																																			C|0.996;T|0.004	0.004	strong		0.602	UNC5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372166.1	XM_030300		T	176305523	C	T	176305523	2	4	22	1	0	0	0	0	0	0	0	1	17006	564	20	2		2	UNC5A	5	176305523	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	293555	176305523	4609737	1348	4249											
MXD3	83463	hgsc.bcm.edu	37	chr5	176734945	176734945	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccttgagctgtcgggcccgCtgctcctgatcctccagctt	3	12	10	16	2	0	2	0	2	0	0	5	2	4	2	5	1	3	4	5	1	0	2	rs35691394	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:176734945C>A	ENST00000439742.2	-	5	820	c.342G>T	c.(340-342)caG>caT	p.Q114H	MXD3_ENST00000427908.2_Missense_Mutation_p.Q114H|MXD3_ENST00000423571.2_Missense_Mutation_p.Q114H|MXD3_ENST00000513063.1_Missense_Mutation_p.Q114H	NM_031300.3	NP_112590.1	Q9BW11	MAD3_HUMAN	MAX dimerization protein 3	114			Q -> H (in dbSNP:rs35691394).		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)			GTCGGGCCCGCTGCTCCTGAT	0.711													C|||	7	0.00139776	0.0053	0.0	5008	,	,		15589	0.0		0.0	False		,,,				2504	0.0				p.Q114H		Atlas-SNP	.											.	MXD3	13	.	0			c.G342T						PASS	.	C	HIS/GLN,HIS/GLN	29,4071		0,29,2021	5	6	5		342,342	4.1	1	5	dbSNP_126	5	1,8135		0,1,4067	no	missense,missense	MXD3	NM_001142935.1,NM_031300.3	24,24	0,30,6088	AA,AC,CC		0.0123,0.7073,0.2452	possibly-damaging,possibly-damaging	114/194,114/207	176734945	30,12206	2050	4068	6118	SO:0001583	missense	83463	exon5			GGCCCGCTGCTCC	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.342G>T	5.37:g.176734945C>A	ENSP00000401867:p.Gln114His	23	0	0		39	22	0.564103	NM_001142935	B4E0J1|Q53HK1|Q7Z4Y0|Q8NDJ7|Q96ME3	Missense_Mutation	SNP	ENST00000439742.2	37	CCDS4416.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	19.48	3.835342	0.71373	0.007073	1.23E-4	ENSG00000213347	ENST00000427908;ENST00000423571;ENST00000439742;ENST00000303165;ENST00000513063;ENST00000513169;ENST00000502529	D;D;D;D;T;T	0.88975	-2.45;-2.45;-2.45;-2.45;0.88;0.9	5.0	4.13	0.48395	Helix-loop-helix DNA-binding (3);	0.422928	0.25416	N	0.030831	D	0.87249	0.6130	L	0.44542	1.39	0.33730	D	0.618086	D;D;D;D	0.71674	0.998;0.989;0.981;0.99	P;P;P;P	0.62560	0.904;0.769;0.687;0.825	D	0.90640	0.4574	10	0.59425	D	0.04	-0.452	10.1788	0.42955	0.0:0.8454:0.0:0.1546	rs35691394	114;105;114;114	Q9BW11-3;F8W9D2;Q9BW11;B4E0J1	.;.;MAD3_HUMAN;.	H	114;114;114;105;114;31;104	ENSP00000416921:Q114H;ENSP00000389716:Q114H;ENSP00000401867:Q114H;ENSP00000421463:Q114H;ENSP00000427104:Q31H;ENSP00000425029:Q104H	ENSP00000307720:Q105H	Q	-	3	2	MXD3	176667551	0.001000	0.12720	0.979000	0.43373	0.681000	0.39784	1.288000	0.33296	1.226000	0.43582	0.561000	0.74099	CAG	C|0.997;A|0.003	0.003	strong		0.711	MXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253427.1			A	176734945	C	A	176734945	3	1	22	1	0	0	0	0	1	0	0	0	10009	796	28	4	367	4	MXD3	5	176734945	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	429422	176734945	4180315	1349	4250											
RGS14	10636	hgsc.bcm.edu	37	chr5	176798996	176798996	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccgcccaagggcccagctccGaggagaccccaccacagacc	10	1	10	20	2	0	2	0	0	0	2	1	4	1	2	8	2	1	1	8	2	1	0	rs149981884	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:176798996G>A	ENST00000408923.3	+	15	1809	c.1621G>A	c.(1621-1623)Gag>Aag	p.E541K	RGS14_ENST00000506944.1_3'UTR	NM_006480.4	NP_006471.2	O43566	RGS14_HUMAN	regulator of G-protein signaling 14	541					cell division (GO:0051301)|chromosome segregation (GO:0007059)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mitotic nuclear division (GO:0007067)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of synaptic plasticity (GO:0031914)|nucleocytoplasmic transport (GO:0006913)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of GTPase activity (GO:0043547)|positive regulation of neurogenesis (GO:0050769)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|response to oxidative stress (GO:0006979)|spindle organization (GO:0007051)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual learning (GO:0008542)|zygote asymmetric cell division (GO:0010070)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|microtubule (GO:0005874)|nuclear body (GO:0016604)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|spindle (GO:0005819)|spindle pole (GO:0000922)	GDP-dissociation inhibitor activity (GO:0005092)|GTPase activator activity (GO:0005096)|microtubule binding (GO:0008017)|receptor signaling complex scaffold activity (GO:0030159)|receptor signaling protein activity (GO:0005057)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(3)|upper_aerodigestive_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)			GCCCAGCTCCGAGGAGACCCC	0.632													C|||	36	0.0071885	0.0265	0.0	5008	,	,		15334	0.0		0.001	False		,,,				2504	0.0				p.E541K	NSCLC(47;353 1896 28036)	Atlas-SNP	.											.	RGS14	34	.	0			c.G1621A						PASS	.	C	LYS/GLU	74,3978		0,74,1952	109	131	124		1621	2.9	0	5	dbSNP_134	124	3,8353		0,3,4175	yes	missense	RGS14	NM_006480.4	56	0,77,6127	AA,AG,GG		0.0359,1.8263,0.6206	benign	541/567	176798996	77,12331	2026	4178	6204	SO:0001583	missense	10636	exon15			AGCTCCGAGGAGA	AF037195	CCDS43405.1	5q35.3	2008-02-05	2007-08-14		ENSG00000169220	ENSG00000169220		"Regulators of G-protein signaling"	9996	protein-coding gene	gene with protein product		602513	"regulator of G-protein signalling 14"				Standard	NM_006480		Approved		uc003mgf.3	O43566	OTTHUMG00000163324	ENST00000408923.3:c.1621G>A	5.37:g.176798996G>A	ENSP00000386229:p.Glu541Lys	66	0	0		80	44	0.55	NM_006480	O43565|Q506M1|Q6ZWA4|Q8TD62	Missense_Mutation	SNP	ENST00000408923.3	37	CCDS43405.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	C	5.842	0.339577	0.11069	0.018263	3.59E-4	ENSG00000169220	ENST00000408923;ENST00000336477	T	0.37584	1.19	4.84	2.9	0.33743	.	1.710450	0.02865	N	0.130773	T	0.09818	0.0241	N	0.14661	0.345	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	0.21827	-1.0234	10	0.06625	T	0.88	-0.2211	2.9504	0.05860	0.0:0.4578:0.2389:0.3033	.	312;389;541	B3KUX0;O43566-5;O43566	.;.;RGS14_HUMAN	K	541;322	ENSP00000386229:E541K	ENSP00000336864:E322K	E	+	1	0	RGS14	176731602	0.001000	0.12720	0.009000	0.14445	0.018000	0.09664	1.463000	0.35277	0.678000	0.31325	-0.756000	0.03474	GAG	G|0.995;A|0.005	0.005	strong		0.632	RGS14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372676.1	NM_006480		A	176798996	G	A	176798996	3	1	22	1	0	0	0	0	1	0	0	0	13312	1059	37	1	1679	1	RGS14	5	176798996	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	64051	176798996	4116264	1350	4251											
DBN1	1627	hgsc.bcm.edu	37	chr5	176885145	176885145	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccagctcctcaagggctgAgggcagagttggggtctggg	6	8	17	10	0	2	2	1	1	1	1	4	2	4	2	2	5	1	4	2	5	1	1	rs139935466	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:176885145A>C	ENST00000309007.5	-	12	1909	c.1690T>G	c.(1690-1692)Tca>Gca	p.S564A	DBN1_ENST00000292385.5_Missense_Mutation_p.S566A|DBN1_ENST00000393563.4_Missense_Mutation_p.S296A|DBN1_ENST00000393565.1_Missense_Mutation_p.S610A|DBN1_ENST00000512501.1_Missense_Mutation_p.S296A	NM_004395.3	NP_004386	Q16643	DREB_HUMAN	drebrin 1	564					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)			TCAAGGGCTGAGGGCAGAGTT	0.642													A|||	23	0.00459265	0.0151	0.0014	5008	,	,		15225	0.0		0.002	False		,,,				2504	0.0				p.S566A		Atlas-SNP	.											.	DBN1	122	.	0			c.T1696G						PASS	.	A	ALA/SER,ALA/SER	45,4361		1,43,2159	35	40	39		1690,1696	2.1	1	5	dbSNP_134	39	0,8592		0,0,4296	yes	missense,missense	DBN1	NM_004395.3,NM_080881.2	99,99	1,43,6455	CC,CA,AA		0.0,1.0213,0.3462	possibly-damaging,possibly-damaging	564/650,566/652	176885145	45,12953	2203	4296	6499	SO:0001583	missense	1627	exon13			GGGCTGAGGGCAG		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.1690T>G	5.37:g.176885145A>C	ENSP00000308532:p.Ser564Ala	117	0	0		107	43	0.401869	NM_080881	A8MV58|B2RBG0|Q9UFZ5	Missense_Mutation	SNP	ENST00000309007.5	37	CCDS4420.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	A	3.494	-0.103186	0.06967	0.010213	0.0	ENSG00000113758	ENST00000309007;ENST00000292385;ENST00000393565;ENST00000512501;ENST00000393563	T;T;T;T;T	0.32023	1.48;1.48;1.47;1.47;1.5	4.71	2.09	0.27110	.	1.730350	0.02752	N	0.117546	T	0.09686	0.0238	N	0.08118	0	0.18873	N	0.999983	P;B;B;B	0.35107	0.484;0.401;0.005;0.247	B;B;B;B	0.34038	0.174;0.115;0.004;0.107	T	0.24584	-1.0156	10	0.37606	T	0.19	-8.9664	9.4796	0.38893	0.7209:0.0:0.0:0.2791	.	514;610;564;566	B3KSQ7;A8MV58;Q16643;Q16643-2	.;.;DREB_HUMAN;.	A	564;566;610;296;296	ENSP00000308532:S564A;ENSP00000292385:S566A;ENSP00000377195:S610A;ENSP00000423208:S296A;ENSP00000377193:S296A	ENSP00000292385:S566A	S	-	1	0	DBN1	176817751	0.998000	0.40836	0.954000	0.39281	0.247000	0.25773	1.322000	0.33689	0.916000	0.36871	0.379000	0.24179	TCA	A|0.995;C|0.005	0.005	strong		0.642	DBN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253429.2	NM_080881		C	176885145	A	C	176885145	3	2	22	1	0	0	0	0	1	0	0	0	4254	304	11	5	271	5	DBN1	5	176885145	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	86149	176885145	4030115	1351	4252											
DOK3	79930	hgsc.bcm.edu	37	chr5	176936822	176936822	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggttcagctgggcacgcGcgtctgatcgcagtctggct	4	10	14	13	4	3	1	1	1	2	0	4	1	3	1	1	3	1	5	1	3	0	1	rs371788222		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:176936822G>A	ENST00000357198.4	-	1	36	c.32C>T	c.(31-33)gCg>gTg	p.A11V	DOK3_ENST00000377112.4_Intron|DOK3_ENST00000312943.6_Intron|DOK3_ENST00000501403.2_Intron	NM_024872.2	NP_079148.2	Q7L591	DOK3_HUMAN	docking protein 3	11					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)			CTGGGCACGCGCGTCTGATCG	0.711																																					p.A11V		Atlas-SNP	.											DOK3,NS,carcinoma,-1,1	DOK3	41	1	0			c.C32T						PASS	.	G	,,VAL/ALA	1,4403	2.1+/-5.4	0,1,2201	52	52	52		,,32	2.3	0	5		52	0,8600		0,0,4300	no	intron,intron,missense	DOK3	NM_001144875.1,NM_001144876.1,NM_024872.2	,,64	0,1,6501	AA,AG,GG		0.0,0.0227,0.0077	,,benign	,,11/497	176936822	1,13003	2202	4300	6502	SO:0001583	missense	79930	exon1			GCACGCGCGTCTG	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	ENST00000357198.4:c.32C>T	5.37:g.176936822G>A	ENSP00000349727:p.Ala11Val	253	1	0.00395257		310	144	0.464516	NM_024872	E9PAT0|H7BXS0|Q8N864|Q9BQB3|Q9H666	Missense_Mutation	SNP	ENST00000357198.4	37	CCDS4426.1	.	.	.	.	.	.	.	.	.	.	G	13.18	2.161465	0.38119	2.27E-4	0.0	ENSG00000146094	ENST00000357198	T	0.20200	2.09	3.22	2.34	0.29019	.	1.986640	0.03416	U	0.205582	T	0.12263	0.0298	N	0.08118	0	0.20563	N	0.999886	B	0.25955	0.138	B	0.11329	0.006	T	0.21381	-1.0247	10	0.87932	D	0	-23.7375	6.3296	0.21262	0.1376:0.0:0.8624:0.0	.	11	Q7L591	DOK3_HUMAN	V	11	ENSP00000349727:A11V	ENSP00000349727:A11V	A	-	2	0	DOK3	176869428	.	.	0.005000	0.12908	0.011000	0.07611	.	.	0.915000	0.36847	0.491000	0.48974	GCG	.	.	weak		0.711	DOK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253420.4	NM_024872		A	176936822	G	A	176936822	3	1	22	1	0	0	0	0	1	0	0	0	4700	1087	38	1	1834	1	DOK3	5	176936822	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	51677	176936822	3978438	1352	4253											
PROP1	5626	hgsc.bcm.edu	37	chr5	177421275	177421275	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cggcccctctgtcctccttgCggggagaaccttgatctccc	4	10	10	17	2	2	2	0	1	2	1	5	3	4	2	6	3	2	0	6	3	1	2	rs2233784	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:177421275C>T	ENST00000308304.2	-	2	482	c.174G>A	c.(172-174)ccG>ccA	p.P58P		NM_006261.4	NP_006252	O75360	PROP1_HUMAN	PROP paired-like homeobox 1	58					blood vessel development (GO:0001568)|canonical Wnt signaling pathway (GO:0060070)|cell migration (GO:0016477)|central nervous system development (GO:0007417)|dorsal/ventral pattern formation (GO:0009953)|hypophysis morphogenesis (GO:0048850)|hypothalamus cell differentiation (GO:0021979)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|somatotropin secreting cell differentiation (GO:0060126)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(2)|lung(9)|stomach(1)	13	all_cancers(89;0.00176)|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)			GTCCTCCTTGCGGGGAGAACC	0.662													c|||	125	0.0249601	0.0908	0.0072	5008	,	,		15546	0.0		0.0	False		,,,				2504	0.0				p.P58P		Atlas-SNP	.											PROP1,NS,carcinoma,-2,1	PROP1	28	1	0			c.G174A						PASS	.	T		357,4043		13,331,1856	25	26	26		174	-6.3	0	5	dbSNP_98	26	3,8597		0,3,4297	no	coding-synonymous	PROP1	NM_006261.4		13,334,6153	TT,TC,CC		0.0349,8.1136,2.7692		58/227	177421275	360,12640	2200	4300	6500	SO:0001819	synonymous_variant	5626	exon2			TCCTTGCGGGGAG	AF076215	CCDS4430.1	5q35.3	2011-06-20	2007-07-12		ENSG00000175325	ENSG00000175325		"Homeoboxes / PRD class"	9455	protein-coding gene	gene with protein product		601538	"prophet of Pit1, paired-like homeodomain transcription factor"			9462743	Standard	NM_006261		Approved		uc003mif.1	O75360	OTTHUMG00000130887	ENST00000308304.2:c.174G>A	5.37:g.177421275C>T		107	0	0		131	68	0.519084	NM_006261		Silent	SNP	ENST00000308304.2	37	CCDS4430.1																																																																																			C|0.969;T|0.031	0.031	strong		0.662	PROP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253472.1	NM_006261		T	177421275	C	T	177421275	2	4	22	1	0	0	0	0	0	0	0	1	12569	755	27	1		1	PROP1	5	177421275	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	484453	177421275	3493985	1353	4254											
ZNF354C	30832	hgsc.bcm.edu	37	chr5	178505831	178505831	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgtggaatttgagagcgAgatagaagaagagcaagaga	17	6	15	3	1	0	6	0	1	0	6	0	10	0	7	0	1	3	2	0	1	5	2	rs57271258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:178505831A>G	ENST00000315475.6	+	5	704	c.398A>G	c.(397-399)gAg>gGg	p.E133G		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E133G(1)		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)		TTTGAGAGCGAGATAGAAGAA	0.378													G|||	122	0.024361	0.0862	0.0115	5008	,	,		20349	0.0		0.0	False		,,,				2504	0.0				p.E133G		Atlas-SNP	.											ZNF354C,caecum,carcinoma,0,1	ZNF354C	77	1	1	Substitution - Missense(1)	large_intestine(1)	c.A398G						PASS	.	G	GLY/GLU	312,4094	788.4+/-414.9	9,294,1900	90	95	93		398	1	0	5	dbSNP_129	93	0,8600		0,0,4300	yes	missense	ZNF354C	NM_014594.1	98	9,294,6200	GG,GA,AA		0.0,7.0813,2.3989	benign	133/555	178505831	312,12694	2203	4300	6503	SO:0001583	missense	30832	exon5			AGAGCGAGATAGA		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.398A>G	5.37:g.178505831A>G	ENSP00000324064:p.Glu133Gly	187	0	0		179	99	0.553073	NM_014594	Q6P4P9|Q8NFX1	Missense_Mutation	SNP	ENST00000315475.6	37	CCDS4443.1	30	0.013736263736263736	27	0.054878048780487805	3	0.008287292817679558	0	0.0	0	0.0	G	7.305	0.613748	0.14066	0.070813	0.0	ENSG00000177932	ENST00000315475	T	0.05786	3.39	3.87	1.04	0.20106	.	.	.	.	.	T	0.00241	0.0007	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48747	-0.9008	9	0.16896	T	0.51	1.603	3.2954	0.06964	0.3129:0.0:0.505:0.182	rs57271258	133	Q86Y25	Z354C_HUMAN	G	133	ENSP00000324064:E133G	ENSP00000324064:E133G	E	+	2	0	ZNF354C	178438437	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.082000	0.03400	-0.148000	0.11234	-0.930000	0.02707	GAG	A|0.974;G|0.026	0.026	strong		0.378	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2			G	178505831	A	G	178505831	3	3	22	1	0	0	0	0	1	0	0	0	17881	304	11	3	412	3	ZNF354C	5	178505831	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1084556	178505831	2409429	1354	4255											
SQSTM1	8878	hgsc.bcm.edu	37	chr5	179260661	179260661	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttcaaaagaagtggacccGtctacaggtgaactccagtc	12	9	9	11	1	3	2	1	1	2	1	5	3	4	3	2	2	2	0	2	2	5	2	rs10058037	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:179260661G>A	ENST00000389805.4	+	7	1222	c.1044G>A	c.(1042-1044)ccG>ccA	p.P348P	SQSTM1_ENST00000510187.1_Intron|SQSTM1_ENST00000376929.3_Silent_p.P264P|SQSTM1_ENST00000402874.3_Silent_p.P264P|SQSTM1_ENST00000360718.5_Silent_p.P264P	NM_003900.4	NP_003891.1	Q13501	SQSTM_HUMAN	sequestosome 1	348	Interaction with NTRK1. {ECO:0000250}.				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)			AAGTGGACCCGTCTACAGGTG	0.542													G|||	165	0.0329473	0.118	0.0086	5008	,	,		19610	0.001		0.001	False		,,,				2504	0.001				p.P348P		Atlas-SNP	.											SQSTM1,NS,carcinoma,+1,1	SQSTM1	30	1	0			c.G1044A						PASS	.	G	,,	415,3991	205.8+/-227.6	17,381,1805	93	87	89		792,792,1044	-10.5	0	5	dbSNP_119	89	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	SQSTM1	NM_001142298.1,NM_001142299.1,NM_003900.4	,,	17,383,6103	AA,AG,GG		0.0233,9.419,3.2062	,,	264/357,264/357,348/441	179260661	417,12589	2203	4300	6503	SO:0001819	synonymous_variant	8878	exon7			GGACCCGTCTACA	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.1044G>A	5.37:g.179260661G>A		82	0	0		82	36	0.439024	NM_003900	A6NFN7|B2R661|B3KUW5|Q13446|Q9BUV7|Q9BVS6|Q9UEU1	Silent	SNP	ENST00000389805.4	37	CCDS34317.1																																																																																			G|0.960;A|0.040	0.040	strong		0.542	SQSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319344.1			A	179260661	G	A	179260661	2	1	22	1	0	0	0	0	0	0	0	1	15145	1132	40	1		1	SQSTM1	5	179260661	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	754830	179260661	1654599	1355	4256											
C5orf45	51149	hgsc.bcm.edu	37	chr5	179285781	179285781	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcagcgtagcacccgagaacGctgaagcgacgccatccctg	10	4	12	15	5	0	2	0	1	0	1	1	4	1	2	3	0	4	4	3	0	3	1	rs199537217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:179285781G>A	ENST00000292586.6	-	1	106	c.16C>T	c.(16-18)Cgt>Tgt	p.R6C	C5orf45_ENST00000521333.1_Missense_Mutation_p.R6C|C5orf45_ENST00000520698.1_Missense_Mutation_p.R6C|C5orf45_ENST00000403396.2_Missense_Mutation_p.A21V|C5orf45_ENST00000518219.1_Missense_Mutation_p.R6C|CTC-241N9.1_ENST00000499601.2_5'Flank|C5orf45_ENST00000518235.1_Missense_Mutation_p.R6C|C5orf45_ENST00000376931.2_Missense_Mutation_p.R6C|C5orf45_ENST00000523084.1_5'UTR	NM_016175.3	NP_057259.2	Q6NTE8	CE045_HUMAN	chromosome 5 open reading frame 45	6										breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12						ACCCGAGAACGCTGAAGCGAC	0.721													G|||	4	0.000798722	0.003	0.0	5008	,	,		14523	0.0		0.0	False		,,,				2504	0.0				p.R6C		Atlas-SNP	.											.	C5orf45	23	.	0			c.C16T						PASS	.	G	CYS/ARG,CYS/ARG	7,3989		0,7,1991	12	14	13		16,16	3.4	0	5		13	0,7610		0,0,3805	yes	missense,missense	C5orf45	NM_001017987.2,NM_016175.3	180,180	0,7,5796	AA,AG,GG		0.0,0.1752,0.0603	probably-damaging,probably-damaging	6/289,6/344	179285781	7,11599	1998	3805	5803	SO:0001583	missense	51149	exon1			GAGAACGCTGAAG		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.16C>T	5.37:g.179285781G>A	ENSP00000292586:p.Arg6Cys	59	0	0		50	27	0.54	NM_016175	B5MD09|E9PAK6|Q7Z3D8|Q9BUC1|Q9UN54	Missense_Mutation	SNP	ENST00000292586.6	37	CCDS34319.1	3|3	0.0013736263736263737|0.0013736263736263737	3|3	0.006097560975609756|0.006097560975609756	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	13.22|13.22	2.172040|2.172040	0.38315|0.38315	0.001752|0.001752	0.0|0.0	ENSG00000161010|ENSG00000161010	ENST00000403396|ENST00000518235;ENST00000520698;ENST00000376931;ENST00000518219;ENST00000292586;ENST00000521333	T|T;D;D;D;T;D	0.28454|0.82619	1.61|3.13;-1.63;-1.63;-1.63;3.13;-1.63	3.43|3.43	3.43|3.43	0.39272|0.39272	.|.	.|1.497770	.|0.04096	.|N	.|0.312148	T|T	0.70945|0.70945	0.3282|0.3282	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	1|1	.|D;D;D;D	.|0.60160	.|0.968;0.968;0.987;0.986	.|B;B;B;B	.|0.43809	.|0.432;0.335;0.432;0.432	T|T	0.67841|0.67841	-0.5566|-0.5566	7|10	0.87932|0.87932	D|D	0|0	-1.0479|-1.0479	10.2343|10.2343	0.43273|0.43273	0.1009:0.0:0.8991:0.0|0.1009:0.0:0.8991:0.0	.|.	.|6;6;6;6	.|E7EMV9;B7Z1T6;E9PAK6;Q6NTE8	.|.;.;.;CE045_HUMAN	V|C	21|6	ENSP00000384599:A21V|ENSP00000430298:R6C;ENSP00000427849:R6C;ENSP00000366130:R6C;ENSP00000428460:R6C;ENSP00000292586:R6C;ENSP00000429651:R6C	ENSP00000384599:A21V|ENSP00000292586:R6C	A|R	-|-	2|1	0|0	C5orf45|C5orf45	179218387|179218387	0.016000|0.016000	0.18221|0.18221	0.007000|0.007000	0.13788|0.13788	0.001000|0.001000	0.01503|0.01503	1.350000|1.350000	0.34010|0.34010	2.211000|2.211000	0.71520|0.71520	0.561000|0.561000	0.74099|0.74099	GCG|CGT	G|0.999;A|0.001	0.001	strong		0.721	C5orf45-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373760.2	NM_016175		A	179285781	G	A	179285781	3	1	22	1	0	0	0	0	1	0	0	0	2306	1087	38	1	1043	1	C5orf45	5	179285781	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	25120	179285781	1629479	1356	4257											
TBC1D9B	23061	hgsc.bcm.edu	37	chr5	179297262	179297262	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcaggcactcactcatcccTgtcacgaactccttgaagtt	9	11	7	14	1	3	1	3	1	0	0	5	2	5	1	2	1	2	3	2	1	2	2	rs407437	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:179297262T>C	ENST00000356834.3	-	16	2755	c.2718A>G	c.(2716-2718)acA>acG	p.T906T	TBC1D9B_ENST00000519746.1_Silent_p.T82T|TBC1D9B_ENST00000355235.3_Silent_p.T906T|TBC1D9B_ENST00000444477.2_Silent_p.T64T	NM_198868.2	NP_942568.2	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	906	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.					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)			CACTCATCCCTGTCACGAACT	0.602													C|||	622	0.124201	0.444	0.0432	5008	,	,		19694	0.0		0.005	False		,,,				2504	0.0				p.T906T		Atlas-SNP	.											.	TBC1D9B	157	.	0			c.A2718G						PASS	.	C	,	1539,2867	670.9+/-402.4	283,973,947	104	111	109		2718,2718	-10.3	0.5	5	dbSNP_80	109	15,8585	818.5+/-406.9	0,15,4285	no	coding-synonymous,coding-synonymous	TBC1D9B	NM_015043.3,NM_198868.2	,	283,988,5232	CC,CT,TT		0.1744,34.9296,11.9483	,	906/1234,906/1251	179297262	1554,11452	2203	4300	6503	SO:0001819	synonymous_variant	23061	exon16			CATCCCTGTCACG	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.2718A>G	5.37:g.179297262T>C		104	0	0		70	30	0.428571	NM_198868	D3DWQ5|D3DWQ6|O75163|Q53EY0|Q6MZI2|Q96H49	Silent	SNP	ENST00000356834.3	37	CCDS43408.1																																																																																			T|0.882;C|0.118	0.118	strong		0.602	TBC1D9B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253501.3	NM_015043		C	179297262	T	C	179297262	2	2	22	1	0	0	0	0	0	0	0	1	15643	1567	55	3		3	TBC1D9B	5	179297262	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	11481	179297262	1617998	1357	4258											
TBC1D9B	23061	hgsc.bcm.edu	37	chr5	179297352	179297352	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagaggtgtgtgggagccAcaggcccagggtgtcaggct	8	6	18	9	0	1	1	1	0	0	1	1	2	1	2	2	5	2	2	2	5	0	0	rs384668	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:179297352A>G	ENST00000356834.3	-	16	2665	c.2628T>C	c.(2626-2628)tgT>tgC	p.C876C	TBC1D9B_ENST00000519746.1_Silent_p.C52C|TBC1D9B_ENST00000355235.3_Silent_p.C876C|TBC1D9B_ENST00000444477.2_Silent_p.C34C	NM_198868.2	NP_942568.2	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	876						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)			TGTGGGAGCCACAGGCCCAGG	0.617													G|||	623	0.124401	0.444	0.0432	5008	,	,		19003	0.001		0.005	False		,,,				2504	0.0				p.C876C		Atlas-SNP	.											.	TBC1D9B	157	.	0			c.T2628C						PASS	.	G	,	1543,2863	671.2+/-402.4	287,969,947	99	102	101		2628,2628	-7.3	0.3	5	dbSNP_80	101	15,8585	818.3+/-406.9	0,15,4285	no	coding-synonymous,coding-synonymous	TBC1D9B	NM_015043.3,NM_198868.2	,	287,984,5232	GG,GA,AA		0.1744,35.0204,11.9791	,	876/1234,876/1251	179297352	1558,11448	2203	4300	6503	SO:0001819	synonymous_variant	23061	exon16			GGAGCCACAGGCC	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.2628T>C	5.37:g.179297352A>G		119	0	0		120	56	0.466667	NM_198868	D3DWQ5|D3DWQ6|O75163|Q53EY0|Q6MZI2|Q96H49	Silent	SNP	ENST00000356834.3	37	CCDS43408.1																																																																																			A|0.890;G|0.110	0.110	strong		0.617	TBC1D9B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253501.3	NM_015043		G	179297352	A	G	179297352	2	3	22	1	0	0	0	0	0	0	0	1	15643	157	6	3		3	TBC1D9B	5	179297352	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	90	179297352	1617908	1358	4259											
TBC1D9B	23061	hgsc.bcm.edu	37	chr5	179300131	179300131	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgctgacctcataggacacTttcaggagctcaaagatgtc	11	10	10	10	0	3	2	3	1	0	1	4	4	3	4	1	2	2	2	1	2	2	2	rs269469	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:179300131T>C	ENST00000356834.3	-	13	2341	c.2304A>G	c.(2302-2304)aaA>aaG	p.K768K	TBC1D9B_ENST00000519746.1_5'Flank|TBC1D9B_ENST00000355235.3_Silent_p.K768K|TBC1D9B_ENST00000444477.2_5'Flank	NM_198868.2	NP_942568.2	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	768						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)			CATAGGACACTTTCAGGAGCT	0.612													T|||	624	0.124601	0.4455	0.0432	5008	,	,		17765	0.0		0.005	False		,,,				2504	0.0				p.K768K		Atlas-SNP	.											.	TBC1D9B	157	.	0			c.A2304G						PASS	.	T	,	1538,2866	480.4+/-358.8	282,974,946	56	56	56		2304,2304	-0.1	1	5	dbSNP_79	56	15,8585	9.1+/-34.3	0,15,4285	no	coding-synonymous,coding-synonymous	TBC1D9B	NM_015043.3,NM_198868.2	,	282,989,5231	CC,CT,TT		0.1744,34.9228,11.9425	,	768/1234,768/1251	179300131	1553,11451	2202	4300	6502	SO:0001819	synonymous_variant	23061	exon13			GGACACTTTCAGG	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.2304A>G	5.37:g.179300131T>C		144	0	0		139	60	0.431655	NM_198868	D3DWQ5|D3DWQ6|O75163|Q53EY0|Q6MZI2|Q96H49	Silent	SNP	ENST00000356834.3	37	CCDS43408.1																																																																																			T|0.899;C|0.101	0.101	strong		0.612	TBC1D9B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253501.3	NM_015043		C	179300131	T	C	179300131	2	2	22	1	0	0	0	0	0	0	0	1	15643	1606	56	3		3	TBC1D9B	5	179300131	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2779	179300131	1615129	1359	4260											
RNF130	55819	hgsc.bcm.edu	37	chr5	179393867	179393867	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccccatcctgaggaagaggTgagatccccgaagttcgaag	11	7	12	11	2	0	3	0	2	0	2	4	7	3	4	5	2	0	1	5	2	3	1	rs10060093	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:179393867T>C	ENST00000261947.4	-	7	1487	c.1089A>G	c.(1087-1089)tcA>tcG	p.S363S	RNF130_ENST00000521389.1_Silent_p.S363S|CTC-563A5.2_ENST00000510240.1_RNA|RNF130_ENST00000522208.2_Silent_p.S363S	NM_001280801.1	NP_001267730.1			ring finger protein 130											breast(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	17	all_cancers(89;5.49e-05)|all_epithelial(37;1.94e-05)|Renal(175;0.000159)|Lung NSC(126;0.00118)|all_lung(126;0.00212)	all_cancers(40;0.0294)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GAGGAAGAGGTGAGATCCCCG	0.582													C|||	123	0.0245607	0.0893	0.0029	5008	,	,		17689	0.002		0.001	False		,,,				2504	0.0				p.S363S	GBM(24;432 554 38471 39699 51728)	Atlas-SNP	.											.	RNF130	49	.	0			c.A1089G						PASS	.	C		291,4115	799.7+/-415.5	9,273,1921	100	91	94		1089	-6.4	0.4	5	dbSNP_119	94	4,8596	819.1+/-406.8	0,4,4296	no	coding-synonymous	RNF130	NM_018434.4		9,277,6217	CC,CT,TT		0.0465,6.6046,2.2682		363/420	179393867	295,12711	2203	4300	6503	SO:0001819	synonymous_variant	55819	exon7			AAGAGGTGAGATC	AF155650	CCDS4451.1, CCDS64340.1	5q35.3	2013-01-09			ENSG00000113269	ENSG00000113269		"RING-type (C3HC4) zinc fingers"	18280	protein-coding gene	gene with protein product						10806348	Standard	NM_018434		Approved	GP, G1RZFP, GOLIATH	uc003mll.1	Q86XS8	OTTHUMG00000130909	ENST00000261947.4:c.1089A>G	5.37:g.179393867T>C		148	0	0		182	82	0.450549	NM_018434		Silent	SNP	ENST00000261947.4	37																																																																																				T|0.972;C|0.028	0.028	strong		0.582	RNF130-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374205.1	NM_018434		C	179393867	T	C	179393867	2	2	22	1	0	0	0	0	0	0	0	1	13453	1683	59	3		3	RNF130	5	179393867	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	93736	179393867	1521393	1360	4261											
FLT4	2324	hgsc.bcm.edu	37	chr5	180043439	180043439	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtcacagatcttcaccacGtcgctttccgacagcagaat	12	9	7	13	3	3	2	2	0	1	2	5	3	4	2	2	0	1	2	2	0	2	2	rs56127961	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180043439G>A	ENST00000261937.6	-	23	3225	c.3147C>T	c.(3145-3147)gaC>gaT	p.D1049D	FLT4_ENST00000502649.1_Silent_p.D1049D|FLT4_ENST00000393347.3_Silent_p.D1049D	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	1049	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		D -> N (in dbSNP:rs56310180). {ECO:0000269|PubMed:17344846}.		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)	TCTTCACCACGTCGCTTTCCG	0.622													G|||	72	0.014377	0.053	0.0014	5008	,	,		19924	0.001		0.0	False		,,,				2504	0.0				p.D1049D	Colon(97;1075 1466 27033 27547 35871)	Atlas-SNP	.											.	FLT4	356	.	0			c.C3147T						PASS	.	G	,	183,4223	116.7+/-154.6	5,173,2025	126	115	118		3147,3147	-5.8	0.4	5	dbSNP_129	118	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	FLT4	NM_002020.4,NM_182925.4	,	5,173,6325	AA,AG,GG		0.0,4.1534,1.407	,	1049/1299,1049/1364	180043439	183,12823	2203	4300	6503	SO:0001819	synonymous_variant	2324	exon23			CACCACGTCGCTT	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.3147C>T	5.37:g.180043439G>A		154	0	0		193	94	0.487047	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Silent	SNP	ENST00000261937.6	37	CCDS4457.1																																																																																			G|0.982;A|0.018	0.018	strong		0.622	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4			A	180043439	G	A	180043439	2	1	22	1	0	0	0	0	0	0	0	1	5952	1136	40	1		1	FLT4	5	180043439	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	649572	180043439	871821	1361	4262											
FLT4	2324	hgsc.bcm.edu	37	chr5	180058720	180058720	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtcaccggtgtcgatgacGtgtgactcctccgtgatgtt	5	13	12	11	4	1	3	1	3	0	0	4	4	3	3	3	1	0	1	3	1	0	1	rs150736691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180058720G>A	ENST00000261937.6	-	2	195	c.117C>T	c.(115-117)caC>caT	p.H39H	FLT4_ENST00000424276.2_5'UTR|FLT4_ENST00000502649.1_Silent_p.H39H|FLT4_ENST00000393347.3_Silent_p.H39H	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	39	Ig-like C2-type 1.				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)	TGTCGATGACGTGTGACTCCT	0.637																																					p.H39H	Colon(97;1075 1466 27033 27547 35871)	Atlas-SNP	.											.	FLT4	356	.	0			c.C117T						PASS	.	G	,	20,4384	27.2+/-55.0	0,20,2182	114	95	101		117,117	1.4	0	5	dbSNP_134	101	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	FLT4	NM_002020.4,NM_182925.4	,	0,20,6482	AA,AG,GG		0.0,0.4541,0.1538	,	39/1299,39/1364	180058720	20,12984	2202	4300	6502	SO:0001819	synonymous_variant	2324	exon2			GATGACGTGTGAC	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.117C>T	5.37:g.180058720G>A		45	0	0		51	30	0.588235	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Silent	SNP	ENST00000261937.6	37	CCDS4457.1																																																																																			G|0.999;A|0.001	0.001	strong		0.637	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4			A	180058720	G	A	180058720	2	1	22	1	0	0	0	0	0	0	0	1	5952	1136	40	1		1	FLT4	5	180058720	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	15281	180058720	856540	1362	4263											
MGAT1	4245	hgsc.bcm.edu	37	chr5	180219838	180219838	+	Missense_Mutation	SNP	C	C	T																															gggtgaggctggcggggtcgCcatcgagagcgctgactgag																								rs61743256	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180219838C>T	ENST00000446023.2	-	3	884	c.134G>A	c.(133-135)gGc>gAc	p.G45D	MGAT1_ENST00000307826.4_Missense_Mutation_p.G45D|MGAT1_ENST00000333055.3_Missense_Mutation_p.G45D|MGAT1_ENST00000427865.2_Missense_Mutation_p.G45D|MGAT1_ENST00000393340.3_Missense_Mutation_p.G45D	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	45					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)			GGCGGGGTCGCCATCGAGAGC	0.677													T|||	81	0.0161741	0.0333	0.0029	5008	,	,		13792	0.001		0.0	False		,,,				2504	0.0348				p.G45D		Atlas-SNP	.											.	MGAT1	48	.	0			c.G134A						PASS	.	T	ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY	77,4251		0,77,2087	9	10	10		134,134,134,134,134	3.4	0	5	dbSNP_129	10	1,8491		0,1,4245	yes	missense,missense,missense,missense,missense	MGAT1	NM_001114617.1,NM_001114618.1,NM_001114619.1,NM_001114620.1,NM_002406.3	94,94,94,94,94	0,78,6332	TT,TC,CC		0.0118,1.7791,0.6084	benign,benign,benign,benign,benign	45/446,45/446,45/446,45/446,45/446	180219838	78,12742	2164	4246	6410	SO:0001583	missense	4245	exon3			GGGTCGCCATCGA	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.134G>A	5.37:g.180219838C>T	ENSP00000404718:p.Gly45Asp	72	0	0		82	32	0.390244	NM_001114617	A8K404|B3KRU8|D3DWR1|Q6IBE3	Missense_Mutation	SNP	ENST00000446023.2	37	CCDS4458.1	15	0.006868131868131868	14	0.028455284552845527	1	0.0027624309392265192	0	0.0	0	0.0	T	0.001	-3.025352	0.00041	0.017791	1.18E-4	ENSG00000131446	ENST00000333055;ENST00000307826;ENST00000446023;ENST00000393340;ENST00000452920;ENST00000427865;ENST00000504671;ENST00000506889;ENST00000514283;ENST00000512695;ENST00000506269;ENST00000514438;ENST00000502678;ENST00000513431	D;D;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;-1.63;-1.63	4.71	3.41	0.39046	.	0.694372	0.14686	N	0.304491	T	0.44726	0.1307	L	0.34521	1.04	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.40346	-0.9568	10	0.08599	T	0.76	-8.3269	4.0209	0.09665	0.0:0.2398:0.1766:0.5835	.	45	P26572	MGAT1_HUMAN	D	45	ENSP00000332073:G45D;ENSP00000311888:G45D;ENSP00000404718:G45D;ENSP00000377010:G45D;ENSP00000402838:G45D;ENSP00000424891:G45D;ENSP00000425988:G45D;ENSP00000424382:G45D;ENSP00000427116:G45D;ENSP00000422906:G45D;ENSP00000421738:G45D;ENSP00000422588:G45D;ENSP00000423401:G45D	ENSP00000311888:G45D	G	-	2	0	MGAT1	180152444	0.000000	0.05858	0.020000	0.16555	0.026000	0.11368	0.260000	0.18424	0.282000	0.22254	-0.535000	0.04281	GGC	C|0.993;T|0.007	0.007	strong		0.677	MGAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368189.1	NM_001114618		T	180219838	C	T	180219838	3	4	22	1	0	0	0	0	1	0	0	0	9551	739	26	2	1207	2	MGAT1	5	180219838	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	161118	180219838	695422	1363	4264	55	2									
MGAT1	4245	hgsc.bcm.edu	37	chr5	180219842	180219842	+	Missense_Mutation	SNP	C	C	T																															gaggctggcggggtcgccatCgagagcgctgactgagggtg																								rs34344788	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180219842C>T	ENST00000446023.2	-	3	880	c.130G>A	c.(130-132)Gat>Aat	p.D44N	MGAT1_ENST00000307826.4_Missense_Mutation_p.D44N|MGAT1_ENST00000333055.3_Missense_Mutation_p.D44N|MGAT1_ENST00000427865.2_Missense_Mutation_p.D44N|MGAT1_ENST00000393340.3_Missense_Mutation_p.D44N	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	44					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)			GGGTCGCCATCGAGAGCGCTG	0.677													C|||	46	0.0091853	0.0333	0.0029	5008	,	,		14178	0.0		0.0	False		,,,				2504	0.0				p.D44N		Atlas-SNP	.											.	MGAT1	48	.	0			c.G130A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	81,4255		0,81,2087	10	11	10		130,130,130,130,130	3	0	5	dbSNP_126	10	1,8491		0,1,4245	yes	missense,missense,missense,missense,missense	MGAT1	NM_001114617.1,NM_001114618.1,NM_001114619.1,NM_001114620.1,NM_002406.3	23,23,23,23,23	0,82,6332	TT,TC,CC		0.0118,1.8681,0.6392	benign,benign,benign,benign,benign	44/446,44/446,44/446,44/446,44/446	180219842	82,12746	2168	4246	6414	SO:0001583	missense	4245	exon3			CGCCATCGAGAGC	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.130G>A	5.37:g.180219842C>T	ENSP00000404718:p.Asp44Asn	76	0	0		87	36	0.413793	NM_001114617	A8K404|B3KRU8|D3DWR1|Q6IBE3	Missense_Mutation	SNP	ENST00000446023.2	37	CCDS4458.1	15	0.006868131868131868	14	0.028455284552845527	1	0.0027624309392265192	0	0.0	0	0.0	C	0.065	-1.214664	0.01555	0.018681	1.18E-4	ENSG00000131446	ENST00000333055;ENST00000307826;ENST00000446023;ENST00000393340;ENST00000452920;ENST00000427865;ENST00000504671;ENST00000506889;ENST00000514283;ENST00000512695;ENST00000506269;ENST00000514438;ENST00000502678;ENST00000513431	T;T;T;T;T;T;T;T;T;T;T;T;T	0.81330	-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48	4.75	2.97	0.34412	.	0.746358	0.12755	N	0.441841	T	0.39682	0.1087	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.26224	-1.0109	10	0.15952	T	0.53	-3.9185	10.5598	0.45140	0.0:0.8532:0.0:0.1468	rs34344788	44	P26572	MGAT1_HUMAN	N	44	ENSP00000332073:D44N;ENSP00000311888:D44N;ENSP00000404718:D44N;ENSP00000377010:D44N;ENSP00000402838:D44N;ENSP00000424891:D44N;ENSP00000425988:D44N;ENSP00000424382:D44N;ENSP00000427116:D44N;ENSP00000422906:D44N;ENSP00000421738:D44N;ENSP00000422588:D44N;ENSP00000423401:D44N	ENSP00000311888:D44N	D	-	1	0	MGAT1	180152448	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	0.842000	0.27627	0.691000	0.31592	-1.523000	0.00931	GAT	C|0.993;T|0.007	0.007	strong		0.677	MGAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368189.1	NM_001114618		T	180219842	C	T	180219842	3	4	22	1	0	0	0	0	1	0	0	0	9551	884	31	1	1211	1	MGAT1	5	180219842	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4	180219842	695418	1364	4265	55	2									
TRIM41	90933	hgsc.bcm.edu	37	chr5	180661274	180661274	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cggcggcaggaggttgctgaCcatcccaagcgcttctcggc	6	7	14	14	4	1	1	0	1	1	0	3	2	2	2	2	5	2	4	2	5	1	2	rs78013120	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180661274C>G	ENST00000315073.5	+	6	2102	c.1392C>G	c.(1390-1392)gaC>gaG	p.D464E	TRIM41_ENST00000351937.5_Missense_Mutation_p.D464E|TRIM41_ENST00000510072.1_3'UTR	NM_033549.4	NP_291027.3	Q8WV44	TRI41_HUMAN	tripartite motif containing 41	464	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)			AGGTTGCTGACCATCCCAAGC	0.726													C|||	23	0.00459265	0.0174	0.0	5008	,	,		8455	0.0		0.0	False		,,,				2504	0.0				p.D464E		Atlas-SNP	.											.	TRIM41	96	.	0			c.C1392G						PASS	.	C	GLU/ASP,GLU/ASP	72,4296		0,72,2112	21	24	23		1392,1392	3.1	1	5	dbSNP_133	23	0,8498		0,0,4249	yes	missense,missense	TRIM41	NM_033549.3,NM_201627.1	45,45	0,72,6361	GG,GC,CC		0.0,1.6484,0.5596	possibly-damaging,possibly-damaging	464/631,464/519	180661274	72,12794	2184	4249	6433	SO:0001583	missense	90933	exon6			TGCTGACCATCCC	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.1392C>G	5.37:g.180661274C>G	ENSP00000320869:p.Asp464Glu	40	0	0		50	28	0.56	NM_201627	B3KNJ6|D3DWR9|Q5BKT0|Q7L484|Q96Q10|Q9BSL8	Missense_Mutation	SNP	ENST00000315073.5	37	CCDS4466.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	18.88	3.716930	0.68844	0.016484	0.0	ENSG00000146063	ENST00000515499;ENST00000351937;ENST00000315073;ENST00000438174	T;T;T	0.14391	2.51;2.51;2.51	4.97	3.14	0.36123	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);B30.2/SPRY domain (1);	0.183072	0.38837	N	0.001552	T	0.09247	0.0228	M	0.62088	1.915	0.26095	N	0.980893	P;B	0.51791	0.948;0.001	P;B	0.48627	0.584;0.005	T	0.04386	-1.0955	10	0.48119	T	0.1	.	7.2565	0.26179	0.1752:0.7342:0.0:0.0907	.	464;464	Q8WV44;Q8WV44-2	TRI41_HUMAN;.	E	174;464;464;149	ENSP00000426803:D174E;ENSP00000336749:D464E;ENSP00000320869:D464E	ENSP00000320869:D464E	D	+	3	2	TRIM41	180593880	0.827000	0.29292	1.000000	0.80357	0.981000	0.71138	1.423000	0.34837	0.645000	0.30675	0.557000	0.71058	GAC	C|0.995;G|0.005	0.005	strong		0.726	TRIM41-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253574.3	NM_201627		G	180661274	C	G	180661274	3	3	22	1	0	0	0	0	1	0	0	0	16531	506	18	4	1414	4	TRIM41	5	180661274	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	441432	180661274	253986	1365	4266											
GNB2L1	10399	hgsc.bcm.edu	37	chr5	180665123	180665123	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atcttgatgctggggcctgtGgcagcacacagccagtagcg	8	8	14	11	1	1	1	0	1	1	0	1	1	1	1	2	3	4	4	2	3	1	2	rs11540200	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180665123G>A	ENST00000512805.1	-	6	1161	c.753C>T	c.(751-753)gcC>gcT	p.A251A	GNB2L1_ENST00000511566.1_Intron|GNB2L1_ENST00000376817.4_Silent_p.A207A|GNB2L1_ENST00000505461.1_5'Flank|GNB2L1_ENST00000504726.1_Intron|GNB2L1_ENST00000511900.1_Silent_p.A203A|GNB2L1_ENST00000514455.1_Silent_p.A35A	NM_006098.4	NP_006089.1	P63244	GBLP_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1	251					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)		TGGGGCCTGTGGCAGCACACA	0.522													G|||	104	0.0207668	0.0772	0.0029	5008	,	,		19698	0.0		0.0	False		,,,				2504	0.0				p.A251A		Atlas-SNP	.											.	GNB2L1	22	.	0			c.C753T						PASS	.	G		300,4106	161.4+/-193.6	13,274,1916	140	125	130		753	2.2	1	5	dbSNP_120	130	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	GNB2L1	NM_006098.4		13,277,6213	AA,AG,GG		0.0349,6.8089,2.3297		251/318	180665123	303,12703	2203	4300	6503	SO:0001819	synonymous_variant	10399	exon6			GCCTGTGGCAGCA	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.753C>T	5.37:g.180665123G>A		158	0	0		168	75	0.446429	NM_006098	B3KTJ0|D3DWS0|P25388|P99049|Q53HU2|Q5J8M6|Q5VLR4|Q6FH47	Silent	SNP	ENST00000512805.1	37	CCDS34324.1	38|38	0.0173992673992674|0.0173992673992674	38|38	0.07723577235772358|0.07723577235772358	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	9.424|9.424	1.083839|1.083839	0.20309|0.20309	0.068089|0.068089	3.49E-4|3.49E-4	ENSG00000204628|ENSG00000204628	ENST00000509148;ENST00000502905;ENST00000504128|ENST00000507756;ENST00000509535	.|.	.|.	.|.	5.91|5.91	2.24|2.24	0.28232|0.28232	.|.	.|.	.|.	.|.	.|.	T|T	0.04770|0.04770	0.0129|0.0129	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.01630|0.01630	-1.1308|-1.1308	4|4	.|.	.|.	.|.	-15.4052|-15.4052	4.7881|4.7881	0.13234|0.13234	0.2979:0.0:0.5646:0.1376|0.2979:0.0:0.5646:0.1376	rs11540200;rs17851237|rs11540200;rs17851237	.|.	.|.	.|.	Y|L	25;132;158|182;109	.|.	.|.	H|P	-|-	1|2	0|0	GNB2L1|GNB2L1	180597729|180597729	0.998000|0.998000	0.40836|0.40836	0.973000|0.973000	0.42090|0.42090	0.780000|0.780000	0.44128|0.44128	0.478000|0.478000	0.22212|0.22212	0.142000|0.142000	0.18901|0.18901	-0.812000|-0.812000	0.03155|0.03155	CAC|CCA	G|0.977;A|0.023	0.023	strong		0.522	GNB2L1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372943.2	NM_006098		A	180665123	G	A	180665123	2	1	22	1	0	0	0	0	0	0	0	1	6526	1335	47	2		2	GNB2L1	5	180665123	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3849	180665123	250137	1366	4267											
IRF4	3662	hgsc.bcm.edu	37	chr6	393330	393330	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctggaagcacgcgggcaagCaggactacaaccgcgaggag	12	2	15	12	4	0	0	0	0	0	0	0	4	0	3	2	4	4	3	2	4	4	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:393330C>A	ENST00000380956.4	+	2	304	c.178C>A	c.(178-180)Cag>Aag	p.Q60K	IRF4_ENST00000495137.1_Intron	NM_001195286.1|NM_002460.3	NP_001182215.1|NP_002451.2	Q15306	IRF4_HUMAN	interferon regulatory factor 4	60					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)	p.Q60K(1)		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)		CGCGGGCAAGCAGGACTACAA	0.692			T	IGH@	MM																																p.Q60K		Atlas-SNP	.		Dom	yes		6	6p25-p23	3662	interferon regulatory factor 4		L	IRF4_ENST00000380956,NS,lymphoid_neoplasm,-2,2	IRF4	65	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C178A						PASS	.						29	26	27					6																	393330		2201	4300	6501	SO:0001583	missense	3662	exon2			GGCAAGCAGGACT	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.178C>A	6.37:g.393330C>A	ENSP00000370343:p.Gln60Lys	69	0	0		75	31	0.413333	NM_001195286	Q5VUI7|Q99660	Missense_Mutation	SNP	ENST00000380956.4	37	CCDS4469.1	.	.	.	.	.	.	.	.	.	.	C	34	5.402639	0.96030	.	.	ENSG00000137265	ENST00000380956;ENST00000412334	D	0.97505	-4.41	4.58	4.58	0.56647	Interferon regulatory factor, conserved site (1);Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (4);	0.115641	0.64402	D	0.000010	D	0.97297	0.9116	L	0.53561	1.675	0.80722	D	1	P;P;D	0.69078	0.852;0.624;0.997	P;P;D	0.74348	0.813;0.61;0.983	D	0.96246	0.9179	10	0.30854	T	0.27	-22.6787	17.6301	0.88104	0.0:1.0:0.0:0.0	.	60;60;60	F2Z3D5;Q15306-2;Q15306	.;.;IRF4_HUMAN	K	60;90	ENSP00000370343:Q60K	ENSP00000370343:Q60K	Q	+	1	0	IRF4	338330	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.909000	0.75735	2.399000	0.81585	0.306000	0.20318	CAG	.	.	none		0.692	IRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043638.1			A	393330	C	A	393330	3	1	22	1	0	0	0	0	1	0	0	0	7841	711	25	4	180	4	IRF4	6	393330	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10		393330	170721737	1367	4268											
FOXC1	2296	hgsc.bcm.edu	37	chr6	1611085	1611085	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aacctctcgctcaacgagtgCttcgtcaaggtgccgcgcga	8	8	11	14	6	3	0	2	0	1	0	5	2	3	0	2	1	4	2	2	1	3	1	rs2230096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:1611085C>T	ENST00000380874.2	+	1	405	c.405C>T	c.(403-405)tgC>tgT	p.C135C		NM_001453.2	NP_001444.2	Q12948	FOXC1_HUMAN	forkhead box C1	135					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)		TCAACGAGTGCTTCGTCAAGG	0.602													c|||	160	0.0319489	0.115	0.0101	5008	,	,		11123	0.0		0.001	False		,,,				2504	0.0				p.C135C	Pancreas(133;719 1821 3197 26645 35015)	Atlas-SNP	.											.	FOXC1	19	.	0			c.C405T						PASS	.	C		454,3952	215.1+/-234.2	26,402,1775	85	94	91		405	3.7	1	6	dbSNP_98	91	4,8596	2.2+/-6.3	0,4,4296	no	coding-synonymous	FOXC1	NM_001453.2		26,406,6071	TT,TC,CC		0.0465,10.3041,3.5215		135/554	1611085	458,12548	2203	4300	6503	SO:0001819	synonymous_variant	2296	exon1			CGAGTGCTTCGTC	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.405C>T	6.37:g.1611085C>T		270	0	0		295	130	0.440678	NM_001453	Q86UP7|Q9BYM1|Q9NUE5|Q9UDD0|Q9UP06	Silent	SNP	ENST00000380874.2	37	CCDS4473.1																																																																																			C|0.970;T|0.030	0.030	strong		0.602	FOXC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043450.1			T	1611085	C	T	1611085	2	4	22	1	0	0	0	0	0	0	0	1	6002	805	28	2		2	FOXC1	6	1611085	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1217755	1611085	169503982	1368	4269											
FOXC1	2296	hgsc.bcm.edu	37	chr6	1612243	1612243	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggatcggcttgaacaactcTccagtgaacgggaatagtag	13	8	12	8	2	1	2	0	2	1	0	3	4	1	4	1	3	3	2	1	3	6	3	rs73406891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:1612243T>G	ENST00000380874.2	+	1	1563	c.1563T>G	c.(1561-1563)tcT>tcG	p.S521S		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)		TGAACAACTCTCCAGTGAACG	0.602													T|||	160	0.0319489	0.115	0.0101	5008	,	,		9192	0.0		0.001	False		,,,				2504	0.0				p.S521S	Pancreas(133;719 1821 3197 26645 35015)	Atlas-SNP	.											.	FOXC1	19	.	0			c.T1563G						PASS	.	T		452,3950	202.1+/-225.0	23,406,1772	64	47	52		1563	-4.6	1	6	dbSNP_130	52	4,8594	1.2+/-3.3	0,4,4295	no	coding-synonymous	FOXC1	NM_001453.2		23,410,6067	GG,GT,TT		0.0465,10.2681,3.5077		521/554	1612243	456,12544	2201	4299	6500	SO:0001819	synonymous_variant	2296	exon1			CAACTCTCCAGTG	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.1563T>G	6.37:g.1612243T>G		43	0	0		61	24	0.393443	NM_001453	Q86UP7|Q9BYM1|Q9NUE5|Q9UDD0|Q9UP06	Silent	SNP	ENST00000380874.2	37	CCDS4473.1																																																																																			T|0.963;G|0.037	0.037	strong		0.602	FOXC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043450.1			G	1612243	T	G	1612243	2	3	22	1	0	0	0	0	0	0	0	1	6002	1538	54	5		5	FOXC1	6	1612243	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1158	1612243	169502824	1369	4270											
BPHL	670	hgsc.bcm.edu	37	chr6	3152760	3152760	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcaaacacaacctgcattTgcgttttgcagatgaattca	13	11	8	9	1	1	2	1	1	0	1	1	2	1	2	1	1	5	4	1	1	3	4	rs2231370	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:3152760T>C	ENST00000380379.5	+	7	876	c.827T>C	c.(826-828)tTg>tCg	p.L276S	RP1-40E16.11_ENST00000447644.1_RNA|BPHL_ENST00000434640.1_Missense_Mutation_p.L259S|BPHL_ENST00000380368.2_3'UTR|BPHL_ENST00000380375.3_Missense_Mutation_p.L259S|TUBB2A_ENST00000489942.1_5'Flank|BPHL_ENST00000464040.1_3'UTR	NM_004332.2	NP_004323.2	Q86WA6	BPHL_HUMAN	biphenyl hydrolase-like (serine hydrolase)	276					cellular amino acid metabolic process (GO:0006520)|response to toxic substance (GO:0009636)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			endometrium(4)|kidney(1)|large_intestine(2)|lung(6)	13	Ovarian(93;0.0386)	all_hematologic(90;0.108)				AACCTGCATTTGCGTTTTGCA	0.438													T|||	250	0.0499201	0.1747	0.0173	5008	,	,		21159	0.001		0.005	False		,,,				2504	0.001				p.L276S		Atlas-SNP	.											.	BPHL	32	.	0			c.T827C						PASS	.	T	SER/LEU	588,3818	261.0+/-264.0	42,504,1657	168	153	158		827	4.7	0.1	6	dbSNP_98	158	31,8569	21.0+/-64.5	0,31,4269	yes	missense	BPHL	NM_004332.2	145	42,535,5926	CC,CT,TT		0.3605,13.3454,4.7593	probably-damaging	276/292	3152760	619,12387	2203	4300	6503	SO:0001583	missense	670	exon7			TGCATTTGCGTTT	X81372	CCDS4483.2	6p25	2008-08-29	2008-08-29		ENSG00000137274	ENSG00000137274			1094	protein-coding gene	gene with protein product	"breast epithelial mucin-associated antigen"	603156		MCNAA		7759552, 9721218, 15832508	Standard	NM_004332		Approved	Bph-rp	uc003mva.3	Q86WA6	OTTHUMG00000014140	ENST00000380379.5:c.827T>C	6.37:g.3152760T>C	ENSP00000369739:p.Leu276Ser	146	0	0		168	84	0.5	NM_004332	Q00306|Q13855|Q3KP51	Missense_Mutation	SNP	ENST00000380379.5	37	CCDS4483.2	104	0.047619047619047616	92	0.18699186991869918	5	0.013812154696132596	1	0.0017482517482517483	6	0.0079155672823219	T	19.10	3.761514	0.69763	0.133454	0.003605	ENSG00000137274	ENST00000434640;ENST00000380375;ENST00000380379	T;T;T	0.72051	-0.62;-0.62;-0.62	5.9	4.74	0.60224	.	0.069235	0.64402	D	0.000014	T	0.77061	0.4075	M	0.73430	2.235	0.22354	P	0.999176454	D;D	0.76494	0.999;0.999	D;D	0.79784	0.993;0.988	T	0.80801	-0.1220	9	0.56958	D	0.05	-17.8489	11.8569	0.52441	0.0:0.0677:0.0:0.9323	rs2231370;rs52831698;rs2231370	276;259	Q86WA6;Q86WA6-2	BPHL_HUMAN;.	S	259;259;276	ENSP00000390472:L259S;ENSP00000369734:L259S;ENSP00000369739:L276S	ENSP00000369734:L259S	L	+	2	0	BPHL	3097759	0.996000	0.38824	0.080000	0.20451	0.991000	0.79684	5.961000	0.70356	1.064000	0.40671	0.528000	0.53228	TTG	T|0.949;C|0.051	0.051	strong		0.438	BPHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039670.5			C	3152760	T	C	3152760	3	2	22	1	0	0	0	0	1	0	0	0	1491	1821	63	3	853	3	BPHL	6	3152760	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1540517	3152760	167962307	1370	4271											
PECI	10455	hgsc.bcm.edu	37	chr6	4119492	4119492	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttggcctaggtgactaaaTggtgtatgaaatgttgcctg	9	14	12	6	0	0	2	0	2	0	0	0	2	0	2	2	3	1	2	2	3	5	5	rs10708	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:4119492T>C	ENST00000380118.3	-	8	849	c.813A>G	c.(811-813)ccA>ccG	p.P271P	ECI2_ENST00000465828.1_Silent_p.P241P|ECI2_ENST00000413766.2_Silent_p.P104P|ECI2_ENST00000380125.2_Silent_p.P241P|C6orf201_ENST00000430835.2_Intron|C6orf201_ENST00000333388.5_Intron|C6orf201_ENST00000380175.4_Intron|ECI2_ENST00000361538.2_Silent_p.P241P			O75521	ECI2_HUMAN	enoyl-CoA delta isomerase 2	271	ECH-like.				fatty acid catabolic process (GO:0009062)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	dodecenoyl-CoA delta-isomerase activity (GO:0004165)|fatty-acyl-CoA binding (GO:0000062)|receptor binding (GO:0005102)			endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	11						GGTGACTAAATGGTGTATGAA	0.378													T|||	214	0.0427316	0.1536	0.0159	5008	,	,		18618	0.0		0.0	False		,,,				2504	0.0				p.P271P		Atlas-SNP	.											.	ECI2	59	.	0			c.A813G						PASS	.	T	,,,	590,3816	258.9+/-262.7	51,488,1664	77	79	78		,723,723,813	-5.8	0.7	6	dbSNP_130	78	6,8594	5.0+/-18.6	0,6,4294	no	intron,coding-synonymous,coding-synonymous,coding-synonymous	ECI2,C6orf201	NM_001085401.1,NM_001166010.1,NM_006117.2,NM_206836.2	,,,	51,494,5958	CC,CT,TT		0.0698,13.3908,4.5825	,,,	,241/365,241/365,271/395	4119492	596,12410	2203	4300	6503	SO:0001819	synonymous_variant	10455	exon8			ACTAAATGGTGTA	AF069301	CCDS4490.1, CCDS43420.1, CCDS43420.2	6p24.3	2011-03-15	2011-03-15	2011-03-15	ENSG00000198721	ENSG00000198721			14601	protein-coding gene	gene with protein product	"acyl-Coenzyme A binding domain containing 2", " Hepatocellular carcinoma-associated antigen 88"	608024	"peroxisomal D3,D2-enoyl-CoA isomerase"	PECI		10419495	Standard	NM_206836		Approved	ACBD2, DRS1, HCA88	uc003mwf.3	O75521	OTTHUMG00000014158	ENST00000380118.3:c.813A>G	6.37:g.4119492T>C		80	0	0		56	27	0.482143	NM_206836	Q5JYK5|Q5JYK7|Q7L124|Q8N0X0|Q9BUE9|Q9H0T9|Q9NQH1|Q9NYH7|Q9UN55	Silent	SNP	ENST00000380118.3	37	CCDS43420.2																																																																																			T|0.962;C|0.038	0.038	strong		0.378	ECI2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039716.4	NM_006117		C	4119492	T	C	4119492	2	2	22	1	0	0	0	0	0	0	0	1	11725	1451	51	3		3	PECI	6	4119492	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	966732	4119492	166995575	1371	4272											
C6orf201	404220	hgsc.bcm.edu	37	chr6	4122279	4122279	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagctaaagggacacaaacAggtacatgcaaagttgccag	17	5	10	9	0	0	0	0	0	0	0	0	1	0	1	1	2	5	4	1	2	5	3	rs17137678	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:4122279A>G	ENST00000380175.4	+	4	1146	c.381A>G	c.(379-381)acA>acG	p.T127T	ECI2_ENST00000465828.1_Intron|ECI2_ENST00000413766.2_Intron|ECI2_ENST00000380125.2_Intron|C6orf201_ENST00000430835.2_Splice_Site_p.T127T|C6orf201_ENST00000333388.5_Splice_Site_p.T130T|ECI2_ENST00000361538.2_Intron|ECI2_ENST00000380118.3_Intron	NM_001085401.2	NP_001078870.1	Q7Z4U5	CF201_HUMAN	chromosome 6 open reading frame 201	127										central_nervous_system(1)|endometrium(3)|lung(2)	6	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				GGACACAAACAGGTACATGCA	0.418													A|||	125	0.0249601	0.09	0.0086	5008	,	,		15796	0.0		0.0	False		,,,				2504	0.0				p.T127T		Atlas-SNP	.											.	C6orf201	17	.	0			c.A381G						PASS	.	A	,,,	308,3458		23,262,1598	63	61	62		381,,,	3.2	0.2	6	dbSNP_123	62	4,8226		0,4,4111	yes	coding-synonymous-near-splice,intron,intron,intron	ECI2,C6orf201	NM_001085401.1,NM_001166010.1,NM_006117.2,NM_206836.2	,,,	23,266,5709	GG,GA,AA		0.0486,8.1784,2.6009	,,,	127/141,,,	4122279	312,11684	1883	4115	5998	SO:0001630	splice_region_variant	404220	exon4			ACAAACAGGTACA	BC047663	CCDS43419.1	6p25.2	2012-02-21			ENSG00000185689	ENSG00000185689			21620	protein-coding gene	gene with protein product							Standard	NM_001085401		Approved	dJ1013A10.5	uc003mwa.4	Q7Z4U5	OTTHUMG00000014160	ENST00000380175.4:c.382+1A>G	6.37:g.4122279A>G		209	0	0		210	114	0.542857	NM_001085401	A6NLI6|Q6NXN5	Silent	SNP	ENST00000380175.4	37	CCDS43419.1																																																																																			A|0.978;G|0.022	0.022	strong		0.418	C6orf201-001	KNOWN	NMD_exception|basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000314019.2	NM_001085401	Silent	G	4122279	A	G	4122279	5	3	22	1	0	0	0	0	0	0	1	0	2353	202	7	3	391	3	C6orf201	6	4122279	Splice_Site	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2787	4122279	166992788	1372	4273											
CDYL	9425	hgsc.bcm.edu	37	chr6	4892381	4892381	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agccccgttaagagcaggacCgcagtggacggctttcagag	10	6	14	11	3	1	2	1	0	0	2	1	4	1	4	3	3	2	4	3	3	1	2	rs734783	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:4892381C>T	ENST00000328908.5	+	4	752	c.621C>T	c.(619-621)acC>acT	p.T207T	CDYL_ENST00000449732.2_Silent_p.T21T|CDYL_ENST00000397588.3_Silent_p.T153T|CDYL_ENST00000472453.1_Intron|CDYL_ENST00000343762.5_Silent_p.T21T			Q9Y232	CDYL1_HUMAN	chromodomain protein, Y-like	207	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)		AGAGCAGGACCGCAGTGGACG	0.587													C|||	250	0.0499201	0.18	0.0159	5008	,	,		19239	0.0		0.001	False		,,,				2504	0.0				p.T153T		Atlas-SNP	.											.	CDYL	74	.	0			c.C459T						PASS	.	C	,,	664,3742	284.3+/-277.5	59,546,1598	66	67	67		63,63,459	3.8	0.8	6	dbSNP_86	67	20,8580	14.6+/-50.1	0,20,4280	no	coding-synonymous,coding-synonymous,coding-synonymous	CDYL	NM_001143970.1,NM_001143971.1,NM_004824.3	,,	59,566,5878	TT,TC,CC		0.2326,15.0704,5.2591	,,	21/413,21/413,153/545	4892381	684,12322	2203	4300	6503	SO:0001819	synonymous_variant	9425	exon2			CAGGACCGCAGTG	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.621C>T	6.37:g.4892381C>T		54	0	0		91	47	0.516484	NM_004824	A8K6D6|B4DLG4|Q0VDG7|Q32NC5|Q5VX99|Q6P7T5|Q9BWZ2|Q9Y424	Silent	SNP	ENST00000328908.5	37																																																																																				C|0.956;T|0.044	0.044	strong		0.587	CDYL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000039736.1	NM_004824		T	4892381	C	T	4892381	2	4	22	1	0	0	0	0	0	0	0	1	3187	639	23	1		1	CDYL	6	4892381	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	770102	4892381	166222686	1373	4274											
RPP40	10799	hgsc.bcm.edu	37	chr6	4996611	4996611	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttggctgatgctcctgaatTtggtacttggaaaaatatga	11	15	10	5	0	0	3	0	3	0	0	1	4	1	4	1	3	2	3	1	3	5	5	rs61730291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:4996611T>G	ENST00000380051.2	-	6	647	c.603A>C	c.(601-603)caA>caC	p.Q201H	RPP40_ENST00000464646.1_Missense_Mutation_p.Q141H|RPP40_ENST00000319533.5_Missense_Mutation_p.Q178H	NM_006638.2	NP_006629.2	O75818	RPP40_HUMAN	ribonuclease P/MRP 40kDa subunit	201					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)				GCTCCTGAATTTGGTACTTGG	0.473													T|||	158	0.0315495	0.115	0.0086	5008	,	,		19568	0.0		0.0	False		,,,				2504	0.0				p.Q201H		Atlas-SNP	.											.	RPP40	36	.	0			c.A603C						PASS	.	T	HIS/GLN	431,3975	209.8+/-230.5	23,385,1795	105	101	103		603	-5.1	0.6	6	dbSNP_129	103	0,8600		0,0,4300	yes	missense	RPP40	NM_006638.2	24	23,385,6095	GG,GT,TT		0.0,9.7821,3.3139	benign	201/364	4996611	431,12575	2203	4300	6503	SO:0001583	missense	10799	exon6			CTGAATTTGGTAC	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.603A>C	6.37:g.4996611T>G	ENSP00000369391:p.Gln201His	132	0	0		98	47	0.479592	NM_006638	Q5VX97|Q8WVK8	Missense_Mutation	SNP	ENST00000380051.2	37	CCDS34333.1	61	0.027930402930402932	58	0.11788617886178862	3	0.008287292817679558	0	0.0	0	0.0	T	13.36	2.213743	0.39102	0.097821	0.0	ENSG00000124787	ENST00000380051;ENST00000319533;ENST00000464646	T;T;T	0.44083	0.93;0.93;0.93	5.23	-5.06	0.02946	.	0.748127	0.13823	N	0.360291	T	0.13841	0.0335	M	0.67953	2.075	0.29984	N	0.817458	B;B	0.09022	0.001;0.002	B;B	0.12156	0.003;0.007	T	0.12016	-1.0564	10	0.44086	T	0.13	-1.8359	2.4943	0.04618	0.1158:0.3526:0.2381:0.2936	.	178;201	O75818-2;O75818	.;RPP40_HUMAN	H	201;178;141	ENSP00000369391:Q201H;ENSP00000317998:Q178H;ENSP00000419431:Q141H	ENSP00000317998:Q178H	Q	-	3	2	RPP40	4941610	0.466000	0.25823	0.631000	0.29282	0.902000	0.53008	-0.492000	0.06467	-0.982000	0.03515	-0.321000	0.08615	CAA	T|0.971;G|0.029	0.029	strong		0.473	RPP40-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039733.2	NM_006638		G	4996611	T	G	4996611	3	3	22	1	0	0	0	0	1	0	0	0	13629	1838	64	5	500	5	RPP40	6	4996611	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	104230	4996611	166118456	1374	4275											
RREB1	6239	hgsc.bcm.edu	37	chr6	7231280	7231280	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccttctcttcctgtaacttTggggcccagcggaatcctgg	5	12	10	14	1	1	0	0	0	1	0	4	1	3	1	4	4	2	1	4	4	2	4	rs115093903	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7231280T>C	ENST00000349384.6	+	10	3262	c.2948T>C	c.(2947-2949)tTg>tCg	p.L983S	RREB1_ENST00000379933.3_Missense_Mutation_p.L983S|RREB1_ENST00000379938.2_Missense_Mutation_p.L983S|RREB1_ENST00000334984.6_Missense_Mutation_p.L983S	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	983	Pro-rich.				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)				CCTGTAACTTTGGGGCCCAGC	0.692													T|||	74	0.0147764	0.0545	0.0029	5008	,	,		12856	0.0		0.0	False		,,,				2504	0.0				p.L983S		Atlas-SNP	.											.	RREB1	242	.	0			c.T2948C						PASS	.	T	SER/LEU,SER/LEU,SER/LEU,SER/LEU	180,4222		4,172,2025	18	21	20		2948,2948,2948,2948	3.3	0	6	dbSNP_132	20	0,8600		0,0,4300	no	missense,missense,missense,missense	RREB1	NM_001003698.3,NM_001003699.3,NM_001003700.1,NM_001168344.1	145,145,145,145	4,172,6325	CC,CT,TT		0.0,4.0891,1.3844	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	983/1688,983/1743,983/1477,983/1688	7231280	180,12822	2201	4300	6501	SO:0001583	missense	6239	exon10			TAACTTTGGGGCC	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.2948T>C	6.37:g.7231280T>C	ENSP00000305560:p.Leu983Ser	85	0	0		74	36	0.486486	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	18	0.008241758241758242	18	0.036585365853658534	0	0.0	0	0.0	0	0.0	T	12.76	2.034987	0.35893	0.040891	0.0	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984	T;T;T;T	0.11495	2.89;2.85;2.89;2.77	5.74	3.35	0.38373	.	0.784404	0.10919	N	0.619695	T	0.03095	0.0091	L	0.43152	1.355	0.09310	N	1	B;B;B	0.32245	0.277;0.361;0.038	B;B;B	0.32289	0.143;0.107;0.037	T	0.46105	-0.9215	10	0.22109	T	0.4	-0.1912	8.4336	0.32773	0.0:0.1663:0.0:0.8337	.	983;983;983	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	S	983	ENSP00000369265:L983S;ENSP00000369270:L983S;ENSP00000305560:L983S;ENSP00000335574:L983S	ENSP00000335574:L983S	L	+	2	0	RREB1	7176279	0.264000	0.24093	0.003000	0.11579	0.012000	0.07955	1.900000	0.39828	0.442000	0.26555	0.533000	0.62120	TTG	T|0.989;C|0.011	0.011	strong		0.692	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1			C	7231280	T	C	7231280	3	2	22	1	0	0	0	0	1	0	0	0	13694	1821	63	3	2974	3	RREB1	6	7231280	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2234669	7231280	163883787	1375	4276											
RREB1	6239	hgsc.bcm.edu	37	chr6	7231736	7231736	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctcccgctccagccagcaGcccagaggctgcctctccca	6	5	9	21	1	1	1	0	0	1	1	4	1	3	1	7	1	4	3	7	1	0	0	rs116295722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7231736G>T	ENST00000349384.6	+	10	3718	c.3404G>T	c.(3403-3405)aGc>aTc	p.S1135I	RREB1_ENST00000379933.3_Missense_Mutation_p.S1135I|RREB1_ENST00000379938.2_Missense_Mutation_p.S1135I|RREB1_ENST00000334984.6_Missense_Mutation_p.S1135I	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1135					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)				CCAGCCAGCAGCCCAGAGGCT	0.687													G|||	12	0.00239617	0.0091	0.0	5008	,	,		13021	0.0		0.0	False		,,,				2504	0.0				p.S1135I		Atlas-SNP	.											.	RREB1	242	.	0			c.G3404T						PASS	.	G	ILE/SER,ILE/SER,ILE/SER,ILE/SER	17,4291		0,17,2137	8	12	11		3404,3404,3404,3404	5.7	1	6	dbSNP_132	11	1,8493		0,1,4246	yes	missense,missense,missense,missense	RREB1	NM_001003698.3,NM_001003699.3,NM_001003700.1,NM_001168344.1	142,142,142,142	0,18,6383	TT,TG,GG		0.0118,0.3946,0.1406	probably-damaging,probably-damaging,probably-damaging,probably-damaging	1135/1688,1135/1743,1135/1477,1135/1688	7231736	18,12784	2154	4247	6401	SO:0001583	missense	6239	exon10			CCAGCAGCCCAGA	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.3404G>T	6.37:g.7231736G>T	ENSP00000305560:p.Ser1135Ile	104	0	0		110	58	0.527273	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	17.76	3.469337	0.63625	0.003946	1.18E-4	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984	T;T;T;T	0.13307	2.6;2.7;2.6;2.6	5.73	5.73	0.89815	.	0.089674	0.47455	D	0.000240	T	0.21186	0.0510	M	0.62723	1.935	0.38993	D	0.959191	D;D;D	0.67145	0.993;0.993;0.996	P;P;D	0.65010	0.9;0.855;0.931	T	0.00778	-1.1570	10	0.72032	D	0.01	-50.0022	10.0245	0.42063	0.1544:0.0:0.8456:0.0	.	1135;1135;1135	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	I	1135	ENSP00000369265:S1135I;ENSP00000369270:S1135I;ENSP00000305560:S1135I;ENSP00000335574:S1135I	ENSP00000335574:S1135I	S	+	2	0	RREB1	7176735	0.693000	0.27728	0.999000	0.59377	0.626000	0.37791	1.532000	0.36029	2.695000	0.91970	0.655000	0.94253	AGC	G|0.997;T|0.003	0.003	strong		0.687	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1			T	7231736	G	T	7231736	3	4	22	1	0	0	0	0	1	0	0	0	13694	971	34	4	3430	4	RREB1	6	7231736	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	456	7231736	163883331	1376	4277											
RREB1	6239	hgsc.bcm.edu	37	chr6	7246994	7246994	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagggcgacggcgaggcaggCgccgggggcgcggcctcgca	5	1	22	13	8	0	0	0	0	0	0	1	3	0	0	2	7	0	2	2	7	0	0	rs187908583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7246994C>T	ENST00000349384.6	+	11	4460	c.4146C>T	c.(4144-4146)ggC>ggT	p.G1382G	RREB1_ENST00000379933.3_Silent_p.G1382G|RREB1_ENST00000379938.2_Silent_p.G1437G|RREB1_ENST00000334984.6_Intron	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1382					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)				GCGAGGCAGGCGCCGGGGGCG	0.692													C|||	33	0.00658946	0.025	0.0	5008	,	,		11874	0.0		0.0	False		,,,				2504	0.0				p.G1437G		Atlas-SNP	.											.	RREB1	242	.	0			c.C4311T						PASS	.	C	,,,	60,4166		0,60,2053	11	13	13		4146,4311,,4146	-3.5	0	6		13	1,8303		0,1,4151	no	coding-synonymous,coding-synonymous,intron,coding-synonymous	RREB1	NM_001003698.3,NM_001003699.3,NM_001003700.1,NM_001168344.1	,,,	0,61,6204	TT,TC,CC		0.012,1.4198,0.4868	,,,	1382/1688,1437/1743,,1382/1688	7246994	61,12469	2113	4152	6265	SO:0001819	synonymous_variant	6239	exon12			GGCAGGCGCCGGG	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.4146C>T	6.37:g.7246994C>T		14	0	0		16	10	0.625	NM_001003699	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Silent	SNP	ENST00000349384.6	37	CCDS34336.1																																																																																			C|0.993;T|0.007	0.007	strong		0.692	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1			T	7246994	C	T	7246994	2	4	22	1	0	0	0	0	0	0	0	1	13694	755	27	1		1	RREB1	6	7246994	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	15258	7246994	163868073	1377	4278											
CAGE1	285782	hgsc.bcm.edu	37	chr6	7379031	7379031	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgtatttgcagaaacactaGtttccattggattttcttcc	9	17	6	9	0	1	1	0	0	1	1	3	2	3	2	2	1	2	3	2	1	3	8	rs10223538	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7379031G>A	ENST00000512086.1	-	4	708	c.506C>T	c.(505-507)aCt>aTt	p.T169I	CAGE1_ENST00000502583.1_Missense_Mutation_p.T169I|CAGE1_ENST00000509324.1_Intron|CAGE1_ENST00000338150.4_Missense_Mutation_p.T169I|CAGE1_ENST00000379918.4_Missense_Mutation_p.T169I|CAGE1_ENST00000296742.7_Missense_Mutation_p.T33I			Q8TC20	CAGE1_HUMAN	cancer antigen 1	169			T -> I (in dbSNP:rs10223538).							breast(1)|cervix(1)|endometrium(3)|kidney(2)|lung(11)|urinary_tract(1)	19	Ovarian(93;0.0418)					AGAAACACTAGTTTCCATTGG	0.388													G|||	216	0.043131	0.1543	0.0159	5008	,	,		16170	0.0		0.0	False		,,,				2504	0.001				p.T169I		Atlas-SNP	.											.	CAGE1	165	.	0			c.C506T						PASS	.	G	ILE/THR,ILE/THR,ILE/THR	470,3226		30,410,1408	123	121	122		506,506,98	0.7	0.5	6	dbSNP_119	122	5,8187		0,5,4091	yes	missense,missense,missense	CAGE1	NM_001170692.1,NM_001170693.1,NM_205864.2	89,89,89	30,415,5499	AA,AG,GG		0.061,12.7165,3.9956	possibly-damaging,possibly-damaging,possibly-damaging	169/840,169/825,33/642	7379031	475,11413	1848	4096	5944	SO:0001583	missense	285782	exon4			ACACTAGTTTCCA	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.506C>T	6.37:g.7379031G>A	ENSP00000427583:p.Thr169Ile	169	0	0		149	72	0.483221	NM_001170693	D6RCT9|Q5TAM0|Q86TM4|Q8N7R5	Missense_Mutation	SNP	ENST00000512086.1	37		74	0.03388278388278388	69	0.1402439024390244	5	0.013812154696132596	0	0.0	0	0.0	G	13.88	2.367959	0.42003	0.127165	6.1E-4	ENSG00000164304	ENST00000541116;ENST00000379918;ENST00000502583;ENST00000296742;ENST00000512086;ENST00000338150;ENST00000542431;ENST00000512691	T;T;T;T;T;T	0.36878	1.23;1.23;1.23;1.23;1.23;1.23	5.23	0.698	0.18087	.	0.571069	0.16966	N	0.192296	T	0.12817	0.0311	L	0.56769	1.78	0.09310	N	1	B	0.20052	0.041	B	0.21917	0.037	T	0.26189	-1.0110	10	0.87932	D	0	-2.6713	2.1016	0.03681	0.1193:0.3601:0.3254:0.1953	rs10223538;rs52806665;rs10223538	169	Q8TC20	CAGE1_HUMAN	I	169;169;169;33;169;169;169;181	ENSP00000369250:T169I;ENSP00000425493:T169I;ENSP00000296742:T33I;ENSP00000427583:T169I;ENSP00000338107:T169I;ENSP00000423789:T181I	ENSP00000296742:T33I	T	-	2	0	CAGE1	7324030	0.274000	0.24191	0.457000	0.27056	0.637000	0.38172	0.554000	0.23407	0.271000	0.22005	0.655000	0.94253	ACT	G|0.944;A|0.056	0.056	strong		0.388	CAGE1-008	PUTATIVE	non_canonical_conserved|basic	protein_coding	protein_coding	OTTHUMT00000367136.1	NM_175745		A	7379031	G	A	7379031	3	1	22	1	0	0	0	0	1	0	0	0	2574	1029	36	2	2163	2	CAGE1	6	7379031	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	132037	7379031	163736036	1378	4279											
DSP	1832	hgsc.bcm.edu	37	chr6	7565596	7565596	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgaacctcctgtgcagaaagCgtcctttgagaggatggatc	10	10	12	9	1	0	3	0	2	0	2	3	6	2	5	3	2	3	1	3	2	2	1	rs139509870	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7565596C>T	ENST00000379802.3	+	7	1123	c.782C>T	c.(781-783)gCg>gTg	p.A261V	DSP_ENST00000418664.2_Missense_Mutation_p.A261V	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	261	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)		GTGCAGAAAGCGTCCTTTGAG	0.473													C|||	2	0.000399361	0.0	0.0029	5008	,	,		19062	0.0		0.0	False		,,,				2504	0.0				p.A261V		Atlas-SNP	.											.	DSP	306	.	0			c.C782T						PASS	.	C	VAL/ALA,VAL/ALA	5,4401	9.9+/-24.2	0,5,2198	106	95	98		782,782	4.6	0.7	6	dbSNP_134	98	0,8600		0,0,4300	no	missense,missense	DSP	NM_001008844.1,NM_004415.2	64,64	0,5,6498	TT,TC,CC		0.0,0.1135,0.0384	benign,benign	261/2273,261/2872	7565596	5,13001	2203	4300	6503	SO:0001583	missense	1832	exon7			AGAAAGCGTCCTT	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.782C>T	6.37:g.7565596C>T	ENSP00000369129:p.Ala261Val	58	0	0		50	22	0.44	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	37	CCDS4501.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	14.58	2.579212	0.46006	0.001135	0.0	ENSG00000096696	ENST00000379802;ENST00000418664;ENST00000397483	D;D	0.92752	-3.1;-3.1	5.42	4.55	0.56014	.	0.366306	0.23134	N	0.051542	T	0.74854	0.3771	L	0.29908	0.895	0.25172	N	0.990271	B;B	0.26483	0.15;0.15	B;B	0.14578	0.006;0.011	T	0.66484	-0.5912	10	0.45353	T	0.12	.	7.1237	0.25458	0.1483:0.7018:0.0:0.1499	.	308;261	Q4LE79;P15924	.;DESP_HUMAN	V	261;261;66	ENSP00000369129:A261V;ENSP00000396591:A261V	ENSP00000369129:A261V	A	+	2	0	DSP	7510595	0.687000	0.27671	0.682000	0.30024	0.913000	0.54294	1.332000	0.33805	1.284000	0.44531	0.563000	0.77884	GCG	C|1.000;T|0.000	0.000	strong		0.473	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		T	7565596	C	T	7565596	3	4	22	1	0	0	0	0	1	0	0	0	4783	768	27	1	808	1	DSP	6	7565596	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	186565	7565596	163549471	1379	4280											
DSP	1832	hgsc.bcm.edu	37	chr6	7576569	7576569	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcaagcaattgaggaattaTcgtgataactatcaggcttt	14	13	8	6	1	2	2	2	2	0	0	3	3	2	3	0	2	2	2	0	2	6	5	rs146407262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7576569T>C	ENST00000379802.3	+	19	3014	c.2673T>C	c.(2671-2673)taT>taC	p.Y891Y	DSP_ENST00000418664.2_Silent_p.Y891Y	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	891	Globular 1.				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)		TGAGGAATTATCGTGATAACT	0.383													T|||	35	0.00698882	0.0257	0.0014	5008	,	,		18556	0.0		0.0	False		,,,				2504	0.0				p.Y891Y		Atlas-SNP	.											.	DSP	306	.	0			c.T2673C						PASS	.	T	,	100,4306	79.9+/-118.3	1,98,2104	107	110	109		2673,2673	-6.6	0.9	6	dbSNP_134	109	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	DSP	NM_001008844.1,NM_004415.2	,	1,98,6404	CC,CT,TT		0.0,2.2696,0.7689	,	891/2273,891/2872	7576569	100,12906	2203	4300	6503	SO:0001819	synonymous_variant	1832	exon19			GAATTATCGTGAT	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.2673T>C	6.37:g.7576569T>C		89	0	0		85	38	0.447059	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Silent	SNP	ENST00000379802.3	37	CCDS4501.1																																																																																			T|0.991;C|0.009	0.009	strong		0.383	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		C	7576569	T	C	7576569	2	2	22	1	0	0	0	0	0	0	0	1	4783	1442	50	3		3	DSP	6	7576569	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	10973	7576569	163538498	1380	4281											
DSP	1832	hgsc.bcm.edu	37	chr6	7585795	7585795	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cgcacagaggctgcaagacaCcagcagctatgccaaaatcc	14	4	9	14	1	0	2	0	0	0	2	1	2	1	2	3	1	4	5	3	1	4	1	rs34884895	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7585795C>A	ENST00000379802.3	+	24	8641	c.8300C>A	c.(8299-8301)aCc>aAc	p.T2767N	DSP_ENST00000418664.2_Missense_Mutation_p.T2168N	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2767	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)		CTGCAAGACACCAGCAGCTAT	0.512													C|||	35	0.00698882	0.0257	0.0014	5008	,	,		807	0.0		0.0	False		,,,				2504	0.0				p.T2767N		Atlas-SNP	.											.	DSP	306	.	0			c.C8300A						PASS	.	C	ASN/THR,ASN/THR	100,4306	79.3+/-117.8	1,98,2104	70	80	77		6503,8300	2.2	1	6	dbSNP_126	77	0,8600		0,0,4300	yes	missense,missense	DSP	NM_001008844.1,NM_004415.2	65,65	1,98,6404	AA,AC,CC		0.0,2.2696,0.7689	possibly-damaging,possibly-damaging	2168/2273,2767/2872	7585795	100,12906	2203	4300	6503	SO:0001583	missense	1832	exon24			AAGACACCAGCAG	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.8300C>A	6.37:g.7585795C>A	ENSP00000369129:p.Thr2767Asn	90	0	0		90	49	0.544444	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	37	CCDS4501.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	C	15.09	2.730333	0.48939	0.022696	0.0	ENSG00000096696	ENST00000379802;ENST00000418664	T;T	0.73258	-0.73;-0.73	5.49	2.23	0.28157	.	0.171164	0.41396	D	0.000892	T	0.64283	0.2584	L	0.60455	1.87	0.22292	N	0.999227	D;P	0.67145	0.996;0.899	D;P	0.68483	0.958;0.689	T	0.57562	-0.7790	10	0.26408	T	0.33	.	8.2741	0.31862	0.0:0.6483:0.0:0.3517	rs34884895	2215;2767	Q4LE79;P15924	.;DESP_HUMAN	N	2767;2168	ENSP00000369129:T2767N;ENSP00000396591:T2168N	ENSP00000369129:T2767N	T	+	2	0	DSP	7530794	0.206000	0.23470	1.000000	0.80357	0.997000	0.91878	0.743000	0.26231	0.204000	0.20548	0.561000	0.74099	ACC	C|0.991;A|0.009	0.009	strong		0.512	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		A	7585795	C	A	7585795	3	1	22	1	0	0	0	0	1	0	0	0	4783	507	18	4	8394	4	DSP	6	7585795	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	9226	7585795	163529272	1381	4282											
TXNDC5	81567	hgsc.bcm.edu	37	chr6	7883386	7883386	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caactgtgttcctaaagttcGtctttcgcttggctcaggac	7	14	9	11	2	2	0	1	0	1	0	5	1	3	1	1	2	1	4	1	2	3	5	rs9502656	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7883386G>A	ENST00000379757.4	-	10	1327	c.1290C>T	c.(1288-1290)gaC>gaT	p.D430D	TXNDC5_ENST00000539054.1_Silent_p.D358D|BLOC1S5-TXNDC5_ENST00000439343.2_3'UTR|TXNDC5_ENST00000473453.1_Silent_p.D322D	NM_030810.3	NP_110437.2	Q8NBS9	TXND5_HUMAN	thioredoxin domain containing 5 (endoplasmic reticulum)	430					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)					CCTAAAGTTCGTCTTTCGCTT	0.557													G|||	375	0.0748802	0.2466	0.0331	5008	,	,		17755	0.0		0.0209	False		,,,				2504	0.0051				p.D430D	Ovarian(119;1430 1625 3928 26125 34589)	Atlas-SNP	.											.	TXNDC5	33	.	0			c.C1290T						PASS	.	G	,	895,3511	345.9+/-308.8	94,707,1402	159	117	131		966,1290	-10.3	0	6	dbSNP_119	131	184,8416	82.9+/-145.4	4,176,4120	no	coding-synonymous,coding-synonymous	TXNDC5	NM_001145549.2,NM_030810.3	,	98,883,5522	AA,AG,GG		2.1395,20.3132,8.2962	,	322/325,430/433	7883386	1079,11927	2203	4300	6503	SO:0001819	synonymous_variant	81567	exon10			AAGTTCGTCTTTC	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.1290C>T	6.37:g.7883386G>A		67	0	0		65	25	0.384615	NM_030810	B2RDM2|Q5TCQ0|Q8ND33|Q8TCT2|Q9BVH9	Silent	SNP	ENST00000379757.4	37	CCDS4505.1																																																																																			G|0.920;A|0.080	0.080	strong		0.557	TXNDC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039792.1	NM_030810		A	7883386	G	A	7883386	2	1	22	1	0	0	0	0	0	0	0	1	16814	1136	40	1		1	TXNDC5	6	7883386	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	297591	7883386	163231681	1382	4283											
TMEM14B	81853	hgsc.bcm.edu	37	chr6	10751379	10751379	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cttctaggcagcgtgccgtcCctggctgcagggctgctctt	3	11	13	14	2	2	0	0	0	2	0	3	0	3	0	2	3	4	5	2	3	1	3	rs1046427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:10751379C>T	ENST00000379542.5	+	4	281	c.114C>T	c.(112-114)tcC>tcT	p.S38S	TMEM14B_ENST00000379530.3_Intron|TMEM14B_ENST00000461342.1_Intron|TMEM14B_ENST00000473276.1_Intron|TMEM14B_ENST00000481240.1_Intron|TMEM14B_ENST00000475942.1_Silent_p.S38S|SYCP2L_ENST00000543878.1_Intron|TMEM14B_ENST00000491103.1_3'UTR|TMEM14B_ENST00000467317.1_Silent_p.S38S|RP11-637O19.3_ENST00000480294.1_Intron|RNA5SP203_ENST00000410451.1_RNA	NM_030969.3	NP_112231.3	Q9NUH8	TM14B_HUMAN	transmembrane protein 14B	38						integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(2)|skin(2)	11	Ovarian(93;0.107)|Breast(50;0.137)	all_hematologic(90;0.135)				GCGTGCCGTCCCTGGCTGCAG	0.542													C|||	117	0.0233626	0.0779	0.0115	5008	,	,		20713	0.0		0.004	False		,,,				2504	0.002				p.S38S		Atlas-SNP	.											.	TMEM14B	19	.	0			c.C114T						PASS	.	C	,	262,4142	148.4+/-182.8	15,232,1955	129	112	118		,114	3.1	0.9	6	dbSNP_86	118	28,8572	18.5+/-59.3	0,28,4272	no	intron,coding-synonymous	TMEM14B	NM_001127711.1,NM_030969.3	,	15,260,6227	TT,TC,CC		0.3256,5.9491,2.2301	,	,38/115	10751379	290,12714	2202	4300	6502	SO:0001819	synonymous_variant	81853	exon4			GCCGTCCCTGGCT	AL024498	CCDS4515.1, CCDS47372.1, CCDS75395.1, CCDS75396.1, CCDS75397.1	6p25.1-p23	2008-08-12			ENSG00000137210	ENSG00000137210			21384	protein-coding gene	gene with protein product							Standard	NM_030969		Approved	MGC1223	uc003mzk.4	Q9NUH8	OTTHUMG00000014246	ENST00000379542.5:c.114C>T	6.37:g.10751379C>T		110	0	0		122	59	0.483607	NM_030969	Q5THN7|Q5THN8|Q96IX7|Q9BVN8	Silent	SNP	ENST00000379542.5	37	CCDS4515.1																																																																																			C|0.979;T|0.021	0.021	strong		0.542	TMEM14B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039836.1	NM_030969		T	10751379	C	T	10751379	2	4	22	1	0	0	0	0	0	0	0	1	16079	610	22	2		2	TMEM14B	6	10751379	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2867993	10751379	160363688	1383	4284											
MAK	4117	hgsc.bcm.edu	37	chr6	10792040	10792040	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgaagatagtctgaccccaaCgcctcctaccacttttatga	11	11	6	13	1	1	4	0	3	1	1	2	4	2	4	5	0	2	0	5	0	5	4	rs62000445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:10792040C>A	ENST00000313243.2	-	10	1566	c.1184G>T	c.(1183-1185)cGt>cTt	p.R395L	MAK_ENST00000354489.2_Missense_Mutation_p.R395L|SYCP2L_ENST00000543878.1_Intron|MAK_ENST00000536370.1_3'UTR|MAK_ENST00000538030.1_Missense_Mutation_p.R395L|MAK_ENST00000474039.1_Missense_Mutation_p.R395L|RP11-637O19.3_ENST00000480294.1_Intron			P20794	MAK_HUMAN	male germ cell-associated kinase	395					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)				CTGACCCCAACGCCTCCTACC	0.448													C|||	48	0.00958466	0.0348	0.0029	5008	,	,		17957	0.0		0.0	False		,,,				2504	0.0				p.R395L		Atlas-SNP	.											MAK,NS,carcinoma,-1,1	MAK	47	1	0			c.G1184T						PASS	.	C	LEU/ARG,LEU/ARG	125,4281	93.4+/-132.2	3,119,2081	114	104	107		1184,1184	5	0.9	6	dbSNP_129	107	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	MAK	NM_001242385.1,NM_005906.4	102,102	3,120,6380	AA,AC,CC		0.0116,2.837,0.9688	probably-damaging,probably-damaging	395/584,395/624	10792040	126,12880	2203	4300	6503	SO:0001583	missense	4117	exon10			CCCCAACGCCTCC		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.1184G>T	6.37:g.10792040C>A	ENSP00000313021:p.Arg395Leu	133	0	0		150	73	0.486667	NM_005906	F1T0K6|G1FL29|Q547D0|Q9NUH7	Missense_Mutation	SNP	ENST00000313243.2	37	CCDS4516.1	21	0.009615384615384616	20	0.04065040650406504	1	0.0027624309392265192	0	0.0	0	0.0	C	22.3	4.265065	0.80358	0.02837	1.16E-4	ENSG00000111837	ENST00000313243;ENST00000354489;ENST00000538030	T;T;T	0.77877	-1.13;-1.13;-0.92	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	D	0.86230	0.5883	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.87928	0.2708	10	0.87932	D	0	.	16.8762	0.86052	0.0:1.0:0.0:0.0	.	395	P20794	MAK_HUMAN	L	395	ENSP00000313021:R395L;ENSP00000346484:R395L;ENSP00000442250:R395L	ENSP00000313021:R395L	R	-	2	0	MAK	10900026	0.999000	0.42202	0.902000	0.35471	0.522000	0.34438	5.363000	0.66104	2.487000	0.83934	0.655000	0.94253	CGT	C|0.991;A|0.009	0.009	strong		0.448	MAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039841.1	NM_005906		A	10792040	C	A	10792040	3	1	22	1	0	0	0	0	1	0	0	0	9206	536	19	4	707	4	MAK	6	10792040	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	40661	10792040	160323027	1384	4285											
NEDD9	4739	hgsc.bcm.edu	37	chr6	11190859	11190859	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcaagggcctgctggagccGctgaagtctctcaatagctg	8	9	12	12	1	3	1	2	1	1	0	4	2	3	2	2	2	3	3	2	2	4	1	rs61755989	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:11190859G>A	ENST00000379446.5	-	5	1409	c.1243C>T	c.(1243-1245)Cgg>Tgg	p.R415W	NEDD9_ENST00000504387.1_Missense_Mutation_p.R415W|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	415					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)			TGCTGGAGCCGCTGAAGTCTC	0.537													G|||	104	0.0207668	0.0741	0.0072	5008	,	,		19658	0.0		0.001	False		,,,				2504	0.0				p.R415W		Atlas-SNP	.											.	NEDD9	191	.	0			c.C1243T						PASS	.	G	TRP/ARG,TRP/ARG	272,4134	152.9+/-186.6	8,256,1939	68	64	65		1243,1243	3.2	0.3	6	dbSNP_129	65	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	NEDD9	NM_001142393.1,NM_006403.3	101,101	8,258,6237	AA,AG,GG		0.0233,6.1734,2.1067	benign,benign	415/835,415/835	11190859	274,12732	2203	4300	6503	SO:0001583	missense	4739	exon6			GGAGCCGCTGAAG	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.1243C>T	6.37:g.11190859G>A	ENSP00000368759:p.Arg415Trp	95	0	0		105	51	0.485714	NM_001142393	A8K9G7|A8MSJ9|G5E9Y9|Q5T9R4|Q5XKI0	Missense_Mutation	SNP	ENST00000379446.5	37	CCDS4520.1	32	0.014652014652014652	29	0.05894308943089431	3	0.008287292817679558	0	0.0	0	0.0	G	8.301	0.819834	0.16678	0.061734	2.33E-4	ENSG00000111859	ENST00000379446;ENST00000504387	T;T	0.27256	1.68;1.68	5.92	3.16	0.36331	Serine rich protein interaction (1);	0.147556	0.64402	N	0.000009	T	0.12689	0.0308	M	0.77103	2.36	0.80722	D	1	B;B;B	0.33512	0.415;0.294;0.403	B;B;B	0.29176	0.081;0.099;0.045	T	0.02966	-1.1088	10	0.59425	D	0.04	-11.9291	5.1672	0.15092	0.1975:0.0:0.5527:0.2498	.	415;415;415	G5E9Y9;A8K9G7;Q14511	.;.;CASL_HUMAN	W	415	ENSP00000368759:R415W;ENSP00000422871:R415W	ENSP00000368759:R415W	R	-	1	2	NEDD9	11298845	0.969000	0.33509	0.350000	0.25708	0.084000	0.17831	1.794000	0.38774	0.395000	0.25257	-0.182000	0.12963	CGG	G|0.981;A|0.019	0.019	strong		0.537	NEDD9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039853.2	NM_006403		A	11190859	G	A	11190859	3	1	22	1	0	0	0	0	1	0	0	0	10322	1086	38	1	1273	1	NEDD9	6	11190859	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	398819	11190859	159924208	1385	4286											
NOL7	51406	hgsc.bcm.edu	37	chr6	13615767	13615767	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggaaggggacgatgagttTgacgatgaggccccggagga	11	5	19	6	3	0	3	0	3	0	0	0	10	0	7	2	6	0	1	2	6	1	1	rs75029999	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:13615767T>C	ENST00000451315.2	+	1	209	c.177T>C	c.(175-177)ttT>ttC	p.F59F	AL441883.1_ENST00000600057.1_3'UTR|RP1-223E5.4_ENST00000566170.1_RNA	NM_016167.3	NP_057251.2	Q9UMY1	NOL7_HUMAN	nucleolar protein 7, 27kDa	59						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)			ACGATGAGTTTGACGATGAGG	0.706											OREG0017200	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	40	0.00798722	0.028	0.0043	5008	,	,		15084	0.0		0.0	False		,,,				2504	0.0				p.F59F		Atlas-SNP	.											.	NOL7	18	.	0			c.T177C						PASS	.	T		71,4223		1,69,2077	8	10	9		177	-7.7	0	6	dbSNP_132	9	1,8465		0,1,4232	no	coding-synonymous	NOL7	NM_016167.3		1,70,6309	CC,CT,TT		0.0118,1.6535,0.5643		59/258	13615767	72,12688	2147	4233	6380	SO:0001819	synonymous_variant	51406	exon1			TGAGTTTGACGAT	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	ENST00000451315.2:c.177T>C	6.37:g.13615767T>C		48	0	0	688	67	32	0.477612	NM_016167	Q5T297|Q9Y3U7	Silent	SNP	ENST00000451315.2	37	CCDS4528.1																																																																																			T|0.994;C|0.006	0.006	strong		0.706	NOL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039904.1	NM_016167		C	13615767	T	C	13615767	2	2	22	1	0	0	0	0	0	0	0	1	10535	1809	63	3		3	NOL7	6	13615767	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2424908	13615767	157499300	1386	4287											
CD83	9308	hgsc.bcm.edu	37	chr6	14135394	14135394	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttctaaagctggcatggaacGagcttttctcccagttacct	9	13	8	11	1	2	0	0	0	2	0	3	2	2	1	2	2	4	4	2	2	4	5	rs2230193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:14135394G>A	ENST00000379153.3	+	5	716	c.545G>A	c.(544-546)cGa>cAa	p.R182Q		NM_001040280.1|NM_001251901.1|NM_004233.3	NP_001035370.1|NP_001238830.1|NP_004224.1	Q01151	CD83_HUMAN	CD83 molecule	182			R -> Q (in dbSNP:rs2230193).		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)				GGCATGGAACGAGCTTTTCTC	0.403													.|||	74	0.0147764	0.0545	0.0014	5008	,	,		21026	0.0		0.0	False		,,,				2504	0.001				p.R182Q		Atlas-SNP	.											.	CD83	23	.	0			c.G545A						PASS	.	G	GLN/ARG,GLN/ARG	202,4204	126.1+/-163.2	4,194,2005	103	105	104		542,545	-4	0	6	dbSNP_98	104	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	CD83	NM_001040280.1,NM_004233.3	43,43	4,200,6299	AA,AG,GG		0.0698,4.5847,1.5993	benign,benign	181/205,182/206	14135394	208,12798	2203	4300	6503	SO:0001583	missense	9308	exon5			TGGAACGAGCTTT	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.545G>A	6.37:g.14135394G>A	ENSP00000368450:p.Arg182Gln	104	0	0		106	48	0.45283	NM_004233	Q5THX9	Missense_Mutation	SNP	ENST00000379153.3	37	CCDS4532.1	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	G	9.394	1.076332	0.20227	0.045847	6.98E-4	ENSG00000112149	ENST00000379153	T	0.48201	0.82	5.0	-3.99	0.04069	.	1.449440	0.04161	N	0.322989	T	0.09862	0.0242	N	0.17082	0.46	0.09310	N	1	B	0.21147	0.052	B	0.10450	0.005	T	0.10200	-1.0640	10	0.25106	T	0.35	-23.8615	5.7782	0.18292	0.4997:0.2613:0.239:0.0	rs2230193;rs16874698;rs52804483;rs16874698	182	Q01151	CD83_HUMAN	Q	182	ENSP00000368450:R182Q	ENSP00000368450:R182Q	R	+	2	0	CD83	14243373	0.210000	0.23517	0.017000	0.16124	0.481000	0.33189	0.050000	0.14120	-0.988000	0.03489	-0.150000	0.13652	CGA	G|0.982;A|0.018	0.018	strong		0.403	CD83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039916.1			A	14135394	G	A	14135394	3	1	22	1	0	0	0	0	1	0	0	0	3043	1058	37	1	563	1	CD83	6	14135394	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	519627	14135394	156979673	1387	4288											
JARID2	3720	hgsc.bcm.edu	37	chr6	15517415	15517415	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtacaagagaacgaaaacgtCgtgttctgtctggagtgtgc	11	10	13	7	3	2	1	0	0	2	1	3	4	2	2	0	1	4	2	0	1	5	2	rs11970076	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:15517415C>T	ENST00000341776.2	+	17	3718	c.3474C>T	c.(3472-3474)gtC>gtT	p.V1158V	JARID2_ENST00000397311.3_Silent_p.V986V	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	1158					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)				ACGAAAACGTCGTGTTCTGTC	0.597													C|||	80	0.0159744	0.0575	0.0043	5008	,	,		17419	0.0		0.001	False		,,,				2504	0.0				p.V1158V		Atlas-SNP	.											.	JARID2	135	.	0			c.C3474T						PASS	.	C		229,4177	134.1+/-170.4	6,217,1980	179	140	153		3474	-3.5	1	6	dbSNP_120	153	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	JARID2	NM_004973.2		6,220,6277	TT,TC,CC		0.0349,5.1975,1.7838		1158/1247	15517415	232,12774	2203	4300	6503	SO:0001819	synonymous_variant	3720	exon17			AAACGTCGTGTTC	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.3474C>T	6.37:g.15517415C>T		78	0	0		136	74	0.544118	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Silent	SNP	ENST00000341776.2	37	CCDS4533.1																																																																																			C|0.983;T|0.017	0.017	strong		0.597	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973		T	15517415	C	T	15517415	2	4	22	1	0	0	0	0	0	0	0	1	7954	871	31	1		1	JARID2	6	15517415	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1382021	15517415	155597652	1388	4289											
DTNBP1	84062	hgsc.bcm.edu	37	chr6	15523388	15523388	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaagaaggtggcttggctcTtaattctgagggatttggaa	11	12	14	4	0	2	3	0	1	2	2	2	5	2	5	0	5	0	2	0	5	4	4	rs73369534	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:15523388T>C	ENST00000344537.5	-	10	1046	c.874A>G	c.(874-876)Aga>Gga	p.R292G	DTNBP1_ENST00000462989.2_Missense_Mutation_p.R136G|DTNBP1_ENST00000355917.3_Missense_Mutation_p.R293G	NM_032122.4	NP_115498.2	Q96EV8	DTBP1_HUMAN	dystrobrevin binding protein 1	292	Dysbindin.				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)			GGCTTGGCTCTTAATTCTGAG	0.532									Hermansky-Pudlak syndrome				t|||	140	0.0279553	0.0998	0.0086	5008	,	,		19166	0.0		0.002	False		,,,				2504	0.0				p.R292G		Atlas-SNP	.											.	DTNBP1	56	.	0			c.A874G						PASS	.	T	GLY/ARG	400,4006	196.4+/-220.7	18,364,1821	154	163	160		874	2.4	0	6	dbSNP_130	160	5,8595	4.3+/-15.6	0,5,4295	yes	missense	DTNBP1	NM_032122.4	125	18,369,6116	CC,CT,TT		0.0581,9.0785,3.1139	possibly-damaging	292/352	15523388	405,12601	2203	4300	6503	SO:0001583	missense	84062	exon10	Familial Cancer Database	HPS, HPS1-8	TGGCTCTTAATTC	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.874A>G	6.37:g.15523388T>C	ENSP00000341680:p.Arg292Gly	136	0	0		133	55	0.413534	NM_032122	A8K3V3|Q5THY3|Q5THY4|Q96NV2|Q9H0U2|Q9H3J5	Missense_Mutation	SNP	ENST00000344537.5	37	CCDS4534.1	37	0.01694139194139194	33	0.06707317073170732	4	0.011049723756906077	0	0.0	0	0.0	t	12.91	2.078161	0.36662	0.090785	5.81E-4	ENSG00000047579	ENST00000344537;ENST00000462989;ENST00000355917;ENST00000397306;ENST00000509674	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	5.42	2.43	0.29744	.	1.442950	0.04672	N	0.410792	T	0.21387	0.0515	M	0.75447	2.3	0.09310	N	1	B	0.25390	0.125	B	0.31390	0.129	T	0.44081	-0.9351	10	0.49607	T	0.09	.	10.1887	0.43013	0.0:0.118:0.41:0.472	.	292	Q96EV8	DTBP1_HUMAN	G	292;136;293;211;109	ENSP00000341680:R292G;ENSP00000427239:R136G;ENSP00000348183:R293G;ENSP00000421797:R109G	ENSP00000341680:R292G	R	-	1	2	DTNBP1	15631367	0.149000	0.22717	0.000000	0.03702	0.104000	0.19210	2.937000	0.48979	0.621000	0.30232	-0.224000	0.12420	AGA	T|0.967;C|0.033	0.033	strong		0.532	DTNBP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000039933.2	NM_032122		C	15523388	T	C	15523388	3	2	22	1	0	0	0	0	1	0	0	0	4792	1617	56	3	185	3	DTNBP1	6	15523388	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	5973	15523388	155591679	1389	4290											
DTNBP1	84062	hgsc.bcm.edu	37	chr6	15533469	15533469	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagccccagcccccactcGcctcgccgctctgcaatctg	6	6	8	21	3	2	0	0	0	2	0	4	0	2	0	6	0	4	3	6	0	1	0	rs61739410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:15533469G>A	ENST00000344537.5	-	8	840		c.e8+1		DTNBP1_ENST00000462989.2_Splice_Site|DTNBP1_ENST00000355917.3_Splice_Site|DTNBP1_ENST00000338950.5_Splice_Site	NM_032122.4	NP_115498.2	Q96EV8	DTBP1_HUMAN	dystrobrevin binding protein 1						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)			GCCCCCACTCGCCTCGCCGCT	0.627									Hermansky-Pudlak syndrome				G|||	140	0.0279553	0.0991	0.0086	5008	,	,		13972	0.0		0.002	False		,,,				2504	0.001				.		Atlas-SNP	.											.	DTNBP1	56	.	0			c.667+2C>T						PASS	.	G	,	389,4017	194.0+/-219.0	16,357,1830	70	61	64		,	1.8	0.5	6	dbSNP_129	64	6,8594	5.0+/-18.6	0,6,4294	yes	splice-5,splice-5	DTNBP1	NM_032122.4,NM_183040.2	,	16,363,6124	AA,AG,GG		0.0698,8.8289,3.0371	,	,	15533469	395,12611	2203	4300	6503	SO:0001630	splice_region_variant	84062	exon9	Familial Cancer Database	HPS, HPS1-8	CCACTCGCCTCGC	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.667+1C>T	6.37:g.15533469G>A		79	0	0		100	45	0.45	NM_032122	A8K3V3|Q5THY3|Q5THY4|Q96NV2|Q9H0U2|Q9H3J5	Splice_Site	SNP	ENST00000344537.5	37	CCDS4534.1	35	0.016025641025641024	30	0.06097560975609756	5	0.013812154696132596	0	0.0	0	0.0	G	4.160	0.028237	0.08054	0.088289	6.98E-4	ENSG00000047579	ENST00000344537;ENST00000462989;ENST00000355917;ENST00000397306;ENST00000509674;ENST00000511762;ENST00000338950;ENST00000543749	.	.	.	5.49	1.75	0.24633	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.453	0.32882	0.4003:0.0:0.5997:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DTNBP1	15641448	1.000000	0.71417	0.499000	0.27577	0.023000	0.10783	2.892000	0.48625	0.001000	0.14605	-0.218000	0.12543	.	G|0.969;A|0.031	0.031	strong		0.627	DTNBP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000039933.2	NM_032122	Intron	A	15533469	G	A	15533469	5	1	22	1	0	0	0	0	0	0	1	0	4792	1101	38	1	499	1	DTNBP1	6	15533469	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	10081	15533469	155581598	1390	4291											
ATXN1	6310	hgsc.bcm.edu	37	chr6	16328115	16328115	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggatcagctgtgatgggaTgaagctggcataggttccac	9	9	16	7	0	1	2	1	2	0	0	2	4	2	4	1	5	2	4	1	5	2	2	rs143125796	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:16328115T>C	ENST00000244769.4	-	8	1363	c.427A>G	c.(427-429)Atc>Gtc	p.I143V	ATXN1_ENST00000436367.1_Missense_Mutation_p.I143V	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	143					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)				TGTGATGGGATGAAGCTGGCA	0.657													T|||	2	0.000399361	0.0015	0.0	5008	,	,		14675	0.0		0.0	False		,,,				2504	0.0				p.I143V		Atlas-SNP	.											.	ATXN1	117	.	0			c.A427G						PASS	.	T	VAL/ILE,VAL/ILE	4,4402	8.1+/-20.4	0,4,2199	73	79	77		427,427	1	1	6	dbSNP_134	77	0,8600		0,0,4300	no	missense,missense	ATXN1	NM_000332.3,NM_001128164.1	29,29	0,4,6499	CC,CT,TT		0.0,0.0908,0.0308	possibly-damaging,possibly-damaging	143/816,143/816	16328115	4,13002	2203	4300	6503	SO:0001583	missense	6310	exon7			ATGGGATGAAGCT	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.427A>G	6.37:g.16328115T>C	ENSP00000244769:p.Ile143Val	42	0	0		51	24	0.470588	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	T	8.212	0.800596	0.16397	9.08E-4	0.0	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.45276	0.9;0.9	5.11	1.04	0.20106	.	0.101815	0.64402	D	0.000004	T	0.14874	0.0359	L	0.46157	1.445	0.41711	D	0.989452	B	0.27229	0.172	B	0.18871	0.023	T	0.04635	-1.0937	10	0.38643	T	0.18	-15.4984	7.2098	0.25927	0.0:0.0733:0.2756:0.6511	.	143	P54253	ATX1_HUMAN	V	143	ENSP00000244769:I143V;ENSP00000416360:I143V	ENSP00000244769:I143V	I	-	1	0	ATXN1	16436094	1.000000	0.71417	1.000000	0.80357	0.147000	0.21601	3.031000	0.49728	0.264000	0.21851	-0.456000	0.05471	ATC	T|0.999;C|0.001	0.001	strong		0.657	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332		C	16328115	T	C	16328115	3	2	22	1	0	0	0	0	1	0	0	0	1209	1464	51	3	2028	3	ATXN1	6	16328115	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	794646	16328115	154786952	1391	4292											
CAP2	10486	hgsc.bcm.edu	37	chr6	17426846	17426846	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaccctccgtggaagccttTgacaagctgatggacagtat	10	9	11	11	1	0	2	0	2	0	0	1	4	1	4	3	2	2	3	3	2	3	2	rs59744718	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:17426846T>C	ENST00000229922.2	+	3	679	c.147T>C	c.(145-147)ttT>ttC	p.F49F	CAP2_ENST00000465994.1_Silent_p.F49F|CAP2_ENST00000489374.1_Silent_p.F49F|CAP2_ENST00000378990.2_Silent_p.F49F|CAP2_ENST00000493172.1_Silent_p.F49F	NM_006366.2	NP_006357.1	P40123	CAP2_HUMAN	CAP, adenylate cyclase-associated protein, 2 (yeast)	49					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)			TGGAAGCCTTTGACAAGCTGA	0.537													T|||	173	0.0345447	0.0915	0.0173	5008	,	,		18857	0.0308		0.003	False		,,,				2504	0.0061				p.F49F		Atlas-SNP	.											.	CAP2	61	.	0			c.T147C						PASS	.	T		352,4054	181.9+/-209.8	13,326,1864	113	102	105		147	1.8	1	6	dbSNP_129	105	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	CAP2	NM_006366.2		13,340,6150	CC,CT,TT		0.1628,7.9891,2.8141		49/478	17426846	366,12640	2203	4300	6503	SO:0001819	synonymous_variant	10486	exon3			AGCCTTTGACAAG	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.147T>C	6.37:g.17426846T>C		117	0	0		153	153	1	NM_006366	B2R5Y3|B7Z1C4|B7Z214|Q6IAY2	Silent	SNP	ENST00000229922.2	37	CCDS4539.1																																																																																			T|0.967;C|0.033	0.033	strong		0.537	CAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039952.2			C	17426846	T	C	17426846	2	2	22	1	0	0	0	0	0	0	0	1	2622	1809	63	3		3	CAP2	6	17426846	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1098731	17426846	153688221	1392	4293											
CAP2	10486	hgsc.bcm.edu	37	chr6	17507504	17507504	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtttaatcatctttcggcCgtcagcgaaagcatccctgc	9	12	8	12	3	3	0	2	0	1	0	5	1	4	0	2	1	3	2	2	1	2	3	rs146710056	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:17507504C>G	ENST00000229922.2	+	5	937	c.405C>G	c.(403-405)gcC>gcG	p.A135A	CAP2_ENST00000465994.1_Silent_p.A135A|CAP2_ENST00000489374.1_Intron|CAP2_ENST00000378990.2_Silent_p.A109A|CAP2_ENST00000493172.1_Intron	NM_006366.2	NP_006357.1	P40123	CAP2_HUMAN	CAP, adenylate cyclase-associated protein, 2 (yeast)	135					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)			ATCTTTCGGCCGTCAGCGAAA	0.483													C|||	4	0.000798722	0.003	0.0	5008	,	,		19667	0.0		0.0	False		,,,				2504	0.0				p.A135A		Atlas-SNP	.											.	CAP2	61	.	0			c.C405G						PASS	.	C		18,4388	26.2+/-53.5	0,18,2185	128	102	111		405	-3.8	0.8	6	dbSNP_134	111	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CAP2	NM_006366.2		0,19,6484	GG,GC,CC		0.0116,0.4085,0.1461		135/478	17507504	19,12987	2203	4300	6503	SO:0001819	synonymous_variant	10486	exon5			TTCGGCCGTCAGC	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.405C>G	6.37:g.17507504C>G		134	0	0		128	66	0.515625	NM_006366	B2R5Y3|B7Z1C4|B7Z214|Q6IAY2	Silent	SNP	ENST00000229922.2	37	CCDS4539.1																																																																																			C|0.998;G|0.002	0.002	strong		0.483	CAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039952.2			G	17507504	C	G	17507504	2	3	22	1	0	0	0	0	0	0	0	1	2622	639	23	4		4	CAP2	6	17507504	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	80658	17507504	153607563	1393	4294											
MBOAT1	154141	hgsc.bcm.edu	37	chr6	20109842	20109842	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacttacttgtataagctgaTggtcggttcaactgccaaca	12	12	8	9	1	1	1	1	1	0	0	2	1	1	1	1	2	6	3	1	2	6	5	rs2065649	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:20109842T>C	ENST00000324607.7	-	12	1512	c.1348A>G	c.(1348-1350)Atc>Gtc	p.I450V	MBOAT1_ENST00000541730.1_Missense_Mutation_p.I301V	NM_001080480.1	NP_001073949.1	Q6ZNC8	MBOA1_HUMAN	membrane bound O-acyltransferase domain containing 1	450			I -> V (in dbSNP:rs2065649).		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)			TATAAGCTGATGGTCGGTTCA	0.468													T|||	239	0.0477236	0.1641	0.0259	5008	,	,		18796	0.0		0.004	False		,,,				2504	0.0				p.I450V		Atlas-SNP	.											.	MBOAT1	48	.	0			c.A1348G						PASS	.	T	VAL/ILE	691,3715	289.5+/-280.5	54,583,1566	149	133	139		1348	3	1	6	dbSNP_94	139	13,8587	9.8+/-36.6	0,13,4287	yes	missense	MBOAT1	NM_001080480.1	29	54,596,5853	CC,CT,TT		0.1512,15.6832,5.4129	benign	450/496	20109842	704,12302	2203	4300	6503	SO:0001583	missense	154141	exon12			AGCTGATGGTCGG	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.1348A>G	6.37:g.20109842T>C	ENSP00000324944:p.Ile450Val	113	0	0		102	47	0.460784	NM_001080480	A9EDQ5|B4DL59|B4E3J4|Q86XC2|Q8N9R5	Missense_Mutation	SNP	ENST00000324607.7	37	CCDS34346.1	75	0.034340659340659344	66	0.13414634146341464	9	0.024861878453038673	0	0.0	0	0.0	T	12.51	1.960413	0.34565	0.156832	0.001512	ENSG00000172197	ENST00000541730;ENST00000324607	T;T	0.18502	2.21;2.68	5.38	2.96	0.34315	.	0.312699	0.38548	N	0.001653	T	0.06142	0.0159	L	0.61036	1.89	0.09310	P	0.9999999999999988	B;B	0.18741	0.03;0.006	B;B	0.20577	0.03;0.003	T	0.17198	-1.0377	9	0.39692	T	0.17	-7.5096	4.338	0.11095	0.0:0.238:0.164:0.598	rs2065649;rs2065649	301;450	Q6ZNC8-2;Q6ZNC8	.;MBOA1_HUMAN	V	301;450	ENSP00000441568:I301V;ENSP00000324944:I450V	ENSP00000324944:I450V	I	-	1	0	MBOAT1	20217821	0.259000	0.24043	0.995000	0.50966	0.991000	0.79684	-0.065000	0.11617	0.409000	0.25649	0.533000	0.62120	ATC	T|0.949;C|0.051	0.051	strong		0.468	MBOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039980.1			C	20109842	T	C	20109842	3	2	22	1	0	0	0	0	1	0	0	0	9365	1464	51	3	147	3	MBOAT1	6	20109842	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2602338	20109842	151005225	1394	4295											
MRS2	57380	hgsc.bcm.edu	37	chr6	24418749	24418749	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgggaaccttctctctttcGctctttggactaatgggagt	7	15	10	9	1	3	0	0	0	3	0	5	3	3	3	1	3	1	1	1	3	2	4	rs141564147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:24418749G>A	ENST00000378386.3	+	9	1143	c.1050G>A	c.(1048-1050)tcG>tcA	p.S350S	MRS2_ENST00000378353.1_Silent_p.S350S|MRS2_ENST00000543597.1_Silent_p.S59S|MRS2_ENST00000443868.2_Silent_p.S353S|MRS2_ENST00000483634.1_3'UTR|MRS2_ENST00000535061.1_Silent_p.S300S|MRS2_ENST00000274747.7_3'UTR	NM_020662.2	NP_065713.1	Q9HD23	MRS2_HUMAN	MRS2 magnesium transporter	350						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						TCTCTCTTTCGCTCTTTGGAC	0.443													G|||	18	0.00359425	0.0129	0.0014	5008	,	,		15837	0.0		0.0	False		,,,				2504	0.0				p.S350S		Atlas-SNP	.											.	MRS2	31	.	0			c.G1050A						PASS	.	G		50,4356	50.9+/-86.3	1,48,2154	171	167	168		1050	-10.8	0	6	dbSNP_134	168	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	MRS2	NM_020662.2		1,51,6451	AA,AG,GG		0.0349,1.1348,0.4075		350/444	24418749	53,12953	2203	4300	6503	SO:0001819	synonymous_variant	57380	exon9			TCTTTCGCTCTTT	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.1050G>A	6.37:g.24418749G>A		278	0	0		261	118	0.452107	NM_020662	A8K4U3|B3KNN2|B4DQL2|Q5T3Y1|Q6NTG4|Q96KF8|Q9BVP1	Silent	SNP	ENST00000378386.3	37	CCDS4552.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	G	9.599	1.128145	0.20959	0.011348	3.49E-4	ENSG00000124532	ENST00000446191	.	.	.	5.41	-10.8	0.00216	.	.	.	.	.	T	0.13670	0.0331	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43393	-0.9394	4	.	.	.	-16.4762	0.5483	0.00658	0.2381:0.1624:0.2797:0.3198	.	.	.	.	H	169	.	.	R	+	2	0	MRS2	24526728	0.008000	0.16893	0.026000	0.17262	0.987000	0.75469	-1.057000	0.03486	-2.703000	0.00397	-0.163000	0.13421	CGC	G|0.996;A|0.004	0.004	strong		0.443	MRS2-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040002.1			A	24418749	G	A	24418749	2	1	22	1	0	0	0	0	0	0	0	1	9860	1074	38	1		1	MRS2	6	24418749	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4308907	24418749	146696318	1395	4296											
KIAA0319	9856	hgsc.bcm.edu	37	chr6	24596433	24596433	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctcccggtagtcatctgAgtactcagacatctcctcta	9	11	7	14	1	5	2	2	1	3	1	7	2	6	2	2	1	2	3	2	1	3	3	rs73727343	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:24596433A>C	ENST00000378214.3	-	3	993	c.469T>G	c.(469-471)Tca>Gca	p.S157A	KIAA0319_ENST00000535378.1_Missense_Mutation_p.S148A|KIAA0319_ENST00000430948.2_Missense_Mutation_p.S112A|KIAA0319_ENST00000543707.1_Missense_Mutation_p.S157A|KIAA0319_ENST00000537886.1_Missense_Mutation_p.S157A	NM_001168375.1|NM_014809.3	NP_001161847.1|NP_055624.2	Q5VV43	K0319_HUMAN	KIAA0319	157				S -> A (in Ref. 1; BAA20777 and 5; AAI52461). {ECO:0000305}.	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						TAGTCATCTGAGTACTCAGAC	0.597													A|||	134	0.0267572	0.0961	0.0072	5008	,	,		17776	0.0		0.002	False		,,,				2504	0.0				p.S157A		Atlas-SNP	.											.	KIAA0319	117	.	0			c.T469G						PASS	.	A	ALA/SER,ALA/SER,ALA/SER,ALA/SER,ALA/SER	322,4084	170.5+/-200.9	9,304,1890	75	79	78		442,469,334,469,469	-3.2	0.1	6	dbSNP_130	78	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense,missense	KIAA0319	NM_001168374.1,NM_001168375.1,NM_001168376.1,NM_001168377.1,NM_014809.3	99,99,99,99,99	9,307,6187	CC,CA,AA		0.0349,7.3082,2.4988	benign,benign,benign,benign,benign	148/1064,157/1073,112/1028,157/1012,157/1073	24596433	325,12681	2203	4300	6503	SO:0001583	missense	9856	exon3			CATCTGAGTACTC	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.469T>G	6.37:g.24596433A>C	ENSP00000367459:p.Ser157Ala	55	0	0		54	25	0.462963	NM_001168377	A7MD37|B2RTU7|B4DHA7|B4DK75|B7ZML3|F5H123|Q9UJC8|Q9Y4G7	Missense_Mutation	SNP	ENST00000378214.3	37	CCDS34348.1	65	0.02976190476190476	58	0.11788617886178862	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	A	4.600	0.111504	0.08831	0.073082	3.49E-4	ENSG00000137261	ENST00000537886;ENST00000535378;ENST00000430948;ENST00000378214;ENST00000543707	T;T;T;T;T	0.06371	3.31;3.32;3.32;3.31;3.31	4.43	-3.24	0.05094	.	1.418230	0.04637	N	0.404692	T	0.01156	0.0038	L	0.29908	0.895	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.10450	0.005;0.003;0.001	T	0.48375	-0.9041	10	0.29301	T	0.29	-0.0017	0.6264	0.00786	0.3156:0.2275:0.2714:0.1855	.	157;148;157	F5H123;Q5VV43-2;Q5VV43	.;.;K0319_HUMAN	A	157;148;112;157;157	ENSP00000439700:S157A;ENSP00000442403:S148A;ENSP00000401086:S112A;ENSP00000367459:S157A;ENSP00000437656:S157A	ENSP00000367459:S157A	S	-	1	0	KIAA0319	24704412	0.000000	0.05858	0.057000	0.19452	0.884000	0.51177	-1.251000	0.02882	-0.187000	0.10516	0.421000	0.28195	TCA	A|0.970;C|0.030	0.030	strong		0.597	KIAA0319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040009.1	NM_014809		C	24596433	A	C	24596433	3	2	22	1	0	0	0	0	1	0	0	0	8177	304	11	5	2825	5	KIAA0319	6	24596433	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	177684	24596433	146518634	1396	4297											
LRRC16A	55604	hgsc.bcm.edu	37	chr6	25606442	25606442	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcccctcctgcagtcccccaAacccagtctggcagcacggc	7	5	9	20	1	1	0	0	0	1	0	3	0	3	0	6	2	3	3	6	2	1	0	rs201300946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:25606442A>G	ENST00000329474.6	+	35	4156	c.3788A>G	c.(3787-3789)aAa>aGa	p.K1263R		NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	1263					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						CAGTCCCCCAAACCCAGTCTG	0.582													A|||	5	0.000998403	0.0038	0.0	5008	,	,		16648	0.0		0.0	False		,,,				2504	0.0				p.K1263R		Atlas-SNP	.											.	LRRC16A	168	.	0			c.A3788G						PASS	.	A	ARG/LYS,ARG/LYS	10,3848		0,10,1919	42	50	47		3770,3788	5.8	1	6		47	0,8290		0,0,4145	yes	missense,missense	LRRC16A	NM_001173977.1,NM_017640.5	26,26	0,10,6064	GG,GA,AA		0.0,0.2592,0.0823	probably-damaging,probably-damaging	1257/1366,1263/1372	25606442	10,12138	1929	4145	6074	SO:0001583	missense	55604	exon35			CCCCCAAACCCAG	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.3788A>G	6.37:g.25606442A>G	ENSP00000331983:p.Lys1263Arg	99	0	0		116	53	0.456897	NM_017640	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	Missense_Mutation	SNP	ENST00000329474.6	37	CCDS54973.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.846082	0.91277	0.002592	0.0	ENSG00000079691	ENST00000329474;ENST00000399313	T	0.18657	2.2	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.35422	0.0931	M	0.65975	2.015	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.999	D;D;D	0.80764	0.993;0.993;0.994	T	0.05257	-1.0896	10	0.38643	T	0.18	-24.4349	16.2375	0.82384	1.0:0.0:0.0:0.0	.	1263;1257;1218	Q5VZK9;B2RTQ5;Q5VZK9-2	LR16A_HUMAN;.;.	R	1263;1218	ENSP00000331983:K1263R	ENSP00000331983:K1263R	K	+	2	0	LRRC16A	25714421	1.000000	0.71417	0.997000	0.53966	0.878000	0.50629	6.167000	0.71902	2.222000	0.72286	0.533000	0.62120	AAA	.	.	weak		0.582	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040045.2	NM_017640		G	25606442	A	G	25606442	3	3	22	1	0	0	0	0	1	0	0	0	8980	14	1	3	3926	3	LRRC16A	6	25606442	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1010009	25606442	145508625	1397	4298											
HIST1H3B	8358	hgsc.bcm.edu	37	chr6	26031962	26031962	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ttagcatggatggcgcaaagGtttgtgtcctcaaagagccc	10	10	12	9	1	1	1	1	0	0	1	2	2	2	2	2	3	2	3	2	3	3	2	rs34966100	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:26031962G>A	ENST00000244661.2	-	1	326	c.327C>T	c.(325-327)aaC>aaT	p.N109N		NM_003537.3	NP_003528.1	P68431	H31_HUMAN	histone cluster 1, H3b	109					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						TGGCGCAAAGGTTTGTGTCCT	0.527													G|||	176	0.0351438	0.1203	0.013	5008	,	,		18951	0.0		0.004	False		,,,				2504	0.0041				p.N109N		Atlas-SNP	.											.	HIST1H3B	59	.	0			c.C327T						PASS	.	G		396,4010	198.4+/-222.2	12,372,1819	78	79	79		327	4.2	1	6	dbSNP_126	79	55,8545	34.3+/-88.2	0,55,4245	no	coding-synonymous	HIST1H3B	NM_003537.3		12,427,6064	AA,AG,GG		0.6395,8.9877,3.4676		109/137	26031962	451,12555	2203	4300	6503	SO:0001819	synonymous_variant	8358	exon1			GCAAAGGTTTGTG	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.327C>T	6.37:g.26031962G>A		113	0	0		141	59	0.41844	NM_003537	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000244661.2	37	CCDS4573.1																																																																																			G|0.966;A|0.034	0.034	strong		0.527	HIST1H3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040077.1	NM_003537		A	26031962	G	A	26031962	2	1	22	1	0	0	0	0	0	0	0	1	7165	1252	44	2		2	HIST1H3B	6	26031962	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	425520	26031962	145083105	1398	4299											
HIST1H4C	8364	hgsc.bcm.edu	37	chr6	26104382	26104382	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttagagaacgttattcgagaCgccgtcacctatacggagca	12	9	10	10	5	1	2	1	0	0	2	2	5	1	3	2	1	3	2	2	1	5	5	rs2229767	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:26104382C>T	ENST00000377803.2	+	1	279	c.207C>T	c.(205-207)gaC>gaT	p.D69D		NM_003542.3	NP_003533.1	P62805	H4_HUMAN	histone cluster 1, H4c	69					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						TTATTCGAGACGCCGTCACCT	0.542													c|||	175	0.0349441	0.1248	0.013	5008	,	,		17220	0.0		0.001	False		,,,				2504	0.0				p.D69D		Atlas-SNP	.											.	HIST1H4C	14	.	0			c.C207T						PASS	.	T		437,3969		27,383,1793	74	66	69		207	0.8	1	6	dbSNP_98	69	29,8571		0,29,4271	no	coding-synonymous	HIST1H4C	NM_003542.3		27,412,6064	TT,TC,CC		0.3372,9.9183,3.583		69/104	26104382	466,12540	2203	4300	6503	SO:0001819	synonymous_variant	8364	exon1			TCGAGACGCCGTC	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.207C>T	6.37:g.26104382C>T		97	0	0		171	81	0.473684	NM_003542	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Silent	SNP	ENST00000377803.2	37	CCDS4583.1																																																																																			C|0.963;T|0.037	0.037	strong		0.542	HIST1H4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040092.2	NM_003542		T	26104382	C	T	26104382	2	4	22	1	0	0	0	0	0	0	0	1	7176	535	19	1		1	HIST1H4C	6	26104382	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	72420	26104382	145010685	1399	4300											
HIST1H2BD	3017	hgsc.bcm.edu	37	chr6	26158456	26158456	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggctccaagaaggcggtgaCtaaggctcagaagaaggacg	13	4	16	8	2	1	4	1	1	0	3	2	5	2	5	1	5	0	2	1	5	5	1	rs62623440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:26158456C>T	ENST00000289316.2	+	1	83	c.59C>T	c.(58-60)aCt>aTt	p.T20I	HIST1H2BD_ENST00000377777.4_Missense_Mutation_p.T20I	NM_138720.2	NP_619790.1	P58876	H2B1D_HUMAN	histone cluster 1, H2bd	20					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						AAGGCGGTGACTAAGGCTCAG	0.527													C|||	47	0.00938498	0.0348	0.0014	5008	,	,		19251	0.0		0.0	False		,,,				2504	0.0				p.T20I		Atlas-SNP	.											.	HIST1H2BD	45	.	0			c.C59T						PASS	.	C	ILE/THR,ILE/THR	128,4278		1,126,2076	126	124	124		59,59	4.1	1	6	dbSNP_129	124	1,8599		0,1,4299	yes	missense,missense	HIST1H2BD	NM_021063.3,NM_138720.2	89,89	1,127,6375	TT,TC,CC		0.0116,2.9051,0.9918	probably-damaging,probably-damaging	20/127,20/127	26158456	129,12877	2203	4300	6503	SO:0001583	missense	3017	exon1			CGGTGACTAAGGC	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.59C>T	6.37:g.26158456C>T	ENSP00000289316:p.Thr20Ile	174	0	0		145	61	0.42069	NM_021063		Missense_Mutation	SNP	ENST00000289316.2	37	CCDS4587.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	.	15.37	2.814326	0.50527	0.029051	1.16E-4	ENSG00000158373	ENST00000377777;ENST00000289316	T;T	0.23754	1.89;1.89	4.95	4.07	0.47477	Histone-fold (2);	0.000000	0.42821	D	0.000655	T	0.19604	0.0471	M	0.79805	2.47	0.36491	D	0.868429	P	0.39216	0.664	B	0.39935	0.314	T	0.08554	-1.0716	10	0.72032	D	0.01	.	9.0973	0.36647	0.0:0.7713:0.147:0.0817	rs62623440	20	P58876	H2B1D_HUMAN	I	20	ENSP00000367008:T20I;ENSP00000289316:T20I	ENSP00000289316:T20I	T	+	2	0	HIST1H2BD	26266435	1.000000	0.71417	1.000000	0.80357	0.480000	0.33159	3.805000	0.55575	1.392000	0.46585	0.644000	0.83932	ACT	C|0.990;T|0.010	0.010	strong		0.527	HIST1H2BD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040088.1	NM_021063		T	26158456	C	T	26158456	3	4	22	1	0	0	0	0	1	0	0	0	7152	565	20	2	61	2	HIST1H2BD	6	26158456	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	54074	26158456	144956611	1400	4301											
HIST1H2BE	8344	hgsc.bcm.edu	37	chr6	26184082	26184082	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gggctccaagaaggccgtgaCcaaggcgcagaagaaggacg	13	2	16	10	3	0	4	0	1	0	3	1	5	1	5	3	4	0	2	3	4	5	0	rs61978632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:26184082C>G	ENST00000356530.3	+	1	125	c.59C>G	c.(58-60)aCc>aGc	p.T20S		NM_003523.2	NP_003514.2	P62807	H2B1C_HUMAN	histone cluster 1, H2be	20					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)			endometrium(1)|large_intestine(2)|lung(1)	4						AAGGCCGTGACCAAGGCGCAG	0.557													C|||	202	0.0403355	0.1339	0.0216	5008	,	,		19019	0.0		0.002	False		,,,				2504	0.0082				p.T20S		Atlas-SNP	.											.	HIST1H2BE	10	.	0			c.C59G						PASS	.	C	SER/THR	444,3962		21,402,1780	121	113	116		59	5.1	1	6	dbSNP_129	116	31,8569		0,31,4269	no	missense	HIST1H2BE	NM_003523.2	58	21,433,6049	GG,GC,CC		0.3605,10.0772,3.6522	benign	20/127	26184082	475,12531	2203	4300	6503	SO:0001583	missense	8344	exon1			CCGTGACCAAGGC	Z80780	CCDS4588.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197697	ENSG00000274290		"Histones / Replication-dependent"	4753	protein-coding gene	gene with protein product		602805	"H2B histone family, member H", "histone 1, H2be"	H2BFH		9119399, 12408966	Standard	NM_003523		Approved	H2B/h, H2B.h	uc003ngt.3	P62807	OTTHUMG00000014427	ENST00000356530.3:c.59C>G	6.37:g.26184082C>G	ENSP00000348924:p.Thr20Ser	225	0	0		213	105	0.492958	NM_003523	P02278|Q3B872|Q4VB69|Q93078|Q93080	Missense_Mutation	SNP	ENST00000356530.3	37	CCDS4588.1	72	0.03296703296703297	64	0.13008130081300814	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	.	17.23	3.336510	0.60963	0.100772	0.003605	ENSG00000197697	ENST00000356530	T	0.22539	1.95	5.08	5.08	0.68730	.	0.000000	0.35040	U	0.003493	T	0.34308	0.0893	.	.	.	0.25861	P	0.9838228	.	.	.	.	.	.	T	0.09100	-1.0690	6	0.59425	D	0.04	.	17.8237	0.88657	0.0:1.0:0.0:0.0	rs61978632	.	.	.	S	20	ENSP00000348924:T20S	ENSP00000348924:T20S	T	+	2	0	HIST1H2BE	26292061	1.000000	0.71417	1.000000	0.80357	0.377000	0.30045	5.752000	0.68728	2.526000	0.85167	0.603000	0.83216	ACC	C|0.965;G|0.035	0.035	strong		0.557	HIST1H2BE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040090.1	NM_003523		G	26184082	C	G	26184082	3	3	22	1	0	0	0	0	1	0	0	0	7153	507	18	4	61	4	HIST1H2BE	6	26184082	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	25626	26184082	144930985	1401	4302											
HIST1H2BH	8345	hgsc.bcm.edu	37	chr6	26252148	26252148	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tacaacaagcgttcgaccatCacctccagggagatccagac	13	6	8	14	2	1	2	1	0	0	2	4	4	3	2	4	1	3	1	4	1	3	2	rs61746493	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:26252148C>T	ENST00000356350.2	+	1	270	c.270C>T	c.(268-270)atC>atT	p.I90I	HIST1H3F_ENST00000446824.2_5'Flank	NM_003524.2	NP_003515.1	Q93079	H2B1H_HUMAN	histone cluster 1, H2bh	90					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(3)|breast(2)|large_intestine(1)|lung(3)|ovary(3)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	17						GTTCGACCATCACCTCCAGGG	0.597													C|||	185	0.0369409	0.1309	0.0144	5008	,	,		18322	0.0		0.002	False		,,,				2504	0.0				p.I90I		Atlas-SNP	.											.	HIST1H2BH	36	.	0			c.C270T						PASS	.	C		426,3980		22,382,1799	85	89	88		270	3.7	1	6	dbSNP_129	88	27,8573		0,27,4273	no	coding-synonymous	HIST1H2BH	NM_003524.2		22,409,6072	TT,TC,CC		0.314,9.6686,3.483		90/127	26252148	453,12553	2203	4300	6503	SO:0001819	synonymous_variant	8345	exon1			GACCATCACCTCC	Z80781	CCDS4601.1	6p21.3	2011-01-27	2006-10-11	2003-02-14	ENSG00000197459	ENSG00000275713		"Histones / Replication-dependent"	4755	protein-coding gene	gene with protein product		602806	"H2B histone family, member J", "histone 1, H2bh"	H2BFJ		9119399, 12408966	Standard	NM_003524		Approved	H2B/j	uc003nhh.3	Q93079	OTTHUMG00000014447	ENST00000356350.2:c.270C>T	6.37:g.26252148C>T		136	0	0		171	91	0.532164	NM_003524	B2R541|Q4VB74	Silent	SNP	ENST00000356350.2	37	CCDS4601.1																																																																																			C|0.968;T|0.032	0.032	strong		0.597	HIST1H2BH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040110.1	NM_003524		T	26252148	C	T	26252148	2	4	22	1	0	0	0	0	0	0	0	1	7156	816	29	2		2	HIST1H2BH	6	26252148	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	68066	26252148	144862919	1402	4303											
BTN3A2	11118	hgsc.bcm.edu	37	chr6	26374571	26374571	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaggtggagaggagtcttcGtccgataccaataagtcagc	11	9	13	8	2	2	1	1	0	1	1	4	4	3	2	2	3	2	1	2	3	4	4	rs115820857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:26374571G>A	ENST00000356386.2	+	9	1169	c.981G>A	c.(979-981)tcG>tcA	p.S327S	BTN3A2_ENST00000377708.2_Silent_p.S327S|BTN3A2_ENST00000527422.1_Silent_p.S327S|BTN3A2_ENST00000396934.3_Silent_p.S304S|BTN3A2_ENST00000396948.1_Silent_p.S327S|BTN3A2_ENST00000508906.2_Silent_p.S285S	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	327				S -> L (in Ref. 2; AAC02655). {ECO:0000305}.	interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						AGGAGTCTTCGTCCGATACCA	0.473													G|||	75	0.014976	0.0552	0.0029	5008	,	,		16013	0.0		0.0	False		,,,				2504	0.0				p.S327S		Atlas-SNP	.											.	BTN3A2	44	.	0			c.G981A						PASS	.	G	,,,,	168,4238	110.8+/-149.0	1,166,2036	196	161	173		981,981,912,855,981	-1.2	0	6	dbSNP_132	173	12,8588	8.4+/-32.0	0,12,4288	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BTN3A2	NM_001197246.1,NM_001197247.1,NM_001197248.1,NM_001197249.1,NM_007047.3	,,,,	1,178,6324	AA,AG,GG		0.1395,3.813,1.384	,,,,	327/335,327/335,304/312,285/293,327/335	26374571	180,12826	2203	4300	6503	SO:0001819	synonymous_variant	11118	exon7			GTCTTCGTCCGAT	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.981G>A	6.37:g.26374571G>A		215	0	0		216	96	0.444444	NM_001197246	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Silent	SNP	ENST00000356386.2	37	CCDS4605.1																																																																																			G|0.988;A|0.012	0.012	strong		0.473	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2			A	26374571	G	A	26374571	2	1	22	1	0	0	0	0	0	0	0	1	1565	1132	40	1		1	BTN3A2	6	26374571	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	122423	26374571	144740496	1403	4304											
HIST1H2AL	8332	hgsc.bcm.edu	37	chr6	27833342	27833342	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggagctggcgggcaacgcCgcccgcgacaacaagaagac	11	2	14	14	5	0	2	0	0	0	2	0	4	0	3	2	3	3	2	2	3	4	0	rs11966705	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:27833342C>T	ENST00000357320.2	+	1	309	c.210C>T	c.(208-210)gcC>gcT	p.A70A		NM_003511.2	NP_003502.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2al	70						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)			breast(1)|endometrium(1)|large_intestine(2)|lung(3)|urinary_tract(2)	9						CGGGCAACGCCGCCCGCGACA	0.657													C|||	123	0.0245607	0.0703	0.0144	5008	,	,		15159	0.005		0.0119	False		,,,				2504	0.0031				p.A70A		Atlas-SNP	.											.	HIST1H2AL	14	.	0			c.C210T						PASS	.	C		329,4077		11,307,1885	78	83	81		210	1.8	1	6	dbSNP_120	81	48,8552		0,48,4252	no	coding-synonymous	HIST1H2AL	NM_003511.2		11,355,6137	TT,TC,CC		0.5581,7.4671,2.8987		70/131	27833342	377,12629	2203	4300	6503	SO:0001819	synonymous_variant	8332	exon1			CAACGCCGCCCGC	X83549	CCDS4634.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000198374	ENSG00000276903		"Histones / Replication-dependent"	4730	protein-coding gene	gene with protein product		602793	"H2A histone family, member I", "histone 1, H2al"	H2AFI		9439656, 9031620, 12408966	Standard	NM_003511		Approved	H2A/i, dJ193B12.9	uc003njw.3	P0C0S8	OTTHUMG00000014492	ENST00000357320.2:c.210C>T	6.37:g.27833342C>T		245	0	0		248	122	0.491935	NM_003511	P02261|Q2M1R2|Q76PA6	Silent	SNP	ENST00000357320.2	37	CCDS4634.1																																																																																			C|0.975;T|0.025	0.025	strong		0.657	HIST1H2AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040160.1	NM_003511		T	27833342	C	T	27833342	2	4	22	1	0	0	0	0	0	0	0	1	7147	639	23	1		1	HIST1H2AL	6	27833342	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1458771	27833342	143281725	1404	4305											
OR2B2	81697	hgsc.bcm.edu	37	chr6	27879093	27879093	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acaaaaataggacaacttgcGgagaagttagtaaggtaagt	18	8	11	4	1	0	1	0	0	0	1	0	3	0	2	0	3	2	3	0	3	8	5	rs73392698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:27879093G>A	ENST00000303324.2	-	1	1081	c.1005C>T	c.(1003-1005)tcC>tcT	p.S335S		NM_033057.2	NP_149046.2	Q9GZK3	OR2B2_HUMAN	olfactory receptor, family 2, subfamily B, member 2	335						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						GACAACTTGCGGAGAAGTTAG	0.318													G|||	86	0.0171725	0.0582	0.0101	5008	,	,		18973	0.0		0.002	False		,,,				2504	0.0				p.S335S		Atlas-SNP	.											.	OR2B2	54	.	0			c.C1005T						PASS	.	G		226,4180	133.3+/-169.7	3,220,1980	81	84	83		1005	-2.2	0	6	dbSNP_130	83	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous	OR2B2	NM_033057.2		3,225,6275	AA,AG,GG		0.0581,5.1294,1.7761		335/358	27879093	231,12775	2203	4300	6503	SO:0001819	synonymous_variant	81697	exon1			ACTTGCGGAGAAG	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.1005C>T	6.37:g.27879093G>A		59	0	0		55	31	0.563636	NM_033057	B2RNH2|Q9GZL2|Q9Y299	Silent	SNP	ENST00000303324.2	37	CCDS4641.1																																																																																			G|0.984;A|0.016	0.016	strong		0.318	OR2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040163.1			A	27879093	G	A	27879093	2	1	22	1	0	0	0	0	0	0	0	1	10998	1103	39	1		1	OR2B2	6	27879093	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	45751	27879093	143235974	1405	4306											
ZKSCAN4	387032	hgsc.bcm.edu	37	chr6	28219695	28219695	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccaccttcacggtcaggaGccccgtctggtcttctgcag	5	10	10	16	2	5	0	2	0	3	0	6	1	6	1	4	3	2	1	4	3	0	2	rs62638680	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:28219695G>A	ENST00000377294.2	-	1	307	c.64C>T	c.(64-66)Ctc>Ttc	p.L22F	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						ACGGTCAGGAGCCCCGTCTGG	0.637													G|||	179	0.0357428	0.1082	0.0187	5008	,	,		15084	0.006		0.0139	False		,,,				2504	0.0031				p.L22F		Atlas-SNP	.											.	ZKSCAN4	42	.	0			c.C64T						PASS	.	G	PHE/LEU	433,3917		24,385,1766	63	69	67		64	-0.6	0.1	6	dbSNP_129	67	51,8447		0,51,4198	yes	missense	ZKSCAN4	NM_019110.3	22	24,436,5964	AA,AG,GG		0.6001,9.954,3.7671	benign	22/546	28219695	484,12364	2175	4249	6424	SO:0001583	missense	387032	exon1			TCAGGAGCCCCGT	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.64C>T	6.37:g.28219695G>A	ENSP00000366509:p.Leu22Phe	82	0	0		102	101	0.990196	NM_019110	B2RE32|Q5U7L4	Missense_Mutation	SNP	ENST00000377294.2	37	CCDS4647.1	77	0.035256410256410256	52	0.10569105691056911	9	0.024861878453038673	5	0.008741258741258742	11	0.014511873350923483	G	16.83	3.231677	0.58777	0.09954	0.006001	ENSG00000187626	ENST00000377294	T	0.08896	3.04	4.21	-0.602	0.11634	.	.	.	.	.	T	0.02047	0.0064	L	0.27053	0.805	0.09310	N	0.999995	P	0.46706	0.883	P	0.44732	0.459	T	0.39901	-0.9591	9	0.46703	T	0.11	.	3.0342	0.06116	0.0972:0.1668:0.458:0.278	.	22	Q969J2	ZKSC4_HUMAN	F	22	ENSP00000366509:L22F	ENSP00000366509:L22F	L	-	1	0	ZKSCAN4	28327674	0.000000	0.05858	0.050000	0.19076	0.678000	0.39670	-0.612000	0.05616	0.044000	0.15775	0.563000	0.77884	CTC	G|0.968;A|0.032	0.032	strong		0.637	ZKSCAN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040179.1	NM_019110		A	28219695	G	A	28219695	3	1	22	1	0	0	0	0	1	0	0	0	17704	971	34	2	1593	2	ZKSCAN4	6	28219695	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	340602	28219695	142895372	1406	4307											
ZKSCAN3	80317	hgsc.bcm.edu	37	chr6	28331573	28331573	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgaaaagcaggagaaccaTggcagcctggtctccctggg	11	6	14	10	0	1	2	0	1	1	1	2	4	1	2	3	4	3	2	3	4	3	0	rs213227	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:28331573T>A	ENST00000377255.3	+	6	1035	c.738T>A	c.(736-738)caT>caA	p.H246Q	ZKSCAN3_ENST00000341464.5_Missense_Mutation_p.H98Q|ZKSCAN3_ENST00000252211.2_Missense_Mutation_p.H246Q	NM_001242894.1	NP_001229823.1	Q9BRR0	ZKSC3_HUMAN	zinc finger with KRAB and SCAN domains 3	246	KRAB.		H -> Q (in dbSNP:rs213227).		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						AGGAGAACCATGGCAGCCTGG	0.463													T|||	244	0.048722	0.1278	0.0346	5008	,	,		18669	0.0119		0.0189	False		,,,				2504	0.0204				p.H246Q		Atlas-SNP	.											.	ZKSCAN3	50	.	0			c.T738A						PASS	.	T	GLN/HIS,GLN/HIS,GLN/HIS	459,3947		25,409,1769	81	74	76		738,294,738	0.5	0	6	dbSNP_79	76	135,8465		1,133,4166	yes	missense,missense,missense	ZKSCAN3	NM_001242894.1,NM_001242895.1,NM_024493.3	24,24,24	26,542,5935	AA,AT,TT		1.5698,10.4176,4.5671	benign,benign,benign	246/539,98/391,246/539	28331573	594,12412	2203	4300	6503	SO:0001583	missense	80317	exon5			GAACCATGGCAGC	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.738T>A	6.37:g.28331573T>A	ENSP00000366465:p.His246Gln	91	0	0		100	47	0.47	NM_024493	B2R8W2|B3KVC0|H7BXX1|Q5VXH3|Q92972|Q9H4T3	Missense_Mutation	SNP	ENST00000377255.3	37	CCDS4650.1	90	0.04120879120879121	53	0.10772357723577236	14	0.03867403314917127	11	0.019230769230769232	12	0.0158311345646438	.	12.65	2.001597	0.35320	0.104176	0.015698	ENSG00000189298	ENST00000252211;ENST00000341464;ENST00000377255	T;T;T	0.01725	4.67;4.67;4.67	2.98	0.46	0.16684	Krueppel-associated box (3);	.	.	.	.	T	0.00468	0.0015	L	0.29908	0.895	0.80722	P	0.0	P	0.35821	0.523	B	0.33392	0.163	T	0.47983	-0.9074	8	0.25751	T	0.34	.	3.8184	0.08825	0.0:0.2424:0.4061:0.3515	rs213227;rs61181430;rs213227	246	Q9BRR0	ZKSC3_HUMAN	Q	246;98;246	ENSP00000252211:H246Q;ENSP00000341883:H98Q;ENSP00000366465:H246Q	ENSP00000252211:H246Q	H	+	3	2	ZKSCAN3	28439552	0.000000	0.05858	0.002000	0.10522	0.920000	0.55202	-0.612000	0.05616	0.086000	0.17137	0.460000	0.39030	CAT	T|0.958;A|0.042	0.042	strong		0.463	ZKSCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040189.3	NM_024493		A	28331573	T	A	28331573	3	1	22	1	0	0	0	0	1	0	0	0	17703	1461	51	5	752	5	ZKSCAN3	6	28331573	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	111878	28331573	142783494	1407	4308											
OR2J3	442186	hgsc.bcm.edu	37	chr6	29080386	29080386	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaccactgggcttcagaaagTgtttggaacatgtggagctc	11	10	12	8	0	1	1	1	0	0	1	2	3	1	3	1	3	3	3	1	3	3	2	rs79293918	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29080386T>C	ENST00000377169.1	+	1	719	c.719T>C	c.(718-720)gTg>gCg	p.V240A		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	240						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						CTTCAGAAAGTGTTTGGAACA	0.448													T|||	116	0.0231629	0.0651	0.0101	5008	,	,		22544	0.0079		0.0119	False		,,,				2504	0.0031				p.V240A		Atlas-SNP	.											.	OR2J3	53	.	0			c.T719C						PASS	.	T	ALA/VAL	185,2355		4,177,1089	118	123	121		719	1.6	0.9	6	dbSNP_131	121	26,5120		0,26,2547	yes	missense	OR2J3	NM_001005216.2	64	4,203,3636	CC,CT,TT		0.5052,7.2835,2.7453	possibly-damaging	240/312	29080386	211,7475	1270	2573	3843	SO:0001583	missense	442186	exon1			AGAAAGTGTTTGG		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.719T>C	6.37:g.29080386T>C	ENSP00000366374:p.Val240Ala	386	0	0		370	177	0.478378	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Missense_Mutation	SNP	ENST00000377169.1	37	CCDS43433.1	54	0.024725274725274724	32	0.06504065040650407	6	0.016574585635359115	6	0.01048951048951049	10	0.013192612137203167	T	0.005	-2.139654	0.00335	0.072835	0.005052	ENSG00000204701	ENST00000377169	T	0.00009	9.47	2.78	1.63	0.23807	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.00123	-2.06	0.40080	D	0.976121	B	0.09022	0.002	B	0.13407	0.009	T	0.00849	-1.1541	9	0.02654	T	1	.	3.5019	0.07676	0.0:0.4818:0.0:0.5182	.	240	O76001	OR2J3_HUMAN	A	240	ENSP00000366374:V240A	ENSP00000366374:V240A	V	+	2	0	OR2J3	29188365	0.981000	0.34729	0.937000	0.37676	0.020000	0.10135	1.790000	0.38734	1.268000	0.44264	0.358000	0.22013	GTG	T|0.981;C|0.019	0.019	strong		0.448	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2			C	29080386	T	C	29080386	3	2	22	1	0	0	0	0	1	0	0	0	11013	1696	59	3	721	3	OR2J3	6	29080386	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	748813	29080386	142034681	1408	4309											
OR11A1	26531	hgsc.bcm.edu	37	chr6	29395180	29395180	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccctccagcatttttggcAtcactgcggaggtgtagaga	9	10	12	10	1	1	1	1	0	0	1	2	3	2	2	2	3	3	3	2	3	1	3	rs61978565	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29395180A>G	ENST00000377149.1	-	5	711	c.239T>C	c.(238-240)aTg>aCg	p.M80T	OR5V1_ENST00000377154.1_Intron|OR11A1_ENST00000377147.2_Missense_Mutation_p.M80T|OR11A1_ENST00000377148.1_Missense_Mutation_p.M80T			Q9GZK7	O11A1_HUMAN	olfactory receptor, family 11, subfamily A, 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)	p.M80T(1)		cervix(1)|large_intestine(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	19						CATTTTTGGCATCACTGCGGA	0.483													A|||	219	0.04373	0.1384	0.0115	5008	,	,		19957	0.0119		0.0129	False		,,,				2504	0.0031				p.M80T		Atlas-SNP	.											OR11A1,NS,carcinoma,0,1	OR11A1	30	1	1	Substitution - Missense(1)	pancreas(1)	c.T239C						PASS	.	A	THR/MET	369,2651		26,317,1167	70	63	66		239	3.8	0.9	6	dbSNP_129	66	34,5384		0,34,2675	yes	missense	OR11A1	NM_013937.2	81	26,351,3842	GG,GA,AA		0.6275,12.2185,4.776	benign	80/316	29395180	403,8035	1510	2709	4219	SO:0001583	missense	26531	exon1			TTTGGCATCACTG		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.239T>C	6.37:g.29395180A>G	ENSP00000366354:p.Met80Thr	60	0	0		75	44	0.586667	NM_013937	A2BF33|A6NFQ3|B0S7T2|Q5ST16|Q9GZK8	Missense_Mutation	SNP	ENST00000377149.1	37	CCDS34363.1	102	0.046703296703296704	74	0.15040650406504066	7	0.019337016574585635	10	0.017482517482517484	11	0.014511873350923483	A	8.985	0.976299	0.18736	0.122185	0.006275	ENSG00000204694	ENST00000377148;ENST00000377149;ENST00000377147	T;T;T	0.02974	4.09;4.09;4.09	3.78	3.78	0.43462	GPCR, rhodopsin-like superfamily (1);	0.297272	0.18047	U	0.153413	T	0.00524	0.0017	N	0.01209	-0.955	0.18873	N	0.999989	B	0.13594	0.008	B	0.14578	0.011	T	0.51028	-0.8757	10	0.56958	D	0.05	-9.2563	11.5265	0.50582	1.0:0.0:0.0:0.0	.	80	Q9GZK7	O11A1_HUMAN	T	80	ENSP00000366353:M80T;ENSP00000366354:M80T;ENSP00000366352:M80T	ENSP00000366352:M80T	M	-	2	0	OR11A1	29503159	0.000000	0.05858	0.925000	0.36789	0.702000	0.40608	0.971000	0.29396	1.569000	0.49696	0.333000	0.21579	ATG	A|0.957;G|0.043	0.043	strong		0.483	OR11A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000193778.1			G	29395180	A	G	29395180	3	3	22	1	0	0	0	0	1	0	0	0	10933	217	8	3	712	3	OR11A1	6	29395180	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	314794	29395180	141719887	1409	4310											
OR2H1	26716	hgsc.bcm.edu	37	chr6	29429732	29429732	+	Silent	SNP	T	T	C																															ccaatgtactttttcctctcTgacctctccttcttggacct																								rs61732184	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29429732T>C	ENST00000377136.1	+	4	651	c.186T>C	c.(184-186)tcT>tcC	p.S62S	OR2H1_ENST00000396792.2_Silent_p.S62S|OR2H1_ENST00000442615.1_Silent_p.S62S|OR2H1_ENST00000377132.1_Silent_p.S62S|OR2H1_ENST00000377133.1_Silent_p.S62S|OR2H1_ENST00000473369.1_Intron			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, 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)			large_intestine(5)|lung(12)	17						TTTTCCTCTCTGACCTCTCCT	0.527													T|||	174	0.0347444	0.1044	0.013	5008	,	,		20433	0.0119		0.0119	False		,,,				2504	0.0031				p.S62S		Atlas-SNP	.											.	OR2H1	38	.	0			c.T186C						PASS	.	T		301,2721		17,267,1227	138	135	136		186	0	1	6	dbSNP_129	136	33,5385		0,33,2676	no	coding-synonymous	OR2H1	NM_030883.3		17,300,3903	CC,CT,TT		0.6091,9.9603,3.9573		62/317	29429732	334,8106	1511	2709	4220	SO:0001819	synonymous_variant	26716	exon3			CCTCTCTGACCTC	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.186T>C	6.37:g.29429732T>C		256	0	0		303	139	0.458746	NM_030883	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Silent	SNP	ENST00000377136.1	37	CCDS4660.1																																																																																			T|0.964;C|0.036	0.036	strong		0.527	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3			C	29429732	T	C	29429732	2	2	22	1	0	0	0	0	0	0	0	1	11010	1567	55	3		3	OR2H1	6	29429732	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	34552	29429732	141685335	1410	4311	56	2									
OR2H1	26716	hgsc.bcm.edu	37	chr6	29429733	29429733	+	Missense_Mutation	SNP	G	G	A																															caatgtactttttcctctctGacctctccttcttggacctc																								rs61732185	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29429733G>A	ENST00000377136.1	+	4	652	c.187G>A	c.(187-189)Gac>Aac	p.D63N	OR2H1_ENST00000396792.2_Missense_Mutation_p.D63N|OR2H1_ENST00000442615.1_Missense_Mutation_p.D63N|OR2H1_ENST00000377132.1_Missense_Mutation_p.D63N|OR2H1_ENST00000377133.1_Missense_Mutation_p.D63N|OR2H1_ENST00000473369.1_Intron			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, member 1	63			D -> N (in allele 6M1-16*02; dbSNP:rs61732185). {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)			large_intestine(5)|lung(12)	17						TTTCCTCTCTGACCTCTCCTT	0.532													G|||	174	0.0347444	0.1044	0.013	5008	,	,		20350	0.0119		0.0119	False		,,,				2504	0.0031				p.D63N		Atlas-SNP	.											.	OR2H1	38	.	0			c.G187A						PASS	.	G	ASN/ASP	301,2721		17,267,1227	137	134	135		187	0.4	1	6	dbSNP_129	135	33,5385		0,33,2676	yes	missense	OR2H1	NM_030883.3	23	17,300,3903	AA,AG,GG		0.6091,9.9603,3.9573	benign	63/317	29429733	334,8106	1511	2709	4220	SO:0001583	missense	26716	exon3			CTCTCTGACCTCT	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.187G>A	6.37:g.29429733G>A	ENSP00000366340:p.Asp63Asn	257	0	0		303	143	0.471947	NM_030883	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Missense_Mutation	SNP	ENST00000377136.1	37	CCDS4660.1	88	0.040293040293040296	60	0.12195121951219512	8	0.022099447513812154	10	0.017482517482517484	10	0.013192612137203167	G	1.564	-0.535865	0.04082	0.099603	0.006091	ENSG00000204688	ENST00000377136;ENST00000377133;ENST00000442615;ENST00000377132;ENST00000396792	T;T;T;T;T	0.00940	5.52;5.52;5.52;5.52;5.52	2.88	0.407	0.16371	GPCR, rhodopsin-like superfamily (1);	0.156786	0.30126	N	0.010354	T	0.00039	0.0001	N	0.00003	-3.425	0.24176	N	0.995605	B	0.02656	0.0	B	0.01281	0.0	T	0.12604	-1.0541	10	0.02654	T	1	.	4.2744	0.10802	0.6269:0.1713:0.2018:0.0	rs61732185	63	Q9GZK4	OR2H1_HUMAN	N	63	ENSP00000366340:D63N;ENSP00000366337:D63N;ENSP00000393254:D63N;ENSP00000366336:D63N;ENSP00000380010:D63N	ENSP00000366336:D63N	D	+	1	0	OR2H1	29537712	0.036000	0.19791	0.986000	0.45419	0.919000	0.55068	1.592000	0.36676	0.072000	0.16694	-0.354000	0.07668	GAC	G|0.964;A|0.036	0.036	strong		0.532	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3			A	29429733	G	A	29429733	3	1	22	1	0	0	0	0	1	0	0	0	11010	1290	45	2	189	2	OR2H1	6	29429733	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1	29429733	141685334	1411	4312	56	2									
OR2H1	26716	hgsc.bcm.edu	37	chr6	29430356	29430356	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tatgcccaagggaggggcaaGttctttggtctcttctatgc	7	13	12	9	0	3	0	0	0	3	0	4	1	3	1	1	4	2	2	1	4	4	5	rs371076908|rs148433584	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29430356G>C	ENST00000377136.1	+	4	1275	c.810G>C	c.(808-810)aaG>aaC	p.K270N	OR2H1_ENST00000396792.2_Missense_Mutation_p.K270N|OR2H1_ENST00000442615.1_Missense_Mutation_p.K270N|OR2H1_ENST00000377132.1_Missense_Mutation_p.K270N|OR2H1_ENST00000377133.1_Missense_Mutation_p.K270N|OR2H1_ENST00000473369.1_3'UTR			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, member 1	270						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						GGAGGGGCAAGTTCTTTGGTC	0.522													G|||	22	0.00439297	0.0159	0.0014	5008	,	,		21364	0.0		0.0	False		,,,				2504	0.0				p.K270N		Atlas-SNP	.											.	OR2H1	38	.	0			c.G810C						PASS	.	G	ASN/LYS	42,2980		0,42,1469	113	115	114		810	2.2	0.9	6	dbSNP_134	114	0,5418		0,0,2709	no	missense	OR2H1	NM_030883.3	94	0,42,4178	CC,CG,GG		0.0,1.3898,0.4976	probably-damaging	270/317	29430356	42,8398	1511	2709	4220	SO:0001583	missense	26716	exon3			GGGCAAGTTCTTT	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.810G>C	6.37:g.29430356G>C	ENSP00000366340:p.Lys270Asn	464	0	0		453	227	0.501104	NM_030883	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Missense_Mutation	SNP	ENST00000377136.1	37	CCDS4660.1	7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	G	10.39	1.335640	0.24253	0.013898	0.0	ENSG00000204688	ENST00000377136;ENST00000377133;ENST00000442615;ENST00000377132;ENST00000396792	T;T;T;T;T	0.00207	8.55;8.55;8.55;8.55;8.55	3.09	2.22	0.28083	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42682	D	0.000675	T	0.00241	0.0007	M	0.87617	2.895	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.32824	-0.9892	10	0.87932	D	0	.	6.4805	0.22060	0.322:0.0:0.678:0.0	.	270	Q9GZK4	OR2H1_HUMAN	N	270	ENSP00000366340:K270N;ENSP00000366337:K270N;ENSP00000393254:K270N;ENSP00000366336:K270N;ENSP00000380010:K270N	ENSP00000366336:K270N	K	+	3	2	OR2H1	29538335	0.000000	0.05858	0.935000	0.37517	0.315000	0.28087	-1.183000	0.03079	0.870000	0.35726	-0.199000	0.12753	AAG	G|0.995;C|0.005	0.005	strong		0.522	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3			C	29430356	G	C	29430356	3	2	22	1	0	0	0	0	1	0	0	0	11010	1020	36	4	812	4	OR2H1	6	29430356	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	623	29430356	141684711	1412	4313											
HLA-A	3105	hgsc.bcm.edu	37	chr6	29910660	29910660	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgacagcgacgccgcgagccAgaggatggagccgcgggcgc	8	1	18	14	8	0	1	0	0	0	1	0	6	0	3	3	3	3	0	3	3	0	0	rs41559117	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29910660A>G	ENST00000396634.1	+	4	541	c.200A>G	c.(199-201)cAg>cGg	p.Q67R	HLA-A_ENST00000376809.5_Missense_Mutation_p.Q67R|HLA-A_ENST00000376806.5_Missense_Mutation_p.Q67R|HLA-A_ENST00000376802.2_Missense_Mutation_p.Q67R			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	67	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)			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						GCCGCGAGCCAGAGGATGGAG	0.682									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)			a|||	114	0.0227636	0.0575	0.0288	5008	,	,		14823	0.002		0.007	False		,,,				2504	0.0092				p.Q67R		Atlas-SNP	.											.	HLA-A	89	.	0			c.A200G						PASS	.	A	ARG/GLN	189,4215		2,185,2015	48	46	46		200	-0.8	0.2	6	dbSNP_127	46	76,8522		0,76,4223	no	missense	HLA-A	NM_002116.7	43	2,261,6238	GG,GA,AA		0.8839,4.2916,2.0381	possibly-damaging	67/366	29910660	265,12737	2202	4299	6501	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CGAGCCAGAGGAT	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.200A>G	6.37:g.29910660A>G	ENSP00000379873:p.Gln67Arg	134	0	0		219	54	0.246575	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	36	0.016483516483516484	22	0.044715447154471545	8	0.022099447513812154	2	0.0034965034965034965	4	0.005277044854881266	.	6.554	0.470589	0.12461	0.042916	0.008839	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00705	5.81;5.81;5.81;5.81	3.72	-0.813	0.10850	MHC class I, alpha chain, alpha1/alpha2 (3);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	.	.	.	.	T	0.00580	0.0019	N	0.21545	0.675	0.09310	N	1	B;D;B;D;B	0.54772	0.0;0.968;0.001;0.968;0.0	B;D;B;D;B	0.75484	0.006;0.986;0.006;0.986;0.006	T	0.55673	-0.8104	9	0.49607	T	0.09	.	5.0607	0.14555	0.5529:0.3361:0.0:0.1109	rs41559117	67;67;67;67;67	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	R	67	ENSP00000379873:Q67R;ENSP00000366002:Q67R;ENSP00000366005:Q67R;ENSP00000365998:Q67R	ENSP00000348012:Q67R	Q	+	2	0	HLA-A	30018639	0.000000	0.05858	0.192000	0.23308	0.357000	0.29423	-1.236000	0.02925	0.031000	0.15407	-1.821000	0.00599	CAG	A|0.977;C|0.002;G|0.021	0.021	strong		0.682	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116		G	29910660	A	G	29910660	3	3	22	1	0	0	0	0	1	0	0	0	7204	188	7	3	206	3	HLA-A	6	29910660	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	480304	29910660	141204407	1413	4314											
TRIM15	89870	hgsc.bcm.edu	37	chr6	30139971	30139971	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcgagatcccgcgcggcGtgagagtcgccctggactac	7	6	15	13	6	0	3	0	2	0	2	2	6	1	4	2	2	2	0	2	2	1	1	rs115649931	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30139971G>C	ENST00000376694.4	+	7	1712	c.1243G>C	c.(1243-1245)Gtg>Ctg	p.V415L	TRIM15_ENST00000376688.1_Intron	NM_033229.2	NP_150232.2	Q9C019	TRI15_HUMAN	tripartite motif containing 15	415	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						CCCGCGCGGCGTGAGAGTCGC	0.682													G|||	26	0.00519169	0.0182	0.0029	5008	,	,		12909	0.0		0.0	False		,,,				2504	0.0				p.V415L		Atlas-SNP	.											.	TRIM15	34	.	0			c.G1243C						PASS	.	G	LEU/VAL	53,2929		0,53,1438	16	13	14		1243	3.7	0	6	dbSNP_133	14	0,5354		0,0,2677	yes	missense	TRIM15	NM_033229.2	32	0,53,4115	CC,CG,GG		0.0,1.7773,0.6358	probably-damaging	415/466	30139971	53,8283	1491	2677	4168	SO:0001583	missense	89870	exon7			CGCGGCGTGAGAG	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.1243G>C	6.37:g.30139971G>C	ENSP00000365884:p.Val415Leu	41	0	0		57	32	0.561404	NM_033229	A2BEC9|O95604|Q8IUX9|Q9C018	Missense_Mutation	SNP	ENST00000376694.4	37	CCDS4677.1	.	.	.	.	.	.	.	.	.	.	G	12.18	1.859376	0.32884	0.017773	0.0	ENSG00000204610	ENST00000376695;ENST00000376694	T	0.74002	-0.8	4.54	3.67	0.42095	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	0.39759	U	0.001266	T	0.51126	0.1656	L	0.58669	1.825	0.48087	D	0.999587	B	0.33448	0.412	B	0.32393	0.145	T	0.54702	-0.8254	10	0.45353	T	0.12	.	5.7541	0.18162	0.1022:0.0:0.7065:0.1913	.	415	Q9C019	TRI15_HUMAN	L	346;415	ENSP00000365884:V415L	ENSP00000365884:V415L	V	+	1	0	TRIM15	30247950	0.042000	0.20092	0.011000	0.14972	0.017000	0.09413	0.313000	0.19415	0.886000	0.36113	0.478000	0.44815	GTG	G|0.990;C|0.010	0.010	strong		0.682	TRIM15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076026.2	NM_033229		C	30139971	G	C	30139971	3	2	22	1	0	0	0	0	1	0	0	0	16505	1145	40	4	1269	4	TRIM15	6	30139971	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	229311	30139971	140975096	1414	4315											
PRR3	80742	hgsc.bcm.edu	37	chr6	30529622	30529622	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctctccagctcttcacagaGgtcctccaggatcaagggga	9	9	10	13	0	4	1	2	0	2	1	8	3	7	3	3	4	1	1	3	4	1	1	rs3888778	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30529622G>A	ENST00000376560.3	+	3	640	c.181G>A	c.(181-183)Ggt>Agt	p.G61S	PRR3_ENST00000498336.1_3'UTR|PRR3_ENST00000376557.3_Missense_Mutation_p.G40S	NM_025263.3	NP_079539.2	P79522	PRR3_HUMAN	proline rich 3	61	Pro-rich.		G -> S (in dbSNP:rs3888778). {ECO:0000269|PubMed:15489334}.				metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			lung(1)|ovary(1)	2						TCTTCACAGAGGTCCTCCAGG	0.507													G|||	166	0.033147	0.0862	0.0259	5008	,	,		17768	0.0208		0.0109	False		,,,				2504	0.002				p.G61S		Atlas-SNP	.											.	PRR3	5	.	0			c.G181A						PASS	.	G	SER/GLY,SER/GLY	137,2249		3,131,1059	9	9	9		118,181	3.9	1	6	dbSNP_108	9	47,4983		0,47,2468	yes	missense,missense	PRR3	NM_001077497.2,NM_025263.3	56,56	3,178,3527	AA,AG,GG		0.9344,5.7418,2.4811	possibly-damaging,possibly-damaging	40/168,61/189	30529622	184,7232	1193	2515	3708	SO:0001583	missense	80742	exon3			CACAGAGGTCCTC	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.181G>A	6.37:g.30529622G>A	ENSP00000365744:p.Gly61Ser	62	0	0		63	33	0.52381	NM_025263	A1A4H4|Q5RJB5|Q5STN6	Missense_Mutation	SNP	ENST00000376560.3	37	CCDS43440.1	75	0.034340659340659344	41	0.08333333333333333	10	0.027624309392265192	17	0.02972027972027972	7	0.009234828496042216	G	18.14	3.558222	0.65538	0.057418	0.009344	ENSG00000204576	ENST00000376560;ENST00000376555;ENST00000376557	T;T	0.61392	0.79;0.11	4.8	3.93	0.45458	.	0.000000	0.44097	D	0.000490	T	0.28665	0.0710	N	0.14661	0.345	0.35071	D	0.762444	D;P	0.55385	0.971;0.952	P;B	0.46585	0.521;0.322	T	0.33471	-0.9867	10	0.87932	D	0	-4.6812	8.9334	0.35684	0.1014:0.0:0.8986:0.0	rs3888778;rs4559118;rs3888778	40;61	P79522-2;P79522	.;PRR3_HUMAN	S	61;126;40	ENSP00000365744:G61S;ENSP00000365740:G40S	ENSP00000365738:G126S	G	+	1	0	PRR3	30637601	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.111000	0.57838	1.243000	0.43853	0.655000	0.94253	GGT	G|0.963;A|0.037	0.037	strong		0.507	PRR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076033.2	NM_025263		A	30529622	G	A	30529622	3	1	22	1	0	0	0	0	1	0	0	0	12610	1000	35	2	191	2	PRR3	6	30529622	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	389651	30529622	140585445	1415	4316											
PPP1R10	5514	hgsc.bcm.edu	37	chr6	30570374	30570374	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggccaccccgcatagggtcGcccgggccatcccagaaggg	7	3	15	16	3	0	1	0	0	0	1	2	1	1	1	6	4	0	1	6	4	2	1	rs35689098	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30570374G>A	ENST00000376511.2	-	19	2604	c.2052C>T	c.(2050-2052)ggC>ggT	p.G684G		NM_002714.3	NP_002705.2	Q96QC0	PP1RA_HUMAN	protein phosphatase 1, regulatory subunit 10	684	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						GCATAGGGTCGCCCGGGCCAT	0.677													G|||	138	0.0275559	0.0915	0.0159	5008	,	,		15303	0.001		0.001	False		,,,				2504	0.0041				p.G684G		Atlas-SNP	.											.	PPP1R10	60	.	0			c.C2052T						PASS	.	G		164,2534		1,162,1186	7	10	9		2052	-0.1	0.9	6	dbSNP_126	9	11,5013		0,11,2501	no	coding-synonymous	PPP1R10	NM_002714.2		1,173,3687	AA,AG,GG		0.2189,6.0786,2.2663		684/941	30570374	175,7547	1349	2512	3861	SO:0001819	synonymous_variant	5514	exon19			AGGGTCGCCCGGG	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.2052C>T	6.37:g.30570374G>A		20	0	0		26	13	0.5	NM_002714	O00405	Silent	SNP	ENST00000376511.2	37	CCDS4681.1																																																																																			G|0.970;A|0.030	0.030	strong		0.677	PPP1R10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076556.2	NM_002714		A	30570374	G	A	30570374	2	1	22	1	0	0	0	0	0	0	0	1	12364	1074	38	1		1	PPP1R10	6	30570374	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	40752	30570374	140544693	1416	4317											
MDC1	9656	hgsc.bcm.edu	37	chr6	30668374	30668374	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	agtggaatggagcaatgaggGaagtcctgagggcatgtgat	12	8	17	4	0	0	3	0	3	0	0	1	6	1	6	1	4	1	2	1	4	3	0	rs9468812	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30668374G>A	ENST00000376406.3	-	15	6785	c.6138C>T	c.(6136-6138)ttC>ttT	p.F2046F	MDC1_ENST00000376405.2_Silent_p.F1782F|MDC1-AS1_ENST00000442150.1_RNA	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	2046	BRCT 2. {ECO:0000255|PROSITE- ProRule:PRU00033}.|Required for nuclear localization (NLS2).				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						AGCAATGAGGGAAGTCCTGAG	0.542								Other conserved DNA damage response genes					G|||	234	0.0467252	0.1278	0.0432	5008	,	,		16633	0.0208		0.0129	False		,,,				2504	0.001				p.F2046F		Atlas-SNP	.											.	MDC1	218	.	0			c.C6138T						PASS	.	G		320,2702		21,278,1212	114	107	109		6138	-4.1	0	6	dbSNP_119	109	63,5355		0,63,2646	no	coding-synonymous	MDC1	NM_014641.2		21,341,3858	AA,AG,GG		1.1628,10.589,4.5379		2046/2090	30668374	383,8057	1511	2709	4220	SO:0001819	synonymous_variant	9656	exon15			ATGAGGGAAGTCC	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.6138C>T	6.37:g.30668374G>A		107	0	0		102	50	0.490196	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Silent	SNP	ENST00000376406.3	37	CCDS34384.1																																																																																			G|0.958;A|0.042	0.042	strong		0.542	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641		A	30668374	G	A	30668374	2	1	22	1	0	0	0	0	0	0	0	1	9412	1165	41	2		2	MDC1	6	30668374	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	98000	30668374	140446693	1417	4318											
MDC1	9656	hgsc.bcm.edu	37	chr6	30673013	30673013	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggggtcttgacagaggacAtatttgtcctgctcctagtg	8	12	12	9	0	1	2	0	1	1	1	3	3	3	3	2	3	1	1	2	3	2	4	rs61733213	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30673013A>G	ENST00000376406.3	-	10	4594	c.3947T>C	c.(3946-3948)aTg>aCg	p.M1316T	MDC1_ENST00000376405.2_Missense_Mutation_p.M1052T|MDC1-AS1_ENST00000442150.1_RNA	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1316	Interaction with the PRKDC complex.|Pro-rich.			Missing (in Ref. 2; CAH18685). {ECO:0000305}.	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						GACAGAGGACATATTTGTCCT	0.597								Other conserved DNA damage response genes					a|||	234	0.0467252	0.1278	0.0432	5008	,	,		19113	0.0208		0.0129	False		,,,				2504	0.001				p.M1316T		Atlas-SNP	.											.	MDC1	218	.	0			c.T3947C						PASS	.	C	THR/MET	480,3926	224.9+/-240.9	34,412,1757	141	152	148		3947	-1.8	0	6	dbSNP_129	148	95,8505	52.3+/-112.8	1,93,4206	no	missense	MDC1	NM_014641.2	81	35,505,5963	GG,GA,AA		1.1047,10.8942,4.421	benign	1316/2090	30673013	575,12431	2203	4300	6503	SO:0001583	missense	9656	exon10			GAGGACATATTTG	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.3947T>C	6.37:g.30673013A>G	ENSP00000365588:p.Met1316Thr	322	1	0.00310559		363	186	0.512397	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Missense_Mutation	SNP	ENST00000376406.3	37	CCDS34384.1	100	0.045787545787545784	59	0.11991869918699187	16	0.04419889502762431	17	0.02972027972027972	8	0.010554089709762533	a	2.633	-0.285988	0.05605	0.108942	0.011047	ENSG00000137337	ENST00000376406;ENST00000376405	T;T	0.05139	3.49;3.49	3.32	-1.81	0.07882	.	0.445015	0.16677	N	0.204131	T	0.00637	0.0021	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	0.42103	-0.9471	10	0.12103	T	0.63	.	3.1868	0.06603	0.299:0.311:0.0:0.3899	.	1052;1316	Q14676-2;Q14676	.;MDC1_HUMAN	T	1316;1052	ENSP00000365588:M1316T;ENSP00000365587:M1052T	ENSP00000365587:M1052T	M	-	2	0	MDC1	30780992	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.173000	0.03108	-0.789000	0.04498	-3.196000	0.00055	ATG	A|0.958;G|0.042	0.042	strong		0.597	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641		G	30673013	A	G	30673013	3	3	22	1	0	0	0	0	1	0	0	0	9412	217	8	3	2346	3	MDC1	6	30673013	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	4639	30673013	140442054	1418	4319											
CCHCR1	54535	hgsc.bcm.edu	37	chr6	31118304	31118304	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acccgcacctgcagcagctcCgcggtggcatgcaggctgtc	6	6	13	16	3	0	0	0	0	0	0	2	0	1	0	3	3	4	7	3	3	0	0	rs139910767		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31118304C>T	ENST00000376266.5	-	7	995	c.873G>A	c.(871-873)gcG>gcA	p.A291A	CCHCR1_ENST00000480060.1_Intron|CCHCR1_ENST00000451521.2_Silent_p.A344A|CCHCR1_ENST00000396263.2_Silent_p.A291A|CCHCR1_ENST00000396268.3_Silent_p.A380A	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	291					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						GCAGCAGCTCCGCGGTGGCAT	0.657													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19191	0.0		0.0	False		,,,				2504	0.0				p.A380A		Atlas-SNP	.											.	CCHCR1	68	.	0			c.G1140A						PASS	.	C	,,	3,3019		0,3,1508	48	34	39		1032,1140,873	-9.5	0	6	dbSNP_134	39	0,5414		0,0,2707	no	coding-synonymous,coding-synonymous,coding-synonymous	CCHCR1	NM_001105563.1,NM_001105564.1,NM_019052.3	,,	0,3,4215	TT,TC,CC		0.0,0.0993,0.0356	,,	344/836,380/872,291/783	31118304	3,8433	1511	2707	4218	SO:0001819	synonymous_variant	54535	exon7			CAGCTCCGCGGTG	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.873G>A	6.37:g.31118304C>T		76	0	0		93	45	0.483871	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Silent	SNP	ENST00000376266.5	37	CCDS4695.1																																																																																			C|0.999;T|0.001	0.001	strong		0.657	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052		T	31118304	C	T	31118304	2	4	22	1	0	0	0	0	0	0	0	1	2879	639	23	1		1	CCHCR1	6	31118304	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	445291	31118304	139996763	1419	4320											
HLA-C	3107	hgsc.bcm.edu	37	chr6	31237275	31237275	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgccatcacttacacgcaGcctgagagcagctccctcct	8	7	8	18	2	1	1	1	1	0	1	3	2	3	1	5	0	4	3	5	0	1	1	rs41559915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31237275G>A	ENST00000376228.5	-	6	1057	c.1043C>T	c.(1042-1044)gCt>gTt	p.A348V	HLA-C_ENST00000383329.3_Missense_Mutation_p.A354V	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	354					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)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						CTTACACGCAGCCTGAGAGCA	0.557													G|||	167	0.0333466	0.0605	0.013	5008	,	,		18640	0.0069		0.006	False		,,,				2504	0.0665				p.A348V		Atlas-SNP	.											HLA-C_ENST00000383329,NS,carcinoma,-1,2	HLA-C	92	2	0			c.C1043T						PASS	.	G	VAL/ALA	216,4190		7,202,1994	64	68	67		1043	1.8	0	6	dbSNP_127	67	39,8561		0,39,4261	yes	missense	HLA-C	NM_002117.5	64	7,241,6255	AA,AG,GG		0.4535,4.9024,1.9606	benign	348/367	31237275	255,12751	2203	4300	6503	SO:0001583	missense	3107	exon6			CACGCAGCCTGAG	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4933	protein-coding gene	gene with protein product		142840	"psoriasis susceptibility 1"	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.1043C>T	6.37:g.31237275G>A	ENSP00000365402:p.Ala348Val	157	0	0		155	81	0.522581	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	33	0.01510989010989011	22	0.044715447154471545	5	0.013812154696132596	1	0.0017482517482517483	5	0.006596306068601583	.	11.21	1.572853	0.28092	0.049024	0.004535	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000539307	T;T	0.04317	3.65;3.65	2.67	1.75	0.24633	MHC class I, alpha chain, C-terminal (1);	.	.	.	.	T	0.13243	0.0321	M	0.93106	3.38	0.09310	N	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.85130	0.997;0.997;0.997	T	0.03898	-1.0994	9	0.72032	D	0.01	.	6.7409	0.23435	0.0:0.0:0.7201:0.2799	rs41559915	348;354;348	A6H578;A2AEA2;P10321	.;.;1C07_HUMAN	V	348;354;385	ENSP00000365402:A348V;ENSP00000372819:A354V	ENSP00000365402:A348V	A	-	2	0	HLA-C	31345254	0.040000	0.19996	0.002000	0.10522	0.176000	0.22953	1.465000	0.35299	0.670000	0.31165	0.298000	0.19748	GCT	G|0.981;A|0.019	0.019	strong		0.557	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117		A	31237275	G	A	31237275	3	1	22	1	0	0	0	0	1	0	0	0	7206	971	34	2	69	2	HLA-C	6	31237275	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	118971	31237275	139877792	1420	4321											
MICA	100507436	hgsc.bcm.edu	37	chr6	31379802	31379802	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgcagggcttccagcttctAtccccggaatatcatactga	10	11	8	12	1	2	1	1	1	1	0	4	2	4	2	3	2	3	3	3	2	4	5	rs41546915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31379802A>G	ENST00000449934.2	+	4	746	c.692A>G	c.(691-693)tAt>tGt	p.Y231C	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)				TCCAGCTTCTATCCCCGGAAT	0.587													a|||	3	0.000599042	0.0023	0.0	5008	,	,		19291	0.0		0.0	False		,,,				2504	0.0				p.Y231C		Atlas-SNP	.											.	MICA	21	.	0			c.A692G						PASS	.						18	22	21					6																	31379802		692	1591	2283	SO:0001583	missense	100507436	exon4			GCTTCTATCCCCG	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	ENST00000449934.2:c.692A>G	6.37:g.31379802A>G	ENSP00000413079:p.Tyr231Cys	129	0	0		79	39	0.493671	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	.	.	.	.	.	.	.	.	.	.	a	12.79	2.044981	0.36085	.	.	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.04317	3.65;3.65	2.38	-2.63	0.06133	.	1.496520	0.04824	N	0.437454	T	0.13586	0.0329	H	0.95294	3.65	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.06807	-1.0806	10	0.87932	D	0	.	3.1987	0.06643	0.4334:0.1971:0.0:0.3695	rs41546915	93;231	Q5SS58;Q96QC4	.;.	C	93;231;188;231;122	ENSP00000413079:Y231C;ENSP00000402410:Y122C	ENSP00000365394:Y231C	Y	+	2	0	MICA	31487781	0.626000	0.27120	0.004000	0.12327	0.037000	0.13140	-0.027000	0.12371	-0.196000	0.10366	0.365000	0.22127	TAT	.	.	weak		0.587	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519		G	31379802	A	G	31379802	3	3	22	1	0	0	0	0	1	0	0	0	9577	449	16	3	706	3	MICA	6	31379802	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	142527	31379802	139735265	1421	4322											
VARS	7407	hgsc.bcm.edu	37	chr6	31747833	31747833	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	actgggcagtggtgacggccGggaagtcgtaggcctggaag	8	6	19	8	3	0	1	0	1	0	0	1	3	0	3	2	6	0	2	2	6	3	1	rs1076827	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31747833G>A	ENST00000375663.3	-	26	3463	c.3023C>T	c.(3022-3024)cCg>cTg	p.P1008L	VWA7_ENST00000467576.1_5'Flank|VWA7_ENST00000375688.4_5'Flank|Y_RNA_ENST00000364685.1_RNA|VARS_ENST00000482996.1_5'Flank|VWA7_ENST00000375686.3_5'Flank|VWA7_ENST00000447450.1_5'Flank	NM_006295.2	NP_006286.1	P26640	SYVC_HUMAN	valyl-tRNA synthetase	1008			P -> L (in dbSNP:rs1076827).		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)	GGTGACGGCCGGGAAGTCGTA	0.627													G|||	95	0.0189696	0.0658	0.0101	5008	,	,		17107	0.0		0.0	False		,,,				2504	0.001				p.P1008L		Atlas-SNP	.											.	VARS	76	.	0			c.C3023T						PASS	.	G	LEU/PRO	261,4145	150.3+/-184.3	5,251,1947	59	61	61		3023	5.2	1	6	dbSNP_86	61	5,8595	4.3+/-15.6	0,5,4295	yes	missense	VARS	NM_006295.2	98	5,256,6242	AA,AG,GG		0.0581,5.9237,2.0452	possibly-damaging	1008/1265	31747833	266,12740	2203	4300	6503	SO:0001583	missense	7407	exon26			ACGGCCGGGAAGT	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.3023C>T	6.37:g.31747833G>A	ENSP00000364815:p.Pro1008Leu	82	0	0		74	37	0.5	NM_006295	B0V1N1|B4DZ61|Q5JQ90|Q96E77|Q9UQM2	Missense_Mutation	SNP	ENST00000375663.3	37	CCDS34412.1	43	0.019688644688644688	40	0.08130081300813008	3	0.008287292817679558	0	0.0	0	0.0	G	12.66	2.003411	0.35320	0.059237	5.81E-4	ENSG00000204394	ENST00000375663	T	0.13420	2.59	5.23	5.23	0.72850	Valyl/Leucyl/Isoleucyl-tRNA synthetase, class I, anticodon-binding (1);Aminoacyl-tRNA synthetase, class 1a, anticodon-binding (1);	0.000000	0.85682	D	0.000000	T	0.14270	0.0345	L	0.48260	1.515	0.80722	D	1	D	0.58268	0.982	P	0.55667	0.781	T	0.05178	-1.0901	10	0.21014	T	0.42	-11.0663	16.2949	0.82765	0.0:0.0:1.0:0.0	rs1076827;rs4368836;rs16867555;rs1076827	1008	P26640	SYVC_HUMAN	L	1008	ENSP00000364815:P1008L	ENSP00000364815:P1008L	P	-	2	0	VARS	31855812	1.000000	0.71417	0.975000	0.42487	0.423000	0.31445	5.547000	0.67249	2.445000	0.82738	0.650000	0.86243	CCG	G|0.978;A|0.022	0.022	strong		0.627	VARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076619.2	NM_006295		A	31747833	G	A	31747833	3	1	22	1	0	0	0	0	1	0	0	0	17138	1116	39	1	791	1	VARS	6	31747833	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	368031	31747833	139367234	1422	4323											
C6orf48	50854	hgsc.bcm.edu	37	chr6	31807372	31807373	+	Frame_Shift_Ins	INS	-	-	A																															tgggcatatcctaagaacttINSacaactttcctgtattatcc																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31807372_31807373insA	ENST00000375640.3	+	4	887_888	c.160_161insA	c.(160-162)tacfs	p.Y54fs	SNORD52_ENST00000364884.1_RNA|C6orf48_ENST00000395788.3_Frame_Shift_Ins_p.Y54fs|C6orf48_ENST00000375642.2_Frame_Shift_Ins_p.Y54fs|C6orf48_ENST00000375633.1_Frame_Shift_Ins_p.Y54fs|C6orf48_ENST00000375641.2_Frame_Shift_Ins_p.Y54fs|C6orf48_ENST00000375639.2_Frame_Shift_Ins_p.Y54fs|C6orf48_ENST00000375638.3_Frame_Shift_Ins_p.Y54fs|C6orf48_ENST00000395789.1_Frame_Shift_Ins_p.Y54fs|C6orf48_ENST00000375635.2_Frame_Shift_Ins_p.Y54fs	NM_001040438.1	NP_001035528.1	Q9UBA6	G8_HUMAN	chromosome 6 open reading frame 48	54										breast(1)|large_intestine(1)|lung(1)|skin(1)	4						CCTAAGAACTTACAACTTTCCT	0.391																																					p.Y54_N55delinsX		Pindel,Atlas-Indel	.											.	C6orf48	8	.	0			c.160_161insA						PASS	.																																			SO:0001589	frameshift_variant	50854	exon5			.	AJ249732	CCDS34416.1	6p21.33	2011-12-13			ENSG00000204387	ENSG00000204387			19078	protein-coding gene	gene with protein product		605447				8096093	Standard	NM_001287483		Approved	D6S57, G8	uc003rjy.2	Q9UBA6	OTTHUMG00000031175	ENST00000375640.3:c.161dupA	6.37:g.31807373_31807373dupA	ENSP00000364791:p.Tyr54fs	119	0	.		120	41	0.342	NM_001040437	Q9BW21|Q9UBA7|Q9UBA8	Frame_Shift_Ins	INS	ENST00000375640.3	37	CCDS34416.1																																																																																			.	.	none		0.391	C6orf48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076332.2	NM_001040437		A	31807373	-	A	31807372	7	5	22	1	0	1	1	0	0	0	0	0	2367	1754	61	0	166	0	C6orf48	6	31807372	Frame_Shift_Ins	INS	-	TCGA-G8-6324-01A-11D-2210-10	59539	31807372	139307695	1423	4324											
SKIV2L	6499	hgsc.bcm.edu	37	chr6	31928039	31928039	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	ccctggtctcttttggctgtCctgggagccccagtcccatc	3	12	10	16	0	1	0	0	0	1	0	5	1	3	1	5	3	1	1	5	3	0	2	rs11541400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31928039C>G	ENST00000375394.2	+	4	392	c.279C>G	c.(277-279)gtC>gtG	p.V93V	SKIV2L_ENST00000488648.1_3'UTR|NELFE_ENST00000375425.5_5'Flank|SKIV2L_ENST00000544581.1_Intron|NELFE_ENST00000444811.2_5'Flank|NELFE_ENST00000375429.3_5'Flank	NM_006929.4	NP_008860.4	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like (S. cerevisiae)	93					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						TTTTGGCTGTCCTGGGAGCCC	0.517													C|||	22	0.00439297	0.0121	0.0058	5008	,	,		19192	0.0		0.002	False		,,,				2504	0.0				p.V93V		Atlas-SNP	.											.	SKIV2L	97	.	0			c.C279G						PASS	.	C		28,2994		0,28,1483	140	173	161		279	0.1	0	6	dbSNP_120	161	33,5385		0,33,2676	no	coding-synonymous	SKIV2L	NM_006929.4		0,61,4159	GG,GC,CC		0.6091,0.9265,0.7227		93/1247	31928039	61,8379	1511	2709	4220	SO:0001819	synonymous_variant	6499	exon4			GGCTGTCCTGGGA		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.279C>G	6.37:g.31928039C>G		113	0	0		116	53	0.456897	NM_006929	O15005|Q12902|Q15476|Q5ST66	Silent	SNP	ENST00000375394.2	37	CCDS4731.1																																																																																			C|0.993;G|0.007	0.007	strong		0.517	SKIV2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076264.3			G	31928039	C	G	31928039	2	3	22	1	0	0	0	0	0	0	0	1	14374	842	30	4		4	SKIV2L	6	31928039	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	120667	31928039	139187028	1424	4325											
TNXB	7148	hgsc.bcm.edu	37	chr6	32014190	32014190	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctggaggtctcctcagccacGgtcagttcccccaggtgggg	5	8	14	14	1	3	0	2	0	1	0	5	1	4	1	4	6	1	1	4	6	0	1	rs116701346	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32014190G>A	ENST00000375244.3	-	31	10569	c.10368C>T	c.(10366-10368)acC>acT	p.T3456T	TNXB_ENST00000375247.2_Silent_p.T3454T|TNXB_ENST00000451343.1_5'Flank			P22105	TENX_HUMAN	tenascin XB	3501	Fibronectin type-III 26. {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						CCTCAGCCACGGTCAGTTCCC	0.632													G|||	18	0.00359425	0.0129	0.0014	5008	,	,		18563	0.0		0.0	False		,,,				2504	0.0				p.T3454T		Atlas-SNP	.											.	TNXB	553	.	0			c.C10362T						PASS	.	G		13,2817		0,13,1402	27	32	30		10362	-4.5	0.2	6	dbSNP_132	30	2,5274		0,2,2636	no	coding-synonymous	TNXB	NM_019105.6		0,15,4038	AA,AG,GG		0.0379,0.4594,0.185		3454/4243	32014190	15,8091	1415	2638	4053	SO:0001819	synonymous_variant	7148	exon31			AGCCACGGTCAGT	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.10368C>T	6.37:g.32014190G>A		82	0	0		79	47	0.594937	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	37																																																																																				G|0.996;A|0.004	0.004	strong		0.632	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		A	32014190	G	A	32014190	2	1	22	1	0	0	0	0	0	0	0	1	16361	1103	39	1		1	TNXB	6	32014190	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	86151	32014190	139100877	1425	4326											
TNXB	7148	hgsc.bcm.edu	37	chr6	32023903	32023903	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcggctcctcagggggctccGgggcctcagtgctgagttcc	3	8	16	14	2	2	1	2	1	0	0	5	1	5	1	4	5	1	4	4	5	0	1	rs440160	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32023903G>C	ENST00000375244.3	-	24	8393	c.8192C>G	c.(8191-8193)cCg>cGg	p.P2731R	TNXB_ENST00000375247.2_Missense_Mutation_p.P2731R			P22105	TENX_HUMAN	tenascin XB	2789	Fibronectin type-III 19. {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						AGGGGGCTCCGGGGCCTCAGT	0.642													G|||	223	0.0445288	0.1036	0.0605	5008	,	,		14531	0.001		0.0427	False		,,,				2504	0.0				p.P2731R		Atlas-SNP	.											.	TNXB	553	.	0			c.C8192G						PASS	.	G	ARG/PRO	201,2183		10,181,1001	40	47	45		8192	4.5	1	6	dbSNP_80	45	209,4793		4,201,2296	no	missense	TNXB	NM_019105.6	103	14,382,3297	CC,CG,GG		4.1783,8.4312,5.551	probably-damaging	2731/4243	32023903	410,6976	1192	2501	3693	SO:0001583	missense	7148	exon24			GGCTCCGGGGCCT	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.8192C>G	6.37:g.32023903G>C	ENSP00000364393:p.Pro2731Arg	101	0	0		126	63	0.5	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		94	0.04304029304029304	42	0.08536585365853659	22	0.06077348066298342	1	0.0017482517482517483	29	0.03825857519788918	G	15.03	2.713296	0.48517	0.084312	0.041783	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.61510	0.47;0.1	4.48	4.48	0.54585	.	.	.	.	.	T	0.65974	0.2743	M	0.82923	2.615	0.28078	N	0.932303	D	0.61080	0.989	P	0.61070	0.883	T	0.60722	-0.7207	9	0.62326	D	0.03	.	12.0664	0.53590	0.0:0.1746:0.8254:0.0	rs440160;rs3948802	2731	P22105-3	.	R	2731	ENSP00000364393:P2731R;ENSP00000364396:P2731R	ENSP00000364393:P2731R	P	-	2	0	TNXB	32131881	0.037000	0.19845	0.989000	0.46669	0.396000	0.30629	0.607000	0.24209	2.317000	0.78254	0.456000	0.33151	CCG	G|0.931;C|0.069	0.069	strong		0.642	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		C	32023903	G	C	32023903	3	2	22	1	0	0	0	0	1	0	0	0	16361	1116	39	4	6605	4	TNXB	6	32023903	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	9713	32023903	139091164	1426	4327											
TNXB	7148	hgsc.bcm.edu	37	chr6	32032689	32032689	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtggtctggctccaggccCgagatggtgaccccatcctc	5	10	12	14	1	1	2	0	1	1	1	4	3	3	2	5	4	0	1	5	4	0	1	rs35206129	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32032689C>T	ENST00000375244.3	-	19	6951	c.6750G>A	c.(6748-6750)tcG>tcA	p.S2250S	TNXB_ENST00000375247.2_Silent_p.S2250S			P22105	TENX_HUMAN	tenascin XB	2322	Fibronectin type-III 14. {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						GCTCCAGGCCCGAGATGGTGA	0.612													C|||	18	0.00359425	0.0129	0.0014	5008	,	,		17765	0.0		0.0	False		,,,				2504	0.0				p.S2250S		Atlas-SNP	.											.	TNXB	553	.	0			c.G6750A						PASS	.	C		11,2531		0,11,1260	49	55	53		6750	-9.6	0.7	6	dbSNP_126	53	0,5100		0,0,2550	no	coding-synonymous	TNXB	NM_019105.6		0,11,3810	TT,TC,CC		0.0,0.4327,0.1439		2250/4243	32032689	11,7631	1271	2550	3821	SO:0001819	synonymous_variant	7148	exon19			CAGGCCCGAGATG	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.6750G>A	6.37:g.32032689C>T		128	0	0		133	64	0.481203	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	37																																																																																				C|0.995;T|0.005	0.005	strong		0.612	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		T	32032689	C	T	32032689	2	4	22	1	0	0	0	0	0	0	0	1	16361	639	23	1		1	TNXB	6	32032689	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	8786	32032689	139082378	1427	4328											
TNXB	7148	hgsc.bcm.edu	37	chr6	32041621	32041621	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaactggccctcggggactGtccaggagaggcccacagag	10	4	14	13	1	0	2	0	0	0	2	2	4	1	3	3	5	1	0	3	5	1	0	rs6910390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32041621G>A	ENST00000375244.3	-	12	4685	c.4484C>T	c.(4483-4485)aCa>aTa	p.T1495I	TNXB_ENST00000375247.2_Missense_Mutation_p.T1495I			P22105	TENX_HUMAN	tenascin XB	1582	Fibronectin type-III 7. {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						CTCGGGGACTGTCCAGGAGAG	0.627													G|||	27	0.00539137	0.0159	0.0058	5008	,	,		13775	0.0		0.002	False		,,,				2504	0.0				p.T1495I		Atlas-SNP	.											.	TNXB	553	.	0			c.C4484T						PASS	.	G	ILE/THR	33,2523		1,31,1246	29	31	30		4484	1.5	0.1	6	dbSNP_116	30	30,5096		0,30,2533	yes	missense	TNXB	NM_019105.6	89	1,61,3779	AA,AG,GG		0.5853,1.2911,0.8201	benign	1495/4243	32041621	63,7619	1278	2563	3841	SO:0001583	missense	7148	exon12			GGGACTGTCCAGG	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.4484C>T	6.37:g.32041621G>A	ENSP00000364393:p.Thr1495Ile	182	0	0		190	100	0.526316	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		18	0.008241758241758242	11	0.022357723577235773	3	0.008287292817679558	1	0.0017482517482517483	3	0.00395778364116095	G	4.859	0.159720	0.09287	0.012911	0.005853	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.59083	0.29;0.29	5.46	1.54	0.23209	.	0.993930	0.08149	N	0.990366	T	0.44456	0.1294	M	0.82823	2.61	0.19945	N	0.999944	B	0.28552	0.215	B	0.36845	0.234	T	0.51934	-0.8642	10	0.38643	T	0.18	.	7.6751	0.28481	0.3741:0.0:0.6259:0.0	rs6910390	1495	P22105-3	.	I	1495	ENSP00000364393:T1495I;ENSP00000364396:T1495I	ENSP00000364393:T1495I	T	-	2	0	TNXB	32149599	0.384000	0.25164	0.076000	0.20297	0.007000	0.05969	0.499000	0.22546	-0.013000	0.14199	-1.178000	0.01721	ACA	G|0.992;A|0.008	0.008	strong		0.627	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		A	32041621	G	A	32041621	3	1	22	1	0	0	0	0	1	0	0	0	16361	1377	48	2	10361	2	TNXB	6	32041621	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	8932	32041621	139073446	1428	4329											
TNXB	7148	hgsc.bcm.edu	37	chr6	32046832	32046832	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcacgcccacggcggacacCgggcccacgcgctgcccctc	5	3	12	21	6	1	0	1	0	0	0	2	1	1	1	5	3	1	1	5	3	0	0	rs61998180	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32046832C>T	ENST00000375244.3	-	11	4554	c.4353G>A	c.(4351-4353)ccG>ccA	p.P1451P	TNXB_ENST00000375247.2_Silent_p.P1451P|RNA5SP206_ENST00000516703.1_RNA			P22105	TENX_HUMAN	tenascin XB	1538					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)	p.P1538P(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CGGCGGACACCGGGCCCACGC	0.662													C|||	18	0.00359425	0.0129	0.0014	5008	,	,		15860	0.0		0.0	False		,,,				2504	0.0				p.P1451P		Atlas-SNP	.											TNXB_ENST00000375247,NS,carcinoma,0,1	TNXB	553	1	1	Substitution - coding silent(1)	breast(1)	c.G4353A						PASS	.	C		11,2573		0,11,1281	38	43	41		4353	-2.3	0.8	6	dbSNP_129	41	0,5136		0,0,2568	no	coding-synonymous	TNXB	NM_019105.6		0,11,3849	TT,TC,CC		0.0,0.4257,0.1425		1451/4243	32046832	11,7709	1292	2568	3860	SO:0001819	synonymous_variant	7148	exon11			GGACACCGGGCCC	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.4353G>A	6.37:g.32046832C>T		86	0	0		137	71	0.518248	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	37																																																																																				C|0.987;T|0.013	0.013	weak		0.662	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105		T	32046832	C	T	32046832	2	4	22	1	0	0	0	0	0	0	0	1	16361	639	23	1		1	TNXB	6	32046832	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	5211	32046832	139068235	1429	4330											
ATF6B	1388	hgsc.bcm.edu	37	chr6	32093922	32093922	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcatcagaggtggggataacGttgatctggacggtttcaaa	11	11	13	6	2	4	2	3	1	1	1	4	4	4	4	0	5	1	2	0	5	2	3	rs204894	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32093922G>A	ENST00000375203.3	-	5	482	c.450C>T	c.(448-450)aaC>aaT	p.N150N	ATF6B_ENST00000468502.1_5'UTR|ATF6B_ENST00000375201.4_Silent_p.N147N	NM_001136153.1|NM_004381.4	NP_001129625.1|NP_004372.3	Q99941	ATF6B_HUMAN	activating transcription factor 6 beta	150					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						TGGGGATAACGTTGATCTGGA	0.512													G|||	244	0.048722	0.115	0.0648	5008	,	,		15085	0.001		0.0457	False		,,,				2504	0.0				p.N150N		Atlas-SNP	.											.	ATF6B	40	.	0			c.C450T						PASS	.	G	,	453,3953	216.4+/-235.1	21,411,1771	157	137	144		441,450	-0.3	1	6	dbSNP_79	144	404,8196	127.2+/-185.5	7,390,3903	yes	coding-synonymous,coding-synonymous	ATF6B	NM_001136153.1,NM_004381.4	,	28,801,5674	AA,AG,GG		4.6977,10.2814,6.5893	,	147/701,150/704	32093922	857,12149	2203	4300	6503	SO:0001819	synonymous_variant	1388	exon5			GATAACGTTGATC		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.450C>T	6.37:g.32093922G>A		120	0	0		132	70	0.530303	NM_004381	B0UYX6|Q13269|Q14343|Q14345|Q5SSW7|Q99635|Q99637|Q9H3V9|Q9H3W1|Q9NPL0	Silent	SNP	ENST00000375203.3	37	CCDS4737.1																																																																																			G|0.945;A|0.055	0.055	strong		0.512	ATF6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076638.2			A	32093922	G	A	32093922	2	1	22	1	0	0	0	0	0	0	0	1	1085	1136	40	1		1	ATF6B	6	32093922	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	47090	32093922	139021145	1430	4331											
FKBPL	63943	hgsc.bcm.edu	37	chr6	32096528	32096528	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcagccaaacatcttgcgcaGaccctgagccagccctgcat	10	7	8	16	1	2	2	1	1	1	1	2	2	2	2	4	0	6	2	4	0	1	1	rs61747172	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32096528G>A	ENST00000375156.3	-	2	1300	c.1030C>T	c.(1030-1032)Ctg>Ttg	p.L344L	ATF6B_ENST00000468502.1_5'Flank|ATF6B_ENST00000375203.3_5'Flank|ATF6B_ENST00000375201.4_5'Flank	NM_022110.3	NP_071393.2	Q9UIM3	FKBPL_HUMAN	FK506 binding protein like	344					chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)|response to radiation (GO:0009314)	endoplasmic reticulum membrane (GO:0005789)	FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)										ATCTTGCGCAGACCCTGAGCC	0.537													G|||	10	0.00199681	0.0068	0.0014	5008	,	,		19239	0.0		0.0	False		,,,				2504	0.0				p.L344L		Atlas-SNP	.											.	FKBPL	25	.	0			c.C1030T						PASS	.	G		14,4392	21.2+/-45.6	0,14,2189	191	203	199		1030	3.1	0.9	6	dbSNP_129	199	0,8600		0,0,4300	no	coding-synonymous	FKBPL	NM_022110.3		0,14,6489	AA,AG,GG		0.0,0.3177,0.1076		344/350	32096528	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	63943	exon2			TGCGCAGACCCTG	AF139374	CCDS4738.1	6p21.3	2013-12-13	2001-11-28		ENSG00000204315	ENSG00000204315		"Tetratricopeptide (TTC) repeat domain containing"	13949	protein-coding gene	gene with protein product	"WAF-1/CIP1 stabilizing protein 39"		"FK506-binding protein like"			9056895	Standard	NM_022110		Approved	DIR1, NG7, WISp39	uc003nzr.3	Q9UIM3	OTTHUMG00000031129	ENST00000375156.3:c.1030C>T	6.37:g.32096528G>A		144	0	0		160	83	0.51875	NM_022110	A8K5V3|B0UYX8|Q9H5G3	Silent	SNP	ENST00000375156.3	37	CCDS4738.1																																																																																			G|0.998;A|0.002	0.002	strong		0.537	FKBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076221.2			A	32096528	G	A	32096528	2	1	22	1	0	0	0	0	0	0	0	1	5924	933	33	2		2	FKBPL	6	32096528	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2606	32096528	139018539	1431	4332											
FKBPL	63943	hgsc.bcm.edu	37	chr6	32097089	32097089	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gcatttctctatgagctcccCccaagtttcctccctccatg	6	13	5	17	0	1	1	0	1	1	0	6	1	5	1	6	0	1	3	6	0	2	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32097089C>T	ENST00000375156.3	-	2	739	c.469G>A	c.(469-471)Ggg>Agg	p.G157R	ATF6B_ENST00000468502.1_5'Flank|ATF6B_ENST00000375203.3_5'Flank|ATF6B_ENST00000375201.4_5'Flank	NM_022110.3	NP_071393.2	Q9UIM3	FKBPL_HUMAN	FK506 binding protein like	157					chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)|response to radiation (GO:0009314)	endoplasmic reticulum membrane (GO:0005789)	FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)										ATGAGCTCCCCCCAAGTTTCC	0.592																																					p.G157R		Atlas-SNP	.											.	FKBPL	25	.	0			c.G469A						PASS	.						188	201	196					6																	32097089		2203	4300	6503	SO:0001583	missense	63943	exon2			GCTCCCCCCAAGT	AF139374	CCDS4738.1	6p21.3	2013-12-13	2001-11-28		ENSG00000204315	ENSG00000204315		"Tetratricopeptide (TTC) repeat domain containing"	13949	protein-coding gene	gene with protein product	"WAF-1/CIP1 stabilizing protein 39"		"FK506-binding protein like"			9056895	Standard	NM_022110		Approved	DIR1, NG7, WISp39	uc003nzr.3	Q9UIM3	OTTHUMG00000031129	ENST00000375156.3:c.469G>A	6.37:g.32097089C>T	ENSP00000364298:p.Gly157Arg	103	0	0		94	51	0.542553	NM_022110	A8K5V3|B0UYX8|Q9H5G3	Missense_Mutation	SNP	ENST00000375156.3	37	CCDS4738.1	.	.	.	.	.	.	.	.	.	.	C	18.73	3.686625	0.68157	.	.	ENSG00000204315	ENST00000375156	T	0.80994	-1.44	5.23	3.46	0.39613	.	0.000000	0.42548	D	0.000691	T	0.47820	0.1466	N	0.24115	0.695	0.38007	D	0.934418	B	0.32829	0.386	B	0.29353	0.101	T	0.42172	-0.9467	10	0.23891	T	0.37	-13.8519	9.3205	0.37962	0.0:0.8274:0.0:0.1726	.	157	Q9UIM3	FKBPL_HUMAN	R	157	ENSP00000364298:G157R	ENSP00000364298:G157R	G	-	1	0	FKBPL	32205067	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.754000	0.47532	0.793000	0.33875	0.462000	0.41574	GGG	.	.	none		0.592	FKBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076221.2			T	32097089	C	T	32097089	3	4	22	1	0	0	0	0	1	0	0	0	5924	623	22	2	584	2	FKBPL	6	32097089	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	561	32097089	139017978	1432	4333											
AGPAT1	10554	hgsc.bcm.edu	37	chr6	32139186	32139186	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gaagaagtacttggcactggGgctgcagaaccacagggtgg	11	6	16	8	0	0	2	0	0	0	2	0	3	0	2	1	5	3	4	1	5	4	2	rs11964847	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32139186G>A	ENST00000395499.1	-	2	667	c.88C>T	c.(88-90)Ccc>Tcc	p.P30S	AGPAT1_ENST00000490711.1_5'UTR|AGPAT1_ENST00000336984.6_Missense_Mutation_p.P30S|AGPAT1_ENST00000375107.3_Missense_Mutation_p.P30S|AGPAT1_ENST00000395496.1_Missense_Mutation_p.P30S|PPT2-EGFL8_ENST00000422437.1_3'UTR|AGPAT1_ENST00000375104.2_Missense_Mutation_p.P30S|AGPAT1_ENST00000412465.2_5'UTR|AGPAT1_ENST00000395497.1_Missense_Mutation_p.P30S			Q99943	PLCA_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 1	30			P -> S (in dbSNP:rs11964847).		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						TTGGCACTGGGGCTGCAGAAC	0.597													G|||	14	0.00279553	0.0098	0.0014	5008	,	,		19885	0.0		0.0	False		,,,				2504	0.0				p.P30S		Atlas-SNP	.											AGPAT1,NS,carcinoma,+1,1	AGPAT1	22	1	0			c.C88T						PASS	.	G	SER/PRO,SER/PRO	15,3007		0,15,1496	90	69	76		88,88	2	1	6	dbSNP_120	76	0,5418		0,0,2709	yes	missense,missense	AGPAT1	NM_006411.3,NM_032741.4	74,74	0,15,4205	AA,AG,GG		0.0,0.4964,0.1777	benign,benign	30/284,30/284	32139186	15,8425	1511	2709	4220	SO:0001583	missense	10554	exon2			CACTGGGGCTGCA	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.88C>T	6.37:g.32139186G>A	ENSP00000378877:p.Pro30Ser	136	0	0		133	65	0.488722	NM_006411	A2BFI5|Q5BL03	Missense_Mutation	SNP	ENST00000395499.1	37	CCDS4744.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	4.129	0.022157	0.08006	0.004964	0.0	ENSG00000204310	ENST00000395496;ENST00000375107;ENST00000395499;ENST00000375104;ENST00000395497;ENST00000336984	T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92	5.11	1.98	0.26296	.	0.468866	0.25546	N	0.029922	T	0.04092	0.0114	N	0.01705	-0.755	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.30001	-0.9993	10	0.09590	T	0.72	-13.782	2.9511	0.05862	0.1065:0.3516:0.3918:0.1502	rs11964847;rs11964847	30	Q99943	PLCA_HUMAN	S	30	ENSP00000378874:P30S;ENSP00000364248:P30S;ENSP00000378877:P30S;ENSP00000364245:P30S;ENSP00000378875:P30S;ENSP00000337463:P30S	ENSP00000337463:P30S	P	-	1	0	AGPAT1	32247164	0.970000	0.33590	1.000000	0.80357	0.998000	0.95712	0.297000	0.19101	1.132000	0.42129	0.561000	0.74099	CCC	G|0.995;A|0.005	0.005	strong		0.597	AGPAT1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268941.1	NM_006411		A	32139186	G	A	32139186	3	1	22	1	0	0	0	0	1	0	0	0	386	1232	43	2	787	2	AGPAT1	6	32139186	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	42097	32139186	138975881	1433	4334											
NOTCH4	4855	hgsc.bcm.edu	37	chr6	32184785	32184785	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atcaaggcagctggctccaaCgggacatgggtcactcaggc	10	6	13	12	1	3	0	3	0	0	0	4	1	4	1	1	5	2	3	1	5	2	0	rs11963697	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32184785C>G	ENST00000375023.3	-	11	1936	c.1798G>C	c.(1798-1800)Gtt>Ctt	p.V600L	NOTCH4_ENST00000465528.1_5'Flank	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	600	EGF-like 15; 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						CTGGCTCCAACGGGACATGGG	0.567													C|||	14	0.00279553	0.0098	0.0014	5008	,	,		19616	0.0		0.0	False		,,,				2504	0.0				p.V600L		Atlas-SNP	.											.	NOTCH4	201	.	0			c.G1798C						PASS	.	C	LEU/VAL	14,3008		0,14,1497	120	92	102		1798	-7.7	0	6	dbSNP_120	102	0,5418		0,0,2709	yes	missense	NOTCH4	NM_004557.3	32	0,14,4206	GG,GC,CC		0.0,0.4633,0.1659	benign	600/2004	32184785	14,8426	1511	2709	4220	SO:0001583	missense	4855	exon11			CTCCAACGGGACA		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.1798G>C	6.37:g.32184785C>G	ENSP00000364163:p.Val600Leu	178	0	0		210	95	0.452381	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Missense_Mutation	SNP	ENST00000375023.3	37	CCDS34420.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	5.110	0.205944	0.09704	0.004633	0.0	ENSG00000204301	ENST00000375023	D	0.92299	-3.01	4.07	-7.74	0.01241	EGF-like calcium-binding, conserved site (1);EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	1.351570	0.05567	N	0.570461	T	0.75324	0.3834	L	0.29908	0.895	0.09310	N	1	B;B	0.21606	0.058;0.006	B;B	0.31191	0.125;0.003	T	0.72168	-0.4372	10	0.72032	D	0.01	.	7.0248	0.24934	0.0:0.3431:0.3629:0.294	rs11963697;rs11963697	600;600	Q6P3V5;Q99466	.;NOTC4_HUMAN	L	600	ENSP00000364163:V600L	ENSP00000364163:V600L	V	-	1	0	NOTCH4	32292763	0.000000	0.05858	0.001000	0.08648	0.070000	0.16714	-2.805000	0.00758	-1.167000	0.02779	-0.251000	0.11542	GTT	C|0.989;G|0.011;T|0.000	0.011	strong		0.567	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			G	32184785	C	G	32184785	3	3	22	1	0	0	0	0	1	0	0	0	10560	536	19	4	4293	4	NOTCH4	6	32184785	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	45599	32184785	138930282	1434	4335											
BTNL2	56244	hgsc.bcm.edu	37	chr6	32370859	32370859	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggatgcgatgctcagacaCggccagcagcttctctcccc	7	9	10	15	2	2	1	1	0	1	1	4	3	3	2	3	2	4	3	3	2	0	2	rs9461742	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32370859C>T	ENST00000374993.1	-	3	561	c.562G>A	c.(562-564)Gtg>Atg	p.V188M	BTNL2_ENST00000374995.3_Splice_Site_p.V148I|BTNL2_ENST00000454136.3_Missense_Mutation_p.V188M|BTNL2_ENST00000540315.1_Intron|BTNL2_ENST00000414363.1_Intron|BTNL2_ENST00000429232.2_Intron|BTNL2_ENST00000544175.1_Intron	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	188	Ig-like V-type 2.		V -> M (in dbSNP:rs9461742).			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						TGCTCAGACACGGCCAGCAGC	0.587													C|||	29	0.00579073	0.0182	0.0058	5008	,	,		19224	0.0		0.0	False		,,,				2504	0.001				p.V188M		Atlas-SNP	.											.	BTNL2	50	.	0			c.G562A						PASS	.	C	MET/VAL	39,2983		0,39,1472	85	79	81		562	-8.9	0	6	dbSNP_119	81	4,5412		0,4,2704	no	missense	BTNL2	NM_019602.1	21	0,43,4176	TT,TC,CC		0.0739,1.2905,0.5096	probably-damaging	188/456	32370859	43,8395	1511	2708	4219	SO:0001583	missense	56244	exon3			CAGACACGGCCAG	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.562G>A	6.37:g.32370859C>T	ENSP00000364132:p.Val188Met	168	0	0		194	92	0.474227	NM_019602	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Missense_Mutation	SNP	ENST00000374993.1	37		14|14	0.00641025641025641|0.00641025641025641	12|12	0.024390243902439025|0.024390243902439025	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	C|C	8.531|8.531	0.871030|0.871030	0.17322|0.17322	0.012905|0.012905	7.39E-4|7.39E-4	ENSG00000204290|ENSG00000204290	ENST00000374995|ENST00000468270;ENST00000374993	T|T	0.02177|0.75704	4.41|-0.96	4.44|4.44	-8.89|-8.89	0.00785|0.00785	.|CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	2.023030|2.023030	0.02292|0.02292	N|N	0.070382|0.070382	T|T	0.43787|0.43787	0.1263|0.1263	L|L	0.50333|0.50333	1.59|1.59	0.09310|0.09310	N|N	1|1	.|P	.|0.50156	.|0.932	.|P	.|0.45232	.|0.474	T|T	0.61926|0.61926	-0.6962|-0.6962	8|10	0.27785|0.35671	T|T	0.31|0.21	.|.	3.5087|3.5087	0.07700|0.07700	0.2462:0.1048:0.4451:0.2038|0.2462:0.1048:0.4451:0.2038	rs9461742;rs9461742|rs9461742;rs9461742	.|188	.|Q9UIR0	.|BTNL2_HUMAN	I|M	148|188	ENSP00000364134:V148I|ENSP00000364132:V188M	ENSP00000364134:V148I|ENSP00000364132:V188M	V|V	-|-	1|1	0|0	BTNL2|BTNL2	32478837|32478837	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.015000|0.015000	0.08874|0.08874	-8.769000|-8.769000	0.00017|0.00017	-2.865000|-2.865000	0.00325|0.00325	-0.172000|-0.172000	0.13284|0.13284	GTT|GTG	C|0.992;T|0.008	0.008	strong		0.587	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602		T	32370859	C	T	32370859	3	4	22	1	0	0	0	0	1	0	0	0	1567	536	19	1	821	1	BTNL2	6	32370859	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	186074	32370859	138744208	1435	4336											
HLA-DRB1	3123	hgsc.bcm.edu	37	chr6	32548534	32548534	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcctcacctttctgattcCtgaagtagatgaacagcccg	9	11	8	13	1	2	4	1	3	1	1	4	4	4	4	4	0	2	2	4	0	3	3	rs71547382		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32548534C>T	ENST00000360004.5	-	4	857	c.752G>A	c.(751-753)aGg>aAg	p.R251K		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	251					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)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						TTTCTGATTCCTGAAGTAGAT	0.537										Multiple Myeloma(14;0.17)																											p.R251K		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.G752A						PASS	.																																			SO:0001583	missense	3123	exon4			TGATTCCTGAAGT	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.752G>A	6.37:g.32548534C>T	ENSP00000353099:p.Arg251Lys	191	0	0		439	28	0.0637813	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	12.57	1.976489	0.34848	.	.	ENSG00000196126	ENST00000360004	T	0.00635	6.06	3.98	1.66	0.24008	.	0.334220	0.32578	N	0.005907	T	0.00241	0.0007	L	0.33710	1.025	0.28819	N	0.897785	B;B;B	0.18166	0.026;0.026;0.0	B;B;B	0.17979	0.02;0.02;0.001	T	0.44757	-0.9307	10	0.38643	T	0.18	.	6.6584	0.23000	0.0:0.6946:0.0:0.3054	.	251;251;251	P04229;Q29974;P01911	2B11_HUMAN;2B1G_HUMAN;2B1F_HUMAN	K	251	ENSP00000353099:R251K	ENSP00000353099:R251K	R	-	2	0	HLA-DRB1	32656512	0.000000	0.05858	0.929000	0.37066	0.845000	0.48019	-0.186000	0.09670	0.802000	0.34089	0.453000	0.30009	AGG	C|1.000;|0.000	.	weak		0.537	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124		T	32548534	C	T	32548534	3	4	22	1	0	0	0	0	1	0	0	0	7217	681	24	2	60	2	HLA-DRB1	6	32548534	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	177675	32548534	138566533	1436	4337											
HLA-DMA	3108	hgsc.bcm.edu	37	chr6	32917126	32917126	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacacccaggccaaaggccaCgccacacagcacattctcca	13	3	6	19	1	1	0	0	0	1	0	2	0	1	0	5	2	1	1	5	2	1	1	rs9469319	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32917126C>T	ENST00000374843.4	-	4	788	c.703G>A	c.(703-705)Gtg>Atg	p.V235M	HLA-DMA_ENST00000464392.1_5'UTR|HLA-DMA_ENST00000395305.3_Missense_Mutation_p.V140M|XXbac-BPG181M17.5_ENST00000429234.1_Intron|HLA-DMA_ENST00000395303.3_Missense_Mutation_p.V201M	NM_006120.3	NP_006111.2	P28067	DMA_HUMAN	major histocompatibility complex, class II, DM alpha	235			V -> M (in dbSNP:rs9469319).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|chaperone mediated protein folding requiring cofactor (GO:0051085)|immunoglobulin mediated immune response (GO:0016064)|inner ear development (GO:0048839)|peptide antigen assembly with MHC class II protein complex (GO:0002503)|positive regulation of immune response (GO:0050778)|positive regulation of T cell differentiation (GO:0045582)|positive thymic T cell selection (GO:0045059)|protein transport (GO:0015031)	cell surface (GO:0009986)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)	MHC class II protein complex binding (GO:0023026)			kidney(1)|large_intestine(2)|lung(8)	11						CCAAAGGCCACGCCACACAGC	0.592													C|||	11	0.00219649	0.0076	0.0014	5008	,	,		19854	0.0		0.0	False		,,,				2504	0.0				p.V235M		Atlas-SNP	.											.	HLA-DMA	20	.	0			c.G703A						PASS	.	C	MET/VAL	21,4385	28.1+/-56.4	0,21,2182	91	85	87		703	-2.8	0	6	dbSNP_119	87	1,8599	1.2+/-3.3	0,1,4299	yes	missense	HLA-DMA	NM_006120.3	21	0,22,6481	TT,TC,CC		0.0116,0.4766,0.1692	possibly-damaging	235/262	32917126	22,12984	2203	4300	6503	SO:0001583	missense	3108	exon4			AGGCCACGCCACA		CCDS4761.1	6p21.3	2013-01-11			ENSG00000204257	ENSG00000204257		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4934	protein-coding gene	gene with protein product		142855				1922385	Standard	NM_006120		Approved	D6S222E, RING6	uc003ocm.2	P28067	OTTHUMG00000031173	ENST00000374843.4:c.703G>A	6.37:g.32917126C>T	ENSP00000363976:p.Val235Met	87	0	0		100	50	0.5	NM_006120	Q29639|Q29640	Missense_Mutation	SNP	ENST00000374843.4	37	CCDS4761.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	11.77	1.739075	0.30774	0.004766	1.16E-4	ENSG00000204257	ENST00000395305;ENST00000395303;ENST00000374843;ENST00000456800	T;T;T;T	0.01821	5.12;4.62;5.63;5.55	5.0	-2.84	0.05751	.	0.963671	0.08623	N	0.918117	T	0.00724	0.0024	M	0.71581	2.175	0.09310	N	1	P	0.52316	0.952	B	0.37780	0.258	T	0.41840	-0.9486	10	0.87932	D	0	.	1.2422	0.01965	0.127:0.2689:0.2786:0.3255	rs9469319;rs9469319	235	Q31604	.	M	140;201;235;265	ENSP00000378716:V140M;ENSP00000378714:V201M;ENSP00000363976:V235M;ENSP00000409668:V265M	ENSP00000363976:V235M	V	-	1	0	HLA-DMA	33025104	0.000000	0.05858	0.006000	0.13384	0.598000	0.36846	-1.977000	0.01495	-0.428000	0.07339	0.551000	0.68910	GTG	C|0.997;T|0.003	0.003	strong		0.592	HLA-DMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076325.2	NM_006120		T	32917126	C	T	32917126	3	4	22	1	0	0	0	0	1	0	0	0	7207	536	19	1	90	1	HLA-DMA	6	32917126	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	368592	32917126	138197941	1437	4338											
HLA-DOA	3111	hgsc.bcm.edu	37	chr6	32975896	32975896	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtcaaagcgggcaaagtcAccaaactcaggcagacgcca	14	3	12	12	2	3	1	3	0	0	1	3	1	3	1	2	3	2	2	2	3	3	0	rs364950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32975896A>G	ENST00000229829.5	-	2	300	c.225T>C	c.(223-225)ggT>ggC	p.G75G	HLA-DOA_ENST00000450833.2_Silent_p.G45G|HLA-DOA_ENST00000495532.1_5'UTR	NM_002119.3	NP_002110.1	P06340	DOA_HUMAN	major histocompatibility complex, class II, DO alpha	75	Alpha-1.				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)|regulation of T cell differentiation (GO:0045580)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)	MHC class II protein complex binding (GO:0023026)|MHC class II receptor activity (GO:0032395)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(1)	9						GGGCAAAGTCACCAAACTCAG	0.612													G|||	401	0.0800719	0.233	0.0749	5008	,	,		16847	0.0		0.0408	False		,,,				2504	0.0				p.G75G		Atlas-SNP	.											.	HLA-DOA	22	.	0			c.T225C						PASS	.	G		616,2406		51,514,946	58	52	54		225	1.6	0.1	6	dbSNP_80	54	141,5277		1,139,2569	no	coding-synonymous	HLA-DOA	NM_002119.3		52,653,3515	GG,GA,AA		2.6024,20.3839,8.9692		75/251	32975896	757,7683	1511	2709	4220	SO:0001819	synonymous_variant	3111	exon2			AAAGTCACCAAAC	M31525	CCDS4763.1	6p21.3	2013-01-11		2001-10-05	ENSG00000204252	ENSG00000204252		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4936	protein-coding gene	gene with protein product		142930		HLA-DZA, HLA-DNA		2370084	Standard	XM_005272804		Approved	HLA-D0-alpha	uc003ocr.3	P06340	OTTHUMG00000031211	ENST00000229829.5:c.225T>C	6.37:g.32975896A>G		78	0	0		88	39	0.443182	NM_002119	Q58HU0|Q58HU1|Q5STC7|Q9TQC6|Q9TQC7|Q9TQC8|Q9TQC9|Q9TQD0|Q9TQD1|Q9TQD2|Q9TQD3	Silent	SNP	ENST00000229829.5	37	CCDS4763.1																																																																																			A|0.906;G|0.094	0.094	strong		0.612	HLA-DOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076426.2	NM_002119		G	32975896	A	G	32975896	2	3	22	1	0	0	0	0	0	0	0	1	7209	146	6	3		3	HLA-DOA	6	32975896	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	58770	32975896	138139171	1438	4339											
HLA-DOA	3111	hgsc.bcm.edu	37	chr6	32976013	32976013	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccgtaagactggtagaaggcGggtccgtaggagcccatgtg	9	7	16	9	3	0	2	0	0	0	2	1	3	1	3	3	4	1	3	3	4	4	3	rs78635760|rs41541116|rs538455361	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32976013G>A	ENST00000229829.5	-	2	183	c.108C>T	c.(106-108)ccC>ccT	p.P36P	HLA-DOA_ENST00000450833.2_Silent_p.P6P|HLA-DOA_ENST00000495532.1_5'Flank	NM_002119.3	NP_002110.1	P06340	DOA_HUMAN	major histocompatibility complex, class II, DO alpha	36	Alpha-1.				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)|regulation of T cell differentiation (GO:0045580)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)	MHC class II protein complex binding (GO:0023026)|MHC class II receptor activity (GO:0032395)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(1)	9						GGTAGAAGGCGGGTCCGTAGG	0.522													G|||	65	0.0129792	0.0454	0.0072	5008	,	,		19086	0.0		0.0	False		,,,				2504	0.0				p.P36P		Atlas-SNP	.											HLA-DOA,colon,carcinoma,0,1	HLA-DOA	22	1	0			c.C108T						PASS	.	G		140,2880		7,126,1377	47	49	48		108	0.4	1	6	dbSNP_131	48	3,5411		0,3,2704	no	coding-synonymous	HLA-DOA	NM_002119.3		7,129,4081	AA,AG,GG		0.0554,4.6358,1.6955		36/251	32976013	143,8291	1510	2707	4217	SO:0001819	synonymous_variant	3111	exon2			GAAGGCGGGTCCG	M31525	CCDS4763.1	6p21.3	2013-01-11		2001-10-05	ENSG00000204252	ENSG00000204252		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4936	protein-coding gene	gene with protein product		142930		HLA-DZA, HLA-DNA		2370084	Standard	XM_005272804		Approved	HLA-D0-alpha	uc003ocr.3	P06340	OTTHUMG00000031211	ENST00000229829.5:c.108C>T	6.37:g.32976013G>A		66	0	0		89	60	0.674157	NM_002119	Q58HU0|Q58HU1|Q5STC7|Q9TQC6|Q9TQC7|Q9TQC8|Q9TQC9|Q9TQD0|Q9TQD1|Q9TQD2|Q9TQD3	Silent	SNP	ENST00000229829.5	37	CCDS4763.1	24	0.01098901098901099	21	0.042682926829268296	3	0.008287292817679558	0	0.0	0	0.0	G	11.11	1.541489	0.27563	0.046358	5.54E-4	ENSG00000204252	ENST00000432150	.	.	.	4.4	0.402	0.16344	.	0.265318	0.38720	N	0.001589	T	0.45577	0.1349	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48875	-0.8996	6	0.87932	D	0	.	5.2858	0.15700	0.0:0.0992:0.3715:0.5293	.	.	.	.	L	36	.	ENSP00000412819:P36L	P	-	2	0	HLA-DOA	33083991	0.970000	0.33590	0.999000	0.59377	0.977000	0.68977	-0.448000	0.06820	-0.008000	0.14320	-0.271000	0.10264	CCG	G|0.984;A|0.016	0.016	strong		0.522	HLA-DOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076426.2	NM_002119		A	32976013	G	A	32976013	2	1	22	1	0	0	0	0	0	0	0	1	7209	1103	39	1		1	HLA-DOA	6	32976013	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	117	32976013	138139054	1439	4340											
RXRB	6257	hgsc.bcm.edu	37	chr6	33162507	33162507	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atctccatgaggaaggtgtcGatgggggtgtcaccaatgag	10	9	15	7	1	2	2	1	2	1	0	4	4	2	3	2	4	0	0	2	4	2	0			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33162507G>A	ENST00000374680.3	-	10	1765	c.1554C>T	c.(1552-1554)atC>atT	p.I518I	RXRB_ENST00000544186.1_Silent_p.I332I|COL11A2_ENST00000374712.1_5'Flank|COL11A2_ENST00000374713.1_5'Flank|COL11A2_ENST00000361917.1_5'Flank|COL11A2_ENST00000374708.4_5'Flank|COL11A2_ENST00000395197.1_5'Flank|COL11A2_ENST00000341947.2_5'Flank|COL11A2_ENST00000395194.1_5'Flank|COL11A2_ENST00000357486.1_5'Flank|COL11A2_ENST00000374714.1_5'Flank|RXRB_ENST00000374685.4_Silent_p.I522I	NM_001270401.1|NM_021976.4	NP_001257330.1|NP_068811.1	P28702	RXRB_HUMAN	retinoid X receptor, beta	518	Ligand-binding. {ECO:0000250}.				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)	GGAAGGTGTCGATGGGGGTGT	0.547																																					p.I522I		Atlas-SNP	.											RXRB,colon,carcinoma,0,1	RXRB	34	1	0			c.C1566T						PASS	.						97	88	91					6																	33162507		1511	2709	4220	SO:0001819	synonymous_variant	6257	exon10			GGTGTCGATGGGG	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.1554C>T	6.37:g.33162507G>A		60	0	0		90	42	0.466667	NM_001270401	P28703|Q59G65|Q5JP92|Q5STQ1	Silent	SNP	ENST00000374680.3	37	CCDS4768.1																																																																																			.	.	none		0.547	RXRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076642.2	NM_021976		A	33162507	G	A	33162507	2	1	22	1	0	0	0	0	0	0	0	1	13779	1048	37	1		1	RXRB	6	33162507	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	186494	33162507	137952560	1440	4341											
ZBTB22	9278	hgsc.bcm.edu	37	chr6	33283945	33283945	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	gctttccagatgtggcccctCcactgccaacgacaggggct	7	8	11	15	1	0	1	0	0	0	1	2	2	2	1	5	3	2	2	5	3	1	1	rs35663442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33283945C>G	ENST00000431845.2	-	2	900	c.749G>C	c.(748-750)gGa>gCa	p.G250A	TAPBP_ENST00000475304.1_5'Flank|TAPBP_ENST00000489157.1_5'Flank|TAPBP_ENST00000434618.2_5'Flank|TAPBP_ENST00000426633.2_5'Flank|TAPBP_ENST00000456592.2_5'Flank|ZBTB22_ENST00000418724.1_Missense_Mutation_p.G250A	NM_005453.4	NP_005444.4	O15209	ZBT22_HUMAN	zinc finger and BTB domain containing 22	250			G -> A (in dbSNP:rs35663442).		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						TGTGGCCCCTCCACTGCCAAC	0.627													C|||	54	0.0107827	0.0393	0.0029	5008	,	,		17213	0.0		0.0	False		,,,				2504	0.0				p.G250A		Atlas-SNP	.											.	ZBTB22	48	.	0			c.G749C						PASS	.	C	ALA/GLY,ALA/GLY	144,4262	101.2+/-139.8	5,134,2064	47	46	46		749,749	2.1	0.5	6	dbSNP_126	46	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	ZBTB22	NM_001145338.1,NM_005453.4	60,60	5,138,6360	GG,GC,CC		0.0465,3.2683,1.1379	benign,benign	250/635,250/635	33283945	148,12858	2203	4300	6503	SO:0001583	missense	9278	exon2			GCCCCTCCACTGC	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.749G>C	6.37:g.33283945C>G	ENSP00000407545:p.Gly250Ala	60	0	0		72	25	0.347222	NM_001145338	B0V007|Q5HYV4|Q5STL0|Q5STR7|Q8WV82	Missense_Mutation	SNP	ENST00000431845.2	37	CCDS4775.1	21	0.009615384615384616	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	0	0.0	C	2.540	-0.306538	0.05458	0.032683	4.65E-4	ENSG00000236104	ENST00000418724;ENST00000431845	T;T	0.07800	3.16;3.16	3.99	2.14	0.27477	.	0.253027	0.20824	N	0.085014	T	0.00875	0.0029	N	0.12182	0.205	0.28027	N	0.934308	B	0.06786	0.001	B	0.04013	0.001	T	0.46721	-0.9171	10	0.06757	T	0.87	.	4.0063	0.09603	0.0:0.5646:0.2105:0.2249	rs35663442	250	O15209	ZBT22_HUMAN	A	250	ENSP00000404403:G250A;ENSP00000407545:G250A	ENSP00000404403:G250A	G	-	2	0	ZBTB22	33391923	0.000000	0.05858	0.470000	0.27216	0.392000	0.30506	0.632000	0.24583	0.325000	0.23359	0.297000	0.19635	GGA	C|0.989;G|0.011	0.011	strong		0.627	ZBTB22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076183.2			G	33283945	C	G	33283945	3	3	22	1	0	0	0	0	1	0	0	0	17545	855	30	4	1159	4	ZBTB22	6	33283945	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	121438	33283945	137831122	1441	4342											
SYNGAP1	8831	hgsc.bcm.edu	37	chr6	33393583	33393583	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cacctcccctagatacacccCctactgatccgggaccggag	9	6	8	18	2	0	2	0	1	0	1	2	4	2	4	7	2	2	0	7	2	3	3	rs73402305	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33393583C>T	ENST00000418600.2	+	3	299	c.198C>T	c.(196-198)ccC>ccT	p.P66P	SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000293748.5_Silent_p.P66P	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	66					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						AGATACACCCCCTACTGATCC	0.697													c|||	259	0.0517173	0.1921	0.0058	5008	,	,		9030	0.0		0.001	False		,,,				2504	0.0				p.P66P		Atlas-SNP	.											SYNGAP1_ENST00000293748,NS,carcinoma,+2,2	SYNGAP1	202	2	0			c.C198T						PASS	.	C		653,3753	259.8+/-263.3	41,571,1591	47	40	43		198	0.8	1	6	dbSNP_131	43	8,8592	5.0+/-18.6	0,8,4292	no	coding-synonymous	SYNGAP1	NM_006772.2		41,579,5883	TT,TC,CC		0.093,14.8207,5.0823		66/1344	33393583	661,12345	2203	4300	6503	SO:0001819	synonymous_variant	8831	exon3			ACACCCCCTACTG	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.198C>T	6.37:g.33393583C>T		183	0	0		168	77	0.458333	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Silent	SNP	ENST00000418600.2	37	CCDS34434.2																																																																																			C|0.937;T|0.063	0.063	strong		0.697	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407		T	33393583	C	T	33393583	2	4	22	1	0	0	0	0	0	0	0	1	15462	610	22	2		2	SYNGAP1	6	33393583	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	109638	33393583	137721484	1442	4343											
ZBTB9	221504	hgsc.bcm.edu	37	chr6	33423698	33423698	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgcaccacttgagcttcctgCccctcctgcactgcccccca	5	9	6	21	0	0	1	0	1	0	0	2	1	2	1	8	0	5	3	8	0	0	2	rs9469425	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33423698C>G	ENST00000395064.2	+	2	1089	c.821C>G	c.(820-822)gCc>gGc	p.A274G		NM_152735.3	NP_689948.1	Q96C00	ZBTB9_HUMAN	zinc finger and BTB domain containing 9	274	Pro-rich.		A -> G (in dbSNP:rs9469425).		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						GAGCTTCCTGCCCCTCCTGCA	0.567													C|||	344	0.0686901	0.2534	0.013	5008	,	,		19073	0.0		0.0	False		,,,				2504	0.0				p.A274G		Atlas-SNP	.											.	ZBTB9	23	.	0			c.C821G						PASS	.	C	GLY/ALA	876,3530	338.6+/-305.4	75,726,1402	58	61	60		821	4.4	0.1	6	dbSNP_119	60	8,8592	6.4+/-24.3	0,8,4292	yes	missense	ZBTB9	NM_152735.3	60	75,734,5694	GG,GC,CC		0.093,19.882,6.7969	possibly-damaging	274/474	33423698	884,12122	2203	4300	6503	SO:0001583	missense	221504	exon2			TTCCTGCCCCTCC	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.821C>G	6.37:g.33423698C>G	ENSP00000378503:p.Ala274Gly	82	0	0		58	35	0.603448	NM_152735	A2AB19	Missense_Mutation	SNP	ENST00000395064.2	37	CCDS4780.1	139	0.06364468864468864	136	0.2764227642276423	3	0.008287292817679558	0	0.0	0	0.0	C	6.353	0.433225	0.12045	0.19882	9.3E-4	ENSG00000213588	ENST00000395064	T	0.07114	3.22	5.28	4.39	0.52855	.	3.470690	0.02755	U	0.117890	T	0.03095	0.0091	L	0.29908	0.895	0.54753	P	1.6000000000016E-5	B	0.24186	0.099	B	0.22601	0.04	T	0.30937	-0.9961	9	0.33940	T	0.23	.	11.5797	0.50883	0.0:0.8205:0.1795:0.0	rs9469425	274	Q96C00	ZBTB9_HUMAN	G	274	ENSP00000378503:A274G	ENSP00000378503:A274G	A	+	2	0	ZBTB9	33531676	0.051000	0.20477	0.114000	0.21550	0.988000	0.76386	1.337000	0.33862	1.419000	0.47118	0.655000	0.94253	GCC	C|0.921;G|0.079	0.079	strong		0.567	ZBTB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276533.1	NM_152735		G	33423698	C	G	33423698	3	3	22	1	0	0	0	0	1	0	0	0	17573	739	26	4	823	4	ZBTB9	6	33423698	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	30115	33423698	137691369	1443	4344											
ZNF76	7629	hgsc.bcm.edu	37	chr6	35263009	35263009	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaccctggagacaacagtgtCggagagtggctgctgagtcc	9	7	15	10	1	0	3	0	1	0	2	2	6	1	3	2	3	2	2	2	3	1	0	rs73745177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:35263009C>T	ENST00000373953.3	+	14	1963	c.1697C>T	c.(1696-1698)tCg>tTg	p.S566L	ZNF76_ENST00000339411.5_Missense_Mutation_p.S511L|ZNF76_ENST00000440666.2_Missense_Mutation_p.S540L|DEF6_ENST00000542066.1_5'Flank|DEF6_ENST00000316637.5_5'Flank	NM_003427.3	NP_003418.2	P36508	ZNF76_HUMAN	zinc finger protein 76	566					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						ACAACAGTGTCGGAGAGTGGC	0.627													C|||	27	0.00539137	0.0151	0.0086	5008	,	,		19071	0.0		0.0	False		,,,				2504	0.001				p.S566L	Esophageal Squamous(52;92 1039 20612 23956 34676)	Atlas-SNP	.											.	ZNF76	37	.	0			c.C1697T						PASS	.	C	LEU/SER	71,4333	62.9+/-100.1	0,71,2131	58	45	49		1697	5.9	0.3	6	dbSNP_130	49	4,8596	2.2+/-6.3	0,4,4296	yes	missense	ZNF76	NM_003427.3	145	0,75,6427	TT,TC,CC		0.0465,1.6122,0.5767	benign	566/571	35263009	75,12929	2202	4300	6502	SO:0001583	missense	7629	exon14			CAGTGTCGGAGAG	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.1697C>T	6.37:g.35263009C>T	ENSP00000363064:p.Ser566Leu	52	0	0		40	18	0.45	NM_003427	Q9BQB2	Missense_Mutation	SNP	ENST00000373953.3	37	CCDS4801.1	9	0.004120879120879121	6	0.012195121951219513	3	0.008287292817679558	0	0.0	0	0.0	C	16.72	3.202287	0.58234	0.016122	4.65E-4	ENSG00000065029	ENST00000373953;ENST00000440666;ENST00000339411	T;T;T	0.10005	2.95;2.95;2.92	5.91	5.91	0.95273	.	0.306088	0.18150	N	0.150126	T	0.04137	0.0115	N	0.22421	0.69	0.09310	N	1	B;B	0.23806	0.046;0.091	B;B	0.12837	0.008;0.007	T	0.24225	-1.0166	10	0.72032	D	0.01	.	17.0178	0.86424	0.0:1.0:0.0:0.0	.	511;566	P36508-2;P36508	.;ZNF76_HUMAN	L	566;540;511	ENSP00000363064:S566L;ENSP00000392243:S540L;ENSP00000344097:S511L	ENSP00000344097:S511L	S	+	2	0	ZNF76	35370987	0.090000	0.21635	0.330000	0.25442	0.994000	0.84299	2.471000	0.45127	2.793000	0.96121	0.655000	0.94253	TCG	C|0.994;T|0.006	0.006	strong		0.627	ZNF76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040279.2	NM_003427		T	35263009	C	T	35263009	3	4	22	1	0	0	0	0	1	0	0	0	18150	893	31	1	1747	1	ZNF76	6	35263009	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1839311	35263009	135852058	1444	4345											
FANCE	2178	hgsc.bcm.edu	37	chr6	35424008	35424010	+	In_Frame_Del	DEL	GGA	GGA	-																															cactggaatccctggcagatGgaggaagtgcatctcctatt																								rs45451605|rs397897540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:35424008_35424010delGGA	ENST00000229769.2	+	2	918_920	c.733_735delGGA	c.(733-735)ggadel	p.G246del		NM_021922.2	NP_068741.1	Q9HB96	FANCE_HUMAN	Fanconi anemia, complementation group E	246	Interaction with FANCC.				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						CCTGGCAGATGGAGGAAGTGCAT	0.507			"N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia					17	0.00339457	0.0113	0.0014	5008	,	,		22003	0.0		0.0	False		,,,				2504	0.001				p.244_245del		Pindel,Atlas-Indel	.	yes	Rec		Fanconi anaemia E	6	6p21-p22	2178	"Fanconi anemia, complementation group E"		L	.	FANCE	45	.	0			c.732_734del						PASS	.			70,4194		2,66,2064						-4.1	0		dbSNP_127	120	5,8249		0,5,4122	no	coding	FANCE	NM_021922.2		2,71,6186	A1A1,A1R,RR		0.0606,1.6417,0.5991				75,12443				SO:0001651	inframe_deletion	2178	exon2	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	.	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.733_735delGGA	6.37:g.35424011_35424013delGGA	ENSP00000229769:p.Gly246del	138	0	.		142	42	0.296	NM_021922	A8K907|Q4ZGH2	In_Frame_Del	DEL	ENST00000229769.2	37	CCDS4805.1																																																																																			GGA|0.979;-|0.021	0.021	strong		0.507	FANCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040282.1			-	35424010	GGA	-	35424008	7	5	22	1	0	1	0	1	0	0	0	0	5674	1349	47	0	739	0	FANCE	6	35424008	In_Frame_Del	DEL	GGA	TCGA-G8-6324-01A-11D-2210-10	160999	35424008	135691059	1445	4346											
C6orf81	221481	hgsc.bcm.edu	37	chr6	35705059	35705059	+	Intron	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgcatcgcccgtgagtgtccGggccctggggagagggctct	4	8	17	12	3	1	2	0	1	1	1	3	3	2	2	3	4	1	2	3	4	0	0	rs56183341	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:35705059G>A	ENST00000373866.3	+	1	185				ARMC12_ENST00000373869.3_Intron|RP3-510O8.4_ENST00000452048.1_RNA|ARMC12_ENST00000288065.2_Silent_p.P58P			Q5T9G4	ARM12_HUMAN	armadillo repeat containing 12							nucleus (GO:0005634)											GTGAGTGTCCGGGCCCTGGGG	0.612											OREG0017379	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	43	0.00858626	0.0295	0.0014	5008	,	,		19230	0.0		0.0	False		,,,				2504	0.0031				p.P58P		Atlas-SNP	.											.	.	.	.	0			c.G174A						PASS	.	G		106,4300	81.9+/-120.4	1,104,2098	68	64	65		174	-0.4	0	6	dbSNP_129	65	0,8600		0,0,4300	no	coding-synonymous	C6orf81	NM_145028.3		1,104,6398	AA,AG,GG		0.0,2.4058,0.815		58/368	35705059	106,12900	2203	4300	6503	SO:0001627	intron_variant	221481	exon1			GTGTCCGGGCCCT	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.163+11G>A	6.37:g.35705059G>A		116	0	0	857	116	56	0.482759	NM_145028	Q8NEB2|Q96LL8	Silent	SNP	ENST00000373866.3	37																																																																																				G|0.992;A|0.008	0.008	strong		0.612	ARMC12-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040311.2	NM_145028		A	35705059	G	A	35705059	1	1	22	0	1	0	0	0	0	0	0	0	2374	1103	39	1		1	C6orf81	6	35705059	Intron	SNP	G	TCGA-G8-6324-01A-11D-2210-10	281051	35705059	135410008	1446	4347											
C6orf81	221481	hgsc.bcm.edu	37	chr6	35716613	35716613	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcccggccctcctcctgccAgcccagtcgttcctacttta	5	10	7	19	2	0	0	0	0	0	0	4	0	3	0	7	1	4	1	7	1	2	4	rs73729781	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:35716613A>G	ENST00000373866.3	+	6	1011	c.989A>G	c.(988-990)cAg>cGg	p.Q330R	ARMC12_ENST00000373869.3_Missense_Mutation_p.Q320R|ARMC12_ENST00000288065.2_Missense_Mutation_p.Q357R			Q5T9G4	ARM12_HUMAN	armadillo repeat containing 12	330						nucleus (GO:0005634)											TCCTCCTGCCAGCCCAGTCGT	0.488													A|||	26	0.00519169	0.0189	0.0014	5008	,	,		17917	0.0		0.0	False		,,,				2504	0.0				p.Q357R		Atlas-SNP	.											.	.	.	.	0			c.A1070G						PASS	.	A	ARG/GLN	63,4343	57.4+/-93.9	0,63,2140	44	47	46		1070	-9.5	0	6	dbSNP_130	46	0,8600		0,0,4300	yes	missense	C6orf81	NM_145028.3	43	0,63,6440	GG,GA,AA		0.0,1.4299,0.4844	benign	357/368	35716613	63,12943	2203	4300	6503	SO:0001583	missense	221481	exon6			CCTGCCAGCCCAG	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.989A>G	6.37:g.35716613A>G	ENSP00000362973:p.Gln330Arg	69	0	0		75	43	0.573333	NM_145028	Q8NEB2|Q96LL8	Missense_Mutation	SNP	ENST00000373866.3	37		10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	A	1.845	-0.466582	0.04476	0.014299	0.0	ENSG00000157343	ENST00000373869;ENST00000288065;ENST00000373866	T;T	0.39997	1.05;1.07	4.77	-9.54	0.00572	.	1.744990	0.03118	N	0.163415	T	0.02267	0.0070	N	0.01874	-0.695	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.07102	-1.0790	10	0.02654	T	1	.	1.28	0.02039	0.1771:0.3484:0.2459:0.2287	.	320;357	Q5T9G4-3;Q5T9G4-2	.;.	R	320;357;330	ENSP00000288065:Q357R;ENSP00000362973:Q330R	ENSP00000288065:Q357R	Q	+	2	0	C6orf81	35824591	0.000000	0.05858	0.001000	0.08648	0.269000	0.26545	-0.566000	0.05922	-1.836000	0.01190	-0.400000	0.06385	CAG	A|0.995;G|0.005	0.005	strong		0.488	ARMC12-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040311.2	NM_145028		G	35716613	A	G	35716613	3	3	22	1	0	0	0	0	1	0	0	0	2374	188	7	3	1092	3	C6orf81	6	35716613	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	11554	35716613	135398454	1447	4348											
SLC26A8	116369	hgsc.bcm.edu	37	chr6	35987425	35987425	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcttaacatcatatgcgaaTgagtttcgcctggacttaga	11	12	9	9	3	1	2	1	1	0	1	2	4	1	3	1	1	2	2	1	1	4	4	rs61743377	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:35987425T>C	ENST00000490799.1	-	2	413	c.60A>G	c.(58-60)tcA>tcG	p.S20S	SLC26A8_ENST00000394602.2_Silent_p.S20S|SLC26A8_ENST00000355574.2_Silent_p.S20S	NM_052961.3	NP_443193.1			solute carrier family 26 (anion exchanger), member 8											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(16)|ovary(3)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	46						CATATGCGAATGAGTTTCGCC	0.448													T|||	74	0.0147764	0.0552	0.0014	5008	,	,		18599	0.0		0.0	False		,,,				2504	0.0				p.S20S		Atlas-SNP	.											.	SLC26A8	95	.	0			c.A60G						PASS	.	T	,,	234,4172	136.9+/-172.8	5,224,1974	182	140	154		60,60,60	-2.6	0	6	dbSNP_129	154	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC26A8	NM_001193476.1,NM_052961.3,NM_138718.2	,,	5,225,6273	CC,CT,TT		0.0116,5.3109,1.8069	,,	20/971,20/971,20/866	35987425	235,12771	2203	4300	6503	SO:0001819	synonymous_variant	116369	exon2			TGCGAATGAGTTT	AF331522	CCDS4813.1, CCDS4814.1	6p21	2013-07-18	2013-07-18		ENSG00000112053	ENSG00000112053		"Solute carriers"	14468	protein-coding gene	gene with protein product		608480	"solute carrier family 26, member 8"			11834742, 11829495	Standard	NM_001193476		Approved		uc003olm.3	Q96RN1	OTTHUMG00000014586	ENST00000490799.1:c.60A>G	6.37:g.35987425T>C		227	0	0		205	89	0.434146	NM_052961		Silent	SNP	ENST00000490799.1	37	CCDS4813.1																																																																																			T|0.986;C|0.014	0.014	strong		0.448	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040325.2			C	35987425	T	C	35987425	2	2	22	1	0	0	0	0	0	0	0	1	14538	1451	51	3		3	SLC26A8	6	35987425	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	270812	35987425	135127642	1448	4349											
MAPK13	5603	hgsc.bcm.edu	37	chr6	36104468	36104468	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggcgcgacatgcagacgcCgagatgactggctacgtggt	8	7	15	11	5	0	3	0	1	0	2	0	5	0	3	1	3	2	2	1	3	1	1	rs115013068	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36104468C>G	ENST00000211287.4	+	7	793	c.531C>G	c.(529-531)gcC>gcG	p.A177A	MAPK13_ENST00000373766.5_Silent_p.A177A|MAPK13_ENST00000373759.1_Silent_p.A99A|MAPK13_ENST00000373761.6_Silent_p.A167A	NM_002754.4	NP_002745.1	O15264	MK13_HUMAN	mitogen-activated protein kinase 13	177	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-6 production (GO:0032755)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(2)|prostate(2)|skin(1)	12						ATGCAGACGCCGAGATGACTG	0.577													C|||	54	0.0107827	0.034	0.013	5008	,	,		20219	0.0		0.0	False		,,,				2504	0.0				p.A177A		Atlas-SNP	.											.	MAPK13	65	.	0			c.C531G						PASS	.	C		134,4272	94.4+/-133.1	3,128,2072	29	29	29		531	-10.2	0	6	dbSNP_132	29	0,8600		0,0,4300	no	coding-synonymous	MAPK13	NM_002754.3		3,128,6372	GG,GC,CC		0.0,3.0413,1.0303		177/366	36104468	134,12872	2203	4300	6503	SO:0001819	synonymous_variant	5603	exon7			AGACGCCGAGATG	Y10488	CCDS4818.1	6p21	2011-06-09			ENSG00000156711	ENSG00000156711	2.7.11.1	"Mitogen-activated protein kinase cascade / Kinases"	6875	protein-coding gene	gene with protein product		602899		PRKM13		9295308, 9218798	Standard	NM_002754		Approved	SAPK4, p38delta	uc003ols.4	O15264	OTTHUMG00000014587	ENST00000211287.4:c.531C>G	6.37:g.36104468C>G		169	0	0		187	98	0.524064	NM_002754	O14739|O15124|Q5U4A5|Q6FI46|Q9UNU0	Silent	SNP	ENST00000211287.4	37	CCDS4818.1																																																																																			C|0.990;G|0.010	0.010	strong		0.577	MAPK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040328.1			G	36104468	C	G	36104468	2	3	22	1	0	0	0	0	0	0	0	1	9284	639	23	4		4	MAPK13	6	36104468	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	117043	36104468	135010599	1449	4350											
BRPF3	27154	hgsc.bcm.edu	37	chr6	36177597	36177597	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggctgccatggagctggagCtgatgccattcaatgttctg	8	11	13	9	0	2	1	1	1	1	0	2	3	2	3	2	3	4	4	2	3	1	2	rs73730485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36177597C>T	ENST00000357641.6	+	5	2024	c.1771C>T	c.(1771-1773)Ctg>Ttg	p.L591L	BRPF3_ENST00000534694.1_Silent_p.L591L|BRPF3_ENST00000534400.1_Silent_p.L591L|BRPF3_ENST00000543502.1_Silent_p.L591L|BRPF3_ENST00000339717.7_Silent_p.L591L|BRPF3_ENST00000443324.2_Silent_p.L591L	NM_015695.2	NP_056510.2	Q9ULD4	BRPF3_HUMAN	bromodomain and PHD finger containing, 3	591					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						GGAGCTGGAGCTGATGCCATT	0.507													C|||	53	0.0105831	0.0393	0.0014	5008	,	,		20080	0.0		0.0	False		,,,				2504	0.0				p.L591L		Atlas-SNP	.											.	BRPF3	93	.	0			c.C1771T						PASS	.	C		186,4220	118.8+/-156.5	4,178,2021	96	84	88		1771	3.2	1	6	dbSNP_130	88	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	BRPF3	NM_015695.2		4,179,6320	TT,TC,CC		0.0116,4.2215,1.4378		591/1206	36177597	187,12819	2203	4300	6503	SO:0001819	synonymous_variant	27154	exon5			CTGGAGCTGATGC	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.1771C>T	6.37:g.36177597C>T		88	0	0		114	53	0.464912	NM_015695	A6ND56|A6NJE2|B7ZLN5|E7EX85|Q17RB6|Q5R3K8	Silent	SNP	ENST00000357641.6	37	CCDS34437.1																																																																																			C|0.987;T|0.013	0.013	strong		0.507	BRPF3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040335.3	NM_015695		T	36177597	C	T	36177597	2	4	22	1	0	0	0	0	0	0	0	1	1523	796	28	2		2	BRPF3	6	36177597	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	73129	36177597	134937470	1450	4351											
PNPLA1	285848	hgsc.bcm.edu	37	chr6	36269946	36269946	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacagccactggcctcttcaActccactttctctaagtggc	8	11	6	16	0	3	0	1	0	2	0	5	0	4	0	3	2	2	0	3	2	2	3	rs145856102	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36269946A>G	ENST00000394571.2	+	6	1084	c.1084A>G	c.(1084-1086)Act>Gct	p.T362A	PNPLA1_ENST00000312917.5_Missense_Mutation_p.T276A|PNPLA1_ENST00000388715.3_Missense_Mutation_p.T267A	NM_001145717.1	NP_001139189.2	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	362	Pro-rich.				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						GGCCTCTTCAACTCCACTTTC	0.562											OREG0017382	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T362A		Atlas-SNP	.											.	PNPLA1	92	.	0			c.A1084G						PASS	.	A	ALA/THR,ALA/THR,ALA/THR	18,4388	25.3+/-52.1	0,18,2185	130	125	127		826,1084,799	0.2	0	6	dbSNP_134	127	0,8600		0,0,4300	yes	missense,missense,missense	PNPLA1	NM_001145716.1,NM_001145717.1,NM_173676.2	58,58,58	0,18,6485	GG,GA,AA		0.0,0.4085,0.1384	benign,benign,benign	276/447,362/533,267/438	36269946	18,12988	2203	4300	6503	SO:0001583	missense	285848	exon6			TCTTCAACTCCAC		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.1084A>G	6.37:g.36269946A>G	ENSP00000378072:p.Thr362Ala	132	0	0	861	133	63	0.473684	NM_001145717	A3RMU3|J3JS20|Q2A6N1|Q3SY95|Q3SY96|Q5R3L2	Missense_Mutation	SNP	ENST00000394571.2	37	CCDS54997.1	.	.	.	.	.	.	.	.	.	.	A	0.635	-0.815820	0.02776	0.004085	0.0	ENSG00000180316	ENST00000388715;ENST00000312917;ENST00000457797;ENST00000394571	T;T;T;T	0.27256	1.91;1.91;1.68;1.68	5.4	0.208	0.15221	.	2.180320	0.02285	N	0.069728	T	0.03136	0.0092	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	0.25641	-1.0126	10	0.18710	T	0.47	0.729	2.0907	0.03656	0.1506:0.4124:0.2712:0.1658	.	362;276	Q8N8W4;Q8N8W4-3	PLPL1_HUMAN;.	A	267;276;363;362	ENSP00000373367:T267A;ENSP00000321116:T276A;ENSP00000391868:T363A;ENSP00000378072:T362A	ENSP00000321116:T276A	T	+	1	0	PNPLA1	36377924	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.120000	0.15647	0.002000	0.14630	-1.513000	0.00942	ACT	A|0.998;G|0.002	0.002	strong		0.562	PNPLA1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_173676		G	36269946	A	G	36269946	3	3	22	1	0	0	0	0	1	0	0	0	12173	43	2	3	1133	3	PNPLA1	6	36269946	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	92349	36269946	134845121	1451	4352											
ETV7	51513	hgsc.bcm.edu	37	chr6	36339176	36339176	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccccctgggtcctgcagcCgagctctgcacagtgacata	8	7	11	15	1	1	1	0	1	1	0	2	3	2	1	4	1	4	3	4	1	1	1	rs34306145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36339176C>T	ENST00000340181.4	-	5	836	c.595G>A	c.(595-597)Ggc>Agc	p.G199S	ETV7_ENST00000373737.4_Intron|ETV7_ENST00000538992.1_Missense_Mutation_p.G48S|ETV7_ENST00000373738.1_Missense_Mutation_p.G144S|ETV7_ENST00000339796.5_Missense_Mutation_p.G199S	NM_001207037.1|NM_001207040.1|NM_016135.3	NP_001193966.1|NP_001193969.1|NP_057219.1	Q9Y603	ETV7_HUMAN	ets variant 7	199			G -> S (in dbSNP:rs34306145).		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						GTCCTGCAGCCGAGCTCTGCA	0.637													C|||	60	0.0119808	0.0446	0.0	5008	,	,		18231	0.0		0.0	False		,,,				2504	0.001				p.G199S		Atlas-SNP	.											.	ETV7	31	.	0			c.G595A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY,,SER/GLY,SER/GLY,SER/GLY,SER/GLY	155,4251	98.5+/-137.1	4,147,2052	48	42	44		595,430,418,,430,352,142,595	-4.3	0	6	dbSNP_126	44	0,8600		0,0,4300	yes	missense,missense,missense,intron,missense,missense,missense,missense	ETV7	NM_001207035.1,NM_001207036.1,NM_001207037.1,NM_001207038.1,NM_001207039.1,NM_001207040.1,NM_001207041.1,NM_016135.3	56,56,56,,56,56,56,56	4,147,6352	TT,TC,CC		0.0,3.5179,1.1918	benign,benign,benign,,benign,benign,benign,benign	199/318,144/287,140/283,,144/263,118/261,48/191,199/342	36339176	155,12851	2203	4300	6503	SO:0001583	missense	51513	exon5			TGCAGCCGAGCTC	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.595G>A	6.37:g.36339176C>T	ENSP00000341843:p.Gly199Ser	58	0	0		49	20	0.408163	NM_001207035	B3KVC2|B4DVB6|B4E1G4|Q5R3L3|Q5R3L4|Q9NZ65|Q9NZ66|Q9NZ68|Q9NZR8|Q9UNJ7|Q9Y5K4|Q9Y604	Missense_Mutation	SNP	ENST00000340181.4	37	CCDS4819.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	C	6.332	0.429441	0.11987	0.035179	0.0	ENSG00000010030	ENST00000339796;ENST00000340181;ENST00000373738;ENST00000538992	T;T;T;T	0.13307	2.6;2.6;2.6;2.6	3.49	-4.27	0.03744	.	1.429630	0.04667	N	0.409962	T	0.03739	0.0106	N	0.17082	0.46	0.09310	N	1	B;D;B;P;B	0.69078	0.101;0.997;0.012;0.708;0.229	B;P;B;B;B	0.52481	0.056;0.7;0.017;0.087;0.014	T	0.25152	-1.0140	10	0.09084	T	0.74	.	11.3935	0.49827	0.0:0.3082:0.0:0.6918	rs34306145	140;144;199;144;199	Q9Y603-2;Q9Y603-4;Q9Y603;Q9Y603-6;Q9Y603-5	.;.;ETV7_HUMAN;.;.	S	199;199;144;48	ENSP00000342260:G199S;ENSP00000341843:G199S;ENSP00000362843:G144S;ENSP00000440592:G48S	ENSP00000342260:G199S	G	-	1	0	ETV7	36447154	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.280000	0.08468	-1.429000	0.01987	-2.010000	0.00438	GGC	C|0.987;T|0.013	0.013	strong		0.637	ETV7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040341.1	NM_016135		T	36339176	C	T	36339176	3	4	22	1	0	0	0	0	1	0	0	0	5286	652	23	1	446	1	ETV7	6	36339176	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	69230	36339176	134775891	1452	4353											
ETV7	51513	hgsc.bcm.edu	37	chr6	36341251	36341251	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttccggggggactggagagtGctgggtgggcgtcttcagcc	4	9	19	9	2	2	1	1	0	1	1	3	3	3	2	2	6	2	1	2	6	0	2	rs9470262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36341251G>A	ENST00000340181.4	-	4	653	c.412C>T	c.(412-414)Cac>Tac	p.H138Y	ETV7_ENST00000373737.4_Missense_Mutation_p.H138Y|ETV7_ENST00000538992.1_5'UTR|ETV7_ENST00000373738.1_Missense_Mutation_p.H83Y|ETV7_ENST00000339796.5_Missense_Mutation_p.H138Y	NM_001207037.1|NM_001207040.1|NM_016135.3	NP_001193966.1|NP_001193969.1|NP_057219.1	Q9Y603	ETV7_HUMAN	ets variant 7	138			H -> Y (in dbSNP:rs9470262).		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						ACTGGAGAGTGCTGGGTGGGC	0.602													G|||	59	0.0117812	0.0446	0.0	5008	,	,		11025	0.0		0.0	False		,,,				2504	0.0				p.H138Y		Atlas-SNP	.											.	ETV7	31	.	0			c.C412T						PASS	.	G	TYR/HIS,TYR/HIS,TYR/HIS,TYR/HIS,TYR/HIS,TYR/HIS,,TYR/HIS	156,4250		3,150,2050	27	25	25		412,247,235,412,247,169,,412	2.4	0	6	dbSNP_119	25	0,8598		0,0,4299	yes	missense,missense,missense,missense,missense,missense,utr-5,missense	ETV7	NM_001207035.1,NM_001207036.1,NM_001207037.1,NM_001207038.1,NM_001207039.1,NM_001207040.1,NM_001207041.1,NM_016135.3	83,83,83,83,83,83,,83	3,150,6349	AA,AG,GG		0.0,3.5406,1.1996	benign,benign,benign,benign,benign,benign,,benign	138/318,83/287,79/283,138/265,83/263,57/261,,138/342	36341251	156,12848	2203	4299	6502	SO:0001583	missense	51513	exon4			GAGAGTGCTGGGT	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.412C>T	6.37:g.36341251G>A	ENSP00000341843:p.His138Tyr	130	0	0		142	63	0.443662	NM_001207035	B3KVC2|B4DVB6|B4E1G4|Q5R3L3|Q5R3L4|Q9NZ65|Q9NZ66|Q9NZ68|Q9NZR8|Q9UNJ7|Q9Y5K4|Q9Y604	Missense_Mutation	SNP	ENST00000340181.4	37	CCDS4819.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	G	9.065	0.995354	0.19043	0.035406	0.0	ENSG00000010030	ENST00000339796;ENST00000340181;ENST00000373737;ENST00000373738	T;T;T;T	0.13538	2.96;2.96;2.58;2.68	3.37	2.43	0.29744	.	7.870880	0.00616	U	0.000429	T	0.02727	0.0082	N	0.24115	0.695	0.34145	D	0.66687	B;B;B;B;B;B	0.33135	0.399;0.167;0.255;0.091;0.263;0.34	B;B;B;B;B;B	0.31686	0.134;0.065;0.041;0.105;0.044;0.134	T	0.34825	-0.9813	10	0.02654	T	1	.	9.2275	0.37416	0.0:0.0:0.503:0.497	rs9470262;rs52802542;rs9470262	79;138;83;138;83;138	Q9Y603-2;Q9Y603-7;Q9Y603-4;Q9Y603;Q9Y603-6;Q9Y603-5	.;.;.;ETV7_HUMAN;.;.	Y	138;138;138;83	ENSP00000342260:H138Y;ENSP00000341843:H138Y;ENSP00000362842:H138Y;ENSP00000362843:H83Y	ENSP00000342260:H138Y	H	-	1	0	ETV7	36449229	0.000000	0.05858	0.007000	0.13788	0.022000	0.10575	0.108000	0.15396	1.446000	0.47643	0.456000	0.33151	CAC	G|0.988;A|0.012	0.012	strong		0.602	ETV7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040341.1	NM_016135		A	36341251	G	A	36341251	3	1	22	1	0	0	0	0	1	0	0	0	5286	1319	46	2	633	2	ETV7	6	36341251	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2075	36341251	134773816	1453	4354											
CDKN1A	1026	hgsc.bcm.edu	37	chr6	36652135	36652135	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacggggccccggcgaggccGggatgagttgggaggaggca	7	3	21	10	4	0	1	0	1	0	0	0	5	0	4	3	8	0	2	3	8	0	1	rs566071526		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36652135G>A	ENST00000405375.1	+	2	492	c.257G>A	c.(256-258)cGg>cAg	p.R86Q	CDKN1A_ENST00000244741.5_Missense_Mutation_p.R86Q|CDKN1A_ENST00000478800.1_3'UTR|CDKN1A_ENST00000448526.2_Missense_Mutation_p.R120Q|CDKN1A_ENST00000373711.2_Missense_Mutation_p.R86Q	NM_001220778.1	NP_001207707.1	P38936	CDN1A_HUMAN	cyclin-dependent kinase inhibitor 1A (p21, Cip1)	86					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						CGGCGAGGCCGGGATGAGTTG	0.652													G|||	1	0.000199681	0.0	0.0	5008	,	,		18244	0.001		0.0	False		,,,				2504	0.0				p.R86Q		Atlas-SNP	.											CDKN1A,NS,carcinoma,+1,1	CDKN1A	27	1	0			c.G257A						PASS	.						25	25	25					6																	36652135		2203	4300	6503	SO:0001583	missense	1026	exon2			GAGGCCGGGATGA	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.257G>A	6.37:g.36652135G>A	ENSP00000384849:p.Arg86Gln	41	0	0		54	23	0.425926	NM_001220778	Q14010|Q6FI05|Q9BUT4	Missense_Mutation	SNP	ENST00000405375.1	37	CCDS4824.1	.	.	.	.	.	.	.	.	.	.	G	4.718	0.133545	0.09032	.	.	ENSG00000124762	ENST00000448526;ENST00000244741;ENST00000405375;ENST00000373711	T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05	5.16	0.313	0.15842	.	1.118360	0.06876	N	0.801660	T	0.25121	0.0610	L	0.34521	1.04	0.09310	N	1	B;B;B	0.24882	0.113;0.064;0.037	B;B;B	0.16289	0.015;0.006;0.006	T	0.21759	-1.0236	10	0.51188	T	0.08	-1.0186	4.3301	0.11059	0.3607:0.161:0.4783:0.0	.	120;86;86	B4DQP9;P38936;Q96LE1	.;CDN1A_HUMAN;.	Q	120;86;86;86	ENSP00000409259:R120Q;ENSP00000244741:R86Q;ENSP00000384849:R86Q;ENSP00000362815:R86Q	ENSP00000244741:R86Q	R	+	2	0	CDKN1A	36760113	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.096000	0.11059	-0.131000	0.11578	0.511000	0.50034	CGG	.	.	none		0.652	CDKN1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040354.1	NM_078467		A	36652135	G	A	36652135	3	1	22	1	0	0	0	0	1	0	0	0	3160	1116	39	1	259	1	CDKN1A	6	36652135	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	310884	36652135	134462932	1454	4355											
PI16	221476	hgsc.bcm.edu	37	chr6	36930795	36930795	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgggcgactgaagcatcagActctaggaaaatgggtactc	12	7	12	10	2	2	2	1	1	1	1	3	4	2	3	1	3	2	2	1	3	5	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36930795A>T	ENST00000373674.3	+	5	1005	c.677A>T	c.(676-678)gAc>gTc	p.D226V	PI16_ENST00000491324.1_3'UTR	NM_001199159.1|NM_153370.2	NP_001186088.1|NP_699201.2	Q6UXB8	PI16_HUMAN	peptidase inhibitor 16	226					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						GAAGCATCAGACTCTAGGAAA	0.547																																					p.D226V		Atlas-SNP	.											.	PI16	50	.	0			c.A677T						PASS	.						87	81	83					6																	36930795		2203	4300	6503	SO:0001583	missense	221476	exon6			CATCAGACTCTAG		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.677A>T	6.37:g.36930795A>T	ENSP00000362778:p.Asp226Val	93	0	0		130	54	0.415385	NM_001199159	Q6ZVG9|Q8IYL8|Q8NBK0|Q8TCB8	Missense_Mutation	SNP	ENST00000373674.3	37	CCDS34440.1	.	.	.	.	.	.	.	.	.	.	A	4.768	0.142776	0.09083	.	.	ENSG00000164530	ENST00000536757;ENST00000373674;ENST00000539035	T	0.06849	3.25	4.56	-5.47	0.02600	.	1.282230	0.05284	N	0.519917	T	0.00936	0.0031	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.001;0.002	T	0.46176	-0.9210	10	0.35671	T	0.21	.	2.847	0.05546	0.4899:0.2078:0.1969:0.1054	.	226;226	Q6UXB8;Q6UXB8-2	PI16_HUMAN;.	V	226;226;78	ENSP00000362778:D226V	ENSP00000362778:D226V	D	+	2	0	PI16	37038773	0.000000	0.05858	0.000000	0.03702	0.103000	0.19146	-1.147000	0.03188	-1.317000	0.02292	-1.155000	0.01812	GAC	.	.	none		0.547	PI16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040380.1	NM_153370		T	36930795	A	T	36930795	3	4	22	1	0	0	0	0	1	0	0	0	11878	275	10	5	695	5	PI16	6	36930795	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	278660	36930795	134184272	1455	4356											
FTSJD2	23070	hgsc.bcm.edu	37	chr6	37426429	37426429	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagctgagcttctgtacttTgctgatgtctgcgcaggccc	6	12	12	11	1	2	2	0	2	2	0	2	3	2	2	1	1	5	5	1	1	2	3	rs35608753	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:37426429T>C	ENST00000373451.4	+	9	983	c.819T>C	c.(817-819)ttT>ttC	p.F273F		NM_015050.2	NP_055865.1	Q8N1G2	CMTR1_HUMAN	cap methyltransferase 1	273	RrmJ-type SAM-dependent 2'-O-MTase. {ECO:0000255|PROSITE-ProRule:PRU00945}.				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)										TTCTGTACTTTGCTGATGTCT	0.527													T|||	46	0.0091853	0.031	0.0072	5008	,	,		19737	0.0		0.0	False		,,,				2504	0.0				p.F273F		Atlas-SNP	.											.	FTSJD2	64	.	0			c.T819C						PASS	.	T		196,4210	122.5+/-159.9	3,190,2010	87	77	80		819	3.5	1	6	dbSNP_126	80	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FTSJD2	NM_015050.2		3,191,6309	CC,CT,TT		0.0116,4.4485,1.5147		273/836	37426429	197,12809	2203	4300	6503	SO:0001819	synonymous_variant	23070	exon9			GTACTTTGCTGAT	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.819T>C	6.37:g.37426429T>C		99	0	0		156	67	0.429487	NM_015050	A8K949|Q14670|Q96FJ9	Silent	SNP	ENST00000373451.4	37	CCDS4835.1																																																																																			T|0.986;C|0.014	0.014	strong		0.527	CMTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040408.1	NM_015050		C	37426429	T	C	37426429	2	2	22	1	0	0	0	0	0	0	0	1	6099	1809	63	3		3	FTSJD2	6	37426429	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	495634	37426429	133688638	1456	4357											
KCNK17	89822	hgsc.bcm.edu	37	chr6	39267315	39267315	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggagtgggactctggctccCggtcaggtccctgtctccag	4	9	15	13	1	3	0	1	0	2	0	6	2	5	2	3	5	0	1	3	5	0	0	rs2758910	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:39267315C>T	ENST00000373231.4	-	5	1119	c.887G>A	c.(886-888)cGg>cAg	p.R296Q	KCNK17_ENST00000453413.2_3'UTR	NM_031460.3	NP_113648.2	Q96T54	KCNKH_HUMAN	potassium channel, subfamily K, member 17	296			R -> Q (in dbSNP:rs2758910).		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						CTCTGGCTCCCGGTCAGGTCC	0.587													c|||	39	0.00778754	0.0287	0.0014	5008	,	,		20167	0.0		0.0	False		,,,				2504	0.0				p.R296Q		Atlas-SNP	.											KCNK17,NS,carcinoma,-1,1	KCNK17	61	1	0			c.G887A						PASS	.	T	,GLN/ARG	142,4264	101.2+/-139.8	1,140,2062	90	79	83		,887	-2.5	0	6	dbSNP_100	83	0,8600		0,0,4300	yes	utr-3,missense	KCNK17	NM_001135111.1,NM_031460.3	,43	1,140,6362	TT,TC,CC		0.0,3.2229,1.0918	,benign	,296/333	39267315	142,12864	2203	4300	6503	SO:0001583	missense	89822	exon5			GGCTCCCGGTCAG	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.887G>A	6.37:g.39267315C>T	ENSP00000362328:p.Arg296Gln	151	0	0		165	80	0.484848	NM_031460	E9PB46|Q5TCF4|Q8TAW4|Q9BXD1|Q9H592	Missense_Mutation	SNP	ENST00000373231.4	37	CCDS4842.1	13	0.005952380952380952	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	0	0.0	c	10.09	1.254922	0.22965	0.032229	0.0	ENSG00000124780	ENST00000373231	T	0.15603	2.41	4.25	-2.45	0.06481	.	.	.	.	.	T	0.01765	0.0056	N	0.14661	0.345	0.09310	N	1	B	0.12013	0.005	B	0.06405	0.002	T	0.47262	-0.9131	9	0.11182	T	0.66	.	5.3132	0.15841	0.0:0.4054:0.1426:0.452	rs2758910;rs52820365;rs2758910	296	Q96T54	KCNKH_HUMAN	Q	296	ENSP00000362328:R296Q	ENSP00000362328:R296Q	R	-	2	0	KCNK17	39375293	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.463000	0.06696	-0.926000	0.03770	-0.119000	0.15052	CGG	C|0.989;T|0.011	0.011	strong		0.587	KCNK17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040453.2	NM_031460		T	39267315	C	T	39267315	3	4	22	1	0	0	0	0	1	0	0	0	8073	652	23	1	115	1	KCNK17	6	39267315	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1840886	39267315	131847752	1457	4358											
KIF6	221458	hgsc.bcm.edu	37	chr6	39688551	39688551	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggtaagatgatttccaagcTaggtattaatttttcatctt	11	18	7	5	0	2	2	1	1	1	1	3	2	3	2	1	2	1	3	1	2	5	8	rs114269617	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:39688551T>C	ENST00000287152.7	-	2	197	c.103A>G	c.(103-105)Agc>Ggc	p.S35G	KIF6_ENST00000538893.1_Missense_Mutation_p.S35G|KIF6_ENST00000373216.3_Missense_Mutation_p.S35G|KIF6_ENST00000373215.3_Missense_Mutation_p.S35G	NM_145027.4	NP_659464.3	Q6ZMV9	KIF6_HUMAN	kinesin family member 6	35	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						ATTTCCAAGCTAGGTATTAAT	0.318													T|||	48	0.00958466	0.0325	0.0014	5008	,	,		18134	0.0		0.004	False		,,,				2504	0.0				p.S35G		Atlas-SNP	.											.	KIF6	233	.	0			c.A103G						PASS	.	T	GLY/SER	184,4222	117.5+/-155.4	2,180,2021	97	101	100		103	0.2	0.4	6	dbSNP_132	100	3,8597	1.2+/-3.3	0,3,4297	yes	missense	KIF6	NM_145027.4	56	2,183,6318	CC,CT,TT		0.0349,4.1761,1.4378	possibly-damaging	35/815	39688551	187,12819	2203	4300	6503	SO:0001583	missense	221458	exon2			CCAAGCTAGGTAT	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.103A>G	6.37:g.39688551T>C	ENSP00000287152:p.Ser35Gly	68	0	0		59	31	0.525424	NM_145027	Q2MDE3|Q2MDE4|Q5T8J6|Q6ZWE3|Q86T87|Q8WTV4	Missense_Mutation	SNP	ENST00000287152.7	37	CCDS4844.1	27	0.012362637362637362	23	0.046747967479674794	0	0.0	0	0.0	4	0.005277044854881266	T	11.68	1.711929	0.30322	0.041761	3.49E-4	ENSG00000164627	ENST00000287152;ENST00000373216;ENST00000373215;ENST00000538893	T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68	6.06	0.196	0.15159	Kinesin, motor domain (3);	.	.	.	.	T	0.43590	0.1254	L	0.47190	1.495	0.09310	N	1	B;B;B	0.25390	0.021;0.005;0.125	B;B;B	0.34452	0.018;0.008;0.183	T	0.46992	-0.9151	9	0.42905	T	0.14	.	4.8731	0.13642	0.3772:0.0982:0.0:0.5246	.	35;35;35	E7EUN7;F6VGH2;Q6ZMV9	.;.;KIF6_HUMAN	G	35	ENSP00000287152:S35G;ENSP00000362312:S35G;ENSP00000362311:S35G;ENSP00000441435:S35G	ENSP00000287152:S35G	S	-	1	0	KIF6	39796529	0.318000	0.24598	0.387000	0.26183	0.989000	0.77384	0.951000	0.29135	0.492000	0.27815	0.533000	0.62120	AGC	T|0.984;C|0.016	0.016	strong		0.318	KIF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040455.2	NM_145027		C	39688551	T	C	39688551	3	2	22	1	0	0	0	0	1	0	0	0	8317	1522	53	3	2429	3	KIF6	6	39688551	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	421236	39688551	131426516	1458	4359											
DAAM2	23500	hgsc.bcm.edu	37	chr6	39847153	39847153	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcatgggcctgcccctccCtcaggacccctaccccagca	6	5	9	21	1	1	0	1	0	0	0	2	1	2	1	8	3	3	2	8	3	1	1	rs150676991	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:39847153C>A	ENST00000398904.2	+	14	1927	c.1745C>A	c.(1744-1746)cCt>cAt	p.P582H	DAAM2_ENST00000274867.4_Missense_Mutation_p.P582H|RP11-61I13.3_ENST00000607675.1_RNA|DAAM2_ENST00000538976.1_Missense_Mutation_p.P582H			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	582	FH1.|Pro-rich.				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)					CTGCCCCTCCCTCAGGACCCC	0.652													C|||	2	0.000399361	0.0015	0.0	5008	,	,		12540	0.0		0.0	False		,,,				2504	0.0				p.P582H		Atlas-SNP	.											.	DAAM2	101	.	0			c.C1745A						PASS	.	C	HIS/PRO,HIS/PRO	8,3826		0,8,1909	44	46	45		1745,1745	5.2	0.9	6	dbSNP_134	45	14,8208		0,14,4097	yes	missense,missense	DAAM2	NM_001201427.1,NM_015345.3	77,77	0,22,6006	AA,AC,CC		0.1703,0.2087,0.1825	benign,benign	582/1069,582/1068	39847153	22,12034	1917	4111	6028	SO:0001583	missense	23500	exon14			CCCTCCCTCAGGA	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.1745C>A	6.37:g.39847153C>A	ENSP00000381876:p.Pro582His	216	0	0		250	110	0.44	NM_015345	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	37	CCDS56426.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	16.94	3.261074	0.59431	0.002087	0.001703	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976	D;D;D	0.84146	-1.81;-1.81;-1.79	5.15	5.15	0.70609	Actin-binding FH2 (1);	0.215647	0.39407	N	0.001370	T	0.65302	0.2678	N	0.08118	0	0.80722	D	1	P;B	0.40875	0.731;0.38	B;B	0.42555	0.391;0.159	T	0.73799	-0.3869	10	0.46703	T	0.11	.	13.0249	0.58808	0.0:0.9199:0.0:0.0801	.	582;582	G5EA45;Q86T65	.;DAAM2_HUMAN	H	582	ENSP00000274867:P582H;ENSP00000381876:P582H;ENSP00000437808:P582H	ENSP00000274867:P582H	P	+	2	0	DAAM2	39955131	0.989000	0.36119	0.881000	0.34555	0.838000	0.47535	3.359000	0.52292	2.383000	0.81215	0.650000	0.86243	CCT	C|0.998;A|0.002	0.002	strong		0.652	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1			A	39847153	C	A	39847153	3	1	22	1	0	0	0	0	1	0	0	0	4218	681	24	4	1795	4	DAAM2	6	39847153	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	158602	39847153	131267914	1459	4360											
LRFN2	57497	hgsc.bcm.edu	37	chr6	40400823	40400823	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acggcaaacgccatgccaaaCgctagcaggccaccaagcag	14	2	10	15	3	0	0	0	0	0	0	0	0	0	0	4	2	5	4	4	2	4	1	rs61731039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:40400823C>T	ENST00000338305.6	-	2	572	c.30G>A	c.(28-30)gcG>gcA	p.A10A		NM_020737.1	NP_065788.1	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III domain containing 2	10						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)					CCATGCCAAACGCTAGCAGGC	0.597													c|||	248	0.0495208	0.1785	0.0144	5008	,	,		18737	0.0		0.002	False		,,,				2504	0.0				p.A10A		Atlas-SNP	.											LRFN2,NS,carcinoma,-1,1	LRFN2	133	1	0			c.G30A						PASS	.	T		702,3704	266.8+/-267.5	63,576,1564	36	38	37		30	-1.2	1	6	dbSNP_129	37	13,8587	9.1+/-34.3	0,13,4287	no	coding-synonymous	LRFN2	NM_020737.1		63,589,5851	TT,TC,CC		0.1512,15.9328,5.4975		10/790	40400823	715,12291	2203	4300	6503	SO:0001819	synonymous_variant	57497	exon2			GCCAAACGCTAGC	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.30G>A	6.37:g.40400823C>T		69	0	0		69	35	0.507246	NM_020737	A5PKU3|Q5SYP9	Silent	SNP	ENST00000338305.6	37	CCDS34443.1																																																																																			C|0.950;T|0.050	0.050	strong		0.597	LRFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040488.1	XM_166372		T	40400823	C	T	40400823	2	4	22	1	0	0	0	0	0	0	0	1	8947	523	19	1		1	LRFN2	6	40400823	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	553670	40400823	130714244	1460	4361											
TREML1	340205	hgsc.bcm.edu	37	chr6	41117586	41117586	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggtgagtcaagcctaatgTgtggtacatccaaaggcaat	12	10	12	7	0	1	1	1	1	0	0	2	1	2	1	2	3	2	2	2	3	5	2	rs34254490	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:41117586T>G	ENST00000426005.2	-	6	735	c.692A>C	c.(691-693)cAc>cCc	p.H231P	TREML1_ENST00000373127.4_3'UTR|TREML1_ENST00000437044.2_Missense_Mutation_p.H120P	NM_178174.2	NP_835468.1	Q86YW5	TRML1_HUMAN	triggering receptor expressed on myeloid cells-like 1	231	Pro-rich.		H -> P (in dbSNP:rs34254490).		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)					AAGCCTAATGTGTGGTACATC	0.507													T|||	138	0.0275559	0.1029	0.0029	5008	,	,		19751	0.0		0.0	False		,,,				2504	0.0				p.H231P		Atlas-SNP	.											.	TREML1	20	.	0			c.A692C						PASS	.	T	PRO/HIS	347,4059	175.9+/-205.1	18,311,1874	174	154	161		692	4.5	0	6	dbSNP_126	161	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TREML1	NM_178174.2	77	18,312,6173	GG,GT,TT		0.0116,7.8756,2.6757	benign	231/312	41117586	348,12658	2203	4300	6503	SO:0001583	missense	340205	exon6			CTAATGTGTGGTA	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.692A>C	6.37:g.41117586T>G	ENSP00000402855:p.His231Pro	138	0	0		148	77	0.52027	NM_178174	Q496B3|Q8IWY1|Q8IWY2	Missense_Mutation	SNP	ENST00000426005.2	37	CCDS4851.1	49	0.022435897435897436	49	0.09959349593495935	0	0.0	0	0.0	0	0.0	T	12.67	2.007412	0.35415	0.078756	1.16E-4	ENSG00000161911	ENST00000373127;ENST00000437044	T	0.46819	0.86	5.71	4.52	0.55395	.	0.532842	0.17347	N	0.177556	T	0.16385	0.0394	N	0.19112	0.55	0.09310	N	1	B;B	0.22683	0.073;0.072	B;B	0.25405	0.06;0.027	T	0.18053	-1.0349	10	0.66056	D	0.02	.	9.718	0.40286	0.0:0.0:0.1745:0.8255	rs34254490;rs60023904	120;231	Q86YW5-3;Q86YW5	.;TRML1_HUMAN	P	231;120	ENSP00000400405:H120P	ENSP00000362219:H231P	H	-	2	0	TREML1	41225564	0.001000	0.12720	0.001000	0.08648	0.184000	0.23303	0.517000	0.22832	0.954000	0.37851	0.533000	0.62120	CAC	T|0.975;G|0.025	0.025	strong		0.507	TREML1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043538.2	NM_178174		G	41117586	T	G	41117586	3	3	22	1	0	0	0	0	1	0	0	0	16487	1696	59	5	245	5	TREML1	6	41117586	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	716763	41117586	129997481	1461	4362											
TREM1	54210	hgsc.bcm.edu	37	chr6	41243926	41243926	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	aagaccaggctcttactcagGaatccaccagccaggagaat	14	6	9	12	0	2	2	1	0	1	2	3	4	3	3	4	3	2	1	4	3	4	1	rs2234245	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:41243926G>C	ENST00000244709.4	-	4	705	c.642C>G	c.(640-642)ttC>ttG	p.F214L	TREM1_ENST00000334475.6_Missense_Mutation_p.S150C|TREM1_ENST00000589614.1_Intron	NM_018643.3	NP_061113.1	Q9NP99	TREM1_HUMAN	triggering receptor expressed on myeloid cells 1	214			F -> L (in dbSNP:rs2234245).		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)					TCTTACTCAGGAATCCACCAG	0.547													G|||	140	0.0279553	0.1006	0.0101	5008	,	,		19431	0.0		0.0	False		,,,				2504	0.0				p.F214L		Atlas-SNP	.											.	TREM1	38	.	0			c.C642G						PASS	.	G	CYS/SER,LEU/PHE	299,4107	162.5+/-194.5	11,277,1915	174	143	154		449,642	1	0.1	6	dbSNP_98	154	7,8593	5.0+/-18.6	0,7,4293	yes	missense,missense	TREM1	NM_001242590.1,NM_018643.3	112,22	11,284,6208	CC,CG,GG		0.0814,6.7862,2.3528	possibly-damaging,possibly-damaging	150/151,214/235	41243926	306,12700	2203	4300	6503	SO:0001583	missense	54210	exon4			ACTCAGGAATCCA	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.642C>G	6.37:g.41243926G>C	ENSP00000244709:p.Phe214Leu	90	0	0		102	48	0.470588	NM_018643	B4DWG2|K7EJW1|Q53FL8|Q5T2C9|Q86YU1	Missense_Mutation	SNP	ENST00000244709.4	37	CCDS4854.1	46|46	0.021062271062271064|0.021062271062271064	41|41	0.08333333333333333|0.08333333333333333	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	0|0	0.0|0.0	G|G	18.63|18.63	3.665281|3.665281	0.67700|0.67700	0.067862|0.067862	8.14E-4|8.14E-4	ENSG00000124731|ENSG00000124731	ENST00000244709|ENST00000334475	T|T	0.04194|0.14144	3.68|2.53	4.86|4.86	1.0|1.0	0.19881|0.19881	.|.	0.883988|.	0.09394|.	N|.	0.808190|.	T|T	0.04543|0.04543	0.0124|0.0124	.|.	.|.	.|.	0.20196|0.20196	N|N	0.999924|0.999924	B|P	0.02656|0.41546	0.0|0.754	B|B	0.01281|0.41299	0.0|0.353	T|T	0.30650|0.30650	-0.9971|-0.9971	9|8	0.02654|0.87932	T|D	1|0	-4.1779|-4.1779	4.7266|4.7266	0.12943|0.12943	0.2677:0.1574:0.5749:0.0|0.2677:0.1574:0.5749:0.0	rs2234245|rs2234245	214|150	Q9NP99|Q9NP99-2	TREM1_HUMAN|.	L|C	214|150	ENSP00000244709:F214L|ENSP00000334284:S150C	ENSP00000244709:F214L|ENSP00000334284:S150C	F|S	-|-	3|2	2|0	TREM1|TREM1	41351904|41351904	0.593000|0.593000	0.26840|0.26840	0.056000|0.056000	0.19401|0.19401	0.730000|0.730000	0.41778|0.41778	0.268000|0.268000	0.18571|0.18571	0.059000|0.059000	0.16252|0.16252	0.655000|0.655000	0.94253|0.94253	TTC|TCC	G|0.979;C|0.021	0.021	strong		0.547	TREM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040505.2	NM_018643		C	41243926	G	C	41243926	3	2	22	1	0	0	0	0	1	0	0	0	16485	1165	41	4	66	4	TREM1	6	41243926	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	126340	41243926	129871141	1462	4363											
NCR2	9436	hgsc.bcm.edu	37	chr6	41318578	41318578	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaaggactaagataagcgaTgatgatgatgaacacacttt	16	9	10	6	1	0	5	0	4	0	1	0	7	0	6	0	1	2	1	0	1	4	3	rs115509322	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:41318578T>C	ENST00000373089.5	+	5	895	c.807T>C	c.(805-807)gaT>gaC	p.D269D	NCR2_ENST00000373086.3_3'UTR|NCR2_ENST00000373083.4_3'UTR	NM_004828.3	NP_004819.2	O95944	NCTR2_HUMAN	natural cytotoxicity triggering receptor 2	269	Poly-Asp.				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)					agataagcgatgatgatgatg	0.398													T|||	43	0.00858626	0.0272	0.0058	5008	,	,		22654	0.0		0.003	False		,,,				2504	0.0				p.D269D		Atlas-SNP	.											.	NCR2	44	.	0			c.T807C						PASS	.	T	,,	118,4288	89.7+/-128.4	1,116,2086	95	89	91		,,807	-2.5	0	6	dbSNP_132	91	17,8583	12.6+/-44.7	0,17,4283	no	utr-3,utr-3,coding-synonymous	NCR2	NM_001199509.1,NM_001199510.1,NM_004828.3	,,	1,133,6369	CC,CT,TT		0.1977,2.6782,1.038	,,	,,269/277	41318578	135,12871	2203	4300	6503	SO:0001819	synonymous_variant	9436	exon5			AAGCGATGATGAT	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.807T>C	6.37:g.41318578T>C		45	0	0		42	19	0.452381	NM_004828	Q9H562|Q9H563|Q9H564|Q9UMT1|Q9UMT2	Silent	SNP	ENST00000373089.5	37	CCDS4855.1																																																																																			T|0.990;C|0.010	0.010	strong		0.398	NCR2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040511.3			C	41318578	T	C	41318578	2	2	22	1	0	0	0	0	0	0	0	1	10247	1461	51	3		3	NCR2	6	41318578	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	74652	41318578	129796489	1463	4364											
PRICKLE4	29964	hgsc.bcm.edu	37	chr6	41753136	41753136	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agcccgggcaggggaacagcGctgctggcaccagccttgct	7	5	15	14	2	0	0	0	0	0	0	0	1	0	1	3	4	6	5	3	4	1	1	rs35880970	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:41753136G>A	ENST00000394260.1	+	3	320	c.320G>A	c.(319-321)cGc>cAc	p.R107H	PRICKLE4_ENST00000463606.1_3'UTR|PRICKLE4_ENST00000359201.5_Missense_Mutation_p.R147H|TOMM6_ENST00000398881.3_5'Flank|PRICKLE4_ENST00000394263.1_Missense_Mutation_p.R147H|PRICKLE4_ENST00000458694.1_Missense_Mutation_p.R147H|PRICKLE4_ENST00000394259.1_Missense_Mutation_p.R107H|TOMM6_ENST00000398884.3_5'Flank			Q2TBC4	PRIC4_HUMAN	prickle homolog 4 (Drosophila)	107	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.					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)			GGGGAACAGCGCTGCTGGCAC	0.602													G|||	81	0.0161741	0.0537	0.0072	5008	,	,		17211	0.0		0.001	False		,,,				2504	0.0041				p.R147H		Atlas-SNP	.											.	PRICKLE4	29	.	0			c.G440A						PASS	.	G	HIS/ARG	225,4181	134.1+/-170.4	6,213,1984	51	50	50		440	2.9	0.6	6	dbSNP_126	50	17,8583	11.2+/-40.8	0,17,4283	yes	missense	PRICKLE4	NM_013397.5	29	6,230,6267	AA,AG,GG		0.1977,5.1067,1.8607	benign	147/385	41753136	242,12764	2203	4300	6503	SO:0001583	missense	29964	exon6			AACAGCGCTGCTG	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.320G>A	6.37:g.41753136G>A	ENSP00000377803:p.Arg107His	89	0	0		79	77	0.974684	NM_013397	A2A3M0|A6PVU1|B3KQ15|Q5T3D4|Q9NSV1	Missense_Mutation	SNP	ENST00000394260.1	37		32	0.014652014652014652	28	0.056910569105691054	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	G	1.735	-0.493181	0.04322	0.051067	0.001977	ENSG00000124593	ENST00000458694;ENST00000359201;ENST00000394263;ENST00000394259;ENST00000394260	D;D;D;D;D	0.87491	-2.26;-2.26;-2.26;-2.26;-2.26	4.71	2.91	0.33838	.	0.859014	0.09926	N	0.737859	T	0.63988	0.2558	L	0.35542	1.07	0.09310	N	1	B	0.25169	0.119	B	0.22601	0.04	T	0.55817	-0.8081	10	0.42905	T	0.14	-6.1033	4.9115	0.13823	0.084:0.1478:0.6159:0.1523	rs35880970	147	Q2TBC4-3	.	H	147;147;147;107;107	ENSP00000404911:R147H;ENSP00000352128:R147H;ENSP00000377806:R147H;ENSP00000377802:R107H;ENSP00000377803:R107H	ENSP00000335185:R147H	R	+	2	0	PRICKLE4	41861114	0.024000	0.19004	0.631000	0.29282	0.275000	0.26752	0.519000	0.22862	0.587000	0.29643	-0.258000	0.10820	CGC	G|0.982;A|0.018	0.018	strong		0.602	PRICKLE4-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000303948.1	NM_013397		A	41753136	G	A	41753136	3	1	22	1	0	0	0	0	1	0	0	0	12501	1087	38	1	454	1	PRICKLE4	6	41753136	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	434558	41753136	129361931	1464	4365											
USP49	25862	hgsc.bcm.edu	37	chr6	41774340	41774340	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgaggagcgcgctgcggcaGgaccacgtcctcacccgaag	8	4	14	15	5	1	1	1	1	0	0	2	4	2	3	3	3	2	2	3	3	1	0	rs111948785	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:41774340G>T	ENST00000394253.3	-	3	711	c.382C>A	c.(382-384)Ctg>Atg	p.L128M	USP49_ENST00000297229.2_Missense_Mutation_p.L128M|USP49_ENST00000373009.3_Missense_Mutation_p.L128M|USP49_ENST00000373006.1_Missense_Mutation_p.L128M|USP49_ENST00000373010.1_Missense_Mutation_p.L128M			Q70CQ1	UBP49_HUMAN	ubiquitin specific peptidase 49	128					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)			CGCTGCGGCAGGACCACGTCC	0.687													G|||	81	0.0161741	0.0537	0.0072	5008	,	,		12628	0.0		0.001	False		,,,				2504	0.0041				p.L128M		Atlas-SNP	.											.	USP49	58	.	0			c.C382A						PASS	.	G	MET/LEU	222,4184		6,210,1987	23	24	23		382	4.6	0.1	6	dbSNP_132	23	14,8582		0,14,4284	yes	missense	USP49	NM_018561.3	15	6,224,6271	TT,TG,GG		0.1629,5.0386,1.8151	benign	128/641	41774340	236,12766	2203	4298	6501	SO:0001583	missense	25862	exon4			GCGGCAGGACCAC	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.382C>A	6.37:g.41774340G>T	ENSP00000377797:p.Leu128Met	33	0	0		37	37	1	NM_018561	Q5T3D9|Q5T3E0|Q96CK4	Missense_Mutation	SNP	ENST00000394253.3	37		.	.	.	.	.	.	.	.	.	.	G	9.151	1.016215	0.19355	0.050386	0.001629	ENSG00000164663	ENST00000394253;ENST00000373010;ENST00000373009;ENST00000373006;ENST00000297229	T;T;T;T;T	0.06933	3.72;3.24;3.72;3.5;3.5	4.6	4.6	0.57074	.	0.851504	0.10514	N	0.665818	T	0.01905	0.0060	N	0.12182	0.205	0.09310	N	1	B	0.13594	0.008	B	0.16722	0.016	T	0.44513	-0.9323	10	0.33940	T	0.23	-1.5488	10.2169	0.43173	0.0:0.0:0.7493:0.2507	.	128	Q70CQ1-2	.	M	128	ENSP00000377797:L128M;ENSP00000362101:L128M;ENSP00000362100:L128M;ENSP00000362097:L128M;ENSP00000297229:L128M	ENSP00000297229:L128M	L	-	1	2	USP49	41882318	0.566000	0.26618	0.076000	0.20297	0.974000	0.67602	2.655000	0.46707	2.376000	0.81061	0.655000	0.94253	CTG	A|0.000;G|0.986;T|0.014	0.014	strong		0.687	USP49-007	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000316513.3	NM_018561		T	41774340	G	T	41774340	3	4	22	1	0	0	0	0	1	0	0	0	17095	991	35	4	1556	4	USP49	6	41774340	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	21204	41774340	129340727	1465	4366											
GUCA1A	2978	hgsc.bcm.edu	37	chr6	42141360	42141360	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaggcctgagcaatgggcaaCgtgatggagggaaagtcagt	13	6	16	6	1	1	2	1	2	0	0	1	4	1	4	1	4	2	2	1	4	4	0	rs116114043	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42141360C>T	ENST00000394237.1	+	3	985	c.9C>T	c.(7-9)aaC>aaT	p.N3N	GUCA1A_ENST00000053469.4_Silent_p.N3N|GUCA1A_ENST00000372958.1_Silent_p.N3N|GUCA1A_ENST00000541991.1_Silent_p.N3N			P43080	GUC1A_HUMAN	guanylate cyclase activator 1A (retina)	3					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)			CAATGGGCAACGTGATGGAGG	0.607													C|||	20	0.00399361	0.0151	0.0	5008	,	,		20437	0.0		0.0	False		,,,				2504	0.0				p.N3N		Atlas-SNP	.											.	GUCA1A	18	.	0			c.C9T						PASS	.	C		59,4347	56.8+/-93.2	0,59,2144	117	97	104		9	2.2	1	6	dbSNP_132	104	0,8600		0,0,4300	no	coding-synonymous	GUCA1A	NM_000409.3		0,59,6444	TT,TC,CC		0.0,1.3391,0.4536		3/202	42141360	59,12947	2203	4300	6503	SO:0001819	synonymous_variant	2978	exon3			GGGCAACGTGATG		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.9C>T	6.37:g.42141360C>T		54	0	0		36	19	0.527778	NM_000409	B3KWT4|Q7Z6T1|Q9NU14	Silent	SNP	ENST00000394237.1	37	CCDS4864.1																																																																																			C|0.995;T|0.005	0.005	strong		0.607	GUCA1A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316582.1			T	42141360	C	T	42141360	2	4	22	1	0	0	0	0	0	0	0	1	6897	535	19	1		1	GUCA1A	6	42141360	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	367020	42141360	128973707	1466	4367											
TRERF1	55809	hgsc.bcm.edu	37	chr6	42233529	42233529	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgggctctcccatcaggtaGgtgcatctaattttgagcca	8	12	10	11	0	3	1	1	1	2	0	4	1	3	1	2	3	2	3	2	3	2	4	rs79466811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42233529G>A	ENST00000372922.4	-	6	2006	c.1444C>T	c.(1444-1446)Cta>Tta	p.L482L	TRERF1_ENST00000541110.1_Silent_p.L482L|TRERF1_ENST00000354325.2_Silent_p.L482L|TRERF1_ENST00000372917.4_Silent_p.L482L|TRERF1_ENST00000340840.2_Silent_p.L482L	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	482	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)			CCATCAGGTAGGTGCATCTAA	0.502													G|||	84	0.0167732	0.0605	0.0058	5008	,	,		18570	0.0		0.0	False		,,,				2504	0.0				p.L482L		Atlas-SNP	.											.	TRERF1	124	.	0			c.C1444T						PASS	.	G		239,4167	140.8+/-176.2	6,227,1970	56	54	55		1444	1.8	1	6	dbSNP_132	55	3,8597	3.7+/-12.6	0,3,4297	no	coding-synonymous	TRERF1	NM_033502.2		6,230,6267	AA,AG,GG		0.0349,5.4244,1.8607		482/1201	42233529	242,12764	2203	4300	6503	SO:0001819	synonymous_variant	55809	exon6			CAGGTAGGTGCAT	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.1444C>T	6.37:g.42233529G>A		87	0	0		96	42	0.4375	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Silent	SNP	ENST00000372922.4	37	CCDS4867.1																																																																																			G|0.981;A|0.019	0.019	strong		0.502	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502		A	42233529	G	A	42233529	2	1	22	1	0	0	0	0	0	0	0	1	16490	991	35	2		2	TRERF1	6	42233529	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	92169	42233529	128881538	1467	4368											
UBR2	23304	hgsc.bcm.edu	37	chr6	42562027	42562027	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catgaacttaacacctctgaAattgaggaagaagaggtaaa	18	8	9	6	0	1	5	0	3	1	2	1	6	1	6	1	2	2	1	1	2	7	3	rs6905054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42562027A>T	ENST00000372899.1	+	4	774	c.516A>T	c.(514-516)gaA>gaT	p.E172D	UBR2_ENST00000372901.1_Missense_Mutation_p.E172D|UBR2_ENST00000372903.2_Missense_Mutation_p.E172D	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	172			E -> D (in dbSNP:rs6905054).		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)			ACACCTCTGAAATTGAGGAAG	0.363													A|||	166	0.033147	0.1089	0.0072	5008	,	,		17588	0.0099		0.0	False		,,,				2504	0.0072				p.E172D		Atlas-SNP	.											.	UBR2	134	.	0			c.A516T						PASS	.	A	ASP/GLU,ASP/GLU	360,4046	185.0+/-212.2	14,332,1857	113	110	111		516,516	5.2	1	6	dbSNP_116	111	2,8598	1.2+/-3.3	0,2,4298	yes	missense,missense	UBR2	NM_001184801.1,NM_015255.2	45,45	14,334,6155	TT,TA,AA		0.0233,8.1707,2.7833	benign,benign	172/440,172/1756	42562027	362,12644	2203	4300	6503	SO:0001583	missense	23304	exon4			CTCTGAAATTGAG	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.516A>T	6.37:g.42562027A>T	ENSP00000361990:p.Glu172Asp	64	0	0		66	22	0.333333	NM_001184801	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	37	CCDS4870.1	58	0.026556776556776556	50	0.1016260162601626	0	0.0	8	0.013986013986013986	0	0.0	A	11.03	1.518060	0.27211	0.081707	2.33E-4	ENSG00000024048	ENST00000372903;ENST00000372899;ENST00000372901	T;T;T	0.73152	-0.72;0.27;0.27	5.17	5.17	0.71159	.	0.218116	0.47093	D	0.000242	T	0.34571	0.0902	N	0.22421	0.69	0.09310	P	0.9999999999999195	B;B	0.09022	0.001;0.002	B;B	0.12837	0.001;0.008	T	0.13415	-1.0510	9	0.11485	T	0.65	-28.0504	11.0648	0.47968	0.9248:0.0:0.0752:0.0	rs6905054;rs52816446;rs61683407;rs6905054	172;172	Q8IWV8;Q8IWV8-2	UBR2_HUMAN;.	D	172	ENSP00000361994:E172D;ENSP00000361990:E172D;ENSP00000361992:E172D	ENSP00000361990:E172D	E	+	3	2	UBR2	42670005	1.000000	0.71417	0.995000	0.50966	0.998000	0.95712	1.373000	0.34272	1.953000	0.56701	0.459000	0.35465	GAA	A|0.966;T|0.034	0.034	strong		0.363	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255		T	42562027	A	T	42562027	3	4	22	1	0	0	0	0	1	0	0	0	16917	11	1	5	530	5	UBR2	6	42562027	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	328498	42562027	128553040	1468	4369											
PRPH2	5961	hgsc.bcm.edu	37	chr6	42666244	42666244	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcccaattgtaatggtcAcctggtggtgggagaggaga	10	8	16	7	0	1	2	1	0	0	2	1	4	1	2	2	5	1	2	2	5	2	2	rs140406696		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42666244A>C	ENST00000230381.5	-	3	1069	c.830T>G	c.(829-831)gTg>gGg	p.V277G		NM_000322.4	NP_000313.2	P23942	PRPH2_HUMAN	peripherin 2 (retinal degeneration, slow)	277					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)			TGTAATGGTCACCTGGTGGTG	0.572													A|||	1	0.000199681	0.0008	0.0	5008	,	,		19706	0.0		0.0	False		,,,				2504	0.0				p.V277G		Atlas-SNP	.											.	PRPH2	47	.	0			c.T830G						PASS	.	A	GLY/VAL	5,4401	9.9+/-24.2	0,5,2198	74	73	73		830	5	0.9	6	dbSNP_134	73	0,8600		0,0,4300	yes	missense-near-splice	PRPH2	NM_000322.4	109	0,5,6498	CC,CA,AA		0.0,0.1135,0.0384	benign	277/347	42666244	5,13001	2203	4300	6503	SO:0001630	splice_region_variant	5961	exon3			ATGGTCACCTGGT		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.829-1T>G	6.37:g.42666244A>C		76	0	0		82	40	0.487805	NM_000322	Q5TFH5|Q6DK65	Missense_Mutation	SNP	ENST00000230381.5	37	CCDS4871.1	.	.	.	.	.	.	.	.	.	.	A	15.09	2.730591	0.48939	0.001135	0.0	ENSG00000112619	ENST00000230381	D	0.81739	-1.53	5.0	5.0	0.66597	.	0.243684	0.40818	N	0.001012	T	0.74261	0.3693	L	0.46157	1.445	0.58432	D	0.999993	P	0.41673	0.759	P	0.46585	0.521	T	0.79167	-0.1915	10	0.66056	D	0.02	.	14.6991	0.69145	1.0:0.0:0.0:0.0	.	277	P23942	PRPH2_HUMAN	G	277	ENSP00000230381:V277G	ENSP00000230381:V277G	V	-	2	0	PRPH2	42774222	0.998000	0.40836	0.926000	0.36857	0.031000	0.12232	4.115000	0.57865	1.858000	0.53909	0.533000	0.62120	GTG	A|1.000;C|0.000	0.000	weak		0.572	PRPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040556.1	NM_000322	Missense_Mutation	C	42666244	A	C	42666244	5	2	22	1	0	0	0	0	0	0	1	0	12589	173	6	5	214	5	PRPH2	6	42666244	Splice_Site	SNP	A	TCGA-G8-6324-01A-11D-2210-10	104217	42666244	128448823	1469	4370											
PRPH2	5961	hgsc.bcm.edu	37	chr6	42689940	42689940	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacatcgctcctctttcggaGttcaatcttcaggaacagtc	9	12	7	13	2	4	0	2	0	2	0	8	2	5	2	1	2	1	2	1	2	2	3	rs61755770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42689940G>A	ENST00000230381.5	-	1	372	c.133C>T	c.(133-135)Ctc>Ttc	p.L45F		NM_000322.4	NP_000313.2	P23942	PRPH2_HUMAN	peripherin 2 (retinal degeneration, slow)	45			L -> F (in RP7; in combination with a null mutation of ROM1; dbSNP:rs61755770).		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)			CTCTTTCGGAGTTCAATCTTC	0.512													G|||	30	0.00599042	0.0212	0.0029	5008	,	,		20575	0.0		0.0	False		,,,				2504	0.0				p.L45F		Atlas-SNP	.											.	PRPH2	47	.	0			c.C133T	GRCh37	CM951114	PRPH2	M	rs61755770	PASS	.	G	PHE/LEU	68,4338	61.7+/-98.7	0,68,2135	109	93	98	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	133	4.7	1	6	dbSNP_129	98	0,8600		0,0,4300	yes	missense	PRPH2	NM_000322.4	22	0,68,6435	AA,AG,GG		0.0,1.5433,0.5228	probably-damaging	45/347	42689940	68,12938	2203	4300	6503	SO:0001583	missense	5961	exon1			TTCGGAGTTCAAT		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.133C>T	6.37:g.42689940G>A	ENSP00000230381:p.Leu45Phe	94	0	0		121	68	0.561983	NM_000322	Q5TFH5|Q6DK65	Missense_Mutation	SNP	ENST00000230381.5	37	CCDS4871.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	G	20.2	3.948475	0.73787	0.015433	0.0	ENSG00000112619	ENST00000230381	T	0.80393	-1.37	5.61	4.71	0.59529	.	0.000000	0.85682	D	0.000000	D	0.87845	0.6280	M	0.85859	2.78	0.58432	D	0.999991	D	0.60160	0.987	D	0.66497	0.944	D	0.87105	0.2181	10	0.40728	T	0.16	.	15.9296	0.79648	0.0:0.0:0.8645:0.1355	rs61755770	45	P23942	PRPH2_HUMAN	F	45	ENSP00000230381:L45F	ENSP00000230381:L45F	L	-	1	0	PRPH2	42797918	1.000000	0.71417	0.951000	0.38953	0.943000	0.58893	6.097000	0.71452	2.631000	0.89168	0.655000	0.94253	CTC	G|0.994;A|0.006	0.006	strong		0.512	PRPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040556.1	NM_000322		A	42689940	G	A	42689940	3	1	22	1	0	0	0	0	1	0	0	0	12589	1029	36	2	919	2	PRPH2	6	42689940	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	23696	42689940	128425127	1470	4371											
PTCRA	171558	hgsc.bcm.edu	37	chr6	42893328	42893328	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgcccagcacaggcctggTgctcaagatctgccctcagg	7	8	11	15	0	3	1	2	0	1	1	3	1	3	1	3	3	4	2	3	3	1	1	rs115331994	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42893328T>C	ENST00000304672.1	+	4	835	c.754T>C	c.(754-756)Tgc>Cgc	p.C252R	PTCRA_ENST00000446507.1_Missense_Mutation_p.C145R|PTCRA_ENST00000441198.1_Missense_Mutation_p.C227R	NM_001243168.1|NM_138296.2	NP_001230097.1|NP_612153.2	Q6ISU1	PTCRA_HUMAN	pre T-cell antigen receptor alpha	252					negative regulation of thymocyte apoptotic process (GO:0070244)	integral component of membrane (GO:0016021)				large_intestine(2)|lung(4)|ovary(2)	8	Colorectal(47;0.196)		all cancers(41;0.000731)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|OV - Ovarian serous cystadenocarcinoma(102;0.0218)|Kidney(15;0.0388)			ACAGGCCTGGTGCTCAAGATC	0.642													T|||	44	0.00878594	0.0257	0.0	5008	,	,		2807	0.0		0.0	False		,,,				2504	0.0102				p.C267R		Atlas-SNP	.											.	PTCRA	24	.	0			c.T799C						PASS	.	T	ARG/CYS	60,4338		0,60,2139	36	30	32		754	-8.4	0	6	dbSNP_132	32	2,8594		0,2,4296	yes	missense	PTCRA	NM_138296.2	180	0,62,6435	CC,CT,TT		0.0233,1.3643,0.4771	possibly-damaging	252/282	42893328	62,12932	2199	4298	6497	SO:0001583	missense	171558	exon4			GCCTGGTGCTCAA	AF084941	CCDS4874.1, CCDS59019.1, CCDS59020.1, CCDS75457.1	6p21.3	2008-02-05			ENSG00000171611	ENSG00000171611			21290	protein-coding gene	gene with protein product		606817				8618853, 9842925	Standard	NM_138296		Approved	PTA, PT-ALPHA	uc021yzp.1	Q6ISU1	OTTHUMG00000014709	ENST00000304672.1:c.754T>C	6.37:g.42893328T>C	ENSP00000304447:p.Cys252Arg	62	0	0		85	50	0.588235	NM_001243168	Q5TFZ7	Missense_Mutation	SNP	ENST00000304672.1	37	CCDS4874.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	T	12.26	1.885331	0.33255	0.013643	2.33E-4	ENSG00000171611	ENST00000304672;ENST00000441198;ENST00000446507;ENST00000418903	T;T;T	0.55413	1.23;1.19;0.52	4.17	-8.35	0.00984	.	2.132630	0.02556	N	0.096213	T	0.09774	0.0240	N	0.14661	0.345	0.09310	N	0.999999	B;B;B	0.23806	0.091;0.005;0.005	B;B;B	0.22152	0.038;0.008;0.003	T	0.03166	-1.1065	10	0.72032	D	0.01	.	1.2025	0.01888	0.3397:0.3089:0.1915:0.1599	.	145;227;252	Q6ISU1-2;Q6ISU1-3;Q6ISU1	.;.;PTCRA_HUMAN	R	252;227;145;98	ENSP00000304447:C252R;ENSP00000409550:C227R;ENSP00000392288:C145R	ENSP00000304447:C252R	C	+	1	0	PTCRA	43001306	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-4.585000	0.00212	-3.458000	0.00159	0.533000	0.62120	TGC	T|0.994;C|0.006	0.006	strong		0.642	PTCRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040565.2	NM_138296		C	42893328	T	C	42893328	3	2	22	1	0	0	0	0	1	0	0	0	12747	1696	59	3	768	3	PTCRA	6	42893328	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	203388	42893328	128221739	1471	4372											
GNMT	27232	hgsc.bcm.edu	37	chr6	42930877	42930877	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgcgggcagggggcctactGgtcattgatcatcgcaacta	8	9	14	10	2	2	1	2	1	0	0	3	1	2	1	1	4	3	2	1	4	3	3	rs147291064	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42930877G>A	ENST00000372808.3	+	4	529	c.519G>A	c.(517-519)ctG>ctA	p.L173L		NM_018960.4	NP_061833.1	Q14749	GNMT_HUMAN	glycine N-methyltransferase	173					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)	GGGGCCTACTGGTCATTGATC	0.602													G|||	47	0.00938498	0.034	0.0029	5008	,	,		11061	0.0		0.0	False		,,,				2504	0.0				p.L173L		Atlas-SNP	.											.	GNMT	13	.	0			c.G519A						PASS	.	G		88,4318	74.7+/-112.8	0,88,2115	42	40	41		519	3.9	1	6	dbSNP_134	41	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	GNMT	NM_018960.4		0,91,6412	AA,AG,GG		0.0349,1.9973,0.6997		173/296	42930877	91,12915	2203	4300	6503	SO:0001819	synonymous_variant	27232	exon4			CCTACTGGTCATT	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.519G>A	6.37:g.42930877G>A		65	0	0		82	39	0.47561	NM_018960	Q5T8W2|Q9NNZ1|Q9NS24	Silent	SNP	ENST00000372808.3	37	CCDS4876.1																																																																																			G|0.993;A|0.007	0.007	strong		0.602	GNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040568.1	NM_018960		A	42930877	G	A	42930877	2	1	22	1	0	0	0	0	0	0	0	1	6548	1335	47	2		2	GNMT	6	42930877	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	37549	42930877	128184190	1472	4373											
PEX6	5190	hgsc.bcm.edu	37	chr6	42932080	42932080	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ccctggggggctcctagcagGcagcaaacttgcgctggatg	7	7	15	12	1	0	0	0	0	0	0	1	1	1	1	2	5	4	5	2	5	2	2	rs115180949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42932080G>A	ENST00000304611.8	-	17	3005	c.2936C>T	c.(2935-2937)gCc>gTc	p.A979V	PEX6_ENST00000244546.4_3'UTR	NM_000287.3	NP_000278.3	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6	979					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)			CTCCTAGCAGGCAGCAAACTT	0.637													G|||	47	0.00938498	0.034	0.0029	5008	,	,		17507	0.0		0.0	False		,,,				2504	0.0				p.A979V		Atlas-SNP	.											.	PEX6	44	.	0			c.C2936T						PASS	.	G	VAL/ALA	85,4321		0,85,2118	36	38	37		2936	5	1	6	dbSNP_132	37	3,8595		0,3,4296	yes	missense	PEX6	NM_000287.3	64	0,88,6414	AA,AG,GG		0.0349,1.9292,0.6767	possibly-damaging	979/981	42932080	88,12916	2203	4299	6502	SO:0001583	missense	5190	exon17			TAGCAGGCAGCAA	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.2936C>T	6.37:g.42932080G>A	ENSP00000303511:p.Ala979Val	107	0	0		98	45	0.459184	NM_000287	Q5T8W1|Q8WYQ0|Q8WYQ1|Q8WYQ2|Q99476	Missense_Mutation	SNP	ENST00000304611.8	37	CCDS4877.1	16	0.007326007326007326	15	0.03048780487804878	1	0.0027624309392265192	0	0.0	0	0.0	G	36	5.602210	0.96614	0.019292	3.49E-4	ENSG00000124587	ENST00000304611	D	0.95377	-3.69	5.9	5.03	0.67393	.	0.307721	0.39985	N	0.001217	D	0.93119	0.7809	L	0.33485	1.01	0.80722	D	1	D	0.57257	0.979	P	0.52554	0.702	D	0.93230	0.6616	10	0.52906	T	0.07	-12.279	15.0391	0.71774	0.0698:0.0:0.9302:0.0	.	979	Q13608	PEX6_HUMAN	V	979	ENSP00000303511:A979V	ENSP00000303511:A979V	A	-	2	0	PEX6	43040058	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	5.035000	0.64158	2.803000	0.96430	0.609000	0.83330	GCC	G|0.993;A|0.007	0.007	strong		0.637	PEX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040569.1	NM_000287		A	42932080	G	A	42932080	3	1	22	1	0	0	0	0	1	0	0	0	11759	1203	42	2	10	2	PEX6	6	42932080	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1203	42932080	128182987	1473	4374											
SRF	6722	hgsc.bcm.edu	37	chr6	43146105	43146105	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacatgatgtaccctagcccGcatgcggtgatgtatgcccc	8	9	10	14	2	0	2	0	2	0	0	0	2	0	2	4	1	4	3	4	1	3	3	rs140883192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43146105G>T	ENST00000265354.4	+	5	1594	c.1236G>T	c.(1234-1236)ccG>ccT	p.P412P	SRF_ENST00000457278.2_Silent_p.P208P	NM_003131.2	NP_003122.1	P11831	SRF_HUMAN	serum response factor (c-fos serum response element-binding transcription factor)	412					angiogenesis involved in wound healing (GO:0060055)|associative learning (GO:0008306)|cardiac myofibril assembly (GO:0055003)|cardiac vascular smooth muscle cell differentiation (GO:0060947)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-matrix adhesion (GO:0007160)|cellular response to glucose stimulus (GO:0071333)|cellular senescence (GO:0090398)|contractile actin filament bundle assembly (GO:0030038)|developmental growth (GO:0048589)|dorsal aorta morphogenesis (GO:0035912)|epithelial cell-cell adhesion (GO:0090136)|epithelial structure maintenance (GO:0010669)|erythrocyte development (GO:0048821)|eyelid development in camera-type eye (GO:0061029)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula formation (GO:0060347)|hematopoietic stem cell differentiation (GO:0060218)|hippocampus development (GO:0021766)|long term synaptic depression (GO:0060292)|long-term memory (GO:0007616)|megakaryocyte development (GO:0035855)|mesoderm formation (GO:0001707)|morphogenesis of an epithelial sheet (GO:0002011)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|neuron development (GO:0048666)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|patterning of blood vessels (GO:0001569)|platelet activation (GO:0030168)|platelet formation (GO:0030220)|positive regulation of cell differentiation (GO:0045597)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription by glucose (GO:0046016)|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 initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription via serum response element binding (GO:0010735)|positive thymic T cell selection (GO:0045059)|primitive streak formation (GO:0090009)|regulation of cell adhesion (GO:0030155)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of water loss via skin (GO:0033561)|response to cytokine (GO:0034097)|response to hormone (GO:0009725)|response to hypoxia (GO:0001666)|response to toxic substance (GO:0009636)|sarcomere organization (GO:0045214)|skin morphogenesis (GO:0043589)|stress fiber assembly (GO:0043149)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|tight junction assembly (GO:0070830)|transcription from RNA polymerase II promoter (GO:0006366)|trophectodermal cell differentiation (GO:0001829)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|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)|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)|serum response element binding (GO:0010736)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	12			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.011)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			ACCCTAGCCCGCATGCGGTGA	0.607													G|||	31	0.0061901	0.0219	0.0014	5008	,	,		20467	0.0		0.001	False		,,,				2504	0.0				p.P412P		Atlas-SNP	.											.	SRF	24	.	0			c.G1236T						PASS	.	G		57,4349	55.5+/-91.7	0,57,2146	102	75	84		1236	4.7	1	6	dbSNP_134	84	0,8600		0,0,4300	no	coding-synonymous	SRF	NM_003131.2		0,57,6446	TT,TG,GG		0.0,1.2937,0.4383		412/509	43146105	57,12949	2203	4300	6503	SO:0001819	synonymous_variant	6722	exon5			TAGCCCGCATGCG	J03161	CCDS4889.1	6p	2008-02-05			ENSG00000112658	ENSG00000112658			11291	protein-coding gene	gene with protein product		600589				3203386	Standard	NM_003131		Approved	MCM1	uc003oui.3	P11831	OTTHUMG00000014722	ENST00000265354.4:c.1236G>T	6.37:g.43146105G>T		57	0	0		63	28	0.444444	NM_003131	Q5T648	Silent	SNP	ENST00000265354.4	37	CCDS4889.1																																																																																			G|0.997;T|0.003	0.003	strong		0.607	SRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040581.1	NM_003131		T	43146105	G	T	43146105	2	4	22	1	0	0	0	0	0	0	0	1	15158	1074	38	4		4	SRF	6	43146105	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	214025	43146105	127968962	1474	4375											
CUL9	23113	hgsc.bcm.edu	37	chr6	43152366	43152366	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tttcctcgagatccaggaggCctggatgaagtggcaatggg	9	9	15	8	1	0	2	0	1	0	1	3	5	2	4	3	5	0	1	3	5	2	1	rs41274928	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43152366C>A	ENST00000252050.4	+	2	402	c.318C>A	c.(316-318)ggC>ggA	p.G106G	CUL9_ENST00000372647.2_Silent_p.G106G|CUL9_ENST00000354495.3_Silent_p.G106G	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	106					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						ATCCAGGAGGCCTGGATGAAG	0.607													C|||	248	0.0495208	0.1112	0.0288	5008	,	,		20915	0.003		0.0288	False		,,,				2504	0.0501				p.G106G		Atlas-SNP	.											.	CUL9	248	.	0			c.C318A						PASS	.	C		459,3947	217.1+/-235.6	32,395,1776	89	96	94		318	0.7	1	6	dbSNP_127	94	267,8333	101.9+/-163.1	2,263,4035	no	coding-synonymous	CUL9	NM_015089.2		34,658,5811	AA,AC,CC		3.1047,10.4176,5.582		106/2518	43152366	726,12280	2203	4300	6503	SO:0001819	synonymous_variant	23113	exon2			AGGAGGCCTGGAT	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.318C>A	6.37:g.43152366C>A		156	0	0		184	95	0.516304	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	37	CCDS4890.1																																																																																			C|0.948;A|0.052	0.052	strong		0.607	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		A	43152366	C	A	43152366	2	1	22	1	0	0	0	0	0	0	0	1	4063	726	26	4		4	CUL9	6	43152366	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6261	43152366	127962701	1475	4376											
CUL9	23113	hgsc.bcm.edu	37	chr6	43154064	43154064	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaattctccagccgtagtggCtatggagaatatgtgcagca	11	10	12	8	1	1	1	0	0	1	1	2	3	1	1	2	2	3	4	2	2	5	4	rs79828871	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43154064C>T	ENST00000252050.4	+	4	1206	c.1122C>T	c.(1120-1122)ggC>ggT	p.G374G	CUL9_ENST00000372647.2_Silent_p.G374G|CUL9_ENST00000354495.3_Silent_p.G374G	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	374					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						GCCGTAGTGGCTATGGAGAAT	0.577													C|||	187	0.0373403	0.1331	0.0144	5008	,	,		19600	0.0		0.001	False		,,,				2504	0.0				p.G374G		Atlas-SNP	.											.	CUL9	248	.	0			c.C1122T						PASS	.	C		441,3965	212.8+/-232.6	12,417,1774	74	73	73		1122	3.7	1	6	dbSNP_131	73	0,8600		0,0,4300	no	coding-synonymous	CUL9	NM_015089.2		12,417,6074	TT,TC,CC		0.0,10.0091,3.3907		374/2518	43154064	441,12565	2203	4300	6503	SO:0001819	synonymous_variant	23113	exon4			TAGTGGCTATGGA	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.1122C>T	6.37:g.43154064C>T		118	0	0		140	58	0.414286	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	37	CCDS4890.1																																																																																			C|0.967;T|0.033	0.033	strong		0.577	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		T	43154064	C	T	43154064	2	4	22	1	0	0	0	0	0	0	0	1	4063	784	28	2		2	CUL9	6	43154064	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1698	43154064	127961003	1476	4377											
TTBK1	84630	hgsc.bcm.edu	37	chr6	43251608	43251608	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggccaccatctcccccagaCgccatgctatgccaggctct	7	8	8	18	1	2	1	0	0	2	1	3	1	2	1	6	2	2	2	6	2	1	1	rs146633224	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43251608C>T	ENST00000259750.4	+	14	3213	c.3130C>T	c.(3130-3132)Cgc>Tgc	p.R1044C		NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	1044					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)			CTCCCCCAGACGCCATGCTAT	0.662													C|||	16	0.00319489	0.0098	0.0043	5008	,	,		14735	0.0		0.0	False		,,,				2504	0.0				p.R1044C		Atlas-SNP	.											.	TTBK1	124	.	0			c.C3130T						PASS	.	C	CYS/ARG	39,4331		0,39,2146	31	29	30		3130	4	0.6	6	dbSNP_134	30	8,8470		0,8,4231	yes	missense	TTBK1	NM_032538.1	180	0,47,6377	TT,TC,CC		0.0944,0.8924,0.3658	possibly-damaging	1044/1322	43251608	47,12801	2185	4239	6424	SO:0001583	missense	84630	exon14			CCCAGACGCCATG	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.3130C>T	6.37:g.43251608C>T	ENSP00000259750:p.Arg1044Cys	99	0	0		99	44	0.444444	NM_032538	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Missense_Mutation	SNP	ENST00000259750.4	37	CCDS34455.1	6	0.0027472527472527475	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	9.159	1.018106	0.19355	0.008924	9.44E-4	ENSG00000146216	ENST00000259750	T	0.54279	0.58	4.84	3.96	0.45880	.	1.368680	0.04907	N	0.452377	T	0.29914	0.0748	L	0.52573	1.65	0.21740	N	0.99957	B	0.06786	0.001	B	0.04013	0.001	T	0.37407	-0.9707	10	0.87932	D	0	.	8.0444	0.30540	0.0:0.7512:0.1604:0.0883	.	1044	Q5TCY1	TTBK1_HUMAN	C	1044	ENSP00000259750:R1044C	ENSP00000259750:R1044C	R	+	1	0	TTBK1	43359586	0.000000	0.05858	0.580000	0.28601	0.346000	0.29079	0.210000	0.17455	1.155000	0.42497	0.462000	0.41574	CGC	C|0.997;T|0.003	0.003	strong		0.662	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3			T	43251608	C	T	43251608	3	4	22	1	0	0	0	0	1	0	0	0	16691	536	19	1	3180	1	TTBK1	6	43251608	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	97544	43251608	127863459	1477	4378											
ABCC10	89845	hgsc.bcm.edu	37	chr6	43411700	43411700	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgagattctgccactggtaCaagctgtccccaaagcctgg	9	9	10	13	0	1	1	0	1	1	1	2	2	2	1	4	2	4	2	4	2	3	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43411700C>T	ENST00000372530.4	+	11	2661	c.2446C>T	c.(2446-2448)Caa>Taa	p.Q816*	ABCC10_ENST00000244533.3_Nonsense_Mutation_p.Q788*	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	816	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				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)	GCCACTGGTACAAGCTGTCCC	0.542																																					p.Q816X		Atlas-SNP	.											.	ABCC10	118	.	0			c.C2446T						PASS	.						150	145	147					6																	43411700		2203	4300	6503	SO:0001587	stop_gained	89845	exon11			CTGGTACAAGCTG	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.2446C>T	6.37:g.43411700C>T	ENSP00000361608:p.Gln816*	91	0	0		83	45	0.542169	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Nonsense_Mutation	SNP	ENST00000372530.4	37	CCDS56430.1	.	.	.	.	.	.	.	.	.	.	C	42	9.524227	0.99195	.	.	ENSG00000124574	ENST00000372530;ENST00000244533	.	.	.	5.67	5.67	0.87782	.	0.128063	0.52532	D	0.000071	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	-28.5185	13.6285	0.62181	0.0:0.7989:0.2011:0.0	.	.	.	.	X	816;788	.	ENSP00000244533:Q788X	Q	+	1	0	ABCC10	43519678	0.921000	0.31238	0.981000	0.43875	0.798000	0.45092	3.288000	0.51739	2.673000	0.90976	0.655000	0.94253	CAA	.	.	none		0.542	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450		T	43411700	C	T	43411700	4	4	22	1	0	0	0	0	0	1	0	0	50	479	17	2	2396	2	ABCC10	6	43411700	Nonsense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	160092	43411700	127703367	1478	4379											
ABCC10	89845	hgsc.bcm.edu	37	chr6	43412935	43412935	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtttctacctcaccgtgtaTgcgaccattgctggtgtaaa	8	13	9	11	3	2	0	1	0	1	0	2	1	2	0	3	1	3	4	3	1	4	5	rs2125740	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43412935T>C	ENST00000372530.4	+	14	3128	c.2913T>C	c.(2911-2913)taT>taC	p.Y971Y	ABCC10_ENST00000244533.3_Silent_p.Y943Y	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	971	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)	TCACCGTGTATGCGACCATTG	0.602													T|||	271	0.0541134	0.1974	0.0115	5008	,	,		17679	0.0		0.002	False		,,,				2504	0.0				p.Y971Y		Atlas-SNP	.											.	ABCC10	118	.	0			c.T2913C						PASS	.	T	,	845,3561	334.7+/-303.5	72,701,1430	132	102	112		2913,2829	-6	0.3	6	dbSNP_96	112	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous,coding-synonymous	ABCC10	NM_001198934.1,NM_033450.2	,	72,706,5725	CC,CT,TT		0.0581,19.1784,6.5354	,	971/1493,943/1465	43412935	850,12156	2203	4300	6503	SO:0001819	synonymous_variant	89845	exon14			CGTGTATGCGACC	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.2913T>C	6.37:g.43412935T>C		225	0	0		234	103	0.440171	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Silent	SNP	ENST00000372530.4	37	CCDS56430.1																																																																																			T|0.940;C|0.060	0.060	strong		0.602	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450		C	43412935	T	C	43412935	2	2	22	1	0	0	0	0	0	0	0	1	50	1471	51	3		3	ABCC10	6	43412935	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1235	43412935	127702132	1479	4380											
ABCC10	89845	hgsc.bcm.edu	37	chr6	43413669	43413669	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tctgtgctccgggccacaggGgccacctacaggtgtgtgaa	7	8	14	12	1	1	1	0	1	1	0	2	1	2	1	4	4	2	1	4	4	2	1	rs112977568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43413669G>A	ENST00000372530.4	+	15	3578	c.3363G>A	c.(3361-3363)ggG>ggA	p.G1121G	ABCC10_ENST00000244533.3_Silent_p.G1093G	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	1121	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)	GGGCCACAGGGGCCACCTACA	0.622													G|||	37	0.00738818	0.0272	0.0	5008	,	,		18669	0.0		0.001	False		,,,				2504	0.0				p.G1121G		Atlas-SNP	.											.	ABCC10	118	.	0			c.G3363A						PASS	.	G	,	106,4248		1,104,2072	21	23	22		3363,3279	3.4	1	6	dbSNP_132	22	0,8536		0,0,4268	no	coding-synonymous,coding-synonymous	ABCC10	NM_001198934.1,NM_033450.2	,	1,104,6340	AA,AG,GG		0.0,2.4345,0.8223	,	1121/1493,1093/1465	43413669	106,12784	2177	4268	6445	SO:0001819	synonymous_variant	89845	exon15			CACAGGGGCCACC	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.3363G>A	6.37:g.43413669G>A		104	0	0		87	45	0.517241	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Silent	SNP	ENST00000372530.4	37	CCDS56430.1																																																																																			G|0.992;A|0.008	0.008	strong		0.622	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450		A	43413669	G	A	43413669	2	1	22	1	0	0	0	0	0	0	0	1	50	1219	43	2		2	ABCC10	6	43413669	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	734	43413669	127701398	1480	4381											
C6orf154	221424	hgsc.bcm.edu	37	chr6	43475195	43475195	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caaccctctgggttcttaccGctggggcacatccaggagct	7	9	11	14	1	2	0	0	0	2	0	3	1	3	1	3	4	3	4	3	4	2	2	rs61746927	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43475195G>A	ENST00000372441.1	-	5	1779	c.879C>T	c.(877-879)agC>agT	p.S293S		NM_001012974.1	NP_001012992.1	Q5JTD7	LRC73_HUMAN	leucine rich repeat containing 73	293																	GGTTCTTACCGCTGGGGCACA	0.632													G|||	74	0.0147764	0.0469	0.0144	5008	,	,		18063	0.0		0.002	False		,,,				2504	0.0				p.S293S		Atlas-SNP	.											.	.	.	.	0			c.C879T						PASS	.	G		237,4169	134.9+/-171.1	9,219,1975	33	38	36		879	-1.7	0.9	6	dbSNP_129	36	4,8596	3.7+/-12.6	0,4,4296	yes	coding-synonymous-near-splice	C6orf154	NM_001012974.1		9,223,6271	AA,AG,GG		0.0465,5.379,1.853		293/317	43475195	241,12765	2203	4300	6503	SO:0001630	splice_region_variant	221424	exon5			CTTACCGCTGGGG		CCDS34456.1	6p21.1	2011-11-25	2011-11-25	2011-11-25	ENSG00000204052	ENSG00000204052			21375	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 154"	C6orf154			Standard	NM_001012974		Approved	dJ337H4.2	uc003ovk.2	Q5JTD7	OTTHUMG00000014737	ENST00000372441.1:c.880+1C>T	6.37:g.43475195G>A		50	0	0		52	25	0.480769	NM_001012974		Silent	SNP	ENST00000372441.1	37	CCDS34456.1																																																																																			G|0.980;A|0.020	0.020	strong		0.632	LRRC73-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040635.1	NM_001012974	Silent	A	43475195	G	A	43475195	5	1	22	1	0	0	0	0	0	0	1	0	2341	1101	38	1	79	1	C6orf154	6	43475195	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	61526	43475195	127639872	1481	4382											
SLC35B2	347734	hgsc.bcm.edu	37	chr6	44223292	44223292	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaccaggaactgcgagtcCgtaaagcgctcacccggtga	11	5	12	13	4	1	1	1	1	0	0	2	3	2	2	3	2	4	3	3	2	3	1	rs35112470	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:44223292C>T	ENST00000393812.3	-	4	593	c.450G>A	c.(448-450)acG>acA	p.T150T	SLC35B2_ENST00000538577.1_Silent_p.T57T|SLC35B2_ENST00000393810.1_3'UTR|SLC35B2_ENST00000537814.1_Silent_p.T17T|SLC35B2_ENST00000495706.1_5'UTR|MIR4647_ENST00000583964.1_RNA	NM_178148.2	NP_835361.1	Q8TB61	S35B2_HUMAN	solute carrier family 35 (adenosine 3'-phospho 5'-phosphosulfate transporter), member B2	150					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)			ACTGCGAGTCCGTAAAGCGCT	0.587													C|||	114	0.0227636	0.0855	0.0014	5008	,	,		18748	0.0		0.0	False		,,,				2504	0.0				p.T150T		Atlas-SNP	.											.	SLC35B2	40	.	0			c.G450A						PASS	.	C		296,4110	162.2+/-194.2	7,282,1914	94	93	93		450	-11.6	0.5	6	dbSNP_126	93	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	SLC35B2	NM_178148.2		7,289,6207	TT,TC,CC		0.0814,6.7181,2.3297		150/433	44223292	303,12703	2203	4300	6503	SO:0001819	synonymous_variant	347734	exon4			CGAGTCCGTAAAG	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.450G>A	6.37:g.44223292C>T		114	0	0		126	72	0.571429	NM_178148	B4DDU9|F5H7Y9|Q2VY06|Q53GA3|Q5T9W1|Q5T9W2|Q7Z2G3|Q8NBK6|Q96AR6	Silent	SNP	ENST00000393812.3	37	CCDS34462.1																																																																																			C|0.977;T|0.023	0.023	strong		0.587	SLC35B2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040724.2			T	44223292	C	T	44223292	2	4	22	1	0	0	0	0	0	0	0	1	14591	639	23	1		1	SLC35B2	6	44223292	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	748097	44223292	126891775	1482	4383											
TCTE1	202500	hgsc.bcm.edu	37	chr6	44249939	44249939	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtggcggtgggctcagacaGctcattgccaccgaggtgca	7	8	15	11	2	2	1	2	0	0	1	2	2	2	1	2	4	3	3	2	4	0	1	rs34405945	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:44249939G>A	ENST00000371505.4	-	4	1326	c.1204C>T	c.(1204-1206)Ctg>Ttg	p.L402L	TCTE1_ENST00000371504.1_Intron|TCTE1_ENST00000371503.3_Intron|RP11-444E17.6_ENST00000505802.1_Intron|TMEM151B_ENST00000438774.2_Intron	NM_182539.3	NP_872345.2	Q5JU00	TCTE1_HUMAN	t-complex-associated-testis-expressed 1	402										breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(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)			GGCTCAGACAGCTCATTGCCA	0.602													G|||	60	0.0119808	0.0446	0.0014	5008	,	,		18613	0.0		0.0	False		,,,				2504	0.0				p.L402L		Atlas-SNP	.											.	TCTE1	77	.	0			c.C1204T						PASS	.	G		113,4293	85.8+/-124.5	0,113,2090	159	127	138		1204	2.4	1	6	dbSNP_126	138	1,8599		0,1,4299	yes	coding-synonymous	TCTE1	NM_182539.3		0,114,6389	AA,AG,GG		0.0116,2.5647,0.8765		402/502	44249939	114,12892	2203	4300	6503	SO:0001819	synonymous_variant	202500	exon4			CAGACAGCTCATT	BC035022	CCDS4910.1	6q21.1	2014-07-18			ENSG00000146221	ENSG00000146221			11693	protein-coding gene	gene with protein product		186975				2568335, 8646886	Standard	NM_182539		Approved	D6S46, MGC33600, FAP155	uc003oxi.2	Q5JU00	OTTHUMG00000014763	ENST00000371505.4:c.1204C>T	6.37:g.44249939G>A		135	0	0		183	98	0.535519	NM_182539	B4DX59|Q8IYS6	Silent	SNP	ENST00000371505.4	37	CCDS4910.1																																																																																			G|0.988;A|0.012	0.012	strong		0.602	TCTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040736.1	NM_182539		A	44249939	G	A	44249939	2	1	22	1	0	0	0	0	0	0	0	1	15732	962	34	2		2	TCTE1	6	44249939	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	26647	44249939	126865128	1483	4384											
AARS2	57505	hgsc.bcm.edu	37	chr6	44270189	44270189	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgccacatcccggctccccAgactcagccgctcagtggcc	6	5	9	21	3	2	1	2	0	0	1	4	1	4	1	7	2	1	2	7	2	0	0	rs35967387	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:44270189A>T	ENST00000244571.4	-	18	2428	c.2426T>A	c.(2425-2427)cTg>cAg	p.L809Q	AARS2_ENST00000491573.1_5'Flank|RP11-444E17.6_ENST00000505802.1_Intron|TMEM151B_ENST00000438774.2_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)			CCGGCTCCCCAGACTCAGCCG	0.632													T|||	114	0.0227636	0.0847	0.0029	5008	,	,		18406	0.0		0.0	False		,,,				2504	0.0				p.L809Q		Atlas-SNP	.											.	AARS2	77	.	0			c.T2426A						PASS	.	T	GLN/LEU	256,4150	795.4+/-415.3	5,246,1952	41	46	44		2426	0.2	1	6	dbSNP_126	44	1,8599		0,1,4299	yes	missense	AARS2	NM_020745.2	113	5,247,6251	TT,TA,AA		0.0116,5.8103,1.976	benign	809/986	44270189	257,12749	2203	4300	6503	SO:0001583	missense	57505	exon18			CTCCCCAGACTCA	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.2426T>A	6.37:g.44270189A>T	ENSP00000244571:p.Leu809Gln	133	0	0		131	66	0.503817	NM_020745		Missense_Mutation	SNP	ENST00000244571.4	37	CCDS34464.1	48	0.02197802197802198	47	0.09552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	T	1.128	-0.653372	0.03480	0.058103	1.16E-4	ENSG00000124608	ENST00000244571	T	0.63913	-0.07	5.32	0.155	0.14906	.	1.197330	0.05517	N	0.561479	T	0.09113	0.0225	N	0.01048	-1.04	0.22947	N	0.998524	B	0.02656	0.0	B	0.01281	0.0	T	0.09250	-1.0683	10	0.12103	T	0.63	-10.1928	4.7087	0.12861	0.2367:0.3061:0.0:0.4572	rs35967387	809	Q5JTZ9	SYAM_HUMAN	Q	809	ENSP00000244571:L809Q	ENSP00000244571:L809Q	L	-	2	0	AARS2	44378167	0.362000	0.24980	0.961000	0.40146	0.084000	0.17831	-0.656000	0.05342	-0.185000	0.10550	-0.983000	0.02560	CTG	A|0.977;T|0.023	0.023	strong		0.632	AARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040741.2	NM_020745		T	44270189	A	T	44270189	3	4	22	1	0	0	0	0	1	0	0	0	20	188	7	5	551	5	AARS2	6	44270189	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	20250	44270189	126844878	1484	4385											
AARS2	57505	hgsc.bcm.edu	37	chr6	44279824	44279824	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctcaccttaaaatattcaccCccaaaggcccaattgccaag	14	8	4	15	0	2	0	2	0	0	0	2	0	2	0	5	1	1	0	5	1	6	4	rs75506489	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:44279824C>T	ENST00000244571.4	-	2	422	c.420G>A	c.(418-420)ggG>ggA	p.G140G	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)			AATATTCACCCCCAAAGGCCC	0.483													C|||	108	0.0215655	0.0809	0.0014	5008	,	,		21967	0.0		0.0	False		,,,				2504	0.0				p.G140G		Atlas-SNP	.											.	AARS2	77	.	0			c.G420A						PASS	.	C		220,4186	132.5+/-169.0	3,214,1986	177	170	172		420	1.7	1	6	dbSNP_132	172	1,8599		0,1,4299	no	coding-synonymous	AARS2	NM_020745.2		3,215,6285	TT,TC,CC		0.0116,4.9932,1.6992		140/986	44279824	221,12785	2203	4300	6503	SO:0001819	synonymous_variant	57505	exon2			TTCACCCCCAAAG	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.420G>A	6.37:g.44279824C>T		125	0	0		137	53	0.386861	NM_020745		Silent	SNP	ENST00000244571.4	37	CCDS34464.1																																																																																			C|0.980;T|0.020	0.020	strong		0.483	AARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040741.2	NM_020745		T	44279824	C	T	44279824	2	4	22	1	0	0	0	0	0	0	0	1	20	610	22	2		2	AARS2	6	44279824	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	9635	44279824	126835243	1485	4386											
CDC5L	988	hgsc.bcm.edu	37	chr6	44387305	44387305	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcgacaagttgtacagacTccaaacacagttctctctac	13	9	6	13	1	2	1	0	0	2	1	4	2	3	1	1	0	4	3	1	0	4	4	rs11571982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:44387305T>C	ENST00000371477.3	+	9	1511	c.1212T>C	c.(1210-1212)acT>acC	p.T404T		NM_001253.3	NP_001244.1	Q99459	CDC5L_HUMAN	cell division cycle 5-like	404	Interaction with PPP1R8.				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)			TTGTACAGACTCCAAACACAG	0.398													T|||	58	0.0115815	0.0393	0.0086	5008	,	,		20954	0.0		0.0	False		,,,				2504	0.0				p.T404T		Atlas-SNP	.											.	CDC5L	86	.	0			c.T1212C						PASS	.	T		140,4266	100.3+/-138.9	1,138,2064	154	138	143		1212	0.3	1	6	dbSNP_120	143	0,8600		0,0,4300	no	coding-synonymous	CDC5L	NM_001253.2		1,138,6364	CC,CT,TT		0.0,3.1775,1.0764		404/803	44387305	140,12866	2203	4300	6503	SO:0001819	synonymous_variant	988	exon9			ACAGACTCCAAAC	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.1212T>C	6.37:g.44387305T>C		144	0	0		126	61	0.484127	NM_001253	Q76N46|Q99974	Silent	SNP	ENST00000371477.3	37	CCDS4912.1																																																																																			T|0.989;C|0.011	0.011	strong		0.398	CDC5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040743.1			C	44387305	T	C	44387305	2	2	22	1	0	0	0	0	0	0	0	1	3084	1538	54	3		3	CDC5L	6	44387305	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	107481	44387305	126727762	1486	4387											
GPR110	266977	hgsc.bcm.edu	37	chr6	46976924	46976924	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gccacaatagccagtgcaggGacaacaaaagccaggagtgg	15	3	13	10	0	0	0	0	0	0	0	0	2	0	2	3	3	4	1	3	3	5	1	rs45511696	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:46976924G>A	ENST00000371253.2	-	11	2462	c.2247C>T	c.(2245-2247)gtC>gtT	p.V749V	GPR110_ENST00000449332.2_5'UTR|GPR110_ENST00000283297.5_Silent_p.V552V	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	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)			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						CCAGTGCAGGGACAACAAAAG	0.493													G|||	186	0.0371406	0.0787	0.0389	5008	,	,		22252	0.0		0.0447	False		,,,				2504	0.0102				p.V749V		Atlas-SNP	.											.	GPR110	102	.	0			c.C2247T						PASS	.	G		375,4031	188.5+/-214.9	14,347,1842	92	97	95		2247	1.2	0.5	6	dbSNP_127	95	328,8272	115.3+/-175.2	7,314,3979	no	coding-synonymous	GPR110	NM_153840.2		21,661,5821	AA,AG,GG		3.814,8.5111,5.4052		749/911	46976924	703,12303	2203	4300	6503	SO:0001819	synonymous_variant	266977	exon11			TGCAGGGACAACA	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.2247C>T	6.37:g.46976924G>A		126	0	0		135	69	0.511111	NM_153840	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Silent	SNP	ENST00000371253.2	37	CCDS34471.1																																																																																			G|0.952;A|0.048	0.048	strong		0.493	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840		A	46976924	G	A	46976924	2	1	22	1	0	0	0	0	0	0	0	1	6635	1161	41	2		2	GPR110	6	46976924	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2589619	46976924	124138143	1487	4388											
GPR110	266977	hgsc.bcm.edu	37	chr6	46977783	46977783	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtctgacccaattaacacaCggcctctgatgggaatagat	12	9	10	10	1	2	3	0	2	2	1	2	4	2	4	2	3	1	0	2	3	4	2	rs45598235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:46977783C>T	ENST00000371253.2	-	11	1603	c.1388G>A	c.(1387-1389)cGt>cAt	p.R463H	GPR110_ENST00000449332.2_5'UTR|GPR110_ENST00000283297.5_Missense_Mutation_p.R266H	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	463					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						AATTAACACACGGCCTCTGAT	0.438													C|||	186	0.0371406	0.0787	0.0389	5008	,	,		20334	0.0		0.0447	False		,,,				2504	0.0102				p.R463H		Atlas-SNP	.											GPR110,NS,carcinoma,0,1	GPR110	102	1	0			c.G1388A						PASS	.	C	HIS/ARG	378,4028	190.9+/-216.7	14,350,1839	97	92	94		1388	-3.6	0	6	dbSNP_127	94	328,8272	115.3+/-175.2	7,314,3979	yes	missense	GPR110	NM_153840.2	29	21,664,5818	TT,TC,CC		3.814,8.5792,5.4283	benign	463/911	46977783	706,12300	2203	4300	6503	SO:0001583	missense	266977	exon11			AACACACGGCCTC	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.1388G>A	6.37:g.46977783C>T	ENSP00000360299:p.Arg463His	134	0	0		176	85	0.482955	NM_153840	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Missense_Mutation	SNP	ENST00000371253.2	37	CCDS34471.1	83	0.038003663003663	43	0.08739837398373984	13	0.03591160220994475	0	0.0	27	0.03562005277044855	C	8.205	0.798930	0.16397	0.085792	0.03814	ENSG00000153292	ENST00000371252;ENST00000371253;ENST00000283297	T;T	0.34472	1.37;1.36	5.2	-3.63	0.04529	.	1.386990	0.04430	N	0.369085	T	0.04588	0.0125	N	0.02202	-0.64	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28996	-1.0026	10	0.35671	T	0.21	-0.5469	6.9695	0.24640	0.0:0.2802:0.2071:0.5127	rs45598235	463	Q5T601	GP110_HUMAN	H	463;463;266	ENSP00000360299:R463H;ENSP00000283297:R266H	ENSP00000283297:R266H	R	-	2	0	GPR110	47085742	0.000000	0.05858	0.022000	0.16811	0.063000	0.16089	-0.885000	0.04161	-0.181000	0.10619	-1.467000	0.01014	CGT	C|0.952;T|0.048	0.048	strong		0.438	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840		T	46977783	C	T	46977783	3	4	22	1	0	0	0	0	1	0	0	0	6635	536	19	1	1364	1	GPR110	6	46977783	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	859	46977783	124137284	1488	4389											
GPR110	266977	hgsc.bcm.edu	37	chr6	46977894	46977894	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttccagtcaatgaatttcCgagaaaaattcagaggaaga	16	10	8	7	1	2	4	2	1	0	3	4	6	4	5	2	1	0	0	2	1	5	3	rs115292676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:46977894C>T	ENST00000371253.2	-	11	1492	c.1277G>A	c.(1276-1278)cGg>cAg	p.R426Q	GPR110_ENST00000449332.2_5'UTR|GPR110_ENST00000283297.5_Missense_Mutation_p.R229Q	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	426					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						AATGAATTTCCGAGAAAAATT	0.428													C|||	59	0.0117812	0.0431	0.0014	5008	,	,		19836	0.0		0.0	False		,,,				2504	0.001				p.R426Q		Atlas-SNP	.											GPR110,colon,carcinoma,-1,2	GPR110	102	2	0			c.G1277A						PASS	.	C	GLN/ARG	135,4271	97.1+/-135.8	4,127,2072	80	77	78		1277	1.6	0.1	6	dbSNP_132	78	7,8593	5.7+/-21.5	0,7,4293	yes	missense	GPR110	NM_153840.2	43	4,134,6365	TT,TC,CC		0.0814,3.064,1.0918	possibly-damaging	426/911	46977894	142,12864	2203	4300	6503	SO:0001583	missense	266977	exon11			AATTTCCGAGAAA	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.1277G>A	6.37:g.46977894C>T	ENSP00000360299:p.Arg426Gln	180	0	0		178	100	0.561798	NM_153840	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Missense_Mutation	SNP	ENST00000371253.2	37	CCDS34471.1	17	0.007783882783882784	17	0.034552845528455285	0	0.0	0	0.0	0	0.0	C	8.645	0.896884	0.17686	0.03064	8.14E-4	ENSG00000153292	ENST00000371252;ENST00000371253;ENST00000283297	T;T	0.32515	1.45;1.45	5.35	1.57	0.23409	.	0.603370	0.14993	N	0.286596	T	0.08935	0.0221	M	0.67953	2.075	0.09310	N	1	B	0.22604	0.072	B	0.09377	0.004	T	0.38200	-0.9672	10	0.09843	T	0.71	-0.0889	5.8064	0.18442	0.0:0.5882:0.1282:0.2836	.	426	Q5T601	GP110_HUMAN	Q	426;426;229	ENSP00000360299:R426Q;ENSP00000283297:R229Q	ENSP00000283297:R229Q	R	-	2	0	GPR110	47085853	0.000000	0.05858	0.104000	0.21259	0.823000	0.46562	-0.323000	0.07997	0.340000	0.23745	0.555000	0.69702	CGG	C|0.989;T|0.011	0.011	strong		0.428	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840		T	46977894	C	T	46977894	3	4	22	1	0	0	0	0	1	0	0	0	6635	652	23	1	1475	1	GPR110	6	46977894	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	111	46977894	124137173	1489	4390											
TNFRSF21	27242	hgsc.bcm.edu	37	chr6	47251772	47251772	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caatggcactgggatcctgcCggggcccctttttcagagtc	6	10	12	13	1	1	1	1	0	0	1	3	2	2	2	4	4	1	1	4	4	1	2	rs148459670	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:47251772C>T	ENST00000296861.2	-	3	1538	c.1145G>A	c.(1144-1146)cGg>cAg	p.R382Q		NM_014452.3	NP_055267.1	O75509	TNR21_HUMAN	tumor necrosis factor receptor superfamily, member 21	382					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)			GGGATCCTGCCGGGGCCCCTT	0.527													C|||	2	0.000399361	0.0015	0.0	5008	,	,		17459	0.0		0.0	False		,,,				2504	0.0				p.R382Q		Atlas-SNP	.											.	TNFRSF21	61	.	0			c.G1145A						PASS	.	C	GLN/ARG	3,4403	6.2+/-15.9	0,3,2200	91	99	96		1145	6.2	1	6	dbSNP_134	96	0,8600		0,0,4300	yes	missense	TNFRSF21	NM_014452.3	43	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	probably-damaging	382/656	47251772	3,13003	2203	4300	6503	SO:0001583	missense	27242	exon3			TCCTGCCGGGGCC	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.1145G>A	6.37:g.47251772C>T	ENSP00000296861:p.Arg382Gln	227	0	0		269	137	0.509294	NM_014452	B2RDI9|Q0D2P5|Q96D86	Missense_Mutation	SNP	ENST00000296861.2	37	CCDS4921.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.892611	0.91889	6.81E-4	0.0	ENSG00000146072	ENST00000296861;ENST00000419206	T	0.66099	-0.19	6.17	6.17	0.99709	.	0.162308	0.56097	D	0.000032	T	0.65450	0.2692	L	0.59436	1.845	0.47374	D	0.999408	D	0.71674	0.998	P	0.56788	0.806	T	0.68689	-0.5342	10	0.87932	D	0	.	13.9957	0.64397	0.0:0.9315:0.0:0.0685	.	382	O75509	TNR21_HUMAN	Q	382;71	ENSP00000296861:R382Q	ENSP00000296861:R382Q	R	-	2	0	TNFRSF21	47359731	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.682000	0.54656	2.941000	0.99782	0.655000	0.94253	CGG	C|1.000;T|0.000	0.000	strong		0.527	TNFRSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040814.1	NM_014452		T	47251772	C	T	47251772	3	4	22	1	0	0	0	0	1	0	0	0	16310	652	23	1	838	1	TNFRSF21	6	47251772	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	273878	47251772	123863295	1490	4391											
MUT	4594	hgsc.bcm.edu	37	chr6	49409599	49409599	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	actttctccaaattcctggcGatatgctccactcaccattc	9	13	4	15	1	2	0	1	0	1	0	6	1	4	0	4	1	1	1	4	1	2	4	rs140727018	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:49409599G>A	ENST00000274813.3	-	10	1889	c.1762C>T	c.(1762-1764)Cgc>Tgc	p.R588C		NM_000255.3	NP_000246.2	P22033	MUTA_HUMAN	methylmalonyl CoA mutase	588					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)	AATTCCTGGCGATATGCTCCA	0.388													G|||	2	0.000399361	0.0015	0.0	5008	,	,		10715	0.0		0.0	False		,,,				2504	0.0				p.R588C		Atlas-SNP	.											.	MUT	70	.	0			c.C1762T						PASS	.	G	CYS/ARG	16,4390	23.3+/-48.9	0,16,2187	231	210	217		1762	4.7	1	6	dbSNP_134	217	0,8600		0,0,4300	yes	missense	MUT	NM_000255.3	180	0,16,6487	AA,AG,GG		0.0,0.3631,0.123	probably-damaging	588/751	49409599	16,12990	2203	4300	6503	SO:0001583	missense	4594	exon10			CCTGGCGATATGC		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.1762C>T	6.37:g.49409599G>A	ENSP00000274813:p.Arg588Cys	237	0	0		256	134	0.523438	NM_000255	A8K953|Q5SYZ3|Q96B11|Q9UD64	Missense_Mutation	SNP	ENST00000274813.3	37	CCDS4924.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	22.7	4.329566	0.81690	0.003631	0.0	ENSG00000146085	ENST00000274813;ENST00000540138	D	0.95069	-3.6	5.59	4.72	0.59763	Cobalamin (vitamin B12)-binding (2);	0.000000	0.85682	D	0.000000	D	0.96156	0.8747	M	0.76170	2.325	0.80722	D	1	D	0.89917	1.0	D	0.73708	0.981	D	0.96378	0.9279	10	0.59425	D	0.04	-20.2086	15.0369	0.71754	0.0:0.0:0.8569:0.1431	.	588	P22033	MUTA_HUMAN	C	588;35	ENSP00000274813:R588C	ENSP00000274813:R588C	R	-	1	0	MUT	49517558	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.507000	0.81676	1.345000	0.45676	0.585000	0.79938	CGC	G|0.999;A|0.001	0.001	strong		0.388	MUT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040854.1			A	49409599	G	A	49409599	3	1	22	1	0	0	0	0	1	0	0	0	10000	1058	37	1	506	1	MUT	6	49409599	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2157827	49409599	121705468	1491	4392											
CRISP2	7180	hgsc.bcm.edu	37	chr6	49666100	49666100	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tataatgtccaacaactgcaTtgggactctttggtcctaca	11	13	7	10	0	1	0	0	0	1	0	3	1	3	1	2	2	4	1	2	2	5	5	rs34457011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:49666100T>C	ENST00000339139.4	-	7	628	c.392A>G	c.(391-393)aAt>aGt	p.N131S		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	131	SCP.		N -> S (in dbSNP:rs34457011).		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)			AACAACTGCATTGGGACTCTT	0.408													T|||	35	0.00698882	0.0257	0.0014	5008	,	,		19608	0.0		0.0	False		,,,				2504	0.0				p.N131S		Atlas-SNP	.											.	CRISP2	53	.	0			c.A392G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN	102,4304	82.4+/-120.9	2,98,2103	124	114	117		392,392,392,392,392	-1.4	0	6	dbSNP_126	117	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense	CRISP2	NM_001142407.1,NM_001142408.1,NM_001142417.1,NM_001142435.1,NM_003296.2	46,46,46,46,46	2,98,6403	CC,CT,TT		0.0,2.315,0.7843	benign,benign,benign,benign,benign	131/244,131/244,131/244,131/244,131/244	49666100	102,12904	2203	4300	6503	SO:0001583	missense	7180	exon7			ACTGCATTGGGAC	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.392A>G	6.37:g.49666100T>C	ENSP00000339155:p.Asn131Ser	113	0	0		137	59	0.430657	NM_001142408	A8K8M0|Q53FF2|Q5U8Z9|Q7Z7B2	Missense_Mutation	SNP	ENST00000339139.4	37	CCDS4928.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	T	9.996	1.232230	0.22626	0.02315	0.0	ENSG00000124490	ENST00000339139;ENST00000211238	T	0.09630	2.96	5.26	-1.44	0.08856	CAP domain (3);	0.986209	0.08313	N	0.965097	T	0.02230	0.0069	L	0.33189	0.99	0.09310	N	1	B;B	0.20052	0.02;0.041	B;B	0.22152	0.038;0.038	T	0.47598	-0.9105	10	0.33940	T	0.23	.	5.0274	0.14393	0.0:0.3052:0.282:0.4128	rs34457011	131;131	Q7Z7B2;P16562	.;CRIS2_HUMAN	S	131	ENSP00000339155:N131S	ENSP00000211238:N131S	N	-	2	0	CRISP2	49774059	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.986000	0.03747	-0.396000	0.07703	-0.379000	0.06801	AAT	T|0.991;C|0.009	0.009	strong		0.408	CRISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040870.2	NM_003296		C	49666100	T	C	49666100	3	2	22	1	0	0	0	0	1	0	0	0	3882	1493	52	3	355	3	CRISP2	6	49666100	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	256501	49666100	121448967	1492	4393											
DEFB110	245913	hgsc.bcm.edu	37	chr6	49989622	49989622	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgtgacccaaaagtgcagAataaagaaaaaaagttgaat	21	8	8	4	0	0	4	0	2	0	2	0	4	0	4	1	0	1	2	1	0	9	3	rs9473719	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:49989622A>G	ENST00000371148.2	-	1	72	c.27T>C	c.(25-27)atT>atC	p.I9I	DEFB110_ENST00000393660.2_Silent_p.I9I	NM_001037497.1	NP_001032586.1	Q30KQ9	DB110_HUMAN	defensin, beta 110 locus	9					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(1)|lung(1)|ovary(1)	3	Lung NSC(77;0.042)					AAAAGTGCAGAATAAAGAAAA	0.313													A|||	75	0.014976	0.056	0.0014	5008	,	,		16040	0.0		0.0	False		,,,				2504	0.0				p.I9I		Atlas-SNP	.											.	DEFB110	5	.	0			c.T27C						PASS	.	A	,	200,4202	113.8+/-151.8	5,190,2006	32	36	35		27,27	3.5	1	6	dbSNP_119	35	1,8591	1.2+/-3.3	0,1,4295	no	coding-synonymous,coding-synonymous	DEFB110	NM_001037497.1,NM_001037728.2	,	5,191,6301	GG,GA,AA		0.0116,4.5434,1.5469	,	9/68,9/63	49989622	201,12793	2201	4296	6497	SO:0001819	synonymous_variant	245913	exon1			GTGCAGAATAAAG	DQ012014, BC148541	CCDS43473.1, CCDS34475.1	6p12.3	2010-11-26	2010-11-26		ENSG00000203970	ENSG00000203970		"Defensins, beta"	18091	protein-coding gene	gene with protein product			"defensin, beta 110"			11854508, 16033865	Standard	NM_001037728		Approved	DEFB-10, DEFB-11, DEFB111	uc003pac.3	Q30KQ9	OTTHUMG00000160208	ENST00000371148.2:c.27T>C	6.37:g.49989622A>G		86	0	0		89	46	0.516854	NM_001037728	Q30KR0	Silent	SNP	ENST00000371148.2	37	CCDS34475.1																																																																																			A|0.986;G|0.014	0.014	strong		0.313	DEFB110-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359664.1	NM_001037728		G	49989622	A	G	49989622	2	3	22	1	0	0	0	0	0	0	0	1	4402	242	9	3		3	DEFB110	6	49989622	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	323522	49989622	121125445	1493	4394											
GCLC	2729	hgsc.bcm.edu	37	chr6	53365102	53365102	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tactcctctgcagcgagctcCgtgctgttctgggccttgcc	3	12	11	15	2	2	0	0	0	2	0	4	1	4	0	4	1	6	4	4	1	1	3	rs17881359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:53365102C>T	ENST00000229416.6	-	14	2007	c.1524G>A	c.(1522-1524)acG>acA	p.T508T	RP1-27K12.4_ENST00000508884.1_RNA	NM_001197115.1|NM_001498.3	NP_001184044.1|NP_001489.1	P48506	GSH1_HUMAN	glutamate-cysteine ligase, catalytic subunit	508					apoptotic mitochondrial changes (GO:0008637)|cell redox homeostasis (GO:0045454)|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)|L-ascorbic acid metabolic process (GO:0019852)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|regulation of blood vessel size (GO:0050880)|regulation of mitochondrial depolarization (GO:0051900)|response to arsenic-containing substance (GO:0046685)|response to heat (GO:0009408)|response to hormone (GO:0009725)|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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|glutamate-cysteine ligase complex (GO:0017109)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|coenzyme binding (GO:0050662)|glutamate binding (GO:0016595)|glutamate-cysteine ligase activity (GO:0004357)|magnesium ion binding (GO:0000287)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22	Lung NSC(77;0.0137)				L-Cysteine(DB00151)|Vitamin E(DB00163)	CAGCGAGCTCCGTGCTGTTCT	0.567													C|||	28	0.00559105	0.0204	0.0014	5008	,	,		18765	0.0		0.0	False		,,,				2504	0.0				p.T508T		Atlas-SNP	.											.	GCLC	58	.	0			c.G1524A						PASS	.	C	,	76,4330	67.0+/-104.6	0,76,2127	148	129	136		1410,1524	-10.5	0	6	dbSNP_124	136	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	GCLC	NM_001197115.1,NM_001498.3	,	0,76,6427	TT,TC,CC		0.0,1.7249,0.5843	,	470/600,508/638	53365102	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	2729	exon14			GAGCTCCGTGCTG	M90656	CCDS4952.1, CCDS75471.1	6p12	2008-02-05				ENSG00000001084	6.3.2.2		4311	protein-coding gene	gene with protein product		606857		GLCLC, GLCL		1350904	Standard	NM_001498		Approved	GCS	uc003pbw.2	P48506		ENST00000229416.6:c.1524G>A	6.37:g.53365102C>T		179	0	0		176	82	0.465909	NM_001498	Q14399	Silent	SNP	ENST00000229416.6	37	CCDS4952.1																																																																																			C|0.994;T|0.006	0.006	strong		0.567	GCLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359710.2			T	53365102	C	T	53365102	2	4	22	1	0	0	0	0	0	0	0	1	6303	639	23	1		1	GCLC	6	53365102	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3375480	53365102	117749965	1494	4395											
FAM83B	222584	hgsc.bcm.edu	37	chr6	54805074	54805074	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tcacgggaaggctatgtaagCcaccacaacacacctgccca	13	5	8	15	1	1	0	1	0	0	0	1	1	1	1	4	2	3	2	4	2	4	2	rs9475076	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:54805074C>G	ENST00000306858.7	+	5	1421	c.1305C>G	c.(1303-1305)agC>agG	p.S435R	RP3-523K23.2_ENST00000562834.1_RNA	NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	435			S -> R (in dbSNP:rs9475076).							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)					GCTATGTAAGCCACCACAACA	0.448													C|||	288	0.057508	0.2088	0.0144	5008	,	,		18486	0.0		0.002	False		,,,				2504	0.0				p.S435R		Atlas-SNP	.											.	FAM83B	186	.	0			c.C1305G						PASS	.	C	ARG/SER	795,3611	321.0+/-296.9	67,661,1475	65	69	67		1305	0.8	0	6	dbSNP_119	67	16,8584	10.5+/-38.8	0,16,4284	yes	missense	FAM83B	NM_001010872.1	110	67,677,5759	GG,GC,CC		0.186,18.0436,6.2356	benign	435/1012	54805074	811,12195	2203	4300	6503	SO:0001583	missense	222584	exon5			TGTAAGCCACCAC	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.1305C>G	6.37:g.54805074C>G	ENSP00000304078:p.Ser435Arg	80	0	0		110	54	0.490909	NM_001010872	Q2M1P3|Q96DQ2	Missense_Mutation	SNP	ENST00000306858.7	37	CCDS34479.1	112	0.05128205128205128	105	0.21341463414634146	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	C	1.045	-0.677640	0.03378	0.180436	0.00186	ENSG00000168143	ENST00000306858	T	0.08546	3.08	5.56	0.802	0.18686	.	1.270360	0.05003	N	0.469411	T	0.02807	0.0084	L	0.47716	1.5	0.80722	P	0.0	P	0.34780	0.468	B	0.27500	0.08	T	0.43572	-0.9383	9	0.42905	T	0.14	-0.061	9.8787	0.41220	0.0:0.4374:0.0:0.5626	rs9475076;rs52793316;rs9475076	435	Q5T0W9	FA83B_HUMAN	R	435	ENSP00000304078:S435R	ENSP00000304078:S435R	S	+	3	2	FAM83B	54913033	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.071000	0.14594	-0.074000	0.12820	-0.137000	0.14449	AGC	C|0.945;G|0.055	0.055	strong		0.448	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139		G	54805074	C	G	54805074	3	3	22	1	0	0	0	0	1	0	0	0	5642	738	26	4	1319	4	FAM83B	6	54805074	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1439972	54805074	116309993	1495	4396											
COL21A1	81578	hgsc.bcm.edu	37	chr6	55925698	55925698	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaatacatacgggcttcccAtccaaacctgggggtccctg	10	8	10	13	1	0	1	0	0	0	1	3	1	3	1	4	3	3	1	4	3	4	3	rs545860371		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:55925698A>C	ENST00000244728.5	-	26	2740	c.2343T>G	c.(2341-2343)gaT>gaG	p.D781E	COL21A1_ENST00000535941.1_Missense_Mutation_p.D781E|COL21A1_ENST00000467045.1_5'UTR|COL21A1_ENST00000370819.1_Missense_Mutation_p.D778E|COL21A1_ENST00000370808.2_Missense_Mutation_p.D181E	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	781	Collagen-like 5.				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)			CGGGCTTCCCATCCAAACCTG	0.473													A|||	1	0.000199681	0.0	0.0	5008	,	,		15984	0.001		0.0	False		,,,				2504	0.0				p.D781E		Atlas-SNP	.											.	COL21A1	201	.	0			c.T2343G						PASS	.						44	43	43					6																	55925698		1837	4081	5918	SO:0001583	missense	81578	exon26			CTTCCCATCCAAA	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.2343T>G	6.37:g.55925698A>C	ENSP00000244728:p.Asp781Glu	96	0	0		92	23	0.25	NM_030820	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Missense_Mutation	SNP	ENST00000244728.5	37	CCDS55025.1	.	.	.	.	.	.	.	.	.	.	A	11.01	1.513616	0.27123	.	.	ENSG00000124749	ENST00000244728;ENST00000370819;ENST00000535941;ENST00000370811;ENST00000370808	D;D;D;D	0.93133	-3.17;-3.17;-3.17;-3.16	4.9	3.74	0.42951	.	0.191909	0.35739	N	0.003010	T	0.80336	0.4604	N	0.25201	0.72	0.32304	N	0.56468	D;D;P;D	0.57571	0.975;0.98;0.789;0.98	P;P;B;P	0.52454	0.573;0.699;0.444;0.699	T	0.75255	-0.3382	10	0.07644	T	0.81	.	4.3365	0.11089	0.6951:0.0:0.1586:0.1463	.	181;781;781;138	Q96P44-2;B7ZLK3;Q96P44;B3KU30	.;.;COLA1_HUMAN;.	E	781;778;781;778;181	ENSP00000244728:D781E;ENSP00000359855:D778E;ENSP00000444384:D781E;ENSP00000359844:D181E	ENSP00000244728:D781E	D	-	3	2	COL21A1	56033657	1.000000	0.71417	0.996000	0.52242	0.986000	0.74619	1.167000	0.31847	0.830000	0.34757	0.533000	0.62120	GAT	.	.	none		0.473	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2			C	55925698	A	C	55925698	3	2	22	1	0	0	0	0	1	0	0	0	3682	214	8	5	550	5	COL21A1	6	55925698	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1120624	55925698	115189369	1496	4397											
LGSN	51557	hgsc.bcm.edu	37	chr6	64004905	64004905	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttgtccttcttaatgtgtTcatgctgttggcttcagtct	4	19	8	10	0	4	0	2	0	2	0	5	0	5	0	2	1	1	4	2	1	1	6	rs2459568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:64004905T>A	ENST00000370657.4	-	2	109	c.76A>T	c.(76-78)Aac>Tac	p.N26Y	LGSN_ENST00000370658.5_Missense_Mutation_p.N26Y			Q5TDP6	LGSN_HUMAN	lengsin, lens protein with glutamine synthetase domain	26			N -> Y (in dbSNP:rs2459568).		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						CTTAATGTGTTCATGCTGTTG	0.343													T|||	68	0.0135783	0.0499	0.0029	5008	,	,		18219	0.0		0.0	False		,,,				2504	0.0				p.N26Y		Atlas-SNP	.											.	LGSN	82	.	0			c.A76T						PASS	.	T	TYR/ASN,TYR/ASN	174,4232	114.2+/-152.2	4,166,2033	267	240	249		76,76	1.8	0	6	dbSNP_100	249	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	LGSN	NM_001143940.1,NM_016571.2	143,143	4,169,6330	AA,AT,TT		0.0349,3.9492,1.3609	benign,benign	26/209,26/510	64004905	177,12829	2203	4300	6503	SO:0001583	missense	51557	exon2			ATGTGTTCATGCT	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.76A>T	6.37:g.64004905T>A	ENSP00000359691:p.Asn26Tyr	302	0	0		362	163	0.450276	NM_016571	A1L421|Q0PVN9|Q0PVP0|Q9NYJ0	Missense_Mutation	SNP	ENST00000370657.4	37	CCDS4964.1	16	0.007326007326007326	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	0	0.0	T	2.447	-0.327180	0.05350	0.039492	3.49E-4	ENSG00000146166	ENST00000370658;ENST00000370657	T;T	0.26660	1.72;1.83	4.71	1.8	0.24995	.	0.346161	0.36409	N	0.002618	T	0.02848	0.0085	N	0.02011	-0.69	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.10450	0.005;0.001;0.0	T	0.41142	-0.9525	10	0.46703	T	0.11	-6.0146	7.4053	0.26987	0.498:0.0:0.0:0.502	rs2459568;rs52826076;rs2459568	26;26;26	Q5TDP6-3;Q5TDP6-2;Q5TDP6	.;.;LGSN_HUMAN	Y	26	ENSP00000359692:N26Y;ENSP00000359691:N26Y	ENSP00000359691:N26Y	N	-	1	0	LGSN	64062864	0.001000	0.12720	0.003000	0.11579	0.007000	0.05969	0.975000	0.29449	0.746000	0.32786	-0.403000	0.06358	AAC	T|0.988;A|0.012	0.012	strong		0.343	LGSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041076.2	NM_016571		A	64004905	T	A	64004905	3	1	22	1	0	0	0	0	1	0	0	0	8768	1783	62	5	1465	5	LGSN	6	64004905	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	8079207	64004905	107110162	1497	4398											
PTP4A1	7803	hgsc.bcm.edu	37	chr6	64289968	64289968	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ttttttcctcccagaaagcgGcgtggagcttttaacagcaa	10	12	9	10	2	0	1	0	0	0	1	2	2	2	2	2	2	4	2	2	2	3	5	rs1618240	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:64289968G>T	ENST00000370651.3	+	6	1564	c.411G>T	c.(409-411)cgG>cgT	p.R137R	PTP4A1_ENST00000370650.2_Silent_p.R112R	NM_003463.3	NP_003454.1	Q93096	TP4A1_HUMAN	protein tyrosine phosphatase type IVA, member 1	137	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)			CCAGAAAGCGGCGTGGAGCTT	0.403													G|||	100	0.0199681	0.0741	0.0029	5008	,	,		16055	0.0		0.0	False		,,,				2504	0.0				p.R137R	Pancreas(91;1019 1502 28028 38110 51645)	Atlas-SNP	.											.	PTP4A1	13	.	0			c.G411T						PASS	.	G		253,4153	143.5+/-178.5	12,229,1962	85	87	87		411	4	1	6	dbSNP_89	87	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	PTP4A1	NM_003463.3		12,232,6259	TT,TG,GG		0.0349,5.7422,1.9683		137/174	64289968	256,12750	2203	4300	6503	SO:0001819	synonymous_variant	7803	exon6			AAAGCGGCGTGGA	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.411G>T	6.37:g.64289968G>T		32	0	0		29	16	0.551724	NM_003463	B2R6C8|O00648|Q49A54	Silent	SNP	ENST00000370651.3	37	CCDS4965.1																																																																																			G|0.980;T|0.020	0.020	strong		0.403	PTP4A1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041083.2			T	64289968	G	T	64289968	2	4	22	1	0	0	0	0	0	0	0	1	12783	1190	42	4		4	PTP4A1	6	64289968	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	285063	64289968	106825099	1498	4399											
PTP4A1	7803	hgsc.bcm.edu	37	chr6	64289996	64289996	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cttttaacagcaagcaacttCtgtatttggagaagtatcgt	12	14	8	7	1	1	1	0	0	1	1	2	2	1	1	0	1	4	4	0	1	6	6	rs1681943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:64289996C>T	ENST00000370651.3	+	6	1592	c.439C>T	c.(439-441)Ctg>Ttg	p.L147L	PTP4A1_ENST00000370650.2_Silent_p.L122L	NM_003463.3	NP_003454.1	Q93096	TP4A1_HUMAN	protein tyrosine phosphatase type IVA, member 1	147	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)			CAAGCAACTTCTGTATTTGGA	0.393													c|||	111	0.0221645	0.0825	0.0029	5008	,	,		16877	0.0		0.0	False		,,,				2504	0.0				p.L147L	Pancreas(91;1019 1502 28028 38110 51645)	Atlas-SNP	.											.	PTP4A1	13	.	0			c.C439T						PASS	.	C		303,4103	162.2+/-194.2	14,275,1914	101	101	101		439	-0.7	1	6	dbSNP_89	101	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	PTP4A1	NM_003463.3		14,278,6211	TT,TC,CC		0.0349,6.877,2.3528		147/174	64289996	306,12700	2203	4300	6503	SO:0001819	synonymous_variant	7803	exon6			CAACTTCTGTATT	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.439C>T	6.37:g.64289996C>T		45	0	0		42	23	0.547619	NM_003463	B2R6C8|O00648|Q49A54	Silent	SNP	ENST00000370651.3	37	CCDS4965.1																																																																																			C|0.980;T|0.020	0.020	strong		0.393	PTP4A1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041083.2			T	64289996	C	T	64289996	2	4	22	1	0	0	0	0	0	0	0	1	12783	912	32	2		2	PTP4A1	6	64289996	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	28	64289996	106825071	1499	4400											
FAM135A	57579	hgsc.bcm.edu	37	chr6	71234960	71234960	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagaagcaaagtgtctttctAttggagaatcattaactaaa	17	12	7	5	0	3	2	1	0	2	2	3	3	3	2	0	1	2	1	0	1	8	5	rs9455142	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:71234960A>G	ENST00000418814.2	+	15	2787	c.2173A>G	c.(2173-2175)Att>Gtt	p.I725V	FAM135A_ENST00000457062.2_Missense_Mutation_p.I512V|FAM135A_ENST00000505868.1_Missense_Mutation_p.I725V|FAM135A_ENST00000370479.3_Missense_Mutation_p.I512V|FAM135A_ENST00000505769.1_Intron|FAM135A_ENST00000361499.3_Missense_Mutation_p.I529V	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	725			I -> V (in dbSNP:rs9455142).							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						GTGTCTTTCTATTGGAGAATC	0.313													A|||	102	0.0203674	0.0726	0.0058	5008	,	,		20204	0.0		0.002	False		,,,				2504	0.0				p.I725V		Atlas-SNP	.											.	FAM135A	181	.	0			c.A2173G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE	299,4105	154.8+/-188.1	6,287,1909	47	52	51		1585,2173,1534	-12.1	0	6	dbSNP_119	51	4,8590	3.0+/-9.4	0,4,4293	yes	missense,missense,missense	FAM135A	NM_001105531.2,NM_001162529.1,NM_020819.4	29,29,29	6,291,6202	GG,GA,AA		0.0465,6.7893,2.3311	benign,benign,benign	529/1320,725/1516,512/1303	71234960	303,12695	2202	4297	6499	SO:0001583	missense	57579	exon13			CTTTCTATTGGAG	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.2173A>G	6.37:g.71234960A>G	ENSP00000410768:p.Ile725Val	65	0	0		60	22	0.366667	NM_001162529	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Missense_Mutation	SNP	ENST00000418814.2	37	CCDS55028.1	46	0.021062271062271064	43	0.08739837398373984	3	0.008287292817679558	0	0.0	0	0.0	A	0.009	-1.845019	0.00568	0.067893	4.65E-4	ENSG00000082269	ENST00000418814;ENST00000370479;ENST00000457062;ENST00000361499;ENST00000505868	T;T;T;T;T	0.38722	1.12;1.12;1.12;1.12;1.12	6.07	-12.1	0.00011	.	1.270720	0.04845	N	0.441304	T	0.06416	0.0165	N	0.03948	-0.315	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;0.001	T	0.38542	-0.9656	10	0.23891	T	0.37	.	18.3851	0.90464	0.7861:0.0739:0.1401:0.0	rs9455142;rs52822960;rs9455142	725;725;529;512	Q9P2D6-4;Q9P2D6;Q9P2D6-2;Q9P2D6-3	.;F135A_HUMAN;.;.	V	725;512;512;529;725	ENSP00000410768:I725V;ENSP00000359510:I512V;ENSP00000409201:I512V;ENSP00000354913:I529V;ENSP00000423307:I725V	ENSP00000354913:I529V	I	+	1	0	FAM135A	71291681	0.000000	0.05858	0.000000	0.03702	0.896000	0.52359	-0.852000	0.04308	-2.772000	0.00364	-0.959000	0.02639	ATT	A|0.974;G|0.026	0.026	strong		0.313	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819		G	71234960	A	G	71234960	3	3	22	1	0	0	0	0	1	0	0	0	5453	449	16	3	2301	3	FAM135A	6	71234960	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	6944964	71234960	99880107	1500	4401											
FAM135A	57579	hgsc.bcm.edu	37	chr6	71235647	71235647	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tgtgtaaaggcttccagagtCctgataaatctaataactct	13	13	7	8	0	2	2	0	1	2	1	4	2	4	2	2	1	1	2	2	1	6	5	rs16869301	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:71235647C>T	ENST00000418814.2	+	15	3474	c.2860C>T	c.(2860-2862)Cct>Tct	p.P954S	FAM135A_ENST00000457062.2_Missense_Mutation_p.P741S|FAM135A_ENST00000505868.1_Missense_Mutation_p.P954S|FAM135A_ENST00000370479.3_Missense_Mutation_p.P741S|FAM135A_ENST00000505769.1_Missense_Mutation_p.P534S|FAM135A_ENST00000361499.3_Missense_Mutation_p.P758S	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	954			P -> S (in dbSNP:rs16869301).							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						CTTCCAGAGTCCTGATAAATC	0.353													C|||	102	0.0203674	0.0726	0.0058	5008	,	,		19255	0.0		0.002	False		,,,				2504	0.0				p.P954S		Atlas-SNP	.											.	FAM135A	181	.	0			c.C2860T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO	296,4110	158.9+/-191.5	7,282,1914	52	55	54		2272,2860,2221	0.9	1	6	dbSNP_123	54	4,8590	3.7+/-12.6	0,4,4293	yes	missense,missense,missense	FAM135A	NM_001105531.2,NM_001162529.1,NM_020819.4	74,74,74	7,286,6207	TT,TC,CC		0.0465,6.7181,2.3077	benign,benign,benign	758/1320,954/1516,741/1303	71235647	300,12700	2203	4297	6500	SO:0001583	missense	57579	exon13			CAGAGTCCTGATA	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.2860C>T	6.37:g.71235647C>T	ENSP00000410768:p.Pro954Ser	96	0	0		99	41	0.414141	NM_001162529	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Missense_Mutation	SNP	ENST00000418814.2	37	CCDS55028.1	46	0.021062271062271064	43	0.08739837398373984	3	0.008287292817679558	0	0.0	0	0.0	C	0.006	-2.070499	0.00379	0.067181	4.65E-4	ENSG00000082269	ENST00000418814;ENST00000370479;ENST00000505769;ENST00000457062;ENST00000361499;ENST00000505868	T;T;T;T;T;T	0.21031	2.35;2.35;2.03;2.35;2.34;2.34	5.96	0.852	0.18995	.	0.426506	0.24048	N	0.042035	T	0.04907	0.0132	L	0.38531	1.155	0.20703	N	0.999861	B;B;B;B	0.21821	0.061;0.002;0.003;0.009	B;B;B;B	0.16289	0.015;0.004;0.011;0.01	T	0.35624	-0.9781	10	0.36615	T	0.2	.	7.0338	0.24983	0.0:0.5415:0.2138:0.2447	rs16869301;rs52792378;rs16869301	954;954;758;741	Q9P2D6-4;Q9P2D6;Q9P2D6-2;Q9P2D6-3	.;F135A_HUMAN;.;.	S	954;741;534;741;758;954	ENSP00000410768:P954S;ENSP00000359510:P741S;ENSP00000423785:P534S;ENSP00000409201:P741S;ENSP00000354913:P758S;ENSP00000423307:P954S	ENSP00000354913:P758S	P	+	1	0	FAM135A	71292368	0.903000	0.30736	0.997000	0.53966	0.055000	0.15305	0.715000	0.25822	0.405000	0.25532	-0.136000	0.14681	CCT	C|0.974;T|0.026	0.026	strong		0.353	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819		T	71235647	C	T	71235647	3	4	22	1	0	0	0	0	1	0	0	0	5453	855	30	2	2988	2	FAM135A	6	71235647	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	687	71235647	99879420	1501	4402											
FAM135A	57579	hgsc.bcm.edu	37	chr6	71245978	71245978	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	taaagctttattggacattcGttgggcaatttaataattcg	12	16	8	5	2	0	0	0	0	0	0	2	1	0	1	0	2	1	3	0	2	6	10	rs9446260	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:71245978G>A	ENST00000418814.2	+	19	4595	c.3981G>A	c.(3979-3981)tcG>tcA	p.S1327S	FAM135A_ENST00000457062.2_Silent_p.S1114S|FAM135A_ENST00000505868.1_Silent_p.S1327S|FAM135A_ENST00000370479.3_Silent_p.S1114S|FAM135A_ENST00000505769.1_Silent_p.S907S|FAM135A_ENST00000361499.3_Silent_p.S1131S	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	1327										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						TTGGACATTCGTTGGGCAATT	0.333													G|||	128	0.0255591	0.0923	0.0058	5008	,	,		16102	0.0		0.002	False		,,,				2504	0.0				p.S1327S		Atlas-SNP	.											.	FAM135A	181	.	0			c.G3981A						PASS	.	G	,,	389,4015	196.4+/-220.7	12,365,1825	112	115	114		3393,3981,3342	-11	0.2	6	dbSNP_119	114	4,8594	3.7+/-12.6	0,4,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	FAM135A	NM_001105531.2,NM_001162529.1,NM_020819.4	,,	12,369,6120	AA,AG,GG		0.0465,8.8329,3.0226	,,	1131/1320,1327/1516,1114/1303	71245978	393,12609	2202	4299	6501	SO:0001819	synonymous_variant	57579	exon17			ACATTCGTTGGGC	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.3981G>A	6.37:g.71245978G>A		80	0	0		82	39	0.47561	NM_001162529	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Silent	SNP	ENST00000418814.2	37	CCDS55028.1																																																																																			G|0.972;A|0.028	0.028	strong		0.333	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819		A	71245978	G	A	71245978	2	1	22	1	0	0	0	0	0	0	0	1	5453	1132	40	1		1	FAM135A	6	71245978	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	10331	71245978	99869089	1502	4403											
FAM135A	57579	hgsc.bcm.edu	37	chr6	71248046	71248046	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttcgcttttgcagctgacAtgtcgagatcactcagaccc	8	11	10	12	2	2	3	2	1	0	2	4	4	2	3	1	1	2	4	1	1	0	3	rs9455152	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:71248046A>G	ENST00000418814.2	+	20	4784	c.4170A>G	c.(4168-4170)acA>acG	p.T1390T	FAM135A_ENST00000457062.2_Silent_p.T1177T|FAM135A_ENST00000505868.1_Silent_p.T1390T|FAM135A_ENST00000370479.3_Silent_p.T1177T|FAM135A_ENST00000505769.1_Silent_p.T970T|FAM135A_ENST00000361499.3_Silent_p.T1194T	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	1390										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						TGCAGCTGACATGTCGAGATC	0.323													A|||	101	0.0201677	0.0726	0.0043	5008	,	,		14384	0.0		0.002	False		,,,				2504	0.0				p.T1390T		Atlas-SNP	.											.	FAM135A	181	.	0			c.A4170G						PASS	.	A	,,	299,4107	162.5+/-194.5	7,285,1911	59	61	60		3582,4170,3531	2.9	1	6	dbSNP_119	60	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	FAM135A	NM_001105531.2,NM_001162529.1,NM_020819.4	,,	7,289,6207	GG,GA,AA		0.0465,6.7862,2.3297	,,	1194/1320,1390/1516,1177/1303	71248046	303,12703	2203	4300	6503	SO:0001819	synonymous_variant	57579	exon18			GCTGACATGTCGA	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.4170A>G	6.37:g.71248046A>G		204	0	0		174	96	0.551724	NM_001162529	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Silent	SNP	ENST00000418814.2	37	CCDS55028.1																																																																																			A|0.974;G|0.026	0.026	strong		0.323	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819		G	71248046	A	G	71248046	2	3	22	1	0	0	0	0	0	0	0	1	5453	204	8	3		3	FAM135A	6	71248046	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2068	71248046	99867021	1503	4404											
DDX43	55510	hgsc.bcm.edu	37	chr6	74125283	74125283	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agggttgcctctgaattgatTaatattctggaaagagcaaa	14	12	10	5	0	2	3	0	2	2	1	2	4	2	4	1	2	2	2	1	2	5	5	rs138615882	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:74125283T>C	ENST00000370336.4	+	15	1967	c.1809T>C	c.(1807-1809)atT>atC	p.I603I	MB21D1_ENST00000370318.1_Intron	NM_018665.2	NP_061135.2	Q9NXZ2	DDX43_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43	603	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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						CTGAATTGATTAATATTCTGG	0.383													T|||	13	0.00259585	0.0098	0.0	5008	,	,		16489	0.0		0.0	False		,,,				2504	0.0				p.I603I		Atlas-SNP	.											.	DDX43	69	.	0			c.T1809C						PASS	.	T		33,4373	37.6+/-69.7	1,31,2171	110	109	109		1809	0.9	1	6	dbSNP_134	109	0,8600		0,0,4300	no	coding-synonymous	DDX43	NM_018665.2		1,31,6471	CC,CT,TT		0.0,0.749,0.2537		603/649	74125283	33,12973	2203	4300	6503	SO:0001819	synonymous_variant	55510	exon15			ATTGATTAATATT		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.1809T>C	6.37:g.74125283T>C		61	0	0		78	43	0.551282	NM_018665	B4E0C8|Q6NXR1	Silent	SNP	ENST00000370336.4	37	CCDS4977.1																																																																																			T|0.997;C|0.003	0.003	strong		0.383	DDX43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041219.3	NM_018665		C	74125283	T	C	74125283	2	2	22	1	0	0	0	0	0	0	0	1	4365	1742	61	3		3	DDX43	6	74125283	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2877237	74125283	96989784	1504	4405											
CD109	135228	hgsc.bcm.edu	37	chr6	74407182	74407182	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cggaggaaatgtgactattgGggtggagcttctggaacact	10	10	15	6	1	1	1	0	1	1	0	1	5	1	5	0	6	2	1	0	6	3	3	rs9446983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:74407182G>T	ENST00000287097.5	+	2	246	c.134G>T	c.(133-135)gGg>gTg	p.G45V	RP11-553A21.3_ENST00000428865.2_RNA|CD109_ENST00000437994.2_Missense_Mutation_p.G45V|CD109_ENST00000422508.2_Missense_Mutation_p.G45V			Q6YHK3	CD109_HUMAN	CD109 molecule	45			G -> V (in dbSNP:rs9446983).		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						GTGACTATTGGGGTGGAGCTT	0.522													G|||	75	0.014976	0.056	0.0014	5008	,	,		18228	0.0		0.0	False		,,,				2504	0.0				p.G45V		Atlas-SNP	.											CD109,NS,carcinoma,-1,1	CD109	170	1	0			c.G134T						PASS	.	G	VAL/GLY,VAL/GLY,VAL/GLY	158,4248	106.9+/-145.3	1,156,2046	118	118	118		134,134,134	5.3	1	6	dbSNP_119	118	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	109,109,109	1,157,6345	TT,TG,GG		0.0116,3.586,1.2225	possibly-damaging,possibly-damaging,possibly-damaging	45/1429,45/1369,45/1446	74407182	159,12847	2203	4300	6503	SO:0001583	missense	135228	exon2			CTATTGGGGTGGA	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.134G>T	6.37:g.74407182G>T	ENSP00000287097:p.Gly45Val	118	0	0		93	51	0.548387	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	37	CCDS4982.1	33	0.01510989010989011	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	0	0.0	G	19.50	3.840234	0.71488	0.03586	1.16E-4	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.26810	1.98;1.71;1.98	5.31	5.31	0.75309	.	0.090017	0.44285	D	0.000473	T	0.26448	0.0646	N	0.19112	0.55	0.47778	D	0.99951	D;D;P;P	0.89917	1.0;0.999;0.508;0.938	D;D;B;P	0.97110	1.0;0.984;0.176;0.706	T	0.03077	-1.1075	10	0.38643	T	0.18	.	16.0095	0.80391	0.0:0.0:1.0:0.0	rs9446983;rs52825035;rs9446983	45;45;45;45	Q6YHK3-2;Q6YHK3-3;Q6YHK3-4;Q6YHK3	.;.;.;CD109_HUMAN	V	45	ENSP00000388062:G45V;ENSP00000404475:G45V;ENSP00000287097:G45V	ENSP00000287097:G45V	G	+	2	0	CD109	74463903	1.000000	0.71417	0.998000	0.56505	0.711000	0.40976	3.673000	0.54591	2.779000	0.95612	0.655000	0.94253	GGG	G|0.986;T|0.014	0.014	strong		0.522	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493		T	74407182	G	T	74407182	3	4	22	1	0	0	0	0	1	0	0	0	2965	1232	43	4	140	4	CD109	6	74407182	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	281899	74407182	96707885	1505	4406											
CD109	135228	hgsc.bcm.edu	37	chr6	74521948	74521948	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttgctgtggtacagccaacGgcagttaatatttccgcaaa	11	11	9	10	2	0	0	0	0	0	0	1	0	1	0	2	2	4	5	2	2	5	5	rs61063525	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:74521948G>T	ENST00000287097.5	+	29	3835	c.3723G>T	c.(3721-3723)acG>acT	p.T1241T	CD109_ENST00000422508.2_Silent_p.T1164T|CD109_ENST00000437994.2_Silent_p.T1224T			Q6YHK3	CD109_HUMAN	CD109 molecule	1241			T -> M (in dbSNP:rs2917862). {ECO:0000269|PubMed:11861284, ECO:0000269|PubMed:17974005}.		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						TACAGCCAACGGCAGTTAATA	0.328													T|||	132	0.0263578	0.0953	0.0086	5008	,	,		20405	0.0		0.0	False		,,,				2504	0.0				p.T1241T		Atlas-SNP	.											.	CD109	170	.	0			c.G3723T						PASS	.	T	,,	324,4082	796.3+/-415.4	13,298,1892	146	139	142		3672,3492,3723	0	0	6	dbSNP_129	142	5,8595	818.7+/-406.8	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	,,	13,303,6187	TT,TG,GG		0.0581,7.3536,2.5296	,,	1224/1429,1164/1369,1241/1446	74521948	329,12677	2203	4300	6503	SO:0001819	synonymous_variant	135228	exon29			GCCAACGGCAGTT	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.3723G>T	6.37:g.74521948G>T		187	0	0		193	84	0.435233	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Silent	SNP	ENST00000287097.5	37	CCDS4982.1																																																																																			G|0.971;T|0.029	0.029	strong		0.328	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493		T	74521948	G	T	74521948	2	4	22	1	0	0	0	0	0	0	0	1	2965	1103	39	4		4	CD109	6	74521948	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	114766	74521948	96593119	1506	4407											
CD109	135228	hgsc.bcm.edu	37	chr6	74524724	74524724	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctcaatgttgtatataatgtGaaggcttctgggtcttctag	9	16	10	6	0	4	1	1	1	3	0	4	1	4	1	0	2	0	3	0	2	6	7	rs59555720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:74524724G>A	ENST00000287097.5	+	30	3901	c.3789G>A	c.(3787-3789)gtG>gtA	p.V1263V	CD109_ENST00000422508.2_Silent_p.V1186V|CD109_ENST00000437994.2_Silent_p.V1246V			Q6YHK3	CD109_HUMAN	CD109 molecule	1263					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						TATATAATGTGAAGGCTTCTG	0.308													G|||	132	0.0263578	0.0953	0.0086	5008	,	,		15195	0.0		0.0	False		,,,				2504	0.0				p.V1263V		Atlas-SNP	.											.	CD109	170	.	0			c.G3789A						PASS	.	G	,,	321,4085	168.7+/-199.5	13,295,1895	80	87	84		3738,3558,3789	5.4	1	6	dbSNP_129	84	5,8593	4.3+/-15.6	0,5,4294	no	coding-synonymous,coding-synonymous,coding-synonymous	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	,,	13,300,6189	AA,AG,GG		0.0582,7.2855,2.5069	,,	1246/1429,1186/1369,1263/1446	74524724	326,12678	2203	4299	6502	SO:0001819	synonymous_variant	135228	exon30			TAATGTGAAGGCT	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.3789G>A	6.37:g.74524724G>A		67	0	0		66	36	0.545455	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Silent	SNP	ENST00000287097.5	37	CCDS4982.1																																																																																			G|0.971;A|0.029	0.029	strong		0.308	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493		A	74524724	G	A	74524724	2	1	22	1	0	0	0	0	0	0	0	1	2965	1277	45	2		2	CD109	6	74524724	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2776	74524724	96590343	1507	4408											
CD109	135228	hgsc.bcm.edu	37	chr6	74524757	74524757	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttctagaagacgaagatcTatccaaaatcaagaagcctt	16	10	6	9	1	4	4	1	0	3	4	5	5	5	4	2	0	1	0	2	0	8	4	rs58562849	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:74524757T>G	ENST00000287097.5	+	30	3934	c.3822T>G	c.(3820-3822)tcT>tcG	p.S1274S	CD109_ENST00000422508.2_Silent_p.S1197S|CD109_ENST00000437994.2_Silent_p.S1257S			Q6YHK3	CD109_HUMAN	CD109 molecule	1274					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						GACGAAGATCTATCCAAAATC	0.328													T|||	132	0.0263578	0.0953	0.0086	5008	,	,		14879	0.0		0.0	False		,,,				2504	0.0				p.S1274S		Atlas-SNP	.											.	CD109	170	.	0			c.T3822G						PASS	.	T	,,	323,4083	172.3+/-202.3	13,297,1893	99	101	100		3771,3591,3822	-5.2	0	6	dbSNP_129	100	5,8591	4.3+/-15.6	0,5,4293	no	coding-synonymous,coding-synonymous,coding-synonymous	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	,,	13,302,6186	GG,GT,TT		0.0582,7.3309,2.5227	,,	1257/1429,1197/1369,1274/1446	74524757	328,12674	2203	4298	6501	SO:0001819	synonymous_variant	135228	exon30			AAGATCTATCCAA	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.3822T>G	6.37:g.74524757T>G		73	0	0		56	33	0.589286	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Silent	SNP	ENST00000287097.5	37	CCDS4982.1																																																																																			T|0.971;G|0.029	0.029	strong		0.328	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493		G	74524757	T	G	74524757	2	3	22	1	0	0	0	0	0	0	0	1	2965	1509	53	5		5	CD109	6	74524757	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	33	74524757	96590310	1508	4409											
COL12A1	1303	hgsc.bcm.edu	37	chr6	75899300	75899300	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgccacctttatatggaattTtttttattgcagcaagaagt	11	17	7	6	0	0	1	0	0	0	1	0	2	0	2	2	1	3	2	2	1	6	8	rs75535959	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:75899300T>G	ENST00000322507.8	-	6	935	c.626A>C	c.(625-627)aAa>aCa	p.K209T	COL12A1_ENST00000483888.2_Missense_Mutation_p.K209T|COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000416123.2_Missense_Mutation_p.K209T	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	209	VWFA 1. {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						ATATGGAATTTTTTTTATTGC	0.318													T|||	138	0.0275559	0.1006	0.0072	5008	,	,		18044	0.0		0.0	False		,,,				2504	0.0				p.K209T		Atlas-SNP	.											.	COL12A1	385	.	0			c.A626C						PASS	.	T	THR/LYS,	278,3348		12,254,1547	123	114	117		626,	0.4	1	6	dbSNP_131	117	2,8142		0,2,4070	yes	missense,intron	COL12A1	NM_004370.5,NM_080645.2	78,	12,256,5617	GG,GT,TT		0.0246,7.6669,2.3789	benign,	209/3064,	75899300	280,11490	1813	4072	5885	SO:0001583	missense	1303	exon6			GGAATTTTTTTTA	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.626A>C	6.37:g.75899300T>G	ENSP00000325146:p.Lys209Thr	74	0	0		91	50	0.549451	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	53	0.024267399267399268	50	0.1016260162601626	3	0.008287292817679558	0	0.0	0	0.0	T	7.405	0.633502	0.14322	0.076669	2.46E-4	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000416123;ENST00000483888	T;T;T	0.78481	-1.18;-1.18;-1.18	5.65	0.435	0.16544	von Willebrand factor, type A (3);	0.422713	0.24285	N	0.039863	T	0.43433	0.1247	L	0.31926	0.97	0.25462	N	0.987905	B	0.14438	0.01	B	0.16289	0.015	T	0.38950	-0.9637	10	0.22706	T	0.39	.	10.6931	0.45884	0.0:0.4407:0.0:0.5593	.	209	Q99715	COCA1_HUMAN	T	209	ENSP00000325146:K209T;ENSP00000412864:K209T;ENSP00000421216:K209T	ENSP00000325146:K209T	K	-	2	0	COL12A1	75956020	0.989000	0.36119	0.995000	0.50966	0.916000	0.54674	0.615000	0.24329	-0.134000	0.11516	0.533000	0.62120	AAA	T|0.984;G|0.016	0.016	strong		0.318	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		G	75899300	T	G	75899300	3	3	22	1	0	0	0	0	1	0	0	0	3671	1841	64	5	8809	5	COL12A1	6	75899300	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1374543	75899300	95215767	1509	4410											
FILIP1	27145	hgsc.bcm.edu	37	chr6	76022541	76022541	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tatctgaataggggatgtggGcctgtctgcaaatgcgcctc	8	11	13	9	1	2	1	0	1	2	0	3	2	2	2	2	3	2	1	2	3	4	2	rs34807169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:76022541G>A	ENST00000237172.7	-	5	3337	c.3007C>T	c.(3007-3009)Ccc>Tcc	p.P1003S	FILIP1_ENST00000498523.1_5'UTR|FILIP1_ENST00000393004.2_Missense_Mutation_p.P1003S|FILIP1_ENST00000370020.1_Missense_Mutation_p.P904S	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	1003			P -> S (in dbSNP:rs34807169).							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						GGGGATGTGGGCCTGTCTGCA	0.502													G|||	151	0.0301518	0.1112	0.0058	5008	,	,		19431	0.0		0.0	False		,,,				2504	0.0				p.P1003S		Atlas-SNP	.											.	FILIP1	173	.	0			c.C3007T						PASS	.	G	SER/PRO	365,4041	187.1+/-213.8	15,335,1853	117	111	113		3007	5.1	1	6	dbSNP_126	113	5,8595	4.3+/-15.6	0,5,4295	yes	missense	FILIP1	NM_015687.2	74	15,340,6148	AA,AG,GG		0.0581,8.2842,2.8448	probably-damaging	1003/1214	76022541	370,12636	2203	4300	6503	SO:0001583	missense	27145	exon5			ATGTGGGCCTGTC	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.3007C>T	6.37:g.76022541G>A	ENSP00000237172:p.Pro1003Ser	241	1	0.00414938		237	109	0.459916	NM_015687	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Missense_Mutation	SNP	ENST00000237172.7	37	CCDS4984.1	60	0.027472527472527472	57	0.11585365853658537	3	0.008287292817679558	0	0.0	0	0.0	G	15.74	2.922149	0.52653	0.082842	5.81E-4	ENSG00000118407	ENST00000393004;ENST00000237172;ENST00000370020	T;T;T	0.19532	2.14;2.14;2.15	6.03	5.14	0.70334	.	0.273243	0.42548	D	0.000686	T	0.11452	0.0279	L	0.53249	1.67	0.53688	D	0.999977	B;B;B	0.31680	0.335;0.073;0.12	B;B;B	0.32624	0.058;0.103;0.149	T	0.05115	-1.0905	10	0.16420	T	0.52	-8.9487	17.2101	0.86928	0.0:0.1259:0.8741:0.0	rs34807169	1003;1003;1003	A8K2G7;Q7Z7B0;Q7Z7B0-2	.;FLIP1_HUMAN;.	S	1003;1003;904	ENSP00000376728:P1003S;ENSP00000237172:P1003S;ENSP00000359037:P904S	ENSP00000237172:P1003S	P	-	1	0	FILIP1	76079261	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	4.086000	0.57664	1.518000	0.48934	0.655000	0.94253	CCC	G|0.973;A|0.027	0.027	strong		0.502	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179		A	76022541	G	A	76022541	3	1	22	1	0	0	0	0	1	0	0	0	5902	1203	42	2	642	2	FILIP1	6	76022541	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	123241	76022541	95092526	1510	4411											
SENP6	26054	hgsc.bcm.edu	37	chr6	76373002	76373002	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actggaccattattaagaacGtcaattcatcagaattctgg	14	12	7	8	1	4	2	3	0	1	2	4	3	4	3	1	2	1	0	1	2	5	4	rs16886792	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:76373002G>A	ENST00000447266.2	+	9	1240	c.762G>A	c.(760-762)acG>acA	p.T254T	SENP6_ENST00000370014.3_Silent_p.T254T|SENP6_ENST00000327284.8_Silent_p.T247T|SENP6_ENST00000370010.2_Silent_p.T247T	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	254					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)				TATTAAGAACGTCAATTCATC	0.353													G|||	71	0.0141773	0.053	0.0014	5008	,	,		17025	0.0		0.0	False		,,,				2504	0.0				p.T254T		Atlas-SNP	.											.	SENP6	189	.	0			c.G762A						PASS	.	G	,	190,3488		6,178,1655	108	102	104		741,762	-6.3	1	6	dbSNP_123	104	2,8180		0,2,4089	no	coding-synonymous,coding-synonymous	SENP6	NM_001100409.1,NM_015571.2	,	6,180,5744	AA,AG,GG		0.0244,5.1659,1.6189	,	247/1106,254/1113	76373002	192,11668	1839	4091	5930	SO:0001819	synonymous_variant	26054	exon9			AAGAACGTCAATT		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.762G>A	6.37:g.76373002G>A		88	0	0		114	57	0.5	NM_015571	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Silent	SNP	ENST00000447266.2	37	CCDS47454.1																																																																																			G|0.985;A|0.015	0.015	strong		0.353	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571		A	76373002	G	A	76373002	2	1	22	1	0	0	0	0	0	0	0	1	14065	1132	40	1		1	SENP6	6	76373002	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	350461	76373002	94742065	1511	4412											
PHIP	55023	hgsc.bcm.edu	37	chr6	79700648	79700648	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgttttcttttctcttctgaCctgtaagtctttatttcttc	4	24	4	9	0	5	1	0	1	5	0	7	1	5	1	1	0	0	2	1	0	2	10	rs149171291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:79700648C>T	ENST00000275034.4	-	20	2423	c.2256G>A	c.(2254-2256)agG>agA	p.R752R		NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	752					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)		TCTCTTCTGACCTGTAAGTCT	0.313													C|||	10	0.00199681	0.0068	0.0014	5008	,	,		17543	0.0		0.0	False		,,,				2504	0.0				p.R752R		Atlas-SNP	.											.	PHIP	177	.	0			c.G2256A						PASS	.	C		29,4377	35.2+/-66.4	0,29,2174	110	110	110		2256	-0.4	1	6	dbSNP_134	110	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	PHIP	NM_017934.5		0,30,6472	TT,TC,CC		0.0116,0.6582,0.2307		752/1822	79700648	30,12974	2203	4299	6502	SO:0001819	synonymous_variant	55023	exon20			TTCTGACCTGTAA	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.2256G>A	6.37:g.79700648C>T		243	1	0.00411523		220	101	0.459091	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000275034.4	37	CCDS4987.1																																																																																			C|0.997;T|0.003	0.003	strong		0.313	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2			T	79700648	C	T	79700648	2	4	22	1	0	0	0	0	0	0	0	1	11851	506	18	2		2	PHIP	6	79700648	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3327646	79700648	91414419	1512	4413											
PRSS35	167681	hgsc.bcm.edu	37	chr6	84233325	84233325	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcatttgaggcagatgctaaGatgatggtaaatacagtgtg	13	11	13	4	0	0	4	0	2	0	2	0	4	0	4	0	2	2	4	0	2	4	4	rs147168330	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:84233325G>A	ENST00000369700.3	+	2	342	c.165G>A	c.(163-165)aaG>aaA	p.K55K	PRSS35_ENST00000536636.1_Silent_p.K55K	NM_153362.2	NP_699193.2	Q8N3Z0	PRS35_HUMAN	protease, serine, 35	55						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)		CAGATGCTAAGATGATGGTAA	0.453													G|||	19	0.00379393	0.0144	0.0	5008	,	,		18836	0.0		0.0	False		,,,				2504	0.0				p.K55K		Atlas-SNP	.											.	PRSS35	60	.	0			c.G165A						PASS	.	G	,	32,4374	38.4+/-70.7	0,32,2171	129	127	128		165,165	2	0	6	dbSNP_134	128	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PRSS35	NM_001170423.1,NM_153362.2	,	0,32,6471	AA,AG,GG		0.0,0.7263,0.246	,	55/414,55/414	84233325	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	167681	exon2			TGCTAAGATGATG	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.165G>A	6.37:g.84233325G>A		209	0	0		198	84	0.424242	NM_153362	A8K7B3|Q9BQP6	Silent	SNP	ENST00000369700.3	37	CCDS4999.1																																																																																			G|0.997;A|0.003	0.003	strong		0.453	PRSS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041352.1	NM_153362		A	84233325	G	A	84233325	2	1	22	1	0	0	0	0	0	0	0	1	12636	933	33	2		2	PRSS35	6	84233325	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4532677	84233325	86881742	1513	4414											
SNAP91	9892	hgsc.bcm.edu	37	chr6	84303273	84303273	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtagtggtggtggcagcggcGgtggcagcagtagtggcagc	6	7	21	7	2	0	0	0	0	0	0	0	0	0	0	0	7	3	6	0	7	2	2	rs181491904	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:84303273G>A	ENST00000439399.2	-	18	1936	c.1620C>T	c.(1618-1620)acC>acT	p.T540T	SNAP91_ENST00000521743.1_Silent_p.T540T|SNAP91_ENST00000428679.2_Silent_p.T540T|SNAP91_ENST00000520302.1_Silent_p.T538T|SNAP91_ENST00000437520.1_Intron|SNAP91_ENST00000520213.1_Intron|SNAP91_ENST00000195649.6_Silent_p.T540T|SNAP91_ENST00000369694.2_Silent_p.T540T|SNAP91_ENST00000521485.1_Silent_p.T540T	NM_014841.2	NP_055656.1	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	540	Ala-rich.|Thr-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)		tggcagcggcggtggcagcag	0.577													G|||	20	0.00399361	0.0151	0.0	5008	,	,		15737	0.0		0.0	False		,,,				2504	0.0				p.T540T		Atlas-SNP	.											.	SNAP91	199	.	0			c.C1620T						PASS	.	G	,,,	20,4206		0,20,2093	15	21	19		1620,1614,,1620	2.3	0.1	6		19	1,8333		0,1,4166	no	coding-synonymous,coding-synonymous,intron,coding-synonymous	SNAP91	NM_001242792.1,NM_001242793.1,NM_001242794.1,NM_014841.2	,,,	0,21,6259	AA,AG,GG		0.012,0.4733,0.1672	,,,	540/908,538/878,,540/908	84303273	21,12539	2113	4167	6280	SO:0001819	synonymous_variant	9892	exon17			AGCGGCGGTGGCA	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.1620C>T	6.37:g.84303273G>A		96	0	0		105	57	0.542857	NM_001242792	A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	Silent	SNP	ENST00000439399.2	37	CCDS47455.1																																																																																			G|0.995;A|0.005	0.005	strong		0.577	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1			A	84303273	G	A	84303273	2	1	22	1	0	0	0	0	0	0	0	1	14848	1103	39	1		1	SNAP91	6	84303273	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	69948	84303273	86811794	1514	4415											
KIAA1009	22832	hgsc.bcm.edu	37	chr6	84856409	84856409	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttggccatttcttacctcTttctgtagaatttcttctcg	5	21	5	10	1	5	1	0	0	5	1	6	1	5	1	2	1	1	1	2	1	3	8	rs9449804	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:84856409T>C	ENST00000403245.3	-	25	3981	c.3867A>G	c.(3865-3867)aaA>aaG	p.K1289K	KIAA1009_ENST00000461137.1_5'UTR|KIAA1009_ENST00000257766.4_Silent_p.K1213K	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)		TTCTTACCTCTTTCTGTAGAA	0.308													T|||	454	0.090655	0.2973	0.036	5008	,	,		16911	0.006		0.0169	False		,,,				2504	0.0133				p.K1289K		Atlas-SNP	.											.	KIAA1009	119	.	0			c.A3867G						PASS	.	T		1113,3285		164,785,1250	32	32	32		3867	-4.6	0.9	6	dbSNP_119	32	131,8451		6,119,4166	no	coding-synonymous	KIAA1009	NM_014895.2		170,904,5416	CC,CT,TT		1.5265,25.307,9.584		1289/1404	84856409	1244,11736	2199	4291	6490	SO:0001819	synonymous_variant	22832	exon25			TACCTCTTTCTGT																												ENST00000403245.3:c.3867A>G	6.37:g.84856409T>C		65	0	0		54	25	0.462963	NM_014895		Silent	SNP	ENST00000403245.3	37	CCDS34494.2																																																																																			T|0.900;C|0.100	0.100	strong		0.308	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1			C	84856409	T	C	84856409	2	2	22	1	0	0	0	0	0	0	0	1	8212	1606	56	3		3	KIAA1009	6	84856409	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	553136	84856409	86258658	1515	4416											
KIAA1009	22832	hgsc.bcm.edu	37	chr6	84925636	84925636	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagctcacatttgttccaagAagtcctaggtacacaattta	13	13	6	9	0	1	1	1	0	0	1	3	1	3	1	2	1	2	3	2	1	7	7	rs9449840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:84925636A>C	ENST00000403245.3	-	4	291	c.177T>G	c.(175-177)ctT>ctG	p.L59L	KIAA1009_ENST00000257766.4_5'UTR	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)		TTGTTCCAAGAAGTCCTAGGT	0.328													C|||	366	0.0730831	0.2602	0.0245	5008	,	,		16242	0.002		0.001	False		,,,				2504	0.002				p.L59L		Atlas-SNP	.											.	KIAA1009	119	.	0			c.T177G						PASS	.	C		1020,3368		119,782,1293	37	36	36		177	-3	0	6	dbSNP_119	36	6,8568		0,6,4281	no	coding-synonymous	KIAA1009	NM_014895.2		119,788,5574	CC,CA,AA		0.07,23.2452,7.9154		59/1404	84925636	1026,11936	2194	4287	6481	SO:0001819	synonymous_variant	22832	exon4			TCCAAGAAGTCCT																												ENST00000403245.3:c.177T>G	6.37:g.84925636A>C		74	0	0		62	31	0.5	NM_014895		Silent	SNP	ENST00000403245.3	37	CCDS34494.2																																																																																			A|0.936;C|0.064	0.064	strong		0.328	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1			C	84925636	A	C	84925636	2	2	22	1	0	0	0	0	0	0	0	1	8212	233	9	5		5	KIAA1009	6	84925636	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	69227	84925636	86189431	1516	4417											
NT5E	4907	hgsc.bcm.edu	37	chr6	86195098	86195098	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagtttgatgaaagaggaaaCgtcatctcttcccatggaaa	14	10	10	7	1	2	3	1	2	1	1	4	6	3	5	1	2	1	1	1	2	3	2	rs35478984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:86195098C>T	ENST00000257770.3	+	4	946	c.897C>T	c.(895-897)aaC>aaT	p.N299N	NT5E_ENST00000369651.3_Silent_p.N299N	NM_002526.3	NP_002517.1	P21589	5NTD_HUMAN	5'-nucleotidase, ecto (CD73)	299					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)			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)	AAAGAGGAAACGTCATCTCTT	0.438													C|||	97	0.019369	0.0703	0.0058	5008	,	,		20130	0.0		0.0	False		,,,				2504	0.0				p.N299N	Melanoma(140;797 1765 2035 2752 18208)	Atlas-SNP	.											.	NT5E	56	.	0			c.C897T						PASS	.	C	,	287,4119	159.6+/-192.1	8,271,1924	151	136	141		897,897	-0.1	0.9	6	dbSNP_126	141	2,8598	3.0+/-9.4	0,2,4298	no	coding-synonymous,coding-synonymous	NT5E	NM_001204813.1,NM_002526.3	,	8,273,6222	TT,TC,CC		0.0233,6.5138,2.2221	,	299/525,299/575	86195098	289,12717	2203	4300	6503	SO:0001819	synonymous_variant	4907	exon4			AGGAAACGTCATC	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.897C>T	6.37:g.86195098C>T		109	0	0		109	47	0.431193	NM_001204813	B3KQI8|O75520|Q5W116	Silent	SNP	ENST00000257770.3	37	CCDS5002.1	44	0.020146520146520148	42	0.08536585365853659	2	0.0055248618784530384	0	0.0	0	0.0	C	6.940	0.543124	0.13250	0.065138	2.33E-4	ENSG00000135318	ENST00000416334	.	.	.	5.36	-0.104	0.13605	.	.	.	.	.	T	0.44561	0.1299	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42732	-0.9434	4	.	.	.	-7.7038	11.3536	0.49602	0.0:0.1944:0.0:0.8056	rs35478984	.	.	.	M	64	.	.	T	+	2	0	NT5E	86251817	0.963000	0.33076	0.937000	0.37676	0.836000	0.47400	0.030000	0.13688	-0.211000	0.10124	-1.744000	0.00683	ACG	C|0.977;T|0.023	0.023	strong		0.438	NT5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041388.1			T	86195098	C	T	86195098	2	4	22	1	0	0	0	0	0	0	0	1	10702	535	19	1		1	NT5E	6	86195098	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1269462	86195098	84919969	1517	4418											
RARS2	57038	hgsc.bcm.edu	37	chr6	88229953	88229953	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttggaatacttgctgaaaatGctttttttgtcctttatctg	8	20	7	6	0	1	1	0	1	1	0	2	2	2	2	1	1	3	2	1	1	5	8	rs138460258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:88229953G>A	ENST00000369536.5	-	13	1102	c.1057C>T	c.(1057-1059)Cat>Tat	p.H353Y	RARS2_ENST00000497828.1_5'Flank	NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	353					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)		TGCTGAAAATGCTTTTTTTGT	0.333													G|||	3	0.000599042	0.0015	0.0014	5008	,	,		17566	0.0		0.0	False		,,,				2504	0.0				p.H353Y		Atlas-SNP	.											.	RARS2	61	.	0			c.C1057T						PASS	.	G	TYR/HIS	1,4405	2.1+/-5.4	0,1,2202	203	194	197		1057	5.8	1	6	dbSNP_134	197	0,8600		0,0,4300	no	missense	RARS2	NM_020320.3	83	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	353/579	88229953	1,13005	2203	4300	6503	SO:0001583	missense	57038	exon13			GAAAATGCTTTTT	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.1057C>T	6.37:g.88229953G>A	ENSP00000358549:p.His353Tyr	78	0	0		52	27	0.519231	NM_020320	B2RDT7|Q96FU5|Q9H8K8	Missense_Mutation	SNP	ENST00000369536.5	37	CCDS5011.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	25.9	4.688534	0.88639	2.27E-4	0.0	ENSG00000146282	ENST00000369536	T	0.62232	0.04	5.76	5.76	0.90799	Arginyl-tRNA synthetase, class Ia, core (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	T	0.79701	0.4491	M	0.84082	2.675	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.81291	-0.0999	10	0.72032	D	0.01	.	19.975	0.97300	0.0:0.0:1.0:0.0	.	353	Q5T160	SYRM_HUMAN	Y	353	ENSP00000358549:H353Y	ENSP00000358549:H353Y	H	-	1	0	RARS2	88286672	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.939000	0.92951	2.724000	0.93272	0.585000	0.79938	CAT	G|1.000;A|0.000	0.000	strong		0.333	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320		A	88229953	G	A	88229953	3	1	22	1	0	0	0	0	1	0	0	0	13074	1319	46	2	711	2	RARS2	6	88229953	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2034855	88229953	82885114	1518	4419											
RARS2	57038	hgsc.bcm.edu	37	chr6	88279282	88279282	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgatgtgatcaagttttcTggtggaagattcaacactct	11	15	9	6	0	4	3	2	2	2	1	4	4	4	4	0	2	1	1	0	2	3	4	rs7748563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:88279282T>C	ENST00000369536.5	-	2	108	c.63A>G	c.(61-63)ccA>ccG	p.P21P		NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	21					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)		TCAAGTTTTCTGGTGGAAGAT	0.313													T|||	68	0.0135783	0.0477	0.0058	5008	,	,		18264	0.0		0.001	False		,,,				2504	0.0				p.P21P		Atlas-SNP	.											.	RARS2	61	.	0			c.A63G						PASS	.	T		160,4246	107.8+/-146.2	5,150,2048	110	113	112		63	2.8	1	6	dbSNP_116	112	0,8600		0,0,4300	no	coding-synonymous	RARS2	NM_020320.3		5,150,6348	CC,CT,TT		0.0,3.6314,1.2302		21/579	88279282	160,12846	2203	4300	6503	SO:0001819	synonymous_variant	57038	exon2			GTTTTCTGGTGGA	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.63A>G	6.37:g.88279282T>C		137	0	0		157	71	0.452229	NM_020320	B2RDT7|Q96FU5|Q9H8K8	Silent	SNP	ENST00000369536.5	37	CCDS5011.1	23	0.010531135531135532	20	0.04065040650406504	3	0.008287292817679558	0	0.0	0	0.0	T	14.17	2.456129	0.43634	0.036314	0.0	ENSG00000146282	ENST00000369523	.	.	.	5.2	2.75	0.32379	.	.	.	.	.	T	0.41026	0.1141	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33137	-0.9880	5	0.39692	T	0.17	.	5.3844	0.16211	0.0:0.0915:0.177:0.7315	rs7748563;rs7748563	.	.	.	G	9	.	ENSP00000358536:R9G	R	-	1	2	RARS2	88336001	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	0.869000	0.27996	0.374000	0.24650	0.528000	0.53228	AGA	T|0.987;C|0.013	0.013	strong		0.313	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320		C	88279282	T	C	88279282	2	2	22	1	0	0	0	0	0	0	0	1	13074	1567	55	3		3	RARS2	6	88279282	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	49329	88279282	82835785	1519	4420											
AKIRIN2	55122	hgsc.bcm.edu	37	chr6	88385579	88385579	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcaaaggtgaaatacttacaGctagcaggctgttctccata	13	11	8	9	0	2	1	1	1	1	0	3	1	2	1	1	2	4	4	1	2	6	5	rs63749091	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:88385579G>A	ENST00000257787.5	-	4	1124	c.600C>T	c.(598-600)agC>agT	p.S200S		NM_018064.3	NP_060534.1	Q53H80	AKIR2_HUMAN	akirin 2	200					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						AATACTTACAGCTAGCAGGCT	0.303													A|||	164	0.0327476	0.1165	0.0144	5008	,	,		19800	0.0		0.0	False		,,,				2504	0.0				p.S200S		Atlas-SNP	.											.	AKIRIN2	13	.	0			c.C600T						PASS	.	A		466,3938	782.5+/-414.6	26,414,1762	71	69	70		600	4.6	1	6	dbSNP_129	70	1,8599	818.3+/-406.9	0,1,4299	yes	coding-synonymous-near-splice	AKIRIN2	NM_018064.3		26,415,6061	AA,AG,GG		0.0116,10.5813,3.5912		200/204	88385579	467,12537	2202	4300	6502	SO:0001630	splice_region_variant	55122	exon4			CTTACAGCTAGCA	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.601+1C>T	6.37:g.88385579G>A		107	0	0		133	61	0.458647	NM_018064	Q9BQB1	Silent	SNP	ENST00000257787.5	37	CCDS5013.1																																																																																			G|0.968;A|0.032	0.032	strong		0.303	AKIRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041455.1	NM_018064	Silent	A	88385579	G	A	88385579	5	1	22	1	0	0	0	0	0	0	1	0	462	985	34	2	19	2	AKIRIN2	6	88385579	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	106297	88385579	82729488	1520	4421											
MDN1	23195	hgsc.bcm.edu	37	chr6	90424458	90424458	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tctccatgaacaggatccatCgagaggaaaagtctagaaaa	17	7	9	8	1	2	3	0	1	2	2	5	6	3	5	2	2	1	0	2	2	6	1	rs114422841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:90424458C>T	ENST00000369393.3	-	46	6988	c.6873G>A	c.(6871-6873)tcG>tcA	p.S2291S	MDN1_ENST00000428876.1_Silent_p.S2291S			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	2291					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)		CAGGATCCATCGAGAGGAAAA	0.433													C|||	13	0.00259585	0.0083	0.0	5008	,	,		20221	0.0		0.001	False		,,,				2504	0.001				p.S2291S		Atlas-SNP	.											.	MDN1	478	.	0			c.G6873A						PASS	.	C		54,4352	52.3+/-87.9	0,54,2149	67	64	65		6873	-4	1	6	dbSNP_132	65	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	MDN1	NM_014611.1		0,56,6447	TT,TC,CC		0.0233,1.2256,0.4306		2291/5597	90424458	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	23195	exon46			ATCCATCGAGAGG	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.6873G>A	6.37:g.90424458C>T		71	0	0		64	35	0.546875	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	37	CCDS5024.1																																																																																			C|0.996;T|0.004	0.004	strong		0.433	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			T	90424458	C	T	90424458	2	4	22	1	0	0	0	0	0	0	0	1	9424	871	31	1		1	MDN1	6	90424458	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2038879	90424458	80690609	1521	4422											
MDN1	23195	hgsc.bcm.edu	37	chr6	90461235	90461235	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcatctattgtaggctcctTgtctcccaccgcaatccagt	7	13	6	15	1	3	0	1	0	2	0	6	0	5	0	4	1	0	3	4	1	3	4	rs115558420	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:90461235T>C	ENST00000369393.3	-	23	3257	c.3142A>G	c.(3142-3144)Aag>Gag	p.K1048E	MDN1_ENST00000428876.1_Missense_Mutation_p.K1048E			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	1048					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)		GTAGGCTCCTTGTCTCCCACC	0.478													T|||	9	0.00179712	0.0068	0.0	5008	,	,		18332	0.0		0.0	False		,,,				2504	0.0				p.K1048E		Atlas-SNP	.											MDN1,NS,carcinoma,+2,1	MDN1	478	1	0			c.A3142G						PASS	.	T	GLU/LYS	41,4365	44.6+/-78.6	0,41,2162	155	133	140		3142	4.5	1	6	dbSNP_132	140	0,8600		0,0,4300	yes	missense	MDN1	NM_014611.1	56	0,41,6462	CC,CT,TT		0.0,0.9305,0.3152	possibly-damaging	1048/5597	90461235	41,12965	2203	4300	6503	SO:0001583	missense	23195	exon23			GCTCCTTGTCTCC	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.3142A>G	6.37:g.90461235T>C	ENSP00000358400:p.Lys1048Glu	165	0	0		186	90	0.483871	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	T	15.19	2.759315	0.49468	0.009305	0.0	ENSG00000112159	ENST00000369393;ENST00000428876;ENST00000439638	T;T;T	0.39592	1.07;1.07;1.07	5.71	4.48	0.54585	.	0.162096	0.53938	D	0.000057	T	0.13200	0.0320	N	0.22421	0.69	0.38581	D	0.950177	B;B	0.19331	0.035;0.003	B;B	0.15484	0.008;0.013	T	0.06409	-1.0828	10	0.14656	T	0.56	.	12.5357	0.56140	0.0:0.0:0.1389:0.8611	.	975;1048	Q5T795;Q9NU22	.;MDN1_HUMAN	E	1048;1048;975	ENSP00000358400:K1048E;ENSP00000413970:K1048E;ENSP00000409664:K975E	ENSP00000358400:K1048E	K	-	1	0	MDN1	90517956	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	3.063000	0.49978	2.172000	0.68678	0.533000	0.62120	AAG	T|0.997;C|0.003	0.003	strong		0.478	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			C	90461235	T	C	90461235	3	2	22	1	0	0	0	0	1	0	0	0	9424	1821	63	3	13968	3	MDN1	6	90461235	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	36777	90461235	80653832	1522	4423											
EPHA7	2045	hgsc.bcm.edu	37	chr6	93982100	93982100	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaaagctcgacactccgctgCagtactctctccttcattac	9	11	6	15	2	2	0	1	0	1	0	6	2	4	0	2	0	4	4	2	0	3	3	rs34302170	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:93982100C>T	ENST00000369303.4	-	6	1549	c.1365G>A	c.(1363-1365)ctG>ctA	p.L455L		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	455	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		CACTCCGCTGCAGTACTCTCT	0.438													C|||	206	0.0411342	0.152	0.0029	5008	,	,		18429	0.0		0.003	False		,,,				2504	0.0				p.L455L		Atlas-SNP	.											.	EPHA7	251	.	0			c.G1365A						PASS	.	C		517,3889	237.7+/-249.4	30,457,1716	204	194	197		1365	5.7	1	6	dbSNP_126	197	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	EPHA7	NM_004440.3		30,464,6009	TT,TC,CC		0.0814,11.734,4.0289		455/999	93982100	524,12482	2203	4300	6503	SO:0001819	synonymous_variant	2045	exon6			CCGCTGCAGTACT	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.1365G>A	6.37:g.93982100C>T		224	0	0		174	92	0.528736	NM_004440	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Silent	SNP	ENST00000369303.4	37	CCDS5031.1																																																																																			C|0.963;T|0.037	0.037	strong		0.438	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1			T	93982100	C	T	93982100	2	4	22	1	0	0	0	0	0	0	0	1	5174	697	25	2		2	EPHA7	6	93982100	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3520865	93982100	77132967	1523	4424											
KLHL32	114792	hgsc.bcm.edu	37	chr6	97533193	97533193	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aagagcgaccgcctgacctcCctgagtgaagagcagatctg	11	6	12	12	2	1	6	0	3	1	3	2	7	2	6	4	0	2	1	4	0	2	0	rs551403903		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:97533193C>A	ENST00000369261.4	+	6	966	c.603C>A	c.(601-603)tcC>tcA	p.S201S	KLHL32_ENST00000536676.1_Silent_p.S165S|KLHL32_ENST00000544166.1_Intron|KLHL32_ENST00000539200.1_Silent_p.S132S	NM_052904.3	NP_443136.2	Q96NJ5	KLH32_HUMAN	kelch-like family member 32	201										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)		GCCTGACCTCCCTGAGTGAAG	0.527																																					p.S201S		Atlas-SNP	.											KLHL32,mouth,carcinoma,+1,1	KLHL32	85	1	0			c.C603A						PASS	.						57	57	57					6																	97533193		2203	4300	6503	SO:0001819	synonymous_variant	114792	exon6			GACCTCCCTGAGT	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.603C>A	6.37:g.97533193C>A		52	0	0		83	4	0.0481928	NM_052904	B7Z346|B7Z4E2|E1P528|Q5THT0|Q96PY7	Silent	SNP	ENST00000369261.4	37	CCDS5038.1																																																																																			.	.	none		0.527	KLHL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041570.1	NM_052904		A	97533193	C	A	97533193	2	1	22	1	0	0	0	0	0	0	0	1	8395	610	22	4		4	KLHL32	6	97533193	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3551093	97533193	73581874	1524	4425											
FBXL4	26235	hgsc.bcm.edu	37	chr6	99374436	99374436	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctccgggatgataggtttcTagaacatgtacagctgtagg	10	11	13	7	1	1	2	0	1	1	1	2	3	2	3	1	3	3	5	1	3	5	5	rs17058965	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:99374436T>C	ENST00000369244.2	-	4	857	c.429A>G	c.(427-429)ctA>ctG	p.L143L	FBXL4_ENST00000229971.1_Silent_p.L143L	NM_001278716.1	NP_001265645.1	Q9UKA2	FBXL4_HUMAN	F-box and leucine-rich repeat protein 4	143					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)		GATAGGTTTCTAGAACATGTA	0.418													T|||	21	0.00419329	0.0151	0.0014	5008	,	,		19281	0.0		0.0	False		,,,				2504	0.0				p.L143L		Atlas-SNP	.											.	FBXL4	54	.	0			c.A429G						PASS	.	T		59,4347	57.4+/-93.9	0,59,2144	93	82	86		429	1.5	1	6	dbSNP_123	86	0,8600		0,0,4300	no	coding-synonymous	FBXL4	NM_012160.3		0,59,6444	CC,CT,TT		0.0,1.3391,0.4536		143/622	99374436	59,12947	2203	4300	6503	SO:0001819	synonymous_variant	26235	exon3			GGTTTCTAGAACA	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.429A>G	6.37:g.99374436T>C		152	0	0		157	78	0.496815	NM_012160	B2R7Q5|E1P530|O95919|Q5BJH0|Q9UJU0	Silent	SNP	ENST00000369244.2	37	CCDS5041.1																																																																																			T|0.996;C|0.004	0.004	strong		0.418	FBXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041587.2			C	99374436	T	C	99374436	2	2	22	1	0	0	0	0	0	0	0	1	5729	1509	53	3		3	FBXL4	6	99374436	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1841243	99374436	71740631	1525	4426											
SCML4	256380	hgsc.bcm.edu	37	chr6	108029133	108029133	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcggcgtccttcacaaaccaCaccacgtcctccacagtcca	10	7	5	19	3	1	0	1	0	0	0	6	0	5	0	6	1	1	0	6	1	1	1	rs61742583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:108029133C>T	ENST00000369020.3	-	7	1301	c.1056G>A	c.(1054-1056)gtG>gtA	p.V352V	SCML4_ENST00000369022.2_Silent_p.V294V|SCML4_ENST00000369025.2_Silent_p.V110V	NM_198081.3	NP_932347.2	Q8N228	SCML4_HUMAN	sex comb on midleg-like 4 (Drosophila)	352	SAM.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(1)	25		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)		TCACAAACCACACCACGTCCT	0.627													C|||	64	0.0127796	0.0477	0.0014	5008	,	,		18965	0.0		0.0	False		,,,				2504	0.0				p.V352V		Atlas-SNP	.											.	SCML4	65	.	0			c.G1056A						PASS	.	C		75,1309		0,75,617	54	63	60		1056	2.7	0.9	6	dbSNP_129	60	0,3182		0,0,1591	no	coding-synonymous	SCML4	NM_198081.3		0,75,2208	TT,TC,CC		0.0,5.4191,1.6426		352/415	108029133	75,4491	692	1591	2283	SO:0001819	synonymous_variant	256380	exon7			AAACCACACCACG		CCDS5060.2, CCDS69163.1, CCDS75500.1	6q21	2013-01-10			ENSG00000146285	ENSG00000146285		"Sterile alpha motif (SAM) domain containing"	21397	protein-coding gene	gene with protein product							Standard	NM_001286409		Approved	dJ47M23.1	uc010kdf.3	Q8N228	OTTHUMG00000015313	ENST00000369020.3:c.1056G>A	6.37:g.108029133C>T		138	0	0		171	78	0.45614	NM_198081	B0QZ10|B0QZ11|B7ZBX3|Q5JXD0|Q5T0T6|Q8IYY6	Silent	SNP	ENST00000369020.3	37	CCDS5060.2																																																																																			C|0.991;T|0.009	0.009	strong		0.627	SCML4-005	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000041700.3	XM_171128		T	108029133	C	T	108029133	2	4	22	1	0	0	0	0	0	0	0	1	13926	465	17	2		2	SCML4	6	108029133	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	8654697	108029133	63085934	1526	4427											
SEC63	11231	hgsc.bcm.edu	37	chr6	108214734	108214735	+	In_Frame_Ins	INS	-	-	GTA																															gtttctgttgctttgactgtINSggtaatagcacaggtgtagg																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:108214734_108214735insGTA	ENST00000369002.4	-	16	1804_1805	c.1625_1626insTAC	c.(1624-1626)cca>ccTACa	p.542_543insT		NM_007214.4	NP_009145.1	Q9UGP8	SEC63_HUMAN	SEC63 homolog (S. cerevisiae)	542					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.P542Q(1)		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)		GCTTTGACTGTGGTAATAGCAC	0.322																																					p.P542delinsPT		Pindel,Atlas-Indel	.											.	SEC63	79	.	1	Substitution - Missense(1)	lung(1)	c.1626_1627insTAC						PASS	.			6,4258		0,6,2126						-3.9	0.9			138	0,8254		0,0,4127	no	coding	SEC63	NM_007214.4		0,6,6253	A1A1,A1R,RR		0.0,0.1407,0.0479				6,12512				SO:0001652	inframe_insertion	11231	exon16			.	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.1625_1626insTAC	6.37:g.108214734_108214735insGTA	ENSP00000357998:p.Pro542_Gln543insThr	104	0	.		110	39	0.355	NM_007214	O95380|Q5THN4|Q86VS9|Q8IWL0|Q9NTE0	In_Frame_Ins	INS	ENST00000369002.4	37	CCDS5061.1																																																																																			.	.	none		0.322	SEC63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041705.4	NM_007214		GTA	108214735	-	GTA	108214734	7	5	22	1	0	1	1	0	0	0	0	0	14020	1683	59	0	680	0	SEC63	6	108214734	In_Frame_Ins	INS	-	TCGA-G8-6324-01A-11D-2210-10	185601	108214734	62900333	1527	4428											
SMPD2	6610	hgsc.bcm.edu	37	chr6	109764875	109764877	+	In_Frame_Del	DEL	GGA	GGA	-																															tgctgtgtgtcctggcggctGgaggaggggccggggaagct																								rs142982624|rs370460899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:109764875_109764877delGGA	ENST00000258052.3	+	10	1398_1400	c.1039_1041delGGA	c.(1039-1041)ggadel	p.G349del	PPIL6_ENST00000440797.2_5'Flank|PPIL6_ENST00000424445.2_5'Flank|PPIL6_ENST00000521072.2_5'Flank	NM_003080.2	NP_003071.2	O60906	NSMA_HUMAN	sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase)	349					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)		CCTGGCGGCTGGAGGAGGGGCCG	0.635														223	0.0445288	0.1573	0.0159	5008	,	,		16679	0.0		0.004	False		,,,				2504	0.0				p.346_347del		Pindel,Atlas-Indel	.											.	SMPD2	25	.	0			c.1038_1040del						PASS	.			602,3662		46,510,1576						-8.7	0		dbSNP_134	49	14,8240		3,8,4116	no	coding	SMPD2	NM_003080.2		49,518,5692	A1A1,A1R,RR		0.1696,14.1182,4.9209				616,11902				SO:0001651	inframe_deletion	6610	exon10			.	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.1039_1041delGGA	6.37:g.109764878_109764880delGGA	ENSP00000258052:p.Gly349del	123	0	.		102	34	0.333	NM_003080	Q5TED1|Q9BWR3	In_Frame_Del	DEL	ENST00000258052.3	37	CCDS5075.1																																																																																			GGA|0.957;-|0.043	0.043	strong		0.635	SMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041755.1			-	109764877	GGA	-	109764875	7	5	22	1	0	1	0	1	0	0	0	0	14820	1349	47	0	1077	0	SMPD2	6	109764875	In_Frame_Del	DEL	GGA	TCGA-G8-6324-01A-11D-2210-10	1550141	109764875	61350192	1528	4429											
ZBTB24	9841	hgsc.bcm.edu	37	chr6	109787596	109787596	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aatgctgctggcatctgaagCatgcttctccttgctatgaa	9	13	9	10	0	2	2	0	2	2	0	3	2	2	2	1	1	5	6	1	1	4	3	rs2232448	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:109787596C>T	ENST00000230122.3	-	7	1719	c.1552G>A	c.(1552-1554)Gct>Act	p.A518T	MICAL1_ENST00000368952.4_5'Flank	NM_001164313.1|NM_014797.2	NP_001157785.1|NP_055612.2	O43167	ZBT24_HUMAN	zinc finger and BTB domain containing 24	518			A -> T (in dbSNP:rs2232448).		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)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	22		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;0.0154)|all cancers(137;0.0216)|OV - Ovarian serous cystadenocarcinoma(136;0.0242)|BRCA - Breast invasive adenocarcinoma(108;0.059)		GCATCTGAAGCATGCTTCTCC	0.463													C|||	418	0.0834665	0.2776	0.0346	5008	,	,		19894	0.0		0.0099	False		,,,				2504	0.0174				p.A518T		Atlas-SNP	.											.	ZBTB24	64	.	0			c.G1552A						PASS	.	C	THR/ALA	1041,3365	383.0+/-324.7	128,785,1290	120	111	114		1552	0.9	0	6	dbSNP_98	114	129,8471	64.9+/-127.2	0,129,4171	yes	missense	ZBTB24	NM_014797.2	58	128,914,5461	TT,TC,CC		1.5,23.6269,8.9958	benign	518/698	109787596	1170,11836	2203	4300	6503	SO:0001583	missense	9841	exon7			CTGAAGCATGCTT	AB007901	CCDS34509.1	6q21	2014-09-17	2004-04-15	2004-04-16	ENSG00000112365	ENSG00000112365		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	21143	protein-coding gene	gene with protein product	"POZ (BTB) and AT hook containing zinc finger 2"	614064	"zinc finger protein 450"	ZNF450		9455477	Standard	NM_014797		Approved	KIAA0441, BIF1, PATZ2	uc003ptl.1	O43167	OTTHUMG00000015349	ENST00000230122.3:c.1552G>A	6.37:g.109787596C>T	ENSP00000230122:p.Ala518Thr	112	0	0		132	77	0.583333	NM_014797	Q17RC6|Q5TED5|Q8N455	Missense_Mutation	SNP	ENST00000230122.3	37	CCDS34509.1	150	0.06868131868131869	131	0.266260162601626	14	0.03867403314917127	0	0.0	5	0.006596306068601583	C	5.706	0.314802	0.10789	0.236269	0.015	ENSG00000112365	ENST00000230122	T	0.11277	2.79	6.06	0.896	0.19253	.	1.043490	0.07456	N	0.899772	T	0.01189	0.0039	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.47420	-0.9119	9	0.62326	D	0.03	0.2747	0.4792	0.00545	0.2407:0.3331:0.1937:0.2325	rs2232448;rs52798886;rs57567548;rs2232448	518	O43167	ZBT24_HUMAN	T	518	ENSP00000230122:A518T	ENSP00000230122:A518T	A	-	1	0	ZBTB24	109894289	0.000000	0.05858	0.000000	0.03702	0.170000	0.22686	0.142000	0.16096	0.444000	0.26612	0.655000	0.94253	GCT	C|0.918;T|0.082	0.082	strong		0.463	ZBTB24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041758.1	NM_014797		T	109787596	C	T	109787596	3	4	22	1	0	0	0	0	1	0	0	0	17546	710	25	2	545	2	ZBTB24	6	109787596	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	22721	109787596	61327471	1529	4430											
RPF2	84154	hgsc.bcm.edu	37	chr6	111310252	111310252	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgcactgaaaaaaccatacGgtgtactatataaaaagtaa	20	9	6	6	1	0	1	0	1	0	0	0	1	0	1	1	1	4	3	1	1	11	6	rs6909298	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:111310252G>A	ENST00000441448.2	+	3	270	c.178G>A	c.(178-180)Ggt>Agt	p.G60S		NM_032194.1	NP_115570.1	Q9H7B2	RPF2_HUMAN	ribosome production factor 2 homolog (S. cerevisiae)	60	Brix. {ECO:0000255|PROSITE- ProRule:PRU00034}.		G -> S (in dbSNP:rs6909298).			nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|ovary(2)	7						AAAACCATACGGTGTACTATA	0.254													G|||	113	0.0225639	0.0809	0.0086	5008	,	,		15215	0.0		0.0	False		,,,				2504	0.0				p.G60S		Atlas-SNP	.											.	RPF2	26	.	0			c.G178A						PASS	.	G	SER/GLY	308,4064	152.2+/-185.9	17,274,1895	41	44	43		178	3.1	0.9	6	dbSNP_116	43	0,8588		0,0,4294	yes	missense	RPF2	NM_032194.1	56	17,274,6189	AA,AG,GG		0.0,7.0448,2.3765	benign	60/307	111310252	308,12652	2186	4294	6480	SO:0001583	missense	84154	exon3			CCATACGGTGTAC	AK024740	CCDS5088.1	6q21	2009-09-25	2009-09-25	2009-09-25	ENSG00000197498	ENSG00000197498			20870	protein-coding gene	gene with protein product	"ribosomal processing factor 2 homolog (S. cerevisiae)"		"brix domain containing 1"	BXDC1		12048200	Standard	NM_032194		Approved	FLJ21087, bA397G5.4	uc003pun.3	Q9H7B2	OTTHUMG00000015368	ENST00000441448.2:c.178G>A	6.37:g.111310252G>A	ENSP00000402338:p.Gly60Ser	113	0	0		133	66	0.496241	NM_032194	Q5VXN1|Q8N4A1	Missense_Mutation	SNP	ENST00000441448.2	37	CCDS5088.1	41	0.018772893772893772	41	0.08333333333333333	0	0.0	0	0.0	0	0.0	g	6.952	0.545509	0.13312	0.070448	0.0	ENSG00000197498	ENST00000441448;ENST00000368864;ENST00000425871	T;T;T	0.18960	2.18;2.18;2.18	4.92	3.11	0.35812	Brix domain (3);	0.105052	0.64402	D	0.000005	T	0.02380	0.0073	N	0.00765	-1.205	0.36277	D	0.855568	B	0.06786	0.001	B	0.10450	0.005	T	0.27297	-1.0078	10	0.33940	T	0.23	-35.436	11.9222	0.52797	0.1536:0.0:0.8463:0.0	rs6909298;rs52791590;rs6909298	60	Q9H7B2	RPF2_HUMAN	S	60;21;27	ENSP00000402338:G60S;ENSP00000357857:G21S;ENSP00000414026:G27S	ENSP00000357857:G21S	G	+	1	0	RPF2	111416945	1.000000	0.71417	0.914000	0.36105	0.019000	0.09904	4.189000	0.58358	1.209000	0.43321	-0.448000	0.05591	GGT	G|0.977;A|0.023	0.023	strong		0.254	RPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041813.2	NM_032194		A	111310252	G	A	111310252	3	1	22	1	0	0	0	0	1	0	0	0	13562	1116	39	1	188	1	RPF2	6	111310252	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1522656	111310252	59804815	1530	4431											
REV3L	5980	hgsc.bcm.edu	37	chr6	111695304	111695304	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgtctttgcaatgcaaaaaAttaggggtatatgcttggtc	11	14	10	6	0	1	0	0	0	1	0	2	0	1	0	0	3	3	4	0	3	7	5	rs3218589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:111695304A>G	ENST00000358835.3	-	14	4708	c.4254T>C	c.(4252-4254)aaT>aaC	p.N1418N	REV3L_ENST00000368805.1_Silent_p.N1418N|REV3L_ENST00000435970.1_Silent_p.N1340N|REV3L_ENST00000368802.3_Silent_p.N1418N			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	1418					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)		AATGCAAAAAATTAGGGGTAT	0.388								DNA polymerases (catalytic subunits)					A|||	6	0.00119808	0.0045	0.0	5008	,	,		19794	0.0		0.0	False		,,,				2504	0.0				p.N1418N		Atlas-SNP	.											.	REV3L	386	.	0			c.T4254C						PASS	.	A		18,4388	25.3+/-52.1	0,18,2185	149	133	138		4254	3.7	1	6	dbSNP_106	138	0,8600		0,0,4300	no	coding-synonymous	REV3L	NM_002912.3		0,18,6485	GG,GA,AA		0.0,0.4085,0.1384		1418/3131	111695304	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	5980	exon13			CAAAAAATTAGGG	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.4254T>C	6.37:g.111695304A>G		122	0	0		147	76	0.517007	NM_002912	O43214|Q5TC33	Silent	SNP	ENST00000358835.3	37	CCDS5091.2																																																																																			A|0.999;G|0.001	0.001	strong		0.388	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		G	111695304	A	G	111695304	2	3	22	1	0	0	0	0	0	0	0	1	13255	98	4	3		3	REV3L	6	111695304	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	385052	111695304	59419763	1531	4432											
LAMA4	3910	hgsc.bcm.edu	37	chr6	112513025	112513025	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caggtgcttccaatgagtaaGgggtttccatagtaaccggg	10	10	13	8	1	0	1	0	1	0	0	2	1	2	1	3	4	2	4	3	4	4	5	rs61742228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:112513025G>A	ENST00000230538.7	-	6	928	c.531C>T	c.(529-531)ccC>ccT	p.P177P	LAMA4_ENST00000389463.4_Silent_p.P177P|LAMA4_ENST00000522006.1_Silent_p.P177P|LAMA4_ENST00000524032.1_5'UTR|LAMA4_ENST00000424408.2_Silent_p.P177P	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	177	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				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)		CAATGAGTAAGGGGTTTCCAT	0.393													G|||	60	0.0119808	0.0446	0.0014	5008	,	,		21553	0.0		0.0	False		,,,				2504	0.0				p.P177P		Atlas-SNP	.											.	LAMA4	227	.	0			c.C531T						PASS	.	G	,,	188,4218	109.5+/-147.8	8,172,2023	68	63	64		531,531,531	4	1	6	dbSNP_129	64	2,8598		0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	LAMA4	NM_001105206.1,NM_001105207.1,NM_002290.3	,,	8,174,6321	AA,AG,GG		0.0233,4.2669,1.4609	,,	177/1824,177/1817,177/1817	112513025	190,12816	2203	4300	6503	SO:0001819	synonymous_variant	3910	exon6			GAGTAAGGGGTTT		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.531C>T	6.37:g.112513025G>A		97	0	0		100	51	0.51	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Silent	SNP	ENST00000230538.7	37	CCDS43491.1																																																																																			G|0.985;A|0.015	0.015	strong		0.393	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206		A	112513025	G	A	112513025	2	1	22	1	0	0	0	0	0	0	0	1	8617	987	35	2		2	LAMA4	6	112513025	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	817721	112513025	58602042	1532	4433											
DSE	29940	hgsc.bcm.edu	37	chr6	116720466	116720466	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtttttcatatatttgctttGctttgtgtcagcctacatca	7	20	6	8	0	3	0	3	0	0	0	3	0	3	0	1	0	4	3	1	0	3	8	rs76186865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:116720466G>T	ENST00000331677.3	+	3	497	c.53G>T	c.(52-54)tGc>tTc	p.C18F	DSE_ENST00000452085.3_Missense_Mutation_p.C18F|DSE_ENST00000540275.1_3'UTR|DSE_ENST00000359564.2_Missense_Mutation_p.C18F|DSE_ENST00000537543.1_Missense_Mutation_p.C37F			Q9UL01	DSE_HUMAN	dermatan sulfate epimerase	18					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)		TATTTGCTTTGCTTTGTGTCA	0.498													G|||	175	0.0349441	0.1263	0.0058	5008	,	,		17864	0.0		0.004	False		,,,				2504	0.0				p.C18F		Atlas-SNP	.											.	DSE	98	.	0			c.G53T						PASS	.	G	PHE/CYS,PHE/CYS	409,3997	201.1+/-224.2	28,353,1822	78	72	74		53,53	4.8	0.1	6	dbSNP_131	74	23,8577	16.0+/-53.3	1,21,4278	yes	missense,missense	DSE	NM_001080976.1,NM_013352.2	205,205	29,374,6100	TT,TG,GG		0.2674,9.2828,3.3215	benign,benign	18/959,18/959	116720466	432,12574	2203	4300	6503	SO:0001583	missense	29940	exon2			TGCTTTGCTTTGT	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.53G>T	6.37:g.116720466G>T	ENSP00000332151:p.Cys18Phe	100	0	0		78	34	0.435897	NM_001080976	Q5R3K6	Missense_Mutation	SNP	ENST00000331677.3	37	CCDS5107.1	70	0.03205128205128205	67	0.13617886178861788	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	7.264	0.605736	0.14002	0.092828	0.002674	ENSG00000111817	ENST00000430252;ENST00000452085;ENST00000537543;ENST00000331677;ENST00000359564	T;T;T;T;T	0.22336	1.96;1.96;1.96;1.96;1.96	5.65	4.76	0.60689	.	0.151973	0.64402	D	0.000006	T	0.10766	0.0263	L	0.36672	1.1	0.44373	D	0.997279	B;B	0.18968	0.032;0.013	B;B	0.18561	0.022;0.009	T	0.02424	-1.1161	10	0.62326	D	0.03	-6.9295	15.1889	0.73028	0.0684:0.0:0.9316:0.0	.	37;18	B7Z765;Q9UL01	.;DSE_HUMAN	F	18;18;37;18;18	ENSP00000397597:C18F;ENSP00000404049:C18F;ENSP00000441152:C37F;ENSP00000332151:C18F;ENSP00000352567:C18F	ENSP00000332151:C18F	C	+	2	0	DSE	116827159	1.000000	0.71417	0.104000	0.21259	0.051000	0.14879	5.884000	0.69729	2.941000	0.99782	0.655000	0.94253	TGC	G|0.970;T|0.030	0.030	strong		0.498	DSE-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041940.2	NM_013352		T	116720466	G	T	116720466	3	4	22	1	0	0	0	0	1	0	0	0	4776	1319	46	4	55	4	DSE	6	116720466	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4207441	116720466	54394601	1533	4434											
DSE	29940	hgsc.bcm.edu	37	chr6	116758004	116758004	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagactgaggaggccattgaCaggatttttgccatatcaca	12	10	10	9	0	1	3	1	2	0	1	1	5	1	5	2	3	1	0	2	3	1	4	rs367781233		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:116758004C>T	ENST00000331677.3	+	7	2817	c.2373C>T	c.(2371-2373)gaC>gaT	p.D791D	DSE_ENST00000452085.3_Silent_p.D791D|DSE_ENST00000359564.2_Silent_p.D791D|DSE_ENST00000537543.1_Silent_p.D810D			Q9UL01	DSE_HUMAN	dermatan sulfate epimerase	791					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)		AGGCCATTGACAGGATTTTTG	0.473																																					p.D791D		Atlas-SNP	.											.	DSE	98	.	0			c.C2373T						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	68	72	70		2373,2373	1.9	1	6		70	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	DSE	NM_001080976.1,NM_013352.2	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	791/959,791/959	116758004	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	29940	exon6			CATTGACAGGATT	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.2373C>T	6.37:g.116758004C>T		113	0	0		142	64	0.450704	NM_001080976	Q5R3K6	Silent	SNP	ENST00000331677.3	37	CCDS5107.1																																																																																			.	.	weak		0.473	DSE-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041940.2	NM_013352		T	116758004	C	T	116758004	2	4	22	1	0	0	0	0	0	0	0	1	4776	477	17	2		2	DSE	6	116758004	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	37538	116758004	54357063	1534	4435											
FAM26F	441168	hgsc.bcm.edu	37	chr6	116783585	116783585	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ccaaggcgtcggacgtgcagGacctcctgaaggatctgaag	10	6	14	11	3	1	2	0	2	1	0	3	5	2	5	3	4	1	1	3	4	3	0	rs76716752	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:116783585G>C	ENST00000368605.1	+	2	588	c.493G>C	c.(493-495)Gac>Cac	p.D165H	RP1-93H18.6_ENST00000476099.1_RNA|FAM26F_ENST00000368606.3_Intron	NM_001010919.1	NP_001010919.1	Q5R3K3	FA26F_HUMAN	family with sequence similarity 26, member F	165					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				large_intestine(2)|lung(1)	3				GBM - Glioblastoma multiforme(226;0.0402)|all cancers(137;0.0627)|OV - Ovarian serous cystadenocarcinoma(136;0.0655)|Epithelial(106;0.231)		GGACGTGCAGGACCTCCTGAA	0.716													G|||	243	0.0485224	0.1747	0.0086	5008	,	,		12495	0.0		0.006	False		,,,				2504	0.0				p.S165P		Atlas-SNP	.											.	FAM26F	12	.	0			c.T493C						PASS	.	G	HIS/ASP	207,1869		8,191,839	3	2	2		493	0.7	0	6	dbSNP_131	2	9,2855		0,9,1423	yes	missense	FAM26F	NM_001010919.1	81	8,200,2262	CC,CG,GG		0.3142,9.9711,4.3725	possibly-damaging	165/316	116783585	216,4724	1038	1432	2470	SO:0001583	missense	441168	exon2			GTGCAGGACCTCC	AF086130	CCDS34519.1, CCDS64506.1	6q22.1	2007-06-20			ENSG00000188820	ENSG00000188820			33391	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 187"	C6orf187			Standard	NM_001010919		Approved	RP1-93H18.5, OTTHUMP00000017061, OTTHUMP00000017062, dJ93H18.5	uc003pwv.4	Q5R3K3	OTTHUMG00000015438	ENST00000368605.1:c.493G>C	6.37:g.116783585G>C	ENSP00000357594:p.Asp165His	15	0	0		33	33	1	NM_001010919	B9EJB0|Q5R3K4	Missense_Mutation	SNP	ENST00000368605.1	37	CCDS34519.1	91	0.041666666666666664	84	0.17073170731707318	3	0.008287292817679558	0	0.0	4	0.005277044854881266	G	22.3	4.278004	0.80692	0.099711	0.003142	ENSG00000188820	ENST00000368605	T	0.17528	2.27	4.82	0.664	0.17890	.	1.210450	0.05680	N	0.590259	T	0.09598	0.0236	L	0.46157	1.445	0.09310	N	1	D	0.57257	0.979	P	0.47915	0.561	T	0.33189	-0.9878	10	0.48119	T	0.1	-3.4085	9.6311	0.39780	0.4247:0.0:0.5753:0.0	.	165	Q5R3K3	FA26F_HUMAN	H	165	ENSP00000357594:D165H	ENSP00000357594:D165H	D	+	1	0	FAM26F	116890278	0.017000	0.18338	0.001000	0.08648	0.784000	0.44337	1.686000	0.37669	-0.058000	0.13177	0.313000	0.20887	GAC	G|0.954;C|0.046	0.046	strong		0.716	FAM26F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041946.1	NM_001010919		C	116783585	G	C	116783585	3	2	22	1	0	0	0	0	1	0	0	0	5559	1174	41	4	495	4	FAM26F	6	116783585	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	25581	116783585	54331482	1535	4436											
GPRC6A	222545	hgsc.bcm.edu	37	chr6	117127551	117127551	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acctcccatggttgaaaggcGttggggttctgacagtcacg	8	10	13	10	2	2	2	1	2	1	0	3	2	3	2	2	4	0	3	2	4	1	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:117127551G>A	ENST00000310357.3	-	3	1338	c.1317C>T	c.(1315-1317)aaC>aaT	p.N439N	GPRC6A_ENST00000368549.3_Silent_p.N439N|GPRC6A_ENST00000530250.1_Intron	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	439					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)		GTTGAAAGGCGTTGGGGTTCT	0.438																																					p.N439N		Atlas-SNP	.											.	GPRC6A	152	.	0			c.C1317T						PASS	.						96	85	88					6																	117127551		2203	4299	6502	SO:0001819	synonymous_variant	222545	exon3			AAAGGCGTTGGGG	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.1317C>T	6.37:g.117127551G>A		75	0	0		88	4	0.0454545	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Silent	SNP	ENST00000310357.3	37	CCDS5112.1																																																																																			.	.	none		0.438	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2			A	117127551	G	A	117127551	2	1	22	1	0	0	0	0	0	0	0	1	6737	1136	40	1		1	GPRC6A	6	117127551	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	343966	117127551	53987516	1536	4437											
GPRC6A	222545	hgsc.bcm.edu	37	chr6	117130561	117130561	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctatgacagccttaactctTggcatgtagctggaatagtc	10	12	9	10	0	1	1	0	1	1	0	2	2	1	2	2	2	3	3	2	2	5	5	rs76688215	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:117130561T>G	ENST00000310357.3	-	2	435	c.414A>C	c.(412-414)ccA>ccC	p.P138P	GPRC6A_ENST00000368549.3_Silent_p.P138P|GPRC6A_ENST00000530250.1_Silent_p.P138P	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	138					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)		CCTTAACTCTTGGCATGTAGC	0.443													T|||	76	0.0151757	0.0545	0.0029	5008	,	,		19458	0.0		0.002	False		,,,				2504	0.0				p.P138P		Atlas-SNP	.											.	GPRC6A	152	.	0			c.A414C						PASS	.	T		161,4245	109.9+/-148.2	3,155,2045	96	91	93		414	0.9	1	6	dbSNP_132	93	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	GPRC6A	NM_148963.2		3,159,6341	GG,GT,TT		0.0465,3.6541,1.2686		138/927	117130561	165,12841	2203	4300	6503	SO:0001819	synonymous_variant	222545	exon2			AACTCTTGGCATG	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.414A>C	6.37:g.117130561T>G		113	0	0		135	63	0.466667	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Silent	SNP	ENST00000310357.3	37	CCDS5112.1																																																																																			T|0.984;G|0.016	0.016	strong		0.443	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2			G	117130561	T	G	117130561	2	3	22	1	0	0	0	0	0	0	0	1	6737	1799	63	5		5	GPRC6A	6	117130561	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	3010	117130561	53984506	1537	4438											
ROS1	6098	hgsc.bcm.edu	37	chr6	117681560	117681560	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctggccccttagatgtaaaGgccctaacctaaagaaaagg	14	7	9	11	0	0	2	0	0	0	2	0	2	0	2	5	3	1	1	5	3	8	4	rs140639104	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:117681560G>T	ENST00000368508.3	-	22	3588	c.3390C>A	c.(3388-3390)gcC>gcA	p.A1130A	GOPC_ENST00000467125.1_Intron|ROS1_ENST00000368507.3_Silent_p.A1125A	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	1130	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)		TAGATGTAAAGGCCCTAACCT	0.368			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"								G|||	12	0.00239617	0.0083	0.0014	5008	,	,		17507	0.0		0.0	False		,,,				2504	0.0				p.A1130A		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	.	ROS1	728	.	0			c.C3390A						PASS	.	G		37,4369	41.6+/-74.8	0,37,2166	81	76	78		3390	1.1	1	6	dbSNP_134	78	0,8600		0,0,4300	no	coding-synonymous	ROS1	NM_002944.2		0,37,6466	TT,TG,GG		0.0,0.8398,0.2845		1130/2348	117681560	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	6098	exon22			TGTAAAGGCCCTA	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.3390C>A	6.37:g.117681560G>T		75	0	0		73	24	0.328767	NM_002944	Q15368|Q5TDB5	Silent	SNP	ENST00000368508.3	37	CCDS5116.1																																																																																			G|0.998;T|0.002	0.002	strong		0.368	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			T	117681560	G	T	117681560	2	4	22	1	0	0	0	0	0	0	0	1	13546	987	35	4		4	ROS1	6	117681560	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	550999	117681560	53433507	1538	4439											
C6orf204	387119	hgsc.bcm.edu	37	chr6	118791804	118791804	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttagaaagctttccttgcaTagactagaatttttaaaaaa	16	15	5	5	0	0	3	0	0	0	3	1	3	1	3	1	0	2	2	1	0	8	9	rs7743702	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:118791804T>C	ENST00000368491.3	-	11	2539	c.1918A>G	c.(1918-1920)Atg>Gtg	p.M640V	CEP85L_ENST00000368488.5_Missense_Mutation_p.M643V	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like	640			M -> V (in dbSNP:rs7743702).			centrosome (GO:0005813)|cytoplasm (GO:0005737)											TTTCCTTGCATAGACTAGAAT	0.318													T|||	166	0.033147	0.059	0.0173	5008	,	,		15160	0.0		0.0189	False		,,,				2504	0.0583				p.M643V		Atlas-SNP	.											.	CEP85L	26	.	0			c.A1927G						PASS	.	T	VAL/MET,VAL/MET	199,3401		4,191,1605	74	70	72		1918,1927	1.6	1	6	dbSNP_116	72	166,7950		2,162,3894	yes	missense,missense	C6orf204	NM_001042475.2,NM_001178035.1	21,21	6,353,5499	CC,CT,TT		2.0453,5.5278,3.1154	benign,benign	640/806,643/809	118791804	365,11351	1800	4058	5858	SO:0001583	missense	387119	exon12			CTTGCATAGACTA	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.1918A>G	6.37:g.118791804T>C	ENSP00000357477:p.Met640Val	127	0	0		131	69	0.526718	NM_001178035	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	Missense_Mutation	SNP	ENST00000368491.3	37	CCDS43498.1	46	0.021062271062271064	26	0.052845528455284556	6	0.016574585635359115	0	0.0	14	0.018469656992084433	T	12.46	1.943229	0.34283	0.055278	0.020453	ENSG00000111860	ENST00000368491;ENST00000368488	T;T	0.10960	2.82;2.82	5.69	1.6	0.23607	.	0.484848	0.22127	N	0.064253	T	0.02304	0.0071	L	0.36672	1.1	0.29229	N	0.873412	B	0.21225	0.053	B	0.18561	0.022	T	0.36601	-0.9741	10	0.49607	T	0.09	-6.4463	2.3369	0.04250	0.257:0.0736:0.133:0.5364	rs7743702;rs52838185;rs7743702	640	Q5SZL2	CF204_HUMAN	V	640;643	ENSP00000357477:M640V;ENSP00000357474:M643V	ENSP00000357474:M643V	M	-	1	0	C6orf204	118898497	0.926000	0.31397	1.000000	0.80357	0.939000	0.58152	0.058000	0.14301	0.932000	0.37266	0.533000	0.62120	ATG	T|0.975;C|0.025	0.025	strong		0.318	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475		C	118791804	T	C	118791804	3	2	22	1	0	0	0	0	1	0	0	0	2355	1406	49	3	511	3	C6orf204	6	118791804	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1110244	118791804	52323263	1539	4440											
C6orf204	387119	hgsc.bcm.edu	37	chr6	118803091	118803091	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttatttttttcttccagaatCtgcagctaaggagaaatgtt	11	17	7	6	0	2	2	0	0	2	2	3	3	3	2	1	1	2	3	1	1	4	7	rs9489410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:118803091C>G	ENST00000368491.3	-	8	2217	c.1596G>C	c.(1594-1596)caG>caC	p.Q532H	CEP85L_ENST00000368488.5_Missense_Mutation_p.Q535H	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like	532			Q -> H (in dbSNP:rs9489410).			centrosome (GO:0005813)|cytoplasm (GO:0005737)											CTTCCAGAATCTGCAGCTAAG	0.318													C|||	166	0.033147	0.059	0.0173	5008	,	,		11959	0.0		0.0189	False		,,,				2504	0.0583				p.Q535H		Atlas-SNP	.											.	CEP85L	26	.	0			c.G1605C						PASS	.	C	HIS/GLN,HIS/GLN	194,3380		4,186,1597	67	57	60		1596,1605	2.3	1	6	dbSNP_119	60	164,7956		1,162,3897	yes	missense,missense	C6orf204	NM_001042475.2,NM_001178035.1	24,24	5,348,5494	GG,GC,CC		2.0197,5.4281,3.0614	probably-damaging,probably-damaging	532/806,535/809	118803091	358,11336	1787	4060	5847	SO:0001583	missense	387119	exon9			CAGAATCTGCAGC	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.1596G>C	6.37:g.118803091C>G	ENSP00000357477:p.Gln532His	59	0	0		72	32	0.444444	NM_001178035	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	Missense_Mutation	SNP	ENST00000368491.3	37	CCDS43498.1	46	0.021062271062271064	26	0.052845528455284556	6	0.016574585635359115	0	0.0	14	0.018469656992084433	C	16.03	3.005806	0.54254	0.054281	0.020197	ENSG00000111860	ENST00000368491;ENST00000368488;ENST00000434604	T;T;T	0.11821	2.74;2.74;2.74	5.24	2.29	0.28610	.	0.061562	0.64402	D	0.000004	T	0.16642	0.0400	L	0.56769	1.78	0.34826	D	0.73918	D;D	0.76494	0.999;0.999	D;D	0.69479	0.964;0.964	T	0.02588	-1.1137	10	0.72032	D	0.01	-5.1646	9.1618	0.37028	0.0:0.6637:0.0:0.3363	rs9489410;rs52802289;rs9489410	535;532	F8W6J2;Q5SZL2	.;CF204_HUMAN	H	532;535;535	ENSP00000357477:Q532H;ENSP00000357474:Q535H;ENSP00000392131:Q535H	ENSP00000357474:Q535H	Q	-	3	2	C6orf204	118909784	1.000000	0.71417	0.999000	0.59377	0.937000	0.57800	0.983000	0.29552	0.219000	0.20840	0.561000	0.74099	CAG	C|0.982;G|0.018	0.018	strong		0.318	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475		G	118803091	C	G	118803091	3	3	22	1	0	0	0	0	1	0	0	0	2355	912	32	4	845	4	C6orf204	6	118803091	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	11287	118803091	52311976	1540	4441											
C6orf204	387119	hgsc.bcm.edu	37	chr6	118812811	118812813	+	Intron	DEL	TGT	TGT	-																															ataattatatgctgaggaaaTgttgttgacctaattcaact																								rs71866282	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:118812811_118812813delTGT	ENST00000368491.3	-	6	2059				CEP85L_ENST00000368488.5_Intron|CEP85L_ENST00000392500.3_In_Frame_Del_p.Q494del|CEP85L_ENST00000419517.2_In_Frame_Del_p.Q491del|CEP85L_ENST00000360290.3_In_Frame_Del_p.Q389del	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like							centrosome (GO:0005813)|cytoplasm (GO:0005737)											GCTGAGGAAATGTTGTTGACCTA	0.32														166	0.033147	0.059	0.0173	5008	,	,		18299	0.0		0.0189	False		,,,				2504	0.0583				p.492_492del		Pindel,Atlas-Indel	.											.	CEP85L	26	.	0			c.1474_1476del						PASS	.		,,	241,4015		6,229,1893					,,	3.5	0		dbSNP_130	43	164,8084		2,160,3962	no	coding,intron,intron	C6orf204	NM_206921.2,NM_001178035.1,NM_001042475.2	,,	8,389,5855	A1A1,A1R,RR		1.9884,5.6626,3.239	,,	,,		405,12099				SO:0001627	intron_variant	387119	exon6			.	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.1437+35ACA>-	6.37:g.118812814_118812816delTGT		77	0	.		70	30	0.429	NM_206921	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	In_Frame_Del	DEL	ENST00000368491.3	37	CCDS43498.1																																																																																			TGT|0.979;-|0.021	0.021	strong		0.32	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475		-	118812813	TGT	-	118812811	6	5	22	0	1	1	0	1	0	0	0	0	2355	1464	51	0		0	C6orf204	6	118812811	Intron	DEL	TGT	TCGA-G8-6324-01A-11D-2210-10	9720	118812811	52302256	1541	4442											
C6orf204	387119	hgsc.bcm.edu	37	chr6	118887215	118887215	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccaccctggccacagttaTccggggcagtgagtttggat	7	10	13	11	1	0	1	0	1	0	0	1	2	1	2	4	4	1	3	4	4	1	2	rs9489444	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:118887215T>A	ENST00000368491.3	-	3	1118	c.497A>T	c.(496-498)gAt>gTt	p.D166V	CEP85L_ENST00000368488.5_Missense_Mutation_p.D169V|CEP85L_ENST00000392500.3_Missense_Mutation_p.D169V|CEP85L_ENST00000419517.2_Missense_Mutation_p.D166V|CEP85L_ENST00000360290.3_Missense_Mutation_p.D64V|CEP85L_ENST00000472713.1_5'UTR	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like	166			D -> V (in dbSNP:rs9489444).			centrosome (GO:0005813)|cytoplasm (GO:0005737)											GCCACAGTTATCCGGGGCAGT	0.498													T|||	191	0.038139	0.121	0.0144	5008	,	,		20125	0.0099		0.004	False		,,,				2504	0.0072				p.D169V		Atlas-SNP	.											.	CEP85L	26	.	0			c.A506T						PASS	.	T	VAL/ASP,VAL/ASP,VAL/ASP	363,4043	186.0+/-213.0	18,327,1858	134	122	126		497,506,497	2.1	0	6	dbSNP_119	126	36,8564	24.6+/-71.5	0,36,4264	yes	missense,missense,missense	C6orf204	NM_001042475.2,NM_001178035.1,NM_206921.2	152,152,152	18,363,6122	AA,AT,TT		0.4186,8.2388,3.0678	benign,benign,benign	166/806,169/809,166/497	118887215	399,12607	2203	4300	6503	SO:0001583	missense	387119	exon4			CAGTTATCCGGGG	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.497A>T	6.37:g.118887215T>A	ENSP00000357477:p.Asp166Val	175	0	0		202	114	0.564356	NM_001178035	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	Missense_Mutation	SNP	ENST00000368491.3	37	CCDS43498.1	72	0.03296703296703297	60	0.12195121951219512	6	0.016574585635359115	3	0.005244755244755245	3	0.00395778364116095	T	4.848	0.157562	0.09236	0.082388	0.004186	ENSG00000111860	ENST00000368491;ENST00000368488;ENST00000434604;ENST00000392500;ENST00000360290;ENST00000419517	T;T;T;T;T;T	0.25912	2.94;2.93;2.35;2.11;1.77;2.12	5.86	2.12	0.27331	.	0.629920	0.16930	N	0.193714	T	0.04998	0.0134	N	0.24115	0.695	0.47308	P	6.110000000000282E-4	B;B;B;B;B	0.18610	0.029;0.023;0.013;0.005;0.005	B;B;B;B;B	0.15052	0.011;0.012;0.012;0.007;0.004	T	0.32322	-0.9911	9	0.38643	T	0.18	-0.0495	4.4874	0.11797	0.1127:0.0771:0.117:0.6932	rs9489444;rs52812528;rs9489444	64;169;166;169;166	B4DYT2;Q5SZL2-2;G3V0H3;F8W6J2;Q5SZL2	.;.;.;.;CF204_HUMAN	V	166;169;169;169;64;166	ENSP00000357477:D166V;ENSP00000357474:D169V;ENSP00000392131:D169V;ENSP00000376288:D169V;ENSP00000353434:D64V;ENSP00000393317:D166V	ENSP00000353434:D64V	D	-	2	0	C6orf204	118993908	0.760000	0.28428	0.001000	0.08648	0.018000	0.09664	1.002000	0.29796	0.130000	0.18549	0.533000	0.62120	GAT	T|0.964;A|0.036	0.036	strong		0.498	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475		A	118887215	T	A	118887215	3	1	22	1	0	0	0	0	1	0	0	0	2355	1435	50	5	2018	5	C6orf204	6	118887215	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	74404	118887215	52227852	1542	4443											
C6orf204	387119	hgsc.bcm.edu	37	chr6	118953755	118953755	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gattcattagcaggtagccaTgctgatgaataatctgggcc	11	11	11	8	0	2	2	1	2	1	0	2	3	2	2	2	2	3	3	2	2	4	4	rs9320659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:118953755T>C	ENST00000368491.3	-	2	714	c.93A>G	c.(91-93)gcA>gcG	p.A31A	CEP85L_ENST00000368488.5_Silent_p.A34A|CEP85L_ENST00000392500.3_Silent_p.A34A|CEP85L_ENST00000419517.2_Silent_p.A31A|CEP85L_ENST00000360290.3_5'UTR	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like	31						centrosome (GO:0005813)|cytoplasm (GO:0005737)											CAGGTAGCCATGCTGATGAAT	0.388													T|||	163	0.0325479	0.0582	0.0159	5008	,	,		17382	0.0		0.0179	False		,,,				2504	0.0583				p.A34A		Atlas-SNP	.											.	CEP85L	26	.	0			c.A102G						PASS	.	T	,,	199,3547		4,191,1678	79	74	76		93,102,93	1.9	1	6	dbSNP_119	76	163,8055		2,159,3948	no	coding-synonymous,coding-synonymous,coding-synonymous	C6orf204	NM_001042475.2,NM_001178035.1,NM_206921.2	,,	6,350,5626	CC,CT,TT		1.9835,5.3123,3.0257	,,	31/806,34/809,31/497	118953755	362,11602	1873	4109	5982	SO:0001819	synonymous_variant	387119	exon3			TAGCCATGCTGAT	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.93A>G	6.37:g.118953755T>C		83	0	0		57	31	0.54386	NM_001178035	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	Silent	SNP	ENST00000368491.3	37	CCDS43498.1																																																																																			T|0.980;C|0.020	0.020	strong		0.388	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475		C	118953755	T	C	118953755	2	2	22	1	0	0	0	0	0	0	0	1	2355	1451	51	3		3	C6orf204	6	118953755	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	66540	118953755	52161312	1543	4444											
C6orf170	221322	hgsc.bcm.edu	37	chr6	121576518	121576518	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagaaacagaatcagaaccCtctactggagtaggaattct	16	8	9	8	0	3	3	1	0	2	3	3	6	3	5	1	2	3	1	1	2	7	3	rs201833154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:121576518C>G	ENST00000398212.2	-	17	2023	c.1974G>C	c.(1972-1974)gaG>gaC	p.E658D	TBC1D32_ENST00000275159.6_Missense_Mutation_p.E658D	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	658					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)										AATCAGAACCCTCTACTGGAG	0.289													C|||	7	0.00139776	0.0053	0.0	5008	,	,		8412	0.0		0.0	False		,,,				2504	0.0				p.E658D		Atlas-SNP	.											C6orf170,colon,carcinoma,-2,1	C6orf170	146	1	0			c.G1974C						PASS	.	C	ASP/GLU	21,3563		0,21,1771	55	55	55		1974	-6.1	0	6		55	0,8094		0,0,4047	yes	missense	C6orf170	NM_152730.4	45	0,21,5818	GG,GC,CC		0.0,0.5859,0.1798	benign	658/1258	121576518	21,11657	1792	4047	5839	SO:0001583	missense	221322	exon17			AGAACCCTCTACT	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.1974G>C	6.37:g.121576518C>G	ENSP00000381270:p.Glu658Asp	136	0	0		141	73	0.51773	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	37	CCDS43501.1	.	.	.	.	.	.	.	.	.	.	C	6.113	0.389161	0.11581	0.005859	0.0	ENSG00000146350	ENST00000275159;ENST00000398212	T;T	0.17370	2.28;2.28	5.81	-6.14	0.02111	.	0.553654	0.18121	N	0.151042	T	0.02571	0.0078	L	0.38175	1.15	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.40701	-0.9549	10	0.22109	T	0.4	.	6.2469	0.20823	0.1049:0.2255:0.0805:0.5892	.	658;658	Q96NH3-4;Q96NH3	.;BROMI_HUMAN	D	658	ENSP00000275159:E658D;ENSP00000381270:E658D	ENSP00000275159:E658D	E	-	3	2	C6orf170	121618217	0.000000	0.05858	0.006000	0.13384	0.982000	0.71751	-1.136000	0.03222	-1.369000	0.02147	-0.150000	0.13652	GAG	.	.	weak		0.289	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730		G	121576518	C	G	121576518	3	3	22	1	0	0	0	0	1	0	0	0	2346	680	24	4	1863	4	C6orf170	6	121576518	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2622763	121576518	49538549	1544	4445											
TRDN	10345	hgsc.bcm.edu	37	chr6	123759243	123759243	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caatggcagtttccttctcaCttttctttttgatatcttct	6	21	4	10	0	4	1	1	1	4	0	6	1	5	1	1	1	0	2	1	1	2	8	rs35766971	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:123759243C>T	ENST00000398178.3	-	12	1037	c.1016G>A	c.(1015-1017)aGt>aAt	p.S339N	TRDN_ENST00000334268.4_Missense_Mutation_p.S339N|RP11-532N4.2_ENST00000427828.1_RNA|RP11-532N4.2_ENST00000587106.2_RNA|RP11-532N4.2_ENST00000418467.2_RNA|RP11-532N4.2_ENST00000434768.1_RNA|RP11-532N4.2_ENST00000587049.1_RNA|RP11-532N4.2_ENST00000589182.1_RNA	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin	339			S -> N (in dbSNP:rs35766971).		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)		TTCCTTCTCACTTTTCTTTTT	0.353													C|||	66	0.0131789	0.0477	0.0043	5008	,	,		19093	0.0		0.0	False		,,,				2504	0.0				p.S340N		Atlas-SNP	.											TRDN,posterior_fossa,glioma,0,1	TRDN	88	1	0			c.G1019A						PASS	.	C	ASN/SER	123,3559		1,121,1719	124	119	121		1016	3.7	0.6	6	dbSNP_126	121	1,8137		0,1,4068	yes	missense	TRDN	NM_006073.2	46	1,122,5787	TT,TC,CC		0.0123,3.3406,1.0491	benign	339/730	123759243	124,11696	1841	4069	5910	SO:0001583	missense	10345	exon12			TTCTCACTTTTCT	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.1016G>A	6.37:g.123759243C>T	ENSP00000381240:p.Ser339Asn	64	0	0		58	29	0.5	NM_001251987	A5D6W5|F5H2W7|Q6NSB8	Missense_Mutation	SNP	ENST00000398178.3	37	CCDS55053.1	19	0.0086996336996337	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	C	12.94	2.089922	0.36855	0.033406	1.23E-4	ENSG00000186439	ENST00000398178;ENST00000398161;ENST00000334268	T;T	0.62788	-0.0;-0.0	5.49	3.72	0.42706	.	0.724189	0.13174	N	0.408030	T	0.25457	0.0619	L	0.27053	0.805	0.43499	D	0.995746	B;B;B	0.23650	0.089;0.089;0.089	B;B;B	0.22152	0.025;0.025;0.038	T	0.09122	-1.0689	10	0.19590	T	0.45	6.1703	6.726	0.23357	0.125:0.3677:0.5073:0.0	rs35766971	339;340;339	Q5SWK9;Q8IVK2;Q13061	.;.;TRDN_HUMAN	N	339	ENSP00000381240:S339N;ENSP00000333984:S339N	ENSP00000333984:S339N	S	-	2	0	TRDN	123800942	0.970000	0.33590	0.602000	0.28890	0.991000	0.79684	1.640000	0.37186	0.812000	0.34326	0.650000	0.86243	AGT	C|0.991;T|0.009	0.009	strong		0.353	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				T	123759243	C	T	123759243	3	4	22	1	0	0	0	0	1	0	0	0	16483	565	20	2	1293	2	TRDN	6	123759243	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2182725	123759243	47355824	1545	4446											
TRMT11	60487	hgsc.bcm.edu	37	chr6	126319453	126319453	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cacaagaagagaaaatcaagCgaatagatgtaagtaaattt	21	8	8	4	1	1	3	1	0	0	3	1	5	1	3	0	0	1	2	0	0	10	4			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:126319453C>T	ENST00000334379.5	+	5	500	c.379C>T	c.(379-381)Cga>Tga	p.R127*	TRMT11_ENST00000368332.3_Nonsense_Mutation_p.R127*|TRMT11_ENST00000450358.1_Nonsense_Mutation_p.R127*	NM_001031712.2	NP_001026882.2	Q7Z4G4	TRM11_HUMAN	tRNA methyltransferase 11 homolog (S. cerevisiae)	127					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)		GAAAATCAAGCGAATAGATGT	0.303																																					p.R127X		Atlas-SNP	.											TRMT11,NS,carcinoma,-1,2	TRMT11	43	2	0			c.C379T						PASS	.						38	37	37					6																	126319453		2166	4290	6456	SO:0001587	stop_gained	60487	exon5			ATCAAGCGAATAG	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.379C>T	6.37:g.126319453C>T	ENSP00000333934:p.Arg127*	35	0	0		48	12	0.25	NM_001031712	E1P570|Q5JY11|Q6PGQ5|Q9HC13	Nonsense_Mutation	SNP	ENST00000334379.5	37	CCDS35496.1	.	.	.	.	.	.	.	.	.	.	C	36	5.666307	0.96745	.	.	ENSG00000066651	ENST00000334379;ENST00000450358;ENST00000368332;ENST00000444121;ENST00000446681	.	.	.	5.95	4.04	0.47022	.	0.174050	0.50627	D	0.000111	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07990	T	0.79	-10.3198	12.802	0.57591	0.508:0.492:0.0:0.0	.	.	.	.	X	127;127;127;64;64	.	ENSP00000333934:R127X	R	+	1	2	TRMT11	126361146	1.000000	0.71417	0.963000	0.40424	0.939000	0.58152	5.384000	0.66225	1.483000	0.48342	0.655000	0.94253	CGA	.	.	none		0.303	TRMT11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_021820		T	126319453	C	T	126319453	4	4	22	1	0	0	0	0	0	1	0	0	16577	760	27	1	397	1	TRMT11	6	126319453	Nonsense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2560210	126319453	44795614	1546	4447											
C6orf174	387104	hgsc.bcm.edu	37	chr6	127797389	127797389	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggatgttggcttcttcctcCaccagccttagccgtagctt	6	13	9	13	1	1	0	0	0	1	0	3	1	3	1	5	2	3	4	5	2	2	6	rs61741826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:127797389C>T	ENST00000525778.1	-	6	2527	c.1782G>A	c.(1780-1782)gtG>gtA	p.V594V	SOGA3_ENST00000465909.2_Silent_p.V594V|SOGA3_ENST00000481848.2_Silent_p.V594V|SOGA3_ENST00000474293.2_5'Flank|SOGA3_ENST00000556132.1_Silent_p.V594V|SOGA3_ENST00000368268.2_Silent_p.V594V			Q5TF21	SOGA3_HUMAN	SOGA family member 3	594					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											CTTCTTCCTCCACCAGCCTTA	0.577													C|||	9	0.00179712	0.0068	0.0	5008	,	,		18875	0.0		0.0	False		,,,				2504	0.0				p.V594V		Atlas-SNP	.											.	.	.	.	0			c.G1782A						PASS	.	C		14,4244		0,14,2115	120	129	126		1782	4.7	1	6	dbSNP_129	126	0,8480		0,0,4240	no	coding-synonymous	C6orf174	NM_001012279.2		0,14,6355	TT,TC,CC		0.0,0.3288,0.1099		594/948	127797389	14,12724	2129	4240	6369	SO:0001819	synonymous_variant	387104	exon6			TTCCTCCACCAGC	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.1782G>A	6.37:g.127797389C>T		89	0	0		85	38	0.447059	NM_001012279		Silent	SNP	ENST00000525778.1	37	CCDS43505.1																																																																																			C|0.999;T|0.001	0.001	strong		0.577	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279		T	127797389	C	T	127797389	2	4	22	1	0	0	0	0	0	0	0	1	2347	581	21	2		2	C6orf174	6	127797389	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1477936	127797389	43317678	1547	4448											
LAMA2	3908	hgsc.bcm.edu	37	chr6	129824406	129824406	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catgatccccaccaaaatcaAtgatggccagtggcacaagg	14	6	9	12	0	1	2	1	2	0	0	2	2	2	2	4	3	0	1	4	3	4	0	rs73599293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:129824406A>G	ENST00000421865.2	+	60	8577	c.8528A>G	c.(8527-8529)aAt>aGt	p.N2843S		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2843	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)		ACCAAAATCAATGATGGCCAG	0.493													A|||	96	0.0191693	0.0673	0.0086	5008	,	,		20534	0.0		0.001	False		,,,				2504	0.0				p.N2843S		Atlas-SNP	.											.	LAMA2	481	.	0			c.A8528G						PASS	.	A	SER/ASN,SER/ASN	305,4101	166.2+/-197.5	11,283,1909	81	76	78		8528,8516	5.9	1	6	dbSNP_130	78	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	LAMA2	NM_000426.3,NM_001079823.1	46,46	11,287,6205	GG,GA,AA		0.0465,6.9224,2.3758	probably-damaging,probably-damaging	2843/3123,2839/3119	129824406	309,12697	2203	4300	6503	SO:0001583	missense	3908	exon60			AAATCAATGATGG	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.8528A>G	6.37:g.129824406A>G	ENSP00000400365:p.Asn2843Ser	38	0	0		46	26	0.565217	NM_000426	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	23	0.010531135531135532	19	0.03861788617886179	4	0.011049723756906077	0	0.0	0	0.0	A	14.58	2.577584	0.45902	0.069224	4.65E-4	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865;ENST00000443169	T	0.71222	-0.55	5.86	5.86	0.93980	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	0.000000	0.85682	D	0.000000	T	0.76593	0.4009	L	0.54863	1.705	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.76329	-0.2999	9	.	.	.	.	16.2479	0.82454	1.0:0.0:0.0:0.0	.	2844;2843	A6NF00;P24043	.;LAMA2_HUMAN	S	2843;2842;2843;861	ENSP00000400365:N2843S	.	N	+	2	0	LAMA2	129866099	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	7.796000	0.85898	2.241000	0.73720	0.533000	0.62120	AAT	A|0.980;G|0.020	0.020	strong		0.493	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			G	129824406	A	G	129824406	3	3	22	1	0	0	0	0	1	0	0	0	8615	101	4	3	8766	3	LAMA2	6	129824406	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2027017	129824406	41290661	1548	4449											
AKAP7	9465	hgsc.bcm.edu	37	chr6	131490324	131490324	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gggaaaacatttgactttgcCctttcaagggattggtactt	10	14	10	7	0	1	1	1	1	0	0	1	3	1	3	1	3	3	1	1	3	4	6	rs115301121	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:131490324C>T	ENST00000431975.2	+	5	598	c.500C>T	c.(499-501)cCc>cTc	p.P167L	AKAP7_ENST00000366358.2_Intron|AKAP7_ENST00000541650.1_Missense_Mutation_p.P166L|AKAP7_ENST00000368123.4_Missense_Mutation_p.P145L	NM_016377.3	NP_057461.2	Q9P0M2	AKA7G_HUMAN	A kinase (PRKA) anchor protein 7	167						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)		TTGACTTTGCCCTTTCAAGGG	0.373													C|||	26	0.00519169	0.0197	0.0	5008	,	,		17471	0.0		0.0	False		,,,				2504	0.0				p.P167L		Atlas-SNP	.											.	AKAP7	61	.	0			c.C500T						PASS	.	C	LEU/PRO	80,4326	68.7+/-106.4	3,74,2126	130	133	132		500	5.9	1	6	dbSNP_132	132	2,8598	1.2+/-3.3	0,2,4298	yes	missense	AKAP7	NM_016377.3	98	3,76,6424	TT,TC,CC		0.0233,1.8157,0.6305	benign	167/349	131490324	82,12924	2203	4300	6503	SO:0001583	missense	9465	exon5			CTTTGCCCTTTCA	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.500C>T	6.37:g.131490324C>T	ENSP00000405252:p.Pro167Leu	188	0	0		210	104	0.495238	NM_016377	B4DUC3|Q9HCZ8	Missense_Mutation	SNP	ENST00000431975.2	37	CCDS5142.2	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	C	25.2	4.613160	0.87359	0.018157	2.33E-4	ENSG00000118507	ENST00000431975;ENST00000541650;ENST00000368123	T;T;T	0.62941	-0.01;-0.01;-0.01	5.9	5.9	0.94986	RNA ligase/cyclic nucleotide phosphodiesterase (1);Protein kinase A anchor protein, nuclear localisation signal domain (1);	0.159801	0.56097	D	0.000021	T	0.63022	0.2476	M	0.73598	2.24	0.58432	D	0.999999	D;P	0.53312	0.959;0.945	P;P	0.50440	0.62;0.641	T	0.62077	-0.6930	10	0.33141	T	0.24	-11.449	15.779	0.78246	0.0:1.0:0.0:0.0	.	166;167	F5GXD1;Q9P0M2	.;AKA7G_HUMAN	L	167;166;145	ENSP00000405252:P167L;ENSP00000441048:P166L;ENSP00000357105:P145L	ENSP00000357105:P145L	P	+	2	0	AKAP7	131532017	0.998000	0.40836	1.000000	0.80357	0.984000	0.73092	4.775000	0.62346	2.788000	0.95919	0.650000	0.86243	CCC	C|0.993;T|0.007	0.007	strong		0.373	AKAP7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042209.2	NM_004842		T	131490324	C	T	131490324	3	4	22	1	0	0	0	0	1	0	0	0	456	623	22	2	448	2	AKAP7	6	131490324	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1665918	131490324	39624743	1549	4450											
OR2A4	79541	hgsc.bcm.edu	37	chr6	132021722	132021722	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaagaggctgtgaaacagcaGgagatatttcttctgctcct	12	11	10	8	0	2	3	0	1	2	2	3	4	3	3	1	2	3	3	1	2	3	3	rs145289654	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:132021722G>A	ENST00000315453.2	-	1	913	c.820C>T	c.(820-822)Ctg>Ttg	p.L274L	ENPP3_ENST00000357639.3_Intron|ENPP3_ENST00000414305.1_Intron|ENPP3_ENST00000358229.5_Intron	NM_030908.1	NP_112170.1	O95047	OR2A4_HUMAN	olfactory receptor, family 2, subfamily A, member 4	274					positive regulation of cytokinesis (GO:0032467)|regulation of actin cytoskeleton organization (GO:0032956)	cleavage furrow (GO:0032154)|Flemming body (GO:0090543)|integral component of membrane (GO:0016021)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(1)|ovary(1)|skin(1)	3	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.018)|OV - Ovarian serous cystadenocarcinoma(155;0.041)		TGAAACAGCAGGAGATATTTC	0.453													g|||	76	0.0151757	0.0545	0.0058	5008	,	,		22576	0.0		0.0	False		,,,				2504	0.0				p.L274L		Atlas-SNP	.											.	OR2A4	17	.	0			c.C820T						PASS	.	G	,	198,3340		56,86,1627	20	30	27		,820	0.7	0.9	6	dbSNP_134	27	0,8486		0,0,4243	no	intron,coding-synonymous	ENPP3,OR2A4	NM_005021.3,NM_030908.1	,	56,86,5870	AA,AG,GG		0.0,5.5964,1.6467	,	,274/311	132021722	198,11826	1769	4243	6012	SO:0001819	synonymous_variant	79541	exon1			ACAGCAGGAGATA	AC005587	CCDS5149.1	6q23	2012-08-09	2003-05-22		ENSG00000180658	ENSG00000180658		"GPCR / Class A : Olfactory receptors"	14729	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily A, member 10"	OR2A10			Standard	NM_030908		Approved		uc011ecd.2	O95047	OTTHUMG00000016316	ENST00000315453.2:c.820C>T	6.37:g.132021722G>A		770	2	0.0025974		935	254	0.271658	NM_030908	Q0VAR3|Q6IF18|Q9NQN0	Silent	SNP	ENST00000315453.2	37	CCDS5149.1																																																																																			G|0.995;A|0.005	0.005	strong		0.453	OR2A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109221.1	NM_030908		A	132021722	G	A	132021722	2	1	22	1	0	0	0	0	0	0	0	1	10988	991	35	2		2	OR2A4	6	132021722	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	531398	132021722	39093345	1550	4451											
TAAR1	134864	hgsc.bcm.edu	37	chr6	132967032	132967032	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actatcagattgccaacgagTgtggtcagaattatgagcac	13	10	10	8	1	2	3	2	1	0	2	2	4	2	3	1	1	3	1	1	1	4	3	rs73775159	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:132967032T>G	ENST00000275216.1	-	1	110	c.111A>C	c.(109-111)acA>acC	p.T37T		NM_138327.1	NP_612200.1	Q96RJ0	TAAR1_HUMAN	trace amine associated receptor 1	37					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)	TGCCAACGAGTGTGGTCAGAA	0.383													T|||	59	0.0117812	0.0431	0.0029	5008	,	,		20615	0.0		0.0	False		,,,				2504	0.0				p.T37T		Atlas-SNP	.											.	TAAR1	41	.	0			c.A111C						PASS	.	T		160,4246	108.2+/-146.6	1,158,2044	168	165	166		111	-3	0	6	dbSNP_130	166	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	TAAR1	NM_138327.1		1,160,6342	GG,GT,TT		0.0233,3.6314,1.2456		37/340	132967032	162,12844	2203	4300	6503	SO:0001819	synonymous_variant	134864	exon1			AACGAGTGTGGTC	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.111A>C	6.37:g.132967032T>G		221	0	0		272	144	0.529412	NM_138327	Q2M1W5|Q3MIH8|Q5VUQ1	Silent	SNP	ENST00000275216.1	37	CCDS5158.1																																																																																			T|0.989;G|0.011	0.011	strong		0.383	TAAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042259.1	NM_138327		G	132967032	T	G	132967032	2	3	22	1	0	0	0	0	0	0	0	1	15504	1683	59	5		5	TAAR1	6	132967032	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	945310	132967032	38148035	1551	4452											
VNN1	8876	hgsc.bcm.edu	37	chr6	133004281	133004281	+	Nonstop_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agagaaaaagtcaatattctAccaacttaatgagcatacaa	20	9	5	7	0	2	2	1	1	1	1	2	3	2	2	1	0	4	1	1	0	9	5	rs61729583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:133004281A>G	ENST00000367928.4	-	7	1553	c.1540T>C	c.(1540-1542)Tag>Cag	p.*514Q		NM_004666.2	NP_004657.2	O95497	VNN1_HUMAN	vanin 1	0					acute inflammatory response (GO:0002526)|cellular component movement (GO:0006928)|chronic inflammatory response (GO:0002544)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|pantothenate metabolic process (GO:0015939)|positive regulation of T cell differentiation in thymus (GO:0033089)|response to oxidative stress (GO:0006979)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	GPI anchor binding (GO:0034235)|pantetheine hydrolase activity (GO:0017159)			NS(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	31	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.0027)|GBM - Glioblastoma multiforme(226;0.0189)		TCAATATTCTACCAACTTAAT	0.333													A|||	148	0.0295527	0.1082	0.0058	5008	,	,		16408	0.0		0.001	False		,,,				2504	0.0				p.X514Q		Atlas-SNP	.											.	VNN1	69	.	0			c.T1540C						PASS	.	A	GLN/stop	395,4011	196.7+/-221.0	18,359,1826	94	89	90		1540	4.7	0.9	6	dbSNP_129	90	4,8596	3.0+/-9.4	0,4,4296	yes	stop-lost	VNN1	NM_004666.2		18,363,6122	GG,GA,AA		0.0465,8.965,3.0678		514/514	133004281	399,12607	2203	4300	6503	SO:0001578	stop_lost	8876	exon7			TATTCTACCAACT	AJ132099	CCDS5159.1	6q23-q24	2013-02-13			ENSG00000112299	ENSG00000112299	3.5.1.92	"Vanins"	12705	protein-coding gene	gene with protein product		603570				9790769	Standard	NM_004666		Approved	Tiff66	uc003qdo.3	O95497	OTTHUMG00000015587	ENST00000367928.4:c.1540T>C	6.37:g.133004281A>G	ENSP00000356905:p.*514Gluext*13	71	0	0		87	36	0.413793	NM_004666	A8K310|Q4JFW6|Q4VAS7|Q4VAS8|Q4VAS9|Q9UF16|Q9UJF4	Missense_Mutation	SNP	ENST00000367928.4	37	CCDS5159.1	47	0.02152014652014652	44	0.08943089430894309	3	0.008287292817679558	0	0.0	0	0.0	A	10.88	1.475064	0.26511	0.08965	4.65E-4	ENSG00000112299	ENST00000367928	.	.	.	5.86	4.71	0.59529	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.1002	0.36664	0.917:0.0:0.083:0.0	.	.	.	.	Q	514	.	.	X	-	1	0	VNN1	133045974	0.003000	0.15002	0.944000	0.38274	0.058000	0.15608	1.546000	0.36179	2.237000	0.73441	0.528000	0.53228	TAG	A|0.971;G|0.029	0.029	strong		0.333	VNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042263.1			G	133004281	A	G	133004281	4	3	22	1	0	0	0	0	0	0	0	0	17197	404	14	3	5	3	VNN1	6	133004281	Nonstop_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	37249	133004281	38110786	1552	4453											
VNN1	8876	hgsc.bcm.edu	37	chr6	133013576	133013576	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccttgtttcctgatgagagcGcttctatactgctggcatag	7	14	10	10	1	1	2	0	2	1	1	2	3	2	2	2	1	3	4	2	1	3	6	rs34535050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:133013576G>T	ENST00000367928.4	-	5	987	c.974C>A	c.(973-975)gCg>gAg	p.A325E		NM_004666.2	NP_004657.2	O95497	VNN1_HUMAN	vanin 1	325	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.		A -> E (in dbSNP:rs34535050). {ECO:0000269|Ref.4}.		acute inflammatory response (GO:0002526)|cellular component movement (GO:0006928)|chronic inflammatory response (GO:0002544)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|pantothenate metabolic process (GO:0015939)|positive regulation of T cell differentiation in thymus (GO:0033089)|response to oxidative stress (GO:0006979)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	GPI anchor binding (GO:0034235)|pantetheine hydrolase activity (GO:0017159)			NS(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	31	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.0027)|GBM - Glioblastoma multiforme(226;0.0189)		TGATGAGAGCGCTTCTATACT	0.448													G|||	124	0.0247604	0.09	0.0058	5008	,	,		18388	0.0		0.001	False		,,,				2504	0.0				p.A325E		Atlas-SNP	.											.	VNN1	69	.	0			c.C974A						PASS	.	G	GLU/ALA	329,4077	173.7+/-203.5	15,299,1889	76	74	75		974	4.1	0	6	dbSNP_126	75	3,8597	2.2+/-6.3	0,3,4297	yes	missense	VNN1	NM_004666.2	107	15,302,6186	TT,TG,GG		0.0349,7.4671,2.5527	benign	325/514	133013576	332,12674	2203	4300	6503	SO:0001583	missense	8876	exon5			GAGAGCGCTTCTA	AJ132099	CCDS5159.1	6q23-q24	2013-02-13			ENSG00000112299	ENSG00000112299	3.5.1.92	"Vanins"	12705	protein-coding gene	gene with protein product		603570				9790769	Standard	NM_004666		Approved	Tiff66	uc003qdo.3	O95497	OTTHUMG00000015587	ENST00000367928.4:c.974C>A	6.37:g.133013576G>T	ENSP00000356905:p.Ala325Glu	63	0	0		67	33	0.492537	NM_004666	A8K310|Q4JFW6|Q4VAS7|Q4VAS8|Q4VAS9|Q9UF16|Q9UJF4	Missense_Mutation	SNP	ENST00000367928.4	37	CCDS5159.1	39	0.017857142857142856	36	0.07317073170731707	3	0.008287292817679558	0	0.0	0	0.0	G	0.747	-0.774241	0.02951	0.074671	3.49E-4	ENSG00000112299	ENST00000367928	D	0.87256	-2.23	5.85	4.05	0.47172	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (1);	1.202920	0.05711	N	0.595981	T	0.67316	0.2880	L	0.46157	1.445	0.09310	N	1	B	0.15141	0.012	B	0.20767	0.031	T	0.55082	-0.8196	10	0.15952	T	0.53	-14.8515	5.0557	0.14531	0.067:0.23:0.4724:0.2306	rs34535050	325	O95497	VNN1_HUMAN	E	325	ENSP00000356905:A325E	ENSP00000356905:A325E	A	-	2	0	VNN1	133055269	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.013000	0.13310	0.796000	0.33947	0.563000	0.77884	GCG	G|0.975;T|0.025	0.025	strong		0.448	VNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042263.1			T	133013576	G	T	133013576	3	4	22	1	0	0	0	0	1	0	0	0	17197	1087	38	4	579	4	VNN1	6	133013576	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	9295	133013576	38101491	1553	4454											
VNN1	8876	hgsc.bcm.edu	37	chr6	133015257	133015257	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgtccccaatatttgccaCaacatagatagagttgttct	11	14	6	10	0	1	2	0	0	1	2	2	2	2	2	3	0	2	2	3	0	5	7	rs45610032	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:133015257C>G	ENST00000367928.4	-	3	419	c.406G>C	c.(406-408)Gtg>Ctg	p.V136L		NM_004666.2	NP_004657.2	O95497	VNN1_HUMAN	vanin 1	136	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.		V -> L (in dbSNP:rs45610032). {ECO:0000269|Ref.4}.		acute inflammatory response (GO:0002526)|cellular component movement (GO:0006928)|chronic inflammatory response (GO:0002544)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|pantothenate metabolic process (GO:0015939)|positive regulation of T cell differentiation in thymus (GO:0033089)|response to oxidative stress (GO:0006979)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	GPI anchor binding (GO:0034235)|pantetheine hydrolase activity (GO:0017159)			NS(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	31	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.0027)|GBM - Glioblastoma multiforme(226;0.0189)		ATATTTGCCACAACATAGATA	0.438													C|||	38	0.00758786	0.0265	0.0043	5008	,	,		16984	0.0		0.0	False		,,,				2504	0.0				p.V136L		Atlas-SNP	.											.	VNN1	69	.	0			c.G406C						PASS	.	C	LEU/VAL	119,4287	90.2+/-128.9	3,113,2087	155	139	144		406	6.1	1	6	dbSNP_127	144	5,8595	3.7+/-12.6	0,5,4295	no	missense	VNN1	NM_004666.2	32	3,118,6382	GG,GC,CC		0.0581,2.7009,0.9534	benign	136/514	133015257	124,12882	2203	4300	6503	SO:0001583	missense	8876	exon3			TTGCCACAACATA	AJ132099	CCDS5159.1	6q23-q24	2013-02-13			ENSG00000112299	ENSG00000112299	3.5.1.92	"Vanins"	12705	protein-coding gene	gene with protein product		603570				9790769	Standard	NM_004666		Approved	Tiff66	uc003qdo.3	O95497	OTTHUMG00000015587	ENST00000367928.4:c.406G>C	6.37:g.133015257C>G	ENSP00000356905:p.Val136Leu	224	0	0		233	115	0.493562	NM_004666	A8K310|Q4JFW6|Q4VAS7|Q4VAS8|Q4VAS9|Q9UF16|Q9UJF4	Missense_Mutation	SNP	ENST00000367928.4	37	CCDS5159.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	C	25.6	4.658625	0.88154	0.027009	5.81E-4	ENSG00000112299	ENST00000367928	D	0.89485	-2.52	6.07	6.07	0.98685	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (4);	0.000000	0.64402	D	0.000004	D	0.90140	0.6919	M	0.76002	2.32	0.58432	D	0.999998	P	0.37141	0.584	B	0.44044	0.439	D	0.89290	0.3618	10	0.52906	T	0.07	-8.8184	20.6439	0.99570	0.0:1.0:0.0:0.0	rs45610032	136	O95497	VNN1_HUMAN	L	136	ENSP00000356905:V136L	ENSP00000356905:V136L	V	-	1	0	VNN1	133056950	1.000000	0.71417	0.969000	0.41365	0.874000	0.50279	6.622000	0.74233	2.890000	0.99128	0.650000	0.86243	GTG	C|0.992;G|0.008	0.008	strong		0.438	VNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042263.1			G	133015257	C	G	133015257	3	3	22	1	0	0	0	0	1	0	0	0	17197	478	17	4	1155	4	VNN1	6	133015257	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1681	133015257	38099810	1554	4455											
TCF21	6943	hgsc.bcm.edu	37	chr6	134210600	134210600	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggagatgttggaatgtgacgGgttgaaaatggattcgaaca	13	10	15	3	2	0	3	0	2	0	1	1	7	0	5	0	4	1	2	0	4	4	3	rs56412384	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:134210600G>T	ENST00000367882.4	+	1	325	c.65G>T	c.(64-66)gGg>gTg	p.G22V	RP3-323P13.2_ENST00000607033.1_RNA|RP3-323P13.2_ENST00000606544.1_RNA|TCF21_ENST00000237316.3_Missense_Mutation_p.G22V|RP3-323P13.2_ENST00000607641.1_RNA|RP3-323P13.2_ENST00000607573.1_RNA	NM_003206.3	NP_003197.2	O43680	TCF21_HUMAN	transcription factor 21	22					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)		GAATGTGACGGGTTGAAAATG	0.567													G|||	298	0.0595048	0.2057	0.0259	5008	,	,		17673	0.004		0.001	False		,,,				2504	0.0031				p.G22V		Atlas-SNP	.											TCF21,NS,carcinoma,+1,1	TCF21	30	1	0			c.G65T	GRCh37	HM050002	TCF21	M	rs56412384	scavenged	.	G	VAL/GLY,VAL/GLY	766,3640	311.6+/-292.2	84,598,1521	97	102	100		65,65	3.5	1	6	dbSNP_129	100	17,8583	11.9+/-42.8	0,17,4283	yes	missense,missense	TCF21	NM_003206.3,NM_198392.2	109,109	84,615,5804	TT,TG,GG		0.1977,17.3854,6.0203	benign,benign	22/180,22/180	134210600	783,12223	2203	4300	6503	SO:0001583	missense	6943	exon1			GTGACGGGTTGAA	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.65G>T	6.37:g.134210600G>T	ENSP00000356857:p.Gly22Val	93	1	0.0107527		107	106	0.990654	NM_003206	E1P581|O43545|Q6ICV0|Q9BZ14	Missense_Mutation	SNP	ENST00000367882.4	37	CCDS5167.1	108	0.04945054945054945	94	0.1910569105691057	10	0.027624309392265192	3	0.005244755244755245	1	0.0013192612137203166	G	10.95	1.496669	0.26861	0.173854	0.001977	ENSG00000118526	ENST00000367882;ENST00000237316	D;D	0.96200	-3.94;-3.94	4.43	3.53	0.40419	.	0.306082	0.28566	N	0.014896	D	0.85660	0.5748	L	0.36672	1.1	0.09310	P	0.99999762263	B	0.13594	0.008	B	0.11329	0.006	T	0.76484	-0.2942	9	0.15952	T	0.53	-15.4673	12.9612	0.58460	0.0:0.1708:0.8291:0.0	rs56412384;rs61729590	22	O43680	TCF21_HUMAN	V	22	ENSP00000356857:G22V;ENSP00000237316:G22V	ENSP00000237316:G22V	G	+	2	0	TCF21	134252293	1.000000	0.71417	0.997000	0.53966	0.798000	0.45092	5.440000	0.66563	0.797000	0.33971	0.313000	0.20887	GGG	G|0.944;T|0.056	0.056	strong		0.567	TCF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042292.1	NM_198392		T	134210600	G	T	134210600	3	4	22	1	0	0	0	0	1	0	0	0	15706	1232	43	4	67	4	TCF21	6	134210600	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1195343	134210600	36904467	1555	4456											
ALDH8A1	64577	hgsc.bcm.edu	37	chr6	135254034	135254034	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agctttttgcagtggggagcGctcagctgggtgatccgctc	5	11	15	10	2	1	1	1	1	0	0	3	2	2	2	1	3	4	5	1	3	0	2	rs114000920	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:135254034G>A	ENST00000265605.2	-	5	797	c.729C>T	c.(727-729)agC>agT	p.S243S	ALDH8A1_ENST00000367845.2_Silent_p.S243S|ALDH8A1_ENST00000367847.2_Silent_p.S193S	NM_022568.3	NP_072090.1	Q9H2A2	AL8A1_HUMAN	aldehyde dehydrogenase 8 family, member A1	243					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)		AGTGGGGAGCGCTCAGCTGGG	0.647													G|||	58	0.0115815	0.0416	0.0043	5008	,	,		17286	0.0		0.0	False		,,,				2504	0.0				p.S243S		Atlas-SNP	.											.	ALDH8A1	68	.	0			c.C729T						PASS	.	G	,,	126,4280	91.6+/-130.3	2,122,2079	68	70	69		579,729,729	-2.7	1	6	dbSNP_132	69	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	ALDH8A1	NM_001193480.1,NM_022568.3,NM_170771.2	,,	2,124,6377	AA,AG,GG		0.0233,2.8597,0.9842	,,	193/438,243/488,243/434	135254034	128,12878	2203	4300	6503	SO:0001819	synonymous_variant	64577	exon5			GGGAGCGCTCAGC	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.729C>T	6.37:g.135254034G>A		92	0	0		79	43	0.544304	NM_022568	B7Z521|O60793|Q24JS9|Q53GT3|Q5TI80	Silent	SNP	ENST00000265605.2	37	CCDS5171.1																																																																																			G|0.987;A|0.013	0.013	strong		0.647	ALDH8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042334.2			A	135254034	G	A	135254034	2	1	22	1	0	0	0	0	0	0	0	1	505	1078	38	1		1	ALDH8A1	6	135254034	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1043434	135254034	35861033	1556	4457											
ALDH8A1	64577	hgsc.bcm.edu	37	chr6	135271178	135271178	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttccagcatcaaaagtgcgTttgttccagccatagcaagg	11	11	9	10	1	1	0	1	0	0	0	3	0	3	0	3	1	4	4	3	1	4	4	rs56954234	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:135271178T>C	ENST00000265605.2	-	1	82	c.14A>G	c.(13-15)aAc>aGc	p.N5S	ALDH8A1_ENST00000367845.2_Missense_Mutation_p.N5S|ALDH8A1_ENST00000367847.2_Missense_Mutation_p.N5S	NM_022568.3	NP_072090.1	Q9H2A2	AL8A1_HUMAN	aldehyde dehydrogenase 8 family, member A1	5					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)		CAAAAGTGCGTTTGTTCCAGC	0.453													T|||	71	0.0141773	0.0514	0.0043	5008	,	,		19775	0.0		0.0	False		,,,				2504	0.0				p.N5S		Atlas-SNP	.											.	ALDH8A1	68	.	0			c.A14G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN	141,4265	98.9+/-137.6	3,135,2065	102	102	102		14,14,14	-1.8	0	6	dbSNP_129	102	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense	ALDH8A1	NM_001193480.1,NM_022568.3,NM_170771.2	46,46,46	3,138,6362	CC,CT,TT		0.0349,3.2002,1.1072	benign,benign,benign	5/438,5/488,5/434	135271178	144,12862	2203	4300	6503	SO:0001583	missense	64577	exon1			AGTGCGTTTGTTC	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.14A>G	6.37:g.135271178T>C	ENSP00000265605:p.Asn5Ser	87	0	0		110	43	0.390909	NM_022568	B7Z521|O60793|Q24JS9|Q53GT3|Q5TI80	Missense_Mutation	SNP	ENST00000265605.2	37	CCDS5171.1	33	0.01510989010989011	30	0.06097560975609756	3	0.008287292817679558	0	0.0	0	0.0	T	14.25	2.479974	0.44044	0.032002	3.49E-4	ENSG00000118514	ENST00000265605;ENST00000367845;ENST00000367847	T;T;T	0.75154	-0.91;-0.88;-0.87	6.14	-1.83	0.07833	.	1.633190	0.02930	N	0.139121	T	0.28699	0.0711	N	0.11560	0.145	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.07121	-1.0789	10	0.21014	T	0.42	.	6.0545	0.19804	0.1131:0.3306:0.0:0.5563	rs56954234;rs61731728	5;5;5	B7Z521;Q9H2A2-2;Q9H2A2	.;.;AL8A1_HUMAN	S	5	ENSP00000265605:N5S;ENSP00000356819:N5S;ENSP00000356821:N5S	ENSP00000265605:N5S	N	-	2	0	ALDH8A1	135312871	0.000000	0.05858	0.000000	0.03702	0.932000	0.56968	0.157000	0.16402	-0.524000	0.06400	0.529000	0.55759	AAC	T|0.985;C|0.015	0.015	strong		0.453	ALDH8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042334.2			C	135271178	T	C	135271178	3	2	22	1	0	0	0	0	1	0	0	0	505	1725	60	3	1477	3	ALDH8A1	6	135271178	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	17144	135271178	35843889	1557	4458											
HBS1L	10767	hgsc.bcm.edu	37	chr6	135358398	135358398	+	Intron	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gtgaaactggcagatgactgGttacaaaggtcagataaagt	15	9	12	5	0	1	4	1	2	0	2	1	4	1	4	0	3	2	2	0	3	5	2	rs116294454	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:135358398G>A	ENST00000367837.5	-	4	637				HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000367824.4_Intron|HBS1L_ENST00000367820.2_Intron|HBS1L_ENST00000367826.2_Intron|HBS1L_ENST00000415177.2_Intron|HBS1L_ENST00000367822.5_Silent_p.N399N|HBS1L_ENST00000314674.3_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)		CAGATGACTGGTTACAAAGGT	0.408													G|||	88	0.0175719	0.0628	0.0072	5008	,	,		19700	0.0		0.0	False		,,,				2504	0.0				p.N399N		Atlas-SNP	.											.	HBS1L	75	.	0			c.C1197T						PASS	.	G	,,	48,1336		1,46,645	138	114	122		,1197,	3.8	0.5	6	dbSNP_132	122	2,3180		0,2,1589	no	intron,coding-synonymous,intron	HBS1L	NM_001145158.1,NM_001145207.1,NM_006620.3	,,	1,48,2234	AA,AG,GG		0.0629,3.4682,1.0951	,,	,399/633,	135358398	50,4516	692	1591	2283	SO:0001627	intron_variant	10767	exon5			TGACTGGTTACAA	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+2312C>T	6.37:g.135358398G>A		77	0	0		98	48	0.489796	NM_001145207	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Silent	SNP	ENST00000367837.5	37	CCDS5173.1																																																																																			G|0.978;A|0.022	0.022	strong		0.408	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2			A	135358398	G	A	135358398	1	1	22	0	1	0	0	0	0	0	0	0	6996	1252	44	2		2	HBS1L	6	135358398	Intron	SNP	G	TCGA-G8-6324-01A-11D-2210-10	87220	135358398	35756669	1558	4459											
HBS1L	10767	hgsc.bcm.edu	37	chr6	135359073	135359073	+	Intron	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	actgagctagcaaaatcaaaGggtttgctactataatccaa	16	10	7	8	0	1	1	1	1	0	0	2	1	2	1	1	1	4	4	1	1	8	5	rs115458424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:135359073G>A	ENST00000367837.5	-	4	637				HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000367824.4_Intron|HBS1L_ENST00000367820.2_Intron|HBS1L_ENST00000367826.2_Intron|HBS1L_ENST00000415177.2_Intron|HBS1L_ENST00000367822.5_Silent_p.P174P|HBS1L_ENST00000525067.1_Missense_Mutation_p.P112L|HBS1L_ENST00000314674.3_Silent_p.P174P	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)		CAAAATCAAAGGGTTTGCTAC	0.343													G|||	91	0.0181709	0.0628	0.0072	5008	,	,		21502	0.0		0.001	False		,,,				2504	0.002				p.P174P		Atlas-SNP	.											.	HBS1L	75	.	0			c.C522T						PASS	.						100	73	81					6																	135359073		692	1590	2282	SO:0001627	intron_variant	10767	exon5			ATCAAAGGGTTTG	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+1637C>T	6.37:g.135359073G>A		115	0	0		126	70	0.555556	NM_001145207	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Silent	SNP	ENST00000367837.5	37	CCDS5173.1	38	0.0173992673992674	33	0.06707317073170732	5	0.013812154696132596	0	0.0	0	0.0	G	1.871	-0.460307	0.04508	.	.	ENSG00000112339	ENST00000525067	.	.	.	5.23	-0.875	0.10628	.	.	.	.	.	T	0.18257	0.0438	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	T	0.33059	-0.9883	5	0.87932	D	0	.	3.928	0.09272	0.3333:0.0:0.2811:0.3855	.	.	.	.	L	112	.	ENSP00000435608:P112L	P	-	2	0	HBS1L	135400766	0.568000	0.26635	0.283000	0.24790	0.501000	0.33797	0.566000	0.23593	-0.076000	0.12775	0.650000	0.86243	CCT	G|0.979;A|0.021	0.021	strong		0.343	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2			A	135359073	G	A	135359073	1	1	22	0	1	0	0	0	0	0	0	0	6996	987	35	2		2	HBS1L	6	135359073	Intron	SNP	G	TCGA-G8-6324-01A-11D-2210-10	675	135359073	35755994	1559	4460											
FAM54A	113115	hgsc.bcm.edu	37	chr6	136560948	136560948	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctaatgcgctcgtcactcaaGccaaaggaacctacaaacaa	16	6	6	13	2	2	0	2	0	0	0	3	1	2	1	2	1	5	1	2	1	7	2	rs10484485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:136560948G>A	ENST00000420702.1	-	6	914	c.525C>T	c.(523-525)ggC>ggT	p.G175G	MTFR2_ENST00000451457.2_Silent_p.G175G	NM_001099286.1	NP_001092756.1	Q6P444	MTFR2_HUMAN	mitochondrial fission regulator 2	175					aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	mitochondrion (GO:0005739)											CGTCACTCAAGCCAAAGGAAC	0.428													G|||	293	0.0585064	0.208	0.0231	5008	,	,		19229	0.0		0.002	False		,,,				2504	0.0				p.G175G		Atlas-SNP	.											.	.	.	.	0			c.C525T						PASS	.	G	,	786,3620	311.6+/-292.2	74,638,1491	38	33	35		525,525	1.3	0	6	dbSNP_119	35	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	FAM54A	NM_001099286.1,NM_138419.3	,	74,643,5786	AA,AG,GG		0.0581,17.8393,6.0818	,	175/386,175/386	136560948	791,12215	2203	4300	6503	SO:0001819	synonymous_variant	113115	exon6			ACTCAAGCCAAAG	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.525C>T	6.37:g.136560948G>A		56	0	0		75	37	0.493333	NM_138419	A8K8D8|E1P585|Q5JWR7|Q6ZUE8|Q7L3U6|Q9BZ39	Silent	SNP	ENST00000420702.1	37	CCDS5176.1																																																																																			G|0.939;A|0.061	0.061	strong		0.428	MTFR2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042378.2	NM_138419		A	136560948	G	A	136560948	2	1	22	1	0	0	0	0	0	0	0	1	5590	958	34	2		2	FAM54A	6	136560948	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1201875	136560948	34554119	1560	4461											
FAM54A	113115	hgsc.bcm.edu	37	chr6	136570221	136570221	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccagcatctctcttaagataTtcagtatgagagacattgat	13	13	7	8	0	3	4	1	2	2	2	4	5	3	4	1	0	1	2	1	0	3	5	rs147085272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:136570221T>C	ENST00000420702.1	-	2	406	c.17A>G	c.(16-18)aAt>aGt	p.N6S	MTFR2_ENST00000445767.2_5'UTR|MTFR2_ENST00000451457.2_Missense_Mutation_p.N6S	NM_001099286.1	NP_001092756.1	Q6P444	MTFR2_HUMAN	mitochondrial fission regulator 2	6					aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	mitochondrion (GO:0005739)											TCTTAAGATATTCAGTATGAG	0.358													T|||	49	0.00978435	0.0356	0.0029	5008	,	,		19511	0.0		0.0	False		,,,				2504	0.0				p.N6S		Atlas-SNP	.											.	.	.	.	0			c.A17G						PASS	.	T	SER/ASN,SER/ASN	124,4282	91.6+/-130.3	5,114,2084	81	76	78		17,17	1	0.1	6	dbSNP_134	78	0,8600		0,0,4300	yes	missense,missense	FAM54A	NM_001099286.1,NM_138419.3	46,46	5,114,6384	CC,CT,TT		0.0,2.8143,0.9534	benign,benign	6/386,6/386	136570221	124,12882	2203	4300	6503	SO:0001583	missense	113115	exon2			AAGATATTCAGTA	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.17A>G	6.37:g.136570221T>C	ENSP00000395232:p.Asn6Ser	47	0	0		42	16	0.380952	NM_138419	A8K8D8|E1P585|Q5JWR7|Q6ZUE8|Q7L3U6|Q9BZ39	Missense_Mutation	SNP	ENST00000420702.1	37	CCDS5176.1	31	0.014194139194139194	30	0.06097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	T	12.20	1.867291	0.32977	0.028143	0.0	ENSG00000146410	ENST00000451457;ENST00000420702	T;T	0.42900	0.96;0.96	4.85	0.955	0.19602	.	0.442859	0.25285	N	0.031765	T	0.11793	0.0287	L	0.36672	1.1	0.25226	N	0.989865	B	0.14438	0.01	B	0.12156	0.007	T	0.23226	-1.0194	10	0.87932	D	0	-9.0671	3.8762	0.09058	0.0:0.2276:0.1828:0.5896	.	6	Q6P444	FA54A_HUMAN	S	6	ENSP00000407010:N6S;ENSP00000395232:N6S	ENSP00000356758:N6S	N	-	2	0	FAM54A	136611914	0.991000	0.36638	0.053000	0.19242	0.995000	0.86356	0.177000	0.16801	-0.006000	0.14370	0.482000	0.46254	AAT	T|0.988;C|0.012	0.012	strong		0.358	MTFR2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042378.2	NM_138419		C	136570221	T	C	136570221	3	2	22	1	0	0	0	0	1	0	0	0	5590	1493	52	3	1168	3	FAM54A	6	136570221	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	9273	136570221	34544846	1561	4462											
SLC35D3	340146	hgsc.bcm.edu	37	chr6	137245567	137245567	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gaggcgcagctaagtggagaCcagctgccgttcgtgatgga	9	7	16	9	3	0	2	0	1	0	1	1	5	0	3	2	3	3	4	2	3	1	2	rs116512494	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:137245567C>A	ENST00000331858.4	+	2	1149	c.984C>A	c.(982-984)gaC>gaA	p.D328E		NM_001008783.1	NP_001008783.1	Q5M8T2	S35D3_HUMAN	solute carrier family 35, member D3	328					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)		TAAGTGGAGACCAGCTGCCGT	0.622													C|||	50	0.00998403	0.0371	0.0014	5008	,	,		17722	0.0		0.0	False		,,,				2504	0.0				p.D328E		Atlas-SNP	.											.	SLC35D3	33	.	0			c.C984A						PASS	.	C	GLU/ASP	110,4296	78.3+/-116.7	1,108,2094	28	30	29		984	0.3	1	6	dbSNP_132	29	0,8600		0,0,4300	yes	missense	SLC35D3	NM_001008783.1	45	1,108,6394	AA,AC,CC		0.0,2.4966,0.8458	benign	328/417	137245567	110,12896	2203	4300	6503	SO:0001583	missense	340146	exon2			TGGAGACCAGCTG		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.984C>A	6.37:g.137245567C>A	ENSP00000333591:p.Asp328Glu	88	0	0		105	59	0.561905	NM_001008783	B4DI58|Q5QNZ6|Q6NX71	Missense_Mutation	SNP	ENST00000331858.4	37	CCDS34544.1	34	0.015567765567765568	33	0.06707317073170732	1	0.0027624309392265192	0	0.0	0	0.0	C	12.85	2.061537	0.36373	0.024966	0.0	ENSG00000182747	ENST00000331858	T	0.54279	0.58	5.99	0.297	0.15762	.	0.219154	0.44902	D	0.000414	T	0.14141	0.0342	N	0.19112	0.55	0.35092	D	0.764393	B	0.06786	0.001	B	0.04013	0.001	T	0.03306	-1.1050	10	0.37606	T	0.19	-11.3298	5.2593	0.15563	0.134:0.399:0.0:0.467	.	328	Q5M8T2	S35D3_HUMAN	E	328	ENSP00000333591:D328E	ENSP00000333591:D328E	D	+	3	2	SLC35D3	137287260	0.998000	0.40836	0.996000	0.52242	0.699000	0.40488	0.450000	0.21762	0.106000	0.17784	0.609000	0.83330	GAC	C|0.988;A|0.012	0.012	strong		0.622	SLC35D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042389.2	XM_294017		A	137245567	C	A	137245567	3	1	22	1	0	0	0	0	1	0	0	0	14598	506	18	4	990	4	SLC35D3	6	137245567	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	675346	137245567	33869500	1562	4463											
TNFAIP3	7128	hgsc.bcm.edu	37	chr6	138196066	138196066	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtactgaggaaggcgctgtTcagcacgctcaaggaaacag	12	6	14	9	2	2	1	2	1	0	0	2	3	2	3	0	4	3	5	0	4	4	2	rs2230926	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:138196066T>G	ENST00000237289.4	+	3	446	c.380T>G	c.(379-381)tTc>tGc	p.F127C		NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	127	OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.|TRAF-binding.		F -> C (in dbSNP:rs2230926). {ECO:0000269|Ref.3}.		apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|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 interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|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 protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)|p.L126fs*87(1)|p.W113_F140del(1)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		AAGGCGCTGTTCAGCACGCTC	0.498			"D, N, F"		"marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"								T|||	699	0.139577	0.4092	0.0778	5008	,	,		19066	0.0506		0.0239	False		,,,				2504	0.0297				p.F127C	GBM(130;153 1739 22295 28918 47987)	Atlas-SNP	.		Rec	yes		6	6q23	7128	"tumor necrosis factor, alpha-induced protein 3"		L	TNFAIP3,eye,lymphoid_neoplasm,0,1	TNFAIP3	340	1	27	Whole gene deletion(25)|Deletion - In frame(1)|Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(27)	c.T380G	GRCh37	CM083789	TNFAIP3	M	rs2230926	PASS	.	T	CYS/PHE	1570,2836	491.8+/-362.2	290,990,923	120	109	112	http://omim.org/entry/612378|http://www.ncbi.nlm.nih.gov/pubmed?term	380	-0.1	0.9	6	dbSNP_98	112	276,8324	103.6+/-164.7	10,256,4034	yes	missense	TNFAIP3	NM_006290.2	205	300,1246,4957	GG,GT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	3.2093,35.6332,14.1934	benign	127/791	138196066	1846,11160	2203	4300	6503	SO:0001583	missense	7128	exon3			CGCTGTTCAGCAC	M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"OTU domain containing"	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.380T>G	6.37:g.138196066T>G	ENSP00000237289:p.Phe127Cys	164	0	0		180	94	0.522222	NM_001270507	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Missense_Mutation	SNP	ENST00000237289.4	37	CCDS5187.1	270	0.12362637362637363	185	0.37601626016260165	27	0.07458563535911603	41	0.07167832167832168	17	0.022427440633245383	T	12.83	2.055887	0.36277	0.356332	0.032093	ENSG00000118503	ENST00000420009;ENST00000237289;ENST00000535574;ENST00000535332;ENST00000539356;ENST00000544646;ENST00000536070	T;T	0.30714	1.52;1.52	5.97	-0.0566	0.13805	Ovarian tumour, otubain (2);	0.318945	0.38897	N	0.001540	T	0.06554	0.0168	L	0.31926	0.97	0.29434	P	0.85964	B	0.13594	0.008	B	0.17722	0.019	T	0.23154	-1.0196	9	0.32370	T	0.25	-4.7828	3.4675	0.07555	0.2368:0.0676:0.1098:0.5858	rs2230926;rs5029942;rs52802446;rs61407535;rs2230926	127	P21580	TNAP3_HUMAN	C	127	ENSP00000401562:F127C;ENSP00000237289:F127C	ENSP00000237289:F127C	F	+	2	0	TNFAIP3	138237759	1.000000	0.71417	0.922000	0.36590	0.934000	0.57294	1.341000	0.33907	0.125000	0.18397	0.533000	0.62120	TTC	T|0.857;G|0.143	0.143	strong		0.498	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1			G	138196066	T	G	138196066	3	3	22	1	0	0	0	0	1	0	0	0	16289	1783	62	5	386	5	TNFAIP3	6	138196066	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	950499	138196066	32919001	1563	4464											
PBOV1	59351	hgsc.bcm.edu	37	chr6	138539372	138539372	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tttttactttttctttttttCgaaataccttgtagcagaat	9	22	4	6	1	1	1	0	0	1	1	2	2	1	1	1	0	3	2	1	0	5	11	rs73774688	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:138539372C>T	ENST00000527246.2	-	1	255	c.161G>A	c.(160-162)cGa>cAa	p.R54Q	KIAA1244_ENST00000251691.4_Intron	NM_021635.2	NP_067648.1	Q9GZY1	PBOV1_HUMAN	prostate and breast cancer overexpressed 1	54						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)		TTCTTTTTTTCGAAATACCTt	0.398													C|||	33	0.00658946	0.0234	0.0029	5008	,	,		20845	0.0		0.0	False		,,,				2504	0.0				p.R54Q		Atlas-SNP	.											PBOV1_ENST00000527246,NS,carcinoma,-1,2	PBOV1	12	2	0			c.G161A						PASS	.	C	GLN/ARG,	107,4299	69.2+/-107.0	0,107,2096	124	121	122		161,	0.7	0	6	dbSNP_130	122	0,8600		0,0,4300	yes	missense,intron	KIAA1244,PBOV1	NM_021635.2,NM_020340.4	43,	0,107,6396	TT,TC,CC		0.0,2.4285,0.8227	probably-damaging,	54/136,	138539372	107,12899	2203	4300	6503	SO:0001583	missense	59351	exon1			TTTTTTCGAAATA	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.161G>A	6.37:g.138539372C>T	ENSP00000432353:p.Arg54Gln	178	0	0		160	75	0.46875	NM_021635		Missense_Mutation	SNP	ENST00000527246.2	37	CCDS5190.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	C	6.594	0.478015	0.12521	0.024285	0.0	ENSG00000254440	ENST00000527246	T	0.43294	0.95	2.62	0.733	0.18289	.	.	.	.	.	T	0.05868	0.0153	N	0.08118	0	0.09310	N	1	D	0.56035	0.974	B	0.32342	0.144	T	0.16394	-1.0404	9	0.87932	D	0	.	5.1595	0.15054	0.0:0.6937:0.0:0.3063	.	54	Q9GZY1	PBOV1_HUMAN	Q	54	ENSP00000432353:R54Q	ENSP00000432353:R54Q	R	-	2	0	PBOV1	138581065	0.004000	0.15560	0.005000	0.12908	0.122000	0.20287	0.148000	0.16224	0.034000	0.15491	-0.880000	0.02959	CGA	C|0.991;T|0.009	0.009	strong		0.398	PBOV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392617.1	NM_021635		T	138539372	C	T	138539372	3	4	22	1	0	0	0	0	1	0	0	0	11499	884	31	1	250	1	PBOV1	6	138539372	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	343306	138539372	32575695	1564	4465											
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138584014	138584014	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaggagctgaaggatggggCtgagtggagccgagattcca	10	7	18	6	1	0	4	0	3	0	1	1	8	1	7	2	5	2	2	2	5	1	1	rs116596107	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:138584014C>G	ENST00000251691.4	+	12	1560	c.1394C>G	c.(1393-1395)gCt>gGt	p.A465G		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)		AAGGATGGGGCTGAGTGGAGC	0.612													C|||	4	0.000798722	0.003	0.0	5008	,	,		21357	0.0		0.0	False		,,,				2504	0.0				p.A465G		Atlas-SNP	.											.	KIAA1244	236	.	0			c.C1394G						PASS	.	C	GLY/ALA	37,4369	42.3+/-75.8	0,37,2166	94	72	80		1394	1.7	0.1	6	dbSNP_132	80	0,8600		0,0,4300	yes	missense	KIAA1244	NM_020340.4	60	0,37,6466	GG,GC,CC		0.0,0.8398,0.2845	benign	465/2178	138584014	37,12969	2203	4300	6503	SO:0001583	missense	57221	exon12			ATGGGGCTGAGTG	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.1394C>G	6.37:g.138584014C>G	ENSP00000251691:p.Ala465Gly	142	0	0		122	65	0.532787	NM_020340		Missense_Mutation	SNP	ENST00000251691.4	37	CCDS5189.2	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	9.329	1.060068	0.19987	0.008398	0.0	ENSG00000112379	ENST00000251691	T	0.18960	2.18	5.62	1.68	0.24146	.	0.330121	0.29544	N	0.011855	T	0.05456	0.0144	L	0.36672	1.1	0.20074	N	0.999932	B	0.02656	0.0	B	0.04013	0.001	T	0.39761	-0.9598	10	0.23302	T	0.38	-25.5355	11.5601	0.50772	0.0:0.4804:0.4521:0.0675	.	465	Q5TH69	BIG3_HUMAN	G	465	ENSP00000251691:A465G	ENSP00000251691:A465G	A	+	2	0	KIAA1244	138625707	0.965000	0.33210	0.081000	0.20488	0.953000	0.61014	2.466000	0.45084	0.266000	0.21894	0.655000	0.94253	GCT	C|0.998;G|0.002	0.002	strong		0.612	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		G	138584014	C	G	138584014	3	3	22	1	0	0	0	0	1	0	0	0	8226	797	28	4	1440	4	KIAA1244	6	138584014	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	44642	138584014	32531053	1565	4466											
CCDC28A	25901	hgsc.bcm.edu	37	chr6	139094936	139094936	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggagctgcggaggagcgggtCccgggatgtgaccggggctc	5	5	21	10	4	0	1	0	1	0	0	2	5	1	5	2	7	3	2	2	7	0	0	rs34538642	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:139094936C>A	ENST00000332797.6	+	1	280	c.125C>A	c.(124-126)tCc>tAc	p.S42Y		NM_015439.2	NP_056254.1	Q8IWP9	CC28A_HUMAN	coiled-coil domain containing 28A	42			S -> Y (in dbSNP:rs34538642).							autonomic_ganglia(1)|large_intestine(3)|lung(8)|ovary(1)	13				OV - Ovarian serous cystadenocarcinoma(155;0.000201)|GBM - Glioblastoma multiforme(68;0.000306)		AGGAGCGGGTCCCGGGATGTG	0.632													C|||	298	0.0595048	0.2148	0.0187	5008	,	,		16083	0.0		0.001	False		,,,				2504	0.0				p.S42Y		Atlas-SNP	.											.	CCDC28A	34	.	0			c.C125A						PASS	.	C	TYR/SER	746,3660	301.3+/-286.8	70,606,1527	83	103	96		125	-9.6	0	6	dbSNP_126	96	10,8590	7.7+/-29.5	0,10,4290	yes	missense	CCDC28A	NM_015439.2	144	70,616,5817	AA,AC,CC		0.1163,16.9315,5.8127	benign	42/275	139094936	756,12250	2203	4300	6503	SO:0001583	missense	25901	exon1			GCGGGTCCCGGGA	AY167571	CCDS5192.1	6q23.1-q24.1	2008-02-05	2005-09-12	2005-09-12	ENSG00000024862	ENSG00000024862			21098	protein-coding gene	gene with protein product		615353	"chromosome 6 open reading frame 80"	C6orf80			Standard	NM_015439		Approved	CCRL1AP, DKFZp586D0623	uc003qie.3	Q8IWP9	OTTHUMG00000015683	ENST00000332797.6:c.125C>A	6.37:g.139094936C>A	ENSP00000332716:p.Ser42Tyr	203	0	0		270	126	0.466667	NM_015439	E1P591|Q32NC7|Q66K67|Q96E23|Q9Y430	Missense_Mutation	SNP	ENST00000332797.6	37	CCDS5192.1	98	0.04487179487179487	95	0.19308943089430894	3	0.008287292817679558	0	0.0	0	0.0	C	4.671	0.124775	0.08931	0.169315	0.001163	ENSG00000024862	ENST00000332797	T	0.26067	1.76	4.79	-9.58	0.00559	.	5.212620	0.00597	N	0.000373	T	0.01730	0.0055	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.22382	-1.0218	9	0.07175	T	0.84	6.5122	2.2197	0.03969	0.342:0.154:0.3568:0.1471	rs34538642	42	Q8IWP9	CC28A_HUMAN	Y	42	ENSP00000332716:S42Y	ENSP00000332716:S42Y	S	+	2	0	CCDC28A	139136629	0.000000	0.05858	0.000000	0.03702	0.068000	0.16541	-0.827000	0.04424	-2.758000	0.00371	-0.268000	0.10319	TCC	C|0.946;A|0.054	0.054	strong		0.632	CCDC28A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042444.1	NM_015439		A	139094936	C	A	139094936	3	1	22	1	0	0	0	0	1	0	0	0	2804	855	30	4	127	4	CCDC28A	6	139094936	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	510922	139094936	32020131	1566	4467											
ECT2L	345930	hgsc.bcm.edu	37	chr6	139170412	139170412	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttcattctccagatggtgAtggagagtgtgaaggctggt	8	13	15	5	0	2	4	1	2	1	2	3	5	2	4	1	4	0	2	1	4	1	2	rs75962473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:139170412A>G	ENST00000423192.1	+	8	1071	c.910A>G	c.(910-912)Atg>Gtg	p.M304V	ECT2L_ENST00000541398.1_Missense_Mutation_p.M235V|ECT2L_ENST00000367682.2_Missense_Mutation_p.M304V			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like	304							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						CCAGATGGTGATGGAGAGTGT	0.398			"N, Splice, Mis"		ETP ALL								G|||	67	0.0133786	0.0477	0.0058	5008	,	,		15878	0.0		0.0	False		,,,				2504	0.0				p.M304V		Atlas-SNP	.		Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	.	ECT2L	75	.	0			c.A910G						PASS	.	G	VAL/MET,VAL/MET	132,3612		4,124,1744	213	193	199		910,910	3.8	0.7	6	dbSNP_131	199	4,8222		0,4,4109	yes	missense,missense	ECT2L	NM_001077706.2,NM_001195037.2	21,21	4,128,5853	GG,GA,AA		0.0486,3.5256,1.1362	benign,benign	304/905,304/905	139170412	136,11834	1872	4113	5985	SO:0001583	missense	345930	exon8			ATGGTGATGGAGA		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.910A>G	6.37:g.139170412A>G	ENSP00000387388:p.Met304Val	120	0	0		132	69	0.522727	NM_001195037	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Missense_Mutation	SNP	ENST00000423192.1	37	CCDS43508.1	23	0.010531135531135532	20	0.04065040650406504	3	0.008287292817679558	0	0.0	0	0.0	G	0.004	-2.271576	0.00257	0.035256	4.86E-4	ENSG00000203734	ENST00000423192;ENST00000367682;ENST00000541398	T;T;T	0.72942	0.41;0.41;-0.7	5.6	3.8	0.43715	.	1.849090	0.04925	N	0.455693	T	0.14056	0.0340	N	0.01109	-1.01	0.19300	N	0.999979	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34950	-0.9808	10	0.02654	T	1	-0.0057	7.1142	0.25407	0.1538:0.1408:0.7055:0.0	.	235;304	F5H7S9;Q008S8	.;ECT2L_HUMAN	V	304;304;235	ENSP00000387388:M304V;ENSP00000356655:M304V;ENSP00000442307:M235V	ENSP00000356655:M304V	M	+	1	0	ECT2L	139212105	1.000000	0.71417	0.718000	0.30602	0.010000	0.07245	0.951000	0.29135	0.406000	0.25560	-0.186000	0.12905	ATG	A|0.992;G|0.008	0.008	strong		0.398	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706		G	139170412	A	G	139170412	3	3	22	1	0	0	0	0	1	0	0	0	4904	333	12	3	936	3	ECT2L	6	139170412	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	75476	139170412	31944655	1567	4468											
HECA	51696	hgsc.bcm.edu	37	chr6	139488364	139488364	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	gccctgtgccaccgggcgctCccggtgttcgaacagttccc	4	8	12	17	4	0	0	0	0	0	0	3	1	2	0	5	2	2	3	5	2	1	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:139488364C>G	ENST00000367658.2	+	2	1500	c.1215C>G	c.(1213-1215)ctC>ctG	p.L405L	RP1-225E12.2_ENST00000588638.1_RNA|RP1-225E12.2_ENST00000587577.1_RNA|RP1-225E12.2_ENST00000591102.1_RNA|RP1-225E12.2_ENST00000586229.1_RNA|RP1-225E12.2_ENST00000585447.1_RNA|RP1-225E12.2_ENST00000588529.1_RNA|RP1-225E12.2_ENST00000415194.2_RNA|RP1-225E12.3_ENST00000585874.1_RNA|RP1-225E12.2_ENST00000586266.1_RNA|RP1-225E12.2_ENST00000590679.1_RNA|RP1-225E12.2_ENST00000589192.1_RNA	NM_016217.2	NP_057301.1	Q9UBI9	HDC_HUMAN	headcase homolog (Drosophila)	405					respiratory tube development (GO:0030323)	membrane (GO:0016020)				endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)	15				GBM - Glioblastoma multiforme(68;0.000252)|OV - Ovarian serous cystadenocarcinoma(155;0.000387)		ACCGGGCGCTCCCGGTGTTCG	0.557																																					p.L405L		Atlas-SNP	.											.	HECA	45	.	0			c.C1215G						PASS	.						62	57	59					6																	139488364		2203	4300	6503	SO:0001819	synonymous_variant	51696	exon2			GGCGCTCCCGGTG	AB033492	CCDS5194.1	6q23-q24	2010-11-25			ENSG00000112406	ENSG00000112406			21041	protein-coding gene	gene with protein product		607977				11696983, 19643820	Standard	NM_016217		Approved	HDCL, hHDC, HDC, dJ225E12.1	uc003qin.3	Q9UBI9	OTTHUMG00000015686	ENST00000367658.2:c.1215C>G	6.37:g.139488364C>G		95	0	0		96	59	0.614583	NM_016217		Silent	SNP	ENST00000367658.2	37	CCDS5194.1																																																																																			.	.	none		0.557	HECA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042456.1	NM_016217		G	139488364	C	G	139488364	2	3	22	1	0	0	0	0	0	0	0	1	7047	842	30	4		4	HECA	6	139488364	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	317952	139488364	31626703	1568	4469											
FUCA2	2519	hgsc.bcm.edu	37	chr6	143816869	143816869	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacattagtcagggctagaGcccagccccatttacacggc	10	8	9	14	1	2	1	2	0	0	1	2	1	2	1	3	2	3	1	3	2	3	4	rs151156975		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:143816869G>A	ENST00000002165.6	-	7	1434	c.1379C>T	c.(1378-1380)gCt>gTt	p.A460V	RP1-20N2.6_ENST00000591892.1_RNA|RP1-20N2.6_ENST00000610068.1_RNA|RP1-20N2.6_ENST00000589563.1_RNA	NM_032020.4	NP_114409.2	Q9BTY2	FUCO2_HUMAN	fucosidase, alpha-L- 2, plasma	460					fucose metabolic process (GO:0006004)|glycoside catabolic process (GO:0016139)|regulation of entry of bacterium into host cell (GO:2000535)|response to bacterium (GO:0009617)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				OV - Ovarian serous cystadenocarcinoma(155;7.45e-06)|GBM - Glioblastoma multiforme(68;0.0142)		CAGGGCTAGAGCCCAGCCCCA	0.453																																					p.A460V		Atlas-SNP	.											.	FUCA2	28	.	0			c.C1379T						PASS	.	G	VAL/ALA	0,4406		0,0,2203	98	82	87		1379	5.4	0.8	6	dbSNP_134	87	1,8599	1.2+/-3.3	0,1,4299	no	missense	FUCA2	NM_032020.4	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	460/468	143816869	1,13005	2203	4300	6503	SO:0001583	missense	2519	exon7			GCTAGAGCCCAGC	BC003060	CCDS5200.1	6q24	2012-10-02			ENSG00000001036	ENSG00000001036	3.2.1.51		4008	protein-coding gene	gene with protein product		136820				6590153	Standard	NM_032020		Approved	MGC1314, dJ20N2.5	uc003qjm.3	Q9BTY2	OTTHUMG00000015728	ENST00000002165.6:c.1379C>T	6.37:g.143816869G>A	ENSP00000002165:p.Ala460Val	109	0	0		120	66	0.55	NM_032020	E9PEB6|Q7Z6V1|Q7Z6Y2|Q8NBK4	Missense_Mutation	SNP	ENST00000002165.6	37	CCDS5200.1	.	.	.	.	.	.	.	.	.	.	G	2.438	-0.329383	0.05314	0.0	1.16E-4	ENSG00000001036	ENST00000002165	T	0.50001	0.76	5.44	5.44	0.79542	.	0.495248	0.23750	N	0.044936	T	0.10423	0.0255	N	0.05383	-0.06	0.80722	D	1	B	0.02656	0.0	B	0.08055	0.003	T	0.12041	-1.0563	10	0.02654	T	1	-0.6766	12.588	0.56428	0.0758:0.0:0.9242:0.0	.	460	Q9BTY2	FUCO2_HUMAN	V	460	ENSP00000002165:A460V	ENSP00000002165:A460V	A	-	2	0	FUCA2	143858562	0.998000	0.40836	0.842000	0.33263	0.068000	0.16541	6.197000	0.72100	2.575000	0.86900	0.650000	0.86243	GCT	G|1.000;A|0.000	0.000	weak		0.453	FUCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042521.2	NM_032020		A	143816869	G	A	143816869	3	1	22	1	0	0	0	0	1	0	0	0	6103	971	34	2	28	2	FUCA2	6	143816869	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4328505	143816869	27298198	1569	4470											
SHPRH	257218	hgsc.bcm.edu	37	chr6	146276280	146276280	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagccacttcttcctttagaCtatcacttagaatgatataa	13	14	5	9	0	2	3	1	1	1	2	3	4	3	3	2	0	1	0	2	0	6	8	rs182151362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:146276280C>T	ENST00000367505.2	-	2	443	c.179G>A	c.(178-180)aGt>aAt	p.S60N	SHPRH_ENST00000367503.3_Missense_Mutation_p.S60N|SHPRH_ENST00000438092.2_Missense_Mutation_p.S60N|SHPRH_ENST00000275233.7_Missense_Mutation_p.S60N			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	60					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)		TTCCTTTAGACTATCACTTAG	0.408													C|||	22	0.00439297	0.0144	0.0014	5008	,	,		18451	0.0		0.002	False		,,,				2504	0.0				p.S60N		Atlas-SNP	.											.	SHPRH	169	.	0			c.G179A						PASS	.	C	ASN/SER,ASN/SER	53,3687		0,53,1817	106	97	100		179,179	1.9	0	6		100	4,8210		0,4,4103	yes	missense,missense	SHPRH	NM_001042683.2,NM_173082.3	46,46	0,57,5920	TT,TC,CC		0.0487,1.4171,0.4768	benign,benign	60/1684,60/1660	146276280	57,11897	1870	4107	5977	SO:0001583	missense	257218	exon2			TTTAGACTATCAC	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.179G>A	6.37:g.146276280C>T	ENSP00000356475:p.Ser60Asn	86	0	0		115	52	0.452174	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	ENST00000367505.2	37	CCDS43513.2	4	0.0018315018315018315	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	C	4.394	0.072688	0.08436	0.014171	4.87E-4	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233	T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09	5.66	1.9	0.25705	.	0.291823	0.32068	N	0.006636	T	0.34250	0.0891	L	0.50333	1.59	0.09310	N	1	B;B	0.31548	0.22;0.328	B;B	0.32864	0.073;0.154	T	0.21690	-1.0238	10	0.49607	T	0.09	0.0517	8.8158	0.34996	0.0:0.6472:0.0:0.3528	.	60;60	Q149N8;Q149N8-4	SHPRH_HUMAN;.	N	60	ENSP00000356475:S60N;ENSP00000356473:S60N;ENSP00000412797:S60N;ENSP00000275233:S60N	ENSP00000275233:S60N	S	-	2	0	SHPRH	146317973	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	0.321000	0.19558	0.332000	0.23536	-0.136000	0.14681	AGT	C|0.998;T|0.002	0.002	strong		0.408	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082		T	146276280	C	T	146276280	3	4	22	1	0	0	0	0	1	0	0	0	14306	565	20	2	5032	2	SHPRH	6	146276280	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2459411	146276280	24838787	1570	4471											
GRM1	2911	hgsc.bcm.edu	37	chr6	146755561	146755561	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	tgtacccgcccccgccacctCcgcagcacctgcagatgctg	6	6	9	20	3	0	1	0	0	0	1	1	1	1	1	7	0	4	5	7	0	1	1	rs146753539	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:146755561C>G	ENST00000282753.1	+	8	3449	c.3214C>G	c.(3214-3216)Ccg>Gcg	p.P1072A	GRM1_ENST00000492807.2_3'UTR|GRM1_ENST00000507907.1_3'UTR|GRM1_ENST00000355289.4_3'UTR|GRM1_ENST00000392299.2_3'UTR|GRM1_ENST00000361719.2_Missense_Mutation_p.P1072A			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	1072	Gln/Pro-rich.				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)		CCCGCCACCTCCGCAGCACCT	0.682													C|||	28	0.00559105	0.0174	0.0043	5008	,	,		14178	0.0		0.002	False		,,,				2504	0.0				p.P1072A		Atlas-SNP	.											GRM1,NS,carcinoma,-1,1	GRM1	419	1	0			c.C3214G						PASS	.	C	ALA/PRO,	67,4321		0,67,2127	29	33	32		3214,	2.9	0.5	6	dbSNP_134	32	12,8572		0,12,4280	yes	missense,utr-3	GRM1	NM_000838.3,NM_001114329.1	27,	0,79,6407	GG,GC,CC		0.1398,1.5269,0.609	benign,	1072/1195,	146755561	79,12893	2194	4292	6486	SO:0001583	missense	2911	exon9			CCACCTCCGCAGC	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.3214C>G	6.37:g.146755561C>G	ENSP00000282753:p.Pro1072Ala	63	0	0		68	23	0.338235	NM_000838	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Missense_Mutation	SNP	ENST00000282753.1	37	CCDS5209.1	13	0.005952380952380952	10	0.02032520325203252	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	C	9.887	1.203100	0.22121	0.015269	0.001398	ENSG00000152822	ENST00000361719;ENST00000282753	D;D	0.87809	-2.3;-2.3	5.71	2.87	0.33458	.	0.283949	0.40144	N	0.001180	T	0.65386	0.2686	L	0.29908	0.895	0.22142	N	0.999333	B	0.13594	0.008	B	0.16722	0.016	T	0.60383	-0.7274	10	0.51188	T	0.08	.	9.181	0.37141	0.0:0.7456:0.1201:0.1343	.	1072	Q13255	GRM1_HUMAN	A	1072	ENSP00000354896:P1072A;ENSP00000282753:P1072A	ENSP00000282753:P1072A	P	+	1	0	GRM1	146797254	0.024000	0.19004	0.468000	0.27192	0.601000	0.36947	0.978000	0.29488	0.730000	0.32425	0.462000	0.41574	CCG	C|0.993;G|0.007	0.007	strong		0.682	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838		G	146755561	C	G	146755561	3	3	22	1	0	0	0	0	1	0	0	0	6805	855	30	4	3309	4	GRM1	6	146755561	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	479281	146755561	24359506	1571	4472											
TAB2	23118	hgsc.bcm.edu	37	chr6	149699333	149699333	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taccaccatggaagagaaggAagtaggatgaatggaagtag	17	6	14	4	0	0	2	0	1	0	1	0	7	0	6	2	4	1	2	2	4	8	3	rs13215304	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:149699333A>G	ENST00000367456.1	+	4	859	c.282A>G	c.(280-282)ggA>ggG	p.G94G	TAB2_ENST00000286332.5_Silent_p.G94G|TAB2_ENST00000536230.1_Silent_p.G62G|TAB2_ENST00000538427.1_Silent_p.G94G|TAB2_ENST00000392282.1_Silent_p.G94G			Q9NYJ8	TAB2_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 2	94					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						GAAGAGAAGGAAGTAGGATGA	0.428													A|||	55	0.0109824	0.0	0.0288	5008	,	,		20789	0.001		0.0328	False		,,,				2504	0.001				p.G94G		Atlas-SNP	.											TAB2,NS,carcinoma,+2,1	TAB2	55	1	0			c.A282G						scavenged	.	A		32,4374	36.0+/-67.5	0,32,2171	132	115	120		282	3.3	1	6	dbSNP_121	120	268,8332	103.1+/-164.3	4,260,4036	no	coding-synonymous	TAB2	NM_015093.4		4,292,6207	GG,GA,AA		3.1163,0.7263,2.3066		94/694	149699333	300,12706	2203	4300	6503	SO:0001819	synonymous_variant	23118	exon5			AGAAGGAAGTAGG	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.282A>G	6.37:g.149699333A>G		132	1	0.00757576		141	70	0.496454	NM_015093	B2RCC4|E1P5A0|O94838|Q6I9W8|Q76N06|Q9UFP7	Silent	SNP	ENST00000367456.1	37	CCDS5214.1																																																																																			A|0.977;G|0.023	0.023	strong		0.428	TAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042633.3			G	149699333	A	G	149699333	2	3	22	1	0	0	0	0	0	0	0	1	15511	233	9	3		3	TAB2	6	149699333	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2943772	149699333	21415734	1572	4473											
ZC3H12D	340152	hgsc.bcm.edu	37	chr6	149777914	149777914	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggagacgatgacgccgtcctGctcgtaggccaccttcacga	8	7	12	14	5	1	2	1	1	0	1	3	5	2	2	4	2	1	2	4	2	1	2	rs200917878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:149777914G>T	ENST00000409806.3	-	4	886	c.568C>A	c.(568-570)Cag>Aag	p.Q190K	ZC3H12D_ENST00000542614.1_Missense_Mutation_p.Q190K|ZC3H12D_ENST00000416573.2_Missense_Mutation_p.Q190K|ZC3H12D_ENST00000389942.5_Missense_Mutation_p.Q190K			A2A288	ZC12D_HUMAN	zinc finger CCCH-type containing 12D	190					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)		ACGCCGTCCTGCTCGTAGGCC	0.627													G|||	13	0.00259585	0.0076	0.0029	5008	,	,		12923	0.001		0.0	False		,,,				2504	0.0				p.Q190K		Atlas-SNP	.											.	ZC3H12D	21	.	0			c.C568A						PASS	.	G	LYS/GLN	63,4247		1,61,2093	85	95	92		568	1.6	1	6		92	1,8539		0,1,4269	yes	missense	ZC3H12D	NM_207360.2	53	1,62,6362	TT,TG,GG		0.0117,1.4617,0.4981	benign	190/528	149777914	64,12786	2155	4270	6425	SO:0001583	missense	340152	exon4			CGTCCTGCTCGTA			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.568C>A	6.37:g.149777914G>T	ENSP00000386616:p.Gln190Lys	61	0	0		53	23	0.433962	NM_207360	A1L178|B2RXF4|B7WNU7|B9ZZP9|B9ZZQ0|Q6ZRW2	Missense_Mutation	SNP	ENST00000409806.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.37|10.37	1.330416|1.330416	0.24167|0.24167	0.014617|0.014617	1.17E-4|1.17E-4	ENSG00000178199|ENSG00000178199	ENST00000458251|ENST00000389942;ENST00000416573;ENST00000409806;ENST00000542614	.|T;T;T;T	.|0.38560	.|1.13;1.13;1.13;1.13	4.84|4.84	1.63|1.63	0.23807|0.23807	.|Ribonuclease Zc3h12a-like (1);	.|0.660796	.|0.14612	.|N	.|0.308967	T|T	0.01387|0.01387	0.0045|0.0045	N|N	0.00035|0.00035	-2.545|-2.545	0.20403|0.20403	N|N	0.999907|0.999907	.|B;B	.|0.10296	.|0.003;0.0	.|B;B	.|0.08055	.|0.003;0.001	T|T	0.47328|0.47328	-0.9126|-0.9126	5|10	.|0.02654	.|T	.|1	-11.5336|-11.5336	5.6416|5.6416	0.17567|0.17567	0.183:0.0:0.4125:0.4045|0.183:0.0:0.4125:0.4045	.|.	.|190;190	.|A2A288;B7WNU7	.|ZC12D_HUMAN;.	E|K	31|190	.|ENSP00000374592:Q190K;ENSP00000408686:Q190K;ENSP00000386616:Q190K;ENSP00000440813:Q190K	.|ENSP00000374592:Q190K	A|Q	-|-	2|1	0|0	ZC3H12D|ZC3H12D	149819607|149819607	0.890000|0.890000	0.30428|0.30428	0.999000|0.999000	0.59377|0.59377	0.998000|0.998000	0.95712|0.95712	1.503000|1.503000	0.35715|0.35715	0.574000|0.574000	0.29417|0.29417	0.561000|0.561000	0.74099|0.74099	GCA|CAG	.	.	weak		0.627	ZC3H12D-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000286400.2	NM_207360		T	149777914	G	T	149777914	3	4	22	1	0	0	0	0	1	0	0	0	17579	1328	46	4	1027	4	ZC3H12D	6	149777914	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	78581	149777914	21337153	1573	4474											
LRP11	84918	hgsc.bcm.edu	37	chr6	150158486	150158486	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caactcacgattctggcagaAgtcttcatcagacccatcag	12	9	7	13	1	6	2	4	0	2	2	6	3	6	2	1	1	1	1	1	1	2	2	rs375299752		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:150158486A>G	ENST00000239367.2	-	4	1032	c.1027T>C	c.(1027-1029)Ttc>Ctc	p.F343L	LRP11_ENST00000463728.1_5'Flank|LRP11_ENST00000546019.1_Missense_Mutation_p.F88L	NM_032832.5	NP_116221.3	Q86VZ4	LRP11_HUMAN	low density lipoprotein receptor-related protein 11	343	LDL-receptor class A. {ECO:0000255|PROSITE-ProRule:PRU00124}.					integral component of membrane (GO:0016021)				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)		TTCTGGCAGAAGTCTTCATCA	0.517																																					p.F343L		Atlas-SNP	.											.	LRP11	27	.	0			c.T1027C						PASS	.	A	LEU/PHE	2,4404	4.2+/-10.8	0,2,2201	122	101	108		1027	5.3	0.9	6		108	0,8600		0,0,4300	no	missense	LRP11	NM_032832.5	22	0,2,6501	GG,GA,AA		0.0,0.0454,0.0154	probably-damaging	343/501	150158486	2,13004	2203	4300	6503	SO:0001583	missense	84918	exon4			GGCAGAAGTCTTC	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.1027T>C	6.37:g.150158486A>G	ENSP00000239367:p.Phe343Leu	120	0	0		107	41	0.383178	NM_032832	Q5VYC0|Q96SN6	Missense_Mutation	SNP	ENST00000239367.2	37	CCDS5220.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.958758	0.92726	4.54E-4	0.0	ENSG00000120256	ENST00000239367;ENST00000546019	D;D	0.95272	-3.66;-3.66	5.32	5.32	0.75619	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.93416	0.7900	N	0.24115	0.695	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94587	0.7784	10	0.51188	T	0.08	-22.8051	14.5589	0.68120	1.0:0.0:0.0:0.0	.	343	Q86VZ4	LRP11_HUMAN	L	343;88	ENSP00000239367:F343L;ENSP00000440196:F88L	ENSP00000239367:F343L	F	-	1	0	LRP11	150200179	1.000000	0.71417	0.923000	0.36655	0.767000	0.43475	8.118000	0.89577	2.134000	0.65973	0.455000	0.32223	TTC	.	.	weak		0.517	LRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042664.1	NM_032832		G	150158486	A	G	150158486	3	3	22	1	0	0	0	0	1	0	0	0	8962	72	3	3	491	3	LRP11	6	150158486	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	380572	150158486	20956581	1574	4475											
TIAM2	26230	hgsc.bcm.edu	37	chr6	155486535	155486535	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcaaggagaagagaccttctAtaactcaggtgagcttttca	13	10	10	8	0	3	3	2	1	1	2	3	5	3	3	1	2	2	2	1	2	4	5	rs62621836	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:155486535A>G	ENST00000461783.3	+	11	3626	c.2353A>G	c.(2353-2355)Ata>Gta	p.I785V	TIAM2_ENST00000318981.5_Missense_Mutation_p.I785V|TIAM2_ENST00000529824.2_Missense_Mutation_p.I785V|TIAM2_ENST00000456144.1_Missense_Mutation_p.I785V|TIAM2_ENST00000456877.2_Missense_Mutation_p.I97V|TIAM2_ENST00000528391.2_Missense_Mutation_p.I97V|TIAM2_ENST00000367174.2_Missense_Mutation_p.I137V|TIAM2_ENST00000360366.4_Missense_Mutation_p.I785V			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	785					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)		GAGACCTTCTATAACTCAGGT	0.448													A|||	100	0.0199681	0.0719	0.0072	5008	,	,		19834	0.0		0.0	False		,,,				2504	0.0				p.I785V		Atlas-SNP	.											.	TIAM2	161	.	0			c.A2353G						PASS	.	A	VAL/ILE	301,4105	165.4+/-196.9	7,287,1909	68	64	65		2353	-4.4	0	6	dbSNP_129	65	2,8598	1.2+/-3.3	0,2,4298	yes	missense	TIAM2	NM_012454.3	29	7,289,6207	GG,GA,AA		0.0233,6.8316,2.3297	benign	785/1702	155486535	303,12703	2203	4300	6503	SO:0001583	missense	26230	exon8			CCTTCTATAACTC		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.2353A>G	6.37:g.155486535A>G	ENSP00000437188:p.Ile785Val	96	0	0		114	59	0.517544	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Missense_Mutation	SNP	ENST00000461783.3	37	CCDS34558.1	21	0.009615384615384616	20	0.04065040650406504	1	0.0027624309392265192	0	0.0	0	0.0	A	10.77	1.443893	0.25987	0.068316	2.33E-4	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000528535;ENST00000456144;ENST00000318981;ENST00000367174;ENST00000360366;ENST00000529824;ENST00000456877;ENST00000528391	T;T;T;T;T;T;T;T;T	0.06142	3.48;3.39;3.44;3.48;3.4;3.57;3.44;3.34;3.4	5.01	-4.42	0.03579	.	0.494314	0.23646	N	0.045965	T	0.01558	0.0050	M	0.61703	1.905	0.20196	N	0.999928	B;B;B;B	0.10296	0.0;0.003;0.003;0.002	B;B;B;B	0.12837	0.008;0.006;0.003;0.003	T	0.48670	-0.9015	10	0.17832	T	0.49	.	6.285	0.21029	0.3957:0.2475:0.3568:0.0	rs62621836	97;785;785;785	E9PKT1;Q8IVF5-2;Q8IVF5-5;Q8IVF5	.;.;.;TIAM2_HUMAN	V	785;1031;785;785;785;137;785;785;97;97	ENSP00000437188:I785V;ENSP00000434901:I785V;ENSP00000407746:I785V;ENSP00000327315:I785V;ENSP00000356142:I137V;ENSP00000353528:I785V;ENSP00000433348:I785V;ENSP00000407183:I97V;ENSP00000435335:I97V	ENSP00000327315:I785V	I	+	1	0	TIAM2	155528227	0.000000	0.05858	0.010000	0.14722	0.881000	0.50899	-0.215000	0.09279	-1.006000	0.03412	-0.274000	0.10170	ATA	A|0.979;G|0.021	0.021	strong		0.448	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454		G	155486535	A	G	155486535	3	3	22	1	0	0	0	0	1	0	0	0	15906	449	16	3	2375	3	TIAM2	6	155486535	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	5328049	155486535	15628532	1575	4476											
ARID1B	57492	hgsc.bcm.edu	37	chr6	157099402	157099403	+	In_Frame_Ins	INS	-	-	CAGCAG																															agcagcagctaaaccagttcINScagcagcagcagcagcagca																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:157099402_157099403insCAGCAG	ENST00000350026.5	+	1	340_341	c.339_340insCAGCAG	c.(340-342)cag>CAGCAGcag	p.114_114Q>QQQ	ARID1B_ENST00000275248.4_In_Frame_Ins_p.56_56Q>QQQ|RP11-230C9.3_ENST00000604792.1_RNA|ARID1B_ENST00000367148.1_In_Frame_Ins_p.114_114Q>QQQ|MIR4466_ENST00000606121.1_RNA|RP11-230C9.2_ENST00000603191.1_lincRNA|ARID1B_ENST00000346085.5_In_Frame_Ins_p.114_114Q>QQQ	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	114	Gln-rich.|Poly-Gln.				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)		TAAACCAGTTCcagcagcagca	0.639																																					p.F113delinsFQQ		Atlas-Indel	.											.	ARID1B	320	.	0			c.339_340insCAGCAG						PASS	.																																			SO:0001652	inframe_insertion	57492	exon1			.	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.352_357dupCAGCAG	6.37:g.157099403_157099408dupCAGCAG	ENSP00000055163:p.GlnGln130dup	30	0	0		27	12	0.444444	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	In_Frame_Ins	INS	ENST00000350026.5	37	CCDS5251.2																																																																																			.	.	none		0.639	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		CAGCAG	157099403	-	CAGCAG	157099402	7	5	22	1	0	1	1	0	0	0	0	0	914	854	30	0	341	0	ARID1B	6	157099402	In_Frame_Ins	INS	-	TCGA-G8-6324-01A-11D-2210-10	1612867	157099402	14015665	1576	4477											
ARID1B	57492	hgsc.bcm.edu	37	chr6	157505478	157505478	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtacctgtttgcctttgaGtgcaagatcgaacgtgggga	9	11	13	8	2	0	2	0	1	0	1	1	4	0	3	2	2	4	3	2	2	3	3	rs61745451	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:157505478G>A	ENST00000350026.5	+	12	3421	c.3420G>A	c.(3418-3420)gaG>gaA	p.E1140E	ARID1B_ENST00000275248.4_Silent_p.E1135E|ARID1B_ENST00000346085.5_Silent_p.E1153E|ARID1B_ENST00000367148.1_Silent_p.E1193E	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1140	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				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)		TTGCCTTTGAGTGCAAGATCG	0.567													G|||	68	0.0135783	0.0492	0.0014	5008	,	,		18188	0.0		0.002	False		,,,				2504	0.0				p.E1153E		Atlas-SNP	.											.	ARID1B	320	.	0			c.G3459A						PASS	.	G	,	141,4265	99.8+/-138.5	1,139,2063	80	77	78		3420,3459	5.9	1	6	dbSNP_129	78	3,8589	3.0+/-9.4	0,3,4293	no	coding-synonymous,coding-synonymous	ARID1B	NM_017519.2,NM_020732.3	,	1,142,6356	AA,AG,GG		0.0349,3.2002,1.1079	,	1140/2237,1153/2250	157505478	144,12854	2203	4296	6499	SO:0001819	synonymous_variant	57492	exon13			CTTTGAGTGCAAG	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.3420G>A	6.37:g.157505478G>A		150	0	0		162	75	0.462963	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Silent	SNP	ENST00000350026.5	37	CCDS5251.2																																																																																			G|0.989;A|0.011	0.011	strong		0.567	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732		A	157505478	G	A	157505478	2	1	22	1	0	0	0	0	0	0	0	1	914	1020	36	2		2	ARID1B	6	157505478	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	406076	157505478	13609589	1577	4478											
FNDC1	84624	hgsc.bcm.edu	37	chr6	159647584	159647584	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcgctgcatcttgggatgcGctaccagagactgaggggaa	9	8	15	9	2	1	2	0	1	1	1	2	5	1	4	1	3	3	3	1	3	2	2	rs12110595	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:159647584G>A	ENST00000297267.9	+	9	1352	c.1152G>A	c.(1150-1152)gcG>gcA	p.A384A	FNDC1_ENST00000480856.1_3'UTR|FNDC1_ENST00000340366.6_Silent_p.A384A	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	384	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)		CTTGGGATGCGCTACCAGAGA	0.473													G|||	264	0.0527157	0.1876	0.0216	5008	,	,		20701	0.001		0.0	False		,,,				2504	0.0				p.A384A		Atlas-SNP	.											.	FNDC1	250	.	0			c.G1152A						PASS	.	G		716,3112		66,584,1264	97	94	95		1152	-10.6	0	6	dbSNP_120	95	8,8254		0,8,4123	no	coding-synonymous	FNDC1	NM_032532.2		66,592,5387	AA,AG,GG		0.0968,18.7043,5.9884		384/1895	159647584	724,11366	1914	4131	6045	SO:0001819	synonymous_variant	84624	exon9			GGATGCGCTACCA	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.1152G>A	6.37:g.159647584G>A		85	0	0		50	17	0.34	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Silent	SNP	ENST00000297267.9	37	CCDS47512.1	111	0.050824175824175824	103	0.20934959349593496	8	0.022099447513812154	0	0.0	0	0.0	G	7.656	0.683920	0.14907	0.187043	9.68E-4	ENSG00000164694	ENST00000329629	T	0.03181	4.02	5.29	-10.6	0.00265	.	0.279587	0.34777	N	0.003696	T	0.00845	0.0028	.	.	.	0.09310	P	0.999999999722547	.	.	.	.	.	.	T	0.17899	-1.0354	6	0.40728	T	0.16	-5.1754	3.7308	0.08492	0.176:0.081:0.3814:0.3616	rs12110595;rs57583348;rs12110595	.	.	.	T	343	ENSP00000333297:A343T	ENSP00000333297:A343T	A	+	1	0	FNDC1	159567572	0.002000	0.14202	0.028000	0.17463	0.773000	0.43773	-1.392000	0.02523	-2.325000	0.00638	-1.283000	0.01379	GCT	G|0.929;A|0.071	0.071	strong		0.473	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		A	159647584	G	A	159647584	2	1	22	1	0	0	0	0	0	0	0	1	5976	1074	38	1		1	FNDC1	6	159647584	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2142106	159647584	11467483	1578	4479											
FNDC1	84624	hgsc.bcm.edu	37	chr6	159654408	159654408	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggctcaggatgttcaacagaGcacagacgcggacacggagg	12	4	15	10	3	2	2	2	0	0	2	2	5	2	5	0	5	2	3	0	5	1	1	rs73799344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:159654408G>A	ENST00000297267.9	+	11	3064	c.2864G>A	c.(2863-2865)aGc>aAc	p.S955N	FNDC1_ENST00000340366.6_Missense_Mutation_p.S892N	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	955					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)		GTTCAACAGAGCACAGACGCG	0.617													G|||	259	0.0517173	0.1846	0.0216	5008	,	,		18211	0.0		0.0	False		,,,				2504	0.0				p.S955N		Atlas-SNP	.											.	FNDC1	250	.	0			c.G2864A						PASS	.	G	ASN/SER	784,3552		68,648,1452	57	68	64		2864	3.8	0.1	6	dbSNP_130	64	8,8520		0,8,4256	yes	missense	FNDC1	NM_032532.2	46	68,656,5708	AA,AG,GG		0.0938,18.0812,6.1567	benign	955/1895	159654408	792,12072	2168	4264	6432	SO:0001583	missense	84624	exon11			AACAGAGCACAGA	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.2864G>A	6.37:g.159654408G>A	ENSP00000297267:p.Ser955Asn	50	0	0		55	25	0.454545	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	107	0.04899267399267399	99	0.20121951219512196	8	0.022099447513812154	0	0.0	0	0.0	G	16.37	3.104157	0.56291	0.180812	9.38E-4	ENSG00000164694	ENST00000297267;ENST00000340366	T;T	0.10005	2.92;3.77	3.81	3.81	0.43845	.	0.352689	0.24945	N	0.034358	T	0.06735	0.0172	L	0.29908	0.895	0.58432	P	1.999999999946489E-6	D;P	0.57257	0.979;0.734	P;B	0.56563	0.801;0.398	T	0.27839	-1.0062	9	0.13108	T	0.6	-19.0686	11.4852	0.50350	0.0:0.0:1.0:0.0	.	892;955	Q4ZHG4-2;Q4ZHG4	.;FNDC1_HUMAN	N	955;892	ENSP00000297267:S955N;ENSP00000342460:S892N	ENSP00000297267:S955N	S	+	2	0	FNDC1	159574398	0.523000	0.26274	0.140000	0.22221	0.635000	0.38103	1.701000	0.37825	2.423000	0.82170	0.561000	0.74099	AGC	G|0.959;A|0.041	0.041	strong		0.617	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		A	159654408	G	A	159654408	3	1	22	1	0	0	0	0	1	0	0	0	5976	971	34	2	2906	2	FNDC1	6	159654408	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6824	159654408	11460659	1579	4480											
FNDC1	84624	hgsc.bcm.edu	37	chr6	159654720	159654720	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcggacccttacacggcgaGctccagagggatgctcccca	8	6	11	16	3	0	1	0	0	0	1	3	4	2	3	4	3	3	2	4	3	1	1	rs115529940	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:159654720G>C	ENST00000297267.9	+	11	3376	c.3176G>C	c.(3175-3177)aGc>aCc	p.S1059T	FNDC1_ENST00000340366.6_Missense_Mutation_p.S996T	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1059					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)		TACACGGCGAGCTCCAGAGGG	0.701													G|||	62	0.0123802	0.0439	0.0058	5008	,	,		14068	0.0		0.0	False		,,,				2504	0.0				p.S1059T		Atlas-SNP	.											.	FNDC1	250	.	0			c.G3176C						PASS	.	G	THR/SER	102,3642		2,98,1772	9	12	11		3176	0.4	0.1	6	dbSNP_132	11	1,7791		0,1,3895	yes	missense	FNDC1	NM_032532.2	58	2,99,5667	CC,CG,GG		0.0128,2.7244,0.8929	benign	1059/1895	159654720	103,11433	1872	3896	5768	SO:0001583	missense	84624	exon11			CGGCGAGCTCCAG	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.3176G>C	6.37:g.159654720G>C	ENSP00000297267:p.Ser1059Thr	37	0	0		45	9	0.2	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	25|25	0.011446886446886446|0.011446886446886446	23|23	0.046747967479674794|0.046747967479674794	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	G|G	12.73|12.73	2.026772|2.026772	0.35797|0.35797	0.027244|0.027244	1.28E-4|1.28E-4	ENSG00000164694|ENSG00000164694	ENST00000329629|ENST00000297267;ENST00000340366	.|T;T	.|0.09538	.|2.97;3.87	4.86|4.86	0.374|0.374	0.16183|0.16183	.|.	.|0.613338	.|0.15407	.|N	.|0.263994	T|T	0.01870|0.01870	0.0059|0.0059	L|L	0.27053|0.27053	0.805|0.805	0.09310|0.09310	N|N	1|1	.|P;P	.|0.40731	.|0.728;0.608	.|B;B	.|0.36092	.|0.217;0.115	T|T	0.42548|0.42548	-0.9445|-0.9445	5|10	.|0.51188	.|T	.|0.08	-5.582|-5.582	2.6419|2.6419	0.04973|0.04973	0.3758:0.0:0.4119:0.2123|0.3758:0.0:0.4119:0.2123	.|.	.|996;1059	.|Q4ZHG4-2;Q4ZHG4	.|.;FNDC1_HUMAN	D|T	954|1059;996	.|ENSP00000297267:S1059T;ENSP00000342460:S996T	.|ENSP00000297267:S1059T	E|S	+|+	3|2	2|0	FNDC1|FNDC1	159574710|159574710	0.096000|0.096000	0.21769|0.21769	0.052000|0.052000	0.19188|0.19188	0.053000|0.053000	0.15095|0.15095	0.113000|0.113000	0.15499|0.15499	0.445000|0.445000	0.26639|0.26639	0.561000|0.561000	0.74099|0.74099	GAG|AGC	G|0.986;C|0.014	0.014	strong		0.701	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		C	159654720	G	C	159654720	3	2	22	1	0	0	0	0	1	0	0	0	5976	971	34	4	3218	4	FNDC1	6	159654720	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	312	159654720	11460347	1580	4481											
IGF2R	3482	hgsc.bcm.edu	37	chr6	160469542	160469542	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgggctgcaaccgatatgcAtcggcttgccagatgaagta	10	8	12	11	3	0	2	0	1	0	1	1	3	0	2	3	2	4	5	3	2	4	3	rs8191809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:160469542A>G	ENST00000356956.1	+	18	2629	c.2481A>G	c.(2479-2481)gcA>gcG	p.A827A		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	827					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)	ACCGATATGCATCGGCTTGCC	0.493													A|||	48	0.00958466	0.0348	0.0029	5008	,	,		21284	0.0		0.0	False		,,,				2504	0.0				p.A827A		Atlas-SNP	.											.	IGF2R	251	.	0			c.A2481G						PASS	.	A		112,4294	85.8+/-124.5	0,112,2091	98	82	87		2481	-7.3	0	6	dbSNP_117	87	0,8600		0,0,4300	no	coding-synonymous	IGF2R	NM_000876.2		0,112,6391	GG,GA,AA		0.0,2.542,0.8611		827/2492	160469542	112,12894	2203	4300	6503	SO:0001819	synonymous_variant	3482	exon18			ATATGCATCGGCT	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.2481A>G	6.37:g.160469542A>G		65	0	0		68	33	0.485294	NM_000876	Q7Z7G9|Q96PT5	Silent	SNP	ENST00000356956.1	37	CCDS5273.1																																																																																			A|0.988;G|0.012	0.012	strong		0.493	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		G	160469542	A	G	160469542	2	3	22	1	0	0	0	0	0	0	0	1	7585	204	8	3		3	IGF2R	6	160469542	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	814822	160469542	10645525	1581	4482											
IGF2R	3482	hgsc.bcm.edu	37	chr6	160482929	160482929	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgggaaccagcgcttctccaCcaggatcacgtttgagtgtg	8	10	12	11	2	2	1	1	1	1	0	3	3	2	3	3	2	2	2	3	2	1	2	rs8191844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:160482929C>G	ENST00000356956.1	+	25	3699	c.3551C>G	c.(3550-3552)aCc>aGc	p.T1184S		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	1184			T -> S (in dbSNP:rs8191844). {ECO:0000269|Ref.5}.		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)	CGCTTCTCCACCAGGATCACG	0.522													C|||	40	0.00798722	0.0287	0.0029	5008	,	,		18416	0.0		0.0	False		,,,				2504	0.0				p.T1184S		Atlas-SNP	.											.	IGF2R	251	.	0			c.C3551G						PASS	.	C	SER/THR	127,4279	93.0+/-131.7	1,125,2077	159	148	152		3551	5.5	1	6	dbSNP_117	152	0,8600		0,0,4300	yes	missense	IGF2R	NM_000876.2	58	1,125,6377	GG,GC,CC		0.0,2.8824,0.9765	probably-damaging	1184/2492	160482929	127,12879	2203	4300	6503	SO:0001583	missense	3482	exon25			TCTCCACCAGGAT	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.3551C>G	6.37:g.160482929C>G	ENSP00000349437:p.Thr1184Ser	156	0	0		152	73	0.480263	NM_000876	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	37	CCDS5273.1	14	0.00641025641025641	12	0.024390243902439025	2	0.0055248618784530384	0	0.0	0	0.0	C	23.0	4.365286	0.82463	0.028824	0.0	ENSG00000197081	ENST00000356956	T	0.04275	3.66	5.5	5.5	0.81552	Mannose-6-phosphate receptor, binding (1);	0.000000	0.85682	D	0.000000	T	0.14270	0.0345	M	0.75615	2.305	0.52501	D	0.999957	D	0.89917	1.0	D	0.87578	0.998	T	0.01810	-1.1269	10	0.32370	T	0.25	-13.6676	17.5389	0.87841	0.0:1.0:0.0:0.0	rs8191844;rs52837912;rs8191844	1184	P11717	MPRI_HUMAN	S	1184	ENSP00000349437:T1184S	ENSP00000349437:T1184S	T	+	2	0	IGF2R	160402919	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.514000	0.67043	2.735000	0.93741	0.655000	0.94253	ACC	C|0.991;G|0.009	0.009	strong		0.522	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876		G	160482929	C	G	160482929	3	3	22	1	0	0	0	0	1	0	0	0	7585	507	18	4	3649	4	IGF2R	6	160482929	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	13387	160482929	10632138	1582	4483											
LPA	4018	hgsc.bcm.edu	37	chr6	160977167	160977167	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aatgtgcctcgataactctgGccattaccatggtagcactg	10	11	9	11	1	1	0	0	0	1	0	2	1	1	0	3	2	4	2	3	2	4	3	rs375904594		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:160977167G>T	ENST00000316300.5	-	30	4907	c.4863C>A	c.(4861-4863)ggC>ggA	p.G1621G	LPA_ENST00000447678.1_Silent_p.G1621G			P08519	APOA_HUMAN	lipoprotein, Lp(a)	4129	Kringle 15. {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)	GATAACTCTGGCCATTACCAT	0.483																																					p.G1621G		Atlas-SNP	.											LPA,right_upper_lobe,carcinoma,-1,1	LPA	237	1	0			c.C4863A						scavenged	.	T		0,4376		0,0,2188	154	156	155		4863	-5.5	0	6		155	1,8599		0,1,4299	no	coding-synonymous	LPA	NM_005577.2		0,1,6487	TT,TG,GG		0.0116,0.0,0.0077		1621/2041	160977167	1,12975	2188	4300	6488	SO:0001819	synonymous_variant	4018	exon31			ACTCTGGCCATTA	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.4863C>A	6.37:g.160977167G>T		342	2	0.00584795		361	33	0.0914127	NM_005577	Q5VTD7|Q9UD88	Silent	SNP	ENST00000316300.5	37	CCDS43523.1																																																																																			.	.	weak		0.483	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		T	160977167	G	T	160977167	2	4	22	1	0	0	0	0	0	0	0	1	8912	1190	42	4		4	LPA	6	160977167	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	494238	160977167	10137900	1583	4484											
LPA	4018	hgsc.bcm.edu	37	chr6	161026103	161026103	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgggtagtatgctggggtccGactatgcgagtgtggtgtca	6	12	17	6	2	1	0	1	0	0	0	2	2	2	0	1	4	2	3	1	4	3	3	rs189364869	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:161026103G>A	ENST00000316300.5	-	18	2964	c.2920C>T	c.(2920-2922)Cgg>Tgg	p.R974W	LPA_ENST00000447678.1_Missense_Mutation_p.R974W			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3482	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)	GCTGGGGTCCGACTATGCGAG	0.443													G|||	4	0.000798722	0.003	0.0	5008	,	,		21608	0.0		0.0	False		,,,				2504	0.0				p.R974W		Atlas-SNP	.											.	LPA	237	.	0			c.C2920T						PASS	.	G	TRP/ARG	12,4376	17.9+/-39.9	0,12,2182	367	381	376		2920	0.9	0	6		376	0,8596		0,0,4298	no	missense	LPA	NM_005577.2	101	0,12,6480	AA,AG,GG		0.0,0.2735,0.0924	probably-damaging	974/2041	161026103	12,12972	2194	4298	6492	SO:0001583	missense	4018	exon19			GGGTCCGACTATG	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.2920C>T	6.37:g.161026103G>A	ENSP00000321334:p.Arg974Trp	49	0	0		73	30	0.410959	NM_005577	Q5VTD7|Q9UD88	Missense_Mutation	SNP	ENST00000316300.5	37	CCDS43523.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	g	7.632	0.679154	0.14907	0.002735	0.0	ENSG00000198670	ENST00000316300;ENST00000447678	T;T	0.62941	-0.01;-0.01	2.16	0.902	0.19290	Kringle (4);Kringle-like fold (1);	.	.	.	.	T	0.61022	0.2314	M	0.78456	2.415	0.09310	N	1	D	0.89917	1.0	D	0.77557	0.99	T	0.47911	-0.9080	9	0.36615	T	0.2	.	5.0035	0.14277	0.0:0.0:0.3278:0.6722	.	3482	P08519	APOA_HUMAN	W	974	ENSP00000321334:R974W;ENSP00000395608:R974W	ENSP00000321334:R974W	R	-	1	2	LPA	160946093	0.049000	0.20398	0.002000	0.10522	0.135000	0.20990	0.804000	0.27098	0.095000	0.17434	0.184000	0.17185	CGG	G|0.999;A|0.001	0.001	strong		0.443	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577		A	161026103	G	A	161026103	3	1	22	1	0	0	0	0	1	0	0	0	8912	1057	37	1	3290	1	LPA	6	161026103	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	48936	161026103	10088964	1584	4485											
PARK2	5071	hgsc.bcm.edu	37	chr6	162475167	162475167	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggattggcattcaccactcaTccggtttggaattaaaacat	12	12	8	9	1	2	0	2	0	0	0	3	2	3	2	2	4	1	2	2	4	3	4	rs9456735	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:162475167T>G	ENST00000366898.1	-	5	676	c.574A>C	c.(574-576)Atg>Ctg	p.M192L	PARK2_ENST00000366892.1_Missense_Mutation_p.M192L|PARK2_ENST00000366894.1_Start_Codon_SNP_p.M1L|PARK2_ENST00000366897.1_Intron|PARK2_ENST00000338468.3_Start_Codon_SNP_p.M1L|PARK2_ENST00000366896.1_Intron	NM_004562.2	NP_004553.2	O60260	PRKN2_HUMAN	parkin RBR E3 ubiquitin protein ligase	192			M -> L (in PARK2; unknown pathological significance; dbSNP:rs9456735). {ECO:0000269|PubMed:11971093}.|M -> V (in PARK2; unknown pathological significance; dbSNP:rs9456735). {ECO:0000269|PubMed:12629236}.		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)		TCACCACTCATCCGGTTTGGA	0.398													T|||	95	0.0189696	0.0681	0.0029	5008	,	,		18248	0.0		0.003	False		,,,				2504	0.0				p.M192L		Atlas-SNP	.											.	PARK2	96	.	0			c.A574C	GRCh37	CM024241|CM030925	PARK2	M	rs9456735	PASS	.	T	LEU/MET,,	252,4154	146.1+/-180.8	8,236,1959	141	123	129		574,,	5.4	1	6	dbSNP_119	129	1,8599	1.2+/-3.3	0,1,4299	yes	missense,intron,intron	PARK2	NM_004562.2,NM_013987.2,NM_013988.2	15,,	8,237,6258	GG,GT,TT		0.0116,5.7195,1.9453	benign,,	192/466,,	162475167	253,12753	2203	4300	6503	SO:0001583	missense	5071	exon5			CACTCATCCGGTT		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.574A>C	6.37:g.162475167T>G	ENSP00000355865:p.Met192Leu	98	0	0		97	53	0.546392	NM_004562	A3FG77|A8K975|D3JZW7|D3K2X0|Q5TFV8|Q5VVX4|Q6Q2I6|Q8NI41|Q8NI43|Q8NI44|Q8WW07	Missense_Mutation	SNP	ENST00000366898.1	37	CCDS5281.1	43	0.019688644688644688	40	0.08130081300813008	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	T	14.04	2.416234	0.42918	0.057195	1.16E-4	ENSG00000185345	ENST00000366898;ENST00000366894;ENST00000338468;ENST00000392134;ENST00000366892;ENST00000366895	D;D;D;D	0.90385	-2.58;-2.33;-2.33;-2.66	5.39	5.39	0.77823	.	0.199863	0.45867	D	0.000329	T	0.79364	0.4433	L	0.41236	1.265	0.29921	N	0.822717	B;B;B	0.17268	0.021;0.001;0.016	B;B;B	0.17722	0.019;0.001;0.003	T	0.74583	-0.3617	10	0.54805	T	0.06	.	11.8193	0.52228	0.0:0.0:0.0:1.0	rs9456735;rs52822498;rs9456735	192;192;1	O60260-5;O60260;Q8NI42	.;PRKN2_HUMAN;.	L	192;1;1;1;192;113	ENSP00000355865:M192L;ENSP00000355860:M1L;ENSP00000343589:M1L;ENSP00000355858:M192L	ENSP00000343589:M1L	M	-	1	0	PARK2	162395157	0.984000	0.35163	0.997000	0.53966	0.944000	0.59088	2.591000	0.46163	2.043000	0.60533	0.533000	0.62120	ATG	T|0.977;G|0.023	0.023	strong		0.398	PARK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042995.1			G	162475167	T	G	162475167	3	3	22	1	0	0	0	0	1	0	0	0	11458	1435	50	5	855	5	PARK2	6	162475167	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1449064	162475167	8639900	1585	4486											
TCP10L2	401285	hgsc.bcm.edu	37	chr6	167585652	167585652	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgctggagggtcagctcgAggccagggagcccaaggagg	9	4	19	9	1	1	0	1	0	0	0	2	5	1	3	2	6	3	2	2	6	1	0	rs59203630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:167585652A>C	ENST00000366832.2	+	2	151	c.20A>C	c.(19-21)gAg>gCg	p.E7A		NM_001145121.1	NP_001138593.1	B9ZVM9	TCP2L_HUMAN	t-complex 10-like 2	7										endometrium(1)|kidney(2)|lung(3)	6						GGTCAGCTCGAGGCCAGGGAG	0.672													A|||	197	0.0393371	0.1422	0.013	5008	,	,		18107	0.0		0.0	False		,,,				2504	0.0				p.E7A		Atlas-SNP	.											.	TCP10L2	41	.	0			c.A20C						PASS	.	A	ALA/GLU	207,1177		20,167,505	21	31	28		20	-2.1	0	6	dbSNP_129	28	0,3182		0,0,1591	no	missense	TCP10L2	NM_001145121.1	107	20,167,2096	CC,CA,AA		0.0,14.9566,4.5335	possibly-damaging	7/354	167585652	207,4359	692	1591	2283	SO:0001583	missense	401285	exon2			AGCTCGAGGCCAG		CCDS47514.1	6q27	2012-09-20	2012-09-20		ENSG00000166984	ENSG00000166984			21254	protein-coding gene	gene with protein product			"t-complex 10-like 2 (mouse)"				Standard	NM_001145121		Approved	bA517H2.3	uc010kkp.3	B9ZVM9	OTTHUMG00000016014	ENST00000366832.2:c.20A>C	6.37:g.167585652A>C	ENSP00000355797:p.Glu7Ala	183	0	0		177	173	0.977401	NM_001145121		Missense_Mutation	SNP	ENST00000366832.2	37	CCDS47514.1	75	0.034340659340659344	73	0.1483739837398374	2	0.0055248618784530384	0	0.0	0	0.0	a	11.90	1.775977	0.31411	0.149566	0.0	ENSG00000166984	ENST00000486697;ENST00000366832	T	0.20200	2.09	2.61	-2.13	0.07144	.	.	.	.	.	T	0.10852	0.0265	L	0.51422	1.61	0.80722	P	0.0	D	0.58268	0.982	P	0.52554	0.702	T	0.04811	-1.0925	8	0.62326	D	0.03	.	3.0393	0.06133	0.4685:0.2327:0.2987:0.0	rs59203630	7	B9ZVM9	TCP2L_HUMAN	A	7	ENSP00000355797:E7A	ENSP00000283507:E7A	E	+	2	0	TCP10L2	167505642	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.176000	0.16782	-0.554000	0.06150	-0.863000	0.03009	GAG	A|0.966;C|0.034	0.034	strong		0.672	TCP10L2-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043112.5	XR_040749		C	167585652	A	C	167585652	3	2	22	1	0	0	0	0	1	0	0	0	15727	304	11	5	22	5	TCP10L2	6	167585652	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	5110485	167585652	3529415	1586	4487											
TTLL2	83887	hgsc.bcm.edu	37	chr6	167755063	167755063	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aagcaggcaactttgttcttGtttttcctttcaatgaagca	10	16	7	8	0	2	1	1	1	1	0	3	1	3	1	1	1	3	5	1	1	4	6	rs34931196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:167755063G>A	ENST00000239587.5	+	3	1763	c.1675G>A	c.(1675-1677)Gtt>Att	p.V559I		NM_031949.4	NP_114155.4	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	559			V -> I (in dbSNP:rs34931196).		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)		CTTTGTTCTTGTTTTTCCTTT	0.468													G|||	140	0.0279553	0.1036	0.0043	5008	,	,		20361	0.0		0.0	False		,,,				2504	0.0				p.V559I		Atlas-SNP	.											.	TTLL2	82	.	0			c.G1675A						PASS	.	G	ILE/VAL	347,4059	179.7+/-208.2	15,317,1871	92	89	90		1675	1.7	0.9	6	dbSNP_126	90	4,8596	3.7+/-12.6	0,4,4296	yes	missense	TTLL2	NM_031949.4	29	15,321,6167	AA,AG,GG		0.0465,7.8756,2.6988	benign	559/593	167755063	351,12655	2203	4300	6503	SO:0001583	missense	83887	exon3			GTTCTTGTTTTTC	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.1675G>A	6.37:g.167755063G>A	ENSP00000239587:p.Val559Ile	177	0	0		166	67	0.403614	NM_031949	B2RB11|B3KS77|Q7Z6R8|Q86X22	Missense_Mutation	SNP	ENST00000239587.5	37	CCDS5301.1	52	0.023809523809523808	50	0.1016260162601626	2	0.0055248618784530384	0	0.0	0	0.0	G	0.039	-1.293630	0.01375	0.078756	4.65E-4	ENSG00000120440	ENST00000239587;ENST00000540954	T	0.02121	4.44	4.04	1.67	0.24075	.	0.415985	0.21849	N	0.068208	T	0.00300	0.0009	N	0.04203	-0.255	0.21627	N	0.99962	B	0.06786	0.001	B	0.04013	0.001	T	0.41734	-0.9492	10	0.02654	T	1	.	6.3218	0.21223	0.6774:0.0:0.3226:0.0	rs34931196	559	Q9BWV7	TTLL2_HUMAN	I	559;486	ENSP00000239587:V559I	ENSP00000239587:V559I	V	+	1	0	TTLL2	167675053	1.000000	0.71417	0.874000	0.34290	0.452000	0.32318	0.911000	0.28584	0.164000	0.19529	-0.339000	0.08088	GTT	G|0.970;A|0.030	0.030	strong		0.468	TTLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043127.3	NM_031949		A	167755063	G	A	167755063	3	1	22	1	0	0	0	0	1	0	0	0	16742	1377	48	2	1685	2	TTLL2	6	167755063	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	169411	167755063	3360004	1587	4488											
THBS2	7058	hgsc.bcm.edu	37	chr6	169648723	169648723	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccagggagaccacatgccggGtgccgtcaatccagtaggtg	9	6	14	12	2	1	1	1	0	0	1	2	2	2	1	5	3	2	1	5	3	2	1	rs36088849	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:169648723G>C	ENST00000366787.3	-	4	647	c.398C>G	c.(397-399)aCc>aGc	p.T133S		NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	133	Heparin-binding. {ECO:0000255}.|Laminin G-like.		T -> S (in dbSNP:rs36088849).		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)		CACATGCCGGGTGCCGTCAAT	0.652													G|||	119	0.023762	0.0885	0.0029	5008	,	,		18772	0.0		0.0	False		,,,				2504	0.0				p.T133S	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-SNP	.											.	THBS2	230	.	0			c.C398G						PASS	.	G	SER/THR	345,4061	168.7+/-199.5	15,315,1873	84	70	75		398	0.2	0	6	dbSNP_126	75	3,8597	3.0+/-9.4	0,3,4297	yes	missense	THBS2	NM_003247.2	58	15,318,6170	CC,CG,GG		0.0349,7.8302,2.6757	benign	133/1173	169648723	348,12658	2203	4300	6503	SO:0001583	missense	7058	exon4			TGCCGGGTGCCGT		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.398C>G	6.37:g.169648723G>C	ENSP00000355751:p.Thr133Ser	84	0	0		110	60	0.545455	NM_003247	A6H8N1|A7E232|Q5RI52	Missense_Mutation	SNP	ENST00000366787.3	37	CCDS34574.1	35	0.016025641025641024	34	0.06910569105691057	1	0.0027624309392265192	0	0.0	0	0.0	G	1.088	-0.664792	0.03428	0.078302	3.49E-4	ENSG00000186340	ENST00000366787	T	0.01998	4.51	4.61	0.151	0.14888	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G, thrombospondin-type, N-terminal (1);	1.763740	0.03486	U	0.215882	T	0.00384	0.0012	N	0.04203	-0.255	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46952	-0.9154	10	0.22706	T	0.39	-3.9265	3.3224	0.07054	0.1616:0.2494:0.4685:0.1205	rs36088849	133	P35442	TSP2_HUMAN	S	133	ENSP00000355751:T133S	ENSP00000355751:T133S	T	-	2	0	THBS2	169390648	0.018000	0.18449	0.000000	0.03702	0.012000	0.07955	1.512000	0.35812	0.080000	0.16959	0.563000	0.77884	ACC	G|0.977;C|0.023	0.023	strong		0.652	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247		C	169648723	G	C	169648723	3	2	22	1	0	0	0	0	1	0	0	0	15869	1261	44	4	3200	4	THBS2	6	169648723	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1893660	169648723	1466344	1588	4489											
PHF10	55274	hgsc.bcm.edu	37	chr6	170105725	170105725	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tacttaccactattctcacaTtgggagcagtgtataagtga	12	13	8	8	0	1	1	1	1	1	0	2	2	1	2	1	1	3	2	1	1	5	7	rs4286788	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:170105725T>C	ENST00000339209.4	-	10	1332	c.1209A>G	c.(1207-1209)caA>caG	p.Q403Q	C6orf120_ENST00000332290.2_3'UTR|PHF10_ENST00000366780.4_Silent_p.Q401Q	NM_018288.3|NM_133325.2	NP_060758.2|NP_579866.2	Q8WUB8	PHF10_HUMAN	PHD finger protein 10	403					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)		TATTCTCACATTGGGAGCAGT	0.353													T|||	21	0.00419329	0.0151	0.0014	5008	,	,		19342	0.0		0.0	False		,,,				2504	0.0				p.Q403Q		Atlas-SNP	.											.	PHF10	76	.	0			c.A1209G						PASS	.	T	,,	63,4343	59.3+/-96.0	0,63,2140	114	110	111		,1209,1203	-0.5	1	6	dbSNP_111	111	0,8600		0,0,4300	no	utr-3,coding-synonymous,coding-synonymous	PHF10,C6orf120	NM_001029863.1,NM_018288.3,NM_133325.2	,,	0,63,6440	CC,CT,TT		0.0,1.4299,0.4844	,,	,403/499,401/497	170105725	63,12943	2203	4300	6503	SO:0001819	synonymous_variant	55274	exon10			CTCACATTGGGAG	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.1209A>G	6.37:g.170105725T>C		166	0	0		140	63	0.45	NM_018288	Q2YDA3|Q53HG8|Q9BXD2|Q9NV26	Silent	SNP	ENST00000339209.4	37	CCDS5308.2																																																																																			T|0.995;C|0.005	0.005	strong		0.353	PHF10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346732.1	NM_018288		C	170105725	T	C	170105725	2	2	22	1	0	0	0	0	0	0	0	1	11830	1490	52	3		3	PHF10	6	170105725	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	457002	170105725	1009342	1589	4490											
C6orf70	55780	hgsc.bcm.edu	37	chr6	170155460	170155460	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ttcacatttcttatctctgaCcaaggggcaatttgaaattc	11	15	6	9	0	3	2	1	2	2	0	5	2	3	2	1	2	0	1	1	2	4	5	rs61735516	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:170155460C>A	ENST00000366773.3	+	3	290	c.257C>A	c.(256-258)aCc>aAc	p.T86N	ERMARD_ENST00000392095.4_5'UTR|ERMARD_ENST00000366772.2_Missense_Mutation_p.T86N|ERMARD_ENST00000418781.3_Missense_Mutation_p.T86N|ERMARD_ENST00000588451.1_5'UTR	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	86					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											TTATCTCTGACCAAGGGGCAA	0.458													C|||	45	0.00898562	0.0318	0.0043	5008	,	,		16421	0.0		0.0	False		,,,				2504	0.0				p.T86N		Atlas-SNP	.											.	C6orf70	63	.	0			c.C257A						PASS	.	C	ASN/THR	167,4239	111.2+/-149.4	1,165,2037	152	142	146		257	2.9	0.1	6	dbSNP_129	146	2,8598	2.2+/-6.3	0,2,4298	yes	missense	C6orf70	NM_018341.1	65	1,167,6335	AA,AC,CC		0.0233,3.7903,1.2994	possibly-damaging	86/679	170155460	169,12837	2203	4300	6503	SO:0001583	missense	55780	exon3			CTCTGACCAAGGG	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.257C>A	6.37:g.170155460C>A	ENSP00000355735:p.Thr86Asn	268	0	0		297	149	0.501683	NM_018341	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Missense_Mutation	SNP	ENST00000366773.3	37	CCDS34576.1	22	0.010073260073260074	20	0.04065040650406504	2	0.0055248618784530384	0	0.0	0	0.0	C	9.157	1.017709	0.19355	0.037903	2.33E-4	ENSG00000130023	ENST00000366773;ENST00000366772;ENST00000418781	T	0.48201	0.82	5.72	2.91	0.33838	.	0.384232	0.25050	N	0.033534	T	0.26846	0.0657	L	0.56769	1.78	0.35175	D	0.771965	B;B	0.20052	0.041;0.006	B;B	0.16722	0.016;0.007	T	0.07731	-1.0757	10	0.56958	D	0.05	.	11.748	0.51832	0.1294:0.6211:0.2494:0.0	rs61735516	86;86	Q5T6L9-2;Q5T6L9	.;CF070_HUMAN	N	86	ENSP00000355735:T86N	ENSP00000355734:T86N	T	+	2	0	C6orf70	169897385	0.815000	0.29118	0.085000	0.20634	0.078000	0.17371	0.775000	0.26689	0.308000	0.22923	-0.310000	0.09108	ACC	C|0.987;A|0.013	0.013	strong		0.458	ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2	NM_018341		A	170155460	C	A	170155460	3	1	22	1	0	0	0	0	1	0	0	0	2372	507	18	4	267	4	C6orf70	6	170155460	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	49735	170155460	959607	1590	4491											
PDCD2	5134	hgsc.bcm.edu	37	chr6	170892759	170892759	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggagacacactgattctccTgtttctgggggaggattctc	7	13	12	9	0	3	2	0	1	3	1	5	5	3	4	1	4	0	1	1	4	0	3	rs73258640	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:170892759T>A	ENST00000541970.1	-	2	438	c.360A>T	c.(358-360)acA>acT	p.T120T	PDCD2_ENST00000443345.2_Silent_p.T87T|PDCD2_ENST00000542896.1_Silent_p.T120T|PDCD2_ENST00000392090.2_Silent_p.T87T|PDCD2_ENST00000537445.1_Silent_p.T87T|PDCD2_ENST00000453163.2_Silent_p.T120T	NM_001199462.1|NM_002598.3	NP_001186391.1|NP_002589.2	Q16342	PDCD2_HUMAN	programmed cell death 2	120					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)		CTGATTCTCCTGTTTCTGGGG	0.433													.|||	61	0.0121805	0.0439	0.0029	5008	,	,		17113	0.0		0.001	False		,,,				2504	0.0				p.T120T	Colon(60;1476 1726 39478)	Atlas-SNP	.											.	PDCD2	13	.	0			c.A360T						PASS	.	T	,,,,,	162,4244		5,152,2046	63	62	62		360,261,261,261,360,360	-2.4	0	6	dbSNP_130	62	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDCD2	NM_001199461.1,NM_001199462.1,NM_001199463.1,NM_001199464.1,NM_002598.3,NM_144781.2	,,,,,	5,152,6346	AA,AT,TT		0.0,3.6768,1.2456	,,,,,	120/222,87/312,87/196,87/189,120/345,120/229	170892759	162,12844	2203	4300	6503	SO:0001819	synonymous_variant	5134	exon2			TTCTCCTGTTTCT	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.360A>T	6.37:g.170892759T>A		90	0	0		95	43	0.452632	NM_002598	E9PCU7|F5GYS7|Q58HM9|Q58HN0|Q9UH12	Silent	SNP	ENST00000541970.1	37	CCDS5316.1																																																																																			T|0.985;A|0.015	0.015	strong		0.433	PDCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043269.2	NM_002598		A	170892759	T	A	170892759	2	1	22	1	0	0	0	0	0	0	0	1	11628	1567	55	5		5	PDCD2	6	170892759	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	737299	170892759	222308	1591	4492											
PRKAR1B	5575	hgsc.bcm.edu	37	chr7	720274	720274	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcggcgggccttcaccacAgggttcgggggggtgggcga	4	5	21	11	5	1	0	1	0	0	0	2	1	1	0	2	8	0	1	2	8	0	2	rs200458521	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:720274A>G	ENST00000406797.1	-	3	441	c.267T>C	c.(265-267)ccT>ccC	p.P89P	PRKAR1B_ENST00000544935.1_Silent_p.P89P|PRKAR1B_ENST00000537384.1_Silent_p.P89P|PRKAR1B_ENST00000403562.1_Silent_p.P89P|PRKAR1B_ENST00000360274.4_Silent_p.P89P	NM_001164761.1	NP_001158233.1	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, beta	89	Dimerization and phosphorylation.				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)		CCTTCACCACAGGGTTCGGGG	0.632													a|||	9	0.00179712	0.0061	0.0014	5008	,	,		15949	0.0		0.0	False		,,,				2504	0.0				p.P89P		Atlas-SNP	.											.	PRKAR1B	32	.	0			c.T267C						PASS	.	A	,,,,,	22,4384	24.3+/-50.5	0,22,2181	51	51	51		267,267,267,267,267,267	-9.8	0.1	7		51	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRKAR1B	NM_001164758.1,NM_001164759.1,NM_001164760.1,NM_001164761.1,NM_001164762.1,NM_002735.2	,,,,,	0,22,6481	GG,GA,AA		0.0,0.4993,0.1692	,,,,,	89/382,89/382,89/382,89/382,89/382,89/382	720274	22,12984	2203	4300	6503	SO:0001819	synonymous_variant	5575	exon3			CACCACAGGGTTC	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.267T>C	7.37:g.720274A>G		52	0	0		35	14	0.4	NM_001164760	Q8N422	Silent	SNP	ENST00000406797.1	37	CCDS34579.1																																																																																			A|0.998;G|0.002	0.002	strong		0.632	PRKAR1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322525.1			G	720274	A	G	720274	2	3	22	1	0	0	0	0	0	0	0	1	12516	175	7	3		3	PRKAR1B	7	720274	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10		720274	158418389	1592	4493											
SUN1	23353	hgsc.bcm.edu	37	chr7	878583	878583	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggctgtgggtgccgacagcGgcaccagcagcgctgtctcc	6	6	15	14	3	1	0	0	0	1	0	2	1	1	0	3	3	4	4	3	3	0	0	rs114826023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:878583G>T	ENST00000405266.1	+	2	250	c.226G>T	c.(226-228)Ggc>Tgc	p.G76C	SUN1_ENST00000401592.1_Missense_Mutation_p.G76C|SUN1_ENST00000389574.3_Missense_Mutation_p.G26C|SUN1_ENST00000456758.2_Missense_Mutation_p.G134C|SUN1_ENST00000425407.2_Missense_Mutation_p.G26C|SUN1_ENST00000457378.2_Missense_Mutation_p.G97C|SUN1_ENST00000403868.1_Missense_Mutation_p.G76C|SUN1_ENST00000469755.1_3'UTR|SUN1_ENST00000452783.2_Missense_Mutation_p.G76C			O94901	SUN1_HUMAN	Sad1 and UNC84 domain containing 1	76	LMNA-binding.				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						TGCCGACAGCGGCACCAGCAG	0.602													G|||	15	0.00299521	0.0113	0.0	5008	,	,		18035	0.0		0.0	False		,,,				2504	0.0				p.G97C		Atlas-SNP	.											.	SUN1	157	.	0			c.G289T						PASS	.	G	CYS/GLY,CYS/GLY,CYS/GLY,CYS/GLY,CYS/GLY	16,4036		0,16,2010	34	33	34		226,226,289,226,76	-2.4	0	7	dbSNP_132	34	0,8402		0,0,4201	yes	missense,missense,missense,missense,missense	SUN1	NM_001130965.2,NM_001171944.1,NM_001171945.1,NM_001171946.1,NM_025154.5	159,159,159,159,159	0,16,6211	TT,TG,GG		0.0,0.3949,0.1285	benign,benign,benign,benign,benign	76/786,76/683,97/279,76/258,26/703	878583	16,12438	2026	4201	6227	SO:0001583	missense	23353	exon4			GACAGCGGCACCA	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.226G>T	7.37:g.878583G>T	ENSP00000384116:p.Gly76Cys	39	0	0		38	16	0.421053	NM_001171945	A5PL20|B3KMV7|B4DZF7|B7WNY4|B7WP53|E9PDU4|E9PF23|F8WD13|Q96CZ7|Q9HA14|Q9UH98	Missense_Mutation	SNP	ENST00000405266.1	37		10	0.004578754578754579	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	8.524	0.869408	0.17322	0.003949	0.0	ENSG00000164828	ENST00000456758;ENST00000389574;ENST00000457378;ENST00000452783;ENST00000435699;ENST00000440380;ENST00000439679;ENST00000424128;ENST00000457598;ENST00000421580;ENST00000405266;ENST00000401592;ENST00000403868;ENST00000297445;ENST00000425407;ENST00000450881	T;T;T;T;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;0.88;0.88;0.88;0.88	4.42	-2.43	0.06522	.	2.242240	0.01866	N	0.036910	T	0.06600	0.0169	N	0.00677	-1.265	0.09310	N	1	B;B;B;B;B	0.11235	0.0;0.001;0.001;0.004;0.0	B;B;B;B;B	0.12156	0.004;0.003;0.0;0.007;0.002	T	0.10474	-1.0628	10	0.46703	T	0.11	-1.7076	1.8943	0.03254	0.3095:0.0848:0.3628:0.2429	.	76;76;97;26;76	E9PDU4;E9PF23;F8WD13;O94901-5;O94901-3	.;.;.;.;.	C	134;26;97;76;76;76;76;76;76;76;76;76;76;76;26;51	ENSP00000388743:G134C;ENSP00000374225:G26C;ENSP00000395952:G97C;ENSP00000413439:G76C;ENSP00000388430:G76C;ENSP00000413188:G76C;ENSP00000404965:G76C;ENSP00000394381:G76C;ENSP00000384116:G76C;ENSP00000384015:G76C;ENSP00000383947:G76C;ENSP00000392309:G26C;ENSP00000392595:G51C	ENSP00000297445:G76C	G	+	1	0	SUN1	845109	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.218000	0.09240	-0.617000	0.05664	-0.266000	0.10368	GGC	G|0.997;T|0.003	0.003	strong		0.602	SUN1-001	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000322566.1	NM_025154		T	878583	G	T	878583	3	4	22	1	0	0	0	0	1	0	0	0	15406	1116	39	4	299	4	SUN1	7	878583	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	158309	878583	158260080	1593	4494											
SUN1	23353	hgsc.bcm.edu	37	chr7	883088	883088	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctgtccgagcgcaaggacGtgctcacggcgcaccccgcg	6	5	14	16	7	1	0	1	0	0	0	2	2	2	1	3	2	3	4	3	2	1	0	rs116520953	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:883088G>A	ENST00000405266.1	+	5	613	c.589G>A	c.(589-591)Gtg>Atg	p.V197M	SUN1_ENST00000401592.1_Missense_Mutation_p.V197M|SUN1_ENST00000389574.3_Missense_Mutation_p.V147M|SUN1_ENST00000456758.2_Missense_Mutation_p.V255M|SUN1_ENST00000425407.2_Missense_Mutation_p.V147M|SUN1_ENST00000457378.2_Missense_Mutation_p.V218M|SUN1_ENST00000403868.1_Missense_Mutation_p.V197M|SUN1_ENST00000452783.2_Intron			O94901	SUN1_HUMAN	Sad1 and UNC84 domain containing 1	197					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						GCGCAAGGACGTGCTCACGGC	0.592													.|||	32	0.00638978	0.0234	0.0014	5008	,	,		13852	0.0		0.0	False		,,,				2504	0.0				p.V218M		Atlas-SNP	.											.	SUN1	157	.	0			c.G652A						PASS	.	G	MET/VAL,,MET/VAL,MET/VAL,MET/VAL	82,3924		2,78,1923	94	112	107		589,,652,589,439	-0.1	0	7	dbSNP_132	107	1,8309		0,1,4154	yes	missense,intron,missense,missense,missense	SUN1	NM_001130965.2,NM_001171944.1,NM_001171945.1,NM_001171946.1,NM_025154.5	21,,21,21,21	2,79,6077	AA,AG,GG		0.012,2.0469,0.6739	benign,,benign,benign,benign	197/786,,218/279,197/258,147/703	883088	83,12233	2003	4155	6158	SO:0001583	missense	23353	exon7			AAGGACGTGCTCA	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.589G>A	7.37:g.883088G>A	ENSP00000384116:p.Val197Met	63	0	0		73	43	0.589041	NM_001171945	A5PL20|B3KMV7|B4DZF7|B7WNY4|B7WP53|E9PDU4|E9PF23|F8WD13|Q96CZ7|Q9HA14|Q9UH98	Missense_Mutation	SNP	ENST00000405266.1	37		7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	G	15.86	2.959220	0.53400	0.020469	1.2E-4	ENSG00000164828	ENST00000456758;ENST00000389574;ENST00000457378;ENST00000405266;ENST00000401592;ENST00000403868;ENST00000297445;ENST00000425407;ENST00000429178	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	4.4	-0.0819	0.13701	.	1.178380	0.05856	N	0.622191	T	0.11707	0.0285	N	0.19112	0.55	0.09310	N	1	B;P;P;B	0.37038	0.038;0.532;0.579;0.079	B;B;B;B	0.27380	0.035;0.079;0.045;0.024	T	0.09907	-1.0653	10	0.33141	T	0.24	-2.952	5.938	0.19177	0.2089:0.0:0.6586:0.1325	.	197;218;147;197	E9PF23;F8WD13;O94901-5;O94901-3	.;.;.;.	M	255;147;218;197;197;197;197;147;28	ENSP00000388743:V255M;ENSP00000374225:V147M;ENSP00000395952:V218M;ENSP00000384116:V197M;ENSP00000384015:V197M;ENSP00000383947:V197M;ENSP00000392309:V147M;ENSP00000409909:V28M	ENSP00000297445:V197M	V	+	1	0	SUN1	849614	0.003000	0.15002	0.000000	0.03702	0.084000	0.17831	0.577000	0.23758	-0.272000	0.09259	0.591000	0.81541	GTG	G|0.996;A|0.004	0.004	strong		0.592	SUN1-001	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000322566.1	NM_025154		A	883088	G	A	883088	3	1	22	1	0	0	0	0	1	0	0	0	15406	1145	40	1	674	1	SUN1	7	883088	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4505	883088	158255575	1594	4495											
MICALL2	79778	hgsc.bcm.edu	37	chr7	1481983	1481983	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggtactgctcgtgctcagcGgggctggcggttccatcctc	4	10	14	13	3	1	0	1	0	0	0	5	0	3	0	2	5	4	5	2	5	1	2	rs4075307	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:1481983G>A	ENST00000297508.7	-	7	1731	c.1556C>T	c.(1555-1557)cCg>cTg	p.P519L	MICALL2_ENST00000405088.4_Missense_Mutation_p.P307L	NM_182924.3	NP_891554.1	Q8IY33	MILK2_HUMAN	MICAL-like 2	519	Mediates targeting to the cell plasma membrane. {ECO:0000250}.		P -> L (in dbSNP:rs4075307).		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)		CGTGCTCAGCGGGGCTGGCGG	0.647													G|||	174	0.0347444	0.1241	0.013	5008	,	,		14709	0.0		0.001	False		,,,				2504	0.0				p.P519L		Atlas-SNP	.											.	MICALL2	63	.	0			c.C1556T						PASS	.		LEU/PRO	437,3969	208.8+/-229.8	24,389,1790	121	118	119		1556	1.3	0	7	dbSNP_108	119	5,8595	3.7+/-12.6	0,5,4295	yes	missense	MICALL2	NM_182924.3	98	24,394,6085	AA,AG,GG		0.0581,9.9183,3.3984	possibly-damaging	519/905	1481983	442,12564	2203	4300	6503	SO:0001583	missense	79778	exon7			CTCAGCGGGGCTG	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.1556C>T	7.37:g.1481983G>A	ENSP00000297508:p.Pro519Leu	86	0	0		76	76	1	NM_182924	D3YTD2|Q7RTP4|Q7Z655|Q8TEQ4|Q9H5F9	Missense_Mutation	SNP	ENST00000297508.7	37	CCDS5324.1	55	0.025183150183150184	50	0.1016260162601626	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	13.70	2.314588	0.40996	0.099183	5.81E-4	ENSG00000164877	ENST00000405088;ENST00000297508	T;T	0.69806	2.37;-0.43	3.76	1.29	0.21616	.	0.235349	0.21901	N	0.067446	T	0.01156	0.0038	L	0.32530	0.975	0.09310	N	0.999999	B;D	0.53312	0.136;0.959	B;B	0.33690	0.006;0.168	T	0.04140	-1.0974	10	0.17832	T	0.49	.	3.0549	0.06181	0.2049:0.2804:0.5147:0.0	rs4075307;rs16870427;rs4075307	519;307	Q8IY33;D3YTD2	MILK2_HUMAN;.	L	307;519	ENSP00000385928:P307L;ENSP00000297508:P519L	ENSP00000297508:P519L	P	-	2	0	MICALL2	1448509	0.001000	0.12720	0.001000	0.08648	0.008000	0.06430	0.665000	0.25083	0.674000	0.31244	0.561000	0.74099	CCG	G|0.965;A|0.035	0.035	strong		0.647	MICALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239223.2	NM_182924		A	1481983	G	A	1481983	3	1	22	1	0	0	0	0	1	0	0	0	9583	1116	39	1	1202	1	MICALL2	7	1481983	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	598895	1481983	157656680	1595	4496											
MICALL2	79778	hgsc.bcm.edu	37	chr7	1488317	1488317	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	taggtcaagatgctcagccgGtcaggcaccttcaaggccac	10	7	11	13	1	4	1	4	0	0	1	4	1	4	1	3	4	2	2	3	4	3	2	rs78897087	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:1488317G>A	ENST00000297508.7	-	3	448	c.273C>T	c.(271-273)gaC>gaT	p.D91D	MICALL2_ENST00000405088.4_Intron	NM_182924.3	NP_891554.1	Q8IY33	MILK2_HUMAN	MICAL-like 2	91	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.|Forms an intramolecular interaction with the C-terminal coiled coil domain keeping the protein in a closed conformation. {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)		TGCTCAGCCGGTCAGGCACCT	0.657													G|||	158	0.0315495	0.1135	0.0115	5008	,	,		15745	0.0		0.0	False		,,,				2504	0.0				p.D91D		Atlas-SNP	.											.	MICALL2	63	.	0			c.C273T						PASS	.			390,4016	190.9+/-216.7	20,350,1833	97	89	92		273	3.2	1	7	dbSNP_132	92	4,8594	3.7+/-12.6	0,4,4295	no	coding-synonymous	MICALL2	NM_182924.3		20,354,6128	AA,AG,GG		0.0465,8.8516,3.0298		91/905	1488317	394,12610	2203	4299	6502	SO:0001819	synonymous_variant	79778	exon3			CAGCCGGTCAGGC	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.273C>T	7.37:g.1488317G>A		123	0	0		122	122	1	NM_182924	D3YTD2|Q7RTP4|Q7Z655|Q8TEQ4|Q9H5F9	Silent	SNP	ENST00000297508.7	37	CCDS5324.1																																																																																			G|0.968;A|0.032	0.032	strong		0.657	MICALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239223.2	NM_182924		A	1488317	G	A	1488317	2	1	22	1	0	0	0	0	0	0	0	1	9583	1252	44	2		2	MICALL2	7	1488317	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6334	1488317	157650346	1596	4497											
INTS1	26173	hgsc.bcm.edu	37	chr7	1538174	1538174	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgcccaggttgtccttgtgCgcgctcagcagctccctggg	3	10	14	14	2	1	0	1	0	0	0	3	0	3	0	3	2	4	4	3	2	0	2	rs143126716	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:1538174C>T	ENST00000404767.3	-	10	1384	c.1299G>A	c.(1297-1299)gcG>gcA	p.A433A	INTS1_ENST00000389470.4_Silent_p.A561A|INTS1_ENST00000493531.1_5'Flank	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	433					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)		TGTCCTTGTGCGCGCTCAGCA	0.652													C|||	63	0.0125799	0.0431	0.0086	5008	,	,		10067	0.0		0.0	False		,,,				2504	0.0				p.A433A		Atlas-SNP	.											INTS1,NS,carcinoma,-1,1	INTS1	145	1	0			c.G1299A						PASS	.			125,4145		4,117,2014	85	97	93		1299	-9.7	0	7	dbSNP_134	93	6,8488		0,6,4241	no	coding-synonymous	INTS1	NM_001080453.2		4,123,6255	TT,TC,CC		0.0706,2.9274,1.0263		433/2191	1538174	131,12633	2135	4247	6382	SO:0001819	synonymous_variant	26173	exon10			CTTGTGCGCGCTC	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.1299G>A	7.37:g.1538174C>T		131	0	0		166	166	1	NM_001080453	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Silent	SNP	ENST00000404767.3	37	CCDS47526.1																																																																																			C|0.988;T|0.012	0.012	strong		0.652	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1			T	1538174	C	T	1538174	2	4	22	1	0	0	0	0	0	0	0	1	7784	755	27	1		1	INTS1	7	1538174	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	49857	1538174	157600489	1597	4498											
FTSJ2	8379	hgsc.bcm.edu	37	chr7	2275177	2275177	+	5'Flank	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agaagatctaccccaagcacGaagccaacaggagagctggg	15	3	12	11	1	1	3	0	0	1	3	1	5	1	3	3	2	5	2	3	2	5	1	rs11547272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2275177G>A	ENST00000406869.1	-	0	0				FTSJ2_ENST00000242257.8_Silent_p.F107F|MAD1L1_ENST00000265854.7_5'Flank|FTSJ2_ENST00000440306.2_Missense_Mutation_p.S142L|FTSJ2_ENST00000486040.1_5'UTR|MAD1L1_ENST00000402746.1_5'Flank|MAD1L1_ENST00000399654.2_5'Flank|FTSJ2_ENST00000407040.1_Silent_p.F13F			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)		CCCCAAGCACGAAGCCAACAG	0.448													G|||	73	0.0145767	0.0537	0.0029	5008	,	,		22055	0.0		0.0	False		,,,				2504	0.0				p.F107F		Atlas-SNP	.											.	FTSJ2	22	.	0			c.C321T						PASS	.	G		246,4160	136.9+/-172.8	7,232,1964	49	47	48		321	-5.2	0.8	7	dbSNP_120	48	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	FTSJ2	NM_013393.1		7,235,6261	AA,AG,GG		0.0349,5.5833,1.9145		107/247	2275177	249,12757	2203	4300	6503	SO:0001631	upstream_gene_variant	29960	exon3			AAGCACGAAGCCA	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		7.37:g.2275177G>A	Exception_encountered	35	0	0		42	29	0.690476	NM_013393	B3KR41|Q13312|Q75MI0|Q86UM4|Q9UNH0	Silent	SNP	ENST00000406869.1	37	CCDS43539.1	30	0.013736263736263736	28	0.056910569105691054	2	0.0055248618784530384	0	0.0	0	0.0	G	15.89	2.967220	0.53507	0.055833	3.49E-4	ENSG00000122687	ENST00000440306	T	0.30714	1.52	5.47	-5.18	0.02840	.	.	.	.	.	T	0.05181	0.0138	.	.	.	0.22710	N	0.99883	.	.	.	.	.	.	T	0.39961	-0.9588	6	0.87932	D	0	.	14.6466	0.68764	0.5757:0.0:0.4243:0.0	rs11547272	.	.	.	L	142	ENSP00000392343:S142L	ENSP00000392343:S142L	S	-	2	0	FTSJ2	2241703	0.001000	0.12720	0.835000	0.33067	0.981000	0.71138	-1.403000	0.02497	-1.417000	0.02017	-0.137000	0.14449	TCG	G|0.982;C|0.000;A|0.018	0.018	strong		0.448	MAD1L1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322871.1	NM_003550		A	2275177	G	A	2275177	1	1	22	0	1	0	0	0	0	0	0	0	6096	1049	37	1		1	FTSJ2	7	2275177	5'Flank	SNP	G	TCGA-G8-6324-01A-11D-2210-10	737003	2275177	156863486	1598	4499											
CHST12	55501	hgsc.bcm.edu	37	chr7	2472599	2472599	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggctacgactggtccccgCgcgacgcccggcgcagccca	6	3	14	18	7	0	0	0	0	0	0	1	3	1	0	4	3	2	2	4	3	1	1	rs17132395	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2472599C>A	ENST00000258711.6	+	2	460	c.325C>A	c.(325-327)Cgc>Agc	p.R109S		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	109			R -> S (in dbSNP:rs17132395).		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)		CTGGTCCCCGCGCGACGCCCG	0.711													C|||	141	0.028155	0.0976	0.0159	5008	,	,		13900	0.0		0.001	False		,,,				2504	0.0				p.R109S		Atlas-SNP	.											.	CHST12	39	.	0			c.C325A						PASS	.	C	SER/ARG	357,4031		15,327,1852	19	25	23		325	5	0	7	dbSNP_123	23	2,8568		0,2,4283	no	missense	CHST12	NM_018641.4	110	15,329,6135	AA,AC,CC		0.0233,8.1358,2.7705	benign	109/415	2472599	359,12599	2194	4285	6479	SO:0001583	missense	55501	exon2			TCCCCGCGCGACG	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.325C>A	7.37:g.2472599C>A	ENSP00000258711:p.Arg109Ser	10	0	0		10	8	0.8	NM_018641	A4D1Z9|Q502W3|Q9NXY7	Missense_Mutation	SNP	ENST00000258711.6	37	CCDS5333.1	53	0.024267399267399268	48	0.0975609756097561	5	0.013812154696132596	0	0.0	0	0.0	C	4.045	0.006027	0.07866	0.081358	2.33E-4	ENSG00000136213	ENST00000258711;ENST00000432336	T;T	0.61742	0.08;0.92	4.98	4.98	0.66077	.	0.798952	0.11372	N	0.570741	T	0.01029	0.0034	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.06405	0.002	T	0.00870	-1.1533	10	0.08837	T	0.75	1.0898	13.2418	0.60002	0.1591:0.8409:0.0:0.0	rs17132395;rs17132395	109	Q9NRB3	CHSTC_HUMAN	S	109	ENSP00000258711:R109S;ENSP00000411207:R109S	ENSP00000258711:R109S	R	+	1	0	CHST12	2439125	0.002000	0.14202	0.022000	0.16811	0.456000	0.32438	1.538000	0.36094	2.304000	0.77564	0.561000	0.74099	CGC	C|0.976;A|0.024	0.024	strong		0.711	CHST12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060170.3	NM_018641		A	2472599	C	A	2472599	3	1	22	1	0	0	0	0	1	0	0	0	3402	768	27	4	327	4	CHST12	7	2472599	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	197422	2472599	156666064	1599	4500											
CHST12	55501	hgsc.bcm.edu	37	chr7	2472662	2472662	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	agcggaggagcgtgctgcggGgcttctgcgccaactccagc	6	6	16	13	4	1	0	0	0	1	0	2	2	2	2	2	4	7	2	2	4	1	1	rs11537796	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2472662G>C	ENST00000258711.6	+	2	523	c.388G>C	c.(388-390)Ggc>Cgc	p.G130R		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	130					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)		CGTGCTGCGGGGCTTCTGCGC	0.701													G|||	141	0.028155	0.0968	0.0159	5008	,	,		14367	0.0		0.002	False		,,,				2504	0.0				p.G130R		Atlas-SNP	.											.	CHST12	39	.	0			c.G388C						PASS	.	G	ARG/GLY	361,4045		25,311,1867	35	37	37		388	4.2	0.3	7	dbSNP_120	37	2,8598		0,2,4298	yes	missense	CHST12	NM_018641.4	125	25,313,6165	CC,CG,GG		0.0233,8.1934,2.791	benign	130/415	2472662	363,12643	2203	4300	6503	SO:0001583	missense	55501	exon2			CTGCGGGGCTTCT	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.388G>C	7.37:g.2472662G>C	ENSP00000258711:p.Gly130Arg	17	0	0		21	10	0.47619	NM_018641	A4D1Z9|Q502W3|Q9NXY7	Missense_Mutation	SNP	ENST00000258711.6	37	CCDS5333.1	55	0.025183150183150184	48	0.0975609756097561	5	0.013812154696132596	0	0.0	2	0.002638522427440633	G	2.483	-0.319175	0.05386	0.081934	2.33E-4	ENSG00000136213	ENST00000258711;ENST00000432336	T;T	0.60548	0.18;1.03	5.09	4.18	0.49190	.	0.697828	0.14301	N	0.328271	T	0.01387	0.0045	N	0.22421	0.69	0.25416	N	0.988316	B	0.19583	0.037	B	0.18871	0.023	T	0.00978	-1.1493	10	0.17832	T	0.49	-6.2778	13.8779	0.63665	0.0:0.2917:0.7083:0.0	rs11537796	130	Q9NRB3	CHSTC_HUMAN	R	130	ENSP00000258711:G130R;ENSP00000411207:G130R	ENSP00000258711:G130R	G	+	1	0	CHST12	2439188	0.021000	0.18746	0.287000	0.24848	0.689000	0.40095	1.514000	0.35834	1.095000	0.41419	0.561000	0.74099	GGC	G|0.970;C|0.030	0.030	strong		0.701	CHST12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060170.3	NM_018641		C	2472662	G	C	2472662	3	2	22	1	0	0	0	0	1	0	0	0	3402	1232	43	4	390	4	CHST12	7	2472662	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	63	2472662	156666001	1600	4501											
IQCE	23288	hgsc.bcm.edu	37	chr7	2611908	2611908	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ggcggcactcctgactgtctGacagacaccttcagagtgaa	10	8	11	12	1	2	5	1	3	1	2	3	5	3	5	2	2	0	1	2	2	1	1	rs147584030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2611908G>C	ENST00000402050.2	+	5	526	c.342G>C	c.(340-342)ctG>ctC	p.L114L	IQCE_ENST00000438376.2_Silent_p.L98L|IQCE_ENST00000404984.1_Silent_p.L63L|IQCE_ENST00000325979.7_Silent_p.L49L	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	114						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)		CTGACTGTCTGACAGACACCT	0.607													G|||	42	0.00838658	0.0303	0.0029	5008	,	,		18614	0.0		0.0	False		,,,				2504	0.0				p.L114L		Atlas-SNP	.											.	IQCE	66	.	0			c.G342C						PASS	.	G	,	116,3980		1,114,1933	51	55	54		294,342	3.3	0	7	dbSNP_134	54	4,8406		0,4,4201	no	coding-synonymous,coding-synonymous	IQCE	NM_001100390.1,NM_152558.3	,	1,118,6134	CC,CG,GG		0.0476,2.832,0.9595	,	98/680,114/696	2611908	120,12386	2048	4205	6253	SO:0001819	synonymous_variant	23288	exon5			CTGTCTGACAGAC	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.342G>C	7.37:g.2611908G>C		51	0	0		65	29	0.446154	NM_152558	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Silent	SNP	ENST00000402050.2	37	CCDS43542.1																																																																																			G|0.994;C|0.006	0.006	strong		0.607	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558		C	2611908	G	C	2611908	2	2	22	1	0	0	0	0	0	0	0	1	7815	1277	45	4		4	IQCE	7	2611908	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	139246	2611908	156526755	1601	4502											
AMZ1	155185	hgsc.bcm.edu	37	chr7	2752026	2752026	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccaggaggcgggggagccGtcagtgtgggaggacacccc	8	3	19	11	2	1	0	1	0	0	0	1	4	1	4	4	6	2	0	4	6	0	0	rs61743920	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2752026G>A	ENST00000312371.4	+	7	1379	c.1011G>A	c.(1009-1011)ccG>ccA	p.P337P	AMZ1_ENST00000489665.1_Intron|AMZ1_ENST00000407112.1_Missense_Mutation_p.V281I	NM_133463.1	NP_597720.1	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1	337							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)		CGGGGGAGCCGTCAGTGTGGG	0.672													G|||	54	0.0107827	0.0386	0.0029	5008	,	,		15627	0.001		0.0	False		,,,				2504	0.0				p.P337P		Atlas-SNP	.											.	AMZ1	41	.	0			c.G1011A						PASS	.	G		160,4240	98.5+/-137.1	4,152,2044	23	28	26		1011	3	0	7	dbSNP_129	26	7,8591	5.7+/-21.5	0,7,4292	no	coding-synonymous	AMZ1	NM_133463.1		4,159,6336	AA,AG,GG		0.0814,3.6364,1.2848		337/499	2752026	167,12831	2200	4299	6499	SO:0001819	synonymous_variant	155185	exon7			GGAGCCGTCAGTG	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.1011G>A	7.37:g.2752026G>A		55	0	0		40	22	0.55	NM_133463	B3KRS0|Q8TF51	Silent	SNP	ENST00000312371.4	37	CCDS34589.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	G	5.330	0.246159	0.10130	0.036364	8.14E-4	ENSG00000174945	ENST00000407112	T	0.35421	1.31	4.85	2.96	0.34315	.	.	.	.	.	T	0.05273	0.0140	.	.	.	0.09310	N	0.999999	B	0.20459	0.045	B	0.13407	0.009	T	0.16808	-1.0390	8	0.23302	T	0.38	-30.2079	7.4751	0.27371	0.0927:0.1681:0.7392:0.0	rs61743920	281	B3KRS0	.	I	281	ENSP00000386020:V281I	ENSP00000386020:V281I	V	+	1	0	AMZ1	2718552	0.000000	0.05858	0.027000	0.17364	0.064000	0.16182	-0.564000	0.05936	0.412000	0.25729	0.462000	0.41574	GTC	G|0.988;A|0.012	0.012	strong		0.672	AMZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325244.1	NM_133463		A	2752026	G	A	2752026	2	1	22	1	0	0	0	0	0	0	0	1	596	1132	40	1		1	AMZ1	7	2752026	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	140118	2752026	156386637	1602	4503											
GNA12	2768	hgsc.bcm.edu	37	chr7	2834754	2834754	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaatgccaagcttatctcgTgcatcaacaagaacccttga	13	9	8	11	1	2	2	1	1	1	1	3	3	2	3	2	1	5	2	2	1	6	2	rs2230877	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2834754T>C	ENST00000275364.3	-	2	495	c.333A>G	c.(331-333)gcA>gcG	p.A111A	GNA12_ENST00000544127.1_Silent_p.A35A|GNA12_ENST00000407904.3_Silent_p.A52A	NM_007353.2	NP_031379.2	Q03113	GNA12_HUMAN	guanine nucleotide binding protein (G protein) alpha 12	111					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)		GCTTATCTCGTGCATCAACAA	0.468													T|||	99	0.0197684	0.0514	0.0101	5008	,	,		21010	0.0		0.0159	False		,,,				2504	0.0082				p.A111A		Atlas-SNP	.											.	GNA12	35	.	0			c.A333G						PASS	.	T		207,4199	127.8+/-164.7	6,195,2002	131	128	129		333	-11.2	0.5	7	dbSNP_123	129	77,8523	45.8+/-104.6	1,75,4224	no	coding-synonymous	GNA12	NM_007353.2		7,270,6226	CC,CT,TT		0.8953,4.6981,2.1836		111/382	2834754	284,12722	2203	4300	6503	SO:0001819	synonymous_variant	2768	exon2			ATCTCGTGCATCA	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.333A>G	7.37:g.2834754T>C		70	0	0		90	47	0.522222	NM_007353	A4D204|B3KXS2|B7Z3F7|Q2T9L1|Q5PPR5|Q86UM8|Q8TD71|Q9UDU9	Silent	SNP	ENST00000275364.3	37	CCDS5335.1																																																																																			T|0.980;C|0.020	0.020	strong		0.468	GNA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241608.1	NM_007353		C	2834754	T	C	2834754	2	2	22	1	0	0	0	0	0	0	0	1	6508	1683	59	3		3	GNA12	7	2834754	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	82728	2834754	156303909	1603	4504											
CARD11	84433	hgsc.bcm.edu	37	chr7	2969689	2969689	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctagggctggcgtccgtgccTtcttcctcgtgccccttggc	1	12	12	16	3	1	0	0	0	1	0	4	0	3	0	5	3	2	1	5	3	1	4	rs41515445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2969689T>G	ENST00000396946.4	-	12	1993	c.1590A>C	c.(1588-1590)gaA>gaC	p.E530D		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	530					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)		CGTCCGTGCCTTCTTCCTCGT	0.622			Mis		DLBCL								T|||	141	0.028155	0.1036	0.0058	5008	,	,		16650	0.0		0.0	False		,,,				2504	0.0				p.E530D		Atlas-SNP	.		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	.	CARD11	339	.	0			c.A1590C						PASS	.	T	ASP/GLU	398,4008	195.3+/-220.0	17,364,1822	115	78	91		1590	-5.4	0	7	dbSNP_127	91	2,8598	1.2+/-3.3	0,2,4298	yes	missense	CARD11	NM_032415.4	45	17,366,6120	GG,GT,TT		0.0233,9.0331,3.0755	benign	530/1155	2969689	400,12606	2203	4300	6503	SO:0001583	missense	84433	exon12			CGTGCCTTCTTCC	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.1590A>C	7.37:g.2969689T>G	ENSP00000380150:p.Glu530Asp	111	0	0		123	62	0.504065	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	50	0.022893772893772892	46	0.09349593495934959	4	0.011049723756906077	0	0.0	0	0.0	T	4.090	0.014638	0.07959	0.090331	2.33E-4	ENSG00000198286	ENST00000396946;ENST00000355508	T;T	0.30981	1.51;2.48	3.85	-5.41	0.02648	.	1.090360	0.06781	N	0.785380	T	0.00384	0.0012	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.23868	-1.0176	10	0.02654	T	1	-2.0525	5.5885	0.17287	0.3319:0.0:0.5015:0.1665	rs41515445;rs58644294	530	Q9BXL7	CAR11_HUMAN	D	530;2	ENSP00000380150:E530D;ENSP00000347695:E2D	ENSP00000347695:E2D	E	-	3	2	CARD11	2936215	0.001000	0.12720	0.000000	0.03702	0.021000	0.10359	-0.891000	0.04135	-0.959000	0.03618	0.459000	0.35465	GAA	T|0.972;G|0.028	0.028	strong		0.622	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		G	2969689	T	G	2969689	3	3	22	1	0	0	0	0	1	0	0	0	2647	1606	56	5	1930	5	CARD11	7	2969689	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	134935	2969689	156168974	1604	4505											
SDK1	221935	hgsc.bcm.edu	37	chr7	3991479	3991479	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgtccgcggacaccgggccAtacgtctgcgaggcggcgct	6	5	15	15	8	1	0	0	0	1	0	2	2	2	1	3	4	2	1	3	4	1	1	rs6961589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:3991479A>G	ENST00000404826.2	+	7	1216	c.1077A>G	c.(1075-1077)ccA>ccG	p.P359P	SDK1_ENST00000389531.3_Silent_p.P359P	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	359	Ig-like C2-type 3.				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)		ACACCGGGCCATACGTCTGCG	0.602													G|||	341	0.0680911	0.2398	0.0303	5008	,	,		16870	0.0		0.002	False		,,,				2504	0.001				p.P359P		Atlas-SNP	.											.	SDK1	361	.	0			c.A1077G						PASS	.	G		958,3448	731.8+/-410.3	104,750,1349	52	52	52		1077	0.9	0	7	dbSNP_116	52	9,8591	817.5+/-406.9	0,9,4291	no	coding-synonymous	SDK1	NM_152744.3		104,759,5640	GG,GA,AA		0.1047,21.7431,7.435		359/2214	3991479	967,12039	2203	4300	6503	SO:0001819	synonymous_variant	221935	exon7			CGGGCCATACGTC	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.1077A>G	7.37:g.3991479A>G		25	0	0		38	15	0.394737	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	ENST00000404826.2	37	CCDS34590.1	110	0.05036630036630037	102	0.2073170731707317	6	0.016574585635359115	0	0.0	2	0.002638522427440633	G	0.457	-0.890886	0.02491	0.217431	0.001047	ENSG00000146555	ENST00000426596	.	.	.	4.87	0.937	0.19494	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.22253	P	0.999251882	.	.	.	.	.	.	T	0.24190	-1.0167	3	.	.	.	.	3.246	0.06797	0.1411:0.2537:0.474:0.1313	rs6961589;rs17134087;rs6961589	.	.	.	R	78	.	.	H	+	2	0	SDK1	3958005	0.838000	0.29461	0.001000	0.08648	0.000000	0.00434	1.014000	0.29950	-0.265000	0.09352	-2.011000	0.00436	CAT	A|0.926;G|0.074	0.074	strong		0.602	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		G	3991479	A	G	3991479	2	3	22	1	0	0	0	0	0	0	0	1	13983	204	8	3		3	SDK1	7	3991479	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1021790	3991479	155147184	1605	4506											
SDK1	221935	hgsc.bcm.edu	37	chr7	4116697	4116697	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acgcacaccctgaacagcacGacgcacgagtacaagatcca	15	3	8	15	4	0	2	0	1	0	1	1	4	1	2	2	0	3	4	2	0	3	1	rs61735695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:4116697G>A	ENST00000404826.2	+	21	3217	c.3078G>A	c.(3076-3078)acG>acA	p.T1026T	SDK1_ENST00000389531.3_Silent_p.T1026T	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1026	Fibronectin type-III 4. {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)		TGAACAGCACGACGCACGAGT	0.567													G|||	56	0.0111821	0.0408	0.0029	5008	,	,		21381	0.0		0.0	False		,,,				2504	0.0				p.T1026T		Atlas-SNP	.											SDK1,NS,carcinoma,+1,2	SDK1	361	2	0			c.G3078A						PASS	.	G		134,4272	96.7+/-135.4	2,130,2071	171	132	145		3078	-6.5	0	7	dbSNP_129	145	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SDK1	NM_152744.3		2,131,6370	AA,AG,GG		0.0116,3.0413,1.038		1026/2214	4116697	135,12871	2203	4300	6503	SO:0001819	synonymous_variant	221935	exon21			CAGCACGACGCAC	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.3078G>A	7.37:g.4116697G>A		134	0	0		129	56	0.434109	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	ENST00000404826.2	37	CCDS34590.1																																																																																			G|0.990;A|0.010	0.010	strong		0.567	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744		A	4116697	G	A	4116697	2	1	22	1	0	0	0	0	0	0	0	1	13983	1045	37	1		1	SDK1	7	4116697	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	125218	4116697	155021966	1606	4507											
TNRC18	84629	hgsc.bcm.edu	37	chr7	5352731	5352731	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcgctgcagttacggcccccGgtgccgcagcccccgtcccc	3	5	12	21	5	0	0	0	0	0	0	1	0	1	0	7	2	4	4	7	2	1	1	rs114222264	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:5352731G>A	ENST00000430969.1	-	27	8139	c.7791C>T	c.(7789-7791)acC>acT	p.T2597T	TNRC18_ENST00000399537.4_Silent_p.T2597T	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2597	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)		TACGGCCCCCGGTGCCGCAGC	0.682													G|||	191	0.038139	0.1407	0.0029	5008	,	,		7259	0.0		0.003	False		,,,				2504	0.0				p.T2597T		Atlas-SNP	.											.	TNRC18	311	.	0			c.C7791T						PASS	.	G		243,2437		9,225,1106	7	12	11		7791	-3.8	0	7	dbSNP_132	11	2,6206		0,2,3102	no	coding-synonymous	TNRC18	NM_001080495.2		9,227,4208	AA,AG,GG		0.0322,9.0672,2.7565		2597/2969	5352731	245,8643	1340	3104	4444	SO:0001819	synonymous_variant	84629	exon27			GCCCCCGGTGCCG	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.7791C>T	7.37:g.5352731G>A		20	0	0		23	8	0.347826	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	37	CCDS47534.1																																																																																			G|0.964;A|0.036	0.036	strong		0.682	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	5352731	G	A	5352731	2	1	22	1	0	0	0	0	0	0	0	1	16354	1103	39	1		1	TNRC18	7	5352731	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1236034	5352731	153785932	1607	4508											
TNRC18	84629	hgsc.bcm.edu	37	chr7	5353252	5353252	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	catggtgatgaggggtgctgGggccagggaggtggcaggag	7	6	23	5	0	0	2	0	2	0	0	0	4	0	4	1	9	1	2	1	9	0	0	rs58819185	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:5353252G>C	ENST00000430969.1	-	27	7618	c.7270C>G	c.(7270-7272)Cca>Gca	p.P2424A	TNRC18_ENST00000399537.4_Missense_Mutation_p.P2424A	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2424	Pro-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)		AGGGGTGCTGGGGCCAGGGAG	0.726													G|||	321	0.0640974	0.2322	0.0144	5008	,	,		11967	0.0		0.004	False		,,,				2504	0.0				p.P2424A		Atlas-SNP	.											.	TNRC18	311	.	0			c.C7270G						PASS	.	G	ALA/PRO	536,2586		36,464,1061	11	12	11		7270	0.1	0.1	7	dbSNP_129	11	1,7155		0,1,3577	no	missense	TNRC18	NM_001080495.2	27	36,465,4638	CC,CG,GG		0.014,17.1685,5.2248	benign	2424/2969	5353252	537,9741	1561	3578	5139	SO:0001583	missense	84629	exon27			GTGCTGGGGCCAG	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.7270C>G	7.37:g.5353252G>C	ENSP00000395538:p.Pro2424Ala	119	0	0		155	66	0.425806	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	37	CCDS47534.1	109|109	0.04990842490842491|0.04990842490842491	101|101	0.20528455284552846|0.20528455284552846	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	4|4	0.005277044854881266|0.005277044854881266	g|g	0|0	-2.731061|-2.731061	0.00089|0.00089	0.171685|0.171685	1.4E-4|1.4E-4	ENSG00000182095|ENSG00000182095	ENST00000399537;ENST00000430969|ENST00000328270	T;T|.	0.12147|.	2.71;2.71|.	3.33|3.33	0.0546|0.0546	0.14311|0.14311	.|.	.|.	.|.	.|.	.|.	T|T	0.00039|0.00039	0.0001|0.0001	N|N	0.14661|0.14661	0.345|0.345	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.28004|0.28004	-1.0057|-1.0057	8|4	0.08381|.	T|.	0.77|.	.|.	8.9408|8.9408	0.35729|0.35729	0.0:0.4024:0.4584:0.1392|0.0:0.4024:0.4584:0.1392	rs58819185|rs58819185	2424|.	O15417|.	TNC18_HUMAN|.	A|R	2424|237	ENSP00000382452:P2424A;ENSP00000395538:P2424A|.	ENSP00000382452:P2424A|.	P|P	-|-	1|2	0|0	TNRC18|TNRC18	5319778|5319778	0.807000|0.807000	0.29009|0.29009	0.131000|0.131000	0.22000|0.22000	0.055000|0.055000	0.15305|0.15305	2.373000|2.373000	0.44266|0.44266	-0.063000|-0.063000	0.13065|0.13065	-3.803000|-3.803000	0.00020|0.00020	CCA|CCC	G|0.943;C|0.057	0.057	strong		0.726	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				C	5353252	G	C	5353252	3	2	22	1	0	0	0	0	1	0	0	0	16354	1232	43	4	1652	4	TNRC18	7	5353252	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	521	5353252	153785411	1608	4509											
TNRC18	84629	hgsc.bcm.edu	37	chr7	5410814	5410814	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcggctctgtgatcttggaGggggacaagcggatgggctt	7	9	18	7	2	2	1	0	1	2	0	2	4	2	4	0	6	2	2	0	6	1	2	rs114987874	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:5410814G>C	ENST00000430969.1	-	11	3759	c.3411C>G	c.(3409-3411)ccC>ccG	p.P1137P	TNRC18_ENST00000399537.4_Silent_p.P1137P	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1137	Pro-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)		TGATCTTGGAGGGGGACAAGC	0.697													G|||	122	0.024361	0.0847	0.0101	5008	,	,		13301	0.0		0.003	False		,,,				2504	0.0				p.P1137P		Atlas-SNP	.											.	TNRC18	311	.	0			c.C3411G						PASS	.	G		322,3598		8,306,1646	15	17	16		3411	0.2	1	7	dbSNP_132	16	16,8234		0,16,4109	no	coding-synonymous	TNRC18	NM_001080495.2		8,322,5755	CC,CG,GG		0.1939,8.2143,2.7773		1137/2969	5410814	338,11832	1960	4125	6085	SO:0001819	synonymous_variant	84629	exon11			CTTGGAGGGGGAC	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.3411C>G	7.37:g.5410814G>C		79	0	0		83	33	0.39759	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	37	CCDS47534.1																																																																																			G|0.984;C|0.016	0.016	strong		0.697	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				C	5410814	G	C	5410814	2	2	22	1	0	0	0	0	0	0	0	1	16354	987	35	4		4	TNRC18	7	5410814	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	57562	5410814	153727849	1609	4510											
TNRC18	84629	hgsc.bcm.edu	37	chr7	5417093	5417093	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcggggtcggcagaccaGcgacctgagcccgccagcgc	6	3	16	16	5	0	2	0	1	0	1	1	3	0	2	4	3	4	2	4	3	0	0	rs60530083	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:5417093G>T	ENST00000430969.1	-	7	2718	c.2370C>A	c.(2368-2370)cgC>cgA	p.R790R	TNRC18_ENST00000399537.4_Silent_p.R790R	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	790							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)		CGGCAGACCAGCGACCTGAGC	0.701													G|||	138	0.0275559	0.0514	0.0058	5008	,	,		11884	0.0139		0.002	False		,,,				2504	0.0511				p.R790R		Atlas-SNP	.											.	TNRC18	311	.	0			c.C2370A						PASS	.	G		181,3615		4,173,1721	8	11	10		2370	-0.9	0.9	7	dbSNP_129	10	21,8133		0,21,4056	no	coding-synonymous	TNRC18	NM_001080495.2		4,194,5777	TT,TG,GG		0.2575,4.7682,1.6904		790/2969	5417093	202,11748	1898	4077	5975	SO:0001819	synonymous_variant	84629	exon7			AGACCAGCGACCT	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.2370C>A	7.37:g.5417093G>T		28	0	0		53	32	0.603774	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	37	CCDS47534.1																																																																																			G|0.985;T|0.015	0.015	strong		0.701	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				T	5417093	G	T	5417093	2	4	22	1	0	0	0	0	0	0	0	1	16354	958	34	4		4	TNRC18	7	5417093	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6279	5417093	153721570	1610	4511											
RNF216	54476	hgsc.bcm.edu	37	chr7	5765034	5765034	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttccactggtttctggtgaCagctcctgccattttttaat	6	18	7	10	0	1	1	0	1	1	0	3	1	3	1	3	2	2	2	3	2	1	5	rs77500990	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:5765034C>T	ENST00000425013.2	-	8	1478	c.1254G>A	c.(1252-1254)ctG>ctA	p.L418L	RNF216_ENST00000389902.3_Silent_p.L475L	NM_207111.3|NM_207116.2	NP_996994.1|NP_996999.1	Q9NWF9	RN216_HUMAN	ring finger protein 216	418					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)		TTTCTGGTGACAGCTCCTGCC	0.368													c|||	17	0.00339457	0.0129	0.0	5008	,	,		20317	0.0		0.0	False		,,,				2504	0.0				p.L475L		Atlas-SNP	.											.	RNF216	71	.	0			c.G1425A						PASS	.	C	,	52,4354	51.6+/-87.1	0,52,2151	143	123	130		1425,1254	-3	1	7	dbSNP_131	130	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous,coding-synonymous	RNF216	NM_207111.3,NM_207116.2	,	0,58,6445	TT,TC,CC		0.0698,1.1802,0.4459	,	475/924,418/867	5765034	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	54476	exon8			TGGTGACAGCTCC	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.1254G>A	7.37:g.5765034C>T		144	0	0		150	79	0.526667	NM_207111	Q6Y691|Q75ML7|Q7Z2H7|Q7Z7C1|Q8NHW7|Q9NYT1	Silent	SNP	ENST00000425013.2	37	CCDS34595.1																																																																																			C|0.996;T|0.004	0.004	strong		0.368	RNF216-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000340374.1	NM_207111		T	5765034	C	T	5765034	2	4	22	1	0	0	0	0	0	0	0	1	13495	465	17	2		2	RNF216	7	5765034	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	347941	5765034	153373629	1611	4512											
PMS2	5395	hgsc.bcm.edu	37	chr7	6026787	6026787	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gtcagttttaggcgctttctCctgagagtccacatgttcct	6	15	9	11	1	2	1	1	1	1	1	5	2	4	1	3	1	0	3	3	1	1	4	rs115052399	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:6026787C>T	ENST00000265849.7	-	11	1714	c.1609G>A	c.(1609-1611)Gag>Aag	p.E537K	PMS2_ENST00000406569.3_Missense_Mutation_p.E537K|PMS2_ENST00000441476.2_Missense_Mutation_p.E431K|PMS2_ENST00000382321.4_Intron|PMS2_ENST00000469652.1_Intron	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	537					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|single base insertion or deletion binding (GO:0032138)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		GGCGCTTTCTCCTGAGAGTCC	0.537			"Mis, N, F"			"colorectal, endometrial, ovarian, medulloblastoma, glioma"		Direct reversal of damage;Mismatch excision repair (MMR)	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				C|||	28	0.00559105	0.0204	0.0014	5008	,	,		15948	0.0		0.0	False		,,,				2504	0.0				p.E537K		Atlas-SNP	.	yes	Rec		"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	7	7p22	5395	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)		E	.	PMS2	88	.	0			c.G1609A						PASS	.	C	LYS/GLU	55,4351		0,55,2148	78	85	83		1609	3.7	0	7	dbSNP_132	83	0,8596		0,0,4298	no	missense	PMS2	NM_000535.5	56	0,55,6446	TT,TC,CC		0.0,1.2483,0.423	benign	537/863	6026787	55,12947	2203	4298	6501	SO:0001583	missense	5395	exon11	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	CTTTCTCCTGAGA		CCDS5343.1	7p22.1	2014-09-17	2001-11-28		ENSG00000122512	ENSG00000122512			9122	protein-coding gene	gene with protein product		600259	"postmeiotic segregation increased (S. cerevisiae) 2"	PMSL2		8072530	Standard	NM_000535		Approved	H_DJ0042M02.9, HNPCC4	uc003spl.3	P54278	OTTHUMG00000023135	ENST00000265849.7:c.1609G>A	7.37:g.6026787C>T	ENSP00000265849:p.Glu537Lys	89	0	0		102	48	0.470588	NM_000535	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Missense_Mutation	SNP	ENST00000265849.7	37	CCDS5343.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	c	11.03	1.519693	0.27211	0.012483	0.0	ENSG00000122512	ENST00000265849;ENST00000382322;ENST00000441476;ENST00000406569	T;T;D	0.87179	1.1;1.1;-2.22	5.85	3.72	0.42706	.	0.843000	0.10493	N	0.668254	T	0.67449	0.2894	L	0.38838	1.175	0.09310	N	0.999999	B;B;B	0.21071	0.023;0.001;0.051	B;B;B	0.19391	0.011;0.003;0.025	T	0.58086	-0.7698	10	0.09338	T	0.73	-16.5088	10.2582	0.43410	0.0:0.7388:0.1388:0.1224	.	537;537;431	P54278-3;P54278;C9J167	.;PMS2_HUMAN;.	K	537;490;431;537	ENSP00000265849:E537K;ENSP00000392843:E431K;ENSP00000384308:E537K	ENSP00000265849:E537K	E	-	1	0	PMS2	5993313	0.001000	0.12720	0.016000	0.15963	0.016000	0.09150	0.250000	0.18235	1.474000	0.48178	0.650000	0.86243	GAG	C|0.995;T|0.005	0.005	strong		0.537	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535		T	6026787	C	T	6026787	3	4	22	1	0	0	0	0	1	0	0	0	12152	864	30	2	999	2	PMS2	7	6026787	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	261753	6026787	153111876	1612	4513											
RSPH10B	728194	hgsc.bcm.edu	37	chr7	6838173	6838176	+	Stop_Codon_Del	DEL	AGAG	AGAG	-																															cagcaagaagaagaaaaagtAgagagacacgaggacacaca																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGAG	AGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:6838173_6838176delAGAG	ENST00000403107.1	+	0	2999_3002				CCZ1B_ENST00000597208.1_5'Flank|RSPH10B2_ENST00000359718.3_3'UTR|RSPH10B2_ENST00000297186.3_Stop_Codon_Del|CCZ1B_ENST00000316731.8_3'UTR|RSPH10B2_ENST00000433859.2_Stop_Codon_Del|RSPH10B2_ENST00000404077.1_Stop_Codon_Del			B2RC85	R10B2_HUMAN	radial spoke head 10 homolog B2 (Chlamydomonas)											breast(3)|endometrium(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|skin(2)	15						AAGAAAAAGTAGAGAGACACGAGG	0.49																																					p.871_871del		Atlas-Indel	.											.	RSPH10B	28	.	0			c.2611_2884del						PASS	.																																			SO:0001567	stop_retained_variant	222967	exon21			.		CCDS43552.1	7p22.1	2008-07-04			ENSG00000169402	ENSG00000169402			34385	protein-coding gene	gene with protein product							Standard	NM_001099697		Approved		uc003sqw.1	B2RC85	OTTHUMG00000151856	Exception_encountered	7.37:g.6838173_6838176delAGAG		497	0	0		379	34	0.0897098	NM_173565	A6NMW7|B2RXI4|B2RXJ0|Q86ST9|Q8NE68	Frame_Shift_Del	DEL	ENST00000403107.1	37	CCDS43552.1																																																																																			.	.	none		0.49	RSPH10B2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324184.4	NM_001099697		-	6838176	AGAG	-	6838173	7	5	22	1	0	1	0	1	0	0	0	0	13718	433	15	0	5375	0	RSPH10B	7	6838173	Stop_Codon_Del	DEL	AGAG	TCGA-G8-6324-01A-11D-2210-10	811386	6838173	152300490	1613	4514											
COL28A1	340267	hgsc.bcm.edu	37	chr7	7410391	7410391	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttttgaggctctggagtagAttcactgagttcttcccctg	6	16	10	9	0	3	3	1	2	2	1	4	4	4	4	2	2	0	3	2	2	1	6	rs76240858	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:7410391A>C	ENST00000399429.3	-	33	3171	c.3031T>G	c.(3031-3033)Tct>Gct	p.S1011A		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	1011					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)		TCTGGAGTAGATTCACTGAGT	0.373													A|||	17	0.00339457	0.0113	0.0	5008	,	,		16003	0.0		0.002	False		,,,				2504	0.0				p.S1011A		Atlas-SNP	.											.	COL28A1	113	.	0			c.T3031G						PASS	.	A	ALA/SER	37,3663		0,37,1813	127	116	120		3031	0.1	0	7	dbSNP_131	120	2,8168		0,2,4083	yes	missense	COL28A1	NM_001037763.2	99	0,39,5896	CC,CA,AA		0.0245,1.0,0.3286	possibly-damaging	1011/1126	7410391	39,11831	1850	4085	5935	SO:0001583	missense	340267	exon33			GAGTAGATTCACT	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.3031T>G	7.37:g.7410391A>C	ENSP00000382356:p.Ser1011Ala	84	0	0		97	32	0.329897	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Missense_Mutation	SNP	ENST00000399429.3	37	CCDS43553.1	9	0.004120879120879121	8	0.016260162601626018	0	0.0	0	0.0	1	0.0013192612137203166	A	10.22	1.291183	0.23564	0.01	2.45E-4	ENSG00000215018	ENST00000399429	D	0.88509	-2.39	3.85	0.134	0.14771	.	1.902650	0.03097	U	0.160580	T	0.69415	0.3108	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.60556	-0.7240	10	0.18710	T	0.47	0.0019	6.0507	0.19785	0.6632:0.0:0.3368:0.0	.	1011	Q2UY09	COSA1_HUMAN	A	1011	ENSP00000382356:S1011A	ENSP00000382356:S1011A	S	-	1	0	COL28A1	7376916	0.764000	0.28473	0.033000	0.17914	0.275000	0.26752	0.791000	0.26915	0.014000	0.14944	-0.290000	0.09829	TCT	A|0.997;C|0.003	0.003	strong		0.373	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763		C	7410391	A	C	7410391	3	2	22	1	0	0	0	0	1	0	0	0	3688	333	12	5	358	5	COL28A1	7	7410391	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	572218	7410391	151728272	1614	4515											
COL28A1	340267	hgsc.bcm.edu	37	chr7	7571420	7571420	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaggagcgaccaggagtcaaTtggaaaatcttgtcactcaa	15	8	10	8	1	4	0	3	0	1	0	4	4	4	3	1	3	1	0	1	3	5	2	rs17168526	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:7571420T>C	ENST00000399429.3	-	3	380	c.240A>G	c.(238-240)caA>caG	p.Q80Q		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	80	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)		CAGGAGTCAATTGGAAAATCT	0.418													T|||	127	0.0253594	0.0923	0.0058	5008	,	,		18415	0.0		0.001	False		,,,				2504	0.0				p.Q80Q		Atlas-SNP	.											.	COL28A1	113	.	0			c.A240G						PASS	.	T		280,3454		9,262,1596	70	69	70		240	-8.4	0	7	dbSNP_123	70	6,8210		0,6,4102	no	coding-synonymous	COL28A1	NM_001037763.2		9,268,5698	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	0.073,7.4987,2.3933		80/1126	7571420	286,11664	1867	4108	5975	SO:0001819	synonymous_variant	340267	exon3			AGTCAATTGGAAA	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.240A>G	7.37:g.7571420T>C		283	0	0		318	131	0.41195	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Silent	SNP	ENST00000399429.3	37	CCDS43553.1																																																																																			T|0.969;C|0.031	0.031	strong		0.418	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763		C	7571420	T	C	7571420	2	2	22	1	0	0	0	0	0	0	0	1	3688	1490	52	3		3	COL28A1	7	7571420	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	161029	7571420	151567243	1615	4516											
TMEM195	392636	hgsc.bcm.edu	37	chr7	15458194	15458194	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagttttacctctgtatggaTccaaaattggtaaagaagat	15	13	8	5	0	1	2	0	0	1	2	2	3	2	3	2	2	1	3	2	2	8	5	rs146442781	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:15458194T>A	ENST00000342526.3	-	5	767	c.598A>T	c.(598-600)Atc>Ttc	p.I200F		NM_001004320.1	NP_001004320.1	Q6ZNB7	ALKMO_HUMAN	alkylglycerol monooxygenase	200					ether lipid metabolic process (GO:0046485)|fatty acid biosynthetic process (GO:0006633)|membrane lipid metabolic process (GO:0006643)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glyceryl-ether monooxygenase activity (GO:0050479)|iron ion binding (GO:0005506)	p.I200V(1)		breast(1)|kidney(1)|large_intestine(6)|liver(1)|lung(30)|prostate(1)|skin(2)	42						TCTGTATGGATCCAAAATTGG	0.348													T|||	22	0.00439297	0.0151	0.0029	5008	,	,		13274	0.0		0.0	False		,,,				2504	0.0				p.I200F		Atlas-SNP	.											AGMO,NS,carcinoma,0,1	AGMO	98	1	1	Substitution - Missense(1)	prostate(1)	c.A598T						scavenged	.	T	PHE/ILE	50,4350		0,50,2150	35	42	40		598	5.8	1	7	dbSNP_134	40	0,8574		0,0,4287	yes	missense	AGMO	NM_001004320.1	21	0,50,6437	AA,AT,TT		0.0,1.1364,0.3854	probably-damaging	200/446	15458194	50,12924	2200	4287	6487	SO:0001583	missense	392636	exon5			TATGGATCCAAAA		CCDS34604.1	7p21.1	2013-03-04	2011-01-31	2011-01-31	ENSG00000187546	ENSG00000187546	1.14.16.5	"Fatty acid hydroxylase domain containing"	33784	protein-coding gene	gene with protein product		613738	"transmembrane protein 195"	TMEM195		20643956	Standard	NM_001004320		Approved	FLJ16237	uc003stb.1	Q6ZNB7	OTTHUMG00000152387	ENST00000342526.3:c.598A>T	7.37:g.15458194T>A	ENSP00000341662:p.Ile200Phe	140	1	0.00714286		162	81	0.5	NM_001004320	A4D114|A6NCH5	Missense_Mutation	SNP	ENST00000342526.3	37	CCDS34604.1	7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	T	22.8	4.342517	0.81911	0.011364	0.0	ENSG00000187546	ENST00000342526	D	0.84730	-1.89	5.8	5.8	0.92144	Fatty acid hydroxylase (1);	0.000000	0.85682	D	0.000000	D	0.91751	0.7391	M	0.93462	3.42	0.80722	D	1	D	0.56035	0.974	P	0.61328	0.887	D	0.93409	0.6767	10	0.72032	D	0.01	-30.639	16.1416	0.81528	0.0:0.0:0.0:1.0	.	200	Q6ZNB7	ALKMO_HUMAN	F	200	ENSP00000341662:I200F	ENSP00000341662:I200F	I	-	1	0	AGMO	15424719	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	5.600000	0.67599	2.209000	0.71365	0.482000	0.46254	ATC	T|0.997;A|0.003	0.003	strong		0.348	AGMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326049.2	NM_001004320		A	15458194	T	A	15458194	3	1	22	1	0	0	0	0	1	0	0	0	16132	1435	50	5	775	5	TMEM195	7	15458194	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	7886774	15458194	143680469	1616	4517											
AHR	196	hgsc.bcm.edu	37	chr7	17379157	17379157	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gaaatgatttttctggtgagGttgacttcagagacattgac	11	14	11	5	0	2	5	1	4	1	1	2	7	2	5	0	2	0	1	0	2	1	5	rs4986826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:17379157G>A	ENST00000242057.4	+	10	2351	c.1708G>A	c.(1708-1710)Gtt>Att	p.V570I		NM_001621.4	NP_001612.1	P35869	AHR_HUMAN	aryl hydrocarbon receptor	570			V -> I (in dbSNP:rs4986826). {ECO:0000269|PubMed:10739168, ECO:0000269|PubMed:11689007}.		apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|cell cycle (GO:0007049)|circadian regulation of gene expression (GO:0032922)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|regulation of B cell proliferation (GO:0030888)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to toxic substance (GO:0009636)|response to xenobiotic stimulus (GO:0009410)|transcription from RNA polymerase II promoter (GO:0006366)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosolic aryl hydrocarbon receptor complex (GO:0034752)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|Hsp90 protein binding (GO:0051879)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|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)|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)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|urinary_tract(3)	33	Lung NSC(10;0.0392)|all_lung(11;0.0754)				Atorvastatin(DB01076)|Flutamide(DB00499)|Ginseng(DB01404)|Leflunomide(DB01097)|Mexiletine(DB00379)|Nimodipine(DB00393)	TTCTGGTGAGGTTGACTTCAG	0.363													G|||	113	0.0225639	0.0756	0.0144	5008	,	,		21431	0.0		0.002	False		,,,				2504	0.001				p.V570I		Atlas-SNP	.											.	AHR	89	.	0			c.G1708A						PASS	.	G	ILE/VAL	285,4121	151.8+/-185.6	14,257,1932	67	71	69		1708	3.4	0.4	7	dbSNP_111	69	17,8583	11.9+/-42.8	0,17,4283	yes	missense	AHR	NM_001621.4	29	14,274,6215	AA,AG,GG		0.1977,6.4685,2.322	benign	570/849	17379157	302,12704	2203	4300	6503	SO:0001583	missense	196	exon10			GGTGAGGTTGACT	L19872	CCDS5366.1	7p15	2013-05-21			ENSG00000106546	ENSG00000106546		"Basic helix-loop-helix proteins"	348	protein-coding gene	gene with protein product		600253				8125016	Standard	NM_001621		Approved	bHLHe76	uc011jxz.1	P35869	OTTHUMG00000149967	ENST00000242057.4:c.1708G>A	7.37:g.17379157G>A	ENSP00000242057:p.Val570Ile	53	0	0		43	27	0.627907	NM_001621	A4D130|Q13728|Q13803|Q13804	Missense_Mutation	SNP	ENST00000242057.4	37	CCDS5366.1	49	0.022435897435897436	41	0.08333333333333333	8	0.022099447513812154	0	0.0	0	0.0	G	9.679	1.148672	0.21288	0.064685	0.001977	ENSG00000106546	ENST00000242057	T	0.24723	1.84	6.16	3.44	0.39384	.	0.396190	0.28322	N	0.015763	T	0.01489	0.0048	M	0.63428	1.95	0.18873	N	0.999986	B	0.31009	0.303	B	0.33799	0.17	T	0.02132	-1.1208	10	0.38643	T	0.18	.	12.061	0.53562	0.15:0.0:0.85:0.0	rs4986826;rs52830926;rs58070269;rs4986826	570	P35869	AHR_HUMAN	I	570	ENSP00000242057:V570I	ENSP00000242057:V570I	V	+	1	0	AHR	17345682	0.908000	0.30866	0.408000	0.26446	0.911000	0.54048	1.786000	0.38694	0.498000	0.27948	0.650000	0.86243	GTT	G|0.974;A|0.026	0.026	strong		0.363	AHR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314620.2	NM_001621		A	17379157	G	A	17379157	3	1	22	1	0	0	0	0	1	0	0	0	416	1261	44	2	1746	2	AHR	7	17379157	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1920963	17379157	141759506	1617	4518											
HDAC9	9734	hgsc.bcm.edu	37	chr7	18914209	18914209	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctctaggagggtacaaagtGacggcaaaatgtaagtacct	14	8	11	8	1	1	1	0	1	1	0	1	2	1	2	2	3	2	4	2	3	7	4	rs17140166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:18914209G>T	ENST00000432645.2	+	21	2784	c.2784G>T	c.(2782-2784)gtG>gtT	p.V928V	HDAC9_ENST00000401921.1_Silent_p.V887V|HDAC9_ENST00000441542.2_Silent_p.V931V|HDAC9_ENST00000406451.4_Silent_p.V928V	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	928	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)	GGTACAAAGTGACGGCAAAAT	0.443													G|||	94	0.01877	0.0681	0.0029	5008	,	,		18680	0.0		0.002	False		,,,				2504	0.0				p.V931V		Atlas-SNP	.											.	HDAC9	560	.	0			c.G2793T						PASS	.	G	,,	258,3528		7,244,1642	67	62	64		2784,2784,2793	1.4	1	7	dbSNP_123	64	4,8238		0,4,4117	no	coding-synonymous,coding-synonymous,coding-synonymous	HDAC9	NM_058176.2,NM_178423.1,NM_178425.2	,,	7,248,5759	TT,TG,GG		0.0485,6.8146,2.1783	,,	928/1012,928/1067,931/1070	18914209	262,11766	1893	4121	6014	SO:0001819	synonymous_variant	9734	exon21			CAAAGTGACGGCA	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.2784G>T	7.37:g.18914209G>T		64	0	0		80	35	0.4375	NM_178425	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Silent	SNP	ENST00000432645.2	37	CCDS47555.1																																																																																			G|0.975;T|0.025	0.025	strong		0.443	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1			T	18914209	G	T	18914209	2	4	22	1	0	0	0	0	0	0	0	1	7023	1277	45	4		4	HDAC9	7	18914209	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1535052	18914209	140224454	1618	4519											
MACC1	346389	hgsc.bcm.edu	37	chr7	20199835	20199835	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacgaagggtgaaagcatccGgccaattgtgaagcaagtct	13	7	12	9	2	1	2	0	2	1	0	2	3	2	2	2	2	2	2	2	2	5	1	rs17142503	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:20199835G>A	ENST00000400331.5	-	5	457	c.149C>T	c.(148-150)cCg>cTg	p.P50L	MACC1_ENST00000589011.1_Missense_Mutation_p.P50L|MACC1_ENST00000332878.4_Missense_Mutation_p.P50L	NM_182762.3	NP_877439.3	Q6ZN28	MACC1_HUMAN	metastasis associated in colon cancer 1	50			P -> L (in dbSNP:rs17142503).		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						GAAAGCATCCGGCCAATTGTG	0.398													G|||	117	0.0233626	0.0802	0.0043	5008	,	,		16736	0.001		0.001	False		,,,				2504	0.0061				p.P50L		Atlas-SNP	.											MACC1,colon,carcinoma,-1,1	MACC1	99	1	0			c.C149T						PASS	.	G	LEU/PRO	269,4137	140.0+/-175.5	6,257,1940	75	76	76		149	4.9	0.1	7	dbSNP_123	76	6,8594	5.0+/-18.6	0,6,4294	yes	missense	MACC1	NM_182762.3	98	6,263,6234	AA,AG,GG		0.0698,6.1053,2.1144	benign	50/853	20199835	275,12731	2203	4300	6503	SO:0001583	missense	346389	exon5			GCATCCGGCCAAT		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.149C>T	7.37:g.20199835G>A	ENSP00000383185:p.Pro50Leu	56	0	0		69	36	0.521739	NM_182762	A8MUS5|B2RNR9|Q6ZQN8|Q7Z5A5	Missense_Mutation	SNP	ENST00000400331.5	37	CCDS5369.1	23	0.010531135531135532	20	0.04065040650406504	2	0.0055248618784530384	1	0.0017482517482517483	0	0.0	G	10.20	1.284308	0.23392	0.061053	6.98E-4	ENSG00000183742	ENST00000400331;ENST00000332878	T;T	0.09538	2.97;2.97	5.82	4.95	0.65309	.	0.520649	0.21203	N	0.078429	T	0.01029	0.0034	L	0.40543	1.245	0.44469	D	0.997404	P	0.52692	0.955	B	0.42087	0.375	T	0.12192	-1.0557	10	0.54805	T	0.06	-2.2911	10.037	0.42135	0.0689:0.0:0.795:0.1362	rs17142503;rs17142503	50	Q6ZN28	MACC1_HUMAN	L	50	ENSP00000383185:P50L;ENSP00000328410:P50L	ENSP00000328410:P50L	P	-	2	0	MACC1	20166360	0.878000	0.30173	0.135000	0.22099	0.025000	0.11179	3.709000	0.54853	1.484000	0.48361	-0.198000	0.12761	CCG	G|0.982;A|0.018	0.018	strong		0.398	MACC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250202.5	NM_182762		A	20199835	G	A	20199835	3	1	22	1	0	0	0	0	1	0	0	0	9152	1116	39	1	2421	1	MACC1	7	20199835	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1285626	20199835	138938828	1619	4520											
ABCB5	340273	hgsc.bcm.edu	37	chr7	20725366	20725366	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtcaatgacatattctacTgaaagaaagaccaactcact	17	9	6	9	0	3	4	2	2	1	2	3	5	3	4	1	0	2	0	1	0	6	3	rs115722120	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:20725366T>G	ENST00000404938.2	+	16	2569	c.1917T>G	c.(1915-1917)acT>acG	p.T639T	ABCB5_ENST00000258738.6_Silent_p.T194T	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	639					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						CATATTCTACTGAAAGAAAGA	0.368													T|||	18	0.00359425	0.0129	0.0	5008	,	,		16557	0.0		0.001	False		,,,				2504	0.0				p.T639T		Atlas-SNP	.											.	ABCB5	357	.	0			c.T1917G						PASS	.	T	,	61,4345	58.1+/-94.6	0,61,2142	94	85	88		1917,582	1.8	0	7	dbSNP_132	88	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ABCB5	NM_001163941.1,NM_178559.5	,	0,61,6442	GG,GT,TT		0.0,1.3845,0.469	,	639/1258,194/813	20725366	61,12945	2203	4300	6503	SO:0001819	synonymous_variant	340273	exon16			TTCTACTGAAAGA	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.1917T>G	7.37:g.20725366T>G		181	0	0		185	85	0.459459	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Silent	SNP	ENST00000404938.2	37	CCDS55090.1																																																																																			T|0.995;G|0.005	0.005	strong		0.368	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559		G	20725366	T	G	20725366	2	3	22	1	0	0	0	0	0	0	0	1	44	1567	55	5		5	ABCB5	7	20725366	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	525531	20725366	138413297	1620	4521											
ABCB5	340273	hgsc.bcm.edu	37	chr7	20766752	20766752	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtatgaagagatgcttcaGactcaacacaggtgattata	15	11	9	6	0	2	4	2	2	0	2	2	5	2	4	0	1	2	2	0	1	5	4	rs35885925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:20766752G>T	ENST00000404938.2	+	22	3367	c.2715G>T	c.(2713-2715)caG>caT	p.Q905H	ABCB5_ENST00000258738.6_Missense_Mutation_p.Q460H	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	905	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.		Q -> H (in dbSNP:rs35885925).		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						AGATGCTTCAGACTCAACACA	0.358													G|||	104	0.0207668	0.0756	0.0058	5008	,	,		18547	0.0		0.0	False		,,,				2504	0.0				p.Q905H		Atlas-SNP	.											.	ABCB5	357	.	0			c.G2715T						PASS	.	G	HIS/GLN,HIS/GLN	270,4136	154.0+/-187.5	9,252,1942	99	105	103		2715,1380	1.6	0.7	7	dbSNP_126	103	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	ABCB5	NM_001163941.1,NM_178559.5	24,24	9,254,6240	TT,TG,GG		0.0233,6.128,2.0913	possibly-damaging,possibly-damaging	905/1258,460/813	20766752	272,12734	2203	4300	6503	SO:0001583	missense	340273	exon22			GCTTCAGACTCAA	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.2715G>T	7.37:g.20766752G>T	ENSP00000384881:p.Gln905His	76	0	0		50	27	0.54	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	37	CCDS55090.1	36	0.016483516483516484	35	0.07113821138211382	1	0.0027624309392265192	0	0.0	0	0.0	G	5.753	0.323381	0.10900	0.06128	2.33E-4	ENSG00000004846	ENST00000404938;ENST00000258738	D;D	0.90197	-2.63;-2.63	4.43	1.61	0.23674	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.332317	0.24615	N	0.037015	T	0.39545	0.1082	L	0.55990	1.75	0.23260	N	0.998027	B;B;B	0.18310	0.027;0.01;0.003	B;B;B	0.21546	0.035;0.025;0.021	T	0.62900	-0.6756	10	0.46703	T	0.11	.	6.0759	0.19915	0.1851:0.1728:0.6421:0.0	rs35885925;rs57355100	905;83;460	A7BKA4;A0ASV4;Q2M3G0	.;.;ABCB5_HUMAN	H	905;460	ENSP00000384881:Q905H;ENSP00000258738:Q460H	ENSP00000258738:Q460H	Q	+	3	2	ABCB5	20733277	0.952000	0.32445	0.664000	0.29753	0.655000	0.38815	1.962000	0.40442	0.362000	0.24319	0.655000	0.94253	CAG	G|0.979;T|0.021	0.021	strong		0.358	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559		T	20766752	G	T	20766752	3	4	22	1	0	0	0	0	1	0	0	0	44	933	33	4	2838	4	ABCB5	7	20766752	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	41386	20766752	138371911	1621	4522											
GPNMB	10457	hgsc.bcm.edu	37	chr7	23300352	23300352	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggaccttgtccgccaccGccaccaccacccagaccttc	8	5	6	22	2	0	1	0	0	0	1	2	2	1	2	10	1	0	0	10	1	0	2	rs35115002	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:23300352G>T	ENST00000381990.2	+	6	1139	c.978G>T	c.(976-978)ccG>ccT	p.P326P	GPNMB_ENST00000539136.1_Silent_p.P227P|GPNMB_ENST00000258733.4_Silent_p.P326P|GPNMB_ENST00000453162.2_Silent_p.P268P	NM_001005340.1|NM_002510.2	NP_001005340.1|NP_002501.1	Q14956	GPNMB_HUMAN	glycoprotein (transmembrane) nmb	326	PKD. {ECO:0000255|PROSITE- ProRule:PRU00151}.|Poly-Pro.				bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|negative regulation of cell proliferation (GO:0008285)|osteoblast differentiation (GO:0001649)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)			breast(5)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(3)|stomach(2)	41			GBM - Glioblastoma multiforme(13;0.154)			GTCCGCCACCGCCACCACCAC	0.493													G|||	11	0.00219649	0.0083	0.0	5008	,	,		18491	0.0		0.0	False		,,,				2504	0.0				p.P326P		Atlas-SNP	.											.	GPNMB	88	.	0			c.G978T						PASS	.	G	,	58,4348	56.2+/-92.4	0,58,2145	119	128	125		978,978	-0.3	0	7	dbSNP_126	125	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	GPNMB	NM_001005340.1,NM_002510.2	,	0,58,6445	TT,TG,GG		0.0,1.3164,0.4459	,	326/573,326/561	23300352	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	10457	exon6			GCCACCGCCACCA	X76534	CCDS5380.1, CCDS34610.1	7p	2008-07-18			ENSG00000136235	ENSG00000136235			4462	protein-coding gene	gene with protein product	"transmembrane glycoprotein", "glycoprotein NMB", "glycoprotein nmb-like protein", "osteoactivin"	604368				7814155	Standard	NM_002510		Approved	NMB, HGFIN	uc003swc.3	Q14956	OTTHUMG00000022811	ENST00000381990.2:c.978G>T	7.37:g.23300352G>T		83	0	0		73	40	0.547945	NM_002510	A4D155|Q6UVX1|Q8N1A1	Silent	SNP	ENST00000381990.2	37	CCDS34610.1																																																																																			G|0.995;T|0.005	0.005	strong		0.493	GPNMB-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327152.1	NM_001005340		T	23300352	G	T	23300352	2	4	22	1	0	0	0	0	0	0	0	1	6628	1074	38	4		4	GPNMB	7	23300352	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2533600	23300352	135838311	1622	4523											
HNRNPA2B1	3181	hgsc.bcm.edu	37	chr7	26236235	26236235	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttgtctagacaaagccttTcttacttctgcattatgacc	9	16	5	11	0	4	2	0	1	4	1	4	2	4	2	2	0	3	1	2	0	4	6	rs34317198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:26236235T>C	ENST00000354667.4	-	6	723	c.555A>G	c.(553-555)agA>agG	p.R185R	HNRNPA2B1_ENST00000356674.7_Silent_p.R173R	NM_031243.2	NP_112533.1	P22626	ROA2_HUMAN	heterogeneous nuclear ribonucleoprotein A2/B1	185	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				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						ACAAAGCCTTTCTTACTTCTG	0.323			T	ETV1	prostate								T|||	259	0.0517173	0.1861	0.0173	5008	,	,		19739	0.0		0.001	False		,,,				2504	0.0				p.R185R		Atlas-SNP	.		Dom	yes		7	7p15	3181	heterogeneous nuclear ribonucleoprotein A2/B1		E	.	HNRNPA2B1	70	.	0			c.A555G						PASS	.	T	,	677,3729	285.5+/-278.2	40,597,1566	168	179	176		519,555	4.9	1	7	dbSNP_126	176	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous,coding-synonymous	HNRNPA2B1	NM_002137.3,NM_031243.2	,	40,603,5860	CC,CT,TT		0.0698,15.3654,5.2514	,	173/342,185/354	26236235	683,12323	2203	4300	6503	SO:0001819	synonymous_variant	3181	exon6			AGCCTTTCTTACT	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.555A>G	7.37:g.26236235T>C		195	0	0		170	78	0.458824	NM_031243	A8K064|P22627|Q9UC98|Q9UDJ2	Silent	SNP	ENST00000354667.4	37	CCDS43557.1																																																																																			T|0.935;C|0.065	0.065	strong		0.323	HNRNPA2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214109.1	NM_002137		C	26236235	T	C	26236235	2	2	22	1	0	0	0	0	0	0	0	1	7268	1780	62	3		3	HNRNPA2B1	7	26236235	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2935883	26236235	132902428	1623	4524											
WIPF3	644150	hgsc.bcm.edu	37	chr7	29924002	29924002	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccccgccgcccccgctccccCcttatgcttcttgctccccg	1	9	6	25	4	1	0	0	0	1	0	3	0	3	0	10	0	2	3	10	0	1	3	rs371924598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:29924002C>A	ENST00000409290.1	+	4	892	c.892C>A	c.(892-894)Cct>Act	p.P298T	WIPF3_ENST00000242140.5_Missense_Mutation_p.P298T|WIPF3_ENST00000409123.1_Missense_Mutation_p.P298T	NM_001080529.2	NP_001073998.2	A6NGB9	WIPF3_HUMAN	WAS/WASL interacting protein family, member 3	298	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						CCCGCTCCCCCCTTATGCTTC	0.672													C|||	18	0.00359425	0.0129	0.0	5008	,	,		5386	0.001		0.0	False		,,,				2504	0.0				p.P298T		Atlas-SNP	.											.	WIPF3	46	.	0			c.C892A						PASS	.	C	THR/PRO	24,3134		0,24,1555	4	4	4		892	1	0	7		4	2,7334		0,2,3666	no	missense	WIPF3	NM_001080529.2	38	0,26,5221	AA,AC,CC		0.0273,0.76,0.2478	benign	298/484	29924002	26,10468	1579	3668	5247	SO:0001583	missense	644150	exon5			CTCCCCCCTTATG	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.892C>A	7.37:g.29924002C>A	ENSP00000386878:p.Pro298Thr	117	0	0		140	69	0.492857	NM_001080529	B8ZZV2	Missense_Mutation	SNP	ENST00000409290.1	37	CCDS56472.1	.	.	.	.	.	.	.	.	.	.	C	6.789	0.514559	0.12944	0.0076	2.73E-4	ENSG00000122574	ENST00000409123;ENST00000409290;ENST00000242140	T;T;T	0.43688	0.94;0.94;0.94	4.02	0.979	0.19745	.	0.460073	0.18939	N	0.126985	T	0.16300	0.0392	N	0.12746	0.255	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.15350	-1.0440	10	0.21014	T	0.42	.	11.6236	0.51132	0.4549:0.5451:0.0:0.0	.	298	A6NGB9	WIPF3_HUMAN	T	298	ENSP00000386790:P298T;ENSP00000386878:P298T;ENSP00000242140:P298T	ENSP00000242140:P298T	P	+	1	0	WIPF3	29890527	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.063000	0.11655	-0.325000	0.08577	-1.624000	0.00789	CCT	.	.	weak		0.672	WIPF3-002	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327705.1			A	29924002	C	A	29924002	3	1	22	1	0	0	0	0	1	0	0	0	17384	623	22	4	906	4	WIPF3	7	29924002	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3687767	29924002	129214661	1624	4525											
FKBP14	55033	hgsc.bcm.edu	37	chr7	30054492	30054492	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccatgtttttcaaactccttCtttaaatatgctttaaccta	11	18	2	10	0	2	0	1	0	1	0	3	0	3	0	3	0	3	2	3	0	6	9	rs142474407	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:30054492C>T	ENST00000222803.5	-	4	670	c.495G>A	c.(493-495)aaG>aaA	p.K165K	AC007285.6_ENST00000419103.1_RNA|AC007285.6_ENST00000422239.1_RNA	NM_017946.3	NP_060416.1	Q9NWM8	FKB14_HUMAN	FK506 binding protein 14, 22 kDa	165	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein folding (GO:0061077)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|large_intestine(2)|lung(2)	5						CAAACTCCTTCTTTAAATATG	0.348													C|||	10	0.00199681	0.0076	0.0	5008	,	,		14950	0.0		0.0	False		,,,				2504	0.0				p.K165K		Atlas-SNP	.											.	FKBP14	18	.	0			c.G495A						PASS	.	C		39,4367	38.4+/-70.7	1,37,2165	85	80	82		495	5	1	7	dbSNP_134	82	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FKBP14	NM_017946.2		1,38,6464	TT,TC,CC		0.0116,0.8852,0.3076		165/212	30054492	40,12966	2203	4300	6503	SO:0001819	synonymous_variant	55033	exon4			CTCCTTCTTTAAA	AK000738	CCDS5423.1	7p15	2014-09-17	2002-08-29		ENSG00000106080	ENSG00000106080		"EF-hand domain containing"	18625	protein-coding gene	gene with protein product		614505	"FK506 binding protein 14 (22 kDa)"			12036304	Standard	NM_017946		Approved	FLJ20731, FKBP22	uc003tal.2	Q9NWM8	OTTHUMG00000023442	ENST00000222803.5:c.495G>A	7.37:g.30054492C>T		63	0	0		66	42	0.636364	NM_017946		Silent	SNP	ENST00000222803.5	37	CCDS5423.1																																																																																			C|0.997;T|0.003	0.003	strong		0.348	FKBP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214229.1	NM_017946		T	30054492	C	T	30054492	2	4	22	1	0	0	0	0	0	0	0	1	5912	912	32	2		2	FKBP14	7	30054492	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	130490	30054492	129084171	1625	4526											
NOD1	10392	hgsc.bcm.edu	37	chr7	30491081	30491081	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcgcagcatccagatgaacGtgggcatggcctgcacctgg	9	6	14	12	2	0	2	0	1	0	1	1	2	1	2	3	3	4	4	3	3	1	0	rs151170709	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:30491081G>A	ENST00000222823.4	-	6	2477	c.1952C>T	c.(1951-1953)aCg>aTg	p.T651M		NM_006092.2	NP_006083.1	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain containing 1	651					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						CCAGATGAACGTGGGCATGGC	0.622													G|||	4	0.000798722	0.003	0.0	5008	,	,		18686	0.0		0.0	False		,,,				2504	0.0				p.T651M		Atlas-SNP	.											.	NOD1	79	.	0			c.C1952T						PASS	.	G	MET/THR	18,4388	26.2+/-53.5	0,18,2185	44	45	45		1952	5.6	1	7	dbSNP_134	45	0,8600		0,0,4300	yes	missense	NOD1	NM_006092.2	81	0,18,6485	AA,AG,GG		0.0,0.4085,0.1384	probably-damaging	651/954	30491081	18,12988	2203	4300	6503	SO:0001583	missense	10392	exon6			ATGAACGTGGGCA	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.1952C>T	7.37:g.30491081G>A	ENSP00000222823:p.Thr651Met	53	0	0		63	34	0.539683	NM_006092	B4DTU3|Q549U4|Q8IWF5	Missense_Mutation	SNP	ENST00000222823.4	37	CCDS5427.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	17.46	3.395795	0.62177	0.004085	0.0	ENSG00000106100	ENST00000222823	T	0.71103	-0.54	5.61	5.61	0.85477	.	0.192032	0.52532	D	0.000072	T	0.70046	0.3179	M	0.63428	1.95	0.80722	D	1	D	0.71674	0.998	P	0.54706	0.759	T	0.74636	-0.3599	10	0.49607	T	0.09	.	12.283	0.54776	0.0:0.0:0.7325:0.2675	.	651	Q9Y239	NOD1_HUMAN	M	651	ENSP00000222823:T651M	ENSP00000222823:T651M	T	-	2	0	NOD1	30457606	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.689000	0.68234	2.652000	0.90054	0.655000	0.94253	ACG	G|0.998;A|0.002	0.002	strong		0.622	NOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250443.2			A	30491081	G	A	30491081	3	1	22	1	0	0	0	0	1	0	0	0	10525	1145	40	1	945	1	NOD1	7	30491081	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	436589	30491081	128647582	1626	4527											
INMT	11185	hgsc.bcm.edu	37	chr7	30793532	30793532	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaccccagcggtgaaattcGcctgtgagctggaaggaaac	11	6	14	10	2	0	2	0	2	0	0	1	5	0	5	3	4	3	1	3	4	3	1	rs76338133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:30793532G>A	ENST00000013222.5	+	2	356	c.340G>A	c.(340-342)Gcc>Acc	p.A114T	INMT_ENST00000484180.1_3'UTR|INMT_ENST00000409539.1_Missense_Mutation_p.A113T|INMT-FAM188B_ENST00000458257.1_Missense_Mutation_p.A113T	NM_001199219.1|NM_006774.4	NP_001186148.1|NP_006765.4	O95050	INMT_HUMAN	indolethylamine N-methyltransferase	114					amine metabolic process (GO:0009308)|methylation (GO:0032259)|response to toxic substance (GO:0009636)	cytosol (GO:0005829)	amine N-methyltransferase activity (GO:0030748)|thioether S-methyltransferase activity (GO:0004790)			kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|stomach(1)	23						GGTGAAATTCGCCTGTGAGCT	0.577													G|||	66	0.0131789	0.0461	0.0072	5008	,	,		19308	0.0		0.0	False		,,,				2504	0.0				p.A114T		Atlas-SNP	.											.	INMT	38	.	0			c.G340A						PASS	.	G	THR/ALA,THR/ALA	191,4215	118.8+/-156.5	1,189,2013	55	63	60		337,340	3	0.1	7	dbSNP_131	60	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	INMT	NM_001199219.1,NM_006774.4	58,58	1,191,6311	AA,AG,GG		0.0233,4.335,1.4839	possibly-damaging,possibly-damaging	113/263,114/264	30793532	193,12813	2203	4300	6503	SO:0001583	missense	11185	exon2			AAATTCGCCTGTG		CCDS5430.1, CCDS56479.1	7p14.3	2011-08-30			ENSG00000241644	ENSG00000241644	2.1.1.49		6069	protein-coding gene	gene with protein product		604854				10552930	Standard	NM_001199219		Approved		uc003tbs.1	O95050	OTTHUMG00000167163	ENST00000013222.5:c.340G>A	7.37:g.30793532G>A	ENSP00000013222:p.Ala114Thr	71	0	0		76	35	0.460526	NM_006774	B8ZZ69|Q3KP49|Q9P1Y2|Q9UBY4|Q9UHQ0	Missense_Mutation	SNP	ENST00000013222.5	37	CCDS5430.1	27	0.012362637362637362	23	0.046747967479674794	4	0.011049723756906077	0	0.0	0	0.0	G	20.3	3.970206	0.74246	0.04335	2.33E-4	ENSG00000241644	ENST00000013222;ENST00000409539	T;T	0.03745	3.82;3.82	3.94	3.01	0.34805	.	0.359516	0.21052	N	0.080972	T	0.00524	0.0017	L	0.47716	1.5	0.26856	N	0.968062	P;P	0.42993	0.797;0.797	B;B	0.30855	0.121;0.121	T	0.44190	-0.9344	10	0.62326	D	0.03	-22.6315	8.8685	0.35300	0.1195:0.0:0.8805:0.0	.	113;114	B8ZZ69;O95050	.;INMT_HUMAN	T	114;113	ENSP00000013222:A114T;ENSP00000386961:A113T	ENSP00000013222:A114T	A	+	1	0	INMT	30760057	0.724000	0.28038	0.090000	0.20809	0.481000	0.33189	3.811000	0.55620	0.927000	0.37143	0.561000	0.74099	GCC	G|0.984;A|0.016	0.016	strong		0.577	INMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214993.3	NM_006774		A	30793532	G	A	30793532	3	1	22	1	0	0	0	0	1	0	0	0	7754	1087	38	1	346	1	INMT	7	30793532	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	302451	30793532	128345131	1627	4528											
INMT	11185	hgsc.bcm.edu	37	chr7	30795419	30795419	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tactctgtcaccaatgctgcCaacaatggggtctgcttcat	9	12	8	12	0	4	0	2	0	2	0	4	0	4	0	2	2	5	2	2	2	4	2	rs35221354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:30795419C>T	ENST00000013222.5	+	3	760	c.744C>T	c.(742-744)gcC>gcT	p.A248A	INMT_ENST00000484180.1_3'UTR|INMT_ENST00000409539.1_Silent_p.A247A|INMT-FAM188B_ENST00000458257.1_Intron	NM_001199219.1|NM_006774.4	NP_001186148.1|NP_006765.4	O95050	INMT_HUMAN	indolethylamine N-methyltransferase	248					amine metabolic process (GO:0009308)|methylation (GO:0032259)|response to toxic substance (GO:0009636)	cytosol (GO:0005829)	amine N-methyltransferase activity (GO:0030748)|thioether S-methyltransferase activity (GO:0004790)			kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|stomach(1)	23						CCAATGCTGCCAACAATGGGG	0.592													C|||	272	0.0543131	0.1921	0.0259	5008	,	,		20160	0.0		0.0	False		,,,				2504	0.0				p.A248A		Atlas-SNP	.											INMT,NS,carcinoma,+1,1	INMT	38	1	0			c.C744T						PASS	.	C	,	710,3696	297.3+/-284.7	54,602,1547	99	96	97		741,744	3.4	0.1	7	dbSNP_126	97	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous,coding-synonymous	INMT	NM_001199219.1,NM_006774.4	,	54,609,5840	TT,TC,CC		0.0814,16.1144,5.5128	,	247/263,248/264	30795419	717,12289	2203	4300	6503	SO:0001819	synonymous_variant	11185	exon3			TGCTGCCAACAAT		CCDS5430.1, CCDS56479.1	7p14.3	2011-08-30			ENSG00000241644	ENSG00000241644	2.1.1.49		6069	protein-coding gene	gene with protein product		604854				10552930	Standard	NM_001199219		Approved		uc003tbs.1	O95050	OTTHUMG00000167163	ENST00000013222.5:c.744C>T	7.37:g.30795419C>T		78	0	0		71	30	0.422535	NM_006774	B8ZZ69|Q3KP49|Q9P1Y2|Q9UBY4|Q9UHQ0	Silent	SNP	ENST00000013222.5	37	CCDS5430.1																																																																																			C|0.947;T|0.053	0.053	strong		0.592	INMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214993.3	NM_006774		T	30795419	C	T	30795419	2	4	22	1	0	0	0	0	0	0	0	1	7754	581	21	2		2	INMT	7	30795419	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1887	30795419	128343244	1628	4529											
CCDC129	223075	hgsc.bcm.edu	37	chr7	31691582	31691582	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgagcaactgcaaacgttacGtgaggccctgaggcagcagg	11	5	14	11	3	0	2	0	2	0	0	0	3	0	2	1	3	6	5	1	3	3	1	rs80081783	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:31691582G>A	ENST00000407970.3	+	13	2779	c.2741G>A	c.(2740-2742)cGt>cAt	p.R914H	CCDC129_ENST00000409210.1_Missense_Mutation_p.R822H|CCDC129_ENST00000451887.2_Missense_Mutation_p.R940H|CCDC129_ENST00000319386.3_Missense_Mutation_p.R766H	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	914										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						CAAACGTTACGTGAGGCCCTG	0.478													G|||	30	0.00599042	0.0227	0.0	5008	,	,		17400	0.0		0.0	False		,,,				2504	0.0				p.R940H		Atlas-SNP	.											LOC223075,right_lower_lobe,carcinoma,-1,2	CCDC129	127	2	0			c.G2819A						PASS	.	G	HIS/ARG	56,4350	55.5+/-91.7	0,56,2147	69	60	63		2741	5.2	0	7	dbSNP_133	63	0,8600		0,0,4300	yes	missense	CCDC129	NM_194300.2	29	0,56,6447	AA,AG,GG		0.0,1.271,0.4306	probably-damaging	914/1045	31691582	56,12950	2203	4300	6503	SO:0001583	missense	223075	exon13			CGTTACGTGAGGC	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.2741G>A	7.37:g.31691582G>A	ENSP00000384416:p.Arg914His	168	0	0		153	77	0.503268	NM_001257968	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Missense_Mutation	SNP	ENST00000407970.3	37	CCDS5435.2	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	26.1	4.700031	0.88924	0.01271	0.0	ENSG00000180347	ENST00000319386;ENST00000407970;ENST00000451887;ENST00000538406;ENST00000409210	T;T;T;T	0.56103	0.48;0.48;0.48;0.48	5.21	5.21	0.72293	.	0.000000	0.50627	D	0.000101	T	0.55862	0.1947	M	0.71581	2.175	0.09310	N	0.999998	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.79784	0.966;0.993;0.993;0.984	T	0.59910	-0.7365	10	0.87932	D	0	-17.7013	14.263	0.66097	0.0:0.0:1.0:0.0	.	940;924;914;766	F5H3V5;F5H2J8;Q6ZRS4;Q6ZRS4-2	.;.;CC129_HUMAN;.	H	766;914;940;924;822	ENSP00000313062:R766H;ENSP00000384416:R914H;ENSP00000395835:R940H;ENSP00000387214:R822H	ENSP00000313062:R766H	R	+	2	0	CCDC129	31658107	0.944000	0.32072	0.031000	0.17742	0.664000	0.39144	2.657000	0.46724	2.437000	0.82529	0.561000	0.74099	CGT	G|0.995;A|0.005	0.005	strong		0.478	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300		A	31691582	G	A	31691582	3	1	22	1	0	0	0	0	1	0	0	0	2766	1145	40	1	2787	1	CCDC129	7	31691582	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	896163	31691582	127447081	1629	4530											
BBS9	27241	hgsc.bcm.edu	37	chr7	33545253	33545253	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctacaagaagacactcaagAattggtaaggacctgaaagc	17	6	10	8	0	1	4	1	1	0	3	1	5	1	5	1	2	2	2	1	2	7	3	rs140882212		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:33545253A>G	ENST00000242067.6	+	20	2815	c.2294A>G	c.(2293-2295)gAa>gGa	p.E765G	BBS9_ENST00000354265.4_Missense_Mutation_p.E730G|BBS9_ENST00000396127.2_Missense_Mutation_p.E730G|BBS9_ENST00000355070.2_Missense_Mutation_p.E760G|BBS9_ENST00000350941.3_Missense_Mutation_p.E725G	NM_198428.2	NP_940820.1	Q3SYG4	PTHB1_HUMAN	Bardet-Biedl syndrome 9	765	Interaction with LZTL1.				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)			GACACTCAAGAATTGGTAAGG	0.468									Bardet-Biedl syndrome				A|||	1	0.000199681	0.0008	0.0	5008	,	,		17434	0.0		0.0	False		,,,				2504	0.0				p.E765G		Atlas-SNP	.											.	BBS9	194	.	0			c.A2294G						PASS	.	A	GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU	4,4402	6.2+/-15.9	0,4,2199	38	38	38		2189,2279,2174,2294	5.6	1	7	dbSNP_134	38	0,8600		0,0,4300	yes	missense,missense,missense,missense	BBS9	NM_001033604.1,NM_001033605.1,NM_014451.3,NM_198428.2	98,98,98,98	0,4,6499	GG,GA,AA		0.0,0.0908,0.0308	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	730/853,760/883,725/848,765/888	33545253	4,13002	2203	4300	6503	SO:0001583	missense	27241	exon20	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	CTCAAGAATTGGT		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.2294A>G	7.37:g.33545253A>G	ENSP00000242067:p.Glu765Gly	41	0	0		59	34	0.576271	NM_198428	E9PDC9|P78514|Q7KYS6|Q7KYS7|Q8N570|Q99844|Q99854|Q9Y699|Q9Y6A0	Missense_Mutation	SNP	ENST00000242067.6	37	CCDS43566.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	16.89	3.246980	0.59103	9.08E-4	0.0	ENSG00000122507	ENST00000242067;ENST00000350941;ENST00000396127;ENST00000355070;ENST00000354265;ENST00000396132	T;T;T;T;T	0.15952	2.38;2.38;2.38;2.38;2.38	5.61	5.61	0.85477	.	0.060219	0.64402	D	0.000004	T	0.24198	0.0586	L	0.46741	1.465	0.80722	D	1	P;P;D;P;P	0.54601	0.877;0.929;0.967;0.929;0.923	P;P;P;P;P	0.49252	0.501;0.501;0.604;0.501;0.501	T	0.00684	-1.1611	10	0.45353	T	0.12	-25.845	15.0016	0.71476	1.0:0.0:0.0:0.0	.	765;725;760;730;765	Q3SYG4-3;Q3SYG4-2;E9PDC9;Q3SYG4-4;Q3SYG4	.;.;.;.;PTHB1_HUMAN	G	765;725;730;760;730;765	ENSP00000242067:E765G;ENSP00000313122:E725G;ENSP00000379433:E730G;ENSP00000347182:E760G;ENSP00000346214:E730G	ENSP00000242067:E765G	E	+	2	0	BBS9	33511778	1.000000	0.71417	0.990000	0.47175	0.956000	0.61745	7.327000	0.79147	2.146000	0.66826	0.459000	0.35465	GAA	A|1.000;G|0.000	0.000	strong		0.468	BBS9-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329064.1			G	33545253	A	G	33545253	3	3	22	1	0	0	0	0	1	0	0	0	1342	246	9	3	2368	3	BBS9	7	33545253	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1853671	33545253	125593410	1630	4531											
BMPER	168667	hgsc.bcm.edu	37	chr7	33946464	33946464	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tgtgaaaatgaaggtgaagtCctccagattccatttatcac	13	12	8	8	0	1	4	1	3	0	1	4	4	4	4	3	1	0	0	3	1	5	3	rs112068976	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:33946464C>T	ENST00000297161.2	+	3	542	c.168C>T	c.(166-168)gtC>gtT	p.V56V	BMPER_ENST00000426693.1_Silent_p.V56V	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	56	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						AAGGTGAAGTCCTCCAGATTC	0.378													C|||	4	0.000798722	0.003	0.0	5008	,	,		18193	0.0		0.0	False		,,,				2504	0.0				p.V56V		Atlas-SNP	.											BMPER,NS,carcinoma,+1,1	BMPER	131	1	0			c.C168T						PASS	.	C		15,4391	22.3+/-47.3	0,15,2188	142	130	134		168	-6.9	0.3	7	dbSNP_132	134	0,8600		0,0,4300	no	coding-synonymous	BMPER	NM_133468.3		0,15,6488	TT,TC,CC		0.0,0.3404,0.1153		56/686	33946464	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	168667	exon3			TGAAGTCCTCCAG		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.168C>T	7.37:g.33946464C>T		107	0	0		95	51	0.536842	NM_133468	A8K1P8|Q8TF36	Silent	SNP	ENST00000297161.2	37	CCDS5442.1																																																																																			C|0.999;T|0.001	0.001	strong		0.378	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2	NM_133468		T	33946464	C	T	33946464	2	4	22	1	0	0	0	0	0	0	0	1	1468	842	30	2		2	BMPER	7	33946464	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	401211	33946464	125192199	1631	4532											
NPSR1	387129	hgsc.bcm.edu	37	chr7	34917759	34917759	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acgagagaactggaagggtaCttggccaggtgtaccttcct	10	9	13	9	1	0	1	0	0	0	1	1	4	1	2	3	4	3	2	3	4	4	4	rs13230135	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:34917759C>T	ENST00000359791.1	+	9	1225	c.1097C>T	c.(1096-1098)aCt>aTt	p.T366I	NPSR1_ENST00000531252.1_Missense_Mutation_p.T355I	NM_207173.1	NP_997056.1	Q6W5P4	NPSR1_HUMAN	neuropeptide S receptor 1	0						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)	TGGAAGGGTACTTGGCCAGGT	0.572													C|||	45	0.00898562	0.031	0.0043	5008	,	,		17115	0.0		0.0	False		,,,				2504	0.001				p.T366I		Atlas-SNP	.											.	NPSR1	134	.	0			c.C1097T						PASS	.	C	ILE/THR	157,4249	99.8+/-138.5	2,153,2048	76	60	65		1097	-1.2	0	7	dbSNP_121	65	3,8597	3.0+/-9.4	0,3,4297	no	missense	NPSR1	NM_207173.1	89	2,156,6345	TT,TC,CC		0.0349,3.5633,1.2302		366/378	34917759	160,12846	2203	4300	6503	SO:0001583	missense	387129	exon9			AGGGTACTTGGCC	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	ENST00000359791.1:c.1097C>T	7.37:g.34917759C>T	ENSP00000352839:p.Thr366Ile	224	0	0		288	146	0.506944	NM_207173	A2RTZ4|Q2XP58|Q56H76|Q56H77|Q56H78|Q6JSL4|Q6JSL5|Q6JSL6|Q6JSL7|Q6JSL8|Q6W5P3|Q6ZMB8	Missense_Mutation	SNP	ENST00000359791.1	37	CCDS5443.1	17	0.007783882783882784	14	0.028455284552845527	3	0.008287292817679558	0	0.0	0	0.0	C	8.876	0.950372	0.18431	0.035633	3.49E-4	ENSG00000187258	ENST00000359791;ENST00000531252	T;T	0.72167	-0.63;-0.25	2.64	-1.25	0.09405	.	.	.	.	.	T	0.13798	0.0334	N	0.08118	0	0.09310	N	1	B;B;B	0.26975	0.165;0.003;0.003	B;B;B	0.18561	0.022;0.006;0.006	T	0.07578	-1.0765	9	0.46703	T	0.11	.	3.1688	0.06545	0.0:0.3835:0.2193:0.3971	rs13230135	300;355;366	B7ZMA2;Q6W5P4-5;Q6W5P4-4	.;.;.	I	366;355	ENSP00000352839:T366I;ENSP00000433258:T355I	ENSP00000352839:T366I	T	+	2	0	NPSR1	34884284	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.050000	0.11904	-0.336000	0.08438	-0.324000	0.08512	ACT	C|0.987;T|0.013	0.013	strong		0.572	NPSR1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000216838.1	NM_207173		T	34917759	C	T	34917759	3	4	22	1	0	0	0	0	1	0	0	0	10609	565	20	2	1226	2	NPSR1	7	34917759	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	971295	34917759	124220904	1632	4533											
DPY19L1	23333	hgsc.bcm.edu	37	chr7	34978926	34978926	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	taatgtggatgattcacaatGggccgaagtgcagagagctt	12	10	13	6	1	1	2	1	1	0	1	1	5	1	3	1	2	2	2	1	2	3	3	rs377307859		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:34978926G>A	ENST00000310974.4	-	20	1851	c.1707C>T	c.(1705-1707)ccC>ccT	p.P569P	MIR548N_ENST00000408742.1_RNA	NM_015283.1	NP_056098.1	Q2PZI1	D19L1_HUMAN	dpy-19-like 1 (C. elegans)	569						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						GATTCACAATGGGCCGAAGTG	0.507																																					p.P569P		Atlas-SNP	.											.	DPY19L1	56	.	0			c.C1707T						PASS	.	G		1,4179		0,1,2089	120	112	115		1707	-0.4	0	7		115	0,8478		0,0,4239	no	coding-synonymous	DPY19L1	NM_015283.1		0,1,6328	AA,AG,GG		0.0,0.0239,0.0079		569/676	34978926	1,12657	2090	4239	6329	SO:0001819	synonymous_variant	23333	exon20			CACAATGGGCCGA	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.1707C>T	7.37:g.34978926G>A		113	0	0		138	71	0.514493	NM_015283	O94954|Q4G151	Silent	SNP	ENST00000310974.4	37	CCDS43567.1	.	.	.	.	.	.	.	.	.	.	G	9.689	1.151487	0.21371	2.39E-4	0.0	ENSG00000173852	ENST00000428054	.	.	.	5.9	-0.415	0.12355	.	.	.	.	.	T	0.41282	0.1152	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21109	-1.0255	4	.	.	.	-12.4763	1.5429	0.02559	0.2774:0.217:0.3812:0.1244	.	.	.	.	Y	19	.	.	H	-	1	0	DPY19L1	34945451	0.075000	0.21258	0.018000	0.16275	0.856000	0.48823	0.068000	0.14531	-0.382000	0.07870	-0.150000	0.13652	CAT	.	.	weak		0.507	DPY19L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337506.1			A	34978926	G	A	34978926	2	1	22	1	0	0	0	0	0	0	0	1	4742	1335	47	2		2	DPY19L1	7	34978926	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	61167	34978926	124159737	1633	4534											
GLI3	2737	hgsc.bcm.edu	37	chr7	42004897	42004897	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ggggccactggctgcctgttGagacagttcccatactgcgg	6	9	14	12	1	0	1	0	1	0	1	1	2	1	1	3	4	3	3	3	4	1	3	rs35448119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:42004897G>C	ENST00000395925.3	-	15	3858	c.3774C>G	c.(3772-3774)ctC>ctG	p.L1258L	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	1258					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						GCTGCCTGTTGAGACAGTTCC	0.627									Pallister-Hall syndrome;Greig Cephalopolysyndactyly				G|||	69	0.013778	0.0484	0.0072	5008	,	,		16948	0.0		0.0	False		,,,				2504	0.0				p.L1258L		Atlas-SNP	.											.	GLI3	312	.	0			c.C3774G						PASS	.	G		195,4211	123.3+/-160.7	7,181,2015	62	65	64	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3774	-9.7	0	7	dbSNP_126	64	0,8600		0,0,4300	no	coding-synonymous	GLI3	NM_000168.5		7,181,6315	CC,CG,GG		0.0,4.4258,1.4993		1258/1581	42004897	195,12811	2203	4300	6503	SO:0001819	synonymous_variant	2737	exon15	Familial Cancer Database	;	CCTGTTGAGACAG		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.3774C>G	7.37:g.42004897G>C		100	0	0		88	41	0.465909	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Silent	SNP	ENST00000395925.3	37	CCDS5465.1																																																																																			G|0.984;C|0.016	0.016	strong		0.627	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		C	42004897	G	C	42004897	2	2	22	1	0	0	0	0	0	0	0	1	6447	1277	45	4		4	GLI3	7	42004897	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	7025971	42004897	117133766	1634	4535											
MRPL32	64983	hgsc.bcm.edu	37	chr7	42971998	42971998	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagggaaaatggcgctggccAtgctggtcttggtggtttcg	6	11	16	8	2	1	0	0	0	1	0	2	1	1	1	1	6	1	3	1	6	2	2	rs111980169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:42971998A>G	ENST00000223324.2	+	1	200	c.13A>G	c.(13-15)Atg>Gtg	p.M5V	PSMA2_ENST00000442788.1_5'Flank|PSMA2_ENST00000223321.4_5'Flank|PSMA2_ENST00000538645.1_5'Flank|PSMA2_ENST00000445517.1_5'Flank	NM_031903.2	NP_114109.1	Q9BYC8	RM32_HUMAN	mitochondrial ribosomal protein L32	5					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrial ribosome (GO:0005761)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)	10						GGCGCTGGCCATGCTGGTCTT	0.637													A|||	23	0.00459265	0.0174	0.0	5008	,	,		15207	0.0		0.0	False		,,,				2504	0.0				p.M5V		Atlas-SNP	.											.	MRPL32	25	.	0			c.A13G						PASS	.	A	VAL/MET	44,4362	46.7+/-81.2	0,44,2159	57	60	59		13	-11.6	0	7	dbSNP_132	59	0,8600		0,0,4300	yes	missense	MRPL32	NM_031903.2	21	0,44,6459	GG,GA,AA		0.0,0.9986,0.3383	benign	5/189	42971998	44,12962	2203	4300	6503	SO:0001583	missense	64983	exon1			CTGGCCATGCTGG	AB051343	CCDS5468.1	7p14	2012-09-13			ENSG00000106591	ENSG00000106591		"Mitochondrial ribosomal proteins / large subunits"	14035	protein-coding gene	gene with protein product		611839				11543634	Standard	NM_031903		Approved	HSPC283, L32mt, MRP-L32, bMRP-59b	uc003tia.3	Q9BYC8	OTTHUMG00000155180	ENST00000223324.2:c.13A>G	7.37:g.42971998A>G	ENSP00000223324:p.Met5Val	99	0	0		96	51	0.53125	NM_031903	Q96Q68|Q9P098	Missense_Mutation	SNP	ENST00000223324.2	37	CCDS5468.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	A	11.56	1.675863	0.29783	0.009986	0.0	ENSG00000106591	ENST00000223324	.	.	.	5.97	-11.6	0.00059	.	1.135090	0.06109	N	0.666822	T	0.09730	0.0239	L	0.42245	1.32	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28427	-1.0044	9	0.02654	T	1	-2.6256	2.0049	0.03475	0.1081:0.2514:0.2373:0.4032	.	5	Q9BYC8	RM32_HUMAN	V	5	.	ENSP00000223324:M5V	M	+	1	0	MRPL32	42938523	0.000000	0.05858	0.005000	0.12908	0.224000	0.24922	-1.230000	0.02942	-1.610000	0.01583	0.477000	0.44152	ATG	A|0.995;G|0.005	0.005	strong		0.637	MRPL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338669.1	NM_031903		G	42971998	A	G	42971998	3	3	22	1	0	0	0	0	1	0	0	0	9804	217	8	3	15	3	MRPL32	7	42971998	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	967101	42971998	116166665	1635	4536											
MRPS24	64951	hgsc.bcm.edu	37	chr7	43906544	43906544	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaaggaaaacatcctccacCgttcgctctgcggcatggtc	9	8	10	14	4	1	0	0	0	1	0	5	2	3	1	3	3	2	3	3	3	3	1	rs9154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:43906544C>T	ENST00000317534.5	-	4	319	c.258G>A	c.(256-258)acG>acA	p.T86T	URGCP-MRPS24_ENST00000603700.1_3'UTR|MRPS24_ENST00000467084.1_5'UTR	NM_032014.2	NP_114403.1	Q96EL2	RT24_HUMAN	mitochondrial ribosomal protein S24	86					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrial small ribosomal subunit (GO:0005763)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.T86T(1)		large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	5						CATCCTCCACCGTTCGCTCTG	0.557													C|||	248	0.0495208	0.1831	0.0058	5008	,	,		17550	0.0		0.002	False		,,,				2504	0.0				p.T86T		Atlas-SNP	.											MRPS24,colon,carcinoma,-1,2	MRPS24	9	2	1	Substitution - coding silent(1)	lung(1)	c.G258A						PASS	.	C	,	694,3712	291.0+/-281.2	51,592,1560	68	64	65		,258	-10.5	0.1	7	dbSNP_52	65	5,8595	4.3+/-15.6	0,5,4295	no	utr-3,coding-synonymous	MRPS24,URGCP-MRPS24	NM_001204871.1,NM_032014.2	,	51,597,5855	TT,TC,CC		0.0581,15.7512,5.3744	,	,86/168	43906544	699,12307	2203	4300	6503	SO:0001819	synonymous_variant	64951	exon4			CTCCACCGTTCGC	AB061207	CCDS5473.1	7p14	2012-09-13			ENSG00000062582	ENSG00000062582		"Mitochondrial ribosomal proteins / small subunits"	14510	protein-coding gene	gene with protein product		611986				8127713, 11279123	Standard	NM_032014		Approved	MRP-S24, HSPC335	uc003tit.1	Q96EL2	OTTHUMG00000023175	ENST00000317534.5:c.258G>A	7.37:g.43906544C>T		55	0	0		68	28	0.411765	NM_032014	A4D1U9|P82668|Q96Q23|Q9P047	Silent	SNP	ENST00000317534.5	37	CCDS5473.1																																																																																			C|0.953;T|0.047	0.047	strong		0.557	MRPS24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250949.1	NM_032014		T	43906544	C	T	43906544	2	4	22	1	0	0	0	0	0	0	0	1	9844	639	23	1		1	MRPS24	7	43906544	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	934546	43906544	115232119	1636	4537											
MRPS24	64951	hgsc.bcm.edu	37	chr7	43908661	43908661	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccccttgcttacgcgtactcGggccgcccggttctaggagc	4	9	12	16	5	1	0	0	0	1	0	2	1	1	1	4	3	4	3	4	3	3	5	rs17854882	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:43908661G>T	ENST00000317534.5	-	3	182	c.121C>A	c.(121-123)Cga>Aga	p.R41R	URGCP-MRPS24_ENST00000603700.1_Missense_Mutation_p.P86Q|MRPS24_ENST00000467084.1_5'UTR	NM_032014.2	NP_114403.1	Q96EL2	RT24_HUMAN	mitochondrial ribosomal protein S24	41					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrial small ribosomal subunit (GO:0005763)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	5						ACGCGTACTCGGGCCGCCCGG	0.647													G|||	150	0.0299521	0.112	0.0014	5008	,	,		10791	0.0		0.001	False		,,,				2504	0.0				p.P86Q		Atlas-SNP	.											.	.	.	.	0			c.C257A						PASS	.	G	GLN/PRO,	422,3984	205.8+/-227.6	21,380,1802	58	53	55		257,121	2.7	0.9	7	dbSNP_123	55	3,8597	3.0+/-9.4	0,3,4297	yes	missense,coding-synonymous	MRPS24,URGCP-MRPS24	NM_001204871.1,NM_032014.2	76,	21,383,6099	TT,TG,GG		0.0349,9.5778,3.2677	,	86/111,41/168	43908661	425,12581	2203	4300	6503	SO:0001819	synonymous_variant	0	exon6			GTACTCGGGCCGC	AB061207	CCDS5473.1	7p14	2012-09-13			ENSG00000062582	ENSG00000062582		"Mitochondrial ribosomal proteins / small subunits"	14510	protein-coding gene	gene with protein product		611986				8127713, 11279123	Standard	NM_032014		Approved	MRP-S24, HSPC335	uc003tit.1	Q96EL2	OTTHUMG00000023175	ENST00000317534.5:c.121C>A	7.37:g.43908661G>T		83	0	0		151	73	0.483444	NM_001204871	A4D1U9|P82668|Q96Q23|Q9P047	Missense_Mutation	SNP	ENST00000317534.5	37	CCDS5473.1																																																																																			G|0.971;T|0.029	0.029	strong		0.647	MRPS24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250949.1	NM_032014		T	43908661	G	T	43908661	2	4	22	1	0	0	0	0	0	0	0	1	9844	1124	39	4		4	MRPS24	7	43908661	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2117	43908661	115230002	1637	4538											
DBNL	28988	hgsc.bcm.edu	37	chr7	44096482	44096482	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagtggccgcttccaggacGtgggaccccaggccccagtg	7	5	15	14	2	0	1	0	0	0	1	1	3	1	3	6	4	0	1	6	4	0	1	rs61735009	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:44096482G>A	ENST00000448521.1	+	5	552	c.454G>A	c.(454-456)Gtg>Atg	p.V152M	DBNL_ENST00000497184.1_3'UTR|DBNL_ENST00000468694.1_Missense_Mutation_p.V152M|DBNL_ENST00000494774.1_Missense_Mutation_p.V152M|DBNL_ENST00000456905.1_Intron|DBNL_ENST00000490734.2_Missense_Mutation_p.V57M|DBNL_ENST00000440166.1_Missense_Mutation_p.V49M|DBNL_ENST00000452943.1_Missense_Mutation_p.V127M	NM_001014436.2	NP_001014436.1	Q9UJU6	DBNL_HUMAN	drebrin-like	152					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)	p.V152L(1)		breast(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|stomach(1)	12						CTTCCAGGACGTGGGACCCCA	0.617													G|||	73	0.0145767	0.0552	0.0	5008	,	,		19626	0.0		0.0	False		,,,				2504	0.0				p.V152M	NSCLC(68;573 1327 18604 34760 37992)	Atlas-SNP	.											.	DBNL	26	.	1	Substitution - Missense(1)	lung(1)	c.G454A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL	188,4218	120.8+/-158.4	4,180,2019	101	93	96		454,454,454	-6.3	0	7	dbSNP_129	96	0,8600		0,0,4300	yes	missense,missense,missense	DBNL	NM_001014436.2,NM_001122956.1,NM_014063.6	21,21,21	4,180,6319	AA,AG,GG		0.0,4.2669,1.4455	benign,benign,benign	152/431,152/440,152/432	44096482	188,12818	2203	4300	6503	SO:0001583	missense	28988	exon5			CAGGACGTGGGAC	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.454G>A	7.37:g.44096482G>A	ENSP00000411701:p.Val152Met	66	0	0		104	45	0.432692	NM_001122956	A4D2I9|B4DEM2|C9J7P1|P84070|Q6IAI8|Q96F30|Q96K74|Q9HBN8|Q9NR72	Missense_Mutation	SNP	ENST00000448521.1	37	CCDS34623.1	23|23	0.010531135531135532|0.010531135531135532	23|23	0.046747967479674794|0.046747967479674794	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	6.385|6.385	0.439110|0.439110	0.12104|0.12104	0.042669|0.042669	0.0|0.0	ENSG00000136279|ENSG00000136279	ENST00000432854|ENST00000448521;ENST00000440166;ENST00000452943;ENST00000468694;ENST00000494774;ENST00000490734;ENST00000539475	.|T;T;T;T;T;T	.|0.30714	.|1.91;2.23;2.23;1.52;1.91;2.22	4.9|4.9	-6.34|-6.34	0.01982|0.01982	.|.	.|1.052620	.|0.07283	.|N	.|0.871083	T|T	0.02230|0.02230	0.0069|0.0069	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	.|B;B;B;B;B;B;B;B	.|0.25772	.|0.021;0.021;0.02;0.134;0.082;0.119;0.005;0.012	.|B;B;B;B;B;B;B;B	.|0.15052	.|0.005;0.003;0.005;0.012;0.003;0.008;0.001;0.004	T|T	0.25502|0.25502	-1.0130|-1.0130	5|10	.|0.41790	.|T	.|0.15	0.0525|0.0525	8.2112|8.2112	0.31483|0.31483	0.2474:0.0:0.6024:0.1502|0.2474:0.0:0.6024:0.1502	rs61735009|rs61735009	.|49;100;82;57;127;152;152;152	.|B4DEM2;B4DXL9;B4DDU5;C9J7P1;B4DDD6;Q9UJU6-3;Q9UJU6;Q9UJU6-2	.|.;.;.;.;.;.;DBNL_HUMAN;.	H|M	80|152;49;127;152;152;57;82	.|ENSP00000411701:V152M;ENSP00000415173:V49M;ENSP00000405343:V127M;ENSP00000417653:V152M;ENSP00000419992:V152M;ENSP00000417749:V57M	.|ENSP00000415173:V49M	R|V	+|+	2|1	0|0	DBNL|DBNL	44063007|44063007	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.088000|0.088000	0.18126|0.18126	-0.206000|-0.206000	0.09398|0.09398	-0.667000|-0.667000	0.05303|0.05303	-0.696000|-0.696000	0.03686|0.03686	CGT|GTG	A|0.013;C|0.000;G|0.987	0.013	strong		0.617	DBNL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339572.2	NM_014063		A	44096482	G	A	44096482	3	1	22	1	0	0	0	0	1	0	0	0	4257	1145	40	1	472	1	DBNL	7	44096482	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	187821	44096482	115042181	1638	4539											
PGAM2	5224	hgsc.bcm.edu	37	chr7	44104805	44104805	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cagatcttcacctgctcctcCccgtgcttggcggccgtttc	3	12	9	17	3	2	1	1	0	1	1	5	1	4	1	5	2	2	3	5	2	0	3	rs112828964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:44104805C>T	ENST00000297283.3	-	1	381	c.324G>A	c.(322-324)ggG>ggA	p.G108G	AC017116.11_ENST00000445938.1_RNA	NM_000290.3	NP_000281.2	P15259	PGAM2_HUMAN	phosphoglycerate mutase 2 (muscle)	108					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|response to mercury ion (GO:0046689)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|striated muscle contraction (GO:0006941)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity (GO:0046538)|bisphosphoglycerate 2-phosphatase activity (GO:0004083)|bisphosphoglycerate mutase activity (GO:0004082)|cofactor binding (GO:0048037)|phosphoglycerate mutase activity (GO:0004619)			large_intestine(2)|lung(4)|ovary(1)|stomach(1)	8						CCTGCTCCTCCCCGTGCTTGG	0.632													C|||	159	0.0317492	0.1188	0.0029	5008	,	,		16305	0.0		0.0	False		,,,				2504	0.0				p.G108G		Atlas-SNP	.											.	PGAM2	20	.	0			c.G324A						PASS	.	C		422,3984	206.5+/-228.1	19,384,1800	62	61	62		324	-4.1	0.9	7	dbSNP_132	62	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	PGAM2	NM_000290.3		19,386,6098	TT,TC,CC		0.0233,9.5778,3.26		108/254	44104805	424,12582	2203	4300	6503	SO:0001819	synonymous_variant	5224	exon1			CTCCTCCCCGTGC		CCDS34624.1	7p13-p12	2008-11-17			ENSG00000164708	ENSG00000164708	5.4.2.1, 3.1.3.13, 5.4.2.4		8889	protein-coding gene	gene with protein product		612931					Standard	NM_000290		Approved	PGAM-M	uc003tjs.3	P15259	OTTHUMG00000155355	ENST00000297283.3:c.324G>A	7.37:g.44104805C>T		256	0	0		280	131	0.467857	NM_000290		Silent	SNP	ENST00000297283.3	37	CCDS34624.1																																																																																			C|0.968;T|0.032	0.032	strong		0.632	PGAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339614.1			T	44104805	C	T	44104805	2	4	22	1	0	0	0	0	0	0	0	1	11783	610	22	2		2	PGAM2	7	44104805	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	8323	44104805	115033858	1639	4540											
PGAM2	5224	hgsc.bcm.edu	37	chr7	44104913	44104913	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccacatctggtccgtgccGtccaggatggcccagagggt	7	7	14	13	2	1	1	0	0	1	1	3	2	3	2	5	4	2	0	5	4	0	0	rs111656877	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:44104913G>A	ENST00000297283.3	-	1	273	c.216C>T	c.(214-216)gaC>gaT	p.D72D	AC017116.11_ENST00000445938.1_RNA	NM_000290.3	NP_000281.2	P15259	PGAM2_HUMAN	phosphoglycerate mutase 2 (muscle)	72					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|response to mercury ion (GO:0046689)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|striated muscle contraction (GO:0006941)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity (GO:0046538)|bisphosphoglycerate 2-phosphatase activity (GO:0004083)|bisphosphoglycerate mutase activity (GO:0004082)|cofactor binding (GO:0048037)|phosphoglycerate mutase activity (GO:0004619)			large_intestine(2)|lung(4)|ovary(1)|stomach(1)	8						GGTCCGTGCCGTCCAGGATGG	0.627													G|||	52	0.0103834	0.0371	0.0029	5008	,	,		17290	0.0		0.0	False		,,,				2504	0.001				p.D72D		Atlas-SNP	.											.	PGAM2	20	.	0			c.C216T						PASS	.	G		218,4188	131.4+/-167.9	7,204,1992	93	78	83		216	-11.9	0	7	dbSNP_132	83	0,8600		0,0,4300	no	coding-synonymous	PGAM2	NM_000290.3		7,204,6292	AA,AG,GG		0.0,4.9478,1.6761		72/254	44104913	218,12788	2203	4300	6503	SO:0001819	synonymous_variant	5224	exon1			CGTGCCGTCCAGG		CCDS34624.1	7p13-p12	2008-11-17			ENSG00000164708	ENSG00000164708	5.4.2.1, 3.1.3.13, 5.4.2.4		8889	protein-coding gene	gene with protein product		612931					Standard	NM_000290		Approved	PGAM-M	uc003tjs.3	P15259	OTTHUMG00000155355	ENST00000297283.3:c.216C>T	7.37:g.44104913G>A		109	0	0		121	57	0.471074	NM_000290		Silent	SNP	ENST00000297283.3	37	CCDS34624.1																																																																																			G|0.984;A|0.016	0.016	strong		0.627	PGAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339614.1			A	44104913	G	A	44104913	2	1	22	1	0	0	0	0	0	0	0	1	11783	1136	40	1		1	PGAM2	7	44104913	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	108	44104913	115033750	1640	4541											
POLM	27434	hgsc.bcm.edu	37	chr7	44116207	44116207	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gtcagcagtcttcacaccgaCcccgaagatctgggtgaaga	11	7	11	12	2	4	3	2	1	2	2	4	5	4	3	3	1	1	1	3	1	2	1	rs28382653	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:44116207C>A	ENST00000242248.5	-	6	837	c.736G>T	c.(736-738)Gtc>Ttc	p.V246F	POLM_ENST00000395831.3_Intron|POLM_ENST00000335195.6_Missense_Mutation_p.V246F|POLM_ENST00000492971.1_5'UTR	NM_013284.2	NP_037416.1	Q9NP87	DPOLM_HUMAN	polymerase (DNA directed), mu	246			V -> F (in dbSNP:rs28382653). {ECO:0000269|Ref.3}.		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						TTCACACCGACCCCGAAGATC	0.607								DNA polymerases (catalytic subunits)					C|||	52	0.0103834	0.0378	0.0029	5008	,	,		19742	0.0		0.0	False		,,,				2504	0.0				p.V246F		Atlas-SNP	.											.	POLM	50	.	0			c.G736T						PASS	.	C	PHE/VAL	220,4186	132.5+/-169.0	7,206,1990	97	92	94		736	5.7	1	7	dbSNP_125	94	0,8600		0,0,4300	yes	missense	POLM	NM_013284.2	50	7,206,6290	AA,AC,CC		0.0,4.9932,1.6915	probably-damaging	246/495	44116207	220,12786	2203	4300	6503	SO:0001583	missense	27434	exon6			CACCGACCCCGAA	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.736G>T	7.37:g.44116207C>A	ENSP00000242248:p.Val246Phe	69	0	0		93	42	0.451613	NM_013284	D3DVK4|Q6P5X8|Q86WQ9	Missense_Mutation	SNP	ENST00000242248.5	37	CCDS34625.1	21	0.009615384615384616	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	0	0.0	C	18.48	3.633258	0.67015	0.049932	0.0	ENSG00000122678	ENST00000335195;ENST00000242248	T;T	0.59502	0.26;0.26	5.68	5.68	0.88126	DNA-directed DNA polymerase X (1);DNA polymerase lambda, fingers domain (2);	.	.	.	.	T	0.40272	0.1110	M	0.82056	2.57	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.994;1.0	T	0.68066	-0.5507	9	0.87932	D	0	.	15.2786	0.73764	0.0:1.0:0.0:0.0	rs28382653	246;246	Q6P5X8;Q9NP87	.;DPOLM_HUMAN	F	246	ENSP00000335141:V246F;ENSP00000242248:V246F	ENSP00000242248:V246F	V	-	1	0	POLM	44082732	0.998000	0.40836	0.995000	0.50966	0.809000	0.45718	4.994000	0.63901	2.672000	0.90937	0.650000	0.86243	GTC	C|0.983;A|0.017	0.017	strong		0.607	POLM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339594.1	NM_013284		A	44116207	C	A	44116207	3	1	22	1	0	0	0	0	1	0	0	0	12215	507	18	4	772	4	POLM	7	44116207	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	11294	44116207	115022456	1641	4542											
AEBP1	165	hgsc.bcm.edu	37	chr7	44146151	44146151	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcatcttggacagtgcctcCggaaaagaccaaagacaaag	15	6	10	10	1	1	2	0	0	1	2	2	4	2	4	3	2	2	1	3	2	4	1	rs75107445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:44146151C>T	ENST00000223357.3	+	2	565	c.260C>T	c.(259-261)cCg>cTg	p.P87L		NM_001129.3	NP_001120.3	Q8IUX7	AEBP1_HUMAN	AE binding protein 1	87	Pro-rich.				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						ACAGTGCCTCCGGAAAAGACC	0.587													C|||	9	0.00179712	0.0061	0.0	5008	,	,		15644	0.0		0.0	False		,,,				2504	0.001				p.P87L		Atlas-SNP	.											AEBP1,larynx,carcinoma,-1,1	AEBP1	102	1	0			c.C260T						PASS	.	C	LEU/PRO	23,4365	26.2+/-53.5	0,23,2171	36	45	42		260	1.9	0.1	7	dbSNP_131	42	0,8586		0,0,4293	yes	missense	AEBP1	NM_001129.3	98	0,23,6464	TT,TC,CC		0.0,0.5242,0.1773	benign	87/1159	44146151	23,12951	2194	4293	6487	SO:0001583	missense	165	exon2			TGCCTCCGGAAAA	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.260C>T	7.37:g.44146151C>T	ENSP00000223357:p.Pro87Leu	40	0	0		46	19	0.413043	NM_001129	Q14113|Q59ER7|Q6ZSC7|Q7KZ79	Missense_Mutation	SNP	ENST00000223357.3	37	CCDS5476.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	16.09	3.025082	0.54683	0.005242	0.0	ENSG00000106624	ENST00000223357;ENST00000449162	D	0.94828	-3.53	4.9	1.92	0.25849	.	0.598172	0.14954	N	0.288777	D	0.84853	0.5564	L	0.27053	0.805	0.34323	D	0.68679	B	0.14805	0.011	B	0.08055	0.003	T	0.81575	-0.0870	10	0.87932	D	0	-1.0442	6.299	0.21101	0.0:0.6427:0.0:0.3573	.	87	Q8IUX7	AEBP1_HUMAN	L	87;3	ENSP00000223357:P87L	ENSP00000223357:P87L	P	+	2	0	AEBP1	44112676	0.000000	0.05858	0.071000	0.20095	0.651000	0.38670	0.214000	0.17541	0.079000	0.16929	0.462000	0.41574	CCG	C|0.999;T|0.001	0.001	strong		0.587	AEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250993.2	NM_001129		T	44146151	C	T	44146151	3	4	22	1	0	0	0	0	1	0	0	0	349	652	23	1	266	1	AEBP1	7	44146151	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	29944	44146151	114992512	1642	4543											
ZMIZ2	83637	hgsc.bcm.edu	37	chr7	44804989	44804989	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagctggaagccagtgcccGtgaagcctgacatgcacatc	10	6	12	13	1	0	2	0	2	0	0	1	3	0	3	3	1	5	3	3	1	2	0	rs114574038	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:44804989G>A	ENST00000309315.4	+	16	2176	c.2053G>A	c.(2053-2055)Gtg>Atg	p.V685M	ZMIZ2_ENST00000441627.1_Missense_Mutation_p.V685M|ZMIZ2_ENST00000413916.1_Missense_Mutation_p.V627M|ZMIZ2_ENST00000265346.7_Missense_Mutation_p.V659M|ZMIZ2_ENST00000433667.1_Missense_Mutation_p.V653M	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2	685					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						GCCAGTGCCCGTGAAGCCTGA	0.637													G|||	47	0.00938498	0.0333	0.0043	5008	,	,		15398	0.0		0.0	False		,,,				2504	0.0				p.V685M	NSCLC(20;604 852 1948 16908 50522)	Atlas-SNP	.											.	ZMIZ2	82	.	0			c.G2053A						PASS	.	G	MET/VAL,MET/VAL	122,4158		1,120,2019	37	40	39		2053,1975	3.2	0.9	7	dbSNP_132	39	2,8500		0,2,4249	yes	missense,missense	ZMIZ2	NM_031449.3,NM_174929.2	21,21	1,122,6268	AA,AG,GG		0.0235,2.8505,0.9701	possibly-damaging,possibly-damaging	685/921,659/895	44804989	124,12658	2140	4251	6391	SO:0001583	missense	83637	exon16			GTGCCCGTGAAGC	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.2053G>A	7.37:g.44804989G>A	ENSP00000311778:p.Val685Met	68	0	0		77	34	0.441558	NM_031449	A4D2K7|D3DVL1|O94790|Q0VGB4|Q659A8|Q6JKL5|Q8WTX8|Q96Q01|Q9BQH7	Missense_Mutation	SNP	ENST00000309315.4	37	CCDS43576.1	20	0.009157509157509158	16	0.032520325203252036	2	0.0055248618784530384	2	0.0034965034965034965	0	0.0	G	19.81	3.896626	0.72639	0.028505	2.35E-4	ENSG00000122515	ENST00000413916;ENST00000309315;ENST00000441627;ENST00000433667;ENST00000265346;ENST00000414051	T;T;T;T;T	0.32753	1.44;1.45;1.45;1.45;1.44	5.14	3.18	0.36537	.	0.277121	0.24642	N	0.036798	T	0.19446	0.0467	M	0.73598	2.24	0.52501	D	0.999953	P;P;P	0.50156	0.932;0.888;0.932	P;P;P	0.54100	0.656;0.557;0.742	T	0.06463	-1.0825	10	0.45353	T	0.12	-7.8333	7.1482	0.25595	0.284:0.0:0.716:0.0	.	659;685;627	Q8NF64-2;Q8NF64;Q8NF64-3	.;ZMIZ2_HUMAN;.	M	627;685;685;653;659;688	ENSP00000409648:V627M;ENSP00000311778:V685M;ENSP00000414723:V685M;ENSP00000396601:V653M;ENSP00000265346:V659M	ENSP00000265346:V659M	V	+	1	0	ZMIZ2	44771514	0.800000	0.28916	0.881000	0.34555	0.984000	0.73092	1.202000	0.32271	1.398000	0.46701	0.561000	0.74099	GTG	G|0.990;A|0.010	0.010	strong		0.637	ZMIZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341790.1	NM_031449		A	44804989	G	A	44804989	3	1	22	1	0	0	0	0	1	0	0	0	17712	1145	40	1	2111	1	ZMIZ2	7	44804989	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	658838	44804989	114333674	1643	4544											
TNS3	64759	hgsc.bcm.edu	37	chr7	47343079	47343079	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagtccttcctggtaccggAgaactcagcgctgaggggac	8	7	15	11	2	1	2	1	1	0	1	3	5	3	4	3	5	3	2	3	5	2	2	rs61731305	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:47343079A>G	ENST00000398879.1	-	22	3292	c.2926T>C	c.(2926-2928)Tcc>Ccc	p.S976P	TNS3_ENST00000355730.3_Missense_Mutation_p.S736P|TNS3_ENST00000311160.9_Missense_Mutation_p.S976P			Q68CZ2	TENS3_HUMAN	tensin 3	976					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						CTGGTACCGGAGAACTCAGCG	0.652													A|||	50	0.00998403	0.0371	0.0014	5008	,	,		16308	0.0		0.0	False		,,,				2504	0.0				p.S976P		Atlas-SNP	.											.	TNS3	140	.	0			c.T2926C						PASS	.	A	PRO/SER	110,3944		1,108,1918	24	30	28		2926	-4.5	0	7	dbSNP_129	28	1,8365		0,1,4182	yes	missense	TNS3	NM_022748.11	74	1,109,6100	GG,GA,AA		0.012,2.7134,0.8937	benign	976/1446	47343079	111,12309	2027	4183	6210	SO:0001583	missense	64759	exon22			TACCGGAGAACTC	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.2926T>C	7.37:g.47343079A>G	ENSP00000381854:p.Ser976Pro	73	0	0		94	55	0.585106	NM_022748	B2RNV1|Q6IPQ2|Q8IZW7|Q8NAD0|Q96PE0|Q96S48	Missense_Mutation	SNP	ENST00000398879.1	37	CCDS5506.2	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	A	7.817	0.717014	0.15372	0.027134	1.2E-4	ENSG00000136205	ENST00000311160;ENST00000538633;ENST00000398879;ENST00000355730;ENST00000545849;ENST00000457718	D;D;D;D	0.94828	-3.07;-3.07;-3.53;-3.23	5.34	-4.47	0.03525	.	1.008340	0.07998	N	0.988200	T	0.56891	0.2016	N	0.08118	0	0.24069	N	0.995984	B	0.02656	0.0	B	0.04013	0.001	T	0.65516	-0.6149	10	0.25751	T	0.34	-5.9377	1.8322	0.03132	0.4155:0.1339:0.3198:0.1308	.	976	Q68CZ2	TENS3_HUMAN	P	976;1086;976;736;432;1079	ENSP00000312143:S976P;ENSP00000381854:S976P;ENSP00000347968:S736P;ENSP00000414358:S1079P	ENSP00000312143:S976P	S	-	1	0	TNS3	47309604	0.942000	0.31987	0.002000	0.10522	0.058000	0.15608	0.267000	0.18552	-0.660000	0.05352	0.528000	0.53228	TCC	A|0.989;G|0.011	0.011	strong		0.652	TNS3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157253.1	NM_022748		G	47343079	A	G	47343079	3	3	22	1	0	0	0	0	1	0	0	0	16359	304	11	3	1451	3	TNS3	7	47343079	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2538090	47343079	111795584	1644	4545											
C7orf65	401335	hgsc.bcm.edu	37	chr7	47698737	47698737	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctatacataaatggtttcActgacccctggaaggatgct	11	12	9	9	0	1	1	1	1	0	0	1	3	1	3	2	3	3	3	2	3	5	4	rs114109572	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:47698737A>C	ENST00000408988.2	+	3	402	c.367A>C	c.(367-369)Act>Cct	p.T123P		NM_001123065.1	NP_001116537.1	Q6ZTY9	CG065_HUMAN	chromosome 7 open reading frame 65	123										endometrium(1)|lung(2)	3						AAATGGTTTCACTGACCCCTG	0.537													A|||	8	0.00159744	0.0061	0.0	5008	,	,		19526	0.0		0.0	False		,,,				2504	0.0				p.T123P		Atlas-SNP	.											.	C7orf65	18	.	0			c.A367C						PASS	.	A	PRO/THR	16,3120		0,16,1552	126	114	118		367	0.6	0	7	dbSNP_132	118	0,7164		0,0,3582	yes	missense	C7orf65	NM_001123065.1	38	0,16,5134	CC,CA,AA		0.0,0.5102,0.1553	probably-damaging	123/152	47698737	16,10284	1568	3582	5150	SO:0001583	missense	401335	exon3			GGTTTCACTGACC		CCDS43580.1	7p12.3	2009-02-11			ENSG00000221845	ENSG00000221845			34432	protein-coding gene	gene with protein product							Standard	NM_001123065		Approved	FLJ44108	uc010kyp.1	Q6ZTY9	OTTHUMG00000155550	ENST00000408988.2:c.367A>C	7.37:g.47698737A>C	ENSP00000386198:p.Thr123Pro	100	0	0		83	35	0.421687	NM_001123065	A4D2F8	Missense_Mutation	SNP	ENST00000408988.2	37	CCDS43580.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	A	6.306	0.424633	0.11928	0.005102	0.0	ENSG00000221845	ENST00000408988	.	.	.	0.559	0.559	0.17272	.	.	.	.	.	T	0.26011	0.0634	N	0.08118	0	0.09310	N	1	D	0.69078	0.997	D	0.68483	0.958	T	0.16928	-1.0386	7	0.87932	D	0	.	.	.	.	.	123	Q6ZTY9	CG065_HUMAN	P	123	.	ENSP00000386198:T123P	T	+	1	0	C7orf65	47665262	0.000000	0.05858	0.008000	0.14137	0.008000	0.06430	0.017000	0.13399	0.469000	0.27268	0.459000	0.35465	ACT	A|0.999;C|0.001	0.001	strong		0.537	C7orf65-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340616.1	NM_001123065		C	47698737	A	C	47698737	3	2	22	1	0	0	0	0	1	0	0	0	2413	159	6	5	377	5	C7orf65	7	47698737	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	355658	47698737	111439926	1645	4546											
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47924233	47924233	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatggtattgcttcttgaatGtcactgtaataggcttcaaa	11	15	9	6	0	3	1	2	1	1	0	3	2	3	1	0	2	1	4	0	2	5	7	rs79566365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:47924233G>A	ENST00000289672.2	-	19	3278	c.3228C>T	c.(3226-3228)gaC>gaT	p.D1076D		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1076	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						CTTCTTGAATGTCACTGTAAT	0.448													A|||	194	0.038738	0.1377	0.0101	5008	,	,		20921	0.0		0.004	False		,,,				2504	0.001				p.D1076D		Atlas-SNP	.											.	PKD1L1	328	.	0			c.C3228T						PASS	.	A		641,3765	767.0+/-413.5	47,547,1609	147	131	136		3228	-4.3	0	7	dbSNP_132	136	85,8515	815.6+/-407.0	1,83,4216	no	coding-synonymous	PKD1L1	NM_138295.3		48,630,5825	AA,AG,GG		0.9884,14.5483,5.582		1076/2850	47924233	726,12280	2203	4300	6503	SO:0001819	synonymous_variant	168507	exon19			TTGAATGTCACTG	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.3228C>T	7.37:g.47924233G>A		87	0	0		92	36	0.391304	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																			G|0.951;A|0.049	0.049	strong		0.448	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		A	47924233	G	A	47924233	2	1	22	1	0	0	0	0	0	0	0	1	11973	1368	48	2		2	PKD1L1	7	47924233	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	225496	47924233	111214430	1646	4547											
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47925485	47925485	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttccccttggagctgaagTggcaggttggccaagggtca	7	9	16	9	0	1	1	1	1	0	0	2	2	2	2	3	6	1	4	3	6	2	3	rs113527998	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:47925485T>G	ENST00000289672.2	-	18	3054	c.3004A>C	c.(3004-3006)Act>Cct	p.T1002P		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1002	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						GGAGCTGAAGTGGCAGGTTGG	0.607													G|||	199	0.0397364	0.1407	0.0101	5008	,	,		16333	0.0		0.005	False		,,,				2504	0.001				p.T1002P		Atlas-SNP	.											.	PKD1L1	328	.	0			c.A3004C						PASS	.	G	PRO/THR	657,3749	765.5+/-413.4	51,555,1597	86	87	86		3004	0.5	0	7	dbSNP_132	86	85,8515	815.6+/-407.0	1,83,4216	yes	missense	PKD1L1	NM_138295.3	38	52,638,5813	GG,GT,TT		0.9884,14.9115,5.7051	benign	1002/2850	47925485	742,12264	2203	4300	6503	SO:0001583	missense	168507	exon18			CTGAAGTGGCAGG	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.3004A>C	7.37:g.47925485T>G	ENSP00000289672:p.Thr1002Pro	185	0	0		198	81	0.409091	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	88	0.040293040293040296	81	0.16463414634146342	4	0.011049723756906077	0	0.0	3	0.00395778364116095	G	8.197	0.797394	0.16327	0.149115	0.009884	ENSG00000158683	ENST00000289672	T	0.20332	2.08	4.97	0.5	0.16919	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	2744.040000	0.00166	N	0.000000	T	0.00039	0.0001	N	0.00707	-1.245	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.25779	-1.0122	9	0.29301	T	0.29	0.945	0.5519	0.00664	0.2174:0.1517:0.32:0.3108	.	1002	Q8TDX9	PK1L1_HUMAN	P	1002	ENSP00000289672:T1002P	ENSP00000289672:T1002P	T	-	1	0	PKD1L1	47892010	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.139000	0.16036	-0.344000	0.08338	-0.132000	0.14878	ACT	T|0.950;G|0.050	0.050	strong		0.607	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		G	47925485	T	G	47925485	3	3	22	1	0	0	0	0	1	0	0	0	11973	1696	59	5	5705	5	PKD1L1	7	47925485	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1252	47925485	111213178	1647	4548											
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47925609	47925609	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gatgactctgaaatggcaccGagtcccagcgagccaagcag	12	5	12	12	2	1	2	0	2	1	0	2	5	2	2	3	1	3	2	3	1	2	0	rs78480673	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:47925609G>A	ENST00000289672.2	-	18	2930	c.2880C>T	c.(2878-2880)ctC>ctT	p.L960L		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	960	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						AAATGGCACCGAGTCCCAGCG	0.488													g|||	194	0.038738	0.1377	0.0101	5008	,	,		17976	0.0		0.004	False		,,,				2504	0.001				p.L960L		Atlas-SNP	.											PKD1L1,NS,carcinoma,0,2	PKD1L1	328	2	0			c.C2880T						PASS	.	A		638,3768	272.8+/-271.0	47,544,1612	60	56	58		2880	-9.9	0	7	dbSNP_132	58	85,8515	48.1+/-107.5	1,83,4216	no	coding-synonymous	PKD1L1	NM_138295.3		48,627,5828	AA,AG,GG		0.9884,14.4803,5.559		960/2850	47925609	723,12283	2203	4300	6503	SO:0001819	synonymous_variant	168507	exon18			GGCACCGAGTCCC	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.2880C>T	7.37:g.47925609G>A		115	0	0		128	65	0.507812	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																			G|0.951;A|0.049	0.049	strong		0.488	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		A	47925609	G	A	47925609	2	1	22	1	0	0	0	0	0	0	0	1	11973	1045	37	1		1	PKD1L1	7	47925609	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	124	47925609	111213054	1648	4549											
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47927650	47927650	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccaggaataagacagattcGgtatttcactgcagtcctca	12	10	8	11	1	2	2	2	0	0	2	4	3	3	3	2	2	1	2	2	2	3	4	rs79105203	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:47927650G>A	ENST00000289672.2	-	17	2824	c.2774C>T	c.(2773-2775)cCg>cTg	p.P925L		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	925	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						AGACAGATTCGGTATTTCACT	0.398													G|||	230	0.0459265	0.1641	0.0115	5008	,	,		21650	0.0		0.004	False		,,,				2504	0.001				p.P925L		Atlas-SNP	.											PKD1L1,colon,carcinoma,0,1	PKD1L1	328	1	0			c.C2774T						scavenged	.	G	LEU/PRO	738,3668	302.1+/-287.2	68,602,1533	123	115	118		2774	-4.2	0	7	dbSNP_132	118	85,8515	48.1+/-107.5	1,83,4216	yes	missense	PKD1L1	NM_138295.3	98	69,685,5749	AA,AG,GG		0.9884,16.7499,6.3278	benign	925/2850	47927650	823,12183	2203	4300	6503	SO:0001583	missense	168507	exon17			AGATTCGGTATTT	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.2774C>T	7.37:g.47927650G>A	ENSP00000289672:p.Pro925Leu	125	1	0.008		98	54	0.55102	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	100	0.045787545787545784	92	0.18699186991869918	5	0.013812154696132596	0	0.0	3	0.00395778364116095	G	7.863	0.726477	0.15439	0.167499	0.009884	ENSG00000158683	ENST00000289672	T	0.69306	-0.39	5.65	-4.17	0.03857	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	1.960750	0.02041	N	0.049260	T	0.00109	0.0003	L	0.27053	0.805	0.80722	P	0.0	B	0.17268	0.021	B	0.10450	0.005	T	0.04635	-1.0937	9	0.37606	T	0.19	0.0986	5.9318	0.19142	0.1912:0.0:0.3612:0.4476	.	925	Q8TDX9	PK1L1_HUMAN	L	925	ENSP00000289672:P925L	ENSP00000289672:P925L	P	-	2	0	PKD1L1	47894175	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.980000	0.01492	-0.571000	0.06014	-0.978000	0.02582	CCG	G|0.945;A|0.055	0.055	strong		0.398	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		A	47927650	G	A	47927650	3	1	22	1	0	0	0	0	1	0	0	0	11973	1116	39	1	5939	1	PKD1L1	7	47927650	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2041	47927650	111211013	1649	4550											
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47933494	47933494	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cctgagagtcgccccagggtCgtcagggtcgaaggactggg	7	6	17	11	3	1	1	1	1	0	1	4	4	1	2	3	4	0	0	3	4	1	0	rs17131915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:47933494C>T	ENST00000289672.2	-	15	2484	c.2434G>A	c.(2434-2436)Gac>Aac	p.D812N		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	812	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.		D -> N (in dbSNP:rs17131915).		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						GCCCCAGGGTCGTCAGGGTCG	0.612													T|||	104	0.0207668	0.0741	0.0014	5008	,	,		17811	0.005		0.0	False		,,,				2504	0.0				p.D812N		Atlas-SNP	.											.	PKD1L1	328	.	0			c.G2434A						PASS	.	T	ASN/ASP	237,4169		5,227,1971	47	36	40		2434	-8.5	0	7	dbSNP_123	40	0,8600		0,0,4300	yes	missense	PKD1L1	NM_138295.3	23	5,227,6271	TT,TC,CC		0.0,5.379,1.8222	benign	812/2850	47933494	237,12769	2203	4300	6503	SO:0001583	missense	168507	exon15			CAGGGTCGTCAGG	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.2434G>A	7.37:g.47933494C>T	ENSP00000289672:p.Asp812Asn	46	0	0		37	16	0.432432	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	46	0.021062271062271064	41	0.08333333333333333	1	0.0027624309392265192	4	0.006993006993006993	0	0.0	N	8.513	0.867001	0.17250	0.05379	0.0	ENSG00000158683	ENST00000289672	T	0.69306	-0.39	5.12	-8.54	0.00912	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	1.892900	0.03306	N	0.189835	T	0.01254	0.0041	N	0.00707	-1.245	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.09143	-1.0688	10	0.26408	T	0.33	-0.013	0.2929	0.00261	0.2928:0.2218:0.2594:0.226	rs17131915;rs52800675;rs17131915	812	Q8TDX9	PK1L1_HUMAN	N	812	ENSP00000289672:D812N	ENSP00000289672:D812N	D	-	1	0	PKD1L1	47900019	0.000000	0.05858	0.002000	0.10522	0.571000	0.35966	-3.364000	0.00496	-1.993000	0.00974	-0.389000	0.06534	GAC	C|0.974;T|0.026	0.026	strong		0.612	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		T	47933494	C	T	47933494	3	4	22	1	0	0	0	0	1	0	0	0	11973	884	31	1	6287	1	PKD1L1	7	47933494	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	5844	47933494	111205169	1650	4551											
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47955167	47955167	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttgtaggtggacatatccaActgaaaatgtaaaagatgaa	17	11	9	4	0	0	3	0	2	0	1	1	4	1	4	1	2	1	2	1	2	8	4	rs17131941	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:47955167A>G	ENST00000289672.2	-	8	1140	c.1090T>C	c.(1090-1092)Ttg>Ctg	p.L364L		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	364					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						GACATAtccaactgaaaatgt	0.323													A|||	90	0.0179712	0.0658	0.0043	5008	,	,		16011	0.0		0.0	False		,,,				2504	0.0				p.L364L		Atlas-SNP	.											.	PKD1L1	328	.	0			c.T1090C						PASS	.	A		173,4233	113.3+/-151.4	3,167,2033	78	76	77		1090	0.4	0	7	dbSNP_123	77	0,8600		0,0,4300	no	coding-synonymous	PKD1L1	NM_138295.3		3,167,6333	GG,GA,AA		0.0,3.9265,1.3302		364/2850	47955167	173,12833	2203	4300	6503	SO:0001819	synonymous_variant	168507	exon8			TATCCAACTGAAA	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.1090T>C	7.37:g.47955167A>G		46	0	0		43	24	0.55814	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																			A|0.981;G|0.019	0.019	strong		0.323	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		G	47955167	A	G	47955167	2	3	22	1	0	0	0	0	0	0	0	1	11973	40	2	3		3	PKD1L1	7	47955167	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	21673	47955167	111183496	1651	4552											
HUS1	3364	hgsc.bcm.edu	37	chr7	48008869	48008869	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttgtaacacatactaattcaGtttctattttcaaattcaat	14	18	2	7	0	4	0	3	0	1	0	4	0	4	0	0	0	2	2	0	0	6	10	rs138848570	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:48008869G>C	ENST00000258774.5	-	6	610	c.587C>G	c.(586-588)aCt>aGt	p.T196S	HUS1_ENST00000432325.1_Missense_Mutation_p.T175S	NM_004507.3	NP_004498.1	O60921	HUS1_HUMAN	HUS1 checkpoint homolog (S. pombe)	196					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)|double-strand break repair via homologous recombination (GO:0000724)|embryo development (GO:0009790)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of DNA replication (GO:0008156)|protein phosphorylation (GO:0006468)|regulation of protein phosphorylation (GO:0001932)|response to UV (GO:0009411)	checkpoint clamp complex (GO:0030896)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(3)|ovary(2)|prostate(1)	13		Breast(660;0.00139)				TACTAATTCAGTTTCTATTTT	0.294								Direct reversal of damage;Other conserved DNA damage response genes			OREG0018063	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	21	0.00419329	0.0159	0.0	5008	,	,		20315	0.0		0.0	False		,,,				2504	0.0				p.T196S	Ovarian(103;466 1517 21788 34610 43890)	Atlas-SNP	.											.	HUS1	36	.	0			c.C587G						PASS	.	G	SER/THR	20,4378	28.1+/-56.4	1,18,2180	95	99	98		587	5.2	1	7	dbSNP_134	98	0,8600		0,0,4300	yes	missense	HUS1	NM_004507.3	58	1,18,6480	CC,CG,GG		0.0,0.4548,0.1539	benign	196/281	48008869	20,12978	2199	4300	6499	SO:0001583	missense	3364	exon6			AATTCAGTTTCTA	Y16893	CCDS34635.1	7p13-p12	2008-08-08	2001-11-28		ENSG00000136273	ENSG00000136273			5309	protein-coding gene	gene with protein product	"hus1+-like protein"	603760	"HUS1 (S. pombe) checkpoint homolog"			9878245, 9524127	Standard	NM_004507		Approved		uc003tod.2	O60921	OTTHUMG00000155645	ENST00000258774.5:c.587C>G	7.37:g.48008869G>C	ENSP00000258774:p.Thr196Ser	51	0	0	951	53	21	0.396226	NM_004507	B4DFI9	Missense_Mutation	SNP	ENST00000258774.5	37	CCDS34635.1	23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	G	16.67	3.187502	0.57909	0.004548	0.0	ENSG00000136273	ENST00000258774;ENST00000432325;ENST00000432627	T;T;T	0.13196	2.61;2.61;2.61	5.19	5.19	0.71726	.	0.052227	0.85682	N	0.000000	T	0.02888	0.0086	L	0.46567	1.45	0.54753	D	0.999987	B	0.30033	0.266	B	0.40228	0.323	T	0.07829	-1.0752	10	0.22109	T	0.4	-12.6777	16.5638	0.84573	0.0:0.0:1.0:0.0	.	196	O60921	HUS1_HUMAN	S	196;175;175	ENSP00000258774:T196S;ENSP00000416588:T175S;ENSP00000404855:T175S	ENSP00000258774:T196S	T	-	2	0	HUS1	47975394	1.000000	0.71417	0.951000	0.38953	0.999000	0.98932	7.975000	0.88055	2.563000	0.86464	0.655000	0.94253	ACT	G|0.996;C|0.004	0.004	strong		0.294	HUS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340952.1	NM_004507		C	48008869	G	C	48008869	3	2	22	1	0	0	0	0	1	0	0	0	7468	1029	36	4	267	4	HUS1	7	48008869	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	53702	48008869	111129794	1652	4553											
ABCA13	154664	hgsc.bcm.edu	37	chr7	48452147	48452147	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgcatcagctgcacctgacGggctatgggatctcagacac	9	8	11	13	1	2	2	2	1	1	1	3	3	2	3	1	2	3	4	1	2	1	1	rs369363967	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:48452147G>A	ENST00000435803.1	+	41	12450	c.12426G>A	c.(12424-12426)acG>acA	p.T4142T		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4142					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						TGCACCTGACGGGCTATGGGA	0.478													G|||	4	0.000798722	0.0023	0.0014	5008	,	,		17632	0.0		0.0	False		,,,				2504	0.0				p.T4142T		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G12426A						PASS	.	G		24,3846		0,24,1911	80	75	77		12426	-9.9	0	7		77	0,8308		0,0,4154	no	coding-synonymous	ABCA13	NM_152701.3		0,24,6065	AA,AG,GG		0.0,0.6202,0.1971		4142/5059	48452147	24,12154	1935	4154	6089	SO:0001819	synonymous_variant	154664	exon41			CCTGACGGGCTAT	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.12426G>A	7.37:g.48452147G>A		121	0	0		152	85	0.559211	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1																																																																																			.	.	weak		0.478	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48452147	G	A	48452147	2	1	22	1	0	0	0	0	0	0	0	1	31	1103	39	1		1	ABCA13	7	48452147	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	443278	48452147	110686516	1653	4554											
GRB10	2887	hgsc.bcm.edu	37	chr7	50672017	50672017	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccctgtttacctgtacttaGggtagaagggtggaggggac	8	10	16	7	0	0	1	0	0	0	1	0	3	0	3	2	5	2	3	2	5	5	5	rs200886440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:50672017G>A	ENST00000401949.1	-	16	1916	c.1447C>T	c.(1447-1449)Cta>Tta	p.L483L	GRB10_ENST00000402578.1_Silent_p.L425L|GRB10_ENST00000335866.3_Silent_p.L425L|GRB10_ENST00000439599.1_Silent_p.L477L|GRB10_ENST00000402497.1_Silent_p.L425L|GRB10_ENST00000406641.1_Silent_p.L425L|GRB10_ENST00000403097.1_Silent_p.L477L|GRB10_ENST00000357271.5_Silent_p.L437L|GRB10_ENST00000398812.2_Silent_p.L483L|GRB10_ENST00000407526.1_Silent_p.L425L|GRB10_ENST00000398810.2_Silent_p.L425L			Q13322	GRB10_HUMAN	growth factor receptor-bound protein 10	483					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)					CCTGTACTTAGGGTAGAAGGG	0.493									Russell-Silver syndrome				G|||	3	0.000599042	0.0023	0.0	5008	,	,		21445	0.0		0.0	False		,,,				2504	0.0				p.L483L		Atlas-SNP	.											.	GRB10	155	.	0			c.C1447T						PASS	.	G	,,,	2,4002		0,2,2000	140	141	141		1309,1273,1273,1447	1.1	0.3	7		141	0,8338		0,0,4169	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GRB10	NM_001001549.2,NM_001001550.2,NM_001001555.2,NM_005311.4	,,,	0,2,6169	AA,AG,GG		0.0,0.05,0.0162	,,,	437/549,425/537,425/537,483/595	50672017	2,12340	2002	4169	6171	SO:0001819	synonymous_variant	2887	exon13	Familial Cancer Database	Silver-Russell Dwarfism, Silver-Russell syndrome, SRS, Russel-Silver Dwarfism	TACTTAGGGTAGA		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.1447C>T	7.37:g.50672017G>A		115	0	0		133	63	0.473684	NM_005311	A4D258|A7VJ95|A8K0E6|D3DVM9|O00427|O00701|O75222|Q92606|Q92907|Q92948	Silent	SNP	ENST00000401949.1	37	CCDS43582.1																																																																																			G|0.999;A|0.001	0.001	strong		0.493	GRB10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319157.1			A	50672017	G	A	50672017	2	1	22	1	0	0	0	0	0	0	0	1	6765	991	35	2		2	GRB10	7	50672017	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2219870	50672017	108466646	1654	4555											
GRB10	2887	hgsc.bcm.edu	37	chr7	50742326	50742326	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagggatgcattcatatcgtTcaccagggcttccaggtcca	9	10	10	12	1	2	0	2	0	0	0	5	1	4	1	3	3	1	3	3	3	1	4	rs185094083	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:50742326T>C	ENST00000401949.1	-	6	638	c.169A>G	c.(169-171)Aac>Gac	p.N57D	GRB10_ENST00000402578.1_5'UTR|GRB10_ENST00000335866.3_5'UTR|GRB10_ENST00000439599.1_Missense_Mutation_p.N51D|GRB10_ENST00000402497.1_5'UTR|GRB10_ENST00000406641.1_5'UTR|GRB10_ENST00000403097.1_Missense_Mutation_p.N51D|GRB10_ENST00000357271.5_Missense_Mutation_p.N57D|GRB10_ENST00000398812.2_Missense_Mutation_p.N57D|GRB10_ENST00000407526.1_5'UTR|GRB10_ENST00000398810.2_5'UTR			Q13322	GRB10_HUMAN	growth factor receptor-bound protein 10	57					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)					TTCATATCGTTCACCAGGGCT	0.522									Russell-Silver syndrome				T|||	14	0.00279553	0.0106	0.0	5008	,	,		21544	0.0		0.0	False		,,,				2504	0.0				p.N57D		Atlas-SNP	.											.	GRB10	155	.	0			c.A169G						PASS	.	T	ASP/ASN,,,ASP/ASN	21,4061		0,21,2020	57	59	59		169,,,169	4.5	1	7		59	1,8411		0,1,4205	yes	missense,utr-5,utr-5,missense	GRB10	NM_001001549.2,NM_001001550.2,NM_001001555.2,NM_005311.4	23,,,23	0,22,6225	CC,CT,TT		0.0119,0.5145,0.1761	probably-damaging,,,probably-damaging	57/549,,,57/595	50742326	22,12472	2041	4206	6247	SO:0001583	missense	2887	exon3	Familial Cancer Database	Silver-Russell Dwarfism, Silver-Russell syndrome, SRS, Russel-Silver Dwarfism	TATCGTTCACCAG		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.169A>G	7.37:g.50742326T>C	ENSP00000385770:p.Asn57Asp	66	0	0		67	26	0.38806	NM_005311	A4D258|A7VJ95|A8K0E6|D3DVM9|O00427|O00701|O75222|Q92606|Q92907|Q92948	Missense_Mutation	SNP	ENST00000401949.1	37	CCDS43582.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	T	25.0	4.597321	0.87055	0.005145	1.19E-4	ENSG00000106070	ENST00000398812;ENST00000439599;ENST00000403097;ENST00000357271;ENST00000401949;ENST00000439044	D;D;D;D;D;T	0.87571	-1.97;-1.97;-1.97;-2.27;-1.97;-1.14	5.67	4.53	0.55603	.	0.083534	0.85682	N	0.000000	T	0.78194	0.4245	L	0.55481	1.735	0.80722	D	1	B;B;B	0.28933	0.228;0.027;0.074	B;B;B	0.24006	0.05;0.024;0.025	T	0.76653	-0.2880	10	0.37606	T	0.19	-25.4018	11.6266	0.51149	0.0:0.0693:0.0:0.9307	.	51;57;57	Q13322-4;Q13322-2;Q13322	.;.;GRB10_HUMAN	D	57;51;51;57;57;51	ENSP00000381793:N57D;ENSP00000406716:N51D;ENSP00000385544:N51D;ENSP00000349818:N57D;ENSP00000385770:N57D;ENSP00000413023:N51D	ENSP00000349818:N57D	N	-	1	0	GRB10	50709820	1.000000	0.71417	0.990000	0.47175	0.689000	0.40095	5.866000	0.69590	1.097000	0.41459	0.533000	0.62120	AAC	T|0.999;C|0.001	0.001	strong		0.522	GRB10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319157.1			C	50742326	T	C	50742326	3	2	22	1	0	0	0	0	1	0	0	0	6765	1783	62	3	1671	3	GRB10	7	50742326	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	70309	50742326	108396337	1655	4556											
COBL	23242	hgsc.bcm.edu	37	chr7	51096992	51096992	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gacgtcatgggaagcggggtGcagggcaggtacttcctccc	7	7	16	11	2	1	0	1	0	0	0	3	2	3	1	2	5	3	3	2	5	2	2	rs61737866	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:51096992G>A	ENST00000265136.7	-	10	1966	c.1801C>T	c.(1801-1803)Cac>Tac	p.H601Y	COBL_ENST00000395542.2_Missense_Mutation_p.H683Y	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	601				H -> Y (in Ref. 5; AAH45771). {ECO:0000305}.	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)					GAAGCGGGGTGCAGGGCAGGT	0.562													G|||	130	0.0259585	0.0976	0.0	5008	,	,		20023	0.0		0.001	False		,,,				2504	0.0				p.H601Y	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											.	COBL	167	.	0			c.C1801T						PASS	.	G	TYR/HIS	393,4013	196.4+/-220.7	22,349,1832	79	70	73		1801	-7	0	7	dbSNP_129	73	4,8596	3.0+/-9.4	0,4,4296	yes	missense	COBL	NM_015198.3	83	22,353,6128	AA,AG,GG		0.0465,8.9197,3.0524	benign	601/1262	51096992	397,12609	2203	4300	6503	SO:0001583	missense	23242	exon10			CGGGGTGCAGGGC	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.1801C>T	7.37:g.51096992G>A	ENSP00000265136:p.His601Tyr	207	0	0		249	112	0.449799	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Missense_Mutation	SNP	ENST00000265136.7	37	CCDS34637.1	40|40	0.018315018315018316|0.018315018315018316	39|39	0.07926829268292683|0.07926829268292683	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	G|G	0.509|0.509	-0.867489|-0.867489	0.02590|0.02590	0.089197|0.089197	4.65E-4|4.65E-4	ENSG00000106078|ENSG00000106078	ENST00000452534|ENST00000265136;ENST00000445054;ENST00000431948;ENST00000395542;ENST00000457306	.|T;T;T;T	.|0.21734	.|1.99;1.99;1.99;1.99	5.59|5.59	-6.98|-6.98	0.01611|0.01611	.|.	.|2.903440	.|0.00947	.|N	.|0.002915	T|T	0.00271|0.00271	0.0008|0.0008	N|N	0.02539|0.02539	-0.55|-0.55	0.09310|0.09310	N|N	1|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|T	0.36866|0.36866	-0.9730|-0.9730	5|10	.|0.02654	.|T	.|1	.|.	11.0652|11.0652	0.47972|0.47972	0.6443:0.0913:0.2644:0.0|0.6443:0.0913:0.2644:0.0	.|.	.|601;658;601;683;143	.|O75128-3;O75128-7;O75128;O75128-2;O75128-6	.|.;.;COBL_HUMAN;.;.	V|Y	576|601;493;486;683;99	.|ENSP00000265136:H601Y;ENSP00000401204:H493Y;ENSP00000413498:H486Y;ENSP00000378912:H683Y	.|ENSP00000265136:H601Y	A|H	-|-	2|1	0|0	COBL|COBL	51064486|51064486	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.066000|0.066000	0.14489|0.14489	-1.290000|-1.290000	0.02372|0.02372	-0.145000|-0.145000	0.13849|0.13849	GCA|CAC	G|0.974;A|0.026	0.026	strong		0.562	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198		A	51096992	G	A	51096992	3	1	22	1	0	0	0	0	1	0	0	0	3655	1319	46	2	2000	2	COBL	7	51096992	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	354666	51096992	108041671	1656	4557											
POM121L12	285877	hgsc.bcm.edu	37	chr7	53103540	53103540	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggcccctgaggtccctgaCtcagagccatattcagtact	8	10	9	14	0	2	3	2	2	0	1	3	3	3	3	4	2	2	1	4	2	2	3	rs78135827	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:53103540C>G	ENST00000408890.4	+	1	192	c.176C>G	c.(175-177)aCt>aGt	p.T59S		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	59										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						AGGTCCCTGACTCAGAGCCAT	0.706													C|||	168	0.0335463	0.1248	0.0043	5008	,	,		12626	0.0		0.0	False		,,,				2504	0.0				p.T59S		Atlas-SNP	.											POM121L12,NS,carcinoma,0,1	POM121L12	146	1	0			c.C176G						PASS	.	C	SER/THR	438,3494		27,384,1555	29	35	33		176	-1.1	0	7	dbSNP_131	33	4,8306		0,4,4151	yes	missense	POM121L12	NM_182595.3	58	27,388,5706	GG,GC,CC		0.0481,11.1394,3.6105	probably-damaging	59/297	53103540	442,11800	1966	4155	6121	SO:0001583	missense	285877	exon1			CCCTGACTCAGAG		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.176C>G	7.37:g.53103540C>G	ENSP00000386133:p.Thr59Ser	57	0	0		78	33	0.423077	NM_182595	Q8NDI9	Missense_Mutation	SNP	ENST00000408890.4	37	CCDS43584.1	74	0.03388278388278388	71	0.1443089430894309	2	0.0055248618784530384	1	0.0017482517482517483	0	0.0	C	0.374	-0.932216	0.02359	0.111394	4.81E-4	ENSG00000221900	ENST00000408890	T	0.22539	1.95	1.81	-1.11	0.09840	.	.	.	.	.	T	0.00073	0.0002	N	0.08118	0	0.80722	P	0.0	B	0.16603	0.018	B	0.20767	0.031	T	0.41052	-0.9530	8	0.22109	T	0.4	.	2.491	0.04610	0.0:0.3885:0.2856:0.3259	.	59	Q8N7R1	P1L12_HUMAN	S	59	ENSP00000386133:T59S	ENSP00000386133:T59S	T	+	2	0	POM121L12	53071034	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.353000	0.20130	-0.287000	0.09064	0.313000	0.20887	ACT	C|0.965;G|0.035	0.035	strong		0.706	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595		G	53103540	C	G	53103540	3	3	22	1	0	0	0	0	1	0	0	0	12250	565	20	4	178	4	POM121L12	7	53103540	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2006548	53103540	106035123	1657	4558											
EGFR	1956	hgsc.bcm.edu	37	chr7	55238087	55238087	+	Intron	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aatgatggcagcgtgtcccaCcagagcgggagcccagctgc	9	5	14	13	2	0	2	0	1	0	1	1	3	1	3	3	2	5	2	3	2	1	0	rs10258429	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:55238087C>T	ENST00000275493.2	+	16	2057				EGFR_ENST00000454757.2_Intron|EGFR_ENST00000455089.1_Intron|EGFR_ENST00000344576.2_Silent_p.H656H|EGFR_ENST00000442591.1_Intron	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor						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)	GCGTGTCCCACCAGAGCGGGA	0.512		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			C|||	563	0.11242	0.2398	0.049	5008	,	,		20745	0.0496		0.0736	False		,,,				2504	0.09				p.H656H		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.C1968T						PASS	.	C	,	922,3484	352.1+/-311.5	101,720,1382	108	89	95		,1968	2.4	0	7	dbSNP_119	95	606,7994	158.6+/-212.1	23,560,3717	no	intron,coding-synonymous	EGFR	NM_005228.3,NM_201284.1	,	124,1280,5099	TT,TC,CC		7.0465,20.926,11.7484	,	,656/706	55238087	1528,11478	2203	4300	6503	SO:0001627	intron_variant	1956	exon16	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	GTCCCACCAGAGC		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.1881-781C>T	7.37:g.55238087C>T		161	0	0		147	79	0.537415	NM_201284	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																			C|0.889;T|0.111	0.111	strong		0.512	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		T	55238087	C	T	55238087	1	4	22	0	1	0	0	0	0	0	0	0	4969	506	18	2		2	EGFR	7	55238087	Intron	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2134547	55238087	103900576	1658	4559											
SUMF2	25870	hgsc.bcm.edu	37	chr7	56140760	56140761	+	Frame_Shift_Del	DEL	TT	TT	-																															ggagctttgtctttgaggacTttgtctctgatgagctgaga																								rs146946713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:56140760_56140761delTT	ENST00000413756.1	+	3	318_319	c.295_296delTT	c.(295-297)tttfs	p.F99fs	SUMF2_ENST00000342190.6_Frame_Shift_Del_p.F118fs|SUMF2_ENST00000275607.9_Frame_Shift_Del_p.F11fs|SUMF2_ENST00000395436.2_Frame_Shift_Del_p.F118fs|SUMF2_ENST00000437307.2_Frame_Shift_Del_p.F99fs|SUMF2_ENST00000434526.2_Frame_Shift_Del_p.F118fs|SUMF2_ENST00000395435.2_Frame_Shift_Del_p.F118fs			Q8NBJ7	SUMF2_HUMAN	sulfatase modifying factor 2	99					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)			CTTTGAGGACTTTGTCTCTGAT	0.48														49	0.00978435	0.034	0.0058	5008	,	,		19873	0.0		0.0	False		,,,				2504	0.0				p.117_118del		Pindel,Atlas-Indel	.											.	SUMF2	56	.	0			c.351_352del						PASS	.		,,,,	133,4131		2,129,2001					,,,,	0.9	0.9		dbSNP_134	120	0,8254		0,0,4127	yes	frameshift,frameshift,frameshift,frameshift,frameshift	SUMF2	NM_015411.2,NM_001146333.1,NM_001130069.2,NM_001042470.1,NM_001042469.1	,,,,	2,129,6128	A1A1,A1R,RR		0.0,3.1191,1.0625	,,,,	,,,,		133,12385				SO:0001589	frameshift_variant	25870	exon3			.	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.295_296delTT	7.37:g.56140760_56140761delTT	ENSP00000406445:p.Phe99fs	105	0	.		101	43	0.426	NM_001130069	B4DU41|B4DWQ0|Q14DW5|Q53ZE3|Q96BH2|Q9BRN3|Q9BWI1|Q9Y405	Frame_Shift_Del	DEL	ENST00000413756.1	37																																																																																				TT|0.993;-|0.007	0.007	strong		0.48	SUMF2-013	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000341457.2	NM_015411		-	56140761	TT	-	56140760	7	5	22	1	0	1	0	1	0	0	0	0	15401	1609	56	0	362	0	SUMF2	7	56140760	Frame_Shift_Del	DEL	TT	TCGA-G8-6324-01A-11D-2210-10	902673	56140760	102997903	1659	4560											
ZNF479	90827	hgsc.bcm.edu	37	chr7	57187997	57187997	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtgtagggtttctctccagtAtgaattctcctatgtctcat	7	17	8	9	0	3	1	1	1	3	0	7	1	4	1	2	1	0	3	2	1	4	5	rs146543279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:57187997A>T	ENST00000331162.4	-	5	1395	c.1125T>A	c.(1123-1125)caT>caA	p.H375Q		NM_033273.1	NP_150376.1	Q96JC4	ZN479_HUMAN	zinc finger protein 479	375					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)			TCTCTCCAGTATGAATTCTCC	0.438													.|||	12	0.00239617	0.0091	0.0	5008	,	,		21893	0.0		0.0	False		,,,				2504	0.0				p.H375Q		Atlas-SNP	.											.	ZNF479	193	.	0			c.T1125A						PASS	.	A	GLN/HIS	39,4097		0,39,2029	42	43	43		1125	0.9	0	7	dbSNP_134	43	0,8454		0,0,4227	no	missense	ZNF479	NM_033273.1	24	0,39,6256	TT,TA,AA		0.0,0.9429,0.3098	probably-damaging	375/525	57187997	39,12551	2068	4227	6295	SO:0001583	missense	90827	exon5			TCCAGTATGAATT	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.1125T>A	7.37:g.57187997A>T	ENSP00000333776:p.His375Gln	242	0	0		281	143	0.508897	NM_033273		Missense_Mutation	SNP	ENST00000331162.4	37	CCDS43590.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	a	11.55	1.671267	0.29693	0.009429	0.0	ENSG00000185177	ENST00000331162	T	0.66995	-0.24	0.946	0.946	0.19549	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.71685	0.3369	M	0.86268	2.805	0.24579	N	0.993888	D	0.55385	0.971	D	0.65773	0.938	T	0.62501	-0.6841	9	0.87932	D	0	.	2.9462	0.05847	0.6852:0.0:0.3148:0.0	.	375	Q96JC4	ZN479_HUMAN	Q	375	ENSP00000333776:H375Q	ENSP00000333776:H375Q	H	-	3	2	ZNF479	57191939	0.998000	0.40836	0.011000	0.14972	0.010000	0.07245	0.567000	0.23608	0.339000	0.23719	0.329000	0.21502	CAT	A|0.998;T|0.002	0.002	strong		0.438	ZNF479-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345302.1	XM_291202		T	57187997	A	T	57187997	3	4	22	1	0	0	0	0	1	0	0	0	17948	446	16	5	453	5	ZNF479	7	57187997	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1047237	57187997	101950666	1660	4561											
ZNF679	168417	hgsc.bcm.edu	37	chr7	63727210	63727210	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aagtcttgctaatcataagaGtatgcatactggagagaaac	16	10	9	6	0	2	2	1	0	1	2	2	4	2	3	0	1	4	3	0	1	6	5	rs142919190	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:63727210G>A	ENST00000421025.1	+	5	1468	c.1199G>A	c.(1198-1200)aGt>aAt	p.S400N	ZNF679_ENST00000255746.4_Missense_Mutation_p.S400N	NM_001159524.1|NM_153363.2	NP_001152996.1|NP_699194.2	Q8IYX0	ZN679_HUMAN	zinc finger protein 679	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)|skin(1)|stomach(1)	18						AATCATAAGAGTATGCATACT	0.338													.|||	38	0.00758786	0.0287	0.0	5008	,	,		18314	0.0		0.0	False		,,,				2504	0.0				p.S400N		Atlas-SNP	.											ZNF679,NS,carcinoma,0,1	ZNF679	80	1	0			c.G1199A						PASS	.	G	ASN/SER	29,1355		0,29,663	26	25	25		1199	0.8	0.5	7	dbSNP_134	25	0,3182		0,0,1591	no	missense	ZNF679	NM_153363.2	46	0,29,2254	AA,AG,GG		0.0,2.0954,0.6351	benign	400/412	63727210	29,4537	692	1591	2283	SO:0001583	missense	168417	exon5			ATAAGAGTATGCA	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.1199G>A	7.37:g.63727210G>A	ENSP00000416809:p.Ser400Asn	24	0	0		34	20	0.588235	NM_153363		Missense_Mutation	SNP	ENST00000421025.1	37	CCDS47592.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	11.97	1.796444	0.31777	0.020954	0.0	ENSG00000197123	ENST00000421025;ENST00000255746	T;T	0.01139	5.28;5.28	0.819	0.819	0.18785	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00496	0.0016	N	0.11818	0.18	0.21020	N	0.999808	B	0.25007	0.116	B	0.28011	0.085	T	0.49560	-0.8927	9	0.62326	D	0.03	.	6.9957	0.24780	0.0:0.0:1.0:0.0	.	400	Q8IYX0	ZN679_HUMAN	N	400	ENSP00000416809:S400N;ENSP00000255746:S400N	ENSP00000255746:S400N	S	+	2	0	ZNF679	63364645	0.000000	0.05858	0.476000	0.27291	0.477000	0.33069	-0.030000	0.12308	0.191000	0.20236	0.194000	0.17425	AGT	G|0.997;A|0.003	0.003	strong		0.338	ZNF679-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344317.2	NM_153363		A	63727210	G	A	63727210	3	1	22	1	0	0	0	0	1	0	0	0	18101	1029	36	2	1213	2	ZNF679	7	63727210	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6539213	63727210	95411453	1661	4562											
ZNF107	51427	hgsc.bcm.edu	37	chr7	64168641	64168641	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctcctcaacccttaatagAcataagataattcatactgg	14	12	5	10	0	2	2	2	0	0	2	3	2	3	2	2	1	3	1	2	1	6	6	rs73363327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:64168641A>G	ENST00000395391.1	+	4	3334	c.1959A>G	c.(1957-1959)agA>agG	p.R653R	ZNF107_ENST00000423627.1_Silent_p.R653R|ZNF107_ENST00000344930.3_Silent_p.R653R			Q9UII5	ZN107_HUMAN	zinc finger protein 107	653					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)				CCCTTAATAGACATAAGATAA	0.363													a|||	131	0.0261581	0.0983	0.0014	5008	,	,		18481	0.0		0.0	False		,,,				2504	0.0				p.R653R		Atlas-SNP	.											.	ZNF107	107	.	0			c.A1959G						PASS	.	A	,	297,4075		9,279,1898	30	34	33		1959,1959	-0.3	0.1	7	dbSNP_131	33	3,8583		0,3,4290	no	coding-synonymous,coding-synonymous	ZNF107	NM_001013746.1,NM_016220.3	,	9,282,6188	GG,GA,AA		0.0349,6.7932,2.3152	,	653/784,653/784	64168641	300,12658	2186	4293	6479	SO:0001819	synonymous_variant	51427	exon7			TAATAGACATAAG	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.1959A>G	7.37:g.64168641A>G		44	0	0		25	9	0.36	NM_016220		Silent	SNP	ENST00000395391.1	37	CCDS5527.1																																																																																			A|0.985;G|0.015	0.015	strong		0.363	ZNF107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251593.1	NM_016220		G	64168641	A	G	64168641	2	3	22	1	0	0	0	0	0	0	0	1	17730	272	10	3		3	ZNF107	7	64168641	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	441431	64168641	94970022	1662	4563											
ASL	435	hgsc.bcm.edu	37	chr7	65551782	65551782	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggctgctggaggtgcggaaGcggatcaatgtcctgcccct	6	8	15	12	3	1	0	1	0	0	0	2	3	2	3	3	5	4	2	3	5	2	0	rs115468878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:65551782G>A	ENST00000304874.9	+	8	678	c.576G>A	c.(574-576)aaG>aaA	p.K192K	ASL_ENST00000380839.4_Intron|AC068533.7_ENST00000450043.1_5'Flank|ASL_ENST00000395332.3_Silent_p.K192K|ASL_ENST00000395331.3_Silent_p.K192K	NM_000048.3	NP_000039.2	P04424	ARLY_HUMAN	argininosuccinate lyase	192					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)	AGGTGCGGAAGCGGATCAATG	0.687													g|||	29	0.00579073	0.0212	0.0014	5008	,	,		17651	0.0		0.0	False		,,,				2504	0.0				p.K192K		Atlas-SNP	.											.	ASL	39	.	0			c.G576A						PASS	.	A	,,,	95,4307		1,93,2107	27	28	28		576,576,576,	1.8	1	7	dbSNP_132	28	0,8584		0,0,4292	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	ASL	NM_000048.3,NM_001024943.1,NM_001024944.1,NM_001024946.1	,,,	1,93,6399	AA,AG,GG		0.0,2.1581,0.7316	,,,	192/465,192/465,192/445,	65551782	95,12891	2201	4292	6493	SO:0001819	synonymous_variant	435	exon8			GCGGAAGCGGATC		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.576G>A	7.37:g.65551782G>A		90	0	0		74	35	0.472973	NM_000048	E7EMI0|E9PE48|Q6LDS5|Q96HS2	Silent	SNP	ENST00000304874.9	37	CCDS5531.1																																																																																			G|0.993;A|0.007	0.007	strong		0.687	ASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251695.2	NM_000048		A	65551782	G	A	65551782	2	1	22	1	0	0	0	0	0	0	0	1	1044	962	34	2		2	ASL	7	65551782	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1383141	65551782	93586881	1663	4564											
KCTD7	154881	hgsc.bcm.edu	37	chr7	66094184	66094184	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cggggcacgcgctgcccctgCtgccacaggaggtacccggg	5	4	16	16	4	0	0	0	0	0	0	0	1	0	1	4	5	4	4	4	5	1	1	rs587780370		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:66094184C>T	ENST00000275532.3	+	1	317	c.133C>T	c.(133-135)Ctg>Ttg	p.L45L	KCTD7_ENST00000443322.1_Silent_p.L45L	NM_001167961.2|NM_153033.4	NP_001161433.1|NP_694578.1	Q96MP8	KCTD7_HUMAN	potassium channel tetramerization domain containing 7	45					cell death (GO:0008219)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|urinary_tract(1)	16						GCTGCCCCTGCTGCCACAGGA	0.776																																					p.L45L		Atlas-SNP	.											KCTD7,brain,glioma,-2,1	KCTD7	26	1	0			c.C133T						scavenged	.																																			SO:0001819	synonymous_variant	154881	exon1			CCCCTGCTGCCAC	AK056631	CCDS5534.1, CCDS55117.1	7q11.21	2014-09-17	2013-06-20		ENSG00000243335	ENSG00000243335			21957	protein-coding gene	gene with protein product		611725	"potassium channel tetramerisation domain containing 7"			12477932	Standard	NM_001167961		Approved	FLJ32069, EPM3, CLN14	uc003tve.3	Q96MP8	OTTHUMG00000129543	ENST00000275532.3:c.133C>T	7.37:g.66094184C>T		2	0	0		8	5	0.625	NM_001167961	A4D2M4|Q8IVR0	Silent	SNP	ENST00000275532.3	37	CCDS5534.1																																																																																			.	.	none		0.776	KCTD7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251733.2	NM_153033		T	66094184	C	T	66094184	2	4	22	1	0	0	0	0	0	0	0	1	8123	796	28	2		2	KCTD7	7	66094184	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	542402	66094184	93044479	1664	4565											
NSUN5	55695	hgsc.bcm.edu	37	chr7	72717686	72717686	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggaggcagtgctcggcaccCgggaacgtgctcaggcctcg	6	5	16	14	5	1	0	1	0	0	0	3	2	1	2	2	5	3	4	2	5	1	0	rs145622470	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:72717686C>T	ENST00000252594.6	-	9	1212	c.1197G>A	c.(1195-1197)ccG>ccA	p.P399P	NSUN5_ENST00000310326.8_Silent_p.P399P|NSUN5_ENST00000438747.2_Silent_p.P399P|NSUN5_ENST00000428206.1_Silent_p.P361P			Q96P11	NSUN5_HUMAN	NOP2/Sun domain family, member 5	399					rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	8		Lung NSC(55;0.163)				GCTCGGCACCCGGGAACGTGC	0.642													.|||	35	0.00698882	0.025	0.0029	5008	,	,		16592	0.0		0.0	False		,,,				2504	0.0				p.P399P		Atlas-SNP	.											.	NSUN5	47	.	0			c.G1197A						PASS	.	C	,,,	92,4314		0,92,2111	49	48	48		1197,1083,1197,1197	-4.7	0	7	dbSNP_134	48	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NSUN5	NM_001168347.1,NM_001168348.1,NM_018044.3,NM_148956.2	,,,	0,92,6411	TT,TC,CC		0.0,2.0881,0.7074	,,,	399/471,361/392,399/430,399/467	72717686	92,12914	2203	4300	6503	SO:0001819	synonymous_variant	55695	exon9			GGCACCCGGGAAC	AF420249	CCDS5546.1, CCDS5547.1, CCDS55118.1, CCDS55119.1	7q11.23	2010-04-08	2009-11-23	2005-01-14	ENSG00000130305	ENSG00000130305		"NOP2/Sun domain containing"	16385	protein-coding gene	gene with protein product	"NOP2/Sun domain family, member 5A"	615732	"Williams Beuren syndrome chromosome region 20A", "NOL1/NOP2/Sun domain family, member 5"	WBSCR20, WBSCR20A		11978965, 12073013	Standard	NM_148956		Approved	NOL1R, p120, (NOL1), FLJ10267, NSUN5A, Ynl022cL	uc011kev.2	Q96P11	OTTHUMG00000129869	ENST00000252594.6:c.1197G>A	7.37:g.72717686C>T		111	0	0		131	70	0.534351	NM_148956	B3KX04|B4DP79|G3V0G9|Q6ZUI8|Q96HT9|Q9NW70	Silent	SNP	ENST00000252594.6	37	CCDS5547.1																																																																																			C|0.993;T|0.007	0.007	strong		0.642	NSUN5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252113.1	NM_148956		T	72717686	C	T	72717686	2	4	22	1	0	0	0	0	0	0	0	1	10690	639	23	1		1	NSUN5	7	72717686	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6623502	72717686	86420977	1665	4566											
NSUN5	55695	hgsc.bcm.edu	37	chr7	72719048	72719048	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cagcagctccggcatcaaggGgtccaggagaaaatgcttcc	11	6	12	12	1	1	1	1	0	0	1	4	2	4	1	3	4	3	4	3	4	3	1	rs34913552	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:72719048G>A	ENST00000252594.6	-	5	562	c.547C>T	c.(547-549)Ccc>Tcc	p.P183S	NSUN5_ENST00000310326.8_Missense_Mutation_p.P183S|NSUN5_ENST00000438747.2_Missense_Mutation_p.P183S|NSUN5_ENST00000428206.1_Missense_Mutation_p.P145S			Q96P11	NSUN5_HUMAN	NOP2/Sun domain family, member 5	183			P -> S (in dbSNP:rs34913552).		rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	8		Lung NSC(55;0.163)				GGCATCAAGGGGTCCAGGAGA	0.567													g|||	189	0.0377396	0.1377	0.0101	5008	,	,		19720	0.0		0.0	False		,,,				2504	0.0				p.P183S		Atlas-SNP	.											.	NSUN5	47	.	0			c.C547T						PASS	.	A	SER/PRO,SER/PRO,SER/PRO,SER/PRO	445,3961	174.4+/-204.0	16,413,1774	19	20	20		547,433,547,547	-2.3	0.1	7	dbSNP_126	20	1,8579		0,1,4289	no	missense,missense,missense,missense	NSUN5	NM_001168347.1,NM_001168348.1,NM_018044.3,NM_148956.2	74,74,74,74	16,414,6063	AA,AG,GG		0.0117,10.0999,3.4345	benign,benign,benign,benign	183/471,145/392,183/430,183/467	72719048	446,12540	2203	4290	6493	SO:0001583	missense	55695	exon5			TCAAGGGGTCCAG	AF420249	CCDS5546.1, CCDS5547.1, CCDS55118.1, CCDS55119.1	7q11.23	2010-04-08	2009-11-23	2005-01-14	ENSG00000130305	ENSG00000130305		"NOP2/Sun domain containing"	16385	protein-coding gene	gene with protein product	"NOP2/Sun domain family, member 5A"	615732	"Williams Beuren syndrome chromosome region 20A", "NOL1/NOP2/Sun domain family, member 5"	WBSCR20, WBSCR20A		11978965, 12073013	Standard	NM_148956		Approved	NOL1R, p120, (NOL1), FLJ10267, NSUN5A, Ynl022cL	uc011kev.2	Q96P11	OTTHUMG00000129869	ENST00000252594.6:c.547C>T	7.37:g.72719048G>A	ENSP00000252594:p.Pro183Ser	568	0	0		496	155	0.3125	NM_148956	B3KX04|B4DP79|G3V0G9|Q6ZUI8|Q96HT9|Q9NW70	Missense_Mutation	SNP	ENST00000252594.6	37	CCDS5547.1	70	0.03205128205128205	59	0.11991869918699187	4	0.011049723756906077	3	0.005244755244755245	4	0.005277044854881266	g	0.011	-1.725772	0.00694	0.100999	1.17E-4	ENSG00000130305	ENST00000428206;ENST00000252594;ENST00000438747;ENST00000310326	T;T;T;T	0.09911	2.93;2.93;2.93;2.93	4.31	-2.31	0.06765	.	0.500976	0.23395	N	0.048648	T	0.00144	0.0004	M	0.69463	2.115	0.09310	N	1	B;B;B;B	0.23185	0.002;0.066;0.081;0.017	B;B;B;B	0.20384	0.01;0.029;0.021;0.018	T	0.42189	-0.9466	10	0.13853	T	0.58	.	7.9291	0.29891	0.3346:0.1027:0.5626:0.0	rs34913552	183;145;183;183	B4DP79;G3V0G9;Q96P11;Q96P11-2	.;.;NSUN5_HUMAN;.	S	145;183;183;183	ENSP00000393081:P145S;ENSP00000252594:P183S;ENSP00000388464:P183S;ENSP00000309126:P183S	ENSP00000252594:P183S	P	-	1	0	NSUN5	72356984	0.893000	0.30496	0.076000	0.20297	0.032000	0.12392	0.935000	0.28924	-0.731000	0.04862	-1.478000	0.00992	CCC	G|0.971;A|0.029	0.029	strong		0.567	NSUN5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252113.1	NM_148956		A	72719048	G	A	72719048	3	1	22	1	0	0	0	0	1	0	0	0	10690	1232	43	2	898	2	NSUN5	7	72719048	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1362	72719048	86419615	1666	4567											
MLXIPL	51085	hgsc.bcm.edu	37	chr7	73020328	73020328	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tcggacaaaaagcaattgagGtccaggagctgccgcccacc	12	5	11	13	2	0	1	0	1	0	0	2	3	1	3	4	3	3	2	4	3	3	1	rs34922362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:73020328G>T	ENST00000313375.3	-	6	779	c.732C>A	c.(730-732)gaC>gaA	p.D244E	MLXIPL_ENST00000434326.1_Intron|MLXIPL_ENST00000354613.1_Missense_Mutation_p.D244E|MLXIPL_ENST00000395189.1_Intron|MLXIPL_ENST00000429400.2_Missense_Mutation_p.D244E|MLXIPL_ENST00000414749.2_Missense_Mutation_p.D244E	NM_032951.2|NM_032953.2	NP_116569.1|NP_116571.1	Q9NP71	MLXPL_HUMAN	MLX interacting protein-like	244			D -> E (in dbSNP:rs34922362).		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)				AGCAATTGAGGTCCAGGAGCT	0.637													G|||	110	0.0219649	0.0825	0.0014	5008	,	,		17810	0.0		0.0	False		,,,				2504	0.0				p.D244E		Atlas-SNP	.											.	MLXIPL	54	.	0			c.C732A						PASS	.	G	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	239,4165		6,227,1969	33	32	32		732,732,732,732	1.8	1	7	dbSNP_126	32	0,8594		0,0,4297	yes	missense,missense,missense,missense	MLXIPL	NM_032951.2,NM_032952.2,NM_032953.2,NM_032954.2	45,45,45,45	6,227,6266	TT,TG,GG		0.0,5.4269,1.8387	benign,benign,benign,benign	244/853,244/834,244/851,244/832	73020328	239,12759	2202	4297	6499	SO:0001583	missense	51085	exon6			ATTGAGGTCCAGG	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.732C>A	7.37:g.73020328G>T	ENSP00000320886:p.Asp244Glu	73	0	0		76	33	0.434211	NM_032954	C5HU02|C5HU03|C5HU04|Q96E48|Q9BY03|Q9BY04|Q9BY05|Q9BY06|Q9Y2P3	Missense_Mutation	SNP	ENST00000313375.3	37	CCDS5553.1	47	0.02152014652014652	46	0.09349593495934959	1	0.0027624309392265192	0	0.0	0	0.0	G	13.57	2.277764	0.40294	0.054269	0.0	ENSG00000009950	ENST00000414749;ENST00000429400;ENST00000313375;ENST00000354613;ENST00000456640	T;T;T;T;T	0.59364	1.81;1.85;1.82;1.83;0.27	3.68	1.79	0.24919	.	0.068000	0.56097	D	0.000024	T	0.03305	0.0096	L	0.59436	1.845	0.80722	D	1	P;D;D;D	0.54207	0.941;0.965;0.965;0.965	B;P;P;P	0.47015	0.333;0.534;0.534;0.534	T	0.01432	-1.1356	10	0.87932	D	0	-11.5469	5.3046	0.15797	0.2859:0.0:0.7141:0.0	rs34922362	244;244;244;244	Q9NP71;Q9NP71-2;Q9NP71-3;Q9NP71-4	MLXPL_HUMAN;.;.;.	E	244;244;244;244;206	ENSP00000412330:D244E;ENSP00000406296:D244E;ENSP00000320886:D244E;ENSP00000346629:D244E;ENSP00000402615:D206E	ENSP00000320886:D244E	D	-	3	2	MLXIPL	72658264	1.000000	0.71417	0.986000	0.45419	0.877000	0.50540	2.652000	0.46682	0.221000	0.20879	0.313000	0.20887	GAC	G|0.978;T|0.022	0.022	strong		0.637	MLXIPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252262.1	NM_032951		T	73020328	G	T	73020328	3	4	22	1	0	0	0	0	1	0	0	0	9646	1252	44	4	1874	4	MLXIPL	7	73020328	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	301280	73020328	86118335	1667	4568											
ABHD11	83451	hgsc.bcm.edu	37	chr7	73151643	73151643	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatggccctcatggctgccaCataggttgcaaagtgggaga	10	8	14	9	0	1	1	1	0	0	1	1	3	1	1	2	4	2	3	2	4	2	2	rs61745525|rs386714666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:73151643C>T	ENST00000222800.3	-	4	610	c.541G>A	c.(541-543)Gtg>Atg	p.V181M	LINC00035_ENST00000427153.1_RNA|ABHD11_ENST00000458339.1_Intron|ABHD11_ENST00000437775.2_Missense_Mutation_p.V174M|ABHD11_ENST00000395147.4_Intron|ABHD11_ENST00000468998.1_5'Flank	NM_148912.2	NP_683710.1	Q8NFV4	ABHDB_HUMAN	abhydrolase domain containing 11	181						mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			breast(1)|endometrium(1)|large_intestine(1)|lung(1)	4		Lung NSC(55;0.0908)|all_lung(88;0.198)				ATGGCTGCCACATAGGTTGCA	0.557													C|||	228	0.0455272	0.1649	0.0144	5008	,	,		21333	0.0		0.0	False		,,,				2504	0.0				p.V181M		Atlas-SNP	.											.	ABHD11	11	.	0			c.G541A						PASS	.	C	,MET/VAL,MET/VAL	436,3970		29,378,1796	89	73	79		,541,520	-9.2	0	7	dbSNP_129	79	3,8597		0,3,4297	yes	intron,missense,missense	ABHD11	NM_001145364.1,NM_148912.2,NM_148913.2	,21,21	29,381,6093	TT,TC,CC		0.0349,9.8956,3.3754	,benign,benign	,181/316,174/309	73151643	439,12567	2203	4300	6503	SO:0001583	missense	83451	exon4			CTGCCACATAGGT	AF217971	CCDS5558.1, CCDS47607.1, CCDS47608.1, CCDS75615.1	7q11.23	2010-08-05	2005-01-24	2005-01-27	ENSG00000106077	ENSG00000106077		"Abhydrolase domain containing"	16407	protein-coding gene	gene with protein product			"Williams Beuren syndrome chromosome region 21"	WBSCR21		12073013	Standard	NR_026910		Approved	PP1226	uc003tzb.3	Q8NFV4	OTTHUMG00000130029	ENST00000222800.3:c.541G>A	7.37:g.73151643C>T	ENSP00000222800:p.Val181Met	59	0	0		63	63	1	NM_148912	H7BYM8|Q6PJU0|Q8N722|Q8N723|Q8NFV2|Q8NFV3|Q9HBS8	Missense_Mutation	SNP	ENST00000222800.3	37	CCDS5558.1	73	0.033424908424908424	67	0.13617886178861788	6	0.016574585635359115	0	0.0	0	0.0	C	6.139	0.393893	0.11638	0.098956	3.49E-4	ENSG00000106077	ENST00000437775;ENST00000222800	T;T	0.68479	-0.33;-0.33	4.62	-9.25	0.00666	.	0.399068	0.28388	N	0.015523	T	0.00328	0.0010	L	0.31578	0.945	0.09310	P	0.99999999628235	B;B	0.18310	0.027;0.017	B;B	0.19666	0.015;0.026	T	0.01456	-1.1350	9	0.36615	T	0.2	-0.2939	3.1353	0.06437	0.2531:0.453:0.1175:0.1763	.	174;181	Q8NFV4-4;Q8NFV4	.;ABHDB_HUMAN	M	174;181	ENSP00000416970:V174M;ENSP00000222800:V181M	ENSP00000222800:V181M	V	-	1	0	ABHD11	72789579	0.406000	0.25344	0.004000	0.12327	0.014000	0.08584	-0.283000	0.08433	-1.427000	0.01992	-0.367000	0.07326	GTG	C|0.963;T|0.037	0.037	strong		0.557	ABHD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252306.1			T	73151643	C	T	73151643	3	4	22	1	0	0	0	0	1	0	0	0	75	478	17	2	418	2	ABHD11	7	73151643	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	131315	73151643	85987020	1668	4569											
WBSCR27	155368	hgsc.bcm.edu	37	chr7	73249092	73249092	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctcacttcctcaacctgggtCgccttccactttcggtacag	6	12	7	16	2	2	0	2	0	0	0	6	0	4	0	4	2	2	1	4	2	2	4	rs73369956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:73249092C>T	ENST00000297873.4	-	6	768	c.719G>A	c.(718-720)cGa>cAa	p.R240Q		NM_152559.2	NP_689772.2	Q8N6F8	WBS27_HUMAN	Williams Beuren syndrome chromosome region 27	240										NS(1)|central_nervous_system(1)|lung(2)|prostate(1)	5		Lung NSC(55;0.159)				CAACCTGGGTCGCCTTCCACT	0.632													C|||	173	0.0345447	0.1263	0.0072	5008	,	,		17029	0.0		0.001	False		,,,				2504	0.0				p.R240Q		Atlas-SNP	.											.	WBSCR27	21	.	0			c.G719A						PASS	.	C	GLN/ARG	448,3958	210.2+/-230.7	22,404,1777	47	43	44		719	-4.9	0	7	dbSNP_130	44	2,8598	2.2+/-6.3	0,2,4298	yes	missense	WBSCR27	NM_152559.2	43	22,406,6075	TT,TC,CC		0.0233,10.168,3.4599	benign	240/246	73249092	450,12556	2203	4300	6503	SO:0001583	missense	155368	exon6			CTGGGTCGCCTTC	AF534110	CCDS5561.1	7q11.23	2004-07-05			ENSG00000165171	ENSG00000165171			19068	protein-coding gene	gene with protein product		612546					Standard	NM_152559		Approved		uc003tzj.2	Q8N6F8	OTTHUMG00000130033	ENST00000297873.4:c.719G>A	7.37:g.73249092C>T	ENSP00000297873:p.Arg240Gln	111	0	0		103	103	1	NM_152559		Missense_Mutation	SNP	ENST00000297873.4	37	CCDS5561.1	61	0.027930402930402932	58	0.11788617886178862	3	0.008287292817679558	0	0.0	0	0.0	C	9.306	1.054385	0.19907	0.10168	2.33E-4	ENSG00000165171	ENST00000297873	T	0.36520	1.25	4.67	-4.88	0.03113	.	0.739448	0.13097	N	0.414080	T	0.00144	0.0004	N	0.02011	-0.69	0.09310	N	1	B	0.10296	0.003	B	0.01281	0.0	T	0.25398	-1.0133	10	0.19147	T	0.46	-0.2142	2.1565	0.03814	0.1345:0.2371:0.1332:0.4952	.	240	Q8N6F8	WBS27_HUMAN	Q	240	ENSP00000297873:R240Q	ENSP00000297873:R240Q	R	-	2	0	WBSCR27	72887028	0.000000	0.05858	0.000000	0.03702	0.104000	0.19210	-3.365000	0.00496	-0.582000	0.05929	0.549000	0.68633	CGA	C|0.962;T|0.038	0.038	strong		0.632	WBSCR27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252312.1	NM_152559		T	73249092	C	T	73249092	3	4	22	1	0	0	0	0	1	0	0	0	17281	884	31	1	22	1	WBSCR27	7	73249092	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	97449	73249092	85889571	1669	4570											
WBSCR27	155368	hgsc.bcm.edu	37	chr7	73254871	73254871	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagctggaggaagcctggAgcccgcagctggggtagggg	7	5	20	9	1	0	0	0	0	0	0	0	3	0	3	2	7	5	5	2	7	2	1	rs61741292	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:73254871A>G	ENST00000297873.4	-	4	310	c.261T>C	c.(259-261)gcT>gcC	p.A87A		NM_152559.2	NP_689772.2	Q8N6F8	WBS27_HUMAN	Williams Beuren syndrome chromosome region 27	87										NS(1)|central_nervous_system(1)|lung(2)|prostate(1)	5		Lung NSC(55;0.159)				GGAAGCCTGGAGCCCGCAGCT	0.672													A|||	173	0.0345447	0.1263	0.0072	5008	,	,		14138	0.0		0.001	False		,,,				2504	0.0				p.A87A		Atlas-SNP	.											.	WBSCR27	21	.	0			c.T261C						PASS	.	A		341,3999		14,313,1843	14	17	16		261	-0.2	1	7	dbSNP_129	16	2,8534		0,2,4266	no	coding-synonymous	WBSCR27	NM_152559.2		14,315,6109	GG,GA,AA		0.0234,7.8571,2.6639		87/246	73254871	343,12533	2170	4268	6438	SO:0001819	synonymous_variant	155368	exon4			GCCTGGAGCCCGC	AF534110	CCDS5561.1	7q11.23	2004-07-05			ENSG00000165171	ENSG00000165171			19068	protein-coding gene	gene with protein product		612546					Standard	NM_152559		Approved		uc003tzj.2	Q8N6F8	OTTHUMG00000130033	ENST00000297873.4:c.261T>C	7.37:g.73254871A>G		111	0	0		95	95	1	NM_152559		Silent	SNP	ENST00000297873.4	37	CCDS5561.1																																																																																			A|0.974;G|0.026	0.026	strong		0.672	WBSCR27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252312.1	NM_152559		G	73254871	A	G	73254871	2	3	22	1	0	0	0	0	0	0	0	1	17281	291	11	3		3	WBSCR27	7	73254871	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	5779	73254871	85883792	1670	4571											
HIP1	3092	hgsc.bcm.edu	37	chr7	75221693	75221693	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tagccccaggaactcacgttCgggtgtccatctcggaggag	8	8	13	12	3	2	0	1	0	1	0	5	3	3	3	3	4	2	1	3	4	2	2	rs144446822	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:75221693C>T	ENST00000336926.6	-	3	350	c.324G>A	c.(322-324)ccG>ccA	p.P108P	HIP1_ENST00000434438.2_Silent_p.P108P	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	108	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						AACTCACGTTCGGGTGTCCAT	0.597			T	PDGFRB	CMML								C|||	6	0.00119808	0.0045	0.0	5008	,	,		20231	0.0		0.0	False		,,,				2504	0.0				p.P108P		Atlas-SNP	.		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	.	HIP1	91	.	0			c.G324A						PASS	.	C		15,4391	22.3+/-47.3	0,15,2188	59	50	53		324	-11.6	0	7	dbSNP_134	53	0,8600		0,0,4300	no	coding-synonymous	HIP1	NM_005338.5		0,15,6488	TT,TC,CC		0.0,0.3404,0.1153		108/1038	75221693	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	3092	exon3			CACGTTCGGGTGT	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.324G>A	7.37:g.75221693C>T		49	0	0		54	35	0.648148	NM_005338	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Silent	SNP	ENST00000336926.6	37	CCDS34669.1																																																																																			C|0.999;T|0.001	0.001	strong		0.597	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338		T	75221693	C	T	75221693	2	4	22	1	0	0	0	0	0	0	0	1	7123	871	31	1		1	HIP1	7	75221693	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1966822	75221693	83916970	1671	4572											
MDH2	4191	hgsc.bcm.edu	37	chr7	75684273	75684273	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atcgcgcacacacccggagtGgccgcagatctgagccacat	10	5	11	15	4	1	2	0	1	1	1	2	3	1	3	3	2	1	2	3	2	0	0	rs77424348	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:75684273G>A	ENST00000315758.5	+	2	286	c.192G>A	c.(190-192)gtG>gtA	p.V64V	MDH2_ENST00000432020.2_Silent_p.V64V|MDH2_ENST00000443006.1_Intron|MDH2_ENST00000490105.1_3'UTR	NM_005918.2	NP_005909.2	P40926	MDHM_HUMAN	malate dehydrogenase 2, NAD (mitochondrial)	64					carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|internal protein amino acid acetylation (GO:0006475)|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)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	L-malate dehydrogenase activity (GO:0030060)|malate dehydrogenase (NADP+) activity (GO:0046554)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(2)	14						CACCCGGAGTGGCCGCAGATC	0.612													g|||	28	0.00559105	0.0204	0.0014	5008	,	,		14182	0.0		0.0	False		,,,				2504	0.0				p.V64V		Atlas-SNP	.											.	MDH2	35	.	0			c.G192A						PASS	.	G		112,4294	86.8+/-125.4	3,106,2094	77	78	78		192	2.3	1	7	dbSNP_132	78	1,8599		0,1,4299	no	coding-synonymous	MDH2	NM_005918.2		3,107,6393	AA,AG,GG		0.0116,2.542,0.8688		64/339	75684273	113,12893	2203	4300	6503	SO:0001819	synonymous_variant	4191	exon2			CGGAGTGGCCGCA		CCDS5581.1, CCDS64691.1, CCDS75622.1	7q11.23	2013-09-20			ENSG00000146701	ENSG00000146701	1.1.1.37		6971	protein-coding gene	gene with protein product		154100					Standard	NM_005918		Approved		uc003ueo.3	P40926	OTTHUMG00000023827	ENST00000315758.5:c.192G>A	7.37:g.75684273G>A		69	0	0		77	54	0.701299	NM_005918	A8K414|B2RE78|B4DE44|E9PDB2|O43682	Silent	SNP	ENST00000315758.5	37	CCDS5581.1																																																																																			G|0.984;A|0.016	0.016	strong		0.612	MDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252851.1			A	75684273	G	A	75684273	2	1	22	1	0	0	0	0	0	0	0	1	9419	1335	47	2		2	MDH2	7	75684273	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	462580	75684273	83454390	1672	4573											
DTX2	113878	hgsc.bcm.edu	37	chr7	76109877	76109877	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caggtgtacaccagccccgcGgctgtggccgtgtgggaatg	6	7	16	12	3	0	0	0	0	0	0	0	1	0	1	4	4	2	2	4	4	2	1	rs149301449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:76109877G>A	ENST00000324432.5	+	4	561	c.51G>A	c.(49-51)gcG>gcA	p.A17A	DTX2_ENST00000446600.1_Intron|DTX2_ENST00000446820.2_Silent_p.A17A|DTX2_ENST00000472426.1_3'UTR|AC007078.4_ENST00000479299.2_RNA|DTX2_ENST00000430490.2_Silent_p.A17A|DTX2_ENST00000307569.8_Silent_p.A17A|DTX2_ENST00000413936.2_Silent_p.A17A	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	17	WWE 1. {ECO:0000255|PROSITE- ProRule:PRU00248}.				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						CCAGCCCCGCGGCTGTGGCCG	0.642													.|||	15	0.00299521	0.0083	0.0014	5008	,	,		18307	0.003		0.0	False		,,,				2504	0.0				p.A17A		Atlas-SNP	.											.	DTX2	64	.	0			c.G51A						PASS	.	G	,,,	16,4390		0,16,2187	28	29	29		51,51,51,51	4.2	1	7	dbSNP_134	29	0,8592		0,0,4296	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DTX2	NM_001102594.1,NM_001102595.1,NM_001102596.1,NM_020892.2	,,,	0,16,6483	AA,AG,GG		0.0,0.3631,0.1231	,,,	17/623,17/623,17/576,17/623	76109877	16,12982	2203	4296	6499	SO:0001819	synonymous_variant	113878	exon1			CCCCGCGGCTGTG		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.51G>A	7.37:g.76109877G>A		214	0	0		238	135	0.567227	NM_001102596	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Silent	SNP	ENST00000324432.5	37	CCDS5587.1																																																																																			G|0.997;A|0.003	0.003	strong		0.642	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2			A	76109877	G	A	76109877	2	1	22	1	0	0	0	0	0	0	0	1	4796	1103	39	1		1	DTX2	7	76109877	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	425604	76109877	83028786	1673	4574											
DTX2	113878	hgsc.bcm.edu	37	chr7	76132805	76132805	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gagaagacggggacccagccCcagggaaagatggaggtatt	13	4	16	8	1	0	3	0	0	0	3	0	7	0	6	3	5	1	1	3	5	3	2	rs73703182	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:76132805C>G	ENST00000324432.5	+	10	1962	c.1452C>G	c.(1450-1452)ccC>ccG	p.P484P	DTX2_ENST00000446600.1_Silent_p.P393P|DTX2_ENST00000446820.2_Silent_p.P437P|DTX2_ENST00000430490.2_Silent_p.P484P|DTX2_ENST00000307569.8_Silent_p.P437P|DTX2_ENST00000413936.2_Silent_p.P484P	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	484					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						GGACCCAGCCCCAGGGAAAGA	0.572													.|||	88	0.0175719	0.0651	0.0029	5008	,	,		18601	0.0		0.0	False		,,,				2504	0.0				p.P484P		Atlas-SNP	.											.	DTX2	64	.	0			c.C1452G						PASS	.	C	,,,	241,4159		11,219,1970	70	66	67		1452,1452,1311,1452	3	1	7	dbSNP_130	67	2,8592		0,2,4295	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DTX2	NM_001102594.1,NM_001102595.1,NM_001102596.1,NM_020892.2	,,,	11,221,6265	GG,GC,CC		0.0233,5.4773,1.8701	,,,	484/623,484/623,437/576,484/623	76132805	243,12751	2200	4297	6497	SO:0001819	synonymous_variant	113878	exon9			CCAGCCCCAGGGA		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.1452C>G	7.37:g.76132805C>G		183	0	0		173	95	0.549133	NM_001102594	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Silent	SNP	ENST00000324432.5	37	CCDS5587.1																																																																																			C|0.977;G|0.023	0.023	strong		0.572	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2			G	76132805	C	G	76132805	2	3	22	1	0	0	0	0	0	0	0	1	4796	610	22	4		4	DTX2	7	76132805	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	22928	76132805	83005858	1674	4575											
POMZP3	22932	hgsc.bcm.edu	37	chr7	76240877	76240877	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctttgttacagcattgacAgatgtcagccaggccttcca	10	11	8	12	0	1	2	1	1	0	1	2	2	2	2	4	1	3	2	4	1	1	4	rs73365247	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:76240877A>T	ENST00000310842.4	-	6	1153	c.469T>A	c.(469-471)Tgt>Agt	p.C157S	UPK3B_ENST00000443097.2_Intron|POMZP3_ENST00000275569.4_Intron|UPK3B_ENST00000419923.2_Intron|AC004980.7_ENST00000418663.1_RNA	NM_012230.3	NP_036362.3	Q6PJE2	POZP3_HUMAN	POM121 and ZP3 fusion	157										kidney(3)|lung(2)	5		Myeloproliferative disorder(862;0.204)				CAGCATTGACAGATGTCAGCC	0.517													a|||	295	0.0589058	0.2148	0.0144	5008	,	,		18707	0.001		0.0	False		,,,				2504	0.0				p.C157S		Atlas-SNP	.											.	POMZP3	19	.	0			c.T469A						PASS	.	A	SER/CYS,	887,3517		137,613,1452	74	76	75		469,	0.8	0.8	7	dbSNP_130	75	16,8566		1,14,4276	no	missense,intron	POMZP3	NM_012230.3,NM_152992.2	112,	138,627,5728	TT,TA,AA		0.1864,20.1408,6.9536	probably-damaging,	157/188,	76240877	903,12083	2202	4291	6493	SO:0001583	missense	22932	exon6			ATTGACAGATGTC	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.469T>A	7.37:g.76240877A>T	ENSP00000309233:p.Cys157Ser	226	0	0		284	110	0.387324	NM_012230	F6STJ3|Q12903|Q9BWB4	Missense_Mutation	SNP	ENST00000310842.4	37	CCDS43606.1	143|143	0.06547619047619048|0.06547619047619048	138|138	0.2804878048780488|0.2804878048780488	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	0|0	0.0|0.0	N|N	17.67|17.67	3.447194|3.447194	0.63178|0.63178	0.201408|0.201408	0.001864|0.001864	ENSG00000146707|ENSG00000146707	ENST00000310842|ENST00000441393	T|.	0.65732|.	-0.17|.	0.786|0.786	0.786|0.786	0.18590|0.18590	.|.	0.000000|.	0.85682|.	U|.	0.000000|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.88310|0.88310	2.945|2.945	0.09310|0.09310	P|P	0.9999947731|0.9999947731	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|T	0.04650|0.04650	-1.0936|-1.0936	9|4	0.87932|.	D|.	0|.	.|.	3.9669|3.9669	0.09436|0.09436	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	157|.	Q6PJE2|.	POZP3_HUMAN|.	S|Q	157|93	ENSP00000309233:C157S|.	ENSP00000309233:C157S|.	C|L	-|-	1|2	0|0	POMZP3|POMZP3	76078813|76078813	1.000000|1.000000	0.71417|0.71417	0.795000|0.795000	0.32087|0.32087	0.753000|0.753000	0.42808|0.42808	2.176000|2.176000	0.42500|0.42500	0.612000|0.612000	0.30071|0.30071	0.305000|0.305000	0.20034|0.20034	TGT|CTG	A|0.957;T|0.043	0.043	strong		0.517	POMZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341775.1	NM_012230		T	76240877	A	T	76240877	3	4	22	1	0	0	0	0	1	0	0	0	12256	188	7	5	105	5	POMZP3	7	76240877	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	108072	76240877	82897786	1675	4576											
PION	54103	hgsc.bcm.edu	37	chr7	77010661	77010661	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgggcgacatggatacgaaaTtgttcaatatctttaaaaga	15	12	9	5	2	2	1	1	0	1	1	2	4	2	2	0	2	1	1	0	2	6	6	rs17152629	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:77010661T>C	ENST00000257626.7	-	8	615	c.537A>G	c.(535-537)caA>caG	p.Q179Q		NM_017439.3	NP_059135.2	A4D1B5	GSAP_HUMAN	gamma-secretase activating protein	179					positive regulation of beta-amyloid formation (GO:1902004)|regulation of proteolysis (GO:0030162)	trans-Golgi network (GO:0005802)	beta-amyloid binding (GO:0001540)										GGATACGAAATTGTTCAATAT	0.284													T|||	157	0.0313498	0.1104	0.0144	5008	,	,		18372	0.001		0.0	False		,,,				2504	0.0				p.Q179Q		Atlas-SNP	.											.	PION	74	.	0			c.A537G						PASS	.	T		349,3271		20,309,1481	66	63	64		537	-1.6	0.2	7	dbSNP_123	64	3,8131		0,3,4064	no	coding-synonymous	PION	NM_017439.3		20,312,5545	CC,CT,TT		0.0369,9.6409,2.9947		179/855	77010661	352,11402	1810	4067	5877	SO:0001819	synonymous_variant	54103	exon8			ACGAAATTGTTCA		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.537A>G	7.37:g.77010661T>C		43	0	0		37	15	0.405405	NM_017439	A4D1B6|Q3MJC0|Q8ND73|Q9UMH3|Q9Y4L9	Silent	SNP	ENST00000257626.7	37	CCDS34672.2																																																																																			T|0.965;C|0.035	0.035	strong		0.284	GSAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318672.2	NM_017439		C	77010661	T	C	77010661	2	2	22	1	0	0	0	0	0	0	0	1	11943	1490	52	3		3	PION	7	77010661	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	769784	77010661	82128002	1676	4577											
RSBN1L	222194	hgsc.bcm.edu	37	chr7	77325919	77325919	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gttctctgtccgccaagaagGtccggactgaggagaagaag	11	7	14	9	2	1	4	0	1	1	3	4	6	3	5	3	3	0	1	3	3	4	1	rs79095281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:77325919G>A	ENST00000334955.8	+	1	160	c.133G>A	c.(133-135)Gtc>Atc	p.V45I	RSBN1L-AS1_ENST00000440088.1_lincRNA|RSBN1L_ENST00000445288.1_5'Flank	NM_198467.2	NP_940869.2	Q6PCB5	RSBNL_HUMAN	round spermatid basic protein 1-like	45						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						CGCCAAGAAGGTCCGGACTGA	0.677													G|||	139	0.0277556	0.1029	0.0043	5008	,	,		14173	0.0		0.0	False		,,,				2504	0.0				p.V45I		Atlas-SNP	.											.	RSBN1L	74	.	0			c.G133A						PASS	.	G	ILE/VAL	329,3439		19,291,1574	34	45	41		133	2.1	1	7	dbSNP_131	41	3,8221		0,3,4109	yes	missense	RSBN1L	NM_198467.2	29	19,294,5683	AA,AG,GG		0.0365,8.7314,2.7685	benign	45/847	77325919	332,11660	1884	4112	5996	SO:0001583	missense	222194	exon1			AAGAAGGTCCGGA	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.133G>A	7.37:g.77325919G>A	ENSP00000334040:p.Val45Ile	60	0	0		67	39	0.58209	NM_198467	C9K0P1|Q6ZS58|Q6ZVI9|Q86X48	Missense_Mutation	SNP	ENST00000334955.8	37	CCDS43607.1	47	0.02152014652014652	45	0.09146341463414634	2	0.0055248618784530384	0	0.0	0	0.0	G	12.96	2.095669	0.36952	0.087314	3.65E-4	ENSG00000187257	ENST00000334955	.	.	.	4.02	2.14	0.27477	.	0.551396	0.14695	N	0.303893	T	0.01124	0.0037	N	0.14661	0.345	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.03184	-1.1063	9	0.19147	T	0.46	-2.8559	7.0249	0.24934	0.2286:0.0:0.7714:0.0	.	45	Q6PCB5	RSBNL_HUMAN	I	45	.	ENSP00000334040:V45I	V	+	1	0	RSBN1L	77163855	0.998000	0.40836	0.998000	0.56505	0.557000	0.35523	0.398000	0.20899	0.421000	0.25980	0.313000	0.20887	GTC	G|0.973;A|0.027	0.027	strong		0.677	RSBN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340455.3	NM_198467		A	77325919	G	A	77325919	3	1	22	1	0	0	0	0	1	0	0	0	13712	1261	44	2	135	2	RSBN1L	7	77325919	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	315258	77325919	81812744	1677	4578											
GNAI1	2770	hgsc.bcm.edu	37	chr7	79828573	79828573	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caactctttgtgctagctggAgctgctgaagaaggctttat	9	13	11	8	0	1	2	0	1	1	1	1	3	1	3	0	2	5	5	0	2	5	4	rs6970347	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:79828573A>G	ENST00000351004.3	+	4	709	c.336A>G	c.(334-336)ggA>ggG	p.G112G	GNAI1_ENST00000457358.2_Silent_p.G60G	NM_002069.5	NP_002060.4	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	112					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						TGCTAGCTGGAGCTGCTGAAG	0.413													A|||	92	0.0183706	0.0673	0.0043	5008	,	,		18019	0.0		0.0	False		,,,				2504	0.0				p.G112G		Atlas-SNP	.											.	GNAI1	44	.	0			c.A336G						PASS	.	A		284,4122	157.8+/-190.6	14,256,1933	116	110	112		336	-3	1	7	dbSNP_116	112	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	GNAI1	NM_002069.5		14,258,6231	GG,GA,AA		0.0233,6.4458,2.199		112/355	79828573	286,12720	2203	4300	6503	SO:0001819	synonymous_variant	2770	exon4			AGCTGGAGCTGCT	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.336A>G	7.37:g.79828573A>G		122	0	0		78	40	0.512821	NM_002069	A8KA88|B4E2V1|C9J3A4|P04898|P11015|P31871|Q5U074|Q8TAN5|Q9UGA4	Silent	SNP	ENST00000351004.3	37	CCDS5595.1																																																																																			A|0.982;G|0.018	0.018	strong		0.413	GNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253254.1	NM_002069		G	79828573	A	G	79828573	2	3	22	1	0	0	0	0	0	0	0	1	6512	291	11	3		3	GNAI1	7	79828573	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2502654	79828573	79310090	1678	4579											
CD36	948	hgsc.bcm.edu	37	chr7	80300449	80300449	+	Nonsense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaaaaaattgtacatcataTggtgtgctagacatcagcaa	16	11	7	7	0	3	1	3	0	0	1	3	1	3	1	0	1	3	3	0	1	7	4	rs3211938	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:80300449T>G	ENST00000435819.1	+	13	1659	c.975T>G	c.(973-975)taT>taG	p.Y325*	CD36_ENST00000534394.1_Nonsense_Mutation_p.Y249*|CD36_ENST00000544133.1_Intron|CD36_ENST00000309881.7_Nonsense_Mutation_p.Y325*|CD36_ENST00000538969.1_Nonsense_Mutation_p.Y265*|CD36_ENST00000394788.3_Nonsense_Mutation_p.Y325*|CD36_ENST00000433696.2_Nonsense_Mutation_p.Y286*|CD36_ENST00000447544.2_Nonsense_Mutation_p.Y325*|CD36_ENST00000432207.1_Nonsense_Mutation_p.Y325*			P16671	CD36_HUMAN	CD36 molecule (thrombospondin receptor)	325					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						GTACATCATATGGTGTGCTAG	0.363													T|||	155	0.0309505	0.1157	0.0029	5008	,	,		16040	0.0		0.0	False		,,,				2504	0.0				p.Y325X		Atlas-SNP	.											.	CD36	185	.	0			c.T975G	GRCh37	CM001647	CD36	M	rs3211938	PASS	.	T	stop/TYR,stop/TYR,stop/TYR,stop/TYR,stop/TYR	361,4045	182.6+/-210.3	16,329,1858	76	75	75	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	975,975,975,975,975	-0.8	0.5	7	dbSNP_105	75	2,8598	1.2+/-3.3	0,2,4298	yes	stop-gained,stop-gained,stop-gained,stop-gained,stop-gained	CD36	NM_000072.3,NM_001001547.2,NM_001001548.2,NM_001127443.1,NM_001127444.1	,,,,	16,331,6156	GG,GT,TT		0.0233,8.1934,2.791	,,,,	325/473,325/473,325/473,325/473,325/473	80300449	363,12643	2203	4300	6503	SO:0001587	stop_gained	948	exon8			ATCATATGGTGTG	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.975T>G	7.37:g.80300449T>G	ENSP00000399421:p.Tyr325*	49	0	0		47	47	1	NM_001127444	D9IX66|D9IX67|D9IX68|D9IX69|Q13966|Q16093|Q8TCV7|Q9BPZ8|Q9BQC2|Q9BZM8|Q9BZN3|Q9BZN4|Q9BZN5	Nonsense_Mutation	SNP	ENST00000435819.1	37	CCDS34673.1	72	0.03296703296703297	72	0.14634146341463414	0	0.0	0	0.0	0	0.0	T	35	5.563074	0.96527	0.081934	2.33E-4	ENSG00000135218	ENST00000435819;ENST00000309881;ENST00000534394;ENST00000394788;ENST00000447544;ENST00000432207;ENST00000419819;ENST00000538969;ENST00000433696	.	.	.	5.57	-0.823	0.10815	.	0.163457	0.53938	D	0.000054	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	-13.6549	9.8443	0.41017	0.0:0.3443:0.0:0.6557	rs3211938;rs10372565;rs17154273;rs3211938	.	.	.	X	325;325;249;325;325;325;325;265;286	.	.	Y	+	3	2	CD36	80138385	0.999000	0.42202	0.528000	0.27938	0.976000	0.68499	0.485000	0.22324	-0.378000	0.07918	0.397000	0.26171	TAT	T|0.967;G|0.033	0.033	strong		0.363	CD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339767.6	NM_001001547		G	80300449	T	G	80300449	4	3	22	1	0	0	0	0	0	1	0	0	3009	1471	51	5	1005	5	CD36	7	80300449	Nonsense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	471876	80300449	78838214	1679	4580											
HGF	3082	hgsc.bcm.edu	37	chr7	81388042	81388042	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggtcaaattcatggccaaaTtcttttttcactccacttga	11	15	5	10	0	4	1	3	1	1	0	5	1	5	1	2	2	0	0	2	2	2	6	rs5745635	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:81388042T>C	ENST00000222390.5	-	3	559	c.333A>G	c.(331-333)gaA>gaG	p.E111E	HGF_ENST00000423064.2_Silent_p.E111E|HGF_ENST00000457544.2_Silent_p.E111E|HGF_ENST00000354224.6_Silent_p.E111E|HGF_ENST00000444829.2_Silent_p.E111E|HGF_ENST00000453411.1_Silent_p.E111E|HGF_ENST00000453018.1_Silent_p.E8E	NM_000601.4	NP_000592.3	P14210	HGF_HUMAN	hepatocyte growth factor (hepapoietin A; scatter factor)	111	PAN. {ECO:0000255|PROSITE- ProRule:PRU00315}.				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						CATGGCCAAATTCTTTTTTCA	0.313													C|||	518	0.103435	0.3139	0.0317	5008	,	,		14939	0.0079		0.006	False		,,,				2504	0.0685				p.E111E		Atlas-SNP	.											HGF,spleen,lymphoid_neoplasm,-2,1	HGF	171	1	0			c.A333G						PASS	.	C	,,,,	1261,3145	702.0+/-406.8	174,913,1116	108	107	107		333,333,333,333,333	-3	0.1	7	dbSNP_114	107	92,8504	814.1+/-407.0	1,90,4207	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HGF	NM_000601.4,NM_001010931.1,NM_001010932.1,NM_001010933.1,NM_001010934.1	,,,,	175,1003,5323	CC,CT,TT		1.0703,28.6201,10.4061	,,,,	111/729,111/291,111/724,111/286,111/211	81388042	1353,11649	2203	4298	6501	SO:0001819	synonymous_variant	3082	exon3			GCCAAATTCTTTT		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.333A>G	7.37:g.81388042T>C		159	0	0		148	148	1	NM_000601	A1L3U6|Q02935|Q13494|Q14519|Q3KRB2|Q8TCE2|Q9BYL9|Q9BYM0|Q9UDU6	Silent	SNP	ENST00000222390.5	37	CCDS5597.1																																																																																			T|0.896;C|0.104	0.104	strong		0.313	HGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253315.2	NM_000601		C	81388042	T	C	81388042	2	2	22	1	0	0	0	0	0	0	0	1	7094	1490	52	3		3	HGF	7	81388042	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1087593	81388042	77750621	1680	4581											
PCLO	27445	hgsc.bcm.edu	37	chr7	82585803	82585803	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tctctttatggtccttgctgGaaggaatatcttgttggcta	7	17	10	7	0	2	0	0	0	2	0	4	2	3	2	1	4	1	3	1	4	5	7	rs114445550	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:82585803G>C	ENST00000333891.9	-	5	4803	c.4466C>G	c.(4465-4467)tCc>tGc	p.S1489C	PCLO_ENST00000423517.2_Missense_Mutation_p.S1489C	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						GTCCTTGCTGGAAGGAATATC	0.358													G|||	19	0.00379393	0.0144	0.0	5008	,	,		21243	0.0		0.0	False		,,,				2504	0.0				p.S1489C		Atlas-SNP	.											.	PCLO	1506	.	0			c.C4466G						PASS	.	G	CYS/SER,CYS/SER	50,3644		0,50,1797	112	103	106		4466,4466	3.6	0	7	dbSNP_132	106	0,8172		0,0,4086	yes	missense,missense	PCLO	NM_014510.2,NM_033026.5	112,112	0,50,5883	CC,CG,GG		0.0,1.3535,0.4214	possibly-damaging,possibly-damaging	1489/4936,1489/5143	82585803	50,11816	1847	4086	5933	SO:0001583	missense	27445	exon5			TTGCTGGAAGGAA	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.4466C>G	7.37:g.82585803G>C	ENSP00000334319:p.Ser1489Cys	120	0	0		139	71	0.510791	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	0.586	-0.834971	0.02713	0.013535	0.0	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.17370	2.28;2.28	5.43	3.57	0.40892	.	.	.	.	.	T	0.17408	0.0418	L	0.47716	1.5	0.09310	N	0.999996	P;P	0.49253	0.921;0.921	P;P	0.50378	0.518;0.639	T	0.04041	-1.0982	9	0.87932	D	0	.	10.4646	0.44600	0.0726:0.1355:0.7919:0.0	.	1489;1489	Q9Y6V0-5;Q9Y6V0-6	.;.	C	1420;1489;1489	ENSP00000334319:S1489C;ENSP00000388393:S1489C	ENSP00000334319:S1489C	S	-	2	0	PCLO	82423739	0.976000	0.34144	0.012000	0.15200	0.080000	0.17528	3.139000	0.50577	1.265000	0.44215	0.650000	0.86243	TCC	G|0.997;C|0.003	0.003	strong		0.358	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		C	82585803	G	C	82585803	3	2	22	1	0	0	0	0	1	0	0	0	11592	1174	41	4	11063	4	PCLO	7	82585803	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1197761	82585803	76552860	1681	4582											
PCLO	27445	hgsc.bcm.edu	37	chr7	82764924	82764924	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggaactggagccagatcccCgcctagagctcttttcattt	8	11	9	13	2	2	2	1	0	1	2	3	4	3	4	4	2	3	1	4	2	2	4	rs138200846	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:82764924C>T	ENST00000333891.9	-	3	2279	c.1942G>A	c.(1942-1944)Ggg>Agg	p.G648R	PCLO_ENST00000423517.2_Missense_Mutation_p.G648R	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						GCCAGATCCCCGCCTAGAGCT	0.453													C|||	35	0.00698882	0.0242	0.0043	5008	,	,		14124	0.0		0.0	False		,,,				2504	0.0				p.G648R		Atlas-SNP	.											.	PCLO	1506	.	0			c.G1942A						PASS	.	C	ARG/GLY,ARG/GLY	88,3802		0,88,1857	57	57	57		1942,1942	5.3	1	7	dbSNP_134	57	1,8259		0,1,4129	yes	missense,missense	PCLO	NM_014510.2,NM_033026.5	125,125	0,89,5986	TT,TC,CC		0.0121,2.2622,0.7325	probably-damaging,probably-damaging	648/4936,648/5143	82764924	89,12061	1945	4130	6075	SO:0001583	missense	27445	exon3			GATCCCCGCCTAG	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.1942G>A	7.37:g.82764924C>T	ENSP00000334319:p.Gly648Arg	159	0	0		155	83	0.535484	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	10	0.004578754578754579	8	0.016260162601626018	2	0.0055248618784530384	0	0.0	0	0.0	C	7.181	0.589683	0.13812	0.022622	1.21E-4	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.17528	2.27;2.27	5.31	5.31	0.75309	.	.	.	.	.	T	0.11153	0.0272	L	0.34521	1.04	0.25271	N	0.989512	D;D	0.69078	0.997;0.997	P;P	0.50970	0.655;0.655	T	0.04481	-1.0948	9	0.87932	D	0	.	12.3476	0.55130	0.0:0.9226:0.0:0.0774	.	648;648	Q9Y6V0-5;Q9Y6V0-6	.;.	R	594;648;648	ENSP00000334319:G648R;ENSP00000388393:G648R	ENSP00000334319:G648R	G	-	1	0	PCLO	82602860	0.380000	0.25131	0.990000	0.47175	0.708000	0.40852	2.840000	0.48215	2.485000	0.83878	0.591000	0.81541	GGG	C|0.995;T|0.005	0.005	strong		0.453	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		T	82764924	C	T	82764924	3	4	22	1	0	0	0	0	1	0	0	0	11592	652	23	1	13595	1	PCLO	7	82764924	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	179121	82764924	76373739	1682	4583											
PCLO	27445	hgsc.bcm.edu	37	chr7	82785096	82785096	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgattctccccttactatGtctgcctgtttagtctgagg	6	16	8	11	0	3	2	0	2	3	0	4	2	3	2	3	1	2	1	3	1	3	5	rs61744360	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:82785096G>A	ENST00000333891.9	-	2	1198	c.861C>T	c.(859-861)gaC>gaT	p.D287D	PCLO_ENST00000423517.2_Silent_p.D287D	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						CCCTTACTATGTCTGCCTGTT	0.512													G|||	12	0.00239617	0.0068	0.0029	5008	,	,		18830	0.0		0.0	False		,,,				2504	0.001				p.D287D		Atlas-SNP	.											.	PCLO	1506	.	0			c.C861T						PASS	.	G	,	25,4119		0,25,2047	122	111	114		861,861	-1	0	7	dbSNP_129	114	0,8422		0,0,4211	no	coding-synonymous,coding-synonymous	PCLO	NM_014510.2,NM_033026.5	,	0,25,6258	AA,AG,GG		0.0,0.6033,0.1989	,	287/4936,287/5143	82785096	25,12541	2072	4211	6283	SO:0001819	synonymous_variant	27445	exon2			TACTATGTCTGCC	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.861C>T	7.37:g.82785096G>A		264	1	0.00378788		270	125	0.462963	NM_014510		Silent	SNP	ENST00000333891.9	37	CCDS47630.1																																																																																			G|0.998;A|0.002	0.002	strong		0.512	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82785096	G	A	82785096	2	1	22	1	0	0	0	0	0	0	0	1	11592	1368	48	2		2	PCLO	7	82785096	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	20172	82785096	76353567	1683	4584											
SEMA3E	9723	hgsc.bcm.edu	37	chr7	83035289	83035289	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaaaatatgtgtcaattccAttcattcctggtactgagca	12	14	6	9	0	3	1	3	1	0	0	5	1	5	1	2	1	2	2	2	1	5	5	rs28505908	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:83035289A>G	ENST00000307792.3	-	8	1367	c.900T>C	c.(898-900)aaT>aaC	p.N300N	SEMA3E_ENST00000427262.1_Silent_p.N240N	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	300	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)				TGTCAATTCCATTCATTCCTG	0.353													A|||	60	0.0119808	0.0454	0.0	5008	,	,		18888	0.0		0.0	False		,,,				2504	0.0				p.N300N		Atlas-SNP	.											.	SEMA3E	125	.	0			c.T900C						PASS	.	A	,	154,4252	106.0+/-144.5	1,152,2050	159	145	150		720,900	3.3	1	7	dbSNP_125	150	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	SEMA3E	NM_001178129.1,NM_012431.2	,	1,154,6348	GG,GA,AA		0.0233,3.4952,1.1994	,	240/716,300/776	83035289	156,12850	2203	4300	6503	SO:0001819	synonymous_variant	9723	exon8			AATTCCATTCATT	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.900T>C	7.37:g.83035289A>G		89	0	0		104	51	0.490385	NM_012431	B4E1P1|Q75M94|Q75M97	Silent	SNP	ENST00000307792.3	37	CCDS34674.1																																																																																			A|0.987;G|0.013	0.013	strong		0.353	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431		G	83035289	A	G	83035289	2	3	22	1	0	0	0	0	0	0	0	1	14043	214	8	3		3	SEMA3E	7	83035289	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	250193	83035289	76103374	1684	4585											
SEMA3D	223117	hgsc.bcm.edu	37	chr7	84697540	84697540	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agcaaaaggctgctgaggatCgaaaggacatttcagtctgc	13	8	12	8	1	2	1	1	1	1	0	3	4	2	3	0	3	3	3	0	3	3	1	rs148351346	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:84697540C>T	ENST00000284136.6	-	5	599	c.556G>A	c.(556-558)Gat>Aat	p.D186N	SEMA3D_ENST00000444867.1_Missense_Mutation_p.D186N	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	186	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						TGCTGAGGATCGAAAGGACAT	0.343													C|||	2	0.000399361	0.0015	0.0	5008	,	,		17192	0.0		0.0	False		,,,				2504	0.0				p.D186N	Ovarian(63;442 1191 17318 29975 31528)	Atlas-SNP	.											.	SEMA3D	177	.	0			c.G556A						PASS	.	C	ASN/ASP	13,4393	20.2+/-43.8	0,13,2190	103	102	102		556	5.5	1	7	dbSNP_134	102	0,8600		0,0,4300	yes	missense	SEMA3D	NM_152754.2	23	0,13,6490	TT,TC,CC		0.0,0.2951,0.1	probably-damaging	186/778	84697540	13,12993	2203	4300	6503	SO:0001583	missense	223117	exon5			GAGGATCGAAAGG	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.556G>A	7.37:g.84697540C>T	ENSP00000284136:p.Asp186Asn	99	0	0		98	46	0.469388	NM_152754	A6NK46|Q6UW77|Q8NCQ1	Missense_Mutation	SNP	ENST00000284136.6	37	CCDS34676.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	33	5.213062	0.95069	0.002951	0.0	ENSG00000153993	ENST00000284136;ENST00000444867	T;T	0.15017	2.46;2.46	5.49	5.49	0.81192	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.28499	0.0705	M	0.72479	2.2	0.80722	D	1	D;P	0.59357	0.985;0.769	P;B	0.54238	0.746;0.404	T	0.01276	-1.1398	10	0.40728	T	0.16	.	19.7307	0.96181	0.0:1.0:0.0:0.0	.	186;186	C9JYT6;O95025	.;SEM3D_HUMAN	N	186	ENSP00000284136:D186N;ENSP00000401366:D186N	ENSP00000284136:D186N	D	-	1	0	SEMA3D	84535476	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.435000	0.80391	2.707000	0.92482	0.655000	0.94253	GAT	C|0.999;T|0.001	0.001	strong		0.343	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754		T	84697540	C	T	84697540	3	4	22	1	0	0	0	0	1	0	0	0	14042	884	31	1	1829	1	SEMA3D	7	84697540	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1662251	84697540	74441123	1685	4586											
GRM3	2913	hgsc.bcm.edu	37	chr7	86479694	86479694	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cttctcttgtaggtgcagacGacaaccatgtgcatctctgt	8	13	9	11	1	2	1	0	0	2	1	4	2	2	1	1	1	3	3	1	1	2	3	rs76035289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:86479694G>A	ENST00000361669.2	+	5	3499	c.2400G>A	c.(2398-2400)acG>acA	p.T800T	GRM3_ENST00000439827.1_Missense_Mutation_p.D445N|GRM3_ENST00000394720.2_Missense_Mutation_p.D443N|GRM3_ENST00000536043.1_Silent_p.T672T|GRM3_ENST00000546348.1_Silent_p.T392T	NM_000840.2	NP_000831.2	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3	800					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)					AGGTGCAGACGACAACCATGT	0.458													G|||	68	0.0135783	0.0469	0.0058	5008	,	,		21770	0.001		0.001	False		,,,				2504	0.0				p.T800T	GBM(52;969 1098 3139 52280)	Atlas-SNP	.											.	GRM3	237	.	0			c.G2400A						PASS	.	G		178,4228	115.0+/-153.0	2,174,2027	218	151	173		2400	-11.9	0.1	7	dbSNP_131	173	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	GRM3	NM_000840.2		2,181,6320	AA,AG,GG		0.0814,4.0399,1.4224		800/880	86479694	185,12821	2203	4300	6503	SO:0001819	synonymous_variant	2913	exon5			GCAGACGACAACC		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.2400G>A	7.37:g.86479694G>A		162	0	0		156	82	0.525641	NM_000840	Q2PNZ6|Q75MV4|Q75N17|Q86YG6|Q8TBH9	Silent	SNP	ENST00000361669.2	37	CCDS5600.1	30	0.013736263736263736	29	0.05894308943089431	0	0.0	0	0.0	1	0.0013192612137203166	G	9.085	1.000326	0.19121	0.040399	8.14E-4	ENSG00000198822	ENST00000439827;ENST00000394720	D;D	0.85773	-2.03;-2.03	5.97	-11.9	0.00025	.	.	.	.	.	T	0.21841	0.0526	.	.	.	0.09310	N	0.999991	B	0.02656	0.0	B	0.01281	0.0	T	0.49799	-0.8901	8	0.66056	D	0.02	.	2.9374	0.05819	0.4424:0.2623:0.1692:0.1262	.	445	G5E9K2	.	N	445;443	ENSP00000398767:D445N;ENSP00000378209:D443N	ENSP00000378209:D443N	D	+	1	0	GRM3	86317630	0.000000	0.05858	0.132000	0.22025	0.766000	0.43426	-1.862000	0.01653	-2.006000	0.00958	-1.779000	0.00650	GAC	G|0.985;A|0.015	0.015	strong		0.458	GRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253362.2			A	86479694	G	A	86479694	2	1	22	1	0	0	0	0	0	0	0	1	6807	1045	37	1		1	GRM3	7	86479694	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1782154	86479694	72658969	1686	4587											
CROT	54677	hgsc.bcm.edu	37	chr7	86986863	86986863	+	Intron	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataaggggtcttgatccagaTgctaagagagggttcttgga	11	11	14	5	0	2	3	0	1	2	2	3	5	3	4	1	4	1	2	1	4	2	5	rs75642989	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:86986863T>C	ENST00000331536.3	+	4	300				CROT_ENST00000412227.2_Intron|CROT_ENST00000442291.1_Intron|CROT_ENST00000419147.2_Silent_p.D52D	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)	ttgatccagatgctaagagag	0.483													C|||	89	0.0177716	0.0658	0.0029	5008	,	,		19249	0.0		0.0	False		,,,				2504	0.0				p.D52D		Atlas-SNP	.											.	CROT	81	.	0			c.T156C						PASS	.	C	,	61,1323		2,57,633	146	124	130		156,	0.2	0	7	dbSNP_132	130	1,3181		0,1,1590	no	coding-synonymous,intron	CROT	NM_001143935.1,NM_021151.3	,	2,58,2223	CC,CT,TT		0.0314,4.4075,1.3579	,	52/641,	86986863	62,4504	692	1591	2283	SO:0001627	intron_variant	54677	exon4			TCCAGATGCTAAG		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.116-1659T>C	7.37:g.86986863T>C		59	0	0		72	37	0.513889	NM_001143935	A4D1D6|E7EQF2|Q86V17|Q8IUW9|Q9Y6I2	Silent	SNP	ENST00000331536.3	37	CCDS5604.1																																																																																			T|0.986;C|0.014	0.014	strong		0.483	CROT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253485.1	NM_021151		C	86986863	T	C	86986863	1	2	22	0	1	0	0	0	0	0	0	0	3896	1461	51	3		3	CROT	7	86986863	Intron	SNP	T	TCGA-G8-6324-01A-11D-2210-10	507169	86986863	72151800	1687	4588											
ABCB1	5243	hgsc.bcm.edu	37	chr7	87179256	87179256	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gacattttcacggccatagcGaatgttttcagctatcgtgg	9	13	10	9	3	2	0	2	0	0	0	3	2	2	0	1	2	2	2	1	2	3	6	rs142600685		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:87179256G>A	ENST00000265724.3	-	14	1882	c.1465C>T	c.(1465-1467)Cgc>Tgc	p.R489C	ABCB1_ENST00000543898.1_Missense_Mutation_p.R425C	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	489	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)	CGGCCATAGCGAATGTTTTCA	0.428													G|||	1	0.000199681	0.0008	0.0	5008	,	,		20930	0.0		0.0	False		,,,				2504	0.0				p.R489C		Atlas-SNP	.											ABCB1,NS,carcinoma,0,2	ABCB1	263	2	0			c.C1465T						PASS	.	G	CYS/ARG	6,4400	11.4+/-27.6	0,6,2197	236	218	224		1465	5.3	1	7	dbSNP_134	224	0,8600		0,0,4300	yes	missense	ABCB1	NM_000927.4	180	0,6,6497	AA,AG,GG		0.0,0.1362,0.0461	probably-damaging	489/1281	87179256	6,13000	2203	4300	6503	SO:0001583	missense	5243	exon14			CATAGCGAATGTT	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.1465C>T	7.37:g.87179256G>A	ENSP00000265724:p.Arg489Cys	139	0	0		136	57	0.419118	NM_000927	A8K294|B5AK60|Q12755|Q14812	Missense_Mutation	SNP	ENST00000265724.3	37	CCDS5608.1	.	.	.	.	.	.	.	.	.	.	G	19.60	3.858540	0.71834	0.001362	0.0	ENSG00000085563	ENST00000543174;ENST00000265724;ENST00000543898	D;D	0.90955	-2.76;-2.76	6.16	5.29	0.74685	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.048148	0.85682	D	0.000000	D	0.93074	0.7795	M	0.64260	1.97	0.80722	D	1	B;P	0.49862	0.256;0.929	B;P	0.56216	0.116;0.794	D	0.93216	0.6604	10	0.54805	T	0.06	-11.5298	15.7393	0.77876	0.0651:0.0:0.9349:0.0	.	425;489	B5AK60;P08183	.;MDR1_HUMAN	C	270;489;425	ENSP00000265724:R489C;ENSP00000444095:R425C	ENSP00000265724:R489C	R	-	1	0	ABCB1	87017192	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	2.779000	0.47734	1.622000	0.50330	0.650000	0.86243	CGC	G|0.999;A|0.001	0.001	strong		0.428	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927		A	87179256	G	A	87179256	3	1	22	1	0	0	0	0	1	0	0	0	40	1058	37	1	2441	1	ABCB1	7	87179256	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	192393	87179256	71959407	1688	4589											
ZNF804B	219578	hgsc.bcm.edu	37	chr7	88963401	88963401	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aagcaaatgcttccttcagcCcaccaaacatttacaaccat	15	9	3	14	0	1	0	1	0	0	0	2	0	2	0	4	0	6	2	4	0	5	4	rs141118086	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:88963401C>T	ENST00000333190.4	+	4	1714	c.1105C>T	c.(1105-1107)Cca>Tca	p.P369S		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	369							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)			TTCCTTCAGCCCACCAAACAT	0.393										HNSCC(36;0.09)			C|||	81	0.0161741	0.0575	0.0058	5008	,	,		18756	0.0		0.001	False		,,,				2504	0.0				p.P369S		Atlas-SNP	.											.	ZNF804B	322	.	0			c.C1105T						PASS	.	C	SER/PRO	239,4165	136.1+/-172.1	7,225,1970	43	48	46		1105	3.1	0.8	7	dbSNP_134	46	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ZNF804B	NM_181646.2	74	7,226,6269	TT,TC,CC		0.0116,5.4269,1.8456	probably-damaging	369/1350	88963401	240,12764	2202	4300	6502	SO:0001583	missense	219578	exon4			TTCAGCCCACCAA	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.1105C>T	7.37:g.88963401C>T	ENSP00000329638:p.Pro369Ser	87	0	0		83	34	0.409639	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	26	0.011904761904761904	24	0.04878048780487805	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	11.61	1.688835	0.29962	0.054269	1.16E-4	ENSG00000182348	ENST00000333190	T	0.05199	3.48	4.86	3.07	0.35406	.	0.639011	0.14589	N	0.310354	T	0.01092	0.0036	M	0.67953	2.075	0.09310	N	1	B	0.34372	0.451	B	0.23150	0.044	T	0.17623	-1.0363	10	0.41790	T	0.15	-1.6547	11.2317	0.48916	0.0:0.8527:0.0:0.1473	.	369	A4D1E1	Z804B_HUMAN	S	369	ENSP00000329638:P369S	ENSP00000329638:P369S	P	+	1	0	ZNF804B	88801337	0.052000	0.20516	0.793000	0.32043	0.997000	0.91878	1.203000	0.32284	0.670000	0.31165	0.655000	0.94253	CCA	C|0.986;T|0.014	0.014	strong		0.393	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		T	88963401	C	T	88963401	3	4	22	1	0	0	0	0	1	0	0	0	18186	623	22	2	1119	2	ZNF804B	7	88963401	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1784145	88963401	70175262	1689	4590											
ZNF804B	219578	hgsc.bcm.edu	37	chr7	88964162	88964162	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagttctaaatgatatagaTgaggacctatcttttccttc	11	15	7	8	0	2	3	0	2	2	1	4	4	3	4	2	1	0	2	2	1	5	8	rs150870900	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:88964162T>G	ENST00000333190.4	+	4	2475	c.1866T>G	c.(1864-1866)gaT>gaG	p.D622E		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	622							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)			ATGATATAGATGAGGACCTAT	0.383										HNSCC(36;0.09)			T|||	31	0.0061901	0.0204	0.0058	5008	,	,		19603	0.0		0.0	False		,,,				2504	0.0				p.D622E		Atlas-SNP	.											.	ZNF804B	322	.	0			c.T1866G						PASS	.	T	GLU/ASP	63,4343	59.3+/-96.0	0,63,2140	74	78	77		1866	-1.2	0	7	dbSNP_134	77	0,8600		0,0,4300	yes	missense	ZNF804B	NM_181646.2	45	0,63,6440	GG,GT,TT		0.0,1.4299,0.4844	benign	622/1350	88964162	63,12943	2203	4300	6503	SO:0001583	missense	219578	exon4			TATAGATGAGGAC	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.1866T>G	7.37:g.88964162T>G	ENSP00000329638:p.Asp622Glu	83	0	0		102	46	0.45098	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	T	0.048	-1.259050	0.01445	0.014299	0.0	ENSG00000182348	ENST00000333190	T	0.04454	3.62	5.49	-1.24	0.09435	.	0.337088	0.29376	N	0.012335	T	0.01189	0.0039	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.46205	-0.9208	10	0.02654	T	1	-6.4004	6.3638	0.21443	0.0:0.1906:0.325:0.4844	.	622	A4D1E1	Z804B_HUMAN	E	622	ENSP00000329638:D622E	ENSP00000329638:D622E	D	+	3	2	ZNF804B	88802098	0.211000	0.23529	0.002000	0.10522	0.037000	0.13140	-0.303000	0.08210	-0.334000	0.08463	0.533000	0.62120	GAT	T|0.996;G|0.004	0.004	strong		0.383	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		G	88964162	T	G	88964162	3	3	22	1	0	0	0	0	1	0	0	0	18186	1461	51	5	1880	5	ZNF804B	7	88964162	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	761	88964162	70174501	1690	4591											
ZNF804B	219578	hgsc.bcm.edu	37	chr7	88965040	88965040	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaaccacagaatcaaacaCtgcagaaggagagaggaccc	19	2	10	10	0	1	4	1	0	0	4	1	7	1	6	2	2	3	1	2	2	4	0	rs56948780	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:88965040C>T	ENST00000333190.4	+	4	3353	c.2744C>T	c.(2743-2745)aCt>aTt	p.T915I		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	915			T -> I (in dbSNP:rs56948780).				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)			GAATCAAACACTGCAGAAGGA	0.433										HNSCC(36;0.09)			T|||	199	0.0397364	0.1445	0.0101	5008	,	,		18290	0.0		0.001	False		,,,				2504	0.0				p.T915I		Atlas-SNP	.											.	ZNF804B	322	.	0			c.C2744T						PASS	.	T	ILE/THR	522,3884	769.0+/-413.6	33,456,1714	93	99	97		2744	2.7	0	7	dbSNP_129	97	7,8593	818.2+/-406.9	0,7,4293	yes	missense	ZNF804B	NM_181646.2	89	33,463,6007	TT,TC,CC		0.0814,11.8475,4.0674	benign	915/1350	88965040	529,12477	2203	4300	6503	SO:0001583	missense	219578	exon4			CAAACACTGCAGA	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.2744C>T	7.37:g.88965040C>T	ENSP00000329638:p.Thr915Ile	135	0	0		130	65	0.5	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	67	0.030677655677655676	63	0.12804878048780488	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	T	0.047	-1.263638	0.01445	0.118475	8.14E-4	ENSG00000182348	ENST00000333190	T	0.04406	3.63	5.02	2.67	0.31697	.	1.602880	0.03170	N	0.170660	T	0.00039	0.0001	N	0.01168	-0.975	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41875	-0.9484	10	0.02654	T	1	3.734	4.3373	0.11092	0.1723:0.2578:0.0:0.5699	rs56948780	915	A4D1E1	Z804B_HUMAN	I	915	ENSP00000329638:T915I	ENSP00000329638:T915I	T	+	2	0	ZNF804B	88802976	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	0.929000	0.28844	0.092000	0.17331	-0.254000	0.11334	ACT	C|0.964;T|0.036	0.036	strong		0.433	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		T	88965040	C	T	88965040	3	4	22	1	0	0	0	0	1	0	0	0	18186	565	20	2	2758	2	ZNF804B	7	88965040	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	878	88965040	70173623	1691	4592											
ZNF804B	219578	hgsc.bcm.edu	37	chr7	88965992	88965992	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catagcagtcacctccctatTgctcatctacatcctctttc	8	14	3	16	0	4	0	2	0	2	0	7	0	6	0	3	0	3	2	3	0	3	5	rs115968745	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:88965992T>G	ENST00000333190.4	+	4	4305	c.3696T>G	c.(3694-3696)atT>atG	p.I1232M		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	1232							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)			ACCTCCCTATTGCTCATCTAC	0.468										HNSCC(36;0.09)			T|||	32	0.00638978	0.0212	0.0058	5008	,	,		20365	0.0		0.0	False		,,,				2504	0.0				p.I1232M		Atlas-SNP	.											.	ZNF804B	322	.	0			c.T3696G						PASS	.	T	MET/ILE	63,4343	59.3+/-96.0	0,63,2140	209	180	190		3696	-9.7	0.4	7	dbSNP_132	190	0,8600		0,0,4300	yes	missense	ZNF804B	NM_181646.2	10	0,63,6440	GG,GT,TT		0.0,1.4299,0.4844	possibly-damaging	1232/1350	88965992	63,12943	2203	4300	6503	SO:0001583	missense	219578	exon4			CCCTATTGCTCAT	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.3696T>G	7.37:g.88965992T>G	ENSP00000329638:p.Ile1232Met	169	0	0		193	93	0.481865	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	T	8.308	0.821452	0.16678	0.014299	0.0	ENSG00000182348	ENST00000333190	T	0.05319	3.46	4.84	-9.68	0.00528	.	0.284991	0.30611	N	0.009243	T	0.02342	0.0072	L	0.51422	1.61	0.09310	N	1	D	0.56035	0.974	P	0.48030	0.564	T	0.00807	-1.1558	10	0.56958	D	0.05	-13.7335	4.6179	0.12435	0.0977:0.4312:0.0933:0.3778	.	1232	A4D1E1	Z804B_HUMAN	M	1232	ENSP00000329638:I1232M	ENSP00000329638:I1232M	I	+	3	3	ZNF804B	88803928	0.240000	0.23847	0.392000	0.26245	0.014000	0.08584	-0.152000	0.10159	-1.527000	0.01758	-0.899000	0.02877	ATT	T|0.996;G|0.004	0.004	strong		0.468	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		G	88965992	T	G	88965992	3	3	22	1	0	0	0	0	1	0	0	0	18186	1800	63	5	3710	5	ZNF804B	7	88965992	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	952	88965992	70172671	1692	4593											
FZD1	8321	hgsc.bcm.edu	37	chr7	90895944	90895944	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tacgctatcccctgccctcaCctccaggcgggcggaggcgc	5	6	12	18	4	1	0	1	0	0	0	3	1	3	1	5	4	2	1	5	4	2	2	rs2232161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:90895944C>T	ENST00000287934.2	+	1	2162	c.1749C>T	c.(1747-1749)caC>caT	p.H583H		NM_003505.1	NP_003496.1	Q9UP38	FZD1_HUMAN	frizzled class receptor 1	583					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)			CCTGCCCTCACCTCCAGGCGG	0.637													C|||	85	0.0169728	0.0605	0.0072	5008	,	,		13904	0.0		0.0	False		,,,				2504	0.0				p.H583H		Atlas-SNP	.											FZD1,NS,carcinoma,0,2	FZD1	64	2	0			c.C1749T						PASS	.	C		238,4168	130.2+/-166.9	9,220,1974	30	28	29		1749	2.9	1	7	dbSNP_98	29	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FZD1	NM_003505.1		9,221,6273	TT,TC,CC		0.0116,5.4017,1.8376		583/648	90895944	239,12767	2203	4300	6503	SO:0001819	synonymous_variant	8321	exon1			CCCTCACCTCCAG	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.1749C>T	7.37:g.90895944C>T		70	0	0		76	36	0.473684	NM_003505	A4D1E8|O94815|Q549T8	Silent	SNP	ENST00000287934.2	37	CCDS5620.1																																																																																			C|0.983;T|0.017	0.017	strong		0.637	FZD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059367.2	NM_003505		T	90895944	C	T	90895944	2	4	22	1	0	0	0	0	0	0	0	1	6136	506	18	2		2	FZD1	7	90895944	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1929952	90895944	68242719	1693	4594											
AKAP9	10142	hgsc.bcm.edu	37	chr7	91622249	91622249	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgaacaaggagcacaagaCagtccgactcatctagagat	15	7	9	10	1	3	3	1	1	2	2	4	6	4	4	1	1	2	1	1	1	4	1	rs138567837		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:91622249C>A	ENST00000359028.2	+	6	717	c.492C>A	c.(490-492)gaC>gaA	p.D164E	AKAP9_ENST00000358100.2_Missense_Mutation_p.D164E|AKAP9_ENST00000356239.3_Missense_Mutation_p.D152E|AKAP9_ENST00000394564.1_Missense_Mutation_p.D152E			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	164					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)			GAGCACAAGACAGTCCGACTC	0.388			T	BRAF	papillary thyroid								C|||	1	0.000199681	0.0008	0.0	5008	,	,		16096	0.0		0.0	False		,,,				2504	0.0				p.D152E		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.C456A						PASS	.	C	GLU/ASP,GLU/ASP	4,4402	8.1+/-20.4	0,4,2199	107	105	106		456,456	1.5	1	7	dbSNP_134	106	0,8600		0,0,4300	yes	missense,missense	AKAP9	NM_005751.4,NM_147185.2	45,45	0,4,6499	AA,AC,CC		0.0,0.0908,0.0308	benign,benign	152/3908,152/3900	91622249	4,13002	2203	4300	6503	SO:0001583	missense	10142	exon5			ACAAGACAGTCCG	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.492C>A	7.37:g.91622249C>A	ENSP00000351922:p.Asp164Glu	87	0	0		74	33	0.445946	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	9.491	1.100713	0.20552	9.08E-4	0.0	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394565;ENST00000394564;ENST00000438114	T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6	5.37	1.53	0.23141	.	0.681654	0.12148	N	0.495208	T	0.16981	0.0408	N	0.14661	0.345	0.09310	N	1	B;B;B;B	0.19817	0.013;0.01;0.039;0.005	B;B;B;B	0.15870	0.008;0.006;0.014;0.008	T	0.24584	-1.0156	10	0.30854	T	0.27	.	8.8667	0.35291	0.0:0.6341:0.0:0.3659	.	152;152;164;152	Q99996-2;Q99996-3;A4D1E4;Q6PJH3	.;.;.;.	E	152;164;164;164;164;152;103	ENSP00000348573:D152E;ENSP00000351922:D164E;ENSP00000350813:D164E;ENSP00000378065:D152E;ENSP00000391704:D103E	ENSP00000348573:D152E	D	+	3	2	AKAP9	91460185	0.943000	0.32029	0.981000	0.43875	0.717000	0.41224	0.068000	0.14531	0.061000	0.16311	-0.150000	0.13652	GAC	C|1.000;A|0.000	0.000	strong		0.388	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		A	91622249	C	A	91622249	3	1	22	1	0	0	0	0	1	0	0	0	459	477	17	4	474	4	AKAP9	7	91622249	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	726305	91622249	67516414	1694	4595											
PEX1	5189	hgsc.bcm.edu	37	chr7	92118654	92118654	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcactaatggatggtcttgtGtgaccaagtgcagtcattaa	11	13	10	7	0	3	1	2	1	1	0	3	2	3	2	1	2	1	1	1	2	3	3	rs34825053	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:92118654G>A	ENST00000248633.4	-	23	3815	c.3720C>T	c.(3718-3720)caC>caT	p.H1240H	AC007566.10_ENST00000427458.1_RNA|PEX1_ENST00000438045.1_Silent_p.H918H|PEX1_ENST00000428214.1_Silent_p.H1183H|AC007566.10_ENST00000441539.1_RNA	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1	1240					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)			ATGGTCTTGTGTGACCAAGTG	0.388													G|||	21	0.00419329	0.0151	0.0014	5008	,	,		15394	0.0		0.0	False		,,,				2504	0.0				p.H1240H		Atlas-SNP	.											.	PEX1	102	.	0			c.C3720T						PASS	.	G		71,4335	64.1+/-101.4	1,69,2133	144	115	125		3720	2.3	0.9	7	dbSNP_126	125	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PEX1	NM_000466.2		1,70,6432	AA,AG,GG		0.0116,1.6114,0.5536		1240/1284	92118654	72,12934	2203	4300	6503	SO:0001819	synonymous_variant	5189	exon23			TCTTGTGTGACCA	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.3720C>T	7.37:g.92118654G>A		122	0	0		140	61	0.435714	NM_000466	A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Silent	SNP	ENST00000248633.4	37	CCDS5627.1																																																																																			G|0.992;A|0.008	0.008	strong		0.388	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466		A	92118654	G	A	92118654	2	1	22	1	0	0	0	0	0	0	0	1	11744	1368	48	2		2	PEX1	7	92118654	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	496405	92118654	67020009	1695	4596											
CDK6	1021	hgsc.bcm.edu	37	chr7	92462572	92462572	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgaacaccttcccataggcGccctccccgatctccgccac	7	8	6	20	3	1	1	0	1	1	0	4	2	3	1	7	1	1	0	7	1	2	3	rs189208543	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:92462572G>A	ENST00000265734.4	-	2	477	c.66C>T	c.(64-66)ggC>ggT	p.G22G	CDK6_ENST00000491250.1_5'Flank|CDK6_ENST00000424848.2_Silent_p.G22G	NM_001259.6	NP_001250.1	Q00534	CDK6_HUMAN	cyclin-dependent kinase 6	22	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				astrocyte development (GO:0014002)|cell cycle arrest (GO:0007050)|cell dedifferentiation (GO:0043697)|cell division (GO:0051301)|dentate gyrus development (GO:0021542)|G1/S transition of mitotic cell cycle (GO:0000082)|generation of neurons (GO:0048699)|gliogenesis (GO:0042063)|hematopoietic stem cell differentiation (GO:0060218)|lateral ventricle development (GO:0021670)|mitotic cell cycle (GO:0000278)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular senescence (GO:2000773)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of osteoblast differentiation (GO:0045668)|Notch signaling pathway (GO:0007219)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of gene expression (GO:0010628)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of erythrocyte differentiation (GO:0045646)|regulation of gene expression (GO:0010468)|response to virus (GO:0009615)|T cell differentiation in thymus (GO:0033077)|type B pancreatic cell development (GO:0003323)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|ruffle (GO:0001726)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|urinary_tract(1)	11	all_cancers(62;8.72e-12)|all_epithelial(64;3.65e-10)|Breast(17;0.000675)|all_lung(186;0.0392)|Lung NSC(181;0.053)|all_neural(327;0.219)|all_hematologic(106;0.237)		STAD - Stomach adenocarcinoma(4;6.16e-07)|GBM - Glioblastoma multiforme(5;1.2e-06)|all cancers(6;3.1e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			TCCCATAGGCGCCCTCCCCGA	0.706			T	MLLT10	ALL								G|||	7	0.00139776	0.0053	0.0	5008	,	,		13163	0.0		0.0	False		,,,				2504	0.0				p.G22G		Atlas-SNP	.		Dom	yes		7	7q21-q22	1021	cyclin-dependent kinase 6		L	.	CDK6	30	.	0			c.C66T						PASS	.	G	,	1,4401		0,1,2200	26	19	21		66,66	2.5	1	7		21	0,8594		0,0,4297	no	coding-synonymous,coding-synonymous	CDK6	NM_001145306.1,NM_001259.6	,	0,1,6497	AA,AG,GG		0.0,0.0227,0.0077	,	22/327,22/327	92462572	1,12995	2201	4297	6498	SO:0001819	synonymous_variant	1021	exon2			ATAGGCGCCCTCC		CCDS5628.1	7q21-q22	2011-11-08			ENSG00000105810	ENSG00000105810		"Cyclin-dependent kinases"	1777	protein-coding gene	gene with protein product		603368				1639063	Standard	NM_001259		Approved	PLSTIRE	uc010lez.3	Q00534	OTTHUMG00000131697	ENST00000265734.4:c.66C>T	7.37:g.92462572G>A		67	0	0		94	45	0.478723	NM_001259	A4D1G0	Silent	SNP	ENST00000265734.4	37	CCDS5628.1																																																																																			G|0.998;A|0.002	0.002	strong		0.706	CDK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254605.2			A	92462572	G	A	92462572	2	1	22	1	0	0	0	0	0	0	0	1	3150	1074	38	1		1	CDK6	7	92462572	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	343918	92462572	66676091	1696	4597											
CCDC132	55610	hgsc.bcm.edu	37	chr7	92926102	92926102	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgcttggaactgatttgtctAtattcaaatatgatgatttc	11	18	7	5	0	2	3	1	3	1	0	3	4	2	4	0	1	2	1	0	1	5	7	rs374290264		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:92926102A>G	ENST00000305866.5	+	15	1344	c.1216A>G	c.(1216-1218)Ata>Gta	p.I406V	CCDC132_ENST00000317751.6_Missense_Mutation_p.I137V|CCDC132_ENST00000535481.1_Missense_Mutation_p.I126V|CCDC132_ENST00000541136.1_Missense_Mutation_p.I217V|CCDC132_ENST00000544910.1_Missense_Mutation_p.I376V	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	406						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)			TGATTTGTCTATATTCAAATA	0.294																																					p.I406V		Atlas-SNP	.											.	CCDC132	136	.	0			c.A1216G						PASS	.	A	VAL/ILE	2,3616		0,2,1807	89	86	87		1216	4.8	1	7		87	0,8124		0,0,4062	no	missense	CCDC132	NM_017667.2	29	0,2,5869	GG,GA,AA		0.0,0.0553,0.017	benign	406/965	92926102	2,11740	1809	4062	5871	SO:0001583	missense	55610	exon15			TTGTCTATATTCA	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.1216A>G	7.37:g.92926102A>G	ENSP00000307666:p.Ile406Val	67	0	0		75	32	0.426667	NM_017667	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Missense_Mutation	SNP	ENST00000305866.5	37	CCDS43617.1	.	.	.	.	.	.	.	.	.	.	A	9.350	1.065336	0.20067	5.53E-4	0.0	ENSG00000004766	ENST00000305866;ENST00000544910;ENST00000541136;ENST00000535481;ENST00000317751	T	0.41065	1.01	4.82	4.82	0.62117	.	0.178206	0.47455	D	0.000238	T	0.22205	0.0535	N	0.03608	-0.345	0.27582	N	0.949545	B;B;B	0.12630	0.001;0.006;0.0	B;B;B	0.10450	0.001;0.005;0.0	T	0.10800	-1.0614	10	0.30078	T	0.28	-3.5357	14.7032	0.69168	1.0:0.0:0.0:0.0	.	126;376;406	B4DS55;F5H5U7;Q96JG6	.;.;CC132_HUMAN	V	406;376;217;126;137	ENSP00000325582:I137V	ENSP00000307666:I406V	I	+	1	0	CCDC132	92764038	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.164000	0.77533	1.951000	0.56629	0.455000	0.32223	ATA	.	.	weak		0.294	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667		G	92926102	A	G	92926102	3	3	22	1	0	0	0	0	1	0	0	0	2769	449	16	3	1316	3	CCDC132	7	92926102	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	463530	92926102	66212561	1697	4598											
COL1A2	1278	hgsc.bcm.edu	37	chr7	94028386	94028386	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccggagatagaggaccacGtggagaaagggtgtgtaatt	13	7	16	5	2	0	3	0	0	0	3	0	6	0	4	2	4	1	1	2	4	3	3	rs139528613	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:94028386G>A	ENST00000297268.6	+	4	593	c.122G>A	c.(121-123)cGt>cAt	p.R41H		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	41					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)	p.R41L(1)	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)	AGAGGACCACGTGGAGAAAGG	0.373										HNSCC(75;0.22)			G|||	15	0.00299521	0.0113	0.0	5008	,	,		15654	0.0		0.0	False		,,,				2504	0.0				p.R41H		Atlas-SNP	.											.	COL1A2	240	.	1	Substitution - Missense(1)	lung(1)	c.G122A						PASS	.	G	HIS/ARG	54,4352	54.2+/-90.2	0,54,2149	125	124	125		122	5.8	1	7	dbSNP_134	125	1,8599	1.2+/-3.3	0,1,4299	yes	missense	COL1A2	NM_000089.3	29	0,55,6448	AA,AG,GG		0.0116,1.2256,0.4229	probably-damaging	41/1367	94028386	55,12951	2203	4300	6503	SO:0001583	missense	1278	exon4			GACCACGTGGAGA	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.122G>A	7.37:g.94028386G>A	ENSP00000297268:p.Arg41His	81	0	0		76	44	0.578947	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	37	CCDS34682.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	19.99	3.928117	0.73327	0.012256	1.16E-4	ENSG00000164692	ENST00000297268	D	0.93712	-3.27	5.85	5.85	0.93711	.	.	.	.	.	D	0.93350	0.7880	L	0.55103	1.725	0.43430	D	0.995594	D;D	0.69078	0.997;0.994	D;P	0.63033	0.91;0.727	D	0.93121	0.6525	9	0.72032	D	0.01	.	14.6939	0.69107	0.071:0.0:0.929:0.0	.	41;41	B4DTF5;P08123	.;CO1A2_HUMAN	H	41	ENSP00000297268:R41H	ENSP00000297268:R41H	R	+	2	0	COL1A2	93866322	0.971000	0.33674	1.000000	0.80357	0.993000	0.82548	2.827000	0.48112	2.941000	0.99782	0.655000	0.94253	CGT	G|0.996;A|0.004	0.004	strong		0.373	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		A	94028386	G	A	94028386	3	1	22	1	0	0	0	0	1	0	0	0	3680	1145	40	1	136	1	COL1A2	7	94028386	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1102284	94028386	65110277	1698	4599											
COL1A2	1278	hgsc.bcm.edu	37	chr7	94057007	94057007	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggtggttatgactttggttaCgatggagacttctacagggc	8	13	14	6	1	1	2	0	1	1	1	1	4	1	2	0	5	2	2	0	5	3	5	rs34691365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:94057007C>T	ENST00000297268.6	+	49	3807	c.3336C>T	c.(3334-3336)taC>taT	p.Y1112Y		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	1112					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)	ACTTTGGTTACGATGGAGACT	0.547										HNSCC(75;0.22)			C|||	27	0.00539137	0.0197	0.0	5008	,	,		18009	0.0		0.001	False		,,,				2504	0.0				p.Y1112Y		Atlas-SNP	.											.	COL1A2	240	.	0			c.C3336T						PASS	.	C		58,4348	56.2+/-92.4	1,56,2146	96	97	97		3336	-4.7	0.1	7	dbSNP_126	97	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	COL1A2	NM_000089.3		1,57,6445	TT,TC,CC		0.0116,1.3164,0.4536		1112/1367	94057007	59,12947	2203	4300	6503	SO:0001819	synonymous_variant	1278	exon49			TGGTTACGATGGA	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.3336C>T	7.37:g.94057007C>T		106	0	0		132	67	0.507576	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Silent	SNP	ENST00000297268.6	37	CCDS34682.1																																																																																			C|0.995;T|0.005	0.005	strong		0.547	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089		T	94057007	C	T	94057007	2	4	22	1	0	0	0	0	0	0	0	1	3680	547	19	1		1	COL1A2	7	94057007	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	28621	94057007	65081656	1699	4600											
PON2	5445	hgsc.bcm.edu	37	chr7	95039394	95039394	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atagaaatgtgccggtccaaCagctgtgatgtcattcacac	12	10	9	10	1	2	2	2	1	0	1	3	2	3	2	2	1	3	1	2	1	3	2	rs17876152	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:95039394C>G	ENST00000222572.3	-	6	760	c.514G>C	c.(514-516)Gtt>Ctt	p.V172L	PON2_ENST00000536183.1_Missense_Mutation_p.V193L|PON2_ENST00000483292.1_5'UTR|PON2_ENST00000433091.2_Missense_Mutation_p.V160L			Q15165	PON2_HUMAN	paraoxonase 2	172			V -> L (in dbSNP:rs17876152). {ECO:0000269|Ref.5}.		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)			GCCGGTCCAACAGCTGTGATG	0.358													C|||	54	0.0107827	0.0378	0.0014	5008	,	,		15286	0.0		0.002	False		,,,				2504	0.001				p.V172L	GBM(42;803 823 13649 23368 31463)	Atlas-SNP	.											.	PON2	32	.	0			c.G514C						PASS	.	C	LEU/VAL,LEU/VAL	149,4257	104.3+/-142.8	2,145,2056	82	78	79		514,478	5	1	7	dbSNP_124	79	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	PON2	NM_000305.2,NM_001018161.1	32,32	2,147,6354	GG,GC,CC		0.0233,3.3818,1.161	benign,benign	172/355,160/343	95039394	151,12855	2203	4300	6503	SO:0001583	missense	5445	exon6			GTCCAACAGCTGT	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.514G>C	7.37:g.95039394C>G	ENSP00000222572:p.Val172Leu	83	0	0		108	58	0.537037	NM_000305	A4D1H7|B2RCP9|B4DJD5|O15114|O15115|O75856|Q5FBX7|Q86YL0	Missense_Mutation	SNP	ENST00000222572.3	37	CCDS5640.1	18	0.008241758241758242	18	0.036585365853658534	0	0.0	0	0.0	0	0.0	C	9.490	1.100457	0.20552	0.033818	2.33E-4	ENSG00000105854	ENST00000536183;ENST00000355659;ENST00000433091;ENST00000222572	T;T;T	0.40756	2.27;1.02;2.27	4.97	4.97	0.65823	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.11067	0.0270	L	0.58302	1.8	0.51767	D	0.999939	B;B	0.12013	0.005;0.005	B;B	0.18263	0.021;0.021	T	0.03240	-1.1057	10	0.20519	T	0.43	-18.3381	10.5089	0.44849	0.0:0.7892:0.1357:0.0752	rs17876152;rs58276578	172;172	A4D1H7;Q15165	.;PON2_HUMAN	L	193;170;160;172	ENSP00000440282:V193L;ENSP00000404622:V160L;ENSP00000222572:V172L	ENSP00000222572:V172L	V	-	1	0	PON2	94877330	0.359000	0.24955	1.000000	0.80357	0.502000	0.33828	0.451000	0.21779	2.754000	0.94517	0.650000	0.86243	GTT	C|0.983;G|0.017	0.017	strong		0.358	PON2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333142.1	NM_000305		G	95039394	C	G	95039394	3	3	22	1	0	0	0	0	1	0	0	0	12258	478	17	4	566	4	PON2	7	95039394	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	982387	95039394	64099269	1700	4601											
SLC25A13	10165	hgsc.bcm.edu	37	chr7	95820500	95820500	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agttccatgttgttaaggagCgaattaaatccattaaaata	16	13	7	5	1	0	0	0	0	0	0	2	2	2	1	2	1	1	3	2	1	7	6	rs78247004	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:95820500C>T	ENST00000265631.5	-	7	811	c.675G>A	c.(673-675)tcG>tcA	p.S225S	SLC25A13_ENST00000416240.2_Silent_p.S225S|SLC25A13_ENST00000542654.1_Silent_p.S117S			Q9UJS0	CMC2_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 13	225					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)	TGTTAAGGAGCGAATTAAATC	0.368													C|||	58	0.0115815	0.0439	0.0	5008	,	,		16454	0.0		0.0	False		,,,				2504	0.0				p.S225S		Atlas-SNP	.											SLC25A13,NS,carcinoma,-1,2	SLC25A13	131	2	0			c.G675A						PASS	.	C	,	161,4245	108.6+/-147.0	4,153,2046	147	145	146		675,675	-10.4	0.1	7	dbSNP_132	146	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SLC25A13	NM_001160210.1,NM_014251.2	,	4,153,6346	TT,TC,CC		0.0,3.6541,1.2379	,	225/677,225/676	95820500	161,12845	2203	4300	6503	SO:0001819	synonymous_variant	10165	exon7			AAGGAGCGAATTA	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.675G>A	7.37:g.95820500C>T		77	0	0		67	34	0.507463	NM_001160210	O14566|O14575|Q546F9|Q9NZW1|Q9UNI7	Silent	SNP	ENST00000265631.5	37	CCDS5645.1																																																																																			C|0.985;T|0.015	0.015	strong		0.368	SLC25A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059395.2	NM_014251		T	95820500	C	T	95820500	2	4	22	1	0	0	0	0	0	0	0	1	14490	755	27	1		1	SLC25A13	7	95820500	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	781106	95820500	63318163	1701	4602											
LMTK2	22853	hgsc.bcm.edu	37	chr7	97822990	97822990	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcggtctgcctcccaacccGgtcattgtcatctcagatgc	7	10	9	15	2	4	1	3	0	2	1	6	1	5	1	3	2	4	0	3	2	1	1	rs56064038	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:97822990G>A	ENST00000297293.5	+	11	3506	c.3213G>A	c.(3211-3213)ccG>ccA	p.P1071P		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	1071					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)					CTCCCAACCCGGTCATTGTCA	0.632													G|||	76	0.0151757	0.0567	0.0014	5008	,	,		17179	0.0		0.0	False		,,,				2504	0.0				p.P1071P		Atlas-SNP	.											.	LMTK2	228	.	0			c.G3213A						PASS	.	G		192,4214	118.8+/-156.5	3,186,2014	34	33	34		3213	-10.7	0.1	7	dbSNP_129	34	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	LMTK2	NM_014916.3		3,189,6311	AA,AG,GG		0.0349,4.3577,1.4993		1071/1504	97822990	195,12811	2203	4300	6503	SO:0001819	synonymous_variant	22853	exon11			CAACCCGGTCATT	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.3213G>A	7.37:g.97822990G>A		49	0	0		54	25	0.462963	NM_014916	A4D272|Q75MG7|Q9UPS3	Silent	SNP	ENST00000297293.5	37	CCDS5654.1																																																																																			G|0.985;A|0.015	0.015	strong		0.632	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334560.1	NM_014916		A	97822990	G	A	97822990	2	1	22	1	0	0	0	0	0	0	0	1	8868	1103	39	1		1	LMTK2	7	97822990	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2002490	97822990	61315673	1702	4603											
TRRAP	8295	hgsc.bcm.edu	37	chr7	98558922	98558922	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aactatgggaatatctgcacGggcctagaagtgctgagctt	11	10	12	8	1	1	2	0	1	1	1	1	3	1	3	1	2	4	3	1	2	6	4	rs34983214	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:98558922G>A	ENST00000359863.4	+	45	6716	c.6507G>A	c.(6505-6507)acG>acA	p.T2169T	TRRAP_ENST00000355540.3_Silent_p.T2151T|TRRAP_ENST00000446306.3_Silent_p.T2150T	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	2169	Interaction with TP53.				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)			ATATCTGCACGGGCCTAGAAG	0.507													G|||	32	0.00638978	0.0219	0.0029	5008	,	,		14881	0.0		0.001	False		,,,				2504	0.0				p.T2169T		Atlas-SNP	.											.	TRRAP	863	.	0			c.G6507A						PASS	.	G		78,4328	68.1+/-105.8	0,78,2125	162	161	162		6453	-10.9	0	7	dbSNP_126	162	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TRRAP	NM_003496.3		0,80,6423	AA,AG,GG		0.0233,1.7703,0.6151		2151/3831	98558922	80,12926	2203	4300	6503	SO:0001819	synonymous_variant	8295	exon45			CTGCACGGGCCTA	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.6507G>A	7.37:g.98558922G>A		81	0	0		94	46	0.489362	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Silent	SNP	ENST00000359863.4	37	CCDS59066.1	18	0.008241758241758242	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	7.407	0.633881	0.14322	0.017703	2.33E-4	ENSG00000196367	ENST00000456197	.	.	.	5.47	-10.9	0.00192	.	.	.	.	.	T	0.12860	0.0312	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37842	-0.9688	4	.	.	.	.	1.7278	0.02925	0.4473:0.1858:0.2241:0.1428	rs34983214	.	.	.	Q	1891	.	.	R	+	2	0	TRRAP	98396858	0.000000	0.05858	0.019000	0.16419	0.892000	0.51952	-2.537000	0.00939	-2.796000	0.00354	-0.136000	0.14681	CGG	G|0.993;A|0.007	0.007	strong		0.507	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		A	98558922	G	A	98558922	2	1	22	1	0	0	0	0	0	0	0	1	16616	1103	39	1		1	TRRAP	7	98558922	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	735932	98558922	60579741	1703	4604											
ZNF498	221785	hgsc.bcm.edu	37	chr7	99226981	99226981	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	caggcagtgcgcctgggcttCctcctccccagcacggtgcc	4	7	12	18	2	0	0	0	0	0	0	3	0	3	0	6	3	3	3	6	3	0	1	rs10239632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99226981C>G	ENST00000394152.2	+	8	1300	c.973C>G	c.(973-975)Cct>Gct	p.P325A	ZSCAN25_ENST00000466948.1_Intron|ZSCAN25_ENST00000262941.6_Missense_Mutation_p.P253A|ZSCAN25_ENST00000334715.3_Missense_Mutation_p.P325A	NM_145115.2	NP_660090.2	Q6NSZ9	ZSC25_HUMAN	zinc finger and SCAN domain containing 25	325			P -> A (in dbSNP:rs10239632).		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)										GCCTGGGCTTCCTCCTCCCCA	0.627													C|||	185	0.0369409	0.1263	0.0216	5008	,	,		17584	0.0		0.003	False		,,,				2504	0.0				p.P325A		Atlas-SNP	.											.	.	.	.	0			c.C973G						PASS	.	C	ALA/PRO	449,3957	211.8+/-231.9	28,393,1782	59	54	56		973	2.7	0	7	dbSNP_119	56	7,8593	3.7+/-12.6	0,7,4293	yes	missense	ZNF498	NM_145115.2	27	28,400,6075	GG,GC,CC		0.0814,10.1906,3.5061	benign	325/545	99226981	456,12550	2203	4300	6503	SO:0001583	missense	221785	exon8			GGGCTTCCTCCTC	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.973C>G	7.37:g.99226981C>G	ENSP00000377708:p.Pro325Ala	52	0	0		58	35	0.603448	NM_145115	A4D290|D6W5T5|Q14C82|Q14C99|Q5EBM9|Q6DJZ0|Q6N032|Q6ZML3	Missense_Mutation	SNP	ENST00000394152.2	37	CCDS5671.2	82	0.037545787545787544	71	0.1443089430894309	10	0.027624309392265192	0	0.0	1	0.0013192612137203166	C	0.010	-1.757120	0.00657	0.101906	8.14E-4	ENSG00000197037	ENST00000394152;ENST00000334715;ENST00000262941	T;T;T	0.08807	3.06;3.06;3.05	4.82	2.66	0.31614	.	0.503847	0.16909	N	0.194576	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.42616	-0.9441	9	0.09590	T	0.72	-0.7741	2.5036	0.04639	0.2459:0.4907:0.1618:0.1016	rs10239632;rs10239632	253;325	Q6NSZ9-2;Q6NSZ9	.;ZN498_HUMAN	A	325;325;253	ENSP00000377708:P325A;ENSP00000334800:P325A;ENSP00000262941:P253A	ENSP00000262941:P253A	P	+	1	0	ZNF498	99064917	0.000000	0.05858	0.006000	0.13384	0.006000	0.05464	0.695000	0.25527	1.140000	0.42260	-0.502000	0.04539	CCT	C|0.966;G|0.034	0.034	strong		0.627	ZSCAN25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157203.4	NM_145115		G	99226981	C	G	99226981	3	3	22	1	0	0	0	0	1	0	0	0	17962	855	30	4	991	4	ZNF498	7	99226981	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	668059	99226981	59911682	1704	4605											
ZNF498	221785	hgsc.bcm.edu	37	chr7	99227027	99227027	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cctgcctgacgaagtcaaaaCccacagctccttctggaagc	11	7	8	15	1	2	1	1	1	1	0	3	3	3	2	4	1	4	1	4	1	4	1	rs142120776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99227027C>T	ENST00000394152.2	+	8	1346	c.1019C>T	c.(1018-1020)aCc>aTc	p.T340I	ZSCAN25_ENST00000466948.1_Intron|ZSCAN25_ENST00000262941.6_Missense_Mutation_p.T268I|ZSCAN25_ENST00000334715.3_Missense_Mutation_p.T340I	NM_145115.2	NP_660090.2	Q6NSZ9	ZSC25_HUMAN	zinc finger and SCAN domain containing 25	340					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)										GAAGTCAAAACCCACAGCTCC	0.617													C|||	14	0.00279553	0.0106	0.0	5008	,	,		18729	0.0		0.0	False		,,,				2504	0.0				p.T340I		Atlas-SNP	.											.	.	.	.	0			c.C1019T						PASS	.	C	ILE/THR	48,4358	47.5+/-82.1	0,48,2155	57	50	52		1019	3.9	0	7	dbSNP_134	52	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ZNF498	NM_145115.2	89	0,49,6454	TT,TC,CC		0.0116,1.0894,0.3767	possibly-damaging	340/545	99227027	49,12957	2203	4300	6503	SO:0001583	missense	221785	exon8			TCAAAACCCACAG	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.1019C>T	7.37:g.99227027C>T	ENSP00000377708:p.Thr340Ile	57	0	0		59	28	0.474576	NM_145115	A4D290|D6W5T5|Q14C82|Q14C99|Q5EBM9|Q6DJZ0|Q6N032|Q6ZML3	Missense_Mutation	SNP	ENST00000394152.2	37	CCDS5671.2	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	8.033	0.762232	0.15914	0.010894	1.16E-4	ENSG00000197037	ENST00000394152;ENST00000334715;ENST00000262941	T;T;T	0.09073	3.03;3.03;3.02	3.89	3.89	0.44902	.	0.669254	0.13160	N	0.409125	T	0.03520	0.0101	N	0.11364	0.135	0.09310	N	1	B;B	0.26195	0.144;0.089	B;B	0.21546	0.025;0.035	T	0.35724	-0.9777	10	0.23891	T	0.37	-2.1444	14.1776	0.65552	0.0:1.0:0.0:0.0	.	268;340	Q6NSZ9-2;Q6NSZ9	.;ZN498_HUMAN	I	340;340;268	ENSP00000377708:T340I;ENSP00000334800:T340I;ENSP00000262941:T268I	ENSP00000262941:T268I	T	+	2	0	ZNF498	99064963	0.017000	0.18338	0.018000	0.16275	0.514000	0.34195	1.627000	0.37050	2.454000	0.82982	0.561000	0.74099	ACC	C|0.998;T|0.002	0.002	strong		0.617	ZSCAN25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157203.4	NM_145115		T	99227027	C	T	99227027	3	4	22	1	0	0	0	0	1	0	0	0	17962	507	18	2	1037	2	ZNF498	7	99227027	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	46	99227027	59911636	1705	4606											
CYP3A5	1577	hgsc.bcm.edu	37	chr7	99262835	99262835	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaaccaaattttaggaacttCttagtgctctccacaaaggg	14	11	7	9	0	2	0	0	0	2	0	3	1	2	1	2	2	3	1	2	2	6	4	rs10264272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99262835C>T	ENST00000222982.4	-	7	723	c.624G>A	c.(622-624)aaG>aaA	p.K208K	CYP3A5_ENST00000339843.2_3'UTR|CYP3A5_ENST00000343703.5_Silent_p.K198K|CYP3A5_ENST00000480723.1_5'Flank	NM_000777.3	NP_000768.1	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 5	208					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)	TTAGGAACTTCTTAGTGCTCT	0.378													C|||	223	0.0445288	0.1543	0.0231	5008	,	,		18786	0.0		0.003	False		,,,				2504	0.0				p.K208K		Atlas-SNP	.											.	CYP3A5	46	.	0			c.G624A	GRCh37	CS015291	CYP3A5	S	rs10264272	PASS	.	C		530,3876	238.4+/-249.8	43,444,1716	113	108	110		624	2.9	0	7	dbSNP_119	110	7,8593	3.7+/-12.6	0,7,4293	no	coding-synonymous	CYP3A5	NM_000777.3		43,451,6009	TT,TC,CC		0.0814,12.0291,4.1289		208/503	99262835	537,12469	2203	4300	6503	SO:0001819	synonymous_variant	1577	exon7			GAACTTCTTAGTG	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.624G>A	7.37:g.99262835C>T		136	0	0		160	72	0.45	NM_000777	A4D289|B7Z5I7|Q53WY8|Q75MV0|Q9HB56	Silent	SNP	ENST00000222982.4	37	CCDS5672.1																																																																																			C|0.952;T|0.048	0.048	strong		0.378	CYP3A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345469.1			T	99262835	C	T	99262835	2	4	22	1	0	0	0	0	0	0	0	1	4182	912	32	2		2	CYP3A5	7	99262835	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	35808	99262835	59875828	1706	4607											
CYP3A7	1551	hgsc.bcm.edu	37	chr7	99317993	99317993	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcactgttttgatcatgtcGggatctgtgatagccagcat	9	13	11	8	1	2	2	1	2	1	0	3	3	2	3	1	1	3	3	1	1	1	3	rs45466796	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99317993G>A	ENST00000336374.2	-	4	263	c.261C>T	c.(259-261)ccC>ccT	p.P87P		NM_000765.3	NP_000756.2	P24462	CP3A7_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 7	87					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)			autonomic_ganglia(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	32	Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228)				Alfentanil(DB00802)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amlodipine(DB00381)|Aprepitant(DB00673)|Aripiprazole(DB01238)|Astemizole(DB00637)|Atorvastatin(DB01076)|Buprenorphine(DB00921)|Buspirone(DB00490)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clotrimazole(DB00257)|Cocaine(DB00907)|Codeine(DB00318)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diltiazem(DB00343)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Eplerenone(DB00700)|Erythromycin(DB00199)|Estradiol(DB00783)|Ethosuximide(DB00593)|Ethylmorphine(DB01466)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluticasone Propionate(DB00588)|Fluvoxamine(DB00176)|Gestodene(DB06730)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nifedipine(DB01115)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Salmeterol(DB00938)|Saquinavir(DB01232)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Testosterone(DB00624)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	TGATCATGTCGGGATCTGTGA	0.388													G|||	111	0.0221645	0.0802	0.0072	5008	,	,		18474	0.0		0.0	False		,,,				2504	0.0				p.P87P		Atlas-SNP	.											.	CYP3A7	59	.	0			c.C261T						PASS	.	G		281,4125	156.3+/-189.4	8,265,1930	129	117	121		261	-2.8	0	7	dbSNP_127	121	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	CYP3A7	NM_000765.3		8,267,6228	AA,AG,GG		0.0233,6.3777,2.1759		87/504	99317993	283,12723	2203	4300	6503	SO:0001819	synonymous_variant	1551	exon4			CATGTCGGGATCT	AF315325	CCDS5673.1	7q21-q22.1	2007-12-14	2003-01-14		ENSG00000160870	ENSG00000160870		"Cytochrome P450s"	2640	protein-coding gene	gene with protein product		605340	"cytochrome P450, subfamily IIIA, polypeptide 7"			2722762	Standard	NM_000765		Approved	CP37, P450-HFLA		P24462	OTTHUMG00000156726	ENST00000336374.2:c.261C>T	7.37:g.99317993G>A		251	0	0		299	142	0.474916	NM_000765	A4D288|Q9H241	Silent	SNP	ENST00000336374.2	37	CCDS5673.1																																																																																			G|0.983;A|0.017	0.017	strong		0.388	CYP3A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345484.1			A	99317993	G	A	99317993	2	1	22	1	0	0	0	0	0	0	0	1	4183	1103	39	1		1	CYP3A7	7	99317993	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	55158	99317993	59820670	1707	4608											
CYP3A43	64816	hgsc.bcm.edu	37	chr7	99463556	99463556	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgaaattagacaatctaccaAttcttcaaccagaaaaacct	18	10	3	10	0	3	3	1	1	2	2	3	3	3	3	3	0	3	0	3	0	8	4	rs540214188	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99463556A>T	ENST00000354829.2	+	13	1547	c.1444A>T	c.(1444-1446)Att>Ttt	p.I482F	CYP3A43_ENST00000342499.4_3'UTR|CYP3A43_ENST00000415413.1_Missense_Mutation_p.I271F|CYP3A43_ENST00000312017.5_3'UTR|CYP3A43_ENST00000222382.5_Missense_Mutation_p.I483F|CYP3A43_ENST00000417625.1_Missense_Mutation_p.I372F|CYP3A43_ENST00000444905.1_3'UTR|CYP3A43_ENST00000477658.1_3'UTR	NM_022820.3|NM_057095.1	NP_073731.1|NP_476436.1	Q9HB55	CP343_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 43	482			Missing (in allele CYP3A43*2).		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)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(1)	19	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)				Dexamethasone(DB01234)|Dolutegravir(DB08930)|Ethosuximide(DB00593)|Oxazepam(DB00842)|Phenelzine(DB00780)|Praziquantel(DB01058)|Rifampicin(DB01045)|Rifapentine(DB01201)|Testosterone(DB00624)|Troleandomycin(DB01361)|Zalcitabine(DB00943)	CAATCTACCAATTCTTCAACC	0.338													A|||	292	0.0583067	0.2035	0.0216	5008	,	,		18384	0.001		0.002	False		,,,				2504	0.0051				p.I483F		Atlas-SNP	.											.	CYP3A43	52	.	0			c.A1447T						PASS	.						87	97	93					7																	99463556		2184	4300	6484	SO:0001583	missense	64816	exon13			CTACCAATTCTTC	AF319634	CCDS5675.1, CCDS5676.1, CCDS5677.1, CCDS64723.1	7q21.1	2007-12-14	2003-01-14		ENSG00000021461	ENSG00000021461		"Cytochrome P450s"	17450	protein-coding gene	gene with protein product		606534	"cytochrome P450, subfamily IIIA, polypeptide 43"			11160876, 11266076	Standard	NM_022820		Approved		uc003ury.1	Q9HB55	OTTHUMG00000156498	ENST00000354829.2:c.1444A>T	7.37:g.99463556A>T	ENSP00000346887:p.Ile482Phe	113	0	0		75	12	0.16	NM_022820	Q495Y1|Q75MK2|Q75MK3|Q9HB52|Q9HB53|Q9HB54|Q9HB57	Missense_Mutation	SNP	ENST00000354829.2	37	CCDS5676.1	.	.	.	.	.	.	.	.	.	.	A	10.34	1.321913	0.23994	.	.	ENSG00000021461	ENST00000354829;ENST00000417625;ENST00000415413;ENST00000222382	T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31	3.17	-6.34	0.01982	.	0.885559	0.09500	N	0.793766	T	0.24928	0.0605	N	0.01019	-1.045	0.22127	N	0.999348	B;B;B	0.11235	0.002;0.001;0.004	B;B;B	0.15052	0.003;0.006;0.012	T	0.16541	-1.0399	10	0.23891	T	0.37	.	0.423	0.00459	0.3831:0.1534:0.2286:0.2349	.	372;483;482	Q495Y1;Q75MK2;Q9HB55	.;.;CP343_HUMAN	F	482;372;271;483	ENSP00000346887:I482F;ENSP00000416581:I372F;ENSP00000401521:I271F;ENSP00000222382:I483F	ENSP00000222382:I483F	I	+	1	0	CYP3A43	99301492	0.000000	0.05858	0.000000	0.03702	0.483000	0.33249	-8.694000	0.00017	-2.343000	0.00623	0.172000	0.16884	ATT	.	.	none		0.338	CYP3A43-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000344379.1			T	99463556	A	T	99463556	3	4	22	1	0	0	0	0	1	0	0	0	4181	101	4	5	1497	5	CYP3A43	7	99463556	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	145563	99463556	59675107	1708	4609											
OR2AE1	81392	hgsc.bcm.edu	37	chr7	99473801	99473801	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggagagtataaatcagagAattcaatgtgggcgtaatga	15	9	12	5	2	2	3	2	1	0	2	2	5	2	3	1	2	0	2	1	2	6	4	rs73403577	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99473801A>G	ENST00000316368.2	-	1	879	c.856T>C	c.(856-858)Tct>Cct	p.S286P		NM_001005276.1	NP_001005276.1	Q8NHA4	O2AE1_HUMAN	olfactory receptor, family 2, subfamily AE, 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)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(2)	11	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					TAAATCAGAGAATTCAATGTG	0.453													G|||	372	0.0742812	0.2557	0.0288	5008	,	,		20421	0.001		0.002	False		,,,				2504	0.0112				p.S286P		Atlas-SNP	.											OR2AE1,rectum,carcinoma,+1,1	OR2AE1	32	1	0			c.T856C						PASS	.	G	PRO/SER	952,3454	734.8+/-410.6	103,746,1354	112	116	115		856	2.7	0.2	7	dbSNP_130	115	22,8578	818.3+/-406.9	0,22,4278	yes	missense	OR2AE1	NM_001005276.1	74	103,768,5632	GG,GA,AA		0.2558,21.6069,7.4889	benign	286/324	99473801	974,12032	2203	4300	6503	SO:0001583	missense	81392	exon1			TCAGAGAATTCAA	AC011904	CCDS34696.1	7q22.1	2014-02-19	2002-02-28		ENSG00000244623	ENSG00000244623		"GPCR / Class A : Olfactory receptors"	15087	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily AE, member 2"	OR2AE2			Standard	NM_001005276		Approved		uc003usc.1	Q8NHA4	OTTHUMG00000156650	ENST00000316368.2:c.856T>C	7.37:g.99473801A>G	ENSP00000313936:p.Ser286Pro	169	0	0		150	74	0.493333	NM_001005276	B2RPD2	Missense_Mutation	SNP	ENST00000316368.2	37	CCDS34696.1	140	0.0641025641025641	127	0.258130081300813	12	0.03314917127071823	0	0.0	1	0.0013192612137203166	G	0.005	-2.228017	0.00280	0.216069	0.002558	ENSG00000244623	ENST00000316368	T	0.14516	2.5	3.56	2.68	0.31781	GPCR, rhodopsin-like superfamily (1);	0.201466	0.24843	N	0.035141	T	0.00012	0.0000	N	0.00081	-2.22	0.51012	P	9.099999999995223E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.43475	-0.9389	9	0.02654	T	1	.	7.3678	0.26783	0.0999:0.1697:0.7304:0.0	.	286	Q8NHA4	O2AE1_HUMAN	P	286	ENSP00000313936:S286P	ENSP00000313936:S286P	S	-	1	0	OR2AE1	99311737	1.000000	0.71417	0.200000	0.23457	0.127000	0.20565	2.295000	0.43576	0.508000	0.28173	-3.352000	0.00042	TCT	A|0.933;G|0.067	0.067	strong		0.453	OR2AE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345053.1			G	99473801	A	G	99473801	3	3	22	1	0	0	0	0	1	0	0	0	10992	246	9	3	119	3	OR2AE1	7	99473801	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	10245	99473801	59664862	1709	4610											
OR2AE1	81392	hgsc.bcm.edu	37	chr7	99474007	99474007	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cactttgaaggatgaagacaTaggatgtagaaatcaggaag	17	8	12	4	0	1	4	1	2	0	2	1	7	1	7	0	3	0	1	0	3	6	3	rs60737583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99474007T>C	ENST00000316368.2	-	1	673	c.650A>G	c.(649-651)tAt>tGt	p.Y217C		NM_001005276.1	NP_001005276.1	Q8NHA4	O2AE1_HUMAN	olfactory receptor, family 2, subfamily AE, member 1	217			Y -> C (in dbSNP:rs60737583).			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(2)|lung(3)|prostate(2)	11	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					GATGAAGACATAGGATGTAGA	0.488													T|||	372	0.0742812	0.2557	0.0288	5008	,	,		23905	0.001		0.002	False		,,,				2504	0.0112				p.Y217C		Atlas-SNP	.											.	OR2AE1	32	.	0			c.A650G						PASS	.	T	CYS/TYR	953,3453	361.1+/-315.5	103,747,1353	113	95	101		650	3.6	0.1	7	dbSNP_129	101	22,8578	14.0+/-48.4	0,22,4278	yes	missense	OR2AE1	NM_001005276.1	194	103,769,5631	CC,CT,TT		0.2558,21.6296,7.4965	probably-damaging	217/324	99474007	975,12031	2203	4300	6503	SO:0001583	missense	81392	exon1			AAGACATAGGATG	AC011904	CCDS34696.1	7q22.1	2014-02-19	2002-02-28		ENSG00000244623	ENSG00000244623		"GPCR / Class A : Olfactory receptors"	15087	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily AE, member 2"	OR2AE2			Standard	NM_001005276		Approved		uc003usc.1	Q8NHA4	OTTHUMG00000156650	ENST00000316368.2:c.650A>G	7.37:g.99474007T>C	ENSP00000313936:p.Tyr217Cys	91	0	0		91	42	0.461538	NM_001005276	B2RPD2	Missense_Mutation	SNP	ENST00000316368.2	37	CCDS34696.1	140	0.0641025641025641	127	0.258130081300813	12	0.03314917127071823	0	0.0	1	0.0013192612137203166	T	13.17	2.158510	0.38119	0.216296	0.002558	ENSG00000244623	ENST00000316368	T	0.00520	6.85	3.62	3.62	0.41486	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36444	N	0.002597	T	0.00012	0.0000	H	0.95611	3.695	0.26077	P	0.9811449	D	0.89917	1.0	D	0.91635	0.999	T	0.23261	-1.0193	9	0.72032	D	0.01	.	10.8339	0.46675	0.0:0.0:0.0:1.0	rs60737583	217	Q8NHA4	O2AE1_HUMAN	C	217	ENSP00000313936:Y217C	ENSP00000313936:Y217C	Y	-	2	0	OR2AE1	99311943	1.000000	0.71417	0.058000	0.19502	0.189000	0.23516	5.082000	0.64450	1.877000	0.54381	0.405000	0.27470	TAT	T|0.932;C|0.068	0.068	strong		0.488	OR2AE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345053.1			C	99474007	T	C	99474007	3	2	22	1	0	0	0	0	1	0	0	0	10992	1406	49	3	325	3	OR2AE1	7	99474007	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	206	99474007	59664656	1710	4611											
CNPY4	245812	hgsc.bcm.edu	37	chr7	99722173	99722173	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aggagtttgaagacattgtgGgagactggtacttccaccat	11	11	12	7	0	0	3	0	1	0	2	1	5	1	4	2	3	1	2	2	3	2	4	rs60551236	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99722173G>A	ENST00000262932.3	+	5	634	c.502G>A	c.(502-504)Gga>Aga	p.G168R	CNPY4_ENST00000480692.1_3'UTR|RP11-506M12.1_ENST00000494221.1_RNA|MBLAC1_ENST00000398075.2_5'Flank	NM_152755.1	NP_689968.1	Q8N129	CNPY4_HUMAN	canopy FGF signaling regulator 4	168	Glu-rich.		G -> R (in dbSNP:rs60551236).			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)					AGACATTGTGGGAGACTGGTA	0.507													G|||	109	0.0217652	0.0794	0.0058	5008	,	,		20245	0.0		0.0	False		,,,				2504	0.0				p.G168R		Atlas-SNP	.											.	CNPY4	18	.	0			c.G502A						PASS	.	G	ARG/GLY	343,4063	179.7+/-208.2	14,315,1874	105	105	105		502	5.9	1	7	dbSNP_129	105	2,8598	1.2+/-3.3	0,2,4298	yes	missense	CNPY4	NM_152755.1	125	14,317,6172	AA,AG,GG		0.0233,7.7848,2.6526	possibly-damaging	168/249	99722173	345,12661	2203	4300	6503	SO:0001583	missense	245812	exon5			ATTGTGGGAGACT	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.502G>A	7.37:g.99722173G>A	ENSP00000262932:p.Gly168Arg	100	0	0		96	46	0.479167	NM_152755	Q8WUN9	Missense_Mutation	SNP	ENST00000262932.3	37	CCDS34701.1	27	0.012362637362637362	26	0.052845528455284556	1	0.0027624309392265192	0	0.0	0	0.0	G	29.2	4.986631	0.93106	0.077848	2.33E-4	ENSG00000166997	ENST00000262932	T	0.34859	1.34	5.94	5.94	0.96194	.	0.106425	0.64402	D	0.000007	T	0.02304	0.0071	N	0.08118	0	0.43489	D	0.995729	D	0.64830	0.994	D	0.66497	0.944	T	0.04400	-1.0954	10	0.23302	T	0.38	-10.3151	15.8634	0.79043	0.0:0.0:1.0:0.0	rs60551236	168	Q8N129	CNPY4_HUMAN	R	168	ENSP00000262932:G168R	ENSP00000262932:G168R	G	+	1	0	CNPY4	99560109	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	7.907000	0.87430	2.826000	0.97356	0.561000	0.74099	GGA	G|0.979;A|0.021	0.021	strong		0.507	CNPY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337224.4	NM_152755		A	99722173	G	A	99722173	3	1	22	1	0	0	0	0	1	0	0	0	3632	1233	43	2	520	2	CNPY4	7	99722173	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	248166	99722173	59416490	1711	4612											
MBLAC1	255374	hgsc.bcm.edu	37	chr7	99725466	99725466	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gctacctgccccacgggctgGgtgaggggcagcccctgcgc	4	5	16	16	2	0	1	0	1	0	0	0	1	0	1	5	4	4	3	5	4	1	1	rs78225840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99725466G>T	ENST00000398075.2	+	2	847	c.448G>T	c.(448-450)Ggt>Tgt	p.G150C	RP11-506M12.1_ENST00000494221.1_RNA	NM_203397.1	NP_981942.1	A4D2B0	MBLC1_HUMAN	metallo-beta-lactamase domain containing 1	150							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|skin(1)	7						CCACGGGCTGGGTGAGGGGCA	0.746													G|||	125	0.0249601	0.09	0.0086	5008	,	,		12011	0.0		0.0	False		,,,				2504	0.0				p.G150C		Atlas-SNP	.											.	MBLAC1	13	.	0			c.G448T						PASS	.	G	CYS/GLY	289,3345		6,277,1534	9	11	10		448	-1.4	0	7	dbSNP_131	10	2,8064		0,2,4031	yes	missense	MBLAC1	NM_203397.1	159	6,279,5565	TT,TG,GG		0.0248,7.9527,2.4872	benign	150/267	99725466	291,11409	1817	4033	5850	SO:0001583	missense	255374	exon2			GGGCTGGGTGAGG	BC031288	CCDS43620.1	7q22	2014-02-12	2009-04-08		ENSG00000214309	ENSG00000214309			22180	protein-coding gene	gene with protein product							Standard	XM_005250250		Approved	MGC49416	uc003utp.3	A4D2B0	OTTHUMG00000154846	ENST00000398075.2:c.448G>T	7.37:g.99725466G>T	ENSP00000381150:p.Gly150Cys	32	0	0		49	27	0.55102	NM_203397	Q8N5X8	Missense_Mutation	SNP	ENST00000398075.2	37	CCDS43620.1	37	0.01694139194139194	31	0.06300813008130081	3	0.008287292817679558	3	0.005244755244755245	0	0.0	G	8.154	0.788075	0.16258	0.079527	2.48E-4	ENSG00000214309	ENST00000398075	T	0.30448	1.53	4.35	-1.38	0.09027	Beta-lactamase-like (2);	0.393038	0.20783	N	0.085752	T	0.00936	0.0031	L	0.46819	1.47	0.09310	N	1	B	0.10296	0.003	B	0.17979	0.02	T	0.11060	-1.0603	10	0.38643	T	0.18	.	1.2154	0.01913	0.4798:0.1516:0.204:0.1646	.	150	A4D2B0	MBLC1_HUMAN	C	150	ENSP00000381150:G150C	ENSP00000381150:G150C	G	+	1	0	MBLAC1	99563402	0.000000	0.05858	0.005000	0.12908	0.332000	0.28634	0.180000	0.16860	-0.294000	0.08973	0.561000	0.74099	GGT	G|0.980;T|0.020	0.020	strong		0.746	MBLAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337353.1	NM_203397		T	99725466	G	T	99725466	3	4	22	1	0	0	0	0	1	0	0	0	9360	1232	43	4	450	4	MBLAC1	7	99725466	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3293	99725466	59413197	1712	4613											
GPC2	221914	hgsc.bcm.edu	37	chr7	99773879	99773879	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgtgaaccagaaaggagccGctgtcctccaccaggcctcg	9	6	12	14	2	0	2	0	1	0	1	3	3	2	3	6	2	2	1	6	2	2	0	rs74662631	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99773879G>A	ENST00000292377.2	-	2	443	c.276C>T	c.(274-276)agC>agT	p.S92S	STAG3_ENST00000426455.1_5'Flank|STAG3_ENST00000394018.2_5'Flank|GPC2_ENST00000471050.1_5'Flank|STAG3_ENST00000317296.5_5'Flank	NM_152742.1	NP_689955.1	Q8N158	GPC2_HUMAN	glypican 2	92					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)|neuron differentiation (GO:0030182)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	anchored component of membrane (GO:0031225)|endoplasmic reticulum (GO:0005783)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(3)	18	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GAAAGGAGCCGCTGTCCTCCA	0.587													G|||	87	0.0173722	0.0628	0.0058	5008	,	,		14063	0.0		0.0	False		,,,				2504	0.0				p.S92S		Atlas-SNP	.											.	GPC2	49	.	0			c.C276T						PASS	.	G		233,4173	138.4+/-174.2	6,221,1976	54	45	48		276	-4	0.4	7	dbSNP_132	48	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GPC2	NM_152742.1		6,222,6275	AA,AG,GG		0.0116,5.2882,1.7992		92/580	99773879	234,12772	2203	4300	6503	SO:0001819	synonymous_variant	221914	exon2			GGAGCCGCTGTCC	BX375153	CCDS5689.1	7q22.1	2007-02-16	2007-02-15		ENSG00000213420	ENSG00000213420		"Proteoglycans / Cell Surface : Glypicans"	4450	protein-coding gene	gene with protein product	"glypican proteoglycan 2, cerebroglycan proteoglycan"		"glypican 2 (cerebroglycan)"			8294498	Standard	NM_152742		Approved	cerebroglycan, FLJ38962, DKFZp547M109	uc003utv.3	Q8N158	OTTHUMG00000154894	ENST00000292377.2:c.276C>T	7.37:g.99773879G>A		231	0	0		276	136	0.492754	NM_152742	A4D2A7	Silent	SNP	ENST00000292377.2	37	CCDS5689.1																																																																																			G|0.985;A|0.015	0.015	strong		0.587	GPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337556.1	NM_152742		A	99773879	G	A	99773879	2	1	22	1	0	0	0	0	0	0	0	1	6606	1078	38	1		1	GPC2	7	99773879	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	48413	99773879	59364784	1713	4614											
AGFG2	3268	hgsc.bcm.edu	37	chr7	100151719	100151719	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attccttctcctccaagcccGtcagtcagtctcacgctcgg	6	11	7	17	3	4	0	3	0	2	0	9	0	6	0	4	1	1	1	4	1	1	2	rs61742738	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100151719G>A	ENST00000300176.4	+	5	711	c.589G>A	c.(589-591)Gtc>Atc	p.V197I	AGFG2_ENST00000262935.4_Intron|AGFG2_ENST00000474713.1_3'UTR	NM_006076.4	NP_006067.3	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2	197					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						CTCCAAGCCCGTCAGTCAGTC	0.597													G|||	203	0.0405351	0.143	0.0144	5008	,	,		19840	0.001		0.003	False		,,,				2504	0.0				p.V197I		Atlas-SNP	.											.	AGFG2	44	.	0			c.G589A						PASS	.	G	ILE/VAL	588,3818	259.2+/-262.9	40,508,1655	69	62	64		589	3.3	1	7	dbSNP_129	64	15,8585	10.5+/-38.8	0,15,4285	yes	missense	AGFG2	NM_006076.4	29	40,523,5940	AA,AG,GG		0.1744,13.3454,4.6363	benign	197/482	100151719	603,12403	2203	4300	6503	SO:0001583	missense	3268	exon5			AAGCCCGTCAGTC	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.589G>A	7.37:g.100151719G>A	ENSP00000300176:p.Val197Ile	83	0	0		86	43	0.5	NM_006076	O75429|Q96AB9|Q96GL4	Missense_Mutation	SNP	ENST00000300176.4	37	CCDS5697.1	76	0.0347985347985348	69	0.1402439024390244	5	0.013812154696132596	0	0.0	2	0.002638522427440633	G	6.520	0.464149	0.12402	0.133454	0.001744	ENSG00000106351	ENST00000300176	T	0.22945	1.93	5.1	3.31	0.37934	.	0.980801	0.08316	N	0.964634	T	0.00144	0.0004	N	0.25485	0.75	0.09310	P	0.9999999999537761	B	0.14438	0.01	B	0.06405	0.002	T	0.22695	-1.0209	9	0.23891	T	0.37	-29.7338	8.266	0.31815	0.1791:0.0:0.8209:0.0	rs61742738	197	O95081	AGFG2_HUMAN	I	197	ENSP00000300176:V197I	ENSP00000300176:V197I	V	+	1	0	AGFG2	99989655	0.823000	0.29233	0.979000	0.43373	0.187000	0.23431	1.897000	0.39799	0.877000	0.35895	-0.125000	0.14975	GTC	G|0.959;A|0.041	0.041	strong		0.597	AGFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342769.1	NM_006076		A	100151719	G	A	100151719	3	1	22	1	0	0	0	0	1	0	0	0	381	1145	40	1	607	1	AGFG2	7	100151719	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	377840	100151719	58986944	1714	4615											
SLC12A9	56996	hgsc.bcm.edu	37	chr7	100456506	100456506	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gccgtgatgaattttgccagCgtctttgctgtcctctttaa	6	16	9	10	2	2	2	0	2	2	0	3	2	3	2	3	0	3	1	3	0	2	5	rs78261122	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100456506C>T	ENST00000354161.3	+	6	932	c.807C>T	c.(805-807)agC>agT	p.S269S	SLC12A9_ENST00000540482.1_Silent_p.S269S|SLC12A9_ENST00000428758.1_Silent_p.S269S|SLC12A9_ENST00000275729.3_Silent_p.S180S|SLC12A9_ENST00000415287.1_Silent_p.S180S	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9	269				S -> N (in Ref. 1; AAF88060). {ECO:0000305}.	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)					ATTTTGCCAGCGTCTTTGCTG	0.587													C|||	32	0.00638978	0.0242	0.0	5008	,	,		19182	0.0		0.0	False		,,,				2504	0.0				p.S269S		Atlas-SNP	.											.	SLC12A9	81	.	0			c.C807T						PASS	.	C		102,4304	80.9+/-119.3	3,96,2104	99	77	84		807	-2.4	1	7	dbSNP_132	84	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	SLC12A9	NM_020246.2		3,99,6401	TT,TC,CC		0.0349,2.315,0.8073		269/915	100456506	105,12901	2203	4300	6503	SO:0001819	synonymous_variant	56996	exon6			TGCCAGCGTCTTT	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.807C>T	7.37:g.100456506C>T		148	0	0		196	90	0.459184	NM_001267812	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Silent	SNP	ENST00000354161.3	37	CCDS5707.1																																																																																			C|0.994;T|0.006	0.006	strong		0.587	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246		T	100456506	C	T	100456506	2	4	22	1	0	0	0	0	0	0	0	1	14405	767	27	1		1	SLC12A9	7	100456506	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	304787	100456506	58682157	1715	4616											
MUC17	140453	hgsc.bcm.edu	37	chr7	100675367	100675367	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattaacaagtatgcctgccAgcaccatgaaggtggccagt	12	8	10	11	0	0	1	0	1	0	0	0	1	0	1	4	2	4	2	4	2	4	2	rs116801454	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100675367A>G	ENST00000306151.4	+	3	734	c.670A>G	c.(670-672)Agc>Ggc	p.S224G		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	224	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)					TATGCCTGCCAGCACCATGAA	0.473													A|||	67	0.0133786	0.0492	0.0029	5008	,	,		23907	0.0		0.0	False		,,,				2504	0.0				p.S224G		Atlas-SNP	.											.	MUC17	804	.	0			c.A670G						PASS	.	A	GLY/SER	208,4198	127.8+/-164.7	5,198,2000	175	178	177		670	-0.9	0	7	dbSNP_132	177	2,8598	1.2+/-3.3	0,2,4298	yes	missense	MUC17	NM_001040105.1	56	5,200,6298	GG,GA,AA		0.0233,4.7208,1.6146	possibly-damaging	224/4494	100675367	210,12796	2203	4300	6503	SO:0001583	missense	140453	exon3			CCTGCCAGCACCA	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.670A>G	7.37:g.100675367A>G	ENSP00000302716:p.Ser224Gly	99	0	0		107	46	0.429907	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	24	0.01098901098901099	24	0.04878048780487805	0	0.0	0	0.0	0	0.0	A	1.401	-0.578226	0.03854	0.047208	2.33E-4	ENSG00000169876	ENST00000306151	T	0.02552	4.25	0.801	-0.886	0.10590	.	.	.	.	.	T	0.00210	0.0006	N	0.08118	0	0.09310	N	1	P	0.51933	0.949	B	0.34138	0.176	T	0.46843	-0.9162	9	0.23302	T	0.38	.	2.6539	0.05007	0.5677:0.0:0.0:0.4323	.	224	Q685J3	MUC17_HUMAN	G	224	ENSP00000302716:S224G	ENSP00000302716:S224G	S	+	1	0	MUC17	100462087	0.006000	0.16342	0.000000	0.03702	0.006000	0.05464	0.201000	0.17276	-0.273000	0.09246	0.165000	0.16767	AGC	A|0.987;G|0.013	0.013	strong		0.473	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		G	100675367	A	G	100675367	3	3	22	1	0	0	0	0	1	0	0	0	9983	188	7	3	680	3	MUC17	7	100675367	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	218861	100675367	58463296	1716	4617											
MUC17	140453	hgsc.bcm.edu	37	chr7	100678032	100678032	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgcctgtcagcaccaggcTggtggtcagttctgaggcta	6	11	14	10	0	3	1	2	1	1	0	3	1	3	1	2	4	2	4	2	4	1	2	rs147173571		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100678032T>C	ENST00000306151.4	+	3	3399	c.3335T>C	c.(3334-3336)cTg>cCg	p.L1112P		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1112	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)					AGCACCAGGCTGGTGGTCAGT	0.512																																					p.L1112P		Atlas-SNP	.											.	MUC17	804	.	0			c.T3335C						PASS	.						494	394	428					7																	100678032		2203	4300	6503	SO:0001583	missense	140453	exon3			CCAGGCTGGTGGT	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.3335T>C	7.37:g.100678032T>C	ENSP00000302716:p.Leu1112Pro	163	0	0		352	33	0.09375	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	0.149	-1.093913	0.01858	.	.	ENSG00000169876	ENST00000306151	T	0.03212	4.01	0.693	-0.391	0.12446	.	.	.	.	.	T	0.01320	0.0043	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48055	-0.9068	8	0.25751	T	0.34	.	.	.	.	.	1112	Q685J3	MUC17_HUMAN	P	1112	ENSP00000302716:L1112P	ENSP00000302716:L1112P	L	+	2	0	MUC17	100464752	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-6.070000	0.00082	-0.165000	0.10908	-1.364000	0.01208	CTG	.	.	weak		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		C	100678032	T	C	100678032	3	2	22	1	0	0	0	0	1	0	0	0	9983	1580	55	3	3345	3	MUC17	7	100678032	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2665	100678032	58460631	1717	4618											
MUC17	140453	hgsc.bcm.edu	37	chr7	100678693	100678693	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcatgccaacctcaacttaTagtgaaggaagaactccttt	14	10	7	10	0	1	2	1	1	0	1	2	3	2	3	3	1	5	1	3	1	7	3	rs78176991	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100678693T>C	ENST00000306151.4	+	3	4060	c.3996T>C	c.(3994-3996)taT>taC	p.Y1332Y		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1332	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)					CCTCAACTTATAGTGAAGGAA	0.448																																					p.Y1332Y		Atlas-SNP	.											.	MUC17	804	.	0			c.T3996C						PASS	.						241	232	235					7																	100678693		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			AACTTATAGTGAA	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.3996T>C	7.37:g.100678693T>C		148	0	0		144	16	0.111111	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			T|0.994;C|0.006	0.006	strong		0.448	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		C	100678693	T	C	100678693	2	2	22	1	0	0	0	0	0	0	0	1	9983	1413	49	3		3	MUC17	7	100678693	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	661	100678693	58459970	1718	4619											
MUC17	140453	hgsc.bcm.edu	37	chr7	100680336	100680336	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgtcagcaccacaacagtggCcagttctgaaaccaacaccc	13	6	7	15	0	2	1	1	1	1	0	2	1	2	1	4	1	4	2	4	1	3	1	rs74687161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100680336C>T	ENST00000306151.4	+	3	5703	c.5639C>T	c.(5638-5640)gCc>gTc	p.A1880V		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1880	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)					ACAACAGTGGCCAGTTCTGAA	0.498													-|||	251	0.0501198	0.1823	0.0144	5008	,	,		24216	0.0		0.0	False		,,,				2504	0.0				p.A1880V		Atlas-SNP	.											.	MUC17	804	.	0			c.C5639T						PASS	.	C	VAL/ALA	665,3741		90,485,1628	240	251	247		5639	-0.3	0	7	dbSNP_131	247	6,8594		0,6,4294	no	missense	MUC17	NM_001040105.1	64	90,491,5922	TT,TC,CC		0.0698,15.0931,5.1592	benign	1880/4494	100680336	671,12335	2203	4300	6503	SO:0001583	missense	140453	exon3			CAGTGGCCAGTTC	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.5639C>T	7.37:g.100680336C>T	ENSP00000302716:p.Ala1880Val	130	0	0		120	59	0.491667	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	79	0.036172161172161175	77	0.1565040650406504	2	0.0055248618784530384	0	0.0	0	0.0	c	3.374	-0.127886	0.06753	0.150931	6.98E-4	ENSG00000169876	ENST00000306151	T	0.02656	4.21	0.824	-0.353	0.12594	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.16802	0.019	B	0.08055	0.003	T	0.45977	-0.9224	8	0.18276	T	0.48	.	5.508	0.16864	0.0:0.7655:0.0:0.2345	.	1880	Q685J3	MUC17_HUMAN	V	1880	ENSP00000302716:A1880V	ENSP00000302716:A1880V	A	+	2	0	MUC17	100467056	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.179000	0.16840	-0.086000	0.12550	0.134000	0.15878	GCC	C|0.958;T|0.042	0.042	strong		0.498	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		T	100680336	C	T	100680336	3	4	22	1	0	0	0	0	1	0	0	0	9983	739	26	2	5649	2	MUC17	7	100680336	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1643	100680336	58458327	1719	4620											
MUC17	140453	hgsc.bcm.edu	37	chr7	100682831	100682831	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaattctgaggctagcaccCtttcaacaactcctgttgac	10	11	6	14	0	2	2	1	2	1	0	3	2	3	2	3	1	3	3	3	1	4	4	rs34223735		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100682831C>G	ENST00000306151.4	+	3	8198	c.8134C>G	c.(8134-8136)Ctt>Gtt	p.L2712V		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2712	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)					GGCTAGCACCCTTTCAACAAC	0.493																																					p.L2712V		Atlas-SNP	.											.	MUC17	804	.	0			c.C8134G						PASS	.						257	264	262					7																	100682831		2203	4300	6503	SO:0001583	missense	140453	exon3			AGCACCCTTTCAA	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.8134C>G	7.37:g.100682831C>G	ENSP00000302716:p.Leu2712Val	120	0	0		146	9	0.0616438	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	0.020	-1.446165	0.01089	.	.	ENSG00000169876	ENST00000306151	T	0.04049	3.72	0.0465	0.0465	0.14256	.	.	.	.	.	T	0.02494	0.0076	N	0.17082	0.46	0.09310	N	1	B	0.17667	0.023	B	0.09377	0.004	T	0.48875	-0.8996	9	0.14656	T	0.56	.	3.6497	0.08198	2.0E-4:0.5059:0.4937:2.0E-4	rs34223735	2712	Q685J3	MUC17_HUMAN	V	2712	ENSP00000302716:L2712V	ENSP00000302716:L2712V	L	+	1	0	MUC17	100469551	0.018000	0.18449	0.005000	0.12908	0.081000	0.17604	-0.783000	0.04638	0.132000	0.18615	0.134000	0.15878	CTT	.	.	weak		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		G	100682831	C	G	100682831	3	3	22	1	0	0	0	0	1	0	0	0	9983	681	24	4	8144	4	MUC17	7	100682831	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2495	100682831	58455832	1720	4621											
MUC17	140453	hgsc.bcm.edu	37	chr7	100683156	100683156	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagtatgcctgtcaaccacaCgccagtggccagttctgagg	9	9	11	12	1	2	1	1	1	1	0	2	1	2	1	4	2	2	2	4	2	3	3	rs79046921	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100683156C>T	ENST00000306151.4	+	3	8523	c.8459C>T	c.(8458-8460)aCg>aTg	p.T2820M		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2820	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)					GTCAACCACACGCCAGTGGCC	0.493																																					p.T2820M		Atlas-SNP	.											MUC17,colon,carcinoma,-1,2	MUC17	804	2	0			c.C8459T						scavenged	.	C	MET/THR	620,3786	270.1+/-269.4	46,528,1629	241	247	245		8459	0.9	0	7	dbSNP_131	245	6,8594	3.0+/-9.4	0,6,4294	yes	missense	MUC17	NM_001040105.1	81	46,534,5923	TT,TC,CC		0.0698,14.0717,4.8132	probably-damaging	2820/4494	100683156	626,12380	2203	4300	6503	SO:0001583	missense	140453	exon3			ACCACACGCCAGT	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.8459C>T	7.37:g.100683156C>T	ENSP00000302716:p.Thr2820Met	117	1	0.00854701		143	77	0.538462	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	77	0.035256410256410256	74	0.15040650406504066	3	0.008287292817679558	0	0.0	0	0.0	C	6.722	0.501948	0.12822	0.140717	6.98E-4	ENSG00000169876	ENST00000306151	T	0.02015	4.5	0.911	0.911	0.19343	.	.	.	.	.	T	0.00039	0.0001	N	0.20986	0.625	0.80722	P	0.0	D	0.76494	0.999	D	0.64877	0.93	T	0.53265	-0.8463	8	0.62326	D	0.03	.	7.81	0.29226	0.0:1.0:0.0:0.0	.	2820	Q685J3	MUC17_HUMAN	M	2820	ENSP00000302716:T2820M	ENSP00000302716:T2820M	T	+	2	0	MUC17	100469876	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.791000	0.26915	0.801000	0.34066	0.134000	0.15878	ACG	A|0.000;C|0.960;T|0.040	0.040	strong		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		T	100683156	C	T	100683156	3	4	22	1	0	0	0	0	1	0	0	0	9983	536	19	1	8469	1	MUC17	7	100683156	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	325	100683156	58455507	1721	4622											
ALKBH4	54784	hgsc.bcm.edu	37	chr7	102098035	102098035	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtgaggaccagcagggagcGggcgggtaaggggatggcca	9	3	22	7	2	0	1	0	1	0	0	0	4	0	4	2	8	2	2	2	8	1	1	rs150409598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:102098035G>A	ENST00000292566.3	-	3	754	c.715C>T	c.(715-717)Cgc>Tgc	p.R239C		NM_017621.3	NP_060091.1	Q9NXW9	ALKB4_HUMAN	alkB, alkylation repair homolog 4 (E. coli)	239					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						AGCAGGGAGCGGGCGGGTAAG	0.701													G|||	22	0.00439297	0.0144	0.0029	5008	,	,		15602	0.0		0.0	False		,,,				2504	0.001				p.R239C		Atlas-SNP	.											.	ALKBH4	21	.	0			c.C715T						PASS	.	G	CYS/ARG	17,4385		0,17,2184	20	19	19		715	3	1	7	dbSNP_134	19	0,8590		0,0,4295	no	missense	ALKBH4	NM_017621.3	180	0,17,6479	AA,AG,GG		0.0,0.3862,0.1308	probably-damaging	239/303	102098035	17,12975	2201	4295	6496	SO:0001583	missense	54784	exon3			GGGAGCGGGCGGG	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.715C>T	7.37:g.102098035G>A	ENSP00000292566:p.Arg239Cys	58	0	0		48	28	0.583333	NM_017621	Q53H92|Q9H6A4	Missense_Mutation	SNP	ENST00000292566.3	37	CCDS5723.1	16	0.007326007326007326	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	0	0.0	G	15.57	2.873700	0.51695	0.003862	0.0	ENSG00000160993	ENST00000292566	T	0.15718	2.4	5.08	3.05	0.35203	Oxoglutarate/iron-dependent oxygenase (1);	0.100392	0.64402	N	0.000011	T	0.11153	0.0272	M	0.89658	3.05	0.80722	D	1	P	0.49447	0.924	P	0.45577	0.486	T	0.02805	-1.1108	10	0.59425	D	0.04	-5.0926	7.4982	0.27503	0.0954:0.0:0.6433:0.2613	.	239	Q9NXW9	ALKB4_HUMAN	C	239	ENSP00000292566:R239C	ENSP00000292566:R239C	R	-	1	0	ALKBH4	101885040	0.994000	0.37717	0.991000	0.47740	0.438000	0.31896	1.036000	0.30228	1.137000	0.42214	0.561000	0.74099	CGC	G|0.996;A|0.004	0.004	strong		0.701	ALKBH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349503.1	NM_017621		A	102098035	G	A	102098035	3	1	22	1	0	0	0	0	1	0	0	0	529	1116	39	1	197	1	ALKBH4	7	102098035	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1414879	102098035	57040628	1722	4623											
LRWD1	222229	hgsc.bcm.edu	37	chr7	102106459	102106459	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccttgtgccagttccccaaGctcgaggaactcagcctgga	8	8	11	14	1	1	0	1	0	0	0	3	3	2	2	5	2	4	2	5	2	2	2	rs146433593	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:102106459G>A	ENST00000292616.5	+	2	428	c.276G>A	c.(274-276)aaG>aaA	p.K92K	MIR5090_ENST00000582533.1_RNA|ALKBH4_ENST00000292566.3_5'Flank	NM_152892.1	NP_690852.1	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain containing 1	92					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						AGTTCCCCAAGCTCGAGGAAC	0.637													G|||	18	0.00359425	0.0136	0.0	5008	,	,		19209	0.0		0.0	False		,,,				2504	0.0				p.K92K		Atlas-SNP	.											.	LRWD1	41	.	0			c.G276A						PASS	.	G		59,4347	57.4+/-93.9	0,59,2144	46	45	45		276	-5.5	0	7	dbSNP_134	45	0,8600		0,0,4300	no	coding-synonymous	LRWD1	NM_152892.1		0,59,6444	AA,AG,GG		0.0,1.3391,0.4536		92/648	102106459	59,12947	2203	4300	6503	SO:0001819	synonymous_variant	222229	exon2			CCCCAAGCTCGAG	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.276G>A	7.37:g.102106459G>A		96	0	0		108	56	0.518519	NM_152892	A8K4K2|B2R9G2|Q8N0T9|Q8WV43|Q96GJ2	Silent	SNP	ENST00000292616.5	37	CCDS34715.1																																																																																			G|0.995;A|0.005	0.005	strong		0.637	LRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349493.1	NM_152892		A	102106459	G	A	102106459	2	1	22	1	0	0	0	0	0	0	0	1	9056	962	34	2		2	LRWD1	7	102106459	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	8424	102106459	57032204	1723	4624											
RELN	5649	hgsc.bcm.edu	37	chr7	103124265	103124265	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagctgtccgtctgcgacAtgctcccaatttgcaaaaca	10	10	8	13	2	1	0	0	0	1	0	3	1	3	0	2	0	6	4	2	0	3	1	rs150638029	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:103124265A>G	ENST00000428762.1	-	62	10175	c.10016T>C	c.(10015-10017)aTg>aCg	p.M3339T	RELN_ENST00000343529.5_Missense_Mutation_p.M3339T|CTB-107G13.1_ENST00000422488.1_RNA|RELN_ENST00000424685.2_Missense_Mutation_p.M3339T|RELN_ENST00000473945.1_5'UTR|RN7SKP86_ENST00000410454.1_RNA	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	3339					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)		CGTCTGCGACATGCTCCCAAT	0.453																																					p.M3339T	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.T10016C						PASS	.	A	THR/MET,THR/MET	2,4404	4.2+/-10.8	0,2,2201	106	99	101		10016,10016	2.9	0	7	dbSNP_134	101	0,8600		0,0,4300	no	missense,missense	RELN	NM_005045.3,NM_173054.2	81,81	0,2,6501	GG,GA,AA		0.0,0.0454,0.0154	benign,benign	3339/3461,3339/3459	103124265	2,13004	2203	4300	6503	SO:0001583	missense	5649	exon62			TGCGACATGCTCC		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.10016T>C	7.37:g.103124265A>G	ENSP00000392423:p.Met3339Thr	91	0	0		92	50	0.543478	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	A	3.338	-0.135242	0.06711	4.54E-4	0.0	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000424828;ENST00000448171	T;T;T	0.20463	2.07;2.07;2.07	5.64	2.87	0.33458	.	0.695276	0.14403	N	0.321778	T	0.08403	0.0209	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39354	-0.9618	10	0.17832	T	0.49	.	8.0051	0.30321	0.4314:0.0:0.5686:0.0	.	3339;3339	P78509-2;P78509	.;RELN_HUMAN	T	3339;3339;3339;856;3339	ENSP00000392423:M3339T;ENSP00000345694:M3339T;ENSP00000388446:M3339T	ENSP00000345694:M3339T	M	-	2	0	RELN	102911501	0.017000	0.18338	0.013000	0.15412	0.558000	0.35554	1.440000	0.35024	0.327000	0.23409	-1.055000	0.02315	ATG	A|1.000;G|0.000	0.000	strong		0.453	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		G	103124265	A	G	103124265	3	3	22	1	0	0	0	0	1	0	0	0	13235	217	8	3	382	3	RELN	7	103124265	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1017806	103124265	56014398	1724	4625											
RELN	5649	hgsc.bcm.edu	37	chr7	103205949	103205949	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcatttcaaactgcaaaaaGgtagatgctgacacatgaaa	17	9	7	8	0	2	3	2	2	0	1	2	3	2	3	0	1	3	3	0	1	5	2	rs78221963	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:103205949G>C	ENST00000428762.1	-	34	5145	c.4986C>G	c.(4984-4986)acC>acG	p.T1662T	RELN_ENST00000424685.2_Silent_p.T1662T|RELN_ENST00000343529.5_Silent_p.T1662T	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1662					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)		ACTGCAAAAAGGTAGATGCTG	0.423													G|||	41	0.0081869	0.0303	0.0014	5008	,	,		18251	0.0		0.0	False		,,,				2504	0.0				p.T1662T	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.C4986G						PASS	.	G	,	65,4341	59.9+/-96.7	0,65,2138	77	70	72		4986,4986	4	1	7	dbSNP_132	72	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	RELN	NM_005045.3,NM_173054.2	,	0,66,6437	CC,CG,GG		0.0116,1.4753,0.5075	,	1662/3461,1662/3459	103205949	66,12940	2203	4300	6503	SO:0001819	synonymous_variant	5649	exon34			CAAAAAGGTAGAT		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.4986C>G	7.37:g.103205949G>C		70	0	0		65	31	0.476923	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Silent	SNP	ENST00000428762.1	37	CCDS47680.1																																																																																			G|0.993;C|0.007	0.007	strong		0.423	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		C	103205949	G	C	103205949	2	2	22	1	0	0	0	0	0	0	0	1	13235	987	35	4		4	RELN	7	103205949	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	81684	103205949	55932714	1725	4626											
RELN	5649	hgsc.bcm.edu	37	chr7	103251218	103251218	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atggtaaatacttgctgatgTaaattcctgacaacttggca	13	13	8	7	0	0	2	0	2	0	0	1	2	1	2	1	2	3	4	1	2	6	6	rs3025962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:103251218T>C	ENST00000428762.1	-	22	3091	c.2932A>G	c.(2932-2934)Aca>Gca	p.T978A	RELN_ENST00000424685.2_Missense_Mutation_p.T978A|RELN_ENST00000343529.5_Missense_Mutation_p.T978A	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	978			T -> A (in dbSNP:rs3025962).		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)		CTTGCTGATGTAAATTCCTGA	0.413													T|||	92	0.0183706	0.0651	0.0086	5008	,	,		18923	0.0		0.0	False		,,,				2504	0.0				p.T978A	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.A2932G						PASS	.	T	ALA/THR,ALA/THR	211,4195	131.0+/-167.6	4,203,1996	146	123	131		2932,2932	6.1	1	7	dbSNP_102	131	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense	RELN	NM_005045.3,NM_173054.2	58,58	4,206,6293	CC,CT,TT		0.0349,4.7889,1.6454	probably-damaging,probably-damaging	978/3461,978/3459	103251218	214,12792	2203	4300	6503	SO:0001583	missense	5649	exon22			CTGATGTAAATTC		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.2932A>G	7.37:g.103251218T>C	ENSP00000392423:p.Thr978Ala	73	0	0		75	34	0.453333	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	T	23.6	4.434312	0.83776	0.047889	3.49E-4	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.24908	1.83;2.09;1.83	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.06325	0.0163	M	0.61703	1.905	0.58432	D	0.999994	D;D	0.76494	0.999;0.982	D;D	0.83275	0.996;0.952	T	0.01235	-1.1410	10	0.62326	D	0.03	.	15.2149	0.73258	0.0:0.0:0.0:1.0	rs3025962;rs52799777;rs3025962	978;978	P78509-2;P78509	.;RELN_HUMAN	A	978	ENSP00000392423:T978A;ENSP00000345694:T978A;ENSP00000388446:T978A	ENSP00000345694:T978A	T	-	1	0	RELN	103038454	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	7.358000	0.79466	2.333000	0.79357	0.533000	0.62120	ACA	T|0.978;C|0.022	0.022	strong		0.413	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		C	103251218	T	C	103251218	3	2	22	1	0	0	0	0	1	0	0	0	13235	1638	57	3	7626	3	RELN	7	103251218	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	45269	103251218	55887445	1726	4627											
ORC5L	5001	hgsc.bcm.edu	37	chr7	103844599	103844599	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttattcttacctctaaagtTttcaacaacgtttgtgttac	10	19	4	8	1	3	0	1	0	2	0	3	0	3	0	1	0	4	3	1	0	7	9	rs2307413	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:103844599T>A	ENST00000297431.4	-	2	298	c.156A>T	c.(154-156)aaA>aaT	p.K52N	ORC5_ENST00000545943.1_5'UTR|ORC5_ENST00000447452.2_Missense_Mutation_p.K52N|ORC5_ENST00000485726.1_5'UTR	NM_002553.3	NP_002544.1	O43913	ORC5_HUMAN	origin recognition complex, subunit 5	52			K -> N (in dbSNP:rs2307413).		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						CCTCTAAAGTTTTCAACAACG	0.299													T|||	72	0.014377	0.053	0.0029	5008	,	,		17463	0.0		0.0	False		,,,				2504	0.0				p.K52N		Atlas-SNP	.											.	ORC5	48	.	0			c.A156T						PASS	.	T	ASN/LYS,ASN/LYS	219,4183	128.6+/-165.4	8,203,1990	59	60	59		156,156	2.7	1	7	dbSNP_100	59	2,8594	1.2+/-3.3	0,2,4296	yes	missense,missense	ORC5	NM_002553.3,NM_181747.3	94,94	8,205,6286	AA,AT,TT		0.0233,4.975,1.7003	benign,benign	52/436,52/325	103844599	221,12777	2201	4298	6499	SO:0001583	missense	5001	exon2			TAAAGTTTTCAAC		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.156A>T	7.37:g.103844599T>A	ENSP00000297431:p.Lys52Asn	123	0	0		115	58	0.504348	NM_002553	A4D0P8|O60590|O95268	Missense_Mutation	SNP	ENST00000297431.4	37	CCDS5734.1	33	0.01510989010989011	31	0.06300813008130081	2	0.0055248618784530384	0	0.0	0	0.0	T	10.43	1.347141	0.24426	0.04975	2.33E-4	ENSG00000164815	ENST00000297431;ENST00000447452	T;T	0.62941	-0.01;-0.01	5.16	2.74	0.32292	.	0.189382	0.56097	D	0.000033	T	0.05364	0.0142	N	0.17474	0.49	0.80722	D	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.08055	0.002;0.003;0.002	T	0.02431	-1.1160	10	0.23302	T	0.38	.	3.8148	0.08811	0.1211:0.0725:0.371:0.4354	rs2307413;rs16873425;rs52800217;rs2307413	52;52;52	A4D0P7;O43913-2;O43913	.;.;ORC5_HUMAN	N	52	ENSP00000297431:K52N;ENSP00000395747:K52N	ENSP00000297431:K52N	K	-	3	2	ORC5	103631835	0.995000	0.38212	1.000000	0.80357	0.913000	0.54294	0.264000	0.18497	0.294000	0.22547	-0.438000	0.05819	AAA	T|0.985;A|0.015	0.015	strong		0.299	ORC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348286.1	NM_002553		A	103844599	T	A	103844599	3	1	22	1	0	0	0	0	1	0	0	0	11274	1838	64	5	1301	5	ORC5L	7	103844599	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	593381	103844599	55294064	1727	4628											
RINT1	60561	hgsc.bcm.edu	37	chr7	105182995	105182995	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aacagccatttgctgactgcGcaaccttggatggacgatct	10	10	10	11	2	1	1	0	1	1	0	1	4	1	3	2	2	5	2	2	2	2	2	rs7805216	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:105182995G>A	ENST00000257700.2	+	4	645	c.414G>A	c.(412-414)gcG>gcA	p.A138A	RINT1_ENST00000477285.1_3'UTR	NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	138					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						TGCTGACTGCGCAACCTTGGA	0.403													G|||	307	0.0613019	0.2209	0.0187	5008	,	,		16144	0.0		0.002	False		,,,				2504	0.0				p.A138A		Atlas-SNP	.											.	RINT1	65	.	0			c.G414A						PASS	.	G		770,3636	312.7+/-292.7	65,640,1498	120	112	115		414	-10	0.1	7	dbSNP_116	115	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	RINT1	NM_021930.4		65,646,5792	AA,AG,GG		0.0698,17.4762,5.9665		138/793	105182995	776,12230	2203	4300	6503	SO:0001819	synonymous_variant	60561	exon4			GACTGCGCAACCT	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.414G>A	7.37:g.105182995G>A		180	0	0		218	106	0.486239	NM_021930	Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	Silent	SNP	ENST00000257700.2	37	CCDS34726.1																																																																																			G|0.939;A|0.061	0.061	strong		0.403	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348686.1	NM_021930		A	105182995	G	A	105182995	2	1	22	1	0	0	0	0	0	0	0	1	13391	1074	38	1		1	RINT1	7	105182995	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1338396	105182995	53955668	1728	4629											
PRKAR2B	5577	hgsc.bcm.edu	37	chr7	106791447	106791447	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaagctttattgagtcactGccattccttaaatctttgga	11	15	7	8	0	2	1	1	1	1	0	3	3	3	2	2	1	2	1	2	1	4	6	rs3729878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:106791447G>A	ENST00000265717.4	+	7	1081	c.822G>A	c.(820-822)ctG>ctA	p.L274L		NM_002736.2	NP_002727.2	P31323	KAP3_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, beta	274					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						TTGAGTCACTGCCATTCCTTA	0.303													G|||	196	0.0391374	0.1422	0.0115	5008	,	,		14361	0.0		0.0	False		,,,				2504	0.0				p.L274L		Atlas-SNP	.											.	PRKAR2B	34	.	0			c.G822A						PASS	.	G		532,3874	238.4+/-249.8	30,472,1701	72	74	73		822	4.6	1	7	dbSNP_107	73	9,8587	7.1+/-27.0	0,9,4289	no	coding-synonymous	PRKAR2B	NM_002736.2		30,481,5990	AA,AG,GG		0.1047,12.0744,4.1609		274/419	106791447	541,12461	2203	4298	6501	SO:0001819	synonymous_variant	5577	exon7			GTCACTGCCATTC		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.822G>A	7.37:g.106791447G>A		201	0	0		209	95	0.454545	NM_002736	A4D0R9	Silent	SNP	ENST00000265717.4	37	CCDS5740.1																																																																																			G|0.953;A|0.047	0.047	strong		0.303	PRKAR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268386.1			A	106791447	G	A	106791447	2	1	22	1	0	0	0	0	0	0	0	1	12518	1306	46	2		2	PRKAR2B	7	106791447	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1608452	106791447	52347216	1729	4630											
COG5	10466	hgsc.bcm.edu	37	chr7	106938740	106938740	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccataagtcattataaagaCgtaataatttagggtattct	15	15	6	5	1	2	1	1	0	1	1	3	1	3	1	1	1	0	2	1	1	8	9	rs35258567	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:106938740C>T	ENST00000347053.3	-	12	1303	c.1253G>A	c.(1252-1254)cGt>cAt	p.R418H	COG5_ENST00000393603.2_Missense_Mutation_p.R418H|COG5_ENST00000297135.3_Missense_Mutation_p.R418H	NM_181733.2	NP_859422.2	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5	418					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						ATTATAAAGACGTAATAATTT	0.343													C|||	7	0.00139776	0.0053	0.0	5008	,	,		12763	0.0		0.0	False		,,,				2504	0.0				p.R418H		Atlas-SNP	.											COG5,colon,carcinoma,-1,1	COG5	78	1	0			c.G1253A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG	15,4391	22.3+/-47.3	0,15,2188	89	84	86		1253,1253,1253	4.8	1	7	dbSNP_126	86	0,8600		0,0,4300	yes	missense,missense,missense	COG5	NM_001161520.1,NM_006348.3,NM_181733.2	29,29,29	0,15,6488	TT,TC,CC		0.0,0.3404,0.1153	probably-damaging,probably-damaging,probably-damaging	418/824,418/861,418/840	106938740	15,12991	2203	4300	6503	SO:0001583	missense	10466	exon12			TAAAGACGTAATA	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.1253G>A	7.37:g.106938740C>T	ENSP00000334703:p.Arg418His	104	0	0		125	58	0.464	NM_006348	A4D0R6|A4D0R7|O14555|O95008|Q6NUL5	Missense_Mutation	SNP	ENST00000347053.3	37	CCDS5743.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	14.56	2.571964	0.45798	0.003404	0.0	ENSG00000164597	ENST00000347053;ENST00000297135;ENST00000393603	T;T;T	0.71934	-0.61;-0.61;-0.61	5.68	4.8	0.61643	.	0.055380	0.64402	D	0.000001	T	0.67173	0.2865	M	0.76170	2.325	0.49687	D	0.999819	B;P	0.41366	0.203;0.747	B;B	0.31495	0.026;0.131	T	0.72191	-0.4365	10	0.56958	D	0.05	-11.5895	14.608	0.68495	0.0:0.9302:0.0:0.0698	rs35258567	418;418	Q9UP83;Q9UP83-2	COG5_HUMAN;.	H	418	ENSP00000334703:R418H;ENSP00000297135:R418H;ENSP00000377228:R418H	ENSP00000297135:R418H	R	-	2	0	COG5	106725976	1.000000	0.71417	1.000000	0.80357	0.471000	0.32888	4.194000	0.58393	1.417000	0.47077	-0.142000	0.14014	CGT	C|0.999;T|0.001	0.001	strong		0.343	COG5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060216.4			T	106938740	C	T	106938740	3	4	22	1	0	0	0	0	1	0	0	0	3663	536	19	1	1377	1	COG5	7	106938740	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	147293	106938740	52199923	1730	4631											
COG5	10466	hgsc.bcm.edu	37	chr7	107204371	107204371	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgccgggttgatgtcgtcagCagcagaacggctccgcccag	7	7	14	13	4	1	2	1	1	0	1	3	2	2	2	3	2	4	4	3	2	1	1	rs73419464	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:107204371C>T	ENST00000347053.3	-	1	114	c.64G>A	c.(64-66)Gct>Act	p.A22T	DUS4L_ENST00000498786.1_Intron|DUS4L_ENST00000265720.3_5'Flank|COG5_ENST00000297135.3_Missense_Mutation_p.A22T|DUS4L_ENST00000402620.1_5'Flank|COG5_ENST00000393603.2_Missense_Mutation_p.A22T	NM_181733.2	NP_859422.2	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5	22					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						ATGTCGTCAGCAGCAGAACGG	0.697													C|||	152	0.0303514	0.1089	0.0101	5008	,	,		12302	0.0		0.0	False		,,,				2504	0.001				p.A22T		Atlas-SNP	.											.	COG5	78	.	0			c.G64A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	347,4057		15,317,1870	18	18	18		64,64,64	1.7	0.4	7	dbSNP_130	18	7,8587		0,7,4290	yes	missense,missense,missense	COG5	NM_181733.2,NM_006348.3,NM_001161520.1	58,58,58	15,324,6160	TT,TC,CC		0.0815,7.8792,2.7235	benign,benign,benign	22/840,22/861,22/824	107204371	354,12644	2202	4297	6499	SO:0001583	missense	10466	exon1			CGTCAGCAGCAGA	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.64G>A	7.37:g.107204371C>T	ENSP00000334703:p.Ala22Thr	93	0	0		112	64	0.571429	NM_006348	A4D0R6|A4D0R7|O14555|O95008|Q6NUL5	Missense_Mutation	SNP	ENST00000347053.3	37	CCDS5743.1	62	0.028388278388278388	57	0.11585365853658537	5	0.013812154696132596	0	0.0	0	0.0	C	14.15	2.449883	0.43531	0.078792	8.15E-4	ENSG00000164597	ENST00000347053;ENST00000297135;ENST00000393603	T;T;T	0.18502	2.22;2.21;2.21	4.76	1.72	0.24424	.	0.904518	0.09273	N	0.824937	T	0.00144	0.0004	N	0.08118	0	0.21355	N	0.999718	B;B	0.21905	0.037;0.062	B;B	0.20184	0.013;0.028	T	0.38067	-0.9678	10	0.28530	T	0.3	-1.6692	12.2534	0.54611	0.0:0.4485:0.5515:0.0	.	22;22	Q9UP83;Q9UP83-2	COG5_HUMAN;.	T	22	ENSP00000334703:A22T;ENSP00000297135:A22T;ENSP00000377228:A22T	ENSP00000297135:A22T	A	-	1	0	COG5	106991607	0.002000	0.14202	0.354000	0.25760	0.206000	0.24218	0.304000	0.19228	0.574000	0.29417	0.591000	0.81541	GCT	C|0.970;T|0.030	0.030	strong		0.697	COG5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060216.4			T	107204371	C	T	107204371	3	4	22	1	0	0	0	0	1	0	0	0	3663	710	25	2	2610	2	COG5	7	107204371	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	265631	107204371	51934292	1731	4632											
SLC26A4	5172	hgsc.bcm.edu	37	chr7	107342294	107342294	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggcatcataagtgatgctgTttcaacaaataatgcttttg	12	15	8	6	0	2	1	2	1	0	0	2	1	2	1	0	1	3	4	0	1	4	5	rs17154335	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:107342294T>G	ENST00000265715.3	+	17	2050	c.1826T>G	c.(1825-1827)gTt>gGt	p.V609G	SLC26A4_ENST00000544569.1_Missense_Mutation_p.V196G|SLC26A4_ENST00000480841.1_3'UTR|SLC26A4_ENST00000543100.1_Missense_Mutation_p.V178G|SLC26A4_ENST00000541474.1_Missense_Mutation_p.V170G	NM_000441.1	NP_000432.1	O43511	S26A4_HUMAN	solute carrier family 26 (anion exchanger), member 4	609	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.		V -> G (in dbSNP:rs17154335). {ECO:0000269|PubMed:15689455, ECO:0000269|PubMed:19204907}.		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						AGTGATGCTGTTTCAACAAAT	0.343									Pendred syndrome				G|||	229	0.0457268	0.1657	0.0115	5008	,	,		21715	0.0		0.002	False		,,,				2504	0.0				p.V609G		Atlas-SNP	.											.	SLC26A4	117	.	0			c.T1826G	GRCh37	CM050323	SLC26A4	M	rs17154335	PASS	.	G	GLY/VAL	629,3777	767.8+/-413.5	43,543,1617	97	96	96	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1826	5.8	0.9	7	dbSNP_123	96	7,8593	818.9+/-406.8	0,7,4293	yes	missense	SLC26A4	NM_000441.1	109	43,550,5910	GG,GT,TT		0.0814,14.276,4.8901	benign	609/781	107342294	636,12370	2203	4300	6503	SO:0001583	missense	5172	exon17	Familial Cancer Database	Goiter-Deafness syndrome	ATGCTGTTTCAAC	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.1826T>G	7.37:g.107342294T>G	ENSP00000265715:p.Val609Gly	89	0	0		92	43	0.467391	NM_000441	B7Z266|O43170	Missense_Mutation	SNP	ENST00000265715.3	37	CCDS5746.1	78	0.03571428571428571	71	0.1443089430894309	7	0.019337016574585635	0	0.0	0	0.0	G	14.16	2.453089	0.43531	0.14276	8.14E-4	ENSG00000091137	ENST00000265715;ENST00000541474;ENST00000544569;ENST00000543100	D;D;D;D	0.94793	-3.2;-3.47;-3.52;-3.51	5.83	5.83	0.93111	Sulphate transporter/antisigma-factor antagonist STAS (3);	0.120219	0.56097	N	0.000035	T	0.02304	0.0071	N	0.00237	-1.79	0.30149	P	0.80322	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.57493	-0.7802	9	0.20046	T	0.44	.	16.5365	0.84373	0.0:0.0:0.8681:0.1319	rs17154335;rs17154335	170;196;609	F5H104;B7Z6M6;O43511	.;.;S26A4_HUMAN	G	609;170;196;178	ENSP00000265715:V609G;ENSP00000439743:V170G;ENSP00000437427:V196G;ENSP00000441209:V178G	ENSP00000265715:V609G	V	+	2	0	SLC26A4	107129530	1.000000	0.71417	0.889000	0.34880	0.977000	0.68977	3.712000	0.54875	1.478000	0.48253	-0.121000	0.15023	GTT	T|0.952;G|0.048	0.048	strong		0.343	SLC26A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337148.1	NM_000441		G	107342294	T	G	107342294	3	3	22	1	0	0	0	0	1	0	0	0	14534	1725	60	5	1888	5	SLC26A4	7	107342294	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	137923	107342294	51796369	1732	4633											
LAMB1	3912	hgsc.bcm.edu	37	chr7	107591720	107591720	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aagagttcctggcactcgctGcaggtgcggcctccaaaccc	8	7	11	15	2	0	1	0	0	0	1	3	1	2	1	4	3	3	4	4	3	2	1	rs25660	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:107591720G>A	ENST00000222399.6	-	24	3572	c.3342C>T	c.(3340-3342)tgC>tgT	p.C1114C	LAMB1_ENST00000393561.1_Silent_p.C1138C	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	1114	Laminin EGF-like 12. {ECO:0000255|PROSITE-ProRule:PRU00460}.				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						GGCACTCGCTGCAGGTGCGGC	0.607													G|||	229	0.0457268	0.1694	0.0043	5008	,	,		16184	0.0		0.002	False		,,,				2504	0.0				p.C1114C		Atlas-SNP	.											.	LAMB1	185	.	0			c.C3342T						PASS	.	G		632,3774	269.2+/-268.9	40,552,1611	54	50	51		3342	4.1	1	7	dbSNP_72	51	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous	LAMB1	NM_002291.2		40,557,5906	AA,AG,GG		0.0581,14.3441,4.8977		1114/1787	107591720	637,12369	2203	4300	6503	SO:0001819	synonymous_variant	3912	exon24			CTCGCTGCAGGTG	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.3342C>T	7.37:g.107591720G>A		152	0	0		150	150	1	NM_002291	Q14D91	Silent	SNP	ENST00000222399.6	37	CCDS5750.1																																																																																			G|0.957;A|0.043	0.043	strong		0.607	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291		A	107591720	G	A	107591720	2	1	22	1	0	0	0	0	0	0	0	1	8619	1311	46	2		2	LAMB1	7	107591720	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	249426	107591720	51546943	1733	4634											
LAMB4	22798	hgsc.bcm.edu	37	chr7	107706208	107706208	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caagcactatactgcataccCgtataaccttgaagacaatt	15	10	5	11	1	0	2	0	1	0	1	0	2	0	2	2	0	5	3	2	0	8	7	rs73725316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:107706208C>T	ENST00000388781.3	-	21	2918	c.2835G>A	c.(2833-2835)acG>acA	p.T945T	LAMB4_ENST00000388780.3_Splice_Site_p.T945T|LAMB4_ENST00000205386.4_Splice_Site_p.T945T	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	945	Laminin EGF-like 9. {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						ACTGCATACCCGTATAACCTT	0.373													C|||	42	0.00838658	0.0303	0.0029	5008	,	,		20016	0.0		0.0	False		,,,				2504	0.0				p.T945T		Atlas-SNP	.											.	LAMB4	253	.	0			c.G2835A						PASS	.	C		113,4293	85.3+/-124.0	2,109,2092	123	116	118		2835	2.2	0.6	7	dbSNP_130	118	0,8600		0,0,4300	yes	coding-synonymous-near-splice	LAMB4	NM_007356.2		2,109,6392	TT,TC,CC		0.0,2.5647,0.8688		945/1762	107706208	113,12893	2203	4300	6503	SO:0001630	splice_region_variant	22798	exon21			CATACCCGTATAA	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.2836+1G>A	7.37:g.107706208C>T		118	0	0		108	51	0.472222	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Silent	SNP	ENST00000388781.3	37	CCDS34732.1																																																																																			C|0.992;T|0.008	0.008	strong		0.373	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857	Silent	T	107706208	C	T	107706208	5	4	22	1	0	0	0	0	0	0	1	0	8622	666	23	1	2506	1	LAMB4	7	107706208	Splice_Site	SNP	C	TCGA-G8-6324-01A-11D-2210-10	114488	107706208	51432455	1734	4635											
LAMB4	22798	hgsc.bcm.edu	37	chr7	107756510	107756510	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccacaggtagaagaagccAtaagctgcgtgttcctgccc	10	7	11	13	1	0	2	0	0	0	2	1	2	1	2	4	1	4	3	4	1	4	3	rs35644375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:107756510A>G	ENST00000388781.3	-	3	214	c.131T>C	c.(130-132)aTg>aCg	p.M44T	LAMB4_ENST00000388780.3_Missense_Mutation_p.M44T|LAMB4_ENST00000205386.4_Missense_Mutation_p.M44T|LAMB4_ENST00000414450.2_Missense_Mutation_p.M44T|LAMB4_ENST00000418464.1_Missense_Mutation_p.M44T	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	44	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.		M -> T (in dbSNP:rs35644375).		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						AGAAGAAGCCATAAGCTGCGT	0.512													G|||	503	0.100439	0.3631	0.0317	5008	,	,		19458	0.0		0.001	False		,,,				2504	0.0				p.M44T		Atlas-SNP	.											.	LAMB4	253	.	0			c.T131C						PASS	.	G	THR/MET	1279,3127	700.8+/-406.7	186,907,1110	105	106	106		131	2.8	0	7	dbSNP_126	106	32,8568	817.9+/-406.9	0,32,4268	yes	missense	LAMB4	NM_007356.2	81	186,939,5378	GG,GA,AA		0.3721,29.0286,10.08	benign	44/1762	107756510	1311,11695	2203	4300	6503	SO:0001583	missense	22798	exon3			GAAGCCATAAGCT	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.131T>C	7.37:g.107756510A>G	ENSP00000373433:p.Met44Thr	92	0	0		101	41	0.405941	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	37	CCDS34732.1	190	0.08699633699633699	177	0.3597560975609756	13	0.03591160220994475	0	0.0	0	0.0	G	0.019	-1.450644	0.01080	0.290286	0.003721	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000388780;ENST00000418464;ENST00000414450	T;T;T;T;T	0.73789	-0.78;-0.78;-0.78;-0.78;-0.78	5.6	2.81	0.32909	Laminin, N-terminal (3);	0.560407	0.16178	N	0.225961	T	0.00012	0.0000	N	0.00099	-2.14	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.26849	-1.0091	9	0.06625	T	0.88	.	6.7977	0.23734	0.2544:0.0:0.6319:0.1136	rs35644375;rs60836843	44	A4D0S4	LAMB4_HUMAN	T	44	ENSP00000205386:M44T;ENSP00000373433:M44T;ENSP00000373432:M44T;ENSP00000402353:M44T;ENSP00000402265:M44T	ENSP00000205386:M44T	M	-	2	0	LAMB4	107543746	0.000000	0.05858	0.003000	0.11579	0.082000	0.17680	0.434000	0.21494	0.049000	0.15920	-0.735000	0.03563	ATG	A|0.908;G|0.092	0.092	strong		0.512	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		G	107756510	A	G	107756510	3	3	22	1	0	0	0	0	1	0	0	0	8622	217	8	3	5282	3	LAMB4	7	107756510	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	50302	107756510	51382153	1735	4636											
NRCAM	4897	hgsc.bcm.edu	37	chr7	107790417	107790417	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgagctttcgtttccttcagCcggctctttctctttcttac	3	19	6	13	2	4	1	1	1	3	0	7	1	5	1	2	1	3	3	2	1	1	6	rs74708699	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:107790417C>T	ENST00000425651.2	-	30	3852	c.3853G>A	c.(3853-3855)Gct>Act	p.A1285T	NRCAM_ENST00000351718.4_Missense_Mutation_p.A1164T|NRCAM_ENST00000379024.4_Missense_Mutation_p.A1173T|NRCAM_ENST00000379028.3_Missense_Mutation_p.A1285T|NRCAM_ENST00000413765.2_Missense_Mutation_p.A1161T|NRCAM_ENST00000522550.2_5'UTR	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	1285					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						TTTCCTTCAGCCGGCTCTTTC	0.428													C|||	36	0.0071885	0.0272	0.0	5008	,	,		15356	0.0		0.0	False		,,,				2504	0.0				p.A1285T		Atlas-SNP	.											.	NRCAM	267	.	0			c.G3853A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	115,4291	87.8+/-126.4	0,115,2088	161	150	154		3853,3574,3517,3481,3490	5.3	0.5	7	dbSNP_131	154	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense,missense,missense,missense	NRCAM	NM_001037132.2,NM_001193582.1,NM_001193583.1,NM_001193584.1,NM_005010.4	58,58,58,58,58	0,118,6385	TT,TC,CC		0.0349,2.6101,0.9073	benign,benign,benign,benign,benign	1285/1305,1192/1212,1173/1193,1161/1181,1164/1184	107790417	118,12888	2203	4300	6503	SO:0001583	missense	4897	exon30			CTTCAGCCGGCTC		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.3853G>A	7.37:g.107790417C>T	ENSP00000401244:p.Ala1285Thr	214	0	0		175	93	0.531429	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Missense_Mutation	SNP	ENST00000425651.2	37	CCDS47686.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	12.19	1.863087	0.32884	0.026101	3.49E-4	ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000413765;ENST00000437386;ENST00000351718;ENST00000379024;ENST00000425651	T;T;T;T;T	0.58940	0.34;0.57;0.3;0.35;0.34	6.17	5.3	0.74995	.	0.344041	0.33290	N	0.005080	T	0.15912	0.0383	N	0.14661	0.345	0.80722	D	1	B;B;B;B;B;B;P	0.47106	0.01;0.001;0.144;0.021;0.036;0.001;0.89	B;B;B;B;B;B;B	0.37833	0.021;0.002;0.17;0.011;0.016;0.004;0.259	T	0.09228	-1.0684	10	0.13108	T	0.6	.	15.699	0.77528	0.0:0.9348:0.0:0.0652	.	1289;131;1161;1173;1164;1285;68	Q92823-5;B4DFP9;Q92823-3;E9PDA4;Q92823-4;Q92823;Q6QRP2	.;.;.;.;.;NRCAM_HUMAN;.	T	1289;1285;1161;129;1164;1173;1285	ENSP00000368314:A1285T;ENSP00000407858:A1161T;ENSP00000325269:A1164T;ENSP00000368310:A1173T;ENSP00000401244:A1285T	ENSP00000325269:A1164T	A	-	1	0	NRCAM	107577653	1.000000	0.71417	0.514000	0.27761	0.983000	0.72400	5.115000	0.64655	1.630000	0.50440	0.655000	0.94253	GCT	C|0.990;T|0.010	0.010	strong		0.428	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132		T	107790417	C	T	107790417	3	4	22	1	0	0	0	0	1	0	0	0	10653	739	26	2	65	2	NRCAM	7	107790417	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	33907	107790417	51348246	1736	4637											
DNAJB9	4189	hgsc.bcm.edu	37	chr7	108213545	108213545	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagaagcgttttgaaaatcaTttccagacacgccaggatgg	14	9	10	8	2	1	3	1	1	0	2	2	4	2	4	2	2	1	1	2	2	4	3	rs376971670		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:108213545T>C	ENST00000249356.3	+	3	966	c.420T>C	c.(418-420)caT>caC	p.H140H	DNAJB9_ENST00000465725.1_Intron	NM_012328.2	NP_036460.1	Q9UBS3	DNJB9_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 9	140					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						TTGAAAATCATTTCCAGACAC	0.363																																					p.H140H		Atlas-SNP	.											DNAJB9,NS,carcinoma,+1,1	DNAJB9	25	1	0			c.T420C						PASS	.	T		2,4404	4.2+/-10.8	0,2,2201	110	109	109		420	0.7	1	7		109	0,8600		0,0,4300	no	coding-synonymous	DNAJB9	NM_012328.2		0,2,6501	CC,CT,TT		0.0,0.0454,0.0154		140/224	108213545	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	4189	exon3			AAATCATTTCCAG	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.420T>C	7.37:g.108213545T>C		172	0	0		176	83	0.471591	NM_012328		Silent	SNP	ENST00000249356.3	37	CCDS5752.1																																																																																			.	.	weak		0.363	DNAJB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337414.1			C	108213545	T	C	108213545	2	2	22	1	0	0	0	0	0	0	0	1	4629	1490	52	3		3	DNAJB9	7	108213545	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	423128	108213545	50925118	1737	4638											
LRRN3	54674	hgsc.bcm.edu	37	chr7	110763563	110763563	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaaagcatctctttttacgaTaacaggcttattaaagtacc	14	13	6	8	1	1	0	0	0	1	0	2	2	1	0	1	1	4	3	1	1	7	7	rs214865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:110763563T>C	ENST00000422987.3	+	2	1566	c.735T>C	c.(733-735)gaT>gaC	p.D245D	LRRN3_ENST00000451085.1_Silent_p.D245D|IMMP2L_ENST00000437687.1_Intron|IMMP2L_ENST00000452895.1_Intron|IMMP2L_ENST00000450877.1_Intron|IMMP2L_ENST00000415362.1_Intron|IMMP2L_ENST00000489381.1_Intron|IMMP2L_ENST00000447215.1_Intron|IMMP2L_ENST00000405709.2_Intron|LRRN3_ENST00000308478.5_Silent_p.D245D|IMMP2L_ENST00000331762.3_Intron	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	245					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)		CTTTTTACGATAACAGGCTTA	0.358													C|||	472	0.0942492	0.3011	0.0418	5008	,	,		18738	0.002		0.0298	False		,,,				2504	0.0133				p.D245D		Atlas-SNP	.											.	LRRN3	132	.	0			c.T735C						PASS	.	C	,,,	1203,3203	693.7+/-405.7	159,885,1159	55	59	57		735,735,735,	3.2	1	7	dbSNP_79	57	236,8360	793.0+/-407.5	3,230,4065	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	LRRN3,IMMP2L	NM_001099658.1,NM_001099660.1,NM_018334.4,NM_032549.3	,,,	162,1115,5224	CC,CT,TT		2.7455,27.3037,11.0675	,,,	245/709,245/709,245/709,	110763563	1439,11563	2203	4298	6501	SO:0001819	synonymous_variant	54674	exon2			TTACGATAACAGG	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.735T>C	7.37:g.110763563T>C		107	0	0		144	75	0.520833	NM_018334	O43377|Q6I9V8|Q8IYQ6	Silent	SNP	ENST00000422987.3	37	CCDS5754.1																																																																																			T|0.892;C|0.108	0.108	strong		0.358	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334		C	110763563	T	C	110763563	2	2	22	1	0	0	0	0	0	0	0	1	9045	1403	49	3		3	LRRN3	7	110763563	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2550018	110763563	48375100	1738	4639											
DOCK4	9732	hgsc.bcm.edu	37	chr7	111400275	111400275	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agatggtctcatcgggctggTtggcgtgctgcatggcgatg	5	11	17	8	3	1	1	1	0	1	1	3	2	1	1	0	5	2	4	0	5	0	1	rs374962931		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:111400275T>C	ENST00000437633.1	-	39	4353	c.4097A>G	c.(4096-4098)aAc>aGc	p.N1366S	DOCK4_ENST00000428084.1_Missense_Mutation_p.N1375S|DOCK4_ENST00000494651.2_Missense_Mutation_p.N249S	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	1366	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)				ATCGGGCTGGTTGGCGTGCTG	0.552																																					p.N1366S		Atlas-SNP	.											.	DOCK4	365	.	0			c.A4097G						PASS	.	T	SER/ASN	2,4310		0,2,2154	184	186	185		4097	4.6	1	7		185	0,8506		0,0,4253	no	missense	DOCK4	NM_014705.3	46	0,2,6407	CC,CT,TT		0.0,0.0464,0.0156	benign	1366/1967	111400275	2,12816	2156	4253	6409	SO:0001583	missense	9732	exon39			GGCTGGTTGGCGT		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.4097A>G	7.37:g.111400275T>C	ENSP00000404179:p.Asn1366Ser	128	0	0		139	63	0.453237	NM_014705	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	37	CCDS47688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.83|11.83	1.755933|1.755933	0.31137|0.31137	4.64E-4|4.64E-4	0.0|0.0	ENSG00000128512|ENSG00000128512	ENST00000352877;ENST00000428084;ENST00000494651;ENST00000437633;ENST00000342288|ENST00000423057;ENST00000445943	T;T;T|.	0.05996|.	4.12;3.36;4.12|.	4.62|4.62	4.62|4.62	0.57501|0.57501	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.53965|0.53965	0.1829|0.1829	L|L	0.29908|0.29908	0.895|0.895	0.49798|0.49798	D|D	0.999821|0.999821	B;B;B;B;B|.	0.28998|.	0.112;0.178;0.22;0.23;0.178|.	B;B;B;B;B|.	0.30716|.	0.023;0.051;0.119;0.119;0.084|.	T|T	0.50931|0.50931	-0.8769|-0.8769	10|5	0.02654|.	T|.	1|.	.|.	14.4645|14.4645	0.67475|0.67475	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	273;249;1411;1366;1375|.	B7Z2K9;F5GXW1;Q149N5;Q8N1I0;Q8N1I0-2|.	.;.;.;DOCK4_HUMAN;.|.	S|A	1354;1375;249;1366;1363|827;1399	ENSP00000410746:N1375S;ENSP00000440944:N249S;ENSP00000404179:N1366S|.	ENSP00000345432:N1363S|.	N|T	-|-	2|1	0|0	DOCK4|DOCK4	111187511|111187511	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.086000|6.086000	0.71352|0.71352	2.066000|2.066000	0.61787|0.61787	0.482000|0.482000	0.46254|0.46254	AAC|ACC	.	.	weak		0.552	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705		C	111400275	T	C	111400275	3	2	22	1	0	0	0	0	1	0	0	0	4691	1725	60	3	1859	3	DOCK4	7	111400275	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	636712	111400275	47738388	1739	4640											
GPR85	54329	hgsc.bcm.edu	37	chr7	112724147	112724147	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcttcatttttcttcgatcGtggacgaaaaatatcagctt	10	15	8	8	3	3	0	2	0	1	0	5	3	3	1	0	2	1	2	0	2	3	6	rs28392728	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:112724147G>A	ENST00000297146.3	-	3	1233	c.630C>T	c.(628-630)caC>caT	p.H210H	GPR85_ENST00000449591.1_Silent_p.H210H|GPR85_ENST00000501255.2_Silent_p.H210H|GPR85_ENST00000487573.1_5'Flank|GPR85_ENST00000424100.1_Silent_p.H210H	NM_001146266.1	NP_001139738.1	P60893	GPR85_HUMAN	G protein-coupled receptor 85	210					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						TTCTTCGATCGTGGACGAAAA	0.498													G|||	97	0.019369	0.0703	0.0058	5008	,	,		19678	0.0		0.0	False		,,,				2504	0.0				p.H210H		Atlas-SNP	.											.	GPR85	49	.	0			c.C630T						PASS	.	G	,,,	296,4110	162.2+/-194.2	11,274,1918	56	55	55		630,630,630,630	-1.6	0.9	7	dbSNP_125	55	3,8597	1.2+/-3.3	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GPR85	NM_001146265.1,NM_001146266.1,NM_001146267.1,NM_018970.6	,,,	11,277,6215	AA,AG,GG		0.0349,6.7181,2.2989	,,,	210/371,210/371,210/371,210/371	112724147	299,12707	2203	4300	6503	SO:0001819	synonymous_variant	54329	exon3			TCGATCGTGGACG	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.630C>T	7.37:g.112724147G>A		91	0	0		94	39	0.414894	NM_001146265	Q9JHI6|Q9NPD1	Silent	SNP	ENST00000297146.3	37	CCDS5758.1																																																																																			G|0.978;A|0.022	0.022	strong		0.498	GPR85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346650.2			A	112724147	G	A	112724147	2	1	22	1	0	0	0	0	0	0	0	1	6723	1136	40	1		1	GPR85	7	112724147	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1323872	112724147	46414516	1740	4641											
PPP1R3A	5506	hgsc.bcm.edu	37	chr7	113519267	113519267	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttggaaaagataatcattcCtcaaaacatttccagttctt	14	14	4	9	0	3	1	2	0	1	1	5	2	5	2	2	1	1	1	2	1	5	6	rs35067467	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:113519267C>T	ENST00000284601.3	-	4	1948	c.1880G>A	c.(1879-1881)aGg>aAg	p.R627K		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	627			R -> K (in dbSNP:rs35067467).		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						ATAATCATTCCTCAAAACATT	0.393													C|||	187	0.0373403	0.1339	0.0115	5008	,	,		20272	0.0		0.002	False		,,,				2504	0.0				p.R627K		Atlas-SNP	.											.	PPP1R3A	317	.	0			c.G1880A						PASS	.	C	LYS/ARG	455,3951	213.5+/-233.1	22,411,1770	83	81	82		1880	-3.9	0	7	dbSNP_126	82	9,8591	6.4+/-24.3	0,9,4291	yes	missense	PPP1R3A	NM_002711.3	26	22,420,6061	TT,TC,CC		0.1047,10.3268,3.5676	benign	627/1123	113519267	464,12542	2203	4300	6503	SO:0001583	missense	5506	exon4			TCATTCCTCAAAA	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.1880G>A	7.37:g.113519267C>T	ENSP00000284601:p.Arg627Lys	253	0	0		238	121	0.508403	NM_002711	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Missense_Mutation	SNP	ENST00000284601.3	37	CCDS5759.1	68	0.031135531135531136	61	0.12398373983739837	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	C	0.023	-1.404787	0.01155	0.103268	0.001047	ENSG00000154415	ENST00000284601	T	0.15256	2.44	6.02	-3.93	0.04143	.	1.218990	0.05550	N	0.567306	T	0.00178	0.0005	L	0.31294	0.92	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39881	-0.9592	9	0.15499	T	0.54	-0.3547	9.053	0.36387	0.0:0.3009:0.11:0.5891	rs35067467	627	Q16821	PPR3A_HUMAN	K	627	ENSP00000284601:R627K	ENSP00000284601:R627K	R	-	2	0	PPP1R3A	113306503	0.000000	0.05858	0.000000	0.03702	0.122000	0.20287	-0.502000	0.06390	-0.652000	0.05408	-1.106000	0.02097	AGG	C|0.959;T|0.041	0.041	strong		0.393	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711		T	113519267	C	T	113519267	3	4	22	1	0	0	0	0	1	0	0	0	12383	681	24	2	1492	2	PPP1R3A	7	113519267	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	795120	113519267	45619396	1741	4642											
MET	4233	hgsc.bcm.edu	37	chr7	116340269	116340269	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aacgacttcttcaacaagatCgtcaacaaaaacaatgtgag	18	8	6	9	2	3	2	2	1	1	1	4	3	3	2	0	0	4	0	0	0	7	2	rs28444388	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:116340269C>T	ENST00000318493.6	+	2	1318	c.1131C>T	c.(1129-1131)atC>atT	p.I377I	MET_ENST00000436117.2_Silent_p.I377I|MET_ENST00000397752.3_Silent_p.I377I			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)			TCAACAAGATCGTCAACAAAA	0.433			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				C|||	311	0.0621006	0.2262	0.013	5008	,	,		19263	0.0		0.002	False		,,,				2504	0.001				p.I377I		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.C1131T						PASS	.	C	,	744,3114		78,588,1263	105	97	100		1131,1131	-7.2	0.7	7	dbSNP_125	100	9,8271		0,9,4131	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	78,597,5394	TT,TC,CC		0.1087,19.2846,6.2037	,	377/1391,377/1409	116340269	753,11385	1929	4140	6069	SO:0001819	synonymous_variant	4233	exon2	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	CAAGATCGTCAAC	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.1131C>T	7.37:g.116340269C>T		36	0	0		42	17	0.404762	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			C|0.967;T|0.033	0.033	strong		0.433	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			T	116340269	C	T	116340269	2	4	22	1	0	0	0	0	0	0	0	1	9494	874	31	1		1	MET	7	116340269	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2821002	116340269	42798394	1742	4643											
ING3	54556	hgsc.bcm.edu	37	chr7	120610847	120610849	+	In_Frame_Del	DEL	AAC	AAC	-																															gtacaagaaatctctcaacaAacaactgtagtgccagaatc																								rs539687500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:120610847_120610849delAAC	ENST00000315870.5	+	10	1162_1164	c.1014_1016delAAC	c.(1012-1017)caaaca>caa	p.T340del	ING3_ENST00000431467.1_In_Frame_Del_p.T325del	NM_019071.2	NP_061944.2	Q9NXR8	ING3_HUMAN	inhibitor of growth family, member 3	340					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)					TCTCTCAACAAACAACTGTAGTG	0.394														6	0.00119808	0.0045	0.0	5008	,	,		17162	0.0		0.0	False		,,,				2504	0.0				p.338_339del		Pindel,Atlas-Indel	.											.	ING3	36	.	0			c.1013_1015del						PASS	.																																			SO:0001651	inframe_deletion	54556	exon10			.	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.1014_1016delAAC	7.37:g.120610850_120610852delAAC	ENSP00000320566:p.Thr340del	112	0	.		92	37	0.402	NM_019071	A8K790|O60394|Q567P3|Q6GMT3|Q7Z762|Q969G0|Q96DT4|Q9HC99|Q9P081	In_Frame_Del	DEL	ENST00000315870.5	37	CCDS5778.1																																																																																			.	.	none		0.394	ING3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280453.2	NM_019071		-	120610849	AAC	-	120610847	7	5	22	1	0	1	0	1	0	0	0	0	7746	11	1	0	1068	0	ING3	7	120610847	In_Frame_Del	DEL	AAC	TCGA-G8-6324-01A-11D-2210-10	4270578	120610847	38527816	1743	4644											
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121652964	121652964	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtggtaccttctttgtacagTaatgatgagttgttccaaac	10	15	9	7	0	1	2	0	2	1	0	2	2	2	2	2	1	3	5	2	1	4	7	rs139671030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:121652964T>C	ENST00000393386.2	+	12	4275	c.3864T>C	c.(3862-3864)agT>agC	p.S1288S	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	1288					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						CTTTGTACAGTAATGATGAGT	0.398													T|||	22	0.00439297	0.0166	0.0	5008	,	,		20087	0.0		0.0	False		,,,				2504	0.0				p.S1288S		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.T3864C						PASS	.	T	,,	46,4360	45.3+/-79.5	0,46,2157	74	69	70		,,3864	-1.6	0	7	dbSNP_134	70	0,8600		0,0,4300	yes	intron,intron,coding-synonymous	PTPRZ1	NM_001206838.1,NM_001206839.1,NM_002851.2	,,	0,46,6457	CC,CT,TT		0.0,1.044,0.3537	,,	,,1288/2316	121652964	46,12960	2203	4300	6503	SO:0001819	synonymous_variant	5803	exon12			GTACAGTAATGAT	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.3864T>C	7.37:g.121652964T>C		116	0	0		114	52	0.45614	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Silent	SNP	ENST00000393386.2	37	CCDS34740.1																																																																																			T|0.997;C|0.003	0.003	strong		0.398	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		C	121652964	T	C	121652964	2	2	22	1	0	0	0	0	0	0	0	1	12829	1635	57	3		3	PTPRZ1	7	121652964	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1042117	121652964	37485699	1744	4645											
SLC13A1	6561	hgsc.bcm.edu	37	chr7	122787306	122787306	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agtaggcaatgcacaaacacGtaagtttacgtgtcacgtgg	13	9	11	8	3	1	0	1	0	0	0	1	0	1	0	0	2	3	5	0	2	5	4	rs10231144	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:122787306G>A	ENST00000194130.2	-	7	758	c.719C>T	c.(718-720)aCg>aTg	p.T240M	SLC13A1_ENST00000539873.1_3'UTR	NM_022444.3	NP_071889.2	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 1	240			T -> M (in dbSNP:rs10231144).		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)	GCACAAACACGTAAGTTTACG	0.413													A|||	31	0.0061901	0.0227	0.0014	5008	,	,		20613	0.0		0.0	False		,,,				2504	0.0				p.T240M		Atlas-SNP	.											.	SLC13A1	110	.	0			c.C719T						PASS	.	A	MET/THR	92,4314	818.0+/-416.3	0,92,2111	236	180	199		719	5	1	7	dbSNP_119	199	1,8599		0,1,4299	yes	missense	SLC13A1	NM_022444.3	81	0,93,6410	AA,AG,GG		0.0116,2.0881,0.7151	benign	240/596	122787306	93,12913	2203	4300	6503	SO:0001583	missense	6561	exon7			AAACACGTAAGTT		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.719C>T	7.37:g.122787306G>A	ENSP00000194130:p.Thr240Met	95	0	0		136	79	0.580882	NM_022444	Q9H5Z0	Missense_Mutation	SNP	ENST00000194130.2	37	CCDS5786.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	A	3.455	-0.111112	0.06881	0.020881	1.16E-4	ENSG00000081800	ENST00000194130	T	0.63913	-0.07	5.0	5.0	0.66597	.	0.085242	0.85682	N	0.000000	T	0.05914	0.0154	N	0.00030	-2.605	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.04946	-1.0916	10	0.13108	T	0.6	.	9.0284	0.36243	0.9119:0.0:0.0881:0.0	rs10231144;rs52791983;rs57837984;rs10231144	240;240	A4D0X1;Q9BZW2	.;S13A1_HUMAN	M	240	ENSP00000194130:T240M	ENSP00000194130:T240M	T	-	2	0	SLC13A1	122574542	1.000000	0.71417	0.997000	0.53966	0.706000	0.40770	6.172000	0.71932	0.772000	0.33382	-0.360000	0.07572	ACG	G|0.989;A|0.011	0.011	strong		0.413	SLC13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347404.1	NM_022444		A	122787306	G	A	122787306	3	1	22	1	0	0	0	0	1	0	0	0	14406	1145	40	1	1104	1	SLC13A1	7	122787306	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1134342	122787306	36351357	1745	4646											
ASB15	142685	hgsc.bcm.edu	37	chr7	123267200	123267200	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tttggcggatgatggggcgtCggtgctgtttgaggcagcag	5	11	19	6	3	0	2	0	2	0	0	1	3	0	3	0	6	2	4	0	6	0	2	rs73718440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:123267200C>T	ENST00000451558.1	+	11	1255	c.734C>T	c.(733-735)tCg>tTg	p.S245L	RP11-390E23.3_ENST00000429396.1_RNA|ASB15_ENST00000451215.1_Missense_Mutation_p.S245L|RP11-390E23.3_ENST00000440504.1_RNA|ASB15_ENST00000540573.1_Missense_Mutation_p.S245L|ASB15_ENST00000275699.3_Missense_Mutation_p.S245L|RP11-390E23.3_ENST00000451016.1_RNA|ASB15_ENST00000434204.1_Missense_Mutation_p.S245L|RP11-390E23.3_ENST00000422401.1_RNA|RP11-390E23.3_ENST00000418409.1_RNA			Q8WXK1	ASB15_HUMAN	ankyrin repeat and SOCS box containing 15	245					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|kidney(1)|large_intestine(1)|lung(6)|skin(3)	12						GATGGGGCGTCGGTGCTGTTT	0.488													C|||	39	0.00778754	0.0295	0.0	5008	,	,		17121	0.0		0.0	False		,,,				2504	0.0				p.S245L		Atlas-SNP	.											.	ASB15	94	.	0			c.C734T						PASS	.	C	LEU/SER	96,4310	78.8+/-117.2	0,96,2107	178	141	153		734	5.6	0.8	7	dbSNP_130	153	1,8599		0,1,4299	yes	missense	ASB15	NM_080928.3	145	0,97,6406	TT,TC,CC		0.0116,2.1788,0.7458	probably-damaging	245/589	123267200	97,12909	2203	4300	6503	SO:0001583	missense	142685	exon7			GGGCGTCGGTGCT	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.734C>T	7.37:g.123267200C>T	ENSP00000397655:p.Ser245Leu	277	0	0		315	149	0.473016	NM_080928	Q3ZCP3|Q3ZCP5|Q68D37	Missense_Mutation	SNP	ENST00000451558.1	37	CCDS34742.1	15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	C	19.14	3.770300	0.69992	0.021788	1.16E-4	ENSG00000146809	ENST00000451558;ENST00000434204;ENST00000451215;ENST00000540573;ENST00000542545;ENST00000275699	T;T;T;T;T	0.16897	2.31;2.31;2.31;2.31;2.31	5.57	5.57	0.84162	Ankyrin repeat-containing domain (4);	0.000000	0.56097	D	0.000022	T	0.16557	0.0398	L	0.48642	1.525	0.46317	D	0.99898	D	0.89917	1.0	D	0.81914	0.995	T	0.00964	-1.1498	10	0.87932	D	0	-24.7501	19.5537	0.95331	0.0:1.0:0.0:0.0	.	245	Q8WXK1	ASB15_HUMAN	L	245;245;245;245;34;245	ENSP00000397655:S245L;ENSP00000390963:S245L;ENSP00000416433:S245L;ENSP00000438643:S245L;ENSP00000275699:S245L	ENSP00000275699:S245L	S	+	2	0	ASB15	123054436	0.989000	0.36119	0.802000	0.32245	0.453000	0.32348	3.285000	0.51716	2.614000	0.88457	0.557000	0.71058	TCG	C|0.993;T|0.007	0.007	strong		0.488	ASB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347493.1			T	123267200	C	T	123267200	3	4	22	1	0	0	0	0	1	0	0	0	1019	893	31	1	756	1	ASB15	7	123267200	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	479894	123267200	35871463	1746	4647											
ASB15	142685	hgsc.bcm.edu	37	chr7	123269280	123269280	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taatgtcaattgttattttaTgcatgtgaatgacactcgtt	11	18	7	5	1	1	2	1	2	0	0	2	2	1	2	0	0	1	3	0	0	5	6	rs73718442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:123269280T>C	ENST00000451558.1	+	12	1753	c.1232T>C	c.(1231-1233)aTg>aCg	p.M411T	ASB15_ENST00000451215.1_Missense_Mutation_p.M411T|ASB15_ENST00000540573.1_Missense_Mutation_p.M411T|ASB15_ENST00000275699.3_Missense_Mutation_p.M411T|ASB15_ENST00000434204.1_Missense_Mutation_p.M411T			Q8WXK1	ASB15_HUMAN	ankyrin repeat and SOCS box containing 15	411					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|kidney(1)|large_intestine(1)|lung(6)|skin(3)	12						TGTTATTTTATGCATGTGAAT	0.418													T|||	42	0.00838658	0.0303	0.0	5008	,	,		21984	0.001		0.001	False		,,,				2504	0.0				p.M411T		Atlas-SNP	.											.	ASB15	94	.	0			c.T1232C						PASS	.	T	THR/MET	102,4304	81.9+/-120.4	1,100,2102	151	134	140		1232	6.2	1	7	dbSNP_130	140	1,8599		0,1,4299	yes	missense	ASB15	NM_080928.3	81	1,101,6401	CC,CT,TT		0.0116,2.315,0.7919	benign	411/589	123269280	103,12903	2203	4300	6503	SO:0001583	missense	142685	exon8			ATTTTATGCATGT	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.1232T>C	7.37:g.123269280T>C	ENSP00000397655:p.Met411Thr	129	0	0		129	66	0.511628	NM_080928	Q3ZCP3|Q3ZCP5|Q68D37	Missense_Mutation	SNP	ENST00000451558.1	37	CCDS34742.1	15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	T	6.119	0.390139	0.11581	0.02315	1.16E-4	ENSG00000146809	ENST00000451558;ENST00000434204;ENST00000451215;ENST00000540573;ENST00000542545;ENST00000275699	T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2	6.17	6.17	0.99709	Ankyrin repeat-containing domain (2);	0.000000	0.85682	D	0.000000	T	0.25827	0.0629	L	0.43152	1.355	0.37857	D	0.929585	B	0.15473	0.013	B	0.09377	0.004	T	0.40739	-0.9547	10	0.06625	T	0.88	-21.3197	12.4321	0.55578	0.1256:0.0:0.0:0.8744	.	411	Q8WXK1	ASB15_HUMAN	T	411;411;411;411;200;411	ENSP00000397655:M411T;ENSP00000390963:M411T;ENSP00000416433:M411T;ENSP00000438643:M411T;ENSP00000275699:M411T	ENSP00000275699:M411T	M	+	2	0	ASB15	123056516	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	1.015000	0.29963	2.371000	0.80710	0.533000	0.62120	ATG	T|0.992;C|0.008	0.008	strong		0.418	ASB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347493.1			C	123269280	T	C	123269280	3	2	22	1	0	0	0	0	1	0	0	0	1019	1464	51	3	1258	3	ASB15	7	123269280	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2080	123269280	35869383	1747	4648											
POT1	25913	hgsc.bcm.edu	37	chr7	124464037	124464037	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagattacatcttctgcaacTgtggtgtcaaaaatctgata	13	14	7	7	0	4	2	1	1	3	1	4	2	4	2	0	1	3	1	0	1	6	4	rs17147565	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:124464037T>G	ENST00000357628.3	-	19	2482	c.1884A>C	c.(1882-1884)acA>acC	p.T628T	POT1_ENST00000393329.1_Silent_p.T497T	NM_015450.2	NP_056265.2	Q9NUX5	POTE1_HUMAN	protection of telomeres 1	628					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						CTTCTGCAACTGTGGTGTCAA	0.363													T|||	144	0.028754	0.1044	0.0086	5008	,	,		18834	0.0		0.0	False		,,,				2504	0.0				p.T628T	Esophageal Squamous(149;1032 1141 16047 36610 40540 42429 44687 51642)	Atlas-SNP	.											POT1_ENST00000357628,NS,carcinoma,-2,2	POT1	186	2	0			c.A1884C						PASS	.	T	,	448,3956	212.5+/-232.4	28,392,1782	192	166	175		1491,1884	-0.8	0.9	7	dbSNP_123	175	2,8592	2.2+/-6.3	0,2,4295	no	coding-synonymous,coding-synonymous	POT1	NM_001042594.1,NM_015450.2	,	28,394,6077	GG,GT,TT		0.0233,10.1726,3.4621	,	497/504,628/635	124464037	450,12548	2202	4297	6499	SO:0001819	synonymous_variant	25913	exon19			TGCAACTGTGGTG	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.1884A>C	7.37:g.124464037T>G		200	0	0		194	102	0.525773	NM_015450	O95018|Q5MJ36|Q9H662|Q9NW19|Q9UG95	Silent	SNP	ENST00000357628.3	37	CCDS5793.1	52	0.023809523809523808	49	0.09959349593495935	3	0.008287292817679558	0	0.0	0	0.0	T	9.568	1.120153	0.20877	0.101726	2.33E-4	ENSG00000128513	ENST00000436534	.	.	.	5.95	-0.844	0.10741	.	.	.	.	.	T	0.01940	0.0061	.	.	.	0.58432	D	0.999991	.	.	.	.	.	.	T	0.02917	-1.1094	4	.	.	.	0.0241	5.3043	0.15795	0.1235:0.3184:0.0:0.5581	rs17147565;rs17147565	.	.	.	R	127	.	.	S	-	1	0	POT1	124251273	0.779000	0.28652	0.918000	0.36340	0.990000	0.78478	0.164000	0.16542	-0.092000	0.12417	0.533000	0.62120	AGT	T|0.970;G|0.030	0.030	strong		0.363	POT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347861.1			G	124464037	T	G	124464037	2	3	22	1	0	0	0	0	0	0	0	1	12269	1567	55	5		5	POT1	7	124464037	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1194757	124464037	34674626	1748	4649											
GRM8	2918	hgsc.bcm.edu	37	chr7	126173902	126173902	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	caggctgcagacagacgccgGgtgagtatgttctctatgag	9	9	14	9	2	1	4	0	2	1	2	2	4	1	4	1	2	1	4	1	2	2	3	rs61753365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:126173902G>C	ENST00000339582.2	-	9	2342	c.1534C>G	c.(1534-1536)Ccg>Gcg	p.P512A	GRM8_ENST00000480995.1_Intron|GRM8_ENST00000358373.3_Missense_Mutation_p.P512A|GRM8_ENST00000444921.2_Missense_Mutation_p.P512A			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	512					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)				ACAGACGCCGGGTGAGTATGT	0.488										HNSCC(24;0.065)			G|||	89	0.0177716	0.0635	0.0072	5008	,	,		17794	0.0		0.0	False		,,,				2504	0.0				p.P512A		Atlas-SNP	.											GRM8,NS,carcinoma,+2,1	GRM8	377	1	0			c.C1534G						scavenged	.	G	ALA/PRO,ALA/PRO	274,4132	149.2+/-183.4	11,252,1940	53	57	56		1534,1534	5.8	1	7	dbSNP_129	56	3,8597		0,3,4297	yes	missense,missense	GRM8	NM_000845.2,NM_001127323.1	27,27	11,255,6237	CC,CG,GG		0.0349,6.2188,2.1298	probably-damaging,probably-damaging	512/909,512/909	126173902	277,12729	2203	4300	6503	SO:0001583	missense	2918	exon8			ACGCCGGGTGAGT		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.1534C>G	7.37:g.126173902G>C	ENSP00000344173:p.Pro512Ala	99	1	0.010101		111	54	0.486486	NM_000845	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	Missense_Mutation	SNP	ENST00000339582.2	37	CCDS5794.1	32	0.014652014652014652	29	0.05894308943089431	3	0.008287292817679558	0	0.0	0	0.0	G	20.9	4.059053	0.76074	0.062188	3.49E-4	ENSG00000179603	ENST00000339582;ENST00000444921;ENST00000358373	D;D;D	0.92699	-3.09;-3.09;-3.09	5.8	5.8	0.92144	GPCR, family 3, nine cysteines domain (1);	0.000000	0.85682	D	0.000000	D	0.85805	0.5782	H	0.94582	3.555	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.86401	0.1742	10	0.87932	D	0	.	19.0428	0.93008	0.0:0.0:1.0:0.0	rs61753365	512;512	O00222-2;O00222	.;GRM8_HUMAN	A	512	ENSP00000344173:P512A;ENSP00000409790:P512A;ENSP00000351142:P512A	ENSP00000344173:P512A	P	-	1	0	GRM8	125961138	1.000000	0.71417	0.971000	0.41717	0.816000	0.46133	9.859000	0.99545	2.758000	0.94735	0.643000	0.83706	CCG	G|0.968;C|0.032	0.032	strong		0.488	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4			C	126173902	G	C	126173902	3	2	22	1	0	0	0	0	1	0	0	0	6812	1232	43	4	1254	4	GRM8	7	126173902	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1709865	126173902	32964761	1749	4650											
ZNF800	168850	hgsc.bcm.edu	37	chr7	127026184	127026184	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtggttgctgtaacaaaggAggatctccaggttccaggat	11	10	13	7	0	1	0	0	0	1	0	3	3	2	3	2	5	2	4	2	5	2	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:127026184A>C	ENST00000393313.1	-	3	678	c.87T>G	c.(85-87)ccT>ccG	p.P29P	ZNF800_ENST00000265827.3_Silent_p.P29P|ZNF800_ENST00000393312.1_Silent_p.P29P			Q2TB10	ZN800_HUMAN	zinc finger protein 800	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)			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						GTAACAAAGGAGGATCTCCAG	0.343																																					p.P29P		Atlas-SNP	.											.	ZNF800	78	.	0			c.T87G						PASS	.						110	104	106					7																	127026184		2203	4300	6503	SO:0001819	synonymous_variant	168850	exon3			CAAAGGAGGATCT	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.87T>G	7.37:g.127026184A>C		72	0	0		83	42	0.506024	NM_176814	Q9HBN0	Silent	SNP	ENST00000393313.1	37	CCDS5795.1																																																																																			.	.	none		0.343	ZNF800-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141823.1	NM_176814		C	127026184	A	C	127026184	2	2	22	1	0	0	0	0	0	0	0	1	18184	291	11	5		5	ZNF800	7	127026184	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	852282	127026184	32112479	1750	4651											
FAM40B	57464	hgsc.bcm.edu	37	chr7	129098602	129098602	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaggaacaagttcatcGgattcaccctggggcagtaa	12	8	12	9	1	2	1	2	1	0	0	3	3	2	3	1	4	2	4	1	4	3	3	rs571423095		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:129098602G>A	ENST00000249344.2	+	11	1364	c.1324G>A	c.(1324-1326)Gga>Aga	p.G442R	STRIP2_ENST00000435494.2_Missense_Mutation_p.G442R	NM_020704.2	NP_065755.1	Q9ULQ0	STRP2_HUMAN	striatin interacting protein 2	442					cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)		p.G442R(1)									CAAGTTCATCGGATTCACCCT	0.517													G|||	1	0.000199681	0.0	0.0014	5008	,	,		17567	0.0		0.0	False		,,,				2504	0.0				p.G442R		Atlas-SNP	.											FAM40B,lymph_node,lymphoid_neoplasm,0,1	.	.	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G1324A						PASS	.						110	95	100					7																	129098602		2203	4300	6503	SO:0001583	missense	57464	exon11			TTCATCGGATTCA	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.1324G>A	7.37:g.129098602G>A	ENSP00000249344:p.Gly442Arg	141	0	0		112	45	0.401786	NM_020704	Q8WUZ4	Missense_Mutation	SNP	ENST00000249344.2	37	CCDS34752.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.608630	0.87258	.	.	ENSG00000128578	ENST00000249344;ENST00000435494;ENST00000450266	T;T	0.48836	0.8;0.8	5.34	5.34	0.76211	.	0.102042	0.64402	D	0.000002	T	0.73087	0.3542	M	0.85099	2.735	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.76016	-0.3113	10	0.54805	T	0.06	-3.4152	18.3766	0.90437	0.0:0.0:1.0:0.0	.	442;442	Q9ULQ0;Q9ULQ0-2	FA40B_HUMAN;.	R	442;442;113	ENSP00000249344:G442R;ENSP00000392393:G442R	ENSP00000249344:G442R	G	+	1	0	FAM40B	128885838	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.747000	0.98863	2.655000	0.90218	0.561000	0.74099	GGA	.	.	none		0.517	STRIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349418.1	NM_001134336		A	129098602	G	A	129098602	3	1	22	1	0	0	0	0	1	0	0	0	5569	1117	39	1	1366	1	FAM40B	7	129098602	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2072418	129098602	30040061	1751	4652											
PLXNA4	91584	hgsc.bcm.edu	37	chr7	131864657	131864657	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgtacaccatccccggggaGtactccatgccaccgacacg	10	6	9	16	3	0	0	0	0	0	0	2	2	2	1	6	2	3	2	6	2	2	2	rs374317794	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:131864657G>A	ENST00000359827.3	-	20	4625	c.3663C>T	c.(3661-3663)taC>taT	p.Y1221Y	PLXNA4_ENST00000321063.4_Silent_p.Y1221Y			Q9HCM2	PLXA4_HUMAN	plexin A4	1221	IPT/TIG 4.				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						TCCCCGGGGAGTACTCCATGC	0.637													G|||	6	0.00119808	0.0045	0.0	5008	,	,		16981	0.0		0.0	False		,,,				2504	0.0				p.Y1221Y		Atlas-SNP	.											.	PLXNA4	873	.	0			c.C3663T						PASS	.	G		9,4255		0,9,2123	15	17	17		3663	4	1	7		17	0,8480		0,0,4240	no	coding-synonymous	PLXNA4	NM_020911.1		0,9,6363	AA,AG,GG		0.0,0.2111,0.0706		1221/1895	131864657	9,12735	2132	4240	6372	SO:0001819	synonymous_variant	91584	exon20			CGGGGAGTACTCC	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.3663C>T	7.37:g.131864657G>A		49	0	0		56	26	0.464286	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	37	CCDS43646.1																																																																																			.	.	weak		0.637	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		A	131864657	G	A	131864657	2	1	22	1	0	0	0	0	0	0	0	1	12131	1024	36	2		2	PLXNA4	7	131864657	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2766055	131864657	27274006	1752	4653											
PLXNA4	91584	hgsc.bcm.edu	37	chr7	132193225	132193225	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcaccaagaccttcaggtcGctggagagcttgtaaatccg	10	9	11	11	2	2	2	2	0	0	2	4	3	3	2	3	2	1	3	3	2	3	3	rs78248128	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:132193225G>A	ENST00000359827.3	-	2	1190	c.228C>T	c.(226-228)agC>agT	p.S76S	PLXNA4_ENST00000321063.4_Silent_p.S76S|PLXNA4_ENST00000378539.5_Silent_p.S76S|PLXNA4_ENST00000423507.2_Silent_p.S76S			Q9HCM2	PLXA4_HUMAN	plexin A4	76	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						CCTTCAGGTCGCTGGAGAGCT	0.587													G|||	189	0.0377396	0.1293	0.013	5008	,	,		18830	0.0		0.004	False		,,,				2504	0.0051				p.S76S		Atlas-SNP	.											.	PLXNA4	873	.	0			c.C228T						PASS	.	G	,,	450,3956	214.8+/-234.0	26,398,1779	57	60	59		228,228,228	-4.6	1	7	dbSNP_131	59	23,8577	16.0+/-53.3	1,21,4278	no	coding-synonymous,coding-synonymous,coding-synonymous	PLXNA4	NM_001105543.1,NM_020911.1,NM_181775.3	,,	27,419,6057	AA,AG,GG		0.2674,10.2133,3.6368	,,	76/493,76/1895,76/523	132193225	473,12533	2203	4300	6503	SO:0001819	synonymous_variant	91584	exon2			CAGGTCGCTGGAG	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.228C>T	7.37:g.132193225G>A		110	0	0		158	92	0.582278	NM_001105543	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	37	CCDS43646.1																																																																																			G|0.966;A|0.034	0.034	strong		0.587	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		A	132193225	G	A	132193225	2	1	22	1	0	0	0	0	0	0	0	1	12131	1078	38	1		1	PLXNA4	7	132193225	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	328568	132193225	26945438	1753	4654											
CHCHD3	54927	hgsc.bcm.edu	37	chr7	132470419	132470419	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tatcctcccttctcaagcatGctctgcaagaaaaacagaaa	15	9	5	12	0	2	2	1	0	2	2	5	2	4	2	2	0	4	3	2	0	6	2	rs147050556	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:132470419G>A	ENST00000262570.5	-	8	807	c.663C>T	c.(661-663)agC>agT	p.S221S	CHCHD3_ENST00000476546.1_5'UTR|CHCHD3_ENST00000448878.1_Silent_p.S226S	NM_017812.2	NP_060282.1	Q9NX63	MIC19_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 3	221					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						TCTCAAGCATGCTCTGCAAGA	0.353													G|||	5	0.000998403	0.0038	0.0	5008	,	,		19096	0.0		0.0	False		,,,				2504	0.0				p.S221S		Atlas-SNP	.											.	CHCHD3	21	.	0			c.C663T						PASS	.	G		18,4388	25.3+/-52.1	0,18,2185	100	95	97		663	5.8	1	7	dbSNP_134	97	0,8600		0,0,4300	no	coding-synonymous	CHCHD3	NM_017812.2		0,18,6485	AA,AG,GG		0.0,0.4085,0.1384		221/228	132470419	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	54927	exon8			AAGCATGCTCTGC	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.663C>T	7.37:g.132470419G>A		329	0	0		324	186	0.574074	NM_017812		Silent	SNP	ENST00000262570.5	37	CCDS5828.1																																																																																			G|0.998;A|0.002	0.002	strong		0.353	CHCHD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000338899.1	NM_017812		A	132470419	G	A	132470419	2	1	22	1	0	0	0	0	0	0	0	1	3319	1310	46	2		2	CHCHD3	7	132470419	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	277194	132470419	26668244	1754	4655											
EXOC4	60412	hgsc.bcm.edu	37	chr7	133682285	133682285	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	agccacacgaacacggatctCcccccagtgtcagagcagat	12	5	9	15	2	2	2	1	0	1	2	3	4	2	3	4	1	3	1	4	1	1	0	rs34608222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:133682285C>T	ENST00000253861.4	+	15	2276	c.2247C>T	c.(2245-2247)ctC>ctT	p.L749L	EXOC4_ENST00000545148.1_Silent_p.L359L|EXOC4_ENST00000539845.1_Silent_p.L648L|EXOC4_ENST00000541309.1_Silent_p.L37L	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	749					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)				ACACGGATCTCCCCCCAGTGT	0.458													C|||	62	0.0123802	0.0439	0.0043	5008	,	,		19403	0.0		0.001	False		,,,				2504	0.0				p.L749L		Atlas-SNP	.											.	EXOC4	118	.	0			c.C2247T						PASS	.	C		209,4197	126.6+/-163.6	9,191,2003	141	114	123		2247	-2.3	0.6	7	dbSNP_126	123	0,8600		0,0,4300	no	coding-synonymous	EXOC4	NM_021807.3		9,191,6303	TT,TC,CC		0.0,4.7435,1.607		749/975	133682285	209,12797	2203	4300	6503	SO:0001819	synonymous_variant	60412	exon15			GGATCTCCCCCCA	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.2247C>T	7.37:g.133682285C>T		106	0	0		117	56	0.478632	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Silent	SNP	ENST00000253861.4	37	CCDS5829.1																																																																																			C|0.986;T|0.014	0.014	strong		0.458	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807		T	133682285	C	T	133682285	2	4	22	1	0	0	0	0	0	0	0	1	5308	842	30	2		2	EXOC4	7	133682285	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1211866	133682285	25456378	1755	4656											
EXOC4	60412	hgsc.bcm.edu	37	chr7	133749077	133749077	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgctttacaacacagctgaCgagctcctgaacctggtggt	10	10	10	11	1	0	2	0	2	0	0	1	3	1	2	2	2	6	3	2	2	3	2	rs139944066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:133749077C>T	ENST00000253861.4	+	18	2750	c.2721C>T	c.(2719-2721)gaC>gaT	p.D907D	EXOC4_ENST00000545148.1_Silent_p.D517D|EXOC4_ENST00000539845.1_Silent_p.D806D|EXOC4_ENST00000541309.1_Silent_p.D195D	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	907					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)				ACACAGCTGACGAGCTCCTGA	0.577													C|||	11	0.00219649	0.0083	0.0	5008	,	,		21152	0.0		0.0	False		,,,				2504	0.0				p.D907D		Atlas-SNP	.											.	EXOC4	118	.	0			c.C2721T						PASS	.	C		21,4385	28.1+/-56.4	0,21,2182	90	76	81		2721	-8.4	0.4	7	dbSNP_134	81	0,8600		0,0,4300	no	coding-synonymous	EXOC4	NM_021807.3		0,21,6482	TT,TC,CC		0.0,0.4766,0.1615		907/975	133749077	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	60412	exon18			AGCTGACGAGCTC	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.2721C>T	7.37:g.133749077C>T		94	0	0		118	52	0.440678	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Silent	SNP	ENST00000253861.4	37	CCDS5829.1																																																																																			C|0.997;T|0.003	0.003	strong		0.577	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807		T	133749077	C	T	133749077	2	4	22	1	0	0	0	0	0	0	0	1	5308	535	19	1		1	EXOC4	7	133749077	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	66792	133749077	25389586	1756	4657											
LRGUK	136332	hgsc.bcm.edu	37	chr7	133881794	133881794	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatcacaagtatggattaaaTagggacaccgtagaaggtat	17	9	10	5	1	1	1	1	0	0	1	1	3	1	3	1	3	0	3	1	3	9	5	rs35258804	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:133881794T>C	ENST00000285928.2	+	13	1551	c.1482T>C	c.(1480-1482)aaT>aaC	p.N494N		NM_144648.1	NP_653249.1	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain containing	494	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.					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						ATGGATTAAATAGGGACACCG	0.358													T|||	188	0.0375399	0.1324	0.013	5008	,	,		18959	0.0		0.001	False		,,,				2504	0.0031				p.N494N		Atlas-SNP	.											.	LRGUK	113	.	0			c.T1482C						PASS	.	T		484,3922	226.9+/-242.2	40,404,1759	164	154	158		1482	0.7	0.4	7	dbSNP_126	158	22,8578	16.0+/-53.3	0,22,4278	no	coding-synonymous	LRGUK	NM_144648.1		40,426,6037	CC,CT,TT		0.2558,10.985,3.8905		494/826	133881794	506,12500	2203	4300	6503	SO:0001819	synonymous_variant	136332	exon13			ATTAAATAGGGAC	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.1482T>C	7.37:g.133881794T>C		135	0	0		98	54	0.55102	NM_144648	Q2M3I1	Silent	SNP	ENST00000285928.2	37	CCDS5830.1																																																																																			T|0.963;C|0.037	0.037	strong		0.358	LRGUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339442.1	NM_144648		C	133881794	T	C	133881794	2	2	22	1	0	0	0	0	0	0	0	1	8952	1403	49	3		3	LRGUK	7	133881794	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	132717	133881794	25256869	1757	4658											
TMEM140	55281	hgsc.bcm.edu	37	chr7	134849690	134849690	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttactcatcctcttgcttaTagccatggctgtgttccctc	5	16	6	14	0	2	0	1	0	1	0	5	0	4	0	3	1	3	3	3	1	3	5	rs76023601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:134849690T>C	ENST00000275767.3	+	2	720	c.497T>C	c.(496-498)aTa>aCa	p.I166T	C7orf49_ENST00000459937.1_Intron	NM_018295.3	NP_060765.4	Q9NV12	TM140_HUMAN	transmembrane protein 140	166						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(2)	5						CTCTTGCTTATAGCCATGGCT	0.567													T|||	9	0.00179712	0.0061	0.0	5008	,	,		20525	0.001		0.0	False		,,,				2504	0.0				p.I166T		Atlas-SNP	.											.	TMEM140	18	.	0			c.T497C						PASS	.	T	THR/ILE	27,4379	30.8+/-60.4	0,27,2176	48	48	48		497	0.2	0	7	dbSNP_131	48	0,8600		0,0,4300	yes	missense	TMEM140	NM_018295.3	89	0,27,6476	CC,CT,TT		0.0,0.6128,0.2076	benign	166/186	134849690	27,12979	2203	4300	6503	SO:0001583	missense	55281	exon2			TGCTTATAGCCAT	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.497T>C	7.37:g.134849690T>C	ENSP00000275767:p.Ile166Thr	146	0	0		214	98	0.457944	NM_018295	A4D1P9|Q8WUC3	Missense_Mutation	SNP	ENST00000275767.3	37	CCDS5837.1	4	0.0018315018315018315	3	0.006097560975609756	0	0.0	1	0.0017482517482517483	0	0.0	T	11.24	1.579014	0.28180	0.006128	0.0	ENSG00000146859	ENST00000275767;ENST00000456488	T	0.20069	2.1	5.28	0.166	0.14999	.	1.753430	0.02512	N	0.091627	T	0.08358	0.0208	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.28618	-1.0038	10	0.62326	D	0.03	-1.1492	5.0072	0.14293	0.0:0.1578:0.2972:0.545	.	166	Q9NV12	TM140_HUMAN	T	166;129	ENSP00000275767:I166T	ENSP00000275767:I166T	I	+	2	0	TMEM140	134500230	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.605000	0.24179	-0.098000	0.12285	-0.258000	0.10820	ATA	T|0.998;C|0.002	0.002	strong		0.567	TMEM140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340017.2	NM_018295		C	134849690	T	C	134849690	3	2	22	1	0	0	0	0	1	0	0	0	16070	1406	49	3	499	3	TMEM140	7	134849690	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	967896	134849690	24288973	1758	4659											
DGKI	9162	hgsc.bcm.edu	37	chr7	137150665	137150665	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cacactcaccccgaggcttgTtccaccaccaggtcaggcat	9	7	8	17	1	2	0	2	0	0	0	3	1	3	0	5	3	0	3	5	3	0	2	rs35245703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:137150665T>C	ENST00000288490.5	-	27	2625	c.2625A>G	c.(2623-2625)gaA>gaG	p.E875E	DGKI_ENST00000446122.1_Silent_p.E857E|DGKI_ENST00000424189.2_Silent_p.E888E|DGKI_ENST00000453654.2_Silent_p.E585E	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	875					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						CCGAGGCTTGTTCCACCACCA	0.542													C|||	480	0.0958466	0.3555	0.013	5008	,	,		17525	0.0		0.001	False		,,,				2504	0.0				p.E875E		Atlas-SNP	.											.	DGKI	335	.	0			c.A2625G						PASS	.	C		1335,3071	695.8+/-406.0	210,915,1078	64	62	63		2625	2.9	1	7	dbSNP_126	63	5,8595	819.0+/-406.8	0,5,4295	no	coding-synonymous	DGKI	NM_004717.2		210,920,5373	CC,CT,TT		0.0581,30.2996,10.3029		875/1066	137150665	1340,11666	2203	4300	6503	SO:0001819	synonymous_variant	9162	exon27			GGCTTGTTCCACC	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.2625A>G	7.37:g.137150665T>C		92	0	0		76	28	0.368421	NM_004717	A4D1Q9|Q9NZ49	Silent	SNP	ENST00000288490.5	37	CCDS5845.1																																																																																			T|0.910;C|0.090	0.090	strong		0.542	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717		C	137150665	T	C	137150665	2	2	22	1	0	0	0	0	0	0	0	1	4473	1722	60	3		3	DGKI	7	137150665	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2300975	137150665	21987998	1759	4660											
DGKI	9162	hgsc.bcm.edu	37	chr7	137263067	137263067	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgttgaatttctctggattTgcttctgtgaaagaggaaaa	11	15	10	5	0	2	3	0	2	2	1	3	5	2	5	0	2	1	2	0	2	4	4	rs61751966	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:137263067T>A	ENST00000288490.5	-	16	1647	c.1647A>T	c.(1645-1647)gcA>gcT	p.A549A	DGKI_ENST00000446122.1_Silent_p.A549A|DGKI_ENST00000424189.2_Silent_p.A549A|DGKI_ENST00000453654.2_Silent_p.A249A	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	549					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						TCTCTGGATTTGCTTCTGTGA	0.373													T|||	88	0.0175719	0.0325	0.0058	5008	,	,		19858	0.0		0.0089	False		,,,				2504	0.0327				p.A549A		Atlas-SNP	.											DGKI_ENST00000288490,NS,carcinoma,-2,2	DGKI	335	2	0			c.A1647T						PASS	.	T		99,4305	78.8+/-117.2	0,99,2103	67	68	68		1647	2.7	1	7	dbSNP_129	68	57,8541	35.9+/-90.5	1,55,4243	no	coding-synonymous	DGKI	NM_004717.2		1,154,6346	AA,AT,TT		0.6629,2.248,1.1998		549/1066	137263067	156,12846	2202	4299	6501	SO:0001819	synonymous_variant	9162	exon16			TGGATTTGCTTCT	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.1647A>T	7.37:g.137263067T>A		98	0	0		123	63	0.512195	NM_004717	A4D1Q9|Q9NZ49	Silent	SNP	ENST00000288490.5	37	CCDS5845.1																																																																																			T|0.987;A|0.013	0.013	strong		0.373	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717		A	137263067	T	A	137263067	2	1	22	1	0	0	0	0	0	0	0	1	4473	1799	63	5		5	DGKI	7	137263067	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	112402	137263067	21875596	1760	4661											
ATP6V0A4	50617	hgsc.bcm.edu	37	chr7	138417642	138417642	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgatgtttgtagaggggtgCgttggaagagtcactgtagt	8	13	16	4	1	1	3	1	1	0	2	1	4	1	4	0	3	1	4	0	3	3	4	rs73730479	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:138417642C>T	ENST00000310018.2	-	17	2170	c.1888G>A	c.(1888-1890)Gca>Aca	p.A630T	ATP6V0A4_ENST00000393054.1_Missense_Mutation_p.A630T|ATP6V0A4_ENST00000353492.4_Missense_Mutation_p.A630T	NM_020632.2|NM_130840.2	NP_065683.2|NP_570855.2	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a4	630					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						TAGAGGGGTGCGTTGGAAGAG	0.373													C|||	210	0.0419329	0.121	0.0245	5008	,	,		16608	0.0268		0.002	False		,,,				2504	0.0041				p.A630T		Atlas-SNP	.											.	ATP6V0A4	93	.	0			c.G1888A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	470,3936	220.0+/-237.6	22,426,1755	99	96	97		1888,1888,1888	1.5	0	7	dbSNP_130	97	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense,missense	ATP6V0A4	NM_020632.2,NM_130840.2,NM_130841.2	58,58,58	22,432,6049	TT,TC,CC		0.0698,10.6673,3.6598	benign,benign,benign	630/841,630/841,630/841	138417642	476,12530	2203	4300	6503	SO:0001583	missense	50617	exon16			GGGGTGCGTTGGA	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.1888G>A	7.37:g.138417642C>T	ENSP00000308122:p.Ala630Thr	108	0	0		90	38	0.422222	NM_130841	A4D1R4|A8KA80|Q32M47	Missense_Mutation	SNP	ENST00000310018.2	37	CCDS5849.1	92	0.04212454212454213	61	0.12398373983739837	9	0.024861878453038673	20	0.03496503496503497	2	0.002638522427440633	C	9.110	1.006311	0.19199	0.106673	6.98E-4	ENSG00000105929	ENST00000310018;ENST00000393054;ENST00000353492	D;D;D	0.85702	-2.02;-2.02;-2.02	5.88	1.49	0.22878	.	0.899723	0.09437	N	0.802370	T	0.02807	0.0084	L	0.37750	1.13	0.09310	N	1	P	0.47350	0.894	B	0.34452	0.183	T	0.01639	-1.1306	10	0.17369	T	0.5	-0.0025	8.1138	0.30930	0.0:0.5837:0.215:0.2013	.	630	Q9HBG4	VPP4_HUMAN	T	630	ENSP00000308122:A630T;ENSP00000376774:A630T;ENSP00000253856:A630T	ENSP00000308122:A630T	A	-	1	0	ATP6V0A4	138068182	0.000000	0.05858	0.001000	0.08648	0.020000	0.10135	0.199000	0.17237	0.383000	0.24910	0.655000	0.94253	GCA	C|0.963;T|0.037	0.037	strong		0.373	ATP6V0A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347514.1	NM_020632		T	138417642	C	T	138417642	3	4	22	1	0	0	0	0	1	0	0	0	1170	768	27	1	658	1	ATP6V0A4	7	138417642	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1154575	138417642	20721021	1761	4662											
ATP6V0A4	50617	hgsc.bcm.edu	37	chr7	138417682	138417682	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttaaacagaaacatgttgatGaagtggatgaggatgctggg	14	10	14	3	0	0	4	0	3	0	1	0	6	0	6	0	3	3	2	0	3	4	2	rs143883618	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:138417682G>A	ENST00000310018.2	-	17	2130	c.1848C>T	c.(1846-1848)ttC>ttT	p.F616F	ATP6V0A4_ENST00000393054.1_Silent_p.F616F|ATP6V0A4_ENST00000353492.4_Silent_p.F616F	NM_020632.2|NM_130840.2	NP_065683.2|NP_570855.2	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a4	616					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						ACATGTTGATGAAGTGGATGA	0.398													G|||	24	0.00479233	0.0182	0.0	5008	,	,		17290	0.0		0.0	False		,,,				2504	0.0				p.F616F		Atlas-SNP	.											.	ATP6V0A4	93	.	0			c.C1848T						PASS	.	G	,,	74,4332	65.3+/-102.7	0,74,2129	116	110	112		1848,1848,1848	2.8	1	7	dbSNP_134	112	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	ATP6V0A4	NM_020632.2,NM_130840.2,NM_130841.2	,,	0,74,6429	AA,AG,GG		0.0,1.6795,0.569	,,	616/841,616/841,616/841	138417682	74,12932	2203	4300	6503	SO:0001819	synonymous_variant	50617	exon16			GTTGATGAAGTGG	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.1848C>T	7.37:g.138417682G>A		144	0	0		124	63	0.508065	NM_130841	A4D1R4|A8KA80|Q32M47	Silent	SNP	ENST00000310018.2	37	CCDS5849.1																																																																																			G|0.995;A|0.005	0.005	strong		0.398	ATP6V0A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347514.1	NM_020632		A	138417682	G	A	138417682	2	1	22	1	0	0	0	0	0	0	0	1	1170	1281	45	2		2	ATP6V0A4	7	138417682	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	40	138417682	20720981	1762	4663											
ZC3HAV1L	92092	hgsc.bcm.edu	37	chr7	138713674	138713674	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgaggttgcagtagccataCagggcttcccctttgttgta	7	14	11	9	0	0	1	0	1	0	0	1	1	1	1	3	2	3	6	3	2	3	8	rs7800990	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:138713674C>G	ENST00000275766.1	-	3	545	c.534G>C	c.(532-534)ctG>ctC	p.L178L		NM_080660.3	NP_542391.2	Q96H79	ZCCHL_HUMAN	zinc finger CCCH-type, antiviral 1-like	178										NS(2)|endometrium(2)|large_intestine(1)|lung(4)|skin(1)	10						AGTAGCCATACAGGGCTTCCC	0.433													G|||	185	0.0369409	0.1354	0.0072	5008	,	,		23164	0.0		0.001	False		,,,				2504	0.0				p.L178L		Atlas-SNP	.											.	ZC3HAV1L	15	.	0			c.G534C						PASS	.	G		554,3852	774.6+/-414.0	28,498,1677	71	69	70		534	-5.1	0	7	dbSNP_116	70	4,8596	819.0+/-406.8	0,4,4296	no	coding-synonymous	ZC3HAV1L	NM_080660.3		28,502,5973	GG,GC,CC		0.0465,12.5738,4.2903		178/301	138713674	558,12448	2203	4300	6503	SO:0001819	synonymous_variant	92092	exon3			GCCATACAGGGCT	BC008842	CCDS5850.1	7q34	2006-07-03	2006-07-03	2006-07-03	ENSG00000146858	ENSG00000146858			22423	protein-coding gene	gene with protein product			"chromosome 7 open reading frame 39"	C7orf39			Standard	NM_080660		Approved	MGC14289	uc003vum.1	Q96H79	OTTHUMG00000157229	ENST00000275766.1:c.534G>C	7.37:g.138713674C>G		93	0	0		78	43	0.551282	NM_080660	Q8WUD9	Silent	SNP	ENST00000275766.1	37	CCDS5850.1																																																																																			C|0.961;G|0.039	0.039	strong		0.433	ZC3HAV1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348090.1	NM_080660		G	138713674	C	G	138713674	2	3	22	1	0	0	0	0	0	0	0	1	17591	465	17	4		4	ZC3HAV1L	7	138713674	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	295992	138713674	20424989	1763	4664											
LUC7L2	100996928	hgsc.bcm.edu	37	chr7	139090515	139090515	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagtagagaaagcacgggcAaagaaaagagaagcagaggt	20	2	15	4	1	0	4	0	0	0	4	0	7	0	4	0	2	2	4	0	2	7	1	rs74758604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:139090515A>G	ENST00000354926.4	+	5	846	c.492A>G	c.(490-492)gcA>gcG	p.A164A	C7orf55-LUC7L2_ENST00000263545.6_Silent_p.A163A|C7orf55-LUC7L2_ENST00000541170.3_Silent_p.A161A|LUC7L2_ENST00000541515.3_Silent_p.A230A	NM_001270643.1|NM_016019.4	NP_001257572.1|NP_057103.2			C7orf55-LUC7L2 readthrough																		AAGCACGGGCAAAGAAAAGAG	0.368													A|||	80	0.0159744	0.0582	0.0029	5008	,	,		17933	0.0		0.001	False		,,,				2504	0.0				p.A230A		Atlas-SNP	.											LUC7L2,NS,carcinoma,+2,1	.	.	1	0			c.A690G						PASS	.	A		171,3519		5,161,1679	100	103	102		492	1.4	1	7	dbSNP_132	102	1,8165		0,1,4082	no	coding-synonymous	LUC7L2	NM_016019.3		5,162,5761	GG,GA,AA		0.0122,4.6341,1.4507		164/393	139090515	172,11684	1845	4083	5928	SO:0001819	synonymous_variant	100996928	exon6			ACGGGCAAAGAAA		CCDS59084.1	7q34	2013-02-14			ENSG00000146963	ENSG00000146963			44671	other	readthrough							Standard	NM_001244584		Approved		uc011kqt.3		OTTHUMG00000151717	ENST00000354926.4:c.492A>G	7.37:g.139090515A>G		139	0	0		133	62	0.466165	NM_001244584		Silent	SNP	ENST00000354926.4	37	CCDS43656.1																																																																																			A|0.981;G|0.019	0.019	strong		0.368	C7orf55-LUC7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323618.2			G	139090515	A	G	139090515	2	3	22	1	0	0	0	0	0	0	0	1	9092	117	5	3		3	LUC7L2	7	139090515	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	376841	139090515	20048148	1764	4665											
CLEC2L	154790	hgsc.bcm.edu	37	chr7	139225215	139225215	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggcggtgctggctgtgatTcagagccagaaggagctggt	8	8	18	7	1	1	3	1	1	0	2	1	5	1	4	1	5	3	3	1	5	1	1	rs112553913	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:139225215T>C	ENST00000422142.2	+	3	486	c.414T>C	c.(412-414)atT>atC	p.I138I		NM_001080511.2	NP_001073980.2	P0C7M8	CLC2L_HUMAN	C-type lectin domain family 2, member L	138	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.					integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(1)|kidney(2)|lung(1)	5	Melanoma(164;0.233)					TGGCTGTGATTCAGAGCCAGA	0.592													T|||	149	0.0297524	0.1097	0.0014	5008	,	,		17539	0.0		0.003	False		,,,				2504	0.0				p.I138I		Atlas-SNP	.											.	CLEC2L	14	.	0			c.T414C						PASS	.	T		311,3699		9,293,1703	13	17	16		414	-4.7	1	7	dbSNP_132	16	7,8351		0,7,4172	no	coding-synonymous	CLEC2L	NM_001080511.2		9,300,5875	CC,CT,TT		0.0838,7.7556,2.5712		138/215	139225215	318,12050	2005	4179	6184	SO:0001819	synonymous_variant	154790	exon3			TGTGATTCAGAGC	AK057548	CCDS47724.1	7q34	2011-05-18			ENSG00000236279	ENSG00000236279		"C-type lectin domain containing"	21969	protein-coding gene	gene with protein product							Standard	NM_001080511		Approved	FLJ32986	uc010lnd.3	P0C7M8	OTTHUMG00000164900	ENST00000422142.2:c.414T>C	7.37:g.139225215T>C		139	0	0		126	67	0.531746	NM_001080511		Silent	SNP	ENST00000422142.2	37	CCDS47724.1	60	0.027472527472527472	58	0.11788617886178862	0	0.0	0	0.0	2	0.002638522427440633	T	9.732	1.162489	0.21538	0.077556	8.38E-4	ENSG00000236279	ENST00000521281	.	.	.	4.81	-4.68	0.03309	.	.	.	.	.	T	0.01124	0.0037	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33599	-0.9862	4	.	.	.	-13.0213	11.495	0.50402	0.0:0.2389:0.0:0.7611	.	.	.	.	S	62	.	.	F	+	2	0	CLEC2L	138875755	0.368000	0.25031	0.986000	0.45419	0.949000	0.60115	-1.179000	0.03090	-0.764000	0.04651	-0.376000	0.06991	TTC	T|0.972;C|0.028	0.028	strong		0.592	CLEC2L-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380878.1	NM_001080511		C	139225215	T	C	139225215	2	2	22	1	0	0	0	0	0	0	0	1	3511	1771	62	3		3	CLEC2L	7	139225215	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	134700	139225215	19913448	1765	4666											
TBXAS1	6916	hgsc.bcm.edu	37	chr7	139661964	139661964	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cactttcttttgccacctacCtactggccaccaaccctgac	8	11	4	18	0	1	1	0	1	1	0	1	1	1	1	6	1	4	0	6	1	3	5	rs4529	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:139661964C>G	ENST00000336425.5	+	13	1455	c.1066C>G	c.(1066-1068)Cta>Gta	p.L356V	TBXAS1_ENST00000448866.1_Missense_Mutation_p.L356V|TBXAS1_ENST00000411653.1_Missense_Mutation_p.L356V|TBXAS1_ENST00000414508.2_Missense_Mutation_p.L357V|TBXAS1_ENST00000458722.1_Missense_Mutation_p.L402V|TBXAS1_ENST00000462275.1_3'UTR|TBXAS1_ENST00000436047.2_Missense_Mutation_p.L357V|TBXAS1_ENST00000263552.6_Missense_Mutation_p.L357V|TBXAS1_ENST00000425687.1_Missense_Mutation_p.L289V|TBXAS1_ENST00000416849.2_Missense_Mutation_p.L403V			P24557	THAS_HUMAN	thromboxane A synthase 1 (platelet)	356			L -> V (in allele CYP5A1*5; dbSNP:rs4529). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:11465543}.		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)	TGCCACCTACCTACTGGCCAC	0.502													C|||	209	0.0417332	0.1543	0.0058	5008	,	,		18923	0.0		0.001	False		,,,				2504	0.0				p.L403V		Atlas-SNP	.											.	TBXAS1	121	.	0			c.C1207G						PASS	.	C	VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU	512,3894	236.1+/-248.4	24,464,1715	111	98	102		1069,1069,1207,865,1069	4.2	1	7	dbSNP_52	102	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense,missense	TBXAS1	NM_001061.4,NM_001130966.2,NM_001166253.1,NM_001166254.1,NM_030984.3	32,32,32,32,32	24,467,6012	GG,GC,CC		0.0349,11.6205,3.9597	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	357/535,357/535,403/581,289/467,357/461	139661964	515,12491	2203	4300	6503	SO:0001583	missense	6916	exon10			ACCTACCTACTGG	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.1066C>G	7.37:g.139661964C>G	ENSP00000338087:p.Leu356Val	136	0	0		114	55	0.482456	NM_001166253	B4DJG6|E7EMU9|E7EP08|E7ESB5|O14987|Q16843|Q16844|Q8IUN1|Q96CN2|Q9GZW4|Q9HD77|Q9HD78|Q9HD79|Q9HD80|Q9HD81|Q9HD82|Q9HD83|Q9HD84	Missense_Mutation	SNP	ENST00000336425.5	37		66	0.03021978021978022	62	0.12601626016260162	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	C	16.28	3.079361	0.55753	0.116205	3.49E-4	ENSG00000059377	ENST00000425687;ENST00000263552;ENST00000336425;ENST00000416849;ENST00000436047;ENST00000414508;ENST00000448866;ENST00000458722;ENST00000411653	T;T;T;T;T;T;T;T;T	0.70399	-0.48;-0.48;-0.48;-0.48;-0.48;-0.48;-0.48;-0.48;-0.48	5.98	4.15	0.48705	.	0.000000	0.85682	D	0.000000	T	0.02533	0.0077	M	0.71920	2.185	0.80722	D	1	P;D;P;D;P;P;P	0.63880	0.937;0.993;0.85;0.992;0.878;0.923;0.923	P;D;P;P;P;P;P	0.65573	0.896;0.936;0.775;0.811;0.722;0.696;0.696	T	0.46076	-0.9217	10	0.18276	T	0.48	.	5.3733	0.16152	0.2612:0.5412:0.1263:0.0712	rs4529;rs52804680;rs57867324;rs4529	337;403;308;289;357;357;356	B4DVP1;E7EP08;B4E0M5;E7ESB5;E7EMU9;Q53F23;P24557	.;.;.;.;.;.;THAS_HUMAN	V	289;357;356;403;357;357;356;402;356	ENSP00000388736:L289V;ENSP00000263552:L357V;ENSP00000338087:L356V;ENSP00000389414:L403V;ENSP00000392361:L357V;ENSP00000392702:L357V;ENSP00000402536:L356V;ENSP00000411274:L402V;ENSP00000411326:L356V	ENSP00000263552:L357V	L	+	1	2	TBXAS1	139308433	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	2.191000	0.42640	0.826000	0.34661	0.655000	0.94253	CTA	C|0.953;G|0.047	0.047	strong		0.502	TBXAS1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000348373.1			G	139661964	C	G	139661964	3	3	22	1	0	0	0	0	1	0	0	0	15679	680	24	4	1245	4	TBXAS1	7	139661964	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	436749	139661964	19476699	1766	4667											
SLC37A3	84255	hgsc.bcm.edu	37	chr7	140048445	140048445	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctatgatccctccaacgtcGtaccaaatggacagcttgtc	10	10	7	14	2	0	1	0	1	0	0	4	2	2	2	4	1	3	2	4	1	4	3	rs73472776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140048445G>A	ENST00000326232.9	-	10	1208	c.1005C>T	c.(1003-1005)taC>taT	p.Y335Y	SLC37A3_ENST00000447932.2_Silent_p.Y335Y|SLC37A3_ENST00000429996.2_3'UTR|SLC37A3_ENST00000340308.3_Silent_p.Y335Y	NM_207113.1	NP_996996.1	Q8NCC5	SPX3_HUMAN	solute carrier family 37, member 3	335					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)					CTCCAACGTCGTACCAAATGG	0.443													G|||	156	0.0311502	0.1104	0.0144	5008	,	,		17310	0.0		0.0	False		,,,				2504	0.0				p.Y335Y	Esophageal Squamous(133;211 1716 4665 11387 37873)	Atlas-SNP	.											.	SLC37A3	80	.	0			c.C1005T						PASS	.	G	,	461,3945	220.4+/-237.8	24,413,1766	129	119	123		1005,1005	2	1	7	dbSNP_130	123	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	SLC37A3	NM_032295.2,NM_207113.1	,	24,416,6063	AA,AG,GG		0.0349,10.463,3.5676	,	335/444,335/495	140048445	464,12542	2203	4300	6503	SO:0001819	synonymous_variant	84255	exon10			AACGTCGTACCAA	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.1005C>T	7.37:g.140048445G>A		57	0	0		56	29	0.517857	NM_207113	Q6PIU7|Q86SS4|Q9BQG7	Silent	SNP	ENST00000326232.9	37	CCDS5859.1	61	0.027930402930402932	57	0.11585365853658537	4	0.011049723756906077	0	0.0	0	0.0	G	8.221	0.802514	0.16397	0.10463	3.49E-4	ENSG00000157800	ENST00000485734;ENST00000485861	.	.	.	5.26	2.05	0.26809	.	.	.	.	.	T	0.01124	0.0037	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.00386	-1.1772	4	.	.	.	-14.7147	6.5083	0.22208	0.4561:0.0:0.5439:0.0	.	.	.	.	M	114;172	.	.	T	-	2	0	SLC37A3	139694914	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	0.648000	0.24828	0.613000	0.30089	0.462000	0.41574	ACG	G|0.961;A|0.039	0.039	strong		0.443	SLC37A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348492.1	NM_032295		A	140048445	G	A	140048445	2	1	22	1	0	0	0	0	0	0	0	1	14614	1140	40	1		1	SLC37A3	7	140048445	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	386481	140048445	19090218	1767	4668											
SLC37A3	84255	hgsc.bcm.edu	37	chr7	140051116	140051116	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgcctggtagaagcttatcGccttgacttgggcaacagaa	11	10	11	9	1	0	3	0	1	0	2	1	3	0	3	2	2	3	3	2	2	5	4	rs76089276	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140051116G>A	ENST00000326232.9	-	9	1042	c.839C>T	c.(838-840)gCg>gTg	p.A280V	SLC37A3_ENST00000447932.2_Missense_Mutation_p.A280V|SLC37A3_ENST00000429996.2_3'UTR|SLC37A3_ENST00000340308.3_Missense_Mutation_p.A280V	NM_207113.1	NP_996996.1	Q8NCC5	SPX3_HUMAN	solute carrier family 37, member 3	280					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)					GAAGCTTATCGCCTTGACTTG	0.468													G|||	167	0.0333466	0.1188	0.0115	5008	,	,		20455	0.0		0.002	False		,,,				2504	0.0				p.A280V	Esophageal Squamous(133;211 1716 4665 11387 37873)	Atlas-SNP	.											.	SLC37A3	80	.	0			c.C839T						PASS	.	G	VAL/ALA,VAL/ALA	454,3952	216.4+/-235.1	19,416,1768	152	129	137		839,839	5.2	1	7	dbSNP_131	137	8,8592	5.0+/-18.6	0,8,4292	yes	missense,missense	SLC37A3	NM_032295.2,NM_207113.1	64,64	19,424,6060	AA,AG,GG		0.093,10.3041,3.5522	probably-damaging,probably-damaging	280/444,280/495	140051116	462,12544	2203	4300	6503	SO:0001583	missense	84255	exon9			CTTATCGCCTTGA	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.839C>T	7.37:g.140051116G>A	ENSP00000321498:p.Ala280Val	171	0	0		187	83	0.44385	NM_207113	Q6PIU7|Q86SS4|Q9BQG7	Missense_Mutation	SNP	ENST00000326232.9	37	CCDS5859.1	71|71	0.03250915750915751|0.03250915750915751	66|66	0.13414634146341464|0.13414634146341464	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	0|0	0.0|0.0	G|G	20.6|20.6	4.022383|4.022383	0.75275|0.75275	0.103041|0.103041	9.3E-4|9.3E-4	ENSG00000157800|ENSG00000157800	ENST00000340308;ENST00000447932;ENST00000326232|ENST00000485734	T;T;T|.	0.58060|.	0.36;0.36;0.36|.	5.2|5.2	5.2|5.2	0.72013|0.72013	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.04407|.	0.0121|.	M|M	0.86097|0.86097	2.795|2.795	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.79108|.	0.981;0.992;0.979|.	T|.	0.49716|.	-0.8910|.	10|.	0.62326|.	D|.	0.03|.	-43.077|-43.077	18.7136|18.7136	0.91667|0.91667	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	280;280;280|.	Q8NCC5-2;Q8NCC5-3;Q8NCC5|.	.;.;SPX3_HUMAN|.	V|X	280|59	ENSP00000343358:A280V;ENSP00000397481:A280V;ENSP00000321498:A280V|.	ENSP00000321498:A280V|.	A|R	-|-	2|1	0|2	SLC37A3|SLC37A3	139697585|139697585	1.000000|1.000000	0.71417|0.71417	0.951000|0.951000	0.38953|0.38953	0.262000|0.262000	0.26303|0.26303	7.710000|7.710000	0.84655|0.84655	2.575000|2.575000	0.86900|0.86900	0.563000|0.563000	0.77884|0.77884	GCG|CGA	G|0.969;A|0.031	0.031	strong		0.468	SLC37A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348492.1	NM_032295		A	140051116	G	A	140051116	3	1	22	1	0	0	0	0	1	0	0	0	14614	1087	38	1	822	1	SLC37A3	7	140051116	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2671	140051116	19087547	1768	4669											
RAB19	401409	hgsc.bcm.edu	37	chr7	140125878	140125878	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tatggggagagtgccctgaaCggcctccccctggactccag	7	7	13	14	1	0	2	0	1	0	1	2	4	2	3	5	4	2	0	5	4	2	1	rs4585665	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140125878C>T	ENST00000356407.3	+	3	650	c.582C>T	c.(580-582)aaC>aaT	p.N194N	RAB19_ENST00000537763.1_Silent_p.N194N|RAB19_ENST00000275874.5_Silent_p.N241N			A4D1S5	RAB19_HUMAN	RAB19, member RAS oncogene family	194					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			breast(3)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	9	Melanoma(164;0.0142)					GTGCCCTGAACGGCCTCCCCC	0.562													C|||	61	0.0121805	0.0439	0.0043	5008	,	,		18656	0.0		0.0	False		,,,				2504	0.0				p.N194N		Atlas-SNP	.											.	RAB19	21	.	0			c.C582T						PASS	.	C		126,4280	93.0+/-131.7	2,122,2079	77	72	74		582	0.4	0	7	dbSNP_111	74	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	RAB19	NM_001008749.2		2,124,6377	TT,TC,CC		0.0233,2.8597,0.9842		194/218	140125878	128,12878	2203	4300	6503	SO:0001819	synonymous_variant	401409	exon4			CCTGAACGGCCTC		CCDS34762.1, CCDS34762.2	7q34	2014-05-09			ENSG00000146955	ENSG00000146955		"RAB, member RAS oncogene"	19982	protein-coding gene	gene with protein product							Standard	NM_001008749		Approved	RAB19B	uc010lni.2	A4D1S5	OTTHUMG00000157410	ENST00000356407.3:c.582C>T	7.37:g.140125878C>T		81	0	0		91	41	0.450549	NM_001008749	A4D1S6|B2RTS6|B5MDR2|Q9UL27	Silent	SNP	ENST00000356407.3	37	CCDS34762.2																																																																																			C|0.989;T|0.011	0.011	strong		0.562	RAB19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348740.1			T	140125878	C	T	140125878	2	4	22	1	0	0	0	0	0	0	0	1	12919	535	19	1		1	RAB19	7	140125878	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	74762	140125878	19012785	1769	4670											
MKRN1	23608	hgsc.bcm.edu	37	chr7	140158960	140158960	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agctgcttctttgtctccacGgcggtttgctctttctctga	3	17	9	12	2	4	1	0	1	4	0	6	1	4	1	1	2	3	4	1	2	0	4	rs61736379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140158960G>A	ENST00000255977.2	-	4	842	c.618C>T	c.(616-618)gcC>gcT	p.A206A	MKRN1_ENST00000481705.1_5'Flank|MKRN1_ENST00000480552.1_Intron|MKRN1_ENST00000443720.2_Silent_p.A206A|MKRN1_ENST00000437223.2_Intron|MKRN1_ENST00000474576.1_Silent_p.A142A	NM_013446.3	NP_038474.2	Q9UHC7	MKRN1_HUMAN	makorin ring finger protein 1	206					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)					TTGTCTCCACGGCGGTTTGCT	0.537													g|||	32	0.00638978	0.0227	0.0029	5008	,	,		17416	0.0		0.0	False		,,,				2504	0.0				p.A206A		Atlas-SNP	.											.	MKRN1	35	.	0			c.C618T						PASS	.	G	,	83,4323	70.9+/-108.8	1,81,2121	133	130	131		618,618	-9.8	0	7	dbSNP_129	131	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	MKRN1	NM_001145125.1,NM_013446.3	,	1,81,6421	AA,AG,GG		0.0,1.8838,0.6382	,	206/330,206/483	140158960	83,12923	2203	4300	6503	SO:0001819	synonymous_variant	23608	exon4			CTCCACGGCGGTT	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.618C>T	7.37:g.140158960G>A		198	0	0		260	125	0.480769	NM_013446	A4D1T7|B3KXB4|Q256Y7|Q59G11|Q6GSF1|Q9H0G0|Q9UEZ7|Q9UHW2	Silent	SNP	ENST00000255977.2	37	CCDS5860.1																																																																																			G|0.993;A|0.007	0.007	strong		0.537	MKRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348752.1	NM_013446		A	140158960	G	A	140158960	2	1	22	1	0	0	0	0	0	0	0	1	9615	1103	39	1		1	MKRN1	7	140158960	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	33082	140158960	18979703	1770	4671											
DENND2A	27147	hgsc.bcm.edu	37	chr7	140221878	140221878	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaggcttcagacaccacctcGttcaaggggctggactctgg	9	8	12	12	1	3	1	2	0	1	1	4	2	3	2	2	5	0	3	2	5	2	2	rs61737088	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140221878G>A	ENST00000275884.6	-	17	3105	c.2688C>T	c.(2686-2688)aaC>aaT	p.N896N	DENND2A_ENST00000537639.1_Silent_p.N896N|DENND2A_ENST00000496613.1_Silent_p.N896N			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	896	dDENN. {ECO:0000255|PROSITE- ProRule:PRU00306}.				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)					ACACCACCTCGTTCAAGGGGC	0.582													G|||	62	0.0123802	0.0446	0.0029	5008	,	,		15621	0.0		0.001	False		,,,				2504	0.0				p.N896N		Atlas-SNP	.											.	DENND2A	132	.	0			c.C2688T						PASS	.	G		141,3909		3,135,1887	49	53	52		2688	-3.1	0.7	7	dbSNP_129	52	3,8365		0,3,4181	no	coding-synonymous	DENND2A	NM_015689.3		3,138,6068	AA,AG,GG		0.0359,3.4815,1.1596		896/1010	140221878	144,12274	2025	4184	6209	SO:0001819	synonymous_variant	27147	exon16			CACCTCGTTCAAG	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.2688C>T	7.37:g.140221878G>A		42	0	0		57	29	0.508772	NM_015689	C9JUI3|Q1RMD5|Q86XY0	Silent	SNP	ENST00000275884.6	37	CCDS43659.1																																																																																			G|0.993;A|0.007	0.007	strong		0.582	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689		A	140221878	G	A	140221878	2	1	22	1	0	0	0	0	0	0	0	1	4431	1136	40	1		1	DENND2A	7	140221878	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	62918	140221878	18916785	1771	4672											
DENND2A	27147	hgsc.bcm.edu	37	chr7	140225578	140225578	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aggaaccggctgttgacgagGtcaaccacaaggacctatga	13	6	12	10	2	1	2	1	2	0	0	1	5	1	4	3	4	2	2	3	4	4	2	rs61737086	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140225578G>A	ENST00000275884.6	-	15	2937	c.2520C>T	c.(2518-2520)gaC>gaT	p.D840D	DENND2A_ENST00000537639.1_Silent_p.D840D|DENND2A_ENST00000496613.1_Silent_p.D840D			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	840	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)					TGTTGACGAGGTCAACCACAA	0.537													G|||	248	0.0495208	0.171	0.0101	5008	,	,		18548	0.0		0.0	False		,,,				2504	0.0153				p.D840D		Atlas-SNP	.											.	DENND2A	132	.	0			c.C2520T						PASS	.	G		507,3455		30,447,1504	49	53	52		2520	2.6	1	7	dbSNP_129	52	4,8336		0,4,4166	no	coding-synonymous	DENND2A	NM_015689.3		30,451,5670	AA,AG,GG		0.048,12.7966,4.1538		840/1010	140225578	511,11791	1981	4170	6151	SO:0001819	synonymous_variant	27147	exon14			GACGAGGTCAACC	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.2520C>T	7.37:g.140225578G>A		92	0	0		111	60	0.540541	NM_015689	C9JUI3|Q1RMD5|Q86XY0	Silent	SNP	ENST00000275884.6	37	CCDS43659.1																																																																																			G|0.968;A|0.032	0.032	strong		0.537	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689		A	140225578	G	A	140225578	2	1	22	1	0	0	0	0	0	0	0	1	4431	1252	44	2		2	DENND2A	7	140225578	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3700	140225578	18913085	1772	4673											
DENND2A	27147	hgsc.bcm.edu	37	chr7	140227184	140227184	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agcccgatgaggaagggcgtCggcgagcacacgatgtcgac	10	4	16	11	6	0	1	0	1	0	0	2	6	0	2	1	3	2	1	1	3	1	0	rs76760136	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140227184C>T	ENST00000275884.6	-	14	2856	c.2439G>A	c.(2437-2439)ccG>ccA	p.P813P	DENND2A_ENST00000537639.1_Silent_p.P813P|DENND2A_ENST00000496613.1_Silent_p.P813P			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	813	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)					GGAAGGGCGTCGGCGAGCACA	0.672													C|||	35	0.00698882	0.0257	0.0014	5008	,	,		17558	0.0		0.0	False		,,,				2504	0.0				p.P813P		Atlas-SNP	.											.	DENND2A	132	.	0			c.G2439A						PASS	.	C		59,4119		0,59,2030	12	18	16		2439	-2.2	0.4	7	dbSNP_132	16	0,8420		0,0,4210	no	coding-synonymous	DENND2A	NM_015689.3		0,59,6240	TT,TC,CC		0.0,1.4122,0.4683		813/1010	140227184	59,12539	2089	4210	6299	SO:0001819	synonymous_variant	27147	exon13			GGGCGTCGGCGAG	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.2439G>A	7.37:g.140227184C>T		243	0	0		209	113	0.54067	NM_015689	C9JUI3|Q1RMD5|Q86XY0	Silent	SNP	ENST00000275884.6	37	CCDS43659.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	C	10.80	1.452752	0.26074	0.014122	0.0	ENSG00000146966	ENST00000469373	T	0.36340	1.26	5.04	-2.21	0.06973	.	.	.	.	.	T	0.29458	0.0734	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43228	-0.9404	6	0.87932	D	0	-17.1724	10.9649	0.47406	0.0:0.2873:0.2046:0.5082	.	.	.	.	Q	141	ENSP00000420145:R141Q	ENSP00000417673:R794Q	R	-	2	0	DENND2A	139873653	0.155000	0.22806	0.413000	0.26509	0.012000	0.07955	-0.761000	0.04751	-0.836000	0.04229	-1.134000	0.01955	CGA	C|0.995;T|0.005	0.005	strong		0.672	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689		T	140227184	C	T	140227184	2	4	22	1	0	0	0	0	0	0	0	1	4431	871	31	1		1	DENND2A	7	140227184	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1606	140227184	18911479	1773	4674											
ADCK2	90956	hgsc.bcm.edu	37	chr7	140374482	140374482	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagattggcagccgagtcctGggagttttgccaggcatcaa	10	9	13	9	1	1	1	1	0	0	1	2	3	2	2	3	3	2	3	3	3	2	3	rs142577491	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140374482G>C	ENST00000072869.4	+	2	1183	c.1005G>C	c.(1003-1005)ctG>ctC	p.L335L	ADCK2_ENST00000476491.1_Silent_p.L335L	NM_052853.3	NP_443085.2	Q7Z695	ADCK2_HUMAN	aarF domain containing kinase 2	335	Protein kinase.					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)					GCCGAGTCCTGGGAGTTTTGC	0.542													C|||	6	0.00119808	0.0038	0.0014	5008	,	,		18388	0.0		0.0	False		,,,				2504	0.0				p.L335L		Atlas-SNP	.											.	ADCK2	37	.	0			c.G1005C						PASS	.	C		15,4391	823.8+/-416.5	0,15,2188	113	95	101		1005	-11.2	0	7	dbSNP_134	101	0,8600		0,0,4300	no	coding-synonymous	ADCK2	NM_052853.3		0,15,6488	CC,CG,GG		0.0,0.3404,0.1153		335/627	140374482	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	90956	exon2			AGTCCTGGGAGTT	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.1005G>C	7.37:g.140374482G>C		113	0	0		124	71	0.572581	NM_052853	Q96CN6|Q9Y6T5	Silent	SNP	ENST00000072869.4	37	CCDS5861.1	2	9.157509157509158E-4	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	C	8.385	0.838441	0.16891	0.003404	0.0	ENSG00000133597	ENST00000483369	.	.	.	5.61	-11.2	0.00127	.	.	.	.	.	T	0.57755	0.2075	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.71537	-0.4563	4	.	.	.	-48.0441	14.5211	0.67851	0.0:0.1623:0.6463:0.1913	.	.	.	.	R	173	.	.	G	+	1	0	ADCK2	140020951	0.066000	0.20996	0.001000	0.08648	0.874000	0.50279	-0.756000	0.04777	-2.611000	0.00445	-1.093000	0.02169	GGG	G|0.999;C|0.001	0.001	strong		0.542	ADCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348734.1	NM_052853		C	140374482	G	C	140374482	2	2	22	1	0	0	0	0	0	0	0	1	289	1335	47	4		4	ADCK2	7	140374482	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	147298	140374482	18764181	1774	4675											
BRAF	673	hgsc.bcm.edu	37	chr7	140449150	140449150	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcaattcatacagaacaatTccaaatgcatatacatctga	18	11	3	9	0	3	2	2	1	1	1	4	2	4	2	1	0	4	1	1	0	7	5	rs9648696	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140449150T>C	ENST00000288602.6	-	16	1989	c.1929A>G	c.(1927-1929)ggA>ggG	p.G643G		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	643	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|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 stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	ACAGAACAATTCCAAATGCAT	0.348		61	"Mis, T, O"	"AKAP9, KIAA1549"	"melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome				C|||	1758	0.351038	0.7451	0.1585	5008	,	,		17576	0.1825		0.1531	False		,,,				2504	0.3323				p.G643G	Colon(40;35 892 2973 5743 27438)	Atlas-SNP	.		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	.	BRAF	36346	.	0			c.A1929G						PASS	.	C		2904,1502	476.8+/-357.7	963,978,262	105	108	107		1929	2.1	1	7	dbSNP_119	107	1258,7342	758.6+/-407.5	114,1030,3156	no	coding-synonymous	BRAF	NM_004333.4		1077,2008,3418	CC,CT,TT		14.6279,34.0899,32.0006		643/767	140449150	4162,8844	2203	4300	6503	SO:0001819	synonymous_variant	673	exon16	Familial Cancer Database	CFC, CFCS	AACAATTCCAAAT	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1929A>G	7.37:g.140449150T>C		141	0	0		148	148	1	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Silent	SNP	ENST00000288602.6	37	CCDS5863.1	611	0.27976190476190477	355	0.7215447154471545	58	0.16022099447513813	91	0.1590909090909091	107	0.14116094986807387	C	9.723	1.160251	0.21454	0.659101	0.146279	ENSG00000157764	ENST00000496384	.	.	.	5.02	2.11	0.27256	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.33317	-0.9873	3	.	.	.	.	5.8585	0.18732	0.0:0.5864:0.1264:0.2872	rs9648696;rs10238189;rs60896634	.	.	.	G	251	.	.	E	-	2	0	BRAF	140095619	1.000000	0.71417	0.998000	0.56505	0.947000	0.59692	1.503000	0.35715	-0.010000	0.14271	-0.355000	0.07637	GAA	T|0.696;C|0.304	0.304	strong		0.348	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		C	140449150	T	C	140449150	2	2	22	1	0	0	0	0	0	0	0	1	1498	1770	62	3		3	BRAF	7	140449150	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	74668	140449150	18689513	1775	4676											
BRAF	673	hgsc.bcm.edu	37	chr7	140481425	140481425	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatgatccagatccaattctTtgtcccactgtaatctgccc	10	13	5	13	0	2	2	0	1	2	1	5	2	5	2	4	0	1	1	4	0	3	3	rs56216404	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140481425T>C	ENST00000288602.6	-	11	1443	c.1383A>G	c.(1381-1383)caA>caG	p.Q461Q		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	461	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|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 stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	ATCCAATTCTTTGTCCCACTG	0.393		61	"Mis, T, O"	"AKAP9, KIAA1549"	"melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome				T|||	27	0.00539137	0.0204	0.0	5008	,	,		15131	0.0		0.0	False		,,,				2504	0.0				p.Q461Q	Colon(40;35 892 2973 5743 27438)	Atlas-SNP	.		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	.	BRAF	36346	.	0			c.A1383G						PASS	.	T		41,4365	43.1+/-76.7	0,41,2162	170	145	154		1383	-3.9	1	7	dbSNP_129	154	0,8596		0,0,4298	no	coding-synonymous	BRAF	NM_004333.4		0,41,6460	CC,CT,TT		0.0,0.9305,0.3153		461/767	140481425	41,12961	2203	4298	6501	SO:0001819	synonymous_variant	673	exon11	Familial Cancer Database	CFC, CFCS	AATTCTTTGTCCC	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1383A>G	7.37:g.140481425T>C		103	0	0		112	59	0.526786	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Silent	SNP	ENST00000288602.6	37	CCDS5863.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	T	9.986	1.229394	0.22542	0.009305	0.0	ENSG00000157764	ENST00000496384	.	.	.	5.62	-3.94	0.04130	.	.	.	.	.	T	0.26593	0.0650	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40887	-0.9539	4	.	.	.	.	7.9193	0.29837	0.1332:0.5351:0.0:0.3317	rs56216404;rs61730028	.	.	.	R	69	.	.	K	-	2	0	BRAF	140127894	0.871000	0.30034	0.970000	0.41538	0.993000	0.82548	-0.010000	0.12743	-0.751000	0.04734	-0.481000	0.04817	AAA	T|0.995;C|0.005	0.005	strong		0.393	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		C	140481425	T	C	140481425	2	2	22	1	0	0	0	0	0	0	0	1	1498	1838	64	3		3	BRAF	7	140481425	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	32275	140481425	18657238	1776	4677											
MGAM	8972	hgsc.bcm.edu	37	chr7	141719078	141719078	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgctactattccaagaatcAtagctaccatgtagagggca	13	10	9	9	0	1	2	1	0	0	2	2	2	2	2	2	1	4	4	2	1	7	6	rs114936410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:141719078A>G	ENST00000549489.2	+	4	502	c.407A>G	c.(406-408)cAt>cGt	p.H136R	MGAM_ENST00000475668.2_Missense_Mutation_p.H136R	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	136					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)	TCCAAGAATCATAGCTACCAT	0.502													A|||	33	0.00658946	0.0234	0.0029	5008	,	,		18070	0.0		0.0	False		,,,				2504	0.0				p.H136R		Atlas-SNP	.											.	MGAM	767	.	0			c.A407G						PASS	.	A	ARG/HIS	70,4000		2,66,1967	86	90	89		407	3.7	1	7	dbSNP_132	89	0,8392		0,0,4196	yes	missense	MGAM	NM_004668.2	29	2,66,6163	GG,GA,AA		0.0,1.7199,0.5617	possibly-damaging	136/1858	141719078	70,12392	2035	4196	6231	SO:0001583	missense	8972	exon4			AGAATCATAGCTA	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.407A>G	7.37:g.141719078A>G	ENSP00000447378:p.His136Arg	46	0	0		38	15	0.394737	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	37	CCDS47727.1	21	0.009615384615384616	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	0	0.0	A	11.07	1.531130	0.27387	0.017199	0.0	ENSG00000257335	ENST00000465654;ENST00000549489;ENST00000497673;ENST00000475668;ENST00000548812	T;D;T	0.85339	-0.82;-1.97;0.55	4.85	3.7	0.42460	Glycoside hydrolase-type carbohydrate-binding (1);P-type trefoil (2);	0.276318	0.26251	N	0.025446	T	0.50752	0.1634	M	0.63843	1.955	0.32573	N	0.529585	P	0.44195	0.828	B	0.34385	0.181	T	0.74287	-0.3714	10	0.51188	T	0.08	.	8.8349	0.35107	0.9101:0.0:0.0899:0.0	.	136	O43451	MGA_HUMAN	R	136;136;136;136;13	ENSP00000419372:H136R;ENSP00000447378:H136R;ENSP00000417103:H136R	ENSP00000316431:H13R	H	+	2	0	MGAM	141365547	1.000000	0.71417	1.000000	0.80357	0.285000	0.27093	6.413000	0.73308	0.992000	0.38840	-0.476000	0.04901	CAT	A|0.990;G|0.010	0.010	strong		0.502	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			G	141719078	A	G	141719078	3	3	22	1	0	0	0	0	1	0	0	0	9550	217	8	3	417	3	MGAM	7	141719078	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1237653	141719078	17419585	1777	4678											
MGAM	8972	hgsc.bcm.edu	37	chr7	141736732	141736732	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctatacaccctcttcttccGtgctcacagccgaggggaca	8	9	8	16	2	3	0	1	0	2	0	4	2	4	1	4	2	3	1	4	2	2	4	rs116034282	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:141736732G>A	ENST00000549489.2	+	18	2281	c.2186G>A	c.(2185-2187)cGt>cAt	p.R729H	MGAM_ENST00000475668.2_Missense_Mutation_p.R729H	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	729	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)	CTCTTCTTCCGTGCTCACAGC	0.493													G|||	56	0.0111821	0.0401	0.0043	5008	,	,		19313	0.0		0.0	False		,,,				2504	0.0				p.R729H		Atlas-SNP	.											.	MGAM	767	.	0			c.G2186A						PASS	.	G	HIS/ARG	129,3941		3,123,1909	199	203	202		2186	-1	0	7	dbSNP_132	202	0,8388		0,0,4194	yes	missense	MGAM	NM_004668.2	29	3,123,6103	AA,AG,GG		0.0,3.1695,1.0355	possibly-damaging	729/1858	141736732	129,12329	2035	4194	6229	SO:0001583	missense	8972	exon18			TCTTCCGTGCTCA	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.2186G>A	7.37:g.141736732G>A	ENSP00000447378:p.Arg729His	81	0	0		100	46	0.46	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	37	CCDS47727.1	28	0.01282051282051282	26	0.052845528455284556	2	0.0055248618784530384	0	0.0	0	0.0	G	12.77	2.038656	0.35989	0.031695	0.0	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	D	0.91464	-2.85	5.81	-0.982	0.10266	Glycoside hydrolase, superfamily (1);	0.281671	0.23492	N	0.047582	T	0.44159	0.1280	N	0.20685	0.6	0.09310	N	1	B	0.30021	0.265	B	0.22753	0.041	T	0.54748	-0.8247	10	0.32370	T	0.25	.	11.754	0.51866	0.5808:0.0:0.4192:0.0	.	729	O43451	MGA_HUMAN	H	729;729;606	ENSP00000447378:R729H	ENSP00000316431:R606H	R	+	2	0	MGAM	141383201	0.034000	0.19679	0.000000	0.03702	0.991000	0.79684	0.534000	0.23098	-0.502000	0.06596	-0.145000	0.13849	CGT	G|0.986;A|0.014	0.014	strong		0.493	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			A	141736732	G	A	141736732	3	1	22	1	0	0	0	0	1	0	0	0	9550	1145	40	1	2252	1	MGAM	7	141736732	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	17654	141736732	17401931	1778	4679											
MGAM	8972	hgsc.bcm.edu	37	chr7	141750613	141750613	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgttacagtgaaacacaaTggtgtcccaagtcagacttc	14	10	8	9	0	1	2	1	1	0	1	3	2	2	2	1	1	2	1	1	1	5	2	rs145430437	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:141750613T>A	ENST00000549489.2	+	24	2849	c.2754T>A	c.(2752-2754)aaT>aaA	p.N918K	MGAM_ENST00000475668.2_Missense_Mutation_p.N918K	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	918					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)	TGAAACACAATGGTGTCCCAA	0.373													t|||	53	0.0105831	0.0378	0.0043	5008	,	,		20002	0.0		0.0	False		,,,				2504	0.0				p.N918K		Atlas-SNP	.											.	MGAM	767	.	0			c.T2754A						PASS	.	T	LYS/ASN	121,3617		1,119,1749	105	95	98		2754	0.9	0.1	7	dbSNP_134	98	0,8200		0,0,4100	no	missense	MGAM	NM_004668.2	94	1,119,5849	AA,AT,TT		0.0,3.237,1.0136	possibly-damaging	918/1858	141750613	121,11817	1869	4100	5969	SO:0001583	missense	8972	exon24			ACACAATGGTGTC	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.2754T>A	7.37:g.141750613T>A	ENSP00000447378:p.Asn918Lys	261	0	0		259	112	0.432432	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	37	CCDS47727.1	27	0.012362637362637362	25	0.0508130081300813	2	0.0055248618784530384	0	0.0	0	0.0	T	16.84	3.233340	0.58886	0.03237	0.0	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	D	0.89746	-2.56	5.81	0.868	0.19090	.	0.000000	0.53938	D	0.000059	T	0.57140	0.2033	M	0.86028	2.79	0.09310	N	1	P	0.45768	0.866	B	0.34590	0.186	T	0.69258	-0.5192	10	0.72032	D	0.01	.	9.1608	0.37021	0.0:0.3617:0.0:0.6383	.	918	O43451	MGA_HUMAN	K	918;918;795	ENSP00000447378:N918K	ENSP00000316431:N795K	N	+	3	2	MGAM	141397082	0.061000	0.20836	0.090000	0.20809	0.275000	0.26752	-0.197000	0.09518	-0.065000	0.13021	-0.479000	0.04858	AAT	T|0.988;A|0.012	0.012	strong		0.373	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			A	141750613	T	A	141750613	3	1	22	1	0	0	0	0	1	0	0	0	9550	1461	51	5	2844	5	MGAM	7	141750613	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	13881	141750613	17388050	1779	4680											
MGAM	8972	hgsc.bcm.edu	37	chr7	141754625	141754625	+	Silent	SNP	C	C	T																															cccagcatgccatccagcacCcctgagggtcaactctatga																								rs115294234	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:141754625C>T	ENST00000549489.2	+	27	3326	c.3231C>T	c.(3229-3231)acC>acT	p.T1077T	MGAM_ENST00000475668.2_Silent_p.T1077T	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1077	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)	CATCCAGCACCCCTGAGGGTC	0.448													c|||	56	0.0111821	0.0401	0.0043	5008	,	,		19007	0.0		0.0	False		,,,				2504	0.0				p.T1077T		Atlas-SNP	.											.	MGAM	767	.	0			c.C3231T						PASS	.	C		137,3699		4,129,1785	142	135	137		3231	1.1	0.2	7	dbSNP_132	137	0,8226		0,0,4113	no	coding-synonymous	MGAM	NM_004668.2		4,129,5898	TT,TC,CC		0.0,3.5714,1.1358		1077/1858	141754625	137,11925	1918	4113	6031	SO:0001819	synonymous_variant	8972	exon27			CAGCACCCCTGAG	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.3231C>T	7.37:g.141754625C>T		169	0	0		190	95	0.5	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000549489.2	37	CCDS47727.1																																																																																			C|0.985;T|0.015	0.015	strong		0.448	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			T	141754625	C	T	141754625	2	4	22	1	0	0	0	0	0	0	0	1	9550	610	22	2		2	MGAM	7	141754625	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4012	141754625	17384038	1780	4681	57	2									
MGAM	8972	hgsc.bcm.edu	37	chr7	141754629	141754629	+	Missense_Mutation	SNP	G	G	C																															gcatgccatccagcacccctGagggtcaactctatgatgtg																								rs145885349	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:141754629G>C	ENST00000549489.2	+	27	3330	c.3235G>C	c.(3235-3237)Gag>Cag	p.E1079Q	MGAM_ENST00000475668.2_Missense_Mutation_p.E1079Q	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1079	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)	CAGCACCCCTGAGGGTCAACT	0.448													g|||	21	0.00419329	0.0151	0.0014	5008	,	,		18921	0.0		0.0	False		,,,				2504	0.0				p.E1079Q		Atlas-SNP	.											MGAM_ENST00000549489,caecum,carcinoma,-2,3	MGAM	767	3	0			c.G3235C						PASS	.	G	GLN/GLU	46,3784		0,46,1869	135	129	131		3235	2.3	0	7	dbSNP_134	131	0,8230		0,0,4115	no	missense	MGAM	NM_004668.2	29	0,46,5984	CC,CG,GG		0.0,1.201,0.3814	possibly-damaging	1079/1858	141754629	46,12014	1915	4115	6030	SO:0001583	missense	8972	exon27			ACCCCTGAGGGTC	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.3235G>C	7.37:g.141754629G>C	ENSP00000447378:p.Glu1079Gln	169	0	0		191	94	0.492147	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	37	CCDS47727.1	6	0.0027472527472527475	4	0.008130081300813009	2	0.0055248618784530384	0	0.0	0	0.0	G	11.01	1.514051	0.27123	0.01201	0.0	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	T	0.30714	1.52	4.24	2.31	0.28768	Glycoside hydrolase-type carbohydrate-binding (1);	0.422018	0.17369	N	0.176760	T	0.28001	0.0690	M	0.76838	2.35	0.09310	N	1	B	0.15719	0.014	B	0.11329	0.006	T	0.28235	-1.0050	10	0.54805	T	0.06	.	12.7162	0.57117	0.0:0.3182:0.6818:0.0	.	1079	O43451	MGA_HUMAN	Q	1079;1079;956	ENSP00000447378:E1079Q	ENSP00000316431:E956Q	E	+	1	0	MGAM	141401098	0.000000	0.05858	0.001000	0.08648	0.119000	0.20118	0.690000	0.25451	0.207000	0.20607	-0.515000	0.04445	GAG	G|0.997;C|0.003	0.003	strong		0.448	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			C	141754629	G	C	141754629	3	2	22	1	0	0	0	0	1	0	0	0	9550	1291	45	4	3337	4	MGAM	7	141754629	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4	141754629	17384034	1781	4682	57	2									
EPHB6	2051	hgsc.bcm.edu	37	chr7	142562011	142562011	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcctggcacctcaaacgCtggaccaaggtggacacaat	11	7	9	14	1	1	0	1	0	0	0	3	2	3	2	4	4	1	2	4	4	3	0	rs8177141	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:142562011C>T	ENST00000392957.2	+	7	1240	c.453C>T	c.(451-453)cgC>cgT	p.R151R	EPHB6_ENST00000442129.1_Silent_p.R151R|EPHB6_ENST00000411471.2_Intron	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	151	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.					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)					ACCTCAAACGCTGGACCAAGG	0.627													C|||	122	0.024361	0.0847	0.0144	5008	,	,		17524	0.0		0.0	False		,,,				2504	0.0				p.R151R		Atlas-SNP	.											EPHB6,right_lower_lobe,carcinoma,-2,1	EPHB6	168	1	0			c.C453T						PASS	.	C		332,4074	168.3+/-199.2	19,294,1890	58	62	61		453	4.7	1	7	dbSNP_117	61	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	EPHB6	NM_004445.3		19,297,6187	TT,TC,CC		0.0349,7.5352,2.5757		151/1022	142562011	335,12671	2203	4300	6503	SO:0001819	synonymous_variant	2051	exon7			CAAACGCTGGACC	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.453C>T	7.37:g.142562011C>T		99	0	0		106	60	0.566038	NM_004445	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Silent	SNP	ENST00000392957.2	37	CCDS5873.2																																																																																			C|0.970;T|0.030	0.030	strong		0.627	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			T	142562011	C	T	142562011	2	4	22	1	0	0	0	0	0	0	0	1	5180	784	28	2		2	EPHB6	7	142562011	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	807382	142562011	16576652	1782	4683											
TRPV6	55503	hgsc.bcm.edu	37	chr7	142573332	142573332	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgaagcagatgatgtacagCagatatatggcacccagcat	14	8	11	8	0	0	4	0	2	0	2	0	4	0	4	1	1	4	5	1	1	4	3	rs4987664	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:142573332C>T	ENST00000359396.3	-	8	1256	c.1011G>A	c.(1009-1011)ctG>ctA	p.L337L	RP11-114L10.2_ENST00000438839.1_RNA	NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	337					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)					TGATGTACAGCAGATATATGG	0.597													C|||	105	0.0209665	0.0726	0.013	5008	,	,		18895	0.0		0.0	False		,,,				2504	0.0				p.L337L		Atlas-SNP	.											.	TRPV6	108	.	0			c.G1011A						PASS	.	C		312,4094	167.3+/-198.3	17,278,1908	150	147	148		1011	1.6	0.4	7	dbSNP_113	148	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TRPV6	NM_018646.2		17,280,6206	TT,TC,CC		0.0233,7.0813,2.4143		337/726	142573332	314,12692	2203	4300	6503	SO:0001819	synonymous_variant	55503	exon8			GTACAGCAGATAT	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.1011G>A	7.37:g.142573332C>T		47	0	0		49	28	0.571429	NM_018646	A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Silent	SNP	ENST00000359396.3	37	CCDS5874.1																																																																																			C|0.971;T|0.029	0.029	strong		0.597	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274		T	142573332	C	T	142573332	2	4	22	1	0	0	0	0	0	0	0	1	16615	697	25	2		2	TRPV6	7	142573332	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	11321	142573332	16565331	1783	4684											
TRPV6	55503	hgsc.bcm.edu	37	chr7	142573613	142573613	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtcgaggtcagtggtccataCgtccactgggtgtgcttccg	5	11	14	11	3	1	0	1	0	0	0	5	1	4	0	3	3	2	1	3	3	1	2	rs79832568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:142573613C>T	ENST00000359396.3	-	7	1052	c.807G>A	c.(805-807)acG>acA	p.T269T	RP11-114L10.2_ENST00000438839.1_RNA	NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	269					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)					GTGGTCCATACGTCCACTGGG	0.532													C|||	117	0.0233626	0.0779	0.0144	5008	,	,		10275	0.0		0.004	False		,,,				2504	0.0				p.T269T		Atlas-SNP	.											.	TRPV6	108	.	0			c.G807A						PASS	.	C		327,4079	172.7+/-202.6	19,289,1895	214	162	180		807	-9.9	0	7	dbSNP_131	180	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	TRPV6	NM_018646.2		19,303,6181	TT,TC,CC		0.1628,7.4217,2.6219		269/726	142573613	341,12665	2203	4300	6503	SO:0001819	synonymous_variant	55503	exon7			TCCATACGTCCAC	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.807G>A	7.37:g.142573613C>T		167	0	0		170	83	0.488235	NM_018646	A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Silent	SNP	ENST00000359396.3	37	CCDS5874.1																																																																																			C|0.976;T|0.024	0.024	strong		0.532	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274		T	142573613	C	T	142573613	2	4	22	1	0	0	0	0	0	0	0	1	16615	523	19	1		1	TRPV6	7	142573613	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	281	142573613	16565050	1784	4685											
KEL	3792	hgsc.bcm.edu	37	chr7	142640004	142640004	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccaacgtctgcagcattctcTaagaatgtgagggagtcatt	11	11	10	9	1	3	2	1	1	2	1	4	3	3	3	1	1	3	2	1	1	3	3	rs8176039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:142640004T>C	ENST00000355265.2	-	17	2373	c.1899A>G	c.(1897-1899)ttA>ttG	p.L633L		NM_000420.2	NP_000411.1	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	633					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)					CAGCATTCTCTAAGAATGTGA	0.517													C|||	353	0.0704872	0.2519	0.0274	5008	,	,		21440	0.0		0.001	False		,,,				2504	0.0				p.L633L		Atlas-SNP	.											.	KEL	128	.	0			c.A1899G						PASS	.	C		957,3449	735.8+/-410.7	105,747,1351	103	94	97	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1899	1.8	0.2	7	dbSNP_117	97	10,8590	818.3+/-406.9	0,10,4290	no	coding-synonymous	KEL	NM_000420.2		105,757,5641	CC,CT,TT		0.1163,21.7204,7.435		633/733	142640004	967,12039	2203	4300	6503	SO:0001819	synonymous_variant	3792	exon17			ATTCTCTAAGAAT	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.1899A>G	7.37:g.142640004T>C		113	0	0		129	64	0.496124	NM_000420	B2RBV4|Q96RS8|Q99885	Silent	SNP	ENST00000355265.2	37	CCDS34766.1																																																																																			A|0.102;C|0.060	0.060	strong		0.517	KEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347671.2	NM_000420		C	142640004	T	C	142640004	2	2	22	1	0	0	0	0	0	0	0	1	8151	1519	53	3		3	KEL	7	142640004	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	66391	142640004	16498659	1785	4686											
EPHA1	2041	hgsc.bcm.edu	37	chr7	143088592	143088592	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctgcaaagaatgcgcttctgGtgcccgggcagtgtgattcc	7	10	13	11	2	1	2	0	1	1	1	2	2	2	2	2	2	3	3	2	2	2	2	rs56307701	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:143088592G>A	ENST00000275815.3	-	18	2975	c.2889C>T	c.(2887-2889)caC>caT	p.H963H	EPHA1_ENST00000458129.1_5'Flank	NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	963	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)				TGCGCTTCTGGTGCCCGGGCA	0.632													G|||	60	0.0119808	0.0446	0.0014	5008	,	,		16965	0.0		0.0	False		,,,				2504	0.0				p.H963H		Atlas-SNP	.											.	EPHA1	193	.	0			c.C2889T						PASS	.	G		187,4219	118.4+/-156.1	3,181,2019	89	59	69		2889	3.4	1	7	dbSNP_129	69	4,8596	2.2+/-6.3	0,4,4296	no	coding-synonymous	EPHA1	NM_005232.4		3,185,6315	AA,AG,GG		0.0465,4.2442,1.4686		963/977	143088592	191,12815	2203	4300	6503	SO:0001819	synonymous_variant	2041	exon18			CTTCTGGTGCCCG	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.2889C>T	7.37:g.143088592G>A		134	0	0		175	84	0.48	NM_005232	A1L3V3|B5A966|B5A967|Q15405	Silent	SNP	ENST00000275815.3	37	CCDS5884.1																																																																																			G|0.988;A|0.013	0.013	strong		0.632	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1			A	143088592	G	A	143088592	2	1	22	1	0	0	0	0	0	0	0	1	5167	1252	44	2		2	EPHA1	7	143088592	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	448588	143088592	16050071	1786	4687											
OR2A5	393046	hgsc.bcm.edu	37	chr7	143747796	143747796	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgtcccatgcacaatgcagaCctttttatacatggcttttg	9	15	7	10	0	0	1	0	0	0	1	1	1	1	1	2	1	3	3	2	1	3	6	rs61741408	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:143747796C>A	ENST00000408906.2	+	1	336	c.302C>A	c.(301-303)aCc>aAc	p.T101N		NM_012365.1	NP_036497.1	Q96R48	OR2A5_HUMAN	olfactory receptor, family 2, subfamily A, member 5	101						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L103fs*14(1)		cervix(1)|endometrium(3)|large_intestine(5)|lung(23)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	38	Melanoma(164;0.0783)					ACAATGCAGACCTTTTTATAC	0.428													C|||	16	0.00319489	0.0121	0.0	5008	,	,		24203	0.0		0.0	False		,,,				2504	0.0				p.T101N		Atlas-SNP	.											OR2A5,colon,carcinoma,+1,5	OR2A5	78	5	1	Deletion - Frameshift(1)	lung(1)	c.C302A						PASS	.	C	ASN/THR	58,4162		0,58,2052	151	149	150		302	4.5	1	7	dbSNP_129	150	1,8505		0,1,4252	yes	missense	OR2A5	NM_012365.1	65	0,59,6304	AA,AC,CC		0.0118,1.3744,0.4636	benign	101/312	143747796	59,12667	2110	4253	6363	SO:0001583	missense	393046	exon1			TGCAGACCTTTTT	U86278	CCDS43668.1	7q35	2013-09-20	2003-11-24		ENSG00000221836	ENSG00000221836		"GPCR / Class A : Olfactory receptors"	8232	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily A, member 5"	OR2A8, OR2A26		9500546	Standard	NM_012365		Approved	OR7-138, OR7-141	uc011ktw.2	Q96R48	OTTHUMG00000158006	ENST00000408906.2:c.302C>A	7.37:g.143747796C>A	ENSP00000386208:p.Thr101Asn	159	0	0		165	85	0.515152	NM_012365	B9EGX2|O43885|O43888	Missense_Mutation	SNP	ENST00000408906.2	37	CCDS43668.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	C	10.44	1.350249	0.24512	0.013744	1.18E-4	ENSG00000221836	ENST00000408906	T	0.02974	4.09	5.37	4.47	0.54385	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.03390	0.0098	M	0.71036	2.16	0.31492	N	0.665835	B	0.27932	0.194	B	0.27262	0.078	T	0.00896	-1.1523	9	0.66056	D	0.02	.	8.4796	0.33034	0.0:0.8307:0.0:0.1693	rs61741408	101	Q96R48	OR2A5_HUMAN	N	101	ENSP00000386208:T101N	ENSP00000386208:T101N	T	+	2	0	OR2A5	143378729	0.000000	0.05858	0.994000	0.49952	0.301000	0.27625	0.546000	0.23284	2.797000	0.96272	0.650000	0.86243	ACC	C|0.997;A|0.003	0.003	strong		0.428	OR2A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349986.1			A	143747796	C	A	143747796	3	1	22	1	0	0	0	0	1	0	0	0	10990	507	18	4	304	4	OR2A5	7	143747796	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	659204	143747796	15390867	1787	4688											
OR2A1	346528	hgsc.bcm.edu	37	chr7	144015524	144015527	+	Frame_Shift_Del	DEL	TGTT	TGTT	-																															gcatgacgcagacctttctcTgtttgagttttggacacagc																								rs559439902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGTT	TGTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:144015524_144015527delTGTT	ENST00000408951.1	+	1	307_310	c.307_310delTGTT	c.(307-312)tgtttgfs	p.CL103fs	OR2A1-AS1_ENST00000478925.1_RNA|OR2A1-AS1_ENST00000476560.1_RNA|OR2A1-AS1_ENST00000496968.1_RNA|OR2A1-AS1_ENST00000475089.1_RNA|OR2A1-AS1_ENST00000467944.1_RNA|OR2A1-AS1_ENST00000463561.1_RNA|OR2A1-AS1_ENST00000478806.1_RNA|OR2A1-AS1_ENST00000486094.1_RNA|OR2A1-AS1_ENST00000461843.1_RNA|OR2A1-AS1_ENST00000488041.1_RNA|OR2A1-AS1_ENST00000489488.1_RNA|OR2A1-AS1_ENST00000493539.1_RNA|OR2A1-AS1_ENST00000487102.1_RNA	NM_001005287.1	NP_001005287.1	Q8NGT9	OR2A1_HUMAN	olfactory receptor, family 2, subfamily A, member 1	103						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(3)|skin(2)	6	Melanoma(164;0.14)					GACCTTTCTCTGTTTGAGTTTTGG	0.569														126	0.0251597	0.0908	0.0086	5008	,	,		44510	0.0		0.0	False		,,,				2504	0.0				p.102_103del		Atlas-Indel	.											.	OR2A1	10	.	0			c.306_309del						PASS	.			296,3480		1,294,1593						-5.2	0.1			171	15,6777		4,7,3385	no	frameshift	OR2A1	NM_001005287.1		5,301,4978	A1A1,A1R,RR		0.2208,7.839,2.9428				311,10257				SO:0001589	frameshift_variant	346528	exon1			.		CCDS43673.1	7q35	2013-09-20			ENSG00000221970	ENSG00000221970		"GPCR / Class A : Olfactory receptors"	8229	protein-coding gene	gene with protein product							Standard	NM_001005287		Approved		uc011kub.2	Q8NGT9	OTTHUMG00000158005	ENST00000408951.1:c.307_310delTGTT	7.37:g.144015524_144015527delTGTT	ENSP00000386175:p.Cys103fs	626	0	0		1136	133	0.117077	NM_001005287	Q6IF44|Q96R46	Frame_Shift_Del	DEL	ENST00000408951.1	37	CCDS43673.1																																																																																			.	.	none		0.569	OR2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349985.1			-	144015527	TGTT	-	144015524	7	5	22	1	0	1	0	1	0	0	0	0	10983	1580	55	0	309	0	OR2A1	7	144015524	Frame_Shift_Del	DEL	TGTT	TCGA-G8-6324-01A-11D-2210-10	267728	144015524	15123139	1788	4689											
CNTNAP2	26047	hgsc.bcm.edu	37	chr7	146829390	146829390	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acggtgcctgtctttttcaaCgctacaagttacctggaggt	8	13	10	10	2	2	0	1	0	1	0	2	1	2	1	2	3	4	2	2	3	4	4	rs78543192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:146829390C>T	ENST00000361727.3	+	8	1653	c.1137C>T	c.(1135-1137)aaC>aaT	p.N379N		NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	379					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)			TCTTTTTCAACGCTACAAGTT	0.458										HNSCC(39;0.1)			T|||	30	0.00599042	0.0219	0.0014	5008	,	,		20040	0.0		0.0	False		,,,				2504	0.0				p.N379N		Atlas-SNP	.											CNTNAP2,colon,carcinoma,0,2	CNTNAP2	392	2	0			c.C1137T						PASS	.	T		66,4340	820.5+/-416.4	0,66,2137	126	121	122		1137	3.3	1	7	dbSNP_132	122	0,8600		0,0,4300	no	coding-synonymous	CNTNAP2	NM_014141.5		0,66,6437	TT,TC,CC		0.0,1.498,0.5075		379/1332	146829390	66,12940	2203	4300	6503	SO:0001819	synonymous_variant	26047	exon8			TTTCAACGCTACA	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.1137C>T	7.37:g.146829390C>T		110	0	0		116	51	0.439655	NM_014141	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Silent	SNP	ENST00000361727.3	37	CCDS5889.1																																																																																			C|0.995;T|0.005	0.005	strong		0.458	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1			T	146829390	C	T	146829390	2	4	22	1	0	0	0	0	0	0	0	1	3649	535	19	1		1	CNTNAP2	7	146829390	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2813866	146829390	12309273	1789	4690											
PDIA4	9601	hgsc.bcm.edu	37	chr7	148701245	148701245	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttcccaccacgaccttgaCgggtcccttgttgttcttgg	4	14	9	14	2	1	1	0	1	1	0	3	2	3	1	4	2	0	2	4	2	0	6	rs61739277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:148701245C>T	ENST00000286091.4	-	10	1811	c.1579G>A	c.(1579-1581)Gtc>Atc	p.V527I		NM_004911.4	NP_004902.1	P13667	PDIA4_HUMAN	protein disulfide isomerase family A, member 4	527	Thioredoxin 3. {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)			ACGACCTTGACGGGTCCCTTG	0.567													C|||	47	0.00938498	0.034	0.0029	5008	,	,		12360	0.0		0.0	False		,,,				2504	0.0				p.V527I		Atlas-SNP	.											.	PDIA4	57	.	0			c.G1579A						PASS	.	C	ILE/VAL	104,4302	83.4+/-121.9	1,102,2100	167	152	157		1579	4.9	0.8	7	dbSNP_129	157	0,8600		0,0,4300	yes	missense	PDIA4	NM_004911.4	29	1,102,6400	TT,TC,CC		0.0,2.3604,0.7996	benign	527/646	148701245	104,12902	2203	4300	6503	SO:0001583	missense	9601	exon10			CCTTGACGGGTCC	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.1579G>A	7.37:g.148701245C>T	ENSP00000286091:p.Val527Ile	208	0	0		175	78	0.445714	NM_004911	A8K4K6|Q549T6	Missense_Mutation	SNP	ENST00000286091.4	37	CCDS5893.1	13	0.005952380952380952	11	0.022357723577235773	2	0.0055248618784530384	0	0.0	0	0.0	C	15.92	2.975631	0.53720	0.023604	0.0	ENSG00000155660	ENST00000286091	T	0.26810	1.71	5.81	4.92	0.64577	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.056360	0.64402	D	0.000001	T	0.25306	0.0615	M	0.77406	2.37	0.80722	D	1	B	0.28419	0.211	B	0.40410	0.328	T	0.30268	-0.9984	10	0.72032	D	0.01	.	15.1664	0.72828	0.0:0.9316:0.0:0.0684	.	527	P13667	PDIA4_HUMAN	I	527	ENSP00000286091:V527I	ENSP00000286091:V527I	V	-	1	0	PDIA4	148332178	1.000000	0.71417	0.785000	0.31869	0.119000	0.20118	5.851000	0.69481	2.751000	0.94390	0.555000	0.69702	GTC	C|0.992;T|0.008	0.008	strong		0.567	PDIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317077.1	NM_004911		T	148701245	C	T	148701245	3	4	22	1	0	0	0	0	1	0	0	0	11679	536	19	1	362	1	PDIA4	7	148701245	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1871855	148701245	10437418	1790	4691											
ZNF212	7988	hgsc.bcm.edu	37	chr7	148947564	148947564	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgcagaggcggctggagaaCgtggagaacctgctgcgcaa	10	5	16	10	3	0	3	0	0	0	3	0	5	0	3	1	4	5	4	1	4	3	0	rs138413836	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:148947564C>T	ENST00000335870.2	+	2	467	c.339C>T	c.(337-339)aaC>aaT	p.N113N		NM_012256.3	NP_036388.2	Q9UDV6	ZN212_HUMAN	zinc finger protein 212	113					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)			GGCTGGAGAACGTGGAGAACC	0.617													C|||	13	0.00259585	0.0091	0.0014	5008	,	,		15049	0.0		0.0	False		,,,				2504	0.0				p.N113N		Atlas-SNP	.											.	ZNF212	28	.	0			c.C339T						PASS	.	C		33,4373	37.6+/-69.7	0,33,2170	68	83	78		339	3.2	1	7	dbSNP_134	78	0,8600		0,0,4300	no	coding-synonymous	ZNF212	NM_012256.3		0,33,6470	TT,TC,CC		0.0,0.749,0.2537		113/496	148947564	33,12973	2203	4300	6503	SO:0001819	synonymous_variant	7988	exon2			GGAGAACGTGGAG	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.339C>T	7.37:g.148947564C>T		87	0	0		104	59	0.567308	NM_012256	B2RCF4|Q13396|Q8N664	Silent	SNP	ENST00000335870.2	37	CCDS5896.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	9.867	1.197790	0.22037	0.00749	0.0	ENSG00000170260	ENST00000481584	.	.	.	5.95	3.17	0.36434	.	.	.	.	.	T	0.49115	0.1538	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44922	-0.9296	4	.	.	.	-30.1409	7.8161	0.29260	0.0:0.7392:0.0:0.2608	.	.	.	.	C	11	.	.	R	+	1	0	ZNF212	148578497	0.992000	0.36948	1.000000	0.80357	0.983000	0.72400	1.139000	0.31504	0.412000	0.25729	-0.222000	0.12452	CGT	C|0.999;T|0.001	0.001	strong		0.617	ZNF212-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352710.1	NM_012256		T	148947564	C	T	148947564	2	4	22	1	0	0	0	0	0	0	0	1	17783	535	19	1		1	ZNF212	7	148947564	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	246319	148947564	10191099	1791	4692											
ZNF746	155061	hgsc.bcm.edu	37	chr7	149174758	149174758	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggctgcccacgcctccacGcccagggcctgctgctcctg	3	6	11	21	3	0	0	0	0	0	0	2	0	2	0	7	2	3	3	7	2	0	0	rs61746598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149174758G>A	ENST00000340622.3	-	5	889	c.609C>T	c.(607-609)ggC>ggT	p.G203G	ZNF746_ENST00000458143.2_Silent_p.G203G			Q6NUN9	ZN746_HUMAN	zinc finger protein 746	203					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)			ACGCCTCCACGCCCAGGGCCT	0.667													G|||	174	0.0347444	0.1248	0.013	5008	,	,		16240	0.0		0.0	False		,,,				2504	0.0				p.G203G		Atlas-SNP	.											.	ZNF746	68	.	0			c.C609T						PASS	.	G	,	528,3878	228.1+/-243.1	33,462,1708	27	30	29		609,609	-6.2	0.7	7	dbSNP_129	29	3,8597	3.0+/-9.4	0,3,4297	yes	coding-synonymous,coding-synonymous	ZNF746	NM_001163474.1,NM_152557.4	,	33,465,6005	AA,AG,GG		0.0349,11.9837,4.0827	,	203/646,203/645	149174758	531,12475	2203	4300	6503	SO:0001819	synonymous_variant	155061	exon5			CTCCACGCCCAGG	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.609C>T	7.37:g.149174758G>A		69	0	0		85	47	0.552941	NM_001163474	A8K6Z9|Q6ZRF9	Silent	SNP	ENST00000340622.3	37	CCDS5897.1																																																																																			G|0.960;A|0.040	0.040	strong		0.667	ZNF746-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352730.1	NM_152557		A	149174758	G	A	149174758	2	1	22	1	0	0	0	0	0	0	0	1	18144	1074	38	1		1	ZNF746	7	149174758	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	227194	149174758	9963905	1792	4693											
ZNF467	168544	hgsc.bcm.edu	37	chr7	149462055	149462055	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	acggcgcaggcgtgggggcgGctgccagtgtgcaccgcctg	4	5	19	13	5	0	0	0	0	0	0	0	0	0	0	3	5	2	3	3	5	0	0	rs863021	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149462055G>A	ENST00000302017.3	-	5	1949	c.1536C>T	c.(1534-1536)agC>agT	p.S512S	ZNF467_ENST00000484747.1_Intron	NM_207336.1	NP_997219.1	Q7Z7K2	ZN467_HUMAN	zinc finger protein 467	512					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)			CGTGGGGGCGGCTGCCAGTGT	0.726													G|||	330	0.0658946	0.239	0.0173	5008	,	,		8834	0.0		0.002	False		,,,				2504	0.0				p.S512S		Atlas-SNP	.											.	ZNF467	50	.	0			c.C1536T						PASS	.	G		861,3477		106,649,1414	16	21	19		1536	-4.4	1	7	dbSNP_86	19	20,8504		1,18,4243	no	coding-synonymous	ZNF467	NM_207336.1		107,667,5657	AA,AG,GG		0.2346,19.8479,6.8496		512/596	149462055	881,11981	2169	4262	6431	SO:0001819	synonymous_variant	168544	exon5			GGGGCGGCTGCCA	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.1536C>T	7.37:g.149462055G>A		4	0	0		17	8	0.470588	NM_207336		Silent	SNP	ENST00000302017.3	37	CCDS5899.1																																																																																			G|0.947;A|0.053	0.053	strong		0.726	ZNF467-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349833.1	NM_207336		A	149462055	G	A	149462055	2	1	22	1	0	0	0	0	0	0	0	1	17942	1194	42	2		2	ZNF467	7	149462055	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	287297	149462055	9676608	1793	4694											
SSPO	23145	hgsc.bcm.edu	37	chr7	149480091	149480092	+	RNA	INS	-	-	C																															gtagcctacatcaccctggaINScccccgccatgcccaccagg																								rs144883973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149480091_149480092insC	ENST00000378016.2	+	0	2057_2058							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)			ATCACCCTGGACCCCCGCCATG	0.653													CCCCC|CCCCC|CCCCCC|insertion	131	0.0261581	0.0946	0.0086	5008	,	,		17227	0.0		0.0	False		,,,				2504	0.0				p.D686fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.2057_2058insC						PASS	.			263,3523		27,209,1657						4.2	1		dbSNP_134	31	27,7833		1,25,3904	no	frameshift	SSPO	NM_198455.2		28,234,5561	A1A1,A1R,RR		0.3435,6.9466,2.4901				290,11356						23145	exon15			.	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.149480096_149480096dupC		217	0	.		217	71	0.327	NM_198455	Q76B61	Frame_Shift_Ins	INS	ENST00000378016.2	37																																																																																				-|0.979;C|0.021	0.021	strong		0.653	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				C	149480092	-	C	149480091	6	5	22	0	1	1	1	0	0	0	0	0	15204	275	10	0		0	SSPO	7	149480091	RNA	INS	-	TCGA-G8-6324-01A-11D-2210-10	18036	149480091	9658572	1794	4695			4	27		21	21	45981	N	T_G_C_-	2.256038e-05
SSPO	23145	hgsc.bcm.edu	37	chr7	149481205	149481205	+	RNA	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcccctggcagtgccaccaTgaaggagtgcaaccgctggt	8	7	13	13	1	0	1	0	1	0	0	0	2	0	2	5	3	4	3	5	3	2	0	rs73727609	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149481205T>C	ENST00000378016.2	+	0	2687							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)			AGTGCCACCATGAAGGAGTGC	0.652													T|||	76	0.0151757	0.056	0.0029	5008	,	,		17147	0.0		0.0	False		,,,				2504	0.0				p.M896T		Atlas-SNP	.											.	.	.	.	0			c.T2687C						PASS	.	T		157,3863		1,155,1854	14	18	17		2689	1.3	0	7	dbSNP_130	17	2,8280		0,2,4139	yes	coding-notMod3	SSPO	NM_198455.2		1,157,5993	CC,CT,TT		0.0241,3.9055,1.2925			149481205	159,12143	2010	4141	6151			23145	exon18			CCACCATGAAGGA	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.149481205T>C		55	0	0		65	28	0.430769	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				T|0.986;C|0.014	0.014	strong		0.652	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				C	149481205	T	C	149481205	1	2	22	0	1	0	0	0	0	0	0	0	15204	1464	51	3		3	SSPO	7	149481205	RNA	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1114	149481205	9657458	1795	4696			4	27		21	21	45981	N	T_G_C_-	2.256038e-05
SSPO	23145	hgsc.bcm.edu	37	chr7	149484830	149484830	+	RNA	DEL	G	G	-																															cgctcttcacattatgccacGcggaggtccccccgcagcag																								rs137977793	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149484830delG	ENST00000378016.2	+	0	3652							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)			ATTATGCCACGCGGAGGTCCC	0.667													G|G|-|deletion	82	0.0163738	0.0598	0.0029	5008	,	,		17852	0.0		0.001	False		,,,				2504	0.0				p.H1217fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.3651delC						PASS	.			183,3691		17,149,1771	8	12	11			-4	0	7	dbSNP_134	11	3,7937		1,1,3968	no	frameshift	SSPO	NM_198455.2		18,150,5739	A1A1,A1R,RR		0.0378,4.7238,1.5744			149484830	186,11628	2003	4151	6154			23145	exon25			.	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.149484830delG		52	0	.		46	11	0.239	NM_198455	Q76B61	Frame_Shift_Del	DEL	ENST00000378016.2	37																																																																																				G|0.985;-|0.015	0.015	strong		0.667	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				-	149484830	G	-	149484830	6	5	22	0	1	1	0	1	0	0	0	0	15204	1087	38	0		0	SSPO	7	149484830	RNA	DEL	G	TCGA-G8-6324-01A-11D-2210-10	3625	149484830	9653833	1796	4697			4	27		21	21	45981	N	T_G_C_-	2.256038e-05
SSPO	23145	hgsc.bcm.edu	37	chr7	149485987	149485987	+	RNA	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgacaaccaggacgactgTggcgatggctctgatgagga	10	8	15	8	2	1	3	0	3	1	0	1	7	1	5	1	4	1	1	1	4	1	0	rs893597	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149485987T>A	ENST00000378016.2	+	0	4206							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)			AGGACGACTGTGGCGATGGCT	0.582													T|||	131	0.0261581	0.0946	0.0086	5008	,	,		22616	0.0		0.0	False		,,,				2504	0.0				p.C1402X		Atlas-SNP	.											.	.	.	.	0			c.T4206A						PASS	.	T		277,4091		10,257,1917	83	87	86		4210	1.2	1	7	dbSNP_86	86	4,8564		0,4,4280	yes	coding-notMod3	SSPO	NM_198455.2		10,261,6197	AA,AT,TT		0.0467,6.3416,2.1722			149485987	281,12655	2184	4284	6468			23145	exon29			CGACTGTGGCGAT	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.149485987T>A		146	0	0		190	90	0.473684	NM_198455	Q76B61	Nonsense_Mutation	SNP	ENST00000378016.2	37																																																																																				T|0.977;A|0.023	0.023	strong		0.582	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				A	149485987	T	A	149485987	1	1	22	0	1	0	0	0	0	0	0	0	15204	1702	59	5		5	SSPO	7	149485987	RNA	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1157	149485987	9652676	1797	4698			4	27		21	21	45981	N	T_G_C_-	2.256038e-05
SSPO	23145	hgsc.bcm.edu	37	chr7	149486367	149486367	+	RNA	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggagatggcacggatgagcCgagctatccgtgcccccagg	8	6	15	12	3	0	2	0	1	0	1	1	5	1	3	4	4	3	2	4	4	1	1	rs855692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149486367C>A	ENST00000378016.2	+	0	4343							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)			ACGGATGAGCCGAGCTATCCG	0.687													A|||	158	0.0315495	0.1029	0.0115	5008	,	,		16290	0.004		0.0	False		,,,				2504	0.0102				p.P1448Q		Atlas-SNP	.											.	.	.	.	0			c.C4343A						PASS	.	A		317,4079		13,291,1894	24	28	27		4347	0.9	0.5	7	dbSNP_86	27	5,8583		0,5,4289	yes	coding-notMod3	SSPO	NM_198455.2		13,296,6183	AA,AC,CC		0.0582,7.2111,2.48			149486367	322,12662	2198	4294	6492			23145	exon30			ATGAGCCGAGCTA	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.149486367C>A		81	0	0		87	47	0.54023	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.968;A|0.032	0.032	strong		0.687	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				A	149486367	C	A	149486367	1	1	22	0	1	0	0	0	0	0	0	0	15204	652	23	4		4	SSPO	7	149486367	RNA	SNP	C	TCGA-G8-6324-01A-11D-2210-10	380	149486367	9652296	1798	4699			4	27		21	21	45981	N	T_G_C_-	2.256038e-05
SSPO	23145	hgsc.bcm.edu	37	chr7	149486420	149486420	+	RNA	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gtgccgatggacgctgcctgCcgccggccctgctctgcgat	3	8	14	16	5	1	0	0	0	1	0	1	3	1	1	5	2	5	2	5	2	0	0	rs855693	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149486420C>G	ENST00000378016.2	+	0	4396							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)			ACGCTGCCTGCCGCCGGCCCT	0.677													C|||	135	0.0269569	0.0976	0.0086	5008	,	,		16567	0.0		0.0	False		,,,				2504	0.0				p.P1466A		Atlas-SNP	.											.	.	.	.	0			c.C4396G						PASS	.	C		238,4158		9,220,1969	20	24	22		4400	4.6	1	7	dbSNP_86	22	4,8582		0,4,4289	yes	coding-notMod3	SSPO	NM_198455.2		9,224,6258	GG,GC,CC		0.0466,5.414,1.8641			149486420	242,12740	2198	4293	6491			23145	exon30			TGCCTGCCGCCGG	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.149486420C>G		87	0	0		92	46	0.5	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.979;G|0.021	0.021	strong		0.677	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				G	149486420	C	G	149486420	1	3	22	0	1	0	0	0	0	0	0	0	15204	739	26	4		4	SSPO	7	149486420	RNA	SNP	C	TCGA-G8-6324-01A-11D-2210-10	53	149486420	9652243	1799	4700			4	27		21	21	45981	N	T_G_C_-	2.256038e-05
SSPO	23145	hgsc.bcm.edu	37	chr7	149486726	149486726	+	RNA	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccggggaggtgtcctgtgtTgatggcacctgcctgggggc	3	9	18	11	1	0	1	0	1	0	0	1	2	1	2	4	6	1	2	4	6	0	1	rs855695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149486726T>C	ENST00000378016.2	+	0	4500							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)			TGTCCTGTGTTGATGGCACCT	0.637													C|||	161	0.0321486	0.1059	0.0115	5008	,	,		18130	0.004		0.0	False		,,,				2504	0.0092				p.V1500V		Atlas-SNP	.											.	.	.	.	0			c.T4500C						PASS	.	C		300,3736		11,278,1729	24	31	29		4504	-9.6	0	7	dbSNP_86	29	6,8338		0,6,4166	yes	coding-notMod3	SSPO	NM_198455.2		11,284,5895	CC,CT,TT		0.0719,7.4331,2.4717			149486726	306,12074	2018	4172	6190			23145	exon31			CTGTGTTGATGGC	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.149486726T>C		140	0	0		127	77	0.606299	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				T|0.974;C|0.026	0.026	strong		0.637	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				C	149486726	T	C	149486726	1	2	22	0	1	0	0	0	0	0	0	0	15204	1799	63	3		3	SSPO	7	149486726	RNA	SNP	T	TCGA-G8-6324-01A-11D-2210-10	306	149486726	9651937	1800	4701			4	27		21	21	45981	N	T_G_C_-	2.256038e-05
SSPO	23145	hgsc.bcm.edu	37	chr7	149488909	149488909	+	RNA	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccccctgcctcacagtggaCggtgaatggagcacctggtc	7	8	12	14	1	1	1	1	1	0	0	3	3	2	3	4	4	2	1	4	4	1	0	rs893600	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149488909C>T	ENST00000378016.2	+	0	5250							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)			TCACAGTGGACGGTGAATGGA	0.657													C|||	131	0.0261581	0.0946	0.0086	5008	,	,		18103	0.0		0.0	False		,,,				2504	0.0				p.D1750D		Atlas-SNP	.											.	.	.	.	0			c.C5250T						PASS	.	C		247,3859		6,235,1812	14	18	16		5254	-5.8	0.4	7	dbSNP_86	16	6,8318		0,6,4156	yes	coding-notMod3	SSPO	NM_198455.2		6,241,5968	TT,TC,CC		0.0721,6.0156,2.0354			149488909	253,12177	2053	4162	6215			23145	exon35			AGTGGACGGTGAA	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.149488909C>T		188	0	0		159	77	0.484277	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				C|0.979;T|0.021	0.021	strong		0.657	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				T	149488909	C	T	149488909	1	4	22	0	1	0	0	0	0	0	0	0	15204	535	19	1		1	SSPO	7	149488909	RNA	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2183	149488909	9649754	1801	4702			4	27		21	21	45981	N	T_G_C_-	2.256038e-05
SSPO	23145	hgsc.bcm.edu	37	chr7	149488991	149488991	+	RNA	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcggcaacggcagtgccacTcaccccagaatgggggccgc	8	3	14	16	4	1	1	1	0	0	1	1	1	1	1	4	4	2	2	4	4	2	0	rs893601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149488991T>C	ENST00000378016.2	+	0	5332							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)			GCAGTGCCACTCACCCCAGAA	0.662													C|||	202	0.0403355	0.1029	0.0144	5008	,	,		16534	0.004		0.003	False		,,,				2504	0.0501				p.S1778P		Atlas-SNP	.											.	.	.	.	0			c.T5332C						PASS	.	C		297,3797		12,273,1762	19	23	22		5336	4.8	0.1	7	dbSNP_86	22	18,8330		0,18,4156	yes	coding-notMod3	SSPO	NM_198455.2		12,291,5918	CC,CT,TT		0.2156,7.2545,2.5317			149488991	315,12127	2047	4174	6221			23145	exon35			TGCCACTCACCCC	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.149488991T>C		95	0	0		83	40	0.481928	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				T|0.976;C|0.024	0.024	strong		0.662	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				C	149488991	T	C	149488991	1	2	22	0	1	0	0	0	0	0	0	0	15204	1551	54	3		3	SSPO	7	149488991	RNA	SNP	T	TCGA-G8-6324-01A-11D-2210-10	82	149488991	9649672	1802	4703			4	27		21	21	45981	N	T_G_C_-	2.256038e-05
SSPO	23145	hgsc.bcm.edu	37	chr7	149489037	149489037	+	RNA	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctgcactgcccggaggccTgcacagcacccgccagacca	8	4	11	18	2	0	1	0	0	0	1	0	2	0	2	5	2	5	4	5	2	0	0	rs1635802	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149489037T>C	ENST00000378016.2	+	0	5378							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)			CCCGGAGGCCTGCACAGCACC	0.652													C|||	202	0.0403355	0.1029	0.0144	5008	,	,		16636	0.004		0.003	False		,,,				2504	0.0501				p.L1793P		Atlas-SNP	.											.	.	.	.	0			c.T5378C						PASS	.	C		308,3816		12,284,1766	25	30	28		5382	3.9	0	7	dbSNP_89	28	19,8349		0,19,4165	no	coding-notMod3	SSPO	NM_198455.2		12,303,5931	CC,CT,TT		0.2271,7.4685,2.6177			149489037	327,12165	2062	4184	6246			23145	exon35			GAGGCCTGCACAG	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.149489037T>C		60	0	0		75	38	0.506667	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				T|0.977;C|0.023	0.023	strong		0.652	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				C	149489037	T	C	149489037	1	2	22	0	1	0	0	0	0	0	0	0	15204	1580	55	3		3	SSPO	7	149489037	RNA	SNP	T	TCGA-G8-6324-01A-11D-2210-10	46	149489037	9649626	1803	4704			4	27		21	21	45981	N	T_G_C_-	2.256038e-05
SSPO	23145	hgsc.bcm.edu	37	chr7	149489048	149489048	+	RNA	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggaggcctgcacagcaccCgccagaccagtgagttgaag	10	4	13	14	2	0	3	0	2	0	1	0	4	0	4	5	2	2	3	5	2	1	1	rs893602	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149489048C>T	ENST00000378016.2	+	0	5389							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)			GCACAGCACCCGCCAGACCAG	0.652													C|||	131	0.0261581	0.0946	0.0086	5008	,	,		18478	0.0		0.0	False		,,,				2504	0.0				p.R1797C		Atlas-SNP	.											.	.	.	.	0			c.C5389T						PASS	.	C		257,3869		9,239,1815	28	32	31		5393	3	0	7	dbSNP_86	31	4,8368		0,4,4182	yes	coding-notMod3	SSPO	NM_198455.2		9,243,5997	TT,TC,CC		0.0478,6.2288,2.0883			149489048	261,12237	2063	4186	6249			23145	exon35			AGCACCCGCCAGA	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.149489048C>T		60	0	0		77	37	0.480519	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.979;T|0.021	0.021	strong		0.652	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				T	149489048	C	T	149489048	1	4	22	0	1	0	0	0	0	0	0	0	15204	652	23	1		1	SSPO	7	149489048	RNA	SNP	C	TCGA-G8-6324-01A-11D-2210-10	11	149489048	9649615	1804	4705			4	27		21	21	45981	N	T_G_C_-	2.256038e-05
SSPO	23145	hgsc.bcm.edu	37	chr7	149489443	149489443	+	RNA	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggggtggtgtgtgtggcccCggcagtgcccctgcctggtg	2	9	19	11	1	0	0	0	0	0	0	0	0	0	0	5	6	2	1	5	6	0	0	rs893603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149489443C>A	ENST00000378016.2	+	0	5596							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)			TGTGTGGCCCCGGCAGTGCCC	0.697													C|||	202	0.0403355	0.1029	0.0144	5008	,	,		16052	0.004		0.003	False		,,,				2504	0.0501				p.R1866R		Atlas-SNP	.											.	.	.	.	0			c.C5596A						PASS	.	C		301,3865		12,277,1794	13	21	19		5600	-1.9	0.1	7	dbSNP_86	19	18,8382		0,18,4182	no	coding-notMod3	SSPO	NM_198455.2		12,295,5976	AA,AC,CC		0.2143,7.2252,2.5386			149489443	319,12247	2083	4200	6283			23145	exon37			TGGCCCCGGCAGT	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.149489443C>A		81	0	0		112	37	0.330357	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				C|0.975;A|0.025	0.025	strong		0.697	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				A	149489443	C	A	149489443	1	1	22	0	1	0	0	0	0	0	0	0	15204	643	23	4		4	SSPO	7	149489443	RNA	SNP	C	TCGA-G8-6324-01A-11D-2210-10	395	149489443	9649220	1805	4706			4	27		21	21	45981	N	T_G_C_-	2.256038e-05
SSPO	23145	hgsc.bcm.edu	37	chr7	149493519	149493519	+	RNA	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggactttcggccgcatggtgCaggcgaggtttgtcagggtg	5	10	18	8	3	1	0	1	0	0	0	2	2	1	1	1	6	1	3	1	6	0	2	rs57595625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149493519C>T	ENST00000378016.2	+	0	6595							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)			CCGCATGGTGCAGGCGAGGTT	0.617													C|||	145	0.0289537	0.1059	0.0072	5008	,	,		18965	0.0		0.0	False		,,,				2504	0.0				p.Q2199X		Atlas-SNP	.											.	.	.	.	0			c.C6595T						PASS	.	C		345,3947		8,329,1809	100	114	110		6599	3.6	1	7	dbSNP_129	110	3,8491		0,3,4244	yes	coding-notMod3	SSPO	NM_198455.2		8,332,6053	TT,TC,CC		0.0353,8.0382,2.7217			149493519	348,12438	2146	4247	6393			23145	exon44			ATGGTGCAGGCGA	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.149493519C>T		135	0	0		139	73	0.52518	NM_198455	Q76B61	Nonsense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.972;T|0.028	0.028	strong		0.617	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				T	149493519	C	T	149493519	1	4	22	0	1	0	0	0	0	0	0	0	15204	711	25	2		2	SSPO	7	149493519	RNA	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4076	149493519	9645144	1806	4707			4	27		21	21	45981	N	T_G_C_-	2.256038e-05
SSPO	23145	hgsc.bcm.edu	37	chr7	149498945	149498945	+	RNA	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcaagggccctctgttcccCgagccagctgagctgtggca	6	8	12	15	1	2	1	1	1	1	0	3	2	3	1	4	2	3	4	4	2	1	1	rs73727615	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149498945C>T	ENST00000378016.2	+	0	7397							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)			CTCTGTTCCCCGAGCCAGCTG	0.657													C|||	90	0.0179712	0.0635	0.0086	5008	,	,		18616	0.0		0.0	False		,,,				2504	0.0				p.P2466L		Atlas-SNP	.											.	.	.	.	0			c.C7397T						PASS	.	C		208,4004		3,202,1901	31	34	33		7401	2.5	0.1	7	dbSNP_130	33	3,8429		0,3,4213	no	coding-notMod3	SSPO	NM_198455.2		3,205,6114	TT,TC,CC		0.0356,4.9383,1.6688			149498945	211,12433	2106	4216	6322			23145	exon50			GTTCCCCGAGCCA	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.149498945C>T		105	0	0		78	44	0.564103	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.982;T|0.018	0.018	strong		0.657	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				T	149498945	C	T	149498945	1	4	22	0	1	0	0	0	0	0	0	0	15204	652	23	1		1	SSPO	7	149498945	RNA	SNP	C	TCGA-G8-6324-01A-11D-2210-10	5426	149498945	9639718	1807	4708			4	27		21	21	45981	N	T_G_C_-	2.256038e-05
SSPO	23145	hgsc.bcm.edu	37	chr7	149499254	149499254	+	RNA	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggcagctgcccgcgtgaccGgttccgaagccagtcctgct	5	7	14	15	4	0	1	0	1	0	0	2	2	2	1	5	2	4	4	5	2	1	1	rs59522380	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149499254G>A	ENST00000378016.2	+	0	7622							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)			CCGCGTGACCGGTTCCGAAGC	0.687													G|||	298	0.0595048	0.2171	0.0159	5008	,	,		15602	0.0		0.0	False		,,,				2504	0.0				p.R2541Q		Atlas-SNP	.											.	.	.	.	0			c.G7622A						PASS	.	G		441,3035		13,415,1310	4	6	5		7626	-4	0	7	dbSNP_129	5	7,7421		0,7,3707	no	coding-notMod3	SSPO	NM_198455.2		13,422,5017	AA,AG,GG		0.0942,12.687,4.1086			149499254	448,10456	1738	3714	5452			23145	exon51			GTGACCGGTTCCG	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.149499254G>A		26	0	0		44	21	0.477273	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				G|0.945;A|0.055	0.055	strong		0.687	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				A	149499254	G	A	149499254	1	1	22	0	1	0	0	0	0	0	0	0	15204	1116	39	1		1	SSPO	7	149499254	RNA	SNP	G	TCGA-G8-6324-01A-11D-2210-10	309	149499254	9639409	1808	4709			4	27		21	21	45981	N	T_G_C_-	2.256038e-05
SSPO	23145	hgsc.bcm.edu	37	chr7	149506195	149506195	+	RNA	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggtggtggctacaggaacCgcacccgaggcagcagctgc	8	5	16	12	2	0	0	0	0	0	0	0	2	0	1	2	5	5	5	2	5	2	1	rs73727627	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149506195C>T	ENST00000378016.2	+	0	9187							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)			CTACAGGAACCGCACCCGAGG	0.682													C|||	125	0.0249601	0.0772	0.0115	5008	,	,		13530	0.001		0.002	False		,,,				2504	0.0123				p.R3063C		Atlas-SNP	.											.	.	.	.	0			c.C9187T						PASS	.	C		235,3871		4,227,1822	16	24	22		9195	5.2	1	7	dbSNP_130	22	32,8324		0,32,4146	no	coding-notMod3	SSPO	NM_198455.2		4,259,5968	TT,TC,CC		0.383,5.7233,2.1425			149506195	267,12195	2053	4178	6231			23145	exon63			AGGAACCGCACCC	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.149506195C>T		259	1	0.003861		292	154	0.527397	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.978;T|0.022	0.022	strong		0.682	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				T	149506195	C	T	149506195	1	4	22	0	1	0	0	0	0	0	0	0	15204	652	23	1		1	SSPO	7	149506195	RNA	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6941	149506195	9632468	1809	4710			4	27		21	21	45981	N	T_G_C_-	2.256038e-05
SSPO	23145	hgsc.bcm.edu	37	chr7	149509048	149509048	+	RNA	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggagccagtgttcagcctcCtgtggccctgcccggtgcca	4	9	13	15	1	1	0	1	0	0	0	2	1	2	1	6	3	4	1	6	3	0	1	rs115723456	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149509048C>T	ENST00000378016.2	+	0	9594							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)			GTTCAGCCTCCTGTGGCCCTG	0.697													C|||	70	0.0139776	0.053	0.0	5008	,	,		15590	0.0		0.0	False		,,,				2504	0.0				p.S3198S		Atlas-SNP	.											.	.	.	.	0			c.C9594T						PASS	.	C		162,3908		5,152,1878	30	35	34		9604	0.7	1	7	dbSNP_132	34	0,8344		0,0,4172	no	coding-notMod3	SSPO	NM_198455.2		5,152,6050	TT,TC,CC		0.0,3.9803,1.305			149509048	162,12252	2035	4172	6207			23145	exon68			AGCCTCCTGTGGC	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.149509048C>T		83	0	0		104	52	0.5	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				C|0.989;T|0.011	0.011	strong		0.697	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				T	149509048	C	T	149509048	1	4	22	0	1	0	0	0	0	0	0	0	15204	668	24	2		2	SSPO	7	149509048	RNA	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2853	149509048	9629615	1810	4711			4	27		21	21	45981	N	T_G_C_-	2.256038e-05
SSPO	23145	hgsc.bcm.edu	37	chr7	149512267	149512267	+	RNA	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctttcttcctgcgtagactgCgggggtggccagagtctgca	5	11	14	11	2	2	2	0	0	2	2	3	2	3	2	2	3	3	2	2	3	1	3	rs142728666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149512267C>T	ENST00000378016.2	+	0	10587							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)			GCGTAGACTGCGGGGGTGGCC	0.667													C|||	46	0.0091853	0.0219	0.0029	5008	,	,		17602	0.0		0.002	False		,,,				2504	0.0133				p.C3529C		Atlas-SNP	.											.	.	.	.	0			c.C10587T						PASS	.	C		80,4040		1,78,1981	37	44	42		10597	-3	0.8	7	dbSNP_134	42	16,8358		0,16,4171	yes	coding-notMod3	SSPO	NM_198455.2		1,94,6152	TT,TC,CC		0.1911,1.9417,0.7684			149512267	96,12398	2060	4187	6247			23145	exon75			AGACTGCGGGGGT	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.149512267C>T		81	0	0		75	33	0.44	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				C|0.996;T|0.004	0.004	strong		0.667	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				T	149512267	C	T	149512267	1	4	22	0	1	0	0	0	0	0	0	0	15204	776	27	1		1	SSPO	7	149512267	RNA	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3219	149512267	9626396	1811	4712			4	27		21	21	45981	N	T_G_C_-	2.256038e-05
SSPO	23145	hgsc.bcm.edu	37	chr7	149519007	149519007	+	RNA	DEL	G	G	-																															actgccctgtctcctgtggaGgtggaaaccaggtccgaacc																								rs568158666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149519007delG	ENST00000378016.2	+	0	12811							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)			CTCCTGTGGAGGTGGAAACCA	0.682													GG|GG|G|deletion	26	0.00519169	0.0197	0.0	5008	,	,		16479	0.0		0.0	False		,,,				2504	0.0				p.G4270fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.12810delA						PASS	.			63,3869		2,59,1905	16	19	18			3.2	1	7		18	2,7986		1,0,3993	no	frameshift	SSPO	NM_198455.2		3,59,5898	A1A1,A1R,RR		0.025,1.6022,0.5453			149519007	65,11855	2040	4183	6223			23145	exon90			.	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.149519007delG		181	0	.		198	54	0.273	NM_198455	Q76B61	Frame_Shift_Del	DEL	ENST00000378016.2	37																																																																																				.	.	none		0.682	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				-	149519007	G	-	149519007	6	5	22	0	1	1	0	1	0	0	0	0	15204	1000	35	0		0	SSPO	7	149519007	RNA	DEL	G	TCGA-G8-6324-01A-11D-2210-10	6740	149519007	9619656	1812	4713			4	27		21	21	45981	N	T_G_C_-	2.256038e-05
SSPO	23145	hgsc.bcm.edu	37	chr7	149522163	149522163	+	RNA	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gccctctgtggaggaggctgCcgggagccatgggctcaaga	7	6	17	11	1	2	1	1	0	1	1	2	4	2	4	3	5	2	2	3	5	1	0	rs73727642	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149522163C>G	ENST00000378016.2	+	0	13950							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)			GAGGAGGCTGCCGGGAGCCAT	0.652													C|||	192	0.0383387	0.1354	0.0187	5008	,	,		15887	0.0		0.0	False		,,,				2504	0.0				p.C4650W		Atlas-SNP	.											.	.	.	.	0			c.C13950G						PASS	.	C		374,3424		21,332,1546	19	25	23		13964	3.5	0.4	7	dbSNP_130	23	7,8195		0,7,4094	yes	coding-notMod3	SSPO	NM_198455.2		21,339,5640	GG,GC,CC		0.0853,9.8473,3.175			149522163	381,11619	1899	4101	6000			23145	exon96			AGGCTGCCGGGAG	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.149522163C>G		85	0	0		66	23	0.348485	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.974;G|0.026	0.026	strong		0.652	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				G	149522163	C	G	149522163	1	3	22	0	1	0	0	0	0	0	0	0	15204	747	26	4		4	SSPO	7	149522163	RNA	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3156	149522163	9616500	1813	4714			4	27		21	21	45981	N	T_G_C_-	2.256038e-05
SSPO	23145	hgsc.bcm.edu	37	chr7	149526071	149526071	+	RNA	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagctgctgtccctcttgccGcagggaggctccgggtatgg	4	9	16	12	2	1	0	0	0	1	0	3	2	3	1	3	4	3	5	3	4	1	2	rs142321773	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149526071G>A	ENST00000378016.2	+	0	15128							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)			CCCTCTTGCCGCAGGGAGGCT	0.667													G|||	21	0.00419329	0.0159	0.0	5008	,	,		14491	0.0		0.0	False		,,,				2504	0.0				p.R5042H		Atlas-SNP	.											.	.	.	.	0			c.G15125A						PASS	.	G	HIS/ARG	46,4080		1,44,2018	42	53	49		15144	-1.8	0	7	dbSNP_134	49	1,8405		0,1,4202	no	missense	SSPO	NM_198455.2	29	1,45,6220	AA,AG,GG		0.0119,1.1149,0.375	benign	5042/5148	149526071	47,12485	2063	4203	6266			23145	exon107			CTTGCCGCAGGGA	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.149526071G>A		129	0	0		114	56	0.491228	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				G|0.997;A|0.003	0.003	strong		0.667	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				A	149526071	G	A	149526071	1	1	22	0	1	0	0	0	0	0	0	0	15204	1087	38	1		1	SSPO	7	149526071	RNA	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3908	149526071	9612592	1814	4715			4	27		21	21	45981	N	T_G_C_-	2.256038e-05
REPIN1	29803	hgsc.bcm.edu	37	chr7	150068981	150068981	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gctctggggccccggcccagGggccgccccgcggtgaccgc	2	3	17	19	5	1	1	0	1	1	0	1	1	1	1	7	6	0	1	7	6	0	0	rs149624173	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150068981G>A	ENST00000425389.2	+	1	729	c.651G>A	c.(649-651)agG>agA	p.R217R	REPIN1_ENST00000397281.2_Silent_p.R217R|REPIN1_ENST00000444957.1_Silent_p.R217R|REPIN1_ENST00000479668.1_3'UTR|REPIN1_ENST00000540729.1_Silent_p.R217R|REPIN1_ENST00000489432.2_Silent_p.R274R|REPIN1_ENST00000466559.1_3'UTR|RP4-584D14.5_ENST00000488310.1_RNA	NM_014374.3	NP_055189.2	Q9BWE0	REPI1_HUMAN	replication initiator 1	217					DNA replication (GO:0006260)|regulation of fatty acid transport (GO:2000191)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cytosolic ribosome (GO:0022626)|lipid particle (GO:0005811)|nuclear membrane (GO:0031965)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	14	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.011)			cccggcccaggggccgccccg	0.716													G|||	21	0.00419329	0.0159	0.0	5008	,	,		9749	0.0		0.0	False		,,,				2504	0.0				p.R274R		Atlas-SNP	.											.	REPIN1	74	.	0			c.G822A						PASS	.	G	,,,	38,3468		0,38,1715	8	10	9		822,651,651,651	1.7	0.9	7	dbSNP_134	9	0,7798		0,0,3899	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	REPIN1	NM_001099695.1,NM_001099696.2,NM_013400.3,NM_014374.3	,,,	0,38,5614	AA,AG,GG		0.0,1.0839,0.3362	,,,	274/625,217/568,217/568,217/568	150068981	38,11266	1753	3899	5652	SO:0001819	synonymous_variant	29803	exon3			GCCCAGGGGCCGC	AF201303	CCDS43677.1, CCDS47745.1	7q36.1	2013-01-08	2003-08-07	2003-08-08				"Zinc fingers, C2H2-type"	17922	protein-coding gene	gene with protein product	"replication initiation region protein (60kD)", "zinc finger protein AP4", "zinc finger protein 464 (RIP60)"		"zinc finger protein 464 (RIP60)"	ZNF464		10606657	Standard	NM_013400		Approved	RIP60, AP4, H_DJ0584D14.12, Zfp464	uc010lpr.1	Q9BWE0		ENST00000425389.2:c.651G>A	7.37:g.150068981G>A		7	0	0		7	4	0.571429	NM_001099695	C9J3L7|D3DWZ1|Q7LE03|Q9BUZ6|Q9NZH2|Q9UMP5	Silent	SNP	ENST00000425389.2	37	CCDS43677.1																																																																																			G|0.994;A|0.006	0.006	strong		0.716	REPIN1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376940.1	NM_014374		A	150068981	G	A	150068981	2	1	22	1	0	0	0	0	0	0	0	1	13242	1223	43	2		2	REPIN1	7	150068981	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	542910	150068981	9069682	1815	4716											
GIMAP8	155038	hgsc.bcm.edu	37	chr7	150164189	150164189	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatcattattgtcttcactCggaaggatgatttgggggat	10	14	11	6	1	3	1	2	1	1	0	4	4	3	4	0	4	0	0	0	4	2	4	rs143212982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150164189C>A	ENST00000307271.3	+	2	977	c.403C>A	c.(403-405)Cgg>Agg	p.R135R		NM_175571.2	NP_783161.1	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	135	AIG1-type G 1.					cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(26)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		TGTCTTCACTCGGAAGGATGA	0.463																																					p.R135R		Atlas-SNP	.											GIMAP8,NS,carcinoma,-1,1	GIMAP8	136	1	0			c.C403A						PASS	.	C		37,4369	41.6+/-74.8	0,37,2166	79	75	76		403	-4.4	0	7	dbSNP_134	76	1,8599	1.2+/-3.3	0,1,4299	yes	coding-synonymous	GIMAP8	NM_175571.2		0,38,6465	AA,AC,CC		0.0116,0.8398,0.2922		135/666	150164189	38,12968	2203	4300	6503	SO:0001819	synonymous_variant	155038	exon2			TTCACTCGGAAGG	AL834361	CCDS34777.1	7q36.1	2014-04-04			ENSG00000171115	ENSG00000171115		"GTPases, IMAP"	21792	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 9"					15474311	Standard	XM_005249951		Approved	DKFZp667I133, hIAN6, IAN9	uc003whj.3	Q8ND71	OTTHUMG00000158327	ENST00000307271.3:c.403C>A	7.37:g.150164189C>A		180	0	0		201	104	0.517413	NM_175571		Silent	SNP	ENST00000307271.3	37	CCDS34777.1																																																																																			A|0.002;C|0.998;G|0.001	0.002	strong		0.463	GIMAP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350701.1	NM_175571		A	150164189	C	A	150164189	2	1	22	1	0	0	0	0	0	0	0	1	6393	875	31	4		4	GIMAP8	7	150164189	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	95208	150164189	8974474	1816	4717											
GIMAP6	474344	hgsc.bcm.edu	37	chr7	150324976	150324976	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaagttttgctgggtatatTggtaagccttgttgctgtaa	9	16	12	4	0	0	0	0	0	0	0	0	1	0	0	1	2	3	7	1	2	5	9	rs11977216	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150324976T>C	ENST00000328902.5	-	3	926	c.710A>G	c.(709-711)cAa>cGa	p.Q237R	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	237	AIG1-type G.		Q -> R (in dbSNP:rs11977216).			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)		CTGGGTATATTGGTAAGCCTT	0.512													T|||	163	0.0325479	0.1203	0.0058	5008	,	,		23011	0.0		0.0	False		,,,				2504	0.0				p.Q307R		Atlas-SNP	.											.	GIMAP6	60	.	0			c.A920G						PASS	.	T	ARG/GLN	479,3927	224.9+/-240.9	27,425,1751	164	152	156		710	0	0	7	dbSNP_120	156	4,8596	3.7+/-12.6	0,4,4296	yes	missense	GIMAP6	NM_024711.5	43	27,429,6047	CC,CT,TT		0.0465,10.8715,3.7137	benign	237/293	150324976	483,12523	2203	4300	6503	SO:0001583	missense	474344	exon3			GTATATTGGTAAG	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.710A>G	7.37:g.150324976T>C	ENSP00000330374:p.Gln237Arg	324	0	0		290	128	0.441379	NM_001244072	C9J7B6|D3DWZ4|Q5ZPR6|Q9H612	Missense_Mutation	SNP	ENST00000328902.5	37	CCDS34778.1	47	0.02152014652014652	44	0.08943089430894309	3	0.008287292817679558	0	0.0	0	0.0	T	2.860	-0.236349	0.05944	0.108715	4.65E-4	ENSG00000133561	ENST00000328902;ENST00000392862	T	0.05199	3.48	4.05	-0.00736	0.14009	AIG1 (1);	0.847263	0.10486	N	0.668996	T	0.00073	0.0002	N	0.04994	-0.135	0.09310	N	0.999999	B;B	0.18013	0.002;0.025	B;B	0.18263	0.021;0.018	T	0.47923	-0.9079	10	0.11794	T	0.64	.	3.0119	0.06047	0.3789:0.1102:0.0:0.5109	rs11977216;rs52790742;rs56467483;rs58007032;rs11977216	237;157	Q6P9H5;Q6P9H5-2	GIMA6_HUMAN;.	R	237;298	ENSP00000330374:Q237R	ENSP00000330374:Q237R	Q	-	2	0	GIMAP6	149955909	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.176000	0.09811	-0.160000	0.11002	-0.336000	0.08194	CAA	T|0.964;C|0.036	0.036	strong		0.512	GIMAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353457.1	NM_024711		C	150324976	T	C	150324976	3	2	22	1	0	0	0	0	1	0	0	0	6391	1812	63	3	172	3	GIMAP6	7	150324976	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	160787	150324976	8813687	1817	4718											
GIMAP6	474344	hgsc.bcm.edu	37	chr7	150325177	150325177	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	catagtcttccagggagccgCcagccaggtcttccttccgg	6	9	11	15	2	2	0	0	0	2	0	5	1	5	1	6	3	2	0	6	3	1	4	rs11974345	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150325177C>T	ENST00000328902.5	-	3	725	c.509G>A	c.(508-510)gGc>gAc	p.G170D	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	170	AIG1-type G.		G -> D (in dbSNP:rs11974345).			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)		CAGGGAGCCGCCAGCCAGGTC	0.612													C|||	163	0.0325479	0.1203	0.0058	5008	,	,		16861	0.0		0.0	False		,,,				2504	0.0				p.G240D		Atlas-SNP	.											GIMAP6,NS,carcinoma,+1,1	GIMAP6	60	1	0			c.G719A						PASS	.	C	ASP/GLY	480,3926	224.6+/-240.7	28,424,1751	110	112	112		509	-1.6	0	7	dbSNP_120	112	4,8596	3.7+/-12.6	0,4,4296	yes	missense	GIMAP6	NM_024711.5	94	28,428,6047	TT,TC,CC		0.0465,10.8942,3.7214	benign	170/293	150325177	484,12522	2203	4300	6503	SO:0001583	missense	474344	exon3			GAGCCGCCAGCCA	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.509G>A	7.37:g.150325177C>T	ENSP00000330374:p.Gly170Asp	47	0	0		52	23	0.442308	NM_001244072	C9J7B6|D3DWZ4|Q5ZPR6|Q9H612	Missense_Mutation	SNP	ENST00000328902.5	37	CCDS34778.1	47	0.02152014652014652	44	0.08943089430894309	3	0.008287292817679558	0	0.0	0	0.0	C	10.17	1.277158	0.23307	0.108942	4.65E-4	ENSG00000133561	ENST00000328902;ENST00000392862	T	0.32272	1.46	4.29	-1.56	0.08532	AIG1 (1);	0.323921	0.26719	N	0.022855	T	0.00241	0.0007	N	0.16708	0.43	0.09310	N	1	B;B	0.18863	0.003;0.031	B;B	0.17433	0.018;0.011	T	0.20240	-1.0281	10	0.12766	T	0.61	.	3.9744	0.09468	0.0:0.2878:0.3552:0.357	rs11974345;rs52826484;rs60915768;rs11974345	170;90	Q6P9H5;Q6P9H5-2	GIMA6_HUMAN;.	D	170;231	ENSP00000330374:G170D	ENSP00000330374:G170D	G	-	2	0	GIMAP6	149956110	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.081000	0.03403	-0.159000	0.11021	-0.304000	0.09214	GGC	C|0.960;T|0.040	0.040	strong		0.612	GIMAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353457.1	NM_024711		T	150325177	C	T	150325177	3	4	22	1	0	0	0	0	1	0	0	0	6391	739	26	2	373	2	GIMAP6	7	150325177	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	201	150325177	8813486	1818	4719											
GIMAP2	26157	hgsc.bcm.edu	37	chr7	150390255	150390255	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctttgcatactgcacagcaTgtgcaatttgttttgttgct	7	17	9	8	0	0	0	0	0	0	0	0	0	0	0	0	0	6	8	0	0	2	6	rs115945256	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150390255T>C	ENST00000223293.5	+	3	975	c.881T>C	c.(880-882)aTg>aCg	p.M294T		NM_015660.2	NP_056475.1	Q9UG22	GIMA2_HUMAN	GTPase, IMAP family member 2	294						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)		CTGCACAGCATGTGCAATTTG	0.323													T|||	24	0.00479233	0.0098	0.0014	5008	,	,		22226	0.004		0.0	False		,,,				2504	0.0061				p.M294T		Atlas-SNP	.											.	GIMAP2	39	.	0			c.T881C						PASS	.	T	THR/MET	58,4348	57.4+/-93.9	1,56,2146	117	108	111		881	2.1	0	7	dbSNP_132	111	0,8600		0,0,4300	yes	missense	GIMAP2	NM_015660.2	81	1,56,6446	CC,CT,TT		0.0,1.3164,0.4459	possibly-damaging	294/338	150390255	58,12948	2203	4300	6503	SO:0001583	missense	26157	exon3			ACAGCATGTGCAA	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.881T>C	7.37:g.150390255T>C	ENSP00000223293:p.Met294Thr	119	0	0		126	55	0.436508	NM_015660	Q96L25	Missense_Mutation	SNP	ENST00000223293.5	37	CCDS5905.1	7	0.003205128205128205	4	0.008130081300813009	0	0.0	3	0.005244755244755245	0	0.0	T	3.694	-0.062952	0.07273	0.013164	0.0	ENSG00000106560	ENST00000223293	T	0.05382	3.45	3.32	2.14	0.27477	.	1.629670	0.03647	N	0.240382	T	0.03739	0.0106	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.37663	-0.9696	10	0.87932	D	0	.	5.2908	0.15725	0.0:0.1378:0.0:0.8622	.	294	Q9UG22	GIMA2_HUMAN	T	294	ENSP00000223293:M294T	ENSP00000223293:M294T	M	+	2	0	GIMAP2	150021188	0.004000	0.15560	0.005000	0.12908	0.008000	0.06430	0.560000	0.23500	0.491000	0.27793	0.533000	0.62120	ATG	T|0.995;C|0.005	0.005	strong		0.323	GIMAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348948.1	NM_015660		C	150390255	T	C	150390255	3	2	22	1	0	0	0	0	1	0	0	0	6388	1464	51	3	887	3	GIMAP2	7	150390255	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	65078	150390255	8748408	1819	4720											
GIMAP5	55340	hgsc.bcm.edu	37	chr7	150439554	150439554	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgctacctgctctctgccccGgggccccacgtcctgcttct	2	11	9	19	2	2	0	0	0	2	0	4	0	3	0	6	2	5	3	6	2	1	2	rs61751040	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150439554G>A	ENST00000358647.3	+	3	694	c.327G>A	c.(325-327)ccG>ccA	p.P109P	GIMAP5_ENST00000479556.1_3'UTR	NM_018384.4	NP_060854.2	Q96F15	GIMA5_HUMAN	GTPase, IMAP family member 5	109	AIG1-type G.				myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of T cell activation (GO:0050868)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0032831)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of membrane potential (GO:0045838)|positive regulation of natural killer cell cytokine production (GO:0002729)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|regulation of mitochondrial membrane permeability (GO:0046902)|T cell differentiation (GO:0030217)|T cell homeostasis (GO:0043029)|temperature homeostasis (GO:0001659)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|urinary_tract(2)	19			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TCTCTGCCCCGGGGCCCCACG	0.592													G|||	297	0.0593051	0.1785	0.0173	5008	,	,		18120	0.0159		0.0	False		,,,				2504	0.0337				p.P313P		Atlas-SNP	.											GIMAP5,NS,carcinoma,+1,1	.	.	1	0			c.G939A						scavenged	.	G	,	661,3745	280.5+/-275.4	42,577,1584	75	76	76		939,327	-8.3	0	7	dbSNP_129	76	12,8588	8.4+/-32.0	0,12,4288	no	coding-synonymous,coding-synonymous	GIMAP5,GIMAP1-GIMAP5	NM_001199577.1,NM_018384.4	,	42,589,5872	AA,AG,GG		0.1395,15.0023,5.1745	,	313/512,109/308	150439554	673,12333	2203	4300	6503	SO:0001819	synonymous_variant	0	exon6			TGCCCCGGGGCCC	AK002158	CCDS5907.1	7q36.1	2014-04-04	2004-10-29	2004-10-30	ENSG00000196329	ENSG00000196329		"GTPases, IMAP"	18005	protein-coding gene	gene with protein product	"immune-associated nucleotide-binding protein 5"	608086	"immune associated nucleotide 4 like 1 (mouse)"	IAN4L1			Standard	NM_018384		Approved	HIMAP3, IAN5		Q96F15	OTTHUMG00000157542	ENST00000358647.3:c.327G>A	7.37:g.150439554G>A		95	1	0.0105263		109	52	0.477064	NM_001199577	D3DWZ5|Q6IA75|Q96NE4|Q9NUK9	Silent	SNP	ENST00000358647.3	37	CCDS5907.1																																																																																			G|0.953;A|0.047	0.047	strong		0.592	GIMAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349108.2	NM_018384		A	150439554	G	A	150439554	2	1	22	1	0	0	0	0	0	0	0	1	6390	1103	39	1		1	GIMAP5	7	150439554	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	49299	150439554	8699109	1820	4721											
TMEM176A	55365	hgsc.bcm.edu	37	chr7	150498773	150498773	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gcgctgcggccccgggccacCcaggccaggggcagcagccg	5	1	17	18	4	0	0	0	0	0	0	0	0	0	0	6	5	3	3	6	5	0	0	rs10239586	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150498773C>T	ENST00000484928.1	+	2	716	c.135C>T	c.(133-135)acC>acT	p.T45T	TMEM176A_ENST00000461345.1_Intron|TMEM176B_ENST00000450753.2_5'Flank|TMEM176A_ENST00000004103.3_Silent_p.T45T|TMEM176B_ENST00000447204.2_5'Flank|TMEM176B_ENST00000492607.1_5'Flank|TMEM176B_ENST00000434545.1_5'Flank|TMEM176B_ENST00000326442.5_5'Flank			Q96HP8	T176A_HUMAN	transmembrane protein 176A	45					negative regulation of dendritic cell differentiation (GO:2001199)	integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|lung(7)|ovary(2)|stomach(1)	12			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCCGGGCCACCCAGGCCAGGG	0.711													C|||	33	0.00658946	0.025	0.0	5008	,	,		12886	0.0		0.0	False		,,,				2504	0.0				p.T45T		Atlas-SNP	.											.	TMEM176A	35	.	0			c.C135T						PASS	.	C		60,4254		0,60,2097	8	9	8		135	3	0	7	dbSNP_119	8	0,8462		0,0,4231	no	coding-synonymous	TMEM176A	NM_018487.2		0,60,6328	TT,TC,CC		0.0,1.3908,0.4696		45/236	150498773	60,12716	2157	4231	6388	SO:0001819	synonymous_variant	55365	exon2			GGCCACCCAGGCC	AF258340	CCDS5909.1	7q36.1	2006-09-04			ENSG00000002933	ENSG00000002933			24930	protein-coding gene	gene with protein product		610334				12097419, 8889548	Standard	NM_018487		Approved	HCA112	uc003whx.1	Q96HP8	OTTHUMG00000158114	ENST00000484928.1:c.135C>T	7.37:g.150498773C>T		28	0	0		30	17	0.566667	NM_018487	D3DX00|Q9NYC7	Silent	SNP	ENST00000484928.1	37	CCDS5909.1																																																																																			C|0.993;T|0.007	0.007	strong		0.711	TMEM176A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350222.1	NM_018487		T	150498773	C	T	150498773	2	4	22	1	0	0	0	0	0	0	0	1	16107	610	22	2		2	TMEM176A	7	150498773	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	59219	150498773	8639890	1821	4722											
TMEM176A	55365	hgsc.bcm.edu	37	chr7	150500832	150500832	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgcctgccgcatctccagctCgagtgactggaacactccag	8	8	10	15	2	1	1	0	1	1	0	4	3	2	2	4	1	4	2	4	1	1	0	rs76937000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150500832C>T	ENST00000484928.1	+	5	1048	c.467C>T	c.(466-468)tCg>tTg	p.S156L	TMEM176A_ENST00000461345.1_Missense_Mutation_p.S97L|TMEM176A_ENST00000004103.3_Missense_Mutation_p.S156L|TMEM176B_ENST00000447204.2_5'Flank			Q96HP8	T176A_HUMAN	transmembrane protein 176A	156					negative regulation of dendritic cell differentiation (GO:2001199)	integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|lung(7)|ovary(2)|stomach(1)	12			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ATCTCCAGCTCGAGTGACTGG	0.517													C|||	100	0.0199681	0.0741	0.0029	5008	,	,		18259	0.0		0.0	False		,,,				2504	0.0				p.S156L		Atlas-SNP	.											.	TMEM176A	35	.	0			c.C467T						PASS	.	C	LEU/SER	286,4120	159.6+/-192.1	11,264,1928	64	66	65		467	1.5	0	7	dbSNP_131	65	3,8597	2.2+/-6.3	0,3,4297	yes	missense	TMEM176A	NM_018487.2	145	11,267,6225	TT,TC,CC		0.0349,6.4911,2.2221	possibly-damaging	156/236	150500832	289,12717	2203	4300	6503	SO:0001583	missense	55365	exon5			CCAGCTCGAGTGA	AF258340	CCDS5909.1	7q36.1	2006-09-04			ENSG00000002933	ENSG00000002933			24930	protein-coding gene	gene with protein product		610334				12097419, 8889548	Standard	NM_018487		Approved	HCA112	uc003whx.1	Q96HP8	OTTHUMG00000158114	ENST00000484928.1:c.467C>T	7.37:g.150500832C>T	ENSP00000417626:p.Ser156Leu	50	0	0		75	38	0.506667	NM_018487	D3DX00|Q9NYC7	Missense_Mutation	SNP	ENST00000484928.1	37	CCDS5909.1	38	0.0173992673992674	36	0.07317073170731707	2	0.0055248618784530384	0	0.0	0	0.0	C	9.342	1.063261	0.20067	0.064911	3.49E-4	ENSG00000002933	ENST00000484928;ENST00000004103;ENST00000461345;ENST00000475536;ENST00000468689	T;T;T;T;T	0.12774	3.16;3.16;2.65;2.85;4.31	2.47	1.51	0.23008	.	5.604390	0.00166	N	0.000010	T	0.00936	0.0031	M	0.64997	1.995	0.09310	N	1	P	0.44627	0.839	B	0.29663	0.105	T	0.34403	-0.9830	10	0.62326	D	0.03	-1.4451	6.1594	0.20356	0.301:0.699:0.0:0.0	.	156	Q96HP8	T176A_HUMAN	L	156;156;97;108;97	ENSP00000417626:S156L;ENSP00000004103:S156L;ENSP00000420818:S97L;ENSP00000417834:S108L;ENSP00000420081:S97L	ENSP00000004103:S156L	S	+	2	0	TMEM176A	150131765	0.000000	0.05858	0.006000	0.13384	0.003000	0.03518	-0.768000	0.04715	0.569000	0.29329	0.555000	0.69702	TCG	C|0.977;T|0.023	0.023	strong		0.517	TMEM176A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350222.1	NM_018487		T	150500832	C	T	150500832	3	4	22	1	0	0	0	0	1	0	0	0	16107	893	31	1	481	1	TMEM176A	7	150500832	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2059	150500832	8637831	1822	4723											
NOS3	4846	hgsc.bcm.edu	37	chr7	150710392	150710392	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaccatctctaccgcgacgaGgtgcagaacgcccagcagcg	10	4	12	15	5	1	1	0	0	1	1	2	4	1	1	3	1	5	2	3	1	2	1	rs3730011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150710392G>A	ENST00000297494.3	+	25	3537	c.3180G>A	c.(3178-3180)gaG>gaA	p.E1060E	ATG9B_ENST00000377974.2_3'UTR|NOS3_ENST00000461406.1_Silent_p.E854E|NOS3_ENST00000477227.1_3'UTR|ATG9B_ENST00000444312.1_3'UTR|ATG9B_ENST00000494791.1_5'UTR|ATG9B_ENST00000605938.1_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)		ACCGCGACGAGGTGCAGAACG	0.642											OREG0018443	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	18	0.00359425	0.0136	0.0	5008	,	,		13957	0.0		0.0	False		,,,				2504	0.0				p.E1060E		Atlas-SNP	.											NOS3,NS,carcinoma,+2,1	NOS3	131	1	0			c.G3180A						PASS	.	G	,	49,4357	50.2+/-85.5	1,47,2155	77	72	74		3180,	4.2	1	7	dbSNP_107	74	0,8600		0,0,4300	no	coding-synonymous,utr-3	NOS3,ATG9B	NM_000603.4,NM_173681.5	,	1,47,6455	AA,AG,GG		0.0,1.1121,0.3767	,	1060/1204,	150710392	49,12957	2203	4300	6503	SO:0001819	synonymous_variant	4846	exon25			CGACGAGGTGCAG		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.3180G>A	7.37:g.150710392G>A		68	0	0	1734	75	41	0.546667	NM_000603	Q495E5	Silent	SNP	ENST00000297494.3	37	CCDS5912.1																																																																																			G|0.995;A|0.005	0.005	strong		0.642	NOS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350750.2	NM_000603		A	150710392	G	A	150710392	2	1	22	1	0	0	0	0	0	0	0	1	10553	991	35	2		2	NOS3	7	150710392	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	209560	150710392	8428271	1823	4724											
ABCB8	11194	hgsc.bcm.edu	37	chr7	150730712	150730712	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtactctgatggctaccgcaGctcctccctcctccgggccg	4	9	10	18	3	1	1	0	1	1	0	5	1	5	1	6	2	3	4	6	2	2	2	rs6975981	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150730712G>A	ENST00000297504.6	+	3	233	c.167G>A	c.(166-168)aGc>aAc	p.S56N	ABCB8_ENST00000477719.1_Missense_Mutation_p.S39N|ABCB8_ENST00000477092.1_Missense_Mutation_p.S39N|ABCB8_ENST00000356058.4_Missense_Mutation_p.S76N|ABCB8_ENST00000542328.1_Intron|ABCB8_ENST00000493338.1_3'UTR|ABCB8_ENST00000358849.4_Missense_Mutation_p.S39N|ABCB8_ENST00000498578.1_Missense_Mutation_p.S39N			Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 8	56					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)	GGCTACCGCAGCTCCTCCCTC	0.677													G|||	161	0.0321486	0.1157	0.0115	5008	,	,		16274	0.0		0.0	False		,,,				2504	0.0				p.S39N		Atlas-SNP	.											.	ABCB8	65	.	0			c.G116A						PASS	.	G	ASN/SER	340,4066	168.7+/-199.5	13,314,1876	41	45	44		116	2.2	0	7	dbSNP_116	44	10,8590	7.7+/-29.5	0,10,4290	yes	missense	ABCB8	NM_007188.3	46	13,324,6166	AA,AG,GG		0.1163,7.7167,2.6911	benign	39/719	150730712	350,12656	2203	4300	6503	SO:0001583	missense	11194	exon2			ACCGCAGCTCCTC	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.167G>A	7.37:g.150730712G>A	ENSP00000297504:p.Ser56Asn	118	0	0		107	49	0.457944	NM_007188	A5D8W3|B2RBL8|B3KND2|B4DG02|G3XAP3|O95787|Q53GM0	Missense_Mutation	SNP	ENST00000297504.6	37		65	0.02976190476190476	61	0.12398373983739837	4	0.011049723756906077	0	0.0	0	0.0	G	10.99	1.505996	0.26949	0.077167	0.001163	ENSG00000197150	ENST00000461373;ENST00000358849;ENST00000360651;ENST00000297504;ENST00000498578;ENST00000356058;ENST00000477719;ENST00000477092	D;D;D;D;D;D	0.91011	-2.65;-2.66;-2.77;-2.01;-2.07;-2.1	4.07	2.23	0.28157	.	0.502250	0.22050	N	0.065324	T	0.05410	0.0143	N	0.24115	0.695	0.09310	N	1	B;B;B;B;P	0.40000	0.079;0.361;0.277;0.361;0.698	B;B;B;B;B	0.38562	0.035;0.051;0.109;0.081;0.276	T	0.29212	-1.0019	10	0.38643	T	0.18	0.0796	5.7097	0.17929	0.1091:0.1985:0.6924:0.0	rs6975981;rs60484309	39;56;39;39;76	A5D8W3;Q9NUT2;Q9NUT2-2;C9JTY4;E7ENE8	.;ABCB8_HUMAN;.;.;.	N	76;39;39;56;39;76;39;39	ENSP00000351717:S39N;ENSP00000297504:S56N;ENSP00000418271:S39N;ENSP00000348353:S76N;ENSP00000419891:S39N;ENSP00000419558:S39N	ENSP00000297504:S56N	S	+	2	0	ABCB8	150361645	0.849000	0.29639	0.002000	0.10522	0.015000	0.08874	1.842000	0.39250	0.474000	0.27392	0.561000	0.74099	AGC	G|0.973;A|0.027	0.027	strong		0.677	ABCB8-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351733.2	NM_007188		A	150730712	G	A	150730712	3	1	22	1	0	0	0	0	1	0	0	0	47	971	34	2	122	2	ABCB8	7	150730712	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	20320	150730712	8407951	1824	4725											
SLC4A2	6522	hgsc.bcm.edu	37	chr7	150763616	150763621	+	In_Frame_Del	DEL	GGAGGC	GGAGGC	-																															ctgcctagaacccaggtggaGgaggcggaggcggaggcggt																								rs150330052|rs199537782|rs374531279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGAGGC	GGAGGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150763616_150763621delGGAGGC	ENST00000485713.1	+	6	1631_1636	c.591_596delGGAGGC	c.(589-597)gaggaggcg>gag	p.EA202del	SLC4A2_ENST00000413384.2_In_Frame_Del_p.EA202del|SLC4A2_ENST00000310317.5_In_Frame_Del_p.EA120del|SLC4A2_ENST00000461735.1_In_Frame_Del_p.EA188del|SLC4A2_ENST00000392826.2_In_Frame_Del_p.EA193del	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	202	Pro-rich.		E -> V (in dbSNP:rs2229551). {ECO:0000269|Ref.2}.		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)		CCCAGGTGGAGGAGGCGGAGGCGGAG	0.733														191	0.038139	0.1316	0.0173	5008	,	,		15101	0.001		0.003	False		,,,				2504	0.001				p.197_199del		Pindel,Atlas-Indel	.											.	SLC4A2	98	.	0			c.590_595del						PASS	.		,,,	390,3074		94,202,1436					,,,	4.7	1		dbSNP_130	8	34,6758		8,18,3370	no	coding,coding,coding,coding	SLC4A2	NM_003040.3,NM_001199694.1,NM_001199693.1,NM_001199692.1	,,,	102,220,4806	A1A1,A1R,RR		0.5006,11.2587,4.1342	,,,	,,,		424,9832				SO:0001651	inframe_deletion	6522	exon6			.		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.591_596delGGAGGC	7.37:g.150763622_150763627delGGAGGC	ENSP00000419412:p.Glu202_Ala203del	56	0	.		49	12	0.245	NM_001199692	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	In_Frame_Del	DEL	ENST00000485713.1	37	CCDS5917.1																																																																																			GGAGGC|0.962;-|0.038	0.038	strong		0.733	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040		-	150763621	GGAGGC	-	150763616	7	5	22	1	0	1	0	1	0	0	0	0	14669	991	35	0	609	0	SLC4A2	7	150763616	In_Frame_Del	DEL	GGAGGC	TCGA-G8-6324-01A-11D-2210-10	32904	150763616	8375047	1825	4726											
SLC4A2	6522	hgsc.bcm.edu	37	chr7	150768849	150768849	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctccagggcgtggtcttctgCctgctgggtgcccagcccct	2	10	13	16	1	2	0	0	0	2	0	3	0	3	0	5	3	4	1	5	3	0	1	rs11542749	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150768849C>T	ENST00000485713.1	+	15	3305	c.2265C>T	c.(2263-2265)tgC>tgT	p.C755C	SLC4A2_ENST00000413384.2_Silent_p.C755C|SLC4A2_ENST00000310317.5_Silent_p.C673C|SLC4A2_ENST00000461735.1_Silent_p.C741C|RP11-148K1.12_ENST00000485974.1_RNA|SLC4A2_ENST00000392826.2_Silent_p.C746C	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	755	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)		TGGTCTTCTGCCTGCTGGGTG	0.617													C|||	332	0.0662939	0.2027	0.036	5008	,	,		15252	0.0		0.0298	False		,,,				2504	0.0092				p.C755C		Atlas-SNP	.											.	SLC4A2	98	.	0			c.C2265T						PASS	.	C	,,,	593,3813	259.8+/-263.3	40,513,1650	83	90	88		2265,2238,2223,2265	1.9	1	7	dbSNP_120	88	256,8344	100.1+/-161.6	4,248,4048	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC4A2	NM_001199692.1,NM_001199693.1,NM_001199694.1,NM_003040.3	,,,	44,761,5698	TT,TC,CC		2.9767,13.4589,6.5278	,,,	755/1242,746/1233,741/1228,755/1242	150768849	849,12157	2203	4300	6503	SO:0001819	synonymous_variant	6522	exon15			CTTCTGCCTGCTG		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.2265C>T	7.37:g.150768849C>T		104	0	0		160	81	0.50625	NM_003040	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Silent	SNP	ENST00000485713.1	37	CCDS5917.1																																																																																			C|0.927;T|0.073	0.073	strong		0.617	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040		T	150768849	C	T	150768849	2	4	22	1	0	0	0	0	0	0	0	1	14669	747	26	2		2	SLC4A2	7	150768849	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	5233	150768849	8369814	1826	4727											
GBX1	2636	hgsc.bcm.edu	37	chr7	150846188	150846188	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgctgggtctcctgctgatgCctccagcttctcctcatctg	3	14	9	15	0	4	1	1	1	3	0	7	1	5	1	4	1	4	3	4	1	0	1	rs11975799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150846188C>T	ENST00000297537.4	-	2	579	c.580G>A	c.(580-582)Gca>Aca	p.A194T	GBX1_ENST00000475831.1_5'Flank	NM_001098834.1	NP_001092304.1	Q14549	GBX1_HUMAN	gastrulation brain homeobox 1	194			A -> T (in dbSNP:rs11975799).		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)		CCTGCTGATGCCTCCAGCTTC	0.582													C|||	117	0.0233626	0.0764	0.0072	5008	,	,		16501	0.006		0.0	False		,,,				2504	0.0051				p.A194T		Atlas-SNP	.											.	GBX1	21	.	0			c.G580A						PASS	.	C	THR/ALA	219,3991		9,201,1895	204	220	215		580	0.8	0.8	7	dbSNP_120	215	4,8462		0,4,4229	yes	missense	GBX1	NM_001098834.1	58	9,205,6124	TT,TC,CC		0.0472,5.2019,1.7592	benign	194/364	150846188	223,12453	2105	4233	6338	SO:0001583	missense	2636	exon2			CTGATGCCTCCAG	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.580G>A	7.37:g.150846188C>T	ENSP00000297537:p.Ala194Thr	21	0	0		24	15	0.625	NM_001098834		Missense_Mutation	SNP	ENST00000297537.4	37	CCDS43682.1	41	0.018772893772893772	33	0.06707317073170732	4	0.011049723756906077	4	0.006993006993006993	0	0.0	C	13.43	2.233908	0.39498	0.052019	4.72E-4	ENSG00000164900	ENST00000297537	D	0.91894	-2.93	4.95	0.769	0.18492	.	0.952841	0.08341	U	0.960876	T	0.27489	0.0675	N	0.08118	0	0.42774	D	0.993847	B	0.10296	0.003	B	0.06405	0.002	T	0.57165	-0.7858	10	0.19147	T	0.46	-4.7045	3.1719	0.06555	0.1248:0.4649:0.2571:0.1532	rs11975799;rs11975799	194	Q14549	GBX1_HUMAN	T	194	ENSP00000297537:A194T	ENSP00000297537:A194T	A	-	1	0	GBX1	150477121	0.997000	0.39634	0.847000	0.33407	0.987000	0.75469	1.560000	0.36331	0.141000	0.18875	-0.373000	0.07131	GCA	C|0.979;T|0.021	0.021	strong		0.582	GBX1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352029.1			T	150846188	C	T	150846188	3	4	22	1	0	0	0	0	1	0	0	0	6288	739	26	2	514	2	GBX1	7	150846188	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	77339	150846188	8292475	1827	4728											
CHPF2	54480	hgsc.bcm.edu	37	chr7	150935367	150935367	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagatcacccccagggccccCgggggctggccctgaccccc	5	3	13	20	1	1	2	1	1	0	1	1	3	1	2	7	4	0	1	7	4	0	0	rs76509585	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150935367C>T	ENST00000035307.2	+	4	3432	c.1919C>T	c.(1918-1920)cCg>cTg	p.P640L	CHPF2_ENST00000495645.1_Missense_Mutation_p.P632L|MIR671_ENST00000390183.1_RNA|RP4-548D19.3_ENST00000607902.1_RNA	NM_019015.1	NP_061888.1	Q9P2E5	CHPF2_HUMAN	chondroitin polymerizing factor 2	640	Gly/Pro-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)|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						CCAGGGCCCCCGGGGGCTGGC	0.657													C|||	77	0.0153754	0.0545	0.0072	5008	,	,		13615	0.0		0.0	False		,,,				2504	0.0				p.P640L		Atlas-SNP	.											.	CHPF2	52	.	0			c.C1919T						PASS	.	C	LEU/PRO	169,4233		1,167,2033	19	22	21		1919	2.9	0	7	dbSNP_131	21	1,8597		0,1,4298	yes	missense	CHPF2	NM_019015.1	98	1,168,6331	TT,TC,CC		0.0116,3.8392,1.3077	probably-damaging	640/773	150935367	170,12830	2201	4299	6500	SO:0001583	missense	54480	exon4			GGCCCCCGGGGGC	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.1919C>T	7.37:g.150935367C>T	ENSP00000035307:p.Pro640Leu	36	0	0		38	10	0.263158	NM_019015	B2DBD8|Q6P2I4|Q6UXD2	Missense_Mutation	SNP	ENST00000035307.2	37	CCDS34779.1	23	0.010531135531135532	21	0.042682926829268296	2	0.0055248618784530384	0	0.0	0	0.0	C	10.20	1.283741	0.23392	0.038392	1.16E-4	ENSG00000033100	ENST00000495645;ENST00000035307	T;T	0.15372	2.43;2.43	4.81	2.92	0.33932	.	0.129772	0.36002	N	0.002859	T	0.01627	0.0052	N	0.08118	0	0.21147	N	0.999775	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.32214	-0.9915	10	0.30078	T	0.28	-5.8196	9.1096	0.36718	0.0:0.8523:0.0:0.1477	.	640;632	Q9P2E5;G5E9W2	CHPF2_HUMAN;.	L	632;640	ENSP00000418914:P632L;ENSP00000035307:P640L	ENSP00000035307:P640L	P	+	2	0	CHPF2	150566300	0.009000	0.17119	0.015000	0.15790	0.410000	0.31052	0.945000	0.29056	0.573000	0.29400	0.655000	0.94253	CCG	C|0.988;T|0.012	0.012	strong		0.657	CHPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348648.2	NM_019015		T	150935367	C	T	150935367	3	4	22	1	0	0	0	0	1	0	0	0	3371	652	23	1	1933	1	CHPF2	7	150935367	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	89179	150935367	8203296	1828	4729											
PRKAG2	51422	hgsc.bcm.edu	37	chr7	151257665	151257665	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacagggaaataatacccacAatactatctgcttcatttac	15	11	5	10	0	2	0	1	0	1	0	2	2	2	1	1	1	4	1	1	1	7	7	rs28763998	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:151257665A>G	ENST00000287878.4	-	15	2127	c.1623T>C	c.(1621-1623)atT>atC	p.I541I	PRKAG2_ENST00000418337.2_Silent_p.I300I|PRKAG2_ENST00000392801.2_Silent_p.I497I|PRKAG2_ENST00000433631.2_Silent_p.I416I|PRKAG2_ENST00000492843.1_Silent_p.I417I	NM_016203.3	NP_057287.2	Q9UGJ0	AAKG2_HUMAN	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	541	CBS 4. {ECO:0000255|PROSITE- ProRule:PRU00703}.				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)	TAATACCCACAATACTATCTG	0.448													A|||	220	0.0439297	0.1596	0.013	5008	,	,		18994	0.0		0.0	False		,,,				2504	0.0				p.I541I		Atlas-SNP	.											.	PRKAG2	86	.	0			c.T1623C						PASS	.	A	,,	526,3880	242.1+/-252.3	28,470,1705	126	122	123		1491,1623,900	-5.7	0.2	7	dbSNP_125	123	2,8598	2.2+/-6.3	0,2,4298	yes	coding-synonymous,coding-synonymous,coding-synonymous	PRKAG2	NM_001040633.1,NM_016203.3,NM_024429.1	,,	28,472,6003	GG,GA,AA		0.0233,11.9383,4.0597	,,	497/526,541/570,300/329	151257665	528,12478	2203	4300	6503	SO:0001819	synonymous_variant	51422	exon15			ACCCACAATACTA	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.1623T>C	7.37:g.151257665A>G		119	0	0		100	45	0.45	NM_016203	Q53Y07|Q6NUI0|Q75MP4|Q9NUZ9|Q9UDN8|Q9ULX8	Silent	SNP	ENST00000287878.4	37	CCDS5928.1																																																																																			A|0.955;G|0.045	0.045	strong		0.448	PRKAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348440.2	NM_016203		G	151257665	A	G	151257665	2	3	22	1	0	0	0	0	0	0	0	1	12513	126	5	3		3	PRKAG2	7	151257665	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	322298	151257665	7880998	1829	4730											
MLL3	58508	hgsc.bcm.edu	37	chr7	151859495	151859495	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgggcaggactctgtctcagCcttttccagttttatctctt	5	17	8	11	0	3	0	1	0	3	0	6	1	4	1	2	2	1	2	2	2	1	5	rs115580901	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:151859495C>G	ENST00000262189.6	-	43	11385	c.11167G>C	c.(11167-11169)Gct>Cct	p.A3723P	KMT2C_ENST00000355193.2_Missense_Mutation_p.A3723P	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	3723					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)										TCTGTCTCAGCCTTTTCCAGT	0.478													C|||	9	0.00179712	0.0061	0.0014	5008	,	,		19613	0.0		0.0	False		,,,				2504	0.0				p.A3723P		Atlas-SNP	.											.	MLL3	1564	.	0			c.G11167C						PASS	.	C	PRO/ALA	19,4387	26.2+/-53.5	0,19,2184	177	181	180		11167	-2	0	7	dbSNP_133	180	0,8600		0,0,4300	yes	missense	MLL3	NM_170606.2	27	0,19,6484	GG,GC,CC		0.0,0.4312,0.1461	benign	3723/4912	151859495	19,12987	2203	4300	6503	SO:0001583	missense	58508	exon43			TCTCAGCCTTTTC	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.11167G>C	7.37:g.151859495C>G	ENSP00000262189:p.Ala3723Pro	158	0	0		176	93	0.528409	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	3|3	0.0013736263736263737|0.0013736263736263737	3|3	0.006097560975609756|0.006097560975609756	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	5.391|5.391	0.257270|0.257270	0.10239|0.10239	0.004312|0.004312	0.0|0.0	ENSG00000055609|ENSG00000055609	ENST00000262189;ENST00000355193;ENST00000424877|ENST00000360104	D;D;D|.	0.89415|.	-1.83;-1.81;-2.51|.	5.51|5.51	-2.01|-2.01	0.07410|0.07410	.|.	0.151901|.	0.29660|.	U|.	0.011527|.	T|T	0.18341|0.18341	0.0440|0.0440	L|L	0.29908|0.29908	0.895|0.895	0.29679|0.29679	N|N	0.841841|0.841841	B;B;B|.	0.10296|.	0.002;0.001;0.003|.	B;B;B|.	0.09377|.	0.003;0.003;0.004|.	T|T	0.24440|0.24440	-1.0160|-1.0160	10|5	0.37606|.	T|.	0.19|.	.|.	2.0729|2.0729	0.03618|0.03618	0.1792:0.4224:0.1773:0.2212|0.1792:0.4224:0.1773:0.2212	.|.	3723;2784;3723|.	Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3|.	MLL3_HUMAN;.;.|.	P|A	3723;3723;309|1228	ENSP00000262189:A3723P;ENSP00000347325:A3723P;ENSP00000410411:A309P|.	ENSP00000262189:A3723P|.	A|G	-|-	1|2	0|0	MLL3|MLL3	151490428|151490428	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.471000|0.471000	0.32888|0.32888	-0.542000|-0.542000	0.06091|0.06091	-1.225000|-1.225000	0.02578|0.02578	-1.938000|-1.938000	0.00498|0.00498	GCT|GGC	C|0.998;G|0.002	0.002	strong		0.478	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			G	151859495	C	G	151859495	3	3	22	1	0	0	0	0	1	0	0	0	9631	739	26	4	3636	4	MLL3	7	151859495	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	601830	151859495	7279168	1830	4731											
MLL3	58508	hgsc.bcm.edu	37	chr7	151970811	151970811	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctttcaggagcttggtcaaTgtgttctggacaaagcagga	10	12	12	7	0	4	0	2	0	2	0	4	3	4	3	0	4	2	3	0	4	2	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:151970811T>C	ENST00000262189.6	-	7	1209	c.991A>G	c.(991-993)Att>Gtt	p.I331V	KMT2C_ENST00000355193.2_Missense_Mutation_p.I331V	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	331					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)										GCTTGGTCAATGTGTTCTGGA	0.393																																					p.I331V		Atlas-SNP	.											.	MLL3	1564	.	0			c.A991G						PASS	.																																			SO:0001583	missense	58508	exon7			GGTCAATGTGTTC	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.991A>G	7.37:g.151970811T>C	ENSP00000262189:p.Ile331Val	725	0	0		801	39	0.0486891	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	T	14.18	2.458970	0.43634	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.83992	-1.79;-1.79	4.78	4.78	0.61160	Zinc finger, PHD-type (1);Protein kinase C-like, phorbol ester/diacylglycerol binding (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.44097	U	0.000493	T	0.72993	0.3530	L	0.34521	1.04	0.80722	D	1	P	0.39094	0.659	B	0.34873	0.191	T	0.71537	-0.4563	10	0.21014	T	0.42	.	14.599	0.68427	0.0:0.0:0.0:1.0	.	331	Q8NEZ4	MLL3_HUMAN	V	331	ENSP00000262189:I331V;ENSP00000347325:I331V	ENSP00000262189:I331V	I	-	1	0	MLL3	151601744	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.185000	0.58330	1.924000	0.55735	0.477000	0.44152	ATT	.	.	none		0.393	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			C	151970811	T	C	151970811	3	2	22	1	0	0	0	0	1	0	0	0	9631	1464	51	3	13956	3	MLL3	7	151970811	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	111316	151970811	7167852	1831	4732											
NOM1	64434	hgsc.bcm.edu	37	chr7	156745224	156745224	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	catgtgaggcaagctgaggaGacagtggacttcaagaaaaa	16	6	13	6	0	1	4	1	2	0	2	1	6	1	5	0	3	1	2	0	3	4	1	rs59371845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:156745224G>A	ENST00000275820.3	+	2	1059	c.1044G>A	c.(1042-1044)gaG>gaA	p.E348E		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	348						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)		AAGCTGAGGAGACAGTGGACT	0.393													G|||	267	0.0533147	0.1906	0.0202	5008	,	,		21925	0.0		0.001	False		,,,				2504	0.0				p.E348E		Atlas-SNP	.											.	NOM1	73	.	0			c.G1044A						PASS	.	G		715,3691	298.1+/-285.1	53,609,1541	104	94	98		1044	1	0	7	dbSNP_129	98	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	NOM1	NM_138400.1		53,613,5837	AA,AG,GG		0.0465,16.2279,5.5282		348/861	156745224	719,12287	2203	4300	6503	SO:0001819	synonymous_variant	64434	exon2			TGAGGAGACAGTG	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.1044G>A	7.37:g.156745224G>A		170	0	0		166	81	0.487952	NM_138400	Q96I08	Silent	SNP	ENST00000275820.3	37	CCDS34787.1																																																																																			G|0.950;A|0.050	0.050	strong		0.393	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400		A	156745224	G	A	156745224	2	1	22	1	0	0	0	0	0	0	0	1	10539	933	33	2		2	NOM1	7	156745224	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4774413	156745224	2393439	1832	4733											
PTPRN2	5799	hgsc.bcm.edu	37	chr7	157931151	157931151	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cagctccaggccactcaggcCcctcacctcagccggctgcc	6	5	9	21	1	3	0	3	0	0	0	4	0	4	0	7	3	3	2	7	3	0	0	rs150508509	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:157931151C>G	ENST00000389418.4	-	7	976	c.967G>C	c.(967-969)Ggc>Cgc	p.G323R	PTPRN2_ENST00000409483.1_Missense_Mutation_p.G285R|PTPRN2_ENST00000389416.4_Missense_Mutation_p.G306R|PTPRN2_ENST00000404321.2_Missense_Mutation_p.G346R|PTPRN2_ENST00000389413.3_Missense_Mutation_p.G323R	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	323				G -> R (in Ref. 2; CAA69880). {ECO:0000305}.	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)		CCACTCAGGCCCCTCACCTCA	0.632													C|||	93	0.0185703	0.053	0.0058	5008	,	,		19317	0.0		0.0	False		,,,				2504	0.0194				p.G323R		Atlas-SNP	.											.	PTPRN2	243	.	0			c.G967C						PASS	.		ARG/GLY,ARG/GLY,ARG/GLY	217,4189	127.0+/-164.0	3,211,1989	62	64	64		967,916,967	-4.9	0	7	dbSNP_134	64	1,8599		0,1,4299	yes	missense,missense,missense	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	125,125,125	3,212,6288	GG,GC,CC		0.0116,4.9251,1.6761	benign,benign,benign	323/1016,306/999,323/987	157931151	218,12788	2203	4300	6503	SO:0001583	missense	5799	exon7			TCAGGCCCCTCAC	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.967G>C	7.37:g.157931151C>G	ENSP00000374069:p.Gly323Arg	93	0	0		101	35	0.346535	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	29	0.013278388278388278	26	0.052845528455284556	3	0.008287292817679558	0	0.0	0	0.0	C	3.517	-0.098660	0.07010	0.049251	1.16E-4	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.02552	4.25;4.27;4.26;4.26;4.25	4.11	-4.94	0.03057	.	.	.	.	.	T	0.00271	0.0008	N	0.12746	0.255	0.09310	N	1	B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.0;0.001;0.0;0.0	T	0.48269	-0.9050	9	0.15499	T	0.54	.	5.6925	0.17837	0.0:0.3821:0.1927:0.4252	.	346;285;323;306;323	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	R	285;323;306;323;346	ENSP00000387114:G285R;ENSP00000374064:G323R;ENSP00000374067:G306R;ENSP00000374069:G323R;ENSP00000385464:G346R	ENSP00000374064:G323R	G	-	1	0	PTPRN2	157623912	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.128000	0.15810	-1.148000	0.02847	-0.312000	0.09012	GGC	C|0.981;G|0.019	0.019	strong		0.632	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1			G	157931151	C	G	157931151	3	3	22	1	0	0	0	0	1	0	0	0	12823	623	22	4	2148	4	PTPRN2	7	157931151	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1185927	157931151	1207512	1833	4734											
PTPRN2	5799	hgsc.bcm.edu	37	chr7	157959794	157959794	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctctgggcagcataggcacTgagggccgccatcagatggt	8	7	14	12	1	2	2	1	1	1	1	2	2	2	2	3	4	1	3	3	4	1	1	rs73745196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:157959794T>C	ENST00000389418.4	-	6	748	c.739A>G	c.(739-741)Agt>Ggt	p.S247G	PTPRN2_ENST00000409483.1_Missense_Mutation_p.S209G|PTPRN2_ENST00000389416.4_Missense_Mutation_p.S230G|PTPRN2_ENST00000404321.2_Missense_Mutation_p.S270G|PTPRN2_ENST00000389413.3_Missense_Mutation_p.S247G	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	247				S -> G (in Ref. 2; CAA69880). {ECO:0000305}.	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)		GCATAGGCACTGAGGGCCGCC	0.662													C|||	100	0.0199681	0.0688	0.0086	5008	,	,		16162	0.0		0.003	False		,,,				2504	0.0				p.S247G		Atlas-SNP	.											.	PTPRN2	243	.	0			c.A739G						PASS	.		GLY/SER,GLY/SER,GLY/SER	297,4109	770.2+/-413.7	12,273,1918	27	23	25		739,688,739	-0.8	0	7	dbSNP_130	25	0,8600		0,0,4300	yes	missense,missense,missense	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	56,56,56	12,273,6218	CC,CT,TT		0.0,6.7408,2.2836	benign,benign,benign	247/1016,230/999,247/987	157959794	297,12709	2203	4300	6503	SO:0001583	missense	5799	exon6			AGGCACTGAGGGC	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.739A>G	7.37:g.157959794T>C	ENSP00000374069:p.Ser247Gly	87	0	0		64	35	0.546875	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	49	0.022435897435897436	42	0.08536585365853659	4	0.011049723756906077	0	0.0	3	0.00395778364116095	C	0.036	-1.306812	0.01353	0.067408	0.0	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.02916	4.12;4.13;4.12;4.12;4.11	4.59	-0.828	0.10799	.	0.484707	0.13807	N	0.361341	T	0.00073	0.0002	N	0.04203	-0.255	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	0.48080	-0.9066	10	0.19147	T	0.46	.	10.525	0.44943	0.0:0.1914:0.0:0.8086	.	270;209;247;230;247	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	G	209;247;230;247;270	ENSP00000387114:S209G;ENSP00000374064:S247G;ENSP00000374067:S230G;ENSP00000374069:S247G;ENSP00000385464:S270G	ENSP00000374064:S247G	S	-	1	0	PTPRN2	157652555	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.189000	0.09629	-0.624000	0.05611	-1.071000	0.02255	AGT	T|0.974;C|0.026	0.026	strong		0.662	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1			C	157959794	T	C	157959794	3	2	22	1	0	0	0	0	1	0	0	0	12823	1580	55	3	2380	3	PTPRN2	7	157959794	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	28643	157959794	1178869	1834	4735			5	28	8433723	3	3	95	N	T_G	9.093627e-05
PTPRN2	5799	hgsc.bcm.edu	37	chr7	157959870	157959870	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatctggctggagctggccGagggtccgcggcaggaggtc	5	7	18	11	3	2	0	1	0	1	0	4	3	3	2	2	7	1	3	2	7	0	0	rs112343839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:157959870G>T	ENST00000389418.4	-	6	672	c.663C>A	c.(661-663)ctC>ctA	p.L221L	PTPRN2_ENST00000409483.1_Silent_p.L183L|PTPRN2_ENST00000389416.4_Silent_p.L204L|PTPRN2_ENST00000404321.2_Silent_p.L244L|PTPRN2_ENST00000389413.3_Silent_p.L221L	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	221					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)		GGAGCTGGCCGAGGGTCCGCG	0.667													G|||	49	0.00978435	0.034	0.0043	5008	,	,		16342	0.0		0.001	False		,,,				2504	0.0				p.L221L		Atlas-SNP	.											.	PTPRN2	243	.	0			c.C663A						PASS	.		,,	161,4245	105.6+/-144.1	5,151,2047	40	39	39		663,612,663	-1.8	0	7	dbSNP_132	39	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	,,	5,151,6347	TT,TG,GG		0.0,3.6541,1.2379	,,	221/1016,204/999,221/987	157959870	161,12845	2203	4300	6503	SO:0001819	synonymous_variant	5799	exon6			CTGGCCGAGGGTC	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.663C>A	7.37:g.157959870G>T		76	0	0		63	33	0.52381	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Silent	SNP	ENST00000389418.4	37	CCDS5947.1																																																																																			G|0.985;T|0.015	0.015	strong		0.667	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1			T	157959870	G	T	157959870	2	4	22	1	0	0	0	0	0	0	0	1	12823	1045	37	4		4	PTPRN2	7	157959870	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	76	157959870	1178793	1835	4736			5	28	8433723	3	3	95	N	T_G	9.093627e-05
PTPRN2	5799	hgsc.bcm.edu	37	chr7	157959888	157959888	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccgagggtccgcggcaggagGtcctcgcggagctgggtccg	4	5	19	13	6	0	0	0	0	0	0	4	3	3	2	4	6	1	2	4	6	0	0	rs73745197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:157959888G>A	ENST00000389418.4	-	6	654	c.645C>T	c.(643-645)gaC>gaT	p.D215D	PTPRN2_ENST00000409483.1_Silent_p.D177D|PTPRN2_ENST00000389416.4_Silent_p.D198D|PTPRN2_ENST00000404321.2_Silent_p.D238D|PTPRN2_ENST00000389413.3_Silent_p.D215D	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	215					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)		GCGGCAGGAGGTCCTCGCGGA	0.652													G|||	100	0.0199681	0.0688	0.0086	5008	,	,		15889	0.0		0.003	False		,,,				2504	0.0				p.D215D		Atlas-SNP	.											.	PTPRN2	243	.	0			c.C645T						PASS	.		,,	303,4101	159.2+/-191.8	12,279,1911	42	42	42		645,594,645	2.3	0	7	dbSNP_130	42	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	,,	12,279,6211	AA,AG,GG		0.0,6.8801,2.3301	,,	215/1016,198/999,215/987	157959888	303,12701	2202	4300	6502	SO:0001819	synonymous_variant	5799	exon6			CAGGAGGTCCTCG	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.645C>T	7.37:g.157959888G>A		80	0	0		70	40	0.571429	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Silent	SNP	ENST00000389418.4	37	CCDS5947.1																																																																																			G|0.973;A|0.027	0.027	strong		0.652	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1			A	157959888	G	A	157959888	2	1	22	1	0	0	0	0	0	0	0	1	12823	1252	44	2		2	PTPRN2	7	157959888	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	18	157959888	1178775	1836	4737			5	28	8433723	3	3	95	N	T_G	9.093627e-05
ARHGEF10	9639	hgsc.bcm.edu	37	chr8	1808343	1808343	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctgcgccacgtccctggaCgaagaaggtactgctaccct	9	8	10	14	3	1	1	0	0	1	1	2	3	2	2	3	2	4	2	3	2	4	2	rs147914724	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:1808343C>T	ENST00000398564.1	+	4	546	c.546C>T	c.(544-546)gaC>gaT	p.D182D	ARHGEF10_ENST00000518288.1_Silent_p.D182D|ARHGEF10_ENST00000398560.1_Silent_p.D182D|ARHGEF10_ENST00000262112.6_Silent_p.D182D|ARHGEF10_ENST00000520359.1_Silent_p.D158D|ARHGEF10_ENST00000349830.3_Silent_p.D158D			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	182					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)	p.D182D(1)		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)		CGTCCCTGGACGAAGAAGGTA	0.657													C|||	2	0.000399361	0.0008	0.0	5008	,	,		17485	0.0		0.0	False		,,,				2504	0.001				p.D158D		Atlas-SNP	.											ARHGEF10_ENST00000398564,colon,carcinoma,0,1	ARHGEF10	255	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C474T						PASS	.	C		14,4392	21.2+/-45.6	0,14,2189	80	72	74		474	-10.6	0	8	dbSNP_134	74	0,8600		0,0,4300	no	coding-synonymous	ARHGEF10	NM_014629.2		0,14,6489	TT,TC,CC		0.0,0.3177,0.1076		158/1345	1808343	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	9639	exon4			CCTGGACGAAGAA	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.546C>T	8.37:g.1808343C>T		67	0	0		95	41	0.431579	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Silent	SNP	ENST00000398564.1	37																																																																																				C|0.999;T|0.001	0.001	strong		0.657	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding				T	1808343	C	T	1808343	2	4	22	1	0	0	0	0	0	0	0	1	894	535	19	1		1	ARHGEF10	8	1808343	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10		1808343	144555679	1837	4738											
ARHGEF10	9639	hgsc.bcm.edu	37	chr8	1905222	1905222	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctctctagagcacagatcAgaggacagcaccatctatga	14	7	9	11	0	3	4	1	1	2	3	4	5	3	5	1	1	3	3	1	1	2	2	rs146227529	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:1905222A>G	ENST00000398564.1	+	29	3903	c.3903A>G	c.(3901-3903)tcA>tcG	p.S1301S	ARHGEF10_ENST00000518288.1_Silent_p.S1300S|ARHGEF10_ENST00000521927.1_3'UTR|ARHGEF10_ENST00000262112.6_Silent_p.S1272S|ARHGEF10_ENST00000520359.1_Silent_p.S1238S|ARHGEF10_ENST00000349830.3_Silent_p.S1276S			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	1301	Ser-rich.				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)		AGCACAGATCAGAGGACAGCA	0.572													A|||	16	0.00319489	0.0106	0.0029	5008	,	,		17994	0.0		0.0	False		,,,				2504	0.0				p.S1276S		Atlas-SNP	.											.	ARHGEF10	255	.	0			c.A3828G						PASS	.	A		40,4366	44.6+/-78.6	1,38,2164	71	67	68		3828	-11.4	0	8	dbSNP_134	68	0,8600		0,0,4300	no	coding-synonymous	ARHGEF10	NM_014629.2		1,38,6464	GG,GA,AA		0.0,0.9079,0.3076		1276/1345	1905222	40,12966	2203	4300	6503	SO:0001819	synonymous_variant	9639	exon29			CAGATCAGAGGAC	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.3903A>G	8.37:g.1905222A>G		67	0	0		72	38	0.527778	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Silent	SNP	ENST00000398564.1	37																																																																																				A|0.996;G|0.004	0.004	strong		0.572	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding				G	1905222	A	G	1905222	2	3	22	1	0	0	0	0	0	0	0	1	894	175	7	3		3	ARHGEF10	8	1905222	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	96879	1905222	144458800	1838	4739											
MYOM2	9172	hgsc.bcm.edu	37	chr8	2050564	2050564	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gagcctgtgctggtagaggcGagaccaggtaaggcttacaa	11	7	15	8	1	0	2	0	0	0	2	0	4	0	2	2	4	3	4	2	4	4	3	rs34460811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:2050564G>A	ENST00000262113.4	+	21	2868	c.2727G>A	c.(2725-2727)gcG>gcA	p.A909A	MYOM2_ENST00000523438.1_Silent_p.A334A	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	909	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.|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)		TGGTAGAGGCGAGACCAGGTA	0.498													G|||	45	0.00898562	0.0333	0.0014	5008	,	,		21003	0.0		0.0	False		,,,				2504	0.0				p.A909A		Atlas-SNP	.											.	MYOM2	251	.	0			c.G2727A						PASS	.	G		115,4291	86.8+/-125.4	2,111,2090	61	53	55		2727	-7.8	0.2	8	dbSNP_126	55	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MYOM2	NM_003970.2		2,112,6389	AA,AG,GG		0.0116,2.6101,0.8919		909/1466	2050564	116,12890	2203	4300	6503	SO:0001819	synonymous_variant	9172	exon21			AGAGGCGAGACCA		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.2727G>A	8.37:g.2050564G>A		53	0	0		53	21	0.396226	NM_003970	Q7Z3Y2	Silent	SNP	ENST00000262113.4	37	CCDS5957.1																																																																																			G|0.991;A|0.009	0.009	strong		0.498	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970		A	2050564	G	A	2050564	2	1	22	1	0	0	0	0	0	0	0	1	10101	1045	37	1		1	MYOM2	8	2050564	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	145342	2050564	144313458	1839	4740											
MYOM2	9172	hgsc.bcm.edu	37	chr8	2088697	2088697	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agaatcggggggagtgaagaGatggcttggctgcagatatg	11	8	18	4	1	0	4	0	1	0	3	1	6	0	5	0	5	1	3	0	5	3	2	rs34735757	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:2088697G>C	ENST00000262113.4	+	33	3993	c.3852G>C	c.(3850-3852)gaG>gaC	p.E1284D	MYOM2_ENST00000523438.1_Missense_Mutation_p.E709D|MYOM2_ENST00000520298.1_3'UTR	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	1284			E -> D (in dbSNP:rs34735757).		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)		GGAGTGAAGAGATGGCTTGGC	0.458													G|||	55	0.0109824	0.0386	0.0043	5008	,	,		15452	0.001		0.0	False		,,,				2504	0.0				p.E1284D		Atlas-SNP	.											.	MYOM2	251	.	0			c.G3852C						PASS	.	G	ASP/GLU	155,4251	106.9+/-145.3	1,153,2049	121	116	118		3852	-1.4	0.7	8	dbSNP_126	118	1,8599		0,1,4299	yes	missense	MYOM2	NM_003970.2	45	1,154,6348	CC,CG,GG		0.0116,3.5179,1.1994	benign	1284/1466	2088697	156,12850	2203	4300	6503	SO:0001583	missense	9172	exon33			TGAAGAGATGGCT		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.3852G>C	8.37:g.2088697G>C	ENSP00000262113:p.Glu1284Asp	68	0	0		76	35	0.460526	NM_003970	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	37	CCDS5957.1	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	G	11.14	1.551354	0.27739	0.035179	1.16E-4	ENSG00000036448	ENST00000262113;ENST00000523438	T;T	0.34667	1.35;1.35	5.02	-1.4	0.08968	Immunoglobulin-like fold (1);	0.345909	0.29473	N	0.012055	T	0.03739	0.0106	L	0.28556	0.865	0.29986	N	0.817304	B	0.06786	0.001	B	0.06405	0.002	T	0.06285	-1.0835	10	0.24483	T	0.36	.	0.3472	0.00343	0.231:0.2232:0.1729:0.373	rs34735757	1284	P54296	MYOM2_HUMAN	D	1284;709	ENSP00000262113:E1284D;ENSP00000428396:E709D	ENSP00000262113:E1284D	E	+	3	2	MYOM2	2076104	0.995000	0.38212	0.652000	0.29579	0.922000	0.55478	0.369000	0.20416	-0.371000	0.08004	0.655000	0.94253	GAG	G|0.986;C|0.014	0.014	strong		0.458	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970		C	2088697	G	C	2088697	3	2	22	1	0	0	0	0	1	0	0	0	10101	933	33	4	3978	4	MYOM2	8	2088697	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	38133	2088697	144275325	1840	4741											
CSMD1	64478	hgsc.bcm.edu	37	chr8	3245054	3245054	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtggttccactggtggttcCtctcacagacgaggggctcg	5	10	14	12	3	1	1	1	0	1	1	5	2	3	1	2	5	0	3	2	5	0	2	rs73657835	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:3245054C>T	ENST00000520002.1	-	19	3302	c.2747G>A	c.(2746-2748)aGg>aAg	p.R916K	CSMD1_ENST00000537824.1_Missense_Mutation_p.R915K|CSMD1_ENST00000539096.1_Missense_Mutation_p.R915K|CSMD1_ENST00000400186.3_Missense_Mutation_p.R916K|CSMD1_ENST00000602557.1_Missense_Mutation_p.R916K|CSMD1_ENST00000602723.1_Missense_Mutation_p.R916K|CSMD1_ENST00000542608.1_Missense_Mutation_p.R915K			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	916	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)		CTGGTGGTTCCTCTCACAGAC	0.597													C|||	175	0.0349441	0.1225	0.0173	5008	,	,		18677	0.0		0.001	False		,,,				2504	0.0				p.R915K		Atlas-SNP	.											CSMD1_ENST00000537824,NS,carcinoma,+1,2	CSMD1	1469	2	0			c.G2744A						PASS	.	C	LYS/ARG	365,3837		16,333,1752	43	49	47		2744	1.2	0.1	8	dbSNP_130	47	0,8430		0,0,4215	yes	missense	CSMD1	NM_033225.5	26	16,333,5967	TT,TC,CC		0.0,8.6863,2.8895	benign	915/3565	3245054	365,12267	2101	4215	6316	SO:0001583	missense	64478	exon18			TGGTTCCTCTCAC			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.2747G>A	8.37:g.3245054C>T	ENSP00000430733:p.Arg916Lys	86	0	0		84	42	0.5	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		73	0.033424908424908424	67	0.13617886178861788	6	0.016574585635359115	0	0.0	0	0.0	C	0.079	-1.186530	0.01620	0.086863	0.0	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.62788	-0.0;-0.0;-0.0;-0.0;-0.0	5.11	1.25	0.21368	Complement control module (2);Sushi/SCR/CCP (3);	0.221554	0.38959	N	0.001512	T	0.00178	0.0005	N	0.01277	-0.915	0.09310	N	0.999999	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.003	T	0.08659	-1.0711	10	0.02654	T	1	.	8.3499	0.32297	0.0:0.6186:0.0:0.3814	.	916;916;916	E5RIG2;Q96PZ7;Q96PZ7-4	.;CSMD1_HUMAN;.	K	916;916;778;915;915;915	ENSP00000383047:R916K;ENSP00000430733:R916K;ENSP00000441462:R915K;ENSP00000446243:R915K;ENSP00000441675:R915K	ENSP00000320445:R778K	R	-	2	0	CSMD1	3232461	0.012000	0.17670	0.095000	0.20976	0.375000	0.29983	0.150000	0.16263	-0.053000	0.13289	-0.157000	0.13467	AGG	C|0.966;T|0.034	0.034	strong		0.597	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		T	3245054	C	T	3245054	3	4	22	1	0	0	0	0	1	0	0	0	3946	681	24	2	8162	2	CSMD1	8	3245054	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1156357	3245054	143118968	1841	4742											
CSMD1	64478	hgsc.bcm.edu	37	chr8	3432586	3432586	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagattggatccacatgttcTcgctggaaacacatagaaac	14	9	8	10	1	1	2	0	0	1	2	3	4	2	4	1	2	2	2	1	2	3	3	rs146006696	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:3432586T>G	ENST00000520002.1	-	11	1783	c.1228A>C	c.(1228-1230)Aga>Cga	p.R410R	CSMD1_ENST00000537824.1_Silent_p.R409R|CSMD1_ENST00000539096.1_Silent_p.R409R|CSMD1_ENST00000400186.3_Silent_p.R410R|CSMD1_ENST00000602557.1_Silent_p.R410R|CSMD1_ENST00000602723.1_Silent_p.R410R|CSMD1_ENST00000542608.1_Silent_p.R409R			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	410						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)		CCACATGTTCTCGCTGGAAAC	0.413													T|||	54	0.0107827	0.0393	0.0029	5008	,	,		20627	0.0		0.0	False		,,,				2504	0.0				p.R409R		Atlas-SNP	.											.	CSMD1	1469	.	0			c.A1225C						PASS	.	T		97,3963		2,93,1935	60	68	65		1225	2.6	0.8	8	dbSNP_134	65	0,8358		0,0,4179	no	coding-synonymous	CSMD1	NM_033225.5		2,93,6114	GG,GT,TT		0.0,2.3892,0.7811		409/3565	3432586	97,12321	2030	4179	6209	SO:0001819	synonymous_variant	64478	exon10			ATGTTCTCGCTGG			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.1228A>C	8.37:g.3432586T>G		60	0	0		75	31	0.413333	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37																																																																																				T|0.988;G|0.012	0.012	strong		0.413	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		G	3432586	T	G	3432586	2	3	22	1	0	0	0	0	0	0	0	1	3946	1559	54	5		5	CSMD1	8	3432586	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	187532	3432586	142931436	1842	4743											
DEFB1	1672	hgsc.bcm.edu	37	chr8	6728298	6728298	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acattgccctccactgctgaCgcaattgtaatgatcagatc	11	11	7	12	1	1	3	1	2	0	1	3	3	2	3	2	0	2	3	2	0	2	3	rs2738047|rs397732952	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:6728298C>T	ENST00000297439.3	-	2	276	c.112G>A	c.(112-114)Gtc>Atc	p.V38I		NM_005218.3	NP_005209.1	P60022	DEFB1_HUMAN	defensin, beta 1	38			V -> I (in dbSNP:rs2738047).		acute inflammatory response (GO:0002526)|antibacterial humoral response (GO:0019731)|chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|response to bacterium (GO:0009617)|response to testosterone (GO:0033574)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				lung(1)	1			STAD - Stomach adenocarcinoma(24;0.0984)	COAD - Colon adenocarcinoma(149;0.0162)|READ - Rectum adenocarcinoma(644;0.128)		CCACTGCTGACGCAATTGTAA	0.498													C|||	199	0.0397364	0.1384	0.0043	5008	,	,		18887	0.0069		0.002	False		,,,				2504	0.0041				p.V38I	Pancreas(35;916 948 9612 33610 36642)	Atlas-SNP	.											.	DEFB1	4	.	0			c.G112A	GRCh37	CM020372	DEFB1	M	rs2738047	PASS	.	C	ILE/VAL	545,3861	249.6+/-257.0	36,473,1694	122	99	107		112	2.2	0	8	dbSNP_100	107	6,8594	5.0+/-18.6	0,6,4294	yes	missense	DEFB1	NM_005218.3	29	36,479,5988	TT,TC,CC		0.0698,12.3695,4.2365	benign	38/69	6728298	551,12455	2203	4300	6503	SO:0001583	missense	1672	exon2			TGCTGACGCAATT	X92744	CCDS5959.1	8p23.1	2012-03-27			ENSG00000164825	ENSG00000164825		"Defensins, beta"	2766	protein-coding gene	gene with protein product		602056				7628632	Standard	NM_005218		Approved	HBD-1, DEFB-1, DEFB101, HBD1, BD1, MGC51822	uc003wqs.2	P60022	OTTHUMG00000090367	ENST00000297439.3:c.112G>A	8.37:g.6728298C>T	ENSP00000297439:p.Val38Ile	122	0	0		128	71	0.554688	NM_005218	Q09753	Missense_Mutation	SNP	ENST00000297439.3	37	CCDS5959.1	62	0.028388278388278388	56	0.11382113821138211	0	0.0	6	0.01048951048951049	0	0.0	C	13.89	2.373486	0.42105	0.123695	6.98E-4	ENSG00000164825	ENST00000297439	T	0.21543	2.0	4.24	2.16	0.27623	.	1.226530	0.06201	N	0.683220	T	0.00178	0.0005	.	.	.	0.09310	N	1	P	0.49696	0.927	B	0.29440	0.102	T	0.28870	-1.0030	9	0.41790	T	0.15	-4.8641	9.8265	0.40914	0.0:0.589:0.411:0.0	rs2738047;rs52816296;rs60091306;rs2738047	38	P60022	DEFB1_HUMAN	I	38	ENSP00000297439:V38I	ENSP00000297439:V38I	V	-	1	0	DEFB1	6715708	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	0.025000	0.13577	1.041000	0.40125	0.563000	0.77884	GTC	T|0.041;C|0.959	0.041	strong		0.498	DEFB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251292.1	NM_005218		T	6728298	C	T	6728298	3	4	22	1	0	0	0	0	1	0	0	0	4396	536	19	1	98	1	DEFB1	8	6728298	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3295712	6728298	139635724	1843	4744											
SGK223	157285	hgsc.bcm.edu	37	chr8	8175868	8175868	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgccgcacagcgcctcctcCgaggtgcccggctgctgcac	4	6	13	18	4	0	0	0	0	0	0	2	1	2	0	5	2	5	4	5	2	0	0	rs114026601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:8175868C>T	ENST00000520004.1	-	6	4281	c.4017G>A	c.(4015-4017)tcG>tcA	p.S1339S	SGK223_ENST00000330777.4_Silent_p.S1339S			Q86YV5	SG223_HUMAN		1343							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GCGCCTCCTCCGAGGTGCCCG	0.682													C|||	123	0.0245607	0.0885	0.0072	5008	,	,		13730	0.0		0.001	False		,,,				2504	0.0				p.S1339S	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.G4017A						PASS	.	C		318,3830		13,292,1769	64	73	70		4017	-6.6	0.1	8	dbSNP_132	70	1,8381		0,1,4190	no	coding-synonymous	SGK223	NM_001080826.1		13,293,5959	TT,TC,CC		0.0119,7.6663,2.5459		1339/1403	8175868	319,12211	2074	4191	6265	SO:0001819	synonymous_variant	0	exon5			CTCCTCCGAGGTG																												ENST00000520004.1:c.4017G>A	8.37:g.8175868C>T		91	0	0		109	68	0.623853	NM_001080826	Q8N3N5	Silent	SNP	ENST00000520004.1	37	CCDS43706.1																																																																																			C|0.988;T|0.012	0.012	strong		0.682	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1			T	8175868	C	T	8175868	2	4	22	1	0	0	0	0	0	0	0	1	14225	639	23	1		1	SGK223	8	8175868	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1447570	8175868	138188154	1844	4745											
SGK223	157285	hgsc.bcm.edu	37	chr8	8176051	8176051	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggcggcaggtcctcctgccgGtagtctctctcccgcagctg	3	9	13	16	3	2	0	0	0	2	0	6	0	4	0	4	4	2	4	4	4	1	1	rs114220337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:8176051G>A	ENST00000520004.1	-	6	4098	c.3834C>T	c.(3832-3834)taC>taT	p.Y1278Y	SGK223_ENST00000330777.4_Silent_p.Y1278Y			Q86YV5	SG223_HUMAN		1282	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										CCTCCTGCCGGTAGTCTCTCT	0.647													G|||	123	0.0245607	0.0885	0.0072	5008	,	,		10988	0.0		0.001	False		,,,				2504	0.0				p.Y1278Y	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											SgK223,caecum,carcinoma,0,2	.	.	2	0			c.C3834T						PASS	.	G		299,3693		13,273,1710	16	21	19		3834	2.7	1	8	dbSNP_132	19	0,8286		0,0,4143	no	coding-synonymous	SGK223	NM_001080826.1		13,273,5853	AA,AG,GG		0.0,7.49,2.4353		1278/1403	8176051	299,11979	1996	4143	6139	SO:0001819	synonymous_variant	0	exon5			CTGCCGGTAGTCT																												ENST00000520004.1:c.3834C>T	8.37:g.8176051G>A		44	0	0		44	27	0.613636	NM_001080826	Q8N3N5	Silent	SNP	ENST00000520004.1	37	CCDS43706.1																																																																																			G|0.980;A|0.020	0.020	strong		0.647	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1			A	8176051	G	A	8176051	2	1	22	1	0	0	0	0	0	0	0	1	14225	1256	44	2		2	SGK223	8	8176051	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	183	8176051	138187971	1845	4746											
SGK223	157285	hgsc.bcm.edu	37	chr8	8176540	8176540	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagcacacgcgccgctcgtaCgcctcgggctccgcctggtg	5	6	13	17	7	0	0	0	0	0	0	3	0	1	0	4	2	2	4	4	2	2	1	rs116402506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:8176540C>T	ENST00000520004.1	-	6	3609	c.3345G>A	c.(3343-3345)gcG>gcA	p.A1115A	SGK223_ENST00000330777.4_Silent_p.A1115A			Q86YV5	SG223_HUMAN		1117	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GCCGCTCGTACGCCTCGGGCT	0.667													C|||	318	0.0634984	0.2231	0.0274	5008	,	,		10206	0.0		0.003	False		,,,				2504	0.001				p.A1115A	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.G3345A						PASS	.	C		726,3448		70,586,1431	77	86	83		3345	-11	0	8	dbSNP_132	83	13,8401		0,13,4194	no	coding-synonymous	SGK223	NM_001080826.1		70,599,5625	TT,TC,CC		0.1545,17.3934,5.8707		1115/1403	8176540	739,11849	2087	4207	6294	SO:0001819	synonymous_variant	0	exon5			CTCGTACGCCTCG																												ENST00000520004.1:c.3345G>A	8.37:g.8176540C>T		32	0	0		46	26	0.565217	NM_001080826	Q8N3N5	Silent	SNP	ENST00000520004.1	37	CCDS43706.1																																																																																			C|0.970;T|0.030	0.030	strong		0.667	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1			T	8176540	C	T	8176540	2	4	22	1	0	0	0	0	0	0	0	1	14225	523	19	1		1	SGK223	8	8176540	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	489	8176540	138187482	1846	4747											
SGK223	157285	hgsc.bcm.edu	37	chr8	8176770	8176770	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgttaaagtgcacgggcaCggacgggctgcagtaggaga	11	6	17	7	3	0	1	0	0	0	1	0	4	0	2	0	4	2	6	0	4	3	2	rs28533138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:8176770C>T	ENST00000520004.1	-	6	3379	c.3115G>A	c.(3115-3117)Gtg>Atg	p.V1039M	SGK223_ENST00000330777.4_Missense_Mutation_p.V1039M			Q86YV5	SG223_HUMAN		1041	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										TGCACGGGCACGGACGGGCTG	0.617													C|||	160	0.0319489	0.115	0.0086	5008	,	,		14630	0.0		0.002	False		,,,				2504	0.0				p.V1039M	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.G3115A						PASS	.	C	MET/VAL	347,3795		11,325,1735	41	49	46		3115	5.3	1	8	dbSNP_125	46	14,8330		0,14,4158	yes	missense	SGK223	NM_001080826.1	21	11,339,5893	TT,TC,CC		0.1678,8.3776,2.8912	probably-damaging	1039/1403	8176770	361,12125	2071	4172	6243	SO:0001583	missense	0	exon5			CGGGCACGGACGG																												ENST00000520004.1:c.3115G>A	8.37:g.8176770C>T	ENSP00000428054:p.Val1039Met	93	0	0		96	44	0.458333	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	58	0.026556776556776556	55	0.11178861788617886	3	0.008287292817679558	0	0.0	0	0.0	C	18.72	3.684827	0.68157	0.083776	0.001678	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.32515	1.45;1.45	5.33	5.33	0.75918	Protein kinase, catalytic domain (1);	0.318706	0.31809	N	0.007027	T	0.00496	0.0016	L	0.27053	0.805	0.46028	D	0.998827	D	0.58268	0.982	P	0.45449	0.481	T	0.00225	-1.1901	10	0.72032	D	0.01	.	14.0559	0.64769	0.0:0.8492:0.1508:0.0	rs28533138	1039	Q86YV5	SG223_HUMAN	M	1039	ENSP00000330930:V1039M;ENSP00000428054:V1039M	ENSP00000330930:V1039M	V	-	1	0	AC068353.1	8214180	1.000000	0.71417	0.959000	0.39883	0.726000	0.41606	4.871000	0.63042	2.670000	0.90874	0.467000	0.42956	GTG	C|0.982;T|0.018	0.018	strong		0.617	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1			T	8176770	C	T	8176770	3	4	22	1	0	0	0	0	1	0	0	0	14225	536	19	1	1097	1	SGK223	8	8176770	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	230	8176770	138187252	1847	4748											
CLDN23	137075	hgsc.bcm.edu	37	chr8	8559917	8559917	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcgggccgggatgcggacGccggtggtgatgacgctggg	4	5	22	10	7	0	2	0	2	0	0	0	4	0	4	2	7	1	1	2	7	0	0	rs61754917	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:8559917G>A	ENST00000519106.1	+	1	470	c.9G>A	c.(7-9)acG>acA	p.T3T		NM_194284.2	NP_919260.2	Q96B33	CLD23_HUMAN	claudin 23	3					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)			endometrium(2)	2		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.071)|READ - Rectum adenocarcinoma(644;0.238)		GGATGCGGACGCCGGTGGTGA	0.736													G|||	31	0.0061901	0.0219	0.0029	5008	,	,		12030	0.0		0.0	False		,,,				2504	0.0				p.T3T		Atlas-SNP	.											.	CLDN23	5	.	0			c.G9A						PASS	.	G		90,3868		0,90,1889	9	13	11		9	2.2	1	8	dbSNP_129	11	0,8248		0,0,4124	no	coding-synonymous	CLDN23	NM_194284.2		0,90,6013	AA,AG,GG		0.0,2.2739,0.7373		3/293	8559917	90,12116	1979	4124	6103	SO:0001819	synonymous_variant	137075	exon1			GCGGACGCCGGTG	AK123547	CCDS55195.1	8p23.1	2006-04-12				ENSG00000253958		"Claudins"	17591	protein-coding gene	gene with protein product		609203				12736707	Standard	NM_194284		Approved	CLDNL	uc003wsi.3	Q96B33		ENST00000519106.1:c.9G>A	8.37:g.8559917G>A		6	0	0		7	6	0.857143	NM_194284	Q08AJ3	Silent	SNP	ENST00000519106.1	37	CCDS55195.1																																																																																			G|0.995;A|0.005	0.005	strong		0.736	CLDN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374721.1	NM_194284		A	8559917	G	A	8559917	2	1	22	1	0	0	0	0	0	0	0	1	3486	1074	38	1		1	CLDN23	8	8559917	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	383147	8559917	137804105	1848	4749											
ERI1	90459	hgsc.bcm.edu	37	chr8	8869129	8869129	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatgctgaaagagagcaattTtgctgacagttattatgact	13	13	10	5	0	0	4	0	3	0	1	0	6	0	4	0	0	3	4	0	0	4	4	rs112570397	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:8869129T>G	ENST00000523898.1	+	4	1044	c.365T>G	c.(364-366)tTt>tGt	p.F122C	ERI1_ENST00000519292.1_Missense_Mutation_p.F122C|ERI1_ENST00000250263.7_Missense_Mutation_p.F122C			Q8IV48	ERI1_HUMAN	exoribonuclease 1	122					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						GAGAGCAATTTTGCTGACAGT	0.348													G|||	41	0.0081869	0.0303	0.0014	5008	,	,		17758	0.0		0.0	False		,,,				2504	0.0				p.F122C		Atlas-SNP	.											.	ERI1	20	.	0			c.T365G						PASS	.	G	CYS/PHE	121,4285	813.8+/-416.2	1,119,2083	82	82	82		365	1.7	0	8	dbSNP_132	82	0,8600		0,0,4300	yes	missense	ERI1	NM_153332.3	205	1,119,6383	GG,GT,TT		0.0,2.7463,0.9303	benign	122/350	8869129	121,12885	2203	4300	6503	SO:0001583	missense	90459	exon3			GCAATTTTGCTGA	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.365T>G	8.37:g.8869129T>G	ENSP00000429615:p.Phe122Cys	51	0	0		75	45	0.6	NM_153332	A8K4U7|Q9NSX3	Missense_Mutation	SNP	ENST00000523898.1	37	CCDS5972.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	G	10.23	1.293512	0.23564	0.027463	0.0	ENSG00000104626	ENST00000523898;ENST00000250263;ENST00000519292	T;T;T	0.43688	0.94;0.94;0.94	5.79	1.69	0.24217	.	1.091090	0.06714	N	0.773725	T	0.09992	0.0245	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18272	-1.0342	10	0.46703	T	0.11	-26.669	3.9327	0.09293	0.1405:0.3665:0.3736:0.1193	.	122	Q8IV48	ERI1_HUMAN	C	122	ENSP00000429615:F122C;ENSP00000250263:F122C;ENSP00000430190:F122C	ENSP00000250263:F122C	F	+	2	0	ERI1	8906539	0.000000	0.05858	0.000000	0.03702	0.943000	0.58893	-0.253000	0.08794	0.078000	0.16900	-0.231000	0.12243	TTT	T|0.991;G|0.009	0.009	strong		0.348	ERI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251471.2	NM_153332		G	8869129	T	G	8869129	3	3	22	1	0	0	0	0	1	0	0	0	5229	1841	64	5	375	5	ERI1	8	8869129	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	309212	8869129	137494893	1849	4750											
RP1L1	94137	hgsc.bcm.edu	37	chr8	10464465	10464465	+	Silent	SNP	G	G	A																															cccactgcctcagtgggggcGagacttccgagtgcctggtc																								rs112520779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10464465G>A	ENST00000382483.3	-	4	7366	c.7143C>T	c.(7141-7143)ctC>ctT	p.L2381L		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	2461					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)		CAGTGGGGGCGAGACTTCCGA	0.547													G|||	14	0.00279553	0.0106	0.0	5008	,	,		17836	0.0		0.0	False		,,,				2504	0.0				p.L2381L		Atlas-SNP	.											RP1L1,NS,carcinoma,-2,1	RP1L1	453	1	0			c.C7143T						PASS	.	G		26,3806		0,26,1890	109	115	113		7143	-6.4	0	8	dbSNP_132	113	0,8232		0,0,4116	no	coding-synonymous	RP1L1	NM_178857.5		0,26,6006	AA,AG,GG		0.0,0.6785,0.2155		2381/2401	10464465	26,12038	1916	4116	6032	SO:0001819	synonymous_variant	94137	exon4			GGGGGCGAGACTT	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.7143C>T	8.37:g.10464465G>A		52	0	0		65	43	0.661538	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																			A|0.002;G|0.998;T|0.000	0.002	strong		0.547	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			A	10464465	G	A	10464465	2	1	22	1	0	0	0	0	0	0	0	1	13548	1045	37	1		1	RP1L1	8	10464465	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1595336	10464465	135899557	1850	4751	58	2									
RP1L1	94137	hgsc.bcm.edu	37	chr8	10464474	10464474	+	Silent	SNP	G	G	T																															tcagtgggggcgagacttccGagtgcctggtcctcttgtag																								rs113172380	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10464474G>T	ENST00000382483.3	-	4	7357	c.7134C>A	c.(7132-7134)ctC>ctA	p.L2378L		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	2458					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)		CGAGACTTCCGAGTGCCTGGT	0.532													G|||	15	0.00299521	0.0113	0.0	5008	,	,		17727	0.0		0.0	False		,,,				2504	0.0				p.L2378L		Atlas-SNP	.											RP1L1,NS,carcinoma,-2,1	RP1L1	453	1	0			c.C7134A						PASS	.	G		27,3811		0,27,1892	110	114	113		7134	-7.2	0	8	dbSNP_132	113	0,8234		0,0,4117	no	coding-synonymous	RP1L1	NM_178857.5		0,27,6009	TT,TG,GG		0.0,0.7035,0.2237		2378/2401	10464474	27,12045	1919	4117	6036	SO:0001819	synonymous_variant	94137	exon4			ACTTCCGAGTGCC	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.7134C>A	8.37:g.10464474G>T		56	0	0		68	46	0.676471	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																			G|0.996;T|0.004	0.004	strong		0.532	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			T	10464474	G	T	10464474	2	4	22	1	0	0	0	0	0	0	0	1	13548	1045	37	4		4	RP1L1	8	10464474	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	9	10464474	135899548	1851	4752	58	2									
RP1L1	94137	hgsc.bcm.edu	37	chr8	10467130	10467130	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cagccccctgggtgggttggGcctgcgtgtgctcttggccc	1	10	16	14	1	1	0	0	0	1	0	1	0	1	0	4	4	3	2	4	4	0	2	rs138261433	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10467130G>A	ENST00000382483.3	-	4	4701	c.4478C>T	c.(4477-4479)gCc>gTc	p.A1493V		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1573					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)		GGTGGGTTGGGCCTGCGTGTG	0.647													G|||	22	0.00439297	0.0159	0.0014	5008	,	,		16042	0.0		0.0	False		,,,				2504	0.0				p.A1493V		Atlas-SNP	.											.	RP1L1	453	.	0			c.C4478T						PASS	.	G	VAL/ALA	69,3877		0,69,1904	33	38	37		4478	-5.1	0	8	dbSNP_134	37	2,8318		0,2,4158	yes	missense	RP1L1	NM_178857.5	64	0,71,6062	AA,AG,GG		0.024,1.7486,0.5788	benign	1493/2401	10467130	71,12195	1973	4160	6133	SO:0001583	missense	94137	exon4			GGTTGGGCCTGCG	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.4478C>T	8.37:g.10467130G>A	ENSP00000371923:p.Ala1493Val	36	0	0		48	24	0.5	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	3.081	-0.189007	0.06299	0.017486	2.4E-4	ENSG00000183638	ENST00000382483	T	0.03860	3.78	4.78	-5.14	0.02875	.	1.690280	0.03804	N	0.264929	T	0.01092	0.0036	N	0.14661	0.345	0.09310	N	1	B	0.26483	0.15	B	0.19946	0.027	T	0.41680	-0.9495	10	0.09338	T	0.73	-0.4613	4.2452	0.10669	0.4089:0.0:0.2703:0.3208	.	1493	A6NKC6	.	V	1493	ENSP00000371923:A1493V	ENSP00000371923:A1493V	A	-	2	0	RP1L1	10504540	0.017000	0.18338	0.000000	0.03702	0.013000	0.08279	0.131000	0.15870	-1.100000	0.03030	0.561000	0.74099	GCC	G|0.998;A|0.002	0.002	strong		0.647	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			A	10467130	G	A	10467130	3	1	22	1	0	0	0	0	1	0	0	0	13548	1203	42	2	2728	2	RP1L1	8	10467130	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2656	10467130	135896892	1852	4753											
RP1L1	94137	hgsc.bcm.edu	37	chr8	10470130	10470130	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggctccctccagctttcCgctcagcccctatctgggca	5	9	8	19	1	2	0	1	0	1	0	5	0	5	0	6	2	2	4	6	2	1	2	rs79401306	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10470130C>T	ENST00000382483.3	-	4	1701	c.1478G>A	c.(1477-1479)cGg>cAg	p.R493Q		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	493					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)		TCCAGCTTTCCGCTCAGCCCC	0.721													C|||	103	0.0205671	0.0764	0.0029	5008	,	,		15146	0.0		0.0	False		,,,				2504	0.0				p.R493Q		Atlas-SNP	.											.	RP1L1	453	.	0			c.G1478A						PASS	.	C	GLN/ARG	205,3593		6,193,1700	26	30	29		1478	-2.6	0	8	dbSNP_131	29	3,8241		0,3,4119	yes	missense	RP1L1	NM_178857.5	43	6,196,5819	TT,TC,CC		0.0364,5.3976,1.7273	possibly-damaging	493/2401	10470130	208,11834	1899	4122	6021	SO:0001583	missense	94137	exon4			GCTTTCCGCTCAG	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.1478G>A	8.37:g.10470130C>T	ENSP00000371923:p.Arg493Gln	24	0	0		33	11	0.333333	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	44	0.020146520146520148	44	0.08943089430894309	0	0.0	0	0.0	0	0.0	C	7.544	0.661253	0.14645	0.053976	3.64E-4	ENSG00000183638	ENST00000382483	T	0.04083	3.71	4.06	-2.57	0.06248	.	.	.	.	.	T	0.00109	0.0003	N	0.08118	0	0.09310	N	1	B	0.16396	0.017	B	0.04013	0.001	T	0.45190	-0.9278	9	0.41790	T	0.15	14.544	4.0305	0.09706	0.1672:0.3134:0.0:0.5194	.	493	A6NKC6	.	Q	493	ENSP00000371923:R493Q	ENSP00000371923:R493Q	R	-	2	0	RP1L1	10507540	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.619000	0.05572	-0.838000	0.04218	0.561000	0.74099	CGG	C|0.987;T|0.013	0.013	strong		0.721	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			T	10470130	C	T	10470130	3	4	22	1	0	0	0	0	1	0	0	0	13548	652	23	1	5728	1	RP1L1	8	10470130	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3000	10470130	135893892	1853	4754											
RP1L1	94137	hgsc.bcm.edu	37	chr8	10470764	10470764	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagggcccaccggggggtTgctaggaccaggcctttctg	6	7	16	12	1	1	0	0	0	1	0	1	1	1	1	4	6	2	3	4	6	1	3	rs75814156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10470764T>G	ENST00000382483.3	-	4	1067	c.844A>C	c.(844-846)Aac>Cac	p.N282H		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	282					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)		ACCGGGGGGTTGCTAGGACCA	0.672													T|||	113	0.0225639	0.084	0.0029	5008	,	,		15048	0.0		0.0	False		,,,				2504	0.0				p.N282H		Atlas-SNP	.											RP1L1,NS,carcinoma,+2,1	RP1L1	453	1	0			c.A844C						PASS	.	T	HIS/ASN	236,3690		8,220,1735	55	62	60		844	0.6	0	8	dbSNP_131	60	2,8288		0,2,4143	yes	missense	RP1L1	NM_178857.5	68	8,222,5878	GG,GT,TT		0.0241,6.0112,1.9483	probably-damaging	282/2401	10470764	238,11978	1963	4145	6108	SO:0001583	missense	94137	exon4			GGGGGTTGCTAGG	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.844A>C	8.37:g.10470764T>G	ENSP00000371923:p.Asn282His	48	0	0		40	13	0.325	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	49	0.022435897435897436	49	0.09959349593495935	0	0.0	0	0.0	0	0.0	T	13.74	2.326457	0.41197	0.060112	2.41E-4	ENSG00000183638	ENST00000382483	T	0.04360	3.64	4.67	0.552	0.17230	.	0.788418	0.10319	N	0.688987	T	0.00144	0.0004	N	0.14661	0.345	0.09310	N	1	D	0.58970	0.984	P	0.46796	0.527	T	0.49960	-0.8883	10	0.59425	D	0.04	-5.163	5.688	0.17813	0.0:0.5952:0.1546:0.2502	.	282	A6NKC6	.	H	282	ENSP00000371923:N282H	ENSP00000371923:N282H	N	-	1	0	RP1L1	10508174	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.263000	0.18478	-0.050000	0.13356	-0.643000	0.03959	AAC	T|0.984;G|0.016	0.016	strong		0.672	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			G	10470764	T	G	10470764	3	3	22	1	0	0	0	0	1	0	0	0	13548	1812	63	5	6362	5	RP1L1	8	10470764	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	634	10470764	135893258	1854	4755											
RP1L1	94137	hgsc.bcm.edu	37	chr8	10470794	10470794	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aggcctttctggcagccgtgGcgtgctgcctggcggagacc	4	8	16	13	3	1	1	0	0	1	1	1	2	1	1	4	5	3	2	4	5	0	1	rs77833234	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10470794G>C	ENST00000382483.3	-	4	1037	c.814C>G	c.(814-816)Cca>Gca	p.P272A		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	272					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)		GGCAGCCGTGGCGTGCTGCCT	0.647													G|||	19	0.00379393	0.0144	0.0	5008	,	,		15506	0.0		0.0	False		,,,				2504	0.0				p.P272A		Atlas-SNP	.											.	RP1L1	453	.	0			c.C814G						PASS	.	G	ALA/PRO	38,3946		0,38,1954	53	59	57		814	0.2	0	8	dbSNP_131	57	2,8342		0,2,4170	no	missense	RP1L1	NM_178857.5	27	0,40,6124	CC,CG,GG		0.024,0.9538,0.3245	probably-damaging	272/2401	10470794	40,12288	1992	4172	6164	SO:0001583	missense	94137	exon4			GCCGTGGCGTGCT	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.814C>G	8.37:g.10470794G>C	ENSP00000371923:p.Pro272Ala	33	0	0		21	9	0.428571	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	20	0.009157509157509158	13	0.026422764227642278	2	0.0055248618784530384	2	0.0034965034965034965	3	0.00395778364116095	G	1.225	-0.625730	0.03610	0.009538	2.4E-4	ENSG00000183638	ENST00000382483	T	0.04194	3.68	5.33	0.147	0.14838	.	1.942830	0.03465	N	0.212853	T	0.01287	0.0042	L	0.38175	1.15	0.09310	N	1	B	0.22683	0.073	B	0.20767	0.031	T	0.43048	-0.9415	10	0.21014	T	0.42	-0.1152	0.8756	0.01223	0.251:0.3733:0.1891:0.1866	.	272	A6NKC6	.	A	272	ENSP00000371923:P272A	ENSP00000371923:P272A	P	-	1	0	RP1L1	10508204	0.087000	0.21565	0.000000	0.03702	0.005000	0.04900	1.861000	0.39438	0.162000	0.19483	-0.293000	0.09583	CCA	G|0.993;C|0.007	0.007	strong		0.647	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			C	10470794	G	C	10470794	3	2	22	1	0	0	0	0	1	0	0	0	13548	1203	42	4	6392	4	RP1L1	8	10470794	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	30	10470794	135893228	1855	4756											
C8orf74	203076	hgsc.bcm.edu	37	chr8	10555263	10555263	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cagtatgtcctgggccaggaCcagcaggtcgacctgaccgt	8	7	13	13	2	0	1	0	1	0	0	2	3	1	2	5	3	1	2	5	3	1	1	rs147047803	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10555263C>G	ENST00000304519.5	+	3	425	c.396C>G	c.(394-396)gaC>gaG	p.D132E	RP1L1_ENST00000329335.3_Intron	NM_001040032.1	NP_001035121	Q6P047	CH074_HUMAN	chromosome 8 open reading frame 74	132										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	13				COAD - Colon adenocarcinoma(149;0.0811)		TGGGCCAGGACCAGCAGGTCG	0.622													C|||	11	0.00219649	0.0083	0.0	5008	,	,		17486	0.0		0.0	False		,,,				2504	0.0				p.D132E		Atlas-SNP	.											.	C8orf74	28	.	0			c.C396G						PASS	.	C	GLU/ASP	33,4233		0,33,2100	163	169	167		396	-3.2	0.2	8	dbSNP_134	167	0,8450		0,0,4225	yes	missense	C8orf74	NM_001040032.1	45	0,33,6325	GG,GC,CC		0.0,0.7736,0.2595	benign	132/295	10555263	33,12683	2133	4225	6358	SO:0001583	missense	203076	exon3			CCAGGACCAGCAG	BC038534	CCDS47800.1	8p23.1	2012-04-17			ENSG00000171060	ENSG00000171060			32296	protein-coding gene	gene with protein product							Standard	NM_001040032		Approved		uc003wtd.1	Q6P047	OTTHUMG00000163807	ENST00000304519.5:c.396C>G	8.37:g.10555263C>G	ENSP00000307129:p.Asp132Glu	79	0	0		97	44	0.453608	NM_001040032	A2RUD6	Missense_Mutation	SNP	ENST00000304519.5	37	CCDS47800.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	C	0.118	-1.129786	0.01756	0.007736	0.0	ENSG00000171060	ENST00000304519	T	0.28666	1.6	5.2	-3.25	0.05079	.	0.639609	0.15360	N	0.266446	T	0.08133	0.0203	N	0.16656	0.425	0.09310	N	1	B	0.14012	0.009	B	0.11329	0.006	T	0.22695	-1.0209	10	0.15499	T	0.54	.	2.1908	0.03898	0.1217:0.2888:0.3579:0.2316	.	132	Q6P047	CH074_HUMAN	E	132	ENSP00000307129:D132E	ENSP00000307129:D132E	D	+	3	2	C8orf74	10592673	0.006000	0.16342	0.207000	0.23584	0.043000	0.13939	-1.025000	0.03600	-0.299000	0.08909	-1.334000	0.01262	GAC	C|0.997;G|0.003	0.003	strong		0.622	C8orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375675.1	NM_001040032		G	10555263	C	G	10555263	3	3	22	1	0	0	0	0	1	0	0	0	2438	506	18	4	406	4	C8orf74	8	10555263	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	84469	10555263	135808759	1856	4757											
MTMR9	66036	hgsc.bcm.edu	37	chr8	11142529	11142529	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgtcctcccggcaggacaaTacggaggagctgtggctcct	7	8	13	13	2	0	0	0	0	0	0	3	3	3	3	3	5	2	3	3	5	2	1	rs61752023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11142529T>C	ENST00000221086.3	+	1	605	c.132T>C	c.(130-132)aaT>aaC	p.N44N	MTMR9_ENST00000526292.1_5'Flank	NM_015458.3	NP_056273.2	Q96QG7	MTMR9_HUMAN	myotubularin related protein 9	44						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)		GGCAGGACAATACGGAGGAGC	0.657													C|||	214	0.0427316	0.1573	0.0072	5008	,	,		12961	0.0		0.001	False		,,,				2504	0.0				p.N44N		Atlas-SNP	.											.	MTMR9	58	.	0			c.T132C						PASS	.	C		609,3797	765.8+/-413.4	36,537,1630	36	38	37		132	3	1	8	dbSNP_129	37	2,8598	817.5+/-406.9	0,2,4298	no	coding-synonymous	MTMR9	NM_015458.3		36,539,5928	CC,CT,TT		0.0233,13.8221,4.6978		44/550	11142529	611,12395	2203	4300	6503	SO:0001819	synonymous_variant	66036	exon1			GGACAATACGGAG	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.132T>C	8.37:g.11142529T>C		91	0	0		101	53	0.524752	NM_015458	B7Z291|Q52LU3|Q8WW11|Q96QG6|Q9NX50	Silent	SNP	ENST00000221086.3	37	CCDS5979.1																																																																																			T|0.958;C|0.042	0.042	strong		0.657	MTMR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207307.2	NM_015458		C	11142529	T	C	11142529	2	2	22	1	0	0	0	0	0	0	0	1	9959	1403	49	3		3	MTMR9	8	11142529	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	587266	11142529	135221493	1857	4758											
GATA4	2626	hgsc.bcm.edu	37	chr8	11614559	11614559	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagacggagcctggcctgtcAtctcactacgggcacagcag	10	6	12	13	2	2	1	2	0	1	1	3	2	2	2	2	3	3	2	2	3	2	1	rs112435835	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11614559A>G	ENST00000335135.4	+	6	1671	c.1113A>G	c.(1111-1113)tcA>tcG	p.S371S	GATA4_ENST00000528712.1_Silent_p.S165S|GATA4_ENST00000532059.1_Silent_p.S372S	NM_002052.3	NP_002043.2	P43694	GATA4_HUMAN	GATA binding protein 4	371					atrial septum morphogenesis (GO:0060413)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|atrioventricular valve morphogenesis (GO:0003181)|blood coagulation (GO:0007596)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac ventricle morphogenesis (GO:0003208)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to glucose stimulus (GO:0071333)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube anterior/posterior pattern specification (GO:0035054)|endocardial cushion development (GO:0003197)|endoderm development (GO:0007492)|endoderm formation (GO:0001706)|epithelial cell fate commitment (GO:0072148)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|intestinal epithelial cell differentiation (GO:0060575)|lung lobe formation (GO:0060464)|male gonad development (GO:0008584)|negative regulation of autophagy (GO:0010507)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|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 cardiac muscle cell contraction (GO:0086004)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to mechanical stimulus (GO:0009612)|seminiferous tubule development (GO:0072520)|Sertoli cell differentiation (GO:0060008)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|enhancer sequence-specific DNA binding (GO:0001158)|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)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(10)	13	all_epithelial(15;0.0839)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.199)		CTGGCCTGTCATCTCACTACG	0.662													A|||	51	0.0101837	0.0371	0.0029	5008	,	,		20298	0.0		0.0	False		,,,				2504	0.0				p.S371S		Atlas-SNP	.											.	GATA4	29	.	0			c.A1113G						PASS	.	A		94,4312	76.8+/-115.0	2,90,2111	90	70	76		1113	-11.7	0	8	dbSNP_132	76	0,8600		0,0,4300	no	coding-synonymous	GATA4	NM_002052.3		2,90,6411	GG,GA,AA		0.0,2.1335,0.7227		371/443	11614559	94,12912	2203	4300	6503	SO:0001819	synonymous_variant	2626	exon6			CCTGTCATCTCAC	AK097060	CCDS5983.1	8p23.1-p22	2013-01-25	2001-11-28		ENSG00000136574	ENSG00000136574		"GATA zinc finger domain containing"	4173	protein-coding gene	gene with protein product		600576	"GATA-binding protein 4"			7665171	Standard	NM_002052		Approved		uc003wuc.2	P43694	OTTHUMG00000090800	ENST00000335135.4:c.1113A>G	8.37:g.11614559A>G		301	0	0		259	132	0.509652	NM_002052	B7ZKX0|B7ZKZ4|Q3MJ45|Q5IFM8	Silent	SNP	ENST00000335135.4	37	CCDS5983.1																																																																																			A|0.993;G|0.007	0.007	strong		0.662	GATA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207587.2	NM_002052		G	11614559	A	G	11614559	2	3	22	1	0	0	0	0	0	0	0	1	6264	204	8	3		3	GATA4	8	11614559	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	472030	11614559	134749463	1858	4759											
NEIL2	252969	hgsc.bcm.edu	37	chr8	11640853	11640853	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	caagccttagaagctctaggCcaggctcagcctgtctgcta	9	9	10	13	0	3	1	1	0	2	1	3	1	3	1	3	2	4	3	3	2	5	3	rs112549959	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11640853C>T	ENST00000284503.6	+	4	1232	c.633C>T	c.(631-633)ggC>ggT	p.G211G	NEIL2_ENST00000528323.1_Silent_p.G95G|NEIL2_ENST00000455213.2_Silent_p.G211G|NEIL2_ENST00000436750.3_Silent_p.G211G|NEIL2_ENST00000403422.3_Silent_p.G150G	NM_145043.2	NP_659480.1	Q969S2	NEIL2_HUMAN	nei endonuclease VIII-like 2 (E. coli)	211					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)		AAGCTCTAGGCCAGGCTCAGC	0.517								Base excision repair (BER), DNA glycosylases					C|||	22	0.00439297	0.0159	0.0014	5008	,	,		23388	0.0		0.0	False		,,,				2504	0.0				p.G211G		Atlas-SNP	.											.	NEIL2	14	.	0			c.C633T						PASS	.	C	,,,	45,4361	48.2+/-83.0	0,45,2158	119	104	109		633,450,285,633	-3.7	0.1	8	dbSNP_132	109	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NEIL2	NM_001135746.1,NM_001135747.1,NM_001135748.1,NM_145043.2	,,,	0,45,6458	TT,TC,CC		0.0,1.0213,0.346	,,,	211/333,150/272,95/217,211/333	11640853	45,12961	2203	4300	6503	SO:0001819	synonymous_variant	252969	exon4			TCTAGGCCAGGCT	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.633C>T	8.37:g.11640853C>T		180	0	0		207	97	0.468599	NM_001135746	B4DFR7|Q7Z3Q7|Q8N842|Q8NG52	Silent	SNP	ENST00000284503.6	37	CCDS5984.1																																																																																			C|0.996;T|0.004	0.004	strong		0.517	NEIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207583.3	NM_145043		T	11640853	C	T	11640853	2	4	22	1	0	0	0	0	0	0	0	1	10328	726	26	2		2	NEIL2	8	11640853	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	26294	11640853	134723169	1859	4760											
NEIL2	252969	hgsc.bcm.edu	37	chr8	11643731	11643731	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggctcacctggtggtgcccGcagtgccagccccagttgtc	5	8	13	15	1	1	0	1	0	0	0	2	0	1	0	5	3	3	3	5	3	0	1	rs113110839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11643731G>A	ENST00000284503.6	+	5	1547	c.948G>A	c.(946-948)ccG>ccA	p.P316P	NEIL2_ENST00000528323.1_Silent_p.P200P|NEIL2_ENST00000455213.2_Silent_p.P316P|NEIL2_ENST00000436750.3_Silent_p.P316P|NEIL2_ENST00000403422.3_Silent_p.P255P	NM_145043.2	NP_659480.1	Q969S2	NEIL2_HUMAN	nei endonuclease VIII-like 2 (E. coli)	316					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)		GGTGGTGCCCGCAGTGCCAGC	0.612								Base excision repair (BER), DNA glycosylases					G|||	23	0.00459265	0.0166	0.0014	5008	,	,		17965	0.0		0.0	False		,,,				2504	0.0				p.P316P		Atlas-SNP	.											.	NEIL2	14	.	0			c.G948A						PASS	.	G	,,,	42,4362		0,42,2160	23	21	22		948,765,600,948	-10.7	0.2	8	dbSNP_132	22	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NEIL2	NM_001135746.1,NM_001135747.1,NM_001135748.1,NM_145043.2	,,,	0,42,6459	AA,AG,GG		0.0,0.9537,0.323	,,,	316/333,255/272,200/217,316/333	11643731	42,12960	2202	4299	6501	SO:0001819	synonymous_variant	252969	exon5			GTGCCCGCAGTGC	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.948G>A	8.37:g.11643731G>A		199	0	0		235	126	0.53617	NM_001135746	B4DFR7|Q7Z3Q7|Q8N842|Q8NG52	Silent	SNP	ENST00000284503.6	37	CCDS5984.1																																																																																			G|0.996;A|0.004	0.004	strong		0.612	NEIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207583.3	NM_145043		A	11643731	G	A	11643731	2	1	22	1	0	0	0	0	0	0	0	1	10328	1074	38	1		1	NEIL2	8	11643731	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2878	11643731	134720291	1860	4761											
DEFB136	613210	hgsc.bcm.edu	37	chr8	11831557	11831557	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgtatcctggcggacacccGaagaaacatacggctttctg	10	9	10	12	3	1	1	0	0	1	1	2	3	2	2	2	3	2	2	2	3	4	3	rs73538682	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11831557G>A	ENST00000382209.2	-	2	125	c.126C>T	c.(124-126)ttC>ttT	p.F42F		NM_001033018.2	NP_001028190.2	Q30KP8	DB136_HUMAN	defensin, beta 136	42					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(2)|large_intestine(1)|lung(4)	7			STAD - Stomach adenocarcinoma(15;0.033)	COAD - Colon adenocarcinoma(149;0.163)		GCGGACACCCGAAGAAACATA	0.473													G|||	147	0.029353	0.1067	0.0058	5008	,	,		20997	0.0		0.002	False		,,,				2504	0.0				p.F42F		Atlas-SNP	.											.	DEFB136	16	.	0			c.C126T						PASS	.	G		356,3638		15,326,1656	169	174	173		126	-2.5	0.7	8	dbSNP_130	173	5,8353		0,5,4174	no	coding-synonymous	DEFB136	NM_001033018.2		15,331,5830	AA,AG,GG		0.0598,8.9134,2.9226		42/79	11831557	361,11991	1997	4179	6176	SO:0001819	synonymous_variant	613210	exon2			ACACCCGAAGAAA	DQ012026	CCDS43709.1	8p23.1	2011-07-19			ENSG00000205884	ENSG00000205884		"Defensins, beta"	34433	protein-coding gene	gene with protein product						16033865	Standard	NM_001033018		Approved	DEFB137	uc011kxm.2	Q30KP8	OTTHUMG00000158720	ENST00000382209.2:c.126C>T	8.37:g.11831557G>A		173	1	0.00578035		141	141	1	NM_001033018	Q4QY36	Silent	SNP	ENST00000382209.2	37	CCDS43709.1																																																																																			G|0.980;A|0.020	0.020	strong		0.473	DEFB136-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351889.1	NM_001033018		A	11831557	G	A	11831557	2	1	22	1	0	0	0	0	0	0	0	1	4422	1049	37	1		1	DEFB136	8	11831557	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	187826	11831557	134532465	1861	4762											
DEFB135	613209	hgsc.bcm.edu	37	chr8	11842019	11842019	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggccaaaatgtctaaaaaacGaacaatatcgtattttgtgt	16	12	7	6	2	1	0	0	0	1	0	2	1	1	0	1	1	2	1	1	1	9	5	rs73663074	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11842019G>A	ENST00000382208.2	+	2	154	c.154G>A	c.(154-156)Gaa>Aaa	p.E52K		NM_001033017.2	NP_001028189.2	Q30KP9	DB135_HUMAN	defensin, beta 135	52					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(1)|large_intestine(2)|prostate(1)	4						TCTAAAAAACGAACAATATCG	0.388													G|||	220	0.0439297	0.1422	0.013	5008	,	,		20406	0.0		0.0	False		,,,				2504	0.0235				p.E52K		Atlas-SNP	.											.	DEFB135	7	.	0			c.G154A						PASS	.	G	LYS/GLU	467,3281		28,411,1435	112	110	111		154	3.3	0.1	8	dbSNP_130	111	10,8190		0,10,4090	yes	missense	DEFB135	NM_001033017.2	56	28,421,5525	AA,AG,GG		0.122,12.46,3.9923	possibly-damaging	52/78	11842019	477,11471	1874	4100	5974	SO:0001583	missense	613209	exon2			AAAAACGAACAAT	DQ012025	CCDS43710.1	8p23.1	2009-05-27			ENSG00000205883	ENSG00000205883		"Defensins, beta"	32400	protein-coding gene	gene with protein product						16033865	Standard	NM_001033017		Approved		uc003wuw.1	Q30KP9	OTTHUMG00000158719	ENST00000382208.2:c.154G>A	8.37:g.11842019G>A	ENSP00000371643:p.Glu52Lys	105	0	0		103	57	0.553398	NM_001033017	Q4QY37	Missense_Mutation	SNP	ENST00000382208.2	37	CCDS43710.1	89	0.04075091575091575	86	0.17479674796747968	3	0.008287292817679558	0	0.0	0	0.0	G	17.23	3.337441	0.60963	0.1246	0.00122	ENSG00000205883	ENST00000382208	T	0.73575	-0.76	3.34	3.34	0.38264	.	0.000000	0.33005	N	0.005386	T	0.01029	0.0034	.	.	.	0.80722	P	0.0	D	0.89917	1.0	D	0.87578	0.998	T	0.47328	-0.9126	8	0.87932	D	0	-25.449	10.4608	0.44578	0.0:0.0:1.0:0.0	.	52	Q30KP9	DB135_HUMAN	K	52	ENSP00000371643:E52K	ENSP00000371643:E52K	E	+	1	0	DEFB135	11879428	0.515000	0.26210	0.053000	0.19242	0.001000	0.01503	2.965000	0.49200	2.157000	0.67596	0.561000	0.74099	GAA	G|0.959;A|0.041	0.041	strong		0.388	DEFB135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351888.1	NM_001033017		A	11842019	G	A	11842019	3	1	22	1	0	0	0	0	1	0	0	0	4421	1059	37	1	160	1	DEFB135	8	11842019	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	10462	11842019	134522003	1862	4763											
USP17L2	377630	hgsc.bcm.edu	37	chr8	11995004	11995004	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggctctttccaccaagcgCtcgtccaactcgggtgcctg	5	10	11	15	3	1	0	0	0	1	0	5	0	3	0	4	2	3	2	4	2	2	1	rs186311075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11995004C>T	ENST00000333796.3	-	1	1582	c.1266G>A	c.(1264-1266)gaG>gaA	p.E422E	FAM66D_ENST00000434078.2_RNA	NM_001256869.1|NM_001256871.1|NM_001256872.1|NM_001256873.1|NM_001256874.1|NM_201402.2	NP_001243798.1|NP_001243800.1|NP_001243801.1|NP_001243802.1|NP_001243803.1|NP_958804.2	Q6R6M4	U17L2_HUMAN	ubiquitin specific peptidase 17-like family member 2	422	Mediates interaction with SUDS3.				apoptotic process (GO:0006915)|CAAX-box protein processing (GO:0071586)|cell cycle checkpoint (GO:0000075)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of histone deacetylation (GO:0031064)|negative regulation of protein processing (GO:0010955)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of Ras GTPase activity (GO:0034261)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of RIG-I signaling pathway (GO:1900246)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of apoptotic process (GO:0042981)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of defense response to virus by host (GO:0050691)|regulation of ruffle assembly (GO:1900027)|ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(1)|kidney(1)|large_intestine(11)|liver(1)|lung(8)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	29						CCACCAAGCGCTCGTCCAACT	0.562													C|||	51	0.0101837	0.0363	0.0043	5008	,	,		20092	0.0		0.0	False		,,,				2504	0.0				p.E422E		Atlas-SNP	.											.	USP17L2	47	.	0			c.G1266A						PASS	.	C		58,3128		3,52,1538	59	65	63		1266	0.7	0	8		63	5,7101		1,3,3549	no	coding-synonymous	USP17L2	NM_201402.2		4,55,5087	TT,TC,CC		0.0704,1.8205,0.6121		422/531	11995004	63,10229	1593	3553	5146	SO:0001819	synonymous_variant	377630	exon1			CAAGCGCTCGTCC	BC156290	CCDS43713.1	8p23.1	2012-10-09	2012-10-09		ENSG00000223443	ENSG00000223443			34434	protein-coding gene	gene with protein product	"deubiquitinating enzyme 3"	610186	"ubiquitin specific peptidase 17-like 2"				Standard	NM_201402		Approved	DUB3	uc003wvc.1	Q6R6M4	OTTHUMG00000165295	ENST00000333796.3:c.1266G>A	8.37:g.11995004C>T		95	0	0		131	27	0.206107	NM_201402		Silent	SNP	ENST00000333796.3	37	CCDS43713.1																																																																																			C|0.992;T|0.008	0.008	strong		0.562	USP17L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383303.2	NM_201402		T	11995004	C	T	11995004	2	4	22	1	0	0	0	0	0	0	0	1	17063	796	28	2		2	USP17L2	8	11995004	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	152985	11995004	134369018	1863	4764											
USP17L2	377630	hgsc.bcm.edu	37	chr8	11996074	11996074	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctactcagaggaagcttctTcctgggagcaagctgtcttg	8	11	12	10	0	3	1	1	0	2	1	4	3	4	3	1	2	4	4	1	2	3	4	rs142023572	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11996074T>C	ENST00000333796.3	-	1	512	c.196A>G	c.(196-198)Aag>Gag	p.K66E	FAM66D_ENST00000434078.2_RNA	NM_001256869.1|NM_001256871.1|NM_001256872.1|NM_001256873.1|NM_001256874.1|NM_201402.2	NP_001243798.1|NP_001243800.1|NP_001243801.1|NP_001243802.1|NP_001243803.1|NP_958804.2	Q6R6M4	U17L2_HUMAN	ubiquitin specific peptidase 17-like family member 2	66				K -> E (in Ref. 1; AAR91701). {ECO:0000305}.	apoptotic process (GO:0006915)|CAAX-box protein processing (GO:0071586)|cell cycle checkpoint (GO:0000075)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of histone deacetylation (GO:0031064)|negative regulation of protein processing (GO:0010955)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of Ras GTPase activity (GO:0034261)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of RIG-I signaling pathway (GO:1900246)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of apoptotic process (GO:0042981)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of defense response to virus by host (GO:0050691)|regulation of ruffle assembly (GO:1900027)|ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(1)|kidney(1)|large_intestine(11)|liver(1)|lung(8)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	29						GGAAGCTTCTTCCTGGGAGCA	0.577													t|||	237	0.0473243	0.1679	0.0173	5008	,	,		18470	0.0		0.001	False		,,,				2504	0.002				p.K66E		Atlas-SNP	.											USP17L2,bladder,carcinoma,+2,1	USP17L2	47	1	0			c.A196G						scavenged	.						43	58	53					8																	11996074		1243	2766	4009	SO:0001583	missense	377630	exon1			GCTTCTTCCTGGG	BC156290	CCDS43713.1	8p23.1	2012-10-09	2012-10-09		ENSG00000223443	ENSG00000223443			34434	protein-coding gene	gene with protein product	"deubiquitinating enzyme 3"	610186	"ubiquitin specific peptidase 17-like 2"				Standard	NM_201402		Approved	DUB3	uc003wvc.1	Q6R6M4	OTTHUMG00000165295	ENST00000333796.3:c.196A>G	8.37:g.11996074T>C	ENSP00000333329:p.Lys66Glu	120	0	0		124	50	0.403226	NM_201402		Missense_Mutation	SNP	ENST00000333796.3	37	CCDS43713.1	135	0.061813186813186816	73	0.1483739837398374	17	0.04696132596685083	21	0.03671328671328671	24	0.0316622691292876	t	4.441	0.081611	0.08533	.	.	ENSG00000223443	ENST00000333796	T	0.11169	2.8	0.36	0.36	0.16097	.	0.863387	0.09306	N	0.820218	T	0.00039	0.0001	.	.	.	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.41413	-0.9510	8	0.02654	T	1	.	2.3221	0.04213	0.0:0.39:0.3289:0.2811	.	66	Q6R6M4	U17L2_HUMAN	E	66	ENSP00000333329:K66E	ENSP00000333329:K66E	K	-	1	0	USP17L2	12033483	0.166000	0.22962	0.015000	0.15790	0.015000	0.08874	0.848000	0.27710	-0.366000	0.08064	-0.368000	0.07277	AAG	T|0.955;C|0.045	0.045	strong		0.577	USP17L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383303.2	NM_201402		C	11996074	T	C	11996074	3	2	22	1	0	0	0	0	1	0	0	0	17063	1792	62	3	1400	3	USP17L2	8	11996074	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1070	11996074	134367948	1864	4765											
C8orf79	57604	hgsc.bcm.edu	37	chr8	12879016	12879016	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cccttgaaaaacacagaagtTtgggccagtagcactgtaac	14	8	9	10	0	0	2	0	1	0	1	0	2	0	2	2	1	3	4	2	1	5	4	rs75377133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:12879016T>A	ENST00000524591.2	+	5	1317	c.828T>A	c.(826-828)gtT>gtA	p.V276V	KIAA1456_ENST00000447063.2_Intron	NM_001099677.1|NM_020844.2	NP_001093147.1|NP_065895.2	Q9P272	K1456_HUMAN	KIAA1456	276							methyltransferase activity (GO:0008168)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7						ACACAGAAGTTTGGGCCAGTA	0.418													T|||	107	0.0213658	0.0794	0.0014	5008	,	,		19745	0.0		0.001	False		,,,				2504	0.0				p.V276V		Atlas-SNP	.											.	KIAA1456	20	.	0			c.T828A						PASS	.	T	,	301,3443		12,277,1583	81	78	79		450,828	-9.9	0	8	dbSNP_132	79	3,8199		0,3,4098	no	coding-synonymous,coding-synonymous	KIAA1456	NM_001099677.1,NM_020844.2	,	12,280,5681	AA,AT,TT		0.0366,8.0395,2.5448	,	150/329,276/455	12879016	304,11642	1872	4101	5973	SO:0001819	synonymous_variant	57604	exon5			AGAAGTTTGGGCC	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.828T>A	8.37:g.12879016T>A		91	0	0		112	47	0.419643	NM_020844	Q96AW6	Silent	SNP	ENST00000524591.2	37	CCDS47808.1																																																																																			T|0.989;A|0.011	0.011	strong		0.418	KIAA1456-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383262.2	NM_001099677		A	12879016	T	A	12879016	2	1	22	1	0	0	0	0	0	0	0	1	2440	1828	64	5		5	C8orf79	8	12879016	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	882942	12879016	133485006	1865	4766											
DLC1	10395	hgsc.bcm.edu	37	chr8	13357331	13357331	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gctgtcattttcgtccacatCctttgaaagatgacccattg	9	14	7	11	1	1	3	1	2	0	1	4	3	3	3	3	0	0	1	3	0	1	4	rs35173269	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:13357331C>T	ENST00000276297.4	-	2	659	c.250G>A	c.(250-252)Gat>Aat	p.D84N	DLC1_ENST00000511869.1_Missense_Mutation_p.D84N|DLC1_ENST00000316609.5_Missense_Mutation_p.D84N	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	84					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						TCGTCCACATCCTTTGAAAGA	0.453													C|||	62	0.0123802	0.0454	0.0014	5008	,	,		20510	0.0		0.001	False		,,,				2504	0.0				p.D84N		Atlas-SNP	.											.	DLC1	411	.	0			c.G250A						PASS	.	C	ASN/ASP,ASN/ASP	215,4191	132.1+/-168.6	8,199,1996	224	226	226		250,250	4.7	0.1	8	dbSNP_126	226	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	DLC1	NM_024767.3,NM_182643.2	23,23	8,202,6293	TT,TC,CC		0.0349,4.8797,1.6761	benign,benign	84/464,84/1529	13357331	218,12788	2203	4300	6503	SO:0001583	missense	10395	exon2			CCACATCCTTTGA	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.250G>A	8.37:g.13357331C>T	ENSP00000276297:p.Asp84Asn	63	0	0		65	34	0.523077	NM_182643	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Missense_Mutation	SNP	ENST00000276297.4	37	CCDS5989.1	20	0.009157509157509158	19	0.03861788617886179	0	0.0	0	0.0	1	0.0013192612137203166	C	11.29	1.596099	0.28445	0.048797	3.49E-4	ENSG00000164741	ENST00000276297;ENST00000316609;ENST00000511869	T;T;T	0.32753	1.44;1.44;1.44	5.55	4.68	0.58851	.	0.542075	0.15368	N	0.266008	T	0.03136	0.0092	N	0.14661	0.345	0.21147	N	0.99977	B;B;B	0.22211	0.039;0.066;0.039	B;B;B	0.24006	0.032;0.05;0.023	T	0.10291	-1.0636	10	0.72032	D	0.01	.	10.6747	0.45778	0.0:0.8543:0.0:0.1457	rs35173269;rs61757613	84;84;84	E9PF76;Q96QB1-3;Q96QB1	.;.;RHG07_HUMAN	N	84	ENSP00000276297:D84N;ENSP00000321034:D84N;ENSP00000425878:D84N	ENSP00000276297:D84N	D	-	1	0	DLC1	13401702	1.000000	0.71417	0.145000	0.22337	0.066000	0.16364	3.124000	0.50461	1.500000	0.48636	0.655000	0.94253	GAT	C|0.981;T|0.019	0.019	strong		0.453	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094		T	13357331	C	T	13357331	3	4	22	1	0	0	0	0	1	0	0	0	4552	855	30	2	4489	2	DLC1	8	13357331	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	478315	13357331	133006691	1866	4767											
ZDHHC2	51201	hgsc.bcm.edu	37	chr8	17067959	17067959	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggatcctgaacaagcatctaCtcctgcagggctgaattcca	11	9	9	12	0	1	2	0	2	1	0	4	3	4	3	3	2	4	3	3	2	4	2	rs190630185	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:17067959C>G	ENST00000262096.8	+	10	1615	c.920C>G	c.(919-921)aCt>aGt	p.T307S		NM_016353.4	NP_057437.1	Q9UIJ5	ZDHC2_HUMAN	zinc finger, DHHC-type containing 2	307					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)		CAAGCATCTACTCCTGCAGGG	0.328													C|||	8	0.00159744	0.0	0.0	5008	,	,		16046	0.0		0.008	False		,,,				2504	0.0				p.T307S		Atlas-SNP	.											.	ZDHHC2	25	.	0			c.C920G						PASS	.	C	SER/THR	1,3667		0,1,1833	69	64	65		920	5.5	1	8		65	28,8156		0,28,4064	yes	missense	ZDHHC2	NM_016353.4	58	0,29,5897	GG,GC,CC		0.3421,0.0273,0.2447	benign	307/368	17067959	29,11823	1834	4092	5926	SO:0001583	missense	51201	exon10			CATCTACTCCTGC	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.920C>G	8.37:g.17067959C>G	ENSP00000262096:p.Thr307Ser	58	0	0		76	37	0.486842	NM_016353	D3DSP5	Missense_Mutation	SNP	ENST00000262096.8	37	CCDS47810.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	8.049	0.765606	0.15914	2.73E-4	0.003421	ENSG00000104219	ENST00000262096	T	0.41758	0.99	5.53	5.53	0.82687	.	0.075692	0.51477	D	0.000086	T	0.23210	0.0561	N	0.22421	0.69	0.43160	D	0.994945	B	0.11235	0.004	B	0.08055	0.003	T	0.13710	-1.0499	10	0.08179	T	0.78	-3.0288	19.8416	0.96692	0.0:1.0:0.0:0.0	.	307	Q9UIJ5	ZDHC2_HUMAN	S	307	ENSP00000262096:T307S	ENSP00000262096:T307S	T	+	2	0	ZDHHC2	17112330	0.998000	0.40836	0.996000	0.52242	0.427000	0.31564	4.020000	0.57189	2.774000	0.95407	0.585000	0.79938	ACT	C|0.997;G|0.003	0.003	strong		0.328	ZDHHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376014.2	NM_016353		G	17067959	C	G	17067959	3	3	22	1	0	0	0	0	1	0	0	0	17625	565	20	4	958	4	ZDHHC2	8	17067959	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3710628	17067959	129296063	1867	4768											
PDGFRL	5157	hgsc.bcm.edu	37	chr8	17434813	17434813	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tggtgcacgaagcgctggagGatggtgagtgactctgggcg	7	8	19	7	3	1	2	0	2	1	0	1	5	1	4	0	5	2	2	0	5	1	0	rs114432448	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:17434813G>A	ENST00000541323.1	+	2	497	c.52G>A	c.(52-54)Gat>Aat	p.D18N	PDGFRL_ENST00000398074.3_Missense_Mutation_p.D18N|PDGFRL_ENST00000251630.6_Missense_Mutation_p.D18N	NM_006207.2	NP_006198.1	Q15198	PGFRL_HUMAN	platelet-derived growth factor receptor-like	18					G-protein coupled receptor signaling pathway (GO:0007186)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)	extracellular region (GO:0005576)	platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)	9				Colorectal(111;0.0752)		AGCGCTGGAGGATGGTGAGTG	0.677											OREG0018579	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	61	0.0121805	0.0431	0.0058	5008	,	,		10540	0.0		0.0	False		,,,				2504	0.0				p.D18N		Atlas-SNP	.											.	PDGFRL	27	.	0			c.G52A						PASS	.	G	ASN/ASP	171,4235	109.5+/-147.8	4,163,2036	54	51	52		52	0.6	0.7	8	dbSNP_132	52	0,8600		0,0,4300	yes	missense	PDGFRL	NM_006207.2	23	4,163,6336	AA,AG,GG		0.0,3.8811,1.3148	benign	18/376	17434813	171,12835	2203	4300	6503	SO:0001583	missense	5157	exon2			CTGGAGGATGGTG	D37965	CCDS6003.1	8p22-p21.3	2013-01-29			ENSG00000104213	ENSG00000104213		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	8805	protein-coding gene	gene with protein product		604584					Standard	NM_006207		Approved	PRLTS	uc003wxr.3	Q15198	OTTHUMG00000130818	ENST00000541323.1:c.52G>A	8.37:g.17434813G>A	ENSP00000444211:p.Asp18Asn	152	0	0	718	140	68	0.485714	NM_006207	A8K085|Q6FH04	Missense_Mutation	SNP	ENST00000541323.1	37	CCDS6003.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	G	3.726	-0.056629	0.07362	0.038811	0.0	ENSG00000104213	ENST00000251630;ENST00000541323;ENST00000398074	T;T;T	0.32023	1.47;1.47;1.47	3.59	0.567	0.17325	.	0.436898	0.23854	N	0.043902	T	0.02848	0.0085	N	0.22421	0.69	0.27009	N	0.964738	B	0.02656	0.0	B	0.01281	0.0	T	0.20538	-1.0272	10	0.09843	T	0.71	-12.0401	3.4884	0.07629	0.388:0.1982:0.4137:0.0	.	18	Q15198	PGFRL_HUMAN	N	18	ENSP00000251630:D18N;ENSP00000444211:D18N;ENSP00000381149:D18N	ENSP00000251630:D18N	D	+	1	0	PDGFRL	17479098	0.860000	0.29831	0.667000	0.29798	0.381000	0.30169	0.234000	0.17930	0.097000	0.17492	0.462000	0.41574	GAT	G|0.987;A|0.013	0.013	strong		0.677	PDGFRL-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253366.3	NM_006207		A	17434813	G	A	17434813	3	1	22	1	0	0	0	0	1	0	0	0	11672	1174	41	2	54	2	PDGFRL	8	17434813	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	366854	17434813	128929209	1868	4769											
MTUS1	57509	hgsc.bcm.edu	37	chr8	17612064	17612064	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttgtctgtgctaatgaccAtatcatttgcatcccaagtc	9	16	6	10	0	2	1	1	1	1	0	4	1	3	1	2	0	2	2	2	0	3	5	rs75253845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:17612064A>C	ENST00000262102.6	-	2	1477	c.1253T>G	c.(1252-1254)aTg>aGg	p.M418R	MTUS1_ENST00000381869.3_Missense_Mutation_p.M418R|MTUS1_ENST00000519263.1_Missense_Mutation_p.M418R|MTUS1_ENST00000381862.3_Missense_Mutation_p.M418R	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	418					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)		GCTAATGACCATATCATTTGC	0.443													A|||	134	0.0267572	0.0991	0.0043	5008	,	,		19985	0.0		0.0	False		,,,				2504	0.0				p.M418R		Atlas-SNP	.											.	MTUS1	144	.	0			c.T1253G						PASS	.	A	ARG/MET,ARG/MET	262,3548		9,244,1652	97	92	93		1253,1253	-3.9	0	8	dbSNP_131	93	0,8240		0,0,4120	yes	missense,missense	MTUS1	NM_001001924.2,NM_001001925.2	91,91	9,244,5772	CC,CA,AA		0.0,6.8766,2.1743	benign,benign	418/1271,418/1217	17612064	262,11788	1905	4120	6025	SO:0001583	missense	57509	exon2			ATGACCATATCAT	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.1253T>G	8.37:g.17612064A>C	ENSP00000262102:p.Met418Arg	147	0	0		134	68	0.507463	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	45	0.020604395604395604	44	0.08943089430894309	1	0.0027624309392265192	0	0.0	0	0.0	A	0.005	-2.138056	0.00335	0.068766	0.0	ENSG00000129422	ENST00000381869;ENST00000262102;ENST00000519263;ENST00000381862	T;T;T;T	0.17854	3.24;3.27;3.24;2.25	5.0	-3.89	0.04193	.	1.334190	0.04473	N	0.376484	T	0.00356	0.0011	N	0.24115	0.695	0.09310	N	1	B;B;B	0.30824	0.296;0.296;0.296	B;B;B	0.27380	0.079;0.037;0.053	T	0.23048	-1.0199	10	0.66056	D	0.02	1.3614	1.2801	0.02039	0.384:0.2677:0.2254:0.1229	.	418;418;418	Q9ULD2-5;Q9ULD2-2;Q9ULD2	.;.;MTUS1_HUMAN	R	418	ENSP00000371293:M418R;ENSP00000262102:M418R;ENSP00000430167:M418R;ENSP00000371286:M418R	ENSP00000262102:M418R	M	-	2	0	MTUS1	17656344	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	0.074000	0.14662	-0.755000	0.04709	-0.336000	0.08194	ATG	A|0.978;C|0.022	0.022	strong		0.443	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		C	17612064	A	C	17612064	3	2	22	1	0	0	0	0	1	0	0	0	9974	217	8	5	2934	5	MTUS1	8	17612064	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	177251	17612064	128751958	1869	4770											
SH2D4A	63898	hgsc.bcm.edu	37	chr8	19221784	19221784	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcaggggcatatcctcaaaAacctcttaggtaagaagcca	14	8	8	11	0	3	1	2	0	1	1	4	1	4	1	3	3	2	2	3	3	6	3	rs35319139	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:19221784A>G	ENST00000265807.3	+	7	1319	c.908A>G	c.(907-909)aAa>aGa	p.K303R	SH2D4A_ENST00000518040.1_Missense_Mutation_p.K258R|SH2D4A_ENST00000519207.1_Missense_Mutation_p.K303R	NM_001174160.1|NM_022071.3	NP_001167631.1|NP_071354.2	Q9H788	SH24A_HUMAN	SH2 domain containing 4A	303					negative regulation of phosphatase activity (GO:0010923)	cytoplasm (GO:0005737)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|stomach(1)	16				Colorectal(111;0.0732)		TATCCTCAAAAACCTCTTAGG	0.473													A|||	113	0.0225639	0.0825	0.0043	5008	,	,		16415	0.0		0.001	False		,,,				2504	0.0				p.K303R		Atlas-SNP	.											.	SH2D4A	49	.	0			c.A908G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS	338,4068	177.6+/-206.5	7,324,1872	52	50	51		908,773,908	2.1	0	8	dbSNP_126	51	0,8600		0,0,4300	yes	missense,missense,missense	SH2D4A	NM_001174159.1,NM_001174160.1,NM_022071.3	26,26,26	7,324,6172	GG,GA,AA		0.0,7.6714,2.5988	benign,benign,benign	303/455,258/410,303/455	19221784	338,12668	2203	4300	6503	SO:0001583	missense	63898	exon7			CTCAAAAACCTCT	AY190323	CCDS6009.1, CCDS55206.1	8p21	2013-02-14			ENSG00000104611	ENSG00000104611		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits", "SH2 domain containing"	26102	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 38"	614968					Standard	NM_022071		Approved	FLJ20967, SH2A, PPP1R38	uc003wzc.3	Q9H788	OTTHUMG00000097005	ENST00000265807.3:c.908A>G	8.37:g.19221784A>G	ENSP00000265807:p.Lys303Arg	89	0	0		67	32	0.477612	NM_022071	B4DDR1|Q5XKC1|Q6NXE9|Q86YM2|Q96C88|Q9H7F7	Missense_Mutation	SNP	ENST00000265807.3	37	CCDS6009.1	36	0.016483516483516484	34	0.06910569105691057	2	0.0055248618784530384	0	0.0	0	0.0	A	6.884	0.532610	0.13127	0.076714	0.0	ENSG00000104611	ENST00000265807;ENST00000518040;ENST00000519207	T;T;T	0.12672	2.66;2.66;2.66	5.75	2.12	0.27331	.	0.818608	0.11013	N	0.609227	T	0.00300	0.0009	N	0.04203	-0.255	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.45440	-0.9261	10	0.11794	T	0.64	.	4.2604	0.10739	0.6516:0.1741:0.1743:0.0	rs35319139	258;303	B4DDR1;Q9H788	.;SH24A_HUMAN	R	303;258;303	ENSP00000265807:K303R;ENSP00000429482:K258R;ENSP00000428684:K303R	ENSP00000265807:K303R	K	+	2	0	SH2D4A	19266064	0.000000	0.05858	0.000000	0.03702	0.779000	0.44077	0.275000	0.18698	0.443000	0.26582	0.460000	0.39030	AAA	A|0.973;G|0.027	0.027	strong		0.473	SH2D4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214094.1	NM_022071		G	19221784	A	G	19221784	3	3	22	1	0	0	0	0	1	0	0	0	14250	14	1	3	980	3	SH2D4A	8	19221784	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1609720	19221784	127142238	1870	4771											
LZTS1	11178	hgsc.bcm.edu	37	chr8	20107325	20107325	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcgctgtccccacgtgccaGctgctgcagggccttctcca	4	8	12	17	2	1	0	0	0	1	0	3	0	2	0	5	2	4	4	5	2	0	1	rs114929298	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:20107325G>C	ENST00000381569.1	-	4	2056	c.1699C>G	c.(1699-1701)Ctg>Gtg	p.L567V	LZTS1_ENST00000522290.1_Missense_Mutation_p.L508V|LZTS1_ENST00000265801.6_Missense_Mutation_p.L567V			Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1	567					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)		CCACGTGCCAGCTGCTGCAGG	0.617													g|||	19	0.00379393	0.0144	0.0	5008	,	,		18009	0.0		0.0	False		,,,				2504	0.0				p.L567V		Atlas-SNP	.											.	LZTS1	72	.	0			c.C1699G						PASS	.		VAL/LEU	46,4360	48.2+/-83.0	1,44,2158	86	87	87		1699	4.4	1	8	dbSNP_132	87	0,8600		0,0,4300	yes	missense	LZTS1	NM_021020.2	32	1,44,6458	CC,CG,GG		0.0,1.044,0.3537	probably-damaging	567/597	20107325	46,12960	2203	4300	6503	SO:0001583	missense	11178	exon3			GTGCCAGCTGCTG	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.1699C>G	8.37:g.20107325G>C	ENSP00000370981:p.Leu567Val	135	0	0		121	71	0.586777	NM_021020	D3DSQ6|Q9Y5V7|Q9Y5V8|Q9Y5V9|Q9Y5W0|Q9Y5W1|Q9Y5W2	Missense_Mutation	SNP	ENST00000381569.1	37	CCDS6015.1	12	0.005494505494505495	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	g	13.50	2.257140	0.39896	0.01044	0.0	ENSG00000061337	ENST00000381569;ENST00000265801;ENST00000522290;ENST00000360248	T;T;T	0.31769	1.59;1.59;1.48	5.28	4.4	0.53042	.	0.075319	0.53938	D	0.000043	T	0.17408	0.0418	N	0.08118	0	0.58432	D	0.99999	P;D	0.76494	0.884;0.999	B;D	0.66847	0.41;0.947	T	0.08351	-1.0726	10	0.36615	T	0.2	-20.5699	12.9504	0.58397	0.0808:0.0:0.9192:0.0	.	508;567	Q9Y250-4;Q9Y250	.;LZTS1_HUMAN	V	567;567;508;544	ENSP00000370981:L567V;ENSP00000265801:L567V;ENSP00000429263:L508V	ENSP00000265801:L567V	L	-	1	2	LZTS1	20151605	1.000000	0.71417	1.000000	0.80357	0.779000	0.44077	3.266000	0.51569	2.454000	0.82982	0.543000	0.68304	CTG	G|0.995;C|0.005	0.005	strong		0.617	LZTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214122.1	NM_021020		C	20107325	G	C	20107325	3	2	22	1	0	0	0	0	1	0	0	0	9147	962	34	4	95	4	LZTS1	8	20107325	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	885541	20107325	126256697	1871	4772											
LGI3	203190	hgsc.bcm.edu	37	chr8	22005939	22005939	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cgagccccgggagggcagggCctgcacctccgagaagcggg	7	2	18	14	4	0	1	0	0	0	1	1	4	1	2	5	4	3	2	5	4	1	0	rs559732127		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22005939C>T	ENST00000306317.2	-	8	1670	c.1381G>A	c.(1381-1383)Gcc>Acc	p.A461T	LGI3_ENST00000424267.2_Missense_Mutation_p.A437T	NM_139278.2	NP_644807.1	Q8N145	LGI3_HUMAN	leucine-rich repeat LGI family, member 3	461					exocytosis (GO:0006887)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|extracellular region (GO:0005576)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	catalytic activity (GO:0003824)			endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	17				Colorectal(74;0.00189)|COAD - Colon adenocarcinoma(73;0.0612)|READ - Rectum adenocarcinoma(644;0.0999)		GAGGGCAGGGCCTGCACCTCC	0.657													C|||	1	0.000199681	0.0008	0.0	5008	,	,		15389	0.0		0.0	False		,,,				2504	0.0				p.A461T		Atlas-SNP	.											.	LGI3	44	.	0			c.G1381A						PASS	.						30	30	30					8																	22005939		2203	4300	6503	SO:0001583	missense	203190	exon8			GCAGGGCCTGCAC	AJ487518	CCDS6025.1	8p21.2	2008-07-28			ENSG00000168481	ENSG00000168481			18711	protein-coding gene	gene with protein product		608302				12023020, 18628660	Standard	NM_139278		Approved		uc003xav.3	Q8N145	OTTHUMG00000131599	ENST00000306317.2:c.1381G>A	8.37:g.22005939C>T	ENSP00000302297:p.Ala461Thr	48	0	0		46	21	0.456522	NM_139278	A5PLP2|Q86TL4|Q8N296	Missense_Mutation	SNP	ENST00000306317.2	37	CCDS6025.1	.	.	.	.	.	.	.	.	.	.	C	13.05	2.122032	0.37436	.	.	ENSG00000168481	ENST00000306317;ENST00000424267	T;T	0.78924	-1.22;-1.22	5.19	5.19	0.71726	Six-bladed beta-propeller, TolB-like (1);	0.062211	0.64402	D	0.000004	T	0.49372	0.1553	N	0.01686	-0.76	0.35162	D	0.770725	B;B	0.16396	0.017;0.008	B;B	0.18561	0.022;0.012	T	0.55970	-0.8056	10	0.12430	T	0.62	-31.0187	9.7807	0.40647	0.0:0.9063:0.0:0.0937	.	437;461	A5PLP2;Q8N145	.;LGI3_HUMAN	T	461;437	ENSP00000302297:A461T;ENSP00000399121:A437T	ENSP00000302297:A461T	A	-	1	0	LGI3	22061884	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.203000	0.51075	2.396000	0.81511	0.561000	0.74099	GCC	.	.	none		0.657	LGI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254482.1			T	22005939	C	T	22005939	3	4	22	1	0	0	0	0	1	0	0	0	8762	739	26	2	269	2	LGI3	8	22005939	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1898614	22005939	124358083	1872	4773											
LGI3	203190	hgsc.bcm.edu	37	chr8	22009053	22009053	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcaacatagtcccacttcaGgatggtgcaggcactgactc	10	9	9	13	0	2	1	2	1	0	0	4	2	3	2	1	3	2	2	1	3	2	2	rs35142808	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22009053G>A	ENST00000306317.2	-	7	1067	c.778C>T	c.(778-780)Ctg>Ttg	p.L260L	LGI3_ENST00000424267.2_Silent_p.L236L	NM_139278.2	NP_644807.1	Q8N145	LGI3_HUMAN	leucine-rich repeat LGI family, member 3	260					exocytosis (GO:0006887)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|extracellular region (GO:0005576)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	catalytic activity (GO:0003824)			endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	17				Colorectal(74;0.00189)|COAD - Colon adenocarcinoma(73;0.0612)|READ - Rectum adenocarcinoma(644;0.0999)		TCCCACTTCAGGATGGTGCAG	0.602													G|||	174	0.0347444	0.1203	0.0043	5008	,	,		19819	0.0		0.003	False		,,,				2504	0.0092				p.L260L		Atlas-SNP	.											.	LGI3	44	.	0			c.C778T						PASS	.	G		467,3939	219.4+/-237.2	32,403,1768	87	89	89		778	4.2	0.8	8	dbSNP_126	89	25,8575	17.9+/-57.8	1,23,4276	no	coding-synonymous	LGI3	NM_139278.2		33,426,6044	AA,AG,GG		0.2907,10.5992,3.7829		260/549	22009053	492,12514	2203	4300	6503	SO:0001819	synonymous_variant	203190	exon7			ACTTCAGGATGGT	AJ487518	CCDS6025.1	8p21.2	2008-07-28			ENSG00000168481	ENSG00000168481			18711	protein-coding gene	gene with protein product		608302				12023020, 18628660	Standard	NM_139278		Approved		uc003xav.3	Q8N145	OTTHUMG00000131599	ENST00000306317.2:c.778C>T	8.37:g.22009053G>A		96	0	0		113	55	0.486726	NM_139278	A5PLP2|Q86TL4|Q8N296	Silent	SNP	ENST00000306317.2	37	CCDS6025.1																																																																																			G|0.968;A|0.032	0.032	strong		0.602	LGI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254482.1			A	22009053	G	A	22009053	2	1	22	1	0	0	0	0	0	0	0	1	8762	991	35	2		2	LGI3	8	22009053	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3114	22009053	124354969	1873	4774											
BMP1	649	hgsc.bcm.edu	37	chr8	22059413	22059413	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	tgccgcagtggcttcgtcctCcatgacaacaagcacgactg	9	8	10	14	3	0	1	0	1	0	0	3	2	2	1	3	1	3	3	3	1	2	1	rs28710878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22059413C>G	ENST00000306385.5	+	16	2875	c.2205C>G	c.(2203-2205)ctC>ctG	p.L735L	BMP1_ENST00000354870.5_3'UTR	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1	735	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of cartilage development (GO:0061036)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(3)	30				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)		GCTTCGTCCTCCATGACAACA	0.587													C|||	171	0.0341454	0.1218	0.0144	5008	,	,		20500	0.0		0.0	False		,,,				2504	0.0				p.L735L		Atlas-SNP	.											.	BMP1	131	.	0			c.C2205G						PASS	.	C		457,3949	210.8+/-231.2	22,413,1768	97	69	78		2205	-2	0.9	8	dbSNP_125	78	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	BMP1	NM_006129.4		22,415,6066	GG,GC,CC		0.0233,10.3722,3.5291		735/987	22059413	459,12547	2203	4300	6503	SO:0001819	synonymous_variant	649	exon16			CGTCCTCCATGAC		CCDS6026.1, CCDS34856.1	8p21	2013-02-06	2004-08-09		ENSG00000168487	ENSG00000168487	3.4.24.19	"Bone morphogenetic proteins"	1067	protein-coding gene	gene with protein product	"procollagen C-endopeptidase"	112264	"procollagen C-endopeptidase"	PCOLC		2004778	Standard	NM_006129		Approved		uc003xbg.3	P13497	OTTHUMG00000097761	ENST00000306385.5:c.2205C>G	8.37:g.22059413C>G		64	0	0		88	39	0.443182	NM_006129	A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Silent	SNP	ENST00000306385.5	37	CCDS6026.1																																																																																			C|0.970;G|0.030	0.030	strong		0.587	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132		G	22059413	C	G	22059413	2	3	22	1	0	0	0	0	0	0	0	1	1456	842	30	4		4	BMP1	8	22059413	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	50360	22059413	124304609	1874	4775											
POLR3D	661	hgsc.bcm.edu	37	chr8	22107707	22107707	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgggcaaggtgactctggaCgtgaccatgggaactgcctg	8	9	15	9	1	1	2	0	2	1	0	1	4	1	4	2	4	2	1	2	4	2	1	rs34435413	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22107707C>T	ENST00000397802.4	+	7	1256	c.1041C>T	c.(1039-1041)gaC>gaT	p.D347D	POLR3D_ENST00000306433.4_Silent_p.D347D			P05423	RPC4_HUMAN	polymerase (RNA) III (DNA directed) polypeptide D, 44kDa	347					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)		TGACTCTGGACGTGACCATGG	0.567													C|||	19	0.00379393	0.0144	0.0	5008	,	,		19108	0.0		0.0	False		,,,				2504	0.0				p.D347D		Atlas-SNP	.											.	POLR3D	26	.	0			c.C1041T						PASS	.	C		78,4328	68.1+/-105.8	0,78,2125	82	73	76		1041	-10.8	0.5	8	dbSNP_126	76	0,8600		0,0,4300	no	coding-synonymous	POLR3D	NM_001722.2		0,78,6425	TT,TC,CC		0.0,1.7703,0.5997		347/399	22107707	78,12928	2203	4300	6503	SO:0001819	synonymous_variant	661	exon8			TCTGGACGTGACC	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.1041C>T	8.37:g.22107707C>T		97	0	0		112	52	0.464286	NM_001722	Q6FI28|Q9BPV7|Q9BPZ1|Q9BXB3	Silent	SNP	ENST00000397802.4	37	CCDS34858.1																																																																																			C|0.993;T|0.007	0.007	strong		0.567	POLR3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375434.2	NM_001722		T	22107707	C	T	22107707	2	4	22	1	0	0	0	0	0	0	0	1	12240	535	19	1		1	POLR3D	8	22107707	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	48294	22107707	124256315	1875	4776											
KIAA1967	57805	hgsc.bcm.edu	37	chr8	22472473	22472473	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgtaccgccatccgctgtgcGcaggcccagactggcattga	7	7	12	15	4	0	2	0	1	0	1	1	2	1	2	4	2	2	4	4	2	1	2	rs112997942	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22472473G>A	ENST00000308511.4	+	11	1413	c.1164G>A	c.(1162-1164)gcG>gcA	p.A388A	RP11-582J16.5_ENST00000521025.1_RNA|CCAR2_ENST00000389279.3_Silent_p.A388A|CCAR2_ENST00000520861.1_Silent_p.A63A			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	388					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage checkpoint (GO:2000003)|regulation of circadian rhythm (GO:0042752)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of protein stability (GO:0031647)|response to UV (GO:0009411)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|DBIRD complex (GO:0044609)|mitochondrial matrix (GO:0005759)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)										TCCGCTGTGCGCAGGCCCAGA	0.627													G|||	37	0.00738818	0.0265	0.0029	5008	,	,		20145	0.0		0.0	False		,,,				2504	0.0				p.A388A		Atlas-SNP	.											.	KIAA1967	72	.	0			c.G1164A						PASS	.	G		87,4317	67.0+/-104.6	0,87,2115	46	34	38		1164	-11.1	0	8	dbSNP_132	38	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KIAA1967	NM_021174.5		0,88,6414	AA,AG,GG		0.0116,1.9755,0.6767		388/924	22472473	88,12916	2202	4300	6502	SO:0001819	synonymous_variant	57805	exon11			CTGTGCGCAGGCC	AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941			23360	protein-coding gene	gene with protein product	"deleted in breast cancer"	607359	"KIAA1967"	KIAA1967		12370419	Standard	NM_021174		Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.1164G>A	8.37:g.22472473G>A		86	0	0		107	52	0.485981	NM_021174	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Silent	SNP	ENST00000308511.4	37	CCDS34863.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	G	9.159	1.018179	0.19355	0.019755	1.16E-4	ENSG00000158941	ENST00000520738	.	.	.	5.53	-11.1	0.00147	.	.	.	.	.	T	0.25531	0.0621	.	.	.	0.40931	D	0.984397	.	.	.	.	.	.	T	0.49351	-0.8949	4	.	.	.	-11.8395	5.7525	0.18154	0.4761:0.2759:0.182:0.066	.	.	.	.	H	80	.	.	R	+	2	0	KIAA1967	22528418	0.000000	0.05858	0.010000	0.14722	0.924000	0.55760	-2.064000	0.01387	-2.862000	0.00326	-0.793000	0.03317	CGC	G|0.993;A|0.007	0.007	strong		0.627	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174		A	22472473	G	A	22472473	2	1	22	1	0	0	0	0	0	0	0	1	8274	1074	38	1		1	KIAA1967	8	22472473	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	364766	22472473	123891549	1876	4777											
KIAA1967	57805	hgsc.bcm.edu	37	chr8	22473646	22473646	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctgaacctgagaaggaggAggcggccaaggaagaagcca	15	2	15	9	1	0	3	0	2	0	2	0	7	0	6	4	5	2	0	4	5	5	0	rs143150726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22473646A>C	ENST00000308511.4	+	14	1979	c.1730A>C	c.(1729-1731)gAg>gCg	p.E577A	RP11-582J16.5_ENST00000521025.1_RNA|CCAR2_ENST00000389279.3_Missense_Mutation_p.E577A|CCAR2_ENST00000520861.1_Missense_Mutation_p.E252A			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	577					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage checkpoint (GO:2000003)|regulation of circadian rhythm (GO:0042752)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of protein stability (GO:0031647)|response to UV (GO:0009411)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|DBIRD complex (GO:0044609)|mitochondrial matrix (GO:0005759)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)										GAGAAGGAGGAGGCGGCCAAG	0.532													A|||	11	0.00219649	0.0045	0.0	5008	,	,		17062	0.003		0.0	False		,,,				2504	0.002				p.E577A		Atlas-SNP	.											.	KIAA1967	72	.	0			c.A1730C						PASS	.	A	ALA/GLU	14,4392	22.3+/-47.3	0,14,2189	91	87	88		1730	4.2	1	8	dbSNP_134	88	1,8599	1.2+/-3.3	0,1,4299	yes	missense	KIAA1967	NM_021174.5	107	0,15,6488	CC,CA,AA		0.0116,0.3177,0.1153	probably-damaging	577/924	22473646	15,12991	2203	4300	6503	SO:0001583	missense	57805	exon14			AGGAGGAGGCGGC	AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941			23360	protein-coding gene	gene with protein product	"deleted in breast cancer"	607359	"KIAA1967"	KIAA1967		12370419	Standard	NM_021174		Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.1730A>C	8.37:g.22473646A>C	ENSP00000310670:p.Glu577Ala	113	0	0		116	44	0.37931	NM_021174	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Missense_Mutation	SNP	ENST00000308511.4	37	CCDS34863.1	5	0.0022893772893772895	2	0.0040650406504065045	0	0.0	3	0.005244755244755245	0	0.0	A	15.25	2.777147	0.49786	0.003177	1.16E-4	ENSG00000158941	ENST00000308511;ENST00000389279;ENST00000520861	T;T;T	0.34667	1.37;1.37;1.35	5.41	4.24	0.50183	.	0.332894	0.27991	N	0.017029	T	0.16557	0.0398	N	0.19112	0.55	0.37034	D	0.896847	B;B	0.14805	0.011;0.007	B;B	0.16722	0.016;0.004	T	0.09840	-1.0656	10	0.23302	T	0.38	-22.2627	10.6868	0.45848	0.8393:0.1607:0.0:0.0	.	252;577	G3V119;Q8N163	.;K1967_HUMAN	A	577;577;252	ENSP00000310670:E577A;ENSP00000373930:E577A;ENSP00000429773:E252A	ENSP00000310670:E577A	E	+	2	0	KIAA1967	22529591	1.000000	0.71417	0.972000	0.41901	0.846000	0.48090	4.106000	0.57804	1.041000	0.40125	0.460000	0.39030	GAG	A|0.998;C|0.002	0.002	strong		0.532	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174		C	22473646	A	C	22473646	3	2	22	1	0	0	0	0	1	0	0	0	8274	304	11	5	1780	5	KIAA1967	8	22473646	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1173	22473646	123890376	1877	4778											
KIAA1967	57805	hgsc.bcm.edu	37	chr8	22476717	22476717	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaccaataagacgctggcggCagagatgcaggagctgcgag	13	4	15	9	3	0	2	0	0	0	2	0	5	0	3	1	3	4	4	1	3	3	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22476717C>T	ENST00000308511.4	+	20	2825	c.2576C>T	c.(2575-2577)gCa>gTa	p.A859V	BIN3_ENST00000519335.1_5'Flank|RP11-582J16.5_ENST00000521025.1_RNA|CCAR2_ENST00000389279.3_Missense_Mutation_p.A859V|CCAR2_ENST00000520861.1_Missense_Mutation_p.A534V			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	859	Interaction with NR1D1. {ECO:0000269|PubMed:23398316}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage checkpoint (GO:2000003)|regulation of circadian rhythm (GO:0042752)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of protein stability (GO:0031647)|response to UV (GO:0009411)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|DBIRD complex (GO:0044609)|mitochondrial matrix (GO:0005759)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)										ACGCTGGCGGCAGAGATGCAG	0.642																																					p.A859V		Atlas-SNP	.											.	KIAA1967	72	.	0			c.C2576T						PASS	.						16	16	16					8																	22476717		2197	4296	6493	SO:0001583	missense	57805	exon20			TGGCGGCAGAGAT	AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941			23360	protein-coding gene	gene with protein product	"deleted in breast cancer"	607359	"KIAA1967"	KIAA1967		12370419	Standard	NM_021174		Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.2576C>T	8.37:g.22476717C>T	ENSP00000310670:p.Ala859Val	92	0	0		107	51	0.476636	NM_021174	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Missense_Mutation	SNP	ENST00000308511.4	37	CCDS34863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.81|14.81	2.646522|2.646522	0.47258|0.47258	.|.	.|.	ENSG00000158941|ENSG00000158941	ENST00000308511;ENST00000389279;ENST00000520861|ENST00000520738	T;T;T|.	0.00453|.	7.33;7.33;7.33|.	5.44|5.44	4.57|4.57	0.56435|0.56435	.|.	0.147376|.	0.43260|.	D|.	0.000594|.	T|.	0.30916|.	0.0780|.	N|N	0.19112|0.19112	0.55|0.55	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|.	0.19160|.	-1.0314|.	10|.	0.36615|.	T|.	0.2|.	-8.609|-8.609	9.9844|9.9844	0.41832|0.41832	0.0:0.9094:0.0:0.0906|0.0:0.9094:0.0:0.0906	.|.	534;859|.	G3V119;Q8N163|.	.;K1967_HUMAN|.	V|X	859;859;534|551	ENSP00000310670:A859V;ENSP00000373930:A859V;ENSP00000429773:A534V|.	ENSP00000310670:A859V|.	A|Q	+|+	2|1	0|0	KIAA1967|KIAA1967	22532662|22532662	0.011000|0.011000	0.17503|0.17503	0.022000|0.022000	0.16811|0.16811	0.782000|0.782000	0.44232|0.44232	1.737000|1.737000	0.38197|0.38197	1.534000|1.534000	0.49203|0.49203	0.655000|0.655000	0.94253|0.94253	GCA|CAG	.	.	none		0.642	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174		T	22476717	C	T	22476717	3	4	22	1	0	0	0	0	1	0	0	0	8274	710	25	2	2650	2	KIAA1967	8	22476717	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3071	22476717	123887305	1878	4779											
TNFRSF10C	8794	hgsc.bcm.edu	37	chr8	22960654	22960654	+	Missense_Mutation	SNP	C	C	T																															catggcccggatccccaagaCcctaaagttcgtcgtcgtca																								rs10107826|rs374790272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22960654C>T	ENST00000356864.3	+	1	552	c.20C>T	c.(19-21)aCc>aTc	p.T7I	TNFRSF10C_ENST00000397703.2_Missense_Mutation_p.T47I|TNFRSF10C_ENST00000520607.1_Intron|TNFRSF10C_ENST00000540813.1_5'UTR	NM_003841.3	NP_003832	O14798	TR10C_HUMAN	tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain	7					apoptotic process (GO:0006915)|signal transduction (GO:0007165)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(6)|lung(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	15		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		ATCCCCAAGACCCTAAAGTTC	0.711													C|||	208	0.0415335	0.149	0.0101	5008	,	,		14783	0.0		0.004	False		,,,				2504	0.0				p.T7I		Atlas-SNP	.											.	TNFRSF10C	30	.	0			c.C20T						PASS	.	C	ILE/THR	443,3961	170.9+/-201.2	25,393,1784	79	59	66		20	0.6	0	8	dbSNP_119	66	12,8584	5.7+/-21.5	0,12,4286	yes	missense	TNFRSF10C	NM_003841.3	89	25,405,6070	TT,TC,CC		0.1396,10.059,3.5	probably-damaging	7/260	22960654	455,12545	2202	4298	6500	SO:0001583	missense	8794	exon1			CCAAGACCCTAAA	AF012536	CCDS6037.1	8p22-p21	2006-02-22			ENSG00000173535	ENSG00000173535		"Tumor necrosis factor receptor superfamily", "CD molecules"	11906	protein-coding gene	gene with protein product		603613				9314565, 9325248	Standard	NM_003841		Approved	DcR1, TRAILR3, LIT, TRID, CD263	uc003xcy.3	O14798	OTTHUMG00000097844	ENST00000356864.3:c.20C>T	8.37:g.22960654C>T	ENSP00000349324:p.Thr7Ile	75	0	0		82	40	0.487805	NM_003841	O14755|Q08AS6|Q6FH98|Q6UXM5	Missense_Mutation	SNP	ENST00000356864.3	37	CCDS6037.1	56	0.02564102564102564	50	0.1016260162601626	4	0.011049723756906077	0	0.0	2	0.002638522427440633	C	4.995	0.184796	0.09495	0.10059	0.001396	ENSG00000173535	ENST00000397703;ENST00000356864;ENST00000544885	T	0.62364	0.03	1.76	0.639	0.17747	.	2.630870	0.02547	U	0.095275	T	0.01627	0.0052	N	0.19112	0.55	0.52099	P	5.100000000002325E-5	B	0.21225	0.053	B	0.06405	0.002	T	0.08186	-1.0734	9	0.52906	T	0.07	.	4.4054	0.11407	0.0:0.717:0.0:0.283	rs10107826;rs10107826	7	O14798	TR10C_HUMAN	I	47;7;7	ENSP00000349324:T7I	ENSP00000349324:T7I	T	+	2	0	TNFRSF10C	23016599	0.000000	0.05858	0.001000	0.08648	0.053000	0.15095	-0.737000	0.04877	-0.010000	0.14271	0.205000	0.17691	ACC	C|0.958;T|0.042	0.042	strong		0.711	TNFRSF10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215134.3			T	22960654	C	T	22960654	3	4	22	1	0	0	0	0	1	0	0	0	16297	507	18	2	22	2	TNFRSF10C	8	22960654	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	483937	22960654	123403368	1879	4780	59	2									
TNFRSF10C	8794	hgsc.bcm.edu	37	chr8	22960655	22960655	+	Silent	SNP	C	C	T																															atggcccggatccccaagacCctaaagttcgtcgtcgtcat																								rs10107827|rs374790272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22960655C>T	ENST00000356864.3	+	1	553	c.21C>T	c.(19-21)acC>acT	p.T7T	TNFRSF10C_ENST00000397703.2_Silent_p.T47T|TNFRSF10C_ENST00000520607.1_Intron|TNFRSF10C_ENST00000540813.1_5'UTR	NM_003841.3	NP_003832	O14798	TR10C_HUMAN	tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain	7					apoptotic process (GO:0006915)|signal transduction (GO:0007165)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(6)|lung(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	15		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		TCCCCAAGACCCTAAAGTTCG	0.716													C|||	208	0.0415335	0.149	0.0101	5008	,	,		14742	0.0		0.004	False		,,,				2504	0.0				p.T7T		Atlas-SNP	.											.	TNFRSF10C	30	.	0			c.C21T						PASS	.	C		438,3966	169.8+/-200.3	25,388,1789	80	59	66		21	0.8	0	8	dbSNP_119	66	12,8586	5.0+/-18.6	0,12,4287	no	coding-synonymous	TNFRSF10C	NM_003841.3		25,400,6076	TT,TC,CC		0.1396,9.9455,3.461		7/260	22960655	450,12552	2202	4299	6501	SO:0001819	synonymous_variant	8794	exon1			CAAGACCCTAAAG	AF012536	CCDS6037.1	8p22-p21	2006-02-22			ENSG00000173535	ENSG00000173535		"Tumor necrosis factor receptor superfamily", "CD molecules"	11906	protein-coding gene	gene with protein product		603613				9314565, 9325248	Standard	NM_003841		Approved	DcR1, TRAILR3, LIT, TRID, CD263	uc003xcy.3	O14798	OTTHUMG00000097844	ENST00000356864.3:c.21C>T	8.37:g.22960655C>T		77	0	0		82	40	0.487805	NM_003841	O14755|Q08AS6|Q6FH98|Q6UXM5	Silent	SNP	ENST00000356864.3	37	CCDS6037.1																																																																																			.	.	alt		0.716	TNFRSF10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215134.3			T	22960655	C	T	22960655	2	4	22	1	0	0	0	0	0	0	0	1	16297	610	22	2		2	TNFRSF10C	8	22960655	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1	22960655	123403367	1880	4781	59	2									
ENTPD4	9583	hgsc.bcm.edu	37	chr8	23299225	23299225	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggaatgttaacttccacaaCggcctcatcatctagaaaga	15	9	7	10	1	3	2	2	0	1	2	4	3	4	3	2	2	2	1	2	2	5	3	rs34849865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:23299225C>T	ENST00000358689.4	-	8	974	c.739G>A	c.(739-741)Gtt>Att	p.V247I	ENTPD4_ENST00000356206.6_Missense_Mutation_p.V247I|ENTPD4_ENST00000417069.2_Missense_Mutation_p.V247I	NM_001128930.2|NM_004901.4	NP_001122402.1|NP_004892.1	Q9Y227	ENTP4_HUMAN	ectonucleoside triphosphate diphosphohydrolase 4	247					UDP catabolic process (GO:0006256)	cytoplasmic vesicle (GO:0031410)|integral component of Golgi membrane (GO:0030173)|intracellular membrane-bounded organelle (GO:0043231)	uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	25		Prostate(55;0.114)		Colorectal(74;0.0161)|COAD - Colon adenocarcinoma(73;0.0649)		ACTTCCACAACGGCCTCATCA	0.473													C|||	26	0.00519169	0.0197	0.0	5008	,	,		21884	0.0		0.0	False		,,,				2504	0.0				p.V247I		Atlas-SNP	.											.	ENTPD4	56	.	0			c.G739A						PASS	.	C	ILE/VAL,ILE/VAL	101,4305	81.9+/-120.4	1,99,2103	65	56	59		739,739	3.1	0.4	8	dbSNP_126	59	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	ENTPD4	NM_001128930.2,NM_004901.4	29,29	1,101,6401	TT,TC,CC		0.0233,2.2923,0.7919	benign,benign	247/609,247/617	23299225	103,12903	2203	4300	6503	SO:0001583	missense	9583	exon8			CCACAACGGCCTC	AJ131358	CCDS6041.1, CCDS47827.1	8p21.3	2014-05-16	2004-09-22	2004-09-22	ENSG00000197217	ENSG00000197217			14573	protein-coding gene	gene with protein product		607577	"lysosomal apyrase-like 1"	LYSAL1		10393803, 9205841	Standard	NM_001128930		Approved	LALP70, LAP70, KIAA0392, NTPDase-4, UDPase	uc003xdl.3	Q9Y227	OTTHUMG00000097852	ENST00000358689.4:c.739G>A	8.37:g.23299225C>T	ENSP00000351520:p.Val247Ile	55	0	0		59	39	0.661017	NM_004901	D3DSS3|O15092	Missense_Mutation	SNP	ENST00000358689.4	37	CCDS6041.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	C	12.07	1.826131	0.32237	0.022923	2.33E-4	ENSG00000197217	ENST00000356206;ENST00000358689;ENST00000417069	T;T;T	0.14144	2.57;2.53;2.58	5.87	3.1	0.35709	.	0.431567	0.26307	N	0.025140	T	0.05686	0.0149	L	0.49126	1.545	0.31429	N	0.673388	B;B;B	0.13594	0.008;0.003;0.003	B;B;B	0.15870	0.014;0.003;0.005	T	0.12192	-1.0557	10	0.25751	T	0.34	-13.4993	8.0326	0.30474	0.0:0.7229:0.1325:0.1446	rs34849865	247;247;247	Q8NE73;Q9Y227-2;Q9Y227	.;.;ENTP4_HUMAN	I	247	ENSP00000348536:V247I;ENSP00000351520:V247I;ENSP00000408573:V247I	ENSP00000348536:V247I	V	-	1	0	ENTPD4	23355170	0.005000	0.15991	0.412000	0.26496	0.832000	0.47134	0.266000	0.18534	0.385000	0.24970	0.655000	0.94253	GTT	C|0.993;T|0.007	0.007	strong		0.473	ENTPD4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215142.1	NM_004901		T	23299225	C	T	23299225	3	4	22	1	0	0	0	0	1	0	0	0	5143	536	19	1	1135	1	ENTPD4	8	23299225	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	338570	23299225	123064797	1881	4782											
SLC25A37	51312	hgsc.bcm.edu	37	chr8	23429093	23429093	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgggctggccggggccctcGccgcggccgccacgaccccc	2	2	16	21	7	0	0	0	0	0	0	1	1	0	0	7	5	0	1	7	5	0	0	rs116050502	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:23429093G>T	ENST00000519973.1	+	4	940	c.742G>T	c.(742-744)Gcc>Tcc	p.A248S	FP15737_ENST00000399967.3_5'Flank	NM_016612.2	NP_057696.2	Q9NYZ2	MFRN1_HUMAN	solute carrier family 25 (mitochondrial iron transporter), member 37	248					iron ion homeostasis (GO:0055072)|mitochondrial iron ion transport (GO:0048250)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	iron ion transmembrane transporter activity (GO:0005381)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|urinary_tract(1)	15		Prostate(55;0.114)		Colorectal(74;0.0198)|COAD - Colon adenocarcinoma(73;0.0751)		CGGGGCCCTCGCCGCGGCCGC	0.662													G|||	33	0.00658946	0.025	0.0	5008	,	,		12709	0.0		0.0	False		,,,				2504	0.0				p.A248S		Atlas-SNP	.											.	SLC25A37	27	.	0			c.G742T						PASS	.	G	SER/ALA	93,3715		1,91,1812	22	26	25		742	5.8	0.2	8	dbSNP_132	25	1,8197		0,1,4098	yes	missense	SLC25A37	NM_016612.2	99	1,92,5910	TT,TG,GG		0.0122,2.4422,0.7829	possibly-damaging	248/339	23429093	94,11912	1904	4099	6003	SO:0001583	missense	51312	exon4			GCCCTCGCCGCGG	AF495725	CCDS47828.1	8p21.2	2013-05-22	2012-03-29		ENSG00000147454	ENSG00000147454		"Solute carriers"	29786	protein-coding gene	gene with protein product	"mitoferrin"	610387	"solute carrier family 25, member 37"			16511496	Standard	XM_006716352		Approved	MSCP, MFRN, MFRN1	uc003xdo.3	Q9NYZ2	OTTHUMG00000163865	ENST00000519973.1:c.742G>T	8.37:g.23429093G>T	ENSP00000429200:p.Ala248Ser	50	0	0		65	40	0.615385	NM_016612	A2RU93|Q53FT7|Q69YJ8|Q969S1|Q9P0J2	Missense_Mutation	SNP	ENST00000519973.1	37	CCDS47828.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	20.5	3.994188	0.74703	0.024422	1.22E-4	ENSG00000147454	ENST00000519973	T	0.79653	-1.29	5.8	5.8	0.92144	Mitochondrial carrier domain (2);	0.049561	0.85682	D	0.000000	T	0.80149	0.4570	L	0.54965	1.715	0.58432	D	0.999999	D	0.58970	0.984	D	0.69479	0.964	D	0.84394	0.0556	10	0.66056	D	0.02	-8.3551	18.6148	0.91299	0.0:0.0:1.0:0.0	.	248	Q9NYZ2	MFRN1_HUMAN	S	248	ENSP00000429200:A248S	ENSP00000429200:A248S	A	+	1	0	SLC25A37	23485038	1.000000	0.71417	0.214000	0.23707	0.949000	0.60115	5.096000	0.64535	2.740000	0.93945	0.650000	0.86243	GCC	G|0.994;T|0.006	0.006	strong		0.662	SLC25A37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376039.1	NM_016612		T	23429093	G	T	23429093	3	4	22	1	0	0	0	0	1	0	0	0	14516	1087	38	4	756	4	SLC25A37	8	23429093	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	129868	23429093	122934929	1882	4783											
ADAM28	10863	hgsc.bcm.edu	37	chr8	24184088	24184088	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaacagaacttgctggaacGactgtgggtcttgcatttat	10	12	11	8	1	1	1	0	0	1	1	1	3	1	2	0	2	5	3	0	2	4	4	rs113950884	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24184088G>T	ENST00000265769.4	+	10	1022	c.912G>T	c.(910-912)acG>acT	p.T304T	RP11-624C23.1_ENST00000518988.1_RNA|ADAM28_ENST00000518516.1_3'UTR|ADAM28_ENST00000397649.3_Silent_p.T51T|RP11-624C23.1_ENST00000523700.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|ADAM28_ENST00000540823.1_Silent_p.T71T|ADAM28_ENST00000437154.2_Silent_p.T304T|RP11-624C23.1_ENST00000523578.1_RNA	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	304	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)		TTGCTGGAACGACTGTGGGTC	0.348													G|||	3	0.000599042	0.0023	0.0	5008	,	,		17957	0.0		0.0	False		,,,				2504	0.0				p.T304T	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											.	ADAM28	100	.	0			c.G912T						PASS	.	G	,	20,4386	27.2+/-55.0	0,20,2183	316	276	289		912,912	-11	0	8	dbSNP_132	289	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ADAM28	NM_014265.4,NM_021777.3	,	0,20,6483	TT,TG,GG		0.0,0.4539,0.1538	,	304/776,304/541	24184088	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	10863	exon10			TGGAACGACTGTG	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.912G>T	8.37:g.24184088G>T		217	0	0		216	106	0.490741	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Silent	SNP	ENST00000265769.4	37	CCDS34865.1																																																																																			G|0.998;T|0.002	0.002	strong		0.348	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778		T	24184088	G	T	24184088	2	4	22	1	0	0	0	0	0	0	0	1	246	1045	37	4		4	ADAM28	8	24184088	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	754995	24184088	122179934	1883	4784											
ADAM28	10863	hgsc.bcm.edu	37	chr8	24184128	24184129	+	In_Frame_Ins	INS	-	-	ATC																															gtctacaatgtgttctccttINSattctgttggcgttgttcag																								rs111491080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24184128_24184129insATC	ENST00000265769.4	+	10	1062_1063	c.952_953insATC	c.(952-954)tat>tATCat	p.318_319insH	RP11-624C23.1_ENST00000518988.1_RNA|ADAM28_ENST00000518516.1_3'UTR|ADAM28_ENST00000397649.3_In_Frame_Ins_p.65_66insH|RP11-624C23.1_ENST00000523700.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|ADAM28_ENST00000540823.1_In_Frame_Ins_p.85_86insH|ADAM28_ENST00000437154.2_In_Frame_Ins_p.318_319insH|RP11-624C23.1_ENST00000523578.1_RNA	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	318	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)		GTGTTCTCCTTATTCTGTTGGC	0.332														3	0.000599042	0.0023	0.0	5008	,	,		18291	0.0		0.0	False		,,,				2504	0.0				p.Y318delinsYH	NSCLC(193;488 2149 22258 34798 40734)	Pindel,Atlas-Indel	.											.	ADAM28	100	.	0			c.952_953insATC						PASS	.		,	20,4244		0,20,2112					,	4.3	1		dbSNP_132	294	0,8252		0,0,4126	no	coding,coding	ADAM28	NM_021777.3,NM_014265.4	,	0,20,6238	A1A1,A1R,RR		0.0,0.469,0.1598	,	,		20,12496				SO:0001652	inframe_insertion	10863	exon10			.	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	8.37:g.24184128_24184129insATC	ENSP00000265769:p.Tyr318_Ser319insHis	269	0	.		282	83	0.294	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	In_Frame_Ins	INS	ENST00000265769.4	37	CCDS34865.1																																																																																			-|0.500;ATC|0.500	0.500	weak		0.332	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778		ATC	24184129	-	ATC	24184128	7	5	22	1	0	1	1	0	0	0	0	0	246	1754	61	0	990	0	ADAM28	8	24184128	In_Frame_Ins	INS	-	TCGA-G8-6324-01A-11D-2210-10	40	24184128	122179894	1884	4785											
ADAMDEC1	27299	hgsc.bcm.edu	37	chr8	24250809	24250809	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagttcaatatcagatgaTcttaaatggagaagaaatca	18	11	8	4	0	4	5	3	2	1	3	4	6	4	5	0	1	0	1	0	1	7	3	rs77012108	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24250809T>C	ENST00000256412.4	+	3	462	c.242T>C	c.(241-243)aTc>aCc	p.I81T	RP11-624C23.1_ENST00000519689.1_RNA|ADAMDEC1_ENST00000522298.1_Missense_Mutation_p.I2T|RP11-624C23.1_ENST00000523578.1_RNA|ADAMDEC1_ENST00000538205.1_Missense_Mutation_p.I2T	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	81					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)		TATCAGATGATCTTAAATGGA	0.303													t|||	120	0.0239617	0.087	0.0072	5008	,	,		16054	0.0		0.0	False		,,,				2504	0.0				p.I81T	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											ADAMDEC1,arm,malignant_melanoma,-1,1	ADAMDEC1	69	1	0			c.T242C						PASS	.	C	THR/ILE,THR/ILE,THR/ILE	356,4050	176.6+/-205.7	19,318,1866	64	68	66		5,5,242	-10.9	0	8	dbSNP_131	66	2,8594	2.2+/-6.3	0,2,4296	yes	missense,missense,missense	ADAMDEC1	NM_001145271.1,NM_001145272.1,NM_014479.3	89,89,89	19,320,6162	CC,CT,TT		0.0233,8.0799,2.7534	benign,benign,benign	2/392,2/392,81/471	24250809	358,12644	2203	4298	6501	SO:0001583	missense	27299	exon3			AGATGATCTTAAA	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.242T>C	8.37:g.24250809T>C	ENSP00000256412:p.Ile81Thr	124	0	0		127	68	0.535433	NM_014479	B7ZAK5	Missense_Mutation	SNP	ENST00000256412.4	37	CCDS6044.1	44	0.020146520146520148	41	0.08333333333333333	3	0.008287292817679558	0	0.0	0	0.0	t	0.013	-1.643647	0.00792	0.080799	2.33E-4	ENSG00000134028	ENST00000256412;ENST00000538205;ENST00000522298	T;T;T	0.04758	3.56;4.16;4.16	5.47	-10.9	0.00192	Peptidase M12B, propeptide (1);	1.393200	0.04190	N	0.328203	T	0.00144	0.0004	N	0.10837	0.055	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.41088	-0.9528	10	0.09843	T	0.71	0.1711	6.3932	0.21599	0.0997:0.5309:0.2221:0.1472	.	81	O15204	ADEC1_HUMAN	T	81;2;2	ENSP00000256412:I81T;ENSP00000442592:I2T;ENSP00000428993:I2T	ENSP00000256412:I81T	I	+	2	0	ADAMDEC1	24306754	0.000000	0.05858	0.001000	0.08648	0.254000	0.26022	-2.948000	0.00679	-1.756000	0.01318	-0.359000	0.07587	ATC	T|0.973;C|0.027	0.027	strong		0.303	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479		C	24250809	T	C	24250809	3	2	22	1	0	0	0	0	1	0	0	0	254	1435	50	3	252	3	ADAMDEC1	8	24250809	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	66681	24250809	122113213	1885	4786											
ADAMDEC1	27299	hgsc.bcm.edu	37	chr8	24251659	24251659	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taccacgaaacctgagaacaTggtagggtccgaatactttg	13	9	10	9	2	0	1	0	1	0	1	1	4	1	1	3	2	4	1	3	2	6	4	rs7007084	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24251659T>C	ENST00000256412.4	+	4	582	c.362T>C	c.(361-363)aTg>aCg	p.M121T	RP11-624C23.1_ENST00000519689.1_RNA|ADAMDEC1_ENST00000522298.1_Splice_Site_p.M42T|RP11-624C23.1_ENST00000523578.1_RNA|ADAMDEC1_ENST00000538205.1_Splice_Site_p.M42T	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	121			M -> T (in dbSNP:rs7007084).		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)		CCTGAGAACATGGTAGGGTCC	0.423													T|||	133	0.0265575	0.0968	0.0072	5008	,	,		18292	0.0		0.0	False		,,,				2504	0.0				p.M121T	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											.	ADAMDEC1	69	.	0			c.T362C						PASS	.	T	THR/MET,THR/MET,THR/MET	391,4015	191.6+/-217.2	21,349,1833	72	68	69		125,125,362	-0.3	0.2	8	dbSNP_116	69	3,8597	3.0+/-9.4	0,3,4297	yes	missense-near-splice,missense-near-splice,missense-near-splice	ADAMDEC1	NM_001145271.1,NM_001145272.1,NM_014479.3	81,81,81	21,352,6130	CC,CT,TT		0.0349,8.8743,3.0294	benign,benign,benign	42/392,42/392,121/471	24251659	394,12612	2203	4300	6503	SO:0001630	splice_region_variant	27299	exon4			AGAACATGGTAGG	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.363+1T>C	8.37:g.24251659T>C		76	0	0		65	32	0.492308	NM_014479	B7ZAK5	Missense_Mutation	SNP	ENST00000256412.4	37	CCDS6044.1	49	0.022435897435897436	46	0.09349593495934959	3	0.008287292817679558	0	0.0	0	0.0	T	0.640	-0.813614	0.02798	0.088743	3.49E-4	ENSG00000134028	ENST00000256412;ENST00000538205;ENST00000522298	T;T;T	0.05139	3.49;3.49;3.49	5.46	-0.309	0.12769	Peptidase M12B, propeptide (1);	0.592394	0.17862	N	0.159489	T	0.00144	0.0004	N	0.17872	0.535	0.09310	N	0.999996	B	0.11235	0.004	B	0.08055	0.003	T	0.43718	-0.9374	10	0.37606	T	0.19	-3.7358	1.3321	0.02137	0.3046:0.0864:0.1576:0.4513	rs7007084;rs52800945;rs7007084	121	O15204	ADEC1_HUMAN	T	121;42;42	ENSP00000256412:M121T;ENSP00000442592:M42T;ENSP00000428993:M42T	ENSP00000256412:M121T	M	+	2	0	ADAMDEC1	24307604	0.195000	0.23338	0.163000	0.22734	0.026000	0.11368	0.147000	0.16202	0.072000	0.16694	-0.371000	0.07208	ATG	T|0.967;C|0.033	0.033	strong		0.423	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479	Missense_Mutation	C	24251659	T	C	24251659	5	2	22	1	0	0	0	0	0	0	1	0	254	1478	51	3	376	3	ADAMDEC1	8	24251659	Splice_Site	SNP	T	TCGA-G8-6324-01A-11D-2210-10	850	24251659	122112363	1886	4787											
ADAMDEC1	27299	hgsc.bcm.edu	37	chr8	24256389	24256389	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taaatgctctttccacagatAtataacaccatagatgttca	15	13	4	9	0	2	2	1	0	1	2	3	2	3	2	2	0	2	2	2	0	6	7	rs7001097	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24256389A>T	ENST00000256412.4	+	9	985	c.765A>T	c.(763-765)atA>atT	p.I255I	RP11-624C23.1_ENST00000519689.1_RNA|ADAMDEC1_ENST00000522298.1_Silent_p.I176I|RP11-624C23.1_ENST00000523578.1_RNA|ADAMDEC1_ENST00000538205.1_Silent_p.I176I	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	255	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)		TTCCACAGATATATAACACCA	0.413													T|||	88	0.0175719	0.0635	0.0058	5008	,	,		20707	0.0		0.0	False		,,,				2504	0.0				p.I255I	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											.	ADAMDEC1	69	.	0			c.A765T						PASS	.	T	,,	261,4145	803.2+/-415.7	11,239,1953	92	91	91		528,528,765	0.2	0.9	8	dbSNP_116	91	2,8598	818.9+/-406.8	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	ADAMDEC1	NM_001145271.1,NM_001145272.1,NM_014479.3	,,	11,241,6251	TT,TA,AA		0.0233,5.9237,2.0221	,,	176/392,176/392,255/471	24256389	263,12743	2203	4300	6503	SO:0001819	synonymous_variant	27299	exon9			ACAGATATATAAC	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.765A>T	8.37:g.24256389A>T		80	0	0		113	51	0.451327	NM_014479	B7ZAK5	Silent	SNP	ENST00000256412.4	37	CCDS6044.1																																																																																			A|0.977;T|0.023	0.023	strong		0.413	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479		T	24256389	A	T	24256389	2	4	22	1	0	0	0	0	0	0	0	1	254	439	16	5		5	ADAMDEC1	8	24256389	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	4730	24256389	122107633	1887	4788											
ADAMDEC1	27299	hgsc.bcm.edu	37	chr8	24256512	24256512	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcctgagatggcacagttcTaacctggggaaaaagatcca	13	9	10	9	0	1	2	0	1	1	2	3	4	3	3	3	3	1	2	3	3	3	3	rs7005258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24256512T>C	ENST00000256412.4	+	9	1108	c.888T>C	c.(886-888)tcT>tcC	p.S296S	RP11-624C23.1_ENST00000519689.1_RNA|ADAMDEC1_ENST00000522298.1_Silent_p.S217S|RP11-624C23.1_ENST00000523578.1_RNA|ADAMDEC1_ENST00000538205.1_Silent_p.S217S	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	296	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)		GGCACAGTTCTAACCTGGGGA	0.517													C|||	88	0.0175719	0.0635	0.0058	5008	,	,		18805	0.0		0.0	False		,,,				2504	0.0				p.S296S	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											.	ADAMDEC1	69	.	0			c.T888C						PASS	.	C	,,	261,4145	803.2+/-415.7	11,239,1953	102	90	94		651,651,888	-0.3	0	8	dbSNP_116	94	2,8598	819.2+/-406.8	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	ADAMDEC1	NM_001145271.1,NM_001145272.1,NM_014479.3	,,	11,241,6251	CC,CT,TT		0.0233,5.9237,2.0221	,,	217/392,217/392,296/471	24256512	263,12743	2203	4300	6503	SO:0001819	synonymous_variant	27299	exon9			CAGTTCTAACCTG	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.888T>C	8.37:g.24256512T>C		114	0	0		133	56	0.421053	NM_014479	B7ZAK5	Silent	SNP	ENST00000256412.4	37	CCDS6044.1																																																																																			T|0.977;C|0.023	0.023	strong		0.517	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479		C	24256512	T	C	24256512	2	2	22	1	0	0	0	0	0	0	0	1	254	1509	53	3		3	ADAMDEC1	8	24256512	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	123	24256512	122107510	1888	4789											
ADAMDEC1	27299	hgsc.bcm.edu	37	chr8	24259600	24259600	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	aagactgtgattgtggctctCctaaggtattatttattaga	11	16	9	5	0	1	3	0	1	1	2	2	3	1	3	1	2	0	2	1	2	6	7	rs76707982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24259600C>T	ENST00000256412.4	+	12	1535	c.1315C>T	c.(1315-1317)Cct>Tct	p.P439S	RP11-624C23.1_ENST00000519689.1_RNA|ADAMDEC1_ENST00000522298.1_Missense_Mutation_p.P360S|RP11-624C23.1_ENST00000523578.1_RNA|ADAMDEC1_ENST00000538205.1_Missense_Mutation_p.P360S	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	439	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				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)		TTGTGGCTCTCCTAAGGTATT	0.368													C|||	72	0.014377	0.053	0.0029	5008	,	,		16709	0.0		0.0	False		,,,				2504	0.0				p.P439S	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											ADAMDEC1_ENST00000256412,NS,malignant_melanoma,-1,1	ADAMDEC1	69	1	0			c.C1315T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO	219,4187	127.8+/-164.7	6,207,1990	77	79	78		1078,1078,1315	3.4	1	8	dbSNP_131	78	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	ADAMDEC1	NM_001145271.1,NM_001145272.1,NM_014479.3	74,74,74	6,208,6289	TT,TC,CC		0.0116,4.9705,1.6915	probably-damaging,probably-damaging,probably-damaging	360/392,360/392,439/471	24259600	220,12786	2203	4300	6503	SO:0001583	missense	27299	exon12			GGCTCTCCTAAGG	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.1315C>T	8.37:g.24259600C>T	ENSP00000256412:p.Pro439Ser	53	0	0		61	39	0.639344	NM_014479	B7ZAK5	Missense_Mutation	SNP	ENST00000256412.4	37	CCDS6044.1	29	0.013278388278388278	28	0.056910569105691054	1	0.0027624309392265192	0	0.0	0	0.0	C	12.49	1.952501	0.34471	0.049705	1.16E-4	ENSG00000134028	ENST00000256412;ENST00000538205;ENST00000522298	T;T;T	0.10860	2.83;2.83;2.83	6.16	3.43	0.39272	Blood coagulation inhibitor, Disintegrin (3);	0.377504	0.26176	N	0.025893	T	0.01156	0.0038	L	0.47190	1.495	0.44188	D	0.997006	P	0.35192	0.489	B	0.39935	0.314	T	0.20472	-1.0274	10	0.38643	T	0.18	-5.4888	8.4866	0.33076	0.0:0.7617:0.0:0.2383	.	439	O15204	ADEC1_HUMAN	S	439;360;360	ENSP00000256412:P439S;ENSP00000442592:P360S;ENSP00000428993:P360S	ENSP00000256412:P439S	P	+	1	0	ADAMDEC1	24315545	0.000000	0.05858	1.000000	0.80357	0.989000	0.77384	-0.002000	0.12924	0.486000	0.27676	0.650000	0.86243	CCT	C|0.983;T|0.017	0.017	strong		0.368	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479		T	24259600	C	T	24259600	3	4	22	1	0	0	0	0	1	0	0	0	254	855	30	2	1361	2	ADAMDEC1	8	24259600	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3088	24259600	122104422	1889	4790											
ADAMDEC1	27299	hgsc.bcm.edu	37	chr8	24261518	24261518	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgtgtgtgctttgaaggaGtgtaccaatctctgctgtga	7	15	13	6	0	1	2	0	2	1	0	2	3	1	3	1	1	3	3	1	1	3	2	rs61731545	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24261518G>A	ENST00000256412.4	+	13	1543	c.1323G>A	c.(1321-1323)gaG>gaA	p.E441E	RP11-624C23.1_ENST00000519689.1_RNA|ADAMDEC1_ENST00000522298.1_Silent_p.E362E|RP11-624C23.1_ENST00000523578.1_RNA|ADAMDEC1_ENST00000538205.1_Silent_p.E362E	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	441	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				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)		CTTTGAAGGAGTGTACCAATC	0.433													A|||	87	0.0173722	0.0628	0.0058	5008	,	,		17414	0.0		0.0	False		,,,				2504	0.0				p.E441E	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											.	ADAMDEC1	69	.	0			c.G1323A						PASS	.	A	,,	259,4147	802.9+/-415.7	10,239,1954	210	177	188		1086,1086,1323	-2.6	0.7	8	dbSNP_129	188	2,8598	818.9+/-406.8	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	ADAMDEC1	NM_001145271.1,NM_001145272.1,NM_014479.3	,,	10,241,6252	AA,AG,GG		0.0233,5.8783,2.0068	,,	362/392,362/392,441/471	24261518	261,12745	2203	4300	6503	SO:0001819	synonymous_variant	27299	exon13			GAAGGAGTGTACC	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.1323G>A	8.37:g.24261518G>A		113	0	0		121	61	0.504132	NM_014479	B7ZAK5	Silent	SNP	ENST00000256412.4	37	CCDS6044.1																																																																																			G|0.979;A|0.021	0.021	strong		0.433	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479		A	24261518	G	A	24261518	2	1	22	1	0	0	0	0	0	0	0	1	254	1020	36	2		2	ADAMDEC1	8	24261518	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1918	24261518	122102504	1890	4791											
ADAM7	8756	hgsc.bcm.edu	37	chr8	24349482	24349482	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	attttcctgagatgtgcactGgccactcgcctgcctgtcct	5	13	9	14	1	0	1	0	1	0	1	3	2	2	1	5	1	2	1	5	1	0	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24349482G>A	ENST00000175238.6	+	14	1506	c.1423G>A	c.(1423-1425)Ggc>Agc	p.G475S	ADAM7_ENST00000520720.1_Missense_Mutation_p.G247S|RP11-624C23.1_ENST00000519689.1_RNA|ADAM7_ENST00000380789.1_Missense_Mutation_p.G475S|RP11-561E1.1_ENST00000519364.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	475	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)		GATGTGCACTGGCCACTCGCC	0.463																																					p.G475S		Atlas-SNP	.											ADAM7,colon,carcinoma,-2,1	ADAM7	165	1	0			c.G1423A						PASS	.																																			SO:0001583	missense	8756	exon14			TGCACTGGCCACT	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.1423G>A	8.37:g.24349482G>A	ENSP00000175238:p.Gly475Ser	130	0	0		97	57	0.587629	NM_003817	A8K8X7|O75959|Q6PEJ6	Missense_Mutation	SNP	ENST00000175238.6	37	CCDS6045.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.891293	0.91889	.	.	ENSG00000069206	ENST00000175238;ENST00000380789;ENST00000520720;ENST00000335595	T;T;T	0.57107	0.42;0.42;0.42	5.78	5.78	0.91487	Blood coagulation inhibitor, Disintegrin (6);	0.000000	0.56097	D	0.000026	D	0.83889	0.5352	H	0.98487	4.245	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.89755	0.3943	10	0.87932	D	0	.	17.5062	0.87746	0.0:0.0:1.0:0.0	.	247;475	E5RK87;Q9H2U9	.;ADAM7_HUMAN	S	475;475;247;290	ENSP00000175238:G475S;ENSP00000370166:G475S;ENSP00000430400:G247S	ENSP00000175238:G475S	G	+	1	0	ADAM7	24405372	1.000000	0.71417	0.997000	0.53966	0.784000	0.44337	7.643000	0.83403	2.749000	0.94314	0.655000	0.94253	GGC	.	.	none		0.463	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817		A	24349482	G	A	24349482	3	1	22	1	0	0	0	0	1	0	0	0	251	1348	47	2	1477	2	ADAM7	8	24349482	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	87964	24349482	122014540	1891	4792											
NEFM	4741	hgsc.bcm.edu	37	chr8	24771318	24771318	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcctccaagatgagctacacGttggactcgctgggcaaccc	9	7	11	14	2	0	2	0	1	0	1	2	3	1	3	3	2	3	4	3	2	3	2	rs61735462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24771318G>A	ENST00000221166.5	+	1	794	c.12G>A	c.(10-12)acG>acA	p.T4T	RP11-624C23.1_ENST00000519689.1_RNA|NEFM_ENST00000433454.2_5'Flank|NEFM_ENST00000437366.2_Silent_p.T4T|NEFM_ENST00000521540.1_3'UTR|NEFM_ENST00000518131.1_Silent_p.T4T|GS1-72M22.1_ENST00000607058.1_RNA			P07197	NFM_HUMAN	neurofilament, medium polypeptide	4	Head.				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)	p.?(1)		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)		TGAGCTACACGTTGGACTCGC	0.697													g|||	42	0.00838658	0.031	0.0	5008	,	,		13480	0.0		0.001	False		,,,				2504	0.0				p.T4T		Atlas-SNP	.											.	NEFM	115	.	1	Unknown(1)	breast(1)	c.G12A						PASS	.			92,4278		0,92,2093	13	16	15		12	-0.2	0.9	8	dbSNP_129	15	3,8561		0,3,4279	no	coding-synonymous	NEFM	NM_005382.2		0,95,6372	AA,AG,GG		0.035,2.1053,0.7345		4/917	24771318	95,12839	2185	4282	6467	SO:0001819	synonymous_variant	4741	exon1			CTACACGTTGGAC	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.12G>A	8.37:g.24771318G>A		68	0	0		81	34	0.419753	NM_005382	B4DGN2|E9PBF7|Q4QRK6	Silent	SNP	ENST00000221166.5	37	CCDS6046.1																																																																																			G|0.992;A|0.008	0.008	strong		0.697	NEFM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254954.2	NM_005382		A	24771318	G	A	24771318	2	1	22	1	0	0	0	0	0	0	0	1	10325	1132	40	1		1	NEFM	8	24771318	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	421836	24771318	121592704	1892	4793											
DOCK5	80005	hgsc.bcm.edu	37	chr8	25149590	25149590	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagcagatgacgtacagcctGatcgagtggcggtcccagat	10	7	13	11	3	0	4	0	2	0	2	2	5	1	4	2	2	3	2	2	2	1	1	rs35475676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:25149590G>A	ENST00000276440.7	+	6	416	c.372G>A	c.(370-372)ctG>ctA	p.L124L	DOCK5_ENST00000481100.1_Silent_p.L124L	NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	124					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)		CGTACAGCCTGATCGAGTGGC	0.483													G|||	59	0.0117812	0.0416	0.0058	5008	,	,		18104	0.0		0.0	False		,,,				2504	0.0				p.L124L	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											.	DOCK5	167	.	0			c.G372A						PASS	.	G		213,4193	121.7+/-159.2	8,197,1998	38	36	36		372	3.7	1	8	dbSNP_126	36	0,8600		0,0,4300	yes	coding-synonymous	DOCK5	NM_024940.6		8,197,6298	AA,AG,GG		0.0,4.8343,1.6377		124/1871	25149590	213,12793	2203	4300	6503	SO:0001819	synonymous_variant	80005	exon6			CAGCCTGATCGAG		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.372G>A	8.37:g.25149590G>A		96	0	0		111	51	0.459459	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Silent	SNP	ENST00000276440.7	37	CCDS6047.1																																																																																			G|0.983;A|0.017	0.017	strong		0.483	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940		A	25149590	G	A	25149590	2	1	22	1	0	0	0	0	0	0	0	1	4692	1277	45	2		2	DOCK5	8	25149590	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	378272	25149590	121214432	1893	4794											
CLU	1191	hgsc.bcm.edu	37	chr8	27457507	27457507	+	Silent	SNP	G	G	C																															cgccgcagcttagcctgggaGgggttgttggtggaacagtc																								rs9331937	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:27457507G>C	ENST00000316403.10	-	7	1359	c.954C>G	c.(952-954)ccC>ccG	p.P318P	CLU_ENST00000405140.3_Silent_p.P318P|CLU_ENST00000523500.1_Silent_p.P318P|CLU_ENST00000546343.1_Silent_p.P329P|CLU_ENST00000560366.1_Silent_p.P370P			P10909	CLUS_HUMAN	clusterin	318					blood coagulation (GO:0007596)|cell morphogenesis (GO:0000902)|central nervous system myelin maintenance (GO:0032286)|chaperone-mediated protein complex assembly (GO:0051131)|chaperone-mediated protein folding (GO:0061077)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|lipid metabolic process (GO:0006629)|microglial cell activation (GO:0001774)|microglial cell proliferation (GO:0061518)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of protein homooligomerization (GO:0032463)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of neurofibrillary tangle assembly (GO:1902998)|positive regulation of neuron death (GO:1901216)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of tau-protein kinase activity (GO:1902949)|positive regulation of tumor necrosis factor production (GO:0032760)|protein import (GO:0017038)|protein stabilization (GO:0050821)|regulation of beta-amyloid clearance (GO:1900221)|regulation of neuron death (GO:1901214)|regulation of neuronal signal transduction (GO:1902847)|release of cytochrome c from mitochondria (GO:0001836)|response to misfolded protein (GO:0051788)|response to virus (GO:0009615)|reverse cholesterol transport (GO:0043691)	apical dendrite (GO:0097440)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|spherical high-density lipoprotein particle (GO:0034366)	misfolded protein binding (GO:0051787)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)	21		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|Colorectal(74;0.132)		TAGCCTGGGAGGGGTTGTTGG	0.522													G|||	144	0.028754	0.1059	0.0058	5008	,	,		20885	0.0		0.0	False		,,,				2504	0.0				p.P318P		Atlas-SNP	.											.	CLU	54	.	0			c.C954G						PASS	.	G		375,4031	191.2+/-216.9	12,351,1840	57	54	55		954	-8.3	0	8	dbSNP_119	55	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	CLU	NM_203339.2		12,353,6138	CC,CG,GG		0.0233,8.5111,2.8987		318/450	27457507	377,12629	2203	4300	6503	SO:0001819	synonymous_variant	1191	exon7			CTGGGAGGGGTTG	M64722	CCDS47832.1	8p21-p12	2012-11-30	2006-02-10		ENSG00000120885	ENSG00000120885			2095	protein-coding gene	gene with protein product	"complement lysis inhibitor", "sulfated glycoprotein 2", "testosterone-repressed prostate message 2", "apolipoprotein J"	185430	"clusterin (complement lysis inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone-repressed prostate message 2, apolipoprotein J)"	CLI, APOJ		1585460	Standard	NR_038335		Approved	SGP-2, SP-40, TRPM-2, KUB1, CLU1, CLU2	uc003xfz.2	P10909	OTTHUMG00000102114	ENST00000316403.10:c.954C>G	8.37:g.27457507G>C		84	0	0		86	38	0.44186	NM_001831	B2R9Q1|B3KSE6|P11380|P11381|Q2TU75|Q5HYC1|Q7Z5B9	Silent	SNP	ENST00000316403.10	37	CCDS47832.1	54|54	0.024725274725274724|0.024725274725274724	51|51	0.10365853658536585|0.10365853658536585	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	G|G	5.885|5.885	0.347360|0.347360	0.11126|0.11126	0.085111|0.085111	2.33E-4|2.33E-4	ENSG00000120885|ENSG00000120885	ENST00000522098|ENST00000521770	.|T	.|0.38401	.|1.14	5.62|5.62	-8.32|-8.32	0.00996|0.00996	.|.	.|0.050523	.|0.85682	.|D	.|0.000000	T|T	0.00724|0.00724	0.0024|0.0024	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.38134|0.38134	-0.9675|-0.9675	4|7	.|0.87932	.|D	.|0	-28.8002|-28.8002	0.2978|0.2978	0.00268|0.00268	0.2607:0.255:0.2311:0.2532|0.2607:0.255:0.2311:0.2532	rs9331937;rs9331937|rs9331937;rs9331937	.|.	.|.	.|.	V|R	181|9	.|ENSP00000428033:P9R	.|ENSP00000428033:P9R	L|P	-|-	1|2	0|0	CLU|CLU	27513424|27513424	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.009000|0.009000	0.06853|0.06853	-3.122000|-3.122000	0.00594|0.00594	-1.333000|-1.333000	0.02247|0.02247	0.655000|0.655000	0.94253|0.94253	CTC|CCT	G|0.973;C|0.027	0.027	strong		0.522	CLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219953.3	NM_001831		C	27457507	G	C	27457507	2	2	22	1	0	0	0	0	0	0	0	1	3570	987	35	4		4	CLU	8	27457507	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2307917	27457507	118906515	1894	4795	60	2									
CLU	1191	hgsc.bcm.edu	37	chr8	27457512	27457512	+	Missense_Mutation	SNP	T	T	G																															cagcttagcctgggaggggtTgttggtggaacagtctgccc																								rs9331936	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:27457512T>G	ENST00000316403.10	-	7	1354	c.949A>C	c.(949-951)Aac>Cac	p.N317H	CLU_ENST00000405140.3_Missense_Mutation_p.N317H|CLU_ENST00000523500.1_Missense_Mutation_p.N317H|CLU_ENST00000546343.1_Missense_Mutation_p.N328H|CLU_ENST00000560366.1_Missense_Mutation_p.N369H			P10909	CLUS_HUMAN	clusterin	317			N -> H (in dbSNP:rs9331936). {ECO:0000269|Ref.6}.		blood coagulation (GO:0007596)|cell morphogenesis (GO:0000902)|central nervous system myelin maintenance (GO:0032286)|chaperone-mediated protein complex assembly (GO:0051131)|chaperone-mediated protein folding (GO:0061077)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|lipid metabolic process (GO:0006629)|microglial cell activation (GO:0001774)|microglial cell proliferation (GO:0061518)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of protein homooligomerization (GO:0032463)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of neurofibrillary tangle assembly (GO:1902998)|positive regulation of neuron death (GO:1901216)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of tau-protein kinase activity (GO:1902949)|positive regulation of tumor necrosis factor production (GO:0032760)|protein import (GO:0017038)|protein stabilization (GO:0050821)|regulation of beta-amyloid clearance (GO:1900221)|regulation of neuron death (GO:1901214)|regulation of neuronal signal transduction (GO:1902847)|release of cytochrome c from mitochondria (GO:0001836)|response to misfolded protein (GO:0051788)|response to virus (GO:0009615)|reverse cholesterol transport (GO:0043691)	apical dendrite (GO:0097440)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|spherical high-density lipoprotein particle (GO:0034366)	misfolded protein binding (GO:0051787)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)	21		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|Colorectal(74;0.132)		TGGGAGGGGTTGTTGGTGGAA	0.527													T|||	327	0.0652955	0.2398	0.013	5008	,	,		20819	0.0		0.001	False		,,,				2504	0.0				p.N317H		Atlas-SNP	.											.	CLU	54	.	0			c.A949C						PASS	.	T	HIS/ASN	869,3537	336.3+/-304.3	81,707,1415	57	53	54		949	-1.3	0	8	dbSNP_119	54	10,8590	7.1+/-27.0	0,10,4290	yes	missense	CLU	NM_203339.2	68	81,717,5705	GG,GT,TT		0.1163,19.7231,6.7584	probably-damaging	317/450	27457512	879,12127	2203	4300	6503	SO:0001583	missense	1191	exon7			AGGGGTTGTTGGT	M64722	CCDS47832.1	8p21-p12	2012-11-30	2006-02-10		ENSG00000120885	ENSG00000120885			2095	protein-coding gene	gene with protein product	"complement lysis inhibitor", "sulfated glycoprotein 2", "testosterone-repressed prostate message 2", "apolipoprotein J"	185430	"clusterin (complement lysis inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone-repressed prostate message 2, apolipoprotein J)"	CLI, APOJ		1585460	Standard	NR_038335		Approved	SGP-2, SP-40, TRPM-2, KUB1, CLU1, CLU2	uc003xfz.2	P10909	OTTHUMG00000102114	ENST00000316403.10:c.949A>C	8.37:g.27457512T>G	ENSP00000315130:p.Asn317His	78	0	0		81	45	0.555556	NM_001831	B2R9Q1|B3KSE6|P11380|P11381|Q2TU75|Q5HYC1|Q7Z5B9	Missense_Mutation	SNP	ENST00000316403.10	37	CCDS47832.1	135|135	0.061813186813186816|0.061813186813186816	131|131	0.266260162601626|0.266260162601626	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	0|0	0.0|0.0	T|T	15.93|15.93	2.978011|2.978011	0.53720|0.53720	0.197231|0.197231	0.001163|0.001163	ENSG00000120885|ENSG00000120885	ENST00000316403;ENST00000546343;ENST00000405140;ENST00000523500;ENST00000380446;ENST00000520012|ENST00000522098	T;T;T|.	0.24350|.	1.86;1.86;1.86|.	5.62|5.62	-1.32|-1.32	0.09201|0.09201	Clusterin, C-terminal (1);|.	0.361968|.	0.34603|.	N|.	0.003825|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.76838|0.76838	2.35|2.35	0.80722|0.80722	P|P	0.0|0.0	D;D;D;D|.	0.76494|.	0.998;0.999;0.999;0.999|.	D;D;D;D|.	0.72338|.	0.972;0.974;0.974;0.977|.	T|T	0.11591|0.11591	-1.0581|-1.0581	9|4	0.62326|.	D|.	0.03|.	-24.2564|-24.2564	5.937|5.937	0.19171|0.19171	0.0:0.4821:0.1723:0.3456|0.0:0.4821:0.1723:0.3456	rs9331936;rs11555230|rs9331936;rs11555230	182;369;328;317|.	E7ETA7;P10909-2;P10909-5;P10909|.	.;.;.;CLUS_HUMAN|.	H|P	369;328;317;317;142;182|179	ENSP00000446413:N328H;ENSP00000385419:N317H;ENSP00000429620:N317H|.	ENSP00000315130:N369H|.	N|Q	-|-	1|2	0|0	CLU|CLU	27513429|27513429	1.000000|1.000000	0.71417|0.71417	0.002000|0.002000	0.10522|0.10522	0.004000|0.004000	0.04260|0.04260	2.424000|2.424000	0.44714|0.44714	-0.154000|-0.154000	0.11118|0.11118	-0.250000|-0.250000	0.11733|0.11733	AAC|CAA	T|0.922;G|0.078	0.078	strong		0.527	CLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219953.3	NM_001831		G	27457512	T	G	27457512	3	3	22	1	0	0	0	0	1	0	0	0	3570	1812	63	5	412	5	CLU	8	27457512	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	5	27457512	118906510	1895	4796	60	2									
CLU	1191	hgsc.bcm.edu	37	chr8	27468005	27468005	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tactcaccctggagctcattGtctgagaccgtctggtcccc	6	11	9	15	1	4	1	2	1	2	1	5	3	5	2	4	2	2	1	4	2	1	2	rs9331892	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:27468005G>A	ENST00000316403.10	-	2	489	c.84C>T	c.(82-84)gaC>gaT	p.D28D	CLU_ENST00000405140.3_Silent_p.D28D|CLU_ENST00000523500.1_Silent_p.D28D|CLU_ENST00000546343.1_Silent_p.D39D|CLU_ENST00000560366.1_Silent_p.D80D			P10909	CLUS_HUMAN	clusterin	28				D -> S (in Ref. 9; AA sequence and 13; AA sequence). {ECO:0000305}.	blood coagulation (GO:0007596)|cell morphogenesis (GO:0000902)|central nervous system myelin maintenance (GO:0032286)|chaperone-mediated protein complex assembly (GO:0051131)|chaperone-mediated protein folding (GO:0061077)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|lipid metabolic process (GO:0006629)|microglial cell activation (GO:0001774)|microglial cell proliferation (GO:0061518)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of protein homooligomerization (GO:0032463)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of neurofibrillary tangle assembly (GO:1902998)|positive regulation of neuron death (GO:1901216)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of tau-protein kinase activity (GO:1902949)|positive regulation of tumor necrosis factor production (GO:0032760)|protein import (GO:0017038)|protein stabilization (GO:0050821)|regulation of beta-amyloid clearance (GO:1900221)|regulation of neuron death (GO:1901214)|regulation of neuronal signal transduction (GO:1902847)|release of cytochrome c from mitochondria (GO:0001836)|response to misfolded protein (GO:0051788)|response to virus (GO:0009615)|reverse cholesterol transport (GO:0043691)	apical dendrite (GO:0097440)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|spherical high-density lipoprotein particle (GO:0034366)	misfolded protein binding (GO:0051787)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)	21		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|Colorectal(74;0.132)		GGAGCTCATTGTCTGAGACCG	0.562													G|||	286	0.0571086	0.2095	0.013	5008	,	,		20395	0.0		0.0	False		,,,				2504	0.0				p.D28D		Atlas-SNP	.											.	CLU	54	.	0			c.C84T						PASS	.	G		775,3631	313.3+/-293.0	65,645,1493	114	103	107		84	2.2	0	8	dbSNP_119	107	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	CLU	NM_203339.2		65,653,5785	AA,AG,GG		0.093,17.5897,6.0203		28/450	27468005	783,12223	2203	4300	6503	SO:0001819	synonymous_variant	1191	exon2			CTCATTGTCTGAG	M64722	CCDS47832.1	8p21-p12	2012-11-30	2006-02-10		ENSG00000120885	ENSG00000120885			2095	protein-coding gene	gene with protein product	"complement lysis inhibitor", "sulfated glycoprotein 2", "testosterone-repressed prostate message 2", "apolipoprotein J"	185430	"clusterin (complement lysis inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone-repressed prostate message 2, apolipoprotein J)"	CLI, APOJ		1585460	Standard	NR_038335		Approved	SGP-2, SP-40, TRPM-2, KUB1, CLU1, CLU2	uc003xfz.2	P10909	OTTHUMG00000102114	ENST00000316403.10:c.84C>T	8.37:g.27468005G>A		116	0	0		138	53	0.384058	NM_001831	B2R9Q1|B3KSE6|P11380|P11381|Q2TU75|Q5HYC1|Q7Z5B9	Silent	SNP	ENST00000316403.10	37	CCDS47832.1																																																																																			G|0.944;A|0.056	0.056	strong		0.562	CLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219953.3	NM_001831		A	27468005	G	A	27468005	2	1	22	1	0	0	0	0	0	0	0	1	3570	1368	48	2		2	CLU	8	27468005	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	10493	27468005	118896017	1896	4797											
PBK	55872	hgsc.bcm.edu	37	chr8	27668587	27668587	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttgtcagtaataacaccattCtcctccacagcttctttggg	9	14	6	12	0	3	0	1	0	2	0	5	0	4	0	3	1	2	2	3	1	2	6	rs17057901	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:27668587C>G	ENST00000301905.4	-	7	1123	c.660G>C	c.(658-660)gaG>gaC	p.E220D	ESCO2_ENST00000397418.2_Intron|PBK_ENST00000522944.1_Missense_Mutation_p.E231D	NM_018492.2	NP_060962.2	Q96KB5	TOPK_HUMAN	PDZ binding kinase	220	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		E -> D (in dbSNP:rs17057901).		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)		TAACACCATTCTCCTCCACAG	0.428													C|||	105	0.0209665	0.0741	0.0101	5008	,	,		19638	0.0		0.0	False		,,,				2504	0.0				p.E220D		Atlas-SNP	.											.	PBK	29	.	0			c.G660C						PASS	.	C	ASP/GLU	299,4107	163.6+/-195.4	12,275,1916	134	114	121		660	-1.1	0.8	8	dbSNP_123	121	4,8596	3.7+/-12.6	0,4,4296	yes	missense	PBK	NM_018492.2	45	12,279,6212	GG,GC,CC		0.0465,6.7862,2.3297	benign	220/323	27668587	303,12703	2203	4300	6503	SO:0001583	missense	55872	exon7			ACCATTCTCCTCC	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.660G>C	8.37:g.27668587C>G	ENSP00000301905:p.Glu220Asp	176	0	0		139	67	0.482014	NM_018492	B4DX68|D3DST2|Q9NPD9|Q9NYL7|Q9NZK6	Missense_Mutation	SNP	ENST00000301905.4	37	CCDS6063.1	31	0.014194139194139194	28	0.056910569105691054	3	0.008287292817679558	0	0.0	0	0.0	C	13.60	2.284682	0.40394	0.067862	4.65E-4	ENSG00000168078	ENST00000301905;ENST00000522944	T;T	0.33654	1.4;1.4	5.49	-1.13	0.09775	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.043945	0.85682	D	0.000000	T	0.01661	0.0053	N	0.21448	0.665	0.44843	D	0.997853	B;B	0.24675	0.109;0.04	B;B	0.35312	0.2;0.075	T	0.06770	-1.0808	10	0.15066	T	0.55	-24.1822	10.3658	0.44024	0.0:0.4018:0.0:0.5982	rs17057901;rs17057901	231;220	B4DX68;Q96KB5	.;TOPK_HUMAN	D	220;231	ENSP00000301905:E220D;ENSP00000428489:E231D	ENSP00000301905:E220D	E	-	3	2	PBK	27724506	0.005000	0.15991	0.807000	0.32361	0.928000	0.56348	-0.940000	0.03929	-0.140000	0.11394	0.655000	0.94253	GAG	C|0.978;G|0.022	0.022	strong		0.428	PBK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219952.2	NM_018492		G	27668587	C	G	27668587	3	3	22	1	0	0	0	0	1	0	0	0	11497	912	32	4	316	4	PBK	8	27668587	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	200582	27668587	118695435	1897	4798											
SCARA5	286133	hgsc.bcm.edu	37	chr8	27779652	27779672	+	In_Frame_Del	DEL	GCAGCGGAGCCTGCAGCAGCC	GCAGCGGAGCCTGCAGCAGCC	-																															ctgctccgtcaggtccgcttGcagcggagcctgcagcagcc																								rs556775167|rs370651084|rs544481270	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GCAGCGGAGCCTGCAGCAGCC	GCAGCGGAGCCTGCAGCAGCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:27779652_27779672delGCAGCGGAGCCTGCAGCAGCC	ENST00000354914.3	-	4	817_837	c.332_352delGGCTGCTGCAGGCTCCGCTGC	c.(331-354)cggctgctgcaggctccgctgcaa>caa	p.RLLQAPL111del	SCARA5_ENST00000518030.1_In_Frame_Del_p.RLLQAPL68del|SCARA5_ENST00000301906.4_In_Frame_Del_p.RLLQAPL68del|SCARA5_ENST00000524352.1_In_Frame_Del_p.RLLQAPL111del|SCARA5_ENST00000380385.2_Intron	NM_173833.5	NP_776194.2	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5	111					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)		AGGTCCGCTTGCAGCGGAGCCTGCAGCAGCCGCAGCTGCAA	0.67														4	0.000798722	0.003	0.0	5008	,	,		20679	0.0		0.0	False		,,,				2504	0.0				p.111_118del		Pindel,Atlas-Indel	.											.	SCARA5	53	.	0			c.333_353del						PASS	.			5,4237		1,3,2117						3.1	1			13	9,8227		3,3,4112	no	coding	SCARA5	NM_173833.5		4,6,6229	A1A1,A1R,RR		0.1093,0.1179,0.1122				14,12464				SO:0001651	inframe_deletion	286133	exon4			.	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.332_352delGGCTGCTGCAGGCTCCGCTGC	8.37:g.27779652_27779672delGCAGCGGAGCCTGCAGCAGCC	ENSP00000346990:p.Arg111_Leu117del	97	0	.		53	26	0.491	NM_173833	Q6UXZ1|Q7Z4A1|Q8N4Z7	In_Frame_Del	DEL	ENST00000354914.3	37	CCDS6064.1																																																																																			.	.	none		0.67	SCARA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255223.2	NM_173833		-	27779672	GCAGCGGAGCCTGCAGCAGCC	-	27779652	7	5	22	1	0	1	0	1	0	0	0	0	13895	1328	46	0	1159	0	SCARA5	8	27779652	In_Frame_Del	DEL	GCAGCGGAGCCTGCAGCAGCC	TCGA-G8-6324-01A-11D-2210-10	111065	27779652	118584370	1898	4799											
C8orf80	389643	hgsc.bcm.edu	37	chr8	27925220	27925220	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgctcagctcctccgtcctAtgcaggagtttggtcaggtt	5	13	11	12	1	2	0	2	0	0	0	5	1	5	1	3	3	3	5	3	3	1	3	rs114951850	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:27925220A>G	ENST00000413272.2	-	6	664	c.522T>C	c.(520-522)caT>caC	p.H174H	NUGGC_ENST00000341513.6_Silent_p.H174H	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	174					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)										CCTCCGTCCTATGCAGGAGTT	0.547													A|||	104	0.0207668	0.0756	0.0058	5008	,	,		18753	0.0		0.0	False		,,,				2504	0.0				p.H174H		Atlas-SNP	.											.	.	.	.	0			c.T522C						PASS	.	A		193,3875		6,181,1847	68	69	69		522	-2.4	0	8	dbSNP_132	69	5,8431		0,5,4213	no	coding-synonymous	C8orf80	NM_001010906.1		6,186,6060	GG,GA,AA		0.0593,4.7443,1.5835		174/797	27925220	198,12306	2034	4218	6252	SO:0001819	synonymous_variant	389643	exon6			CGTCCTATGCAGG	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.522T>C	8.37:g.27925220A>G		212	0	0		247	130	0.526316	NM_001010906	Q6ZP73	Silent	SNP	ENST00000413272.2	37	CCDS47833.1																																																																																			A|0.985;G|0.015	0.015	strong		0.547	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906		G	27925220	A	G	27925220	2	3	22	1	0	0	0	0	0	0	0	1	2441	446	16	3		3	C8orf80	8	27925220	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	145568	27925220	118438802	1899	4800											
FBXO16	157574	hgsc.bcm.edu	37	chr8	28321153	28321153	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacaacgacaaaggctccgAgggtccaggaaagaaaagat	17	3	12	9	2	0	2	0	0	0	2	2	5	2	3	2	3	1	2	2	3	5	0	rs7822086	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:28321153A>G	ENST00000380254.2	-	4	466	c.318T>C	c.(316-318)ccT>ccC	p.P106P	FBXO16_ENST00000518734.1_Silent_p.P94P|FBXO16_ENST00000517436.1_5'UTR|FBXO16_ENST00000346498.2_Silent_p.P94P	NM_001258211.1|NM_172366.3	NP_001245140.1|NP_758954.1	Q8IX29	FBX16_HUMAN	F-box protein 16	106	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.									large_intestine(2)|ovary(1)	3		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.121)|Kidney(114;0.144)|Colorectal(74;0.249)		AAAGGCTCCGAGGGTCCAGGA	0.443													G|||	308	0.0615016	0.2194	0.0101	5008	,	,		20959	0.005		0.001	False		,,,				2504	0.0051				p.P106P		Atlas-SNP	.											.	FBXO16	29	.	0			c.T318C						PASS	.	G		735,3671	720.3+/-409.0	73,589,1541	55	53	54		318	2.7	1	8	dbSNP_116	54	8,8592	818.7+/-406.8	0,8,4292	no	coding-synonymous	FBXO16	NM_172366.2		73,597,5833	GG,GA,AA		0.093,16.6818,5.7127		106/293	28321153	743,12263	2203	4300	6503	SO:0001819	synonymous_variant	157574	exon4			GCTCCGAGGGTCC	AF453435	CCDS6068.1, CCDS59099.1	8p21.1	2008-02-05	2004-06-15		ENSG00000214050	ENSG00000214050		"F-boxes /  "other""	13618	protein-coding gene	gene with protein product		608519	"F-box only protein 16"			12243353	Standard	NM_172366		Approved	FBX16	uc003xgu.4	Q8IX29	OTTHUMG00000102147	ENST00000380254.2:c.318T>C	8.37:g.28321153A>G		172	0	0		133	58	0.43609	NM_172366	Q3T1B2|Q3T1B3|Q3T1B4	Silent	SNP	ENST00000380254.2	37	CCDS6068.1																																																																																			A|0.932;G|0.068	0.068	strong		0.443	FBXO16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219988.2	NM_172366		G	28321153	A	G	28321153	2	3	22	1	0	0	0	0	0	0	0	1	5737	291	11	3		3	FBXO16	8	28321153	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	395933	28321153	118042869	1900	4801											
FZD3	7976	hgsc.bcm.edu	37	chr8	28413375	28413375	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tccactcaaggaacatccacCcatgcttcttcaactcagct	11	10	4	16	0	4	0	3	0	1	0	6	1	6	1	3	1	4	2	3	1	3	2	rs62001924	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:28413375C>T	ENST00000240093.3	+	7	2152	c.1674C>T	c.(1672-1674)acC>acT	p.T558T	FZD3_ENST00000537916.1_Silent_p.T558T	NM_017412.3	NP_059108.1	Q9NPG1	FZD3_HUMAN	frizzled class receptor 3	558					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)		GAACATCCACCCATGCTTCTT	0.488													C|||	76	0.0151757	0.0575	0.0	5008	,	,		19431	0.0		0.0	False		,,,				2504	0.0				p.T558T		Atlas-SNP	.											.	FZD3	65	.	0			c.C1674T						PASS	.	C	,	204,4202	124.9+/-162.1	3,198,2002	95	77	83		1674,1674	0.3	1	8	dbSNP_129	83	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	FZD3	NM_017412.3,NM_145866.1	,	3,198,6302	TT,TC,CC		0.0,4.63,1.5685	,	558/667,558/667	28413375	204,12802	2203	4300	6503	SO:0001819	synonymous_variant	7976	exon7			ATCCACCCATGCT	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.1674C>T	8.37:g.28413375C>T		124	0	0		100	58	0.58	NM_017412	A8K615	Silent	SNP	ENST00000240093.3	37	CCDS6069.1																																																																																			C|0.984;T|0.016	0.016	strong		0.488	FZD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219986.2	NM_145866		T	28413375	C	T	28413375	2	4	22	1	0	0	0	0	0	0	0	1	6139	610	22	2		2	FZD3	8	28413375	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	92222	28413375	117950647	1901	4802											
TMEM66	51669	hgsc.bcm.edu	37	chr8	29927182	29927182	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gaactcagacttaaagcctgGgggaggaggtcctgctgagt	10	8	15	8	0	1	2	1	1	0	1	2	5	2	4	2	4	3	1	2	4	3	1	rs34416759	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:29927182G>A	ENST00000256255.6	-	3	933	c.676C>T	c.(676-678)Cca>Tca	p.P226S	TMEM66_ENST00000536273.1_Missense_Mutation_p.P54S|TMEM66_ENST00000545648.1_Missense_Mutation_p.P54S	NM_016127.4	NP_057211.4	Q96BY9	SARAF_HUMAN		226					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)		TTAAAGCCTGGGGGAGGAGGT	0.507													G|||	44	0.00878594	0.031	0.0043	5008	,	,		18064	0.0		0.0	False		,,,				2504	0.0				p.P226S		Atlas-SNP	.											.	TMEM66	23	.	0			c.C676T						PASS	.	G	SER/PRO	135,4271	95.3+/-134.0	4,127,2072	119	102	108		676	-0.4	0	8	dbSNP_126	108	0,8600		0,0,4300	yes	missense	TMEM66	NM_016127.4	74	4,127,6372	AA,AG,GG		0.0,3.064,1.038	benign	226/340	29927182	135,12871	2203	4300	6503	SO:0001583	missense	51669	exon3			AGCCTGGGGGAGG																												ENST00000256255.6:c.676C>T	8.37:g.29927182G>A	ENSP00000256255:p.Pro226Ser	126	0	0		159	64	0.402516	NM_016127	B3KQQ4|B7Z9J1|D3DSU7|H9MHJ8|H9MHJ9|Q53HE8|Q9UNZ3|Q9Y683	Missense_Mutation	SNP	ENST00000256255.6	37	CCDS6074.1	16|16	0.007326007326007326|0.007326007326007326	15|15	0.03048780487804878|0.03048780487804878	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	G|G	13.64|13.64	2.296786|2.296786	0.40594|0.40594	0.03064|0.03064	0.0|0.0	ENSG00000133872|ENSG00000133872	ENST00000518296|ENST00000256255;ENST00000545648;ENST00000541035;ENST00000536273;ENST00000523127;ENST00000522794	T|T;T;T;T;T	0.58940|0.57752	0.3|0.38;0.38;0.38;0.38;0.38	5.82|5.82	-0.4|-0.4	0.12411|0.12411	.|.	0.360290|0.360290	0.32244|0.32244	N|N	0.006371|0.006371	T|T	0.21427|0.21427	0.0516|0.0516	L|L	0.61036|0.61036	1.89|1.89	0.41958|0.41958	D|D	0.990696|0.990696	.|B;B	.|0.25390	.|0.125;0.125	.|B;B	.|0.27170	.|0.077;0.077	T|T	0.09751|0.09751	-1.0660|-1.0660	8|10	0.72032|0.48119	D|T	0.01|0.1	-4.2187|-4.2187	7.801|7.801	0.29174|0.29174	0.0663:0.457:0.3642:0.1125|0.0663:0.457:0.3642:0.1125	rs34416759|rs34416759	.|226;226	.|B3KQQ4;Q96BY9	.|.;TMM66_HUMAN	L|S	95|226;54;190;54;124;190	ENSP00000427769:P95L|ENSP00000256255:P226S;ENSP00000441351:P54S;ENSP00000441723:P54S;ENSP00000428323:P124S;ENSP00000429630:P190S	ENSP00000427769:P95L|ENSP00000256255:P226S	P|P	-|-	2|1	0|0	TMEM66|TMEM66	30046724|30046724	0.985000|0.985000	0.35326|0.35326	0.020000|0.020000	0.16555|0.16555	0.991000|0.991000	0.79684|0.79684	1.791000|1.791000	0.38744|0.38744	-0.381000|-0.381000	0.07882|0.07882	-0.182000|-0.182000	0.12963|0.12963	CCC|CCA	G|0.990;A|0.010	0.010	strong		0.507	TMEM66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257254.4			A	29927182	G	A	29927182	3	1	22	1	0	0	0	0	1	0	0	0	16210	1232	43	2	359	2	TMEM66	8	29927182	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1513807	29927182	116436840	1902	4803											
LEPROTL1	619373	hgsc.bcm.edu	37	chr8	29994923	29994923	+	Intron	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagagtgtccactcaacccGtgctgaggctggcagacagt	9	7	13	12	1	1	3	1	1	0	2	2	3	2	3	2	2	2	4	2	2	1	0	rs77053651	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:29994923G>A	ENST00000320542.3	-	2	429				LEPROTL1_ENST00000523116.1_Missense_Mutation_p.V139M|LEPROTL1_ENST00000442880.2_3'UTR	NM_001100916.1	NP_001094386.1	Q96T53	MBOA4_HUMAN	membrane bound O-acyltransferase domain containing 4						cellular protein metabolic process (GO:0044267)|peptidyl-serine octanoylation (GO:0018191)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	serine O-acyltransferase activity (GO:0016412)			endometrium(1)	1						CACTCAACCCGTGCTGAGGCT	0.562													G|||	82	0.0163738	0.056	0.0101	5008	,	,		19995	0.0		0.001	False		,,,				2504	0.0				p.V139M		Atlas-SNP	.											.	LEPROTL1	16	.	0			c.G415A						PASS	.	G	,MET/VAL	82,1302		3,76,613	51	44	46		,415	-1.1	0	8	dbSNP_132	46	1,3181		0,1,1590	yes	intron,missense	LEPROTL1,MBOAT4	NM_001100916.1,NM_001128208.1	,21	3,77,2203	AA,AG,GG		0.0314,5.9249,1.8178	,benign	,139/170	29994923	83,4483	692	1591	2283	SO:0001627	intron_variant	23484	exon4			CAACCCGTGCTGA	AF359269	CCDS47835.1	8p12	2008-08-04	2006-06-29	2006-06-29	ENSG00000177669	ENSG00000177669			32311	protein-coding gene	gene with protein product	"ghrelin O-acyltransferase"	611940	"O-acyltransferase (membrane bound) domain containing 4"	OACT4		18443287	Standard	NM_001100916		Approved	FKSG89, GOAT	uc010lvg.3	Q96T53	OTTHUMG00000163824	ENST00000320542.3:c.344+1124C>T	8.37:g.29994923G>A		118	0	0		135	56	0.414815	NM_001128208	B1Q003	Missense_Mutation	SNP	ENST00000320542.3	37	CCDS47835.1	33	0.01510989010989011	29	0.05894308943089431	4	0.011049723756906077	0	0.0	0	0.0	G	13.55	2.271741	0.40194	0.059249	3.14E-4	ENSG00000104660	ENST00000523116	.	.	.	3.84	-1.13	0.09775	.	.	.	.	.	T	0.01523	0.0049	N	0.08118	0	0.09310	N	0.999999	B	0.16396	0.017	B	0.08055	0.003	T	0.23297	-1.0192	7	.	.	.	.	7.2794	0.26302	0.5248:0.0:0.4752:0.0	.	139	E9PHP8	.	M	139	.	.	V	+	1	0	LEPROTL1	30114465	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-0.030000	0.12308	-0.204000	0.10235	-0.469000	0.05056	GTG	G|0.984;A|0.016	0.016	strong		0.562	MBOAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375795.1			A	29994923	G	A	29994923	1	1	22	0	1	0	0	0	0	0	0	0	8742	1145	40	1		1	LEPROTL1	8	29994923	Intron	SNP	G	TCGA-G8-6324-01A-11D-2210-10	67741	29994923	116369099	1903	4804											
WRN	7486	hgsc.bcm.edu	37	chr8	30954338	30954338	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tactgttcaggtaacatgggCctgctccagcaacttgaggc	9	10	11	11	0	1	1	1	1	0	0	2	1	2	1	2	3	5	4	2	3	3	4	rs11574263	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:30954338C>T	ENST00000298139.5	+	17	2202	c.1953C>T	c.(1951-1953)ggC>ggT	p.G651G		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	651	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)		GTAACATGGGCCTGCTCCAGC	0.338			"Mis, N, F, S"			"osteosarcoma, meningioma, others"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome				C|||	20	0.00399361	0.0144	0.0014	5008	,	,		16879	0.0		0.0	False		,,,				2504	0.0				p.G651G	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.C1953T						PASS	.	C		78,4328	67.0+/-104.6	2,74,2127	92	91	91		1953	2.1	0	8	dbSNP_120	91	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	WRN	NM_000553.4		2,76,6425	TT,TC,CC		0.0233,1.7703,0.6151		651/1433	30954338	80,12926	2203	4300	6503	SO:0001819	synonymous_variant	7486	exon17	Familial Cancer Database	WS, Adult Progeria	CATGGGCCTGCTC		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.1953C>T	8.37:g.30954338C>T		28	0	0		29	12	0.413793	NM_000553	A1KYY9	Silent	SNP	ENST00000298139.5	37	CCDS6082.1																																																																																			C|0.997;T|0.003	0.003	strong		0.338	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1			T	30954338	C	T	30954338	2	4	22	1	0	0	0	0	0	0	0	1	17417	726	26	2		2	WRN	8	30954338	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	959415	30954338	115409684	1904	4805											
GPR124	25960	hgsc.bcm.edu	37	chr8	37690615	37690615	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccctgggcgggggtgccccGggcacccgagcctcccgccg	2	3	16	20	5	0	0	0	0	0	0	1	1	1	0	8	4	2	1	8	4	0	0	rs61738775	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:37690615G>A	ENST00000412232.2	+	9	1198	c.1185G>A	c.(1183-1185)ccG>ccA	p.P395P	GPR124_ENST00000315215.7_Silent_p.P395P	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124	395					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)			GGGGTGCCCCGGGCACCCGAG	0.682													G|||	321	0.0640974	0.2284	0.0159	5008	,	,		11914	0.005		0.002	False		,,,				2504	0.001				p.P395P		Atlas-SNP	.											.	GPR124	85	.	0			c.G1185A						PASS	.	G		846,3560	318.5+/-295.7	69,708,1426	41	47	45		1185	-10.2	0.3	8	dbSNP_129	45	8,8592	5.0+/-18.6	0,8,4292	no	coding-synonymous	GPR124	NM_032777.9		69,716,5718	AA,AG,GG		0.093,19.2011,6.5662		395/1339	37690615	854,12152	2203	4300	6503	SO:0001819	synonymous_variant	25960	exon9			TGCCCCGGGCACC	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.1185G>A	8.37:g.37690615G>A		14	0	0		17	15	0.882353	NM_032777	A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	Silent	SNP	ENST00000412232.2	37	CCDS6097.2																																																																																			G|0.934;A|0.066	0.066	strong		0.682	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343331.2			A	37690615	G	A	37690615	2	1	22	1	0	0	0	0	0	0	0	1	6646	1103	39	1		1	GPR124	8	37690615	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6736277	37690615	108673407	1905	4806											
WHSC1L1	54904	hgsc.bcm.edu	37	chr8	38205133	38205133	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctttcatgctttgatttcGtgtgctcacttgcctgtact	4	19	8	10	1	2	1	2	1	0	0	3	1	2	1	1	0	5	4	1	0	1	5	rs13034	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:38205133G>A	ENST00000317025.8	-	2	1074	c.557C>T	c.(556-558)aCg>aTg	p.T186M	WHSC1L1_ENST00000433384.2_Missense_Mutation_p.T186M|WHSC1L1_ENST00000527502.1_Missense_Mutation_p.T186M|WHSC1L1_ENST00000316985.3_Missense_Mutation_p.T186M	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1	186			T -> M (in dbSNP:rs13034).		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)			CTTTGATTTCGTGTGCTCACT	0.373			T	NUP98	AML								G|||	74	0.0147764	0.0552	0.0014	5008	,	,		19666	0.0		0.0	False		,,,				2504	0.0				p.T186M		Atlas-SNP	.		Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	.	WHSC1L1	137	.	0			c.C557T						PASS	.	G	MET/THR,MET/THR	236,4170	139.6+/-175.2	5,226,1972	179	163	168		557,557	3	1	8	dbSNP_52	168	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	WHSC1L1	NM_017778.2,NM_023034.1	81,81	5,228,6270	AA,AG,GG		0.0233,5.3563,1.8299	benign,benign	186/646,186/1438	38205133	238,12768	2203	4300	6503	SO:0001583	missense	54904	exon2			GATTTCGTGTGCT	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.557C>T	8.37:g.38205133G>A	ENSP00000313983:p.Thr186Met	224	0	0		189	86	0.455026	NM_017778	B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	Missense_Mutation	SNP	ENST00000317025.8	37	CCDS43729.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	G	10.27	1.303287	0.23736	0.053563	2.33E-4	ENSG00000147548	ENST00000433384;ENST00000317025;ENST00000446459;ENST00000527502;ENST00000316985;ENST00000529223	D;D;D;T;T	0.95238	-3.64;-3.65;-3.65;-0.15;0.87	5.7	2.96	0.34315	.	0.453371	0.17834	U	0.160431	T	0.65719	0.2718	L	0.29908	0.895	0.33540	D	0.594756	B;B;B;B	0.25390	0.125;0.079;0.078;0.06	B;B;B;B	0.18561	0.008;0.009;0.022;0.005	T	0.79662	-0.1710	10	0.66056	D	0.02	.	11.7413	0.51794	0.1932:0.0:0.8068:0.0	rs13034	186;186;186;186	B7ZL11;Q9BZ95-2;Q9BZ95-3;Q9BZ95	.;.;.;NSD3_HUMAN	M	186;186;123;186;186;186	ENSP00000393284:T186M;ENSP00000313983:T186M;ENSP00000434730:T186M;ENSP00000313410:T186M;ENSP00000435422:T186M	ENSP00000313410:T186M	T	-	2	0	WHSC1L1	38324290	0.999000	0.42202	0.997000	0.53966	0.896000	0.52359	1.040000	0.30278	0.348000	0.23949	-0.916000	0.02749	ACG	G|0.983;A|0.017	0.017	strong		0.373	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381924.3	NM_023034		A	38205133	G	A	38205133	3	1	22	1	0	0	0	0	1	0	0	0	17378	1145	40	1	3935	1	WHSC1L1	8	38205133	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	514518	38205133	108158889	1906	4807											
TACC1	6867	hgsc.bcm.edu	37	chr8	38677242	38677242	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atagaaacgaaggattccacGgatatctcggcagtcctcgg	12	8	11	10	4	1	1	0	0	1	1	5	4	3	3	2	4	1	1	2	4	4	3	rs16887780	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:38677242G>A	ENST00000317827.4	+	3	859	c.480G>A	c.(478-480)acG>acA	p.T160T	TACC1_ENST00000518415.1_Silent_p.T115T|TACC1_ENST00000379931.3_Silent_p.T160T|TACC1_ENST00000443286.2_Silent_p.T176T|TACC1_ENST00000522752.1_Intron|TACC1_ENST00000276520.8_Intron|TACC1_ENST00000330691.6_Intron|TACC1_ENST00000520615.1_5'UTR|TACC1_ENST00000520340.1_Silent_p.T124T|TACC1_ENST00000520973.1_5'UTR|TACC1_ENST00000348567.4_Intron|TACC1_ENST00000519416.1_5'UTR|TACC1_ENST00000520611.1_5'Flank	NM_006283.2	NP_006274.2	O75410	TACC1_HUMAN	transforming, acidic coiled-coil containing protein 1	160	Interaction with TDRD7.				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)			AGGATTCCACGGATATCTCGG	0.493													G|||	61	0.0121805	0.0454	0.0014	5008	,	,		20225	0.0		0.0	False		,,,				2504	0.0				p.T160T		Atlas-SNP	.											.	TACC1	98	.	0			c.G480A						PASS	.	G	,,	120,4286	89.7+/-128.4	1,118,2084	101	101	101		,,480	-1.6	0	8	dbSNP_123	101	1,8599	1.2+/-3.3	0,1,4299	yes	intron,utr-5,coding-synonymous	TACC1	NM_001122824.1,NM_001146216.2,NM_006283.2	,,	1,119,6383	AA,AG,GG		0.0116,2.7236,0.9303	,,	,,160/806	38677242	121,12885	2203	4300	6503	SO:0001819	synonymous_variant	6867	exon3			TTCCACGGATATC	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.480G>A	8.37:g.38677242G>A		225	1	0.00444444		230	117	0.508696	NM_006283	B2RBD9|D3DSX6|Q6Y687|Q86YG7|Q8IUJ2|Q8IUJ3|Q8IUJ4|Q8IZG2|Q8NEY7|Q9UPP9	Silent	SNP	ENST00000317827.4	37	CCDS6109.1																																																																																			G|0.991;A|0.009	0.009	strong		0.493	TACC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376768.1	NM_006283		A	38677242	G	A	38677242	2	1	22	1	0	0	0	0	0	0	0	1	15516	1103	39	1		1	TACC1	8	38677242	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	472109	38677242	107686780	1907	4808											
ADAM32	203102	hgsc.bcm.edu	37	chr8	39091546	39091546	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgtagactacaaattgcctcGaacagttccagatccactgg	12	10	8	11	1	0	2	0	0	0	2	3	3	2	2	3	1	3	2	3	1	4	4	rs114068623	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:39091546G>A	ENST00000379907.4	+	16	1890	c.1763G>A	c.(1762-1764)cGa>cAa	p.R588Q	ADAM32_ENST00000519315.1_Missense_Mutation_p.R482Q|ADAM32_ENST00000437682.2_Missense_Mutation_p.R489Q	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	588						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)			AAATTGCCTCGAACAGTTCCA	0.353													G|||	42	0.00838658	0.0318	0.0	5008	,	,		13545	0.0		0.0	False		,,,				2504	0.0				p.R588Q		Atlas-SNP	.											.	ADAM32	70	.	0			c.G1763A						PASS	.	G	GLN/ARG	96,3584		1,94,1745	63	55	58		1763	-9.3	0	8	dbSNP_132	58	0,8154		0,0,4077	yes	missense	ADAM32	NM_145004.5	43	1,94,5822	AA,AG,GG		0.0,2.6087,0.8112	possibly-damaging	588/788	39091546	96,11738	1840	4077	5917	SO:0001583	missense	203102	exon16			TGCCTCGAACAGT	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.1763G>A	8.37:g.39091546G>A	ENSP00000369238:p.Arg588Gln	90	0	0		82	46	0.560976	NM_145004	Q8TC42	Missense_Mutation	SNP	ENST00000379907.4	37	CCDS47846.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	G	5.640	0.302788	0.10678	0.026087	0.0	ENSG00000197140	ENST00000437682;ENST00000519315;ENST00000379907	T;T;T	0.21361	2.01;2.01;2.01	4.66	-9.32	0.00643	ADAM, cysteine-rich (2);	10.959300	0.00735	U	0.000979	T	0.01905	0.0060	N	0.05383	-0.06	0.09310	N	1	P;P;P	0.51351	0.559;0.944;0.694	B;B;B	0.38755	0.148;0.281;0.067	T	0.41034	-0.9531	10	0.11182	T	0.66	.	2.6264	0.04930	0.1635:0.1349:0.4716:0.23	.	489;482;588	E7EPX8;E7ER82;Q8TC27	.;.;ADA32_HUMAN	Q	489;482;588	ENSP00000405978:R489Q;ENSP00000429422:R482Q;ENSP00000369238:R588Q	ENSP00000369238:R588Q	R	+	2	0	ADAM32	39210703	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.001000	0.00652	-2.751000	0.00374	-0.781000	0.03364	CGA	G|0.990;A|0.010	0.010	strong		0.353	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004		A	39091546	G	A	39091546	3	1	22	1	0	0	0	0	1	0	0	0	249	1058	37	1	1825	1	ADAM32	8	39091546	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	414304	39091546	107272476	1908	4809											
ADAM18	8749	hgsc.bcm.edu	37	chr8	39468128	39468128	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttgagcatataatttatcAaatgaaaaataatgatccaa	20	13	4	4	0	1	3	1	3	0	0	2	3	2	3	1	0	1	1	1	0	8	6	rs73605945	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:39468128A>T	ENST00000265707.5	+	6	470	c.425A>T	c.(424-426)cAa>cTa	p.Q142L	ADAM18_ENST00000520772.1_Missense_Mutation_p.Q142L|ADAM18_ENST00000379866.1_Missense_Mutation_p.Q142L|ADAM18_ENST00000541111.1_Intron	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	142					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)			ATAATTTATCAAATGAAAAAT	0.328													A|||	181	0.0361422	0.1203	0.0144	5008	,	,		15463	0.0		0.0089	False		,,,				2504	0.0031				p.Q142L		Atlas-SNP	.											.	ADAM18	169	.	0			c.A425T						PASS	.	A	LEU/GLN,LEU/GLN	505,3901	221.7+/-238.7	22,461,1720	47	49	48		425,425	4.1	1	8	dbSNP_130	48	49,8547	29.0+/-79.6	0,49,4249	yes	missense,missense	ADAM18	NM_001190956.1,NM_014237.2	113,113	22,510,5969	TT,TA,AA		0.57,11.4616,4.2609	probably-damaging,probably-damaging	142/183,142/740	39468128	554,12448	2203	4298	6501	SO:0001583	missense	8749	exon6			TTTATCAAATGAA	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.425A>T	8.37:g.39468128A>T	ENSP00000265707:p.Gln142Leu	289	0	0		280	125	0.446429	NM_001190956	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	37	CCDS6113.1	75	0.034340659340659344	66	0.13414634146341464	6	0.016574585635359115	0	0.0	3	0.00395778364116095	A	15.82	2.946102	0.53079	0.114616	0.0057	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000520772;ENST00000522198	T;T;T	0.12465	5.29;4.82;2.68	5.25	4.07	0.47477	.	0.000000	0.47093	D	0.000245	T	0.00144	0.0004	N	0.08118	0	0.80722	D	1	D;D;D	0.63046	0.98;0.967;0.992	P;P;P	0.60286	0.872;0.749;0.84	T	0.34179	-0.9839	10	0.41790	T	0.15	.	7.8609	0.29509	0.9058:0.0:0.0942:0.0	.	142;142;142	Q9Y3Q7-2;Q9Y3Q7;Q6IRW9	.;ADA18_HUMAN;.	L	142;142;142;98	ENSP00000265707:Q142L;ENSP00000369195:Q142L;ENSP00000429908:Q142L	ENSP00000265707:Q142L	Q	+	2	0	ADAM18	39587285	1.000000	0.71417	1.000000	0.80357	0.291000	0.27294	2.766000	0.47629	2.206000	0.71126	0.533000	0.62120	CAA	A|0.964;T|0.036	0.036	strong		0.328	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237		T	39468128	A	T	39468128	3	4	22	1	0	0	0	0	1	0	0	0	239	130	5	5	447	5	ADAM18	8	39468128	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	376582	39468128	106895894	1909	4810											
ADAM18	8749	hgsc.bcm.edu	37	chr8	39537616	39537616	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaaatgctaataaaagtgaCgctcaatctacagtttattc	17	12	5	7	1	2	1	1	1	1	0	3	1	2	1	0	0	2	3	0	0	8	6	rs28454772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:39537616C>T	ENST00000265707.5	+	16	1737	c.1692C>T	c.(1690-1692)gaC>gaT	p.D564D	ADAM18_ENST00000379866.1_Silent_p.D540D|ADAM18_ENST00000541111.1_5'UTR	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	564	Cys-rich.				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)			ATAAAAGTGACGCTCAATCTA	0.383													c|||	402	0.0802716	0.2723	0.0317	5008	,	,		19440	0.002		0.0099	False		,,,				2504	0.0082				p.D564D		Atlas-SNP	.											ADAM18,colon,carcinoma,0,1	ADAM18	169	1	0			c.C1692T						PASS	.	A		1031,3375	381.6+/-324.1	128,775,1300	113	101	105		1692	0.3	0	8	dbSNP_125	105	60,8540	35.9+/-90.5	0,60,4240	no	coding-synonymous	ADAM18	NM_014237.2		128,835,5540	TT,TC,CC		0.6977,23.3999,8.3884		564/740	39537616	1091,11915	2203	4300	6503	SO:0001819	synonymous_variant	8749	exon16			AAGTGACGCTCAA	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.1692C>T	8.37:g.39537616C>T		126	0	0		127	67	0.527559	NM_014237	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Silent	SNP	ENST00000265707.5	37	CCDS6113.1																																																																																			C|0.914;T|0.086	0.086	strong		0.383	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237		T	39537616	C	T	39537616	2	4	22	1	0	0	0	0	0	0	0	1	239	535	19	1		1	ADAM18	8	39537616	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	69488	39537616	106826406	1910	4811											
ADAM18	8749	hgsc.bcm.edu	37	chr8	39581395	39581395	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagaaatgaaataagtaaaTcatgtaacagagagaatgca	23	7	8	3	0	1	4	1	1	0	3	1	5	1	4	0	0	2	3	0	0	8	3	rs79109719	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:39581395T>A	ENST00000265707.5	+	19	2191	c.2146T>A	c.(2146-2148)Tca>Aca	p.S716T	ADAM18_ENST00000523755.1_3'UTR|ADAM18_ENST00000379866.1_Missense_Mutation_p.S692T|ADAM18_ENST00000541111.1_Missense_Mutation_p.S130T	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	716					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)			AATAAGTAAATCATGTAACAG	0.308													T|||	141	0.028155	0.0998	0.0101	5008	,	,		14093	0.0		0.002	False		,,,				2504	0.0				p.S716T		Atlas-SNP	.											.	ADAM18	169	.	0			c.T2146A						PASS	.		THR/SER	403,4001	192.3+/-217.7	22,359,1821	99	104	102		2146	2.3	0	8	dbSNP_131	102	3,8591	2.2+/-6.3	0,3,4294	yes	missense	ADAM18	NM_014237.2	58	22,362,6115	AA,AT,TT		0.0349,9.1508,3.1236	benign	716/740	39581395	406,12592	2202	4297	6499	SO:0001583	missense	8749	exon19			AGTAAATCATGTA	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.2146T>A	8.37:g.39581395T>A	ENSP00000265707:p.Ser716Thr	79	0	0		70	70	1	NM_014237	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	37	CCDS6113.1	57	0.0260989010989011	51	0.10365853658536585	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	T	4.809	0.150384	0.09185	0.091508	3.49E-4	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000541111	D;D;D	0.93366	-3.21;-3.21;-3.21	4.77	2.32	0.28847	.	2.401010	0.01912	N	0.039915	T	0.34135	0.0887	L	0.56769	1.78	0.09310	N	1	B;B	0.22604	0.072;0.043	B;B	0.33960	0.173;0.084	T	0.61778	-0.6993	10	0.22706	T	0.39	.	5.2918	0.15731	0.0:0.0953:0.1793:0.7254	.	692;716	Q9Y3Q7-2;Q9Y3Q7	.;ADA18_HUMAN	T	716;692;130	ENSP00000265707:S716T;ENSP00000369195:S692T;ENSP00000444729:S130T	ENSP00000265707:S716T	S	+	1	0	ADAM18	39700552	0.004000	0.15560	0.003000	0.11579	0.007000	0.05969	0.525000	0.22956	0.376000	0.24707	0.451000	0.29950	TCA	T|0.968;A|0.032	0.032	strong		0.308	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237		A	39581395	T	A	39581395	3	1	22	1	0	0	0	0	1	0	0	0	239	1435	50	5	2220	5	ADAM18	8	39581395	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	43779	39581395	106782627	1911	4812											
ADAM18	8749	hgsc.bcm.edu	37	chr8	39581417	39581417	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtaacagagagaatgcagAgtataatcggtaaatatgat	18	10	10	3	1	0	4	0	1	0	3	1	5	0	4	0	1	2	4	0	1	7	5	rs76378145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:39581417A>G	ENST00000265707.5	+	19	2213	c.2168A>G	c.(2167-2169)gAg>gGg	p.E723G	ADAM18_ENST00000523755.1_3'UTR|ADAM18_ENST00000379866.1_Missense_Mutation_p.E699G|ADAM18_ENST00000541111.1_Missense_Mutation_p.E137G	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	723					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)			GAGAATGCAGAGTATAATCGG	0.274													A|||	127	0.0253594	0.0893	0.0101	5008	,	,		14686	0.0		0.002	False		,,,				2504	0.0				p.E723G		Atlas-SNP	.											.	ADAM18	169	.	0			c.A2168G						PASS	.		GLY/GLU	371,4033	172.3+/-202.3	20,331,1851	84	89	87		2168	3.6	0	8	dbSNP_132	87	2,8588	2.2+/-6.3	0,2,4293	yes	missense	ADAM18	NM_014237.2	98	20,333,6144	GG,GA,AA		0.0233,8.4242,2.8706	benign	723/740	39581417	373,12621	2202	4295	6497	SO:0001583	missense	8749	exon19			ATGCAGAGTATAA	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.2168A>G	8.37:g.39581417A>G	ENSP00000265707:p.Glu723Gly	55	0	0		52	52	1	NM_014237	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	37	CCDS6113.1	51	0.023351648351648352	45	0.09146341463414634	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	a	9.078	0.998571	0.19121	0.084242	2.33E-4	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000541111	D;D;D	0.93953	-3.32;-3.32;-3.32	4.77	3.61	0.41365	.	0.638567	0.13741	N	0.365922	T	0.38241	0.1033	M	0.68593	2.085	0.09310	N	1	B;B	0.27910	0.193;0.046	B;B	0.27170	0.077;0.035	T	0.67333	-0.5697	10	0.52906	T	0.07	.	7.6055	0.28100	0.9001:0.0:0.0999:0.0	.	699;723	Q9Y3Q7-2;Q9Y3Q7	.;ADA18_HUMAN	G	723;699;137	ENSP00000265707:E723G;ENSP00000369195:E699G;ENSP00000444729:E137G	ENSP00000265707:E723G	E	+	2	0	ADAM18	39700574	0.174000	0.23070	0.007000	0.13788	0.001000	0.01503	2.076000	0.41548	0.933000	0.37291	-0.393000	0.06486	GAG	A|0.972;G|0.028	0.028	strong		0.274	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237		G	39581417	A	G	39581417	3	3	22	1	0	0	0	0	1	0	0	0	239	304	11	3	2242	3	ADAM18	8	39581417	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	22	39581417	106782605	1912	4813											
ANK1	286	hgsc.bcm.edu	37	chr8	41522407	41522407	+	Intron	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgctctcccccagctccttGtccagctcctggtggatgtg	3	12	10	16	1	1	0	0	0	1	0	6	1	4	1	5	2	2	3	5	2	0	1	rs112350393	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:41522407G>C	ENST00000347528.4	-	40	5478				ANK1_ENST00000396945.1_Intron|RP11-930P14.1_ENST00000520418.1_RNA|ANK1_ENST00000352337.4_Intron|ANK1_ENST00000265709.8_Intron|ANK1_ENST00000457297.1_Missense_Mutation_p.D45E|ANK1_ENST00000379758.2_Intron|ANK1_ENST00000522231.1_Missense_Mutation_p.D45E|ANK1_ENST00000314214.8_Missense_Mutation_p.D45E|RP11-930P14.1_ENST00000585088.1_RNA|ANK1_ENST00000289734.7_Intron|ANK1_ENST00000522543.1_Missense_Mutation_p.D45E|ANK1_ENST00000396942.1_Intron|RP11-930P14.1_ENST00000522388.1_RNA	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic						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)			CCAGCTCCTTGTCCAGCTCCT	0.612													G|||	147	0.029353	0.1104	0.0014	5008	,	,		18468	0.0		0.0	False		,,,				2504	0.0				p.D45E		Atlas-SNP	.											.	ANK1	497	.	0			c.C135G						PASS	.	G	,GLU/ASP,,,,,GLU/ASP,GLU/ASP	405,4001	200.8+/-224.0	31,343,1829	80	58	65		,135,,,,,135,135	4.6	1	8	dbSNP_132	65	4,8596	3.0+/-9.4	0,4,4296	yes	intron,missense,intron,intron,intron,intron,missense,missense	ANK1	NM_000037.3,NM_001142445.1,NM_001142446.1,NM_020475.2,NM_020476.2,NM_020477.2,NM_020478.4,NM_020480.4	,45,,,,,45,45	31,347,6125	CC,CG,GG		0.0465,9.192,3.1447	,,,,,,,	,45/157,,,,,45/156,45/110	41522407	409,12597	2203	4300	6503	SO:0001627	intron_variant	286	exon1			CTCCTTGTCCAGC	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.5395-1147C>G	8.37:g.41522407G>C		68	0	0		63	28	0.444444	NM_020478	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Missense_Mutation	SNP	ENST00000347528.4	37	CCDS6119.1	36	0.016483516483516484	36	0.07317073170731707	0	0.0	0	0.0	0	0.0	G	24.8	4.569350	0.86439	0.09192	4.65E-4	ENSG00000029534	ENST00000457297;ENST00000522231;ENST00000522543;ENST00000314214;ENST00000348036;ENST00000335651	D;D;D	0.87334	-1.81;-2.24;-2.19	5.51	4.63	0.57726	.	.	.	.	.	T	0.41534	0.1163	M	0.67953	2.075	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.83275	0.996;0.994;0.996;0.996	T	0.72087	-0.4396	9	0.72032	D	0.01	.	12.8445	0.57821	0.078:0.0:0.9219:0.0	.	45;45;45;45	Q6PK32;A0PJN8;Q53ER1;E5RFL7	.;.;.;.	E	45	ENSP00000428750:D45E;ENSP00000430368:D45E;ENSP00000319123:D45E	ENSP00000319123:D45E	D	-	3	2	ANK1	41641564	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	4.545000	0.60698	2.585000	0.87301	0.563000	0.77884	GAC	G|0.969;C|0.031	0.031	strong		0.612	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		C	41522407	G	C	41522407	1	2	22	0	1	0	0	0	0	0	0	0	620	1368	48	4		4	ANK1	8	41522407	Intron	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1940990	41522407	104841615	1913	4814											
ANK1	286	hgsc.bcm.edu	37	chr8	41552840	41552840	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcaaagtgcgggatctccacGattacagggctgaggcaagg	11	6	15	9	2	1	1	0	1	1	0	2	3	1	2	1	4	2	3	1	4	3	1	rs34969689	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:41552840G>A	ENST00000347528.4	-	27	3053	c.2970C>T	c.(2968-2970)atC>atT	p.I990I	ANK1_ENST00000396945.1_Silent_p.I990I|ANK1_ENST00000352337.4_Silent_p.I990I|ANK1_ENST00000265709.8_Silent_p.I1031I|ANK1_ENST00000379758.2_Silent_p.I990I|ANK1_ENST00000289734.7_Silent_p.I990I|ANK1_ENST00000396942.1_Silent_p.I990I	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	990	ZU5 1. {ECO:0000255|PROSITE- ProRule:PRU00485}.				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)			GGATCTCCACGATTACAGGGC	0.642													G|||	71	0.0141773	0.0522	0.0014	5008	,	,		20368	0.0		0.0	False		,,,				2504	0.001				p.I1031I		Atlas-SNP	.											.	ANK1	497	.	0			c.C3093T						PASS	.	G	,,,,	167,4239	109.9+/-148.2	2,163,2038	94	79	84		2970,3093,2970,2970,2970	-4	1	8	dbSNP_126	84	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ANK1	NM_000037.3,NM_001142446.1,NM_020475.2,NM_020476.2,NM_020477.2	,,,,	2,166,6335	AA,AG,GG		0.0349,3.7903,1.3071	,,,,	990/1881,1031/1898,990/1857,990/1882,990/1720	41552840	170,12836	2203	4300	6503	SO:0001819	synonymous_variant	286	exon28			CTCCACGATTACA	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.2970C>T	8.37:g.41552840G>A		173	0	0		180	85	0.472222	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Silent	SNP	ENST00000347528.4	37	CCDS6119.1	22	0.010073260073260074	21	0.042682926829268296	1	0.0027624309392265192	0	0.0	0	0.0	G	8.916	0.959980	0.18507	0.037903	3.49E-4	ENSG00000029534	ENST00000520299	.	.	.	4.99	-4.02	0.04034	.	.	.	.	.	T	0.21674	0.0522	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43734	-0.9373	4	.	.	.	.	9.6086	0.39648	0.649:0.1048:0.2461:0.0	rs34969689	.	.	.	C	312	.	.	R	-	1	0	ANK1	41671997	0.000000	0.05858	0.956000	0.39512	0.803000	0.45373	-2.206000	0.01231	-0.779000	0.04560	-0.251000	0.11542	CGT	G|0.987;A|0.013	0.013	strong		0.642	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		A	41552840	G	A	41552840	2	1	22	1	0	0	0	0	0	0	0	1	620	1048	37	1		1	ANK1	8	41552840	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	30433	41552840	104811182	1914	4815											
KIAA0146	23514	hgsc.bcm.edu	37	chr8	48511729	48511729	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggggtcagcagggggccagCtcaggacacacagacccagc	11	2	15	13	0	2	1	2	0	0	1	2	2	2	2	2	5	3	2	2	5	0	0			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:48511729C>T	ENST00000297423.4	+	10	1899	c.1515C>T	c.(1513-1515)agC>agT	p.S505S	SPIDR_ENST00000521214.1_3'UTR|SPIDR_ENST00000518074.1_Silent_p.S445S|SPIDR_ENST00000541342.1_Silent_p.S435S	NM_001080394.2|NM_001282916.1	NP_001073863.1|NP_001269845.1	Q14159	SPIDR_HUMAN	scaffolding protein involved in DNA repair	505					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)											AGGGGGCCAGCTCAGGACACA	0.592																																					p.S505S		Atlas-SNP	.											.	KIAA0146	64	.	0			c.C1515T						PASS	.						29	36	33					8																	48511729		2051	4183	6234	SO:0001819	synonymous_variant	23514	exon10			GGCCAGCTCAGGA	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.1515C>T	8.37:g.48511729C>T		102	0	0		101	41	0.405941	NM_001080394	B4DFV2|B4E0Y6|Q96BI5	Silent	SNP	ENST00000297423.4	37	CCDS43737.1	.	.	.	.	.	.	.	.	.	.	C	3.747	-0.052466	0.07362	.	.	ENSG00000164808	ENST00000519401	.	.	.	4.68	0.555	0.17247	.	.	.	.	.	T	0.23846	0.0577	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.24764	-1.0151	4	.	.	.	.	3.972	0.09457	0.1661:0.488:0.0:0.3459	.	.	.	.	V	187	.	.	A	+	2	0	KIAA0146	48674282	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.473000	0.06615	0.134000	0.18681	0.585000	0.79938	GCT	.	.	none		0.592	SPIDR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377611.1	NM_001080394		T	48511729	C	T	48511729	2	4	22	1	0	0	0	0	0	0	0	1	8166	796	28	2		2	KIAA0146	8	48511729	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6958889	48511729	97852293	1915	4816											
PXDNL	137902	hgsc.bcm.edu	37	chr8	52320786	52320786	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggcagccgaatccacggccGcagaataagccgcggagaag	12	3	14	12	5	0	2	0	0	0	2	1	4	1	2	4	3	2	2	4	3	4	1	rs74731075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:52320786G>A	ENST00000356297.4	-	17	3498	c.3398C>T	c.(3397-3399)gCg>gTg	p.A1133V	PXDNL_ENST00000543296.1_Missense_Mutation_p.A1133V	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	1133					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)				ATCCACGGCCGCAGAATAAGC	0.547													G|||	131	0.0261581	0.0946	0.0072	5008	,	,		14026	0.0		0.001	False		,,,				2504	0.0				p.A1133V		Atlas-SNP	.											.	PXDNL	414	.	0			c.C3398T						PASS	.	G	VAL/ALA	264,3518		11,242,1638	73	79	77		3398	1.3	0	8	dbSNP_131	77	5,8231		0,5,4113	yes	missense	PXDNL	NM_144651.4	64	11,247,5751	AA,AG,GG		0.0607,6.9804,2.2383	benign	1133/1464	52320786	269,11749	1891	4118	6009	SO:0001583	missense	137902	exon17			ACGGCCGCAGAAT		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.3398C>T	8.37:g.52320786G>A	ENSP00000348645:p.Ala1133Val	68	0	0		81	40	0.493827	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	51|51	0.023351648351648352|0.023351648351648352	48|48	0.0975609756097561|0.0975609756097561	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	G|G	0.006|0.006	-2.030686|-2.030686	0.00410|0.00410	0.069804|0.069804	6.07E-4|6.07E-4	ENSG00000147485|ENSG00000147485	ENST00000356297;ENST00000543296|ENST00000522933	T;T|.	0.69040|.	-0.37;-0.37|.	3.82|3.82	1.31|1.31	0.21738|0.21738	.|.	0.495534|.	0.16394|.	N|.	0.216355|.	T|T	0.00109|0.00109	0.0003|0.0003	N|N	0.00055|0.00055	-2.37|-2.37	0.25903|0.25903	N|N	0.983334|0.983334	B|.	0.11235|.	0.004|.	B|.	0.01281|.	0.0|.	T|T	0.35425|0.35425	-0.9789|-0.9789	10|5	0.02654|.	T|.	1|.	.|.	3.9194|3.9194	0.09237|0.09237	0.6521:0.2101:0.1378:0.0|0.6521:0.2101:0.1378:0.0	.|.	1133|.	A1KZ92|.	PXDNL_HUMAN|.	V|W	1133|252	ENSP00000348645:A1133V;ENSP00000444865:A1133V|.	ENSP00000348645:A1133V|.	A|R	-|-	2|1	0|2	PXDNL|PXDNL	52483339|52483339	1.000000|1.000000	0.71417|0.71417	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	6.058000|6.058000	0.71126|0.71126	-0.039000|-0.039000	0.13602|0.13602	-0.175000|-0.175000	0.13238|0.13238	GCG|CGG	G|0.973;A|0.027	0.027	strong		0.547	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		A	52320786	G	A	52320786	3	1	22	1	0	0	0	0	1	0	0	0	12863	1087	38	1	1021	1	PXDNL	8	52320786	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3809057	52320786	94043236	1916	4817											
PXDNL	137902	hgsc.bcm.edu	37	chr8	52321293	52321293	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatggcggccagagccagaTgctcgttggcccggtggtcc	5	7	16	13	3	0	2	0	0	0	2	2	2	1	2	4	5	2	3	4	5	0	1	rs562911693		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:52321293T>A	ENST00000356297.4	-	17	2991	c.2891A>T	c.(2890-2892)cAt>cTt	p.H964L	PXDNL_ENST00000543296.1_Missense_Mutation_p.H964L	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	964					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)				CAGAGCCAGATGCTCGTTGGC	0.647																																					p.H964L		Atlas-SNP	.											.	PXDNL	414	.	0			c.A2891T						PASS	.						13	15	14					8																	52321293		1980	4147	6127	SO:0001583	missense	137902	exon17			GCCAGATGCTCGT		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.2891A>T	8.37:g.52321293T>A	ENSP00000348645:p.His964Leu	106	0	0		103	54	0.524272	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	7.567|7.567	0.665851|0.665851	0.14710|0.14710	.|.	.|.	ENSG00000147485|ENSG00000147485	ENST00000356297;ENST00000543296|ENST00000522933	T;T|.	0.71698|.	-0.59;-0.59|.	3.73|3.73	1.18|1.18	0.20946|0.20946	.|.	0.164545|.	0.29508|.	N|.	0.011960|.	T|T	0.19208|0.19208	0.0461|0.0461	N|N	0.17082|0.17082	0.46|0.46	0.26667|0.26667	N|N	0.971805|0.971805	B|.	0.11235|.	0.004|.	B|.	0.17979|.	0.02|.	T|T	0.24657|0.24657	-1.0154|-1.0154	10|5	0.59425|.	D|.	0.04|.	.|.	3.9824|3.9824	0.09501|0.09501	0.1835:0.1097:0.0:0.7068|0.1835:0.1097:0.0:0.7068	.|.	964|.	A1KZ92|.	PXDNL_HUMAN|.	L|F	964|83	ENSP00000348645:H964L;ENSP00000444865:H964L|.	ENSP00000348645:H964L|.	H|I	-|-	2|1	0|0	PXDNL|PXDNL	52483846|52483846	1.000000|1.000000	0.71417|0.71417	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	5.173000|5.173000	0.65010|0.65010	-0.052000|-0.052000	0.13311|0.13311	-0.371000|-0.371000	0.07208|0.07208	CAT|ATC	.	.	none		0.647	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		A	52321293	T	A	52321293	3	1	22	1	0	0	0	0	1	0	0	0	12863	1464	51	5	1528	5	PXDNL	8	52321293	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	507	52321293	94042729	1917	4818											
LYPLA1	10434	hgsc.bcm.edu	37	chr8	54967638	54967638	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acctgagaaaaccctcccaaAataattctgttagaaggaat	17	9	6	9	0	1	2	0	1	1	2	2	4	2	3	3	1	1	1	3	1	8	3	rs76859468	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:54967638A>C	ENST00000316963.3	-	6	535	c.342T>G	c.(340-342)atT>atG	p.I114M	LYPLA1_ENST00000343231.6_Missense_Mutation_p.I98M|LYPLA1_ENST00000519926.1_5'UTR|LYPLA1_ENST00000522007.1_Intron	NM_001279360.1|NM_006330.2	NP_001266289.1|NP_006321.1	O75608	LYPA1_HUMAN	lysophospholipase I	114					fatty acid metabolic process (GO:0006631)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|nitric oxide metabolic process (GO:0046209)|protein depalmitoylation (GO:0002084)|regulation of nitric-oxide synthase activity (GO:0050999)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	lysophospholipase activity (GO:0004622)|palmitoyl-(protein) hydrolase activity (GO:0008474)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(3)	6		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;8.48e-07)|Epithelial(17;9.29e-05)|all cancers(17;0.000689)			ACCCTCCCAAAATAATTCTGT	0.328													A|||	56	0.0111821	0.0401	0.0043	5008	,	,		16168	0.0		0.0	False		,,,				2504	0.0				p.I114M		Atlas-SNP	.											.	LYPLA1	15	.	0			c.T342G						PASS	.	A	MET/ILE	211,4195	127.4+/-164.3	6,199,1998	60	58	59		342	5.2	1	8	dbSNP_131	59	1,8591	1.2+/-3.3	0,1,4295	yes	missense	LYPLA1	NM_006330.2	10	6,200,6293	CC,CA,AA		0.0116,4.7889,1.631	benign	114/231	54967638	212,12786	2203	4296	6499	SO:0001583	missense	10434	exon6			TCCCAAAATAATT	AF081281	CCDS6157.1, CCDS64899.1, CCDS75738.1, CCDS75739.1	8q11.23-q12.1	2008-05-15			ENSG00000120992	ENSG00000120992	3.1.1.5		6737	protein-coding gene	gene with protein product		605599				10064899	Standard	NM_006330		Approved	LPL1	uc003xry.3	O75608	OTTHUMG00000164313	ENST00000316963.3:c.342T>G	8.37:g.54967638A>C	ENSP00000320043:p.Ile114Met	212	0	0		223	108	0.484305	NM_006330	O43202|Q9UQF9	Missense_Mutation	SNP	ENST00000316963.3	37	CCDS6157.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	A	12.13	1.846250	0.32606	0.047889	1.16E-4	ENSG00000120992	ENST00000316963;ENST00000523751;ENST00000343231;ENST00000521171;ENST00000518546;ENST00000521352;ENST00000519926;ENST00000521898	T;T;T;T;T	0.27720	1.65;1.65;1.65;1.65;1.65	5.23	5.23	0.72850	Phospholipase/carboxylesterase/thioesterase (1);	0.223460	0.46145	D	0.000313	T	0.05547	0.0146	L	0.45744	1.44	0.80722	D	1	B;B;B	0.33549	0.417;0.392;0.073	B;B;B	0.41666	0.363;0.259;0.105	T	0.05649	-1.0872	10	0.51188	T	0.08	-5.5049	5.7137	0.17948	0.7698:0.0:0.0798:0.1504	.	114;98;114	B4DP64;O75608-2;O75608	.;.;LYPA1_HUMAN	M	114;114;98;23;98;50;114;92	ENSP00000320043:I114M;ENSP00000344477:I98M;ENSP00000428729:I98M;ENSP00000428306:I50M;ENSP00000430791:I92M	ENSP00000320043:I114M	I	-	3	3	LYPLA1	55130191	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.404000	0.34623	2.103000	0.63969	0.528000	0.53228	ATT	A|0.983;C|0.017	0.017	strong		0.328	LYPLA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378238.1			C	54967638	A	C	54967638	3	2	22	1	0	0	0	0	1	0	0	0	9125	10	1	5	366	5	LYPLA1	8	54967638	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2646345	54967638	91396384	1918	4819											
MRPL15	29088	hgsc.bcm.edu	37	chr8	55047893	55047893	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccgggccctggacctactccGgggcctgccgcgtgtgagcc	3	6	15	17	4	0	1	0	1	0	0	1	2	1	2	7	4	3	0	7	4	1	1	rs200980911	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:55047893G>A	ENST00000260102.4	+	1	124	c.50G>A	c.(49-51)cGg>cAg	p.R17Q		NM_014175.3	NP_054894.1	Q9P015	RM15_HUMAN	mitochondrial ribosomal protein L15	17					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)			GACCTACTCCGGGGCCTGCCG	0.677													g|||	8	0.00159744	0.0045	0.0029	5008	,	,		12630	0.0		0.0	False		,,,				2504	0.0				p.R17Q		Atlas-SNP	.											.	MRPL15	26	.	0			c.G50A						PASS	.	G	GLN/ARG	20,4078		0,20,2029	11	13	12		50	5.1	0.5	8		12	0,8010		0,0,4005	yes	missense	MRPL15	NM_014175.3	43	0,20,6034	AA,AG,GG		0.0,0.488,0.1652	benign	17/297	55047893	20,12088	2049	4005	6054	SO:0001583	missense	29088	exon1			TACTCCGGGGCCT	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.50G>A	8.37:g.55047893G>A	ENSP00000260102:p.Arg17Gln	237	0	0		222	106	0.477477	NM_014175	Q96Q54|Q9H0Y1	Missense_Mutation	SNP	ENST00000260102.4	37	CCDS6158.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	G	19.81	3.897077	0.72639	0.00488	0.0	ENSG00000137547	ENST00000260102;ENST00000519831	.	.	.	5.07	5.07	0.68467	.	0.111607	0.64402	D	0.000010	T	0.68714	0.3031	L	0.52759	1.655	0.45648	D	0.998575	D	0.69078	0.997	D	0.70227	0.968	T	0.73827	-0.3860	9	0.54805	T	0.06	-19.3451	18.8755	0.92332	0.0:0.0:1.0:0.0	.	17	Q9P015	RM15_HUMAN	Q	17	.	ENSP00000260102:R17Q	R	+	2	0	MRPL15	55210446	0.990000	0.36364	0.459000	0.27081	0.769000	0.43574	5.342000	0.65970	2.533000	0.85409	0.650000	0.86243	CGG	G|0.997;A|0.003	0.003	strong		0.677	MRPL15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378254.1	NM_014175		A	55047893	G	A	55047893	3	1	22	1	0	0	0	0	1	0	0	0	9789	1116	39	1	52	1	MRPL15	8	55047893	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	80255	55047893	91316129	1919	4820											
PENK	5179	hgsc.bcm.edu	37	chr8	57354380	57354380	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttccggtttgctattttcTctgagggtgctggtgccatc	3	17	11	10	1	2	1	0	1	2	0	5	1	3	1	2	3	3	3	2	3	1	5	rs76702938	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:57354380T>C	ENST00000314922.3	-	2	331	c.255A>G	c.(253-255)agA>agG	p.R85R	PENK_ENST00000523274.1_5'UTR|PENK_ENST00000451791.2_Silent_p.R85R	NM_006211.3	NP_006202.1	P01210	PENK_HUMAN	proenkephalin	85					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)			TGCTATTTTCTCTGAGGGTGC	0.468													T|||	12	0.00239617	0.0091	0.0	5008	,	,		17675	0.0		0.0	False		,,,				2504	0.0				p.R85R		Atlas-SNP	.											.	PENK	59	.	0			c.A255G						PASS	.	T	,	15,4391	21.2+/-45.6	0,15,2188	98	100	99		255,255	1.5	0	8	dbSNP_132	99	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PENK	NM_001135690.1,NM_006211.3	,	0,15,6488	CC,CT,TT		0.0,0.3404,0.1153	,	85/268,85/268	57354380	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	5179	exon4			ATTTTCTCTGAGG		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.255A>G	8.37:g.57354380T>C		115	0	0		107	58	0.542056	NM_001135690	B2RC23|Q6FHC6|Q6FHE6	Silent	SNP	ENST00000314922.3	37	CCDS6168.1																																																																																			T|0.999;C|0.001	0.001	strong		0.468	PENK-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378645.1			C	57354380	T	C	57354380	2	2	22	1	0	0	0	0	0	0	0	1	11736	1548	54	3		3	PENK	8	57354380	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2306487	57354380	89009642	1920	4821											
TOX	9760	hgsc.bcm.edu	37	chr8	59727966	59727966	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggttcccaaggggctgctgCatggtgagcggctggtgctg	4	10	18	9	1	0	1	0	1	0	0	1	1	1	1	1	6	4	6	1	6	1	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:59727966C>T	ENST00000361421.1	-	7	1543	c.1323G>A	c.(1321-1323)atG>atA	p.M441I	RNU4-50P_ENST00000364361.1_RNA	NM_014729.2	NP_055544.1	O94900	TOX_HUMAN	thymocyte selection-associated high mobility group box	441						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)				GGGGCTGCTGCATGGTGAGCG	0.577																																					p.M441I	Pancreas(161;610 1969 17913 21374 22725)	Atlas-SNP	.											.	TOX	83	.	0			c.G1323A						PASS	.						69	73	72					8																	59727966		2203	4300	6503	SO:0001583	missense	9760	exon7			CTGCTGCATGGTG		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.1323G>A	8.37:g.59727966C>T	ENSP00000354842:p.Met441Ile	274	0	0		334	166	0.497006	NM_014729	Q96AV5	Missense_Mutation	SNP	ENST00000361421.1	37	CCDS34897.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.447063	0.63178	.	.	ENSG00000198846	ENST00000361421;ENST00000456290	T	0.12255	2.7	5.98	5.98	0.97165	.	0.196250	0.56097	D	0.000022	T	0.32675	0.0837	L	0.55213	1.73	0.80722	D	1	P	0.45126	0.851	P	0.58391	0.838	T	0.00031	-1.2282	9	.	.	.	.	20.4366	0.99092	0.0:1.0:0.0:0.0	.	441	O94900	TOX_HUMAN	I	441;191	ENSP00000354842:M441I	.	M	-	3	0	TOX	59890520	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	6.711000	0.74675	2.837000	0.97791	0.591000	0.81541	ATG	.	.	none		0.577	TOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378307.1	NM_014729		T	59727966	C	T	59727966	3	4	22	1	0	0	0	0	1	0	0	0	16392	710	25	2	269	2	TOX	8	59727966	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2373586	59727966	86636056	1921	4822											
ARMC1	55156	hgsc.bcm.edu	37	chr8	66517549	66517549	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagctttcataaccttggtTgatgctattgctgatgccaa	9	15	9	8	0	1	3	1	3	0	0	1	3	1	3	2	1	5	4	2	1	3	6	rs16932266	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:66517549T>C	ENST00000276569.3	-	6	850	c.606A>G	c.(604-606)tcA>tcG	p.S202S	ARMC1_ENST00000458464.2_Silent_p.S100S	NM_018120.4	NP_060590.1	Q9NVT9	ARMC1_HUMAN	armadillo repeat containing 1	202					metal ion transport (GO:0030001)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|large_intestine(1)|lung(8)|skin(1)	14			Epithelial(68;0.103)|OV - Ovarian serous cystadenocarcinoma(28;0.235)			TAACCTTGGTTGATGCTATTG	0.323													T|||	109	0.0217652	0.0257	0.0288	5008	,	,		18451	0.0248		0.0159	False		,,,				2504	0.0143				p.S202S		Atlas-SNP	.											.	ARMC1	22	.	0			c.A606G						PASS	.	T		105,4301	81.4+/-119.9	2,101,2100	114	110	111		606	-0.1	1	8	dbSNP_123	111	126,8474	65.3+/-127.6	1,124,4175	no	coding-synonymous	ARMC1	NM_018120.4		3,225,6275	CC,CT,TT		1.4651,2.3831,1.7761		202/283	66517549	231,12775	2203	4300	6503	SO:0001819	synonymous_variant	55156	exon6			CTTGGTTGATGCT	BC011607	CCDS6181.1, CCDS69490.1	8q12.3	2013-02-14			ENSG00000104442	ENSG00000104442		"Armadillo repeat containing"	17684	protein-coding gene	gene with protein product							Standard	XM_005251264		Approved	FLJ10511, Arcp	uc003xvl.3	Q9NVT9	OTTHUMG00000164374	ENST00000276569.3:c.606A>G	8.37:g.66517549T>C		190	0	0		193	103	0.533679	NM_018120	B4E2W7|Q9H018|Q9H820	Silent	SNP	ENST00000276569.3	37	CCDS6181.1																																																																																			T|0.984;C|0.016	0.016	strong		0.323	ARMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378480.1	NM_018120		C	66517549	T	C	66517549	2	2	22	1	0	0	0	0	0	0	0	1	949	1799	63	3		3	ARMC1	8	66517549	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	6789583	66517549	79846473	1922	4823											
C8orf45	157777	hgsc.bcm.edu	37	chr8	67809160	67809160	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagggctgttttatgcggCttctagacagttcacaactg	9	13	11	8	1	2	2	1	1	1	1	2	2	2	2	0	2	2	4	0	2	4	5	rs35595089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:67809160C>G	ENST00000422365.2	+	12	1763	c.1592C>G	c.(1591-1593)gCt>gGt	p.A531G	MCMDC2_ENST00000313616.5_Missense_Mutation_p.A531G|MCMDC2_ENST00000396592.3_Missense_Mutation_p.A531G|MCMDC2_ENST00000541540.1_Missense_Mutation_p.A468G	NM_173518.4	NP_775789.3	Q4G0Z9	MCMD2_HUMAN	minichromosome maintenance domain containing 2	531					DNA replication (GO:0006260)		ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(2)|kidney(2)|lung(5)	9						TTTTATGCGGCTTCTAGACAG	0.408													C|||	30	0.00599042	0.0227	0.0	5008	,	,		13579	0.0		0.0	False		,,,				2504	0.0				p.A531G		Atlas-SNP	.											.	MCMDC2	84	.	0			c.C1592G						PASS	.	C	GLY/ALA,GLY/ALA,GLY/ALA	93,4313	76.2+/-114.5	2,89,2112	100	100	100		1592,1592,1592	4.6	1	8	dbSNP_126	100	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	C8orf45	NM_001136160.1,NM_001136161.1,NM_173518.4	60,60,60	2,90,6411	GG,GC,CC		0.0116,2.1108,0.7227	possibly-damaging,possibly-damaging,possibly-damaging	531/633,531/591,531/682	67809160	94,12912	2203	4300	6503	SO:0001583	missense	157777	exon12			ATGCGGCTTCTAG	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.1592C>G	8.37:g.67809160C>G	ENSP00000413632:p.Ala531Gly	146	0	0		119	59	0.495798	NM_173518	B4DYZ3|B4DZM4|B4E293|Q6P533|Q7Z3P4	Missense_Mutation	SNP	ENST00000422365.2	37	CCDS6197.2	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	10.04	1.240474	0.22711	0.021108	1.16E-4	ENSG00000178460	ENST00000396592;ENST00000422365;ENST00000313616;ENST00000541540	T;T;T;T	0.30182	1.54;1.54;1.54;1.54	5.51	4.57	0.56435	.	0.315894	0.33075	N	0.005315	T	0.12944	0.0314	L	0.40543	1.245	0.26863	N	0.967917	P;P;P	0.36354	0.493;0.549;0.549	B;B;B	0.41036	0.234;0.346;0.272	T	0.07233	-1.0783	10	0.22706	T	0.39	-9.108	6.8758	0.24147	0.1753:0.7144:0.0:0.1103	rs35595089;rs57404017	468;531;531	Q4G0Z9-4;Q4G0Z9;B4DXX4	.;CH045_HUMAN;.	G	531;531;531;468	ENSP00000379837:A531G;ENSP00000413632:A531G;ENSP00000317234:A531G;ENSP00000445629:A468G	ENSP00000317234:A531G	A	+	2	0	C8orf45	67971714	0.967000	0.33354	0.996000	0.52242	0.225000	0.24961	2.515000	0.45512	2.763000	0.94921	0.650000	0.86243	GCT	C|0.993;G|0.007	0.007	strong		0.408	MCMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347350.1	NM_173518		G	67809160	C	G	67809160	3	3	22	1	0	0	0	0	1	0	0	0	2432	797	28	4	1634	4	C8orf45	8	67809160	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1291611	67809160	78554862	1923	4824											
PREX2	80243	hgsc.bcm.edu	37	chr8	69104701	69104701	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggactgctgtcagtttcctcGgagctgtgcaacaggctggg	6	10	15	10	1	1	0	1	0	0	0	3	2	2	2	1	4	4	5	1	4	1	1	rs116570374	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:69104701G>A	ENST00000288368.4	+	37	4822	c.4545G>A	c.(4543-4545)tcG>tcA	p.S1515S		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	1515					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						CAGTTTCCTCGGAGCTGTGCA	0.557													G|||	28	0.00559105	0.0204	0.0014	5008	,	,		12376	0.0		0.0	False		,,,				2504	0.0				p.S1515S		Atlas-SNP	.											.	PREX2	614	.	0			c.G4545A						PASS	.	G		93,4313	75.7+/-113.9	1,91,2111	57	47	50		4545	-3.1	1	8	dbSNP_132	50	2,8598		0,2,4298	no	coding-synonymous	PREX2	NM_024870.2		1,93,6409	AA,AG,GG		0.0233,2.1108,0.7304		1515/1607	69104701	95,12911	2203	4300	6503	SO:0001819	synonymous_variant	80243	exon37			TTCCTCGGAGCTG	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.4545G>A	8.37:g.69104701G>A		65	0	0		101	51	0.504951	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Silent	SNP	ENST00000288368.4	37	CCDS6201.1																																																																																			G|0.993;A|0.007	0.007	strong		0.557	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170		A	69104701	G	A	69104701	2	1	22	1	0	0	0	0	0	0	0	1	12489	1103	39	1		1	PREX2	8	69104701	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1295541	69104701	77259321	1924	4825											
STAU2	27067	hgsc.bcm.edu	37	chr8	74526081	74526081	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtaagacggtggtcgcagcGcgcttcttggagagtttttt	6	14	14	7	4	1	2	0	0	1	2	2	3	1	2	0	3	1	4	0	3	1	6	rs28728027	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:74526081G>A	ENST00000521451.1	-	4	505	c.129C>T	c.(127-129)cgC>cgT	p.R43R	STAU2_ENST00000522509.1_Silent_p.R231R|STAU2_ENST00000521727.1_Silent_p.R243R|STAU2_ENST00000517542.1_Silent_p.R225R|STAU2_ENST00000522695.1_Silent_p.R231R|STAU2_ENST00000521210.1_Silent_p.R159R|STAU2_ENST00000519961.1_Silent_p.R263R|STAU2_ENST00000524300.1_Silent_p.R263R|STAU2_ENST00000523558.1_Silent_p.R91R|STAU2_ENST00000355780.5_Silent_p.R231R			Q9NUL3	STAU2_HUMAN	staufen double-stranded RNA binding protein 2	263	DRBM 1. {ECO:0000255|PROSITE- ProRule:PRU00266}.				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)			TGGTCGCAGCGCGCTTCTTGG	0.418													G|||	28	0.00559105	0.0189	0.0043	5008	,	,		15334	0.0		0.0	False		,,,				2504	0.0				p.R263R		Atlas-SNP	.											STAU2_ENST00000524300,NS,carcinoma,-1,3	STAU2	148	3	0			c.C789T						PASS	.	G	,,,,,,	79,4327	68.1+/-105.8	1,77,2125	88	83	85		789,693,477,273,693,675,693	-11.9	0.3	8	dbSNP_125	85	3,8597	2.2+/-6.3	0,3,4297	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	STAU2	NM_001164380.1,NM_001164381.1,NM_001164382.1,NM_001164383.1,NM_001164384.1,NM_001164385.1,NM_014393.2	,,,,,,	1,80,6422	AA,AG,GG		0.0349,1.793,0.6305	,,,,,,	263/571,231/539,159/505,91/399,231/480,225/474,231/480	74526081	82,12924	2203	4300	6503	SO:0001819	synonymous_variant	27067	exon9			CGCAGCGCGCTTC	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.129C>T	8.37:g.74526081G>A		79	0	0		56	26	0.464286	NM_001164380	B7Z1I6|B7Z292|B7Z8B4|E7ER74|E9PEI3|E9PF26|E9PF50|Q6AHY7|Q96HM0|Q96HM1|Q9NVI5|Q9UGG6	Silent	SNP	ENST00000521451.1	37																																																																																				G|0.995;A|0.005	0.005	strong		0.418	STAU2-006	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000379006.4	NM_001164380		A	74526081	G	A	74526081	2	1	22	1	0	0	0	0	0	0	0	1	15288	1074	38	1		1	STAU2	8	74526081	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5421380	74526081	71837941	1925	4826											
PSKH2	85481	hgsc.bcm.edu	37	chr8	87060793	87060793	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacttagaagactgtgcagaTccaggactctgagagtgggg	11	8	15	7	0	1	4	0	1	1	4	2	7	2	5	1	3	1	1	1	3	2	1	rs28483271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:87060793T>A	ENST00000276616.2	-	3	1130	c.1056A>T	c.(1054-1056)ggA>ggT	p.G352G		NM_033126.1	NP_149117.1	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	352							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)			ACTGTGCAGATCCAGGACTCT	0.498													T|||	124	0.0247604	0.0885	0.0101	5008	,	,		16173	0.0		0.0	False		,,,				2504	0.0				p.G352G		Atlas-SNP	.											.	PSKH2	79	.	0			c.A1056T						PASS	.	T		302,4104	164.0+/-195.7	9,284,1910	113	117	115		1056	0	0.5	8	dbSNP_125	115	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PSKH2	NM_033126.1		9,285,6209	AA,AT,TT		0.0116,6.8543,2.3297		352/386	87060793	303,12703	2203	4300	6503	SO:0001819	synonymous_variant	85481	exon3			TGCAGATCCAGGA	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.1056A>T	8.37:g.87060793T>A		150	0	0		142	69	0.485915	NM_033126	A0AV22	Silent	SNP	ENST00000276616.2	37	CCDS6240.1																																																																																			T|0.966;A|0.034	0.034	strong		0.498	PSKH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374628.1	NM_033126		A	87060793	T	A	87060793	2	1	22	1	0	0	0	0	0	0	0	1	12677	1422	50	5		5	PSKH2	8	87060793	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	12534712	87060793	59303229	1926	4827											
PSKH2	85481	hgsc.bcm.edu	37	chr8	87076651	87076651	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctccattaccatgtaaactTgatcctcagtctcaaagatc	12	12	5	12	0	2	2	2	1	1	1	6	2	4	2	3	0	2	2	3	0	4	3	rs16879427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:87076651T>C	ENST00000276616.2	-	2	469	c.395A>G	c.(394-396)cAa>cGa	p.Q132R	PSKH2_ENST00000517981.1_5'UTR	NM_033126.1	NP_149117.1	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	132	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		Q -> R (in dbSNP:rs16879427). {ECO:0000269|PubMed:17344846}.				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)			CATGTAAACTTGATCCTCAGT	0.542													C|||	503	0.100439	0.3533	0.036	5008	,	,		15987	0.0		0.005	False		,,,				2504	0.0061				p.Q132R		Atlas-SNP	.											PSKH2,right_upper_lobe,carcinoma,-1,1	PSKH2	79	1	0			c.A395G						PASS	.	C	ARG/GLN	1304,3102	697.8+/-406.3	192,920,1091	86	82	83		395	2.5	0	8	dbSNP_123	83	19,8581	818.4+/-406.9	0,19,4281	yes	missense	PSKH2	NM_033126.1	43	192,939,5372	CC,CT,TT		0.2209,29.596,10.1722	benign	132/386	87076651	1323,11683	2203	4300	6503	SO:0001583	missense	85481	exon2			TAAACTTGATCCT	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.395A>G	8.37:g.87076651T>C	ENSP00000276616:p.Gln132Arg	110	0	0		142	70	0.492958	NM_033126	A0AV22	Missense_Mutation	SNP	ENST00000276616.2	37	CCDS6240.1	186	0.08516483516483517	172	0.34959349593495936	12	0.03314917127071823	0	0.0	2	0.002638522427440633	C	0.021	-1.427937	0.01117	0.29596	0.002209	ENSG00000147613	ENST00000276616	T	0.64803	-0.12	5.22	2.46	0.29980	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	0.00012	0.0000	N	0.10874	0.06	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.28586	-1.0039	8	0.07175	T	0.84	.	9.205	0.37285	0.0:0.6926:0.0:0.3074	rs16879427;rs52809304;rs16879427	132	Q96QS6	KPSH2_HUMAN	R	132	ENSP00000276616:Q132R	ENSP00000276616:Q132R	Q	-	2	0	PSKH2	87145767	0.895000	0.30542	0.003000	0.11579	0.206000	0.24218	1.883000	0.39658	-0.015000	0.14150	-0.702000	0.03669	CAA	T|0.874;C|0.126	0.126	strong		0.542	PSKH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374628.1	NM_033126		C	87076651	T	C	87076651	3	2	22	1	0	0	0	0	1	0	0	0	12677	1812	63	3	768	3	PSKH2	8	87076651	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	15858	87076651	59287371	1927	4828											
ATP6V0D2	245972	hgsc.bcm.edu	37	chr8	87162515	87162515	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agaacgtagcggatcattacGgagtatgtgatgacactggc	12	9	13	7	3	1	3	1	2	0	1	1	5	1	5	0	3	3	2	0	3	4	3	rs10094744	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:87162515G>A	ENST00000285393.3	+	6	956	c.814G>A	c.(814-816)Gga>Aga	p.G272R	CTD-3118D11.2_ENST00000522679.1_RNA	NM_152565.1	NP_689778.1	Q8N8Y2	VA0D2_HUMAN	ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d2	272			G -> R (in dbSNP:rs10094744).		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						GGATCATTACGGAGTATGTGA	0.453													G|||	152	0.0303514	0.1089	0.0115	5008	,	,		18274	0.0		0.0	False		,,,				2504	0.0				p.G272R		Atlas-SNP	.											.	ATP6V0D2	61	.	0			c.G814A						PASS	.	G	ARG/GLY	421,3985	204.5+/-226.7	19,383,1801	100	90	94		814	5.3	0.1	8	dbSNP_119	94	5,8595	4.3+/-15.6	0,5,4295	yes	missense	ATP6V0D2	NM_152565.1	125	19,388,6096	AA,AG,GG		0.0581,9.5552,3.2754	benign	272/351	87162515	426,12580	2203	4300	6503	SO:0001583	missense	245972	exon6			CATTACGGAGTAT	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.814G>A	8.37:g.87162515G>A	ENSP00000285393:p.Gly272Arg	107	0	0		101	45	0.445545	NM_152565		Missense_Mutation	SNP	ENST00000285393.3	37	CCDS6241.1	37	0.01694139194139194	35	0.07113821138211382	2	0.0055248618784530384	0	0.0	0	0.0	G	14.33	2.504335	0.44558	0.095552	5.81E-4	ENSG00000147614	ENST00000285393	T	0.29917	1.55	6.17	5.27	0.74061	.	0.585174	0.17628	N	0.167492	T	0.00724	0.0024	L	0.48642	1.525	0.23689	N	0.997107	D	0.53462	0.96	B	0.38194	0.267	T	0.01940	-1.1243	10	0.40728	T	0.16	-22.0686	16.0952	0.81114	0.0:0.0:0.8659:0.1341	rs10094744;rs52810720;rs10094744	272	Q8N8Y2	VA0D2_HUMAN	R	272	ENSP00000285393:G272R	ENSP00000285393:G272R	G	+	1	0	ATP6V0D2	87231631	0.153000	0.22777	0.096000	0.21009	0.040000	0.13550	3.075000	0.50073	2.941000	0.99782	0.655000	0.94253	GGA	G|0.970;A|0.030	0.030	strong		0.453	ATP6V0D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374651.1	NM_152565		A	87162515	G	A	87162515	3	1	22	1	0	0	0	0	1	0	0	0	1174	1117	39	1	836	1	ATP6V0D2	8	87162515	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	85864	87162515	59201507	1928	4829											
WWP1	11059	hgsc.bcm.edu	37	chr8	87414308	87414308	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctacaagcactctagtccaAaactcatgctgctcgtatgt	11	11	6	13	1	2	0	1	0	1	0	4	0	3	0	2	0	5	4	2	0	6	3	rs10106066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:87414308A>G	ENST00000517970.1	+	8	907	c.600A>G	c.(598-600)caA>caG	p.Q200Q	WWP1_ENST00000341922.2_Intron|WWP1_ENST00000265428.4_Silent_p.Q200Q|WWP1_ENST00000349423.2_Intron	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	200					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						CTCTAGTCCAAAACTCATGCT	0.408													A|||	265	0.0529153	0.1921	0.013	5008	,	,		16493	0.0		0.001	False		,,,				2504	0.001				p.Q200Q		Atlas-SNP	.											.	WWP1	97	.	0			c.A600G						PASS	.	A		678,3728	286.0+/-278.5	47,584,1572	119	105	109		600	-4.8	0	8	dbSNP_119	109	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	WWP1	NM_007013.3		47,589,5867	GG,GA,AA		0.0581,15.3881,5.2514		200/923	87414308	683,12323	2203	4300	6503	SO:0001819	synonymous_variant	11059	exon8			AGTCCAAAACTCA	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.600A>G	8.37:g.87414308A>G		216	1	0.00462963		196	104	0.530612	NM_007013	O00307|Q5YLC1|Q96BP4	Silent	SNP	ENST00000517970.1	37	CCDS6242.1																																																																																			.	.	weak		0.408	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013		G	87414308	A	G	87414308	2	3	22	1	0	0	0	0	0	0	0	1	17430	11	1	3		3	WWP1	8	87414308	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	251793	87414308	58949714	1929	4830											
CPNE3	8895	hgsc.bcm.edu	37	chr8	87558846	87558846	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gaatttgaatgcataaatgaGaaaaaaaggcaaaagaaaaa	25	6	8	2	0	0	3	0	2	0	2	0	5	0	3	0	1	1	2	0	1	11	2	rs41333046	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:87558846G>C	ENST00000521271.1	+	10	918	c.756G>C	c.(754-756)gaG>gaC	p.E252D	CPNE3_ENST00000198765.4_Missense_Mutation_p.E252D	NM_003909.3	NP_003900.1	O75131	CPNE3_HUMAN	copine III	252			E -> D (in dbSNP:rs41333046).		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						GCATAAATGAGAAAAAAAGGC	0.308													G|||	571	0.114018	0.41	0.0303	5008	,	,		17040	0.004		0.003	False		,,,				2504	0.001				p.E252D		Atlas-SNP	.											CPNE3,NS,carcinoma,0,1	CPNE3	65	1	0			c.G756C						PASS	.	G	ASP/GLU	1372,3034	453.4+/-350.3	207,958,1038	90	103	98		756	1.6	1	8	dbSNP_127	98	14,8586	8.4+/-32.0	0,14,4286	yes	missense	CPNE3	NM_003909.3	45	207,972,5324	CC,CG,GG		0.1628,31.1394,10.6566	benign	252/538	87558846	1386,11620	2203	4300	6503	SO:0001583	missense	8895	exon10			AAATGAGAAAAAA	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.756G>C	8.37:g.87558846G>C	ENSP00000430934:p.Glu252Asp	265	0	0		270	141	0.522222	NM_003909	A8KA47|Q8IYA1	Missense_Mutation	SNP	ENST00000521271.1	37	CCDS6243.1	199|199	0.09111721611721611|0.09111721611721611	186|186	0.3780487804878049|0.3780487804878049	11|11	0.03038674033149171|0.03038674033149171	1|1	0.0017482517482517483|0.0017482517482517483	1|1	0.0013192612137203166|0.0013192612137203166	G|G	14.05|14.05	2.420410|2.420410	0.42918|0.42918	0.311394|0.311394	0.001628|0.001628	ENSG00000085719|ENSG00000085719	ENST00000198765;ENST00000521271|ENST00000517391	T;T|.	0.39787|.	1.06;1.06|.	5.52|5.52	1.62|1.62	0.23740|0.23740	C2 calcium/lipid-binding domain, CaLB (1);|.	0.106801|.	0.64402|.	D|.	0.000001|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.45352|0.45352	1.415|1.415	0.27719|0.27719	P|P	0.9451934|0.9451934	B|.	0.32051|.	0.354|.	B|.	0.26614|.	0.071|.	T|T	0.40739|0.40739	-0.9547|-0.9547	9|4	0.59425|.	D|.	0.04|.	-12.9148|-12.9148	9.7986|9.7986	0.40751|0.40751	0.5228:0.0:0.4772:0.0|0.5228:0.0:0.4772:0.0	rs41333046|rs41333046	252|.	O75131|.	CPNE3_HUMAN|.	D|T	252|141	ENSP00000198765:E252D;ENSP00000430934:E252D|.	ENSP00000198765:E252D|.	E|R	+|+	3|2	2|0	CPNE3|CPNE3	87627962|87627962	0.931000|0.931000	0.31567|0.31567	0.998000|0.998000	0.56505|0.56505	0.984000|0.984000	0.73092|0.73092	0.121000|0.121000	0.15667|0.15667	0.078000|0.078000	0.16900|0.16900	-0.355000|-0.355000	0.07637|0.07637	GAG|AGA	G|0.888;C|0.112	0.112	strong		0.308	CPNE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374994.1			C	87558846	G	C	87558846	3	2	22	1	0	0	0	0	1	0	0	0	3815	933	33	4	786	4	CPNE3	8	87558846	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	144538	87558846	58805176	1930	4831											
CNGB3	54714	hgsc.bcm.edu	37	chr8	87680282	87680282	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgctgtttggaagtttaattCgctttaagtactctgttaaa	10	18	8	5	1	1	0	0	0	1	0	2	1	1	1	0	1	2	6	0	1	6	8	rs16916632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:87680282C>T	ENST00000320005.5	-	5	655	c.608G>A	c.(607-609)cGa>cAa	p.R203Q		NM_019098.4	NP_061971.3	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	203			R -> Q (in ACHM3; unknown pathological significance; dbSNP:rs16916632). {ECO:0000269|PubMed:15712225}.		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						AAGTTTAATTCGCTTTAAGTA	0.398													C|||	278	0.0555112	0.1952	0.0101	5008	,	,		14978	0.003		0.0	False		,,,				2504	0.0102				p.R203Q		Atlas-SNP	.											.	CNGB3	176	.	0			c.G608A						PASS	.	C	GLN/ARG	679,3727	286.0+/-278.5	46,587,1570	238	228	231		608	-6.8	0	8	dbSNP_123	231	2,8598	1.2+/-3.3	0,2,4298	yes	missense	CNGB3	NM_019098.4	43	46,589,5868	TT,TC,CC		0.0233,15.4108,5.236	benign	203/810	87680282	681,12325	2203	4300	6503	SO:0001583	missense	54714	exon5			TTAATTCGCTTTA	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.608G>A	8.37:g.87680282C>T	ENSP00000316605:p.Arg203Gln	163	0	0		185	86	0.464865	NM_019098	C9JA51|Q9NRE9	Missense_Mutation	SNP	ENST00000320005.5	37	CCDS6244.1	73	0.033424908424908424	72	0.14634146341463414	1	0.0027624309392265192	0	0.0	0	0.0	C	12.18	1.862010	0.32884	0.154108	2.33E-4	ENSG00000170289	ENST00000320005	D	0.97016	-4.21	6.1	-6.81	0.01704	.	1.625600	0.03560	N	0.226891	T	0.07369	0.0186	L	0.40543	1.245	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.68375	-0.5425	9	0.23891	T	0.37	.	13.0899	0.59162	0.1009:0.116:0.0:0.7831	rs16916632;rs52789907;rs16916632	203;203	Q9NQW8-2;Q9NQW8	.;CNGB3_HUMAN	Q	203	ENSP00000316605:R203Q	ENSP00000316605:R203Q	R	-	2	0	CNGB3	87749398	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.590000	0.05760	-1.332000	0.02249	-0.143000	0.13931	CGA	C|0.951;T|0.049	0.049	strong		0.398	CNGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375107.1	NM_019098		T	87680282	C	T	87680282	3	4	22	1	0	0	0	0	1	0	0	0	3603	884	31	1	1877	1	CNGB3	8	87680282	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	121436	87680282	58683740	1931	4832											
DCAF4L2	138009	hgsc.bcm.edu	37	chr8	88885256	88885256	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	catgcacgggtaggtaggcgGagttattcacatgaccttcg	9	10	13	9	3	1	1	1	1	0	0	2	2	1	2	1	4	1	4	1	4	3	5	rs146716352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:88885256G>A	ENST00000319675.3	-	1	1040	c.944C>T	c.(943-945)tCc>tTc	p.S315F		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2	315										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						TAGGTAGGCGGAGTTATTCAC	0.542													G|||	11	0.00219649	0.0083	0.0	5008	,	,		19579	0.0		0.0	False		,,,				2504	0.0				p.S315F		Atlas-SNP	.											.	DCAF4L2	187	.	0			c.C944T						PASS	.	G	PHE/SER	45,4361	46.7+/-81.2	0,45,2158	108	102	104		944	0.1	0	8	dbSNP_134	104	0,8600		0,0,4300	yes	missense	DCAF4L2	NM_152418.3	155	0,45,6458	AA,AG,GG		0.0,1.0213,0.346	benign	315/396	88885256	45,12961	2203	4300	6503	SO:0001583	missense	138009	exon1			TAGGCGGAGTTAT	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.944C>T	8.37:g.88885256G>A	ENSP00000316496:p.Ser315Phe	199	0	0		185	87	0.47027	NM_152418		Missense_Mutation	SNP	ENST00000319675.3	37	CCDS6245.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	14.00	2.405976	0.42715	0.010213	0.0	ENSG00000176566	ENST00000319675	T	0.22945	1.93	1.39	0.0752	0.14398	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.113194	0.64402	D	0.000008	T	0.07773	0.0195	N	0.14661	0.345	0.22096	N	0.999368	B	0.25521	0.128	B	0.25614	0.062	T	0.24548	-1.0157	10	0.22706	T	0.39	.	5.3547	0.16055	0.0:0.0:0.3197:0.6803	.	315	Q8NA75	DC4L2_HUMAN	F	315	ENSP00000316496:S315F	ENSP00000316496:S315F	S	-	2	0	DCAF4L2	88954372	1.000000	0.71417	0.009000	0.14445	0.009000	0.06853	2.530000	0.45641	-0.175000	0.10725	-0.518000	0.04402	TCC	G|0.997;A|0.003	0.003	strong		0.542	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	NM_152418		A	88885256	G	A	88885256	3	1	22	1	0	0	0	0	1	0	0	0	4274	1174	41	2	247	2	DCAF4L2	8	88885256	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1204974	88885256	57478766	1932	4833											
TMEM64	169200	hgsc.bcm.edu	37	chr8	91637929	91637929	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgattccacctccagaaaaTgttagggtcctcttgttgta	9	15	8	9	0	1	2	0	1	1	1	4	2	4	2	4	1	0	3	4	1	4	6	rs75193995	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:91637929T>C	ENST00000458549.2	-	3	1290	c.1113A>G	c.(1111-1113)acA>acG	p.T371T	TMEM64_ENST00000519519.1_Silent_p.T110T|TMEM64_ENST00000418210.2_Silent_p.T319T	NM_001008495.3	NP_001008495.2	Q6YI46	TMM64_HUMAN	transmembrane protein 64	371					cytosolic calcium ion homeostasis (GO:0051480)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|regulation of ATPase activity (GO:0043462)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)	2			BRCA - Breast invasive adenocarcinoma(11;0.0598)			CTCCAGAAAATGTTAGGGTCC	0.408													T|||	27	0.00539137	0.0197	0.0014	5008	,	,		16021	0.0		0.0	False		,,,				2504	0.0				p.T371T		Atlas-SNP	.											.	TMEM64	31	.	0			c.A1113G						PASS	.	T	,	60,4346	57.4+/-93.9	2,56,2145	101	92	95		1113,957	-2.3	1	8	dbSNP_132	95	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	TMEM64	NM_001008495.3,NM_001146273.1	,	2,57,6444	CC,CT,TT		0.0116,1.3618,0.469	,	371/381,319/329	91637929	61,12945	2203	4300	6503	SO:0001819	synonymous_variant	169200	exon3			AGAAAATGTTAGG	AL834364	CCDS34920.2, CCDS55260.1	8q21.3	2005-08-09			ENSG00000180694	ENSG00000180694			25441	protein-coding gene	gene with protein product							Standard	NM_001008495		Approved	DKFZp762C1112	uc003yen.2	Q6YI46	OTTHUMG00000157185	ENST00000458549.2:c.1113A>G	8.37:g.91637929T>C		207	0	0		174	77	0.442529	NM_001008495	B4DUC0|F5GXM4|Q2HIZ7|Q8N3G6	Silent	SNP	ENST00000458549.2	37	CCDS34920.2																																																																																			T|0.995;C|0.005	0.005	strong		0.408	TMEM64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347825.1	NM_001008495		C	91637929	T	C	91637929	2	2	22	1	0	0	0	0	0	0	0	1	16208	1451	51	3		3	TMEM64	8	91637929	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2752673	91637929	54726093	1933	4834											
TMEM64	169200	hgsc.bcm.edu	37	chr8	91638019	91638019	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcagttccatttcacaagcTacaatagctgcattcaattc	12	14	4	11	0	3	0	3	0	0	0	5	0	4	0	1	0	4	4	1	0	5	7	rs61741096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:91638019T>C	ENST00000458549.2	-	3	1200	c.1023A>G	c.(1021-1023)gtA>gtG	p.V341V	TMEM64_ENST00000519519.1_Silent_p.V80V|TMEM64_ENST00000418210.2_Silent_p.V289V	NM_001008495.3	NP_001008495.2	Q6YI46	TMM64_HUMAN	transmembrane protein 64	341					cytosolic calcium ion homeostasis (GO:0051480)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|regulation of ATPase activity (GO:0043462)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)	2			BRCA - Breast invasive adenocarcinoma(11;0.0598)			TTTCACAAGCTACAATAGCTG	0.353													T|||	24	0.00479233	0.0174	0.0	5008	,	,		17444	0.0		0.001	False		,,,				2504	0.0				p.V341V		Atlas-SNP	.											.	TMEM64	31	.	0			c.A1023G						PASS	.	T	,	57,4349	52.9+/-88.7	0,57,2146	95	87	89		1023,867	0.2	1	8	dbSNP_129	89	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous	TMEM64	NM_001008495.3,NM_001146273.1	,	0,58,6445	CC,CT,TT		0.0116,1.2937,0.4459	,	341/381,289/329	91638019	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	169200	exon3			ACAAGCTACAATA	AL834364	CCDS34920.2, CCDS55260.1	8q21.3	2005-08-09			ENSG00000180694	ENSG00000180694			25441	protein-coding gene	gene with protein product							Standard	NM_001008495		Approved	DKFZp762C1112	uc003yen.2	Q6YI46	OTTHUMG00000157185	ENST00000458549.2:c.1023A>G	8.37:g.91638019T>C		156	0	0		151	68	0.450331	NM_001008495	B4DUC0|F5GXM4|Q2HIZ7|Q8N3G6	Silent	SNP	ENST00000458549.2	37	CCDS34920.2																																																																																			T|0.996;C|0.004	0.004	strong		0.353	TMEM64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347825.1	NM_001008495		C	91638019	T	C	91638019	2	2	22	1	0	0	0	0	0	0	0	1	16208	1509	53	3		3	TMEM64	8	91638019	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	90	91638019	54726003	1934	4835											
PDP1	54704	hgsc.bcm.edu	37	chr8	94935623	94935623	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcatgcatcaccaacagccaAtagctgttggtggctacaag	12	8	10	11	0	1	0	1	0	0	0	1	0	1	0	2	2	5	5	2	2	5	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:94935623A>G	ENST00000297598.4	+	2	1605	c.1336A>G	c.(1336-1338)Ata>Gta	p.I446V	PDP1_ENST00000520728.1_Missense_Mutation_p.I446V|PDP1_ENST00000517764.1_Missense_Mutation_p.I446V|PDP1_ENST00000396200.3_Missense_Mutation_p.I471V	NM_001161781.1|NM_018444.3	NP_001155253.1|NP_060914.2	Q9P0J1	PDP1_HUMAN	pyruvate dehyrogenase phosphatase catalytic subunit 1	446					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						CCAACAGCCAATAGCTGTTGG	0.493																																					p.I471V		Atlas-SNP	.											PDP1,caecum,carcinoma,-2,1	PDP1	97	1	0			c.A1411G						PASS	.						80	80	80					8																	94935623		2203	4300	6503	SO:0001583	missense	54704	exon3			CAGCCAATAGCTG	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.1336A>G	8.37:g.94935623A>G	ENSP00000297598:p.Ile446Val	159	0	0		221	117	0.529412	NM_001161780	B3KX71|J3KPU0|Q5U5K1	Missense_Mutation	SNP	ENST00000297598.4	37	CCDS6259.1	.	.	.	.	.	.	.	.	.	.	A	5.314	0.243239	0.10077	.	.	ENSG00000164951	ENST00000297598;ENST00000520728;ENST00000396200;ENST00000517764	T;T;T;T	0.41065	1.03;1.03;1.01;1.03	6.03	6.03	0.97812	Protein phosphatase 2C-like (3);	0.127835	0.64402	D	0.000016	T	0.16896	0.0406	N	0.02247	-0.625	0.42964	D	0.994412	B;B	0.12013	0.005;0.001	B;B	0.10450	0.005;0.005	T	0.18871	-1.0323	10	0.02654	T	1	-7.6316	12.4101	0.55461	0.86:0.14:0.0:0.0	.	497;446	B4DYX8;Q9P0J1	.;PDP1_HUMAN	V	446;446;471;446	ENSP00000297598:I446V;ENSP00000428317:I446V;ENSP00000379503:I471V;ENSP00000430380:I446V	ENSP00000297598:I446V	I	+	1	0	PDP1	95004799	1.000000	0.71417	0.994000	0.49952	0.997000	0.91878	4.348000	0.59379	2.308000	0.77769	0.533000	0.62120	ATA	.	.	none		0.493	PDP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378415.2	NM_018444		G	94935623	A	G	94935623	3	3	22	1	0	0	0	0	1	0	0	0	11694	101	4	3	1519	3	PDP1	8	94935623	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	3297604	94935623	51428399	1935	4836											
DPY19L4	286148	hgsc.bcm.edu	37	chr8	95746883	95746883	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttatttcaacgctttgcaaaGattttcattggctgtcttgc	8	18	7	8	1	3	1	2	0	1	1	3	1	3	1	0	1	3	3	0	1	3	7	rs113391412	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:95746883G>A	ENST00000414645.2	+	3	252	c.153G>A	c.(151-153)aaG>aaA	p.K51K		NM_181787.2	NP_861452.2	Q7Z388	D19L4_HUMAN	dpy-19-like 4 (C. elegans)	51						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)	21	Breast(36;3.85e-06)					GCTTTGCAAAGATTTTCATTG	0.348													G|||	49	0.00978435	0.0363	0.0014	5008	,	,		19614	0.0		0.0	False		,,,				2504	0.0				p.K51K		Atlas-SNP	.											.	DPY19L4	60	.	0			c.G153A						PASS	.	G		136,4270	93.9+/-132.6	1,134,2068	89	84	85		153	4.2	1	8	dbSNP_132	85	0,8600		0,0,4300	no	coding-synonymous	DPY19L4	NM_181787.2		1,134,6368	AA,AG,GG		0.0,3.0867,1.0457		51/724	95746883	136,12870	2203	4300	6503	SO:0001819	synonymous_variant	286148	exon3			TGCAAAGATTTTC		CCDS34924.1	8q22.1	2006-11-24			ENSG00000156162	ENSG00000156162			27829	protein-coding gene	gene with protein product		613895					Standard	NM_181787		Approved		uc003ygx.2	Q7Z388	OTTHUMG00000164589	ENST00000414645.2:c.153G>A	8.37:g.95746883G>A		90	0	0		114	67	0.587719	NM_181787	Q6ZW32|Q6ZW42|Q7Z329	Silent	SNP	ENST00000414645.2	37	CCDS34924.1																																																																																			G|0.988;A|0.012	0.012	strong		0.348	DPY19L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379339.1	NM_181787		A	95746883	G	A	95746883	2	1	22	1	0	0	0	0	0	0	0	1	4745	933	33	2		2	DPY19L4	8	95746883	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	811260	95746883	50617139	1936	4837											
TP53INP1	94241	hgsc.bcm.edu	37	chr8	95942773	95942773	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ttgtgcttgacttgccgaggGtggcaatccctggtaagatt	7	13	13	8	1	0	2	0	1	0	1	1	3	1	2	2	3	2	3	2	3	2	5	rs77630257	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:95942773G>A	ENST00000342697.4	-	4	1064	c.657C>T	c.(655-657)caC>caT	p.H219H	TP53INP1_ENST00000378776.4_Silent_p.H164H|TP53INP1_ENST00000448464.2_3'UTR|NDUFAF6_ENST00000396113.1_Intron	NM_033285.3	NP_150601.1	Q96A56	T53I1_HUMAN	tumor protein p53 inducible nuclear protein 1	219					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)					CTTGCCGAGGGTGGCAATCCC	0.473													G|||	42	0.00838658	0.0303	0.0029	5008	,	,		19735	0.0		0.0	False		,,,				2504	0.0				p.H219H		Atlas-SNP	.											.	TP53INP1	22	.	0			c.C657T						PASS	.	G	,	125,4281	92.5+/-131.2	1,123,2079	205	211	209		,657	5.2	1	8	dbSNP_132	209	0,8600		0,0,4300	no	utr-3,coding-synonymous	TP53INP1	NM_001135733.1,NM_033285.3	,	1,123,6379	AA,AG,GG		0.0,2.837,0.9611	,	,219/241	95942773	125,12881	2203	4300	6503	SO:0001819	synonymous_variant	94241	exon4			CCGAGGGTGGCAA	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.657C>T	8.37:g.95942773G>A		195	0	0		201	82	0.40796	NM_033285	B2RCE5|Q969R9	Silent	SNP	ENST00000342697.4	37	CCDS6265.1																																																																																			A|0.010;G|0.990	0.010	strong		0.473	TP53INP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379818.1			A	95942773	G	A	95942773	2	1	22	1	0	0	0	0	0	0	0	1	16403	1252	44	2		2	TP53INP1	8	95942773	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	195890	95942773	50421249	1937	4838											
MTERFD1	51001	hgsc.bcm.edu	37	chr8	97263180	97263180	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agagaaaattgcatgattttTtgtcaggaatgctcccagtt	12	14	9	6	0	1	2	1	1	0	1	2	4	2	3	1	1	2	3	1	1	3	5	rs112357919	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:97263180T>G	ENST00000287025.3	-	4	729	c.631A>C	c.(631-633)Aaa>Caa	p.K211Q	MTERFD1_ENST00000524341.1_Missense_Mutation_p.K21Q|MTERFD1_ENST00000522822.1_Missense_Mutation_p.K90Q|MTERFD1_ENST00000523821.1_Missense_Mutation_p.K211Q	NM_015942.3	NP_057026.3	Q96E29	MTEF3_HUMAN		211					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)					GCATGATTTTTTGTCAGGAAT	0.363													T|||	215	0.0429313	0.1566	0.0101	5008	,	,		12111	0.0		0.001	False		,,,				2504	0.0				p.K211Q		Atlas-SNP	.											.	MTERFD1	50	.	0			c.A631C						PASS	.	T	GLN/LYS	602,3804	263.1+/-265.3	36,530,1637	113	116	115		631	6	1	8	dbSNP_132	115	3,8597	3.0+/-9.4	0,3,4297	yes	missense	MTERFD1	NM_015942.3	53	36,533,5934	GG,GT,TT		0.0349,13.6632,4.6517	probably-damaging	211/418	97263180	605,12401	2203	4300	6503	SO:0001583	missense	51001	exon4			GATTTTTTGTCAG																												ENST00000287025.3:c.631A>C	8.37:g.97263180T>G	ENSP00000287025:p.Lys211Gln	169	0	0		163	82	0.503067	NM_015942	B3KMG6|G3V130|Q9Y301	Missense_Mutation	SNP	ENST00000287025.3	37	CCDS6270.1	79	0.036172161172161175	76	0.15447154471544716	3	0.008287292817679558	0	0.0	0	0.0	T	22.3	4.273758	0.80580	0.136632	3.49E-4	ENSG00000156469	ENST00000523821;ENST00000522822;ENST00000524341;ENST00000287025	T;T;T;T	0.17213	2.73;2.73;2.29;2.73	5.98	5.98	0.97165	.	0.191366	0.51477	D	0.000091	T	0.00210	0.0006	M	0.69823	2.125	0.20821	P	0.999846152	D;D	0.65815	0.995;0.995	P;P	0.58820	0.846;0.799	T	0.01298	-1.1392	9	0.33940	T	0.23	-9.9875	15.0407	0.71788	0.0:0.0:0.0:1.0	.	211;211	E5RIK9;Q96E29	.;MTER1_HUMAN	Q	211;90;21;211	ENSP00000429400:K211Q;ENSP00000430138:K90Q;ENSP00000429267:K21Q;ENSP00000287025:K211Q	ENSP00000287025:K211Q	K	-	1	0	MTERFD1	97332356	1.000000	0.71417	0.963000	0.40424	0.946000	0.59487	4.381000	0.59587	2.289000	0.77006	0.482000	0.46254	AAA	T|0.958;G|0.042	0.042	strong		0.363	MTERFD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379876.1			G	97263180	T	G	97263180	3	3	22	1	0	0	0	0	1	0	0	0	9928	1850	64	5	642	5	MTERFD1	8	97263180	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1320407	97263180	49100842	1938	4839											
TSPYL5	85453	hgsc.bcm.edu	37	chr8	98289922	98289922	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cgcgccagcctgcacctgtgCcgcctgggtgtcttccccga	3	8	12	18	4	1	0	0	0	1	0	2	1	2	0	7	1	3	1	7	1	0	1	rs200123082	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:98289922C>T	ENST00000322128.3	-	1	254	c.151G>A	c.(151-153)Gca>Aca	p.A51T		NM_033512.2	NP_277047.2	Q86VY4	TSYL5_HUMAN	TSPY-like 5	51					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)					TGCACCTGTGCCGCCTGGGTG	0.746													C|||	37	0.00738818	0.0257	0.0043	5008	,	,		10609	0.0		0.0	False		,,,				2504	0.0				p.A51T		Atlas-SNP	.											.	TSPYL5	48	.	0			c.G151A						PASS	.	C	THR/ALA	59,4045		1,57,1994	5	7	6		151	1.2	0	8		6	2,8036		0,2,4017	yes	missense	TSPYL5	NM_033512.2	58	1,59,6011	TT,TC,CC		0.0249,1.4376,0.5024	possibly-damaging	51/418	98289922	61,12081	2052	4019	6071	SO:0001583	missense	85453	exon1			CCTGTGCCGCCTG	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.151G>A	8.37:g.98289922C>T	ENSP00000322802:p.Ala51Thr	29	0	0		32	18	0.5625	NM_033512	B3KRF0|Q9C0B3	Missense_Mutation	SNP	ENST00000322128.3	37	CCDS34927.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	C	2.842	-0.240359	0.05944	0.014376	2.49E-4	ENSG00000180543	ENST00000322128	T	0.23754	1.89	4.03	1.24	0.21308	.	0.260319	0.20293	N	0.095194	T	0.04998	0.0134	N	0.20986	0.625	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.32719	-0.9896	10	0.02654	T	1	-1.04	3.5525	0.07851	0.1976:0.5914:0.0:0.211	.	51	Q86VY4	TSYL5_HUMAN	T	51	ENSP00000322802:A51T	ENSP00000322802:A51T	A	-	1	0	TSPYL5	98359098	0.996000	0.38824	0.014000	0.15608	0.014000	0.08584	2.417000	0.44653	0.261000	0.21753	-0.258000	0.10820	GCA	C|0.994;T|0.006	0.006	strong		0.746	TSPYL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380611.1	NM_033512		T	98289922	C	T	98289922	3	4	22	1	0	0	0	0	1	0	0	0	16677	739	26	2	1106	2	TSPYL5	8	98289922	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1026742	98289922	48074100	1939	4840											
MATN2	4147	hgsc.bcm.edu	37	chr8	99028811	99028811	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccacggttgtgaacattcGtgtgtaagcagtgaagattc	11	11	12	7	2	0	3	0	2	0	1	2	4	0	3	1	1	2	3	1	1	3	4	rs79255841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:99028811G>A	ENST00000520016.1	+	10	1741	c.1617G>A	c.(1615-1617)tcG>tcA	p.S539S	MATN2_ENST00000521689.1_Silent_p.S539S|MATN2_ENST00000522025.2_Silent_p.S255S|MATN2_ENST00000524308.1_Silent_p.S498S|MATN2_ENST00000254898.5_Silent_p.S539S			O00339	MATN2_HUMAN	matrilin 2	539	EGF-like 8. {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)			GTGAACATTCGTGTGTAAGCA	0.418													G|||	139	0.0277556	0.0953	0.0187	5008	,	,		19696	0.0		0.0	False		,,,				2504	0.0				p.S539S		Atlas-SNP	.											MATN2_ENST00000520016,NS,carcinoma,+1,2	MATN2	165	2	0			c.G1617A						PASS	.	G	,	355,3435		11,333,1551	108	102	104		1617,1617	-11.3	0	8	dbSNP_132	104	4,8248		0,4,4122	no	coding-synonymous,coding-synonymous	MATN2	NM_002380.3,NM_030583.2	,	11,337,5673	AA,AG,GG		0.0485,9.3668,2.9812	,	539/957,539/938	99028811	359,11683	1895	4126	6021	SO:0001819	synonymous_variant	4147	exon11			ACATTCGTGTGTA	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.1617G>A	8.37:g.99028811G>A		208	0	0		204	104	0.509804	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Silent	SNP	ENST00000520016.1	37	CCDS55264.1	41	0.018772893772893772	35	0.07113821138211382	6	0.016574585635359115	0	0.0	0	0.0	G	0.127	-1.118394	0.01785	0.093668	4.85E-4	ENSG00000132561	ENST00000518154;ENST00000517321	.	.	.	5.67	-11.3	0.00108	.	.	.	.	.	T	0.01156	0.0038	.	.	.	0.52099	D	0.999946	.	.	.	.	.	.	T	0.30851	-0.9964	4	.	.	.	-0.062	1.117	0.01716	0.232:0.3145:0.2304:0.2231	.	.	.	.	M	322;14	.	.	V	+	1	0	MATN2	99097987	0.000000	0.05858	0.012000	0.15200	0.010000	0.07245	-6.461000	0.00065	-2.310000	0.00650	-1.185000	0.01705	GTG	G|0.976;A|0.024	0.024	strong		0.418	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1			A	99028811	G	A	99028811	2	1	22	1	0	0	0	0	0	0	0	1	9343	1132	40	1		1	MATN2	8	99028811	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	738889	99028811	47335211	1940	4841											
PABPC1	26986	hgsc.bcm.edu	37	chr8	101721705	101721705	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctgtgggatagctgccatGaagtaacctgaaggaggtgc	11	8	14	8	0	0	2	0	2	0	0	0	4	0	4	3	3	4	2	3	3	4	2	rs201017624	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:101721705G>T	ENST00000318607.5	-	8	2355	c.1227C>A	c.(1225-1227)ttC>ttA	p.F409L	AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000519596.1_5'UTR|PABPC1_ENST00000519004.1_Missense_Mutation_p.F364L|PABPC1_ENST00000522387.1_Missense_Mutation_p.F377L	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	409					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)			TAGCTGCCATGAAGTAACCTG	0.488													g|||	1288	0.257188	0.2943	0.2089	5008	,	,		21380	0.2649		0.2107	False		,,,				2504	0.2812				p.F409L		Atlas-SNP	.											.	PABPC1	76	.	0			c.C1227A						PASS	.						101	92	95					8																	101721705		2203	4300	6503	SO:0001583	missense	26986	exon8			TGCCATGAAGTAA	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.1227C>A	8.37:g.101721705G>T	ENSP00000313007:p.Phe409Leu	200	0	0		264	48	0.181818	NM_002568	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	g|g|g	17.00|17.00|17.00	3.276204|3.276204|3.276204	0.59649|0.59649|0.59649	.|.|.	.|.|.	ENSG00000070756|ENSG00000070756|ENSG00000070756	ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387|ENST00000519596|ENST00000517403;ENST00000519100	T;T;T|.|.	0.29142|.|.	1.67;1.58;2.65|.|.	5.37|5.37|5.37	4.5|4.5|4.5	0.54988|0.54988|0.54988	.|.|.	0.000000|.|.	0.64402|.|.	D|.|.	0.000001|.|.	T|T|.	0.61160|0.61160|.	0.2325|0.2325|.	L|L|L	0.46819|0.46819|0.46819	1.47|1.47|1.47	0.58432|0.58432|0.58432	D|D|D	0.999997|0.999997|0.999997	B;B;B|.|.	0.23937|.|.	0.094;0.024;0.009|.|.	B;B;B|.|.	0.19946|.|.	0.027;0.01;0.013|.|.	T|T|.	0.58747|0.58747|.	-0.7582|-0.7582|.	10|5|.	0.49607|.|.	T|.|.	0.09|.|.	.|.|.	14.6297|14.6297|14.6297	0.68647|0.68647|0.68647	0.0702:0.0:0.9298:0.0|0.0702:0.0:0.9298:0.0|0.0702:0.0:0.9298:0.0	.|.|.	377;409;409|.|.	E7ERJ7;B3KT93;P11940|.|.	.;.;PABP1_HUMAN|.|.	L|N|X	409;409;364;377|242|62;278	ENSP00000313007:F409L;ENSP00000429594:F364L;ENSP00000429395:F377L|.|.	ENSP00000313007:F409L|.|.	F|H|S	-|-|-	3|1|2	2|0|0	PABPC1|PABPC1|PABPC1	101790881|101790881|101790881	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	7.998000|7.998000|7.998000	0.88491|0.88491|0.88491	1.419000|1.419000|1.419000	0.47118|0.47118|0.47118	-0.119000|-0.119000|-0.119000	0.15052|0.15052|0.15052	TTC|CAT|TCA	G|0.944;T|0.057	0.057	strong		0.488	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568		T	101721705	G	T	101721705	3	4	22	1	0	0	0	0	1	0	0	0	11372	1281	45	4	711	4	PABPC1	8	101721705	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2692894	101721705	44642317	1941	4842											
RRM2B	50484	hgsc.bcm.edu	37	chr8	103251034	103251034	+	Intron	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgtgactgcggtgagggggaAgacgcaacagcaacatttac	12	6	14	9	3	0	3	0	2	0	1	0	4	0	4	0	3	5	2	0	3	4	2	rs72554092	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:103251034A>C	ENST00000251810.3	-	1	292				KB-431C1.4_ENST00000520820.1_RNA|RRM2B_ENST00000519317.1_Intron|RRM2B_ENST00000395912.2_Intron|RRM2B_ENST00000519962.1_Intron	NM_001172478.1|NM_015713.4	NP_001165949.1|NP_056528.2	Q7LG56	RIR2B_HUMAN	ribonucleotide reductase M2 B (TP53 inducible)						deoxyribonucleoside diphosphate metabolic process (GO:0009186)|deoxyribonucleoside triphosphate metabolic process (GO:0009200)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA repair (GO:0006281)|kidney development (GO:0001822)|mitochondrial DNA replication (GO:0006264)|negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902254)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|renal system process (GO:0003014)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	9	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;0.000728)		Cladribine(DB00242)	GTGAGGGGGAAGACGCAACAG	0.637								Modulation of nucleotide pools					A|||	104	0.0207668	0.0764	0.0029	5008	,	,		13321	0.0		0.0	False		,,,				2504	0.001				p.L6R		Atlas-SNP	.											.	RRM2B	31	.	0			c.T17G						PASS	.	A	ARG/LEU,,	414,3992	200.4+/-223.7	20,374,1809	63	62	62		17,,	-4.6	0	8	dbSNP_130	62	2,8598	2.2+/-6.3	0,2,4298	yes	missense,intron,intron	RRM2B	NM_001172477.1,NM_001172478.1,NM_015713.4	102,,	20,376,6107	CC,CA,AA		0.0233,9.3963,3.1985	,,	6/424,,	103251034	416,12590	2203	4300	6503	SO:0001627	intron_variant	50484	exon1			GGGGGAAGACGCA	AB036532	CCDS34932.1, CCDS55267.1	8q23.1	2014-09-17			ENSG00000048392	ENSG00000048392			17296	protein-coding gene	gene with protein product		604712				10716435, 10980602, 17486094	Standard	NM_015713		Approved	p53R2	uc022azl.1	Q7LG56	OTTHUMG00000164776	ENST00000251810.3:c.48+20T>G	8.37:g.103251034A>C		28	0	0		26	15	0.576923	NM_001172477	B4E2N4|Q17R22|Q75PQ6|Q75PQ7|Q75PY8|Q75PY9|Q86YE3|Q9NPD6|Q9NTD8|Q9NUW3	Missense_Mutation	SNP	ENST00000251810.3	37	CCDS34932.1																																																																																			A|0.975;C|0.025	0.025	strong		0.637	RRM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380191.3			C	103251034	A	C	103251034	1	2	22	0	1	0	0	0	0	0	0	0	13698	72	3	5		5	RRM2B	8	103251034	Intron	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1529329	103251034	43112988	1942	4843											
ODF1	4956	hgsc.bcm.edu	37	chr8	103573024	103573024	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcccctgcaacccctgcaGcccctgcaacccgtgcagcc	7	4	8	22	1	0	0	0	0	0	0	0	0	0	0	8	0	9	4	8	0	2	0	rs568456031|rs143802899|rs111689913|rs58232162|rs386728348	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:103573024G>A	ENST00000285402.3	+	2	821	c.665G>A	c.(664-666)aGc>aAc	p.S222N	ODF1_ENST00000518835.1_Missense_Mutation_p.S15N	NM_024410.3	NP_077721.2	Q14990	ODFP1_HUMAN	outer dense fiber of sperm tails 1	222	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)			aacccctgcagcccctgcaac	0.567													A|||	442	0.0882588	0.3011	0.0303	5008	,	,		16173	0.0129		0.0099	False		,,,				2504	0.0				p.S222N		Atlas-SNP	.											.	ODF1	55	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.G665A						PASS	.	A	ASN/SER	1013,3353		178,657,1348	60	59	59		665	-4.1	0	8	dbSNP_132	59	30,8398		1,28,4185	no	missense	ODF1	NM_024410.3	46	179,685,5533	AA,AG,GG		0.356,23.202,8.1523	benign	222/251	103573024	1043,11751	2183	4214	6397	SO:0001583	missense	4956	exon2			CCTGCAGCCCCTG	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.665G>A	8.37:g.103573024G>A	ENSP00000285402:p.Ser222Asn	145	0	0		106	42	0.396226	NM_024410	Q3SX72	Missense_Mutation	SNP	ENST00000285402.3	37	CCDS6293.1	188	0.08608058608058608	164	0.3333333333333333	11	0.03038674033149171	9	0.015734265734265736	4	0.005277044854881266	A	0.034	-1.317862	0.01320	0.23202	0.00356	ENSG00000155087	ENST00000285402;ENST00000518835	D;T	0.86164	-2.08;1.89	4.92	-4.11	0.03928	.	1.048210	0.07416	N	0.893166	T	0.00012	0.0000	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.00688	-1.1609	10	0.22706	T	0.39	-12.522	13.0969	0.59197	0.6974:0.0:0.3026:0.0	.	222	Q14990	ODFP1_HUMAN	N	222;15	ENSP00000285402:S222N;ENSP00000430023:S15N	ENSP00000285402:S222N	S	+	2	0	ODF1	103642200	0.004000	0.15560	0.004000	0.12327	0.002000	0.02628	-1.097000	0.03349	-1.135000	0.02895	-1.581000	0.00855	AGC	G|0.893;A|0.107	0.107	strong		0.567	ODF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379884.1			A	103573024	G	A	103573024	3	1	22	1	0	0	0	0	1	0	0	0	10835	971	34	2	671	2	ODF1	8	103573024	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	321990	103573024	42790998	1943	4844											
ODF1	4956	hgsc.bcm.edu	37	chr8	103573086	103573086	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gttatccctgtggaagccgaTtttcctgtaggaagatgatt	9	14	11	7	1	0	2	0	1	0	1	2	5	2	4	3	2	1	2	3	2	4	5	rs11995900	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:103573086T>C	ENST00000285402.3	+	2	883	c.727T>C	c.(727-729)Ttt>Ctt	p.F243L	ODF1_ENST00000518835.1_Missense_Mutation_p.F36L	NM_024410.3	NP_077721.2	Q14990	ODFP1_HUMAN	outer dense fiber of sperm tails 1	243			F -> L (in dbSNP:rs11995900).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|outer dense fiber (GO:0001520)				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)			TGGAAGCCGATTTTCCTGTAG	0.537													T|||	386	0.0770767	0.2587	0.0303	5008	,	,		19863	0.0129		0.0099	False		,,,				2504	0.0				p.F243L		Atlas-SNP	.											.	ODF1	55	.	0			c.T727C						PASS	.	T	LEU/PHE	1038,3368	365.1+/-317.3	121,796,1286	93	100	97		727	4	1	8	dbSNP_120	97	37,8563	22.8+/-68.1	0,37,4263	yes	missense	ODF1	NM_024410.3	22	121,833,5549	CC,CT,TT		0.4302,23.5588,8.2654	benign	243/251	103573086	1075,11931	2203	4300	6503	SO:0001583	missense	4956	exon2			AGCCGATTTTCCT	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.727T>C	8.37:g.103573086T>C	ENSP00000285402:p.Phe243Leu	93	0	0		79	31	0.392405	NM_024410	Q3SX72	Missense_Mutation	SNP	ENST00000285402.3	37	CCDS6293.1	170	0.07783882783882784	146	0.2967479674796748	11	0.03038674033149171	9	0.015734265734265736	4	0.005277044854881266	T	15.81	2.942523	0.53079	0.235588	0.004302	ENSG00000155087	ENST00000285402;ENST00000518835	T;T	0.29655	1.56;1.73	5.18	3.95	0.45737	.	0.114042	0.40302	N	0.001133	T	0.00012	0.0000	N	0.22421	0.69	0.32344	P	0.559367	B	0.11235	0.004	B	0.12156	0.007	T	0.24083	-1.0170	9	0.87932	D	0	-31.0421	8.7103	0.34380	0.1694:0.0:0.0:0.8306	rs11995900;rs52827661;rs59122996;rs11995900	243	Q14990	ODFP1_HUMAN	L	243;36	ENSP00000285402:F243L;ENSP00000430023:F36L	ENSP00000285402:F243L	F	+	1	0	ODF1	103642262	0.945000	0.32115	1.000000	0.80357	0.997000	0.91878	2.400000	0.44504	2.106000	0.64143	0.528000	0.53228	TTT	T|0.911;C|0.089	0.089	strong		0.537	ODF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379884.1			C	103573086	T	C	103573086	3	2	22	1	0	0	0	0	1	0	0	0	10835	1493	52	3	733	3	ODF1	8	103573086	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	62	103573086	42790936	1944	4845											
ATP6V1C1	528	hgsc.bcm.edu	37	chr8	104054603	104054603	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcttggttggcttgtcagaTgaactggctaaactggatgc	8	13	13	7	0	2	2	1	1	1	1	2	3	2	3	0	4	3	3	0	4	3	4	rs7009365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:104054603T>C	ENST00000395862.3	+	3	327	c.168T>C	c.(166-168)gaT>gaC	p.D56D	ATP6V1C1_ENST00000518738.1_Silent_p.D56D|ATP6V1C1_ENST00000521514.1_5'UTR|ATP6V1C1_ENST00000518857.1_Intron	NM_001695.4	NP_001686.1	P21283	VATC1_HUMAN	ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C1	56					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)			GCTTGTCAGATGAACTGGCTA	0.373													T|||	382	0.076278	0.2685	0.0375	5008	,	,		19747	0.0		0.0	False		,,,				2504	0.001				p.D56D		Atlas-SNP	.											.	ATP6V1C1	33	.	0			c.T168C						PASS	.	T		917,3489	353.1+/-312.0	113,691,1399	226	216	220		168	0.8	1	8	dbSNP_116	220	10,8590	4.3+/-15.6	1,8,4291	no	coding-synonymous	ATP6V1C1	NM_001695.4		114,699,5690	CC,CT,TT		0.1163,20.8125,7.1275		56/383	104054603	927,12079	2203	4300	6503	SO:0001819	synonymous_variant	528	exon3			GTCAGATGAACTG	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.168T>C	8.37:g.104054603T>C		201	0	0		157	82	0.522293	NM_001695		Silent	SNP	ENST00000395862.3	37	CCDS6296.1																																																																																			T|0.922;C|0.078	0.078	strong		0.373	ATP6V1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380101.1	NM_001695		C	104054603	T	C	104054603	2	2	22	1	0	0	0	0	0	0	0	1	1180	1461	51	3		3	ATP6V1C1	8	104054603	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	481517	104054603	42309419	1945	4846											
BAALC	79870	hgsc.bcm.edu	37	chr8	104240275	104240275	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caccattaatgtaacagataGcatccaacagatggacagaa	18	7	7	9	0	0	3	0	0	0	3	1	4	1	4	2	1	3	2	2	1	5	3	rs34542607	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:104240275G>C	ENST00000297574.6	+	4	630	c.491G>C	c.(490-492)aGc>aCc	p.S164T	RP11-318M2.2_ENST00000499522.2_RNA|BAALC_ENST00000309982.5_Missense_Mutation_p.S129T|BAALC_ENST00000438105.2_3'UTR|RP11-318M2.2_ENST00000523614.2_RNA|BAALC_ENST00000523754.1_3'UTR|RP11-318M2.3_ENST00000523775.1_RNA			Q8WXS3	BAALC_HUMAN	brain and acute leukemia, cytoplasmic	164			S -> T (in dbSNP:rs34542607).			cytoplasm (GO:0005737)|membrane (GO:0016020)				kidney(1)|large_intestine(3)|lung(3)	7			OV - Ovarian serous cystadenocarcinoma(57;3.49e-05)|STAD - Stomach adenocarcinoma(118;0.133)			GTAACAGATAGCATCCAACAG	0.408													G|||	124	0.0247604	0.0908	0.0058	5008	,	,		24074	0.0		0.0	False		,,,				2504	0.0				p.S129T		Atlas-SNP	.											.	BAALC	15	.	0			c.G386C						PASS	.	G	,THR/SER	395,4011	198.1+/-222.0	21,353,1829	127	109	115		,386	3.9	0.9	8	dbSNP_126	115	1,8599	1.2+/-3.3	0,1,4299	yes	utr-3,missense	BAALC	NM_001024372.1,NM_024812.2	,58	21,354,6128	CC,CG,GG		0.0116,8.965,3.0447	,benign	,129/146	104240275	396,12610	2203	4300	6503	SO:0001583	missense	79870	exon3			CAGATAGCATCCA	AF363578	CCDS6297.1, CCDS47906.1	8q22.3	2008-07-29			ENSG00000164929	ENSG00000164929			14333	protein-coding gene	gene with protein product		606602				11707601	Standard	NM_024812		Approved		uc003yld.3	Q8WXS3	OTTHUMG00000164782	ENST00000297574.6:c.491G>C	8.37:g.104240275G>C	ENSP00000297574:p.Ser164Thr	72	0	0		81	47	0.580247	NM_024812	Q8WTP6|Q8WXS0|Q8WXS1|Q8WXS2|Q9HA93	Missense_Mutation	SNP	ENST00000297574.6	37		56	0.02564102564102564	55	0.11178861788617886	1	0.0027624309392265192	0	0.0	0	0.0	G	12.02	1.813455	0.32053	0.08965	1.16E-4	ENSG00000164929	ENST00000309982;ENST00000297574	T;T	0.50813	0.73;0.73	4.8	3.9	0.45041	.	0.129605	0.48286	D	0.000192	T	0.00524	0.0017	.	.	.	0.80722	D	1	P;B	0.40970	0.734;0.447	B;B	0.32342	0.14;0.144	T	0.01894	-1.1252	9	0.22109	T	0.4	-12.8881	8.4904	0.33098	0.1123:0.0:0.8877:0.0	rs34542607	164;129	Q8WXS3;Q8WXS3-2	BAALC_HUMAN;.	T	129;164	ENSP00000312457:S129T;ENSP00000297574:S164T	ENSP00000297574:S164T	S	+	2	0	BAALC	104309451	1.000000	0.71417	0.886000	0.34754	0.987000	0.75469	2.175000	0.42491	1.113000	0.41760	0.591000	0.81541	AGC	G|0.971;C|0.029	0.029	strong		0.408	BAALC-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000380257.1			C	104240275	G	C	104240275	3	2	22	1	0	0	0	0	1	0	0	0	1279	971	34	4	396	4	BAALC	8	104240275	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	185672	104240275	42123747	1946	4847											
RIMS2	9699	hgsc.bcm.edu	37	chr8	104513156	104513156	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cggggccgcctggctcccatCccggcggcctctcagccgcc	2	5	13	21	5	1	0	1	0	1	0	4	0	3	0	7	5	1	1	7	5	0	0	rs78505067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:104513156C>A	ENST00000406091.3	+	1	42	c.42C>A	c.(40-42)atC>atA	p.I14I	RP11-1C8.4_ENST00000517376.1_RNA|RP11-1C8.4_ENST00000523422.1_RNA	NM_001100117.2	NP_001093587.1	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	14					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)			TGGCTCCCATCCCGGCGGCCT	0.677										HNSCC(12;0.0054)			C|||	38	0.00758786	0.0257	0.0058	5008	,	,		10505	0.0		0.0	False		,,,				2504	0.0				p.I14I		Atlas-SNP	.											.	RIMS2	1357	.	0			c.C42A						PASS	.	C		67,3591		1,65,1763	14	17	16		42	1.2	1	8	dbSNP_132	16	0,8116		0,0,4058	no	coding-synonymous	RIMS2	NM_001100117.2		1,65,5821	AA,AC,CC		0.0,1.8316,0.5691		14/1350	104513156	67,11707	1829	4058	5887	SO:0001819	synonymous_variant	9699	exon1			TCCCATCCCGGCG	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.42C>A	8.37:g.104513156C>A		80	0	0		95	47	0.494737	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Silent	SNP	ENST00000406091.3	37	CCDS55269.1																																																																																			C|0.994;A|0.006	0.006	strong		0.677	RIMS2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001100117		A	104513156	C	A	104513156	2	1	22	1	0	0	0	0	0	0	0	1	13383	845	30	4		4	RIMS2	8	104513156	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	272881	104513156	41850866	1947	4848											
RIMS2	9699	hgsc.bcm.edu	37	chr8	104897606	104897606	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agaggaatattcacagtatgCtacttcggataccgcaatgc	13	10	9	9	2	1	1	1	0	0	1	2	3	1	3	1	2	4	3	1	2	6	6	rs146399863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:104897606C>G	ENST00000436393.2	+	2	354	c.113C>G	c.(112-114)gCt>gGt	p.A38G	RIMS2_ENST00000507740.1_Missense_Mutation_p.A68G|RIMS2_ENST00000522174.1_3'UTR|RIMS2_ENST00000406091.3_Missense_Mutation_p.A260G|RIMS2_ENST00000262231.10_Missense_Mutation_p.A68G			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	291	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)			TCACAGTATGCTACTTCGGAT	0.398										HNSCC(12;0.0054)			C|||	2	0.000399361	0.0015	0.0	5008	,	,		21790	0.0		0.0	False		,,,				2504	0.0				p.A260G		Atlas-SNP	.											.	RIMS2	1357	.	0			c.C779G						PASS	.	C	GLY/ALA,GLY/ALA	6,3780		0,6,1887	92	83	86		779,203	4.4	1	8	dbSNP_134	86	0,8240		0,0,4120	yes	missense,missense	RIMS2	NM_001100117.2,NM_014677.4	60,60	0,6,6007	GG,GC,CC		0.0,0.1585,0.0499	benign,benign	260/1350,68/1164	104897606	6,12020	1893	4120	6013	SO:0001583	missense	9699	exon4			AGTATGCTACTTC	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.113C>G	8.37:g.104897606C>G	ENSP00000390665:p.Ala38Gly	75	0	0		84	45	0.535714	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Missense_Mutation	SNP	ENST00000436393.2	37		2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	14.15	2.450412	0.43531	0.001585	0.0	ENSG00000176406	ENST00000504942;ENST00000329869;ENST00000406091;ENST00000402998;ENST00000515551;ENST00000262231;ENST00000507740;ENST00000408894;ENST00000436393	T;T;T;T;T;T;T	0.37584	1.19;1.19;2.19;2.26;2.25;2.18;2.62	5.31	4.42	0.53409	.	.	.	.	.	T	0.41419	0.1158	L	0.51422	1.61	0.80722	D	1	B;P;P;P;P	0.45902	0.278;0.676;0.868;0.694;0.559	B;B;P;B;B	0.48141	0.248;0.273;0.568;0.332;0.361	T	0.31138	-0.9954	9	0.54805	T	0.06	.	12.9673	0.58492	0.0:0.9206:0.0:0.0794	.	291;38;68;68;260	Q9UQ26;D6RA03;Q9UQ26-1;Q9UQ26-3;F8WD47	RIMS2_HUMAN;.;.;.;.	G	260;291;260;291;68;68;68;68;38	ENSP00000427018:A260G;ENSP00000384892:A260G;ENSP00000425205:A68G;ENSP00000262231:A68G;ENSP00000423559:A68G;ENSP00000386228:A68G;ENSP00000390665:A38G	ENSP00000262231:A68G	A	+	2	0	RIMS2	104966782	1.000000	0.71417	0.973000	0.42090	0.970000	0.65996	4.441000	0.59981	1.204000	0.43247	0.460000	0.39030	GCT	C|0.999;G|0.001	0.001	strong		0.398	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117		G	104897606	C	G	104897606	3	3	22	1	0	0	0	0	1	0	0	0	13383	797	28	4	919	4	RIMS2	8	104897606	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	384450	104897606	41466416	1948	4849											
LRP12	29967	hgsc.bcm.edu	37	chr8	105503401	105503401	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtactctgagttgaggaacTtgcacatgctcctactgtcg	8	12	11	10	1	1	2	0	2	1	0	3	3	2	3	1	2	5	4	1	2	3	4	rs16871494	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:105503401T>C	ENST00000276654.5	-	7	2188	c.2080A>G	c.(2080-2082)Agt>Ggt	p.S694G	LRP12_ENST00000424843.2_Missense_Mutation_p.S675G|LRP12_ENST00000518375.1_5'UTR	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	694			S -> G (in dbSNP:rs16871494).		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)			GTTGAGGAACTTGCACATGCT	0.532													T|||	177	0.0353435	0.1286	0.0072	5008	,	,		19333	0.0		0.002	False		,,,				2504	0.0				p.S694G		Atlas-SNP	.											.	LRP12	124	.	0			c.A2080G						PASS	.	T	GLY/SER,GLY/SER	469,3937	220.4+/-237.8	15,439,1749	99	84	90		2023,2080	3.1	0.8	8	dbSNP_123	90	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	LRP12	NM_001135703.2,NM_013437.4	56,56	15,444,6044	CC,CT,TT		0.0581,10.6446,3.6445	benign,benign	675/841,694/860	105503401	474,12532	2203	4300	6503	SO:0001583	missense	29967	exon7			AGGAACTTGCACA	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.2080A>G	8.37:g.105503401T>C	ENSP00000276654:p.Ser694Gly	170	0	0		189	93	0.492063	NM_013437	A8K137|B4DRQ2	Missense_Mutation	SNP	ENST00000276654.5	37	CCDS6303.1	80	0.03663003663003663	78	0.15853658536585366	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	8.256	0.809999	0.16537	0.106446	5.81E-4	ENSG00000147650	ENST00000424843;ENST00000276654;ENST00000520873	D;D	0.85484	-1.99;-1.94	5.49	3.13	0.36017	.	0.595743	0.20652	N	0.088183	T	0.00608	0.0020	N	0.14661	0.345	0.09310	N	0.999997	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.00857	-1.1538	10	0.38643	T	0.18	-5.7539	8.0472	0.30555	0.0:0.2201:0.0:0.7799	rs16871494;rs52835469;rs16871494	675;694	Q9Y561-2;Q9Y561	.;LRP12_HUMAN	G	675;694;59	ENSP00000399148:S675G;ENSP00000276654:S694G	ENSP00000276654:S694G	S	-	1	0	LRP12	105572577	0.961000	0.32948	0.772000	0.31596	0.845000	0.48019	1.626000	0.37039	0.482000	0.27582	0.528000	0.53228	AGT	T|0.957;C|0.043	0.043	strong		0.532	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1	NM_013437		C	105503401	T	C	105503401	3	2	22	1	0	0	0	0	1	0	0	0	8963	1609	56	3	503	3	LRP12	8	105503401	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	605795	105503401	40860621	1949	4850											
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110408347	110408347	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgatcagacagatttcccCgtcagagttctagttggagg	9	13	11	8	1	3	4	2	1	1	3	4	5	4	5	2	2	0	2	2	2	1	5	rs6469258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:110408347C>T	ENST00000378402.5	+	11	1007	c.903C>T	c.(901-903)ccC>ccT	p.P301P		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	301	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)			CAGATTTCCCCGTCAGAGTTC	0.393										HNSCC(38;0.096)			C|||	138	0.0275559	0.1006	0.0072	5008	,	,		17027	0.0		0.0	False		,,,				2504	0.0				p.P301P		Atlas-SNP	.											PKHD1L1,NS,carcinoma,+2,1	PKHD1L1	522	1	0			c.C903T						PASS	.	C		335,3603		16,303,1650	74	64	67		903	2.1	0.8	8	dbSNP_116	67	1,8335		0,1,4167	no	coding-synonymous	PKHD1L1	NM_177531.4		16,304,5817	TT,TC,CC		0.012,8.5069,2.7375		301/4244	110408347	336,11938	1969	4168	6137	SO:0001819	synonymous_variant	93035	exon11			TTTCCCCGTCAGA	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.903C>T	8.37:g.110408347C>T		61	0	0		49	25	0.510204	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																			C|0.975;T|0.025	0.025	strong		0.393	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		T	110408347	C	T	110408347	2	4	22	1	0	0	0	0	0	0	0	1	11981	639	23	1		1	PKHD1L1	8	110408347	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4904946	110408347	35955675	1950	4851											
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110413806	110413806	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcagatgatattcatctgcaGaaaggaaaagagtaaggctt	16	10	10	5	0	3	4	2	1	1	3	3	5	3	5	0	2	1	3	0	2	5	4	rs200316129	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:110413806G>A	ENST00000378402.5	+	14	1466	c.1362G>A	c.(1360-1362)caG>caA	p.Q454Q		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	454					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.Q456Q(1)		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)			TTCATCTGCAGAAAGGAAAAG	0.313										HNSCC(38;0.096)			G|||	2	0.000399361	0.0015	0.0	5008	,	,		13925	0.0		0.0	False		,,,				2504	0.0				p.Q454Q		Atlas-SNP	.											PKHD1L1,NS,carcinoma,0,1	PKHD1L1	522	1	1	Substitution - coding silent(1)	breast(1)	c.G1362A						PASS	.	G		2,3624		0,2,1811	76	69	71		1362	3.4	1	8		71	0,8154		0,0,4077	no	coding-synonymous	PKHD1L1	NM_177531.4		0,2,5888	AA,AG,GG		0.0,0.0552,0.017		454/4244	110413806	2,11778	1813	4077	5890	SO:0001819	synonymous_variant	93035	exon14			TCTGCAGAAAGGA	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.1362G>A	8.37:g.110413806G>A		136	0	0		107	56	0.523364	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																			G|1.000;A|0.000	0.000	strong		0.313	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		A	110413806	G	A	110413806	2	1	22	1	0	0	0	0	0	0	0	1	11981	933	33	2		2	PKHD1L1	8	110413806	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5459	110413806	35950216	1951	4852											
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110491801	110491801	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttatggtcaaatgattctttTtggcaatcatcacgagaaaa	14	14	7	6	1	4	2	3	1	1	1	4	3	4	2	0	2	0	1	0	2	5	4	rs116618272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:110491801T>C	ENST00000378402.5	+	54	9215	c.9111T>C	c.(9109-9111)ttT>ttC	p.F3037F		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3037	G8 2. {ECO:0000255|PROSITE- ProRule:PRU00817}.				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)			ATGATTCTTTTTGGCAATCAT	0.328										HNSCC(38;0.096)			T|||	39	0.00778754	0.0287	0.0014	5008	,	,		20916	0.0		0.0	False		,,,				2504	0.0				p.F3037F		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.T9111C						PASS	.	T		56,3594		1,54,1770	127	111	116		9111	-2.1	1	8	dbSNP_132	116	0,8152		0,0,4076	no	coding-synonymous	PKHD1L1	NM_177531.4		1,54,5846	CC,CT,TT		0.0,1.5342,0.4745		3037/4244	110491801	56,11746	1825	4076	5901	SO:0001819	synonymous_variant	93035	exon54			TTCTTTTTGGCAA	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.9111T>C	8.37:g.110491801T>C		89	0	0		87	40	0.45977	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																			T|0.993;C|0.007	0.007	strong		0.328	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		C	110491801	T	C	110491801	2	2	22	1	0	0	0	0	0	0	0	1	11981	1838	64	3		3	PKHD1L1	8	110491801	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	77995	110491801	35872221	1952	4853											
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110492328	110492328	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggagctgcagaatcttcttAcagagaagttgttttgaatg	12	13	11	5	0	2	3	0	1	2	2	2	5	2	4	0	1	3	4	0	1	4	5	rs140472257	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:110492328A>C	ENST00000378402.5	+	55	9391	c.9287A>C	c.(9286-9288)tAc>tCc	p.Y3096S		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3096	G8 2. {ECO:0000255|PROSITE- ProRule:PRU00817}.				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)			GAATCTTCTTACAGAGAAGTT	0.348										HNSCC(38;0.096)			A|||	43	0.00858626	0.0303	0.0043	5008	,	,		17254	0.0		0.0	False		,,,				2504	0.0				p.Y3096S		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.A9287C						PASS	.	A	SER/TYR	59,3605		0,59,1773	51	52	52		9287	3.8	0.2	8	dbSNP_134	52	0,8158		0,0,4079	yes	missense	PKHD1L1	NM_177531.4	144	0,59,5852	CC,CA,AA		0.0,1.6103,0.4991	benign	3096/4244	110492328	59,11763	1832	4079	5911	SO:0001583	missense	93035	exon55			CTTCTTACAGAGA	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.9287A>C	8.37:g.110492328A>C	ENSP00000367655:p.Tyr3096Ser	149	0	0		138	58	0.42029	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	A	8.551	0.875589	0.17395	0.016103	0.0	ENSG00000205038	ENST00000378402	D	0.85411	-1.98	5.01	3.83	0.44106	G8 domain (2);	0.589185	0.17371	N	0.176674	T	0.69557	0.3124	M	0.76574	2.34	0.22213	N	0.999281	B	0.20164	0.042	B	0.32022	0.139	T	0.69176	-0.5214	10	0.36615	T	0.2	.	10.3982	0.44214	0.8352:0.1648:0.0:0.0	.	3096	Q86WI1	PKHL1_HUMAN	S	3096	ENSP00000367655:Y3096S	ENSP00000367655:Y3096S	Y	+	2	0	PKHD1L1	110561504	0.951000	0.32395	0.236000	0.24074	0.176000	0.22953	3.178000	0.50879	0.840000	0.34995	-0.323000	0.08544	TAC	A|0.993;C|0.007	0.007	strong		0.348	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		C	110492328	A	C	110492328	3	2	22	1	0	0	0	0	1	0	0	0	11981	391	14	5	9505	5	PKHD1L1	8	110492328	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	527	110492328	35871694	1953	4854											
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110539175	110539175	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccagataatgactgtagtaaTtagctgtctggttggaagaa	13	12	11	5	0	1	3	0	1	1	2	1	4	1	4	1	2	1	4	1	2	6	5	rs141977750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:110539175T>A	ENST00000378402.5	+	77	12751	c.12647T>A	c.(12646-12648)aTt>aAt	p.I4216N		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	4216					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)			ACTGTAGTAATTAGCTGTCTG	0.418										HNSCC(38;0.096)			T|||	46	0.0091853	0.0325	0.0043	5008	,	,		17708	0.0		0.0	False		,,,				2504	0.0				p.I4216N		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.T12647A						PASS	.	T	ASN/ILE	77,3947		0,77,1935	93	98	96		12647	1.8	0	8	dbSNP_134	96	0,8418		0,0,4209	yes	missense	PKHD1L1	NM_177531.4	149	0,77,6144	AA,AT,TT		0.0,1.9135,0.6189	benign	4216/4244	110539175	77,12365	2012	4209	6221	SO:0001583	missense	93035	exon77			TAGTAATTAGCTG	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.12647T>A	8.37:g.110539175T>A	ENSP00000367655:p.Ile4216Asn	162	0	0		204	105	0.514706	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	16	0.007326007326007326	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	0	0.0	T	7.650	0.682659	0.14907	0.019135	0.0	ENSG00000205038	ENST00000378402;ENST00000526472	D;D	0.87412	-2.25;-2.08	5.64	1.83	0.25207	.	0.492124	0.18017	N	0.154354	T	0.52933	0.1765	N	0.24115	0.695	0.09310	N	1	B	0.34015	0.435	B	0.27170	0.077	T	0.58312	-0.7658	10	0.72032	D	0.01	.	7.5255	0.27653	0.0:0.253:0.0:0.747	.	4216	Q86WI1	PKHL1_HUMAN	N	4216;1144	ENSP00000367655:I4216N;ENSP00000437376:I1144N	ENSP00000367655:I4216N	I	+	2	0	PKHD1L1	110608351	0.002000	0.14202	0.001000	0.08648	0.122000	0.20287	0.151000	0.16283	0.068000	0.16574	0.528000	0.53228	ATT	T|0.993;A|0.007	0.007	strong		0.418	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		A	110539175	T	A	110539175	3	1	22	1	0	0	0	0	1	0	0	0	11981	1493	52	5	12953	5	PKHD1L1	8	110539175	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	46847	110539175	35824847	1954	4855											
CSMD3	114788	hgsc.bcm.edu	37	chr8	113275878	113275878	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcatacttacgtaagcactgCggtacttcaccactccaggt	10	11	7	13	2	2	0	2	0	0	0	3	0	3	0	2	2	5	3	2	2	4	5	rs16883323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:113275878C>T	ENST00000297405.5	-	61	10096	c.9852G>A	c.(9850-9852)ccG>ccA	p.P3284P	CSMD3_ENST00000455883.2_Silent_p.P3115P|CSMD3_ENST00000343508.3_Silent_p.P3244P|CSMD3_ENST00000352409.3_Silent_p.P3214P	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3284	Sushi 25. {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						GTAAGCACTGCGGTACTTCAC	0.398										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			C|||	180	0.0359425	0.1324	0.0072	5008	,	,		16096	0.0		0.0	False		,,,				2504	0.0				p.P3284P		Atlas-SNP	.											CSMD3_ENST00000343508,caecum,carcinoma,0,4	CSMD3	2325	4	0			c.G9852A						PASS	.	C	,,	438,3968	208.8+/-229.8	21,396,1786	86	72	77		9345,9852,9732	-2.2	1	8	dbSNP_123	77	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	,,	21,401,6081	TT,TC,CC		0.0581,9.941,3.4061	,,	3115/3539,3284/3708,3244/3668	113275878	443,12563	2203	4300	6503	SO:0001819	synonymous_variant	114788	exon61			GCACTGCGGTACT	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.9852G>A	8.37:g.113275878C>T		65	0	0		70	36	0.514286	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																			C|0.969;T|0.031	0.031	strong		0.398	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	113275878	C	T	113275878	2	4	22	1	0	0	0	0	0	0	0	1	3948	755	27	1		1	CSMD3	8	113275878	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2736703	113275878	33088144	1955	4856											
CSMD3	114788	hgsc.bcm.edu	37	chr8	113662508	113662508	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acagtagagccaatggagaaAtcatgaccatagcgacggcc	15	5	11	10	2	1	3	1	1	0	2	1	5	1	3	3	2	2	1	3	2	4	2	rs7839690	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:113662508A>G	ENST00000297405.5	-	19	3319	c.3075T>C	c.(3073-3075)gaT>gaC	p.D1025D	CSMD3_ENST00000455883.2_Silent_p.D921D|CSMD3_ENST00000343508.3_Silent_p.D985D|CSMD3_ENST00000352409.3_Silent_p.D1025D	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1025	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						CAATGGAGAAATCATGACCAT	0.433										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			A|||	132	0.0263578	0.0968	0.0058	5008	,	,		14812	0.0		0.0	False		,,,				2504	0.0				p.D1025D		Atlas-SNP	.											CSMD3_ENST00000343508,colon,carcinoma,-2,2	CSMD3	2325	2	0			c.T3075C						PASS	.	A	,,	311,4095	166.2+/-197.5	10,291,1902	147	147	147		2763,3075,2955	2.3	1	8	dbSNP_116	147	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	,,	10,296,6197	GG,GA,AA		0.0581,7.0586,2.4296	,,	921/3539,1025/3708,985/3668	113662508	316,12690	2203	4300	6503	SO:0001819	synonymous_variant	114788	exon19			GGAGAAATCATGA	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.3075T>C	8.37:g.113662508A>G		225	0	0		219	90	0.410959	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																			A|0.972;G|0.028	0.028	strong		0.433	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		G	113662508	A	G	113662508	2	3	22	1	0	0	0	0	0	0	0	1	3948	98	4	3		3	CSMD3	8	113662508	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	386630	113662508	32701514	1956	4857											
CSMD3	114788	hgsc.bcm.edu	37	chr8	113668453	113668453	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatagaaggtatataaaattActgctactaaatagaaactg	20	11	6	4	0	0	2	0	0	0	2	0	2	0	2	0	1	4	2	0	1	13	8	rs11992014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:113668453A>G	ENST00000297405.5	-	18	3178	c.2934T>C	c.(2932-2934)agT>agC	p.S978S	CSMD3_ENST00000455883.2_Silent_p.S874S|CSMD3_ENST00000343508.3_Silent_p.S938S|CSMD3_ENST00000352409.3_Silent_p.S978S	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	978	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						ATATAAAATTACTGCTACTAA	0.348										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			A|||	156	0.0311502	0.1112	0.0115	5008	,	,		12832	0.0		0.001	False		,,,				2504	0.0				p.S978S		Atlas-SNP	.											CSMD3_ENST00000343508,NS,carcinoma,-2,2	CSMD3	2325	2	0			c.T2934C						PASS	.	A	,,	382,4024	189.5+/-215.6	17,348,1838	67	74	72		2622,2934,2814	2.5	1	8	dbSNP_120	72	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	,,	17,353,6133	GG,GA,AA		0.0581,8.67,2.9755	,,	874/3539,978/3708,938/3668	113668453	387,12619	2203	4300	6503	SO:0001819	synonymous_variant	114788	exon18			AAAATTACTGCTA	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.2934T>C	8.37:g.113668453A>G		95	0	0		132	132	1	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																			A|0.971;G|0.029	0.029	strong		0.348	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		G	113668453	A	G	113668453	2	3	22	1	0	0	0	0	0	0	0	1	3948	388	14	3		3	CSMD3	8	113668453	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	5945	113668453	32695569	1957	4858											
CSMD3	114788	hgsc.bcm.edu	37	chr8	114111156	114111156	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagggctggatatgatgccaCtggatcctctcattgttcct	7	14	10	10	0	1	1	1	1	1	0	4	3	3	3	3	3	1	2	3	3	2	4	rs73701331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:114111156C>T	ENST00000297405.5	-	5	990	c.746G>A	c.(745-747)aGt>aAt	p.S249N	CSMD3_ENST00000519485.1_5'UTR|CSMD3_ENST00000455883.2_Missense_Mutation_p.S249N|CSMD3_ENST00000343508.3_Missense_Mutation_p.S209N|CSMD3_ENST00000352409.3_Missense_Mutation_p.S249N	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	249	CUB 2. {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						TATGATGCCACTGGATCCTCT	0.388										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			C|||	47	0.00938498	0.034	0.0	5008	,	,		16287	0.002		0.0	False		,,,				2504	0.0				p.S249N		Atlas-SNP	.											.	CSMD3	2325	.	0			c.G746A						PASS	.	C	ASN/SER,ASN/SER,ASN/SER	106,4300	82.9+/-121.4	2,102,2099	124	107	112		746,746,626	5.3	1	8	dbSNP_130	112	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	46,46,46	2,103,6398	TT,TC,CC		0.0116,2.4058,0.8227	possibly-damaging,possibly-damaging,possibly-damaging	249/3539,249/3708,209/3668	114111156	107,12899	2203	4300	6503	SO:0001583	missense	114788	exon5			ATGCCACTGGATC	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.746G>A	8.37:g.114111156C>T	ENSP00000297405:p.Ser249Asn	109	0	0		125	63	0.504	NM_052900	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	15	0.006868131868131868	14	0.028455284552845527	0	0.0	1	0.0017482517482517483	0	0.0	C	17.36	3.370151	0.61624	0.024058	1.16E-4	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000455883;ENST00000352409	T;T;T;T	0.18502	2.21;2.21;2.21;2.21	5.32	5.32	0.75619	CUB (5);	0.058984	0.64402	D	0.000003	T	0.09686	0.0238	L	0.27944	0.81	0.30352	N	0.784714	P;P;D;P	0.65815	0.763;0.844;0.995;0.753	B;B;D;P	0.75020	0.288;0.445;0.985;0.671	T	0.05920	-1.0856	10	0.02654	T	1	.	19.3517	0.94389	0.0:1.0:0.0:0.0	.	249;249;249;209	Q7Z407-3;Q7Z407-4;Q7Z407;Q7Z407-2	.;.;CSMD3_HUMAN;.	N	209;249;249;249	ENSP00000345799:S209N;ENSP00000297405:S249N;ENSP00000412263:S249N;ENSP00000343124:S249N	ENSP00000297405:S249N	S	-	2	0	CSMD3	114180332	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	4.889000	0.63171	2.660000	0.90430	0.591000	0.81541	AGT	C|0.990;T|0.010	0.010	strong		0.388	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		T	114111156	C	T	114111156	3	4	22	1	0	0	0	0	1	0	0	0	3948	565	20	2	10645	2	CSMD3	8	114111156	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	442703	114111156	32252866	1958	4859											
TRPS1	7227	hgsc.bcm.edu	37	chr8	116631902	116631902	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcatctgcctctgctctttgCggagacttcaagggctcaca	7	12	9	13	1	6	1	3	0	3	1	6	2	6	1	1	2	3	2	1	2	1	2	rs7823278	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:116631902C>A	ENST00000220888.5	-	2	543	c.384G>T	c.(382-384)ccG>ccT	p.P128P	TRPS1_ENST00000395715.3_Silent_p.P141P|TRPS1_ENST00000519076.1_Silent_p.P82P|TRPS1_ENST00000519674.1_Silent_p.P128P|TRPS1_ENST00000520276.1_Silent_p.P132P			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	128					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)			CTGCTCTTTGCGGAGACTTCA	0.522									Langer-Giedion syndrome				A|||	844	0.16853	0.5734	0.049	5008	,	,		18881	0.0		0.002	False		,,,				2504	0.0511				p.P141P		Atlas-SNP	.											TRPS1_ENST00000395715,NS,carcinoma,-1,2	TRPS1	516	2	0			c.G423T						PASS	.	A		1632,2214		341,950,632	58	58	58		423	5.8	1	8	dbSNP_116	58	20,8250		0,20,4115	no	coding-synonymous	TRPS1	NM_014112.2		341,970,4747	AA,AC,CC		0.2418,42.4337,13.6349		141/1295	116631902	1652,10464	1923	4135	6058	SO:0001819	synonymous_variant	7227	exon3	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	TCTTTGCGGAGAC	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.384G>T	8.37:g.116631902C>A		97	0	0		110	110	1	NM_014112	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Silent	SNP	ENST00000220888.5	37																																																																																				C|0.873;A|0.127	0.127	strong		0.522	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112		A	116631902	C	A	116631902	2	1	22	1	0	0	0	0	0	0	0	1	16608	755	27	4		4	TRPS1	8	116631902	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2520746	116631902	29732120	1959	4860											
RAD21	5885	hgsc.bcm.edu	37	chr8	117864867	117864867	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaaattctttgaggaattcAtccaaattatctgcctctcc	11	15	4	11	0	5	1	2	1	3	0	7	2	6	2	3	1	1	0	3	1	4	4	rs75160167	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:117864867A>C	ENST00000297338.2	-	10	1529	c.1242T>G	c.(1240-1242)gaT>gaG	p.D414E	RAD21_ENST00000518055.1_5'Flank|RAD21_ENST00000523986.1_5'Flank	NM_006265.2	NP_006256.1	O60216	RAD21_HUMAN	RAD21 homolog (S. pombe)	414					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)					TGAGGAATTCATCCAAATTAT	0.403													A|||	36	0.0071885	0.0265	0.0014	5008	,	,		15827	0.0		0.0	False		,,,				2504	0.0				p.D414E		Atlas-SNP	.											.	RAD21	95	.	0			c.T1242G						PASS	.	A	GLU/ASP	88,4318	74.1+/-112.3	0,88,2115	115	112	113		1242	5.5	1	8	dbSNP_131	113	0,8600		0,0,4300	yes	missense	RAD21	NM_006265.2	45	0,88,6415	CC,CA,AA		0.0,1.9973,0.6766	benign	414/632	117864867	88,12918	2203	4300	6503	SO:0001583	missense	5885	exon10			GAATTCATCCAAA	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.1242T>G	8.37:g.117864867A>C	ENSP00000297338:p.Asp414Glu	197	0	0		203	86	0.423645	NM_006265	A8K0E0|Q15001|Q99568	Missense_Mutation	SNP	ENST00000297338.2	37	CCDS6321.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	A	13.90	2.373790	0.42105	0.019973	0.0	ENSG00000164754	ENST00000297338	T	0.50277	0.75	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.18341	0.0440	L	0.32530	0.975	0.80722	D	1	B	0.28900	0.227	B	0.21360	0.034	T	0.12967	-1.0527	10	0.02654	T	1	-14.1824	15.669	0.77258	1.0:0.0:0.0:0.0	.	414	O60216	RAD21_HUMAN	E	414	ENSP00000297338:D414E	ENSP00000297338:D414E	D	-	3	2	RAD21	117934048	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.009000	0.57110	2.092000	0.63282	0.460000	0.39030	GAT	A|0.992;C|0.008	0.008	strong		0.403	RAD21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381184.1	NM_006265		C	117864867	A	C	117864867	3	2	22	1	0	0	0	0	1	0	0	0	12996	214	8	5	673	5	RAD21	8	117864867	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1232965	117864867	28499155	1960	4861											
MAL2	114569	hgsc.bcm.edu	37	chr8	120233968	120233968	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgttcctctctggcatggtgGctcaaattgatgctaactgg	7	14	11	9	0	2	1	1	1	1	0	4	1	3	1	1	4	2	4	1	4	2	3	rs2303398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:120233968G>A	ENST00000276681.6	+	3	376	c.274G>A	c.(274-276)Gct>Act	p.A92T	RP11-4K16.2_ENST00000522828.1_lincRNA|MAL2_ENST00000521748.1_3'UTR	NM_052886.2	NP_443118.1	Q969L2	MAL2_HUMAN	mal, T-cell differentiation protein 2 (gene/pseudogene)	92	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.		A -> T (in dbSNP:rs2303398).			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)						all_cancers(13;1.91e-26)|Lung NSC(37;8.61e-08)|Ovarian(258;0.018)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000967)			TGGCATGGTGGCTCAAATTGA	0.433													A|||	563	0.11242	0.3238	0.0331	5008	,	,		19676	0.0308		0.0	False		,,,				2504	0.0828				p.A92T		Atlas-SNP	.											.	.	.	.	0			c.G274A						PASS	.	A	THR/ALA	1171,2763		182,807,978	128	127	127		275	5.2	1	8	dbSNP_100	127	21,8295		0,21,4137	yes	missense	MAL2	NM_052886.2	58	182,828,5115	AA,AG,GG		0.2525,29.7661,9.7306	benign	92/177	120233968	1192,11058	1967	4158	6125	SO:0001583	missense	114569	exon3			ATGGTGGCTCAAA	AL117612	CCDS75780.1	8q23	2011-01-26	2011-01-26			ENSG00000147676			13634	protein-coding gene	gene with protein product	"MAL proteolipid protein 2"	609684				11549320	Standard	NM_052886		Approved		uc003yop.3	Q969L2		ENST00000276681.6:c.274G>A	8.37:g.120233968G>A	ENSP00000475434:p.Ala92Thr	138	0	0		135	88	0.651852	NM_052886	B2R520|Q6ZMD9	Missense_Mutation	SNP	ENST00000276681.6	37																																																																																				G|0.895;A|0.105	0.105	strong		0.433	MAL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052886		A	120233968	G	A	120233968	3	1	22	1	0	0	0	0	1	0	0	0	9209	1203	42	2	281	2	MAL2	8	120233968	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2369101	120233968	26130054	1961	4862											
ENPP2	5168	hgsc.bcm.edu	37	chr8	120575112	120575112	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcacattgcagctctcctcGttgtcaggccggtgaggcag	6	10	12	13	2	3	1	2	1	1	0	5	1	3	1	2	3	2	4	2	3	0	2	rs61740048	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:120575112G>A	ENST00000075322.6	-	24	2464	c.2406C>T	c.(2404-2406)aaC>aaT	p.N802N	ENPP2_ENST00000427067.2_Silent_p.N823N|ENPP2_ENST00000522826.1_Silent_p.N827N|ENPP2_ENST00000522167.1_Silent_p.N437N|ENPP2_ENST00000259486.6_Silent_p.N854N	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	802					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)	p.N854N(1)		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)			AGCTCTCCTCGTTGTCAGGCC	0.478													G|||	21	0.00419329	0.0159	0.0	5008	,	,		19836	0.0		0.0	False		,,,				2504	0.0				p.N854N	Melanoma(20;305 879 2501 4818 31020)	Atlas-SNP	.											ENPP2_ENST00000522826,colon,carcinoma,0,7	ENPP2	254	7	1	Substitution - coding silent(1)	kidney(1)	c.C2562T						PASS	.	G	,,	48,4358	48.2+/-83.0	0,48,2155	109	97	101		2406,2481,2562	-6	0.2	8	dbSNP_129	101	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	ENPP2	NM_001040092.1,NM_001130863.1,NM_006209.3	,,	0,49,6454	AA,AG,GG		0.0116,1.0894,0.3767	,,	802/864,827/889,854/916	120575112	49,12957	2203	4300	6503	SO:0001819	synonymous_variant	5168	exon25			CTCCTCGTTGTCA	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.2406C>T	8.37:g.120575112G>A		101	0	0		121	61	0.504132	NM_006209	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Silent	SNP	ENST00000075322.6	37	CCDS34936.1																																																																																			G|0.997;A|0.003	0.003	strong		0.478	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1			A	120575112	G	A	120575112	2	1	22	1	0	0	0	0	0	0	0	1	5132	1136	40	1		1	ENPP2	8	120575112	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	341144	120575112	25788910	1962	4863											
TAF2	6873	hgsc.bcm.edu	37	chr8	120793332	120793332	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaaagctcataaagttgttTgttttcacaatgtttggaca	12	16	8	5	0	2	1	2	1	0	0	2	2	2	2	0	1	1	5	0	1	4	6	rs28619538	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:120793332T>C	ENST00000378164.2	-	17	2512	c.2214A>G	c.(2212-2214)acA>acG	p.T738T		NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	738					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)			TAAAGTTGTTTGTTTTCACAA	0.348													T|||	117	0.0233626	0.0825	0.0086	5008	,	,		16206	0.0		0.002	False		,,,				2504	0.0				p.T738T		Atlas-SNP	.											.	TAF2	204	.	0			c.A2214G						PASS	.	T		271,4135	152.9+/-186.6	5,261,1937	79	84	82		2214	2.8	1	8	dbSNP_125	82	35,8565	24.0+/-70.4	0,35,4265	no	coding-synonymous	TAF2	NM_003184.3		5,296,6202	CC,CT,TT		0.407,6.1507,2.3528		738/1200	120793332	306,12700	2203	4300	6503	SO:0001819	synonymous_variant	6873	exon17			GTTGTTTGTTTTC	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.2214A>G	8.37:g.120793332T>C		75	0	0		62	36	0.580645	NM_003184	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Silent	SNP	ENST00000378164.2	37	CCDS34937.1																																																																																			T|0.977;C|0.023	0.023	strong		0.348	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184		C	120793332	T	C	120793332	2	2	22	1	0	0	0	0	0	0	0	1	15539	1799	63	3		3	TAF2	8	120793332	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	218220	120793332	25570690	1963	4864											
ZHX1	11244	hgsc.bcm.edu	37	chr8	124265676	124265676	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatcaataacttcatcttcCtcctcattttcctcaaataa	12	16	0	13	0	6	0	5	0	1	0	9	0	9	0	3	0	1	0	3	0	4	6	rs34145851	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:124265676C>T	ENST00000522655.1	-	3	3051	c.2511G>A	c.(2509-2511)gaG>gaA	p.E837E	ZHX1_ENST00000297857.2_Silent_p.E837E|ZHX1_ENST00000395571.3_Silent_p.E837E|ZHX1-C8ORF76_ENST00000357082.4_Intron|ZHX1_ENST00000522595.1_5'Flank			Q9UKY1	ZHX1_HUMAN	zinc fingers and homeoboxes 1	837	Required for repressor activity.				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)			CTTCATCTTCCTCCTCATTTT	0.398													C|||	69	0.013778	0.0514	0.0014	5008	,	,		18508	0.0		0.0	False		,,,				2504	0.0				p.E837E		Atlas-SNP	.											ZHX1,NS,carcinoma,-2,1	ZHX1	89	1	0			c.G2511A						PASS	.	C	,,	194,4212	122.9+/-160.3	4,186,2013	210	202	205		2511,,2511	1.6	1	8	dbSNP_126	205	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,intron,coding-synonymous	ZHX1,ZHX1-C8ORF76	NM_001017926.2,NM_001204180.1,NM_007222.4	,,	4,187,6312	TT,TC,CC		0.0116,4.4031,1.4993	,,	837/874,,837/874	124265676	195,12811	2203	4300	6503	SO:0001819	synonymous_variant	11244	exon3			ATCTTCCTCCTCA	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.2511G>A	8.37:g.124265676C>T		325	0	0		311	149	0.4791	NM_007222	Q8IWD8	Silent	SNP	ENST00000522655.1	37	CCDS6342.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	C	5.662	0.306815	0.10733	0.044031	1.16E-4	ENSG00000165156	ENST00000520474	.	.	.	5.95	1.57	0.23409	.	.	.	.	.	T	0.20170	0.0485	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.09997	-1.0649	4	.	.	.	-14.7224	5.1468	0.14989	0.1123:0.5612:0.198:0.1285	rs34145851	.	.	.	K	522	.	.	R	-	2	0	ZHX1	124334857	0.995000	0.38212	0.997000	0.53966	0.983000	0.72400	0.381000	0.20619	0.384000	0.24942	0.491000	0.48974	AGG	C|0.986;T|0.014	0.014	strong		0.398	ZHX1-003	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000381759.1			T	124265676	C	T	124265676	2	4	22	1	0	0	0	0	0	0	0	1	17690	680	24	2		2	ZHX1	8	124265676	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3472344	124265676	22098346	1964	4865											
ATAD2	29028	hgsc.bcm.edu	37	chr8	124357302	124357302	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgctgttctcttagcttcaCgaatcacctagtagagagag	10	12	10	9	1	3	2	2	0	1	2	4	4	3	2	1	0	2	4	1	0	4	5	rs78548009	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:124357302C>T	ENST00000287394.5	-	19	2647	c.2540G>A	c.(2539-2541)cGt>cAt	p.R847H	MIR548AA1_ENST00000384971.2_RNA|RNU6-875P_ENST00000516488.1_RNA|ATAD2_ENST00000521903.1_Missense_Mutation_p.R165H	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	847					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)	p.R847H(1)		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)			CTTAGCTTCACGAATCACCTA	0.398													C|||	7	0.00139776	0.0015	0.0	5008	,	,		17101	0.0		0.0	False		,,,				2504	0.0051				p.R847H		Atlas-SNP	.											ATAD2,NS,carcinoma,0,1	ATAD2	160	1	1	Substitution - Missense(1)	endometrium(1)	c.G2540A						PASS	.	C	HIS/ARG	8,4398	14.3+/-33.2	0,8,2195	175	150	159		2540	4.7	1	8	dbSNP_131	159	0,8600		0,0,4300	yes	missense	ATAD2	NM_014109.3	29	0,8,6495	TT,TC,CC		0.0,0.1816,0.0615	probably-damaging	847/1391	124357302	8,12998	2203	4300	6503	SO:0001583	missense	29028	exon19			GCTTCACGAATCA	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.2540G>A	8.37:g.124357302C>T	ENSP00000287394:p.Arg847His	61	0	0		76	44	0.578947	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Missense_Mutation	SNP	ENST00000287394.5	37	CCDS6343.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	C	19.10	3.761292	0.69763	0.001816	0.0	ENSG00000156802	ENST00000287394;ENST00000521903	D;D	0.82803	-1.65;-1.65	5.58	4.7	0.59300	.	0.888358	0.09837	N	0.749398	D	0.87783	0.6264	L	0.58101	1.795	0.37045	D	0.897316	D	0.63880	0.993	P	0.56514	0.8	D	0.85289	0.1066	10	0.46703	T	0.11	-4.8315	14.7146	0.69257	0.0:0.9301:0.0:0.0699	.	847	Q6PL18	ATAD2_HUMAN	H	847;165	ENSP00000287394:R847H;ENSP00000429213:R165H	ENSP00000287394:R847H	R	-	2	0	ATAD2	124426483	0.983000	0.35010	1.000000	0.80357	0.436000	0.31835	0.289000	0.18957	1.359000	0.45940	0.655000	0.94253	CGT	C|0.999;T|0.001	0.001	strong		0.398	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109		T	124357302	C	T	124357302	3	4	22	1	0	0	0	0	1	0	0	0	1071	536	19	1	1672	1	ATAD2	8	124357302	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	91626	124357302	22006720	1965	4866											
FER1L6	654463	hgsc.bcm.edu	37	chr8	124987404	124987404	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacaggtcatcagttctgcAacaagtgggccctgctcaca	10	9	9	13	0	5	0	4	0	1	0	5	0	5	0	1	2	3	3	1	2	2	1	rs77810887	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:124987404A>G	ENST00000522917.1	+	8	747	c.541A>G	c.(541-543)Aac>Gac	p.N181D	FER1L6_ENST00000399018.1_Missense_Mutation_p.N181D	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	181						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)			TCAGTTCTGCAACAAGTGGGC	0.557													G|||	75	0.014976	0.056	0.0014	5008	,	,		19342	0.0		0.0	False		,,,				2504	0.0				p.N181D		Atlas-SNP	.											.	FER1L6	268	.	0			c.A541G						PASS	.	G	ASP/ASN	198,3804		4,190,1807	93	91	92		541	5.5	1	8	dbSNP_131	92	0,8352		0,0,4176	yes	missense	FER1L6	NM_001039112.2	23	4,190,5983	GG,GA,AA		0.0,4.9475,1.6027	benign	181/1858	124987404	198,12156	2001	4176	6177	SO:0001583	missense	654463	exon8			TTCTGCAACAAGT	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.541A>G	8.37:g.124987404A>G	ENSP00000428280:p.Asn181Asp	252	0	0		288	150	0.520833	NM_001039112		Missense_Mutation	SNP	ENST00000522917.1	37	CCDS43767.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	G	8.521	0.868834	0.17322	0.049475	0.0	ENSG00000214814	ENST00000522917;ENST00000399018	T;T	0.80480	-1.38;-1.38	5.5	5.5	0.81552	C2 calcium/lipid-binding domain, CaLB (1);FerIin domain (1);	0.220886	0.37012	N	0.002292	T	0.24812	0.0602	N	0.10760	0.04	0.22342	N	0.999181	B	0.02656	0.0	B	0.06405	0.002	T	0.24404	-1.0161	10	0.28530	T	0.3	.	14.8757	0.70493	0.069:0.0:0.931:0.0	.	181	Q2WGJ9	FR1L6_HUMAN	D	181	ENSP00000428280:N181D;ENSP00000381982:N181D	ENSP00000381982:N181D	N	+	1	0	FER1L6	125056585	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.931000	0.40134	1.487000	0.48415	-0.215000	0.12644	AAC	A|0.988;G|0.012	0.012	strong		0.557	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112		G	124987404	A	G	124987404	3	3	22	1	0	0	0	0	1	0	0	0	5823	130	5	3	567	3	FER1L6	8	124987404	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	630102	124987404	21376618	1966	4867											
MTSS1	9788	hgsc.bcm.edu	37	chr8	125575047	125575047	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttgggggcctctggcggcatGggggatggtgacttggactg	4	10	20	7	1	1	1	0	1	1	0	1	3	1	3	1	8	0	1	1	8	0	2	rs16899702	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:125575047G>T	ENST00000518547.1	-	10	1484	c.1011C>A	c.(1009-1011)ccC>ccA	p.P337P	MTSS1_ENST00000354184.4_Silent_p.P137P|MTSS1_ENST00000524090.1_Silent_p.P227P|MTSS1_ENST00000378017.3_Silent_p.P337P|MTSS1_ENST00000325064.5_Silent_p.P341P|MTSS1_ENST00000395508.2_Silent_p.P71P|MTSS1_ENST00000523587.1_5'UTR|NDUFB9_ENST00000522532.1_Intron|MTSS1_ENST00000431961.2_Silent_p.P137P	NM_001282971.1|NM_014751.4	NP_001269900.1|NP_055566.3	O43312	MTSS1_HUMAN	metastasis suppressor 1	337	Ser-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)			CTGGCGGCATGGGGGATGGTG	0.607													G|||	305	0.0609026	0.2201	0.0144	5008	,	,		18723	0.001		0.003	False		,,,				2504	0.0				p.P337P	Esophageal Squamous(160;622 1893 3862 8546 12509)	Atlas-SNP	.											.	MTSS1	79	.	0			c.C1011A						PASS	.	G		702,3704	291.8+/-281.7	69,564,1570	58	55	56		1011	-1	1	8	dbSNP_123	56	19,8581	14.0+/-48.4	0,19,4281	no	coding-synonymous	MTSS1	NM_014751.4		69,583,5851	TT,TG,GG		0.2209,15.9328,5.5436		337/756	125575047	721,12285	2203	4300	6503	SO:0001819	synonymous_variant	9788	exon10			CGGCATGGGGGAT	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.1011C>A	8.37:g.125575047G>T		88	0	0		93	50	0.537634	NM_014751	J3KNK6|Q8TCA2|Q96RX2	Silent	SNP	ENST00000518547.1	37	CCDS6353.1	116	0.05311355311355311	107	0.21747967479674796	8	0.022099447513812154	1	0.0017482517482517483	0	0.0	G	1.045	-0.677528	0.03378	0.159328	0.002209	ENSG00000170873	ENST00000519168;ENST00000523179	.	.	.	5.6	-0.986	0.10252	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.26780	-1.0093	3	.	.	.	-14.8982	2.3089	0.04181	0.1747:0.1927:0.435:0.1977	rs16899702;rs16899702	.	.	.	N	85;185	.	.	H	-	1	0	MTSS1	125644228	0.683000	0.27633	0.995000	0.50966	0.047000	0.14425	-0.264000	0.08658	-0.095000	0.12351	-0.156000	0.13503	CAT	G|0.936;T|0.064	0.064	strong		0.607	MTSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109625.3	NM_014751		T	125575047	G	T	125575047	2	4	22	1	0	0	0	0	0	0	0	1	9971	1335	47	4		4	MTSS1	8	125575047	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	587643	125575047	20788975	1967	4868											
KIAA0196	9897	hgsc.bcm.edu	37	chr8	126079867	126079867	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aactcaaattgtgcagtatcTaacagcagctggaagaggat	15	9	10	7	0	2	1	1	0	1	1	2	3	2	3	0	2	5	4	0	2	5	3	rs10429323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:126079867T>C	ENST00000318410.7	-	10	1594	c.1245A>G	c.(1243-1245)ttA>ttG	p.L415L	KIAA0196_ENST00000517845.1_Silent_p.L267L	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	415					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)			GTGCAGTATCTAACAGCAGCT	0.358													C|||	160	0.0319489	0.1157	0.0101	5008	,	,		15835	0.0		0.0	False		,,,				2504	0.0				p.L415L		Atlas-SNP	.											.	KIAA0196	90	.	0			c.A1245G						PASS	.	C		358,4048	793.9+/-415.2	17,324,1862	166	155	158		1245	4.7	1	8	dbSNP_119	158	1,8599	819.2+/-406.8	0,1,4299	no	coding-synonymous	KIAA0196	NM_014846.3		17,325,6161	CC,CT,TT		0.0116,8.1253,2.7603		415/1160	126079867	359,12647	2203	4300	6503	SO:0001819	synonymous_variant	9897	exon10			AGTATCTAACAGC		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.1245A>G	8.37:g.126079867T>C		132	0	0		150	72	0.48	NM_014846	A8K4R7|Q3KQX5|Q8TBQ2	Silent	SNP	ENST00000318410.7	37	CCDS6355.1	51	0.023351648351648352	45	0.09146341463414634	6	0.016574585635359115	0	0.0	0	0.0	C	8.635	0.894613	0.17613	0.081253	1.16E-4	ENSG00000164961	ENST00000523273	.	.	.	5.61	4.7	0.59300	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-12.6356	10.9586	0.47372	0.1293:0.8033:0.0:0.0675	rs10429323;rs10429323	.	.	.	W	32	.	.	X	-	2	0	KIAA0196	126149049	0.998000	0.40836	0.996000	0.52242	0.751000	0.42716	0.645000	0.24782	1.393000	0.46605	-0.320000	0.08662	TAG	T|0.971;C|0.029	0.029	strong		0.358	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846		C	126079867	T	C	126079867	2	2	22	1	0	0	0	0	0	0	0	1	8170	1519	53	3		3	KIAA0196	8	126079867	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	504820	126079867	20284155	1968	4869											
KIAA0196	9897	hgsc.bcm.edu	37	chr8	126087351	126087351	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atccccatgtaaatactaatTacctgaaagaggagacattc	16	10	6	9	0	0	3	0	1	0	2	2	4	1	3	3	1	2	1	3	1	6	5	rs79464415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:126087351T>G	ENST00000318410.7	-	8	1216	c.867A>C	c.(865-867)gtA>gtC	p.V289V	KIAA0196_ENST00000517845.1_Silent_p.V141V	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	289					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)			AAATACTAATTACCTGAAAGA	0.363													T|||	36	0.0071885	0.0272	0.0	5008	,	,		18432	0.0		0.0	False		,,,				2504	0.0				p.V289V		Atlas-SNP	.											.	KIAA0196	90	.	0			c.A867C						PASS	.	T		72,4334	64.7+/-102.0	0,72,2131	106	106	106		867	-3.3	1	8	dbSNP_131	106	1,8599		0,1,4299	no	coding-synonymous	KIAA0196	NM_014846.3		0,73,6430	GG,GT,TT		0.0116,1.6341,0.5613		289/1160	126087351	73,12933	2203	4300	6503	SO:0001819	synonymous_variant	9897	exon8			ACTAATTACCTGA		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.867A>C	8.37:g.126087351T>G		116	0	0		71	39	0.549296	NM_014846	A8K4R7|Q3KQX5|Q8TBQ2	Silent	SNP	ENST00000318410.7	37	CCDS6355.1																																																																																			T|0.994;G|0.006	0.006	strong		0.363	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846		G	126087351	T	G	126087351	2	3	22	1	0	0	0	0	0	0	0	1	8170	1741	61	5		5	KIAA0196	8	126087351	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	7484	126087351	20276671	1969	4870											
TRIB1	10221	hgsc.bcm.edu	37	chr8	126448674	126448674	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcagaccagattgttccagaGtaccaggaggacagtgacat	13	8	11	9	0	1	4	1	1	0	3	2	6	2	6	3	2	1	2	3	2	1	3	rs16900603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:126448674G>T	ENST00000519576.1	+	2	650	c.387G>T	c.(385-387)gaG>gaT	p.E129D	TRIB1_ENST00000311922.3_Missense_Mutation_p.E360D|TRIB1_ENST00000520847.1_Missense_Mutation_p.E194D					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)			TTGTTCCAGAGTACCAGGAGG	0.473													G|||	147	0.029353	0.1051	0.0101	5008	,	,		20227	0.0		0.001	False		,,,				2504	0.0				p.E360D		Atlas-SNP	.											.	TRIB1	73	.	0			c.G1080T						PASS	.	G	ASP/GLU	353,4053	181.5+/-209.5	15,323,1865	83	85	84		1080	2.7	1	8	dbSNP_123	84	4,8596	3.7+/-12.6	0,4,4296	yes	missense	TRIB1	NM_025195.2	45	15,327,6161	TT,TG,GG		0.0465,8.0118,2.7449	benign	360/373	126448674	357,12649	2203	4300	6503	SO:0001583	missense	10221	exon3			TCCAGAGTACCAG	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		ENST00000519576.1:c.387G>T	8.37:g.126448674G>T	ENSP00000428879:p.Glu129Asp	114	0	0		134	75	0.559702	NM_025195		Missense_Mutation	SNP	ENST00000519576.1	37		39	0.017857142857142856	35	0.07113821138211382	4	0.011049723756906077	0	0.0	0	0.0	G	0.601	-0.829096	0.02734	0.080118	4.65E-4	ENSG00000173334	ENST00000311922;ENST00000520847;ENST00000519576	T;T;T	0.47177	0.88;0.85;1.12	5.88	2.65	0.31530	.	0.241181	0.21003	N	0.081838	T	0.00936	0.0031	N	0.08118	0	0.23903	N	0.996519	B	0.11235	0.004	B	0.10450	0.005	T	0.17410	-1.0370	10	0.02654	T	1	-15.0092	5.2841	0.15692	0.0985:0.2463:0.5295:0.1257	rs16900603;rs52815805;rs16900603	360	Q96RU8	TRIB1_HUMAN	D	360;194;129	ENSP00000312150:E360D;ENSP00000429063:E194D;ENSP00000428879:E129D	ENSP00000312150:E360D	E	+	3	2	TRIB1	126517856	0.026000	0.19158	0.998000	0.56505	0.850000	0.48378	-0.005000	0.12855	0.811000	0.34303	-0.305000	0.09177	GAG	G|0.974;T|0.026	0.026	strong		0.473	TRIB1-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000381433.1	NM_025195		T	126448674	G	T	126448674	3	4	22	1	0	0	0	0	1	0	0	0	16497	1020	36	4	1090	4	TRIB1	8	126448674	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	361323	126448674	19915348	1970	4871											
POU5F1B	5462	hgsc.bcm.edu	37	chr8	128428592	128428592	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	agcagaagaggatcaccctgGgatatacacaggccgatgtg	13	6	13	9	1	1	2	1	0	0	2	1	5	1	4	2	3	2	1	2	3	3	2	rs140000439	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:128428592G>A	ENST00000465342.2	+	2	1638	c.481G>A	c.(481-483)Gga>Aga	p.G161R	CASC8_ENST00000501396.1_RNA|CASC8_ENST00000502082.1_RNA|POU5F1B_ENST00000391675.1_Missense_Mutation_p.G161R|CASC8_ENST00000523825.1_RNA			Q06416	P5F1B_HUMAN	POU class 5 homeobox 1B	161	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						GATCACCCTGGGATATACACA	0.522													g|||	78	0.0155751	0.053	0.0115	5008	,	,		17902	0.0		0.0	False		,,,				2504	0.0				p.G161R		Atlas-SNP	.											.	POU5F1B	32	.	0			c.G481A						PASS	.	G	ARG/GLY	73,1311		2,69,621	47	54	52		481	1.1	0.8	8	dbSNP_134	52	0,3182		0,0,1591	no	missense	POU5F1B	NM_001159542.1	125	2,69,2212	AA,AG,GG		0.0,5.2746,1.5988	probably-damaging	161/360	128428592	73,4493	692	1591	2283	SO:0001583	missense	5462	exon1			ACCCTGGGATATA	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.481G>A	8.37:g.128428592G>A	ENSP00000419298:p.Gly161Arg	155	0	0		161	81	0.503106	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	37	CCDS55274.1	32	0.014652014652014652	28	0.056910569105691054	4	0.011049723756906077	0	0.0	0	0.0	G	23.4	4.412629	0.83340	0.052746	0.0	ENSG00000212993	ENST00000465342;ENST00000391675	T;T	0.77877	-1.13;-1.13	1.14	1.14	0.20703	POU-specific (4);Lambda repressor-like, DNA-binding (2);POU (1);	0.000000	0.40144	N	0.001164	T	0.50137	0.1598	M	0.87682	2.9	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74328	-0.3701	10	0.87932	D	0	.	8.3083	0.32055	0.0:0.0:1.0:0.0	.	161	Q06416	P5F1B_HUMAN	R	161	ENSP00000419298:G161R;ENSP00000375557:G161R	ENSP00000375557:G161R	G	+	1	0	POU5F1B	128497774	1.000000	0.71417	0.759000	0.31340	0.727000	0.41649	6.555000	0.73928	0.968000	0.38212	0.134000	0.15878	GGA	G|0.985;A|0.015	0.015	strong		0.522	POU5F1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349649.2	NM_001159542		A	128428592	G	A	128428592	3	1	22	1	0	0	0	0	1	0	0	0	12291	1233	43	2	483	2	POU5F1B	8	128428592	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1979918	128428592	17935430	1971	4872											
POU5F1B	5462	hgsc.bcm.edu	37	chr8	128428721	128428721	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgtgtaagctgcggcccttgCtgcagaagtgggtggaggaa	8	9	17	7	1	0	1	0	0	0	1	0	3	0	3	1	4	4	4	1	4	3	2	rs192151034	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:128428721C>T	ENST00000465342.2	+	2	1767	c.610C>T	c.(610-612)Ctg>Ttg	p.L204L	CASC8_ENST00000501396.1_RNA|CASC8_ENST00000502082.1_RNA|POU5F1B_ENST00000391675.1_Silent_p.L204L|CASC8_ENST00000523825.1_RNA			Q06416	P5F1B_HUMAN	POU class 5 homeobox 1B	204	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						GCGGCCCTTGCTGCAGAAGTG	0.502													c|||	78	0.0155751	0.053	0.0115	5008	,	,		19515	0.0		0.0	False		,,,				2504	0.0				p.L204L		Atlas-SNP	.											.	POU5F1B	32	.	0			c.C610T						PASS	.	C		73,1311		2,69,621	17	21	20		610	1.1	0.8	8		20	0,3180		0,0,1590	no	coding-synonymous	POU5F1B	NM_001159542.1		2,69,2211	TT,TC,CC		0.0,5.2746,1.5995		204/360	128428721	73,4491	692	1590	2282	SO:0001819	synonymous_variant	5462	exon1			CCCTTGCTGCAGA	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.610C>T	8.37:g.128428721C>T		124	0	0		159	86	0.540881	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	37	CCDS55274.1																																																																																			C|0.985;T|0.015	0.015	strong		0.502	POU5F1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349649.2	NM_001159542		T	128428721	C	T	128428721	2	4	22	1	0	0	0	0	0	0	0	1	12291	796	28	2		2	POU5F1B	8	128428721	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	129	128428721	17935301	1972	4873											
GSDMC	56169	hgsc.bcm.edu	37	chr8	130762324	130762324	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagtttctttaggatggcAccaccagggccatccaaatg	11	10	10	10	0	1	1	0	1	1	0	2	2	2	2	4	3	0	2	4	3	3	3	rs35085916	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:130762324A>G	ENST00000276708.4	-	12	2006	c.1125T>C	c.(1123-1125)ggT>ggC	p.G375G		NM_031415.2	NP_113603.1	Q9BYG8	GSDMC_HUMAN	gasdermin C	375						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						TTAGGATGGCACCACCAGGGC	0.368													A|||	87	0.0173722	0.0628	0.0058	5008	,	,		18988	0.0		0.0	False		,,,				2504	0.0				p.G375G		Atlas-SNP	.											.	GSDMC	71	.	0			c.T1125C						PASS	.	A		286,4120	153.3+/-186.9	9,268,1926	36	36	36		1125	0.7	0	8	dbSNP_126	36	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	GSDMC	NM_031415.2		9,272,6222	GG,GA,AA		0.0465,6.4911,2.2297		375/509	130762324	290,12716	2203	4300	6503	SO:0001819	synonymous_variant	56169	exon12			GATGGCACCACCA	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.1125T>C	8.37:g.130762324A>G		102	0	0		111	67	0.603604	NM_031415	Q5XKF3|Q6P494	Silent	SNP	ENST00000276708.4	37	CCDS6360.1																																																																																			A|0.981;G|0.019	0.019	strong		0.368	GSDMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380586.1			G	130762324	A	G	130762324	2	3	22	1	0	0	0	0	0	0	0	1	6827	146	6	3		3	GSDMC	8	130762324	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2333603	130762324	15601698	1973	4874											
GSDMC	56169	hgsc.bcm.edu	37	chr8	130762732	130762732	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgagcatggccaggatactgTagaacatgacatcctgaaca	14	8	10	9	0	0	4	0	3	0	1	1	5	1	5	2	2	4	2	2	2	4	2	rs76700535	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:130762732T>C	ENST00000276708.4	-	11	1909	c.1028A>G	c.(1027-1029)tAc>tGc	p.Y343C		NM_031415.2	NP_113603.1	Q9BYG8	GSDMC_HUMAN	gasdermin C	343						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						CAGGATACTGTAGAACATGAC	0.473													T|||	53	0.0105831	0.0393	0.0014	5008	,	,		20490	0.0		0.0	False		,,,				2504	0.0				p.Y343C		Atlas-SNP	.											.	GSDMC	71	.	0			c.A1028G						PASS	.	T	CYS/TYR	190,4216	120.0+/-157.7	6,178,2019	136	119	125		1028	-4	0	8	dbSNP_131	125	1,8599	1.2+/-3.3	0,1,4299	yes	missense	GSDMC	NM_031415.2	194	6,179,6318	CC,CT,TT		0.0116,4.3123,1.4686	probably-damaging	343/509	130762732	191,12815	2203	4300	6503	SO:0001583	missense	56169	exon11			ATACTGTAGAACA	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.1028A>G	8.37:g.130762732T>C	ENSP00000276708:p.Tyr343Cys	101	0	0		117	47	0.401709	NM_031415	Q5XKF3|Q6P494	Missense_Mutation	SNP	ENST00000276708.4	37	CCDS6360.1	25	0.011446886446886446	25	0.0508130081300813	0	0.0	0	0.0	0	0.0	T	9.583	1.124120	0.20959	0.043123	1.16E-4	ENSG00000147697	ENST00000276708	T	0.22134	1.97	5.14	-4.01	0.04045	.	1.565630	0.03508	N	0.219111	T	0.02688	0.0081	N	0.08118	0	0.09310	N	1	D	0.59357	0.985	P	0.55667	0.781	T	0.12993	-1.0526	10	0.38643	T	0.18	.	8.1941	0.31385	0.0:0.1621:0.5701:0.2678	.	343	Q9BYG8	GSDMC_HUMAN	C	343	ENSP00000276708:Y343C	ENSP00000276708:Y343C	Y	-	2	0	GSDMC	130831914	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-0.577000	0.05847	-0.432000	0.07297	-0.389000	0.06534	TAC	T|0.985;C|0.015	0.015	strong		0.473	GSDMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380586.1			C	130762732	T	C	130762732	3	2	22	1	0	0	0	0	1	0	0	0	6827	1638	57	3	514	3	GSDMC	8	130762732	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	408	130762732	15601290	1974	4875											
OC90	729330	hgsc.bcm.edu	37	chr8	133036743	133036743	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcatctatcttccatgaagAggcccgatccccaagggacc	10	7	10	14	1	2	2	0	1	2	1	4	4	4	3	5	3	0	1	5	3	3	2	rs11991659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133036743A>G	ENST00000443356.2	-	15	1553	c.1467T>C	c.(1465-1467)ccT>ccC	p.P489P	OC90_ENST00000603859.1_Silent_p.P473P|OC90_ENST00000254627.3_Silent_p.P473P|OC90_ENST00000262283.5_Silent_p.P685P			Q02509	OC90_HUMAN	otoconin 90	489					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)			TTCCATGAAGAGGCCCGATCC	0.577													G|||	252	0.0503195	0.174	0.013	5008	,	,		19645	0.002		0.008	False		,,,				2504	0.0031				p.P473P		Atlas-SNP	.											OC90_ENST00000262283,brain,primitive_neuroectodermal_tumour-medulloblastoma,-1,2	OC90	163	2	0			c.T1419C						PASS	.	G		470,3414		23,424,1495	23	26	25		1419	0.9	0	8	dbSNP_120	25	67,8215		1,65,4075	no	coding-synonymous	OC90	NM_001080399.2		24,489,5570	GG,GA,AA		0.809,12.1009,4.4139		473/478	133036743	537,11629	1942	4141	6083	SO:0001819	synonymous_variant	729330	exon14			ATGAAGAGGCCCG	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.1467T>C	8.37:g.133036743A>G		52	0	0		34	20	0.588235	NM_001080399	B4DNG8	Silent	SNP	ENST00000443356.2	37																																																																																				A|0.952;G|0.048	0.048	strong		0.577	OC90-201	KNOWN	basic	protein_coding	protein_coding		NM_001080399		G	133036743	A	G	133036743	2	3	22	1	0	0	0	0	0	0	0	1	10823	291	11	3		3	OC90	8	133036743	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2274011	133036743	13327279	1975	4876											
OC90	729330	hgsc.bcm.edu	37	chr8	133044172	133044172	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctcttccttcttgtccacaGtaacagccataagactcaaa	12	11	4	14	0	3	1	1	0	2	1	5	1	5	1	4	0	2	1	4	0	3	5	rs6989686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133044172G>A	ENST00000443356.2	-	13	1121	c.1035C>T	c.(1033-1035)taC>taT	p.Y345Y	OC90_ENST00000603859.1_Silent_p.Y329Y|OC90_ENST00000254627.3_Silent_p.Y329Y|OC90_ENST00000262283.5_Silent_p.Y541Y			Q02509	OC90_HUMAN	otoconin 90	345	Phospholipase A2-like 2.				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)			CTTGTCCACAGTAACAGCCAT	0.542													G|||	45	0.00898562	0.0325	0.0029	5008	,	,		19082	0.0		0.0	False		,,,				2504	0.0				p.Y329Y		Atlas-SNP	.											.	OC90	163	.	0			c.C987T						PASS	.	G		111,3919		1,109,1905	57	60	59		987	4.1	1	8	dbSNP_116	59	1,8369		0,1,4184	no	coding-synonymous	OC90	NM_001080399.2		1,110,6089	AA,AG,GG		0.0119,2.7543,0.9032		329/478	133044172	112,12288	2015	4185	6200	SO:0001819	synonymous_variant	729330	exon12			TCCACAGTAACAG	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.1035C>T	8.37:g.133044172G>A		130	0	0		144	65	0.451389	NM_001080399	B4DNG8	Silent	SNP	ENST00000443356.2	37																																																																																				G|0.994;A|0.006	0.006	strong		0.542	OC90-201	KNOWN	basic	protein_coding	protein_coding		NM_001080399		A	133044172	G	A	133044172	2	1	22	1	0	0	0	0	0	0	0	1	10823	1024	36	2		2	OC90	8	133044172	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	7429	133044172	13319850	1976	4877											
OC90	729330	hgsc.bcm.edu	37	chr8	133053909	133053909	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agcacagggaaattggtgaaGacagcctgcagccaggtgaa	14	5	14	8	0	0	3	0	2	0	1	0	4	0	4	2	3	4	2	2	3	3	1	rs115883855	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133053909G>C	ENST00000443356.2	-	5	293	c.207C>G	c.(205-207)gtC>gtG	p.V69V	OC90_ENST00000603859.1_Silent_p.V69V|OC90_ENST00000254627.3_Silent_p.V69V|OC90_ENST00000262283.5_Silent_p.V265V			Q02509	OC90_HUMAN	otoconin 90	69					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)			AATTGGTGAAGACAGCCTGCA	0.577													G|||	53	0.0105831	0.0386	0.0029	5008	,	,		17110	0.0		0.0	False		,,,				2504	0.0				p.V69V		Atlas-SNP	.											OC90_ENST00000262283,caecum,carcinoma,0,2	OC90	163	2	0			c.C207G						PASS	.	G		121,3849		1,119,1865	33	33	33		207	2.8	1	8	dbSNP_132	33	0,8330		0,0,4165	no	coding-synonymous	OC90	NM_001080399.2		1,119,6030	CC,CG,GG		0.0,3.0479,0.9837		69/478	133053909	121,12179	1985	4165	6150	SO:0001819	synonymous_variant	729330	exon5			GGTGAAGACAGCC	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.207C>G	8.37:g.133053909G>C		121	0	0		139	70	0.503597	NM_001080399	B4DNG8	Silent	SNP	ENST00000443356.2	37																																																																																				G|0.989;C|0.011	0.011	strong		0.577	OC90-201	KNOWN	basic	protein_coding	protein_coding		NM_001080399		C	133053909	G	C	133053909	2	2	22	1	0	0	0	0	0	0	0	1	10823	929	33	4		4	OC90	8	133053909	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	9737	133053909	13310113	1977	4878											
TG	7038	hgsc.bcm.edu	37	chr8	133898949	133898949	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	aatcttctcaaagaagccatCcgagcaatttttccctcccg	11	11	5	14	2	2	1	1	0	2	1	6	2	5	1	4	0	2	1	4	0	4	3	rs61741629	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133898949C>T	ENST00000220616.4	+	9	1372	c.1332C>T	c.(1330-1332)atC>atT	p.I444I	TG_ENST00000377869.1_Silent_p.I444I	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	444					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)		AAGAAGCCATCCGAGCAATTT	0.502													C|||	124	0.0247604	0.0923	0.0029	5008	,	,		18045	0.0		0.0	False		,,,				2504	0.0				p.I444I		Atlas-SNP	.											.	TG	416	.	0			c.C1332T						PASS	.	C		332,4074	169.1+/-199.8	19,294,1890	73	80	78		1332	-1	0	8	dbSNP_129	78	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TG	NM_003235.4		19,296,6188	TT,TC,CC		0.0233,7.5352,2.568		444/2769	133898949	334,12672	2203	4300	6503	SO:0001819	synonymous_variant	7038	exon9			AGCCATCCGAGCA	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.1332C>T	8.37:g.133898949C>T		48	0	0		68	42	0.617647	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1																																																																																			C|0.971;T|0.029	0.029	strong		0.502	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		T	133898949	C	T	133898949	2	4	22	1	0	0	0	0	0	0	0	1	15828	845	30	2		2	TG	8	133898949	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	845040	133898949	12465073	1978	4879											
TG	7038	hgsc.bcm.edu	37	chr8	133899438	133899438	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acggtactcagctcccagacCtgtgagcagacacctgaaag	12	6	10	13	1	1	4	1	2	0	2	2	4	2	4	3	1	3	3	3	1	2	1	rs61742713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133899438C>T	ENST00000220616.4	+	9	1861	c.1821C>T	c.(1819-1821)acC>acT	p.T607T	TG_ENST00000377869.1_Silent_p.T607T	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	607	Thyroglobulin type-1 5. {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)		GCTCCCAGACCTGTGAGCAGA	0.473													C|||	108	0.0215655	0.0802	0.0029	5008	,	,		21407	0.0		0.0	False		,,,				2504	0.0				p.T607T		Atlas-SNP	.											.	TG	416	.	0			c.C1821T						PASS	.	C		290,4116	160.0+/-192.4	12,266,1925	148	132	137		1821	5	0.7	8	dbSNP_129	137	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TG	NM_003235.4		12,268,6223	TT,TC,CC		0.0233,6.5819,2.2451		607/2769	133899438	292,12714	2203	4300	6503	SO:0001819	synonymous_variant	7038	exon9			CCAGACCTGTGAG	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.1821C>T	8.37:g.133899438C>T		141	0	0		149	77	0.516779	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1																																																																																			C|0.974;T|0.026	0.026	strong		0.473	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		T	133899438	C	T	133899438	2	4	22	1	0	0	0	0	0	0	0	1	15828	668	24	2		2	TG	8	133899438	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	489	133899438	12464584	1979	4880											
TG	7038	hgsc.bcm.edu	37	chr8	133953676	133953676	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctggattgtacaaccccAttgtgttctcagcctcagga	8	14	8	11	0	3	0	2	0	2	0	4	2	3	2	3	2	3	2	3	2	2	5	rs61744679	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133953676A>G	ENST00000220616.4	+	26	5162	c.5122A>G	c.(5122-5124)Att>Gtt	p.I1708V	TG_ENST00000542445.1_Intron|TG_ENST00000377869.1_Missense_Mutation_p.I1651V	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1708					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)		GTACAACCCCATTGTGTTCTC	0.502													A|||	140	0.0279553	0.1014	0.0086	5008	,	,		22921	0.0		0.0	False		,,,				2504	0.0				p.I1708V		Atlas-SNP	.											.	TG	416	.	0			c.A5122G						PASS	.	A	VAL/ILE	382,4024	193.0+/-218.2	19,344,1840	170	143	153		5122	-0.3	0	8	dbSNP_129	153	3,8597	3.0+/-9.4	0,3,4297	yes	missense	TG	NM_003235.4	29	19,347,6137	GG,GA,AA		0.0349,8.67,2.9602	benign	1708/2769	133953676	385,12621	2203	4300	6503	SO:0001583	missense	7038	exon26			AACCCCATTGTGT	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.5122A>G	8.37:g.133953676A>G	ENSP00000220616:p.Ile1708Val	241	0	0		286	144	0.503497	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	61	0.027930402930402932	57	0.11585365853658537	4	0.011049723756906077	0	0.0	0	0.0	A	0	-2.653927	0.00109	0.0867	3.49E-4	ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616	T;T	0.60548	0.18;0.18	5.81	-0.269	0.12930	.	1.039030	0.07593	N	0.922337	T	0.00210	0.0006	N	0.00268	-1.735	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.12604	-1.0541	10	0.02654	T	1	.	4.2539	0.10708	0.2662:0.0:0.4355:0.2983	rs61744679	1708	P01266	THYG_HUMAN	V	1651;514;1708	ENSP00000367100:I1651V;ENSP00000220616:I1708V	ENSP00000220616:I1708V	I	+	1	0	TG	134022858	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	0.340000	0.19892	0.055000	0.16094	-1.652000	0.00757	ATT	A|0.964;G|0.036	0.036	strong		0.502	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		G	133953676	A	G	133953676	3	3	22	1	0	0	0	0	1	0	0	0	15828	217	8	3	5224	3	TG	8	133953676	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	54238	133953676	12410346	1980	4881											
TG	7038	hgsc.bcm.edu	37	chr8	133953740	133953740	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttctgtcttcttgcatgcgAccgtgatctgtgttgcgatg	4	16	11	10	3	4	1	0	1	4	0	4	3	4	1	1	0	3	2	1	0	0	4	rs61744749	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133953740A>C	ENST00000220616.4	+	26	5226	c.5186A>C	c.(5185-5187)gAc>gCc	p.D1729A	TG_ENST00000542445.1_Intron|TG_ENST00000377869.1_Missense_Mutation_p.D1672A	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1729					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)		CTTGCATGCGACCGTGATCTG	0.527													A|||	140	0.0279553	0.1014	0.0086	5008	,	,		23318	0.0		0.0	False		,,,				2504	0.0				p.D1729A		Atlas-SNP	.											TG,NS,carcinoma,+1,1	TG	416	1	0			c.A5186C						PASS	.	A	ALA/ASP	382,4024	193.0+/-218.2	19,344,1840	176	141	153		5186	5.6	1	8	dbSNP_129	153	3,8597	3.0+/-9.4	0,3,4297	yes	missense	TG	NM_003235.4	126	19,347,6137	CC,CA,AA		0.0349,8.67,2.9602	possibly-damaging	1729/2769	133953740	385,12621	2203	4300	6503	SO:0001583	missense	7038	exon26			CATGCGACCGTGA	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.5186A>C	8.37:g.133953740A>C	ENSP00000220616:p.Asp1729Ala	292	1	0.00342466		311	147	0.472669	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	61	0.027930402930402932	57	0.11585365853658537	4	0.011049723756906077	0	0.0	0	0.0	A	11.79	1.743661	0.30865	0.0867	3.49E-4	ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616	T;T	0.70282	-0.47;-0.47	5.61	5.61	0.85477	.	0.387653	0.24873	N	0.034902	T	0.02230	0.0069	M	0.72118	2.19	0.36596	D	0.874396	B	0.31581	0.329	B	0.27170	0.077	T	0.47898	-0.9081	10	0.66056	D	0.02	.	12.1945	0.54290	1.0:0.0:0.0:0.0	rs61744749	1729	P01266	THYG_HUMAN	A	1672;535;1729	ENSP00000367100:D1672A;ENSP00000220616:D1729A	ENSP00000220616:D1729A	D	+	2	0	TG	134022922	0.998000	0.40836	0.981000	0.43875	0.150000	0.21749	3.679000	0.54634	2.142000	0.66516	0.379000	0.24179	GAC	A|0.964;C|0.036	0.036	strong		0.527	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		C	133953740	A	C	133953740	3	2	22	1	0	0	0	0	1	0	0	0	15828	275	10	5	5288	5	TG	8	133953740	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	64	133953740	12410282	1981	4882											
TG	7038	hgsc.bcm.edu	37	chr8	134042164	134042164	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatttggcggggaccctcggCgcgtgtccctggcagcagac	5	7	16	13	4	0	1	0	0	0	1	2	3	1	2	2	5	1	2	2	5	0	1	rs61742878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:134042164C>T	ENST00000220616.4	+	41	7175	c.7135C>T	c.(7135-7137)Cgc>Tgc	p.R2379C	TG_ENST00000542445.1_Missense_Mutation_p.R749C|TG_ENST00000377869.1_Missense_Mutation_p.R2322C|TG_ENST00000519543.1_Missense_Mutation_p.R512C	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2379					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)		GGACCCTCGGCGCGTGTCCCT	0.667													C|||	22	0.00439297	0.0166	0.0	5008	,	,		14003	0.0		0.0	False		,,,				2504	0.0				p.R2379C		Atlas-SNP	.											TG,NS,carcinoma,0,4	TG	416	4	0			c.C7135T						PASS	.	C	CYS/ARG	54,4352	54.2+/-90.2	0,54,2149	47	49	48		7135	4.2	0.6	8	dbSNP_129	48	0,8596		0,0,4298	yes	missense	TG	NM_003235.4	180	0,54,6447	TT,TC,CC		0.0,1.2256,0.4153	probably-damaging	2379/2769	134042164	54,12948	2203	4298	6501	SO:0001583	missense	7038	exon41			CCTCGGCGCGTGT	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.7135C>T	8.37:g.134042164C>T	ENSP00000220616:p.Arg2379Cys	106	0	0		124	49	0.395161	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	7|7	0.003205128205128205|0.003205128205128205	7|7	0.014227642276422764|0.014227642276422764	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	15.00|15.00	2.701863|2.701863	0.48307|0.48307	0.012256|0.012256	0.0|0.0	ENSG00000042832|ENSG00000042832	ENST00000519178;ENST00000518108|ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445;ENST00000519543	.|T;T;T;T	.|0.65364	.|-0.15;-0.15;-0.15;-0.15	5.13|5.13	4.22|4.22	0.49857|0.49857	.|Carboxylesterase, type B (1);	.|0.761860	.|0.12170	.|N	.|0.493098	T|T	0.69993|0.69993	0.3173|0.3173	M|M	0.72576|0.72576	2.205|2.205	0.09310|0.09310	N|N	0.999993|0.999993	.|D;D;D	.|0.89917	.|1.0;0.999;0.999	.|D;P;D	.|0.63192	.|0.912;0.899;0.912	T|T	0.63853|0.63853	-0.6543|-0.6543	5|10	.|0.87932	.|D	.|0	.|.	13.7454|13.7454	0.62872|0.62872	0.1544:0.8456:0.0:0.0|0.1544:0.8456:0.0:0.0	rs61742878|rs61742878	.|512;749;2379	.|E7EVM0;F5GWW5;P01266	.|.;.;THYG_HUMAN	V|C	834;174|2322;1185;2379;749;512	.|ENSP00000367100:R2322C;ENSP00000220616:R2379C;ENSP00000441693:R749C;ENSP00000430430:R512C	.|ENSP00000220616:R2379C	A|R	+|+	2|1	0|0	TG|TG	134111346|134111346	0.060000|0.060000	0.20803|0.20803	0.550000|0.550000	0.28217|0.28217	0.384000|0.384000	0.30261|0.30261	2.504000|2.504000	0.45416|0.45416	2.407000|2.407000	0.81776|0.81776	0.485000|0.485000	0.47835|0.47835	GCG|CGC	C|0.995;T|0.005	0.005	strong		0.667	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		T	134042164	C	T	134042164	3	4	22	1	0	0	0	0	1	0	0	0	15828	768	27	1	7297	1	TG	8	134042164	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	88424	134042164	12321858	1982	4883											
TG	7038	hgsc.bcm.edu	37	chr8	134108459	134108459	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atccaatgcagctcctggccGtgagtggccctttccactac	7	10	9	15	1	0	1	0	1	0	0	3	1	3	1	5	2	3	2	5	2	2	2	rs61730222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:134108459G>C	ENST00000220616.4	+	43	7454	c.7414G>C	c.(7414-7416)Gtg>Ctg	p.V2472L	SLA_ENST00000338087.5_Intron|SLA_ENST00000524345.1_Intron|SLA_ENST00000395352.3_Intron|TG_ENST00000542445.1_Missense_Mutation_p.V842L|SLA_ENST00000518565.1_Intron|TG_ENST00000377869.1_Missense_Mutation_p.V2415L|TG_ENST00000519543.1_Missense_Mutation_p.V605L|SLA_ENST00000517648.1_Intron	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2472					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.V2472M(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)		GCTCCTGGCCGTGAGTGGCCC	0.502													G|||	90	0.0179712	0.0658	0.0043	5008	,	,		21243	0.0		0.0	False		,,,				2504	0.0				p.V2472L		Atlas-SNP	.											TG,colon,carcinoma,0,2	TG	416	2	1	Substitution - Missense(1)	large_intestine(1)	c.G7414C						PASS	.	G	,,LEU/VAL	250,4156	146.9+/-181.5	5,240,1958	171	160	164		,,7414	3.4	1	8	dbSNP_129	164	2,8598	1.2+/-3.3	0,2,4298	no	intron,intron,missense	SLA,TG	NM_001045556.2,NM_001045557.2,NM_003235.4	,,32	5,242,6256	CC,CG,GG		0.0233,5.6741,1.9376	,,possibly-damaging	,,2472/2769	134108459	252,12754	2203	4300	6503	SO:0001583	missense	7038	exon43			CTGGCCGTGAGTG	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.7414G>C	8.37:g.134108459G>C	ENSP00000220616:p.Val2472Leu	159	0	0		181	85	0.469613	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	42|42	0.019230769230769232|0.019230769230769232	39|39	0.07926829268292683|0.07926829268292683	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	G|G	19.35|19.35	3.810956|3.810956	0.70797|0.70797	0.056741|0.056741	2.33E-4|2.33E-4	ENSG00000042832|ENSG00000042832	ENST00000519178|ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445;ENST00000519543	.|T;T;T;T	.|0.66815	.|-0.23;-0.23;-0.23;-0.23	5.46|5.46	3.42|3.42	0.39159|0.39159	.|Carboxylesterase, type B (1);	.|0.800184	.|0.11276	.|N	.|0.580893	T|T	0.05318|0.05318	0.0141|0.0141	L|L	0.33137|0.33137	0.985|0.985	0.80722|0.80722	D|D	1|1	.|P;B;P	.|0.45283	.|0.855;0.142;0.526	.|B;B;B	.|0.41571	.|0.36;0.014;0.172	T|T	0.11867|0.11867	-1.0570|-1.0570	5|10	.|0.66056	.|D	.|0.02	.|.	5.3896|5.3896	0.16237|0.16237	0.2809:0.0:0.7191:0.0|0.2809:0.0:0.7191:0.0	rs61730222|rs61730222	.|605;842;2472	.|E7EVM0;F5GWW5;P01266	.|.;.;THYG_HUMAN	P|L	927|2415;1278;2472;842;605	.|ENSP00000367100:V2415L;ENSP00000220616:V2472L;ENSP00000441693:V842L;ENSP00000430430:V605L	.|ENSP00000220616:V2472L	R|V	+|+	2|1	0|0	TG|TG	134177641|134177641	0.999000|0.999000	0.42202|0.42202	0.989000|0.989000	0.46669|0.46669	0.954000|0.954000	0.61252|0.61252	4.049000|4.049000	0.57397|0.57397	1.300000|1.300000	0.44818|0.44818	0.655000|0.655000	0.94253|0.94253	CGT|GTG	G|0.978;C|0.022	0.022	strong		0.502	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		C	134108459	G	C	134108459	3	2	22	1	0	0	0	0	1	0	0	0	15828	1145	40	4	7584	4	TG	8	134108459	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	66295	134108459	12255563	1983	4884											
ST3GAL1	6482	hgsc.bcm.edu	37	chr8	134478178	134478178	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctatctcaggcccataagaAgactccctcaggttgcccga	10	9	8	14	1	3	2	2	0	2	2	5	3	4	2	3	2	1	1	3	2	3	3	rs112787936	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:134478178A>G	ENST00000319914.5	-	5	1489	c.462T>C	c.(460-462)tcT>tcC	p.S154S	ST3GAL1_ENST00000399640.2_Silent_p.S154S|ST3GAL1_ENST00000521180.1_Silent_p.S154S|ST3GAL1_ENST00000522652.1_Silent_p.S154S			Q11201	SIA4A_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	154					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)			GCCCATAAGAAGACTCCCTCA	0.622													A|||	75	0.014976	0.0552	0.0029	5008	,	,		18246	0.0		0.0	False		,,,				2504	0.0				p.S154S		Atlas-SNP	.											.	ST3GAL1	39	.	0			c.T462C						PASS	.	A	,	201,4205	123.7+/-161.0	5,191,2007	94	93	93		462,462	1.8	0.3	8	dbSNP_132	93	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	ST3GAL1	NM_003033.3,NM_173344.2	,	5,193,6305	GG,GA,AA		0.0233,4.562,1.5608	,	154/341,154/341	134478178	203,12803	2203	4300	6503	SO:0001819	synonymous_variant	6482	exon6			ATAAGAAGACTCC	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.462T>C	8.37:g.134478178A>G		146	0	0		160	82	0.5125	NM_173344	O60677|Q9UN51	Silent	SNP	ENST00000319914.5	37	CCDS6373.1																																																																																			A|0.984;G|0.016	0.016	strong		0.622	ST3GAL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379132.1	NM_003033		G	134478178	A	G	134478178	2	3	22	1	0	0	0	0	0	0	0	1	15229	59	3	3		3	ST3GAL1	8	134478178	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	369719	134478178	11885844	1984	4885											
ZFAT	57623	hgsc.bcm.edu	37	chr8	135613947	135613947	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggtttgacctgagacacCtgctgggatctgggtcacca	7	10	13	11	0	2	2	1	2	1	1	2	4	2	3	3	3	1	2	3	3	0	1	rs35003767	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:135613947C>T	ENST00000377838.3	-	6	2189	c.2015G>A	c.(2014-2016)aGg>aAg	p.R672K	ZFAT_ENST00000520356.1_Missense_Mutation_p.R660K|ZFAT-AS1_ENST00000505776.1_RNA|ZFAT_ENST00000520214.1_Missense_Mutation_p.R660K|ZFAT_ENST00000429442.2_Missense_Mutation_p.R660K|ZFAT_ENST00000523399.1_Missense_Mutation_p.R610K|ZFAT_ENST00000520727.1_Missense_Mutation_p.R660K	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	672			R -> K (in dbSNP:rs35003767).		hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|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)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			CCTGAGACACCTGCTGGGATC	0.602													C|||	119	0.023762	0.0855	0.0086	5008	,	,		19293	0.0		0.0	False		,,,				2504	0.0				p.R672K		Atlas-SNP	.											.	ZFAT	265	.	0			c.G2015A						PASS	.	C	LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG	224,3798		7,210,1794	60	66	64		1979,1979,1829,1979,2015	-2.1	0	8	dbSNP_126	64	2,8378		0,2,4188	yes	missense,missense,missense,missense,missense	ZFAT	NM_001029939.3,NM_001167583.2,NM_001174157.1,NM_001174158.1,NM_020863.3	26,26,26,26,26	7,212,5982	TT,TC,CC		0.0239,5.5694,1.8223	benign,benign,benign,benign,benign	660/1232,660/1232,610/1182,660/1146,672/1244	135613947	226,12176	2011	4190	6201	SO:0001583	missense	57623	exon6			AGACACCTGCTGG	BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827		"Zinc fingers, C2H2-type"	19899	protein-coding gene	gene with protein product		610931	"zinc finger protein 406"	ZNF406, ZFAT1		10819331, 18329245	Standard	NM_020863		Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.2015G>A	8.37:g.135613947C>T	ENSP00000367069:p.Arg672Lys	83	0	0		82	39	0.47561	NM_020863	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Missense_Mutation	SNP	ENST00000377838.3	37	CCDS47924.1	59	0.027014652014652016	56	0.11382113821138211	3	0.008287292817679558	0	0.0	0	0.0	C	0.009	-1.816281	0.00595	0.055694	2.39E-4	ENSG00000066827	ENST00000520356;ENST00000520727;ENST00000429442;ENST00000377838;ENST00000520214;ENST00000318135;ENST00000523399;ENST00000398946	T;T;T;T;T;T	0.08282	3.18;3.12;3.13;3.11;3.12;3.12	4.76	-2.14	0.07123	.	1.175010	0.06093	N	0.663981	T	0.00109	0.0003	N	0.19112	0.55	0.09310	N	1	B;B;B;B	0.16396	0.001;0.017;0.002;0.001	B;B;B;B	0.15870	0.001;0.014;0.002;0.0	T	0.37731	-0.9693	10	0.05436	T	0.98	-1.7605	2.7057	0.05161	0.1238:0.3172:0.3665:0.1925	rs35003767	610;660;660;672	E9PER3;E9PBN4;Q9P243-3;Q9P243	.;.;.;ZFAT_HUMAN	K	660;660;660;672;660;559;610;660	ENSP00000427879:R660K;ENSP00000427831:R660K;ENSP00000394501:R660K;ENSP00000367069:R672K;ENSP00000428483:R660K;ENSP00000429091:R610K	ENSP00000326997:R559K	R	-	2	0	ZFAT	135683129	0.000000	0.05858	0.000000	0.03702	0.217000	0.24651	-2.263000	0.01174	-0.055000	0.13244	0.561000	0.74099	AGG	C|0.971;T|0.029	0.029	strong		0.602	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939		T	135613947	C	T	135613947	3	4	22	1	0	0	0	0	1	0	0	0	17647	681	24	2	1760	2	ZFAT	8	135613947	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1135769	135613947	10750075	1985	4886											
TRAPPC9	83696	hgsc.bcm.edu	37	chr8	140743460	140743460	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccgaggcaggccgactggccGgacggctgcacctgagcagg	7	3	17	14	4	0	1	0	1	0	0	0	4	0	2	4	6	2	4	4	6	0	0	rs148857575	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:140743460G>A	ENST00000438773.2	-	23	3424	c.3291C>T	c.(3289-3291)tcC>tcT	p.S1097S	TRAPPC9_ENST00000389328.4_Silent_p.S1195S|TRAPPC9_ENST00000522504.1_5'UTR|TRAPPC9_ENST00000389327.3_Silent_p.S1088S	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	1097					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						CCGACTGGCCGGACGGCTGCA	0.622													G|||	12	0.00239617	0.0083	0.0014	5008	,	,		14736	0.0		0.0	False		,,,				2504	0.0				p.S1195S		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.C3585T						PASS	.	G	,	30,4376	36.8+/-68.6	0,30,2173	38	38	38		3291,3585	-9.9	0	8	dbSNP_134	38	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	TRAPPC9	NM_001160372.1,NM_031466.5	,	0,30,6473	AA,AG,GG		0.0,0.6809,0.2307	,	1097/1149,1195/1247	140743460	30,12976	2203	4300	6503	SO:0001819	synonymous_variant	83696	exon23			CTGGCCGGACGGC	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.3291C>T	8.37:g.140743460G>A		76	0	0		85	43	0.505882	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Silent	SNP	ENST00000438773.2	37	CCDS55278.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	0.021	-1.421690	0.01126	0.006809	0.0	ENSG00000167632	ENST00000520857	.	.	.	4.93	-9.86	0.00473	.	.	.	.	.	T	0.35624	0.0938	.	.	.	0.38039	D	0.935405	.	.	.	.	.	.	T	0.56792	-0.7920	4	.	.	.	.	6.719	0.23321	0.0688:0.4132:0.3666:0.1514	.	.	.	.	W	941	.	.	R	-	1	2	TRAPPC9	140812642	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-3.021000	0.00642	-4.055000	0.00078	-3.274000	0.00048	CGG	G|0.998;A|0.002	0.002	strong		0.622	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466		A	140743460	G	A	140743460	2	1	22	1	0	0	0	0	0	0	0	1	16480	1103	39	1		1	TRAPPC9	8	140743460	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5129513	140743460	5620562	1986	4887											
TRAPPC9	83696	hgsc.bcm.edu	37	chr8	140999002	140999002	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgacggtcagctcatgctcGgtggagttgaagacatccag	9	9	13	10	2	2	3	2	2	0	1	4	4	3	4	1	3	2	3	1	3	1	1	rs28710457	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:140999002G>A	ENST00000438773.2	-	19	2875	c.2742C>T	c.(2740-2742)acC>acT	p.T914T	TRAPPC9_ENST00000389328.4_Silent_p.T1012T|TRAPPC9_ENST00000389327.3_Silent_p.T905T	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	914					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						GCTCATGCTCGGTGGAGTTGA	0.567													G|||	54	0.0107827	0.0378	0.0014	5008	,	,		19691	0.003		0.0	False		,,,				2504	0.0				p.T1012T		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.C3036T						PASS	.	G	,	125,3835		1,123,1856	29	26	27		2742,3036	-9.6	0.5	8	dbSNP_125	27	1,7655		0,1,3827	no	coding-synonymous,coding-synonymous	TRAPPC9	NM_001160372.1,NM_031466.5	,	1,124,5683	AA,AG,GG		0.0131,3.1566,1.0847	,	914/1149,1012/1247	140999002	126,11490	1980	3828	5808	SO:0001819	synonymous_variant	83696	exon19			ATGCTCGGTGGAG	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.2742C>T	8.37:g.140999002G>A		49	0	0		62	30	0.483871	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Silent	SNP	ENST00000438773.2	37	CCDS55278.1	21	0.009615384615384616	17	0.034552845528455285	1	0.0027624309392265192	3	0.005244755244755245	0	0.0	G	6.618	0.482489	0.12581	0.031566	1.31E-4	ENSG00000167632	ENST00000520857	.	.	.	5.62	-9.63	0.00544	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.9498	0.14008	0.0885:0.1092:0.2516:0.5507	rs28710457	.	.	.	X	758	.	.	R	-	1	2	TRAPPC9	141068184	0.262000	0.24073	0.460000	0.27093	0.679000	0.39708	-0.500000	0.06405	-2.040000	0.00916	-2.131000	0.00343	CGA	G|0.986;A|0.014	0.014	strong		0.567	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466		A	140999002	G	A	140999002	2	1	22	1	0	0	0	0	0	0	0	1	16480	1103	39	1		1	TRAPPC9	8	140999002	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	255542	140999002	5365020	1987	4888											
SLC45A4	57210	hgsc.bcm.edu	37	chr8	142228386	142228386	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtcgctcatgctgcgcgaCggcttgatcagcaccacggc	7	7	13	14	5	2	1	2	1	0	0	3	2	2	1	1	3	3	4	1	3	0	1	rs61995881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:142228386C>T	ENST00000024061.3	-	4	1507	c.1200G>A	c.(1198-1200)ccG>ccA	p.P400P	SLC45A4_ENST00000519067.1_Silent_p.P400P|SLC45A4_ENST00000433583.2_Silent_p.P393P|SLC45A4_ENST00000517878.1_Silent_p.P451P	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)			TGCTGCGCGACGGCTTGATCA	0.677													C|||	69	0.013778	0.0461	0.0086	5008	,	,		15669	0.0		0.0	False		,,,				2504	0.002				p.P400P		Atlas-SNP	.											.	SLC45A4	71	.	0			c.G1200A						PASS	.	C		212,4194	124.9+/-162.1	7,198,1998	46	44	45		1200	-2.3	0.9	8	dbSNP_129	45	0,8598		0,0,4299	no	coding-synonymous	SLC45A4	NM_001080431.1		7,198,6297	TT,TC,CC		0.0,4.8116,1.6303		400/799	142228386	212,12792	2203	4299	6502	SO:0001819	synonymous_variant	57210	exon4			GCGCGACGGCTTG	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.1200G>A	8.37:g.142228386C>T		32	0	0		46	28	0.608696	NM_001080431	Q6ZRI2|Q9ULU3	Silent	SNP	ENST00000024061.3	37	CCDS34948.1																																																																																			C|0.986;T|0.014	0.014	strong		0.677	SLC45A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378571.3	XM_050325		T	142228386	C	T	142228386	2	4	22	1	0	0	0	0	0	0	0	1	14658	523	19	1		1	SLC45A4	8	142228386	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1229384	142228386	4135636	1988	4889											
BAI1	575	hgsc.bcm.edu	37	chr8	143599594	143599594	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggtcatcatctacgtgtcCgtgtggaggtgggtgccgcc	4	11	15	11	3	3	0	2	0	1	0	4	1	4	1	3	4	2	0	3	4	1	1	rs75573695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:143599594C>T	ENST00000517894.1	+	19	3807	c.2913C>T	c.(2911-2913)tcC>tcT	p.S971S	BAI1_ENST00000323289.5_Silent_p.S971S			O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	971					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)					TCTACGTGTCCGTGTGGAGGT	0.632													C|||	247	0.0493211	0.1142	0.0187	5008	,	,		14503	0.0258		0.002	False		,,,				2504	0.0562				p.S971S		Atlas-SNP	.											.	BAI1	146	.	0			c.C2913T						PASS	.	C		384,4012	181.2+/-209.3	15,354,1829	148	152	151		2913	-3.8	1	8	dbSNP_132	151	9,8573	6.4+/-24.3	0,9,4282	no	coding-synonymous	BAI1	NM_001702.2		15,363,6111	TT,TC,CC		0.1049,8.7352,3.0282		971/1585	143599594	393,12585	2198	4291	6489	SO:0001819	synonymous_variant	575	exon18			CGTGTCCGTGTGG	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.2913C>T	8.37:g.143599594C>T		160	0	0		145	67	0.462069	NM_001702		Silent	SNP	ENST00000517894.1	37																																																																																				C|0.964;T|0.036	0.036	strong		0.632	BAI1-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379963.3	NM_001702		T	143599594	C	T	143599594	2	4	22	1	0	0	0	0	0	0	0	1	1298	639	23	1		1	BAI1	8	143599594	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1371208	143599594	2764428	1989	4890											
JRK	8629	hgsc.bcm.edu	37	chr8	143746107	143746107	+	RNA	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacacacaacctctgctggCgacgtggcagcagggggccg	8	4	14	15	3	1	0	0	0	1	0	1	1	1	0	3	4	3	3	3	4	1	0	rs61747165	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:143746107C>T	ENST00000507178.2	-	0	1703							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)				cctctgctggcgacgtggcag	0.682													C|||	63	0.0125799	0.0469	0.0014	5008	,	,		16019	0.0		0.0	False		,,,				2504	0.0				p.S457S		Atlas-SNP	.											.	.	.	.	0			c.G1371A						PASS	.	C	,	147,3827		0,147,1840	17	19	18		1371,1371	-6.5	0	8	dbSNP_129	18	1,8225		0,1,4112	no	coding-synonymous,coding-synonymous	JRK	NM_001077527.1,NM_003724.2	,	0,148,5952	TT,TC,CC		0.0122,3.699,1.2131	,	457/557,457/569	143746107	148,12052	1987	4113	6100			8629	exon2			TGCTGGCGACGTG	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			8.37:g.143746107C>T		25	0	0		52	38	0.730769	NM_003724	O75565	Silent	SNP	ENST00000507178.2	37																																																																																				C|0.992;T|0.008	0.008	strong		0.682	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724		T	143746107	C	T	143746107	1	4	22	0	1	0	0	0	0	0	0	0	7973	755	27	1		1	JRK	8	143746107	RNA	SNP	C	TCGA-G8-6324-01A-11D-2210-10	146513	143746107	2617915	1990	4891											
JRK	8629	hgsc.bcm.edu	37	chr8	143746399	143746399	+	RNA	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccacgctgaatatggcatcgTtcatgttgtagcgggcatgg	8	11	13	9	3	1	1	1	1	0	0	2	1	1	1	1	3	1	6	1	3	3	4	rs73379623	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:143746399T>C	ENST00000507178.2	-	0	1411							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)				tatggcatcgttcatgttgta	0.602													T|||	63	0.0125799	0.0469	0.0014	5008	,	,		18767	0.0		0.0	False		,,,				2504	0.0				p.N360S		Atlas-SNP	.											.	.	.	.	0			c.A1079G						PASS	.	T	SER/ASN,SER/ASN	137,3981		0,137,1922	9	10	10		1079,1079	1.4	0	8	dbSNP_130	10	1,8401		0,1,4200	yes	missense,missense	JRK	NM_001077527.1,NM_003724.2	46,46	0,138,6122	CC,CT,TT		0.0119,3.3269,1.1022	benign,benign	360/557,360/569	143746399	138,12382	2059	4201	6260			8629	exon2			GCATCGTTCATGT	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			8.37:g.143746399T>C		89	0	0		91	43	0.472527	NM_003724	O75565	Missense_Mutation	SNP	ENST00000507178.2	37																																																																																				T|0.992;C|0.008	0.008	strong		0.602	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724		C	143746399	T	C	143746399	1	2	22	0	1	0	0	0	0	0	0	0	7973	1725	60	3		3	JRK	8	143746399	RNA	SNP	T	TCGA-G8-6324-01A-11D-2210-10	292	143746399	2617623	1991	4892											
JRK	8629	hgsc.bcm.edu	37	chr8	143746414	143746414	+	RNA	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	catcgttcatgttgtagcggGcatgggggccctgcaggggg	5	9	18	9	2	1	0	1	0	0	0	2	0	1	0	1	5	2	5	1	5	1	3	rs115218091	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:143746414G>A	ENST00000507178.2	-	0	1396							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)				gttgtagcgggcatgggggcc	0.617													G|||	63	0.0125799	0.0469	0.0014	5008	,	,		18410	0.0		0.0	False		,,,				2504	0.0				p.A355V		Atlas-SNP	.											.	.	.	.	0			c.C1064T						PASS	.	G	VAL/ALA,VAL/ALA	67,3943		0,67,1938	8	9	9		1064,1064	3.7	0	8	dbSNP_132	9	1,8323		0,1,4161	yes	missense,missense	JRK	NM_001077527.1,NM_003724.2	64,64	0,68,6099	AA,AG,GG		0.012,1.6708,0.5513	benign,benign	355/557,355/569	143746414	68,12266	2005	4162	6167			8629	exon2			TAGCGGGCATGGG	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			8.37:g.143746414G>A		90	0	0		88	38	0.431818	NM_003724	O75565	Missense_Mutation	SNP	ENST00000507178.2	37																																																																																				G|0.991;A|0.009	0.009	strong		0.617	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724		A	143746414	G	A	143746414	1	1	22	0	1	0	0	0	0	0	0	0	7973	1203	42	2		2	JRK	8	143746414	RNA	SNP	G	TCGA-G8-6324-01A-11D-2210-10	15	143746414	2617608	1992	4893											
JRK	8629	hgsc.bcm.edu	37	chr8	143746722	143746722	+	RNA	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttcccctgggccttataggcGacgggcaggtgctggatgcc	5	9	15	12	2	0	0	0	0	0	0	1	2	1	1	4	5	2	2	4	5	2	3	rs60195180	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:143746722G>A	ENST00000507178.2	-	0	1088							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)				ccttataggcgacgggcaggt	0.577													G|||	63	0.0125799	0.0469	0.0014	5008	,	,		18089	0.0		0.0	False		,,,				2504	0.0				p.V252V		Atlas-SNP	.											.	.	.	.	0			c.C756T						PASS	.	G	,	90,2688		0,90,1299	13	15	14		756,756	-7.2	0	8	dbSNP_129	14	3,5557		0,3,2777	no	coding-synonymous,coding-synonymous	JRK	NM_001077527.1,NM_003724.2	,	0,93,4076	AA,AG,GG		0.054,3.2397,1.1154	,	252/557,252/569	143746722	93,8245	1389	2780	4169			8629	exon2			ATAGGCGACGGGC	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			8.37:g.143746722G>A		99	0	0		107	43	0.401869	NM_003724	O75565	Silent	SNP	ENST00000507178.2	37																																																																																				G|0.992;A|0.008	0.008	strong		0.577	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724		A	143746722	G	A	143746722	1	1	22	0	1	0	0	0	0	0	0	0	7973	1045	37	1		1	JRK	8	143746722	RNA	SNP	G	TCGA-G8-6324-01A-11D-2210-10	308	143746722	2617300	1993	4894											
SLURP1	57152	hgsc.bcm.edu	37	chr8	143822612	143822612	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagcagaagatcaggtgggcGgccccgatgctgtcggggtc	7	6	17	11	3	1	2	1	0	0	2	3	3	1	2	2	5	2	2	2	5	1	0	rs62636564	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:143822612G>A	ENST00000246515.1	-	3	286	c.261C>T	c.(259-261)gcC>gcT	p.A87A		NM_020427.2	NP_065160.1	P55000	SLUR1_HUMAN	secreted LY6/PLAUR domain containing 1	87					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)					TCAGGTGGGCGGCCCCGATGC	0.662													G|||	111	0.0221645	0.0802	0.0072	5008	,	,		15680	0.0		0.0	False		,,,				2504	0.0				p.A87A		Atlas-SNP	.											.	SLURP1	16	.	0			c.C261T						PASS	.	G		250,4156	143.5+/-178.5	7,236,1960	43	45	45		261	-7.5	0	8	dbSNP_129	45	5,8593	4.3+/-15.6	0,5,4294	no	coding-synonymous	SLURP1	NM_020427.2		7,241,6254	AA,AG,GG		0.0582,5.6741,1.9609		87/104	143822612	255,12749	2203	4299	6502	SO:0001819	synonymous_variant	57152	exon3			GTGGGCGGCCCCG	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.261C>T	8.37:g.143822612G>A		74	0	0		79	41	0.518987	NM_020427	Q53YJ6|Q6PUA6|Q92483	Silent	SNP	ENST00000246515.1	37	CCDS6387.1																																																																																			G|0.979;A|0.021	0.021	strong		0.662	SLURP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379741.1	NM_020427		A	143822612	G	A	143822612	2	1	22	1	0	0	0	0	0	0	0	1	14771	1103	39	1		1	SLURP1	8	143822612	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	75890	143822612	2541410	1994	4895											
CYP11B1	1584	hgsc.bcm.edu	37	chr8	143958291	143958291	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agccgctctccaaaaagagcCaagttgctggctgcggggag	10	6	14	11	2	1	1	0	0	1	1	2	2	1	2	3	3	4	4	3	3	3	1	rs61751154		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:143958291C>T	ENST00000292427.4	-	4	638	c.606G>A	c.(604-606)ttG>ttA	p.L202L	CYP11B1_ENST00000377675.3_Silent_p.L273L|CYP11B1_ENST00000517471.1_Silent_p.L202L	NM_000497.3	NP_000488.3	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 1	202					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)	CAAAAAGAGCCAAGTTGCTGG	0.642									Familial Hyperaldosteronism type I				.|||	1	0.000199681	0.0008	0.0	5008	,	,		19690	0.0		0.0	False		,,,				2504	0.0				p.L202L		Atlas-SNP	.											CYP11B1,right_lower_lobe,carcinoma,0,1	CYP11B1	128	1	0			c.G606A						scavenged	.						37	38	38					8																	143958291		2203	4300	6503	SO:0001819	synonymous_variant	1584	exon4	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	AAGAGCCAAGTTG	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.606G>A	8.37:g.143958291C>T		140	1	0.00714286		184	24	0.130435	NM_000497	Q14095|Q4VAQ8|Q4VAQ9|Q9UML2	Silent	SNP	ENST00000292427.4	37	CCDS6392.1																																																																																			C|0.025;T|0.975	0.975	strong		0.642	CYP11B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379475.2			T	143958291	C	T	143958291	2	4	22	1	0	0	0	0	0	0	0	1	4147	593	21	2		2	CYP11B1	8	143958291	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	135679	143958291	2405731	1995	4896											
C8orf31	286122	hgsc.bcm.edu	37	chr8	144126087	144126087	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	acctgccctctgccctggcaCcccagggactcactgccaaa	8	6	8	19	0	2	0	1	0	1	0	2	1	2	1	6	2	3	1	6	2	1	0	rs73717943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144126087C>A	ENST00000395172.1	+	4	560	c.208C>A	c.(208-210)Ccc>Acc	p.P70T	C8orf31_ENST00000517653.1_3'UTR	NM_173687.2	NP_775958.1	Q8N9H6	CH031_HUMAN	chromosome 8 open reading frame 31	70										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)					TGCCCTGGCACCCCAGGGACT	0.627													c|||	115	0.0229633	0.084	0.0058	5008	,	,		14974	0.0		0.0	False		,,,				2504	0.0				p.P70T		Atlas-SNP	.											.	C8orf31	18	.	0			c.C208A						PASS	.	C	THR/PRO	323,4083	170.1+/-200.6	7,309,1887	69	60	63		208	-2.7	0	8	dbSNP_130	63	2,8598	2.2+/-6.3	0,2,4298	yes	missense	C8orf31	NM_173687.2	38	7,311,6185	AA,AC,CC		0.0233,7.3309,2.4988	benign	70/133	144126087	325,12681	2203	4300	6503	SO:0001583	missense	286122	exon4			CTGGCACCCCAGG		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.208C>A	8.37:g.144126087C>A	ENSP00000378601:p.Pro70Thr	57	0	0		59	33	0.559322	NM_173687	Q6GMU7	Missense_Mutation	SNP	ENST00000395172.1	37	CCDS6395.1	46	0.021062271062271064	43	0.08739837398373984	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	c	0.019	-1.466214	0.01053	0.073309	2.33E-4	ENSG00000177335	ENST00000395172	T	0.57595	0.39	1.37	-2.73	0.05950	.	.	.	.	.	T	0.00875	0.0029	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.08055	0.003	T	0.05500	-1.0881	9	0.87932	D	0	.	0.828	0.01124	0.2674:0.3758:0.1668:0.19	.	70	Q8N9H6	CH031_HUMAN	T	70	ENSP00000378601:P70T	ENSP00000378601:P70T	P	+	1	0	C8orf31	144197462	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.991000	0.01478	-2.249000	0.00702	-1.735000	0.00691	CCC	C|0.973;A|0.027	0.027	strong		0.627	C8orf31-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380167.1	NM_173687		A	144126087	C	A	144126087	3	1	22	1	0	0	0	0	1	0	0	0	2422	507	18	4	218	4	C8orf31	8	144126087	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	167796	144126087	2237935	1996	4897											
RHPN1	114822	hgsc.bcm.edu	37	chr8	144464073	144464073	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtgacggagctgaaggctGcgggagaggcgggcgccagc	7	4	21	9	4	0	3	0	2	0	1	0	5	0	4	1	6	3	2	1	6	1	0	rs34746679	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144464073G>A	ENST00000289013.6	+	14	1833	c.1732G>A	c.(1732-1734)Gcg>Acg	p.A578T		NM_052924.2	NP_443156.2	Q8TCX5	RHPN1_HUMAN	rhophilin, Rho GTPase binding protein 1	603	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)			GCTGAAGGCTGCGGGAGAGGC	0.682													G|||	39	0.00778754	0.0287	0.0014	5008	,	,		15201	0.0		0.0	False		,,,				2504	0.0				p.A578T		Atlas-SNP	.											RHPN1_ENST00000289013,NS,carcinoma,-1,2	RHPN1	76	2	0			c.G1732A						PASS	.	G	THR/ALA	90,4180		3,84,2048	29	46	41		1732	1.7	0	8	dbSNP_126	41	3,8489		0,3,4243	yes	missense	RHPN1	NM_052924.2	58	3,87,6291	AA,AG,GG		0.0353,2.1077,0.7287	benign	578/671	144464073	93,12669	2135	4246	6381	SO:0001583	missense	114822	exon14			AAGGCTGCGGGAG	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.1732G>A	8.37:g.144464073G>A	ENSP00000289013:p.Ala578Thr	125	0	0		139	79	0.568345	NM_052924	Q8TAV1|Q96PV9	Missense_Mutation	SNP	ENST00000289013.6	37	CCDS47927.1	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	G	6.274	0.418750	0.11870	0.021077	3.53E-4	ENSG00000158106	ENST00000289013	T	0.27557	1.66	4.59	1.73	0.24493	.	0.587122	0.17709	N	0.164651	T	0.04092	0.0114	N	0.25789	0.76	0.09310	N	1	B	0.17852	0.024	B	0.17979	0.02	T	0.16719	-1.0393	10	0.25751	T	0.34	-10.2882	6.9391	0.24483	0.4169:0.0:0.5831:0.0	rs34746679	578	Q8TCX5-2	.	T	578	ENSP00000289013:A578T	ENSP00000289013:A578T	A	+	1	0	RHPN1	144535216	0.000000	0.05858	0.001000	0.08648	0.017000	0.09413	0.119000	0.15626	0.349000	0.23975	0.462000	0.41574	GCG	G|0.989;A|0.011	0.011	strong		0.682	RHPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381417.1			A	144464073	G	A	144464073	3	1	22	1	0	0	0	0	1	0	0	0	13365	1319	46	2	1786	2	RHPN1	8	144464073	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	337986	144464073	1899949	1997	4898											
GSDMD	79792	hgsc.bcm.edu	37	chr8	144641514	144641514	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcctcaggagcatggggtcGgcctttgagcgggtagtccg	5	9	16	11	3	1	1	1	1	0	0	4	2	3	2	3	5	2	2	3	5	1	2	rs7840446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144641514G>T	ENST00000526406.1	+	5	892	c.9G>T	c.(7-9)tcG>tcT	p.S3S	GSDMD_ENST00000533063.1_Silent_p.S51S|GSDMD_ENST00000262580.4_Silent_p.S3S	NM_001166237.1	NP_001159709.1	P57764	GSDMD_HUMAN	gasdermin D	3					cellular response to extracellular stimulus (GO:0031668)					breast(1)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	12						GCATGGGGTCGGCCTTTGAGC	0.627													G|||	165	0.0329473	0.121	0.0058	5008	,	,		10930	0.0		0.001	False		,,,				2504	0.0				p.S3S		Atlas-SNP	.											.	GSDMD	28	.	0			c.G9T						PASS	.	G	,	383,4023	190.2+/-216.2	15,353,1835	63	58	60		9,9	-9.4	0	8	dbSNP_116	60	4,8594	3.0+/-9.4	0,4,4295	no	coding-synonymous,coding-synonymous	GSDMD	NM_001166237.1,NM_024736.6	,	15,357,6130	TT,TG,GG		0.0465,8.6927,2.976	,	3/485,3/485	144641514	387,12617	2203	4299	6502	SO:0001819	synonymous_variant	79792	exon5			GGGGTCGGCCTTT	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.9G>T	8.37:g.144641514G>T		74	0	0		79	48	0.607595	NM_001166237	D3DWJ9|Q96Q98	Silent	SNP	ENST00000526406.1	37	CCDS34956.1																																																																																			G|0.971;T|0.029	0.029	strong		0.627	GSDMD-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382046.3	NM_024736		T	144641514	G	T	144641514	2	4	22	1	0	0	0	0	0	0	0	1	6828	1103	39	4		4	GSDMD	8	144641514	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	177441	144641514	1722508	1998	4899											
C8orf73	642475	hgsc.bcm.edu	37	chr8	144652780	144652780	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtagaagcccctcgtggcTcccacgcagcccgaaacagc	9	4	12	16	3	0	1	0	0	0	1	2	2	1	1	4	2	4	3	4	2	3	1	rs11990485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144652780T>A	ENST00000398882.3	-	5	1024	c.768A>T	c.(766-768)ggA>ggT	p.G256G	MROH6_ENST00000524906.1_5'Flank|MROH6_ENST00000532704.1_5'Flank|RP11-661A12.9_ENST00000531730.1_RNA|MROH6_ENST00000533679.1_5'Flank|MROH6_ENST00000534459.1_5'Flank	NM_001100878.1	NP_001094348.1	A6NGR9	MROH6_HUMAN	maestro heat-like repeat family member 6	256																	CCCTCGTGGCTCCCACGCAGC	0.662													T|||	70	0.0139776	0.0522	0.0014	5008	,	,		12771	0.0		0.0	False		,,,				2504	0.0				p.G256G		Atlas-SNP	.											.	.	.	.	0			c.A768T						PASS	.	T		171,3991		2,167,1912	30	35	34		768	-0.9	1	8	dbSNP_120	34	1,8441		0,1,4220	no	coding-synonymous	C8orf73	NM_001100878.1		2,168,6132	AA,AT,TT		0.0118,4.1086,1.3646		256/720	144652780	172,12432	2081	4221	6302	SO:0001819	synonymous_variant	642475	exon5			CGTGGCTCCCACG	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.768A>T	8.37:g.144652780T>A		14	0	0		27	14	0.518519	NM_001100878	A8MWB1	Silent	SNP	ENST00000398882.3	37	CCDS47928.1																																																																																			T|0.989;A|0.011	0.011	strong		0.662	MROH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382330.3	NM_001100878		A	144652780	T	A	144652780	2	1	22	1	0	0	0	0	0	0	0	1	2437	1538	54	5		5	C8orf73	8	144652780	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	11266	144652780	1711242	1999	4900											
EEF1D	1936	hgsc.bcm.edu	37	chr8	144671489	144671489	+	Intron	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	caggcgcaccttccctggggGatggccgtcaaacagggcct	7	6	14	14	2	1	0	1	0	0	0	2	1	2	1	4	5	1	1	4	5	1	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144671489G>C	ENST00000529272.1	-	2	397				EEF1D_ENST00000395119.3_Intron|EEF1D_ENST00000526838.1_Intron|EEF1D_ENST00000528610.1_Intron|EEF1D_ENST00000524624.1_Intron|EEF1D_ENST00000532400.1_Intron|EEF1D_ENST00000419152.2_Intron|EEF1D_ENST00000532741.1_Missense_Mutation_p.P305A|EEF1D_ENST00000531621.1_Intron|EEF1D_ENST00000423316.2_Missense_Mutation_p.P255A|EEF1D_ENST00000442189.2_Missense_Mutation_p.P255A|EEF1D_ENST00000317198.6_Intron			P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)						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)			TTCCCTGGGGGATGGCCGTCA	0.697																																					p.P255A		Atlas-SNP	.											.	EEF1D	48	.	0			c.C763G						PASS	.						5	7	6					8																	144671489		2037	4109	6146	SO:0001627	intron_variant	1936	exon3			CTGGGGGATGGCC	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.4-2470C>G	8.37:g.144671489G>C		59	0	0		64	25	0.390625	NM_001130053	B4DDU4|D3DWK3|E9PBQ9|Q4VBZ6|Q969J1|Q96I38	Missense_Mutation	SNP	ENST00000529272.1	37	CCDS6405.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.470797	0.43942	.	.	ENSG00000104529	ENST00000532741;ENST00000442189;ENST00000423316;ENST00000356793;ENST00000337369;ENST00000526710;ENST00000531281	.	.	.	4.4	4.4	0.53042	.	0.309039	0.29940	N	0.010803	T	0.51312	0.1667	L	0.44542	1.39	0.80722	D	1	P;P;P	0.50528	0.894;0.894;0.936	B;B;P	0.50405	0.437;0.437;0.64	T	0.50381	-0.8835	9	0.45353	T	0.12	.	9.8627	0.41125	0.0939:0.0:0.9061:0.0	.	255;305;255	D3DWK1;E9PRY8;P29692-2	.;.;.	A	305;255;255;207;255;255;255	.	ENSP00000338323:P255A	P	-	1	0	EEF1D	144742632	1.000000	0.71417	0.988000	0.46212	0.875000	0.50365	3.368000	0.52357	2.277000	0.76020	0.561000	0.74099	CCC	.	.	none		0.697	EEF1D-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382592.2	NM_032378		C	144671489	G	C	144671489	1	2	22	0	1	0	0	0	0	0	0	0	4928	1174	41	4		4	EEF1D	8	144671489	Intron	SNP	G	TCGA-G8-6324-01A-11D-2210-10	18709	144671489	1692533	2000	4901											
EPPK1	83481	hgsc.bcm.edu	37	chr8	144942097	144942097	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagttctggattgcaacacGtgtctcgtggcctcattgat	7	13	11	10	2	3	1	1	1	2	0	4	2	3	2	1	2	2	3	1	2	1	3	rs73375119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144942097G>A	ENST00000525985.1	-	2	5396	c.5325C>T	c.(5323-5325)caC>caT	p.H1775H				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)			ATTGCAACACGTGTCTCGTGG	0.522													G|||	67	0.0133786	0.0477	0.0043	5008	,	,		20496	0.0		0.001	False		,,,				2504	0.0				p.H1775H		Atlas-SNP	.											EPPK1,NS,NS,-1,1	EPPK1	199	1	0			c.C5325T						PASS	.	G		178,3790		4,170,1810	125	120	122		5325	-10.2	0	8	dbSNP_130	122	1,8341		0,1,4170	no	coding-synonymous	EPPK1	NM_031308.1		4,171,5980	AA,AG,GG		0.012,4.4859,1.4541		1775/2420	144942097	179,12131	1984	4171	6155	SO:0001819	synonymous_variant	83481	exon1			CAACACGTGTCTC	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.5325C>T	8.37:g.144942097G>A		247	1	0.00404858		260	132	0.507692	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				G|0.984;A|0.016	0.016	strong		0.522	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		A	144942097	G	A	144942097	2	1	22	1	0	0	0	0	0	0	0	1	5192	1136	40	1		1	EPPK1	8	144942097	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	270608	144942097	1421925	2001	4902											
EPPK1	83481	hgsc.bcm.edu	37	chr8	144942934	144942934	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaccacctgccgcagggcCgcagccctcccagaccgaca	8	3	10	20	3	0	2	0	1	0	1	1	3	1	2	7	1	2	2	7	1	0	0	rs114155737	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144942934C>T	ENST00000525985.1	-	2	4559	c.4488G>A	c.(4486-4488)gcG>gcA	p.A1496A				P58107	EPIPL_HUMAN	epiplakin 1	1496						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)			GCCGCAGGGCCGCAGCCCTCC	0.672													C|||	59	0.0117812	0.0416	0.0043	5008	,	,		17427	0.0		0.001	False		,,,				2504	0.0				p.A1496A		Atlas-SNP	.											.	EPPK1	199	.	0			c.G4488A						PASS	.	C		163,4153		2,159,1997	19	22	21		4488	-9	0	8	dbSNP_132	21	4,8516		0,4,4256	no	coding-synonymous	EPPK1	NM_031308.1		2,163,6253	TT,TC,CC		0.0469,3.7766,1.301		1496/2420	144942934	167,12669	2158	4260	6418	SO:0001819	synonymous_variant	83481	exon1			CAGGGCCGCAGCC	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.4488G>A	8.37:g.144942934C>T		33	0	0		25	16	0.64	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				C|0.987;T|0.013	0.013	strong		0.672	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		T	144942934	C	T	144942934	2	4	22	1	0	0	0	0	0	0	0	1	5192	639	23	1		1	EPPK1	8	144942934	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	837	144942934	1421088	2002	4903											
EPPK1	83481	hgsc.bcm.edu	37	chr8	144946271	144946271	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccagtggcctgtccactagcCccttcttcatggcctggaaa	7	10	9	15	0	2	0	1	0	1	0	3	1	3	1	6	3	1	0	6	3	2	3	rs58368323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144946271C>T	ENST00000525985.1	-	2	1222	c.1151G>A	c.(1150-1152)gGg>gAg	p.G384E				P58107	EPIPL_HUMAN	epiplakin 1	384						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)			GTCCACTAGCCCCTTCTTCAT	0.672													C|||	224	0.0447284	0.1604	0.013	5008	,	,		15903	0.0		0.003	False		,,,				2504	0.0				p.G384E		Atlas-SNP	.											.	EPPK1	199	.	0			c.G1151A						PASS	.	C	GLU/GLY	400,3414		19,362,1526	6	7	7		1151	-1.4	0.7	8	dbSNP_129	7	6,8126		0,6,4060	yes	missense	EPPK1	NM_031308.1	98	19,368,5586	TT,TC,CC		0.0738,10.4877,3.3986	benign	384/2420	144946271	406,11540	1907	4066	5973	SO:0001583	missense	83481	exon1			ACTAGCCCCTTCT	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.1151G>A	8.37:g.144946271C>T	ENSP00000436337:p.Gly384Glu	95	0	0		72	34	0.472222	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		83	0.038003663003663	70	0.14227642276422764	4	0.011049723756906077	2	0.0034965034965034965	7	0.009234828496042216	C	9.565	1.119374	0.20877	0.104877	7.38E-4	ENSG00000227184	ENST00000525985	T	0.72835	-0.69	4.96	-1.43	0.08884	.	.	.	.	.	T	0.00524	0.0017	N	0.25789	0.76	0.09310	N	0.999997	B	0.12013	0.005	B	0.09377	0.004	T	0.00870	-1.1533	9	0.16896	T	0.51	.	10.042	0.42164	0.0:0.6982:0.0:0.3018	rs58368323	384	E9PPU0	.	E	384	ENSP00000436337:G384E	ENSP00000436337:G384E	G	-	2	0	EPPK1	145018259	0.000000	0.05858	0.663000	0.29738	0.564000	0.35744	-0.181000	0.09740	-0.542000	0.06249	-0.409000	0.06214	GGG	C|0.961;T|0.039	0.039	strong		0.672	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		T	144946271	C	T	144946271	3	4	22	1	0	0	0	0	1	0	0	0	5192	623	22	2	6115	2	EPPK1	8	144946271	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3337	144946271	1417751	2003	4904											
PLEC	5339	hgsc.bcm.edu	37	chr8	144991428	144991428	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcatggacttgaccacgccGtccgaggaggagatggtgat	10	8	14	9	3	1	3	1	2	0	1	2	7	2	5	3	4	0	0	3	4	0	1	rs11998271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144991428G>A	ENST00000322810.4	-	32	13141	c.12972C>T	c.(12970-12972)gaC>gaT	p.D4324D	PLEC_ENST00000398774.2_Silent_p.D4155D|PLEC_ENST00000354958.2_Silent_p.D4165D|PLEC_ENST00000345136.3_Silent_p.D4187D|PLEC_ENST00000357649.2_Silent_p.D4191D|PLEC_ENST00000354589.3_Silent_p.D4187D|PLEC_ENST00000436759.2_Silent_p.D4214D|PLEC_ENST00000527096.1_Silent_p.D4210D|PLEC_ENST00000356346.3_Silent_p.D4173D	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	4324	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						TGACCACGCCGTCCGAGGAGG	0.622													G|||	419	0.0836661	0.3011	0.0173	5008	,	,		18486	0.001		0.002	False		,,,				2504	0.0061				p.D4324D		Atlas-SNP	.											.	PLEC	1144	.	0			c.C12972T						PASS	.	G	,,,,,,,	1134,3084		148,838,1123	56	63	61		12642,12519,12495,12972,12465,12561,12573,12561	-4.4	0.9	8	dbSNP_120	61	5,8413		0,5,4204	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	148,843,5327	AA,AG,GG		0.0594,26.8848,9.0139	,,,,,,,	4214/4575,4173/4534,4165/4526,4324/4685,4155/4516,4187/4548,4191/4552,4187/4548	144991428	1139,11497	2109	4209	6318	SO:0001819	synonymous_variant	5339	exon32			CACGCCGTCCGAG	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.12972C>T	8.37:g.144991428G>A		40	0	0		42	22	0.52381	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			G|0.957;A|0.043	0.043	strong		0.622	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		A	144991428	G	A	144991428	2	1	22	1	0	0	0	0	0	0	0	1	12061	1136	40	1		1	PLEC	8	144991428	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	45157	144991428	1372594	2004	4905											
PLEC	5339	hgsc.bcm.edu	37	chr8	145006866	145006866	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggtaggcaccccgggtggcGggggagagctggccctgcaa	6	4	19	12	3	0	1	0	0	0	1	0	2	0	1	3	7	2	4	3	7	2	1	rs185978075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145006866G>A	ENST00000322810.4	-	15	2332	c.2163C>T	c.(2161-2163)ccC>ccT	p.P721P	PLEC_ENST00000398774.2_Silent_p.P552P|PLEC_ENST00000354958.2_Silent_p.P562P|PLEC_ENST00000345136.3_Silent_p.P584P|PLEC_ENST00000357649.2_Silent_p.P588P|PLEC_ENST00000354589.3_Silent_p.P584P|PLEC_ENST00000436759.2_Silent_p.P611P|PLEC_ENST00000527096.1_Silent_p.P607P|PLEC_ENST00000356346.3_Silent_p.P570P	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	721	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						CCCGGGTGGCGGGGGAGAGCT	0.716													A|||	61	0.0121805	0.0424	0.0072	5008	,	,		14613	0.0		0.0	False		,,,				2504	0.0				p.P721P		Atlas-SNP	.											.	PLEC	1144	.	0			c.C2163T						PASS	.	A	,,,,,,,	99,3883		3,93,1895	10	14	13		1833,1710,1686,2163,1656,1752,1764,1752	-9.7	0	8		13	2,8238		0,2,4118	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	3,95,6013	AA,AG,GG		0.0243,2.4862,0.8264	,,,,,,,	611/4575,570/4534,562/4526,721/4685,552/4516,584/4548,588/4552,584/4548	145006866	101,12121	1991	4120	6111	SO:0001819	synonymous_variant	5339	exon15			GGTGGCGGGGGAG	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.2163C>T	8.37:g.145006866G>A		39	0	0		56	27	0.482143	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			G|0.994;A|0.006	0.006	strong		0.716	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		A	145006866	G	A	145006866	2	1	22	1	0	0	0	0	0	0	0	1	12061	1103	39	1		1	PLEC	8	145006866	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	15438	145006866	1357156	2005	4906											
PLEC	5339	hgsc.bcm.edu	37	chr8	145007409	145007409	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gggtgccgtccatccttgagGgtctgcacgtcgttgaagag	6	10	15	10	3	1	3	0	2	1	1	4	3	3	3	3	2	2	2	3	2	1	2	rs115081018	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145007409G>A	ENST00000322810.4	-	13	1954	c.1785C>T	c.(1783-1785)acC>acT	p.T595T	PLEC_ENST00000398774.2_Silent_p.T426T|PLEC_ENST00000354958.2_Silent_p.T436T|PLEC_ENST00000345136.3_Silent_p.T458T|PLEC_ENST00000357649.2_Silent_p.T462T|PLEC_ENST00000354589.3_Silent_p.T458T|PLEC_ENST00000436759.2_Silent_p.T485T|PLEC_ENST00000527096.1_Silent_p.T481T|PLEC_ENST00000356346.3_Silent_p.T444T	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	595	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						CATCCTTGAGGGTCTGCACGT	0.677													G|||	83	0.0165735	0.059	0.0072	5008	,	,		16349	0.0		0.0	False		,,,				2504	0.0				p.T595T		Atlas-SNP	.											.	PLEC	1144	.	0			c.C1785T						PASS	.	G	,,,,,,,	160,3982		4,152,1915	63	72	69		1455,1332,1308,1785,1278,1374,1386,1374	1	1	8	dbSNP_132	69	4,8358		0,4,4177	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	4,156,6092	AA,AG,GG		0.0478,3.8629,1.3116	,,,,,,,	485/4575,444/4534,436/4526,595/4685,426/4516,458/4548,462/4552,458/4548	145007409	164,12340	2071	4181	6252	SO:0001819	synonymous_variant	5339	exon13			CTTGAGGGTCTGC	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.1785C>T	8.37:g.145007409G>A		118	0	0		119	62	0.521008	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			G|0.988;A|0.012	0.012	strong		0.677	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		A	145007409	G	A	145007409	2	1	22	1	0	0	0	0	0	0	0	1	12061	1219	43	2		2	PLEC	8	145007409	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	543	145007409	1356613	2006	4907											
RECQL4	9684	hgsc.bcm.edu	37	chr8	145740622	145740622	+	5'Flank	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctggaacacctcagccggCgtctctgcagacacagatgt	9	7	11	14	2	2	2	1	0	1	2	3	3	2	3	3	2	3	1	3	2	1	0	rs34948955	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145740622C>T	ENST00000292524.1	+	0	0				RECQL4_ENST00000532237.1_5'UTR|LRRC14_ENST00000529022.1_5'Flank|CTD-2517M22.17_ENST00000580385.1_RNA|RECQL4_ENST00000428558.2_Silent_p.T465T	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)			CCTCAGCCGGCGTCTCTGCAG	0.622													C|||	8	0.00159744	0.0	0.0014	5008	,	,		20490	0.0		0.007	False		,,,				2504	0.0				p.T465T		Atlas-SNP	.											RECQL4,brain,glioma,0,2	RECQL4	75	2	0			c.G1395A						scavenged	.	C		5,4245		0,5,2120	25	32	29		1395	-10.8	0	8	dbSNP_126	29	70,8422		0,70,4176	no	coding-synonymous	RECQL4	NM_004260.3		0,75,6296	TT,TC,CC		0.8243,0.1176,0.5886		465/1209	145740622	75,12667	2125	4246	6371	SO:0001631	upstream_gene_variant	9401	exon8			AGCCGGCGTCTCT	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		8.37:g.145740622C>T	Exception_encountered	111	1	0.00900901		115	49	0.426087	NM_004260	A8K0A8|D3DWM8	Silent	SNP	ENST00000292524.1	37	CCDS6432.1																																																																																			C|0.997;T|0.003	0.003	strong		0.622	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665		T	145740622	C	T	145740622	1	4	22	0	1	0	0	0	0	0	0	0	13217	755	27	1		1	RECQL4	8	145740622	5'Flank	SNP	C	TCGA-G8-6324-01A-11D-2210-10	733213	145740622	623400	2007	4908											
LRRC14	9684	hgsc.bcm.edu	37	chr8	145745268	145745268	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcgcgagttggtacacacGtggcccttcccgctgctcag	5	9	12	15	4	1	0	1	0	0	0	2	1	2	0	2	2	3	4	2	2	1	3	rs116791876	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145745268G>A	ENST00000292524.1	+	2	305	c.159G>A	c.(157-159)acG>acA	p.T53T	RECQL4_ENST00000532237.1_5'Flank|LRRC14_ENST00000529022.1_Silent_p.T53T|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	53										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)			TGGTACACACGTGGCCCTTCC	0.627													G|||	31	0.0061901	0.0212	0.0043	5008	,	,		21870	0.0		0.0	False		,,,				2504	0.0				p.T53T		Atlas-SNP	.											.	LRRC14	25	.	0			c.G159A						PASS	.	G		61,4345	58.1+/-94.6	0,61,2142	98	95	96		159	-8.8	0	8	dbSNP_132	96	1,8599	1.2+/-3.3	0,1,4299	yes	coding-synonymous	LRRC14	NM_014665.2		0,62,6441	AA,AG,GG		0.0116,1.3845,0.4767		53/494	145745268	62,12944	2203	4300	6503	SO:0001819	synonymous_variant	9684	exon3			ACACACGTGGCCC	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.159G>A	8.37:g.145745268G>A		147	0	0		144	85	0.590278	NM_001272036	A8K0A8|D3DWM8	Silent	SNP	ENST00000292524.1	37	CCDS6432.1																																																																																			G|0.994;A|0.006	0.006	strong		0.627	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665		A	145745268	G	A	145745268	2	1	22	1	0	0	0	0	0	0	0	1	8977	1132	40	1		1	LRRC14	8	145745268	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4646	145745268	618754	2008	4909											
LRRC24	441381	hgsc.bcm.edu	37	chr8	145748075	145748075	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagtcgttgacgaacagcgcTccctcccccggaggcccccg	6	6	11	18	5	0	1	0	1	0	0	3	3	2	2	5	2	2	2	5	2	2	2	rs112652028	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145748075T>G	ENST00000529415.2	-	5	1443	c.1326A>C	c.(1324-1326)ggA>ggC	p.G442G	LRRC14_ENST00000528528.1_3'UTR|LRRC24_ENST00000533758.1_Silent_p.G439G|LRRC14_ENST00000292524.1_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													G|||	75	0.014976	0.0522	0.0072	5008	,	,		9844	0.0		0.0	False		,,,				2504	0.001				p.G442G		Atlas-SNP	.											.	LRRC24	11	.	0			c.A1326C						PASS	.	G	,	155,4189		3,149,2020	13	14	14		1326,	3.1	1	8	dbSNP_132	14	2,8570		0,2,4284	no	coding-synonymous,utr-3	LRRC14,LRRC24	NM_001024678.3,NM_014665.2	,	3,151,6304	GG,GT,TT		0.0233,3.5681,1.2155	,	442/514,	145748075	157,12759	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>C	8.37:g.145748075T>G		49	0	0		53	21	0.396226	NM_001024678		Silent	SNP	ENST00000529415.2	37	CCDS34969.1																																																																																			T|0.986;G|0.014	0.014	strong		0.682	LRRC24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382501.2	NM_001024678		G	145748075	T	G	145748075	2	3	22	1	0	0	0	0	0	0	0	1	8988	1538	54	5		5	LRRC24	8	145748075	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2807	145748075	615947	2009	4910											
MGC70857	414919	hgsc.bcm.edu	37	chr8	145753431	145753431	+	Frame_Shift_Del	DEL	T	T	-																															tgaagcaggtgatgaaattcTtcattttggaatcatccagg																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145753431delT	ENST00000524821.1	-	2	397	c.182delA	c.(181-183)aagfs	p.K61fs	C8orf82_ENST00000313465.5_Frame_Shift_Del_p.K61fs|LRRC24_ENST00000529415.2_5'Flank|LRRC24_ENST00000533758.1_5'Flank			Q6P1X6	CH082_HUMAN	chromosome 8 open reading frame 82	61										endometrium(1)|urinary_tract(1)	2						GATGAAATTCTTCATTTTGGA	0.582																																					p.K61fs		Pindel,Atlas-Indel	.											C8orf82,bladder,carcinoma,0,1	C8orf82	7	1	0			c.183delG						PASS	.			1,4263		0,1,2131	86	84	85			3.7	1	8		85	0,8254		0,0,4127	no	frameshift	C8orf82	NM_001001795.1		0,1,6258	A1A1,A1R,RR		0.0,0.0235,0.0080			145753431	1,12517	2203	4300	6503	SO:0001589	frameshift_variant	414919	exon2			.		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.182delA	8.37:g.145753431delT	ENSP00000436621:p.Lys61fs	51	0	.		57	28	0.491	NM_001001795	Q6GMR2|Q6P2Q7	Frame_Shift_Del	DEL	ENST00000524821.1	37	CCDS34970.1																																																																																			.	.	none		0.582	C8orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382503.1	NM_001001795		-	145753431	T	-	145753431	7	5	22	1	0	1	0	1	0	0	0	0	9562	1609	56	0	476	0	MGC70857	8	145753431	Frame_Shift_Del	DEL	T	TCGA-G8-6324-01A-11D-2210-10	5356	145753431	610591	2010	4911											
FOXD4	2298	hgsc.bcm.edu	37	chr9	117637	117637	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcgcgggggatcttgacgaaGcagtcgttcagcgagaggtt	8	9	16	8	5	2	2	1	1	1	1	4	5	2	3	0	3	2	3	0	3	1	3	rs138098441	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117637G>A	ENST00000382500.2	-	1	780	c.483C>T	c.(481-483)tgC>tgT	p.C161C		NM_207305.4	NP_997188.2	Q12950	FOXD4_HUMAN	forkhead box D4	161					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)			endometrium(5)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	14	all_lung(41;0.218)	all_cancers(5;0.0395)|Acute lymphoblastic leukemia(5;1.91e-07)|all_hematologic(5;1.95e-06)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		TCTTGACGAAGCAGTCGTTCA	0.637													.|||	119	0.023762	0.0847	0.0101	5008	,	,		14103	0.0		0.0	False		,,,				2504	0.0				p.C161C		Atlas-SNP	.											.	FOXD4	75	.	0			c.C483T						PASS	.	G		293,4087		3,287,1900	104	143	130		483	2.2	1	9	dbSNP_134	130	1,8567		0,1,4283	no	coding-synonymous	FOXD4	NM_207305.3		3,288,6183	AA,AG,GG		0.0117,6.6895,2.2706		161/440	117637	294,12654	2190	4284	6474	SO:0001819	synonymous_variant	2298	exon1			GACGAAGCAGTCG	U13223	CCDS34975.1	9p24.3	2014-09-17			ENSG00000170122	ENSG00000170122		"Forkhead boxes"	3805	protein-coding gene	gene with protein product		601092		FKHL9		7957066, 8825632, 12234674	Standard	NM_207305		Approved	FREAC5, FOXD4a	uc003zfz.4	Q12950	OTTHUMG00000021015	ENST00000382500.2:c.483C>T	9.37:g.117637G>A		219	0	0		228	115	0.504386	NM_207305	B2RN05|B9EGL7|Q5VVK1|Q8WXT6	Silent	SNP	ENST00000382500.2	37	CCDS34975.1																																																																																			G|0.974;A|0.026	0.026	strong		0.637	FOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055433.1	NM_207305		A	117637	G	A	117637	2	1	22	1	0	0	0	0	0	0	0	1	6007	963	34	2		2	FOXD4	9	117637	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10		117637	141095794	2011	4912											
DOCK8	81704	hgsc.bcm.edu	37	chr9	328144	328144	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcttctcagtcacctacccGtcctcagacatctacctggt	7	12	6	16	1	5	1	3	0	3	1	7	1	6	1	4	1	2	0	4	1	2	3	rs35746964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:328144G>A	ENST00000453981.1	+	9	1129	c.1017G>A	c.(1015-1017)ccG>ccA	p.P339P	DOCK8_ENST00000469391.1_Silent_p.P271P|DOCK8_ENST00000432829.2_Silent_p.P271P			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	339					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)		TCACCTACCCGTCCTCAGACA	0.493													G|||	11	0.00219649	0.0083	0.0	5008	,	,		20591	0.0		0.0	False		,,,				2504	0.0				p.P339P		Atlas-SNP	.											DOCK8_ENST00000453981,colon,carcinoma,0,2	DOCK8	401	2	0			c.G1017A						PASS	.	G	,,	41,4365	44.6+/-78.6	0,41,2162	100	82	88		813,813,1017	-8.7	0.6	9	dbSNP_126	88	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	,,	0,42,6461	AA,AG,GG		0.0116,0.9305,0.3229	,,	271/2000,271/2032,339/2100	328144	42,12964	2203	4300	6503	SO:0001819	synonymous_variant	81704	exon9			CTACCCGTCCTCA	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.1017G>A	9.37:g.328144G>A		157	0	0		146	80	0.547945	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Silent	SNP	ENST00000453981.1	37	CCDS6440.2																																																																																			G|0.996;A|0.004	0.004	strong		0.493	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307		A	328144	G	A	328144	2	1	22	1	0	0	0	0	0	0	0	1	4695	1132	40	1		1	DOCK8	9	328144	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	210507	328144	140885287	2012	4913											
DOCK8	81704	hgsc.bcm.edu	37	chr9	382646	382646	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gacctcgcggggacacactcCgcagcagacgaggaagtgaa	12	3	14	12	4	0	2	0	1	0	1	2	6	1	4	2	3	1	2	2	3	2	0	rs116523732	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:382646C>T	ENST00000453981.1	+	22	2851	c.2739C>T	c.(2737-2739)tcC>tcT	p.S913S	DOCK8_ENST00000382329.1_Silent_p.S380S|DOCK8_ENST00000382331.1_Silent_p.S215S|DOCK8_ENST00000469391.1_Silent_p.S845S|DOCK8_ENST00000432829.2_Silent_p.S845S			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	913					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)		GGACACACTCCGCAGCAGACG	0.507													C|||	56	0.0111821	0.0386	0.0072	5008	,	,		20060	0.0		0.0	False		,,,				2504	0.0				p.S913S		Atlas-SNP	.											.	DOCK8	401	.	0			c.C2739T						PASS	.	C	,,	139,4267	98.9+/-137.6	2,135,2066	61	53	56		2535,2535,2739	-6.7	0	9	dbSNP_132	56	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	,,	2,137,6364	TT,TC,CC		0.0233,3.1548,1.0841	,,	845/2000,845/2032,913/2100	382646	141,12865	2203	4300	6503	SO:0001819	synonymous_variant	81704	exon22			ACACTCCGCAGCA	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.2739C>T	9.37:g.382646C>T		96	0	0		118	62	0.525424	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Silent	SNP	ENST00000453981.1	37	CCDS6440.2																																																																																			C|0.991;T|0.009	0.009	strong		0.507	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307		T	382646	C	T	382646	2	4	22	1	0	0	0	0	0	0	0	1	4695	639	23	1		1	DOCK8	9	382646	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	54502	382646	140830785	2013	4914											
DMRT2	10655	hgsc.bcm.edu	37	chr9	1056517	1056517	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccacctgccttgatttaacCatgcagtattcagggtctgg	8	12	9	12	0	2	1	1	1	1	0	2	1	2	1	4	2	3	2	4	2	2	5	rs16928356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:1056517C>G	ENST00000358146.2	+	3	930	c.930C>G	c.(928-930)acC>acG	p.T310T	DMRT2_ENST00000382255.3_3'UTR|DMRT2_ENST00000302441.6_Silent_p.T310T|DMRT2_ENST00000259622.6_3'UTR|DMRT2_ENST00000382251.3_Silent_p.T310T			Q9Y5R5	DMRT2_HUMAN	doublesex and mab-3 related transcription factor 2	310					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)		TTGATTTAACCATGCAGTATT	0.438													C|||	263	0.052516	0.1876	0.0173	5008	,	,		20652	0.0		0.003	False		,,,				2504	0.0				p.T310T		Atlas-SNP	.											.	DMRT2	70	.	0			c.C930G						PASS	.	C	,,	699,3707	291.5+/-281.6	55,589,1559	85	88	87		,,930	3.7	1	9	dbSNP_123	87	3,8597	1.2+/-3.3	0,3,4297	no	utr-3,utr-3,coding-synonymous	DMRT2	NM_001130865.2,NM_006557.6,NM_181872.4	,,	55,592,5856	GG,GC,CC		0.0349,15.8647,5.3975	,,	,,310/562	1056517	702,12304	2203	4300	6503	SO:0001819	synonymous_variant	10655	exon4			TTTAACCATGCAG	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.930C>G	9.37:g.1056517C>G		160	0	0		138	137	0.992754	NM_181872	B1ANC0|B9EGJ1|Q9NPG6|Q9NQR6	Silent	SNP	ENST00000358146.2	37	CCDS6444.1																																																																																			C|0.951;G|0.049	0.049	strong		0.438	DMRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051492.1	NM_006557		G	1056517	C	G	1056517	2	3	22	1	0	0	0	0	0	0	0	1	4588	581	21	4		4	DMRT2	9	1056517	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	673871	1056517	140156914	2014	4915											
SMARCA2	6595	hgsc.bcm.edu	37	chr9	2029196	2029196	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agtgtctcccatcctatgccGacgatggggtccacagactt	8	10	10	13	2	1	1	0	0	1	1	4	3	3	1	4	2	1	0	4	2	1	2	rs10964470	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:2029196G>A	ENST00000382203.1	+	2	383	c.174G>A	c.(172-174)ccG>ccA	p.P58P	SMARCA2_ENST00000349721.2_Silent_p.P58P|SMARCA2_ENST00000357248.2_Silent_p.P58P|SMARCA2_ENST00000382194.1_Silent_p.P58P			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	58					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)		ATCCTATGCCGACGATGGGGT	0.527													G|||	245	0.0489217	0.1778	0.0115	5008	,	,		19068	0.0		0.002	False		,,,				2504	0.0				p.P58P		Atlas-SNP	.											.	SMARCA2	313	.	0			c.G174A						PASS	.	G	,	635,3771	271.0+/-269.9	44,547,1612	42	36	38		174,174	-11.2	0	9	dbSNP_120	38	2,8598	1.2+/-3.3	0,2,4298	yes	coding-synonymous,coding-synonymous	SMARCA2	NM_003070.3,NM_139045.2	,	44,549,5910	AA,AG,GG		0.0233,14.4122,4.8977	,	58/1591,58/1573	2029196	637,12369	2203	4300	6503	SO:0001819	synonymous_variant	6595	exon2			TATGCCGACGATG	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.174G>A	9.37:g.2029196G>A		91	0	0		111	56	0.504505	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Silent	SNP	ENST00000382203.1	37	CCDS34977.1																																																																																			G|0.950;A|0.050	0.050	strong		0.527	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070		A	2029196	G	A	2029196	2	1	22	1	0	0	0	0	0	0	0	1	14784	1045	37	1		1	SMARCA2	9	2029196	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	972679	2029196	139184235	2015	4916											
SMARCA2	6595	hgsc.bcm.edu	37	chr9	2039779	2039779	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caacaacagcagcagcaacaGcagcagcagcagcagcagca	17	0	10	14	0	0	0	0	0	0	0	0	0	0	0	0	0	13	10	0	0	3	0	rs376509101|rs62639301	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:2039779G>A	ENST00000382203.1	+	4	878	c.669G>A	c.(667-669)caG>caA	p.Q223Q	SMARCA2_ENST00000349721.2_Silent_p.Q223Q|SMARCA2_ENST00000491574.1_3'UTR|SMARCA2_ENST00000357248.2_Silent_p.Q223Q|RP11-264I13.2_ENST00000426860.1_RNA|SMARCA2_ENST00000382194.1_Silent_p.Q223Q			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	223	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)		agcagcaacagcagcagcagc	0.642																																					p.Q223Q		Atlas-SNP	.											SMARCA2_ENST00000349721,NS,carcinoma,0,2	SMARCA2	313	2	0			c.G669A						scavenged	.						10	13	12					9																	2039779		2187	4260	6447	SO:0001819	synonymous_variant	6595	exon4			GCAACAGCAGCAG	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.669G>A	9.37:g.2039779G>A		66	1	0.0151515		98	51	0.520408	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Silent	SNP	ENST00000382203.1	37	CCDS34977.1																																																																																			G|0.889;A|0.111	0.111	strong		0.642	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070		A	2039779	G	A	2039779	2	1	22	1	0	0	0	0	0	0	0	1	14784	962	34	2		2	SMARCA2	9	2039779	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	10583	2039779	139173652	2016	4917											
VLDLR	7436	hgsc.bcm.edu	37	chr9	2643175	2643175	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aataggcaatataacatgtaGtcccgacgagttcacctgct	13	10	8	10	2	1	0	1	0	0	0	2	2	2	0	2	1	2	4	2	1	6	5	rs34080096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:2643175G>C	ENST00000382100.3	+	5	820	c.464G>C	c.(463-465)aGt>aCt	p.S155T	VLDLR_ENST00000382099.2_Missense_Mutation_p.S155T|RP11-125B21.2_ENST00000599229.1_RNA	NM_003383.3	NP_003374.3	P98155	VLDLR_HUMAN	very low density lipoprotein receptor	155	LDL-receptor class A 4. {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)		ATAACATGTAGTCCCGACGAG	0.473													G|||	15	0.00299521	0.0106	0.0014	5008	,	,		20805	0.0		0.0	False		,,,				2504	0.0				p.S155T		Atlas-SNP	.											.	VLDLR	68	.	0			c.G464C						PASS	.	G	THR/SER,THR/SER	36,4370	40.8+/-73.8	0,36,2167	116	122	120		464,464	4.6	0	9	dbSNP_126	120	0,8600		0,0,4300	yes	missense,missense	VLDLR	NM_001018056.1,NM_003383.3	58,58	0,36,6467	CC,CG,GG		0.0,0.8171,0.2768	benign,benign	155/846,155/874	2643175	36,12970	2203	4300	6503	SO:0001583	missense	7436	exon5			CATGTAGTCCCGA		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.464G>C	9.37:g.2643175G>C	ENSP00000371532:p.Ser155Thr	40	0	0		38	22	0.578947	NM_003383	B2RMZ7|D3DRH6|Q5VVF6	Missense_Mutation	SNP	ENST00000382100.3	37	CCDS6446.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	13.70	2.315185	0.40996	0.008171	0.0	ENSG00000147852	ENST00000382100;ENST00000382096;ENST00000382099	D;D;D	0.95588	-3.75;-3.75;-3.75	5.5	4.61	0.57282	.	0.091415	0.48286	D	0.000195	D	0.86789	0.6017	L	0.28776	0.89	0.80722	D	1	B;B;B	0.14805	0.003;0.004;0.011	B;B;B	0.29353	0.013;0.022;0.101	D	0.85668	0.1293	10	0.33940	T	0.23	.	14.3118	0.66422	0.0706:0.0:0.9294:0.0	rs34080096	155;155;155	P98155-2;Q5VVF5;P98155	.;.;VLDLR_HUMAN	T	155;114;155	ENSP00000371532:S155T;ENSP00000371528:S114T;ENSP00000371531:S155T	ENSP00000371528:S114T	S	+	2	0	VLDLR	2633175	1.000000	0.71417	0.028000	0.17463	0.199000	0.23934	5.517000	0.67061	1.558000	0.49541	0.655000	0.94253	AGT	G|0.996;C|0.004	0.004	strong		0.473	VLDLR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051519.2	NM_003383		C	2643175	G	C	2643175	3	2	22	1	0	0	0	0	1	0	0	0	17189	1029	36	4	482	4	VLDLR	9	2643175	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	603396	2643175	138570256	2017	4918											
KCNV2	169522	hgsc.bcm.edu	37	chr9	2729705	2729705	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttggaagcaacccacagcTcaccccaagacaagagaatt	15	5	8	13	0	1	2	1	0	0	2	1	4	1	3	3	1	3	3	3	1	5	2	rs112673841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:2729705T>C	ENST00000382082.3	+	2	1854	c.1616T>C	c.(1615-1617)cTc>cCc	p.L539P		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	539					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)		AACCCACAGCTCACCCCAAGA	0.433													C|||	68	0.0135783	0.0492	0.0043	5008	,	,		19814	0.0		0.0	False		,,,				2504	0.0				p.L539P		Atlas-SNP	.											.	KCNV2	72	.	0			c.T1616C						PASS	.	C	PRO/LEU	195,4211	808.3+/-415.9	2,191,2010	92	87	89		1616	3.5	0	9	dbSNP_132	89	4,8596	819.1+/-406.8	0,4,4296	yes	missense	KCNV2	NM_133497.3	98	2,195,6306	CC,CT,TT		0.0465,4.4258,1.5301	benign	539/546	2729705	199,12807	2203	4300	6503	SO:0001583	missense	169522	exon2			CACAGCTCACCCC	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.1616T>C	9.37:g.2729705T>C	ENSP00000371514:p.Leu539Pro	93	0	0		103	52	0.504854	NM_133497	Q5T6X0	Missense_Mutation	SNP	ENST00000382082.3	37	CCDS6447.1	175	0.08012820512820513	58	0.11788617886178862	16	0.04419889502762431	36	0.06293706293706294	65	0.08575197889182058	C	0.271	-0.992832	0.02162	0.044258	4.65E-4	ENSG00000168263	ENST00000382082	D	0.96716	-4.1	5.47	3.52	0.40303	.	5.982730	0.00424	N	0.000068	T	0.08980	0.0222	N	0.00538	-1.39	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.70938	-0.4736	10	0.23302	T	0.38	.	5.3373	0.15965	0.2188:0.5872:0.1183:0.0758	.	539	Q8TDN2	KCNV2_HUMAN	P	539	ENSP00000371514:L539P	ENSP00000371514:L539P	L	+	2	0	KCNV2	2719705	0.000000	0.05858	0.010000	0.14722	0.081000	0.17604	0.370000	0.20433	1.461000	0.47929	-0.119000	0.15052	CTC	T|0.962;C|0.038	0.038	strong		0.433	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497		C	2729705	T	C	2729705	3	2	22	1	0	0	0	0	1	0	0	0	8104	1551	54	3	1622	3	KCNV2	9	2729705	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	86530	2729705	138483726	2018	4919											
KIAA0020	9933	hgsc.bcm.edu	37	chr9	2811522	2811522	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggcgtgttcttgcaggtagcTtaacaaagctggagaaatgg	11	10	14	6	1	1	1	0	0	1	1	1	2	1	1	0	4	4	5	0	4	4	4	rs60717199	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:2811522T>A	ENST00000397885.2	-	15	1680	c.1474A>T	c.(1474-1476)Agc>Tgc	p.S492C		NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020	492	PUM-HD. {ECO:0000255|PROSITE- ProRule:PRU00318}.					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)		TGCAGGTAGCTTAACAAAGCT	0.473													T|||	109	0.0217652	0.0764	0.0101	5008	,	,		19686	0.0		0.001	False		,,,				2504	0.0				p.S492C		Atlas-SNP	.											.	KIAA0020	56	.	0			c.A1474T						PASS	.	T	CYS/SER	263,4143	148.8+/-183.1	7,249,1947	148	137	140		1474	4.8	0.8	9	dbSNP_129	140	3,8597	3.0+/-9.4	0,3,4297	yes	missense	KIAA0020	NM_014878.4	112	7,252,6244	AA,AT,TT		0.0349,5.9691,2.0452	probably-damaging	492/649	2811522	266,12740	2203	4300	6503	SO:0001583	missense	9933	exon15			GGTAGCTTAACAA	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.1474A>T	9.37:g.2811522T>A	ENSP00000380982:p.Ser492Cys	107	0	0		102	42	0.411765	NM_014878	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Missense_Mutation	SNP	ENST00000397885.2	37	CCDS6448.2	35	0.016025641025641024	32	0.06504065040650407	3	0.008287292817679558	0	0.0	0	0.0	T	19.38	3.816861	0.70912	0.059691	3.49E-4	ENSG00000080608	ENST00000397885	T	0.46063	0.88	5.97	4.84	0.62591	CPL (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.452768	0.30676	N	0.009106	T	0.07773	0.0195	M	0.63843	1.955	0.29221	N	0.87392	P;P	0.43607	0.544;0.812	P;P	0.54856	0.656;0.762	T	0.18147	-1.0346	10	0.66056	D	0.02	-29.6696	9.6157	0.39690	0.0:0.1502:0.0:0.8498	rs60717199	352;492	B2RDG4;Q15397	.;K0020_HUMAN	C	492	ENSP00000380982:S492C	ENSP00000380982:S492C	S	-	1	0	KIAA0020	2801522	1.000000	0.71417	0.841000	0.33234	0.884000	0.51177	2.579000	0.46059	1.089000	0.41292	0.533000	0.62120	AGC	T|0.980;A|0.020	0.020	strong		0.473	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878		A	2811522	T	A	2811522	3	1	22	1	0	0	0	0	1	0	0	0	8161	1609	56	5	488	5	KIAA0020	9	2811522	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	81817	2811522	138401909	2019	4920											
KIAA0020	9933	hgsc.bcm.edu	37	chr9	2837218	2837218	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctggaattttctcttcttgTtgaatttatttgccggctgg	5	19	10	7	1	2	1	0	1	2	0	3	2	2	2	1	3	1	3	1	3	3	8	rs112185565	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:2837218T>C	ENST00000397885.2	-	3	472	c.266A>G	c.(265-267)aAc>aGc	p.N89S		NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020	89						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)		TCTCTTCTTGTTGAATTTATT	0.433													T|||	2	0.000399361	0.0015	0.0	5008	,	,		18588	0.0		0.0	False		,,,				2504	0.0				p.N89S		Atlas-SNP	.											.	KIAA0020	56	.	0			c.A266G						PASS	.	T	SER/ASN	6,3742		0,6,1868	226	222	223		266	-3.1	0.8	9	dbSNP_132	223	0,8196		0,0,4098	yes	missense	KIAA0020	NM_014878.4	46	0,6,5966	CC,CT,TT		0.0,0.1601,0.0502	benign	89/649	2837218	6,11938	1874	4098	5972	SO:0001583	missense	9933	exon3			TTCTTGTTGAATT	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.266A>G	9.37:g.2837218T>C	ENSP00000380982:p.Asn89Ser	196	0	0		246	110	0.447154	NM_014878	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Missense_Mutation	SNP	ENST00000397885.2	37	CCDS6448.2	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	2.871	-0.234057	0.05983	0.001601	0.0	ENSG00000080608	ENST00000397885	T	0.11277	2.79	3.73	-3.09	0.05331	.	1.455670	0.03867	N	0.274933	T	0.06554	0.0168	N	0.22421	0.69	0.09310	N	0.999993	B	0.02656	0.0	B	0.01281	0.0	T	0.38394	-0.9663	10	0.09084	T	0.74	-4.4541	7.1421	0.25562	0.0:0.4276:0.1305:0.4419	.	89	Q15397	K0020_HUMAN	S	89	ENSP00000380982:N89S	ENSP00000380982:N89S	N	-	2	0	KIAA0020	2827218	0.005000	0.15991	0.824000	0.32777	0.991000	0.79684	-0.410000	0.07151	-0.634000	0.05538	-0.263000	0.10527	AAC	T|0.999;C|0.001	0.001	strong		0.433	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878		C	2837218	T	C	2837218	3	2	22	1	0	0	0	0	1	0	0	0	8161	1725	60	3	1744	3	KIAA0020	9	2837218	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	25696	2837218	138376213	2020	4921											
GLIS3	169792	hgsc.bcm.edu	37	chr9	4118262	4118262	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caccatgtggttgaccaggcCtggctgcaggccgccgtgct	5	8	14	14	2	0	1	0	1	0	0	0	1	0	1	5	4	2	4	5	4	0	1	rs75462592	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:4118262C>A	ENST00000324333.10	-	3	944	c.751G>T	c.(751-753)Ggc>Tgc	p.G251C	GLIS3_ENST00000381971.3_Missense_Mutation_p.G406C	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3	251					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)		TTGACCAGGCCTGGCTGCAGG	0.721													C|||	66	0.0131789	0.0469	0.0058	5008	,	,		10239	0.0		0.0	False		,,,				2504	0.0				p.G406C		Atlas-SNP	.											.	GLIS3	152	.	0			c.G1216T						PASS	.	C	CYS/GLY,CYS/GLY	67,3403		1,65,1669	5	6	5		1216,751	5.5	0.4	9	dbSNP_131	5	2,6878		0,2,3438	yes	missense,missense	GLIS3	NM_001042413.1,NM_152629.3	159,159	1,67,5107	AA,AC,CC		0.0291,1.9308,0.6667	possibly-damaging,possibly-damaging	406/931,251/776	4118262	69,10281	1735	3440	5175	SO:0001583	missense	169792	exon4			CCAGGCCTGGCTG	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.751G>T	9.37:g.4118262C>A	ENSP00000325494:p.Gly251Cys	10	0	0		24	18	0.75	NM_001042413	B1AL19|Q1PHK5	Missense_Mutation	SNP	ENST00000324333.10	37	CCDS6451.1	15	0.006868131868131868	14	0.028455284552845527	1	0.0027624309392265192	0	0.0	0	0.0	C	12.40	1.925708	0.34002	0.019308	2.91E-4	ENSG00000107249	ENST00000324333;ENST00000381971	T;T	0.10960	2.84;2.82	5.49	5.49	0.81192	.	0.299519	0.22308	U	0.061772	T	0.04770	0.0129	N	0.22421	0.69	0.09310	N	0.999999	D;D	0.57257	0.979;0.964	P;B	0.50378	0.639;0.436	T	0.05115	-1.0905	10	0.38643	T	0.18	.	19.359	0.94428	0.0:1.0:0.0:0.0	.	406;251	Q8NEA6-2;Q8NEA6	.;GLIS3_HUMAN	C	251;406	ENSP00000325494:G251C;ENSP00000371398:G406C	ENSP00000325494:G251C	G	-	1	0	GLIS3	4108262	0.000000	0.05858	0.385000	0.26158	0.649000	0.38597	1.002000	0.29796	2.555000	0.86185	0.655000	0.94253	GGC	C|0.993;A|0.007	0.007	strong		0.721	GLIS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051559.1	NM_152629		A	4118262	C	A	4118262	3	1	22	1	0	0	0	0	1	0	0	0	6455	681	24	4	1608	4	GLIS3	9	4118262	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1281044	4118262	137095169	2021	4922											
C9orf68	55064	hgsc.bcm.edu	37	chr9	4625546	4625546	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tgtgatgtagataaaggcctCcgtgactcatgtctttcttc	8	15	9	9	1	3	3	1	2	2	1	5	3	4	3	2	1	0	1	2	1	3	4	rs12338523	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:4625546C>T	ENST00000454239.2	-	7	695	c.450G>A	c.(448-450)cgG>cgA	p.R150R	SPATA6L_ENST00000381890.5_Silent_p.R164R|SPATA6L_ENST00000475086.1_Silent_p.R92R|SPATA6L_ENST00000223517.5_5'UTR|SPATA6L_ENST00000381895.5_Silent_p.R27R			Q8N4H0	SPA6L_HUMAN	spermatogenesis associated 6-like	150																	ATAAAGGCCTCCGTGACTCAT	0.294													T|||	73	0.0145767	0.0499	0.0101	5008	,	,		15547	0.0		0.0	False		,,,				2504	0.0				p.R92R		Atlas-SNP	.											.	SPATA6L	3	.	0			c.G276A						PASS	.	T		130,3480		1,128,1676	62	63	63		276	-1.8	0	9	dbSNP_120	63	2,8128		0,2,4063	no	coding-synonymous	C9orf68	NM_001039395.3		1,130,5739	TT,TC,CC		0.0246,3.6011,1.1244		92/335	4625546	132,11608	1805	4065	5870	SO:0001819	synonymous_variant	55064	exon5			AGGCCTCCGTGAC	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.450G>A	9.37:g.4625546C>T		78	0	0		98	52	0.530612	NM_001039395	B4DIY4|Q5JVJ5|Q8IY90	Silent	SNP	ENST00000454239.2	37																																																																																				C|0.994;T|0.006	0.006	strong		0.294	SPATA6L-202	KNOWN	basic	protein_coding	protein_coding		NM_017985		T	4625546	C	T	4625546	2	4	22	1	0	0	0	0	0	0	0	1	2493	842	30	2		2	C9orf68	9	4625546	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	507284	4625546	136587885	2022	4923											
JAK2	3717	hgsc.bcm.edu	37	chr9	5050706	5050706	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcggcatgattttgtgcaCggatggataaaagtacctgt	10	12	13	6	2	0	1	0	1	0	0	0	3	0	3	1	4	2	3	1	4	3	4	rs2230722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:5050706C>T	ENST00000381652.3	+	6	983	c.489C>T	c.(487-489)caC>caT	p.H163H	JAK2_ENST00000539801.1_Silent_p.H163H|JAK2_ENST00000544510.1_Silent_p.H14H	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	163	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)	ATTTTGTGCACGGATGGATAA	0.343		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial				T|||	1794	0.358227	0.4887	0.3905	5008	,	,		15245	0.2708		0.3002	False		,,,				2504	0.3088				p.H163H		Atlas-SNP	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	35466	.	0			c.C489T						PASS	.	T		2047,2359	609.9+/-391.4	488,1071,644	110	123	118		489	-0.9	0.9	9	dbSNP_119	118	2589,6011	689.4+/-404.4	366,1857,2077	no	coding-synonymous	JAK2	NM_004972.3		854,2928,2721	TT,TC,CC		30.1047,46.4594,35.6451		163/1133	5050706	4636,8370	2203	4300	6503	SO:0001819	synonymous_variant	3717	exon6	Familial Cancer Database		TGTGCACGGATGG		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.489C>T	9.37:g.5050706C>T		86	0	0		74	32	0.432432	NM_004972	O14636|O75297	Silent	SNP	ENST00000381652.3	37	CCDS6457.1																																																																																			C|0.647;T|0.353	0.353	strong		0.343	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			T	5050706	C	T	5050706	2	4	22	1	0	0	0	0	0	0	0	1	7947	535	19	1		1	JAK2	9	5050706	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	425160	5050706	136162725	2023	4924											
INSL6	11172	hgsc.bcm.edu	37	chr9	5185365	5185365	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcggtttgcgggctttcgaActggtatgggctgtaggctt	5	13	16	7	3	0	0	0	0	0	0	1	1	0	0	0	5	3	6	0	5	3	5	rs2149554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:5185365A>G	ENST00000381641.3	-	1	303	c.238T>C	c.(238-240)Ttc>Ctc	p.F80L		NM_007179.2	NP_009110.2	Q9Y581	INSL6_HUMAN	insulin-like 6	80			F -> L (in dbSNP:rs2149554).		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)		GGGCTTTCGAACTGGTATGGG	0.537													A|||	503	0.100439	0.3646	0.0274	5008	,	,		16500	0.0		0.001	False		,,,				2504	0.001				p.F80L		Atlas-SNP	.											INSL6,NS,carcinoma,+2,1	INSL6	35	1	0			c.T238C						scavenged	.	A	LEU/PHE	1275,3131	436.4+/-344.6	176,923,1104	118	126	123		238	0.5	0	9	dbSNP_96	123	10,8590	6.4+/-24.3	0,10,4290	yes	missense	INSL6	NM_007179.2	22	176,933,5394	GG,GA,AA		0.1163,28.9378,9.8801	benign	80/214	5185365	1285,11721	2203	4300	6503	SO:0001583	missense	11172	exon1			TTTCGAACTGGTA	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.238T>C	9.37:g.5185365A>G	ENSP00000371054:p.Phe80Leu	84	1	0.0119048		117	61	0.521368	NM_007179	A0AVS0|Q9NS16	Missense_Mutation	SNP	ENST00000381641.3	37	CCDS6458.1	184	0.08424908424908426	174	0.35365853658536583	10	0.027624309392265192	0	0.0	0	0.0	A	5.443	0.266871	0.10294	0.289378	0.001163	ENSG00000120210	ENST00000381641	T	0.40476	1.03	4.39	0.455	0.16649	Insulin-like (3);	3.103370	0.00944	N	0.002876	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.06786	0.001	B	0.10450	0.005	T	0.29427	-1.0012	9	0.11485	T	0.65	-13.6373	3.4873	0.07625	0.5569:0.1995:0.2435:0.0	rs2149554;rs52816055;rs56640305;rs2149554	80	Q9Y581	INSL6_HUMAN	L	80	ENSP00000371054:F80L	ENSP00000371054:F80L	F	-	1	0	INSL6	5175365	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.553000	0.06012	0.067000	0.16545	0.533000	0.62120	TTC	A|0.897;G|0.103	0.103	strong		0.537	INSL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051608.3	NM_007179		G	5185365	A	G	5185365	3	3	22	1	0	0	0	0	1	0	0	0	7779	43	2	3	411	3	INSL6	9	5185365	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	134659	5185365	136028066	2024	4925											
INSL4	3641	hgsc.bcm.edu	37	chr9	5233664	5233664	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacttcacagaaatggtgtcAacctccaacaacaaagatgg	16	8	7	10	0	2	2	2	0	0	2	3	2	3	2	2	2	4	0	2	2	6	2	rs7030463	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:5233664A>G	ENST00000239316.4	+	2	312	c.207A>G	c.(205-207)tcA>tcG	p.S69S		NM_002195.1	NP_002186.1	Q14641	INSL4_HUMAN	insulin-like 4 (placenta)	69					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	insulin-like growth factor receptor binding (GO:0005159)|receptor binding (GO:0005102)			endometrium(2)|lung(2)|skin(1)|urinary_tract(1)	6	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0201)|Lung(218;0.14)		AAATGGTGTCAACCTCCAACA	0.398													A|||	163	0.0325479	0.121	0.0043	5008	,	,		21594	0.0		0.0	False		,,,				2504	0.0				p.S69S		Atlas-SNP	.											INSL4,right_upper_lobe,carcinoma,+2,1	INSL4	20	1	0			c.A207G						PASS	.	A		394,4012	197.4+/-221.5	15,364,1824	62	58	59		207	1.8	0.3	9	dbSNP_116	59	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	INSL4	NM_002195.1		15,366,6122	GG,GA,AA		0.0233,8.9424,3.0447		69/140	5233664	396,12610	2203	4300	6503	SO:0001819	synonymous_variant	3641	exon2			GGTGTCAACCTCC		CCDS6459.1	9p24	2008-02-05			ENSG00000120211	ENSG00000120211			6087	protein-coding gene	gene with protein product		600910				8666396, 9730618	Standard	NM_002195		Approved	EPIL	uc003ziy.3	Q14641	OTTHUMG00000019494	ENST00000239316.4:c.207A>G	9.37:g.5233664A>G		55	0	0		61	33	0.540984	NM_002195	A8K678|Q5W127	Silent	SNP	ENST00000239316.4	37	CCDS6459.1																																																																																			A|0.967;G|0.033	0.033	strong		0.398	INSL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051616.2	NM_002195		G	5233664	A	G	5233664	2	3	22	1	0	0	0	0	0	0	0	1	7777	117	5	3		3	INSL4	9	5233664	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	48299	5233664	135979767	2025	4926											
GLDC	2731	hgsc.bcm.edu	37	chr9	6587176	6587176	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagacctggtcataacctgtGagttcacacaaatccttctc	11	11	6	13	0	3	2	2	1	1	1	5	2	4	2	3	1	1	1	3	1	2	3	rs74461075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:6587176G>A	ENST00000321612.6	-	15	1965	c.1815C>T	c.(1813-1815)ctC>ctT	p.L605L		NM_000170.2	NP_000161.2	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	605					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)	CATAACCTGTGAGTTCACACA	0.418													G|||	71	0.0141773	0.0514	0.0043	5008	,	,		19260	0.0		0.0	False		,,,				2504	0.0				p.L605L		Atlas-SNP	.											.	GLDC	118	.	0			c.C1815T						PASS	.	G		173,4233	112.9+/-151.0	3,167,2033	117	112	114		1815	3.5	1	9	dbSNP_131	114	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	GLDC	NM_000170.2		3,169,6331	AA,AG,GG		0.0233,3.9265,1.3455		605/1021	6587176	175,12831	2203	4300	6503	SO:0001819	synonymous_variant	2731	exon15			ACCTGTGAGTTCA	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.1815C>T	9.37:g.6587176G>A		125	0	0		135	64	0.474074	NM_000170	Q2M2F8	Silent	SNP	ENST00000321612.6	37	CCDS34987.1																																																																																			G|0.987;A|0.013	0.013	strong		0.418	GLDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051674.2	NM_000170		A	6587176	G	A	6587176	2	1	22	1	0	0	0	0	0	0	0	1	6441	1277	45	2		2	GLDC	9	6587176	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1353512	6587176	134626255	2026	4927											
KDM4C	23081	hgsc.bcm.edu	37	chr9	6986589	6986589	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagaagagagtgatgtggagAgccatgggaatggccttgaa	13	7	17	4	0	0	5	0	2	0	3	0	9	0	6	2	3	1	0	2	3	3	1	rs111451391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:6986589A>C	ENST00000381309.3	+	11	2165	c.1600A>C	c.(1600-1602)Agc>Cgc	p.S534R	KDM4C_ENST00000543771.1_Missense_Mutation_p.S534R|KDM4C_ENST00000536108.1_Missense_Mutation_p.S353R|KDM4C_ENST00000428870.2_Missense_Mutation_p.S221R|KDM4C_ENST00000535193.1_Missense_Mutation_p.S556R|KDM4C_ENST00000442236.2_Intron|KDM4C_ENST00000381306.3_Missense_Mutation_p.S534R	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	534					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						TGATGTGGAGAGCCATGGGAA	0.498													A|||	63	0.0125799	0.0023	0.0865	5008	,	,		19983	0.0		0.0	False		,,,				2504	0.0				p.S556R		Atlas-SNP	.											KDM4C,NS,carcinoma,-2,1	KDM4C	186	1	0			c.A1666C						scavenged	.	A	ARG/SER,ARG/SER,ARG/SER,ARG/SER	5,4401	9.9+/-24.2	0,5,2198	101	90	94		1600,1600,1666,1600	4.2	1	9	dbSNP_132	94	1,8599		0,1,4299	yes	missense,missense,missense,missense	KDM4C	NM_001146694.1,NM_001146695.1,NM_001146696.1,NM_015061.3	110,110,110,110	0,6,6497	CC,CA,AA		0.0116,0.1135,0.0461	benign,benign,benign,benign	534/1048,534/814,556/836,534/1057	6986589	6,13000	2203	4300	6503	SO:0001583	missense	23081	exon11			GTGGAGAGCCATG	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.1600A>C	9.37:g.6986589A>C	ENSP00000370710:p.Ser534Arg	162	1	0.00617284		174	89	0.511494	NM_001146696	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	37	CCDS6471.1	31	0.014194139194139194	1	0.0020325203252032522	30	0.08287292817679558	0	0.0	0	0.0	A	13.15	2.149919	0.37923	0.001135	1.16E-4	ENSG00000107077	ENST00000535193;ENST00000543771;ENST00000381309;ENST00000381306;ENST00000536108;ENST00000428870	T;T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6;0.6	5.3	4.17	0.49024	.	2.061340	0.01784	N	0.031882	T	0.04952	0.0133	M	0.66939	2.045	0.29043	N	0.884963	P;P;B;P	0.42203	0.773;0.603;0.112;0.603	B;B;B;B	0.38616	0.277;0.202;0.064;0.246	T	0.14671	-1.0464	10	0.13470	T	0.59	-1.3627	8.4932	0.33112	0.8984:0.0:0.1016:0.0	.	534;556;534;534	F5H347;F5H7P0;Q9H3R0;Q9H3R0-2	.;.;KDM4C_HUMAN;.	R	556;534;534;534;353;221	ENSP00000442382:S556R;ENSP00000445427:S534R;ENSP00000370710:S534R;ENSP00000370707:S534R;ENSP00000440656:S353R;ENSP00000405739:S221R	ENSP00000370707:S534R	S	+	1	0	KDM4C	6976589	1.000000	0.71417	0.979000	0.43373	0.845000	0.48019	4.096000	0.57734	1.040000	0.40099	0.533000	0.62120	AGC	A|0.995;C|0.004;T|0.000	0.004	strong		0.498	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061		C	6986589	A	C	6986589	3	2	22	1	0	0	0	0	1	0	0	0	8139	304	11	5	1708	5	KDM4C	9	6986589	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	399413	6986589	134226842	2027	4928											
KDM4C	23081	hgsc.bcm.edu	37	chr9	7013874	7013874	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gagggaaagactaagcccctCataccagagatgtgttttat	13	10	10	8	0	1	2	1	0	0	2	1	5	1	3	3	1	2	1	3	1	4	4	rs35006356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:7013874C>T	ENST00000381309.3	+	14	2620	c.2055C>T	c.(2053-2055)ctC>ctT	p.L685L	KDM4C_ENST00000543771.1_Silent_p.L685L|KDM4C_ENST00000536108.1_Silent_p.L504L|KDM4C_ENST00000428870.2_Silent_p.L372L|KDM4C_ENST00000535193.1_Silent_p.L707L|KDM4C_ENST00000442236.2_Silent_p.L430L|KDM4C_ENST00000381306.3_Silent_p.L685L	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	685					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						CTAAGCCCCTCATACCAGAGA	0.388													C|||	36	0.0071885	0.0265	0.0	5008	,	,		19797	0.0		0.001	False		,,,				2504	0.0				p.L707L		Atlas-SNP	.											.	KDM4C	186	.	0			c.C2121T						PASS	.	C	,,,	96,4310	77.8+/-116.1	1,94,2108	118	114	115		2055,2055,2121,2055	1.3	1	9	dbSNP_126	115	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KDM4C	NM_001146694.1,NM_001146695.1,NM_001146696.1,NM_015061.3	,,,	1,94,6408	TT,TC,CC		0.0,2.1788,0.7381	,,,	685/1048,685/814,707/836,685/1057	7013874	96,12910	2203	4300	6503	SO:0001819	synonymous_variant	23081	exon14			GCCCCTCATACCA	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.2055C>T	9.37:g.7013874C>T		76	0	0		67	35	0.522388	NM_001146696	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Silent	SNP	ENST00000381309.3	37	CCDS6471.1																																																																																			C|0.993;T|0.007	0.007	strong		0.388	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061		T	7013874	C	T	7013874	2	4	22	1	0	0	0	0	0	0	0	1	8139	813	29	2		2	KDM4C	9	7013874	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	27285	7013874	134199557	2028	4929											
FREM1	158326	hgsc.bcm.edu	37	chr9	14824088	14824088	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttggtatgctgtccaccaTaaataatttcccagcatcca	11	14	5	11	0	0	0	0	0	0	0	3	0	3	0	4	1	2	3	4	1	4	6	rs7864984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:14824088T>C	ENST00000380880.3	-	12	2887	c.2104A>G	c.(2104-2106)Atg>Gtg	p.M702V	FREM1_ENST00000380881.4_Missense_Mutation_p.M703V|FREM1_ENST00000422223.2_Missense_Mutation_p.M702V			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	702					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)		CTGTCCACCATAAATAATTTC	0.393													T|||	185	0.0369409	0.1309	0.0086	5008	,	,		20998	0.0		0.004	False		,,,				2504	0.002				p.M702V		Atlas-SNP	.											.	FREM1	261	.	0			c.A2104G						PASS	.	T	VAL/MET	360,3416		13,334,1541	63	60	61		2104	0.8	0.8	9	dbSNP_116	61	16,8218		0,16,4101	yes	missense	FREM1	NM_144966.5	21	13,350,5642	CC,CT,TT		0.1943,9.5339,3.1307	benign	702/2180	14824088	376,11634	1888	4117	6005	SO:0001583	missense	158326	exon13			CCACCATAAATAA	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.2104A>G	9.37:g.14824088T>C	ENSP00000370262:p.Met702Val	91	0	0		92	44	0.478261	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	55	0.025183150183150184	51	0.10365853658536585	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	T	7.670	0.686751	0.14973	0.095339	0.001943	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.25414	1.8;1.8;1.8	5.83	0.775	0.18527	.	0.246267	0.48767	D	0.000171	T	0.00580	0.0019	M	0.71581	2.175	0.28563	N	0.911019	B	0.22211	0.066	B	0.17098	0.017	T	0.20538	-1.0272	10	0.17832	T	0.49	-9.8199	8.6558	0.34062	0.1862:0.0:0.3315:0.4823	rs7864984;rs57027040;rs7864984	702	Q5H8C1	FREM1_HUMAN	V	703;702;702	ENSP00000370263:M703V;ENSP00000412940:M702V;ENSP00000370262:M702V	ENSP00000370257:M705V	M	-	1	0	FREM1	14814088	0.995000	0.38212	0.842000	0.33263	0.462000	0.32619	0.335000	0.19806	-0.394000	0.07727	-3.035000	0.00072	ATG	T|0.978;C|0.022	0.022	strong		0.393	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		C	14824088	T	C	14824088	3	2	22	1	0	0	0	0	1	0	0	0	6052	1406	49	3	4589	3	FREM1	9	14824088	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	7810214	14824088	126389343	2029	4930											
FREM1	158326	hgsc.bcm.edu	37	chr9	14857744	14857744	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacacttcagttttgctctcAgttctagaatgtacagcact	10	14	7	10	0	3	1	2	0	2	1	4	2	3	1	0	0	3	5	0	0	3	6	rs145369669	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:14857744A>C	ENST00000380880.3	-	5	1418	c.635T>G	c.(634-636)cTg>cGg	p.L212R	FREM1_ENST00000380881.4_Missense_Mutation_p.L212R|FREM1_ENST00000422223.2_Missense_Mutation_p.L212R			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	212					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)		TTTTGCTCTCAGTTCTAGAAT	0.428													A|||	18	0.00359425	0.0136	0.0	5008	,	,		19720	0.0		0.0	False		,,,				2504	0.0				p.L212R		Atlas-SNP	.											.	FREM1	261	.	0			c.T635G						PASS	.	A	ARG/LEU	53,3683		0,53,1815	71	70	70		635	4.9	1	9	dbSNP_134	70	0,8198		0,0,4099	yes	missense	FREM1	NM_144966.5	102	0,53,5914	CC,CA,AA		0.0,1.4186,0.4441	benign	212/2180	14857744	53,11881	1868	4099	5967	SO:0001583	missense	158326	exon6			GCTCTCAGTTCTA	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.635T>G	9.37:g.14857744A>C	ENSP00000370262:p.Leu212Arg	59	0	0		84	43	0.511905	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	a	6.809	0.518344	0.13005	0.014186	0.0	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.11385	2.78;2.78;2.78	6.03	4.86	0.63082	.	0.387478	0.27668	N	0.018341	T	0.04634	0.0126	N	0.22421	0.69	0.09310	N	0.999998	P	0.51791	0.948	B	0.39876	0.312	T	0.36237	-0.9756	10	0.25751	T	0.34	-4.1637	10.3897	0.44162	0.7497:0.0:0.0:0.2503	.	212	Q5H8C1	FREM1_HUMAN	R	212	ENSP00000370263:L212R;ENSP00000412940:L212R;ENSP00000370262:L212R	ENSP00000370257:L212R	L	-	2	0	FREM1	14847744	0.590000	0.26815	0.952000	0.39060	0.064000	0.16182	4.254000	0.58798	2.314000	0.78098	0.456000	0.33151	CTG	A|0.997;C|0.003	0.003	strong		0.428	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		C	14857744	A	C	14857744	3	2	22	1	0	0	0	0	1	0	0	0	6052	188	7	5	6086	5	FREM1	9	14857744	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	33656	14857744	126355687	2030	4931											
FREM1	158326	hgsc.bcm.edu	37	chr9	14863863	14863863	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attggacaaccattgtgaacAtacttgacttcgttgggaag	12	12	10	7	1	0	2	0	2	0	0	1	4	0	4	1	2	3	1	1	2	4	6	rs61740262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:14863863A>G	ENST00000380880.3	-	3	1056	c.273T>C	c.(271-273)taT>taC	p.Y91Y	FREM1_ENST00000380881.4_Silent_p.Y91Y|FREM1_ENST00000422223.2_Silent_p.Y91Y			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	91					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)		CATTGTGAACATACTTGACTT	0.393													A|||	159	0.0317492	0.112	0.013	5008	,	,		22501	0.0		0.001	False		,,,				2504	0.001				p.Y91Y		Atlas-SNP	.											.	FREM1	261	.	0			c.T273C						PASS	.	A		313,3603		19,275,1664	115	113	113		273	2.9	0.8	9	dbSNP_129	113	12,8276		0,12,4132	yes	coding-synonymous	FREM1	NM_144966.5		19,287,5796	GG,GA,AA		0.1448,7.9928,2.6631		91/2180	14863863	325,11879	1958	4144	6102	SO:0001819	synonymous_variant	158326	exon4			GTGAACATACTTG	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.273T>C	9.37:g.14863863A>G		107	0	0		121	65	0.53719	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	37	CCDS47952.1																																																																																			A|0.975;G|0.025	0.025	strong		0.393	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		G	14863863	A	G	14863863	2	3	22	1	0	0	0	0	0	0	0	1	6052	224	8	3		3	FREM1	9	14863863	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	6119	14863863	126349568	2031	4932											
TTC39B	158219	hgsc.bcm.edu	37	chr9	15191209	15191209	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctattcccagaaaatccaatAaattctagtagtctgataat	16	13	4	8	0	2	2	0	1	2	1	4	2	4	2	2	0	0	1	2	0	9	7	rs74818741	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:15191209A>G	ENST00000512701.2	-	10	1011	c.975T>C	c.(973-975)ttT>ttC	p.F325F	TTC39B_ENST00000541445.1_3'UTR|TTC39B_ENST00000355694.2_Silent_p.F259F|TTC39B_ENST00000297615.5_Silent_p.F256F|TTC39B_ENST00000380850.4_Silent_p.F325F|TTC39B_ENST00000507993.1_Silent_p.F160F|TTC39B_ENST00000507285.1_Silent_p.F160F			Q5VTQ0	TT39B_HUMAN	tetratricopeptide repeat domain 39B	325										NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)	21						AAAATCCAATAAATTCTAGTA	0.323													A|||	137	0.0273562	0.1014	0.0043	5008	,	,		17741	0.0		0.0	False		,,,				2504	0.0				p.F325F		Atlas-SNP	.											.	TTC39B	83	.	0			c.T975C						PASS	.	A	,,,,	346,4060	176.9+/-206.0	13,320,1870	69	73	72		969,975,768,480,975	1.3	1	9	dbSNP_132	72	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTC39B	NM_001168339.1,NM_001168340.1,NM_001168341.1,NM_001168342.1,NM_152574.2	,,,,	13,321,6168	GG,GA,AA		0.0116,7.8529,2.6684	,,,,	323/681,325/670,256/614,160/518,325/683	15191209	347,12657	2203	4299	6502	SO:0001819	synonymous_variant	158219	exon10			TCCAATAAATTCT	AK091187	CCDS6477.1, CCDS6477.2, CCDS55294.1, CCDS55295.1, CCDS55296.1	9p22.2	2013-01-11	2008-06-23	2008-06-23	ENSG00000155158	ENSG00000155158		"Tetratricopeptide (TTC) repeat domain containing"	23704	protein-coding gene	gene with protein product		613574	"chromosome 9 open reading frame 52"	C9orf52			Standard	NM_001168339		Approved	FLJ33868	uc003zlr.2	Q5VTQ0	OTTHUMG00000019581	ENST00000512701.2:c.975T>C	9.37:g.15191209A>G		110	0	0		98	49	0.5	NM_001168340	A5PLN1|B4DQ10|B4DQX4|B4DW93|Q8IVR7|Q8IXZ6|Q8N267	Silent	SNP	ENST00000512701.2	37	CCDS6477.2																																																																																			A|0.969;G|0.031	0.031	strong		0.323	TTC39B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051758.3	NM_152574		G	15191209	A	G	15191209	2	3	22	1	0	0	0	0	0	0	0	1	16723	359	13	3		3	TTC39B	9	15191209	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	327346	15191209	126022222	2032	4933											
ACER2	340485	hgsc.bcm.edu	37	chr9	19450598	19450598	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcccctatgtgtccctcctGtgtgccaacaagaaatcatc	9	11	7	14	0	1	1	1	0	0	1	5	1	4	1	5	0	2	0	5	0	4	1	rs7855739	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:19450598G>C	ENST00000340967.2	+	6	818	c.792G>C	c.(790-792)ctG>ctC	p.L264L	RP11-363E7.4_ENST00000563205.1_RNA	NM_001010887.2	NP_001010887.2	Q5QJU3	ACER2_HUMAN	alkaline ceramidase 2	264					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to drug (GO:0035690)|ceramide metabolic process (GO:0006672)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of protein glycosylation in Golgi (GO:0090285)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	ceramidase activity (GO:0017040)|dihydroceramidase activity (GO:0071633)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)	13						TGTCCCTCCTGTGTGCCAACA	0.517													G|||	375	0.0748802	0.2579	0.0216	5008	,	,		19358	0.003		0.0	False		,,,				2504	0.0164				p.L264L		Atlas-SNP	.											.	ACER2	24	.	0			c.G792C						PASS	.	G		1024,3382	378.7+/-323.0	131,762,1310	145	131	136		792	-0.3	0.9	9	dbSNP_116	136	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	ACER2	NM_001010887.2		131,770,5602	CC,CG,GG		0.093,23.241,7.9348		264/276	19450598	1032,11974	2203	4300	6503	SO:0001819	synonymous_variant	340485	exon6			CCTCCTGTGTGCC	AK123581	CCDS34992.1	9p21.3	2013-01-25	2008-12-19	2008-12-19	ENSG00000177076	ENSG00000177076	3.5.1.23	"Alkaline ceramidase"	23675	protein-coding gene	gene with protein product		613492	"N-acylsphingosine amidohydrolase 3-like"	ASAH3L		18945876	Standard	XM_005251447		Approved	FLJ41587	uc003zny.1	Q5QJU3	OTTHUMG00000019644	ENST00000340967.2:c.792G>C	9.37:g.19450598G>C		282	1	0.0035461		330	328	0.993939	NM_001010887	A2A3R8|Q569G5|Q5VZR7|Q71RD2	Silent	SNP	ENST00000340967.2	37	CCDS34992.1																																																																																			G|0.933;C|0.067	0.067	strong		0.517	ACER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051864.1	XM_294540		C	19450598	G	C	19450598	2	2	22	1	0	0	0	0	0	0	0	1	139	1364	48	4		4	ACER2	9	19450598	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4259389	19450598	121762833	2033	4934											
KIAA1797	54914	hgsc.bcm.edu	37	chr9	20820346	20820346	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtataggacaaattctacgAataatacaactacttggaac	17	11	6	7	1	1	0	0	0	1	0	1	3	1	2	0	2	5	1	0	2	10	8	rs147147351		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:20820346A>T	ENST00000380249.1	+	15	1948	c.1584A>T	c.(1582-1584)cgA>cgT	p.R528R	FOCAD_ENST00000338382.6_Silent_p.R528R|FOCAD_ENST00000605086.1_5'UTR	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	528						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											AAATTCTACGAATAATACAAC	0.378													A|||	1	0.000199681	0.0008	0.0	5008	,	,		17668	0.0		0.0	False		,,,				2504	0.0				p.R528R		Atlas-SNP	.											KIAA1797,rectum,carcinoma,+1,1	.	.	1	0			c.A1584T						PASS	.	A		3,4403	6.2+/-15.9	0,3,2200	101	96	98		1584	1.8	1	9	dbSNP_134	98	0,8600		0,0,4300	no	coding-synonymous	KIAA1797	NM_017794.3		0,3,6500	TT,TA,AA		0.0,0.0681,0.0231		528/1802	20820346	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	54914	exon15			TCTACGAATAATA	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.1584A>T	9.37:g.20820346A>T		127	0	0		123	55	0.447154	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Silent	SNP	ENST00000380249.1	37	CCDS34993.1																																																																																			A|1.000;T|0.000	0.000	strong		0.378	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794		T	20820346	A	T	20820346	2	4	22	1	0	0	0	0	0	0	0	1	8267	233	9	5		5	KIAA1797	9	20820346	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1369748	20820346	120393085	2034	4935											
KIAA1797	54914	hgsc.bcm.edu	37	chr9	20978439	20978439	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgggtgacaccaccactgAtccacagtctgagtgtatgt	9	11	11	10	0	1	3	0	3	1	0	2	3	2	3	3	1	0	1	3	1	1	1	rs149031092		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:20978439A>C	ENST00000380249.1	+	39	4727	c.4363A>C	c.(4363-4365)Atc>Ctc	p.I1455L	FOCAD_ENST00000338382.6_Missense_Mutation_p.I1455L|FOCAD_ENST00000605086.1_Missense_Mutation_p.I891L	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	1455						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											ACCACCACTGATCCACAGTCT	0.458													A|||	1	0.000199681	0.0008	0.0	5008	,	,		19302	0.0		0.0	False		,,,				2504	0.0				p.I1455L		Atlas-SNP	.											.	.	.	.	0			c.A4363C						PASS	.	A	LEU/ILE	3,4403	6.2+/-15.9	0,3,2200	77	71	73		4363	-1	0.1	9	dbSNP_134	73	0,8600		0,0,4300	no	missense	KIAA1797	NM_017794.3	5	0,3,6500	CC,CA,AA		0.0,0.0681,0.0231	benign	1455/1802	20978439	3,13003	2203	4300	6503	SO:0001583	missense	54914	exon39			CCACTGATCCACA	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.4363A>C	9.37:g.20978439A>C	ENSP00000369599:p.Ile1455Leu	138	0	0		152	80	0.526316	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	37	CCDS34993.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	12.27	1.888125	0.33348	6.81E-4	0.0	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.21543	2.0;2.0	6.06	-0.993	0.10228	.	0.598323	0.18257	N	0.146776	T	0.15435	0.0372	L	0.51422	1.61	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.16897	-1.0387	10	0.39692	T	0.17	-0.8041	5.9075	0.19008	0.399:0.252:0.349:0.0	.	1455	Q5VW36	K1797_HUMAN	L	1455	ENSP00000369599:I1455L;ENSP00000344307:I1455L	ENSP00000344307:I1455L	I	+	1	0	KIAA1797	20968439	0.409000	0.25368	0.067000	0.19924	0.828000	0.46876	0.494000	0.22467	-0.159000	0.11021	0.533000	0.62120	ATC	A|1.000;C|0.000	0.000	strong		0.458	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794		C	20978439	A	C	20978439	3	2	22	1	0	0	0	0	1	0	0	0	8267	333	12	5	4505	5	KIAA1797	9	20978439	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	158093	20978439	120234992	2035	4936											
IFNA4	3441	hgsc.bcm.edu	37	chr9	21187146	21187146	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	catcaggggagtctcttccaCcccaacctcctgtatcacac	9	9	6	17	0	3	0	2	0	1	0	6	1	5	1	5	2	1	1	5	2	2	2	rs201186279		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21187146C>T	ENST00000421715.1	-	1	452	c.385G>A	c.(385-387)Gtg>Atg	p.V129M		NM_021068.2	NP_066546.1	P05014	IFNA4_HUMAN	interferon, alpha 4	129					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)	p.V129M(1)		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)		GTCTCTTCCACCCCAACCTCC	0.458													C|||	1	0.000199681	0.0	0.0014	5008	,	,		19919	0.0		0.0	False		,,,				2504	0.0				p.V129M	NSCLC(154;890 1986 23660 27800 51138)	Atlas-SNP	.											IFNA4,NS,carcinoma,0,1	IFNA4	34	1	1	Substitution - Missense(1)	endometrium(1)	c.G385A						scavenged	.						35	38	37					9																	21187146		2182	4253	6435	SO:0001583	missense	3441	exon1			CTTCCACCCCAAC		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.385G>A	9.37:g.21187146C>T	ENSP00000412897:p.Val129Met	513	2	0.00389864		736	68	0.0923913	NM_021068	P13358|Q14CS4|Q5VV15	Missense_Mutation	SNP	ENST00000421715.1	37	CCDS6498.1	.	.	.	.	.	.	.	.	.	.	-	4.271	0.049496	0.08243	.	.	ENSG00000236637	ENST00000421715	T	0.03441	3.93	2.96	-5.93	0.02254	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	1.507550	0.03550	N	0.225260	T	0.05593	0.0147	M	0.73319	2.225	0.09310	N	1	B	0.18741	0.03	B	0.28305	0.088	T	0.38351	-0.9665	10	0.52906	T	0.07	.	1.8132	0.03095	0.1267:0.2025:0.3717:0.2991	.	129	P05014	IFNA4_HUMAN	M	129	ENSP00000412897:V129M	ENSP00000412897:V129M	V	-	1	0	IFNA4	21177146	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.851000	0.01669	-1.988000	0.00980	-1.417000	0.01113	GTG	.	.	weak		0.458	IFNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051889.1	NM_021068		T	21187146	C	T	21187146	3	4	22	1	0	0	0	0	1	0	0	0	7548	507	18	2	188	2	IFNA4	9	21187146	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	208707	21187146	120026285	2036	4937											
IFNA10	3446	hgsc.bcm.edu	37	chr9	21206724	21206724	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcttccaccccaacctcctGtatcacacatgcttccaggt	8	11	4	18	0	2	0	1	0	1	0	5	0	5	0	6	1	2	2	6	1	2	3	rs145785282	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21206724G>A	ENST00000357374.2	-	1	418	c.373C>T	c.(373-375)Cag>Tag	p.Q125*		NM_002171.1	NP_002162.1	P01566	IFN10_HUMAN	interferon, alpha 10	125					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)			endometrium(1)|large_intestine(3)|liver(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	16				Lung(24;1.26e-23)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.17)		CCAACCTCCTGTATCACACAT	0.463													g|||	48	0.00958466	0.0325	0.0043	5008	,	,		19993	0.0		0.002	False		,,,				2504	0.0				p.Q125X		Atlas-SNP	.											.	IFNA10	29	.	0			c.C373T						PASS	.	G	stop/GLN	104,4300		2,100,2100	69	76	73		373	0.4	0	9	dbSNP_134	73	4,8556		0,4,4276	no	stop-gained	IFNA10	NM_002171.1		2,104,6376	AA,AG,GG		0.0467,2.3615,0.8331		125/190	21206724	108,12856	2202	4280	6482	SO:0001587	stop_gained	3446	exon1			CCTCCTGTATCAC		CCDS6499.1	9p22	2010-08-24			ENSG00000186803	ENSG00000186803		"Interferons"	5418	protein-coding gene	gene with protein product		147577				1385305	Standard	NM_002171		Approved	IFN-alphaC	uc003zoq.1	P01566	OTTHUMG00000019658	ENST00000357374.2:c.373C>T	9.37:g.21206724G>A	ENSP00000369566:p.Gln125*	599	0	0		702	210	0.299145	NM_002171	Q5VV13	Nonsense_Mutation	SNP	ENST00000357374.2	37	CCDS6499.1	.	.	.	.	.	.	.	.	.	.	-	12.34	1.908152	0.33721	0.023615	4.67E-4	ENSG00000186803	ENST00000357374	.	.	.	3.75	0.383	0.16239	.	0.485956	0.22193	N	0.063355	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	7.857	0.29489	0.0:0.3253:0.508:0.1667	.	.	.	.	X	125	.	ENSP00000369566:Q125X	Q	-	1	0	IFNA10	21196724	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.002000	0.13061	0.171000	0.19730	-0.667000	0.03836	CAG	G|0.996;A|0.004	0.004	strong		0.463	IFNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051887.1	NM_002171		A	21206724	G	A	21206724	4	1	22	1	0	0	0	0	0	1	0	0	7541	1386	48	2	200	2	IFNA10	9	21206724	Nonsense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	19578	21206724	120006707	2037	4938											
IFNA14	3448	hgsc.bcm.edu	37	chr9	21239578	21239578	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctgtatcacacaggcttcCaggtcattcatttgctggaa	9	13	8	11	0	3	0	3	0	0	0	5	1	5	1	2	3	1	3	2	3	2	4	rs141933410		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21239578C>T	ENST00000380222.2	-	1	400	c.357G>A	c.(355-357)ctG>ctA	p.L119L		NM_002172.2	NP_002163.2	P01570	IFN14_HUMAN	interferon, alpha 14	119					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)		CACAGGCTTCCAGGTCATTCA	0.448																																					p.L119L		Atlas-SNP	.											.	IFNA14	29	.	0			c.G357A						PASS	.						150	156	154					9																	21239578		2203	4300	6503	SO:0001819	synonymous_variant	3448	exon1			GGCTTCCAGGTCA		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.357G>A	9.37:g.21239578C>T		360	0	0		429	43	0.100233	NM_002172	Q5VZ56|Q7M4S1	Silent	SNP	ENST00000380222.2	37	CCDS6501.1																																																																																			C|0.999;G|0.000;T|0.001	0.001	strong		0.448	IFNA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051894.1	NM_002172		T	21239578	C	T	21239578	2	4	22	1	0	0	0	0	0	0	0	1	7543	581	21	2		2	IFNA14	9	21239578	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	32854	21239578	119973853	2038	4939											
IFNA5	3442	hgsc.bcm.edu	37	chr9	21305048	21305048	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcttgagccttctggaactGgttgccatcaaactcctcct	7	12	9	13	0	2	1	1	1	1	0	4	2	4	2	4	3	4	2	4	3	2	3	rs138121530	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21305048G>C	ENST00000259555.4	-	1	264	c.208C>G	c.(208-210)Cag>Gag	p.Q70E		NM_002169.2	NP_002160.1	P01569	IFNA5_HUMAN	interferon, alpha 5	70					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)		TTCTGGAACTGGTTGCCATCA	0.473													G|||	60	0.0119808	0.0439	0.0029	5008	,	,		23310	0.0		0.0	False		,,,				2504	0.0				p.Q70E		Atlas-SNP	.											.	IFNA5	21	.	0			c.C208G						PASS	.	G	GLU/GLN	212,4194	131.0+/-167.6	3,206,1994	139	130	133		208	4.2	0	9	dbSNP_134	133	2,8598	2.2+/-6.3	0,2,4298	no	missense	IFNA5	NM_002169.2	29	3,208,6292	CC,CG,GG		0.0233,4.8116,1.6454	benign	70/190	21305048	214,12792	2203	4300	6503	SO:0001583	missense	3442	exon1			GGAACTGGTTGCC		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.208C>G	9.37:g.21305048G>C	ENSP00000259555:p.Gln70Glu	332	0	0		288	138	0.479167	NM_002169	Q52LX3	Missense_Mutation	SNP	ENST00000259555.4	37	CCDS6502.1	18	0.008241758241758242	18	0.036585365853658534	0	0.0	0	0.0	0	0.0	G	13.34	2.206733	0.39003	0.048116	2.33E-4	ENSG00000147873	ENST00000259555	T	0.04275	3.66	4.16	4.16	0.48862	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.474897	0.22261	N	0.062416	T	0.02610	0.0079	M	0.85373	2.75	0.09310	N	1	B	0.25743	0.133	P	0.45712	0.491	T	0.02596	-1.1136	10	0.72032	D	0.01	.	10.4841	0.44711	0.0:0.1982:0.8018:0.0	.	70	P01569	IFNA5_HUMAN	E	70	ENSP00000259555:Q70E	ENSP00000259555:Q70E	Q	-	1	0	IFNA5	21295048	0.002000	0.14202	0.014000	0.15608	0.007000	0.05969	1.019000	0.30014	2.052000	0.61016	0.537000	0.68136	CAG	G|0.984;C|0.016	0.016	strong		0.473	IFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051893.1	NM_002169		C	21305048	G	C	21305048	3	2	22	1	0	0	0	0	1	0	0	0	7549	1357	47	4	365	4	IFNA5	9	21305048	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	65470	21305048	119908383	2039	4940											
IFNA6	3443	hgsc.bcm.edu	37	chr9	21350487	21350487	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatggagtcctcattcatcaGgggagtccctcccacccaca	9	8	9	15	0	3	0	3	0	0	0	6	3	6	2	4	3	0	0	4	3	0	1	rs61736258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21350487G>A	ENST00000380210.1	-	1	890	c.400C>T	c.(400-402)Ctg>Ttg	p.L134L		NM_021002.2	NP_066282.1	P05013	IFNA6_HUMAN	interferon, alpha 6	134					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)			large_intestine(3)|lung(7)|skin(1)	11				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)		TCATTCATCAGGGGAGTCCCT	0.498													G|||	124	0.0247604	0.09	0.0072	5008	,	,		20965	0.0		0.0	False		,,,				2504	0.0				p.L134L		Atlas-SNP	.											.	IFNA6	27	.	0			c.C400T						PASS	.	G		351,4055	181.2+/-209.3	15,321,1867	200	202	202		400	0.6	0	9	dbSNP_129	202	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	IFNA6	NM_021002.2		15,323,6165	AA,AG,GG		0.0233,7.9664,2.7141		134/190	21350487	353,12653	2203	4300	6503	SO:0001819	synonymous_variant	3443	exon1			TCATCAGGGGAGT		CCDS6504.1	9p22	2010-12-10			ENSG00000120235	ENSG00000120235		"Interferons"	5427	protein-coding gene	gene with protein product		147566				1385305	Standard	NM_021002		Approved	IFN-alphaK	uc011lni.2	P05013	OTTHUMG00000019676	ENST00000380210.1:c.400C>T	9.37:g.21350487G>A		371	0	0		361	179	0.495845	NM_021002	Q5VYQ1	Silent	SNP	ENST00000380210.1	37	CCDS6504.1																																																																																			G|0.971;A|0.029	0.029	strong		0.498	IFNA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051905.1	NM_021002		A	21350487	G	A	21350487	2	1	22	1	0	0	0	0	0	0	0	1	7550	991	35	2		2	IFNA6	9	21350487	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	45439	21350487	119862944	2040	4941											
IFNA13	3447	hgsc.bcm.edu	37	chr9	21367519	21367519	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctgctctgacaacctcccagGcacaagggctgtatttcttc	8	11	8	14	0	2	1	0	1	2	0	4	1	3	1	2	2	2	4	2	2	3	3	rs145283706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21367519G>C	ENST00000449498.1	-	1	556	c.491C>G	c.(490-492)gCc>gGc	p.A164G		NM_006900.3	NP_008831.3	P01562	IFNA1_HUMAN	interferon, alpha 13	163					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)			breast(2)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)|skin(1)	9				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0173)		AACCTCCCAGGCACAAGGGCT	0.443																																					p.A164G		Atlas-SNP	.											.	IFNA13	19	.	0			c.C491G						PASS	.						108	102	104					9																	21367519		2202	4280	6482	SO:0001583	missense	3447	exon1			TCCCAGGCACAAG		CCDS6505.2	9p22	2010-12-10			ENSG00000233816	ENSG00000233816		"Interferons"	5419	protein-coding gene	gene with protein product		147578				1385305	Standard	NM_006900		Approved		uc003zpa.2	P01562	OTTHUMG00000019675	ENST00000449498.1:c.491C>G	9.37:g.21367519G>C	ENSP00000394494:p.Ala164Gly	569	1	0.00175747		592	229	0.386824	NM_006900	D4Q9M8|Q14605|Q2M1L8|Q52LB8|Q5VYQ2|Q7M4Q1|Q8WZ68|Q9UMJ3	Missense_Mutation	SNP	ENST00000449498.1	37	CCDS6505.2	.	.	.	.	.	.	.	.	.	.	G	19.57	3.852515	0.71719	.	.	ENSG00000233816	ENST00000449498	T	0.18960	2.18	2.56	1.64	0.23874	.	0.126331	0.52532	D	0.000075	T	0.50446	0.1616	M	0.92317	3.295	0.27386	N	0.95527	P	0.39847	0.691	D	0.65140	0.932	T	0.42899	-0.9424	10	0.87932	D	0	.	6.7704	0.23591	0.1469:0.0:0.8531:0.0	.	164	E9PB07	.	G	164	ENSP00000394494:A164G	ENSP00000394494:A164G	A	-	2	0	IFNA13	21357519	1.000000	0.71417	0.994000	0.49952	0.928000	0.56348	2.320000	0.43797	0.402000	0.25451	0.313000	0.20887	GCC	G|0.832;C|0.168	0.168	strong		0.443	IFNA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051904.2	NM_006900		C	21367519	G	C	21367519	3	2	22	1	0	0	0	0	1	0	0	0	7542	1203	42	4	85	4	IFNA13	9	21367519	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	17032	21367519	119845912	2041	4942											
C9orf82	79886	hgsc.bcm.edu	37	chr9	26842506	26842506	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ttctcaatgtctttctccagGtcatctatctgaccagcttc	7	16	5	13	0	6	1	2	1	5	0	9	1	6	1	2	1	1	1	2	1	2	4	rs10967558	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:26842506G>A	ENST00000333916.5	-	6	967	c.879C>T	c.(877-879)gaC>gaT	p.D293D	CAAP1_ENST00000535437.1_Silent_p.D148D|CAAP1_ENST00000520187.1_3'UTR	NM_001167575.1|NM_024828.3	NP_001161047.1|NP_079104.3	Q9H8G2	CAAP1_HUMAN	caspase activity and apoptosis inhibitor 1	293					apoptotic process (GO:0006915)												CTTTCTCCAGGTCATCTATCT	0.502													G|||	242	0.0483227	0.1747	0.0144	5008	,	,		18187	0.0		0.001	False		,,,				2504	0.0				p.D293D		Atlas-SNP	.											.	.	.	.	0			c.C879T						PASS	.	G	,	585,3821	259.5+/-263.1	32,521,1650	244	228	233		444,879	2.9	1	9	dbSNP_120	233	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous	C9orf82	NM_001167575.1,NM_024828.3	,	32,525,5946	AA,AG,GG		0.0465,13.2773,4.5287	,	148/217,293/362	26842506	589,12417	2203	4300	6503	SO:0001819	synonymous_variant	79886	exon6			CTCCAGGTCATCT	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.879C>T	9.37:g.26842506G>A		289	0	0		295	140	0.474576	NM_024828	B4DWT4|D3DRK4|Q5VY32|Q6IPE6|Q96C59	Silent	SNP	ENST00000333916.5	37	CCDS6516.1																																																																																			G|0.941;A|0.059	0.059	strong		0.502	CAAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051954.1	NM_024828		A	26842506	G	A	26842506	2	1	22	1	0	0	0	0	0	0	0	1	2501	1252	44	2		2	C9orf82	9	26842506	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5474987	26842506	114370925	2042	4943											
C9orf82	79886	hgsc.bcm.edu	37	chr9	26861106	26861106	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggttgcttattctctctcaCggatgaagcagaatctatac	11	13	8	9	1	3	2	1	1	3	1	5	3	3	3	0	2	3	3	0	2	5	5	rs12342214	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:26861106C>T	ENST00000333916.5	-	5	785	c.697G>A	c.(697-699)Gtg>Atg	p.V233M	CAAP1_ENST00000535437.1_Missense_Mutation_p.V88M|CAAP1_ENST00000520187.1_Intron|CAAP1_ENST00000495958.1_5'UTR	NM_001167575.1|NM_024828.3	NP_001161047.1|NP_079104.3	Q9H8G2	CAAP1_HUMAN	caspase activity and apoptosis inhibitor 1	233			V -> M (in dbSNP:rs12342214).		apoptotic process (GO:0006915)												TTCTCTCTCACGGATGAAGCA	0.318													T|||	257	0.0513179	0.1868	0.013	5008	,	,		15800	0.0		0.001	False		,,,				2504	0.0				p.V233M		Atlas-SNP	.											.	.	.	.	0			c.G697A						PASS	.	T	MET/VAL,MET/VAL	602,3804	769.0+/-413.6	30,542,1631	95	104	101		262,697	0.6	0.4	9	dbSNP_120	101	3,8597	818.4+/-406.9	0,3,4297	yes	missense,missense	C9orf82	NM_001167575.1,NM_024828.3	21,21	30,545,5928	TT,TC,CC		0.0349,13.6632,4.6517	benign,benign	88/217,233/362	26861106	605,12401	2203	4300	6503	SO:0001583	missense	79886	exon5			CTCTCACGGATGA	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.697G>A	9.37:g.26861106C>T	ENSP00000369431:p.Val233Met	175	0	0		170	72	0.423529	NM_024828	B4DWT4|D3DRK4|Q5VY32|Q6IPE6|Q96C59	Missense_Mutation	SNP	ENST00000333916.5	37	CCDS6516.1	94	0.04304029304029304	89	0.18089430894308944	5	0.013812154696132596	0	0.0	0	0.0	T	11.16	1.556553	0.27827	0.136632	3.49E-4	ENSG00000120159	ENST00000333916;ENST00000535437	T;T	0.44881	0.91;0.92	5.71	0.612	0.17591	.	0.254994	0.31381	N	0.007741	T	0.00039	0.0001	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.06405	0.002	T	0.18272	-1.0342	9	0.33940	T	0.23	0.0412	1.6248	0.02721	0.1489:0.2564:0.3337:0.261	rs12342214;rs52805377;rs12342214	233	Q9H8G2	CI082_HUMAN	M	233;88	ENSP00000369431:V233M;ENSP00000444885:V88M	ENSP00000369431:V233M	V	-	1	0	C9orf82	26851106	0.831000	0.29352	0.434000	0.26772	0.937000	0.57800	-0.048000	0.11944	-0.404000	0.07610	-1.904000	0.00526	GTG	C|0.939;T|0.061	0.061	strong		0.318	CAAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051954.1	NM_024828		T	26861106	C	T	26861106	3	4	22	1	0	0	0	0	1	0	0	0	2501	536	19	1	396	1	C9orf82	9	26861106	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	18600	26861106	114352325	2043	4944											
DDX58	23586	hgsc.bcm.edu	37	chr9	32492529	32492529	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgccatcatccccttagtaGagcaaatctaagcaaggtaa	14	9	7	11	0	2	1	1	0	1	1	3	1	3	1	3	1	3	4	3	1	6	4	rs55789327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:32492529G>A	ENST00000379883.2	-	4	588	c.431C>T	c.(430-432)tCt>tTt	p.S144F	DDX58_ENST00000545044.1_Intron|DDX58_ENST00000379882.1_Missense_Mutation_p.S99F|DDX58_ENST00000542096.1_Missense_Mutation_p.S73F|DDX58_ENST00000379868.1_Intron	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	144	CARD 2.				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)		CCCCTTAGTAGAGCAAATCTA	0.373													G|||	239	0.0477236	0.1104	0.0072	5008	,	,		21117	0.0407		0.0	False		,,,				2504	0.0481				p.S144F		Atlas-SNP	.											.	DDX58	82	.	0			c.C431T						PASS	.	G	PHE/SER	349,4057	179.4+/-207.9	15,319,1869	120	115	117		431	-2	0	9	dbSNP_129	117	6,8594	5.0+/-18.6	0,6,4294	yes	missense	DDX58	NM_014314.3	155	15,325,6163	AA,AG,GG		0.0698,7.921,2.7295	benign	144/926	32492529	355,12651	2203	4300	6503	SO:0001583	missense	23586	exon4			TTAGTAGAGCAAA	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.431C>T	9.37:g.32492529G>A	ENSP00000369213:p.Ser144Phe	208	0	0		203	108	0.53202	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Missense_Mutation	SNP	ENST00000379883.2	37	CCDS6526.1	82	0.037545787545787544	54	0.10975609756097561	4	0.011049723756906077	24	0.04195804195804196	0	0.0	G	8.541	0.873187	0.17322	0.07921	6.98E-4	ENSG00000107201	ENST00000379882;ENST00000379883;ENST00000542096;ENST00000542960	T;T;T	0.35789	1.29;1.29;1.29	5.22	-2.04	0.07343	.	1.364960	0.05002	N	0.469210	T	0.00384	0.0012	N	0.20685	0.6	0.09310	N	1	B;B;B	0.10296	0.003;0.002;0.002	B;B;B	0.09377	0.004;0.002;0.002	T	0.21109	-1.0255	10	0.56958	D	0.05	0.2274	1.0358	0.01548	0.407:0.1539:0.2819:0.1572	rs55789327	99;73;144	O95786-2;B3KWW1;O95786	.;.;DDX58_HUMAN	F	99;144;73;144	ENSP00000369212:S99F;ENSP00000369213:S144F;ENSP00000442160:S73F	ENSP00000369212:S99F	S	-	2	0	DDX58	32482529	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.367000	0.07553	-0.191000	0.10448	-0.157000	0.13467	TCT	G|0.972;A|0.028	0.028	strong		0.373	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314		A	32492529	G	A	32492529	3	1	22	1	0	0	0	0	1	0	0	0	4377	942	33	2	2406	2	DDX58	9	32492529	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5631423	32492529	108720902	2044	4945											
APTX	54840	hgsc.bcm.edu	37	chr9	32984803	32984803	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtaagaccagccaatggtaaCgggcctttgggtatttatcc	10	11	11	9	1	0	1	0	0	0	1	1	1	1	1	4	3	2	3	4	3	5	6	rs150886026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:32984803C>T	ENST00000379819.1	-	6	637	c.638G>A	c.(637-639)cGt>cAt	p.R213H	APTX_ENST00000463596.1_Missense_Mutation_p.R199H|APTX_ENST00000468275.1_Missense_Mutation_p.R199H|APTX_ENST00000309615.3_Missense_Mutation_p.R213H|APTX_ENST00000476858.1_Missense_Mutation_p.R159H|APTX_ENST00000379813.3_Missense_Mutation_p.R199H|APTX_ENST00000397172.3_Missense_Mutation_p.R141H|APTX_ENST00000379825.2_Missense_Mutation_p.R213H|APTX_ENST00000379817.2_Missense_Mutation_p.R199H|APTX_ENST00000436040.2_Intron			Q7Z2E3	APTX_HUMAN	aprataxin	213	HIT. {ECO:0000255|PROSITE- ProRule:PRU00464}.		R -> H (in AOA; dbSNP:rs150886026). {ECO:0000269|PubMed:11586300}.		cell death (GO:0008219)|cellular response to DNA damage stimulus (GO:0006974)|dephosphorylation (GO:0016311)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA ligation (GO:0006266)|double-strand break repair (GO:0006302)|polynucleotide 3' dephosphorylation (GO:0098506)|regulation of protein stability (GO:0031647)|response to hydrogen peroxide (GO:0042542)|single strand break repair (GO:0000012)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA 5'-adenosine monophosphate hydrolase activity (GO:0033699)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|phosphoglycolate phosphatase activity (GO:0008967)|phosphoprotein binding (GO:0051219)|polynucleotide 3'-phosphatase activity (GO:0046403)|protein N-terminus binding (GO:0047485)			endometrium(1)|lung(1)|ovary(2)|prostate(2)	6			LUSC - Lung squamous cell carcinoma(29;0.0302)	GBM - Glioblastoma multiforme(74;0.105)		CCAATGGTAACGGGCCTTTGG	0.473								Editing and processing nucleases					C|||	31	0.0061901	0.0197	0.0058	5008	,	,		21579	0.0		0.0	False		,,,				2504	0.001				p.R213H		Atlas-SNP	.											.	APTX	44	.	0			c.G638A	GRCh37	CM012895	APTX	M	rs150886026	PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	80,4326	69.2+/-107.0	0,80,2123	162	146	152		638,596,476,596,422,434,638,596	4	0.8	9	dbSNP_134	152	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense,missense,missense	APTX	NM_001195248.1,NM_001195249.1,NM_001195250.1,NM_001195251.1,NM_001195252.1,NM_001195254.1,NM_175069.2,NM_175073.2	29,29,29,29,29,29,29,29	0,80,6423	TT,TC,CC		0.0,1.8157,0.6151	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	213/357,199/343,159/303,199/293,141/285,145/289,213/307,199/343	32984803	80,12926	2203	4300	6503	SO:0001583	missense	54840	exon6			TGGTAACGGGCCT	AK000164	CCDS47956.1, CCDS56568.1, CCDS75827.1	9p13.3	2014-01-28	2003-04-03		ENSG00000137074	ENSG00000137074			15984	protein-coding gene	gene with protein product		606350	"ataxia 1, early onset with hypoalbuminemia"	AXA1		11586299, 11586300	Standard	NM_175069		Approved	FLJ20157, AOA, AOA1, EAOH, EOAHA	uc003zry.3	Q7Z2E3	OTTHUMG00000019759	ENST00000379819.1:c.638G>A	9.37:g.32984803C>T	ENSP00000369147:p.Arg213His	108	0	0		112	63	0.5625	NM_001195248	A8MTN4|D3DRK9|D3DRL0|Q0P662|Q5T781|Q5T782|Q5T784|Q6JV81|Q6JV82|Q6JV85|Q7Z2F3|Q7Z336|Q7Z5R5|Q7Z6V7|Q7Z6V8|Q9NXM5	Missense_Mutation	SNP	ENST00000379819.1	37		9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	C	13.81	2.348650	0.41599	0.018157	0.0	ENSG00000137074	ENST00000379825;ENST00000309615;ENST00000397172;ENST00000379817;ENST00000379819;ENST00000468275;ENST00000463596;ENST00000476858;ENST00000344355;ENST00000379813;ENST00000379812;ENST00000473221;ENST00000477119	D;D;D;D;D;D;D;D;D;D;D;D	0.95656	-3.77;-3.77;-2.86;-2.86;-2.86;-2.86;-2.86;-2.86;-2.86;-3.77;-3.77;-3.77	5.81	3.96	0.45880	Histidine triad motif (1);Histidine triad-like motif (1);	0.047355	0.85682	D	0.000000	D	0.92257	0.7544	M	0.64170	1.965	0.80722	D	1	D;P;P;P;P	0.64830	0.994;0.864;0.632;0.769;0.632	P;B;B;B;B	0.55785	0.784;0.304;0.288;0.352;0.288	D	0.91337	0.5094	10	0.52906	T	0.07	-11.4381	11.0972	0.48152	0.0:0.8459:0.0:0.1541	.	159;141;213;145;213	C9JZ40;Q7Z2E3-3;Q5T782;Q7Z2E3-5;Q7Z2E3	.;.;.;.;APTX_HUMAN	H	213;213;141;199;213;199;199;159;194;199;141;159;145	ENSP00000369153:R213H;ENSP00000311547:R213H;ENSP00000380357:R141H;ENSP00000369145:R199H;ENSP00000369147:R213H;ENSP00000420263:R199H;ENSP00000419846:R199H;ENSP00000419042:R159H;ENSP00000369141:R199H;ENSP00000369140:R141H;ENSP00000419020:R159H;ENSP00000417649:R145H	ENSP00000311547:R213H	R	-	2	0	APTX	32974803	1.000000	0.71417	0.798000	0.32154	0.012000	0.07955	6.082000	0.71318	1.451000	0.47736	0.655000	0.94253	CGT	C|0.994;T|0.006	0.006	strong		0.473	APTX-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000052028.2	NM_017692		T	32984803	C	T	32984803	3	4	22	1	0	0	0	0	1	0	0	0	820	536	19	1	453	1	APTX	9	32984803	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	492274	32984803	108228628	2045	4946											
AQP7	364	hgsc.bcm.edu	37	chr9	33385134	33385134	+	3'UTR	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agatcccatcttgggcaataCggttatcccgtggtcttcat	8	13	9	11	2	3	1	1	0	2	1	5	1	5	1	2	3	1	2	2	3	3	4	rs61073250	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:33385134C>T	ENST00000537089.1	-	0	1298				AQP7_ENST00000377425.4_3'UTR			O14520	AQP7_HUMAN	aquaporin 7						excretion (GO:0007588)|generation of precursor metabolites and energy (GO:0006091)|glycerol transport (GO:0015793)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glycerol channel activity (GO:0015254)|water channel activity (GO:0015250)			NS(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(4)|skin(2)|stomach(1)	17			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		TTGGGCAATACGGTTATCCCG	0.562													c|||	234	0.0467252	0.1732	0.0072	5008	,	,		18995	0.0		0.0	False		,,,				2504	0.0				p.V300I		Atlas-SNP	.											.	AQP7	58	.	0			c.G898A						PASS	.	C	ILE/VAL	519,3887	236.1+/-248.4	25,469,1709	142	140	141		898	0.9	0	9	dbSNP_129	141	8,8592	6.4+/-24.3	0,8,4292	no	missense	AQP7	NM_001170.1	29	25,477,6001	TT,TC,CC		0.093,11.7794,4.052	benign	300/343	33385134	527,12479	2203	4300	6503	SO:0001624	3_prime_UTR_variant	364	exon8			GCAATACGGTTAT	AB006190	CCDS6541.1	9p13	2008-02-05			ENSG00000165269	ENSG00000165269		"Ion channels / Aquaporins"	640	protein-coding gene	gene with protein product		602974		AQP7L		9252401	Standard	NM_001170		Approved	AQP9, AQPap	uc003zst.3	O14520	OTTHUMG00000019773	ENST00000537089.1:c.*482G>A	9.37:g.33385134C>T		113	0	0		150	87	0.58	NM_001170	Q08E94|Q5T5L9|Q8NHM3	Missense_Mutation	SNP	ENST00000537089.1	37		76	0.0347985347985348	73	0.1483739837398374	3	0.008287292817679558	0	0.0	0	0.0	c	10.83	1.461549	0.26248	0.117794	9.3E-4	ENSG00000165269	ENST00000379507;ENST00000297988	D;D	0.86164	-2.07;-2.08	3.75	0.85	0.18980	.	.	.	.	.	T	0.01124	0.0037	L	0.32530	0.975	0.09310	N	1	B	0.26602	0.154	B	0.17098	0.017	T	0.04128	-1.0975	9	0.39692	T	0.17	0.5079	3.07	0.06227	0.2121:0.5537:0.0:0.2342	rs61073250	300	O14520	AQP7_HUMAN	I	299;300	ENSP00000368821:V299I;ENSP00000297988:V300I	ENSP00000297988:V300I	V	-	1	0	AQP7	33375134	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.123000	0.10611	-0.001000	0.14495	-0.354000	0.07668	GTA	C|0.964;T|0.036	0.036	strong		0.562	AQP7-202	KNOWN	basic	protein_coding	protein_coding		NM_001170		T	33385134	C	T	33385134	1	4	22	0	1	0	0	0	0	0	0	0	831	536	19	1		1	AQP7	9	33385134	3'UTR	SNP	C	TCGA-G8-6324-01A-11D-2210-10	400331	33385134	107828297	2046	4947											
UBAP2	55833	hgsc.bcm.edu	37	chr9	33927880	33927880	+	Nonstop_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cagaggctgttcgcggtgttCatgctactggacaggctggc	6	10	15	10	2	1	1	1	0	0	1	2	2	1	2	0	5	2	5	0	5	1	3	rs16935295	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:33927880C>G	ENST00000418786.2	-	17	2152	c.2060G>C	c.(2059-2061)tGa>tCa	p.*687S	UBAP2_ENST00000539807.1_Missense_Mutation_p.M517I|UBAP2_ENST00000449054.1_Missense_Mutation_p.M762I|UBAP2_ENST00000379238.1_Missense_Mutation_p.M762I|UBAP2_ENST00000379235.1_Start_Codon_SNP_p.M1I|UBAP2_ENST00000360802.1_Missense_Mutation_p.M762I|UBAP2_ENST00000379239.4_Missense_Mutation_p.M495I					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)		TCGCGGTGTTCATGCTACTGG	0.637													C|||	151	0.0301518	0.1104	0.0058	5008	,	,		19308	0.0		0.001	False		,,,				2504	0.0				p.M762I		Atlas-SNP	.											.	UBAP2	82	.	0			c.G2286C						PASS	.	C	ILE/MET	448,3958	214.8+/-234.0	24,400,1779	90	87	88		2286	4.8	0.7	9	dbSNP_123	88	6,8594	5.0+/-18.6	0,6,4294	yes	missense	UBAP2	NM_018449.2	10	24,406,6073	GG,GC,CC		0.0698,10.168,3.4907	benign	762/1120	33927880	454,12552	2203	4300	6503	SO:0001578	stop_lost	55833	exon20			GGTGTTCATGCTA	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	ENST00000418786.2:c.2060G>C	9.37:g.33927880C>G		140	0	0		142	88	0.619718	NM_018449		Missense_Mutation	SNP	ENST00000418786.2	37		43|43	0.019688644688644688|0.019688644688644688	40|40	0.08130081300813008|0.08130081300813008	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	C|C	11.68|11.68	1.711377|1.711377	0.30322|0.30322	0.10168|0.10168	6.98E-4|6.98E-4	ENSG00000137073|ENSG00000137073	ENST00000379238;ENST00000449054;ENST00000360802;ENST00000431417;ENST00000379235;ENST00000379239;ENST00000539807;ENST00000351580|ENST00000418786	T;T;T;T;T;T|.	0.33216|.	1.66;1.66;1.66;1.42;1.66;1.66|.	5.77|5.77	4.85|4.85	0.62838|0.62838	.|.	0.315392|.	0.42682|.	D|.	0.000678|.	T|.	0.02267|.	0.0070|.	L|L	0.50919|0.50919	1.6|1.6	0.09310|0.09310	N|N	1|1	B;B;B;B;B|.	0.12013|.	0.005;0.002;0.002;0.002;0.003|.	B;B;B;B;B|.	0.09377|.	0.004;0.004;0.004;0.004;0.002|.	T|.	0.00761|.	-1.1577|.	10|.	0.23891|.	T|.	0.37|.	-1.1258|-1.1258	16.2411|16.2411	0.82409|0.82409	0.0:0.8668:0.1332:0.0|0.0:0.8668:0.1332:0.0	rs16935295;rs52823002;rs16935295|rs16935295;rs52823002;rs16935295	687;517;495;671;762|.	F5H4D5;F5H2U4;A6NCA8;F5H2C8;Q5T6F2|.	.;.;.;.;UBAP2_HUMAN|.	I|S	762;762;762;671;1;495;517;198|687	ENSP00000368540:M762I;ENSP00000416932:M762I;ENSP00000354039:M762I;ENSP00000368537:M1I;ENSP00000368541:M495I;ENSP00000439329:M517I|.	ENSP00000259602:M198I|.	M|X	-|-	3|2	0|2	UBAP2|UBAP2	33917880|33917880	1.000000|1.000000	0.71417|0.71417	0.710000|0.710000	0.30468|0.30468	0.061000|0.061000	0.15899|0.15899	1.399000|1.399000	0.34566|0.34566	1.383000|1.383000	0.46405|0.46405	0.655000|0.655000	0.94253|0.94253	ATG|TGA	C|0.965;G|0.035	0.035	strong		0.637	UBAP2-203	KNOWN	basic	protein_coding	protein_coding		NM_018449		G	33927880	C	G	33927880	4	3	22	1	0	0	0	0	0	0	0	0	16852	826	29	4	1113	4	UBAP2	9	33927880	Nonstop_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	542746	33927880	107285551	2047	4948											
UNC13B	10497	hgsc.bcm.edu	37	chr9	35398900	35398900	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccaggtacggattgatgaGtgtgttcgacaaatggccga	10	11	13	7	3	0	2	0	2	0	0	2	5	1	3	2	3	1	2	2	3	2	4	rs12339582	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35398900G>T	ENST00000378495.3	+	32	3918	c.3696G>T	c.(3694-3696)gaG>gaT	p.E1232D	UNC13B_ENST00000378496.4_Missense_Mutation_p.E1232D|UNC13B_ENST00000396787.1_Missense_Mutation_p.E1244D|UNC13B_ENST00000481299.1_3'UTR	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	1232			E -> D (in dbSNP:rs12339582).		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)			GGATTGATGAGTGTGTTCGAC	0.582													G|||	153	0.0305511	0.1067	0.0043	5008	,	,		21512	0.0079		0.001	False		,,,				2504	0.0				p.E1232D		Atlas-SNP	.											.	UNC13B	153	.	0			c.G3696T						PASS	.	G	ASP/GLU	379,4027	191.9+/-217.4	16,347,1840	126	129	128		3696	4.1	1	9	dbSNP_120	128	4,8596	3.7+/-12.6	0,4,4296	yes	missense	UNC13B	NM_006377.3	45	16,351,6136	TT,TG,GG		0.0465,8.6019,2.9448	benign	1232/1592	35398900	383,12623	2203	4300	6503	SO:0001583	missense	10497	exon32			TGATGAGTGTGTT	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.3696G>T	9.37:g.35398900G>T	ENSP00000367756:p.Glu1232Asp	186	0	0		200	88	0.44	NM_006377	Q5VYM8	Missense_Mutation	SNP	ENST00000378495.3	37	CCDS6579.1	69	0.03159340659340659	62	0.12601626016260162	2	0.0055248618784530384	4	0.006993006993006993	1	0.0013192612137203166	G	13.61	2.288018	0.40494	0.086019	4.65E-4	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496;ENST00000535471	T;T;T	0.10099	2.91;2.91;2.91	5.94	4.07	0.47477	.	0.102509	0.64402	D	0.000003	T	0.00073	0.0002	N	0.25332	0.735	0.50171	D	0.999858	B;B	0.15473	0.013;0.011	B;B	0.14023	0.009;0.01	T	0.52223	-0.8604	10	0.24483	T	0.36	-27.2563	7.8494	0.29446	0.1495:0.1355:0.715:0.0	rs12339582;rs17849224;rs12339582	1232;1232	F8W8M9;O14795	.;UN13B_HUMAN	D	1244;1232;1232;819	ENSP00000380006:E1244D;ENSP00000367756:E1232D;ENSP00000367757:E1232D	ENSP00000367756:E1232D	E	+	3	2	UNC13B	35388900	0.992000	0.36948	1.000000	0.80357	0.998000	0.95712	0.238000	0.18004	1.493000	0.48517	0.557000	0.71058	GAG	G|0.960;T|0.040	0.040	strong		0.582	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377		T	35398900	G	T	35398900	3	4	22	1	0	0	0	0	1	0	0	0	17000	1020	36	4	3822	4	UNC13B	9	35398900	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1471020	35398900	105814531	2048	4949											
TESK1	7016	hgsc.bcm.edu	37	chr9	35608962	35608962	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cccccatcaccagaatcaccCcccaactggggggacaatct	11	5	7	18	0	3	1	2	0	1	1	3	2	3	2	6	3	1	0	6	3	3	0	rs148341917	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35608962C>T	ENST00000336395.5	+	10	1354	c.1104C>T	c.(1102-1104)ccC>ccT	p.P368P	MIR4667_ENST00000578933.1_RNA|CD72_ENST00000490239.1_5'Flank|TESK1_ENST00000498522.1_3'UTR	NM_006285.2	NP_006276.2	Q15569	TESK1_HUMAN	testis-specific kinase 1	368					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)			CAGAATCACCCCCCAACTGGG	0.607													C|||	30	0.00599042	0.0129	0.0014	5008	,	,		17980	0.001		0.002	False		,,,				2504	0.0092				p.P368P		Atlas-SNP	.											.	TESK1	46	.	0			c.C1104T						PASS	.	C		63,4343	58.7+/-95.3	0,63,2140	63	70	68		1104	3.4	1	9	dbSNP_134	68	25,8575	17.3+/-56.4	0,25,4275	no	coding-synonymous	TESK1	NM_006285.2		0,88,6415	TT,TC,CC		0.2907,1.4299,0.6766		368/627	35608962	88,12918	2203	4300	6503	SO:0001819	synonymous_variant	7016	exon10			ATCACCCCCCAAC	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.1104C>T	9.37:g.35608962C>T		59	0	0		73	38	0.520548	NM_006285	Q8IXZ8	Silent	SNP	ENST00000336395.5	37	CCDS6580.1																																																																																			C|0.994;T|0.006	0.006	strong		0.607	TESK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052314.1	NM_006285		T	35608962	C	T	35608962	2	4	22	1	0	0	0	0	0	0	0	1	15782	610	22	2		2	TESK1	9	35608962	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	210062	35608962	105604469	2049	4950											
CCDC107	203260	hgsc.bcm.edu	37	chr9	35661057	35661057	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	gacatggaacctagctacttCctgggaggtggggcggggac	8	7	17	9	1	0	0	0	0	0	0	1	4	1	3	2	7	3	1	2	7	3	3	rs10441685	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35661057C>G	ENST00000426546.2	+	5	791	c.725C>G	c.(724-726)tCc>tGc	p.S242C	CCDC107_ENST00000378407.3_3'UTR|CCDC107_ENST00000378409.3_Missense_Mutation_p.S215C|ARHGEF39_ENST00000343259.3_3'UTR|ARHGEF39_ENST00000378395.2_3'UTR|CCDC107_ENST00000378406.1_3'UTR|ARHGEF39_ENST00000490970.1_5'Flank|ARHGEF39_ENST00000378387.3_3'UTR|CCDC107_ENST00000421582.2_3'UTR|CCDC107_ENST00000327351.2_3'UTR	NM_001195200.1|NM_001195201.1|NM_001195217.1|NM_174923.2	NP_001182129.1|NP_001182130.1|NP_001182146.1|NP_777583.2	Q8WV48	CC107_HUMAN	coiled-coil domain containing 107	242			S -> C (in dbSNP:rs10441685).			integral component of membrane (GO:0016021)				endometrium(1)|lung(3)|skin(1)	5	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CTAGCTACTTCCTGGGAGGTG	0.597													C|||	358	0.0714856	0.1982	0.0216	5008	,	,		19531	0.0139		0.0338	False		,,,				2504	0.0337				p.S242C		Atlas-SNP	.											.	CCDC107	12	.	0			c.C725G						PASS	.	C	CYS/SER,,,,CYS/SER	698,3708	290.4+/-280.9	47,604,1552	72	71	71		644,,,,725	4.4	0	9	dbSNP_119	71	229,8371	93.1+/-155.1	2,225,4073	no	missense,utr-3,utr-3,utr-3,missense	C9orf100,CCDC107	NM_001195200.1,NM_001195201.1,NM_001195217.1,NM_032818.2,NM_174923.2	112,,,,112	49,829,5625	GG,GC,CC		2.6628,15.842,7.1275	possibly-damaging,,,,possibly-damaging	215/257,,,,242/284	35661057	927,12079	2203	4300	6503	SO:0001583	missense	203260	exon5			CTACTTCCTGGGA	AK075523	CCDS6583.1, CCDS56573.1, CCDS56574.1, CCDS56575.1	9q13.3	2008-02-05			ENSG00000159884	ENSG00000159884			28465	protein-coding gene	gene with protein product						12477932	Standard	NM_174923		Approved	MGC31967	uc011lox.2	Q8WV48	OTTHUMG00000019868	ENST00000426546.2:c.725C>G	9.37:g.35661057C>G	ENSP00000414964:p.Ser242Cys	119	0	0		116	52	0.448276	NM_174923	A6XND6|Q5T4R5|Q5T4R8|Q5T4R9|Q86VB6|Q8N2E4	Missense_Mutation	SNP	ENST00000426546.2	37	CCDS6583.1	145	0.06639194139194139	99	0.20121951219512196	10	0.027624309392265192	9	0.015734265734265736	27	0.03562005277044855	C	10.84	1.464832	0.26335	0.15842	0.026628	ENSG00000159884	ENST00000426546;ENST00000378409	T;T	0.39592	1.48;1.07	5.34	4.44	0.53790	.	0.688813	0.13667	N	0.371165	T	0.00039	0.0001	L	0.34521	1.04	0.40203	P	0.022464999999999957	D;D	0.61697	0.99;0.99	P;P	0.53549	0.729;0.729	T	0.06058	-1.0848	9	0.48119	T	0.1	-0.1448	9.9115	0.41408	0.0:0.9082:0.0:0.0918	rs10441685	215;242	F8W8S5;Q8WV48	.;CC107_HUMAN	C	242;215	ENSP00000414964:S242C;ENSP00000367665:S215C	ENSP00000367665:S215C	S	+	2	0	CCDC107	35651057	0.014000	0.17966	0.007000	0.13788	0.048000	0.14542	1.958000	0.40402	1.487000	0.48415	0.655000	0.94253	TCC	C|0.929;G|0.071	0.071	strong		0.597	CCDC107-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052325.1	NM_174923		G	35661057	C	G	35661057	3	3	22	1	0	0	0	0	1	0	0	0	2744	855	30	4	743	4	CCDC107	9	35661057	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	52095	35661057	105552374	2050	4951											
CCDC107	203260	hgsc.bcm.edu	37	chr9	35661088	35661088	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gggcggggactacggagaagGtgcagccaggctgtggcaaa	10	4	19	8	2	0	1	0	0	0	1	0	3	0	2	1	7	3	3	1	7	3	1	rs10441686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35661088G>A	ENST00000426546.2	+	5	822	c.756G>A	c.(754-756)agG>agA	p.R252R	CCDC107_ENST00000378407.3_3'UTR|CCDC107_ENST00000378409.3_Silent_p.R225R|ARHGEF39_ENST00000343259.3_3'UTR|ARHGEF39_ENST00000378395.2_3'UTR|CCDC107_ENST00000378406.1_3'UTR|ARHGEF39_ENST00000490970.1_5'Flank|ARHGEF39_ENST00000378387.3_3'UTR|CCDC107_ENST00000421582.2_3'UTR|CCDC107_ENST00000327351.2_3'UTR	NM_001195200.1|NM_001195201.1|NM_001195217.1|NM_174923.2	NP_001182129.1|NP_001182130.1|NP_001182146.1|NP_777583.2	Q8WV48	CC107_HUMAN	coiled-coil domain containing 107	252						integral component of membrane (GO:0016021)				endometrium(1)|lung(3)|skin(1)	5	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TACGGAGAAGGTGCAGCCAGG	0.572													G|||	357	0.0712859	0.1982	0.0216	5008	,	,		19466	0.0139		0.0328	False		,,,				2504	0.0337				p.R252R		Atlas-SNP	.											.	CCDC107	12	.	0			c.G756A						PASS	.	G	,,,,	694,3712	290.7+/-281.1	47,600,1556	63	64	64		675,,,,756	0.4	1	9	dbSNP_119	64	229,8371	93.8+/-155.7	2,225,4073	no	coding-synonymous,utr-3,utr-3,utr-3,coding-synonymous	C9orf100,CCDC107	NM_001195200.1,NM_001195201.1,NM_001195217.1,NM_032818.2,NM_174923.2	,,,,	49,825,5629	AA,AG,GG		2.6628,15.7512,7.0967	,,,,	225/257,,,,252/284	35661088	923,12083	2203	4300	6503	SO:0001819	synonymous_variant	203260	exon5			GAGAAGGTGCAGC	AK075523	CCDS6583.1, CCDS56573.1, CCDS56574.1, CCDS56575.1	9q13.3	2008-02-05			ENSG00000159884	ENSG00000159884			28465	protein-coding gene	gene with protein product						12477932	Standard	NM_174923		Approved	MGC31967	uc011lox.2	Q8WV48	OTTHUMG00000019868	ENST00000426546.2:c.756G>A	9.37:g.35661088G>A		133	0	0		134	64	0.477612	NM_174923	A6XND6|Q5T4R5|Q5T4R8|Q5T4R9|Q86VB6|Q8N2E4	Silent	SNP	ENST00000426546.2	37	CCDS6583.1																																																																																			G|0.925;A|0.075	0.075	strong		0.572	CCDC107-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052325.1	NM_174923		A	35661088	G	A	35661088	2	1	22	1	0	0	0	0	0	0	0	1	2744	1252	44	2		2	CCDC107	9	35661088	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	31	35661088	105552343	2051	4952											
TLN1	7094	hgsc.bcm.edu	37	chr9	35714269	35714269	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtccggagttcagccagcgcGgtgcccaggttcttggcaca	6	8	14	13	3	2	0	1	0	1	0	3	1	3	1	3	4	3	3	3	4	0	3	rs35844106	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35714269G>A	ENST00000314888.9	-	24	3440	c.3087C>T	c.(3085-3087)acC>acT	p.T1029T	TLN1_ENST00000540444.1_Silent_p.T1029T	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1029					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)			CAGCCAGCGCGGTGCCCAGGT	0.582													G|||	22	0.00439297	0.0166	0.0	5008	,	,		21795	0.0		0.0	False		,,,				2504	0.0				p.T1029T		Atlas-SNP	.											.	TLN1	185	.	0			c.C3087T						PASS	.	G		63,4343	58.1+/-94.6	0,63,2140	58	55	56		3087	-11.8	0	9	dbSNP_126	56	0,8600		0,0,4300	yes	coding-synonymous	TLN1	NM_006289.3		0,63,6440	AA,AG,GG		0.0,1.4299,0.4844		1029/2542	35714269	63,12943	2203	4300	6503	SO:0001819	synonymous_variant	7094	exon24			CAGCGCGGTGCCC	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.3087C>T	9.37:g.35714269G>A		98	0	0		87	45	0.517241	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Silent	SNP	ENST00000314888.9	37	CCDS35009.1																																																																																			G|0.995;A|0.005	0.005	strong		0.582	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		A	35714269	G	A	35714269	2	1	22	1	0	0	0	0	0	0	0	1	15962	1103	39	1		1	TLN1	9	35714269	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	53181	35714269	105499162	2052	4953											
MSMP	692094	hgsc.bcm.edu	37	chr9	35754052	35754052	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtgctggaggagtagagaCatcaccaagcagatgatccc	12	6	14	9	0	1	3	1	1	0	2	2	6	2	5	2	3	2	3	2	3	2	1	rs189235807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35754052C>T	ENST00000436428.2	-	1	214	c.75G>A	c.(73-75)atG>atA	p.M25I	RP11-112J3.15_ENST00000425499.2_RNA|MSMP_ENST00000414286.1_Intron|RGP1_ENST00000378078.4_3'UTR	NM_001044264.2	NP_001037729.1	Q1L6U9	MSMP_HUMAN	microseminoprotein, prostate associated	25						cytoplasm (GO:0005737)|extracellular space (GO:0005615)				endometrium(2)|kidney(1)|lung(3)|prostate(3)	9						GGAGTAGAGACATCACCAAGC	0.577													C|||	11	0.00219649	0.0076	0.0	5008	,	,		19648	0.0		0.0	False		,,,				2504	0.001				p.M25I		Atlas-SNP	.											.	MSMP	15	.	0			c.G75A						PASS	.	C	ILE/MET	14,4138		0,14,2062	158	168	165		75	-7.9	0.5	9		165	0,8454		0,0,4227	yes	missense	MSMP	NM_001044264.2	10	0,14,6289	TT,TC,CC		0.0,0.3372,0.1111	benign	25/140	35754052	14,12592	2076	4227	6303	SO:0001583	missense	692094	exon1			TAGAGACATCACC	DQ012170	CCDS43797.1	9p13.3	2012-10-02			ENSG00000215183	ENSG00000215183			29663	protein-coding gene	gene with protein product		612191				17338636	Standard	NM_001044264		Approved	PC-3, PSMP	uc003zyb.2	Q1L6U9	OTTHUMG00000019882	ENST00000436428.2:c.75G>A	9.37:g.35754052C>T	ENSP00000419194:p.Met25Ile	161	0	0		139	63	0.453237	NM_001044264		Missense_Mutation	SNP	ENST00000436428.2	37	CCDS43797.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	8.661	0.900498	0.17686	0.003372	0.0	ENSG00000215183	ENST00000436428	T	0.40476	1.03	5.92	-7.93	0.01156	.	1.391910	0.05859	N	0.622637	T	0.12050	0.0293	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20907	-1.0261	10	0.08599	T;T	0.76;0.76	.	4.3929	0.11350	0.1292:0.1236:0.4683:0.2788	.	25	Q1L6U9	MSMP_HUMAN	I	25	ENSP00000419194:M25I	ENSP00000419194:M25I;ENSP00000419194:M25I	M	-	3	0	MSMP	35744052	0.000000	0.05858	0.494000	0.27515	0.988000	0.76386	-3.267000	0.00533	-0.951000	0.03654	-0.140000	0.14226	ATG	C|1.000;T|0.000	0.000	strong		0.577	MSMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052384.2	NM_001044264		T	35754052	C	T	35754052	3	4	22	1	0	0	0	0	1	0	0	0	9893	478	17	2	356	2	MSMP	9	35754052	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	39783	35754052	105459379	2053	4954											
SPAG8	4882	hgsc.bcm.edu	37	chr9	35811215	35811215	+	IGR	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagaggaggcactggccccgCggcaaagtttcatagcaaac	12	6	12	11	2	1	1	1	0	0	1	1	2	1	2	2	4	2	4	2	4	4	3	rs73444820	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35811215C>T	ENST00000342694.2	+	0	3686				AL133410.1_ENST00000582432.1_RNA|HINT2_ENST00000474908.1_5'Flank|SPAG8_ENST00000484764.1_Silent_p.P274P|SPAG8_ENST00000396638.2_Silent_p.P276P|SPAG8_ENST00000340291.2_Silent_p.P276P|SPAG8_ENST00000479751.1_5'UTR	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)	ACTGGCCCCGCGGCAAAGTTT	0.507													c|||	99	0.0197684	0.0734	0.0029	5008	,	,		17255	0.0		0.0	False		,,,				2504	0.0				p.P276P		Atlas-SNP	.											SPAG8_ENST00000396638,caecum,carcinoma,0,2	SPAG8	67	2	0			c.G828A						scavenged	.	C	,	276,4130	148.0+/-182.4	7,262,1934	95	109	104		828,828	0.7	1	9	dbSNP_130	104	3,8597	3.0+/-9.4	0,3,4297	yes	coding-synonymous,coding-synonymous	SPAG8	NM_001039592.1,NM_172312.1	,	7,265,6231	TT,TC,CC		0.0349,6.2642,2.1452	,	276/486,276/502	35811215	279,12727	2203	4300	6503	SO:0001628	intergenic_variant	26206	exon2			GCCCCGCGGCAAA	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		9.37:g.35811215C>T		89	1	0.011236		100	71	0.71	NM_001039592	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Silent	SNP	ENST00000342694.2	37	CCDS6590.1	26	0.011904761904761904	26	0.052845528455284556	0	0.0	0	0.0	0	0.0	c	6.691	0.496043	0.12762	0.062642	3.49E-4	ENSG00000137098	ENST00000497810	.	.	.	5.65	0.724	0.18236	.	.	.	.	.	T	0.11410	0.0278	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.05500	-1.0881	4	.	.	.	-7.0172	7.2861	0.26340	0.0:0.4303:0.0:0.5697	.	.	.	.	H	274	.	.	R	-	2	0	SPAG8	35801215	0.477000	0.25909	0.964000	0.40570	0.648000	0.38561	-1.146000	0.03191	0.200000	0.20447	-0.285000	0.09966	CGC	C|0.978;T|0.022	0.022	strong		0.507	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1			T	35811215	C	T	35811215	1	4	22	0	1	0	0	0	0	0	0	0	14999	755	27	1		1	SPAG8	9	35811215	IGR	SNP	C	TCGA-G8-6324-01A-11D-2210-10	57163	35811215	105402216	2054	4955											
SPAG8	4882	hgsc.bcm.edu	37	chr9	35811749	35811749	+	IGR	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtgggtaaagccgggtccCgcacagggctccccaagaag	9	6	14	12	2	0	1	0	0	0	1	2	1	2	1	4	3	1	3	4	3	4	2	rs79261709	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35811749C>T	ENST00000342694.2	+	0	3686				TMEM8B_ENST00000377996.1_5'Flank|AL133410.1_ENST00000582432.1_RNA|HINT2_ENST00000474908.1_5'Flank|SPAG8_ENST00000484764.1_Silent_p.A96A|SPAG8_ENST00000396638.2_Silent_p.A98A|SPAG8_ENST00000340291.2_Silent_p.A98A|SPAG8_ENST00000479751.1_5'Flank	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)	AGCCGGGTCCCGCACAGGGCT	0.547													c|||	68	0.0135783	0.0492	0.0043	5008	,	,		17978	0.0		0.0	False		,,,				2504	0.0				p.A98A		Atlas-SNP	.											.	SPAG8	67	.	0			c.G294A						PASS	.	C	,	184,4222	115.0+/-153.0	2,180,2021	56	68	64		294,294	-2.2	0	9	dbSNP_131	64	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SPAG8	NM_001039592.1,NM_172312.1	,	2,180,6321	TT,TC,CC		0.0,4.1761,1.4147	,	98/486,98/502	35811749	184,12822	2203	4300	6503	SO:0001628	intergenic_variant	26206	exon2			GGGTCCCGCACAG	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		9.37:g.35811749C>T		80	0	0		76	44	0.578947	NM_001039592	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Silent	SNP	ENST00000342694.2	37	CCDS6590.1	19	0.0086996336996337	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	c	5.786	0.329334	0.10956	0.041761	0.0	ENSG00000137098	ENST00000497810	.	.	.	5.3	-2.21	0.06973	.	.	.	.	.	T	0.04003	0.0112	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.20538	-1.0272	4	.	.	.	3.7726	0.3647	0.00370	0.3138:0.2293:0.2557:0.2013	.	.	.	.	Q	96	.	.	R	-	2	0	SPAG8	35801749	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.424000	0.07025	-0.264000	0.09365	-0.710000	0.03640	CGG	C|0.988;T|0.012	0.012	strong		0.547	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1			T	35811749	C	T	35811749	1	4	22	0	1	0	0	0	0	0	0	0	14999	639	23	1		1	SPAG8	9	35811749	IGR	SNP	C	TCGA-G8-6324-01A-11D-2210-10	534	35811749	105401682	2055	4956											
TMEM8B	51754	hgsc.bcm.edu	37	chr9	35842480	35842480	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaccagccactgcccccagaAccgccatcccttggaacccc	10	4	6	21	1	0	1	0	0	0	1	1	2	1	2	9	1	5	0	9	1	3	1	rs7037450	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35842480A>G	ENST00000377991.4	+	7	1060	c.45A>G	c.(43-45)gaA>gaG	p.E15E	TMEM8B_ENST00000377996.1_Silent_p.E15E|TMEM8B_ENST00000473947.1_Intron|TMEM8B_ENST00000377988.2_Silent_p.E15E|TMEM8B_ENST00000439587.2_Silent_p.E15E	NM_001042589.2	NP_001036054.1	A6NDV4	TMM8B_HUMAN	transmembrane protein 8B	15					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						TGCCCCCAGAACCGCCATCCC	0.701													G|||	154	0.0307508	0.1089	0.0101	5008	,	,		17224	0.0		0.003	False		,,,				2504	0.0				p.E15E		Atlas-SNP	.											.	TMEM8B	53	.	0			c.A45G						PASS	.	G	,,	474,3932	759.4+/-412.9	36,402,1765	32	33	32		45,45,45	4.8	1	9	dbSNP_116	32	21,8577	804.0+/-407.3	0,21,4278	no	coding-synonymous,coding-synonymous,coding-synonymous	TMEM8B	NM_001042589.1,NM_001042590.1,NM_016446.3	,,	36,423,6043	GG,GA,AA		0.2442,10.7581,3.8065	,,	15/473,15/473,15/339	35842480	495,12509	2203	4299	6502	SO:0001819	synonymous_variant	51754	exon6			CCCAGAACCGCCA	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.45A>G	9.37:g.35842480A>G		115	0	0		105	52	0.495238	NM_001042590	B3KQF3|O75539|Q49AB1|Q4KMX5|Q5TCW5|Q9HBY2|Q9P0U7	Silent	SNP	ENST00000377991.4	37	CCDS43800.1																																																																																			A|0.962;G|0.038	0.038	strong		0.701	TMEM8B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052388.2	NM_016446		G	35842480	A	G	35842480	2	3	22	1	0	0	0	0	0	0	0	1	16230	40	2	3		3	TMEM8B	9	35842480	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	30731	35842480	105370951	2056	4957											
TMEM8B	51754	hgsc.bcm.edu	37	chr9	35845998	35845998	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgcgccaggaaaacgtgacGgtgtttggatgcttgactca	9	10	14	8	3	1	2	1	2	0	0	1	4	1	4	1	3	3	2	1	3	2	2	rs34807292	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35845998G>C	ENST00000377991.4	+	8	1321	c.306G>C	c.(304-306)acG>acC	p.T102T	TMEM8B_ENST00000377996.1_Silent_p.T102T|TMEM8B_ENST00000473947.1_3'UTR|TMEM8B_ENST00000377988.2_Silent_p.T102T|TMEM8B_ENST00000439587.2_Silent_p.T102T	NM_001042589.2	NP_001036054.1	A6NDV4	TMM8B_HUMAN	transmembrane protein 8B	102					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						AAAACGTGACGGTGTTTGGAT	0.617													G|||	127	0.0253594	0.0908	0.0072	5008	,	,		16083	0.0		0.002	False		,,,				2504	0.0				p.T102T		Atlas-SNP	.											.	TMEM8B	53	.	0			c.G306C						PASS	.	G	,,	386,4020	191.9+/-217.4	17,352,1834	114	95	102		306,306,306	-2.7	1	9	dbSNP_126	102	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	TMEM8B	NM_001042589.1,NM_001042590.1,NM_016446.3	,,	17,353,6133	CC,CG,GG		0.0116,8.7608,2.9755	,,	102/473,102/473,102/339	35845998	387,12619	2203	4300	6503	SO:0001819	synonymous_variant	51754	exon7			CGTGACGGTGTTT	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.306G>C	9.37:g.35845998G>C		65	0	0		50	24	0.48	NM_001042590	B3KQF3|O75539|Q49AB1|Q4KMX5|Q5TCW5|Q9HBY2|Q9P0U7	Silent	SNP	ENST00000377991.4	37	CCDS43800.1																																																																																			G|0.969;C|0.031	0.031	strong		0.617	TMEM8B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052388.2	NM_016446		C	35845998	G	C	35845998	2	2	22	1	0	0	0	0	0	0	0	1	16230	1103	39	4		4	TMEM8B	9	35845998	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3518	35845998	105367433	2057	4958											
HRCT1	646962	hgsc.bcm.edu	37	chr9	35906601	35906601	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cctccaccaccaccaccaccCccaccgccaccatccccgcc	8	2	2	29	2	0	0	0	0	0	0	2	0	2	0	14	0	0	0	14	0	0	0	rs565823201|rs112212538		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35906601C>A	ENST00000354323.2	+	1	413	c.317C>A	c.(316-318)cCc>cAc	p.P106H	LINC00961_ENST00000443779.1_lincRNA	NM_001039792.1	NP_001034881.1	Q6UXD1	HRCT1_HUMAN	histidine rich carboxyl terminus 1	106	His-rich.					integral component of membrane (GO:0016021)				NS(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(1)	4						caccaccacccccaccgccac	0.677																																					p.P106H		Atlas-SNP	.											.	HRCT1	14	.	0			c.C317A						PASS	.						6	6	6					9																	35906601		1795	3578	5373	SO:0001583	missense	646962	exon1			ACCACCCCCACCG		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.317C>A	9.37:g.35906601C>A	ENSP00000346283:p.Pro106His	37	0	0		36	22	0.611111	NM_001039792	B7ZBJ1	Missense_Mutation	SNP	ENST00000354323.2	37	CCDS35012.1	337	0.1543040293040293	82	0.16666666666666666	47	0.1298342541436464	45	0.07867132867132867	163	0.21503957783641162	C	1.568	-0.535019	0.04082	.	.	ENSG00000196196	ENST00000354323	.	.	.	0.571	-1.14	0.09741	.	2.262810	0.02394	N	0.080002	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	P	0.36944	0.574	B	0.32465	0.146	T	0.09751	-1.0660	7	0.87932	D	0	-19.8215	.	.	.	.	106	Q6UXD1	HRCT1_HUMAN	H	106	.	ENSP00000346283:P106H	P	+	2	0	HRCT1	35896601	0.000000	0.05858	0.011000	0.14972	0.341000	0.28922	-0.113000	0.10774	-1.188000	0.02705	-0.718000	0.03613	CCC	C|0.846;A|0.154	0.154	strong		0.677	HRCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334099.1	NM_001039792		A	35906601	C	A	35906601	3	1	22	1	0	0	0	0	1	0	0	0	7362	623	22	4	319	4	HRCT1	9	35906601	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	60603	35906601	105306830	2058	4959											
OR2S2	56656	hgsc.bcm.edu	37	chr9	35957728	35957728	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggttgcagatggccacatagCgatcaaatgccatcatgctc	11	9	10	11	1	2	1	2	0	0	1	3	2	2	1	2	2	4	3	2	2	2	2	rs2233563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35957728C>T	ENST00000341959.2	-	1	423	c.368G>A	c.(367-369)cGc>cAc	p.R123H		NM_019897.2	NP_063950.2	Q9NQN1	OR2S1_HUMAN	olfactory receptor, family 2, subfamily S, member 2	123			R -> H (in dbSNP:rs2233563).		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(2)|large_intestine(2)|lung(8)|ovary(1)|skin(1)|stomach(1)	17			LUSC - Lung squamous cell carcinoma(32;0.00613)|STAD - Stomach adenocarcinoma(86;0.194)			GGCCACATAGCGATCAAATGC	0.557													C|||	122	0.024361	0.0915	0.0014	5008	,	,		24963	0.0		0.0	False		,,,				2504	0.0				p.R123H	Pancreas(172;293 2036 17878 24427 30946)	Atlas-SNP	.											.	OR2S2	46	.	0			c.G368A						PASS	.	C	HIS/ARG	351,4055	182.9+/-210.6	14,323,1866	94	80	85		368	0.8	0.2	9	dbSNP_98	85	3,8597	3.0+/-9.4	0,3,4297	yes	missense	OR2S2	NM_019897.2	29	14,326,6163	TT,TC,CC		0.0349,7.9664,2.7218	possibly-damaging	123/320	35957728	354,12652	2203	4300	6503	SO:0001583	missense	56656	exon1			ACATAGCGATCAA	AL135841	CCDS6596.2	9p13.3	2012-08-09			ENSG00000122718	ENSG00000122718		"GPCR / Class A : Olfactory receptors"	8276	protein-coding gene	gene with protein product							Standard	NM_019897		Approved		uc011lpi.2	Q9NQN1	OTTHUMG00000019891	ENST00000341959.2:c.368G>A	9.37:g.35957728C>T	ENSP00000344040:p.Arg123His	103	0	0		100	57	0.57	NM_019897	Q2M3L0|Q6IF19|Q96R42	Missense_Mutation	SNP	ENST00000341959.2	37	CCDS6596.2	45	0.020604395604395604	45	0.09146341463414634	0	0.0	0	0.0	0	0.0	C	10.24	1.295956	0.23650	0.079664	3.49E-4	ENSG00000122718	ENST00000341959	T	0.77489	-1.1	4.32	0.775	0.18527	GPCR, rhodopsin-like superfamily (1);	0.388525	0.22144	N	0.064012	T	0.11110	0.0271	M	0.88310	2.945	0.25060	N	0.991077	P	0.47034	0.889	B	0.36504	0.226	T	0.48747	-0.9008	10	0.72032	D	0.01	.	8.045	0.30545	0.0:0.6808:0.0:0.3192	rs2233563;rs2233563	123	Q9NQN1	OR2S1_HUMAN	H	123	ENSP00000344040:R123H	ENSP00000344040:R123H	R	-	2	0	OR2S2	35947728	0.990000	0.36364	0.195000	0.23364	0.101000	0.19017	1.416000	0.34759	0.125000	0.18397	0.655000	0.94253	CGC	C|0.975;T|0.025	0.025	strong		0.557	OR2S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052400.2	NM_019897		T	35957728	C	T	35957728	3	4	22	1	0	0	0	0	1	0	0	0	11024	768	27	1	595	1	OR2S2	9	35957728	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	51127	35957728	105255703	2059	4960											
CLTA	1211	hgsc.bcm.edu	37	chr9	36197564	36197564	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcagatgctgttgatggagtAatgaatggtgaatactacca	13	11	12	5	0	0	4	0	3	0	1	0	5	0	5	1	2	3	4	1	2	5	4	rs138682143	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:36197564A>G	ENST00000242285.6	+	2	354	c.234A>G	c.(232-234)gtA>gtG	p.V78V	CLTA_ENST00000540080.1_Intron|CLTA_ENST00000466396.1_Intron|CLTA_ENST00000345519.5_Silent_p.V78V|CLTA_ENST00000396603.2_Silent_p.V78V|CLTA_ENST00000470744.1_Silent_p.V78V|CLTA_ENST00000433436.2_Silent_p.V78V|CLTA_ENST00000538225.1_Silent_p.V78V			P09496	CLCA_HUMAN	clathrin, light chain A	78					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)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-Golgi vesicle-mediated transport (GO:0006892)	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)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	clathrin heavy chain binding (GO:0032050)|peptide binding (GO:0042277)|structural molecule activity (GO:0005198)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(1)	6			STAD - Stomach adenocarcinoma(86;0.228)			TTGATGGAGTAATGAATGGTG	0.383																																					p.V78V		Atlas-SNP	.											.	CLTA	18	.	0			c.A234G						PASS	.	A	,,,,,	10,4396	16.8+/-37.8	0,10,2193	254	237	243		234,234,234,,234,234	0.6	1	9	dbSNP_134	243	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous	CLTA	NM_001076677.2,NM_001184760.1,NM_001184761.1,NM_001184762.1,NM_001833.3,NM_007096.3	,,,,,	0,10,6493	GG,GA,AA		0.0,0.227,0.0769	,,,,,	78/237,78/231,78/169,,78/219,78/249	36197564	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	1211	exon2			TGGAGTAATGAAT		CCDS6600.1, CCDS6601.1, CCDS43802.1, CCDS55306.1, CCDS55307.1	9p13.3	2010-05-11	2010-05-11		ENSG00000122705	ENSG00000122705			2090	protein-coding gene	gene with protein product		118960	"clathrin, light polypeptide (Lca)"			7713494	Standard	NM_007096		Approved	Lca	uc003zzc.3	P09496	OTTHUMG00000019896	ENST00000242285.6:c.234A>G	9.37:g.36197564A>G		178	0	0		189	109	0.57672	NM_001184761	A8K4W3|B4DIN1|F5H6N3|Q2XPN5|Q53XZ1	Silent	SNP	ENST00000242285.6	37	CCDS6601.1																																																																																			A|0.998;G|0.002	0.002	strong		0.383	CLTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052405.1	NM_007096		G	36197564	A	G	36197564	2	3	22	1	0	0	0	0	0	0	0	1	3566	349	13	3		3	CLTA	9	36197564	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	239836	36197564	105015867	2060	4961											
FBXO10	26267	hgsc.bcm.edu	37	chr9	37537892	37537892	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggccatggacctggatgtGcccgttctcaaagttgcagt	7	10	13	11	2	1	0	1	0	1	0	2	2	1	2	3	3	2	3	3	3	1	2	rs7044561	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:37537892G>T	ENST00000432825.2	-	3	682	c.634C>A	c.(634-636)Cac>Aac	p.H212N	FBXO10_ENST00000543968.1_5'Flank|RP11-613M10.8_ENST00000544475.1_5'UTR|FBXO10_ENST00000541829.1_Intron	NM_012166.2	NP_036298.2	Q9UK96	FBX10_HUMAN	F-box protein 10	212			H -> N (found in a patient with lymphoma; dbSNP:rs7044561). {ECO:0000269|PubMed:23431138}.		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)		ACCTGGATGTGCCCGTTCTCA	0.488													G|||	76	0.0151757	0.0575	0.0	5008	,	,		21854	0.0		0.0	False		,,,				2504	0.0				p.H212N		Atlas-SNP	.											.	FBXO10	75	.	0			c.C634A						PASS	.	G	ASN/HIS	171,3729		8,155,1787	85	85	85		634	5.3	1	9	dbSNP_116	85	5,8263		0,5,4129	yes	missense	FBXO10	NM_012166.2	68	8,160,5916	TT,TG,GG		0.0605,4.3846,1.4464	benign	212/957	37537892	176,11992	1950	4134	6084	SO:0001583	missense	26267	exon3			GGATGTGCCCGTT	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.634C>A	9.37:g.37537892G>T	ENSP00000403802:p.His212Asn	137	0	0		149	75	0.503356	NM_012166	Q08AL3|Q08AL4|Q5JRT8|Q9UKC3	Missense_Mutation	SNP	ENST00000432825.2	37	CCDS47966.1	22	0.010073260073260074	22	0.044715447154471545	0	0.0	0	0.0	0	0.0	G	16.84	3.233921	0.58886	0.043846	6.05E-4	ENSG00000147912	ENST00000432825	T	0.40756	1.02	5.3	5.3	0.74995	Pectin lyase fold/virulence factor (1);Pectin lyase fold (1);	0.054328	0.85682	D	0.000000	T	0.06462	0.0166	N	0.14661	0.345	0.80722	D	1	B	0.25105	0.118	B	0.23852	0.049	T	0.05484	-1.0882	10	0.02654	T	1	-29.9635	18.0885	0.89466	0.0:0.0:1.0:0.0	rs7044561;rs52804171;rs7044561	212	Q9UK96	FBX10_HUMAN	N	212	ENSP00000403802:H212N	ENSP00000276960:H212N	H	-	1	0	FBXO10	37527892	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.345000	0.97053	2.631000	0.89168	0.655000	0.94253	CAC	G|0.983;T|0.017	0.017	strong		0.488	FBXO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052472.3			T	37537892	G	T	37537892	3	4	22	1	0	0	0	0	1	0	0	0	5734	1319	46	4	2272	4	FBXO10	9	37537892	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1340328	37537892	103675539	2061	4962											
FRMPD1	22844	hgsc.bcm.edu	37	chr9	37745562	37745562	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagatcccaccacatccccCtagagaccctcaaggacaga	13	4	7	17	0	1	3	1	0	0	3	3	5	3	4	5	1	0	1	5	1	2	1	rs62640016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:37745562C>T	ENST00000539465.1	+	16	4126	c.3533C>T	c.(3532-3534)cCt>cTt	p.P1178L	RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000377765.3_Missense_Mutation_p.P1178L			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	1178						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.P1178H(1)		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)		CCACATCCCCCTAGAGACCCT	0.483													C|||	81	0.0161741	0.0605	0.0014	5008	,	,		19697	0.0		0.0	False		,,,				2504	0.0				p.P1178L		Atlas-SNP	.											FRMPD1,scalp,carcinoma,+1,1	FRMPD1	237	1	1	Substitution - Missense(1)	lung(1)	c.C3533T						PASS	.	C	LEU/PRO	164,4242	104.7+/-143.2	3,158,2042	52	55	54		3533	3.2	0	9	dbSNP_129	54	0,8598		0,0,4299	yes	missense	FRMPD1	NM_014907.2	98	3,158,6341	TT,TC,CC		0.0,3.7222,1.2612	possibly-damaging	1178/1579	37745562	164,12840	2203	4299	6502	SO:0001583	missense	22844	exon16			ATCCCCCTAGAGA	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.3533C>T	9.37:g.37745562C>T	ENSP00000444411:p.Pro1178Leu	75	0	0		78	41	0.525641	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	37	CCDS6612.1	23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	C	11.39	1.625940	0.28889	0.037222	0.0	ENSG00000070601	ENST00000377765;ENST00000539465	T;T	0.06768	3.26;3.26	4.24	3.24	0.37175	.	1.039780	0.07531	N	0.912167	T	0.00998	0.0033	N	0.24115	0.695	0.19300	N	0.999977	B	0.06786	0.001	B	0.04013	0.001	T	0.15925	-1.0420	10	0.56958	D	0.05	-9.9948	8.5566	0.33485	0.2299:0.7701:0.0:0.0	rs62640016	1178	Q5SYB0	FRPD1_HUMAN	L	1178	ENSP00000366995:P1178L;ENSP00000444411:P1178L	ENSP00000366995:P1178L	P	+	2	0	FRMPD1	37735562	0.005000	0.15991	0.037000	0.18230	0.034000	0.12701	1.541000	0.36126	2.298000	0.77334	0.561000	0.74099	CCT	C|0.986;T|0.014	0.014	strong		0.483	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		T	37745562	C	T	37745562	3	4	22	1	0	0	0	0	1	0	0	0	6065	681	24	2	3591	2	FRMPD1	9	37745562	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	207670	37745562	103467869	2062	4963											
ZNF658	26149	hgsc.bcm.edu	37	chr9	40774091	40774091	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgaatgaggtgtgctttcCggtaaaaggattttctgcat	9	14	12	6	1	1	2	0	2	1	0	2	3	2	3	1	3	2	4	1	3	3	4	rs79262629	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:40774091C>T	ENST00000602553.1	-	5	1478	c.1184G>A	c.(1183-1185)cGg>cAg	p.R395Q	ZNF658_ENST00000441795.1_Missense_Mutation_p.R393Q|ZNF658_ENST00000377626.3_Missense_Mutation_p.R395Q			Q5TYW1	ZN658_HUMAN	zinc finger protein 658	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	46				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		GTGTGCTTTCCGGTAAAAGGA	0.393													C|||	70	0.0139776	0.0522	0.0	5008	,	,		20923	0.001		0.0	False		,,,				2504	0.0				p.R395Q		Atlas-SNP	.											ZNF658,lower_third,carcinoma,-1,1	ZNF658	100	1	0			c.G1184A						scavenged	.	C	GLN/ARG	152,4254	103.4+/-141.9	2,148,2053	218	217	218		1184	-0.9	0	9	dbSNP_131	218	2,8598	2.2+/-6.3	0,2,4298	yes	missense	ZNF658	NM_033160.5	43	2,150,6351	TT,TC,CC		0.0233,3.4498,1.1841	benign	395/1060	40774091	154,12852	2203	4300	6503	SO:0001583	missense	26149	exon5			GCTTTCCGGTAAA	AA482262	CCDS75846.1	9p13.1	2013-01-08			ENSG00000196409	ENSG00000274349		"Zinc fingers, C2H2-type", "-"	25226	protein-coding gene	gene with protein product							Standard	NM_033160		Approved	MGC35232, DKFZp572C163, FLJ32813	uc004abs.2	Q5TYW1	OTTHUMG00000013392	ENST00000602553.1:c.1184G>A	9.37:g.40774091C>T	ENSP00000473484:p.Arg395Gln	532	2	0.0037594		543	183	0.337017	NM_033160	Q6PIP3|Q96M55|Q9H9S6|Q9UG02	Missense_Mutation	SNP	ENST00000602553.1	37	CCDS35023.1	18	0.008241758241758242	18	0.036585365853658534	0	0.0	0	0.0	0	0.0	c	0.018	-1.473237	0.01044	0.034498	2.33E-4	ENSG00000196409	ENST00000441795;ENST00000377626	T;T	0.14893	2.47;2.47	1.8	-0.939	0.10408	Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00936	0.0031	N	0.01473	-0.845	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41805	-0.9488	9	0.07990	T	0.79	.	5.7522	0.18152	0.0:0.5247:0.0:0.4753	.	395;395	Q5TYW1-2;Q5TYW1	.;ZN658_HUMAN	Q	393;395	ENSP00000408462:R393Q;ENSP00000366853:R395Q	ENSP00000366853:R395Q	R	-	2	0	ZNF658	40764091	0.000000	0.05858	0.000000	0.03702	0.211000	0.24417	-0.970000	0.03810	-0.174000	0.10743	-0.820000	0.03113	CGG	C|0.990;T|0.010	0.010	strong		0.393	ZNF658-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467800.1	NM_033160		T	40774091	C	T	40774091	3	4	22	1	0	0	0	0	1	0	0	0	18084	652	23	1	1999	1	ZNF658	9	40774091	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3028529	40774091	100439340	2063	4964											
ZNF658	26149	hgsc.bcm.edu	37	chr9	40784132	40784132	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacctctggttcaggaattcAtcttctaaagaccatggctc	10	13	7	11	0	5	1	2	0	3	1	6	2	5	2	2	3	1	2	2	3	4	5	rs142151197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:40784132A>G	ENST00000602553.1	-	4	507	c.213T>C	c.(211-213)gaT>gaC	p.D71D	ZNF658_ENST00000441795.1_Silent_p.D69D|ZNF658_ENST00000377626.3_Silent_p.D71D			Q5TYW1	ZN658_HUMAN	zinc finger protein 658	71	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(3)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	46				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		TCAGGAATTCATCTTCTAAAG	0.433													A|||	68	0.0135783	0.0514	0.0	5008	,	,		13262	0.0		0.0	False		,,,				2504	0.0				p.D71D		Atlas-SNP	.											.	ZNF658	100	.	0			c.T213C						PASS	.	A		146,4260	97.1+/-135.8	1,144,2058	32	36	34		213	-3.4	0	9	dbSNP_134	34	2,8592	2.2+/-6.3	0,2,4295	no	coding-synonymous	ZNF658	NM_033160.5		1,146,6353	GG,GA,AA		0.0233,3.3137,1.1385		71/1060	40784132	148,12852	2203	4297	6500	SO:0001819	synonymous_variant	26149	exon4			GAATTCATCTTCT	AA482262	CCDS75846.1	9p13.1	2013-01-08			ENSG00000196409	ENSG00000274349		"Zinc fingers, C2H2-type", "-"	25226	protein-coding gene	gene with protein product							Standard	NM_033160		Approved	MGC35232, DKFZp572C163, FLJ32813	uc004abs.2	Q5TYW1	OTTHUMG00000013392	ENST00000602553.1:c.213T>C	9.37:g.40784132A>G		233	0	0		264	93	0.352273	NM_033160	Q6PIP3|Q96M55|Q9H9S6|Q9UG02	Silent	SNP	ENST00000602553.1	37	CCDS35023.1																																																																																			.	.	weak		0.433	ZNF658-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467800.1	NM_033160		G	40784132	A	G	40784132	2	3	22	1	0	0	0	0	0	0	0	1	18084	214	8	3		3	ZNF658	9	40784132	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	10041	40784132	100429299	2064	4965											
FOXD4L3	286380	hgsc.bcm.edu	37	chr9	70919085	70919085	+	Frame_Shift_Del	DEL	C	C	-																															ctcccaccaagggcgcggtgCtgggcgggcacctgtcggcc																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:70919085delC	ENST00000342833.2	+	1	1810	c.1218delC	c.(1216-1218)tgcfs	p.C406fs		NM_199135.4	NP_954586.4	Q6VB84	FX4L3_HUMAN	forkhead box D4-like 3	406						nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			ovary(1)	1				all cancers(8;0.00136)|Epithelial(8;0.0288)|GBM - Glioblastoma multiforme(74;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		GGGCGCGGTGCTGGGCGGGCA	0.677																																					p.C406fs		Atlas-Indel	.											.	FOXD4L3	7	.	0			c.1217delG						PASS	.						2	3	2					9																	70919085		917	2379	3296	SO:0001589	frameshift_variant	286380	exon1			.	AY344642	CCDS43833.1	9q13	2008-05-13				ENSG00000187559			18523	protein-coding gene	gene with protein product		611086				12421752	Standard	NM_199135		Approved	OTTHUMG00000019959, FOXD6	uc004agm.1	Q6VB84	OTTHUMG00000019959	ENST00000342833.2:c.1218delC	9.37:g.70919085delC	ENSP00000341961:p.Cys406fs	668	0	0		931	76	0.0816327	NM_199135	Q5JTX9	Frame_Shift_Del	DEL	ENST00000342833.2	37	CCDS43833.1																																																																																			.	.	none		0.677	FOXD4L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052539.2	NM_199358		-	70919085	C	-	70919085	7	5	22	1	0	1	0	1	0	0	0	0	6009	805	28	0	1220	0	FOXD4L3	9	70919085	Frame_Shift_Del	DEL	C	TCGA-G8-6324-01A-11D-2210-10	30134953	70919085	70294346	2065	4966											
TJP2	9414	hgsc.bcm.edu	37	chr9	71844124	71844124	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcaaccaaaagcagccccgaGaacttttcttcgtcctagtc	11	10	6	14	2	2	1	1	0	1	1	5	2	3	1	4	0	4	1	4	0	5	4	rs41277901	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:71844124G>A	ENST00000377245.4	+	10	1686	c.1478G>A	c.(1477-1479)aGa>aAa	p.R493K	TJP2_ENST00000265384.7_Missense_Mutation_p.R493K|TJP2_ENST00000453658.2_Missense_Mutation_p.R470K|TJP2_ENST00000535702.1_Missense_Mutation_p.R497K|TJP2_ENST00000348208.4_Missense_Mutation_p.R493K|TJP2_ENST00000539225.1_Missense_Mutation_p.R524K	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	493					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						GCAGCCCCGAGAACTTTTCTT	0.393													G|||	60	0.0119808	0.0356	0.0115	5008	,	,		19298	0.0		0.005	False		,,,				2504	0.0				p.R524K		Atlas-SNP	.											.	TJP2	120	.	0			c.G1571A						PASS	.	G	LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG	153,4253	106.5+/-144.9	0,153,2050	215	200	205		1409,1490,1571,1478,1478,1478	4	0.3	9	dbSNP_127	205	14,8586	11.2+/-40.8	0,14,4286	yes	missense,missense,missense,missense,missense,missense	TJP2	NM_001170414.1,NM_001170415.1,NM_001170416.1,NM_001170630.1,NM_004817.3,NM_201629.3	26,26,26,26,26,26	0,167,6336	AA,AG,GG		0.1628,3.4725,1.284	benign,benign,benign,benign,benign,benign	470/1021,497/1158,524/1222,493/994,493/1191,493/1044	71844124	167,12839	2203	4300	6503	SO:0001583	missense	9414	exon10			CCCCGAGAACTTT	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.1478G>A	9.37:g.71844124G>A	ENSP00000366453:p.Arg493Lys	228	0	0		254	70	0.275591	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Missense_Mutation	SNP	ENST00000377245.4	37	CCDS6627.1	19	0.0086996336996337	13	0.026422764227642278	3	0.008287292817679558	0	0.0	3	0.00395778364116095	G	13.41	2.227582	0.39399	0.034725	0.001628	ENSG00000119139	ENST00000453658;ENST00000377245;ENST00000348208;ENST00000265384;ENST00000535702;ENST00000539225	T;T;T;T;T;T	0.08807	3.06;3.06;3.05;3.05;3.08;3.11	5.85	4.02	0.46733	PDZ/DHR/GLGF (1);	0.162144	0.56097	D	0.000036	T	0.01870	0.0059	L	0.29908	0.895	0.33647	D	0.608025	B;B;B;B;B	0.29136	0.234;0.007;0.004;0.007;0.021	B;B;B;B;B	0.28465	0.09;0.01;0.003;0.004;0.018	T	0.29731	-1.0002	10	0.24483	T	0.36	.	9.1425	0.36912	0.2159:0.0:0.7841:0.0	rs41277901;rs61731595	524;497;493;493;493	F5H301;F5H886;Q9UDY2-2;Q9UDY2;Q9UDY2-5	.;.;.;ZO2_HUMAN;.	K	470;493;493;493;497;524	ENSP00000392178:R470K;ENSP00000366453:R493K;ENSP00000345893:R493K;ENSP00000265384:R493K;ENSP00000442090:R497K;ENSP00000438262:R524K	ENSP00000265384:R493K	R	+	2	0	TJP2	71033944	1.000000	0.71417	0.285000	0.24819	0.979000	0.70002	4.172000	0.58243	1.481000	0.48307	0.557000	0.71058	AGA	G|0.988;A|0.012	0.012	strong		0.393	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629		A	71844124	G	A	71844124	3	1	22	1	0	0	0	0	1	0	0	0	15945	942	33	2	1673	2	TJP2	9	71844124	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	925039	71844124	69369307	2066	4967											
TJP2	9414	hgsc.bcm.edu	37	chr9	71851080	71851080	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggtagacacactgtatgaCggcaagctgggcaactggct	10	8	14	9	1	0	2	0	1	0	1	0	2	0	2	0	4	2	6	0	4	4	2	rs12340440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:71851080C>T	ENST00000377245.4	+	13	2125	c.1917C>T	c.(1915-1917)gaC>gaT	p.D639D	TJP2_ENST00000265384.7_Silent_p.D639D|TJP2_ENST00000453658.2_Silent_p.D616D|TJP2_ENST00000535702.1_Silent_p.D643D|TJP2_ENST00000348208.4_Silent_p.D639D|TJP2_ENST00000539225.1_Silent_p.D670D	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	639	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				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						CACTGTATGACGGCAAGCTGG	0.502													C|||	75	0.014976	0.0545	0.0043	5008	,	,		19727	0.0		0.0	False		,,,				2504	0.0				p.D670D		Atlas-SNP	.											TJP2,colon,carcinoma,0,1	TJP2	120	1	0			c.C2010T						scavenged	.	C	,,,,,	188,4218	120.4+/-158.0	5,178,2020	106	97	100		1848,1929,2010,1917,1917,1917	-3.3	1	9	dbSNP_120	100	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TJP2	NM_001170414.1,NM_001170415.1,NM_001170416.1,NM_001170630.1,NM_004817.3,NM_201629.3	,,,,,	5,179,6319	TT,TC,CC		0.0116,4.2669,1.4532	,,,,,	616/1021,643/1158,670/1222,639/994,639/1191,639/1044	71851080	189,12817	2203	4300	6503	SO:0001819	synonymous_variant	9414	exon13			GTATGACGGCAAG	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.1917C>T	9.37:g.71851080C>T		54	1	0.0185185		57	36	0.631579	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Silent	SNP	ENST00000377245.4	37	CCDS6627.1																																																																																			C|0.983;T|0.017	0.017	strong		0.502	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629		T	71851080	C	T	71851080	2	4	22	1	0	0	0	0	0	0	0	1	15945	535	19	1		1	TJP2	9	71851080	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6956	71851080	69362351	2067	4968											
TRPM3	80036	hgsc.bcm.edu	37	chr9	73151130	73151133	+	Frame_Shift_Del	DEL	TCTC	TCTC	-																															gtgatgttgttggacagggtTctctctgagttatcaccctc																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCTC	TCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:73151130_73151133delTCTC	ENST00000377110.3	-	25	5103_5106	c.4860_4863delGAGA	c.(4858-4863)gagagafs	p.ER1620fs	TRPM3_ENST00000396292.4_Frame_Shift_Del_p.ER1492fs|TRPM3_ENST00000358082.3_Frame_Shift_Del_p.ER1482fs|TRPM3_ENST00000377105.1_Frame_Shift_Del_p.ER1479fs|TRPM3_ENST00000377111.2_Intron|TRPM3_ENST00000396280.5_Frame_Shift_Del_p.ER1469fs|TRPM3_ENST00000408909.2_Frame_Shift_Del_p.ER1479fs|TRPM3_ENST00000357533.2_Frame_Shift_Del_p.ER1624fs|TRPM3_ENST00000377106.1_Frame_Shift_Del_p.ER1492fs|TRPM3_ENST00000396285.1_Frame_Shift_Del_p.ER1479fs|TRPM3_ENST00000423814.3_Frame_Shift_Del_p.ER1647fs|TRPM3_ENST00000360823.2_Frame_Shift_Del_p.ER1482fs			Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	1645					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						TGGACAGGGTTCTCTCTGAGTTAT	0.544																																					p.1621_1622del		Pindel,Atlas-Indel	.											.	TRPM3	700	.	0			c.4861_4864del						PASS	.		,,,,,,	5,4259		0,5,2127					,,,,,,	-3.5	0.6			363	0,8254		0,0,4127	no	frameshift,frameshift,frameshift,frameshift,frameshift,frameshift,frameshift	TRPM3	NM_206947.3,NM_206946.3,NM_206945.3,NM_206944.3,NM_024971.5,NM_020952.4,NM_001007471.2	,,,,,,	0,5,6254	A1A1,A1R,RR		0.0,0.1173,0.0399	,,,,,,	,,,,,,		5,12513				SO:0001589	frameshift_variant	80036	exon25			.	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.4860_4863delGAGA	9.37:g.73151130_73151133delTCTC	ENSP00000366314:p.Glu1620fs	439	0	.		453	86	0.19	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Frame_Shift_Del	DEL	ENST00000377110.3	37	CCDS43835.1																																																																																			.	.	none		0.544	TRPM3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214158.3	NM_206945		-	73151133	TCTC	-	73151130	7	5	22	1	0	1	0	1	0	0	0	0	16602	1780	62	0	264	0	TRPM3	9	73151130	Frame_Shift_Del	DEL	TCTC	TCGA-G8-6324-01A-11D-2210-10	1300050	73151130	68062301	2068	4969											
TRPM6	140803	hgsc.bcm.edu	37	chr9	77418802	77418802	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcctgaggagtgtctctggtGctgggaaaggttttgaacaa	9	12	14	6	0	1	2	0	2	1	0	3	4	2	4	1	4	2	2	1	4	3	2	rs115354606	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:77418802G>A	ENST00000360774.1	-	15	1876	c.1639C>T	c.(1639-1641)Cac>Tac	p.H547Y	TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000376864.4_Splice_Site_p.H547Y|TRPM6_ENST00000449912.2_Splice_Site_p.H542Y|TRPM6_ENST00000451710.3_Splice_Site_p.H547Y|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000361255.3_Splice_Site_p.H542Y	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	547					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						TGTCTCTGGTGCTGGGAAAGG	0.388													G|||	164	0.0327476	0.1127	0.0187	5008	,	,		17133	0.0		0.002	False		,,,				2504	0.0				p.H547Y		Atlas-SNP	.											.	TRPM6	377	.	0			c.C1639T						PASS	.	G	TYR/HIS,TYR/HIS,TYR/HIS	400,4006	201.1+/-224.2	18,364,1821	142	135	137		1624,1624,1639	2.7	0.7	9	dbSNP_132	137	9,8591	6.4+/-24.3	0,9,4291	yes	missense-near-splice,missense-near-splice,missense-near-splice	TRPM6	NM_001177310.1,NM_001177311.1,NM_017662.4	83,83,83	18,373,6112	AA,AG,GG		0.1047,9.0785,3.1447	benign,benign,benign	542/2018,542/2018,547/2023	77418802	409,12597	2203	4300	6503	SO:0001630	splice_region_variant	140803	exon15			TCTGGTGCTGGGA	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.1639-1C>T	9.37:g.77418802G>A		82	0	0		88	61	0.693182	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	37	CCDS6647.1	67	0.030677655677655676	58	0.11788617886178862	8	0.022099447513812154	0	0.0	1	0.0013192612137203166	G	16.51	3.143177	0.57044	0.090785	0.001047	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000449912;ENST00000361255;ENST00000376864;ENST00000312449;ENST00000448641	T;T;T;T;T	0.73575	-0.76;-0.76;-0.76;-0.76;-0.76	5.51	2.69	0.31865	.	0.768746	0.12808	N	0.437439	T	0.03390	0.0098	M	0.67953	2.075	0.36472	P	0.132695	D;B	0.54397	0.966;0.402	P;B	0.49421	0.61;0.196	T	0.47799	-0.9089	9	0.62326	D	0.03	.	6.3637	0.21443	0.2288:0.1334:0.6379:0.0	.	547;542	Q9BX84;Q9BX84-3	TRPM6_HUMAN;.	Y	547;547;542;542;547;210;210	ENSP00000354006:H547Y;ENSP00000407341:H547Y;ENSP00000396672:H542Y;ENSP00000354962:H542Y;ENSP00000366060:H547Y	ENSP00000309693:H210Y	H	-	1	0	TRPM6	76608622	0.107000	0.21998	0.717000	0.30585	0.861000	0.49209	0.067000	0.14510	0.302000	0.22762	0.563000	0.77884	CAC	G|0.969;A|0.031	0.031	strong		0.388	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662	Missense_Mutation	A	77418802	G	A	77418802	5	1	22	1	0	0	0	0	0	0	1	0	16605	1333	46	2	4529	2	TRPM6	9	77418802	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4267672	77418802	63794629	2069	4970											
PCSK5	5125	hgsc.bcm.edu	37	chr9	78506181	78506181	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcgggggctgcctgctcccCgtgtgtcggacgcgcgtcta	2	9	15	15	6	1	0	0	0	1	0	4	1	2	1	3	3	2	2	3	3	1	1	rs34813806	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:78506181C>A	ENST00000545128.1	+	1	622	c.84C>A	c.(82-84)ccC>ccA	p.P28P	PCSK5_ENST00000376752.4_Silent_p.P28P|PCSK5_ENST00000376767.3_Silent_p.P28P	NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	28					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						GCCTGCTCCCCGTGTGTCGGA	0.677													C|||	55	0.0109824	0.0386	0.0058	5008	,	,		12564	0.0		0.0	False		,,,				2504	0.0				p.P28P		Atlas-SNP	.											.	PCSK5	329	.	0			c.C84A						PASS	.	C	,	116,4290	76.8+/-115.0	3,110,2090	42	51	48		84,84	-4	1	9	dbSNP_126	48	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous,coding-synonymous	PCSK5	NM_001190482.1,NM_006200.3	,	3,116,6384	AA,AC,CC		0.0698,2.6328,0.938	,	28/1861,28/914	78506181	122,12884	2203	4300	6503	SO:0001819	synonymous_variant	5125	exon1			GCTCCCCGTGTGT		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.84C>A	9.37:g.78506181C>A		74	0	0		104	77	0.740385	NM_006200	F5H2G7|Q13527|Q96EP4	Silent	SNP	ENST00000545128.1	37	CCDS55320.1																																																																																			C|0.990;A|0.010	0.010	strong		0.677	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	78506181	C	A	78506181	2	1	22	1	0	0	0	0	0	0	0	1	11612	639	23	4		4	PCSK5	9	78506181	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1087379	78506181	62707250	2070	4971											
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79319725	79319725	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggtaaatcagaattatctgTttctacttcccagtcaacgt	11	15	6	9	1	4	1	2	0	2	1	5	1	5	1	1	1	2	2	1	1	6	5	rs375144440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:79319725T>C	ENST00000376718.3	-	8	7588	c.7465A>G	c.(7465-7467)Aca>Gca	p.T2489A	PRUNE2_ENST00000428286.1_Missense_Mutation_p.T2130A	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2489					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						GAATTATCTGTTTCTACTTCC	0.448											OREG0019258	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	2	0.000399361	0.0015	0.0	5008	,	,		20535	0.0		0.0	False		,,,				2504	0.0				p.T2489A		Atlas-SNP	.											.	PRUNE2	331	.	0			c.A7465G						PASS	.	T	ALA/THR	5,3131		0,5,1563	72	60	64		7465	-1.6	0.2	9		64	0,7162		0,0,3581	no	missense	PRUNE2	NM_015225.2	58	0,5,5144	CC,CT,TT		0.0,0.1594,0.0486	benign	2489/3089	79319725	5,10293	1568	3581	5149	SO:0001583	missense	158471	exon8			TATCTGTTTCTAC	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.7465A>G	9.37:g.79319725T>C	ENSP00000365908:p.Thr2489Ala	132	0	0	1190	149	104	0.697987	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	37	CCDS47982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	6.828|6.828	0.521980|0.521980	0.13005|0.13005	0.001594|0.001594	0.0|0.0	ENSG00000106772|ENSG00000106772	ENST00000426088|ENST00000376718;ENST00000428286;ENST00000422033	.|T;T	.|0.47869	.|0.83;0.83	5.66|5.66	-1.6|-1.6	0.08426|0.08426	.|.	.|0.512611	.|0.18219	.|N	.|0.147951	T|T	0.31295|0.31295	0.0792|0.0792	L|L	0.48362|0.48362	1.52|1.52	0.25662|0.25662	N|N	0.985999|0.985999	.|B	.|0.15141	.|0.012	.|B	.|0.11329	.|0.006	T|T	0.15235|0.15235	-1.0444|-1.0444	5|10	.|0.21540	.|T	.|0.41	-0.3544|-0.3544	4.9213|4.9213	0.13871|0.13871	0.3138:0.2585:0.0:0.4276|0.3138:0.2585:0.0:0.4276	.|.	.|2489	.|Q8WUY3	.|PRUN2_HUMAN	S|A	1810|2489;2130;2488	.|ENSP00000365908:T2489A;ENSP00000397425:T2130A	.|ENSP00000365908:T2489A	N|T	-|-	2|1	0|0	PRUNE2|PRUNE2	78509545|78509545	0.492000|0.492000	0.26027|0.26027	0.226000|0.226000	0.23910|0.23910	0.731000|0.731000	0.41821|0.41821	0.124000|0.124000	0.15728|0.15728	-0.097000|-0.097000	0.12307|0.12307	0.533000|0.533000	0.62120|0.62120	AAC|ACA	.	.	weak		0.448	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		C	79319725	T	C	79319725	3	2	22	1	0	0	0	0	1	0	0	0	12653	1725	60	3	1849	3	PRUNE2	9	79319725	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	813544	79319725	61893706	2071	4972											
VPS13A	23230	hgsc.bcm.edu	37	chr9	79875104	79875104	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcattccaaaacctgaaccAgtaactgaagtatctgcccc	14	8	6	13	0	1	2	0	2	1	0	2	2	2	2	5	0	5	3	5	0	6	3	rs73466058	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:79875104A>G	ENST00000360280.3	+	23	2651	c.2391A>G	c.(2389-2391)ccA>ccG	p.P797P	VPS13A_ENST00000376636.3_Silent_p.P797P|VPS13A_ENST00000376634.4_Silent_p.P797P|VPS13A_ENST00000357409.5_Silent_p.P797P	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	797					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						AACCTGAACCAGTAACTGAAG	0.313													A|||	72	0.014377	0.0537	0.0014	5008	,	,		13428	0.0		0.0	False		,,,				2504	0.0				p.P797P		Atlas-SNP	.											.	VPS13A	735	.	0			c.A2391G						PASS	.	A	,,,	182,4224	118.0+/-155.7	3,176,2024	72	73	73		2391,2391,2391,2391	1.9	0	9	dbSNP_130	73	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	VPS13A	NM_001018037.1,NM_001018038.2,NM_015186.3,NM_033305.2	,,,	3,177,6322	GG,GA,AA		0.0116,4.1307,1.4073	,,,	797/3136,797/3070,797/3096,797/3175	79875104	183,12821	2203	4299	6502	SO:0001819	synonymous_variant	23230	exon23			TGAACCAGTAACT	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.2391A>G	9.37:g.79875104A>G		145	0	0		150	93	0.62	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Silent	SNP	ENST00000360280.3	37	CCDS6655.1																																																																																			A|0.987;G|0.013	0.013	strong		0.313	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		G	79875104	A	G	79875104	2	3	22	1	0	0	0	0	0	0	0	1	17204	175	7	3		3	VPS13A	9	79875104	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	555379	79875104	61338327	2072	4973											
VPS13A	23230	hgsc.bcm.edu	37	chr9	79929004	79929004	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cttcaaaactgatgatctcaCcatggtgctgtatagtccag	11	12	8	10	0	2	2	2	2	1	0	4	2	3	2	2	1	2	2	2	1	4	3	rs140993797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:79929004C>T	ENST00000360280.3	+	36	4471	c.4211C>T	c.(4210-4212)aCc>aTc	p.T1404I	VPS13A_ENST00000376636.3_Missense_Mutation_p.T1365I|VPS13A_ENST00000376634.4_Missense_Mutation_p.T1404I|VPS13A_ENST00000357409.5_Missense_Mutation_p.T1404I|VPS13A_ENST00000423463.2_3'UTR	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	1404					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						GATGATCTCACCATGGTGCTG	0.388																																					p.T1404I		Atlas-SNP	.											.	VPS13A	735	.	0			c.C4211T						PASS	.	C	ILE/THR,ILE/THR,ILE/THR,ILE/THR	3,4403	6.2+/-15.9	0,3,2200	115	86	96		4094,4211,4211,4211	4.5	1	9	dbSNP_134	96	0,8600		0,0,4300	yes	missense,missense,missense,missense	VPS13A	NM_001018037.1,NM_001018038.2,NM_015186.3,NM_033305.2	89,89,89,89	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	benign,benign,benign,benign	1365/3136,1404/3070,1404/3096,1404/3175	79929004	3,13003	2203	4300	6503	SO:0001583	missense	23230	exon36			ATCTCACCATGGT	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.4211C>T	9.37:g.79929004C>T	ENSP00000353422:p.Thr1404Ile	77	0	0		94	62	0.659574	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	37	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	C	15.27	2.782618	0.49891	6.81E-4	0.0	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.47528	1.02;0.84;0.93;1.02	5.44	4.53	0.55603	.	0.285219	0.33290	N	0.005074	T	0.38799	0.1054	L	0.29908	0.895	0.80722	D	1	B;B;B;B	0.22414	0.002;0.019;0.069;0.033	B;B;B;B	0.27715	0.008;0.027;0.082;0.06	T	0.17930	-1.0353	10	0.37606	T	0.19	.	14.5567	0.68106	0.0:0.9276:0.0:0.0724	.	1365;1404;1404;1404	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	I	1404;1365;1404;1404	ENSP00000365821:T1404I;ENSP00000365823:T1365I;ENSP00000353422:T1404I;ENSP00000349985:T1404I	ENSP00000349985:T1404I	T	+	2	0	VPS13A	79118824	0.999000	0.42202	1.000000	0.80357	0.995000	0.86356	2.410000	0.44592	1.399000	0.46721	0.650000	0.86243	ACC	C|1.000;T|0.000	0.000	strong		0.388	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		T	79929004	C	T	79929004	3	4	22	1	0	0	0	0	1	0	0	0	17204	507	18	2	4353	2	VPS13A	9	79929004	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	53900	79929004	61284427	2073	4974											
VPS13A	23230	hgsc.bcm.edu	37	chr9	79936579	79936579	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaaaaatggagaaagtttaaGtatggattatatccgaacca	18	10	9	4	1	0	1	0	0	0	1	1	5	1	2	2	2	1	2	2	2	8	5	rs73467962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:79936579G>A	ENST00000360280.3	+	44	6007	c.5747G>A	c.(5746-5748)aGt>aAt	p.S1916N	VPS13A_ENST00000376636.3_Missense_Mutation_p.S1877N|VPS13A_ENST00000376634.4_Missense_Mutation_p.S1916N|VPS13A_ENST00000357409.5_Missense_Mutation_p.S1916N	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	1916					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						GAAAGTTTAAGTATGGATTAT	0.343													G|||	72	0.014377	0.0537	0.0014	5008	,	,		16144	0.0		0.0	False		,,,				2504	0.0				p.S1916N		Atlas-SNP	.											.	VPS13A	735	.	0			c.G5747A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER,ASN/SER	183,4223	118.4+/-156.1	3,177,2023	84	82	82		5630,5747,5747,5747	1.9	1	9	dbSNP_130	82	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense	VPS13A	NM_001018037.1,NM_001018038.2,NM_015186.3,NM_033305.2	46,46,46,46	3,178,6322	AA,AG,GG		0.0116,4.1534,1.4147	benign,benign,benign,benign	1877/3136,1916/3070,1916/3096,1916/3175	79936579	184,12822	2203	4300	6503	SO:0001583	missense	23230	exon44			GTTTAAGTATGGA	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.5747G>A	9.37:g.79936579G>A	ENSP00000353422:p.Ser1916Asn	99	0	0		125	75	0.6	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	37	CCDS6655.1	19|19	0.0086996336996337|0.0086996336996337	19|19	0.03861788617886179|0.03861788617886179	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	6.184|6.184	0.402055|0.402055	0.11696|0.11696	0.041534|0.041534	1.16E-4|1.16E-4	ENSG00000197969|ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409|ENST00000419472	T;T;T;T|.	0.47869|.	1.0;0.83;0.91;1.0|.	5.8|5.8	1.87|1.87	0.25490|0.25490	.|.	0.321368|.	0.38111|.	N|.	0.001815|.	T|T	0.08044|0.08044	0.0201|0.0201	N|N	0.11560|0.11560	0.145|0.145	0.80722|0.80722	D|D	1|1	B;B;B;B;B|.	0.16802|.	0.004;0.005;0.019;0.019;0.019|.	B;B;B;B;B|.	0.18871|.	0.006;0.012;0.01;0.023;0.023|.	T|T	0.01899|0.01899	-1.1251|-1.1251	10|5	0.37606|.	T|.	0.19|.	.|.	5.1895|5.1895	0.15203|0.15203	0.3604:0.1441:0.4955:0.0|0.3604:0.1441:0.4955:0.0	.|.	168;1877;1916;1916;1916|.	B1ALW4;Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4|.	.;.;VP13A_HUMAN;.;.|.	N|I	1916;1877;1916;1916|169	ENSP00000365821:S1916N;ENSP00000365823:S1877N;ENSP00000353422:S1916N;ENSP00000349985:S1916N|.	ENSP00000349985:S1916N|.	S|V	+|+	2|1	0|0	VPS13A|VPS13A	79126399|79126399	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.867000|0.867000	0.49689|0.49689	1.688000|1.688000	0.37690|0.37690	0.347000|0.347000	0.23924|0.23924	-0.373000|-0.373000	0.07131|0.07131	AGT|GTA	G|0.987;A|0.013	0.013	strong		0.343	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186		A	79936579	G	A	79936579	3	1	22	1	0	0	0	0	1	0	0	0	17204	1029	36	2	5921	2	VPS13A	9	79936579	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	7575	79936579	61276852	2074	4975											
VPS13A	23230	hgsc.bcm.edu	37	chr9	79959197	79959197	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctattgcgtctagataacgaGgtaagtttttttttcttttt	8	21	7	5	2	2	1	0	0	2	1	2	2	2	1	0	1	2	2	0	1	4	11	rs73449933	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:79959197G>A	ENST00000360280.3	+	51	7415	c.7155G>A	c.(7153-7155)gaG>gaA	p.E2385E	VPS13A_ENST00000376636.3_Splice_Site_p.E2346E|VPS13A_ENST00000376634.4_Splice_Site_p.E2385E|VPS13A_ENST00000357409.5_Splice_Site_p.E2385E	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	2385					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						TAGATAACGAGGTAAGTTTTT	0.289													G|||	71	0.0141773	0.053	0.0014	5008	,	,		13508	0.0		0.0	False		,,,				2504	0.0				p.E2385E		Atlas-SNP	.											.	VPS13A	735	.	0			c.G7155A						PASS	.	G	,,,	169,4237	101.2+/-139.8	3,163,2037	80	91	87		7038,7155,7155,7155	2.7	1	9	dbSNP_130	87	1,8585	1.2+/-3.3	0,1,4292	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	VPS13A	NM_001018037.1,NM_001018038.2,NM_015186.3,NM_033305.2	,,,	3,164,6329	AA,AG,GG		0.0116,3.8357,1.3085	,,,	2346/3136,2385/3070,2385/3096,2385/3175	79959197	170,12822	2203	4293	6496	SO:0001630	splice_region_variant	23230	exon51			TAACGAGGTAAGT	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.7155+1G>A	9.37:g.79959197G>A		69	0	0		81	57	0.703704	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Silent	SNP	ENST00000360280.3	37	CCDS6655.1																																																																																			G|0.986;A|0.014	0.014	strong		0.289	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	Silent	A	79959197	G	A	79959197	5	1	22	1	0	0	0	0	0	0	1	0	17204	1014	35	2	7357	2	VPS13A	9	79959197	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	22618	79959197	61254234	2075	4976											
GNA14	9630	hgsc.bcm.edu	37	chr9	80144099	80144099	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgaacccctttctgtcttcGtcgctgtaaccagacccatg	7	12	8	14	2	2	2	0	1	2	1	4	2	2	2	4	0	2	2	4	0	2	3	rs12346870	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:80144099G>A	ENST00000341700.6	-	2	708	c.195C>T	c.(193-195)gaC>gaT	p.D65D	RP11-466A17.1_ENST00000439145.1_RNA	NM_004297.3	NP_004288.1	O95837	GNA14_HUMAN	guanine nucleotide binding protein (G protein), alpha 14	65					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						TTCTGTCTTCGTCGCTGTAAC	0.448													G|||	114	0.0227636	0.0809	0.0086	5008	,	,		21370	0.0		0.001	False		,,,				2504	0.0				p.D65D		Atlas-SNP	.											.	GNA14	50	.	0			c.C195T						PASS	.	G		273,4133	154.0+/-187.5	12,249,1942	339	317	324		195	-0.6	1	9	dbSNP_120	324	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	GNA14	NM_004297.3		12,251,6240	AA,AG,GG		0.0233,6.1961,2.1144		65/356	80144099	275,12731	2203	4300	6503	SO:0001819	synonymous_variant	9630	exon2			GTCTTCGTCGCTG	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.195C>T	9.37:g.80144099G>A		291	0	0		324	213	0.657407	NM_004297	B1ALW3	Silent	SNP	ENST00000341700.6	37	CCDS6657.1																																																																																			G|0.976;A|0.024	0.024	strong		0.448	GNA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052759.1			A	80144099	G	A	80144099	2	1	22	1	0	0	0	0	0	0	0	1	6510	1136	40	1		1	GNA14	9	80144099	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	184902	80144099	61069332	2076	4977											
CEP78	84131	hgsc.bcm.edu	37	chr9	80881357	80881357	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttgttttgtttttccttctaGtttcagaaaattacaggtga	9	20	7	5	0	2	2	1	1	1	1	3	2	3	2	1	1	1	3	1	1	4	9	rs146563928	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:80881357G>C	ENST00000424347.2	+	15	2086		c.e15-1		CEP78_ENST00000376597.4_Splice_Site|CEP78_ENST00000277082.5_Splice_Site|CEP78_ENST00000415759.2_Splice_Site|CEP78_ENST00000376598.2_Splice_Site			Q5JTW2	CEP78_HUMAN	centrosomal protein 78kDa						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						TTTCCTTCTAGTTTCAGAAAA	0.378													G|||	2	0.000399361	0.0	0.0014	5008	,	,		18264	0.0		0.001	False		,,,				2504	0.0				.		Atlas-SNP	.											.	CEP78	79	.	0			c.1849-1G>C						PASS	.	G	,	1,3681		0,1,1840	40	40	40		,	4	1	9	dbSNP_134	40	21,8139		0,21,4059	yes	splice-3,splice-3	CEP78	NM_001098802.1,NM_032171.1	,	0,22,5899	CC,CG,GG		0.2574,0.0272,0.1858	,	,	80881357	22,11820	1841	4080	5921	SO:0001630	splice_region_variant	84131	exon16			CTTCTAGTTTCAG	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.1798-1G>C	9.37:g.80881357G>C		34	0	0		29	10	0.344828	NM_001098802	A1A4S8|E9PHX5|Q5BJE3|Q5JTW0|Q5JTW1|Q9H9N3	Splice_Site	SNP	ENST00000424347.2	37		2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	14.72	2.618270	0.46736	2.72E-4	0.002574	ENSG00000148019	ENST00000424347;ENST00000415085;ENST00000415759;ENST00000376597;ENST00000277082;ENST00000376598	.	.	.	6.07	4.01	0.46588	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.3193	0.26517	0.1296:0.1641:0.7063:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CEP78	80071177	0.987000	0.35691	0.999000	0.59377	0.943000	0.58893	1.038000	0.30254	2.885000	0.99019	0.655000	0.94253	.	G|0.999;C|0.001	0.001	strong		0.378	CEP78-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000052766.2	XM_095991	Intron	C	80881357	G	C	80881357	5	2	22	1	0	0	0	0	0	0	1	0	3264	1043	36	4	1910	4	CEP78	9	80881357	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	737258	80881357	60332074	2077	4978											
GOLM1	51280	hgsc.bcm.edu	37	chr9	88650332	88650332	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgtccgtcggggatgacaagCtggtctcgctcagggccctc	5	9	14	13	3	2	1	1	1	1	0	6	2	3	2	2	4	1	2	2	4	1	0	rs61741197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:88650332C>G	ENST00000388712.3	-	8	1134	c.966G>C	c.(964-966)caG>caC	p.Q322H	GOLM1_ENST00000388711.3_Missense_Mutation_p.Q322H|GOLM1_ENST00000257504.6_5'Flank	NM_016548.3	NP_057632.2	Q8NBJ4	GOLM1_HUMAN	golgi membrane protein 1	322					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						GGATGACAAGCTGGTCTCGCT	0.652											OREG0019278	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	249	0.0497204	0.1823	0.0115	5008	,	,		15263	0.0		0.0	False		,,,				2504	0.0				p.Q322H		Atlas-SNP	.											.	GOLM1	36	.	0			c.G966C						PASS	.	C	HIS/GLN,HIS/GLN	673,3733	284.6+/-277.7	59,555,1589	76	84	81		966,966	2.7	1	9	dbSNP_129	81	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	GOLM1	NM_016548.3,NM_177937.2	24,24	59,556,5888	GG,GC,CC		0.0116,15.2746,5.1822	possibly-damaging,possibly-damaging	322/402,322/402	88650332	674,12332	2203	4300	6503	SO:0001583	missense	51280	exon8			GACAAGCTGGTCT	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.966G>C	9.37:g.88650332C>G	ENSP00000373364:p.Gln322His	93	0	0	1261	104	71	0.682692	NM_016548	Q6IAF4|Q9NRB9	Missense_Mutation	SNP	ENST00000388712.3	37	CCDS35054.1	90	0.04120879120879121	84	0.17073170731707318	6	0.016574585635359115	0	0.0	0	0.0	C	11.23	1.576207	0.28092	0.152746	1.16E-4	ENSG00000135052	ENST00000388712;ENST00000388711	T;T	0.47177	0.85;0.85	4.54	2.7	0.31948	.	0.524964	0.19303	N	0.117587	T	0.00241	0.0007	L	0.56769	1.78	0.33372	P	0.42634399999999995	D	0.64830	0.994	D	0.64321	0.924	T	0.06625	-1.0816	9	0.40728	T	0.16	-0.0466	6.3297	0.21262	0.0:0.7825:0.0:0.2175	rs61741197	322	Q8NBJ4	GOLM1_HUMAN	H	322	ENSP00000373364:Q322H;ENSP00000373363:Q322H	ENSP00000373363:Q322H	Q	-	3	2	GOLM1	87840152	1.000000	0.71417	0.997000	0.53966	0.445000	0.32107	1.172000	0.31908	1.282000	0.44496	0.462000	0.41574	CAG	C|0.947;G|0.053	0.053	strong		0.652	GOLM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052904.2	NM_177937		G	88650332	C	G	88650332	3	3	22	1	0	0	0	0	1	0	0	0	6575	796	28	4	251	4	GOLM1	9	88650332	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	7768975	88650332	52563099	2078	4979											
ROR2	4920	hgsc.bcm.edu	37	chr9	94499797	94499797	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacccatcctcgtggtaatcAtccctggtaagaaacacaca	14	8	6	13	1	1	1	1	0	0	1	4	1	3	1	3	2	2	2	3	2	4	2	rs16907720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:94499797A>G	ENST00000375708.3	-	5	696	c.498T>C	c.(496-498)gaT>gaC	p.D166D	ROR2_ENST00000550066.1_5'UTR|ROR2_ENST00000375715.1_Silent_p.D26D	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	166					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						CGTGGTAATCATCCCTGGTAA	0.512													A|||	361	0.0720847	0.1959	0.0504	5008	,	,		16550	0.0		0.0537	False		,,,				2504	0.0133				p.D166D		Atlas-SNP	.											.	ROR2	167	.	0			c.T498C						PASS	.	A		757,3649	309.1+/-290.9	63,631,1509	80	73	75		498	-4.9	0.8	9	dbSNP_123	75	573,8027	153.7+/-208.1	19,535,3746	no	coding-synonymous	ROR2	NM_004560.3		82,1166,5255	GG,GA,AA		6.6628,17.1811,10.226		166/944	94499797	1330,11676	2203	4300	6503	SO:0001819	synonymous_variant	4920	exon5			GTAATCATCCCTG	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.498T>C	9.37:g.94499797A>G		50	0	0		38	26	0.684211	NM_004560	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Silent	SNP	ENST00000375708.3	37	CCDS6691.1																																																																																			A|0.902;G|0.098	0.098	strong		0.512	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1			G	94499797	A	G	94499797	2	3	22	1	0	0	0	0	0	0	0	1	13542	214	8	3		3	ROR2	9	94499797	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	5849465	94499797	46713634	2079	4980											
NOL8	55035	hgsc.bcm.edu	37	chr9	95076833	95076833	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagctgtctttgtcaaagcCtatgttgtgagtctttgcac	7	15	10	9	0	3	1	1	1	2	0	3	1	3	1	1	0	3	4	1	0	2	4	rs373764183		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95076833C>G	ENST00000535387.1	-	6	2073	c.2074G>C	c.(2074-2076)Ggc>Cgc	p.G692R	NOL8_ENST00000542053.1_Missense_Mutation_p.G624R|NOL8_ENST00000545558.1_Missense_Mutation_p.G692R|NOL8_ENST00000358855.4_Missense_Mutation_p.G624R|NOL8_ENST00000442668.2_Missense_Mutation_p.G692R					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						TTGTCAAAGCCTATGTTGTGA	0.433																																					p.G692R		Atlas-SNP	.											.	NOL8	118	.	0			c.G2074C						PASS	.	C	ARG/GLY	1,3761		0,1,1880	37	33	35		2074	1.5	0	9		35	0,8226		0,0,4113	no	missense	NOL8	NM_017948.5	125	0,1,5993	GG,GC,CC		0.0,0.0266,0.0083	probably-damaging	692/1168	95076833	1,11987	1881	4113	5994	SO:0001583	missense	55035	exon7			CAAAGCCTATGTT	AB109030	CCDS47993.1, CCDS59135.1	9q22.32	2013-02-12	2004-01-12	2004-01-14	ENSG00000198000	ENSG00000198000		"RNA binding motif (RRM) containing"	23387	protein-coding gene	gene with protein product		611534	"chromosome 9 open reading frame 34"	C9orf34		12477932	Standard	NM_017948		Approved	FLJ20736, Nop132	uc022bjx.1	Q76FK4	OTTHUMG00000020221	ENST00000535387.1:c.2074G>C	9.37:g.95076833C>G	ENSP00000441300:p.Gly692Arg	76	0	0		97	65	0.670103	NM_017948		Missense_Mutation	SNP	ENST00000535387.1	37	CCDS47993.1	.	.	.	.	.	.	.	.	.	.	C	11.25	1.582405	0.28180	2.66E-4	0.0	ENSG00000198000	ENST00000442668;ENST00000375594;ENST00000358855;ENST00000545558;ENST00000535387;ENST00000542053;ENST00000432670	T;T;T;T;T;T	0.49720	0.77;0.77;0.77;0.77;0.77;0.77	5.48	1.52	0.23074	.	1.217900	0.05599	N	0.576075	T	0.33556	0.0867	L	0.29908	0.895	0.09310	N	1	P	0.41265	0.744	B	0.39068	0.289	T	0.21793	-1.0235	10	0.52906	T	0.07	0.5806	1.5277	0.02529	0.1481:0.4632:0.1439:0.2448	.	692	Q76FK4	NOL8_HUMAN	R	692;694;624;692;692;624;692	ENSP00000401177:G692R;ENSP00000351723:G624R;ENSP00000441140:G692R;ENSP00000441300:G692R;ENSP00000440709:G624R;ENSP00000414112:G692R	ENSP00000351723:G624R	G	-	1	0	NOL8	94116654	0.000000	0.05858	0.000000	0.03702	0.089000	0.18198	0.191000	0.17076	0.018000	0.15052	0.561000	0.74099	GGC	.	.	weak		0.433	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948		G	95076833	C	G	95076833	3	3	22	1	0	0	0	0	1	0	0	0	10536	681	24	4	1473	4	NOL8	9	95076833	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	577036	95076833	46136598	2080	4981											
NOL8	55035	hgsc.bcm.edu	37	chr9	95077498	95077498	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tggcattatactcctcacctCcttcagagtcagctaattct	9	14	5	13	0	4	1	3	0	1	1	6	1	6	1	3	1	2	2	3	1	3	5	rs58545014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95077498C>T	ENST00000535387.1	-	6	1408	c.1409G>A	c.(1408-1410)gGa>gAa	p.G470E	NOL8_ENST00000542053.1_Missense_Mutation_p.G402E|NOL8_ENST00000545558.1_Missense_Mutation_p.G470E|NOL8_ENST00000358855.4_Missense_Mutation_p.G402E|NOL8_ENST00000442668.2_Missense_Mutation_p.G470E					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						CTCCTCACCTCCTTCAGAGTC	0.433													C|||	166	0.033147	0.1172	0.0159	5008	,	,		20446	0.0		0.0	False		,,,				2504	0.0				p.G470E		Atlas-SNP	.											.	NOL8	118	.	0			c.G1409A						PASS	.	C	GLU/GLY	379,3445		15,349,1548	67	62	63		1409	-2.3	0	9	dbSNP_129	63	9,8283		0,9,4137	yes	missense	NOL8	NM_017948.5	98	15,358,5685	TT,TC,CC		0.1085,9.9111,3.2024	benign	470/1168	95077498	388,11728	1912	4146	6058	SO:0001583	missense	55035	exon7			TCACCTCCTTCAG	AB109030	CCDS47993.1, CCDS59135.1	9q22.32	2013-02-12	2004-01-12	2004-01-14	ENSG00000198000	ENSG00000198000		"RNA binding motif (RRM) containing"	23387	protein-coding gene	gene with protein product		611534	"chromosome 9 open reading frame 34"	C9orf34		12477932	Standard	NM_017948		Approved	FLJ20736, Nop132	uc022bjx.1	Q76FK4	OTTHUMG00000020221	ENST00000535387.1:c.1409G>A	9.37:g.95077498C>T	ENSP00000441300:p.Gly470Glu	178	0	0		161	118	0.732919	NM_017948		Missense_Mutation	SNP	ENST00000535387.1	37	CCDS47993.1	73	0.033424908424908424	67	0.13617886178861788	6	0.016574585635359115	0	0.0	0	0.0	C	2.889	-0.230150	0.05983	0.099111	0.001085	ENSG00000198000	ENST00000442668;ENST00000375594;ENST00000358855;ENST00000545558;ENST00000535387;ENST00000542053;ENST00000432670	T;T;T;T;T;T	0.15256	2.71;2.7;2.71;2.93;2.7;2.44	5.69	-2.34	0.06704	.	1.014810	0.07869	N	0.967526	T	0.00039	0.0001	N	0.16656	0.425	0.80722	P	0.0	B	0.15141	0.012	B	0.11329	0.006	T	0.41124	-0.9526	9	0.10377	T	0.69	-5.5238	1.3463	0.02164	0.171:0.3053:0.1593:0.3644	rs58545014;rs61740235	470	Q76FK4	NOL8_HUMAN	E	470;472;402;470;470;402;470	ENSP00000401177:G470E;ENSP00000351723:G402E;ENSP00000441140:G470E;ENSP00000441300:G470E;ENSP00000440709:G402E;ENSP00000414112:G470E	ENSP00000351723:G402E	G	-	2	0	NOL8	94117319	0.000000	0.05858	0.000000	0.03702	0.182000	0.23217	-1.648000	0.01995	-0.302000	0.08869	-0.345000	0.07892	GGA	C|0.972;T|0.028	0.028	strong		0.433	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948		T	95077498	C	T	95077498	3	4	22	1	0	0	0	0	1	0	0	0	10536	855	30	2	2138	2	NOL8	9	95077498	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	665	95077498	46135933	2081	4982											
NOL8	55035	hgsc.bcm.edu	37	chr9	95078413	95078413	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtattttgagggatcatatTtgatgatgttacgcaagtca	12	15	10	4	1	2	3	2	3	0	0	2	4	2	4	0	1	1	3	0	1	4	6	rs41305617	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95078413T>C	ENST00000535387.1	-	6	493	c.494A>G	c.(493-495)aAa>aGa	p.K165R	NOL8_ENST00000542053.1_Missense_Mutation_p.K97R|NOL8_ENST00000545558.1_Missense_Mutation_p.K165R|NOL8_ENST00000358855.4_Missense_Mutation_p.K97R|NOL8_ENST00000442668.2_Missense_Mutation_p.K165R					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						GGGATCATATTTGATGATGTT	0.363													T|||	47	0.00938498	0.0023	0.0144	5008	,	,		20765	0.0		0.0338	False		,,,				2504	0.0				p.K165R		Atlas-SNP	.											.	NOL8	118	.	0			c.A494G						PASS	.	T	ARG/LYS	16,3702		0,16,1843	96	85	89		494	5.1	1	9	dbSNP_127	89	231,7979		3,225,3877	yes	missense	NOL8	NM_017948.5	26	3,241,5720	CC,CT,TT		2.8136,0.4303,2.0708	probably-damaging	165/1168	95078413	247,11681	1859	4105	5964	SO:0001583	missense	55035	exon7			TCATATTTGATGA	AB109030	CCDS47993.1, CCDS59135.1	9q22.32	2013-02-12	2004-01-12	2004-01-14	ENSG00000198000	ENSG00000198000		"RNA binding motif (RRM) containing"	23387	protein-coding gene	gene with protein product		611534	"chromosome 9 open reading frame 34"	C9orf34		12477932	Standard	NM_017948		Approved	FLJ20736, Nop132	uc022bjx.1	Q76FK4	OTTHUMG00000020221	ENST00000535387.1:c.494A>G	9.37:g.95078413T>C	ENSP00000441300:p.Lys165Arg	223	0	0		242	91	0.376033	NM_017948		Missense_Mutation	SNP	ENST00000535387.1	37	CCDS47993.1	33	0.01510989010989011	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	24	0.0316622691292876	T	21.3	4.129430	0.77549	0.004303	0.028136	ENSG00000198000	ENST00000442668;ENST00000375594;ENST00000358855;ENST00000545558;ENST00000535387;ENST00000542053;ENST00000432670;ENST00000433029;ENST00000421075;ENST00000411621;ENST00000535807	T;T;T;T;T;T;T;T	0.54479	2.12;2.06;2.12;2.32;2.06;1.84;0.57;0.66	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.40815	0.1132	L	0.39147	1.195	0.47659	D	0.999482	D	0.89917	1.0	D	0.87578	0.998	T	0.60949	-0.7161	10	0.87932	D	0	-23.0153	15.1284	0.72500	0.0:0.0:0.0:1.0	rs41305617	165	Q76FK4	NOL8_HUMAN	R	165;167;97;165;165;97;165;165;165;97;97	ENSP00000401177:K165R;ENSP00000351723:K97R;ENSP00000441140:K165R;ENSP00000441300:K165R;ENSP00000440709:K97R;ENSP00000414112:K165R;ENSP00000412471:K165R;ENSP00000390143:K165R	ENSP00000351723:K97R	K	-	2	0	NOL8	94118234	1.000000	0.71417	1.000000	0.80357	0.536000	0.34869	7.001000	0.76297	2.021000	0.59480	0.528000	0.53228	AAA	T|0.986;C|0.014	0.014	strong		0.363	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948		C	95078413	T	C	95078413	3	2	22	1	0	0	0	0	1	0	0	0	10536	1841	64	3	3053	3	NOL8	9	95078413	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	915	95078413	46135018	2082	4983											
NOL8	55035	hgsc.bcm.edu	37	chr9	95081569	95081569	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tccactcctcctgtcttttcTaacaagttggcgttacctgt	6	16	6	13	1	2	0	0	0	2	0	5	0	5	0	4	1	2	2	4	1	3	5	rs16908298	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95081569T>C	ENST00000535387.1	-	4	350	c.351A>G	c.(349-351)ttA>ttG	p.L117L	NOL8_ENST00000542053.1_Silent_p.L49L|NOL8_ENST00000545558.1_Silent_p.L117L|NOL8_ENST00000358855.4_Silent_p.L49L|NOL8_ENST00000442668.2_Silent_p.L117L|NOL8_ENST00000543985.1_5'Flank					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						CTGTCTTTTCTAACAAGTTGG	0.428													T|||	166	0.033147	0.1172	0.0159	5008	,	,		20037	0.0		0.0	False		,,,				2504	0.0				p.L117L		Atlas-SNP	.											.	NOL8	118	.	0			c.A351G						PASS	.	T		382,3474		15,352,1561	183	167	172		351	-3.3	0	9	dbSNP_123	172	9,8229		0,9,4110	no	coding-synonymous	NOL8	NM_017948.5		15,361,5671	CC,CT,TT		0.1092,9.9066,3.233		117/1168	95081569	391,11703	1928	4119	6047	SO:0001819	synonymous_variant	55035	exon5			CTTTTCTAACAAG	AB109030	CCDS47993.1, CCDS59135.1	9q22.32	2013-02-12	2004-01-12	2004-01-14	ENSG00000198000	ENSG00000198000		"RNA binding motif (RRM) containing"	23387	protein-coding gene	gene with protein product		611534	"chromosome 9 open reading frame 34"	C9orf34		12477932	Standard	NM_017948		Approved	FLJ20736, Nop132	uc022bjx.1	Q76FK4	OTTHUMG00000020221	ENST00000535387.1:c.351A>G	9.37:g.95081569T>C		284	0	0		241	156	0.647303	NM_017948		Silent	SNP	ENST00000535387.1	37	CCDS47993.1																																																																																			T|0.969;C|0.031	0.031	strong		0.428	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948		C	95081569	T	C	95081569	2	2	22	1	0	0	0	0	0	0	0	1	10536	1519	53	3		3	NOL8	9	95081569	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	3156	95081569	46131862	2083	4984											
ECM2	1842	hgsc.bcm.edu	37	chr9	95267938	95267938	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggcttcactgagattgttTccttccaattctaaggtgac	8	16	8	9	0	2	2	1	2	1	1	4	3	4	2	2	2	0	2	2	2	2	7	rs35161698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95267938T>C	ENST00000344604.5	-	7	1490	c.1341A>G	c.(1339-1341)ggA>ggG	p.G447G	CENPP_ENST00000375587.3_Intron|ECM2_ENST00000444490.2_Silent_p.G425G	NM_001197295.1|NM_001393.3	NP_001184224.1|NP_001384.1	O94769	ECM2_HUMAN	extracellular matrix protein 2, female organ and adipocyte specific	447					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						TGAGATTGTTTCCTTCCAATT	0.323													T|||	117	0.0233626	0.0802	0.0159	5008	,	,		15033	0.0		0.0	False		,,,				2504	0.0				p.G447G		Atlas-SNP	.											.	ECM2	147	.	0			c.A1341G						PASS	.	T	,,,	294,4112	144.2+/-179.2	6,282,1915	80	85	83		,1275,1275,1341	5.8	1	9	dbSNP_126	83	8,8592	5.7+/-21.5	0,8,4292	no	intron,coding-synonymous,coding-synonymous,coding-synonymous	ECM2,CENPP	NM_001012267.1,NM_001197295.1,NM_001197296.1,NM_001393.3	,,,	6,290,6207	CC,CT,TT		0.093,6.6727,2.322	,,,	,425/678,425/644,447/700	95267938	302,12704	2203	4300	6503	SO:0001819	synonymous_variant	1842	exon7			ATTGTTTCCTTCC	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.1341A>G	9.37:g.95267938T>C		117	0	0		99	62	0.626263	NM_001393	B2R730|E2PU11|Q5T9F2|Q7Z3D0	Silent	SNP	ENST00000344604.5	37	CCDS6698.1																																																																																			T|0.978;C|0.022	0.022	strong		0.323	ECM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053091.1	NM_001393		C	95267938	T	C	95267938	2	2	22	1	0	0	0	0	0	0	0	1	4900	1770	62	3		3	ECM2	9	95267938	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	186369	95267938	45945493	2084	4985											
IPPK	64768	hgsc.bcm.edu	37	chr9	95411816	95411816	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaattaggaaggcacatagcGtaaccactgagagtatccag	16	7	10	8	1	0	1	0	1	0	1	1	3	1	2	2	2	2	3	2	2	6	4	rs16908484	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95411816G>A	ENST00000287996.3	-	5	609	c.333C>T	c.(331-333)taC>taT	p.Y111Y		NM_022755.5	NP_073592.1	Q9H8X2	IPPK_HUMAN	inositol 1,3,4,5,6-pentakisphosphate 2-kinase	111					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						GGCACATAGCGTAACCACTGA	0.512													G|||	59	0.0117812	0.0424	0.0043	5008	,	,		19264	0.0		0.0	False		,,,				2504	0.0				p.Y111Y		Atlas-SNP	.											.	IPPK	34	.	0			c.C333T						PASS	.	G		156,4250	106.0+/-144.5	1,154,2048	165	127	140		333	-1.9	1	9	dbSNP_123	140	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	IPPK	NM_022755.5		1,155,6347	AA,AG,GG		0.0116,3.5406,1.2071		111/492	95411816	157,12849	2203	4300	6503	SO:0001819	synonymous_variant	64768	exon5			CATAGCGTAACCA	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.333C>T	9.37:g.95411816G>A		113	0	0		116	69	0.594828	NM_022755	Q5T9F7|Q9H7V8	Silent	SNP	ENST00000287996.3	37	CCDS6699.1																																																																																			G|0.986;A|0.014	0.014	strong		0.512	IPPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053101.1	NM_022755		A	95411816	G	A	95411816	2	1	22	1	0	0	0	0	0	0	0	1	7810	1140	40	1		1	IPPK	9	95411816	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	143878	95411816	45801615	2085	4986											
FGD3	89846	hgsc.bcm.edu	37	chr9	95766336	95766336	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctccagaagtcatcatgggCatattctctaacatctcctc	10	12	5	14	0	4	1	2	0	2	1	8	1	5	1	3	1	1	1	3	1	3	3	rs201073654		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95766336C>T	ENST00000375482.3	+	5	1093	c.597C>T	c.(595-597)ggC>ggT	p.G199G	FGD3_ENST00000337352.6_Silent_p.G199G|FGD3_ENST00000416701.2_Silent_p.G199G	NM_001083536.1	NP_001077005.1	Q5JSP0	FGD3_HUMAN	FYVE, RhoGEF and PH domain containing 3	199	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						TCATCATGGGCATATTCTCTA	0.582											OREG0019318	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G199G		Atlas-SNP	.											.	FGD3	116	.	0			c.C597T						PASS	.	C	,	1,4183		0,1,2091	77	81	80		597,597	-0.6	1	9		80	0,8488		0,0,4244	no	coding-synonymous,coding-synonymous	FGD3	NM_001083536.1,NM_033086.2	,	0,1,6335	TT,TC,CC		0.0,0.0239,0.0079	,	199/726,199/726	95766336	1,12671	2092	4244	6336	SO:0001819	synonymous_variant	89846	exon5			CATGGGCATATTC	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.597C>T	9.37:g.95766336C>T		99	0	0	1315	93	60	0.645161	NM_001083536	F8W7P2|Q4VX84|Q7Z7D9|Q8N5G1	Silent	SNP	ENST00000375482.3	37	CCDS43849.1																																																																																			C|1.000;T|0.000	0.000	strong		0.582	FGD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055493.1	NM_033086		T	95766336	C	T	95766336	2	4	22	1	0	0	0	0	0	0	0	1	5842	697	25	2		2	FGD3	9	95766336	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	354520	95766336	45447095	2086	4987											
FGD3	89846	hgsc.bcm.edu	37	chr9	95768396	95768396	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcaagaactttgaccgagcCgtagggctggtgagcacgtg	9	8	15	9	3	1	3	1	2	0	1	1	4	1	3	2	2	3	3	2	2	3	2	rs199786328		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95768396C>T	ENST00000375482.3	+	6	1267	c.771C>T	c.(769-771)gcC>gcT	p.A257A	FGD3_ENST00000337352.6_Silent_p.A257A|FGD3_ENST00000416701.2_Silent_p.A257A	NM_001083536.1	NP_001077005.1	Q5JSP0	FGD3_HUMAN	FYVE, RhoGEF and PH domain containing 3	257	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						TTGACCGAGCCGTAGGGCTGG	0.587																																					p.A257A		Atlas-SNP	.											.	FGD3	116	.	0			c.C771T						PASS	.	C	,	1,4327		0,1,2163	64	71	69		771,771	-7.4	0	9		69	0,8568		0,0,4284	no	coding-synonymous,coding-synonymous	FGD3	NM_001083536.1,NM_033086.2	,	0,1,6447	TT,TC,CC		0.0,0.0231,0.0078	,	257/726,257/726	95768396	1,12895	2164	4284	6448	SO:0001819	synonymous_variant	89846	exon6			CCGAGCCGTAGGG	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.771C>T	9.37:g.95768396C>T		68	0	0		85	56	0.658824	NM_001083536	F8W7P2|Q4VX84|Q7Z7D9|Q8N5G1	Silent	SNP	ENST00000375482.3	37	CCDS43849.1																																																																																			C|1.000;T|0.000	0.000	strong		0.587	FGD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055493.1	NM_033086		T	95768396	C	T	95768396	2	4	22	1	0	0	0	0	0	0	0	1	5842	639	23	1		1	FGD3	9	95768396	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2060	95768396	45445035	2087	4988											
C9orf3	84909	hgsc.bcm.edu	37	chr9	97563076	97563076	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcacatggaatacccctgcCgcttccagaatgcttctgcc	8	10	8	15	1	2	1	1	0	1	1	3	2	3	2	5	1	4	2	5	1	3	3	rs34557833	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:97563076C>T	ENST00000375315.2	+	4	1156	c.1156C>T	c.(1156-1158)Cgc>Tgc	p.R386C	C9orf3_ENST00000297979.5_Missense_Mutation_p.R386C|C9orf3_ENST00000277198.2_Missense_Mutation_p.R386C|C9orf3_ENST00000395357.2_Missense_Mutation_p.R6C	NM_001193329.1	NP_001180258.1	Q8N6M6	AMPO_HUMAN	chromosome 9 open reading frame 3	386			R -> C (in dbSNP:rs34557833).		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)		ATACCCCTGCCGCTTCCAGAA	0.507													C|||	30	0.00599042	0.0227	0.0	5008	,	,		20701	0.0		0.0	False		,,,				2504	0.0				p.R386C		Atlas-SNP	.											.	C9orf3	100	.	0			c.C1156T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG	58,4348	56.2+/-92.4	0,58,2145	102	94	97		1156,1156,1156	4.4	1	9	dbSNP_126	97	0,8600		0,0,4300	yes	missense,missense,missense	C9orf3	NM_001193329.1,NM_001193331.2,NM_032823.5	180,180,180	0,58,6445	TT,TC,CC		0.0,1.3164,0.4459	possibly-damaging,possibly-damaging,possibly-damaging	386/820,386/567,386/721	97563076	58,12948	2203	4300	6503	SO:0001583	missense	84909	exon5			CCCTGCCGCTTCC	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.1156C>T	9.37:g.97563076C>T	ENSP00000364464:p.Arg386Cys	130	0	0		141	88	0.624114	NM_001193331	Q5T9B1|Q5T9B3|Q5T9B4|Q8WUL6|Q96M23|Q96SS1	Missense_Mutation	SNP	ENST00000375315.2	37	CCDS55328.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	C	23.3	4.397577	0.83120	0.013164	0.0	ENSG00000148120	ENST00000277198;ENST00000297979;ENST00000375315;ENST00000424143;ENST00000428313;ENST00000395357	T;T;T;T;T;T	0.15952	4.18;2.39;2.74;2.43;2.38;4.18	5.28	4.38	0.52667	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.24084	0.0583	M	0.63843	1.955	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;0.995;0.998	T	0.13710	-1.0499	10	0.72032	D	0.01	-13.0857	15.6642	0.77213	0.1375:0.8625:0.0:0.0	rs34557833	386;386;386;386	Q8N6M6;Q8N6M6-4;Q8N6M6-2;Q8N6M6-3	AMPO_HUMAN;.;.;.	C	386;386;386;209;168;6	ENSP00000277198:R386C;ENSP00000297979:R386C;ENSP00000364464:R386C;ENSP00000402171:R209C;ENSP00000401854:R168C;ENSP00000378763:R6C	ENSP00000277198:R386C	R	+	1	0	C9orf3	96602897	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	4.291000	0.59025	1.432000	0.47375	0.650000	0.86243	CGC	C|0.995;T|0.005	0.005	strong		0.507	C9orf3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032823		T	97563076	C	T	97563076	3	4	22	1	0	0	0	0	1	0	0	0	2479	652	23	1	1170	1	C9orf3	9	97563076	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1794680	97563076	43650355	2088	4989											
C9orf21	195827	hgsc.bcm.edu	37	chr9	99417000	99417000	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aactcacttgtaagaaactcCtggggattttggccagatcc	11	11	9	10	0	1	2	1	0	0	2	3	3	3	3	3	3	2	1	3	3	3	4	rs9886834|rs77297714	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:99417000C>T	ENST00000375234.3	-	2	247	c.248G>A	c.(247-249)aGg>aAg	p.R83K	AAED1_ENST00000464512.1_5'UTR	NM_153698.1	NP_714542.1	Q7RTV5	AAED1_HUMAN	AhpC/TSA antioxidant enzyme domain containing 1	83			R -> K (in dbSNP:rs9886834).														TAAGAAACTCCTGGGGATTTT	0.572													T|||	410	0.081869	0.2912	0.0259	5008	,	,		16276	0.0		0.002	False		,,,				2504	0.0051				p.R83K		Atlas-SNP	.											.	.	.	.	0			c.G248A						PASS	.	T	LYS/ARG	1109,3283		125,859,1212	59	58	58		248	-1.6	0.8	9	dbSNP_119	58	16,8558		0,16,4271	yes	missense	C9orf21	NM_153698.1	26	125,875,5483	TT,TC,CC		0.1866,25.2505,8.6765	benign	83/227	99417000	1125,11841	2196	4287	6483	SO:0001583	missense	195827	exon2			AAACTCCTGGGGA	BK000255	CCDS35073.1	9q22.32	2013-01-07	2012-03-06	2012-03-06	ENSG00000158122	ENSG00000158122			16881	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 21"	C9orf21			Standard	XM_005251783		Approved		uc004awm.3	Q7RTV5	OTTHUMG00000020299	ENST00000375234.3:c.248G>A	9.37:g.99417000C>T	ENSP00000364382:p.Arg83Lys	90	0	0		69	41	0.594203	NM_153698	B2RMW4|Q5JU02	Missense_Mutation	SNP	ENST00000375234.3	37	CCDS35073.1	132|132	0.06043956043956044|0.06043956043956044	124|124	0.25203252032520324|0.25203252032520324	8|8	0.022099447513812154|0.022099447513812154	0|0	0.0|0.0	0|0	0.0|0.0	T|T	0.325|0.325	-0.959491|-0.959491	0.02267|0.02267	0.252505|0.252505	0.001866|0.001866	ENSG00000158122|ENSG00000158122	ENST00000411939|ENST00000375234;ENST00000375233	.|T	.|0.39592	.|1.07	4.79|4.79	-1.64|-1.64	0.08318|0.08318	.|Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant (1);Thioredoxin-like fold (2);	.|0.514983	.|0.21661	.|N	.|0.071010	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02539|0.02539	-0.55|-0.55	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.20240|0.20240	-1.0281|-1.0281	4|9	.|0.02654	.|T	.|1	-1.013|-1.013	5.5316|5.5316	0.16987|0.16987	0.1376:0.4036:0.0:0.4588|0.1376:0.4036:0.0:0.4588	rs9886834;rs11538195;rs57315001;rs9886834|rs9886834;rs11538195;rs57315001;rs9886834	.|83	.|Q7RTV5	.|CI021_HUMAN	R|K	11|83	.|ENSP00000364382:R83K	.|ENSP00000364381:R83K	G|R	-|-	1|2	0|0	C9orf21|C9orf21	98456821|98456821	0.175000|0.175000	0.23083|0.23083	0.814000|0.814000	0.32528|0.32528	0.098000|0.098000	0.18820|0.18820	-0.008000|-0.008000	0.12788|0.12788	-0.858000|-0.858000	0.04110|0.04110	-1.916000|-1.916000	0.00518|0.00518	GGA|AGG	C|0.901;T|0.099	0.099	strong		0.572	AAED1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053273.1	NM_153698		T	99417000	C	T	99417000	3	4	22	1	0	0	0	0	1	0	0	0	2475	681	24	2	452	2	C9orf21	9	99417000	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1853924	99417000	41796431	2089	4990											
ZNF510	22869	hgsc.bcm.edu	37	chr9	99521150	99521150	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tattcattgcattcataagaTttctccccactgtgagtcct	9	16	5	11	0	3	2	2	1	1	1	5	2	4	2	3	0	1	1	3	0	2	6	rs61735521	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:99521150T>C	ENST00000375231.1	-	6	2612	c.1962A>G	c.(1960-1962)aaA>aaG	p.K654K	ZNF510_ENST00000223428.4_Silent_p.K654K			Q9Y2H8	ZN510_HUMAN	zinc finger protein 510	654					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)				ATTCATAAGATTTCTCCCCAC	0.383													T|||	174	0.0347444	0.1278	0.0072	5008	,	,		18490	0.0		0.0	False		,,,				2504	0.0				p.K654K		Atlas-SNP	.											.	ZNF510	59	.	0			c.A1962G						PASS	.	T		448,3958	211.8+/-231.9	22,404,1777	101	107	105		1962	-0.6	0	9	dbSNP_129	105	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ZNF510	NM_014930.1		22,406,6075	CC,CT,TT		0.0233,10.168,3.4599		654/684	99521150	450,12556	2203	4300	6503	SO:0001819	synonymous_variant	22869	exon6			ATAAGATTTCTCC	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.1962A>G	9.37:g.99521150T>C		148	0	0		162	103	0.635802	NM_014930	Q5SZP5	Silent	SNP	ENST00000375231.1	37	CCDS35074.1																																																																																			T|0.970;C|0.030	0.030	strong		0.383	ZNF510-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053287.1	NM_014930		C	99521150	T	C	99521150	2	2	22	1	0	0	0	0	0	0	0	1	17969	1490	52	3		3	ZNF510	9	99521150	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	104150	99521150	41692281	2090	4991											
ZNF510	22869	hgsc.bcm.edu	37	chr9	99522508	99522508	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcacatacattaccgcaacCtattttctttgttgaatagt	11	16	4	10	1	2	1	1	1	1	0	2	1	2	1	2	0	3	2	2	0	6	8	rs61731162	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:99522508C>T	ENST00000375231.1	-	6	1254	c.604G>A	c.(604-606)Ggt>Agt	p.G202S	ZNF510_ENST00000223428.4_Missense_Mutation_p.G202S|ZNF510_ENST00000472201.1_5'Flank			Q9Y2H8	ZN510_HUMAN	zinc finger protein 510	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)			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)				TTACCGCAACCTATTTTCTTT	0.294													C|||	172	0.034345	0.1263	0.0072	5008	,	,		17618	0.0		0.0	False		,,,				2504	0.0				p.G202S		Atlas-SNP	.											.	ZNF510	59	.	0			c.G604A						PASS	.	C	SER/GLY	441,3957	195.0+/-219.7	22,397,1780	39	44	42		604	0	0	9	dbSNP_129	42	2,8588	2.2+/-6.3	0,2,4293	yes	missense	ZNF510	NM_014930.1	56	22,399,6073	TT,TC,CC		0.0233,10.0273,3.4108	benign	202/684	99522508	443,12545	2199	4295	6494	SO:0001583	missense	22869	exon6			CGCAACCTATTTT	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.604G>A	9.37:g.99522508C>T	ENSP00000364379:p.Gly202Ser	116	0	0		108	67	0.62037	NM_014930	Q5SZP5	Missense_Mutation	SNP	ENST00000375231.1	37	CCDS35074.1	53	0.024267399267399268	50	0.1016260162601626	3	0.008287292817679558	0	0.0	0	0.0	c	10.85	1.467776	0.26335	0.100273	2.33E-4	ENSG00000081386	ENST00000375231;ENST00000223428	T;T	0.05139	3.49;3.49	3.02	0.0252	0.14144	.	.	.	.	.	T	0.00109	0.0003	N	0.12569	0.235	0.09310	N	1	B	0.26002	0.139	B	0.19946	0.027	T	0.48305	-0.9047	9	0.18710	T	0.47	.	2.8749	0.05628	0.3758:0.3954:0.0:0.2288	.	202	Q9Y2H8	ZN510_HUMAN	S	202	ENSP00000364379:G202S;ENSP00000223428:G202S	ENSP00000223428:G202S	G	-	1	0	ZNF510	98562329	0.000000	0.05858	0.001000	0.08648	0.318000	0.28184	0.101000	0.15251	0.012000	0.14892	0.655000	0.94253	GGT	C|0.973;T|0.027	0.027	strong		0.294	ZNF510-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053287.1	NM_014930		T	99522508	C	T	99522508	3	4	22	1	0	0	0	0	1	0	0	0	17969	681	24	2	1451	2	ZNF510	9	99522508	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1358	99522508	41690923	2091	4992											
ZNF782	158431	hgsc.bcm.edu	37	chr9	99581440	99581440	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgaaggatttccctcctgTgagagttttgtgagtgattc	7	15	12	7	0	0	4	0	4	0	1	3	6	2	5	2	1	0	2	2	1	1	4	rs35403084	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:99581440T>C	ENST00000481138.1	-	6	1526	c.865A>G	c.(865-867)Aca>Gca	p.T289A	ZNF782_ENST00000535338.1_Missense_Mutation_p.T157A|ZNF782_ENST00000466833.1_5'Flank	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	289			T -> A (in dbSNP:rs35403084).		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)				TTCCCTCCTGTGAGAGTTTTG	0.363													T|||	174	0.0347444	0.1278	0.0072	5008	,	,		19195	0.0		0.0	False		,,,				2504	0.0				p.T289A		Atlas-SNP	.											.	ZNF782	64	.	0			c.A865G						PASS	.	T	ALA/THR	440,3966	207.8+/-229.1	21,398,1784	84	88	86		865	0.7	0	9	dbSNP_126	86	2,8598	2.2+/-6.3	0,2,4298	yes	missense	ZNF782	NM_001001662.1	58	21,400,6082	CC,CT,TT		0.0233,9.9864,3.3984	benign	289/700	99581440	442,12564	2203	4300	6503	SO:0001583	missense	158431	exon6			CTCCTGTGAGAGT	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.865A>G	9.37:g.99581440T>C	ENSP00000419397:p.Thr289Ala	81	0	0		92	57	0.619565	NM_001001662	B2RNR0	Missense_Mutation	SNP	ENST00000481138.1	37	CCDS35075.1	55|55	0.025183150183150184|0.025183150183150184	52|52	0.10569105691056911|0.10569105691056911	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	T|T	11.19|11.19	1.564629|1.564629	0.27915|0.27915	0.099864|0.099864	2.33E-4|2.33E-4	ENSG00000196597|ENSG00000196597	ENST00000289032|ENST00000481138;ENST00000535338	.|T;T	.|0.05996	.|3.5;3.36	3.29|3.29	0.74|0.74	0.18330|0.18330	.|Zinc finger, C2H2 (1);	.|1.047330	.|0.07644	.|N	.|0.930840	T|T	0.00144|0.00144	0.0004|0.0004	L|L	0.45051|0.45051	1.395|1.395	0.20821|0.20821	N|N	0.999841|0.999841	.|P	.|0.37525	.|0.598	.|B	.|0.32211	.|0.142	T|T	0.44757|0.44757	-0.9307|-0.9307	5|10	.|0.42905	.|T	.|0.14	.|.	8.5445|8.5445	0.33413|0.33413	0.0:0.0:0.3768:0.6232|0.0:0.0:0.3768:0.6232	rs35403084|rs35403084	.|289	.|Q6ZMW2	.|ZN782_HUMAN	R|A	277|289;157	.|ENSP00000419397:T289A;ENSP00000440624:T157A	.|ENSP00000419397:T289A	H|T	-|-	2|1	0|0	ZNF782|ZNF782	98621261|98621261	0.044000|0.044000	0.20184|0.20184	0.000000|0.000000	0.03702|0.03702	0.137000|0.137000	0.21094|0.21094	1.139000|1.139000	0.31504|0.31504	0.142000|0.142000	0.18901|0.18901	0.524000|0.524000	0.50904|0.50904	CAC|ACA	T|0.971;C|0.029	0.029	strong		0.363	ZNF782-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356810.1	NM_001001662		C	99581440	T	C	99581440	3	2	22	1	0	0	0	0	1	0	0	0	18170	1696	59	3	1238	3	ZNF782	9	99581440	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	58932	99581440	41631991	2092	4993											
XPA	7507	hgsc.bcm.edu	37	chr9	100449436	100449436	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgatgtggattcttcttcAcaataaatttaagaggtggc	13	14	9	5	0	3	2	1	1	2	1	3	3	3	3	0	3	0	0	0	3	5	6	rs143374902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:100449436A>G	ENST00000375128.4	-	4	561	c.497T>C	c.(496-498)gTg>gCg	p.V166A		NM_000380.3	NP_000371.1	P23025	XPA_HUMAN	xeroderma pigmentosum, complementation group A	166					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)|nucleotide-excision repair, DNA damage removal (GO:0000718)|response to oxidative stress (GO:0006979)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercellular bridge (GO:0045171)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(4)|large_intestine(1)|lung(4)|prostate(1)	11		Acute lymphoblastic leukemia(62;0.158)				ATTCTTCTTCACAATAAATTT	0.313			"Mis, N, F, S"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				A|||	10	0.00199681	0.0076	0.0	5008	,	,		15259	0.0		0.0	False		,,,				2504	0.0				p.V166A		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (A)	9	9q22.3	7507	"xeroderma pigmentosum, complementation group A"		E	.	XPA	21	.	0			c.T497C						PASS	.	A	ALA/VAL	48,4358	48.9+/-83.8	0,48,2155	119	126	123		497	5.4	1	9	dbSNP_134	123	0,8596		0,0,4298	yes	missense	XPA	NM_000380.3	64	0,48,6453	GG,GA,AA		0.0,1.0894,0.3692	benign	166/274	100449436	48,12954	2203	4298	6501	SO:0001583	missense	7507	exon4	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	TTCTTCACAATAA	D14533	CCDS6729.1	9q22.3	2014-09-17			ENSG00000136936	ENSG00000136936			12814	protein-coding gene	gene with protein product		611153					Standard	NM_000380		Approved	XPAC, XP1	uc004axr.4	P23025	OTTHUMG00000020330	ENST00000375128.4:c.497T>C	9.37:g.100449436A>G	ENSP00000364270:p.Val166Ala	76	0	0		71	55	0.774648	NM_000380	Q5T1U9|Q6LCW7|Q6LD02	Missense_Mutation	SNP	ENST00000375128.4	37	CCDS6729.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	15.65	2.896170	0.52121	0.010894	0.0	ENSG00000136936	ENST00000375128	T	0.59224	0.28	5.42	5.42	0.78866	DNA binding domain, putative (1);XPA C- terminal (1);	0.212392	0.44483	D	0.000454	T	0.48624	0.1510	L	0.48362	1.52	0.45852	D	0.998718	B	0.24426	0.103	B	0.36766	0.232	T	0.53063	-0.8491	10	0.40728	T	0.16	.	13.2937	0.60284	1.0:0.0:0.0:0.0	.	166	P23025	XPA_HUMAN	A	166	ENSP00000364270:V166A	ENSP00000364270:V166A	V	-	2	0	XPA	99489257	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.905000	0.92613	2.196000	0.70406	0.533000	0.62120	GTG	A|0.996;G|0.004	0.004	strong		0.313	XPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053332.1	NM_000380		G	100449436	A	G	100449436	3	3	22	1	0	0	0	0	1	0	0	0	17455	159	6	3	336	3	XPA	9	100449436	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	867996	100449436	40763995	2093	4994											
GALNT12	79695	hgsc.bcm.edu	37	chr9	101594219	101594219	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agggagaggatacggatgcaAtcccccgtcgatgtcatcag	11	7	13	10	3	2	1	2	0	0	1	4	5	3	3	2	3	2	1	2	3	2	1	rs16917929	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:101594219A>G	ENST00000375011.3	+	4	897	c.897A>G	c.(895-897)caA>caG	p.Q299Q		NM_024642.4	NP_078918.3	Q8IXK2	GLT12_HUMAN	polypeptide N-acetylgalactosaminyltransferase 12	299					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)				TACGGATGCAATCCCCCGTCG	0.572													A|||	206	0.0411342	0.1513	0.0086	5008	,	,		14266	0.0		0.0	False		,,,				2504	0.0				p.Q299Q		Atlas-SNP	.											.	GALNT12	37	.	0			c.A897G						PASS	.	A		592,3814	257.7+/-262.0	43,506,1654	65	49	54		897	-4	0.6	9	dbSNP_123	54	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	GALNT12	NM_024642.4		43,509,5951	GG,GA,AA		0.0349,13.4362,4.5748		299/582	101594219	595,12411	2203	4300	6503	SO:0001819	synonymous_variant	79695	exon4			GATGCAATCCCCC	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.897A>G	9.37:g.101594219A>G		98	0	0		89	56	0.629214	NM_024642	Q5TCF7|Q8NG54|Q96CT9|Q9H771	Silent	SNP	ENST00000375011.3	37	CCDS6737.1																																																																																			A|0.954;G|0.046	0.046	strong		0.572	GALNT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053382.1	NM_024642		G	101594219	A	G	101594219	2	3	22	1	0	0	0	0	0	0	0	1	6218	98	4	3		3	GALNT12	9	101594219	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1144783	101594219	39619212	2094	4995											
COL15A1	1306	hgsc.bcm.edu	37	chr9	101816873	101816873	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcaggtgttaaaggagagaAaggatcctggggtcttcctg	10	9	16	6	0	1	1	0	0	1	1	3	4	3	3	2	6	0	2	2	6	3	2	rs35642150	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:101816873A>G	ENST00000375001.3	+	32	3389	c.2966A>G	c.(2965-2967)aAa>aGa	p.K989R		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	989	Triple-helical region 6 (COL6).		K -> R (in dbSNP:rs35642150).		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)				AAAGGAGAGAAAGGATCCTGG	0.433													A|||	71	0.0141773	0.0514	0.0043	5008	,	,		19547	0.0		0.0	False		,,,				2504	0.0				p.K989R		Atlas-SNP	.											.	COL15A1	211	.	0			c.A2966G						PASS	.	A	ARG/LYS	123,4283	91.1+/-129.8	1,121,2081	79	84	82		2966	5.7	1	9	dbSNP_126	82	1,8599	1.2+/-3.3	0,1,4299	yes	missense	COL15A1	NM_001855.3	26	1,122,6380	GG,GA,AA		0.0116,2.7916,0.9534	probably-damaging	989/1389	101816873	124,12882	2203	4300	6503	SO:0001583	missense	1306	exon32			GAGAGAAAGGATC	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.2966A>G	9.37:g.101816873A>G	ENSP00000364140:p.Lys989Arg	131	0	0		134	94	0.701493	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	37	CCDS35081.1	23	0.010531135531135532	21	0.042682926829268296	2	0.0055248618784530384	0	0.0	0	0.0	A	16.86	3.239791	0.58995	0.027916	1.16E-4	ENSG00000204291	ENST00000375001	T	0.30448	1.53	5.67	5.67	0.87782	C-type lectin fold (1);	0.172969	0.41396	D	0.000883	T	0.13030	0.0316	L	0.33753	1.03	0.41059	D	0.985365	D	0.63880	0.993	D	0.72625	0.978	T	0.02560	-1.1141	10	0.20046	T	0.44	-17.3435	12.5857	0.56416	1.0:0.0:0.0:0.0	rs35642150	989	P39059	COFA1_HUMAN	R	989	ENSP00000364140:K989R	ENSP00000364140:K989R	K	+	2	0	COL15A1	100856694	0.999000	0.42202	1.000000	0.80357	0.990000	0.78478	1.712000	0.37940	2.288000	0.76882	0.533000	0.62120	AAA	A|0.988;G|0.012	0.012	strong		0.433	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855		G	101816873	A	G	101816873	3	3	22	1	0	0	0	0	1	0	0	0	3674	14	1	3	3092	3	COL15A1	9	101816873	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	222654	101816873	39396558	2095	4996											
ZNF189	7743	hgsc.bcm.edu	37	chr9	104170580	104170580	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tactggtgagaaaccttttcAgtgcaatgaatgtgggaaaa	14	11	11	5	0	1	2	1	2	0	1	1	4	1	3	1	2	3	1	1	2	6	3	rs148414030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:104170580A>G	ENST00000339664.2	+	3	659	c.530A>G	c.(529-531)cAg>cGg	p.Q177R	ZNF189_ENST00000259395.4_Missense_Mutation_p.Q135R|ZNF189_ENST00000374861.3_Missense_Mutation_p.Q163R	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	177					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)				AAACCTTTTCAGTGCAATGAA	0.408													A|||	6	0.00119808	0.0045	0.0	5008	,	,		21632	0.0		0.0	False		,,,				2504	0.0				p.Q177R		Atlas-SNP	.											.	ZNF189	79	.	0			c.A530G						PASS	.	A	ARG/GLN,ARG/GLN	19,4387	25.3+/-52.1	0,19,2184	82	82	82		530,404	4.6	1	9	dbSNP_134	82	0,8600		0,0,4300	yes	missense,missense	ZNF189	NM_003452.2,NM_197977.1	43,43	0,19,6484	GG,GA,AA		0.0,0.4312,0.1461	benign,benign	177/627,135/585	104170580	19,12987	2203	4300	6503	SO:0001583	missense	7743	exon3			CTTTTCAGTGCAA	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.530A>G	9.37:g.104170580A>G	ENSP00000342019:p.Gln177Arg	157	0	0		158	102	0.64557	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Missense_Mutation	SNP	ENST00000339664.2	37	CCDS6754.1	.	.	.	.	.	.	.	.	.	.	A	9.515	1.106655	0.20714	0.004312	0.0	ENSG00000136870	ENST00000374861;ENST00000339664;ENST00000259395	T;T;T	0.19105	2.17;2.17;2.17	4.55	4.55	0.56014	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.46442	D	0.000288	T	0.18841	0.0452	N	0.13235	0.315	0.27578	N	0.949673	B;B;B	0.34372	0.056;0.451;0.262	B;P;B	0.47102	0.115;0.537;0.115	T	0.10359	-1.0633	10	0.54805	T	0.06	.	7.7508	0.28896	0.8138:0.0:0.0:0.1862	.	162;163;177	B7ZLK9;Q5T7D8;O75820	.;.;ZN189_HUMAN	R	163;177;135	ENSP00000363995:Q163R;ENSP00000342019:Q177R;ENSP00000259395:Q135R	ENSP00000259395:Q135R	Q	+	2	0	ZNF189	103210401	0.000000	0.05858	0.995000	0.50966	0.991000	0.79684	0.093000	0.15086	2.272000	0.75746	0.460000	0.39030	CAG	A|0.998;G|0.002	0.002	strong		0.408	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452		G	104170580	A	G	104170580	3	3	22	1	0	0	0	0	1	0	0	0	17769	188	7	3	540	3	ZNF189	9	104170580	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2353707	104170580	37042851	2096	4997											
GRIN3A	116443	hgsc.bcm.edu	37	chr9	104385646	104385646	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgagaagtttgcagtcagcAtctattgacacttcataatc	12	13	8	8	0	3	2	2	2	1	1	4	3	3	2	0	0	2	3	0	0	3	5	rs138253972	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:104385646A>G	ENST00000361820.3	-	5	3168	c.2568T>C	c.(2566-2568)gaT>gaC	p.D856D		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	856					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)	TGCAGTCAGCATCTATTGACA	0.413													A|||	5	0.000998403	0.0023	0.0029	5008	,	,		18756	0.0		0.0	False		,,,				2504	0.0				p.D856D		Atlas-SNP	.											.	GRIN3A	186	.	0			c.T2568C						PASS	.	A		7,4399	12.9+/-30.5	0,7,2196	165	149	154		2568	1.7	1	9	dbSNP_134	154	0,8600		0,0,4300	no	coding-synonymous	GRIN3A	NM_133445.2		0,7,6496	GG,GA,AA		0.0,0.1589,0.0538		856/1116	104385646	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	116443	exon5			GTCAGCATCTATT		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.2568T>C	9.37:g.104385646A>G		169	0	0		183	121	0.661202	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Silent	SNP	ENST00000361820.3	37	CCDS6758.1																																																																																			A|1.000;G|0.000	0.000	strong		0.413	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1			G	104385646	A	G	104385646	2	3	22	1	0	0	0	0	0	0	0	1	6792	214	8	3		3	GRIN3A	9	104385646	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	215066	104385646	36827785	2097	4998											
GRIN3A	116443	hgsc.bcm.edu	37	chr9	104432462	104432462	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atggcccaaaggttcattagAaaccttccagtccaacattt	13	11	6	11	0	1	1	1	0	0	1	3	1	3	1	4	2	2	1	4	2	4	4	rs200841145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:104432462A>G	ENST00000361820.3	-	3	2832	c.2232T>C	c.(2230-2232)ttT>ttC	p.F744F		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	744					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)	GGTTCATTAGAAACCTTCCAG	0.433													A|||	3	0.000599042	0.0015	0.0014	5008	,	,		19652	0.0		0.0	False		,,,				2504	0.0				p.F744F		Atlas-SNP	.											.	GRIN3A	186	.	0			c.T2232C						PASS	.	A		3,4403	6.2+/-15.9	0,3,2200	90	86	87		2232	5.4	1	9		87	0,8600		0,0,4300	no	coding-synonymous	GRIN3A	NM_133445.2		0,3,6500	GG,GA,AA		0.0,0.0681,0.0231		744/1116	104432462	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	116443	exon3			CATTAGAAACCTT		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.2232T>C	9.37:g.104432462A>G		96	0	0		79	48	0.607595	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Silent	SNP	ENST00000361820.3	37	CCDS6758.1																																																																																			A|1.000;G|0.000	0.000	strong		0.433	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1			G	104432462	A	G	104432462	2	3	22	1	0	0	0	0	0	0	0	1	6792	243	9	3		3	GRIN3A	9	104432462	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	46816	104432462	36780969	2098	4999											
SMC2	10592	hgsc.bcm.edu	37	chr9	106888978	106888978	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagagagagcatacatcttaCaaacaacagcttgaagctgt	17	8	8	8	0	1	3	0	1	1	2	1	4	1	3	0	0	7	3	0	0	6	3	rs6479217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:106888978C>T	ENST00000286398.7	+	19	2796	c.2508C>T	c.(2506-2508)taC>taT	p.Y836Y	SMC2_ENST00000374793.3_Silent_p.Y836Y|SMC2_ENST00000303219.8_Silent_p.Y836Y|SMC2_ENST00000374787.3_Silent_p.Y836Y	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	836					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						ATACATCTTACAAACAACAGC	0.348													C|||	326	0.0650958	0.2209	0.013	5008	,	,		16974	0.0129		0.007	False		,,,				2504	0.0051				p.Y836Y		Atlas-SNP	.											.	SMC2	127	.	0			c.C2508T						PASS	.	C	,,	745,3661	303.5+/-288.0	55,635,1513	82	83	83		2508,2508,2508	-0.1	0	9	dbSNP_116	83	62,8538	38.8+/-94.9	0,62,4238	no	coding-synonymous,coding-synonymous,coding-synonymous	SMC2	NM_001042550.1,NM_001042551.1,NM_006444.2	,,	55,697,5751	TT,TC,CC		0.7209,16.9088,6.2048	,,	836/1198,836/1198,836/1198	106888978	807,12199	2203	4300	6503	SO:0001819	synonymous_variant	10592	exon19			ATCTTACAAACAA	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.2508C>T	9.37:g.106888978C>T		43	0	0		41	8	0.195122	NM_006444	Q6IEE0|Q9P1P2	Silent	SNP	ENST00000286398.7	37	CCDS35086.1																																																																																			C|0.935;T|0.065	0.065	strong		0.348	SMC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053470.1			T	106888978	C	T	106888978	2	4	22	1	0	0	0	0	0	0	0	1	14798	489	17	2		2	SMC2	9	106888978	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2456516	106888978	34324453	2099	5000											
SMC2	10592	hgsc.bcm.edu	37	chr9	106901506	106901506	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtggatggtgtttctacagtAgccagatttactcaatgtca	10	14	10	7	0	3	1	2	0	1	1	3	2	3	2	1	2	3	2	1	2	4	5	rs16923746	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:106901506A>G	ENST00000286398.7	+	25	3792	c.3504A>G	c.(3502-3504)gtA>gtG	p.V1168V	SMC2_ENST00000374793.3_Silent_p.V1168V|SMC2_ENST00000374787.3_Silent_p.V1168V	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	1168					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						TTTCTACAGTAGCCAGATTTA	0.363													A|||	326	0.0650958	0.2209	0.013	5008	,	,		15837	0.0129		0.007	False		,,,				2504	0.0051				p.V1168V		Atlas-SNP	.											.	SMC2	127	.	0			c.A3504G						PASS	.	A	,,	742,3664	302.7+/-287.5	56,630,1517	89	89	89		3504,3504,3504	-3	1	9	dbSNP_123	89	62,8538	39.3+/-95.6	0,62,4238	no	coding-synonymous,coding-synonymous,coding-synonymous	SMC2	NM_001042550.1,NM_001042551.1,NM_006444.2	,,	56,692,5755	GG,GA,AA		0.7209,16.8407,6.1818	,,	1168/1198,1168/1198,1168/1198	106901506	804,12202	2203	4300	6503	SO:0001819	synonymous_variant	10592	exon25			TACAGTAGCCAGA	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.3504A>G	9.37:g.106901506A>G		177	0	0		194	66	0.340206	NM_006444	Q6IEE0|Q9P1P2	Silent	SNP	ENST00000286398.7	37	CCDS35086.1																																																																																			A|0.935;G|0.065	0.065	strong		0.363	SMC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053470.1			G	106901506	A	G	106901506	2	3	22	1	0	0	0	0	0	0	0	1	14798	407	15	3		3	SMC2	9	106901506	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	12528	106901506	34311925	2100	5001											
OR13F1	138805	hgsc.bcm.edu	37	chr9	107266813	107266813	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aactttgtttcagggagaaaCactatttcattctcagggtg	11	14	9	7	0	3	1	3	0	1	1	4	2	3	1	0	2	2	1	0	2	3	5	rs61754949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107266813C>T	ENST00000334726.2	+	1	359	c.270C>T	c.(268-270)aaC>aaT	p.N90N		NM_001004485.1	NP_001004485.1	Q8NGS4	O13F1_HUMAN	olfactory receptor, family 13, subfamily F, member 1	90						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(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						CAGGGAGAAACACTATTTCAT	0.517													C|||	55	0.0109824	0.0401	0.0029	5008	,	,		20598	0.0		0.0	False		,,,				2504	0.0				p.N90N		Atlas-SNP	.											.	OR13F1	75	.	0			c.C270T						PASS	.	C		161,4245	108.2+/-146.6	3,155,2045	132	117	122		270	2.2	0.9	9	dbSNP_129	122	0,8600		0,0,4300	no	coding-synonymous	OR13F1	NM_001004485.1		3,155,6345	TT,TC,CC		0.0,3.6541,1.2379		90/320	107266813	161,12845	2203	4300	6503	SO:0001819	synonymous_variant	138805	exon1			GAGAAACACTATT		CCDS35087.1	9q31.1	2013-09-24			ENSG00000186881	ENSG00000186881		"GPCR / Class A : Olfactory receptors"	14723	protein-coding gene	gene with protein product							Standard	NM_001004485		Approved		uc011lvm.2	Q8NGS4	OTTHUMG00000020404	ENST00000334726.2:c.270C>T	9.37:g.107266813C>T		196	0	0		168	47	0.279762	NM_001004485	Q6IF50	Silent	SNP	ENST00000334726.2	37	CCDS35087.1																																																																																			C|0.987;T|0.013	0.013	strong		0.517	OR13F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053475.1			T	107266813	C	T	107266813	2	4	22	1	0	0	0	0	0	0	0	1	10950	477	17	2		2	OR13F1	9	107266813	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	365307	107266813	33946618	2101	5002											
OR13C4	138804	hgsc.bcm.edu	37	chr9	107289352	107289352	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaatccaagatgcttgctaTgatcagaacaccattgccaa	15	9	7	10	0	1	4	1	1	0	3	2	4	2	4	3	0	4	2	3	0	5	3	rs61738891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107289352T>C	ENST00000277216.3	-	1	138	c.139A>G	c.(139-141)Ata>Gta	p.I47V		NM_001001919.1	NP_001001919.1	Q8NGS5	O13C4_HUMAN	olfactory receptor, family 13, subfamily C, member 4	47						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(2)|lung(14)|skin(1)	18						ATGCTTGCTATGATCAGAACA	0.438													T|||	43	0.00858626	0.0318	0.0014	5008	,	,		22015	0.0		0.0	False		,,,				2504	0.0				p.I47V		Atlas-SNP	.											.	OR13C4	55	.	0			c.A139G						PASS	.	T	VAL/ILE	119,4287	89.2+/-127.9	1,117,2085	149	127	134		139	1.9	0.6	9	dbSNP_129	134	0,8600		0,0,4300	yes	missense	OR13C4	NM_001001919.1	29	1,117,6385	CC,CT,TT		0.0,2.7009,0.915	benign	47/319	107289352	119,12887	2203	4300	6503	SO:0001583	missense	138804	exon1			TTGCTATGATCAG		CCDS35088.1	9q31.1	2013-09-24			ENSG00000148136	ENSG00000148136		"GPCR / Class A : Olfactory receptors"	14722	protein-coding gene	gene with protein product							Standard	NM_001001919		Approved		uc011lvn.2	Q8NGS5	OTTHUMG00000020407	ENST00000277216.3:c.139A>G	9.37:g.107289352T>C	ENSP00000277216:p.Ile47Val	86	0	0		82	32	0.390244	NM_001001919	Q6IF51|Q96R41	Missense_Mutation	SNP	ENST00000277216.3	37	CCDS35088.1	13	0.005952380952380952	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	0	0.0	T	4.428	0.079162	0.08533	0.027009	0.0	ENSG00000148136	ENST00000277216;ENST00000545903	T	0.03889	3.77	4.45	1.9	0.25705	GPCR, rhodopsin-like superfamily (1);	0.410669	0.20335	U	0.094356	T	0.00815	0.0027	N	0.10782	0.045	0.09310	N	1	B	0.14805	0.011	B	0.15052	0.012	T	0.44772	-0.9306	10	0.40728	T	0.16	.	3.6631	0.08246	0.3365:0.0958:0.0:0.5676	.	47	Q8NGS5	O13C4_HUMAN	V	47;76	ENSP00000277216:I47V	ENSP00000277216:I47V	I	-	1	0	OR13C4	106329173	0.000000	0.05858	0.607000	0.28956	0.763000	0.43281	-0.351000	0.07711	0.256000	0.21614	0.482000	0.46254	ATA	T|0.992;C|0.008	0.008	strong		0.438	OR13C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053478.1			C	107289352	T	C	107289352	3	2	22	1	0	0	0	0	1	0	0	0	10945	1464	51	3	819	3	OR13C4	9	107289352	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	22539	107289352	33924079	2102	5003											
OR13C5	138799	hgsc.bcm.edu	37	chr9	107361009	107361009	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgcttctcccctccgaagagCtaattttgaagatgctcaaa	11	12	7	11	1	2	3	1	1	1	2	4	4	3	3	3	0	3	3	3	0	4	4	rs73508187	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107361009C>G	ENST00000374779.2	-	1	779	c.686G>C	c.(685-687)aGc>aCc	p.S229T		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	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(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						CTCCGAAGAGCTAATTTTGAA	0.428													C|||	65	0.0129792	0.0454	0.0072	5008	,	,		22160	0.0		0.0	False		,,,				2504	0.0				p.S229T		Atlas-SNP	.											.	OR13C5	60	.	0			c.G686C						PASS	.	C	THR/SER	125,4281	92.5+/-131.2	0,125,2078	122	115	117		686	-1.2	0	9	dbSNP_130	117	1,8599	1.2+/-3.3	0,1,4299	yes	missense	OR13C5	NM_001004482.1	58	0,126,6377	GG,GC,CC		0.0116,2.837,0.9688	benign	229/319	107361009	126,12880	2203	4300	6503	SO:0001583	missense	138799	exon1			GAAGAGCTAATTT		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.686G>C	9.37:g.107361009C>G	ENSP00000363911:p.Ser229Thr	183	0	0		210	132	0.628571	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Missense_Mutation	SNP	ENST00000374779.2	37	CCDS35091.1	27	0.012362637362637362	25	0.0508130081300813	2	0.0055248618784530384	0	0.0	0	0.0	C	10.96	1.499301	0.26861	0.02837	1.16E-4	ENSG00000255800	ENST00000374779	T	0.38722	1.12	4.03	-1.21	0.09524	GPCR, rhodopsin-like superfamily (1);	1.008970	0.07986	U	0.986370	T	0.05777	0.0151	L	0.29908	0.895	0.09310	N	1	B	0.22800	0.075	B	0.32022	0.139	T	0.36915	-0.9728	10	0.59425	D	0.04	.	5.1916	0.15212	0.0:0.2959:0.4158:0.2883	.	229	Q8NGS8	O13C5_HUMAN	T	229	ENSP00000363911:S229T	ENSP00000363911:S229T	S	-	2	0	OR13C5	106400830	0.000000	0.05858	0.000000	0.03702	0.174000	0.22865	-5.456000	0.00121	-0.113000	0.11958	0.423000	0.28283	AGC	C|0.990;G|0.010	0.010	strong		0.428	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482		G	107361009	C	G	107361009	3	3	22	1	0	0	0	0	1	0	0	0	10946	797	28	4	272	4	OR13C5	9	107361009	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	71657	107361009	33852422	2103	5004											
OR13C5	138799	hgsc.bcm.edu	37	chr9	107361038	107361038	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagatgctcaaaatgattaaCgtgtaagagacaataattaa	20	10	7	4	1	1	3	1	1	0	2	1	4	1	3	0	0	2	2	0	0	8	4	rs75872480	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107361038C>T	ENST00000374779.2	-	1	750	c.657G>A	c.(655-657)acG>acA	p.T219T		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	219						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						AAATGATTAACGTGTAAGAGA	0.428													C|||	14	0.00279553	0.0106	0.0	5008	,	,		22708	0.0		0.0	False		,,,				2504	0.0				p.T219T		Atlas-SNP	.											OR13C5,NS,haematopoietic_neoplasm,-1,1	OR13C5	60	1	0			c.G657A						PASS	.	C		24,4382	30.8+/-60.4	0,24,2179	131	124	127		657	-8.1	0	9	dbSNP_131	127	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	OR13C5	NM_001004482.1		0,25,6478	TT,TC,CC		0.0116,0.5447,0.1922		219/319	107361038	25,12981	2203	4300	6503	SO:0001819	synonymous_variant	138799	exon1			GATTAACGTGTAA		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.657G>A	9.37:g.107361038C>T		173	0	0		212	134	0.632075	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Silent	SNP	ENST00000374779.2	37	CCDS35091.1																																																																																			C|0.998;T|0.002	0.002	strong		0.428	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482		T	107361038	C	T	107361038	2	4	22	1	0	0	0	0	0	0	0	1	10946	523	19	1		1	OR13C5	9	107361038	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	29	107361038	33852393	2104	5005											
ABCA1	19	hgsc.bcm.edu	37	chr9	107547872	107547872	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctggacaggcttcaggtcCgggttggaccctgctattcg	5	11	13	12	2	1	0	1	0	0	0	4	2	3	2	3	5	1	3	3	5	1	4	rs61741359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107547872C>T	ENST00000374736.3	-	49	6844	c.6450G>A	c.(6448-6450)ccG>ccA	p.P2150P		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	2150			P -> L (in HDLD2). {ECO:0000269|PubMed:11086027}.		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)	GCTTCAGGTCCGGGTTGGACC	0.418													C|||	57	0.0113818	0.0386	0.0072	5008	,	,		17972	0.0		0.001	False		,,,				2504	0.0				p.P2150P		Atlas-SNP	.											.	ABCA1	244	.	0			c.G6450A						PASS	.	C		172,4234	112.5+/-150.6	0,172,2031	85	87	87		6450	2.2	1	9	dbSNP_129	87	0,8600		0,0,4300	yes	coding-synonymous	ABCA1	NM_005502.3		0,172,6331	TT,TC,CC		0.0,3.9038,1.3225		2150/2262	107547872	172,12834	2203	4300	6503	SO:0001819	synonymous_variant	19	exon49			CAGGTCCGGGTTG	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.6450G>A	9.37:g.107547872C>T		70	0	0		71	54	0.760563	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Silent	SNP	ENST00000374736.3	37	CCDS6762.1																																																																																			C|0.985;T|0.015	0.015	strong		0.418	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		T	107547872	C	T	107547872	2	4	22	1	0	0	0	0	0	0	0	1	28	639	23	1		1	ABCA1	9	107547872	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	186834	107547872	33665559	2105	5006											
ABCA1	19	hgsc.bcm.edu	37	chr9	107578478	107578478	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gaaatgcccaggtctgagagCcggtcatcaatctcatgaaa	13	8	10	10	1	4	2	3	2	2	1	5	4	4	2	2	2	2	0	2	2	3	0	rs2230807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107578478C>T	ENST00000374736.3	-	25	4078	c.3684G>A	c.(3682-3684)cgG>cgA	p.R1228R		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	1228					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)	GGTCTGAGAGCCGGTCATCAA	0.488													C|||	316	0.063099	0.2269	0.0231	5008	,	,		18611	0.0		0.0	False		,,,				2504	0.0				p.R1228R		Atlas-SNP	.											.	ABCA1	244	.	0			c.G3684A						PASS	.	C		778,3628	314.7+/-293.7	70,638,1495	159	165	163		3684	-2.1	1	9	dbSNP_98	163	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous	ABCA1	NM_005502.3		70,647,5786	TT,TC,CC		0.1047,17.6577,6.0511		1228/2262	107578478	787,12219	2203	4300	6503	SO:0001819	synonymous_variant	19	exon25			TGAGAGCCGGTCA	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.3684G>A	9.37:g.107578478C>T		148	0	0		158	87	0.550633	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Silent	SNP	ENST00000374736.3	37	CCDS6762.1																																																																																			T|0.049;G|0.134	0.049	strong		0.488	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502		T	107578478	C	T	107578478	2	4	22	1	0	0	0	0	0	0	0	1	28	726	26	2		2	ABCA1	9	107578478	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	30606	107578478	33634953	2106	5007											
KLF4	9314	hgsc.bcm.edu	37	chr9	110249415	110249415	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccttttccggggccacgaTcgtcttcccctctttggctt	2	15	9	15	3	2	0	0	0	2	0	6	1	5	0	5	3	0	1	5	3	0	5	rs45596731	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:110249415T>C	ENST00000374672.4	-	4	1631	c.1158A>G	c.(1156-1158)cgA>cgG	p.R386R		NM_004235.4	NP_004226.3	O43474	KLF4_HUMAN	Kruppel-like factor 4 (gut)	420	Pro-rich.				cellular response to cycloheximide (GO:0071409)|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 peptide (GO:1901653)|epidermal cell differentiation (GO:0009913)|epidermis morphogenesis (GO:0048730)|fat cell differentiation (GO:0045444)|mesodermal cell fate determination (GO:0007500)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000342)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of muscle hyperplasia (GO:0014740)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of response to cytokine stimulus (GO:0060761)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of hemoglobin biosynthetic process (GO:0046985)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic camera-type eye development (GO:0031077)|post-embryonic hemopoiesis (GO:0035166)|regulation of cell differentiation (GO:0045595)|response to retinoic acid (GO:0032526)|stem cell maintenance (GO:0019827)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|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)|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)|sequence-specific DNA binding transcription factor recruiting transcription factor activity (GO:0001010)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(5)|large_intestine(1)|lung(3)|pancreas(1)|prostate(2)	16						GGGGCCACGATCGTCTTCCCC	0.597													T|||	18	0.00359425	0.0129	0.0014	5008	,	,		17148	0.0		0.0	False		,,,				2504	0.0				p.R386R		Atlas-SNP	.											.	KLF4	106	.	0			c.A1158G						PASS	.	T		51,4355	52.3+/-87.9	0,51,2152	192	175	180		1158	4.4	1	9	dbSNP_127	180	0,8600		0,0,4300	no	coding-synonymous	KLF4	NM_004235.4		0,51,6452	CC,CT,TT		0.0,1.1575,0.3921		386/480	110249415	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	9314	exon4			CCACGATCGTCTT	AF022184	CCDS6770.2	9q31	2013-01-08			ENSG00000136826	ENSG00000136826		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	6348	protein-coding gene	gene with protein product		602253				9422764, 16372018	Standard	NM_004235		Approved	EZF, GKLF	uc004bdg.3	O43474	OTTHUMG00000020449	ENST00000374672.4:c.1158A>G	9.37:g.110249415T>C		270	1	0.0037037		269	171	0.635688	NM_004235	B2R8S4|B3KT79|L0R3I6|L0R4N5|P78338|Q5T3J8|Q5T3J9|Q8N717|Q9UNP3	Silent	SNP	ENST00000374672.4	37	CCDS6770.2																																																																																			T|0.996;C|0.004	0.004	strong		0.597	KLF4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053556.2	NM_004235		C	110249415	T	C	110249415	2	2	22	1	0	0	0	0	0	0	0	1	8357	1422	50	3		3	KLF4	9	110249415	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2670937	110249415	30964016	2107	5008											
EPB41L4B	54566	hgsc.bcm.edu	37	chr9	112017883	112017883	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggaagaatgcgtggtgctcAactgcacacttccaaaggtg	11	8	12	10	2	1	1	1	0	0	1	2	2	2	2	1	3	4	2	1	3	4	1	rs73529389	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:112017883A>G	ENST00000374566.3	-	11	1594	c.1077T>C	c.(1075-1077)gtT>gtC	p.V359V	EPB41L4B_ENST00000374557.4_Silent_p.V359V	NM_019114.3	NP_061987.3	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B	359	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				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						CGTGGTGCTCAACTGCACACT	0.532													G|||	30	0.00599042	0.0219	0.0014	5008	,	,		20496	0.0		0.0	False		,,,				2504	0.0				p.V359V		Atlas-SNP	.											.	EPB41L4B	111	.	0			c.T1077C						PASS	.	G	,	79,3947		0,79,1934	131	125	127		1077,1077	-11.6	0	9	dbSNP_130	127	0,8322		0,0,4161	no	coding-synonymous,coding-synonymous	EPB41L4B	NM_018424.2,NM_019114.3	,	0,79,6095	GG,GA,AA		0.0,1.9622,0.6398	,	359/519,359/901	112017883	79,12269	2013	4161	6174	SO:0001819	synonymous_variant	54566	exon11			GTGCTCAACTGCA	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.1077T>C	9.37:g.112017883A>G		107	0	0		116	34	0.293103	NM_019114	Q5T4G5|Q5T4G6|Q9H328|Q9P2V3	Silent	SNP	ENST00000374566.3	37	CCDS43859.1																																																																																			A|0.997;G|0.003	0.003	strong		0.532	EPB41L4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053592.1	NM_018424		G	112017883	A	G	112017883	2	3	22	1	0	0	0	0	0	0	0	1	5158	117	5	3		3	EPB41L4B	9	112017883	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1768468	112017883	29195548	2108	5009											
SVEP1	79987	hgsc.bcm.edu	37	chr9	113149612	113149612	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggttccattttctgtgcagTgtgcctcagatggcccttca	6	14	10	11	0	3	1	2	0	1	1	4	1	4	1	3	2	2	2	3	2	0	4	rs114581956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:113149612T>C	ENST00000401783.2	-	42	10349	c.10013A>G	c.(10012-10014)cAc>cGc	p.H3338R	SVEP1_ENST00000374469.1_Missense_Mutation_p.H3315R|SVEP1_ENST00000297826.5_Missense_Mutation_p.H1264R	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	3338	Sushi 32. {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						TTCTGTGCAGTGTGCCTCAGA	0.468													T|||	47	0.00938498	0.0333	0.0029	5008	,	,		17065	0.0		0.001	False		,,,				2504	0.0				p.H3338R		Atlas-SNP	.											.	SVEP1	326	.	0			c.A10013G						PASS	.	T	ARG/HIS	94,3784		1,92,1846	140	140	140		10013	1.4	0	9	dbSNP_132	140	0,8258		0,0,4129	yes	missense	SVEP1	NM_153366.3	29	1,92,5975	CC,CT,TT		0.0,2.4239,0.7746	benign	3338/3572	113149612	94,12042	1939	4129	6068	SO:0001583	missense	79987	exon42			GTGCAGTGTGCCT	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.10013A>G	9.37:g.113149612T>C	ENSP00000384917:p.His3338Arg	247	0	0		241	80	0.33195	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	27	0.012362637362637362	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	3.480	-0.106077	0.06924	0.024239	0.0	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826	T;T;T	0.63580	-0.05;-0.05;-0.05	5.09	1.42	0.22433	Complement control module (2);Sushi/SCR/CCP (3);	0.889971	0.09909	N	0.740049	T	0.08133	0.0203	N	0.11892	0.195	0.09310	N	0.999999	B	0.18013	0.025	B	0.22152	0.038	T	0.09662	-1.0664	10	0.21014	T	0.42	.	3.9589	0.09403	0.1226:0.0714:0.1426:0.6634	.	3338	Q4LDE5	SVEP1_HUMAN	R	3338;3315;1264	ENSP00000384917:H3338R;ENSP00000363593:H3315R;ENSP00000297826:H1264R	ENSP00000297826:H1264R	H	-	2	0	SVEP1	112189433	0.005000	0.15991	0.021000	0.16686	0.386000	0.30323	1.484000	0.35508	0.055000	0.16094	0.529000	0.55759	CAC	T|0.987;C|0.013	0.013	strong		0.468	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	113149612	T	C	113149612	3	2	22	1	0	0	0	0	1	0	0	0	15435	1696	59	3	730	3	SVEP1	9	113149612	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1131729	113149612	28063819	2109	5010											
SVEP1	79987	hgsc.bcm.edu	37	chr9	113169116	113169116	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttggagcaccgtgcaagaTgtagccctcgtgacagtgga	9	10	13	9	2	0	2	0	1	0	1	1	4	0	4	2	2	3	3	2	2	2	3	rs16914996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:113169116T>C	ENST00000401783.2	-	38	9100	c.8764A>G	c.(8764-8766)Atc>Gtc	p.I2922V	SVEP1_ENST00000374469.1_Missense_Mutation_p.I2899V|SVEP1_ENST00000297826.5_Missense_Mutation_p.I848V	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2922	Sushi 25. {ECO:0000255|PROSITE- ProRule:PRU00302}.		I -> V (in dbSNP:rs16914996).		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						CCGTGCAAGATGTAGCCCTCG	0.527													T|||	207	0.0413339	0.149	0.0144	5008	,	,		21879	0.0		0.0	False		,,,				2504	0.0				p.I2922V		Atlas-SNP	.											.	SVEP1	326	.	0			c.A8764G						PASS	.	T	VAL/ILE	495,3643		27,441,1601	141	142	141		8764	-1.4	0	9	dbSNP_123	141	5,8423		0,5,4209	yes	missense	SVEP1	NM_153366.3	29	27,446,5810	CC,CT,TT		0.0593,11.9623,3.979	benign	2922/3572	113169116	500,12066	2069	4214	6283	SO:0001583	missense	79987	exon38			GCAAGATGTAGCC	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.8764A>G	9.37:g.113169116T>C	ENSP00000384917:p.Ile2922Val	66	0	0		74	52	0.702703	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	74	0.03388278388278388	71	0.1443089430894309	3	0.008287292817679558	0	0.0	0	0.0	T	0.008	-1.879969	0.00537	0.119623	5.93E-4	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826	T;T;T	0.61859	0.07;0.07;0.07	5.41	-1.41	0.08941	Complement control module (2);Sushi/SCR/CCP (3);	1.252220	0.05177	N	0.500598	T	0.00178	0.0005	N	0.01146	-0.985	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.03651	-1.1016	9	0.17369	T	0.5	.	6.9527	0.24554	0.1169:0.3452:0.0:0.5379	rs16914996;rs52792614;rs16914996	2922	Q4LDE5	SVEP1_HUMAN	V	2922;2899;848	ENSP00000384917:I2922V;ENSP00000363593:I2899V;ENSP00000297826:I848V	ENSP00000297826:I848V	I	-	1	0	SVEP1	112208937	0.000000	0.05858	0.002000	0.10522	0.079000	0.17450	-1.006000	0.03671	-0.630000	0.05567	-0.326000	0.08463	ATC	T|0.943;C|0.057	0.057	strong		0.527	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	113169116	T	C	113169116	3	2	22	1	0	0	0	0	1	0	0	0	15435	1464	51	3	1995	3	SVEP1	9	113169116	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	19504	113169116	28044315	2110	5011											
SVEP1	79987	hgsc.bcm.edu	37	chr9	113169816	113169816	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggttccccagaagttcataTcctggattacaggtgtatga	10	12	11	8	0	1	2	1	1	0	1	3	3	3	3	3	3	1	3	3	3	4	5	rs116159392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:113169816T>C	ENST00000401783.2	-	38	8400	c.8064A>G	c.(8062-8064)ggA>ggG	p.G2688G	SVEP1_ENST00000374469.1_Silent_p.G2665G|SVEP1_ENST00000297826.5_Silent_p.G614G	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2688	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						GAAGTTCATATCCTGGATTAC	0.453													T|||	207	0.0413339	0.149	0.0144	5008	,	,		22581	0.0		0.0	False		,,,				2504	0.0				p.G2688G		Atlas-SNP	.											SVEP1,NS,carcinoma,0,1	SVEP1	326	1	0			c.A8064G						PASS	.	T		461,3353		27,407,1473	169	166	167		8064	-6.8	0.9	9	dbSNP_132	167	5,8265		0,5,4130	no	coding-synonymous	SVEP1	NM_153366.3		27,412,5603	CC,CT,TT		0.0605,12.087,3.8563		2688/3572	113169816	466,11618	1907	4135	6042	SO:0001819	synonymous_variant	79987	exon38			TTCATATCCTGGA	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.8064A>G	9.37:g.113169816T>C		151	0	0		118	75	0.635593	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	37	CCDS48004.1																																																																																			T|0.959;C|0.041	0.041	strong		0.453	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	113169816	T	C	113169816	2	2	22	1	0	0	0	0	0	0	0	1	15435	1422	50	3		3	SVEP1	9	113169816	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	700	113169816	28043615	2111	5012											
SVEP1	79987	hgsc.bcm.edu	37	chr9	113170323	113170323	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggttgcaagagtaggtaacGgtctgtccatagtgtaggtc	9	11	14	7	2	1	1	0	0	1	1	3	1	2	1	1	4	2	5	1	4	5	5	rs111722103	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:113170323G>A	ENST00000401783.2	-	38	7893	c.7557C>T	c.(7555-7557)acC>acT	p.T2519T	SVEP1_ENST00000374469.1_Silent_p.T2496T|SVEP1_ENST00000297826.5_Silent_p.T445T	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2519	Sushi 19. {ECO:0000255|PROSITE- ProRule:PRU00302}.			T -> I (in Ref. 6; CAD97901). {ECO:0000305}.	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						AGTAGGTAACGGTCTGTCCAT	0.488													G|||	154	0.0307508	0.1097	0.013	5008	,	,		21854	0.0		0.0	False		,,,				2504	0.0				p.T2519T		Atlas-SNP	.											SVEP1,NS,carcinoma,0,1	SVEP1	326	1	0			c.C7557T						PASS	.	G		334,3532		13,308,1612	49	48	49		7557	-1.3	0	9	dbSNP_132	49	5,8261		0,5,4128	no	coding-synonymous	SVEP1	NM_153366.3		13,313,5740	AA,AG,GG		0.0605,8.6394,2.7943		2519/3572	113170323	339,11793	1933	4133	6066	SO:0001819	synonymous_variant	79987	exon38			GGTAACGGTCTGT	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.7557C>T	9.37:g.113170323G>A		90	0	0		90	66	0.733333	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	37	CCDS48004.1																																																																																			G|0.977;A|0.023	0.023	strong		0.488	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	113170323	G	A	113170323	2	1	22	1	0	0	0	0	0	0	0	1	15435	1103	39	1		1	SVEP1	9	113170323	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	507	113170323	28043108	2112	5013											
SVEP1	79987	hgsc.bcm.edu	37	chr9	113233738	113233738	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcggctataagtatttctgaTgcaagctgaaaggaatacat	14	12	9	6	1	1	2	0	2	1	0	2	3	1	3	0	2	3	4	0	2	7	5	rs61732942	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:113233738T>C	ENST00000401783.2	-	16	3240	c.2904A>G	c.(2902-2904)gcA>gcG	p.A968A	SVEP1_ENST00000302728.8_Silent_p.A968A|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374469.1_Silent_p.A945A	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	968					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						GTATTTCTGATGCAAGCTGAA	0.428													T|||	210	0.0419329	0.1513	0.0144	5008	,	,		16743	0.0		0.0	False		,,,				2504	0.0				p.A968A		Atlas-SNP	.											.	SVEP1	326	.	0			c.A2904G						PASS	.	T		458,3258		27,404,1427	122	112	115		2904	-11	0.2	9	dbSNP_129	115	5,8209		0,5,4102	no	coding-synonymous	SVEP1	NM_153366.3		27,409,5529	CC,CT,TT		0.0609,12.3251,3.881		968/3572	113233738	463,11467	1858	4107	5965	SO:0001819	synonymous_variant	79987	exon16			TTCTGATGCAAGC	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.2904A>G	9.37:g.113233738T>C		249	1	0.00401606		267	181	0.677903	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	37	CCDS48004.1																																																																																			T|0.963;C|0.037	0.037	strong		0.428	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	113233738	T	C	113233738	2	2	22	1	0	0	0	0	0	0	0	1	15435	1451	51	3		3	SVEP1	9	113233738	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	63415	113233738	27979693	2113	5014											
SVEP1	79987	hgsc.bcm.edu	37	chr9	113265448	113265448	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tataacatttcccttgtagaAcagctgatgtggccatgttt	10	15	8	8	0	0	2	0	1	0	1	1	2	1	2	2	1	3	3	2	1	4	6	rs10120982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:113265448A>G	ENST00000401783.2	-	6	1689	c.1353T>C	c.(1351-1353)tgT>tgC	p.C451C	SVEP1_ENST00000302728.8_Silent_p.C451C|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374461.1_Silent_p.C428C|SVEP1_ENST00000374469.1_Silent_p.C428C	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	451	Sushi 2. {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						CCCTTGTAGAACAGCTGATGT	0.393													A|||	56	0.0111821	0.0378	0.0072	5008	,	,		20793	0.0		0.001	False		,,,				2504	0.0				p.C451C		Atlas-SNP	.											SVEP1,NS,carcinoma,-1,2	SVEP1	326	2	0			c.T1353C						PASS	.	A		130,3830		4,122,1854	152	149	150		1353	0.9	1	9	dbSNP_119	150	2,8308		0,2,4153	no	coding-synonymous	SVEP1	NM_153366.3		4,124,6007	GG,GA,AA		0.0241,3.2828,1.0758		451/3572	113265448	132,12138	1980	4155	6135	SO:0001819	synonymous_variant	79987	exon6			TGTAGAACAGCTG	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.1353T>C	9.37:g.113265448A>G		186	0	0		202	59	0.292079	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	37	CCDS48004.1																																																																																			A|0.992;G|0.008	0.008	strong		0.393	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	113265448	A	G	113265448	2	3	22	1	0	0	0	0	0	0	0	1	15435	41	2	3		3	SVEP1	9	113265448	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	31710	113265448	27947983	2114	5015											
OR2K2	26248	hgsc.bcm.edu	37	chr9	114089883	114089883	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aacataggggtaagcactccGtaaagcaacgagatgatttt	15	9	10	7	2	0	2	0	1	0	1	1	3	1	2	1	2	4	4	1	2	6	5	rs61748722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:114089883G>A	ENST00000374428.1	-	1	917	c.918C>T	c.(916-918)taC>taT	p.Y306Y	OR2K2_ENST00000302681.1_Silent_p.Y277Y			Q8NGT1	OR2K2_HUMAN	olfactory receptor, family 2, subfamily K, member 2	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)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)	20						TAAGCACTCCGTAAAGCAACG	0.383													A|||	74	0.0147764	0.053	0.0058	5008	,	,		22259	0.0		0.0	False		,,,				2504	0.0				p.Y277Y		Atlas-SNP	.											.	OR2K2	77	.	0			c.C831T						PASS	.	A		233,4173	805.1+/-415.8	5,223,1975	131	124	126		831	4.6	1	9	dbSNP_129	126	1,8599	819.2+/-406.8	0,1,4299	no	coding-synonymous	OR2K2	NM_205859.1		5,224,6274	AA,AG,GG		0.0116,5.2882,1.7992		277/317	114089883	234,12772	2203	4300	6503	SO:0001819	synonymous_variant	26248	exon1			CACTCCGTAAAGC	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.918C>T	9.37:g.114089883G>A		167	0	0		171	123	0.719298	NM_205859	Q2TA61|Q5VYK4|Q6IFI5	Silent	SNP	ENST00000374428.1	37																																																																																				G|0.982;A|0.018	0.018	strong		0.383	OR2K2-201	KNOWN	basic	protein_coding	protein_coding		NM_205859		A	114089883	G	A	114089883	2	1	22	1	0	0	0	0	0	0	0	1	11014	1140	40	1		1	OR2K2	9	114089883	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	824435	114089883	27123548	2115	5016											
OR2K2	26248	hgsc.bcm.edu	37	chr9	114090277	114090277	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aacccgtcacccaggagaccGtagccatccgtgcacagacg	11	4	10	16	4	1	2	1	0	0	2	2	3	2	2	5	1	3	2	5	1	2	1	rs73656223	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:114090277G>A	ENST00000374428.1	-	1	523	c.524C>T	c.(523-525)aCg>aTg	p.T175M	OR2K2_ENST00000302681.1_Missense_Mutation_p.T146M			Q8NGT1	OR2K2_HUMAN	olfactory receptor, family 2, subfamily K, member 2	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)|central_nervous_system(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)	20						CCAGGAGACCGTAGCCATCCG	0.547													G|||	74	0.0147764	0.053	0.0058	5008	,	,		21286	0.0		0.0	False		,,,				2504	0.0				p.T146M		Atlas-SNP	.											.	OR2K2	77	.	0			c.C437T						PASS	.	G	MET/THR	226,4180	116.7+/-154.6	5,216,1982	99	80	86		437	1.1	0	9	dbSNP_130	86	1,8599	1.2+/-3.3	0,1,4299	yes	missense	OR2K2	NM_205859.1	81	5,217,6281	AA,AG,GG		0.0116,5.1294,1.7453	benign	146/317	114090277	227,12779	2203	4300	6503	SO:0001583	missense	26248	exon1			GAGACCGTAGCCA	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.524C>T	9.37:g.114090277G>A	ENSP00000363550:p.Thr175Met	85	0	0		78	44	0.564103	NM_205859	Q2TA61|Q5VYK4|Q6IFI5	Missense_Mutation	SNP	ENST00000374428.1	37		25	0.011446886446886446	22	0.044715447154471545	3	0.008287292817679558	0	0.0	0	0.0	G	4.460	0.085171	0.08583	0.051294	1.16E-4	ENSG00000171133	ENST00000302681;ENST00000374428	T;T	0.37752	1.18;1.18	4.92	1.09	0.20402	GPCR, rhodopsin-like superfamily (1);	1.107710	0.07088	U	0.838300	T	0.04092	0.0114	N	0.20986	0.625	0.09310	N	1	B	0.18461	0.028	B	0.14578	0.011	T	0.20371	-1.0277	10	0.72032	D	0.01	.	6.3971	0.21618	0.1168:0.2929:0.5903:0.0	.	175	Q8NGT1	OR2K2_HUMAN	M	146;175	ENSP00000305055:T146M;ENSP00000363550:T175M	ENSP00000305055:T146M	T	-	2	0	OR2K2	113130098	0.000000	0.05858	0.000000	0.03702	0.242000	0.25591	0.116000	0.15561	0.150000	0.19136	-0.423000	0.05987	ACG	G|0.982;A|0.018	0.018	strong		0.547	OR2K2-201	KNOWN	basic	protein_coding	protein_coding		NM_205859		A	114090277	G	A	114090277	3	1	22	1	0	0	0	0	1	0	0	0	11014	1145	40	1	516	1	OR2K2	9	114090277	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	394	114090277	27123154	2116	5017											
C9orf84	158401	hgsc.bcm.edu	37	chr9	114454735	114454735	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaggtgacgaaatttgcggTgattttgttatggaagaaga	12	13	14	2	2	0	5	0	3	0	2	0	7	0	6	0	3	1	1	0	3	4	4	rs73656294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:114454735T>C	ENST00000318737.4	-	25	3458	c.3330A>G	c.(3328-3330)tcA>tcG	p.S1110S	C9orf84_ENST00000394779.3_Silent_p.S1071S|C9orf84_ENST00000374287.3_Silent_p.S1110S|C9orf84_ENST00000394777.4_Silent_p.S1036S	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	1110										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						AAATTTGCGGTGATTTTGTTA	0.323													T|||	67	0.0133786	0.0477	0.0058	5008	,	,		18851	0.0		0.0	False		,,,				2504	0.0				p.S1110S		Atlas-SNP	.											.	C9orf84	207	.	0			c.A3330G						PASS	.	T	,	151,4255		2,147,2054	53	58	57		3213,3330	3	1	9	dbSNP_130	57	1,8589		0,1,4294	no	coding-synonymous,coding-synonymous	C9orf84	NM_001080551.1,NM_173521.3	,	2,148,6348	CC,CT,TT		0.0116,3.4271,1.1696	,	1071/1406,1110/1445	114454735	152,12844	2203	4295	6498	SO:0001819	synonymous_variant	158401	exon25			TTGCGGTGATTTT	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.3330A>G	9.37:g.114454735T>C		57	0	0		40	9	0.225	NM_173521	A2A2V3|Q2M1H8|Q96M73	Silent	SNP	ENST00000318737.4	37	CCDS6781.3																																																																																			T|0.988;C|0.012	0.012	strong		0.323	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521		C	114454735	T	C	114454735	2	2	22	1	0	0	0	0	0	0	0	1	2502	1683	59	3		3	C9orf84	9	114454735	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	364458	114454735	26758696	2117	5018											
PRPF4	9128	hgsc.bcm.edu	37	chr9	116041316	116041316	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcgagcccggcagatcaaTgtttccacagatgactcaga	13	7	10	11	2	2	4	2	1	0	3	3	5	3	4	2	1	2	2	2	1	2	1	rs146246780	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116041316T>C	ENST00000374198.4	+	3	402	c.300T>C	c.(298-300)aaT>aaC	p.N100N	PRPF4_ENST00000374199.4_Silent_p.N99N	NM_001244926.1|NM_004697.4	NP_001231855.1|NP_004688.2	O43172	PRP4_HUMAN	pre-mRNA processing factor 4	100				HISERQAEVLAEFERRKRARQINVST -> ISASDRQKYWL SLREGSEPGRSMFPP (in Ref. 3; AAC02261). {ECO:0000305}.	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						GGCAGATCAATGTTTCCACAG	0.473													T|||	7	0.00139776	0.0045	0.0014	5008	,	,		15580	0.0		0.0	False		,,,				2504	0.0				p.N100N		Atlas-SNP	.											.	PRPF4	56	.	0			c.T300C						PASS	.	T		14,4392	21.2+/-45.6	0,14,2189	95	91	92		300	0.2	1	9	dbSNP_134	92	0,8600		0,0,4300	no	coding-synonymous	PRPF4	NM_004697.3		0,14,6489	CC,CT,TT		0.0,0.3177,0.1076		100/523	116041316	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	9128	exon3			GATCAATGTTTCC	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.300T>C	9.37:g.116041316T>C		76	0	0		97	57	0.587629	NM_004697	O43445|O43864|Q5T1M8|Q96DG2|Q96IK4	Silent	SNP	ENST00000374198.4	37	CCDS6791.1																																																																																			T|0.999;C|0.001	0.001	strong		0.473	PRPF4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053708.2	NM_004697		C	116041316	T	C	116041316	2	2	22	1	0	0	0	0	0	0	0	1	12582	1461	51	3		3	PRPF4	9	116041316	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1586581	116041316	25172115	2118	5019											
PRPF4	9128	hgsc.bcm.edu	37	chr9	116053895	116053895	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccgatgggcagctcatagcCacttgctcatatgacaggac	10	9	10	12	1	2	1	2	1	0	0	3	3	3	2	2	2	3	3	2	2	2	3	rs146201781	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116053895C>T	ENST00000374198.4	+	14	1626	c.1524C>T	c.(1522-1524)gcC>gcT	p.A508A	PRPF4_ENST00000374199.4_Silent_p.A507A	NM_001244926.1|NM_004697.4	NP_001231855.1|NP_004688.2	O43172	PRP4_HUMAN	pre-mRNA processing factor 4	508					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						AGCTCATAGCCACTTGCTCAT	0.517													C|||	7	0.00139776	0.0045	0.0014	5008	,	,		19015	0.0		0.0	False		,,,				2504	0.0				p.A508A		Atlas-SNP	.											.	PRPF4	56	.	0			c.C1524T						PASS	.	C		14,4392	21.2+/-45.6	0,14,2189	88	80	83		1524	3.9	1	9	dbSNP_134	83	0,8600		0,0,4300	no	coding-synonymous	PRPF4	NM_004697.3		0,14,6489	TT,TC,CC		0.0,0.3177,0.1076		508/523	116053895	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	9128	exon14			CATAGCCACTTGC	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.1524C>T	9.37:g.116053895C>T		102	0	0		122	78	0.639344	NM_004697	O43445|O43864|Q5T1M8|Q96DG2|Q96IK4	Silent	SNP	ENST00000374198.4	37	CCDS6791.1																																																																																			C|0.999;T|0.001	0.001	strong		0.517	PRPF4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053708.2	NM_004697		T	116053895	C	T	116053895	2	4	22	1	0	0	0	0	0	0	0	1	12582	581	21	2		2	PRPF4	9	116053895	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	12579	116053895	25159536	2119	5020											
WDR31	114987	hgsc.bcm.edu	37	chr9	116085148	116085148	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgtcaccacatcccacagAagcagggtgttgtcccgaga	10	7	10	14	1	1	2	1	0	0	2	3	3	3	2	4	1	1	2	4	1	1	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116085148A>C	ENST00000374193.4	-	7	759	c.513T>G	c.(511-513)ctT>ctG	p.L171L	WDR31_ENST00000374195.3_Silent_p.L46L|WDR31_ENST00000341761.4_Silent_p.L170L|WDR31_ENST00000461942.1_5'UTR	NM_001012361.2|NM_145241.3	NP_001012361.1|NP_660284.1	Q8NA23	WDR31_HUMAN	WD repeat domain 31	171										NS(1)|large_intestine(1)|lung(2)|prostate(2)	6						CATCCCACAGAAGCAGGGTGT	0.527																																					p.L171L		Atlas-SNP	.											.	WDR31	23	.	0			c.T513G						PASS	.						124	104	111					9																	116085148		2203	4300	6503	SO:0001819	synonymous_variant	114987	exon7			CCACAGAAGCAGG	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.513T>G	9.37:g.116085148A>C		176	0	0		195	68	0.348718	NM_001012361	Q5W0T9|Q96EG8	Silent	SNP	ENST00000374193.4	37	CCDS35110.1																																																																																			.	.	none		0.527	WDR31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053734.2	NM_145241		C	116085148	A	C	116085148	2	2	22	1	0	0	0	0	0	0	0	1	17301	233	9	5		5	WDR31	9	116085148	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	31253	116085148	25128283	2120	5021											
BSPRY	54836	hgsc.bcm.edu	37	chr9	116131916	116131916	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcacagaggacatacggatcGatgagaggacagtcagcccc	13	4	13	11	2	1	2	1	1	0	2	2	7	1	5	2	3	2	1	2	3	1	1	rs377189582		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116131916G>A	ENST00000374183.4	+	6	742	c.703G>A	c.(703-705)Gat>Aat	p.D235N	BSPRY_ENST00000462085.1_3'UTR	NM_017688.2	NP_060158.2	Q5W0U4	BSPRY_HUMAN	B-box and SPRY domain containing	235	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)	cell leading edge (GO:0031252)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|lung(4)|urinary_tract(1)	8						CATACGGATCGATGAGAGGAC	0.562																																					p.D235N		Atlas-SNP	.											.	BSPRY	21	.	0			c.G703A						PASS	.						85	85	85					9																	116131916		2012	4204	6216	SO:0001583	missense	54836	exon6			CGGATCGATGAGA	AJ276691	CCDS43868.1	9q33.1	2008-02-05			ENSG00000119411	ENSG00000119411			18232	protein-coding gene	gene with protein product						10978534, 11099500	Standard	NM_017688		Approved	FLJ20150	uc004bhg.4	Q5W0U4	OTTHUMG00000021006	ENST00000374183.4:c.703G>A	9.37:g.116131916G>A	ENSP00000363298:p.Asp235Asn	59	0	0		67	50	0.746269	NM_017688	B3KS19|Q96DJ2|Q9H4E4|Q9NXN0	Missense_Mutation	SNP	ENST00000374183.4	37	CCDS43868.1	.	.	.	.	.	.	.	.	.	.	G	19.66	3.868407	0.72065	.	.	ENSG00000119411	ENST00000374183	T	0.61274	0.12	5.6	4.7	0.59300	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	0.047007	0.85682	D	0.000000	T	0.67951	0.2948	M	0.92317	3.295	0.58432	D	0.999992	P	0.44195	0.828	B	0.41174	0.349	T	0.76429	-0.2962	10	0.59425	D	0.04	-17.9828	13.9619	0.64185	0.0733:0.0:0.9267:0.0	.	235	Q5W0U4	BSPRY_HUMAN	N	235	ENSP00000363298:D235N	ENSP00000363298:D235N	D	+	1	0	BSPRY	115171737	1.000000	0.71417	0.645000	0.29479	0.973000	0.67179	4.224000	0.58593	1.355000	0.45865	0.561000	0.74099	GAT	.	.	alt		0.562	BSPRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055399.1	NM_017688		A	116131916	G	A	116131916	3	1	22	1	0	0	0	0	1	0	0	0	1534	1058	37	1	725	1	BSPRY	9	116131916	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	46768	116131916	25081515	2121	5022											
RGS3	5998	hgsc.bcm.edu	37	chr9	116224452	116224452	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aacttctccagccaggaagaGgatcacgcatgccaaagtcc	13	6	9	13	1	2	1	1	0	1	1	4	3	3	3	4	2	3	1	4	2	3	1	rs16933949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116224452G>A	ENST00000374140.2	+	4	595	c.386G>A	c.(385-387)aGg>aAg	p.R129K	RGS3_ENST00000317613.6_5'Flank|RGS3_ENST00000350696.5_Missense_Mutation_p.R129K	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	129			R -> K (in dbSNP:rs16933949).		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						GCCAGGAAGAGGATCACGCAT	0.537													G|||	288	0.057508	0.2088	0.0159	5008	,	,		16916	0.0		0.001	False		,,,				2504	0.0				p.R129K		Atlas-SNP	.											.	RGS3	251	.	0			c.G386A						PASS	.	G	LYS/ARG	726,3434		72,582,1426	77	81	79		386	-1.2	0	9	dbSNP_123	79	4,8432		0,4,4214	yes	missense	RGS3	NM_144488.4	26	72,586,5640	AA,AG,GG		0.0474,17.4519,5.7955	possibly-damaging	129/1199	116224452	730,11866	2080	4218	6298	SO:0001583	missense	5998	exon4			GGAAGAGGATCAC	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.386G>A	9.37:g.116224452G>A	ENSP00000363255:p.Arg129Lys	95	0	0		105	72	0.685714	NM_144488	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	37	CCDS43869.1	100	0.045787545787545784	93	0.18902439024390244	7	0.019337016574585635	0	0.0	0	0.0	G	6.337	0.430283	0.12045	0.174519	4.74E-4	ENSG00000138835	ENST00000374140;ENST00000350696	T;T	0.41065	1.01;1.01	4.39	-1.25	0.09405	.	.	.	.	.	T	0.00039	0.0001	N	0.12182	0.205	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.15321	-1.0441	8	0.87932	D	0	.	7.8729	0.29576	0.5369:0.0:0.4631:0.0	rs16933949;rs59024905;rs16933949	129	P49796	RGS3_HUMAN	K	129	ENSP00000363255:R129K;ENSP00000259406:R129K	ENSP00000259406:R129K	R	+	2	0	RGS3	115264273	0.022000	0.18835	0.003000	0.11579	0.862000	0.49288	0.044000	0.13992	-0.349000	0.08274	0.591000	0.81541	AGG	G|0.957;A|0.043	0.043	strong		0.537	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790		A	116224452	G	A	116224452	3	1	22	1	0	0	0	0	1	0	0	0	13321	1000	35	2	396	2	RGS3	9	116224452	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	92536	116224452	24988979	2122	5023											
RGS3	5998	hgsc.bcm.edu	37	chr9	116356389	116356389	+	Intron	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctgtctgagtcccagcccCggcttgtgcctgggagtcca	4	10	12	15	1	1	1	0	1	1	0	4	2	4	2	6	2	2	1	6	2	0	1	rs57845277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116356389C>T	ENST00000374140.2	+	23	3289				RGS3_ENST00000343817.5_Intron|RGS3_ENST00000374134.3_Intron|RGS3_ENST00000462143.1_Intron|RGS3_ENST00000394646.3_Intron|RGS3_ENST00000462403.1_Missense_Mutation_p.R64W|RGS3_ENST00000350696.5_Intron|RGS3_ENST00000342620.5_Intron	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3						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						GTCCCAGCCCCGGCTTGTGCC	0.637													C|||	54	0.0107827	0.0393	0.0029	5008	,	,		15146	0.0		0.0	False		,,,				2504	0.0				p.R64W		Atlas-SNP	.											.	RGS3	251	.	0			c.C190T						PASS	.	C	,,,,TRP/ARG	146,4260		5,136,2062	66	74	71		,,,,190	-5.5	0	9	dbSNP_129	71	1,8599		0,1,4299	no	intron,intron,intron,intron,missense	RGS3	NM_021106.3,NM_130795.2,NM_134427.1,NM_144488.4,NM_144489.2	,,,,101	5,137,6361	TT,TC,CC		0.0116,3.3137,1.1302	,,,,	,,,,64/312	116356389	147,12859	2203	4300	6503	SO:0001627	intron_variant	5998	exon1			CAGCCCCGGCTTG	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.3081-321C>T	9.37:g.116356389C>T		273	0	0		259	94	0.362934	NM_144489	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	37	CCDS43869.1	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	C	1.749	-0.489752	0.04352	0.033137	1.16E-4	ENSG00000138835	ENST00000462403	T	0.62232	0.04	4.25	-5.51	0.02568	.	.	.	.	.	T	0.12390	0.0301	N	0.08118	0	0.20074	N	0.999939	B	0.02656	0.0	B	0.01281	0.0	T	0.09707	-1.0662	9	0.87932	D	0	.	0.1774	0.00120	0.2449:0.2726:0.1703:0.3122	rs57845277	64	Q5VZ06	.	W	64	ENSP00000436168:R64W	ENSP00000436168:R64W	R	+	1	2	RGS3	115396210	0.000000	0.05858	0.010000	0.14722	0.220000	0.24768	-2.218000	0.01219	-1.939000	0.01044	-1.946000	0.00489	CGG	C|0.988;T|0.012	0.012	strong		0.637	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790		T	116356389	C	T	116356389	1	4	22	0	1	0	0	0	0	0	0	0	13321	643	23	1		1	RGS3	9	116356389	Intron	SNP	C	TCGA-G8-6324-01A-11D-2210-10	131937	116356389	24857042	2123	5024											
RGS3	5998	hgsc.bcm.edu	37	chr9	116356549	116356549	+	Intron	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggccccaaggtggggggccCtacagagatgctccgaggca	8	4	16	13	2	0	1	0	0	0	1	1	3	1	1	4	6	2	2	4	6	2	1	rs113405588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116356549C>G	ENST00000374140.2	+	23	3289				RGS3_ENST00000343817.5_Intron|RGS3_ENST00000374134.3_Intron|RGS3_ENST00000462143.1_Intron|RGS3_ENST00000394646.3_Intron|RGS3_ENST00000462403.1_Missense_Mutation_p.P117R|RGS3_ENST00000350696.5_Intron|RGS3_ENST00000342620.5_Intron	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3						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						GTGGGGGGCCCTACAGAGATG	0.662													C|||	68	0.0135783	0.0492	0.0043	5008	,	,		13726	0.0		0.0	False		,,,				2504	0.0				p.P117R		Atlas-SNP	.											.	RGS3	251	.	0			c.C350G						PASS	.	C	,,,,ARG/PRO	206,4196		8,190,2003	37	45	42		,,,,350	5.2	0.8	9	dbSNP_132	42	1,8595		0,1,4297	yes	intron,intron,intron,intron,missense	RGS3	NM_021106.3,NM_130795.2,NM_134427.1,NM_144488.4,NM_144489.2	,,,,103	8,191,6300	GG,GC,CC		0.0116,4.6797,1.5926	,,,,	,,,,117/312	116356549	207,12791	2201	4298	6499	SO:0001627	intron_variant	5998	exon1			GGGGCCCTACAGA	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.3081-161C>G	9.37:g.116356549C>G		75	0	0		72	42	0.583333	NM_144489	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	37	CCDS43869.1	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	C	14.66	2.600389	0.46423	0.046797	1.16E-4	ENSG00000138835	ENST00000462403	T	0.65364	-0.15	5.23	5.23	0.72850	.	.	.	.	.	T	0.09949	0.0244	N	0.14661	0.345	0.47819	D	0.99952	P	0.41313	0.745	B	0.36418	0.224	T	0.14200	-1.0481	9	0.49607	T	0.09	.	11.4969	0.50413	0.1792:0.8208:0.0:0.0	.	117	Q5VZ06	.	R	117	ENSP00000436168:P117R	ENSP00000436168:P117R	P	+	2	0	RGS3	115396370	0.373000	0.25073	0.808000	0.32385	0.977000	0.68977	2.249000	0.43169	2.442000	0.82660	0.558000	0.71614	CCT	C|0.988;G|0.012	0.012	strong		0.662	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790		G	116356549	C	G	116356549	1	3	22	0	1	0	0	0	0	0	0	0	13321	681	24	4		4	RGS3	9	116356549	Intron	SNP	C	TCGA-G8-6324-01A-11D-2210-10	160	116356549	24856882	2124	5025											
ZNF618	114991	hgsc.bcm.edu	37	chr9	116811184	116811184	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgcatgtacaaccaggtgaaGgtgaaagtgacctgtgcctt	11	9	12	9	1	0	3	0	3	0	0	0	3	0	3	3	2	3	2	3	2	4	2	rs7852282	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116811184G>A	ENST00000374126.5	+	15	1701	c.1602G>A	c.(1600-1602)aaG>aaA	p.K534K	ZNF618_ENST00000470105.1_3'UTR|ZNF618_ENST00000288466.7_Silent_p.K441K			Q5T7W0	ZN618_HUMAN	zinc finger protein 618	534					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						ACCAGGTGAAGGTGAAAGTGA	0.587													G|||	338	0.067492	0.2375	0.0303	5008	,	,		21657	0.0		0.0	False		,,,				2504	0.0031				p.K441K		Atlas-SNP	.											.	ZNF618	184	.	0			c.G1323A						PASS	.	G		796,3538		77,642,1448	27	30	29		1323	3.5	1	9	dbSNP_116	29	18,8520		0,18,4251	no	coding-synonymous	ZNF618	NM_133374.2		77,660,5699	AA,AG,GG		0.2108,18.3664,6.3238		441/862	116811184	814,12058	2167	4269	6436	SO:0001819	synonymous_variant	114991	exon14			GGTGAAGGTGAAA	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.1602G>A	9.37:g.116811184G>A		55	0	0		60	38	0.633333	NM_133374	B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49	Silent	SNP	ENST00000374126.5	37																																																																																				G|0.921;A|0.079	0.079	strong		0.587	ZNF618-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000053749.1	XM_054983		A	116811184	G	A	116811184	2	1	22	1	0	0	0	0	0	0	0	1	18057	991	35	2		2	ZNF618	9	116811184	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	454635	116811184	24402247	2125	5026											
COL27A1	85301	hgsc.bcm.edu	37	chr9	116930013	116930013	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcctcagctggacgaaggccGggagccctgcacccccggga	7	3	15	16	3	1	0	1	0	0	0	1	4	1	3	5	4	3	2	5	4	1	0	rs74339956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116930013G>A	ENST00000356083.3	+	3	569	c.178G>A	c.(178-180)Ggg>Agg	p.G60R		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	60					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						GACGAAGGCCGGGAGCCCTGC	0.677													G|||	70	0.0139776	0.0522	0.0014	5008	,	,		16813	0.0		0.0	False		,,,				2504	0.0				p.G60R		Atlas-SNP	.											.	COL27A1	200	.	0			c.G178A						PASS	.	G	ARG/GLY	211,4195	122.5+/-159.9	6,199,1998	71	84	80		178	2.3	1	9	dbSNP_131	80	0,8598		0,0,4299	yes	missense	COL27A1	NM_032888.2	125	6,199,6297	AA,AG,GG		0.0,4.7889,1.6226	benign	60/1861	116930013	211,12793	2203	4299	6502	SO:0001583	missense	85301	exon3			AAGGCCGGGAGCC	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.178G>A	9.37:g.116930013G>A	ENSP00000348385:p.Gly60Arg	84	0	0		102	37	0.362745	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	37	CCDS6802.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	G	9.795	1.179007	0.21787	0.047889	0.0	ENSG00000196739	ENST00000356083;ENST00000357257;ENST00000374106;ENST00000451716	T;T	0.03242	4.0;4.0	5.32	2.3	0.28687	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	.	.	.	.	T	0.00300	0.0009	N	0.01576	-0.805	0.24118	N	0.995813	B	0.02656	0.0	B	0.01281	0.0	T	0.48885	-0.8995	9	0.32370	T	0.25	.	6.932	0.24447	0.0:0.5451:0.36:0.095	.	60	Q8IZC6	CORA1_HUMAN	R	60;60;7;7	ENSP00000348385:G60R;ENSP00000391328:G7R	ENSP00000348385:G60R	G	+	1	0	COL27A1	115969834	0.010000	0.17322	1.000000	0.80357	0.271000	0.26615	1.569000	0.36428	0.627000	0.30340	-0.516000	0.04426	GGG	G|0.985;A|0.015	0.015	strong		0.677	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888		A	116930013	G	A	116930013	3	1	22	1	0	0	0	0	1	0	0	0	3687	1116	39	1	188	1	COL27A1	9	116930013	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	118829	116930013	24283418	2126	5027											
COL27A1	85301	hgsc.bcm.edu	37	chr9	116958283	116958283	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccgggaatccaggacctccGggacgaaaggtactgtttgg	9	8	14	10	3	0	0	0	0	0	0	3	4	3	3	4	5	1	2	4	5	3	2	rs10982098	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116958283G>A	ENST00000356083.3	+	7	2506	c.2115G>A	c.(2113-2115)ccG>ccA	p.P705P		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	705	Collagen-like 2.|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						CAGGACCTCCGGGACGAAAGG	0.592													G|||	39	0.00778754	0.0295	0.0	5008	,	,		19536	0.0		0.0	False		,,,				2504	0.0				p.P705P		Atlas-SNP	.											.	COL27A1	200	.	0			c.G2115A						PASS	.	G		101,4305	79.3+/-117.8	2,97,2104	160	134	143		2115	1.2	0.4	9	dbSNP_120	143	0,8600		0,0,4300	no	coding-synonymous	COL27A1	NM_032888.2		2,97,6404	AA,AG,GG		0.0,2.2923,0.7766		705/1861	116958283	101,12905	2203	4300	6503	SO:0001819	synonymous_variant	85301	exon7			ACCTCCGGGACGA	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.2115G>A	9.37:g.116958283G>A		78	0	0		77	27	0.350649	NM_032888	Q66K43|Q96JF7	Silent	SNP	ENST00000356083.3	37	CCDS6802.1																																																																																			G|0.993;A|0.007	0.007	strong		0.592	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888		A	116958283	G	A	116958283	2	1	22	1	0	0	0	0	0	0	0	1	3687	1103	39	1		1	COL27A1	9	116958283	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	28270	116958283	24255148	2127	5028											
COL27A1	85301	hgsc.bcm.edu	37	chr9	117068826	117068826	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agctatccagaccggctggtGctggaccagggaggagagat	10	6	16	9	1	0	2	0	0	0	2	1	6	1	5	3	5	2	3	3	5	1	1	rs1249762	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117068826G>A	ENST00000356083.3	+	58	5356	c.4965G>A	c.(4963-4965)gtG>gtA	p.V1655V		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1655					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						ACCGGCTGGTGCTGGACCAGG	0.587											OREG0019417	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	112	0.0223642	0.0847	0.0	5008	,	,		14302	0.0		0.0	False		,,,				2504	0.0				p.V1655V		Atlas-SNP	.											.	COL27A1	200	.	0			c.G4965A						PASS	.	G		298,4108	162.9+/-194.8	12,274,1917	61	64	63		4965	4.4	1	9	dbSNP_87	63	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	COL27A1	NM_032888.2		12,275,6216	AA,AG,GG		0.0116,6.7635,2.2989		1655/1861	117068826	299,12707	2203	4300	6503	SO:0001819	synonymous_variant	85301	exon58			GCTGGTGCTGGAC	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.4965G>A	9.37:g.117068826G>A		62	0	0	1478	73	31	0.424658	NM_032888	Q66K43|Q96JF7	Silent	SNP	ENST00000356083.3	37	CCDS6802.1																																																																																			G|0.974;A|0.026	0.026	strong		0.587	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888		A	117068826	G	A	117068826	2	1	22	1	0	0	0	0	0	0	0	1	3687	1306	46	2		2	COL27A1	9	117068826	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	110543	117068826	24144605	2128	5029											
ORM1	5004	hgsc.bcm.edu	37	chr9	117088618	117088620	+	In_Frame_Del	DEL	AGG	AGG	-																															gcacgagaaggagaggaaacAggaggagggggaatcctagc																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117088618_117088620delAGG	ENST00000259396.8	+	6	665_667	c.587_589delAGG	c.(586-591)caggag>cag	p.E198del		NM_000607.2	NP_000598.2	P02763	A1AG1_HUMAN	orosomucoid 1	198					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)	GAGAGGAAACAGGAGGAGGGGGA	0.581																																					p.196_196del		Atlas-Indel	.											.	ORM1	20	.	0			c.586_588del						PASS	.																																			SO:0001651	inframe_deletion	5004	exon6			.		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.587_589delAGG	9.37:g.117088624_117088626delAGG	ENSP00000259396:p.Glu198del	915	0	0		979	178	0.181818	NM_000607	B7ZKQ5|Q5T539|Q5U067|Q8TC16	In_Frame_Del	DEL	ENST00000259396.8	37	CCDS6803.1																																																																																			.	.	none		0.581	ORM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055426.1			-	117088620	AGG	-	117088618	7	5	22	1	0	1	0	1	0	0	0	0	11276	188	7	0	609	0	ORM1	9	117088618	In_Frame_Del	DEL	AGG	TCGA-G8-6324-01A-11D-2210-10	19792	117088618	24124813	2129	5030											
ORM2	5005	hgsc.bcm.edu	37	chr9	117093856	117093856	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttctcttccagagggaggccGagaacatgttgctcacctgc	8	10	11	12	1	2	2	1	0	1	2	4	4	3	3	3	2	3	2	3	2	1	3	rs142633392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117093856G>A	ENST00000431067.2	+	4	374	c.338G>A	c.(337-339)cGa>cAa	p.R113Q	ORM2_ENST00000412657.1_3'UTR	NM_000608.2	NP_000599.1	P19652	A1AG2_HUMAN	orosomucoid 2	113					acute-phase response (GO:0006953)|regulation of immune system process (GO:0002682)|transport (GO:0006810)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(1)	7		Myeloproliferative disorder(63;0.163)			Chlorpromazine(DB00477)|Oxycodone(DB00497)|Thalidomide(DB01041)	GAGGGAGGCCGAGAACATGTT	0.537													-|||	29	0.00579073	0.0197	0.0029	5008	,	,		18793	0.0		0.001	False		,,,				2504	0.0				p.R113Q	NSCLC(65;867 1308 1814 2391 12508)	Atlas-SNP	.											.	ORM2	13	.	0			c.G338A						PASS	.	G	GLN/ARG	77,4329		1,75,2127	132	116	121		338	-5.9	0	9	dbSNP_134	121	0,8600		0,0,4300	yes	missense	ORM2	NM_000608.2	43	1,75,6427	AA,AG,GG		0.0,1.7476,0.592		113/202	117093856	77,12929	2203	4300	6503	SO:0001583	missense	5005	exon4			GAGGCCGAGAACA		CCDS6804.1	9q32	2013-09-19			ENSG00000228278	ENSG00000228278		"Lipocalins"	8499	protein-coding gene	gene with protein product	"alpha-1-acid glycoprotein, type 2"	138610				4711474, 2970990	Standard	NM_000608		Approved	AGP-B, AGP-B', AGP2		P19652	OTTHUMG00000021014	ENST00000431067.2:c.338G>A	9.37:g.117093856G>A	ENSP00000394936:p.Arg113Gln	208	0	0		216	135	0.625	NM_000608	B2R5L2|Q16571|Q5T538|Q6IB74	Missense_Mutation	SNP	ENST00000431067.2	37	CCDS6804.1	10	0.004578754578754579	8	0.016260162601626018	2	0.0055248618784530384	0	0.0	0	0.0	-	0.084	-1.178327	0.01633	0.017476	0.0	ENSG00000228278	ENST00000431067	T	0.08008	3.14	2.95	-5.9	0.02275	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	1.906400	0.02445	N	0.084964	T	0.03095	0.0091	L	0.37561	1.115	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.24476	-1.0159	10	0.20519	T	0.43	4.2497	6.8017	0.23754	0.121:0.0928:0.6382:0.148	.	113	P19652	A1AG2_HUMAN	Q	113	ENSP00000394936:R113Q	ENSP00000394936:R113Q	R	+	2	0	ORM2	116133677	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.988000	0.00319	-4.920000	0.00027	-2.326000	0.00250	CGA	G|0.995;A|0.005	0.005	strong		0.537	ORM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055432.1	NM_000608		A	117093856	G	A	117093856	3	1	22	1	0	0	0	0	1	0	0	0	11277	1058	37	1	352	1	ORM2	9	117093856	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5238	117093856	24119575	2130	5031											
ORM2	5005	hgsc.bcm.edu	37	chr9	117094119	117094119	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctgcagctgacaagccagaGacgaccaaggagcaactggg	13	3	13	12	1	0	2	0	1	0	1	0	5	0	3	3	2	5	3	3	2	3	0	rs148394636	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117094119G>A	ENST00000431067.2	+	5	486	c.450G>A	c.(448-450)gaG>gaA	p.E150E	ORM2_ENST00000412657.1_3'UTR	NM_000608.2	NP_000599.1	P19652	A1AG2_HUMAN	orosomucoid 2	150					acute-phase response (GO:0006953)|regulation of immune system process (GO:0002682)|transport (GO:0006810)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(1)	7		Myeloproliferative disorder(63;0.163)			Chlorpromazine(DB00477)|Oxycodone(DB00497)|Thalidomide(DB01041)	ACAAGCCAGAGACGACCAAGG	0.602													G|||	399	0.0796725	0.2943	0.0144	5008	,	,		17341	0.0		0.0	False		,,,				2504	0.0				p.E150E	NSCLC(65;867 1308 1814 2391 12508)	Atlas-SNP	.											.	ORM2	13	.	0			c.G450A						PASS	.	G		955,3451	347.2+/-309.4	112,731,1360	59	63	62		450	-2.4	0	9	dbSNP_134	62	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous	ORM2	NM_000608.2		112,732,5656	AA,AG,GG		0.0116,21.675,7.3538		150/202	117094119	956,12044	2203	4297	6500	SO:0001819	synonymous_variant	5005	exon5			GCCAGAGACGACC		CCDS6804.1	9q32	2013-09-19			ENSG00000228278	ENSG00000228278		"Lipocalins"	8499	protein-coding gene	gene with protein product	"alpha-1-acid glycoprotein, type 2"	138610				4711474, 2970990	Standard	NM_000608		Approved	AGP-B, AGP-B', AGP2		P19652	OTTHUMG00000021014	ENST00000431067.2:c.450G>A	9.37:g.117094119G>A		176	0	0		182	46	0.252747	NM_000608	B2R5L2|Q16571|Q5T538|Q6IB74	Silent	SNP	ENST00000431067.2	37	CCDS6804.1																																																																																			G|0.931;A|0.069	0.069	strong		0.602	ORM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055432.1	NM_000608		A	117094119	G	A	117094119	2	1	22	1	0	0	0	0	0	0	0	1	11277	933	33	2		2	ORM2	9	117094119	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	263	117094119	24119312	2131	5032											
ORM2	5005	hgsc.bcm.edu	37	chr9	117094159	117094159	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gagagttctacgaagctctcGactgcttgtgcattcccagg	8	11	11	11	2	2	1	0	0	2	1	4	4	3	1	1	1	4	4	1	1	2	4	rs148221879	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117094159G>A	ENST00000431067.2	+	5	526	c.490G>A	c.(490-492)Gac>Aac	p.D164N	ORM2_ENST00000412657.1_3'UTR	NM_000608.2	NP_000599.1	P19652	A1AG2_HUMAN	orosomucoid 2	164					acute-phase response (GO:0006953)|regulation of immune system process (GO:0002682)|transport (GO:0006810)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(1)	7		Myeloproliferative disorder(63;0.163)			Chlorpromazine(DB00477)|Oxycodone(DB00497)|Thalidomide(DB01041)	CGAAGCTCTCGACTGCTTGTG	0.572													G|||	14	0.00279553	0.0083	0.0014	5008	,	,		18564	0.0		0.001	False		,,,				2504	0.001				p.D164N	NSCLC(65;867 1308 1814 2391 12508)	Atlas-SNP	.											.	ORM2	13	.	0			c.G490A						PASS	.	G	ASN/ASP	54,4352	53.6+/-89.4	1,52,2150	103	99	100		490	-5.1	0	9	dbSNP_134	100	0,8600		0,0,4300	yes	missense	ORM2	NM_000608.2	23	1,52,6450	AA,AG,GG		0.0,1.2256,0.4152		164/202	117094159	54,12952	2203	4300	6503	SO:0001583	missense	5005	exon5			GCTCTCGACTGCT		CCDS6804.1	9q32	2013-09-19			ENSG00000228278	ENSG00000228278		"Lipocalins"	8499	protein-coding gene	gene with protein product	"alpha-1-acid glycoprotein, type 2"	138610				4711474, 2970990	Standard	NM_000608		Approved	AGP-B, AGP-B', AGP2		P19652	OTTHUMG00000021014	ENST00000431067.2:c.490G>A	9.37:g.117094159G>A	ENSP00000394936:p.Asp164Asn	194	0	0		215	152	0.706977	NM_000608	B2R5L2|Q16571|Q5T538|Q6IB74	Missense_Mutation	SNP	ENST00000431067.2	37	CCDS6804.1	3	0.0013736263736263737	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	G	14.61	2.587382	0.46110	0.012256	0.0	ENSG00000228278	ENST00000431067	T	0.07567	3.18	3.83	-5.07	0.02938	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	1.832830	0.02642	N	0.105407	T	0.03827	0.0108	L	0.36672	1.1	0.09310	N	1	P	0.39748	0.686	B	0.27076	0.076	T	0.35822	-0.9773	10	0.24483	T	0.36	-2.7618	10.116	0.42591	0.3551:0.0:0.6449:0.0	.	164	P19652	A1AG2_HUMAN	N	164	ENSP00000394936:D164N	ENSP00000394936:D164N	D	+	1	0	ORM2	116133980	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-1.487000	0.02310	-1.079000	0.03113	0.544000	0.68410	GAC	G|0.997;A|0.003	0.003	strong		0.572	ORM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055432.1	NM_000608		A	117094159	G	A	117094159	3	1	22	1	0	0	0	0	1	0	0	0	11277	1058	37	1	508	1	ORM2	9	117094159	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	40	117094159	24119272	2132	5033											
ORM2	5005	hgsc.bcm.edu	37	chr9	117094200	117094200	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagatgtcatgtacaccgaCtggaaaaaggtaaacgcaag	16	7	10	8	2	2	1	2	0	0	1	2	3	2	2	1	2	2	3	1	2	6	2	rs1826232	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117094200C>T	ENST00000431067.2	+	5	567	c.531C>T	c.(529-531)gaC>gaT	p.D177D	ORM2_ENST00000412657.1_3'UTR	NM_000608.2	NP_000599.1	P19652	A1AG2_HUMAN	orosomucoid 2	177					acute-phase response (GO:0006953)|regulation of immune system process (GO:0002682)|transport (GO:0006810)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(1)	7		Myeloproliferative disorder(63;0.163)			Chlorpromazine(DB00477)|Oxycodone(DB00497)|Thalidomide(DB01041)	TGTACACCGACTGGAAAAAGG	0.567													T|||	747	0.149161	0.4894	0.0403	5008	,	,		18828	0.0605		0.002	False		,,,				2504	0.0092				p.D177D	NSCLC(65;867 1308 1814 2391 12508)	Atlas-SNP	.											ORM2,face,carcinoma,-2,1	ORM2	13	1	0			c.C531T						PASS	.	T		1790,2616	641.6+/-397.5	383,1024,796	92	92	92		531	-4.5	0	9	dbSNP_92	92	20,8580	818.0+/-406.9	0,20,4280	no	coding-synonymous	ORM2	NM_000608.2		383,1044,5076	TT,TC,CC		0.2326,40.6264,13.9167		177/202	117094200	1810,11196	2203	4300	6503	SO:0001819	synonymous_variant	5005	exon5			CACCGACTGGAAA		CCDS6804.1	9q32	2013-09-19			ENSG00000228278	ENSG00000228278		"Lipocalins"	8499	protein-coding gene	gene with protein product	"alpha-1-acid glycoprotein, type 2"	138610				4711474, 2970990	Standard	NM_000608		Approved	AGP-B, AGP-B', AGP2		P19652	OTTHUMG00000021014	ENST00000431067.2:c.531C>T	9.37:g.117094200C>T		136	0	0		160	49	0.30625	NM_000608	B2R5L2|Q16571|Q5T538|Q6IB74	Silent	SNP	ENST00000431067.2	37	CCDS6804.1																																																																																			C|0.873;T|0.127	0.127	strong		0.567	ORM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055432.1	NM_000608		T	117094200	C	T	117094200	2	4	22	1	0	0	0	0	0	0	0	1	11277	564	20	2		2	ORM2	9	117094200	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	41	117094200	24119231	2133	5034											
ORM2	5005	hgsc.bcm.edu	37	chr9	117095395	117095397	+	In_Frame_Del	DEL	AGG	AGG	-																															gcacgagaaggagaggaaacAggaggagggggaatcctagc																								rs530796283|rs537714275	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117095395_117095397delAGG	ENST00000431067.2	+	6	623_625	c.587_589delAGG	c.(586-591)caggag>cag	p.E198del		NM_000608.2	NP_000599.1	P19652	A1AG2_HUMAN	orosomucoid 2	198					acute-phase response (GO:0006953)|regulation of immune system process (GO:0002682)|transport (GO:0006810)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(1)	7		Myeloproliferative disorder(63;0.163)			Chlorpromazine(DB00477)|Oxycodone(DB00497)|Thalidomide(DB01041)	GAGAGGAAACAGGAGGAGGGGGA	0.581														13	0.00259585	0.0083	0.0014	5008	,	,		22543	0.0		0.001	False		,,,				2504	0.0				p.196_196del	NSCLC(65;867 1308 1814 2391 12508)	Atlas-Indel	.											.	ORM2	13	.	0			c.586_588del						PASS	.			39,3131		1,37,1547						1.8	0			15	1,5925		0,1,2962	no	coding	ORM2	NM_000608.2		1,38,4509	A1A1,A1R,RR		0.0169,1.2303,0.4398				40,9056				SO:0001651	inframe_deletion	5005	exon6			.		CCDS6804.1	9q32	2013-09-19			ENSG00000228278	ENSG00000228278		"Lipocalins"	8499	protein-coding gene	gene with protein product	"alpha-1-acid glycoprotein, type 2"	138610				4711474, 2970990	Standard	NM_000608		Approved	AGP-B, AGP-B', AGP2		P19652	OTTHUMG00000021014	ENST00000431067.2:c.587_589delAGG	9.37:g.117095401_117095403delAGG	ENSP00000394936:p.Glu198del	871	0	0		888	290	0.326577	NM_000608	B2R5L2|Q16571|Q5T538|Q6IB74	In_Frame_Del	DEL	ENST00000431067.2	37	CCDS6804.1																																																																																			.	.	none		0.581	ORM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055432.1	NM_000608		-	117095397	AGG	-	117095395	7	5	22	1	0	1	0	1	0	0	0	0	11277	188	7	0	609	0	ORM2	9	117095395	In_Frame_Del	DEL	AGG	TCGA-G8-6324-01A-11D-2210-10	1195	117095395	24118036	2134	5035											
AKNA	80709	hgsc.bcm.edu	37	chr9	117099574	117099574	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggctgaggtaggtcctgcAggcgcatagtacctgaggag	8	8	17	8	1	0	2	0	2	0	0	1	3	1	3	2	5	2	5	2	5	3	3	rs148856699	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117099574A>G	ENST00000307564.4	-	22	4241	c.4080T>C	c.(4078-4080)ccT>ccC	p.P1360P	AKNA_ENST00000374075.5_Silent_p.P1279P|AKNA_ENST00000374088.3_Silent_p.P1360P|AKNA_ENST00000492875.1_5'UTR|AKNA_ENST00000374079.4_Silent_p.P305P|AKNA_ENST00000223791.3_Silent_p.P820P	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	1360					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						TAGGTCCTGCAGGCGCATAGT	0.652													G|||	29	0.00579073	0.0197	0.0029	5008	,	,		10995	0.0		0.001	False		,,,				2504	0.0				p.P1360P		Atlas-SNP	.											.	AKNA	119	.	0			c.T4080C						PASS	.	G		77,4329	810.3+/-416.0	1,75,2127	41	44	43		4080	-5.6	0	9	dbSNP_134	43	0,8598		0,0,4299	no	coding-synonymous	AKNA	NM_030767.4		1,75,6426	GG,GA,AA		0.0,1.7476,0.5921		1360/1440	117099574	77,12927	2203	4299	6502	SO:0001819	synonymous_variant	80709	exon22			TCCTGCAGGCGCA	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.4080T>C	9.37:g.117099574A>G		136	0	0		147	99	0.673469	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Silent	SNP	ENST00000307564.4	37	CCDS6805.1	10	0.004578754578754579	8	0.016260162601626018	2	0.0055248618784530384	0	0.0	0	0.0	G	8.193	0.796449	0.16327	0.017476	0.0	ENSG00000106948	ENST00000320310	.	.	.	5.0	-5.55	0.02536	.	.	.	.	.	T	0.09202	0.0227	.	.	.	0.21822	N	0.999529	.	.	.	.	.	.	T	0.24476	-1.0159	4	.	.	.	-1.4841	3.3389	0.07111	0.561:0.1076:0.2123:0.119	.	.	.	.	P	371	.	.	L	-	2	0	AKNA	116139395	0.000000	0.05858	0.014000	0.15608	0.849000	0.48306	-0.506000	0.06359	-1.037000	0.03283	-0.349000	0.07799	CTG	A|0.995;G|0.005	0.005	strong		0.652	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767		G	117099574	A	G	117099574	2	3	22	1	0	0	0	0	0	0	0	1	463	175	7	3		3	AKNA	9	117099574	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	4179	117099574	24113857	2135	5036											
AKNA	80709	hgsc.bcm.edu	37	chr9	117103900	117103900	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgggggcgctgttgccagaTaccacagtccggggggtggg	5	7	19	10	2	0	1	0	0	0	1	1	1	1	1	3	6	2	2	3	6	1	2	rs2787344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117103900T>C	ENST00000307564.4	-	21	4141	c.3980A>G	c.(3979-3981)tAt>tGt	p.Y1327C	AKNA_ENST00000374075.5_Missense_Mutation_p.Y1246C|AKNA_ENST00000374088.3_Missense_Mutation_p.Y1327C|AKNA_ENST00000492875.1_5'UTR|AKNA_ENST00000374079.4_Missense_Mutation_p.Y272C|AKNA_ENST00000223791.3_Missense_Mutation_p.Y787C	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	1327			Y -> C (in dbSNP:rs2787344).		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						TGTTGCCAGATACCACAGTCC	0.622													T|||	395	0.0788738	0.2897	0.0173	5008	,	,		15911	0.0		0.0	False		,,,				2504	0.0				p.Y1327C		Atlas-SNP	.											.	AKNA	119	.	0			c.A3980G						PASS	.	T	CYS/TYR	981,3425	369.1+/-318.9	102,777,1324	56	62	60		3980	5.5	1	9	dbSNP_100	60	6,8594	4.3+/-15.6	0,6,4294	yes	missense	AKNA	NM_030767.4	194	102,783,5618	CC,CT,TT		0.0698,22.2651,7.5888	probably-damaging	1327/1440	117103900	987,12019	2203	4300	6503	SO:0001583	missense	80709	exon21			GCCAGATACCACA	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.3980A>G	9.37:g.117103900T>C	ENSP00000303769:p.Tyr1327Cys	103	0	0		126	40	0.31746	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	37	CCDS6805.1	141|141	0.06456043956043957|0.06456043956043957	135|135	0.27439024390243905|0.27439024390243905	6|6	0.016574585635359115|0.016574585635359115	0|0	0.0|0.0	0|0	0.0|0.0	T|T	16.55|16.55	3.154873|3.154873	0.57259|0.57259	0.222651|0.222651	6.98E-4|6.98E-4	ENSG00000106948|ENSG00000106948	ENST00000320310|ENST00000307564;ENST00000374079;ENST00000374088;ENST00000223791;ENST00000374075	.|T;T;T;T;T	.|0.39592	.|1.99;1.07;1.99;1.73;1.97	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	.|0.000000	.|0.53938	.|D	.|0.000059	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.36672|0.36672	1.1|1.1	0.27590|0.27590	P|P	0.9492969|0.9492969	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.998;0.999	T|T	0.10567|0.10567	-1.0624|-1.0624	5|9	0.51188|0.72032	T|D	0.08|0.01	-18.4356|-18.4356	12.2902|12.2902	0.54815|0.54815	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs2787344;rs2787344|rs2787344;rs2787344	.|1327;1246	.|Q7Z591;Q7Z591-2	.|AKNA_HUMAN;.	V|C	338|1327;272;1327;787;1246	.|ENSP00000303769:Y1327C;ENSP00000363192:Y272C;ENSP00000363201:Y1327C;ENSP00000223791:Y787C;ENSP00000363188:Y1246C	ENSP00000314538:I338V|ENSP00000223791:Y787C	I|Y	-|-	1|2	0|0	AKNA|AKNA	116143721|116143721	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.450000|0.450000	0.32258|0.32258	4.341000|4.341000	0.59335|0.59335	2.209000|2.209000	0.71365|0.71365	0.533000|0.533000	0.62120|0.62120	ATC|TAT	T|0.919;C|0.081	0.081	strong		0.622	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767		C	117103900	T	C	117103900	3	2	22	1	0	0	0	0	1	0	0	0	463	1406	49	3	347	3	AKNA	9	117103900	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	4326	117103900	24109531	2136	5037											
AKNA	80709	hgsc.bcm.edu	37	chr9	117104368	117104368	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggacactgaagggtatcagcGggaggcggtcccagtgggtc	8	6	18	9	2	1	1	1	1	0	0	3	3	2	3	1	6	1	1	1	6	2	1	rs73548990	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117104368G>A	ENST00000307564.4	-	20	3956	c.3795C>T	c.(3793-3795)ccC>ccT	p.P1265P	AKNA_ENST00000374075.5_Silent_p.P1184P|AKNA_ENST00000374088.3_Silent_p.P1265P|AKNA_ENST00000492875.1_5'UTR|AKNA_ENST00000374079.4_Silent_p.P210P|AKNA_ENST00000223791.3_Silent_p.P725P	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	1265					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						GGGTATCAGCGGGAGGCGGTC	0.567													G|||	130	0.0259585	0.093	0.0072	5008	,	,		18549	0.0		0.002	False		,,,				2504	0.0				p.P1265P		Atlas-SNP	.											.	AKNA	119	.	0			c.C3795T						PASS	.	G		303,4103	164.0+/-195.7	7,289,1907	52	51	51		3795	1.6	0	9	dbSNP_130	51	1,8599		0,1,4299	no	coding-synonymous	AKNA	NM_030767.4		7,290,6206	AA,AG,GG		0.0116,6.877,2.3374		1265/1440	117104368	304,12702	2203	4300	6503	SO:0001819	synonymous_variant	80709	exon20			ATCAGCGGGAGGC	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.3795C>T	9.37:g.117104368G>A		79	0	0		50	34	0.68	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Silent	SNP	ENST00000307564.4	37	CCDS6805.1	56	0.02564102564102564	51	0.10365853658536585	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	4.086	0.013849	0.07959	0.06877	1.16E-4	ENSG00000106948	ENST00000320310	.	.	.	4.95	1.61	0.23674	.	0.482521	0.19304	N	0.117578	T	0.01189	0.0039	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.03130	-1.1069	6	0.87932	D	0	-5.6524	5.4261	0.16427	0.1935:0.0:0.6201:0.1863	.	.	.	.	L	276	.	ENSP00000314538:P276L	P	-	2	0	AKNA	116144189	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-1.483000	0.02318	0.275000	0.22094	-0.244000	0.11960	CCG	G|0.978;A|0.022	0.022	strong		0.567	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767		A	117104368	G	A	117104368	2	1	22	1	0	0	0	0	0	0	0	1	463	1103	39	1		1	AKNA	9	117104368	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	468	117104368	24109063	2137	5038											
AKNA	80709	hgsc.bcm.edu	37	chr9	117110112	117110112	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgggctgccctggagtggcTggtgcaggctgtcttccagc	3	10	16	12	1	1	0	0	0	1	0	3	1	2	1	2	5	3	4	2	5	0	1	rs1265891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117110112T>C	ENST00000307564.4	-	16	3451	c.3290A>G	c.(3289-3291)cAg>cGg	p.Q1097R	AKNA_ENST00000374075.5_Missense_Mutation_p.Q1016R|AKNA_ENST00000374088.3_Missense_Mutation_p.Q1097R|AKNA_ENST00000492875.1_5'Flank|AKNA_ENST00000374079.4_Missense_Mutation_p.Q42R|AKNA_ENST00000223791.3_Missense_Mutation_p.Q557R	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	1097			Q -> R (in dbSNP:rs1265891).		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						CTGGAGTGGCTGGTGCAGGCT	0.667													C|||	1051	0.209864	0.6891	0.0605	5008	,	,		14024	0.0526		0.003	False		,,,				2504	0.0429				p.Q1097R		Atlas-SNP	.											.	AKNA	119	.	0			c.A3290G						PASS	.	C	ARG/GLN	2091,2139		503,1085,527	15	15	15		3290	-3.5	0	9	dbSNP_87	15	21,8365		0,21,4172	no	missense	AKNA	NM_030767.4	43	503,1106,4699	CC,CT,TT		0.2504,49.4326,16.7406	benign	1097/1440	117110112	2112,10504	2115	4193	6308	SO:0001583	missense	80709	exon16			AGTGGCTGGTGCA	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.3290A>G	9.37:g.117110112T>C	ENSP00000303769:p.Gln1097Arg	138	1	0.00724638		101	101	1	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	37	CCDS6805.1	398	0.18223443223443223	337	0.6849593495934959	27	0.07458563535911603	32	0.055944055944055944	2	0.002638522427440633	C	6.830	0.522364	0.13066	0.494326	0.002504	ENSG00000106948	ENST00000307564;ENST00000374079;ENST00000320310;ENST00000374088;ENST00000223791;ENST00000374075	T;T;T;T;T	0.17370	2.74;2.28;2.74;2.51;2.74	5.44	-3.52	0.04682	.	1.042290	0.07587	N	0.921372	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40459	-0.9562	9	0.02654	T	1	-2.0827	6.3932	0.21599	0.0:0.2694:0.3256:0.405	rs1265891;rs52814197;rs1265891	1097;1016	Q7Z591;Q7Z591-2	AKNA_HUMAN;.	R	1097;42;109;1097;557;1016	ENSP00000303769:Q1097R;ENSP00000363192:Q42R;ENSP00000363201:Q1097R;ENSP00000223791:Q557R;ENSP00000363188:Q1016R	ENSP00000223791:Q557R	Q	-	2	0	AKNA	116149933	0.001000	0.12720	0.019000	0.16419	0.639000	0.38242	-0.315000	0.08081	-0.930000	0.03752	-0.726000	0.03593	CAG	T|0.754;C|0.246	0.246	strong		0.667	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767		C	117110112	T	C	117110112	3	2	22	1	0	0	0	0	1	0	0	0	463	1580	55	3	1057	3	AKNA	9	117110112	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	5744	117110112	24103319	2138	5039											
AKNA	80709	hgsc.bcm.edu	37	chr9	117129921	117129921	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gttctccggaagccaccccaGggtgggcatgctggtaagcg	7	7	15	12	2	1	0	0	0	1	0	2	1	1	1	4	4	3	4	4	4	2	2	rs62640865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117129921G>C	ENST00000307564.4	-	6	1791	c.1630C>G	c.(1630-1632)Ctg>Gtg	p.L544V	AKNA_ENST00000374075.5_Missense_Mutation_p.L463V|AKNA_ENST00000374088.3_Missense_Mutation_p.L544V|AKNA_ENST00000312033.3_Missense_Mutation_p.L544V|AKNA_ENST00000223791.3_Missense_Mutation_p.L4V	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	544					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						AGCCACCCCAGGGTGGGCATG	0.607													G|||	180	0.0359425	0.1324	0.0072	5008	,	,		20087	0.0		0.0	False		,,,				2504	0.0				p.L544V		Atlas-SNP	.											.	AKNA	119	.	0			c.C1630G						PASS	.	G	VAL/LEU	445,3961	213.8+/-233.3	20,405,1778	50	50	50		1630	3.2	0	9	dbSNP_129	50	3,8597	2.2+/-6.3	0,3,4297	yes	missense	AKNA	NM_030767.4	32	20,408,6075	CC,CG,GG		0.0349,10.0999,3.4446	benign	544/1440	117129921	448,12558	2203	4300	6503	SO:0001583	missense	80709	exon6			ACCCCAGGGTGGG	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.1630C>G	9.37:g.117129921G>C	ENSP00000303769:p.Leu544Val	72	0	0		76	32	0.421053	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	37	CCDS6805.1	71	0.03250915750915751	68	0.13821138211382114	3	0.008287292817679558	0	0.0	0	0.0	G	8.010	0.757277	0.15846	0.100999	3.49E-4	ENSG00000106948	ENST00000307564;ENST00000394582;ENST00000374088;ENST00000223791;ENST00000374075;ENST00000312033	T;T;T;T;T	0.30714	2.72;2.72;2.46;2.72;1.52	5.05	3.17	0.36434	.	0.310451	0.23710	N	0.045338	T	0.00109	0.0003	N	0.14661	0.345	0.09310	N	0.999998	B;B	0.17268	0.005;0.021	B;B	0.15484	0.004;0.013	T	0.21042	-1.0257	10	0.30078	T	0.28	-0.342	6.9494	0.24536	0.0931:0.1751:0.7318:0.0	rs62640865	544;463	Q7Z591;Q7Z591-2	AKNA_HUMAN;.	V	544;385;544;4;463;544	ENSP00000303769:L544V;ENSP00000363201:L544V;ENSP00000223791:L4V;ENSP00000363188:L463V;ENSP00000309222:L544V	ENSP00000223791:L4V	L	-	1	2	AKNA	116169742	0.004000	0.15560	0.002000	0.10522	0.008000	0.06430	1.056000	0.30480	0.802000	0.34089	0.655000	0.94253	CTG	G|0.957;C|0.043	0.043	strong		0.607	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767		C	117129921	G	C	117129921	3	2	22	1	0	0	0	0	1	0	0	0	463	991	35	4	2757	4	AKNA	9	117129921	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	19809	117129921	24083510	2139	5040											
AKNA	80709	hgsc.bcm.edu	37	chr9	117130838	117130838	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcaccattcccgtgtggatgCtgtggttgggctggggtggg	3	11	19	8	1	0	0	0	0	0	0	1	1	1	1	2	6	1	4	2	6	0	2	rs138188658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117130838C>T	ENST00000307564.4	-	5	1615	c.1454G>A	c.(1453-1455)aGc>aAc	p.S485N	AKNA_ENST00000374075.5_Missense_Mutation_p.S404N|AKNA_ENST00000374088.3_Missense_Mutation_p.S485N|AKNA_ENST00000312033.3_Missense_Mutation_p.S485N|AKNA_ENST00000223791.3_5'UTR	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	485					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						CGTGTGGATGCTGTGGTTGGG	0.652													C|||	18	0.00359425	0.0113	0.0029	5008	,	,		18213	0.0		0.001	False		,,,				2504	0.0				p.S485N		Atlas-SNP	.											.	AKNA	119	.	0			c.G1454A						PASS	.	C	ASN/SER	61,4345	56.8+/-93.2	0,61,2142	80	54	63		1454	4	0.6	9	dbSNP_134	63	0,8600		0,0,4300	yes	missense	AKNA	NM_030767.4	46	0,61,6442	TT,TC,CC		0.0,1.3845,0.469	probably-damaging	485/1440	117130838	61,12945	2203	4300	6503	SO:0001583	missense	80709	exon5			TGGATGCTGTGGT	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.1454G>A	9.37:g.117130838C>T	ENSP00000303769:p.Ser485Asn	104	0	0		120	66	0.55	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	37	CCDS6805.1	5	0.0022893772893772895	3	0.006097560975609756	2	0.0055248618784530384	0	0.0	0	0.0	C	6.631	0.484937	0.12641	0.013845	0.0	ENSG00000106948	ENST00000307564;ENST00000394582;ENST00000374088;ENST00000374075;ENST00000312033	T;T;T;T	0.33654	2.63;2.63;2.63;1.4	4.87	3.97	0.46021	.	0.575422	0.18059	N	0.153006	T	0.23886	0.0578	L	0.56769	1.78	0.09310	N	0.999995	B;B	0.30937	0.079;0.301	B;B	0.27715	0.037;0.082	T	0.15780	-1.0425	10	0.41790	T	0.15	-10.4751	7.9366	0.29933	0.1595:0.755:0.0:0.0855	.	485;404	Q7Z591;Q7Z591-2	AKNA_HUMAN;.	N	485;326;485;404;485	ENSP00000303769:S485N;ENSP00000363201:S485N;ENSP00000363188:S404N;ENSP00000309222:S485N	ENSP00000303769:S485N	S	-	2	0	AKNA	116170659	0.924000	0.31332	0.604000	0.28916	0.007000	0.05969	0.647000	0.24812	1.279000	0.44446	-0.140000	0.14226	AGC	C|0.996;T|0.004	0.004	strong		0.652	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767		T	117130838	C	T	117130838	3	4	22	1	0	0	0	0	1	0	0	0	463	797	28	2	2937	2	AKNA	9	117130838	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	917	117130838	24082593	2140	5041											
TNFSF15	9966	hgsc.bcm.edu	37	chr9	117568219	117568219	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctgctcctggccttgggcCtgcagctgccgtgctctggc	1	11	14	15	1	1	0	0	0	1	0	2	0	2	0	4	3	6	5	4	3	0	1	rs150191342	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117568219C>T	ENST00000374045.4	-	1	187	c.74G>A	c.(73-75)aGg>aAg	p.R25K		NM_001204344.1|NM_005118.3	NP_001191273.1|NP_005109.2	O95150	TNF15_HUMAN	tumor necrosis factor (ligand) superfamily, member 15	25					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|cytokine metabolic process (GO:0042107)|immune response (GO:0006955)|positive regulation of cytokine secretion (GO:0050715)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|skin(1)	11						GGCCTTGGGCCTGCAGCTGCC	0.627													C|||	20	0.00399361	0.0151	0.0	5008	,	,		17651	0.0		0.0	False		,,,				2504	0.0				p.R25K		Atlas-SNP	.											.	TNFSF15	23	.	0			c.G74A						PASS	.	C	LYS/ARG	54,4352	53.6+/-89.4	1,52,2150	64	58	60		74	3.2	0.5	9	dbSNP_134	60	0,8600		0,0,4300	yes	missense	TNFSF15	NM_005118.3	26	1,52,6450	TT,TC,CC		0.0,1.2256,0.4152	benign	25/252	117568219	54,12952	2203	4300	6503	SO:0001583	missense	9966	exon1			TTGGGCCTGCAGC	AF039390	CCDS6809.1	9q32	2008-07-21			ENSG00000181634	ENSG00000181634		"Tumor necrosis factor (ligand) superfamily"	11931	protein-coding gene	gene with protein product	"vascular endothelial cell growth inhibitor", "TNF superfamily ligand TL1A", "TNF ligand-related molecule 1", "vascular endothelial growth inhibitor-192A"	604052				9434163	Standard	NM_005118		Approved	TL1, VEGI, TL1A, VEGI192A, MGC129934, MGC129935	uc004bjh.3	O95150	OTTHUMG00000021011	ENST00000374045.4:c.74G>A	9.37:g.117568219C>T	ENSP00000363157:p.Arg25Lys	104	0	0		108	75	0.694444	NM_005118	Q3SX69|Q5VJK8|Q5VWH1|Q8NFE9	Missense_Mutation	SNP	ENST00000374045.4	37	CCDS6809.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	12.31	1.898972	0.33535	0.012256	0.0	ENSG00000181634	ENST00000374045	T	0.28069	1.63	5.11	3.23	0.37069	.	2.547720	0.01464	N	0.015995	T	0.14700	0.0355	N	0.24115	0.695	0.48696	D	0.999692	B	0.20261	0.043	B	0.19946	0.027	T	0.44862	-0.9300	10	0.02654	T	1	-17.7812	6.6172	0.22782	0.0:0.7011:0.1969:0.102	.	25	O95150	TNF15_HUMAN	K	25	ENSP00000363157:R25K	ENSP00000363157:R25K	R	-	2	0	TNFSF15	116608040	0.122000	0.22280	0.461000	0.27105	0.699000	0.40488	0.565000	0.23578	0.616000	0.30141	0.484000	0.47621	AGG	C|0.996;T|0.004	0.004	strong		0.627	TNFSF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055424.2	NM_005118		T	117568219	C	T	117568219	3	4	22	1	0	0	0	0	1	0	0	0	16323	681	24	2	697	2	TNFSF15	9	117568219	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	437381	117568219	23645212	2141	5042											
TNC	3371	hgsc.bcm.edu	37	chr9	117810651	117810651	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctaagctccagcttcctctgGgttcctgaaagtgtgaattc	8	13	9	11	0	1	2	0	2	1	0	5	2	4	2	3	1	2	3	3	1	3	4	rs146504512	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117810651G>A	ENST00000350763.4	-	16	5151	c.4740C>T	c.(4738-4740)acC>acT	p.T1580T	TNC_ENST00000535648.1_Intron|TNC_ENST00000537320.1_Intron|TNC_ENST00000345230.3_Intron|TNC_ENST00000481475.1_5'UTR|TNC_ENST00000341037.4_Intron|TNC_ENST00000340094.3_Silent_p.T1216T|TNC_ENST00000423613.2_Intron|TNC_ENST00000346706.3_Intron|TNC_ENST00000542877.1_Intron	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1580	Fibronectin type-III 11. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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						GCTTCCTCTGGGTTCCTGAAA	0.527													G|||	26	0.00519169	0.0144	0.0072	5008	,	,		18220	0.0		0.001	False		,,,				2504	0.001				p.T1580T		Atlas-SNP	.											.	TNC	282	.	0			c.C4740T						PASS	.	G		39,4367	43.8+/-77.6	0,39,2164	89	82	84		4740	3.1	1	9	dbSNP_134	84	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	TNC	NM_002160.3		0,47,6456	AA,AG,GG		0.093,0.8852,0.3614		1580/2202	117810651	47,12959	2203	4300	6503	SO:0001819	synonymous_variant	3371	exon16			CCTCTGGGTTCCT		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.4740C>T	9.37:g.117810651G>A		68	0	0		79	37	0.468354	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Silent	SNP	ENST00000350763.4	37	CCDS6811.1																																																																																			G|0.996;A|0.004	0.004	strong		0.527	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160		A	117810651	G	A	117810651	2	1	22	1	0	0	0	0	0	0	0	1	16285	1219	43	2		2	TNC	9	117810651	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	242432	117810651	23402780	2142	5043											
TNC	3371	hgsc.bcm.edu	37	chr9	117848368	117848368	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cataaatccttcatggcacaCgcactgcccattcacacagc	12	8	5	16	1	2	0	2	0	0	0	3	0	3	0	2	1	2	2	2	1	2	3	rs61729478	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117848368C>T	ENST00000350763.4	-	3	2053	c.1642G>A	c.(1642-1644)Gtg>Atg	p.V548M	TNC_ENST00000535648.1_Missense_Mutation_p.V548M|TNC_ENST00000537320.1_Missense_Mutation_p.V548M|TNC_ENST00000345230.3_Missense_Mutation_p.V548M|TNC_ENST00000341037.4_Missense_Mutation_p.V548M|TNC_ENST00000340094.3_Missense_Mutation_p.V548M|TNC_ENST00000423613.2_Missense_Mutation_p.V548M|TNC_ENST00000346706.3_Missense_Mutation_p.V548M|TNC_ENST00000542877.1_Missense_Mutation_p.V548M	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	548	EGF-like 13. {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						TCATGGCACACGCACTGCCCA	0.587													C|||	32	0.00638978	0.0038	0.0072	5008	,	,		21065	0.0		0.0119	False		,,,				2504	0.0102				p.V548M		Atlas-SNP	.											.	TNC	282	.	0			c.G1642A						PASS	.	C	MET/VAL	41,4365	44.6+/-78.6	0,41,2162	106	76	86		1642	4.1	0.9	9	dbSNP_129	86	123,8477	63.1+/-125.2	1,121,4178	yes	missense	TNC	NM_002160.3	21	1,162,6340	TT,TC,CC		1.4302,0.9305,1.261	benign	548/2202	117848368	164,12842	2203	4300	6503	SO:0001583	missense	3371	exon3			GGCACACGCACTG		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.1642G>A	9.37:g.117848368C>T	ENSP00000265131:p.Val548Met	181	0	0		165	108	0.654545	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	37	CCDS6811.1	15	0.006868131868131868	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	10	0.013192612137203167	C	9.105	1.005034	0.19199	0.009305	0.014302	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000442945;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877	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	5.95	4.13	0.48395	EGF, extracellular (1);Epidermal growth factor-like (1);EGF-like region, conserved site (2);	0.111211	0.64402	N	0.000008	T	0.16471	0.0396	M	0.79614	2.46	0.51767	D	0.999938	D;P	0.55385	0.971;0.52	P;B	0.49953	0.627;0.223	T	0.01245	-1.1407	10	0.59425	D	0.04	.	12.6844	0.56940	0.0:0.8672:0.0:0.1328	.	548;548	E9PC84;P24821	.;TENA_HUMAN	M	548	ENSP00000344400:V548M;ENSP00000438152:V548M;ENSP00000344555:V548M;ENSP00000345861:V548M;ENSP00000265131:V548M;ENSP00000339553:V548M;ENSP00000411406:V548M;ENSP00000443478:V548M;ENSP00000442242:V548M	ENSP00000344400:V548M	V	-	1	0	TNC	116888189	0.008000	0.16893	0.874000	0.34290	0.117000	0.20001	0.248000	0.18198	0.867000	0.35654	-0.222000	0.12452	GTG	C|0.990;T|0.010	0.010	strong		0.587	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160		T	117848368	C	T	117848368	3	4	22	1	0	0	0	0	1	0	0	0	16285	536	19	1	5067	1	TNC	9	117848368	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	37717	117848368	23365063	2143	5044											
PAPPA	5069	hgsc.bcm.edu	37	chr9	118950208	118950208	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atctcctgggagctggacgtGctggaggtgagcaactcctc	7	9	14	11	1	1	1	0	1	1	0	4	4	2	4	2	4	4	3	2	4	1	0	rs80284365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:118950208G>T	ENST00000328252.3	+	2	1560	c.1191G>T	c.(1189-1191)gtG>gtT	p.V397V	PAPPA_ENST00000534838.1_5'Flank	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	397	Metalloprotease.				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						AGCTGGACGTGCTGGAGGTGA	0.582													G|||	222	0.0443291	0.1581	0.0115	5008	,	,		19158	0.0		0.003	False		,,,				2504	0.002				p.V397V		Atlas-SNP	.											.	PAPPA	243	.	0			c.G1191T						PASS	.	G		626,3780	270.7+/-269.8	45,536,1622	71	61	64		1191	1	1	9	dbSNP_132	64	32,8568	20.4+/-63.3	1,30,4269	no	coding-synonymous	PAPPA	NM_002581.3		46,566,5891	TT,TG,GG		0.3721,14.2079,5.0592		397/1628	118950208	658,12348	2203	4300	6503	SO:0001819	synonymous_variant	5069	exon2			GGACGTGCTGGAG		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.1191G>T	9.37:g.118950208G>T		77	0	0		78	52	0.666667	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Silent	SNP	ENST00000328252.3	37	CCDS6813.1																																																																																			G|0.955;T|0.045	0.045	strong		0.582	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581		T	118950208	G	T	118950208	2	4	22	1	0	0	0	0	0	0	0	1	11441	1306	46	4		4	PAPPA	9	118950208	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1101840	118950208	22263223	2144	5045											
ASTN2	23245	hgsc.bcm.edu	37	chr9	119249690	119249690	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgactgagtagatactgaCttcagggacctctccatggc	10	10	11	10	0	2	4	1	3	1	1	3	6	2	5	2	2	1	1	2	2	2	3	rs16933591	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:119249690C>T	ENST00000313400.4	-	20	3545	c.3445G>A	c.(3445-3447)Gtc>Atc	p.V1149I	ASTN2_ENST00000361209.2_Missense_Mutation_p.V1098I|ASTN2_ENST00000288520.5_Missense_Mutation_p.V250I|ASTN2_ENST00000361477.3_Missense_Mutation_p.V201I|ASTN2_ENST00000341734.4_Missense_Mutation_p.V201I|ASTN2_ENST00000373996.3_Missense_Mutation_p.V1145I			O75129	ASTN2_HUMAN	astrotactin 2	1149	Fibronectin type-III.		V -> I (in dbSNP:rs16933591).		negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)		p.V1098F(1)|p.V201F(1)		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						TAGATACTGACTTCAGGGACC	0.507													C|||	101	0.0201677	0.0741	0.0043	5008	,	,		17865	0.0		0.0	False		,,,				2504	0.0				p.V1098I		Atlas-SNP	.											ASTN2_ENST00000361477,NS,carcinoma,0,1	ASTN2	307	1	2	Substitution - Missense(2)	lung(2)	c.G3292A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	262,4144	150.7+/-184.7	5,252,1946	118	106	110		601,3292,748,601,601	3.6	1	9	dbSNP_123	110	2,8598	1.2+/-3.3	0,2,4298	yes	missense,missense,missense,missense,missense	ASTN2	NM_001184734.1,NM_014010.4,NM_198186.3,NM_198187.3,NM_198188.2	29,29,29,29,29	5,254,6244	TT,TC,CC		0.0233,5.9464,2.0298	benign,benign,benign,benign,benign	201/376,1098/1289,250/441,201/403,201/396	119249690	264,12742	2203	4300	6503	SO:0001583	missense	23245	exon19			TACTGACTTCAGG	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.3445G>A	9.37:g.119249690C>T	ENSP00000314038:p.Val1149Ile	70	0	0		79	50	0.632911	NM_014010	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Missense_Mutation	SNP	ENST00000313400.4	37		38	0.0173992673992674	36	0.07317073170731707	2	0.0055248618784530384	0	0.0	0	0.0	C	12.97	2.096981	0.37048	0.059464	2.33E-4	ENSG00000148219	ENST00000313400;ENST00000373996;ENST00000288520;ENST00000341734;ENST00000373986;ENST00000361209;ENST00000361477	T;T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95;0.95	5.49	3.6	0.41247	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.383922	0.28225	N	0.016137	T	0.01320	0.0043	N	0.08118	0	0.29275	N	0.870436	B;B;B;B;B;B;B	0.15473	0.013;0.0;0.006;0.0;0.01;0.0;0.0	B;B;B;B;B;B;B	0.11329	0.006;0.0;0.001;0.001;0.005;0.0;0.0	T	0.06338	-1.0832	10	0.20519	T	0.43	-28.4103	5.7264	0.18015	0.0:0.6328:0.0:0.3672	rs16933591;rs52796427;rs16933591	201;201;1098;1149;1145;201;250	B7ZKP4;B7ZKP5;O75129-2;O75129;O75129-3;O75129-6;O75129-4	.;.;.;ASTN2_HUMAN;.;.;.	I	1149;1145;250;201;872;1098;201	ENSP00000314038:V1149I;ENSP00000363108:V1145I;ENSP00000288520:V250I;ENSP00000339925:V201I;ENSP00000363098:V872I;ENSP00000354504:V1098I;ENSP00000355116:V201I	ENSP00000288520:V250I	V	-	1	0	ASTN2	118289511	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.748000	0.47483	1.436000	0.47453	0.655000	0.94253	GTC	C|0.979;T|0.021	0.021	strong		0.507	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010		T	119249690	C	T	119249690	3	4	22	1	0	0	0	0	1	0	0	0	1065	565	20	2	631	2	ASTN2	9	119249690	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	299482	119249690	21963741	2145	5046											
TRAF1	7185	hgsc.bcm.edu	37	chr9	123671613	123671613	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgccatctccattcaggtaCagccgcaggcacaacttgta	10	9	9	13	1	2	0	1	0	1	0	3	0	2	0	3	2	4	4	3	2	3	4	rs112060909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:123671613C>T	ENST00000373887.3	-	7	3372	c.927G>A	c.(925-927)ctG>ctA	p.L309L	TRAF1_ENST00000546084.1_Silent_p.L187L|TRAF1_ENST00000540010.1_Silent_p.L309L	NM_005658.4	NP_005649.1	Q13077	TRAF1_HUMAN	TNF receptor-associated factor 1	309	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				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						CATTCAGGTACAGCCGCAGGC	0.547													C|||	68	0.0135783	0.0492	0.0043	5008	,	,		20674	0.0		0.0	False		,,,				2504	0.0				p.L309L		Atlas-SNP	.											.	TRAF1	42	.	0			c.G927A						PASS	.	C	,,	179,4227	117.1+/-155.0	3,173,2027	173	163	167		927,561,927	-0.2	1	9	dbSNP_132	167	6,8594	5.7+/-21.5	0,6,4294	no	coding-synonymous,coding-synonymous,coding-synonymous	TRAF1	NM_001190945.1,NM_001190947.1,NM_005658.4	,,	3,179,6321	TT,TC,CC		0.0698,4.0626,1.4224	,,	309/417,187/295,309/417	123671613	185,12821	2203	4300	6503	SO:0001819	synonymous_variant	7185	exon7			CAGGTACAGCCGC	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.927G>A	9.37:g.123671613C>T		109	0	0		127	48	0.377953	NM_005658	B4DJ77|Q658U1|Q8NF13	Silent	SNP	ENST00000373887.3	37	CCDS6825.1																																																																																			C|0.983;T|0.017	0.017	strong		0.547	TRAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053843.1	NM_005658		T	123671613	C	T	123671613	2	4	22	1	0	0	0	0	0	0	0	1	16452	465	17	2		2	TRAF1	9	123671613	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4421923	123671613	17541818	2146	5047											
GSN	2934	hgsc.bcm.edu	37	chr9	124091256	124091256	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatggatgcccatcctcctcGcctctttgcctgctccaaca	6	11	7	17	1	1	0	0	0	1	0	5	2	4	1	6	1	4	1	6	1	1	1	rs9696578	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:124091256G>T	ENST00000373818.4	+	14	2072	c.2003G>T	c.(2002-2004)cGc>cTc	p.R668L	GSN_ENST00000436847.1_Missense_Mutation_p.R628L|GSN_ENST00000373823.3_Missense_Mutation_p.R617L|GSN_ENST00000373807.1_Missense_Mutation_p.R399L|GSN_ENST00000545652.1_Missense_Mutation_p.R625L|GSN_ENST00000341272.2_Missense_Mutation_p.R617L|GSN_ENST00000412819.1_Missense_Mutation_p.R617L|GSN_ENST00000394353.2_Missense_Mutation_p.R628L|GSN_ENST00000373808.2_Missense_Mutation_p.R617L|GSN_ENST00000449733.1_Missense_Mutation_p.R617L|GSN_ENST00000373806.1_Missense_Mutation_p.R93L	NM_000177.4|NM_001258029.1	NP_000168.1|NP_001244958.1	P06396	GELS_HUMAN	gelsolin	668	Actin-binding, Ca-sensitive. {ECO:0000255}.		R -> L (in dbSNP:rs9696578).		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						CATCCTCCTCGCCTCTTTGCC	0.622													G|||	18	0.00359425	0.0129	0.0	5008	,	,		21562	0.0		0.001	False		,,,				2504	0.0				p.R668L		Atlas-SNP	.											.	GSN	81	.	0			c.G2003T						PASS	.	G	LEU/ARG,LEU/ARG,LEU/ARG,LEU/ARG,LEU/ARG,LEU/ARG,LEU/ARG,LEU/ARG	46,4360	49.6+/-84.7	0,46,2157	89	74	79		2003,1850,1850,1850,1850,1883,1883,1850	4.7	1	9	dbSNP_119	79	1,8599	2.2+/-6.3	0,1,4299	yes	missense,missense,missense,missense,missense,missense,missense,missense	GSN	NM_000177.4,NM_001127662.1,NM_001127663.1,NM_001127664.1,NM_001127665.1,NM_001127666.1,NM_001127667.1,NM_198252.2	102,102,102,102,102,102,102,102	0,47,6456	TT,TG,GG		0.0116,1.044,0.3614	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	668/783,617/732,617/732,617/732,617/732,628/743,628/743,617/732	124091256	47,12959	2203	4300	6503	SO:0001583	missense	2934	exon14			CTCCTCGCCTCTT	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.2003G>T	9.37:g.124091256G>T	ENSP00000362924:p.Arg668Leu	38	0	0		49	25	0.510204	NM_000177	A2A418|A8MUD1|A8MYN7|B7Z373|B7Z5V1|F5H1A8|Q5T0I2|Q8WVV7	Missense_Mutation	SNP	ENST00000373818.4	37	CCDS6828.1	7	0.003205128205128205	6	0.012195121951219513	0	0.0	0	0.0	1	0.0013192612137203166	G	27.6	4.842728	0.91197	0.01044	1.16E-4	ENSG00000148180	ENST00000373823;ENST00000436847;ENST00000394353;ENST00000449733;ENST00000412819;ENST00000341272;ENST00000373808;ENST00000394352;ENST00000456109;ENST00000545652;ENST00000373818;ENST00000373807;ENST00000373806;ENST00000373805	T;T;T;T;T;T;T;T;T;T;T	0.57595	1.62;1.62;1.62;1.62;1.62;1.62;1.62;1.62;1.62;2.41;0.39	5.56	4.66	0.58398	.	0.110224	0.64402	D	0.000005	T	0.74527	0.3728	H	0.94964	3.605	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	0.994;0.999;0.999;0.992;0.999	D	0.84690	0.0722	10	0.87932	D	0	-20.0116	15.541	0.76048	0.0:0.1383:0.8617:0.0	rs9696578;rs9696578	641;625;628;399;668	B7Z9A0;F5H1A8;B7Z373;Q5T0H9;P06396	.;.;.;.;GELS_HUMAN	L	617;628;628;617;617;617;617;601;591;625;668;399;93;93	ENSP00000362929:R617L;ENSP00000411293:R628L;ENSP00000377882:R628L;ENSP00000409358:R617L;ENSP00000416586:R617L;ENSP00000340888:R617L;ENSP00000362914:R617L;ENSP00000445823:R625L;ENSP00000362924:R668L;ENSP00000362913:R399L;ENSP00000362912:R93L	ENSP00000340888:R617L	R	+	2	0	GSN	123131077	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	9.362000	0.97126	1.322000	0.45245	0.655000	0.94253	CGC	G|0.993;T|0.007	0.007	strong		0.622	GSN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053861.1	NM_000177		T	124091256	G	T	124091256	3	4	22	1	0	0	0	0	1	0	0	0	6834	1087	38	4	2085	4	GSN	9	124091256	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	419643	124091256	17122175	2147	5048											
STOM	2040	hgsc.bcm.edu	37	chr9	124110368	124110368	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcacaggtagtttcacatcCttaatttccacacgctccac	10	12	5	14	1	1	0	1	0	0	0	4	0	4	0	3	1	1	4	3	1	2	4	rs115702601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:124110368C>T	ENST00000286713.2	-	6	602	c.585G>A	c.(583-585)aaG>aaA	p.K195K	AL161784.1_ENST00000594963.1_Silent_p.S46S|STOM_ENST00000538954.1_Silent_p.K144K|STOM_ENST00000347359.2_Intron	NM_001270526.1|NM_004099.5	NP_001257455.1|NP_004090.4	P27105	STOM_HUMAN	stomatin	195					protein homooligomerization (GO:0051260)|regulation of acid-sensing ion channel activity (GO:1901585)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|vesicle (GO:0031982)				endometrium(1)|large_intestine(1)|lung(3)|urinary_tract(1)	6				OV - Ovarian serous cystadenocarcinoma(323;0.00107)|GBM - Glioblastoma multiforme(294;0.0137)		GTTTCACATCCTTAATTTCCA	0.493													C|||	19	0.00379393	0.0136	0.0	5008	,	,		16533	0.0		0.001	False		,,,				2504	0.0				p.K195K		Atlas-SNP	.											.	STOM	15	.	0			c.G585A						PASS	.	C	,	50,4356	52.3+/-87.9	0,50,2153	123	121	122		585,	1.5	1	9	dbSNP_132	122	1,8599	2.2+/-6.3	0,1,4299	no	coding-synonymous,intron	STOM	NM_004099.4,NM_198194.1	,	0,51,6452	TT,TC,CC		0.0116,1.1348,0.3921	,	195/289,	124110368	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	2040	exon6			CACATCCTTAATT		CCDS6830.1, CCDS6831.1, CCDS75892.1	9q34.1	2008-07-21	2002-11-11	2002-11-15	ENSG00000148175	ENSG00000148175			3383	protein-coding gene	gene with protein product		133090	"erythrocyte membrane protein band 7.2 (stomatin)"	EPB7, EPB72		1883838	Standard	NM_198194		Approved	BND7	uc004blh.4	P27105	OTTHUMG00000020590	ENST00000286713.2:c.585G>A	9.37:g.124110368C>T		123	0	0		100	55	0.55	NM_001270526	B1AM77|Q14087|Q15609|Q5VX96|Q96FK4	Silent	SNP	ENST00000286713.2	37	CCDS6830.1																																																																																			C|0.996;T|0.004	0.004	strong		0.493	STOM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053889.1	NM_004099		T	124110368	C	T	124110368	2	4	22	1	0	0	0	0	0	0	0	1	15327	680	24	2		2	STOM	9	124110368	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	19112	124110368	17103063	2148	5049											
TTLL11	158135	hgsc.bcm.edu	37	chr9	124633018	124633018	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccagcgaatggtttttcaagCtgctgagacctgaagcacac	11	9	10	11	1	1	2	1	2	0	1	1	4	1	2	2	1	4	4	2	1	3	2	rs16911064	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:124633018C>T	ENST00000321582.5	-	7	1948	c.1761G>A	c.(1759-1761)caG>caA	p.Q587Q	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						GTTTTTCAAGCTGCTGAGACC	0.488													C|||	88	0.0175719	0.0613	0.0058	5008	,	,		21797	0.0		0.003	False		,,,				2504	0.0				p.Q587Q		Atlas-SNP	.											.	TTLL11	67	.	0			c.G1761A						PASS	.	C		96,1288		2,92,598	142	125	130		1761	1.6	0.8	9	dbSNP_123	130	0,3182		0,0,1591	no	coding-synonymous	TTLL11	NM_001139442.1		2,92,2189	TT,TC,CC		0.0,6.9364,2.1025		587/801	124633018	96,4470	692	1591	2283	SO:0001819	synonymous_variant	158135	exon7			TTCAAGCTGCTGA	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.1761G>A	9.37:g.124633018C>T		159	0	0		132	67	0.507576	NM_001139442		Silent	SNP	ENST00000321582.5	37	CCDS48012.1																																																																																			C|0.983;T|0.017	0.017	strong		0.488	TTLL11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_088486		T	124633018	C	T	124633018	2	4	22	1	0	0	0	0	0	0	0	1	16739	796	28	2		2	TTLL11	9	124633018	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	522650	124633018	16580413	2149	5050											
TTLL11	158135	hgsc.bcm.edu	37	chr9	124855220	124855220	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cccctcctcagccgcactggGctgcgccggggccggggcca	3	4	15	19	4	1	0	1	0	0	0	2	0	2	0	7	5	2	2	7	5	0	0	rs61742325	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:124855220G>A	ENST00000373776.3	-	1	665	c.478C>T	c.(478-480)Ccc>Tcc	p.P160S	TTLL11_ENST00000474723.1_5'UTR|TTLL11_ENST00000321582.5_Missense_Mutation_p.P160S	NM_194252.2	NP_919228.2	Q8NHH1	TTL11_HUMAN	tubulin tyrosine ligase-like family, member 11	160					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						GCCGCACTGGGCTGCGCCGGG	0.766													G|||	247	0.0493211	0.1808	0.0115	5008	,	,		11208	0.0		0.0	False		,,,				2504	0.0				p.P160S		Atlas-SNP	.											.	TTLL11	67	.	0			c.C478T						PASS	.	G	SER/PRO,SER/PRO	440,3254		12,416,1419	5	6	6		478,478	0.4	0.2	9	dbSNP_129	6	1,7393		0,1,3696	no	missense,missense	TTLL11	NM_001139442.1,NM_194252.2	74,74	12,417,5115	AA,AG,GG		0.0135,11.9112,3.9773	possibly-damaging,possibly-damaging	160/801,160/539	124855220	441,10647	1847	3697	5544	SO:0001583	missense	158135	exon1			CACTGGGCTGCGC	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.478C>T	9.37:g.124855220G>A	ENSP00000362881:p.Pro160Ser	5	0	0		14	14	1	NM_001139442		Missense_Mutation	SNP	ENST00000373776.3	37	CCDS6834.2	98	0.04487179487179487	90	0.18292682926829268	8	0.022099447513812154	0	0.0	0	0.0	G	8.451	0.853131	0.17106	0.119112	1.35E-4	ENSG00000175764	ENST00000321582;ENST00000373776	T;T	0.08458	3.24;3.09	4.73	0.383	0.16239	.	8.202900	0.00520	U	0.000189	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.16396	0.017;0.01	B;B	0.10450	0.005;0.003	T	0.41360	-0.9513	8	.	.	.	.	3.3638	0.07196	0.0901:0.2587:0.426:0.2252	.	160;160	F8W6M1;Q8NHH1	.;TTL11_HUMAN	S	160	ENSP00000321346:P160S;ENSP00000362881:P160S	.	P	-	1	0	TTLL11	123895041	0.067000	0.21026	0.156000	0.22583	0.281000	0.26958	0.757000	0.26433	0.382000	0.24878	-0.379000	0.06801	CCC	G|0.955;A|0.045	0.045	strong		0.766	TTLL11-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053907.1	XM_088486		A	124855220	G	A	124855220	3	1	22	1	0	0	0	0	1	0	0	0	16739	1203	42	2	2038	2	TTLL11	9	124855220	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	222202	124855220	16358211	2150	5051											
OR1J1	347168	hgsc.bcm.edu	37	chr9	125239449	125239449	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atagagaccaataattgtccGataatagatagtcaccactg	16	10	7	8	1	1	2	1	0	0	2	2	4	2	2	3	0	0	0	3	0	6	6	rs192344372	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:125239449G>A	ENST00000259357.2	-	1	786	c.757C>T	c.(757-759)Cgg>Tgg	p.R253W	RP11-542K23.9_ENST00000412262.2_RNA	NM_001004451.1	NP_001004451.1	Q8NGS3	OR1J1_HUMAN	olfactory receptor, family 1, subfamily J, 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)			endometrium(1)|large_intestine(4)|lung(6)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	16						ATAATTGTCCGATAATAGATA	0.453													C|||	3	0.000599042	0.0023	0.0	5008	,	,		23406	0.0		0.0	False		,,,				2504	0.0				p.R253W		Atlas-SNP	.											OR1J1,colon,carcinoma,0,1	OR1J1	46	1	0			c.C757T						PASS	.						135	129	131					9																	125239449		2203	4300	6503	SO:0001583	missense	347168	exon1			TTGTCCGATAATA	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.757C>T	9.37:g.125239449G>A	ENSP00000259357:p.Arg253Trp	125	0	0		137	92	0.671533	NM_001004451	A3KFL8|Q6IF10|Q96R88	Missense_Mutation	SNP	ENST00000259357.2	37	CCDS35120.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	18.97	3.734988	0.69189	.	.	ENSG00000136834	ENST00000259357	T	0.37058	1.22	4.93	4.93	0.64822	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000015	T	0.23965	0.0580	N	0.24115	0.695	0.35696	D	0.81525	P	0.36874	0.572	B	0.26614	0.071	T	0.35176	-0.9799	10	0.87932	D	0	.	14.8875	0.70582	0.0:0.8554:0.1446:0.0	.	253	Q8NGS3	OR1J1_HUMAN	W	253	ENSP00000259357:R253W	ENSP00000259357:R253W	R	-	1	2	OR1J1	124279270	0.076000	0.21285	1.000000	0.80357	0.049000	0.14656	1.108000	0.31123	1.482000	0.48325	-0.181000	0.13052	CGG	G|0.999;A|0.001	0.001	strong		0.453	OR1J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053931.1			A	125239449	G	A	125239449	3	1	22	1	0	0	0	0	1	0	0	0	10968	1057	37	1	214	1	OR1J1	9	125239449	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	384229	125239449	15973982	2151	5052											
OR1J2	26740	hgsc.bcm.edu	37	chr9	125274015	125274015	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagtagagcaacatttttctCttggtgacatctgacttttt	9	17	7	8	0	2	3	0	2	2	1	3	3	2	3	0	1	2	2	0	1	2	6	rs150890302	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:125274015C>T	ENST00000335302.5	+	1	935	c.935C>T	c.(934-936)tCt>tTt	p.S312F		NM_054107.1	NP_473448.1	Q8NGS2	OR1J2_HUMAN	olfactory receptor, family 1, subfamily J, 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)			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						ACATTTTTCTCTTGGTGACAT	0.378													C|||	11	0.00219649	0.0076	0.0014	5008	,	,		20140	0.0		0.0	False		,,,				2504	0.0				p.S312F		Atlas-SNP	.											.	OR1J2	64	.	0			c.C935T						PASS	.	C	PHE/SER	35,4371	29.0+/-57.7	0,35,2168	39	42	41		935	-0.7	0	9	dbSNP_134	41	0,8600		0,0,4300	yes	missense	OR1J2	NM_054107.1	155	0,35,6468	TT,TC,CC		0.0,0.7944,0.2691	benign	312/314	125274015	35,12971	2203	4300	6503	SO:0001583	missense	26740	exon1			TTTTCTCTTGGTG		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.935C>T	9.37:g.125274015C>T	ENSP00000335575:p.Ser312Phe	117	0	0		96	36	0.375	NM_054107	A3KFL9|Q6IF14|Q96R90|Q9NZP1	Missense_Mutation	SNP	ENST00000335302.5	37	CCDS35121.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	10.26	1.301654	0.23736	0.007944	0.0	ENSG00000197233	ENST00000335302	T	0.01505	4.82	4.67	-0.71	0.11234	.	2.214490	0.02811	U	0.124264	T	0.00845	0.0028	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.47114	-0.9142	10	0.52906	T	0.07	.	1.4467	0.02366	0.1417:0.3067:0.138:0.4137	.	312	Q8NGS2	OR1J2_HUMAN	F	312	ENSP00000335575:S312F	ENSP00000335575:S312F	S	+	2	0	OR1J2	124313836	0.000000	0.05858	0.000000	0.03702	0.120000	0.20174	-1.098000	0.03346	0.218000	0.20820	0.632000	0.83419	TCT	C|0.998;T|0.002	0.002	strong		0.378	OR1J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053932.1			T	125274015	C	T	125274015	3	4	22	1	0	0	0	0	1	0	0	0	10969	913	32	2	937	2	OR1J2	9	125274015	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	34566	125274015	15939416	2152	5053											
OR1L1	26737	hgsc.bcm.edu	37	chr9	125424164	125424164	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcagacactcgtctccagaCgcccatgtacttctttctaa	9	12	5	15	2	4	2	1	0	3	2	6	2	4	2	2	0	1	1	2	0	2	4	rs111803762	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:125424164C>T	ENST00000373686.1	+	1	320	c.320C>T	c.(319-321)aCg>aTg	p.T107M	OR1L1_ENST00000309623.1_Missense_Mutation_p.T57M			Q8NH94	OR1L1_HUMAN	olfactory receptor, family 1, subfamily L, member 1	107						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(4)|ovary(1)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)	17						CGTCTCCAGACGCCCATGTAC	0.463													.|||	67	0.0133786	0.0477	0.0058	5008	,	,		21488	0.0		0.0	False		,,,				2504	0.0				p.T57M		Atlas-SNP	.											OR1L1,caecum,carcinoma,0,1	OR1L1	54	1	0			c.C170T						PASS	.	C	MET/THR	147,4259	102.1+/-140.7	3,141,2059	133	124	127		170	1	0.2	9	dbSNP_132	127	1,8599		0,1,4299	yes	missense	OR1L1	NM_001005236.3	81	3,142,6358	TT,TC,CC		0.0116,3.3364,1.1379	probably-damaging	57/311	125424164	148,12858	2203	4300	6503	SO:0001583	missense	26737	exon1			TCCAGACGCCCAT		CCDS35127.1, CCDS35127.2	9q33.2	2013-09-20			ENSG00000173679	ENSG00000173679		"GPCR / Class A : Olfactory receptors"	8213	protein-coding gene	gene with protein product				OR1L2			Standard	NM_001005236		Approved	OR9-C	uc022bmz.1	Q8NH94	OTTHUMG00000020618	ENST00000373686.1:c.320C>T	9.37:g.125424164C>T	ENSP00000362790:p.Thr107Met	155	0	0		226	151	0.668142	NM_001005236	Q5T7Z3|Q6IFN2	Missense_Mutation	SNP	ENST00000373686.1	37		27	0.012362637362637362	26	0.052845528455284556	1	0.0027624309392265192	0	0.0	0	0.0	C	14.01	2.408566	0.42715	0.033364	1.16E-4	ENSG00000173679	ENST00000373686;ENST00000309623	T;T	0.00481	7.11;7.11	3.11	1.01	0.19927	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00178	0.0005	L	0.58428	1.81	0.09310	N	0.999997	D	0.59357	0.985	P	0.55391	0.775	T	0.54077	-0.8347	9	0.72032	D	0.01	.	9.8389	0.40987	0.511:0.489:0.0:0.0	.	107	Q8NH94	OR1L1_HUMAN	M	107;57	ENSP00000362790:T107M;ENSP00000310773:T57M	ENSP00000310773:T57M	T	+	2	0	OR1L1	124463985	0.000000	0.05858	0.188000	0.23233	0.075000	0.17131	-1.376000	0.02561	0.095000	0.17434	0.313000	0.20887	ACG	C|0.987;T|0.013	0.013	strong		0.463	OR1L1-201	KNOWN	basic	protein_coding	protein_coding				T	125424164	C	T	125424164	3	4	22	1	0	0	0	0	1	0	0	0	10972	536	19	1	172	1	OR1L1	9	125424164	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	150149	125424164	15789267	2153	5054											
OR1L1	26737	hgsc.bcm.edu	37	chr9	125424277	125424277	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agacaaagaccatctcttacAgtgagtgtctgacccagatg	13	9	9	10	0	2	5	0	2	2	3	3	5	2	5	2	0	1	0	2	0	2	1	rs70157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:125424277A>G	ENST00000373686.1	+	1	433	c.433A>G	c.(433-435)Agt>Ggt	p.S145G	OR1L1_ENST00000309623.1_Missense_Mutation_p.S95G			Q8NH94	OR1L1_HUMAN	olfactory receptor, family 1, subfamily L, member 1	145			S -> G (in dbSNP:rs70157). {ECO:0000269|PubMed:14983052, 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)			breast(1)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)	17						CATCTCTTACAGTGAGTGTCT	0.428													.|||	649	0.129593	0.4713	0.036	5008	,	,		24856	0.0		0.001	False		,,,				2504	0.0				p.S95G		Atlas-SNP	.											.	OR1L1	54	.	0			c.A283G						PASS	.	G	GLY/SER	1689,2717	654.4+/-399.7	329,1031,843	202	199	200		283	1.1	0	9	dbSNP_79	200	10,8590	818.9+/-406.8	0,10,4290	yes	missense	OR1L1	NM_001005236.3	56	329,1041,5133	GG,GA,AA		0.1163,38.3341,13.0632	benign	95/311	125424277	1699,11307	2203	4300	6503	SO:0001583	missense	26737	exon1			TCTTACAGTGAGT		CCDS35127.1, CCDS35127.2	9q33.2	2013-09-20			ENSG00000173679	ENSG00000173679		"GPCR / Class A : Olfactory receptors"	8213	protein-coding gene	gene with protein product				OR1L2			Standard	NM_001005236		Approved	OR9-C	uc022bmz.1	Q8NH94	OTTHUMG00000020618	ENST00000373686.1:c.433A>G	9.37:g.125424277A>G	ENSP00000362790:p.Ser145Gly	169	0	0		180	114	0.633333	NM_001005236	Q5T7Z3|Q6IFN2	Missense_Mutation	SNP	ENST00000373686.1	37		228	0.1043956043956044	217	0.4410569105691057	11	0.03038674033149171	0	0.0	0	0.0	G	2.229	-0.376473	0.05000	0.383341	0.001163	ENSG00000173679	ENST00000373686;ENST00000309623	T;T	0.00402	7.56;7.56	3.11	1.14	0.20703	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.11756	0.17	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.22941	-1.0202	8	0.46703	T	0.11	.	1.3175	0.02110	0.2108:0.169:0.4474:0.1728	rs70157;rs700052;rs56487442;rs70157	145	Q8NH94	OR1L1_HUMAN	G	145;95	ENSP00000362790:S145G;ENSP00000310773:S95G	ENSP00000310773:S95G	S	+	1	0	OR1L1	124464098	0.000000	0.05858	0.002000	0.10522	0.015000	0.08874	-3.542000	0.00436	-0.119000	0.11830	-0.642000	0.03964	AGT	A|0.860;G|0.140	0.140	strong		0.428	OR1L1-201	KNOWN	basic	protein_coding	protein_coding				G	125424277	A	G	125424277	3	3	22	1	0	0	0	0	1	0	0	0	10972	188	7	3	285	3	OR1L1	9	125424277	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	113	125424277	15789154	2154	5055											
CRB2	286204	hgsc.bcm.edu	37	chr9	126133252	126133252	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccccatagaggtcccacgtgCgctgatggtgaggaataagc	10	7	13	11	2	0	3	0	2	0	1	1	4	1	4	3	3	2	1	3	3	3	2	rs55965026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:126133252C>T	ENST00000373631.3	+	7	1921	c.1920C>T	c.(1918-1920)tgC>tgT	p.C640C	CRB2_ENST00000373629.2_Silent_p.C308C|CRB2_ENST00000359999.3_Silent_p.C640C	NM_173689.5	NP_775960.4	Q5IJ48	CRUM2_HUMAN	crumbs family member 2	640	EGF-like 10. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cardiovascular system development (GO:0072358)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|mesoderm formation (GO:0001707)|negative regulation of endopeptidase activity (GO:0010951)|notochord formation (GO:0014028)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|somitogenesis (GO:0001756)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)			NS(2)|breast(1)|cervix(1)|endometrium(2)|lung(11)|ovary(1)|prostate(2)|skin(3)	23						GTCCCACGTGCGCTGATGGTG	0.617													C|||	160	0.0319489	0.0893	0.0159	5008	,	,		19920	0.0		0.0229	False		,,,				2504	0.0082				p.C640C		Atlas-SNP	.											.	CRB2	86	.	0			c.C1920T						PASS	.	C		332,4074	168.3+/-199.2	12,308,1883	56	61	59		1920	-3.2	0.1	9	dbSNP_129	59	257,8343	97.9+/-159.5	8,241,4051	no	coding-synonymous	CRB2	NM_173689.5		20,549,5934	TT,TC,CC		2.9884,7.5352,4.5287		640/1286	126133252	589,12417	2203	4300	6503	SO:0001819	synonymous_variant	286204	exon7			CACGTGCGCTGAT	AK095783	CCDS6852.2	9q33.2	2014-02-06	2014-02-06		ENSG00000148204	ENSG00000148204			18688	protein-coding gene	gene with protein product		609720	"crumbs homolog 2 (Drosophila)"			14767562	Standard	XM_005251934		Approved	FLJ38464, FLJ16786	uc004bnx.1	Q5IJ48	OTTHUMG00000020638	ENST00000373631.3:c.1920C>T	9.37:g.126133252C>T		59	0	0		51	33	0.647059	NM_173689	A2A3N4|Q0QD46|Q5JS41|Q5JS43|Q6ZTA9|Q6ZWI6	Silent	SNP	ENST00000373631.3	37	CCDS6852.2																																																																																			C|0.962;T|0.038	0.038	strong		0.617	CRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053990.3	NM_173689		T	126133252	C	T	126133252	2	4	22	1	0	0	0	0	0	0	0	1	3851	776	27	1		1	CRB2	9	126133252	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	708975	126133252	15080179	2155	5056											
NR5A1	2516	hgsc.bcm.edu	37	chr9	127245070	127245070	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcttgcagcatttcgatgagCaggttgttgcggggcatctc	6	12	14	9	2	1	1	0	1	1	0	3	2	1	1	0	3	4	7	0	3	0	4	rs79833327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:127245070C>T	ENST00000373588.4	-	7	1549	c.1353G>A	c.(1351-1353)ctG>ctA	p.L451L		NM_004959.4	NP_004950.2	Q13285	STF1_HUMAN	nuclear receptor subfamily 5, group A, member 1	451	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						TTTCGATGAGCAGGTTGTTGC	0.697													C|||	45	0.00898562	0.0333	0.0014	5008	,	,		11167	0.0		0.0	False		,,,				2504	0.0				p.L451L		Atlas-SNP	.											.	NR5A1	32	.	0			c.G1353A						PASS	.	C		214,4188	122.1+/-159.5	5,204,1992	64	45	51		1353	3.9	1	9	dbSNP_131	51	2,8594		0,2,4296	no	coding-synonymous	NR5A1	NM_004959.4		5,206,6288	TT,TC,CC		0.0233,4.8614,1.6618		451/462	127245070	216,12782	2201	4298	6499	SO:0001819	synonymous_variant	2516	exon7			GATGAGCAGGTTG	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.1353G>A	9.37:g.127245070C>T		113	0	0		115	42	0.365217	NM_004959	O15196|Q5T6F5	Silent	SNP	ENST00000373588.4	37	CCDS6856.1																																																																																			C|0.983;T|0.017	0.017	strong		0.697	NR5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054029.1	NM_004959		T	127245070	C	T	127245070	2	4	22	1	0	0	0	0	0	0	0	1	10644	697	25	2		2	NR5A1	9	127245070	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1111818	127245070	13968361	2156	5057											
NR5A1	2516	hgsc.bcm.edu	37	chr9	127262864	127262864	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggcggcgggggcacccccatCgggggccctgtctccagctt	3	6	16	16	3	1	0	0	0	1	0	3	0	1	0	4	6	1	2	4	6	0	1	rs1110062	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:127262864C>T	ENST00000373588.4	-	4	571	c.375G>A	c.(373-375)ccG>ccA	p.P125P		NM_004959.4	NP_004950.2	Q13285	STF1_HUMAN	nuclear receptor subfamily 5, group A, member 1	125					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						GCACCCCCATCGGGGGCCCTG	0.682													C|||	436	0.0870607	0.3154	0.0245	5008	,	,		12705	0.002		0.0	False		,,,				2504	0.0				p.P125P		Atlas-SNP	.											.	NR5A1	32	.	0			c.G375A						PASS	.	C		1188,3052		158,872,1090	19	22	21		375	-9.1	0	9	dbSNP_86	21	9,8255		0,9,4123	no	coding-synonymous	NR5A1	NM_004959.4		158,881,5213	TT,TC,CC		0.1089,28.0189,9.5729		125/462	127262864	1197,11307	2120	4132	6252	SO:0001819	synonymous_variant	2516	exon4			CCCCATCGGGGGC	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.375G>A	9.37:g.127262864C>T		36	0	0		53	53	1	NM_004959	O15196|Q5T6F5	Silent	SNP	ENST00000373588.4	37	CCDS6856.1																																																																																			C|0.948;T|0.052	0.052	strong		0.682	NR5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054029.1	NM_004959		T	127262864	C	T	127262864	2	4	22	1	0	0	0	0	0	0	0	1	10644	871	31	1		1	NR5A1	9	127262864	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	17794	127262864	13950567	2157	5058											
GAPVD1	26130	hgsc.bcm.edu	37	chr9	128099784	128099784	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	atgaagagcgagaactccctCcagctgcagccattggtgct	10	8	11	12	1	0	3	0	1	0	2	2	4	2	3	3	1	6	3	3	1	2	1	rs62637637	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:128099784C>T	ENST00000495955.1	+	17	3081	c.2791C>T	c.(2791-2793)Cca>Tca	p.P931S	GAPVD1_ENST00000297933.6_Missense_Mutation_p.P931S|GAPVD1_ENST00000312123.9_Missense_Mutation_p.P910S|GAPVD1_ENST00000394105.2_Missense_Mutation_p.P958S|GAPVD1_ENST00000394104.2_Missense_Mutation_p.P931S|GAPVD1_ENST00000470056.1_Missense_Mutation_p.P931S|GAPVD1_ENST00000394083.2_Missense_Mutation_p.P910S|GAPVD1_ENST00000265956.4_Missense_Mutation_p.P905S			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	931				P -> S (in Ref. 6; AAH13635). {ECO:0000305}.	endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of protein transport (GO:0051223)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	GTPase activating protein binding (GO:0032794)|GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						AGAACTCCCTCCAGCTGCAGC	0.532													C|||	30	0.00599042	0.0219	0.0014	5008	,	,		18533	0.0		0.0	False		,,,				2504	0.0				p.P958S		Atlas-SNP	.											.	GAPVD1	124	.	0			c.C2872T						PASS	.	C	SER/PRO	68,4338	62.9+/-100.1	1,66,2136	70	69	70		2872	5.3	0.9	9	dbSNP_129	70	0,8600		0,0,4300	yes	missense	GAPVD1	NM_015635.2	74	1,66,6436	TT,TC,CC		0.0,1.5433,0.5228	benign	958/1488	128099784	68,12938	2203	4300	6503	SO:0001583	missense	26130	exon16			CTCCCTCCAGCTG		CCDS65130.1, CCDS65131.1, CCDS65132.1	9q34.11	2008-02-05			ENSG00000165219	ENSG00000165219			23375	protein-coding gene	gene with protein product		611714					Standard	XM_005251901		Approved	DKFZP434C212, KIAA1521	uc004bpr.3	Q14C86	OTTHUMG00000020678	ENST00000495955.1:c.2791C>T	9.37:g.128099784C>T	ENSP00000419063:p.Pro931Ser	119	0	0		136	33	0.242647	NM_015635	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Missense_Mutation	SNP	ENST00000495955.1	37		14|14	0.00641025641025641|0.00641025641025641	13|13	0.026422764227642278|0.026422764227642278	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	C|C	8.329|8.329	0.826071|0.826071	0.16749|0.16749	0.015433|0.015433	0.0|0.0	ENSG00000165219|ENSG00000165219	ENST00000470056;ENST00000394105;ENST00000394104;ENST00000265956;ENST00000394083;ENST00000495955;ENST00000467750;ENST00000297933;ENST00000312123|ENST00000436712	.|.	.|.	.|.	6.17|6.17	5.26|5.26	0.73747|0.73747	.|.	0.267957|.	0.43416|.	D|.	0.000568|.	T|T	0.15955|0.15955	0.0384|0.0384	N|N	0.19112|0.19112	0.55|0.55	0.32006|0.32006	N|N	0.602735|0.602735	B;B;B;B;B;B|.	0.15930|.	0.002;0.002;0.001;0.001;0.001;0.015|.	B;B;B;B;B;B|.	0.12837|.	0.006;0.004;0.004;0.004;0.004;0.008|.	T|T	0.35895|0.35895	-0.9770|-0.9770	9|5	0.15066|.	T|.	0.55|.	.|.	11.4079|11.4079	0.49908|0.49908	0.1307:0.6166:0.2527:0.0|0.1307:0.6166:0.2527:0.0	rs62637637|rs62637637	905;931;931;910;931;958|.	Q14C86-5;Q14C86;Q14C86-3;Q14C86-4;Q14C86-2;Q14C86-6|.	.;GAPD1_HUMAN;.;.;.;.|.	S|F	931;958;931;905;910;931;931;931;910|767	.|.	ENSP00000265956:P905S|.	P|S	+|+	1|2	0|0	GAPVD1|GAPVD1	127139605|127139605	0.914000|0.914000	0.31030|0.31030	0.948000|0.948000	0.38648|0.38648	0.162000|0.162000	0.22319|0.22319	2.148000|2.148000	0.42235|0.42235	1.586000|1.586000	0.49944|0.49944	0.655000|0.655000	0.94253|0.94253	CCA|TCC	C|0.993;T|0.007	0.007	strong		0.532	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1			T	128099784	C	T	128099784	3	4	22	1	0	0	0	0	1	0	0	0	6247	855	30	2	2930	2	GAPVD1	9	128099784	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	836920	128099784	13113647	2158	5059											
MAPKAP1	79109	hgsc.bcm.edu	37	chr9	128206855	128206855	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tagtcgtgattgcttagataCgtgagtttaaatattgcgtg	10	16	11	4	3	0	3	0	2	0	1	1	3	0	3	0	0	3	2	0	0	6	8	rs35549826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:128206855C>T	ENST00000373498.1	-	10	1436	c.1368G>A	c.(1366-1368)acG>acA	p.T456T	MAPKAP1_ENST00000394063.1_Silent_p.T264T|MAPKAP1_ENST00000373511.2_Silent_p.T409T|MAPKAP1_ENST00000265960.3_Silent_p.T456T|MAPKAP1_ENST00000373497.5_Silent_p.T169T|MAPKAP1_ENST00000373503.3_Silent_p.T264T|MAPKAP1_ENST00000350766.3_Silent_p.T420T|MAPKAP1_ENST00000483937.1_5'UTR			Q9BPZ7	SIN1_HUMAN	mitogen-activated protein kinase associated protein 1	456					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						TGCTTAGATACGTGAGTTTAA	0.453													c|||	29	0.00579073	0.0212	0.0014	5008	,	,		20762	0.0		0.0	False		,,,				2504	0.0				p.T456T		Atlas-SNP	.											MAPKAP1_ENST00000265960,NS,carcinoma,-1,4	MAPKAP1	68	4	0			c.G1368A						scavenged	.	T	,,,,	63,4343	59.9+/-96.7	1,61,2141	167	147	154		1368,1227,792,792,1260	-6.7	0.7	9	dbSNP_126	154	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MAPKAP1	NM_001006617.1,NM_001006619.1,NM_001006620.1,NM_001006621.1,NM_024117.3	,,,,	1,62,6440	TT,TC,CC		0.0116,1.4299,0.4921	,,,,	456/523,409/476,264/331,264/331,420/487	128206855	64,12942	2203	4300	6503	SO:0001819	synonymous_variant	79109	exon11			TAGATACGTGAGT	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.1368G>A	9.37:g.128206855C>T		112	1	0.00892857		166	67	0.403614	NM_001006617	A8K1Z5|B1AMA4|B7Z309|Q00426|Q5JSV5|Q5JSV6|Q5JSV9|Q658R0|Q699U1|Q699U2|Q699U3|Q699U4|Q6GVJ0|Q6GVJ1|Q6GVJ2	Silent	SNP	ENST00000373498.1	37	CCDS35140.1	13	0.005952380952380952	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	0	0.0	c	4.720	0.133973	0.09032	0.014299	1.16E-4	ENSG00000119487	ENST00000444226	.	.	.	5.91	-6.66	0.01789	.	.	.	.	.	T	0.34948	0.0915	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53457	-0.8436	4	.	.	.	-6.8579	10.2871	0.43573	0.0:0.2969:0.167:0.5361	rs35549826	.	.	.	I	28	.	.	V	-	1	0	MAPKAP1	127246676	0.012000	0.17670	0.657000	0.29651	0.643000	0.38383	-1.022000	0.03611	-1.316000	0.02295	-4.302000	0.00007	GTA	C|0.994;T|0.006	0.006	strong		0.453	MAPKAP1-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054092.1			T	128206855	C	T	128206855	2	4	22	1	0	0	0	0	0	0	0	1	9297	523	19	1		1	MAPKAP1	9	128206855	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	107071	128206855	13006576	2159	5060											
SLC2A8	29988	hgsc.bcm.edu	37	chr9	130162230	130162230	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	ccagcagtccgggggttgctCggctcctgtgtgcagctaat	5	10	14	12	2	0	0	0	0	0	0	3	0	2	0	3	3	4	6	3	3	1	2	rs36057295	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:130162230C>G	ENST00000373371.3	+	4	560	c.471C>G	c.(469-471)ctC>ctG	p.L157L	SLC2A8_ENST00000373360.3_Silent_p.L157L|SLC2A8_ENST00000373352.1_5'UTR	NM_001271712.1|NM_014580.3	NP_001258641.1|NP_055395.2	Q9NY64	GTR8_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 8	157					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|male meiosis I (GO:0007141)|response to hypoxia (GO:0001666)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	glucose binding (GO:0005536)|glucose transmembrane transporter activity (GO:0005355)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)	11						GGGGGTTGCTCGGCTCCTGTG	0.557													C|||	130	0.0259585	0.0968	0.0029	5008	,	,		17695	0.0		0.0	False		,,,				2504	0.0				p.L157L		Atlas-SNP	.											.	SLC2A8	27	.	0			c.C471G						PASS	.	C		315,4091	169.1+/-199.8	9,297,1897	137	134	135		471	-5.9	1	9	dbSNP_126	135	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SLC2A8	NM_014580.3		9,299,6195	GG,GC,CC		0.0233,7.1493,2.4373		157/478	130162230	317,12689	2203	4300	6503	SO:0001819	synonymous_variant	29988	exon4			GTTGCTCGGCTCC	AJ245937	CCDS6870.1, CCDS65138.1, CCDS75903.1	9q33.3	2013-05-22	2008-09-02		ENSG00000136856	ENSG00000136856		"Solute carriers"	13812	protein-coding gene	gene with protein product		605245	"solute carrier family 2 (facilitated glucose transporter) member 8"			10671487, 10821868	Standard	NM_014580		Approved	GLUTX1, GLUT8	uc004bqu.4	Q9NY64	OTTHUMG00000020702	ENST00000373371.3:c.471C>G	9.37:g.130162230C>G		155	0	0		108	32	0.296296	NM_014580	Q8WUZ9|Q9NSC4	Silent	SNP	ENST00000373371.3	37	CCDS6870.1	38	0.0173992673992674	37	0.07520325203252033	1	0.0027624309392265192	0	0.0	0	0.0	C	1.094	-0.663174	0.03428	0.071493	2.33E-4	ENSG00000136856	ENST00000419132	.	.	.	5.35	-5.92	0.02261	.	.	.	.	.	T	0.04003	0.0112	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40701	-0.9549	4	.	.	.	.	7.9566	0.30047	0.0948:0.1228:0.603:0.1794	rs36057295	.	.	.	W	67	.	.	S	+	2	0	SLC2A8	129202051	0.005000	0.15991	0.967000	0.41034	0.066000	0.16364	-2.012000	0.01451	-0.659000	0.05359	-0.302000	0.09304	TCG	C|0.975;G|0.025	0.025	strong		0.557	SLC2A8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054177.1	NM_014580		G	130162230	C	G	130162230	2	3	22	1	0	0	0	0	0	0	0	1	14566	871	31	4		4	SLC2A8	9	130162230	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1955375	130162230	11051201	2160	5061											
LRSAM1	90678	hgsc.bcm.edu	37	chr9	130263362	130263362	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgagtctgtgaggccatcCgctccccctgcagagctgga	6	8	12	15	1	1	3	0	2	1	1	3	4	3	4	5	2	2	3	5	2	0	0			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:130263362C>T	ENST00000323301.4	+	24	2590	c.1986C>T	c.(1984-1986)tcC>tcT	p.S662S	LRSAM1_ENST00000300417.6_Silent_p.S662S|LRSAM1_ENST00000483302.1_3'UTR|LRSAM1_ENST00000373322.1_Silent_p.S662S|LRSAM1_ENST00000373324.4_Silent_p.S635S	NM_138361.5	NP_612370.3	Q6UWE0	LRSM1_HUMAN	leucine rich repeat and sterile alpha motif containing 1	662					cell death (GO:0008219)|negative regulation of endocytosis (GO:0045806)|protein autoubiquitination (GO:0051865)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|ubiquitin-dependent endocytosis (GO:0070086)|viral budding (GO:0046755)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(2)	16						TGAGGCCATCCGCTCCCCCTG	0.662																																					p.S662S		Atlas-SNP	.											.	LRSAM1	40	.	0			c.C1986T						PASS	.						57	55	56					9																	130263362		2203	4300	6503	SO:0001819	synonymous_variant	90678	exon25			GCCATCCGCTCCC	AK056203	CCDS6873.1, CCDS55347.1	9q34.13	2014-09-17			ENSG00000148356	ENSG00000148356		"Sterile alpha motif (SAM) domain containing"	25135	protein-coding gene	gene with protein product		610933				12975309	Standard	NM_001005373		Approved	FLJ31641	uc004brd.2	Q6UWE0	OTTHUMG00000020701	ENST00000323301.4:c.1986C>T	9.37:g.130263362C>T		63	0	0		68	20	0.294118	NM_001005373	Q5VVV0|Q8NB40|Q96GT5|Q96MX5|Q96MZ7	Silent	SNP	ENST00000323301.4	37	CCDS6873.1																																																																																			.	.	none		0.662	LRSAM1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054164.1	NM_138361		T	130263362	C	T	130263362	2	4	22	1	0	0	0	0	0	0	0	1	9052	639	23	1		1	LRSAM1	9	130263362	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	101132	130263362	10950069	2161	5062											
TTC16	158248	hgsc.bcm.edu	37	chr9	130485476	130485476	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggccaggatgctgctccagAagatggtggcccaggcccag	9	5	15	12	0	0	2	0	0	0	2	1	3	1	3	4	5	2	2	4	5	1	0	rs115363266	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:130485476A>C	ENST00000373289.3	+	7	816	c.736A>C	c.(736-738)Aag>Cag	p.K246Q	PTRH1_ENST00000419060.1_Intron|PTRH1_ENST00000429848.1_Intron|TTC16_ENST00000393748.4_Missense_Mutation_p.K70Q|TTC16_ENST00000489226.1_3'UTR	NM_144965.1	NP_659402.1	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	246										central_nervous_system(2)|endometrium(3)|lung(7)|ovary(3)|pancreas(2)|prostate(4)|skin(1)	22						GCTGCTCCAGAAGATGGTGGC	0.662													A|||	136	0.0271565	0.0983	0.0086	5008	,	,		19586	0.0		0.0	False		,,,				2504	0.0				p.K246Q		Atlas-SNP	.											.	TTC16	55	.	0			c.A736C						PASS	.	A	GLN/LYS	459,3947	211.5+/-231.7	30,399,1774	55	56	55		736	0.1	0.1	9	dbSNP_132	55	0,8600		0,0,4300	yes	missense	TTC16	NM_144965.1	53	30,399,6074	CC,CA,AA		0.0,10.4176,3.5291	benign	246/874	130485476	459,12547	2203	4300	6503	SO:0001583	missense	158248	exon7			CTCCAGAAGATGG	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.736A>C	9.37:g.130485476A>C	ENSP00000362386:p.Lys246Gln	118	0	0		100	62	0.62	NM_144965	B4DYG4|B5ME24|Q5JU66|Q96M72	Missense_Mutation	SNP	ENST00000373289.3	37	CCDS6875.1	69|69	0.03159340659340659|0.03159340659340659	66|66	0.13414634146341464|0.13414634146341464	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	A|A	7.212|7.212	0.595622|0.595622	0.13875|0.13875	0.104176|0.104176	0.0|0.0	ENSG00000167094|ENSG00000167094	ENST00000373288|ENST00000373289;ENST00000393748;ENST00000316259	.|T	.|0.54866	.|0.55	5.08|5.08	0.119|0.119	0.14685|0.14685	.|Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	.|1.102050	.|0.06828	.|N	.|0.793373	T|T	0.00637|0.00637	0.0021|0.0021	L|L	0.53249|0.53249	1.67|1.67	0.09310|0.09310	N|N	1|1	.|P;B;P	.|0.51351	.|0.944;0.022;0.944	.|B;B;B	.|0.44044	.|0.439;0.013;0.439	T|T	0.02491|0.02491	-1.1151|-1.1151	6|10	0.87932|0.46703	D|T	0|0.11	-1.776|-1.776	7.3747|7.3747	0.26821|0.26821	0.6016:0.0:0.3984:0.0|0.6016:0.0:0.3984:0.0	.|.	.|233;198;246	.|B4DZ42;B4DH05;Q8NEE8	.|.;.;TTC16_HUMAN	A|Q	71|246;70;191	.|ENSP00000362386:K246Q	ENSP00000362385:E71A|ENSP00000319048:K191Q	E|K	+|+	2|1	0|0	TTC16|TTC16	129525297|129525297	0.005000|0.005000	0.15991|0.15991	0.113000|0.113000	0.21522|0.21522	0.358000|0.358000	0.29455|0.29455	0.441000|0.441000	0.21611|0.21611	-0.113000|-0.113000	0.11958|0.11958	0.374000|0.374000	0.22700|0.22700	GAA|AAG	A|0.962;C|0.038	0.038	strong		0.662	TTC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054224.1	NM_144965		C	130485476	A	C	130485476	3	2	22	1	0	0	0	0	1	0	0	0	16698	247	9	5	762	5	TTC16	9	130485476	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	222114	130485476	10727955	2162	5063											
CIZ1	25792	hgsc.bcm.edu	37	chr9	130938650	130938650	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatcctctgtctccaggacGtcccggggcacgggcagcag	6	7	13	15	3	3	0	1	0	2	0	6	1	5	1	3	4	1	3	3	4	0	0	rs45475893	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:130938650G>A	ENST00000393608.1	-	11	2125	c.1923C>T	c.(1921-1923)gaC>gaT	p.D641D	CIZ1_ENST00000476727.2_Intron|CIZ1_ENST00000538431.1_Silent_p.D641D|CIZ1_ENST00000325721.8_Silent_p.D612D|CIZ1_ENST00000357558.5_Silent_p.D613D|CIZ1_ENST00000372948.3_Silent_p.D585D|CIZ1_ENST00000372954.1_Silent_p.D561D|CIZ1_ENST00000372938.5_Silent_p.D641D|CIZ1_ENST00000541172.1_Silent_p.D540D|CIZ1_ENST00000277465.4_Silent_p.D613D	NM_012127.2	NP_036259.2	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1	641					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						TCTCCAGGACGTCCCGGGGCA	0.637													G|||	22	0.00439297	0.0151	0.0029	5008	,	,		19335	0.0		0.0	False		,,,				2504	0.0				p.D671D		Atlas-SNP	.											.	CIZ1	75	.	0			c.C2013T						PASS	.	G	,,,,	75,4331	67.0+/-104.6	0,75,2128	98	103	101		1755,1923,1740,1683,1923	-8.3	0	9	dbSNP_127	101	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CIZ1	NM_001131015.1,NM_001131016.1,NM_001131017.1,NM_001131018.1,NM_012127.2	,,,,	0,76,6427	AA,AG,GG		0.0116,1.7022,0.5843	,,,,	585/843,641/899,580/838,561/819,641/899	130938650	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	25792	exon11			CAGGACGTCCCGG	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.1923C>T	9.37:g.130938650G>A		102	0	0		119	86	0.722689	NM_001257975	A8K9J8|B4E131|B7ZAS8|Q5SYW3|Q5SYW5|Q8WU72|Q9H868|Q9NYM8|Q9UHK4|Q9Y3F9|Q9Y3G0	Silent	SNP	ENST00000393608.1	37	CCDS6894.1																																																																																			G|0.994;A|0.006	0.006	strong		0.637	CIZ1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054399.1	NM_012127		A	130938650	G	A	130938650	2	1	22	1	0	0	0	0	0	0	0	1	3443	1136	40	1		1	CIZ1	9	130938650	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	453174	130938650	10274781	2163	5064											
CIZ1	25792	hgsc.bcm.edu	37	chr9	130941451	130941451	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tctggagaggtctgtgtttgCgcctgcttctgcagctttgg	3	15	14	9	1	3	1	0	0	3	1	3	2	3	1	1	3	4	4	1	3	0	3	rs45536439	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:130941451C>T	ENST00000393608.1	-	8	1237	c.1035G>A	c.(1033-1035)gcG>gcA	p.A345A	CIZ1_ENST00000476727.2_Intron|CIZ1_ENST00000538431.1_Silent_p.A345A|CIZ1_ENST00000325721.8_Silent_p.A316A|CIZ1_ENST00000357558.5_Silent_p.A345A|CIZ1_ENST00000372948.3_Silent_p.A345A|CIZ1_ENST00000372954.1_Silent_p.A321A|CIZ1_ENST00000372938.5_Silent_p.A345A|CIZ1_ENST00000541172.1_Silent_p.A244A|CIZ1_ENST00000277465.4_Silent_p.A345A	NM_012127.2	NP_036259.2	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1	345	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						TCTGTGTTTGCGCCTGCTTCT	0.617													C|||	174	0.0347444	0.1225	0.0159	5008	,	,		20540	0.0		0.001	False		,,,				2504	0.0				p.A375A		Atlas-SNP	.											.	CIZ1	75	.	0			c.G1125A						PASS	.	C	,,,,	553,3853	248.7+/-256.4	38,477,1688	63	64	64		1035,1035,1020,963,1035	-5.6	0.9	9	dbSNP_127	64	13,8587	7.7+/-29.5	0,13,4287	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CIZ1	NM_001131015.1,NM_001131016.1,NM_001131017.1,NM_001131018.1,NM_012127.2	,,,,	38,490,5975	TT,TC,CC		0.1512,12.5511,4.3518	,,,,	345/843,345/899,340/838,321/819,345/899	130941451	566,12440	2203	4300	6503	SO:0001819	synonymous_variant	25792	exon8			TGTTTGCGCCTGC	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.1035G>A	9.37:g.130941451C>T		118	0	0		118	70	0.59322	NM_001257975	A8K9J8|B4E131|B7ZAS8|Q5SYW3|Q5SYW5|Q8WU72|Q9H868|Q9NYM8|Q9UHK4|Q9Y3F9|Q9Y3G0	Silent	SNP	ENST00000393608.1	37	CCDS6894.1																																																																																			C|0.961;T|0.039	0.039	strong		0.617	CIZ1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054399.1	NM_012127		T	130941451	C	T	130941451	2	4	22	1	0	0	0	0	0	0	0	1	3443	755	27	1		1	CIZ1	9	130941451	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2801	130941451	10271980	2164	5065											
CIZ1	25792	hgsc.bcm.edu	37	chr9	130948018	130948018	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggtgtgaggctgggggctgcGaggcctggggatgccatgcc	4	7	21	9	1	0	1	0	1	0	0	0	3	0	2	3	7	3	2	3	7	0	0	rs45545033	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:130948018G>A	ENST00000393608.1	-	5	598	c.396C>T	c.(394-396)ctC>ctT	p.L132L	CIZ1_ENST00000476727.2_5'UTR|CIZ1_ENST00000538431.1_Silent_p.L132L|CIZ1_ENST00000372948.3_Silent_p.L132L|CIZ1_ENST00000372954.1_Silent_p.L108L|CIZ1_ENST00000372938.5_Silent_p.L132L|CIZ1_ENST00000541172.1_Silent_p.L31L|CIZ1_ENST00000277465.4_Silent_p.L132L|CIZ1_ENST00000357558.5_Silent_p.L132L|CIZ1_ENST00000325721.8_Silent_p.L108L	NM_012127.2	NP_036259.2	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1	132					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						TGGGGGCTGCGAGGCCTGGGG	0.602													G|||	162	0.0323482	0.1165	0.0115	5008	,	,		16972	0.0		0.0	False		,,,				2504	0.0				p.L162L		Atlas-SNP	.											.	CIZ1	75	.	0			c.C486T						PASS	.	G	,,,,	520,3886	238.4+/-249.8	36,448,1719	38	38	38		396,396,396,324,396	0.2	0	9	dbSNP_127	38	8,8592	3.7+/-12.6	0,8,4292	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CIZ1	NM_001131015.1,NM_001131016.1,NM_001131017.1,NM_001131018.1,NM_012127.2	,,,,	36,456,6011	AA,AG,GG		0.093,11.8021,4.0597	,,,,	132/843,132/899,132/838,108/819,132/899	130948018	528,12478	2203	4300	6503	SO:0001819	synonymous_variant	25792	exon5			GGCTGCGAGGCCT	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.396C>T	9.37:g.130948018G>A		49	0	0		63	43	0.68254	NM_001257975	A8K9J8|B4E131|B7ZAS8|Q5SYW3|Q5SYW5|Q8WU72|Q9H868|Q9NYM8|Q9UHK4|Q9Y3F9|Q9Y3G0	Silent	SNP	ENST00000393608.1	37	CCDS6894.1																																																																																			G|0.962;A|0.038	0.038	strong		0.602	CIZ1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054399.1	NM_012127		A	130948018	G	A	130948018	2	1	22	1	0	0	0	0	0	0	0	1	3443	1045	37	1		1	CIZ1	9	130948018	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6567	130948018	10265413	2165	5066											
ODF2	4957	hgsc.bcm.edu	37	chr9	131260808	131260808	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gaaaacacgggaatgtgggaCcctggcaaggcagttggaga	13	5	16	7	1	0	1	0	0	0	1	0	5	0	3	1	5	1	3	1	5	4	1	rs16930426	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131260808C>G	ENST00000434106.3	+	19	2492	c.2129C>G	c.(2128-2130)aCc>aGc	p.T710S	ODF2_ENST00000444119.2_Missense_Mutation_p.T686S|ODF2_ENST00000351030.3_Missense_Mutation_p.T705S|ODF2_ENST00000393527.3_Missense_Mutation_p.T686S|ODF2_ENST00000372807.5_Missense_Mutation_p.T705S|ODF2_ENST00000604420.1_Missense_Mutation_p.T710S	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	710			T -> S (in dbSNP:rs16930426).		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						GAATGTGGGACCctggcaagg	0.542													C|||	106	0.0211661	0.0749	0.0086	5008	,	,		20036	0.0		0.001	False		,,,				2504	0.0				p.T774S		Atlas-SNP	.											.	ODF2	227	.	0			c.C2321G						PASS	.	C	SER/THR,SER/THR,SER/THR,SER/THR,SER/THR	330,4076	173.0+/-202.9	15,300,1888	73	62	66		2114,2129,2057,2129,2321	3.8	0.3	9	dbSNP_123	66	4,8596	3.0+/-9.4	0,4,4296	yes	missense,missense,missense,missense,missense	ODF2	NM_001242352.1,NM_001242353.1,NM_002540.4,NM_153433.1,NM_153435.1	58,58,58,58,58	15,304,6184	GG,GC,CC		0.0465,7.4898,2.568	benign,benign,benign,benign,benign	705/825,710/830,686/806,710/830,774/894	131260808	334,12672	2203	4300	6503	SO:0001583	missense	4957	exon19			GTGGGACCCTGGC	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.2129C>G	9.37:g.131260808C>G	ENSP00000403453:p.Thr710Ser	128	0	0		117	76	0.649573	NM_153435	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Missense_Mutation	SNP	ENST00000434106.3	37	CCDS56588.1	45	0.020604395604395604	41	0.08333333333333333	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	C	9.645	1.139924	0.21205	0.074898	4.65E-4	ENSG00000136811	ENST00000351030;ENST00000372796;ENST00000303890	T;T;T	0.20069	2.1;2.11;2.1	5.67	3.8	0.43715	.	1.035180	0.07583	N	0.920674	T	0.00468	0.0015	N	0.01576	-0.805	0.25699	N	0.985609	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	0.09997	-1.0649	10	0.05721	T	0.95	-0.0175	15.5266	0.75915	0.0:0.6681:0.3319:0.0	rs16930426;rs52827709;rs16930426	705;55;710;686	Q5BJF6-4;Q6PJQ8;Q5BJF6;Q5BJF6-3	.;.;ODFP2_HUMAN;.	S	705;710;686	ENSP00000342581:T705S;ENSP00000361882:T710S;ENSP00000307781:T686S	ENSP00000307781:T686S	T	+	2	0	ODF2	130300629	0.000000	0.05858	0.265000	0.24526	0.689000	0.40095	0.677000	0.25262	0.685000	0.31468	-0.211000	0.12701	ACC	C|0.971;G|0.029	0.029	strong		0.542	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3			G	131260808	C	G	131260808	3	3	22	1	0	0	0	0	1	0	0	0	10836	507	18	4	2317	4	ODF2	9	131260808	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	312790	131260808	9952623	2166	5067											
SPTAN1	6709	hgsc.bcm.edu	37	chr9	131362361	131362361	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctctttctttgaataggaTgaaactgattccaagacagc	12	13	7	9	0	2	4	0	3	2	1	4	5	4	5	2	1	2	0	2	1	4	4	rs945831	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131362361T>C	ENST00000372731.4	+	27	3656	c.3546T>C	c.(3544-3546)gaT>gaC	p.D1182D	SPTAN1_ENST00000358161.5_Silent_p.D1182D|SPTAN1_ENST00000372739.3_Silent_p.D1182D	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1182					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						TTGAATAGGATGAAACTGATT	0.433													T|||	175	0.0349441	0.1263	0.0115	5008	,	,		18973	0.0		0.0	False		,,,				2504	0.0				p.D1182D	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.T3546C						PASS	.	T	,,	478,3928	223.3+/-239.8	28,422,1753	124	113	117		3546,3486,3546	6.1	1	9	dbSNP_86	117	8,8592	5.0+/-18.6	0,8,4292	no	coding-synonymous,coding-synonymous,coding-synonymous	SPTAN1	NM_001130438.2,NM_001195532.1,NM_003127.3	,,	28,430,6045	CC,CT,TT		0.093,10.8488,3.7367	,,	1182/2478,1162/2453,1182/2473	131362361	486,12520	2203	4300	6503	SO:0001819	synonymous_variant	6709	exon27			ATAGGATGAAACT	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.3546T>C	9.37:g.131362361T>C		202	0	0		229	93	0.406114	NM_003127	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Silent	SNP	ENST00000372731.4	37	CCDS6905.1																																																																																			T|0.963;C|0.037	0.037	strong		0.433	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		C	131362361	T	C	131362361	2	2	22	1	0	0	0	0	0	0	0	1	15132	1461	51	3		3	SPTAN1	9	131362361	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	101553	131362361	9851070	2167	5068											
SPTAN1	6709	hgsc.bcm.edu	37	chr9	131395568	131395568	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagggccgcgagctccccacCgcgttcgactacgtggagtt	7	7	13	14	6	0	0	0	0	0	0	2	3	1	1	4	2	2	3	4	2	2	3	rs2228952	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131395568C>T	ENST00000372731.4	+	56	7484	c.7374C>T	c.(7372-7374)acC>acT	p.T2458T	SPTAN1_ENST00000358161.5_Silent_p.T2463T|WDR34_ENST00000483181.1_5'Flank|SPTAN1_ENST00000372739.3_Silent_p.T2463T	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	2458					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						AGCTCCCCACCGCGTTCGACT	0.632													C|||	116	0.0231629	0.0817	0.0101	5008	,	,		17940	0.0		0.001	False		,,,				2504	0.0				p.T2463T	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.C7389T						PASS	.	C	,,	348,4058	182.9+/-210.6	11,326,1866	83	72	76		7389,7314,7374	-10.7	0	9	dbSNP_98	76	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	SPTAN1	NM_001130438.2,NM_001195532.1,NM_003127.3	,,	11,331,6161	TT,TC,CC		0.0581,7.8983,2.7141	,,	2463/2478,2438/2453,2458/2473	131395568	353,12653	2203	4300	6503	SO:0001819	synonymous_variant	6709	exon57			CCCCACCGCGTTC	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.7374C>T	9.37:g.131395568C>T		80	0	0		77	52	0.675325	NM_001130438	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Silent	SNP	ENST00000372731.4	37	CCDS6905.1																																																																																			C|0.967;T|0.033	0.033	strong		0.632	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		T	131395568	C	T	131395568	2	4	22	1	0	0	0	0	0	0	0	1	15132	639	23	1		1	SPTAN1	9	131395568	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	33207	131395568	9817863	2168	5069											
WDR34	89891	hgsc.bcm.edu	37	chr9	131398633	131398633	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggacctccaccacggccgaCggctgctggggacgcaggtc	6	4	16	15	4	0	0	0	0	0	0	2	3	1	2	4	6	1	3	4	6	0	0	rs61744155	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131398633C>T	ENST00000372715.2	-	4	690	c.630G>A	c.(628-630)ccG>ccA	p.P210P	WDR34_ENST00000483181.1_5'Flank	NM_052844.3	NP_443076.2	Q96EX3	WDR34_HUMAN	WD repeat domain 34	210						axoneme (GO:0005930)|centriole (GO:0005814)|ciliary basal body (GO:0036064)				central_nervous_system(2)|lung(5)|skin(1)|urinary_tract(1)	9						CCACGGCCGACGGCTGCTGGG	0.682													C|||	77	0.0153754	0.056	0.0043	5008	,	,		16542	0.0		0.0	False		,,,				2504	0.0				p.P210P		Atlas-SNP	.											.	WDR34	29	.	0			c.G630A						PASS	.	C		252,4150	136.5+/-172.5	10,232,1959	56	49	51		630	-5.2	0	9	dbSNP_129	51	5,8589	3.7+/-12.6	0,5,4292	no	coding-synonymous	WDR34	NM_052844.3		10,237,6251	TT,TC,CC		0.0582,5.7247,1.9775		210/537	131398633	257,12739	2201	4297	6498	SO:0001819	synonymous_variant	89891	exon4			GGCCGACGGCTGC	BC011874	CCDS6906.2	9q34.11	2013-11-15	2013-02-19	2013-02-19	ENSG00000119333	ENSG00000119333		"WD repeat domain containing"	28296	protein-coding gene	gene with protein product		613363				19521662, 21953912, 24183451	Standard	NM_052844		Approved	DIC5, MGC20486, bA216B9.3, FAP133	uc004bvq.1	Q96EX3	OTTHUMG00000020750	ENST00000372715.2:c.630G>A	9.37:g.131398633C>T		92	0	0		110	30	0.272727	NM_052844	Q5VXV4|Q9BV46	Silent	SNP	ENST00000372715.2	37	CCDS6906.2																																																																																			C|0.978;T|0.022	0.022	strong		0.682	WDR34-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054463.1	NM_052844		T	131398633	C	T	131398633	2	4	22	1	0	0	0	0	0	0	0	1	17303	523	19	1		1	WDR34	9	131398633	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3065	131398633	9814798	2169	5070											
PKN3	29941	hgsc.bcm.edu	37	chr9	131467782	131467782	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgagctgcgggagctgcaCgcccgaatcctgctgcccgg	5	5	16	15	5	0	0	0	0	0	0	1	3	1	1	3	3	6	4	3	3	1	0	rs55665019	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131467782C>T	ENST00000291906.4	+	2	618	c.225C>T	c.(223-225)caC>caT	p.H75H		NM_013355.3	NP_037487.2	Q6P5Z2	PKN3_HUMAN	protein kinase N3	75					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						GGGAGCTGCACGCCCGAATCC	0.706													C|||	530	0.105831	0.3767	0.0317	5008	,	,		15403	0.0069		0.003	False		,,,				2504	0.0				p.H75H		Atlas-SNP	.											.	PKN3	62	.	0			c.C225T						PASS	.	C		1131,3035		106,919,1058	4	4	4		225	-10.4	0.1	9	dbSNP_129	4	36,8126		0,36,4045	no	coding-synonymous	PKN3	NM_013355.3		106,955,5103	TT,TC,CC		0.4411,27.1483,9.4663		75/890	131467782	1167,11161	2083	4081	6164	SO:0001819	synonymous_variant	29941	exon2			GCTGCACGCCCGA	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.225C>T	9.37:g.131467782C>T		10	0	0		15	11	0.733333	NM_013355	Q9UM03	Silent	SNP	ENST00000291906.4	37	CCDS6908.1																																																																																			C|0.909;T|0.091	0.091	strong		0.706	PKN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054487.1	NM_013355		T	131467782	C	T	131467782	2	4	22	1	0	0	0	0	0	0	0	1	11990	535	19	1		1	PKN3	9	131467782	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	69149	131467782	9745649	2170	5071											
ENDOG	2021	hgsc.bcm.edu	37	chr9	131584649	131584649	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tacgtaaagtaccaggtcatCggcaagaaccacgtggcagt	13	7	11	10	3	1	1	1	0	0	1	2	1	1	1	2	3	3	4	2	3	6	3	rs55985529	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131584649C>T	ENST00000372642.4	+	3	865	c.654C>T	c.(652-654)atC>atT	p.I218I	C9orf114_ENST00000361256.5_3'UTR	NM_004435.2	NP_004426.2	Q14249	NUCG_HUMAN	endonuclease G	218					apoptotic DNA fragmentation (GO:0006309)|DNA recombination (GO:0006310)|in utero embryonic development (GO:0001701)|positive regulation of apoptotic process (GO:0043065)|response to antibiotic (GO:0046677)|response to tumor necrosis factor (GO:0034612)	mitochondrion (GO:0005739)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|nucleic acid binding (GO:0003676)										ACCAGGTCATCGGCAAGAACC	0.592													C|||	136	0.0271565	0.0961	0.0101	5008	,	,		20205	0.0		0.002	False		,,,				2504	0.0				p.I218I		Atlas-SNP	.											.	ENDOG	8	.	0			c.C654T						PASS	.	C	,	338,4068	177.3+/-206.3	10,318,1875	88	78	82		654,	-11.3	0	9	dbSNP_129	82	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous,utr-3	ENDOG,C9orf114	NM_004435.2,NM_016390.2	,	10,323,6170	TT,TC,CC		0.0581,7.6714,2.6372	,	218/298,	131584649	343,12663	2203	4300	6503	SO:0001819	synonymous_variant	2021	exon3			GGTCATCGGCAAG	X79444	CCDS6912.1	9q34.1	2008-06-04			ENSG00000167136	ENSG00000167136			3346	protein-coding gene	gene with protein product		600440				7789991	Standard	NM_004435		Approved		uc004bwc.3	Q14249	OTTHUMG00000020763	ENST00000372642.4:c.654C>T	9.37:g.131584649C>T		105	0	0		107	66	0.616822	NM_004435	Q5T281|Q9BSP2	Silent	SNP	ENST00000372642.4	37	CCDS6912.1																																																																																			C|0.970;T|0.030	0.030	strong		0.592	ENDOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054505.1	NM_004435		T	131584649	C	T	131584649	2	4	22	1	0	0	0	0	0	0	0	1	5117	874	31	1		1	ENDOG	9	131584649	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	116867	131584649	9628782	2171	5072											
NUP188	23511	hgsc.bcm.edu	37	chr9	131755891	131755891	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atcgatactggtgcccacccCtgctgcatcgtgccgccatt	6	10	9	16	3	0	0	0	0	0	0	2	1	0	0	5	1	5	2	5	1	1	2	rs17485583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131755891C>T	ENST00000372577.2	+	27	2956	c.2935C>T	c.(2935-2937)Ctg>Ttg	p.L979L		NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	979					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						GTGCCCACCCCTGCTGCATCG	0.562													C|||	169	0.033746	0.1203	0.0115	5008	,	,		20683	0.0		0.002	False		,,,				2504	0.0				p.L979L		Atlas-SNP	.											.	NUP188	140	.	0			c.C2935T						PASS	.	C		452,3954	218.1+/-236.3	17,418,1768	169	137	148		2935	5.6	1	9	dbSNP_123	148	6,8594	3.7+/-12.6	0,6,4294	no	coding-synonymous	NUP188	NM_015354.1		17,424,6062	TT,TC,CC		0.0698,10.2587,3.5215		979/1750	131755891	458,12548	2203	4300	6503	SO:0001819	synonymous_variant	23511	exon27			CCACCCCTGCTGC	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.2935C>T	9.37:g.131755891C>T		234	0	0		218	140	0.642202	NM_015354	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Silent	SNP	ENST00000372577.2	37	CCDS35156.1																																																																																			C|0.962;T|0.038	0.038	strong		0.562	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2			T	131755891	C	T	131755891	2	4	22	1	0	0	0	0	0	0	0	1	10767	680	24	2		2	NUP188	9	131755891	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	171242	131755891	9457540	2172	5073											
CRAT	1384	hgsc.bcm.edu	37	chr9	131860421	131860421	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	taggtggcacatgcctgtccGtagatcctggtgggaaatgg	8	10	15	8	1	0	1	0	0	0	1	2	2	2	2	3	5	1	2	3	5	3	2	rs16930895	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131860421G>A	ENST00000318080.2	-	11	1629	c.1335C>T	c.(1333-1335)taC>taT	p.Y445Y	RP11-247A12.1_ENST00000434250.1_RNA	NM_000755.3|NM_001257363.1	NP_000746|NP_001244292.1	P43155	CACP_HUMAN	carnitine O-acetyltransferase	445					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)	ATGCCTGTCCGTAGATCCTGG	0.642													G|||	198	0.0395367	0.1445	0.0086	5008	,	,		20455	0.0		0.001	False		,,,				2504	0.0				p.Y445Y		Atlas-SNP	.											.	CRAT	43	.	0			c.C1335T						PASS	.	G		605,3801	264.1+/-265.8	34,537,1632	113	114	114		1335	1.2	0.6	9	dbSNP_123	114	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	CRAT	NM_000755.3		34,540,5929	AA,AG,GG		0.0349,13.7313,4.6748		445/627	131860421	608,12398	2203	4300	6503	SO:0001819	synonymous_variant	1384	exon11			CTGTCCGTAGATC	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.1335C>T	9.37:g.131860421G>A		53	0	0		37	17	0.459459	NM_000755	Q5T952|Q9BW16	Silent	SNP	ENST00000318080.2	37	CCDS6919.1	82	0.037545787545787544	77	0.1565040650406504	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	5.678	0.309678	0.10733	0.137313	3.49E-4	ENSG00000095321	ENST00000455396	.	.	.	5.65	1.21	0.21127	.	.	.	.	.	T	0.00241	0.0007	.	.	.	0.09310	P	0.999999999693856	.	.	.	.	.	.	T	0.10706	-1.0618	3	.	.	.	-22.048	9.4792	0.38891	0.4152:0.0:0.5848:0.0	rs16930895;rs17486087;rs16930895	.	.	.	W	44	.	.	R	-	1	2	CRAT	130900242	0.002000	0.14202	0.565000	0.28409	0.678000	0.39670	-0.028000	0.12350	0.332000	0.23536	0.561000	0.74099	CGG	G|0.943;A|0.057	0.057	strong		0.642	CRAT-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253700.1			A	131860421	G	A	131860421	2	1	22	1	0	0	0	0	0	0	0	1	3849	1140	40	1		1	CRAT	9	131860421	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	104530	131860421	9353010	2173	5074											
C9orf50	375759	hgsc.bcm.edu	37	chr9	132377769	132377769	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctgtctgcttacctgagcGtctgcgctcccagtagcgga	5	11	11	14	3	2	1	0	1	2	0	4	2	4	2	3	1	5	3	3	1	2	2	rs117566704	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:132377769G>A	ENST00000372478.4	-	4	1075	c.874C>T	c.(874-876)Cgc>Tgc	p.R292C	NTMT1_ENST00000372486.1_Intron	NM_199350.3	NP_955382.3	Q5SZB4	CI050_HUMAN	chromosome 9 open reading frame 50	292										central_nervous_system(1)|endometrium(4)|large_intestine(2)|ovary(1)|skin(1)|urinary_tract(1)	10		Ovarian(14;0.00556)				TTACCTGAGCGTCTGCGCTCC	0.642													g|||	3	0.000599042	0.0015	0.0	5008	,	,		18538	0.0		0.0	False		,,,				2504	0.001				p.R292C		Atlas-SNP	.											.	C9orf50	25	.	0			c.C874T						PASS	.		CYS/ARG	11,4395	17.9+/-39.9	0,11,2192	53	45	48		874	0.8	0	9	dbSNP_132	48	0,8600		0,0,4300	yes	missense	C9orf50	NM_199350.3	180	0,11,6492	AA,AG,GG		0.0,0.2497,0.0846	benign	292/432	132377769	11,12995	2203	4300	6503	SO:0001583	missense	375759	exon4			CTGAGCGTCTGCG	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.874C>T	9.37:g.132377769G>A	ENSP00000361556:p.Arg292Cys	62	0	0		63	35	0.555556	NM_199350	Q2M1I2|Q8NA65	Missense_Mutation	SNP	ENST00000372478.4	37	CCDS35159.1	.	.	.	.	.	.	.	.	.	.	g	6.146	0.395061	0.11638	0.002497	0.0	ENSG00000179058	ENST00000372478	T	0.18657	2.2	3.17	0.799	0.18667	.	1.485060	0.04472	N	0.376207	T	0.11196	0.0273	N	0.05124	-0.11	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30238	-0.9985	10	0.46703	T	0.11	1.6017	5.7707	0.18251	0.5791:0.0:0.4209:0.0	.	292	Q5SZB4	CI050_HUMAN	C	292	ENSP00000361556:R292C	ENSP00000361556:R292C	R	-	1	0	C9orf50	131417590	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	0.457000	0.21875	-0.097000	0.12307	-1.479000	0.00991	CGC	A|0.001;C|0.002;G|0.998	0.001	strong		0.642	C9orf50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054593.1	NM_199350		A	132377769	G	A	132377769	3	1	22	1	0	0	0	0	1	0	0	0	2489	1145	40	1	437	1	C9orf50	9	132377769	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	517348	132377769	8835662	2174	5075											
PTGES	9536	hgsc.bcm.edu	37	chr9	132510960	132510960	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagcgttccacgtcggggtcGctcctgcaatactgggggcc	5	8	14	14	4	0	0	0	0	0	0	4	0	2	0	3	4	3	3	3	4	2	2	rs3205181	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:132510960G>A	ENST00000340607.4	-	2	217	c.183C>T	c.(181-183)agC>agT	p.S61S	PTGES_ENST00000481476.1_5'UTR	NM_004878.4	NP_004869.1	O14684	PTGES_HUMAN	prostaglandin E synthase	61					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)				CGTCGGGGTCGCTCCTGCAAT	0.607													G|||	132	0.0263578	0.093	0.0115	5008	,	,		16751	0.0		0.001	False		,,,				2504	0.0				p.S61S		Atlas-SNP	.											.	PTGES	7	.	0			c.C183T						PASS	.	G		367,4039	185.7+/-212.7	14,339,1850	49	42	44		183	-12.2	0	9	dbSNP_105	44	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	PTGES	NM_004878.4		14,345,6144	AA,AG,GG		0.0698,8.3296,2.8679		61/153	132510960	373,12633	2203	4300	6503	SO:0001819	synonymous_variant	9536	exon2			GGGGTCGCTCCTG	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.183C>T	9.37:g.132510960G>A		49	0	0		71	48	0.676056	NM_004878	O14900|Q5SZC0	Silent	SNP	ENST00000340607.4	37	CCDS6927.1																																																																																			G|0.969;A|0.031	0.031	strong		0.607	PTGES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054599.2	NM_004878		A	132510960	G	A	132510960	2	1	22	1	0	0	0	0	0	0	0	1	12759	1078	38	1		1	PTGES	9	132510960	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	133191	132510960	8702471	2175	5076											
GPR107	57720	hgsc.bcm.edu	37	chr9	132854643	132854643	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctgggaccatctggattcaTatccttcgaaaacgacggta	11	11	9	10	3	3	0	1	0	2	0	5	4	4	2	2	3	1	1	2	3	4	4	rs34227818	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:132854643T>C	ENST00000372406.1	+	9	1353	c.846T>C	c.(844-846)caT>caC	p.H282H	GPR107_ENST00000347136.6_Silent_p.H282H|GPR107_ENST00000372410.3_Silent_p.H282H	NM_001136557.1	NP_001130029.1	Q5VW38	GP107_HUMAN	G protein-coupled receptor 107	282						integral component of membrane (GO:0016021)				endometrium(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	11		Ovarian(14;0.000531)				TCTGGATTCATATCCTTCGAA	0.423													T|||	120	0.0239617	0.0825	0.0144	5008	,	,		15888	0.0		0.001	False		,,,				2504	0.0				p.H282H		Atlas-SNP	.											.	GPR107	30	.	0			c.T846C						PASS	.	T	,,	325,4081	173.0+/-202.9	5,315,1883	147	144	145		846,846,846	2.2	1	9	dbSNP_126	145	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous	GPR107	NM_001136557.1,NM_001136558.1,NM_020960.4	,,	5,322,6176	CC,CT,TT		0.0814,7.3763,2.5527	,,	282/601,282/572,282/553	132854643	332,12674	2203	4300	6503	SO:0001819	synonymous_variant	57720	exon9			GATTCATATCCTT	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.846T>C	9.37:g.132854643T>C		163	0	0		203	126	0.62069	NM_001136557	A6NJ53|Q2TB81|Q5JPA3|Q5VW39|Q96T26|Q9H658|Q9HCE8	Silent	SNP	ENST00000372406.1	37	CCDS48041.1																																																																																			T|0.980;C|0.020	0.020	strong		0.423	GPR107-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054643.2			C	132854643	T	C	132854643	2	2	22	1	0	0	0	0	0	0	0	1	6631	1403	49	3		3	GPR107	9	132854643	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	343683	132854643	8358788	2176	5077											
ABL1	25	hgsc.bcm.edu	37	chr9	133759546	133759546	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgcagcagctccttccgggaGatggacggccagccggagcg	7	4	16	14	5	0	1	0	0	0	1	2	4	2	3	4	4	4	3	4	4	0	1	rs34717358	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:133759546G>A	ENST00000318560.5	+	11	2250	c.1869G>A	c.(1867-1869)gaG>gaA	p.E623E		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	623					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)	CCTTCCGGGAGATGGACGGCC	0.602			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"								G|||	116	0.0231629	0.0613	0.0245	5008	,	,		16665	0.0		0.0179	False		,,,				2504	0.0				p.E642E		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.G1926A						PASS	.	G	,	232,4174		6,220,1977	46	56	52		1869,1926	4.7	1	9	dbSNP_126	52	145,8455		0,145,4155	no	coding-synonymous,coding-synonymous	ABL1	NM_005157.4,NM_007313.2	,	6,365,6132	AA,AG,GG		1.686,5.2655,2.8987	,	623/1131,642/1150	133759546	377,12629	2203	4300	6503	SO:0001819	synonymous_variant	25	exon11			CCGGGAGATGGAC	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.1869G>A	9.37:g.133759546G>A		52	0	0		80	63	0.7875	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																			G|0.971;A|0.029	0.029	strong		0.602	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		A	133759546	G	A	133759546	2	1	22	1	0	0	0	0	0	0	0	1	92	933	33	2		2	ABL1	9	133759546	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	904903	133759546	7453885	2177	5078											
ABL1	25	hgsc.bcm.edu	37	chr9	133760592	133760592	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gccacagtccgccaagccgtCggggacccccatcagcccag	8	3	11	19	3	1	0	1	0	0	0	3	1	2	1	7	2	2	0	7	2	1	0	rs2229067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:133760592C>T	ENST00000318560.5	+	11	3296	c.2915C>T	c.(2914-2916)tCg>tTg	p.S972L		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	972	F-actin-binding.|Pro-rich.		S -> L (in dbSNP:rs2229067). {ECO:0000269|PubMed:17344846, ECO:0000269|Ref.4}.		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)	GCCAAGCCGTCGGGGACCCCC	0.672			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"								C|||	93	0.0185703	0.0431	0.0245	5008	,	,		15811	0.0		0.0189	False		,,,				2504	0.0				p.S991L		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.C2972T						PASS	.	C	LEU/SER,LEU/SER	190,4214	111.6+/-149.8	4,182,2016	41	51	48		2915,2972	2.4	0	9	dbSNP_98	48	172,8420	75.7+/-138.4	0,172,4124	yes	missense,missense	ABL1	NM_005157.4,NM_007313.2	145,145	4,354,6140	TT,TC,CC		2.0019,4.3143,2.7855	benign,benign	972/1131,991/1150	133760592	362,12634	2202	4296	6498	SO:0001583	missense	25	exon11			AGCCGTCGGGGAC	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.2915C>T	9.37:g.133760592C>T	ENSP00000323315:p.Ser972Leu	95	0	0		96	60	0.625	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Missense_Mutation	SNP	ENST00000318560.5	37	CCDS35166.1	39	0.017857142857142856	16	0.032520325203252036	9	0.024861878453038673	0	0.0	14	0.018469656992084433	C	9.404	1.078707	0.20227	0.043143	0.020019	ENSG00000097007	ENST00000444970;ENST00000372348;ENST00000318560	T;T	0.11495	2.77;2.77	5.27	2.43	0.29744	F-actin binding (1);	1.170500	0.05873	N	0.625078	T	0.01800	0.0057	N	0.22421	0.69	0.09310	N	1	B;B	0.11235	0.001;0.004	B;B	0.12156	0.004;0.007	T	0.35871	-0.9771	10	0.42905	T	0.14	.	7.9383	0.29944	0.0:0.6637:0.0:0.3363	rs2229067;rs2229067	972;1009	P00519;Q59FK4	ABL1_HUMAN;.	L	787;991;972	ENSP00000361423:S991L;ENSP00000323315:S972L	ENSP00000323315:S972L	S	+	2	0	ABL1	132750413	0.000000	0.05858	0.009000	0.14445	0.707000	0.40811	0.591000	0.23969	0.613000	0.30089	-0.258000	0.10820	TCG	C|0.971;T|0.029	0.029	strong		0.672	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		T	133760592	C	T	133760592	3	4	22	1	0	0	0	0	1	0	0	0	92	893	31	1	3097	1	ABL1	9	133760592	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1046	133760592	7452839	2178	5079											
ABL1	25	hgsc.bcm.edu	37	chr9	133761001	133761001	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgacagcaggcagtggtccAgcggccactcaggacttcag	9	5	14	13	2	2	0	2	0	0	0	3	2	3	1	2	4	2	2	2	4	0	1	rs1056171	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:133761001A>G	ENST00000318560.5	+	11	3705	c.3324A>G	c.(3322-3324)ccA>ccG	p.P1108P		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	1108	F-actin-binding.				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)	GCAGTGGTCCAGCGGCCACTC	0.557			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"								G|||	3276	0.654153	0.882	0.6974	5008	,	,		18771	0.5952		0.4881	False		,,,				2504	0.547				p.P1127P		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	ABL1,scalp,carcinoma,+2,1	ABL1	1632	1	0			c.A3381G						PASS	.	G	,	3592,814	300.1+/-286.2	1470,652,81	29	34	32		3324,3381	-10.5	0.2	9	dbSNP_86	32	4015,4585	586.5+/-392.0	924,2167,1209	no	coding-synonymous,coding-synonymous	ABL1	NM_005157.4,NM_007313.2	,	2394,2819,1290	GG,GA,AA		46.686,18.4748,41.5116	,	1108/1131,1127/1150	133761001	7607,5399	2203	4300	6503	SO:0001819	synonymous_variant	25	exon11			TGGTCCAGCGGCC	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.3324A>G	9.37:g.133761001A>G		141	1	0.0070922		122	122	1	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																			A|0.391;G|0.609	0.609	strong		0.557	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		G	133761001	A	G	133761001	2	3	22	1	0	0	0	0	0	0	0	1	92	175	7	3		3	ABL1	9	133761001	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	409	133761001	7452430	2179	5080											
QRFP	347148	hgsc.bcm.edu	37	chr9	133768921	133768921	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggtcttctcccccgcagcaGggaggaagccggtggcctca	6	7	14	14	2	3	0	1	0	2	0	4	2	3	2	4	5	2	2	4	5	1	1	rs140393161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:133768921G>A	ENST00000343079.1	-	1	304	c.305C>T	c.(304-306)cCt>cTt	p.P102L		NM_198180.1	NP_937823.1			pyroglutamylated RFamide peptide											cervix(1)|endometrium(3)|lung(1)|skin(2)	7	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.17e-05)|Epithelial(140;0.000267)		CCCCGCAGCAGGGAGGAAGCC	0.642													G|||	5	0.000998403	0.0038	0.0	5008	,	,		18404	0.0		0.0	False		,,,				2504	0.0				p.P102L		Atlas-SNP	.											.	QRFP	14	.	0			c.C305T						PASS	.	G	LEU/PRO	4,4400	6.2+/-15.9	0,4,2198	57	63	61		305	0.9	0	9	dbSNP_134	61	0,8600		0,0,4300	yes	missense	QRFP	NM_198180.1	98	0,4,6498	AA,AG,GG		0.0,0.0908,0.0308	benign	102/137	133768921	4,13000	2202	4300	6502	SO:0001583	missense	347148	exon1			GCAGCAGGGAGGA	AB109625	CCDS6936.1	9q34.12	2013-02-28			ENSG00000188710	ENSG00000188710		"Endogenous ligands"	29982	protein-coding gene	gene with protein product	"prepro-QRFP"	609795				12714592, 15808908	Standard	NM_198180		Approved	26RFa, P518	uc011mcb.2	P83859	OTTHUMG00000131663	ENST00000343079.1:c.305C>T	9.37:g.133768921G>A	ENSP00000345487:p.Pro102Leu	98	0	0		105	38	0.361905	NM_198180		Missense_Mutation	SNP	ENST00000343079.1	37	CCDS6936.1	5	0.0022893772893772895	3	0.006097560975609756	2	0.0055248618784530384	0	0.0	0	0.0	G	7.215	0.596183	0.13875	9.08E-4	0.0	ENSG00000188710	ENST00000343079	T	0.41065	1.01	4.12	0.912	0.19349	.	0.654924	0.13732	N	0.366612	T	0.19087	0.0458	L	0.37507	1.11	0.09310	N	1	B	0.14438	0.01	B	0.16289	0.015	T	0.18461	-1.0336	10	0.22109	T	0.4	-0.0237	3.2515	0.06816	0.1026:0.1401:0.4738:0.2835	.	102	P83859	OX26_HUMAN	L	102	ENSP00000345487:P102L	ENSP00000345487:P102L	P	-	2	0	QRFP	132758742	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.074000	0.11450	-0.057000	0.13199	0.313000	0.20887	CCT	G|0.999;A|0.001	0.001	strong		0.642	QRFP-001	KNOWN	mRNA_start_NF|mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254566.1	NM_198180		A	133768921	G	A	133768921	3	1	22	1	0	0	0	0	1	0	0	0	12892	1000	35	2	108	2	QRFP	9	133768921	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	7920	133768921	7444510	2180	5081											
POMT1	10585	hgsc.bcm.edu	37	chr9	134393834	134393834	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgagatgtctttttgcaggaAattgtgaacagaggatctga	12	13	12	4	0	2	4	0	3	2	2	2	7	2	6	0	2	2	1	0	2	2	3	rs62620174	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:134393834A>G	ENST00000372228.3	+	14	1520	c.1341A>G	c.(1339-1341)gaA>gaG	p.E447E	RP11-334J6.6_ENST00000415423.1_RNA|POMT1_ENST00000419118.2_Silent_p.E273E|POMT1_ENST00000423007.1_Silent_p.E425E|POMT1_ENST00000354713.4_Silent_p.E395E|POMT1_ENST00000541219.1_Silent_p.E203E|POMT1_ENST00000485278.1_3'UTR|POMT1_ENST00000341012.7_Silent_p.E371E|POMT1_ENST00000402686.3_Silent_p.E425E|POMT1_ENST00000404875.2_Silent_p.E308E	NM_007171.3	NP_009102	Q9Y6A1	POMT1_HUMAN	protein-O-mannosyltransferase 1	447	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)		TTTTGCAGGAAATTGTGAACA	0.418													A|||	111	0.0221645	0.0794	0.0086	5008	,	,		22316	0.0		0.0	False		,,,				2504	0.0				p.E447E		Atlas-SNP	.											.	POMT1	59	.	0			c.A1341G						PASS	.	A	,,,,	283,4123	154.4+/-187.8	8,267,1928	192	202	198		1275,1113,1275,924,1341	0.8	1	9	dbSNP_129	198	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	POMT1	NM_001077365.1,NM_001077366.1,NM_001136113.1,NM_001136114.1,NM_007171.3	,,,,	8,267,6228	GG,GA,AA		0.0,6.4231,2.1759	,,,,	425/726,371/672,425/726,308/609,447/748	134393834	283,12723	2203	4300	6503	SO:0001819	synonymous_variant	10585	exon14			GCAGGAAATTGTG	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.1341A>G	9.37:g.134393834A>G		110	0	0		115	68	0.591304	NM_007171	B3KQG0|B4DIF0|Q5JT01|Q5JT06|Q5JT08|Q8NC91|Q8TCA9|Q9NX32|Q9NX82|Q9UNT2	Silent	SNP	ENST00000372228.3	37	CCDS6943.1																																																																																			A|0.976;G|0.024	0.024	strong		0.418	POMT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054737.1	NM_007171		G	134393834	A	G	134393834	2	3	22	1	0	0	0	0	0	0	0	1	12254	11	1	3		3	POMT1	9	134393834	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	624913	134393834	6819597	2181	5082											
UCK1	83549	hgsc.bcm.edu	37	chr9	134404337	134404337	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gcgagcacaggtaccggcagGcagaactcctcgaaggccgg	10	3	15	13	4	0	1	0	0	0	1	2	3	1	1	3	5	3	4	3	5	3	1	rs11557925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:134404337G>A	ENST00000372215.4	-	5	690	c.597C>T	c.(595-597)tgC>tgT	p.C199C	UCK1_ENST00000372211.3_Silent_p.C204C|UCK1_ENST00000372210.3_Silent_p.C190C|UCK1_ENST00000459858.1_5'UTR|UCK1_ENST00000372208.3_Intron	NM_001261450.1|NM_001261451.1|NM_031432.2	NP_001248379.1|NP_001248380.1|NP_113620.1	Q9HA47	UCK1_HUMAN	uridine-cytidine kinase 1	199					CTP salvage (GO:0044211)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)	cytosol (GO:0005829)	ATP binding (GO:0005524)|nucleoside kinase activity (GO:0019206)|uridine kinase activity (GO:0004849)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|skin(1)|upper_aerodigestive_tract(1)	6				OV - Ovarian serous cystadenocarcinoma(145;2.34e-05)|Epithelial(140;0.000219)		GTACCGGCAGGCAGAACTCCT	0.602													G|||	111	0.0221645	0.0794	0.0086	5008	,	,		17080	0.0		0.0	False		,,,				2504	0.0				p.C204C	Melanoma(42;523 1129 28385 43975 48113)	Atlas-SNP	.											.	UCK1	29	.	0			c.C612T						PASS	.	G	,	281,4125	153.7+/-187.2	8,265,1930	74	57	63		,597	3.7	1	9	dbSNP_120	63	0,8600		0,0,4300	no	intron,coding-synonymous	UCK1	NM_001135954.1,NM_031432.2	,	8,265,6230	AA,AG,GG		0.0,6.3777,2.1605	,	,199/278	134404337	281,12725	2203	4300	6503	SO:0001819	synonymous_variant	83549	exon5			CGGCAGGCAGAAC	AF237290	CCDS6944.1, CCDS48046.1, CCDS59151.1, CCDS59152.1	9q34.1	2008-02-05			ENSG00000130717	ENSG00000130717	2.7.1.48		14859	protein-coding gene	gene with protein product		609328				11306702	Standard	NM_031432		Approved	URK1, FLJ12255	uc031tfj.1	Q9HA47	OTTHUMG00000020823	ENST00000372215.4:c.597C>T	9.37:g.134404337G>A		34	0	0		35	20	0.571429	NM_001261451	Q5JT09|Q5JT10|Q5JT12|Q5JT13|Q6IA74|Q96BJ0	Silent	SNP	ENST00000372215.4	37	CCDS6944.1																																																																																			G|0.976;A|0.024	0.024	strong		0.602	UCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054726.1	NM_031432		A	134404337	G	A	134404337	2	1	22	1	0	0	0	0	0	0	0	1	16938	1195	42	2		2	UCK1	9	134404337	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	10503	134404337	6809094	2182	5083											
C9orf171	389799	hgsc.bcm.edu	37	chr9	135418389	135418389	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctgaggaagtacaagccGcccgtgaagctggacaccct	11	5	12	13	2	0	2	0	2	0	0	0	4	0	4	3	2	4	3	3	2	4	1	rs61308567	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:135418389G>A	ENST00000343036.2	+	6	843	c.795G>A	c.(793-795)ccG>ccA	p.P265P	C9orf171_ENST00000393216.2_Silent_p.P229P	NM_207417.1	NP_997300.1	Q6ZQR2	CI171_HUMAN	chromosome 9 open reading frame 171	265										large_intestine(7)|lung(9)|ovary(4)|prostate(3)	23						AGTACAAGCCGCCCGTGAAGC	0.602													G|||	245	0.0489217	0.1762	0.0173	5008	,	,		16308	0.0		0.0	False		,,,				2504	0.0				p.P265P		Atlas-SNP	.											.	C9orf171	53	.	0			c.G795A						PASS	.	G		590,3816	262.2+/-264.8	37,516,1650	156	136	143		795	-5.2	0.9	9	dbSNP_129	143	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous	C9orf171	NM_207417.1		37,521,5945	AA,AG,GG		0.0581,13.3908,4.5748		265/321	135418389	595,12411	2203	4300	6503	SO:0001819	synonymous_variant	389799	exon6			CAAGCCGCCCGTG	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.795G>A	9.37:g.135418389G>A		88	0	0		68	68	1	NM_207417	Q147X1	Silent	SNP	ENST00000343036.2	37	CCDS6949.1																																																																																			G|0.948;A|0.052	0.052	strong		0.602	C9orf171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254589.1	NM_207417		A	135418389	G	A	135418389	2	1	22	1	0	0	0	0	0	0	0	1	2472	1074	38	1		1	C9orf171	9	135418389	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1014052	135418389	5795042	2183	5084											
DDX31	64794	hgsc.bcm.edu	37	chr9	135493792	135493792	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgtctgcaagactgtggctcGctctcggatttcctgggggc	4	11	14	12	3	2	1	0	0	2	1	5	2	3	2	1	4	1	3	1	4	1	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:135493792G>A	ENST00000372159.3	-	18	2216	c.2065C>T	c.(2065-2067)Cga>Tga	p.R689*	DDX31_ENST00000438527.3_Nonsense_Mutation_p.R560*|DDX31_ENST00000372153.1_Intron	NM_022779.7	NP_073616.6	Q9H8H2	DDX31_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 31	689						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)		ACTGTGGCTCGCTCTCGGATT	0.507																																					p.R689X		Atlas-SNP	.											.	DDX31	76	.	0			c.C2065T						PASS	.						105	93	97					9																	135493792		2203	4300	6503	SO:0001587	stop_gained	64794	exon18			TGGCTCGCTCTCG	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.2065C>T	9.37:g.135493792G>A	ENSP00000361232:p.Arg689*	129	0	0		120	48	0.4	NM_022779	Q5K6N2|Q5K6N3|Q5K6N4|Q5VZJ4|Q5VZJ9|Q96E91|Q96NY2|Q96SX5|Q9H5K6	Nonsense_Mutation	SNP	ENST00000372159.3	37	CCDS6951.1	.	.	.	.	.	.	.	.	.	.	G	40	8.126157	0.98667	.	.	ENSG00000125485	ENST00000372159;ENST00000372155;ENST00000438527	.	.	.	5.7	5.7	0.88788	.	0.264197	0.35320	N	0.003292	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	-6.5596	13.6113	0.62080	0.0:0.0:0.8456:0.1544	.	.	.	.	X	689;689;560	.	ENSP00000361228:R689X	R	-	1	2	DDX31	134483613	1.000000	0.71417	0.965000	0.40720	0.956000	0.61745	3.757000	0.55212	2.686000	0.91538	0.591000	0.81541	CGA	.	.	none		0.507	DDX31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054794.1	NM_138620		A	135493792	G	A	135493792	4	1	22	1	0	0	0	0	0	1	0	0	4358	1095	38	1	502	1	DDX31	9	135493792	Nonsense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	75403	135493792	5719639	2184	5085											
C9orf98	158067	hgsc.bcm.edu	37	chr9	135601126	135601126	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atcccactctcgatgtattcGaagactgtgtatgggtcctg	8	13	10	10	2	1	1	0	0	1	1	5	3	3	1	2	1	0	2	2	1	3	3	rs28477720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:135601126G>A	ENST00000298545.3	-	13	1910	c.1389C>T	c.(1387-1389)ttC>ttT	p.F463F	AK8_ENST00000477396.1_5'UTR	NM_152572.2	NP_689785.1	Q96MA6	KAD8_HUMAN	adenylate kinase 8	463	Adenylate kinase 2.				nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			NS(1)|kidney(2)|large_intestine(4)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(2)	23						CGATGTATTCGAAGACTGTGT	0.532													G|||	151	0.0301518	0.1089	0.0086	5008	,	,		18753	0.0		0.001	False		,,,				2504	0.0				p.F463F		Atlas-SNP	.											.	AK8	45	.	0			c.C1389T						PASS	.	G		452,3954		24,404,1775	80	61	67		1389	-1.5	0.8	9	dbSNP_125	67	3,8597		0,3,4297	no	coding-synonymous	AK8	NM_152572.2		24,407,6072	AA,AG,GG		0.0349,10.2587,3.4984		463/480	135601126	455,12551	2203	4300	6503	SO:0001819	synonymous_variant	158067	exon13			GTATTCGAAGACT	AK093446	CCDS6954.1	9q34.13	2013-04-29	2010-12-07	2010-12-07	ENSG00000165695	ENSG00000165695	2.7.4.3	"Adenylate kinases"	26526	protein-coding gene	gene with protein product		615365	"chromosome 9 open reading frame 98"	C9orf98		21080915	Standard	NM_152572		Approved	FLJ32704	uc004cbu.1	Q96MA6	OTTHUMG00000021009	ENST00000298545.3:c.1389C>T	9.37:g.135601126G>A		127	0	0		117	89	0.760684	NM_152572	A8K821|Q8N9W9	Silent	SNP	ENST00000298545.3	37	CCDS6954.1																																																																																			G|0.966;A|0.034	0.034	strong		0.532	AK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055413.1	NM_152572		A	135601126	G	A	135601126	2	1	22	1	0	0	0	0	0	0	0	1	2511	1049	37	1		1	C9orf98	9	135601126	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	107334	135601126	5612305	2185	5086											
GFI1B	8328	hgsc.bcm.edu	37	chr9	135864547	135864547	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcggcaaaaccttcggccacGctgtgagcctggagcagcac	9	5	13	14	3	0	1	0	1	0	0	1	2	0	2	3	3	4	4	3	3	2	1	rs62638686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:135864547G>A	ENST00000339463.3	+	9	1429	c.610G>A	c.(610-612)Gct>Act	p.A204T	GFI1B_ENST00000372124.1_Intron|GFI1B_ENST00000450530.1_Missense_Mutation_p.A204T|GFI1B_ENST00000372123.1_Intron|GFI1B_ENST00000534944.1_Intron|GFI1B_ENST00000372122.1_Missense_Mutation_p.A204T			Q5VTD9	GFI1B_HUMAN	growth factor independent 1B transcription repressor	204	Interaction with ARIH2.|Mediates interaction with GATA1.				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)		CTTCGGCCACGCTGTGAGCCT	0.662													G|||	75	0.014976	0.0537	0.0043	5008	,	,		19398	0.0		0.001	False		,,,				2504	0.0				p.A204T		Atlas-SNP	.											.	GFI1B	37	.	0			c.G610A						PASS	.	G	,THR/ALA	228,4178	134.5+/-170.7	6,216,1981	63	50	55		,610	2.5	0.3	9	dbSNP_129	55	3,8597	2.2+/-6.3	0,3,4297	yes	intron,missense	GFI1B	NM_001135031.1,NM_004188.4	,58	6,219,6278	AA,AG,GG		0.0349,5.1748,1.7761	,benign	,204/331	135864547	231,12775	2203	4300	6503	SO:0001583	missense	8328	exon5			GGCCACGCTGTGA	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.610G>A	9.37:g.135864547G>A	ENSP00000344782:p.Ala204Thr	112	0	0		121	41	0.338843	NM_004188	O95270|Q5VTD8|Q6FHZ2|Q6T888	Missense_Mutation	SNP	ENST00000339463.3	37	CCDS6957.1	38	0.0173992673992674	34	0.06910569105691057	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	G	13.62	2.290120	0.40494	0.051748	3.49E-4	ENSG00000165702	ENST00000339463;ENST00000450530;ENST00000372122	T;T;T	0.07800	3.16;3.16;3.16	5.42	2.45	0.29901	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.129163	0.51477	D	0.000098	T	0.00524	0.0017	N	0.21142	0.635	0.47245	D	0.99936	B	0.30727	0.292	B	0.31812	0.136	T	0.44877	-0.9299	10	0.72032	D	0.01	-23.2176	14.0232	0.64571	0.0:0.0:0.6057:0.3943	rs62638686	204	Q5VTD9	GFI1B_HUMAN	T	204	ENSP00000344782:A204T;ENSP00000409546:A204T;ENSP00000361195:A204T	ENSP00000344782:A204T	A	+	1	0	GFI1B	134854368	1.000000	0.71417	0.338000	0.25549	0.016000	0.09150	4.773000	0.62331	0.649000	0.30751	-0.122000	0.15005	GCT	A|0.017;G|0.983;T|0.000	0.017	strong		0.662	GFI1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393840.1	NM_004188		A	135864547	G	A	135864547	3	1	22	1	0	0	0	0	1	0	0	0	6348	1087	38	1	624	1	GFI1B	9	135864547	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	263421	135864547	5348884	2186	5087											
RALGDS	5900	hgsc.bcm.edu	37	chr9	135974054	135974054	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctccgtgcttgaccttcaCtcccttggtgaaggtccgct	4	12	11	14	2	1	2	1	2	0	0	4	2	4	2	4	3	1	3	4	3	1	3	rs143209866	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:135974054C>T	ENST00000372050.3	-	18	2686	c.2665G>A	c.(2665-2667)Gtg>Atg	p.V889M	RALGDS_ENST00000542690.1_Missense_Mutation_p.V960M|RALGDS_ENST00000393160.3_Missense_Mutation_p.V834M|RALGDS_ENST00000372047.3_Missense_Mutation_p.V877M|RALGDS_ENST00000372062.3_Missense_Mutation_p.V860M|RALGDS_ENST00000393157.3_Missense_Mutation_p.V888M|RALGDS_ENST00000469972.1_5'UTR	NM_006266.2	NP_006257.1	Q12967	GNDS_HUMAN	ral guanine nucleotide dissociation stimulator	889					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)		TTGACCTTCACTCCCTTGGTG	0.542			T	CIITA	"PMBL, Hodgkin Lymphona, "								C|||	4	0.000798722	0.003	0.0	5008	,	,		21550	0.0		0.0	False		,,,				2504	0.0				p.V889M	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.G2665A						PASS	.	C	MET/VAL,MET/VAL	19,4387	26.2+/-53.5	0,19,2184	116	93	100		2500,2665	2.5	0.8	9	dbSNP_134	100	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	RALGDS	NM_001042368.1,NM_006266.2	21,21	0,20,6483	TT,TC,CC		0.0116,0.4312,0.1538	possibly-damaging,possibly-damaging	834/860,889/915	135974054	20,12986	2203	4300	6503	SO:0001583	missense	5900	exon18			CCTTCACTCCCTT	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.2665G>A	9.37:g.135974054C>T	ENSP00000361120:p.Val889Met	132	0	0		189	65	0.343915	NM_006266	B7Z753|E7ER93|E7ERZ0|Q5T7V4|Q6KH11|Q6PCE1|Q6ZSD5|Q9HAX7|Q9HAY1|Q9HCT1|Q9P2N8	Missense_Mutation	SNP	ENST00000372050.3	37	CCDS6959.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	10.20	1.285630	0.23478	0.004312	1.16E-4	ENSG00000160271	ENST00000372050;ENST00000372047;ENST00000393160;ENST00000393157;ENST00000542690;ENST00000372062	T;T;T;T;T;T	0.40476	1.52;1.04;1.52;1.5;1.68;1.03	5.37	2.55	0.30701	.	0.458064	0.20879	N	0.084033	T	0.34716	0.0907	L	0.46157	1.445	0.19945	N	0.999946	B;P;P;P;P;B	0.51240	0.349;0.943;0.694;0.758;0.943;0.35	B;B;B;B;B;B	0.41271	0.057;0.352;0.295;0.173;0.352;0.077	T	0.18053	-1.0349	10	0.72032	D	0.01	.	9.9724	0.41763	0.0:0.7793:0.0:0.2207	.	960;860;834;888;877;889	F5H6M6;E7ER93;Q6KH11;E7ERZ0;Q6PCE1;Q12967	.;.;.;.;.;GNDS_HUMAN	M	889;877;834;888;960;860	ENSP00000361120:V889M;ENSP00000361117:V877M;ENSP00000376867:V834M;ENSP00000376864:V888M;ENSP00000437518:V960M;ENSP00000361132:V860M	ENSP00000361117:V877M	V	-	1	0	RALGDS	134963875	0.000000	0.05858	0.797000	0.32132	0.292000	0.27327	0.038000	0.13862	0.259000	0.21709	0.561000	0.74099	GTG	C|0.998;T|0.002	0.002	strong		0.542	RALGDS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054837.1	NM_006266		T	135974054	C	T	135974054	3	4	22	1	0	0	0	0	1	0	0	0	13031	565	20	2	83	2	RALGDS	9	135974054	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	109507	135974054	5239377	2187	5088											
GBGT1	26301	hgsc.bcm.edu	37	chr9	136029474	136029474	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tccatccggcgcatggatgtCtcctcccagtgggagtgacc	6	9	12	14	2	1	1	0	1	1	0	5	3	4	3	5	3	0	1	5	3	0	0	rs35808997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136029474C>T	ENST00000372040.3	-	7	845	c.534G>A	c.(532-534)gaG>gaA	p.E178E	RALGDS_ENST00000542690.1_Intron|GBGT1_ENST00000372038.3_3'UTR|GBGT1_ENST00000472281.1_5'UTR|GBGT1_ENST00000372043.3_Missense_Mutation_p.R172K|GBGT1_ENST00000540636.1_Silent_p.E161E	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	178					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)		GCATGGATGTCTCCTCCCAGT	0.607													C|||	364	0.0726837	0.2632	0.0202	5008	,	,		17590	0.0		0.002	False		,,,				2504	0.0				p.E178E		Atlas-SNP	.											.	GBGT1	25	.	0			c.G534A						PASS	.	C		957,3449	360.1+/-315.1	109,739,1355	59	47	51		534	2.9	0.6	9	dbSNP_126	51	6,8592	4.3+/-15.6	0,6,4293	no	coding-synonymous	GBGT1	NM_021996.4		109,745,5648	TT,TC,CC		0.0698,21.7204,7.4054		178/348	136029474	963,12041	2203	4299	6502	SO:0001819	synonymous_variant	26301	exon7			GGATGTCTCCTCC	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.534G>A	9.37:g.136029474C>T		88	0	0		118	69	0.584746	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Silent	SNP	ENST00000372040.3	37	CCDS6960.1	115	0.052655677655677656	109	0.22154471544715448	6	0.016574585635359115	0	0.0	0	0.0	C	6.220	0.408804	0.11812	0.217204	6.98E-4	ENSG00000148288	ENST00000372043	T	0.22134	1.97	5.16	2.91	0.33838	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999742809	.	.	.	.	.	.	T	0.13575	-1.0504	5	0.87932	D	0	-9.1051	9.1909	0.37197	0.0:0.6371:0.2769:0.086	rs35808997;rs62638706	.	.	.	K	172	ENSP00000361113:R172K	ENSP00000361113:R172K	R	-	2	0	GBGT1	135019295	0.950000	0.32346	0.650000	0.29550	0.003000	0.03518	0.078000	0.14761	1.145000	0.42336	-0.479000	0.04858	AGA	C|0.934;T|0.066	0.066	strong		0.607	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996		T	136029474	C	T	136029474	2	4	22	1	0	0	0	0	0	0	0	1	6280	912	32	2		2	GBGT1	9	136029474	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	55420	136029474	5183957	2188	5089											
MED22	6837	hgsc.bcm.edu	37	chr9	136208405	136208405	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcatgggagtgggcaggggCtgccacctgtagggggccag	7	5	20	9	0	0	0	0	0	0	0	0	1	0	1	3	6	2	4	3	6	1	1	rs145653063	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136208405C>T	ENST00000491289.1	-	5	1134	c.553G>A	c.(553-555)Gcc>Acc	p.A185T	MED22_ENST00000471524.1_5'Flank|MED22_ENST00000344469.5_3'UTR|MED22_ENST00000476080.1_3'UTR|MED22_ENST00000343730.5_Missense_Mutation_p.A185T			Q15528	MED22_HUMAN	mediator complex subunit 22	185						cytoplasm (GO:0005737)|mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			endometrium(1)|large_intestine(1)|ovary(1)|urinary_tract(1)	4				OV - Ovarian serous cystadenocarcinoma(145;1.14e-06)|Epithelial(140;8.2e-06)|all cancers(34;6.94e-05)		TGGGCAGGGGCTGCCACCTGT	0.677													C|||	52	0.0103834	0.0378	0.0029	5008	,	,		15147	0.0		0.0	False		,,,				2504	0.0				p.A185T		Atlas-SNP	.											.	MED22	13	.	0			c.G553A						PASS	.	C	THR/ALA,	116,4286	85.3+/-124.0	2,112,2087	22	26	25		553,	1.2	0	9	dbSNP_134	25	5,8589	3.7+/-12.6	0,5,4292	no	missense,utr-3	MED22	NM_133640.3,NM_181491.1	58,	2,117,6379	TT,TC,CC		0.0582,2.6352,0.9311	benign,	185/201,	136208405	121,12875	2201	4297	6498	SO:0001583	missense	6837	exon5			CAGGGGCTGCCAC		CCDS6963.1, CCDS6964.1	9q34.1	2008-02-05	2007-07-30	2007-07-30	ENSG00000148297	ENSG00000148297			11477	protein-coding gene	gene with protein product		185641	"surfeit 5"	SURF5		8499913, 15175163	Standard	NM_133640		Approved	Med24	uc004cdc.3	Q15528	OTTHUMG00000020869	ENST00000491289.1:c.553G>A	9.37:g.136208405C>T	ENSP00000420393:p.Ala185Thr	106	0	0		115	39	0.33913	NM_133640	B3KW83|B3KWX4|O76072|Q5T8U0	Missense_Mutation	SNP	ENST00000491289.1	37	CCDS6963.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	C	0.576	-0.838931	0.02692	0.026352	5.82E-4	ENSG00000148297	ENST00000491289;ENST00000343730	.	.	.	4.15	1.23	0.21249	.	0.579278	0.18389	N	0.142701	T	0.02418	0.0074	N	0.04880	-0.145	0.18873	N	0.999985	B	0.02656	0.0	B	0.01281	0.0	T	0.23154	-1.0196	9	0.05620	T	0.96	-4.6055	2.9823	0.05957	0.1951:0.4783:0.0:0.3266	.	185	Q15528	MED22_HUMAN	T	185	.	ENSP00000342343:A185T	A	-	1	0	MED22	135198226	0.879000	0.30193	0.041000	0.18516	0.049000	0.14656	1.605000	0.36815	0.146000	0.19002	0.563000	0.77884	GCC	C|0.989;T|0.011	0.011	strong		0.677	MED22-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054898.2	NM_133640		T	136208405	C	T	136208405	3	4	22	1	0	0	0	0	1	0	0	0	9449	797	28	2	53	2	MED22	9	136208405	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	178931	136208405	5005026	2189	5090											
DBH	1621	hgsc.bcm.edu	37	chr9	136521749	136521749	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtggacgccggcttcctgcaGaagtacttccacctcatcaa	9	9	9	14	2	2	1	2	0	0	1	4	2	4	2	4	2	2	3	4	2	3	3	rs78516399	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136521749G>A	ENST00000393056.2	+	10	1551	c.1539G>A	c.(1537-1539)caG>caA	p.Q513Q	DBH-AS1_ENST00000425189.1_RNA	NM_000787.3	NP_000778.3	P09172	DOPO_HUMAN	dopamine beta-hydroxylase (dopamine beta-monooxygenase)	513					behavioral response to ethanol (GO:0048149)|blood vessel remodeling (GO:0001974)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cytokine production (GO:0001816)|dopamine catabolic process (GO:0042420)|fear response (GO:0042596)|glucose homeostasis (GO:0042593)|homoiothermy (GO:0042309)|leukocyte mediated immunity (GO:0002443)|leukocyte migration (GO:0050900)|locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|memory (GO:0007613)|norepinephrine biosynthetic process (GO:0042421)|positive regulation of vasoconstriction (GO:0045907)|regulation of cell proliferation (GO:0042127)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|response to amphetamine (GO:0001975)|response to pain (GO:0048265)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|secretory granule lumen (GO:0034774)	catalytic activity (GO:0003824)|copper ion binding (GO:0005507)|dopamine beta-monooxygenase activity (GO:0004500)|L-ascorbic acid binding (GO:0031418)			central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	36				OV - Ovarian serous cystadenocarcinoma(145;2.33e-07)|Epithelial(140;1.5e-06)|all cancers(34;1.66e-05)	Disulfiram(DB00822)|Dopamine(DB00988)|Propylthiouracil(DB00550)|Vitamin C(DB00126)	GCTTCCTGCAGAAGTACTTCC	0.622													G|||	33	0.00658946	0.025	0.0	5008	,	,		17798	0.0		0.0	False		,,,				2504	0.0				p.Q513Q		Atlas-SNP	.											.	DBH	86	.	0			c.G1539A						PASS	.	G		77,4329	68.7+/-106.4	0,77,2126	47	44	45		1539	1.7	1	9	dbSNP_131	45	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DBH	NM_000787.3		0,78,6425	AA,AG,GG		0.0116,1.7476,0.5997		513/618	136521749	78,12928	2203	4300	6503	SO:0001819	synonymous_variant	1621	exon10			CCTGCAGAAGTAC	X13256	CCDS6977.2	9q34	2013-06-03			ENSG00000123454	ENSG00000123454	1.14.17.1		2689	protein-coding gene	gene with protein product		609312					Standard	NM_000787		Approved	DBM	uc004cel.3	P09172	OTTHUMG00000020878	ENST00000393056.2:c.1539G>A	9.37:g.136521749G>A		52	0	0		31	18	0.580645	NM_000787	Q5T381|Q96AG2	Silent	SNP	ENST00000393056.2	37	CCDS6977.2																																																																																			G|0.993;A|0.007	0.007	strong		0.622	DBH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054929.2	NM_000787		A	136521749	G	A	136521749	2	1	22	1	0	0	0	0	0	0	0	1	4252	933	33	2		2	DBH	9	136521749	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	313344	136521749	4691682	2190	5091											
SARDH	1757	hgsc.bcm.edu	37	chr9	136535746	136535746	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caggcgccggcggaggcctgCggcccgctgctgctccaggg	3	4	18	16	5	0	0	0	0	0	0	1	1	1	1	4	6	3	3	4	6	0	0	rs61685718	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136535746C>T	ENST00000371872.4	-	19	2712	c.2455G>A	c.(2455-2457)Gca>Aca	p.A819T	SARDH_ENST00000439388.1_Missense_Mutation_p.A819T|SARDH_ENST00000422262.2_Missense_Mutation_p.A651T|SARDH_ENST00000371868.1_Missense_Mutation_p.A247T	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	819					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)		CGGAGGCCTGCGGCCCGCTGC	0.697													C|||	75	0.014976	0.0545	0.0043	5008	,	,		13059	0.0		0.0	False		,,,				2504	0.0				p.A819T		Atlas-SNP	.											SARDH,colon,carcinoma,0,1	SARDH	112	1	0			c.G2455A						PASS	.	C	THR/ALA,THR/ALA	197,4115		3,191,1962	11	11	11		2455,2455	-10	0	9	dbSNP_129	11	6,8490		0,6,4242	yes	missense,missense	SARDH	NM_001134707.1,NM_007101.3	58,58	3,197,6204	TT,TC,CC		0.0706,4.5686,1.5849	benign,benign	819/919,819/919	136535746	203,12605	2156	4248	6404	SO:0001583	missense	1757	exon19			GGCCTGCGGCCCG		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.2455G>A	9.37:g.136535746C>T	ENSP00000360938:p.Ala819Thr	107	0	0		119	41	0.344538	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Missense_Mutation	SNP	ENST00000371872.4	37	CCDS6978.1	27	0.012362637362637362	24	0.04878048780487805	3	0.008287292817679558	0	0.0	0	0.0	C	5.568	0.289698	0.10567	0.045686	7.06E-4	ENSG00000123453	ENST00000371872;ENST00000371868;ENST00000439388;ENST00000422262	T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05	5.01	-10.0	0.00425	Glycine cleavage T-protein, C-terminal barrel (1);	1.295140	0.05116	N	0.489711	T	0.12774	0.0310	N	0.11131	0.1	0.09310	N	0.999999	B;B	0.09022	0.001;0.002	B;B	0.13407	0.005;0.009	T	0.26224	-1.0109	10	0.30854	T	0.27	5.8048	0.49	0.00562	0.358:0.2261:0.1855:0.2303	rs61685718;rs61745311	819;247	Q9UL12;Q5SYV2	SARDH_HUMAN;.	T	819;247;819;651	ENSP00000360938:A819T;ENSP00000360934:A247T;ENSP00000403084:A819T;ENSP00000415537:A651T	ENSP00000360934:A247T	A	-	1	0	SARDH	135525567	0.000000	0.05858	0.000000	0.03702	0.480000	0.33159	-0.744000	0.04839	-2.619000	0.00441	-0.485000	0.04761	GCA	C|0.987;T|0.013	0.013	strong		0.697	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1			T	136535746	C	T	136535746	3	4	22	1	0	0	0	0	1	0	0	0	13856	768	27	1	313	1	SARDH	9	136535746	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	13997	136535746	4677685	2191	5092											
SARDH	1757	hgsc.bcm.edu	37	chr9	136577770	136577770	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tagccatgcatgtccttctcCgggcgcccatggatgatcca	7	10	10	14	2	1	1	0	1	1	0	4	2	3	2	5	2	2	1	5	2	1	2	rs147188337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136577770C>T	ENST00000371872.4	-	10	1556	c.1299G>A	c.(1297-1299)ccG>ccA	p.P433P	SARDH_ENST00000439388.1_Silent_p.P433P|SARDH_ENST00000422262.2_Silent_p.P265P	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	433					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)		TGTCCTTCTCCGGGCGCCCAT	0.642													C|||	12	0.00239617	0.0091	0.0	5008	,	,		16347	0.0		0.0	False		,,,				2504	0.0				p.P433P		Atlas-SNP	.											.	SARDH	112	.	0			c.G1299A						PASS	.	C	,	54,4352	54.9+/-90.9	0,54,2149	69	68	69		1299,1299	-9.4	0.5	9	dbSNP_134	69	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	SARDH	NM_001134707.1,NM_007101.3	,	0,55,6448	TT,TC,CC		0.0116,1.2256,0.4229	,	433/919,433/919	136577770	55,12951	2203	4300	6503	SO:0001819	synonymous_variant	1757	exon10			CTTCTCCGGGCGC		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.1299G>A	9.37:g.136577770C>T		59	0	0		58	42	0.724138	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Silent	SNP	ENST00000371872.4	37	CCDS6978.1																																																																																			C|0.996;T|0.004	0.004	strong		0.642	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1			T	136577770	C	T	136577770	2	4	22	1	0	0	0	0	0	0	0	1	13856	639	23	1		1	SARDH	9	136577770	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	42024	136577770	4635661	2192	5093											
SARDH	1757	hgsc.bcm.edu	37	chr9	136595253	136595253	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccacacccgcgacccgccgCaccccaaaatcatccgtcca	10	4	5	22	5	1	0	1	0	0	0	4	1	4	0	8	0	0	1	8	0	2	0	rs35457000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136595253C>T	ENST00000371872.4	-	5	1004	c.747G>A	c.(745-747)gtG>gtA	p.V249V	SARDH_ENST00000298628.5_Silent_p.V249V|SARDH_ENST00000439388.1_Silent_p.V249V|SARDH_ENST00000371867.1_Silent_p.V160V|SARDH_ENST00000422262.2_Silent_p.V81V	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	249					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)		CGACCCGCCGCACCCCAAAAT	0.577													C|||	82	0.0163738	0.0598	0.0043	5008	,	,		17220	0.0		0.0	False		,,,				2504	0.0				p.V249V		Atlas-SNP	.											.	SARDH	112	.	0			c.G747A						PASS	.	C	,	174,4232	114.6+/-152.6	5,164,2034	92	85	88		747,747	3.1	1	9	dbSNP_126	88	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	SARDH	NM_001134707.1,NM_007101.3	,	5,166,6332	TT,TC,CC		0.0233,3.9492,1.3532	,	249/919,249/919	136595253	176,12830	2203	4300	6503	SO:0001819	synonymous_variant	1757	exon5			CCGCCGCACCCCA		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.747G>A	9.37:g.136595253C>T		128	0	0		113	40	0.353982	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Silent	SNP	ENST00000371872.4	37	CCDS6978.1																																																																																			C|0.985;T|0.015	0.015	strong		0.577	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1			T	136595253	C	T	136595253	2	4	22	1	0	0	0	0	0	0	0	1	13856	697	25	2		2	SARDH	9	136595253	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	17483	136595253	4618178	2193	5094											
VAV2	7410	hgsc.bcm.edu	37	chr9	136640122	136640122	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcaggtaggtcccgctggcGtgggacttgagcaggttgtc	6	10	16	9	2	1	1	1	1	0	0	3	2	2	2	1	5	1	4	1	5	1	3	rs7875953	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136640122G>A	ENST00000371850.3	-	25	2101	c.2070C>T	c.(2068-2070)caC>caT	p.H690H	VAV2_ENST00000371851.1_Silent_p.H680H|VAV2_ENST00000406606.3_Silent_p.H680H	NM_001134398.1	NP_001127870.1	P52735	VAV2_HUMAN	vav 2 guanine nucleotide exchange factor	690	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(1)	35				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)		TCCCGCTGGCGTGGGACTTGA	0.617													G|||	132	0.0263578	0.0923	0.0115	5008	,	,		18617	0.0		0.002	False		,,,				2504	0.0				p.H690H		Atlas-SNP	.											VAV2_ENST00000371850,colon,carcinoma,0,2	VAV2	165	2	0			c.C2070T						PASS	.	G	,	426,3980	207.2+/-228.6	26,374,1803	71	64	66		2070,2040	-3.2	1	9	dbSNP_116	66	5,8593	3.0+/-9.4	0,5,4294	no	coding-synonymous,coding-synonymous	VAV2	NM_001134398.1,NM_003371.3	,	26,379,6097	AA,AG,GG		0.0582,9.6686,3.3144	,	690/879,680/840	136640122	431,12573	2203	4299	6502	SO:0001819	synonymous_variant	7410	exon25			GCTGGCGTGGGAC		CCDS6979.1, CCDS48053.1	9q34.1	2013-02-14	2007-07-25		ENSG00000160293	ENSG00000160293		"Rho guanine nucleotide exchange factors", "Pleckstrin homology (PH) domain containing", "SH2 domain containing"	12658	protein-coding gene	gene with protein product		600428	"vav 2 oncogene"			7762982	Standard	NM_003371		Approved		uc004ces.3	P52735	OTTHUMG00000020882	ENST00000371850.3:c.2070C>T	9.37:g.136640122G>A		102	0	0		135	86	0.637037	NM_001134398	A2RUM4|A8MQ12|B6ZDF5|Q5SYV3|Q5SYV4|Q5SYV5|Q6N012|Q6PIJ9|Q6Q317	Silent	SNP	ENST00000371850.3	37	CCDS48053.1																																																																																			G|0.963;A|0.037	0.037	strong		0.617	VAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054939.1			A	136640122	G	A	136640122	2	1	22	1	0	0	0	0	0	0	0	1	17147	1136	40	1		1	VAV2	9	136640122	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	44869	136640122	4573309	2194	5095											
COL5A1	1289	hgsc.bcm.edu	37	chr9	137630361	137630361	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctggcccagaaggccccgcGgtgagtatccggctttatcc	6	8	12	15	3	0	2	0	1	0	1	2	2	2	2	6	4	0	2	6	4	3	3	rs61729545	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:137630361G>A	ENST00000371817.3	+	10	1845	c.1431G>A	c.(1429-1431)gcG>gcA	p.A477A		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	477	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)		AAGGCCCCGCGGTGAGTATCC	0.637													G|||	351	0.0700879	0.2549	0.0202	5008	,	,		15920	0.0		0.0	False		,,,				2504	0.0				p.A477A		Atlas-SNP	.											COL5A1,NS,carcinoma,+1,1	COL5A1	323	1	0			c.G1431A						PASS	.	G		894,3512	343.1+/-307.5	90,714,1399	42	46	44		1431	-5.2	0.9	9	dbSNP_129	44	13,8587	7.1+/-27.0	0,13,4287	yes	coding-synonymous-near-splice	COL5A1	NM_000093.3		90,727,5686	AA,AG,GG		0.1512,20.2905,6.9737		477/1839	137630361	907,12099	2203	4300	6503	SO:0001630	splice_region_variant	1289	exon10			CCCCGCGGTGAGT	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.1431+1G>A	9.37:g.137630361G>A		128	0	0		160	100	0.625	NM_000093	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	37	CCDS6982.1																																																																																			G|0.937;A|0.063	0.063	strong		0.637	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	Silent	A	137630361	G	A	137630361	5	1	22	1	0	0	0	0	0	0	1	0	3698	1130	39	1	1469	1	COL5A1	9	137630361	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	990239	137630361	3583070	2195	5096											
KIAA0649	9858	hgsc.bcm.edu	37	chr9	138378308	138378308	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgaggccctgggaggggaggGcaccgccaggggccctggcg	5	3	21	12	2	0	1	0	1	0	0	0	3	0	3	4	8	0	1	4	8	0	0	rs35142799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:138378308G>A	ENST00000356818.2	+	4	2501	c.1952G>A	c.(1951-1953)gGc>gAc	p.G651D	PPP1R26_ENST00000604351.1_Missense_Mutation_p.G651D|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000605660.1_Missense_Mutation_p.G651D|PPP1R26_ENST00000401470.3_Missense_Mutation_p.G651D|PPP1R26_ENST00000605286.1_Missense_Mutation_p.G651D	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	651					negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										GGAGGGGAGGGCACCGCCAGG	0.652													G|||	36	0.0071885	0.0272	0.0	5008	,	,		17736	0.0		0.0	False		,,,				2504	0.0				p.G651D		Atlas-SNP	.											.	.	.	.	0			c.G1952A						PASS	.	G	ASP/GLY	100,4300	73.1+/-111.1	1,98,2101	29	33	31		1952	0.7	0	9	dbSNP_126	31	0,8600		0,0,4300	no	missense	KIAA0649	NM_014811.3	94	1,98,6401	AA,AG,GG		0.0,2.2727,0.7692	benign	651/1210	138378308	100,12900	2200	4300	6500	SO:0001583	missense	9858	exon4			GGGAGGGCACCGC	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.1952G>A	9.37:g.138378308G>A	ENSP00000349274:p.Gly651Asp	120	0	0		147	107	0.727891	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Missense_Mutation	SNP	ENST00000356818.2	37	CCDS6988.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	3.546	-0.092690	0.07053	0.022727	0.0	ENSG00000196422	ENST00000356818	T	0.20738	2.05	4.34	0.693	0.18056	.	0.864323	0.09973	N	0.732016	T	0.07143	0.0181	L	0.29908	0.895	0.09310	N	1	B	0.16396	0.017	B	0.12156	0.007	T	0.26189	-1.0110	10	0.52906	T	0.07	-15.8819	6.8421	0.23969	0.1852:0.6278:0.187:0.0	rs35142799	651	Q5T8A7	PPR26_HUMAN	D	651	ENSP00000349274:G651D	ENSP00000349274:G651D	G	+	2	0	KIAA0649	137518129	0.060000	0.20803	0.001000	0.08648	0.006000	0.05464	1.152000	0.31663	0.249000	0.21456	0.561000	0.74099	GGC	G|0.994;A|0.006	0.006	strong		0.652	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811		A	138378308	G	A	138378308	3	1	22	1	0	0	0	0	1	0	0	0	8196	1203	42	2	1954	2	KIAA0649	9	138378308	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	747947	138378308	2835123	2196	5097											
KIAA0649	9858	hgsc.bcm.edu	37	chr9	138379608	138379608	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ttctcgccgctgctgtccacCcagctcttccactttggaaa	6	12	7	16	2	2	0	0	0	2	0	5	1	4	1	4	1	2	3	4	1	1	3	rs139160467	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:138379608C>T	ENST00000356818.2	+	4	3801	c.3252C>T	c.(3250-3252)acC>acT	p.T1084T	PPP1R26_ENST00000604351.1_Silent_p.T1084T|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000605660.1_Silent_p.T1084T|PPP1R26_ENST00000401470.3_Silent_p.T1084T|PPP1R26_ENST00000605286.1_Silent_p.T1084T	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	1084					negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										TGCTGTCCACCCAGCTCTTCC	0.726													C|||	57	0.0113818	0.0424	0.0014	5008	,	,		14055	0.0		0.0	False		,,,				2504	0.0				p.T1084T		Atlas-SNP	.											.	.	.	.	0			c.C3252T						PASS	.	C		72,3236		0,72,1582	4	5	5		3252	-7.1	0.1	9	dbSNP_134	5	2,7236		0,2,3617	no	coding-synonymous	KIAA0649	NM_014811.3		0,74,5199	TT,TC,CC		0.0276,2.1765,0.7017		1084/1210	138379608	74,10472	1654	3619	5273	SO:0001819	synonymous_variant	9858	exon4			GTCCACCCAGCTC	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.3252C>T	9.37:g.138379608C>T		24	0	0		22	8	0.363636	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Silent	SNP	ENST00000356818.2	37	CCDS6988.1																																																																																			C|0.989;T|0.011	0.011	strong		0.726	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811		T	138379608	C	T	138379608	2	4	22	1	0	0	0	0	0	0	0	1	8196	610	22	2		2	KIAA0649	9	138379608	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1300	138379608	2833823	2197	5098											
KCNT1	57582	hgsc.bcm.edu	37	chr9	138651648	138651648	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcacgcccaagatctggccAtcgcagctgctggtggtcat	7	9	12	13	2	3	1	2	0	1	1	4	1	3	1	2	3	2	3	2	3	1	0	rs61739517	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:138651648A>G	ENST00000263604.3	+	11	921	c.921A>G	c.(919-921)ccA>ccG	p.P307P	KCNT1_ENST00000490355.2_Silent_p.P307P|KCNT1_ENST00000486577.2_Silent_p.P287P|KCNT1_ENST00000487664.1_Silent_p.P281P|KCNT1_ENST00000371757.2_Silent_p.P326P|KCNT1_ENST00000491806.2_Silent_p.P293P|KCNT1_ENST00000488444.2_Silent_p.P307P|KCNT1_ENST00000298480.5_Silent_p.P326P			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	307					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)		AGATCTGGCCATCGCAGCTGC	0.642													A|||	142	0.0283546	0.1051	0.0043	5008	,	,		20814	0.0		0.0	False		,,,				2504	0.0				p.P326P		Atlas-SNP	.											.	KCNT1	139	.	0			c.A978G						PASS	.	A		385,4021	194.0+/-219.0	20,345,1838	137	98	111		978	-9.7	0.7	9	dbSNP_129	111	4,8596	1.2+/-3.3	0,4,4296	no	coding-synonymous	KCNT1	NM_020822.2		20,349,6134	GG,GA,AA		0.0465,8.7381,2.9909		326/1236	138651648	389,12617	2203	4300	6503	SO:0001819	synonymous_variant	57582	exon11			CTGGCCATCGCAG	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.921A>G	9.37:g.138651648A>G		135	0	0		116	39	0.336207	NM_020822	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Silent	SNP	ENST00000263604.3	37																																																																																				A|0.967;G|0.033	0.033	strong		0.642	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822		G	138651648	A	G	138651648	2	3	22	1	0	0	0	0	0	0	0	1	8100	204	8	3		3	KCNT1	9	138651648	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	272040	138651648	2561783	2198	5099											
LHX3	8022	hgsc.bcm.edu	37	chr9	139096782	139096782	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcctgctggggcttacccCgagtcccgcccaaggtgcag	5	8	13	15	2	0	0	0	0	0	0	2	1	2	0	5	3	3	3	5	3	2	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139096782C>T	ENST00000371748.5	-	1	173	c.77G>A	c.(76-78)cGg>cAg	p.R26Q	LHX3_ENST00000371746.3_5'Flank	NM_178138.4	NP_835258.1	Q9UBR4	LHX3_HUMAN	LIM homeobox 3	26					inner ear development (GO:0048839)|lung development (GO:0030324)|medial motor column neuron differentiation (GO:0021526)|motor neuron axon guidance (GO:0008045)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|pituitary gland development (GO:0021983)|placenta development (GO:0001890)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spinal cord association neuron differentiation (GO:0021527)|spinal cord motor neuron cell fate specification (GO:0021520)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		Myeloproliferative disorder(178;0.0511)		Epithelial(140;8.43e-08)|OV - Ovarian serous cystadenocarcinoma(145;1.26e-07)		GGGCTTACCCCGAGTCCCGCC	0.721																																					p.R26Q		Atlas-SNP	.											.	LHX3	23	.	0			c.G77A						PASS	.						15	16	15					9																	139096782		2173	4271	6444	SO:0001583	missense	8022	exon1			TTACCCCGAGTCC	AF096169	CCDS6994.1, CCDS6995.1	9q34.3	2011-06-20			ENSG00000107187	ENSG00000107187		"Homeoboxes / LIM class"	6595	protein-coding gene	gene with protein product		600577				10598593, 10717474	Standard	NM_178138		Approved		uc004cgz.3	Q9UBR4	OTTHUMG00000020924	ENST00000371748.5:c.77G>A	9.37:g.139096782C>T	ENSP00000360813:p.Arg26Gln	39	0	0		36	12	0.333333	NM_178138	Q5TB39|Q5TB40|Q9NZB5|Q9P0I8|Q9P0I9	Missense_Mutation	SNP	ENST00000371748.5	37	CCDS6994.1	.	.	.	.	.	.	.	.	.	.	C	0.014	-1.571243	0.00895	.	.	ENSG00000107187	ENST00000371748	D	0.87729	-2.29	2.48	-3.37	0.04898	.	.	.	.	.	T	0.68805	0.3041	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.55503	-0.8131	9	0.08599	T	0.76	.	5.7854	0.18331	0.0:0.2132:0.172:0.6149	.	26	Q9UBR4	LHX3_HUMAN	Q	26	ENSP00000360813:R26Q	ENSP00000360813:R26Q	R	-	2	0	LHX3	138236603	0.000000	0.05858	0.000000	0.03702	0.239000	0.25481	-1.334000	0.02665	-0.951000	0.03654	-0.350000	0.07774	CGG	.	.	none		0.721	LHX3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055048.3			T	139096782	C	T	139096782	3	4	22	1	0	0	0	0	1	0	0	0	8781	652	23	1	1238	1	LHX3	9	139096782	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	445134	139096782	2116649	2199	5100											
CARD9	64170	hgsc.bcm.edu	37	chr9	139264827	139264827	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgctcctggtggtcccgcagCgcctgccgccagtcctcctc	2	9	11	19	3	0	0	0	0	0	0	5	0	4	0	7	2	3	2	7	2	0	0	rs115057256	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139264827C>T	ENST00000371732.5	-	6	1035	c.870G>A	c.(868-870)gcG>gcA	p.A290A	CARD9_ENST00000371734.3_Silent_p.A290A|CARD9_ENST00000460290.1_5'Flank|CARD9_ENST00000315908.7_Silent_p.A290A	NM_052813.4	NP_434700.2	Q9H257	CARD9_HUMAN	caspase recruitment domain family, member 9	290					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)		GGTCCCGCAGCGCCTGCCGCC	0.687													C|||	50	0.00998403	0.0363	0.0029	5008	,	,		16294	0.0		0.0	False		,,,				2504	0.0				p.A290A		Atlas-SNP	.											CARD9,NS,NS,-1,1	CARD9	47	1	0			c.G870A						PASS	.	C	,	145,4233	94.8+/-133.5	2,141,2046	33	36	35		870,870	-8.2	0.2	9	dbSNP_132	35	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous,coding-synonymous	CARD9	NM_052813.4,NM_052814.3	,	2,142,6343	TT,TC,CC		0.0116,3.312,1.1253	,	290/537,290/493	139264827	146,12828	2189	4298	6487	SO:0001819	synonymous_variant	64170	exon6			CCGCAGCGCCTGC	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.870G>A	9.37:g.139264827C>T		87	0	0		91	71	0.78022	NM_052813	Q5SXM5|Q5SXM6|Q9H854	Silent	SNP	ENST00000371732.5	37	CCDS6997.1																																																																																			C|0.989;T|0.011	0.011	strong		0.687	CARD9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055053.1	NM_052813		T	139264827	C	T	139264827	2	4	22	1	0	0	0	0	0	0	0	1	2654	755	27	1		1	CARD9	9	139264827	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	168045	139264827	1948604	2200	5101											
SNAPC4	6621	hgsc.bcm.edu	37	chr9	139292751	139292751	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctaggtacaaggggcttacCtgcttcagaatctgactcga	10	10	11	10	1	2	2	1	1	1	1	3	3	2	2	1	3	3	4	1	3	5	4	rs7031489	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139292751C>T	ENST00000298532.2	-	1	498	c.130G>A	c.(130-132)Gat>Aat	p.D44N		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)		AGGGGCTTACCTGCTTCAGAA	0.557													C|||	36	0.0071885	0.0257	0.0029	5008	,	,		15053	0.0		0.0	False		,,,				2504	0.0				p.D44N		Atlas-SNP	.											.	SNAPC4	82	.	0			c.G130A						PASS	.	C	ASN/ASP	86,4320	73.1+/-111.1	0,86,2117	105	108	107		130	4.2	0.8	9	dbSNP_116	107	12,8588	9.1+/-34.3	0,12,4288	yes	missense-near-splice	SNAPC4	NM_003086.2	23	0,98,6405	TT,TC,CC		0.1395,1.9519,0.7535	benign	44/1470	139292751	98,12908	2203	4300	6503	SO:0001630	splice_region_variant	6621	exon1			GCTTACCTGCTTC	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.130+1G>A	9.37:g.139292751C>T		88	0	0		91	30	0.32967	NM_003086		Missense_Mutation	SNP	ENST00000298532.2	37	CCDS6998.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	c	12.43	1.935886	0.34189	0.019519	0.001395	ENSG00000165684	ENST00000298532	T	0.28895	1.59	4.18	4.18	0.49190	.	0.853272	0.10561	N	0.660279	T	0.15609	0.0376	L	0.46157	1.445	0.26436	N	0.975854	B	0.32245	0.361	B	0.29440	0.102	T	0.05835	-1.0861	9	.	.	.	-10.7631	14.4014	0.67050	0.0:1.0:0.0:0.0	rs7031489;rs7031489	44	Q5SXM2	SNPC4_HUMAN	N	44	ENSP00000298532:D44N	.	D	-	1	0	SNAPC4	138412572	0.988000	0.35896	0.779000	0.31741	0.410000	0.31052	3.351000	0.52232	2.327000	0.79052	0.651000	0.88453	GAT	C|0.991;T|0.009	0.009	strong		0.557	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	Missense_Mutation	T	139292751	C	T	139292751	5	4	22	1	0	0	0	0	0	0	1	0	14852	695	24	2	4367	2	SNAPC4	9	139292751	Splice_Site	SNP	C	TCGA-G8-6324-01A-11D-2210-10	27924	139292751	1920680	2201	5102											
SEC16A	9919	hgsc.bcm.edu	37	chr9	139370829	139370829	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcccccacgtgtgtaggtgcGggcggacggcctagcccagg	5	5	17	14	4	0	0	0	0	0	0	0	1	0	1	4	5	2	1	4	5	2	2	rs114386206	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139370829G>A	ENST00000371706.3	-	1	738	c.705C>T	c.(703-705)ccC>ccT	p.P235P	SEC16A_ENST00000290037.6_Silent_p.P235P|SEC16A_ENST00000313050.7_Silent_p.P413P|SEC16A_ENST00000431893.2_Silent_p.P235P			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	235					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)		GTGTAGGTGCGGGCGGACGGC	0.592													g|||	19	0.00379393	0.0136	0.0014	5008	,	,		16416	0.0		0.0	False		,,,				2504	0.0				p.P413P		Atlas-SNP	.											.	SEC16A	249	.	0			c.C1239T						PASS	.	C		42,3906		0,42,1932	21	24	23		1239	-7.4	0	9	dbSNP_132	23	9,8283		0,9,4137	no	coding-synonymous	SEC16A	NM_014866.1		0,51,6069	AA,AG,GG		0.1085,1.0638,0.4167		413/2358	139370829	51,12189	1974	4146	6120	SO:0001819	synonymous_variant	9919	exon3			AGGTGCGGGCGGA	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.705C>T	9.37:g.139370829G>A		89	0	0		121	45	0.371901	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Silent	SNP	ENST00000371706.3	37																																																																																				G|0.996;A|0.004	0.004	strong		0.592	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459		A	139370829	G	A	139370829	2	1	22	1	0	0	0	0	0	0	0	1	14001	1103	39	1		1	SEC16A	9	139370829	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	78078	139370829	1842602	2202	5103											
NOTCH1	4851	hgsc.bcm.edu	37	chr9	139390649	139390650	+	Frame_Shift_Del	DEL	AG	AG	-																															gaccactggtcaggggactcAggggacggggtgaggaaggg																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139390649_139390650delAG	ENST00000277541.6	-	34	7616_7617	c.7541_7542delCT	c.(7540-7542)cctfs	p.P2514fs		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	2514					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.P2515fs*4(145)|p.T2512fs*1(1)|p.E2515fs*3(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)		CAGGGGACTCAGGGGACGGGGT	0.663			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)																											p.2514_2515del		Pindel,Atlas-Indel	.		Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	.	NOTCH1	1980	.	147	Complex - frameshift(145)|Deletion - Frameshift(2)	haematopoietic_and_lymphoid_tissue(147)	c.7542_7543del						PASS	.																																			SO:0001589	frameshift_variant	4851	exon34			.	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.7541_7542delCT	9.37:g.139390649_139390650delAG	ENSP00000277541:p.Pro2514fs	113	0	.		118	38	0.322	NM_017617	Q59ED8|Q5SXM3	Frame_Shift_Del	DEL	ENST00000277541.6	37	CCDS43905.1																																																																																			.	.	none		0.663	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		-	139390650	AG	-	139390649	7	5	22	1	0	1	0	1	0	0	0	0	10556	175	7	0	129	0	NOTCH1	9	139390649	Frame_Shift_Del	DEL	AG	TCGA-G8-6324-01A-11D-2210-10	19820	139390649	1822782	2203	5104											
NOTCH1	4851	hgsc.bcm.edu	37	chr9	139390958	139390958	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcggctgtggtggtggtggTggcggctgcaggctttgctg	1	12	21	7	2	0	0	0	0	0	0	0	0	0	0	0	8	3	5	0	8	0	1	rs11574911	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139390958T>C	ENST00000277541.6	-	34	7308	c.7233A>G	c.(7231-7233)ccA>ccG	p.P2411P		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	2411	Poly-Pro.				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.P2412P(1)|p.P2412del(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)		GTGGTGGTGGTGGCGGCTGCA	0.642			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)			T|||	160	0.0319489	0.1112	0.0144	5008	,	,		14401	0.0		0.003	False		,,,				2504	0.0				p.P2411P		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	NOTCH1,NS,lymphoid_neoplasm,0,1	NOTCH1	1980	1	2	Substitution - coding silent(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(2)	c.A7233G						PASS	.	T		313,3979		8,297,1841	22	30	27		7233	-1.5	0	9	dbSNP_120	27	17,8511		0,17,4247	no	coding-synonymous	NOTCH1	NM_017617.3		8,314,6088	CC,CT,TT		0.1993,7.2926,2.5741		2411/2556	139390958	330,12490	2146	4264	6410	SO:0001819	synonymous_variant	4851	exon34			TGGTGGTGGCGGC	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.7233A>G	9.37:g.139390958T>C		26	0	0		31	11	0.354839	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			T|0.968;C|0.032	0.032	strong		0.642	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		C	139390958	T	C	139390958	2	2	22	1	0	0	0	0	0	0	0	1	10556	1683	59	3		3	NOTCH1	9	139390958	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	309	139390958	1822473	2204	5105											
NOTCH1	4851	hgsc.bcm.edu	37	chr9	139391636	139391636	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagcaggcagcccttgccGtcctgggacttcttcctccg	4	10	10	17	2	1	0	0	0	1	0	5	1	5	1	6	2	3	2	6	2	0	3	rs2229974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139391636G>A	ENST00000277541.6	-	34	6630	c.6555C>T	c.(6553-6555)gaC>gaT	p.D2185D		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	2185					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.K2182fs*61(1)|p.S2163_T2283del(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)		AGCCCTTGCCGTCCTGGGACT	0.662			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)			G|||	3481	0.695088	0.6278	0.6542	5008	,	,		16337	0.9494		0.5775	False		,,,				2504	0.6738				p.D2185D		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	.	NOTCH1	1980	.	2	Deletion - Frameshift(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(2)	c.C6555T						PASS	.	G		2777,1589		891,995,297	47	54	52		6555	-0.8	1	9	dbSNP_98	52	4726,3816		1319,2088,864	no	coding-synonymous	NOTCH1	NM_017617.3		2210,3083,1161	AA,AG,GG		44.6734,36.3949,41.8733		2185/2556	139391636	7503,5405	2183	4271	6454	SO:0001819	synonymous_variant	4851	exon34			CTTGCCGTCCTGG	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.6555C>T	9.37:g.139391636G>A		121	0	0		133	77	0.578947	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			G|0.341;A|0.659	0.659	strong		0.662	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		A	139391636	G	A	139391636	2	1	22	1	0	0	0	0	0	0	0	1	10556	1136	40	1		1	NOTCH1	9	139391636	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	678	139391636	1821795	2205	5106											
AGPAT2	10555	hgsc.bcm.edu	37	chr9	139571560	139571560	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcccgcttggcgatctgcacGcagcgctccggaaggacctc	6	7	12	16	5	1	0	0	0	1	0	4	3	3	2	3	3	2	4	3	3	1	1	rs73668354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139571560G>A	ENST00000371696.2	-	3	410	c.345C>T	c.(343-345)tgC>tgT	p.C115C	AGPAT2_ENST00000371694.3_Silent_p.C115C|AGPAT2_ENST00000538402.1_Silent_p.C115C	NM_006412.3	NP_006403.2	O15120	PLCB_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 2	115					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)		CGATCTGCACGCAGCGCTCCG	0.637													G|||	72	0.014377	0.0461	0.013	5008	,	,		15024	0.0		0.002	False		,,,				2504	0.0				p.C115C		Atlas-SNP	.											AGPAT2,NS,carcinoma,0,1	AGPAT2	17	1	0			c.C345T						PASS	.	A	,	183,4223	115.0+/-153.0	2,179,2022	50	57	54		345,345	-3.2	0.7	9	dbSNP_130	54	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous,coding-synonymous	AGPAT2	NM_001012727.1,NM_006412.3	,	2,185,6316	AA,AG,GG		0.0698,4.1534,1.4532	,	115/247,115/279	139571560	189,12817	2203	4300	6503	SO:0001819	synonymous_variant	10555	exon3			CTGCACGCAGCGC	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.345C>T	9.37:g.139571560G>A		120	0	0		116	85	0.732759	NM_001012727	O00516|O15106|Q5VUD3|Q5VUD4|Q9BSV7|Q9BWR7	Silent	SNP	ENST00000371696.2	37	CCDS7003.1																																																																																			G|0.982;A|0.018	0.018	strong		0.637	AGPAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055090.1	NM_006412		A	139571560	G	A	139571560	2	1	22	1	0	0	0	0	0	0	0	1	387	1079	38	1		1	AGPAT2	9	139571560	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	179924	139571560	1641871	2206	5107											
LCN8	138307	hgsc.bcm.edu	37	chr9	139649701	139649701	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcccctgggctcaccaggcCgggccgccaggtagagacca	7	3	15	16	2	1	1	1	0	0	1	1	2	1	1	7	5	0	2	7	5	1	1	rs144857499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139649701C>T	ENST00000371688.3	-	5	711	c.416G>A	c.(415-417)cGg>cAg	p.R139Q	LCN8_ENST00000482893.1_5'UTR	NM_178469.3	NP_848564.2	Q6JVE9	LCN8_HUMAN	lipocalin 8	162					response to hormone (GO:0009725)|transport (GO:0006810)	extracellular region (GO:0005576)				endometrium(1)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)	10	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;5.56e-06)|Epithelial(140;8.32e-05)		CTCACCAGGCCGGGCCGCCAG	0.682													C|||	7	0.00139776	0.0045	0.0014	5008	,	,		14888	0.0		0.0	False		,,,				2504	0.0				p.R139Q		Atlas-SNP	.											.	LCN8	14	.	0			c.G416A						PASS	.	C	GLN/ARG	25,4379	30.8+/-60.4	0,25,2177	39	48	45		416	1.9	0.2	9	dbSNP_134	45	1,8599		0,1,4299	yes	missense	LCN8	NM_178469.3	43	0,26,6476	TT,TC,CC		0.0116,0.5677,0.1999	probably-damaging	139/153	139649701	26,12978	2202	4300	6502	SO:0001583	missense	138307	exon5			CCAGGCCGGGCCG	AK124003	CCDS35183.1	9q34.3	2011-10-24	2005-01-11		ENSG00000204001	ENSG00000204001		"Lipocalins"	27038	protein-coding gene	gene with protein product		612902	"chromosome 9 open reading frame 137", "lipocalin 5"	LCN5			Standard	XM_005266058		Approved		uc004cjb.1	Q6JVE9	OTTHUMG00000020942	ENST00000371688.3:c.416G>A	9.37:g.139649701C>T	ENSP00000360753:p.Arg139Gln	78	0	0		80	55	0.6875	NM_178469	A1L4A8|A6NMN9|Q5T5R4	Missense_Mutation	SNP	ENST00000371688.3	37	CCDS35183.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	9.456	1.091903	0.20471	0.005677	1.16E-4	ENSG00000204001	ENST00000371688	T	0.34667	1.35	2.76	1.85	0.25348	.	.	.	.	.	T	0.14700	0.0355	N	0.24115	0.695	0.09310	N	1	B	0.23490	0.086	B	0.15870	0.014	T	0.15723	-1.0427	9	0.28530	T	0.3	.	5.487	0.16755	0.0:0.8418:0.0:0.1582	.	139	Q6JVE9-2	.	Q	139	ENSP00000360753:R139Q	ENSP00000360753:R139Q	R	-	2	0	LCN8	138769522	0.058000	0.20735	0.229000	0.23960	0.549000	0.35272	0.257000	0.18369	0.731000	0.32448	0.491000	0.48974	CGG	C|0.997;T|0.003	0.003	strong		0.682	LCN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055109.1	NM_178469		T	139649701	C	T	139649701	3	4	22	1	0	0	0	0	1	0	0	0	8695	652	23	1	54	1	LCN8	9	139649701	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	78141	139649701	1563730	2207	5108											
LCN15	389812	hgsc.bcm.edu	37	chr9	139657874	139657874	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	agatgtaaaggacggcgaagGagctgtagtctgtgtccacg	11	8	15	7	3	1	1	0	0	1	1	2	4	2	3	1	3	1	3	1	3	4	2	rs11145871	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139657874G>C	ENST00000316144.5	-	4	377	c.353C>G	c.(352-354)tCc>tGc	p.S118C	LCN15_ENST00000482511.1_5'UTR	NM_203347.1	NP_976222.1	Q6UWW0	LCN15_HUMAN	lipocalin 15	118					lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	small molecule binding (GO:0036094)|transporter activity (GO:0005215)			endometrium(1)|lung(1)	2						GACGGCGAAGGAGCTGTAGTC	0.642													G|||	14	0.00279553	0.0098	0.0014	5008	,	,		8323	0.0		0.0	False		,,,				2504	0.0				p.S118C		Atlas-SNP	.											.	LCN15	11	.	0			c.C353G						PASS	.	G	CYS/SER	55,4351	54.2+/-90.2	1,53,2149	83	75	77		353	3.8	0.3	9	dbSNP_120	77	0,8600		0,0,4300	yes	missense	LCN15	NM_203347.1	112	1,53,6449	CC,CG,GG		0.0,1.2483,0.4229	probably-damaging	118/185	139657874	55,12951	2203	4300	6503	SO:0001583	missense	389812	exon4			GCGAAGGAGCTGT		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.353C>G	9.37:g.139657874G>C	ENSP00000313833:p.Ser118Cys	37	0	0		37	21	0.567568	NM_203347		Missense_Mutation	SNP	ENST00000316144.5	37	CCDS7006.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	G	14.93	2.681579	0.47991	0.012483	0.0	ENSG00000177984	ENST00000316144	T	0.08720	3.06	3.76	3.76	0.43208	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	1.023620	0.07803	N	0.956885	T	0.17577	0.0422	M	0.71581	2.175	0.09310	N	1	D	0.69078	0.997	P	0.58077	0.832	T	0.08700	-1.0709	10	0.62326	D	0.03	.	11.2408	0.48968	0.0:0.0:1.0:0.0	rs11145871	118	Q6UWW0	LCN15_HUMAN	C	118	ENSP00000313833:S118C	ENSP00000313833:S118C	S	-	2	0	LCN15	138777695	0.919000	0.31177	0.273000	0.24645	0.776000	0.43924	2.771000	0.47670	2.104000	0.64026	0.561000	0.74099	TCC	G|0.994;C|0.006	0.006	strong		0.642	LCN15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055114.2	NM_203347		C	139657874	G	C	139657874	3	2	22	1	0	0	0	0	1	0	0	0	8692	1174	41	4	213	4	LCN15	9	139657874	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	8173	139657874	1555557	2208	5109											
LCN15	389812	hgsc.bcm.edu	37	chr9	139657900	139657900	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagtctgtgtccacgatgcgCacgtccaggtagcccaaggc	8	8	12	13	3	1	0	0	0	1	0	3	1	3	0	3	2	2	2	3	2	3	2	rs11145872	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139657900C>G	ENST00000316144.5	-	4	351	c.327G>C	c.(325-327)gtG>gtC	p.V109V	LCN15_ENST00000482511.1_5'UTR	NM_203347.1	NP_976222.1	Q6UWW0	LCN15_HUMAN	lipocalin 15	109					lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	small molecule binding (GO:0036094)|transporter activity (GO:0005215)			endometrium(1)|lung(1)	2						CCACGATGCGCACGTCCAGGT	0.642													C|||	14	0.00279553	0.0098	0.0014	5008	,	,		8406	0.0		0.0	False		,,,				2504	0.0				p.V109V		Atlas-SNP	.											.	LCN15	11	.	0			c.G327C						PASS	.	C		56,4350	54.9+/-90.9	1,54,2148	76	67	70		327	3.9	1	9	dbSNP_120	70	0,8600		0,0,4300	no	coding-synonymous	LCN15	NM_203347.1		1,54,6448	GG,GC,CC		0.0,1.271,0.4306		109/185	139657900	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	389812	exon4			GATGCGCACGTCC		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.327G>C	9.37:g.139657900C>G		36	0	0		32	20	0.625	NM_203347		Silent	SNP	ENST00000316144.5	37	CCDS7006.1																																																																																			C|0.994;G|0.006	0.006	strong		0.642	LCN15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055114.2	NM_203347		G	139657900	C	G	139657900	2	3	22	1	0	0	0	0	0	0	0	1	8692	697	25	4		4	LCN15	9	139657900	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	26	139657900	1555531	2209	5110											
KIAA1984	84960	hgsc.bcm.edu	37	chr9	139698977	139698977	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacatgaggcaaagggaggcGtccttcatcgaggagcgccg	11	5	15	10	4	1	1	1	1	0	0	3	4	2	3	2	4	2	1	2	4	2	1	rs11145892	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139698977G>A	ENST00000338005.6	+	7	725	c.690G>A	c.(688-690)gcG>gcA	p.A230A	KIAA1984_ENST00000371682.3_3'UTR|RP11-216L13.19_ENST00000415992.1_RNA|KIAA1984-AS1_ENST00000414656.1_RNA|RP11-216L13.18_ENST00000471502.1_RNA	NM_001039374.4	NP_001034463.4	Q5T5S1	CC183_HUMAN		230										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)		AAAGGGAGGCGTCCTTCATCG	0.612													G|||	64	0.0127796	0.0424	0.0058	5008	,	,		18627	0.0		0.002	False		,,,				2504	0.002				p.A230A		Atlas-SNP	.											.	KIAA1984	39	.	0			c.G690A						PASS	.	G		120,3832		1,118,1857	39	44	42		690	-5.7	0.4	9	dbSNP_120	42	37,8243		0,37,4103	no	coding-synonymous	KIAA1984	NM_001039374.4		1,155,5960	AA,AG,GG		0.4469,3.0364,1.2835		230/535	139698977	157,12075	1976	4140	6116	SO:0001819	synonymous_variant	84960	exon7			GGAGGCGTCCTTC																												ENST00000338005.6:c.690G>A	9.37:g.139698977G>A		31	0	0		40	27	0.675	NM_001039374	B2RP89|C9JD38|Q6P2D9|Q8NAI4|Q8TF18	Silent	SNP	ENST00000338005.6	37	CCDS43906.1																																																																																			G|0.993;A|0.007	0.007	strong		0.612	KIAA1984-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354899.1			A	139698977	G	A	139698977	2	1	22	1	0	0	0	0	0	0	0	1	8275	1132	40	1		1	KIAA1984	9	139698977	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	41077	139698977	1514454	2210	5111											
C9orf172	389813	hgsc.bcm.edu	37	chr9	139740900	139740900	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgcaccgagaccatgttcaaCgcctgcctctacttcaagtc	9	9	7	16	3	3	1	2	0	1	1	4	2	3	1	4	0	3	2	4	0	3	3	rs147735504	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139740900C>T	ENST00000436881.1	+	1	2034	c.2034C>T	c.(2032-2034)aaC>aaT	p.N678N	PHPT1_ENST00000545326.1_5'Flank|PHPT1_ENST00000371661.1_5'Flank|PHPT1_ENST00000247665.10_5'Flank	NM_001080482.2	NP_001073951.2	C9J069	CI172_HUMAN	chromosome 9 open reading frame 172	678										endometrium(2)|large_intestine(1)|lung(6)	9						CCATGTTCAACGCCTGCCTCT	0.682													c|||	31	0.0061901	0.0227	0.0014	5008	,	,		10471	0.0		0.0	False		,,,				2504	0.0				p.N678N		Atlas-SNP	.											.	C9orf172	23	.	0			c.C2034T						PASS	.	C		90,4048		0,90,1979	23	28	27		2034	3.2	1	9	dbSNP_134	27	1,8323		0,1,4161	no	coding-synonymous	C9orf172	NM_001080482.2		0,91,6140	TT,TC,CC		0.012,2.175,0.7302		678/977	139740900	91,12371	2069	4162	6231	SO:0001819	synonymous_variant	389813	exon1			GTTCAACGCCTGC		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.2034C>T	9.37:g.139740900C>T		41	0	0		38	16	0.421053	NM_001080482		Silent	SNP	ENST00000436881.1	37	CCDS48059.1																																																																																			C|0.994;T|0.006	0.006	strong		0.682	C9orf172-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080482		T	139740900	C	T	139740900	2	4	22	1	0	0	0	0	0	0	0	1	2473	535	19	1		1	C9orf172	9	139740900	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	41923	139740900	1472531	2211	5112											
PHPT1	29085	hgsc.bcm.edu	37	chr9	139745012	139745012	+	Intron	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccccaggatccaccatcaaGgtttgcttgcctgtggaggt	7	10	12	12	0	1	0	1	0	0	0	2	2	2	2	5	4	2	2	5	4	1	2	rs149543778	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139745012G>T	ENST00000247665.10	+	3	622				MAMDC4_ENST00000445819.1_5'Flank|PHPT1_ENST00000492540.1_3'UTR|PHPT1_ENST00000545326.1_Splice_Site_p.G114C|MAMDC4_ENST00000317446.2_5'Flank|PHPT1_ENST00000371661.1_Splice_Site_p.G114C	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)			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)		CCACCATCAAGGTTTGCTTGC	0.637													G|||	26	0.00519169	0.0159	0.0072	5008	,	,		18692	0.0		0.0	False		,,,				2504	0.0				p.G114C		Atlas-SNP	.											.	PHPT1	14	.	0			c.G340T						PASS	.	G	CYS/GLY,	37,3091		0,37,1527	37	38	38		340,	1.5	0	9	dbSNP_134	38	0,7150		0,0,3575	yes	missense-near-splice,intron	PHPT1	NM_001135861.1,NM_014172.4	159,	0,37,5102	TT,TG,GG		0.0,1.1829,0.36	,	114/125,	139745012	37,10241	1564	3575	5139	SO:0001627	intron_variant	29085	exon3			CATCAAGGTTTGC	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.286-195G>T	9.37:g.139745012G>T		50	0	0		61	36	0.590164	NM_001135861	B1AMX0|B1AMX1|Q9H0Y3	Missense_Mutation	SNP	ENST00000247665.10	37	CCDS7009.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	.	11.23	1.576676	0.28092	0.011829	0.0	ENSG00000054148	ENST00000371661;ENST00000545326	.	.	.	1.54	1.54	0.23209	.	.	.	.	.	T	0.54549	0.1865	.	.	.	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.41875	-0.9484	7	0.54805	T	0.06	.	9.0668	0.36469	0.0:0.0:1.0:0.0	.	114	Q9NRX4-2	.	C	114	.	ENSP00000360724:G114C	G	+	1	0	PHPT1	138864833	0.000000	0.05858	0.002000	0.10522	0.044000	0.14063	0.167000	0.16602	1.174000	0.42811	0.462000	0.41574	GGC	G|0.996;T|0.004	0.004	strong		0.637	PHPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055150.1	NM_014172		T	139745012	G	T	139745012	1	4	22	0	1	0	0	0	0	0	0	0	11869	1014	35	4		4	PHPT1	9	139745012	Intron	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4112	139745012	1468419	2212	5113											
TRAF2	7186	hgsc.bcm.edu	37	chr9	139814931	139814931	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gcctgcagccggcagcaccgGctggaccaagacaagattga	11	4	13	13	2	0	3	0	1	0	2	0	4	0	4	4	3	3	4	4	3	2	1	rs17244166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139814931G>T	ENST00000247668.2	+	8	976	c.924G>T	c.(922-924)cgG>cgT	p.R308R	TRAF2_ENST00000536468.1_Silent_p.R308R|TRAF2_ENST00000359662.3_Silent_p.R360R	NM_021138.3	NP_066961.2	Q12933	TRAF2_HUMAN	TNF receptor-associated factor 2	308				Missing (in Ref. 2; BAB70792). {ECO:0000305}.	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)|cellular protein complex assembly (GO:0043623)|cellular response to nitric oxide (GO:0071732)|innate immune response (GO:0045087)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of neuron death (GO:1901215)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|programmed necrotic cell death (GO:0097300)|protein autoubiquitination (GO:0051865)|protein catabolic process (GO:0030163)|protein complex assembly (GO:0006461)|protein heterooligomerization (GO:0051291)|protein homotrimerization (GO:0070207)|protein K63-linked ubiquitination (GO:0070534)|regulation of apoptotic process (GO:0042981)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of immunoglobulin secretion (GO:0051023)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|membrane raft (GO:0045121)|ubiquitin ligase complex (GO:0000151)	CD40 receptor binding (GO:0005174)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein phosphatase binding (GO:0019903)|signal transducer activity (GO:0004871)|sphingolipid binding (GO:0046625)|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(3)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.229)	OV - Ovarian serous cystadenocarcinoma(145;4.48e-06)|Epithelial(140;9.55e-06)		GGCAGCACCGGCTGGACCAAG	0.597													G|||	30	0.00599042	0.0219	0.0014	5008	,	,		15208	0.0		0.0	False		,,,				2504	0.0				p.R308R		Atlas-SNP	.											.	TRAF2	46	.	0			c.G924T						PASS	.	G		114,4290	85.8+/-124.5	1,112,2089	30	33	32		924	-1.9	1	9	dbSNP_123	32	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TRAF2	NM_021138.3		1,113,6388	TT,TG,GG		0.0116,2.5886,0.8843		308/502	139814931	115,12889	2202	4300	6502	SO:0001819	synonymous_variant	7186	exon8			GCACCGGCTGGAC	U12597	CCDS7013.1	9q34	2013-01-09			ENSG00000127191	ENSG00000127191		"RING-type (C3HC4) zinc fingers"	12032	protein-coding gene	gene with protein product		601895				7639698	Standard	NM_021138		Approved	TRAP3	uc004cjv.3	Q12933	OTTHUMG00000020952	ENST00000247668.2:c.924G>T	9.37:g.139814931G>T		61	0	0		77	29	0.376623	NM_021138	A8K107|B4DPJ7|Q7Z337|Q96NT2	Silent	SNP	ENST00000247668.2	37	CCDS7013.1																																																																																			G|0.989;T|0.011	0.011	strong		0.597	TRAF2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055166.1	NM_021138		T	139814931	G	T	139814931	2	4	22	1	0	0	0	0	0	0	0	1	16453	1190	42	4		4	TRAF2	9	139814931	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	69919	139814931	1398500	2213	5114											
LCNL1	401562	hgsc.bcm.edu	37	chr9	139879427	139879428	+	Frame_Shift_Ins	INS	-	-	GG																															cggcccctccctgcccctctINSctccctctcttcgcccctcc																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139879427_139879428insGG	ENST00000408973.2	+	3	1053_1054	c.459_460insGG	c.(460-462)ctcfs	p.L154fs	LCNL1_ENST00000432827.1_Intron	NM_207510.3	NP_997393.3	Q6ZST4	LCNL1_HUMAN	lipocalin-like 1	154																	cctgcccctctctccctctctt	0.678																																					p.S153fs		Atlas-Indel	.											.	LCNL1	4	.	0			c.459_460insGG						PASS	.			103,3313		9,85,1614						-1.1	0			10	3,7317		0,3,3657	no	frameshift	LCNL1	NM_207510.3		9,88,5271	A1A1,A1R,RR		0.041,3.0152,0.9873				106,10630				SO:0001589	frameshift_variant	401562	exon3			.		CCDS43908.1	9q34.3	2014-01-22			ENSG00000214402	ENSG00000214402		"Lipocalins"	34436	protein-coding gene	gene with protein product							Standard	NM_207510		Approved	FLJ45224	uc004ckh.1	Q6ZST4	OTTHUMG00000159546	Exception_encountered	9.37:g.139879427_139879428insGG	ENSP00000386162:p.Leu154fs	314	0	0		217	14	0.0645161	NM_207510		Frame_Shift_Ins	INS	ENST00000408973.2	37	CCDS43908.1																																																																																			.	.	none		0.678	LCNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356128.1	NM_207510		GG	139879428	-	GG	139879427	7	5	22	1	0	1	1	0	0	0	0	0	8697	1538	54	0	469	0	LCNL1	9	139879427	Frame_Shift_Ins	INS	-	TCGA-G8-6324-01A-11D-2210-10	64496	139879427	1334004	2214	5115	61	2									
LCNL1	401562	hgsc.bcm.edu	37	chr9	139879429	139879429	+	Frame_Shift_Del	DEL	T	T	-																															ggcccctccctgcccctctcTccctctcttcgcccctccag																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139879429delT	ENST00000408973.2	+	3	1055	c.461delT	c.(460-462)ctcfs	p.L154fs	LCNL1_ENST00000432827.1_Intron	NM_207510.3	NP_997393.3	Q6ZST4	LCNL1_HUMAN	lipocalin-like 1	154																	tgcccctctctccctctcttc	0.682																																					p.L154fs		Atlas-Indel	.											.	LCNL1	4	.	0			c.460delC						PASS	.						8	11	10					9																	139879429		1791	3853	5644	SO:0001589	frameshift_variant	401562	exon3			.		CCDS43908.1	9q34.3	2014-01-22			ENSG00000214402	ENSG00000214402		"Lipocalins"	34436	protein-coding gene	gene with protein product							Standard	NM_207510		Approved	FLJ45224	uc004ckh.1	Q6ZST4	OTTHUMG00000159546	ENST00000408973.2:c.461delT	9.37:g.139879429delT	ENSP00000386162:p.Leu154fs	315	0	0		209	15	0.0717703	NM_207510		Frame_Shift_Del	DEL	ENST00000408973.2	37	CCDS43908.1																																																																																			.	.	none		0.682	LCNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356128.1	NM_207510		-	139879429	T	-	139879429	7	5	22	1	0	1	0	1	0	0	0	0	8697	1551	54	0	471	0	LCNL1	9	139879429	Frame_Shift_Del	DEL	T	TCGA-G8-6324-01A-11D-2210-10	2	139879429	1334002	2215	5116	61	2									
FUT7	2529	hgsc.bcm.edu	37	chr9	139925459	139925459	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acagtgccagccaccagtgcGttgcgccagaatttctccgt	8	9	10	14	3	1	1	0	0	1	1	2	1	1	1	5	0	4	1	5	0	1	2	rs11145973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139925459G>A	ENST00000314412.6	-	2	1750	c.732C>T	c.(730-732)aaC>aaT	p.N244N	ABCA2_ENST00000371605.3_5'Flank|ABCA2_ENST00000265662.5_5'Flank|ABCA2_ENST00000492260.1_5'Flank|C9orf139_ENST00000314330.2_Intron|ABCA2_ENST00000341511.6_5'Flank	NM_004479.3	NP_004470.1	Q11130	FUT7_HUMAN	fucosyltransferase 7 (alpha (1,3) fucosyltransferase)	244					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)		CCACCAGTGCGTTGCGCCAGA	0.627													g|||	24	0.00479233	0.0166	0.0	5008	,	,		17645	0.0		0.001	False		,,,				2504	0.001				p.N244N		Atlas-SNP	.											.	FUT7	24	.	0			c.C732T						PASS	.		,	89,4317	67.0+/-104.6	2,85,2116	88	104	99		732,	-1.4	0.9	9	dbSNP_120	99	0,8598		0,0,4299	no	coding-synonymous,intron	FUT7,C9orf139	NM_004479.3,NM_207511.1	,	2,85,6415	AA,AG,GG		0.0,2.02,0.6844	,	244/343,	139925459	89,12915	2203	4299	6502	SO:0001819	synonymous_variant	2529	exon2			CAGTGCGTTGCGC	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.732C>T	9.37:g.139925459G>A		76	0	0		98	71	0.72449	NM_004479	B2R7U7|Q6DK54	Silent	SNP	ENST00000314412.6	37	CCDS7022.1																																																																																			G|0.993;A|0.007	0.007	strong		0.627	FUT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055220.1	NM_004479		A	139925459	G	A	139925459	2	1	22	1	0	0	0	0	0	0	0	1	6117	1136	40	1		1	FUT7	9	139925459	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	46030	139925459	1287972	2216	5117											
TPRN	286262	hgsc.bcm.edu	37	chr9	140086940	140086940	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agccgagagctctcgggtctCacgctgctcacaaacgtggc	8	7	12	14	4	3	1	2	0	2	1	5	2	3	1	1	2	4	3	1	2	1	0	rs115446132	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140086940C>T	ENST00000409012.4	-	2	2015	c.1929G>A	c.(1927-1929)gtG>gtA	p.V643V	TPRN_ENST00000321773.2_Silent_p.V582V|TPRN_ENST00000541945.1_5'Flank	NM_001128228.2	NP_001121700.2	Q4KMQ1	TPRN_HUMAN	taperin	643					sensory perception of sound (GO:0007605)	stereocilium (GO:0032420)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)	8						TCTCGGGTCTCACGCTGCTCA	0.642													C|||	20	0.00399361	0.0129	0.0043	5008	,	,		17266	0.0		0.0	False		,,,				2504	0.0				p.V643V		Atlas-SNP	.											.	TPRN	28	.	0			c.G1929A						PASS	.	C		48,4356	46.7+/-81.2	0,48,2154	33	26	28		1929	3	0	9	dbSNP_132	28	0,8596		0,0,4298	no	coding-synonymous	TPRN	NM_001128228.2		0,48,6452	TT,TC,CC		0.0,1.0899,0.3692		643/712	140086940	48,12952	2202	4298	6500	SO:0001819	synonymous_variant	286262	exon2			GGGTCTCACGCTG	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.1929G>A	9.37:g.140086940C>T		93	0	0		71	41	0.577465	NM_001128228	B7ZKU5|Q5VSG5|Q5VSG6|Q6IPP2|Q8NCH2	Silent	SNP	ENST00000409012.4	37	CCDS56594.1																																																																																			C|0.996;T|0.004	0.004	strong		0.642	TPRN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055323.3	NM_173691		T	140086940	C	T	140086940	2	4	22	1	0	0	0	0	0	0	0	1	16436	813	29	2		2	TPRN	9	140086940	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	161481	140086940	1126491	2217	5118											
TMEM203	94107	hgsc.bcm.edu	37	chr9	140099675	140099675	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggcgcacggacacgatggtGgtgaagtaggtgctgagccc	9	6	17	9	3	0	2	0	2	0	0	0	4	0	3	1	5	2	3	1	5	2	1	rs113235610	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140099675G>A	ENST00000343666.5	-	1	415	c.192C>T	c.(190-192)acC>acT	p.T64T	NDOR1_ENST00000371521.4_5'Flank|TMEM203_ENST00000537254.1_Silent_p.T64T|NDOR1_ENST00000427047.2_5'Flank|TPRN_ENST00000541945.1_5'Flank|NDOR1_ENST00000458322.2_5'Flank|NDOR1_ENST00000344894.5_5'Flank	NM_053045.1	NP_444273.1	Q969S6	TM203_HUMAN	transmembrane protein 203	64						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)		ACACGATGGTGGTGAAGTAGG	0.617													G|||	33	0.00658946	0.0212	0.0072	5008	,	,		15733	0.0		0.0	False		,,,				2504	0.0				p.T64T		Atlas-SNP	.											TMEM203,NS,carcinoma,0,1	TMEM203	8	1	0			c.C192T						PASS	.	G		83,4319	70.3+/-108.2	1,81,2119	45	47	46		192	3.1	1	9	dbSNP_132	46	0,8584		0,0,4292	no	coding-synonymous	TMEM203	NM_053045.1		1,81,6411	AA,AG,GG		0.0,1.8855,0.6391		64/137	140099675	83,12903	2201	4292	6493	SO:0001819	synonymous_variant	94107	exon1			GATGGTGGTGAAG	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.192C>T	9.37:g.140099675G>A		77	0	0		80	56	0.7	NM_053045	Q6NW08	Silent	SNP	ENST00000343666.5	37	CCDS35185.1																																																																																			G|0.992;A|0.008	0.008	strong		0.617	TMEM203-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055325.2	NM_053045		A	140099675	G	A	140099675	2	1	22	1	0	0	0	0	0	0	0	1	16143	1335	47	2		2	TMEM203	9	140099675	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	12735	140099675	1113756	2218	5119											
NDOR1	27158	hgsc.bcm.edu	37	chr9	140108468	140108468	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gagacttgtgggacagggttCtggggctgtacccgccgcct	5	9	16	11	2	1	1	0	0	1	1	1	3	1	2	3	4	1	3	3	4	1	3	rs114934623	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140108468C>T	ENST00000344894.5	+	5	543	c.460C>T	c.(460-462)Ctg>Ttg	p.L154L	NDOR1_ENST00000371521.4_Silent_p.L154L|NDOR1_ENST00000427047.2_Intron|NDOR1_ENST00000458322.2_Silent_p.L154L	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)		GGACAGGGTTCTGGGGCTGTA	0.711													C|||	26	0.00519169	0.0182	0.0029	5008	,	,		14886	0.0		0.0	False		,,,				2504	0.0				p.L154L		Atlas-SNP	.											.	NDOR1	71	.	0			c.C460T						PASS	.	C	,,,	43,4245		0,43,2101	18	22	21		460,,460,460	2.3	0.6	9	dbSNP_132	21	0,8378		0,0,4189	no	coding-synonymous,intron,coding-synonymous,coding-synonymous	NDOR1	NM_001144026.1,NM_001144027.1,NM_001144028.1,NM_014434.2	,,,	0,43,6290	TT,TC,CC		0.0,1.0028,0.3395	,,,	154/607,,154/591,154/598	140108468	43,12623	2144	4189	6333	SO:0001819	synonymous_variant	27158	exon5			AGGGTTCTGGGGC	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.460C>T	9.37:g.140108468C>T		36	0	0		69	15	0.217391	NM_001144026		Silent	SNP	ENST00000344894.5	37	CCDS7036.1																																																																																			C|0.994;T|0.006	0.006	strong		0.711	NDOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254704.1	NM_014434		T	140108468	C	T	140108468	2	4	22	1	0	0	0	0	0	0	0	1	10258	912	32	2		2	NDOR1	9	140108468	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	8793	140108468	1104963	2219	5120											
FAM166A	401565	hgsc.bcm.edu	37	chr9	140140188	140140188	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgaacttgggtttggacatGggggacagcacagagcaggg	11	7	17	6	0	0	2	0	1	0	1	0	4	0	4	0	5	3	3	0	5	1	2	rs112239130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140140188G>A	ENST00000344774.4	-	2	228	c.174C>T	c.(172-174)ccC>ccT	p.P58P	FAM166A_ENST00000388932.2_Silent_p.P58P	NM_001001710.1	NP_001001710.1	Q6J272	F166A_HUMAN	family with sequence similarity 166, member A	58						nucleus (GO:0005634)				kidney(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(2)	15						GTTTGGACATGGGGGACAGCA	0.622													G|||	33	0.00658946	0.0234	0.0029	5008	,	,		18282	0.0		0.0	False		,,,				2504	0.0				p.P58P		Atlas-SNP	.											.	FAM166A	44	.	0			c.C174T						PASS	.	G		69,4337	63.5+/-100.7	0,69,2134	55	58	57		174	-2.9	0.3	9	dbSNP_132	57	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	FAM166A	NM_001001710.1		0,70,6432	AA,AG,GG		0.0116,1.566,0.5383		58/318	140140188	70,12934	2203	4299	6502	SO:0001819	synonymous_variant	401565	exon2			GGACATGGGGGAC	BC132916	CCDS35186.1	9q34.3	2008-08-08			ENSG00000188163	ENSG00000188163			33818	protein-coding gene	gene with protein product							Standard	XR_245332		Approved		uc004cmi.1	Q6J272	OTTHUMG00000159545	ENST00000344774.4:c.174C>T	9.37:g.140140188G>A		135	0	0		116	76	0.655172	NM_001001710	A6NND9|Q8N830	Silent	SNP	ENST00000344774.4	37	CCDS35186.1																																																																																			G|0.992;A|0.008	0.008	strong		0.622	FAM166A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356125.1	NM_001001710		A	140140188	G	A	140140188	2	1	22	1	0	0	0	0	0	0	0	1	5486	1335	47	2		2	FAM166A	9	140140188	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	31720	140140188	1073243	2220	5121											
C9orf173	441476	hgsc.bcm.edu	37	chr9	140146526	140146526	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtaccaggtgccgagcccGtccgtacgagagtcctcccc	7	6	12	16	4	0	1	0	0	0	1	3	3	3	1	7	2	4	2	7	2	2	2	rs74822962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140146526G>A	ENST00000412566.1	+	3	351	c.342G>A	c.(340-342)ccG>ccA	p.P114P	C9orf173_ENST00000388931.3_Silent_p.P114P			Q8N7X2	CI173_HUMAN	chromosome 9 open reading frame 173	114								p.P114P(1)		kidney(1)|large_intestine(1)|lung(5)|pancreas(1)	8						TGCCGAGCCCGTCCGTACGAG	0.672													G|||	36	0.0071885	0.0257	0.0029	5008	,	,		16156	0.0		0.0	False		,,,				2504	0.0				p.P114P		Atlas-SNP	.											C9orf173,colon,carcinoma,0,1	C9orf173	19	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G342A						PASS	.	G		64,4044		0,64,1990	40	50	47		342	-7.8	0	9	dbSNP_132	47	1,8369		0,1,4184	no	coding-synonymous	C9orf173	NM_001004353.2		0,65,6174	AA,AG,GG		0.0119,1.5579,0.5209		114/309	140146526	65,12413	2054	4185	6239	SO:0001819	synonymous_variant	441476	exon3			GAGCCCGTCCGTA		CCDS48065.1, CCDS59156.1, CCDS75940.1, CCDS75941.1	9q34.3	2009-10-02			ENSG00000197768	ENSG00000197768			37285	protein-coding gene	gene with protein product							Standard	NM_001256699		Approved	FLJ40246	uc004cmk.2	Q8N7X2		ENST00000412566.1:c.342G>A	9.37:g.140146526G>A		58	0	0		71	52	0.732394	NM_001256701	A2RU24|B7ZM72|B7ZM76|Q8NEA3	Silent	SNP	ENST00000412566.1	37	CCDS48065.1																																																																																			G|0.991;A|0.009	0.009	strong		0.672	C9orf173-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004353		A	140146526	G	A	140146526	2	1	22	1	0	0	0	0	0	0	0	1	2474	1132	40	1		1	C9orf173	9	140146526	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6338	140146526	1066905	2221	5122											
EXD3	54932	hgsc.bcm.edu	37	chr9	140247103	140247103	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgaaccggcggagttccaCagccaccgcagccggcagcc	8	3	12	18	4	0	1	0	1	0	0	1	2	1	2	7	3	4	3	7	3	1	1	rs115998217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140247103C>T	ENST00000340951.4	-	11	1201	c.1006G>A	c.(1006-1008)Gtg>Atg	p.V336M	EXD3_ENST00000342129.4_Missense_Mutation_p.V16M	NM_017820.3	NP_060290.3	Q9NX53	MUT7B_HUMAN	exonuclease 3'-5' domain containing 3	0										NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)	12						CGGAGTTCCACAGCCACCGCA	0.701													C|||	163	0.0325479	0.1142	0.0101	5008	,	,		8184	0.001		0.004	False		,,,				2504	0.0				p.V336M		Atlas-SNP	.											.	EXD3	86	.	0			c.G1006A						PASS	.	C	MET/VAL	259,3395		3,253,1571	5	7	6		1006	-0.7	0	9	dbSNP_132	6	35,7739		0,35,3852	yes	missense	EXD3	NM_017820.3	21	3,288,5423	TT,TC,CC		0.4502,7.0881,2.5726	benign	336/877	140247103	294,11134	1827	3887	5714	SO:0001583	missense	54932	exon11			GTTCCACAGCCAC		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.1006G>A	9.37:g.140247103C>T	ENSP00000340474:p.Val336Met	47	0	0		78	29	0.371795	NM_017820	Q6P1M1|Q8IXT8	Missense_Mutation	SNP	ENST00000340951.4	37	CCDS48066.1	84	0.038461538461538464	78	0.15853658536585366	3	0.008287292817679558	0	0.0	3	0.00395778364116095	C	10.88	1.476873	0.26511	0.070881	0.004502	ENSG00000187609	ENST00000342129;ENST00000340951	T;T	0.64085	-0.08;0.68	3.69	-0.678	0.11353	.	0.954002	0.08598	N	0.921938	T	0.00210	0.0006	N	0.22421	0.69	0.80722	P	0.0	P;P	0.46327	0.876;0.831	B;B	0.41036	0.346;0.254	T	0.01848	-1.1261	9	0.54805	T	0.06	.	4.8317	0.13443	0.0:0.5455:0.1562:0.2983	.	16;336	Q8N9H8-3;Q8N9H8	.;MUT7_HUMAN	M	16;336	ENSP00000343705:V16M;ENSP00000340474:V336M	ENSP00000340474:V336M	V	-	1	0	EXD3	139366924	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.999000	0.03697	-0.415000	0.07484	-0.494000	0.04653	GTG	C|0.960;T|0.040	0.040	strong		0.701	EXD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343182.1	NM_017820		T	140247103	C	T	140247103	3	4	22	1	0	0	0	0	1	0	0	0	5301	478	17	2	1672	2	EXD3	9	140247103	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	100577	140247103	966328	2222	5123											
WDR85	92715	hgsc.bcm.edu	37	chr9	140472034	140472034	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	acggcctaaacggacctgagGctccttaacttccattccac	10	9	7	15	2	0	1	0	1	0	0	3	2	3	2	5	3	2	1	5	3	3	4			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140472034G>C	ENST00000277540.2	-	2	332	c.175C>G	c.(175-177)Cct>Gct	p.P59A	DPH7_ENST00000479650.1_Intron	NM_138778.2	NP_620133.1	Q9BTV6	DPH7_HUMAN	diphthamide biosynthesis 7	59					peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)												CGGACCTGAGGCTCCTTAACT	0.458																																					p.P59A		Atlas-SNP	.											.	WDR85	20	.	0			c.C175G						PASS	.						110	98	102					9																	140472034		2203	4300	6503	SO:0001583	missense	92715	exon2			CCTGAGGCTCCTT	AK075115	CCDS7047.1	9q34.3	2013-06-20	2013-06-20	2013-06-20	ENSG00000148399	ENSG00000148399		"WD repeat domain containing"	25199	protein-coding gene	gene with protein product		613210	"chromosome 9 open reading frame 112", "WD repeat domain 85"	C9orf112, WDR85		23486472	Standard	NM_138778		Approved	FLJ90634, RRT2	uc004cnk.1	Q9BTV6	OTTHUMG00000020991	ENST00000277540.2:c.175C>G	9.37:g.140472034G>C	ENSP00000277540:p.Pro59Ala	106	0	0		133	92	0.691729	NM_138778	Q96AB7	Missense_Mutation	SNP	ENST00000277540.2	37	CCDS7047.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.471496	0.43942	.	.	ENSG00000148399	ENST00000277540	T	0.12569	2.67	5.11	4.2	0.49525	.	0.243332	0.33875	N	0.004464	T	0.09468	0.0233	L	0.32530	0.975	0.29436	N	0.859517	B	0.33549	0.417	B	0.30105	0.111	T	0.11690	-1.0577	10	0.21540	T	0.41	.	10.6122	0.45429	0.0936:0.0:0.9064:0.0	.	59	Q9BTV6	WDR85_HUMAN	A	59	ENSP00000277540:P59A	ENSP00000277540:P59A	P	-	1	0	WDR85	139591855	0.998000	0.40836	0.361000	0.25849	0.016000	0.09150	1.030000	0.30153	2.363000	0.80096	0.455000	0.32223	CCT	.	.	none		0.458	DPH7-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055350.1	NM_138778		C	140472034	G	C	140472034	3	2	22	1	0	0	0	0	1	0	0	0	17348	1203	42	4	1215	4	WDR85	9	140472034	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	224931	140472034	741397	2223	5124											
EHMT1	79813	hgsc.bcm.edu	37	chr9	140671147	140671147	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgtgcctctcgagtcaataaCgccagctattgtccccactg	8	11	8	14	2	2	0	1	0	1	0	4	1	3	0	4	0	3	1	4	0	3	3	rs7868455	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140671147C>T	ENST00000460843.1	+	12	1896	c.1869C>T	c.(1867-1869)aaC>aaT	p.N623N	EHMT1_ENST00000371394.2_3'UTR|EHMT1_ENST00000334856.6_Silent_p.N592N|EHMT1_ENST00000462484.1_Silent_p.N623N	NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	623					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)		GAGTCAATAACGCCAGCTATT	0.527													C|||	315	0.0628994	0.2315	0.0115	5008	,	,		18209	0.0		0.001	False		,,,				2504	0.0				p.N623N		Atlas-SNP	.											.	EHMT1	196	.	0			c.C1869T						PASS	.	C	,	712,3694	297.3+/-284.7	63,586,1554	126	111	116		1869,1869	-6.8	0.8	9	dbSNP_116	116	11,8589	7.7+/-29.5	0,11,4289	no	coding-synonymous,coding-synonymous	EHMT1	NM_001145527.1,NM_024757.4	,	63,597,5843	TT,TC,CC		0.1279,16.1598,5.559	,	623/809,623/1299	140671147	723,12283	2203	4300	6503	SO:0001819	synonymous_variant	79813	exon12			CAATAACGCCAGC	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.1869C>T	9.37:g.140671147C>T		122	0	0		126	126	1	NM_001145527	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Silent	SNP	ENST00000460843.1	37	CCDS7050.2																																																																																			C|0.939;T|0.061	0.061	strong		0.527	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757		T	140671147	C	T	140671147	2	4	22	1	0	0	0	0	0	0	0	1	4985	535	19	1		1	EHMT1	9	140671147	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	199113	140671147	542284	2224	5125											
EHMT1	79813	hgsc.bcm.edu	37	chr9	140707590	140707590	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctctgcaggactcggccccCgacaggcccagccccgtgga	6	4	13	18	3	1	0	0	0	1	0	2	3	1	2	5	4	2	2	5	4	0	0	rs35943616	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140707590C>T	ENST00000460843.1	+	20	3027	c.3000C>T	c.(2998-3000)ccC>ccT	p.P1000P		NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	1000					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)		ACTCGGCCCCCGACAGGCCCA	0.622													C|||	555	0.110823	0.4017	0.0274	5008	,	,		17819	0.005		0.0	False		,,,				2504	0.0				p.P1000P		Atlas-SNP	.											.	EHMT1	196	.	0			c.C3000T						PASS	.	C		1428,2978	446.9+/-348.2	236,956,1011	34	40	38		3000	-9.4	0	9	dbSNP_126	38	12,8588	7.7+/-29.5	1,10,4289	no	coding-synonymous	EHMT1	NM_024757.4		237,966,5300	TT,TC,CC		0.1395,32.4103,11.0718		1000/1299	140707590	1440,11566	2203	4300	6503	SO:0001819	synonymous_variant	79813	exon20			GGCCCCCGACAGG	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.3000C>T	9.37:g.140707590C>T		47	0	0		64	64	1	NM_024757	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Silent	SNP	ENST00000460843.1	37	CCDS7050.2																																																																																			C|0.899;T|0.101	0.101	strong		0.622	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757		T	140707590	C	T	140707590	2	4	22	1	0	0	0	0	0	0	0	1	4985	639	23	1		1	EHMT1	9	140707590	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	36443	140707590	505841	2225	5126											
TUBB8	347688	hgsc.bcm.edu	37	chr10	94562	94562	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcccgcagctcaccgaagatGaagttgtctggcctgaagac	10	7	12	12	2	2	4	1	2	1	2	2	5	2	4	3	1	1	3	3	1	3	1	rs145350711	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:94562G>A	ENST00000309812.4	-	3	332	c.270C>T	c.(268-270)ttC>ttT	p.F90F	TUBB8_ENST00000332708.5_Missense_Mutation_p.S54L|TUBB8_ENST00000413237.3_5'UTR|TUBB8_ENST00000447903.2_Silent_p.F18F	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	90					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)		CACCGAAGATGAAGTTGTCTG	0.637													g|||	2	0.000399361	0.0015	0.0	5008	,	,		15565	0.0		0.0	False		,,,				2504	0.0				p.F90F	Pancreas(192;2041 3010 9013 18103)	Atlas-SNP	.											.	TUBB8	62	.	0			c.C270T						PASS	.	G		16,4386	21.2+/-45.6	0,16,2185	42	52	49		270	0.1	0	10	dbSNP_134	49	0,8596		0,0,4298	no	coding-synonymous	TUBB8	NM_177987.2		0,16,6483	AA,AG,GG		0.0,0.3635,0.1231		90/445	94562	16,12982	2201	4298	6499	SO:0001819	synonymous_variant	347688	exon3			GAAGATGAAGTTG	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.270C>T	10.37:g.94562G>A		107	0	0		111	62	0.558559	NM_177987	Q5SQX9|Q8WZ78	Silent	SNP	ENST00000309812.4	37	CCDS7051.1	.	.	.	.	.	.	.	.	.	.	G	6.257	0.415577	0.11870	0.003635	0.0	ENSG00000173876	ENST00000332708	.	.	.	0.109	0.109	0.14578	.	.	.	.	.	T	0.55497	0.1924	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55598	-0.8116	5	0.87932	D	0	.	2.6667	0.05054	0.4741:0.0:0.5259:0.0	.	.	.	.	L	54	.	ENSP00000371071:S54L	S	-	2	0	RP11-631M21.2	84562	0.988000	0.35896	0.031000	0.17742	0.032000	0.12392	0.081000	0.14823	0.181000	0.19994	0.184000	0.17185	TCA	G|0.999;A|0.001	0.001	strong		0.637	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987		A	94562	G	A	94562	2	1	22	1	0	0	0	0	0	0	0	1	16776	1281	45	2		2	TUBB8	10	94562	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10		94562	135440185	2226	5127											
ADARB2	105	hgsc.bcm.edu	37	chr10	1405835	1405835	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acctccaccgctaccgcgaaGaccggggcatgcaccgggcc	8	3	12	18	5	0	1	0	0	0	1	1	2	1	1	7	3	2	3	7	3	2	1	rs35398040	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:1405835G>A	ENST00000381312.1	-	3	790	c.465C>T	c.(463-465)gtC>gtT	p.V155V	RP11-398B16.2_ENST00000432987.1_RNA	NM_018702.3	NP_061172.1	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2 (non-functional)	155	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)		CTACCGCGAAGACCGGGGCAT	0.692													g|||	72	0.014377	0.0522	0.0043	5008	,	,		9729	0.0		0.0	False		,,,				2504	0.0				p.V155V		Atlas-SNP	.											.	ADARB2	95	.	0			c.C465T						PASS	.			185,4221	107.8+/-146.2	5,175,2023	35	30	32		465	1.2	1	10	dbSNP_126	32	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ADARB2	NM_018702.3		5,176,6322	AA,AG,GG		0.0116,4.1988,1.4301		155/740	1405835	186,12820	2203	4300	6503	SO:0001819	synonymous_variant	105	exon3			CGCGAAGACCGGG	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.465C>T	10.37:g.1405835G>A		74	0	0		115	114	0.991304	NM_018702	B2RPJ5|Q5VUT6|Q5VW42	Silent	SNP	ENST00000381312.1	37	CCDS7058.1																																																																																			G|0.981;A|0.019	0.019	strong		0.692	ADARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046426.1	NM_018702		A	1405835	G	A	1405835	2	1	22	1	0	0	0	0	0	0	0	1	283	929	33	2		2	ADARB2	10	1405835	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1311273	1405835	134128912	2227	5128											
PFKP	5214	hgsc.bcm.edu	37	chr10	3177944	3177944	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ataggaaaaaaatttaccacCgatgattccatttgtgtgct	14	13	7	7	1	0	1	0	1	0	0	1	3	1	2	3	1	2	1	3	1	5	5	rs61731934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:3177944C>T	ENST00000381125.4	+	21	2215	c.2139C>T	c.(2137-2139)acC>acT	p.T713T	PITRM1_ENST00000464395.1_5'Flank|PFKP_ENST00000381075.2_Silent_p.T705T|PFKP_ENST00000381072.1_Silent_p.T131T	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	713	C-terminal regulatory PFK domain 2.				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)		AATTTACCACCGATGATTCCA	0.413													C|||	53	0.0105831	0.0356	0.0043	5008	,	,		18020	0.0		0.001	False		,,,				2504	0.002				p.T713T		Atlas-SNP	.											PFKP_ENST00000381075,NS,carcinoma,+2,2	PFKP	182	2	0			c.C2139T						PASS	.	C	,	224,4182	130.6+/-167.2	9,206,1988	62	63	63		2115,2139	-7.3	0	10	dbSNP_129	63	5,8595	5.0+/-18.6	0,5,4295	yes	coding-synonymous,coding-synonymous	PFKP	NM_001242339.1,NM_002627.4	,	9,211,6283	TT,TC,CC		0.0581,5.084,1.7607	,	705/777,713/785	3177944	229,12777	2203	4300	6503	SO:0001819	synonymous_variant	5214	exon21			TACCACCGATGAT	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.2139C>T	10.37:g.3177944C>T		51	0	0		76	40	0.526316	NM_002627	B3KS15|Q5VSR7|Q5VSR8	Silent	SNP	ENST00000381125.4	37	CCDS7059.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	c	2.293	-0.362014	0.05103	0.05084	5.81E-4	ENSG00000067057	ENST00000433193	.	.	.	5.21	-7.26	0.01466	.	.	.	.	.	T	0.19846	0.0477	.	.	.	0.48288	D	0.999629	.	.	.	.	.	.	T	0.59413	-0.7459	4	.	.	.	.	13.2504	0.60048	0.0:0.5807:0.1633:0.256	rs61731934	.	.	.	L	66	.	.	P	+	2	0	PFKP	3167944	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-5.635000	0.00108	-1.087000	0.03081	-1.012000	0.02466	CCG	C|0.983;T|0.017	0.017	strong		0.413	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627		T	3177944	C	T	3177944	2	4	22	1	0	0	0	0	0	0	0	1	11775	639	23	1		1	PFKP	10	3177944	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1772109	3177944	132356803	2228	5129											
PITRM1	10531	hgsc.bcm.edu	37	chr10	3187831	3187831	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctccgttcctttttactcCgaccgatgcttctaaggaag	7	13	8	13	3	1	0	0	0	1	0	4	3	4	1	5	1	2	2	5	1	3	6	rs34837384	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:3187831C>T	ENST00000224949.4	-	21	2448	c.2414G>A	c.(2413-2415)cGg>cAg	p.R805Q	PITRM1_ENST00000451104.2_Missense_Mutation_p.R707Q|PITRM1_ENST00000464395.1_5'UTR|PITRM1-AS1_ENST00000441377.1_RNA|PITRM1_ENST00000380989.2_Missense_Mutation_p.R806Q|PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000380994.1_Missense_Mutation_p.R363Q|PITRM1-AS1_ENST00000601046.1_RNA			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	805			R -> Q (in dbSNP:rs34837384).		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						CTTTTTACTCCGACCGATGCT	0.547													C|||	45	0.00898562	0.0325	0.0029	5008	,	,		17900	0.0		0.0	False		,,,				2504	0.0				p.R806Q		Atlas-SNP	.											.	PITRM1	109	.	0			c.G2417A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	145,3603		5,135,1734	51	52	52		2417,2120,2414	3.4	0	10	dbSNP_126	52	1,7975		0,1,3987	yes	missense,missense,missense	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	43,43,43	5,136,5721	TT,TC,CC		0.0125,3.8687,1.2453	benign,benign,benign	806/1039,707/940,805/1038	3187831	146,11578	1874	3988	5862	SO:0001583	missense	10531	exon21			TTACTCCGACCGA	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.2414G>A	10.37:g.3187831C>T	ENSP00000224949:p.Arg805Gln	100	0	0		81	41	0.506173	NM_001242307	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	37	CCDS59208.1	15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	c	13.97	2.394997	0.42512	0.038687	1.25E-4	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000380994;ENST00000451104;ENST00000424714	T;T;T;T;T	0.54866	1.57;1.57;1.57;1.57;0.55	5.29	3.43	0.39272	Peptidase M16, C-terminal (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.301189	0.35495	N	0.003174	T	0.14570	0.0352	L	0.46947	1.48	0.09310	N	1	B;B;B;B;B	0.24043	0.017;0.045;0.056;0.056;0.096	B;B;B;B;B	0.26969	0.005;0.046;0.075;0.075;0.075	T	0.08126	-1.0737	10	0.17369	T	0.5	-8.921	12.181	0.54211	0.0:0.8592:0.0:0.1408	rs34837384	798;707;806;805;798	E9PDX6;E7ES23;C9JSL2;Q5JRX3;B4DH07	.;.;.;PREP_HUMAN;.	Q	805;798;806;363;707;24	ENSP00000224949:R805Q;ENSP00000370377:R806Q;ENSP00000370382:R363Q;ENSP00000401201:R707Q;ENSP00000402072:R24Q	ENSP00000224949:R805Q	R	-	2	0	PITRM1	3177831	0.021000	0.18746	0.004000	0.12327	0.004000	0.04260	1.792000	0.38754	0.725000	0.32318	0.462000	0.41574	CGG	C|0.992;T|0.008	0.008	strong		0.547	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2			T	3187831	C	T	3187831	3	4	22	1	0	0	0	0	1	0	0	0	11962	652	23	1	727	1	PITRM1	10	3187831	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	9887	3187831	132346916	2229	5130											
PITRM1	10531	hgsc.bcm.edu	37	chr10	3214939	3214939	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gccgcctcagcacacacaggCcctgccgcccgccgcagcgc	6	2	11	22	5	1	0	1	0	0	0	1	0	1	0	6	1	3	2	6	1	0	0	rs199766052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:3214939C>A	ENST00000224949.4	-	1	60	c.26G>T	c.(25-27)gGc>gTc	p.G9V	PITRM1_ENST00000451104.2_Silent_p.G11G|PITRM1_ENST00000380989.2_Missense_Mutation_p.G9V			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	9					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						CACACACAGGCCCTGCCGCCC	0.751													C|||	58	0.0115815	0.0416	0.0029	5008	,	,		8716	0.0		0.0	False		,,,				2504	0.001				p.G9V		Atlas-SNP	.											.	PITRM1	109	.	0			c.G26T						PASS	.	C	VAL/GLY,,VAL/GLY	125,3595		1,123,1736	4	7	6		26,33,26	-4.6	0	10		6	3,7519		0,3,3758	no	missense,coding-synonymous,missense	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	109,,109	1,126,5494	AA,AC,CC		0.0399,3.3602,1.1386	benign,,benign	9/1039,11/940,9/1038	3214939	128,11114	1860	3761	5621	SO:0001583	missense	10531	exon1			CACAGGCCCTGCC	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.26G>T	10.37:g.3214939C>A	ENSP00000224949:p.Gly9Val	22	0	0		58	29	0.5	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	37	CCDS59208.1	.	.	.	.	.	.	.	.	.	.	C	11.07	1.530296	0.27387	0.033602	3.99E-4	ENSG00000107959	ENST00000224949;ENST00000380989	T;T	0.03920	3.76;3.76	3.31	-4.59	0.03400	.	2.102200	0.01907	N	0.039579	T	0.01092	0.0036	.	.	.	0.09310	N	0.999998	B;B	0.18968	0.032;0.019	B;B	0.19391	0.025;0.011	T	0.42699	-0.9436	9	0.30078	T	0.28	.	7.0117	0.24865	0.2341:0.5702:0.1957:0.0	.	9;9	Q5JRX3-2;Q5JRX3	.;PREP_HUMAN	V	9	ENSP00000224949:G9V;ENSP00000370377:G9V	ENSP00000224949:G9V	G	-	2	0	PITRM1	3204939	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.319000	0.08039	-0.576000	0.05974	0.313000	0.20887	GGC	.	.	weak		0.751	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2			A	3214939	C	A	3214939	3	1	22	1	0	0	0	0	1	0	0	0	11962	739	26	4	3195	4	PITRM1	10	3214939	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	27108	3214939	132319808	2230	5131											
AKR1C2	1646	hgsc.bcm.edu	37	chr10	5043749	5043749	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctctcttcacactgccatctGcaatcttgcttcggatggcc	6	13	7	15	1	4	0	1	0	3	0	6	1	4	1	2	2	3	2	2	2	1	3	rs147648222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:5043749G>A	ENST00000380753.4	-	2	396	c.209C>T	c.(208-210)gCa>gTa	p.A70V	AKR1C2_ENST00000407674.1_Missense_Mutation_p.A70V|AKR1C2_ENST00000455190.1_Missense_Mutation_p.A70V|AKR1C2_ENST00000421196.3_Missense_Mutation_p.A70V	NM_205845.2	NP_995317.1	P52895	AK1C2_HUMAN	aldo-keto reductase family 1, member C2	70					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)	ACTGCCATCTGCAATCTTGCT	0.443													G|||	17	0.00339457	0.0121	0.0	5008	,	,		21154	0.0		0.001	False		,,,				2504	0.0				p.A70V		Atlas-SNP	.											.	AKR1C2	68	.	0			c.C209T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA	44,4362	48.2+/-83.0	1,42,2160	132	114	120		209,209,209	-1.2	0.9	10	dbSNP_134	120	0,8596		0,0,4298	no	missense,missense,missense	AKR1C2	NM_001135241.1,NM_001354.4,NM_205845.1	64,64,64	1,42,6458	AA,AG,GG		0.0,0.9986,0.3384	benign,benign,benign	70/140,70/324,70/324	5043749	44,12958	2203	4298	6501	SO:0001583	missense	1646	exon4			CCATCTGCAATCT	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.209C>T	10.37:g.5043749G>A	ENSP00000370129:p.Ala70Val	297	0	0		328	172	0.52439	NM_001354	A8K2N9|B4DKR9|Q14133|Q5SR16|Q7M4N1|Q96A71	Missense_Mutation	SNP	ENST00000380753.4	37	CCDS7062.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	G	8.905	0.957221	0.18507	0.009986	0.0	ENSG00000151632	ENST00000380753;ENST00000421196;ENST00000407674;ENST00000455190	T;T;T;T	0.52526	0.66;0.66;0.66;0.66	2.35	-1.18	0.09617	NADP-dependent oxidoreductase domain (3);	0.225703	0.28730	N	0.014335	T	0.33177	0.0854	M	0.65498	2.005	0.20821	N	0.999846	B;B;B	0.30526	0.283;0.128;0.063	B;B;B	0.30646	0.118;0.071;0.057	T	0.36744	-0.9735	10	0.62326	D	0.03	.	9.2164	0.37351	0.0:0.0:0.4586:0.5414	.	70;70;70	B4DKR9;B4DK69;P52895	.;.;AK1C2_HUMAN	V	70	ENSP00000370129:A70V;ENSP00000392694:A70V;ENSP00000385221:A70V;ENSP00000408440:A70V	ENSP00000370129:A70V	A	-	2	0	AKR1C2	5033749	0.876000	0.30132	0.896000	0.35187	0.326000	0.28443	3.023000	0.49666	-0.272000	0.09259	0.205000	0.17691	GCA	G|0.998;A|0.002	0.002	strong		0.443	AKR1C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046531.1	NM_001354		A	5043749	G	A	5043749	3	1	22	1	0	0	0	0	1	0	0	0	470	1319	46	2	849	2	AKR1C2	10	5043749	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1828810	5043749	130490998	2231	5132											
UCN3	114131	hgsc.bcm.edu	37	chr10	5416027	5416027	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccaggacacggccaagagtcCccaccgcaccaagttcaccc	11	3	8	19	2	1	1	1	0	0	1	2	2	2	2	7	2	0	2	7	2	2	1	rs201708420	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:5416027C>G	ENST00000380433.3	+	2	572	c.344C>G	c.(343-345)cCc>cGc	p.P115R		NM_053049.2	NP_444277.2	Q969E3	UCN3_HUMAN	urocortin 3	115					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|digestion (GO:0007586)|positive regulation of insulin secretion (GO:0032024)|positive regulation of membrane potential (GO:0045838)|response to corticosterone (GO:0051412)|response to glucose (GO:0009749)|response to immobilization stress (GO:0035902)|response to starvation (GO:0042594)	axon terminus (GO:0043679)|extracellular space (GO:0005615)|varicosity (GO:0043196)				endometrium(1)|large_intestine(1)	2						GCCAAGAGTCCCCACCGCACC	0.642													.|||	4	0.000798722	0.003	0.0	5008	,	,		10358	0.0		0.0	False		,,,				2504	0.0				p.P115R		Atlas-SNP	.											.	UCN3	13	.	0			c.C344G						PASS	.	C	ARG/PRO	4,4402	8.1+/-20.4	0,4,2199	74	76	76		344	1.7	0	10		76	0,8600		0,0,4300	yes	missense	UCN3	NM_053049.2	103	0,4,6499	GG,GC,CC		0.0,0.0908,0.0308	possibly-damaging	115/162	5416027	4,13002	2203	4300	6503	SO:0001583	missense	114131	exon2			AGAGTCCCCACCG	AF361943	CCDS7065.1	10p15.1	2013-02-28	2012-10-17		ENSG00000178473	ENSG00000178473		"Endogenous ligands"	17781	protein-coding gene	gene with protein product	"stresscopin", "prepro-urocortin 3"	605901				11416224	Standard	NM_053049		Approved	UCNIII, SPC	uc001ihx.1	Q969E3	OTTHUMG00000017594	ENST00000380433.3:c.344C>G	10.37:g.5416027C>G	ENSP00000369798:p.Pro115Arg	45	0	0		57	25	0.438596	NM_053049	Q496H2|Q5SR91	Missense_Mutation	SNP	ENST00000380433.3	37	CCDS7065.1	.	.	.	.	.	.	.	.	.	.	C	6.795	0.515627	0.12944	9.08E-4	0.0	ENSG00000178473	ENST00000380433	T	0.30182	1.54	5.49	1.67	0.24075	.	0.332477	0.29884	N	0.010946	T	0.18045	0.0433	N	0.22421	0.69	0.23144	N	0.998221	B	0.23490	0.086	B	0.21360	0.034	T	0.16630	-1.0396	10	0.59425	D	0.04	-11.4379	7.1327	0.25510	0.6324:0.291:0.0767:0.0	.	115	Q969E3	UCN3_HUMAN	R	115	ENSP00000369798:P115R	ENSP00000369798:P115R	P	+	2	0	UCN3	5406027	1.000000	0.71417	0.003000	0.11579	0.007000	0.05969	3.203000	0.51075	0.390000	0.25115	-0.500000	0.04577	CCC	.	.	weak		0.642	UCN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046547.1	NM_053049		G	5416027	C	G	5416027	3	3	22	1	0	0	0	0	1	0	0	0	16944	623	22	4	346	4	UCN3	10	5416027	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	372278	5416027	130118720	2232	5133											
NET1	10276	hgsc.bcm.edu	37	chr10	5498102	5498102	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttctgactcggcccgtcaCacggaacgaacggcactctt	8	8	11	14	5	3	1	1	1	2	0	4	3	3	2	1	4	2	2	1	4	2	2	rs34658946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:5498102C>T	ENST00000355029.4	+	11	1392	c.1250C>T	c.(1249-1251)aCa>aTa	p.T417I	NET1_ENST00000380359.3_Missense_Mutation_p.T363I|NET1_ENST00000484741.1_3'UTR|NET1_ENST00000542715.1_Missense_Mutation_p.T236I	NM_001047160.2	NP_001040625.1	Q7Z628	ARHG8_HUMAN	neuroepithelial cell transforming 1	417	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.		T -> I (in dbSNP:rs34658946).		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						CGGCCCGTCACACGGAACGAA	0.473													C|||	76	0.0151757	0.056	0.0029	5008	,	,		18225	0.0		0.0	False		,,,				2504	0.0				p.T417I		Atlas-SNP	.											.	NET1	82	.	0			c.C1250T						PASS	.	C	ILE/THR,ILE/THR	177,4229	115.4+/-153.4	4,169,2030	88	90	89		1250,1088	4.7	1	10	dbSNP_126	89	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	NET1	NM_001047160.1,NM_005863.3	89,89	4,170,6329	TT,TC,CC		0.0116,4.0172,1.3686	benign,benign	417/597,363/543	5498102	178,12828	2203	4300	6503	SO:0001583	missense	10276	exon11			CCGTCACACGGAA	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.1250C>T	10.37:g.5498102C>T	ENSP00000347134:p.Thr417Ile	65	0	0		55	20	0.363636	NM_001047160	Q12773|Q96D82|Q99903|Q9UEN6	Missense_Mutation	SNP	ENST00000355029.4	37	CCDS41483.1	27	0.012362637362637362	25	0.0508130081300813	2	0.0055248618784530384	0	0.0	0	0.0	C	15.93	2.978394	0.53720	0.040172	1.16E-4	ENSG00000173848	ENST00000355029;ENST00000542715;ENST00000380359	T;T;T	0.31510	1.49;1.49;1.49	5.78	4.69	0.59074	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.43110	D	0.000603	T	0.06050	0.0157	L	0.49350	1.555	0.58432	D	0.999994	B;B	0.23490	0.048;0.086	B;B	0.34138	0.153;0.176	T	0.02491	-1.1151	10	0.48119	T	0.1	-20.9971	10.7957	0.46459	0.0:0.8395:0.0:0.1605	rs34658946	363;417	Q5SQI7;Q7Z628	.;ARHG8_HUMAN	I	417;236;363	ENSP00000347134:T417I;ENSP00000446452:T236I;ENSP00000369717:T363I	ENSP00000347134:T417I	T	+	2	0	NET1	5488102	0.967000	0.33354	0.997000	0.53966	0.951000	0.60555	2.640000	0.46579	2.735000	0.93741	0.557000	0.71058	ACA	C|0.984;T|0.016	0.016	strong		0.473	NET1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046553.3	NM_005863		T	5498102	C	T	5498102	3	4	22	1	0	0	0	0	1	0	0	0	10347	478	17	2	1389	2	NET1	10	5498102	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	82075	5498102	130036645	2233	5134											
ANKRD16	54522	hgsc.bcm.edu	37	chr10	5920244	5920244	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgacctgcacaggccagaTgcagggctgaggggtgacaa	10	5	16	10	0	0	4	0	3	0	1	0	4	0	4	2	4	2	4	2	4	1	0	rs61729846	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:5920244T>C	ENST00000380094.5	-	7	1478	c.935A>G	c.(934-936)cAt>cGt	p.H312R	ANKRD16_ENST00000191063.8_Missense_Mutation_p.I286V|ANKRD16_ENST00000380092.4_Missense_Mutation_p.H312R	NM_019046.2	NP_061919.1	Q6P6B7	ANR16_HUMAN	ankyrin repeat domain 16	312										breast(1)|endometrium(1)|large_intestine(5)|lung(3)|stomach(2)	12						ACAGGCCAGATGCAGGGCTGA	0.502													T|||	310	0.061901	0.2247	0.0173	5008	,	,		19150	0.0		0.001	False		,,,				2504	0.0				p.H312R		Atlas-SNP	.											.	ANKRD16	32	.	0			c.A935G						PASS	.	T	ARG/HIS,VAL/ILE,ARG/HIS	885,3521	343.8+/-307.8	98,689,1416	67	66	66		935,856,935	5	1	10	dbSNP_129	66	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense,missense	ANKRD16	NM_001009941.2,NM_001009943.2,NM_019046.2	29,29,29	98,694,5711	CC,CT,TT		0.0581,20.0862,6.843	probably-damaging,probably-damaging,probably-damaging	312/362,286/305,312/362	5920244	890,12116	2203	4300	6503	SO:0001583	missense	54522	exon7			GCCAGATGCAGGG	AL137614	CCDS31136.1, CCDS31137.1	10p15.1	2013-01-10			ENSG00000134461	ENSG00000134461		"Ankyrin repeat domain containing"	23471	protein-coding gene	gene with protein product							Standard	NM_019046		Approved	DKFZP434N1511	uc010qat.2	Q6P6B7	OTTHUMG00000017610	ENST00000380094.5:c.935A>G	10.37:g.5920244T>C	ENSP00000369436:p.His312Arg	33	0	0		47	30	0.638298	NM_001009941	A6NEF0|F8WEI4|Q9NT01	Missense_Mutation	SNP	ENST00000380094.5	37	CCDS31136.1	102|102	0.046703296703296704|0.046703296703296704	96|96	0.1951219512195122|0.1951219512195122	6|6	0.016574585635359115|0.016574585635359115	0|0	0.0|0.0	0|0	0.0|0.0	T|T	12.88|12.88	2.071823|2.071823	0.36566|0.36566	0.200862|0.200862	5.81E-4|5.81E-4	ENSG00000134461|ENSG00000134461	ENST00000380094;ENST00000380092|ENST00000191063	T;T|T	0.71461|0.58797	-0.57;-0.57|0.31	4.97|4.97	4.97|4.97	0.65823|0.65823	Ankyrin repeat-containing domain (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.00144|0.00144	0.0004|0.0004	M|M	0.85099|0.85099	2.735|2.735	0.35597|0.35597	P|P	0.192465|0.192465	D|B	0.89917|0.19073	1.0|0.033	D|B	0.91635|0.21917	0.999|0.037	T|T	0.20672|0.20672	-1.0268|-1.0268	9|8	0.51188|0.62326	T|D	0.08|0.03	-15.6176|-15.6176	13.4896|13.4896	0.61386|0.61386	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	312|286	Q6P6B7|F8WEI4	ANR16_HUMAN|.	R|V	312|286	ENSP00000369436:H312R;ENSP00000369434:H312R|ENSP00000352361:I286V	ENSP00000369434:H312R|ENSP00000352361:I286V	H|I	-|-	2|1	0|0	ANKRD16|ANKRD16	5960250|5960250	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.852000|0.852000	0.48524|0.48524	6.409000|6.409000	0.73289|0.73289	1.858000|1.858000	0.53909|0.53909	0.254000|0.254000	0.18369|0.18369	CAT|ATC	T|0.928;C|0.072	0.072	strong		0.502	ANKRD16-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046611.2	XM_166138		C	5920244	T	C	5920244	3	2	22	1	0	0	0	0	1	0	0	0	645	1464	51	3	154	3	ANKRD16	10	5920244	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	422142	5920244	129614503	2234	5135											
ITIH5	80760	hgsc.bcm.edu	37	chr10	7628027	7628027	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agaattgtgaagagggcatcCttggtctaggcaaacacaaa	15	8	11	7	0	1	3	0	1	1	2	2	3	2	3	1	3	1	2	1	3	5	3	rs11255206	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:7628027C>T	ENST00000256861.6	-	8	1023	c.945G>A	c.(943-945)aaG>aaA	p.K315K	ITIH5_ENST00000446830.2_Silent_p.K97K|ITIH5_ENST00000434980.1_5'UTR|ITIH5_ENST00000397146.2_Silent_p.K315K|ITIH5_ENST00000298441.6_Silent_p.K101K|ITIH5_ENST00000397145.2_Silent_p.K315K	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	315	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						AGAGGGCATCCTTGGTCTAGG	0.493													C|||	98	0.0195687	0.0643	0.0043	5008	,	,		17370	0.0069		0.002	False		,,,				2504	0.001				p.K315K		Atlas-SNP	.											.	ITIH5	343	.	0			c.G945A						PASS	.	C	,,	215,4191	126.6+/-163.6	5,205,1993	94	84	87		945,945,303	-0.6	1	10	dbSNP_120	87	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	ITIH5	NM_001001851.2,NM_030569.6,NM_032817.5	,,	5,209,6289	TT,TC,CC		0.0465,4.8797,1.6838	,,	315/703,315/943,101/729	7628027	219,12787	2203	4300	6503	SO:0001819	synonymous_variant	80760	exon8			GGCATCCTTGGTC			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.945G>A	10.37:g.7628027C>T		77	0	0		96	41	0.427083	NM_001001851	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Silent	SNP	ENST00000256861.6	37																																																																																				C|0.983;T|0.017	0.017	strong		0.493	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569		T	7628027	C	T	7628027	2	4	22	1	0	0	0	0	0	0	0	1	7916	680	24	2		2	ITIH5	10	7628027	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1707783	7628027	127906720	2235	5136											
GATA3	2625	hgsc.bcm.edu	37	chr10	8100632	8100632	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggagtcgtcccactcccgTggcagcatgaccgccctggg	5	7	13	16	3	0	1	0	1	0	0	3	2	2	2	4	3	1	2	4	3	0	0	rs2228254	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:8100632T>C	ENST00000346208.3	+	3	1061	c.606T>C	c.(604-606)cgT>cgC	p.R202R	GATA3_ENST00000461472.1_3'UTR|GATA3_ENST00000379328.3_Silent_p.R202R			P23771	GATA3_HUMAN	GATA binding protein 3	202					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						CCCACTCCCGTGGCAGCATGA	0.687			"F, N, S"		breast		"HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE)"						T|||	189	0.0377396	0.1392	0.0058	5008	,	,		14132	0.0		0.001	False		,,,				2504	0.0				p.R202R		Atlas-SNP	.		Rec	yes		10	10p15	2625	GATA binding protein 3	yes	E	.	GATA3	182	.	0			c.T606C						PASS	.	T	,	504,3902	227.8+/-242.9	31,442,1730	85	77	80		606,606	-11.1	0.4	10	dbSNP_98	80	2,8596	2.2+/-6.3	0,2,4297	no	coding-synonymous,coding-synonymous	GATA3	NM_001002295.1,NM_002051.2	,	31,444,6027	CC,CT,TT		0.0233,11.4389,3.8911	,	202/445,202/444	8100632	506,12498	2203	4299	6502	SO:0001819	synonymous_variant	2625	exon3			CTCCCGTGGCAGC	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.606T>C	10.37:g.8100632T>C		55	0	0		46	27	0.586957	NM_002051	Q5VWG7|Q5VWG8|Q96J16	Silent	SNP	ENST00000346208.3	37	CCDS7083.1																																																																																			T|0.959;C|0.041	0.041	strong		0.687	GATA3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046719.1	NM_001002295		C	8100632	T	C	8100632	2	2	22	1	0	0	0	0	0	0	0	1	6263	1683	59	3		3	GATA3	10	8100632	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	472605	8100632	127434115	2236	5137											
ECHDC3	79746	hgsc.bcm.edu	37	chr10	11797484	11797484	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gccgcggctgccggctgtcaActggttgccagctgcgacat	5	8	14	14	4	1	0	1	0	0	0	1	1	1	0	3	3	5	4	3	3	1	1	rs34878615	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:11797484A>G	ENST00000379215.4	+	4	679	c.468A>G	c.(466-468)caA>caG	p.Q156Q	ECHDC3_ENST00000496136.1_3'UTR	NM_024693.4	NP_078969	Q96DC8	ECHD3_HUMAN	enoyl CoA hydratase domain containing 3	156						mitochondrion (GO:0005739)	catalytic activity (GO:0003824)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)	4						CCGGCTGTCAACTGGTTGCCA	0.607													A|||	94	0.01877	0.0681	0.0043	5008	,	,		13971	0.0		0.001	False		,,,				2504	0.0				p.Q156Q		Atlas-SNP	.											.	ECHDC3	12	.	0			c.A468G						PASS	.	A		251,4155	144.6+/-179.5	10,231,1962	51	42	45		468	3.4	1	10	dbSNP_126	45	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	ECHDC3	NM_024693.4		10,235,6258	GG,GA,AA		0.0465,5.6968,1.9606		156/304	11797484	255,12751	2203	4300	6503	SO:0001819	synonymous_variant	79746	exon4			CTGTCAACTGGTT	AF275677	CCDS7084.1	10p14	2010-04-30	2010-04-30		ENSG00000134463	ENSG00000134463			23489	protein-coding gene	gene with protein product			"enoyl Coenzyme A hydratase domain containing 3"			12477932	Standard	NM_024693		Approved	FLJ20909	uc001ikw.4	Q96DC8	OTTHUMG00000017675	ENST00000379215.4:c.468A>G	10.37:g.11797484A>G		104	0	0		100	53	0.53	NM_024693	Q53HR9|Q5W0J7|Q8WYY8|Q9BVL8|Q9H7G4	Silent	SNP	ENST00000379215.4	37	CCDS7084.1																																																																																			A|0.981;G|0.019	0.019	strong		0.607	ECHDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046771.1	NM_024693		G	11797484	A	G	11797484	2	3	22	1	0	0	0	0	0	0	0	1	4897	40	2	3		3	ECHDC3	10	11797484	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	3696852	11797484	123737263	2237	5138											
C10orf47	254427	hgsc.bcm.edu	37	chr10	11912381	11912381	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agggaggccctgcggaagctGgggctgctcagggagagttc	7	6	19	9	1	1	1	1	0	0	1	2	4	1	3	1	6	3	4	1	6	1	1	rs191542752	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:11912381G>A	ENST00000277570.5	+	4	1438	c.1284G>A	c.(1282-1284)ctG>ctA	p.L428L	PROSER2-AS1_ENST00000453242.1_RNA|PROSER2_ENST00000379200.1_Silent_p.L232L|PROSER2-AS1_ENST00000445498.1_RNA	NM_153256.3	NP_694988.3	Q86WR7	PRSR2_HUMAN	proline and serine rich 2	428																	TGCGGAAGCTGGGGCTGCTCA	0.726													G|||	45	0.00898562	0.031	0.0058	5008	,	,		11702	0.0		0.0	False		,,,				2504	0.0				p.L428L		Atlas-SNP	.											.	.	.	.	0			c.G1284A						PASS	.	G		34,2126		0,34,1046	1	1	1		1284	-10.4	0.7	10		1	1,4447		0,1,2223	no	coding-synonymous	C10orf47	NM_153256.3		0,35,3269	AA,AG,GG		0.0225,1.5741,0.5297		428/436	11912381	35,6573	1080	2224	3304	SO:0001819	synonymous_variant	254427	exon4			GAAGCTGGGGCTG	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.1284G>A	10.37:g.11912381G>A		20	0	0		19	10	0.526316	NM_153256	D3DRR8|Q5W0J9|Q5W0K0|Q5W0K1|Q5W0K2|Q6PJC8|Q8N317	Silent	SNP	ENST00000277570.5	37	CCDS7085.1																																																																																			G|0.993;A|0.007	0.007	strong		0.726	PROSER2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090189.2	NM_153256		A	11912381	G	A	11912381	2	1	22	1	0	0	0	0	0	0	0	1	1607	1335	47	2		2	C10orf47	10	11912381	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	114897	11912381	123622366	2238	5139											
DHTKD1	55526	hgsc.bcm.edu	37	chr10	12160868	12160868	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gtagaggaactctgccccttCccgttggattctttacagca	8	12	9	12	1	2	1	0	0	2	1	3	3	3	3	3	2	4	3	3	2	3	6	rs12769375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:12160868C>T	ENST00000263035.4	+	15	2585	c.2523C>T	c.(2521-2523)ttC>ttT	p.F841F	U6_ENST00000606801.1_RNA	NM_018706.5	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain containing 1	841					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)			TCTGCCCCTTCCCGTTGGATT	0.448													C|||	48	0.00958466	0.0356	0.0014	5008	,	,		17605	0.0		0.0	False		,,,				2504	0.0				p.F841F		Atlas-SNP	.											.	DHTKD1	104	.	0			c.C2523T						PASS	.	C		153,4253	104.7+/-143.2	4,145,2054	146	143	144		2523	3.2	1	10	dbSNP_121	144	0,8600		0,0,4300	no	coding-synonymous	DHTKD1	NM_018706.5		4,145,6354	TT,TC,CC		0.0,3.4725,1.1764		841/920	12160868	153,12853	2203	4300	6503	SO:0001819	synonymous_variant	55526	exon15			CCCCTTCCCGTTG	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.2523C>T	10.37:g.12160868C>T		83	0	0		78	35	0.448718	NM_018706	Q68CU5|Q9BUM8|Q9HCE2	Silent	SNP	ENST00000263035.4	37	CCDS7087.1																																																																																			C|0.985;T|0.015	0.015	strong		0.448	DHTKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046777.1	NM_018706		T	12160868	C	T	12160868	2	4	22	1	0	0	0	0	0	0	0	1	4502	854	30	2		2	DHTKD1	10	12160868	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	248487	12160868	123373879	2239	5140											
SEC61A2	55176	hgsc.bcm.edu	37	chr10	12200092	12200092	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aactttttagtaaatttactAggacagtgggccgtgagtat	12	14	10	5	1	0	1	0	1	0	0	0	2	0	2	1	2	2	2	1	2	7	8	rs61731911	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:12200092A>G	ENST00000298428.9	+	9	1052	c.963A>G	c.(961-963)ctA>ctG	p.L321L	SEC61A2_ENST00000304267.8_Silent_p.L321L|SEC61A2_ENST00000379033.3_Silent_p.L299L|SEC61A2_ENST00000379020.4_Intron|SEC61A2_ENST00000495368.1_3'UTR	NM_018144.3	NP_060614.2	Q9H9S3	S61A2_HUMAN	Sec61 alpha 2 subunit (S. cerevisiae)	321					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)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ribosome binding (GO:0043022)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Renal(717;0.228)				TAAATTTACTAGGACAGTGGG	0.373													A|||	91	0.0181709	0.0651	0.0072	5008	,	,		16175	0.0		0.0	False		,,,				2504	0.0				p.L321L		Atlas-SNP	.											.	SEC61A2	48	.	0			c.A963G						PASS	.	A	,,	258,4148	145.7+/-180.5	6,246,1951	83	77	79		963,897,963	-1.3	1	10	dbSNP_129	79	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	SEC61A2	NM_001142627.1,NM_001142628.1,NM_018144.3	,,	6,246,6251	GG,GA,AA		0.0,5.8557,1.9837	,,	321/438,299/455,321/477	12200092	258,12748	2203	4300	6503	SO:0001819	synonymous_variant	55176	exon9			TTTACTAGGACAG	AF346603	CCDS7088.1, CCDS44358.1, CCDS44359.1	10p14	2004-01-06			ENSG00000065665	ENSG00000065665			17702	protein-coding gene	gene with protein product							Standard	NM_018144		Approved	FLJ10578	uc001ile.2	Q9H9S3	OTTHUMG00000017679	ENST00000298428.9:c.963A>G	10.37:g.12200092A>G		141	0	0		142	82	0.577465	NM_001142627	A8K8D0|B4DX72|F8W773	Silent	SNP	ENST00000298428.9	37	CCDS7088.1																																																																																			A|0.974;G|0.026	0.026	strong		0.373	SEC61A2-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046795.1	NM_018144		G	12200092	A	G	12200092	2	3	22	1	0	0	0	0	0	0	0	1	14016	407	15	3		3	SEC61A2	10	12200092	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	39224	12200092	123334655	2240	5141											
CDNF	441549	hgsc.bcm.edu	37	chr10	14862140	14862140	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cttccgcaggtcaactgatgCcaagtccagtgttttttcta	8	14	8	11	1	2	1	1	1	1	0	4	1	4	1	3	1	2	2	3	1	3	5	rs61740068	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:14862140C>A	ENST00000378442.1	-	6	600	c.97G>T	c.(97-99)Gca>Tca	p.A33S	CDNF_ENST00000378441.2_5'UTR			Q49AH0	CDNF_HUMAN	cerebral dopamine neurotrophic factor	135						extracellular region (GO:0005576)				breast(2)|large_intestine(2)|lung(1)	5						TCAACTGATGCCAAGTCCAGT	0.418													C|||	76	0.0151757	0.0522	0.0072	5008	,	,		19434	0.0		0.0	False		,,,				2504	0.002				p.A135S		Atlas-SNP	.											.	CDNF	19	.	0			c.G403T						PASS	.	C	SER/ALA	205,4201	127.4+/-164.3	3,199,2001	96	98	97		403	5.9	1	10	dbSNP_129	97	0,8600		0,0,4300	yes	missense	CDNF	NM_001029954.2	99	3,199,6301	AA,AC,CC		0.0,4.6527,1.5762	benign	135/188	14862140	205,12801	2203	4300	6503	SO:0001583	missense	441549	exon4			CTGATGCCAAGTC	BC037872	CCDS31148.1	10p13	2009-06-04	2009-06-04	2009-06-04	ENSG00000185267	ENSG00000185267			24913	protein-coding gene	gene with protein product	"conserved dopamine neurotrophic factor"	611233	"arginine-rich, mutated in early stage tumors-like 1"	ARMETL1		17611540	Standard	NM_001029954		Approved		uc001inb.1	Q49AH0	OTTHUMG00000017713	ENST00000378442.1:c.97G>T	10.37:g.14862140C>A	ENSP00000367703:p.Ala33Ser	166	0	0		128	60	0.46875	NM_001029954	A2RUU0|B4DVW3	Missense_Mutation	SNP	ENST00000378442.1	37		27	0.012362637362637362	24	0.04878048780487805	3	0.008287292817679558	0	0.0	0	0.0	C	3.967	-0.009097	0.07727	0.046527	0.0	ENSG00000185267	ENST00000378442;ENST00000465530	.	.	.	5.9	5.9	0.94986	.	0.284770	0.36519	N	0.002549	T	0.03783	0.0107	N	0.04994	-0.135	0.34379	D	0.692882	B	0.22983	0.078	B	0.21360	0.034	T	0.09185	-1.0686	9	0.02654	T	1	-13.8964	13.0686	0.59048	0.0:0.9231:0.0:0.0769	.	135	Q49AH0	CDNF_HUMAN	S	33;135	.	ENSP00000367703:A33S	A	-	1	0	CDNF	14902146	1.000000	0.71417	0.997000	0.53966	0.555000	0.35460	3.795000	0.55499	2.806000	0.96561	0.655000	0.94253	GCA	C|0.985;A|0.015	0.015	strong		0.418	CDNF-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000046919.1	NM_001029954		A	14862140	C	A	14862140	3	1	22	1	0	0	0	0	1	0	0	0	3170	739	26	4	164	4	CDNF	10	14862140	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2662048	14862140	120672607	2241	5142											
RPP38	10557	hgsc.bcm.edu	37	chr10	15145917	15145917	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatcatccccagagtccccAgtttaagtgtaccatggctt	9	11	7	14	0	1	1	1	0	0	1	3	1	3	1	6	1	1	3	6	1	2	4	rs12249258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:15145917A>C	ENST00000378197.4	+	3	1118	c.604A>C	c.(604-606)Agt>Cgt	p.S202R	RPP38_ENST00000451677.1_Intron|RPP38_ENST00000378202.5_Missense_Mutation_p.S202R|NMT2_ENST00000466201.1_Intron	NM_183005.4	NP_892117.1	P78345	RPP38_HUMAN	ribonuclease P/MRP 38kDa subunit	202			S -> R (in dbSNP:rs12249258).		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						CAGAGTCCCCAGTTTAAGTGT	0.463													A|||	241	0.048123	0.1725	0.013	5008	,	,		20068	0.0		0.004	False		,,,				2504	0.0				p.S202R	GBM(118;1591 1611 9649 34378 50720)	Atlas-SNP	.											.	RPP38	26	.	0			c.A604C						PASS	.	A	ARG/SER,ARG/SER,ARG/SER	543,3863	244.7+/-253.9	41,461,1701	68	69	69		604,604,604	-3	0	10	dbSNP_120	69	5,8595	3.7+/-12.6	0,5,4295	yes	missense,missense,missense	RPP38	NM_001097590.1,NM_006414.3,NM_183005.3	110,110,110	41,466,5996	CC,CA,AA		0.0581,12.3241,4.2134	benign,benign,benign	202/284,202/284,202/284	15145917	548,12458	2203	4300	6503	SO:0001583	missense	10557	exon2			GTCCCCAGTTTAA	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.604A>C	10.37:g.15145917A>C	ENSP00000367439:p.Ser202Arg	92	0	0		87	44	0.505747	NM_001265601	B3KPY0|D3DRT8|Q53F71|Q8NHS8	Missense_Mutation	SNP	ENST00000378197.4	37	CCDS7108.1	96	0.04395604395604396	86	0.17479674796747968	7	0.019337016574585635	0	0.0	3	0.00395778364116095	A	5.707	0.315044	0.10789	0.123241	5.81E-4	ENSG00000152464	ENST00000378203;ENST00000378202;ENST00000378197	T;T;T	0.10192	2.9;2.9;2.9	5.88	-2.97	0.05530	.	1.421770	0.04406	N	0.365158	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.43360	-0.9396	9	0.15952	T	0.53	-0.0859	5.4796	0.16717	0.2215:0.5329:0.1457:0.0999	rs12249258;rs52829912;rs57326558;rs12249258	202	P78345	RPP38_HUMAN	R	202	ENSP00000367445:S202R;ENSP00000367444:S202R;ENSP00000367439:S202R	ENSP00000367439:S202R	S	+	1	0	RPP38	15185923	0.000000	0.05858	0.006000	0.13384	0.561000	0.35649	-0.048000	0.11944	-0.396000	0.07703	0.482000	0.46254	AGT	A|0.946;C|0.054	0.054	strong		0.463	RPP38-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046976.1	NM_006414		C	15145917	A	C	15145917	3	2	22	1	0	0	0	0	1	0	0	0	13628	188	7	5	606	5	RPP38	10	15145917	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	283777	15145917	120388830	2242	5143											
NMT2	9397	hgsc.bcm.edu	37	chr10	15170387	15170387	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcattgttctctgtaaagTcatatttctactcaagtgag	10	17	6	8	0	5	1	3	1	2	0	6	1	5	1	0	0	1	2	0	0	5	7			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:15170387T>C	ENST00000378165.4	-	8	1041	c.961A>G	c.(961-963)Act>Gct	p.T321A	RPP38_ENST00000451677.1_Intron|NMT2_ENST00000378150.1_Missense_Mutation_p.T308A|NMT2_ENST00000540259.1_Missense_Mutation_p.T133A|NMT2_ENST00000535341.1_Missense_Mutation_p.T308A	NM_004808.2	NP_004799.1	O60551	NMT2_HUMAN	N-myristoyltransferase 2	321					intracellular transport of virus (GO:0075733)|N-terminal protein myristoylation (GO:0006499)|phototransduction, visible light (GO:0007603)|protein lipoylation (GO:0009249)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	catalytic activity (GO:0003824)|glycylpeptide N-tetradecanoyltransferase activity (GO:0004379)			breast(3)|endometrium(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(3)	21						CTCTGTAAAGTCATATTTCTA	0.328																																					p.T321A	Melanoma(117;1345 1645 4130 12688 30625)	Atlas-SNP	.											.	NMT2	44	.	0			c.A961G						PASS	.						85	88	87					10																	15170387		2202	4300	6502	SO:0001583	missense	9397	exon8			GTAAAGTCATATT	AF043325	CCDS7109.1	10p13	2006-07-11			ENSG00000152465	ENSG00000152465			7858	protein-coding gene	gene with protein product		603801				9506952	Standard	NM_004808		Approved		uc001inz.1	O60551	OTTHUMG00000017723	ENST00000378165.4:c.961A>G	10.37:g.15170387T>C	ENSP00000367407:p.Thr321Ala	97	0	0		149	6	0.0402685	NM_004808	B0YJ49|Q53Y38|Q5VUC8|Q9BRB4	Missense_Mutation	SNP	ENST00000378165.4	37	CCDS7109.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.582566	0.86748	.	.	ENSG00000152465	ENST00000378165;ENST00000378150;ENST00000378143;ENST00000540259;ENST00000535341	T	0.50813	0.73	5.58	5.58	0.84498	Acyl-CoA N-acyltransferase (2);Myristoyl-CoA:protein N-myristoyltransferase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.77928	0.4204	H	0.95437	3.67	0.80722	D	1	D;D;D	0.65815	0.992;0.995;0.992	D;D;D	0.75020	0.985;0.985;0.985	D	0.85108	0.0961	10	0.87932	D	0	-19.6603	15.7488	0.77967	0.0:0.0:0.0:1.0	.	321;308;321	B2RCF3;Q5VUC6;O60551	.;.;NMT2_HUMAN	A	321;308;352;133;308	ENSP00000367407:T321A	ENSP00000367385:T352A	T	-	1	0	NMT2	15210393	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.115000	0.64714	0.533000	0.62120	ACT	.	.	none		0.328	NMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046958.2	NM_004808		C	15170387	T	C	15170387	3	2	22	1	0	0	0	0	1	0	0	0	10513	1667	58	3	555	3	NMT2	10	15170387	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	24470	15170387	120364360	2243	5144											
PIP4K2A	5305	hgsc.bcm.edu	37	chr10	22830842	22830842	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctatctgggggggttcccacCgggtgggtgccatcgctctc	3	10	15	13	2	2	0	0	0	2	0	5	0	3	0	3	5	1	2	3	5	1	2	rs61731109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:22830842C>T	ENST00000376573.4	-	8	1155	c.927G>A	c.(925-927)ccG>ccA	p.P309P	PIP4K2A_ENST00000323883.7_Silent_p.P169P|PIP4K2A_ENST00000545335.1_Silent_p.P250P	NM_005028.4	NP_005019.2	P48426	PI42A_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	309	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				megakaryocyte development (GO:0035855)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)			endometrium(4)|kidney(13)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	29						GGGTTCCCACCGGGTGGGTGC	0.592													C|||	98	0.0195687	0.0522	0.0101	5008	,	,		18503	0.0		0.0149	False		,,,				2504	0.0072				p.P309P		Atlas-SNP	.											.	PIP4K2A	59	.	0			c.G927A						PASS	.	C		217,4189	133.7+/-170.0	6,205,1992	79	73	75		927	-12.1	0	10	dbSNP_129	75	110,8490	58.3+/-119.8	1,108,4191	no	coding-synonymous	PIP4K2A	NM_005028.4		7,313,6183	TT,TC,CC		1.2791,4.9251,2.5142		309/407	22830842	327,12679	2203	4300	6503	SO:0001819	synonymous_variant	5305	exon8			TCCCACCGGGTGG	S78798	CCDS7141.1	10p12.2	2007-08-21	2007-08-14	2007-08-14	ENSG00000150867	ENSG00000150867			8997	protein-coding gene	gene with protein product		603140	"phosphatidylinositol-4-phosphate 5-kinase, type II, alpha"	PIP5K2A		7852364, 9367159	Standard	NM_005028		Approved	PIP5KIIA, PIP5KIIalpha	uc001irl.4	P48426	OTTHUMG00000017810	ENST00000376573.4:c.927G>A	10.37:g.22830842C>T		109	0	0		98	41	0.418367	NM_005028	B0YJ66|B4DGX2|D3DRV1|P53807|Q5VUX3	Silent	SNP	ENST00000376573.4	37	CCDS7141.1																																																																																			C|0.976;T|0.024	0.024	strong		0.592	PIP4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047193.1	NM_005028		T	22830842	C	T	22830842	2	4	22	1	0	0	0	0	0	0	0	1	11945	639	23	1		1	PIP4K2A	10	22830842	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	7660455	22830842	112703905	2244	5145											
RET	5979	hgsc.bcm.edu	37	chr10	43615094	43615094	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggaggcagccgcaactccagCtccctggaccacccggatga	9	4	12	16	2	0	1	0	1	0	0	2	4	2	4	5	4	3	3	5	4	1	0	rs1800862	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:43615094C>T	ENST00000355710.3	+	14	2740	c.2508C>T	c.(2506-2508)agC>agT	p.S836S	RET_ENST00000340058.5_Silent_p.S836S	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	836	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)	GCAACTCCAGCTCCCTGGACC	0.642		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				C|||	180	0.0359425	0.0129	0.0303	5008	,	,		15331	0.0		0.0586	False		,,,				2504	0.0849				p.S836S	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.C2508T	GRCh37	CM012798	RET	M	rs1800862	PASS	.	C	,	117,4289	83.9+/-122.4	2,113,2088	36	35	35		2508,2508	2.5	1	10	dbSNP_89	35	435,8163	128.3+/-186.6	17,401,3881	no	coding-synonymous,coding-synonymous	RET	NM_020630.4,NM_020975.4	,	19,514,5969	TT,TC,CC		5.0593,2.6555,4.2448	,	836/1073,836/1115	43615094	552,12452	2203	4299	6502	SO:0001819	synonymous_variant	5979	exon14	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	CTCCAGCTCCCTG	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.2508C>T	10.37:g.43615094C>T		113	0	0		124	61	0.491935	NM_020630	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Silent	SNP	ENST00000355710.3	37	CCDS7200.1																																																																																			C|0.960;T|0.040	0.040	strong		0.642	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975		T	43615094	C	T	43615094	2	4	22	1	0	0	0	0	0	0	0	1	13250	796	28	2		2	RET	10	43615094	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	20784252	43615094	91919653	2245	5146											
GPRIN2	9721	hgsc.bcm.edu	37	chr10	46999385	46999385	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctggccagggtggccaggccCctgcaggcctggaaagggac	7	4	17	13	0	0	0	0	0	0	0	0	2	0	2	5	7	1	1	5	7	1	0	rs113256776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:46999385C>T	ENST00000374317.1	+	3	778	c.505C>T	c.(505-507)Cct>Tct	p.P169S	GPRIN2_ENST00000374314.4_Missense_Mutation_p.P169S	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	169										breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						TGGCCAGGCCCCTGCAGGCCT	0.637													C|||	128	0.0255591	0.09	0.0115	5008	,	,		39000	0.0		0.001	False		,,,				2504	0.0				p.P169S		Atlas-SNP	.											.	GPRIN2	94	.	0			c.C505T						PASS	.	C	SER/PRO	231,4175		0,231,1972	39	40	40		505	0.7	0	10	dbSNP_132	40	1,8599		0,1,4299	yes	missense	GPRIN2	NM_014696.3	74	0,232,6271	TT,TC,CC		0.0116,5.2429,1.7838	probably-damaging	169/459	46999385	232,12774	2203	4300	6503	SO:0001583	missense	9721	exon3			CAGGCCCCTGCAG	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.505C>T	10.37:g.46999385C>T	ENSP00000363436:p.Pro169Ser	37	0	0		70	15	0.214286	NM_014696	Q5SVF0	Missense_Mutation	SNP	ENST00000374317.1	37	CCDS31192.1	.	.	.	.	.	.	.	.	.	.	C	9.805	1.181582	0.21787	0.052429	1.16E-4	ENSG00000204175	ENST00000374317;ENST00000374314	T;T	0.03330	3.97;3.97	4.71	0.695	0.18070	.	0.700953	0.12491	N	0.464220	T	0.00695	0.0023	M	0.63428	1.95	0.09310	N	1	B	0.22909	0.077	B	0.20767	0.031	T	0.39165	-0.9627	10	0.87932	D	0	-0.5548	3.3753	0.07235	0.1809:0.5265:0.0:0.2926	.	169	O60269	GRIN2_HUMAN	S	169	ENSP00000363436:P169S;ENSP00000363433:P169S	ENSP00000363433:P169S	P	+	1	0	GPRIN2	46419391	0.000000	0.05858	0.003000	0.11579	0.063000	0.16089	0.087000	0.14958	0.036000	0.15547	0.650000	0.86243	CCT	C|0.975;T|0.025	0.025	strong		0.637	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696		T	46999385	C	T	46999385	3	4	22	1	0	0	0	0	1	0	0	0	6739	623	22	2	507	2	GPRIN2	10	46999385	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3384291	46999385	88535362	2246	5147											
C10orf71	118461	hgsc.bcm.edu	37	chr10	50531520	50531520	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcactatggggacacgacCttgctaagagaaccctgtcc	12	7	10	12	1	0	1	0	0	0	1	1	4	1	2	3	2	3	2	3	2	4	3	rs73307889	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:50531520C>A	ENST00000374144.3	+	3	1218	c.930C>A	c.(928-930)acC>acA	p.T310T	C10orf71_ENST00000323868.4_Silent_p.T310T			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	310										endometrium(1)	1						GGGACACGACCTTGCTAAGAG	0.567													C|||	98	0.0195687	0.0719	0.0043	5008	,	,		19049	0.0		0.0	False		,,,				2504	0.0				p.T310T		Atlas-SNP	.											C10orf71_ENST00000374144,NS,carcinoma,+1,2	C10orf71	179	2	0			c.C930A						scavenged	.	C	,	237,3885		7,223,1831	70	79	76		930,930	-1.9	0	10	dbSNP_130	76	3,8405		0,3,4201	no	coding-synonymous,coding-synonymous	C10orf71	NM_001135196.1,NM_199459.3	,	7,226,6032	AA,AC,CC		0.0357,5.7496,1.9154	,	310/1436,310/720	50531520	240,12290	2061	4204	6265	SO:0001819	synonymous_variant	118461	exon3			CACGACCTTGCTA	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.930C>A	10.37:g.50531520C>A		78	1	0.0128205		72	34	0.472222	NM_001135196	A0AVL8	Silent	SNP	ENST00000374144.3	37	CCDS44387.1																																																																																			C|0.984;A|0.016	0.016	strong		0.567	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459		A	50531520	C	A	50531520	2	1	22	1	0	0	0	0	0	0	0	1	1616	668	24	4		4	C10orf71	10	50531520	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3532135	50531520	85003227	2247	5148											
C10orf71	118461	hgsc.bcm.edu	37	chr10	50531907	50531907	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cccaatgaacattatgatccCccctttaacatcagtaagct	13	11	4	13	0	1	2	1	2	0	0	2	2	2	2	4	0	3	2	4	0	5	4	rs74528495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:50531907C>T	ENST00000374144.3	+	3	1605	c.1317C>T	c.(1315-1317)ccC>ccT	p.P439P	C10orf71_ENST00000323868.4_Silent_p.P439P			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	439										endometrium(1)	1						ATTATGATCCCCCCTTTAACA	0.522													C|||	27	0.00539137	0.0182	0.0043	5008	,	,		17686	0.0		0.0	False		,,,				2504	0.0				p.P439P		Atlas-SNP	.											.	C10orf71	179	.	0			c.C1317T						PASS	.	C	,	53,3975		0,53,1961	84	88	87		1317,1317	-2.9	0.4	10	dbSNP_133	87	1,8371		0,1,4185	no	coding-synonymous,coding-synonymous	C10orf71	NM_001135196.1,NM_199459.3	,	0,54,6146	TT,TC,CC		0.0119,1.3158,0.4355	,	439/1436,439/720	50531907	54,12346	2014	4186	6200	SO:0001819	synonymous_variant	118461	exon3			TGATCCCCCCTTT	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.1317C>T	10.37:g.50531907C>T		97	0	0		98	42	0.428571	NM_001135196	A0AVL8	Silent	SNP	ENST00000374144.3	37	CCDS44387.1																																																																																			C|0.994;T|0.006	0.006	strong		0.522	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459		T	50531907	C	T	50531907	2	4	22	1	0	0	0	0	0	0	0	1	1616	610	22	2		2	C10orf71	10	50531907	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	387	50531907	85002840	2248	5149											
C10orf71	118461	hgsc.bcm.edu	37	chr10	50532155	50532155	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcctcacctctcttgaaagTgcttgatgagaaaactagag	12	12	8	9	0	2	4	1	3	1	2	4	5	3	4	2	0	2	1	2	0	4	4	rs61453891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:50532155T>G	ENST00000374144.3	+	3	1853	c.1565T>G	c.(1564-1566)gTg>gGg	p.V522G	C10orf71_ENST00000323868.4_Missense_Mutation_p.V522G			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	522			V -> G (in dbSNP:rs61453891).							endometrium(1)	1						CTCTTGAAAGTGCTTGATGAG	0.502													T|||	150	0.0299521	0.1067	0.0115	5008	,	,		21076	0.0		0.001	False		,,,				2504	0.0				p.V522G		Atlas-SNP	.											.	C10orf71	179	.	0			c.T1565G						PASS	.	T	GLY/VAL,GLY/VAL	381,3695		19,343,1676	71	75	74		1565,1565	3.6	0.7	10	dbSNP_129	74	6,8358		0,6,4176	yes	missense,missense	C10orf71	NM_001135196.1,NM_199459.3	109,109	19,349,5852	GG,GT,TT		0.0717,9.3474,3.1109	benign,benign	522/1436,522/720	50532155	387,12053	2038	4182	6220	SO:0001583	missense	118461	exon3			TGAAAGTGCTTGA	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.1565T>G	10.37:g.50532155T>G	ENSP00000363259:p.Val522Gly	82	0	0		88	45	0.511364	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	37	CCDS44387.1	49	0.022435897435897436	44	0.08943089430894309	5	0.013812154696132596	0	0.0	0	0.0	T	0.006	-2.028060	0.00410	0.093474	7.17E-4	ENSG00000177354	ENST00000323868;ENST00000374144	T;T	0.13196	2.61;3.75	5.52	3.62	0.41486	.	0.465425	0.15896	N	0.239327	T	0.00109	0.0003	N	0.00170	-1.935	0.37892	D	0.930737	B	0.02656	0.0	B	0.01281	0.0	T	0.35001	-0.9806	10	0.08599	T	0.76	.	4.4351	0.11547	0.071:0.3245:0.3604:0.2441	rs61453891	522	Q711Q0-3	.	G	522	ENSP00000318713:V522G;ENSP00000363259:V522G	ENSP00000318713:V522G	V	+	2	0	C10orf71	50202161	0.998000	0.40836	0.723000	0.30687	0.214000	0.24535	1.664000	0.37439	0.651000	0.30788	-0.202000	0.12741	GTG	T|0.977;G|0.023	0.023	strong		0.502	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459		G	50532155	T	G	50532155	3	3	22	1	0	0	0	0	1	0	0	0	1616	1696	59	5	1567	5	C10orf71	10	50532155	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	248	50532155	85002592	2249	5150											
OGDHL	55753	hgsc.bcm.edu	37	chr10	50954850	50954850	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcgtgtaggagggcaggtcGctcaggtggaaggtctcata	8	9	17	7	2	2	0	2	0	1	0	5	2	2	2	0	6	0	3	0	6	3	2	rs75974530	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:50954850G>A	ENST00000374103.4	-	10	1327	c.1242C>T	c.(1240-1242)agC>agT	p.S414S	OGDHL_ENST00000419399.1_Silent_p.S357S|OGDHL_ENST00000432695.1_Silent_p.S205S	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	414					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						AGGGCAGGTCGCTCAGGTGGA	0.617													G|||	88	0.0175719	0.062	0.0072	5008	,	,		22610	0.0		0.001	False		,,,				2504	0.0				p.S414S		Atlas-SNP	.											.	OGDHL	149	.	0			c.C1242T						PASS	.	G	,,	299,4107	164.4+/-196.0	9,281,1913	151	102	119		1071,615,1242	-11.5	0.2	10	dbSNP_131	119	9,8591	6.4+/-24.3	0,9,4291	no	coding-synonymous,coding-synonymous,coding-synonymous	OGDHL	NM_001143996.1,NM_001143997.1,NM_018245.2	,,	9,290,6204	AA,AG,GG		0.1047,6.7862,2.3681	,,	357/954,205/802,414/1011	50954850	308,12698	2203	4300	6503	SO:0001819	synonymous_variant	55753	exon10			CAGGTCGCTCAGG	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.1242C>T	10.37:g.50954850G>A		114	0	0		126	66	0.52381	NM_018245	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Silent	SNP	ENST00000374103.4	37	CCDS7234.1																																																																																			G|0.976;A|0.024	0.024	strong		0.617	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245		A	50954850	G	A	50954850	2	1	22	1	0	0	0	0	0	0	0	1	10849	1078	38	1		1	OGDHL	10	50954850	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	422695	50954850	84579897	2250	5151											
AGAP7	653268	hgsc.bcm.edu	37	chr10	51465429	51465429	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	acccagcccggtgtccatgtCcttggataggccatcgcttt	6	11	10	14	2	0	0	0	0	0	0	3	1	2	1	5	3	1	1	5	3	1	3	rs183573385	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:51465429C>T	ENST00000374095.5	-	7	1152	c.1027G>A	c.(1027-1029)Gac>Aac	p.D343N		NM_001077685.1	NP_001071153.1	Q5VUJ5	AGAP7_HUMAN		343	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)	11						GTGTCCATGTCCTTGGATAGG	0.562													-|||	17	0.00339457	0.0	0.0043	5008	,	,		17858	0.0		0.0139	False		,,,				2504	0.0				p.D343N		Atlas-SNP	.											.	AGAP7	33	.	0			c.G1027A						PASS	.	C	ASN/ASP	8,4396		0,8,2194	116	137	130		1027		0	10		130	44,8556		0,44,4256	no	missense	AGAP7	NM_001077685.1	23	0,52,6450	TT,TC,CC		0.5116,0.1817,0.3999	benign	343/664	51465429	52,12952	2202	4300	6502	SO:0001583	missense	653268	exon7			CCATGTCCTTGGA																												ENST00000374095.5:c.1027G>A	10.37:g.51465429C>T	ENSP00000363208:p.Asp343Asn	591	0	0		650	348	0.535385	NM_001077685	A6NGH4	Missense_Mutation	SNP	ENST00000374095.5	37	CCDS41524.1	12	0.005494505494505495	0	0.0	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	.	4.603	0.112029	0.08831	0.001817	0.005116	ENSG00000204169	ENST00000374095	T	0.56103	0.48	.	.	.	Pleckstrin homology domain (3);	0.720818	0.12823	N	0.436252	T	0.35393	0.0930	M	0.74647	2.275	0.25300	N	0.98928	B	0.06786	0.001	B	0.15052	0.012	T	0.30937	-0.9961	9	0.27082	T	0.32	.	4.5676	0.12195	0.0:0.6819:0.0:0.3181	.	343	Q5VUJ5	AGAP7_HUMAN	N	343	ENSP00000363208:D343N	ENSP00000363208:D343N	D	-	1	0	AGAP7	51135435	0.999000	0.42202	0.016000	0.15963	0.016000	0.09150	2.917000	0.48821	-1.351000	0.02197	-1.360000	0.01215	GAC	C|0.996;T|0.004	0.004	strong		0.562	AGAP7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048033.1			T	51465429	C	T	51465429	3	4	22	1	0	0	0	0	1	0	0	0	373	855	30	2	968	2	AGAP7	10	51465429	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	510579	51465429	84069318	2251	5152											
PRKG1	5592	hgsc.bcm.edu	37	chr10	53822344	53822344	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtgaagacccagtctttctTagaactttaggaaaaggaga	15	10	10	6	0	2	4	0	1	2	3	2	6	2	5	1	2	1	0	1	2	6	4	rs113994747	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:53822344T>C	ENST00000401604.2	+	7	1037	c.843T>C	c.(841-843)ctT>ctC	p.L281L	PRKG1_ENST00000373975.2_5'UTR|PRKG1_ENST00000373985.1_Silent_p.L269L|PRKG1_ENST00000373980.4_Silent_p.L296L			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	281	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)		CAGTCTTTCTTAGAACTTTAG	0.403													T|||	106	0.0211661	0.0764	0.0058	5008	,	,		15835	0.0		0.001	False		,,,				2504	0.0				p.L296L		Atlas-SNP	.											.	PRKG1	167	.	0			c.T888C						PASS	.	T	,	299,4107	162.9+/-194.8	15,269,1919	65	67	66		843,888	0.8	1	10	dbSNP_132	66	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PRKG1	NM_001098512.2,NM_006258.3	,	15,269,6219	CC,CT,TT		0.0,6.7862,2.2989	,	281/672,296/687	53822344	299,12707	2203	4300	6503	SO:0001819	synonymous_variant	5592	exon7			CTTTCTTAGAACT		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.843T>C	10.37:g.53822344T>C		121	0	0		119	68	0.571429	NM_006258	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Silent	SNP	ENST00000401604.2	37	CCDS44399.1																																																																																			T|0.976;C|0.024	0.024	strong		0.403	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	53822344	T	C	53822344	2	2	22	1	0	0	0	0	0	0	0	1	12534	1741	61	3		3	PRKG1	10	53822344	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2356915	53822344	81712403	2252	5153											
ANK3	288	hgsc.bcm.edu	37	chr10	61830256	61830256	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcgataacttcaagtttactTtggctaaaagagcggtcagc	12	12	9	8	2	2	1	2	0	0	1	3	2	2	1	0	2	4	2	0	2	5	6	rs61732400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:61830256T>C	ENST00000280772.2	-	37	10574	c.10383A>G	c.(10381-10383)caA>caG	p.Q3461Q	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)	3461					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						CAAGTTTACTTTGGCTAAAAG	0.438													T|||	159	0.0317492	0.1135	0.0115	5008	,	,		21138	0.001		0.0	False		,,,				2504	0.0				p.Q3461Q		Atlas-SNP	.											.	ANK3	703	.	0			c.A10383G						PASS	.	T	,,,	449,3957	215.1+/-234.2	19,411,1773	83	80	81		,,,10383	-2.4	1	10	dbSNP_129	81	6,8594	4.3+/-15.6	0,6,4294	no	intron,intron,intron,coding-synonymous	ANK3	NM_001149.3,NM_001204403.1,NM_001204404.1,NM_020987.3	,,,	19,417,6067	CC,CT,TT		0.0698,10.1906,3.4984	,,,	,,,3461/4378	61830256	455,12551	2203	4300	6503	SO:0001819	synonymous_variant	288	exon37			TTTACTTTGGCTA	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.10383A>G	10.37:g.61830256T>C		114	0	0		120	62	0.516667	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	37	CCDS7258.1																																																																																			T|0.970;C|0.030	0.030	strong		0.438	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		C	61830256	T	C	61830256	2	2	22	1	0	0	0	0	0	0	0	1	622	1838	64	3		3	ANK3	10	61830256	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	8007912	61830256	73704491	2253	5154											
DNA2	1763	hgsc.bcm.edu	37	chr10	70218890	70218890	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgcatctgagggaagtcagtCgaagtgtttttatgcatgaa	11	13	12	5	1	2	2	1	2	1	0	3	4	2	3	0	1	2	3	0	1	4	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:70218890C>T	ENST00000358410.3	-	5	740	c.690G>A	c.(688-690)tcG>tcA	p.S230S	DNA2_ENST00000399179.2_Silent_p.S230S|DNA2_ENST00000399180.2_Silent_p.S316S|RNA5SP319_ENST00000362768.1_RNA	NM_001080449.2	NP_001073918.2	P51530	DNA2_HUMAN	DNA replication helicase/nuclease 2	230	Nuclease 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						GGAAGTCAGTCGAAGTGTTTT	0.358																																					p.S230S		Atlas-SNP	.											DNA2L,NS,carcinoma,-1,4	DNA2	76	4	0			c.G690A						PASS	.						88	78	81					10																	70218890		1845	4099	5944	SO:0001819	synonymous_variant	1763	exon5			GTCAGTCGAAGTG	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.690G>A	10.37:g.70218890C>T		91	0	0		103	5	0.0485437	NM_001080449	Q2NKM1|Q5TC49|Q5TC50|Q6P455|Q6PI80|Q7Z6H9|Q8N346	Silent	SNP	ENST00000358410.3	37																																																																																				.	.	none		0.358	DNA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048334.2			T	70218890	C	T	70218890	2	4	22	1	0	0	0	0	0	0	0	1	4598	871	31	1		1	DNA2	10	70218890	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	8388634	70218890	65315857	2254	5155											
TET1	80312	hgsc.bcm.edu	37	chr10	70406747	70406747	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctaaagattctgaactgcccAcctgcagctgtcttggtgag	9	11	10	11	0	2	3	0	2	2	1	2	3	2	3	2	1	4	2	2	1	3	3	rs144156611	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:70406747A>G	ENST00000373644.4	+	4	4470	c.4261A>G	c.(4261-4263)Acc>Gcc	p.T1421A		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1421					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						TGAACTGCCCACCTGCAGCTG	0.368													A|||	43	0.00858626	0.0008	0.0504	5008	,	,		19982	0.0		0.005	False		,,,				2504	0.002				p.T1421A		Atlas-SNP	.											.	TET1	255	.	0			c.A4261G						PASS	.	A	ALA/THR	4,4402	8.1+/-20.4	0,4,2199	61	58	59		4261	-10.4	0	10	dbSNP_134	59	39,8561	24.6+/-71.5	0,39,4261	yes	missense	TET1	NM_030625.2	58	0,43,6460	GG,GA,AA		0.4535,0.0908,0.3306	benign	1421/2137	70406747	43,12963	2203	4300	6503	SO:0001583	missense	80312	exon4			CTGCCCACCTGCA	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.4261A>G	10.37:g.70406747A>G	ENSP00000362748:p.Thr1421Ala	140	0	0		127	54	0.425197	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	22	0.010073260073260074	0	0.0	19	0.052486187845303865	0	0.0	3	0.00395778364116095	A	11.19	1.565969	0.27915	9.08E-4	0.004535	ENSG00000138336	ENST00000373644	T	0.20881	2.04	5.22	-10.4	0.00318	TET cysteine-rich domain (1);	2.737390	0.01161	N	0.006653	T	0.01661	0.0053	L	0.31926	0.97	0.09310	N	1	B	0.14012	0.009	B	0.14023	0.01	T	0.14392	-1.0474	10	0.66056	D	0.02	.	0.6454	0.00817	0.1857:0.2739:0.184:0.3564	.	1421	Q8NFU7	TET1_HUMAN	A	1421	ENSP00000362748:T1421A	ENSP00000362748:T1421A	T	+	1	0	TET1	70076753	0.001000	0.12720	0.000000	0.03702	0.862000	0.49288	-0.836000	0.04382	-2.685000	0.00406	0.455000	0.32223	ACC	A|0.995;G|0.005	0.005	strong		0.368	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		G	70406747	A	G	70406747	3	3	22	1	0	0	0	0	1	0	0	0	15784	159	6	3	4271	3	TET1	10	70406747	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	187857	70406747	65128000	2255	5156											
STOX1	219736	hgsc.bcm.edu	37	chr10	70646139	70646139	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attactatagcgcaagaaaaGccagttttgaagctgaagtc	15	10	9	7	1	0	3	0	2	0	1	1	3	0	3	1	0	4	3	1	0	8	5	rs7904300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:70646139G>A	ENST00000298596.6	+	3	2670	c.2587G>A	c.(2587-2589)Gcc>Acc	p.A863T	STOX1_ENST00000399165.4_Intron|STOX1_ENST00000399169.4_Missense_Mutation_p.A863T|STOX1_ENST00000421961.2_Missense_Mutation_p.A753T|STOX1_ENST00000399162.2_Intron	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	863			A -> T (in dbSNP:rs7904300).			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						CGCAAGAAAAGCCAGTTTTGA	0.423													G|||	145	0.0289537	0.1014	0.0144	5008	,	,		20639	0.0		0.001	False		,,,				2504	0.0				p.A863T		Atlas-SNP	.											.	STOX1	75	.	0			c.G2587A						PASS	.	G	,,THR/ALA,THR/ALA,THR/ALA	385,3671		22,341,1665	81	81	81		,,2587,2257,2587	-1.5	0	10	dbSNP_116	81	4,8436		0,4,4216	yes	intron,intron,missense,missense,missense	STOX1	NM_001130159.2,NM_001130160.2,NM_001130161.2,NM_001130162.2,NM_152709.4	,,58,58,58	22,345,5881	AA,AG,GG		0.0474,9.4921,3.113	,,benign,benign,benign	,,863/990,753/880,863/990	70646139	389,12107	2028	4220	6248	SO:0001583	missense	219736	exon3			AGAAAAGCCAGTT	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.2587G>A	10.37:g.70646139G>A	ENSP00000298596:p.Ala863Thr	88	0	0		105	42	0.4	NM_152709	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Missense_Mutation	SNP	ENST00000298596.6	37	CCDS41535.1	56	0.02564102564102564	52	0.10569105691056911	4	0.011049723756906077	0	0.0	0	0.0	G	7.158	0.585121	0.13749	0.094921	4.74E-4	ENSG00000165730	ENST00000399169;ENST00000298596;ENST00000421961	T;T;T	0.66815	-0.23;-0.23;-0.23	6.17	-1.51	0.08664	.	0.471664	0.25324	N	0.031488	T	0.01695	0.0054	L	0.56769	1.78	0.80722	P	0.0	B	0.19445	0.036	B	0.17098	0.017	T	0.09618	-1.0666	9	0.46703	T	0.11	.	7.4728	0.27359	0.2424:0.2162:0.5415:0.0	rs7904300;rs52803686;rs7904300	863	Q6ZVD7	STOX1_HUMAN	T	863;863;753	ENSP00000382121:A863T;ENSP00000298596:A863T;ENSP00000394509:A753T	ENSP00000298596:A863T	A	+	1	0	STOX1	70316145	0.119000	0.22226	0.000000	0.03702	0.006000	0.05464	0.598000	0.24074	-0.561000	0.06094	0.655000	0.94253	GCC	G|0.968;A|0.032	0.032	strong		0.423	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709		A	70646139	G	A	70646139	3	1	22	1	0	0	0	0	1	0	0	0	15334	971	34	2	2597	2	STOX1	10	70646139	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	239392	70646139	64888608	2256	5157											
KIAA1279	26128	hgsc.bcm.edu	37	chr10	70775329	70775329	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcttgatcttgataaacaGtctgaacttagagctttaag	13	13	9	6	0	2	4	0	3	2	1	2	5	2	4	0	0	4	2	0	0	5	6	rs16926021	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:70775329G>A	ENST00000361983.4	+	7	1125	c.1023G>A	c.(1021-1023)caG>caA	p.Q341Q		NM_015634.3	NP_056449.1	Q96EK5	KBP_HUMAN	KIAA1279	341					cell differentiation (GO:0030154)|mitochondrial transport (GO:0006839)|nervous system development (GO:0007399)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)	kinesin binding (GO:0019894)			breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	14						TTGATAAACAGTCTGAACTTA	0.373													G|||	306	0.0611022	0.2148	0.0303	5008	,	,		18364	0.0		0.001	False		,,,				2504	0.0				p.Q341Q		Atlas-SNP	.											.	KIAA1279	35	.	0			c.G1023A						PASS	.	G		817,3589	310.2+/-291.5	78,661,1464	78	82	80		1023	-2	0.9	10	dbSNP_123	80	11,8589	5.7+/-21.5	0,11,4289	no	coding-synonymous	KIAA1279	NM_015634.3		78,672,5753	AA,AG,GG		0.1279,18.5429,6.3663		341/622	70775329	828,12178	2203	4300	6503	SO:0001819	synonymous_variant	26128	exon7			TAAACAGTCTGAA	BC012180	CCDS7284.1	10q22.1	2008-02-05			ENSG00000198954	ENSG00000198954			23419	protein-coding gene	gene with protein product		609367					Standard	NM_015634		Approved	DKFZP586B0923, TTC20	uc001joy.3	Q96EK5	OTTHUMG00000018363	ENST00000361983.4:c.1023G>A	10.37:g.70775329G>A		53	0	0		52	24	0.461538	NM_015634	A8K5M8|Q9BR89|Q9ULE1|Q9Y428	Silent	SNP	ENST00000361983.4	37	CCDS7284.1																																																																																			G|0.946;A|0.054	0.054	strong		0.373	KIAA1279-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048370.1	NM_015634		A	70775329	G	A	70775329	2	1	22	1	0	0	0	0	0	0	0	1	8230	1020	36	2		2	KIAA1279	10	70775329	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	129190	70775329	64759418	2257	5158											
SUPV3L1	6832	hgsc.bcm.edu	37	chr10	70940052	70940052	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	agaacctgcggcctcgatgtCcttctcccgtgccctattgt	5	12	9	15	3	1	1	0	0	1	1	4	2	2	1	5	1	3	0	5	1	2	3	rs33998366	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:70940052C>T	ENST00000359655.4	+	1	65	c.5C>T	c.(4-6)tCc>tTc	p.S2F	SUPV3L1_ENST00000483572.1_3'UTR	NM_003171.3	NP_003162.2	Q8IYB8	SUV3_HUMAN	suppressor of var1, 3-like 1 (S. cerevisiae)	2			S -> F (in dbSNP:rs33998366).		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						GCCTCGATGTCCTTCTCCCGT	0.692													C|||	218	0.0435304	0.1573	0.013	5008	,	,		16089	0.0		0.001	False		,,,				2504	0.0				p.S2F		Atlas-SNP	.											.	SUPV3L1	61	.	0			c.C5T						PASS	.	C	PHE/SER	537,3867	208.5+/-229.5	33,471,1698	25	29	28		5	4.9	1	10	dbSNP_126	28	2,8596	2.2+/-6.3	0,2,4297	yes	missense	SUPV3L1	NM_003171.3	155	33,473,5995	TT,TC,CC		0.0233,12.1935,4.1455	probably-damaging	2/787	70940052	539,12463	2202	4299	6501	SO:0001583	missense	6832	exon1			CGATGTCCTTCTC	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.5C>T	10.37:g.70940052C>T	ENSP00000352678:p.Ser2Phe	52	0	0		52	24	0.461538	NM_003171	A8K301|O43630	Missense_Mutation	SNP	ENST00000359655.4	37	CCDS7287.1	89	0.04075091575091575	81	0.16463414634146342	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	C	22.0	4.227112	0.79576	0.121935	2.33E-4	ENSG00000156502	ENST00000359655;ENST00000422378	T;T	0.35973	1.43;1.28	5.78	4.88	0.63580	.	0.080168	0.50627	N	0.000116	T	0.00073	0.0002	N	0.22421	0.69	0.31663	N	0.645286	P	0.35077	0.483	B	0.33392	0.163	T	0.02789	-1.1110	10	0.87932	D	0	-0.6733	8.3656	0.32385	0.1559:0.7643:0.0:0.0797	rs33998366	2	Q8IYB8	SUV3_HUMAN	F	2	ENSP00000352678:S2F;ENSP00000409072:S2F	ENSP00000352678:S2F	S	+	2	0	SUPV3L1	70610058	0.672000	0.27530	1.000000	0.80357	0.919000	0.55068	1.022000	0.30052	2.729000	0.93468	0.655000	0.94253	TCC	C|0.961;T|0.039	0.039	strong		0.692	SUPV3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048396.2	NM_003171		T	70940052	C	T	70940052	3	4	22	1	0	0	0	0	1	0	0	0	15417	855	30	2	7	2	SUPV3L1	10	70940052	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	164723	70940052	64594695	2258	5159											
SUPV3L1	6832	hgsc.bcm.edu	37	chr10	70940066	70940066	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgatgtccttctcccgtgccCtattgtgggctcggctcccg	2	12	11	16	4	1	0	0	0	1	0	5	1	3	0	4	2	1	2	4	2	1	3	rs12251842	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:70940066C>T	ENST00000359655.4	+	1	79	c.19C>T	c.(19-21)Cta>Tta	p.L7L	SUPV3L1_ENST00000483572.1_3'UTR	NM_003171.3	NP_003162.2	Q8IYB8	SUV3_HUMAN	suppressor of var1, 3-like 1 (S. cerevisiae)	7					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						CTCCCGTGCCCTATTGTGGGC	0.706													C|||	232	0.0463259	0.1672	0.0144	5008	,	,		16416	0.0		0.001	False		,,,				2504	0.0				p.L7L		Atlas-SNP	.											.	SUPV3L1	61	.	0			c.C19T						PASS	.	C		575,3829	214.1+/-233.5	41,493,1668	25	29	28		19	0.8	0.6	10	dbSNP_120	28	4,8594	2.2+/-6.3	0,4,4295	no	coding-synonymous	SUPV3L1	NM_003171.3		41,497,5963	TT,TC,CC		0.0465,13.0563,4.4532		7/787	70940066	579,12423	2202	4299	6501	SO:0001819	synonymous_variant	6832	exon1			CGTGCCCTATTGT	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.19C>T	10.37:g.70940066C>T		59	0	0		62	27	0.435484	NM_003171	A8K301|O43630	Silent	SNP	ENST00000359655.4	37	CCDS7287.1																																																																																			C|0.962;T|0.038	0.038	strong		0.706	SUPV3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048396.2	NM_003171		T	70940066	C	T	70940066	2	4	22	1	0	0	0	0	0	0	0	1	15417	680	24	2		2	SUPV3L1	10	70940066	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	14	70940066	64594681	2259	5160											
HKDC1	80201	hgsc.bcm.edu	37	chr10	70980243	70980243	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagcaagctgaaggaggacCagatcaagaaggtaaggagg	16	4	15	6	0	2	3	2	1	0	2	2	6	2	6	1	5	2	3	1	5	5	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:70980243C>A	ENST00000354624.5	+	1	185	c.52C>A	c.(52-54)Cag>Aag	p.Q18K	RP11-227H15.4_ENST00000450995.1_RNA|HKDC1_ENST00000395086.2_Missense_Mutation_p.Q18K	NM_025130.3	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	18	Hexokinase type-1 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						GAAGGAGGACCAGATCAAGAA	0.468																																					p.Q18K		Atlas-SNP	.											.	HKDC1	98	.	0			c.C52A						PASS	.						81	76	78					10																	70980243		2203	4300	6503	SO:0001583	missense	80201	exon1			GAGGACCAGATCA		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.52C>A	10.37:g.70980243C>A	ENSP00000346643:p.Gln18Lys	54	0	0		70	37	0.528571	NM_025130	B5MDN9|Q2TB91|Q5VTC7|Q7Z373|Q8WU37|Q96EH2|Q9H5Y9	Missense_Mutation	SNP	ENST00000354624.5	37	CCDS7288.1	.	.	.	.	.	.	.	.	.	.	C	16.98	3.270551	0.59540	.	.	ENSG00000156510	ENST00000354624;ENST00000395087;ENST00000395086	D;D	0.98968	-5.28;-5.28	5.44	5.44	0.79542	Hexokinase, N-terminal (1);	0.149729	0.47093	D	0.000250	D	0.98232	0.9415	M	0.86740	2.835	0.54753	D	0.99998	B	0.14438	0.01	B	0.20184	0.028	D	0.98393	1.0564	10	0.25106	T	0.35	-10.1756	19.279	0.94044	0.0:1.0:0.0:0.0	.	18	Q2TB90	HKDC1_HUMAN	K	18	ENSP00000346643:Q18K;ENSP00000378521:Q18K	ENSP00000346643:Q18K	Q	+	1	0	HKDC1	70650249	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	7.339000	0.79282	2.554000	0.86153	0.655000	0.94253	CAG	.	.	none		0.468	HKDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048389.1	NM_025130		A	70980243	C	A	70980243	3	1	22	1	0	0	0	0	1	0	0	0	7202	595	21	4	54	4	HKDC1	10	70980243	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	40177	70980243	64554504	2260	5161											
KIAA1274	27143	hgsc.bcm.edu	37	chr10	72294192	72294192	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcgacagggctgcccccaCgcaggccaagcccctgccta	7	4	10	20	2	0	0	0	0	0	0	1	1	0	0	7	2	3	2	7	2	2	1	rs141167395	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:72294192C>T	ENST00000263563.6	+	9	1302	c.1034C>T	c.(1033-1035)aCg>aTg	p.T345M		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	345						cytosol (GO:0005829)											GCTGCCCCCACGCAGGCCAAG	0.622													C|||	6	0.00119808	0.0038	0.0	5008	,	,		16332	0.001		0.0	False		,,,				2504	0.0				p.T345M		Atlas-SNP	.											.	.	.	.	0			c.C1034T						PASS	.	C	MET/THR	13,4391	20.2+/-43.8	0,13,2189	38	35	36		1034	-4	0	10	dbSNP_134	36	0,8598		0,0,4299	yes	missense	KIAA1274	NM_014431.2	81	0,13,6488	TT,TC,CC		0.0,0.2952,0.1	benign	345/857	72294192	13,12989	2202	4299	6501	SO:0001583	missense	27143	exon9			CCCCCACGCAGGC	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.1034C>T	10.37:g.72294192C>T	ENSP00000263563:p.Thr345Met	93	0	0		92	40	0.434783	NM_014431	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Missense_Mutation	SNP	ENST00000263563.6	37	CCDS31215.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	C	9.315	1.056639	0.19907	0.002952	0.0	ENSG00000107719	ENST00000263563;ENST00000373214	T	0.24908	1.83	4.62	-3.99	0.04069	.	1.808830	0.02724	N	0.114334	T	0.13628	0.0330	N	0.11201	0.11	0.09310	N	1	B	0.18610	0.029	B	0.15052	0.012	T	0.23619	-1.0183	10	0.45353	T	0.12	0.2671	6.7714	0.23596	0.1154:0.3697:0.0:0.5148	.	345	Q9ULE6	PALD_HUMAN	M	345	ENSP00000263563:T345M	ENSP00000263563:T345M	T	+	2	0	KIAA1274	71964198	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-2.206000	0.01231	-1.208000	0.02634	-0.448000	0.05591	ACG	C|0.999;T|0.001	0.001	strong		0.622	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431		T	72294192	C	T	72294192	3	4	22	1	0	0	0	0	1	0	0	0	8229	536	19	1	1064	1	KIAA1274	10	72294192	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1313949	72294192	63240555	2261	5162											
KIAA1274	27143	hgsc.bcm.edu	37	chr10	72324139	72324139	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgaaggcagcgaaagaggCgcaagaaatgcggaggctgc	13	2	18	8	4	0	2	0	0	0	2	0	5	0	3	0	5	3	3	0	5	4	0			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:72324139C>T	ENST00000263563.6	+	19	2550	c.2282C>T	c.(2281-2283)gCg>gTg	p.A761V		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	761						cytosol (GO:0005829)											GCGAAAGAGGCGCAAGAAATG	0.617																																					p.A761V		Atlas-SNP	.											KIAA1274,NS,carcinoma,-1,1	.	.	1	0			c.C2282T						PASS	.						77	75	76					10																	72324139		2203	4300	6503	SO:0001583	missense	27143	exon19			AAGAGGCGCAAGA	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.2282C>T	10.37:g.72324139C>T	ENSP00000263563:p.Ala761Val	127	0	0		135	60	0.444444	NM_014431	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Missense_Mutation	SNP	ENST00000263563.6	37	CCDS31215.1	.	.	.	.	.	.	.	.	.	.	c	10.63	1.404595	0.25378	.	.	ENSG00000107719	ENST00000263563;ENST00000373214	T	0.29917	1.55	4.9	2.42	0.29668	.	0.426837	0.24803	N	0.035474	T	0.24547	0.0595	L	0.47716	1.5	0.26423	N	0.976068	B	0.18610	0.029	B	0.12156	0.007	T	0.16158	-1.0412	10	0.40728	T	0.16	-12.6907	8.4465	0.32845	0.3575:0.52:0.0:0.1225	.	761	Q9ULE6	PALD_HUMAN	V	761;737	ENSP00000263563:A761V	ENSP00000263563:A761V	A	+	2	0	KIAA1274	71994145	1.000000	0.71417	0.147000	0.22382	0.613000	0.37349	1.533000	0.36040	0.168000	0.19655	-0.410000	0.06199	GCG	.	.	none		0.617	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431		T	72324139	C	T	72324139	3	4	22	1	0	0	0	0	1	0	0	0	8229	768	27	1	2352	1	KIAA1274	10	72324139	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	29947	72324139	63210608	2262	5163											
PRF1	5551	hgsc.bcm.edu	37	chr10	72358407	72358407	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggccctcctcagtgcctccCgccgcgggtcctggctgtcc	1	8	13	19	3	1	0	1	0	0	0	5	0	5	0	7	3	1	1	7	3	0	0	rs140787739	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:72358407C>T	ENST00000441259.1	-	3	1230	c.1070G>A	c.(1069-1071)cGg>cAg	p.R357Q	PRF1_ENST00000373209.2_Missense_Mutation_p.R357Q	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	357	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						CAGTGCCTCCCGCCGCGGGTC	0.697			M			"various leukaemia, lymphoma"	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis				C|||	2	0.000399361	0.0008	0.0	5008	,	,		16023	0.0		0.0	False		,,,				2504	0.001				p.R357Q		Atlas-SNP	.	yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	PRF1,caecum,carcinoma,-1,1	PRF1	64	1	0			c.G1070A						PASS	.	C	GLN/ARG,GLN/ARG	5,4399		0,5,2197	19	23	22		1070,1070	4.9	1	10	dbSNP_134	22	2,8588		0,2,4293	yes	missense,missense	PRF1	NM_001083116.1,NM_005041.4	43,43	0,7,6490	TT,TC,CC		0.0233,0.1135,0.0539	probably-damaging,probably-damaging	357/556,357/556	72358407	7,12987	2202	4295	6497	SO:0001583	missense	5551	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GCCTCCCGCCGCG	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.1070G>A	10.37:g.72358407C>T	ENSP00000398568:p.Arg357Gln	74	0	0		68	35	0.514706	NM_001083116	B2R6X4|Q59F57|Q86WX7	Missense_Mutation	SNP	ENST00000441259.1	37	CCDS7305.1	.	.	.	.	.	.	.	.	.	.	C	18.09	3.547379	0.65311	0.001135	2.33E-4	ENSG00000180644	ENST00000373209;ENST00000441259;ENST00000318971	D;D	0.85013	-1.93;-1.93	5.83	4.92	0.64577	Membrane attack complex component/perforin (MACPF) domain (3);	0.263415	0.37669	N	0.001991	D	0.88463	0.6443	M	0.66378	2.025	0.41451	D	0.987985	D	0.76494	0.999	P	0.61940	0.896	D	0.87239	0.2265	10	0.44086	T	0.13	-49.1524	7.9431	0.29969	0.0:0.8314:0.0:0.1686	.	357	P14222	PERF_HUMAN	Q	357	ENSP00000362305:R357Q;ENSP00000398568:R357Q	ENSP00000316746:R357Q	R	-	2	0	PRF1	72028413	0.050000	0.20438	0.966000	0.40874	0.070000	0.16714	0.384000	0.20668	2.741000	0.93983	0.655000	0.94253	CGG	C|0.999;T|0.001	0.001	strong		0.697	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041		T	72358407	C	T	72358407	3	4	22	1	0	0	0	0	1	0	0	0	12490	652	23	1	601	1	PRF1	10	72358407	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	34268	72358407	63176340	2263	5164											
UNC5B	219699	hgsc.bcm.edu	37	chr10	73039594	73039594	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcaggcactgattctggcagCgaggtgctccctgactcctt	6	10	12	13	1	1	2	0	2	1	0	3	3	3	2	2	3	2	4	2	3	0	2	rs80333477	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73039594C>T	ENST00000335350.6	+	2	512	c.96C>T	c.(94-96)agC>agT	p.S32S	UNC5B_ENST00000373192.4_Silent_p.S32S	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	32					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						ATTCTGGCAGCGAGGTGCTCC	0.657													C|||	79	0.0157748	0.0582	0.0029	5008	,	,		17163	0.0		0.0	False		,,,				2504	0.0				p.S32S		Atlas-SNP	.											.	UNC5B	123	.	0			c.C96T						PASS	.	C		186,4220	118.8+/-156.5	4,178,2021	37	32	34		96	-3.5	0.3	10	dbSNP_132	34	0,8600		0,0,4300	no	coding-synonymous	UNC5B	NM_170744.4		4,178,6321	TT,TC,CC		0.0,4.2215,1.4301		32/946	73039594	186,12820	2203	4300	6503	SO:0001819	synonymous_variant	219699	exon2			TGGCAGCGAGGTG	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.96C>T	10.37:g.73039594C>T		147	0	0		177	97	0.548023	NM_001244889	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Silent	SNP	ENST00000335350.6	37	CCDS7309.1																																																																																			C|0.987;T|0.013	0.013	strong		0.657	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744		T	73039594	C	T	73039594	2	4	22	1	0	0	0	0	0	0	0	1	17007	767	27	1		1	UNC5B	10	73039594	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	681187	73039594	62495153	2264	5165											
UNC5B	219699	hgsc.bcm.edu	37	chr10	73051440	73051440	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacataccctagcgatttcGcccgggacacccacttcctg	8	8	8	17	3	0	0	0	0	0	0	2	2	1	1	4	1	2	1	4	1	2	4	rs10509332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73051440G>A	ENST00000335350.6	+	10	1962	c.1546G>A	c.(1546-1548)Gcc>Acc	p.A516T	UNC5B_ENST00000373192.4_Missense_Mutation_p.A505T	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	516			A -> T (in dbSNP:rs10509332).		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						TAGCGATTTCGCCCGGGACAC	0.682													g|||	174	0.0347444	0.0923	0.013	5008	,	,		16797	0.0		0.0169	False		,,,				2504	0.0266				p.A516T		Atlas-SNP	.											.	UNC5B	123	.	0			c.G1546A						PASS	.		THR/ALA	326,4080	175.9+/-205.1	12,302,1889	49	51	50		1546	-7.4	0	10	dbSNP_119	50	235,8363	96.3+/-158.1	3,229,4067	yes	missense	UNC5B	NM_170744.4	58	15,531,5956	AA,AG,GG		2.7332,7.399,4.3141	benign	516/946	73051440	561,12443	2203	4299	6502	SO:0001583	missense	219699	exon10			GATTTCGCCCGGG	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.1546G>A	10.37:g.73051440G>A	ENSP00000334329:p.Ala516Thr	75	0	0		87	45	0.517241	NM_170744	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Missense_Mutation	SNP	ENST00000335350.6	37	CCDS7309.1	66	0.03021978021978022	44	0.08943089430894309	6	0.016574585635359115	0	0.0	16	0.021108179419525065	g	0.003	-2.576838	0.00131	0.07399	0.027332	ENSG00000107731	ENST00000335350;ENST00000373192	T;T	0.48836	0.86;0.8	3.71	-7.42	0.01388	.	1.034760	0.07589	N	0.921713	T	0.00754	0.0025	N	0.22421	0.69	0.09310	N	1	B;B	0.24483	0.104;0.063	B;B	0.15870	0.014;0.006	T	0.04128	-1.0975	10	0.14656	T	0.56	-3.517	0.8807	0.01233	0.1728:0.2213:0.3114:0.2946	rs10509332;rs10509332	505;516	Q8IZJ1-2;Q8IZJ1	.;UNC5B_HUMAN	T	516;505	ENSP00000334329:A516T;ENSP00000362288:A505T	ENSP00000334329:A516T	A	+	1	0	UNC5B	72721446	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.641000	0.02007	-3.747000	0.00112	-2.851000	0.00103	GCC	G|0.960;A|0.040	0.040	strong		0.682	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744		A	73051440	G	A	73051440	3	1	22	1	0	0	0	0	1	0	0	0	17007	1087	38	1	1584	1	UNC5B	10	73051440	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	11846	73051440	62483307	2265	5166											
CDH23	64072	hgsc.bcm.edu	37	chr10	73377069	73377069	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccccggagttcaacagctcCgagtacagcgtggccatcac	9	6	11	15	3	2	0	2	0	0	0	3	2	3	1	4	2	4	3	4	2	2	2	rs7903475	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73377069C>T	ENST00000224721.6	+	10	1073	c.1068C>T	c.(1066-1068)tcC>tcT	p.S356S	CDH23_ENST00000398842.3_Silent_p.S351S|CDH23_ENST00000461841.3_Silent_p.S396S|CDH23_ENST00000398809.4_Silent_p.S351S|CDH23_ENST00000299366.7_Silent_p.S396S	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	351	Cadherin 4. {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						TCAACAGCTCCGAGTACAGCG	0.547													C|||	368	0.0734824	0.2625	0.0259	5008	,	,		21110	0.0		0.003	False		,,,				2504	0.0				p.S351S		Atlas-SNP	.											.	CDH23	365	.	0			c.C1053T						PASS	.	C	,,,,	967,3407	328.0+/-300.3	116,735,1336	83	86	85	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1053,1053,1053,1053,1053	-10.9	0.2	10	dbSNP_116	85	12,8568	7.7+/-29.5	0,12,4278	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CDH23	NM_001171930.1,NM_001171931.1,NM_001171932.1,NM_022124.5,NM_052836.3	,,,,	116,747,5614	TT,TC,CC		0.1399,22.1079,7.5575	,,,,	351/1382,351/1062,351/407,351/3355,351/531	73377069	979,11975	2187	4290	6477	SO:0001819	synonymous_variant	64072	exon11			CAGCTCCGAGTAC	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.1068C>T	10.37:g.73377069C>T		112	0	0		108	52	0.481481	NM_052836	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																				C|0.932;T|0.068	0.068	strong		0.547	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		T	73377069	C	T	73377069	2	4	22	1	0	0	0	0	0	0	0	1	3110	639	23	1		1	CDH23	10	73377069	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	325629	73377069	62157678	2266	5167											
CDH23	64072	hgsc.bcm.edu	37	chr10	73551088	73551088	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catctgctagagaactgcccGcctggtaagcaggggacagg	10	6	14	11	1	1	1	0	0	1	1	1	3	1	2	2	4	4	3	2	4	3	2	rs55964031	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73551088G>A	ENST00000224721.6	+	46	6269	c.6264G>A	c.(6262-6264)ccG>ccA	p.P2088P		NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2083	Cadherin 20. {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)	p.P2088P(1)		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						AGAACTGCCCGCCTGGTAAGC	0.627													G|||	135	0.0269569	0.0976	0.0072	5008	,	,		16895	0.0		0.001	False		,,,				2504	0.0				p.P2083P		Atlas-SNP	.											CDH23,NS,carcinoma,0,1	CDH23	365	1	1	Substitution - coding silent(1)	prostate(1)	c.G6249A						scavenged	.	G		276,3814		11,254,1780	42	43	43	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6249	-8.6	1	10	dbSNP_129	43	4,8364		0,4,4180	no	coding-synonymous	CDH23	NM_022124.5		11,258,5960	AA,AG,GG		0.0478,6.7482,2.2476		2083/3355	73551088	280,12178	2045	4184	6229	SO:0001819	synonymous_variant	64072	exon45			CTGCCCGCCTGGT	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.6264G>A	10.37:g.73551088G>A		80	1	0.0125		90	44	0.488889	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																				G|0.974;A|0.026	0.026	strong		0.627	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		A	73551088	G	A	73551088	2	1	22	1	0	0	0	0	0	0	0	1	3110	1074	38	1		1	CDH23	10	73551088	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	174019	73551088	61983659	2267	5168											
CDH23	64072	hgsc.bcm.edu	37	chr10	73553177	73553177	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gccattgtcaccattctgatCgatgacatcaatgactcccg	10	11	7	13	2	3	3	2	3	1	0	5	4	4	3	3	0	0	0	3	0	1	2	rs41281332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73553177C>T	ENST00000224721.6	+	47	6512	c.6507C>T	c.(6505-6507)atC>atT	p.I2169I	CDH23_ENST00000398788.3_5'Flank	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2164	Cadherin 20. {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						CCATTCTGATCGATGACATCA	0.597													C|||	131	0.0261581	0.0946	0.0072	5008	,	,		18788	0.0		0.001	False		,,,				2504	0.0				p.I2164I		Atlas-SNP	.											.	CDH23	365	.	0			c.C6492T						PASS	.	C		294,3964		11,272,1846	75	82	80	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6492	-2.9	1	10	dbSNP_127	80	4,8500		0,4,4248	no	coding-synonymous	CDH23	NM_022124.5		11,276,6094	TT,TC,CC		0.047,6.9047,2.3351		2164/3355	73553177	298,12464	2129	4252	6381	SO:0001819	synonymous_variant	64072	exon46			TCTGATCGATGAC	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.6507C>T	10.37:g.73553177C>T		105	0	0		120	63	0.525	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																				C|0.976;T|0.024	0.024	strong		0.597	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		T	73553177	C	T	73553177	2	4	22	1	0	0	0	0	0	0	0	1	3110	874	31	1		1	CDH23	10	73553177	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2089	73553177	61981570	2268	5169											
CDH23	5660	hgsc.bcm.edu	37	chr10	73574948	73574948	+	IGR	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gccactgccttcgagcgcaaCgcccgcacagaatccgccaa	10	4	9	18	5	0	1	0	0	0	1	2	2	1	1	5	0	3	2	5	0	3	1	rs73277900	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73574948C>T	ENST00000394936.3	-	0	2866				CDH23_ENST00000224721.6_Silent_p.N3331N|CDH23_ENST00000475158.1_3'UTR|CDH23_ENST00000398788.3_Silent_p.N1086N			P07602	SAP_HUMAN	prosaposin						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						TCGAGCGCAACGCCCGCACAG	0.637													C|||	106	0.0211661	0.0756	0.0072	5008	,	,		17511	0.0		0.001	False		,,,				2504	0.0				p.N3326N		Atlas-SNP	.											.	CDH23	365	.	0			c.C9978T						PASS	.	C	,,,,	260,4058		7,246,1906	21	28	26	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3258,3153,669,564,9978	-0.8	1	10	dbSNP_130	26	3,8497		0,3,4247	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CDH23	NM_001171933.1,NM_001171934.1,NM_001171935.1,NM_001171936.1,NM_022124.5	,,,,	7,249,6153	TT,TC,CC		0.0353,6.0213,2.0518	,,,,	1086/1115,1051/1080,223/252,188/217,3326/3355	73574948	263,12555	2159	4250	6409	SO:0001628	intergenic_variant	64072	exon68			GCGCAACGCCCGC	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		10.37:g.73574948C>T		59	0	0		54	27	0.5	NM_022124	P07292|P15793|P78538|P78541|P78546|P78547|P78558|Q53Y86|Q6IBQ6|Q92739|Q92740|Q92741|Q92742	Silent	SNP	ENST00000394936.3	37	CCDS7311.1																																																																																			C|0.984;T|0.016	0.016	strong		0.637	PSAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048553.1	NM_002778		T	73574948	C	T	73574948	1	4	22	0	1	0	0	0	0	0	0	0	3110	535	19	1		1	CDH23	10	73574948	IGR	SNP	C	TCGA-G8-6324-01A-11D-2210-10	21771	73574948	61959799	2269	5170											
SPOCK2	9806	hgsc.bcm.edu	37	chr10	73826775	73826775	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tacttgtccaggttgatggcGgccagctccgtctggtccag	5	11	13	12	2	1	1	0	1	1	0	4	1	4	1	4	4	2	2	4	4	1	3	rs7079142	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73826775G>A	ENST00000373109.2	-	8	1257	c.813C>T	c.(811-813)gcC>gcT	p.A271A	SPOCK2_ENST00000460053.1_5'UTR|SPOCK2_ENST00000536168.1_Silent_p.A271A|SPOCK2_ENST00000317376.4_Silent_p.A271A	NM_001244950.1	NP_001231879.1	Q92563	TICN2_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 2	271					extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)|regulation of cell differentiation (GO:0045595)|signal transduction (GO:0007165)|synapse assembly (GO:0007416)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|glycosaminoglycan binding (GO:0005539)			endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						GGTTGATGGCGGCCAGCTCCG	0.582													G|||	46	0.0091853	0.034	0.0014	5008	,	,		18389	0.0		0.0	False		,,,				2504	0.0				p.A271A		Atlas-SNP	.											.	SPOCK2	32	.	0			c.C813T						PASS	.	G		112,4294	85.8+/-124.5	0,112,2091	121	106	111		813	-7.5	0.6	10	dbSNP_116	111	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	SPOCK2	NM_014767.2		0,115,6388	AA,AG,GG		0.0349,2.542,0.8842		271/425	73826775	115,12891	2203	4300	6503	SO:0001819	synonymous_variant	9806	exon8			GATGGCGGCCAGC	AJ001453	CCDS7313.1, CCDS44431.1	10q22.1	2013-09-19			ENSG00000107742	ENSG00000107742			13564	protein-coding gene	gene with protein product		607988				10386950	Standard	NM_014767		Approved	KIAA0275, testican-2	uc001jso.2	Q92563	OTTHUMG00000018430	ENST00000373109.2:c.813C>T	10.37:g.73826775G>A		58	0	0		74	34	0.459459	NM_001244950	C9J767|Q6UW87	Silent	SNP	ENST00000373109.2	37	CCDS7313.1																																																																																			G|0.990;A|0.010	0.010	strong		0.582	SPOCK2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048560.2			A	73826775	G	A	73826775	2	1	22	1	0	0	0	0	0	0	0	1	15095	1103	39	1		1	SPOCK2	10	73826775	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	251827	73826775	61707972	2270	5171											
ANAPC16	119504	hgsc.bcm.edu	37	chr10	73992862	73992862	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctgctgggattcaccccCtcttcaggttgatactgcct	6	12	9	14	0	3	1	2	1	1	0	3	2	3	2	3	2	4	3	3	2	1	4	rs9275	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73992862C>G	ENST00000299381.4	+	4	439	c.321C>G	c.(319-321)ccC>ccG	p.P107P	ANAPC16_ENST00000470481.2_3'UTR	NM_001242546.1|NM_001242547.1|NM_001242548.1|NM_173473.3	NP_001229475.1|NP_001229476.1|NP_001229477.1|NP_775744.1	Q96DE5	APC16_HUMAN	anaphase promoting complex subunit 16	107					mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	anaphase-promoting complex (GO:0005680)|cytoplasm (GO:0005737)				large_intestine(1)|ovary(1)	2						GATTCACCCCCTCTTCAGGTT	0.542													C|||	364	0.0726837	0.2595	0.0274	5008	,	,		14954	0.0		0.002	False		,,,				2504	0.0				p.P107P		Atlas-SNP	.											.	ANAPC16	10	.	0			c.C321G						PASS	.	C	,,,	919,3487	344.1+/-307.9	90,739,1374	66	64	65		321,321,246,321	-0.3	1	10	dbSNP_52	65	13,8587	9.1+/-34.3	0,13,4287	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ANAPC16	NM_001242546.1,NM_001242547.1,NM_001242548.1,NM_173473.3	,,,	90,752,5661	GG,GC,CC		0.1512,20.8579,7.1659	,,,	107/111,107/111,82/86,107/111	73992862	932,12074	2203	4300	6503	SO:0001819	synonymous_variant	119504	exon5			CACCCCCTCTTCA	BC009530	CCDS7314.1, CCDS73147.1	10q22.2	2011-08-12	2010-04-06	2010-04-06	ENSG00000166295	ENSG00000166295		"Anaphase promoting complex subunits"	26976	protein-coding gene	gene with protein product	"centromere protein 27"	613427	"chromosome 10 open reading frame 104"	C10orf104		14702039, 20360068	Standard	NM_001242546		Approved	bA570G20.3, FLJ33728, APC16, CENP-27	uc021psp.1	Q96DE5	OTTHUMG00000018433	ENST00000299381.4:c.321C>G	10.37:g.73992862C>G		40	0	0		45	26	0.577778	NM_001242546		Silent	SNP	ENST00000299381.4	37	CCDS7314.1																																																																																			G|0.064;C|0.936	0.064	strong		0.542	ANAPC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048565.2	NM_173473		G	73992862	C	G	73992862	2	3	22	1	0	0	0	0	0	0	0	1	602	668	24	4		4	ANAPC16	10	73992862	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	166087	73992862	61541885	2271	5172											
CBARA1	10367	hgsc.bcm.edu	37	chr10	74183034	74183034	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttgagctgcctctgcatggcGgtcagcttcttggactgcac	5	12	12	12	1	3	1	1	1	2	0	3	2	3	2	1	3	5	4	1	3	0	3	rs186054834	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:74183034G>A	ENST00000361114.5	-	9	1125	c.1029C>T	c.(1027-1029)acC>acT	p.T343T	MICU1_ENST00000401998.3_Silent_p.T343T|MICU1_ENST00000418483.2_Silent_p.T145T|MICU1_ENST00000398761.4_Silent_p.T345T|MICU1_ENST00000398763.4_Silent_p.T145T	NM_001195518.1|NM_006077.3	NP_001182447.1|NP_006068.2	Q9BPX6	MICU1_HUMAN	mitochondrial calcium uptake 1	343					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)										TCTGCATGGCGGTCAGCTTCT	0.493													G|||	3	0.000599042	0.0023	0.0	5008	,	,		19951	0.0		0.0	False		,,,				2504	0.0				p.T343T		Atlas-SNP	.											.	.	.	.	0			c.C1029T						PASS	.	G	,,	5,3985		0,5,1990	106	100	102		1029,435,1035	-11.3	0.3	10		102	0,8342		0,0,4171	no	coding-synonymous,coding-synonymous,coding-synonymous	MICU1	NM_001195518.1,NM_001195519.1,NM_006077.3	,,	0,5,6161	AA,AG,GG		0.0,0.1253,0.0405	,,	343/477,145/279,345/479	74183034	5,12327	1995	4171	6166	SO:0001819	synonymous_variant	10367	exon9			CATGGCGGTCAGC	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.1029C>T	10.37:g.74183034G>A		164	0	0		160	69	0.43125	NM_001195518	A8MV96|B3KN20|B4DJH9|B4DPI1|B5MBY3|D3YTJ3|O75785|Q9H9N6|Q9UFX0	Silent	SNP	ENST00000361114.5	37	CCDS55715.1																																																																																			G|0.999;A|0.001	0.001	strong		0.493	MICU1-002	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048586.1	NM_006077		A	74183034	G	A	74183034	2	1	22	1	0	0	0	0	0	0	0	1	2698	1103	39	1		1	CBARA1	10	74183034	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	190172	74183034	61351713	2272	5173											
DUPD1	338599	hgsc.bcm.edu	37	chr10	76797660	76797660	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgtcgcctctgctgcaccagCtgcttgtccagctcccggag	4	9	11	17	3	1	0	0	0	1	0	4	1	3	1	4	1	5	5	4	1	0	1	rs1868624	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:76797660C>T	ENST00000338487.5	-	3	596	c.597G>A	c.(595-597)caG>caA	p.Q199Q		NM_001003892.1	NP_001003892.1	Q68J44	DUPD1_HUMAN	dual specificity phosphatase and pro isomerase domain containing 1	199	Tyrosine-protein phosphatase.				protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(2)|lung(5)|ovary(2)|urinary_tract(1)	11	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)					GCTGCACCAGCTGCTTGTCCA	0.657													C|||	34	0.00678914	0.0227	0.0058	5008	,	,		21195	0.0		0.0	False		,,,				2504	0.0				p.Q199Q		Atlas-SNP	.											.	DUPD1	30	.	0			c.G597A						PASS	.	C		89,4317	74.1+/-112.3	0,89,2114	60	60	60		597	4.1	1	10	dbSNP_92	60	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	DUPD1	NM_001003892.1		0,91,6412	TT,TC,CC		0.0233,2.02,0.6997		199/221	76797660	91,12915	2203	4300	6503	SO:0001819	synonymous_variant	338599	exon3			CACCAGCTGCTTG		CCDS31223.1	10q22.3	2011-06-09			ENSG00000188716	ENSG00000188716		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	23481	protein-coding gene	gene with protein product							Standard	NM_001003892		Approved	DUSP27	uc001jwq.1	Q68J44	OTTHUMG00000018512	ENST00000338487.5:c.597G>A	10.37:g.76797660C>T		69	0	0		75	34	0.453333	NM_001003892	B2RP93	Silent	SNP	ENST00000338487.5	37	CCDS31223.1																																																																																			C|0.959;T|0.041	0.041	strong		0.657	DUPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048777.2	XM_291741		T	76797660	C	T	76797660	2	4	22	1	0	0	0	0	0	0	0	1	4806	796	28	2		2	DUPD1	10	76797660	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2614626	76797660	58737087	2273	5174											
DUPD1	338599	hgsc.bcm.edu	37	chr10	76803600	76803602	+	In_Frame_Del	DEL	AGA	AGA	-																															gatgaaggctgccgccgggtAgaagaagacactgaggtcga																								rs571550955|rs370448554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:76803600_76803602delAGA	ENST00000338487.5	-	2	373_375	c.374_376delTCT	c.(373-378)ttctac>tac	p.F125del		NM_001003892.1	NP_001003892.1	Q68J44	DUPD1_HUMAN	dual specificity phosphatase and pro isomerase domain containing 1	125	Tyrosine-protein phosphatase.				protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(2)|lung(5)|ovary(2)|urinary_tract(1)	11	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)					GCCGCCGGGTAGAAGAAGACACT	0.68														33	0.00658946	0.0219	0.0058	5008	,	,		9789	0.0		0.0	False		,,,				2504	0.0				p.125_126del		Pindel,Atlas-Indel	.											.	DUPD1	30	.	0			c.375_377del						PASS	.			103,4161		6,91,2035						2.5	0.2			84	42,8212		16,10,4101	no	coding	DUPD1	NM_001003892.1		22,101,6136	A1A1,A1R,RR		0.5088,2.4156,1.1583				145,12373				SO:0001651	inframe_deletion	338599	exon2			.		CCDS31223.1	10q22.3	2011-06-09			ENSG00000188716	ENSG00000188716		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	23481	protein-coding gene	gene with protein product							Standard	NM_001003892		Approved	DUSP27	uc001jwq.1	Q68J44	OTTHUMG00000018512	ENST00000338487.5:c.374_376delTCT	10.37:g.76803606_76803608delAGA	ENSP00000340609:p.Phe125del	44	0	.		56	18	0.321	NM_001003892	B2RP93	In_Frame_Del	DEL	ENST00000338487.5	37	CCDS31223.1																																																																																			.	.	none		0.68	DUPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048777.2	XM_291741		-	76803602	AGA	-	76803600	7	5	22	1	0	1	0	1	0	0	0	0	4806	420	15	0	294	0	DUPD1	10	76803600	In_Frame_Del	DEL	AGA	TCGA-G8-6324-01A-11D-2210-10	5940	76803600	58731147	2274	5175											
DUSP13	51207	hgsc.bcm.edu	37	chr10	76854463	76854463	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccccgtctcccgccccagtcGgttgtccagaacctggagct	5	8	10	18	3	1	1	0	0	1	1	4	2	2	2	7	2	2	2	7	2	1	1	rs16931996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:76854463G>C	ENST00000472493.2	-	4	646	c.568C>G	c.(568-570)Cga>Gga	p.R190G	DUSP13_ENST00000372702.3_3'UTR|DUSP13_ENST00000478873.2_Missense_Mutation_p.R326G|DUSP13_ENST00000607131.1_Missense_Mutation_p.R283G|DUSP13_ENST00000491677.2_Missense_Mutation_p.R319G|DUSP13_ENST00000464872.1_Missense_Mutation_p.R139G|DUSP13_ENST00000605915.1_Missense_Mutation_p.R212G|DUSP13_ENST00000372700.3_Missense_Mutation_p.R240G	NM_016364.3	NP_057448.3	Q9UII6	DS13B_HUMAN	dual specificity phosphatase 13	190			R -> G (in dbSNP:rs16931996).		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)					CGCCCCAGTCGGTTGTCCAGA	0.642													G|||	149	0.0297524	0.1082	0.0072	5008	,	,		17269	0.0		0.001	False		,,,				2504	0.0				p.R283G	NSCLC(174;1655 2059 12324 40663 42963)	Atlas-SNP	.											.	DUSP13	82	.	0			c.C847G						PASS	.	G	,GLY/ARG,GLY/ARG,GLY/ARG	462,3944	213.8+/-233.3	24,414,1765	47	45	46		,718,847,568	3.6	1	10	dbSNP_123	46	3,8597	3.0+/-9.4	0,3,4297	yes	utr-3,missense,missense,missense	DUSP13	NM_001007271.1,NM_001007272.1,NM_001007273.1,NM_016364.3	,125,125,125	24,417,6062	CC,CG,GG		0.0349,10.4857,3.5753	,probably-damaging,probably-damaging,probably-damaging	,240/249,283/292,190/199	76854463	465,12541	2203	4300	6503	SO:0001583	missense	51207	exon6			CCAGTCGGTTGTC	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	ENST00000472493.2:c.568C>G	10.37:g.76854463G>C	ENSP00000444580:p.Arg190Gly	81	0	0		56	35	0.625	NM_001007273	A8K776|A8K782|B3KPY1|B3KXT0|B4DUK0|Q5JSC6|Q6IAR0|Q96GC2	Missense_Mutation	SNP	ENST00000472493.2	37	CCDS7346.1	59	0.027014652014652016	55	0.11178861788617886	4	0.011049723756906077	0	0.0	0	0.0	G	19.55	3.847958	0.71603	0.104857	3.49E-4	ENSG00000079393	ENST00000308475;ENST00000472493;ENST00000491677;ENST00000372698;ENST00000464872;ENST00000372700	T;T;T;T;T	0.61627	0.09;0.09;0.09;0.09;0.09	5.52	3.61	0.41365	Dual specificity phosphatase, subgroup, catalytic domain (2);	0.557970	0.19913	N	0.103241	T	0.03564	0.0102	M	0.74647	2.275	0.34897	D	0.74614	P;D;B	0.54772	0.556;0.968;0.157	B;P;B	0.54706	0.248;0.759;0.146	T	0.53500	-0.8430	10	0.49607	T	0.09	-3.9628	14.5469	0.68038	0.0:0.0:0.61:0.39	rs16931996;rs52804188;rs16931996	240;319;190	Q9UII6-4;F2Z2C4;Q9UII6	.;.;DUS13_HUMAN	G	190;190;319;283;139;240	ENSP00000311051:R190G;ENSP00000444580:R190G;ENSP00000436312:R319G;ENSP00000434041:R139G;ENSP00000361785:R240G	ENSP00000311051:R190G	R	-	1	2	DUSP13	76524469	0.947000	0.32204	1.000000	0.80357	0.987000	0.75469	1.817000	0.39002	0.635000	0.30488	-0.169000	0.13324	CGA	G|0.956;C|0.044	0.044	strong		0.642	DUSP13-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048786.3			C	76854463	G	C	76854463	3	2	22	1	0	0	0	0	1	0	0	0	4815	1124	39	4	32	4	DUSP13	10	76854463	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	50863	76854463	58680284	2275	5176											
DLG5	9231	hgsc.bcm.edu	37	chr10	79556301	79556301	+	Missense_Mutation	SNP	A	A	G																															ccagaatcaggacaggcctcAgagcggtgcagtccaccttc																								rs74140333	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:79556301A>G	ENST00000372391.2	-	28	5221	c.5216T>C	c.(5215-5217)cTg>cCg	p.L1739P	DLG5_ENST00000459739.1_5'UTR|DLG5_ENST00000372388.2_Missense_Mutation_p.L1399P	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	1739	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)			GACAGGCCTCAGAGCGGTGCA	0.602													A|||	68	0.0135783	0.0499	0.0014	5008	,	,		20065	0.0		0.001	False		,,,				2504	0.0				p.L1739P		Atlas-SNP	.											.	DLG5	154	.	0			c.T5216C						PASS	.	A	PRO/LEU	150,4256	104.3+/-142.8	2,146,2055	100	85	90		5216	3.6	1	10	dbSNP_130	90	2,8598	2.2+/-6.3	0,2,4298	yes	missense	DLG5	NM_004747.3	98	2,148,6353	GG,GA,AA		0.0233,3.4044,1.1687	benign	1739/1920	79556301	152,12854	2203	4300	6503	SO:0001583	missense	9231	exon28			GGCCTCAGAGCGG	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.5216T>C	10.37:g.79556301A>G	ENSP00000361467:p.Leu1739Pro	249	0	0		211	98	0.464455	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Missense_Mutation	SNP	ENST00000372391.2	37	CCDS7353.2	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	A	12.73	2.026468	0.35701	0.034044	2.33E-4	ENSG00000151208	ENST00000372391;ENST00000424842;ENST00000372388	T;T;T	0.20598	2.06;2.06;2.06	5.97	3.63	0.41609	Guanylate kinase/L-type calcium channel (1);	0.000000	0.31519	N	0.007516	T	0.00784	0.0026	N	0.00652	-1.29	0.58432	D	0.999999	B;B	0.10296	0.001;0.003	B;B	0.17433	0.002;0.018	T	0.31586	-0.9938	10	0.24483	T	0.36	.	4.6381	0.12534	0.5759:0.0:0.4241:0.0	.	1739;1399	Q8TDM6;Q8TDM6-2	DLG5_HUMAN;.	P	1739;700;1399	ENSP00000361467:L1739P;ENSP00000394797:L700P;ENSP00000361464:L1399P	ENSP00000361464:L1399P	L	-	2	0	DLG5	79226307	1.000000	0.71417	0.970000	0.41538	0.687000	0.40016	4.450000	0.60041	1.069000	0.40788	0.533000	0.62120	CTG	A|0.989;G|0.011	0.011	strong		0.602	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2			G	79556301	A	G	79556301	3	3	22	1	0	0	0	0	1	0	0	0	4560	188	7	3	563	3	DLG5	10	79556301	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2701838	79556301	55978446	2276	5177	62	2									
DLG5	9231	hgsc.bcm.edu	37	chr10	79556305	79556305	+	Missense_Mutation	SNP	C	C	T																															aatcaggacaggcctcagagCggtgcagtccaccttctgga																								rs74140334	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:79556305C>T	ENST00000372391.2	-	28	5217	c.5212G>A	c.(5212-5214)Gct>Act	p.A1738T	DLG5_ENST00000459739.1_5'UTR|DLG5_ENST00000372388.2_Missense_Mutation_p.A1398T	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	1738	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)			GGCCTCAGAGCGGTGCAGTCC	0.597													C|||	70	0.0139776	0.0514	0.0014	5008	,	,		19795	0.0		0.001	False		,,,				2504	0.0				p.A1738T		Atlas-SNP	.											.	DLG5	154	.	0			c.G5212A						PASS	.	C	THR/ALA	164,4242	110.4+/-148.6	2,160,2041	100	85	90		5212	2.4	0.1	10	dbSNP_130	90	2,8598	2.2+/-6.3	0,2,4298	yes	missense	DLG5	NM_004747.3	58	2,162,6339	TT,TC,CC		0.0233,3.7222,1.2763	benign	1738/1920	79556305	166,12840	2203	4300	6503	SO:0001583	missense	9231	exon28			TCAGAGCGGTGCA	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.5212G>A	10.37:g.79556305C>T	ENSP00000361467:p.Ala1738Thr	241	0	0		210	96	0.457143	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Missense_Mutation	SNP	ENST00000372391.2	37	CCDS7353.2	29	0.013278388278388278	28	0.056910569105691054	1	0.0027624309392265192	0	0.0	0	0.0	C	6.638	0.486271	0.12641	0.037222	2.33E-4	ENSG00000151208	ENST00000372391;ENST00000424842;ENST00000372388	T;T;T	0.16457	2.34;2.34;2.34	5.97	2.38	0.29361	Guanylate kinase/L-type calcium channel (1);	0.200014	0.25233	N	0.032160	T	0.00552	0.0018	N	0.03608	-0.345	0.29378	N	0.863515	B;B	0.27882	0.0;0.192	B;B	0.21360	0.0;0.034	T	0.39333	-0.9619	10	0.02654	T	1	.	8.5372	0.33371	0.6271:0.2508:0.0:0.1221	.	1738;1398	Q8TDM6;Q8TDM6-2	DLG5_HUMAN;.	T	1738;699;1398	ENSP00000361467:A1738T;ENSP00000394797:A699T;ENSP00000361464:A1398T	ENSP00000361464:A1398T	A	-	1	0	DLG5	79226311	0.996000	0.38824	0.059000	0.19551	0.082000	0.17680	3.446000	0.52928	0.153000	0.19213	-0.262000	0.10625	GCT	C|0.988;T|0.012	0.012	strong		0.597	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2			T	79556305	C	T	79556305	3	4	22	1	0	0	0	0	1	0	0	0	4560	768	27	1	567	1	DLG5	10	79556305	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4	79556305	55978442	2277	5178	62	2									
DLG5	9231	hgsc.bcm.edu	37	chr10	79603423	79603423	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgtccatggccgtgtcataCagtttgttgagaatctcgga	8	14	11	8	2	2	1	1	1	1	1	4	3	3	2	2	2	1	2	2	2	2	4	rs12257229	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:79603423C>T	ENST00000372391.2	-	6	911	c.906G>A	c.(904-906)ctG>ctA	p.L302L	DLG5_ENST00000372388.2_Silent_p.L302L	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	302					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)			CCGTGTCATACAGTTTGTTGA	0.532													C|||	497	0.0992412	0.3593	0.0274	5008	,	,		21222	0.0		0.003	False		,,,				2504	0.0				p.L302L		Atlas-SNP	.											.	DLG5	154	.	0			c.G906A						PASS	.	C		1351,3055	449.4+/-349.0	200,951,1052	180	162	168		906	2.6	1	10	dbSNP_120	168	21,8579	14.0+/-48.4	0,21,4279	no	coding-synonymous	DLG5	NM_004747.3		200,972,5331	TT,TC,CC		0.2442,30.6627,10.549		302/1920	79603423	1372,11634	2203	4300	6503	SO:0001819	synonymous_variant	9231	exon6			GTCATACAGTTTG	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.906G>A	10.37:g.79603423C>T		195	0	0		201	94	0.467662	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Silent	SNP	ENST00000372391.2	37	CCDS7353.2																																																																																			C|0.888;T|0.112	0.112	strong		0.532	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2			T	79603423	C	T	79603423	2	4	22	1	0	0	0	0	0	0	0	1	4560	465	17	2		2	DLG5	10	79603423	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	47118	79603423	55931324	2278	5179											
DLG5	9231	hgsc.bcm.edu	37	chr10	79616520	79616520	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccgtgccatgcgtagcaaaGgccaggcgcttgcggagctc	7	6	15	13	4	0	0	0	0	0	0	1	1	0	1	3	3	5	4	3	3	2	2	rs12243930	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:79616520G>C	ENST00000372391.2	-	3	509	c.504C>G	c.(502-504)gcC>gcG	p.A168A	DLG5_ENST00000372388.2_Silent_p.A168A	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	168					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)			GCGTAGCAAAGGCCAGGCGCT	0.592													G|||	720	0.14377	0.5197	0.0432	5008	,	,		18218	0.0		0.003	False		,,,				2504	0.0				p.A168A		Atlas-SNP	.											.	DLG5	154	.	0			c.C504G						PASS	.	G		1939,2467	545.8+/-376.9	450,1039,714	46	48	47		504	4.5	1	10	dbSNP_120	47	24,8576	14.6+/-50.1	0,24,4276	no	coding-synonymous	DLG5	NM_004747.3		450,1063,4990	CC,CG,GG		0.2791,44.0082,15.093		168/1920	79616520	1963,11043	2203	4300	6503	SO:0001819	synonymous_variant	9231	exon3			AGCAAAGGCCAGG	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.504C>G	10.37:g.79616520G>C		206	0	0		198	95	0.479798	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Silent	SNP	ENST00000372391.2	37	CCDS7353.2																																																																																			G|0.857;C|0.143	0.143	strong		0.592	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2			C	79616520	G	C	79616520	2	2	22	1	0	0	0	0	0	0	0	1	4560	987	35	4		4	DLG5	10	79616520	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	13097	79616520	55918227	2279	5180											
POLR3A	11128	hgsc.bcm.edu	37	chr10	79781326	79781326	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctcaggaaaagttagaattTtggccacatgaactggcaca	14	10	9	8	0	1	2	1	1	1	1	2	3	1	3	1	3	1	2	1	3	5	3	rs550436426		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:79781326T>C	ENST00000372371.3	-	8	1300	c.1163A>G	c.(1162-1164)aAa>aGa	p.K388R	POLR3A_ENST00000484760.1_5'Flank	NM_007055.3	NP_008986.2	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide A, 155kDa	388					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)			AGTTAGAATTTTGGCCACATG	0.423													T|||	1	0.000199681	0.0008	0.0	5008	,	,		18712	0.0		0.0	False		,,,				2504	0.0				p.K388R		Atlas-SNP	.											.	POLR3A	104	.	0			c.A1163G						PASS	.						74	71	72					10																	79781326		2203	4300	6503	SO:0001583	missense	11128	exon8			AGAATTTTGGCCA	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.1163A>G	10.37:g.79781326T>C	ENSP00000361446:p.Lys388Arg	77	0	0		69	29	0.42029	NM_007055	Q8IW34|Q8TCW5	Missense_Mutation	SNP	ENST00000372371.3	37	CCDS7354.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.845255	0.91197	.	.	ENSG00000148606	ENST00000372371;ENST00000540842	T	0.68331	-0.32	5.58	5.58	0.84498	RNA polymerase, alpha subunit (1);RNA polymerase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.62258	0.2413	L	0.41906	1.305	0.80722	D	1	P	0.46578	0.88	B	0.44133	0.442	T	0.61705	-0.7008	9	.	.	.	-24.6898	16.0507	0.80760	0.0:0.0:0.0:1.0	.	388	O14802	RPC1_HUMAN	R	388	ENSP00000361446:K388R	.	K	-	2	0	POLR3A	79451332	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.646000	0.83445	2.243000	0.73865	0.528000	0.53228	AAA	.	.	none		0.423	POLR3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048923.1	NM_007055		C	79781326	T	C	79781326	3	2	22	1	0	0	0	0	1	0	0	0	12237	1841	64	3	3105	3	POLR3A	10	79781326	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	164806	79781326	55753421	2280	5181											
RPS24	6229	hgsc.bcm.edu	37	chr10	79814747	79814747	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgcttctccccaccttcctgCctctctggtctgggccacta	3	13	7	18	0	3	0	0	0	3	0	6	0	4	0	6	2	2	1	6	2	1	3	rs76653255	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:79814747C>T	ENST00000440692.1	+	5	991	c.849C>T	c.(847-849)tgC>tgT	p.C283C		NM_001142285.1	NP_001135757.1	P62847	RS24_HUMAN	ribosomal protein S24	0					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)			caccttcctgcctctctggtc	0.542													C|||	318	0.0634984	0.2231	0.0202	5008	,	,		17984	0.0		0.0089	False		,,,				2504	0.0				p.C283C		Atlas-SNP	.											.	RPS24	23	.	0			c.C849T						PASS	.	C		237,1147		17,203,472	37	35	35		849	-4.1	0	10	dbSNP_132	35	7,3175		0,7,1584	yes	coding-synonymous	RPS24	NM_001142285.1		17,210,2056	TT,TC,CC		0.22,17.1243,5.3438		283/290	79814747	244,4322	692	1591	2283	SO:0001819	synonymous_variant	6229	exon5			TTCCTGCCTCTCT	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	ENST00000440692.1:c.849C>T	10.37:g.79814747C>T		134	0	0		108	55	0.509259	NM_001142285	E7EPK6|P16632|Q5T0P7|Q5T0P8|Q7Z3D1	Silent	SNP	ENST00000440692.1	37	CCDS44443.1																																																																																			C|0.947;T|0.053	0.053	strong		0.542	RPS24-202	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001026		T	79814747	C	T	79814747	2	4	22	1	0	0	0	0	0	0	0	1	13650	747	26	2		2	RPS24	10	79814747	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	33421	79814747	55720000	2281	5182											
GHITM	27069	hgsc.bcm.edu	37	chr10	85902479	85902479	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagaactcaaagaggcagcAttggaaccatcgatggaaaa	18	5	10	8	1	1	2	1	0	0	2	2	5	1	4	1	3	3	2	1	3	6	1	rs146877821	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:85902479A>T	ENST00000372134.3	+	3	391	c.198A>T	c.(196-198)gcA>gcT	p.A66A	RP11-338I21.1_ENST00000606511.1_RNA	NM_014394.2	NP_055209.2	Q9H3K2	GHITM_HUMAN	growth hormone inducible transmembrane protein	66					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						AAGAGGCAGCATTGGAACCAT	0.408													A|||	29	0.00579073	0.0212	0.0014	5008	,	,		15827	0.0		0.0	False		,,,				2504	0.0				p.A66A		Atlas-SNP	.											.	GHITM	30	.	0			c.A198T						PASS	.	A		53,3701		0,53,1824	100	102	101		198	-9.6	0	10	dbSNP_134	101	0,8224		0,0,4112	no	coding-synonymous	GHITM	NM_014394.2		0,53,5936	TT,TA,AA		0.0,1.4118,0.4425		66/346	85902479	53,11925	1877	4112	5989	SO:0001819	synonymous_variant	27069	exon3			GGCAGCATTGGAA	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.198A>T	10.37:g.85902479A>T		61	0	0		97	46	0.474227	NM_014394	A8K9Z9|D3DWE0|O95894|Q5VT95|Q9H0P2	Silent	SNP	ENST00000372134.3	37	CCDS41542.1																																																																																			A|0.995;T|0.005	0.005	strong		0.408	GHITM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049125.1	NM_014394		T	85902479	A	T	85902479	2	4	22	1	0	0	0	0	0	0	0	1	6378	204	8	5		5	GHITM	10	85902479	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	6087732	85902479	49632268	2282	5183											
LRIT2	340745	hgsc.bcm.edu	37	chr10	85981756	85981756	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	accgtcatcacagacagctgGatgttctctaaaggagccat	12	9	9	11	1	3	1	2	0	1	1	4	3	3	3	2	2	2	2	2	2	2	2	rs74145770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:85981756G>T	ENST00000372113.4	-	3	1578	c.1573C>A	c.(1573-1575)Cca>Aca	p.P525T	LRIT2_ENST00000538192.1_Missense_Mutation_p.P535T	NM_001017924.2	NP_001017924.1	A6NDA9	LRIT2_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 2	525						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						CAGACAGCTGGATGTTCTCTA	0.592													G|||	227	0.0453275	0.1672	0.0086	5008	,	,		19768	0.0		0.0	False		,,,				2504	0.0				p.P525T		Atlas-SNP	.											.	LRIT2	81	.	0			c.C1573A						PASS	.	G	THR/PRO	600,3806	252.1+/-258.6	50,500,1653	117	105	109		1573	-5.7	0	10	dbSNP_130	109	18,8582	12.6+/-44.7	0,18,4282	yes	missense	LRIT2	NM_001017924.2	38	50,518,5935	TT,TG,GG		0.2093,13.6178,4.7517	benign	525/551	85981756	618,12388	2203	4300	6503	SO:0001583	missense	340745	exon3			CAGCTGGATGTTC		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.1573C>A	10.37:g.85981756G>T	ENSP00000361185:p.Pro525Thr	159	0	0		208	119	0.572115	NM_001017924	B7ZME6	Missense_Mutation	SNP	ENST00000372113.4	37	CCDS31234.1	91	0.041666666666666664	87	0.17682926829268292	4	0.011049723756906077	0	0.0	0	0.0	G	0.610	-0.825514	0.02734	0.136178	0.002093	ENSG00000204033	ENST00000372113;ENST00000538192	T;T	0.16597	2.33;2.33	4.57	-5.65	0.02459	.	1.918670	0.02557	N	0.096284	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.12013	0.005;0.001	B;B	0.06405	0.002;0.001	T	0.31336	-0.9947	9	0.13108	T	0.6	.	3.6424	0.08172	0.1993:0.4518:0.2433:0.1056	.	535;525	B7ZME6;A6NDA9	.;LRIT2_HUMAN	T	525;535	ENSP00000361185:P525T;ENSP00000438264:P535T	ENSP00000361185:P525T	P	-	1	0	LRIT2	85971736	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.226000	0.09139	-1.353000	0.02191	0.655000	0.94253	CCA	G|0.957;T|0.043	0.043	strong		0.592	LRIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049110.4	XM_291697		T	85981756	G	T	85981756	3	4	22	1	0	0	0	0	1	0	0	0	8957	1174	41	4	83	4	LRIT2	10	85981756	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	79277	85981756	49552991	2283	5184											
LRIT2	340745	hgsc.bcm.edu	37	chr10	85982075	85982075	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaaggaggtcatccacagcAtaagtattgattccggggcc	11	8	13	9	1	1	1	1	1	0	0	3	3	3	3	3	5	1	2	3	5	3	4	rs7901410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:85982075A>G	ENST00000372113.4	-	3	1259	c.1254T>C	c.(1252-1254)taT>taC	p.Y418Y	LRIT2_ENST00000538192.1_Silent_p.Y428Y	NM_001017924.2	NP_001017924.1	A6NDA9	LRIT2_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 2	418	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						CATCCACAGCATAAGTATTGA	0.537													A|||	227	0.0453275	0.1672	0.0086	5008	,	,		21319	0.0		0.0	False		,,,				2504	0.0				p.Y418Y		Atlas-SNP	.											.	LRIT2	81	.	0			c.T1254C						PASS	.	A		602,3804	265.9+/-266.9	50,502,1651	121	114	116		1254	-10.1	0	10	dbSNP_116	116	18,8582	12.6+/-44.7	0,18,4282	no	coding-synonymous	LRIT2	NM_001017924.2		50,520,5933	GG,GA,AA		0.2093,13.6632,4.767		418/551	85982075	620,12386	2203	4300	6503	SO:0001819	synonymous_variant	340745	exon3			CACAGCATAAGTA		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.1254T>C	10.37:g.85982075A>G		56	0	0		78	41	0.525641	NM_001017924	B7ZME6	Silent	SNP	ENST00000372113.4	37	CCDS31234.1																																																																																			A|0.945;G|0.055	0.055	strong		0.537	LRIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049110.4	XM_291697		G	85982075	A	G	85982075	2	3	22	1	0	0	0	0	0	0	0	1	8957	224	8	3		3	LRIT2	10	85982075	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	319	85982075	49552672	2284	5185											
LRIT1	26103	hgsc.bcm.edu	37	chr10	85993923	85993923	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtagcagtgctgtgccaccCaaaagggacctgatgctggc	9	7	13	12	1	0	1	0	1	0	0	0	2	0	2	3	2	4	4	3	2	3	1	rs149121025	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:85993923C>T	ENST00000372105.3	-	3	822	c.801G>A	c.(799-801)ttG>ttA	p.L267L		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	267	Ig-like C2-type.					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						CTGTGCCACCCAAAAGGGACC	0.622													C|||	11	0.00219649	0.0083	0.0	5008	,	,		19368	0.0		0.0	False		,,,				2504	0.0				p.L267L		Atlas-SNP	.											LRIT1,NS,haematopoietic_neoplasm,0,1	LRIT1	73	1	0			c.G801A						PASS	.	C		27,4379	34.3+/-65.2	0,27,2176	73	72	72		801	5.9	1	10	dbSNP_134	72	0,8600		0,0,4300	no	coding-synonymous	LRIT1	NM_015613.2		0,27,6476	TT,TC,CC		0.0,0.6128,0.2076		267/624	85993923	27,12979	2203	4300	6503	SO:0001819	synonymous_variant	26103	exon3			GCCACCCAAAAGG	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.801G>A	10.37:g.85993923C>T		59	0	0		94	41	0.43617	NM_015613	Q0QD41|Q9Y4N7	Silent	SNP	ENST00000372105.3	37	CCDS7373.1																																																																																			C|0.998;T|0.002	0.002	strong		0.622	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613		T	85993923	C	T	85993923	2	4	22	1	0	0	0	0	0	0	0	1	8956	593	21	2		2	LRIT1	10	85993923	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	11848	85993923	49540824	2285	5186											
LDB3	11155	hgsc.bcm.edu	37	chr10	88476458	88476458	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccacttgccagggggaccGtccagagggctgagcgattc	8	6	14	13	2	0	2	0	1	0	1	2	4	1	3	4	3	2	1	4	3	0	2	rs113817827		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:88476458G>A	ENST00000361373.4	+	9	1627	c.1606G>A	c.(1606-1608)Gtc>Atc	p.V536I	LDB3_ENST00000458213.2_Missense_Mutation_p.V426I|LDB3_ENST00000429277.2_Missense_Mutation_p.V541I|LDB3_ENST00000352360.5_Missense_Mutation_p.V279I|LDB3_ENST00000263066.6_Missense_Mutation_p.V426I	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						CAGGGGGACCGTCCAGAGGGC	0.667													G|||	1	0.000199681	0.0	0.0	5008	,	,		13034	0.001		0.0	False		,,,				2504	0.0				p.V541I		Atlas-SNP	.											.	LDB3	164	.	0			c.G1621A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL	2,4404	4.2+/-10.8	0,2,2201	33	33	33		1276,1621,1606	-0.3	0.9	10	dbSNP_132	33	0,8600		0,0,4300	no	missense,missense,missense	LDB3	NM_001080114.1,NM_001171610.1,NM_007078.2	29,29,29	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	benign,benign,benign	426/618,541/733,536/728	88476458	2,13004	2203	4300	6503	SO:0001583	missense	11155	exon10			GGGACCGTCCAGA	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.1606G>A	10.37:g.88476458G>A	ENSP00000355296:p.Val536Ile	251	0	0		235	105	0.446809	NM_001171610		Missense_Mutation	SNP	ENST00000361373.4	37	CCDS7377.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	G	13.41	2.227523	0.39399	4.54E-4	0.0	ENSG00000122367	ENST00000539402;ENST00000429277;ENST00000458213;ENST00000352360;ENST00000263066;ENST00000361373	T;T;T;T;T	0.54279	0.82;0.67;0.61;0.67;0.58	4.85	-0.331	0.12679	.	0.302757	0.18155	N	0.149948	T	0.21509	0.0518	N	0.05124	-0.11	0.80722	D	1	B;B;B;P;B	0.38729	0.001;0.003;0.0;0.644;0.0	B;B;B;B;B	0.32805	0.001;0.004;0.001;0.153;0.0	T	0.02852	-1.1102	10	0.35671	T	0.21	.	4.289	0.10869	0.1864:0.0:0.2957:0.5179	.	541;457;279;536;426	B4E3K3;F5H0C2;O75112-3;O75112;O75112-2	.;.;.;LDB3_HUMAN;.	I	457;541;426;279;426;536	ENSP00000401437:V541I;ENSP00000409148:V426I;ENSP00000263067:V279I;ENSP00000263066:V426I;ENSP00000355296:V536I	ENSP00000263066:V426I	V	+	1	0	LDB3	88466438	0.975000	0.34042	0.879000	0.34478	0.874000	0.50279	1.816000	0.38992	0.095000	0.17434	0.555000	0.69702	GTC	G|0.998;A|0.002	0.002	strong		0.667	LDB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049160.2			A	88476458	G	A	88476458	3	1	22	1	0	0	0	0	1	0	0	0	8706	1145	40	1	1976	1	LDB3	10	88476458	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2482535	88476458	47058289	2286	5187											
MINPP1	9562	hgsc.bcm.edu	37	chr10	89312046	89312046	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctttaccactgtgaaaatgcTaagactcctaaagaacaatt	16	11	5	9	0	0	3	0	1	0	2	1	3	1	3	2	0	3	1	2	0	8	5	rs2233169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:89312046T>C	ENST00000371996.4	+	5	1316	c.1275T>C	c.(1273-1275)gcT>gcC	p.A425A	MINPP1_ENST00000536010.1_Silent_p.A224A|MINPP1_ENST00000472891.1_3'UTR|MINPP1_ENST00000371994.4_3'UTR	NM_004897.4	NP_004888.2	Q9UNW1	MINP1_HUMAN	multiple inositol-polyphosphate phosphatase 1	425					bone mineralization (GO:0030282)|dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|ossification (GO:0001503)|polyphosphate metabolic process (GO:0006797)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	acid phosphatase activity (GO:0003993)|bisphosphoglycerate 3-phosphatase activity (GO:0034417)|inositol hexakisphosphate 2-phosphatase activity (GO:0052826)|phosphohistidine phosphatase activity (GO:0008969)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|urinary_tract(2)	5		Colorectal(252;0.122)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00123)		GTGAAAATGCTAAGACTCCTA	0.368													T|||	142	0.0283546	0.0998	0.0086	5008	,	,		20648	0.0		0.002	False		,,,				2504	0.002				p.A425A		Atlas-SNP	.											.	MINPP1	22	.	0			c.T1275C						PASS	.	T	,,	354,4052	181.5+/-209.5	14,326,1863	126	123	124		,672,1275	-4.7	1	10	dbSNP_98	124	11,8589	7.7+/-29.5	0,11,4289	no	utr-3,coding-synonymous,coding-synonymous	MINPP1	NM_001178117.1,NM_001178118.1,NM_004897.4	,,	14,337,6152	CC,CT,TT		0.1279,8.0345,2.8064	,,	,224/287,425/488	89312046	365,12641	2203	4300	6503	SO:0001819	synonymous_variant	9562	exon5			AAATGCTAAGACT	AF046915	CCDS7384.1, CCDS53551.1, CCDS53552.1	10q23	2010-05-04	2010-05-04		ENSG00000107789	ENSG00000107789	3.1.3.62		7102	protein-coding gene	gene with protein product		605391	"multiple inositol polyphosphate histidine phosphatase, 1"			10087200	Standard	NM_004897		Approved	MIPP	uc001keu.3	Q9UNW1	OTTHUMG00000018678	ENST00000371996.4:c.1275T>C	10.37:g.89312046T>C		160	0	0		137	61	0.445255	NM_004897	F5H683|O95172|O95286|Q59EJ2|Q9UGA3	Silent	SNP	ENST00000371996.4	37	CCDS7384.1																																																																																			T|0.975;C|0.025	0.025	strong		0.368	MINPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049221.1			C	89312046	T	C	89312046	2	2	22	1	0	0	0	0	0	0	0	1	9597	1509	53	3		3	MINPP1	10	89312046	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	835588	89312046	46222701	2287	5188											
LIPN	643418	hgsc.bcm.edu	37	chr10	90530683	90530683	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaatctgcaacaataagataCtctggttgatatgtagcgaa	16	11	8	6	1	2	2	0	1	2	1	2	3	2	2	0	1	4	3	0	1	8	5	rs114737713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:90530683C>T	ENST00000404459.1	+	6	754	c.754C>T	c.(754-756)Ctc>Ttc	p.L252F		NM_001102469.1	NP_001095939.1	Q5VXI9	LIPN_HUMAN	lipase, family member N	252					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	hydrolase activity, acting on ester bonds (GO:0016788)			endometrium(1)|kidney(1)|large_intestine(5)|lung(1)|skin(1)	9		Colorectal(252;0.0161)		Colorectal(12;4.83e-05)|COAD - Colon adenocarcinoma(12;6.5e-05)		CAATAAGATACTCTGGTTGAT	0.323													C|||	76	0.0151757	0.0545	0.0043	5008	,	,		17038	0.0		0.001	False		,,,				2504	0.0				p.L252F		Atlas-SNP	.											.	LIPN	28	.	0			c.C754T						PASS	.	C	PHE/LEU	117,3509		2,113,1698	67	64	65		754	1.9	0.4	10	dbSNP_132	65	3,8125		0,3,4061	yes	missense	LIPN	NM_001102469.1	22	2,116,5759	TT,TC,CC		0.0369,3.2267,1.0209	benign	252/399	90530683	120,11634	1813	4064	5877	SO:0001583	missense	643418	exon6			AAGATACTCTGGT		CCDS44456.1	10q23.31	2013-09-20	2007-02-27	2007-02-27	ENSG00000204020	ENSG00000204020			23452	protein-coding gene	gene with protein product		613924	"lipase-like, ab-hydrolase domain containing 4"	LIPL4			Standard	NM_001102469		Approved	bA186O14.3	uc010qmw.2	Q5VXI9	OTTHUMG00000018694	ENST00000404459.1:c.754C>T	10.37:g.90530683C>T	ENSP00000383923:p.Leu252Phe	136	0	0		150	76	0.506667	NM_001102469	A7KIH9	Missense_Mutation	SNP	ENST00000404459.1	37	CCDS44456.1	35	0.016025641025641024	32	0.06504065040650407	3	0.008287292817679558	0	0.0	0	0.0	C	6.188	0.402853	0.11696	0.032267	3.69E-4	ENSG00000204020	ENST00000404459	T	0.62232	0.04	4.86	1.85	0.25348	Alpha/beta hydrolase fold-1 (1);	0.760258	0.11368	N	0.571199	T	0.03783	0.0107	N	0.20845	0.615	0.09310	N	1	B	0.26975	0.165	B	0.25506	0.061	T	0.04635	-1.0937	10	0.10377	T	0.69	-8.2711	5.458	0.16602	0.0:0.4967:0.0:0.5032	.	252	Q5VXI9	LIPN_HUMAN	F	252	ENSP00000383923:L252F	ENSP00000383923:L252F	L	+	1	0	LIPN	90520663	0.003000	0.15002	0.412000	0.26496	0.894000	0.52154	-0.146000	0.10250	0.668000	0.31126	0.650000	0.86243	CTC	C|0.983;T|0.017	0.017	strong		0.323	LIPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049254.2	XM_926751		T	90530683	C	T	90530683	3	4	22	1	0	0	0	0	1	0	0	0	8837	565	20	2	776	2	LIPN	10	90530683	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1218637	90530683	45004064	2288	5189											
KIF20B	9585	hgsc.bcm.edu	37	chr10	91532574	91532574	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaatttcatctcctattgatAtatcaggccaagtggtaagc	13	13	7	8	0	3	1	2	1	1	0	4	1	3	1	2	2	1	1	2	2	6	6	rs150021584	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:91532574A>G	ENST00000371728.3	+	32	5436	c.5371A>G	c.(5371-5373)Ata>Gta	p.I1791V	KIF20B_ENST00000416354.1_Missense_Mutation_p.I1821V|KIF20B_ENST00000478929.1_3'UTR|KIF20B_ENST00000260753.4_Missense_Mutation_p.I1751V	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	1791	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						TCCTATTGATATATCAGGCCA	0.323													A|||	3	0.000599042	0.0023	0.0	5008	,	,		15182	0.0		0.0	False		,,,				2504	0.0				p.I1751V		Atlas-SNP	.											.	KIF20B	191	.	0			c.A5251G						PASS	.	A	VAL/ILE	17,4389	22.3+/-47.3	0,17,2186	137	137	137		5251	4.8	1	10	dbSNP_134	137	0,8600		0,0,4300	yes	missense	KIF20B	NM_016195.2	29	0,17,6486	GG,GA,AA		0.0,0.3858,0.1307	benign	1751/1781	91532574	17,12989	2203	4300	6503	SO:0001583	missense	9585	exon32			ATTGATATATCAG	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.5371A>G	10.37:g.91532574A>G	ENSP00000360793:p.Ile1791Val	407	1	0.002457		389	182	0.467866	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	37		1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	19.08	3.757963	0.69648	0.003858	0.0	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000371728	T;T;T	0.54479	0.57;0.57;0.57	5.91	4.76	0.60689	.	0.125603	0.35235	N	0.003352	T	0.49983	0.1589	M	0.66939	2.045	0.80722	D	1	P;P	0.43287	0.702;0.802	B;B	0.40677	0.182;0.337	T	0.52961	-0.8505	10	0.66056	D	0.02	-7.6635	8.0076	0.30334	0.7238:0.1411:0.0:0.1351	.	1791;1751	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	V	1751;1821;1791	ENSP00000260753:I1751V;ENSP00000411545:I1821V;ENSP00000360793:I1791V	ENSP00000260753:I1751V	I	+	1	0	KIF20B	91522554	1.000000	0.71417	0.991000	0.47740	0.989000	0.77384	2.459000	0.45023	1.027000	0.39758	0.533000	0.62120	ATA	A|0.999;G|0.001	0.001	strong		0.323	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195		G	91532574	A	G	91532574	3	3	22	1	0	0	0	0	1	0	0	0	8296	449	16	3	5373	3	KIF20B	10	91532574	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1001891	91532574	44002173	2289	5190											
HECTD2	143279	hgsc.bcm.edu	37	chr10	93260363	93260363	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatggctatgcaaaaacggaCttaactataaagtgagctct	15	10	9	7	1	1	1	0	1	1	0	1	3	1	2	0	2	4	3	0	2	7	4	rs34553731	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:93260363C>T	ENST00000298068.5	+	19	2149	c.2055C>T	c.(2053-2055)gaC>gaT	p.D685D	HECTD2_ENST00000446394.1_Silent_p.D689D|HECTD2_ENST00000536715.1_Silent_p.D274D|HECTD2_ENST00000371667.1_Silent_p.D335D	NM_182765.3	NP_877497	Q5U5R9	HECD2_HUMAN	HECT domain containing E3 ubiquitin protein ligase 2	685	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						CAAAAACGGACTTAACTATAA	0.418													C|||	61	0.0121805	0.0439	0.0029	5008	,	,		16343	0.0		0.001	False		,,,				2504	0.0				p.D685D	NSCLC(12;376 469 1699 39910 41417)	Atlas-SNP	.											.	HECTD2	60	.	0			c.C2055T						PASS	.	C		205,4201	127.0+/-164.0	5,195,2003	103	95	98		2055	3.9	0.6	10	dbSNP_126	98	6,8594	3.0+/-9.4	0,6,4294	no	coding-synonymous	HECTD2	NM_182765.3		5,201,6297	TT,TC,CC		0.0698,4.6527,1.6223		685/777	93260363	211,12795	2203	4300	6503	SO:0001819	synonymous_variant	143279	exon19			AACGGACTTAACT	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.2055C>T	10.37:g.93260363C>T		50	0	0		61	29	0.47541	NM_182765	Q5VZ97|Q5VZ98|Q5VZ99|Q8N1X7|Q8TCP5	Silent	SNP	ENST00000298068.5	37	CCDS7414.1																																																																																			C|0.985;T|0.015	0.015	strong		0.418	HECTD2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098620.1			T	93260363	C	T	93260363	2	4	22	1	0	0	0	0	0	0	0	1	7049	564	20	2		2	HECTD2	10	93260363	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1727789	93260363	42274384	2290	5191											
CEP55	55165	hgsc.bcm.edu	37	chr10	95262980	95262980	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggccagatatagtactacCacattgcttgaacagctgga	14	9	9	9	0	0	2	0	1	0	1	0	3	0	3	2	2	5	3	2	2	6	6	rs62642530	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:95262980C>T	ENST00000371485.3	+	3	598	c.294C>T	c.(292-294)acC>acT	p.T98T		NM_001127182.1|NM_018131.4	NP_001120654|NP_060601	Q53EZ4	CEP55_HUMAN	centrosomal protein 55kDa	98					establishment of protein localization (GO:0045184)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|midbody (GO:0030496)				kidney(1)|large_intestine(5)|lung(6)|stomach(1)	13		Colorectal(252;0.207)				ATAGTACTACCACATTGCTTG	0.443													C|||	20	0.00399361	0.0129	0.0014	5008	,	,		19829	0.0		0.0	False		,,,				2504	0.002				p.T98T		Atlas-SNP	.											.	CEP55	35	.	0			c.C294T						PASS	.	C	,	38,4368	16.8+/-37.8	0,38,2165	147	131	136		294,294	-10.7	0	10	dbSNP_129	136	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CEP55	NM_001127182.1,NM_018131.4	,	0,38,6465	TT,TC,CC		0.0,0.8625,0.2922	,	98/465,98/465	95262980	38,12968	2203	4300	6503	SO:0001819	synonymous_variant	55165	exon3			TACTACCACATTG	AK001402	CCDS7428.1	10q24.1	2014-02-20	2005-12-01	2005-12-01	ENSG00000138180	ENSG00000138180			1161	protein-coding gene	gene with protein product	"cancer/testis antigen 111"	610000	"chromosome 10 open reading frame 3"	C10orf3		16198290	Standard	NM_018131		Approved	FLJ10540, CT111	uc009xug.3	Q53EZ4	OTTHUMG00000018774	ENST00000371485.3:c.294C>T	10.37:g.95262980C>T		102	0	0		82	43	0.52439	NM_018131	B2RDG8|Q32WF5|Q3MV20|Q5VY28|Q6N034|Q96H32|Q9NVS7	Silent	SNP	ENST00000371485.3	37	CCDS7428.1																																																																																			C|0.996;T|0.004	0.004	strong		0.443	CEP55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049434.1	NM_018131		T	95262980	C	T	95262980	2	4	22	1	0	0	0	0	0	0	0	1	3257	581	21	2		2	CEP55	10	95262980	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2002617	95262980	40271767	2291	5192											
CYP2C8	1558	hgsc.bcm.edu	37	chr10	96818106	96818106	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttacctgctccattttgaTcaggaagcaatcgataaagt	12	13	7	9	1	2	1	1	1	1	0	4	3	3	2	2	1	3	2	2	1	5	4	rs11572103	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:96818106T>A	ENST00000371270.3	-	5	899	c.805A>T	c.(805-807)Atc>Ttc	p.I269F	CYP2C8_ENST00000535898.1_Missense_Mutation_p.I167F|CYP2C8_ENST00000539050.1_Missense_Mutation_p.I183F	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	269			I -> F (in allele CYP2C8*2; only found in African-Americans; dbSNP:rs11572103). {ECO:0000269|PubMed:11668219, ECO:0000269|PubMed:12429347, ECO:0000269|PubMed:15469410, ECO:0000269|Ref.5}.		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)	TCCATTTTGATCAGGAAGCAA	0.358													T|||	274	0.0547125	0.1891	0.0115	5008	,	,		17668	0.0		0.004	False		,,,				2504	0.0123				p.I269F		Atlas-SNP	.											.	CYP2C8	73	.	0			c.A805T	GRCh37	CM016067	CYP2C8	M	rs11572103	PASS	.	T	PHE/ILE,PHE/ILE,PHE/ILE,PHE/ILE	690,3716	289.5+/-280.5	68,554,1581	156	139	145		805,595,499,595	4.2	0.8	10	dbSNP_120	145	30,8570	21.0+/-64.5	0,30,4270	yes	missense,missense,missense,missense	CYP2C8	NM_000770.3,NM_001198853.1,NM_001198854.1,NM_001198855.1	21,21,21,21	68,584,5851	AA,AT,TT		0.3488,15.6605,5.5359	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	269/491,199/421,167/389,199/421	96818106	720,12286	2203	4300	6503	SO:0001583	missense	1558	exon5			TTTTGATCAGGAA	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.805A>T	10.37:g.96818106T>A	ENSP00000360317:p.Ile269Phe	138	0	0		136	73	0.536765	NM_000770	A8K9N8|B0AZN2|B7Z1F6|Q5VX93|Q8WWB1|Q9UCZ9	Missense_Mutation	SNP	ENST00000371270.3	37	CCDS7438.1	85	0.03891941391941392	82	0.16666666666666666	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	T	13.62	2.290753	0.40494	0.156605	0.003488	ENSG00000138115	ENST00000371270;ENST00000535868;ENST00000535898;ENST00000539050	T;T;T	0.68624	-0.34;-0.34;-0.34	4.17	4.17	0.49024	.	0.225081	0.35235	U	0.003341	T	0.00524	0.0017	M	0.66378	2.025	0.23903	P	0.99651506	P;D;D;D	0.59767	0.898;0.961;0.986;0.961	P;P;P;P	0.57101	0.622;0.675;0.795;0.813	T	0.32134	-0.9918	9	0.72032	D	0.01	.	11.4277	0.50020	0.0:0.0:0.0:1.0	rs11572103;rs52833642;rs58027822;rs11572103	183;167;237;269	F5H7Q9;B7Z1F6;B7Z8S1;P10632	.;.;.;CP2C8_HUMAN	F	269;236;167;183	ENSP00000360317:I269F;ENSP00000445062:I167F;ENSP00000442343:I183F	ENSP00000360317:I269F	I	-	1	0	CYP2C8	96808096	0.980000	0.34600	0.793000	0.32043	0.156000	0.22039	1.316000	0.33620	1.642000	0.50584	0.254000	0.18369	ATC	T|0.950;A|0.050	0.050	strong		0.358	CYP2C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049499.2	NM_000770		A	96818106	T	A	96818106	3	1	22	1	0	0	0	0	1	0	0	0	4169	1435	50	5	687	5	CYP2C8	10	96818106	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1555126	96818106	38716641	2292	5193											
SORBS1	10580	hgsc.bcm.edu	37	chr10	97154762	97154762	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctaagtttatggtaccttcGgaagtttgctggatttcagg	8	16	11	6	1	2	0	1	0	1	0	3	2	2	2	1	4	2	4	1	4	4	7	rs17110703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:97154762G>A	ENST00000361941.3	-	12	1319	c.1293C>T	c.(1291-1293)tcC>tcT	p.S431S	SORBS1_ENST00000371241.1_Intron|SORBS1_ENST00000371246.2_Silent_p.S431S|SORBS1_ENST00000371245.3_Intron|SORBS1_ENST00000371247.2_Silent_p.S431S|SORBS1_ENST00000354106.3_Silent_p.S422S|SORBS1_ENST00000474353.2_Intron|SORBS1_ENST00000353505.5_Intron|SORBS1_ENST00000306402.6_Intron|SORBS1_ENST00000371249.2_Intron|SORBS1_ENST00000347291.4_Silent_p.S299S|SORBS1_ENST00000371239.1_Intron|SORBS1_ENST00000371227.4_Intron|SORBS1_ENST00000607232.1_Intron|SORBS1_ENST00000277982.5_Silent_p.S431S|SORBS1_ENST00000393949.1_Silent_p.S422S	NM_001034954.1	NP_001030126			sorbin and SH3 domain containing 1											NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(19)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		TGGTACCTTCGGAAGTTTGCT	0.393													G|||	188	0.0375399	0.1369	0.0086	5008	,	,		19554	0.0		0.001	False		,,,				2504	0.0				p.S431S		Atlas-SNP	.											.	SORBS1	185	.	0			c.C1293T						PASS	.	G	,,,,,,	505,3901	233.6+/-246.7	26,453,1724	237	281	266		1293,1293,,,,,	4.9	1	10	dbSNP_123	266	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous,coding-synonymous,intron,intron,intron,intron,intron	SORBS1	NM_001034954.1,NM_001034955.1,NM_001034956.1,NM_001034957.1,NM_006434.2,NM_015385.2,NM_024991.1	,,,,,,	26,462,6015	AA,AG,GG		0.1047,11.4616,3.952	,,,,,,	431/1293,431/1152,,,,,	97154762	514,12492	2203	4300	6503	SO:0001819	synonymous_variant	10580	exon12			ACCTTCGGAAGTT	AF136381	CCDS7442.1, CCDS31252.1, CCDS31253.1, CCDS31254.1, CCDS31255.1, CCDS31256.1, CCDS73169.1	10q23.33	2011-07-25	2002-05-08		ENSG00000095637	ENSG00000095637			14565	protein-coding gene	gene with protein product	"c-Cbl-associated protein"	605264	"SH3-domain protein 5 (ponsin)"	SH3D5		10085297, 11001060	Standard	XM_005269405		Approved	FLJ12406, CAP, sh3p12, ponsin, KIAA1296	uc001kkp.3	Q9BX66	OTTHUMG00000018812	ENST00000361941.3:c.1293C>T	10.37:g.97154762G>A		228	0	0		214	108	0.504673	NM_001034955		Silent	SNP	ENST00000361941.3	37	CCDS31255.1																																																																																			G|0.952;A|0.048	0.048	strong		0.393	SORBS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049517.1			A	97154762	G	A	97154762	2	1	22	1	0	0	0	0	0	0	0	1	14942	1103	39	1		1	SORBS1	10	97154762	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	336656	97154762	38379985	2293	5194											
CC2D2B	387707	hgsc.bcm.edu	37	chr10	97779510	97779510	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caatggctgtattttttgacTattcaaaggaaagtttctgg	11	16	9	5	0	2	1	1	1	1	0	2	2	2	2	0	3	0	3	0	3	5	7	rs9943393	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:97779510T>C	ENST00000344386.3	+	8	873	c.709T>C	c.(709-711)Tat>Cat	p.Y237H	ENTPD1-AS1_ENST00000416301.1_RNA|RP11-690P14.4_ENST00000475252.2_Intron|ENTPD1-AS1_ENST00000458228.1_RNA|CC2D2B_ENST00000371198.2_Intron|ENTPD1-AS1_ENST00000452728.1_RNA|ENTPD1-AS1_ENST00000454638.1_RNA|ENTPD1-AS1_ENST00000449197.1_RNA|ENTPD1-AS1_ENST00000451364.1_RNA|CC2D2B_ENST00000410012.2_Missense_Mutation_p.Y237H	NM_001001732.3	NP_001001732.2	Q6DHV5	C2D2B_HUMAN	coiled-coil and C2 domain containing 2B	237			Y -> H (in dbSNP:rs9943393).							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)		ATTTTTTGACTATTCAAAGGA	0.338													T|||	67	0.0133786	0.0477	0.0043	5008	,	,		17685	0.0		0.001	False		,,,				2504	0.0				p.Y237H		Atlas-SNP	.											.	CC2D2B	46	.	0			c.T709C						PASS	.	T	HIS/TYR,HIS/TYR	124,3472		7,110,1681	105	107	106		709,709	3.7	1	10	dbSNP_119	106	3,8137		0,3,4067	yes	missense,missense	CC2D2B	NM_001001732.3,NM_001159747.1	83,83	7,113,5748	CC,CT,TT		0.0369,3.4483,1.0821	possibly-damaging,possibly-damaging	237/323,237/402	97779510	127,11609	1798	4070	5868	SO:0001583	missense	387707	exon8			TTTGACTATTCAA	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.709T>C	10.37:g.97779510T>C	ENSP00000343747:p.Tyr237His	271	0	0		288	127	0.440972	NM_001001732	A2A3E9|B4DYD4|E9PCC3|Q5VUS0	Missense_Mutation	SNP	ENST00000344386.3	37	CCDS41555.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	T	14.01	2.407470	0.42715	0.034483	3.69E-4	ENSG00000188649	ENST00000451649;ENST00000410012;ENST00000344386	T;T	0.70399	-0.48;-0.48	4.93	3.73	0.42828	.	.	.	.	.	T	0.22166	0.0534	L	0.44542	1.39	0.26525	N	0.974358	P;B	0.44195	0.828;0.392	B;B	0.42593	0.392;0.141	T	0.31194	-0.9952	9	0.39692	T	0.17	.	7.3082	0.26459	0.2619:0.0:0.0:0.7381	rs9943393;rs9943393	237;237	E9PCC3;Q6DHV5	.;C2D2B_HUMAN	H	237	ENSP00000386988:Y237H;ENSP00000343747:Y237H	ENSP00000343747:Y237H	Y	+	1	0	CC2D2B	97769500	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	2.130000	0.42064	2.072000	0.62099	0.454000	0.30748	TAT	T|0.988;C|0.012	0.012	strong		0.338	CC2D2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049573.3	NM_001001732		C	97779510	T	C	97779510	3	2	22	1	0	0	0	0	1	0	0	0	2731	1522	53	3	735	3	CC2D2B	10	97779510	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	624748	97779510	37755237	2294	5195											
TLL2	7093	hgsc.bcm.edu	37	chr10	98240156	98240156	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcttggtccagtctctggctTtgtcaatgtgaaacagcttc	7	14	10	10	0	2	1	1	1	1	0	5	1	3	1	1	2	2	3	1	2	2	3	rs61738802	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:98240156T>A	ENST00000357947.3	-	2	461	c.236A>T	c.(235-237)aAa>aTa	p.K79I	TLL2_ENST00000469598.1_5'UTR	NM_012465.3	NP_036597.1	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	79					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)		GTCTCTGGCTTTGTCAATGTG	0.502													T|||	19	0.00379393	0.0144	0.0	5008	,	,		22069	0.0		0.0	False		,,,				2504	0.0				p.K79I		Atlas-SNP	.											.	TLL2	122	.	0			c.A236T						PASS	.	T	ILE/LYS	66,4340	61.7+/-98.7	1,64,2138	285	234	251		236	3.4	0.4	10	dbSNP_129	251	1,8599		0,1,4299	yes	missense	TLL2	NM_012465.3	102	1,65,6437	AA,AT,TT		0.0116,1.498,0.5151	benign	79/1016	98240156	67,12939	2203	4300	6503	SO:0001583	missense	7093	exon2			CTGGCTTTGTCAA	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.236A>T	10.37:g.98240156T>A	ENSP00000350630:p.Lys79Ile	250	0	0		256	118	0.460938	NM_012465	A6NDK0|Q2M1H1|Q6PJN5|Q9UQ00	Missense_Mutation	SNP	ENST00000357947.3	37	CCDS7449.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	T	16.21	3.058034	0.55325	0.01498	1.16E-4	ENSG00000095587	ENST00000357947	T	0.16457	2.34	5.74	3.37	0.38596	.	0.384078	0.18126	U	0.150896	T	0.07863	0.0197	L	0.38175	1.15	0.24846	N	0.992434	B	0.34103	0.437	B	0.29716	0.106	T	0.22695	-1.0209	10	0.72032	D	0.01	.	4.0306	0.09708	0.0:0.1654:0.1858:0.6489	rs61738802	79	Q9Y6L7	TLL2_HUMAN	I	79	ENSP00000350630:K79I	ENSP00000350630:K79I	K	-	2	0	TLL2	98230146	0.920000	0.31207	0.364000	0.25888	0.337000	0.28794	1.236000	0.32683	0.959000	0.37980	0.459000	0.35465	AAA	T|0.986;A|0.014	0.014	strong		0.502	TLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049608.1			A	98240156	T	A	98240156	3	1	22	1	0	0	0	0	1	0	0	0	15961	1841	64	5	2891	5	TLL2	10	98240156	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	460646	98240156	37294591	2295	5196											
TM9SF3	56889	hgsc.bcm.edu	37	chr10	98282083	98282083	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cttgttcccatgtaaccaatCgctcctgcaaagataaaata	14	11	5	11	1	0	1	0	0	0	1	3	1	2	1	3	0	2	4	3	0	6	5	rs35359279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:98282083C>T	ENST00000371142.4	-	15	1923	c.1707G>A	c.(1705-1707)gcG>gcA	p.A569A		NM_020123.3	NP_064508.3	Q9HD45	TM9S3_HUMAN	transmembrane 9 superfamily member 3	569						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)		TGTAACCAATCGCTCCTGCAA	0.338													C|||	47	0.00938498	0.0356	0.0	5008	,	,		18641	0.0		0.0	False		,,,				2504	0.0				p.A569A		Atlas-SNP	.											.	TM9SF3	45	.	0			c.G1707A						PASS	.	C		106,4300	82.9+/-121.4	3,100,2100	98	101	100		1707	-2.1	1	10	dbSNP_126	100	3,8595		0,3,4296	no	coding-synonymous	TM9SF3	NM_020123.3		3,103,6396	TT,TC,CC		0.0349,2.4058,0.8382		569/590	98282083	109,12895	2203	4299	6502	SO:0001819	synonymous_variant	56889	exon15			ACCAATCGCTCCT	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.1707G>A	10.37:g.98282083C>T		80	0	0		95	35	0.368421	NM_020123	Q5TB57|Q6UWE7|Q9NWL8|Q9P0G9|Q9UHW8	Silent	SNP	ENST00000371142.4	37	CCDS7450.1																																																																																			C|0.990;T|0.010	0.010	strong		0.338	TM9SF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049610.2	NM_020123		T	98282083	C	T	98282083	2	4	22	1	0	0	0	0	0	0	0	1	15994	871	31	1		1	TM9SF3	10	98282083	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	41927	98282083	37252664	2296	5197											
PIK3AP1	118788	hgsc.bcm.edu	37	chr10	98469734	98469734	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgaggatgtcgcatcctctgGgcacccctggacaagaatga	10	8	12	11	1	1	3	0	2	1	1	3	5	2	5	3	3	0	2	3	3	2	0	rs73334383	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:98469734G>A	ENST00000339364.5	-	2	139	c.20C>T	c.(19-21)cCc>cTc	p.P7L		NM_152309.2	NP_689522.2	Q6ZUJ8	BCAP_HUMAN	phosphoinositide-3-kinase adaptor protein 1	7					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)		GCATCCTCTGGGCACCCCTGG	0.597													G|||	61	0.0121805	0.0416	0.0086	5008	,	,		17446	0.0		0.0	False		,,,				2504	0.0				p.P7L		Atlas-SNP	.											.	PIK3AP1	111	.	0			c.C20T						PASS	.	G	LEU/PRO	128,4168		2,124,2022	52	43	46		20	-9.5	0	10	dbSNP_130	46	2,8428		0,2,4213	yes	missense	PIK3AP1	NM_152309.2	98	2,126,6235	AA,AG,GG		0.0237,2.9795,1.0215	benign	7/806	98469734	130,12596	2148	4215	6363	SO:0001583	missense	118788	exon2			CCTCTGGGCACCC	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.20C>T	10.37:g.98469734G>A	ENSP00000339826:p.Pro7Leu	94	0	0		91	40	0.43956	NM_152309	Q5TB56|Q5VXJ9|Q8N6J6|Q8NAC8	Missense_Mutation	SNP	ENST00000339364.5	37	CCDS31259.1	26	0.011904761904761904	21	0.042682926829268296	5	0.013812154696132596	0	0.0	0	0.0	G	2.065	-0.414443	0.04766	0.029795	2.37E-4	ENSG00000155629	ENST00000339364	T	0.09255	3.0	4.73	-9.46	0.00597	.	2.649450	0.01208	N	0.007761	T	0.00906	0.0030	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.26467	-1.0102	10	0.22109	T	0.4	4.4446	5.2642	0.15589	0.1057:0.174:0.5472:0.173	.	7	Q6ZUJ8	BCAP_HUMAN	L	7	ENSP00000339826:P7L	ENSP00000339826:P7L	P	-	2	0	PIK3AP1	98459724	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.446000	0.06837	-2.205000	0.00742	-0.345000	0.07892	CCC	G|0.987;A|0.013	0.013	strong		0.597	PIK3AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049619.2	NM_152309		A	98469734	G	A	98469734	3	1	22	1	0	0	0	0	1	0	0	0	11917	1232	43	2	2461	2	PIK3AP1	10	98469734	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	187651	98469734	37065013	2297	5198											
C10orf12	26148	hgsc.bcm.edu	37	chr10	98742088	98742088	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtggcctctccctgctcaccTtcctgaagaggacctgccag	6	9	10	16	0	2	2	1	1	1	1	4	3	3	3	6	2	2	1	6	2	1	1	rs7082522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:98742088T>C	ENST00000286067.2	+	1	1048	c.941T>C	c.(940-942)cTt>cCt	p.L314P		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	314			L -> P (in dbSNP:rs7082522).							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)		CCTGCTCACCTTCCTGAAGAG	0.572													T|||	42	0.00838658	0.0234	0.0101	5008	,	,		19340	0.0		0.004	False		,,,				2504	0.0				p.L314P		Atlas-SNP	.											.	C10orf12	94	.	0			c.T941C						PASS	.	T	PRO/LEU	82,4324	69.8+/-107.6	0,82,2121	66	67	67		941	2.5	0.1	10	dbSNP_116	67	19,8581	12.6+/-44.7	0,19,4281	yes	missense	C10orf12	NM_015652.2	98	0,101,6402	CC,CT,TT		0.2209,1.8611,0.7766	benign	314/1248	98742088	101,12905	2203	4300	6503	SO:0001583	missense	26148	exon1			CTCACCTTCCTGA	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.941T>C	10.37:g.98742088T>C	ENSP00000286067:p.Leu314Pro	96	0	0		82	36	0.439024	NM_015652	Q9H945|Q9Y457	Missense_Mutation	SNP	ENST00000286067.2	37	CCDS7452.1	9	0.004120879120879121	5	0.01016260162601626	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	T	6.674	0.492926	0.12702	0.018611	0.002209	ENSG00000155640	ENST00000286067;ENST00000539886	T	0.08720	3.06	6.05	2.49	0.30216	.	0.311072	0.22801	N	0.055461	T	0.02156	0.0067	N	0.14661	0.345	0.20638	N	0.999875	B;B	0.17038	0.006;0.02	B;B	0.16722	0.009;0.016	T	0.40850	-0.9541	10	0.33141	T	0.24	0.0135	8.0912	0.30801	0.0:0.3649:0.0:0.6351	rs7082522;rs7082522	148;314	A0PJI9;Q8N655	.;CJ012_HUMAN	P	314;148	ENSP00000286067:L314P	ENSP00000286067:L314P	L	+	2	0	C10orf12	98732078	0.000000	0.05858	0.055000	0.19348	0.931000	0.56810	-0.378000	0.07446	0.189000	0.20188	0.533000	0.62120	CTT	T|0.994;C|0.006	0.006	strong		0.572	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652		C	98742088	T	C	98742088	3	2	22	1	0	0	0	0	1	0	0	0	1591	1609	56	3	943	3	C10orf12	10	98742088	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	272354	98742088	36792659	2298	5199											
CRTAC1	55118	hgsc.bcm.edu	37	chr10	99667840	99667840	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaagttaggcccattctcAttgtcgcagaagatatccga	12	10	10	9	2	1	2	1	0	1	2	4	4	2	3	2	2	0	2	2	2	4	4	rs35333633	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:99667840A>G	ENST00000370597.3	-	6	1135	c.780T>C	c.(778-780)aaT>aaC	p.N260N	CRTAC1_ENST00000370591.2_Silent_p.N260N|CRTAC1_ENST00000298819.4_Silent_p.N260N	NM_018058.6	NP_060528.3	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1	260						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)		GCCCATTCTCATTGTCGCAGA	0.607													G|||	285	0.0569089	0.2005	0.0231	5008	,	,		20899	0.0		0.004	False		,,,				2504	0.0				p.N260N		Atlas-SNP	.											.	CRTAC1	86	.	0			c.T780C						PASS	.	G	,	725,3681	757.9+/-412.8	68,589,1546	89	68	75		780,780	-2.7	1	10	dbSNP_126	75	7,8593	819.0+/-406.8	0,7,4293	no	coding-synonymous,coding-synonymous	CRTAC1	NM_001206528.2,NM_018058.6	,	68,596,5839	GG,GA,AA		0.0814,16.4548,5.6282	,	260/646,260/662	99667840	732,12274	2203	4300	6503	SO:0001819	synonymous_variant	55118	exon6			ATTCTCATTGTCG	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.780T>C	10.37:g.99667840A>G		115	0	0		153	75	0.490196	NM_001206528	B1ALN4|Q5T4F8|Q8N4H6|Q8TE52|Q9NQ78|Q9NQ80|Q9NW46	Silent	SNP	ENST00000370597.3	37	CCDS31266.1																																																																																			A|0.946;G|0.054	0.054	strong		0.607	CRTAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049754.1	NM_018058		G	99667840	A	G	99667840	2	3	22	1	0	0	0	0	0	0	0	1	3898	214	8	3		3	CRTAC1	10	99667840	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	925752	99667840	35866907	2299	5200											
CRTAC1	55118	hgsc.bcm.edu	37	chr10	99696031	99696031	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccctgccggtcccgcagcGcgtagtagggtgagctgcgc	4	7	15	15	5	0	1	0	1	0	0	2	1	2	1	4	2	4	4	4	2	2	2	rs80014629	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:99696031G>A	ENST00000370597.3	-	3	672	c.317C>T	c.(316-318)gCg>gTg	p.A106V	CRTAC1_ENST00000370591.2_Missense_Mutation_p.A106V|CRTAC1_ENST00000298819.4_Missense_Mutation_p.A106V	NM_018058.6	NP_060528.3	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1	106						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.A106V(1)		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)		GTCCCGCAGCGCGTAGTAGGG	0.617													G|||	7	0.00139776	0.0053	0.0	5008	,	,		18551	0.0		0.0	False		,,,				2504	0.0				p.A106V		Atlas-SNP	.											CRTAC1,NS,carcinoma,0,2	CRTAC1	86	2	1	Substitution - Missense(1)	endometrium(1)	c.C317T						PASS	.	G	VAL/ALA,VAL/ALA	18,4388	24.3+/-50.5	0,18,2185	66	54	58		317,317	4.8	1	10	dbSNP_131	58	0,8600		0,0,4300	yes	missense,missense	CRTAC1	NM_001206528.2,NM_018058.6	64,64	0,18,6485	AA,AG,GG		0.0,0.4085,0.1384	benign,benign	106/646,106/662	99696031	18,12988	2203	4300	6503	SO:0001583	missense	55118	exon3			CGCAGCGCGTAGT	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.317C>T	10.37:g.99696031G>A	ENSP00000359629:p.Ala106Val	132	0	0		112	52	0.464286	NM_001206528	B1ALN4|Q5T4F8|Q8N4H6|Q8TE52|Q9NQ78|Q9NQ80|Q9NW46	Missense_Mutation	SNP	ENST00000370597.3	37	CCDS31266.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	14.45	2.537920	0.45176	0.004085	0.0	ENSG00000095713	ENST00000413387;ENST00000370597;ENST00000298819;ENST00000309155;ENST00000370591	T;T;T;T;T	0.75050	1.37;-0.9;1.27;-0.05;-0.06	4.76	4.76	0.60689	.	0.000000	0.85682	D	0.000000	T	0.65091	0.2658	L	0.57536	1.79	0.80722	D	1	P;P	0.50710	0.68;0.938	B;B	0.43386	0.089;0.418	T	0.68239	-0.5461	10	0.15066	T	0.55	-16.5833	17.7665	0.88480	0.0:0.0:1.0:0.0	.	106;106	Q9NQ79-2;Q9NQ79	.;CRAC1_HUMAN	V	2;106;106;98;106	ENSP00000408445:A2V;ENSP00000359629:A106V;ENSP00000298819:A106V;ENSP00000310810:A98V;ENSP00000359623:A106V	ENSP00000298819:A106V	A	-	2	0	CRTAC1	99686021	1.000000	0.71417	0.958000	0.39756	0.350000	0.29205	7.675000	0.84002	2.204000	0.70986	0.313000	0.20887	GCG	G|0.999;A|0.001	0.001	strong		0.617	CRTAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049754.1	NM_018058		A	99696031	G	A	99696031	3	1	22	1	0	0	0	0	1	0	0	0	3898	1087	38	1	1720	1	CRTAC1	10	99696031	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	28191	99696031	35838716	2300	5201											
CNNM1	26507	hgsc.bcm.edu	37	chr10	101120671	101120671	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttgtttaagctttcggacacGgagatgcgggtgaagatctc	9	12	13	7	3	1	3	0	1	1	2	3	5	1	4	0	3	2	2	0	3	2	4	rs61735150	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:101120671G>A	ENST00000356713.4	+	3	2086	c.1797G>A	c.(1795-1797)acG>acA	p.T599T	CNNM1_ENST00000446890.1_Silent_p.T528T|CNNM1_ENST00000370534.4_Silent_p.T234T|CNNM1_ENST00000370528.3_Silent_p.T528T	NM_020348.2	NP_065081.2	Q9NRU3	CNNM1_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 1	599					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)		TTTCGGACACGGAGATGCGGG	0.542													G|||	20	0.00399361	0.0144	0.0014	5008	,	,		20089	0.0		0.0	False		,,,				2504	0.0				p.T599T		Atlas-SNP	.											CNNM1_ENST00000356713,NS,carcinoma,0,2	CNNM1	101	2	0			c.G1797A						PASS	.	G		86,4320	72.5+/-110.5	0,86,2117	117	111	113		1797	-11.5	0	10	dbSNP_129	113	0,8600		0,0,4300	no	coding-synonymous	CNNM1	NM_020348.2		0,86,6417	AA,AG,GG		0.0,1.9519,0.6612		599/952	101120671	86,12920	2203	4300	6503	SO:0001819	synonymous_variant	26507	exon3			GGACACGGAGATG	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.1797G>A	10.37:g.101120671G>A		75	0	0		93	46	0.494624	NM_020348	Q4QQG7|Q4QQH8|Q4QQP9|Q9NT45	Silent	SNP	ENST00000356713.4	37	CCDS7478.2																																																																																			G|0.992;A|0.008	0.008	strong		0.542	CNNM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049792.2	NM_020348		A	101120671	G	A	101120671	2	1	22	1	0	0	0	0	0	0	0	1	3614	1103	39	1		1	CNNM1	10	101120671	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1424640	101120671	34414076	2301	5202											
ABCC2	1244	hgsc.bcm.edu	37	chr10	101604107	101604107	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgactgataagaggcctcCgccagattggcccagcaaag	11	6	13	11	1	0	4	0	2	0	2	1	4	1	4	4	3	1	1	4	3	2	2	rs17216317	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:101604107C>T	ENST00000370449.4	+	28	3985	c.3872C>T	c.(3871-3873)cCg>cTg	p.P1291L		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	1291			P -> L (altered transporter activity; dbSNP:rs17216317). {ECO:0000269|PubMed:22290738}.		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)	AAGAGGCCTCCGCCAGATTGG	0.532													C|||	55	0.0109824	0.0363	0.0086	5008	,	,		20061	0.0		0.001	False		,,,				2504	0.0				p.P1291L		Atlas-SNP	.											.	ABCC2	160	.	0			c.C3872T						PASS	.		LEU/PRO	145,4261	101.2+/-139.8	3,139,2061	95	89	91		3872	5.8	1	10	dbSNP_126	91	3,8597	2.2+/-6.3	0,3,4297	yes	missense	ABCC2	NM_000392.3	98	3,142,6358	TT,TC,CC		0.0349,3.291,1.1379	probably-damaging	1291/1546	101604107	148,12858	2203	4300	6503	SO:0001583	missense	1244	exon28			GGCCTCCGCCAGA	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.3872C>T	10.37:g.101604107C>T	ENSP00000359478:p.Pro1291Leu	62	0	0		62	33	0.532258	NM_000392	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Missense_Mutation	SNP	ENST00000370449.4	37	CCDS7484.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	C	18.14	3.557532	0.65425	0.03291	3.49E-4	ENSG00000023839	ENST00000370449	D	0.89681	-2.55	5.79	5.79	0.91817	.	0.099134	0.64402	D	0.000001	D	0.84556	0.5498	M	0.65320	2	0.80722	D	1	D	0.69078	0.997	D	0.64687	0.928	D	0.87880	0.2677	10	0.87932	D	0	-8.0E-4	15.6234	0.76829	0.1379:0.8621:0.0:0.0	rs17216317;rs52825311;rs61667815	1291	Q92887	MRP2_HUMAN	L	1291	ENSP00000359478:P1291L	ENSP00000359478:P1291L	P	+	2	0	ABCC2	101594097	1.000000	0.71417	0.968000	0.41197	0.881000	0.50899	5.706000	0.68362	2.733000	0.93635	0.655000	0.94253	CCG	C|0.988;T|0.012	0.012	strong		0.532	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392		T	101604107	C	T	101604107	3	4	22	1	0	0	0	0	1	0	0	0	53	652	23	1	3982	1	ABCC2	10	101604107	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	483436	101604107	33930640	2302	5203											
CPN1	1369	hgsc.bcm.edu	37	chr10	101835764	101835764	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	acgatgcgctggttcctgttCcggaactcctcgcacagaaa	9	9	10	13	4	0	1	0	0	0	1	4	3	3	2	3	2	2	4	3	2	2	2	rs61754515	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:101835764C>G	ENST00000370418.3	-	2	575	c.324G>C	c.(322-324)cgG>cgC	p.R108R		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	108	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)		GGTTCCTGTTCCGGAACTCCT	0.602													C|||	187	0.0373403	0.1324	0.0159	5008	,	,		18603	0.0		0.001	False		,,,				2504	0.0				p.R108R		Atlas-SNP	.											.	CPN1	62	.	0			c.G324C						PASS	.			560,3846	250.3+/-257.4	33,494,1676	143	118	126		324	-2.5	0.1	10	dbSNP_129	126	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	CPN1	NM_001308.2		33,499,5971	GG,GC,CC		0.0581,12.7099,4.3441		108/459	101835764	565,12441	2203	4300	6503	SO:0001819	synonymous_variant	1369	exon2			CCTGTTCCGGAAC	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.324G>C	10.37:g.101835764C>G		91	0	0		88	46	0.522727	NM_001308	B1AP59	Silent	SNP	ENST00000370418.3	37	CCDS7486.1																																																																																			C|0.959;G|0.041	0.041	strong		0.602	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049828.1	NM_001308		G	101835764	C	G	101835764	2	3	22	1	0	0	0	0	0	0	0	1	3811	842	30	4		4	CPN1	10	101835764	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	231657	101835764	33698983	2303	5204											
CWF19L1	55280	hgsc.bcm.edu	37	chr10	101993024	101993024	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	catagggctcaaagtctttcCggaagcggcgagccagggtc	9	7	14	11	3	2	0	1	0	1	0	4	2	3	1	2	4	2	1	2	4	3	2	rs7922946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:101993024C>T	ENST00000354105.4	-	14	1663	c.1577G>A	c.(1576-1578)cGg>cAg	p.R526Q	CWF19L1_ENST00000370379.1_Missense_Mutation_p.R241Q|CWF19L1_ENST00000478047.1_5'UTR|RP11-316M21.6_ENST00000444359.1_RNA	NM_018294.4	NP_060764.3	Q69YN2	C19L1_HUMAN	CWF19-like 1, cell cycle control (S. pombe)	526			R -> Q (in dbSNP:rs7922946).				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)		AAAGTCTTTCCGGAAGCGGCG	0.448													C|||	34	0.00678914	0.0257	0.0	5008	,	,		16484	0.0		0.0	False		,,,				2504	0.0				p.R526Q		Atlas-SNP	.											.	CWF19L1	39	.	0			c.G1577A						PASS	.	C	GLN/ARG	107,4299	83.4+/-121.9	1,105,2097	85	90	88		1577	2.5	1	10	dbSNP_116	88	0,8600		0,0,4300	yes	missense	CWF19L1	NM_018294.4	43	1,105,6397	TT,TC,CC		0.0,2.4285,0.8227	probably-damaging	526/539	101993024	107,12899	2203	4300	6503	SO:0001583	missense	55280	exon14			TCTTTCCGGAAGC	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.1577G>A	10.37:g.101993024C>T	ENSP00000326411:p.Arg526Gln	105	0	0		77	33	0.428571	NM_018294	B4DHX1|D3DR66|Q5W0I3|Q96HC3|Q9H865|Q9NV13	Missense_Mutation	SNP	ENST00000354105.4	37	CCDS7489.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	C	21.5	4.159440	0.78226	0.024285	0.0	ENSG00000095485	ENST00000354105;ENST00000370379	T;T	0.30714	1.52;1.52	5.38	2.55	0.30701	Histidine triad motif (1);Cwf19-like protein, C-terminal domain-2 (1);	0.099847	0.64402	N	0.000004	T	0.31104	0.0786	M	0.79475	2.455	0.43168	D	0.994968	P;D;D	0.76494	0.815;0.993;0.999	B;P;P	0.60173	0.394;0.596;0.87	T	0.19063	-1.0317	10	0.41790	T	0.15	-3.3822	9.1705	0.37078	0.0:0.7604:0.0:0.2396	rs7922946;rs7922946	230;389;526	Q69YN2-2;Q69YN2-3;Q69YN2	.;.;C19L1_HUMAN	Q	526;241	ENSP00000326411:R526Q;ENSP00000359405:R241Q	ENSP00000326411:R526Q	R	-	2	0	CWF19L1	101983014	1.000000	0.71417	0.999000	0.59377	0.652000	0.38707	4.389000	0.59639	0.262000	0.21774	-0.219000	0.12488	CGG	C|0.993;T|0.007	0.007	strong		0.448	CWF19L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018294		T	101993024	C	T	101993024	3	4	22	1	0	0	0	0	1	0	0	0	4073	652	23	1	43	1	CWF19L1	10	101993024	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	157260	101993024	33541723	2304	5205											
BLOC1S2	282991	hgsc.bcm.edu	37	chr10	102046402	102046402	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgggtcgccagtacgccctcGgctgccgccgccatagcgga	5	5	14	17	7	0	0	0	0	0	0	2	1	0	1	5	3	3	2	5	3	2	2	rs12250221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:102046402G>C	ENST00000370372.2	-	1	67	c.15C>G	c.(13-15)gcC>gcG	p.A5A	BLOC1S2_ENST00000361832.2_5'UTR|BLOC1S2_ENST00000441611.1_5'Flank	NM_173809.4	NP_776170.2	Q6QNY1	BL1S2_HUMAN	biogenesis of lysosomal organelles complex-1, subunit 2	5					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)		GTACGCCCTCGGCTGCCGCCG	0.751													-|||	293	0.0585064	0.2148	0.0115	5008	,	,		12869	0.0		0.001	False		,,,				2504	0.0				p.A5A		Atlas-SNP	.											.	BLOC1S2	10	.	0			c.C15G						PASS	.			564,3608		30,504,1552	8	12	11		15	-6.3	0.1	10	dbSNP_120	11	10,8242		0,10,4116	no	coding-synonymous	BLOC1S2	NM_173809.2		30,514,5668	CC,CG,GG		0.1212,13.5187,4.6201		5/143	102046402	574,11850	2086	4126	6212	SO:0001819	synonymous_variant	282991	exon1			GCCCTCGGCTGCC	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.15C>G	10.37:g.102046402G>C		75	0	0		53	22	0.415094	NM_173809	B4DQV2|Q5W040|Q8WUI8	Silent	SNP	ENST00000370372.2	37	CCDS7490.1																																																																																			G|0.949;C|0.051	0.051	strong		0.751	BLOC1S2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049861.2	NM_173809		C	102046402	G	C	102046402	2	2	22	1	0	0	0	0	0	0	0	1	1449	1103	39	4		4	BLOC1S2	10	102046402	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	53378	102046402	33488345	2305	5206											
WNT8B	7479	hgsc.bcm.edu	37	chr10	102242030	102242030	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcctagctctctccccaggcGgtgaagggcaccatgaaacg	9	7	11	14	2	1	2	0	2	1	0	4	2	3	2	4	3	2	2	4	3	3	1	rs9420786	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:102242030G>A	ENST00000343737.5	+	6	641	c.513G>A	c.(511-513)gcG>gcA	p.A171A		NM_003393.3	NP_003384.2	Q93098	WNT8B_HUMAN	wingless-type MMTV integration site family, member 8B	171					cell fate commitment (GO:0045165)|cellular response to retinoic acid (GO:0071300)|determination of dorsal identity (GO:0048263)|gastrulation (GO:0007369)|negative regulation of gene expression (GO:0010629)|nervous system development (GO:0007399)|neuron differentiation (GO:0030182)|positive regulation of gene expression (GO:0010628)|response to estradiol (GO:0032355)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|large_intestine(1)|ovary(1)|skin(1)	4		Colorectal(252;0.117)		Epithelial(162;1.87e-10)|all cancers(201;1.64e-08)		CTCCCCAGGCGGTGAAGGGCA	0.622											OREG0020440	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	90	0.0179712	0.0514	0.0029	5008	,	,		16675	0.002		0.001	False		,,,				2504	0.0174				p.A171A		Atlas-SNP	.											.	WNT8B	31	.	0			c.G513A						PASS	.	G		247,4131		4,239,1946	15	16	16		513	-3.3	0.9	10	dbSNP_119	16	2,8544		0,2,4271	no	coding-synonymous	WNT8B	NM_003393.3		4,241,6217	AA,AG,GG		0.0234,5.6418,1.9266		171/352	102242030	249,12675	2189	4273	6462	SO:0001819	synonymous_variant	7479	exon6			CCAGGCGGTGAAG	X91940	CCDS7494.1	10q24	2003-11-12			ENSG00000075290	ENSG00000075290		"Wingless-type MMTV integration sites"	12789	protein-coding gene	gene with protein product		601396				8661156	Standard	NM_003393		Approved		uc001krb.3	Q93098	OTTHUMG00000018912	ENST00000343737.5:c.513G>A	10.37:g.102242030G>A		17	0	0	1365	29	12	0.413793	NM_003393	O00771|Q5VX55|Q8WYK9	Silent	SNP	ENST00000343737.5	37	CCDS7494.1																																																																																			G|0.978;A|0.022	0.022	strong		0.622	WNT8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049867.1	NM_003393		A	102242030	G	A	102242030	2	1	22	1	0	0	0	0	0	0	0	1	17412	1103	39	1		1	WNT8B	10	102242030	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	195628	102242030	33292717	2306	5207											
SEC31B	25956	hgsc.bcm.edu	37	chr10	102262227	102262227	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggggaggccaaaagtaacCagcttccctccaaactggtg	11	7	11	12	0	0	0	0	0	0	0	2	1	2	1	4	4	3	2	4	4	4	2	rs143541316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:102262227C>G	ENST00000370345.3	-	11	1291	c.1194G>C	c.(1192-1194)ctG>ctC	p.L398L	SEC31B_ENST00000451524.1_Silent_p.L398L|SEC31B_ENST00000494350.1_5'Flank	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	398					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)		CAAAAGTAACCAGCTTCCCTC	0.483													c|||	34	0.00678914	0.0219	0.0043	5008	,	,		19175	0.0		0.002	False		,,,				2504	0.0				p.L398L		Atlas-SNP	.											.	SEC31B	84	.	0			c.G1194C						PASS	.			126,4280	92.5+/-131.2	3,120,2080	40	42	41		1194	4.5	1	10	dbSNP_134	41	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	SEC31B	NM_015490.3		3,126,6374	GG,GC,CC		0.0698,2.8597,1.0149		398/1180	102262227	132,12874	2203	4300	6503	SO:0001819	synonymous_variant	25956	exon11			AGTAACCAGCTTC	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.1194G>C	10.37:g.102262227C>G		42	0	0		40	18	0.45	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Silent	SNP	ENST00000370345.3	37	CCDS7495.1																																																																																			C|0.990;G|0.010	0.010	strong		0.483	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490		G	102262227	C	G	102262227	2	3	22	1	0	0	0	0	0	0	0	1	14014	581	21	4		4	SEC31B	10	102262227	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	20197	102262227	33272520	2307	5208											
LZTS2	84445	hgsc.bcm.edu	37	chr10	102762439	102762439	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagctcctccccgccaccaCggccctcctgggcccacctt	4	6	7	24	2	0	0	0	0	0	0	3	0	3	0	10	2	1	1	10	2	0	1	rs142122181|rs35061268	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:102762439C>T	ENST00000370220.1	+	1	3207	c.144C>T	c.(142-144)caC>caT	p.H48H	LZTS2_ENST00000370223.3_Silent_p.H48H					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)		CCCGCCACCACGGCCCTCCTG	0.682													C|||	6	0.00119808	0.003	0.0014	5008	,	,		16468	0.0		0.001	False		,,,				2504	0.0				p.H48H	Esophageal Squamous(8;38 437 13604 19902 37640)	Atlas-SNP	.											.	LZTS2	57	.	0			c.C144T						PASS	.	C		22,4384		0,22,2181	36	43	41		144	-9.3	0	10	dbSNP_134	41	2,8596		0,2,4297	no	coding-synonymous	LZTS2	NM_032429.2		0,24,6478	TT,TC,CC		0.0233,0.4993,0.1846		48/670	102762439	24,12980	2203	4299	6502	SO:0001819	synonymous_variant	84445	exon2			CCACCACGGCCCT	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.144C>T	10.37:g.102762439C>T		108	0	0		122	70	0.57377	NM_032429		Silent	SNP	ENST00000370220.1	37	CCDS7507.1																																																																																			C|0.998;T|0.002	0.002	strong		0.682	LZTS2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049872.1	XM_046743		T	102762439	C	T	102762439	2	4	22	1	0	0	0	0	0	0	0	1	9148	535	19	1		1	LZTS2	10	102762439	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	500212	102762439	32772308	2308	5209											
SFXN3	81855	hgsc.bcm.edu	37	chr10	102795819	102795819	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtccttcaatgccattgttaActactccaaccgcagtggtg	9	12	8	12	1	1	0	1	0	0	0	3	0	3	0	4	1	4	2	4	1	4	4	rs35361377	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:102795819A>T	ENST00000224807.5	+	5	860	c.404A>T	c.(403-405)aAc>aTc	p.N135I	SFXN3_ENST00000393459.1_Missense_Mutation_p.N131I	NM_030971.3	NP_112233.2	Q9BWM7	SFXN3_HUMAN	sideroflexin 3	135					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	cation transmembrane transporter activity (GO:0008324)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	9		Colorectal(252;0.234)		Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)		GCCATTGTTAACTACTCCAAC	0.572													A|||	59	0.0117812	0.0431	0.0029	5008	,	,		18920	0.0		0.0	False		,,,				2504	0.0				p.N135I		Atlas-SNP	.											.	SFXN3	19	.	0			c.A404T						PASS	.	A	ILE/ASN	161,4245	109.1+/-147.4	3,155,2045	173	153	159		404	5.4	1	10	dbSNP_126	159	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SFXN3	NM_030971.3	149	3,156,6344	TT,TA,AA		0.0116,3.6541,1.2456	probably-damaging	135/326	102795819	162,12844	2203	4300	6503	SO:0001583	missense	81855	exon5			TTGTTAACTACTC	AK074707	CCDS7508.2	10q24.32	2008-09-04			ENSG00000107819	ENSG00000107819		"Sideroflexins"	16087	protein-coding gene	gene with protein product		615571					Standard	NM_030971		Approved	SFX3	uc001ksp.3	Q9BWM7	OTTHUMG00000018921	ENST00000224807.5:c.404A>T	10.37:g.102795819A>T	ENSP00000224807:p.Asn135Ile	113	0	0		116	67	0.577586	NM_030971	Q8NCJ0|Q9NTP4	Missense_Mutation	SNP	ENST00000224807.5	37	CCDS7508.2	21	0.009615384615384616	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	0	0.0	A	29.2	4.982999	0.93044	0.036541	1.16E-4	ENSG00000107819	ENST00000393459;ENST00000224807	T;T	0.54279	0.58;0.58	5.36	5.36	0.76844	.	0.041188	0.85682	D	0.000000	T	0.54886	0.1886	H	0.96111	3.77	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.996;0.996	T	0.80699	-0.1266	10	0.87932	D	0	-24.293	15.3508	0.74384	1.0:0.0:0.0:0.0	rs35361377	139;135;135	B4DRS6;A6NCZ6;Q9BWM7	.;.;SFXN3_HUMAN	I	131;135	ENSP00000377103:N131I;ENSP00000224807:N135I	ENSP00000224807:N135I	N	+	2	0	SFXN3	102785809	1.000000	0.71417	0.991000	0.47740	0.988000	0.76386	9.329000	0.96413	2.024000	0.59613	0.379000	0.24179	AAC	A|0.986;T|0.014	0.014	strong		0.572	SFXN3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_030971		T	102795819	A	T	102795819	3	4	22	1	0	0	0	0	1	0	0	0	14211	43	2	5	418	5	SFXN3	10	102795819	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	33380	102795819	32738928	2309	5210											
NOLC1	9221	hgsc.bcm.edu	37	chr10	103920255	103920255	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctccttctaagccagctggTaccaccaagaattcttcaaa	12	10	6	13	0	3	1	1	0	2	1	4	1	4	1	4	1	3	3	4	1	5	5	rs145855726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:103920255T>A	ENST00000605788.1	+	10	1381	c.1146T>A	c.(1144-1146)ggT>ggA	p.G382G	NOLC1_ENST00000603742.1_Silent_p.G101G|NOLC1_ENST00000405356.1_Silent_p.G392G|NOLC1_ENST00000488254.2_Silent_p.G383G	NM_001284389.1|NM_004741.3	NP_001271318.1|NP_004732.2	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	382	11 X 12 AA approximate repeats of an acidic serine cluster.|Interacts with RPA194.				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)		AGCCAGCTGGTACCACCAAGA	0.542													T|||	7	0.00139776	0.0053	0.0	5008	,	,		20457	0.0		0.0	False		,,,				2504	0.0				p.G382G		Atlas-SNP	.											.	NOLC1	61	.	0			c.T1146A						PASS	.	T		31,4375	36.0+/-67.5	0,31,2172	63	67	66		1146	-1	0	10	dbSNP_134	66	0,8600		0,0,4300	yes	coding-synonymous	NOLC1	NM_004741.3		0,31,6472	AA,AT,TT		0.0,0.7036,0.2384		382/700	103920255	31,12975	2203	4300	6503	SO:0001819	synonymous_variant	9221	exon10			AGCTGGTACCACC	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.1146T>A	10.37:g.103920255T>A		97	0	0		102	51	0.5	NM_004741	Q15030|Q5VV70|Q9BUV3	Silent	SNP	ENST00000605788.1	37	CCDS7530.1																																																																																			T|0.997;A|0.003	0.003	strong		0.542	NOLC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050012.2	NM_004741		A	103920255	T	A	103920255	2	1	22	1	0	0	0	0	0	0	0	1	10538	1625	57	5		5	NOLC1	10	103920255	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1124436	103920255	31614492	2310	5211											
C10orf95	79946	hgsc.bcm.edu	37	chr10	104210861	104210861	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	acacatacatggtcggccccCcaggcggctgctgttcttac	7	9	10	15	2	1	0	0	0	1	0	2	0	1	0	3	4	3	3	3	4	2	3	rs73349055	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:104210861C>A	ENST00000239125.1	-	2	201	c.127G>T	c.(127-129)Ggg>Tgg	p.G43W	RP11-18I14.10_ENST00000494270.2_RNA|RP11-18I14.10_ENST00000473970.2_RNA|RP11-18I14.10_ENST00000596045.1_RNA|RP11-18I14.10_ENST00000596366.1_RNA|RP11-18I14.10_ENST00000492465.2_RNA|RP11-18I14.10_ENST00000594818.1_RNA	NM_024886.1	NP_079162.1	Q9H7T3	CJ095_HUMAN	chromosome 10 open reading frame 95	43										liver(1)	1		Colorectal(252;0.207)		Epithelial(162;8.34e-09)|all cancers(201;1.95e-07)|BRCA - Breast invasive adenocarcinoma(275;0.213)		GGTCGGCCCCCCAGGCGGCTG	0.657													C|||	318	0.0634984	0.2315	0.0144	5008	,	,		11331	0.0		0.002	False		,,,				2504	0.0				p.G43W		Atlas-SNP	.											.	C10orf95	5	.	0			c.G127T						PASS	.	C	TRP/GLY	452,2752		21,410,1171	9	11	10		127	-0.7	0	10	dbSNP_130	10	11,6951		0,11,3470	yes	missense	C10orf95	NM_024886.1	184	21,421,4641	AA,AC,CC		0.158,14.1074,4.5544	probably-damaging	43/258	104210861	463,9703	1602	3481	5083	SO:0001583	missense	79946	exon2			GGCCCCCCAGGCG	AK024342	CCDS7534.1	10q24.32	2014-02-19	2014-02-19	2014-02-19	ENSG00000120055	ENSG00000120055			25880	protein-coding gene	gene with protein product							Standard	NM_024886		Approved	FLJ14280	uc001kvo.1	Q9H7T3	OTTHUMG00000018959	ENST00000239125.1:c.127G>T	10.37:g.104210861C>A	ENSP00000239125:p.Gly43Trp	27	0	0		16	7	0.4375	NM_024886	A0AVQ7	Missense_Mutation	SNP	ENST00000239125.1	37	CCDS7534.1	121	0.0554029304029304	115	0.23373983739837398	6	0.016574585635359115	0	0.0	0	0.0	C	12.67	2.007558	0.35415	0.141074	0.00158	ENSG00000120055	ENST00000239125	.	.	.	4.67	-0.695	0.11291	.	1.984030	0.02659	N	0.107299	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	D	0.63046	0.992	P	0.56751	0.805	T	0.04281	-1.0963	8	0.87932	D	0	-26.9089	1.7389	0.02948	0.1583:0.0984:0.3263:0.417	.	43	Q9H7T3	CJ095_HUMAN	W	43	.	ENSP00000239125:G43W	G	-	1	0	C10orf95	104200851	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.146000	0.16180	-0.211000	0.10124	-0.350000	0.07774	GGG	C|0.954;A|0.046	0.046	strong		0.657	C10orf95-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050065.1	NM_024886		A	104210861	C	A	104210861	3	1	22	1	0	0	0	0	1	0	0	0	1628	623	22	4	650	4	C10orf95	10	104210861	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	290606	104210861	31323886	2311	5212											
SFXN2	118980	hgsc.bcm.edu	37	chr10	104486489	104486489	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cacttcctaaacatcacggaCccccgcactgtctttgtatc	9	11	5	16	2	2	0	1	0	1	0	4	1	3	1	3	1	1	2	3	1	3	4	rs35153373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:104486489C>T	ENST00000369893.5	+	2	263	c.96C>T	c.(94-96)gaC>gaT	p.D32D	SFXN2_ENST00000602785.1_3'UTR	NM_178858.4	NP_849189.1	Q96NB2	SFXN2_HUMAN	sideroflexin 2	32					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)		ACATCACGGACCCCCGCACTG	0.597													C|||	98	0.0195687	0.0719	0.0043	5008	,	,		19104	0.0		0.0	False		,,,				2504	0.0				p.D32D		Atlas-SNP	.											.	SFXN2	40	.	0			c.C96T						PASS	.	C		273,4133	153.3+/-186.9	5,263,1935	91	90	90		96	1.1	1	10	dbSNP_126	90	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SFXN2	NM_178858.4		5,264,6234	TT,TC,CC		0.0116,6.1961,2.1067		32/323	104486489	274,12732	2203	4300	6503	SO:0001819	synonymous_variant	118980	exon2			CACGGACCCCCGC	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.96C>T	10.37:g.104486489C>T		139	0	0		156	77	0.49359	NM_178858	Q5JSM6	Silent	SNP	ENST00000369893.5	37	CCDS7539.1																																																																																			C|0.980;T|0.020	0.020	strong		0.597	SFXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050096.2	XM_058359		T	104486489	C	T	104486489	2	4	22	1	0	0	0	0	0	0	0	1	14210	506	18	2		2	SFXN2	10	104486489	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	275628	104486489	31048258	2312	5213											
SFXN2	118980	hgsc.bcm.edu	37	chr10	104486822	104486822	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tatgactcggccttccacccCgacactggggagaagatgaa	11	7	11	12	2	0	4	0	2	0	2	2	6	1	4	4	3	0	0	4	3	3	2	rs35094483	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:104486822C>T	ENST00000369893.5	+	3	407	c.240C>T	c.(238-240)ccC>ccT	p.P80P	SFXN2_ENST00000602785.1_3'UTR	NM_178858.4	NP_849189.1	Q96NB2	SFXN2_HUMAN	sideroflexin 2	80					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)		CCTTCCACCCCGACACTGGGG	0.597													C|||	166	0.033147	0.121	0.0086	5008	,	,		18582	0.0		0.0	False		,,,				2504	0.0				p.P80P		Atlas-SNP	.											.	SFXN2	40	.	0			c.C240T						PASS	.	C		444,3962	212.2+/-232.1	13,418,1772	84	74	77		240	-5.3	1	10	dbSNP_126	77	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SFXN2	NM_178858.4		13,420,6070	TT,TC,CC		0.0233,10.0772,3.4292		80/323	104486822	446,12560	2203	4300	6503	SO:0001819	synonymous_variant	118980	exon3			CCACCCCGACACT	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.240C>T	10.37:g.104486822C>T		192	0	0		191	190	0.994764	NM_178858	Q5JSM6	Silent	SNP	ENST00000369893.5	37	CCDS7539.1																																																																																			C|0.969;T|0.031	0.031	strong		0.597	SFXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050096.2	XM_058359		T	104486822	C	T	104486822	2	4	22	1	0	0	0	0	0	0	0	1	14210	639	23	1		1	SFXN2	10	104486822	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	333	104486822	31047925	2313	5214											
CALHM2	51063	hgsc.bcm.edu	37	chr10	105207176	105207176	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcacccgagagtgcacctcGgccgtgcgctggaacagctg	8	5	14	14	4	0	1	0	0	0	1	1	3	0	2	3	2	5	4	3	2	1	0	rs2232663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:105207176G>A	ENST00000260743.5	-	4	1228	c.705C>T	c.(703-705)gcC>gcT	p.A235A	CALHM2_ENST00000494180.1_5'Flank|CALHM2_ENST00000369788.3_Silent_p.A235A|RP11-225H22.7_ENST00000608063.1_RNA	NM_015916.4	NP_057000.2	Q9HA72	CAHM2_HUMAN	calcium homeostasis modulator 2	235					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						AGTGCACCTCGGCCGTGCGCT	0.597													G|||	370	0.0738818	0.2663	0.0216	5008	,	,		20251	0.0		0.003	False		,,,				2504	0.0				p.A235A		Atlas-SNP	.											.	CALHM2	30	.	0			c.C705T						PASS	.	G		896,3510	345.7+/-308.6	84,728,1391	67	61	63		705	-8.1	0.7	10	dbSNP_98	63	27,8573	19.2+/-60.6	0,27,4273	no	coding-synonymous	CALHM2	NM_015916.4		84,755,5664	AA,AG,GG		0.314,20.3359,7.0967		235/324	105207176	923,12083	2203	4300	6503	SO:0001819	synonymous_variant	51063	exon4			CACCTCGGCCGTG	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.705C>T	10.37:g.105207176G>A		77	0	0		85	85	1	NM_015916	D3DR94|O95893|Q6ZUV9	Silent	SNP	ENST00000260743.5	37	CCDS7549.1																																																																																			G|0.925;A|0.075	0.075	strong		0.597	CALHM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050159.1	NM_015916		A	105207176	G	A	105207176	2	1	22	1	0	0	0	0	0	0	0	1	2585	1103	39	1		1	CALHM2	10	105207176	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	720354	105207176	30327571	2314	5215											
CALHM1	255022	hgsc.bcm.edu	37	chr10	105215071	105215071	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tacgcggaggccggggcccaCccccagcccagccgttgccc	5	3	13	20	4	0	0	0	0	0	0	0	1	0	1	7	4	4	1	7	4	1	2	rs114015468	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:105215071C>T	ENST00000329905.5	-	2	1125	c.989G>A	c.(988-990)gGt>gAt	p.G330D	CALHM2_ENST00000369788.3_5'Flank|CALHM2_ENST00000260743.5_5'Flank|CALHM2_ENST00000393235.1_5'Flank|RP11-225H22.4_ENST00000411906.1_RNA	NM_001001412.3	NP_001001412.3	Q8IU99	CAHM1_HUMAN	calcium homeostasis modulator 1	330					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						CCGGGGCCCACCCCCAGCCCA	0.662													C|||	63	0.0125799	0.0477	0.0	5008	,	,		17190	0.0		0.0	False		,,,				2504	0.0				p.G330D		Atlas-SNP	.											.	CALHM1	33	.	0			c.G989A						PASS	.	C	ASP/GLY	151,4255	95.7+/-134.4	1,149,2053	30	27	28		989	1.8	0	10	dbSNP_132	28	1,8599	2.2+/-6.3	0,1,4299	yes	missense	CALHM1	NM_001001412.3	94	1,150,6352	TT,TC,CC		0.0116,3.4271,1.1687	benign	330/347	105215071	152,12854	2203	4300	6503	SO:0001583	missense	255022	exon2			GGCCCACCCCCAG	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.989G>A	10.37:g.105215071C>T	ENSP00000329926:p.Gly330Asp	90	0	0		123	75	0.609756	NM_001001412	Q5W091	Missense_Mutation	SNP	ENST00000329905.5	37	CCDS7550.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	C	0.028	-1.354143	0.01256	0.034271	1.16E-4	ENSG00000185933	ENST00000329905	T	0.17054	2.3	4.8	1.83	0.25207	.	1.229190	0.05379	N	0.536826	T	0.01661	0.0053	N	0.08118	0	0.09310	N	1	B	0.22414	0.069	B	0.18561	0.022	T	0.36625	-0.9740	10	0.13108	T	0.6	-4.9354	5.3984	0.16283	0.0:0.5539:0.146:0.3001	.	330	Q8IU99	CAHM1_HUMAN	D	330	ENSP00000329926:G330D	ENSP00000329926:G330D	G	-	2	0	CALHM1	105205061	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.057000	0.11768	0.169000	0.19679	-0.379000	0.06801	GGT	C|0.988;T|0.012	0.012	strong		0.662	CALHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050165.1	NM_001001412		T	105215071	C	T	105215071	3	4	22	1	0	0	0	0	1	0	0	0	2584	507	18	2	55	2	CALHM1	10	105215071	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	7895	105215071	30319676	2315	5216											
COL17A1	1308	hgsc.bcm.edu	37	chr10	105824332	105824332	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggaaggttggcatccaggatCgttgcatcgtaggtgcctga	8	10	15	8	2	0	1	0	1	0	0	3	3	1	3	2	5	2	5	2	5	2	3	rs149012179	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:105824332C>T	ENST00000353479.5	-	10	920	c.630G>A	c.(628-630)acG>acA	p.T210T	COL17A1_ENST00000369733.3_Silent_p.T210T|COL17A1_ENST00000393211.3_Silent_p.T210T	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	210	Necessary for interaction with DST and for the recruitment of DST to hemidesmosome.|Nonhelical region (NC16).		T -> M (in dbSNP:rs805708). {ECO:0000269|PubMed:15489334}.		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)		CATCCAGGATCGTTGCATCGT	0.547													C|||	37	0.00738818	0.0272	0.0014	5008	,	,		15732	0.0		0.0	False		,,,				2504	0.0				p.T210T		Atlas-SNP	.											.	COL17A1	149	.	0			c.G630A						PASS	.	C		90,4316	74.7+/-112.8	0,90,2113	119	81	94		630	-8	0.1	10	dbSNP_134	94	0,8600		0,0,4300	no	coding-synonymous	COL17A1	NM_000494.3		0,90,6413	TT,TC,CC		0.0,2.0427,0.692		210/1498	105824332	90,12916	2203	4300	6503	SO:0001819	synonymous_variant	1308	exon10			CAGGATCGTTGCA	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.630G>A	10.37:g.105824332C>T		141	0	0		156	79	0.50641	NM_000494	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Silent	SNP	ENST00000353479.5	37	CCDS7554.1																																																																																			C|0.993;T|0.007	0.007	strong		0.547	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494		T	105824332	C	T	105824332	2	4	22	1	0	0	0	0	0	0	0	1	3676	871	31	1		1	COL17A1	10	105824332	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	609261	105824332	29710415	2316	5217											
C10orf79	80217	hgsc.bcm.edu	37	chr10	105906077	105906077	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcacacatccaggtcttctcTagatttccgaacagcttctg	9	12	7	13	1	3	1	0	0	3	1	6	2	5	1	2	1	2	2	2	1	2	4	rs369682196		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:105906077T>C	ENST00000357060.3	-	30	3914	c.3799A>G	c.(3799-3801)Aga>Gga	p.R1267G	WDR96_ENST00000428666.1_Intron	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						AGGTCTTCTCTAGATTTCCGA	0.418																																					p.R1267G		Atlas-SNP	.											WDR96,NS,carcinoma,+1,1	WDR96	183	1	0			c.A3799G						PASS	.	T	GLY/ARG	1,4405	2.1+/-5.4	0,1,2202	139	125	130		3799	3.5	0	10		130	0,8600		0,0,4300	no	missense	WDR96	NM_025145.5	125	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign	1267/1666	105906077	1,13005	2203	4300	6503	SO:0001583	missense	80217	exon30			CTTCTCTAGATTT																												ENST00000357060.3:c.3799A>G	10.37:g.105906077T>C	ENSP00000349568:p.Arg1267Gly	127	0	0		167	85	0.508982	NM_025145		Missense_Mutation	SNP	ENST00000357060.3	37	CCDS31281.1	.	.	.	.	.	.	.	.	.	.	T	7.040	0.562289	0.13498	2.27E-4	0.0	ENSG00000197748	ENST00000357060	T	0.14640	2.49	6.07	3.55	0.40652	.	0.466125	0.21837	N	0.068397	T	0.15132	0.0365	M	0.63428	1.95	0.09310	N	1	P	0.43094	0.799	B	0.36092	0.217	T	0.08973	-1.0696	10	0.51188	T	0.08	.	13.497	0.61432	0.0:0.0:0.2551:0.7449	.	1267	Q8NDM7	WDR96_HUMAN	G	1267	ENSP00000349568:R1267G	ENSP00000349568:R1267G	R	-	1	2	WDR96	105896067	0.005000	0.15991	0.036000	0.18154	0.021000	0.10359	1.590000	0.36654	1.078000	0.41014	0.533000	0.62120	AGA	.	.	none		0.418	WDR96-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	105906077	T	C	105906077	3	2	22	1	0	0	0	0	1	0	0	0	1620	1530	53	3	1234	3	C10orf79	10	105906077	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	81745	105906077	29628670	2317	5218											
GSTO2	119391	hgsc.bcm.edu	37	chr10	106058940	106058940	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	atatcagccatgaagtgggaCcccacagtctgtgctcttct	9	11	9	12	0	4	1	1	1	3	0	4	2	4	2	3	1	2	1	3	1	2	2	rs157078	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:106058940C>T	ENST00000338595.2	+	7	950	c.630C>T	c.(628-630)gaC>gaT	p.D210D	GSTO2_ENST00000450629.2_Silent_p.D176D|GSTO2_ENST00000429569.2_Missense_Mutation_p.P113S|GSTO2_ENST00000369707.2_Silent_p.D182D	NM_183239.1	NP_899062.1	Q9H4Y5	GSTO2_HUMAN	glutathione S-transferase omega 2	210	GST C-terminal.				cellular response to arsenic-containing substance (GO:0071243)|glutathione derivative biosynthetic process (GO:1901687)|L-ascorbic acid metabolic process (GO:0019852)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	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)			NS(1)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	11		Colorectal(252;0.178)		Epithelial(162;1.14e-09)|all cancers(201;3.89e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0155)	Glutathione(DB00143)	TGAAGTGGGACCCCACAGTCT	0.522													C|||	247	0.0493211	0.1823	0.0086	5008	,	,		16782	0.0		0.0	False		,,,				2504	0.0				p.D210D		Atlas-SNP	.											.	GSTO2	23	.	0			c.C630T						PASS	.	C	,,,	643,3763	276.0+/-272.9	61,521,1621	104	100	101		528,546,444,630	4.1	1	10	dbSNP_79	101	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GSTO2	NM_001191013.1,NM_001191014.1,NM_001191015.1,NM_183239.1	,,,	61,523,5919	TT,TC,CC		0.0233,14.5937,4.9592	,,,	176/210,182/216,148/182,210/244	106058940	645,12361	2203	4300	6503	SO:0001819	synonymous_variant	119391	exon7			GTGGGACCCCACA	AY191318	CCDS7556.1, CCDS53574.1, CCDS53575.1	10q25.1	2012-06-21			ENSG00000065621	ENSG00000065621	2.5.1.18, 1.8.5.1, 1.20.4.2	"Glutathione S-transferases / Soluble"	23064	protein-coding gene	gene with protein product		612314				12618591	Standard	NM_001191013		Approved		uc001kyb.3	Q9H4Y5	OTTHUMG00000019006	ENST00000338595.2:c.630C>T	10.37:g.106058940C>T		126	0	0		130	61	0.469231	NM_183239	A8K771|B4DJW6|E7ESD6|Q49TW5|Q5GM70|Q5JU15|Q86WP3	Silent	SNP	ENST00000338595.2	37	CCDS7556.1	76	0.0347985347985348	71	0.1443089430894309	5	0.013812154696132596	0	0.0	0	0.0	C	13.14	2.149018	0.37923	0.145937	2.33E-4	ENSG00000065621	ENST00000429569	T	0.13901	2.55	5.9	4.06	0.47325	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.24759	N	0.992935	B	0.12630	0.006	B	0.11329	0.006	T	0.36553	-0.9743	8	0.33141	T	0.24	-34.5724	8.1478	0.31121	0.0:0.8242:0.0:0.1758	rs157078;rs545826;rs157078	113	B4DML4	.	S	113	ENSP00000407381:P113S	ENSP00000407381:P113S	P	+	1	0	GSTO2	106048930	1.000000	0.71417	1.000000	0.80357	0.528000	0.34623	0.617000	0.24359	1.501000	0.48654	0.563000	0.77884	CCC	C|0.952;T|0.048	0.048	strong		0.522	GSTO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050210.2	NM_183239		T	106058940	C	T	106058940	2	4	22	1	0	0	0	0	0	0	0	1	6852	506	18	2		2	GSTO2	10	106058940	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	152863	106058940	29475807	2318	5219											
ADRA2A	150	hgsc.bcm.edu	37	chr10	112838135	112838135	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	tgcgagatctacctggcgctCgacgtgctcttctgcacgtc	5	11	11	14	5	3	1	0	0	3	1	5	3	3	1	1	1	4	3	1	1	1	2	rs142434876	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:112838135C>G	ENST00000280155.2	+	1	1346	c.381C>G	c.(379-381)ctC>ctG	p.L127L		NM_000681.3	NP_000672.3	P08913	ADA2A_HUMAN	adrenoceptor alpha 2A	112					actin cytoskeleton organization (GO:0030036)|activation of MAPK activity by adrenergic receptor signaling pathway (GO:0071883)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|acute inflammatory response (GO:0002526)|adenylate cyclase-inhibiting adrenergic receptor signaling pathway (GO:0071881)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|cellular response to hormone stimulus (GO:0032870)|DNA replication (GO:0006260)|energy reserve metabolic process (GO:0006112)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|fear response (GO:0042596)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|intestinal absorption (GO:0050892)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of adrenergic receptor signaling pathway (GO:0071878)|negative regulation of calcium ion transmembrane transporter activity (GO:1901020)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of insulin secretion (GO:0046676)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of norepinephrine secretion (GO:0010700)|negative regulation of uterine smooth muscle contraction (GO:0070473)|phospholipase C-activating adrenergic receptor signaling pathway (GO:0071882)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine production (GO:0001819)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of potassium ion transport (GO:0043268)|positive regulation of vasodilation (GO:0045909)|positive regulation of wound healing (GO:0090303)|Ras protein signal transduction (GO:0007265)|regulation of insulin secretion (GO:0050796)|regulation of vasoconstriction (GO:0019229)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|thermoception (GO:0050955)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	alpha-1B adrenergic receptor binding (GO:0031692)|alpha-2C adrenergic receptor binding (GO:0031696)|alpha2-adrenergic receptor activity (GO:0004938)|epinephrine binding (GO:0051379)|heterotrimeric G-protein binding (GO:0032795)|norepinephrine binding (GO:0051380)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|thioesterase binding (GO:0031996)			breast(1)|cervix(3)|endometrium(6)|large_intestine(3)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(234;0.0735)|Lung NSC(174;0.238)		Epithelial(162;0.000316)|all cancers(201;0.00501)|BRCA - Breast invasive adenocarcinoma(275;0.118)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Apraclonidine(DB00964)|Aripiprazole(DB01238)|Asenapine(DB06216)|Benzphetamine(DB00865)|Bethanidine(DB00217)|Brimonidine(DB00484)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Desipramine(DB01151)|Dexmedetomidine(DB00633)|Dihydroergotamine(DB00320)|Dipivefrin(DB00449)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinastine(DB00751)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Flupirtine(DB06623)|Guanabenz(DB00629)|Guanfacine(DB01018)|Lisuride(DB00589)|Lofexidine(DB04948)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Methyldopa(DB00968)|Mianserin(DB06148)|Mirtazapine(DB00370)|Naphazoline(DB06711)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phentolamine(DB00692)|Phenylpropanolamine(DB00397)|Pramipexole(DB00413)|Prazosin(DB00457)|Propericiazine(DB01608)|Pseudoephedrine(DB00852)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Tizanidine(DB00697)|Tolazoline(DB00797)|Trazodone(DB00656)|Trimipramine(DB00726)|Xylometazoline(DB06694)|Yohimbine(DB01392)|Ziprasidone(DB00246)	ACCTGGCGCTCGACGTGCTCT	0.602													C|||	4	0.000798722	0.0023	0.0014	5008	,	,		15105	0.0		0.0	False		,,,				2504	0.0				p.L127L	Esophageal Squamous(173;605 2658 7278 49362)	Atlas-SNP	.											.	ADRA2A	38	.	0			c.C381G						PASS	.	C		32,4374	36.8+/-68.6	0,32,2171	94	75	82		381	2.3	1	10	dbSNP_134	82	0,8600		0,0,4300	no	coding-synonymous	ADRA2A	NM_000681.3		0,32,6471	GG,GC,CC		0.0,0.7263,0.246		127/466	112838135	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	150	exon1			GGCGCTCGACGTG	AF284095	CCDS7569.2	10q25.2	2012-08-08	2012-05-09		ENSG00000150594	ENSG00000150594		"GPCR / Class A : Adrenoceptors : alpha"	281	protein-coding gene	gene with protein product	"alpha-2AAR subtype C10", " alpha-2A-adrenergic receptor"	104210	"adrenergic, alpha-2A-, receptor"	ADRA2, ADRA2R			Standard	NM_000681		Approved	ADRAR	uc001kzo.3	P08913	OTTHUMG00000019050	ENST00000280155.2:c.381C>G	10.37:g.112838135C>G		145	0	0		172	97	0.563953	NM_000681	B0LPF6|Q2I8G2|Q2XN99|Q86TH8|Q9BZK1	Silent	SNP	ENST00000280155.2	37	CCDS7569.2																																																																																			C|0.998;G|0.002	0.002	strong		0.602	ADRA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050372.2	NM_000681		G	112838135	C	G	112838135	2	3	22	1	0	0	0	0	0	0	0	1	337	871	31	4		4	ADRA2A	10	112838135	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6779195	112838135	22696612	2319	5220											
ACSL5	51703	hgsc.bcm.edu	37	chr10	114181773	114181773	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggctgacatgaactactttAcagtgaataatgaaggagag	15	10	11	5	0	0	5	0	4	0	1	0	6	0	5	0	2	3	1	0	2	6	4	rs12254915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:114181773A>G	ENST00000393081.1	+	16	1763	c.1456A>G	c.(1456-1458)Aca>Gca	p.T486A	ACSL5_ENST00000354273.4_Missense_Mutation_p.T486A|RP11-324O2.6_ENST00000424422.1_RNA|ACSL5_ENST00000433418.1_Missense_Mutation_p.T486A|ACSL5_ENST00000369410.3_Missense_Mutation_p.T268A|ACSL5_ENST00000354655.4_Missense_Mutation_p.T486A|ACSL5_ENST00000356116.1_Missense_Mutation_p.T542A	NM_203380.1	NP_976314.1	Q9ULC5	ACSL5_HUMAN	acyl-CoA synthetase long-chain family member 5	486			T -> A (in dbSNP:rs12254915).		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)		GAACTACTTTACAGTGAATAA	0.458													A|||	75	0.014976	0.0552	0.0029	5008	,	,		20705	0.0		0.0	False		,,,				2504	0.0				p.T542A		Atlas-SNP	.											.	ACSL5	51	.	0			c.A1624G						PASS	.	A	ALA/THR,ALA/THR,ALA/THR	193,4213	122.9+/-160.3	2,189,2012	135	132	133		1624,1456,1456	0.6	0.7	10	dbSNP_120	133	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	ACSL5	NM_016234.3,NM_203379.1,NM_203380.1	58,58,58	2,190,6311	GG,GA,AA		0.0116,4.3804,1.4916	benign,benign,benign	542/740,486/684,486/684	114181773	194,12812	2203	4300	6503	SO:0001583	missense	51703	exon16			TACTTTACAGTGA	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.1456A>G	10.37:g.114181773A>G	ENSP00000376796:p.Thr486Ala	88	0	0		70	22	0.314286	NM_016234	A6GV77|D3DRB3|Q6UX44|Q9UIU4	Missense_Mutation	SNP	ENST00000393081.1	37	CCDS7573.1	25	0.011446886446886446	23	0.046747967479674794	2	0.0055248618784530384	0	0.0	0	0.0	A	2.991	-0.208102	0.06180	0.043804	1.16E-4	ENSG00000197142	ENST00000354655;ENST00000393081;ENST00000356116;ENST00000433418;ENST00000354273;ENST00000369410	T;T;T;T;T;T	0.09630	2.96;2.96;2.96;2.96;2.96;2.96	5.86	0.636	0.17729	AMP-dependent synthetase/ligase (1);	0.395320	0.28724	N	0.014342	T	0.00356	0.0011	N	0.00405	-1.535	0.09310	N	0.999999	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	0.44283	-0.9338	10	0.02654	T	1	-2.9242	8.9257	0.35639	0.2131:0.0:0.462:0.3249	rs12254915;rs52833907;rs12254915	268;486;542;486	B4DX30;A6GV77;Q9ULC5-3;Q9ULC5	.;.;.;ACSL5_HUMAN	A	486;486;542;486;486;268	ENSP00000346680:T486A;ENSP00000376796:T486A;ENSP00000348429:T542A;ENSP00000403647:T486A;ENSP00000346223:T486A;ENSP00000358418:T268A	ENSP00000346223:T486A	T	+	1	0	ACSL5	114171763	0.994000	0.37717	0.677000	0.29947	0.906000	0.53458	1.059000	0.30517	-0.131000	0.11578	-0.270000	0.10280	ACA	A|0.982;G|0.018	0.018	strong		0.458	ACSL5-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050386.1	NM_016234		G	114181773	A	G	114181773	3	3	22	1	0	0	0	0	1	0	0	0	180	391	14	3	1686	3	ACSL5	10	114181773	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1343638	114181773	21352974	2320	5221											
NRAP	3026	hgsc.bcm.edu	37	chr10	115348749	115348751	+	3'UTR	DEL	CTT	CTT	-																															atggctcacaacagcagggcCttcttctttttgacgtgcag																								rs141729427|rs148467563|rs200486696|rs11575787|rs144589482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:115348749_115348751delCTT	ENST00000351270.3	+	0	2400_2402				NRAP_ENST00000359988.3_In_Frame_Del_p.K1726del|NRAP_ENST00000369358.4_In_Frame_Del_p.K1734del|NRAP_ENST00000369360.3_In_Frame_Del_p.K1699del|NRAP_ENST00000360478.3_In_Frame_Del_p.K1691del|HABP2_ENST00000542051.1_3'UTR	NM_004132.3	NP_004123.1	Q14520	HABP2_HUMAN	hyaluronan binding protein 2						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)	ACAGCAGGGCCTTCTTCTTTTTG	0.537														34	0.00678914	0.025	0.0014	5008	,	,		16073	0.0		0.0	False		,,,				2504	0.0				p.1727_1728del		Pindel,Atlas-Indel	.											.	NRAP	208	.	0			c.5180_5182del						PASS	.		,,,	162,4102		7,148,1977					,,,	3.8	1		dbSNP_120	163	28,8226		11,6,4110	no	coding,coding,utr-3,utr-3	HABP2,NRAP	NM_198060.2,NM_006175.3,NM_004132.3,NM_001177660.1	,,,	18,154,6087	A1A1,A1R,RR		0.3392,3.7992,1.5178	,,,	,,,		190,12328				SO:0001624	3_prime_UTR_variant	4892	exon42			.		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	ENST00000351270.3:c.*623CTT>-	10.37:g.115348755_115348757delCTT		144	0	.		187	61	0.326	NM_001261463	A8K467|B7Z8U5|F5H5M6|O00663	In_Frame_Del	DEL	ENST00000351270.3	37	CCDS7577.1																																																																																			CTT|0.992;-|0.008	0.008	strong		0.537	HABP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050428.1	NM_004132		-	115348751	CTT	-	115348749	6	5	22	0	1	1	0	1	0	0	0	0	10647	680	24	0		0	NRAP	10	115348749	3'UTR	DEL	CTT	TCGA-G8-6324-01A-11D-2210-10	1166976	115348749	20185998	2321	5222											
C10orf81	79949	hgsc.bcm.edu	37	chr10	115531790	115531790	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cctacaagatttatcagaagCcactcaagatgtgaaggaag	16	8	9	8	0	2	4	2	1	0	3	2	5	2	5	2	1	2	0	2	1	7	3	rs143039412		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:115531790C>T	ENST00000369310.3	+	7	1158	c.596C>T	c.(595-597)gCc>gTc	p.A199V	PLEKHS1_ENST00000361048.1_Missense_Mutation_p.A205V|PLEKHS1_ENST00000369312.4_Missense_Mutation_p.A117V|PLEKHS1_ENST00000369309.1_Missense_Mutation_p.A19V|PLEKHS1_ENST00000354462.3_5'UTR	NM_182601.1	NP_872407.1	Q5SXH7	PKHS1_HUMAN	pleckstrin homology domain containing, family S member 1	199																	TTATCAGAAGCCACTCAAGAT	0.353													C|||	1	0.000199681	0.0008	0.0	5008	,	,		21165	0.0		0.0	False		,,,				2504	0.0				p.A205V		Atlas-SNP	.											.	PLEKHS1	19	.	0			c.C614T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	3,4403	4.2+/-10.8	0,3,2200	147	137	140		350,350,614,596	2.6	0	10	dbSNP_134	140	0,8600		0,0,4300	no	missense,missense,missense,missense	C10orf81	NM_001193434.1,NM_001193435.1,NM_024889.4,NM_182601.1	64,64,64,64	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	benign,benign,benign,benign	117/367,117/367,205/364,199/466	115531790	3,13003	2203	4300	6503	SO:0001583	missense	79949	exon8			CAGAAGCCACTCA	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.596C>T	10.37:g.115531790C>T	ENSP00000358316:p.Ala199Val	141	0	0		126	56	0.444444	NM_024889	A8KA02|B3KX00|B6EDE1|Q5SXH8|Q5SXI0|Q6ZQR5|Q8NE42|Q9H5D9	Missense_Mutation	SNP	ENST00000369310.3	37	CCDS53580.1	.	.	.	.	.	.	.	.	.	.	C	12.12	1.843362	0.32606	6.81E-4	0.0	ENSG00000148735	ENST00000361048;ENST00000369312;ENST00000369310;ENST00000369309	T;T;T;T	0.30448	1.53;1.53;1.53;1.53	5.63	2.59	0.31030	.	1.116260	0.06460	N	0.729232	T	0.13970	0.0338	N	0.08118	0	0.09310	N	1	B;B;B;B	0.31077	0.307;0.009;0.049;0.043	B;B;B;B	0.23419	0.046;0.005;0.019;0.03	T	0.17198	-1.0377	10	0.36615	T	0.2	-21.7194	3.245	0.06794	0.1867:0.5589:0.1595:0.095	.	199;199;199;205	Q5SXH7;Q5SXH7-5;Q5SXH7-2;Q5SXH7-4	CJ081_HUMAN;.;.;.	V	205;117;199;19	ENSP00000354332:A205V;ENSP00000358318:A117V;ENSP00000358316:A199V;ENSP00000358315:A19V	ENSP00000354332:A205V	A	+	2	0	C10orf81	115521780	0.002000	0.14202	0.002000	0.10522	0.072000	0.16883	0.513000	0.22770	1.390000	0.46547	0.650000	0.86243	GCC	C|1.000;T|0.000	0.000	weak		0.353	PLEKHS1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050432.1	NM_024889		T	115531790	C	T	115531790	3	4	22	1	0	0	0	0	1	0	0	0	1621	739	26	2	640	2	C10orf81	10	115531790	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	183041	115531790	20002957	2322	5223											
ADRB1	153	hgsc.bcm.edu	37	chr10	115804123	115804123	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcatcgtggcgggcaatgtgCtggtgatcgtggccatcgcc	5	10	15	11	4	1	1	1	1	0	0	4	1	1	1	2	4	1	2	2	4	1	0	rs373125312		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:115804123C>T	ENST00000369295.2	+	1	318	c.232C>T	c.(232-234)Ctg>Ttg	p.L78L		NM_000684.2	NP_000675.1	P08588	ADRB1_HUMAN	adrenoceptor beta 1	78					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|aging (GO:0007568)|apoptotic process (GO:0006915)|brown fat cell differentiation (GO:0050873)|diet induced thermogenesis (GO:0002024)|fear response (GO:0042596)|glycogen catabolic process (GO:0005980)|heat generation (GO:0031649)|lipid homeostasis (GO:0055088)|memory (GO:0007613)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of urine volume (GO:0035811)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cation channel activity (GO:2001259)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of heart rate by epinephrine-norepinephrine (GO:0001996)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of renin secretion into blood stream (GO:1900135)|positive regulation of saliva secretion (GO:0046878)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of the force of heart contraction by norepinephrine (GO:0003061)|protein localization to organelle (GO:0033365)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|response to cold (GO:0009409)|Rho protein signal transduction (GO:0007266)|sensory perception of pain (GO:0019233)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)|wound healing (GO:0042060)	early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|beta-adrenergic receptor activity (GO:0004939)|beta1-adrenergic receptor activity (GO:0004940)|dopamine binding (GO:0035240)|drug binding (GO:0008144)|epinephrine binding (GO:0051379)|norepinephrine binding (GO:0051380)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|receptor signaling protein activity (GO:0005057)			large_intestine(4)|lung(1)|upper_aerodigestive_tract(1)	6		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0124)|all cancers(201;0.0298)	Acebutolol(DB01193)|Alprenolol(DB00866)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Asenapine(DB06216)|Atenolol(DB00335)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dobutamine(DB00841)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Esmolol(DB00187)|Fenoterol(DB01288)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Loxapine(DB00408)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Practolol(DB01297)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Salbutamol(DB01001)|Sotalol(DB00489)|Timolol(DB00373)|Trimipramine(DB00726)	GGGCAATGTGCTGGTGATCGT	0.657																																					p.L78L		Atlas-SNP	.											.	ADRB1	16	.	0			c.C232T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	43	39	40		232	2.1	1	10		40	0,8600		0,0,4300	no	coding-synonymous	ADRB1	NM_000684.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		78/478	115804123	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	153	exon1			AATGTGCTGGTGA	J03019	CCDS7586.1	10q25.3	2012-08-08	2012-05-09		ENSG00000043591	ENSG00000043591		"GPCR / Class A : Adrenoceptors : beta"	285	protein-coding gene	gene with protein product		109630	"adrenergic, beta-1-, receptor"	ADRB1R			Standard	NM_000684		Approved		uc001lba.3	P08588	OTTHUMG00000019079	ENST00000369295.2:c.232C>T	10.37:g.115804123C>T		89	0	0		80	42	0.525	NM_000684	B0LPE2|Q5T5Y4|Q9UKG7|Q9UKG8	Silent	SNP	ENST00000369295.2	37	CCDS7586.1																																																																																			.	.	none		0.657	ADRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050448.1			T	115804123	C	T	115804123	2	4	22	1	0	0	0	0	0	0	0	1	340	796	28	2		2	ADRB1	10	115804123	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	272333	115804123	19730624	2323	5224											
ADRB1	153	hgsc.bcm.edu	37	chr10	115804206	115804206	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccctggccagcgccgacctGgtcatggggctgctggtggt	3	9	16	13	2	1	0	1	0	0	0	2	1	2	0	4	6	2	2	4	6	0	0	rs7921133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:115804206G>T	ENST00000369295.2	+	1	401	c.315G>T	c.(313-315)ctG>ctT	p.L105L		NM_000684.2	NP_000675.1	P08588	ADRB1_HUMAN	adrenoceptor beta 1	105					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|aging (GO:0007568)|apoptotic process (GO:0006915)|brown fat cell differentiation (GO:0050873)|diet induced thermogenesis (GO:0002024)|fear response (GO:0042596)|glycogen catabolic process (GO:0005980)|heat generation (GO:0031649)|lipid homeostasis (GO:0055088)|memory (GO:0007613)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of urine volume (GO:0035811)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cation channel activity (GO:2001259)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of heart rate by epinephrine-norepinephrine (GO:0001996)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of renin secretion into blood stream (GO:1900135)|positive regulation of saliva secretion (GO:0046878)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of the force of heart contraction by norepinephrine (GO:0003061)|protein localization to organelle (GO:0033365)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|response to cold (GO:0009409)|Rho protein signal transduction (GO:0007266)|sensory perception of pain (GO:0019233)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)|wound healing (GO:0042060)	early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|beta-adrenergic receptor activity (GO:0004939)|beta1-adrenergic receptor activity (GO:0004940)|dopamine binding (GO:0035240)|drug binding (GO:0008144)|epinephrine binding (GO:0051379)|norepinephrine binding (GO:0051380)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|receptor signaling protein activity (GO:0005057)			large_intestine(4)|lung(1)|upper_aerodigestive_tract(1)	6		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0124)|all cancers(201;0.0298)	Acebutolol(DB01193)|Alprenolol(DB00866)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Asenapine(DB06216)|Atenolol(DB00335)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dobutamine(DB00841)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Esmolol(DB00187)|Fenoterol(DB01288)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Loxapine(DB00408)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Practolol(DB01297)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Salbutamol(DB01001)|Sotalol(DB00489)|Timolol(DB00373)|Trimipramine(DB00726)	GCGCCGACCTGGTCATGGGGC	0.662													G|||	144	0.028754	0.1044	0.0086	5008	,	,		15320	0.0		0.0	False		,,,				2504	0.0				p.L105L		Atlas-SNP	.											.	ADRB1	16	.	0			c.G315T						PASS	.	G		447,3959	205.8+/-227.6	24,399,1780	57	67	63		315	4.1	1	10	dbSNP_116	63	8,8590	6.4+/-24.3	0,8,4291	no	coding-synonymous	ADRB1	NM_000684.2		24,407,6071	TT,TG,GG		0.093,10.1453,3.4989		105/478	115804206	455,12549	2203	4299	6502	SO:0001819	synonymous_variant	153	exon1			CGACCTGGTCATG	J03019	CCDS7586.1	10q25.3	2012-08-08	2012-05-09		ENSG00000043591	ENSG00000043591		"GPCR / Class A : Adrenoceptors : beta"	285	protein-coding gene	gene with protein product		109630	"adrenergic, beta-1-, receptor"	ADRB1R			Standard	NM_000684		Approved		uc001lba.3	P08588	OTTHUMG00000019079	ENST00000369295.2:c.315G>T	10.37:g.115804206G>T		118	0	0		116	52	0.448276	NM_000684	B0LPE2|Q5T5Y4|Q9UKG7|Q9UKG8	Silent	SNP	ENST00000369295.2	37	CCDS7586.1																																																																																			G|0.963;T|0.037	0.037	strong		0.662	ADRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050448.1			T	115804206	G	T	115804206	2	4	22	1	0	0	0	0	0	0	0	1	340	1335	47	4		4	ADRB1	10	115804206	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	83	115804206	19730541	2324	5225											
ADRB1	153	hgsc.bcm.edu	37	chr10	115805057	115805057	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cttccgcaaggccttccaggGactgctctgctgcgcgcgca	5	8	12	16	4	1	0	0	0	1	0	3	1	3	1	3	2	3	4	3	2	1	2	rs17875445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:115805057G>T	ENST00000369295.2	+	1	1252	c.1166G>T	c.(1165-1167)gGa>gTa	p.G389V		NM_000684.2	NP_000675.1	P08588	ADRB1_HUMAN	adrenoceptor beta 1	389			R -> G (reduced binding to G proteins; dbSNP:rs1801253). {ECO:0000269|PubMed:10212248, ECO:0000269|PubMed:10477438, ECO:0000269|PubMed:15164054, ECO:0000269|Ref.3}.|R -> L. {ECO:0000269|Ref.3}.		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|aging (GO:0007568)|apoptotic process (GO:0006915)|brown fat cell differentiation (GO:0050873)|diet induced thermogenesis (GO:0002024)|fear response (GO:0042596)|glycogen catabolic process (GO:0005980)|heat generation (GO:0031649)|lipid homeostasis (GO:0055088)|memory (GO:0007613)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of urine volume (GO:0035811)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cation channel activity (GO:2001259)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of heart rate by epinephrine-norepinephrine (GO:0001996)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of renin secretion into blood stream (GO:1900135)|positive regulation of saliva secretion (GO:0046878)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of the force of heart contraction by norepinephrine (GO:0003061)|protein localization to organelle (GO:0033365)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|response to cold (GO:0009409)|Rho protein signal transduction (GO:0007266)|sensory perception of pain (GO:0019233)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)|wound healing (GO:0042060)	early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|beta-adrenergic receptor activity (GO:0004939)|beta1-adrenergic receptor activity (GO:0004940)|dopamine binding (GO:0035240)|drug binding (GO:0008144)|epinephrine binding (GO:0051379)|norepinephrine binding (GO:0051380)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|receptor signaling protein activity (GO:0005057)			large_intestine(4)|lung(1)|upper_aerodigestive_tract(1)	6		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0124)|all cancers(201;0.0298)	Acebutolol(DB01193)|Alprenolol(DB00866)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Asenapine(DB06216)|Atenolol(DB00335)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dobutamine(DB00841)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Esmolol(DB00187)|Fenoterol(DB01288)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Loxapine(DB00408)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Practolol(DB01297)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Salbutamol(DB01001)|Sotalol(DB00489)|Timolol(DB00373)|Trimipramine(DB00726)	GCCTTCCAGGGACTGCTCTGC	0.721													G|||	27	0.00539137	0.0197	0.0014	5008	,	,		5822	0.0		0.0	False		,,,				2504	0.0				p.G389V		Atlas-SNP	.											.	ADRB1	16	.	0			c.G1166T						PASS	.	G	VAL/GLY	35,4029		0,35,1997	15	13	13		1166	1.7	1	10	dbSNP_124	13	0,7986		0,0,3993	no	missense	ADRB1	NM_000684.2	109	0,35,5990	TT,TG,GG		0.0,0.8612,0.2905		389/478	115805057	35,12015	2032	3993	6025	SO:0001583	missense	153	exon1			TCCAGGGACTGCT	J03019	CCDS7586.1	10q25.3	2012-08-08	2012-05-09		ENSG00000043591	ENSG00000043591		"GPCR / Class A : Adrenoceptors : beta"	285	protein-coding gene	gene with protein product		109630	"adrenergic, beta-1-, receptor"	ADRB1R			Standard	NM_000684		Approved		uc001lba.3	P08588	OTTHUMG00000019079	ENST00000369295.2:c.1166G>T	10.37:g.115805057G>T	ENSP00000358301:p.Gly389Val	36	0	0		37	17	0.459459	NM_000684	B0LPE2|Q5T5Y4|Q9UKG7|Q9UKG8	Missense_Mutation	SNP	ENST00000369295.2	37	CCDS7586.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	G	8.144	0.785930	0.16189	0.008612	0.0	ENSG00000043591	ENST00000369295	T	0.37235	1.21	3.81	1.72	0.24424	.	0.000000	0.85682	U	0.000000	T	0.26484	0.0647	M	0.64404	1.975	0.36477	D	0.867582	.	.	.	.	.	.	T	0.37079	-0.9721	8	0.62326	D	0.03	.	7.2309	0.26043	0.3079:0.0:0.6921:0.0	rs17875445	.	.	.	V	389	ENSP00000358301:G389V	ENSP00000358301:G389V	G	+	2	0	ADRB1	115795047	1.000000	0.71417	0.998000	0.56505	0.291000	0.27294	3.494000	0.53273	0.129000	0.18514	0.484000	0.47621	GGA	G|0.994;T|0.006	0.006	strong		0.721	ADRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050448.1			T	115805057	G	T	115805057	3	4	22	1	0	0	0	0	1	0	0	0	340	1174	41	4	1168	4	ADRB1	10	115805057	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	851	115805057	19729690	2325	5226											
VWA2	340706	hgsc.bcm.edu	37	chr10	116049199	116049199	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgatccacgtggcagcttaCgccgacctgcggtaccacca	8	7	10	16	4	0	1	0	1	0	0	1	2	1	1	5	2	4	3	5	2	2	2	rs148020287	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:116049199C>T	ENST00000392982.3	+	12	2323	c.2073C>T	c.(2071-2073)taC>taT	p.Y691Y	VWA2_ENST00000603594.1_Silent_p.Y691Y			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	691	VWFA 3. {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)		TGGCAGCTTACGCCGACCTGC	0.642													C|||	29	0.00579073	0.0212	0.0014	5008	,	,		18395	0.0		0.0	False		,,,				2504	0.0				p.Y691Y		Atlas-SNP	.											VWA2,caecum,carcinoma,0,1	VWA2	64	1	0			c.C2073T						PASS	.	C		62,4344	58.7+/-95.3	0,62,2141	126	100	109		2073	-0.5	0.1	10	dbSNP_134	109	0,8600		0,0,4300	no	coding-synonymous	VWA2	NM_198496.1		0,62,6441	TT,TC,CC		0.0,1.4072,0.4767		691/726	116049199	62,12944	2203	4300	6503	SO:0001819	synonymous_variant	340706	exon12			AGCTTACGCCGAC	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.2073C>T	10.37:g.116049199C>T		139	0	0		162	93	0.574074	NM_001272046	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Silent	SNP	ENST00000392982.3	37																																																																																				C|0.994;T|0.006	0.006	strong		0.642	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496		T	116049199	C	T	116049199	2	4	22	1	0	0	0	0	0	0	0	1	17254	547	19	1		1	VWA2	10	116049199	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	244142	116049199	19485548	2326	5227											
AFAP1L2	84632	hgsc.bcm.edu	37	chr10	116056779	116056779	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctttgcctgtgaccacgacCgagagaggcctgttcttgag	7	10	12	12	2	1	3	0	2	1	1	1	6	1	3	5	1	1	1	5	1	0	3	rs62641713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:116056779C>T	ENST00000304129.4	-	18	2417	c.2388G>A	c.(2386-2388)tcG>tcA	p.S796S	AFAP1L2_ENST00000491814.1_5'UTR|AFAP1L2_ENST00000369271.3_Silent_p.S792S|AFAP1L2_ENST00000545353.1_Silent_p.S849S			Q8N4X5	AF1L2_HUMAN	actin filament associated protein 1-like 2	796					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)		TGACCACGACCGAGAGAGGCC	0.567													C|||	206	0.0411342	0.1467	0.0115	5008	,	,		19382	0.001		0.003	False		,,,				2504	0.0				p.S796S		Atlas-SNP	.											.	AFAP1L2	90	.	0			c.G2388A						PASS	.	C	,	664,3742	280.8+/-275.6	62,540,1601	180	157	164		2388,2376	-10.9	0.1	10	dbSNP_129	164	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous,coding-synonymous	AFAP1L2	NM_001001936.1,NM_032550.2	,	62,547,5894	TT,TC,CC		0.0814,15.0704,5.1592	,	796/819,792/815	116056779	671,12335	2203	4300	6503	SO:0001819	synonymous_variant	84632	exon18			CACGACCGAGAGA	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.2388G>A	10.37:g.116056779C>T		297	1	0.003367		337	337	1	NM_001001936	A8K6P7|B3KVQ8|Q2UZW3|Q8TB54|Q96PX4|Q96SY5	Silent	SNP	ENST00000304129.4	37	CCDS31286.1																																																																																			C|0.953;T|0.047	0.047	strong		0.567	AFAP1L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050462.1	NM_032550		T	116056779	C	T	116056779	2	4	22	1	0	0	0	0	0	0	0	1	355	639	23	1		1	AFAP1L2	10	116056779	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	7580	116056779	19477968	2327	5228											
AFAP1L2	84632	hgsc.bcm.edu	37	chr10	116064528	116064528	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggatgcggaaggagtagaGgtggtcggggctggggtctg	7	7	23	4	2	1	1	0	0	1	1	2	5	1	4	0	9	1	2	0	9	2	1	rs73365341	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:116064528G>A	ENST00000304129.4	-	11	1263	c.1234C>T	c.(1234-1236)Ctc>Ttc	p.L412F	AFAP1L2_ENST00000491814.1_5'Flank|AFAP1L2_ENST00000369271.3_Missense_Mutation_p.L412F|AFAP1L2_ENST00000545353.1_Missense_Mutation_p.L465F			Q8N4X5	AF1L2_HUMAN	actin filament associated protein 1-like 2	412	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)		AAGGAGTAGAGGTGGTCGGGG	0.682													G|||	531	0.10603	0.354	0.0375	5008	,	,		12908	0.0		0.0199	False		,,,				2504	0.0174				p.L412F		Atlas-SNP	.											.	AFAP1L2	90	.	0			c.C1234T						PASS	.	G	PHE/LEU,PHE/LEU	1464,2940	461.5+/-352.9	257,950,995	39	38	38		1234,1234	5.3	1	10	dbSNP_130	38	165,8435	76.3+/-139.0	3,159,4138	yes	missense,missense	AFAP1L2	NM_001001936.1,NM_032550.2	22,22	260,1109,5133	AA,AG,GG		1.9186,33.2425,12.5269	probably-damaging,probably-damaging	412/819,412/815	116064528	1629,11375	2202	4300	6502	SO:0001583	missense	84632	exon11			AGTAGAGGTGGTC	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.1234C>T	10.37:g.116064528G>A	ENSP00000303042:p.Leu412Phe	40	0	0		49	49	1	NM_032550	A8K6P7|B3KVQ8|Q2UZW3|Q8TB54|Q96PX4|Q96SY5	Missense_Mutation	SNP	ENST00000304129.4	37	CCDS31286.1	224	0.10256410256410256	195	0.39634146341463417	15	0.04143646408839779	0	0.0	14	0.018469656992084433	G	26.3	4.722438	0.89298	0.332425	0.019186	ENSG00000169129	ENST00000369271;ENST00000304129;ENST00000392974;ENST00000545353	T;T;T	0.75589	-0.95;-0.95;-0.95	5.3	5.3	0.74995	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.62723	1.935	0.09310	P	0.999999814385	D;D;D;D;D	0.89917	1.0;1.0;0.997;1.0;1.0	D;D;D;D;D	0.97110	0.998;0.999;0.984;0.998;1.0	T	0.02104	-1.1213	9	0.45353	T	0.12	-16.927	18.9486	0.92632	0.0:0.0:1.0:0.0	.	465;466;440;412;412	F5GZE1;B7Z2Q0;Q8N4X5-4;Q8N4X5-2;Q8N4X5	.;.;.;.;AF1L2_HUMAN	F	412;412;439;465	ENSP00000358276:L412F;ENSP00000303042:L412F;ENSP00000444511:L465F	ENSP00000303042:L412F	L	-	1	0	AFAP1L2	116054518	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	7.973000	0.88032	2.470000	0.83445	0.563000	0.77884	CTC	G|0.884;A|0.116	0.116	strong		0.682	AFAP1L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050462.1	NM_032550		A	116064528	G	A	116064528	3	1	22	1	0	0	0	0	1	0	0	0	355	1000	35	2	1258	2	AFAP1L2	10	116064528	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	7749	116064528	19470219	2328	5229											
ABLIM1	3983	hgsc.bcm.edu	37	chr10	116203801	116203801	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcttacctgagttgatgggAgaatcgtagcgactggctaa	10	11	13	7	2	0	3	0	2	0	1	1	5	0	3	1	2	3	4	1	2	4	4	rs74158004	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:116203801A>C	ENST00000277895.5	-	17	2017	c.1920T>G	c.(1918-1920)tcT>tcG	p.S640S	ABLIM1_ENST00000533213.2_Silent_p.S580S|ABLIM1_ENST00000369266.3_Silent_p.S317S|ABLIM1_ENST00000369252.4_Silent_p.S580S|ABLIM1_ENST00000392952.3_Silent_p.S317S|ABLIM1_ENST00000369253.2_Silent_p.S263S	NM_002313.5	NP_002304.3	O14639	ABLM1_HUMAN	actin binding LIM protein 1	640					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)		AGTTGATGGGAGAATCGTAGC	0.512													C|||	165	0.0329473	0.1233	0.0029	5008	,	,		16633	0.0		0.0	False		,,,				2504	0.0				p.S640S		Atlas-SNP	.											.	ABLIM1	131	.	0			c.T1920G						PASS	.	C	,,,	418,3988	788.2+/-414.9	31,356,1816	185	183	184		1740,1824,1920,951	-1.1	1	10	dbSNP_130	184	2,8598	819.2+/-406.8	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ABLIM1	NM_001003407.1,NM_001003408.1,NM_002313.5,NM_006720.3	,,,	31,358,6114	CC,CA,AA		0.0233,9.4871,3.2293	,,,	580/719,608/747,640/779,317/456	116203801	420,12586	2203	4300	6503	SO:0001819	synonymous_variant	3983	exon17			GATGGGAGAATCG	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.1920T>G	10.37:g.116203801A>C		112	0	0		124	57	0.459677	NM_002313	A6NI16|A6NJ06|A8MXA9|B3KVH2|Q15039|Q5JVV1|Q5JVV2|Q5T6N2|Q5T6N3|Q5T6N5|Q68CQ9|Q9BUP1	Silent	SNP	ENST00000277895.5	37	CCDS7590.1	57	0.0260989010989011	56	0.11382113821138211	1	0.0027624309392265192	0	0.0	0	0.0	C	7.510	0.654490	0.14580	0.094871	2.33E-4	ENSG00000099204	ENST00000392955	.	.	.	5.79	-1.12	0.09808	.	.	.	.	.	T	0.00967	0.0032	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.04268	-1.0964	4	.	.	.	.	3.7237	0.08466	0.5347:0.1057:0.0608:0.2988	.	.	.	.	R	514	.	.	L	-	2	0	ABLIM1	116193791	0.990000	0.36364	0.988000	0.46212	0.621000	0.37620	0.259000	0.18405	-0.380000	0.07894	-2.704000	0.00135	CTC	A|0.963;C|0.037	0.037	strong		0.512	ABLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050469.3			C	116203801	A	C	116203801	2	2	22	1	0	0	0	0	0	0	0	1	94	291	11	5		5	ABLIM1	10	116203801	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	139273	116203801	19330946	2329	5230											
KCNK18	338567	hgsc.bcm.edu	37	chr10	118969353	118969353	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctgtttgagagatctcatgCgctagagaaacagaacacac	14	8	10	9	1	1	4	1	1	1	3	2	6	1	4	0	0	3	3	0	0	3	2	rs363360	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:118969353C>T	ENST00000334549.1	+	3	698	c.698C>T	c.(697-699)gCg>gTg	p.A233V		NM_181840.1	NP_862823.1	Q7Z418	KCNKI_HUMAN	potassium channel, subfamily K, member 18	233			A -> V (in dbSNP:rs363360). {ECO:0000269|PubMed:20871611}.		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)		AGATCTCATGCGCTAGAGAAA	0.527													C|||	163	0.0325479	0.1165	0.013	5008	,	,		20294	0.0		0.0	False		,,,				2504	0.0				p.A233V		Atlas-SNP	.											KCNK18,colon,carcinoma,0,1	KCNK18	70	1	0			c.C698T						scavenged	.	C	VAL/ALA	421,3985	204.1+/-226.4	22,377,1804	103	99	100		698	2.8	0	10	dbSNP_79	100	3,8597	2.2+/-6.3	0,3,4297	no	missense	KCNK18	NM_181840.1	64	22,380,6101	TT,TC,CC		0.0349,9.5552,3.26	benign	233/385	118969353	424,12582	2203	4300	6503	SO:0001583	missense	338567	exon3			CTCATGCGCTAGA	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.698C>T	10.37:g.118969353C>T	ENSP00000334650:p.Ala233Val	110	1	0.00909091		120	56	0.466667	NM_181840	Q5SQQ8	Missense_Mutation	SNP	ENST00000334549.1	37	CCDS7598.1	67	0.030677655677655676	59	0.11991869918699187	8	0.022099447513812154	0	0.0	0	0.0	C	4.454	0.084176	0.08583	0.095552	3.49E-4	ENSG00000186795	ENST00000334549	T	0.14640	2.49	4.87	2.83	0.33086	.	0.649699	0.15587	N	0.254599	T	0.00144	0.0004	L	0.32530	0.975	0.09310	N	1	P	0.36010	0.532	B	0.27380	0.079	T	0.37957	-0.9683	10	0.31617	T	0.26	.	9.2831	0.37740	0.0:0.648:0.2759:0.0761	rs363360;rs363360	233	Q7Z418	KCNKI_HUMAN	V	233	ENSP00000334650:A233V	ENSP00000334650:A233V	A	+	2	0	KCNK18	118959343	0.289000	0.24334	0.002000	0.10522	0.001000	0.01503	1.454000	0.35178	1.379000	0.46325	0.655000	0.94253	GCG	A|0.000;C|0.963;T|0.037	0.037	strong		0.527	KCNK18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050562.2	NM_181840		T	118969353	C	T	118969353	3	4	22	1	0	0	0	0	1	0	0	0	8074	768	27	1	708	1	KCNK18	10	118969353	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2765552	118969353	16565394	2330	5231											
EMX2	2018	hgsc.bcm.edu	37	chr10	119305282	119305282	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aatcactacgtggtgggcgcCgaaaggaagcagctggcaca	12	5	14	10	3	1	0	1	0	0	0	1	2	1	1	1	4	3	3	1	4	4	1	rs424112	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:119305282C>A	ENST00000553456.3	+	2	1370	c.546C>A	c.(544-546)gcC>gcA	p.A182A	EMX2OS_ENST00000551288.1_RNA|EMX2_ENST00000442245.4_Intron|EMX2_ENST00000546446.1_3'UTR	NM_004098.3	NP_004089.1	Q04743	EMX2_HUMAN	empty spiracles homeobox 2	182					anterior/posterior pattern specification (GO:0009952)|cell proliferation in forebrain (GO:0021846)|cerebral cortex regionalization (GO:0021796)|dentate gyrus development (GO:0021542)|forebrain cell migration (GO:0021885)|neuron differentiation (GO:0030182)|regulation of transcription, DNA-templated (GO:0006355)|renal system development (GO:0072001)|response to drug (GO:0042493)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|prostate(2)	12		Colorectal(252;0.109)|Lung NSC(174;0.179)|all_lung(145;0.22)		all cancers(201;0.0133)		TGGTGGGCGCCGAAAGGAAGC	0.642													C|||	191	0.038139	0.1354	0.0159	5008	,	,		15931	0.0		0.001	False		,,,				2504	0.0				p.A182A		Atlas-SNP	.											.	EMX2	25	.	0			c.C546A						PASS	.	C	,	469,3937	219.7+/-237.4	28,413,1762	46	44	45		,546	-3.2	1	10	dbSNP_80	45	4,8596	3.7+/-12.6	0,4,4296	no	intron,coding-synonymous	EMX2	NM_001165924.1,NM_004098.3	,	28,417,6058	AA,AC,CC		0.0465,10.6446,3.6368	,	,182/253	119305282	473,12533	2203	4300	6503	SO:0001819	synonymous_variant	2018	exon2			GGGCGCCGAAAGG	AF301598	CCDS7601.1, CCDS53583.1	10q26.11	2011-06-20	2007-02-15		ENSG00000170370	ENSG00000170370		"Homeoboxes / ANTP class : NKL subclass"	3341	protein-coding gene	gene with protein product		600035	"empty spiracles homolog 2 (Drosophila)"			7959790	Standard	NM_004098		Approved		uc001ldh.4	Q04743	OTTHUMG00000019123	ENST00000553456.3:c.546C>A	10.37:g.119305282C>A		159	0	0		178	95	0.533708	NM_004098	G3V305|Q96NN8|Q9BQF4	Silent	SNP	ENST00000553456.3	37	CCDS7601.1																																																																																			C|0.962;A|0.038	0.038	strong		0.642	EMX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050569.4	NM_004098		A	119305282	C	A	119305282	2	1	22	1	0	0	0	0	0	0	0	1	5110	639	23	4		4	EMX2	10	119305282	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	335929	119305282	16229465	2331	5232											
C10orf119	79892	hgsc.bcm.edu	37	chr10	121602830	121602830	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ttgatgtgttgcaacttctgGgctaagatcacatgaattct	10	15	9	7	0	3	3	1	2	2	1	3	3	3	3	0	1	2	3	0	1	3	5	rs34297798	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:121602830G>A	ENST00000360003.3	-	9	1105	c.936C>T	c.(934-936)gcC>gcT	p.A312A	MCMBP_ENST00000369077.3_Silent_p.A312A|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	312					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						GCAACTTCTGGGCTAAGATCA	0.483													G|||	44	0.00878594	0.0303	0.0058	5008	,	,		20195	0.0		0.0	False		,,,				2504	0.0				p.A312A		Atlas-SNP	.											.	MCMBP	49	.	0			c.C936T						PASS	.	G		113,4293	86.8+/-125.4	0,113,2090	289	228	249		936	-1.7	1	10	dbSNP_126	249	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	MCMBP	NM_024834.2		0,117,6386	AA,AG,GG		0.0465,2.5647,0.8996		312/643	121602830	117,12889	2203	4300	6503	SO:0001819	synonymous_variant	79892	exon9			CTTCTGGGCTAAG	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.936C>T	10.37:g.121602830G>A		190	0	0		214	111	0.518692	NM_024834	B3KSP7|Q6IA56|Q9BVT9|Q9H916	Silent	SNP	ENST00000360003.3	37	CCDS7617.1																																																																																			G|0.990;A|0.010	0.010	strong		0.483	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834		A	121602830	G	A	121602830	2	1	22	1	0	0	0	0	0	0	0	1	1590	1219	43	2		2	C10orf119	10	121602830	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2297548	121602830	13931917	2332	5233											
WDR11	55717	hgsc.bcm.edu	37	chr10	122649481	122649481	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggaaatcaaaaattaatagCaatgtacaatgatggagctg	19	9	9	4	0	1	1	1	1	0	0	1	3	1	3	0	2	3	3	0	2	8	3	rs150399543	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:122649481C>T	ENST00000263461.6	+	18	2549	c.2303C>T	c.(2302-2304)gCa>gTa	p.A768V	WDR11_ENST00000604509.1_3'UTR	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						AAATTAATAGCAATGTACAAT	0.393													C|||	12	0.00239617	0.0091	0.0	5008	,	,		15112	0.0		0.0	False		,,,				2504	0.0				p.A768V		Atlas-SNP	.											WDR11,NS,carcinoma,-1,1	WDR11	95	1	0			c.C2303T						PASS	.	C	VAL/ALA	30,4376	23.3+/-48.9	0,30,2173	114	108	110		2303	5.5	1	10	dbSNP_134	110	0,8600		0,0,4300	yes	missense	WDR11	NM_018117.11	64	0,30,6473	TT,TC,CC		0.0,0.6809,0.2307	benign	768/1225	122649481	30,12976	2203	4300	6503	SO:0001583	missense	55717	exon18			TAATAGCAATGTA	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.2303C>T	10.37:g.122649481C>T	ENSP00000263461:p.Ala768Val	65	0	0		58	26	0.448276	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000263461.6	37	CCDS7619.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	c	9.054	0.992836	0.18966	0.006809	0.0	ENSG00000120008	ENST00000263461	T	0.50001	0.76	5.49	5.49	0.81192	WD40/YVTN repeat-like-containing domain (1);	0.184844	0.49916	D	0.000125	T	0.11024	0.0269	N	0.00648	-1.295	0.44477	D	0.99741	B;B;B;B	0.06786	0.001;0.0;0.001;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.30357	-0.9981	10	0.02654	T	1	-9.4036	13.0155	0.58754	0.0:0.9262:0.0:0.0738	.	768;768;59;297	Q9BZH6;B2RCJ6;Q9NWV7;Q659C9	WDR11_HUMAN;.;.;.	V	768	ENSP00000263461:A768V	ENSP00000263461:A768V	A	+	2	0	WDR11	122639471	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.417000	0.66423	2.733000	0.93635	0.655000	0.94253	GCA	C|0.997;T|0.003	0.003	strong		0.393	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2			T	122649481	C	T	122649481	3	4	22	1	0	0	0	0	1	0	0	0	17288	710	25	2	2373	2	WDR11	10	122649481	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1046651	122649481	12885266	2333	5234											
FGFR2	2263	hgsc.bcm.edu	37	chr10	123310871	123310871	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagccaccgcatggttggcAttgggttccccccggctggg	4	9	14	14	2	1	0	1	0	0	0	2	0	2	0	5	5	1	5	5	5	0	3	rs755793	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:123310871A>G	ENST00000358487.5	-	5	829	c.557T>C	c.(556-558)aTg>aCg	p.M186T	FGFR2_ENST00000360144.3_Missense_Mutation_p.M97T|FGFR2_ENST00000359354.2_Missense_Mutation_p.M186T|FGFR2_ENST00000356226.4_Missense_Mutation_p.M71T|FGFR2_ENST00000357555.5_Missense_Mutation_p.M97T|FGFR2_ENST00000351936.6_Missense_Mutation_p.M186T|FGFR2_ENST00000369061.4_Missense_Mutation_p.M186T|FGFR2_ENST00000369059.1_Missense_Mutation_p.M71T|FGFR2_ENST00000369056.1_Missense_Mutation_p.M186T|FGFR2_ENST00000369060.4_Missense_Mutation_p.M186T|FGFR2_ENST00000346997.2_Missense_Mutation_p.M186T|FGFR2_ENST00000490349.1_5'UTR|FGFR2_ENST00000457416.2_Missense_Mutation_p.M186T	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	186	Ig-like C2-type 2.		M -> T (in dbSNP:rs755793). {ECO:0000269|PubMed:11781872, ECO:0000269|PubMed:17344846, ECO:0000269|Ref.15}.		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)	CATGGTTGGCATTGGGTTCCC	0.517		5	Mis		"gastric. NSCLC, endometrial"		"Crouzon, Pfeiffer, and Apert syndromes"		Saethre-Chotzen syndrome;Apert syndrome				G|||	629	0.125599	0.3638	0.1066	5008	,	,		15709	0.0645		0.007	False		,,,				2504	0.002				p.M186T		Atlas-SNP	.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	.	FGFR2	758	.	0			c.T557C	GRCh37	CM071761	FGFR2	M	rs755793	PASS	.	G	THR/MET,THR/MET,THR/MET,THR/MET,THR/MET,THR/MET,THR/MET,THR/MET,THR/MET	1295,3111	698.3+/-406.3	194,907,1102	115	107	109		557,557,557,290,212,557,212,290,557	3.9	0.8	10	dbSNP_86	109	15,8585	818.8+/-406.8	0,15,4285	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense	FGFR2	NM_000141.4,NM_001144913.1,NM_001144914.1,NM_001144915.1,NM_001144916.1,NM_001144917.1,NM_001144918.1,NM_001144919.1,NM_022970.3	81,81,81,81,81,81,81,81,81	194,922,5387	GG,GA,AA		0.1744,29.3917,10.0723	benign,benign,benign,benign,benign,benign,benign,benign,benign	186/822,186/770,186/710,97/708,71/707,186/706,71/705,97/681,186/823	123310871	1310,11696	2203	4300	6503	SO:0001583	missense	2263	exon5	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	GTTGGCATTGGGT	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.557T>C	10.37:g.123310871A>G	ENSP00000351276:p.Met186Thr	70	0	0		93	37	0.397849	NM_022970	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	37	CCDS31298.1	263	0.12042124542124542	176	0.35772357723577236	42	0.11602209944751381	40	0.06993006993006994	5	0.006596306068601583	G	0.006	-2.076963	0.00375	0.293917	0.001744	ENSG00000066468	ENST00000357555;ENST00000369062;ENST00000369061;ENST00000358487;ENST00000356226;ENST00000369060;ENST00000369059;ENST00000346997;ENST00000457416;ENST00000351936;ENST00000360144;ENST00000369056;ENST00000369058;ENST00000336553;ENST00000359354	T;T;T;T;T;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;-0.11;-0.11;-0.11;-0.11;-0.11	4.89	3.86	0.44501	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.389842	0.28279	N	0.015928	T	0.00012	0.0000	N	0.00855	-1.145	0.80722	P	0.0	B;B;B;B;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;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B;B;B;B;B;B	0.09377	0.0;0.001;0.0;0.002;0.0;0.0;0.003;0.0;0.004;0.0;0.0;0.002	T	0.29941	-0.9995	9	0.02654	T	1	.	9.2544	0.37575	0.2804:0.0:0.7196:0.0	rs755793;rs52828989;rs60409063;rs755793	205;205;71;186;205;186;97;71;186;205;97;186	D3DRD9;D3DRD4;B5A963;B5A960;D3DRD5;P21802-18;P21802-21;P21802-20;P21802;D3DRE0;P21802-22;P21802-17	.;.;.;.;.;.;.;.;FGFR2_HUMAN;.;.;.	T	97;186;186;186;71;186;71;186;186;186;97;186;186;97;186	ENSP00000350166:M97T;ENSP00000358057:M186T;ENSP00000351276:M186T;ENSP00000348559:M71T;ENSP00000358056:M186T;ENSP00000358055:M71T;ENSP00000263451:M186T;ENSP00000410294:M186T;ENSP00000309878:M186T;ENSP00000353262:M97T;ENSP00000358052:M186T;ENSP00000358054:M186T;ENSP00000337665:M97T;ENSP00000352309:M186T	ENSP00000337665:M97T	M	-	2	0	FGFR2	123300861	0.028000	0.19301	0.838000	0.33150	0.277000	0.26821	1.098000	0.31000	1.065000	0.40693	-0.166000	0.13349	ATG	A|0.878;G|0.122	0.122	strong		0.517	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141		G	123310871	A	G	123310871	3	3	22	1	0	0	0	0	1	0	0	0	5874	217	8	3	2220	3	FGFR2	10	123310871	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	661390	123310871	12223876	2334	5235											
TACC2	10579	hgsc.bcm.edu	37	chr10	123843946	123843946	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaggggggtgctgggcacaCggacgggccccactctcaga	9	4	16	12	2	1	1	1	0	1	1	2	2	1	2	2	6	1	2	2	6	1	0	rs60531929	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:123843946C>T	ENST00000369005.1	+	4	2271	c.1931C>T	c.(1930-1932)aCg>aTg	p.T644M	TACC2_ENST00000453444.2_Missense_Mutation_p.T644M|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515603.1_Missense_Mutation_p.T644M|TACC2_ENST00000515273.1_Missense_Mutation_p.T644M|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000334433.3_Missense_Mutation_p.T644M	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	644					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)				GCTGGGCACACGGACGGGCCC	0.612													C|||	150	0.0299521	0.1036	0.0173	5008	,	,		18351	0.0		0.001	False		,,,				2504	0.0				p.T644M		Atlas-SNP	.											.	TACC2	271	.	0			c.C1931T						PASS	.	C	,MET/THR	445,3961	208.8+/-229.8	26,393,1784	37	35	35		,1931	-10	0	10	dbSNP_129	35	9,8591	5.0+/-18.6	0,9,4291	yes	intron,missense	TACC2	NM_206861.1,NM_206862.2	,81	26,402,6075	TT,TC,CC		0.1047,10.0999,3.4907	,possibly-damaging	,644/2949	123843946	454,12552	2203	4300	6503	SO:0001583	missense	10579	exon4			GGCACACGGACGG	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.1931C>T	10.37:g.123843946C>T	ENSP00000358001:p.Thr644Met	32	0	0		31	16	0.516129	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	47	0.02152014652014652	41	0.08333333333333333	6	0.016574585635359115	0	0.0	0	0.0	C	6.831	0.522532	0.13066	0.100999	0.001047	ENSG00000138162	ENST00000369005;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000453444;ENST00000340076	T;T;T;T;T	0.03413	3.96;3.94;3.94;3.96;3.94	5.02	-10.0	0.00425	.	3.389020	0.01191	N	0.007326	T	0.00073	0.0002	N	0.14661	0.345	0.09310	N	1	P;P;P	0.42757	0.789;0.789;0.789	B;B;B	0.29785	0.107;0.107;0.107	T	0.45659	-0.9246	10	0.45353	T	0.12	11.5241	1.2386	0.01958	0.331:0.1646:0.0943:0.41	rs60531929	644;644;644	E9PBC6;E7EMZ9;O95359	.;.;TACC2_HUMAN	M	644;644;644;644;644;634	ENSP00000358001:T644M;ENSP00000424467:T644M;ENSP00000427618:T644M;ENSP00000334280:T644M;ENSP00000395048:T644M	ENSP00000334280:T644M	T	+	2	0	TACC2	123833936	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.942000	0.00167	-1.779000	0.01280	0.561000	0.74099	ACG	C|0.965;T|0.035	0.035	strong		0.612	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			T	123843946	C	T	123843946	3	4	22	1	0	0	0	0	1	0	0	0	15517	536	19	1	1941	1	TACC2	10	123843946	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	533075	123843946	11690801	2335	5236											
TACC2	10579	hgsc.bcm.edu	37	chr10	123970173	123970173	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccacggattccgtccccaTctctaagtctacactgtccc	7	11	6	17	2	2	0	0	0	2	0	7	1	6	1	5	1	1	0	5	1	2	3	rs7083331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:123970173T>C	ENST00000369005.1	+	9	6573	c.6233T>C	c.(6232-6234)aTc>aCc	p.I2078T	TACC2_ENST00000360561.3_Missense_Mutation_p.I156T|TACC2_ENST00000369004.3_Missense_Mutation_p.I156T|TACC2_ENST00000368999.1_Missense_Mutation_p.I156T|TACC2_ENST00000453444.2_Missense_Mutation_p.I2082T|TACC2_ENST00000369001.1_5'UTR|TACC2_ENST00000358010.1_Missense_Mutation_p.I224T|TACC2_ENST00000515603.1_Missense_Mutation_p.I2033T|TACC2_ENST00000515273.1_Missense_Mutation_p.I2082T|TACC2_ENST00000513429.1_Missense_Mutation_p.I224T|TACC2_ENST00000260733.3_Missense_Mutation_p.I156T|TACC2_ENST00000369000.1_5'UTR|TACC2_ENST00000334433.3_Missense_Mutation_p.I2078T	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	2078			I -> T (in dbSNP:rs7083331).		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)				TCCGTCCCCATCTCTAAGTCT	0.567													T|||	522	0.104233	0.3737	0.0375	5008	,	,		16691	0.0		0.002	False		,,,				2504	0.0				p.I2078T		Atlas-SNP	.											.	TACC2	271	.	0			c.T6233C						PASS	.	T	THR/ILE,THR/ILE,THR/ILE,THR/ILE	1380,3026	456.5+/-351.3	234,912,1057	98	95	96		467,467,671,6233	2.1	0.1	10	dbSNP_116	96	21,8579	14.0+/-48.4	0,21,4279	yes	missense,missense,missense,missense	TACC2	NM_006997.2,NM_206860.1,NM_206861.1,NM_206862.2	89,89,89,89	234,933,5336	CC,CT,TT		0.2442,31.3209,10.772	benign,benign,benign,benign	156/1027,156/997,224/1095,2078/2949	123970173	1401,11605	2203	4300	6503	SO:0001583	missense	10579	exon9			TCCCCATCTCTAA	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.6233T>C	10.37:g.123970173T>C	ENSP00000358001:p.Ile2078Thr	93	0	0		96	46	0.479167	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	188	0.08608058608058608	177	0.3597560975609756	10	0.027624309392265192	0	0.0	1	0.0013192612137203166	T	2.370	-0.344560	0.05208	0.313209	0.002442	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	0.08370	4.02;3.63;4.02;4.04;4.02;3.63;4.02;3.52;3.52;3.52;3.52;3.1	5.5	2.1	0.27182	.	1.500250	0.04801	N	0.433439	T	0.00012	0.0000	N	0.01352	-0.895	0.52099	P	5.8000000000002494E-5	B;B;B;B;B;B;B;B;B	0.13145	0.002;0.007;0.0;0.007;0.007;0.0;0.0;0.001;0.007	B;B;B;B;B;B;B;B;B	0.12156	0.004;0.007;0.001;0.007;0.007;0.002;0.002;0.004;0.007	T	0.47535	-0.9110	9	0.11794	T	0.64	0.8103	7.4447	0.27205	0.0:0.4578:0.0:0.5422	rs7083331;rs52830245;rs7083331	173;2082;156;2033;2082;156;156;224;2078	E9PGB3;E9PBC6;D6RAA5;E7EMZ9;B7ZMJ9;O95359-6;O95359-1;O95359-5;O95359	.;.;.;.;.;.;.;.;TACC2_HUMAN	T	2078;224;2082;2033;2078;224;2082;2068;156;156;156;156;173	ENSP00000358001:I2078T;ENSP00000425062:I224T;ENSP00000424467:I2082T;ENSP00000427618:I2033T;ENSP00000334280:I2078T;ENSP00000350701:I224T;ENSP00000395048:I2082T;ENSP00000353763:I156T;ENSP00000357995:I156T;ENSP00000422815:I156T;ENSP00000260733:I156T;ENSP00000420967:I173T	ENSP00000260733:I156T	I	+	2	0	TACC2	123960163	0.000000	0.05858	0.128000	0.21923	0.313000	0.28021	0.587000	0.23909	0.130000	0.18549	0.533000	0.62120	ATC	T|0.899;C|0.101	0.101	strong		0.567	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			C	123970173	T	C	123970173	3	2	22	1	0	0	0	0	1	0	0	0	15517	1435	50	3	6335	3	TACC2	10	123970173	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	126227	123970173	11564574	2336	5237											
TACC2	10579	hgsc.bcm.edu	37	chr10	123970513	123970513	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagccttattggaggagacGccccttgagcccgctgtggg	6	8	14	13	2	0	2	0	1	0	1	0	4	0	3	5	3	2	1	5	3	1	3	rs35913854	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:123970513G>A	ENST00000369005.1	+	9	6913	c.6573G>A	c.(6571-6573)acG>acA	p.T2191T	TACC2_ENST00000360561.3_Silent_p.T269T|TACC2_ENST00000369004.3_Silent_p.T269T|TACC2_ENST00000368999.1_Silent_p.T269T|TACC2_ENST00000453444.2_Silent_p.T2195T|TACC2_ENST00000369001.1_5'UTR|TACC2_ENST00000358010.1_Silent_p.T337T|TACC2_ENST00000515603.1_Silent_p.T2146T|TACC2_ENST00000515273.1_Silent_p.T2195T|TACC2_ENST00000513429.1_Silent_p.T337T|TACC2_ENST00000260733.3_Silent_p.T269T|TACC2_ENST00000369000.1_5'UTR|TACC2_ENST00000334433.3_Silent_p.T2191T	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	2191					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)				TGGAGGAGACGCCCCTTGAGC	0.597													G|||	369	0.0736821	0.2648	0.0259	5008	,	,		15618	0.0		0.001	False		,,,				2504	0.0				p.T2191T		Atlas-SNP	.											.	TACC2	271	.	0			c.G6573A						PASS	.	G	,,,	913,3491	324.5+/-298.6	109,695,1398	54	66	62		807,807,1011,6573	-11.1	0	10	dbSNP_126	62	14,8586	9.8+/-36.6	0,14,4286	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TACC2	NM_006997.2,NM_206860.1,NM_206861.1,NM_206862.2	,,,	109,709,5684	AA,AG,GG		0.1628,20.7312,7.1286	,,,	269/1027,269/997,337/1095,2191/2949	123970513	927,12077	2202	4300	6502	SO:0001819	synonymous_variant	10579	exon9			GGAGACGCCCCTT	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.6573G>A	10.37:g.123970513G>A		54	0	0		52	23	0.442308	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	37	CCDS7626.1																																																																																			G|0.936;A|0.064	0.064	strong		0.597	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			A	123970513	G	A	123970513	2	1	22	1	0	0	0	0	0	0	0	1	15517	1074	38	1		1	TACC2	10	123970513	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	340	123970513	11564234	2337	5238											
GPR26	2849	hgsc.bcm.edu	37	chr10	125447511	125447511	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgctgtccaagtgcttggcGtacagcaaggccgcatccga	8	8	13	12	3	0	0	0	0	0	0	2	1	2	0	3	2	4	5	3	2	3	2	rs62640899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:125447511G>A	ENST00000284674.1	+	3	902	c.849G>A	c.(847-849)gcG>gcA	p.A283A		NM_153442.3	NP_703143.1	Q8NDV2	GPR26_HUMAN	G protein-coupled receptor 26	283					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)			breast(3)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	20		Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)				AGTGCTTGGCGTACAGCAAGG	0.577													G|||	139	0.0277556	0.1006	0.0072	5008	,	,		17997	0.0		0.001	False		,,,				2504	0.0				p.A283A		Atlas-SNP	.											.	GPR26	47	.	0			c.G849A						PASS	.	G		363,4043	186.4+/-213.3	16,331,1856	91	80	84		849	2.3	1	10	dbSNP_129	84	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	GPR26	NM_153442.3		16,338,6149	AA,AG,GG		0.0814,8.2388,2.8448		283/338	125447511	370,12636	2203	4300	6503	SO:0001819	synonymous_variant	2849	exon3			CTTGGCGTACAGC		CCDS7636.1	10q26.2-q26.3	2012-08-21			ENSG00000154478	ENSG00000154478		"GPCR / Class A : Orphans"	4481	protein-coding gene	gene with protein product		604847					Standard	NM_153442		Approved		uc001lhh.3	Q8NDV2	OTTHUMG00000019204	ENST00000284674.1:c.849G>A	10.37:g.125447511G>A		58	0	0		67	31	0.462687	NM_153442	Q2M2E2	Silent	SNP	ENST00000284674.1	37	CCDS7636.1																																																																																			G|0.970;A|0.030	0.030	strong		0.577	GPR26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050850.1			A	125447511	G	A	125447511	2	1	22	1	0	0	0	0	0	0	0	1	6692	1132	40	1		1	GPR26	10	125447511	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1476998	125447511	10087236	2338	5239											
CPXM2	119587	hgsc.bcm.edu	37	chr10	125651150	125651150	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggagcaccagggccagcgctGgggtagcggtccccgggcgg	5	3	20	13	4	0	0	0	0	0	0	1	1	1	1	4	7	3	3	4	7	1	1	rs112027854	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:125651150G>A	ENST00000241305.3	-	1	180	c.26C>T	c.(25-27)cCa>cTa	p.P9L	CPXM2_ENST00000368854.3_Intron	NM_198148.2	NP_937791.2	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2	9					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)		GGCCAGCGCTGGGGTAGCGGT	0.751													g|||	131	0.0261581	0.0938	0.0101	5008	,	,		8004	0.0		0.0	False		,,,				2504	0.0				p.P9L		Atlas-SNP	.											CPXM2,rectum,carcinoma,0,1	CPXM2	120	1	0			c.C26T						PASS	.		LEU/PRO	153,2681		2,149,1266	4	6	5		26	-2.5	0	10	dbSNP_132	5	3,5397		0,3,2697	no	missense	CPXM2	NM_198148.2	98	2,152,3963	AA,AG,GG		0.0556,5.3987,1.8946	benign	9/757	125651150	156,8078	1417	2700	4117	SO:0001583	missense	119587	exon1			AGCGCTGGGGTAG	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.26C>T	10.37:g.125651150G>A	ENSP00000241305:p.Pro9Leu	12	0	0		18	7	0.388889	NM_198148	B4E3Q2	Missense_Mutation	SNP	ENST00000241305.3	37	CCDS7637.1	.	.	.	.	.	.	.	.	.	.	g	12.37	1.916952	0.33815	0.053987	5.56E-4	ENSG00000121898	ENST00000241305;ENST00000418782	D	0.96716	-4.1	3.45	-2.48	0.06423	.	3.521810	0.01155	N	0.006503	T	0.66406	0.2786	N	0.08118	0	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.78841	-0.2045	10	0.30078	T	0.28	0.0228	7.7622	0.28959	0.6768:0.0:0.3232:0.0	.	9	Q8N436	CPXM2_HUMAN	L	9	ENSP00000241305:P9L	ENSP00000241305:P9L	P	-	2	0	CPXM2	125641140	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	-0.090000	0.11163	-0.418000	0.07450	-0.701000	0.03672	CCA	G|0.500;A|0.500	0.500	weak		0.751	CPXM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050853.1	NM_198148		A	125651150	G	A	125651150	3	1	22	1	0	0	0	0	1	0	0	0	3840	1348	47	2	2300	2	CPXM2	10	125651150	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	203639	125651150	9883597	2339	5240											
ADAM12	8038	hgsc.bcm.edu	37	chr10	127824167	127824167	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acttacctgagaccagaacaCgtgctgagactgactgctga	12	8	10	11	1	0	5	0	4	0	3	0	7	0	5	2	0	4	2	2	0	2	1	rs12098586	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:127824167C>T	ENST00000368679.4	-	5	720	c.411G>A	c.(409-411)acG>acA	p.T137T	ADAM12_ENST00000368676.4_Silent_p.T137T	NM_003474.4	NP_003465.3	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12	137					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)		GACCAGAACACGTGCTGAGAC	0.498													c|||	207	0.0413339	0.1415	0.0259	5008	,	,		19767	0.0		0.002	False		,,,				2504	0.0				p.T137T		Atlas-SNP	.											.	ADAM12	388	.	0			c.G411A						PASS	.	C	,	514,3892	237.4+/-249.2	33,448,1722	161	120	134		411,411	-6.5	0.9	10	dbSNP_120	134	24,8576	17.9+/-57.8	0,24,4276	no	coding-synonymous,coding-synonymous	ADAM12	NM_003474.4,NM_021641.3	,	33,472,5998	TT,TC,CC		0.2791,11.6659,4.1366	,	137/910,137/739	127824167	538,12468	2203	4300	6503	SO:0001819	synonymous_variant	8038	exon5			AGAACACGTGCTG	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.411G>A	10.37:g.127824167C>T		143	0	0		125	61	0.488	NM_021641	O60470|Q5JRP0|Q5JRP1|Q6P9E3|Q6UWB0	Silent	SNP	ENST00000368679.4	37	CCDS7653.1																																																																																			C|0.960;T|0.040	0.040	strong		0.498	ADAM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050961.1			T	127824167	C	T	127824167	2	4	22	1	0	0	0	0	0	0	0	1	236	523	19	1		1	ADAM12	10	127824167	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2173017	127824167	7710580	2340	5241											
DOCK1	1793	hgsc.bcm.edu	37	chr10	128795081	128795081	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gatccagaattaactagcacGattagtctcttcagagctca	13	11	7	10	1	3	2	2	0	1	2	5	4	4	2	1	0	3	2	1	0	4	4	rs79043452	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:128795081G>A	ENST00000280333.6	+	7	652	c.543G>A	c.(541-543)acG>acA	p.T181T		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	181					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)		TAACTAGCACGATTAGTCTCT	0.368													G|||	19	0.00379393	0.0144	0.0	5008	,	,		20216	0.0		0.0	False		,,,				2504	0.0				p.T181T		Atlas-SNP	.											.	DOCK1	188	.	0			c.G543A						PASS	.	G		40,3640		0,40,1800	214	203	206		498	-10.2	0	10	dbSNP_133	206	1,8191		0,1,4095	no	coding-synonymous	DOCK1	NM_001380.3		0,41,5895	AA,AG,GG		0.0122,1.087,0.3454		166/1851	128795081	41,11831	1840	4096	5936	SO:0001819	synonymous_variant	1793	exon7			TAGCACGATTAGT	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.543G>A	10.37:g.128795081G>A		130	0	0		159	79	0.496855	NM_001380	A9Z1Z5	Silent	SNP	ENST00000280333.6	37																																																																																				G|0.997;A|0.003	0.003	strong		0.368	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380		A	128795081	G	A	128795081	2	1	22	1	0	0	0	0	0	0	0	1	4686	1045	37	1		1	DOCK1	10	128795081	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	970914	128795081	6739666	2341	5242											
CLRN3	119467	hgsc.bcm.edu	37	chr10	129676520	129676520	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatgatggttacagtgactaTatttagaagaatgacgagca	15	11	11	4	1	0	5	0	3	0	2	0	7	0	5	0	1	2	2	0	1	6	5	rs34656572	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:129676520T>C	ENST00000368671.3	-	3	736	c.574A>G	c.(574-576)Ata>Gta	p.I192V		NM_152311.3	NP_689524.1	Q8NCR9	CLRN3_HUMAN	clarin 3	192						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	6		all_epithelial(44;0.00168)|all_lung(145;0.0586)|Lung NSC(174;0.0765)|all_neural(114;0.201)|Glioma(114;0.222)|Colorectal(57;0.235)				ACAGTGACTATATTTAGAAGA	0.458													T|||	45	0.00898562	0.0333	0.0014	5008	,	,		22782	0.0		0.0	False		,,,				2504	0.0				p.I192V		Atlas-SNP	.											.	CLRN3	27	.	0			c.A574G						PASS	.	T	VAL/ILE	169,4237	113.3+/-151.4	3,163,2037	220	190	200		574	-6.1	0	10	dbSNP_126	200	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CLRN3	NM_152311.3	29	3,165,6335	CC,CT,TT		0.0233,3.8357,1.3148	benign	192/227	129676520	171,12835	2203	4300	6503	SO:0001583	missense	119467	exon3			TGACTATATTTAG	BC029478	CCDS7656.1	10q26.2	2006-11-24	2006-11-23	2006-11-23	ENSG00000180745	ENSG00000180745			20795	protein-coding gene	gene with protein product			"transmembrane protein 12"	TMEM12		12145752, 12080385	Standard	NM_152311		Approved	MGC32871, USH3AL1	uc001lka.1	Q8NCR9	OTTHUMG00000019253	ENST00000368671.3:c.574A>G	10.37:g.129676520T>C	ENSP00000357660:p.Ile192Val	141	0	0		136	69	0.507353	NM_152311	Q6MZX8	Missense_Mutation	SNP	ENST00000368671.3	37	CCDS7656.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	T	4.071	0.010943	0.07912	0.038357	2.33E-4	ENSG00000180745	ENST00000368671	T	0.75154	-0.91	4.48	-6.08	0.02151	.	0.505264	0.18944	N	0.126863	T	0.21761	0.0524	N	0.21448	0.665	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.24941	-1.0146	10	0.10377	T	0.69	.	16.6501	0.85187	0.0:0.7096:0.0:0.2904	rs34656572	192;124	Q8NCR9;Q8NCR9-2	CLRN3_HUMAN;.	V	192	ENSP00000357660:I192V	ENSP00000357660:I192V	I	-	1	0	CLRN3	129566510	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-2.443000	0.01013	-1.177000	0.02744	-0.263000	0.10527	ATA	T|0.989;C|0.011	0.011	strong		0.458	CLRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050987.1	NM_152311		C	129676520	T	C	129676520	3	2	22	1	0	0	0	0	1	0	0	0	3561	1406	49	3	110	3	CLRN3	10	129676520	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	881439	129676520	5858227	2342	5243											
STK32C	282974	hgsc.bcm.edu	37	chr10	134038817	134038817	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagccggtcccgccgttgaCaaaagagtggaagatctccg	10	7	13	11	4	1	3	0	1	1	2	3	4	2	4	4	2	1	2	4	2	4	2	rs148669059	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:134038817C>T	ENST00000368622.1	-	7	826	c.445G>A	c.(445-447)Gtc>Atc	p.V149I	STK32C_ENST00000368625.4_Missense_Mutation_p.V279I					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)		CCGCCGTTGACAAAAGAGTGG	0.627													C|||	10	0.00199681	0.0068	0.0014	5008	,	,		18797	0.0		0.0	False		,,,				2504	0.0				p.V266I		Atlas-SNP	.											.	STK32C	61	.	0			c.G796A						PASS	.	C	ILE/VAL	38,4360	40.8+/-73.8	0,38,2161	27	30	29		796	4.5	1	10	dbSNP_134	29	2,8592	2.2+/-6.3	0,2,4295	yes	missense	STK32C	NM_173575.2	29	0,40,6456	TT,TC,CC		0.0233,0.864,0.3079	benign	266/487	134038817	40,12952	2199	4297	6496	SO:0001583	missense	282974	exon7			CGTTGACAAAAGA	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.445G>A	10.37:g.134038817C>T	ENSP00000357611:p.Val149Ile	137	0	0		102	54	0.529412	NM_173575		Missense_Mutation	SNP	ENST00000368622.1	37		.	.	.	.	.	.	.	.	.	.	C	18.26	3.583708	0.65992	0.00864	2.33E-4	ENSG00000165752	ENST00000368622;ENST00000298630;ENST00000368625	T;T;T	0.62364	0.03;0.03;0.03	4.49	4.49	0.54785	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.264823	0.24443	N	0.038493	T	0.47655	0.1457	N	0.14661	0.345	0.42125	D	0.991448	P;P;P	0.39376	0.67;0.629;0.577	P;B;B	0.50537	0.643;0.439;0.179	T	0.56962	-0.7892	10	0.46703	T	0.11	.	11.5206	0.50549	0.0:0.7538:0.2461:0.0	.	279;266;149	B7Z7J1;Q86UX6;Q86UX6-2	.;ST32C_HUMAN;.	I	149;266;279	ENSP00000357611:V149I;ENSP00000298630:V266I;ENSP00000357614:V279I	ENSP00000298630:V266I	V	-	1	0	STK32C	133888807	0.991000	0.36638	0.998000	0.56505	0.753000	0.42808	2.948000	0.49066	2.059000	0.61396	0.585000	0.79938	GTC	C|0.996;T|0.004	0.004	strong		0.627	STK32C-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000051068.2	NM_173575		T	134038817	C	T	134038817	3	4	22	1	0	0	0	0	1	0	0	0	15314	478	17	2	688	2	STK32C	10	134038817	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4362297	134038817	1495930	2343	5244											
PWWP2B	170394	hgsc.bcm.edu	37	chr10	134218802	134218802	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccccagggcaagggagaggtGgtcaagatcccctcccgcgt	8	5	14	14	2	1	2	1	0	0	2	3	3	3	2	5	4	0	1	5	4	2	0	rs76160300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:134218802G>T	ENST00000305233.5	+	2	857	c.798G>T	c.(796-798)gtG>gtT	p.V266V	PWWP2B_ENST00000368609.4_Silent_p.V266V	NM_138499.3	NP_612508.3	Q6NUJ5	PWP2B_HUMAN	PWWP domain containing 2B	266										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)		AGGGAGAGGTGGTCAAGATCC	0.701													G|||	36	0.0071885	0.0272	0.0	5008	,	,		12729	0.0		0.0	False		,,,				2504	0.0				p.V266V		Atlas-SNP	.											.	PWWP2B	33	.	0			c.G798T						PASS	.	G	,	107,4271		1,105,2083	15	20	19		798,798	-1.2	1	10	dbSNP_131	19	1,8565		0,1,4282	no	coding-synonymous,coding-synonymous	PWWP2B	NM_001098637.1,NM_138499.3	,	1,106,6365	TT,TG,GG		0.0117,2.444,0.8344	,	266/500,266/591	134218802	108,12836	2189	4283	6472	SO:0001819	synonymous_variant	170394	exon2			AGAGGTGGTCAAG	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.798G>T	10.37:g.134218802G>T		116	0	0		93	52	0.55914	NM_001098637	A6NM90|B5MDQ1|H9KV61|Q5SZI0|Q6ZQX5|Q96F43	Silent	SNP	ENST00000305233.5	37	CCDS7667.2																																																																																			G|0.993;T|0.007	0.007	strong		0.701	PWWP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051075.3	NM_138499		T	134218802	G	T	134218802	2	4	22	1	0	0	0	0	0	0	0	1	12861	1335	47	4		4	PWWP2B	10	134218802	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	179985	134218802	1315945	2344	5245											
PWWP2B	170394	hgsc.bcm.edu	37	chr10	134219291	134219291	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagcagcgacagcctggaCgaggccagatcgtccggctc	8	5	14	14	4	0	1	0	0	0	1	3	4	1	2	3	3	4	3	3	3	0	0	rs139452616	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:134219291C>T	ENST00000305233.5	+	2	1346	c.1287C>T	c.(1285-1287)gaC>gaT	p.D429D	PWWP2B_ENST00000368609.4_Silent_p.D429D	NM_138499.3	NP_612508.3	Q6NUJ5	PWP2B_HUMAN	PWWP domain containing 2B	429										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)		ACAGCCTGGACGAGGCCAGAT	0.697													C|||	57	0.0113818	0.0393	0.0058	5008	,	,		15963	0.0		0.001	False		,,,				2504	0.0				p.D429D		Atlas-SNP	.											.	PWWP2B	33	.	0			c.C1287T						PASS	.	C	,	156,4234	103.4+/-141.9	3,150,2042	30	29	29		1287,1287	-7.2	0.1	10	dbSNP_134	29	2,8594	2.2+/-6.3	0,2,4296	no	coding-synonymous,coding-synonymous	PWWP2B	NM_001098637.1,NM_138499.3	,	3,152,6338	TT,TC,CC		0.0233,3.5535,1.2167	,	429/500,429/591	134219291	158,12828	2195	4298	6493	SO:0001819	synonymous_variant	170394	exon2			CCTGGACGAGGCC	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.1287C>T	10.37:g.134219291C>T		19	0	0		17	12	0.705882	NM_001098637	A6NM90|B5MDQ1|H9KV61|Q5SZI0|Q6ZQX5|Q96F43	Silent	SNP	ENST00000305233.5	37	CCDS7667.2																																																																																			C|0.986;T|0.014	0.014	strong		0.697	PWWP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051075.3	NM_138499		T	134219291	C	T	134219291	2	4	22	1	0	0	0	0	0	0	0	1	12861	535	19	1		1	PWWP2B	10	134219291	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	489	134219291	1315456	2345	5246											
KNDC1	85442	hgsc.bcm.edu	37	chr10	135012583	135012583	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cctgccggggaacgtgatgaCcagagtccagacagtgtccc	9	6	13	13	2	0	4	0	2	0	2	2	5	2	5	5	2	2	0	5	2	1	0	rs111276772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:135012583C>A	ENST00000304613.3	+	14	2592	c.2571C>A	c.(2569-2571)gaC>gaA	p.D857E	KNDC1_ENST00000368571.2_Missense_Mutation_p.D792E|KNDC1_ENST00000368572.2_Missense_Mutation_p.D857E			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	857	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)		AACGTGATGACCAGAGTCCAG	0.741													C|||	102	0.0203674	0.0749	0.0029	5008	,	,		10501	0.0		0.001	False		,,,				2504	0.0				p.D857E		Atlas-SNP	.											.	KNDC1	155	.	0			c.C2571A						PASS	.		GLU/ASP	232,4062		3,226,1918	10	12	11		2571	-3.8	0	10	dbSNP_132	11	5,8501		0,5,4248	yes	missense	KNDC1	NM_152643.6	45	3,231,6166	AA,AC,CC		0.0588,5.4029,1.8516	benign	857/1750	135012583	237,12563	2147	4253	6400	SO:0001583	missense	85442	exon14			TGATGACCAGAGT	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.2571C>A	10.37:g.135012583C>A	ENSP00000304437:p.Asp857Glu	23	0	0		55	28	0.509091	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	37	CCDS7674.1	35	0.016025641025641024	34	0.06910569105691057	1	0.0027624309392265192	0	0.0	0	0.0	C	7.348	0.622286	0.14193	0.054029	5.88E-4	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.18502	2.69;2.69;2.21	1.93	-3.85	0.04243	.	13.355300	0.01309	U	0.010560	T	0.00552	0.0018	N	0.08118	0	0.09310	N	1	B;B;B	0.26195	0.144;0.002;0.106	B;B;B	0.19666	0.026;0.003;0.018	T	0.19614	-1.0300	10	0.22109	T	0.4	.	6.2917	0.21063	0.192:0.2336:0.5744:0.0	.	857;792;857	Q76NI1-4;Q76NI1-2;Q76NI1	.;.;VKIND_HUMAN	E	857;857;792	ENSP00000304437:D857E;ENSP00000357561:D857E;ENSP00000357560:D792E	ENSP00000304437:D857E	D	+	3	2	KNDC1	134862573	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.062000	0.14389	-0.906000	0.03866	-0.828000	0.03084	GAC	C|0.983;A|0.017	0.017	strong		0.741	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		A	135012583	C	A	135012583	3	1	22	1	0	0	0	0	1	0	0	0	8435	506	18	4	2625	4	KNDC1	10	135012583	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	793292	135012583	522164	2346	5247											
ADAM8	101	hgsc.bcm.edu	37	chr10	135077265	135077265	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggtgcgaacgttggcttgAtgacctgggaggaaacagac	10	7	17	7	2	0	3	0	2	0	1	0	6	0	5	1	5	3	2	1	5	2	2	rs3008319	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:135077265A>G	ENST00000445355.3	-	22	2374	c.2324T>C	c.(2323-2325)aTc>aCc	p.I775T	ADAM8_ENST00000485491.2_Intron|ADAM8_ENST00000415217.3_Silent_p.H719H	NM_001109.4	NP_001100.3	P78325	ADAM8_HUMAN	ADAM metallopeptidase domain 8	775			I -> T (in dbSNP:rs3008319).		activation of MAPK activity involved in innate immune response (GO:0035419)|angiogenesis (GO:0001525)|cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|leukocyte migration involved in inflammatory response (GO:0002523)|lymphocyte chemotaxis (GO:0048247)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell adhesion (GO:0045785)|positive regulation of eosinophil migration (GO:2000418)|positive regulation of fibronectin-dependent thymocyte migration (GO:2000415)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of neutrophil extravasation (GO:2000391)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein processing (GO:0010954)|positive regulation of protein secretion (GO:0050714)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000309)|regulation of cell-cell adhesion (GO:0022407)|single organismal cell-cell adhesion (GO:0016337)	alpha9-beta1 integrin-ADAM8 complex (GO:0071133)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dense core granule membrane (GO:0032127)|integral component of plasma membrane (GO:0005887)|phagolysosome (GO:0032010)|plasma membrane (GO:0005886)|podosome (GO:0002102)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein self-association (GO:0043621)|zinc ion binding (GO:0008270)	p.I775T(1)		central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)	17		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;7.72e-06)|OV - Ovarian serous cystadenocarcinoma(35;8.23e-06)|Epithelial(32;1.02e-05)		CGTTGGCTTGATGACCTGGGA	0.642													A|||	341	0.0680911	0.2421	0.0288	5008	,	,		15527	0.0		0.001	False		,,,				2504	0.0				p.I775T		Atlas-SNP	.											ADAM8,NS,carcinoma,0,1	ADAM8	41	1	1	Substitution - Missense(1)	prostate(1)	c.T2324C						PASS	.	A	THR/ILE,,	990,3408		102,786,1311	41	39	40		2324,2157,	1	0.1	10	dbSNP_101	40	12,8580		0,12,4284	yes	missense,coding-synonymous,intron	ADAM8	NM_001109.4,NM_001164489.1,NM_001164490.1	89,,	102,798,5595	GG,GA,AA		0.1397,22.5102,7.7136	benign,,	775/825,719/743,	135077265	1002,11988	2199	4296	6495	SO:0001583	missense	101	exon22			GGCTTGATGACCT	D26579	CCDS31319.2, CCDS58102.1, CCDS58103.1	10q26.3	2014-03-20	2005-08-18		ENSG00000151651	ENSG00000151651		"ADAM metallopeptidase domain containing", "CD molecules"	215	protein-coding gene	gene with protein product		602267	"a disintegrin and metalloproteinase domain 8"			9126482	Standard	NM_001109		Approved	CD156, MS2, CD156a	uc021qbe.1	P78325	OTTHUMG00000019309	ENST00000445355.3:c.2324T>C	10.37:g.135077265A>G	ENSP00000453302:p.Ile775Thr	58	0	0		52	22	0.423077	NM_001109	B4DVM6|H0YL36|H0YLR0|H0YN39	Missense_Mutation	SNP	ENST00000445355.3	37	CCDS31319.2																																																																																			A|0.917;G|0.083	0.083	strong		0.642	ADAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051118.4	NM_001109		G	135077265	A	G	135077265	3	3	22	1	0	0	0	0	1	0	0	0	252	333	12	3	76	3	ADAM8	10	135077265	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	64682	135077265	457482	2347	5248											
TUBGCP2	10844	hgsc.bcm.edu	37	chr10	135106718	135106718	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tggttcacctgcccgtactcGaaggaagacttctcttcaat	9	12	8	12	2	3	1	2	0	1	1	5	3	3	2	2	2	2	2	2	2	4	4	rs3008344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:135106718G>A	ENST00000252936.3	-	6	888	c.849C>T	c.(847-849)ttC>ttT	p.F283F	TUBGCP2_ENST00000417178.2_Silent_p.F153F|TUBGCP2_ENST00000543663.1_Silent_p.F311F|TUBGCP2_ENST00000368563.2_Silent_p.F283F|RP11-122K13.12_ENST00000424450.1_RNA|TUBGCP2_ENST00000368562.1_5'Flank			Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2	283					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)		GCCCGTACTCGAAGGAAGACT	0.547													G|||	16	0.00319489	0.0106	0.0014	5008	,	,		20270	0.0		0.001	False		,,,				2504	0.0				p.F311F		Atlas-SNP	.											.	TUBGCP2	79	.	0			c.C933T						PASS	.	G		48,4358	50.2+/-85.5	0,48,2155	60	58	59		849	-6.7	0.8	10	dbSNP_101	59	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	TUBGCP2	NM_006659.2		0,51,6452	AA,AG,GG		0.0349,1.0894,0.3921		283/903	135106718	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	10844	exon8			GTACTCGAAGGAA	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.849C>T	10.37:g.135106718G>A		60	0	0		58	26	0.448276	NM_001256617	B4DM18|B7ZKL8|F5H4E0|F5H4L0|O43632|Q5VWX7	Silent	SNP	ENST00000252936.3	37	CCDS7676.1																																																																																			G|0.996;A|0.004	0.004	strong		0.547	TUBGCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051148.1			A	135106718	G	A	135106718	2	1	22	1	0	0	0	0	0	0	0	1	16781	1049	37	1		1	TUBGCP2	10	135106718	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	29453	135106718	428029	2348	5249											
NLRP6	171389	hgsc.bcm.edu	37	chr11	284299	284299	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccctgagggcagcccccgcActgacggagctgggcctcct	5	5	14	17	2	0	2	0	2	0	0	1	3	1	3	5	3	2	3	5	3	0	0	rs7108261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:284299A>G	ENST00000312165.5	+	6	2271	c.2271A>G	c.(2269-2271)gcA>gcG	p.A757A	NLRP6_ENST00000534750.1_Silent_p.A756A	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	757					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)		CAGCCCCCGCACTGACGGAGC	0.637													G|||	862	0.172125	0.6165	0.062	5008	,	,		17322	0.0		0.004	False		,,,				2504	0.0				p.A757A		Atlas-SNP	.											NALP6,NS,carcinoma,+1,1	NLRP6	4	1	0			c.A2271G						scavenged	.	G		2265,2141	587.2+/-386.6	600,1065,538	41	43	42		2271	-0.8	0	11	dbSNP_116	42	25,8575	14.6+/-50.1	0,25,4275	yes	coding-synonymous	NLRP6	NM_138329.1		600,1090,4813	GG,GA,AA		0.2907,48.5928,17.6073		757/893	284299	2290,10716	2203	4300	6503	SO:0001819	synonymous_variant	171389	exon6			CCCCGCACTGACG	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.2271A>G	11.37:g.284299A>G		67	1	0.0149254		94	42	0.446809	NM_138329	A8K9F3|E9PJZ8	Silent	SNP	ENST00000312165.5	37	CCDS7693.1																																																																																			A|0.837;G|0.163	0.163	strong		0.637	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329		G	284299	A	G	284299	2	3	22	1	0	0	0	0	0	0	0	1	10490	146	6	3		3	NLRP6	11	284299	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10		284299	134722217	2349	5250											
NLRP6	171389	hgsc.bcm.edu	37	chr11	284477	284477	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggtcggccctcccacagggTacagctgcctgacccccagc	7	5	11	18	1	0	1	0	1	0	0	2	1	1	1	5	3	4	2	5	3	1	1	rs74044411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:284477T>C	ENST00000312165.5	+	7	2375	c.2375T>C	c.(2374-2376)gTa>gCa	p.V792A	NLRP6_ENST00000534750.1_Missense_Mutation_p.V791A|RP11-326C3.2_ENST00000533924.1_RNA	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	792					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)		TCCCACAGGGTACAGCTGCCT	0.697													T|||	324	0.0646965	0.2337	0.0202	5008	,	,		14829	0.0		0.001	False		,,,				2504	0.0				p.V792A		Atlas-SNP	.											.	NLRP6	4	.	0			c.T2375C						PASS	.	T	ALA/VAL	832,3574	301.5+/-286.9	87,658,1458	26	28	27		2375	1.9	0.1	11	dbSNP_130	27	11,8589	7.1+/-27.0	0,11,4289	yes	missense	NLRP6	NM_138329.1	64	87,669,5747	CC,CT,TT		0.1279,18.8833,6.4816	benign	792/893	284477	843,12163	2203	4300	6503	SO:0001583	missense	171389	exon7			ACAGGGTACAGCT	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.2375T>C	11.37:g.284477T>C	ENSP00000309767:p.Val792Ala	87	0	0		79	30	0.379747	NM_138329	A8K9F3|E9PJZ8	Missense_Mutation	SNP	ENST00000312165.5	37	CCDS7693.1	99	0.04532967032967033	90	0.18292682926829268	8	0.022099447513812154	0	0.0	1	0.0013192612137203166	T	10.94	1.491727	0.26774	0.188833	0.001279	ENSG00000174885	ENST00000534750;ENST00000312165	T;T	0.54675	0.56;0.56	3.06	1.93	0.25924	.	1.705140	0.04569	U	0.393007	T	0.00073	0.0002	L	0.40543	1.245	0.09310	N	1	B;B	0.29037	0.006;0.231	B;B	0.22386	0.008;0.039	T	0.07927	-1.0747	10	0.87932	D	0	.	6.1513	0.20313	0.0:0.1362:0.0:0.8638	.	791;792	E9PJZ8;P59044	.;NALP6_HUMAN	A	791;792	ENSP00000433617:V791A;ENSP00000309767:V792A	ENSP00000309767:V792A	V	+	2	0	NLRP6	274477	0.524000	0.26282	0.112000	0.21494	0.161000	0.22273	1.453000	0.35167	1.414000	0.47017	0.374000	0.22700	GTA	T|0.940;C|0.060	0.060	strong		0.697	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329		C	284477	T	C	284477	3	2	22	1	0	0	0	0	1	0	0	0	10490	1638	57	3	2401	3	NLRP6	11	284477	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	178	284477	134722039	2350	5251											
NLRP6	171389	hgsc.bcm.edu	37	chr11	285256	285256	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctggtcatcacacacccagcGctggacggccacccacaacc	10	4	8	19	2	2	0	2	0	0	0	2	1	2	1	4	3	2	1	4	3	1	0	rs144727560	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:285256G>A	ENST00000312165.5	+	8	2631	c.2631G>A	c.(2629-2631)gcG>gcA	p.A877A	RP11-326C3.2_ENST00000525217.1_RNA|RP11-326C3.2_ENST00000534742.1_RNA|NLRP6_ENST00000534750.1_Silent_p.A876A|RP11-326C3.2_ENST00000533924.1_RNA	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	877					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)		CACACCCAGCGCTGGACGGCC	0.597													G|||	19	0.00379393	0.0106	0.0029	5008	,	,		15333	0.0		0.0	False		,,,				2504	0.0031				p.A877A		Atlas-SNP	.											.	NLRP6	4	.	0			c.G2631A						PASS	.	G		49,4357	45.3+/-79.5	0,49,2154	84	69	74		2631	-4.3	0	11	dbSNP_134	74	0,8600		0,0,4300	no	coding-synonymous	NLRP6	NM_138329.1		0,49,6454	AA,AG,GG		0.0,1.1121,0.3767		877/893	285256	49,12957	2203	4300	6503	SO:0001819	synonymous_variant	171389	exon8			CCCAGCGCTGGAC	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.2631G>A	11.37:g.285256G>A		70	0	0		78	36	0.461538	NM_138329	A8K9F3|E9PJZ8	Silent	SNP	ENST00000312165.5	37	CCDS7693.1																																																																																			G|0.995;A|0.005	0.005	strong		0.597	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329		A	285256	G	A	285256	2	1	22	1	0	0	0	0	0	0	0	1	10490	1074	38	1		1	NLRP6	11	285256	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	779	285256	134721260	2351	5252											
IFITM3	10410	hgsc.bcm.edu	37	chr11	320723	320723	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgtggggcgcccccagcaCagccacctcgtgctcctcct	4	8	11	18	2	0	0	0	0	0	0	3	0	2	0	6	2	3	3	6	2	0	1	rs199582787	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:320723C>T	ENST00000399808.4	-	1	327	c.91G>A	c.(91-93)Gtg>Atg	p.V31M	RP11-326C3.11_ENST00000602429.1_RNA|RP11-326C3.14_ENST00000602809.1_lincRNA|RP11-326C3.10_ENST00000534271.1_RNA|RP11-326C3.11_ENST00000508004.2_RNA|RP11-326C3.11_ENST00000602756.1_RNA|IFITM3_ENST00000602735.1_Missense_Mutation_p.V10M|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	1	0			c.G91A						scavenged	.						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	11.37:g.320723C>T	ENSP00000382707:p.Val31Met	98	0	0		97	4	0.0412371	NM_021034	Q53Y76|Q96HK8|Q96J15	Missense_Mutation	SNP	ENST00000399808.4	37	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	.	.	weak		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	22	1	0	0	0	0	1	0	0	0	7537	478	17	2	318	2	IFITM3	11	320723	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	35467	320723	134685793	2352	5253											
B4GALNT4	338707	hgsc.bcm.edu	37	chr11	380390	380390	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcgtggagggcaggctggcCttcgcgcccgtggtcatgcg	3	8	18	12	5	1	0	1	0	0	0	2	1	1	1	2	5	2	2	2	5	0	1	rs115057328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:380390C>T	ENST00000329962.6	+	18	2814	c.2814C>T	c.(2812-2814)gcC>gcT	p.A938A		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	938					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)		GCAGGCTGGCCTTCGCGCCCG	0.682													.|||	22	0.00439297	0.0151	0.0029	5008	,	,		13932	0.0		0.0	False		,,,				2504	0.0				p.A938A		Atlas-SNP	.											.	B4GALNT4	83	.	0			c.C2814T						PASS	.	C		57,4349	51.6+/-87.1	0,57,2146	60	43	49		2814	3.8	1	11	dbSNP_132	49	0,8598		0,0,4299	no	coding-synonymous	B4GALNT4	NM_178537.4		0,57,6445	TT,TC,CC		0.0,1.2937,0.4383		938/1040	380390	57,12947	2203	4299	6502	SO:0001819	synonymous_variant	338707	exon18			GCTGGCCTTCGCG	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.2814C>T	11.37:g.380390C>T		73	0	0		104	64	0.615385	NM_178537	Q96LV2	Silent	SNP	ENST00000329962.6	37	CCDS7694.1																																																																																			C|0.995;T|0.005	0.005	strong		0.682	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537		T	380390	C	T	380390	2	4	22	1	0	0	0	0	0	0	0	1	1269	668	24	2		2	B4GALNT4	11	380390	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	59667	380390	134626126	2353	5254											
LRRC56	115399	hgsc.bcm.edu	37	chr11	549949	549949	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcaggtgctgtggctggctcGctgtggcctcgctgacctgg	2	10	17	12	2	0	1	0	1	0	0	2	1	0	1	2	5	1	6	2	5	0	0	rs371135949		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:549949G>A	ENST00000270115.7	+	7	874	c.374G>A	c.(373-375)cGc>cAc	p.R125H		NM_198075.3	NP_932341.1	Q8IYG6	LRC56_HUMAN	leucine rich repeat containing 56	125										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)		TGGCTGGCTCGCTGTGGCCTC	0.667													G|||	1	0.000199681	0.0	0.0	5008	,	,		18623	0.001		0.0	False		,,,				2504	0.0				p.R125H		Atlas-SNP	.											.	LRRC56	23	.	0			c.G374A						PASS	.	G	HIS/ARG	0,4406		0,0,2203	64	56	59		374	3.8	1	11		59	1,8599	1.2+/-3.3	0,1,4299	no	missense	LRRC56	NM_198075.3	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	125/543	549949	1,13005	2203	4300	6503	SO:0001583	missense	115399	exon7			TGGCTCGCTGTGG		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.374G>A	11.37:g.549949G>A	ENSP00000270115:p.Arg125His	79	0	0		75	27	0.36	NM_198075	Q8N3Q4	Missense_Mutation	SNP	ENST00000270115.7	37	CCDS7700.1	.	.	.	.	.	.	.	.	.	.	G	19.34	3.809742	0.70797	0.0	1.16E-4	ENSG00000161328	ENST00000270115	T	0.09538	2.97	4.71	3.8	0.43715	.	0.119263	0.64402	D	0.000014	T	0.21921	0.0528	L	0.46819	1.47	0.40148	D	0.976912	D	0.89917	1.0	D	0.81914	0.995	T	0.01256	-1.1404	10	0.72032	D	0.01	-17.8379	7.3187	0.26515	0.1956:0.0:0.8044:0.0	.	125	Q8IYG6	LRC56_HUMAN	H	125	ENSP00000270115:R125H	ENSP00000270115:R125H	R	+	2	0	LRRC56	539949	1.000000	0.71417	0.999000	0.59377	0.977000	0.68977	3.731000	0.55013	1.219000	0.43474	-0.186000	0.12905	CGC	.	.	weak		0.667	LRRC56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254969.1	NM_198075		A	549949	G	A	549949	3	1	22	1	0	0	0	0	1	0	0	0	9021	1087	38	1	388	1	LRRC56	11	549949	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	169559	549949	134456567	2354	5255											
LRDD	79751	hgsc.bcm.edu	37	chr11	800186	800186	+	5'Flank	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtctgcgcccttcctctgcCgggcagcctcagcctcctcg	2	9	10	20	4	3	0	1	0	2	0	6	0	5	0	6	1	4	1	6	1	0	1	rs148849040		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:800186C>T	ENST00000531214.1	-	0	0				PIDD_ENST00000411829.2_Missense_Mutation_p.R723Q|PIDD_ENST00000347755.5_Missense_Mutation_p.R740Q	NM_001191060.1	NP_001177989.1	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)		CTTCCTCTGCCGGGCAGCCTC	0.692													C|||	1	0.000199681	0.0008	0.0	5008	,	,		14878	0.0		0.0	False		,,,				2504	0.0				p.R740Q	Colon(93;848 1468 3270 23355 49636)	Atlas-SNP	.											.	PIDD	76	.	0			c.G2219A						PASS	.	C	GLN/ARG,GLN/ARG	5,4369		0,5,2182	15	17	16		2219,2168	3.3	1	11	dbSNP_134	16	0,8574		0,0,4287	yes	missense,missense	PIDD	NM_145886.3,NM_145887.3	43,43	0,5,6469	TT,TC,CC		0.0,0.1143,0.0386	probably-damaging,probably-damaging	740/911,723/894	800186	5,12943	2187	4287	6474	SO:0001631	upstream_gene_variant	55367	exon14			CTCTGCCGGGCAG	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		11.37:g.800186C>T	Exception_encountered	61	0	0		60	41	0.683333	NM_145886	A8K366|C9J1H6|E9PJD3|E9PKB2|E9PL68|E9PN26|E9PNQ3|E9PP01|E9PR97|Q8TBU8	Missense_Mutation	SNP	ENST00000531214.1	37	CCDS7715.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.238462	0.79800	0.001143	0.0	ENSG00000177595	ENST00000411829;ENST00000347755	T;T	0.48201	0.82;0.94	4.24	3.29	0.37713	.	0.138436	0.46145	N	0.000315	T	0.49236	0.1545	L	0.29908	0.895	0.32961	D	0.521066	D;D;D;D	0.76494	0.999;0.999;0.996;0.999	D;P;P;D	0.64776	0.929;0.886;0.806;0.928	T	0.58429	-0.7638	10	0.54805	T	0.06	.	7.9393	0.29948	0.0:0.7476:0.0:0.2524	.	451;740;583;723	Q9HB75-5;Q9HB75;Q9HB75-3;Q9HB75-2	.;PIDD_HUMAN;.;.	Q	723;740	ENSP00000416801:R723Q;ENSP00000337797:R740Q	ENSP00000337797:R740Q	R	-	2	0	PIDD	790186	1.000000	0.71417	0.999000	0.59377	0.828000	0.46876	1.731000	0.38135	2.193000	0.70182	0.462000	0.41574	CGG	C|1.000;T|0.000	0.000	weak		0.692	SLC25A22-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384124.1			T	800186	C	T	800186	1	4	22	0	1	0	0	0	0	0	0	0	8945	652	23	1		1	LRDD	11	800186	5'Flank	SNP	C	TCGA-G8-6324-01A-11D-2210-10	250237	800186	134206330	2355	5256											
MUC6	4588	hgsc.bcm.edu	37	chr11	1017522	1017522	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtagaagttgaggtgactTcaggatggtgtgtggaggaa	10	11	18	2	0	1	3	1	2	0	1	1	6	1	6	0	6	0	2	0	6	3	3	rs199592093		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1017522T>G	ENST00000421673.2	-	31	5329	c.5279A>C	c.(5278-5280)gAa>gCa	p.E1760A		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1760	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)		TGAGGTGACTTCAGGATGGTG	0.567																																					p.E1760A		Atlas-SNP	.											.	MUC6	408	.	0			c.A5279C						PASS	.						751	715	727					11																	1017522		2200	4294	6494	SO:0001583	missense	4588	exon31			GTGACTTCAGGAT	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.5279A>C	11.37:g.1017522T>G	ENSP00000406861:p.Glu1760Ala	957	0	0		1236	124	0.100324	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	-	0.655	-0.808100	0.02819	.	.	ENSG00000184956	ENST00000421673	T	0.20332	2.08	0.235	0.235	0.15431	.	.	.	.	.	T	0.25195	0.0612	L	0.38175	1.15	0.09310	N	1	D	0.67145	0.996	D	0.70227	0.968	T	0.11966	-1.0566	8	0.05833	T	0.94	.	.	.	.	.	1760	Q6W4X9	MUC6_HUMAN	A	1760	ENSP00000406861:E1760A	ENSP00000406861:E1760A	E	-	2	0	MUC6	1007522	0.000000	0.05858	0.002000	0.10522	0.045000	0.14185	-3.356000	0.00499	0.263000	0.21812	0.260000	0.18958	GAA	.	.	weak		0.567	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		G	1017522	T	G	1017522	3	3	22	1	0	0	0	0	1	0	0	0	9989	1783	62	5	2052	5	MUC6	11	1017522	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	217336	1017522	133988994	2356	5257											
MUC6	4588	hgsc.bcm.edu	37	chr11	1017945	1017945	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtcaccaaagaggtggagAaaggtggaacgtgagtggga	14	5	18	4	1	1	3	1	1	0	2	1	7	1	5	1	5	1	0	1	5	3	0			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						PASS	.																																			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	11.37:g.1017945A>G	ENSP00000406861:p.Phe1619Ser	1032	0	0		1212	49	0.040429	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	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	.	.	none		0.542	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		G	1017945	A	G	1017945	3	3	22	1	0	0	0	0	1	0	0	0	9989	246	9	3	2475	3	MUC6	11	1017945	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	423	1017945	133988571	2357	5258											
MUC2	4583	hgsc.bcm.edu	37	chr11	1093228	1093228	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagccatcaccaccaccactAcggtgaccccaaccccaaca	13	3	4	21	1	1	1	1	1	0	0	1	1	1	1	8	1	4	0	8	1	3	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1093228A>G	ENST00000441003.2	+	30	5074	c.5047A>G	c.(5047-5049)Acg>Gcg	p.T1683A	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.T1650A	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)	caccaccactacGGTGacccc	0.632																																					p.T1683A		Atlas-SNP	.											.	MUC2	614	.	0			c.A5047G						PASS	.						85	148	126					11																	1093228		1822	3322	5144	SO:0001583	missense	4583	exon30			ACCACTACGGTGA	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.5047A>G	11.37:g.1093228A>G	ENSP00000415183:p.Thr1683Ala	60	0	0		66	13	0.19697	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	A	3.524	-0.097228	0.07010	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.12465	2.97;2.68	1.75	0.234	0.15390	.	0.000000	0.34750	U	0.003714	T	0.04497	0.0123	.	.	.	0.09310	N	1	B	0.28933	0.228	B	0.21546	0.035	T	0.37126	-0.9719	9	0.11485	T	0.65	.	3.3046	0.06996	0.6291:0.0:0.0:0.3709	.	1683	E7EUV1	.	A	1683;1650	ENSP00000415183:T1683A;ENSP00000351956:T1650A	ENSP00000351956:T1650A	T	+	1	0	MUC2	1083228	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	-0.225000	0.09151	0.813000	0.34350	0.155000	0.16302	ACG	.	.	none		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		G	1093228	A	G	1093228	3	3	22	1	0	0	0	0	1	0	0	0	9984	391	14	3	5165	3	MUC2	11	1093228	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	75283	1093228	133913288	2358	5259											
MUC2	4583	hgsc.bcm.edu	37	chr11	1093362	1093362	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgacacccatctccaccacCactacggtgaccccaacccc	10	4	4	23	2	1	1	0	1	1	0	2	2	1	1	9	1	2	0	9	1	2	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1093362C>G	ENST00000441003.2	+	30	5208	c.5181C>G	c.(5179-5181)acC>acG	p.T1727T	MUC2_ENST00000333592.6_Silent_p.T15T|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Silent_p.T1694T	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)	tctccaccaccactacggtga	0.647																																					p.T1727T		Atlas-SNP	.											.	MUC2	614	.	0			c.C5181G						PASS	.						187	230	215					11																	1093362		1968	3798	5766	SO:0001819	synonymous_variant	4583	exon30			CACCACCACTACG	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.5181C>G	11.37:g.1093362C>G		117	0	0		132	8	0.0606061	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.	.	none		0.647	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		G	1093362	C	G	1093362	2	3	22	1	0	0	0	0	0	0	0	1	9984	581	21	4		4	MUC2	11	1093362	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	134	1093362	133913154	2359	5260											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1268528	1268528	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggtgcgcacagcctggacttCggccacctcgggcatcttgg	5	8	14	14	3	1	0	0	0	1	0	3	1	1	1	3	5	2	2	3	5	0	2	rs202008769	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1268528C>T	ENST00000529681.1	+	31	10476	c.10418C>T	c.(10417-10419)tCg>tTg	p.S3473L	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.S3476L	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3473	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)		GCCTGGACTTCGGCCACCTCG	0.672													-|||	12	0.00239617	0.0083	0.0014	5008	,	,		18693	0.0		0.0	False		,,,				2504	0.0				p.S3473L		Atlas-SNP	.											MUC5B,colon,carcinoma,0,4	MUC5B	473	4	0			c.C10418T						PASS	.	C	LEU/SER	11,4213		0,11,2101	60	85	77		10418	0	0	11		77	2,8406		0,2,4202	no	missense	MUC5B	NM_002458.2	145	0,13,6303	TT,TC,CC		0.0238,0.2604,0.1029	benign	3473/5763	1268528	13,12619	2112	4204	6316	SO:0001583	missense	727897	exon31			GGACTTCGGCCAC	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.10418C>T	11.37:g.1268528C>T	ENSP00000436812:p.Ser3473Leu	462	0	0		657	250	0.380518	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	c	4.864	0.160630	0.09287	0.002604	2.38E-4	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.20598	2.06;2.24	2.0	0.00491	0.14060	.	.	.	.	.	T	0.16811	0.0404	L	0.50333	1.59	0.09310	N	1	B;B	0.33494	0.414;0.001	B;B	0.29716	0.106;0.0	T	0.18745	-1.0327	9	0.87932	D	0	.	5.899	0.18955	0.0:0.6851:0.0:0.3149	.	4001;3476	A7Y9J9;E9PBJ0	.;.	L	3473;3476;3445;3378	ENSP00000436812:S3473L;ENSP00000415793:S3476L	ENSP00000343037:S3445L	S	+	2	0	MUC5B	1225104	0.000000	0.05858	0.002000	0.10522	0.028000	0.11728	-1.189000	0.03061	0.007000	0.14760	-0.712000	0.03635	TCG	.	.	weak		0.672	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		T	1268528	C	T	1268528	3	4	22	1	0	0	0	0	1	0	0	0	9988	893	31	1	10549	1	MUC5B	11	1268528	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	175166	1268528	133737988	2360	5261											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1271582	1271582	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggccacgacacccacagtcaCcagctccaaagccactccct	11	4	6	20	1	1	0	1	0	0	0	3	1	3	0	6	1	2	1	6	1	1	0	rs200110193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1271582C>T	ENST00000529681.1	+	31	13530	c.13472C>T	c.(13471-13473)aCc>aTc	p.T4491I	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.T4494I	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4491	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)		CCCACAGTCACCAGCTCCAAA	0.642													C|||	68	0.0135783	0.0469	0.0086	5008	,	,		18910	0.0		0.0	False		,,,				2504	0.0				p.T4491I		Atlas-SNP	.											.	MUC5B	473	.	0			c.C13472T						PASS	.	C	ILE/THR	95,4235		2,91,2072	114	152	139		13472	0.4	0	11		139	0,8520		0,0,4260	no	missense	MUC5B	NM_002458.2	89	2,91,6332	TT,TC,CC		0.0,2.194,0.7393	probably-damaging	4491/5763	1271582	95,12755	2165	4260	6425	SO:0001583	missense	727897	exon31			CAGTCACCAGCTC	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.13472C>T	11.37:g.1271582C>T	ENSP00000436812:p.Thr4491Ile	827	2	0.00241838		596	279	0.468121	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	-	1.101	-0.661133	0.03454	0.02194	0.0	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844;ENST00000535652	T;T	0.25749	1.78;1.97	0.399	0.399	0.16325	.	.	.	.	.	T	0.22475	0.0542	L	0.60455	1.87	0.09310	N	1	D;D	0.58970	0.984;0.984	P;P	0.59595	0.86;0.86	T	0.08351	-1.0726	8	0.87932	D	0	.	.	.	.	.	4964;4494	A7Y9J9;E9PBJ0	.;.	I	4491;4494;4435;4341;270	ENSP00000436812:T4491I;ENSP00000415793:T4494I	ENSP00000343037:T4435I	T	+	2	0	MUC5B	1228158	0.000000	0.05858	0.019000	0.16419	0.023000	0.10783	-0.180000	0.09754	0.440000	0.26502	0.162000	0.16502	ACC	.	.	weak		0.642	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		T	1271582	C	T	1271582	3	4	22	1	0	0	0	0	1	0	0	0	9988	507	18	2	13603	2	MUC5B	11	1271582	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3054	1271582	133734934	2361	5262											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1272246	1272246	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accccagtgctgaccagcacGgccaccacacccgcagccac	10	2	8	21	2	0	1	0	1	0	0	0	1	0	1	7	1	3	3	7	1	0	0	rs115045504	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1272246G>A	ENST00000529681.1	+	31	14194	c.14136G>A	c.(14134-14136)acG>acA	p.T4712T	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Silent_p.T4715T	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4712	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.		T -> M (in dbSNP:rs2943511). {ECO:0000269|PubMed:9013550}.		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)		tgaccagcacggccaccacac	0.617													g|||	69	0.013778	0.0477	0.0086	5008	,	,		18297	0.0		0.0	False		,,,				2504	0.0				p.T4712T		Atlas-SNP	.											MUC5B,colon,carcinoma,+1,2	MUC5B	473	2	0			c.G14136A						PASS	.	G		97,4189		3,91,2049	108	139	128		14136	-3.3	0	11	dbSNP_132	128	0,8456		0,0,4228	no	coding-synonymous	MUC5B	NM_002458.2		3,91,6277	AA,AG,GG		0.0,2.2632,0.7613		4712/5763	1272246	97,12645	2143	4228	6371	SO:0001819	synonymous_variant	727897	exon31			CAGCACGGCCACC	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.14136G>A	11.37:g.1272246G>A		551	2	0.00362976		520	253	0.486538	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			G|0.988;A|0.012	0.012	strong		0.617	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1272246	G	A	1272246	2	1	22	1	0	0	0	0	0	0	0	1	9988	1103	39	1		1	MUC5B	11	1272246	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	664	1272246	133734270	2362	5263											
KRTAP5-4	387267	hgsc.bcm.edu	37	chr11	1643073	1643073	+	Frame_Shift_Del	DEL	C	C	-																															agccccccttggaacccccaCaagagccatagccccccttg																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1643073delC	ENST00000399682.1	-	1	295	c.251delG	c.(250-252)tgtfs	p.C84fs		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)		GGAACCCCCACAAGAGCCATA	0.667																																					p.C84fs		Atlas-Indel	.											KRTAP5-4,NS,carcinoma,0,1	KRTAP5-4	78	1	0			c.252delT						PASS	.						9	15	13					11																	1643073		682	1575	2257	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.251delG	11.37:g.1643073delC	ENSP00000382590:p.Cys84fs	225	0	0		284	23	0.0809859	NM_001012709		Frame_Shift_Del	DEL	ENST00000399682.1	37																																																																																				.	.	none		0.667	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709		-	1643073	C	-	1643073	7	5	22	1	0	1	0	1	0	0	0	0	8572	478	17	0	439	0	KRTAP5-4	11	1643073	Frame_Shift_Del	DEL	C	TCGA-G8-6324-01A-11D-2210-10	370827	1643073	133363443	2363	5264											
SYT8	90019	hgsc.bcm.edu	37	chr11	1858076	1858076	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgctggaggctcgaggcctgCgtccaggacttgcaggtgag	6	8	17	10	2	0	1	0	1	0	0	2	4	1	3	2	5	3	3	2	5	0	1	rs115217397	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1858076C>T	ENST00000381968.3	+	7	945	c.817C>T	c.(817-819)Cgt>Tgt	p.R273C	TNNI2_ENST00000252898.7_5'Flank|SYT8_ENST00000535046.1_3'UTR|TNNI2_ENST00000381906.1_5'Flank|SYT8_ENST00000341958.3_Missense_Mutation_p.R259C|TNNI2_ENST00000381911.1_5'Flank	NM_138567.3	NP_612634	Q8NBV8	SYT8_HUMAN	synaptotagmin VIII	273	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)		TCGAGGCCTGCGTCCAGGACT	0.682													C|||	38	0.00758786	0.0272	0.0014	5008	,	,		16027	0.0		0.0	False		,,,				2504	0.001				p.R273C		Atlas-SNP	.											.	SYT8	29	.	0			c.C817T						PASS	.	C	CYS/ARG	108,4292	82.4+/-120.9	2,104,2094	37	38	38		817	0.6	0.2	11	dbSNP_132	38	1,8595	1.2+/-3.3	0,1,4297	yes	missense	SYT8	NM_138567.3	180	2,105,6391	TT,TC,CC		0.0116,2.4545,0.8387	probably-damaging	273/402	1858076	109,12887	2200	4298	6498	SO:0001583	missense	90019	exon7			GGCCTGCGTCCAG	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.817C>T	11.37:g.1858076C>T	ENSP00000371394:p.Arg273Cys	55	0	0		57	21	0.368421	NM_138567	A6NFJ4|Q9NSV9	Missense_Mutation	SNP	ENST00000381968.3	37	CCDS7726.2	17|17	0.007783882783882784|0.007783882783882784	17|17	0.034552845528455285|0.034552845528455285	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	c|c	13.17|13.17	2.156344|2.156344	0.38021|0.38021	0.024545|0.024545	1.16E-4|1.16E-4	ENSG00000149043|ENSG00000149043	ENST00000381978|ENST00000381968;ENST00000341958	.|T;T	.|0.69685	.|-0.42;-0.42	3.07|3.07	0.632|0.632	0.17705|0.17705	.|C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	.|.	.|.	.|.	.|.	T|T	0.35278|0.35278	0.0926|0.0926	L|L	0.33245|0.33245	0.995|0.995	0.18873|0.18873	N|N	0.999986|0.999986	.|D;D	.|0.63046	.|0.992;0.992	.|P;P	.|0.51918	.|0.684;0.684	T|T	0.40136|0.40136	-0.9579|-0.9579	5|9	.|0.87932	.|D	.|0	.|.	5.0271|5.0271	0.14391|0.14391	0.6967:0.1957:0.1076:0.0|0.6967:0.1957:0.1076:0.0	.|.	.|273;259	.|Q8NBV8;A6NCR4	.|SYT8_HUMAN;.	V|C	271|273;259	.|ENSP00000371394:R273C;ENSP00000343691:R259C	.|ENSP00000343691:R259C	A|R	+|+	2|1	0|0	SYT8|SYT8	1814652|1814652	0.012000|0.012000	0.17670|0.17670	0.210000|0.210000	0.23637|0.23637	0.473000|0.473000	0.32948|0.32948	-0.050000|-0.050000	0.11904|0.11904	0.015000|0.015000	0.14971|0.14971	0.313000|0.313000	0.20887|0.20887	GCG|CGT	C|0.991;T|0.009	0.009	strong		0.682	SYT8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025013.4			T	1858076	C	T	1858076	3	4	22	1	0	0	0	0	1	0	0	0	15495	768	27	1	843	1	SYT8	11	1858076	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	215003	1858076	133148440	2364	5265											
MRPL23	6150	hgsc.bcm.edu	37	chr11	1972229	1972229	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcccagcccgaggacaccGtgcagttccggatccccatg	7	6	12	16	3	0	0	0	0	0	0	2	3	2	2	6	3	2	2	6	3	0	1	rs377324983		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1972229G>A	ENST00000397298.3	+	2	203	c.118G>A	c.(118-120)Gtg>Atg	p.V40M	MRPL23_ENST00000381514.3_Missense_Mutation_p.V40M|MRPL23_ENST00000397294.3_Missense_Mutation_p.V40M|MRPL23_ENST00000397297.3_Missense_Mutation_p.V40M|MRPL23_ENST00000486931.1_3'UTR|MRPL23_ENST00000381519.1_Missense_Mutation_p.V40M	NM_021134.3	NP_066957.3	Q16540	RM23_HUMAN	mitochondrial ribosomal protein L23	40					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			large_intestine(2)|lung(1)|ovary(1)	4		all_epithelial(84;6.24e-05)|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;0.0026)|Lung(200;0.0171)|LUSC - Lung squamous cell carcinoma(625;0.0842)		CGAGGACACCGTGCAGTTCCG	0.657													G|||	1	0.000199681	0.0	0.0	5008	,	,		15615	0.001		0.0	False		,,,				2504	0.0				p.V40M		Atlas-SNP	.											.	MRPL23	14	.	0			c.G118A						PASS	.						38	31	33					11																	1972229		2198	4297	6495	SO:0001583	missense	6150	exon2			GACACCGTGCAGT	AB051340	CCDS31336.1	11p15.5	2012-09-13			ENSG00000214026	ENSG00000214026		"Mitochondrial ribosomal proteins / large subunits"	10322	protein-coding gene	gene with protein product		600789		RPL23L		8541832	Standard	NM_021134		Approved	L23MRP	uc001lux.3	Q16540	OTTHUMG00000012476	ENST00000397298.3:c.118G>A	11.37:g.1972229G>A	ENSP00000380466:p.Val40Met	64	0	0		70	37	0.528571	NM_021134	A8MT29|Q96Q71	Missense_Mutation	SNP	ENST00000397298.3	37	CCDS31336.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.663671	0.88251	.	.	ENSG00000214026	ENST00000397298;ENST00000381519;ENST00000397297;ENST00000381514;ENST00000397294	T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93	4.46	4.46	0.54185	Ribosomal protein L23/L15e (1);Nucleotide-binding, alpha-beta plait (1);	0.159427	0.41097	U	0.000941	T	0.71921	0.3397	M	0.91196	3.185	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.80522	-0.1345	10	0.72032	D	0.01	.	17.4877	0.87693	0.0:0.0:1.0:0.0	.	40	Q16540	RM23_HUMAN	M	40	ENSP00000380466:V40M;ENSP00000370930:V40M;ENSP00000380465:V40M;ENSP00000370925:V40M;ENSP00000380462:V40M	ENSP00000370925:V40M	V	+	1	0	MRPL23	1928805	1.000000	0.71417	0.996000	0.52242	0.876000	0.50452	5.989000	0.70587	2.199000	0.70637	0.491000	0.48974	GTG	.	.	weak		0.657	MRPL23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034765.2	NM_021134		A	1972229	G	A	1972229	3	1	22	1	0	0	0	0	1	0	0	0	9798	1145	40	1	124	1	MRPL23	11	1972229	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	114153	1972229	133034287	2365	5266											
TH	7054	hgsc.bcm.edu	37	chr11	2190982	2190982	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccttctcctcaaaggccacAgcctccagggggtccccggg	6	7	11	17	1	2	0	1	0	1	0	6	0	5	0	7	4	1	0	7	4	1	1	rs7950050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:2190982A>G	ENST00000381178.1	-	3	321	c.303T>C	c.(301-303)gcT>gcC	p.A101A	TH_ENST00000333684.5_Silent_p.A74A|TH_ENST00000381175.1_Silent_p.A97A|TH_ENST00000352909.3_Silent_p.A70A	NM_199292.2	NP_954986.2	P07101	TY3H_HUMAN	tyrosine hydroxylase	101					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)	CAAAGGCCACAGCCTCCAGGG	0.697													G|||	168	0.0335463	0.1233	0.0058	5008	,	,		14629	0.0		0.001	False		,,,				2504	0.0				p.A101A		Atlas-SNP	.											.	TH	43	.	0			c.T303C						PASS	.	G	,,	522,3882	744.0+/-411.5	23,476,1703	32	34	34		210,303,291	-1.3	0.1	11	dbSNP_116	34	13,8583	796.2+/-407.5	0,13,4285	no	coding-synonymous,coding-synonymous,coding-synonymous	TH	NM_000360.3,NM_199292.2,NM_199293.2	,,	23,489,5988	GG,GA,AA		0.1512,11.8529,4.1154	,,	70/498,101/529,97/525	2190982	535,12465	2202	4298	6500	SO:0001819	synonymous_variant	7054	exon3			GGCCACAGCCTCC	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.303T>C	11.37:g.2190982A>G		121	0	0		116	62	0.534483	NM_199292	B7ZL70|B7ZL73|Q0PWM2|Q0PWM3|Q15585|Q15588|Q15589|Q2M3B4	Silent	SNP	ENST00000381178.1	37	CCDS7731.1																																																																																			A|0.952;G|0.048	0.048	strong		0.697	TH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026597.1	NM_000360		G	2190982	A	G	2190982	2	3	22	1	0	0	0	0	0	0	0	1	15853	175	7	3		3	TH	11	2190982	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	218753	2190982	132815534	2366	5267											
TH	7054	hgsc.bcm.edu	37	chr11	2191006	2191006	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagggggtccccgggctcCgaggggactgcagcggccgc	4	4	18	15	4	0	0	0	0	0	0	3	2	3	1	5	6	2	2	5	6	0	0	rs34510659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:2191006C>T	ENST00000381178.1	-	3	297	c.279G>A	c.(277-279)tcG>tcA	p.S93S	TH_ENST00000333684.5_Silent_p.S66S|TH_ENST00000381175.1_Silent_p.S89S|TH_ENST00000352909.3_Silent_p.S62S	NM_199292.2	NP_954986.2	P07101	TY3H_HUMAN	tyrosine hydroxylase	93					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)	CCCCGGGCTCCGAGGGGACTG	0.711													C|||	122	0.024361	0.0893	0.0058	5008	,	,		13970	0.0		0.0	False		,,,				2504	0.0				p.S93S		Atlas-SNP	.											.	TH	43	.	0			c.G279A						PASS	.	C	,,	343,4043		10,323,1860	17	20	19		186,279,267	-1	0	11	dbSNP_126	19	6,8586		0,6,4290	no	coding-synonymous,coding-synonymous,coding-synonymous	TH	NM_000360.3,NM_199292.2,NM_199293.2	,,	10,329,6150	TT,TC,CC		0.0698,7.8203,2.6892	,,	62/498,93/529,89/525	2191006	349,12629	2193	4296	6489	SO:0001819	synonymous_variant	7054	exon3			GGGCTCCGAGGGG	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.279G>A	11.37:g.2191006C>T		74	0	0		68	40	0.588235	NM_199292	B7ZL70|B7ZL73|Q0PWM2|Q0PWM3|Q15585|Q15588|Q15589|Q2M3B4	Silent	SNP	ENST00000381178.1	37	CCDS7731.1																																																																																			C|0.971;T|0.029	0.029	strong		0.711	TH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026597.1	NM_000360		T	2191006	C	T	2191006	2	4	22	1	0	0	0	0	0	0	0	1	15853	639	23	1		1	TH	11	2191006	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	24	2191006	132815510	2367	5268											
TRPM5	29850	hgsc.bcm.edu	37	chr11	2428434	2428434	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctgagcaggatgaagggcggGgccagggcggggcgctcgtg	6	4	22	9	4	0	2	0	2	0	0	1	3	0	3	1	7	1	2	1	7	1	0	rs369339407		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:2428434G>A	ENST00000155858.6	-	20	3041	c.3033C>T	c.(3031-3033)gcC>gcT	p.A1011A	AC124057.5_ENST00000433035.1_RNA|TRPM5_ENST00000533060.1_Silent_p.A1011A|TRPM5_ENST00000452833.1_Silent_p.A1013A|TRPM5_ENST00000528453.1_Silent_p.A1011A	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)		TGAAGGGCGGGGCCAGGGCGG	0.637																																					p.A1011A	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.C3033T						PASS	.						35	34	34					11																	2428434		2198	4299	6497	SO:0001819	synonymous_variant	29850	exon20			GGGCGGGGCCAGG	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.3033C>T	11.37:g.2428434G>A		101	0	0		123	70	0.569106	NM_014555		Silent	SNP	ENST00000155858.6	37	CCDS31340.1																																																																																			.	.	weak		0.637	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555		A	2428434	G	A	2428434	2	1	22	1	0	0	0	0	0	0	0	1	16604	1219	43	2		2	TRPM5	11	2428434	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	237428	2428434	132578082	2368	5269											
KCNQ1	3784	hgsc.bcm.edu	37	chr11	2683252	2683252	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttcatgagaaccaacagcttCgccgaggacctggacctgga	11	7	11	12	2	1	1	1	1	0	1	2	6	1	4	4	3	3	1	4	3	2	2	rs17215465	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:2683252C>T	ENST00000155840.5	+	11	1563	c.1455C>T	c.(1453-1455)ttC>ttT	p.F485F	KCNQ1_ENST00000335475.5_Silent_p.F358F|KCNQ1OT1_ENST00000597346.1_RNA	NM_000218.2	NP_000209.2	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 1	485					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)	CCAACAGCTTCGCCGAGGACC	0.577													C|||	78	0.0155751	0.0514	0.0029	5008	,	,		17275	0.0		0.001	False		,,,				2504	0.0072				p.F485F		Atlas-SNP	.											.	KCNQ1	60	.	0			c.C1455T						PASS	.	C	,	211,4193	128.6+/-165.4	4,203,1995	170	158	162		1455,1074	-5.4	0	11	dbSNP_125	162	7,8591	5.0+/-18.6	0,7,4292	no	coding-synonymous,coding-synonymous	KCNQ1	NM_000218.2,NM_181798.1	,	4,210,6287	TT,TC,CC		0.0814,4.7911,1.6767	,	485/677,358/550	2683252	218,12784	2202	4299	6501	SO:0001819	synonymous_variant	3784	exon11			CAGCTTCGCCGAG	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.1455C>T	11.37:g.2683252C>T		133	0	0		150	83	0.553333	NM_000218	O00347|O60607|O94787|Q14D14|Q7Z6G9|Q92960|Q9UMN8|Q9UMN9	Silent	SNP	ENST00000155840.5	37	CCDS7736.1																																																																																			C|0.983;T|0.017	0.017	strong		0.577	KCNQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027382.2	NM_000218		T	2683252	C	T	2683252	2	4	22	1	0	0	0	0	0	0	0	1	8091	883	31	1		1	KCNQ1	11	2683252	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	254818	2683252	132323264	2369	5270											
ZNF195	7748	hgsc.bcm.edu	37	chr11	3383015	3383015	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	attgaggcctggctgggcacGgtggttcacacctgtaatcc	7	10	13	11	1	1	1	1	1	0	0	2	1	2	1	3	5	0	4	3	5	1	3	rs7125523	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:3383015G>A	ENST00000399602.4	-	4	457	c.331C>T	c.(331-333)Cgt>Tgt	p.R111C	ZNF195_ENST00000354599.6_Intron|ZNF195_ENST00000526601.1_Missense_Mutation_p.R115C|ZNF195_ENST00000438262.2_Intron|ZNF195_ENST00000005082.9_Missense_Mutation_p.R111C|ZNF195_ENST00000528796.1_Intron|ZNF195_ENST00000343338.7_Intron|ZNF195_ENST00000429541.2_Intron	NM_001130520.2	NP_001123992.1	O14628	ZN195_HUMAN	zinc finger protein 195	111	Spacer.				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)		ggctgggcacggtggttcaca	0.502													g|||	110	0.0219649	0.0794	0.0072	5008	,	,		18477	0.0		0.0	False		,,,				2504	0.0				p.R115C		Atlas-SNP	.											.	ZNF195	77	.	0			c.C343T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG,,,	87,1297		0,87,605	184	176	179		331,331,343,,,	-0.4	0	11	dbSNP_116	179	4,3178		0,4,1587	yes	missense,missense,missense,intron,intron,intron	ZNF195	NM_001130519.2,NM_001130520.2,NM_001242841.1,NM_001242842.1,NM_001242843.1,NM_007152.4	180,180,180,,,	0,91,2192	AA,AG,GG		0.1257,6.2861,1.993	possibly-damaging,possibly-damaging,possibly-damaging,,,	111/607,111/630,115/611,,,	3383015	91,4475	692	1591	2283	SO:0001583	missense	7748	exon5			GGGCACGGTGGTT		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.331C>T	11.37:g.3383015G>A	ENSP00000382511:p.Arg111Cys	39	0	0		50	29	0.58	NM_001242841	A8K234|B3KTK2|B4DEL0|C9JLY9|L7MNK2|Q0VAJ6|Q658N8|Q6ZNA9	Missense_Mutation	SNP	ENST00000399602.4	37	CCDS44522.1	43	0.019688644688644688	39	0.07926829268292683	4	0.011049723756906077	0	0.0	0	0.0	g	0.950	-0.706656	0.03230	0.062861	0.001257	ENSG00000005801	ENST00000399602;ENST00000005082;ENST00000526601;ENST00000533036;ENST00000534569	T;T;T;T;T	0.14766	5.12;5.12;5.12;5.12;2.48	0.225	-0.451	0.12214	.	.	.	.	.	T	0.00271	0.0008	N	0.25992	0.78	0.09310	N	1	B;B;P	0.50710	0.0;0.0;0.938	B;B;B	0.22753	0.0;0.0;0.041	T	0.33727	-0.9857	8	0.56958	D	0.05	.	.	.	.	rs7125523	115;111;111	O14628-6;O14628-5;O14628	.;.;ZN195_HUMAN	C	111;111;115;130;115	ENSP00000382511:R111C;ENSP00000005082:R111C;ENSP00000435828:R115C;ENSP00000433911:R130C;ENSP00000437265:R115C	ENSP00000005082:R111C	R	-	1	0	ZNF195	3339591	0.001000	0.12720	0.002000	0.10522	0.002000	0.02628	-0.653000	0.05360	-1.864000	0.01148	-1.842000	0.00583	CGT	G|0.980;A|0.020	0.020	strong		0.502	ZNF195-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032321.2			A	3383015	G	A	3383015	3	1	22	1	0	0	0	0	1	0	0	0	17773	1116	39	1	1570	1	ZNF195	11	3383015	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	699763	3383015	131623501	2370	5271											
OR51F1	256892	hgsc.bcm.edu	37	chr11	4790868	4790868	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatgcagctatatagactgaTttcacgtgcctcaaaccaga	14	10	7	10	1	2	3	2	1	0	2	2	3	2	3	2	0	4	2	2	0	5	4	rs75972277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:4790868T>C	ENST00000380383.1	-	1	300	c.301A>G	c.(301-303)Atc>Gtc	p.I101V	MMP26_ENST00000477339.1_Intron|OR51F1_ENST00000343430.3_Missense_Mutation_p.I94V|MMP26_ENST00000380390.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	101						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)		TATAGACTGATTTCACGTGCC	0.428													T|||	230	0.0459265	0.1649	0.0159	5008	,	,		22485	0.0		0.001	False		,,,				2504	0.0				p.I94V		Atlas-SNP	.											.	OR51F1	60	.	0			c.A280G						PASS	.	T	VAL/ILE	655,3747	277.2+/-273.6	49,557,1595	78	75	76		280	1.3	0.2	11	dbSNP_132	76	12,8584	7.7+/-29.5	0,12,4286	yes	missense	OR51F1	NM_001004752.1	29	49,569,5881	CC,CT,TT		0.1396,14.8796,5.1316	probably-damaging	94/313	4790868	667,12331	2201	4298	6499	SO:0001583	missense	256892	exon1			GACTGATTTCACG	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.301A>G	11.37:g.4790868T>C	ENSP00000369744:p.Ile101Val	83	0	0		83	33	0.39759	NM_001004752		Missense_Mutation	SNP	ENST00000380383.1	37		96	0.04395604395604396	91	0.18495934959349594	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	t	14.41	2.525656	0.44969	0.148796	0.001396	ENSG00000188069	ENST00000343430;ENST00000380383	T;T	0.00590	6.36;6.36	4.91	1.3	0.21679	GPCR, rhodopsin-like superfamily (1);	0.114787	0.38381	N	0.001718	T	0.00012	0.0000	M	0.87097	2.86	0.24681	N	0.993366	D	0.67145	0.996	D	0.80764	0.994	T	0.45527	-0.9255	10	0.46703	T	0.11	.	8.2938	0.31973	0.0:0.2382:0.0:0.7618	.	101	A6NGY5	O51F1_HUMAN	V	94;101	ENSP00000345163:I94V;ENSP00000369744:I101V	ENSP00000345163:I94V	I	-	1	0	OR51F1	4747444	0.937000	0.31787	0.237000	0.24090	0.676000	0.39594	1.729000	0.38115	0.058000	0.16222	0.473000	0.43528	ATC	T|0.955;C|0.045	0.045	strong		0.428	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752		C	4790868	T	C	4790868	3	2	22	1	0	0	0	0	1	0	0	0	11105	1493	52	3	661	3	OR51F1	11	4790868	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1407853	4790868	130215648	2371	5272											
OR51F1	256892	hgsc.bcm.edu	37	chr11	4791012	4791012	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgatgacaaacaggatcaCgctgttcccagagagggcaa	15	6	11	9	1	1	3	1	2	0	1	2	5	2	4	1	2	1	3	1	2	3	1	rs146706676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:4791012C>T	ENST00000380383.1	-	1	156	c.157G>A	c.(157-159)Gtg>Atg	p.V53M	MMP26_ENST00000477339.1_Intron|OR51F1_ENST00000343430.3_Missense_Mutation_p.V46M|MMP26_ENST00000380390.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	53						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)		AACAGGATCACGCTGTTCCCA	0.478													C|||	4	0.000798722	0.003	0.0	5008	,	,		20537	0.0		0.0	False		,,,				2504	0.0				p.V46M		Atlas-SNP	.											.	OR51F1	60	.	0			c.G136A						PASS	.	C	MET/VAL	15,4387	22.3+/-47.3	0,15,2186	66	63	64		136	1	1	11	dbSNP_134	64	0,8596		0,0,4298	yes	missense	OR51F1	NM_001004752.1	21	0,15,6484	TT,TC,CC		0.0,0.3408,0.1154	benign	46/313	4791012	15,12983	2201	4298	6499	SO:0001583	missense	256892	exon1			GGATCACGCTGTT	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.157G>A	11.37:g.4791012C>T	ENSP00000369744:p.Val53Met	80	0	0		75	34	0.453333	NM_001004752		Missense_Mutation	SNP	ENST00000380383.1	37		.	.	.	.	.	.	.	.	.	.	C	0.094	-1.162853	0.01673	0.003408	0.0	ENSG00000188069	ENST00000343430;ENST00000380383	T;T	0.00451	7.35;7.35	4.81	1.05	0.20165	GPCR, rhodopsin-like superfamily (1);	0.193258	0.36234	N	0.002716	T	0.00109	0.0003	N	0.00595	-1.35	0.22762	N	0.998768	B	0.02656	0.0	B	0.01281	0.0	T	0.26916	-1.0089	10	0.18710	T	0.47	.	3.1994	0.06645	0.1376:0.0783:0.1435:0.6405	.	53	A6NGY5	O51F1_HUMAN	M	46;53	ENSP00000345163:V46M;ENSP00000369744:V53M	ENSP00000345163:V46M	V	-	1	0	OR51F1	4747588	0.000000	0.05858	0.993000	0.49108	0.775000	0.43874	-1.227000	0.02950	0.008000	0.14787	-0.385000	0.06624	GTG	C|0.999;T|0.001	0.001	strong		0.478	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752		T	4791012	C	T	4791012	3	4	22	1	0	0	0	0	1	0	0	0	11105	536	19	1	805	1	OR51F1	11	4791012	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	144	4791012	130215504	2372	5273											
OR51F2	119694	hgsc.bcm.edu	37	chr11	4843119	4843119	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgttgataagaaatgttgcCgtcatgttgccagtcatgct	10	14	10	7	1	2	2	2	1	0	1	2	2	2	2	2	0	3	4	2	0	2	4	rs142530902		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:4843119C>T	ENST00000322110.5	+	1	569	c.504C>T	c.(502-504)gcC>gcT	p.A168A	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004753.1	NP_001004753.1	Q8NH61	O51F2_HUMAN	olfactory receptor, family 51, subfamily F, 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)			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)		GAAATGTTGCCGTCATGTTGC	0.443																																					p.A168A		Atlas-SNP	.											.	OR51F2	72	.	0			c.C504T						PASS	.	C		2,4400	6.2+/-15.9	0,2,2199	336	287	303		504	-1.1	1	11	dbSNP_134	303	0,8596		0,0,4298	no	coding-synonymous	OR51F2	NM_001004753.1		0,2,6497	TT,TC,CC		0.0,0.0454,0.0154		168/343	4843119	2,12996	2201	4298	6499	SO:0001819	synonymous_variant	119694	exon1			TGTTGCCGTCATG	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.504C>T	11.37:g.4843119C>T		134	0	0		143	83	0.58042	NM_001004753	Q6IFI1	Silent	SNP	ENST00000322110.5	37	CCDS31361.1																																																																																			C|1.000;T|0.000	0.000	weak		0.443	OR51F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142181.1	NM_001004753		T	4843119	C	T	4843119	2	4	22	1	0	0	0	0	0	0	0	1	11106	639	23	1		1	OR51F2	11	4843119	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	52107	4843119	130163397	2373	5274											
OR51S1	119692	hgsc.bcm.edu	37	chr11	4869792	4869792	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaaataagcagggggtccAaacccatggctgaaagaacc	17	4	11	9	0	0	3	0	1	0	2	1	3	1	3	3	3	3	2	3	3	6	1	rs57238061	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:4869792A>G	ENST00000322101.2	-	1	722	c.647T>C	c.(646-648)tTg>tCg	p.L216S	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	216						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)		CAGGGGGTCCAAACCCATGGC	0.527													A|||	307	0.0613019	0.2209	0.0202	5008	,	,		18029	0.0		0.001	False		,,,				2504	0.0				p.L216S		Atlas-SNP	.											.	OR51S1	83	.	0			c.T647C						PASS	.	A	SER/LEU	791,3611	318.8+/-295.8	72,647,1482	78	82	80		647	4.1	1	11	dbSNP_129	80	11,8585	8.4+/-32.0	0,11,4287	yes	missense	OR51S1	NM_001004758.1	145	72,658,5769	GG,GA,AA		0.128,17.9691,6.1702	probably-damaging	216/324	4869792	802,12196	2201	4298	6499	SO:0001583	missense	119692	exon1			GGGTCCAAACCCA	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.647T>C	11.37:g.4869792A>G	ENSP00000322754:p.Leu216Ser	77	0	0		83	45	0.542169	NM_001004758	B9EGZ1|Q6IFI2	Missense_Mutation	SNP	ENST00000322101.2	37	CCDS31362.1	113	0.051739926739926737	105	0.21341463414634146	8	0.022099447513812154	0	0.0	0	0.0	A	16.28	3.079144	0.55753	0.179691	0.00128	ENSG00000176922	ENST00000322101	T	0.44482	0.92	5.25	4.09	0.47781	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36002	N	0.002844	T	0.00039	0.0001	L	0.43923	1.385	0.54753	P	1.799999999996249E-5	P	0.39535	0.677	B	0.39419	0.299	T	0.11567	-1.0582	9	0.51188	T	0.08	-6.8936	10.3194	0.43756	0.9202:0.0:0.0798:0.0	rs57238061;rs61746907	216	Q8NGJ8	O51S1_HUMAN	S	216	ENSP00000322754:L216S	ENSP00000322754:L216S	L	-	2	0	OR51S1	4826368	0.007000	0.16637	0.966000	0.40874	0.681000	0.39784	2.118000	0.41949	2.203000	0.70933	0.533000	0.62120	TTG	A|0.944;G|0.056	0.056	strong		0.527	OR51S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142179.1	NM_001004758		G	4869792	A	G	4869792	3	3	22	1	0	0	0	0	1	0	0	0	11114	131	5	3	327	3	OR51S1	11	4869792	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	26673	4869792	130136724	2374	5275											
OR51L1	119682	hgsc.bcm.edu	37	chr11	5020542	5020542	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcttcatccacacattcacAttcctggagtcctcagtgtt	8	15	5	13	0	4	0	3	0	1	0	7	1	7	1	3	1	0	1	3	1	0	5	rs368384016		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5020542A>T	ENST00000321543.1	+	1	330	c.330A>T	c.(328-330)acA>acT	p.T110T		NM_001004755.1	NP_001004755.1	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L, 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)			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)		ACACATTCACATTCCTGGAGT	0.502																																					p.T110T		Atlas-SNP	.											.	OR51L1	60	.	0			c.A330T						PASS	.	A		6,4396	11.4+/-27.6	0,6,2195	296	222	247		330	0	1	11		247	0,8596		0,0,4298	no	coding-synonymous	OR51L1	NM_001004755.1		0,6,6493	TT,TA,AA		0.0,0.1363,0.0462		110/316	5020542	6,12992	2201	4298	6499	SO:0001819	synonymous_variant	119682	exon1			ATTCACATTCCTG	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.330A>T	11.37:g.5020542A>T		374	0	0		423	203	0.479905	NM_001004755	Q6IFE5	Silent	SNP	ENST00000321543.1	37	CCDS31369.1																																																																																			.	.	weak		0.502	OR51L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142812.1	NM_001004755		T	5020542	A	T	5020542	2	4	22	1	0	0	0	0	0	0	0	1	11111	204	8	5		5	OR51L1	11	5020542	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	150750	5020542	129985974	2375	5276											
OR52E2	119678	hgsc.bcm.edu	37	chr11	5080523	5080523	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacaaggactgctgactccAtaagtgtgaagttgtggata	12	10	11	8	0	0	2	0	2	0	0	1	4	1	4	2	2	1	2	2	2	4	3	rs144077173	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5080523A>G	ENST00000321522.2	-	1	334	c.335T>C	c.(334-336)aTg>aCg	p.M112T		NM_001005164.2	NP_001005164.2	Q8NGJ4	O52E2_HUMAN	olfactory receptor, family 52, subfamily E, member 2	112						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)		TGCTGACTCCATAAGTGTGAA	0.468													a|||	3	0.000599042	0.0	0.0	5008	,	,		22727	0.003		0.0	False		,,,				2504	0.0				p.M112T		Atlas-SNP	.											.	OR52E2	63	.	0			c.T335C						PASS	.	G	THR/MET	3,4399	8.1+/-20.4	0,3,2198	75	71	72		335	1.4	0.7	11	dbSNP_134	72	0,8596		0,0,4298	yes	missense	OR52E2	NM_001005164.2	81	0,3,6496	GG,GA,AA		0.0,0.0682,0.0231	benign	112/326	5080523	3,12995	2201	4298	6499	SO:0001583	missense	119678	exon1			GACTCCATAAGTG	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.335T>C	11.37:g.5080523A>G	ENSP00000322088:p.Met112Thr	87	0	0		91	47	0.516484	NM_001005164		Missense_Mutation	SNP	ENST00000321522.2	37	CCDS31371.1	4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	a	2.241	-0.373782	0.05034	6.82E-4	0.0	ENSG00000176787	ENST00000321522	T	0.01613	4.73	3.77	1.43	0.22495	GPCR, rhodopsin-like superfamily (1);	0.185074	0.38111	N	0.001815	T	0.01222	0.0040	L	0.35249	1.045	0.09310	N	1	B	0.23316	0.083	B	0.25291	0.059	T	0.44697	-0.9311	10	0.54805	T	0.06	.	7.9034	0.29748	0.8183:0.0:0.1817:0.0	.	112	Q8NGJ4	O52E2_HUMAN	T	112	ENSP00000322088:M112T	ENSP00000322088:M112T	M	-	2	0	OR52E2	5037099	0.000000	0.05858	0.673000	0.29887	0.113000	0.19764	0.661000	0.25023	0.311000	0.23014	-0.259000	0.10710	ATG	A|0.999;G|0.001	0.001	strong		0.468	OR52E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142815.1	NM_001005164		G	5080523	A	G	5080523	3	3	22	1	0	0	0	0	1	0	0	0	11124	217	8	3	645	3	OR52E2	11	5080523	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	59981	5080523	129925993	2376	5277											
OR51V1	283111	hgsc.bcm.edu	37	chr11	5221132	5221132	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaaacggtgcaccattgtgaGgctaatgatagggatgtaga	14	9	13	5	1	0	3	0	2	0	1	0	4	0	4	1	3	2	3	1	3	5	4	rs61736992	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5221132G>A	ENST00000321255.1	-	1	798	c.799C>T	c.(799-801)Ctc>Ttc	p.L267F		NM_001004760.2	NP_001004760.2	Q9H2C8	O51V1_HUMAN	olfactory receptor, family 51, subfamily V, member 1	267					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)		ACCATTGTGAGGCTAATGATA	0.483													G|||	126	0.0251597	0.0378	0.0086	5008	,	,		19744	0.0		0.0189	False		,,,				2504	0.0521				p.L267F		Atlas-SNP	.											.	OR51V1	77	.	0			c.C799T						PASS	.	G	PHE/LEU	182,4220	116.3+/-154.2	1,180,2020	134	117	123		799	1.4	0	11	dbSNP_129	123	209,8387	89.4+/-151.6	4,201,4093	yes	missense	OR51V1	NM_001004760.2	22	5,381,6113	AA,AG,GG		2.4314,4.1345,3.0082	probably-damaging	267/322	5221132	391,12607	2201	4298	6499	SO:0001583	missense	283111	exon1			TTGTGAGGCTAAT	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.799C>T	11.37:g.5221132G>A	ENSP00000321729:p.Leu267Phe	117	0	0		104	58	0.557692	NM_001004760		Missense_Mutation	SNP	ENST00000321255.1	37	CCDS31375.1	32	0.014652014652014652	15	0.03048780487804878	6	0.016574585635359115	0	0.0	11	0.014511873350923483	G	10.05	1.243241	0.22796	0.041345	0.024314	ENSG00000176742	ENST00000321255	T	0.72835	-0.69	5.27	1.37	0.22104	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40144	N	0.001163	T	0.56992	0.2023	M	0.85373	2.75	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.63972	-0.6516	10	0.87932	D	0	.	8.363	0.32369	0.3867:0.0:0.6133:0.0	.	267	Q9H2C8	O51V1_HUMAN	F	267	ENSP00000321729:L267F	ENSP00000321729:L267F	L	-	1	0	OR51V1	5177708	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	-0.502000	0.06390	0.103000	0.17682	0.655000	0.94253	CTC	G|0.975;A|0.025	0.025	strong		0.483	OR51V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142965.1	NM_001004760		A	5221132	G	A	5221132	3	1	22	1	0	0	0	0	1	0	0	0	11116	1000	35	2	169	2	OR51V1	11	5221132	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	140609	5221132	129785384	2377	5278											
OR51I2	390064	hgsc.bcm.edu	37	chr11	5474894	5474894	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccagcctccatgagcccaTgtactacttcctgtccatgt	7	11	7	16	0	0	1	0	1	0	0	3	1	3	1	6	0	4	1	6	0	2	3	rs74049540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5474894T>C	ENST00000341449.2	+	1	257	c.176T>C	c.(175-177)aTg>aCg	p.M59T	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron	NM_001004754.2	NP_001004754.1	Q9H344	O51I2_HUMAN	olfactory receptor, family 51, subfamily I, member 2	59					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)		CATGAGCCCATGTACTACTTC	0.572													T|||	291	0.058107	0.2118	0.0144	5008	,	,		21590	0.0		0.001	False		,,,				2504	0.0				p.M59T		Atlas-SNP	.											.	OR51I2	76	.	0			c.T176C						PASS	.	T	THR/MET	709,3693	295.6+/-283.7	60,589,1552	109	98	102		176	5.6	1	11	dbSNP_130	102	9,8585	5.0+/-18.6	0,9,4288	yes	missense	OR51I2	NM_001004754.2	81	60,598,5840	CC,CT,TT		0.1047,16.1063,5.5248	possibly-damaging	59/313	5474894	718,12278	2201	4297	6498	SO:0001583	missense	390064	exon1			AGCCCATGTACTA	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.176T>C	11.37:g.5474894T>C	ENSP00000341987:p.Met59Thr	125	0	0		135	64	0.474074	NM_001004754	Q6IF81	Missense_Mutation	SNP	ENST00000341449.2	37	CCDS31383.1	128	0.05860805860805861	123	0.25	5	0.013812154696132596	0	0.0	0	0.0	T	13.85	2.359159	0.41801	0.161063	0.001047	ENSG00000187918	ENST00000341449	T	0.09817	2.94	5.57	5.57	0.84162	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	H	0.94771	3.58	0.25314	P	0.9891777	D	0.55800	0.973	P	0.61201	0.885	T	0.04621	-1.0938	9	0.72032	D	0.01	.	14.7065	0.69194	0.0:0.0:0.0:1.0	.	59	Q9H344	O51I2_HUMAN	T	59	ENSP00000341987:M59T	ENSP00000341987:M59T	M	+	2	0	OR51I2	5431470	1.000000	0.71417	1.000000	0.80357	0.364000	0.29643	4.672000	0.61597	2.340000	0.79590	0.528000	0.53228	ATG	T|0.937;C|0.063	0.063	strong		0.572	OR51I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143385.1	NM_001004754		C	5474894	T	C	5474894	3	2	22	1	0	0	0	0	1	0	0	0	11110	1464	51	3	178	3	OR51I2	11	5474894	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	253762	5474894	129531622	2378	5279											
OR52D1	390066	hgsc.bcm.edu	37	chr11	5510498	5510499	+	Frame_Shift_Ins	INS	-	-	C																															ctgtgagcatatgggcattgINScccgactggcctgtgccaac																								rs571241475|rs386750177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5510498_5510499insC	ENST00000322641.5	+	1	584_585	c.562_563insC	c.(562-564)gccfs	p.A188fs	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron	NM_001005163.2	NP_001005163.1	Q9H346	O52D1_HUMAN	olfactory receptor, family 52, subfamily D, member 1	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)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	22		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.46e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TATGGGCATTGCCCGACTGGCC	0.51													CCC|CCC|CCCC|insertion	9	0.00179712	0.0053	0.0029	5008	,	,		22033	0.0		0.0	False		,,,				2504	0.0				p.A188fs		Atlas-Indel	.											.	OR52D1	66	.	0			c.562_563insC						PASS	.																																			SO:0001589	frameshift_variant	390066	exon1			.	BK004276	CCDS31384.1	11p15.4	2012-08-09			ENSG00000181609	ENSG00000181609		"GPCR / Class A : Olfactory receptors"	15212	protein-coding gene	gene with protein product							Standard	NM_001005163		Approved		uc010qzg.2	Q9H346	OTTHUMG00000066895	ENST00000322641.5:c.565dupC	11.37:g.5510501_5510501dupC	ENSP00000326232:p.Ala188fs	121	0	0		134	54	0.402985	NM_001005163	B9EGY9|Q6IFI6	Frame_Shift_Ins	INS	ENST00000322641.5	37	CCDS31384.1																																																																																			.	.	none		0.51	OR52D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143372.1	NM_001005163		C	5510499	-	C	5510498	7	5	22	1	0	1	1	0	0	0	0	0	11123	1319	46	0	564	0	OR52D1	11	5510498	Frame_Shift_Ins	INS	-	TCGA-G8-6324-01A-11D-2210-10	35604	5510498	129496018	2379	5280											
OR52H1	390067	hgsc.bcm.edu	37	chr11	5566460	5566460	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcctgggaatgtgatttcGcgagcccctagccaaaagat	11	9	10	11	2	0	2	0	1	0	1	2	4	1	3	4	1	2	0	4	1	4	2	rs115541630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5566460G>A	ENST00000322653.4	-	1	319	c.294C>T	c.(292-294)cgC>cgT	p.R98R	HBG2_ENST00000380259.2_Intron	NM_001005289.1	NP_001005289.1	Q8NGJ2	O52H1_HUMAN	olfactory receptor, family 52, subfamily H, member 1	98						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)		ATGTGATTTCGCGAGCCCCTA	0.468													G|||	61	0.0121805	0.0439	0.0043	5008	,	,		22055	0.0		0.0	False		,,,				2504	0.0				p.R98R		Atlas-SNP	.											OR52H1,NS,carcinoma,0,1	OR52H1	46	1	0			c.C294T						PASS	.	G		242,4160	142.7+/-177.9	6,230,1965	73	70	71		294	-9.5	0	11	dbSNP_132	71	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous	OR52H1	NM_001005289.1		6,231,6261	AA,AG,GG		0.0116,5.4975,1.8698		98/321	5566460	243,12753	2201	4297	6498	SO:0001819	synonymous_variant	390067	exon1			GATTTCGCGAGCC	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.294C>T	11.37:g.5566460G>A		104	0	0		117	58	0.495726	NM_001005289	B9EH26|Q6IF79	Silent	SNP	ENST00000322653.4	37	CCDS31386.1																																																																																			G|0.983;A|0.017	0.017	strong		0.468	OR52H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143400.1	NM_001005289		A	5566460	G	A	5566460	2	1	22	1	0	0	0	0	0	0	0	1	11128	1074	38	1		1	OR52H1	11	5566460	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	55962	5566460	129440056	2380	5281											
TRIM22	10346	hgsc.bcm.edu	37	chr11	5719649	5719649	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcaaaagctggaggaaggTgaggtgaatgtgctggataa	13	8	16	4	0	0	2	0	2	0	0	0	5	0	5	0	5	3	3	0	5	5	1	rs78484876	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5719649T>C	ENST00000379965.3	+	4	901	c.624T>C	c.(622-624)ggT>ggC	p.G208G	TRIM5_ENST00000380027.1_Intron	NM_001199573.1|NM_006074.4	NP_001186502.1|NP_006065.2	Q8IYM9	TRI22_HUMAN	tripartite motif containing 22	208					defense response to virus (GO:0051607)|immune response (GO:0006955)|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 trimerization (GO:0070206)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			kidney(3)|large_intestine(8)|lung(9)|prostate(1)|stomach(2)	23		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;7.54e-09)|BRCA - Breast invasive adenocarcinoma(625;0.14)		TGGAGGAAGGTGAGGTGAATG	0.512													T|||	135	0.0269569	0.0825	0.0072	5008	,	,		20336	0.0		0.004	False		,,,				2504	0.0174				p.G208G	GBM(104;491 2336 5222)	Atlas-SNP	.											.	TRIM22	66	.	0			c.T624C						PASS	.	T	,	248,3932		10,228,1852	70	78	76		612,624	-3.5	0	11	dbSNP_132	76	25,8435		0,25,4205	no	coding-synonymous,coding-synonymous	TRIM22	NM_001199573.1,NM_006074.4	,	10,253,6057	CC,CT,TT		0.2955,5.933,2.1598	,	204/495,208/499	5719649	273,12367	2090	4230	6320	SO:0001819	synonymous_variant	10346	exon4			GGAAGGTGAGGTG	X82200	CCDS41612.1	11p15	2013-01-09	2011-01-25		ENSG00000132274	ENSG00000132274		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16379	protein-coding gene	gene with protein product		606559	"tripartite motif-containing 22"			11331580, 11096452	Standard	NM_006074		Approved	STAF50, GPSTAF50, RNF94	uc001mbr.3	Q8IYM9	OTTHUMG00000066904	ENST00000379965.3:c.624T>C	11.37:g.5719649T>C		217	1	0.00460829		239	116	0.485356	NM_006074	Q05CQ0|Q15521	Silent	SNP	ENST00000379965.3	37	CCDS41612.1																																																																																			T|0.990;C|0.010	0.010	strong		0.512	TRIM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143387.2	NM_006074		C	5719649	T	C	5719649	2	2	22	1	0	0	0	0	0	0	0	1	16511	1683	59	3		3	TRIM22	11	5719649	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	153189	5719649	129286867	2381	5282											
OR52L1	338751	hgsc.bcm.edu	37	chr11	6007679	6007679	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccagcaccaccattccgatgCaccctatgacccctggatgc	9	7	7	18	1	0	1	0	1	0	0	1	3	1	2	7	1	3	2	7	1	1	2	rs61742092|rs386750238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6007679C>T	ENST00000332249.4	-	1	536	c.482G>A	c.(481-483)tGc>tAc	p.C161Y		NM_001005173.2	NP_001005173.2	Q8NGH7	O52L1_HUMAN	olfactory receptor, family 52, subfamily L, member 1	161			C -> R (in dbSNP:rs4436524). {ECO:0000269|PubMed:14983052, 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)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|pancreas(1)|skin(3)|soft_tissue(1)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.98e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CATTCCGATGCACCCTATGAC	0.512													.|||	122	0.024361	0.0855	0.013	5008	,	,		23519	0.0		0.0	False		,,,				2504	0.0				p.C161Y	Melanoma(121;653 1666 10547 22796 51255)	Atlas-SNP	.											OR52L1_ENST00000332249,NS,carcinoma,-1,2	OR52L1	100	2	0			c.G482A						PASS	.	C	TYR/CYS	26,4038		3,20,2009	76	73	74		482	0.5	0	11	dbSNP_129	74	2,8378		0,2,4188	no	missense	OR52L1	NM_001005173.2	194	3,22,6197	TT,TC,CC		0.0239,0.6398,0.225	benign	161/330	6007679	28,12416	2032	4190	6222	SO:0001583	missense	338751	exon1			CCGATGCACCCTA	AB065819	CCDS44529.1	11p15.4	2012-08-09			ENSG00000183313	ENSG00000183313		"GPCR / Class A : Olfactory receptors"	14785	protein-coding gene	gene with protein product							Standard	NM_001005173		Approved		uc001mcd.2	Q8NGH7	OTTHUMG00000165374	ENST00000332249.4:c.482G>A	11.37:g.6007679C>T	ENSP00000330338:p.Cys161Tyr	164	0	0		160	70	0.4375	NM_001005173	B2RPA6|Q6IFK9	Missense_Mutation	SNP	ENST00000332249.4	37	CCDS44529.1	32	0.014652014652014652	29	0.05894308943089431	3	0.008287292817679558	0	0.0	0	0.0	C	0.004	-2.262469	0.00262	0.006398	2.39E-4	ENSG00000183313	ENST00000332249	T	0.36520	1.25	3.85	0.545	0.17190	GPCR, rhodopsin-like superfamily (1);	0.486110	0.17495	N	0.172195	T	0.01558	0.0050	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.15867	-1.0422	10	0.18276	T	0.48	.	4.1238	0.10118	0.0:0.4045:0.2702:0.3253	.	161	Q8NGH7	O52L1_HUMAN	Y	161	ENSP00000330338:C161Y	ENSP00000330338:C161Y	C	-	2	0	OR52L1	5964255	0.000000	0.05858	0.027000	0.17364	0.006000	0.05464	-3.285000	0.00526	0.235000	0.21160	0.313000	0.20887	TGC	A|0.000;C|0.988;T|0.012	0.012	strong		0.512	OR52L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383754.1	NM_001005173		T	6007679	C	T	6007679	3	4	22	1	0	0	0	0	1	0	0	0	11134	710	25	2	511	2	OR52L1	11	6007679	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	288030	6007679	128998837	2382	5283											
OR52L1	338751	hgsc.bcm.edu	37	chr11	6007992	6007992	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatggtaacattgcccactaAagcaaggaggtaaaggatgc	16	7	11	7	0	0	0	0	0	0	0	0	2	0	2	1	4	4	3	1	4	7	4	rs115266467	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6007992A>G	ENST00000332249.4	-	1	223	c.169T>C	c.(169-171)Tta>Cta	p.L57L		NM_001005173.2	NP_001005173.2	Q8NGH7	O52L1_HUMAN	olfactory receptor, family 52, subfamily L, member 1	57						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)|kidney(2)|large_intestine(6)|lung(11)|pancreas(1)|skin(3)|soft_tissue(1)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.98e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTGCCCACTAAAGCAAGGAGG	0.512													.|||	116	0.0231629	0.0809	0.013	5008	,	,		22867	0.0		0.0	False		,,,				2504	0.0				p.L57L	Melanoma(121;653 1666 10547 22796 51255)	Atlas-SNP	.											.	OR52L1	100	.	0			c.T169C						PASS	.	G		204,3818		9,186,1816	75	75	75		169	0.5	0.9	11	dbSNP_132	75	6,8360		0,6,4177	no	coding-synonymous	OR52L1	NM_001005173.2		9,192,5993	GG,GA,AA		0.0717,5.0721,1.6952		57/330	6007992	210,12178	2011	4183	6194	SO:0001819	synonymous_variant	338751	exon1			CCACTAAAGCAAG	AB065819	CCDS44529.1	11p15.4	2012-08-09			ENSG00000183313	ENSG00000183313		"GPCR / Class A : Olfactory receptors"	14785	protein-coding gene	gene with protein product							Standard	NM_001005173		Approved		uc001mcd.2	Q8NGH7	OTTHUMG00000165374	ENST00000332249.4:c.169T>C	11.37:g.6007992A>G		135	0	0		163	74	0.453988	NM_001005173	B2RPA6|Q6IFK9	Silent	SNP	ENST00000332249.4	37	CCDS44529.1																																																																																			A|0.989;G|0.011	0.011	strong		0.512	OR52L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383754.1	NM_001005173		G	6007992	A	G	6007992	2	3	22	1	0	0	0	0	0	0	0	1	11134	11	1	3		3	OR52L1	11	6007992	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	313	6007992	128998524	2383	5284											
NLRP14	338323	hgsc.bcm.edu	37	chr11	7064271	7064271	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaggatgcaagagaggagtaTatttaccagttttttgaaga	14	12	12	3	0	0	3	0	1	0	2	0	7	0	5	1	2	2	3	1	2	5	7	rs116753166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:7064271T>C	ENST00000299481.4	+	4	1360	c.1014T>C	c.(1012-1014)taT>taC	p.Y338Y		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	338	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)		GAGAGGAGTATATTTACCAGT	0.398													T|||	87	0.0173722	0.0613	0.0072	5008	,	,		22160	0.0		0.001	False		,,,				2504	0.0				p.Y338Y		Atlas-SNP	.											.	NLRP14	187	.	0			c.T1014C						PASS	.	T		260,4142	146.9+/-181.5	14,232,1955	100	105	103		1014	2.2	0.4	11	dbSNP_132	103	1,8591	1.2+/-3.3	0,1,4295	no	coding-synonymous	NLRP14	NM_176822.3		14,233,6250	CC,CT,TT		0.0116,5.9064,2.0086		338/1094	7064271	261,12733	2201	4296	6497	SO:0001819	synonymous_variant	338323	exon4			GGAGTATATTTAC	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.1014T>C	11.37:g.7064271T>C		127	0	0		166	82	0.493976	NM_176822	Q7RTR6	Silent	SNP	ENST00000299481.4	37	CCDS7776.1																																																																																			T|0.983;C|0.017	0.017	strong		0.398	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822		C	7064271	T	C	7064271	2	2	22	1	0	0	0	0	0	0	0	1	10485	1413	49	3		3	NLRP14	11	7064271	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1056279	7064271	127942245	2384	5285											
PPFIBP2	8495	hgsc.bcm.edu	37	chr11	7673029	7673029	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaggagaagcgagagaaaaTggcctcaccagcttacacac	16	4	10	11	1	1	2	1	0	0	2	1	5	1	2	2	2	3	1	2	2	4	1	rs77873429	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:7673029T>C	ENST00000299492.4	+	23	2778	c.2390T>C	c.(2389-2391)aTg>aCg	p.M797T	PPFIBP2_ENST00000530582.1_3'UTR|PPFIBP2_ENST00000533792.1_Missense_Mutation_p.M639T|PPFIBP2_ENST00000530181.1_Missense_Mutation_p.M654T|PPFIBP2_ENST00000528883.1_Missense_Mutation_p.M685T	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	797					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)		CGAGAGAAAATGGCCTCACCA	0.597													T|||	471	0.0940495	0.2708	0.0476	5008	,	,		19476	0.0149		0.004	False		,,,				2504	0.0624				p.M797T		Atlas-SNP	.											.	PPFIBP2	87	.	0			c.T2390C						PASS	.	T	THR/MET	1144,3258	408.0+/-334.4	146,852,1203	134	129	130		2390	5.8	1	11	dbSNP_131	130	40,8552	27.4+/-76.7	0,40,4256	yes	missense	PPFIBP2	NM_003621.2	81	146,892,5459	CC,CT,TT		0.4655,25.9882,9.1119	benign	797/877	7673029	1184,11810	2201	4296	6497	SO:0001583	missense	8495	exon23			AGAAAATGGCCTC	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.2390T>C	11.37:g.7673029T>C	ENSP00000299492:p.Met797Thr	67	0	0		59	17	0.288136	NM_003621	B7Z433|E9PK77|O75337|Q8WW26	Missense_Mutation	SNP	ENST00000299492.4	37	CCDS31419.1	160	0.07326007326007326	129	0.2621951219512195	15	0.04143646408839779	13	0.022727272727272728	3	0.00395778364116095	T	7.418	0.636121	0.14386	0.259882	0.004655	ENSG00000166387	ENST00000299492;ENST00000537211;ENST00000533792;ENST00000541115;ENST00000528883;ENST00000530181	T;T;T;T	0.29655	1.98;1.57;1.98;1.56	5.77	5.77	0.91146	.	0.127954	0.53938	D	0.000047	T	0.00012	0.0000	L	0.38531	1.155	0.25772	P	0.984823	B;B;B;B;B;B	0.06786	0.0;0.0;0.0;0.001;0.0;0.0	B;B;B;B;B;B	0.06405	0.001;0.001;0.002;0.001;0.002;0.001	T	0.31861	-0.9928	9	0.18276	T	0.48	-17.2519	14.3292	0.66541	0.0:0.0:0.0:1.0	.	685;685;720;639;654;797	E9PK77;B7Z433;F5GWB0;E9PP16;E9PMU1;Q8ND30	.;.;.;.;.;LIPB2_HUMAN	T	797;138;639;720;685;654	ENSP00000299492:M797T;ENSP00000436498:M639T;ENSP00000435469:M685T;ENSP00000437321:M654T	ENSP00000299492:M797T	M	+	2	0	PPFIBP2	7629605	1.000000	0.71417	0.994000	0.49952	0.142000	0.21351	2.644000	0.46613	2.326000	0.78906	0.533000	0.62120	ATG	T|0.914;C|0.086	0.086	strong		0.597	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621		C	7673029	T	C	7673029	3	2	22	1	0	0	0	0	1	0	0	0	12323	1464	51	3	2476	3	PPFIBP2	11	7673029	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	608758	7673029	127333487	2385	5286											
PPFIBP2	8495	hgsc.bcm.edu	37	chr11	7673049	7673049	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tggcctcaccagcttacacaCcactgaccaccacagccaaa	13	5	5	18	0	1	1	1	1	0	0	1	1	1	1	6	1	3	1	6	1	2	1	rs77975665	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:7673049C>G	ENST00000299492.4	+	23	2798	c.2410C>G	c.(2410-2412)Cca>Gca	p.P804A	PPFIBP2_ENST00000530582.1_3'UTR|PPFIBP2_ENST00000533792.1_Missense_Mutation_p.P646A|PPFIBP2_ENST00000530181.1_Missense_Mutation_p.P661A|PPFIBP2_ENST00000528883.1_Missense_Mutation_p.P692A	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	804					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)		AGCTTACACACCACTGACCAC	0.612													C|||	445	0.0888578	0.2542	0.0418	5008	,	,		19239	0.0149		0.004	False		,,,				2504	0.0624				p.P804A		Atlas-SNP	.											.	PPFIBP2	87	.	0			c.C2410G						PASS	.	C	ALA/PRO	1038,3364	381.8+/-324.2	119,800,1282	117	116	117		2410	4.8	1	11	dbSNP_132	117	38,8554	26.3+/-74.7	0,38,4258	yes	missense	PPFIBP2	NM_003621.2	27	119,838,5540	GG,GC,CC		0.4423,23.5802,8.2807	probably-damaging	804/877	7673049	1076,11918	2201	4296	6497	SO:0001583	missense	8495	exon23			TACACACCACTGA	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.2410C>G	11.37:g.7673049C>G	ENSP00000299492:p.Pro804Ala	53	0	0		46	13	0.282609	NM_003621	B7Z433|E9PK77|O75337|Q8WW26	Missense_Mutation	SNP	ENST00000299492.4	37	CCDS31419.1	146|146	0.06684981684981685|0.06684981684981685	118|118	0.23983739837398374|0.23983739837398374	12|12	0.03314917127071823|0.03314917127071823	13|13	0.022727272727272728|0.022727272727272728	3|3	0.00395778364116095|0.00395778364116095	C|C	9.478|9.478	1.097421|1.097421	0.20552|0.20552	0.235802|0.235802	0.004423|0.004423	ENSG00000166387|ENSG00000166387	ENST00000299492;ENST00000537211;ENST00000533792;ENST00000541115;ENST00000528883;ENST00000530181|ENST00000534552	T;T;T;T|.	0.36157|.	1.7;1.28;1.68;1.27|.	5.77|5.77	4.84|4.84	0.62591|0.62591	.|.	0.078622|.	0.53938|.	N|.	0.000047|.	T|T	0.00073|0.00073	0.0002|0.0002	M|M	0.76574|0.76574	2.34|2.34	0.09310|0.09310	P|P	0.99999648842|0.99999648842	B;B;P;B;B;B|.	0.36768|.	0.231;0.009;0.569;0.009;0.009;0.231|.	B;B;B;B;B;B|.	0.37480|.	0.128;0.016;0.251;0.01;0.016;0.08|.	T|T	0.00191|0.00191	-1.1936|-1.1936	9|5	0.15499|0.41790	T|T	0.54|0.15	-9.5207|-9.5207	15.0756|15.0756	0.72074|0.72074	0.0:0.846:0.154:0.0|0.0:0.846:0.154:0.0	.|.	692;692;727;646;661;804|.	E9PK77;B7Z433;F5GWB0;E9PP16;E9PMU1;Q8ND30|.	.;.;.;.;.;LIPB2_HUMAN|.	A|S	804;145;646;727;692;661|35	ENSP00000299492:P804A;ENSP00000436498:P646A;ENSP00000435469:P692A;ENSP00000437321:P661A|.	ENSP00000299492:P804A|ENSP00000436489:T35S	P|T	+|+	1|2	0|0	PPFIBP2|PPFIBP2	7629625|7629625	0.998000|0.998000	0.40836|0.40836	0.987000|0.987000	0.45799|0.45799	0.905000|0.905000	0.53344|0.53344	4.020000|4.020000	0.57189|0.57189	1.525000|1.525000	0.49052|0.49052	0.655000|0.655000	0.94253|0.94253	CCA|ACC	C|0.922;G|0.078	0.078	strong		0.612	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621		G	7673049	C	G	7673049	3	3	22	1	0	0	0	0	1	0	0	0	12323	507	18	4	2496	4	PPFIBP2	11	7673049	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	20	7673049	127333467	2386	5287											
C11orf16	56673	hgsc.bcm.edu	37	chr11	8942889	8942890	+	Frame_Shift_Del	DEL	AT	AT	-																															ggaattcttgttccactgacAtattgcaaggctctgactcc																								rs398102297|rs10583719	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:8942889_8942890delAT	ENST00000326053.5	-	6	1483_1484	c.1377_1378delAT	c.(1375-1380)atatgtfs	p.IC459fs	C11orf16_ENST00000525780.1_Intron	NM_020643.2	NP_065694.2	Q9NQ32	CK016_HUMAN	chromosome 11 open reading frame 16	459										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)		TTCCACTGACATATTGCAAGGC	0.54														164	0.0327476	0.1135	0.0173	5008	,	,		18882	0.0		0.002	False		,,,				2504	0.0				p.460_460del		Pindel,Atlas-Indel	.											.	C11orf16	43	.	0			c.1378_1379del						PASS	.			445,3819		22,401,1709						-1.1	0		dbSNP_119	130	6,8248		0,6,4121	no	frameshift	C11orf16	NM_020643.2		22,407,5830	A1A1,A1R,RR		0.0727,10.4362,3.6028				451,12067				SO:0001589	frameshift_variant	56673	exon6			.	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.1377_1378delAT	11.37:g.8942891_8942892delAT	ENSP00000318999:p.Ile459fs	174	0	.		179	52	0.291	NM_020643	Q53FB2|Q8N6Y9	Frame_Shift_Del	DEL	ENST00000326053.5	37	CCDS7794.1																																																																																			AT|0.978;-|0.022	0.022	strong		0.54	C11orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385626.1	NM_020643		-	8942890	AT	-	8942889	7	5	22	1	0	1	0	1	0	0	0	0	1633	217	8	0	29	0	C11orf16	11	8942889	Frame_Shift_Del	DEL	AT	TCGA-G8-6324-01A-11D-2210-10	1269840	8942889	126063627	2387	5288											
DENND5A	23258	hgsc.bcm.edu	37	chr11	9286515	9286515	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggcgcgcactcacccgacagCtcgtccggctccagcccggt	5	5	12	19	6	1	0	1	0	0	0	4	1	3	0	4	3	2	3	4	3	0	0	rs75717840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:9286515C>T	ENST00000328194.3	-	1	422	c.102G>A	c.(100-102)gaG>gaA	p.E34E	DENND5A_ENST00000530044.1_Silent_p.E34E	NM_001243254.1|NM_015213.3	NP_001230183.1|NP_056028.2	Q6IQ26	DEN5A_HUMAN	DENN/MADD domain containing 5A	34					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						CACCCGACAGCTCGTCCGGCT	0.711													C|||	104	0.0207668	0.0772	0.0029	5008	,	,		8908	0.0		0.0	False		,,,				2504	0.0				p.E34E		Atlas-SNP	.											.	DENND5A	84	.	0			c.G102A						PASS	.	C		216,3890		5,206,1842	6	7	6		102	1.3	0.2	11	dbSNP_132	6	4,8126		0,4,4061	no	coding-synonymous	DENND5A	NM_015213.3		5,210,5903	TT,TC,CC		0.0492,5.2606,1.798		34/1288	9286515	220,12016	2053	4065	6118	SO:0001819	synonymous_variant	23258	exon1			CGACAGCTCGTCC	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.102G>A	11.37:g.9286515C>T		15	0	0		42	25	0.595238	NM_015213	B4DJ15|E9PS91|Q96GN3|Q9H6U7|Q9UFV0|Q9UPR1	Silent	SNP	ENST00000328194.3	37	CCDS31423.1																																																																																			C|0.980;T|0.020	0.020	strong		0.711	DENND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385910.2	NM_015213		T	9286515	C	T	9286515	2	4	22	1	0	0	0	0	0	0	0	1	4438	796	28	2		2	DENND5A	11	9286515	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	343626	9286515	125720001	2388	5289											
TMEM41B	440026	hgsc.bcm.edu	37	chr11	9305136	9305136	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctacaaaagaaggaggtgcGacacctgaaataaaatataa	20	6	9	6	1	0	2	0	1	0	1	0	4	0	3	1	2	2	1	1	2	9	4	rs77349011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:9305136G>A	ENST00000528080.1	-	7	1049	c.711C>T	c.(709-711)gtC>gtT	p.V237V	TMEM41B_ENST00000527813.1_Missense_Mutation_p.S191L	NM_015012.3	NP_055827.1	Q5BJD5	TM41B_HUMAN	transmembrane protein 41B	237					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(1)|prostate(1)|urinary_tract(2)	7				all cancers(16;9.96e-08)|Epithelial(150;4.89e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0972)		AAGGAGGTGCGACACCTGAAA	0.333													G|||	356	0.0710863	0.2557	0.0231	5008	,	,		14041	0.0		0.002	False		,,,				2504	0.0				p.V237V		Atlas-SNP	.											TMEM41B,NS,haematopoietic_neoplasm,0,1	TMEM41B	22	1	0			c.C711T						PASS	.	G		876,3526	335.5+/-303.9	87,702,1412	45	43	44		711	0.6	1	11	dbSNP_131	44	9,8583	7.1+/-27.0	0,9,4287	no	coding-synonymous	TMEM41B	NM_015012.3		87,711,5699	AA,AG,GG		0.1047,19.9,6.8108		237/292	9305136	885,12109	2201	4296	6497	SO:0001819	synonymous_variant	440026	exon7			AGGTGCGACACCT	D26067	CCDS31424.1, CCDS53600.1	11p15.3	2008-02-05			ENSG00000166471	ENSG00000166471			28948	protein-coding gene	gene with protein product						7584026, 7584028	Standard	NM_015012		Approved	KIAA0033	uc001mhn.2	Q5BJD5	OTTHUMG00000165719	ENST00000528080.1:c.711C>T	11.37:g.9305136G>A		58	0	0		33	33	1	NM_015012	D3DQU9|E9PP29|Q15055|Q4G0P0	Silent	SNP	ENST00000528080.1	37	CCDS31424.1	109	0.04990842490842491	102	0.2073170731707317	7	0.019337016574585635	0	0.0	0	0.0	G	11.73	1.724415	0.30593	0.199	0.001047	ENSG00000166471	ENST00000527813	.	.	.	5.55	0.652	0.17823	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.17137	-1.0379	4	0.59425	D	0.04	-12.5515	1.822	0.03112	0.415:0.2125:0.2657:0.1069	.	.	.	.	L	191	.	ENSP00000435685:S191L	S	-	2	0	TMEM41B	9261712	0.806000	0.28996	0.997000	0.53966	0.830000	0.47004	0.020000	0.13466	-0.132000	0.11557	-1.004000	0.02495	TCG	G|0.941;A|0.059	0.059	strong		0.333	TMEM41B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385940.2			A	9305136	G	A	9305136	2	1	22	1	0	0	0	0	0	0	0	1	16180	1045	37	1		1	TMEM41B	11	9305136	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	18621	9305136	125701380	2389	5290											
IPO7	10527	hgsc.bcm.edu	37	chr11	9456506	9456506	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgcccctccttcataattaTgtaacagttgatacagacac	13	12	5	11	0	1	2	1	1	0	1	2	2	2	2	3	0	3	2	3	0	4	6	rs148344816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:9456506T>C	ENST00000379719.3	+	19	2242	c.2100T>C	c.(2098-2100)taT>taC	p.Y700Y	CTD-2371O3.2_ENST00000531111.1_RNA	NM_006391.2	NP_006382.1	O95373	IPO7_HUMAN	importin 7	700					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)		TTCATAATTATGTAACAGTTG	0.308													T|||	6	0.00119808	0.0045	0.0	5008	,	,		19628	0.0		0.0	False		,,,				2504	0.0				p.Y700Y		Atlas-SNP	.											.	IPO7	72	.	0			c.T2100C						PASS	.	T		23,4379	29.9+/-59.1	0,23,2178	119	115	116		2100	3.3	1	11	dbSNP_134	116	0,8588		0,0,4294	no	coding-synonymous	IPO7	NM_006391.2		0,23,6472	CC,CT,TT		0.0,0.5225,0.1771		700/1039	9456506	23,12967	2201	4294	6495	SO:0001819	synonymous_variant	10527	exon19			TAATTATGTAACA	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.2100T>C	11.37:g.9456506T>C		102	0	0		89	55	0.617977	NM_006391	A6NNM5|B2R786|Q1RMF7|Q9H177|Q9NTE3	Silent	SNP	ENST00000379719.3	37	CCDS31425.1																																																																																			T|0.998;C|0.002	0.002	strong		0.308	IPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386022.1	NM_006391		C	9456506	T	C	9456506	2	2	22	1	0	0	0	0	0	0	0	1	7806	1471	51	3		3	IPO7	11	9456506	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	151370	9456506	125550010	2390	5291											
AMPD3	272	hgsc.bcm.edu	37	chr11	10526179	10526179	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgtgagatcgccaggaacagCgtgctgcagagcggcctctc	8	7	14	12	3	1	2	0	1	1	2	3	4	1	3	2	2	5	2	2	2	1	0	rs375685508		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:10526179C>T	ENST00000396554.3	+	14	2468	c.2127C>T	c.(2125-2127)agC>agT	p.S709S	AMPD3_ENST00000444303.2_Silent_p.S541S|AMPD3_ENST00000530864.1_3'UTR	NM_000480.2	NP_000471.1	Q01432	AMPD3_HUMAN	adenosine monophosphate deaminase 3	700					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)		CCAGGAACAGCGTGCTGCAGA	0.587																																					p.S709S		Atlas-SNP	.											.	AMPD3	68	.	0			c.C2127T						PASS	.	C	,,,,	0,4402		0,0,2201	177	141	154		2127,2100,2121,2100,1623	-9.7	0.5	11		154	1,8587	1.2+/-3.3	0,1,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AMPD3	NM_000480.2,NM_001025389.1,NM_001025390.1,NM_001172430.1,NM_001172431.1	,,,,	0,1,6494	TT,TC,CC		0.0116,0.0,0.0077	,,,,	709/777,700/768,707/775,700/768,541/609	10526179	1,12989	2201	4294	6495	SO:0001819	synonymous_variant	272	exon14			GAACAGCGTGCTG	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.2127C>T	11.37:g.10526179C>T		98	0	0		120	43	0.358333	NM_000480	A0AUX0|B7Z2S2|B7Z763|B7Z877	Silent	SNP	ENST00000396554.3	37	CCDS7802.1																																																																																			.	.	weak		0.587	AMPD3-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385783.2	NM_000480		T	10526179	C	T	10526179	2	4	22	1	0	0	0	0	0	0	0	1	587	767	27	1		1	AMPD3	11	10526179	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1069673	10526179	124480337	2391	5292											
EIF4G2	1982	hgsc.bcm.edu	37	chr11	10821185	10821185	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	catttatatatggtttgaggGgatggatccaactttatttg	10	17	10	4	0	0	1	0	1	0	0	1	3	1	3	1	4	1	1	1	4	5	8	rs11542384	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:10821185G>A	ENST00000526148.1	-	19	2748	c.2238C>T	c.(2236-2238)tcC>tcT	p.S746S	EIF4G2_ENST00000339995.5_Silent_p.S746S|EIF4G2_ENST00000396525.2_Silent_p.S708S|SNORD97_ENST00000459187.1_RNA|RP11-685M7.5_ENST00000532365.1_RNA|EIF4G2_ENST00000525681.1_Silent_p.S746S	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)		TGGTTTGAGGGGATGGATCCA	0.378													G|||	614	0.122604	0.4342	0.0504	5008	,	,		20172	0.0		0.005	False		,,,				2504	0.0				p.S746S		Atlas-SNP	.											.	EIF4G2	89	.	0			c.C2238T						PASS	.	G	,,	1686,2716	512.4+/-368.1	337,1012,852	148	145	146		2124,2238,2238	4.6	1	11	dbSNP_120	146	27,8561	17.3+/-56.4	0,27,4267	no	coding-synonymous,coding-synonymous,coding-synonymous	EIF4G2	NM_001042559.2,NM_001172705.1,NM_001418.3	,,	337,1039,5119	AA,AG,GG		0.3144,38.3008,13.1871	,,	708/870,746/908,746/908	10821185	1713,11277	2201	4294	6495	SO:0001819	synonymous_variant	1982	exon19			TTGAGGGGATGGA	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.2238C>T	11.37:g.10821185G>A		191	0	0		198	86	0.434343	NM_001172705		Silent	SNP	ENST00000526148.1	37	CCDS31428.1																																																																																			T|0.000;G|0.885;C|0.000;A|0.115	0.115	strong		0.378	EIF4G2-006	KNOWN	alternative_5_UTR|non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386603.1	NM_001418		A	10821185	G	A	10821185	2	1	22	1	0	0	0	0	0	0	0	1	5039	1219	43	2		2	EIF4G2	11	10821185	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	295006	10821185	124185331	2392	5293											
DKK3	27122	hgsc.bcm.edu	37	chr11	12023868	12023868	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtgaatttctcggtgcacAtggatggtattatttccaac	9	16	9	7	1	1	1	0	1	1	0	3	2	2	2	1	3	2	2	1	3	4	5	rs79628149	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:12023868A>G	ENST00000396505.2	-	3	568	c.330T>C	c.(328-330)caT>caC	p.H110H	DKK3_ENST00000525493.1_Silent_p.H110H|DKK3_ENST00000450094.2_Silent_p.H110H|DKK3_ENST00000527132.1_Intron|DKK3_ENST00000326932.4_Silent_p.H110H	NM_015881.5	NP_056965.3	Q9UBP4	DKK3_HUMAN	dickkopf WNT signaling pathway inhibitor 3	110					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)		CTCGGTGCACATGGATGGTAT	0.433													A|||	45	0.00898562	0.028	0.0101	5008	,	,		18698	0.0		0.001	False		,,,				2504	0.0				p.H110H		Atlas-SNP	.											.	DKK3	35	.	0			c.T330C						PASS	.	A	,,	109,4293	86.3+/-125.0	0,109,2092	308	260	276		330,330,330	-11.1	0.1	11	dbSNP_132	276	0,8588		0,0,4294	no	coding-synonymous,coding-synonymous,coding-synonymous	DKK3	NM_001018057.1,NM_013253.4,NM_015881.5	,,	0,109,6386	GG,GA,AA		0.0,2.4761,0.8391	,,	110/351,110/351,110/351	12023868	109,12881	2201	4294	6495	SO:0001819	synonymous_variant	27122	exon2			GTGCACATGGATG	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.330T>C	11.37:g.12023868A>G		362	1	0.00276243		361	164	0.454294	NM_001018057	A8K1I2|D3DQW1|Q9ULB7	Silent	SNP	ENST00000396505.2	37	CCDS7808.1																																																																																			A|0.991;G|0.009	0.009	strong		0.433	DKK3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385863.1	NM_013253		G	12023868	A	G	12023868	2	3	22	1	0	0	0	0	0	0	0	1	4548	214	8	3		3	DKK3	11	12023868	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1202683	12023868	122982648	2393	5294											
USH1C	10083	hgsc.bcm.edu	37	chr11	17531057	17531057	+	Intron	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagcgccgagggcagtgggCgggtgggagtgaggtcttgg	5	6	22	8	3	1	1	0	1	1	0	1	3	1	2	2	6	1	1	2	6	0	1	rs139996942	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:17531057C>A	ENST00000318024.4	-	16	1393				USH1C_ENST00000527020.1_Intron|USH1C_ENST00000529563.1_Intron|USH1C_ENST00000005226.7_Missense_Mutation_p.R620L|USH1C_ENST00000527720.1_Intron	NM_005709.3	NP_005700.2	Q9Y6N9	USH1C_HUMAN	Usher syndrome 1C (autosomal recessive, severe)						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						GGGCAGTGGGCGGGTGGGAGT	0.637													C|||	55	0.0109824	0.0401	0.0029	5008	,	,		9520	0.0		0.0	False		,,,				2504	0.0				p.R620L		Atlas-SNP	.											USH1C,NS,carcinoma,-1,2	USH1C	157	2	0			c.G1859T	GRCh37	CM024263	ush1cpst	M	rs139996942	scavenged	.	C	,LEU/ARG	139,4261	97.6+/-136.3	3,133,2064	46	46	46		,1859	5.9	1	11	dbSNP_134	46	1,8585	1.2+/-3.3	0,1,4292	yes	intron,missense	USH1C	NM_005709.3,NM_153676.3	,102	3,134,6356	AA,AC,CC		0.0116,3.1591,1.0781	,benign	,620/900	17531057	140,12846	2200	4293	6493	SO:0001627	intron_variant	10083	exon18			AGTGGGCGGGTGG	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.1285-7530G>T	11.37:g.17531057C>A		100	1	0.01		124	64	0.516129	NM_153676	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Missense_Mutation	SNP	ENST00000318024.4	37	CCDS31438.1	23	0.010531135531135532	21	0.042682926829268296	2	0.0055248618784530384	0	0.0	0	0.0	C	15.92	2.975208	0.53720	0.031591	1.16E-4	ENSG00000006611	ENST00000005226	T	0.37411	1.2	5.93	5.93	0.95920	.	0.378995	0.24557	N	0.037515	T	0.10165	0.0249	.	.	.	0.27896	N	0.93916	D	0.54207	0.965	B	0.44224	0.444	T	0.22277	-1.0221	9	0.66056	D	0.02	.	11.2233	0.48869	0.0:0.9172:0.0:0.0828	.	620	Q7RTU8	.	L	620	ENSP00000005226:R620L	ENSP00000005226:R620L	R	-	2	0	USH1C	17487633	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.046000	0.30354	2.814000	0.96858	0.591000	0.81541	CGC	C|0.988;A|0.012	0.012	strong		0.637	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709		A	17531057	C	A	17531057	1	1	22	0	1	0	0	0	0	0	0	0	17049	768	27	4		4	USH1C	11	17531057	Intron	SNP	C	TCGA-G8-6324-01A-11D-2210-10	5507189	17531057	117475459	2394	5295											
MRGPRX3	117195	hgsc.bcm.edu	37	chr11	18159406	18159406	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	aggctgtacgtgaccatcctCctcacagtgctggtcttcct	6	12	9	14	1	2	1	1	1	1	0	5	1	5	1	4	2	2	3	4	2	1	2	rs28628238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:18159406C>G	ENST00000396275.2	+	3	1018	c.657C>G	c.(655-657)ctC>ctG	p.L219L		NM_054031.3	NP_473372.3	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3	219						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						TGACCATCCTCCTCACAGTGC	0.542													.|||	273	0.0545128	0.1952	0.0216	5008	,	,		20315	0.0		0.0	False		,,,				2504	0.0				p.L219L		Atlas-SNP	.											.	MRGPRX3	59	.	0			c.C657G						PASS	.	G		816,3584	748.0+/-411.9	83,650,1467	113	107	109		657	1.3	0.3	11	dbSNP_125	109	5,8581	818.5+/-406.9	0,5,4288	no	coding-synonymous	MRGPRX3	NM_054031.3		83,655,5755	GG,GC,CC		0.0582,18.5455,6.3222		219/323	18159406	821,12165	2200	4293	6493	SO:0001819	synonymous_variant	117195	exon3			CATCCTCCTCACA		CCDS7830.1	11p15.1	2013-10-10			ENSG00000179826	ENSG00000179826		"GPCR / Class A : Orphans"	17980	protein-coding gene	gene with protein product		607229				11551509	Standard	NM_054031		Approved	MRGX3	uc001mnu.3	Q96LB0	OTTHUMG00000166435	ENST00000396275.2:c.657C>G	11.37:g.18159406C>G		123	0	0		138	137	0.992754	NM_054031	B0M0L1|Q8TDE0|Q8TDE1	Silent	SNP	ENST00000396275.2	37	CCDS7830.1																																																																																			C|0.948;G|0.052	0.052	strong		0.542	MRGPRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389767.1	NM_054031		G	18159406	C	G	18159406	2	3	22	1	0	0	0	0	0	0	0	1	9777	842	30	4		4	MRGPRX3	11	18159406	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	628349	18159406	116847110	2395	5296											
HPS5	11234	hgsc.bcm.edu	37	chr11	18330522	18330522	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcacacaagaaggatcgagtAagtgaagatataagtagcct	17	8	10	6	1	1	3	1	1	0	2	2	5	1	4	1	1	1	2	1	1	7	4	rs146455658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:18330522A>G	ENST00000349215.3	-	6	859	c.582T>C	c.(580-582)ctT>ctC	p.L194L	HPS5_ENST00000438420.2_Silent_p.L80L|HPS5_ENST00000531848.1_Silent_p.L80L|HPS5_ENST00000396253.3_Silent_p.L80L	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	194					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						AGGATCGAGTAAGTGAAGATA	0.388									Hermansky-Pudlak syndrome				A|||	2	0.000399361	0.0008	0.0014	5008	,	,		16667	0.0		0.0	False		,,,				2504	0.0				p.L194L		Atlas-SNP	.											.	HPS5	70	.	0			c.T582C						PASS	.	A	,,	15,4383	22.3+/-47.3	0,15,2184	136	118	124		240,582,240	0.2	1	11	dbSNP_134	124	0,8586		0,0,4293	no	coding-synonymous,coding-synonymous,coding-synonymous	HPS5	NM_007216.3,NM_181507.1,NM_181508.1	,,	0,15,6477	GG,GA,AA		0.0,0.3411,0.1155	,,	80/1016,194/1130,80/1016	18330522	15,12969	2199	4293	6492	SO:0001819	synonymous_variant	11234	exon6	Familial Cancer Database	HPS, HPS1-8	TCGAGTAAGTGAA	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.582T>C	11.37:g.18330522A>G		97	0	0		88	40	0.454545	NM_181507	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Silent	SNP	ENST00000349215.3	37	CCDS7836.1																																																																																			A|0.999;G|0.001	0.001	strong		0.388	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1	NM_181507		G	18330522	A	G	18330522	2	3	22	1	0	0	0	0	0	0	0	1	7351	349	13	3		3	HPS5	11	18330522	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	171116	18330522	116675994	2396	5297											
IGSF22	283284	hgsc.bcm.edu	37	chr11	18731905	18731905	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggccactactgagctggaTggcacactgggctgtccagg	7	9	14	11	0	0	1	0	1	0	0	1	2	1	2	2	5	2	3	2	5	1	2	rs114511413	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:18731905T>A	ENST00000513874.1	-	17	2809	c.2670A>T	c.(2668-2670)ccA>ccT	p.P890P	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	888	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.									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						CTGAGCTGGATGGCACACTGG	0.493													T|||	67	0.0133786	0.0484	0.0043	5008	,	,		20918	0.0		0.0	False		,,,				2504	0.0				p.P890P		Atlas-SNP	.											.	IGSF22	211	.	0			c.A2670T						PASS	.	T		123,3791		3,117,1837	119	119	119		2670	-0.4	0.2	11	dbSNP_132	119	3,8295		0,3,4146	no	coding-synonymous	IGSF22	NM_173588.3		3,120,5983	AA,AT,TT		0.0362,3.1426,1.0318		890/1327	18731905	126,12086	1957	4149	6106	SO:0001819	synonymous_variant	283284	exon17			GCTGGATGGCACA	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.2670A>T	11.37:g.18731905T>A		133	0	0		110	53	0.481818	NM_173588	A6NNA0|D6RGV7	Silent	SNP	ENST00000513874.1	37	CCDS41625.2																																																																																			T|0.991;A|0.009	0.009	strong		0.493	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588		A	18731905	T	A	18731905	2	1	22	1	0	0	0	0	0	0	0	1	7609	1451	51	5		5	IGSF22	11	18731905	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	401383	18731905	116274611	2397	5298											
IGSF22	283284	hgsc.bcm.edu	37	chr11	18735480	18735480	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gatgaggccgctgtcttcacGcacacagttggagatggtga	9	9	14	9	2	2	3	1	2	1	1	2	5	2	3	1	3	0	3	1	3	0	2	rs111397851	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:18735480G>A	ENST00000513874.1	-	14	2153	c.2014C>T	c.(2014-2016)Cgt>Tgt	p.R672C	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	672	Ig-like 4.									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						CTGTCTTCACGCACACAGTTG	0.602													g|||	236	0.0471246	0.1415	0.0317	5008	,	,		23327	0.0		0.0258	False		,,,				2504	0.001				p.R672C		Atlas-SNP	.											.	IGSF22	211	.	0			c.C2014T						PASS	.		CYS/ARG	491,3899	207.2+/-228.6	24,443,1728	88	95	93		2014	1	0	11	dbSNP_132	93	219,8353	90.4+/-152.6	3,213,4070	yes	missense	IGSF22	NM_173588.3	180	27,656,5798	AA,AG,GG		2.5548,11.1845,5.4775	probably-damaging	672/1327	18735480	710,12252	2195	4286	6481	SO:0001583	missense	283284	exon14			CTTCACGCACACA	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.2014C>T	11.37:g.18735480G>A	ENSP00000421191:p.Arg672Cys	165	0	0		194	107	0.551546	NM_173588	A6NNA0|D6RGV7	Missense_Mutation	SNP	ENST00000513874.1	37	CCDS41625.2	94	0.04304029304029304	61	0.12398373983739837	15	0.04143646408839779	0	0.0	18	0.023746701846965697	G	11.60	1.686151	0.29962	0.111845	0.025548	ENSG00000179057	ENST00000513874	T	0.46063	0.88	3.98	0.959	0.19624	.	0.000000	0.33327	U	0.005033	T	0.02418	0.0074	H	0.97896	4.1	0.09310	N	1	D	0.89917	1.0	D	0.79784	0.993	T	0.16129	-1.0413	10	0.62326	D	0.03	.	3.8194	0.08828	0.1944:0.0:0.384:0.4215	.	672	D6RGV7	.	C	672	ENSP00000421191:R672C	ENSP00000322422:R672C	R	-	1	0	IGSF22	18692056	0.003000	0.15002	0.002000	0.10522	0.321000	0.28281	0.178000	0.16820	0.027000	0.15297	0.448000	0.29417	CGT	G|0.961;A|0.039	0.039	strong		0.602	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588		A	18735480	G	A	18735480	3	1	22	1	0	0	0	0	1	0	0	0	7609	1087	38	1	2006	1	IGSF22	11	18735480	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3575	18735480	116271036	2398	5299											
IGSF22	283284	hgsc.bcm.edu	37	chr11	18743529	18743529	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccgcagggatgtttgagcTccgggtcactaagctgaaga	9	8	14	10	2	1	3	1	2	0	1	2	4	2	4	2	2	2	4	2	2	2	2	rs115954314	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:18743529T>C	ENST00000513874.1	-	3	308	c.169A>G	c.(169-171)Agc>Ggc	p.S57G	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	57										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						ATGTTTGAGCTCCGGGTCACT	0.627											OREG0020822	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	34	0.00678914	0.025	0.0014	5008	,	,		17155	0.0		0.0	False		,,,				2504	0.0				p.S57G		Atlas-SNP	.											.	IGSF22	211	.	0			c.A169G						PASS	.	T	GLY/SER	74,3986		0,74,1956	74	81	79		169	3	0	11	dbSNP_132	79	1,8327		0,1,4163	yes	missense	IGSF22	NM_173588.3	56	0,75,6119	CC,CT,TT		0.012,1.8227,0.6054	possibly-damaging	57/1327	18743529	75,12313	2030	4164	6194	SO:0001583	missense	283284	exon3			TTGAGCTCCGGGT	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.169A>G	11.37:g.18743529T>C	ENSP00000421191:p.Ser57Gly	50	0	0	90	71	30	0.422535	NM_173588	A6NNA0|D6RGV7	Missense_Mutation	SNP	ENST00000513874.1	37	CCDS41625.2	17	0.007783882783882784	17	0.034552845528455285	0	0.0	0	0.0	0	0.0	T	13.41	2.229888	0.39399	0.018227	1.2E-4	ENSG00000179057	ENST00000513874	T	0.53640	0.61	4.23	3.05	0.35203	.	0.206612	0.23787	U	0.044561	T	0.09423	0.0232	N	0.14661	0.345	0.09310	N	1	B	0.20261	0.043	B	0.17433	0.018	T	0.08700	-1.0709	10	0.28530	T	0.3	.	5.4317	0.16456	0.1745:0.0:0.1813:0.6442	.	57	D6RGV7	.	G	57	ENSP00000421191:S57G	ENSP00000322422:S57G	S	-	1	0	IGSF22	18700105	0.780000	0.28664	0.001000	0.08648	0.989000	0.77384	2.349000	0.44054	0.471000	0.27319	0.533000	0.62120	AGC	T|0.992;C|0.008	0.008	strong		0.627	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588		C	18743529	T	C	18743529	3	2	22	1	0	0	0	0	1	0	0	0	7609	1551	54	3	3895	3	IGSF22	11	18743529	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	8049	18743529	116262987	2399	5300											
NAV2	89797	hgsc.bcm.edu	37	chr11	19735325	19735325	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gcgcccatcctgcacgtgccCccggcccgggcgggccccca	3	3	13	22	5	0	0	0	0	0	0	1	0	1	0	7	3	2	1	7	3	0	0	rs11828836	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:19735325C>A	ENST00000396087.3	+	1	183	c.84C>A	c.(82-84)ccC>ccA	p.P28P	NAV2_ENST00000360655.4_Intron|NAV2_ENST00000396085.1_Silent_p.P28P|NAV2_ENST00000349880.4_Silent_p.P28P|RP11-359E10.1_ENST00000603468.1_lincRNA	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	28					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						TGCACGTgcccccggcccggg	0.662													C|||	112	0.0223642	0.0825	0.0043	5008	,	,		13608	0.0		0.0	False		,,,				2504	0.0				p.P28P		Atlas-SNP	.											.	NAV2	255	.	0			c.C84A						PASS	.	C	,,	269,4121		8,253,1934	20	22	21		,84,84	4.4	1	11	dbSNP_120	21	5,8571		0,5,4283	no	intron,coding-synonymous,coding-synonymous	NAV2	NM_001111018.1,NM_145117.4,NM_182964.5	,,	8,258,6217	AA,AC,CC		0.0583,6.1276,2.1132	,,	,28/2430,28/2433	19735325	274,12692	2195	4288	6483	SO:0001819	synonymous_variant	89797	exon1			CGTGCCCCCGGCC	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.84C>A	11.37:g.19735325C>A		18	0	0		38	28	0.736842	NM_145117	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	37	CCDS58126.1																																																																																			C|0.975;A|0.025	0.025	strong		0.662	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		A	19735325	C	A	19735325	2	1	22	1	0	0	0	0	0	0	0	1	10193	610	22	4		4	NAV2	11	19735325	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	991796	19735325	115271191	2400	5301											
NAV2	89797	hgsc.bcm.edu	37	chr11	20070349	20070349	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaaattcggtggtcatctcCaatcctcatgccaccatgac	12	10	6	13	1	3	1	2	1	1	0	6	1	4	1	4	2	1	0	4	2	3	1	rs78806867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:20070349C>T	ENST00000396087.3	+	16	4146	c.4047C>T	c.(4045-4047)tcC>tcT	p.S1349S	NAV2_ENST00000527559.2_Silent_p.S1278S|NAV2_ENST00000311043.8_Silent_p.S412S|NAV2_ENST00000533917.1_Silent_p.S412S|NAV2_ENST00000360655.4_Silent_p.S1262S|NAV2_ENST00000540292.1_Silent_p.S1280S|NAV2_ENST00000396085.1_Silent_p.S1326S|NAV2_ENST00000349880.4_Silent_p.S1326S|NAV2-AS2_ENST00000533767.1_RNA	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	1349					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						TGGTCATCTCCAATCCTCATG	0.522													C|||	63	0.0125799	0.0454	0.0014	5008	,	,		21187	0.0		0.002	False		,,,				2504	0.0				p.S1349S		Atlas-SNP	.											.	NAV2	255	.	0			c.C4047T						PASS	.	C	,,,	145,4261	101.2+/-139.8	5,135,2063	136	113	121		3786,1236,3978,3978	1.9	1	11	dbSNP_131	121	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NAV2	NM_001111018.1,NM_001111019.1,NM_145117.4,NM_182964.5	,,,	5,136,6362	TT,TC,CC		0.0116,3.291,1.1226	,,,	1262/2366,412/1494,1326/2430,1326/2433	20070349	146,12860	2203	4300	6503	SO:0001819	synonymous_variant	89797	exon16			CATCTCCAATCCT	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.4047C>T	11.37:g.20070349C>T		141	0	0		155	76	0.490323	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	37	CCDS58126.1																																																																																			C|0.988;T|0.012	0.012	strong		0.522	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		T	20070349	C	T	20070349	2	4	22	1	0	0	0	0	0	0	0	1	10193	581	21	2		2	NAV2	11	20070349	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	335024	20070349	114936167	2401	5302											
SLC6A5	9152	hgsc.bcm.edu	37	chr11	20652291	20652291	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acaagcatctttgccggcttCgtcatcttctccgttatcgg	6	14	8	13	4	4	0	1	0	3	0	7	0	4	0	2	2	2	3	2	2	2	4	rs143680068		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:20652291C>T	ENST00000525748.1	+	10	1827	c.1554C>T	c.(1552-1554)ttC>ttT	p.F518F	SLC6A5_ENST00000528440.1_3'UTR	NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	518					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)	TTGCCGGCTTCGTCATCTTCT	0.493													C|||	1	0.000199681	0.0008	0.0	5008	,	,		23670	0.0		0.0	False		,,,				2504	0.0				p.F518F		Atlas-SNP	.											.	SLC6A5	151	.	0			c.C1554T						PASS	.	C		9,4397	15.5+/-35.6	0,9,2194	204	173	183		1554	-9.9	0.5	11	dbSNP_134	183	0,8600		0,0,4300	no	coding-synonymous	SLC6A5	NM_004211.3		0,9,6494	TT,TC,CC		0.0,0.2043,0.0692		518/798	20652291	9,12997	2203	4300	6503	SO:0001819	synonymous_variant	9152	exon10			CGGCTTCGTCATC	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.1554C>T	11.37:g.20652291C>T		316	1	0.00316456		298	138	0.463087	NM_004211	O95288|Q4VAM7|Q9BX77	Silent	SNP	ENST00000525748.1	37	CCDS7854.1																																																																																			C|1.000;T|0.000	0.000	strong		0.493	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211		T	20652291	C	T	20652291	2	4	22	1	0	0	0	0	0	0	0	1	14702	883	31	1		1	SLC6A5	11	20652291	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	581942	20652291	114354225	2402	5303											
GAS2	2620	hgsc.bcm.edu	37	chr11	22770669	22770669	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagggtctttttaaaggtaTggtgtggagcctcctggttt	6	15	13	7	0	1	0	0	0	1	0	2	1	2	1	3	5	1	2	3	5	3	5	rs7122835	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:22770669T>C	ENST00000454584.2	+	6	782	c.477T>C	c.(475-477)taT>taC	p.Y159Y	GAS2_ENST00000278187.3_Silent_p.Y159Y|GAS2_ENST00000433790.1_Silent_p.Y159Y	NM_001143830.1	NP_001137302.1	O43903	GAS2_HUMAN	growth arrest-specific 2	159					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						TTTAAAGGTATGGTGTGGAGC	0.378													t|||	80	0.0159744	0.059	0.0029	5008	,	,		18402	0.0		0.0	False		,,,				2504	0.0				p.Y159Y		Atlas-SNP	.											.	GAS2	46	.	0			c.T477C						PASS	.	C	,,	212,4194	128.6+/-165.4	5,202,1996	73	76	75		477,477,477	4.7	1	11	dbSNP_116	75	3,8595	3.0+/-9.4	0,3,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	GAS2	NM_001143830.1,NM_005256.3,NM_177553.2	,,	5,205,6292	CC,CT,TT		0.0349,4.8116,1.6533	,,	159/314,159/314,159/314	22770669	215,12789	2203	4299	6502	SO:0001819	synonymous_variant	2620	exon6			AAGGTATGGTGTG	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.477T>C	11.37:g.22770669T>C		116	0	0		121	56	0.46281	NM_177553	B2R9C8|D3DQZ0|Q6ICV8|Q7Z3X8	Silent	SNP	ENST00000454584.2	37	CCDS7858.1																																																																																			T|0.988;C|0.012	0.012	strong		0.378	GAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387717.1	NM_177553		C	22770669	T	C	22770669	2	2	22	1	0	0	0	0	0	0	0	1	6253	1471	51	3		3	GAS2	11	22770669	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2118378	22770669	112235847	2403	5304											
SLC5A12	159963	hgsc.bcm.edu	37	chr11	26700344	26700344	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggtaggagatcgagtaccaGgtatcagctattccaggtct	11	10	12	8	1	2	1	1	0	1	1	4	3	3	1	2	4	2	4	2	4	4	5	rs150900623	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:26700344G>C	ENST00000396005.3	-	13	1803	c.1494C>G	c.(1492-1494)acC>acG	p.T498T		NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	498					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						TCGAGTACCAGGTATCAGCTA	0.453													G|||	42	0.00838658	0.031	0.0014	5008	,	,		16935	0.0		0.0	False		,,,				2504	0.0				p.T498T		Atlas-SNP	.											.	SLC5A12	134	.	0			c.C1494G						PASS	.	G		75,3887		0,75,1906	116	114	115		1494	0.2	0.8	11	dbSNP_134	115	0,8338		0,0,4169	no	coding-synonymous	SLC5A12	NM_178498.3		0,75,6075	CC,CG,GG		0.0,1.893,0.6098		498/619	26700344	75,12225	1981	4169	6150	SO:0001819	synonymous_variant	159963	exon13			GTACCAGGTATCA	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.1494C>G	11.37:g.26700344G>C		75	0	0		90	39	0.433333	NM_178498	Q86UC7	Silent	SNP	ENST00000396005.3	37	CCDS7860.2																																																																																			G|0.994;C|0.006	0.006	strong		0.453	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498		C	26700344	G	C	26700344	2	2	22	1	0	0	0	0	0	0	0	1	14679	987	35	4		4	SLC5A12	11	26700344	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3929675	26700344	108306172	2404	5305											
CCDC34	91057	hgsc.bcm.edu	37	chr11	27384449	27384466	+	In_Frame_Del	DEL	TCATCCACGTCTTCCTCA	TCATCCACGTCTTCCTCA	-																															cctctgaatcatgggcatctTcatccacgtcttcctcatca																								rs368035683|rs138931796|rs377198931|rs3207371|rs558321598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCATCCACGTCTTCCTCA	TCATCCACGTCTTCCTCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:27384449_27384466delTCATCCACGTCTTCCTCA	ENST00000328697.6	-	1	949_966	c.276_293delTGAGGAAGACGTGGATGA	c.(274-294)gatgaggaagacgtggatgaa>gaa	p.DEEDVD92del	CCDC34_ENST00000317945.6_In_Frame_Del_p.DEEDVD92del	NM_030771.1	NP_110398.1	Q96HJ3	CCD34_HUMAN	coiled-coil domain containing 34	92	Asp-rich.									endometrium(2)|large_intestine(4)|lung(1)|prostate(1)|urinary_tract(1)	9						ATGGGCATCTTCATCCACGTCTTCCTCATCATCCACGT	0.592														162	0.0323482	0.1097	0.0144	5008	,	,		19380	0.001		0.004	False		,,,				2504	0.002				p.93_98del		Pindel,Atlas-Indel	.											.	CCDC34	48	.	0			c.277_294del						PASS	.		,	353,3911		23,307,1802					,	0.9	0		dbSNP_134	173	50,8204		11,28,4088	no	coding,coding	CCDC34	NM_080654.2,NM_030771.1	,	34,335,5890	A1A1,A1R,RR		0.6058,8.2786,3.2194	,	,		403,12115				SO:0001651	inframe_deletion	91057	exon1			.	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.276_293delTGAGGAAGACGTGGATGA	11.37:g.27384449_27384466delTCATCCACGTCTTCCTCA	ENSP00000330240:p.Asp92_Asp97del	294	0	.		215	39	0.181	NM_030771	B2R8G2|Q8IX69|Q9H2A6|Q9Y599	In_Frame_Del	DEL	ENST00000328697.6	37	CCDS31448.1																																																																																			TCATCCACGTCTTCCTCA|0.966;-|0.034	0.034	strong		0.592	CCDC34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388396.2	NM_030771		-	27384466	TCATCCACGTCTTCCTCA	-	27384449	7	5	22	1	0	1	0	1	0	0	0	0	2809	1783	62	0	936	0	CCDC34	11	27384449	In_Frame_Del	DEL	TCATCCACGTCTTCCTCA	TCGA-G8-6324-01A-11D-2210-10	684105	27384449	107622067	2405	5306											
BDNF	627	hgsc.bcm.edu	37	chr11	27679976	27679976	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctgccttgggcccattcaCgctctccagagtcccatggg	6	9	10	16	1	2	1	1	0	1	1	4	1	3	1	5	2	1	1	5	2	0	2	rs146354977	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:27679976C>T	ENST00000525528.1	-	1	1229	c.136G>A	c.(136-138)Gtg>Atg	p.V46M	BDNF_ENST00000525950.1_Missense_Mutation_p.V46M|BDNF_ENST00000314915.6_Missense_Mutation_p.V54M|BDNF_ENST00000584049.1_5'UTR|BDNF_ENST00000395983.3_Missense_Mutation_p.V46M|BDNF_ENST00000438929.1_Missense_Mutation_p.V128M|BDNF_ENST00000420794.1_Missense_Mutation_p.V46M|BDNF_ENST00000533246.1_Missense_Mutation_p.V46M|BDNF-AS_ENST00000532965.1_RNA|BDNF_ENST00000395980.2_Missense_Mutation_p.V46M|BDNF-AS_ENST00000530686.1_RNA|BDNF_ENST00000418212.1_Missense_Mutation_p.V46M|BDNF-AS_ENST00000502161.2_RNA|BDNF_ENST00000356660.4_Missense_Mutation_p.V46M|BDNF-AS_ENST00000530313.1_RNA|BDNF_ENST00000533131.1_Missense_Mutation_p.V46M|BDNF_ENST00000395978.3_Missense_Mutation_p.V46M|BDNF_ENST00000530861.1_Missense_Mutation_p.V46M|BDNF_ENST00000395981.3_Missense_Mutation_p.V46M|BDNF-AS_ENST00000499008.3_RNA|BDNF-AS_ENST00000501176.2_RNA|BDNF-AS_ENST00000500662.2_RNA|BDNF_ENST00000532997.1_Missense_Mutation_p.V46M|BDNF_ENST00000439476.2_Missense_Mutation_p.V46M|BDNF-AS_ENST00000499568.2_RNA|BDNF_ENST00000395986.2_Missense_Mutation_p.V61M	NM_170735.5	NP_733931.1	P23560	BDNF_HUMAN	brain-derived neurotrophic factor	46					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						GGCCCATTCACGCTCTCCAGA	0.547													C|||	3	0.000599042	0.0023	0.0	5008	,	,		18690	0.0		0.0	False		,,,				2504	0.0				p.V128M		Atlas-SNP	.											.	BDNF	63	.	0			c.G382A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	1,4403	2.1+/-5.4	0,1,2201	149	149	149		136,136,136,136,223,382,136,136,136,136,136,136,160,136,136,181,136	-1.7	1	11	dbSNP_134	149	0,8598		0,0,4299	no	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	BDNF	NM_001143805.1,NM_001143806.1,NM_001143807.1,NM_001143808.1,NM_001143809.1,NM_001143810.1,NM_001143811.1,NM_001143812.1,NM_001143813.1,NM_001143814.1,NM_001143816.1,NM_001709.4,NM_170731.4,NM_170732.4,NM_170733.3,NM_170734.3,NM_170735.5	21,21,21,21,21,21,21,21,21,21,21,21,21,21,21,21,21	0,1,6500	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	46/248,46/248,46/248,46/248,75/277,128/330,46/248,46/248,46/248,46/248,46/248,46/248,54/256,46/248,46/248,61/263,46/248	27679976	1,13001	2202	4299	6501	SO:0001583	missense	627	exon3			CATTCACGCTCTC	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	ENST00000525528.1:c.136G>A	11.37:g.27679976C>T	ENSP00000437138:p.Val46Met	139	0	0		131	61	0.465649	NM_001143810	A7LA85|A7LA92|D3DQZ2|Q598Q1|Q6DN19|Q6YNR2|Q6YNR3|Q9BYY7|Q9UC24	Missense_Mutation	SNP	ENST00000525528.1	37	CCDS7866.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	6.658	0.489860	0.12702	2.27E-4	0.0	ENSG00000176697	ENST00000439476;ENST00000525528;ENST00000395986;ENST00000533131;ENST00000356660;ENST00000418212;ENST00000533246;ENST00000530861;ENST00000395983;ENST00000438929;ENST00000395980;ENST00000532997;ENST00000395981;ENST00000395978;ENST00000525950;ENST00000314915;ENST00000420794;ENST00000528035	T;T;T;T;T;T;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;0.62;0.62;0.62;0.62;0.62;0.62	6.16	-1.67	0.08238	.	0.752012	0.13050	N	0.417798	T	0.20495	0.0493	N	0.14661	0.345	0.26003	N	0.98209	B;B;B;B;B	0.19445	0.012;0.013;0.014;0.002;0.036	B;B;B;B;B	0.16722	0.016;0.002;0.01;0.003;0.01	T	0.20306	-1.0279	10	0.87932	D	0	-29.8815	9.1961	0.37228	0.0:0.2875:0.1522:0.5603	.	75;128;54;46;61	P23560-5;P23560-4;P23560-2;P23560;P23560-3	.;.;.;BDNF_HUMAN;.	M	46;46;61;46;46;46;46;46;46;128;46;46;46;46;46;54;46;46	ENSP00000389345:V46M;ENSP00000437138:V46M;ENSP00000379309:V61M;ENSP00000432727:V46M;ENSP00000349084:V46M;ENSP00000400502:V46M;ENSP00000432376:V46M;ENSP00000435564:V46M;ENSP00000379307:V46M;ENSP00000414303:V128M;ENSP00000379304:V46M;ENSP00000435805:V46M;ENSP00000379305:V46M;ENSP00000379302:V46M;ENSP00000432035:V46M;ENSP00000320002:V54M;ENSP00000389564:V46M	ENSP00000320002:V54M	V	-	1	0	BDNF	27636552	0.977000	0.34250	0.957000	0.39632	0.991000	0.79684	0.156000	0.16382	-0.215000	0.10063	-0.142000	0.14014	GTG	C|0.999;T|0.001	0.001	strong		0.547	BDNF-016	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388135.1	NM_170735		T	27679976	C	T	27679976	3	4	22	1	0	0	0	0	1	0	0	0	1394	536	19	1	611	1	BDNF	11	27679976	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	295527	27679976	107326540	2406	5307											
METT5D1	196074	hgsc.bcm.edu	37	chr11	28351963	28351963	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagcatttcctccctctgctAtttatacacggaaagactta	11	13	6	11	1	1	1	0	0	1	1	3	3	3	2	2	1	3	2	2	1	5	6	rs11030280	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:28351963A>T	ENST00000407364.3	+	7	1151	c.799A>T	c.(799-801)Att>Ttt	p.I267F	METTL15_ENST00000406787.3_Missense_Mutation_p.Y252F|METTL15_ENST00000342303.5_3'UTR|METTL15_ENST00000303459.6_3'UTR			A6NJ78	MET15_HUMAN	methyltransferase like 15	267			I -> F (in dbSNP:rs11030280).				methyltransferase activity (GO:0008168)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	14						TCCCTCTGCTATTTATACACG	0.368													a|||	66	0.0131789	0.0484	0.0029	5008	,	,		18196	0.0		0.0	False		,,,				2504	0.0				p.I267F		Atlas-SNP	.											.	METTL15	63	.	0			c.A799T						PASS	.						26	20	22					11																	28351963		692	1591	2283	SO:0001583	missense	196074	exon7			TCTGCTATTTATA	AL832668	CCDS31450.1, CCDS44559.1, CCDS73269.1	11p14.1	2011-03-02	2011-03-02	2011-03-02	ENSG00000169519	ENSG00000169519			26606	protein-coding gene	gene with protein product			"methyltransferase 5 domain containing 1"	METT5D1		12477932	Standard	NM_152636		Approved	FLJ33979	uc001msh.2	A6NJ78	OTTHUMG00000150448	ENST00000407364.3:c.799A>T	11.37:g.28351963A>T	ENSP00000384369:p.Ile267Phe	229	1	0.00436681		242	117	0.483471	NM_001113528	A8MRS5|B7WNU2|Q3MHD3|Q8N601|Q8NBA7	Missense_Mutation	SNP	ENST00000407364.3	37	CCDS44559.1	16|16	0.007326007326007326|0.007326007326007326	16|16	0.032520325203252036|0.032520325203252036	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	a|a	6.700|6.700	0.497771|0.497771	0.12762|0.12762	.|.	.|.	ENSG00000169519|ENSG00000169519	ENST00000407364|ENST00000406787	T|T	0.22743|0.42513	1.94|0.97	5.32|5.32	-8.55|-8.55	0.00908|0.00908	S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain (2);|.	1.236540|.	0.05563|.	N|.	0.569607|.	T|T	0.04497|0.04497	0.0123|0.0123	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	0.999999|0.999999	B|B	0.15473|0.02656	0.013|0.0	B|B	0.17979|0.04013	0.02|0.001	T|T	0.14227|0.14227	-1.0480|-1.0480	9|8	.|.	.|.	.|.	.|.	1.7987|1.7987	0.03067|0.03067	0.2726:0.3206:0.2653:0.1414|0.2726:0.3206:0.2653:0.1414	rs11030280|rs11030280	267|252	A6NJ78|A6NJ78-4	MET15_HUMAN|.	F|F	267|252	ENSP00000384369:I267F|ENSP00000385507:Y252F	.|.	I|Y	+|+	1|2	0|0	METTL15|METTL15	28308539|28308539	0.002000|0.002000	0.14202|0.14202	0.010000|0.010000	0.14722|0.14722	0.688000|0.688000	0.40055|0.40055	-0.377000|-0.377000	0.07456|0.07456	-0.966000|-0.966000	0.03587|0.03587	-1.125000|-1.125000	0.01998|0.01998	ATT|TAT	A|0.993;T|0.007	0.007	strong		0.368	METTL15-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318135.2	NM_152636		T	28351963	A	T	28351963	3	4	22	1	0	0	0	0	1	0	0	0	9501	449	16	5	865	5	METT5D1	11	28351963	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	671987	28351963	106654553	2407	5308											
EIF3M	10480	hgsc.bcm.edu	37	chr11	32610617	32610617	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtaagatacacagtgtattGcagccttattaaagtggcag	13	12	10	6	0	0	1	0	0	0	1	0	1	0	1	1	1	3	4	1	1	6	6	rs140562244	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:32610617G>T	ENST00000531120.1	+	4	437	c.374G>T	c.(373-375)tGc>tTc	p.C125F	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)					ACAGTGTATTGCAGCCTTATT	0.408																																					p.C125F		Atlas-SNP	.											.	EIF3M	37	.	0			c.G374T						PASS	.	G	PHE/CYS	14,4390	14.3+/-33.2	0,14,2188	115	102	106		374	5.8	1	11	dbSNP_134	106	0,8598		0,0,4299	yes	missense	EIF3M	NM_006360.3	205	0,14,6487	TT,TG,GG		0.0,0.3179,0.1077	benign	125/375	32610617	14,12988	2202	4299	6501	SO:0001583	missense	10480	exon4			TGTATTGCAGCCT	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.374G>T	11.37:g.32610617G>T	ENSP00000436049:p.Cys125Phe	119	0	0		154	21	0.136364	NM_006360		Missense_Mutation	SNP	ENST00000531120.1	37	CCDS7880.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	14.72	2.618767	0.46736	0.003179	0.0	ENSG00000149100	ENST00000531120;ENST00000323213;ENST00000533439	T;T	0.36878	1.23;1.23	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.45498	0.1345	L	0.59436	1.845	0.80722	D	1	D	0.61080	0.989	P	0.62014	0.897	T	0.27536	-1.0071	10	0.12766	T	0.61	-25.8093	20.0797	0.97768	0.0:0.0:1.0:0.0	.	125	Q7L2H7	EIF3M_HUMAN	F	125;62;62	ENSP00000436049:C125F;ENSP00000319910:C62F	ENSP00000319910:C62F	C	+	2	0	EIF3M	32567193	1.000000	0.71417	1.000000	0.80357	0.365000	0.29674	9.476000	0.97823	2.752000	0.94435	0.467000	0.42956	TGC	G|0.998;T|0.002	0.002	strong		0.408	EIF3M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388762.2	NM_006360		T	32610617	G	T	32610617	3	4	22	1	0	0	0	0	1	0	0	0	5025	1319	46	4	388	4	EIF3M	11	32610617	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4258654	32610617	102395899	2408	5309											
EIF3M	493860	hgsc.bcm.edu	37	chr11	32622233	32622233	+	IGR	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcttcactattctgttttctAggcctgttacatgaacagaa	10	15	7	9	0	3	2	1	1	2	1	3	2	3	2	1	1	2	3	1	1	5	7			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:32622233A>T	ENST00000335185.5	-	0	3849				EIF3M_ENST00000531120.1_Splice_Site|EIF3M_ENST00000524896.1_Splice_Site	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73											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)					TCTGTTTTCTAGGCCTGTTAC	0.333																																					.		Atlas-SNP	.											.	EIF3M	37	.	0			c.800-2A>T						PASS	.						65	63	63					11																	32622233		2202	4299	6501	SO:0001628	intergenic_variant	10480	exon9			TTTTCTAGGCCTG	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		11.37:g.32622233A>T		86	0	0		108	12	0.111111	NM_006360	Q6P5Q7|Q6ZMW0|Q86WE7	Splice_Site	SNP	ENST00000335185.5	37	CCDS41630.1	.	.	.	.	.	.	.	.	.	.	A	31	5.076612	0.94000	.	.	ENSG00000149100	ENST00000531120;ENST00000524896;ENST00000526267	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3871	0.83514	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	EIF3M	32578809	1.000000	0.71417	0.634000	0.29324	0.673000	0.39480	8.701000	0.91331	2.270000	0.75569	0.482000	0.46254	.	.	.	none		0.333	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391		T	32622233	A	T	32622233	1	4	22	0	1	0	0	0	0	0	0	0	5025	434	15	5		5	EIF3M	11	32622233	IGR	SNP	A	TCGA-G8-6324-01A-11D-2210-10	11616	32622233	102384283	2409	5310											
NAT10	55226	hgsc.bcm.edu	37	chr11	34133767	34133767	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	accttcggcatgtgtgtgctGcaggtgggtggcttcctcta	4	13	14	10	1	1	0	0	0	1	0	3	0	2	0	2	4	2	4	2	4	1	3	rs36003235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:34133767G>A	ENST00000257829.3	+	4	575	c.369G>A	c.(367-369)ctG>ctA	p.L123L	NAT10_ENST00000527971.1_Silent_p.L123L|NAT10_ENST00000531159.2_Silent_p.L51L	NM_024662.2	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 (GCN5-related)	123						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)				TGTGTGTGCTGCAGGTGGGTG	0.517													G|||	32	0.00638978	0.0219	0.0043	5008	,	,		20244	0.0		0.0	False		,,,				2504	0.0				p.L123L		Atlas-SNP	.											.	NAT10	78	.	0			c.G369A						PASS	.	G	,	49,4355	50.9+/-86.3	0,49,2153	115	82	93		153,369	-2.1	1	11	dbSNP_126	93	1,8595		0,1,4297	no	coding-synonymous,coding-synonymous	NAT10	NM_001144030.1,NM_024662.2	,	0,50,6450	AA,AG,GG		0.0116,1.1126,0.3846	,	51/954,123/1026	34133767	50,12950	2202	4298	6500	SO:0001819	synonymous_variant	55226	exon4			TGTGCTGCAGGTG	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.369G>A	11.37:g.34133767G>A		168	0	0		163	77	0.472393	NM_024662	B4DFD5|E7ESU4|E9PMN9|Q86WK5|Q9C0F4|Q9HA61|Q9NVF2	Silent	SNP	ENST00000257829.3	37	CCDS7889.1																																																																																			G|0.996;A|0.004	0.004	strong		0.517	NAT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388693.1	NM_024662		A	34133767	G	A	34133767	2	1	22	1	0	0	0	0	0	0	0	1	10183	1306	46	2		2	NAT10	11	34133767	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1511534	34133767	100872749	2410	5311											
ABTB2	25841	hgsc.bcm.edu	37	chr11	34176262	34176262	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcacctccaggatgtcagTggtggggatctccatggatt	7	12	12	10	0	3	0	2	0	2	0	6	3	4	3	3	5	0	0	3	5	0	1	rs2473928	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:34176262T>C	ENST00000435224.2	-	15	3176	c.2752A>G	c.(2752-2754)Act>Gct	p.T918A	ABTB2_ENST00000298992.2_Missense_Mutation_p.T732A	NM_145804.2	NP_665803.2	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing 2	918			T -> A (in dbSNP:rs2473928).		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)				AGGATGTCAGTGGTGGGGATC	0.602													C|||	142	0.0283546	0.1044	0.0058	5008	,	,		20312	0.0		0.0	False		,,,				2504	0.0				p.T918A		Atlas-SNP	.											.	ABTB2	101	.	0			c.A2752G						PASS	.	C	ALA/THR	328,4076	796.1+/-415.3	14,300,1888	153	134	140		2752	-0.4	0	11	dbSNP_100	140	3,8593	819.0+/-406.8	0,3,4295	yes	missense	ABTB2	NM_145804.2	58	14,303,6183	CC,CT,TT		0.0349,7.4478,2.5462	benign	918/1026	34176262	331,12669	2202	4298	6500	SO:0001583	missense	25841	exon15			TGTCAGTGGTGGG	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.2752A>G	11.37:g.34176262T>C	ENSP00000410157:p.Thr918Ala	106	0	0		122	69	0.565574	NM_145804	A8K6S9|E9PRW7|Q52LD6|Q6MZW4|Q8NB44	Missense_Mutation	SNP	ENST00000435224.2	37	CCDS7890.2	41	0.018772893772893772	40	0.08130081300813008	1	0.0027624309392265192	0	0.0	0	0.0	C	0.013	-1.626374	0.00813	0.074478	3.49E-4	ENSG00000166016	ENST00000435224;ENST00000298992	T;T	0.65732	-0.17;-0.17	4.79	-0.445	0.12242	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.385085	0.29178	N	0.012911	T	0.02012	0.0063	N	0.20807	0.61	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.07481	-1.0770	10	0.02654	T	1	-15.8719	6.5214	0.22277	0.1139:0.4201:0.0:0.466	rs2473928;rs16925228;rs52811333;rs2473928	732	Q8N961	ABTB2_HUMAN	A	918;732	ENSP00000410157:T918A;ENSP00000298992:T732A	ENSP00000298992:T732A	T	-	1	0	ABTB2	34132838	0.000000	0.05858	0.016000	0.15963	0.433000	0.31745	-0.763000	0.04740	-0.594000	0.05836	-2.820000	0.00109	ACT	T|0.973;C|0.027	0.027	strong		0.602	ABTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388703.3	NM_145804		C	34176262	T	C	34176262	3	2	22	1	0	0	0	0	1	0	0	0	103	1696	59	3	337	3	ABTB2	11	34176262	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	42495	34176262	100830254	2411	5312											
ABTB2	25841	hgsc.bcm.edu	37	chr11	34226140	34226140	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gccaggagggactgctccagGgttcggagctccagctgggc	6	6	17	12	1	0	0	0	0	0	0	3	3	2	3	3	5	3	4	3	5	0	1	rs77165558	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:34226140G>T	ENST00000435224.2	-	2	1405	c.981C>A	c.(979-981)acC>acA	p.T327T	ABTB2_ENST00000530814.1_5'UTR|ABTB2_ENST00000298992.2_Silent_p.T141T	NM_145804.2	NP_665803.2	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing 2	327					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)				ACTGCTCCAGGGTTCGGAGCT	0.637													G|||	142	0.0283546	0.1036	0.0072	5008	,	,		17394	0.0		0.0	False		,,,				2504	0.0				p.T327T		Atlas-SNP	.											ABTB2,NS,carcinoma,-2,1	ABTB2	101	1	0			c.C981A						PASS	.	G		392,4012	193.0+/-218.2	21,350,1831	45	43	44		981	-5.2	1	11	dbSNP_132	44	4,8592	3.0+/-9.4	0,4,4294	no	coding-synonymous	ABTB2	NM_145804.2		21,354,6125	TT,TG,GG		0.0465,8.901,3.0462		327/1026	34226140	396,12604	2202	4298	6500	SO:0001819	synonymous_variant	25841	exon2			CTCCAGGGTTCGG	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.981C>A	11.37:g.34226140G>T		45	0	0		33	17	0.515152	NM_145804	A8K6S9|E9PRW7|Q52LD6|Q6MZW4|Q8NB44	Silent	SNP	ENST00000435224.2	37	CCDS7890.2																																																																																			G|0.972;T|0.028	0.028	strong		0.637	ABTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388703.3	NM_145804		T	34226140	G	T	34226140	2	4	22	1	0	0	0	0	0	0	0	1	103	1219	43	4		4	ABTB2	11	34226140	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	49878	34226140	100780376	2412	5313											
PDHX	8050	hgsc.bcm.edu	37	chr11	34969150	34969150	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gatggaatcttggccaaaatCgtggtaagtttttattttaa	12	16	9	4	1	1	0	0	0	1	0	2	2	1	1	1	3	0	2	1	3	6	7	rs34582941	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:34969150C>T	ENST00000227868.4	+	3	423	c.339C>T	c.(337-339)atC>atT	p.I113I	PDHX_ENST00000430469.2_Silent_p.I113I|PDHX_ENST00000448838.3_Silent_p.I98I			O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	113	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)			TGGCCAAAATCGTGGTAAGTT	0.353													C|||	272	0.0543131	0.1974	0.0159	5008	,	,		15319	0.0		0.0	False		,,,				2504	0.0				p.I113I		Atlas-SNP	.											.	PDHX	40	.	0			c.C339T						PASS	.	C	,,	720,3684	299.3+/-285.7	67,586,1549	163	154	157		294,339,339	-2.9	1	11	dbSNP_126	157	10,8586	5.7+/-21.5	0,10,4288	no	coding-synonymous,coding-synonymous,coding-synonymous	PDHX	NM_001135024.1,NM_001166158.1,NM_003477.2	,,	67,596,5837	TT,TC,CC		0.1163,16.3488,5.6154	,,	98/487,113/275,113/502	34969150	730,12270	2202	4298	6500	SO:0001819	synonymous_variant	8050	exon3			CAAAATCGTGGTA	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.339C>T	11.37:g.34969150C>T		36	0	0		70	33	0.471429	NM_003477	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Silent	SNP	ENST00000227868.4	37	CCDS7896.1																																																																																			C|0.951;T|0.049	0.049	strong		0.353	PDHX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390017.1	NM_003477		T	34969150	C	T	34969150	2	4	22	1	0	0	0	0	0	0	0	1	11676	874	31	1		1	PDHX	11	34969150	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	743010	34969150	100037366	2413	5314											
CD44	960	hgsc.bcm.edu	37	chr11	35223303	35223303	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	attcaccatgagcatcatgaGgaagaagagaccccacattc	15	7	8	11	0	2	4	2	2	0	2	3	6	2	5	3	1	1	1	3	1	2	2	rs11033026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:35223303G>A	ENST00000428726.2	+	9	1245	c.1122G>A	c.(1120-1122)gaG>gaA	p.E374E	CD44_ENST00000360158.4_Intron|CD44_ENST00000433892.2_Intron|CD44_ENST00000415148.2_Silent_p.E331E|CD44_ENST00000526669.2_Intron|CD44_ENST00000352818.4_Intron|CD44_ENST00000449691.2_Silent_p.E374E|CD44_ENST00000437706.2_Silent_p.E374E|CD44_ENST00000278386.6_Intron|CD44_ENST00000433354.2_Silent_p.E375E|CD44_ENST00000434472.2_Intron|CD44_ENST00000263398.6_Intron	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)	374	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)	AGCATCATGAGGAAGAAGAGA	0.473													G|||	473	0.0944489	0.3449	0.0245	5008	,	,		18781	0.0		0.0	False		,,,				2504	0.0				p.E374E		Atlas-SNP	.											.	CD44	48	.	0			c.G1122A						PASS	.	G	,,,,,,,	1185,3219	417.2+/-337.8	174,837,1191	153	129	137		1122,993,,,,,,	-10.3	0.1	11	dbSNP_120	137	12,8584	5.7+/-21.5	0,12,4286	no	coding-synonymous,coding-synonymous,intron,intron,intron,intron,intron,intron	CD44	NM_000610.3,NM_001001389.1,NM_001001390.1,NM_001001391.1,NM_001001392.1,NM_001202555.1,NM_001202556.1,NM_001202557.1	,,,,,,,	174,849,5477	AA,AG,GG		0.1396,26.9074,9.2077	,,,,,,,	374/743,331/700,,,,,,	35223303	1197,11803	2202	4298	6500	SO:0001819	synonymous_variant	960	exon9			TCATGAGGAAGAA	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.1122G>A	11.37:g.35223303G>A		170	0	0		161	160	0.993789	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	37	CCDS7897.1	176	0.08058608058608059	170	0.34552845528455284	6	0.016574585635359115	0	0.0	0	0.0	G	0.022	-1.413724	0.01145	0.269074	0.001396	ENSG00000026508	ENST00000528455	.	.	.	5.14	-10.3	0.00346	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.35450	-0.9788	3	.	.	.	-9.2826	1.2309	0.01943	0.2577:0.2623:0.3217:0.1583	rs11033026;rs11033026	.	.	.	R	226	.	.	G	+	1	0	CD44	35179879	0.000000	0.05858	0.068000	0.19968	0.002000	0.02628	-2.933000	0.00687	-1.585000	0.01634	-1.108000	0.02087	GGA	G|0.883;A|0.117	0.117	strong		0.473	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	NM_000610		A	35223303	G	A	35223303	2	1	22	1	0	0	0	0	0	0	0	1	3019	991	35	2		2	CD44	11	35223303	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	254153	35223303	99783213	2414	5315											
FJX1	24147	hgsc.bcm.edu	37	chr11	35641428	35641428	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacgctcagctgctacagcGccgcctcgacttcctcgcca	6	7	8	20	5	1	0	1	0	0	0	4	1	2	0	5	0	4	3	5	0	1	2	rs12286850	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:35641428G>A	ENST00000317811.4	+	1	1694	c.1244G>A	c.(1243-1245)cGc>cAc	p.R415H	FJX1_ENST00000532914.1_3'UTR	NM_014344.3	NP_055159.2	Q86VR8	FJX1_HUMAN	four jointed box 1 (Drosophila)	415			R -> H (in dbSNP:rs12286850).		retina layer formation (GO:0010842)	extracellular space (GO:0005615)				lung(1)|urinary_tract(1)	2	all_cancers(35;0.177)|all_lung(20;0.0238)|Lung NSC(22;0.0494)|all_epithelial(35;0.0739)	all_hematologic(20;0.107)				CTGCTACAGCGCCGCCTCGAC	0.667													G|||	358	0.0714856	0.2617	0.0159	5008	,	,		13330	0.0		0.001	False		,,,				2504	0.0				p.R415H	Melanoma(161;10 2587 27165 47356)	Atlas-SNP	.											.	FJX1	32	.	0			c.G1244A						PASS	.	G	HIS/ARG	717,3093		68,581,1256	6	7	7		1244	4.3	1	11	dbSNP_120	7	9,8147		0,9,4069	yes	missense	FJX1	NM_014344.3	29	68,590,5325	AA,AG,GG		0.1103,18.8189,6.0672	probably-damaging	415/438	35641428	726,11240	1905	4078	5983	SO:0001583	missense	24147	exon1			TACAGCGCCGCCT	AJ245599	CCDS44570.1	11p13	2012-05-18				ENSG00000179431			17166	protein-coding gene	gene with protein product	"putative secreted ligand homologous to fjx1"	612206				7647465, 10072791	Standard	NM_014344		Approved	FLJ22416, FLJ25593	uc001mwh.3	Q86VR8		ENST00000317811.4:c.1244G>A	11.37:g.35641428G>A	ENSP00000400223:p.Arg415His	57	0	0		47	27	0.574468	NM_014344	B2RCA9|Q9UGK6	Missense_Mutation	SNP	ENST00000317811.4	37	CCDS44570.1	124	0.056776556776556776	118	0.23983739837398374	6	0.016574585635359115	0	0.0	0	0.0	G	13.12	2.141657	0.37825	0.188189	0.001103	ENSG00000179431	ENST00000317811	T	0.80480	-1.38	5.21	4.29	0.51040	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.35833	P	0.174551	B	0.11235	0.004	B	0.08055	0.003	T	0.03354	-1.1045	8	0.51188	T	0.08	-3.1322	7.4212	0.27073	0.1565:0.1395:0.7039:0.0	rs12286850	415	Q86VR8	FJX1_HUMAN	H	415	ENSP00000400223:R415H	ENSP00000400223:R415H	R	+	2	0	FJX1	35598004	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.527000	0.45615	1.184000	0.42957	0.555000	0.69702	CGC	G|0.908;A|0.092	0.092	strong		0.667	FJX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389078.1	NM_014344		A	35641428	G	A	35641428	3	1	22	1	0	0	0	0	1	0	0	0	5909	1087	38	1	1246	1	FJX1	11	35641428	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	418125	35641428	99365088	2415	5316											
TTC17	55761	hgsc.bcm.edu	37	chr11	43413028	43413028	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attttagtcctgaagattatAtagacacagaatctcctgtc	13	14	6	8	0	1	4	0	1	1	3	4	4	2	4	2	0	0	0	2	0	6	5	rs12099204	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:43413028A>C	ENST00000039989.4	+	4	447	c.433A>C	c.(433-435)Ata>Cta	p.I145L	RP11-484D2.4_ENST00000394183.2_RNA|TTC17_ENST00000299240.6_Missense_Mutation_p.I145L	NM_018259.5	NP_060729.2	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17	145			I -> L (in dbSNP:rs12099204).		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						TGAAGATTATATAGACACAGA	0.328													A|||	528	0.105431	0.382	0.0317	5008	,	,		16846	0.0		0.001	False		,,,				2504	0.0				p.I145L		Atlas-SNP	.											.	TTC17	112	.	0			c.A433C						PASS	.	A	LEU/ILE	1459,2947	469.6+/-355.5	256,947,1000	80	82	82		433	5.2	1	11	dbSNP_120	82	9,8591	6.4+/-24.3	0,9,4291	yes	missense	TTC17	NM_018259.5	5	256,956,5291	CC,CA,AA		0.1047,33.1139,11.2871	benign	145/1142	43413028	1468,11538	2203	4300	6503	SO:0001583	missense	55761	exon4			GATTATATAGACA	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.433A>C	11.37:g.43413028A>C	ENSP00000039989:p.Ile145Leu	195	1	0.00512821		203	203	1	NM_018259	G3XAB3|Q8NEC0	Missense_Mutation	SNP	ENST00000039989.4	37	CCDS31466.1	202	0.0924908424908425	193	0.39227642276422764	9	0.024861878453038673	0	0.0	0	0.0	A	12.70	2.015330	0.35511	0.331139	0.001047	ENSG00000052841	ENST00000299240;ENST00000039989	T;T	0.31510	1.49;1.59	5.2	5.2	0.72013	.	0.264075	0.45606	D	0.000357	T	0.00012	0.0000	N	0.08118	0	0.34987	P	0.245382	B;B;B	0.16802	0.011;0.007;0.019	B;B;B	0.17433	0.008;0.006;0.018	T	0.41088	-0.9528	9	0.09338	T	0.73	-16.7019	9.8335	0.40956	0.9228:0.0:0.0772:0.0	rs12099204;rs12099204	145;145;145	Q8NEC0;Q96AE7;G3XAB3	.;TTC17_HUMAN;.	L	145	ENSP00000299240:I145L;ENSP00000039989:I145L	ENSP00000039989:I145L	I	+	1	0	TTC17	43369604	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.614000	0.36911	2.091000	0.63221	0.460000	0.39030	ATA	A|0.883;C|0.117	0.117	strong		0.328	TTC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389577.2	NM_018259		C	43413028	A	C	43413028	3	2	22	1	0	0	0	0	1	0	0	0	16699	449	16	5	447	5	TTC17	11	43413028	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	7771600	43413028	91593488	2416	5317											
EXT2	2132	hgsc.bcm.edu	37	chr11	44129386	44129386	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggcctcattgccactggcAtgtttcagttttggccccat	5	14	10	12	0	2	0	2	0	0	0	2	0	2	0	4	3	1	3	4	3	0	4	rs4755779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:44129386A>G	ENST00000343631.3	+	2	253	c.124A>G	c.(124-126)Atg>Gtg	p.M42V	EXT2_ENST00000395673.3_Missense_Mutation_p.M75V|EXT2_ENST00000533608.1_Missense_Mutation_p.M42V|EXT2_ENST00000358681.4_Missense_Mutation_p.M42V			Q93063	EXT2_HUMAN	exostosin glycosyltransferase 2	42			M -> V (in dbSNP:rs4755779).		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						TGCCACTGGCATGTTTCAGTT	0.527			"Mis, N, F, S"			"exostoses, osteosarcoma"			Hereditary Multiple Exostoses				A|||	65	0.0129792	0.0492	0.0	5008	,	,		19628	0.0		0.0	False		,,,				2504	0.0				p.M75V		Atlas-SNP	.	yes	Rec		Multiple Exostoses Type 2	11	11p12-p11	2132	multiple exostoses type 2 gene		M	.	EXT2	129	.	0			c.A223G						PASS	.	A	VAL/MET,VAL/MET,VAL/MET	215,4191	132.1+/-168.6	3,209,1991	158	164	162		223,124,124	-1.5	1	11	dbSNP_111	162	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	EXT2	NM_000401.3,NM_001178083.1,NM_207122.1	21,21,21	3,210,6290	GG,GA,AA		0.0116,4.8797,1.6608	benign,benign,benign	75/752,42/729,42/719	44129386	216,12790	2203	4300	6503	SO:0001583	missense	2132	exon2	Familial Cancer Database	HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	ACTGGCATGTTTC		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.124A>G	11.37:g.44129386A>G	ENSP00000342656:p.Met42Val	188	0	0		204	98	0.480392	NM_000401	B2R5Z6|C9JU51|J3KPT2|O15288	Missense_Mutation	SNP	ENST00000343631.3	37	CCDS7908.1	24	0.01098901098901099	24	0.04878048780487805	0	0.0	0	0.0	0	0.0	A	9.644	1.139669	0.21205	0.048797	1.16E-4	ENSG00000151348	ENST00000533608;ENST00000532479;ENST00000527014;ENST00000358681;ENST00000395673;ENST00000343631	T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95	5.45	-1.52	0.08637	.	0.204155	0.64402	N	0.000019	T	0.03095	0.0091	N	0.24115	0.695	0.43814	D	0.996377	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	0.17018	-1.0383	10	0.07990	T	0.79	-5.2768	8.2837	0.31915	0.5707:0.1043:0.3249:0.0	rs4755779;rs52810595;rs4755779	42;42;42;42;55	Q6NUL1;C9JU51;Q93063-2;Q93063;D3DR24	.;.;.;EXT2_HUMAN;.	V	42;42;42;42;75;42	ENSP00000431173:M42V;ENSP00000433827:M42V;ENSP00000434716:M42V;ENSP00000351509:M42V;ENSP00000379032:M75V;ENSP00000342656:M42V	ENSP00000342656:M42V	M	+	1	0	EXT2	44085962	1.000000	0.71417	0.996000	0.52242	0.995000	0.86356	1.323000	0.33701	-0.161000	0.10983	0.528000	0.53228	ATG	A|0.981;G|0.019	0.019	strong		0.527	EXT2-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390074.1	NM_000401		G	44129386	A	G	44129386	3	3	22	1	0	0	0	0	1	0	0	0	5326	217	8	3	229	3	EXT2	11	44129386	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	716358	44129386	90877130	2417	5318											
ALX4	60529	hgsc.bcm.edu	37	chr11	44286722	44286722	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgttgttgccgagccaggaCgggttctgaatctgggagag	7	9	16	9	3	2	2	0	1	2	1	2	5	2	3	3	3	2	3	3	3	1	3	rs145904583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:44286722C>T	ENST00000329255.3	-	4	1021	c.918G>A	c.(916-918)ccG>ccA	p.P306P		NM_021926.3	NP_068745.2	Q9H161	ALX4_HUMAN	ALX homeobox 4	306			P -> L. {ECO:0000269|PubMed:22829454}.		anterior/posterior pattern specification (GO:0009952)|digestive tract development (GO:0048565)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal system morphogenesis (GO:0048704)|hair follicle development (GO:0001942)|muscle organ development (GO:0007517)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of apoptotic process (GO:0042981)|skeletal system development (GO:0001501)|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)	p.P306P(1)		central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	16						CGAGCCAGGACGGGTTCTGAA	0.687													C|||	47	0.00938498	0.0325	0.0043	5008	,	,		16566	0.0		0.0	False		,,,				2504	0.001				p.P306P		Atlas-SNP	.											ALX4,NS,carcinoma,0,1	ALX4	58	1	1	Substitution - coding silent(1)	prostate(1)	c.G918A						PASS	.	C		100,4198		1,98,2050	17	16	16		918	-7.6	0.3	11	dbSNP_134	16	5,8425		0,5,4210	no	coding-synonymous	ALX4	NM_021926.3		1,103,6260	TT,TC,CC		0.0593,2.3267,0.825		306/412	44286722	105,12623	2149	4215	6364	SO:0001819	synonymous_variant	60529	exon4			CCAGGACGGGTTC	AF294629	CCDS31468.1	11p11.2	2011-06-20	2008-11-04		ENSG00000052850	ENSG00000052850		"Homeoboxes / PRD class"	450	protein-coding gene	gene with protein product		605420	"parietal foramina 2", "aristaless-like homeobox 4"	PFM2		11017806, 8644736	Standard	NM_021926		Approved	FPP, PFM, KIAA1788	uc001myb.3	Q9H161	OTTHUMG00000166557	ENST00000329255.3:c.918G>A	11.37:g.44286722C>T		267	0	0		221	109	0.493213	NM_021926	Q96JN7|Q9H198|Q9HAY9	Silent	SNP	ENST00000329255.3	37	CCDS31468.1																																																																																			C|0.991;T|0.009	0.009	strong		0.687	ALX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390399.1			T	44286722	C	T	44286722	2	4	22	1	0	0	0	0	0	0	0	1	558	523	19	1		1	ALX4	11	44286722	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	157336	44286722	90719794	2418	5319											
TSPAN18	90139	hgsc.bcm.edu	37	chr11	44931308	44931308	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgggtcatggtggaccccaCcggcttccgggagatcgtgg	5	8	16	12	3	1	1	1	0	0	1	3	3	2	2	4	6	0	1	4	6	0	1	rs34282417	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:44931308C>T	ENST00000520358.2	+	5	531	c.116C>T	c.(115-117)aCc>aTc	p.T39I	TSPAN18_ENST00000340160.3_Missense_Mutation_p.T39I			Q96SJ8	TSN18_HUMAN	tetraspanin 18	39						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(6)|lung(3)	10						GTGGACCCCACCGGCTTCCGG	0.667													C|||	17	0.00339457	0.0121	0.0014	5008	,	,		14867	0.0		0.0	False		,,,				2504	0.0				p.T39I		Atlas-SNP	.											.	TSPAN18	38	.	0			c.C116T						PASS	.	C	ILE/THR	46,4360	47.5+/-82.1	0,46,2157	45	49	48		116	5	1	11	dbSNP_126	48	0,8598		0,0,4299	yes	missense	TSPAN18	NM_130783.4	89	0,46,6456	TT,TC,CC		0.0,1.044,0.3537	probably-damaging	39/249	44931308	46,12958	2203	4299	6502	SO:0001583	missense	90139	exon4			ACCCCACCGGCTT	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.116C>T	11.37:g.44931308C>T	ENSP00000429993:p.Thr39Ile	96	0	0		87	44	0.505747	NM_130783	Q6UY44|Q8NBI9	Missense_Mutation	SNP	ENST00000520358.2	37	CCDS7910.1	9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	C	18.20	3.570526	0.65765	0.01044	0.0	ENSG00000157570	ENST00000533786;ENST00000533202;ENST00000520358;ENST00000520999;ENST00000340160;ENST00000520837	T;T;T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2;-1.2;-1.2	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.67859	0.2938	M	0.67517	2.055	0.80722	D	1	B;P	0.40050	0.143;0.7	B;B	0.42882	0.228;0.401	T	0.76041	-0.3104	10	0.40728	T	0.16	.	18.2971	0.90150	0.0:1.0:0.0:0.0	rs34282417	39;39	Q8WUV1;Q96SJ8	.;TSN18_HUMAN	I	39;39;39;49;39;49	ENSP00000433592:T39I;ENSP00000434625:T39I;ENSP00000429993:T39I;ENSP00000427942:T49I;ENSP00000339820:T39I;ENSP00000430343:T49I	ENSP00000339820:T39I	T	+	2	0	TSPAN18	44887884	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.845000	0.62853	2.319000	0.78375	0.561000	0.74099	ACC	C|0.995;T|0.005	0.005	strong		0.667	TSPAN18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376197.3	NM_130783		T	44931308	C	T	44931308	3	4	22	1	0	0	0	0	1	0	0	0	16657	507	18	2	122	2	TSPAN18	11	44931308	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	644586	44931308	90075208	2419	5320											
TSPAN18	90139	hgsc.bcm.edu	37	chr11	44948263	44948263	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctcaacaccttcgagacctaCgtctacttggccggagccct	8	9	8	16	3	2	1	1	0	1	1	3	3	2	2	4	2	4	0	4	2	3	4	rs34695714	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:44948263C>T	ENST00000520358.2	+	9	1069	c.654C>T	c.(652-654)taC>taT	p.Y218Y	TSPAN18_ENST00000340160.3_Silent_p.Y218Y			Q96SJ8	TSN18_HUMAN	tetraspanin 18	218						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(6)|lung(3)	10						TCGAGACCTACGTCTACTTGG	0.602											OREG0020922	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	129	0.0257588	0.0953	0.0043	5008	,	,		17858	0.0		0.0	False		,,,				2504	0.0				p.Y218Y		Atlas-SNP	.											TSPAN18,colon,carcinoma,+1,1	TSPAN18	38	1	0			c.C654T						PASS	.	C		320,4086	169.8+/-200.3	6,308,1889	217	187	197		654	-1	1	11	dbSNP_126	197	2,8596	2.2+/-6.3	0,2,4297	no	coding-synonymous	TSPAN18	NM_130783.4		6,310,6186	TT,TC,CC		0.0233,7.2628,2.4762		218/249	44948263	322,12682	2203	4299	6502	SO:0001819	synonymous_variant	90139	exon8			GACCTACGTCTAC	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.654C>T	11.37:g.44948263C>T		107	0	0	927	124	65	0.524194	NM_130783	Q6UY44|Q8NBI9	Silent	SNP	ENST00000520358.2	37	CCDS7910.1	58	0.026556776556776556	57	0.11585365853658537	1	0.0027624309392265192	0	0.0	0	0.0	C	3.000	-0.206236	0.06180	0.072628	2.33E-4	ENSG00000157570	ENST00000518429	.	.	.	4.54	-1.0	0.10196	.	.	.	.	.	T	0.00666	0.0022	.	.	.	0.09310	P	0.9999999999999879	.	.	.	.	.	.	T	0.23511	-1.0186	3	.	.	.	.	9.8138	0.40840	0.0:0.4987:0.0:0.5013	rs34695714	.	.	.	C	222	.	.	R	+	1	0	TSPAN18	44904839	0.935000	0.31712	0.991000	0.47740	0.329000	0.28539	0.060000	0.14342	-0.186000	0.10533	0.479000	0.44913	CGT	C|0.972;T|0.028	0.028	strong		0.602	TSPAN18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376197.3	NM_130783		T	44948263	C	T	44948263	2	4	22	1	0	0	0	0	0	0	0	1	16657	547	19	1		1	TSPAN18	11	44948263	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	16955	44948263	90058253	2420	5321											
SLC35C1	55343	hgsc.bcm.edu	37	chr11	45827783	45827783	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgtcggtgtggccttctacaAtgtgggccgctcactcacca	6	10	11	14	3	3	0	2	0	1	0	4	0	3	0	3	3	1	1	3	3	2	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:45827783A>G	ENST00000314134.3	+	1	1827	c.431A>G	c.(430-432)aAt>aGt	p.N144S	SLC35C1_ENST00000456334.1_Missense_Mutation_p.N131S|SLC35C1_ENST00000442528.2_Missense_Mutation_p.N131S	NM_018389.4	NP_060859.4	Q96A29	FUCT1_HUMAN	solute carrier family 35 (GDP-fucose transporter), member C1	144					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)		GCCTTCTACAATGTGGGCCGC	0.587																																					p.N144S		Atlas-SNP	.											.	SLC35C1	23	.	0			c.A431G						PASS	.						137	96	110					11																	45827783		2203	4299	6502	SO:0001583	missense	55343	exon1			TCTACAATGTGGG		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.431A>G	11.37:g.45827783A>G	ENSP00000313318:p.Asn144Ser	63	0	0		77	4	0.0519481	NM_018389	B2RDB2|Q9BV76|Q9NUJ8	Missense_Mutation	SNP	ENST00000314134.3	37	CCDS7914.1	.	.	.	.	.	.	.	.	.	.	A	13.73	2.323167	0.41096	.	.	ENSG00000181830	ENST00000442528;ENST00000456334;ENST00000530670;ENST00000314134;ENST00000530471;ENST00000540685	T;T;T;T	0.37915	1.17;1.17;1.17;1.17	4.64	4.64	0.57946	Drug/metabolite transporter (1);	0.049836	0.85682	D	0.000000	T	0.28732	0.0712	L	0.39898	1.24	0.42596	D	0.993269	B	0.22909	0.077	B	0.26614	0.071	T	0.08289	-1.0729	10	0.23302	T	0.38	-24.5504	10.2877	0.43577	0.8343:0.1656:0.0:0.0	.	144	Q96A29	FUCT1_HUMAN	S	131;131;65;144;131;144	ENSP00000412408:N131S;ENSP00000399779:N131S;ENSP00000313318:N144S;ENSP00000432669:N131S	ENSP00000313318:N144S	N	+	2	0	SLC35C1	45784359	0.978000	0.34361	1.000000	0.80357	0.992000	0.81027	4.671000	0.61590	1.738000	0.51689	0.460000	0.39030	AAT	.	.	none		0.587	SLC35C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390139.1	NM_018389		G	45827783	A	G	45827783	3	3	22	1	0	0	0	0	1	0	0	0	14594	101	4	3	433	3	SLC35C1	11	45827783	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	879520	45827783	89178733	2421	5322											
PEX16	9409	hgsc.bcm.edu	37	chr11	45932458	45932458	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccctgcttacttgtgaccaGgccaacgccagggacgtggt	7	9	12	13	2	0	1	0	1	0	0	1	2	1	2	4	3	3	1	4	3	2	2	rs150774189	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:45932458G>A	ENST00000378750.5	-	10	1186	c.943C>T	c.(943-945)Ctg>Ttg	p.L315L	PEX16_ENST00000532681.1_Silent_p.L220L|PEX16_ENST00000241041.3_Silent_p.L315L			Q9Y5Y5	PEX16_HUMAN	peroxisomal biogenesis factor 16	315	Interaction with PEX19.				ER-dependent peroxisome organization (GO:0032581)|peroxisome membrane biogenesis (GO:0016557)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome membrane (GO:0045046)|protein localization to endoplasmic reticulum (GO:0070972)|protein targeting to peroxisome (GO:0006625)|protein to membrane docking (GO:0022615)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	protein C-terminus binding (GO:0008022)			large_intestine(2)|lung(2)|ovary(2)|skin(1)	7				GBM - Glioblastoma multiforme(35;0.223)		CTTGTGACCAGGCCAACGCCA	0.597													G|||	19	0.00379393	0.0136	0.0014	5008	,	,		18792	0.0		0.0	False		,,,				2504	0.0				p.L315L		Atlas-SNP	.											.	PEX16	24	.	0			c.C943T						PASS	.	G	,	68,4338	62.3+/-99.4	2,64,2137	118	102	108		943,943	3.4	1	11	dbSNP_134	108	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	PEX16	NM_004813.2,NM_057174.2	,	2,64,6436	AA,AG,GG		0.0,1.5433,0.5229	,	315/337,315/347	45932458	68,12936	2203	4299	6502	SO:0001819	synonymous_variant	9409	exon10			TGACCAGGCCAAC	AF118240	CCDS7917.1, CCDS31472.1	11p	2007-12-14			ENSG00000121680	ENSG00000121680			8857	protein-coding gene	gene with protein product		603360				9922452	Standard	NM_057174		Approved		uc001nbt.3	Q9Y5Y5	OTTHUMG00000167005	ENST00000378750.5:c.943C>T	11.37:g.45932458G>A		91	0	0		111	60	0.540541	NM_004813	Q9BWB9	Silent	SNP	ENST00000378750.5	37	CCDS31472.1																																																																																			G|0.995;A|0.005	0.005	strong		0.597	PEX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392398.1	NM_057174		A	45932458	G	A	45932458	2	1	22	1	0	0	0	0	0	0	0	1	11752	991	35	2		2	PEX16	11	45932458	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	104675	45932458	89074058	2422	5323											
DGKZ	8525	hgsc.bcm.edu	37	chr11	46388024	46388024	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcccagggttccagccgccGgcgctccagcactgtgcccc	4	5	13	19	3	0	0	0	0	0	0	2	0	2	0	7	3	3	3	7	3	0	1	rs11827702	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:46388024G>A	ENST00000454345.1	+	2	343	c.218G>A	c.(217-219)cGg>cAg	p.R73Q	DGKZ_ENST00000343674.6_Intron|DGKZ_ENST00000525434.1_3'UTR|DGKZ_ENST00000543978.1_Intron|DGKZ_ENST00000532868.2_Intron|DGKZ_ENST00000421244.2_Intron|DGKZ_ENST00000456247.2_Intron|DGKZ_ENST00000527911.1_Intron|DGKZ_ENST00000395574.3_Intron|DGKZ_ENST00000528615.1_Intron|DGKZ_ENST00000318201.8_Intron	NM_001105540.1	NP_001099010.1	Q13574	DGKZ_HUMAN	diacylglycerol kinase, zeta	73					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)		TCCAGCCGCCGGCGCTCCAGC	0.701													G|||	204	0.0407348	0.1475	0.0101	5008	,	,		12532	0.0		0.001	False		,,,				2504	0.001				p.R73Q		Atlas-SNP	.											.	DGKZ	199	.	0			c.G218A						PASS	.	G	GLN/ARG,,,,,,	346,3634		8,330,1652	13	15	15		218,,,,,,	3.2	1	11	dbSNP_120	15	4,8270		0,4,4133	yes	missense,intron,intron,intron,intron,intron,intron	DGKZ	NM_001105540.1,NM_001199266.1,NM_001199267.1,NM_001199268.1,NM_003646.3,NM_201532.2,NM_201533.3	43,,,,,,	8,334,5785	AA,AG,GG		0.0483,8.6935,2.8562	possibly-damaging,,,,,,	73/1118,,,,,,	46388024	350,11904	1990	4137	6127	SO:0001583	missense	8525	exon2			GCCGCCGGCGCTC	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.218G>A	11.37:g.46388024G>A	ENSP00000412178:p.Arg73Gln	23	0	0		44	26	0.590909	NM_001105540	B7Z2M9|B7Z6M3|E9PPW4|F6UCU9|G3V0F6|J3KNJ6|O00542|Q6ZVG7|Q8IVW9	Missense_Mutation	SNP	ENST00000454345.1	37	CCDS41640.1	68	0.031135531135531136	63	0.12804878048780488	5	0.013812154696132596	0	0.0	0	0.0	G	23.1	4.371425	0.82573	0.086935	4.83E-4	ENSG00000149091	ENST00000454345	T	0.74002	-0.8	4.15	3.15	0.36227	.	2.389100	0.02186	N	0.060943	T	0.03520	0.0101	L	0.34521	1.04	0.80722	D	1	D	0.76494	0.999	P	0.61275	0.886	T	0.57745	-0.7758	10	0.72032	D	0.01	.	12.8442	0.57821	0.0:0.0:0.8362:0.1637	rs11827702	73	Q13574	DGKZ_HUMAN	Q	73	ENSP00000412178:R73Q	ENSP00000412178:R73Q	R	+	2	0	DGKZ	46344600	1.000000	0.71417	1.000000	0.80357	0.539000	0.34962	6.808000	0.75206	2.033000	0.60031	0.462000	0.41574	CGG	G|0.968;A|0.032	0.032	strong		0.701	DGKZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389772.1	NM_001105540		A	46388024	G	A	46388024	3	1	22	1	0	0	0	0	1	0	0	0	4476	1116	39	1	664	1	DGKZ	11	46388024	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	455566	46388024	88618492	2423	5324											
LRP4	4038	hgsc.bcm.edu	37	chr11	46914526	46914526	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctgagatacaacttacccCtccatgggatgcaaggcaat	12	8	9	12	0	0	1	0	1	0	1	1	3	1	2	4	2	4	2	4	2	5	2	rs61741501	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:46914526C>T	ENST00000378623.1	-	13	1937	c.1695G>A	c.(1693-1695)gaG>gaA	p.E565E		NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	565					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)		CAACTTACCCCTCCATGGGAT	0.567													C|||	306	0.0611022	0.2216	0.0173	5008	,	,		17231	0.0		0.001	False		,,,				2504	0.0				p.E565E		Atlas-SNP	.											.	LRP4	160	.	0			c.G1695A						PASS	.	C		763,3639	303.2+/-287.8	67,629,1505	43	41	42		1695	2.7	1	11	dbSNP_129	42	3,8595	2.2+/-6.3	0,3,4296	no	coding-synonymous	LRP4	NM_002334.3		67,632,5801	TT,TC,CC		0.0349,17.333,5.8923		565/1906	46914526	766,12234	2201	4299	6500	SO:0001819	synonymous_variant	4038	exon13			TTACCCCTCCATG	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.1695G>A	11.37:g.46914526C>T		66	0	0		56	29	0.517857	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Silent	SNP	ENST00000378623.1	37	CCDS31478.1																																																																																			C|0.947;T|0.053	0.053	strong		0.567	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334		T	46914526	C	T	46914526	2	4	22	1	0	0	0	0	0	0	0	1	8968	680	24	2		2	LRP4	11	46914526	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	526502	46914526	88091990	2424	5325											
LRP4	4038	hgsc.bcm.edu	37	chr11	46917868	46917868	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaacacaggaactggtccAaggcacattgggggcttcct	10	8	11	12	0	0	0	0	0	0	0	3	1	3	1	3	5	2	2	3	5	3	2	rs7926667	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:46917868A>G	ENST00000378623.1	-	9	1183	c.941T>C	c.(940-942)tTg>tCg	p.L314S		NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	314	LDL-receptor class A 8. {ECO:0000255|PROSITE-ProRule:PRU00124}.		L -> S (in dbSNP:rs7926667).		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)		GAACTGGTCCAAGGCACATTG	0.562													G|||	306	0.0611022	0.2216	0.0173	5008	,	,		20751	0.0		0.001	False		,,,				2504	0.0				p.L314S		Atlas-SNP	.											.	LRP4	160	.	0			c.T941C						PASS	.	G	SER/LEU	769,3633	752.8+/-412.3	67,635,1499	90	86	87		941	6	0.9	11	dbSNP_116	87	3,8595	818.6+/-406.8	0,3,4296	yes	missense	LRP4	NM_002334.3	145	67,638,5795	GG,GA,AA		0.0349,17.4693,5.9385	benign	314/1906	46917868	772,12228	2201	4299	6500	SO:0001583	missense	4038	exon9			TGGTCCAAGGCAC	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.941T>C	11.37:g.46917868A>G	ENSP00000367888:p.Leu314Ser	28	0	0		22	7	0.318182	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	37	CCDS31478.1	100	0.045787545787545784	92	0.18699186991869918	8	0.022099447513812154	0	0.0	0	0.0	G	4.491	0.091136	0.08632	0.174693	3.49E-4	ENSG00000134569	ENST00000378623	T	0.55234	0.53	5.96	5.96	0.96718	.	0.074366	0.56097	N	0.000024	T	0.00039	0.0001	N	0.02368	-0.58	0.42982	P	0.005531999999999981	B	0.02656	0.0	B	0.06405	0.002	T	0.08806	-1.0704	9	0.07482	T	0.82	.	10.2442	0.43330	0.0677:0.0:0.7975:0.1348	rs7926667;rs52792198;rs7926667	314	O75096	LRP4_HUMAN	S	314	ENSP00000367888:L314S	ENSP00000367888:L314S	L	-	2	0	LRP4	46874444	1.000000	0.71417	0.886000	0.34754	0.907000	0.53573	4.687000	0.61708	1.543000	0.49345	-0.119000	0.15052	TTG	A|0.948;G|0.052	0.052	strong		0.562	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334		G	46917868	A	G	46917868	3	3	22	1	0	0	0	0	1	0	0	0	8968	131	5	3	4896	3	LRP4	11	46917868	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	3342	46917868	88088648	2425	5326											
LRP4	4038	hgsc.bcm.edu	37	chr11	46918529	46918529	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgacagcggaactgttctgcCgtacacatggaggtggctgg	8	9	15	9	2	1	1	0	1	1	0	1	3	1	3	1	5	4	3	1	5	2	2	rs879721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:46918529C>T	ENST00000378623.1	-	8	1055	c.813G>A	c.(811-813)acG>acA	p.T271T		NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	271	LDL-receptor class A 7. {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)		ACTGTTCTGCCGTACACATGG	0.552													T|||	309	0.0617013	0.2239	0.0173	5008	,	,		17998	0.0		0.001	False		,,,				2504	0.0				p.T271T		Atlas-SNP	.											.	LRP4	160	.	0			c.G813A						PASS	.	T		770,3632	753.5+/-412.4	68,634,1499	113	100	104		813	-11.6	0	11	dbSNP_86	104	3,8595	819.0+/-406.8	0,3,4296	no	coding-synonymous	LRP4	NM_002334.3		68,637,5795	TT,TC,CC		0.0349,17.492,5.9462		271/1906	46918529	773,12227	2201	4299	6500	SO:0001819	synonymous_variant	4038	exon8			TTCTGCCGTACAC	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.813G>A	11.37:g.46918529C>T		86	0	0		76	35	0.460526	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Silent	SNP	ENST00000378623.1	37	CCDS31478.1																																																																																			C|0.943;T|0.057	0.057	strong		0.552	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334		T	46918529	C	T	46918529	2	4	22	1	0	0	0	0	0	0	0	1	8968	639	23	1		1	LRP4	11	46918529	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	661	46918529	88087987	2426	5327											
PTPRJ	5795	hgsc.bcm.edu	37	chr11	48149352	48149352	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgctattcaggtttttgacGtcaccgctgtgaacatcagt	9	14	9	9	2	3	2	3	2	0	0	3	2	3	2	1	1	2	3	1	1	2	4	rs2229703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:48149352G>A	ENST00000418331.2	+	7	1466	c.1114G>A	c.(1114-1116)Gtc>Atc	p.V372I	PTPRJ_ENST00000440289.2_Missense_Mutation_p.V372I	NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	372	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.		V -> I (in dbSNP:rs2229703).		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)	p.V372L(1)		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						GGTTTTTGACGTCACCGCTGT	0.498													G|||	156	0.0311502	0.1112	0.0115	5008	,	,		23784	0.0		0.0	False		,,,				2504	0.001				p.V372I		Atlas-SNP	.											PTPRJ_ENST00000418331,rectum,carcinoma,-1,5	PTPRJ	225	5	1	Substitution - Missense(1)	kidney(1)	c.G1114A						PASS	.	G	ILE/VAL,ILE/VAL	397,4005	197.7+/-221.8	9,379,1813	108	95	99		1114,1114	-11.5	0	11	dbSNP_98	99	4,8592	1.2+/-3.3	0,4,4294	yes	missense,missense	PTPRJ	NM_001098503.1,NM_002843.3	29,29	9,383,6107	AA,AG,GG		0.0465,9.0186,3.0851	benign,benign	372/540,372/1338	48149352	401,12597	2201	4298	6499	SO:0001583	missense	5795	exon7			TTTGACGTCACCG	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.1114G>A	11.37:g.48149352G>A	ENSP00000400010:p.Val372Ile	73	0	0		96	38	0.395833	NM_001098503	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Missense_Mutation	SNP	ENST00000418331.2	37	CCDS7945.1	53	0.024267399267399268	48	0.0975609756097561	5	0.013812154696132596	0	0.0	0	0.0	G	4.166	0.029336	0.08054	0.090186	4.65E-4	ENSG00000149177	ENST00000278456;ENST00000418331;ENST00000440289	T;T	0.59906	0.23;0.23	5.75	-11.5	0.00074	Fibronectin, type III (4);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00637	0.0021	N	0.04297	-0.235	0.09310	N	1	B;P	0.36027	0.035;0.533	B;B	0.34652	0.024;0.187	T	0.28713	-1.0035	9	0.23302	T	0.38	.	9.7949	0.40728	0.1072:0.3001:0.5182:0.0745	rs2229703;rs16905649;rs56484607;rs16905649	372;372	Q12913;Q6P4H4	PTPRJ_HUMAN;.	I	372	ENSP00000400010:V372I;ENSP00000409733:V372I	ENSP00000278456:V372I	V	+	1	0	PTPRJ	48105928	0.000000	0.05858	0.000000	0.03702	0.188000	0.23474	-1.405000	0.02492	-3.757000	0.00111	-0.136000	0.14681	GTC	G|0.964;A|0.036	0.036	strong		0.498	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1			A	48149352	G	A	48149352	3	1	22	1	0	0	0	0	1	0	0	0	12819	1145	40	1	1140	1	PTPRJ	11	48149352	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1230823	48149352	86857164	2427	5328											
PTPRJ	5795	hgsc.bcm.edu	37	chr11	48166642	48166642	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctatgtgtccttcagtcgCtactcagatgctgtttcctt	6	16	8	11	1	2	1	2	0	0	1	5	1	4	1	2	0	3	4	2	0	2	5	rs34300475	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:48166642C>T	ENST00000418331.2	+	14	3229	c.2877C>T	c.(2875-2877)cgC>cgT	p.R959R		NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	959					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						CCTTCAGTCGCTACTCAGATG	0.532													C|||	350	0.0698882	0.2564	0.013	5008	,	,		22420	0.0		0.002	False		,,,				2504	0.0				p.R959R		Atlas-SNP	.											.	PTPRJ	225	.	0			c.C2877T						PASS	.	C		789,3613	319.1+/-295.9	68,653,1480	164	145	151		2877	2.3	0	11	dbSNP_126	151	5,8591	3.0+/-9.4	0,5,4293	no	coding-synonymous	PTPRJ	NM_002843.3		68,658,5773	TT,TC,CC		0.0582,17.9237,6.1086		959/1338	48166642	794,12204	2201	4298	6499	SO:0001819	synonymous_variant	5795	exon14			CAGTCGCTACTCA	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.2877C>T	11.37:g.48166642C>T		206	0	0		198	100	0.50505	NM_002843	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Silent	SNP	ENST00000418331.2	37	CCDS7945.1																																																																																			C|0.944;T|0.056	0.056	strong		0.532	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1			T	48166642	C	T	48166642	2	4	22	1	0	0	0	0	0	0	0	1	12819	784	28	2		2	PTPRJ	11	48166642	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	17290	48166642	86839874	2428	5329											
OR4X1	390113	hgsc.bcm.edu	37	chr11	48285424	48285424	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttaaaatatggttgctacAaacaatgtgactgaaataat	17	13	6	5	0	0	2	0	2	0	0	0	2	0	2	0	1	3	2	0	1	8	6	rs713323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:48285424A>G	ENST00000320048.1	+	1	12	c.12A>G	c.(10-12)acA>acG	p.T4T		NM_001004726.1	NP_001004726.1	Q8NH49	OR4X1_HUMAN	olfactory receptor, family 4, subfamily X, member 1 (gene/pseudogene)	4						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						TGGTTGCTACAAACAATGTGA	0.428													A|||	80	0.0159744	0.0575	0.0058	5008	,	,		20768	0.0		0.0	False		,,,				2504	0.0				p.T4T		Atlas-SNP	.											.	OR4X1	75	.	0			c.A12G						PASS	.	A		203,4199	125.7+/-162.9	5,193,2003	94	90	91		12	-1.7	0	11	dbSNP_86	91	0,8596		0,0,4298	no	coding-synonymous	OR4X1	NM_001004726.1		5,193,6301	GG,GA,AA		0.0,4.6115,1.5618		4/306	48285424	203,12795	2201	4298	6499	SO:0001819	synonymous_variant	390113	exon1			TGCTACAAACAAT	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.12A>G	11.37:g.48285424A>G		160	0	0		167	82	0.491018	NM_001004726	Q6IF74	Silent	SNP	ENST00000320048.1	37	CCDS31487.1																																																																																			A|0.982;G|0.018	0.018	strong		0.428	OR4X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383373.1	NM_001004726		G	48285424	A	G	48285424	2	3	22	1	0	0	0	0	0	0	0	1	11093	117	5	3		3	OR4X1	11	48285424	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	118782	48285424	86721092	2429	5330											
OR4A5	81318	hgsc.bcm.edu	37	chr11	51411817	51411817	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctattgacaacaacagtgagGcctataaagtaggtgtcagt	14	10	10	7	0	1	2	1	2	0	0	1	2	1	2	1	2	2	1	1	2	7	5	rs144502772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:51411817G>A	ENST00000319760.6	-	1	631	c.579C>T	c.(577-579)ggC>ggT	p.G193G		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, 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)			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)				CAACAGTGAGGCCTATAAAGT	0.428													.|||	30	0.00599042	0.0219	0.0014	5008	,	,		20435	0.0		0.0	False		,,,				2504	0.0				p.G193G		Atlas-SNP	.											.	OR4A5	116	.	0			c.C579T						PASS	.	G		102,4300		2,98,2101	62	55	57		579	-2.1	0.1	11	dbSNP_134	57	0,8590		0,0,4295	no	coding-synonymous	OR4A5	NM_001005272.3		2,98,6396	AA,AG,GG		0.0,2.3171,0.7851		193/316	51411817	102,12890	2201	4295	6496	SO:0001819	synonymous_variant	81318	exon1			AGTGAGGCCTATA	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.579C>T	11.37:g.51411817G>A		88	0	0		105	58	0.552381	NM_001005272	Q6IF84	Silent	SNP	ENST00000319760.6	37	CCDS31497.1																																																																																			G|0.993;A|0.007	0.007	strong		0.428	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272		A	51411817	G	A	51411817	2	1	22	1	0	0	0	0	0	0	0	1	11052	1190	42	2		2	OR4A5	11	51411817	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3126393	51411817	83594699	2430	5331											
OR4A5	81318	hgsc.bcm.edu	37	chr11	51412370	51412370	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaagcccaggaggacaaatTctgtaatattgttattctgt	14	13	8	6	0	2	0	0	0	2	0	2	2	2	2	1	2	1	2	1	2	6	6	rs149177099	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:51412370T>A	ENST00000319760.6	-	1	78	c.26A>T	c.(25-27)gAa>gTa	p.E9V		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	9						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)				GAGGACAAATTCTGTAATATT	0.423													.|||	42	0.00838658	0.0272	0.0086	5008	,	,		18603	0.0		0.0	False		,,,				2504	0.0				p.E9V		Atlas-SNP	.											OR4A5,NS,carcinoma,-1,1	OR4A5	116	1	0			c.A26T						PASS	.	T	VAL/GLU	130,4266		1,128,2069	28	27	27		26	2	0.3	11	dbSNP_134	27	6,8576		0,6,4285	no	missense	OR4A5	NM_001005272.3	121	1,134,6354	AA,AT,TT		0.0699,2.9572,1.0479	probably-damaging	9/316	51412370	136,12842	2198	4291	6489	SO:0001583	missense	81318	exon1			ACAAATTCTGTAA	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.26A>T	11.37:g.51412370T>A	ENSP00000367664:p.Glu9Val	94	0	0		88	38	0.431818	NM_001005272	Q6IF84	Missense_Mutation	SNP	ENST00000319760.6	37	CCDS31497.1	13	0.005952380952380952	10	0.02032520325203252	3	0.008287292817679558	0	0.0	0	0.0	.	4.648	0.120435	0.08881	0.029572	6.99E-4	ENSG00000221840	ENST00000319760	T	0.01139	5.28	2.01	2.01	0.26516	.	0.000000	0.48286	D	0.000188	T	0.00845	0.0028	M	0.84511	2.7	0.09310	N	0.999991	P	0.35714	0.517	B	0.37833	0.259	T	0.24512	-1.0158	10	0.72032	D	0.01	.	7.9849	0.30205	0.0:0.0:0.0:1.0	.	9	Q8NH83	OR4A5_HUMAN	V	9	ENSP00000367664:E9V	ENSP00000367664:E9V	E	-	2	0	OR4A5	51268946	0.027000	0.19231	0.318000	0.25279	0.086000	0.17979	1.684000	0.37649	1.181000	0.42912	0.136000	0.15936	GAA	T|0.990;A|0.010	0.010	strong		0.423	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272		A	51412370	T	A	51412370	3	1	22	1	0	0	0	0	1	0	0	0	11052	1783	62	5	925	5	OR4A5	11	51412370	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	553	51412370	83594146	2431	5332											
OR4A16	81327	hgsc.bcm.edu	37	chr11	55110989	55110989	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agctcttcatagaacacttaCttggtggtgcagaggtcttc	9	13	10	9	0	3	2	1	0	2	2	4	2	3	2	0	3	4	2	0	3	3	5	rs116541488	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55110989C>G	ENST00000314721.2	+	1	363	c.313C>G	c.(313-315)Ctt>Gtt	p.L105V		NM_001005274.1	NP_001005274.1	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A, member 16	105						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						AGAACACTTACTTGGTGGTGC	0.448													.|||	50	0.00998403	0.0333	0.0086	5008	,	,		22391	0.0		0.0	False		,,,				2504	0.0				p.L105V		Atlas-SNP	.											.	OR4A16	120	.	0			c.C313G						PASS	.	C	VAL/LEU	142,4260	100.3+/-138.9	1,140,2060	201	188	192		313	1.4	0.2	11	dbSNP_132	192	5,8587	5.0+/-18.6	0,5,4291	yes	missense	OR4A16	NM_001005274.1	32	1,145,6351	GG,GC,CC		0.0582,3.2258,1.1313	benign	105/329	55110989	147,12847	2201	4296	6497	SO:0001583	missense	81327	exon1			CACTTACTTGGTG	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.313C>G	11.37:g.55110989C>G	ENSP00000325128:p.Leu105Val	307	0	0		289	128	0.442907	NM_001005274	Q6IFL3	Missense_Mutation	SNP	ENST00000314721.2	37	CCDS31499.1	16	0.007326007326007326	13	0.026422764227642278	3	0.008287292817679558	0	0.0	0	0.0	c	0.720	-0.783973	0.02907	0.032258	5.82E-4	ENSG00000181961	ENST00000314721	T	0.00700	5.82	2.57	1.37	0.22104	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00356	0.0011	L	0.41079	1.255	0.09310	N	1	B	0.25007	0.116	B	0.29353	0.101	T	0.48658	-0.9016	9	0.87932	D	0	.	4.5335	0.12017	0.0:0.3127:0.0:0.6873	.	105	Q8NH70	O4A16_HUMAN	V	105	ENSP00000325128:L105V	ENSP00000325128:L105V	L	+	1	0	OR4A16	54867565	0.036000	0.19791	0.157000	0.22605	0.029000	0.11900	0.995000	0.29706	0.240000	0.21263	-0.664000	0.03847	CTT	C|0.988;G|0.012	0.012	strong		0.448	OR4A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391160.1	NM_001005274		G	55110989	C	G	55110989	3	3	22	1	0	0	0	0	1	0	0	0	11050	565	20	4	315	4	OR4A16	11	55110989	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3698619	55110989	79895527	2432	5333											
OR4C16	219428	hgsc.bcm.edu	37	chr11	55340057	55340057	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcctgggtgggatcctgtGtgcattctttagttcagatt	5	16	13	7	0	2	1	1	0	1	1	3	2	3	2	2	3	1	2	2	3	1	5	rs144962866	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55340057G>A	ENST00000314634.3	+	1	454	c.454G>A	c.(454-456)Gtg>Atg	p.V152M		NM_001004701.2	NP_001004701.2	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C, member 16 (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)			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)				GGGATCCTGTGTGCATTCTTT	0.488													g|||	34	0.00678914	0.025	0.0014	5008	,	,		19716	0.0		0.0	False		,,,				2504	0.0				p.V152M		Atlas-SNP	.											.	OR4C16	104	.	0			c.G454A						PASS	.	G	MET/VAL	101,4301	79.9+/-118.3	2,97,2102	149	137	141		454	-2.6	0.3	11	dbSNP_134	141	0,8592		0,0,4296	yes	missense	OR4C16	NM_001004701.2	21	2,97,6398	AA,AG,GG		0.0,2.2944,0.7773	benign	152/311	55340057	101,12893	2201	4296	6497	SO:0001583	missense	219428	exon1			TCCTGTGTGCATT	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.454G>A	11.37:g.55340057G>A	ENSP00000324913:p.Val152Met	144	0	0		159	85	0.534591	NM_001004701	Q6IEV8	Missense_Mutation	SNP	ENST00000314634.3	37	CCDS31502.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	G	9.386	1.074257	0.20227	0.022944	0.0	ENSG00000181935	ENST00000314634	T	0.39997	1.05	4.83	-2.58	0.06228	GPCR, rhodopsin-like superfamily (1);	0.267871	0.27139	N	0.020760	T	0.16428	0.0395	L	0.39566	1.225	0.09310	N	1	B	0.18461	0.028	B	0.32211	0.142	T	0.25363	-1.0134	10	0.62326	D	0.03	.	5.5455	0.17061	0.4732:0.1409:0.3859:0.0	.	152	Q8NGL9	OR4CG_HUMAN	M	152	ENSP00000324913:V152M	ENSP00000324913:V152M	V	+	1	0	OR4C16	55096633	0.000000	0.05858	0.326000	0.25389	0.412000	0.31113	-3.095000	0.00607	-0.293000	0.08986	-0.272000	0.10252	GTG	G|0.994;A|0.006	0.006	strong		0.488	OR4C16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382627.1	NM_001004701		A	55340057	G	A	55340057	3	1	22	1	0	0	0	0	1	0	0	0	11058	1377	48	2	456	2	OR4C16	11	55340057	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	229068	55340057	79666459	2433	5334											
OR4S2	219431	hgsc.bcm.edu	37	chr11	55419147	55419147	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggcccctgtacttttatgtaCatgcgccctgatacgacctt	7	13	8	13	2	0	1	0	1	0	0	0	2	0	1	4	1	4	2	4	1	4	6	rs74538149	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55419147C>T	ENST00000312422.2	+	1	768	c.768C>T	c.(766-768)taC>taT	p.Y256Y		NM_001004059.2	NP_001004059.2	Q8NH73	OR4S2_HUMAN	olfactory receptor, family 4, subfamily S, member 2	256						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)				CTTTTATGTACATGCGCCCTG	0.463													c|||	56	0.0111821	0.0416	0.0014	5008	,	,		14395	0.0		0.0	False		,,,				2504	0.0				p.Y256Y		Atlas-SNP	.											.	OR4S2	89	.	0			c.C768T						PASS	.	C		169,4189		21,127,2031	161	136	145		768	0.1	1	11	dbSNP_132	145	3,8047		0,3,4022	yes	coding-synonymous	OR4S2	NM_001004059.2		21,130,6053	TT,TC,CC		0.0373,3.8779,1.3862		256/312	55419147	172,12236	2179	4025	6204	SO:0001819	synonymous_variant	219431	exon1			TATGTACATGCGC	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.768C>T	11.37:g.55419147C>T		111	1	0.00900901		73	72	0.986301	NM_001004059	Q6IF72	Silent	SNP	ENST00000312422.2	37	CCDS31505.1																																																																																			C|0.988;T|0.012	0.012	strong		0.463	OR4S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391503.1	NM_001004059		T	55419147	C	T	55419147	2	4	22	1	0	0	0	0	0	0	0	1	11092	489	17	2		2	OR4S2	11	55419147	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	79090	55419147	79587369	2434	5335											
OR5L1	219437	hgsc.bcm.edu	37	chr11	55579078	55579078	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttagccaacctgggcatgAttgcactgattcaggtcagc	9	11	11	10	0	2	2	2	2	0	0	2	2	2	2	2	2	4	3	2	2	2	3	rs2869020	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55579078A>T	ENST00000333973.2	+	1	225	c.136A>T	c.(136-138)Att>Ttt	p.I46F		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	46			I -> F (in dbSNP:rs2869020).			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)				CCTGGGCATGATTGCACTGAT	0.493													N|||	121	0.0241613	0.0862	0.0101	5008	,	,		19133	0.0		0.0	False		,,,				2504	0.0				p.I46F		Atlas-SNP	.											.	OR5L1	145	.	0			c.A136T						PASS	.	A	PHE/ILE	307,4093	167.3+/-198.3	16,275,1909	330	288	302		136	0.6	0.1	11	dbSNP_101	302	6,8586	5.7+/-21.5	0,6,4290	yes	missense	OR5L1	NM_001004738.1	21	16,281,6199	TT,TA,AA		0.0698,6.9773,2.4092	benign	46/312	55579078	313,12679	2200	4296	6496	SO:0001583	missense	219437	exon1			GGCATGATTGCAC	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.136A>T	11.37:g.55579078A>T	ENSP00000335529:p.Ile46Phe	238	1	0.00420168		238	107	0.44958	NM_001004738	B2RNK6|Q6IFD0	Missense_Mutation	SNP	ENST00000333973.2	37	CCDS31509.1	43	0.019688644688644688	39	0.07926829268292683	4	0.011049723756906077	0	0.0	0	0.0	a	12.72	2.022276	0.35701	0.069773	6.98E-4	ENSG00000186117	ENST00000333973	T	0.00638	6.04	4.32	0.548	0.17208	GPCR, rhodopsin-like superfamily (1);	0.454491	0.18670	N	0.134475	T	0.00109	0.0003	M	0.84219	2.685	0.09310	N	1	B	0.29612	0.251	B	0.35039	0.194	T	0.39603	-0.9606	10	0.87932	D	0	-7.0075	8.3108	0.32071	0.6568:0.0:0.3432:0.0	rs2869020;rs52812745;rs2869020	46	Q8NGL2	OR5L1_HUMAN	F	46	ENSP00000335529:I46F	ENSP00000335529:I46F	I	+	1	0	OR5L1	55335654	0.000000	0.05858	0.057000	0.19452	0.019000	0.09904	-0.143000	0.10296	-0.167000	0.10871	0.358000	0.22013	ATT	A|0.976;T|0.024	0.024	strong		0.493	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738		T	55579078	A	T	55579078	3	4	22	1	0	0	0	0	1	0	0	0	11179	333	12	5	138	5	OR5L1	11	55579078	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	159931	55579078	79427438	2435	5336											
OR5D18	219438	hgsc.bcm.edu	37	chr11	55587591	55587591	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgttccttggaactgacgtgCtctgctttaaagttatgttt	7	18	9	7	1	1	1	0	1	1	0	2	2	2	2	1	1	3	5	1	1	4	6	rs142792552	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55587591C>T	ENST00000333976.4	+	1	506	c.486C>T	c.(484-486)tgC>tgT	p.C162C		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	162						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)				AACTGACGTGCTCTGCTTTAA	0.453													N|||	7	0.00139776	0.0053	0.0	5008	,	,		18790	0.0		0.0	False		,,,				2504	0.0				p.C162C		Atlas-SNP	.											.	OR5D18	121	.	0			c.C486T						PASS	.	C		43,4357		0,43,2157	203	189	193		486	-0.8	0.2	11	dbSNP_134	193	0,8592		0,0,4296	no	coding-synonymous	OR5D18	NM_001001952.1		0,43,6453	TT,TC,CC		0.0,0.9773,0.331		162/314	55587591	43,12949	2200	4296	6496	SO:0001819	synonymous_variant	219438	exon1			GACGTGCTCTGCT	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.486C>T	11.37:g.55587591C>T		309	1	0.00323625		345	163	0.472464	NM_001001952	Q6IF67|Q6IFD3|Q96RB3	Silent	SNP	ENST00000333976.4	37	CCDS31510.1																																																																																			C|0.997;T|0.003	0.003	strong		0.453	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	NM_001001952		T	55587591	C	T	55587591	2	4	22	1	0	0	0	0	0	0	0	1	11166	805	28	2		2	OR5D18	11	55587591	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	8513	55587591	79418925	2436	5337											
OR5L2	26338	hgsc.bcm.edu	37	chr11	55594980	55594980	+	Frame_Shift_Del	DEL	G	G	-																															acaaagccatctccttcctaGggtgcatggtgcaattctac																								rs571342053|rs144106069	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55594980delG	ENST00000378397.1	+	1	286	c.286delG	c.(286-288)gggfs	p.G96fs		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	96						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)				CTCCTTCCTAGGGTGCATGGT	0.473										HNSCC(27;0.073)			|||unknown(ALL_OTHER_Ns)	28	0.00559105	0.0189	0.0043	5008	,	,		23720	0.0		0.0	False		,,,				2504	0.0				p.L95fs		Pindel,Atlas-Indel	.											OR5L2,NS,carcinoma,+2,2	OR5L2	135	2	0			c.285delA						PASS	.			101,4161		1,99,2031	187	181	183			-0.1	0	11	dbSNP_134	184	4,8248		0,4,4122	no	frameshift	OR5L2	NM_001004739.1		1,103,6153	A1A1,A1R,RR		0.0485,2.3698,0.8391			55594980	105,12409	2200	4296	6496	SO:0001589	frameshift_variant	26338	exon1			.	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.286delG	11.37:g.55594980delG	ENSP00000367650:p.Gly96fs	201	0	.		141	37	0.262	NM_001004739	Q6IF66|Q96RB2	Frame_Shift_Del	DEL	ENST00000378397.1	37	CCDS31511.1																																																																																			G|0.995;-|0.005	0.005	strong		0.473	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739		-	55594980	G	-	55594980	7	5	22	1	0	1	0	1	0	0	0	0	11180	1000	35	0	288	0	OR5L2	11	55594980	Frame_Shift_Del	DEL	G	TCGA-G8-6324-01A-11D-2210-10	7389	55594980	79411536	2437	5338											
OR5L2	26338	hgsc.bcm.edu	37	chr11	55595401	55595401	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctctgcagagagcaggcacaAagctttctccacctgtgcct	9	9	9	14	0	2	1	0	0	2	1	3	2	2	1	3	1	4	4	3	1	1	1	rs148148644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55595401A>G	ENST00000378397.1	+	1	707	c.707A>G	c.(706-708)aAa>aGa	p.K236R		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	236						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)				AGCAGGCACAAAGCTTTCTCC	0.488										HNSCC(27;0.073)			N|||	7	0.00139776	0.0053	0.0	5008	,	,		17988	0.0		0.0	False		,,,				2504	0.0				p.K236R		Atlas-SNP	.											.	OR5L2	135	.	0			c.A707G						PASS	.	A	ARG/LYS	43,4357		0,43,2157	177	150	159		707	5.2	1	11	dbSNP_134	159	0,8592		0,0,4296	yes	missense	OR5L2	NM_001004739.1	26	0,43,6453	GG,GA,AA		0.0,0.9773,0.331	benign	236/312	55595401	43,12949	2200	4296	6496	SO:0001583	missense	26338	exon1			GGCACAAAGCTTT	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.707A>G	11.37:g.55595401A>G	ENSP00000367650:p.Lys236Arg	166	0	0		159	73	0.459119	NM_001004739	Q6IF66|Q96RB2	Missense_Mutation	SNP	ENST00000378397.1	37	CCDS31511.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	.	13.65	2.300050	0.40694	0.009773	0.0	ENSG00000205030	ENST00000378397	T	0.00360	7.86	5.24	5.24	0.73138	GPCR, rhodopsin-like superfamily (1);	0.110656	0.40640	N	0.001045	T	0.00300	0.0009	M	0.62723	1.935	0.39567	D	0.969221	B	0.31581	0.329	B	0.37304	0.246	T	0.77520	-0.2557	10	0.66056	D	0.02	-6.4806	14.3209	0.66487	1.0:0.0:0.0:0.0	.	236	Q8NGL0	OR5L2_HUMAN	R	236	ENSP00000367650:K236R	ENSP00000367650:K236R	K	+	2	0	OR5L2	55351977	1.000000	0.71417	0.998000	0.56505	0.029000	0.11900	2.879000	0.48522	2.115000	0.64714	0.514000	0.50259	AAA	A|0.997;G|0.003	0.003	strong		0.488	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739		G	55595401	A	G	55595401	3	3	22	1	0	0	0	0	1	0	0	0	11180	14	1	3	709	3	OR5L2	11	55595401	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	421	55595401	79411115	2438	5339											
OR5I1	10798	hgsc.bcm.edu	37	chr11	55703523	55703523	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tagcgatcataggccatggcGgccaggatgaaggattctgt	10	9	14	8	2	2	1	1	1	1	0	2	4	2	3	2	5	1	0	2	5	3	3	rs11231594	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55703523G>A	ENST00000301532.3	-	1	353	c.354C>T	c.(352-354)gcC>gcT	p.A118A		NM_006637.1	NP_006628.1	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I, member 1	118					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						AGGCCATGGCGGCCAGGATGA	0.433													G|||	121	0.0241613	0.0862	0.0101	5008	,	,		19053	0.0		0.0	False		,,,				2504	0.0				p.A118A		Atlas-SNP	.											.	OR5I1	110	.	0			c.C354T						PASS	.	G		304,4098	162.9+/-194.8	16,272,1913	52	55	54		354	-2.7	0.3	11	dbSNP_120	54	6,8578	5.7+/-21.5	0,6,4286	no	coding-synonymous	OR5I1	NM_006637.1		16,278,6199	AA,AG,GG		0.0699,6.906,2.3872		118/315	55703523	310,12676	2201	4292	6493	SO:0001819	synonymous_variant	10798	exon1			CATGGCGGCCAGG	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.354C>T	11.37:g.55703523G>A		86	0	0		96	44	0.458333	NM_006637	Q6IEU4	Silent	SNP	ENST00000301532.3	37	CCDS7949.1																																																																																			G|0.974;A|0.026	0.026	strong		0.433	OR5I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391528.1	NM_006637		A	55703523	G	A	55703523	2	1	22	1	0	0	0	0	0	0	0	1	11173	1103	39	1		1	OR5I1	11	55703523	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	108122	55703523	79302993	2439	5340											
OR10AG1	282770	hgsc.bcm.edu	37	chr11	55735091	55735091	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	accatgatatctttgttcctCagggtatatataataggatt	12	16	7	6	0	2	1	1	1	1	0	3	2	3	2	2	2	0	2	2	2	6	9	rs12292026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55735091C>T	ENST00000312345.2	-	1	899	c.849G>A	c.(847-849)ctG>ctA	p.L283L		NM_001005491.1	NP_001005491.1	Q8NH19	O10AG_HUMAN	olfactory receptor, family 10, subfamily AG, member 1	283						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(6)|lung(24)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	40	Esophageal squamous(21;0.0137)					CTTTGTTCCTCAGGGTATATA	0.328													C|||	121	0.0241613	0.0862	0.0101	5008	,	,		18729	0.0		0.0	False		,,,				2504	0.0				p.L283L		Atlas-SNP	.											.	OR10AG1	100	.	0			c.G849A						PASS	.	C		306,4096	161.4+/-193.6	17,272,1912	55	61	59		849	3.2	1	11	dbSNP_120	59	6,8586	5.7+/-21.5	0,6,4290	no	coding-synonymous	OR10AG1	NM_001005491.1		17,278,6202	TT,TC,CC		0.0698,6.9514,2.4011		283/302	55735091	312,12682	2201	4296	6497	SO:0001819	synonymous_variant	282770	exon1			GTTCCTCAGGGTA	AB065594	CCDS31514.1	11q11	2012-08-09			ENSG00000174970	ENSG00000174970		"GPCR / Class A : Olfactory receptors"	19607	protein-coding gene	gene with protein product							Standard	NM_001005491		Approved		uc010rit.2	Q8NH19	OTTHUMG00000166824	ENST00000312345.2:c.849G>A	11.37:g.55735091C>T		115	0	0		106	55	0.518868	NM_001005491	B2RNH4|Q6IEU3	Silent	SNP	ENST00000312345.2	37	CCDS31514.1																																																																																			C|0.974;T|0.026	0.026	strong		0.328	OR10AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391531.1	NM_001005491		T	55735091	C	T	55735091	2	4	22	1	0	0	0	0	0	0	0	1	10906	813	29	2		2	OR10AG1	11	55735091	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	31568	55735091	79271425	2440	5341											
OR8H2	390151	hgsc.bcm.edu	37	chr11	55873401	55873401	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatttatagtcttagaaacAaagaggtgaaaaatgctgtc	16	12	8	5	0	2	3	1	1	1	2	3	3	2	3	0	1	2	1	0	1	7	4	rs115405120	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55873401A>G	ENST00000313503.1	+	1	883	c.883A>G	c.(883-885)Aaa>Gaa	p.K295E		NM_001005200.1	NP_001005200.1	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H, member 2	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)|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)					TCTTAGAAACAAAGAGGTGAA	0.368										HNSCC(53;0.14)			a|||	35	0.00698882	0.0219	0.0086	5008	,	,		17201	0.0		0.0	False		,,,				2504	0.0				p.K295E		Atlas-SNP	.											.	OR8H2	117	.	0			c.A883G						PASS	.	A	GLU/LYS	102,4298	78.8+/-117.2	1,100,2099	81	89	87		883	3.3	1	11	dbSNP_132	87	2,8586	3.0+/-9.4	0,2,4292	yes	missense	OR8H2	NM_001005200.1	56	1,102,6391	GG,GA,AA		0.0233,2.3182,0.8007	possibly-damaging	295/313	55873401	104,12884	2200	4294	6494	SO:0001583	missense	390151	exon1			AGAAACAAAGAGG	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.883A>G	11.37:g.55873401A>G	ENSP00000323982:p.Lys295Glu	121	0	0		111	61	0.54955	NM_001005200	Q6IFC1	Missense_Mutation	SNP	ENST00000313503.1	37	CCDS31518.1	19	0.0086996336996337	16	0.032520325203252036	3	0.008287292817679558	0	0.0	0	0.0	a	8.777	0.927390	0.18056	0.023182	2.33E-4	ENSG00000181767	ENST00000313503	T	0.44083	0.93	3.35	3.35	0.38373	.	0.000000	0.56097	D	0.000025	T	0.18341	0.0440	M	0.76170	2.325	0.25971	N	0.982491	B	0.28378	0.209	B	0.27380	0.079	T	0.35301	-0.9794	10	0.87932	D	0	.	8.3251	0.32151	0.9009:0.0:0.0991:0.0	.	295	Q8N162	OR8H2_HUMAN	E	295	ENSP00000323982:K295E	ENSP00000323982:K295E	K	+	1	0	OR8H2	55629977	0.009000	0.17119	0.992000	0.48379	0.067000	0.16453	2.182000	0.42556	1.497000	0.48584	0.362000	0.22060	AAA	A|0.991;G|0.009	0.009	strong		0.368	OR8H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391540.1	NM_001005200		G	55873401	A	G	55873401	3	3	22	1	0	0	0	0	1	0	0	0	11247	131	5	3	885	3	OR8H2	11	55873401	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	138310	55873401	79133115	2441	5342											
OR8H3	390152	hgsc.bcm.edu	37	chr11	55889918	55889918	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gactgtcagactctgaagagGtccagatggctctgtttatg	9	12	12	8	0	3	4	1	1	2	3	4	5	4	4	1	2	0	2	1	2	2	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55889918G>A	ENST00000313472.3	+	1	70	c.70G>A	c.(70-72)Gtc>Atc	p.V24I		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, 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(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)					CTCTGAAGAGGTCCAGATGGC	0.453																																					p.V24I		Atlas-SNP	.											.	OR8H3	92	.	0			c.G70A						PASS	.						204	194	198					11																	55889918		2201	4296	6497	SO:0001583	missense	390152	exon1			GAAGAGGTCCAGA	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.70G>A	11.37:g.55889918G>A	ENSP00000323928:p.Val24Ile	196	0	0		231	18	0.0779221	NM_001005201	Q6IFB7	Missense_Mutation	SNP	ENST00000313472.3	37	CCDS31519.1	.	.	.	.	.	.	.	.	.	.	G	1.503	-0.551434	0.03996	.	.	ENSG00000181761	ENST00000313472	T	0.01359	4.98	3.43	-6.36	0.01969	.	1.100610	0.06932	N	0.811320	T	0.00552	0.0018	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.49504	-0.8933	10	0.54805	T	0.06	.	2.0752	0.03623	0.3689:0.211:0.3126:0.1075	.	24	Q8N146	OR8H3_HUMAN	I	24	ENSP00000323928:V24I	ENSP00000323928:V24I	V	+	1	0	OR8H3	55646494	0.000000	0.05858	0.104000	0.21259	0.032000	0.12392	-5.175000	0.00144	-0.849000	0.04158	-1.252000	0.01501	GTC	.	.	none		0.453	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201		A	55889918	G	A	55889918	3	1	22	1	0	0	0	0	1	0	0	0	11248	1261	44	2	72	2	OR8H3	11	55889918	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	16517	55889918	79116598	2442	5343											
OR8H3	390152	hgsc.bcm.edu	37	chr11	55890066	55890066	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctgtcatttattgacctcaGttactcaactgtcgtcacac	9	14	5	13	1	4	1	4	1	0	0	5	1	4	1	2	0	2	1	2	0	3	4	rs140843028	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55890066G>A	ENST00000313472.3	+	1	218	c.218G>A	c.(217-219)aGt>aAt	p.S73N		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	73						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)					ATTGACCTCAGTTACTCAACT	0.448													G|||	73	0.0145767	0.0499	0.0101	5008	,	,		20989	0.0		0.0	False		,,,				2504	0.0				p.S73N		Atlas-SNP	.											.	OR8H3	92	.	0			c.G218A						PASS	.	G	ASN/SER	175,4227	115.0+/-153.0	4,167,2030	255	252	253		218	-0.2	0.9	11	dbSNP_134	253	4,8582	4.3+/-15.6	0,4,4289	no	missense	OR8H3	NM_001005201.1	46	4,171,6319	AA,AG,GG		0.0466,3.9755,1.3782	possibly-damaging	73/313	55890066	179,12809	2201	4293	6494	SO:0001583	missense	390152	exon1			ACCTCAGTTACTC	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.218G>A	11.37:g.55890066G>A	ENSP00000323928:p.Ser73Asn	368	0	0		390	160	0.410256	NM_001005201	Q6IFB7	Missense_Mutation	SNP	ENST00000313472.3	37	CCDS31519.1	26	0.011904761904761904	22	0.044715447154471545	4	0.011049723756906077	0	0.0	0	0.0	G	11.76	1.735059	0.30774	0.039755	4.66E-4	ENSG00000181761	ENST00000313472	T	0.01359	4.98	3.44	-0.164	0.13359	GPCR, rhodopsin-like superfamily (1);	0.421176	0.23038	N	0.052645	T	0.00875	0.0029	M	0.86864	2.845	0.09310	N	1	D	0.56287	0.975	P	0.52267	0.694	T	0.26849	-1.0091	10	0.87932	D	0	.	3.7935	0.08730	0.0939:0.291:0.4667:0.1484	.	73	Q8N146	OR8H3_HUMAN	N	73	ENSP00000323928:S73N	ENSP00000323928:S73N	S	+	2	0	OR8H3	55646642	0.006000	0.16342	0.902000	0.35471	0.267000	0.26476	1.600000	0.36762	0.075000	0.16796	0.173000	0.16961	AGT	G|0.986;A|0.014	0.014	weak		0.448	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201		A	55890066	G	A	55890066	3	1	22	1	0	0	0	0	1	0	0	0	11248	1029	36	2	220	2	OR8H3	11	55890066	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	148	55890066	79116450	2443	5344											
OR8J3	81168	hgsc.bcm.edu	37	chr11	55904422	55904422	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtttggggctgcaaatacAtaaatagcattgtcccatag	12	12	10	7	0	0	0	0	0	0	0	1	0	1	0	1	3	3	4	1	3	6	6	rs114758947	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55904422A>G	ENST00000301529.1	-	1	772	c.773T>C	c.(772-774)aTg>aCg	p.M258T		NM_001004064.1	NP_001004064.1	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J, 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)			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)					CTGCAAATACATAAATAGCAT	0.428													A|||	88	0.0175719	0.0628	0.0058	5008	,	,		18131	0.0		0.001	False		,,,				2504	0.0				p.M258T		Atlas-SNP	.											.	OR8J3	112	.	0			c.T773C						PASS	.	A	THR/MET	235,4167	139.2+/-174.8	7,221,1973	138	133	135		773	2.1	0.5	11	dbSNP_132	135	2,8590	2.2+/-6.3	0,2,4294	yes	missense	OR8J3	NM_001004064.1	81	7,223,6267	GG,GA,AA		0.0233,5.3385,1.8239	probably-damaging	258/316	55904422	237,12757	2201	4296	6497	SO:0001583	missense	81168	exon1			AAATACATAAATA		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.773T>C	11.37:g.55904422A>G	ENSP00000301529:p.Met258Thr	183	0	0		236	127	0.538136	NM_001004064	Q6IFB6|Q96RC2	Missense_Mutation	SNP	ENST00000301529.1	37	CCDS31520.1	41	0.018772893772893772	38	0.07723577235772358	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	A	7.537	0.659897	0.14645	0.053385	2.33E-4	ENSG00000167822	ENST00000301529	T	0.00164	8.64	3.27	2.11	0.27256	GPCR, rhodopsin-like superfamily (1);	0.136411	0.52532	D	0.000070	T	0.00039	0.0001	L	0.53561	1.675	0.09310	N	1	D	0.53619	0.961	P	0.62298	0.9	T	0.47169	-0.9138	10	0.72032	D	0.01	.	5.506	0.16854	0.6758:0.0:0.3242:0.0	.	258	Q8NGG0	OR8J3_HUMAN	T	258	ENSP00000301529:M258T	ENSP00000301529:M258T	M	-	2	0	OR8J3	55660998	0.000000	0.05858	0.453000	0.27007	0.065000	0.16274	-0.305000	0.08188	1.272000	0.44329	0.247000	0.18012	ATG	A|0.983;G|0.017	0.017	strong		0.428	OR8J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391542.1	NM_001004064		G	55904422	A	G	55904422	3	3	22	1	0	0	0	0	1	0	0	0	11251	217	8	3	176	3	OR8J3	11	55904422	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	14356	55904422	79102094	2444	5345											
OR8K5	219453	hgsc.bcm.edu	37	chr11	55927591	55927591	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tagaattaccaagatcaacaAaagccaaatgtctgatagaa	20	8	6	7	0	2	4	1	1	1	3	2	4	2	4	2	0	3	0	2	0	10	3	rs2512938	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55927591A>G	ENST00000313447.1	-	1	202	c.203T>C	c.(202-204)tTt>tCt	p.F68S		NM_001004058.2	NP_001004058.2	Q8NH50	OR8K5_HUMAN	olfactory receptor, family 8, subfamily K, member 5	68			F -> S (in dbSNP:rs2512938).			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)				AAGATCAACAAAAGCCAAATG	0.398													.|||	111	0.0221645	0.0779	0.0115	5008	,	,		21695	0.0		0.0	False		,,,				2504	0.0				p.F68S		Atlas-SNP	.											.	OR8K5	82	.	0			c.T203C						PASS	.	A	SER/PHE	280,4122	155.9+/-189.0	9,262,1930	110	109	109		203	2.7	0.9	11	dbSNP_100	109	6,8586	4.3+/-15.6	0,6,4290	yes	missense	OR8K5	NM_001004058.2	155	9,268,6220	GG,GA,AA		0.0698,6.3607,2.201	possibly-damaging	68/308	55927591	286,12708	2201	4296	6497	SO:0001583	missense	219453	exon1			TCAACAAAAGCCA	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.203T>C	11.37:g.55927591A>G	ENSP00000323853:p.Phe68Ser	126	0	0		138	68	0.492754	NM_001004058	Q6IFB5	Missense_Mutation	SNP	ENST00000313447.1	37	CCDS31521.1	44	0.020146520146520148	39	0.07926829268292683	5	0.013812154696132596	0	0.0	0	0.0	A	11.51	1.659357	0.29515	0.063607	6.98E-4	ENSG00000181752	ENST00000313447	T	0.01005	5.45	3.87	2.69	0.31865	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00178	0.0005	M	0.79475	2.455	0.23834	N	0.996718	D	0.56746	0.977	P	0.47744	0.556	T	0.48559	-0.9025	9	0.72032	D	0.01	.	8.9967	0.36057	0.8337:0.0:0.0:0.1663	rs2512938;rs56484064;rs2512938	68	Q8NH50	OR8K5_HUMAN	S	68	ENSP00000323853:F68S	ENSP00000323853:F68S	F	-	2	0	OR8K5	55684167	0.082000	0.21442	0.937000	0.37676	0.050000	0.14768	3.809000	0.55606	0.621000	0.30232	-0.555000	0.04198	TTT	A|0.974;G|0.026	0.026	strong		0.398	OR8K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391543.1	NM_001004058		G	55927591	A	G	55927591	3	3	22	1	0	0	0	0	1	0	0	0	11254	14	1	3	723	3	OR8K5	11	55927591	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	23169	55927591	79078925	2445	5346											
OR5J2	282775	hgsc.bcm.edu	37	chr11	55944501	55944501	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgctttacactgtagccatGtctgatagaaagtgtgtgga	10	14	11	6	0	1	2	0	1	1	1	1	3	1	3	1	1	3	2	1	1	4	5	rs12279899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55944501G>C	ENST00000312298.1	+	1	408	c.408G>C	c.(406-408)atG>atC	p.M136I		NM_001005492.1	NP_001005492.1	Q8NH18	OR5J2_HUMAN	olfactory receptor, family 5, subfamily J, member 2	136			M -> I (in dbSNP:rs12279899).			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)					CTGTAGCCATGTCTGATAGAA	0.453													.|||	111	0.0221645	0.0779	0.0115	5008	,	,		23867	0.0		0.0	False		,,,				2504	0.0				p.M136I		Atlas-SNP	.											.	OR5J2	98	.	0			c.G408C						PASS	.	G	ILE/MET	280,4122	156.6+/-189.7	9,262,1930	164	150	155		408	4.7	0.4	11	dbSNP_120	155	6,8586	4.3+/-15.6	0,6,4290	yes	missense	OR5J2	NM_001005492.1	10	9,268,6220	CC,CG,GG		0.0698,6.3607,2.201	probably-damaging	136/313	55944501	286,12708	2201	4296	6497	SO:0001583	missense	282775	exon1			AGCCATGTCTGAT	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.408G>C	11.37:g.55944501G>C	ENSP00000310788:p.Met136Ile	316	0	0		426	193	0.453052	NM_001005492	Q6IEU5	Missense_Mutation	SNP	ENST00000312298.1	37	CCDS31522.1	44	0.020146520146520148	39	0.07926829268292683	5	0.013812154696132596	0	0.0	0	0.0	G	16.43	3.120975	0.56613	0.063607	6.98E-4	ENSG00000174957	ENST00000312298	T	0.00551	6.65	4.67	4.67	0.58626	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000002	T	0.00073	0.0002	M	0.70595	2.14	0.51482	D	0.999923	P	0.41313	0.745	B	0.36719	0.231	T	0.75425	-0.3322	10	0.66056	D	0.02	.	17.6944	0.88277	0.0:0.0:1.0:0.0	rs12279899;rs52802580;rs12279899	136	Q8NH18	OR5J2_HUMAN	I	136	ENSP00000310788:M136I	ENSP00000310788:M136I	M	+	3	0	OR5J2	55701077	1.000000	0.71417	0.364000	0.25888	0.028000	0.11728	6.151000	0.71806	2.350000	0.79820	0.584000	0.79450	ATG	G|0.979;C|0.021	0.021	strong		0.453	OR5J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391544.1	NM_001005492		C	55944501	G	C	55944501	3	2	22	1	0	0	0	0	1	0	0	0	11174	1377	48	4	410	4	OR5J2	11	55944501	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	16910	55944501	79062015	2446	5347											
OR5T2	219464	hgsc.bcm.edu	37	chr11	55999879	55999879	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tacatcttcagaatggccaaCagaatcaaaccataggagat	17	8	7	9	0	3	3	2	0	1	3	3	4	3	3	2	2	3	0	2	2	6	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55999879C>A	ENST00000313264.4	-	1	858	c.783G>T	c.(781-783)ctG>ctT	p.L261L		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	261						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)					GAATGGCCAACAGAATCAAAC	0.438																																					p.L261L		Atlas-SNP	.											OR5T2,NS,carcinoma,0,1	OR5T2	107	1	0			c.G783T						scavenged	.						129	120	123					11																	55999879		2201	4296	6497	SO:0001819	synonymous_variant	219464	exon1			GGCCAACAGAATC	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.783G>T	11.37:g.55999879C>A		197	1	0.00507614		219	94	0.429224	NM_001004746	B9EGX5|Q6IFC8	Silent	SNP	ENST00000313264.4	37	CCDS31523.1																																																																																			.	.	none		0.438	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746		A	55999879	C	A	55999879	2	1	22	1	0	0	0	0	0	0	0	1	11191	465	17	4		4	OR5T2	11	55999879	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	55378	55999879	79006637	2447	5348											
OR8K1	390157	hgsc.bcm.edu	37	chr11	56113703	56113703	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ttggactccaagctacacacCcccatgtactttttccttag	9	13	5	14	0	0	0	0	0	0	0	2	1	2	1	4	1	3	2	4	1	4	6	rs145394503	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:56113703C>T	ENST00000279783.2	+	1	283	c.189C>T	c.(187-189)acC>acT	p.T63T		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	63						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)					AGCTACACACCCCCATGTACT	0.433										HNSCC(65;0.19)			C|||	35	0.00698882	0.0242	0.0029	5008	,	,		19161	0.0		0.001	False		,,,				2504	0.0				p.T63T		Atlas-SNP	.											.	OR8K1	93	.	0			c.C189T						PASS	.	C		108,4294	83.9+/-122.4	2,104,2095	165	149	154		189	-10	0	11	dbSNP_134	154	3,8589	2.2+/-6.3	0,3,4293	no	coding-synonymous	OR8K1	NM_001002907.1		2,107,6388	TT,TC,CC		0.0349,2.4534,0.8542		63/320	56113703	111,12883	2201	4296	6497	SO:0001819	synonymous_variant	390157	exon1			ACACACCCCCATG	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.189C>T	11.37:g.56113703C>T		216	1	0.00462963		189	94	0.497355	NM_001002907	B9EJB1|Q6IFC3|Q96RC1	Silent	SNP	ENST00000279783.2	37	CCDS31528.1																																																																																			C|0.993;T|0.007	0.007	strong		0.433	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907		T	56113703	C	T	56113703	2	4	22	1	0	0	0	0	0	0	0	1	11252	610	22	2		2	OR8K1	11	56113703	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	113824	56113703	78892813	2448	5349											
OR8K1	390157	hgsc.bcm.edu	37	chr11	56113923	56113923	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tagccatctgtaaacctcttCtgtacgtgatcatcatggca	10	13	7	11	1	5	1	2	1	3	0	5	1	5	1	2	1	3	3	2	1	4	4	rs61745885	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:56113923C>T	ENST00000279783.2	+	1	503	c.409C>T	c.(409-411)Ctg>Ttg	p.L137L		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	137						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L137M(1)		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)					TAAACCTCTTCTGTACGTGAT	0.403										HNSCC(65;0.19)			C|||	35	0.00698882	0.0242	0.0029	5008	,	,		21543	0.0		0.001	False		,,,				2504	0.0				p.L137L		Atlas-SNP	.											OR8K1,shoulder,malignant_melanoma,0,1	OR8K1	93	1	1	Substitution - Missense(1)	skin(1)	c.C409T						PASS	.	C		108,4294	83.4+/-121.9	2,104,2095	213	211	211		409	3.1	0.9	11	dbSNP_129	211	3,8589	2.2+/-6.3	0,3,4293	no	coding-synonymous	OR8K1	NM_001002907.1		2,107,6388	TT,TC,CC		0.0349,2.4534,0.8542		137/320	56113923	111,12883	2201	4296	6497	SO:0001819	synonymous_variant	390157	exon1			CCTCTTCTGTACG	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.409C>T	11.37:g.56113923C>T		152	0	0		148	71	0.47973	NM_001002907	B9EJB1|Q6IFC3|Q96RC1	Silent	SNP	ENST00000279783.2	37	CCDS31528.1																																																																																			C|0.993;T|0.007	0.007	strong		0.403	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907		T	56113923	C	T	56113923	2	4	22	1	0	0	0	0	0	0	0	1	11252	912	32	2		2	OR8K1	11	56113923	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	220	56113923	78892593	2449	5350											
OR8J1	219477	hgsc.bcm.edu	37	chr11	56128226	56128226	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatgtattctctgtgtcttaTtgctcttctaatataatcaa	10	20	4	7	0	5	0	1	0	4	0	6	0	5	0	0	0	1	2	0	0	7	9	rs11823483	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:56128226T>C	ENST00000303039.3	+	1	536	c.504T>C	c.(502-504)taT>taC	p.Y168Y		NM_001005205.2	NP_001005205.2	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J, member 1	168						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)					CTGTGTCTTATTGCTCTTCTA	0.388													T|||	240	0.0479233	0.1687	0.0231	5008	,	,		18982	0.0		0.001	False		,,,				2504	0.0				p.Y168Y		Atlas-SNP	.											.	OR8J1	87	.	0			c.T504C						PASS	.	T		628,3774	272.5+/-270.8	48,532,1621	120	108	112		504	-2.3	1	11	dbSNP_120	112	9,8583	4.3+/-15.6	0,9,4287	no	coding-synonymous	OR8J1	NM_001005205.2		48,541,5908	CC,CT,TT		0.1047,14.2662,4.9023		168/317	56128226	637,12357	2201	4296	6497	SO:0001819	synonymous_variant	219477	exon1			GTCTTATTGCTCT	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.504T>C	11.37:g.56128226T>C		146	0	0		161	73	0.453416	NM_001005205	B2RNQ6|B9EH63|Q6IFC2|Q96RC3	Silent	SNP	ENST00000303039.3	37	CCDS31529.1																																																																																			T|0.955;C|0.045	0.045	strong		0.388	OR8J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391606.2	NM_001005205		C	56128226	T	C	56128226	2	2	22	1	0	0	0	0	0	0	0	1	11250	1500	52	3		3	OR8J1	11	56128226	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	14303	56128226	78878290	2450	5351											
OR8U8	219417	hgsc.bcm.edu	37	chr11	56143952	56143952	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acacagtgatcattcccatgTtgaatcccttaatctatagc	12	13	5	11	0	2	2	1	2	1	0	4	2	4	2	2	0	1	1	2	0	4	5	rs78408319	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:56143952T>C	ENST00000302270.1	+	1	853	c.853T>C	c.(853-855)Ttg>Ctg	p.L285L		NM_001005204.1	NP_001005204.1	Q8NH10	OR8U1_HUMAN	olfactory receptor, family 8, subfamily U, member 1	285						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)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(23)|ovary(4)|skin(1)|stomach(1)	39	Esophageal squamous(21;0.00448)					CATTCCCATGTTGAATCCCTT	0.388													T|||	237	0.0473243	0.1664	0.0231	5008	,	,		18826	0.0		0.001	False		,,,				2504	0.0				p.L285L		Atlas-SNP	.											.	OR8U1	59	.	0			c.T853C						PASS	.	T		535,3441		39,457,1492	139	144	142		853	-11.4	0.2	11	dbSNP_132	142	8,8396		0,8,4194	no	coding-synonymous	OR8U1	NM_001005204.1		39,465,5686	CC,CT,TT		0.0952,13.4557,4.3861		285/310	56143952	543,11837	1988	4202	6190	SO:0001819	synonymous_variant	219417	exon1			CCCATGTTGAATC	AB065603	CCDS41647.1	11q11	2012-08-09			ENSG00000172199	ENSG00000172199		"GPCR / Class A : Olfactory receptors"	19611	protein-coding gene	gene with protein product							Standard	NM_001005204		Approved			Q8NH10	OTTHUMG00000166860	ENST00000302270.1:c.853T>C	11.37:g.56143952T>C		114	0	0		125	60	0.48	NM_001005204		Silent	SNP	ENST00000302270.1	37	CCDS41647.1																																																																																			T|0.973;C|0.027	0.027	strong		0.388	OR8U1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391607.1	NM_001005204		C	56143952	T	C	56143952	2	2	22	1	0	0	0	0	0	0	0	1	11256	1722	60	3		3	OR8U8	11	56143952	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	15726	56143952	78862564	2451	5352											
OR5AK2	390181	hgsc.bcm.edu	37	chr11	56756565	56756565	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tccagatttcaaacactcacGtacttttttctacaacattt	12	16	2	11	1	3	1	2	0	1	1	4	1	4	1	1	0	4	1	1	0	4	7	rs62001001	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:56756565G>A	ENST00000326855.2	+	1	219	c.177G>A	c.(175-177)acG>acA	p.T59T		NM_001005323.1	NP_001005323.1	Q8NH90	O5AK2_HUMAN	olfactory receptor, family 5, subfamily AK, 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)	p.T59T(1)		breast(3)|endometrium(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21						AAACACTCACGTACTTTTTTC	0.363													.|||	58	0.0115815	0.0431	0.0014	5008	,	,		21424	0.0		0.0	False		,,,				2504	0.0				p.T59T		Atlas-SNP	.											OR5AK2,NS,carcinoma,0,1	OR5AK2	45	1	1	Substitution - coding silent(1)	prostate(1)	c.G177A						PASS	.	G		174,4228	113.8+/-151.8	2,170,2029	118	104	109		177	0.4	0.9	11	dbSNP_129	109	3,8589	2.2+/-6.3	0,3,4293	no	coding-synonymous	OR5AK2	NM_001005323.1		2,173,6322	AA,AG,GG		0.0349,3.9527,1.3622		59/310	56756565	177,12817	2201	4296	6497	SO:0001819	synonymous_variant	390181	exon1			ACTCACGTACTTT	AB065496	CCDS31538.1	11q11	2012-08-09			ENSG00000181273	ENSG00000181273		"GPCR / Class A : Olfactory receptors"	15251	protein-coding gene	gene with protein product							Standard	NM_001005323		Approved		uc010rjp.2	Q8NH90	OTTHUMG00000167019	ENST00000326855.2:c.177G>A	11.37:g.56756565G>A		247	0	0		251	116	0.462151	NM_001005323	B2RNZ9	Silent	SNP	ENST00000326855.2	37	CCDS31538.1																																																																																			G|0.987;A|0.013	0.013	strong		0.363	OR5AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392446.1	NM_001005323		A	56756565	G	A	56756565	2	1	22	1	0	0	0	0	0	0	0	1	11151	1132	40	1		1	OR5AK2	11	56756565	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	612613	56756565	78249951	2452	5353											
LRRC55	219527	hgsc.bcm.edu	37	chr11	56949529	56949529	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggcccagcttccctggccCgggccaccccacccagcaat	6	5	10	20	1	0	0	0	0	0	0	1	0	1	0	7	3	2	2	7	3	1	1	rs80306837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:56949529C>T	ENST00000497933.1	+	1	309	c.162C>T	c.(160-162)ccC>ccT	p.P54P		NM_001005210.2	NP_001005210.1	Q6ZSA7	LRC55_HUMAN	leucine rich repeat containing 55	24	LRRNT.				ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|skin(2)	25						TTCCCTGGCCCGGGCCACCCC	0.632													C|||	184	0.0367412	0.1339	0.0101	5008	,	,		18733	0.0		0.0	False		,,,				2504	0.0				p.P54P		Atlas-SNP	.											.	LRRC55	52	.	0			c.C162T						PASS	.	C		516,3886	234.9+/-247.6	28,460,1713	43	38	40		162	-11.3	0.8	11	dbSNP_131	40	4,8588	3.7+/-12.6	0,4,4292	no	coding-synonymous	LRRC55	NM_001005210.2		28,464,6005	TT,TC,CC		0.0466,11.7219,4.0018		54/342	56949529	520,12474	2201	4296	6497	SO:0001819	synonymous_variant	219527	exon1			CTGGCCCGGGCCA		CCDS31539.1	11q12.1	2008-02-05			ENSG00000183908	ENSG00000183908			32324	protein-coding gene	gene with protein product		615213					Standard	NM_001005210		Approved	FLJ45686	uc001njl.2	Q6ZSA7	OTTHUMG00000159309	ENST00000497933.1:c.162C>T	11.37:g.56949529C>T		185	0	0		142	66	0.464789	NM_001005210	A7E2U7|B2RN81	Silent	SNP	ENST00000497933.1	37	CCDS31539.1																																																																																			C|0.952;T|0.048	0.048	strong		0.632	LRRC55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354503.2	NM_001005210		T	56949529	C	T	56949529	2	4	22	1	0	0	0	0	0	0	0	1	9020	639	23	1		1	LRRC55	11	56949529	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	192964	56949529	78056987	2453	5354											
SSRP1	6749	hgsc.bcm.edu	37	chr11	57101000	57101000	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgagttttgaagaaatcagaGagtttctcaaactcctgtgg	12	13	10	6	0	2	4	2	2	1	2	4	5	3	4	1	1	1	2	1	1	3	3	rs7932705	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:57101000G>C	ENST00000278412.2	-	4	521	c.255C>G	c.(253-255)ctC>ctG	p.L85L		NM_003146.2	NP_003137.1	Q08945	SSRP1_HUMAN	structure specific recognition protein 1	85					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						AGAAATCAGAGAGTTTCTCAA	0.468													G|||	76	0.0151757	0.0537	0.0072	5008	,	,		19918	0.0		0.0	False		,,,				2504	0.0				p.L85L	Colon(89;1000 1340 6884 23013 41819)	Atlas-SNP	.											.	SSRP1	75	.	0			c.C255G						PASS	.	G		189,4213	122.1+/-159.5	2,185,2014	90	87	88		255	-0.2	1	11	dbSNP_116	88	5,8587	3.7+/-12.6	0,5,4291	no	coding-synonymous	SSRP1	NM_003146.2		2,190,6305	CC,CG,GG		0.0582,4.2935,1.493		85/710	57101000	194,12800	2201	4296	6497	SO:0001819	synonymous_variant	6749	exon4			ATCAGAGAGTTTC	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.255C>G	11.37:g.57101000G>C		144	0	0		111	63	0.567568	NM_003146	Q5BJG8	Silent	SNP	ENST00000278412.2	37	CCDS7952.1																																																																																			G|0.986;C|0.014	0.014	strong		0.468	SSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392460.1	NM_003146		C	57101000	G	C	57101000	2	2	22	1	0	0	0	0	0	0	0	1	15209	929	33	4		4	SSRP1	11	57101000	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	151471	57101000	77905516	2454	5355											
OR10Q1	219960	hgsc.bcm.edu	37	chr11	57996289	57996289	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	attcagtggctgtggtgaacGcacggaacacaaactcagtg	12	8	12	9	2	2	1	2	1	0	0	2	2	2	2	0	3	3	2	0	3	3	1	rs112800197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:57996289G>A	ENST00000316770.2	-	1	101	c.59C>T	c.(58-60)gCg>gTg	p.A20V		NM_001004471.2	NP_001004471.1	Q8NGQ4	O10Q1_HUMAN	olfactory receptor, family 10, subfamily Q, 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)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)	35		Breast(21;0.0589)				TGTGGTGAACGCACGGAACAC	0.507													g|||	51	0.0101837	0.0378	0.0014	5008	,	,		17105	0.0		0.0	False		,,,				2504	0.0				p.A20V		Atlas-SNP	.											.	OR10Q1	79	.	0			c.C59T						PASS	.	G	VAL/ALA	114,4248		1,112,2068	126	133	130		59	-1.3	0	11	dbSNP_132	130	0,8558		0,0,4279	yes	missense	OR10Q1	NM_001004471.2	64	1,112,6347	AA,AG,GG		0.0,2.6135,0.8824	benign	20/320	57996289	114,12806	2181	4279	6460	SO:0001583	missense	219960	exon1			GTGAACGCACGGA	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.59C>T	11.37:g.57996289G>A	ENSP00000314324:p.Ala20Val	209	0	0		212	103	0.485849	NM_001004471	Q6IFG4	Missense_Mutation	SNP	ENST00000316770.2	37	CCDS31547.1	20	0.009157509157509158	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	0	0.0	G	2.409	-0.335766	0.05278	0.026135	0.0	ENSG00000180475	ENST00000316770	T	0.00330	8.08	4.98	-1.34	0.09143	.	0.376700	0.19161	N	0.121185	T	0.00039	0.0001	N	0.10760	0.04	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33574	-0.9863	10	0.51188	T	0.08	.	7.7104	0.28673	0.3775:0.1422:0.4802:0.0	.	20	Q8NGQ4	O10Q1_HUMAN	V	20	ENSP00000314324:A20V	ENSP00000314324:A20V	A	-	2	0	OR10Q1	57752865	0.000000	0.05858	0.000000	0.03702	0.206000	0.24218	-0.355000	0.07671	-0.439000	0.07222	-0.295000	0.09555	GCG	G|0.991;A|0.009	0.009	strong		0.507	OR10Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394706.1	NM_001004471		A	57996289	G	A	57996289	3	1	22	1	0	0	0	0	1	0	0	0	10925	1087	38	1	904	1	OR10Q1	11	57996289	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	895289	57996289	77010227	2455	5356											
OR5B2	390190	hgsc.bcm.edu	37	chr11	58190228	58190228	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaaaagtgatgtaccagattGgatttacagaaagagagact	18	9	10	4	0	0	5	0	1	0	4	0	7	0	6	1	1	2	1	1	1	5	4	rs77952368	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:58190228G>A	ENST00000302581.2	-	1	558	c.507C>T	c.(505-507)tcC>tcT	p.S169S		NM_001005566.2	NP_001005566.1	Q96R09	OR5B2_HUMAN	olfactory receptor, family 5, subfamily B, member 2	169						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)				GTACCAGATTGGATTTACAGA	0.453													G|||	26	0.00519169	0.0182	0.0029	5008	,	,		22719	0.0		0.0	False		,,,				2504	0.0				p.S169S		Atlas-SNP	.											OR5B2,NS,carcinoma,-1,1	OR5B2	75	1	0			c.C507T						PASS	.	G		59,4343	56.2+/-92.4	1,57,2143	61	57	58		507	1.8	0	11	dbSNP_131	58	1,8589		0,1,4294	no	coding-synonymous	OR5B2	NM_001005566.2		1,58,6437	AA,AG,GG		0.0116,1.3403,0.4618		169/310	58190228	60,12932	2201	4295	6496	SO:0001819	synonymous_variant	390190	exon1			CAGATTGGATTTA	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.507C>T	11.37:g.58190228G>A		60	0	0		72	43	0.597222	NM_001005566	B2RNJ6|B9EGY7|Q6IEV7|Q8NGF5	Silent	SNP	ENST00000302581.2	37	CCDS31550.1																																																																																			G|0.993;A|0.007	0.007	strong		0.453	OR5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394887.2	NM_001005566		A	58190228	G	A	58190228	2	1	22	1	0	0	0	0	0	0	0	1	11159	1335	47	2		2	OR5B2	11	58190228	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	193939	58190228	76816288	2456	5357											
DTX4	23220	hgsc.bcm.edu	37	chr11	58949852	58949852	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggacccaacagcaagacCggaagggtggccctggccac	11	2	13	15	1	0	1	0	0	0	1	0	3	0	3	5	5	2	1	5	5	3	0	rs75403375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:58949852C>T	ENST00000227451.3	+	2	956	c.852C>T	c.(850-852)acC>acT	p.T284T	DTX4_ENST00000532982.1_Silent_p.T178T	NM_015177.1	NP_055992.1	Q9Y2E6	DTX4_HUMAN	deltex 4, E3 ubiquitin ligase	284					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)				ACAGCAAGACCGGAAGGGTGG	0.637													C|||	135	0.0269569	0.0983	0.0072	5008	,	,		19567	0.0		0.0	False		,,,				2504	0.0				p.T284T		Atlas-SNP	.											.	DTX4	84	.	0			c.C852T						PASS	.	C		245,3755		7,231,1762	30	40	37		852	-9.1	0	11	dbSNP_132	37	0,8320		0,0,4160	no	coding-synonymous	DTX4	NM_015177.1		7,231,5922	TT,TC,CC		0.0,6.125,1.9886		284/620	58949852	245,12075	2000	4160	6160	SO:0001819	synonymous_variant	23220	exon2			CAAGACCGGAAGG	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.852C>T	11.37:g.58949852C>T		45	0	0		49	25	0.510204	NM_015177	Q0VF38	Silent	SNP	ENST00000227451.3	37	CCDS44612.1																																																																																			C|0.975;T|0.025	0.025	strong		0.637	DTX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394228.1	XM_166213		T	58949852	C	T	58949852	2	4	22	1	0	0	0	0	0	0	0	1	4799	639	23	1		1	DTX4	11	58949852	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	759624	58949852	76056664	2457	5358											
OR4D9	390199	hgsc.bcm.edu	37	chr11	59282651	59282651	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatagatcttctatcagagaCaaaaaccatctccttcagtg	14	11	6	10	0	5	2	2	0	3	2	6	4	5	2	2	0	1	0	2	0	4	4	rs76276934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:59282651C>T	ENST00000329328.3	+	1	266	c.266C>T	c.(265-267)aCa>aTa	p.T89I		NM_001004711.1	NP_001004711.1	Q8NGE8	OR4D9_HUMAN	olfactory receptor, family 4, subfamily D, member 9	89						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						CTATCAGAGACAAAAACCATC	0.483													c|||	108	0.0215655	0.0802	0.0029	5008	,	,		20793	0.0		0.0	False		,,,				2504	0.0				p.T89I		Atlas-SNP	.											.	OR4D9	47	.	0			c.C266T						PASS	.	C	ILE/THR	263,4139	149.5+/-183.7	9,245,1947	122	118	119		266	-6.1	0	11	dbSNP_131	119	1,8589		0,1,4294	yes	missense	OR4D9	NM_001004711.1	89	9,246,6241	TT,TC,CC		0.0116,5.9746,2.032	benign	89/315	59282651	264,12728	2201	4295	6496	SO:0001583	missense	390199	exon1			CAGAGACAAAAAC	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.266C>T	11.37:g.59282651C>T	ENSP00000328563:p.Thr89Ile	177	0	0		174	88	0.505747	NM_001004711	Q6IFF3	Missense_Mutation	SNP	ENST00000329328.3	37	CCDS31564.1	53	0.024267399267399268	52	0.10569105691056911	1	0.0027624309392265192	0	0.0	0	0.0	C	1.435	-0.569257	0.03910	0.059746	1.16E-4	ENSG00000172742	ENST00000329328	T	0.01397	4.94	4.02	-6.07	0.02158	GPCR, rhodopsin-like superfamily (1);	0.913714	0.08973	U	0.866909	T	0.00039	0.0001	L	0.39085	1.19	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46076	-0.9217	10	0.52906	T	0.07	.	2.2328	0.04001	0.3788:0.3173:0.1962:0.1076	.	89	Q8NGE8	OR4D9_HUMAN	I	89	ENSP00000328563:T89I	ENSP00000328563:T89I	T	+	2	0	OR4D9	59039227	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-2.882000	0.00714	-1.736000	0.01352	-1.265000	0.01443	ACA	C|0.979;T|0.021	0.021	strong		0.483	OR4D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394237.1	NM_001004711		T	59282651	C	T	59282651	3	4	22	1	0	0	0	0	1	0	0	0	11068	478	17	2	268	2	OR4D9	11	59282651	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	332799	59282651	75723865	2458	5359											
OR4D9	390199	hgsc.bcm.edu	37	chr11	59282838	59282838	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atcgtggcttcctgggtgggGggctttgtccactccatagc	4	12	14	11	1	0	0	0	0	0	0	4	0	3	0	3	5	1	2	3	5	1	3	rs75125922	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:59282838G>A	ENST00000329328.3	+	1	453	c.453G>A	c.(451-453)ggG>ggA	p.G151G		NM_001004711.1	NP_001004711.1	Q8NGE8	OR4D9_HUMAN	olfactory receptor, family 4, subfamily D, member 9	151				ASWVGGF -> GFLGGGL (in Ref. 2; AC019093). {ECO:0000305}.		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						CCTGGGTGGGGGGCTTTGTCC	0.547													G|||	180	0.0359425	0.1331	0.0058	5008	,	,		18390	0.0		0.0	False		,,,				2504	0.0				p.G151G		Atlas-SNP	.											.	OR4D9	47	.	0			c.G453A						PASS	.	G		451,3951	215.8+/-234.7	18,415,1768	81	79	79		453	2.1	1	11	dbSNP_131	79	2,8588	1.2+/-3.3	0,2,4293	no	coding-synonymous	OR4D9	NM_001004711.1		18,417,6061	AA,AG,GG		0.0233,10.2453,3.4868		151/315	59282838	453,12539	2201	4295	6496	SO:0001819	synonymous_variant	390199	exon1			GGTGGGGGGCTTT	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.453G>A	11.37:g.59282838G>A		102	0	0		144	72	0.5	NM_001004711	Q6IFF3	Silent	SNP	ENST00000329328.3	37	CCDS31564.1																																																																																			G|0.966;A|0.034	0.034	strong		0.547	OR4D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394237.1	NM_001004711		A	59282838	G	A	59282838	2	1	22	1	0	0	0	0	0	0	0	1	11068	1219	43	2		2	OR4D9	11	59282838	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	187	59282838	75723678	2459	5360											
OR4D9	390199	hgsc.bcm.edu	37	chr11	59282960	59282960	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	caaacttgcctgcactgacaCcttcactctggagctcctga	9	10	7	15	0	2	2	1	2	1	0	3	3	3	3	3	1	4	2	3	1	1	2	rs113146895	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:59282960C>G	ENST00000329328.3	+	1	575	c.575C>G	c.(574-576)aCc>aGc	p.T192S		NM_001004711.1	NP_001004711.1	Q8NGE8	OR4D9_HUMAN	olfactory receptor, family 4, subfamily D, member 9	192						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						TGCACTGACACCTTCACTCTG	0.453													C|||	108	0.0215655	0.0802	0.0029	5008	,	,		21548	0.0		0.0	False		,,,				2504	0.0				p.T192S		Atlas-SNP	.											.	OR4D9	47	.	0			c.C575G						PASS	.	C	SER/THR	263,4139	149.5+/-183.7	9,245,1947	189	162	171		575	3.5	0.1	11	dbSNP_132	171	1,8589		0,1,4294	yes	missense	OR4D9	NM_001004711.1	58	9,246,6241	GG,GC,CC		0.0116,5.9746,2.032	possibly-damaging	192/315	59282960	264,12728	2201	4295	6496	SO:0001583	missense	390199	exon1			CTGACACCTTCAC	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.575C>G	11.37:g.59282960C>G	ENSP00000328563:p.Thr192Ser	176	0	0		169	82	0.485207	NM_001004711	Q6IFF3	Missense_Mutation	SNP	ENST00000329328.3	37	CCDS31564.1	53	0.024267399267399268	52	0.10569105691056911	1	0.0027624309392265192	0	0.0	0	0.0	C	11.61	1.689273	0.29962	0.059746	1.16E-4	ENSG00000172742	ENST00000329328	T	0.00207	8.55	4.44	3.52	0.40303	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42964	U	0.000628	T	0.00012	0.0000	M	0.78916	2.43	0.09310	N	1	D	0.53151	0.958	P	0.59825	0.864	T	0.37174	-0.9717	10	0.72032	D	0.01	-12.673	11.2423	0.48977	0.0:0.9081:0.0:0.0919	.	192	Q8NGE8	OR4D9_HUMAN	S	192	ENSP00000328563:T192S	ENSP00000328563:T192S	T	+	2	0	OR4D9	59039536	0.004000	0.15560	0.109000	0.21407	0.328000	0.28507	0.698000	0.25571	0.977000	0.38444	0.557000	0.71058	ACC	C|0.979;G|0.021	0.021	strong		0.453	OR4D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394237.1	NM_001004711		G	59282960	C	G	59282960	3	3	22	1	0	0	0	0	1	0	0	0	11068	507	18	4	577	4	OR4D9	11	59282960	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	122	59282960	75723556	2460	5361											
OR4D9	390199	hgsc.bcm.edu	37	chr11	59283299	59283299	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaggaaactgaagagacggcTaggacaatcagaaaggattt	17	6	13	5	1	1	3	1	1	0	2	1	8	1	6	0	4	1	1	0	4	5	2	rs79922105	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:59283299T>C	ENST00000329328.3	+	1	914	c.914T>C	c.(913-915)cTa>cCa	p.L305P		NM_001004711.1	NP_001004711.1	Q8NGE8	OR4D9_HUMAN	olfactory receptor, family 4, subfamily D, member 9	305						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						AAGAGACGGCTAGGACAATCA	0.383													T|||	108	0.0215655	0.0802	0.0029	5008	,	,		20633	0.0		0.0	False		,,,				2504	0.0				p.L305P		Atlas-SNP	.											.	OR4D9	47	.	0			c.T914C						PASS	.	T	PRO/LEU	260,4142	140.0+/-175.5	8,244,1949	54	56	55		914	2.3	0	11	dbSNP_132	55	1,8589		0,1,4294	yes	missense	OR4D9	NM_001004711.1	98	8,245,6243	CC,CT,TT		0.0116,5.9064,2.0089	possibly-damaging	305/315	59283299	261,12731	2201	4295	6496	SO:0001583	missense	390199	exon1			GACGGCTAGGACA	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.914T>C	11.37:g.59283299T>C	ENSP00000328563:p.Leu305Pro	69	0	0		83	26	0.313253	NM_001004711	Q6IFF3	Missense_Mutation	SNP	ENST00000329328.3	37	CCDS31564.1	53	0.024267399267399268	52	0.10569105691056911	1	0.0027624309392265192	0	0.0	0	0.0	T	6.379	0.438092	0.12104	0.059064	1.16E-4	ENSG00000172742	ENST00000329328	T	0.38887	1.11	3.47	2.29	0.28610	.	0.257134	0.20056	U	0.100183	T	0.00356	0.0011	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.18263	0.021	T	0.09975	-1.0650	10	0.37606	T	0.19	.	4.1407	0.10191	0.208:0.0:0.2151:0.5769	.	305	Q8NGE8	OR4D9_HUMAN	P	305	ENSP00000328563:L305P	ENSP00000328563:L305P	L	+	2	0	OR4D9	59039875	0.003000	0.15002	0.001000	0.08648	0.002000	0.02628	1.303000	0.33470	0.480000	0.27534	-0.490000	0.04691	CTA	T|0.980;C|0.020	0.020	strong		0.383	OR4D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394237.1	NM_001004711		C	59283299	T	C	59283299	3	2	22	1	0	0	0	0	1	0	0	0	11068	1522	53	3	916	3	OR4D9	11	59283299	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	339	59283299	75723217	2461	5362											
MS4A6A	64231	hgsc.bcm.edu	37	chr11	59943082	59943082	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttccaaccaggctgctatgCacctgaaagagaaatgttgg	12	9	10	10	0	0	2	0	1	0	1	1	3	1	2	3	2	3	4	3	2	4	3	rs138028890	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:59943082C>T	ENST00000530839.1	-	6	834	c.342G>A	c.(340-342)gtG>gtA	p.V114V	MS4A6A_ENST00000420732.2_Silent_p.V114V|MS4A6A_ENST00000323961.3_Silent_p.V114V|MS4A6A_ENST00000412309.2_Silent_p.V142V|MS4A6A_ENST00000528851.1_Silent_p.V114V|MS4A6A_ENST00000529054.1_Silent_p.V142V|MS4A6A_ENST00000426738.2_Silent_p.V69V|MS4A6A_ENST00000529906.1_5'Flank|MS4A6A_ENST00000533023.1_Silent_p.V50V	NM_152852.2	NP_690591.1	Q9H2W1	M4A6A_HUMAN	membrane-spanning 4-domains, subfamily A, member 6A	114						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						GGCTGCTATGCACCTGAAAGA	0.448													C|||	9	0.00179712	0.0068	0.0	5008	,	,		21254	0.0		0.0	False		,,,				2504	0.0				p.V142V		Atlas-SNP	.											.	MS4A6A	85	.	0			c.G426A						PASS	.	C	,,	26,4376	31.7+/-61.6	0,26,2175	95	84	88		342,342,342	-5.1	0	11	dbSNP_134	88	0,8590		0,0,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	MS4A6A	NM_022349.2,NM_152851.1,NM_152852.1	,,	0,26,6470	TT,TC,CC		0.0,0.5906,0.2001	,,	114/226,114/179,114/249	59943082	26,12966	2201	4295	6496	SO:0001819	synonymous_variant	64231	exon6			GCTATGCACCTGA	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.342G>A	11.37:g.59943082C>T		94	0	0		110	64	0.581818	NM_001247999	A8K755|F8W9K1|Q7Z4E8|Q8TBV7|Q8TEZ4|Q8TEZ5|Q96PG6|Q9H2L1|Q9H2N3|Q9H3V1|Q9HC76	Silent	SNP	ENST00000530839.1	37	CCDS7981.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	1.565	-0.535705	0.04082	0.005906	0.0	ENSG00000110077	ENST00000533989	.	.	.	4.99	-5.13	0.02884	.	.	.	.	.	T	0.11196	0.0273	.	.	.	0.18873	N	0.999984	.	.	.	.	.	.	T	0.25187	-1.0139	4	.	.	.	.	0.3632	0.00367	0.2373:0.2707:0.2458:0.2462	.	.	.	.	Y	49	.	.	C	-	2	0	MS4A6A	59699658	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.770000	0.01791	-0.810000	0.04375	-0.976000	0.02587	TGC	C|0.997;T|0.003	0.003	strong		0.448	MS4A6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393848.1			T	59943082	C	T	59943082	2	4	22	1	0	0	0	0	0	0	0	1	9873	697	25	2		2	MS4A6A	11	59943082	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	659783	59943082	75063434	2462	5363											
MS4A7	58475	hgsc.bcm.edu	37	chr11	60161273	60161273	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tttctagagttcattttcctCgacccagtcacaagatcata	11	14	5	11	1	4	2	3	0	1	2	6	3	5	2	2	0	0	1	2	0	3	6	rs372900689		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:60161273C>T	ENST00000300184.3	+	7	858	c.662C>T	c.(661-663)tCg>tTg	p.S221L	MS4A14_ENST00000531787.1_Intron|MS4A7_ENST00000358246.1_Missense_Mutation_p.S176L|MS4A7_ENST00000530234.2_Intron|MS4A14_ENST00000395001.1_5'Flank|MS4A14_ENST00000531783.1_5'Flank|MS4A14_ENST00000300187.6_5'Flank|MS4A7_ENST00000534016.1_Missense_Mutation_p.S176L|MS4A14_ENST00000395005.2_5'Flank	NM_021201.4|NM_206939.1	NP_067024.1|NP_996822.1	Q9GZW8	MS4A7_HUMAN	membrane-spanning 4-domains, subfamily A, member 7	221						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						TCATTTTCCTCGACCCAGTCA	0.348																																					p.S221L		Atlas-SNP	.											.	MS4A7	38	.	0			c.C662T						PASS	.	C	LEU/SER,LEU/SER,LEU/SER,LEU/SER	1,4405	2.1+/-5.4	0,1,2202	103	105	104		527,662,527,662	0	0	11		104	0,8600		0,0,4300	no	missense,missense,missense,missense	MS4A7	NM_206940.1,NM_206939.1,NM_206938.1,NM_021201.4	145,145,145,145	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign,benign,benign	176/196,221/241,176/196,221/241	60161273	1,13005	2203	4300	6503	SO:0001583	missense	58475	exon7			TTTCCTCGACCCA	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.662C>T	11.37:g.60161273C>T	ENSP00000300184:p.Ser221Leu	75	0	0		70	41	0.585714	NM_021201	A6NP53|Q6IAG8	Missense_Mutation	SNP	ENST00000300184.3	37	CCDS7985.1	.	.	.	.	.	.	.	.	.	.	c	0.019	-1.453245	0.01071	2.27E-4	0.0	ENSG00000166927	ENST00000300184;ENST00000358246;ENST00000534016;ENST00000530027	T;T;T;T	0.12984	3.36;2.63;2.63;2.9	3.79	-0.0112	0.13993	.	2.053890	0.03732	N	0.253570	T	0.05640	0.0148	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	0.27434	-1.0074	10	0.02654	T	1	-35.547	3.542	0.07815	0.0:0.2192:0.1969:0.5839	.	176;221	Q9GZW8-2;Q9GZW8	.;MS4A7_HUMAN	L	221;176;176;157	ENSP00000300184:S221L;ENSP00000350983:S176L;ENSP00000434637:S176L;ENSP00000434819:S157L	ENSP00000300184:S221L	S	+	2	0	MS4A7	59917849	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.094000	0.11094	-0.015000	0.14150	-0.592000	0.04112	TCG	.	.	weak		0.348	MS4A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394299.1			T	60161273	C	T	60161273	3	4	22	1	0	0	0	0	1	0	0	0	9875	893	31	1	684	1	MS4A7	11	60161273	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	218191	60161273	74845243	2463	5364											
MS4A14	84689	hgsc.bcm.edu	37	chr11	60183401	60183401	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatatatcacctgaagacttGccatcccaagctctaccagt	12	10	6	13	0	2	2	1	1	1	1	3	3	3	2	4	0	3	1	4	0	5	4	rs376669252		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:60183401G>T	ENST00000300187.6	+	5	1237	c.960G>T	c.(958-960)ttG>ttT	p.L320F	MS4A14_ENST00000395005.2_Missense_Mutation_p.L303F|MS4A14_ENST00000531783.1_Missense_Mutation_p.L353F|MS4A14_ENST00000395001.1_3'UTR|MS4A14_ENST00000531787.1_Missense_Mutation_p.L208F	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14	320						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						CTGAAGACTTGCCATCCCAAG	0.448																																					p.L353F		Atlas-SNP	.											.	MS4A14	120	.	0			c.G1059T						PASS	.	G	PHE/LEU,PHE/LEU	1,4405	2.1+/-5.4	0,1,2202	99	91	94		909,960	-0.6	0	11		94	0,8600		0,0,4300	no	missense,missense	MS4A14	NM_001079692.1,NM_032597.3	22,22	0,1,6502	TT,TG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	303/663,320/680	60183401	1,13005	2203	4300	6503	SO:0001583	missense	84689	exon6			AGACTTGCCATCC	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.960G>T	11.37:g.60183401G>T	ENSP00000300187:p.Leu320Phe	168	0	0		164	77	0.469512	NM_001261828	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Missense_Mutation	SNP	ENST00000300187.6	37	CCDS31569.1	.	.	.	.	.	.	.	.	.	.	G	9.851	1.193578	0.22037	2.27E-4	0.0	ENSG00000166928	ENST00000531787;ENST00000300187;ENST00000395005;ENST00000531783	T;T;T;T	0.39787	1.07;2.31;1.06;2.67	3.83	-0.63	0.11530	.	3.820730	0.00986	N	0.003454	T	0.32071	0.0817	L	0.36672	1.1	0.09310	N	1	P;P	0.40107	0.703;0.578	B;B	0.35413	0.202;0.099	T	0.27331	-1.0077	10	0.52906	T	0.07	-0.0477	5.6589	0.17658	0.0999:0.0:0.3621:0.5381	.	303;320	Q96JA4-2;Q96JA4	.;M4A14_HUMAN	F	208;320;303;353	ENSP00000437222:L208F;ENSP00000300187:L320F;ENSP00000378453:L303F;ENSP00000433761:L353F	ENSP00000300187:L320F	L	+	3	2	MS4A14	59939977	0.000000	0.05858	0.007000	0.13788	0.081000	0.17604	-0.924000	0.03996	-0.103000	0.12175	-0.143000	0.13931	TTG	.	.	weak		0.448	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2			T	60183401	G	T	60183401	3	4	22	1	0	0	0	0	1	0	0	0	9867	1310	46	4	978	4	MS4A14	11	60183401	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	22128	60183401	74823115	2464	5365											
ZP1	22917	hgsc.bcm.edu	37	chr11	60642633	60642633	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcaggtcaccgtaatgaCactgccaggccccaggacat	10	7	9	15	1	2	1	2	1	0	0	3	2	3	2	5	3	1	1	5	3	1	1	rs112864814	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:60642633C>T	ENST00000278853.5	+	11	1686	c.1686C>T	c.(1684-1686)gaC>gaT	p.D562D		NM_207341.2	NP_997224.2	P60852	ZP1_HUMAN	zona pellucida glycoprotein 1 (sperm receptor)	562					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						ACCGTAATGACACTGCCAGGC	0.627													C|||	78	0.0155751	0.056	0.0029	5008	,	,		19463	0.0		0.002	False		,,,				2504	0.0				p.D562D		Atlas-SNP	.											.	ZP1	69	.	0			c.C1686T						PASS	.	C		240,4166	142.3+/-177.5	3,234,1966	69	73	72		1686	-4.2	0	11	dbSNP_132	72	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	ZP1	NM_207341.2		3,235,6264	TT,TC,CC		0.0116,5.4471,1.8533		562/639	60642633	241,12763	2203	4299	6502	SO:0001819	synonymous_variant	22917	exon11			TAATGACACTGCC	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.1686C>T	11.37:g.60642633C>T		99	0	0		126	60	0.47619	NM_207341		Silent	SNP	ENST00000278853.5	37	CCDS31572.1																																																																																			C|0.980;T|0.020	0.020	strong		0.627	ZP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396329.1	NM_207341		T	60642633	C	T	60642633	2	4	22	1	0	0	0	0	0	0	0	1	18230	477	17	2		2	ZP1	11	60642633	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	459232	60642633	74363883	2465	5366											
VWCE	220001	hgsc.bcm.edu	37	chr11	61048322	61048322	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgactccttgattcatgcatGgctcccaggtgccagcaggg	7	9	12	13	1	1	1	1	1	0	0	3	2	3	1	3	3	3	3	3	3	0	2	rs61744427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61048322G>C	ENST00000335613.5	-	8	1559	c.1173C>G	c.(1171-1173)gcC>gcG	p.A391A		NM_152718.2	NP_689931.2	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	391	VWFC 1. {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						ATTCATGCATGGCTCCCAGGT	0.662													G|||	142	0.0283546	0.0613	0.0058	5008	,	,		17203	0.0268		0.001	False		,,,				2504	0.0297				p.A391A		Atlas-SNP	.											.	VWCE	84	.	0			c.C1173G						PASS	.	G		240,4164		3,234,1965	12	14	13		1173	1.2	0.5	11	dbSNP_129	13	3,8587		0,3,4292	no	coding-synonymous	VWCE	NM_152718.2		3,237,6257	CC,CG,GG		0.0349,5.4496,1.8701		391/956	61048322	243,12751	2202	4295	6497	SO:0001819	synonymous_variant	220001	exon8			ATGCATGGCTCCC	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.1173C>G	11.37:g.61048322G>C		51	0	0		67	36	0.537313	NM_152718	A5PKV0|Q7Z7L6|Q86WK8	Silent	SNP	ENST00000335613.5	37	CCDS8002.1																																																																																			G|0.971;C|0.029	0.029	strong		0.662	VWCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398811.1	NM_152718		C	61048322	G	C	61048322	2	2	22	1	0	0	0	0	0	0	0	1	17260	1335	47	4		4	VWCE	11	61048322	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	405689	61048322	73958194	2466	5367											
BEST1	7439	hgsc.bcm.edu	37	chr11	61730414	61730414	+	Intron	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgcattgccctgtgccccacCccagcttcccttgctctgag	4	11	8	18	0	1	1	0	1	1	0	2	1	2	1	6	0	5	3	6	0	0	3	rs115379107	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61730414C>A	ENST00000378043.4	+	10	2382				FTH1_ENST00000529631.1_Intron|BEST1_ENST00000301774.9_Silent_p.T224T|FTH1_ENST00000529191.1_Intron|BEST1_ENST00000449131.2_Silent_p.T536T|BEST1_ENST00000378042.3_Intron|BEST1_ENST00000534553.1_3'UTR	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1						chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|detection of light stimulus involved in visual perception (GO:0050908)|ion transmembrane transport (GO:0034220)|regulation of calcium ion transport (GO:0051924)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	basolateral plasma membrane (GO:0016323)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|urinary_tract(2)	25						TGTGCCCCACCCCAGCTTCCC	0.557													C|||	141	0.028155	0.1014	0.0101	5008	,	,		20189	0.0		0.0	False		,,,				2504	0.0				p.T536T		Atlas-SNP	.											.	BEST1	85	.	0			c.C1608A						PASS	.	C	,	329,4041		12,305,1868	69	76	74		1608,	-0.5	0	11	dbSNP_132	74	0,8586		0,0,4293	no	coding-synonymous,intron	BEST1	NM_001139443.1,NM_004183.3	,	12,305,6161	AA,AC,CC		0.0,7.5286,2.5394	,	536/605,	61730414	329,12627	2185	4293	6478	SO:0001627	intron_variant	7439	exon9			CCCCACCCCAGCT	AF057170	CCDS31580.1, CCDS44623.1	11q12	2013-02-14	2006-10-18	2006-10-18	ENSG00000167995	ENSG00000167995		"Ion channels / Chloride channels : Calcium activated : Bestrophins"	12703	protein-coding gene	gene with protein product	"Best disease"	607854	"vitelliform macular dystrophy 2"	VMD2		1302019, 17003041	Standard	NM_004183		Approved	BMD, BEST, RP50	uc001nsr.2	O76090	OTTHUMG00000167469	ENST00000378043.4:c.1739+49C>A	11.37:g.61730414C>A		201	0	0		163	84	0.515337	NM_001139443	A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	Silent	SNP	ENST00000378043.4	37	CCDS31580.1																																																																																			C|0.974;A|0.026	0.026	strong		0.557	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1	NM_004183		A	61730414	C	A	61730414	1	1	22	0	1	0	0	0	0	0	0	0	1404	610	22	4		4	BEST1	11	61730414	Intron	SNP	C	TCGA-G8-6324-01A-11D-2210-10	682092	61730414	73276102	2467	5368											
BEST1	7439	hgsc.bcm.edu	37	chr11	61730427	61730427	+	Intron	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccccaccccagcttcccttGctctgagcctacccttcctc	4	10	5	22	0	1	1	0	1	1	0	4	1	3	1	8	0	4	2	8	0	1	4	rs115979721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61730427G>T	ENST00000378043.4	+	10	2382				FTH1_ENST00000529631.1_Intron|BEST1_ENST00000301774.9_Missense_Mutation_p.A229S|FTH1_ENST00000529191.1_Intron|BEST1_ENST00000449131.2_Missense_Mutation_p.A541S|BEST1_ENST00000378042.3_Intron|BEST1_ENST00000534553.1_3'UTR	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1						chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|detection of light stimulus involved in visual perception (GO:0050908)|ion transmembrane transport (GO:0034220)|regulation of calcium ion transport (GO:0051924)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	basolateral plasma membrane (GO:0016323)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|urinary_tract(2)	25						AGCTTCCCTTGCTCTGAGCCT	0.562													G|||	107	0.0213658	0.0764	0.0086	5008	,	,		19855	0.0		0.0	False		,,,				2504	0.0				p.A541S		Atlas-SNP	.											.	BEST1	85	.	0			c.G1621T						PASS	.	G	SER/ALA,	74,1310		2,70,620	123	114	116		1621,	-5.3	0	11	dbSNP_132	116	0,3182		0,0,1591	yes	missense,intron	BEST1	NM_001139443.1,NM_004183.3	99,	2,70,2211	TT,TG,GG		0.0,5.3468,1.6207	,	541/605,	61730427	74,4492	692	1591	2283	SO:0001627	intron_variant	7439	exon9			TCCCTTGCTCTGA	AF057170	CCDS31580.1, CCDS44623.1	11q12	2013-02-14	2006-10-18	2006-10-18	ENSG00000167995	ENSG00000167995		"Ion channels / Chloride channels : Calcium activated : Bestrophins"	12703	protein-coding gene	gene with protein product	"Best disease"	607854	"vitelliform macular dystrophy 2"	VMD2		1302019, 17003041	Standard	NM_004183		Approved	BMD, BEST, RP50	uc001nsr.2	O76090	OTTHUMG00000167469	ENST00000378043.4:c.1739+62G>T	11.37:g.61730427G>T		193	0	0		165	81	0.490909	NM_001139443	A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	Missense_Mutation	SNP	ENST00000378043.4	37	CCDS31580.1	40	0.018315018315018316	38	0.07723577235772358	2	0.0055248618784530384	0	0.0	0	0.0	G	12.96	2.094835	0.36952	0.053468	0.0	ENSG00000167995	ENST00000301774;ENST00000449131	T;D	0.97089	-0.32;-4.24	4.13	-5.35	0.02697	.	.	.	.	.	T	0.35098	0.0920	N	0.08118	0	0.09310	N	0.999995	B	0.17268	0.021	B	0.14023	0.01	T	0.73116	-0.4084	8	.	.	.	.	0.3641	0.00369	0.2188:0.2264:0.2454:0.3094	.	541	O76090-3	.	S	229;541	ENSP00000301774:A229S;ENSP00000399709:A541S	.	A	+	1	0	BEST1	61487003	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.419000	0.07071	-1.297000	0.02351	-0.311000	0.09066	GCT	G|0.977;T|0.023	0.023	strong		0.562	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1	NM_004183		T	61730427	G	T	61730427	1	4	22	0	1	0	0	0	0	0	0	0	1404	1319	46	4		4	BEST1	11	61730427	Intron	SNP	G	TCGA-G8-6324-01A-11D-2210-10	13	61730427	73276089	2468	5369											
INCENP	3619	hgsc.bcm.edu	37	chr11	61897542	61897542	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagcgccagaatgctgagcaGcatgtcacccagctcatgtc	10	7	11	13	1	2	2	2	1	0	1	3	3	2	2	2	0	5	4	2	0	1	0	rs145875137	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61897542G>A	ENST00000394818.3	+	4	745	c.543G>A	c.(541-543)caG>caA	p.Q181Q	INCENP_ENST00000278849.4_Silent_p.Q181Q	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	181					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						ATGCTGAGCAGCATGTCACCC	0.617													G|||	13	0.00259585	0.0098	0.0	5008	,	,		16459	0.0		0.0	False		,,,				2504	0.0				p.Q181Q		Atlas-SNP	.											.	INCENP	122	.	0			c.G543A						PASS	.	G	,	50,4354	50.9+/-86.3	0,50,2152	65	56	59		543,543	1.8	0	11	dbSNP_134	59	1,8597		0,1,4298	no	coding-synonymous,coding-synonymous	INCENP	NM_001040694.1,NM_020238.2	,	0,51,6450	AA,AG,GG		0.0116,1.1353,0.3922	,	181/919,181/915	61897542	51,12951	2202	4299	6501	SO:0001819	synonymous_variant	3619	exon4			TGAGCAGCATGTC	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.543G>A	11.37:g.61897542G>A		42	0	0		40	20	0.5	NM_001040694	A8MQD2|Q5Y192	Silent	SNP	ENST00000394818.3	37	CCDS44624.1																																																																																			G|0.996;A|0.004	0.004	strong		0.617	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238		A	61897542	G	A	61897542	2	1	22	1	0	0	0	0	0	0	0	1	7742	962	34	2		2	INCENP	11	61897542	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	167115	61897542	73108974	2469	5370											
INCENP	3619	hgsc.bcm.edu	37	chr11	61906216	61906216	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggaaccccccgaggaggctGagcctgtggcggcagctgag	8	4	17	12	2	0	2	0	2	0	0	0	5	0	4	4	5	3	3	4	5	1	0	rs61751226	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61906216G>A	ENST00000394818.3	+	6	1349	c.1147G>A	c.(1147-1149)Gag>Aag	p.E383K	INCENP_ENST00000278849.4_Missense_Mutation_p.E383K	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	383					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						CGAGGAGGCTGAGCCTGTGGC	0.642													G|||	58	0.0115815	0.0159	0.0	5008	,	,		17187	0.0		0.0	False		,,,				2504	0.0378				p.E383K		Atlas-SNP	.											.	INCENP	122	.	0			c.G1147A						PASS	.	G	LYS/GLU,LYS/GLU	83,4321	72.0+/-110.0	2,79,2121	47	53	51		1147,1147	1.9	0	11	dbSNP_129	51	1,8597		0,1,4298	yes	missense,missense	INCENP	NM_020238.2,NM_001040694.1	56,56	2,80,6419	AA,AG,GG		0.0116,1.8847,0.6461	benign,benign	383/915,383/919	61906216	84,12918	2202	4299	6501	SO:0001583	missense	3619	exon6			GAGGCTGAGCCTG	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.1147G>A	11.37:g.61906216G>A	ENSP00000378295:p.Glu383Lys	44	0	0		50	26	0.52	NM_001040694	A8MQD2|Q5Y192	Missense_Mutation	SNP	ENST00000394818.3	37	CCDS44624.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	9.415	1.081416	0.20309	0.018847	1.16E-4	ENSG00000149503	ENST00000394818;ENST00000278849	T;T	0.16743	2.37;2.32	4.98	1.93	0.25924	.	0.347185	0.24786	N	0.035604	T	0.05731	0.0150	M	0.68952	2.095	0.09310	N	1	P;B;B	0.43788	0.817;0.208;0.132	B;B;B	0.36666	0.23;0.038;0.017	T	0.12682	-1.0538	10	0.08381	T	0.77	.	4.7767	0.13182	0.1895:0.1777:0.6328:0.0	rs61751226	383;383;383	B3KPD3;Q9NQS7-2;Q9NQS7	.;.;INCE_HUMAN	K	383	ENSP00000378295:E383K;ENSP00000278849:E383K	ENSP00000278849:E383K	E	+	1	0	INCENP	61662792	0.351000	0.24887	0.039000	0.18376	0.000000	0.00434	2.664000	0.46783	0.816000	0.34421	-0.768000	0.03414	GAG	G|0.995;A|0.005	0.005	strong		0.642	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238		A	61906216	G	A	61906216	3	1	22	1	0	0	0	0	1	0	0	0	7742	1291	45	2	1165	2	INCENP	11	61906216	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	8674	61906216	73100300	2470	5371											
INCENP	3619	hgsc.bcm.edu	37	chr11	61906397	61906397	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaataactcgtggccccacaAtgacacggagattgccaaca	15	6	8	12	2	0	2	0	1	0	1	1	3	0	2	3	2	3	0	3	2	4	2	rs138049815	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61906397A>G	ENST00000394818.3	+	7	1413	c.1211A>G	c.(1210-1212)aAt>aGt	p.N404S	INCENP_ENST00000278849.4_Missense_Mutation_p.N404S	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	404					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						TGGCCCCACAATGACACGGAG	0.587													A|||	13	0.00259585	0.0098	0.0	5008	,	,		17407	0.0		0.0	False		,,,				2504	0.0				p.N404S		Atlas-SNP	.											.	INCENP	122	.	0			c.A1211G						PASS	.	A	SER/ASN,SER/ASN	48,4356	49.6+/-84.7	0,48,2154	133	122	125		1211,1211	1.4	0.1	11	dbSNP_134	125	1,8597		0,1,4298	yes	missense,missense	INCENP	NM_020238.2,NM_001040694.1	46,46	0,49,6452	GG,GA,AA		0.0116,1.0899,0.3769	benign,benign	404/915,404/919	61906397	49,12953	2202	4299	6501	SO:0001583	missense	3619	exon7			CCCACAATGACAC	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.1211A>G	11.37:g.61906397A>G	ENSP00000378295:p.Asn404Ser	64	0	0		124	68	0.548387	NM_001040694	A8MQD2|Q5Y192	Missense_Mutation	SNP	ENST00000394818.3	37	CCDS44624.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	A	0.939	-0.710017	0.03230	0.010899	1.16E-4	ENSG00000149503	ENST00000394818;ENST00000278849	T;T	0.13196	2.61;2.61	5.24	1.43	0.22495	.	0.301301	0.29113	N	0.013114	T	0.02156	0.0067	N	0.01410	-0.885	0.09310	N	1	B;B;B	0.18610	0.029;0.0;0.0	B;B;B	0.18871	0.023;0.001;0.001	T	0.44605	-0.9317	10	0.07325	T	0.83	.	6.0369	0.19712	0.4261:0.0:0.5739:0.0	.	404;404;404	B3KPD3;Q9NQS7-2;Q9NQS7	.;.;INCE_HUMAN	S	404	ENSP00000378295:N404S;ENSP00000278849:N404S	ENSP00000278849:N404S	N	+	2	0	INCENP	61662973	0.048000	0.20356	0.068000	0.19968	0.006000	0.05464	0.392000	0.20801	0.558000	0.29135	-0.242000	0.12053	AAT	A|0.996;G|0.004	0.004	strong		0.587	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238		G	61906397	A	G	61906397	3	3	22	1	0	0	0	0	1	0	0	0	7742	101	4	3	1233	3	INCENP	11	61906397	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	181	61906397	73100119	2471	5372											
SCGB1D1	10648	hgsc.bcm.edu	37	chr11	61959636	61959636	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atttaaggcacctctggaagCtgttgcagccaagatggaag	12	9	12	8	0	1	1	0	0	1	1	1	3	1	3	2	3	3	4	2	3	4	3	rs116188604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61959636C>T	ENST00000306238.3	+	2	233	c.164C>T	c.(163-165)gCt>gTt	p.A55V		NM_006552.1	NP_006543.1	O95968	SG1D1_HUMAN	secretoglobin, family 1D, member 1	55						extracellular space (GO:0005615)	protein heterodimerization activity (GO:0046982)			endometrium(1)|large_intestine(2)|lung(4)|skin(1)|stomach(1)	9						CCTCTGGAAGCTGTTGCAGCC	0.423													C|||	69	0.013778	0.0484	0.0058	5008	,	,		21854	0.0		0.001	False		,,,				2504	0.0				p.A55V		Atlas-SNP	.											SCGB1D1,NS,carcinoma,0,1	SCGB1D1	18	1	0			c.C164T						PASS	.	C	VAL/ALA	192,4212	122.1+/-159.5	6,180,2016	132	126	128		164	-4.4	0	11	dbSNP_132	128	4,8594	3.7+/-12.6	0,4,4295	yes	missense	SCGB1D1	NM_006552.1	64	6,184,6311	TT,TC,CC		0.0465,4.3597,1.5075	probably-damaging	55/91	61959636	196,12806	2202	4299	6501	SO:0001583	missense	10648	exon2			TGGAAGCTGTTGC	AJ224171	CCDS8015.1	11q13	2011-12-14			ENSG00000168515	ENSG00000168515		"Secretoglobins"	18395	protein-coding gene	gene with protein product	"prostatein-like lipophilin A", "lipophilin A (uteroglobin family member)"	615060				9720917, 10066439, 22155607	Standard	NM_006552		Approved	LPHA, LIPA, MGC71958	uc001nsz.1	O95968	OTTHUMG00000167505	ENST00000306238.3:c.164C>T	11.37:g.61959636C>T	ENSP00000303070:p.Ala55Val	151	0	0		165	88	0.533333	NM_006552		Missense_Mutation	SNP	ENST00000306238.3	37	CCDS8015.1	36	0.016483516483516484	30	0.06097560975609756	3	0.008287292817679558	0	0.0	3	0.00395778364116095	C	13.33	2.203741	0.38905	0.043597	4.65E-4	ENSG00000168515	ENST00000306238	T	0.15372	2.43	3.88	-4.42	0.03579	.	1.484950	0.04929	N	0.456544	T	0.01029	0.0034	.	.	.	0.09310	N	1	P	0.42735	0.788	B	0.37144	0.242	T	0.14309	-1.0477	9	0.51188	T	0.08	.	3.9086	0.09193	0.269:0.2885:0.0:0.4425	.	55	O95968	SG1D1_HUMAN	V	55	ENSP00000303070:A55V	ENSP00000303070:A55V	A	+	2	0	SCGB1D1	61716212	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.404000	0.02494	-1.026000	0.03330	-0.857000	0.03018	GCT	C|0.982;T|0.018	0.018	strong		0.423	SCGB1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394856.1	NM_006552		T	61959636	C	T	61959636	3	4	22	1	0	0	0	0	1	0	0	0	13911	797	28	2	170	2	SCGB1D1	11	61959636	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	53239	61959636	73046880	2472	5373											
AHNAK	79026	hgsc.bcm.edu	37	chr11	62291912	62291912	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgggccctttatatccaaaCtgggagctttaatgtcacct	9	13	8	11	0	1	0	1	0	0	0	2	1	2	1	3	2	2	1	3	2	4	5	rs115362908	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62291912C>T	ENST00000378024.4	-	5	10251	c.9977G>A	c.(9976-9978)aGt>aAt	p.S3326N	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	3326					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)				TATATCCAAACTGGGAGCTTT	0.413													C|||	16	0.00319489	0.0098	0.0043	5008	,	,		19033	0.0		0.0	False		,,,				2504	0.0				p.S3326N		Atlas-SNP	.											.	AHNAK	532	.	0			c.G9977A						PASS	.	C	ASN/SER,	53,4351	52.3+/-87.9	3,47,2152	58	53	55		9977,	1.6	0.1	11	dbSNP_132	55	1,8597	1.2+/-3.3	0,1,4298	yes	missense,intron	AHNAK	NM_001620.1,NM_024060.2	46,	3,48,6450	TT,TC,CC		0.0116,1.2035,0.4153	benign,	3326/5891,	62291912	54,12948	2202	4299	6501	SO:0001583	missense	79026	exon5			TCCAAACTGGGAG	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.9977G>A	11.37:g.62291912C>T	ENSP00000367263:p.Ser3326Asn	80	0	0		76	45	0.592105	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	8	0.003663003663003663	6	0.012195121951219513	2	0.0055248618784530384	0	0.0	0	0.0	C	1.856	-0.463832	0.04476	0.012035	1.16E-4	ENSG00000124942	ENST00000378024	T	0.00672	5.89	4.07	1.61	0.23674	.	.	.	.	.	T	0.00608	0.0020	L	0.28556	0.865	0.09310	N	1	B	0.25719	0.132	B	0.35278	0.199	T	0.48747	-0.9008	9	0.20519	T	0.43	.	6.9065	0.24311	0.0:0.2034:0.0:0.7966	.	3326	Q09666	AHNK_HUMAN	N	3326	ENSP00000367263:S3326N	ENSP00000367263:S3326N	S	-	2	0	AHNAK	62048488	0.000000	0.05858	0.067000	0.19924	0.419000	0.31324	0.794000	0.26958	0.089000	0.17243	0.305000	0.20034	AGT	C|0.996;T|0.004	0.004	strong		0.413	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		T	62291912	C	T	62291912	3	4	22	1	0	0	0	0	1	0	0	0	414	565	20	2	7815	2	AHNAK	11	62291912	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	332276	62291912	72714604	2473	5374											
AHNAK	79026	hgsc.bcm.edu	37	chr11	62295149	62295149	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcatgctgaacttgggcattTtcatcttaggcatcttcagg	8	14	10	9	0	4	1	2	1	2	0	4	1	4	1	0	3	2	4	0	3	2	5	rs61524789	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62295149T>G	ENST00000378024.4	-	5	7014	c.6740A>C	c.(6739-6741)aAa>aCa	p.K2247T	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	2247			K -> T (in dbSNP:rs61524789).		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)				CTTGGGCATTTTCATCTTAGG	0.522													T|||	148	0.0295527	0.1051	0.0101	5008	,	,		20293	0.0		0.002	False		,,,				2504	0.0				p.K2247T		Atlas-SNP	.											.	AHNAK	532	.	0			c.A6740C						PASS	.	T	THR/LYS,	378,4026	192.6+/-218.0	16,346,1840	305	305	305		6740,	3.4	1	11	dbSNP_129	305	3,8595	2.2+/-6.3	0,3,4296	no	missense,intron	AHNAK	NM_001620.1,NM_024060.2	78,	16,349,6136	GG,GT,TT		0.0349,8.5831,2.9303	probably-damaging,	2247/5891,	62295149	381,12621	2202	4299	6501	SO:0001583	missense	79026	exon5			GGCATTTTCATCT	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.6740A>C	11.37:g.62295149T>G	ENSP00000367263:p.Lys2247Thr	210	0	0		274	131	0.478102	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	73	0.033424908424908424	68	0.13821138211382114	3	0.008287292817679558	0	0.0	2	0.002638522427440633	T	16.14	3.038892	0.55003	0.085831	3.49E-4	ENSG00000124942	ENST00000244934;ENST00000378024	T	0.12147	2.71	3.38	3.38	0.38709	.	0.000000	0.39083	U	0.001465	T	0.00440	0.0014	H	0.95470	3.675	0.44660	D	0.997647	D	0.69078	0.997	D	0.77557	0.99	T	0.01743	-1.1283	10	0.62326	D	0.03	.	12.0108	0.53286	0.0:0.0:0.0:1.0	rs61524789	2247	Q09666	AHNK_HUMAN	T	336;2247	ENSP00000367263:K2247T	ENSP00000244934:K336T	K	-	2	0	AHNAK	62051725	1.000000	0.71417	0.997000	0.53966	0.777000	0.43975	5.886000	0.69743	1.546000	0.49388	0.242000	0.17961	AAA	T|0.965;G|0.035	0.035	strong		0.522	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		G	62295149	T	G	62295149	3	3	22	1	0	0	0	0	1	0	0	0	414	1841	64	5	11052	5	AHNAK	11	62295149	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	3237	62295149	72711367	2474	5375											
INTS5	80789	hgsc.bcm.edu	37	chr11	62415285	62415285	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acttgggtggctttaagccaCggccgatgactccagcatgg	8	9	13	11	2	0	1	0	1	0	0	1	2	1	1	3	4	2	2	3	4	1	3	rs149821915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62415285C>T	ENST00000330574.2	-	2	2319	c.2267G>A	c.(2266-2268)cGt>cAt	p.R756H	GANAB_ENST00000346178.4_5'Flank|GANAB_ENST00000534779.1_5'Flank|GANAB_ENST00000540933.1_5'Flank|GANAB_ENST00000356638.3_5'Flank	NM_030628.1	NP_085131.1	Q6P9B9	INT5_HUMAN	integrator complex subunit 5	756					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						CTTTAAGCCACGGCCGATGAC	0.557																																					p.R756H		Atlas-SNP	.											.	INTS5	81	.	0			c.G2267A						PASS	.	C	HIS/ARG	6,4398	11.4+/-27.6	0,6,2196	51	57	55		2267	3.5	1	11	dbSNP_134	55	0,8598		0,0,4299	yes	missense	INTS5	NM_030628.1	29	0,6,6495	TT,TC,CC		0.0,0.1362,0.0461	benign	756/1020	62415285	6,12996	2202	4299	6501	SO:0001583	missense	80789	exon2			AAGCCACGGCCGA	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.2267G>A	11.37:g.62415285C>T	ENSP00000327889:p.Arg756His	118	0	0		143	75	0.524476	NM_030628	Q8N6W5|Q9C0G5	Missense_Mutation	SNP	ENST00000330574.2	37	CCDS8027.1	.	.	.	.	.	.	.	.	.	.	C	7.215	0.596297	0.13875	0.001362	0.0	ENSG00000185085	ENST00000330574	.	.	.	5.43	3.53	0.40419	.	0.200939	0.45867	D	0.000336	T	0.29126	0.0724	L	0.28115	0.83	0.30938	N	0.726113	B	0.10296	0.003	B	0.04013	0.001	T	0.14282	-1.0478	9	0.25106	T	0.35	.	6.0709	0.19889	0.0:0.6759:0.1555:0.1686	.	756	Q6P9B9	INT5_HUMAN	H	756	.	ENSP00000327889:R756H	R	-	2	0	INTS5	62171861	0.146000	0.22672	1.000000	0.80357	0.864000	0.49448	0.847000	0.27696	1.530000	0.49136	-0.145000	0.13849	CGT	C|1.000;T|0.000	0.000	strong		0.557	INTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395327.1	NM_030628		T	62415285	C	T	62415285	3	4	22	1	0	0	0	0	1	0	0	0	7790	536	19	1	796	1	INTS5	11	62415285	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	120136	62415285	72591231	2475	5376											
TMEM223	79064	hgsc.bcm.edu	37	chr11	62559301	62559301	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	catggaagcccagaagacgcCctggcccgcgcagaacagcc	11	2	12	16	3	0	3	0	0	0	3	0	4	0	4	4	2	3	1	4	2	3	0	rs2956139	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62559301C>T	ENST00000307366.7	-	1	192	c.166G>A	c.(166-168)Ggc>Agc	p.G56S	NXF1_ENST00000533048.1_5'Flank|TMEM223_ENST00000525631.1_Missense_Mutation_p.G56S|TMEM223_ENST00000527073.1_5'Flank	NM_001080501.2	NP_001073970.1	A0PJW6	TM223_HUMAN	transmembrane protein 223	56						integral component of membrane (GO:0016021)											CAGAAGACGCCCTGGCCCGCG	0.672													C|||	121	0.0241613	0.0855	0.0086	5008	,	,		14072	0.0		0.002	False		,,,				2504	0.0				p.G56S		Atlas-SNP	.											.	TMEM223	22	.	0			c.G166A						PASS	.	C	SER/GLY	221,3653		5,211,1721	17	26	23		166	5	1	11	dbSNP_101	23	2,8218		0,2,4108	yes	missense	TMEM223	NM_001080501.2	56	5,213,5829	TT,TC,CC		0.0243,5.7047,1.8439	benign	56/203	62559301	223,11871	1937	4110	6047	SO:0001583	missense	79064	exon1			AGACGCCCTGGCC		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.166G>A	11.37:g.62559301C>T	ENSP00000303987:p.Gly56Ser	125	0	0		128	58	0.453125	NM_001080501	Q504S0|Q86YD4|Q8WUC5|Q96HG0	Missense_Mutation	SNP	ENST00000307366.7	37	CCDS44628.1	57|57	0.0260989010989011|0.0260989010989011	53|53	0.10772357723577236|0.10772357723577236	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	C|C	21.4|21.4	4.141694|4.141694	0.77775|0.77775	0.057047|0.057047	2.43E-4|2.43E-4	ENSG00000168569|ENSG00000168569	ENST00000528367|ENST00000525631;ENST00000307366	.|T;T	.|0.41758	.|0.99;0.99	5.94|5.94	5.02|5.02	0.67125|0.67125	.|.	0.275955|0.275955	0.35407|0.35407	N|N	0.003221|0.003221	T|T	0.00608|0.00608	0.0020|0.0020	L|L	0.34521|0.34521	1.04|1.04	0.35563|0.35563	D|D	0.804871|0.804871	.|B	.|0.30281	.|0.275	.|B	.|0.28916	.|0.096	T|T	0.09952|0.09952	-1.0651|-1.0651	6|9	.|.	.|.	.|.	-15.5835|-15.5835	13.3061|13.3061	0.60352|0.60352	0.0:0.9227:0.0:0.0773|0.0:0.9227:0.0:0.0773	rs2956139|rs2956139	.|56	.|A0PJW6	.|TM223_HUMAN	E|S	55|56	.|ENSP00000436670:G56S;ENSP00000303987:G56S	.|.	G|G	-|-	2|1	0|0	TMEM223|TMEM223	62315877|62315877	0.994000|0.994000	0.37717|0.37717	1.000000|1.000000	0.80357|0.80357	0.887000|0.887000	0.51463|0.51463	1.735000|1.735000	0.38176|0.38176	1.499000|1.499000	0.48617|0.48617	0.561000|0.561000	0.74099|0.74099	GGG|GGC	C|0.973;T|0.027	0.027	strong		0.672	TMEM223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395674.1			T	62559301	C	T	62559301	3	4	22	1	0	0	0	0	1	0	0	0	16161	623	22	2	450	2	TMEM223	11	62559301	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	144016	62559301	72447215	2476	5377											
SLC3A2	6520	hgsc.bcm.edu	37	chr11	62648748	62648748	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tacgcacccgctgggcactgCtgctgctcttctggctcggc	3	10	12	16	3	2	0	0	0	2	0	3	0	2	0	1	3	4	7	1	3	1	2	rs73487878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62648748C>T	ENST00000377890.2	+	4	724	c.556C>T	c.(556-558)Ctg>Ttg	p.L186L	SLC3A2_ENST00000338663.7_Silent_p.L85L|SLC3A2_ENST00000377891.2_Silent_p.L187L|SLC3A2_ENST00000535296.1_Silent_p.L155L|SLC3A2_ENST00000377889.2_Silent_p.L124L|SLC3A2_ENST00000377892.1_Silent_p.L217L|SLC3A2_ENST00000536981.1_5'Flank	NM_002394.5	NP_002385.3	P08195	4F2_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 2	186					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						CTGGGCACTGCTGCTGCTCTT	0.687											OREG0021031	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	116	0.0231629	0.0809	0.0101	5008	,	,		13125	0.0		0.002	False		,,,				2504	0.0				p.L187L		Atlas-SNP	.											.	SLC3A2	55	.	0			c.C559T						PASS	.	C	,,,	239,4153		11,217,1968	15	16	16		559,370,253,556	5	1	11	dbSNP_130	16	1,8579		0,1,4289	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC3A2	NM_001012662.2,NM_001012664.2,NM_001013251.2,NM_002394.5	,,,	11,218,6257	TT,TC,CC		0.0117,5.4417,1.8501	,,,	187/632,124/569,85/530,186/631	62648748	240,12732	2196	4290	6486	SO:0001819	synonymous_variant	6520	exon4			GCACTGCTGCTGC		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.556C>T	11.37:g.62648748C>T		57	0	0	1062	73	36	0.493151	NM_001012662	Q13543	Silent	SNP	ENST00000377890.2	37	CCDS8039.2																																																																																			C|0.975;T|0.025	0.025	strong		0.687	SLC3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157306.1	NM_001012661		T	62648748	C	T	62648748	2	4	22	1	0	0	0	0	0	0	0	1	14642	796	28	2		2	SLC3A2	11	62648748	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	89447	62648748	72357768	2477	5378											
SLC22A24	283238	hgsc.bcm.edu	37	chr11	62886706	62886706	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggagaaccctgccaagaagCgcagtatgcagtaaacaagg	15	5	12	9	1	0	2	0	0	0	2	0	3	0	2	2	2	5	4	2	2	7	2	rs116063135	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62886706C>T	ENST00000417740.1	-	3	1049	c.608G>A	c.(607-609)cGc>cAc	p.R203H	SLC22A24_ENST00000326192.5_Missense_Mutation_p.R203H	NM_001136506.2	NP_001129978.2	Q8N4F4	S22AO_HUMAN	solute carrier family 22, member 24	203					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				kidney(1)|stomach(1)	2						TGCCAAGAAGCGCAGTATGCA	0.438													C|||	58	0.0115815	0.0439	0.0	5008	,	,		21113	0.0		0.0	False		,,,				2504	0.0				p.R203H		Atlas-SNP	.											.	SLC22A24	31	.	0			c.G608A						PASS	.	C	HIS/ARG	59,1325		0,59,633	136	120	125		608	1.8	0	11	dbSNP_132	125	1,3181		0,1,1590	yes	missense	SLC22A24	NM_001136506.2	29	0,60,2223	TT,TC,CC		0.0314,4.263,1.3141	probably-damaging	203/553	62886706	60,4506	692	1591	2283	SO:0001583	missense	283238	exon3			AAGAAGCGCAGTA		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.608G>A	11.37:g.62886706C>T	ENSP00000396586:p.Arg203His	165	0	0		162	84	0.518519	NM_001136506		Missense_Mutation	SNP	ENST00000417740.1	37		23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	C	19.33	3.807587	0.70797	0.04263	3.14E-4	ENSG00000197658	ENST00000417740;ENST00000531535;ENST00000326192	D;T	0.90197	-2.63;-0.51	3.77	1.79	0.24919	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	U	0.000000	D	0.83353	0.5236	H	0.96365	3.81	0.09310	N	1	D;D	0.76494	0.999;0.995	D;P	0.66602	0.945;0.843	T	0.80094	-0.1526	10	0.87932	D	0	.	8.3277	0.32167	0.0:0.7891:0.0:0.2109	.	203;203	Q8N4F4;C9JC66	S22AO_HUMAN;.	H	203	ENSP00000396586:R203H;ENSP00000321549:R203H	ENSP00000321549:R203H	R	-	2	0	SLC22A24	62643282	0.007000	0.16637	0.002000	0.10522	0.505000	0.33919	1.812000	0.38952	0.801000	0.34066	0.501000	0.49751	CGC	C|0.988;T|0.012	0.012	strong		0.438	SLC22A24-003	PUTATIVE	non_canonical_polymorphism|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000383747.1	NM_173586		T	62886706	C	T	62886706	3	4	22	1	0	0	0	0	1	0	0	0	14468	768	27	1	1077	1	SLC22A24	11	62886706	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	237958	62886706	72119810	2478	5379											
SLC22A25	387601	hgsc.bcm.edu	37	chr11	62931547	62931547	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gattccagtagctcttccccTtggagtaaaaacagcaacag	13	9	8	11	0	1	0	0	0	1	0	3	2	3	1	3	1	4	4	3	1	5	5	rs114205803	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62931547T>C	ENST00000306494.6	-	9	1394		c.e9-2		SLC22A10_ENST00000525620.1_Intron|SLC22A10_ENST00000535888.1_Intron	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						GCTCTTCCCCTTGGAGTAAAA	0.403													T|||	18	0.00359425	0.0136	0.0	5008	,	,		20838	0.0		0.0	False		,,,				2504	0.0				.		Atlas-SNP	.											.	SLC22A25	87	.	0			c.1395-2A>G						PASS	.	T		48,4354	35.2+/-66.4	1,46,2154	102	113	110			3.9	0.7	11	dbSNP_132	110	0,8596		0,0,4298	yes	splice-3	SLC22A25	NM_199352.3		1,46,6452	CC,CT,TT		0.0,1.0904,0.3693			62931547	48,12950	2201	4298	6499	SO:0001630	splice_region_variant	387601	exon10			TTCCCCTTGGAGT	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.1395-2A>G	11.37:g.62931547T>C		230	0	0		230	91	0.395652	NM_199352		Splice_Site	SNP	ENST00000306494.6	37	CCDS31592.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	T	10.76	1.441510	0.25900	0.010904	0.0	ENSG00000196600	ENST00000306494	.	.	.	3.88	3.88	0.44766	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.2959	0.37815	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLC22A25	62688123	0.077000	0.21312	0.693000	0.30195	0.010000	0.07245	1.743000	0.38258	1.768000	0.52137	0.477000	0.44152	.	T|0.996;C|0.004	0.004	strong		0.403	SLC22A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383519.3	NM_199352	Intron	C	62931547	T	C	62931547	5	2	22	1	0	0	0	0	0	0	1	0	14469	1623	56	3	254	3	SLC22A25	11	62931547	Splice_Site	SNP	T	TCGA-G8-6324-01A-11D-2210-10	44841	62931547	72074969	2479	5380											
SLC22A25	387601	hgsc.bcm.edu	37	chr11	62996774	62996775	+	Frame_Shift_Ins	INS	-	-	A																															ggtcatatacccagccatccINSacacagggctctgtatctgg																								rs112260121	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62996774_62996775insA	ENST00000306494.6	-	1	349_350	c.350_351insT	c.(349-351)gtgfs	p.V117fs	SLC22A10_ENST00000525620.1_Intron|SLC22A25_ENST00000403374.2_5'Flank|SLC22A10_ENST00000535888.1_Intron	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						CCCAGCCATCCACACAGGGCTC	0.51													A|A|AA|insertion	42	0.00838658	0.0318	0.0	5008	,	,		19685	0.0		0.0	False		,,,				2504	0.0				p.V117fs		Pindel,Atlas-Indel	.											.	SLC22A25	87	.	0			c.351_352insT						PASS	.			104,4160		2,100,2030						1.9	1		dbSNP_132	130	4,8250		0,4,4123	yes	frameshift	SLC22A25	NM_199352.3		2,104,6153	A1A1,A1R,RR		0.0485,2.439,0.8628				108,12410				SO:0001589	frameshift_variant	387601	exon1			.	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.351dupT	11.37:g.62996775_62996775dupA	ENSP00000307443:p.Val117fs	235	0	.		200	57	0.285	NM_199352		Frame_Shift_Ins	INS	ENST00000306494.6	37	CCDS31592.1																																																																																			-|0.990;A|0.010	0.010	strong		0.51	SLC22A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383519.3	NM_199352		A	62996775	-	A	62996774	7	5	22	1	0	1	1	0	0	0	0	0	14469	581	21	0	1328	0	SLC22A25	11	62996774	Frame_Shift_Ins	INS	-	TCGA-G8-6324-01A-11D-2210-10	65227	62996774	72009742	2480	5381											
GPR137	572	hgsc.bcm.edu	37	chr11	64051853	64051853	+	5'UTR	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tggaacatgctctgggctgtGaggacaagatgttacgtagt	10	11	14	6	1	1	2	0	1	1	1	1	4	1	4	0	3	3	4	0	3	4	2	rs75052600	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:64051853G>A	ENST00000394532.3	-	0	258				GPR137_ENST00000377702.4_5'Flank|GPR137_ENST00000438980.2_5'Flank|GPR137_ENST00000539851.1_5'Flank|BAD_ENST00000309032.3_Intron|BAD_ENST00000544785.1_5'Flank|GPR137_ENST00000313074.3_5'Flank|GPR137_ENST00000411458.1_Silent_p.V5V|BAD_ENST00000394531.3_Intron	NM_004322.3	NP_004313.1	Q92934	BAD_HUMAN	BCL2-associated agonist of cell death						activation of cysteine-type endopeptidase activity (GO:0097202)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|ADP metabolic process (GO:0046031)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|ATP metabolic process (GO:0046034)|cellular process regulating host cell cycle in response to virus (GO:0060154)|cellular response to chromate (GO:0071247)|cellular response to hypoxia (GO:0071456)|cellular response to lipid (GO:0071396)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|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)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose catabolic process (GO:0006007)|glucose homeostasis (GO:0042593)|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)|pore complex assembly (GO:0046931)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic process by virus (GO:0060139)|positive regulation of autophagy (GO:0010508)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of glucokinase activity (GO:0033133)|positive regulation of insulin secretion (GO:0032024)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane potential (GO:0010918)|positive regulation of neuron death (GO:1901216)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of mitochondrial membrane permeability (GO:0046902)|release of cytochrome c from mitochondria (GO:0001836)|response to amino acid (GO:0043200)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to hydrogen peroxide (GO:0042542)|response to oleic acid (GO:0034201)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|suppression by virus of host apoptotic process (GO:0019050)|type B pancreatic cell proliferation (GO:0044342)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|lipid binding (GO:0008289)|phospholipid binding (GO:0005543)|protein kinase binding (GO:0019901)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)	4						TCTGGGCTGTGAGGACAAGAT	0.647													G|||	95	0.0189696	0.0658	0.0101	5008	,	,		18548	0.0		0.001	False		,,,				2504	0.0				p.V5V		Atlas-SNP	.											.	GPR137	52	.	0			c.G15A						PASS	.	G	,,	193,4209	120.8+/-158.4	8,177,2016	59	64	62		15,,	0.8	0	11	dbSNP_131	62	3,8591	3.0+/-9.4	0,3,4294	no	coding-synonymous,utr-5,intron	BAD,GPR137	NM_001170726.1,NM_004322.3,NM_032989.2	,,	8,180,6310	AA,AG,GG		0.0349,4.3844,1.5082	,,	5/476,,	64051853	196,12800	2201	4297	6498	SO:0001623	5_prime_UTR_variant	56834	exon1			GGCTGTGAGGACA	AF021792	CCDS8065.1	11q13.1	2014-03-07	2008-08-19		ENSG00000002330	ENSG00000002330			936	protein-coding gene	gene with protein product		603167				8929532	Standard	NM_004322		Approved	BCL2L8, BBC2	uc001nzd.3	Q92934	OTTHUMG00000134302	ENST00000394532.3:c.-13C>T	11.37:g.64051853G>A		38	0	0		48	26	0.541667	NM_001170726	O14803|Q6FH21	Silent	SNP	ENST00000394532.3	37	CCDS8065.1																																																																																			G|0.986;A|0.014	0.014	strong		0.647	BAD-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259180.2	NM_032989		A	64051853	G	A	64051853	1	1	22	0	1	0	0	0	0	0	0	0	6653	1277	45	2		2	GPR137	11	64051853	5'UTR	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1055079	64051853	70954663	2481	5382											
PYGM	5837	hgsc.bcm.edu	37	chr11	64520569	64520569	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcaatgacctctgccagcccGgggttacacagaaccagcca	11	5	10	15	1	1	2	0	1	1	1	1	2	1	2	5	2	5	2	5	2	3	1	rs11231865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:64520569G>A	ENST00000164139.3	-	12	1892	c.1494C>T	c.(1492-1494)ccC>ccT	p.P498P	PYGM_ENST00000462303.1_5'Flank|PYGM_ENST00000377432.3_Silent_p.P410P	NM_005609.2	NP_005600.1	P11217	PYGM_HUMAN	phosphorylase, glycogen, muscle	498					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						CTGCCAGCCCGGGGTTACACA	0.572													G|||	177	0.0353435	0.1293	0.0058	5008	,	,		18308	0.0		0.002	False		,,,				2504	0.0				p.P498P		Atlas-SNP	.											.	PYGM	77	.	0			c.C1494T						PASS	.	G	,	539,3863	245.3+/-254.3	24,491,1686	202	231	221		1230,1494	-11.6	0.1	11	dbSNP_120	221	1,8593		0,1,4296	no	coding-synonymous,coding-synonymous	PYGM	NM_001164716.1,NM_005609.2	,	24,492,5982	AA,AG,GG		0.0116,12.2444,4.1551	,	410/755,498/843	64520569	540,12456	2201	4297	6498	SO:0001819	synonymous_variant	5837	exon12			CAGCCCGGGGTTA		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.1494C>T	11.37:g.64520569G>A		200	1	0.005		221	121	0.547511	NM_005609	A0AVK1|A6NDY6	Silent	SNP	ENST00000164139.3	37	CCDS8079.1																																																																																			G|0.963;A|0.037	0.037	strong		0.572	PYGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143254.2	NM_005609		A	64520569	G	A	64520569	2	1	22	1	0	0	0	0	0	0	0	1	12877	1103	39	1		1	PYGM	11	64520569	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	468716	64520569	70485947	2482	5383											
TM7SF2	7108	hgsc.bcm.edu	37	chr11	64882441	64882441	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggtttggcttcatgctggcGtttggggacatggcctgggt	3	13	18	7	1	1	0	1	0	0	0	1	1	1	1	1	7	1	4	1	7	0	3	rs33981236	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:64882441G>A	ENST00000279263.7	+	7	942	c.780G>A	c.(778-780)gcG>gcA	p.A260A	AP003068.12_ENST00000527789.1_RNA|TM7SF2_ENST00000345348.5_Silent_p.A260A|TM7SF2_ENST00000540748.1_Silent_p.A144A|TM7SF2_ENST00000531029.1_3'UTR	NM_003273.2	NP_003264.2	O76062	ERG24_HUMAN	transmembrane 7 superfamily member 2	260					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						TCATGCTGGCGTTTGGGGACA	0.617													G|||	152	0.0303514	0.0681	0.0187	5008	,	,		20654	0.0317		0.003	False		,,,				2504	0.0143				p.A260A		Atlas-SNP	.											TM7SF2,NS,carcinoma,+1,1	TM7SF2	30	1	0			c.G780A						PASS	.	G		201,4019		2,197,1911	171	181	178		780	-2.3	1	11	dbSNP_126	178	14,8428		0,14,4207	no	coding-synonymous	TM7SF2	NM_003273.2		2,211,6118	AA,AG,GG		0.1658,4.763,1.698		260/419	64882441	215,12447	2110	4221	6331	SO:0001819	synonymous_variant	7108	exon7			GCTGGCGTTTGGG	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.780G>A	11.37:g.64882441G>A		130	0	0		174	93	0.534483	NM_003273	A8K4H0|O95982|Q8IY06|Q96E64|Q96GZ1	Silent	SNP	ENST00000279263.7	37	CCDS41669.1	62	0.028388278388278388	33	0.06707317073170732	7	0.019337016574585635	19	0.033216783216783216	3	0.00395778364116095	G	6.877	0.531230	0.13127	0.04763	0.001658	ENSG00000149809	ENST00000528802	.	.	.	5.23	-2.3	0.06785	.	.	.	.	.	T	0.03520	0.0101	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21655	-1.0239	4	.	.	.	-10.0796	0.2725	0.00233	0.2909:0.1876:0.2797:0.2419	rs33981236	.	.	.	H	88	.	.	R	+	2	0	TM7SF2	64639017	0.000000	0.05858	0.991000	0.47740	0.658000	0.38924	-1.832000	0.01696	-0.207000	0.10187	-1.332000	0.01269	CGT	G|0.981;A|0.019	0.019	strong		0.617	TM7SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385234.1	NM_003273		A	64882441	G	A	64882441	2	1	22	1	0	0	0	0	0	0	0	1	15989	1132	40	1		1	TM7SF2	11	64882441	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	361872	64882441	70124075	2483	5384											
CDC42EP2	10435	hgsc.bcm.edu	37	chr11	65088498	65088498	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccgccacaccattcatatTggcagtggcggcggcagtga	8	9	12	12	3	1	1	1	1	0	0	2	1	2	1	3	4	0	2	3	4	1	4	rs4149835	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:65088498T>C	ENST00000544348.1	+	2	735	c.129T>C	c.(127-129)atT>atC	p.I43I	CDC42EP2_ENST00000533419.1_Silent_p.I43I|CDC42EP2_ENST00000279249.2_Silent_p.I43I			O14613	BORG1_HUMAN	CDC42 effector protein (Rho GTPase binding) 2	43	CRIB. {ECO:0000255|PROSITE- ProRule:PRU00057}.				actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	GTP-Rho binding (GO:0017049)|Rho GTPase activator activity (GO:0005100)			lung(1)	1						CCATTCATATTGGCAGTGGCG	0.612													C|||	393	0.0784744	0.2791	0.0303	5008	,	,		19020	0.0		0.003	False		,,,				2504	0.0				p.I43I		Atlas-SNP	.											.	CDC42EP2	13	.	0			c.T129C						PASS	.	C		1061,3341	705.0+/-407.2	120,821,1260	59	59	59		129	-9.5	0.1	11	dbSNP_110	59	9,8585	804.3+/-407.3	0,9,4288	no	coding-synonymous	CDC42EP2	NM_006779.3		120,830,5548	CC,CT,TT		0.1047,24.1027,8.2333		43/211	65088498	1070,11926	2201	4297	6498	SO:0001819	synonymous_variant	10435	exon2			TCATATTGGCAGT	AF098290	CCDS8099.1	11q13	2008-07-18				ENSG00000149798			16263	protein-coding gene	gene with protein product	"CRIB-containing BOGR1 protein"	606132				10490598, 11035016	Standard	NM_006779		Approved	CEP2, BORG1	uc001odl.3	O14613		ENST00000544348.1:c.129T>C	11.37:g.65088498T>C		133	0	0		128	57	0.445312	NM_006779	B2RD85|Q9UNS0	Silent	SNP	ENST00000544348.1	37	CCDS8099.1																																																																																			T|0.914;C|0.086	0.086	strong		0.612	CDC42EP2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387258.1	NM_006779		C	65088498	T	C	65088498	2	2	22	1	0	0	0	0	0	0	0	1	3078	1800	63	3		3	CDC42EP2	11	65088498	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	206057	65088498	69918018	2484	5385											
DPF2	5977	hgsc.bcm.edu	37	chr11	65113459	65113459	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tactgtgacttctgcctgggGgactcaaagattaacaagaa	13	10	10	8	0	2	3	1	1	1	2	2	4	2	4	1	2	3	0	1	2	5	3	rs61736579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:65113459G>T	ENST00000528416.1	+	8	967	c.834G>T	c.(832-834)ggG>ggT	p.G278G	DPF2_ENST00000415073.2_Intron|DPF2_ENST00000532264.1_3'UTR|DPF2_ENST00000252268.4_Silent_p.G292G	NM_006268.4	NP_006259.1	Q92785	REQU_HUMAN	D4, zinc and double PHD fingers family 2	278					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						TCTGCCTGGGGGACTCAAAGA	0.537													G|||	57	0.0113818	0.0295	0.0029	5008	,	,		18964	0.0149		0.001	False		,,,				2504	0.0				p.G278G		Atlas-SNP	.											.	DPF2	54	.	0			c.G834T						PASS	.	G		96,4306	78.3+/-116.7	0,96,2105	118	123	121		834	-7.1	0.6	11	dbSNP_129	121	2,8592	1.2+/-3.3	0,2,4295	no	coding-synonymous	DPF2	NM_006268.4		0,98,6400	TT,TG,GG		0.0233,2.1808,0.7541		278/392	65113459	98,12898	2201	4297	6498	SO:0001819	synonymous_variant	5977	exon8			CCTGGGGGACTCA	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.834G>T	11.37:g.65113459G>T		78	0	0		103	51	0.495146	NM_006268	A8K7C9|B4DT58	Silent	SNP	ENST00000528416.1	37	CCDS8100.1	26	0.011904761904761904	19	0.03861788617886179	0	0.0	7	0.012237762237762238	0	0.0	G	12.47	1.947810	0.34377	0.021808	2.33E-4	ENSG00000133884	ENST00000531989	D	0.90504	-2.68	5.92	-7.09	0.01553	.	0.000000	0.38005	N	0.001851	T	0.61515	0.2353	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69187	-0.5211	7	0.24483	T	0.36	-20.6054	6.2509	0.20845	0.5834:0.0898:0.2361:0.0906	rs61736579	.	.	.	V	41	ENSP00000435887:G41V	ENSP00000435887:G41V	G	+	2	0	DPF2	64870035	0.000000	0.05858	0.648000	0.29521	0.864000	0.49448	-1.570000	0.02140	-1.394000	0.02077	-2.076000	0.00381	GGG	G|0.989;T|0.011	0.011	strong		0.537	DPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387293.3	NM_006268		T	65113459	G	T	65113459	2	4	22	1	0	0	0	0	0	0	0	1	4719	1219	43	4		4	DPF2	11	65113459	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	24961	65113459	69893057	2485	5386											
PCNXL3	399909	hgsc.bcm.edu	37	chr11	65403666	65403666	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcacaagggctgtggcgcCggctgcaatagtggcgggaa	8	7	16	10	3	1	0	1	0	0	0	1	1	1	1	1	5	1	3	1	5	4	2	rs61732727	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:65403666C>T	ENST00000355703.3	+	33	6020	c.5481C>T	c.(5479-5481)gcC>gcT	p.A1827A	SIPA1_ENST00000534313.1_5'Flank|MIR4690_ENST00000578459.1_RNA	NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	1827	Gly-rich.					integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						GCTGTGGCGCCGGCTGCAATA	0.632													C|||	160	0.0319489	0.1112	0.0173	5008	,	,		17328	0.0		0.001	False		,,,				2504	0.0				p.A1827A		Atlas-SNP	.											.	PCNXL3	140	.	0			c.C5481T						PASS	.	C		352,3732		7,338,1697	27	32	30		5481	-7.7	0.9	11	dbSNP_129	30	4,8360		0,4,4178	no	coding-synonymous	PCNXL3	NM_032223.2		7,342,5875	TT,TC,CC		0.0478,8.619,2.8599		1827/2035	65403666	356,12092	2042	4182	6224	SO:0001819	synonymous_variant	399909	exon33			TGGCGCCGGCTGC	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.5481C>T	11.37:g.65403666C>T		138	0	0		151	78	0.516556	NM_032223	Q6MZN8	Silent	SNP	ENST00000355703.3	37	CCDS44650.1																																																																																			C|0.974;T|0.026	0.026	strong		0.632	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223		T	65403666	C	T	65403666	2	4	22	1	0	0	0	0	0	0	0	1	11602	639	23	1		1	PCNXL3	11	65403666	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	290207	65403666	69602850	2486	5387											
RELA	5970	hgsc.bcm.edu	37	chr11	65422374	65422374	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggggccggggccaaggcCgaggcctggctgatctgccc	5	4	19	13	2	1	1	0	1	1	0	1	3	1	2	5	8	1	1	5	8	1	0	rs7116571	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:65422374C>T	ENST00000406246.3	-	11	1392	c.1131G>A	c.(1129-1131)tcG>tcA	p.S377S	RELA_ENST00000525693.1_3'UTR|RELA_ENST00000308639.9_Silent_p.S374S	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	377				QISQASALA -> RSARPRLG (in Ref. 2; CAA80524). {ECO:0000305}.	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						gggccaaggccgaggcCTGGC	0.647													C|||	153	0.0305511	0.1074	0.0159	5008	,	,		14470	0.0		0.0	False		,,,				2504	0.0				p.S377S		Atlas-SNP	.											.	RELA	44	.	0			c.G1131A						PASS	.	C	,	346,4040		7,332,1854	10	10	10		1122,1131	-7.6	0.2	11	dbSNP_116	10	6,8576		0,6,4285	no	coding-synonymous,coding-synonymous	RELA	NM_001145138.1,NM_021975.3	,	7,338,6139	TT,TC,CC		0.0699,7.8887,2.7144	,	374/549,377/552	65422374	352,12616	2193	4291	6484	SO:0001819	synonymous_variant	5970	exon11			CAAGGCCGAGGCC	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.1131G>A	11.37:g.65422374C>T		131	0	0		149	69	0.463087	NM_021975	Q6GTV1|Q6SLK1	Silent	SNP	ENST00000406246.3	37	CCDS31609.1																																																																																			C|0.965;T|0.035	0.035	strong		0.647	RELA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390457.2	NM_021975		T	65422374	C	T	65422374	2	4	22	1	0	0	0	0	0	0	0	1	13231	639	23	1		1	RELA	11	65422374	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	18708	65422374	69584142	2487	5388											
DKFZp761E198	91056	hgsc.bcm.edu	37	chr11	65547775	65547775	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcagaggcgtcgggccacagCtgcgcagggtactccatgct	7	6	15	13	3	0	1	0	0	0	1	2	1	1	1	2	3	4	5	2	3	1	1	rs114368095	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:65547775C>T	ENST00000532090.2	-	2	399	c.189G>A	c.(187-189)caG>caA	p.Q63Q		NM_138368.4	NP_612377.4	Q2VPB7	AP5B1_HUMAN	adaptor-related protein complex 5, beta 1 subunit	63					endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-type membrane coat adaptor complex (GO:0030119)|lysosomal membrane (GO:0005765)				lung(1)	1						CGGGCCACAGCTGCGCAGGGT	0.667													C|||	130	0.0259585	0.0893	0.0173	5008	,	,		13769	0.0		0.0	False		,,,				2504	0.0				p.Q63Q		Atlas-SNP	.											.	AP5B1	40	.	0			c.G189A						PASS	.	C		220,3598		0,220,1689	5	7	6		18	3.2	1	11	dbSNP_132	6	4,8094		0,4,4045	no	coding-synonymous	DKFZp761E198	NM_138368.3		0,224,5734	TT,TC,CC		0.0494,5.7622,1.8798		6/822	65547775	224,11692	1909	4049	5958	SO:0001819	synonymous_variant	91056	exon2			CCACAGCTGCGCA	JQ313135	CCDS58146.1	11q13.1	2012-02-29			ENSG00000254470	ENSG00000254470			25104	protein-coding gene	gene with protein product		614367				22022230	Standard	NM_138368		Approved	PP1030, AP-5, DKFZp761E198	uc031qbm.1	Q2VPB7	OTTHUMG00000166593	ENST00000532090.2:c.189G>A	11.37:g.65547775C>T		41	0	0		51	19	0.372549	NM_138368	A1L0S6|H6WUK2|Q0D2Q2|Q8N3J7|Q8WYH6	Silent	SNP	ENST00000532090.2	37	CCDS58146.1																																																																																			C|0.975;T|0.025	0.025	strong		0.667	AP5B1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390636.2	NM_138368		T	65547775	C	T	65547775	2	4	22	1	0	0	0	0	0	0	0	1	4545	796	28	2		2	DKFZp761E198	11	65547775	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	125401	65547775	69458741	2488	5389											
EIF1AD	84285	hgsc.bcm.edu	37	chr11	65767578	65767578	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggcatgctcaccaggaagcGctgcccttgggctgtctcca	6	8	13	14	1	2	0	1	0	1	0	3	1	2	1	3	3	3	4	3	3	1	1	rs35497370	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:65767578G>A	ENST00000312234.2	-	3	476	c.142C>T	c.(142-144)Cgc>Tgc	p.R48C	BANF1_ENST00000445560.2_5'Flank|EIF1AD_ENST00000533544.1_Missense_Mutation_p.R48C|EIF1AD_ENST00000529964.1_Missense_Mutation_p.R48C|EIF1AD_ENST00000525767.1_5'UTR|BANF1_ENST00000527348.1_5'Flank|EIF1AD_ENST00000527249.1_Missense_Mutation_p.R48C|BANF1_ENST00000533166.1_5'Flank|EIF1AD_ENST00000526451.1_Missense_Mutation_p.R48C|BANF1_ENST00000312175.2_5'Flank	NM_001242481.1|NM_001242482.1|NM_001242483.1|NM_032325.3	NP_001229410.1|NP_001229411.1|NP_001229412.1|NP_115701.2	Q8N9N8	EIF1A_HUMAN	eukaryotic translation initiation factor 1A domain containing	48	S1-like. {ECO:0000255|PROSITE- ProRule:PRU00181}.					intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	translation initiation factor activity (GO:0003743)			lung(5)	5						ACCAGGAAGCGCTGCCCTTGG	0.517													G|||	16	0.00319489	0.0113	0.0014	5008	,	,		21003	0.0		0.0	False		,,,				2504	0.0				p.R48C		Atlas-SNP	.											EIF1AD,colon,carcinoma,+1,1	EIF1AD	10	1	0			c.C142T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	29,4373	36.0+/-67.5	0,29,2172	128	115	119		142,142,142,142,142,142,142	5.3	1	11	dbSNP_126	119	0,8592		0,0,4296	yes	missense,missense,missense,missense,missense,missense,missense	EIF1AD	NM_001242481.1,NM_001242482.1,NM_001242483.1,NM_001242484.1,NM_001242485.1,NM_001242486.1,NM_032325.3	180,180,180,180,180,180,180	0,29,6468	AA,AG,GG		0.0,0.6588,0.2232	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	48/166,48/166,48/166,48/166,48/166,48/166,48/166	65767578	29,12965	2201	4296	6497	SO:0001583	missense	84285	exon3			GGAAGCGCTGCCC	AK094129	CCDS8124.1	11q13.1	2009-05-27				ENSG00000175376			28147	protein-coding gene	gene with protein product						12477932	Standard	NM_001242482		Approved	MGC11102, haponin	uc001ogn.2	Q8N9N8		ENST00000312234.2:c.142C>T	11.37:g.65767578G>A	ENSP00000309175:p.Arg48Cys	110	0	0		91	47	0.516484	NM_001242483	B2R4N5|Q9BSC1	Missense_Mutation	SNP	ENST00000312234.2	37	CCDS8124.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	26.8	4.770117	0.90108	0.006588	0.0	ENSG00000175376	ENST00000526451;ENST00000312234;ENST00000529964;ENST00000533544;ENST00000527249;ENST00000530462;ENST00000532707;ENST00000527051	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	5.31	5.31	0.75309	Nucleic acid-binding, OB-fold-like (1);RNA-binding domain, S1, IF1 type (2);Nucleic acid-binding, OB-fold (1);	0.170574	0.50627	D	0.000112	T	0.51381	0.1671	M	0.62723	1.935	0.80722	D	1	D	0.60575	0.988	P	0.61477	0.889	T	0.58532	-0.7620	10	0.59425	D	0.04	.	16.4684	0.84092	0.0:0.0:1.0:0.0	rs35497370	48	Q8N9N8	EIF1A_HUMAN	C	48	ENSP00000436644:R48C;ENSP00000309175:R48C;ENSP00000435942:R48C;ENSP00000434056:R48C;ENSP00000435439:R48C;ENSP00000435891:R48C;ENSP00000433320:R48C;ENSP00000432135:R48C	ENSP00000309175:R48C	R	-	1	0	EIF1AD	65524154	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.963000	0.49184	2.488000	0.83962	0.561000	0.74099	CGC	G|0.997;A|0.003	0.003	strong		0.517	EIF1AD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391072.1	NM_032325		A	65767578	G	A	65767578	3	1	22	1	0	0	0	0	1	0	0	0	4993	1087	38	1	371	1	EIF1AD	11	65767578	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	219803	65767578	69238938	2489	5390											
RIN1	9610	hgsc.bcm.edu	37	chr11	66099888	66099888	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctggctttgaccccagcatcCccatctccctggcacccttg	5	10	7	19	0	1	1	0	1	1	0	3	1	2	1	6	2	1	3	6	2	0	2	rs61547186	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:66099888C>T	ENST00000311320.4	-	10	2337	c.2211G>A	c.(2209-2211)ggG>ggA	p.G737G	RIN1_ENST00000524804.1_5'Flank|RIN1_ENST00000424433.2_Intron|RIN1_ENST00000530056.1_Silent_p.G571G|RP11-867G23.12_ENST00000526655.1_RNA	NM_004292.2	NP_004283.2	Q13671	RIN1_HUMAN	Ras and Rab interactor 1	737					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						CCCCAGCATCCCCATCTCCCT	0.647													C|||	153	0.0305511	0.1104	0.0101	5008	,	,		17960	0.0		0.0	False		,,,				2504	0.0				p.G737G		Atlas-SNP	.											.	RIN1	64	.	0			c.G2211A						PASS	.	C		437,3963	211.5+/-231.7	17,403,1780	156	151	153		2211	-2.9	0	11	dbSNP_129	153	2,8588	1.2+/-3.3	0,2,4293	no	coding-synonymous	RIN1	NM_004292.2		17,405,6073	TT,TC,CC		0.0233,9.9318,3.3795		737/784	66099888	439,12551	2200	4295	6495	SO:0001819	synonymous_variant	9610	exon10			AGCATCCCCATCT	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.2211G>A	11.37:g.66099888C>T		181	0	0		182	182	1	NM_004292	O15010|Q00427|Q96CC8	Silent	SNP	ENST00000311320.4	37	CCDS31614.1																																																																																			C|0.969;T|0.031	0.031	strong		0.647	RIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392980.2	NM_004292		T	66099888	C	T	66099888	2	4	22	1	0	0	0	0	0	0	0	1	13386	610	22	2		2	RIN1	11	66099888	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	332310	66099888	68906628	2490	5391											
CCS	9973	hgsc.bcm.edu	37	chr11	66366682	66366682	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aggctctcctggaaggcacgGggcggcaggcggtactcaag	8	5	17	11	3	2	0	1	0	1	0	3	1	2	1	1	8	1	4	1	8	3	1	rs61731812	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:66366682G>A	ENST00000533244.1	+	3	649	c.208G>A	c.(208-210)Ggg>Agg	p.G70R	CCS_ENST00000310190.4_Missense_Mutation_p.G51R	NM_005125.1	NP_005116.1	O14618	CCS_HUMAN	copper chaperone for superoxide dismutase	70	HMA. {ECO:0000255|PROSITE- ProRule:PRU00280}.				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						GGAAGGCACGGGGCGGCAGGC	0.642													G|||	21	0.00419329	0.0144	0.0029	5008	,	,		18662	0.0		0.0	False		,,,				2504	0.0				p.G70R		Atlas-SNP	.											.	CCS	22	.	0			c.G208A						PASS	.	G	ARG/GLY	48,4352	50.9+/-86.3	0,48,2152	68	59	62		208	4.9	1	11	dbSNP_129	62	0,8590		0,0,4295	yes	missense	CCS	NM_005125.1	125	0,48,6447	AA,AG,GG		0.0,1.0909,0.3695	probably-damaging	70/275	66366682	48,12942	2200	4295	6495	SO:0001583	missense	9973	exon3			GGCACGGGGCGGC	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.208G>A	11.37:g.66366682G>A	ENSP00000436318:p.Gly70Arg	80	0	0		91	57	0.626374	NM_005125	Q2M366|Q8NEV0	Missense_Mutation	SNP	ENST00000533244.1	37	CCDS8146.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	G	27.6	4.842813	0.91197	0.010909	0.0	ENSG00000173992	ENST00000533244;ENST00000310190	D;D	0.94092	-3.35;-2.58	4.87	4.87	0.63330	Heavy metal-associated domain, HMA (3);	0.000000	0.85682	D	0.000000	D	0.97417	0.9155	H	0.99261	4.49	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96137	0.9097	10	0.87932	D	0	.	13.3773	0.60747	0.0:0.0:1.0:0.0	rs61731812	70	O14618	CCS_HUMAN	R	70;51	ENSP00000436318:G70R;ENSP00000307870:G51R	ENSP00000307870:G51R	G	+	1	0	CCS	66123258	1.000000	0.71417	0.955000	0.39395	0.970000	0.65996	7.533000	0.81994	2.546000	0.85860	0.561000	0.74099	GGG	G|0.996;A|0.004	0.004	strong		0.642	CCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393826.1	NM_005125		A	66366682	G	A	66366682	3	1	22	1	0	0	0	0	1	0	0	0	2954	1232	43	2	218	2	CCS	11	66366682	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	266794	66366682	68639834	2491	5392											
ADRBK1	156	hgsc.bcm.edu	37	chr11	67052322	67052322	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgtctctcgcctcagactaCgccctgggcaaggactgcat	7	9	10	15	2	2	1	1	0	1	1	4	2	2	2	2	2	2	2	2	2	2	1	rs115867067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:67052322C>T	ENST00000308595.5	+	19	1949	c.1659C>T	c.(1657-1659)taC>taT	p.Y553Y	ADRBK1_ENST00000527176.1_3'UTR|ADRBK1_ENST00000526285.1_Intron	NM_001619.3	NP_001610.2	P25098	ARBK1_HUMAN	adrenergic, beta, receptor kinase 1	553					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)	CCTCAGACTACGCCCTGGGCA	0.587													C|||	66	0.0131789	0.0484	0.0029	5008	,	,		15108	0.0		0.0	False		,,,				2504	0.0				p.Y553Y		Atlas-SNP	.											.	ADRBK1	51	.	0			c.C1659T						PASS	.	C		168,4230	108.2+/-146.6	4,160,2035	77	56	63		1659	1	1	11	dbSNP_132	63	1,8589		0,1,4294	no	coding-synonymous	ADRBK1	NM_001619.3		4,161,6329	TT,TC,CC		0.0116,3.8199,1.3012		553/690	67052322	169,12819	2199	4295	6494	SO:0001819	synonymous_variant	156	exon19			AGACTACGCCCTG	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.1659C>T	11.37:g.67052322C>T		52	0	0		76	25	0.328947	NM_001619	B0ZBE1|Q13837|Q6GTT3	Silent	SNP	ENST00000308595.5	37	CCDS8156.1																																																																																			C|0.987;T|0.013	0.013	strong		0.587	ADRBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393153.1	NM_001619		T	67052322	C	T	67052322	2	4	22	1	0	0	0	0	0	0	0	1	343	547	19	1		1	ADRBK1	11	67052322	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	685640	67052322	67954194	2492	5393											
AIP	9049	hgsc.bcm.edu	37	chr11	67258362	67258362	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gtgctggagctggacccagcCctggcgcctgtggtgagccg	4	7	17	13	2	0	1	0	1	0	0	0	3	0	3	4	4	4	2	4	4	0	0	rs35665586|rs267606585	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:67258362C>A	ENST00000279146.3	+	6	1009	c.891C>A	c.(889-891)gcC>gcA	p.A297A	PITPNM1_ENST00000526450.1_5'Flank	NM_003977.2	NP_003968.2	O00170	AIP_HUMAN	aryl hydrocarbon receptor interacting protein	297					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						TGGACCCAGCCCTGGCGCCTG	0.652									Familial Isolated Pituitary Adenoma				C|||	31	0.0061901	0.0219	0.0029	5008	,	,		16963	0.0		0.0	False		,,,				2504	0.0				p.A297A		Atlas-SNP	.											.	AIP	26	.	0			c.C891A						PASS	.	C		70,4322	61.1+/-98.1	1,68,2127	25	27	26		891	4	1	11	dbSNP_126	26	1,8585		0,1,4292	no	coding-synonymous	AIP	NM_003977.2		1,69,6419	AA,AC,CC		0.0116,1.5938,0.5471		297/331	67258362	71,12907	2196	4293	6489	SO:0001819	synonymous_variant	9049	exon6	Familial Cancer Database	FIPA, incl. Familial Isolated Somatotropinomas, FIS, IFS, Familial Acromegaly	CCCAGCCCTGGCG	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.891C>A	11.37:g.67258362C>A		149	0	0		148	70	0.472973	NM_003977	A0SZW3|A0SZW4|A0SZW5|A0SZW6|Q2M3Q2|Q99606	Silent	SNP	ENST00000279146.3	37	CCDS8168.1																																																																																			C|0.995;A|0.005	0.005	strong		0.652	AIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395516.1			A	67258362	C	A	67258362	2	1	22	1	0	0	0	0	0	0	0	1	435	610	22	4		4	AIP	11	67258362	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	206040	67258362	67748154	2493	5394											
PITPNM1	9600	hgsc.bcm.edu	37	chr11	67267636	67267636	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccaaagctggcatcgggggaGgcatctgggcctgggggggc	6	5	20	10	1	1	0	0	0	1	0	2	1	1	1	2	8	1	3	2	8	1	0	rs59249357	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:67267636G>A	ENST00000534749.1	-	5	1085	c.897C>T	c.(895-897)gcC>gcT	p.A299A	PITPNM1_ENST00000436757.2_Silent_p.A299A|PITPNM1_ENST00000356404.3_Silent_p.A299A			O00562	PITM1_HUMAN	phosphatidylinositol transfer protein, membrane-associated 1	299					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						CATCGGGGGAGGCATCTGGGC	0.687													G|||	68	0.0135783	0.0492	0.0043	5008	,	,		14719	0.0		0.0	False		,,,				2504	0.0				p.A299A	GBM(28;144 709 4607 5525)	Atlas-SNP	.											.	PITPNM1	84	.	0			c.C897T						PASS	.						26	32	30					11																	67267636		2172	4257	6429	SO:0001819	synonymous_variant	9600	exon6			GGGGGAGGCATCT	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.897C>T	11.37:g.67267636G>A		15	0	0		29	13	0.448276	NM_001130848	A6NME4|Q6T7X3|Q8TBN3|Q9BZ73	Silent	SNP	ENST00000534749.1	37	CCDS31620.1																																																																																			A|0.006;C|0.005;G|0.988	0.006	strong		0.687	PITPNM1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395520.1	NM_004910		A	67267636	G	A	67267636	2	1	22	1	0	0	0	0	0	0	0	1	11959	987	35	2		2	PITPNM1	11	67267636	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	9274	67267636	67738880	2494	5395											
SAPS3	55291	hgsc.bcm.edu	37	chr11	68341661	68341661	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacagcactgacaagggcccCaacagtgcattagtgcagca	13	5	10	13	0	0	1	0	1	0	0	0	1	0	1	2	1	5	4	2	1	3	1	rs114505709	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:68341661C>A	ENST00000393800.2	+	13	1682	c.1428C>A	c.(1426-1428)ccC>ccA	p.P476P	PPP6R3_ENST00000265636.5_Silent_p.P425P|PPP6R3_ENST00000393801.3_Silent_p.P476P|PPP6R3_ENST00000265637.4_Silent_p.P476P|PPP6R3_ENST00000527403.2_Silent_p.P476P|PPP6R3_ENST00000524904.1_Silent_p.P476P|PPP6R3_ENST00000393799.2_Silent_p.P476P|PPP6R3_ENST00000534534.1_Silent_p.P244P|PPP6R3_ENST00000524845.1_Silent_p.P476P|PPP6R3_ENST00000529710.1_Silent_p.P425P	NM_001164161.1|NM_001164162.1|NM_001164163.1	NP_001157633.1|NP_001157634.1|NP_001157635.1	Q5H9R7	PP6R3_HUMAN	protein phosphatase 6, regulatory subunit 3	476					regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			breast(2)|endometrium(6)|kidney(3)|large_intestine(10)|liver(2)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						ACAAGGGCCCCAACAGTGCAT	0.448													C|||	37	0.00738818	0.025	0.0029	5008	,	,		20069	0.0		0.002	False		,,,				2504	0.0				p.P476P		Atlas-SNP	.											.	PPP6R3	159	.	0			c.C1428A						PASS	.	C	,,,,,	105,4295	80.9+/-119.3	3,99,2098	143	122	129		1428,1428,1428,1428,1275,1275	0.1	1	11	dbSNP_132	129	0,8588		0,0,4294	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PPP6R3	NM_001164160.1,NM_001164161.1,NM_001164162.1,NM_001164163.1,NM_001164164.1,NM_018312.4	,,,,,	3,99,6392	AA,AC,CC		0.0,2.3864,0.8084	,,,,,	476/880,476/874,476/868,476/845,425/792,425/794	68341661	105,12883	2200	4294	6494	SO:0001819	synonymous_variant	55291	exon13			GGGCCCCAACAGT	AF264779	CCDS8182.1, CCDS53671.1, CCDS53672.1, CCDS53673.1, CCDS53674.1, CCDS53675.1	11q13	2012-04-17	2010-06-28	2010-06-28	ENSG00000110075	ENSG00000110075		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"	1173	protein-coding gene	gene with protein product	"sporulation-induced transcript 4-associated protein"	610879	"chromosome 11 open reading frame 23", "SAPS domain family, member 3"	C11orf23, SAPS3		11401438, 16769727	Standard	NM_018312		Approved	SAPLa, DKFZp781E2374, DKFZp781O2362, DKFZp781E17107, SAP190, SAPL, PP6R3, FLJ11058, FLJ43065, KIAA1558, MGC125711, MGC125712	uc001onv.3	Q5H9R7		ENST00000393800.2:c.1428C>A	11.37:g.68341661C>A		54	0	0		68	23	0.338235	NM_001164162	Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3	Silent	SNP	ENST00000393800.2	37	CCDS53672.1																																																																																			C|0.991;A|0.009	0.009	strong		0.448	PPP6R3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395275.1	NM_018312		A	68341661	C	A	68341661	2	1	22	1	0	0	0	0	0	0	0	1	13853	581	21	4		4	SAPS3	11	68341661	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1074025	68341661	66664855	2495	5396											
CPT1A	1374	hgsc.bcm.edu	37	chr11	68529027	68529027	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaaggaaaggggactccacAgcgagatatttagacaccac	15	7	10	9	1	0	2	0	0	0	2	1	5	1	4	2	3	1	0	2	3	4	4	rs2228503	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:68529027A>G	ENST00000265641.5	-	16	2158	c.2004T>C	c.(2002-2004)gcT>gcC	p.A668A	CPT1A_ENST00000376618.2_Silent_p.A668A|CPT1A_ENST00000539743.1_Silent_p.A668A|CPT1A_ENST00000540367.1_Silent_p.A668A|CPT1A_ENST00000537756.2_5'Flank	NM_001876.3	NP_001867.2	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A (liver)	668					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)	p.A668A(1)		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)	GGGACTCCACAGCGAGATATT	0.473													G|||	63	0.0125799	0.0461	0.0014	5008	,	,		19324	0.0		0.001	False		,,,				2504	0.0				p.A668A		Atlas-SNP	.											CPT1A,colon,carcinoma,0,1	CPT1A	89	1	1	Substitution - coding silent(1)	large_intestine(1)	c.T2004C						PASS	.	G	,	117,4283	815.3+/-416.2	2,113,2085	176	173	174		2004,2004	-11.3	0	11	dbSNP_132	174	0,8588		0,0,4294	no	coding-synonymous,coding-synonymous	CPT1A	NM_001031847.2,NM_001876.3	,	2,113,6379	GG,GA,AA		0.0,2.6591,0.9008	,	668/757,668/774	68529027	117,12871	2200	4294	6494	SO:0001819	synonymous_variant	1374	exon16			CTCCACAGCGAGA	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.2004T>C	11.37:g.68529027A>G		119	0	0		111	51	0.459459	NM_001876	Q8TCU0|Q9BWK0	Silent	SNP	ENST00000265641.5	37	CCDS8185.1																																																																																			A|0.991;G|0.009	0.009	strong		0.473	CPT1A-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397457.2	NM_001876		G	68529027	A	G	68529027	2	3	22	1	0	0	0	0	0	0	0	1	3833	175	7	3		3	CPT1A	11	68529027	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	187366	68529027	66477489	2496	5397											
ORAOV1	220064	hgsc.bcm.edu	37	chr11	69490001	69490001	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atcgaatatgtcctgactgcCagccatagcggcaagcagcc	11	7	10	13	2	0	1	0	1	0	0	2	2	1	1	4	1	5	2	4	1	4	2	rs56107468	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:69490001C>T	ENST00000535657.1	-	1	88	c.7G>A	c.(7-9)Ggc>Agc	p.G3S	ORAOV1_ENST00000542341.1_Missense_Mutation_p.G3S|ORAOV1_ENST00000539414.1_Missense_Mutation_p.G3S|ORAOV1_ENST00000279147.4_Missense_Mutation_p.G3S|ORAOV1_ENST00000536870.1_Missense_Mutation_p.G3S			Q8WV07	ORAV1_HUMAN	oral cancer overexpressed 1	3			G -> S (in dbSNP:rs56107468).							NS(1)|endometrium(1)|large_intestine(2)|lung(1)	5	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;5.64e-57)|all cancers(3;5.98e-51)|BRCA - Breast invasive adenocarcinoma(2;5.49e-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)			TCCTGACTGCCAGCCATAGCG	0.677													C|||	111	0.0221645	0.0802	0.0072	5008	,	,		15446	0.0		0.0	False		,,,				2504	0.0				p.G3S		Atlas-SNP	.											.	ORAOV1	11	.	0			c.G7A						PASS	.	C	SER/GLY	279,4109		8,263,1923	28	26	26		7	1.8	0.1	11	dbSNP_129	26	3,8577		0,3,4287	yes	missense	ORAOV1	NM_153451.2	56	8,266,6210	TT,TC,CC		0.035,6.3582,2.1746	benign	3/138	69490001	282,12686	2194	4290	6484	SO:0001583	missense	220064	exon1			GACTGCCAGCCAT		CCDS8192.1	11q13.2	2010-11-23			ENSG00000149716	ENSG00000149716			17589	protein-coding gene	gene with protein product	"oral cancer overexpressed protein 1-A"	607224				12172009	Standard	NM_153451		Approved	TAOS1	uc001opc.3	Q8WV07		ENST00000535657.1:c.7G>A	11.37:g.69490001C>T	ENSP00000446129:p.Gly3Ser	227	0	0		218	101	0.463303	NM_153451	B2R4R2|Q8NFK0	Missense_Mutation	SNP	ENST00000535657.1	37	CCDS8192.1	46	0.021062271062271064	42	0.08536585365853659	4	0.011049723756906077	0	0.0	0	0.0	C	12.95	2.091045	0.36855	0.063582	3.5E-4	ENSG00000149716	ENST00000538554;ENST00000376587;ENST00000279147;ENST00000536870;ENST00000535657;ENST00000539414;ENST00000441922;ENST00000542341;ENST00000355486;ENST00000543023	T;T;T;T;T;T;T	0.44083	0.95;1.04;0.93;1.04;1.03;0.97;1.03	3.78	1.83	0.25207	.	0.922530	0.09022	N	0.859968	T	0.01029	0.0034	L	0.40543	1.245	0.09310	N	1	B;B;B;B	0.34015	0.435;0.034;0.004;0.041	B;B;B;B	0.35510	0.204;0.017;0.01;0.017	T	0.09662	-1.0664	10	0.09338	T	0.73	-25.5519	3.1767	0.06571	0.209:0.5597:0.0:0.2313	rs56107468	3;3;3;3	B4DFA5;F5H6T8;F5GWS9;Q8WV07	.;.;.;ORAV1_HUMAN	S	3	ENSP00000446428:G3S;ENSP00000279147:G3S;ENSP00000441984:G3S;ENSP00000446129:G3S;ENSP00000444112:G3S;ENSP00000409643:G3S;ENSP00000437367:G3S	ENSP00000279147:G3S	G	-	1	0	ORAOV1	69199182	0.000000	0.05858	0.060000	0.19600	0.298000	0.27526	0.050000	0.14120	0.878000	0.35920	0.561000	0.74099	GGC	C|0.978;T|0.022	0.022	strong		0.677	ORAOV1-009	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000396821.1	NM_153451		T	69490001	C	T	69490001	3	4	22	1	0	0	0	0	1	0	0	0	11269	594	21	2	426	2	ORAOV1	11	69490001	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	960974	69490001	65516515	2497	5398											
FGF4	2249	hgsc.bcm.edu	37	chr11	69588798	69588798	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcggtactcaccgagccAtagagcttgcccttgctgct	6	10	10	15	2	1	1	1	0	0	1	1	2	1	1	4	1	7	4	4	1	2	4	rs61738964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:69588798A>G	ENST00000168712.1	-	2	756	c.438T>C	c.(436-438)taT>taC	p.Y146Y	AP001888.1_ENST00000602104.1_5'Flank|FGF4_ENST00000538040.1_Intron	NM_002007.2	NP_001998.1	P08620	FGF4_HUMAN	fibroblast growth factor 4	146					apoptotic process involved in morphogenesis (GO:0060561)|cartilage condensation (GO:0001502)|cell-cell signaling (GO:0007267)|chondroblast differentiation (GO:0060591)|cranial suture morphogenesis (GO:0060363)|embryonic hindlimb morphogenesis (GO:0035116)|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)|mesenchymal cell proliferation (GO:0010463)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|stem cell maintenance (GO:0019827)	cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)			lung(3)	3	Melanoma(5;1.89e-05)		LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)		Pentosan Polysulfate(DB00686)	TCACCGAGCCATAGAGCTTGC	0.657													A|||	31	0.0061901	0.0212	0.0043	5008	,	,		17189	0.0		0.0	False		,,,				2504	0.0				p.Y146Y		Atlas-SNP	.											.	FGF4	13	.	0			c.T438C						PASS	.	A		100,4300	77.8+/-116.1	3,94,2103	38	34	35		438	1.5	1	11	dbSNP_129	35	0,8588		0,0,4294	no	coding-synonymous	FGF4	NM_002007.2		3,94,6397	GG,GA,AA		0.0,2.2727,0.7699		146/207	69588798	100,12888	2200	4294	6494	SO:0001819	synonymous_variant	2249	exon2			CGAGCCATAGAGC	M17446	CCDS8194.1	11q13.3	2014-01-30	2008-08-01		ENSG00000075388	ENSG00000075388		"Endogenous ligands"	3682	protein-coding gene	gene with protein product	"human stomach cancer, transforming factor from FGF-related oncogene", "kaposi sarcoma oncogene", "transforming protein KS3"	164980	"heparin secretory transforming protein 1"	HSTF1		1611909	Standard	NM_002007		Approved	K-FGF, HBGF-4, HST, HST-1, KFGF	uc001opg.1	P08620	OTTHUMG00000167887	ENST00000168712.1:c.438T>C	11.37:g.69588798A>G		131	0	0		174	83	0.477012	NM_002007	B7U994	Silent	SNP	ENST00000168712.1	37	CCDS8194.1																																																																																			A|0.994;G|0.006	0.006	strong		0.657	FGF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396834.2	NM_002007		G	69588798	A	G	69588798	2	3	22	1	0	0	0	0	0	0	0	1	5862	224	8	3		3	FGF4	11	69588798	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	98797	69588798	65417718	2498	5399											
PPFIA1	8500	hgsc.bcm.edu	37	chr11	70200516	70200516	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaccggctgcacaaaggggCgctgcacaccgtcagccacg	10	3	13	15	4	1	1	1	0	0	1	1	1	1	1	3	3	3	4	3	3	1	0	rs139448605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:70200516C>T	ENST00000253925.7	+	17	2488	c.2273C>T	c.(2272-2274)gCg>gTg	p.A758V	PPFIA1_ENST00000389547.3_Missense_Mutation_p.A758V|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	758					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)			CACAAAGGGGCGCTGCACACC	0.567													C|||	50	0.00998403	0.0378	0.0	5008	,	,		15864	0.0		0.0	False		,,,				2504	0.0				p.A758V		Atlas-SNP	.											.	PPFIA1	114	.	0			c.C2273T						PASS	.	C	VAL/ALA,VAL/ALA	116,4284	88.2+/-126.9	0,116,2084	51	44	46		2273,2273	4.4	0	11	dbSNP_134	46	2,8586	1.2+/-3.3	0,2,4292	yes	missense,missense	PPFIA1	NM_003626.2,NM_177423.1	64,64	0,118,6376	TT,TC,CC		0.0233,2.6364,0.9085	benign,benign	758/1203,758/1186	70200516	118,12870	2200	4294	6494	SO:0001583	missense	8500	exon17			AAGGGGCGCTGCA	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.2273C>T	11.37:g.70200516C>T	ENSP00000253925:p.Ala758Val	51	0	0		63	26	0.412698	NM_177423	A6NLE3|Q13135|Q14567|Q8N4I2	Missense_Mutation	SNP	ENST00000253925.7	37	CCDS31627.1	14|14	0.00641025641025641|0.00641025641025641	14|14	0.028455284552845527|0.028455284552845527	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	14.81|14.81	2.646317|2.646317	0.47258|0.47258	0.026364|0.026364	2.33E-4|2.33E-4	ENSG00000131626|ENSG00000131626	ENST00000253925;ENST00000389547;ENST00000544950|ENST00000528750	T;T|.	0.28255|.	1.62;1.62|.	5.36|5.36	4.45|4.45	0.53987|0.53987	.|.	0.314716|.	0.29508|.	N|.	0.011941|.	T|T	0.36580|0.36580	0.0972|0.0972	M|M	0.62723|0.62723	1.935|1.935	0.31697|0.31697	N|N	0.64121|0.64121	B;B|.	0.23377|.	0.012;0.084|.	B;B|.	0.15870|.	0.004;0.014|.	T|T	0.59920|0.59920	-0.7363|-0.7363	10|5	0.29301|.	T|.	0.29|.	.|.	14.198|14.198	0.65684|0.65684	0.0:0.9277:0.0:0.0723|0.0:0.9277:0.0:0.0723	.|.	758;758|.	Q13136;Q13136-2|.	LIPA1_HUMAN;.|.	V|C	758;758;255|201	ENSP00000253925:A758V;ENSP00000374198:A758V|.	ENSP00000253925:A758V|.	A|R	+|+	2|1	0|0	PPFIA1|PPFIA1	69878164|69878164	0.926000|0.926000	0.31397|0.31397	0.009000|0.009000	0.14445|0.14445	0.490000|0.490000	0.33462|0.33462	2.135000|2.135000	0.42112|0.42112	1.272000|1.272000	0.44329|0.44329	0.561000|0.561000	0.74099|0.74099	GCG|CGC	C|0.992;T|0.008	0.008	strong		0.567	PPFIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393905.1	NM_003626		T	70200516	C	T	70200516	3	4	22	1	0	0	0	0	1	0	0	0	12318	768	27	1	2335	1	PPFIA1	11	70200516	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	611718	70200516	64806000	2499	5400											
CTTN	2017	hgsc.bcm.edu	37	chr11	70279759	70279759	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggctttcttttagaggacaGcacctacgatgagtacgaga	11	11	11	8	2	1	3	0	1	1	2	1	6	1	4	1	2	3	3	1	2	3	5	rs56162978	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:70279759G>A	ENST00000301843.8	+	17	1657	c.1451G>A	c.(1450-1452)aGc>aAc	p.S484N	CTTN_ENST00000538675.1_Missense_Mutation_p.S168N|CTTN_ENST00000346329.3_Missense_Mutation_p.S447N|CTTN_ENST00000376561.3_Missense_Mutation_p.S447N	NM_005231.3	NP_005222.2	Q14247	SRC8_HUMAN	cortactin	484					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)		TTAGAGGACAGCACCTACGAT	0.517													G|||	261	0.0521166	0.1884	0.0173	5008	,	,		16431	0.0		0.0	False		,,,				2504	0.0				p.S484N		Atlas-SNP	.											.	CTTN	162	.	0			c.G1451A						PASS	.		ASN/SER,ASN/SER,ASN/SER	788,3612	319.1+/-295.9	55,678,1467	159	153	155		1340,1451,1340	-0.8	0	11	dbSNP_129	155	5,8583	3.7+/-12.6	0,5,4289	yes	missense,missense,missense	CTTN	NM_001184740.1,NM_005231.3,NM_138565.2	46,46,46	55,683,5756	AA,AG,GG		0.0582,17.9091,6.1056	benign,benign,benign	447/635,484/551,447/514	70279759	793,12195	2200	4294	6494	SO:0001583	missense	2017	exon17			AGGACAGCACCTA	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.1451G>A	11.37:g.70279759G>A	ENSP00000301843:p.Ser484Asn	121	0	0		138	64	0.463768	NM_005231	Q8N707|Q96H99	Missense_Mutation	SNP	ENST00000301843.8	37	CCDS41680.1	85	0.03891941391941392	81	0.16463414634146342	4	0.011049723756906077	0	0.0	0	0.0	G	1.497	-0.553053	0.03996	0.179091	5.82E-4	ENSG00000085733	ENST00000346329;ENST00000301843;ENST00000376561;ENST00000538675;ENST00000529736	T;T;T;T;T	0.32753	1.44;1.45;1.48;1.88;1.86	4.86	-0.816	0.10839	Src homology-3 domain (1);	0.722113	0.13537	N	0.380525	T	0.00039	0.0001	N	0.14661	0.345	0.09310	N	1	B;B;B;B	0.09022	0.002;0.0;0.0;0.0	B;B;B;B	0.10450	0.005;0.0;0.0;0.001	T	0.21143	-1.0254	10	0.05525	T	0.97	-27.692	5.4208	0.16400	0.6072:0.1347:0.258:0.0	rs56162978;rs58344286	168;447;484;447	B4E358;Q96H99;Q14247;Q8N707	.;.;SRC8_HUMAN;.	N	447;484;447;168;141	ENSP00000317189:S447N;ENSP00000301843:S484N;ENSP00000365745:S447N;ENSP00000439762:S168N;ENSP00000431421:S141N	ENSP00000301843:S484N	S	+	2	0	CTTN	69957407	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.316000	0.19469	-0.462000	0.06984	-0.891000	0.02926	AGC	G|0.941;A|0.059	0.059	strong		0.517	CTTN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259233.2	NM_138565		A	70279759	G	A	70279759	3	1	22	1	0	0	0	0	1	0	0	0	4046	971	34	2	1509	2	CTTN	11	70279759	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	79243	70279759	64726757	2500	5401											
KRTAP5-8	57830	hgsc.bcm.edu	37	chr11	71249530	71249530	+	Silent	SNP	T	T	C																															agctgctgcaagccctgctgTtcccagtccagctgctgtaa																								rs532438179|rs369043826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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,NS,carcinoma,+1,1	KRTAP5-8	28	1	0			c.T429C						scavenged	.						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	11.37:g.71249530T>C		157	1	0.00636943		229	16	0.069869	NM_021046	Q6L8G7|Q6UTX6	Silent	SNP	ENST00000398534.3	37	CCDS41683.1																																																																																			.	.	none		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	22	1	0	0	0	0	0	0	0	1	8576	1731	60	3		3	KRTAP5-8	11	71249530	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	969771	71249530	63756986	2501	5402	63	2									
KRTAP5-8	57830	hgsc.bcm.edu	37	chr11	71249532	71249532	+	Missense_Mutation	SNP	C	C	G																															ctgctgcaagccctgctgttCccagtccagctgctgtaagc																								rs532438179|rs11234084|rs369043826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71249532C>G	ENST00000398534.3	+	1	462	c.431C>G	c.(430-432)tCc>tGc	p.S144C		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	144	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						CCCTGCTGTTCCCAGTCCAGC	0.612																																					p.S144C		Atlas-SNP	.											.	KRTAP5-8	28	.	0			c.C431G						PASS	.						148	160	156					11																	71249532		2200	4294	6494	SO:0001583	missense	57830	exon1			GCTGTTCCCAGTC	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.431C>G	11.37:g.71249532C>G	ENSP00000420723:p.Ser144Cys	158	0	0		222	9	0.0405405	NM_021046	Q6L8G7|Q6UTX6	Missense_Mutation	SNP	ENST00000398534.3	37	CCDS41683.1	.	.	.	.	.	.	.	.	.	.	-	3.125	-0.179750	0.06380	.	.	ENSG00000241233	ENST00000398534	T	0.01197	5.19	1.57	-2.99	0.05497	.	.	.	.	.	T	0.00552	0.0018	N	0.02213	-0.635	0.21861	N	0.999505	B	0.02656	0.0	B	0.01281	0.0	T	0.44314	-0.9336	9	0.02654	T	1	.	12.0511	0.53507	0.0:0.7645:0.2355:0.0	rs11234084	144	O75690	KRA58_HUMAN	C	144	ENSP00000420723:S144C	ENSP00000420723:S144C	S	+	2	0	KRTAP5-8	70927180	0.000000	0.05858	0.375000	0.26029	0.014000	0.08584	-0.627000	0.05521	-0.723000	0.04915	-0.951000	0.02657	TCC	.	.	weak		0.612	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046		G	71249532	C	G	71249532	3	3	22	1	0	0	0	0	1	0	0	0	8576	855	30	4	433	4	KRTAP5-8	11	71249532	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2	71249532	63756984	2502	5403	63	2									
KRTAP5-9	3846	hgsc.bcm.edu	37	chr11	71259709	71259709	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caatccaccagaaccatgggCtgctgtggctgctccggagg	8	7	13	13	1	0	1	0	0	0	1	2	2	2	2	4	4	3	4	4	4	2	0	rs180808688	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71259709C>T	ENST00000528743.2	+	1	244	c.6C>T	c.(4-6)ggC>ggT	p.G2G		NM_005553.3	NP_005544.4	P26371	KRA59_HUMAN	keratin associated protein 5-9	2					epidermis development (GO:0008544)	keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(6)|prostate(3)	11						GAACCATGGGCTGCTGTGGCT	0.642													c|||	10	0.00199681	0.0068	0.0014	5008	,	,		17898	0.0		0.0	False		,,,				2504	0.0				p.G2G		Atlas-SNP	.											.	KRTAP5-9	19	.	0			c.C6T						PASS	.	C		32,4366		0,32,2167	84	95	91		6	1.6	1	11		91	0,8588		0,0,4294	no	coding-synonymous	KRTAP5-9	NM_005553.3		0,32,6461	TT,TC,CC		0.0,0.7276,0.2464		2/170	71259709	32,12954	2199	4294	6493	SO:0001819	synonymous_variant	3846	exon1			CATGGGCTGCTGT	AB126078	CCDS53677.1	11q13.4	2008-02-05				ENSG00000254997		"Keratin associated proteins"	23604	protein-coding gene	gene with protein product		148021		KRN1		15144888	Standard	NM_005553		Approved	KRTAP5.9, KRTAP5-1	uc001oqs.1	P26371		ENST00000528743.2:c.6C>T	11.37:g.71259709C>T		453	1	0.00220751		521	234	0.449136	NM_005553	Q14564|Q3MIP8	Silent	SNP	ENST00000528743.2	37	CCDS53677.1																																																																																			C|0.999;T|0.001	0.001	strong		0.642	KRTAP5-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393901.2			T	71259709	C	T	71259709	2	4	22	1	0	0	0	0	0	0	0	1	8577	784	28	2		2	KRTAP5-9	11	71259709	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	10177	71259709	63746807	2503	5404											
KRTAP5-9	3846	hgsc.bcm.edu	37	chr11	71259818	71259818	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccccagctgctgtgcacccGtctactgctgcaagcccgtg	5	8	11	17	2	1	0	0	0	1	0	1	0	1	0	4	0	7	5	4	0	2	1	rs146869772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71259818G>A	ENST00000528743.2	+	1	353	c.115G>A	c.(115-117)Gtc>Atc	p.V39I		NM_005553.3	NP_005544.4	P26371	KRA59_HUMAN	keratin associated protein 5-9	39	8 X 4 AA repeats of C-C-X-P.				epidermis development (GO:0008544)	keratin filament (GO:0045095)		p.V39I(1)		kidney(1)|large_intestine(1)|lung(6)|prostate(3)	11						CTGTGCACCCGTCTACTGCTG	0.667													g|||	10	0.00199681	0.0068	0.0014	5008	,	,		17781	0.0		0.0	False		,,,				2504	0.0				p.V39I		Atlas-SNP	.											KRTAP5-9,caecum,carcinoma,0,1	KRTAP5-9	19	1	1	Substitution - Missense(1)	large_intestine(1)	c.G115A						PASS	.	G	ILE/VAL	37,4363		0,37,2163	80	91	87		115	1.6	0	11	dbSNP_134	87	0,8588		0,0,4294	no	missense	KRTAP5-9	NM_005553.3	29	0,37,6457	AA,AG,GG		0.0,0.8409,0.2849	possibly-damaging	39/170	71259818	37,12951	2200	4294	6494	SO:0001583	missense	3846	exon1			GCACCCGTCTACT	AB126078	CCDS53677.1	11q13.4	2008-02-05				ENSG00000254997		"Keratin associated proteins"	23604	protein-coding gene	gene with protein product		148021		KRN1		15144888	Standard	NM_005553		Approved	KRTAP5.9, KRTAP5-1	uc001oqs.1	P26371		ENST00000528743.2:c.115G>A	11.37:g.71259818G>A	ENSP00000431443:p.Val39Ile	293	0	0		324	145	0.447531	NM_005553	Q14564|Q3MIP8	Missense_Mutation	SNP	ENST00000528743.2	37	CCDS53677.1	3	0.0013736263736263737	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	N	4.044	0.005754	0.07866	0.008409	0.0	ENSG00000254997	ENST00000528743	T	0.03745	3.82	1.57	1.57	0.23409	.	.	.	.	.	T	0.04003	0.0112	L	0.42487	1.325	0.09310	N	1	P	0.51537	0.946	P	0.50270	0.636	T	0.38067	-0.9678	9	0.49607	T	0.09	.	6.6099	0.22745	0.0:0.0:1.0:0.0	.	39	P26371	KRA59_HUMAN	I	39	ENSP00000431443:V39I	ENSP00000431443:V39I	V	+	1	0	KRTAP5-9	70937466	0.000000	0.05858	0.015000	0.15790	0.167000	0.22549	-0.373000	0.07494	1.189000	0.43028	0.442000	0.29010	GTC	G|0.999;A|0.001	0.001	strong		0.667	KRTAP5-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393901.2			A	71259818	G	A	71259818	3	1	22	1	0	0	0	0	1	0	0	0	8577	1145	40	1	117	1	KRTAP5-9	11	71259818	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	109	71259818	63746698	2504	5405											
IL18BP	10068	hgsc.bcm.edu	37	chr11	71711438	71711438	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctcctgtgtgcccacgtcGtcactctcctggtcagagcc	4	11	10	16	2	3	1	2	0	1	1	6	1	4	1	4	1	3	1	4	1	0	0	rs376290357		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71711438G>A	ENST00000393703.4	+	3	607	c.70G>A	c.(70-72)Gtc>Atc	p.V24I	IL18BP_ENST00000497194.2_Missense_Mutation_p.V24I|IL18BP_ENST00000393707.4_Missense_Mutation_p.V24I|IL18BP_ENST00000260049.5_Missense_Mutation_p.V24I|IL18BP_ENST00000393705.4_Missense_Mutation_p.V24I|IL18BP_ENST00000531053.1_Missense_Mutation_p.V24I|IL18BP_ENST00000337131.5_Missense_Mutation_p.V24I|IL18BP_ENST00000404792.1_Missense_Mutation_p.V24I	NM_001039660.1	NP_001034749.1	O95998	I18BP_HUMAN	interleukin 18 binding protein	24					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						TGCCCACGTCGTCACTCTCCT	0.617																																					p.V24I		Atlas-SNP	.											.	IL18BP	15	.	0			c.G70A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	3,4255		0,3,2126	98	107	104		70,70,70,70,70,70,70	-8.2	0	11		104	0,8508		0,0,4254	no	missense,missense,missense,missense,missense,missense,missense	IL18BP	NM_001039659.1,NM_001039660.1,NM_001145055.1,NM_001145057.1,NM_005699.3,NM_173042.2,NM_173044.2	29,29,29,29,29,29,29	0,3,6380	AA,AG,GG		0.0,0.0705,0.0235	benign,benign,benign,benign,benign,benign,benign	24/195,24/195,24/116,24/195,24/200,24/195,24/164	71711438	3,12763	2129	4254	6383	SO:0001583	missense	10068	exon3			CACGTCGTCACTC	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.70G>A	11.37:g.71711438G>A	ENSP00000377306:p.Val24Ile	91	0	0		85	44	0.517647	NM_001145057	B3KUZ0|B7WPK4|O95993|O96027|Q9NZA9|Q9UBR7	Missense_Mutation	SNP	ENST00000393703.4	37	CCDS8206.2	.	.	.	.	.	.	.	.	.	.	G	0	-2.676183	0.00102	7.05E-4	0.0	ENSG00000137496	ENST00000393703;ENST00000497194;ENST00000393705;ENST00000337131;ENST00000531053;ENST00000404792;ENST00000260049;ENST00000393707	T;T;T;T;T;T;T	0.35236	1.35;1.32;1.35;1.35;1.32;1.35;1.35	4.08	-8.16	0.01061	.	1.862160	0.02902	N	0.135517	T	0.13329	0.0323	N	0.04043	-0.29	0.09310	N	1	B;B;B	0.12013	0.001;0.005;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.20273	-1.0280	10	0.06099	T	0.92	-2.0645	7.9891	0.30229	0.1145:0.1776:0.6198:0.0881	.	24;24;24	O95998-3;G3V1C5;O95998	.;.;I18BP_HUMAN	I	24	ENSP00000377306:V24I;ENSP00000434717:V24I;ENSP00000377308:V24I;ENSP00000338723:V24I;ENSP00000434835:V24I;ENSP00000384212:V24I;ENSP00000260049:V24I	ENSP00000260049:V24I	V	+	1	0	IL18BP	71389086	0.000000	0.05858	0.000000	0.03702	0.070000	0.16714	-2.169000	0.01269	-3.683000	0.00121	-0.340000	0.08031	GTC	.	.	weak		0.617	IL18BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258012.2	NM_173042		A	71711438	G	A	71711438	3	1	22	1	0	0	0	0	1	0	0	0	7655	1145	40	1	76	1	IL18BP	11	71711438	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	451620	71711438	63295078	2505	5406											
NUMA1	4926	hgsc.bcm.edu	37	chr11	71718413	71718413	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attctaccttggggggcaggCgctgggagataggtgaggct	7	9	18	7	1	1	2	0	1	1	1	1	3	1	2	1	7	1	3	1	7	2	4	rs149588226	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71718413C>T	ENST00000393695.3	-	21	5616	c.5285G>A	c.(5284-5286)cGc>cAc	p.R1762H	NUMA1_ENST00000351960.6_Missense_Mutation_p.R626H|NUMA1_ENST00000358965.6_Missense_Mutation_p.R1748H	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						GGGGGGCAGGCGCTGGGAGAT	0.622			T	RARA	APL								C|||	14	0.00279553	0.0106	0.0	5008	,	,		17501	0.0		0.0	False		,,,				2504	0.0				p.R1762H		Atlas-SNP	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1	142	.	0			c.G5285A						PASS	.	C	HIS/ARG	72,4328	63.5+/-100.7	1,70,2129	40	43	42		5285	4.6	1	11	dbSNP_134	42	0,8586		0,0,4293	yes	missense	NUMA1	NM_006185.2	29	1,70,6422	TT,TC,CC		0.0,1.6364,0.5544	probably-damaging	1762/2116	71718413	72,12914	2200	4293	6493	SO:0001583	missense	4926	exon21			GGCAGGCGCTGGG	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.5285G>A	11.37:g.71718413C>T	ENSP00000377298:p.Arg1762His	79	0	0		85	28	0.329412	NM_006185		Missense_Mutation	SNP	ENST00000393695.3	37	CCDS31633.1	4|4	0.0018315018315018315|0.0018315018315018315	4|4	0.008130081300813009|0.008130081300813009	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	20.5|20.5	3.994037|3.994037	0.74703|0.74703	0.016364|0.016364	0.0|0.0	ENSG00000137497|ENSG00000137497	ENST00000541584|ENST00000351960;ENST00000358965;ENST00000393695;ENST00000359652;ENST00000536544	.|T;T;T	.|0.21543	.|2.0;2.46;2.46	4.58|4.58	4.58|4.58	0.56647|0.56647	.|.	.|0.000000	.|0.56097	.|D	.|0.000035	T|T	0.13329|0.13329	0.0323|0.0323	N|N	0.24115|0.24115	0.695|0.695	0.40559|0.40559	D|D	0.981196|0.981196	.|D;D;D;D	.|0.89917	.|0.999;0.999;0.999;1.0	.|P;D;P;D	.|0.67231	.|0.897;0.95;0.855;0.938	T|T	0.01587|0.01587	-1.1318|-1.1318	5|10	.|0.52906	.|T	.|0.07	.|.	6.077|6.077	0.19921|0.19921	0.0:0.7688:0.0:0.2312|0.0:0.7688:0.0:0.2312	.|.	.|1768;1748;1762;626	.|Q4LE64;Q14980-2;Q14980;Q9BTE9	.|.;.;NUMA1_HUMAN;.	T|H	611|626;1748;1762;1311;735	.|ENSP00000260051:R626H;ENSP00000351851:R1748H;ENSP00000377298:R1762H	.|ENSP00000260051:R626H	A|R	-|-	1|2	0|0	NUMA1|NUMA1	71396061|71396061	0.995000|0.995000	0.38212|0.38212	0.999000|0.999000	0.59377|0.59377	0.988000|0.988000	0.76386|0.76386	1.062000|1.062000	0.30555|0.30555	2.527000|2.527000	0.85204|0.85204	0.561000|0.561000	0.74099|0.74099	GCC|CGC	C|0.995;T|0.005	0.005	strong		0.622	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1			T	71718413	C	T	71718413	3	4	22	1	0	0	0	0	1	0	0	0	10759	768	27	1	1090	1	NUMA1	11	71718413	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6975	71718413	63288103	2506	5407											
NUMA1	4926	hgsc.bcm.edu	37	chr11	71725612	71725612	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccgcagccgttccagctcAttgcccatctgctctgcctc	4	10	8	19	2	3	0	1	0	2	0	5	0	4	0	5	0	5	4	5	0	0	2	rs142372284	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71725612A>G	ENST00000393695.3	-	15	3268	c.2937T>C	c.(2935-2937)aaT>aaC	p.N979N	NUMA1_ENST00000351960.6_Intron|RP11-849H4.4_ENST00000502284.1_RNA|NUMA1_ENST00000358965.6_Silent_p.N979N	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						GTTCCAGCTCATTGCCCATCT	0.672			T	RARA	APL								A|||	14	0.00279553	0.0106	0.0	5008	,	,		17846	0.0		0.0	False		,,,				2504	0.0				p.N979N		Atlas-SNP	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1	142	.	0			c.T2937C						PASS	.	A		71,4329	59.3+/-96.0	1,69,2130	66	73	71		2937	-6	0.9	11	dbSNP_134	71	0,8586		0,0,4293	no	coding-synonymous	NUMA1	NM_006185.2		1,69,6423	GG,GA,AA		0.0,1.6136,0.5467		979/2116	71725612	71,12915	2200	4293	6493	SO:0001819	synonymous_variant	4926	exon15			CAGCTCATTGCCC	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.2937T>C	11.37:g.71725612A>G		54	0	0		87	39	0.448276	NM_006185		Silent	SNP	ENST00000393695.3	37	CCDS31633.1																																																																																			A|0.995;G|0.005	0.005	strong		0.672	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1			G	71725612	A	G	71725612	2	3	22	1	0	0	0	0	0	0	0	1	10759	214	8	3		3	NUMA1	11	71725612	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	7199	71725612	63280904	2507	5408											
LRTOMT	220074	hgsc.bcm.edu	37	chr11	71806515	71806515	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	accacagctgaagtctggaaAcgcatgaacatcaagcccaa	16	5	8	12	1	2	2	1	2	1	0	2	3	2	3	2	1	4	2	2	1	5	0	rs150245488	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71806515A>G	ENST00000289488.2	+	6	906	c.528A>G	c.(526-528)aaA>aaG	p.K176K	LRTOMT_ENST00000307198.7_Intron|LRTOMT_ENST00000419228.1_Intron|LRTOMT_ENST00000439209.1_Intron|LAMTOR1_ENST00000535107.1_Intron|LRTOMT_ENST00000541614.1_Intron|LRTOMT_ENST00000440313.2_Intron|LAMTOR1_ENST00000545249.1_Intron|LRTOMT_ENST00000423494.2_Silent_p.K158K|LRTOMT_ENST00000324866.7_3'UTR|LRTOMT_ENST00000539587.1_Missense_Mutation_p.N42S|LRTOMT_ENST00000447974.1_Intron|LRTOMT_ENST00000538478.1_Silent_p.K176K|LRTOMT_ENST00000435085.1_Intron|LAMTOR1_ENST00000539797.1_5'Flank|LRTOMT_ENST00000539271.1_Missense_Mutation_p.N42S	NM_001271471.2|NM_145309.5	NP_001258400.1|NP_660352.1	Q96E66	LRC51_HUMAN	leucine rich transmembrane and O-methyltransferase domain containing	176						cytoplasm (GO:0005737)				large_intestine(2)|lung(1)|ovary(1)	4						AAGTCTGGAAACGCATGAACA	0.537													A|||	14	0.00279553	0.0106	0.0	5008	,	,		20529	0.0		0.0	False		,,,				2504	0.0				p.K176K		Atlas-SNP	.											.	LRTOMT	20	.	0			c.A528G						PASS	.	A	,,,	72,4328	64.7+/-102.0	1,70,2129	96	69	78		,,474,528	0.6	1	11	dbSNP_134	78	0,8586		0,0,4293	no	intron,intron,coding-synonymous,coding-synonymous	LRTOMT	NM_001145307.2,NM_001145308.2,NM_001205138.1,NM_145309.3	,,,	1,70,6422	GG,GA,AA		0.0,1.6364,0.5544	,,,	,,158/175,176/193	71806515	72,12914	2200	4293	6493	SO:0001819	synonymous_variant	220074	exon6			CTGGAAACGCATG		CCDS8208.1, CCDS44667.1, CCDS44668.1, CCDS55778.1, CCDS59227.1	11q13.4	2014-09-05	2013-08-19	2008-11-27	ENSG00000184154	ENSG00000184154			25033	protein-coding gene	gene with protein product		612414	"leucine rich repeat containing 51", "deafness, autosomal recessive 63"	LRRC51, DFNB63		18794526, 18953341	Standard	NM_145309		Approved	COMT2, CFAP111	uc010rqw.2	Q8WZ04	OTTHUMG00000154887	ENST00000289488.2:c.528A>G	11.37:g.71806515A>G		160	0	0		149	81	0.543624	NM_145309	B2R7X1|B6CZ35|B6CZ36|B6CZ37|B6CZ38|B6CZ39|B7Z5I4	Silent	SNP	ENST00000289488.2	37	CCDS8208.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	14.26	2.483004	0.44147	0.016364	0.0	ENSG00000184154	ENST00000539271;ENST00000539587	.	.	.	5.9	0.652	0.17823	.	.	.	.	.	T	0.47395	0.1443	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58446	-0.7635	5	0.87932	D	0	-16.0144	8.9883	0.36008	0.4707:0.0:0.5292:0.0	.	.	.	.	S	42	.	ENSP00000442267:N42S	N	+	2	0	LRTOMT	71484163	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	0.340000	0.19892	0.072000	0.16694	0.496000	0.49642	AAC	A|0.995;G|0.005	0.005	strong		0.537	LRTOMT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337504.1	NM_145309		G	71806515	A	G	71806515	2	3	22	1	0	0	0	0	0	0	0	1	9055	40	2	3		3	LRTOMT	11	71806515	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	80903	71806515	63200001	2508	5409											
LRTOMT	55004	hgsc.bcm.edu	37	chr11	71817250	71817250	+	5'Flank	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acttgagccacatggggcctGtcaaaggtcagtgttcccta	9	10	11	11	0	2	1	2	1	0	0	3	1	3	1	3	3	1	1	3	3	2	3	rs181092713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71817250G>A	ENST00000278671.5	-	0	0				LRTOMT_ENST00000307198.7_Missense_Mutation_p.V118I|LRTOMT_ENST00000419228.1_Missense_Mutation_p.V78I|LRTOMT_ENST00000439209.1_Intron|LAMTOR1_ENST00000535107.1_5'Flank|LAMTOR1_ENST00000545249.1_5'Flank|snoU13_ENST00000459046.1_RNA|LRTOMT_ENST00000435085.1_Missense_Mutation_p.V118I|LAMTOR1_ENST00000538404.1_5'Flank	NM_017907.2	NP_060377.1	Q6IAA8	LTOR1_HUMAN	late endosomal/lysosomal adaptor, MAPK and MTOR activator 1						cell growth (GO:0016049)|cellular protein localization (GO:0034613)|cellular response to amino acid stimulus (GO:0071230)|cholesterol homeostasis (GO:0042632)|endosome localization (GO:0032439)|endosome organization (GO:0007032)|lysosome localization (GO:0032418)|lysosome organization (GO:0007040)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of TOR signaling (GO:0032008)|regulation of cholesterol efflux (GO:0010874)|regulation of cholesterol esterification (GO:0010872)|regulation of cholesterol import (GO:0060620)|regulation of receptor recycling (GO:0001919)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|late endosome membrane (GO:0031902)|lysosome (GO:0005764)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|Ragulator complex (GO:0071986)				cervix(1)	1						CATGGGGCCTGTCAAAGGTCA	0.562													G|||	14	0.00279553	0.0106	0.0	5008	,	,		18621	0.0		0.0	False		,,,				2504	0.0				p.V118I		Atlas-SNP	.											.	LRTOMT	20	.	0			c.G352A						PASS	.	G	ILE/VAL	21,1363		0,21,671	35	38	37		352	1.4	1	11		37	0,3182		0,0,1591	no	missense	LRTOMT	NM_001145308.2	29	0,21,2262	AA,AG,GG		0.0,1.5173,0.4599	benign	118/292	71817250	21,4545	692	1591	2283	SO:0001631	upstream_gene_variant	220074	exon7			GGGCCTGTCAAAG	AK000632	CCDS8209.1	11q13.4	2011-05-18	2011-02-15	2011-02-15	ENSG00000149357	ENSG00000149357			26068	protein-coding gene	gene with protein product	"p27kip1 releasing factor from RhoA", "protein associated with DRMs and endosomes"	613510	"chromosome 11 open reading frame 59"	C11orf59		12358155	Standard	NM_017907		Approved	FLJ20625, p18, p27RF-Rho, Pdro, Ragulator1	uc001ort.3	Q6IAA8	OTTHUMG00000167869		11.37:g.71817250G>A	Exception_encountered	13	0	0		15	6	0.4	NM_001145309	Q8WZ09|Q9NWT0	Missense_Mutation	SNP	ENST00000278671.5	37	CCDS8209.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	13.30	2.195071	0.38806	0.015173	0.0	ENSG00000184154	ENST00000419228;ENST00000435085;ENST00000307198	T;T;T	0.21734	1.99;1.99;1.99	4.59	1.43	0.22495	.	.	.	.	.	T	0.05364	0.0142	N	0.21240	0.645	0.21445	N	0.99969	B;B	0.06786	0.0;0.001	B;B	0.08055	0.001;0.003	T	0.26573	-1.0099	9	0.38643	T	0.18	-3.0892	2.2276	0.03988	0.1802:0.2893:0.404:0.1265	.	118;78	Q8WZ04;Q8WZ04-2	TOMT_HUMAN;.	I	78;118;118	ENSP00000392233:V78I;ENSP00000409789:V118I;ENSP00000305742:V118I	ENSP00000305742:V78I	V	+	1	0	LRTOMT	71494898	0.617000	0.27043	0.999000	0.59377	0.980000	0.70556	1.049000	0.30392	0.642000	0.30620	0.462000	0.41574	GTC	G|0.998;A|0.002	0.002	strong		0.562	LAMTOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396733.1	NM_017907		A	71817250	G	A	71817250	1	1	22	0	1	0	0	0	0	0	0	0	9055	1377	48	2		2	LRTOMT	11	71817250	5'Flank	SNP	G	TCGA-G8-6324-01A-11D-2210-10	10735	71817250	63189266	2509	5410											
ARAP1	116985	hgsc.bcm.edu	37	chr11	72403832	72403832	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctccacggcctctggctcTgtttgatagaggatcagggt	6	11	13	11	2	3	2	1	1	2	1	4	3	4	3	2	4	0	3	2	4	1	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:72403832T>C	ENST00000393609.3	-	30	4157		c.e30-2		ARAP1_ENST00000393605.3_Splice_Site|ARAP1_ENST00000429686.1_Intron|ARAP1_ENST00000455638.2_Intron|ARAP1_ENST00000334211.8_Splice_Site|ARAP1_ENST00000426523.1_Intron|ARAP1_ENST00000359373.5_Intron|ARAP1_ENST00000495878.1_Intron|ARAP1-AS1_ENST00000542022.1_RNA	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1						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						CCTCTGGCTCTGTTTGATAGA	0.587																																					.	Ovarian(102;1198 1520 13195 17913 37529)	Atlas-SNP	.											.	ARAP1	168	.	0			c.3220-2A>G						PASS	.						46	46	46					11																	72403832		2200	4293	6493	SO:0001630	splice_region_variant	116985	exon29			TGGCTCTGTTTGA	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.3955-2A>G	11.37:g.72403832T>C		48	0	0		64	29	0.453125	NM_015242	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Splice_Site	SNP	ENST00000393609.3	37	CCDS41687.1	.	.	.	.	.	.	.	.	.	.	T	17.85	3.491402	0.64074	.	.	ENSG00000186635	ENST00000393605;ENST00000334211;ENST00000393609	.	.	.	5.73	4.54	0.55810	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.4138	0.32659	0.1738:0.0:0.0:0.8262	.	.	.	.	.	-1	.	.	.	-	.	.	ARAP1	72081480	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.927000	0.40094	2.184000	0.69523	0.448000	0.29417	.	.	.	none		0.587	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118	Intron	C	72403832	T	C	72403832	5	2	22	1	0	0	0	0	0	0	1	0	838	1594	55	3	423	3	ARAP1	11	72403832	Splice_Site	SNP	T	TCGA-G8-6324-01A-11D-2210-10	586582	72403832	62602684	2510	5411											
ARHGEF17	9828	hgsc.bcm.edu	37	chr11	73078685	73078685	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccttggcaccgaggccccGcccctgccaggcctaaaatg	7	5	10	19	2	0	0	0	0	0	0	0	1	0	0	9	3	1	1	9	3	2	2	rs143114785	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:73078685G>A	ENST00000263674.3	+	21	6402	c.6052G>A	c.(6052-6054)Gcc>Acc	p.A2018T		NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	2018					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						CCGAGGCCCCGCCCCTGCCAG	0.647													G|||	42	0.00838658	0.031	0.0014	5008	,	,		16959	0.0		0.0	False		,,,				2504	0.0				p.A2018T		Atlas-SNP	.											.	ARHGEF17	117	.	0			c.G6052A						PASS	.	G	THR/ALA	112,4288	86.8+/-125.4	0,112,2088	69	71	70		6052	-2.7	0	11	dbSNP_134	70	0,8586		0,0,4293	yes	missense	ARHGEF17	NM_014786.3	58	0,112,6381	AA,AG,GG		0.0,2.5455,0.8625	benign	2018/2064	73078685	112,12874	2200	4293	6493	SO:0001583	missense	9828	exon21			GGCCCCGCCCCTG	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.6052G>A	11.37:g.73078685G>A	ENSP00000263674:p.Ala2018Thr	72	0	0		70	37	0.528571	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Missense_Mutation	SNP	ENST00000263674.3	37	CCDS8221.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	G	4.409	0.075520	0.08485	0.025455	0.0	ENSG00000110237	ENST00000263674	T	0.57436	0.4	5.42	-2.69	0.06022	.	0.281147	0.33753	N	0.004585	T	0.07728	0.0194	N	0.02830	-0.485	0.18873	N	0.999987	B	0.06786	0.001	B	0.06405	0.002	T	0.13124	-1.0521	10	0.15499	T	0.54	-2.6535	11.6716	0.51406	0.5979:0.0:0.4021:0.0	.	2018	Q96PE2	ARHGH_HUMAN	T	2018	ENSP00000263674:A2018T	ENSP00000263674:A2018T	A	+	1	0	ARHGEF17	72756333	0.001000	0.12720	0.004000	0.12327	0.145000	0.21501	-0.227000	0.09126	-0.943000	0.03691	-0.459000	0.05422	GCC	G|0.991;A|0.009	0.009	strong		0.647	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786		A	73078685	G	A	73078685	3	1	22	1	0	0	0	0	1	0	0	0	900	1087	38	1	6134	1	ARHGEF17	11	73078685	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	674853	73078685	61927831	2511	5412											
UCP3	7352	hgsc.bcm.edu	37	chr11	73717247	73717247	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggggtgtacacctgcttgaCggagtcatagaggccgatgc	8	8	16	9	2	1	2	1	1	0	1	1	4	1	3	2	4	3	2	2	4	2	3	rs2229707	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:73717247C>T	ENST00000314032.4	-	3	856	c.304G>A	c.(304-306)Gtc>Atc	p.V102I	UCP3_ENST00000426995.2_Missense_Mutation_p.V102I|UCP3_ENST00000348534.4_Missense_Mutation_p.V102I	NM_003356.3	NP_003347.1	P55916	UCP3_HUMAN	uncoupling protein 3 (mitochondrial, proton carrier)	102			V -> I (in obesity; dbSNP:rs2229707). {ECO:0000269|PubMed:9769326}.		aging (GO:0007568)|cellular metabolic process (GO:0044237)|cellular response to hormone stimulus (GO:0032870)|fatty acid metabolic process (GO:0006631)|lipid metabolic process (GO:0006629)|mitochondrial transport (GO:0006839)|proton transport (GO:0015992)|respiratory electron transport chain (GO:0022904)|respiratory gaseous exchange (GO:0007585)|response to activity (GO:0014823)|response to cold (GO:0009409)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|response to superoxide (GO:0000303)|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)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	12	Breast(11;2.08e-05)					ACCTGCTTGACGGAGTCATAG	0.627													C|||	216	0.043131	0.1513	0.013	5008	,	,		19077	0.0		0.005	False		,,,				2504	0.002				p.V102I		Atlas-SNP	.											.	UCP3	31	.	0			c.G304A	GRCh37	CM981987	UCP3	M	rs2229707	PASS	.	C	ILE/VAL,ILE/VAL	524,3876	236.8+/-248.8	36,452,1712	44	43	44	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	304,304	5.8	1	11	dbSNP_98	44	12,8574	9.1+/-34.3	0,12,4281	yes	missense,missense	UCP3	NM_003356.3,NM_022803.2	29,29	36,464,5993	TT,TC,CC		0.1398,11.9091,4.1275	benign,benign	102/313,102/276	73717247	536,12450	2200	4293	6493	SO:0001583	missense	7352	exon3			GCTTGACGGAGTC	AF001787	CCDS8229.1, CCDS44677.1	11q13.4	2013-05-22				ENSG00000175564		"Solute carriers"	12519	protein-coding gene	gene with protein product		602044				9480760, 9196039	Standard	NM_003356		Approved	SLC25A9	uc001our.3	P55916		ENST00000314032.4:c.304G>A	11.37:g.73717247C>T	ENSP00000323740:p.Val102Ile	67	0	0		76	32	0.421053	NM_003356	O60475|Q96HL3	Missense_Mutation	SNP	ENST00000314032.4	37	CCDS8229.1	81	0.03708791208791209	75	0.1524390243902439	3	0.008287292817679558	0	0.0	3	0.00395778364116095	C	15.72	2.915545	0.52546	0.119091	0.001398	ENSG00000175564	ENST00000314032;ENST00000348534;ENST00000426995	T;T;T	0.78816	-1.21;-1.21;-1.21	5.76	5.76	0.90799	Mitochondrial carrier domain (2);	0.054467	0.64402	D	0.000001	T	0.00967	0.0032	L	0.39020	1.185	0.22933	P	0.99854677	B	0.20459	0.045	B	0.23275	0.045	T	0.24764	-1.0151	9	0.59425	D	0.04	-25.6915	19.5566	0.95351	0.0:1.0:0.0:0.0	rs2229707;rs2734830;rs2229707	102	P55916	UCP3_HUMAN	I	102	ENSP00000323740:V102I;ENSP00000343615:V102I;ENSP00000392143:V102I	ENSP00000323740:V102I	V	-	1	0	UCP3	73394895	1.000000	0.71417	0.990000	0.47175	0.261000	0.26267	5.621000	0.67743	2.724000	0.93272	0.561000	0.74099	GTC	C|0.964;T|0.036	0.036	strong		0.627	UCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398200.1	NM_003356		T	73717247	C	T	73717247	3	4	22	1	0	0	0	0	1	0	0	0	16947	536	19	1	658	1	UCP3	11	73717247	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	638562	73717247	61289269	2512	5413											
UCP3	7352	hgsc.bcm.edu	37	chr11	73717263	73717263	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttgacggagtcatagaggccGatgcggatggaggcgaagct	10	7	17	7	4	1	2	1	1	0	1	1	7	1	5	1	5	2	1	1	5	2	2	rs2229706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:73717263G>A	ENST00000314032.4	-	3	840	c.288C>T	c.(286-288)atC>atT	p.I96I	UCP3_ENST00000426995.2_Silent_p.I96I|UCP3_ENST00000348534.4_Silent_p.I96I	NM_003356.3	NP_003347.1	P55916	UCP3_HUMAN	uncoupling protein 3 (mitochondrial, proton carrier)	96					aging (GO:0007568)|cellular metabolic process (GO:0044237)|cellular response to hormone stimulus (GO:0032870)|fatty acid metabolic process (GO:0006631)|lipid metabolic process (GO:0006629)|mitochondrial transport (GO:0006839)|proton transport (GO:0015992)|respiratory electron transport chain (GO:0022904)|respiratory gaseous exchange (GO:0007585)|response to activity (GO:0014823)|response to cold (GO:0009409)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|response to superoxide (GO:0000303)|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)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	12	Breast(11;2.08e-05)					CATAGAGGCCGATGCGGATGG	0.627													G|||	34	0.00678914	0.0242	0.0029	5008	,	,		18530	0.0		0.0	False		,,,				2504	0.0				p.I96I		Atlas-SNP	.											.	UCP3	31	.	0			c.C288T						PASS	.	G	,	102,4298	80.9+/-119.3	1,100,2099	44	43	43		288,288	-4	1	11	dbSNP_98	43	1,8585	1.2+/-3.3	0,1,4292	no	coding-synonymous,coding-synonymous	UCP3	NM_003356.3,NM_022803.2	,	1,101,6391	AA,AG,GG		0.0116,2.3182,0.7932	,	96/313,96/276	73717263	103,12883	2200	4293	6493	SO:0001819	synonymous_variant	7352	exon3			GAGGCCGATGCGG	AF001787	CCDS8229.1, CCDS44677.1	11q13.4	2013-05-22				ENSG00000175564		"Solute carriers"	12519	protein-coding gene	gene with protein product		602044				9480760, 9196039	Standard	NM_003356		Approved	SLC25A9	uc001our.3	P55916		ENST00000314032.4:c.288C>T	11.37:g.73717263G>A		66	0	0		70	39	0.557143	NM_003356	O60475|Q96HL3	Silent	SNP	ENST00000314032.4	37	CCDS8229.1																																																																																			G|0.991;A|0.009	0.009	strong		0.627	UCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398200.1	NM_003356		A	73717263	G	A	73717263	2	1	22	1	0	0	0	0	0	0	0	1	16947	1048	37	1		1	UCP3	11	73717263	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	16	73717263	61289253	2513	5414											
C2CD3	26005	hgsc.bcm.edu	37	chr11	73759251	73759251	+	Splice_Site	SNP	T	T	C																															tcatcaagaattcactcaccTcccaggagaggagaaatcaa																								rs1632242|rs200356969	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:73759251T>C	ENST00000334126.7	-	28	5720	c.5494A>G	c.(5494-5496)Aga>Gga	p.R1832G	C2CD3_ENST00000313663.7_Splice_Site_p.R1832G			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1832			R -> G (in dbSNP:rs1632242).		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)					TTCACTCACCTCCCAGGAGAG	0.438													T|||	243	0.0485224	0.1778	0.0115	5008	,	,		19079	0.0		0.0	False		,,,				2504	0.0				p.R1832G		Atlas-SNP	.											.	C2CD3	288	.	0			c.A5494G						PASS	.						56	52	53					11																	73759251		2200	4293	6493	SO:0001630	splice_region_variant	26005	exon28			CTCACCTCCCAGG	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.5495+1A>G	11.37:g.73759251T>C		97	0	0		99	42	0.424242	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	37		76|76	0.0347985347985348|0.0347985347985348	71|71	0.1443089430894309|0.1443089430894309	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	0|0	0.0|0.0	T|T	11.88|11.88	1.770709|1.770709	0.31320|0.31320	.|.	.|.	ENSG00000168014|ENSG00000168014	ENST00000538361|ENST00000334126;ENST00000313663;ENST00000313681;ENST00000414160	.|T;T;T	.|0.15952	.|2.73;2.77;2.38	4.75|4.75	4.75|4.75	0.60458|0.60458	.|.	.|0.440230	.|0.27172	.|N	.|0.020590	T|T	0.00144|0.00144	0.0004|0.0004	M|M	0.72894|0.72894	2.215|2.215	0.34135|0.34135	P|P	0.334317|0.334317	.|P	.|0.35272	.|0.493	.|B	.|0.33620	.|0.167	T|T	0.09292|0.09292	-1.0681|-1.0681	4|9	.|0.44086	.|T	.|0.13	-5.0634|-5.0634	10.8098|10.8098	0.46540|0.46540	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs1632242;rs52837313;rs1632242|rs1632242;rs52837313;rs1632242	.|1832	.|Q4AC94-1	.|.	G|G	65|1832;1832;1813;640	.|ENSP00000334379:R1832G;ENSP00000323339:R1832G;ENSP00000388750:R640G	.|ENSP00000323339:R1832G	E|R	-|-	2|1	0|2	C2CD3|C2CD3	73436899|73436899	0.997000|0.997000	0.39634|0.39634	0.981000|0.981000	0.43875|0.43875	0.172000|0.172000	0.22775|0.22775	2.829000|2.829000	0.48128|0.48128	2.114000|2.114000	0.64651|0.64651	0.533000|0.533000	0.62120|0.62120	GAG|AGA	T|0.962;C|0.038	0.038	strong		0.438	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531	Missense_Mutation	C	73759251	T	C	73759251	5	2	22	1	0	0	0	0	0	0	1	0	2156	1565	54	3	413	3	C2CD3	11	73759251	Splice_Site	SNP	T	TCGA-G8-6324-01A-11D-2210-10	41988	73759251	61247265	2514	5415	64	2									
C2CD3	26005	hgsc.bcm.edu	37	chr11	73759254	73759254	+	Missense_Mutation	SNP	C	C	A																															tcaagaattcactcacctccCaggagaggagaaatcaagct																								rs1632245	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:73759254C>A	ENST00000334126.7	-	28	5717	c.5491G>T	c.(5491-5493)Ggg>Tgg	p.G1831W	C2CD3_ENST00000313663.7_Missense_Mutation_p.G1831W			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1831			G -> W (in dbSNP:rs1632245).		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)					ACTCACCTCCCAGGAGAGGAG	0.443													C|||	243	0.0485224	0.1778	0.0115	5008	,	,		19111	0.0		0.0	False		,,,				2504	0.0				p.G1831W		Atlas-SNP	.											C2CD3_ENST00000334126,NS,carcinoma,+2,2	C2CD3	288	2	0			c.G5491T						PASS	.						58	53	55					11																	73759254		2200	4293	6493	SO:0001583	missense	26005	exon28			ACCTCCCAGGAGA	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.5491G>T	11.37:g.73759254C>A	ENSP00000334379:p.Gly1831Trp	98	0	0		100	42	0.42	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	37		76|76	0.0347985347985348|0.0347985347985348	71|71	0.1443089430894309|0.1443089430894309	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	0|0	0.0|0.0	C|C	12.63|12.63	1.994257|1.994257	0.35226|0.35226	.|.	.|.	ENSG00000168014|ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681;ENST00000414160|ENST00000538361	T;T;T|.	0.14266|.	2.91;2.93;2.52|.	4.75|4.75	0.796|0.796	0.18648|0.18648	.|.	0.878366|.	0.10272|.	N|.	0.694613|.	T|T	0.00328|0.00328	0.0010|0.0010	L|L	0.47716|0.47716	1.5|1.5	0.42535|0.42535	P|P	0.006946000000000008|0.006946000000000008	D|.	0.60575|.	0.988|.	P|.	0.62089|.	0.898|.	T|T	0.09640|0.09640	-1.0665|-1.0665	9|4	0.72032|.	D|.	0.01|.	.|.	3.8081|3.8081	0.08786|0.08786	0.0:0.518:0.1836:0.2984|0.0:0.518:0.1836:0.2984	rs1632245;rs52791226;rs1632245|rs1632245;rs52791226;rs1632245	1831|.	Q4AC94-1|.	.|.	W|L	1831;1831;1812;639|64	ENSP00000334379:G1831W;ENSP00000323339:G1831W;ENSP00000388750:G639W|.	ENSP00000323339:G1831W|.	G|W	-|-	1|2	0|0	C2CD3|C2CD3	73436902|73436902	0.919000|0.919000	0.31177|0.31177	0.959000|0.959000	0.39883|0.39883	0.175000|0.175000	0.22909|0.22909	0.834000|0.834000	0.27518|0.27518	0.312000|0.312000	0.23038|0.23038	0.655000|0.655000	0.94253|0.94253	GGG|TGG	A|0.037;C|0.963	0.037	strong		0.443	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		A	73759254	C	A	73759254	3	1	22	1	0	0	0	0	1	0	0	0	2156	594	21	4	416	4	C2CD3	11	73759254	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3	73759254	61247262	2515	5416	64	2									
C2CD3	26005	hgsc.bcm.edu	37	chr11	73796683	73796683	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgacttggtattttcatgaTagacagcaaaaataacttct	14	14	6	7	0	2	3	1	2	1	1	2	3	2	3	0	1	2	2	0	1	5	7	rs1095423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:73796683T>C	ENST00000334126.7	-	21	4116	c.3890A>G	c.(3889-3891)tAt>tGt	p.Y1297C	C2CD3_ENST00000313663.7_Missense_Mutation_p.Y1297C			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1297			Y -> C (in dbSNP:rs1095423).		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)					ATTTTCATGATAGACAGCAAA	0.413													T|||	239	0.0477236	0.1747	0.0115	5008	,	,		19547	0.0		0.0	False		,,,				2504	0.0				p.Y1297C		Atlas-SNP	.											.	C2CD3	288	.	0			c.A3890G						PASS	.	T	CYS/TYR	554,3846	248.7+/-256.4	40,474,1686	64	62	63		3890	5.9	1	11	dbSNP_86	63	15,8571	11.2+/-40.8	0,15,4278	yes	missense	C2CD3	NM_015531.4	194	40,489,5964	CC,CT,TT		0.1747,12.5909,4.3816	probably-damaging	1297/1964	73796683	569,12417	2200	4293	6493	SO:0001583	missense	26005	exon21			TCATGATAGACAG	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.3890A>G	11.37:g.73796683T>C	ENSP00000334379:p.Tyr1297Cys	97	0	0		101	47	0.465347	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	37		75	0.034340659340659344	70	0.14227642276422764	5	0.013812154696132596	0	0.0	0	0.0	T	18.08	3.542983	0.65198	0.125909	0.001747	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681;ENST00000414160	T;T;T	0.46063	0.88;0.88;0.88	5.95	5.95	0.96441	.	0.188748	0.48767	D	0.000167	T	0.00754	0.0025	M	0.68317	2.08	0.29764	P	0.835337	D	0.89917	1.0	D	0.91635	0.999	T	0.29427	-1.0012	9	0.72032	D	0.01	-12.7519	11.7864	0.52045	0.1316:0.0:0.0:0.8684	rs1095423;rs1790396;rs52807296;rs61681570;rs1095423	1297	Q4AC94-1	.	C	1297;1297;1297;105	ENSP00000334379:Y1297C;ENSP00000323339:Y1297C;ENSP00000388750:Y105C	ENSP00000323339:Y1297C	Y	-	2	0	C2CD3	73474331	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	3.834000	0.55798	2.268000	0.75426	0.533000	0.62120	TAT	T|0.951;C|0.049	0.049	strong		0.413	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		C	73796683	T	C	73796683	3	2	22	1	0	0	0	0	1	0	0	0	2156	1406	49	3	2045	3	C2CD3	11	73796683	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	37429	73796683	61209833	2516	5417											
CHRDL2	25884	hgsc.bcm.edu	37	chr11	74415606	74415606	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtctgaagtggcgagggaTgaagctcagaggggcgctga	9	6	20	6	2	2	4	1	3	1	1	2	6	2	5	0	5	1	2	0	5	2	0	rs59876990	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:74415606T>C	ENST00000376332.3	-	7	1172	c.676A>G	c.(676-678)Atc>Gtc	p.I226V	CHRDL2_ENST00000534159.1_5'UTR|CHRDL2_ENST00000263671.5_Missense_Mutation_p.I226V	NM_001278473.1	NP_001265402.1	Q6WN34	CRDL2_HUMAN	chordin-like 2	226					cartilage development (GO:0051216)|cell differentiation (GO:0030154)|ossification (GO:0001503)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|prostate(1)|skin(2)	15	Hepatocellular(1;0.098)					TGGCGAGGGATGAAGCTCAGA	0.582													T|||	102	0.0203674	0.0756	0.0029	5008	,	,		14376	0.0		0.0	False		,,,				2504	0.0				p.I226V		Atlas-SNP	.											.	CHRDL2	47	.	0			c.A676G						PASS	.	T	VAL/ILE	246,4154	144.6+/-179.5	7,232,1961	65	62	63		676	-1.4	1	11	dbSNP_129	63	0,8586		0,0,4293	yes	missense	CHRDL2	NM_015424.3	29	7,232,6254	CC,CT,TT		0.0,5.5909,1.8943	benign	226/452	74415606	246,12740	2200	4293	6493	SO:0001583	missense	25884	exon7			GAGGGATGAAGCT	AL110168	CCDS8234.1, CCDS60893.1	11q13.4	2013-09-20			ENSG00000054938	ENSG00000054938			24168	protein-coding gene	gene with protein product		613127				12853144, 12975309	Standard	NM_015424		Approved	BNF1	uc001ovh.3	Q6WN34	OTTHUMG00000165623	ENST00000376332.3:c.676A>G	11.37:g.74415606T>C	ENSP00000365510:p.Ile226Val	223	0	0		229	102	0.445415	NM_015424	A5PKU9|Q6WN30|Q6WN31|Q6WN32|Q7Z5J3	Missense_Mutation	SNP	ENST00000376332.3	37		42	0.019230769230769232	41	0.08333333333333333	1	0.0027624309392265192	0	0.0	0	0.0	T	12.53	1.964712	0.34659	0.055909	0.0	ENSG00000054938	ENST00000263671;ENST00000376332;ENST00000376323;ENST00000393519;ENST00000528789	T;T;T	0.62105	0.94;0.98;0.05	5.39	-1.36	0.09085	.	0.361824	0.31472	N	0.007600	T	0.03871	0.0109	L	0.56769	1.78	0.27110	N	0.962407	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.09377	0.001;0.002;0.004	T	0.06232	-1.0838	10	0.19147	T	0.46	-7.7366	6.1715	0.20421	0.0:0.1511:0.3979:0.451	rs59876990	226;226;226	E9PCG7;Q6WN34;Q6WN34-2	.;CRDL2_HUMAN;.	V	226;226;112;110;226	ENSP00000263671:I226V;ENSP00000365510:I226V;ENSP00000431380:I226V	ENSP00000263671:I226V	I	-	1	0	CHRDL2	74093254	0.983000	0.35010	0.996000	0.52242	0.980000	0.70556	-0.008000	0.12788	-0.250000	0.09555	0.379000	0.24179	ATC	T|0.978;C|0.022	0.022	strong		0.582	CHRDL2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000385391.1			C	74415606	T	C	74415606	3	2	22	1	0	0	0	0	1	0	0	0	3376	1464	51	3	703	3	CHRDL2	11	74415606	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	618923	74415606	60590910	2517	5418											
MOGAT2	80168	hgsc.bcm.edu	37	chr11	75431049	75431049	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccccagccgagatctgcaCtgtgggcttcatagccctcc	6	9	9	17	1	2	1	1	0	1	1	4	2	4	1	5	1	3	2	5	1	1	2	rs35828061	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:75431049C>T	ENST00000198801.5	+	2	174	c.104C>T	c.(103-105)aCt>aTt	p.T35I	MOGAT2_ENST00000526712.1_5'UTR	NM_025098.2	NP_079374.2	Q3SYC2	MOGT2_HUMAN	monoacylglycerol O-acyltransferase 2	35					diacylglycerol biosynthetic process (GO:0006651)|glycerol metabolic process (GO:0006071)|intestinal absorption (GO:0050892)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	2-acylglycerol O-acyltransferase activity (GO:0003846)|acetyltransferase activity (GO:0016407)			NS(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	20	Ovarian(111;0.103)					GAGATCTGCACTGTGGGCTTC	0.592													C|||	122	0.024361	0.0908	0.0	5008	,	,		19209	0.0		0.002	False		,,,				2504	0.0				p.T35I		Atlas-SNP	.											MOGAT2,NS,carcinoma,+1,1	MOGAT2	49	1	0			c.C104T						PASS	.	C	ILE/THR	311,4089	169.8+/-200.3	8,295,1897	165	143	150		104	-7.3	0	11	dbSNP_126	150	6,8580	4.3+/-15.6	0,6,4287	yes	missense	MOGAT2	NM_025098.2	89	8,301,6184	TT,TC,CC		0.0699,7.0682,2.4411	benign	35/335	75431049	317,12669	2200	4293	6493	SO:0001583	missense	80168	exon2			TCTGCACTGTGGG	AY157608	CCDS8240.1	11q13.5	2008-02-05			ENSG00000166391	ENSG00000166391			23248	protein-coding gene	gene with protein product		610270				14970677	Standard	NM_025098		Approved	MGAT2, DGAT2L5, FLJ22644	uc010rru.2	Q3SYC2	OTTHUMG00000165341	ENST00000198801.5:c.104C>T	11.37:g.75431049C>T	ENSP00000198801:p.Thr35Ile	58	0	0		69	31	0.449275	NM_025098	A8K7I3|Q3SYC1|Q6ZQZ2|Q86UH6|Q9H630	Missense_Mutation	SNP	ENST00000198801.5	37	CCDS8240.1	37	0.01694139194139194	37	0.07520325203252033	0	0.0	0	0.0	0	0.0	C	2.919	-0.223665	0.06061	0.070682	6.99E-4	ENSG00000166391	ENST00000198801	T	0.09163	3.01	4.99	-7.32	0.01436	.	1.133530	0.06466	N	0.730377	T	0.00241	0.0007	N	0.04959	-0.14	0.20307	N	0.999911	B;B	0.06786	0.0;0.001	B;B	0.09377	0.0;0.004	T	0.42716	-0.9435	10	0.05833	T	0.94	2.7006	8.1687	0.31241	0.201:0.487:0.0:0.3121	rs35828061;rs61085918	35;35	Q3SYC2;Q3SYC2-3	MOGT2_HUMAN;.	I	35	ENSP00000198801:T35I	ENSP00000198801:T35I	T	+	2	0	MOGAT2	75108697	0.000000	0.05858	0.000000	0.03702	0.551000	0.35334	-2.562000	0.00920	-1.376000	0.02126	-1.300000	0.01332	ACT	C|0.974;T|0.026	0.026	strong		0.592	MOGAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383520.1	NM_025098		T	75431049	C	T	75431049	3	4	22	1	0	0	0	0	1	0	0	0	9704	565	20	2	110	2	MOGAT2	11	75431049	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1015443	75431049	59575467	2518	5419											
CAPN5	726	hgsc.bcm.edu	37	chr11	76796022	76796022	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aaggtgctcttcgaggacccCctcttccccgccactgacga	7	8	9	17	3	2	1	0	1	2	0	4	4	3	2	5	2	1	1	5	2	1	2	rs34236021	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:76796022C>A	ENST00000278559.3	+	2	279	c.90C>A	c.(88-90)ccC>ccA	p.P30P	CAPN5_ENST00000531028.1_Silent_p.P30P|CAPN5_ENST00000456580.2_Silent_p.P30P|CAPN5_ENST00000529629.1_Silent_p.P30P	NM_004055.4	NP_004046.2	O15484	CAN5_HUMAN	calpain 5	30	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				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						TCGAGGACCCCCTCTTCCCCG	0.637													c|||	176	0.0351438	0.1278	0.0072	5008	,	,		14704	0.0		0.002	False		,,,				2504	0.0				p.P30P		Atlas-SNP	.											.	CAPN5	67	.	0			c.C90A						PASS	.	C		424,3976	186.0+/-213.0	16,392,1792	33	37	36		90	0.5	1	11	dbSNP_126	36	9,8575	6.4+/-24.3	0,9,4283	no	coding-synonymous	CAPN5	NM_004055.4		16,401,6075	AA,AC,CC		0.1048,9.6364,3.3349		30/641	76796022	433,12551	2200	4292	6492	SO:0001819	synonymous_variant	726	exon2			GGACCCCCTCTTC		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.90C>A	11.37:g.76796022C>A		85	0	0		73	24	0.328767	NM_004055	O00263	Silent	SNP	ENST00000278559.3	37	CCDS8248.1																																																																																			C|0.973;A|0.027	0.027	strong		0.637	CAPN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382564.2	NM_004055		A	76796022	C	A	76796022	2	1	22	1	0	0	0	0	0	0	0	1	2631	610	22	4		4	CAPN5	11	76796022	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1364973	76796022	58210494	2519	5420											
MYO7A	4647	hgsc.bcm.edu	37	chr11	76922208	76922208	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctctgacaggagttgcccaaGtatctccgaggctaccacaa	11	8	9	13	1	2	1	0	1	2	0	3	3	2	2	3	2	2	3	3	2	4	3	rs111033209	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:76922208G>A	ENST00000409709.3	+	45	6335	c.6063G>A	c.(6061-6063)aaG>aaA	p.K2021K	MYO7A_ENST00000409619.2_Silent_p.K1972K|MYO7A_ENST00000605744.1_3'UTR|MYO7A_ENST00000458637.2_Silent_p.K1983K	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	2021	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						AGTTGCCCAAGTATCTCCGAG	0.617													G|||	155	0.0309505	0.1142	0.0043	5008	,	,		19584	0.0		0.001	False		,,,				2504	0.0				p.K2021K		Atlas-SNP	.											.	MYO7A	164	.	0			c.G6063A						PASS	.	G	,	352,3800		22,308,1746	19	23	22	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6063,5949	1.4	1	11	dbSNP_132	22	6,8398		0,6,4196	no	coding-synonymous,coding-synonymous	MYO7A	NM_000260.3,NM_001127180.1	,	22,314,5942	AA,AG,GG		0.0714,8.4778,2.8512	,	2021/2216,1983/2176	76922208	358,12198	2076	4202	6278	SO:0001819	synonymous_variant	4647	exon45			GCCCAAGTATCTC	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.6063G>A	11.37:g.76922208G>A		83	0	0		62	24	0.387097	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Silent	SNP	ENST00000409709.3	37	CCDS53683.1																																																																																			G|0.966;A|0.034	0.034	strong		0.617	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		A	76922208	G	A	76922208	2	1	22	1	0	0	0	0	0	0	0	1	10091	1020	36	2		2	MYO7A	11	76922208	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	126186	76922208	58084308	2520	5421											
RSF1	51773	hgsc.bcm.edu	37	chr11	77413223	77413223	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatattgccaccaaattcgaTcctttcaggctcctgtgcca	10	12	6	13	1	1	0	1	0	0	0	4	1	3	0	5	1	2	1	5	1	3	4	rs78433827	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:77413223T>C	ENST00000308488.6	-	6	1353	c.1051A>G	c.(1051-1053)Atc>Gtc	p.I351V	RSF1_ENST00000360355.2_Missense_Mutation_p.I320V|RSF1_ENST00000480887.1_Missense_Mutation_p.I99V			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	351	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)			CCAAATTCGATCCTTTCAGGC	0.398													T|||	29	0.00579073	0.0197	0.0043	5008	,	,		18269	0.0		0.0	False		,,,				2504	0.0				p.I351V		Atlas-SNP	.											RSF1,caecum,carcinoma,+2,1	RSF1	105	1	0			c.A1051G						PASS	.	T	VAL/ILE	110,4290	86.8+/-125.4	1,108,2091	149	147	148		1051	-0.2	0	11	dbSNP_131	148	2,8582	2.2+/-6.3	0,2,4290	yes	missense	RSF1	NM_016578.3	29	1,110,6381	CC,CT,TT		0.0233,2.5,0.8626	benign	351/1442	77413223	112,12872	2200	4292	6492	SO:0001583	missense	51773	exon6			ATTCGATCCTTTC	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.1051A>G	11.37:g.77413223T>C	ENSP00000311513:p.Ile351Val	256	1	0.00390625		288	162	0.5625	NM_016578	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Missense_Mutation	SNP	ENST00000308488.6	37	CCDS8253.1	9	0.004120879120879121	6	0.012195121951219513	3	0.008287292817679558	0	0.0	0	0.0	T	0.003	-2.567968	0.00133	0.025	2.33E-4	ENSG00000048649	ENST00000308488;ENST00000480887;ENST00000360355;ENST00000526324;ENST00000528095	D;D;D;D;T	0.84589	-1.85;-1.85;-1.87;-1.86;1.6	5.9	-0.187	0.13268	.	1.083410	0.07199	N	0.857181	T	0.41026	0.1141	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.41124	-0.9526	10	0.21014	T	0.42	3.5725	1.2586	0.01996	0.175:0.2018:0.3389:0.2843	.	351	Q96T23	RSF1_HUMAN	V	351;99;320;152;350	ENSP00000311513:I351V;ENSP00000434509:I99V;ENSP00000353511:I320V;ENSP00000432022:I152V;ENSP00000436408:I350V	ENSP00000311513:I351V	I	-	1	0	RSF1	77090871	0.000000	0.05858	0.014000	0.15608	0.387000	0.30353	-0.043000	0.12043	0.057000	0.16193	-0.313000	0.08912	ATC	T|0.992;C|0.008	0.008	strong		0.398	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578		C	77413223	T	C	77413223	3	2	22	1	0	0	0	0	1	0	0	0	13714	1435	50	3	3318	3	RSF1	11	77413223	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	491015	77413223	57593293	2521	5422											
THRSP	7069	hgsc.bcm.edu	37	chr11	77775157	77775157	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggaccatgggctgctgccgcGggaggagtggcaggccaagg	7	4	20	10	2	0	0	0	0	0	0	0	3	0	3	3	7	2	3	3	7	1	0			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:77775157G>A	ENST00000281030.2	+	1	251	c.230G>A	c.(229-231)cGg>cAg	p.R77Q	NDUFC2-KCTD14_ENST00000530054.1_Intron|NDUFC2-KCTD14_ENST00000528251.1_Intron	NM_003251.3	NP_003242.1	Q92748	THRSP_HUMAN	thyroid hormone responsive	77					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)			CTGCTGCCGCGGGAGGAGTGG	0.632																																					p.R77Q		Atlas-SNP	.											.	THRSP	18	.	0			c.G230A						PASS	.						66	70	68					11																	77775157		2200	4292	6492	SO:0001583	missense	7069	exon1			TGCCGCGGGAGGA	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.230G>A	11.37:g.77775157G>A	ENSP00000281030:p.Arg77Gln	128	0	0		120	62	0.516667	NM_003251	B2R4W7	Missense_Mutation	SNP	ENST00000281030.2	37	CCDS8256.1	.	.	.	.	.	.	.	.	.	.	G	9.274	1.046346	0.19748	.	.	ENSG00000151365	ENST00000281030	.	.	.	4.96	1.88	0.25563	.	0.320599	0.29328	N	0.012474	T	0.18045	0.0433	.	.	.	0.09310	N	1	B	0.25169	0.119	B	0.17722	0.019	T	0.09684	-1.0663	8	0.26408	T	0.33	-4.5778	3.7206	0.08454	0.3124:0.1858:0.5018:0.0	.	77	Q92748	THRSP_HUMAN	Q	77	.	ENSP00000281030:R77Q	R	+	2	0	THRSP	77452805	0.582000	0.26749	0.195000	0.23364	0.730000	0.41778	0.188000	0.17018	0.700000	0.31782	0.561000	0.74099	CGG	.	.	none		0.632	THRSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390939.1	NM_003251		A	77775157	G	A	77775157	3	1	22	1	0	0	0	0	1	0	0	0	15891	1116	39	1	232	1	THRSP	11	77775157	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	361934	77775157	57231359	2522	5423											
USP35	57558	hgsc.bcm.edu	37	chr11	77911224	77911224	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgtccggggagctgccttgTctgtgctcaagtacatgctc	5	12	12	12	2	2	0	1	0	1	0	5	1	3	1	2	2	5	4	2	2	2	2	rs115848453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:77911224T>C	ENST00000529308.1	+	5	1243	c.982T>C	c.(982-984)Tct>Cct	p.S328P	USP35_ENST00000441408.2_5'UTR|USP35_ENST00000526425.1_Missense_Mutation_p.S59P|USP35_ENST00000530267.1_Intron|USP35_ENST00000530535.1_Intron	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	328					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)			AGCTGCCTTGTCTGTGCTCAA	0.602													T|||	28	0.00559105	0.0212	0.0	5008	,	,		18945	0.0		0.0	False		,,,				2504	0.0				p.S328P		Atlas-SNP	.											.	USP35	179	.	0			c.T982C						PASS	.	T	PRO/SER	46,4006		1,44,1981	105	108	107		982	5	1	11	dbSNP_132	107	0,8330		0,0,4165	yes	missense	USP35	NM_020798.2	74	1,44,6146	CC,CT,TT		0.0,1.1352,0.3715	probably-damaging	328/1019	77911224	46,12336	2026	4165	6191	SO:0001583	missense	57558	exon5			GCCTTGTCTGTGC	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.982T>C	11.37:g.77911224T>C	ENSP00000431876:p.Ser328Pro	152	0	0		182	71	0.39011	NM_020798		Missense_Mutation	SNP	ENST00000529308.1	37	CCDS41693.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	T	9.269	1.045301	0.19748	0.011352	0.0	ENSG00000118369	ENST00000528910;ENST00000529308;ENST00000526425	T;T;T	0.68624	-0.34;-0.34;0.91	4.97	4.97	0.65823	Armadillo-like helical (1);	0.253449	0.28161	N	0.016373	T	0.40094	0.1103	N	0.13098	0.295	0.80722	D	1	D	0.53885	0.963	P	0.48425	0.577	T	0.50972	-0.8764	10	0.29301	T	0.29	-4.9719	14.8266	0.70117	0.0:0.0:0.0:1.0	.	328	Q9P2H5	UBP35_HUMAN	P	84;328;59	ENSP00000436001:S84P;ENSP00000431876:S328P;ENSP00000434942:S59P	ENSP00000434942:S59P	S	+	1	0	USP35	77588872	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.519000	0.45546	2.092000	0.63282	0.533000	0.62120	TCT	T|0.995;C|0.005	0.005	strong		0.602	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	XM_290527		C	77911224	T	C	77911224	3	2	22	1	0	0	0	0	1	0	0	0	17081	1667	58	3	996	3	USP35	11	77911224	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	136067	77911224	57095292	2523	5424											
USP35	57558	hgsc.bcm.edu	37	chr11	77921013	77921013	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaagcaccagaggggaaggAgagagggagaaagaggagga	18	0	20	3	0	0	4	0	0	0	4	0	11	0	8	1	6	1	1	1	6	3	0	rs78142936	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:77921013A>G	ENST00000529308.1	+	10	2373	c.2112A>G	c.(2110-2112)ggA>ggG	p.G704G	USP35_ENST00000441408.2_Silent_p.G290G|USP35_ENST00000526425.1_Silent_p.G435G|USP35_ENST00000530267.1_Silent_p.G272G|USP35_ENST00000530535.1_3'UTR	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	704	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)			gaggggaaggagagagggaga	0.547													A|||	394	0.0786741	0.2814	0.0231	5008	,	,		18681	0.0		0.005	False		,,,				2504	0.001				p.G704G		Atlas-SNP	.											.	USP35	179	.	0			c.A2112G						PASS	.	A		976,3208		101,774,1217	46	61	56		2112	0.8	0	11	dbSNP_131	56	25,8435		1,23,4206	no	coding-synonymous	USP35	NM_020798.2		102,797,5423	GG,GA,AA		0.2955,23.327,7.9168		704/1019	77921013	1001,11643	2092	4230	6322	SO:0001819	synonymous_variant	57558	exon10			GGAAGGAGAGAGG	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.2112A>G	11.37:g.77921013A>G		50	0	0		77	41	0.532468	NM_020798		Silent	SNP	ENST00000529308.1	37	CCDS41693.1																																																																																			A|0.935;G|0.065	0.065	strong		0.547	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	XM_290527		G	77921013	A	G	77921013	2	3	22	1	0	0	0	0	0	0	0	1	17081	291	11	3		3	USP35	11	77921013	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	9789	77921013	57085503	2524	5425											
NARS2	79731	hgsc.bcm.edu	37	chr11	78279744	78279744	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccacattttgccttttggaTggactttttatcagctgccc	6	17	7	11	0	1	0	1	0	0	0	2	2	2	2	3	2	3	1	3	2	1	7	rs60510975	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:78279744T>C	ENST00000281038.5	-	3	681	c.306A>G	c.(304-306)ccA>ccG	p.P102P	NARS2_ENST00000528850.1_5'UTR	NM_001243251.1|NM_024678.5	NP_001230180.1|NP_078954.4	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial (putative)	102					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)	GCCTTTTGGATGGACTTTTTA	0.333													T|||	225	0.0449281	0.1657	0.0072	5008	,	,		17073	0.0		0.001	False		,,,				2504	0.0				p.P102P		Atlas-SNP	.											NARS2,lower_third,carcinoma,-2,1	NARS2	62	1	0			c.A306G						PASS	.	T		604,3796	264.1+/-265.8	41,522,1637	182	174	177		306	-1.5	1	11	dbSNP_129	177	3,8579	3.0+/-9.4	0,3,4288	no	coding-synonymous	NARS2	NM_024678.5		41,525,5925	CC,CT,TT		0.035,13.7273,4.6757		102/478	78279744	607,12375	2200	4291	6491	SO:0001819	synonymous_variant	79731	exon3			TTTGGATGGACTT	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.306A>G	11.37:g.78279744T>C		185	0	0		193	97	0.502591	NM_024678	G3V178	Silent	SNP	ENST00000281038.5	37	CCDS8261.1																																																																																			T|0.960;C|0.040	0.040	strong		0.333	NARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391138.2	NM_024678		C	78279744	T	C	78279744	2	2	22	1	0	0	0	0	0	0	0	1	10180	1451	51	3		3	NARS2	11	78279744	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	358731	78279744	56726772	2525	5426											
ODZ4	26011	hgsc.bcm.edu	37	chr11	78387356	78387356	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagtggggctcagtctgcagCgccacctccatgccgttggc	6	8	13	14	2	2	0	1	0	1	0	3	0	3	0	4	3	3	3	4	3	1	1	rs59660398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:78387356C>T	ENST00000278550.7	-	30	5799	c.5337G>A	c.(5335-5337)gcG>gcA	p.A1779A		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1779					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)										CAGTCTGCAGCGCCACCTCCA	0.632													C|||	301	0.0601038	0.2224	0.0101	5008	,	,		15294	0.0		0.0	False		,,,				2504	0.0				p.A1779A		Atlas-SNP	.											.	.	.	.	0			c.G5337A						PASS	.	C		802,3514		60,682,1416	30	37	35		5337	-9.4	0.2	11	dbSNP_129	35	15,8485		0,15,4235	no	coding-synonymous	ODZ4	NM_001098816.2		60,697,5651	TT,TC,CC		0.1765,18.582,6.3748		1779/2770	78387356	817,11999	2158	4250	6408	SO:0001819	synonymous_variant	26011	exon30			CTGCAGCGCCACC	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.5337G>A	11.37:g.78387356C>T		67	0	0		88	39	0.443182	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Silent	SNP	ENST00000278550.7	37	CCDS44688.1																																																																																			C|0.963;T|0.037	0.037	strong		0.632	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			T	78387356	C	T	78387356	2	4	22	1	0	0	0	0	0	0	0	1	10846	755	27	1		1	ODZ4	11	78387356	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	107612	78387356	56619160	2526	5427											
C11orf82	220042	hgsc.bcm.edu	37	chr11	82644059	82644059	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tactcttaagaagactatcaGaatctcaccacacagggaga	16	8	7	10	0	3	4	2	0	2	4	4	5	3	4	1	1	1	0	1	1	5	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:82644059G>C	ENST00000533655.1	+	6	1891	c.1679G>C	c.(1678-1680)aGa>aCa	p.R560T	C11orf82_ENST00000528759.1_3'UTR|C11orf82_ENST00000430323.2_Missense_Mutation_p.R560T|C11orf82_ENST00000525361.1_Intron|C11orf82_ENST00000329143.3_Missense_Mutation_p.R259T	NM_145018.3	NP_659455.3	Q8IXT1	DDIAS_HUMAN		560					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						AAGACTATCAGAATCTCACCA	0.333																																					p.R560T		Atlas-SNP	.											.	C11orf82	71	.	0			c.G1679C						PASS	.						39	40	40					11																	82644059		2203	4297	6500	SO:0001583	missense	220042	exon6			CTATCAGAATCTC																												ENST00000533655.1:c.1679G>C	11.37:g.82644059G>C	ENSP00000435421:p.Arg560Thr	42	0	0		33	17	0.515152	NM_145018	Q96LK6|Q9H856	Missense_Mutation	SNP	ENST00000533655.1	37	CCDS8263.1	.	.	.	.	.	.	.	.	.	.	G	3.431	-0.116076	0.06881	.	.	ENSG00000165490	ENST00000430323;ENST00000533655;ENST00000329143	T;T;T	0.18338	2.48;2.48;2.22	5.73	0.776	0.18532	.	0.891385	0.09988	N	0.730156	T	0.20901	0.0503	L	0.57536	1.79	0.09310	N	1	D	0.56521	0.976	P	0.46685	0.524	T	0.17167	-1.0378	9	.	.	.	.	8.4326	0.32766	0.3684:0.0:0.6316:0.0	.	560	Q8IXT1	NOXIN_HUMAN	T	560;560;259	ENSP00000414687:R560T;ENSP00000435421:R560T;ENSP00000329930:R259T	.	R	+	2	0	C11orf82	82321707	0.000000	0.05858	0.001000	0.08648	0.144000	0.21451	-0.075000	0.11431	0.102000	0.17638	0.655000	0.94253	AGA	.	.	none		0.333	C11orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391936.1			C	82644059	G	C	82644059	3	2	22	1	0	0	0	0	1	0	0	0	1667	942	33	4	1693	4	C11orf82	11	82644059	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4256703	82644059	52362457	2527	5428											
DLG2	1740	hgsc.bcm.edu	37	chr11	83182726	83182726	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatcaagtcgtcattgatccGatccttcatgggccccagga	9	11	9	12	2	3	1	3	1	0	0	6	3	5	2	4	2	0	0	4	2	2	3	rs34857356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:83182726G>T	ENST00000532653.1	-	19	2322	c.2020C>A	c.(2020-2022)Cgg>Agg	p.R674R	DLG2_ENST00000330014.6_Silent_p.R613R|DLG2_ENST00000418306.2_Silent_p.R571R|DLG2_ENST00000524982.1_Silent_p.R688R|DLG2_ENST00000537455.1_Silent_p.R442R|DLG2_ENST00000376104.2_Silent_p.R797R|DLG2_ENST00000543673.1_Silent_p.R797R|DLG2_ENST00000398309.2_Silent_p.R692R|DLG2_ENST00000426717.2_Silent_p.R156R|DLG2_ENST00000404783.3_Silent_p.R170R|DLG2_ENST00000531015.1_Silent_p.R659R|DLG2_ENST00000376106.3_Silent_p.R156R|DLG2_ENST00000280241.8_Silent_p.R731R			Q14168	MPP2_HUMAN	discs, large homolog 2 (Drosophila)	389					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)				TCATTGATCCGATCCTTCATG	0.433													G|||	105	0.0209665	0.0688	0.013	5008	,	,		17636	0.0		0.005	False		,,,				2504	0.0				p.R797R		Atlas-SNP	.											DLG2_ENST00000418306,colon,carcinoma,+2,9	DLG2	448	9	0			c.C2389A						PASS	.	G	,,,,	221,3475		11,199,1638	67	65	65		2389,1711,466,2191,2074	4.2	1	11	dbSNP_126	65	11,8175		0,11,4082	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DLG2	NM_001142699.1,NM_001142700.1,NM_001142702.1,NM_001206769.1,NM_001364.3	,,,,	11,210,5720	TT,TG,GG		0.1344,5.9794,1.9525	,,,,	797/976,571/750,156/335,731/910,692/871	83182726	232,11650	1848	4093	5941	SO:0001819	synonymous_variant	1740	exon24			TGATCCGATCCTT	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.2020C>A	11.37:g.83182726G>T		144	0	0		111	60	0.540541	NM_001142699	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Silent	SNP	ENST00000532653.1	37																																																																																				G|0.984;T|0.016	0.016	strong		0.433	DLG2-009	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000259253.2	NM_001364		T	83182726	G	T	83182726	2	4	22	1	0	0	0	0	0	0	0	1	4557	1057	37	4		4	DLG2	11	83182726	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	538667	83182726	51823790	2528	5429											
SYTL2	54843	hgsc.bcm.edu	37	chr11	85435742	85435742	+	Intron	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gttattaacggagcctcggcCttttctactgtttcttttaa	7	18	7	9	2	2	0	0	0	2	0	3	1	2	1	2	2	3	2	2	2	4	8	rs146372321	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:85435742C>T	ENST00000528231.1	-	7	1737				SYTL2_ENST00000316356.4_Intron|SYTL2_ENST00000525423.1_Silent_p.K586K|SYTL2_ENST00000527523.1_Intron|SYTL2_ENST00000354566.3_Silent_p.K586K|SYTL2_ENST00000389960.4_Intron|SYTL2_ENST00000524452.1_Intron|SYTL2_ENST00000359152.5_Silent_p.K1110K	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)		GAGCCTCGGCCTTTTCTACTG	0.443													C|||	30	0.00599042	0.0219	0.0014	5008	,	,		18228	0.0		0.0	False		,,,				2504	0.0				p.K586K		Atlas-SNP	.											.	SYTL2	231	.	0			c.G1758A						PASS	.	C	,,,,	79,4327	62.3+/-99.4	0,79,2124	67	65	66		,,,1758,1758	1	0.1	11	dbSNP_134	66	0,8598		0,0,4299	no	intron,intron,intron,coding-synonymous,coding-synonymous	SYTL2	NM_001162951.1,NM_001162953.1,NM_032943.3,NM_206927.2,NM_206928.2	,,,,	0,79,6423	TT,TC,CC		0.0,1.793,0.6075	,,,,	,,,586/1273,586/1257	85435742	79,12925	2203	4299	6502	SO:0001627	intron_variant	54843	exon1			CTCGGCCTTTTCT	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+3196G>A	11.37:g.85435742C>T		117	0	0		117	47	0.401709	NM_206927	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Silent	SNP	ENST00000528231.1	37	CCDS53688.1																																																																																			C|0.995;T|0.005	0.005	strong		0.443	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927		T	85435742	C	T	85435742	1	4	22	0	1	0	0	0	0	0	0	0	15498	680	24	2		2	SYTL2	11	85435742	Intron	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2253016	85435742	49570774	2529	5430											
GRM5	2915	hgsc.bcm.edu	37	chr11	88337922	88337922	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cattctcatcgaataggatcGtatctccagaaaccccagta	13	10	6	12	2	2	1	1	0	2	1	6	3	2	2	3	1	1	2	3	1	5	4	rs61741175	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:88337922G>A	ENST00000305447.4	-	4	1507	c.1358C>T	c.(1357-1359)aCg>aTg	p.T453M	GRM5_ENST00000393297.1_Missense_Mutation_p.T453M|GRM5_ENST00000418177.2_Missense_Mutation_p.T453M|GRM5_ENST00000455756.2_Missense_Mutation_p.T453M|GRM5_ENST00000305432.5_Missense_Mutation_p.T453M	NM_001143831.2	NP_001137303.1	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5	453					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)	GAATAGGATCGTATCTCCAGA	0.448													G|||	136	0.0271565	0.0946	0.0144	5008	,	,		20219	0.0		0.001	False		,,,				2504	0.0				p.T453M		Atlas-SNP	.											GRM5_ENST00000418177,right_upper_lobe,carcinoma,+1,2	GRM5	414	2	0			c.C1358T						PASS	.	G	MET/THR,MET/THR	352,4050	181.9+/-209.8	14,324,1863	58	60	59		1358,1358	2.1	1	11	dbSNP_129	59	2,8596	2.2+/-6.3	0,2,4297	yes	missense,missense	GRM5	NM_000842.3,NM_001143831.2	81,81	14,326,6160	AA,AG,GG		0.0233,7.9964,2.7231	benign,benign	453/1181,453/1213	88337922	354,12646	2201	4299	6500	SO:0001583	missense	2915	exon5			AGGATCGTATCTC	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.1358C>T	11.37:g.88337922G>A	ENSP00000306138:p.Thr453Met	49	0	0		54	28	0.518519	NM_000842	Q6J164	Missense_Mutation	SNP	ENST00000305447.4	37	CCDS44694.1	47	0.02152014652014652	43	0.08739837398373984	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	G	9.419	1.082463	0.20309	0.079964	2.33E-4	ENSG00000168959	ENST00000418177;ENST00000455756;ENST00000305432;ENST00000305447;ENST00000393297	D;D;D;D;D	0.82433	-1.61;-1.61;-1.61;-1.61;-1.61	5.77	2.13	0.27403	Extracellular ligand-binding receptor (1);	0.320592	0.41294	N	0.000913	T	0.10121	0.0248	L	0.45137	1.4	0.22479	N	0.999063	B;B	0.19935	0.04;0.002	B;B	0.15484	0.013;0.002	T	0.12041	-1.0563	9	.	.	.	.	9.7316	0.40363	0.7425:0.0:0.2575:0.0	.	453;453	P41594-2;P41594	.;GRM5_HUMAN	M	453	ENSP00000402912:T453M;ENSP00000405690:T453M;ENSP00000305905:T453M;ENSP00000306138:T453M;ENSP00000376975:T453M	.	T	-	2	0	GRM5	87977570	0.706000	0.27856	1.000000	0.80357	0.863000	0.49368	0.371000	0.20450	0.461000	0.27071	-1.721000	0.00707	ACG	G|0.972;A|0.028	0.028	strong		0.448	GRM5-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259226.1	NM_000842		A	88337922	G	A	88337922	3	1	22	1	0	0	0	0	1	0	0	0	6809	1145	40	1	2304	1	GRM5	11	88337922	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2902180	88337922	46668594	2530	5431											
GRM5	2915	hgsc.bcm.edu	37	chr11	88338074	88338074	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	taggccatcgaatagatggcGttgatcacaaatcccatttt	12	12	8	9	2	1	2	1	1	0	1	3	3	2	2	2	2	0	1	2	2	4	5	rs61745770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:88338074G>A	ENST00000305447.4	-	4	1355	c.1206C>T	c.(1204-1206)aaC>aaT	p.N402N	GRM5_ENST00000393297.1_Silent_p.N402N|GRM5_ENST00000418177.2_Silent_p.N402N|GRM5_ENST00000455756.2_Silent_p.N402N|GRM5_ENST00000305432.5_Silent_p.N402N	NM_001143831.2	NP_001137303.1	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5	402					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)	AATAGATGGCGTTGATCACAA	0.458													g|||	136	0.0271565	0.0946	0.0144	5008	,	,		20660	0.0		0.001	False		,,,				2504	0.0				p.N402N		Atlas-SNP	.											.	GRM5	414	.	0			c.C1206T						PASS	.	A	,	353,4049	183.3+/-210.9	14,325,1862	101	86	91		1206,1206	-2.1	1	11	dbSNP_129	91	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	GRM5	NM_000842.3,NM_001143831.2	,	14,325,6161	AA,AG,GG		0.0,8.0191,2.7154	,	402/1181,402/1213	88338074	353,12647	2201	4299	6500	SO:0001819	synonymous_variant	2915	exon5			GATGGCGTTGATC	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.1206C>T	11.37:g.88338074G>A		65	0	0		71	40	0.56338	NM_000842	Q6J164	Silent	SNP	ENST00000305447.4	37	CCDS44694.1																																																																																			G|0.971;A|0.029	0.029	strong		0.458	GRM5-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259226.1	NM_000842		A	88338074	G	A	88338074	2	1	22	1	0	0	0	0	0	0	0	1	6809	1136	40	1		1	GRM5	11	88338074	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	152	88338074	46668442	2531	5432											
FAT3	120114	hgsc.bcm.edu	37	chr11	92534968	92534968	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cttcgcgcaggaagtgtaccGagggaatgtgaaggagagcg	11	6	17	7	4	0	2	0	1	0	1	1	6	0	4	1	3	2	2	1	3	4	2	rs370539148	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:92534968G>A	ENST00000298047.6	+	9	8806	c.8789G>A	c.(8788-8790)cGa>cAa	p.R2930Q	FAT3_ENST00000525166.1_Missense_Mutation_p.R2780Q|FAT3_ENST00000409404.2_Missense_Mutation_p.R2930Q			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2930	Cadherin 27. {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)				GAAGTGTACCGAGGGAATGTG	0.552										TCGA Ovarian(4;0.039)			G|||	4	0.000798722	0.003	0.0	5008	,	,		21033	0.0		0.0	False		,,,				2504	0.0				p.R2930Q		Atlas-SNP	.											.	FAT3	1822	.	0			c.G8789A						PASS	.	G	GLN/ARG	7,4033		0,7,2013	94	93	93		8789	5.1	1	11		93	0,8374		0,0,4187	no	missense	FAT3	NM_001008781.2	43	0,7,6200	AA,AG,GG		0.0,0.1733,0.0564	possibly-damaging	2930/4558	92534968	7,12407	2020	4187	6207	SO:0001583	missense	120114	exon9			TGTACCGAGGGAA	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.8789G>A	11.37:g.92534968G>A	ENSP00000298047:p.Arg2930Gln	98	0	0		90	49	0.544444	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	G	16.93	3.257586	0.59321	0.001733	0.0	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.01725	4.67;4.67;4.67	6.04	5.08	0.68730	.	.	.	.	.	T	0.02455	0.0075	N	0.20766	0.605	0.80722	D	1	D	0.59357	0.985	P	0.52267	0.694	T	0.71206	-0.4661	9	0.24483	T	0.36	.	10.4452	0.44490	0.157:0.0:0.843:0.0	.	2930	Q8TDW7-3	.	Q	2930;2930;2780	ENSP00000298047:R2930Q;ENSP00000387040:R2930Q;ENSP00000432586:R2780Q	ENSP00000298047:R2930Q	R	+	2	0	FAT3	92174616	1.000000	0.71417	1.000000	0.80357	0.719000	0.41307	1.983000	0.40648	1.433000	0.47394	0.563000	0.77884	CGA	.	.	weak		0.552	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		A	92534968	G	A	92534968	3	1	22	1	0	0	0	0	1	0	0	0	5699	1058	37	1	8823	1	FAT3	11	92534968	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4196894	92534968	42471548	2532	5433											
FAT3	120114	hgsc.bcm.edu	37	chr11	92538351	92538351	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggaaggtttgctctgggcCtggtgcaaagtgagtggaag	9	9	18	5	0	1	1	0	1	1	0	1	4	1	3	1	5	2	3	1	5	3	1	rs56843577	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:92538351C>T	ENST00000298047.6	+	10	8946	c.8929C>T	c.(8929-8931)Ctg>Ttg	p.L2977L	FAT3_ENST00000525166.1_Silent_p.L2827L|FAT3_ENST00000409404.2_Silent_p.L2977L			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2977	Cadherin 27. {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)				TGCTCTGGGCCTGGTGCAAAG	0.428										TCGA Ovarian(4;0.039)			C|||	81	0.0161741	0.059	0.0043	5008	,	,		19268	0.0		0.0	False		,,,				2504	0.0				p.L2977L		Atlas-SNP	.											.	FAT3	1822	.	0			c.C8929T						PASS	.	C		197,3563		4,189,1687	80	81	81		8929	5.1	1	11	dbSNP_129	81	0,8218		0,0,4109	no	coding-synonymous	FAT3	NM_001008781.2		4,189,5796	TT,TC,CC		0.0,5.2394,1.6447		2977/4558	92538351	197,11781	1880	4109	5989	SO:0001819	synonymous_variant	120114	exon10			CTGGGCCTGGTGC	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.8929C>T	11.37:g.92538351C>T		172	0	0		178	81	0.455056	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				C|0.988;T|0.012	0.012	strong		0.428	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92538351	C	T	92538351	2	4	22	1	0	0	0	0	0	0	0	1	5699	680	24	2		2	FAT3	11	92538351	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3383	92538351	42468165	2533	5434											
FAT3	120114	hgsc.bcm.edu	37	chr11	92538422	92538422	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaacaggacatttactttctCaatatcactgccactgatgg	12	12	7	10	0	2	1	2	1	1	0	3	3	2	2	1	2	3	0	1	2	4	4	rs59542280	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:92538422C>T	ENST00000298047.6	+	10	9017	c.9000C>T	c.(8998-9000)ctC>ctT	p.L3000L	FAT3_ENST00000525166.1_Silent_p.L2850L|FAT3_ENST00000409404.2_Silent_p.L3000L			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3000	Cadherin 27. {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)				TTTACTTTCTCAATATCACTG	0.488										TCGA Ovarian(4;0.039)			C|||	78	0.0155751	0.0567	0.0043	5008	,	,		16467	0.0		0.0	False		,,,				2504	0.0				p.L3000L		Atlas-SNP	.											.	FAT3	1822	.	0			c.C9000T						PASS	.	C		199,3665		5,189,1738	82	84	83		9000	4.2	1	11	dbSNP_129	83	0,8304		0,0,4152	no	coding-synonymous	FAT3	NM_001008781.2		5,189,5890	TT,TC,CC		0.0,5.1501,1.6354		3000/4558	92538422	199,11969	1932	4152	6084	SO:0001819	synonymous_variant	120114	exon10			CTTTCTCAATATC	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.9000C>T	11.37:g.92538422C>T		150	0	0		140	65	0.464286	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				C|0.988;T|0.012	0.012	strong		0.488	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92538422	C	T	92538422	2	4	22	1	0	0	0	0	0	0	0	1	5699	813	29	2		2	FAT3	11	92538422	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	71	92538422	42468094	2534	5435											
FAT3	120114	hgsc.bcm.edu	37	chr11	92568196	92568196	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcccaagttcagccaagaCgtctacagtgcggttatcag	10	9	9	13	2	3	1	2	0	1	1	4	1	4	1	3	1	3	2	3	1	4	3	rs374591402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:92568196C>T	ENST00000298047.6	+	14	10049	c.10032C>T	c.(10030-10032)gaC>gaT	p.D3344D	FAT3_ENST00000525166.1_Silent_p.D3194D|FAT3_ENST00000409404.2_Silent_p.D3344D			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3344	Cadherin 31. {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)				TCAGCCAAGACGTCTACAGTG	0.527										TCGA Ovarian(4;0.039)			C|||	4	0.000798722	0.0023	0.0	5008	,	,		17326	0.0		0.0	False		,,,				2504	0.001				p.D3344D		Atlas-SNP	.											.	FAT3	1822	.	0			c.C10032T						PASS	.	C		7,3905		0,7,1949	55	55	55		10032	-1.9	1	11		55	0,8324		0,0,4162	no	coding-synonymous	FAT3	NM_001008781.2		0,7,6111	TT,TC,CC		0.0,0.1789,0.0572		3344/4558	92568196	7,12229	1956	4162	6118	SO:0001819	synonymous_variant	120114	exon14			CCAAGACGTCTAC	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.10032C>T	11.37:g.92568196C>T		195	0	0		150	83	0.553333	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				.	.	weak		0.527	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92568196	C	T	92568196	2	4	22	1	0	0	0	0	0	0	0	1	5699	535	19	1		1	FAT3	11	92568196	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	29774	92568196	42438320	2535	5436											
FAT3	120114	hgsc.bcm.edu	37	chr11	92616006	92616006	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgcaactgcacgccgggctaCgtgggccagtactgcgggct	6	7	15	13	4	0	0	0	0	0	0	0	0	0	0	2	3	6	5	2	3	3	2	rs58474174	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:92616006C>T	ENST00000298047.6	+	23	12401	c.12384C>T	c.(12382-12384)taC>taT	p.Y4128Y	FAT3_ENST00000525166.1_Silent_p.Y3978Y|FAT3_ENST00000533797.1_Silent_p.Y463Y|FAT3_ENST00000409404.2_Silent_p.Y4128Y			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	4128	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				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)				CGCCGGGCTACGTGGGCCAGT	0.632										TCGA Ovarian(4;0.039)			C|||	182	0.0363419	0.1309	0.0115	5008	,	,		15044	0.0		0.001	False		,,,				2504	0.0				p.Y4128Y		Atlas-SNP	.											.	FAT3	1822	.	0			c.C12384T						PASS	.	C		392,3806		19,354,1726	62	79	73		12384	1.9	1	11	dbSNP_129	73	2,8424		0,2,4211	no	coding-synonymous	FAT3	NM_001008781.2		19,356,5937	TT,TC,CC		0.0237,9.3378,3.121		4128/4558	92616006	394,12230	2099	4213	6312	SO:0001819	synonymous_variant	120114	exon23			GGGCTACGTGGGC	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.12384C>T	11.37:g.92616006C>T		140	0	0		115	47	0.408696	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				C|0.976;T|0.024	0.024	strong		0.632	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92616006	C	T	92616006	2	4	22	1	0	0	0	0	0	0	0	1	5699	547	19	1		1	FAT3	11	92616006	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	47810	92616006	42390510	2536	5437											
FAT3	120114	hgsc.bcm.edu	37	chr11	92624276	92624276	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	actcagcatcagactcaagtGtagacatcacatcttgggta	13	10	8	10	0	5	2	4	0	1	2	5	2	5	2	0	1	1	3	0	1	3	3	rs371790138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:92624276G>A	ENST00000298047.6	+	27	13784	c.13767G>A	c.(13765-13767)gtG>gtA	p.V4589V	FAT3_ENST00000525166.1_Silent_p.V4439V|FAT3_ENST00000533797.1_Silent_p.V892V|FAT3_ENST00000409404.2_Silent_p.V4557V			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	4589					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)				AGACTCAAGTGTAGACATCAC	0.507										TCGA Ovarian(4;0.039)			G|||	3	0.000599042	0.0023	0.0	5008	,	,		20727	0.0		0.0	False		,,,				2504	0.0				p.V4557V		Atlas-SNP	.											.	FAT3	1822	.	0			c.G13671A						PASS	.	G		9,4135		0,9,2063	43	45	44		13671	3.8	1	11		44	0,8398		0,0,4199	no	coding-synonymous	FAT3	NM_001008781.2		0,9,6262	AA,AG,GG		0.0,0.2172,0.0718		4557/4558	92624276	9,12533	2072	4199	6271	SO:0001819	synonymous_variant	120114	exon25			TCAAGTGTAGACA	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.13767G>A	11.37:g.92624276G>A		60	0	0		48	24	0.5	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				.	.	weak		0.507	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		A	92624276	G	A	92624276	2	1	22	1	0	0	0	0	0	0	0	1	5699	1364	48	2		2	FAT3	11	92624276	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	8270	92624276	42382240	2537	5438											
HEPHL1	341208	hgsc.bcm.edu	37	chr11	93844722	93844722	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gacaacaggattccttactcCaccacatctcctggagtggc	10	9	8	14	0	1	0	0	0	1	0	4	3	3	2	4	3	2	0	4	3	2	2	rs76467816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:93844722C>T	ENST00000315765.9	+	19	3236	c.3228C>T	c.(3226-3228)tcC>tcT	p.S1076S		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	1076	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)				TTCCTTACTCCACCACATCTC	0.428													C|||	147	0.029353	0.1067	0.0086	5008	,	,		20649	0.0		0.0	False		,,,				2504	0.0				p.S1076S		Atlas-SNP	.											.	HEPHL1	144	.	0			c.C3228T						PASS	.	C		310,3668		15,280,1694	48	47	48		3228	-4	0.9	11	dbSNP_131	48	1,8347		0,1,4173	no	coding-synonymous	HEPHL1	NM_001098672.1		15,281,5867	TT,TC,CC		0.012,7.7929,2.5231		1076/1160	93844722	311,12015	1989	4174	6163	SO:0001819	synonymous_variant	341208	exon19			TTACTCCACCACA	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.3228C>T	11.37:g.93844722C>T		205	0	0		194	193	0.994845	NM_001098672	Q3C1W7	Silent	SNP	ENST00000315765.9	37	CCDS44710.1																																																																																			C|0.979;T|0.021	0.021	strong		0.428	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947		T	93844722	C	T	93844722	2	4	22	1	0	0	0	0	0	0	0	1	7064	581	21	2		2	HEPHL1	11	93844722	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1220446	93844722	41161794	2538	5439											
PANX1	24145	hgsc.bcm.edu	37	chr11	93913392	93913392	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgtctgcagagatgagagaGgagcaggggaaccagacggc	13	4	17	7	1	1	4	0	1	1	3	1	8	1	6	1	4	3	2	1	4	1	0	rs74549886	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:93913392G>T	ENST00000227638.3	+	4	1555	c.1170G>T	c.(1168-1170)gaG>gaT	p.E390D	PANX1_ENST00000436171.2_Missense_Mutation_p.E390D	NM_015368.3	NP_056183.2	Q96RD7	PANX1_HUMAN	pannexin 1	390					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)	AGATGAGAGAGGAGCAGGGGA	0.532													G|||	180	0.0359425	0.1286	0.0115	5008	,	,		17647	0.0		0.002	False		,,,				2504	0.0				p.E390D		Atlas-SNP	.											.	PANX1	38	.	0			c.G1170T						PASS	.	G	ASP/GLU	484,3918	225.9+/-241.6	21,442,1738	68	64	66		1170	1	0	11	dbSNP_131	66	6,8590	4.3+/-15.6	0,6,4292	yes	missense	PANX1	NM_015368.3	45	21,448,6030	TT,TG,GG		0.0698,10.995,3.7698	benign	390/427	93913392	490,12508	2201	4298	6499	SO:0001583	missense	24145	exon4			GAGAGAGGAGCAG	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.1170G>T	11.37:g.93913392G>T	ENSP00000227638:p.Glu390Asp	136	0	0		129	56	0.434109	NM_015368	O75968|Q543A0|Q6UW26|Q96AM9|Q96L77|Q96RS5	Missense_Mutation	SNP	ENST00000227638.3	37	CCDS8296.1	62	0.028388278388278388	57	0.11585365853658537	5	0.013812154696132596	0	0.0	0	0.0	G	12.51	1.958933	0.34565	0.10995	6.98E-4	ENSG00000110218	ENST00000227638;ENST00000436171	T;T	0.19250	2.17;2.16	5.22	0.965	0.19661	.	1.495480	0.03723	N	0.252178	T	0.00300	0.0009	M	0.67953	2.075	0.09310	N	1	B;B	0.32573	0.376;0.29	B;B	0.29785	0.049;0.107	T	0.16600	-1.0397	10	0.39692	T	0.17	-15.6543	4.6163	0.12428	0.3593:0.2803:0.3603:0.0	.	390;390	Q96RD7;Q96RD7-2	PANX1_HUMAN;.	D	390	ENSP00000227638:E390D;ENSP00000411461:E390D	ENSP00000227638:E390D	E	+	3	2	PANX1	93553040	0.059000	0.20769	0.005000	0.12908	0.026000	0.11368	0.183000	0.16919	0.606000	0.29965	0.655000	0.94253	GAG	G|0.968;T|0.032	0.032	strong		0.532	PANX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396121.1	NM_015368		T	93913392	G	T	93913392	3	4	22	1	0	0	0	0	1	0	0	0	11429	991	35	4	1184	4	PANX1	11	93913392	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	68670	93913392	41093124	2539	5440											
PIWIL4	143689	hgsc.bcm.edu	37	chr11	94320300	94320300	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gctgatgtgagttacaaagtCctccggaatgagacggttct	10	11	12	8	2	1	3	0	3	1	1	3	5	3	4	2	2	1	3	2	2	3	2	rs145516372	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:94320300C>T	ENST00000299001.6	+	7	1012	c.801C>T	c.(799-801)gtC>gtT	p.V267V	RP11-867G2.8_ENST00000536540.1_RNA|RP11-867G2.8_ENST00000537874.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	267					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)				GTTACAAAGTCCTCCGGAATG	0.433													C|||	51	0.0101837	0.0371	0.0029	5008	,	,		18230	0.0		0.0	False		,,,				2504	0.0				p.V267V		Atlas-SNP	.											.	PIWIL4	70	.	0			c.C801T						PASS	.	C		116,4286	88.7+/-127.4	2,112,2087	188	191	190		801	1.8	0.9	11	dbSNP_134	190	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous	PIWIL4	NM_152431.2		2,113,6384	TT,TC,CC		0.0116,2.6352,0.9001		267/853	94320300	117,12881	2201	4298	6499	SO:0001819	synonymous_variant	143689	exon7			CAAAGTCCTCCGG	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.801C>T	11.37:g.94320300C>T		119	0	0		124	47	0.379032	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Silent	SNP	ENST00000299001.6	37	CCDS31656.1																																																																																			C|0.992;T|0.008	0.008	strong		0.433	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431		T	94320300	C	T	94320300	2	4	22	1	0	0	0	0	0	0	0	1	11969	842	30	2		2	PIWIL4	11	94320300	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	406908	94320300	40686216	2540	5441											
AMOTL1	154810	hgsc.bcm.edu	37	chr11	94602457	94602457	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcctccatagcctccactacGgcagccagcagtgcccacgc	8	6	8	19	2	0	0	0	0	0	0	3	0	3	0	6	1	5	2	6	1	2	2	rs181764487	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:94602457G>A	ENST00000433060.2	+	12	2724	c.2583G>A	c.(2581-2583)acG>acA	p.T861T	AMOTL1_ENST00000317837.9_Silent_p.T448T|AMOTL1_ENST00000317829.8_Silent_p.T811T	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	861					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)				CCTCCACTACGGCAGCCAGCA	0.632													G|||	20	0.00399361	0.0106	0.0072	5008	,	,		14338	0.0		0.0	False		,,,				2504	0.001				p.T861T		Atlas-SNP	.											AMOTL1,NS,carcinoma,+1,2	AMOTL1	95	2	0			c.G2583A						PASS	.	G		24,4298		0,24,2137	25	34	31		2583	-10.3	0	11		31	2,8548		0,2,4273	no	coding-synonymous	AMOTL1	NM_130847.2		0,26,6410	AA,AG,GG		0.0234,0.5553,0.202		861/957	94602457	26,12846	2161	4275	6436	SO:0001819	synonymous_variant	154810	exon12			CACTACGGCAGCC	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.2583G>A	11.37:g.94602457G>A		120	0	0		139	69	0.496403	NM_130847	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Silent	SNP	ENST00000433060.2	37	CCDS44712.1																																																																																			G|0.995;A|0.005	0.005	strong		0.632	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847		A	94602457	G	A	94602457	2	1	22	1	0	0	0	0	0	0	0	1	583	1103	39	1		1	AMOTL1	11	94602457	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	282157	94602457	40404059	2541	5442											
ENDOD1	23052	hgsc.bcm.edu	37	chr11	94862340	94862340	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgtggtgtgttaccaagcAggtgattaatggcatagaaa	12	11	12	6	0	0	2	0	1	0	1	0	2	0	2	2	3	2	3	2	3	5	3	rs188091415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:94862340A>T	ENST00000278505.4	+	2	1218	c.1100A>T	c.(1099-1101)cAg>cTg	p.Q367L		NM_015036.2	NP_055851.1	O94919	ENDD1_HUMAN	endonuclease domain containing 1	367						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)				GTTACCAAGCAGGTGATTAAT	0.438													A|||	5	0.000998403	0.0038	0.0	5008	,	,		21650	0.0		0.0	False		,,,				2504	0.0				p.Q367L		Atlas-SNP	.											.	ENDOD1	26	.	0			c.A1100T						PASS	.	A	LEU/GLN	12,3830		0,12,1909	114	102	106		1100	4.9	1	11		106	0,8256		0,0,4128	yes	missense	ENDOD1	NM_015036.2	113	0,12,6037	TT,TA,AA		0.0,0.3123,0.0992	possibly-damaging	367/501	94862340	12,12086	1921	4128	6049	SO:0001583	missense	23052	exon2			CCAAGCAGGTGAT	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.1100A>T	11.37:g.94862340A>T	ENSP00000278505:p.Gln367Leu	165	0	0		145	89	0.613793	NM_015036	A8K6K8|Q6GQY5|Q8TAQ8	Missense_Mutation	SNP	ENST00000278505.4	37	CCDS41699.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	13.12	2.141283	0.37825	0.003123	0.0	ENSG00000149218	ENST00000278505	T	0.33865	1.39	6.03	4.88	0.63580	.	0.171913	0.40469	N	0.001086	T	0.26991	0.0661	M	0.67953	2.075	0.32644	N	0.52035	B	0.18461	0.028	B	0.17433	0.018	T	0.44360	-0.9333	10	0.87932	D	0	-24.9899	6.2791	0.20997	0.7766:0.0:0.0796:0.1438	.	367	O94919	ENDD1_HUMAN	L	367	ENSP00000278505:Q367L	ENSP00000278505:Q367L	Q	+	2	0	ENDOD1	94501988	0.987000	0.35691	0.993000	0.49108	0.553000	0.35397	1.425000	0.34859	1.066000	0.40716	0.455000	0.32223	CAG	A|0.998;T|0.002	0.002	strong		0.438	ENDOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396545.1	NM_015036		T	94862340	A	T	94862340	3	4	22	1	0	0	0	0	1	0	0	0	5116	188	7	5	1106	5	ENDOD1	11	94862340	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	259883	94862340	40144176	2542	5443											
CNTN5	53942	hgsc.bcm.edu	37	chr11	100226900	100226900	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactctctctccacatcttcGtcatcagtcaccttgctctt	6	15	3	17	1	7	0	3	0	4	0	10	0	7	0	2	0	1	1	2	0	0	3	rs34539243	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:100226900G>A	ENST00000524871.1	+	25	3542	c.3252G>A	c.(3250-3252)tcG>tcA	p.S1084S	CNTN5_ENST00000279463.3_Silent_p.S1084S|CNTN5_ENST00000524560.1_3'UTR|CNTN5_ENST00000528682.1_Silent_p.S1084S|CNTN5_ENST00000418526.2_Silent_p.S1010S	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	1084					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)		CCACATCTTCGTCATCAGTCA	0.418													G|||	88	0.0175719	0.0651	0.0	5008	,	,		20062	0.0		0.002	False		,,,				2504	0.0				p.S1084S		Atlas-SNP	.											.	CNTN5	324	.	0			c.G3252A						PASS	.	G	,	209,3773		7,195,1789	143	139	140		3252,3030	-4.7	0	11	dbSNP_126	140	5,8327		0,5,4161	no	coding-synonymous,coding-synonymous	CNTN5	NM_014361.3,NM_175566.2	,	7,200,5950	AA,AG,GG		0.06,5.2486,1.7379	,	1084/1101,1010/1027	100226900	214,12100	1991	4166	6157	SO:0001819	synonymous_variant	53942	exon24			ATCTTCGTCATCA	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.3252G>A	11.37:g.100226900G>A		115	0	0		94	56	0.595745	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Silent	SNP	ENST00000524871.1	37	CCDS53696.1																																																																																			G|0.988;A|0.012	0.012	strong		0.418	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361		A	100226900	G	A	100226900	2	1	22	1	0	0	0	0	0	0	0	1	3646	1132	40	1		1	CNTN5	11	100226900	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5364560	100226900	34779616	2543	5444											
KIAA1377	57562	hgsc.bcm.edu	37	chr11	101829070	101829070	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaggaaactcagaaactcctCgaagatcaacatctaagcaa	18	6	7	10	1	3	2	2	0	1	2	5	5	4	3	1	1	4	1	1	1	6	1	rs61742070	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:101829070C>T	ENST00000263468.8	+	5	948	c.678C>T	c.(676-678)ctC>ctT	p.L226L	KIAA1377_ENST00000537689.1_Silent_p.L27L	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	226										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)		AGAAACTCCTCGAAGATCAAC	0.343													C|||	49	0.00978435	0.0371	0.0	5008	,	,		18452	0.0		0.0	False		,,,				2504	0.0				p.L226L		Atlas-SNP	.											.	KIAA1377	111	.	0			c.C678T						PASS	.	C		129,4277	90.2+/-128.9	0,129,2074	105	113	110		678	0.7	1	11	dbSNP_129	110	0,8598		0,0,4299	no	coding-synonymous	KIAA1377	NM_020802.2		0,129,6373	TT,TC,CC		0.0,2.9278,0.992		226/1118	101829070	129,12875	2203	4299	6502	SO:0001819	synonymous_variant	57562	exon5			ACTCCTCGAAGAT	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.678C>T	11.37:g.101829070C>T		68	0	0		67	32	0.477612	NM_020802	Q4G0U6	Silent	SNP	ENST00000263468.8	37	CCDS31658.1																																																																																			C|0.989;T|0.011	0.011	strong		0.343	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802		T	101829070	C	T	101829070	2	4	22	1	0	0	0	0	0	0	0	1	8236	871	31	1		1	KIAA1377	11	101829070	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1602170	101829070	33177446	2544	5445											
MMP20	9313	hgsc.bcm.edu	37	chr11	102487643	102487643	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggcttcttgatcacgttcaTtgtggtctggtctaacttcc	6	16	9	10	1	5	1	2	1	3	0	6	1	6	1	1	3	1	2	1	3	1	6	rs61730848	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:102487643T>C	ENST00000260228.2	-	2	286	c.274A>G	c.(274-276)Atg>Gtg	p.M92V	RP11-817J15.2_ENST00000542119.1_RNA	NM_004771.3	NP_004762.2	Q9NPA2	MMP25_HUMAN	matrix metallopeptidase 20	82					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)	ATCACGTTCATTGTGGTCTGG	0.458													T|||	12	0.00239617	0.0083	0.0014	5008	,	,		20171	0.0		0.0	False		,,,				2504	0.0				p.M92V		Atlas-SNP	.											.	MMP20	52	.	0			c.A274G						PASS	.	T	VAL/MET	31,4375	36.8+/-68.6	0,31,2172	174	149	158		274	4	0.4	11	dbSNP_129	158	0,8598		0,0,4299	yes	missense	MMP20	NM_004771.3	21	0,31,6471	CC,CT,TT		0.0,0.7036,0.2384	benign	92/484	102487643	31,12973	2203	4299	6502	SO:0001583	missense	9313	exon2			CGTTCATTGTGGT	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.274A>G	11.37:g.102487643T>C	ENSP00000260228:p.Met92Val	222	0	0		223	91	0.408072	NM_004771	D3DUA8|Q9H3Q0	Missense_Mutation	SNP	ENST00000260228.2	37	CCDS8318.1	3	0.0013736263736263737	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	T	8.312	0.822400	0.16678	0.007036	0.0	ENSG00000137674	ENST00000260228	T	0.34072	1.38	5.09	3.95	0.45737	Peptidoglycan binding-like (2);Metallopeptidase, catalytic domain (1);	0.248296	0.48286	D	0.000186	T	0.22126	0.0533	L	0.48174	1.505	0.31775	N	0.631573	B	0.10296	0.003	B	0.12837	0.008	T	0.24368	-1.0162	10	0.54805	T	0.06	.	7.274	0.26273	0.1337:0.0:0.2769:0.5894	.	92	O60882	MMP20_HUMAN	V	92	ENSP00000260228:M92V	ENSP00000260228:M92V	M	-	1	0	MMP20	101992853	0.016000	0.18221	0.382000	0.26119	0.387000	0.30353	0.103000	0.15292	1.044000	0.40200	0.533000	0.62120	ATG	T|0.998;C|0.002	0.002	strong		0.458	MMP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398012.1			C	102487643	T	C	102487643	3	2	22	1	0	0	0	0	1	0	0	0	9668	1493	52	3	1213	3	MMP20	11	102487643	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	658573	102487643	32518873	2545	5446											
MMP13	4322	hgsc.bcm.edu	37	chr11	102818662	102818662	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaggagagtcttgcctgtaTcctcaaagtgaacagctgca	12	9	10	10	0	2	2	1	1	1	1	3	3	3	2	2	1	4	3	2	1	3	2	rs17860568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:102818662T>C	ENST00000260302.3	-	8	1197	c.1169A>G	c.(1168-1170)gAt>gGt	p.D390G	MMP13_ENST00000340273.4_Missense_Mutation_p.D390G	NM_002427.3	NP_002418.1	P45452	MMP13_HUMAN	matrix metallopeptidase 13 (collagenase 3)	390	Interaction with collagen.		D -> G (in dbSNP:rs17860568). {ECO:0000269|Ref.4}.		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)	CTTGCCTGTATCCTCAAAGTG	0.438													T|||	41	0.0081869	0.0287	0.0014	5008	,	,		16765	0.0		0.002	False		,,,				2504	0.0				p.D390G		Atlas-SNP	.											.	MMP13	75	.	0			c.A1169G						PASS	.	T	GLY/ASP	75,4329	67.0+/-104.6	2,71,2129	135	113	120		1169	2	0.2	11	dbSNP_123	120	1,8597		0,1,4298	yes	missense	MMP13	NM_002427.3	94	2,72,6427	CC,CT,TT		0.0116,1.703,0.5845	benign	390/472	102818662	76,12926	2202	4299	6501	SO:0001583	missense	4322	exon8			CCTGTATCCTCAA	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.1169A>G	11.37:g.102818662T>C	ENSP00000260302:p.Asp390Gly	85	0	0		89	32	0.359551	NM_002427	A8K846|B2RCZ3|Q6NWN6	Missense_Mutation	SNP	ENST00000260302.3	37	CCDS8324.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	T	12.68	2.009730	0.35415	0.01703	1.16E-4	ENSG00000137745	ENST00000260302;ENST00000340273	T;T	0.02863	4.13;4.13	5.82	1.98	0.26296	Hemopexin/matrixin (2);	0.232869	0.49916	D	0.000139	T	0.01061	0.0035	L	0.39566	1.225	0.35073	D	0.762662	B	0.18741	0.03	B	0.30716	0.119	T	0.37407	-0.9707	10	0.44086	T	0.13	.	7.3488	0.26678	0.0:0.1373:0.2092:0.6535	rs17860568	390	P45452	MMP13_HUMAN	G	390	ENSP00000260302:D390G;ENSP00000339672:D390G	ENSP00000260302:D390G	D	-	2	0	MMP13	102323872	0.008000	0.16893	0.234000	0.24042	0.991000	0.79684	1.812000	0.38952	0.479000	0.27511	0.533000	0.62120	GAT	T|0.991;C|0.009	0.009	strong		0.438	MMP13-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386648.1	NM_002427		C	102818662	T	C	102818662	3	2	22	1	0	0	0	0	1	0	0	0	9661	1435	50	3	258	3	MMP13	11	102818662	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	331019	102818662	32187854	2546	5447											
DDI1	414301	hgsc.bcm.edu	37	chr11	103908517	103908517	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gctctttctccatacttgagGatcaacccatggatatgctt	9	14	7	11	0	3	1	1	1	2	0	4	3	3	3	2	2	3	2	2	2	3	5	rs116423827	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:103908517G>A	ENST00000302259.3	+	1	1210	c.967G>A	c.(967-969)Gat>Aat	p.D323N	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)	323							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)		CATACTTGAGGATCAACCCAT	0.448													G|||	30	0.00599042	0.0219	0.0014	5008	,	,		19982	0.0		0.0	False		,,,				2504	0.0				p.D323N		Atlas-SNP	.											.	DDI1	222	.	0			c.G967A						PASS	.	G	ASN/ASP,,	55,4349	54.9+/-90.9	1,53,2148	139	129	133		967,,	5.2	1	11	dbSNP_132	133	1,8597	1.2+/-3.3	0,1,4298	yes	missense,intron,intron	PDGFD,DDI1	NM_001001711.2,NM_025208.4,NM_033135.3	23,,	1,54,6446	AA,AG,GG		0.0116,1.2489,0.4307	possibly-damaging,,	323/397,,	103908517	56,12946	2202	4299	6501	SO:0001583	missense	414301	exon1			CTTGAGGATCAAC		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.967G>A	11.37:g.103908517G>A	ENSP00000302805:p.Asp323Asn	105	0	0		117	41	0.350427	NM_001001711	Q7Z4U6|Q8WTS3	Missense_Mutation	SNP	ENST00000302259.3	37	CCDS31660.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	11.40	1.628901	0.28978	0.012489	1.16E-4	ENSG00000170967	ENST00000302259	T	0.43688	0.94	5.21	5.21	0.72293	Peptidase aspartic (1);Peptidase aspartic, eukaryotic predicted (1);Peptidase aspartic, catalytic (1);	0.165679	0.52532	D	0.000074	T	0.19765	0.0475	N	0.11364	0.135	0.47862	D	0.999536	B	0.26547	0.152	B	0.32090	0.14	T	0.06197	-1.0840	10	0.10636	T	0.68	-21.2941	16.6709	0.85266	0.0:0.0:1.0:0.0	.	323	Q8WTU0	DDI1_HUMAN	N	323	ENSP00000302805:D323N	ENSP00000302805:D323N	D	+	1	0	DDI1	103413727	1.000000	0.71417	0.954000	0.39281	0.097000	0.18754	9.016000	0.93645	2.884000	0.98904	0.655000	0.94253	GAT	G|0.995;A|0.005	0.005	strong		0.448	DDI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387326.1	NM_001001711		A	103908517	G	A	103908517	3	1	22	1	0	0	0	0	1	0	0	0	4330	1174	41	2	969	2	DDI1	11	103908517	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1089855	103908517	31097999	2547	5448											
CASP4	837	hgsc.bcm.edu	37	chr11	104819333	104819333	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagcatcttcctctaggttCtcagatgactgtgaagaggc	10	11	10	10	0	3	4	1	2	3	2	5	4	4	4	1	2	1	2	1	2	2	3	rs55901059	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:104819333C>A	ENST00000444739.2	-	6	1762	c.852G>T	c.(850-852)gaG>gaT	p.E284D	CASP4_ENST00000531333.1_5'Flank|CASP4_ENST00000393150.3_Missense_Mutation_p.E228D	NM_001225.3	NP_001216.1	P49662	CASP4_HUMAN	caspase 4, apoptosis-related cysteine peptidase	284			E -> D (in dbSNP:rs55901059).		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)		CCTCTAGGTTCTCAGATGACT	0.493													c|||	93	0.0185703	0.0688	0.0029	5008	,	,		19215	0.0		0.0	False		,,,				2504	0.0				p.E284D		Atlas-SNP	.											.	CASP4	57	.	0			c.G852T						PASS	.	C	ASP/GLU,ASP/GLU	287,4117	157.8+/-190.6	12,263,1927	157	117	131		852,684	-2.6	0	11	dbSNP_129	131	1,8597		0,1,4298	yes	missense,missense	CASP4	NM_001225.3,NM_033306.2	45,45	12,264,6225	AA,AC,CC		0.0116,6.5168,2.215	benign,benign	284/378,228/322	104819333	288,12714	2202	4299	6501	SO:0001583	missense	837	exon6			TAGGTTCTCAGAT	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.852G>T	11.37:g.104819333C>A	ENSP00000388566:p.Glu284Asp	147	0	0		141	86	0.609929	NM_001225	A2NHL8|A2NHM0	Missense_Mutation	SNP	ENST00000444739.2	37	CCDS8327.1	43	0.019688644688644688	42	0.08536585365853659	1	0.0027624309392265192	0	0.0	0	0.0	C	9.595	1.127085	0.20959	0.065168	1.16E-4	ENSG00000196954	ENST00000444739;ENST00000393150;ENST00000355546	T;T	0.20738	2.05;2.05	5.08	-2.61	0.06171	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase precursor p45, core (1);	1.203310	0.05999	N	0.647483	T	0.00580	0.0019	L	0.37800	1.135	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.32587	-0.9901	10	0.19590	T	0.45	.	12.8207	0.57692	0.0:0.3484:0.58:0.0716	rs55901059;rs61735787	284	P49662	CASP4_HUMAN	D	284;228;237	ENSP00000388566:E284D;ENSP00000376857:E228D	ENSP00000347741:E237D	E	-	3	2	CASP4	104324543	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.270000	0.02831	-0.407000	0.07576	-0.494000	0.04653	GAG	C|0.979;A|0.021	0.021	strong		0.493	CASP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387751.1	NM_001225		A	104819333	C	A	104819333	3	1	22	1	0	0	0	0	1	0	0	0	2675	912	32	4	293	4	CASP4	11	104819333	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	910816	104819333	30187183	2548	5449											
CASP4	837	hgsc.bcm.edu	37	chr11	104825597	104825597	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tttgtcttcagttttagcatCgtaatatttctttttttcct	6	24	4	7	1	3	0	1	0	2	0	5	0	4	0	1	0	1	3	1	0	3	10	rs56226603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:104825597C>T	ENST00000444739.2	-	2	1049	c.139G>A	c.(139-141)Gat>Aat	p.D47N	CASP4_ENST00000531333.1_5'UTR|CASP4_ENST00000393150.3_5'UTR	NM_001225.3	NP_001216.1	P49662	CASP4_HUMAN	caspase 4, apoptosis-related cysteine peptidase	47	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.		D -> N (in dbSNP:rs56226603).		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)		GTTTTAGCATCGTAATATTTC	0.398													C|||	136	0.0271565	0.0946	0.0159	5008	,	,		19636	0.0		0.0	False		,,,				2504	0.0				p.D47N		Atlas-SNP	.											.	CASP4	57	.	0			c.G139A						PASS	.	C	ASN/ASP,	361,4043	185.0+/-212.2	22,317,1863	226	209	215		139,	0	0	11	dbSNP_129	215	1,8597	1.2+/-3.3	0,1,4298	yes	missense,utr-5	CASP4	NM_001225.3,NM_033306.2	23,	22,318,6161	TT,TC,CC		0.0116,8.1971,2.7842	benign,	47/378,	104825597	362,12640	2202	4299	6501	SO:0001583	missense	837	exon2			TAGCATCGTAATA	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.139G>A	11.37:g.104825597C>T	ENSP00000388566:p.Asp47Asn	181	0	0		180	60	0.333333	NM_001225	A2NHL8|A2NHM0	Missense_Mutation	SNP	ENST00000444739.2	37	CCDS8327.1	65	0.02976190476190476	57	0.11585365853658537	8	0.022099447513812154	0	0.0	0	0.0	C	0.022	-1.408830	0.01155	0.081971	1.16E-4	ENSG00000196954	ENST00000444739;ENST00000417440	T;T	0.19394	2.15;2.15	3.04	0.0232	0.14136	DEATH-like (2);Caspase Recruitment (3);	0.704837	0.13761	N	0.364575	T	0.00073	0.0002	N	0.02357	-0.585	0.09310	N	0.999999	B;B;B	0.33288	0.406;0.007;0.002	B;B;B	0.26969	0.075;0.006;0.006	T	0.27123	-1.0083	10	0.02654	T	1	.	6.0472	0.19766	0.0:0.469:0.0:0.531	rs56226603;rs61751520	47;47;47	B4DJH5;B4E2D2;P49662	.;.;CASP4_HUMAN	N	47	ENSP00000388566:D47N;ENSP00000401673:D47N	ENSP00000401673:D47N	D	-	1	0	CASP4	104330807	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.945000	0.03909	0.002000	0.14630	-0.140000	0.14226	GAT	C|0.969;T|0.031	0.031	strong		0.398	CASP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387751.1	NM_001225		T	104825597	C	T	104825597	3	4	22	1	0	0	0	0	1	0	0	0	2675	884	31	1	1022	1	CASP4	11	104825597	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6264	104825597	30180919	2549	5450											
CASP5	838	hgsc.bcm.edu	37	chr11	104871193	104871193	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacttgtgctctggtctggcAgcaaatgccctcagcactga	8	10	11	12	0	3	1	1	1	2	0	3	2	3	1	1	2	4	4	1	2	1	1	rs45501691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:104871193A>G	ENST00000260315.3	-	6	746	c.747T>C	c.(745-747)gcT>gcC	p.A249A	CASP5_ENST00000444749.2_Silent_p.A191A|CASP5_ENST00000393141.2_Silent_p.A262A|CASP5_ENST00000393139.2_3'UTR|CASP5_ENST00000526056.1_Silent_p.A262A|CASP5_ENST00000531367.1_Silent_p.A107A|CASP5_ENST00000418434.1_Silent_p.A107A			P51878	CASP5_HUMAN	caspase 5, apoptosis-related cysteine peptidase	249					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)		CTGGTCTGGCAGCAAATGCCC	0.448													A|||	212	0.0423323	0.1543	0.0115	5008	,	,		17767	0.0		0.0	False		,,,				2504	0.0				p.A262A		Atlas-SNP	.											.	CASP5	213	.	0			c.T786C						PASS	.	A	,,,	601,3803		51,499,1652	98	89	92		573,321,786,747	1.9	0.2	11	dbSNP_127	92	5,8593		0,5,4294	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CASP5	NM_001136109.1,NM_001136110.1,NM_001136112.1,NM_004347.3	,,,	51,504,5946	GG,GA,AA		0.0582,13.6467,4.6608	,,,	191/377,107/293,262/448,249/435	104871193	606,12396	2202	4299	6501	SO:0001819	synonymous_variant	838	exon6			TCTGGCAGCAAAT		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.747T>C	11.37:g.104871193A>G		139	0	0		118	68	0.576271	NM_001136112	B4DKP5|Q0QVY7|Q0QVY8|Q0QVZ0|Q0QVZ1|Q0QVZ2|Q14DD6|Q1HBJ3|Q6DJV7	Silent	SNP	ENST00000260315.3	37	CCDS8328.2																																																																																			A|0.954;G|0.046	0.046	strong		0.448	CASP5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109397.2	NM_004347		G	104871193	A	G	104871193	2	3	22	1	0	0	0	0	0	0	0	1	2676	175	7	3		3	CASP5	11	104871193	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	45596	104871193	30135323	2550	5451											
ALKBH8	91801	hgsc.bcm.edu	37	chr11	107427616	107427616	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgtatcttgcaaatgagtaCggcttgttaggtggcattaa	10	14	11	6	1	1	1	0	1	1	0	1	1	1	1	0	3	2	6	0	3	5	6	rs17107135	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:107427616C>G	ENST00000428149.2	-	3	394	c.243G>C	c.(241-243)ccG>ccC	p.P81P	ALKBH8_ENST00000389568.3_Silent_p.P81P|ALKBH8_ENST00000530933.1_5'UTR|ALKBH8_ENST00000417449.2_Silent_p.P84P|ALKBH8_ENST00000429370.1_Silent_p.P81P	NM_138775.2	NP_620130.2	Q96BT7	ALKB8_HUMAN	alkB, alkylation repair homolog 8 (E. coli)	81	RRM.				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)		CAAATGAGTACGGCTTGTTAG	0.443													G|||	545	0.108826	0.3918	0.036	5008	,	,		14479	0.001		0.001	False		,,,				2504	0.0				p.P81P		Atlas-SNP	.											.	ALKBH8	88	.	0			c.G243C						PASS	.	G		1354,3048	692.3+/-405.5	220,914,1067	130	121	124		243	2.7	1	11	dbSNP_123	124	24,8572	818.1+/-406.9	0,24,4274	no	coding-synonymous	ALKBH8	NM_138775.2		220,938,5341	GG,GC,CC		0.2792,30.7587,10.6016		81/665	107427616	1378,11620	2201	4298	6499	SO:0001819	synonymous_variant	91801	exon3			TGAGTACGGCTTG	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.243G>C	11.37:g.107427616C>G		158	1	0.00632911		152	152	1	NM_138775	B1Q2M0|B4DEF6|Q8N989	Silent	SNP	ENST00000428149.2	37	CCDS8337.2																																																																																			C|0.896;G|0.104	0.104	strong		0.443	ALKBH8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347071.2	NM_138775		G	107427616	C	G	107427616	2	3	22	1	0	0	0	0	0	0	0	1	533	523	19	4		4	ALKBH8	11	107427616	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2556423	107427616	27578900	2551	5452											
ELMOD1	55531	hgsc.bcm.edu	37	chr11	107501428	107501428	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgttgctgctttcacagaaAcatcactgagggattctaaa	12	13	8	8	0	3	2	2	1	1	1	3	3	3	3	0	1	3	3	0	1	3	5	rs201717101	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:107501428A>T	ENST00000265840.7	+	4	431	c.166A>T	c.(166-168)Aca>Tca	p.T56S	ELMOD1_ENST00000531234.1_Missense_Mutation_p.T50S|ELMOD1_ENST00000443271.2_Missense_Mutation_p.T56S	NM_018712.3	NP_061182.3	Q8N336	ELMD1_HUMAN	ELMO/CED-12 domain containing 1	56					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)		TTTCACAGAAACATCACTGAG	0.313													A|||	6	0.00119808	0.0045	0.0	5008	,	,		19465	0.0		0.0	False		,,,				2504	0.0				p.T56S		Atlas-SNP	.											.	ELMOD1	40	.	0			c.A166T						PASS	.	A	SER/THR,SER/THR	8,3684		0,8,1838	93	89	90		166,166	3.2	1	11		90	0,8158		0,0,4079	yes	missense,missense	ELMOD1	NM_001130037.1,NM_018712.3	58,58	0,8,5917	TT,TA,AA		0.0,0.2167,0.0675	benign,benign	56/327,56/335	107501428	8,11842	1846	4079	5925	SO:0001583	missense	55531	exon4			ACAGAAACATCAC	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.166A>T	11.37:g.107501428A>T	ENSP00000265840:p.Thr56Ser	122	0	0		152	58	0.381579	NM_018712	B4E167|G5E9S5|Q9NPW3	Missense_Mutation	SNP	ENST00000265840.7	37	CCDS44723.1	.	.	.	.	.	.	.	.	.	.	A	10.08	1.251659	0.22880	0.002167	0.0	ENSG00000110675	ENST00000531234;ENST00000265840;ENST00000443271	.	.	.	5.62	3.19	0.36642	.	0.250304	0.42294	D	0.000737	T	0.09686	0.0238	N	0.01277	-0.915	0.30939	N	0.726031	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.20538	-1.0272	9	0.08381	T	0.77	.	4.3202	0.11013	0.5821:0.0:0.178:0.2399	.	56;56	Q8N336;G5E9S5	ELMD1_HUMAN;.	S	50;56;56	.	ENSP00000265840:T56S	T	+	1	0	ELMOD1	107006638	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	1.228000	0.32588	0.957000	0.37930	0.533000	0.62120	ACA	.	.	weak		0.313	ELMOD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389406.1	NM_018712		T	107501428	A	T	107501428	3	4	22	1	0	0	0	0	1	0	0	0	5070	43	2	5	176	5	ELMOD1	11	107501428	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	73812	107501428	27505088	2552	5453											
CUL5	8065	hgsc.bcm.edu	37	chr11	107943124	107943124	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tagagccaatgttgaaagacTtggaggaacatatcattagt	15	11	10	5	0	1	3	1	1	0	2	1	5	1	5	1	2	2	1	1	2	6	5	rs111339569	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:107943124T>C	ENST00000393094.2	+	9	1556	c.940T>C	c.(940-942)Ttg>Ctg	p.L314L		NM_003478.3	NP_003469.2	Q93034	CUL5_HUMAN	cullin 5	314					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)		GTTGAAAGACTTGGAGGAACA	0.348													T|||	72	0.014377	0.053	0.0029	5008	,	,		19109	0.0		0.0	False		,,,				2504	0.0				p.L314L		Atlas-SNP	.											.	CUL5	71	.	0			c.T940C						PASS	.	T		204,4198	127.0+/-164.0	4,196,2001	113	111	112		940	3.9	1	11	dbSNP_132	112	1,8595		0,1,4297	no	coding-synonymous	CUL5	NM_003478.3		4,197,6298	CC,CT,TT		0.0116,4.6343,1.5772		314/781	107943124	205,12793	2201	4298	6499	SO:0001819	synonymous_variant	8065	exon9			AAAGACTTGGAGG	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.940T>C	11.37:g.107943124T>C		81	0	0		62	28	0.451613	NM_003478	A8K960|O14766|Q9BZC6	Silent	SNP	ENST00000393094.2	37	CCDS31668.1																																																																																			T|0.987;C|0.013	0.013	strong		0.348	CUL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389429.1			C	107943124	T	C	107943124	2	2	22	1	0	0	0	0	0	0	0	1	4061	1606	56	3		3	CUL5	11	107943124	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	441696	107943124	27063392	2553	5454											
ATM	472	hgsc.bcm.edu	37	chr11	108143299	108143299	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatatatattctctgtaagaAtggccctagtaaattgcctt	13	15	6	7	0	1	1	0	0	1	1	2	1	1	1	2	1	1	2	2	1	9	9	rs3092857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:108143299A>G	ENST00000452508.2	+	22	3307	c.3118A>G	c.(3118-3120)Atg>Gtg	p.M1040V	ATM_ENST00000278616.4_Missense_Mutation_p.M1040V			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1040			M -> V (in B-cell non-Hodgkin lymphoma; dbSNP:rs3092857). {ECO:0000269|PubMed:9288106}.		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.M1040V(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)	CTCTGTAAGAATGGCCCTAGT	0.303			"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)			A|||	71	0.0141773	0.053	0.0014	5008	,	,		17666	0.0		0.0	False		,,,				2504	0.0				p.M1040V		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	ATM_ENST00000278616,colon,carcinoma,-1,7	ATM	1657	7	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.A3118G						PASS	.	A	VAL/MET	177,4225	112.5+/-150.6	1,175,2025	112	117	115	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3118	-1.1	1	11	dbSNP_103	115	0,8596		0,0,4298	yes	missense	ATM	NM_000051.3	21	1,175,6323	GG,GA,AA		0.0,4.0209,1.3617	benign	1040/3057	108143299	177,12821	2201	4298	6499	SO:0001583	missense	472	exon21	Familial Cancer Database	AT, Louis-Bar syndrome	GTAAGAATGGCCC	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.3118A>G	11.37:g.108143299A>G	ENSP00000388058:p.Met1040Val	203	0	0		142	51	0.359155	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	A	0.185	-1.058171	0.01950	0.040209	0.0	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.68624	-0.34;-0.34;-0.34	5.43	-1.09	0.09904	Armadillo-type fold (1);	0.532223	0.22706	N	0.056633	T	0.10380	0.0254	L	0.35723	1.085	0.20926	N	0.999827	B	0.02656	0.0	B	0.01281	0.0	T	0.14531	-1.0469	10	0.02654	T	1	.	6.8803	0.24168	0.4453:0.1325:0.4222:0.0	rs3092857;rs17107892;rs52804880;rs3092857	1040	Q13315	ATM_HUMAN	V	1040	ENSP00000435747:M1040V;ENSP00000278616:M1040V;ENSP00000388058:M1040V	ENSP00000278616:M1040V	M	+	1	0	ATM	107648509	0.995000	0.38212	0.990000	0.47175	0.533000	0.34776	0.324000	0.19610	-0.134000	0.11516	0.533000	0.62120	ATG	A|0.985;G|0.015	0.015	strong		0.303	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		G	108143299	A	G	108143299	3	3	22	1	0	0	0	0	1	0	0	0	1109	101	4	3	3196	3	ATM	11	108143299	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	200175	108143299	26863217	2554	5455											
EXPH5	23086	hgsc.bcm.edu	37	chr11	108380609	108380609	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgtatatagatattgcagaCctgggacctgtttttgtccc	8	15	9	9	0	0	2	0	0	0	2	1	3	1	3	3	1	1	3	3	1	4	7	rs115867994	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:108380609C>T	ENST00000265843.4	-	6	5735	c.5625G>A	c.(5623-5625)agG>agA	p.R1875R	EXPH5_ENST00000428840.1_Silent_p.R1799R|EXPH5_ENST00000525344.1_Silent_p.R1868R|EXPH5_ENST00000443411.1_Silent_p.R1687R	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1875					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)		ATATTGCAGACCTGGGACCTG	0.418													C|||	66	0.0131789	0.0492	0.0014	5008	,	,		19501	0.0		0.0	False		,,,				2504	0.0				p.R1875R		Atlas-SNP	.											.	EXPH5	193	.	0			c.G5625A						PASS	.	C		174,4228	114.6+/-152.6	0,174,2027	62	63	63		5625	2.2	0.2	11	dbSNP_132	63	0,8596		0,0,4298	no	coding-synonymous	EXPH5	NM_015065.2		0,174,6325	TT,TC,CC		0.0,3.9527,1.3387		1875/1990	108380609	174,12824	2201	4298	6499	SO:0001819	synonymous_variant	23086	exon6			TGCAGACCTGGGA		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.5625G>A	11.37:g.108380609C>T		150	0	0		157	74	0.471338	NM_015065	Q2KHM1|Q9Y4D6	Silent	SNP	ENST00000265843.4	37	CCDS8341.1																																																																																			C|0.986;T|0.014	0.014	strong		0.418	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		T	108380609	C	T	108380609	2	4	22	1	0	0	0	0	0	0	0	1	5324	506	18	2		2	EXPH5	11	108380609	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	237310	108380609	26625907	2555	5456											
EXPH5	23086	hgsc.bcm.edu	37	chr11	108380740	108380740	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	ttcattcccaagggtcagtcGactcagggcattgtcaatag	10	11	10	10	1	4	0	4	0	0	0	6	1	5	0	1	2	0	1	1	2	3	4	rs36005552	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:108380740G>C	ENST00000265843.4	-	6	5604	c.5494C>G	c.(5494-5496)Cga>Gga	p.R1832G	EXPH5_ENST00000428840.1_Missense_Mutation_p.R1756G|EXPH5_ENST00000525344.1_Missense_Mutation_p.R1825G|EXPH5_ENST00000443411.1_Missense_Mutation_p.R1644G	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1832					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)		AGGGTCAGTCGACTCAGGGCA	0.443													G|||	30	0.00599042	0.0212	0.0029	5008	,	,		20136	0.0		0.0	False		,,,				2504	0.0				p.R1832G		Atlas-SNP	.											.	EXPH5	193	.	0			c.C5494G						PASS	.	G	GLY/ARG	134,4268	96.2+/-134.9	0,134,2067	63	63	63		5494	0.4	0	11	dbSNP_126	63	0,8596		0,0,4298	yes	missense	EXPH5	NM_015065.2	125	0,134,6365	CC,CG,GG		0.0,3.0441,1.0309	benign	1832/1990	108380740	134,12864	2201	4298	6499	SO:0001583	missense	23086	exon6			TCAGTCGACTCAG		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.5494C>G	11.37:g.108380740G>C	ENSP00000265843:p.Arg1832Gly	115	0	0		89	56	0.629214	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	G	8.864	0.947649	0.18356	0.030441	0.0	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000439956	T;T;T;T	0.03181	4.24;4.17;4.02;4.24	6.17	0.414	0.16406	.	1.706240	0.03093	N	0.160006	T	0.01092	0.0036	L	0.27053	0.805	0.09310	N	1	B	0.14438	0.01	B	0.18263	0.021	T	0.43294	-0.9400	10	0.41790	T	0.15	7.6536	3.311	0.07016	0.1263:0.1752:0.4527:0.2458	rs36005552	1832	Q8NEV8	EXPH5_HUMAN	G	1832;1756;1644;1825;662	ENSP00000265843:R1832G;ENSP00000391966:R1756G;ENSP00000411390:R1644G;ENSP00000432546:R1825G	ENSP00000265843:R1832G	R	-	1	2	EXPH5	107885950	0.000000	0.05858	0.047000	0.18901	0.426000	0.31534	0.086000	0.14935	0.144000	0.18951	0.655000	0.94253	CGA	G|0.990;C|0.010	0.010	strong		0.443	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		C	108380740	G	C	108380740	3	2	22	1	0	0	0	0	1	0	0	0	5324	1066	37	4	479	4	EXPH5	11	108380740	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	131	108380740	26625776	2556	5457											
EXPH5	23086	hgsc.bcm.edu	37	chr11	108383560	108383560	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagcatcaagggaagaatTctttgatggtgaggaatctg	13	10	14	4	0	3	3	1	2	2	1	3	6	3	6	0	4	1	1	0	4	4	2	rs10890850	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:108383560T>A	ENST00000265843.4	-	6	2784	c.2674A>T	c.(2674-2676)Aat>Tat	p.N892Y	EXPH5_ENST00000524840.1_5'Flank|EXPH5_ENST00000428840.1_Missense_Mutation_p.N816Y|EXPH5_ENST00000525344.1_Missense_Mutation_p.N885Y|EXPH5_ENST00000443411.1_Missense_Mutation_p.N704Y	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	892			N -> Y (in dbSNP:rs10890850).		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)		AGGGAAGAATTCTTTGATGGT	0.438													T|||	270	0.0539137	0.1316	0.0115	5008	,	,		19382	0.0119		0.002	False		,,,				2504	0.0757				p.N892Y		Atlas-SNP	.											.	EXPH5	193	.	0			c.A2674T						PASS	.	T	TYR/ASN	493,3909	229.8+/-244.2	29,435,1737	182	167	172		2674	-2	0	11	dbSNP_120	172	9,8587	7.1+/-27.0	0,9,4289	yes	missense	EXPH5	NM_015065.2	143	29,444,6026	AA,AT,TT		0.1047,11.1995,3.8621	benign	892/1990	108383560	502,12496	2201	4298	6499	SO:0001583	missense	23086	exon6			AAGAATTCTTTGA		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.2674A>T	11.37:g.108383560T>A	ENSP00000265843:p.Asn892Tyr	126	0	0		130	86	0.661538	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	59	0.027014652014652016	46	0.09349593495934959	5	0.013812154696132596	7	0.012237762237762238	1	0.0013192612137203166	T	14.92	2.680490	0.47886	0.111995	0.001047	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.04603	4.17;4.1;3.95;4.17;4.02;3.59	5.74	-1.97	0.07503	.	0.712890	0.13437	N	0.387972	T	0.00109	0.0003	L	0.44542	1.39	0.09310	N	1	P	0.49090	0.919	B	0.43445	0.42	T	0.40813	-0.9543	10	0.72032	D	0.01	-0.8859	6.5046	0.22188	0.0:0.4682:0.1578:0.3739	rs10890850;rs10890850	892	Q8NEV8	EXPH5_HUMAN	Y	892;816;704;885;816;704	ENSP00000265843:N892Y;ENSP00000391966:N816Y;ENSP00000411390:N704Y;ENSP00000432546:N885Y;ENSP00000432683:N816Y;ENSP00000446434:N704Y	ENSP00000265843:N892Y	N	-	1	0	EXPH5	107888770	0.000000	0.05858	0.002000	0.10522	0.230000	0.25150	-0.173000	0.09854	-0.270000	0.09285	0.460000	0.39030	AAT	T|0.967;A|0.033	0.033	strong		0.438	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		A	108383560	T	A	108383560	3	1	22	1	0	0	0	0	1	0	0	0	5324	1783	62	5	3299	5	EXPH5	11	108383560	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2820	108383560	26622956	2557	5458											
EXPH5	23086	hgsc.bcm.edu	37	chr11	108384857	108384857	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggtattgctgaagaaagaTctggtaaatgtgttgctttg	12	14	12	3	0	1	3	0	1	1	2	1	3	1	3	0	2	2	5	0	2	6	5	rs116565594	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:108384857T>C	ENST00000265843.4	-	6	1487	c.1377A>G	c.(1375-1377)agA>agG	p.R459R	EXPH5_ENST00000524840.1_5'UTR|EXPH5_ENST00000428840.1_Silent_p.R383R|EXPH5_ENST00000525344.1_Silent_p.R452R|EXPH5_ENST00000443411.1_Silent_p.R271R	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	459					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)		TGAAGAAAGATCTGGTAAATG	0.438													T|||	64	0.0127796	0.0477	0.0014	5008	,	,		22659	0.0		0.0	False		,,,				2504	0.0				p.R459R		Atlas-SNP	.											.	EXPH5	193	.	0			c.A1377G						PASS	.	T		168,4234	112.5+/-150.6	0,168,2033	158	150	152		1377	2.5	1	11	dbSNP_132	152	0,8596		0,0,4298	no	coding-synonymous	EXPH5	NM_015065.2		0,168,6331	CC,CT,TT		0.0,3.8164,1.2925		459/1990	108384857	168,12830	2201	4298	6499	SO:0001819	synonymous_variant	23086	exon6			GAAAGATCTGGTA		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.1377A>G	11.37:g.108384857T>C		136	0	0		116	55	0.474138	NM_015065	Q2KHM1|Q9Y4D6	Silent	SNP	ENST00000265843.4	37	CCDS8341.1																																																																																			T|0.987;C|0.013	0.013	strong		0.438	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		C	108384857	T	C	108384857	2	2	22	1	0	0	0	0	0	0	0	1	5324	1432	50	3		3	EXPH5	11	108384857	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1297	108384857	26621659	2558	5459											
ZC3H12C	85463	hgsc.bcm.edu	37	chr11	110007834	110007834	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggaagcaaagaaaccaccTgatgtggtgcgagaatacca	17	5	11	8	1	0	3	0	1	0	2	0	5	0	4	3	2	4	1	3	2	6	1	rs78240010	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:110007834T>C	ENST00000278590.3	+	2	519	c.468T>C	c.(466-468)ccT>ccC	p.P156P	ZC3H12C_ENST00000528673.1_Silent_p.P157P|ZC3H12C_ENST00000453089.2_Silent_p.P125P	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	156							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)		AGAAACCACCTGATGTGGTGC	0.413													N|||	66	0.0131789	0.0431	0.0043	5008	,	,		22894	0.003		0.0	False		,,,				2504	0.0031				p.P156P		Atlas-SNP	.											.	ZC3H12C	83	.	0			c.T468C						PASS	.	C		127,3593		4,119,1737	71	66	67		468	-8.4	0.9	11	dbSNP_132	67	0,8192		0,0,4096	no	coding-synonymous	ZC3H12C	NM_033390.1		4,119,5833	CC,CT,TT		0.0,3.414,1.0662		156/884	110007834	127,11785	1860	4096	5956	SO:0001819	synonymous_variant	85463	exon2			ACCACCTGATGTG		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.468T>C	11.37:g.110007834T>C		91	0	0		54	24	0.444444	NM_033390	B4DI65|B4DR47	Silent	SNP	ENST00000278590.3	37	CCDS44727.1																																																																																			T|0.992;C|0.008	0.008	strong		0.413	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390		C	110007834	T	C	110007834	2	2	22	1	0	0	0	0	0	0	0	1	17578	1567	55	3		3	ZC3H12C	11	110007834	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1622977	110007834	24998682	2559	5460											
RDX	5962	hgsc.bcm.edu	37	chr11	110118459	110118459	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttaattgtctgctcttcaatTtgttttagacgttccattag	8	20	6	7	1	3	1	1	0	2	1	4	1	4	1	1	0	1	3	1	0	4	8	rs139953187	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:110118459T>C	ENST00000343115.4	-	10	1378	c.1059A>G	c.(1057-1059)caA>caG	p.Q353Q	RDX_ENST00000528900.1_Silent_p.Q6Q|RDX_ENST00000528498.1_Silent_p.Q353Q|RDX_ENST00000405097.1_Silent_p.Q353Q|RDX_ENST00000530301.1_Intron|RDX_ENST00000544551.1_Silent_p.Q217Q	NM_001260494.1|NM_002906.3	NP_001247423.1|NP_002897.1	P35241	RADI_HUMAN	radixin	353	Glu-rich.				actin filament capping (GO:0051693)|apical protein localization (GO:0045176)|establishment of endothelial barrier (GO:0061028)|microvillus assembly (GO:0030033)|positive regulation of gene expression (GO:0010628)	apical part of cell (GO:0045177)|cell tip (GO:0051286)|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)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|stereocilium (GO:0032420)|T-tubule (GO:0030315)	poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	18		all_cancers(61;7.18e-13)|all_epithelial(67;2.61e-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;1.13e-06)|BRCA - Breast invasive adenocarcinoma(274;9.75e-06)|all cancers(92;5.9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0248)		GCTCTTCAATTTGTTTTAGAC	0.308													T|||	53	0.0105831	0.0333	0.0115	5008	,	,		17959	0.0		0.001	False		,,,				2504	0.0				p.Q353Q	Esophageal Squamous(55;25 1062 11040 28755 44273)	Atlas-SNP	.											.	RDX	59	.	0			c.A1059G						PASS	.	T		107,4289	79.3+/-117.8	1,105,2092	134	122	126		1059	2.8	1	11	dbSNP_134	126	1,8587	1.2+/-3.3	0,1,4293	no	coding-synonymous	RDX	NM_002906.3		1,106,6385	CC,CT,TT		0.0116,2.434,0.8318		353/584	110118459	108,12876	2198	4294	6492	SO:0001819	synonymous_variant	5962	exon10			TTCAATTTGTTTT	BC020751	CCDS8343.1, CCDS58171.1, CCDS58172.1, CCDS58173.1, CCDS58174.1	11q23	2008-03-17				ENSG00000137710			9944	protein-coding gene	gene with protein product		179410	"deafness, autosomal recessive 24"	DFNB24		8486357, 17226784	Standard	NM_001260492		Approved		uc031qdy.1	P35241		ENST00000343115.4:c.1059A>G	11.37:g.110118459T>C		193	0	0		163	99	0.607362	NM_001260493	A7YIJ8|A7YIK0|A7YIK3|B7Z9U6|F5H1A7|Q86Y61	Silent	SNP	ENST00000343115.4	37	CCDS8343.1																																																																																			T|0.989;C|0.011	0.011	strong		0.308	RDX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390535.2	NM_002906		C	110118459	T	C	110118459	2	2	22	1	0	0	0	0	0	0	0	1	13213	1838	64	3		3	RDX	11	110118459	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	110625	110118459	24888057	2560	5461											
ARHGAP20	57569	hgsc.bcm.edu	37	chr11	110451470	110451470	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcatctttttgagaaagaaTtgcatcacagctggacttgc	11	14	8	8	0	3	2	2	1	1	2	3	4	3	3	0	1	3	2	0	1	2	5	rs151169911	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:110451470T>C	ENST00000260283.4	-	16	2484	c.2200A>G	c.(2200-2202)Att>Gtt	p.I734V	ARHGAP20_ENST00000357139.3_Missense_Mutation_p.I708V|ARHGAP20_ENST00000529591.1_Missense_Mutation_p.I277V|ARHGAP20_ENST00000527598.1_Missense_Mutation_p.I698V|ARHGAP20_ENST00000528829.1_Missense_Mutation_p.I698V|ARHGAP20_ENST00000533353.1_Missense_Mutation_p.I708V|ARHGAP20_ENST00000524756.1_Missense_Mutation_p.I711V	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	734					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)		TGAGAAAGAATTGCATCACAG	0.448													T|||	3	0.000599042	0.0023	0.0	5008	,	,		21606	0.0		0.0	False		,,,				2504	0.0				p.I734V		Atlas-SNP	.											.	ARHGAP20	150	.	0			c.A2200G						PASS	.	T	VAL/ILE	10,4392	15.5+/-35.6	0,10,2191	66	69	68		2200	-1.6	0	11	dbSNP_134	68	0,8596		0,0,4298	yes	missense	ARHGAP20	NM_020809.2	29	0,10,6489	CC,CT,TT		0.0,0.2272,0.0769	benign	734/1192	110451470	10,12988	2201	4298	6499	SO:0001583	missense	57569	exon16			AAAGAATTGCATC	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.2200A>G	11.37:g.110451470T>C	ENSP00000260283:p.Ile734Val	164	0	0		127	58	0.456693	NM_020809	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Missense_Mutation	SNP	ENST00000260283.4	37	CCDS31673.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	T	4.295	0.054024	0.08291	0.002272	0.0	ENSG00000137727	ENST00000260283;ENST00000357139;ENST00000529591;ENST00000524756;ENST00000528829;ENST00000533353;ENST00000527598	T;T;T;T;T;T;T	0.07908	3.15;3.15;3.18;3.15;3.15;3.15;3.15	5.93	-1.65	0.08291	.	0.430046	0.22922	N	0.054011	T	0.03220	0.0094	N	0.25647	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	0.44205	-0.9343	10	0.06365	T	0.9	.	13.7174	0.62705	0.0:0.7298:0.0:0.2702	.	708;734;711	Q9P2F6-2;Q9P2F6;Q9P2F6-3	.;RHG20_HUMAN;.	V	734;708;277;711;698;708;698	ENSP00000260283:I734V;ENSP00000349660:I708V;ENSP00000437905:I277V;ENSP00000432076:I711V;ENSP00000436319:I698V;ENSP00000436522:I708V;ENSP00000431399:I698V	ENSP00000260283:I734V	I	-	1	0	ARHGAP20	109956680	0.028000	0.19301	0.033000	0.17914	0.860000	0.49131	0.237000	0.17985	-0.263000	0.09378	-0.408000	0.06270	ATT	T|0.999;C|0.001	0.001	strong		0.448	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809		C	110451470	T	C	110451470	3	2	22	1	0	0	0	0	1	0	0	0	870	1493	52	3	1379	3	ARHGAP20	11	110451470	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	333011	110451470	24555046	2561	5462											
C11orf53	341032	hgsc.bcm.edu	37	chr11	111156523	111156523	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccagcacaggggctcaagctGggggtcatccctggctgggg	6	6	17	12	0	2	0	2	0	0	0	3	0	3	0	2	7	2	4	2	7	1	0	rs74649813	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:111156523G>T	ENST00000280325.4	+	4	602	c.455G>T	c.(454-456)tGg>tTg	p.W152L		NM_198498.1	NP_940900.1	Q8IXP5	CK053_HUMAN	chromosome 11 open reading frame 53	152										endometrium(1)|large_intestine(2)|lung(3)|skin(2)	8		all_cancers(61;2.05e-09)|Melanoma(852;4.04e-05)|all_epithelial(67;6.15e-05)|all_hematologic(158;0.000826)|Acute lymphoblastic leukemia(157;0.000966)|all_neural(223;0.0332)|Medulloblastoma(222;0.0425)|Breast(348;0.147)		Epithelial(105;1.7e-06)|BRCA - Breast invasive adenocarcinoma(274;3.16e-06)|all cancers(92;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0507)		GGCTCAAGCTGGGGGTCATCC	0.642													G|||	223	0.0445288	0.1589	0.0187	5008	,	,		21186	0.0		0.0	False		,,,				2504	0.0				p.W152L		Atlas-SNP	.											C11orf53,NS,haematopoietic_neoplasm,-1,1	C11orf53	17	1	0			c.G455T						PASS	.	G	LEU/TRP	526,3876	237.4+/-249.2	36,454,1711	75	72	73		455	5.2	1	11	dbSNP_131	73	3,8591	2.2+/-6.3	0,3,4294	yes	missense	C11orf53	NM_198498.1	61	36,457,6005	TT,TG,GG		0.0349,11.9491,4.0705	probably-damaging	152/237	111156523	529,12467	2201	4297	6498	SO:0001583	missense	341032	exon4			CAAGCTGGGGGTC	BC039669	CCDS31674.1	11q23.1	2012-05-31			ENSG00000150750	ENSG00000150750			30527	protein-coding gene	gene with protein product						12477932	Standard	NM_198498		Approved	MGC50104	uc001plc.3	Q8IXP5	OTTHUMG00000166656	ENST00000280325.4:c.455G>T	11.37:g.111156523G>T	ENSP00000280325:p.Trp152Leu	75	0	0		56	34	0.607143	NM_198498		Missense_Mutation	SNP	ENST00000280325.4	37	CCDS31674.1	86	0.039377289377289376	77	0.1565040650406504	9	0.024861878453038673	0	0.0	0	0.0	G	18.56	3.650861	0.67472	0.119491	3.49E-4	ENSG00000150750	ENST00000280325	.	.	.	5.15	5.15	0.70609	.	0.069080	0.64402	D	0.000009	T	0.00754	0.0025	M	0.67953	2.075	0.24566	P	0.99394883	D	0.89917	1.0	D	0.87578	0.998	T	0.23833	-1.0177	8	0.12103	T	0.63	-12.1586	16.1285	0.81410	0.0:0.0:1.0:0.0	.	152	Q8IXP5	CK053_HUMAN	L	152	.	ENSP00000280325:W152L	W	+	2	0	C11orf53	110661733	1.000000	0.71417	0.995000	0.50966	0.655000	0.38815	6.849000	0.75414	2.402000	0.81655	0.561000	0.74099	TGG	G|0.961;T|0.039	0.039	strong		0.642	C11orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390989.1	NM_198498		T	111156523	G	T	111156523	3	4	22	1	0	0	0	0	1	0	0	0	1650	1357	47	4	465	4	C11orf53	11	111156523	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	705053	111156523	23849993	2562	5463											
SIK2	23235	hgsc.bcm.edu	37	chr11	111594520	111594520	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctgctcctcctctgcccacGcagctacagcagcagcagcc	7	6	9	19	1	1	0	0	0	1	0	3	0	3	0	4	0	8	7	4	0	1	1	rs75997369	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:111594520G>A	ENST00000304987.3	+	15	2621	c.2448G>A	c.(2446-2448)acG>acA	p.T816T		NM_015191.1	NP_056006.1	Q9H0K1	SIK2_HUMAN	salt-inducible kinase 2	816					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						CTCTGCCCACGCAGCTACAGC	0.637													G|||	9	0.00179712	0.0068	0.0	5008	,	,		10597	0.0		0.0	False		,,,				2504	0.0				p.T816T		Atlas-SNP	.											.	SIK2	89	.	0			c.G2448A						PASS	.	G		48,4354	49.6+/-84.7	0,48,2153	64	72	69		2448	-8.7	0	11	dbSNP_131	69	0,8594		0,0,4297	no	coding-synonymous	SIK2	NM_015191.1		0,48,6450	AA,AG,GG		0.0,1.0904,0.3693		816/927	111594520	48,12948	2201	4297	6498	SO:0001819	synonymous_variant	23235	exon15			GCCCACGCAGCTA	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.2448G>A	11.37:g.111594520G>A		82	0	0		57	36	0.631579	NM_015191	A8K5B8|B0YJ94|O94878|Q17RV0|Q6AZE2|Q76N03|Q8NCV7|Q96CZ8	Silent	SNP	ENST00000304987.3	37	CCDS8347.1																																																																																			G|0.997;A|0.003	0.003	strong		0.637	SIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319352.3	NM_015191		A	111594520	G	A	111594520	2	1	22	1	0	0	0	0	0	0	0	1	14333	1074	38	1		1	SIK2	11	111594520	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	437997	111594520	23411996	2563	5464											
DLAT	1737	hgsc.bcm.edu	37	chr11	111908137	111908137	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttgctgactataggccaaccGaagtaacagatttaaaacca	16	9	7	9	1	0	2	0	1	0	1	0	3	0	2	3	1	4	2	3	1	7	6	rs116125936	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:111908137G>A	ENST00000280346.6	+	6	1587	c.928G>A	c.(928-930)Gaa>Aaa	p.E310K	DLAT_ENST00000537636.1_Missense_Mutation_p.E81K|DLAT_ENST00000393051.1_Intron	NM_001931.4	NP_001922.2	P10515	ODP2_HUMAN	dihydrolipoamide S-acetyltransferase	310					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)	mitochondrial matrix (GO:0005759)|mitochondrial pyruvate dehydrogenase complex (GO:0005967)|mitochondrion (GO:0005739)	dihydrolipoyllysine-residue acetyltransferase activity (GO:0004742)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(1)|skin(1)	22		all_cancers(61;4.53e-11)|all_epithelial(67;2.76e-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;4.87e-07)|BRCA - Breast invasive adenocarcinoma(274;6.83e-07)|all cancers(92;9.63e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0557)		TAGGCCAACCGAAGTAACAGA	0.448													G|||	24	0.00479233	0.0166	0.0029	5008	,	,		19194	0.0		0.0	False		,,,				2504	0.0				p.E310K		Atlas-SNP	.											.	DLAT	39	.	0			c.G928A						PASS	.	G	LYS/GLU	97,4305	78.3+/-116.7	0,97,2104	75	75	75		928	6.1	1	11	dbSNP_132	75	0,8594		0,0,4297	yes	missense	DLAT	NM_001931.4	56	0,97,6401	AA,AG,GG		0.0,2.2035,0.7464	benign	310/648	111908137	97,12899	2201	4297	6498	SO:0001583	missense	1737	exon6			CCAACCGAAGTAA	Y00978	CCDS8354.1	11q23.1	2008-02-05	2008-02-04		ENSG00000150768	ENSG00000150768	2.3.1.12		2896	protein-coding gene	gene with protein product	"E2 component of pyruvate dehydrogenase complex"	608770		DLTA		8102256	Standard	NM_001931		Approved	PDC-E2	uc001pmo.3	P10515	OTTHUMG00000133751	ENST00000280346.6:c.928G>A	11.37:g.111908137G>A	ENSP00000280346:p.Glu310Lys	97	0	0		64	21	0.328125	NM_001931	Q16783|Q53EP3	Missense_Mutation	SNP	ENST00000280346.6	37	CCDS8354.1	9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	G	15.75	2.925111	0.52759	0.022035	0.0	ENSG00000150768	ENST00000280346;ENST00000531306;ENST00000537636	T;T;T	0.21932	1.98;1.98;1.98	6.07	6.07	0.98685	Single hybrid motif (1);	0.512867	0.20290	N	0.095276	T	0.08179	0.0204	N	0.19112	0.55	0.40612	D	0.981685	B;B	0.21520	0.057;0.057	B;B	0.19148	0.024;0.024	T	0.16335	-1.0406	10	0.12103	T	0.63	-12.1494	20.6525	0.99598	0.0:0.0:1.0:0.0	.	310;310	Q86YI5;P10515	.;ODP2_HUMAN	K	310;142;81	ENSP00000280346:E310K;ENSP00000433432:E142K;ENSP00000442427:E81K	ENSP00000280346:E310K	E	+	1	0	DLAT	111413347	1.000000	0.71417	0.990000	0.47175	0.975000	0.68041	9.458000	0.97634	2.890000	0.99128	0.585000	0.79938	GAA	G|0.992;A|0.008	0.008	strong		0.448	DLAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258167.1	NM_001931		A	111908137	G	A	111908137	3	1	22	1	0	0	0	0	1	0	0	0	4551	1059	37	1	950	1	DLAT	11	111908137	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	313617	111908137	23098379	2564	5465											
BCO2	83875	hgsc.bcm.edu	37	chr11	112071464	112071464	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggaaccccagtgtaatacgCggtttcatgtggtggaaaaa	12	9	13	7	2	1	0	1	0	0	0	1	2	1	2	2	4	2	2	2	4	5	3	rs115780398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:112071464C>T	ENST00000357685.5	+	7	1129	c.994C>T	c.(994-996)Cgg>Tgg	p.R332W	BCO2_ENST00000526088.1_Missense_Mutation_p.R298W|BCO2_ENST00000393032.2_Missense_Mutation_p.R298W|BCO2_ENST00000532593.1_Missense_Mutation_p.R227W|BCO2_ENST00000531169.1_Missense_Mutation_p.R298W|BCO2_ENST00000361053.4_Missense_Mutation_p.R259W|BCO2_ENST00000438022.1_Missense_Mutation_p.R298W			Q9BYV7	BCDO2_HUMAN	beta-carotene oxygenase 2	332					carotene catabolic process (GO:0016121)|carotene metabolic process (GO:0016119)|carotenoid metabolic process (GO:0016116)|oxidation-reduction process (GO:0055114)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of reactive oxygen species metabolic process (GO:2000377)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)	intracellular (GO:0005622)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			NS(1)|breast(1)|kidney(3)|large_intestine(1)|lung(9)|skin(1)	16						GTGTAATACGCGGTTTCATGT	0.398													C|||	31	0.0061901	0.0212	0.0014	5008	,	,		18093	0.002		0.0	False		,,,				2504	0.0				p.R332W	GBM(177;1916 2099 21049 29541 39946)	Atlas-SNP	.											BCO2,colon,carcinoma,0,1	BCO2	44	1	0			c.C994T						PASS	.	C	TRP/ARG,TRP/ARG	81,4321	69.8+/-107.6	0,81,2120	120	123	122		892,994	0	0	11	dbSNP_132	122	1,8593	1.2+/-3.3	0,1,4296	yes	missense,missense	BCO2	NM_001037290.1,NM_031938.4	101,101	0,82,6416	TT,TC,CC		0.0116,1.8401,0.631	probably-damaging,probably-damaging	298/546,332/580	112071464	82,12914	2201	4297	6498	SO:0001583	missense	83875	exon7			AATACGCGGTTTC	AJ290393	CCDS8358.2, CCDS41716.1, CCDS58181.1, CCDS58182.1, CCDS58183.1	11q23.1	2014-05-12	2008-04-15	2008-04-15	ENSG00000197580	ENSG00000197580	1.13.11.71		18503	protein-coding gene	gene with protein product	"beta-carotene 9',10' oxygenase", "carotenoid-9',10'-cleaving dioxygenase"	611740	"beta-carotene dioxygenase 2"	BCDO2		11278918, 15983114, 15949678	Standard	NM_031938		Approved	FLJ34464, B-DIOX-II	uc001pnf.3	Q9BYV7	OTTHUMG00000167155	ENST00000357685.5:c.994C>T	11.37:g.112071464C>T	ENSP00000350314:p.Arg332Trp	78	0	0		64	35	0.546875	NM_031938	B0YIX5|B4DNC3|E9PBI8|E9PJJ1|Q8IUS0|Q96JC8|Q96JY5	Missense_Mutation	SNP	ENST00000357685.5	37	CCDS8358.2	16	0.007326007326007326	13	0.026422764227642278	1	0.0027624309392265192	2	0.0034965034965034965	0	0.0	C	5.058	0.196301	0.09599	0.018401	1.16E-4	ENSG00000197580	ENST00000357685;ENST00000393032;ENST00000361053;ENST00000438022;ENST00000526088;ENST00000532593;ENST00000531169	D;D;D;D;D;D;D	0.95885	-3.84;-3.84;-3.84;-3.84;-3.84;-3.84;-3.84	5.45	0.0177	0.14113	.	0.629740	0.16560	N	0.209094	D	0.85120	0.5624	L	0.39566	1.225	0.09310	N	1	D;D;D;D	0.63046	0.965;0.99;0.965;0.992	P;P;P;P	0.58970	0.788;0.659;0.788;0.849	T	0.81052	-0.1107	10	0.37606	T	0.19	-11.5438	1.2953	0.02068	0.2227:0.4126:0.1085:0.2562	.	309;259;332;159	C9JEZ9;E9PBI8;Q9BYV7;Q8NAZ7	.;.;BCDO2_HUMAN;.	W	332;298;259;298;298;227;298	ENSP00000350314:R332W;ENSP00000376752:R298W;ENSP00000354338:R259W;ENSP00000414843:R298W;ENSP00000436615:R298W;ENSP00000431802:R227W;ENSP00000437053:R298W	ENSP00000350314:R332W	R	+	1	2	BCO2	111576674	0.000000	0.05858	0.010000	0.14722	0.089000	0.18198	0.047000	0.14056	0.024000	0.15214	-0.203000	0.12734	CGG	C|0.994;T|0.006	0.006	strong		0.398	BCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256570.3	NM_001037290		T	112071464	C	T	112071464	3	4	22	1	0	0	0	0	1	0	0	0	1385	759	27	1	1020	1	BCO2	11	112071464	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	163327	112071464	22935052	2565	5466											
HTR3A	3359	hgsc.bcm.edu	37	chr11	113857661	113857661	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccgtgcctgcttggctgcGtcacctggttctggagagaa	5	10	14	12	2	2	1	1	0	1	1	2	3	2	2	3	3	3	3	3	3	1	2	rs35815285	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:113857661G>A	ENST00000504030.2	+	8	1476	c.1031G>A	c.(1030-1032)cGt>cAt	p.R344H	HTR3A_ENST00000535865.1_Missense_Mutation_p.R88H|HTR3A_ENST00000375498.2_Missense_Mutation_p.R350H|HTR3A_ENST00000299961.5_Missense_Mutation_p.R329H|HTR3A_ENST00000506841.2_Missense_Mutation_p.R376H|HTR3A_ENST00000355556.2_Missense_Mutation_p.R382H			P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A, ionotropic	344			R -> H (in dbSNP:rs35815285). {ECO:0000269|PubMed:16487942}.		cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cellular response to growth factor stimulus (GO:0071363)|digestion (GO:0007586)|ion transmembrane transport (GO:0034220)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	36		all_cancers(61;2.31e-17)|all_epithelial(67;2.1e-10)|all_hematologic(158;4.64e-05)|Melanoma(852;0.000312)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0294)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.71e-06)|Epithelial(105;2.58e-05)|all cancers(92;0.000238)|OV - Ovarian serous cystadenocarcinoma(223;0.191)	Alosetron(DB00969)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Chloroprocaine(DB01161)|Cisapride(DB00604)|Clozapine(DB00363)|Dolasetron(DB00757)|Ergoloid mesylate(DB01049)|Granisetron(DB00889)|Loxapine(DB00408)|Memantine(DB01043)|Methadone(DB00333)|Metoclopramide(DB01233)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Ondansetron(DB00904)|Palonosetron(DB00377)|Procaine(DB00721)|Quetiapine(DB01224)|Rocuronium(DB00728)|Tapentadol(DB06204)|Trimipramine(DB00726)|Tubocurarine(DB01199)|Ziprasidone(DB00246)	GCTTGGCTGCGTCACCTGGTT	0.592													G|||	172	0.034345	0.121	0.0144	5008	,	,		17839	0.0		0.002	False		,,,				2504	0.0				p.R382H		Atlas-SNP	.											HTR3A,NS,carcinoma,+1,1	HTR3A	93	1	0			c.G1145A	GRCh37	CM011786	HTR3A	M	rs35815285	scavenged	.	G	HIS/ARG,HIS/ARG,HIS/ARG	419,3983	205.2+/-227.1	17,385,1799	55	50	52		1049,986,1145	3.5	0.6	11	dbSNP_126	52	6,8586	5.0+/-18.6	0,6,4290	yes	missense,missense,missense	HTR3A	NM_000869.5,NM_001161772.2,NM_213621.3	29,29,29	17,391,6089	AA,AG,GG		0.0698,9.5184,3.2707	possibly-damaging,possibly-damaging,possibly-damaging	350/485,329/464,382/517	113857661	425,12569	2201	4296	6497	SO:0001583	missense	3359	exon7			GGCTGCGTCACCT	D49394	CCDS8365.1, CCDS8366.1, CCDS8365.2, CCDS8366.2, CCDS53710.1	11q23.1-q23.2	2012-05-22	2012-02-03					"5-HT (serotonin) receptors", "Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"	5297	protein-coding gene	gene with protein product		182139	"5-hydroxytryptamine (serotonin) receptor 3A"	HTR3		8530095, 12867984	Standard	NM_000869		Approved	5-HT3R, 5-HT3A	uc010rxb.2	P46098		ENST00000504030.2:c.1031G>A	11.37:g.113857661G>A	ENSP00000424189:p.Arg344His	119	1	0.00840336		119	69	0.579832	NM_213621	B4DSY6|G5E986|O60854|Q7KZM7|Q99918|Q9BSZ9	Missense_Mutation	SNP	ENST00000504030.2	37		59	0.027014652014652016	52	0.10569105691056911	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	G	18.10	3.548612	0.65311	0.095184	6.98E-4	ENSG00000166736	ENST00000504030;ENST00000355556;ENST00000375498;ENST00000506841;ENST00000535865;ENST00000299961	D;T;D;T;D;D	0.87966	-2.32;-0.77;-2.32;-0.77;-2.32;-2.32	5.37	3.51	0.40186	.	0.166108	0.48767	D	0.000170	T	0.12603	0.0306	L	0.45581	1.43	0.44104	D	0.996877	P;D;D	0.58970	0.944;0.98;0.984	P;P;P	0.52957	0.602;0.681;0.714	T	0.55405	-0.8146	10	0.59425	D	0.04	-19.81	6.9616	0.24599	0.3829:0.0:0.6171:0.0	rs35815285	329;382;350	B4DSY6;G5E986;Q7KZM7	.;.;.	H	344;382;350;376;88;329	ENSP00000424189:R344H;ENSP00000347754:R382H;ENSP00000364648:R350H;ENSP00000424776:R376H;ENSP00000437776:R88H;ENSP00000299961:R329H	ENSP00000299961:R329H	R	+	2	0	HTR3A	113362871	1.000000	0.71417	0.646000	0.29493	0.545000	0.35147	4.552000	0.60747	0.765000	0.33221	0.561000	0.74099	CGT	G|0.965;A|0.035	0.035	strong		0.592	HTR3A-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000360822.2	NM_000869		A	113857661	G	A	113857661	3	1	22	1	0	0	0	0	1	0	0	0	7453	1145	40	1	1197	1	HTR3A	11	113857661	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1786197	113857661	21148855	2566	5467											
FAM55A	120400	hgsc.bcm.edu	37	chr11	114393066	114393066	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtcacctgatagccggtcaAtttcccgagggatataatca	11	11	9	10	2	3	1	3	1	0	0	4	3	4	2	3	2	1	0	3	2	4	4	rs34993124	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:114393066A>G	ENST00000424269.1	-	5	1267	c.1268T>C	c.(1267-1269)aTt>aCt	p.I423T	NXPE1_ENST00000251921.2_Missense_Mutation_p.I281T|NXPE1_ENST00000536271.1_Missense_Mutation_p.I139T			Q8N323	NXPE1_HUMAN	neurexophilin and PC-esterase domain family, member 1	423			I -> T (in dbSNP:rs34993124).			extracellular region (GO:0005576)											TAGCCGGTCAATTTCCCGAGG	0.443													A|||	95	0.0189696	0.0651	0.013	5008	,	,		18652	0.0		0.0	False		,,,				2504	0.0				p.I281T		Atlas-SNP	.											.	NXPE1	8	.	0			c.T842C						PASS	.	A	THR/ILE	254,4148	146.1+/-180.8	4,246,1951	147	140	142		842	2.1	0.6	11	dbSNP_126	142	3,8589	3.0+/-9.4	0,3,4293	yes	missense	FAM55A	NM_152315.2	89	4,249,6244	GG,GA,AA		0.0349,5.7701,1.9778	probably-damaging	281/406	114393066	257,12737	2201	4296	6497	SO:0001583	missense	120400	exon6			CGGTCAATTTCCC	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.1268T>C	11.37:g.114393066A>G	ENSP00000411690:p.Ile423Thr	172	0	0		161	74	0.459627	NM_152315	B0YJ13	Missense_Mutation	SNP	ENST00000424269.1	37		38	0.0173992673992674	34	0.06910569105691057	4	0.011049723756906077	0	0.0	0	0.0	A	27.2	4.809928	0.90707	0.057701	3.49E-4	ENSG00000095110	ENST00000536271;ENST00000251921;ENST00000424269	T;T;T	0.27256	1.68;1.68;1.68	4.44	2.07	0.26955	.	0.082106	0.49916	D	0.000132	T	0.07503	0.0189	M	0.92367	3.3	0.28092	N	0.931779	D	0.76494	0.999	D	0.67382	0.951	T	0.10177	-1.0641	10	0.56958	D	0.05	.	8.0262	0.30438	0.8267:0.0:0.1733:0.0	rs34993124	423	Q8N323	FA55A_HUMAN	T	139;281;423	ENSP00000445200:I139T;ENSP00000251921:I281T;ENSP00000411690:I423T	ENSP00000251921:I281T	I	-	2	0	FAM55A	113898276	0.993000	0.37304	0.643000	0.29450	0.931000	0.56810	1.124000	0.31320	0.298000	0.22638	0.528000	0.53228	ATT	A|0.982;G|0.018	0.018	strong		0.443	NXPE1-201	KNOWN	basic	protein_coding	protein_coding		NM_152315		G	114393066	A	G	114393066	3	3	22	1	0	0	0	0	1	0	0	0	5592	101	4	3	379	3	FAM55A	11	114393066	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	535405	114393066	20613450	2567	5468											
FAM55A	120400	hgsc.bcm.edu	37	chr11	114393757	114393757	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttccttgtaaagtataacCaccagggacaggaggcttca	12	11	9	9	0	1	0	1	0	0	0	2	2	2	2	3	3	1	3	3	3	4	7	rs79538449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:114393757C>T	ENST00000424269.1	-	4	951	c.952G>A	c.(952-954)Ggt>Agt	p.G318S	NXPE1_ENST00000251921.2_Missense_Mutation_p.G176S|NXPE1_ENST00000536271.1_Missense_Mutation_p.G34S			Q8N323	NXPE1_HUMAN	neurexophilin and PC-esterase domain family, member 1	318						extracellular region (GO:0005576)											AAAGTATAACCACCAGGGACA	0.363													C|||	16	0.00319489	0.0121	0.0	5008	,	,		19211	0.0		0.0	False		,,,				2504	0.0				p.G176S		Atlas-SNP	.											.	NXPE1	8	.	0			c.G526A						PASS	.	C	SER/GLY	56,4346	56.2+/-92.4	0,56,2145	101	91	95		526	4.4	0.2	11	dbSNP_131	95	1,8591	1.2+/-3.3	0,1,4295	yes	missense	FAM55A	NM_152315.2	56	0,57,6440	TT,TC,CC		0.0116,1.2721,0.4387	probably-damaging	176/406	114393757	57,12937	2201	4296	6497	SO:0001583	missense	120400	exon5			TATAACCACCAGG	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.952G>A	11.37:g.114393757C>T	ENSP00000411690:p.Gly318Ser	145	0	0		166	99	0.596386	NM_152315	B0YJ13	Missense_Mutation	SNP	ENST00000424269.1	37		3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	33	5.276316	0.95459	0.012721	1.16E-4	ENSG00000095110	ENST00000536271;ENST00000251921;ENST00000424269	T;T;T	0.60797	0.55;0.29;0.16	4.4	4.4	0.53042	.	0.000000	0.64402	D	0.000003	T	0.72011	0.3408	M	0.84585	2.705	0.42372	D	0.992458	D	0.89917	1.0	D	0.97110	1.0	T	0.80777	-0.1231	10	0.87932	D	0	.	15.2699	0.73693	0.0:1.0:0.0:0.0	.	318	Q8N323	FA55A_HUMAN	S	34;176;318	ENSP00000445200:G34S;ENSP00000251921:G176S;ENSP00000411690:G318S	ENSP00000251921:G176S	G	-	1	0	FAM55A	113898967	0.425000	0.25498	0.152000	0.22495	0.689000	0.40095	2.280000	0.43443	2.372000	0.80975	0.650000	0.86243	GGT	C|0.997;T|0.003	0.003	strong		0.363	NXPE1-201	KNOWN	basic	protein_coding	protein_coding		NM_152315		T	114393757	C	T	114393757	3	4	22	1	0	0	0	0	1	0	0	0	5592	594	21	2	699	2	FAM55A	11	114393757	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	691	114393757	20612759	2568	5469											
SIDT2	51092	hgsc.bcm.edu	37	chr11	117050007	117050007	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctctgggcttgcccttcttgGtgctcttggtggcctcggtc	0	15	13	13	1	3	0	0	0	3	0	5	0	3	0	2	5	2	2	2	5	0	4	rs61729992	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117050007G>A	ENST00000324225.4	+	1	559	c.28G>A	c.(28-30)Gtg>Atg	p.V10M	SIDT2_ENST00000431081.2_Missense_Mutation_p.V10M	NM_001040455.1	NP_001035545.1	Q8NBJ9	SIDT2_HUMAN	SID1 transmembrane family, member 2	10					cell morphogenesis (GO:0000902)|dsRNA transport (GO:0033227)|glucose homeostasis (GO:0042593)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to glucose (GO:0009749)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell proliferation (GO:0044342)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	RNA transmembrane transporter activity (GO:0051033)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	36	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;0.000219)|all cancers(92;0.00144)		GCCCTTCTTGGTGCTCTTGGT	0.677													G|||	43	0.00858626	0.0303	0.0029	5008	,	,		11337	0.0		0.001	False		,,,				2504	0.0				p.V10M		Atlas-SNP	.											.	SIDT2	82	.	0			c.G28A						PASS	.	G	MET/VAL	83,4319	70.3+/-108.2	0,83,2118	72	66	68		28	2.3	0.1	11	dbSNP_129	68	0,8592		0,0,4296	yes	missense	SIDT2	NM_001040455.1	21	0,83,6414	AA,AG,GG		0.0,1.8855,0.6388	benign	10/833	117050007	83,12911	2201	4296	6497	SO:0001583	missense	51092	exon1			TTCTTGGTGCTCT	AF151799	CCDS31682.1	11q23.3	2008-02-05			ENSG00000149577	ENSG00000149577			24272	protein-coding gene	gene with protein product						10810093, 12975309	Standard	NM_001040455		Approved	CGI-40	uc001pqh.1	Q8NBJ9	OTTHUMG00000167065	ENST00000324225.4:c.28G>A	11.37:g.117050007G>A	ENSP00000314023:p.Val10Met	43	0	0		44	15	0.340909	NM_001040455	Q8NBY7|Q9Y357	Missense_Mutation	SNP	ENST00000324225.4	37	CCDS31682.1	19	0.0086996336996337	16	0.032520325203252036	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	11.97	1.798338	0.31777	0.018855	0.0	ENSG00000149577	ENST00000324225;ENST00000532960;ENST00000525347;ENST00000278951;ENST00000431081;ENST00000392956	T;T;T;T	0.50548	2.12;0.74;2.1;2.12	4.19	2.28	0.28536	.	1.095770	0.07106	N	0.841382	T	0.19644	0.0472	L	0.44542	1.39	0.25313	N	0.989181	B;P;P;B	0.43701	0.126;0.815;0.718;0.232	B;B;B;B	0.43251	0.206;0.413;0.235;0.07	T	0.17806	-1.0357	10	0.62326	D	0.03	-4.7017	5.5137	0.16894	0.1108:0.2032:0.6859:0.0	rs61729992	10;10;10;10	Q8NBJ9-2;F5H8L4;Q8NBJ9;C9JBG5	.;.;SIDT2_HUMAN;.	M	10	ENSP00000314023:V10M;ENSP00000431176:V10M;ENSP00000278951:V10M;ENSP00000399635:V10M	ENSP00000278951:V10M	V	+	1	0	SIDT2	116555217	1.000000	0.71417	0.081000	0.20488	0.384000	0.30261	3.334000	0.52097	0.393000	0.25203	0.561000	0.74099	GTG	G|0.991;A|0.009	0.009	strong		0.677	SIDT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392836.1	NM_015996		A	117050007	G	A	117050007	3	1	22	1	0	0	0	0	1	0	0	0	14318	1261	44	2	30	2	SIDT2	11	117050007	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2656250	117050007	17956509	2569	5470											
SIDT2	51092	hgsc.bcm.edu	37	chr11	117062989	117062989	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtctttggcaaagggaacaCggcgttctggatcgtcttct	7	12	13	9	3	4	0	0	0	4	0	5	2	4	2	0	5	1	2	0	5	2	3	rs12285035	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117062989C>T	ENST00000324225.4	+	20	2423	c.1892C>T	c.(1891-1893)aCg>aTg	p.T631M	SIDT2_ENST00000431081.2_Missense_Mutation_p.T628M|SIDT2_ENST00000532062.1_5'Flank	NM_001040455.1	NP_001035545.1	Q8NBJ9	SIDT2_HUMAN	SID1 transmembrane family, member 2	631			T -> M (in dbSNP:rs12285035).		cell morphogenesis (GO:0000902)|dsRNA transport (GO:0033227)|glucose homeostasis (GO:0042593)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to glucose (GO:0009749)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell proliferation (GO:0044342)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	RNA transmembrane transporter activity (GO:0051033)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	36	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;0.000219)|all cancers(92;0.00144)		AAAGGGAACACGGCGTTCTGG	0.617													C|||	83	0.0165735	0.0575	0.0086	5008	,	,		18145	0.0		0.001	False		,,,				2504	0.0				p.T631M		Atlas-SNP	.											.	SIDT2	82	.	0			c.C1892T						PASS	.	C	MET/THR	214,4188	129.8+/-166.5	6,202,1993	114	97	103		1892	3.4	0.9	11	dbSNP_120	103	2,8590	2.2+/-6.3	0,2,4294	yes	missense	SIDT2	NM_001040455.1	81	6,204,6287	TT,TC,CC		0.0233,4.8614,1.6623	benign	631/833	117062989	216,12778	2201	4296	6497	SO:0001583	missense	51092	exon20			GGAACACGGCGTT	AF151799	CCDS31682.1	11q23.3	2008-02-05			ENSG00000149577	ENSG00000149577			24272	protein-coding gene	gene with protein product						10810093, 12975309	Standard	NM_001040455		Approved	CGI-40	uc001pqh.1	Q8NBJ9	OTTHUMG00000167065	ENST00000324225.4:c.1892C>T	11.37:g.117062989C>T	ENSP00000314023:p.Thr631Met	98	0	0		93	93	1	NM_001040455	Q8NBY7|Q9Y357	Missense_Mutation	SNP	ENST00000324225.4	37	CCDS31682.1	34	0.015567765567765568	29	0.05894308943089431	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	C	9.873	1.199548	0.22121	0.048614	2.33E-4	ENSG00000149577	ENST00000324225;ENST00000278951;ENST00000431081	T;T;T	0.21932	1.98;1.98;1.98	5.47	3.36	0.38483	.	0.304899	0.37761	N	0.001945	T	0.00784	0.0026	N	0.02247	-0.625	0.35238	D	0.777525	B;B;B;B	0.16166	0.013;0.005;0.006;0.016	B;B;B;B	0.15484	0.007;0.003;0.008;0.013	T	0.22661	-1.0210	10	0.32370	T	0.25	-5.8591	8.774	0.34751	0.0:0.6961:0.0:0.3039	rs12285035;rs52809888;rs12285035	652;628;631;652	Q8NBJ9-2;F5H8L4;Q8NBJ9;C9JBG5	.;.;SIDT2_HUMAN;.	M	631;652;628	ENSP00000314023:T631M;ENSP00000278951:T652M;ENSP00000399635:T628M	ENSP00000278951:T652M	T	+	2	0	SIDT2	116568199	0.066000	0.20996	0.886000	0.34754	0.994000	0.84299	0.421000	0.21280	1.308000	0.44962	0.655000	0.94253	ACG	C|0.978;T|0.022	0.022	strong		0.617	SIDT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392836.1	NM_015996		T	117062989	C	T	117062989	3	4	22	1	0	0	0	0	1	0	0	0	14318	536	19	1	1970	1	SIDT2	11	117062989	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	12982	117062989	17943527	2570	5471											
SIDT2	51092	hgsc.bcm.edu	37	chr11	117063020	117063020	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcgtcttctccatcattcaCatcatcgccaccctgctcct	7	13	3	18	2	5	0	3	0	2	0	9	0	6	0	4	0	1	1	4	0	0	2	rs12285062	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117063020C>T	ENST00000324225.4	+	20	2454	c.1923C>T	c.(1921-1923)caC>caT	p.H641H	SIDT2_ENST00000431081.2_Silent_p.H638H|SIDT2_ENST00000532062.1_5'Flank	NM_001040455.1	NP_001035545.1	Q8NBJ9	SIDT2_HUMAN	SID1 transmembrane family, member 2	641					cell morphogenesis (GO:0000902)|dsRNA transport (GO:0033227)|glucose homeostasis (GO:0042593)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to glucose (GO:0009749)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell proliferation (GO:0044342)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	RNA transmembrane transporter activity (GO:0051033)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	36	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;0.000219)|all cancers(92;0.00144)		CCATCATTCACATCATCGCCA	0.632													C|||	40	0.00798722	0.0272	0.0058	5008	,	,		17690	0.0		0.0	False		,,,				2504	0.0				p.H641H		Atlas-SNP	.											.	SIDT2	82	.	0			c.C1923T						PASS	.	C		125,4277	92.0+/-130.7	2,121,2078	122	102	109		1923	0	1	11	dbSNP_120	109	2,8590	2.2+/-6.3	0,2,4294	no	coding-synonymous	SIDT2	NM_001040455.1		2,123,6372	TT,TC,CC		0.0233,2.8396,0.9774		641/833	117063020	127,12867	2201	4296	6497	SO:0001819	synonymous_variant	51092	exon20			CATTCACATCATC	AF151799	CCDS31682.1	11q23.3	2008-02-05			ENSG00000149577	ENSG00000149577			24272	protein-coding gene	gene with protein product						10810093, 12975309	Standard	NM_001040455		Approved	CGI-40	uc001pqh.1	Q8NBJ9	OTTHUMG00000167065	ENST00000324225.4:c.1923C>T	11.37:g.117063020C>T		106	0	0		94	49	0.521277	NM_001040455	Q8NBY7|Q9Y357	Silent	SNP	ENST00000324225.4	37	CCDS31682.1																																																																																			C|0.990;T|0.010	0.010	strong		0.632	SIDT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392836.1	NM_015996		T	117063020	C	T	117063020	2	4	22	1	0	0	0	0	0	0	0	1	14318	477	17	2		2	SIDT2	11	117063020	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	31	117063020	17943496	2571	5472											
TAGLN	6876	hgsc.bcm.edu	37	chr11	117075014	117075014	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggccttcagatgggcagcaAcagaggggcctcccaggccg	8	5	15	13	1	1	2	1	0	0	2	2	2	2	2	4	5	2	2	4	5	1	1	rs12284316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117075014A>G	ENST00000532870.1	+	4	1686	c.545A>G	c.(544-546)aAc>aGc	p.N182S	TAGLN_ENST00000530649.1_Missense_Mutation_p.N182S|TAGLN_ENST00000392951.4_Missense_Mutation_p.N182S|PCSK7_ENST00000529458.1_5'Flank			Q01995	TAGL_HUMAN	transgelin	182			N -> S (in dbSNP:rs12284316).		epithelial cell differentiation (GO:0030855)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)				central_nervous_system(1)|large_intestine(4)|lung(1)|urinary_tract(1)	7	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;1.63e-06)|Epithelial(105;5.49e-05)|all cancers(92;0.000435)		ATGGGCAGCAACAGAGGGGCC	0.612													A|||	15	0.00299521	0.0113	0.0	5008	,	,		18601	0.0		0.0	False		,,,				2504	0.0				p.N182S		Atlas-SNP	.											.	TAGLN	17	.	0			c.A545G						PASS	.	A	SER/ASN,SER/ASN	46,4356	48.2+/-83.0	0,46,2155	80	83	82		545,545	4.6	1	11	dbSNP_120	82	0,8592		0,0,4296	yes	missense,missense	TAGLN	NM_001001522.1,NM_003186.3	46,46	0,46,6451	GG,GA,AA		0.0,1.045,0.354	probably-damaging,probably-damaging	182/202,182/202	117075014	46,12948	2201	4296	6497	SO:0001583	missense	6876	exon5			GCAGCAACAGAGG	M95787	CCDS8381.1	11q23.2	2008-07-21				ENSG00000149591			11553	protein-coding gene	gene with protein product	"SM22-alpha", "transgelin variant 2"	600818				8117285, 1520290	Standard	NM_003186		Approved	SM22, WS3-10, TAGLN1, SMCC, DKFZp686P11128	uc001pqm.3	Q01995		ENST00000532870.1:c.545A>G	11.37:g.117075014A>G	ENSP00000432282:p.Asn182Ser	312	1	0.00320513		255	146	0.572549	NM_001001522	O15542	Missense_Mutation	SNP	ENST00000532870.1	37	CCDS8381.1	6|6	0.0027472527472527475|0.0027472527472527475	6|6	0.012195121951219513|0.012195121951219513	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	A|A	22.5|22.5	4.294103|4.294103	0.81025|0.81025	0.01045|0.01045	0.0|0.0	ENSG00000149591|ENSG00000149591	ENST00000392951;ENST00000525531;ENST00000278968;ENST00000530649;ENST00000532870|ENST00000529622	T;T;T;T;T|.	0.68331|.	-0.32;-0.32;-0.32;-0.32;-0.32|.	4.63|4.63	4.63|4.63	0.57726|0.57726	Calponin homology domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.82231|0.82231	0.4992|0.4992	H|H	0.95745|0.95745	3.715|3.715	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	D|.	0.71414|.	0.973|.	D|D	0.88266|0.88266	0.2926|0.2926	10|5	0.87932|.	D|.	0|.	.|.	13.0278|13.0278	0.58825|0.58825	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	rs12284316|rs12284316	182|.	Q01995|.	TAGL_HUMAN|.	S|A	182|132	ENSP00000376678:N182S;ENSP00000432054:N182S;ENSP00000278968:N182S;ENSP00000431941:N182S;ENSP00000432282:N182S|.	ENSP00000278968:N182S|.	N|T	+|+	2|1	0|0	TAGLN|TAGLN	116580224|116580224	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.966000|0.966000	0.64601|0.64601	8.709000|8.709000	0.91379|0.91379	1.954000|1.954000	0.56735|0.56735	0.402000|0.402000	0.26972|0.26972	AAC|ACA	A|0.996;G|0.004	0.004	strong		0.612	TAGLN-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392864.1	NM_001001522		G	117075014	A	G	117075014	3	3	22	1	0	0	0	0	1	0	0	0	15553	43	2	3	559	3	TAGLN	11	117075014	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	11994	117075014	17931502	2572	5473											
PCSK7	9159	hgsc.bcm.edu	37	chr11	117079687	117079687	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcttcagctccaagctgccGcgccgtgggtgagtgatgga	7	8	15	11	3	1	2	1	2	0	0	2	3	2	3	3	2	4	3	3	2	1	1	rs148329047	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117079687G>A	ENST00000320934.3	-	13	2247	c.1617C>T	c.(1615-1617)cgC>cgT	p.R539R	PCSK7_ENST00000540028.1_Silent_p.R180R|PCSK7_ENST00000529458.1_5'Flank	NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	539					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)		CCAAGCTGCCGCGCCGTGGGT	0.617			T	IGH@	MLCLS								G|||	44	0.00878594	0.031	0.0029	5008	,	,		24069	0.0		0.001	False		,,,				2504	0.0				p.R539R		Atlas-SNP	.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	.	PCSK7	59	.	0			c.C1617T						PASS	.	G		81,4321	62.3+/-99.4	0,81,2120	41	42	41		1617	-9.1	0.2	11	dbSNP_134	41	0,8590		0,0,4295	no	coding-synonymous	PCSK7	NM_004716.2		0,81,6415	AA,AG,GG		0.0,1.8401,0.6235		539/786	117079687	81,12911	2201	4295	6496	SO:0001819	synonymous_variant	9159	exon13			GCTGCCGCGCCGT	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.1617C>T	11.37:g.117079687G>A		393	0	0		246	92	0.373984	NM_004716	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Silent	SNP	ENST00000320934.3	37	CCDS8382.1																																																																																			G|0.991;A|0.009	0.009	strong		0.617	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716		A	117079687	G	A	117079687	2	1	22	1	0	0	0	0	0	0	0	1	11614	1074	38	1		1	PCSK7	11	117079687	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4673	117079687	17926829	2573	5474											
PCSK7	9159	hgsc.bcm.edu	37	chr11	117089801	117089801	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cattcacgagcctccaggcgTtgaggaggccgaaaccgtgc	9	6	13	13	4	1	1	1	1	0	0	2	4	2	2	4	3	3	1	4	3	1	2	rs61729982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117089801T>C	ENST00000320934.3	-	11	2033	c.1403A>G	c.(1402-1404)aAc>aGc	p.N468S	PCSK7_ENST00000540028.1_Missense_Mutation_p.N109S	NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	468	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)		CCTCCAGGCGTTGAGGAGGCC	0.607			T	IGH@	MLCLS								T|||	20	0.00399361	0.0151	0.0	5008	,	,		21331	0.0		0.0	False		,,,				2504	0.0				p.N468S		Atlas-SNP	.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	.	PCSK7	59	.	0			c.A1403G						PASS	.	T	SER/ASN	48,4354	49.6+/-84.7	0,48,2153	67	53	57		1403	5.2	0.9	11	dbSNP_129	57	0,8592		0,0,4296	yes	missense	PCSK7	NM_004716.2	46	0,48,6449	CC,CT,TT		0.0,1.0904,0.3694	benign	468/786	117089801	48,12946	2201	4296	6497	SO:0001583	missense	9159	exon11			CAGGCGTTGAGGA	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.1403A>G	11.37:g.117089801T>C	ENSP00000325917:p.Asn468Ser	44	0	0		41	29	0.707317	NM_004716	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Missense_Mutation	SNP	ENST00000320934.3	37	CCDS8382.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	T	13.08	2.129420	0.37630	0.010904	0.0	ENSG00000160613	ENST00000320934;ENST00000540028;ENST00000543900	D;D	0.83163	-1.69;-1.69	5.2	5.2	0.72013	Peptidase S8/S53, subtilisin/kexin/sedolisin (2);	0.050433	0.85682	D	0.000000	T	0.65688	0.2715	L	0.43923	1.385	0.52501	D	0.999951	B	0.18013	0.025	B	0.17722	0.019	T	0.71583	-0.4549	10	0.59425	D	0.04	-22.611	13.9011	0.63804	0.0:0.0:0.0:1.0	.	468	Q16549	PCSK7_HUMAN	S	468;109;468	ENSP00000325917:N468S;ENSP00000441944:N109S	ENSP00000325917:N468S	N	-	2	0	PCSK7	116595011	0.999000	0.42202	0.924000	0.36721	0.523000	0.34469	3.028000	0.49705	1.977000	0.57605	0.482000	0.46254	AAC	T|0.996;C|0.004	0.004	strong		0.607	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716		C	117089801	T	C	117089801	3	2	22	1	0	0	0	0	1	0	0	0	11614	1725	60	3	982	3	PCSK7	11	117089801	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	10114	117089801	17916715	2574	5475											
PCSK7	9159	hgsc.bcm.edu	37	chr11	117097931	117097931	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagctgttgttgggcacagcCgcgatctctcctgcacatcg	7	10	11	13	3	1	0	0	0	1	0	4	1	2	0	2	1	3	5	2	1	1	2	rs45528535	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117097931C>T	ENST00000320934.3	-	5	1341	c.711G>A	c.(709-711)gcG>gcA	p.A237A		NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	237	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)		TGGGCACAGCCGCGATCTCTC	0.607			T	IGH@	MLCLS						OREG0021371	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	227	0.0453275	0.1415	0.0375	5008	,	,		18045	0.0		0.0119	False		,,,				2504	0.002				p.A237A		Atlas-SNP	.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	PCSK7,NS,carcinoma,-2,1	PCSK7	59	1	0			c.G711A						PASS	.	C		535,3867	243.1+/-252.9	28,479,1694	114	94	101		711	-11.2	0	11	dbSNP_127	101	31,8561	22.2+/-67.0	0,31,4265	no	coding-synonymous	PCSK7	NM_004716.2		28,510,5959	TT,TC,CC		0.3608,12.1536,4.3559		237/786	117097931	566,12428	2201	4296	6497	SO:0001819	synonymous_variant	9159	exon5			CACAGCCGCGATC	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.711G>A	11.37:g.117097931C>T		78	0	0	1478	79	28	0.35443	NM_004716	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Silent	SNP	ENST00000320934.3	37	CCDS8382.1																																																																																			C|0.956;T|0.044	0.044	strong		0.607	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716		T	117097931	C	T	117097931	2	4	22	1	0	0	0	0	0	0	0	1	11614	639	23	1		1	PCSK7	11	117097931	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	8130	117097931	17908585	2575	5476											
BACE1	23621	hgsc.bcm.edu	37	chr11	117186285	117186285	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgcccacggtcatctccacgTagtagccctgccccgacttg	6	9	9	17	3	2	0	1	0	1	0	3	1	2	0	5	1	3	2	5	1	2	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117186285T>C	ENST00000313005.6	-	1	687	c.227A>G	c.(226-228)tAc>tGc	p.Y76C	BACE1_ENST00000428381.2_Missense_Mutation_p.Y76C|BACE1_ENST00000514464.1_5'UTR|BACE1_ENST00000528053.1_Missense_Mutation_p.Y76C|BACE1_ENST00000445823.2_Missense_Mutation_p.Y76C|BACE1_ENST00000513780.1_Missense_Mutation_p.Y76C|AP000892.4_ENST00000504906.1_RNA	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	76					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)		CATCTCCACGTAGTAGCCCTG	0.677																																					p.Y76C		Atlas-SNP	.											.	BACE1	33	.	0			c.A227G						PASS	.						45	44	44					11																	117186285		2201	4296	6497	SO:0001583	missense	23621	exon1			TCCACGTAGTAGC	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.227A>G	11.37:g.117186285T>C	ENSP00000318585:p.Tyr76Cys	151	0	0		87	4	0.045977	NM_138972	A0M8W7|B0YIU9|E9PE65|H7BXJ9|Q9BYB9|Q9BYC0|Q9BYC1|Q9UJT5|Q9ULS1	Missense_Mutation	SNP	ENST00000313005.6	37	CCDS8383.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.420349	0.83559	.	.	ENSG00000186318	ENST00000313005;ENST00000528053;ENST00000428381;ENST00000513780;ENST00000445823	T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82	4.99	4.99	0.66335	Peptidase aspartic (1);Peptidase aspartic, catalytic (1);	0.061196	0.64402	D	0.000002	T	0.72179	0.3428	M	0.89414	3.03	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;0.998;0.982;0.964;0.999	T	0.78186	-0.2302	10	0.87932	D	0	.	12.6208	0.56601	0.0:0.0:0.0:1.0	.	76;76;76;76;76	Q76KP0;P56817;P56817-3;P56817-4;P56817-2	.;BACE1_HUMAN;.;.;.	C	76	ENSP00000318585:Y76C;ENSP00000431848:Y76C;ENSP00000402228:Y76C;ENSP00000424536:Y76C;ENSP00000403685:Y76C	ENSP00000318585:Y76C	Y	-	2	0	BACE1	116691495	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.012000	0.76366	1.866000	0.54105	0.533000	0.62120	TAC	.	.	none		0.677	BACE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361505.1			C	117186285	T	C	117186285	3	2	22	1	0	0	0	0	1	0	0	0	1281	1638	57	3	1314	3	BACE1	11	117186285	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	88354	117186285	17820231	2576	5477											
DSCAML1	57453	hgsc.bcm.edu	37	chr11	117329597	117329597	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agctccacccgctcccgcgtGgtggtgatgttctgcatctc	4	11	11	15	3	2	1	0	1	2	0	5	1	4	1	3	2	2	4	3	2	0	1	rs115831160	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117329597G>C	ENST00000321322.6	-	19	3622	c.3621C>G	c.(3619-3621)acC>acG	p.T1207T	DSCAML1_ENST00000527706.1_Silent_p.T937T	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1147	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		GCTCCCGCGTGGTGGTGATGT	0.652													G|||	5	0.000998403	0.0038	0.0	5008	,	,		20355	0.0		0.0	False		,,,				2504	0.0				p.T1207T		Atlas-SNP	.											.	DSCAML1	286	.	0			c.C3621G						PASS	.	G		14,4388	22.3+/-47.3	0,14,2187	104	95	98		3621	-7.8	0.7	11	dbSNP_132	98	2,8590	2.2+/-6.3	0,2,4294	no	coding-synonymous	DSCAML1	NM_020693.2		0,16,6481	CC,CG,GG		0.0233,0.318,0.1231		1207/2114	117329597	16,12978	2201	4296	6497	SO:0001819	synonymous_variant	57453	exon19			CCGCGTGGTGGTG		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.3621C>G	11.37:g.117329597G>C		100	0	0		118	48	0.40678	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Silent	SNP	ENST00000321322.6	37	CCDS8384.1																																																																																			G|0.999;C|0.001	0.001	strong		0.652	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		C	117329597	G	C	117329597	2	2	22	1	0	0	0	0	0	0	0	1	4771	1335	47	4		4	DSCAML1	11	117329597	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	143312	117329597	17676919	2577	5478											
IL10RA	3587	hgsc.bcm.edu	37	chr11	117870257	117870257	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	agctttgcccatgaccttgcCcctctaggctgtgtggcagc	5	11	11	14	0	1	1	0	1	1	0	1	1	1	1	4	2	4	3	4	2	1	3	rs146193205	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117870257C>T	ENST00000227752.3	+	7	1758	c.1638C>T	c.(1636-1638)gcC>gcT	p.A546A	IL10RA_ENST00000545409.1_Silent_p.A397A|IL10RA_ENST00000541785.1_Silent_p.A526A|IL10RA_ENST00000533700.1_3'UTR	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	546					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)		ATGACCTTGCCCCTCTAGGCT	0.592													C|||	3	0.000599042	0.0023	0.0	5008	,	,		19108	0.0		0.0	False		,,,				2504	0.0				p.A546A		Atlas-SNP	.											.	IL10RA	46	.	0			c.C1638T						PASS	.	C		6,4394	11.4+/-27.6	0,6,2194	51	48	49		1638	-0.1	0	11	dbSNP_134	49	0,8592		0,0,4296	no	coding-synonymous	IL10RA	NM_001558.3		0,6,6490	TT,TC,CC		0.0,0.1364,0.0462		546/579	117870257	6,12986	2200	4296	6496	SO:0001819	synonymous_variant	3587	exon7			CCTTGCCCCTCTA	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.1638C>T	11.37:g.117870257C>T		67	0	0		53	30	0.566038	NM_001558	A8K6I0|B0YJ27	Silent	SNP	ENST00000227752.3	37	CCDS8388.1																																																																																			C|0.999;T|0.001	0.001	strong		0.592	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1			T	117870257	C	T	117870257	2	4	22	1	0	0	0	0	0	0	0	1	7629	610	22	2		2	IL10RA	11	117870257	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	540660	117870257	17136259	2578	5479											
TMPRSS4	56649	hgsc.bcm.edu	37	chr11	117978578	117978578	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagccaggagcttcgcatgcGgaactcaagtgggtaagtga	11	7	14	9	2	1	1	1	1	0	0	2	3	1	3	1	3	4	3	1	3	3	2	rs1894176	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117978578G>A	ENST00000437212.3	+	6	744	c.530G>A	c.(529-531)cGg>cAg	p.R177Q	TMPRSS4_ENST00000523251.1_Missense_Mutation_p.R137Q|TMPRSS4_ENST00000522824.1_Missense_Mutation_p.R172Q|TMPRSS4_ENST00000534111.1_Missense_Mutation_p.R175Q|TMPRSS4_ENST00000522307.1_Missense_Mutation_p.R30Q			Q9NRS4	TMPS4_HUMAN	transmembrane protease, serine 4	177	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.		R -> Q (in dbSNP:rs1894176).		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)		CTTCGCATGCGGAACTCAAGT	0.547													G|||	204	0.0407348	0.1415	0.0216	5008	,	,		19296	0.0		0.002	False		,,,				2504	0.0				p.R177Q		Atlas-SNP	.											TMPRSS4,NS,carcinoma,-1,1	TMPRSS4	46	1	0			c.G530A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	452,3948	216.1+/-234.9	26,400,1774	67	60	62		515,524,410,530	-7.9	0	11	dbSNP_92	62	13,8579	9.1+/-34.3	0,13,4283	yes	missense,missense,missense,missense	TMPRSS4	NM_001083947.1,NM_001173551.1,NM_001173552.1,NM_019894.3	43,43,43,43	26,413,6057	AA,AG,GG		0.1513,10.2727,3.5791	benign,benign,benign,benign	172/433,175/436,137/398,177/438	117978578	465,12527	2200	4296	6496	SO:0001583	missense	56649	exon6			GCATGCGGAACTC	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.530G>A	11.37:g.117978578G>A	ENSP00000416037:p.Arg177Gln	57	0	0		51	35	0.686275	NM_019894	A8MU84|B0YJB0|B7Z8C5|E7ERX8|Q5XKQ6|Q6UX37|Q9NZA5	Missense_Mutation	SNP	ENST00000437212.3	37	CCDS31684.1	84	0.038461538461538464	78	0.15853658536585366	6	0.016574585635359115	0	0.0	0	0.0	G	2.686	-0.274296	0.05679	0.102727	0.001513	ENSG00000137648	ENST00000534111;ENST00000522307;ENST00000523251;ENST00000437212;ENST00000522824;ENST00000522151	T;D;T;T;T;T	0.88201	0.21;-2.35;0.21;0.21;0.21;0.21	5.31	-7.95	0.01148	Speract/scavenger receptor-related (2);	1.636540	0.03489	N	0.216335	T	0.00384	0.0012	N	0.00642	-1.3	0.80722	P	0.0	B;B;B;B;B	0.15719	0.014;0.014;0.008;0.005;0.005	B;B;B;B;B	0.04013	0.001;0.001;0.0;0.001;0.001	T	0.33752	-0.9856	9	0.13108	T	0.6	.	4.6674	0.12673	0.2857:0.1209:0.4751:0.1183	rs1894176;rs1894176	152;137;30;177;175	B7Z900;E7ERX8;E7ESG9;Q9NRS4;Q9NRS4-3	.;.;.;TMPS4_HUMAN;.	Q	175;30;137;177;172;124	ENSP00000435184:R175Q;ENSP00000428814:R30Q;ENSP00000429209:R137Q;ENSP00000416037:R177Q;ENSP00000430547:R172Q;ENSP00000428407:R124Q	ENSP00000416037:R177Q	R	+	2	0	TMPRSS4	117483788	0.000000	0.05858	0.033000	0.17914	0.003000	0.03518	-1.134000	0.03228	-1.008000	0.03404	-1.105000	0.02106	CGG	G|0.955;A|0.045	0.045	strong		0.547	TMPRSS4-004	KNOWN	non_canonical_polymorphism|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377328.2	NM_019894		A	117978578	G	A	117978578	3	1	22	1	0	0	0	0	1	0	0	0	16264	1116	39	1	552	1	TMPRSS4	11	117978578	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	108321	117978578	17027938	2579	5480											
MPZL3	196264	hgsc.bcm.edu	37	chr11	118100634	118100634	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtctcttcatagtctgaaTcctggagggagcaaaacagc	12	10	10	9	0	3	1	1	1	2	0	5	3	4	3	1	2	3	1	1	2	4	2	rs7105729	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:118100634T>A	ENST00000278949.4	-	6	738	c.683A>T	c.(682-684)gAt>gTt	p.D228V	MPZL3_ENST00000527472.1_Splice_Site_p.D216V|MPZL3_ENST00000525386.1_Splice_Site_p.I47F			Q6UWV2	MPZL3_HUMAN	myelin protein zero-like 3	228			D -> V (in dbSNP:rs7105729).		cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|hair cycle (GO:0042633)	integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(1)|large_intestine(1)|lung(2)|stomach(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.046)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		ATAGTCTGAATCCTGGAGGGA	0.453													T|||	223	0.0445288	0.1528	0.0274	5008	,	,		19501	0.0		0.002	False		,,,				2504	0.0				p.D228V		Atlas-SNP	.											.	MPZL3	22	.	0			c.A683T						PASS	.	T	VAL/ASP	613,3787	268.6+/-268.5	54,505,1641	101	93	96		683	5.8	1	11	dbSNP_116	96	7,8585	6.4+/-24.3	0,7,4289	yes	missense-near-splice	MPZL3	NM_198275.1	152	54,512,5930	AA,AT,TT		0.0815,13.9318,4.7722	benign	228/236	118100634	620,12372	2200	4296	6496	SO:0001630	splice_region_variant	196264	exon6			TCTGAATCCTGGA	AK095399	CCDS8392.1, CCDS66241.1	11q23.3	2013-01-11			ENSG00000160588	ENSG00000160588		"Immunoglobulin superfamily / V-set domain containing"	27279	protein-coding gene	gene with protein product		611707				17273165	Standard	NM_198275		Approved		uc001psm.3	Q6UWV2	OTTHUMG00000166966	ENST00000278949.4:c.682-1A>T	11.37:g.118100634T>A		69	0	0		74	49	0.662162	NM_198275	A8K025|B4DLD5|B4E2I8	Missense_Mutation	SNP	ENST00000278949.4	37	CCDS8392.1	92|92	0.04212454212454213|0.04212454212454213	81|81	0.16463414634146342|0.16463414634146342	11|11	0.03038674033149171|0.03038674033149171	0|0	0.0|0.0	0|0	0.0|0.0	T|T	19.48|19.48	3.834812|3.834812	0.71373|0.71373	0.139318|0.139318	8.15E-4|8.15E-4	ENSG00000160588|ENSG00000160588	ENST00000278949;ENST00000527472|ENST00000525386	D;D|.	0.96651|.	-3.93;-4.08|.	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.00271|0.00271	0.0008|0.0008	L|L	0.34521|0.34521	1.04|1.04	0.09310|0.09310	P|P	0.9999999999999915|0.9999999999999915	P;P|.	0.47191|.	0.693;0.891|.	P;P|.	0.45681|.	0.49;0.49|.	T|T	0.11792|0.11792	-1.0573|-1.0573	9|5	0.87932|0.41790	D|T	0|0.15	.|.	12.5017|12.5017	0.55960|0.55960	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs7105729;rs52792812;rs7105729|rs7105729;rs52792812;rs7105729	216;228|.	B4E2I8;Q6UWV2|.	.;MPZL3_HUMAN|.	V|F	228;216|47	ENSP00000278949:D228V;ENSP00000432106:D216V|.	ENSP00000278949:D228V|ENSP00000434636:I47F	D|I	-|-	2|1	0|0	MPZL3|MPZL3	117605844|117605844	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.873000|0.873000	0.50193|0.50193	4.093000|4.093000	0.57714|0.57714	2.215000|2.215000	0.71742|0.71742	0.460000|0.460000	0.39030|0.39030	GAT|ATT	T|0.954;A|0.046	0.046	strong		0.453	MPZL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392109.1	NM_198275	Missense_Mutation	A	118100634	T	A	118100634	5	1	22	1	0	0	0	0	0	0	1	0	9760	1449	50	5	28	5	MPZL3	11	118100634	Splice_Site	SNP	T	TCGA-G8-6324-01A-11D-2210-10	122056	118100634	16905882	2580	5481											
MPZL2	10205	hgsc.bcm.edu	37	chr11	118133334	118133334	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttaaaccgcccactcatgggTtggaagggatctatgtggta	10	11	12	8	1	2	0	1	0	1	0	2	2	2	2	2	4	1	2	2	4	5	4	rs17122002	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:118133334T>C	ENST00000278937.2	-	3	383	c.255A>G	c.(253-255)caA>caG	p.Q85Q	MPZL2_ENST00000438295.2_Silent_p.Q85Q|MPZL2_ENST00000525647.1_5'Flank	NM_005797.3	NP_005788.1	O60487	MPZL2_HUMAN	myelin protein zero-like 2	85	Ig-like V-type.				anatomical structure morphogenesis (GO:0009653)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)|T cell differentiation in thymus (GO:0033077)	cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|skin(1)	11	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;3.04e-05)		CACTCATGGGTTGGAAGGGAT	0.537													T|||	205	0.0409345	0.1467	0.013	5008	,	,		20403	0.0		0.002	False		,,,				2504	0.0				p.Q85Q		Atlas-SNP	.											.	MPZL2	20	.	0			c.A255G						PASS	.	T	,	655,3745	280.8+/-275.6	62,531,1607	62	57	59		255,255	-6.6	0	11	dbSNP_123	59	5,8587	4.3+/-15.6	0,5,4291	no	coding-synonymous,coding-synonymous	MPZL2	NM_005797.3,NM_144765.2	,	62,536,5898	CC,CT,TT		0.0582,14.8864,5.08	,	85/216,85/216	118133334	660,12332	2200	4296	6496	SO:0001819	synonymous_variant	10205	exon3			CATGGGTTGGAAG	AF275945	CCDS8393.1	11q24	2013-01-11	2007-08-01	2007-08-01		ENSG00000149573		"Immunoglobulin superfamily / V-set domain containing"	3496	protein-coding gene	gene with protein product		604873	"epithelial V-like antigen 1"	EVA1		9585423	Standard	NM_005797		Approved	EVA	uc001psn.3	O60487		ENST00000278937.2:c.255A>G	11.37:g.118133334T>C		167	0	0		120	70	0.583333	NM_005797	A8K2R1	Silent	SNP	ENST00000278937.2	37	CCDS8393.1																																																																																			T|0.954;C|0.046	0.046	strong		0.537	MPZL2-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392113.1	NM_005797		C	118133334	T	C	118133334	2	2	22	1	0	0	0	0	0	0	0	1	9759	1722	60	3		3	MPZL2	11	118133334	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	32700	118133334	16873182	2581	5482											
CXCR5	643	hgsc.bcm.edu	37	chr11	118764382	118764382	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctctgccctgccacagagggGcccctcatggcctccttcaa	6	8	9	18	0	3	1	2	0	1	1	4	1	4	1	6	3	2	0	6	3	1	1	rs2230319	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:118764382G>T	ENST00000292174.4	+	2	305	c.129G>T	c.(127-129)ggG>ggT	p.G43G		NM_001716.4|NM_032966.2	NP_001707.1|NP_116743.1	P32302	CXCR5_HUMAN	chemokine (C-X-C motif) receptor 5	43					B cell activation (GO:0042113)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of cytokinesis (GO:0032467)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|G-protein coupled receptor activity (GO:0004930)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(5)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	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)		CCACAGAGGGGCCCCTCATGG	0.597													G|||	275	0.0549121	0.202	0.0101	5008	,	,		17609	0.0		0.001	False		,,,				2504	0.0				p.G43G		Atlas-SNP	.											.	CXCR5	34	.	0			c.G129T						PASS	.	G	,	589,3811	259.8+/-263.3	34,521,1645	87	83	85		129,	-1.9	0.9	11	dbSNP_98	85	8,8582	5.7+/-21.5	0,8,4287	no	coding-synonymous,utr-5	CXCR5	NM_001716.4,NM_032966.2	,	34,529,5932	TT,TG,GG		0.0931,13.3864,4.5958	,	43/373,	118764382	597,12393	2200	4295	6495	SO:0001819	synonymous_variant	643	exon2			AGAGGGGCCCCTC	X68829	CCDS8402.1	11q23.3	2012-08-08	2008-01-22	2008-01-22	ENSG00000160683	ENSG00000160683		"CD molecules", "GPCR / Class A : Chemokine receptors : C-X-C motif"	1060	protein-coding gene	gene with protein product		601613	"Burkitt lymphoma receptor 1, GTP-binding protein", "Burkitt lymphoma receptor 1, GTP binding protein (chemokine (C-X-C motif) receptor 5)"	BLR1		1425907	Standard	NM_001716		Approved	MDR15, CD185	uc001pue.4	P32302	OTTHUMG00000166345	ENST00000292174.4:c.129G>T	11.37:g.118764382G>T		97	0	0		114	67	0.587719	NM_001716	Q14811	Silent	SNP	ENST00000292174.4	37	CCDS8402.1																																																																																			G|0.952;T|0.048	0.048	strong		0.597	CXCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389309.1	NM_001716		T	118764382	G	T	118764382	2	4	22	1	0	0	0	0	0	0	0	1	4096	1190	42	4		4	CXCR5	11	118764382	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	631048	118764382	16242134	2582	5483											
BCL9L	283149	hgsc.bcm.edu	37	chr11	118770054	118770054	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcccccctgtcccctgtgcGttgggatgcagtggaatgtt	4	11	14	12	1	0	0	0	0	0	0	1	2	1	2	5	3	2	3	5	3	1	2	rs12277303	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:118770054G>A	ENST00000334801.3	-	8	4534	c.3570C>T	c.(3568-3570)aaC>aaT	p.N1190N	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	1190	Pro-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)		TCCCCTGTGCGTTGGGATGCA	0.692													G|||	262	0.0523163	0.1921	0.0101	5008	,	,		11201	0.0		0.001	False		,,,				2504	0.0				p.N1190N		Atlas-SNP	.											.	BCL9L	254	.	0			c.C3570T						PASS	.	G		401,3799		5,391,1704	5	6	6		3570	-0.1	0.9	11	dbSNP_120	6	6,8276		0,6,4135	no	coding-synonymous	BCL9L	NM_182557.2		5,397,5839	AA,AG,GG		0.0724,9.5476,3.2607		1190/1500	118770054	407,12075	2100	4141	6241	SO:0001819	synonymous_variant	283149	exon8			CTGTGCGTTGGGA	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.3570C>T	11.37:g.118770054G>A		112	0	0		95	55	0.578947	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Silent	SNP	ENST00000334801.3	37	CCDS8403.1																																																																																			G|0.948;A|0.052	0.052	strong		0.692	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557		A	118770054	G	A	118770054	2	1	22	1	0	0	0	0	0	0	0	1	1382	1136	40	1		1	BCL9L	11	118770054	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5672	118770054	16236462	2583	5484											
BCL9L	283149	hgsc.bcm.edu	37	chr11	118773204	118773204	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggagcagcagtcgctcaatGtctcgcagcgtctggaggga	8	7	15	11	4	3	0	1	0	2	0	5	3	3	3	0	3	3	4	0	3	1	0	rs7119065	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:118773204G>A	ENST00000334801.3	-	6	2212	c.1248C>T	c.(1246-1248)gaC>gaT	p.D416D	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	416	Necessary for interaction with CTNNB1. {ECO:0000250}.|Pro-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)		GTCGCTCAATGTCTCGCAGCG	0.682													G|||	294	0.0587061	0.2156	0.0101	5008	,	,		12409	0.0		0.002	False		,,,				2504	0.0				p.D416D		Atlas-SNP	.											BCL9L_ENST00000392849,right_upper_lobe,carcinoma,-1,2	BCL9L	254	2	0			c.C1248T						PASS	.	G		615,3783		41,533,1625	27	30	29		1248	3.6	1	11	dbSNP_116	29	11,8575		0,11,4282	no	coding-synonymous	BCL9L	NM_182557.2		41,544,5907	AA,AG,GG		0.1281,13.9836,4.8213		416/1500	118773204	626,12358	2199	4293	6492	SO:0001819	synonymous_variant	283149	exon6			CTCAATGTCTCGC	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.1248C>T	11.37:g.118773204G>A		21	0	0		30	19	0.633333	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Silent	SNP	ENST00000334801.3	37	CCDS8403.1																																																																																			G|0.949;A|0.051	0.051	strong		0.682	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557		A	118773204	G	A	118773204	2	1	22	1	0	0	0	0	0	0	0	1	1382	1368	48	2		2	BCL9L	11	118773204	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3150	118773204	16233312	2584	5485											
ABCG4	64137	hgsc.bcm.edu	37	chr11	119027691	119027691	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagagcagccctgagaagaaCgaggtccctgccccatgccc	11	4	11	15	1	0	3	0	1	0	3	1	5	1	3	5	1	5	1	5	1	3	0	rs12271907	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119027691C>G	ENST00000449422.2	+	9	1223	c.1035C>G	c.(1033-1035)aaC>aaG	p.N345K	ABCG4_ENST00000307417.3_Missense_Mutation_p.N345K|AP002956.1_ENST00000599663.1_Intron|ABCG4_ENST00000531739.1_Missense_Mutation_p.N345K	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	345					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)		CTGAGAAGAACGAGGTCCCTG	0.607													C|||	379	0.0756789	0.2685	0.0331	5008	,	,		22013	0.0		0.001	False		,,,				2504	0.0				p.N345K		Atlas-SNP	.											.	ABCG4	77	.	0			c.C1035G						PASS	.	C	LYS/ASN,LYS/ASN	977,3423	367.3+/-318.2	117,743,1340	169	155	159		1035,1035	-11.3	0	11	dbSNP_120	159	7,8583	4.3+/-15.6	0,7,4288	yes	missense,missense	ABCG4	NM_001142505.1,NM_022169.4	94,94	117,750,5628	GG,GC,CC		0.0815,22.2045,7.5751	benign,benign	345/647,345/647	119027691	984,12006	2200	4295	6495	SO:0001583	missense	64137	exon9			GAAGAACGAGGTC	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.1035C>G	11.37:g.119027691C>G	ENSP00000406874:p.Asn345Lys	74	0	0		49	29	0.591837	NM_022169	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Missense_Mutation	SNP	ENST00000449422.2	37	CCDS8415.1	162	0.07417582417582418	154	0.3130081300813008	8	0.022099447513812154	0	0.0	0	0.0	C	9.694	1.152791	0.21371	0.222045	8.15E-4	ENSG00000172350	ENST00000307417;ENST00000449422;ENST00000531739;ENST00000534402	D;D;D;T	0.86562	-2.14;-2.14;-2.14;0.92	5.65	-11.3	0.00108	.	0.718923	0.14549	N	0.312774	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.22604	0.072	B	0.20577	0.03	T	0.08493	-1.0719	9	0.06365	T	0.9	-5.4059	11.0626	0.47957	0.0:0.2915:0.2915:0.4171	rs12271907;rs12271907	345	Q9H172	ABCG4_HUMAN	K	345;345;345;23	ENSP00000304111:N345K;ENSP00000406874:N345K;ENSP00000434318:N345K;ENSP00000434571:N23K	ENSP00000304111:N345K	N	+	3	2	ABCG4	118532901	0.002000	0.14202	0.001000	0.08648	0.350000	0.29205	-2.018000	0.01444	-3.564000	0.00140	-1.778000	0.00651	AAC	C|0.928;G|0.072;T|0.000	0.072	strong		0.607	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169		G	119027691	C	G	119027691	3	3	22	1	0	0	0	0	1	0	0	0	70	535	19	4	1065	4	ABCG4	11	119027691	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	254487	119027691	15978825	2585	5486											
CBL	867	hgsc.bcm.edu	37	chr11	119170362	119170362	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tccagtgagatcgagaacctCatgagtcaggggtactccta	11	9	11	10	1	2	3	2	2	0	2	5	5	4	3	3	2	2	1	3	2	3	2	rs1893177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119170362C>T	ENST00000264033.4	+	16	2968	c.2592C>T	c.(2590-2592)ctC>ctT	p.L864L		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	864	Interaction with CD2AP.|UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				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)		TCGAGAACCTCATGAGTCAGG	0.537			"T, Mis S, O"	MLL	"AML, JMML, MDS"				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies				C|||	172	0.034345	0.1203	0.0187	5008	,	,		19424	0.0		0.0	False		,,,				2504	0.0				p.L864L		Atlas-SNP	.		"Dom, Rec"	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	.	CBL	408	.	0			c.C2592T						PASS	.	C		478,3920	224.9+/-240.9	22,434,1743	217	217	217		2592	4.7	1	11	dbSNP_92	217	1,8589	1.2+/-3.3	0,1,4294	no	coding-synonymous	CBL	NM_005188.2		22,435,6037	TT,TC,CC		0.0116,10.8686,3.688		864/907	119170362	479,12509	2199	4295	6494	SO:0001819	synonymous_variant	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	GAACCTCATGAGT	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.2592C>T	11.37:g.119170362C>T		113	0	0		79	47	0.594937	NM_005188	A3KMP8	Silent	SNP	ENST00000264033.4	37	CCDS8418.1																																																																																			C|0.948;T|0.052	0.052	strong		0.537	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188		T	119170362	C	T	119170362	2	4	22	1	0	0	0	0	0	0	0	1	2702	813	29	2		2	CBL	11	119170362	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	142671	119170362	15836154	2586	5487											
CBL	867	hgsc.bcm.edu	37	chr11	119170480	119170480	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccatttcttctcctgcccatGtagctacctagcacaccatc	8	12	4	17	0	2	0	0	0	2	0	4	0	2	0	5	0	4	3	5	0	3	5	rs17122769	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119170480G>A	ENST00000264033.4	+	16	3086	c.2710G>A	c.(2710-2712)Gta>Ata	p.V904I		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	904	Interaction with CD2AP.		V -> I (in dbSNP:rs17122769).		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)		TCCTGCCCATGTAGCTACCTA	0.493			"T, Mis S, O"	MLL	"AML, JMML, MDS"				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies				G|||	30	0.00599042	0.0219	0.0014	5008	,	,		21109	0.0		0.0	False		,,,				2504	0.0				p.V904I		Atlas-SNP	.		"Dom, Rec"	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	.	CBL	408	.	0			c.G2710A						PASS	.	G	ILE/VAL	65,4333	61.1+/-98.1	0,65,2134	239	244	242		2710	4.9	0.1	11	dbSNP_123	242	2,8588	2.2+/-6.3	0,2,4293	yes	missense	CBL	NM_005188.2	29	0,67,6427	AA,AG,GG		0.0233,1.4779,0.5159	benign	904/907	119170480	67,12921	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	GCCCATGTAGCTA	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.2710G>A	11.37:g.119170480G>A	ENSP00000264033:p.Val904Ile	72	0	0		69	30	0.434783	NM_005188	A3KMP8	Missense_Mutation	SNP	ENST00000264033.4	37	CCDS8418.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	G	11.37	1.617349	0.28801	0.014779	2.33E-4	ENSG00000110395	ENST00000264033	T	0.78816	-1.21	5.8	4.89	0.63831	.	0.120265	0.56097	D	0.000027	T	0.49372	0.1553	N	0.03115	-0.41	0.44677	D	0.997661	B	0.12013	0.005	B	0.14023	0.01	T	0.50499	-0.8821	10	0.30854	T	0.27	-23.714	14.7175	0.69280	0.0692:0.0:0.9308:0.0	rs17122769;rs52793379;rs17122769	904	P22681	CBL_HUMAN	I	904	ENSP00000264033:V904I	ENSP00000264033:V904I	V	+	1	0	CBL	118675690	0.997000	0.39634	0.064000	0.19789	0.936000	0.57629	2.667000	0.46808	1.461000	0.47929	0.655000	0.94253	GTA	G|0.993;A|0.007	0.007	strong		0.493	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188		A	119170480	G	A	119170480	3	1	22	1	0	0	0	0	1	0	0	0	2702	1377	48	2	2772	2	CBL	11	119170480	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	118	119170480	15836036	2587	5488											
MFRP	83552	hgsc.bcm.edu	37	chr11	119216867	119216867	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	ccgtagccctcgaggacgccGacctgcgggttggcaggtgg	5	6	17	13	5	0	0	0	0	0	0	1	3	0	1	4	5	2	3	4	5	1	2	rs139436396	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119216867G>C	ENST00000530681.1	-	3	304	c.160C>G	c.(160-162)Cgg>Ggg	p.R54G	MFRP_ENST00000555262.1_Missense_Mutation_p.R54G|C1QTNF5_ENST00000445041.2_5'UTR|MFRP_ENST00000360167.4_Missense_Mutation_p.R54G|MFRP_ENST00000449574.2_Missense_Mutation_p.R54G|MFRP_ENST00000529147.1_5'UTR	NM_001278431.1	NP_001265360.1	Q9BY79	MFRP_HUMAN	membrane frizzled-related protein	54			R -> G (in dbSNP:rs139436396). {ECO:0000269|PubMed:16352475}.		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)		CGAGGACGCCGACCTGCGGGT	0.642													G|||	55	0.0109824	0.0371	0.0086	5008	,	,		17805	0.0		0.0	False		,,,				2504	0.0				p.R54G		Atlas-SNP	.											.	MFRP	63	.	0			c.C160G						PASS	.	G	,GLY/ARG	111,4267		2,107,2080	19	18	18		,160	4.3	0.8	11	dbSNP_134	18	1,8565		0,1,4282	yes	utr-5,missense	MFRP,C1QTNF5	NM_015645.3,NM_031433.2	,125	2,108,6362	CC,CG,GG		0.0117,2.5354,0.8653	,benign	,54/580	119216867	112,12832	2189	4283	6472	SO:0001583	missense	83552	exon3			GACGCCGACCTGC	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.160C>G	11.37:g.119216867G>C	ENSP00000456533:p.Arg54Gly	48	0	0		46	23	0.5	NM_031433	B0YJ36|B0YJ37|B4DHN8|Q335M3|Q96DQ9	Missense_Mutation	SNP	ENST00000530681.1	37	CCDS8421.1	15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	G	17.80	3.477400	0.63849	0.025354	1.17E-4	ENSG00000235718	ENST00000555262;ENST00000449574;ENST00000360167	T;T;T	0.67698	-0.28;-0.28;1.88	5.24	4.27	0.50696	.	0.647065	0.15397	N	0.264485	T	0.29126	0.0724	L	0.27053	0.805	0.24539	N	0.994075	P;B	0.39157	0.662;0.319	B;B	0.37833	0.259;0.097	T	0.26643	-1.0097	10	0.30078	T	0.28	-13.8891	13.6734	0.62438	0.0:0.1544:0.8456:0.0	.	54;54	B4DHN8;Q9BY79	.;MFRP_HUMAN	G	54	ENSP00000450509:R54G;ENSP00000391664:R54G;ENSP00000353291:R54G	ENSP00000353291:R54G	R	-	1	2	MFRP	118722077	0.010000	0.17322	0.842000	0.33263	0.537000	0.34900	0.833000	0.27504	2.601000	0.87937	0.655000	0.94253	CGG	G|0.990;C|0.010	0.010	strong		0.642	MFRP-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000415179.1	NM_031433		C	119216867	G	C	119216867	3	2	22	1	0	0	0	0	1	0	0	0	9535	1057	37	4	1623	4	MFRP	11	119216867	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	46387	119216867	15789649	2588	5489											
USP2	9099	hgsc.bcm.edu	37	chr11	119243612	119243612	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tccaggtagtcgaccaggtaTtcagggcagctggctgtctg	7	10	14	10	1	2	0	1	0	1	0	4	1	3	0	2	4	1	5	2	4	2	3	rs4938649	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119243612T>C	ENST00000260187.2	-	2	873	c.579A>G	c.(577-579)gaA>gaG	p.E193E	USP2_ENST00000455332.2_Intron|RP11-334E6.3_ENST00000530918.2_RNA	NM_004205.4	NP_004196.4	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2	193	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)		CGACCAGGTATTCAGGGCAGC	0.637													C|||	239	0.0477236	0.1195	0.0274	5008	,	,		17377	0.0407		0.002	False		,,,				2504	0.0194				p.E193E		Atlas-SNP	.											.	USP2	71	.	0			c.A579G						PASS	.	C		503,3895	779.2+/-414.3	28,447,1724	66	69	68		579	1.2	0.9	11	dbSNP_111	68	8,8582	818.2+/-406.9	0,8,4287	no	coding-synonymous	USP2	NM_004205.4		28,455,6011	CC,CT,TT		0.0931,11.437,3.9344		193/606	119243612	511,12477	2199	4295	6494	SO:0001819	synonymous_variant	9099	exon2			CAGGTATTCAGGG	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.579A>G	11.37:g.119243612T>C		55	0	0		46	29	0.630435	NM_004205	B0YJB8|E9PPM2|Q8IUM2|Q8IW04|Q96MB9|Q9BQ21	Silent	SNP	ENST00000260187.2	37	CCDS8422.1																																																																																			T|0.959;C|0.041	0.041	strong		0.637	USP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388361.2	NM_171997		C	119243612	T	C	119243612	2	2	22	1	0	0	0	0	0	0	0	1	17066	1490	52	3		3	USP2	11	119243612	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	26745	119243612	15762904	2589	5490											
USP2	9099	hgsc.bcm.edu	37	chr11	119243912	119243912	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcagtaccccgggtctggctCtctgcccgcttaccaccccc	4	9	8	20	2	3	0	1	0	2	0	4	0	3	0	6	2	3	3	6	2	2	2	rs536224379|rs79464246	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119243912C>T	ENST00000260187.2	-	2	573	c.279G>A	c.(277-279)gaG>gaA	p.E93E	USP2_ENST00000455332.2_Intron|RP11-334E6.3_ENST00000530918.2_RNA	NM_004205.4	NP_004196.4	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2	93	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)		GGGTCTGGCTCTCTGCCCGCT	0.657													C|||	40	0.00798722	0.0265	0.0072	5008	,	,		16244	0.0		0.0	False		,,,				2504	0.0				p.E93E		Atlas-SNP	.											.	USP2	71	.	0			c.G279A						PASS	.	C		107,4291	82.9+/-121.4	2,103,2094	67	76	73		279	4.3	1	11	dbSNP_132	73	1,8589		0,1,4294	no	coding-synonymous	USP2	NM_004205.4		2,104,6388	TT,TC,CC		0.0116,2.4329,0.8315		93/606	119243912	108,12880	2199	4295	6494	SO:0001819	synonymous_variant	9099	exon2			CTGGCTCTCTGCC	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.279G>A	11.37:g.119243912C>T		73	0	0		90	50	0.555556	NM_004205	B0YJB8|E9PPM2|Q8IUM2|Q8IW04|Q96MB9|Q9BQ21	Silent	SNP	ENST00000260187.2	37	CCDS8422.1																																																																																			C|0.991;T|0.009	0.009	strong		0.657	USP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388361.2	NM_171997		T	119243912	C	T	119243912	2	4	22	1	0	0	0	0	0	0	0	1	17066	912	32	2		2	USP2	11	119243912	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	300	119243912	15762604	2590	5491											
PVRL1	5818	hgsc.bcm.edu	37	chr11	119509485	119509485	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gctttgcctgctgggagaagGctccggcttctgggagaggg	5	9	18	9	1	1	2	0	0	1	2	2	4	2	2	2	5	2	4	2	5	1	2	rs73571271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119509485G>A	ENST00000341398.2	-	7	1182	c.1183C>T	c.(1183-1185)Cct>Tct	p.P395S	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)		CTGGGAGAAGGCTCCGGCTTC	0.617													G|||	94	0.01877	0.0643	0.013	5008	,	,		19246	0.0		0.0	False		,,,				2504	0.0				p.P395S		Atlas-SNP	.											.	PVRL1	133	.	0			c.C1183T						PASS	.	G	SER/PRO	274,4124	154.0+/-187.5	4,266,1929	48	46	46		1183	1.5	0	11	dbSNP_130	46	1,8589	1.2+/-3.3	0,1,4294	yes	missense	PVRL1	NM_203285.1	74	4,267,6223	AA,AG,GG		0.0116,6.2301,2.1173		395/459	119509485	275,12713	2199	4295	6494	SO:0001583	missense	5818	exon7			GAGAAGGCTCCGG	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.1183C>T	11.37:g.119509485G>A	ENSP00000344974:p.Pro395Ser	62	0	0		41	21	0.512195	NM_203285	O75465|Q2M3D3|Q9HBE6|Q9HBW2	Missense_Mutation	SNP	ENST00000341398.2	37	CCDS8425.1	41	0.018772893772893772	34	0.06910569105691057	7	0.019337016574585635	0	0.0	0	0.0	G	5.225	0.226965	0.09916	0.062301	1.16E-4	ENSG00000110400	ENST00000341398	T	0.77098	-1.07	3.39	1.49	0.22878	.	.	.	.	.	T	0.13072	0.0317	L	0.40543	1.245	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.14504	-1.0470	9	0.31617	T	0.26	.	5.6558	0.17642	0.257:0.0:0.743:0.0	.	395	Q15223-2	.	S	395	ENSP00000344974:P395S	ENSP00000344974:P395S	P	-	1	0	PVRL1	119014695	0.013000	0.17824	0.002000	0.10522	0.017000	0.09413	1.059000	0.30517	0.413000	0.25759	-0.448000	0.05591	CCT	G|0.978;A|0.022	0.022	strong		0.617	PVRL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388230.1			A	119509485	G	A	119509485	3	1	22	1	0	0	0	0	1	0	0	0	12854	1203	42	2	201	2	PVRL1	11	119509485	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	265573	119509485	15497031	2591	5492											
TRIM29	23650	hgsc.bcm.edu	37	chr11	119996490	119996490	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgcatacattgagcaggtcGtccttgaagttgcctagtga	10	12	11	8	1	0	3	0	3	0	0	2	3	1	3	2	1	4	3	2	1	3	5	rs61753082	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119996490G>A	ENST00000341846.5	-	4	1663	c.1242C>T	c.(1240-1242)gaC>gaT	p.D414D	TRIM29_ENST00000529044.1_Silent_p.D153D|TRIM29_ENST00000524816.3_5'Flank|TRIM29_ENST00000528870.1_5'Flank|TRIM29_ENST00000541857.1_Silent_p.D147D	NM_012101.3	NP_036233.2	Q14134	TRI29_HUMAN	tripartite motif containing 29	414					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)		TGAGCAGGTCGTCCTTGAAGT	0.562													G|||	105	0.0209665	0.0719	0.0144	5008	,	,		11882	0.0		0.0	False		,,,				2504	0.0				p.D414D		Atlas-SNP	.											.	TRIM29	78	.	0			c.C1242T						PASS	.	G		298,4100	162.2+/-194.2	15,268,1916	101	87	92		1242	-8.7	0.6	11	dbSNP_129	92	0,8590		0,0,4295	no	coding-synonymous	TRIM29	NM_012101.3		15,268,6211	AA,AG,GG		0.0,6.7758,2.2944		414/589	119996490	298,12690	2199	4295	6494	SO:0001819	synonymous_variant	23650	exon4			CAGGTCGTCCTTG	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.1242C>T	11.37:g.119996490G>A		151	0	0		118	78	0.661017	NM_012101	Q96AA9|Q9BZY7	Silent	SNP	ENST00000341846.5	37	CCDS8428.1																																																																																			G|0.979;A|0.021	0.021	strong		0.562	TRIM29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277108.2	NM_012101		A	119996490	G	A	119996490	2	1	22	1	0	0	0	0	0	0	0	1	16518	1136	40	1		1	TRIM29	11	119996490	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	487005	119996490	15010026	2592	5493											
OAF	220323	hgsc.bcm.edu	37	chr11	120097551	120097551	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccccgggcagtgcggcaggcGgaggaggttcggggtctgga	5	5	21	10	4	1	0	0	0	1	0	2	3	1	3	2	9	1	3	2	9	0	1	rs873058	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:120097551G>A	ENST00000328965.4	+	3	906	c.393G>A	c.(391-393)gcG>gcA	p.A131A	OAF_ENST00000531220.1_Silent_p.A15A	NM_178507.2	NP_848602.1	Q86UD1	OAF_HUMAN	OAF homolog (Drosophila)	131						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)		TGCGGCAGGCGGAGGAGGTTC	0.612													G|||	71	0.0141773	0.0507	0.0058	5008	,	,		16367	0.0		0.0	False		,,,				2504	0.0				p.A131A		Atlas-SNP	.											.	OAF	12	.	0			c.G393A						PASS	.	G		213,4193	129.0+/-165.8	5,203,1995	64	59	61		393	-10.4	0.6	11	dbSNP_86	61	2,8598		0,2,4298	no	coding-synonymous	OAF	NM_178507.2		5,205,6293	AA,AG,GG		0.0233,4.8343,1.6531		131/274	120097551	215,12791	2203	4300	6503	SO:0001819	synonymous_variant	220323	exon3			GCAGGCGGAGGAG	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.393G>A	11.37:g.120097551G>A		85	0	0		70	45	0.642857	NM_178507		Silent	SNP	ENST00000328965.4	37	CCDS8430.1																																																																																			G|0.982;A|0.018	0.018	strong		0.612	OAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388036.2	NM_178507		A	120097551	G	A	120097551	2	1	22	1	0	0	0	0	0	0	0	1	10807	1103	39	1		1	OAF	11	120097551	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	101061	120097551	14908965	2593	5494											
GRIK4	2900	hgsc.bcm.edu	37	chr11	120811161	120811161	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaattagcattctttaccgcGttcatatggtaagagactta	12	14	8	7	2	2	1	1	0	1	1	2	3	2	1	1	1	2	3	1	1	6	8	rs2230298	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:120811161G>A	ENST00000527524.2	+	14	1869	c.1582G>A	c.(1582-1584)Gtt>Att	p.V528I	GRIK4_ENST00000438375.2_Missense_Mutation_p.V528I	NM_001282470.1	NP_001269399.1	Q16099	GRIK4_HUMAN	glutamate receptor, ionotropic, kainate 4	528			V -> I (in dbSNP:rs35599906). {ECO:0000269|PubMed:8263508}.		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)		TCTTTACCGCGTTCATATGGT	0.388													G|||	151	0.0301518	0.1104	0.0072	5008	,	,		22695	0.0		0.0	False		,,,				2504	0.0				p.V528I		Atlas-SNP	.											.	GRIK4	149	.	0			c.G1582A						PASS	.	G	ILE/VAL	396,4010	195.7+/-220.2	25,346,1832	82	84	83		1582	5.5	1	11	dbSNP_126	83	7,8591	6.4+/-24.3	0,7,4292	yes	missense	GRIK4	NM_014619.2	29	25,353,6124	AA,AG,GG		0.0814,8.9877,3.099	probably-damaging	528/957	120811161	403,12601	2203	4299	6502	SO:0001583	missense	2900	exon12			TACCGCGTTCATA	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.1582G>A	11.37:g.120811161G>A	ENSP00000435648:p.Val528Ile	103	0	0		65	30	0.461538	NM_014619	A8K9L1	Missense_Mutation	SNP	ENST00000527524.2	37	CCDS8433.1	61	0.027930402930402932	59	0.11991869918699187	2	0.0055248618784530384	0	0.0	0	0.0	G	21.3	4.125095	0.77436	0.089877	8.14E-4	ENSG00000149403	ENST00000527524;ENST00000438375	T;T	0.11385	2.78;2.78	5.47	5.47	0.80525	Ionotropic glutamate receptor (1);	0.121890	0.56097	D	0.000035	T	0.00356	0.0011	L	0.39147	1.195	0.80722	D	1	D;D	0.89917	1.0;0.995	D;P	0.68353	0.957;0.871	T	0.00812	-1.1556	10	0.34782	T	0.22	.	18.9072	0.92467	0.0:0.0:1.0:0.0	rs35599906	528;528	A6H8K8;Q16099	.;GRIK4_HUMAN	I	528	ENSP00000435648:V528I;ENSP00000404063:V528I	ENSP00000404063:V528I	V	+	1	0	GRIK4	120316371	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.384000	0.97219	2.579000	0.87056	0.591000	0.81541	GTT	G|0.964;A|0.036	0.036	strong		0.388	GRIK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109760.4	NM_014619		A	120811161	G	A	120811161	3	1	22	1	0	0	0	0	1	0	0	0	6785	1145	40	1	1628	1	GRIK4	11	120811161	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	713610	120811161	14195355	2594	5495											
TECTA	7007	hgsc.bcm.edu	37	chr11	121016424	121016424	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtccctcggagcatgcagaAcagcacctatggtctgtgtg	9	9	12	11	1	1	1	0	0	1	1	3	2	2	2	2	2	4	3	2	2	2	1	rs200852252	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:121016424A>G	ENST00000392793.1	+	12	3975	c.3704A>G	c.(3703-3705)aAc>aGc	p.N1235S	TECTA_ENST00000264037.2_Missense_Mutation_p.N1235S|TECTA_ENST00000478058.1_3'UTR			O75443	TECTA_HUMAN	tectorin alpha	1235	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)		AGCATGCAGAACAGCACCTAT	0.532													A|||	4	0.000798722	0.0015	0.0029	5008	,	,		22478	0.0		0.0	False		,,,				2504	0.0				p.N1235S		Atlas-SNP	.											.	TECTA	329	.	0			c.A3704G						PASS	.	A	SER/ASN	2,4404	4.2+/-10.8	0,2,2201	157	126	136		3704	4.6	1	11		136	0,8598		0,0,4299	no	missense	TECTA	NM_005422.2	46	0,2,6500	GG,GA,AA		0.0,0.0454,0.0154	probably-damaging	1235/2156	121016424	2,13002	2203	4299	6502	SO:0001583	missense	7007	exon11			TGCAGAACAGCAC	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.3704A>G	11.37:g.121016424A>G	ENSP00000376543:p.Asn1235Ser	189	0	0		150	71	0.473333	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	37	CCDS8434.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	A	17.08	3.298372	0.60195	4.54E-4	0.0	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.62788	-0.0;-0.0	5.76	4.57	0.56435	von Willebrand factor, type D domain (3);	0.000000	0.85682	D	0.000000	T	0.72463	0.3463	L	0.55213	1.73	0.40504	D	0.980674	D	0.76494	0.999	D	0.83275	0.996	T	0.70927	-0.4739	10	0.31617	T	0.26	.	12.6018	0.56501	0.8617:0.1383:0.0:0.0	.	1235	O75443	TECTA_HUMAN	S	1235	ENSP00000376543:N1235S;ENSP00000264037:N1235S	ENSP00000264037:N1235S	N	+	2	0	TECTA	120521634	1.000000	0.71417	0.970000	0.41538	0.986000	0.74619	5.257000	0.65473	2.196000	0.70406	0.482000	0.46254	AAC	A|1.000;G|0.000	0.000	strong		0.532	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		G	121016424	A	G	121016424	3	3	22	1	0	0	0	0	1	0	0	0	15762	43	2	3	3746	3	TECTA	11	121016424	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	205263	121016424	13990092	2595	5496											
UBASH3B	84959	hgsc.bcm.edu	37	chr11	122678778	122678778	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgccattttcccccaggaaAtaacatcctgattgtggccc	9	12	7	13	0	0	1	0	1	0	0	2	2	2	2	5	2	2	0	5	2	2	5	rs35343548	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:122678778A>G	ENST00000284273.5	+	13	2081	c.1706A>G	c.(1705-1707)aAt>aGt	p.N569S		NM_032873.4	NP_116262.2	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing B	569	Protein tyrosine phosphatase. {ECO:0000250}.		N -> S (in dbSNP:rs35343548).		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)		CCCCCAGGAAATAACATCCTG	0.473													A|||	33	0.00658946	0.0242	0.0014	5008	,	,		18186	0.0		0.0	False		,,,				2504	0.0				p.N569S		Atlas-SNP	.											.	UBASH3B	73	.	0			c.A1706G						PASS	.	A	SER/ASN	74,4330	66.4+/-103.9	0,74,2128	336	327	330		1706	4.7	1	11	dbSNP_126	330	2,8596		0,2,4297	yes	missense	UBASH3B	NM_032873.4	46	0,76,6425	GG,GA,AA		0.0233,1.6803,0.5845	benign	569/650	122678778	76,12926	2202	4299	6501	SO:0001583	missense	84959	exon13			CAGGAAATAACAT	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.1706A>G	11.37:g.122678778A>G	ENSP00000284273:p.Asn569Ser	176	0	0		130	49	0.376923	NM_032873	Q53GT5|Q53GT8|Q8NBV7|Q96IG9|Q96NZ2	Missense_Mutation	SNP	ENST00000284273.5	37	CCDS31694.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	A	15.55	2.865578	0.51588	0.016803	2.33E-4	ENSG00000154127	ENST00000284273	T	0.27890	1.64	5.85	4.74	0.60224	Histidine phosphatase superfamily, clade-1 (1);	0.130095	0.64402	N	0.000002	T	0.10423	0.0255	L	0.27053	0.805	0.46376	D	0.999012	B	0.06786	0.001	B	0.08055	0.003	T	0.03514	-1.1029	10	0.48119	T	0.1	-8.6767	7.823	0.29298	0.7888:0.1392:0.072:0.0	rs35343548	569	Q8TF42	UBS3B_HUMAN	S	569	ENSP00000284273:N569S	ENSP00000284273:N569S	N	+	2	0	UBASH3B	122183988	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.395000	0.52558	1.061000	0.40601	0.533000	0.62120	AAT	A|0.992;G|0.008	0.008	strong		0.473	UBASH3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387499.1	NM_032873		G	122678778	A	G	122678778	3	3	22	1	0	0	0	0	1	0	0	0	16855	101	4	3	1756	3	UBASH3B	11	122678778	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1662354	122678778	12327738	2596	5497											
HSPA8	3312	hgsc.bcm.edu	37	chr11	122931337	122931337	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgcaatttccttcatcttTgtcagaaccatagaagacac	12	13	5	11	0	4	3	2	0	2	3	5	3	5	3	2	0	2	1	2	0	4	4	rs147610984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:122931337T>C	ENST00000532636.1	-	3	494	c.375A>G	c.(373-375)acA>acG	p.T125T	HSPA8_ENST00000533540.1_Intron|HSPA8_ENST00000534319.1_5'Flank|HSPA8_ENST00000526110.1_Silent_p.T125T|SNORD14D_ENST00000384390.1_RNA|HSPA8_ENST00000526862.1_5'Flank|HSPA8_ENST00000227378.3_Silent_p.T125T|HSPA8_ENST00000534624.1_Silent_p.T125T|HSPA8_ENST00000453788.2_Silent_p.T125T|SNORD14E_ENST00000364009.1_RNA|SNORD14C_ENST00000365382.1_RNA			P11142	HSP7C_HUMAN	heat shock 70kDa protein 8	125					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)		CCTTCATCTTTGTCAGAACCA	0.488													T|||	41	0.0081869	0.0303	0.0014	5008	,	,		19288	0.0		0.0	False		,,,				2504	0.0				p.T125T	Colon(21;486 594 5900 6733 14272)	Atlas-SNP	.											.	HSPA8	168	.	0			c.A375G						PASS	.	T	,	123,4281	91.6+/-130.3	1,121,2080	94	97	96		375,375	-2.6	1	11	dbSNP_134	96	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	HSPA8	NM_006597.4,NM_153201.2	,	1,121,6379	CC,CT,TT		0.0,2.7929,0.946	,	125/647,125/494	122931337	123,12879	2202	4299	6501	SO:0001819	synonymous_variant	3312	exon3			CATCTTTGTCAGA	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.375A>G	11.37:g.122931337T>C		118	0	0		132	56	0.424242	NM_006597	Q9H3R6	Silent	SNP	ENST00000532636.1	37	CCDS8440.1																																																																																			T|0.989;C|0.011	0.011	strong		0.488	HSPA8-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387515.1			C	122931337	T	C	122931337	2	2	22	1	0	0	0	0	0	0	0	1	7425	1799	63	3		3	HSPA8	11	122931337	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	252559	122931337	12075179	2597	5498											
SCN3B	55800	hgsc.bcm.edu	37	chr11	123516316	123516316	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggaaatctttaccgccctcGggcctgtagaaccattccac	10	9	8	14	2	1	1	0	0	1	1	3	2	2	2	5	2	2	1	5	2	4	4	rs115752338	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123516316G>A	ENST00000392770.2	-	2	1000	c.198C>T	c.(196-198)ccC>ccT	p.P66P	SCN3B_ENST00000530277.1_Silent_p.P66P|SCN3B_ENST00000299333.3_Silent_p.P66P	NM_018400.3	NP_060870.1	Q9NY72	SCN3B_HUMAN	sodium channel, voltage-gated, type III, beta subunit	66	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)	TACCGCCCTCGGGCCTGTAGA	0.597													A|||	46	0.0091853	0.0325	0.0043	5008	,	,		19339	0.0		0.0	False		,,,				2504	0.0				p.P66P		Atlas-SNP	.											.	SCN3B	53	.	0			c.C198T						PASS	.	A	,	118,4286	815.4+/-416.2	2,114,2086	131	135	134		198,198	-11.9	0	11	dbSNP_132	134	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	SCN3B	NM_001040151.1,NM_018400.3	,	2,114,6385	AA,AG,GG		0.0,2.6794,0.9076	,	66/216,66/216	123516316	118,12884	2202	4299	6501	SO:0001819	synonymous_variant	55800	exon2			GCCCTCGGGCCTG	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.198C>T	11.37:g.123516316G>A		145	0	0		112	68	0.607143	NM_018400	A5H1I5|Q17RL3|Q9ULR2	Silent	SNP	ENST00000392770.2	37	CCDS8442.1																																																																																			G|0.990;A|0.010	0.010	strong		0.597	SCN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387412.1	NM_018400		A	123516316	G	A	123516316	2	1	22	1	0	0	0	0	0	0	0	1	13934	1103	39	1		1	SCN3B	11	123516316	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	584979	123516316	11490200	2598	5499											
OR10G4	390264	hgsc.bcm.edu	37	chr11	123886648	123886648	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcatgtcctatgatcgctacTtggccatcagttacccgctc	7	13	7	14	2	2	1	2	1	0	0	5	1	3	1	3	1	2	3	3	1	3	4	rs397832341	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123886648T>C	ENST00000320891.4	+	1	367	c.367T>C	c.(367-369)Ttg>Ctg	p.L123L		NM_001004462.1	NP_001004462.1	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G, 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)			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)		TGATCGCTACTTGGCCATCAG	0.567													t|||	2	0.000399361	0.0008	0.0	5008	,	,		23929	0.0		0.0	False		,,,				2504	0.001				p.L123L		Atlas-SNP	.											OR10G4,right_lower_lobe,carcinoma,-2,1	OR10G4	77	1	0			c.T367C						scavenged	.																																			SO:0001819	synonymous_variant	390264	exon1			CGCTACTTGGCCA	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.367T>C	11.37:g.123886648T>C		1243	0	0		939	202	0.215122	NM_001004462	Q6IEW0	Silent	SNP	ENST00000320891.4	37	CCDS31702.1																																																																																			.	.	none		0.567	OR10G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387268.1	NM_001004462		C	123886648	T	C	123886648	2	2	22	1	0	0	0	0	0	0	0	1	10910	1606	56	3		3	OR10G4	11	123886648	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	370332	123886648	11119868	2599	5500											
OR10G8	219869	hgsc.bcm.edu	37	chr11	123900968	123900968	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcgggctgctttgtcctgatAgtgctgtcctatgtgtccat	4	16	11	10	1	0	1	0	1	0	0	4	1	3	1	3	1	2	3	3	1	2	3	rs146815262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123900968A>G	ENST00000431524.1	+	1	672	c.639A>G	c.(637-639)atA>atG	p.I213M		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)		TTGTCCTGATAGTGCTGTCCT	0.552													A|||	5	0.000998403	0.0038	0.0	5008	,	,		21238	0.0		0.0	False		,,,				2504	0.0				p.I213M		Atlas-SNP	.											.	OR10G8	132	.	0			c.A639G						PASS	.	A	MET/ILE	11,4391	17.9+/-39.9	0,11,2190	187	162	171		639	0	0.8	11	dbSNP_134	171	0,8598		0,0,4299	yes	missense	OR10G8	NM_001004464.1	10	0,11,6489	GG,GA,AA		0.0,0.2499,0.0846	probably-damaging	213/312	123900968	11,12989	2201	4299	6500	SO:0001583	missense	219869	exon1			CCTGATAGTGCTG	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.639A>G	11.37:g.123900968A>G	ENSP00000389072:p.Ile213Met	437	0	0		406	224	0.551724	NM_001004464	B2RNJ3|Q6IEV2	Missense_Mutation	SNP	ENST00000431524.1	37	CCDS31704.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	8.778	0.927449	0.18056	0.002499	0.0	ENSG00000234560	ENST00000431524	T	0.00333	8.07	2.91	0.0166	0.14109	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000074	T	0.00754	0.0025	M	0.89601	3.045	0.22571	N	0.998971	D	0.89917	1.0	D	0.97110	1.0	T	0.36089	-0.9762	10	0.72032	D	0.01	.	7.3929	0.26919	0.3109:0.0:0.0:0.6891	.	213	Q8NGN5	O10G8_HUMAN	M	213	ENSP00000389072:I213M	ENSP00000389072:I213M	I	+	3	3	OR10G8	123406178	0.000000	0.05858	0.808000	0.32385	0.060000	0.15804	-2.286000	0.01152	0.282000	0.22254	0.455000	0.32223	ATA	A|0.999;G|0.001	0.001	strong		0.552	OR10G8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387270.1	NM_001004464		G	123900968	A	G	123900968	3	3	22	1	0	0	0	0	1	0	0	0	10912	410	15	3	641	3	OR10G8	11	123900968	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	14320	123900968	11105548	2600	5501											
OR10G7	390265	hgsc.bcm.edu	37	chr11	123909524	123909524	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgtcaatgaaggacaggttgGtgaggaagtagtacatgggg	12	9	17	3	0	1	2	1	2	0	0	1	4	1	4	0	6	1	3	0	6	5	3	rs201246927		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123909524G>A	ENST00000330487.5	-	1	193	c.185C>T	c.(184-186)aCc>aTc	p.T62I		NM_001004463.1	NP_001004463.1	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G, member 7	62						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)		GGACAGGTTGGTGAGGAAGTA	0.547																																					p.T62I		Atlas-SNP	.											OR10G7,NS,carcinoma,+1,1	OR10G7	103	1	0			c.C185T						scavenged	.						21	21	21					11																	123909524		2195	4272	6467	SO:0001583	missense	390265	exon1			AGGTTGGTGAGGA	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.185C>T	11.37:g.123909524G>A	ENSP00000329689:p.Thr62Ile	624	0	0		468	56	0.119658	NM_001004463	Q6IFE8	Missense_Mutation	SNP	ENST00000330487.5	37	CCDS31705.1	58	0.026556776556776556	21	0.042682926829268296	17	0.04696132596685083	17	0.02972027972027972	3	0.00395778364116095	G	9.581	1.123605	0.20959	.	.	ENSG00000182634	ENST00000330487	T	0.01092	5.35	3.53	1.5	0.22942	GPCR, rhodopsin-like superfamily (1);	0.649434	0.13528	N	0.381190	T	0.00241	0.0007	L	0.28694	0.88	0.22213	N	0.999283	B	0.06786	0.001	B	0.15052	0.012	T	0.48875	-0.8996	10	0.66056	D	0.02	.	5.9703	0.19349	0.1371:0.3547:0.5082:0.0	.	62	Q8NGN6	O10G7_HUMAN	I	62	ENSP00000329689:T62I	ENSP00000329689:T62I	T	-	2	0	OR10G7	123414734	0.000000	0.05858	0.928000	0.36995	0.900000	0.52787	-0.620000	0.05565	0.261000	0.21753	0.557000	0.71058	ACC	A|1.000;|0.000	1.000	weak		0.547	OR10G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387271.1	NM_001004463		A	123909524	G	A	123909524	3	1	22	1	0	0	0	0	1	0	0	0	10911	1261	44	2	754	2	OR10G7	11	123909524	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	8556	123909524	11096992	2601	5502											
OR10G7	390265	hgsc.bcm.edu	37	chr11	123909638	123909638	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ccaggaagattccaaagaggGgggcgtccagccctggggca	10	4	16	11	1	0	2	0	0	0	2	2	3	2	3	4	6	1	1	4	6	2	1	rs148218442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123909638G>A	ENST00000330487.5	-	1	79	c.71C>T	c.(70-72)cCc>cTc	p.P24L		NM_001004463.1	NP_001004463.1	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G, member 7	24						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)		TCCAAAGAGGGGGGCGTCCAG	0.572													G|||	62	0.0123802	0.0416	0.0101	5008	,	,		16260	0.0		0.0	False		,,,				2504	0.0				p.P24L		Atlas-SNP	.											OR10G7,NS,carcinoma,+1,1	OR10G7	103	1	0			c.C71T						scavenged	.	G	LEU/PRO	70,4330	56.8+/-93.2	0,70,2130	96	92	94		71	-3.2	0	11	dbSNP_134	94	4,8594	3.0+/-9.4	0,4,4295	no	missense	OR10G7	NM_001004463.1	98	0,74,6425	AA,AG,GG		0.0465,1.5909,0.5693	benign	24/312	123909638	74,12924	2200	4299	6499	SO:0001583	missense	390265	exon1			AAGAGGGGGGCGT	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.71C>T	11.37:g.123909638G>A	ENSP00000329689:p.Pro24Leu	408	2	0.00490196		229	109	0.475983	NM_001004463	Q6IFE8	Missense_Mutation	SNP	ENST00000330487.5	37	CCDS31705.1	20	0.009157509157509158	12	0.024390243902439025	4	0.011049723756906077	0	0.0	4	0.005277044854881266	G	0.023	-1.397240	0.01175	0.015909	4.65E-4	ENSG00000182634	ENST00000330487	T	0.00036	8.86	3.38	-3.23	0.05109	.	1.833280	0.02752	N	0.117583	T	0.00039	0.0001	N	0.01096	-1.015	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.33954	-0.9848	10	0.02654	T	1	.	10.6967	0.45903	0.7947:0.0:0.2053:0.0	.	24	Q8NGN6	O10G7_HUMAN	L	24	ENSP00000329689:P24L	ENSP00000329689:P24L	P	-	2	0	OR10G7	123414848	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.678000	0.05209	-0.661000	0.05345	-0.232000	0.12228	CCC	G|0.992;A|0.008	0.008	strong		0.572	OR10G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387271.1	NM_001004463		A	123909638	G	A	123909638	3	1	22	1	0	0	0	0	1	0	0	0	10911	1232	43	2	868	2	OR10G7	11	123909638	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	114	123909638	11096878	2602	5503											
VWA5A	4013	hgsc.bcm.edu	37	chr11	123989383	123989383	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	actgccccttgagtcctaccGagtacctaggagaggacaag	11	7	11	12	1	0	2	0	1	0	1	1	5	1	3	5	2	3	1	5	2	4	4	rs35215239	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123989383G>A	ENST00000456829.2	+	6	864	c.613G>A	c.(613-615)Gag>Aag	p.E205K	VWA5A_ENST00000392748.1_Missense_Mutation_p.E205K|VWA5A_ENST00000449321.1_Missense_Mutation_p.E205K|VWA5A_ENST00000361352.5_Missense_Mutation_p.E205K|VWA5A_ENST00000392744.4_Missense_Mutation_p.E221K|VWA5A_ENST00000360334.4_Missense_Mutation_p.E205K	NM_001130142.1	NP_001123614.1	O00534	VMA5A_HUMAN	von Willebrand factor A domain containing 5A	205			E -> K (in dbSNP:rs35215239).					p.E205*(1)		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						GAGTCCTACCGAGTACCTAGG	0.517													G|||	109	0.0217652	0.0809	0.0029	5008	,	,		20475	0.0		0.0	False		,,,				2504	0.0				p.E205K		Atlas-SNP	.											VWA5A,larynx,carcinoma,0,1	VWA5A	102	1	1	Substitution - Nonsense(1)	upper_aerodigestive_tract(1)	c.G613A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU	253,4149	145.7+/-180.5	8,237,1956	90	82	85		613,613,613	-2.8	0	11	dbSNP_126	85	3,8595	3.0+/-9.4	0,3,4296	yes	missense,missense,missense	VWA5A	NM_001130142.1,NM_014622.4,NM_198315.2	56,56,56	8,240,6252	AA,AG,GG		0.0349,5.7474,1.9692	benign,benign,benign	205/787,205/787,205/416	123989383	256,12744	2201	4299	6500	SO:0001583	missense	4013	exon5			CCTACCGAGTACC	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.613G>A	11.37:g.123989383G>A	ENSP00000407726:p.Glu205Lys	91	0	0		78	28	0.358974	NM_014622	Q6UN19|Q6UN20|Q9BVF8	Missense_Mutation	SNP	ENST00000456829.2	37	CCDS8444.1	40	0.018315018315018316	39	0.07926829268292683	1	0.0027624309392265192	0	0.0	0	0.0	G	7.535	0.659528	0.14645	0.057474	3.49E-4	ENSG00000110002	ENST00000456829;ENST00000360334;ENST00000392748;ENST00000524524;ENST00000530025;ENST00000361352;ENST00000449321;ENST00000392744	T;T;T;T;T;T	0.22743	3.78;1.94;3.78;2.28;2.28;2.27	5.6	-2.84	0.05751	.	0.832622	0.11287	N	0.579757	T	0.00608	0.0020	L	0.52364	1.645	0.09310	N	1	B;B	0.31859	0.091;0.343	B;B	0.24269	0.023;0.052	T	0.30736	-0.9968	10	0.08599	T	0.76	-11.1706	6.7445	0.23454	0.2766:0.318:0.4054:0.0	rs35215239	221;205	B4DHS6;O00534	.;VMA5A_HUMAN	K	205;205;205;205;205;205;205;221	ENSP00000407726:E205K;ENSP00000353485:E205K;ENSP00000376504:E205K;ENSP00000355070:E205K;ENSP00000404683:E205K;ENSP00000376501:E221K	ENSP00000353485:E205K	E	+	1	0	VWA5A	123494593	0.001000	0.12720	0.003000	0.11579	0.055000	0.15305	-0.395000	0.07287	-0.184000	0.10567	-0.315000	0.08773	GAG	G|0.978;A|0.022	0.022	strong		0.517	VWA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387273.1	NM_014622		A	123989383	G	A	123989383	3	1	22	1	0	0	0	0	1	0	0	0	17257	1059	37	1	627	1	VWA5A	11	123989383	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	79745	123989383	11017133	2603	5504											
OR8G5	219865	hgsc.bcm.edu	37	chr11	124135143	124135143	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcagctctacttcttcctcGtttttgctattgcagagtgt	5	18	7	11	1	3	1	1	0	2	1	5	1	4	1	1	0	4	4	1	0	2	7	rs200012972	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124135143G>A	ENST00000524943.2	+	1	421	c.421G>A	c.(421-423)Gtt>Att	p.V141I	OR8G1_ENST00000341493.2_RNA	NM_001005198.1	NP_001005198.1	Q8NG78	OR8G5_HUMAN	olfactory receptor, family 8, subfamily G, member 5	141						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)		CTTCTTCCTCGTTTTTGCTAT	0.463													g|||	27	0.00539137	0.0197	0.0014	5008	,	,		23436	0.0		0.0	False		,,,				2504	0.0				p.V141I	Ovarian(169;523 1969 8640 31295 51256)	Atlas-SNP	.											.	.	.	.	0			c.G421A						PASS	.	G	ILE/VAL	38,4260		0,38,2111	165	155	158		421	-7.2	0	11		158	0,8562		0,0,4281	no	missense	OR8G5	NM_001005198.1	29	0,38,6392	AA,AG,GG		0.0,0.8841,0.2955		141/347	124135143	38,12822	2149	4281	6430	SO:0001583	missense	219865	exon1			TTCCTCGTTTTTG	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.421G>A	11.37:g.124135143G>A	ENSP00000477014:p.Val141Ile	332	0	0		258	127	0.492248	NM_001005198	B2RND3|Q6IEU6	Missense_Mutation	SNP	ENST00000524943.2	37																																																																																				.	.	weak		0.463	OR8G5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387283.2	NM_001005198		A	124135143	G	A	124135143	3	1	22	1	0	0	0	0	1	0	0	0	11245	1145	40	1	423	1	OR8G5	11	124135143	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	145760	124135143	10871373	2604	5505											
OR8D2	283160	hgsc.bcm.edu	37	chr11	124190036	124190036	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggcagttgaagttctgggcGttgtgtcaagcctgccagga	7	11	15	8	1	2	1	1	1	1	0	2	2	2	2	2	3	2	4	2	3	2	3	rs61735123	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124190036G>A	ENST00000357438.2	-	1	148	c.58C>T	c.(58-60)Cgc>Tgc	p.R20C		NM_001002918.1	NP_001002918.1	Q9GZM6	OR8D2_HUMAN	olfactory receptor, family 8, subfamily D, member 2	20						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)		AGTTCTGGGCGTTGTGTCAAG	0.438													A|||	134	0.0267572	0.093	0.013	5008	,	,		17109	0.001		0.0	False		,,,				2504	0.001				p.R20C		Atlas-SNP	.											.	OR8D2	65	.	0			c.C58T						PASS	.	A	CYS/ARG	378,4022	188.5+/-214.9	16,346,1838	67	67	67		58	-6.8	0	11	dbSNP_129	67	5,8593	4.3+/-15.6	0,5,4294	yes	missense	OR8D2	NM_001002918.1	180	16,351,6132	AA,AG,GG		0.0582,8.5909,2.9466	benign	20/312	124190036	383,12615	2200	4299	6499	SO:0001583	missense	283160	exon1			CTGGGCGTTGTGT	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.58C>T	11.37:g.124190036G>A	ENSP00000350022:p.Arg20Cys	61	0	0		66	28	0.424242	NM_001002918	B9EH49|Q6IFR0	Missense_Mutation	SNP	ENST00000357438.2	37	CCDS31707.1	33	0.01510989010989011	28	0.056910569105691054	5	0.013812154696132596	0	0.0	0	0.0	g	6.776	0.512072	0.12944	0.085909	5.82E-4	ENSG00000197263	ENST00000357438	T	0.00438	7.42	3.42	-6.85	0.01681	.	1.442220	0.04657	N	0.408191	T	0.00012	0.0000	N	0.25380	0.74	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.35943	-0.9768	10	0.72032	D	0.01	.	6.2183	0.20667	0.4743:0.0:0.1929:0.3328	.	20	Q9GZM6	OR8D2_HUMAN	C	20	ENSP00000350022:R20C	ENSP00000350022:R20C	R	-	1	0	OR8D2	123695246	0.000000	0.05858	0.000000	0.03702	0.072000	0.16883	-2.227000	0.01210	-3.085000	0.00249	-0.684000	0.03749	CGC	G|0.972;A|0.028	0.028	strong		0.438	OR8D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387286.1	NM_001002918		A	124190036	G	A	124190036	3	1	22	1	0	0	0	0	1	0	0	0	11241	1145	40	1	880	1	OR8D2	11	124190036	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	54893	124190036	10816480	2605	5506											
OR8B2	26595	hgsc.bcm.edu	37	chr11	124253042	124253042	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	taacagagatcaatgaaggaGagattgaagaggaaatagta	20	7	12	2	0	1	5	1	2	0	3	1	9	1	7	0	2	1	1	0	2	7	4	rs142893914	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124253042G>A	ENST00000375013.2	-	1	216	c.198C>T	c.(196-198)ctC>ctT	p.L66L		NM_001005468.1	NP_001005468.1	Q96RD0	OR8B2_HUMAN	olfactory receptor, family 8, subfamily B, 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)			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)		CAATGAAGGAGAGATTGAAGA	0.398													g|||	90	0.0179712	0.0605	0.0115	5008	,	,		22840	0.0		0.002	False		,,,				2504	0.0				p.L66L		Atlas-SNP	.											.	OR8B2	42	.	0			c.C198T						PASS	.	G		271,4131	153.7+/-187.2	8,255,1938	154	143	147		198	-8.4	0	11	dbSNP_134	147	5,8587	4.3+/-15.6	0,5,4291	no	coding-synonymous	OR8B2	NM_001005468.1		8,260,6229	AA,AG,GG		0.0582,6.1563,2.1241		66/314	124253042	276,12718	2201	4296	6497	SO:0001819	synonymous_variant	26595	exon1			GAAGGAGAGATTG	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.198C>T	11.37:g.124253042G>A		242	0	0		175	87	0.497143	NM_001005468	Q8NGH2	Silent	SNP	ENST00000375013.2	37	CCDS31708.1																																																																																			.	.	weak		0.398	OR8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387290.1	NM_001005468		A	124253042	G	A	124253042	2	1	22	1	0	0	0	0	0	0	0	1	11236	929	33	2		2	OR8B2	11	124253042	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	63006	124253042	10753474	2606	5507											
OR8B12	219858	hgsc.bcm.edu	37	chr11	124413491	124413491	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagagggggatccgcagtccCggctggtgggttaagccttc	7	8	16	10	2	0	1	0	0	0	1	3	2	2	2	3	5	1	3	3	5	2	2	rs61746453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124413491C>T	ENST00000306842.2	-	1	84	c.60G>A	c.(58-60)ccG>ccA	p.P20P		NM_001005195.1	NP_001005195.1	Q8NGG6	OR8BC_HUMAN	olfactory receptor, family 8, subfamily B, member 12	20						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)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		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;0.0213)		TCCGCAGTCCCGGCTGGTGGG	0.542													C|||	139	0.0277556	0.1021	0.0058	5008	,	,		18064	0.0		0.0	False		,,,				2504	0.0				p.P20P		Atlas-SNP	.											OR8B12,bladder,carcinoma,-1,1	OR8B12	66	1	0			c.G60A						PASS	.	C		321,4081	155.5+/-188.7	7,307,1887	47	51	49		60	-5.8	0	11	dbSNP_129	49	16,8582	10.5+/-38.8	0,16,4283	no	coding-synonymous	OR8B12	NM_001005195.1		7,323,6170	TT,TC,CC		0.1861,7.2921,2.5923		20/311	124413491	337,12663	2201	4299	6500	SO:0001819	synonymous_variant	219858	exon1			CAGTCCCGGCTGG		CCDS31711.1	11q24.2	2013-09-24			ENSG00000170953	ENSG00000170953		"GPCR / Class A : Olfactory receptors"	15307	protein-coding gene	gene with protein product							Standard	NM_001005195		Approved		uc010sam.2	Q8NGG6	OTTHUMG00000165922	ENST00000306842.2:c.60G>A	11.37:g.124413491C>T		60	0	0		51	27	0.529412	NM_001005195	B2RNF6|Q6IEW8|Q96RC7	Silent	SNP	ENST00000306842.2	37	CCDS31711.1																																																																																			C|0.974;T|0.026	0.026	strong		0.542	OR8B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387061.1			T	124413491	C	T	124413491	2	4	22	1	0	0	0	0	0	0	0	1	11235	639	23	1		1	OR8B12	11	124413491	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	160449	124413491	10593025	2607	5508											
ROBO4	54538	hgsc.bcm.edu	37	chr11	124764176	124764176	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acttgcacgcagtaggagccTggcatatgggtggcgatttc	8	10	14	9	2	0	0	0	0	0	0	1	2	0	1	1	4	2	4	1	4	2	4	rs11820142	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124764176T>C	ENST00000306534.3	-	8	1724	c.1239A>G	c.(1237-1239)ccA>ccG	p.P413P	ROBO4_ENST00000526899.1_5'Flank|ROBO4_ENST00000533054.1_Silent_p.P268P	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	413	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)			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)		AGTAGGAGCCTGGCATATGGG	0.597													T|||	125	0.0249601	0.0893	0.0086	5008	,	,		3618	0.0		0.001	False		,,,				2504	0.0				p.P413P		Atlas-SNP	.											.	ROBO4	130	.	0			c.A1239G						PASS	.	T		344,4058	179.4+/-207.9	9,326,1866	111	87	95		1239	1.1	1	11	dbSNP_120	95	2,8596	1.2+/-3.3	0,2,4297	no	coding-synonymous	ROBO4	NM_019055.5		9,328,6163	CC,CT,TT		0.0233,7.8146,2.6615		413/1008	124764176	346,12654	2201	4299	6500	SO:0001819	synonymous_variant	54538	exon8			GGAGCCTGGCATA	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.1239A>G	11.37:g.124764176T>C		97	0	0		90	38	0.422222	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Silent	SNP	ENST00000306534.3	37	CCDS8455.1																																																																																			T|0.971;C|0.029	0.029	strong		0.597	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055		C	124764176	T	C	124764176	2	2	22	1	0	0	0	0	0	0	0	1	13531	1567	55	3		3	ROBO4	11	124764176	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	350685	124764176	10242340	2608	5509											
ROBO4	54538	hgsc.bcm.edu	37	chr11	124765511	124765511	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctctgcccacggagctcccTggcctcccggggcagtctgg	3	7	13	18	2	2	0	0	0	2	0	4	1	4	1	5	5	2	2	5	5	0	0	rs60888551	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124765511T>G	ENST00000306534.3	-	6	1363	c.878A>C	c.(877-879)cAg>cCg	p.Q293P	ROBO4_ENST00000526899.1_5'Flank|ROBO4_ENST00000533054.1_Missense_Mutation_p.Q148P	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	293	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)		CGGAGCTCCCTGGCCTCCCGG	0.657													T|||	366	0.0730831	0.2557	0.0202	5008	,	,		15539	0.0		0.0129	False		,,,				2504	0.001				p.Q293P		Atlas-SNP	.											.	ROBO4	130	.	0			c.A878C						PASS	.	T	PRO/GLN	667,3699		42,583,1558	34	43	40		878	0.9	0.6	11	dbSNP_129	40	44,8504		1,42,4231	yes	missense	ROBO4	NM_019055.5	76	43,625,5789	GG,GT,TT		0.5147,15.2771,5.5057	benign	293/1008	124765511	711,12203	2183	4274	6457	SO:0001583	missense	54538	exon6			GCTCCCTGGCCTC	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.878A>C	11.37:g.124765511T>G	ENSP00000304945:p.Gln293Pro	93	0	0		93	31	0.333333	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Missense_Mutation	SNP	ENST00000306534.3	37	CCDS8455.1	127	0.05815018315018315	108	0.21951219512195122	10	0.027624309392265192	0	0.0	9	0.011873350923482849	T	7.456	0.643746	0.14451	0.152771	0.005147	ENSG00000154133	ENST00000306534;ENST00000374963;ENST00000533054	T;T	0.64438	-0.1;0.26	4.72	0.925	0.19424	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.438357	0.17070	N	0.188195	T	0.00039	0.0001	L	0.29908	0.895	0.48341	P	3.670000000000062E-4	B;B	0.10296	0.002;0.003	B;B	0.08055	0.003;0.002	T	0.06303	-1.0834	9	0.30078	T	0.28	.	5.9357	0.19165	0.0:0.0891:0.3409:0.57	rs60888551	183;293	Q8WZ75-3;Q8WZ75	.;ROBO4_HUMAN	P	293;183;148	ENSP00000304945:Q293P;ENSP00000437129:Q148P	ENSP00000304945:Q293P	Q	-	2	0	ROBO4	124270721	0.108000	0.22018	0.642000	0.29436	0.276000	0.26787	0.391000	0.20784	0.293000	0.22520	0.459000	0.35465	CAG	T|0.952;G|0.048	0.048	strong		0.657	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055		G	124765511	T	G	124765511	3	3	22	1	0	0	0	0	1	0	0	0	13531	1580	55	5	2197	5	ROBO4	11	124765511	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1335	124765511	10241005	2609	5510											
HEPACAM	220296	hgsc.bcm.edu	37	chr11	124794763	124794763	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaaagagtcggatacggtcTcgatagtcaggccgcagggt	10	8	14	9	4	3	1	2	0	1	1	5	3	3	2	1	4	1	1	1	4	3	2	rs36089266	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124794763T>G	ENST00000298251.4	-	2	693	c.288A>C	c.(286-288)cgA>cgC	p.R96R		NM_152722.4	NP_689935.2			hepatic and glial cell adhesion molecule											breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22	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;1.54e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308)		GGATACGGTCTCGATAGTCAG	0.587													T|||	27	0.00539137	0.0204	0.0	5008	,	,		21438	0.0		0.0	False		,,,				2504	0.0				p.R96R		Atlas-SNP	.											HEPACAM,NS,carcinoma,-1,4	HEPACAM	64	4	0			c.A288C						PASS	.	T		52,4350	53.6+/-89.4	1,50,2150	142	125	131		288	1.8	1	11	dbSNP_126	131	0,8598		0,0,4299	no	coding-synonymous	HEPACAM	NM_152722.4		1,50,6449	GG,GT,TT		0.0,1.1813,0.4		96/417	124794763	52,12948	2201	4299	6500	SO:0001819	synonymous_variant	220296	exon2			ACGGTCTCGATAG	AK098396	CCDS8456.1	11q24.2	2013-01-29	2011-02-11		ENSG00000165478	ENSG00000165478		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	26361	protein-coding gene	gene with protein product	"glial cell adhesion molecule"	611642	"hepatocyte cell adhesion molecule"			15885354, 15917256	Standard	NM_152722		Approved	FLJ25530, hepaCAM, GLIALCAM	uc001qbk.3	Q14CZ8	OTTHUMG00000165938	ENST00000298251.4:c.288A>C	11.37:g.124794763T>G		127	0	0		111	57	0.513514	NM_152722		Silent	SNP	ENST00000298251.4	37	CCDS8456.1																																																																																			T|0.994;G|0.006	0.006	strong		0.587	HEPACAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387125.1	NM_152722		G	124794763	T	G	124794763	2	3	22	1	0	0	0	0	0	0	0	1	7061	1538	54	5		5	HEPACAM	11	124794763	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	29252	124794763	10211753	2610	5511											
TMEM218	219854	hgsc.bcm.edu	37	chr11	124972114	124972114	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aagatgaacacgcccgcaccGactccgagcacagtgccagc	12	3	10	16	4	0	2	0	1	0	1	1	4	1	2	4	0	4	2	4	0	2	0	rs7114520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124972114G>A	ENST00000279968.4	-	3	347	c.24C>T	c.(22-24)gtC>gtT	p.V8V	TMEM218_ENST00000531909.1_Silent_p.V8V|TMEM218_ENST00000532407.1_Silent_p.V8V|TMEM218_ENST00000527271.1_Silent_p.V8V|TMEM218_ENST00000531262.1_Intron|TMEM218_ENST00000455225.1_Silent_p.V8V|TMEM218_ENST00000526175.1_Silent_p.V8V|TMEM218_ENST00000529583.1_Silent_p.V8V|TMEM218_ENST00000529609.1_Silent_p.V8V|TMEM218_ENST00000532156.1_Silent_p.V8V|TMEM218_ENST00000527766.1_Silent_p.V8V|TMEM218_ENST00000528724.1_Silent_p.V8V			A2RU14	TM218_HUMAN	transmembrane protein 218	8						integral component of membrane (GO:0016021)				breast(1)|large_intestine(2)|lung(1)|prostate(1)	5						CGCCCGCACCGACTCCGAGCA	0.682													G|||	294	0.0587061	0.1861	0.0115	5008	,	,		12552	0.001		0.008	False		,,,				2504	0.0317				p.V43V		Atlas-SNP	.											.	TMEM218	14	.	0			c.C129T						PASS	.	G		735,3661	293.8+/-282.8	52,631,1515	42	43	43		24	0.9	1	11	dbSNP_116	43	70,8520	41.7+/-99.0	0,70,4225	no	coding-synonymous	TMEM218	NM_001080546.1		52,701,5740	AA,AG,GG		0.8149,16.7197,6.199		8/116	124972114	805,12181	2198	4295	6493	SO:0001819	synonymous_variant	219854	exon4			CGCACCGACTCCG		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.24C>T	11.37:g.124972114G>A		88	0	0		79	43	0.544304	NM_001258243	B7ZM48	Silent	SNP	ENST00000279968.4	37	CCDS31715.1																																																																																			G|0.946;A|0.054	0.054	strong		0.682	TMEM218-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386849.1	NM_001080546		A	124972114	G	A	124972114	2	1	22	1	0	0	0	0	0	0	0	1	16156	1045	37	1		1	TMEM218	11	124972114	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	177351	124972114	10034402	2611	5512											
DDX25	29118	hgsc.bcm.edu	37	chr11	125778305	125778305	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cttttctacagaccccagaaCctcatagcacagagccagtc	12	8	6	15	0	2	3	1	0	1	3	3	3	2	3	4	0	4	1	4	0	3	4	rs34007659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:125778305C>T	ENST00000263576.6	+	6	569	c.414C>T	c.(412-414)aaC>aaT	p.N138N	RP11-680F20.9_ENST00000533033.2_RNA|DDX25_ENST00000525943.1_3'UTR	NM_013264.4	NP_037396.3	Q9UHL0	DDX25_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 25	138	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|ovary(2)|upper_aerodigestive_tract(1)	10	all_hematologic(175;0.177)	Breast(109;0.0021)|all_lung(97;0.0203)|Lung NSC(97;0.0203)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.14e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.046)		GACCCCAGAACCTCATAGCAC	0.428													C|||	85	0.0169728	0.0613	0.0043	5008	,	,		20960	0.0		0.001	False		,,,				2504	0.0				p.N138N		Atlas-SNP	.											.	DDX25	65	.	0			c.C414T						PASS	.	C		201,3635		5,191,1722	170	163	165		414	2.3	1	11	dbSNP_126	165	5,8241		0,5,4118	no	coding-synonymous	DDX25	NM_013264.3		5,196,5840	TT,TC,CC		0.0606,5.2398,1.705		138/484	125778305	206,11876	1918	4123	6041	SO:0001819	synonymous_variant	29118	exon6			CCAGAACCTCATA	AF155140	CCDS44766.1	11q24	2012-02-23	2012-02-23		ENSG00000109832	ENSG00000109832		"DEAD-boxes"	18698	protein-coding gene	gene with protein product	"gonadotropin-regulated testicular RNA helicase"	607663	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 25", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 25"			10608860, 15096601	Standard	NM_013264		Approved	GRTH	uc001qcz.5	Q9UHL0	OTTHUMG00000165859	ENST00000263576.6:c.414C>T	11.37:g.125778305C>T		153	0	0		146	83	0.568493	NM_013264	B2R6Z0|Q5XVN2|Q86W81|Q8IYP1	Silent	SNP	ENST00000263576.6	37	CCDS44766.1	31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	C	8.677	0.904182	0.17760	0.052398	6.06E-4	ENSG00000109832	ENST00000530129	.	.	.	5.18	2.26	0.28386	.	.	.	.	.	T	0.10165	0.0249	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.03773	-1.1005	4	.	.	.	-6.705	4.4905	0.11812	0.0:0.4806:0.1565:0.3629	rs34007659	.	.	.	S	150	.	.	P	+	1	0	DDX25	125283515	0.994000	0.37717	1.000000	0.80357	0.995000	0.86356	0.292000	0.19011	0.269000	0.21961	0.591000	0.81541	CCT	C|0.985;T|0.015	0.015	strong		0.428	DDX25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386736.3	NM_013264		T	125778305	C	T	125778305	2	4	22	1	0	0	0	0	0	0	0	1	4354	506	18	2		2	DDX25	11	125778305	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	806191	125778305	9228211	2612	5513											
KIRREL3	84623	hgsc.bcm.edu	37	chr11	126294661	126294661	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tccaggaaggagctgctgtcGctgagggagcctctctggaa	8	8	15	10	1	1	1	0	1	1	0	4	5	2	5	2	4	3	3	2	4	2	0	rs34844660	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:126294661G>A	ENST00000525144.2	-	17	2400	c.2151C>T	c.(2149-2151)agC>agT	p.S717S	KIRREL3_ENST00000529097.2_Silent_p.S705S|KIRREL3_ENST00000416561.2_Silent_p.S184S	NM_032531.3	NP_115920.1	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 (Drosophila)	717	Ser-rich.				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)		AGCTGCTGTCGCTGAGGGAGC	0.627													G|||	69	0.013778	0.0514	0.0014	5008	,	,		19048	0.0		0.0	False		,,,				2504	0.0				p.S717S		Atlas-SNP	.											.	KIRREL3	183	.	0			c.C2151T						PASS	.	G		148,4198		0,148,2025	74	82	79		2151	4	1	11	dbSNP_126	79	0,8562		0,0,4281	no	coding-synonymous	KIRREL3	NM_032531.3		0,148,6306	AA,AG,GG		0.0,3.4054,1.1466		717/779	126294661	148,12760	2173	4281	6454	SO:0001819	synonymous_variant	84623	exon17			GCTGTCGCTGAGG	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.2151C>T	11.37:g.126294661G>A		115	0	0		109	54	0.495413	NM_032531	Q3MIJ7|Q6UWJ9|Q6UWL5|Q96JG0	Silent	SNP	ENST00000525144.2	37	CCDS53723.1																																																																																			G|0.992;A|0.008	0.008	strong		0.627	KIRREL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386479.2	NM_032531		A	126294661	G	A	126294661	2	1	22	1	0	0	0	0	0	0	0	1	8335	1078	38	1		1	KIRREL3	11	126294661	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	516356	126294661	8711855	2613	5514											
ARHGAP32	9743	hgsc.bcm.edu	37	chr11	128994781	128994781	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaatctctggaacatctgcGcctcttgccttaaaaaataa	13	11	7	10	1	3	0	0	0	3	0	4	2	3	2	2	2	3	0	2	2	6	3	rs114955890	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:128994781G>A	ENST00000310343.9	-	3	233	c.234C>T	c.(232-234)ggC>ggT	p.G78G	ARHGAP32_ENST00000524655.1_Silent_p.G4G	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	78					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						GAACATCTGCGCCTCTTGCCT	0.333													G|||	6	0.00119808	0.0045	0.0	5008	,	,		15533	0.0		0.0	False		,,,				2504	0.0				p.G78G		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.C234T						PASS	.	G		17,3115		0,17,1549	108	98	101		234	2.2	1	11	dbSNP_132	101	0,7156		0,0,3578	no	coding-synonymous	ARHGAP32	NM_001142685.1		0,17,5127	AA,AG,GG		0.0,0.5428,0.1652		78/2088	128994781	17,10271	1566	3578	5144	SO:0001819	synonymous_variant	9743	exon3			ATCTGCGCCTCTT	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.234C>T	11.37:g.128994781G>A		42	0	0		59	34	0.576271	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Silent	SNP	ENST00000310343.9	37	CCDS44769.1																																																																																			G|0.998;A|0.002	0.002	strong		0.333	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715		A	128994781	G	A	128994781	2	1	22	1	0	0	0	0	0	0	0	1	881	1074	38	1		1	ARHGAP32	11	128994781	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2700120	128994781	6011735	2614	5515											
TMEM45B	120224	hgsc.bcm.edu	37	chr11	129722512	129722512	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctacattactatcagcgtctCgagatcgtcgaagccgcaat	11	10	8	12	5	2	1	1	0	1	1	5	3	2	1	1	0	4	1	1	0	5	3	rs115605173	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:129722512C>T	ENST00000524567.1	+	2	416	c.135C>T	c.(133-135)ctC>ctT	p.L45L	TMEM45B_ENST00000281441.3_Silent_p.L45L			Q96B21	TM45B_HUMAN	transmembrane protein 45B	45						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)		ATCAGCGTCTCGAGATCGTCG	0.483													C|||	40	0.00798722	0.0272	0.0058	5008	,	,		19521	0.0		0.0	False		,,,				2504	0.0				p.L45L		Atlas-SNP	.											.	TMEM45B	25	.	0			c.C135T						PASS	.	C		118,4284	89.2+/-127.9	1,116,2084	144	133	136		135	-11.3	0	11	dbSNP_132	136	10,8584	7.1+/-27.0	0,10,4287	no	coding-synonymous	TMEM45B	NM_138788.3		1,126,6371	TT,TC,CC		0.1164,2.6806,0.9849		45/276	129722512	128,12868	2201	4297	6498	SO:0001819	synonymous_variant	120224	exon2			GCGTCTCGAGATC	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.135C>T	11.37:g.129722512C>T		235	0	0		248	132	0.532258	NM_138788	A8K2L8	Silent	SNP	ENST00000524567.1	37	CCDS8482.1																																																																																			C|0.991;T|0.009	0.009	strong		0.483	TMEM45B-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386062.1	NM_138788		T	129722512	C	T	129722512	2	4	22	1	0	0	0	0	0	0	0	1	16185	871	31	1		1	TMEM45B	11	129722512	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	727731	129722512	5284004	2615	5516											
NFRKB	4798	hgsc.bcm.edu	37	chr11	129752426	129752426	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcagtactgcttagcggctcGgccaggtcctctgcctctga	5	11	11	14	2	3	1	1	1	2	0	5	1	4	1	3	3	4	3	3	3	2	2	rs76967949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:129752426G>A	ENST00000446488.3	-	9	1105	c.1002C>T	c.(1000-1002)gcC>gcT	p.A334A	NFRKB_ENST00000524746.1_Silent_p.A334A|NFRKB_ENST00000304521.5_Silent_p.A334A|NFRKB_ENST00000524794.1_Silent_p.A359A	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	334					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)		TTAGCGGCTCGGCCAGGTCCT	0.463													G|||	42	0.00838658	0.0295	0.0043	5008	,	,		17616	0.0		0.0	False		,,,				2504	0.0				p.A359A		Atlas-SNP	.											.	NFRKB	101	.	0			c.C1077T						PASS	.	G	,	177,4225	116.3+/-154.2	5,167,2029	95	99	98		1002,1077	-0.8	0.6	11	dbSNP_131	98	5,8589	4.3+/-15.6	0,5,4292	no	coding-synonymous,coding-synonymous	NFRKB	NM_001143835.1,NM_006165.3	,	5,172,6321	AA,AG,GG		0.0582,4.0209,1.4004	,	334/1300,359/1325	129752426	182,12814	2201	4297	6498	SO:0001819	synonymous_variant	4798	exon8			CGGCTCGGCCAGG		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.1002C>T	11.37:g.129752426G>A		89	0	0		85	51	0.6	NM_006165	Q12869|Q15312|Q9H048	Silent	SNP	ENST00000446488.3	37	CCDS44770.1																																																																																			G|0.985;A|0.015	0.015	strong		0.463	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2	NM_006165		A	129752426	G	A	129752426	2	1	22	1	0	0	0	0	0	0	0	1	10393	1103	39	1		1	NFRKB	11	129752426	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	29914	129752426	5254090	2616	5517											
ADAMTS8	11095	hgsc.bcm.edu	37	chr11	130284495	130284495	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtgcccaggcccgcacggCgtgccgtcagcccagggcag	6	3	16	16	4	1	0	1	0	0	0	1	0	1	0	4	4	3	2	4	4	0	0	rs142963990	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:130284495C>T	ENST00000257359.6	-	5	2203	c.1497G>A	c.(1495-1497)acG>acA	p.T499T		NM_007037.4	NP_008968.4	Q9UP79	ATS8_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 8	499	Disintegrin.				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)		GCCCGCACGGCGTGCCGTCAG	0.662													C|||	20	0.00399361	0.0151	0.0	5008	,	,		17513	0.0		0.0	False		,,,				2504	0.0				p.T499T		Atlas-SNP	.											.	ADAMTS8	172	.	0			c.G1497A						PASS	.	C		53,3979		0,53,1963	48	54	52		1497	-11.2	0.2	11	dbSNP_134	52	0,8342		0,0,4171	no	coding-synonymous	ADAMTS8	NM_007037.4		0,53,6134	TT,TC,CC		0.0,1.3145,0.4283		499/890	130284495	53,12321	2016	4171	6187	SO:0001819	synonymous_variant	11095	exon5			GCACGGCGTGCCG	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.1497G>A	11.37:g.130284495C>T		258	1	0.00387597		271	127	0.468635	NM_007037	Q9NZS0	Silent	SNP	ENST00000257359.6	37	CCDS41732.1																																																																																			C|0.996;T|0.004	0.004	strong		0.662	ADAMTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385636.1	NM_007037		T	130284495	C	T	130284495	2	4	22	1	0	0	0	0	0	0	0	1	272	755	27	1		1	ADAMTS8	11	130284495	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	532069	130284495	4722021	2617	5518											
ADAMTS15	170689	hgsc.bcm.edu	37	chr11	130318935	130318935	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctggaggctctgagccagagCgggaggtagtcgttcccatc	7	8	15	11	2	1	2	0	1	1	1	4	4	2	4	2	4	2	3	2	4	1	2	rs146878786	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:130318935C>A	ENST00000299164.2	+	1	67	c.67C>A	c.(67-69)Cgg>Agg	p.R23R		NM_139055.2	NP_620686.1	Q8TE58	ATS15_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 15	23						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)		TGAGCCAGAGCGGGAGGTAGT	0.662													C|||	14	0.00279553	0.0098	0.0014	5008	,	,		14248	0.0		0.0	False		,,,				2504	0.0				p.R23R		Atlas-SNP	.											.	ADAMTS15	103	.	0			c.C67A						PASS	.	C		46,4356	44.6+/-78.6	0,46,2155	29	30	30		67	2.4	0.4	11	dbSNP_134	30	0,8594		0,0,4297	no	coding-synonymous	ADAMTS15	NM_139055.2		0,46,6452	AA,AC,CC		0.0,1.045,0.354		23/951	130318935	46,12950	2201	4297	6498	SO:0001819	synonymous_variant	170689	exon1			CCAGAGCGGGAGG	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.67C>A	11.37:g.130318935C>A		82	0	0		59	24	0.40678	NM_139055	Q32MI6	Silent	SNP	ENST00000299164.2	37	CCDS8488.1																																																																																			C|0.997;A|0.003	0.003	strong		0.662	ADAMTS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385638.1	NM_139055		A	130318935	C	A	130318935	2	1	22	1	0	0	0	0	0	0	0	1	260	759	27	4		4	ADAMTS15	11	130318935	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	34440	130318935	4687581	2618	5519											
IGSF9B	22997	hgsc.bcm.edu	37	chr11	133789790	133789790	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagggtagccggtggccagaGtggtgaagcccatggcgggc	8	5	19	9	2	0	2	0	1	0	1	0	2	0	2	3	6	2	1	3	6	3	1	rs200373794	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:133789790G>C	ENST00000321016.8	-	18	4060	c.3830C>G	c.(3829-3831)aCt>aGt	p.T1277S	IGSF9B_ENST00000533871.2_Missense_Mutation_p.T1277S			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	1277	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)		GGTGGCCAGAGTGGTGAAGCC	0.677													G|||	20	0.00399361	0.0151	0.0	5008	,	,		12387	0.0		0.0	False		,,,				2504	0.0				p.T1277S		Atlas-SNP	.											.	IGSF9B	290	.	0			c.C3830G						PASS	.	G	SER/THR	55,3777		1,53,1862	24	32	30		3830	4.8	0.9	11	dbSNP_132	30	1,8223		0,1,4111	yes	missense	IGSF9B	NM_014987.1	58	1,54,5973	CC,CG,GG		0.0122,1.4353,0.4645	benign	1277/1350	133789790	56,12000	1916	4112	6028	SO:0001583	missense	22997	exon18			GCCAGAGTGGTGA	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.3830C>G	11.37:g.133789790G>C	ENSP00000317980:p.Thr1277Ser	92	0	0		91	46	0.505495	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	37		.	.	.	.	.	.	.	.	.	.	G	12.95	2.091421	0.36952	0.014353	1.22E-4	ENSG00000080854	ENST00000321016;ENST00000533871	T;T	0.65916	0.15;-0.18	4.76	4.76	0.60689	.	0.000000	0.44688	D	0.000431	T	0.37320	0.0999	N	0.12182	0.205	0.38308	D	0.943176	B	0.06786	0.001	B	0.04013	0.001	T	0.35301	-0.9794	10	0.28530	T	0.3	.	17.5598	0.87902	0.0:0.0:1.0:0.0	.	1277	Q9UPX0	TUTLB_HUMAN	S	1277;1119	ENSP00000317980:T1277S;ENSP00000436552:T1119S	ENSP00000317980:T1277S	T	-	2	0	IGSF9B	133295000	1.000000	0.71417	0.926000	0.36857	0.814000	0.46013	8.633000	0.90999	2.484000	0.83849	0.555000	0.69702	ACT	.	.	weak		0.677	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		C	133789790	G	C	133789790	3	2	22	1	0	0	0	0	1	0	0	0	7615	1029	36	4	227	4	IGSF9B	11	133789790	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3470855	133789790	1216726	2619	5520											
NCAPD3	23310	hgsc.bcm.edu	37	chr11	134038949	134038949	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccaggcaaaactccccgaaGctgcaaaggtgagagaaaca	16	3	11	11	1	0	2	0	1	0	1	1	4	1	2	3	2	4	3	3	2	5	0	rs7927108	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:134038949G>T	ENST00000534548.2	-	25	3166	c.3102C>A	c.(3100-3102)agC>agA	p.S1034R		NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	1034			S -> R (in dbSNP:rs7927108).		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)		ACTCCCCGAAGCTGCAAAGGT	0.433													G|||	165	0.0329473	0.1195	0.0101	5008	,	,		20928	0.0		0.0	False		,,,				2504	0.0				p.S1034R		Atlas-SNP	.											.	NCAPD3	141	.	0			c.C3102A						PASS	.	G	ARG/SER	400,4002	198.1+/-222.0	11,378,1812	54	53	53		3102	-4.5	0.4	11	dbSNP_116	53	2,8592	2.2+/-6.3	0,2,4295	yes	missense-near-splice	NCAPD3	NM_015261.2	110	11,380,6107	TT,TG,GG		0.0233,9.0868,3.0933	benign	1034/1499	134038949	402,12594	2201	4297	6498	SO:0001630	splice_region_variant	23310	exon25			CCCGAAGCTGCAA	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.3102-1C>A	11.37:g.134038949G>T		45	0	0		40	16	0.4	NM_015261	A6NFS2|Q4KMQ9	Missense_Mutation	SNP	ENST00000534548.2	37	CCDS31723.1	55	0.025183150183150184	53	0.10772357723577236	2	0.0055248618784530384	0	0.0	0	0.0	G	8.070	0.770068	0.15983	0.090868	2.33E-4	ENSG00000151503	ENST00000534548;ENST00000530396	T;T	0.46063	0.88;0.88	5.57	-4.49	0.03504	Armadillo-like helical (1);Armadillo-type fold (1);	0.288722	0.49305	N	0.000151	T	0.00384	0.0012	L	0.29908	0.895	0.80722	D	1	B	0.23937	0.094	B	0.28638	0.092	T	0.15292	-1.0442	10	0.13853	T	0.58	.	3.0773	0.06251	0.313:0.3092:0.2902:0.0876	rs7927108;rs52805171;rs7927108	1034	P42695	CNDD3_HUMAN	R	1034;70	ENSP00000433681:S1034R;ENSP00000435173:S70R	ENSP00000435173:S70R	S	-	3	2	NCAPD3	133544159	0.168000	0.22989	0.419000	0.26584	0.457000	0.32468	-0.280000	0.08468	-0.683000	0.05190	-0.258000	0.10820	AGC	G|0.966;T|0.034	0.034	strong		0.433	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261	Missense_Mutation	T	134038949	G	T	134038949	5	4	22	1	0	0	0	0	0	0	1	0	10215	985	34	4	1438	4	NCAPD3	11	134038949	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	249159	134038949	967567	2620	5521											
NCAPD3	23310	hgsc.bcm.edu	37	chr11	134048592	134048592	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agaacctctgacctggggggGtggctgagacgctggggcct	6	7	18	10	1	1	3	0	2	1	2	1	4	1	3	3	6	1	2	3	6	1	0	rs34739733	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:134048592G>T	ENST00000534548.2	-	22	2783	c.2719C>A	c.(2719-2721)Ccc>Acc	p.P907T	RP11-700F16.3_ENST00000531710.1_RNA	NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	907			P -> T (in dbSNP:rs34739733).		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)		ACCTGGGGGGGTGGCTGAGAC	0.522													G|||	20	0.00399361	0.0136	0.0029	5008	,	,		18713	0.0		0.0	False		,,,				2504	0.0				p.P907T		Atlas-SNP	.											.	NCAPD3	141	.	0			c.C2719A						PASS	.	G	THR/PRO	55,4347	54.2+/-90.2	0,55,2146	92	94	93		2719	4.1	0	11	dbSNP_126	93	0,8594		0,0,4297	yes	missense	NCAPD3	NM_015261.2	38	0,55,6443	TT,TG,GG		0.0,1.2494,0.4232	benign	907/1499	134048592	55,12941	2201	4297	6498	SO:0001583	missense	23310	exon22			GGGGGGGTGGCTG	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.2719C>A	11.37:g.134048592G>T	ENSP00000433681:p.Pro907Thr	106	0	0		138	66	0.478261	NM_015261	A6NFS2|Q4KMQ9	Missense_Mutation	SNP	ENST00000534548.2	37	CCDS31723.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	G	8.015	0.758394	0.15846	0.012494	0.0	ENSG00000151503	ENST00000534548	T	0.21734	1.99	6.03	4.13	0.48395	Armadillo-like helical (1);Armadillo-type fold (1);	0.330969	0.32918	N	0.005489	T	0.09512	0.0234	L	0.31664	0.95	0.40749	D	0.982908	B	0.33413	0.411	B	0.29353	0.101	T	0.09530	-1.0670	10	0.14656	T	0.56	-4.2164	11.7991	0.52116	0.0:0.1196:0.6321:0.2483	rs34739733	907	P42695	CNDD3_HUMAN	T	907	ENSP00000433681:P907T	ENSP00000434168:P907T	P	-	1	0	NCAPD3	133553802	1.000000	0.71417	0.001000	0.08648	0.115000	0.19883	4.737000	0.62066	0.850000	0.35239	0.655000	0.94253	CCC	G|0.995;T|0.005	0.005	strong		0.522	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261		T	134048592	G	T	134048592	3	4	22	1	0	0	0	0	1	0	0	0	10215	1261	44	4	1833	4	NCAPD3	11	134048592	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	9643	134048592	957924	2621	5522											
NCAPD3	23310	hgsc.bcm.edu	37	chr11	134055275	134055275	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttattctgctgtagtccagcCtgggtgaggagccagcaatc	8	11	12	10	0	1	1	0	1	1	0	3	2	2	2	3	2	4	3	3	2	3	3	rs61744119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:134055275C>T	ENST00000534548.2	-	17	2256	c.2192G>A	c.(2191-2193)aGg>aAg	p.R731K	RP11-700F16.3_ENST00000531710.1_RNA	NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	731					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)		GTAGTCCAGCCTGGGTGAGGA	0.433													c|||	20	0.00399361	0.0136	0.0029	5008	,	,		16996	0.0		0.0	False		,,,				2504	0.0				p.R731K		Atlas-SNP	.											.	NCAPD3	141	.	0			c.G2192A						PASS	.	T	LYS/ARG	55,4347	52.3+/-87.9	0,55,2146	67	64	65		2192	-2.9	0.6	11	dbSNP_129	65	0,8594		0,0,4297	yes	missense	NCAPD3	NM_015261.2	26	0,55,6443	TT,TC,CC		0.0,1.2494,0.4232	benign	731/1499	134055275	55,12941	2201	4297	6498	SO:0001583	missense	23310	exon17			TCCAGCCTGGGTG	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.2192G>A	11.37:g.134055275C>T	ENSP00000433681:p.Arg731Lys	114	0	0		134	74	0.552239	NM_015261	A6NFS2|Q4KMQ9	Missense_Mutation	SNP	ENST00000534548.2	37	CCDS31723.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	c	0.387	-0.925700	0.02377	0.012494	0.0	ENSG00000151503	ENST00000534548	T	0.16743	2.32	5.95	-2.94	0.05581	Armadillo-like helical (1);Armadillo-type fold (1);	0.333488	0.38164	N	0.001795	T	0.01387	0.0045	N	0.00104	-2.125	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45026	-0.9289	10	0.02654	T	1	-5.8849	6.0997	0.20041	0.087:0.072:0.1785:0.6625	.	731	P42695	CNDD3_HUMAN	K	731	ENSP00000433681:R731K	ENSP00000431612:R731K	R	-	2	0	NCAPD3	133560485	0.426000	0.25506	0.571000	0.28486	0.014000	0.08584	0.322000	0.19576	-1.200000	0.02662	-1.563000	0.00883	AGG	C|0.995;T|0.005	0.005	strong		0.433	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261		T	134055275	C	T	134055275	3	4	22	1	0	0	0	0	1	0	0	0	10215	681	24	2	2380	2	NCAPD3	11	134055275	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6683	134055275	951241	2622	5523											
ACAD8	27034	hgsc.bcm.edu	37	chr11	134131033	134131033	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agcgaggggcagggcttcctCattgccgtgagaggactgaa	9	7	16	9	2	1	2	1	2	0	1	2	5	2	3	2	4	2	2	2	4	1	2	rs36115758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:134131033C>T	ENST00000281182.4	+	7	907	c.801C>T	c.(799-801)ctC>ctT	p.L267L	ACAD8_ENST00000524547.1_3'UTR|ACAD8_ENST00000537423.1_Silent_p.L190L|ACAD8_ENST00000543332.1_Silent_p.L169L|ACAD8_ENST00000374752.4_Silent_p.L140L	NM_014384.2	NP_055199.1	Q9UKU7	ACAD8_HUMAN	acyl-CoA dehydrogenase family, member 8	267					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)	AGGGCTTCCTCATTGCCGTGA	0.597													C|||	41	0.0081869	0.0287	0.0043	5008	,	,		18819	0.0		0.0	False		,,,				2504	0.0				p.L267L	GBM(65;238 1125 33403 41853 48889)	Atlas-SNP	.											.	ACAD8	33	.	0			c.C801T						PASS	.	C		84,4318	71.4+/-109.4	1,82,2118	68	65	66		801	0.9	1	11	dbSNP_126	66	0,8594		0,0,4297	no	coding-synonymous	ACAD8	NM_014384.2		1,82,6415	TT,TC,CC		0.0,1.9082,0.6464		267/416	134131033	84,12912	2201	4297	6498	SO:0001819	synonymous_variant	27034	exon7			CTTCCTCATTGCC	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.801C>T	11.37:g.134131033C>T		132	0	0		118	57	0.483051	NM_014384	B7Z5W4|Q6ZWP6|Q9BUS8	Silent	SNP	ENST00000281182.4	37	CCDS8498.1																																																																																			C|0.993;T|0.007	0.007	strong		0.597	ACAD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393607.1	NM_014384		T	134131033	C	T	134131033	2	4	22	1	0	0	0	0	0	0	0	1	110	813	29	2		2	ACAD8	11	134131033	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	75758	134131033	875483	2623	5524											
DCP1B	196513	hgsc.bcm.edu	37	chr12	2102455	2102455	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcatttctgtagagaaggaaAgggtcctggagttggaaatc	12	10	14	5	0	1	1	0	0	1	1	3	5	2	4	1	4	0	3	1	4	4	3	rs150415068	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:2102455A>C	ENST00000280665.6	-	3	373	c.294T>G	c.(292-294)ccT>ccG	p.P98P	DCP1B_ENST00000541700.1_5'UTR|DCP1B_ENST00000397173.4_5'UTR	NM_152640.3	NP_689853.3	Q8IZD4	DCP1B_HUMAN	decapping mRNA 1B	98					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)			AGAGAAGGAAAGGGTCCTGGA	0.403													A|||	4	0.000798722	0.0	0.0014	5008	,	,		19112	0.0		0.003	False		,,,				2504	0.0				p.P98P		Atlas-SNP	.											DCP1B,rectum,carcinoma,0,6	DCP1B	63	6	0			c.T294G						PASS	.	A		2,4404	4.2+/-10.8	0,2,2201	148	156	153		294	0.6	1	12	dbSNP_134	153	19,8581	13.3+/-46.6	0,19,4281	no	coding-synonymous	DCP1B	NM_152640.3		0,21,6482	CC,CA,AA		0.2209,0.0454,0.1615		98/618	2102455	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	196513	exon3			AAGGAAAGGGTCC	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.294T>G	12.37:g.2102455A>C		146	0	0		185	85	0.459459	NM_152640	B4DRD1|Q86XH9|Q96BP8|Q96MZ8	Silent	SNP	ENST00000280665.6	37	CCDS31727.1																																																																																			A|0.998;C|0.002	0.002	strong		0.403	DCP1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398244.1	NM_152640		C	2102455	A	C	2102455	2	2	22	1	0	0	0	0	0	0	0	1	4301	59	3	5		5	DCP1B	12	2102455	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10		2102455	131749440	2624	5525											
TSPAN9	10867	hgsc.bcm.edu	37	chr12	3389559	3389559	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcctggcaggtgaacgagaaCgccaagaaggacctgaagga	14	3	15	9	2	0	4	0	2	0	2	0	7	0	6	3	4	2	1	3	4	5	0	rs877089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:3389559C>T	ENST00000011898.5	+	6	503	c.342C>T	c.(340-342)aaC>aaT	p.N114N	TSPAN9_ENST00000537971.1_Silent_p.N114N|TSPAN9_ENST00000407263.1_Silent_p.N114N|TSPAN9_ENST00000492305.1_3'UTR	NM_006675.4	NP_006666.1	O75954	TSN9_HUMAN	tetraspanin 9	114						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)			TGAACGAGAACGCCAAGAAGG	0.617													c|||	104	0.0207668	0.0598	0.0173	5008	,	,		18186	0.0		0.0099	False		,,,				2504	0.0031				p.N114N		Atlas-SNP	.											.	TSPAN9	20	.	0			c.C342T						PASS	.		,	237,4169	138.4+/-174.2	3,231,1969	136	92	107		342,342	-3.5	1	12	dbSNP_86	107	130,8470	65.6+/-127.9	1,128,4171	no	coding-synonymous,coding-synonymous	TSPAN9	NM_001168320.1,NM_006675.4	,	4,359,6140	TT,TC,CC		1.5116,5.379,2.8218	,	114/240,114/240	3389559	367,12639	2203	4300	6503	SO:0001819	synonymous_variant	10867	exon6			CGAGAACGCCAAG	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.342C>T	12.37:g.3389559C>T		38	0	0		38	13	0.342105	NM_006675	D3DUQ7|Q53FV2|Q6FGJ8	Silent	SNP	ENST00000011898.5	37	CCDS8520.1																																																																																			C|0.974;T|0.026	0.026	strong		0.617	TSPAN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317606.2	NM_006675		T	3389559	C	T	3389559	2	4	22	1	0	0	0	0	0	0	0	1	16669	535	19	1		1	TSPAN9	12	3389559	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1287104	3389559	130462336	2625	5526											
EFCAB4B	84766	hgsc.bcm.edu	37	chr12	3747496	3747496	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatgattctgcggagcggccGggggtacggacccccaggcc	6	5	17	13	4	1	1	0	1	1	0	1	4	1	3	4	6	3	1	4	6	1	2	rs58583720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:3747496G>C	ENST00000440314.2	-	14	1869	c.1396C>G	c.(1396-1398)Cgg>Ggg	p.R466G		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)			CGGAGCGGCCGGGGGTACGGA	0.612													G|||	59	0.0117812	0.0416	0.0058	5008	,	,		14651	0.0		0.0	False		,,,				2504	0.0				p.R466G		Atlas-SNP	.											.	EFCAB4B	100	.	0			c.C1396G						PASS	.	G	GLY/ARG	50,1334		1,48,643	20	24	23		1396	3.5	0	12	dbSNP_129	23	0,3182		0,0,1591	yes	missense	EFCAB4B	NM_001144958.1	125	1,48,2234	CC,CG,GG		0.0,3.6127,1.0951	benign	466/732	3747496	50,4516	692	1591	2283	SO:0001583	missense	84766	exon14			GCGGCCGGGGGTA																												ENST00000440314.2:c.1396C>G	12.37:g.3747496G>C	ENSP00000409382:p.Arg466Gly	72	0	0		81	46	0.567901	NM_001144958	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000440314.2	37	CCDS44803.1	.	.	.	.	.	.	.	.	.	.	G	12.83	2.054114	0.36277	0.036127	0.0	ENSG00000130038	ENST00000440314	T	0.61274	0.12	4.4	3.51	0.40186	.	.	.	.	.	T	0.23926	0.0579	.	.	.	0.36197	D	0.85047	P	0.42620	0.785	P	0.45506	0.483	T	0.53479	-0.8433	8	0.45353	T	0.12	.	10.1568	0.42827	0.0984:0.0:0.9016:0.0	rs58583720	466	Q9BSW2-2	.	G	466	ENSP00000409382:R466G	ENSP00000409382:R466G	R	-	1	2	EFCAB4B	3617757	0.331000	0.24713	0.007000	0.13788	0.194000	0.23727	4.138000	0.58017	1.074000	0.40909	0.557000	0.71058	CGG	A|0.002;C|0.001;G|0.997	0.001	strong		0.612	EFCAB4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398640.2			C	3747496	G	C	3747496	3	2	22	1	0	0	0	0	1	0	0	0	4939	1115	39	4	827	4	EFCAB4B	12	3747496	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	357937	3747496	130104399	2626	5527											
FGF6	2251	hgsc.bcm.edu	37	chr12	4554549	4554549	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	caatctctccagctagcccgGcgcgagacctggacagcagg	9	5	12	15	3	1	1	0	0	1	1	3	3	2	2	3	3	3	2	3	3	2	1	rs17183529	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:4554549G>A	ENST00000228837.2	-	1	231	c.188C>T	c.(187-189)gCc>gTc	p.A63V		NM_020996.1	NP_066276.2	P10767	FGF6_HUMAN	fibroblast growth factor 6	63			A -> V (in dbSNP:rs17183529). {ECO:0000269|Ref.2}.		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.A63V(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)			AGCTAGCCCGGCGCGAGACCT	0.642													G|||	21	0.00419329	0.0159	0.0	5008	,	,		17319	0.0		0.0	False		,,,				2504	0.0				p.A63V		Atlas-SNP	.											FGF6,colon,carcinoma,-1,2	FGF6	40	2	1	Substitution - Missense(1)	large_intestine(1)	c.C188T						PASS	.	G	VAL/ALA	57,4349	51.6+/-87.1	0,57,2146	88	83	85		188	4.1	0	12	dbSNP_123	85	0,8600		0,0,4300	no	missense	FGF6	NM_020996.1	64	0,57,6446	AA,AG,GG		0.0,1.2937,0.4383	benign	63/209	4554549	57,12949	2203	4300	6503	SO:0001583	missense	2251	exon1			AGCCCGGCGCGAG	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.188C>T	12.37:g.4554549G>A	ENSP00000228837:p.Ala63Val	59	0	0		89	44	0.494382	NM_020996	Q0VAE1	Missense_Mutation	SNP	ENST00000228837.2	37	CCDS8527.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	10.67	1.415816	0.25552	0.012937	0.0	ENSG00000111241	ENST00000228837	T	0.26810	1.71	5.0	4.09	0.47781	.	0.553031	0.20578	N	0.089588	T	0.18257	0.0438	L	0.49126	1.545	0.09310	N	0.999998	B	0.30146	0.27	B	0.34991	0.193	T	0.12578	-1.0542	10	0.36615	T	0.2	.	9.216	0.37348	0.0768:0.1473:0.7759:0.0	rs17183529	63	P10767	FGF6_HUMAN	V	63	ENSP00000228837:A63V	ENSP00000228837:A63V	A	-	2	0	FGF6	4424810	0.756000	0.28383	0.004000	0.12327	0.229000	0.25112	3.566000	0.53805	1.215000	0.43411	0.561000	0.74099	GCC	G|0.996;A|0.004	0.004	strong		0.642	FGF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398939.1	NM_020996		A	4554549	G	A	4554549	3	1	22	1	0	0	0	0	1	0	0	0	5864	1203	42	2	450	2	FGF6	12	4554549	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	807053	4554549	129297346	2627	5528											
VWF	7450	hgsc.bcm.edu	37	chr12	6094249	6094249	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcactggtctgcattctggCggaggcgggctacttcacac	7	9	13	12	2	3	0	1	0	2	0	3	1	3	1	0	5	3	3	0	5	1	3	rs62641242	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:6094249C>T	ENST00000261405.5	-	40	7192	c.6938G>A	c.(6937-6939)cGc>cAc	p.R2313H		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	2313	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.				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)	TGCATTCTGGCGGAGGCGGGC	0.597													C|||	5	0.000998403	0.0015	0.0014	5008	,	,		17767	0.0		0.002	False		,,,				2504	0.0				p.R2313H		Atlas-SNP	.											.	VWF	338	.	0			c.G6938A	GRCh37	CM070320	VWF	M	rs62641242	PASS	.	C	HIS/ARG	3,4403	6.2+/-15.9	0,3,2200	92	88	89	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6938	-2.6	0.1	12	dbSNP_129	89	1,8599	1.2+/-3.3	0,1,4299	yes	missense	VWF	NM_000552.3	29	0,4,6499	TT,TC,CC		0.0116,0.0681,0.0308	possibly-damaging	2313/2814	6094249	4,13002	2203	4300	6503	SO:0001583	missense	7450	exon40			TTCTGGCGGAGGC		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.6938G>A	12.37:g.6094249C>T	ENSP00000261405:p.Arg2313His	128	0	0		154	82	0.532468	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	3	0.0013736263736263737	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	6.785	0.513843	0.12944	6.81E-4	1.16E-4	ENSG00000110799	ENST00000261405	T	0.36699	1.24	5.33	-2.61	0.06171	von Willebrand factor, type C (3);	1.093970	0.07212	N	0.859422	T	0.22003	0.0530	N	0.14661	0.345	0.26288	N	0.978165	B	0.17268	0.021	B	0.12837	0.008	T	0.27739	-1.0065	10	0.38643	T	0.18	.	11.7285	0.51722	0.0:0.3397:0.0:0.6603	rs62641242	2313	P04275	VWF_HUMAN	H	2313	ENSP00000261405:R2313H	ENSP00000261405:R2313H	R	-	2	0	VWF	5964510	0.001000	0.12720	0.067000	0.19924	0.135000	0.20990	-0.426000	0.07008	-0.496000	0.06650	0.561000	0.74099	CGC	C|0.999;T|0.001	0.001	strong		0.597	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		T	6094249	C	T	6094249	3	4	22	1	0	0	0	0	1	0	0	0	17261	768	27	1	1555	1	VWF	12	6094249	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1539700	6094249	127757646	2628	5529											
VWF	7450	hgsc.bcm.edu	37	chr12	6103072	6103072	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caacgcagaccccgttggtcCgacagaggtgggcataagag	11	5	14	11	3	0	3	0	0	0	3	1	4	1	3	3	3	1	3	3	3	2	2	rs2229446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:6103072C>T	ENST00000261405.5	-	37	6808	c.6554G>A	c.(6553-6555)cGg>cAg	p.R2185Q		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	2185			R -> Q (in dbSNP:rs2229446).		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)	CCCGTTGGTCCGACAGAGGTG	0.552													C|||	342	0.0682907	0.2428	0.0245	5008	,	,		17441	0.0		0.002	False		,,,				2504	0.002				p.R2185Q		Atlas-SNP	.											VWF,rectum,carcinoma,-1,1	VWF	338	1	0			c.G6554A	GRCh37	CM070322	VWF	M	rs76342212	PASS	.	C	GLN/ARG	877,3529	337.0+/-304.7	89,699,1415	71	60	63		6554	5.3	1	12	dbSNP_131	63	13,8587	8.4+/-32.0	0,13,4287	yes	missense	VWF	NM_000552.3	43	89,712,5702	TT,TC,CC		0.1512,19.9047,6.843	probably-damaging	2185/2814	6103072	890,12116	2203	4300	6503	SO:0001583	missense	7450	exon37			TTGGTCCGACAGA		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.6554G>A	12.37:g.6103072C>T	ENSP00000261405:p.Arg2185Gln	72	0	0		48	23	0.479167	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	110	0.05036630036630037	102	0.2073170731707317	8	0.022099447513812154	0	0.0	0	0.0	C	22.3	4.275153	0.80580	0.199047	0.001512	ENSG00000110799	ENST00000261405	T	0.75367	-0.93	5.3	5.3	0.74995	Uncharacterised domain, cysteine-rich (2);	0.000000	0.40385	N	0.001115	T	0.00241	0.0007	L	0.43646	1.37	0.09310	P	1.0	D	0.89917	1.0	D	0.87578	0.998	T	0.01405	-1.1363	9	0.51188	T	0.08	.	17.9818	0.89144	0.0:1.0:0.0:0.0	rs2229446;rs11537643;rs52798162;rs11537643	2185	P04275	VWF_HUMAN	Q	2185	ENSP00000261405:R2185Q	ENSP00000261405:R2185Q	R	-	2	0	VWF	5973333	0.998000	0.40836	0.994000	0.49952	0.987000	0.75469	3.949000	0.56668	2.482000	0.83794	0.655000	0.94253	CGG	C|0.939;T|0.061	0.061	strong		0.552	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		T	6103072	C	T	6103072	3	4	22	1	0	0	0	0	1	0	0	0	17261	652	23	1	1951	1	VWF	12	6103072	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	8823	6103072	127748823	2629	5530											
VWF	7450	hgsc.bcm.edu	37	chr12	6103281	6103281	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctgccctggccgctgcacAgtccattcctgaacaagtgt	7	10	10	14	1	1	1	0	1	1	0	3	1	3	1	4	1	3	2	4	1	2	1	rs11537642	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:6103281A>T	ENST00000261405.5	-	37	6599	c.6345T>A	c.(6343-6345)acT>acA	p.T2115T		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	2115	VWFD 4. {ECO:0000255|PROSITE- ProRule:PRU00580}.				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)	GCCGCTGCACAGTCCATTCCT	0.557													A|||	277	0.0553115	0.1982	0.0202	5008	,	,		20224	0.0		0.001	False		,,,				2504	0.0				p.T2115T		Atlas-SNP	.											.	VWF	338	.	0			c.T6345A						PASS	.	A		660,3746	280.2+/-275.2	55,550,1598	94	79	84		6345	-10.3	0	12	dbSNP_120	84	4,8596	2.2+/-6.3	0,4,4296	no	coding-synonymous	VWF	NM_000552.3		55,554,5894	TT,TA,AA		0.0465,14.9796,5.1053		2115/2814	6103281	664,12342	2203	4300	6503	SO:0001819	synonymous_variant	7450	exon37			CTGCACAGTCCAT		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.6345T>A	12.37:g.6103281A>T		71	0	0		88	36	0.409091	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																			A|0.955;T|0.045	0.045	strong		0.557	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		T	6103281	A	T	6103281	2	4	22	1	0	0	0	0	0	0	0	1	17261	175	7	5		5	VWF	12	6103281	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	209	6103281	127748614	2630	5531											
VWF	7450	hgsc.bcm.edu	37	chr12	6138575	6138575	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agaccacggagagggctttgCccagcagcagaatgatgtac	12	6	13	10	1	0	4	0	1	0	3	0	5	0	4	2	2	4	4	2	2	2	2	rs141087261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:6138575C>T	ENST00000261405.5	-	22	3154	c.2900G>A	c.(2899-2901)gGc>gAc	p.G967D		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	967	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				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)	GAGGGCTTTGCCCAGCAGCAG	0.547													C|||	47	0.00938498	0.0325	0.0058	5008	,	,		20111	0.0		0.0	False		,,,				2504	0.0				p.G967D		Atlas-SNP	.											.	VWF	338	.	0			c.G2900A						PASS	.	C	ASP/GLY	109,4297	84.8+/-123.5	2,105,2096	140	125	130		2900	3.7	0.9	12	dbSNP_134	130	0,8600		0,0,4300	yes	missense	VWF	NM_000552.3	94	2,105,6396	TT,TC,CC		0.0,2.4739,0.8381	benign	967/2814	6138575	109,12897	2203	4300	6503	SO:0001583	missense	7450	exon22			GCTTTGCCCAGCA		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.2900G>A	12.37:g.6138575C>T	ENSP00000261405:p.Gly967Asp	90	0	0		131	74	0.564885	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	18	0.008241758241758242	16	0.032520325203252036	2	0.0055248618784530384	0	0.0	0	0.0	C	18.66	3.671977	0.67928	0.024739	0.0	ENSG00000110799	ENST00000261405	T	0.61040	0.14	4.58	3.69	0.42338	von Willebrand factor, type D domain (3);	0.382429	0.19030	N	0.124571	T	0.38081	0.1027	L	0.36672	1.1	0.80722	D	1	D	0.52996	0.957	P	0.61800	0.894	T	0.50759	-0.8790	10	0.42905	T	0.14	.	11.8305	0.52293	0.0:0.9149:0.0:0.0851	.	967	P04275	VWF_HUMAN	D	967	ENSP00000261405:G967D	ENSP00000261405:G967D	G	-	2	0	VWF	6008836	1.000000	0.71417	0.913000	0.36048	0.642000	0.38348	5.586000	0.67503	1.152000	0.42452	0.484000	0.47621	GGC	C|0.992;T|0.008	0.008	strong		0.547	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		T	6138575	C	T	6138575	3	4	22	1	0	0	0	0	1	0	0	0	17261	739	26	2	5665	2	VWF	12	6138575	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	35294	6138575	127713320	2631	5532											
VWF	7450	hgsc.bcm.edu	37	chr12	6182828	6182828	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcgctcctgacacatttcAttgatgtgcaggctctggca	8	12	9	12	1	2	2	1	2	1	0	4	2	3	2	1	2	1	4	1	2	0	2	rs1800387	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:6182828A>T	ENST00000261405.5	-	8	1208	c.954T>A	c.(952-954)aaT>aaA	p.N318K		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	318	TIL 1.		N -> K (in dbSNP:rs1800387).		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)	GACACATTTCATTGATGTGCA	0.537													A|||	779	0.155551	0.4705	0.0735	5008	,	,		20376	0.001		0.0328	False		,,,				2504	0.0736				p.N318K		Atlas-SNP	.											.	VWF	338	.	0			c.T954A						PASS	.	A	LYS/ASN	1814,2592	532.8+/-373.5	380,1054,769	121	101	108		954	-3.5	0	12	dbSNP_89	108	222,8378	92.8+/-154.8	1,220,4079	yes	missense	VWF	NM_000552.3	94	381,1274,4848	TT,TA,AA		2.5814,41.1711,15.6543	benign	318/2814	6182828	2036,10970	2203	4300	6503	SO:0001583	missense	7450	exon8			CATTTCATTGATG		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.954T>A	12.37:g.6182828A>T	ENSP00000261405:p.Asn318Lys	77	0	0		88	28	0.318182	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	283	0.1295787545787546	235	0.47764227642276424	30	0.08287292817679558	0	0.0	18	0.023746701846965697	A	13.32	2.203429	0.38905	0.411711	0.025814	ENSG00000110799	ENST00000261405	D	0.90069	-2.61	5.07	-3.54	0.04653	Protease inhibitor I8, cysteine-rich trypsin inhibitor-like (2);	1.028730	0.07777	N	0.952644	T	0.00012	0.0000	L	0.42632	1.34	0.09310	P	0.99999999821589	B;P	0.42161	0.005;0.772	B;B	0.40444	0.02;0.329	T	0.09357	-1.0678	9	0.32370	T	0.25	.	1.2239	0.01929	0.3764:0.2668:0.2306:0.1262	rs1800387;rs56444638;rs1800387	318;318	B4DNX0;P04275	.;VWF_HUMAN	K	318	ENSP00000261405:N318K	ENSP00000261405:N318K	N	-	3	2	VWF	6053089	0.916000	0.31088	0.012000	0.15200	0.881000	0.50899	0.118000	0.15605	-0.694000	0.05113	0.402000	0.26972	AAT	A|0.839;T|0.161	0.161	strong		0.537	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		T	6182828	A	T	6182828	3	4	22	1	0	0	0	0	1	0	0	0	17261	214	8	5	7667	5	VWF	12	6182828	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	44253	6182828	127669067	2632	5533											
ACSM4	341392	hgsc.bcm.edu	37	chr12	7477100	7477100	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcttttcctcttcaggtaccGtattgggccatttgaagtgg	6	16	10	9	1	3	1	1	1	2	0	4	1	4	1	3	3	1	2	3	3	3	7	rs61584783		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:7477100G>A	ENST00000399422.4	+	11	1490	c.1442G>A	c.(1441-1443)cGt>cAt	p.R481H		NM_001080454.1	NP_001073923.1	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member 4	481			R -> H (in dbSNP:rs61584783).		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						TTCAGGTACCGTATTGGGCCA	0.463													G|||	155	0.0309505	0.1127	0.0086	5008	,	,		-128	0.0		0.0	False		,,,				2504	0.0				p.R481H		Atlas-SNP	.											.	ACSM4	98	.	0			c.G1442A						PASS	.	G	HIS/ARG	395,3577		24,347,1615	139	128	132		1442	1.8	1	12	dbSNP_129	132	1,8369		0,1,4184	yes	missense	ACSM4	NM_001080454.1	29	24,348,5799	AA,AG,GG		0.0119,9.9446,3.2086	probably-damaging	481/581	7477100	396,11946	1986	4185	6171	SO:0001583	missense	341392	exon11			GGTACCGTATTGG		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.1442G>A	12.37:g.7477100G>A	ENSP00000382349:p.Arg481His	174	0	0		157	76	0.484076	NM_001080454	A8MTI6	Missense_Mutation	SNP	ENST00000399422.4	37	CCDS44825.1	57	0.0260989010989011	54	0.10975609756097561	3	0.008287292817679558	0	0.0	0	0.0	G	17.40	3.379356	0.61845	0.099446	1.19E-4	ENSG00000215009	ENST00000399422	T	0.15256	2.44	2.74	1.84	0.25277	AMP-dependent synthetase/ligase (1);	0.000000	0.38959	U	0.001517	T	0.01061	0.0035	M	0.92122	3.275	0.40110	D	0.97647	D	0.89917	1.0	D	0.79108	0.992	T	0.00431	-1.1743	10	0.87932	D	0	-4.6674	7.7673	0.28986	0.1334:0.0:0.8666:0.0	rs61584783	481	P0C7M7	ACSM4_HUMAN	H	481	ENSP00000382349:R481H	ENSP00000382349:R481H	R	+	2	0	ACSM4	7368367	1.000000	0.71417	0.984000	0.44739	0.981000	0.71138	6.064000	0.71169	0.721000	0.32231	0.557000	0.71058	CGT	G|0.979;A|0.021	0.021	strong		0.463	ACSM4-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337866.2	NM_001080454		A	7477100	G	A	7477100	3	1	22	1	0	0	0	0	1	0	0	0	186	1145	40	1	1484	1	ACSM4	12	7477100	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1294272	7477100	126374795	2633	5534											
CD163	9332	hgsc.bcm.edu	37	chr12	7636027	7636027	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggccccagcgtctggcaggAcaatcccacaaggaagactc	11	5	11	14	1	1	1	0	0	1	1	3	3	2	3	3	4	1	1	3	4	3	0	rs78817356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:7636027A>G	ENST00000359156.4	-	12	3226	c.3024T>C	c.(3022-3024)tgT>tgC	p.C1008C	CD163_ENST00000396620.3_Silent_p.C1041C|CD163_ENST00000541972.1_Silent_p.C996C|CD163_ENST00000432237.2_Silent_p.C1008C|CD163_ENST00000539632.1_5'UTR	NM_004244.5	NP_004235.4	Q86VB7	C163A_HUMAN	CD163 molecule	1008	SRCR 9. {ECO:0000255|PROSITE- ProRule:PRU00196}.				acute-phase response (GO:0006953)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(6)|pancreas(2)|prostate(1)|skin(5)|urinary_tract(4)	76					WF10(DB05389)	GTCTGGCAGGACAATCCCACA	0.507													A|||	144	0.028754	0.1014	0.013	5008	,	,		-128	0.0		0.001	False		,,,				2504	0.0				p.C1008C		Atlas-SNP	.											.	CD163	221	.	0			c.T3024C						PASS	.	A	,	305,4101	164.4+/-196.0	6,293,1904	131	112	118		3024,3024	0.5	1	12	dbSNP_131	118	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	CD163	NM_004244.5,NM_203416.3	,	6,294,6203	GG,GA,AA		0.0116,6.9224,2.3528	,	1008/1157,1008/1122	7636027	306,12700	2203	4300	6503	SO:0001819	synonymous_variant	9332	exon12			GGCAGGACAATCC	Z22968	CCDS8578.1, CCDS53742.1	12p13	2006-03-28	2006-03-28		ENSG00000177575	ENSG00000177575		"CD molecules"	1631	protein-coding gene	gene with protein product		605545	"CD163 antigen"			10403791, 8370408	Standard	NM_004244		Approved	M130, MM130	uc001qsz.3	Q86VB7	OTTHUMG00000168353	ENST00000359156.4:c.3024T>C	12.37:g.7636027A>G		131	0	0		123	58	0.471545	NM_203416	C9JIG2|Q07898|Q07899|Q07900|Q07901|Q2VLH7	Silent	SNP	ENST00000359156.4	37	CCDS8578.1	42	0.019230769230769232	35	0.07113821138211382	7	0.019337016574585635	0	0.0	0	0.0	A	10.17	1.275594	0.23307	0.069224	1.16E-4	ENSG00000177575	ENST00000537626	.	.	.	5.4	0.458	0.16670	.	.	.	.	.	T	0.08313	0.0207	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.04103	-1.0977	4	.	.	.	.	8.3663	0.32389	0.6729:0.0:0.3271:0.0	.	.	.	.	A	21	.	.	V	-	2	0	CD163	7527294	0.000000	0.05858	0.998000	0.56505	0.984000	0.73092	-0.124000	0.10595	0.121000	0.18284	-0.388000	0.06559	GTC	A|0.978;G|0.022	0.022	strong		0.507	CD163-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399396.2	NM_004244, NM_203416		G	7636027	A	G	7636027	2	3	22	1	0	0	0	0	0	0	0	1	2969	273	10	3		3	CD163	12	7636027	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	158927	7636027	126215868	2634	5535											
CLEC4C	170482	hgsc.bcm.edu	37	chr12	7890040	7890040	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catacctgttcttccctggtGttgatcaccaccagatcagc	8	12	7	14	0	3	2	2	1	1	1	4	2	4	2	4	1	2	2	4	1	1	4	rs77889141	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:7890040G>T	ENST00000542353.1	-	5	856	c.366C>A	c.(364-366)aaC>aaA	p.N122K	CLEC4C_ENST00000354629.5_Missense_Mutation_p.N91K|CLEC4C_ENST00000360345.3_Missense_Mutation_p.N122K|CLEC4C_ENST00000540085.1_Missense_Mutation_p.N91K	NM_130441.2	NP_569708.1	Q8WTT0	CLC4C_HUMAN	C-type lectin domain family 4, member C	122	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				innate immune response (GO:0045087)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				Kidney(36;0.0915)		CTTCCCTGGTGTTGATCACCA	0.408													G|||	88	0.0175719	0.0635	0.0043	5008	,	,		-128	0.0		0.001	False		,,,				2504	0.0				p.N122K		Atlas-SNP	.											.	CLEC4C	44	.	0			c.C366A						PASS	.	G	LYS/ASN,LYS/ASN	235,4171	137.7+/-173.5	10,215,1978	129	126	127		366,273	2.6	0.2	12	dbSNP_131	127	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	CLEC4C	NM_130441.2,NM_203503.1	94,94	10,218,6275	TT,TG,GG		0.0349,5.3336,1.8299	possibly-damaging,possibly-damaging	122/214,91/183	7890040	238,12768	2203	4300	6503	SO:0001583	missense	170482	exon5			CCTGGTGTTGATC	AF325460	CCDS8583.1, CCDS8584.1	12p13.2-p12.3	2008-02-05	2004-02-13	2005-02-11	ENSG00000198178	ENSG00000198178		"C-type lectin domain containing", "CD molecules"	13258	protein-coding gene	gene with protein product		606677	"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 7"	CLECSF11, CLECSF7		11031109, 11536172	Standard	NM_130441		Approved	HECL, DLEC, BDCA2, CD303	uc001qth.1	Q8WTT0	OTTHUMG00000168441	ENST00000542353.1:c.366C>A	12.37:g.7890040G>T	ENSP00000440428:p.Asn122Lys	67	0	0		54	27	0.5	NM_130441	D3DUU3|Q3T1C3|Q6UXS8|Q8WXX8	Missense_Mutation	SNP	ENST00000542353.1	37	CCDS8583.1	21	0.009615384615384616	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	0	0.0	G	10.90	1.482342	0.26598	0.053336	3.49E-4	ENSG00000198178	ENST00000542353;ENST00000354629;ENST00000540085;ENST00000360345;ENST00000537530;ENST00000543765	T;T;T;T;T;T	0.17528	2.27;2.27;2.27;2.27;2.27;2.27	2.62	2.62	0.31277	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	.	.	.	.	T	0.03390	0.0098	L	0.46614	1.455	0.09310	N	1	P;P	0.51057	0.557;0.941	B;P	0.51615	0.169;0.675	T	0.04885	-1.0920	9	0.27082	T	0.32	.	8.9424	0.35738	0.0:0.0:1.0:0.0	.	91;122	Q8WTT0-2;Q8WTT0	.;CLC4C_HUMAN	K	122;91;91;122;44;82	ENSP00000440428:N122K;ENSP00000346648:N91K;ENSP00000445338:N91K;ENSP00000353500:N122K;ENSP00000438649:N44K;ENSP00000442457:N82K	ENSP00000346648:N91K	N	-	3	2	CLEC4C	7781307	0.976000	0.34144	0.165000	0.22776	0.054000	0.15201	1.943000	0.40253	1.784000	0.52394	0.603000	0.83216	AAC	G|0.981;T|0.019	0.019	strong		0.408	CLEC4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399750.1	NM_203503		T	7890040	G	T	7890040	3	4	22	1	0	0	0	0	1	0	0	0	3515	1368	48	4	287	4	CLEC4C	12	7890040	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	254013	7890040	125961855	2635	5536											
CLEC4A	50856	hgsc.bcm.edu	37	chr12	8290881	8290881	+	Nonstop_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatgatgaagatccacttaTgaactgaacattctccatga	15	11	7	8	0	1	7	0	5	1	2	3	7	2	7	2	0	2	0	2	0	4	2	rs74810750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:8290881T>C	ENST00000229332.5	+	6	959	c.712T>C	c.(712-714)Tga>Cga	p.*238R	CLEC4A_ENST00000360500.3_Nonstop_Mutation_p.*199R|CLEC4A_ENST00000352620.3_Nonstop_Mutation_p.*205R|CLEC4A_ENST00000345999.3_Nonstop_Mutation_p.*166R	NM_016184.3|NM_194447.2|NM_194450.2	NP_057268.1|NP_919429.2|NP_919432.1	Q9UMR7	CLC4A_HUMAN	C-type lectin domain family 4, member A	0					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(3)|large_intestine(2)|lung(4)|prostate(1)	11				Kidney(36;0.0915)		GATCCACTTATGAACTGAACA	0.393													t|||	32	0.00638978	0.0227	0.0029	5008	,	,		-128	0.0		0.0	False		,,,				2504	0.0				p.X238R		Atlas-SNP	.											.	CLEC4A	28	.	0			c.T712C						PASS	.	T	ARG/stop,ARG/stop,ARG/stop,ARG/stop	70,4336	64.1+/-101.4	1,68,2134	229	204	212		712,595,496,613	1.6	0.9	12	dbSNP_132	212	2,8598	2.2+/-6.3	0,2,4298	yes	stop-lost,stop-lost,stop-lost,stop-lost	CLEC4A	NM_016184.3,NM_194447.2,NM_194448.2,NM_194450.2	,,,	1,70,6432	CC,CT,TT		0.0233,1.5887,0.5536	,,,	238/238,199/199,166/166,205/205	8290881	72,12934	2203	4300	6503	SO:0001578	stop_lost	50856	exon6			CACTTATGAACTG	AJ133532	CCDS8590.1, CCDS8591.1, CCDS8592.1, CCDS41745.1	12p13	2005-02-09	2005-02-09	2005-02-09	ENSG00000111729	ENSG00000111729		"C-type lectin domain containing"	13257	protein-coding gene	gene with protein product		605306	"C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 6"	CLECSF6		10438934	Standard	NM_016184		Approved	DCIR, DDB27	uc001qtz.1	Q9UMR7	OTTHUMG00000168571	ENST00000229332.5:c.712T>C	12.37:g.8290881T>C	ENSP00000229332:p.*238Argext*6	127	0	0		162	72	0.444444	NM_016184	Q17R69|Q8WXW9|Q9H2Z9|Q9NS33|Q9UI34	Missense_Mutation	SNP	ENST00000229332.5	37	CCDS8590.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	T	7.275	0.607941	0.14002	0.015887	2.33E-4	ENSG00000111729	ENST00000229332;ENST00000345999;ENST00000352620;ENST00000360500	.	.	.	4.12	1.65	0.23941	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.3429	0.32254	0.0:0.0:0.3962:0.6038	.	.	.	.	R	238;166;205;199	.	.	X	+	1	0	CLEC4A	8182148	0.320000	0.24616	0.897000	0.35233	0.152000	0.21847	0.699000	0.25586	0.346000	0.23899	0.477000	0.44152	TGA	T|0.994;C|0.006	0.006	strong		0.393	CLEC4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400257.1	NM_194450		C	8290881	T	C	8290881	4	2	22	1	0	0	0	0	0	0	0	0	3514	1477	51	3	734	3	CLEC4A	12	8290881	Nonstop_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	400841	8290881	125561014	2636	5537											
RIMKLB	57494	hgsc.bcm.edu	37	chr12	8926015	8926015	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atgtgtgtggcattgatctgCtgatgaaagatgacggctcc	9	12	13	7	1	1	5	0	4	1	1	2	5	2	5	1	2	1	3	1	2	1	1	rs386760122|rs2302488	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:8926015C>T	ENST00000538135.1	+	6	1621	c.796C>T	c.(796-798)Ctg>Ttg	p.L266L	RIMKLB_ENST00000299673.5_3'UTR|RIMKLB_ENST00000535829.1_Silent_p.L266L|A2ML1-AS1_ENST00000537288.1_RNA|RIMKLB_ENST00000357529.3_Silent_p.L266L			Q9ULI2	RIMKB_HUMAN	ribosomal modification protein rimK-like family member B	266	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.				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						CATTGATCTGCTGATGAAAGA	0.473													T|||	384	0.0766773	0.2602	0.0259	5008	,	,		-128	0.0159		0.003	False		,,,				2504	0.0031				p.L266L		Atlas-SNP	.											.	RIMKLB	47	.	0			c.C796T						PASS	.	T		905,3245		101,703,1271	189	193	191		796	0.6	0.9	12	dbSNP_100	191	24,8424		0,24,4200	yes	coding-synonymous	RIMKLB	NM_020734.2		101,727,5471	TT,TC,CC		0.2841,21.8072,7.3742		266/387	8926015	929,11669	2075	4224	6299	SO:0001819	synonymous_variant	57494	exon7			GATCTGCTGATGA	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.796C>T	12.37:g.8926015C>T		263	0	0		267	116	0.434457	NM_020734	B7Z834|D3DUV2|Q8N4P4|Q8WTW6	Silent	SNP	ENST00000538135.1	37	CCDS41748.1																																																																																			C|0.911;T|0.089	0.089	strong		0.473	RIMKLB-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398874.1	NM_020734		T	8926015	C	T	8926015	2	4	22	1	0	0	0	0	0	0	0	1	13381	796	28	2		2	RIMKLB	12	8926015	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	635134	8926015	124925880	2637	5538											
A2M	2	hgsc.bcm.edu	37	chr12	9251209	9251209	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccaggaactcaccgaggaCgccgagagctcagcatcagg	11	4	13	13	3	3	1	3	0	0	1	3	5	3	3	3	3	4	2	3	3	1	0	rs185750870		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:9251209C>T	ENST00000318602.7	-	15	2152	c.1845G>A	c.(1843-1845)gcG>gcA	p.A615A		NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	615					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)	TCACCGAGGACGCCGAGAGCT	0.572													C|||	18	0.00359425	0.0129	0.0014	5008	,	,		-128	0.0		0.0	False		,,,				2504	0.0				p.A615A		Atlas-SNP	.											.	A2M	180	.	0			c.G1845A						PASS	.	C		41,4365		0,41,2162	28	28	28		1845	-11.1	0	12		28	1,8597		0,1,4298	no	coding-synonymous	A2M	NM_000014.4		0,42,6460	TT,TC,CC		0.0116,0.9305,0.323		615/1475	9251209	42,12962	2203	4299	6502	SO:0001819	synonymous_variant	2	exon15			CGAGGACGCCGAG	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.1845G>A	12.37:g.9251209C>T		59	0	0		77	42	0.545455	NM_000014	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Silent	SNP	ENST00000318602.7	37	CCDS44827.1																																																																																			C|0.998;T|0.002	0.002	strong		0.572	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014		T	9251209	C	T	9251209	2	4	22	1	0	0	0	0	0	0	0	1	4	523	19	1		1	A2M	12	9251209	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	325194	9251209	124600686	2638	5539											
CLEC12B	387837	hgsc.bcm.edu	37	chr12	10163381	10163381	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctgaagaagtgacctacgCgacactcacatttcaggatt	12	10	9	10	2	3	3	2	2	1	1	3	5	3	4	1	1	1	0	1	1	3	3	rs11833101|rs386760228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:10163381C>T	ENST00000338896.5	+	1	151	c.23C>T	c.(22-24)gCg>gTg	p.A8V	CLEC1B_ENST00000428126.2_Intron|CLEC12B_ENST00000396502.1_Missense_Mutation_p.A8V	NM_001129998.1	NP_001123470.1	Q2HXU8	CL12B_HUMAN	C-type lectin domain family 12, member B	8						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(2)|large_intestine(2)|lung(5)	9						GTGACCTACGCGACACTCACA	0.398													C|||	160	0.0319489	0.1135	0.0144	5008	,	,		20629	0.0		0.0	False		,,,				2504	0.0				p.A8V		Atlas-SNP	.											.	CLEC12B	25	.	0			c.C23T						PASS	.	C	VAL/ALA,VAL/ALA	334,4072	170.1+/-200.6	12,310,1881	61	58	59		23,23	4	0.3	12	dbSNP_120	59	0,8600		0,0,4300	yes	missense,missense	CLEC12B	NM_001129998.1,NM_205852.2	64,64	12,310,6181	TT,TC,CC		0.0,7.5806,2.568	possibly-damaging,possibly-damaging	8/277,8/233	10163381	334,12672	2203	4300	6503	SO:0001583	missense	387837	exon1			CCTACGCGACACT	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.23C>T	12.37:g.10163381C>T	ENSP00000344563:p.Ala8Val	67	0	0		77	28	0.363636	NM_001129998	Q6UWF2|Q6ZRG0	Missense_Mutation	SNP	ENST00000338896.5	37	CCDS44830.1	60	0.027472527472527472	54	0.10975609756097561	6	0.016574585635359115	0	0.0	0	0.0	C	12.83	2.054910	0.36277	0.075806	0.0	ENSG00000256660	ENST00000396502;ENST00000338896	T;T	0.01629	4.72;5.01	4.88	4.0	0.46444	.	0.368895	0.22840	N	0.054991	T	0.00073	0.0002	M	0.69823	2.125	0.18873	N	0.999986	B;P;P	0.44690	0.206;0.454;0.841	B;B;B	0.33690	0.022;0.049;0.168	T	0.50841	-0.8780	10	0.62326	D	0.03	.	9.8308	0.40941	0.0:0.9025:0.0:0.0975	rs11833101;rs56980128	8;8;8	Q2HXU8;Q2HXU8-2;F5H4H7	CL12B_HUMAN;.;.	V	8	ENSP00000379759:A8V;ENSP00000344563:A8V	ENSP00000344563:A8V	A	+	2	0	CLEC12B	10054648	0.000000	0.05858	0.322000	0.25334	0.601000	0.36947	0.634000	0.24614	1.390000	0.46547	0.561000	0.74099	GCG	C|0.976;T|0.024	0.024	strong		0.398	CLEC12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399554.2	NM_205852		T	10163381	C	T	10163381	3	4	22	1	0	0	0	0	1	0	0	0	3500	768	27	1	25	1	CLEC12B	12	10163381	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	912172	10163381	123688514	2639	5540											
TAS2R30	259293	hgsc.bcm.edu	37	chr12	11286688	11286688	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaaaccaactctggagacCgccagagcagtgagaatttg	14	6	11	10	1	1	3	0	1	1	3	1	5	1	3	3	1	4	2	3	1	3	1	rs375822837		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:11286688C>T	ENST00000539585.1	-	1	555	c.156G>A	c.(154-156)gcG>gcA	p.A52A	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_001097643.1	NP_001091112.1	P59541	T2R30_HUMAN	taste receptor, type 2, member 30	52					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)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	13						CTCTGGAGACCGCCAGAGCAG	0.388																																					p.A52A		Atlas-SNP	.											.	TAS2R30	28	.	0			c.G156A						PASS	.	C		2,4110		0,2,2054	78	79	79		156	-5.4	0	12		79	0,8504		0,0,4252	no	coding-synonymous	TAS2R30	NM_001097643.1		0,2,6306	TT,TC,CC		0.0,0.0486,0.0159		52/320	11286688	2,12614	2056	4252	6308	SO:0001819	synonymous_variant	259293	exon1			GGAGACCGCCAGA	AX097746, AF494233	CCDS53750.1	12p13.2	2012-08-22				ENSG00000256188		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	19112	protein-coding gene	gene with protein product		613963	"taste receptor, type 2, member 47"	TAS2R47			Standard	NM_001097643		Approved	T2R30	uc009zhs.1	P59541		ENST00000539585.1:c.156G>A	12.37:g.11286688C>T		305	1	0.00327869		357	187	0.52381	NM_001097643	Q645X7	Silent	SNP	ENST00000539585.1	37	CCDS53750.1																																																																																			.	.	weak		0.388	TAS2R30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400238.1	NM_001097643		T	11286688	C	T	11286688	2	4	22	1	0	0	0	0	0	0	0	1	15588	639	23	1		1	TAS2R30	12	11286688	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1123307	11286688	122565207	2640	5541											
DDX47	51202	hgsc.bcm.edu	37	chr12	12980305	12980305	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgaagcccaaaggtttgcccGaatggtatgcatctttcttt	9	14	9	9	1	2	1	0	1	2	0	2	2	2	1	2	2	3	3	2	2	4	4	rs373273540		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:12980305G>A	ENST00000358007.3	+	11	1254	c.1232G>A	c.(1231-1233)cGa>cAa	p.R411Q	DDX47_ENST00000352940.4_Missense_Mutation_p.R362Q	NM_016355.3	NP_057439.2	Q9H0S4	DDX47_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47	411					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)		AGGTTTGCCCGAATGGTATGC	0.423													G|||	1	0.000199681	0.0	0.0	5008	,	,		21240	0.001		0.0	False		,,,				2504	0.0				p.R411Q		Atlas-SNP	.											DDX47,colon,carcinoma,+1,1	DDX47	37	1	0			c.G1232A						PASS	.						218	216	217					12																	12980305		2203	4300	6503	SO:0001583	missense	51202	exon11			TTGCCCGAATGGT	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.1232G>A	12.37:g.12980305G>A	ENSP00000350698:p.Arg411Gln	118	0	0		116	73	0.62931	NM_016355	B3KXP4|G5E955|Q96GM0|Q96NV8|Q9UI98	Missense_Mutation	SNP	ENST00000358007.3	37	CCDS8655.1	.	.	.	.	.	.	.	.	.	.	G	13.60	2.284152	0.40394	.	.	ENSG00000213782	ENST00000352940;ENST00000358007	T;T	0.26957	2.5;1.7	5.75	3.89	0.44902	.	0.066087	0.64402	D	0.000015	T	0.17704	0.0425	L	0.28649	0.875	0.53688	D	0.999974	B;B	0.20887	0.036;0.049	B;B	0.16722	0.016;0.004	T	0.04203	-1.0969	10	0.13108	T	0.6	-5.9575	12.9654	0.58481	0.0:0.1243:0.7461:0.1296	.	362;411	G5E955;Q9H0S4	.;DDX47_HUMAN	Q	362;411	ENSP00000319578:R362Q;ENSP00000350698:R411Q	ENSP00000319578:R362Q	R	+	2	0	DDX47	12871572	1.000000	0.71417	0.983000	0.44433	0.988000	0.76386	7.657000	0.83745	0.746000	0.32786	0.655000	0.94253	CGA	.	.	weak		0.423	DDX47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400674.1	NM_016355		A	12980305	G	A	12980305	3	1	22	1	0	0	0	0	1	0	0	0	4367	1058	37	1	1274	1	DDX47	12	12980305	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1693617	12980305	120871590	2641	5542											
GPRC5D	55507	hgsc.bcm.edu	37	chr12	13103196	13103196	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atgaggaagagaaatgctaaGagtagcagaattgtgaccac	17	7	12	5	0	0	5	0	2	0	3	0	7	0	6	1	1	2	3	1	1	5	3	rs150759739	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:13103196G>A	ENST00000228887.1	-	1	122	c.123C>T	c.(121-123)ctC>ctT	p.L41L	RP11-392P7.6_ENST00000538231.1_RNA|RP11-392P7.6_ENST00000543515.2_RNA|RP11-392P7.6_ENST00000536029.1_RNA|RP11-392P7.6_ENST00000540198.1_RNA|GPRC5D_ENST00000396333.3_Silent_p.L41L|RP11-392P7.6_ENST00000545914.1_RNA|RP11-392P7.6_ENST00000394742.3_RNA|RP11-392P7.6_ENST00000542078.1_RNA	NM_018654.1	NP_061124.1	Q9NZD1	GPC5D_HUMAN	G protein-coupled receptor, class C, group 5, member D	41						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			kidney(2)|large_intestine(2)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.15)		GAAATGCTAAGAGTAGCAGAA	0.547													G|||	16	0.00319489	0.0106	0.0014	5008	,	,		20686	0.001		0.0	False		,,,				2504	0.0				p.L41L		Atlas-SNP	.											.	GPRC5D	23	.	0			c.C123T						PASS	.	G		39,4367	44.6+/-78.6	0,39,2164	98	91	94		123	5.2	1	12	dbSNP_134	94	0,8600		0,0,4300	no	coding-synonymous	GPRC5D	NM_018654.1		0,39,6464	AA,AG,GG		0.0,0.8852,0.2999		41/346	13103196	39,12967	2203	4300	6503	SO:0001819	synonymous_variant	55507	exon1			TGCTAAGAGTAGC	AF209923	CCDS8658.1	12p13.3	2014-01-30	2014-01-30		ENSG00000111291	ENSG00000111291		"GPCR / Class C : Orphans"	13310	protein-coding gene	gene with protein product		607437	"G protein-coupled receptor, family C, group 5, member D"				Standard	XM_005253421		Approved		uc010shp.2	Q9NZD1	OTTHUMG00000168711	ENST00000228887.1:c.123C>T	12.37:g.13103196G>A		74	0	0		70	48	0.685714	NM_018654	Q3KNV3|Q7Z5J9|Q8TDS6	Silent	SNP	ENST00000228887.1	37	CCDS8658.1																																																																																			G|0.997;A|0.003	0.003	strong		0.547	GPRC5D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400687.1			A	13103196	G	A	13103196	2	1	22	1	0	0	0	0	0	0	0	1	6736	929	33	2		2	GPRC5D	12	13103196	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	122891	13103196	120748699	2642	5543											
ERP27	121506	hgsc.bcm.edu	37	chr12	15070169	15070169	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcatgttctcttcatactcTggggaggccttgttcattat	6	17	9	9	0	4	0	2	0	2	0	5	1	4	1	1	3	2	3	1	3	2	6	rs35203261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:15070169T>A	ENST00000266397.2	-	5	1092	c.519A>T	c.(517-519)ccA>ccT	p.P173P	ERP27_ENST00000544881.1_5'UTR|ERP27_ENST00000540097.1_Silent_p.P72P	NM_152321.2	NP_689534.1	Q96DN0	ERP27_HUMAN	endoplasmic reticulum protein 27	173						endoplasmic reticulum (GO:0005783)				breast(2)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(3)|prostate(2)|skin(1)	19						CTTCATACTCTGGGGAGGCCT	0.458													T|||	123	0.0245607	0.09	0.0043	5008	,	,		20881	0.0		0.0	False		,,,				2504	0.001				p.P173P		Atlas-SNP	.											.	ERP27	37	.	0			c.A519T						PASS	.	T		319,4087	170.5+/-200.9	8,303,1892	216	184	195		519	0.8	1	12	dbSNP_126	195	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	ERP27	NM_152321.2		8,307,6188	AA,AT,TT		0.0465,7.2401,2.4835		173/274	15070169	323,12683	2203	4300	6503	SO:0001819	synonymous_variant	121506	exon5			ATACTCTGGGGAG	AK056677	CCDS8670.1, CCDS73450.1	12p12.3	2011-10-19	2009-02-23	2007-03-26	ENSG00000139055	ENSG00000139055		"Protein disulfide isomerases"	26495	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 8"	610642	"chromosome 12 open reading frame 46", "endoplasmic reticulum protein 27 kDa"	C12orf46		12975309, 16940051	Standard	XM_005253303		Approved	FLJ32115, ERp27, PDIA8	uc001rco.3	Q96DN0	OTTHUMG00000168741	ENST00000266397.2:c.519A>T	12.37:g.15070169T>A		229	0	0		229	102	0.445415	NM_152321		Silent	SNP	ENST00000266397.2	37	CCDS8670.1																																																																																			T|0.980;A|0.020	0.020	strong		0.458	ERP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400868.1	NM_152321		A	15070169	T	A	15070169	2	1	22	1	0	0	0	0	0	0	0	1	5243	1567	55	5		5	ERP27	12	15070169	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1966973	15070169	118781726	2643	5544											
PDE6H	5149	hgsc.bcm.edu	37	chr12	15134337	15134337	+	Frame_Shift_Del	DEL	T	T	-																															tcttccatctcttgcagataTcacagtgatttgtccatggg																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:15134337delT	ENST00000266395.2	+	4	285	c.179delT	c.(178-180)atcfs	p.I60fs		NM_006205.2	NP_006196.1	Q13956	CNCG_HUMAN	phosphodiesterase 6H, cGMP-specific, cone, gamma	60					activation of MAPK activity (GO:0000187)|negative regulation of catalytic activity (GO:0043086)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|response to stimulus (GO:0050896)|visual perception (GO:0007601)		3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|cGMP binding (GO:0030553)|enzyme inhibitor activity (GO:0004857)			endometrium(1)|lung(6)|ovary(1)|skin(2)	10					Sildenafil(DB00203)|Vardenafil(DB00862)	CTTGCAGATATCACAGTGATT	0.498																																					p.I60fs		Pindel,Atlas-Indel	.											.	PDE6H	13	.	0			c.178delA						PASS	.						180	154	163					12																	15134337		2203	4300	6503	SO:0001589	frameshift_variant	5149	exon4			.		CCDS8672.1	12p13	2008-03-18					3.1.4.17	"Phosphodiesterases"	8790	protein-coding gene	gene with protein product		601190				8786098	Standard	NM_006205		Approved		uc001rcr.3	Q13956		ENST00000266395.2:c.179delT	12.37:g.15134337delT	ENSP00000266395:p.Ile60fs	110	0	.		106	33	0.311	NM_006205	Q52LY7	Frame_Shift_Del	DEL	ENST00000266395.2	37	CCDS8672.1																																																																																			.	.	none		0.498	PDE6H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400880.1			-	15134337	T	-	15134337	7	5	22	1	0	1	0	1	0	0	0	0	11659	1435	50	0	189	0	PDE6H	12	15134337	Frame_Shift_Del	DEL	T	TCGA-G8-6324-01A-11D-2210-10	64168	15134337	118717558	2644	5545											
EPS8	2059	hgsc.bcm.edu	37	chr12	15776095	15776095	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggttgacaagtcatacctcCaatgcagctttttgtacagt	11	13	8	9	0	1	1	1	1	0	0	2	1	2	1	2	1	4	4	2	1	4	5	rs1126786	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:15776095C>T	ENST00000281172.5	-	20	2788	c.2352G>A	c.(2350-2352)ttG>ttA	p.L784L	EPS8_ENST00000543523.1_Silent_p.L784L|EPS8_ENST00000543612.1_Silent_p.L784L|EPS8_ENST00000542903.1_Silent_p.L524L|EPS8_ENST00000540613.1_Silent_p.L524L	NM_004447.5	NP_004438.3	Q12929	EPS8_HUMAN	epidermal growth factor receptor pathway substrate 8	784	Effector region. {ECO:0000250}.|Helix bundle 4. {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)		GTCATACCTCCAATGCAGCTT	0.418													T|||	882	0.176118	0.5507	0.0562	5008	,	,		17316	0.0536		0.0209	False		,,,				2504	0.0409				p.L784L		Atlas-SNP	.											.	EPS8	70	.	0			c.G2352A						PASS	.	T		2128,2278	599.1+/-389.2	529,1070,604	131	135	133		2352	-0.9	0.7	12	dbSNP_86	133	204,8396	810.5+/-407.1	2,200,4098	no	coding-synonymous	EPS8	NM_004447.5		531,1270,4702	TT,TC,CC		2.3721,48.2978,17.9302		784/823	15776095	2332,10674	2203	4300	6503	SO:0001819	synonymous_variant	2059	exon20			TACCTCCAATGCA	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.2352G>A	12.37:g.15776095C>T		148	0	0		158	76	0.481013	NM_004447	A6NMC3|A8K6W2|A8KA66|B4DX66|Q8N6J0	Silent	SNP	ENST00000281172.5	37	CCDS31753.1																																																																																			T|0.130;G|0.153;C|0.674;A|0.042	0.130	strong		0.418	EPS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401093.1			T	15776095	C	T	15776095	2	4	22	1	0	0	0	0	0	0	0	1	5196	593	21	2		2	EPS8	12	15776095	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	641758	15776095	118075800	2645	5546											
PIK3C2G	5288	hgsc.bcm.edu	37	chr12	18473933	18473933	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcagttttatctgaatcaacTtctagaatttatgcatattt	12	19	4	6	0	4	2	2	1	2	1	4	2	4	2	0	0	2	2	0	0	7	8	rs201637656		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:18473933T>G	ENST00000266497.5	+	6	1213	c.1175T>G	c.(1174-1176)cTt>cGt	p.L392R	PIK3C2G_ENST00000538779.1_Missense_Mutation_p.L392R|PIK3C2G_ENST00000535651.1_Missense_Mutation_p.L392R|PIK3C2G_ENST00000433979.1_Missense_Mutation_p.L392R|RERGL_ENST00000541632.1_5'Flank			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	392					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)				CTGAATCAACTTCTAGAATTT	0.303																																					p.L392R		Atlas-SNP	.											PIK3C2G_ENST00000433979,NS,carcinoma,+1,2	PIK3C2G	315	2	0			c.T1175G						PASS	.	T	ARG/LEU	3,3597		0,3,1797	50	49	49		1175	4.6	1	12		49	0,8118		0,0,4059	yes	missense	PIK3C2G	NM_004570.4	102	0,3,5856	GG,GT,TT		0.0,0.0833,0.0256	probably-damaging	392/1446	18473933	3,11715	1800	4059	5859	SO:0001583	missense	5288	exon7			ATCAACTTCTAGA	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.1175T>G	12.37:g.18473933T>G	ENSP00000266497:p.Leu392Arg	287	0	0		256	121	0.472656	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	37	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	T	16.78	3.216850	0.58452	8.33E-4	0.0	ENSG00000139144	ENST00000535651;ENST00000433979;ENST00000266497;ENST00000538779	T;T;T;T	0.65916	1.12;-0.18;-0.18;-0.08	4.57	4.57	0.56435	.	0.000000	0.52532	D	0.000071	T	0.72787	0.3504	M	0.63843	1.955	0.42403	D	0.992574	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.71184	0.957;0.972;0.938	T	0.72516	-0.4269	10	0.40728	T	0.16	-22.2094	10.628	0.45519	0.0:0.0:0.0:1.0	.	391;392;392	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	R	392	ENSP00000443850:L392R;ENSP00000404845:L392R;ENSP00000266497:L392R;ENSP00000445381:L392R	ENSP00000266497:L392R	L	+	2	0	PIK3C2G	18365200	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.773000	0.55333	2.281000	0.76405	0.528000	0.53228	CTT	.	.	weak		0.303	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570		G	18473933	T	G	18473933	3	3	22	1	0	0	0	0	1	0	0	0	11920	1609	56	5	1197	5	PIK3C2G	12	18473933	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2697838	18473933	115377962	2646	5547											
PIK3C2G	5288	hgsc.bcm.edu	37	chr12	18499629	18499629	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atccatctaccagctaatcaAtgtctactgtaacagctttt	12	14	4	11	0	3	0	1	0	2	0	4	0	4	0	2	0	5	3	2	0	5	6	rs77656456	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:18499629A>T	ENST00000266497.5	+	10	1522	c.1484A>T	c.(1483-1485)aAt>aTt	p.N495I	PIK3C2G_ENST00000538779.1_Missense_Mutation_p.N495I|PIK3C2G_ENST00000535651.1_Missense_Mutation_p.N495I|PIK3C2G_ENST00000433979.1_Missense_Mutation_p.N495I			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	495	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)				CAGCTAATCAATGTCTACTGT	0.418													A|||	9	0.00179712	0.0061	0.0014	5008	,	,		17734	0.0		0.0	False		,,,				2504	0.0				p.N495I		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.A1484T						PASS	.	A	ILE/ASN	17,3835		0,17,1909	183	183	183		1484	1.6	0	12	dbSNP_131	183	0,8256		0,0,4128	yes	missense	PIK3C2G	NM_004570.4	149	0,17,6037	TT,TA,AA		0.0,0.4413,0.1404	benign	495/1446	18499629	17,12091	1926	4128	6054	SO:0001583	missense	5288	exon11			TAATCAATGTCTA	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.1484A>T	12.37:g.18499629A>T	ENSP00000266497:p.Asn495Ile	119	0	0		149	73	0.489933	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	37	CCDS44839.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	A	10.11	1.260049	0.23051	0.004413	0.0	ENSG00000139144	ENST00000535651;ENST00000433979;ENST00000266497;ENST00000538779	T;T;T;T	0.60797	1.49;0.17;0.17;0.16	3.98	1.61	0.23674	Phosphoinositide 3-kinase, C2 (1);	1.592470	0.03319	N	0.191731	T	0.30727	0.0774	N	0.08118	0	0.09310	N	1	B;B;B	0.30281	0.04;0.066;0.275	B;B;B	0.28232	0.033;0.073;0.087	T	0.35871	-0.9771	10	0.66056	D	0.02	-1.4578	6.9084	0.24321	0.6849:0.0:0.3151:0.0	.	494;495;495	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	I	495	ENSP00000443850:N495I;ENSP00000404845:N495I;ENSP00000266497:N495I;ENSP00000445381:N495I	ENSP00000266497:N495I	N	+	2	0	PIK3C2G	18390896	0.000000	0.05858	0.019000	0.16419	0.908000	0.53690	0.199000	0.17237	0.344000	0.23847	0.454000	0.30748	AAT	A|0.998;T|0.002	0.002	strong		0.418	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570		T	18499629	A	T	18499629	3	4	22	1	0	0	0	0	1	0	0	0	11920	101	4	5	1522	5	PIK3C2G	12	18499629	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	25696	18499629	115352266	2647	5548											
PIK3C2G	5288	hgsc.bcm.edu	37	chr12	18715673	18715673	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctggagtgtttccctgttaaAttgaataacttgatccacac	11	14	7	9	0	0	2	0	2	0	0	2	3	2	3	2	1	1	2	2	1	4	5	rs11044184	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:18715673A>G	ENST00000266497.5	+	25	3542	c.3504A>G	c.(3502-3504)aaA>aaG	p.K1168K	PIK3C2G_ENST00000538779.1_Silent_p.K1209K|PIK3C2G_ENST00000433979.1_Silent_p.K1168K			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	1168	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				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)				TCCCTGTTAAATTGAATAACT	0.383													A|||	273	0.0545128	0.1989	0.0144	5008	,	,		17230	0.0		0.0	False		,,,				2504	0.0				p.K1168K		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.A3504G						PASS	.	A		672,3034		63,546,1244	68	64	65		3504	-0.7	1	12	dbSNP_120	65	5,8185		0,5,4090	no	coding-synonymous	PIK3C2G	NM_004570.4		63,551,5334	GG,GA,AA		0.0611,18.1328,5.691		1168/1446	18715673	677,11219	1853	4095	5948	SO:0001819	synonymous_variant	5288	exon26			TGTTAAATTGAAT	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.3504A>G	12.37:g.18715673A>G		181	0	0		192	85	0.442708	NM_004570	A1L3U0	Silent	SNP	ENST00000266497.5	37	CCDS44839.1																																																																																			A|0.941;G|0.059	0.059	strong		0.383	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570		G	18715673	A	G	18715673	2	3	22	1	0	0	0	0	0	0	0	1	11920	98	4	3		3	PIK3C2G	12	18715673	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	216044	18715673	115136222	2648	5549											
PLEKHA5	54477	hgsc.bcm.edu	37	chr12	19440471	19440471	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttacagtctgttagtccccAgagcctccaagggaaaacgg	11	9	10	11	1	1	1	0	0	1	1	3	2	3	2	4	2	3	1	4	2	5	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:19440471A>G	ENST00000299275.6	+	12	1832	c.1826A>G	c.(1825-1827)cAg>cGg	p.Q609R	PLEKHA5_ENST00000510738.2_3'UTR|PLEKHA5_ENST00000543806.1_Missense_Mutation_p.Q501R|PLEKHA5_ENST00000317589.4_Missense_Mutation_p.Q609R|PLEKHA5_ENST00000309364.4_Missense_Mutation_p.Q609R|PLEKHA5_ENST00000538714.1_Missense_Mutation_p.Q609R|PLEKHA5_ENST00000355397.3_Missense_Mutation_p.Q609R|PLEKHA5_ENST00000539256.1_Missense_Mutation_p.Q367R|PLEKHA5_ENST00000424268.1_Missense_Mutation_p.Q501R|PLEKHA5_ENST00000429027.2_Missense_Mutation_p.Q615R|PLEKHA5_ENST00000359180.3_Missense_Mutation_p.Q609R	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	609					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)					GTTAGTCCCCAGAGCCTCCAA	0.403																																					p.Q615R	Pancreas(196;329 2193 11246 14234 19524)	Atlas-SNP	.											.	PLEKHA5	198	.	0			c.A1844G						PASS	.						105	104	105					12																	19440471		2203	4300	6503	SO:0001583	missense	54477	exon13			GTCCCCAGAGCCT	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.1826A>G	12.37:g.19440471A>G	ENSP00000299275:p.Gln609Arg	175	0	0		160	83	0.51875	NM_001256470	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Missense_Mutation	SNP	ENST00000299275.6	37	CCDS8682.1	.	.	.	.	.	.	.	.	.	.	A	18.64	3.668063	0.67814	.	.	ENSG00000052126	ENST00000317589;ENST00000355397;ENST00000359180;ENST00000542828;ENST00000309364;ENST00000429027;ENST00000299275;ENST00000539256;ENST00000538714;ENST00000424268;ENST00000543806;ENST00000536974	T;T;T;T;T;T;T;T;T;T;T	0.35048	2.5;1.33;2.5;2.5;1.33;2.5;2.5;1.33;1.57;1.57;2.5	5.86	4.73	0.59995	.	0.115083	0.64402	D	0.000011	T	0.52757	0.1754	M	0.70595	2.14	0.39754	D	0.971935	D;D;D;P;D;D;D	0.76494	0.988;0.999;0.998;0.584;0.995;0.986;0.999	P;D;D;B;D;P;D	0.85130	0.883;0.997;0.993;0.445;0.978;0.835;0.997	T	0.52571	-0.8558	10	0.10111	T	0.7	-14.8584	11.3548	0.49609	0.9297:0.0:0.0703:0.0	.	609;501;501;615;615;609;609	Q9HAU0-4;F5H0I0;E7EME8;B4DHK5;E9PHQ3;Q9HAU0;Q9HAU0-2	.;.;.;.;.;PKHA5_HUMAN;.	R	609;609;609;616;609;615;609;367;609;501;501;501	ENSP00000325155:Q609R;ENSP00000347560:Q609R;ENSP00000352104:Q609R;ENSP00000311239:Q609R;ENSP00000404296:Q615R;ENSP00000299275:Q609R;ENSP00000440611:Q367R;ENSP00000439673:Q609R;ENSP00000400411:Q501R;ENSP00000439837:Q501R;ENSP00000440371:Q501R	ENSP00000299275:Q609R	Q	+	2	0	PLEKHA5	19331738	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.067000	0.71193	2.241000	0.73720	0.482000	0.46254	CAG	.	.	none		0.403	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012		G	19440471	A	G	19440471	3	3	22	1	0	0	0	0	1	0	0	0	12068	188	7	3	1872	3	PLEKHA5	12	19440471	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	724798	19440471	114411424	2649	5550											
PDE3A	5139	hgsc.bcm.edu	37	chr12	20522487	20522487	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggtcggctgtgacctggAgcagtgtaaggaggcggcgg	7	6	21	7	3	0	1	0	1	0	0	1	4	0	4	1	8	1	3	1	8	1	1	rs372953537	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:20522487A>G	ENST00000359062.3	+	1	309	c.269A>G	c.(268-270)gAg>gGg	p.E90G	RP11-284H19.1_ENST00000535755.1_RNA	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	90					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)	TGTGACCTGGAGCAGTGTAAG	0.716													A|||	5	0.000998403	0.0038	0.0	5008	,	,		11878	0.0		0.0	False		,,,				2504	0.0				p.E90G		Atlas-SNP	.											.	PDE3A	184	.	0			c.A269G						PASS	.	A	GLY/GLU	6,4166		0,6,2080	5	5	5		269	0	0.5	12		5	0,8264		0,0,4132	no	missense	PDE3A	NM_000921.4	98	0,6,6212	GG,GA,AA		0.0,0.1438,0.0482	possibly-damaging	90/1142	20522487	6,12430	2086	4132	6218	SO:0001583	missense	5139	exon1			ACCTGGAGCAGTG		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.269A>G	12.37:g.20522487A>G	ENSP00000351957:p.Glu90Gly	68	0	0		74	34	0.459459	NM_000921	O60865|Q13348|Q17RD1	Missense_Mutation	SNP	ENST00000359062.3	37	CCDS31754.1	.	.	.	.	.	.	.	.	.	.	A	16.65	3.182736	0.57800	0.001438	0.0	ENSG00000172572	ENST00000359062	T	0.64260	-0.09	5.03	-0.0284	0.13922	.	4.081800	0.00633	N	0.000487	T	0.46639	0.1403	N	0.19112	0.55	0.25845	N	0.984007	B	0.02656	0.0	B	0.01281	0.0	T	0.35871	-0.9771	10	0.59425	D	0.04	.	3.9386	0.09316	0.5223:0.1842:0.2935:0.0	.	90	Q14432	PDE3A_HUMAN	G	90	ENSP00000351957:E90G	ENSP00000351957:E90G	E	+	2	0	PDE3A	20413754	0.929000	0.31497	0.519000	0.27824	0.703000	0.40648	0.632000	0.24583	-0.019000	0.14055	0.449000	0.29647	GAG	.	.	weak		0.716	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2			G	20522487	A	G	20522487	3	3	22	1	0	0	0	0	1	0	0	0	11646	304	11	3	271	3	PDE3A	12	20522487	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1082016	20522487	113329408	2650	5551											
SLCO1B1	10599	hgsc.bcm.edu	37	chr12	21358933	21358933	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	catctcaccctgtctagcagGttgcaaatcttcaagtggca	10	11	8	12	0	4	0	2	0	3	0	5	0	4	0	1	2	2	4	1	2	3	3	rs59502379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:21358933G>C	ENST00000256958.2	+	11	1559	c.1463G>C	c.(1462-1464)gGt>gCt	p.G488A		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	488	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.		G -> A (in dbSNP:rs59502379). {ECO:0000269|PubMed:11477075}.		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)	TGTCTAGCAGGTTGCAAATCT	0.363													G|||	56	0.0111821	0.0408	0.0029	5008	,	,		17184	0.0		0.0	False		,,,				2504	0.0				p.G488A		Atlas-SNP	.											.	SLCO1B1	151	.	0			c.G1463C	GRCh37	CM016147	SLCO1B1	M	rs59502379	PASS	.	G	ALA/GLY	155,4251	104.3+/-142.8	3,149,2051	127	125	126		1463	4.1	1	12	dbSNP_129	126	1,8597	1.2+/-3.3	0,1,4298	yes	missense	SLCO1B1	NM_006446.4	60	3,150,6349	CC,CG,GG		0.0116,3.5179,1.1996	probably-damaging	488/692	21358933	156,12848	2203	4299	6502	SO:0001583	missense	10599	exon11			TAGCAGGTTGCAA		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.1463G>C	12.37:g.21358933G>C	ENSP00000256958:p.Gly488Ala	156	0	0		150	55	0.366667	NM_006446	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Missense_Mutation	SNP	ENST00000256958.2	37	CCDS8685.1	22	0.010073260073260074	22	0.044715447154471545	0	0.0	0	0.0	0	0.0	G	14.57	2.574305	0.45902	0.035179	1.16E-4	ENSG00000134538	ENST00000256958	T	0.04862	3.54	4.06	4.06	0.47325	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	0.11067	0.0270	H	0.96805	3.885	0.48632	D	0.999686	D	0.89917	1.0	D	0.97110	1.0	T	0.44421	-0.9329	10	0.87932	D	0	.	13.1306	0.59380	0.0:0.0:1.0:0.0	rs59502379	488	Q9Y6L6	SO1B1_HUMAN	A	488	ENSP00000256958:G488A	ENSP00000256958:G488A	G	+	2	0	SLCO1B1	21250200	1.000000	0.71417	1.000000	0.80357	0.335000	0.28730	7.474000	0.81024	1.783000	0.52377	0.484000	0.47621	GGT	G|0.988;C|0.012	0.012	strong		0.363	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446		C	21358933	G	C	21358933	3	2	22	1	0	0	0	0	1	0	0	0	14738	1261	44	4	1501	4	SLCO1B1	12	21358933	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	836446	21358933	112492962	2651	5552											
RECQL	5965	hgsc.bcm.edu	37	chr12	21643223	21643223	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctcctttccagccattgttaCgttaatagtttcaagctgaa	10	15	6	10	1	1	1	1	1	0	0	3	1	3	1	3	0	3	4	3	0	5	6	rs1065751	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:21643223C>T	ENST00000444129.2	-	4	772	c.304G>A	c.(304-306)Gta>Ata	p.V102I	RECQL_ENST00000421138.2_Missense_Mutation_p.V102I	NM_002907.3|NM_032941.2	NP_002898.2|NP_116559.1	P46063	RECQ1_HUMAN	RecQ helicase-like	102	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.		V -> I (in dbSNP:rs1065751).		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						GCCATTGTTACGTTAATAGTT	0.368								Other identified genes with known or suspected DNA repair function					C|||	225	0.0449281	0.1634	0.013	5008	,	,		15171	0.0		0.0	False		,,,				2504	0.0				p.V102I		Atlas-SNP	.											.	RECQL	45	.	0			c.G304A						PASS	.	C	ILE/VAL,ILE/VAL	617,3789	266.5+/-267.3	44,529,1630	122	123	123		304,304	5.3	0.1	12	dbSNP_86	123	4,8596	2.2+/-6.3	0,4,4296	yes	missense,missense	RECQL	NM_002907.3,NM_032941.2	29,29	44,533,5926	TT,TC,CC		0.0465,14.0036,4.7747	benign,benign	102/650,102/650	21643223	621,12385	2203	4300	6503	SO:0001583	missense	5965	exon5			TTGTTACGTTAAT	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.304G>A	12.37:g.21643223C>T	ENSP00000416739:p.Val102Ile	128	0	0		115	60	0.521739	NM_032941	A8K6G2	Missense_Mutation	SNP	ENST00000444129.2	37	CCDS31756.1	85	0.03891941391941392	80	0.16260162601626016	5	0.013812154696132596	0	0.0	0	0.0	C	15.74	2.923245	0.52653	0.140036	4.65E-4	ENSG00000004700	ENST00000444129;ENST00000421138;ENST00000396093;ENST00000314748;ENST00000542432;ENST00000536240	T;T;T;T;T;T	0.75477	-0.94;-0.94;2.49;2.49;2.49;0.93	5.29	5.29	0.74685	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.529047	0.19411	N	0.114924	T	0.00552	0.0018	L	0.36672	1.1	0.31263	P	0.6926570000000001	B	0.16166	0.016	B	0.14023	0.01	T	0.23332	-1.0191	9	0.66056	D	0.02	-2.6848	19.2899	0.94095	0.0:1.0:0.0:0.0	rs1065751;rs1065751	102	P46063	RECQ1_HUMAN	I	102	ENSP00000416739:V102I;ENSP00000395449:V102I;ENSP00000379400:V102I;ENSP00000318727:V102I;ENSP00000445555:V102I;ENSP00000439069:V102I	ENSP00000318727:V102I	V	-	1	0	RECQL	21534490	0.985000	0.35326	0.113000	0.21522	0.868000	0.49771	4.862000	0.62976	2.615000	0.88500	0.650000	0.86243	GTA	T|0.045;G|0.039	0.045	strong		0.368	RECQL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402371.1	NM_002907		T	21643223	C	T	21643223	3	4	22	1	0	0	0	0	1	0	0	0	13216	536	19	1	1693	1	RECQL	12	21643223	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	284290	21643223	112208672	2652	5553											
GYS2	2998	hgsc.bcm.edu	37	chr12	21692210	21692210	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accgttggtggtgatgttagTtccacatggaatttatctgg	8	15	12	6	1	1	1	0	1	1	0	2	2	2	2	2	4	0	3	2	4	3	5	rs142883971	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:21692210T>C	ENST00000261195.2	-	15	2126	c.1872A>G	c.(1870-1872)gaA>gaG	p.E624E		NM_021957.3	NP_068776.2	P54840	GYS2_HUMAN	glycogen synthase 2 (liver)	624					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						GTGATGTTAGTTCCACATGGA	0.303													T|||	17	0.00339457	0.0121	0.0014	5008	,	,		16759	0.0		0.0	False		,,,				2504	0.0				p.E624E	Colon(149;9 1820 3690 10544 50424)	Atlas-SNP	.											GYS2,NS,carcinoma,-2,1	GYS2	110	1	0			c.A1872G						PASS	.	T		72,4334	63.5+/-100.7	0,72,2131	166	173	171		1872	-3.7	0	12	dbSNP_134	171	0,8600		0,0,4300	no	coding-synonymous	GYS2	NM_021957.3		0,72,6431	CC,CT,TT		0.0,1.6341,0.5536		624/704	21692210	72,12934	2203	4300	6503	SO:0001819	synonymous_variant	2998	exon15			TGTTAGTTCCACA		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.1872A>G	12.37:g.21692210T>C		88	0	0		91	46	0.505495	NM_021957	A0AVD8	Silent	SNP	ENST00000261195.2	37	CCDS8690.1																																																																																			T|0.995;C|0.005	0.005	strong		0.303	GYS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402396.1	NM_021957		C	21692210	T	C	21692210	2	2	22	1	0	0	0	0	0	0	0	1	6922	1722	60	3		3	GYS2	12	21692210	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	48987	21692210	112159685	2653	5554											
KIAA0528	9847	hgsc.bcm.edu	37	chr12	22680809	22680809	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atctgtaaaggttcatcttgTaagtcttcatcatccaccta	11	15	5	10	0	6	0	3	0	3	0	7	0	7	0	2	1	0	3	2	1	4	6	rs12322490	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:22680809T>C	ENST00000333957.4	-	4	450	c.195A>G	c.(193-195)ttA>ttG	p.L65L	C2CD5_ENST00000536386.1_Silent_p.L65L|C2CD5_ENST00000446597.1_Silent_p.L65L|C2CD5_ENST00000540703.1_5'Flank|C2CD5_ENST00000545552.1_Silent_p.L65L|C2CD5_ENST00000544930.1_5'UTR|C2CD5_ENST00000396028.2_Silent_p.L65L|C2CD5_ENST00000542676.1_Silent_p.L65L	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	65	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				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)										GTTCATCTTGTAAGTCTTCAT	0.303													T|||	229	0.0457268	0.1649	0.0159	5008	,	,		16020	0.0		0.0	False		,,,				2504	0.0				p.L65L		Atlas-SNP	.											.	.	.	.	0			c.A195G						PASS	.	T		560,3846	250.0+/-257.2	37,486,1680	142	130	134		195	0.2	1	12	dbSNP_120	134	7,8593	5.0+/-18.6	0,7,4293	yes	coding-synonymous	KIAA0528	NM_014802.1		37,493,5973	CC,CT,TT		0.0814,12.7099,4.3595		65/1001	22680809	567,12439	2203	4300	6503	SO:0001819	synonymous_variant	9847	exon4			ATCTTGTAAGTCT	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.195A>G	12.37:g.22680809T>C		119	0	0		135	93	0.688889	NM_014802	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Silent	SNP	ENST00000333957.4	37	CCDS31758.1																																																																																			T|0.950;C|0.050	0.050	strong		0.303	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802		C	22680809	T	C	22680809	2	2	22	1	0	0	0	0	0	0	0	1	8191	1635	57	3		3	KIAA0528	12	22680809	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	988599	22680809	111171086	2654	5555											
BCAT1	586	hgsc.bcm.edu	37	chr12	25031515	25031515	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agactagcagatgttgaataTgggacccattcttgatccaa	13	11	9	8	0	1	4	0	2	1	2	2	5	2	5	2	1	1	2	2	1	4	5			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:25031515T>C	ENST00000261192.7	-	5	985	c.459A>G	c.(457-459)ccA>ccG	p.P153P	BCAT1_ENST00000342945.5_Silent_p.P92P|BCAT1_ENST00000538118.1_Silent_p.P152P|BCAT1_ENST00000539282.1_Silent_p.P165P|BCAT1_ENST00000539780.1_Silent_p.P116P|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	153					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)	ATGTTGAATATGGGACCCATT	0.363																																					p.P165P		Atlas-SNP	.											.	BCAT1	44	.	0			c.A495G						PASS	.						94	91	92					12																	25031515		1894	4128	6022	SO:0001819	synonymous_variant	586	exon5			TGAATATGGGACC		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.459A>G	12.37:g.25031515T>C		112	0	0		106	9	0.0849057	NM_001178093	B3KY27|B7Z2M5|B7Z5L0|F5H5E4|Q68DQ7|Q96MY9	Silent	SNP	ENST00000261192.7	37	CCDS44845.1																																																																																			.	.	none		0.363	BCAT1-001	KNOWN	upstream_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402080.1	NM_005504		C	25031515	T	C	25031515	2	2	22	1	0	0	0	0	0	0	0	1	1354	1451	51	3		3	BCAT1	12	25031515	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2350706	25031515	108820380	2655	5556											
IFLTD1	160492	hgsc.bcm.edu	37	chr12	25671871	25671871	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggcaccaagggctgcgattAgggaaaacggttggtgggat	10	8	17	6	2	0	0	0	0	0	0	0	3	0	2	1	6	2	3	1	6	4	2	rs34028410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:25671871A>G	ENST00000282881.6	-	7	1133	c.984T>C	c.(982-984)ccT>ccC	p.P328P	IFLTD1_ENST00000539744.1_Silent_p.P231P|IFLTD1_ENST00000458174.2_Silent_p.P349P|IFLTD1_ENST00000413632.2_Silent_p.P309P|IFLTD1_ENST00000445693.1_Silent_p.P265P	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		328					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)					GGCTGCGATTAGGGAAAACGG	0.448													G|||	88	0.0175719	0.0628	0.0072	5008	,	,		20109	0.0		0.0	False		,,,				2504	0.0				p.P349P		Atlas-SNP	.											.	IFLTD1	121	.	0			c.T1047C						PASS	.	G	,,,	251,4155	803.2+/-415.7	5,241,1957	101	101	101		795,1047,927,984	-2.9	0	12	dbSNP_126	101	1,8599	819.2+/-406.8	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IFLTD1	NM_001145727.1,NM_001145728.1,NM_001145729.1,NM_152590.2	,,,	5,242,6256	GG,GA,AA		0.0116,5.6968,1.9376	,,,	265/326,349/410,309/370,328/389	25671871	252,12754	2203	4300	6503	SO:0001819	synonymous_variant	160492	exon8			GCGATTAGGGAAA																												ENST00000282881.6:c.984T>C	12.37:g.25671871A>G		117	0	0		151	79	0.523179	NM_001145728	B4DL27|B4DY70|Q8IY38	Silent	SNP	ENST00000282881.6	37	CCDS8704.1	20	0.009157509157509158	17	0.034552845528455285	3	0.008287292817679558	0	0.0	0	0.0	G	1.210	-0.629928	0.03610	0.056968	1.16E-4	ENSG00000152936	ENST00000543629	.	.	.	4.95	-2.93	0.05598	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999994	.	.	.	.	.	.	.	.	.	.	.	.	.	-13.2418	0.8046	0.01082	0.3824:0.1182:0.2583:0.241	rs34028410	.	.	.	Q	103	.	.	X	-	1	0	IFLTD1	25563138	0.330000	0.24705	0.000000	0.03702	0.293000	0.27360	0.047000	0.14056	-0.848000	0.04163	-0.930000	0.02707	TAA	A|0.980;G|0.020	0.020	strong		0.448	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1			G	25671871	A	G	25671871	2	3	22	1	0	0	0	0	0	0	0	1	7539	407	15	3		3	IFLTD1	12	25671871	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	640356	25671871	108180024	2656	5557											
IFLTD1	160492	hgsc.bcm.edu	37	chr12	25672877	25672877	+	Missense_Mutation	SNP	C	C	T																															tttttctttagttattgtagCtgtagatgctgtccactgaa																								rs34074522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:25672877C>T	ENST00000282881.6	-	6	1017	c.868G>A	c.(868-870)Gct>Act	p.A290T	IFLTD1_ENST00000539744.1_Missense_Mutation_p.A193T|IFLTD1_ENST00000458174.2_Missense_Mutation_p.A311T|IFLTD1_ENST00000413632.2_Missense_Mutation_p.A271T|IFLTD1_ENST00000445693.1_Missense_Mutation_p.A227T	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		290			A -> T (in dbSNP:rs34074522).		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)					GTTATTGTAGCTGTAGATGCT	0.383													T|||	88	0.0175719	0.0628	0.0072	5008	,	,		13260	0.0		0.0	False		,,,				2504	0.0				p.A311T		Atlas-SNP	.											IFLTD1_ENST00000458174,NS,carcinoma,+1,2	IFLTD1	121	2	0			c.G931A						PASS	.	T	THR/ALA,THR/ALA,THR/ALA,THR/ALA	251,4155	802.9+/-415.7	5,241,1957	210	187	195		679,931,811,868	-0.6	0	12	dbSNP_126	195	1,8599	818.9+/-406.8	0,1,4299	yes	missense,missense,missense,missense	IFLTD1	NM_001145727.1,NM_001145728.1,NM_001145729.1,NM_152590.2	58,58,58,58	5,242,6256	TT,TC,CC		0.0116,5.6968,1.9376	benign,benign,benign,benign	227/326,311/410,271/370,290/389	25672877	252,12754	2203	4300	6503	SO:0001583	missense	160492	exon7			TTGTAGCTGTAGA																												ENST00000282881.6:c.868G>A	12.37:g.25672877C>T	ENSP00000282881:p.Ala290Thr	159	0	0		119	50	0.420168	NM_001145728	B4DL27|B4DY70|Q8IY38	Missense_Mutation	SNP	ENST00000282881.6	37	CCDS8704.1	20|20	0.009157509157509158|0.009157509157509158	17|17	0.034552845528455285|0.034552845528455285	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	T|T	0.198|0.198	-1.047307|-1.047307	0.01981|0.01981	0.056968|0.056968	1.16E-4|1.16E-4	ENSG00000152936|ENSG00000152936	ENST00000282881;ENST00000539744;ENST00000458174;ENST00000445693;ENST00000413632;ENST00000539523;ENST00000545543|ENST00000543629	T;T;T;T;T;T;T|.	0.22336|.	2.67;2.68;2.67;2.66;2.53;1.96;2.54|.	4.68|4.68	-0.618|-0.618	0.11576|0.11576	.|.	.|.	.|.	.|.	.|.	T|T	0.00875|0.00875	0.0029|0.0029	N|N	0.01874|0.01874	-0.695|-0.695	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|.	0.001;0.0;0.0;0.0|.	T|T	0.30179|0.30179	-0.9987|-0.9987	9|5	0.08599|.	T|.	0.76|.	-1.4413|-1.4413	4.4653|4.4653	0.11685|0.11685	0.1606:0.3771:0.0:0.4623|0.1606:0.3771:0.0:0.4623	rs34074522|rs34074522	227;311;271;290|.	Q8N9Z9-3;Q8N9Z9-5;Q8N9Z9-4;Q8N9Z9|.	.;.;.;ILFT1_HUMAN|.	T|N	290;193;311;227;271;7;120|64	ENSP00000282881:A290T;ENSP00000443132:A193T;ENSP00000407353:A311T;ENSP00000407043:A227T;ENSP00000393150:A271T;ENSP00000438160:A7T;ENSP00000443596:A120T|.	ENSP00000282881:A290T|.	A|S	-|-	1|2	0|0	IFLTD1|IFLTD1	25564144|25564144	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	-0.752000|-0.752000	0.04797|0.04797	-0.241000|-0.241000	0.09681|0.09681	-1.163000|-1.163000	0.01768|0.01768	GCT|AGC	C|0.980;T|0.020	0.020	strong		0.383	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1			T	25672877	C	T	25672877	3	4	22	1	0	0	0	0	1	0	0	0	7539	797	28	2	310	2	IFLTD1	12	25672877	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1006	25672877	108179018	2657	5558	65	2									
IFLTD1	160492	hgsc.bcm.edu	37	chr12	25672880	25672880	+	Missense_Mutation	SNP	T	T	C																															ttctttagttattgtagctgTagatgctgtccactgaaaca																								rs34732786	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:25672880T>C	ENST00000282881.6	-	6	1014	c.865A>G	c.(865-867)Aca>Gca	p.T289A	IFLTD1_ENST00000539744.1_Missense_Mutation_p.T192A|IFLTD1_ENST00000458174.2_Missense_Mutation_p.T310A|IFLTD1_ENST00000413632.2_Missense_Mutation_p.T270A|IFLTD1_ENST00000445693.1_Missense_Mutation_p.T226A	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		289			T -> A (in dbSNP:rs34732786).		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)					ATTGTAGCTGTAGATGCTGTC	0.378													T|||	88	0.0175719	0.0628	0.0072	5008	,	,		13206	0.0		0.0	False		,,,				2504	0.0				p.T310A		Atlas-SNP	.											.	IFLTD1	121	.	0			c.A928G						PASS	.	T	ALA/THR,ALA/THR,ALA/THR,ALA/THR	251,4155	146.5+/-181.1	5,241,1957	211	187	195		676,928,808,865	-7	0	12	dbSNP_126	195	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense	IFLTD1	NM_001145727.1,NM_001145728.1,NM_001145729.1,NM_152590.2	58,58,58,58	5,242,6256	CC,CT,TT		0.0116,5.6968,1.9376	benign,benign,benign,benign	226/326,310/410,270/370,289/389	25672880	252,12754	2203	4300	6503	SO:0001583	missense	160492	exon7			TAGCTGTAGATGC																												ENST00000282881.6:c.865A>G	12.37:g.25672880T>C	ENSP00000282881:p.Thr289Ala	160	0	0		121	51	0.421488	NM_001145728	B4DL27|B4DY70|Q8IY38	Missense_Mutation	SNP	ENST00000282881.6	37	CCDS8704.1	20|20	0.009157509157509158|0.009157509157509158	17|17	0.034552845528455285|0.034552845528455285	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	T|T	8.850|8.850	0.944302|0.944302	0.18356|0.18356	0.056968|0.056968	1.16E-4|1.16E-4	ENSG00000152936|ENSG00000152936	ENST00000282881;ENST00000539744;ENST00000458174;ENST00000445693;ENST00000413632;ENST00000539523;ENST00000545543|ENST00000543629	T;T;T;T;T;T;T|.	0.22945|.	2.72;2.75;2.72;2.72;2.54;1.93;2.5|.	4.84|4.84	-7.02|-7.02	0.01589|0.01589	.|.	.|.	.|.	.|.	.|.	T|T	0.02267|0.02267	0.0070|0.0070	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	B;B;B;B|.	0.17667|.	0.023;0.023;0.023;0.013|.	B;B;B;B|.	0.11329|.	0.003;0.006;0.006;0.002|.	T|T	0.21861|0.21861	-1.0233|-1.0233	9|5	0.62326|.	D|.	0.03|.	-0.6199|-0.6199	9.436|9.436	0.38639|0.38639	0.0:0.5472:0.2462:0.2065|0.0:0.5472:0.2462:0.2065	rs34732786|rs34732786	226;310;270;289|.	Q8N9Z9-3;Q8N9Z9-5;Q8N9Z9-4;Q8N9Z9|.	.;.;.;ILFT1_HUMAN|.	A|C	289;192;310;226;270;6;119|63	ENSP00000282881:T289A;ENSP00000443132:T192A;ENSP00000407353:T310A;ENSP00000407043:T226A;ENSP00000393150:T270A;ENSP00000438160:T6A;ENSP00000443596:T119A|.	ENSP00000282881:T289A|.	T|Y	-|-	1|2	0|0	IFLTD1|IFLTD1	25564147|25564147	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.013000|0.013000	0.08279|0.08279	-2.565000|-2.565000	0.00918|0.00918	-1.326000|-1.326000	0.02266|0.02266	0.477000|0.477000	0.44152|0.44152	ACA|TAC	T|0.980;C|0.020	0.020	strong		0.378	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1			C	25672880	T	C	25672880	3	2	22	1	0	0	0	0	1	0	0	0	7539	1638	57	3	313	3	IFLTD1	12	25672880	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	3	25672880	108179015	2658	5559	65	2									
IFLTD1	160492	hgsc.bcm.edu	37	chr12	25672945	25672945	+	Missense_Mutation	SNP	T	T	C																															ctactgaacatctgttaaatTcaacgtcagcatctaatttt																								rs34326830	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:25672945T>C	ENST00000282881.6	-	6	949	c.800A>G	c.(799-801)gAa>gGa	p.E267G	IFLTD1_ENST00000539744.1_Missense_Mutation_p.E170G|IFLTD1_ENST00000458174.2_Missense_Mutation_p.E288G|IFLTD1_ENST00000413632.2_Missense_Mutation_p.E248G|IFLTD1_ENST00000445693.1_Missense_Mutation_p.E204G	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		267			E -> G (in dbSNP:rs34326830).		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)					TCTGTTAAATTCAACGTCAGC	0.388													T|||	88	0.0175719	0.0628	0.0072	5008	,	,		13538	0.0		0.0	False		,,,				2504	0.0				p.E288G		Atlas-SNP	.											.	IFLTD1	121	.	0			c.A863G						PASS	.	T	GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU	251,4155	144.6+/-179.5	5,241,1957	138	121	126		611,863,743,800	5.1	1	12	dbSNP_126	126	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense	IFLTD1	NM_001145727.1,NM_001145728.1,NM_001145729.1,NM_152590.2	98,98,98,98	5,242,6256	CC,CT,TT		0.0116,5.6968,1.9376	probably-damaging,probably-damaging,probably-damaging,probably-damaging	204/326,288/410,248/370,267/389	25672945	252,12754	2203	4300	6503	SO:0001583	missense	160492	exon7			TTAAATTCAACGT																												ENST00000282881.6:c.800A>G	12.37:g.25672945T>C	ENSP00000282881:p.Glu267Gly	169	0	0		155	81	0.522581	NM_001145728	B4DL27|B4DY70|Q8IY38	Missense_Mutation	SNP	ENST00000282881.6	37	CCDS8704.1	20|20	0.009157509157509158|0.009157509157509158	17|17	0.034552845528455285|0.034552845528455285	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	T|T	19.78|19.78	3.891505|3.891505	0.72524|0.72524	0.056968|0.056968	1.16E-4|1.16E-4	ENSG00000152936|ENSG00000152936	ENST00000282881;ENST00000539744;ENST00000458174;ENST00000445693;ENST00000413632;ENST00000545543|ENST00000543629	T;T;T;T;T;T|.	0.18502|.	2.35;2.43;2.33;2.38;2.28;2.21|.	5.05|5.05	5.05|5.05	0.67936|0.67936	.|.	.|.	.|.	.|.	.|.	T|.	0.05410|.	0.0143|.	L|L	0.32530|0.32530	0.975|0.975	0.29530|0.29530	N|N	0.852852|0.852852	P;P;D;D|.	0.76494|.	0.734;0.946;0.972;0.999|.	B;P;P;D|.	0.64144|.	0.421;0.637;0.723;0.922|.	T|.	0.04635|.	-1.0937|.	9|.	0.87932|.	D|.	0|.	4.219|4.219	11.112|11.112	0.48239|0.48239	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs34326830|rs34326830	204;288;248;267|.	Q8N9Z9-3;Q8N9Z9-5;Q8N9Z9-4;Q8N9Z9|.	.;.;.;ILFT1_HUMAN|.	G|W	267;170;288;204;248;97|41	ENSP00000282881:E267G;ENSP00000443132:E170G;ENSP00000407353:E288G;ENSP00000407043:E204G;ENSP00000393150:E248G;ENSP00000443596:E97G|.	ENSP00000282881:E267G|.	E|X	-|-	2|3	0|0	IFLTD1|IFLTD1	25564212|25564212	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.842000|0.842000	0.47809|0.47809	3.758000|3.758000	0.55220|0.55220	2.134000|2.134000	0.65973|0.65973	0.477000|0.477000	0.44152|0.44152	GAA|TGA	T|0.980;C|0.020	0.020	strong		0.388	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1			C	25672945	T	C	25672945	3	2	22	1	0	0	0	0	1	0	0	0	7539	1783	62	3	378	3	IFLTD1	12	25672945	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	65	25672945	108178950	2659	5560	66	2									
IFLTD1	160492	hgsc.bcm.edu	37	chr12	25672955	25672955	+	Missense_Mutation	SNP	C	C	T																															tctgttaaattcaacgtcagCatctaatttttcccacgctt																								rs35450203	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:25672955C>T	ENST00000282881.6	-	6	939	c.790G>A	c.(790-792)Gct>Act	p.A264T	IFLTD1_ENST00000539744.1_Missense_Mutation_p.A167T|IFLTD1_ENST00000458174.2_Missense_Mutation_p.A285T|IFLTD1_ENST00000413632.2_Missense_Mutation_p.A245T|IFLTD1_ENST00000445693.1_Missense_Mutation_p.A201T	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		264			A -> T (in dbSNP:rs35450203).		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)					TCAACGTCAGCATCTAATTTT	0.383													T|||	88	0.0175719	0.0628	0.0072	5008	,	,		13163	0.0		0.0	False		,,,				2504	0.0				p.A285T		Atlas-SNP	.											.	IFLTD1	121	.	0			c.G853A						PASS	.	T	THR/ALA,THR/ALA,THR/ALA,THR/ALA	252,4154	803.0+/-415.7	5,242,1956	123	107	112		601,853,733,790	2.6	1	12	dbSNP_126	112	1,8599	818.9+/-406.8	0,1,4299	yes	missense,missense,missense,missense	IFLTD1	NM_001145727.1,NM_001145728.1,NM_001145729.1,NM_152590.2	58,58,58,58	5,243,6255	TT,TC,CC		0.0116,5.7195,1.9453	benign,benign,benign,benign	201/326,285/410,245/370,264/389	25672955	253,12753	2203	4300	6503	SO:0001583	missense	160492	exon7			CGTCAGCATCTAA																												ENST00000282881.6:c.790G>A	12.37:g.25672955C>T	ENSP00000282881:p.Ala264Thr	158	0	0		159	89	0.559748	NM_001145728	B4DL27|B4DY70|Q8IY38	Missense_Mutation	SNP	ENST00000282881.6	37	CCDS8704.1	20|20	0.009157509157509158|0.009157509157509158	17|17	0.034552845528455285|0.034552845528455285	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	T|T	2.163|2.163	-0.391668|-0.391668	0.04932|0.04932	0.057195|0.057195	1.16E-4|1.16E-4	ENSG00000152936|ENSG00000152936	ENST00000282881;ENST00000539744;ENST00000458174;ENST00000445693;ENST00000413632;ENST00000545543|ENST00000543629	T;T;T;T;T;T|.	0.12569|.	2.92;2.9;2.94;2.89;2.67;2.69|.	5.05|5.05	2.61|2.61	0.31194|0.31194	.|.	.|.	.|.	.|.	.|.	T|T	0.00815|0.00815	0.0027|0.0027	N|N	0.01048|0.01048	-1.04|-1.04	0.19300|0.19300	N|N	0.999978|0.999978	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|T	0.32188|0.32188	-0.9916|-0.9916	9|5	0.02654|.	T|.	1|.	-2.2559|-2.2559	4.0577|4.0577	0.09824|0.09824	0.3165:0.0877:0.0:0.5958|0.3165:0.0877:0.0:0.5958	rs35450203|rs35450203	201;285;245;264|.	Q8N9Z9-3;Q8N9Z9-5;Q8N9Z9-4;Q8N9Z9|.	.;.;.;ILFT1_HUMAN|.	T|Y	264;167;285;201;245;94|38	ENSP00000282881:A264T;ENSP00000443132:A167T;ENSP00000407353:A285T;ENSP00000407043:A201T;ENSP00000393150:A245T;ENSP00000443596:A94T|.	ENSP00000282881:A264T|.	A|C	-|-	1|2	0|0	IFLTD1|IFLTD1	25564222|25564222	0.160000|0.160000	0.22878|0.22878	0.953000|0.953000	0.39169|0.39169	0.671000|0.671000	0.39405|0.39405	0.141000|0.141000	0.16076|0.16076	0.050000|0.050000	0.15949|0.15949	-0.352000|-0.352000	0.07741|0.07741	GCT|TGC	C|0.980;T|0.020	0.020	strong		0.383	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1			T	25672955	C	T	25672955	3	4	22	1	0	0	0	0	1	0	0	0	7539	710	25	2	388	2	IFLTD1	12	25672955	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	10	25672955	108178940	2660	5561	66	2									
IFLTD1	160492	hgsc.bcm.edu	37	chr12	25673001	25673001	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtggataggggtgtaccaCgcaatggcctaatgaaaatg	13	8	13	7	1	0	1	0	1	0	0	0	2	0	2	2	4	1	2	2	4	6	3	rs76419032	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:25673001C>G	ENST00000282881.6	-	6	893	c.744G>C	c.(742-744)gcG>gcC	p.A248A	IFLTD1_ENST00000539744.1_Silent_p.A151A|IFLTD1_ENST00000458174.2_Silent_p.A269A|IFLTD1_ENST00000413632.2_Silent_p.A229A|IFLTD1_ENST00000445693.1_Silent_p.A185A	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		248	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)					GGGTGTACCACGCAATGGCCT	0.343													G|||	88	0.0175719	0.0628	0.0072	5008	,	,		13235	0.0		0.0	False		,,,				2504	0.0				p.A269A		Atlas-SNP	.											.	IFLTD1	121	.	0			c.G807C						PASS	.	G	,,,	248,4158	801.2+/-415.6	5,238,1960	79	67	71		555,807,687,744	0.9	1	12	dbSNP_132	71	1,8599	818.4+/-406.9	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IFLTD1	NM_001145727.1,NM_001145728.1,NM_001145729.1,NM_152590.2	,,,	5,239,6259	GG,GC,CC		0.0116,5.6287,1.9145	,,,	185/326,269/410,229/370,248/389	25673001	249,12757	2203	4300	6503	SO:0001819	synonymous_variant	160492	exon7			GTACCACGCAATG																												ENST00000282881.6:c.744G>C	12.37:g.25673001C>G		108	0	0		112	65	0.580357	NM_001145728	B4DL27|B4DY70|Q8IY38	Silent	SNP	ENST00000282881.6	37	CCDS8704.1	20	0.009157509157509158	17	0.034552845528455285	3	0.008287292817679558	0	0.0	0	0.0	G	1.295	-0.606444	0.03717	0.056287	1.16E-4	ENSG00000152936	ENST00000543629	.	.	.	5.05	0.883	0.19177	.	.	.	.	.	T	0.06371	0.0164	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.07654	-1.0761	4	.	.	.	-5.3188	0.7606	0.01006	0.2856:0.1643:0.3812:0.1689	.	.	.	.	L	23	.	.	V	-	1	0	IFLTD1	25564268	1.000000	0.71417	0.983000	0.44433	0.110000	0.19582	0.968000	0.29357	0.060000	0.16281	-1.126000	0.01995	GTG	C|0.981;G|0.019	0.019	strong		0.343	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1			G	25673001	C	G	25673001	2	3	22	1	0	0	0	0	0	0	0	1	7539	523	19	4		4	IFLTD1	12	25673001	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	46	25673001	108178894	2661	5562											
BHLHE41	79365	hgsc.bcm.edu	37	chr12	26275297	26275297	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggggtatagcagcgggaacGgggcggcagccgccgccggg	6	2	21	12	7	0	0	0	0	0	0	0	1	0	1	3	7	4	3	3	7	3	2	rs121912617	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:26275297G>T	ENST00000242728.4	-	5	1498	c.1151C>A	c.(1150-1152)cCg>cAg	p.P384Q	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	384	Ala/Gly-rich.		P -> R (associated with short sleep phenotype). {ECO:0000269|PubMed:19679812}.		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						CAGCGGGAACGGGGCGGCAGC	0.741													G|||	36	0.0071885	0.0227	0.0086	5008	,	,		4052	0.0		0.0	False		,,,				2504	0.0				p.P384Q		Atlas-SNP	.											.	BHLHE41	20	.	0			c.C1151A						PASS	.						2	3	2					12																	26275297		1465	3164	4629	SO:0001583	missense	79365	exon5			GGGAACGGGGCGG	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.1151C>A	12.37:g.26275297G>T	ENSP00000242728:p.Pro384Gln	4	0	0		5	4	0.8	NM_030762	A2I2N8	Missense_Mutation	SNP	ENST00000242728.4	37	CCDS8706.1	.	.	.	.	.	.	.	.	.	.	G	14.73	2.622122	0.46840	.	.	ENSG00000123095	ENST00000242728	T	0.79141	-1.24	3.09	3.09	0.35607	.	1.892810	0.04121	U	0.316359	T	0.75280	0.3828	L	0.38838	1.175	0.80722	D	1	D	0.53151	0.958	P	0.44860	0.462	T	0.68443	-0.5407	10	0.87932	D	0	.	11.9445	0.52920	0.0:0.0:1.0:0.0	.	384	Q9C0J9	BHE41_HUMAN	Q	384	ENSP00000242728:P384Q	ENSP00000242728:P384Q	P	-	2	0	BHLHE41	26166564	1.000000	0.71417	0.985000	0.45067	0.044000	0.14063	7.845000	0.86875	1.435000	0.47434	0.471000	0.43371	CCG	.	.	alt		0.741	BHLHE41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402714.1	NM_030762		T	26275297	G	T	26275297	3	4	22	1	0	0	0	0	1	0	0	0	1424	1116	39	4	301	4	BHLHE41	12	26275297	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	602296	26275297	107576598	2662	5563											
ITPR2	3709	hgsc.bcm.edu	37	chr12	26774089	26774089	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcaccacctttcacttgactTtcccctatttctccattctc	6	17	1	17	0	4	1	2	1	2	0	7	1	5	1	5	0	0	0	5	0	1	6	rs2230373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:26774089T>G	ENST00000381340.3	-	26	3845	c.3429A>C	c.(3427-3429)gaA>gaC	p.E1143D	RP11-666F17.1_ENST00000414098.2_RNA|ITPR2_ENST00000545902.1_5'Flank	NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1143			E -> D (in dbSNP:rs16931091).		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)	TCACTTGACTTTCCCCTATTT	0.413													T|||	203	0.0405351	0.149	0.0072	5008	,	,		18812	0.0		0.001	False		,,,				2504	0.0				p.E1143D		Atlas-SNP	.											.	ITPR2	270	.	0			c.A3429C						PASS	.	T	ASP/GLU	488,3302		24,440,1431	380	359	366		3429	-0.8	0.6	12	dbSNP_123	366	1,8249		0,1,4124	yes	missense	ITPR2	NM_002223.2	45	24,441,5555	GG,GT,TT		0.0121,12.876,4.0615	benign	1143/2702	26774089	489,11551	1895	4125	6020	SO:0001583	missense	3709	exon26			TTGACTTTCCCCT	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.3429A>C	12.37:g.26774089T>G	ENSP00000370744:p.Glu1143Asp	254	1	0.00393701		281	139	0.494662	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	82	0.037545787545787544	81	0.16463414634146342	1	0.0027624309392265192	0	0.0	0	0.0	T	9.713	1.157689	0.21454	0.12876	1.21E-4	ENSG00000123104	ENST00000381340	D	0.91996	-2.95	4.36	-0.782	0.10961	.	0.222293	0.40554	N	0.001063	T	0.00754	0.0025	N	0.05574	-0.02	0.31748	P	0.634949	B	0.02656	0.0	B	0.01281	0.0	T	0.23726	-1.0180	9	0.14656	T	0.56	.	1.8975	0.03261	0.1237:0.3347:0.2527:0.2889	rs16931091;rs56635647;rs16931091	1143	Q14571	ITPR2_HUMAN	D	1143	ENSP00000370744:E1143D	ENSP00000370744:E1143D	E	-	3	2	ITPR2	26665356	0.003000	0.15002	0.552000	0.28243	0.721000	0.41392	-0.083000	0.11286	-0.216000	0.10048	0.454000	0.30748	GAA	T|0.944;G|0.056	0.056	strong		0.413	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		G	26774089	T	G	26774089	3	3	22	1	0	0	0	0	1	0	0	0	7930	1838	64	5	4804	5	ITPR2	12	26774089	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	498792	26774089	107077806	2663	5564											
ITPR2	3709	hgsc.bcm.edu	37	chr12	26816779	26816779	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgctttaagaattccaaataCctatcaggaataaaaacagc	18	10	5	8	0	1	1	1	0	0	1	2	2	2	2	2	1	4	1	2	1	9	6	rs77639758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:26816779C>T	ENST00000381340.3	-	15	1968	c.1552G>A	c.(1552-1554)Gta>Ata	p.V518I		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	518					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)	ATTCCAAATACCTATCAGGAA	0.338													C|||	19	0.00379393	0.0136	0.0014	5008	,	,		15680	0.0		0.0	False		,,,				2504	0.0				p.V518I		Atlas-SNP	.											.	ITPR2	270	.	0			c.G1552A						PASS	.	C	ILE/VAL	30,3602		0,30,1786	151	148	149		1552	4.5	1	12	dbSNP_131	149	0,8144		0,0,4072	yes	missense-near-splice	ITPR2	NM_002223.2	29	0,30,5858	TT,TC,CC		0.0,0.826,0.2548	benign	518/2702	26816779	30,11746	1816	4072	5888	SO:0001630	splice_region_variant	3709	exon15			CAAATACCTATCA	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.1552-1G>A	12.37:g.26816779C>T		68	0	0		74	38	0.513514	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	4.645	0.119815	0.08881	0.00826	0.0	ENSG00000123104	ENST00000381340	D	0.96885	-4.16	4.5	4.5	0.54988	Intracellular calcium-release channel (1);	0.053381	0.64402	D	0.000001	T	0.78317	0.4264	N	0.01242	-0.935	0.80722	D	1	B	0.02656	0.0	B	0.08055	0.003	T	0.77744	-0.2473	10	0.02654	T	1	.	5.5858	0.17274	0.0:0.7597:0.0:0.2403	.	518	Q14571	ITPR2_HUMAN	I	518	ENSP00000370744:V518I	ENSP00000370744:V518I	V	-	1	0	ITPR2	26708046	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	4.869000	0.63028	2.489000	0.83994	0.655000	0.94253	GTA	C|0.998;T|0.002	0.002	strong		0.338	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	Missense_Mutation	T	26816779	C	T	26816779	5	4	22	1	0	0	0	0	0	0	1	0	7930	521	18	2	6725	2	ITPR2	12	26816779	Splice_Site	SNP	C	TCGA-G8-6324-01A-11D-2210-10	42690	26816779	107035116	2664	5565											
ITPR2	3709	hgsc.bcm.edu	37	chr12	26834833	26834833	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcattctgagttattgtgccGttttctagctttttaactgt	6	21	7	7	1	3	1	1	1	2	0	3	1	3	1	1	0	3	3	1	0	3	9	rs35412320	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:26834833G>A	ENST00000381340.3	-	13	1799	c.1383C>T	c.(1381-1383)aaC>aaT	p.N461N		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	461					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)	TTATTGTGCCGTTTTCTAGCT	0.378													G|||	47	0.00938498	0.0348	0.0014	5008	,	,		19655	0.0		0.0	False		,,,				2504	0.0				p.N461N		Atlas-SNP	.											ITPR2,colon,carcinoma,-2,1	ITPR2	270	1	0			c.C1383T						PASS	.	G		94,3584		1,92,1746	196	185	189		1383	-10.2	0.4	12	dbSNP_126	189	1,8193		0,1,4096	no	coding-synonymous	ITPR2	NM_002223.2		1,93,5842	AA,AG,GG		0.0122,2.5557,0.8002		461/2702	26834833	95,11777	1839	4097	5936	SO:0001819	synonymous_variant	3709	exon13			TGTGCCGTTTTCT	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.1383C>T	12.37:g.26834833G>A		101	0	0		119	44	0.369748	NM_002223	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			G|0.991;A|0.009	0.009	strong		0.378	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223		A	26834833	G	A	26834833	2	1	22	1	0	0	0	0	0	0	0	1	7930	1136	40	1		1	ITPR2	12	26834833	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	18054	26834833	107017062	2665	5566											
TM7SF3	51768	hgsc.bcm.edu	37	chr12	27148324	27148324	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtctgtcccagcgtcacatGgtgggggatctacgcctcta	6	10	13	12	2	4	0	1	0	3	0	5	1	5	1	2	4	2	0	2	4	2	2	rs34735713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:27148324G>C	ENST00000343028.4	-	5	761	c.536C>G	c.(535-537)cCa>cGa	p.P179R	TM7SF3_ENST00000542667.1_5'UTR	NM_016551.2	NP_057635.1	Q9NS93	TM7S3_HUMAN	transmembrane 7 superfamily member 3	179			P -> R (in dbSNP:rs34735713).			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)					AGCGTCACATGGTGGGGGATC	0.468													G|||	109	0.0217652	0.0779	0.0086	5008	,	,		21417	0.0		0.0	False		,,,				2504	0.0				p.P179R		Atlas-SNP	.											.	TM7SF3	41	.	0			c.C536G						PASS	.	G	ARG/PRO	360,4046	183.3+/-210.9	16,328,1859	68	56	60		536	2.5	0	12	dbSNP_126	60	5,8595	3.7+/-12.6	0,5,4295	yes	missense	TM7SF3	NM_016551.2	103	16,333,6154	CC,CG,GG		0.0581,8.1707,2.8064	possibly-damaging	179/571	27148324	365,12641	2203	4300	6503	SO:0001583	missense	51768	exon5			TCACATGGTGGGG	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.536C>G	12.37:g.27148324G>C	ENSP00000342322:p.Pro179Arg	80	0	0		119	61	0.512605	NM_016551	B3KMZ3|Q9NUS4	Missense_Mutation	SNP	ENST00000343028.4	37	CCDS8710.1	32	0.014652014652014652	31	0.06300813008130081	1	0.0027624309392265192	0	0.0	0	0.0	G	13.61	2.289340	0.40494	0.081707	5.81E-4	ENSG00000064115	ENST00000343028;ENST00000543803;ENST00000539741;ENST00000543088	T;T;T;T	0.44881	1.5;0.92;0.91;0.93	4.27	2.45	0.29901	.	0.491723	0.22200	N	0.063241	T	0.01870	0.0059	L	0.60455	1.87	0.09310	N	1	P	0.42409	0.779	B	0.33690	0.168	T	0.02184	-1.1199	10	0.66056	D	0.02	-0.8778	8.9426	0.35740	0.2425:0.0:0.7575:0.0	rs34735713	179	Q9NS93	TM7S3_HUMAN	R	179;77;57;57	ENSP00000342322:P179R;ENSP00000442617:P77R;ENSP00000441027:P57R;ENSP00000444632:P57R	ENSP00000342322:P179R	P	-	2	0	TM7SF3	27039591	0.546000	0.26457	0.001000	0.08648	0.002000	0.02628	3.800000	0.55537	0.574000	0.29417	-0.157000	0.13467	CCA	G|0.971;C|0.029	0.029	strong		0.468	TM7SF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403033.1	NM_016551		C	27148324	G	C	27148324	3	2	22	1	0	0	0	0	1	0	0	0	15990	1348	47	4	1208	4	TM7SF3	12	27148324	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	313491	27148324	106703571	2666	5567											
STK38L	23012	hgsc.bcm.edu	37	chr12	27450671	27450671	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	actatggcaatgacggcaggGactacaacaacctttcctat	13	9	8	11	1	0	1	0	1	0	0	1	2	1	2	2	3	3	2	2	3	6	4	rs56140810	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:27450671G>T	ENST00000389032.3	+	2	187	c.18G>T	c.(16-18)ggG>ggT	p.G6G	STK38L_ENST00000539577.1_Intron	NM_015000.3	NP_055815.1			serine/threonine kinase 38 like											breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)	12	Colorectal(261;0.0847)					TGACGGCAGGGACTACAACAA	0.373													G|||	124	0.0247604	0.0862	0.013	5008	,	,		18491	0.0		0.001	False		,,,				2504	0.0				p.G6G		Atlas-SNP	.											.	STK38L	44	.	0			c.G18T						PASS	.	G		384,4022	185.0+/-212.2	18,348,1837	90	90	90		18	5.2	1	12	dbSNP_129	90	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	STK38L	NM_015000.3		18,352,6133	TT,TG,GG		0.0465,8.7154,2.9832		6/465	27450671	388,12618	2203	4300	6503	SO:0001819	synonymous_variant	23012	exon2			GGCAGGGACTACA	AB023182	CCDS31761.1	12p11.23	2014-04-23			ENSG00000211455	ENSG00000211455			17848	protein-coding gene	gene with protein product	"nuclear Dbf2-related 2"	615836				16488889	Standard	NM_015000		Approved	KIAA0965, NDR2	uc001rhr.3	Q9Y2H1	OTTHUMG00000169284	ENST00000389032.3:c.18G>T	12.37:g.27450671G>T		56	0	0		68	32	0.470588	NM_015000		Silent	SNP	ENST00000389032.3	37	CCDS31761.1																																																																																			G|0.972;T|0.028	0.028	strong		0.373	STK38L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403297.1	NM_015000		T	27450671	G	T	27450671	2	4	22	1	0	0	0	0	0	0	0	1	15319	1161	41	4		4	STK38L	12	27450671	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	302347	27450671	106401224	2667	5568											
ARNTL2	56938	hgsc.bcm.edu	37	chr12	27543028	27543028	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcgcccccttctgcacgaaaGctggtttgcaagttcacagt	8	11	9	13	2	2	0	1	0	1	0	3	1	2	0	2	1	3	5	2	1	2	3	rs113615248	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:27543028G>A	ENST00000266503.5	+	9	793		c.e9-1		ARNTL2_ENST00000542388.1_Splice_Site|ARNTL2_ENST00000544915.1_Splice_Site|ARNTL2_ENST00000311001.5_Splice_Site|RP11-165P7.1_ENST00000500498.2_RNA|ARNTL2_ENST00000546179.1_Splice_Site|ARNTL2_ENST00000261178.5_Splice_Site|ARNTL2_ENST00000395901.2_Splice_Site			Q8WYA1	BMAL2_HUMAN	aryl hydrocarbon receptor nuclear translocator-like 2						circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|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)|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)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	E-box binding (GO:0070888)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(1)|skin(2)|urinary_tract(1)	21	Colorectal(261;0.0847)|Lung SC(9;0.184)					CTGCACGAAAGCTGGTTTGCA	0.383													G|||	31	0.0061901	0.0227	0.0014	5008	,	,		17019	0.0		0.0	False		,,,				2504	0.0				.		Atlas-SNP	.											.	ARNTL2	54	.	0			c.665-1G>A						PASS	.	G		135,4271	96.7+/-135.4	1,133,2069	153	151	152			2.2	0.2	12	dbSNP_132	152	3,8597	3.0+/-9.4	0,3,4297	yes	splice-3	ARNTL2	NM_020183.3		1,136,6366	AA,AG,GG		0.0349,3.064,1.061			27543028	138,12868	2203	4300	6503	SO:0001630	splice_region_variant	56938	exon7			ACGAAAGCTGGTT	AF246961	CCDS8712.1, CCDS58219.1, CCDS58220.1, CCDS58221.1, CCDS58222.1	12p12.2-p11.2	2013-05-21			ENSG00000029153	ENSG00000029153		"Basic helix-loop-helix proteins"	18984	protein-coding gene	gene with protein product		614517				10864977, 10964693	Standard	NM_020183		Approved	BMAL2, MOP9, CLIF, PASD9, bHLHe6	uc001rht.2	Q8WYA1	OTTHUMG00000169257	ENST00000266503.5:c.776-1G>A	12.37:g.27543028G>A		172	0	0		151	78	0.516556	NM_001248005	B7Z429|F5H402|Q8WYA2|Q8WYA3|Q8WYA4|Q96J63|Q9H2M4|Q9NS70|Q9NYQ4|Q9NYQ5	Splice_Site	SNP	ENST00000266503.5	37	CCDS8712.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	G	17.45	3.393650	0.62066	0.03064	3.49E-4	ENSG00000029153	ENST00000544915;ENST00000395901;ENST00000546179;ENST00000311001;ENST00000261178;ENST00000266503;ENST00000457040;ENST00000542388	.	.	.	3.14	2.25	0.28309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.6704	0.34147	0.1092:0.0:0.8908:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARNTL2	27434295	1.000000	0.71417	0.181000	0.23098	0.664000	0.39144	7.551000	0.82182	0.675000	0.31264	0.655000	0.94253	.	G|0.991;A|0.009	0.009	strong		0.383	ARNTL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403162.1	NM_020183	Intron	A	27543028	G	A	27543028	5	1	22	1	0	0	0	0	0	0	1	0	968	985	34	2	809	2	ARNTL2	12	27543028	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	92357	27543028	106308867	2668	5569											
ARNTL2	56938	hgsc.bcm.edu	37	chr12	27543141	27543141	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaaatctctgtcaaagaagaGcatggatgcttacccaactc	15	9	7	10	0	2	2	1	0	1	2	4	3	2	3	1	1	4	2	1	1	6	1	rs74988383	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:27543141G>C	ENST00000266503.5	+	9	906	c.888G>C	c.(886-888)gaG>gaC	p.E296D	ARNTL2_ENST00000542388.1_Missense_Mutation_p.E211D|ARNTL2_ENST00000544915.1_Missense_Mutation_p.E262D|ARNTL2_ENST00000311001.5_Missense_Mutation_p.E282D|RP11-165P7.1_ENST00000500498.2_RNA|ARNTL2_ENST00000546179.1_Missense_Mutation_p.E259D|ARNTL2_ENST00000261178.5_Missense_Mutation_p.E248D|ARNTL2_ENST00000395901.2_Missense_Mutation_p.E259D			Q8WYA1	BMAL2_HUMAN	aryl hydrocarbon receptor nuclear translocator-like 2	296					circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|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)|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)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	E-box binding (GO:0070888)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(1)|skin(2)|urinary_tract(1)	21	Colorectal(261;0.0847)|Lung SC(9;0.184)					TCAAAGAAGAGCATGGATGCT	0.373													G|||	31	0.0061901	0.0227	0.0014	5008	,	,		17221	0.0		0.0	False		,,,				2504	0.0				p.E296D		Atlas-SNP	.											.	ARNTL2	54	.	0			c.G888C						PASS	.	G	ASP/GLU	136,4270	97.1+/-135.8	1,134,2068	94	92	92		888	-2.6	0.3	12	dbSNP_132	92	3,8597	3.0+/-9.4	0,3,4297	yes	missense	ARNTL2	NM_020183.3	45	1,137,6365	CC,CG,GG		0.0349,3.0867,1.0687	benign	296/637	27543141	139,12867	2203	4300	6503	SO:0001583	missense	56938	exon9			AGAAGAGCATGGA	AF246961	CCDS8712.1, CCDS58219.1, CCDS58220.1, CCDS58221.1, CCDS58222.1	12p12.2-p11.2	2013-05-21			ENSG00000029153	ENSG00000029153		"Basic helix-loop-helix proteins"	18984	protein-coding gene	gene with protein product		614517				10864977, 10964693	Standard	NM_020183		Approved	BMAL2, MOP9, CLIF, PASD9, bHLHe6	uc001rht.2	Q8WYA1	OTTHUMG00000169257	ENST00000266503.5:c.888G>C	12.37:g.27543141G>C	ENSP00000266503:p.Glu296Asp	100	0	0		83	43	0.518072	NM_020183	B7Z429|F5H402|Q8WYA2|Q8WYA3|Q8WYA4|Q96J63|Q9H2M4|Q9NS70|Q9NYQ4|Q9NYQ5	Missense_Mutation	SNP	ENST00000266503.5	37	CCDS8712.1	13|13	0.005952380952380952|0.005952380952380952	13|13	0.026422764227642278|0.026422764227642278	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	17.22|17.22	3.334286|3.334286	0.60853|0.60853	0.030867|0.030867	3.49E-4|3.49E-4	ENSG00000029153|ENSG00000029153	ENST00000544915;ENST00000395901;ENST00000546179;ENST00000311001;ENST00000261178;ENST00000266503;ENST00000542388|ENST00000457040	T;T;T;T;T;T;T|.	0.08720|.	3.16;3.17;3.06;3.16;3.18;3.16;3.19|.	3.71|3.71	-2.58|-2.58	0.06228|0.06228	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.37571|0.37571	0.1008|0.1008	M|M	0.70903|0.70903	2.155|2.155	0.38371|0.38371	D|D	0.944876|0.944876	P;D;P;P;B;B|.	0.53151|.	0.907;0.958;0.907;0.907;0.161;0.09|.	P;P;P;P;B;B|.	0.60345|.	0.686;0.873;0.801;0.686;0.137;0.103|.	T|T	0.58601|0.58601	-0.7608|-0.7608	10|5	0.56958|.	D|.	0.05|.	.|.	10.3192|10.3192	0.43756|0.43756	0.6174:0.0:0.3826:0.0|0.6174:0.0:0.3826:0.0	.|.	259;262;259;248;282;296|.	F5H402;Q8WYA1-5;Q8WYA1-3;Q8WYA1-4;Q8WYA1-2;Q8WYA1|.	.;.;.;.;.;BMAL2_HUMAN|.	D|T	262;259;259;282;248;296;211|248	ENSP00000442438:E262D;ENSP00000379238:E259D;ENSP00000438545:E259D;ENSP00000312247:E282D;ENSP00000261178:E248D;ENSP00000266503:E296D;ENSP00000445836:E211D|.	ENSP00000261178:E248D|.	E|S	+|+	3|2	2|0	ARNTL2|ARNTL2	27434408|27434408	0.865000|0.865000	0.29922|0.29922	0.275000|0.275000	0.24674|0.24674	0.946000|0.946000	0.59487|0.59487	-0.103000|-0.103000	0.10940|0.10940	-0.470000|-0.470000	0.06901|0.06901	0.655000|0.655000	0.94253|0.94253	GAG|AGC	G|0.991;C|0.009	0.009	strong		0.373	ARNTL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403162.1	NM_020183		C	27543141	G	C	27543141	3	2	22	1	0	0	0	0	1	0	0	0	968	962	34	4	922	4	ARNTL2	12	27543141	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	113	27543141	106308754	2669	5570											
PPFIBP1	8496	hgsc.bcm.edu	37	chr12	27829369	27829369	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgcctctcaggacagagcTccggcagaaagcaggccatt	10	8	11	12	1	1	2	1	0	1	2	3	3	2	3	3	3	3	3	3	3	1	2	rs35150305	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:27829369T>C	ENST00000318304.8	+	18	1753	c.1470T>C	c.(1468-1470)gcT>gcC	p.A490A	PPFIBP1_ENST00000542629.1_Silent_p.A459A|PPFIBP1_ENST00000537927.1_Silent_p.A337A|PPFIBP1_ENST00000228425.6_Silent_p.A473A	NM_001198916.1|NM_177444.2	NP_001185845.1|NP_803193	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)	490					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)					AGGACAGAGCTCCGGCAGAAA	0.547													T|||	123	0.0245607	0.0915	0.0029	5008	,	,		17752	0.0		0.0	False		,,,				2504	0.0				p.A490A		Atlas-SNP	.											.	PPFIBP1	153	.	0			c.T1470C						PASS	.	T	,,,	340,4066	176.2+/-205.4	9,322,1872	61	63	62		1011,1377,1419,1470	-2.5	0	12	dbSNP_126	62	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PPFIBP1	NM_001198915.1,NM_001198916.1,NM_003622.3,NM_177444.2	,,,	9,325,6169	CC,CT,TT		0.0349,7.7167,2.6372	,,,	337/859,459/981,473/1006,490/1012	27829369	343,12663	2203	4300	6503	SO:0001819	synonymous_variant	8496	exon18			CAGAGCTCCGGCA	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.1470T>C	12.37:g.27829369T>C		93	0	0		130	71	0.546154	NM_177444	O75336|Q86X70|Q9NY03|Q9ULJ0	Silent	SNP	ENST00000318304.8	37	CCDS55812.1																																																																																			T|0.978;C|0.022	0.022	strong		0.547	PPFIBP1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402877.1	NM_003622		C	27829369	T	C	27829369	2	2	22	1	0	0	0	0	0	0	0	1	12322	1538	54	3		3	PPFIBP1	12	27829369	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	286228	27829369	106022526	2670	5571											
PPFIBP1	8496	hgsc.bcm.edu	37	chr12	27842052	27842052	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gccactcatttcaaccttctGattggggctgaggcacagca	9	10	10	12	0	3	2	2	2	1	0	3	2	3	2	2	3	2	3	2	3	1	3	rs61730962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:27842052G>A	ENST00000318304.8	+	26	2902	c.2619G>A	c.(2617-2619)ctG>ctA	p.L873L	PPFIBP1_ENST00000542629.1_Silent_p.L842L|PPFIBP1_ENST00000537927.1_Silent_p.L720L|PPFIBP1_ENST00000228425.6_Silent_p.L867L	NM_001198916.1|NM_177444.2	NP_001185845.1|NP_803193	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)	873	SAM 3. {ECO:0000255|PROSITE- ProRule:PRU00184}.				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)					TCAACCTTCTGATTGGGGCTG	0.473													G|||	274	0.0547125	0.2005	0.0115	5008	,	,		18229	0.0		0.001	False		,,,				2504	0.0				p.L873L		Atlas-SNP	.											.	PPFIBP1	153	.	0			c.G2619A						PASS	.	G	,,,	720,3686	299.0+/-285.6	56,608,1539	130	117	121		2160,2526,2601,2619	4.4	1	12	dbSNP_129	121	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PPFIBP1	NM_001198915.1,NM_001198916.1,NM_003622.3,NM_177444.2	,,,	56,612,5835	AA,AG,GG		0.0465,16.3414,5.5667	,,,	720/859,842/981,867/1006,873/1012	27842052	724,12282	2203	4300	6503	SO:0001819	synonymous_variant	8496	exon26			CCTTCTGATTGGG	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.2619G>A	12.37:g.27842052G>A		137	0	0		167	84	0.502994	NM_177444	O75336|Q86X70|Q9NY03|Q9ULJ0	Silent	SNP	ENST00000318304.8	37	CCDS55812.1																																																																																			G|0.949;A|0.051	0.051	strong		0.473	PPFIBP1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402877.1	NM_003622		A	27842052	G	A	27842052	2	1	22	1	0	0	0	0	0	0	0	1	12322	1277	45	2		2	PPFIBP1	12	27842052	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	12683	27842052	106009843	2671	5572											
C12orf35	55196	hgsc.bcm.edu	37	chr12	32134122	32134122	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaaatttctgtttctgataTgcataatgggacagttgtgg	11	15	10	5	0	2	1	0	1	2	0	2	2	2	2	0	2	1	3	0	2	3	5	rs75434030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:32134122T>C	ENST00000312561.4	+	4	647	c.233T>C	c.(232-234)aTg>aCg	p.M78T	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	78																	GTTTCTGATATGCATAATGGG	0.373													T|||	33	0.00658946	0.0242	0.0014	5008	,	,		22474	0.0		0.0	False		,,,				2504	0.0				p.M78T		Atlas-SNP	.											.	.	.	.	0			c.T233C						PASS	.	T	THR/MET	109,4297	84.8+/-123.5	1,107,2095	85	83	83		233	-1.3	0	12	dbSNP_131	83	1,8599	1.2+/-3.3	0,1,4299	yes	missense	C12orf35	NM_018169.3	81	1,108,6394	CC,CT,TT		0.0116,2.4739,0.8458	possibly-damaging	78/1748	32134122	110,12896	2203	4300	6503	SO:0001583	missense	55196	exon4			CTGATATGCATAA	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.233T>C	12.37:g.32134122T>C	ENSP00000310338:p.Met78Thr	124	0	0		168	91	0.541667	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	37	CCDS8725.2	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	T	10.56	1.385451	0.25031	0.024739	1.16E-4	ENSG00000174718	ENST00000312561;ENST00000381054	T;T	0.09073	3.02;3.02	5.39	-1.28	0.09318	.	0.664905	0.14503	N	0.315631	T	0.01976	0.0062	L	0.29908	0.895	0.09310	N	1	B	0.13145	0.007	B	0.15484	0.013	T	0.40720	-0.9548	9	.	.	.	.	1.6516	0.02773	0.1117:0.2639:0.2202:0.4042	.	78	Q9HCM1	CL035_HUMAN	T	78	ENSP00000310338:M78T;ENSP00000370442:M78T	.	M	+	2	0	C12orf35	32025389	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	-0.467000	0.06664	-0.141000	0.11374	0.528000	0.53228	ATG	T|0.995;C|0.005	0.005	strong		0.373	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169		C	32134122	T	C	32134122	3	2	22	1	0	0	0	0	1	0	0	0	1684	1464	51	3	235	3	C12orf35	12	32134122	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	4292070	32134122	101717773	2672	5573											
PKP2	5318	hgsc.bcm.edu	37	chr12	33031023	33031023	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcccgacagtgagccctGccgtcaggtagttctccttc	5	10	10	16	2	2	1	1	1	1	0	4	2	2	1	5	1	3	2	5	1	1	3	rs62001016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:33031023G>A	ENST00000070846.6	-	3	815	c.791C>T	c.(790-792)gCa>gTa	p.A264V	PKP2_ENST00000340811.4_Missense_Mutation_p.A264V	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	264					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)					AGTGAGCCCTGCCGTCAGGTA	0.647													G|||	58	0.0115815	0.0408	0.0058	5008	,	,		18240	0.0		0.0	False		,,,				2504	0.0				p.A264V		Atlas-SNP	.											.	PKP2	110	.	0			c.C791T						PASS	.	G	VAL/ALA,VAL/ALA	137,4269	96.7+/-135.4	1,135,2067	52	48	49		791,791	3.8	0	12	dbSNP_129	49	0,8600		0,0,4300	yes	missense,missense	PKP2	NM_001005242.2,NM_004572.3	64,64	1,135,6367	AA,AG,GG		0.0,3.1094,1.0534	benign,benign	264/838,264/882	33031023	137,12869	2203	4300	6503	SO:0001583	missense	5318	exon3			AGCCCTGCCGTCA	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.791C>T	12.37:g.33031023G>A	ENSP00000070846:p.Ala264Val	85	0	0		97	47	0.484536	NM_004572	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Missense_Mutation	SNP	ENST00000070846.6	37	CCDS8731.1	24	0.01098901098901099	22	0.044715447154471545	2	0.0055248618784530384	0	0.0	0	0.0	G	1.719	-0.497156	0.04291	0.031094	0.0	ENSG00000057294	ENST00000340811;ENST00000070846;ENST00000537278	T;T	0.81163	-1.46;-1.39	4.73	3.84	0.44239	.	5.091870	0.00357	N	0.000025	T	0.42944	0.1225	N	0.22421	0.69	0.09310	N	1	B;B;B	0.19200	0.034;0.02;0.006	B;B;B	0.21708	0.036;0.016;0.01	T	0.49862	-0.8894	10	0.21540	T	0.41	-14.3867	10.8315	0.46663	0.0896:0.0:0.9104:0.0	.	264;264;264	Q99959-2;A0AV37;Q99959	.;.;PKP2_HUMAN	V	264	ENSP00000342800:A264V;ENSP00000070846:A264V	ENSP00000070846:A264V	A	-	2	0	PKP2	32922290	0.001000	0.12720	0.001000	0.08648	0.008000	0.06430	0.892000	0.28322	0.994000	0.38892	0.650000	0.86243	GCA	G|0.988;A|0.012	0.012	strong		0.647	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572		A	33031023	G	A	33031023	3	1	22	1	0	0	0	0	1	0	0	0	11994	1319	46	2	1902	2	PKP2	12	33031023	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	896901	33031023	100820872	2673	5574											
KIF21A	55605	hgsc.bcm.edu	37	chr12	39734066	39734066	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgcatgttctttttgagcTgcttgaagtctctgcagttc	5	18	9	9	0	2	2	0	2	2	0	4	2	2	2	0	0	4	6	0	0	1	6	rs150241656	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:39734066T>G	ENST00000361418.5	-	16	2226	c.2211A>C	c.(2209-2211)gcA>gcC	p.A737A	KIF21A_ENST00000361961.3_Silent_p.A724A|KIF21A_ENST00000541463.2_Silent_p.A724A|KIF21A_ENST00000544797.2_Silent_p.A724A|KIF21A_ENST00000395670.3_Silent_p.A737A			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	737					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)				CTTTTTGAGCTGCTTGAAGTC	0.363													T|||	6	0.00119808	0.0045	0.0	5008	,	,		18446	0.0		0.0	False		,,,				2504	0.0				p.A737A		Atlas-SNP	.											.	KIF21A	238	.	0			c.A2211C						PASS	.	T	,,,	31,4375	36.8+/-68.6	0,31,2172	125	109	114		2172,2211,2172,2172	-4	0.8	12	dbSNP_134	114	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KIF21A	NM_001173463.1,NM_001173464.1,NM_001173465.1,NM_017641.3	,,,	0,31,6470	GG,GT,TT		0.0,0.7036,0.2384	,,,	724/1638,737/1675,724/1622,724/1662	39734066	31,12971	2203	4298	6501	SO:0001819	synonymous_variant	55605	exon16			TTGAGCTGCTTGA	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.2211A>C	12.37:g.39734066T>G		270	0	0		269	136	0.505576	NM_001173464	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Silent	SNP	ENST00000361418.5	37	CCDS53776.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	10.31	1.314750	0.23908	0.007036	0.0	ENSG00000139116	ENST00000552961	.	.	.	5.22	-4.01	0.04045	.	.	.	.	.	T	0.38665	0.1049	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40327	-0.9569	4	.	.	.	.	5.0229	0.14370	0.5061:0.2038:0.0:0.2901	.	.	.	.	P	85	.	.	Q	-	2	0	KIF21A	38020333	0.026000	0.19158	0.768000	0.31515	0.987000	0.75469	-1.450000	0.02390	-0.615000	0.05679	0.533000	0.62120	CAG	T|0.998;G|0.002	0.002	strong		0.363	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641		G	39734066	T	G	39734066	2	3	22	1	0	0	0	0	0	0	0	1	8297	1567	55	5		5	KIF21A	12	39734066	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	6703043	39734066	94117829	2674	5575											
PRICKLE1	144165	hgsc.bcm.edu	37	chr12	42862431	42862431	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgaacttttttttacctcGtcacatgctgagcaccgtgg	8	14	9	10	2	1	2	1	2	0	0	2	3	1	2	2	1	4	2	2	1	2	4	rs74081707	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:42862431G>A	ENST00000455697.1	-	5	870	c.585C>T	c.(583-585)gaC>gaT	p.D195D	PRICKLE1_ENST00000548696.1_Silent_p.D195D|RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000345127.3_Silent_p.D195D|PRICKLE1_ENST00000552240.1_Silent_p.D195D|PRICKLE1_ENST00000445766.2_Silent_p.D195D	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	195	LIM zinc-binding 2. {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)		TTTTTACCTCGTCACATGCTG	0.403													G|||	153	0.0305511	0.1097	0.0115	5008	,	,		20234	0.0		0.0	False		,,,				2504	0.0				p.D195D		Atlas-SNP	.											.	PRICKLE1	105	.	0			c.C585T						PASS	.	G	,,,	477,3929	223.9+/-240.3	23,431,1749	82	82	82		585,585,585,585	-6.4	0.9	12	dbSNP_130	82	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRICKLE1	NM_001144881.1,NM_001144882.1,NM_001144883.1,NM_153026.2	,,,	23,434,6046	AA,AG,GG		0.0349,10.8261,3.6906	,,,	195/832,195/832,195/832,195/832	42862431	480,12526	2203	4300	6503	SO:0001819	synonymous_variant	144165	exon5			TACCTCGTCACAT	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.585C>T	12.37:g.42862431G>A		90	0	0		81	45	0.555556	NM_001144882	Q14C83|Q71QF8|Q96N00	Silent	SNP	ENST00000455697.1	37	CCDS8742.1																																																																																			G|0.967;A|0.033	0.033	strong		0.403	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1			A	42862431	G	A	42862431	2	1	22	1	0	0	0	0	0	0	0	1	12498	1136	40	1		1	PRICKLE1	12	42862431	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3128365	42862431	90989464	2675	5576											
PUS7L	83448	hgsc.bcm.edu	37	chr12	44130205	44130205	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttactatttgggaaattctcGtcatcaatgtcttcatccaa	11	16	5	9	1	5	0	3	0	2	0	7	1	6	1	1	1	1	0	1	1	5	5	rs12309260	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:44130205G>A	ENST00000416848.2	-	7	2192	c.1704C>T	c.(1702-1704)gaC>gaT	p.D568D	PUS7L_ENST00000431332.3_Silent_p.D255D|PUS7L_ENST00000551923.1_Silent_p.D568D|PUS7L_ENST00000344862.5_Silent_p.D568D	NM_001098615.1|NM_001271826.1	NP_001092085.1|NP_001258755.1	Q9H0K6	PUS7L_HUMAN	pseudouridylate synthase 7 homolog (S. cerevisiae)-like	568	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)		GGAAATTCTCGTCATCAATGT	0.373													G|||	61	0.0121805	0.0431	0.0043	5008	,	,		18654	0.0		0.001	False		,,,				2504	0.0				p.D568D		Atlas-SNP	.											.	PUS7L	73	.	0			c.C1704T						PASS	.	G	,,	178,4228	115.4+/-153.4	2,174,2027	158	146	150		1704,1704,1704	-5.5	0	12	dbSNP_120	150	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	PUS7L	NM_001098614.1,NM_001098615.1,NM_031292.3	,,	2,176,6325	AA,AG,GG		0.0233,4.0399,1.384	,,	568/702,568/702,568/702	44130205	180,12826	2203	4300	6503	SO:0001819	synonymous_variant	83448	exon7			ATTCTCGTCATCA	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.1704C>T	12.37:g.44130205G>A		72	0	0		96	52	0.541667	NM_001098614	B3KUJ1|Q05CU0|Q6AHZ3|Q6NUP2	Silent	SNP	ENST00000416848.2	37	CCDS8743.1																																																																																			G|0.988;A|0.012	0.012	strong		0.373	PUS7L-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403931.1	NM_031292		A	44130205	G	A	44130205	2	1	22	1	0	0	0	0	0	0	0	1	12849	1136	40	1		1	PUS7L	12	44130205	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1267774	44130205	89721690	2676	5577											
ARID2	196528	hgsc.bcm.edu	37	chr12	46245077	46245077	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cagcctgcctctggtgagtcGagtctgattaaacagcttct	8	12	10	11	1	3	2	0	2	3	0	4	3	3	2	2	1	4	1	2	1	2	2	rs7296694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:46245077G>A	ENST00000334344.6	+	15	3343	c.3171G>A	c.(3169-3171)tcG>tcA	p.S1057S	ARID2_ENST00000457135.1_5'Flank|ARID2_ENST00000422737.1_Silent_p.S908S|ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000444670.1_Silent_p.S667S	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1057	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)		CTGGTGAGTCGAGTCTGATTA	0.493			"N, S, F"		hepatocellular carcinoma								G|||	501	0.10004	0.3442	0.0202	5008	,	,		22635	0.004		0.001	False		,,,				2504	0.0276				p.S1057S		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.G3171A						PASS	.	G		1229,3177	426.4+/-341.1	182,865,1156	148	131	137		3171	-11.8	0	12	dbSNP_116	137	9,8591	6.4+/-24.3	0,9,4291	yes	coding-synonymous	ARID2	NM_152641.2		182,874,5447	AA,AG,GG		0.1047,27.8938,9.5187		1057/1836	46245077	1238,11768	2203	4300	6503	SO:0001819	synonymous_variant	196528	exon15			TGAGTCGAGTCTG		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.3171G>A	12.37:g.46245077G>A		116	0	0		120	58	0.483333	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Silent	SNP	ENST00000334344.6	37	CCDS31783.1																																																																																			G|0.905;A|0.095	0.095	strong		0.493	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		A	46245077	G	A	46245077	2	1	22	1	0	0	0	0	0	0	0	1	915	1045	37	1		1	ARID2	12	46245077	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2114872	46245077	87606818	2677	5578											
SFRS2IP	9169	hgsc.bcm.edu	37	chr12	46321417	46321417	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctgtagatctaggatgttcGgtcagcgattcattcttttc	7	17	9	8	2	5	1	2	0	3	1	7	3	5	2	0	2	1	2	0	2	2	7	rs11574971	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:46321417G>A	ENST00000369367.3	-	11	2300	c.2067C>T	c.(2065-2067)acC>acT	p.T689T	SCAF11_ENST00000549162.1_Silent_p.T497T|SCAF11_ENST00000550629.1_5'Flank|SCAF11_ENST00000465950.1_Silent_p.T374T|SCAF11_ENST00000419565.2_Silent_p.T689T	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	689					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						TAGGATGTTCGGTCAGCGATT	0.318													G|||	549	0.109625	0.3775	0.0259	5008	,	,		13728	0.004		0.002	False		,,,				2504	0.0266				p.T689T		Atlas-SNP	.											.	SCAF11	145	.	0			c.C2067T						PASS	.	G		1384,3022	457.5+/-351.6	235,914,1054	160	162	161		2067	1.9	0	12	dbSNP_120	161	14,8586	9.8+/-36.6	0,14,4286	no	coding-synonymous	SCAF11	NM_004719.2		235,928,5340	AA,AG,GG		0.1628,31.4117,10.7489		689/1464	46321417	1398,11608	2203	4300	6503	SO:0001819	synonymous_variant	9169	exon11			ATGTTCGGTCAGC	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.2067C>T	12.37:g.46321417G>A		76	0	0		90	45	0.5	NM_004719	A6NEU9|A6NLW5|Q8IW59	Silent	SNP	ENST00000369367.3	37	CCDS8748.2																																																																																			G|0.894;A|0.106	0.106	strong		0.318	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719		A	46321417	G	A	46321417	2	1	22	1	0	0	0	0	0	0	0	1	14192	1103	39	1		1	SFRS2IP	12	46321417	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	76340	46321417	87530478	2678	5579											
SFRS2IP	9169	hgsc.bcm.edu	37	chr12	46339033	46339033	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caagcaaaaagtaacttactAtgtatccacttcaagtcaca	17	10	4	10	0	2	0	2	0	0	0	3	0	3	0	1	0	3	3	1	0	8	5	rs11183245	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:46339033A>G	ENST00000369367.3	-	6	695	c.462T>C	c.(460-462)caT>caC	p.H154H	SCAF11_ENST00000419565.2_Splice_Site_p.H154H	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	154					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						GTAACTTACTATGTATCCACT	0.318													A|||	66	0.0131789	0.0477	0.0029	5008	,	,		17740	0.0		0.001	False		,,,				2504	0.0				p.H154H		Atlas-SNP	.											.	SCAF11	145	.	0			c.T462C						PASS	.	A		167,3485		4,159,1663	111	105	107		462	-1.8	0	12	dbSNP_120	107	0,8134		0,0,4067	yes	coding-synonymous-near-splice	SCAF11	NM_004719.2		4,159,5730	GG,GA,AA		0.0,4.5728,1.4169		154/1464	46339033	167,11619	1826	4067	5893	SO:0001630	splice_region_variant	9169	exon6			CTTACTATGTATC	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.463+1T>C	12.37:g.46339033A>G		97	0	0		90	42	0.466667	NM_004719	A6NEU9|A6NLW5|Q8IW59	Silent	SNP	ENST00000369367.3	37	CCDS8748.2																																																																																			A|0.972;G|0.028	0.028	strong		0.318	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719	Silent	G	46339033	A	G	46339033	5	3	22	1	0	0	0	0	0	0	1	0	14192	463	16	3	3969	3	SFRS2IP	12	46339033	Splice_Site	SNP	A	TCGA-G8-6324-01A-11D-2210-10	17616	46339033	87512862	2679	5580											
FAM113B	91523	hgsc.bcm.edu	37	chr12	47629179	47629179	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atcttgaaagagctgcagtcGggcgagcacgcccccgacct	9	6	12	14	4	1	2	0	1	1	1	2	4	1	2	3	1	3	3	3	1	1	1	rs79990001	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:47629179G>T	ENST00000546455.1	+	4	1064	c.333G>T	c.(331-333)tcG>tcT	p.S111S	RP11-493L12.3_ENST00000547748.1_RNA|PCED1B_ENST00000432328.1_Silent_p.S111S			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B	111							hydrolase activity (GO:0016787)										AGCTGCAGTCGGGCGAGCACG	0.572													G|||	122	0.024361	0.0877	0.0072	5008	,	,		17862	0.0		0.001	False		,,,				2504	0.0				p.S111S		Atlas-SNP	.											FAM113B,rectum,carcinoma,+1,1	.	.	1	0			c.G333T						PASS	.	G		310,4096	167.3+/-198.3	8,294,1901	104	116	112		333	-8.4	0	12	dbSNP_132	112	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FAM113B	NM_138371.1		8,295,6200	TT,TG,GG		0.0116,7.0359,2.3912		111/433	47629179	311,12695	2203	4300	6503	SO:0001819	synonymous_variant	91523	exon2			GCAGTCGGGCGAG	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.333G>T	12.37:g.47629179G>T		36	0	0		45	25	0.555556	NM_138371	Q96B20	Silent	SNP	ENST00000546455.1	37	CCDS8752.1																																																																																			G|0.974;T|0.026	0.026	strong		0.572	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371		T	47629179	G	T	47629179	2	4	22	1	0	0	0	0	0	0	0	1	5407	1103	39	4		4	FAM113B	12	47629179	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1290146	47629179	86222716	2680	5581											
RPAP3	79657	hgsc.bcm.edu	37	chr12	48075597	48075597	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtctttttcagcttcttcAtatctattgaacatgataaa	12	17	4	8	0	5	2	2	2	3	0	5	2	5	2	0	0	2	1	0	0	5	8	rs36123489	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:48075597A>G	ENST00000005386.3	-	10	1111	c.996T>C	c.(994-996)taT>taC	p.Y332Y	RPAP3_ENST00000432584.3_Silent_p.Y173Y|RPAP3_ENST00000380650.4_Silent_p.Y332Y	NM_024604.2	NP_078880.2	Q9H6T3	RPAP3_HUMAN	RNA polymerase II associated protein 3	332										endometrium(2)|large_intestine(4)|liver(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16	Lung SC(27;0.192)					CAGCTTCTTCATATCTATTGA	0.313													A|||	224	0.0447284	0.1566	0.0231	5008	,	,		18004	0.0		0.001	False		,,,				2504	0.0				p.Y332Y		Atlas-SNP	.											.	RPAP3	45	.	0			c.T996C						PASS	.	A	,,	647,3757	277.8+/-273.9	49,549,1604	61	59	59		996,519,996	1.9	1	12	dbSNP_126	59	12,8584	8.4+/-32.0	0,12,4286	no	coding-synonymous,coding-synonymous,coding-synonymous	RPAP3	NM_001146075.1,NM_001146076.1,NM_024604.2	,,	49,561,5890	GG,GA,AA		0.1396,14.6912,5.0692	,,	332/632,173/507,332/666	48075597	659,12341	2202	4298	6500	SO:0001819	synonymous_variant	79657	exon10			TTCTTCATATCTA	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.996T>C	12.37:g.48075597A>G		68	0	0		96	46	0.479167	NM_024604	B4DRW9|Q6PHR5	Silent	SNP	ENST00000005386.3	37	CCDS8753.1																																																																																			A|0.952;G|0.048	0.048	strong		0.313	RPAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405340.1	NM_024604		G	48075597	A	G	48075597	2	3	22	1	0	0	0	0	0	0	0	1	13558	224	8	3		3	RPAP3	12	48075597	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	446418	48075597	85776298	2681	5582											
ENDOU	8909	hgsc.bcm.edu	37	chr12	48110150	48110150	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgatctctctgaggaaggcGtcctgctcggccagctcctg	6	10	12	13	2	2	2	0	2	2	0	6	3	4	3	3	3	2	2	3	3	1	0	rs61734364	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:48110150G>A	ENST00000422538.3	-	6	806	c.684C>T	c.(682-684)gaC>gaT	p.D228D	ENDOU_ENST00000545824.2_Silent_p.D165D|ENDOU_ENST00000229003.3_Silent_p.D187D|ENDOU_ENST00000542202.1_De_novo_Start_OutOfFrame|RP1-197B17.3_ENST00000547799.1_lincRNA	NM_001172439.1	NP_001165910.1	P21128	ENDOU_HUMAN	endonuclease, polyU-specific	228					female pregnancy (GO:0007565)|immune response (GO:0006955)|proteolysis (GO:0006508)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endoribonuclease activity (GO:0004521)|growth factor activity (GO:0008083)|manganese ion binding (GO:0030145)|polysaccharide binding (GO:0030247)|RNA binding (GO:0003723)|scavenger receptor activity (GO:0005044)|serine-type peptidase activity (GO:0008236)			autonomic_ganglia(1)|endometrium(2)|large_intestine(4)|lung(2)|ovary(3)|pancreas(1)|stomach(1)	14						TGAGGAAGGCGTCCTGCTCGG	0.592											OREG0021752	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	109	0.0217652	0.0756	0.0101	5008	,	,		17569	0.001		0.001	False		,,,				2504	0.0				p.D228D		Atlas-SNP	.											.	ENDOU	39	.	0			c.C684T						PASS	.	G	,,	344,4062	180.5+/-208.7	12,320,1871	136	124	128		684,495,561	-9.6	0	12	dbSNP_129	128	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	ENDOU	NM_001172439.1,NM_001172440.1,NM_006025.3	,,	12,323,6168	AA,AG,GG		0.0349,7.8075,2.668	,,	228/411,165/348,187/370	48110150	347,12659	2203	4300	6503	SO:0001819	synonymous_variant	8909	exon6			GAAGGCGTCCTGC	M32402	CCDS8754.1, CCDS53784.1, CCDS53785.1	12q13.1	2011-08-31			ENSG00000111405	ENSG00000111405		"Serine peptidases / Serine peptidases"	14369	protein-coding gene	gene with protein product		606720				2350438, 1710108, 15755742, 18936097	Standard	NM_006025		Approved	PP11, P11, PRSS26	uc001rpu.2	P21128	OTTHUMG00000169670	ENST00000422538.3:c.684C>T	12.37:g.48110150G>A		193	0	0	952	204	93	0.455882	NM_001172439	B2RBJ3|B3KQS7|B7Z6E1|Q2NKJ4	Silent	SNP	ENST00000422538.3	37	CCDS53785.1																																																																																			A|0.024;G|0.975;T|0.000	0.024	strong		0.592	ENDOU-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000405352.1	NM_006025.2		A	48110150	G	A	48110150	2	1	22	1	0	0	0	0	0	0	0	1	5118	1136	40	1		1	ENDOU	12	48110150	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	34553	48110150	85741745	2682	5583											
RAPGEF3	10411	hgsc.bcm.edu	37	chr12	48134768	48134768	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggtccttggcactcaccAggtccagcccctcagcagag	8	6	10	17	0	2	1	2	0	0	1	4	1	4	1	6	3	2	2	6	3	0	1	rs80097705	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:48134768A>T	ENST00000449771.2	-	20	2067	c.1979T>A	c.(1978-1980)cTg>cAg	p.L660Q	RAPGEF3_ENST00000548919.1_Missense_Mutation_p.L569Q|RAPGEF3_ENST00000171000.4_Missense_Mutation_p.L618Q|RAPGEF3_ENST00000389212.3_Missense_Mutation_p.L660Q|RAPGEF3_ENST00000405493.2_Missense_Mutation_p.L618Q|RP1-197B17.3_ENST00000547799.1_lincRNA|RAPGEF3_ENST00000549151.1_Missense_Mutation_p.L618Q			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	660					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)		GGCACTCACCAGGTCCAGCCC	0.657													A|||	149	0.0297524	0.1059	0.0115	5008	,	,		15902	0.0		0.001	False		,,,				2504	0.0				p.L660Q		Atlas-SNP	.											.	RAPGEF3	98	.	0			c.T1979A						PASS	.	A	GLN/LEU,GLN/LEU,GLN/LEU	441,3965	204.5+/-226.7	16,409,1778	28	26	27		1979,1853,1853	2.8	1	12	dbSNP_131	27	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense	RAPGEF3	NM_001098531.2,NM_001098532.2,NM_006105.5	113,113,113	16,412,6075	TT,TA,AA		0.0349,10.0091,3.4138	benign,benign,benign	660/924,618/882,618/882	48134768	444,12562	2203	4300	6503	SO:0001583	missense	10411	exon20			CTCACCAGGTCCA	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.1979T>A	12.37:g.48134768A>T	ENSP00000395708:p.Leu660Gln	118	0	0		134	61	0.455224	NM_001098531	A8K2G5|E7EQC8|O95634|Q8WVN0	Missense_Mutation	SNP	ENST00000449771.2	37	CCDS41775.1	64	0.029304029304029304	60	0.12195121951219512	4	0.011049723756906077	0	0.0	0	0.0	A	15.33	2.801075	0.50315	0.100091	3.49E-4	ENSG00000079337	ENST00000405493;ENST00000449771;ENST00000541821;ENST00000549151;ENST00000171000;ENST00000389211;ENST00000389212;ENST00000397089;ENST00000548919	T;T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56;1.56	4.0	2.85	0.33270	Guanine-nucleotide dissociation stimulator CDC25 (2);Ras guanine nucleotide exchange factor, domain (1);	0.318780	0.26567	N	0.023652	T	0.00271	0.0008	N	0.25332	0.735	0.25580	P	0.9868038	B	0.13145	0.007	B	0.15484	0.013	T	0.05007	-1.0912	9	0.52906	T	0.07	.	7.9374	0.29937	0.898:0.0:0.102:0.0	.	660	O95398	RPGF3_HUMAN	Q	618;660;307;618;618;618;660;623;569	ENSP00000384521:L618Q;ENSP00000395708:L660Q;ENSP00000448619:L618Q;ENSP00000171000:L618Q;ENSP00000373864:L660Q;ENSP00000448480:L569Q	ENSP00000171000:L618Q	L	-	2	0	RAPGEF3	46421035	0.352000	0.24895	1.000000	0.80357	0.997000	0.91878	1.101000	0.31037	1.609000	0.50190	0.459000	0.35465	CTG	A|0.965;T|0.035	0.035	strong		0.657	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257848.1	NM_006105		T	48134768	A	T	48134768	3	4	22	1	0	0	0	0	1	0	0	0	13060	188	7	5	828	5	RAPGEF3	12	48134768	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	24618	48134768	85717127	2683	5584											
HDAC7	51564	hgsc.bcm.edu	37	chr12	48185449	48185449	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cgtgccgctcagagtggaccGactgcagctcttccagggag	7	7	14	13	3	2	1	1	0	1	1	3	4	3	3	3	2	3	3	3	2	0	1	rs73291234	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:48185449G>A	ENST00000427332.2	-	15	1892	c.1736C>T	c.(1735-1737)tCg>tTg	p.S579L	HDAC7_ENST00000552960.1_Missense_Mutation_p.S601L|HDAC7_ENST00000354334.3_Missense_Mutation_p.S581L|HDAC7_ENST00000380610.4_Missense_Mutation_p.S635L|HDAC7_ENST00000080059.7_Missense_Mutation_p.S618L|HDAC7_ENST00000488927.1_5'UTR			Q8WUI4	HDAC7_HUMAN	histone deacetylase 7	579	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)		AGAGTGGACCGACTGCAGCTC	0.632													G|||	51	0.0101837	0.0356	0.0058	5008	,	,		13311	0.0		0.0	False		,,,				2504	0.0				p.S618L		Atlas-SNP	.											.	HDAC7	71	.	0			c.C1853T						PASS	.	G	LEU/SER,LEU/SER	134,4272	96.2+/-134.9	4,126,2073	41	43	42		1742,1853	3.5	0.8	12	dbSNP_130	42	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	HDAC7	NM_001098416.2,NM_015401.3	145,145	4,127,6372	AA,AG,GG		0.0116,3.0413,1.038	possibly-damaging,possibly-damaging	581/955,618/992	48185449	135,12871	2203	4300	6503	SO:0001583	missense	51564	exon15			TGGACCGACTGCA	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.1736C>T	12.37:g.48185449G>A	ENSP00000404394:p.Ser579Leu	178	0	0		172	79	0.459302	NM_015401	B3KY08|B4DWI0|B4E0Q5|Q6P1W9|Q6W9G7|Q7Z4K2|Q7Z5I1|Q96K01|Q9BR73|Q9H7L0|Q9NW41|Q9NWA9|Q9NYK9|Q9UFU7	Missense_Mutation	SNP	ENST00000427332.2	37		17|17	0.007783882783882784|0.007783882783882784	15|15	0.03048780487804878|0.03048780487804878	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	G|G	16.73|16.73	3.204615|3.204615	0.58234|0.58234	0.030413|0.030413	1.16E-4|1.16E-4	ENSG00000061273|ENSG00000061273	ENST00000548080|ENST00000080059;ENST00000354334;ENST00000552960;ENST00000380610;ENST00000427332	.|T;T;T;T;T	.|0.68903	.|-0.36;-0.36;-0.36;-0.36;-0.36	5.3|5.3	3.48|3.48	0.39840|0.39840	.|.	.|0.194140	.|0.45606	.|N	.|0.000346	T|T	0.19127|0.19127	0.0459|0.0459	N|N	0.02539|0.02539	-0.55|-0.55	0.45295|0.45295	D|D	0.998291|0.998291	.|D;D;D	.|0.59767	.|0.963;0.986;0.978	.|B;P;B	.|0.48627	.|0.209;0.584;0.398	T|T	0.07654|0.07654	-1.0761|-1.0761	5|10	.|0.21540	.|T	.|0.41	.|.	7.5367|7.5367	0.27714|0.27714	0.1551:0.1369:0.708:0.0|0.1551:0.1369:0.708:0.0	.|.	.|618;601;581	.|Q8WUI4-5;Q8WUI4-6;Q8WUI4-7	.|.;.;.	W|L	59|618;581;601;635;579	.|ENSP00000080059:S618L;ENSP00000351326:S581L;ENSP00000448532:S601L;ENSP00000369984:S635L;ENSP00000404394:S579L	.|ENSP00000080059:S618L	R|S	-|-	1|2	2|0	HDAC7|HDAC7	46471716|46471716	1.000000|1.000000	0.71417|0.71417	0.765000|0.765000	0.31456|0.31456	0.970000|0.970000	0.65996|0.65996	5.572000|5.572000	0.67411|0.67411	0.759000|0.759000	0.33084|0.33084	-0.261000|-0.261000	0.10672|0.10672	CGG|TCG	G|0.989;A|0.011	0.011	strong		0.632	HDAC7-013	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000328804.2			A	48185449	G	A	48185449	3	1	22	1	0	0	0	0	1	0	0	0	7021	1059	37	1	1170	1	HDAC7	12	48185449	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	50681	48185449	85666446	2684	5585											
C12orf68	387856	hgsc.bcm.edu	37	chr12	48577925	48577925	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatggaggacggtctgctggAgatcatgaccaaggacggcg	11	6	16	8	3	2	2	1	1	1	1	2	6	2	5	1	6	1	1	1	6	2	0	rs140861476		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:48577925A>G	ENST00000316554.3	+	1	560	c.20A>G	c.(19-21)gAg>gGg	p.E7G		NM_001013635.3	NP_001013657.3	Q52MB2	CC184_HUMAN		7						cytoplasm (GO:0005737)				central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)	4						GGTCTGCTGGAGATCATGACC	0.706																																					p.E7G		Atlas-SNP	.											.	C12orf68	11	.	0			c.A20G						PASS	.	A	GLY/GLU	3,4403		0,3,2200	28	36	33		20	4.9	1	12	dbSNP_134	33	0,8598		0,0,4299	no	missense	C12orf68	NM_001013635.3	98	0,3,6499	GG,GA,AA		0.0,0.0681,0.0231	benign	7/195	48577925	3,13001	2203	4299	6502	SO:0001583	missense	387856	exon1			TGCTGGAGATCAT																												ENST00000316554.3:c.20A>G	12.37:g.48577925A>G	ENSP00000320849:p.Glu7Gly	49	0	0		47	22	0.468085	NM_001013635	Q96MK5|Q96N39	Missense_Mutation	SNP	ENST00000316554.3	37	CCDS31785.1	.	.	.	.	.	.	.	.	.	.	A	14.73	2.623833	0.46840	6.81E-4	0.0	ENSG00000177875	ENST00000316554	T	0.57273	0.41	4.9	4.9	0.64082	.	0.000000	0.52532	D	0.000075	T	0.50939	0.1645	N	0.08118	0	0.35002	D	0.756066	D	0.76494	0.999	D	0.78314	0.991	T	0.66304	-0.5957	10	0.87932	D	0	-21.6442	10.8402	0.46710	1.0:0.0:0.0:0.0	.	7	Q52MB2	CL068_HUMAN	G	7	ENSP00000320849:E7G	ENSP00000320849:E7G	E	+	2	0	C12orf68	46864192	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.151000	0.58105	2.049000	0.60858	0.491000	0.48974	GAG	A|1.000;G|0.000	0.000	weak		0.706	C12orf68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406514.1			G	48577925	A	G	48577925	3	3	22	1	0	0	0	0	1	0	0	0	1712	304	11	3	22	3	C12orf68	12	48577925	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	392476	48577925	85273970	2685	5586											
CCDC65	85478	hgsc.bcm.edu	37	chr12	49308261	49308261	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	agccacttgcacaatgttgaCcagctcttggccctgcagag	9	9	10	13	0	1	2	0	1	1	1	1	2	1	2	3	1	4	4	3	1	1	3	rs143088014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49308261C>T	ENST00000320516.4	+	3	563	c.375C>T	c.(373-375)gaC>gaT	p.D125D	RP11-302B13.5_ENST00000398092.4_Intron|CCDC65_ENST00000266984.5_Silent_p.D125D	NM_033124.4	NP_149115.2	Q8IXS2	CCD65_HUMAN	coiled-coil domain containing 65	125										breast(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	15						ACAATGTTGACCAGCTCTTGG	0.537													C|||	8	0.00159744	0.0053	0.0014	5008	,	,		17358	0.0		0.0	False		,,,				2504	0.0				p.D125D		Atlas-SNP	.											.	CCDC65	41	.	0			c.C375T						PASS	.	C		15,4391	22.3+/-47.3	0,15,2188	85	74	78		375	1.2	1	12	dbSNP_134	78	1,8599		0,1,4299	no	coding-synonymous	CCDC65	NM_033124.4		0,16,6487	TT,TC,CC		0.0116,0.3404,0.123		125/485	49308261	16,12990	2203	4300	6503	SO:0001819	synonymous_variant	85478	exon3			TGTTGACCAGCTC		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.375C>T	12.37:g.49308261C>T		62	0	0		67	25	0.373134	NM_033124	A6NJG5|B2RBE2|Q8N7G4|Q8NA91|Q96JA0	Silent	SNP	ENST00000320516.4	37	CCDS8772.1																																																																																			C|0.999;T|0.001	0.001	strong		0.537	CCDC65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408922.1	NM_033124		T	49308261	C	T	49308261	2	4	22	1	0	0	0	0	0	0	0	1	2839	506	18	2		2	CCDC65	12	49308261	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	730336	49308261	84543634	2686	5587											
CCDC65	85478	hgsc.bcm.edu	37	chr12	49310831	49310831	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gccatggagcagaactatatAgattctgagtatgaaagcaa	16	9	10	6	0	1	4	0	2	1	2	1	5	1	5	1	1	3	3	1	1	7	5	rs140228766	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49310831A>G	ENST00000320516.4	+	4	737	c.549A>G	c.(547-549)atA>atG	p.I183M	RP11-302B13.5_ENST00000398092.4_Intron|CCDC65_ENST00000266984.5_Missense_Mutation_p.I183M	NM_033124.4	NP_149115.2	Q8IXS2	CCD65_HUMAN	coiled-coil domain containing 65	183										breast(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	15						AGAACTATATAGATTCTGAGT	0.433													A|||	8	0.00159744	0.0053	0.0014	5008	,	,		21739	0.0		0.0	False		,,,				2504	0.0				p.I183M		Atlas-SNP	.											.	CCDC65	41	.	0			c.A549G						PASS	.	A	MET/ILE	15,4391	22.3+/-47.3	0,15,2188	107	95	99		549	-3.4	0	12	dbSNP_134	99	1,8599		0,1,4299	yes	missense	CCDC65	NM_033124.4	10	0,16,6487	GG,GA,AA		0.0116,0.3404,0.123	benign	183/485	49310831	16,12990	2203	4300	6503	SO:0001583	missense	85478	exon4			CTATATAGATTCT		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.549A>G	12.37:g.49310831A>G	ENSP00000312706:p.Ile183Met	143	0	0		175	68	0.388571	NM_033124	A6NJG5|B2RBE2|Q8N7G4|Q8NA91|Q96JA0	Missense_Mutation	SNP	ENST00000320516.4	37	CCDS8772.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	A	11.22	1.573482	0.28092	0.003404	1.16E-4	ENSG00000139537	ENST00000266984;ENST00000320516	T;T	0.02472	4.28;4.28	5.32	-3.4	0.04853	.	0.540717	0.18922	N	0.127459	T	0.01454	0.0047	L	0.44542	1.39	0.21220	N	0.999755	B	0.02656	0.0	B	0.06405	0.002	T	0.40059	-0.9583	10	0.46703	T	0.11	-3.8361	1.8254	0.03119	0.4013:0.2222:0.2683:0.1081	.	183	Q8IXS2	CCD65_HUMAN	M	183	ENSP00000266984:I183M;ENSP00000312706:I183M	ENSP00000266984:I183M	I	+	3	3	CCDC65	47597098	0.000000	0.05858	0.049000	0.19019	0.979000	0.70002	-0.846000	0.04336	-0.658000	0.05366	-0.274000	0.10170	ATA	A|0.999;G|0.001	0.001	strong		0.433	CCDC65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408922.1	NM_033124		G	49310831	A	G	49310831	3	3	22	1	0	0	0	0	1	0	0	0	2839	410	15	3	563	3	CCDC65	12	49310831	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2570	49310831	84541064	2687	5588											
FKBP11	51303	hgsc.bcm.edu	37	chr12	49315821	49315821	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgagcttctttttggagacTttgggtctattggcctttct	4	20	10	7	0	3	2	0	1	3	1	3	3	3	2	1	3	1	1	1	3	1	8	rs148302547	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49315821T>C	ENST00000550765.1	-	6	950	c.552A>G	c.(550-552)aaA>aaG	p.K184K	FKBP11_ENST00000444214.2_Silent_p.K82K|RP11-302B13.5_ENST00000398092.4_Intron|CCDC65_ENST00000266984.5_Intron|AC073610.5_ENST00000537495.1_3'UTR	NM_016594.2	NP_057678.1	Q9NYL4	FKB11_HUMAN	FK506 binding protein 11, 19 kDa	184					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						TTTTGGAGACTTTGGGTCTAT	0.403													T|||	8	0.00159744	0.0053	0.0014	5008	,	,		18104	0.0		0.0	False		,,,				2504	0.0				p.K184K		Atlas-SNP	.											FKBP11,colon,carcinoma,-1,1	FKBP11	12	1	0			c.A552G						PASS	.	T	,	15,4391	15.5+/-35.6	0,15,2188	90	91	91		246,552	4.7	1	12	dbSNP_134	91	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous	FKBP11	NM_001143781.1,NM_016594.2	,	0,16,6487	CC,CT,TT		0.0116,0.3404,0.123	,	82/100,184/202	49315821	16,12990	2203	4300	6503	SO:0001819	synonymous_variant	51303	exon6			GGAGACTTTGGGT	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.552A>G	12.37:g.49315821T>C		75	0	0		60	29	0.483333	NM_016594	B4DWB7	Silent	SNP	ENST00000550765.1	37	CCDS8773.1																																																																																			T|0.999;C|0.001	0.001	strong		0.403	FKBP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408927.1	NM_016594		C	49315821	T	C	49315821	2	2	22	1	0	0	0	0	0	0	0	1	5911	1606	56	3		3	FKBP11	12	49315821	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	4990	49315821	84536074	2688	5589											
MLL2	8085	hgsc.bcm.edu	37	chr12	49433356	49433356	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctcctgccgcagggtgttGcgctggatctgctgccgaat	4	12	13	12	3	2	0	0	0	2	0	3	2	2	1	3	2	4	4	3	2	1	2	rs116686402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49433356G>A	ENST00000301067.7	-	32	8090	c.8091C>T	c.(8089-8091)cgC>cgT	p.R2697R	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2697					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)										GCAGGGTGTTGCGCTGGATCT	0.587													G|||	93	0.0185703	0.0696	0.0014	5008	,	,		18946	0.0		0.0	False		,,,				2504	0.0				p.R2697R		Atlas-SNP	.											.	MLL2	1173	.	0			c.C8091T						PASS	.	G		239,3787		8,223,1782	17	19	18		8091	0.2	1	12	dbSNP_132	18	2,8382		0,2,4190	no	coding-synonymous	MLL2	NM_003482.3		8,225,5972	AA,AG,GG		0.0239,5.9364,1.942		2697/5538	49433356	241,12169	2013	4192	6205	SO:0001819	synonymous_variant	8085	exon32			GGTGTTGCGCTGG	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.8091C>T	12.37:g.49433356G>A		30	0	0		43	17	0.395349	NM_003482	O14687	Silent	SNP	ENST00000301067.7	37	CCDS44873.1																																																																																			G|0.986;A|0.014	0.014	strong		0.587	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49433356	G	A	49433356	2	1	22	1	0	0	0	0	0	0	0	1	9630	1306	46	2		2	MLL2	12	49433356	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	117535	49433356	84418539	2689	5590											
LMBR1L	55716	hgsc.bcm.edu	37	chr12	49498635	49498635	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aggagcaggacagcacccagGgcaattgccagggtaaaggt	13	4	15	9	0	0	0	0	0	0	0	0	2	0	2	2	5	3	4	2	5	3	2	rs141166526	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49498635G>T	ENST00000267102.8	-	4	567	c.225C>A	c.(223-225)gcC>gcA	p.A75A	LMBR1L_ENST00000395141.4_Silent_p.A70A|LMBR1L_ENST00000547382.1_Silent_p.A75A|LMBR1L_ENST00000553204.1_5'UTR	NM_018113.2	NP_060583.2	Q6UX01	LMBRL_HUMAN	limb development membrane protein 1-like	75	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						CAGCACCCAGGGCAATTGCCA	0.587													G|||	22	0.00439297	0.0166	0.0	5008	,	,		22882	0.0		0.0	False		,,,				2504	0.0				p.A75A		Atlas-SNP	.											LMBR1L_ENST00000267102,colon,carcinoma,-1,2	LMBR1L	61	2	0			c.C225A						PASS	.	G		50,4356	48.9+/-83.8	0,50,2153	108	78	88		225	5.2	1	12	dbSNP_134	88	0,8600		0,0,4300	no	coding-synonymous	LMBR1L	NM_018113.2		0,50,6453	TT,TG,GG		0.0,1.1348,0.3844		75/490	49498635	50,12956	2203	4300	6503	SO:0001819	synonymous_variant	55716	exon4			ACCCAGGGCAATT	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.225C>A	12.37:g.49498635G>T		76	0	0		67	33	0.492537	NM_018113	Q969J4|Q96BY8|Q96HN8|Q9NT09|Q9NVE1|Q9NVU9|Q9ULP6	Silent	SNP	ENST00000267102.8	37	CCDS8780.2																																																																																			G|0.996;T|0.004	0.004	strong		0.587	LMBR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318696.1	NM_018113		T	49498635	G	T	49498635	2	4	22	1	0	0	0	0	0	0	0	1	8850	1219	43	4		4	LMBR1L	12	49498635	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	65279	49498635	84353260	2690	5591											
FAM186B	84070	hgsc.bcm.edu	37	chr12	49994658	49994658	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	ctgtatttggtctccaggctCctgttctccttgtgttggag	3	17	11	10	0	2	0	0	0	2	0	5	1	3	1	3	3	0	4	3	3	1	5	rs74086906	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49994658C>G	ENST00000257894.2	-	4	926	c.765G>C	c.(763-765)agG>agC	p.R255S	PRPF40B_ENST00000508736.1_3'UTR|FAM186B_ENST00000551047.1_Intron|FAM186B_ENST00000544141.1_Missense_Mutation_p.R165S	NM_032130.2	NP_115506.1	Q8IYM0	F186B_HUMAN	family with sequence similarity 186, member B	255						protein complex (GO:0043234)				breast(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						TCTCCAGGCTCCTGTTCTCCT	0.557													C|||	200	0.0399361	0.1445	0.0115	5008	,	,		20376	0.0		0.001	False		,,,				2504	0.0				p.R255S		Atlas-SNP	.											.	FAM186B	72	.	0			c.G765C						PASS	.	C	SER/ARG	471,3935	223.9+/-240.3	27,417,1759	118	107	111		765	-3.4	0	12	dbSNP_130	111	2,8598	1.2+/-3.3	0,2,4298	yes	missense	FAM186B	NM_032130.2	110	27,419,6057	GG,GC,CC		0.0233,10.69,3.6368	benign	255/894	49994658	473,12533	2203	4300	6503	SO:0001583	missense	84070	exon4			CAGGCTCCTGTTC	AL136748	CCDS8788.1	12q13.12	2008-09-17	2008-09-17	2008-09-17	ENSG00000135436	ENSG00000135436			25296	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 25"	C12orf25		11230166	Standard	NM_032130		Approved	DKFZP434J0113	uc001ruo.3	Q8IYM0	OTTHUMG00000167427	ENST00000257894.2:c.765G>C	12.37:g.49994658C>G	ENSP00000257894:p.Arg255Ser	283	0	0		288	114	0.395833	NM_032130	B4DZ15|Q8TCP7|Q9H0L3	Missense_Mutation	SNP	ENST00000257894.2	37	CCDS8788.1	85	0.03891941391941392	77	0.1565040650406504	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	C	9.727	1.161124	0.21538	0.1069	2.33E-4	ENSG00000135436	ENST00000544141;ENST00000257894	T;T	0.13307	2.6;2.81	5.35	-3.38	0.04883	.	0.418099	0.20622	N	0.088744	T	0.00039	0.0001	L	0.29908	0.895	0.80722	P	0.0	B;B	0.28783	0.222;0.024	B;B	0.20955	0.032;0.015	T	0.37619	-0.9698	8	.	.	.	-11.8042	1.6749	0.02820	0.1249:0.2948:0.1626:0.4177	.	165;255	B4DZ15;Q8IYM0	.;F186B_HUMAN	S	165;255	ENSP00000438569:R165S;ENSP00000257894:R255S	.	R	-	3	2	FAM186B	48280925	0.000000	0.05858	0.019000	0.16419	0.986000	0.74619	-0.460000	0.06720	-0.364000	0.08088	-0.157000	0.13467	AGG	C|0.964;G|0.036	0.036	strong		0.557	FAM186B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394583.2	NM_032130		G	49994658	C	G	49994658	3	3	22	1	0	0	0	0	1	0	0	0	5517	854	30	4	1932	4	FAM186B	12	49994658	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	496023	49994658	83857237	2691	5592											
TMBIM6	7009	hgsc.bcm.edu	37	chr12	50153060	50153060	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcgtcctttttgatactcaActcattattgaaaaggccga	11	15	6	9	2	2	2	2	2	0	0	4	3	3	2	2	1	2	0	2	1	5	6	rs12310796	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:50153060A>G	ENST00000267115.5	+	8	655	c.570A>G	c.(568-570)caA>caG	p.Q190Q	TMBIM6_ENST00000423828.1_Silent_p.Q248Q|TMBIM6_ENST00000549385.1_Silent_p.Q190Q|TMBIM6_ENST00000547798.1_Silent_p.Q153Q|TMBIM6_ENST00000395006.4_Silent_p.Q190Q|TMBIM6_ENST00000552699.1_Silent_p.Q248Q	NM_003217.2	NP_003208.2	P55061	BI1_HUMAN	transmembrane BAX inhibitor motif containing 6	190					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						TTGATACTCAACTCATTATTG	0.418													A|||	27	0.00539137	0.0204	0.0	5008	,	,		20350	0.0		0.0	False		,,,				2504	0.0				p.Q248Q		Atlas-SNP	.											.	TMBIM6	26	.	0			c.A744G						PASS	.	A	,	81,4325	69.2+/-107.0	0,81,2122	212	192	199		744,570	3	1	12	dbSNP_120	199	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	TMBIM6	NM_001098576.1,NM_003217.2	,	0,81,6422	GG,GA,AA		0.0,1.8384,0.6228	,	248/296,190/238	50153060	81,12925	2203	4300	6503	SO:0001819	synonymous_variant	7009	exon8			TACTCAACTCATT	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.570A>G	12.37:g.50153060A>G		142	0	0		128	58	0.453125	NM_001098576	B2R5M4|F8W034|O14938|Q643A7|Q96J50	Silent	SNP	ENST00000267115.5	37	CCDS31797.1																																																																																			A|0.993;G|0.007	0.007	strong		0.418	TMBIM6-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405289.1	NM_003217		G	50153060	A	G	50153060	2	3	22	1	0	0	0	0	0	0	0	1	15998	40	2	3		3	TMBIM6	12	50153060	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	158402	50153060	83698835	2692	5593											
AQP2	359	hgsc.bcm.edu	37	chr12	50344958	50344958	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccagcagacatccgcggggaCctggctgtcaatgctgtgag	8	7	14	12	2	1	2	1	1	0	1	2	3	2	3	3	3	2	3	3	3	1	0	rs60629501	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:50344958C>T	ENST00000199280.3	+	1	430	c.345C>T	c.(343-345)gaC>gaT	p.D115D	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)	115					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						TCCGCGGGGACCTGGCTGTCA	0.627													C|||	61	0.0121805	0.0431	0.0058	5008	,	,		18198	0.0		0.0	False		,,,				2504	0.0				p.D115D		Atlas-SNP	.											.	AQP2	34	.	0			c.C345T						PASS	.	C		173,4225		2,169,2028	16	17	17		345	0.7	1	12	dbSNP_129	17	0,8590		0,0,4295	no	coding-synonymous	AQP2	NM_000486.5		2,169,6323	TT,TC,CC		0.0,3.9336,1.332		115/272	50344958	173,12815	2199	4295	6494	SO:0001819	synonymous_variant	359	exon1			CGGGGACCTGGCT		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.345C>T	12.37:g.50344958C>T		69	0	0		83	43	0.518072	NM_000486	Q9UD68	Silent	SNP	ENST00000199280.3	37	CCDS8792.1																																																																																			C|0.988;T|0.012	0.012	strong		0.627	AQP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405540.1	NM_000486		T	50344958	C	T	50344958	2	4	22	1	0	0	0	0	0	0	0	1	826	506	18	2		2	AQP2	12	50344958	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	191898	50344958	83506937	2693	5594											
RACGAP1	29127	hgsc.bcm.edu	37	chr12	50384469	50384469	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaggccaattctgcatacctAggagtgttcttggtgagggt	9	12	13	7	0	2	1	0	1	2	0	2	2	2	2	2	4	2	2	2	4	4	5	rs56699050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:50384469A>G	ENST00000427314.2	-	18	2044	c.1821T>C	c.(1819-1821)ccT>ccC	p.P607P	RACGAP1_ENST00000434422.1_Silent_p.P607P|RACGAP1_ENST00000454520.2_Silent_p.P607P|RACGAP1_ENST00000548961.1_Intron|RACGAP1_ENST00000547905.1_Silent_p.P607P|RACGAP1_ENST00000551016.1_Silent_p.P607P|RACGAP1_ENST00000312377.5_Silent_p.P607P	NM_013277.3	NP_037409.2			Rac GTPase activating protein 1											cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(6)	14						CTGCATACCTAGGAGTGTTCT	0.403													G|||	407	0.08127	0.2988	0.0173	5008	,	,		18804	0.0		0.0	False		,,,				2504	0.0				p.P607P		Atlas-SNP	.											.	RACGAP1	36	.	0			c.T1821C						PASS	.	G	,,	1092,3314	721.2+/-409.1	136,820,1247	106	109	108		1821,1821,1821	2.9	1	12	dbSNP_129	108	5,8595	819.1+/-406.8	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	RACGAP1	NM_001126103.1,NM_001126104.1,NM_013277.3	,,	136,825,5542	GG,GA,AA		0.0581,24.7844,8.4346	,,	607/633,607/633,607/633	50384469	1097,11909	2203	4300	6503	SO:0001819	synonymous_variant	29127	exon18			ATACCTAGGAGTG		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.1821T>C	12.37:g.50384469A>G		136	0	0		132	70	0.530303	NM_013277		Silent	SNP	ENST00000427314.2	37	CCDS8795.1																																																																																			A|0.918;G|0.082	0.082	strong		0.403	RACGAP1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405997.1	NM_013277		G	50384469	A	G	50384469	2	3	22	1	0	0	0	0	0	0	0	1	12992	407	15	3		3	RACGAP1	12	50384469	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	39511	50384469	83467426	2694	5595											
RACGAP1	29127	hgsc.bcm.edu	37	chr12	50384542	50384542	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggagtcttgagaagctgaTgttcaggagtggtcacaggt	11	10	15	5	0	3	2	2	2	1	1	3	5	3	4	0	4	1	2	0	4	2	2	rs140590023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:50384542T>C	ENST00000427314.2	-	18	1971	c.1748A>G	c.(1747-1749)cAt>cGt	p.H583R	RACGAP1_ENST00000434422.1_Missense_Mutation_p.H583R|RACGAP1_ENST00000454520.2_Missense_Mutation_p.H583R|RACGAP1_ENST00000548961.1_Intron|RACGAP1_ENST00000547905.1_Missense_Mutation_p.H583R|RACGAP1_ENST00000551016.1_Missense_Mutation_p.H583R|RACGAP1_ENST00000312377.5_Missense_Mutation_p.H583R	NM_013277.3	NP_037409.2			Rac GTPase activating protein 1											cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(6)	14						GAGAAGCTGATGTTCAGGAGT	0.448													T|||	7	0.00139776	0.0053	0.0	5008	,	,		18657	0.0		0.0	False		,,,				2504	0.0				p.H583R		Atlas-SNP	.											.	RACGAP1	36	.	0			c.A1748G						PASS	.	T	ARG/HIS,ARG/HIS,ARG/HIS	24,4382	30.8+/-60.4	0,24,2179	99	100	100		1748,1748,1748	4.3	1	12	dbSNP_134	100	0,8600		0,0,4300	yes	missense,missense,missense	RACGAP1	NM_001126103.1,NM_001126104.1,NM_013277.3	29,29,29	0,24,6479	CC,CT,TT		0.0,0.5447,0.1845	benign,benign,benign	583/633,583/633,583/633	50384542	24,12982	2203	4300	6503	SO:0001583	missense	29127	exon18			AGCTGATGTTCAG		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.1748A>G	12.37:g.50384542T>C	ENSP00000404190:p.His583Arg	159	0	0		167	67	0.401198	NM_013277		Missense_Mutation	SNP	ENST00000427314.2	37	CCDS8795.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	10.23	1.292278	0.23564	0.005447	0.0	ENSG00000161800	ENST00000427314;ENST00000312377;ENST00000434422;ENST00000454520;ENST00000551016;ENST00000547905	T;T;T;T;T;T	0.25250	1.81;1.81;1.81;1.81;1.81;1.81	5.44	4.26	0.50523	.	0.261377	0.45606	D	0.000346	T	0.12347	0.0300	L	0.40543	1.245	0.32252	N	0.571354	B	0.02656	0.0	B	0.04013	0.001	T	0.21042	-1.0257	10	0.12103	T	0.63	-5.0933	7.5935	0.28035	0.1299:0.0708:0.0:0.7993	.	583	Q9H0H5	RGAP1_HUMAN	R	583	ENSP00000404190:H583R;ENSP00000309871:H583R;ENSP00000413241:H583R;ENSP00000404808:H583R;ENSP00000449374:H583R;ENSP00000449370:H583R	ENSP00000309871:H583R	H	-	2	0	RACGAP1	48670809	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.825000	0.62708	0.955000	0.37878	0.533000	0.62120	CAT	T|0.998;C|0.002	0.002	strong		0.448	RACGAP1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405997.1	NM_013277		C	50384542	T	C	50384542	3	2	22	1	0	0	0	0	1	0	0	0	12992	1464	51	3	158	3	RACGAP1	12	50384542	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	73	50384542	83467353	2695	5596											
GPD1	2819	hgsc.bcm.edu	37	chr12	50498475	50498475	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaaaaagctgactgagatcAtcaacacgcagcatgagaat	17	6	9	9	1	2	3	2	3	0	2	2	5	2	3	0	0	3	4	0	0	4	0	rs2232202	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:50498475A>G	ENST00000301149.3	+	2	392	c.160A>G	c.(160-162)Atc>Gtc	p.I54V	GPD1_ENST00000547190.1_3'UTR|GPD1_ENST00000548814.1_Missense_Mutation_p.I54V	NM_001257199.1|NM_005276.3	NP_001244128.1|NP_005267.2	P21695	GPDA_HUMAN	glycerol-3-phosphate dehydrogenase 1 (soluble)	54			I -> V (in dbSNP:rs2232202). {ECO:0000269|PubMed:22226083}.		cellular lipid metabolic process (GO:0044255)|cellular response to cAMP (GO:0071320)|cellular response to tumor necrosis factor (GO:0071356)|gluconeogenesis (GO:0006094)|glycerol-3-phosphate catabolic process (GO:0046168)|glycerophosphate shuttle (GO:0006127)|glycerophospholipid biosynthetic process (GO:0046474)|NADH oxidation (GO:0006116)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of glycolytic process (GO:0045821)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycerol-3-phosphate dehydrogenase complex (GO:0009331)|mitochondrion (GO:0005739)	glycerol-3-phosphate dehydrogenase [NAD+] activity (GO:0004367)|glycerol-3-phosphate dehydrogenase activity (GO:0004368)|NAD binding (GO:0051287)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8						GACTGAGATCATCAACACGCA	0.542													A|||	56	0.0111821	0.0424	0.0	5008	,	,		20418	0.0		0.0	False		,,,				2504	0.0				p.I54V	NSCLC(141;1402 1905 9497 13391 44868)	Atlas-SNP	.											.	GPD1	23	.	0			c.A160G						PASS	.	A	VAL/ILE	177,4229	115.4+/-153.4	7,163,2033	126	112	117		160	5.7	1	12	dbSNP_98	117	1,8599		0,1,4299	yes	missense	GPD1	NM_005276.2	29	7,164,6332	GG,GA,AA		0.0116,4.0172,1.3686	probably-damaging	54/350	50498475	178,12828	2203	4300	6503	SO:0001583	missense	2819	exon2			GAGATCATCAACA		CCDS8799.1, CCDS58229.1	12q13.12	2013-09-20			ENSG00000167588	ENSG00000167588	1.1.1.8		4455	protein-coding gene	gene with protein product		138420					Standard	NM_005276		Approved		uc001rvz.4	P21695	OTTHUMG00000169813	ENST00000301149.3:c.160A>G	12.37:g.50498475A>G	ENSP00000301149:p.Ile54Val	130	0	0		98	41	0.418367	NM_005276	F8W1L5|Q8N1B0	Missense_Mutation	SNP	ENST00000301149.3	37	CCDS8799.1	22	0.010073260073260074	22	0.044715447154471545	0	0.0	0	0.0	0	0.0	A	26.3	4.724233	0.89298	0.040172	1.16E-4	ENSG00000167588	ENST00000301149;ENST00000547190;ENST00000548814	T;T	0.63913	-0.07;0.53	5.7	5.7	0.88788	Glycerol-3-phosphate dehydrogenase, NAD-dependent, N-terminal (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.57592	0.2064	M	0.89287	3.02	0.80722	D	1	D;D;D	0.76494	0.986;0.999;0.998	P;D;D	0.85130	0.908;0.99;0.997	T	0.78267	-0.2270	10	0.87932	D	0	-16.3048	16.2858	0.82720	1.0:0.0:0.0:0.0	rs2232202;rs52818556;rs2232202	54;54;54	B4DJ37;F8W1L5;P21695	.;.;GPDA_HUMAN	V	54	ENSP00000301149:I54V;ENSP00000446768:I54V	ENSP00000301149:I54V	I	+	1	0	GPD1	48784742	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.458000	0.80787	2.313000	0.78055	0.454000	0.30748	ATC	A|0.984;G|0.016	0.016	strong		0.542	GPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406018.1			G	50498475	A	G	50498475	3	3	22	1	0	0	0	0	1	0	0	0	6612	217	8	3	166	3	GPD1	12	50498475	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	113933	50498475	83353420	2696	5597											
SLC4A8	9498	hgsc.bcm.edu	37	chr12	51855009	51855009	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttttgtttatcttattgggTccagtagggaaaggtcagca	9	16	11	5	0	2	0	1	0	1	0	3	1	3	1	1	3	1	3	1	3	4	7	rs150970094	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:51855009T>G	ENST00000453097.2	+	9	1252	c.1035T>G	c.(1033-1035)ggT>ggG	p.G345G	SLC4A8_ENST00000514353.3_Silent_p.G292G|SLC4A8_ENST00000358657.3_Silent_p.G372G|SLC4A8_ENST00000535225.2_Silent_p.G292G|SLC4A8_ENST00000394856.1_Silent_p.G292G	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)		TCTTATTGGGTCCAGTAGGGA	0.398													T|||	18	0.00359425	0.0136	0.0	5008	,	,		18676	0.0		0.0	False		,,,				2504	0.0				p.G345G		Atlas-SNP	.											SLC4A8,back,malignant_melanoma,+2,1	SLC4A8	292	1	0			c.T1035G						PASS	.	T	,	38,4368	42.3+/-75.8	0,38,2165	155	142	147		1035,1035	-2.6	1	12	dbSNP_134	147	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SLC4A8	NM_001039960.1,NM_004858.2	,	0,38,6465	GG,GT,TT		0.0,0.8625,0.2922	,	345/1094,345/1045	51855009	38,12968	2203	4300	6503	SO:0001819	synonymous_variant	9498	exon9			ATTGGGTCCAGTA	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.1035T>G	12.37:g.51855009T>G		151	0	0		164	78	0.47561	NM_001039960		Silent	SNP	ENST00000453097.2	37	CCDS44890.1																																																																																			T|0.997;G|0.003	0.003	strong		0.398	SLC4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404356.1	NM_004858		G	51855009	T	G	51855009	2	3	22	1	0	0	0	0	0	0	0	1	14674	1654	58	5		5	SLC4A8	12	51855009	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1356534	51855009	81996886	2697	5598											
ANKRD33	341405	hgsc.bcm.edu	37	chr12	52282865	52282865	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cctcagacaggcctcatggtCgcatgctaccacggcttcca	8	8	9	16	2	2	1	2	0	0	1	4	1	3	1	4	3	2	3	4	3	1	2	rs35851809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52282865C>T	ENST00000340970.4	+	3	377	c.6C>T	c.(4-6)gtC>gtT	p.V2V	ANKRD33_ENST00000547119.1_3'UTR|ANKRD33_ENST00000538991.1_Intron|ANKRD33_ENST00000301190.6_Silent_p.V137V			Q7Z3H0	ANR33_HUMAN	ankyrin repeat domain 33	2					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|skeletal muscle cell differentiation (GO:0035914)	cytosol (GO:0005829)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	22				BRCA - Breast invasive adenocarcinoma(357;0.0969)		GCCTCATGGTCGCATGCTACC	0.607													c|||	7	0.00139776	0.0053	0.0	5008	,	,		18277	0.0		0.0	False		,,,				2504	0.0				p.V137V		Atlas-SNP	.											.	ANKRD33	33	.	0			c.C411T						PASS	.	T	,	29,4377	35.2+/-66.4	1,27,2175	91	96	95		6,411	-1.1	0.7	12	dbSNP_126	95	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ANKRD33	NM_001130015.1,NM_182608.3	,	1,27,6475	TT,TC,CC		0.0,0.6582,0.223	,	2/273,137/453	52282865	29,12977	2203	4300	6503	SO:0001819	synonymous_variant	341405	exon3			CATGGTCGCATGC		CCDS8815.1, CCDS44892.1	12q13.13	2013-01-10	2005-01-07	2005-01-07		ENSG00000167612		"Ankyrin repeat domain containing"	13788	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 7"	C12orf7		20026326	Standard	NM_182608		Approved	DKFZp686O1689, PANKY	uc001rzd.3	Q7Z3H0	OTTHUMG00000169506	ENST00000340970.4:c.6C>T	12.37:g.52282865C>T		135	0	0		93	42	0.451613	NM_182608	Q0VAA7|Q5K619|Q5K621|Q5K622|Q5K623|Q5K624|Q6ZUN0	Silent	SNP	ENST00000340970.4	37	CCDS44892.1																																																																																			C|0.998;T|0.002	0.002	strong		0.607	ANKRD33-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404515.1	NM_182608		T	52282865	C	T	52282865	2	4	22	1	0	0	0	0	0	0	0	1	661	871	31	1		1	ANKRD33	12	52282865	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	427856	52282865	81569030	2698	5599											
ACVRL1	94	hgsc.bcm.edu	37	chr12	52306898	52306898	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaggagaccctgtgaagcCgtctcggggcccgctggtga	6	7	15	13	3	1	3	0	2	1	1	3	4	2	3	4	4	1	1	4	4	1	0	rs199542304	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52306898C>T	ENST00000388922.4	+	3	360	c.77C>T	c.(76-78)cCg>cTg	p.P26L	ACVRL1_ENST00000550683.1_Missense_Mutation_p.P40L|ACVRL1_ENST00000419526.2_Intron	NM_000020.2	NP_000011.2	P37023	ACVL1_HUMAN	activin A receptor type II-like 1	26					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)	CCTGTGAAGCCGTCTCGGGGC	0.657													C|||	2	0.000399361	0.0	0.0	5008	,	,		14365	0.002		0.0	False		,,,				2504	0.0				p.P26L		Atlas-SNP	.											.	ACVRL1	60	.	0			c.C77T						PASS	.	C	LEU/PRO,LEU/PRO	1,4371		0,1,2185	13	15	14		77,77	5.8	0.9	12		14	1,8567		0,1,4283	yes	missense,missense	ACVRL1	NM_000020.2,NM_001077401.1	98,98	0,2,6468	TT,TC,CC		0.0117,0.0229,0.0155	possibly-damaging,possibly-damaging	26/504,26/504	52306898	2,12938	2186	4284	6470	SO:0001583	missense	94	exon3			TGAAGCCGTCTCG	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.77C>T	12.37:g.52306898C>T	ENSP00000373574:p.Pro26Leu	24	0	0		42	12	0.285714	NM_000020	A6NGA8	Missense_Mutation	SNP	ENST00000388922.4	37	CCDS31804.1	.	.	.	.	.	.	.	.	.	.	C	17.59	3.427822	0.62733	2.29E-4	1.17E-4	ENSG00000139567	ENST00000388922;ENST00000267008;ENST00000547400;ENST00000550683	D;D;D	0.92149	-2.98;-2.98;-2.98	5.76	5.76	0.90799	.	0.343290	0.21467	N	0.074075	T	0.80649	0.4663	N	0.08118	0	0.80722	D	1	P	0.43750	0.816	B	0.27380	0.079	D	0.83667	0.0164	10	0.44086	T	0.13	.	15.4529	0.75290	0.0:1.0:0.0:0.0	.	26	P37023	ACVL1_HUMAN	L	26;26;40;40	ENSP00000373574:P26L;ENSP00000446724:P40L;ENSP00000447884:P40L	ENSP00000267008:P26L	P	+	2	0	ACVRL1	50593165	0.004000	0.15560	0.898000	0.35279	0.512000	0.34134	0.741000	0.26202	2.716000	0.92895	0.655000	0.94253	CCG	.	.	weak		0.657	ACVRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404520.2			T	52306898	C	T	52306898	3	4	22	1	0	0	0	0	1	0	0	0	225	652	23	1	83	1	ACVRL1	12	52306898	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	24033	52306898	81544997	2699	5600											
ACVRL1	94	hgsc.bcm.edu	37	chr12	52308344	52308344	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	actgagatctataacacagtGttgctcagacacgacaacat	15	9	7	10	1	2	2	1	1	1	2	2	4	2	2	0	0	3	2	0	0	3	3	rs1058563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52308344G>A	ENST00000388922.4	+	6	1030	c.747G>A	c.(745-747)gtG>gtA	p.V249V	ACVRL1_ENST00000550683.1_Silent_p.V263V|ACVRL1_ENST00000419526.2_Silent_p.V75V	NM_000020.2	NP_000011.2	P37023	ACVL1_HUMAN	activin A receptor type II-like 1	249	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)	ATAACACAGTGTTGCTCAGAC	0.592													G|||	231	0.0461262	0.1619	0.0159	5008	,	,		10490	0.0		0.006	False		,,,				2504	0.0				p.V249V		Atlas-SNP	.											.	ACVRL1	60	.	0			c.G747A						PASS	.	G	,	576,3830	254.3+/-259.9	37,502,1664	94	71	79		747,747	1.9	0.4	12	dbSNP_86	79	17,8583	11.2+/-40.8	0,17,4283	no	coding-synonymous,coding-synonymous	ACVRL1	NM_000020.2,NM_001077401.1	,	37,519,5947	AA,AG,GG		0.1977,13.0731,4.5594	,	249/504,249/504	52308344	593,12413	2203	4300	6503	SO:0001819	synonymous_variant	94	exon6			CACAGTGTTGCTC	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.747G>A	12.37:g.52308344G>A		190	0	0		221	113	0.511312	NM_000020	A6NGA8	Silent	SNP	ENST00000388922.4	37	CCDS31804.1																																																																																			G|0.957;A|0.043	0.043	strong		0.592	ACVRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404520.2			A	52308344	G	A	52308344	2	1	22	1	0	0	0	0	0	0	0	1	225	1364	48	2		2	ACVRL1	12	52308344	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1446	52308344	81543551	2700	5601											
ACVR1B	91	hgsc.bcm.edu	37	chr12	52370181	52370181	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtaggcatcatcgccggcccGgtgttcctcctgttcctcat	4	12	10	15	3	2	0	2	0	0	0	6	0	5	0	5	3	0	4	5	3	1	3	rs115556161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52370181G>A	ENST00000257963.4	+	3	479	c.402G>A	c.(400-402)ccG>ccA	p.P134P	ACVR1B_ENST00000415850.2_Silent_p.P134P|ACVR1B_ENST00000541224.1_Silent_p.P134P|ACVR1B_ENST00000542485.1_Silent_p.P82P|ACVR1B_ENST00000426655.2_Silent_p.P134P	NM_004302.4|NM_020328.3	NP_004293.1|NP_064733.3	P36896	ACV1B_HUMAN	activin A receptor, type IB	134					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)	TCGCCGGCCCGGTGTTCCTCC	0.542													G|||	30	0.00599042	0.0219	0.0014	5008	,	,		19147	0.0		0.0	False		,,,				2504	0.0				p.P134P		Atlas-SNP	.											.	ACVR1B	167	.	0			c.G402A						PASS	.	G	,,	52,4354	52.9+/-88.7	0,52,2151	162	157	159		402,246,402	-10.8	0.7	12	dbSNP_132	159	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	ACVR1B	NM_004302.4,NM_020327.3,NM_020328.3	,,	0,53,6450	AA,AG,GG		0.0116,1.1802,0.4075	,,	134/506,82/454,134/547	52370181	53,12953	2203	4300	6503	SO:0001819	synonymous_variant	91	exon3			CGGCCCGGTGTTC		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.402G>A	12.37:g.52370181G>A		154	0	0		167	85	0.508982	NM_020328	B7Z5L8|B7Z5W5|Q15479|Q15480|Q15481|Q15482	Silent	SNP	ENST00000257963.4	37	CCDS8816.1																																																																																			G|0.994;A|0.006	0.006	strong		0.542	ACVR1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397000.1	NM_020328		A	52370181	G	A	52370181	2	1	22	1	0	0	0	0	0	0	0	1	221	1103	39	1		1	ACVR1B	12	52370181	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	61837	52370181	81481714	2701	5602											
KRT7	3855	hgsc.bcm.edu	37	chr12	52636843	52636843	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aagcatggggacgacctccgGaatacccggaatgagatttc	12	7	12	10	3	0	1	0	1	0	1	2	6	1	4	3	4	2	1	3	4	4	2	rs10564	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52636843G>A	ENST00000331817.5	+	6	1089	c.906G>A	c.(904-906)cgG>cgA	p.R302R	RP3-416H24.1_ENST00000546686.1_RNA	NM_005556.3	NP_005547.3	P08729	K2C7_HUMAN	keratin 7	302	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)	ACGACCTCCGGAATACCCGGA	0.567													G|||	172	0.034345	0.1256	0.0086	5008	,	,		18629	0.0		0.0	False		,,,				2504	0.0				p.R302R		Atlas-SNP	.											KRT7,colon,carcinoma,+1,1	KRT7	48	1	0			c.G906A						PASS	.	G		434,3972	210.8+/-231.2	19,396,1788	74	69	70		906	-0.4	0.5	12	dbSNP_52	70	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	KRT7	NM_005556.3		19,398,6086	AA,AG,GG		0.0233,9.8502,3.3523		302/470	52636843	436,12570	2203	4300	6503	SO:0001819	synonymous_variant	3855	exon6			CCTCCGGAATACC		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.906G>A	12.37:g.52636843G>A		95	0	0		85	44	0.517647	NM_005556	Q92676|Q9BUD8|Q9Y3R7	Silent	SNP	ENST00000331817.5	37	CCDS8822.1																																																																																			G|0.964;A|0.036	0.036	strong		0.567	KRT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404897.1	NM_005556		A	52636843	G	A	52636843	2	1	22	1	0	0	0	0	0	0	0	1	8492	1161	41	2		2	KRT7	12	52636843	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	266662	52636843	81215052	2702	5603											
KRT75	9119	hgsc.bcm.edu	37	chr12	52822464	52822464	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgcggttcatttcagagaTctcttgtttggtgtttcgaa	7	17	10	7	2	3	1	2	0	1	1	5	3	3	1	0	2	1	3	0	2	1	5	rs2232402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52822464T>C	ENST00000252245.5	-	6	1319	c.1099A>G	c.(1099-1101)Atc>Gtc	p.I367V	RP11-1020M18.10_ENST00000548135.1_RNA	NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	367	Coil 2.|Rod.		I -> V (in dbSNP:rs2232402).		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)		ATTTCAGAGATCTCTTGTTTG	0.512													T|||	103	0.0205671	0.0764	0.0029	5008	,	,		21269	0.0		0.0	False		,,,				2504	0.0				p.I367V		Atlas-SNP	.											KRT75,NS,carcinoma,+2,3	KRT75	75	3	0			c.A1099G						PASS	.	T	VAL/ILE	373,4033	189.2+/-215.4	16,341,1846	193	158	170		1099	5.2	1	12	dbSNP_98	170	1,8599		0,1,4299	yes	missense	KRT75	NM_004693.2	29	16,342,6145	CC,CT,TT		0.0116,8.4657,2.8756	probably-damaging	367/552	52822464	374,12632	2203	4300	6503	SO:0001583	missense	9119	exon6			CAGAGATCTCTTG	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.1099A>G	12.37:g.52822464T>C	ENSP00000252245:p.Ile367Val	153	0	0		149	73	0.489933	NM_004693	B4DQU4|Q9NSA9	Missense_Mutation	SNP	ENST00000252245.5	37	CCDS8827.1	34	0.015567765567765568	33	0.06707317073170732	1	0.0027624309392265192	0	0.0	0	0.0	T	18.53	3.644098	0.67244	0.084657	1.16E-4	ENSG00000170454	ENST00000252245	D	0.89617	-2.54	5.18	5.18	0.71444	Prefoldin (1);Filament (1);	0.000000	0.51477	D	0.000081	T	0.59128	0.2171	M	0.81802	2.56	0.42420	D	0.992635	D	0.69078	0.997	D	0.70935	0.971	T	0.77680	-0.2497	10	0.66056	D	0.02	.	15.0403	0.71785	0.0:0.0:0.0:1.0	rs2232402;rs52796316;rs60556458;rs2232402	367	O95678	K2C75_HUMAN	V	367	ENSP00000252245:I367V	ENSP00000252245:I367V	I	-	1	0	KRT75	51108731	1.000000	0.71417	1.000000	0.80357	0.611000	0.37282	5.064000	0.64338	1.966000	0.57179	0.459000	0.35465	ATC	T|0.969;C|0.031	0.031	strong		0.512	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693		C	52822464	T	C	52822464	3	2	22	1	0	0	0	0	1	0	0	0	8497	1435	50	3	572	3	KRT75	12	52822464	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	185621	52822464	81029431	2703	5604											
KRT6C	286887	hgsc.bcm.edu	37	chr12	52865924	52865924	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cggccccgttccccgacgatGctgtccagctgcctcctgag	4	8	11	18	4	0	1	0	1	0	0	3	3	3	1	7	1	3	3	7	1	0	1	rs77218649	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52865924G>A	ENST00000252250.6	-	2	728	c.681C>T	c.(679-681)agC>agT	p.S227S		NM_173086.4	NP_775109.2	P48668	K2C6C_HUMAN	keratin 6C	227	Coil 1B.|Rod.		S -> N (in dbSNP:rs17099602). {ECO:0000269|PubMed:7543104}.		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)		CCCCGACGATGCTGTCCAGCT	0.592													G|||	128	0.0255591	0.0961	0.0014	5008	,	,		17326	0.0		0.0	False		,,,				2504	0.0				p.S227S		Atlas-SNP	.											.	KRT6C	55	.	0			c.C681T						PASS	.	G		354,4050		39,276,1887	135	87	103		681	-2.5	0	12	dbSNP_131	103	4,8524		1,2,4261	no	coding-synonymous	KRT6C	NM_173086.4		40,278,6148	AA,AG,GG		0.0469,8.0381,2.7683		227/565	52865924	358,12574	2202	4264	6466	SO:0001819	synonymous_variant	286887	exon2			GACGATGCTGTCC	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.681C>T	12.37:g.52865924G>A		340	0	0		398	189	0.474874	NM_173086	A1L4L5|P48666|Q2TAZ9|Q7RTN9	Silent	SNP	ENST00000252250.6	37	CCDS8829.1																																																																																			G|0.976;A|0.024	0.024	strong		0.592	KRT6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404976.1	NM_173086		A	52865924	G	A	52865924	2	1	22	1	0	0	0	0	0	0	0	1	8491	1310	46	2		2	KRT6C	12	52865924	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	43460	52865924	80985971	2704	5605											
KRT71	112802	hgsc.bcm.edu	37	chr12	52946424	52946424	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccctagaagacccaccttGtcgatgaaggaggcgaactt	11	7	12	11	2	0	3	0	1	0	2	1	6	0	4	3	3	1	0	3	3	4	3	rs61729863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52946424G>A	ENST00000267119.5	-	1	507	c.438C>T	c.(436-438)gaC>gaT	p.D146D		NM_033448.2	NP_258259.1	Q3SY84	K2C71_HUMAN	keratin 71	146	Coil 1A.|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)		GACCCACCTTGTCGATGAAGG	0.537													G|||	187	0.0373403	0.1339	0.0144	5008	,	,		19941	0.0		0.0	False		,,,				2504	0.0				p.D146D		Atlas-SNP	.											.	KRT71	70	.	0			c.C438T						PASS	.	G		431,3975	208.5+/-229.5	28,375,1800	94	92	92		438	0.9	1	12	dbSNP_129	92	0,8600		0,0,4300	no	coding-synonymous	KRT71	NM_033448.2		28,375,6100	AA,AG,GG		0.0,9.7821,3.3139		146/524	52946424	431,12575	2203	4300	6503	SO:0001819	synonymous_variant	112802	exon1			CACCTTGTCGATG	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.438C>T	12.37:g.52946424G>A		225	0	0		208	87	0.418269	NM_033448	B3KVC1|Q3SY85|Q96DU2	Silent	SNP	ENST00000267119.5	37	CCDS8831.1																																																																																			G|0.970;A|0.030	0.030	strong		0.537	KRT71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396487.1	NM_033448		A	52946424	G	A	52946424	2	1	22	1	0	0	0	0	0	0	0	1	8493	1368	48	2		2	KRT71	12	52946424	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	80500	52946424	80905471	2705	5606											
KRT72	140807	hgsc.bcm.edu	37	chr12	52995127	52995127	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaggccgagcccttgaccCgggcccggaatgaggcggag	8	3	18	12	4	0	2	0	2	0	0	0	6	0	5	4	6	1	0	4	6	1	1	rs61747194	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52995127C>T	ENST00000537672.2	-	1	120	c.110G>A	c.(109-111)cGg>cAg	p.R37Q	KRT72_ENST00000398066.3_5'UTR|KRT72_ENST00000354310.4_Missense_Mutation_p.R37Q|KRT72_ENST00000293745.2_Missense_Mutation_p.R37Q|RP11-641A6.2_ENST00000551089.1_RNA	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	37	Gly-rich.|Head.					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)		GCCCTTGACCCGGGCCCGGAA	0.726													C|||	67	0.0133786	0.0484	0.0029	5008	,	,		12331	0.0		0.001	False		,,,				2504	0.0				p.R37Q		Atlas-SNP	.											.	KRT72	70	.	0			c.G110A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	143,3439		0,143,1648	3	4	3		110,110,110	4	0.1	12	dbSNP_129	3	3,7115		0,3,3556	yes	missense,missense,missense	KRT72	NM_001146225.1,NM_001146226.1,NM_080747.2	43,43,43	0,146,5204	TT,TC,CC		0.0421,3.9922,1.3645	benign,benign,benign	37/512,37/470,37/512	52995127	146,10554	1791	3559	5350	SO:0001583	missense	140807	exon1			TTGACCCGGGCCC	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.110G>A	12.37:g.52995127C>T	ENSP00000441160:p.Arg37Gln	45	0	0		46	21	0.456522	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Missense_Mutation	SNP	ENST00000537672.2	37	CCDS8833.1	29|29	0.013278388278388278|0.013278388278388278	27|27	0.054878048780487805|0.054878048780487805	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	C|C	14.43|14.43	2.532485|2.532485	0.45073|0.45073	0.039922|0.039922	4.21E-4|4.21E-4	ENSG00000170486|ENSG00000170486	ENST00000549979|ENST00000537672;ENST00000293745;ENST00000354310	.|T;T;T	.|0.75260	.|-0.92;-0.92;-0.92	4.04|4.04	4.04|4.04	0.47022|0.47022	.|.	.|0.000000	.|0.53938	.|D	.|0.000058	T|T	0.20740|0.20740	0.0499|0.0499	L|L	0.27053|0.27053	0.805|0.805	0.19575|0.19575	N|N	0.999962|0.999962	.|B;B	.|0.18610	.|0.016;0.029	.|B;B	.|0.21708	.|0.001;0.036	T|T	0.34229|0.34229	-0.9837|-0.9837	5|10	.|0.52906	.|T	.|0.07	.|.	9.2743|9.2743	0.37690|0.37690	0.1593:0.6857:0.155:0.0|0.1593:0.6857:0.155:0.0	.|.	.|37;37	.|B4DEI8;Q14CN4	.|.;K2C72_HUMAN	R|Q	23|37	.|ENSP00000441160:R37Q;ENSP00000293745:R37Q;ENSP00000346269:R37Q	.|ENSP00000293745:R37Q	G|R	-|-	1|2	0|0	KRT72|KRT72	51281394|51281394	.|.	.|.	0.107000|0.107000	0.21349|0.21349	0.130000|0.130000	0.20726|0.20726	.|.	.|.	2.543000|2.543000	0.85770|0.85770	0.561000|0.561000	0.74099|0.74099	GGG|CGG	C|0.987;T|0.013	0.013	strong		0.726	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747		T	52995127	C	T	52995127	3	4	22	1	0	0	0	0	1	0	0	0	8494	652	23	1	1461	1	KRT72	12	52995127	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	48703	52995127	80856768	2706	5607											
KRT73	319101	hgsc.bcm.edu	37	chr12	53005004	53005004	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacctgcttcttcacactcTcaatctccgagcgcagtctt	7	13	5	16	2	6	0	3	0	4	0	8	1	6	0	2	0	2	2	2	0	1	3	rs607426	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53005004T>C	ENST00000305748.3	-	6	1128	c.1094A>G	c.(1093-1095)gAg>gGg	p.E365G	RP11-641A6.2_ENST00000552364.1_RNA|RP11-641A6.2_ENST00000549180.1_RNA|RP11-641A6.2_ENST00000551089.1_RNA	NM_175068.2	NP_778238.1	Q86Y46	K2C73_HUMAN	keratin 73	365	Coil 2.|Rod.		E -> G (in dbSNP:rs607426).			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)		CTTCACACTCTCAATCTCCGA	0.567													T|||	104	0.0207668	0.0764	0.0043	5008	,	,		20476	0.0		0.0	False		,,,				2504	0.0				p.E365G		Atlas-SNP	.											.	KRT73	101	.	0			c.A1094G						PASS	.	T	GLY/GLU	214,4192	129.8+/-166.5	5,204,1994	144	125	131		1094	5.6	1	12	dbSNP_83	131	1,8599		0,1,4299	yes	missense	KRT73	NM_175068.2	98	5,205,6293	CC,CT,TT		0.0116,4.857,1.6531	benign	365/541	53005004	215,12791	2203	4300	6503	SO:0001583	missense	319101	exon6			ACACTCTCAATCT	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.1094A>G	12.37:g.53005004T>C	ENSP00000307014:p.Glu365Gly	218	0	0		211	97	0.459716	NM_175068	Q32MB2	Missense_Mutation	SNP	ENST00000305748.3	37	CCDS8834.1	29	0.013278388278388278	27	0.054878048780487805	2	0.0055248618784530384	0	0.0	0	0.0	T	12.93	2.086766	0.36855	0.04857	1.16E-4	ENSG00000186049	ENST00000305748;ENST00000552855	D;D	0.89746	-2.56;-2.56	5.61	5.61	0.85477	Filament (1);	0.000000	0.53938	D	0.000057	T	0.63896	0.2550	M	0.83603	2.65	0.37997	D	0.934108	B	0.06786	0.001	B	0.13407	0.009	T	0.79019	-0.1974	10	0.44086	T	0.13	.	11.2067	0.48773	0.0:0.0715:0.0:0.9285	rs607426;rs1352442;rs1707745	365	Q86Y46	K2C73_HUMAN	G	365;110	ENSP00000307014:E365G;ENSP00000449081:E110G	ENSP00000307014:E365G	E	-	2	0	KRT73	51291271	0.995000	0.38212	0.995000	0.50966	0.919000	0.55068	3.762000	0.55250	2.276000	0.75962	0.454000	0.30748	GAG	T|0.980;C|0.020	0.020	strong		0.567	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405700.1	NM_175068		C	53005004	T	C	53005004	3	2	22	1	0	0	0	0	1	0	0	0	8495	1551	54	3	544	3	KRT73	12	53005004	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	9877	53005004	80846891	2707	5608											
KRT79	338785	hgsc.bcm.edu	37	chr12	53215684	53215684	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tctggctggacgtcttgaccGtagtggtcttccgcaggatg	5	12	14	10	3	3	1	0	1	3	0	4	3	4	3	2	4	0	3	2	4	1	3	rs73303800	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53215684G>A	ENST00000330553.5	-	9	1614	c.1580C>T	c.(1579-1581)aCg>aTg	p.T527M		NM_175834.2	NP_787028.1	Q5XKE5	K2C79_HUMAN	keratin 79	527	Tail.					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						CGTCTTGACCGTAGTGGTCTT	0.622													G|||	44	0.00878594	0.0318	0.0029	5008	,	,		17021	0.0		0.0	False		,,,				2504	0.0				p.T527M		Atlas-SNP	.											.	KRT79	78	.	0			c.C1580T						PASS	.	G	MET/THR	121,4285	90.6+/-129.3	3,115,2085	58	44	48		1580	4	1	12	dbSNP_130	48	2,8598	1.2+/-3.3	0,2,4298	yes	missense	KRT79	NM_175834.2	81	3,117,6383	AA,AG,GG		0.0233,2.7463,0.9457	probably-damaging	527/536	53215684	123,12883	2203	4300	6503	SO:0001583	missense	338785	exon9			TTGACCGTAGTGG	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.1580C>T	12.37:g.53215684G>A	ENSP00000328358:p.Thr527Met	64	0	0		73	40	0.547945	NM_175834	Q6P465|Q7Z793	Missense_Mutation	SNP	ENST00000330553.5	37	CCDS8839.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	G	18.23	3.578041	0.65878	0.027463	2.33E-4	ENSG00000185640	ENST00000330553	D	0.83075	-1.68	3.97	3.97	0.46021	.	0.000000	0.47852	D	0.000213	T	0.75824	0.3902	M	0.61703	1.905	0.37441	D	0.914404	D	0.89917	1.0	D	0.78314	0.991	D	0.85029	0.0916	10	0.72032	D	0.01	.	11.8409	0.52353	0.0:0.0:1.0:0.0	.	527	Q5XKE5	K2C79_HUMAN	M	527	ENSP00000328358:T527M	ENSP00000328358:T527M	T	-	2	0	KRT79	51501951	0.969000	0.33509	1.000000	0.80357	0.997000	0.91878	1.735000	0.38176	2.516000	0.84829	0.655000	0.94253	ACG	G|0.990;A|0.010	0.010	strong		0.622	KRT79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406376.1	NM_175834		A	53215684	G	A	53215684	3	1	22	1	0	0	0	0	1	0	0	0	8501	1145	40	1	31	1	KRT79	12	53215684	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	210680	53215684	80636211	2708	5609											
KRT78	196374	hgsc.bcm.edu	37	chr12	53242389	53242389	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatctcctgggtctcctgcGtccgcaccacctggaactgg	5	10	11	15	2	2	1	0	1	2	0	5	2	3	2	5	3	2	1	5	3	1	0	rs116117459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53242389G>A	ENST00000304620.4	-	1	389	c.326C>T	c.(325-327)aCg>aTg	p.T109M	KRT78_ENST00000359499.4_5'Flank	NM_173352.2	NP_775487.2	Q8N1N4	K2C78_HUMAN	keratin 78	109	Head.					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						GGTCTCCTGCGTCCGCACCAC	0.567													G|||	67	0.0133786	0.0507	0.0	5008	,	,		16189	0.0		0.0	False		,,,				2504	0.0				p.T109M		Atlas-SNP	.											.	KRT78	41	.	0			c.C326T						PASS	.	G	MET/THR	254,4152	145.7+/-180.5	5,244,1954	106	88	94		326	4.2	1	12	dbSNP_132	94	1,8599	1.2+/-3.3	0,1,4299	yes	missense	KRT78	NM_173352.2	81	5,245,6253	AA,AG,GG		0.0116,5.7649,1.9606	probably-damaging	109/521	53242389	255,12751	2203	4300	6503	SO:0001583	missense	196374	exon1			TCCTGCGTCCGCA	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.326C>T	12.37:g.53242389G>A	ENSP00000306261:p.Thr109Met	142	0	0		187	89	0.475936	NM_173352	A8K4D6|Q5HYM7|Q7RTT2	Missense_Mutation	SNP	ENST00000304620.4	37	CCDS8840.1	31	0.014194139194139194	31	0.06300813008130081	0	0.0	0	0.0	0	0.0	G	20.4	3.978126	0.74360	0.057649	1.16E-4	ENSG00000170423	ENST00000304620	T	0.77877	-1.13	5.18	4.22	0.49857	.	.	.	.	.	T	0.56485	0.1988	M	0.90369	3.11	0.25830	N	0.984172	D	0.89917	1.0	D	0.65874	0.939	T	0.67364	-0.5689	9	0.72032	D	0.01	.	13.5578	0.61770	0.0:0.0:0.8437:0.1563	.	109	Q8N1N4	K2C78_HUMAN	M	109	ENSP00000306261:T109M	ENSP00000306261:T109M	T	-	2	0	KRT78	51528656	0.080000	0.21391	0.977000	0.42913	0.994000	0.84299	2.068000	0.41471	2.575000	0.86900	0.491000	0.48974	ACG	G|0.983;A|0.017	0.017	strong		0.567	KRT78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406380.1	NM_173352		A	53242389	G	A	53242389	3	1	22	1	0	0	0	0	1	0	0	0	8500	1145	40	1	1272	1	KRT78	12	53242389	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	26705	53242389	80609506	2709	5610											
SPRYD3	84926	hgsc.bcm.edu	37	chr12	53467230	53467230	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctgggaacagtccatctgggGacatgggcatgatggtagag	10	8	16	7	0	1	2	0	1	1	1	2	4	2	4	1	5	1	2	1	5	2	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53467230G>T	ENST00000301463.4	-	6	619	c.533C>A	c.(532-534)tCc>tAc	p.S178Y	SPRYD3_ENST00000547837.1_Missense_Mutation_p.S215Y	NM_032840.2	NP_116229.1	Q8NCJ5	SPRY3_HUMAN	SPRY domain containing 3	178	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.									central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	17						TCCATCTGGGGACATGGGCAT	0.607																																					p.S178Y		Atlas-SNP	.											.	SPRYD3	29	.	0			c.C533A						PASS	.						57	43	47					12																	53467230		2203	4292	6495	SO:0001583	missense	84926	exon6			TCTGGGGACATGG	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.533C>A	12.37:g.53467230G>T	ENSP00000301463:p.Ser178Tyr	53	0	0		54	22	0.407407	NM_032840	B9EG99|Q96SK5	Missense_Mutation	SNP	ENST00000301463.4	37	CCDS8845.1	.	.	.	.	.	.	.	.	.	.	G	19.45	3.830680	0.71258	.	.	ENSG00000167778	ENST00000301463;ENST00000547837	T;T	0.60040	0.22;0.22	5.17	5.17	0.71159	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.060021	0.64402	D	0.000002	T	0.60143	0.2246	L	0.42245	1.32	0.53005	D	0.999964	D	0.56968	0.978	P	0.50708	0.648	T	0.59484	-0.7446	10	0.45353	T	0.12	-19.5437	16.5838	0.84722	0.0:0.0:1.0:0.0	.	178	Q8NCJ5	SPRY3_HUMAN	Y	178;215	ENSP00000301463:S178Y;ENSP00000449452:S215Y	ENSP00000301463:S178Y	S	-	2	0	SPRYD3	51753497	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.182000	0.94881	2.861000	0.98227	0.655000	0.94253	TCC	.	.	none		0.607	SPRYD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407264.1	NM_032840		T	53467230	G	T	53467230	3	4	22	1	0	0	0	0	1	0	0	0	15124	1174	41	4	819	4	SPRYD3	12	53467230	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	224841	53467230	80384665	2710	5611											
ESPL1	9700	hgsc.bcm.edu	37	chr12	53680135	53680135	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	acccaagctctccaagcttcCctgaatcataaaacaccccc	13	7	3	18	0	2	1	1	1	1	0	4	1	3	1	5	0	3	2	5	0	5	2	rs61741367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53680135C>T	ENST00000257934.4	+	18	3706	c.3615C>T	c.(3613-3615)tcC>tcT	p.S1205S	ESPL1_ENST00000552462.1_Silent_p.S1205S	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	1205					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						TCCAAGCTTCCCTGAATCATA	0.582													C|||	180	0.0359425	0.1316	0.0086	5008	,	,		17444	0.0		0.0	False		,,,				2504	0.0				p.S1205S	Colon(53;1069 1201 2587 5382)	Atlas-SNP	.											.	ESPL1	158	.	0			c.C3615T						PASS	.	C		503,3903	233.3+/-246.5	36,431,1736	79	87	84		3615	0.4	0.3	12	dbSNP_129	84	7,8593	4.3+/-15.6	0,7,4293	no	coding-synonymous	ESPL1	NM_012291.4		36,438,6029	TT,TC,CC		0.0814,11.4163,3.9213		1205/2121	53680135	510,12496	2203	4300	6503	SO:0001819	synonymous_variant	9700	exon18			AGCTTCCCTGAAT	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.3615C>T	12.37:g.53680135C>T		48	0	0		73	32	0.438356	NM_012291		Silent	SNP	ENST00000257934.4	37	CCDS8852.1																																																																																			C|0.957;T|0.043	0.043	strong		0.582	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291		T	53680135	C	T	53680135	2	4	22	1	0	0	0	0	0	0	0	1	5255	610	22	2		2	ESPL1	12	53680135	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	212905	53680135	80171760	2711	5612											
HOXC10	3226	hgsc.bcm.edu	37	chr12	54379610	54379610	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcgccgaacatctggaatcGcctcagctggggggcaaagt	9	6	14	12	4	2	0	1	0	1	0	3	2	2	1	2	4	2	2	2	4	3	0	rs145093077		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:54379610G>C	ENST00000303460.4	+	1	641	c.567G>C	c.(565-567)tcG>tcC	p.S189S	HOXC-AS3_ENST00000513165.1_RNA|RP11-834C11.12_ENST00000513209.1_5'Flank|HOXC-AS3_ENST00000514702.1_RNA|HOXC-AS3_ENST00000509870.1_RNA|HOXC-AS3_ENST00000567780.1_RNA	NM_017409.3	NP_059105.2	Q9NYD6	HXC10_HUMAN	homeobox C10	189					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						ATCTGGAATCGCCTCAGCTGG	0.647																																					p.S189S		Atlas-SNP	.											.	HOXC10	42	.	0			c.G567C						PASS	.						32	36	35					12																	54379610		2203	4299	6502	SO:0001819	synonymous_variant	3226	exon1			GGAATCGCCTCAG		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.567G>C	12.37:g.54379610G>C		72	0	0		106	49	0.462264	NM_017409	O15219|O15220|Q9BVD5	Silent	SNP	ENST00000303460.4	37	CCDS8868.1																																																																																			G|1.000;A|0.000	.	alt		0.647	HOXC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358952.2			C	54379610	G	C	54379610	2	2	22	1	0	0	0	0	0	0	0	1	7318	1074	38	4		4	HOXC10	12	54379610	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	699475	54379610	79472285	2712	5613											
OR6C76	390326	hgsc.bcm.edu	37	chr12	55820358	55820358	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttatcttccttggctcaacGgagtttttcctcctggcctc	4	17	7	13	1	2	0	1	0	1	0	6	1	5	1	4	3	1	2	4	3	2	6	rs12322458	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:55820358G>A	ENST00000328314.3	+	1	321	c.321G>A	c.(319-321)acG>acA	p.T107T		NM_001005183.1	NP_001005183.1	A6NM76	O6C76_HUMAN	olfactory receptor, family 6, subfamily C, member 76	107						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)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						TTGGCTCAACGGAGTTTTTCC	0.408													g|||	97	0.019369	0.0673	0.0115	5008	,	,		15616	0.0		0.0	False		,,,				2504	0.0				p.T107T		Atlas-SNP	.											.	OR6C76	98	.	0			c.G321A						PASS	.			262,4144	140.0+/-175.5	7,248,1948	116	128	124		321	-1.2	0.7	12	dbSNP_120	124	3,8593	3.0+/-9.4	0,3,4295	no	coding-synonymous	OR6C76	NM_001005183.1		7,251,6243	AA,AG,GG		0.0349,5.9464,2.0381		107/313	55820358	265,12737	2203	4298	6501	SO:0001819	synonymous_variant	390326	exon1			CTCAACGGAGTTT		CCDS31823.1	12q13.2	2013-09-23			ENSG00000185821	ENSG00000185821		"GPCR / Class A : Olfactory receptors"	31305	protein-coding gene	gene with protein product							Standard	NM_001005183		Approved		uc010spm.2	A6NM76	OTTHUMG00000169956	ENST00000328314.3:c.321G>A	12.37:g.55820358G>A		165	0	0		152	72	0.473684	NM_001005183		Silent	SNP	ENST00000328314.3	37	CCDS31823.1																																																																																			G|0.978;A|0.022	0.022	strong		0.408	OR6C76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406675.1	NM_001005183		A	55820358	G	A	55820358	2	1	22	1	0	0	0	0	0	0	0	1	11209	1103	39	1		1	OR6C76	12	55820358	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1440748	55820358	78031537	2713	5614											
OR6C76	390326	hgsc.bcm.edu	37	chr12	55820927	55820927	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaaccagcaggtgaaacaagCatttaaggatgttctgagaa	17	8	10	6	0	1	2	0	2	1	1	1	4	1	3	1	2	4	3	1	2	5	3	rs73327795	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:55820927C>T	ENST00000328314.3	+	1	890	c.890C>T	c.(889-891)gCa>gTa	p.A297V		NM_001005183.1	NP_001005183.1	A6NM76	O6C76_HUMAN	olfactory receptor, family 6, subfamily C, member 76	297						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)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						GTGAAACAAGCATTTAAGGAT	0.353													c|||	104	0.0207668	0.0719	0.013	5008	,	,		14924	0.0		0.0	False		,,,				2504	0.0				p.A297V		Atlas-SNP	.											.	OR6C76	98	.	0			c.C890T						PASS	.		VAL/ALA	273,4133		6,261,1936	35	37	37		890	3.4	0.4	12	dbSNP_130	37	2,8590		0,2,4294	yes	missense	OR6C76	NM_001005183.1	64	6,263,6230	TT,TC,CC		0.0233,6.1961,2.1157	benign	297/313	55820927	275,12723	2203	4296	6499	SO:0001583	missense	390326	exon1			AACAAGCATTTAA		CCDS31823.1	12q13.2	2013-09-23			ENSG00000185821	ENSG00000185821		"GPCR / Class A : Olfactory receptors"	31305	protein-coding gene	gene with protein product							Standard	NM_001005183		Approved		uc010spm.2	A6NM76	OTTHUMG00000169956	ENST00000328314.3:c.890C>T	12.37:g.55820927C>T	ENSP00000328402:p.Ala297Val	70	0	0		54	31	0.574074	NM_001005183		Missense_Mutation	SNP	ENST00000328314.3	37	CCDS31823.1	41	0.018772893772893772	38	0.07723577235772358	3	0.008287292817679558	0	0.0	0	0.0	c	11.52	1.664546	0.29604	0.061961	2.33E-4	ENSG00000185821	ENST00000328314	T	0.44881	0.91	4.25	3.36	0.38483	.	0.000000	0.46442	U	0.000298	T	0.03095	0.0091	M	0.74647	2.275	0.09310	N	1	B	0.33940	0.433	B	0.35899	0.213	T	0.04811	-1.0925	10	0.59425	D	0.04	.	10.1138	0.42579	0.0:0.8992:0.0:0.1008	.	297	A6NM76	O6C76_HUMAN	V	297	ENSP00000328402:A297V	ENSP00000328402:A297V	A	+	2	0	OR6C76	54107194	0.109000	0.22037	0.419000	0.26584	0.684000	0.39900	2.983000	0.49345	1.154000	0.42482	-0.205000	0.12727	GCA	C|0.983;T|0.017	0.017	strong		0.353	OR6C76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406675.1	NM_001005183		T	55820927	C	T	55820927	3	4	22	1	0	0	0	0	1	0	0	0	11209	710	25	2	892	2	OR6C76	12	55820927	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	569	55820927	78030968	2714	5615											
OR6C68	403284	hgsc.bcm.edu	37	chr12	55887054	55887054	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gaatgagcaagttaaacaagCctttcatgactcactcaaaa	17	9	6	9	0	3	2	3	2	0	0	3	3	3	2	1	0	3	2	1	0	7	2	rs56760228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:55887054C>G	ENST00000548615.1	+	1	893	c.893C>G	c.(892-894)gCc>gGc	p.A298G	RP11-110A12.2_ENST00000554049.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA|RP11-110A12.2_ENST00000556750.1_RNA|OR6C68_ENST00000379662.1_Missense_Mutation_p.A303G	NM_001005519.2	NP_001005519.2	A6NDL8	O6C68_HUMAN	olfactory receptor, family 6, subfamily C, member 68	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(2)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	15						GTTAAACAAGCCTTTCATGAC	0.289													C|||	306	0.0611022	0.2163	0.0288	5008	,	,		17663	0.0		0.0	False		,,,				2504	0.0				p.A298G		Atlas-SNP	.											.	OR6C68	36	.	0			c.C893G						PASS	.	G	GLY/ALA	793,3609		73,647,1481	32	36	35		893	3.2	0.2	12	dbSNP_129	35	9,8583		0,9,4287	yes	missense	OR6C68	NM_001005519.2	60	73,656,5768	GG,GC,CC		0.1047,18.0145,6.1721	benign	298/313	55887054	802,12192	2201	4296	6497	SO:0001583	missense	403284	exon1			AACAAGCCTTTCA		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.893C>G	12.37:g.55887054C>G	ENSP00000448811:p.Ala298Gly	61	0	0		62	23	0.370968	NM_001005519		Missense_Mutation	SNP	ENST00000548615.1	37	CCDS31826.2	104	0.047619047619047616	93	0.18902439024390244	11	0.03038674033149171	0	0.0	0	0.0	c	4.988	0.183559	0.09495	0.180145	0.001047	ENSG00000205327	ENST00000379662;ENST00000548615	T;T	0.45276	0.9;0.9	5.03	3.19	0.36642	.	0.288458	0.24461	N	0.038338	T	0.00073	0.0002	M	0.61703	1.905	0.80722	P	0.0	B	0.30914	0.3	B	0.38296	0.27	T	0.09185	-1.0686	9	0.72032	D	0.01	.	7.1754	0.25742	0.1288:0.6768:0.1243:0.0702	rs56760228	298	A6NDL8	O6C68_HUMAN	G	303;298	ENSP00000368983:A303G;ENSP00000448811:A298G	ENSP00000368983:A303G	A	+	2	0	OR6C68	54173321	0.000000	0.05858	0.226000	0.23910	0.035000	0.12851	0.005000	0.13129	0.628000	0.30357	-3.065000	0.00067	GCC	C|0.953;G|0.047	0.047	strong		0.289	OR6C68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406677.1			G	55887054	C	G	55887054	3	3	22	1	0	0	0	0	1	0	0	0	11205	739	26	4	910	4	OR6C68	12	55887054	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	66127	55887054	77964841	2715	5616											
DGKA	1606	hgsc.bcm.edu	37	chr12	56346891	56346891	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagatgggccaaatctatacCaagctcaagaatgctggacg	14	7	11	9	1	2	2	1	0	1	2	2	4	2	3	2	2	3	2	2	2	6	2	rs199663532		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56346891C>T	ENST00000331886.5	+	22	2464	c.2010C>T	c.(2008-2010)acC>acT	p.T670T	DGKA_ENST00000551156.1_Silent_p.T670T|DGKA_ENST00000394147.1_Silent_p.T670T|DGKA_ENST00000549079.2_3'UTR	NM_001345.4	NP_001336.2	P23743	DGKA_HUMAN	diacylglycerol kinase, alpha 80kDa	670					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)	AAATCTATACCAAGCTCAAGA	0.532																																					p.T670T		Atlas-SNP	.											.	DGKA	70	.	0			c.C2010T						PASS	.						112	109	110					12																	56346891		2203	4300	6503	SO:0001819	synonymous_variant	1606	exon22			CTATACCAAGCTC	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.2010C>T	12.37:g.56346891C>T		123	0	0		108	48	0.444444	NM_201554	O75481|O75482|O75483|O95217|Q3ZE25|Q8IZ56|Q8N5Q2	Silent	SNP	ENST00000331886.5	37	CCDS8896.1																																																																																			.	.	none		0.532	DGKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407291.1			T	56346891	C	T	56346891	2	4	22	1	0	0	0	0	0	0	0	1	4467	581	21	2		2	DGKA	12	56346891	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	459837	56346891	77505004	2716	5617											
APOF	319	hgsc.bcm.edu	37	chr12	56755300	56755300	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataggcccccctgacatcccAgccatggtcatcagaaggtc	10	7	9	15	0	2	2	2	1	0	1	4	2	3	2	5	3	1	0	5	3	2	1	rs11575217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56755300A>C	ENST00000398189.3	-	2	767	c.690T>G	c.(688-690)gcT>gcG	p.A230A	STAT2_ENST00000418572.2_5'Flank|STAT2_ENST00000557235.1_5'Flank|STAT2_ENST00000314128.4_5'Flank|APOF_ENST00000541105.1_Silent_p.A212A	NM_001638.2	NP_001629.1	Q13790	APOF_HUMAN	apolipoprotein F	230					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						CTGACATCCCAGCCATGGTCA	0.517													A|||	212	0.0423323	0.1528	0.0144	5008	,	,		20580	0.0		0.0	False		,,,				2504	0.0				p.A230A		Atlas-SNP	.											.	APOF	13	.	0			c.T690G						PASS	.	A		449,3449		26,397,1526	68	70	69		690	-11	0	12	dbSNP_120	69	0,8286		0,0,4143	no	coding-synonymous	APOF	NM_001638.2		26,397,5669	CC,CA,AA		0.0,11.5187,3.6852		230/327	56755300	449,11735	1949	4143	6092	SO:0001819	synonymous_variant	319	exon2			CATCCCAGCCATG	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.690T>G	12.37:g.56755300A>C		150	0	0		126	53	0.420635	NM_001638	Q8TC13	Silent	SNP	ENST00000398189.3	37	CCDS44923.1																																																																																			A|0.945;C|0.055	0.055	strong		0.517	APOF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410076.1			C	56755300	A	C	56755300	2	2	22	1	0	0	0	0	0	0	0	1	803	175	7	5		5	APOF	12	56755300	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	408409	56755300	77096595	2717	5618											
TIMELESS	8914	hgsc.bcm.edu	37	chr12	56815717	56815717	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacactgtcagccagtcccaTctgtaccagatggtggatga	10	9	11	11	0	2	2	1	1	1	1	3	4	3	3	3	2	2	1	3	2	1	1	rs61733875	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56815717T>C	ENST00000553532.1	-	21	2758	c.2608A>G	c.(2608-2610)Atg>Gtg	p.M870V	TIMELESS_ENST00000229201.4_Missense_Mutation_p.M869V|TIMELESS_ENST00000554616.1_Missense_Mutation_p.M367V					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						GCCAGTCCCATCTGTACCAGA	0.557													T|||	255	0.0509185	0.1823	0.0187	5008	,	,		21890	0.0		0.001	False		,,,				2504	0.0				p.M870V		Atlas-SNP	.											.	TIMELESS	107	.	0			c.A2608G						PASS	.	T	VAL/MET	704,3702	295.3+/-283.6	47,610,1546	140	127	131		2608	1.3	0.8	12	dbSNP_129	131	4,8596	3.0+/-9.4	0,4,4296	yes	missense	TIMELESS	NM_003920.3	21	47,614,5842	CC,CT,TT		0.0465,15.9782,5.4436	benign	870/1209	56815717	708,12298	2203	4300	6503	SO:0001583	missense	8914	exon21			GTCCCATCTGTAC	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.2608A>G	12.37:g.56815717T>C	ENSP00000450607:p.Met870Val	71	0	0		114	57	0.5	NM_003920		Missense_Mutation	SNP	ENST00000553532.1	37	CCDS8918.1	111	0.050824175824175824	108	0.21951219512195122	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	T	7.065	0.567067	0.13560	0.159782	4.65E-4	ENSG00000111602	ENST00000229201;ENST00000553532;ENST00000554616	T;T;T	0.11604	2.76;2.76;2.76	5.29	1.26	0.21427	Timeless C-terminal (1);	0.478535	0.21599	N	0.071972	T	0.00012	0.0000	L	0.46157	1.445	0.80722	P	0.0	B	0.17852	0.024	B	0.20955	0.032	T	0.35325	-0.9793	9	0.51188	T	0.08	-2.3118	3.9116	0.09205	0.0713:0.2456:0.3032:0.3798	.	870	Q9UNS1	TIM_HUMAN	V	869;870;367	ENSP00000229201:M869V;ENSP00000450607:M870V;ENSP00000450848:M367V	ENSP00000229201:M870V	M	-	1	0	TIMELESS	55101984	0.560000	0.26570	0.789000	0.31954	0.285000	0.27093	0.692000	0.25482	0.031000	0.15407	-0.973000	0.02599	ATG	T|0.947;C|0.053	0.053	strong		0.557	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920		C	56815717	T	C	56815717	3	2	22	1	0	0	0	0	1	0	0	0	15919	1435	50	3	1054	3	TIMELESS	12	56815717	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	60417	56815717	77036178	2718	5619											
TIMELESS	8914	hgsc.bcm.edu	37	chr12	56822690	56822690	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtgcccaggaggcagcttcCttgcggtcagtcagcatcat	7	9	12	13	2	3	0	3	0	0	0	4	1	4	1	2	3	4	3	2	3	0	2	rs11832580	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56822690C>T	ENST00000553532.1	-	11	1431	c.1281G>A	c.(1279-1281)aaG>aaA	p.K427K	TIMELESS_ENST00000229201.4_Silent_p.K426K|TIMELESS_ENST00000554616.1_Intron					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						AGGCAGCTTCCTTGCGGTCAG	0.532													C|||	256	0.0511182	0.1831	0.0187	5008	,	,		19438	0.0		0.001	False		,,,				2504	0.0				p.K427K		Atlas-SNP	.											.	TIMELESS	107	.	0			c.G1281A						PASS	.	C		702,3704	294.7+/-283.3	45,612,1546	109	95	100		1281	4.4	1	12	dbSNP_120	100	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	TIMELESS	NM_003920.3		45,616,5842	TT,TC,CC		0.0465,15.9328,5.4283		427/1209	56822690	706,12300	2203	4300	6503	SO:0001819	synonymous_variant	8914	exon11			AGCTTCCTTGCGG	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.1281G>A	12.37:g.56822690C>T		127	0	0		119	54	0.453782	NM_003920		Silent	SNP	ENST00000553532.1	37	CCDS8918.1																																																																																			C|0.949;T|0.051	0.051	strong		0.532	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920		T	56822690	C	T	56822690	2	4	22	1	0	0	0	0	0	0	0	1	15919	680	24	2		2	TIMELESS	12	56822690	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6973	56822690	77029205	2719	5620											
MIP	4284	hgsc.bcm.edu	37	chr12	56847384	56847384	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ttcctgcttaccccaaagagGtgccccagggcaagggagaa	11	6	12	12	0	0	2	0	0	0	2	1	3	1	2	5	3	3	2	5	3	4	2	rs36032520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56847384G>A	ENST00000257979.4	-	2	544	c.516C>T	c.(514-516)caC>caT	p.H172H	MIP_ENST00000555551.1_5'UTR	NM_012064.3	NP_036196.1	P30301	MIP_HUMAN	major intrinsic protein of lens fiber	172					canalicular bile acid transport (GO:0015722)|lens development in camera-type eye (GO:0002088)|response to stimulus (GO:0050896)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)|water transport (GO:0006833)	gap junction (GO:0005921)|integral component of plasma membrane (GO:0005887)|intracellular canaliculus (GO:0046691)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|structural constituent of eye lens (GO:0005212)|transporter activity (GO:0005215)|water channel activity (GO:0015250)			kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(3)|urinary_tract(1)	16						CCCCAAAGAGGTGCCCCAGGG	0.562													G|||	9	0.00179712	0.0068	0.0	5008	,	,		20604	0.0		0.0	False		,,,				2504	0.0				p.H172H		Atlas-SNP	.											.	MIP	39	.	0			c.C516T						PASS	.	G		39,4367	43.8+/-77.6	0,39,2164	57	53	54		516	3	1	12	dbSNP_126	54	0,8600		0,0,4300	no	coding-synonymous	MIP	NM_012064.3		0,39,6464	AA,AG,GG		0.0,0.8852,0.2999		172/264	56847384	39,12967	2203	4300	6503	SO:0001819	synonymous_variant	4284	exon2			AAAGAGGTGCCCC		CCDS8919.1	12q13	2012-10-02				ENSG00000135517		"Ion channels / Aquaporins"	7103	protein-coding gene	gene with protein product	aquaporin 0	154050				1840563, 7536742	Standard	NM_012064		Approved	MP26, LIM1, AQP0	uc001slh.3	P30301		ENST00000257979.4:c.516C>T	12.37:g.56847384G>A		85	0	0		84	40	0.47619	NM_012064	Q17R41	Silent	SNP	ENST00000257979.4	37	CCDS8919.1																																																																																			G|0.998;A|0.002	0.002	strong		0.562	MIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409620.1	NM_012064		A	56847384	G	A	56847384	2	1	22	1	0	0	0	0	0	0	0	1	9600	1252	44	2		2	MIP	12	56847384	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	24694	56847384	77004511	2720	5621											
GPR182	11318	hgsc.bcm.edu	37	chr12	57389536	57389536	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcaggcatctgggtcctctcGgccatcatcccgctgcctga	5	9	11	16	2	3	1	1	1	2	0	6	1	5	1	4	3	1	3	4	3	0	0	rs61740222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:57389536G>A	ENST00000300098.1	+	2	762	c.543G>A	c.(541-543)tcG>tcA	p.S181S	RP11-474N8.5_ENST00000556850.1_RNA|HBCBP_ENST00000600202.1_5'Flank	NM_007264.3	NP_009195.1	O15218	GP182_HUMAN	G protein-coupled receptor 182	181					cell surface receptor signaling pathway (GO:0007166)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	15						GGGTCCTCTCGGCCATCATCC	0.642													G|||	65	0.0129792	0.0492	0.0	5008	,	,		19981	0.0		0.0	False		,,,				2504	0.0				p.S181S		Atlas-SNP	.											.	GPR182	35	.	0			c.G543A						PASS	.	G		158,4248	106.5+/-144.9	2,154,2047	61	53	56		543	-8.9	0.1	12	dbSNP_129	56	2,8598		0,2,4298	no	coding-synonymous	GPR182	NM_007264.3		2,156,6345	AA,AG,GG		0.0233,3.586,1.2302		181/405	57389536	160,12846	2203	4300	6503	SO:0001819	synonymous_variant	11318	exon2			CCTCTCGGCCATC	Y13583	CCDS8927.1	12q13.3	2012-08-21	2007-09-24	2007-09-24		ENSG00000166856		"GPCR / Class A : Orphans"	13708	protein-coding gene	gene with protein product		605307	"adrenomedullin receptor"	ADMR		9367907, 9535752	Standard	NM_007264		Approved	hrhAMR, G10D, AM-R	uc001smk.3	O15218		ENST00000300098.1:c.543G>A	12.37:g.57389536G>A		88	0	0		103	53	0.514563	NM_007264		Silent	SNP	ENST00000300098.1	37	CCDS8927.1																																																																																			G|0.987;A|0.013	0.013	strong		0.642	GPR182-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411212.1	NM_007264		A	57389536	G	A	57389536	2	1	22	1	0	0	0	0	0	0	0	1	6685	1103	39	1		1	GPR182	12	57389536	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	542152	57389536	76462359	2721	5622											
TAC3	6866	hgsc.bcm.edu	37	chr12	57406234	57406234	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgattcacatccgtaggagAgtctagggtaaagcgaacag	13	9	12	7	2	2	2	1	1	1	1	3	4	3	2	1	2	2	2	1	2	5	5	rs73334764	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:57406234A>G	ENST00000458521.2	-	6	454	c.295T>C	c.(295-297)Tct>Cct	p.S99P	TAC3_ENST00000415231.1_Missense_Mutation_p.S99P|TAC3_ENST00000441881.1_Missense_Mutation_p.S81P	NM_013251.3	NP_037383.1	Q9UHF0	TKNK_HUMAN	tachykinin 3	99					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						TCCGTAGGAGAGTCTAGGGTA	0.488													A|||	125	0.0249601	0.0893	0.0101	5008	,	,		16633	0.0		0.0	False		,,,				2504	0.0				p.S99P		Atlas-SNP	.											.	TAC3	11	.	0			c.T295C						PASS	.	A	PRO/SER,PRO/SER	347,4059	180.8+/-209.0	17,313,1873	73	66	68		241,295	-0.9	0	12	dbSNP_130	68	2,8598	1.2+/-3.3	0,2,4298	yes	missense,missense	TAC3	NM_001178054.1,NM_013251.3	74,74	17,315,6171	GG,GA,AA		0.0233,7.8756,2.6834	possibly-damaging,possibly-damaging	81/104,99/122	57406234	349,12657	2203	4300	6503	SO:0001583	missense	6866	exon6			TAGGAGAGTCTAG	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.295T>C	12.37:g.57406234A>G	ENSP00000404056:p.Ser99Pro	77	0	0		83	42	0.506024	NM_013251	Q6IAG2|Q71BC6|Q71BC9	Missense_Mutation	SNP	ENST00000458521.2	37	CCDS8928.1	40	0.018315018315018316	36	0.07317073170731707	4	0.011049723756906077	0	0.0	0	0.0	A	10.20	1.285372	0.23478	0.078756	2.33E-4	ENSG00000166863	ENST00000458521;ENST00000441881;ENST00000415231	D;T;D	0.83250	-1.7;-1.07;-1.7	5.0	-0.857	0.10693	.	.	.	.	.	T	0.09512	0.0234	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.15263	-1.0443	9	0.40728	T	0.16	.	6.259	0.20889	0.1768:0.0:0.4637:0.3595	.	99;81	Q9UHF0;Q9UHF0-3	TKNK_HUMAN;.	P	99;81;99	ENSP00000404056:S99P;ENSP00000408208:S81P;ENSP00000402995:S99P	ENSP00000300108:S99P	S	-	1	0	TAC3	55692501	0.002000	0.14202	0.003000	0.11579	0.008000	0.06430	-0.120000	0.10660	0.002000	0.14630	-0.490000	0.04691	TCT	A|0.971;G|0.029	0.029	strong		0.488	TAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346793.1	NM_001006667		G	57406234	A	G	57406234	3	3	22	1	0	0	0	0	1	0	0	0	15514	304	11	3	74	3	TAC3	12	57406234	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	16698	57406234	76445661	2722	5623											
LRP1	4035	hgsc.bcm.edu	37	chr12	57578696	57578696	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggagacaggtgagaaccgCgaggtggttctgtccagcaa	10	7	15	9	2	1	2	0	1	1	2	2	5	2	2	2	4	2	2	2	4	2	1	rs140921686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:57578696C>T	ENST00000243077.3	+	39	6727	c.6261C>T	c.(6259-6261)cgC>cgT	p.R2087R		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	2087					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)	GTGAGAACCGCGAGGTGGTTC	0.542													C|||	18	0.00359425	0.0023	0.0	5008	,	,		21048	0.0149		0.0	False		,,,				2504	0.0				p.R2087R		Atlas-SNP	.											.	LRP1	428	.	0			c.C6261T						PASS	.	C		6,4400	11.4+/-27.6	0,6,2197	189	162	171		6261	-10.3	0.7	12	dbSNP_134	171	0,8600		0,0,4300	no	coding-synonymous	LRP1	NM_002332.2		0,6,6497	TT,TC,CC		0.0,0.1362,0.0461		2087/4545	57578696	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	4035	exon39			GAACCGCGAGGTG	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.6261C>T	12.37:g.57578696C>T		110	0	0		144	79	0.548611	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			C|0.999;T|0.001	0.001	strong		0.542	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		T	57578696	C	T	57578696	2	4	22	1	0	0	0	0	0	0	0	1	8960	755	27	1		1	LRP1	12	57578696	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	172462	57578696	76273199	2723	5624											
LRP1	4035	hgsc.bcm.edu	37	chr12	57603647	57603647	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	taccatcagcacaagcagccCgaaggtgggggcagagggga	12	3	16	10	1	1	1	1	0	0	1	1	3	1	2	2	5	4	3	2	5	3	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:57603647C>T	ENST00000243077.3	+	80	12901	c.12435C>T	c.(12433-12435)ccC>ccT	p.P4145P		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	4145					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)	p.P4145P(1)		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)	ACAAGCAGCCCGAAGGTGGGG	0.632																																					p.P4145P		Atlas-SNP	.											LRP1,bladder,carcinoma,0,1	LRP1	428	1	1	Substitution - coding silent(1)	urinary_tract(1)	c.C12435T						PASS	.						35	37	36					12																	57603647		2203	4300	6503	SO:0001819	synonymous_variant	4035	exon80			GCAGCCCGAAGGT	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.12435C>T	12.37:g.57603647C>T		45	0	0		52	30	0.576923	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			.	.	none		0.632	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		T	57603647	C	T	57603647	2	4	22	1	0	0	0	0	0	0	0	1	8960	639	23	1		1	LRP1	12	57603647	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	24951	57603647	76248248	2724	5625											
SLC26A10	65012	hgsc.bcm.edu	37	chr12	58017665	58017665	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtcctgtcggtgctgctgtGgctggggcccttcttttact	1	15	14	11	1	1	0	0	0	1	0	3	0	2	0	2	5	3	3	2	5	1	3	rs115563091	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:58017665G>A	ENST00000320442.4	+	8	1411	c.1100G>A	c.(1099-1101)tGg>tAg	p.W367*	SLC26A10_ENST00000379218.2_Nonsense_Mutation_p.W367*	NM_133489.2	NP_597996.2	Q8NG04	S2610_HUMAN	solute carrier family 26, member 10	367						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)					GTGCTGCTGTGGCTGGGGCCC	0.562													G|||	6	0.00119808	0.0045	0.0	5008	,	,		18555	0.0		0.0	False		,,,				2504	0.0				p.W367X		Atlas-SNP	.											.	SLC26A10	89	.	0			c.G1100A						PASS	.	G	stop/TRP	21,4385		0,21,2182	98	100	100		1100	3.9	1	12	dbSNP_132	100	0,8600		0,0,4300	yes	stop-gained	SLC26A10	NM_133489.2		0,21,6482	AA,AG,GG		0.0,0.4766,0.1615		367/564	58017665	21,12985	2203	4300	6503	SO:0001587	stop_gained	65012	exon8			TGCTGTGGCTGGG		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.1100G>A	12.37:g.58017665G>A	ENSP00000320217:p.Trp367*	70	0	0		71	40	0.56338	NM_133489	A6NMJ2|B6ZDQ3|Q6ZWI7	Nonsense_Mutation	SNP	ENST00000320442.4	37	CCDS8949.2	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	.	37	6.630732	0.97718	0.004766	0.0	ENSG00000135502	ENST00000320442;ENST00000379218	.	.	.	3.92	3.92	0.45320	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	.	14.2309	0.65892	0.0:0.0:1.0:0.0	.	.	.	.	X	367	.	ENSP00000320217:W367X	W	+	2	0	SLC26A10	56303932	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	4.320000	0.59203	2.471000	0.83476	0.561000	0.74099	TGG	G|0.999;A|0.001	0.001	strong		0.562	SLC26A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250311.2			A	58017665	G	A	58017665	4	1	22	1	0	0	0	0	0	1	0	0	14530	1357	47	2	1130	2	SLC26A10	12	58017665	Nonsense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	414018	58017665	75834230	2725	5626											
SLC26A10	65012	hgsc.bcm.edu	37	chr12	58019388	58019388	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtgcaggggacactgaccCgggtaggactcctggacagg	8	6	17	10	1	0	1	0	1	0	0	1	4	1	4	2	7	1	2	2	7	1	1	rs114079678	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:58019388C>T	ENST00000320442.4	+	14	1863	c.1552C>T	c.(1552-1554)Cgg>Tgg	p.R518W	SLC26A10_ENST00000379218.2_3'UTR|SLC26A10_ENST00000490243.1_Intron	NM_133489.2	NP_597996.2	Q8NG04	S2610_HUMAN	solute carrier family 26, member 10	518	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.					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)					GACACTGACCCGGGTAGGACT	0.587													C|||	6	0.00119808	0.0045	0.0	5008	,	,		19242	0.0		0.0	False		,,,				2504	0.0				p.R518W		Atlas-SNP	.											.	SLC26A10	89	.	0			c.C1552T						PASS	.	C	TRP/ARG	21,4385		0,21,2182	63	58	60		1552	1.2	0.8	12	dbSNP_133	60	1,8599		0,1,4299	yes	missense	SLC26A10	NM_133489.2	101	0,22,6481	TT,TC,CC		0.0116,0.4766,0.1692	probably-damaging	518/564	58019388	22,12984	2203	4300	6503	SO:0001583	missense	65012	exon14			CTGACCCGGGTAG		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.1552C>T	12.37:g.58019388C>T	ENSP00000320217:p.Arg518Trp	81	0	0		82	35	0.426829	NM_133489	A6NMJ2|B6ZDQ3|Q6ZWI7	Missense_Mutation	SNP	ENST00000320442.4	37	CCDS8949.2	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	.	9.455	1.091629	0.20471	0.004766	1.16E-4	ENSG00000135502	ENST00000320442	D	0.89343	-2.5	4.62	1.25	0.21368	Sulphate transporter/antisigma-factor antagonist STAS (4);	.	.	.	.	T	0.81531	0.4842	L	0.56199	1.76	0.41713	D	0.989468	B	0.27316	0.175	B	0.14023	0.01	T	0.76225	-0.3037	9	0.87932	D	0	.	1.6978	0.02866	0.2061:0.4624:0.1995:0.132	.	518	Q8NG04	S2610_HUMAN	W	518	ENSP00000320217:R518W	ENSP00000320217:R518W	R	+	1	2	SLC26A10	56305655	0.903000	0.30736	0.796000	0.32109	0.255000	0.26057	0.125000	0.15749	0.554000	0.29061	0.557000	0.71058	CGG	C|0.999;T|0.001	0.001	strong		0.587	SLC26A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250311.2			T	58019388	C	T	58019388	3	4	22	1	0	0	0	0	1	0	0	0	14530	643	23	1	1606	1	SLC26A10	12	58019388	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1723	58019388	75832507	2726	5627											
DPY19L2	283417	hgsc.bcm.edu	37	chr12	64057543	64057543	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aagaagaaacctaaccatttCagtgcgaaaagtcatctccc	16	8	6	11	1	3	2	2	0	1	2	4	3	3	2	3	0	3	0	3	0	6	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:64057543C>T	ENST00000324472.4	-	3	628	c.445G>A	c.(445-447)Gaa>Aaa	p.E149K	RP11-415I12.3_ENST00000509615.2_RNA	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	149					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.E149*(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)		CTAACCATTTCAGTGCGAAAA	0.333																																					p.E149K		Atlas-SNP	.											DPY19L2,caecum,carcinoma,0,1	DPY19L2	97	1	1	Substitution - Nonsense(1)	large_intestine(1)	c.G445A						scavenged	.						58	55	56					12																	64057543		2203	4299	6502	SO:0001583	missense	283417	exon3			CCATTTCAGTGCG		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.445G>A	12.37:g.64057543C>T	ENSP00000315988:p.Glu149Lys	317	0	0		344	21	0.0610465	NM_173812	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Missense_Mutation	SNP	ENST00000324472.4	37	CCDS31851.1	.	.	.	.	.	.	.	.	.	.	C	15.97	2.990830	0.54041	.	.	ENSG00000177990	ENST00000324472;ENST00000538147	T;T	0.68331	-0.32;-0.32	2.5	2.5	0.30297	.	0.000000	0.85682	U	0.000000	T	0.81230	0.4779	M	0.86740	2.835	0.80722	D	1	D	0.76494	0.999	D	0.76071	0.987	T	0.83031	-0.0162	9	.	.	.	.	10.7323	0.46104	0.0:1.0:0.0:0.0	.	149	Q6NUT2	D19L2_HUMAN	K	149;6	ENSP00000315988:E149K;ENSP00000439567:E6K	.	E	-	1	0	DPY19L2	62343810	1.000000	0.71417	0.999000	0.59377	0.753000	0.42808	6.967000	0.76079	1.389000	0.46526	0.184000	0.17185	GAA	.	.	none		0.333	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812		T	64057543	C	T	64057543	3	4	22	1	0	0	0	0	1	0	0	0	4743	835	29	2	1911	2	DPY19L2	12	64057543	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6038155	64057543	69794352	2727	5628											
DYRK2	8445	hgsc.bcm.edu	37	chr12	68052166	68052166	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgaggggcccaccggagagCagagagtgggggaacgcgct	9	3	19	10	3	0	3	0	1	0	2	0	6	0	4	2	5	2	2	2	5	1	0	rs56178357	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:68052166C>T	ENST00000344096.3	+	3	1892	c.1479C>T	c.(1477-1479)agC>agT	p.S493S	RP11-335O4.3_ENST00000425371.2_RNA|DYRK2_ENST00000393555.3_Silent_p.S420S	NM_006482.2	NP_006473.2	Q92630	DYRK2_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	493	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of NFAT protein import into nucleus (GO:0051534)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of glycogen biosynthetic process (GO:0045725)|protein phosphorylation (GO:0006468)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	30			Lung(24;6.81e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(7;0.000573)		CACCGGAGAGCAGAGAGTGGG	0.572													C|||	538	0.107428	0.382	0.0447	5008	,	,		19022	0.0		0.002	False		,,,				2504	0.0				p.S493S		Atlas-SNP	.											.	DYRK2	63	.	0			c.C1479T						PASS	.	C	,	1334,3072	442.3+/-346.6	195,944,1064	59	62	61		1260,1479	5.2	1	12	dbSNP_129	61	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous,coding-synonymous	DYRK2	NM_003583.3,NM_006482.2	,	195,953,5355	TT,TC,CC		0.1047,30.2769,10.326	,	420/529,493/602	68052166	1343,11663	2203	4300	6503	SO:0001819	synonymous_variant	8445	exon3			GGAGAGCAGAGAG	Y09216	CCDS8978.1, CCDS8979.1	12q15	2008-07-03				ENSG00000127334			3093	protein-coding gene	gene with protein product		603496				9748265	Standard	NM_003583		Approved		uc001str.4	Q92630		ENST00000344096.3:c.1479C>T	12.37:g.68052166C>T		163	0	0		170	85	0.5	NM_006482	B2R9V9|Q9BRB5	Silent	SNP	ENST00000344096.3	37	CCDS8978.1																																																																																			C|0.909;T|0.091	0.091	strong		0.572	DYRK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402218.1			T	68052166	C	T	68052166	2	4	22	1	0	0	0	0	0	0	0	1	4858	709	25	2		2	DYRK2	12	68052166	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3994623	68052166	65799729	2728	5629											
ZFC3H1	196441	hgsc.bcm.edu	37	chr12	72020103	72020103	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacacatttcctgcacctcGtccttggttcctctttttga	5	17	5	14	1	2	1	1	1	1	0	6	1	5	1	4	1	1	2	4	1	0	5	rs56384440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:72020103G>A	ENST00000378743.3	-	22	4612	c.4254C>T	c.(4252-4254)gaC>gaT	p.D1418D		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	1418					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						CCTGCACCTCGTCCTTGGTTC	0.413													G|||	121	0.0241613	0.0862	0.0086	5008	,	,		17082	0.0		0.001	False		,,,				2504	0.0				p.D1418D		Atlas-SNP	.											.	ZFC3H1	172	.	0			c.C4254T						PASS	.	G		253,3587		9,235,1676	185	176	179		4254	-7.2	0.5	12	dbSNP_129	179	3,8243		0,3,4120	no	coding-synonymous	ZFC3H1	NM_144982.4		9,238,5796	AA,AG,GG		0.0364,6.5885,2.1182		1418/1990	72020103	256,11830	1920	4123	6043	SO:0001819	synonymous_variant	196441	exon22			CACCTCGTCCTTG	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.4254C>T	12.37:g.72020103G>A		173	0	0		147	70	0.47619	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Silent	SNP	ENST00000378743.3	37	CCDS41813.1																																																																																			A|0.013;G|0.987	0.013	strong		0.413	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982		A	72020103	G	A	72020103	2	1	22	1	0	0	0	0	0	0	0	1	17648	1136	40	1		1	ZFC3H1	12	72020103	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3967937	72020103	61831792	2729	5630											
TMEM19	55266	hgsc.bcm.edu	37	chr12	72094627	72094627	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagggttggatgaaagcaCtggcatggtggtcaacagcc	10	8	14	9	0	1	1	1	1	0	0	2	2	2	2	2	5	3	3	2	5	2	1	rs74104122	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:72094627C>G	ENST00000266673.5	+	6	1457	c.863C>G	c.(862-864)aCt>aGt	p.T288S		NM_018279.3	NP_060749.2	Q96HH6	TMM19_HUMAN	transmembrane protein 19	288						integral component of membrane (GO:0016021)				large_intestine(1)|lung(8)	9		Breast(359;0.0889)		GBM - Glioblastoma multiforme(134;0.044)		GATGAAAGCACTGGCATGGTG	0.358													C|||	126	0.0251597	0.09	0.0086	5008	,	,		17302	0.0		0.001	False		,,,				2504	0.0				p.T288S		Atlas-SNP	.											.	TMEM19	35	.	0			c.C863G						PASS	.	C	SER/THR	319,4087	170.9+/-201.2	13,293,1897	195	174	181		863	5	1	12	dbSNP_130	181	3,8597	3.0+/-9.4	0,3,4297	yes	missense	TMEM19	NM_018279.3	58	13,296,6194	GG,GC,CC		0.0349,7.2401,2.4758	possibly-damaging	288/337	72094627	322,12684	2203	4300	6503	SO:0001583	missense	55266	exon6			AAAGCACTGGCAT	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.863C>G	12.37:g.72094627C>G	ENSP00000266673:p.Thr288Ser	157	0	0		188	95	0.505319	NM_018279	B2RDL2|Q53FY3|Q9NV41	Missense_Mutation	SNP	ENST00000266673.5	37	CCDS9002.1	45|45	0.020604395604395604|0.020604395604395604	43|43	0.08739837398373984|0.08739837398373984	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	C|C	10.59|10.59	1.393752|1.393752	0.25205|0.25205	0.072401|0.072401	3.49E-4|3.49E-4	ENSG00000139291|ENSG00000139291	ENST00000550787|ENST00000266673;ENST00000546795	.|.	.|.	.|.	5.93|5.93	5.03|5.03	0.67393|0.67393	.|.	.|0.100553	.|0.64402	.|N	.|0.000002	T|T	0.02649|0.02649	0.0080|0.0080	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	.|P	.|0.51537	.|0.946	.|P	.|0.48952	.|0.596	T|T	0.04165|0.04165	-1.0972|-1.0972	5|9	.|0.08837	.|T	.|0.75	-22.104|-22.104	12.1152|12.1152	0.53861|0.53861	0.0:0.8121:0.1216:0.0663|0.0:0.8121:0.1216:0.0663	.|.	.|288	.|Q96HH6	.|TMM19_HUMAN	Q|S	103|288;132	.|.	.|ENSP00000266673:T288S	H|T	+|+	3|2	2|0	TMEM19|TMEM19	70380894|70380894	0.990000|0.990000	0.36364|0.36364	0.993000|0.993000	0.49108|0.49108	0.973000|0.973000	0.67179|0.67179	1.858000|1.858000	0.39408|0.39408	1.463000|1.463000	0.47967|0.47967	0.655000|0.655000	0.94253|0.94253	CAC|ACT	C|0.976;G|0.024	0.024	strong		0.358	TMEM19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404801.1	NM_018279		G	72094627	C	G	72094627	3	3	22	1	0	0	0	0	1	0	0	0	16128	565	20	4	885	4	TMEM19	12	72094627	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	74524	72094627	61757268	2730	5631											
LRRIQ1	84125	hgsc.bcm.edu	37	chr12	85492658	85492658	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatatagcttccatccttggAgaatcttgttttactaagag	12	15	7	7	0	1	2	0	0	1	2	3	3	3	2	2	1	2	2	2	1	6	8	rs139758674	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:85492658A>C	ENST00000393217.2	+	13	3156	c.3095A>C	c.(3094-3096)gAg>gCg	p.E1032A		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1032										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)		CCATCCTTGGAGAATCTTGTT	0.299													A|||	43	0.00858626	0.031	0.0029	5008	,	,		11103	0.0		0.0	False		,,,				2504	0.0				p.E1032A		Atlas-SNP	.											LRRIQ1_ENST00000393217,NS,carcinoma,-1,2	LRRIQ1	512	2	0			c.A3095C						scavenged	.	A	ALA/GLU	79,4325	69.8+/-107.6	1,77,2124	75	78	77		3095	0.4	0	12	dbSNP_134	77	2,8586	2.2+/-6.3	0,2,4292	yes	missense	LRRIQ1	NM_001079910.1	107	1,79,6416	CC,CA,AA		0.0233,1.7938,0.6235	benign	1032/1723	85492658	81,12911	2202	4294	6496	SO:0001583	missense	84125	exon13			CCTTGGAGAATCT	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.3095A>C	12.37:g.85492658A>C	ENSP00000376910:p.Glu1032Ala	92	1	0.0108696		94	47	0.5	NM_001079910	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	37	CCDS41816.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	A	6.385	0.439095	0.12104	0.017938	2.33E-4	ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393217	T	0.23348	1.91	5.18	0.447	0.16608	.	1.889910	0.03114	N	0.162924	T	0.08537	0.0212	N	0.20574	0.59	0.09310	N	1	B;B	0.25667	0.063;0.131	B;B	0.22386	0.039;0.039	T	0.21211	-1.0252	10	0.56958	D	0.05	.	4.26	0.10737	0.6323:0.0:0.2269:0.1408	.	1032;1007	Q96JM4;C9JI57	LRIQ1_HUMAN;.	A	1032;1007;1032	ENSP00000376910:E1032A	ENSP00000256007:E1032A	E	+	2	0	LRRIQ1	84016789	0.569000	0.26643	0.003000	0.11579	0.778000	0.44026	1.102000	0.31050	-0.162000	0.10964	0.477000	0.44152	GAG	A|0.995;C|0.005	0.005	strong		0.299	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		C	85492658	A	C	85492658	3	2	22	1	0	0	0	0	1	0	0	0	9038	304	11	5	3141	5	LRRIQ1	12	85492658	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	13398031	85492658	48359237	2731	5632											
KITLG	4254	hgsc.bcm.edu	37	chr12	88912624	88912624	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gacaattgtactaccatctcGcttatccaacaatgacttgg	12	12	6	11	1	1	1	0	1	1	0	3	2	2	1	2	1	3	2	2	1	6	5	rs17015782	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:88912624G>A	ENST00000228280.5	-	4	395	c.213C>T	c.(211-213)agC>agT	p.S71S	KITLG_ENST00000378535.4_5'UTR|KITLG_ENST00000347404.5_Silent_p.S71S|KITLG_ENST00000357116.4_Intron	NM_000899.4	NP_000890.1	P21583	SCF_HUMAN	KIT ligand	71					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						CTACCATCTCGCTTATCCAAC	0.353									Testicular Cancer, Familial Clustering of				G|||	52	0.0103834	0.0378	0.0029	5008	,	,		20000	0.0		0.0	False		,,,				2504	0.0				p.S71S		Atlas-SNP	.											.	KITLG	26	.	0			c.C213T						PASS	.	G	,	154,4252	106.0+/-144.5	2,150,2051	76	74	75		213,213	-10.1	0	12	dbSNP_123	75	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	KITLG	NM_000899.4,NM_003994.5	,	2,150,6351	AA,AG,GG		0.0,3.4952,1.1841	,	71/274,71/246	88912624	154,12852	2203	4300	6503	SO:0001819	synonymous_variant	4254	exon4	Familial Cancer Database		CATCTCGCTTATC	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.213C>T	12.37:g.88912624G>A		83	0	0		94	41	0.43617	NM_003994	A0AV09|A8K2Q4|B7ZLM4|Q16487|Q68DZ2|Q7M4N8|Q9UQK7	Silent	SNP	ENST00000228280.5	37	CCDS31868.1																																																																																			G|0.988;A|0.012	0.012	strong		0.353	KITLG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406424.2	NM_003994		A	88912624	G	A	88912624	2	1	22	1	0	0	0	0	0	0	0	1	8339	1078	38	1		1	KITLG	12	88912624	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3419966	88912624	44939271	2732	5633											
GALNT4	8693	hgsc.bcm.edu	37	chr12	89916781	89916781	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccatctttgggacaattttGcattcccacataattttttt	9	18	4	10	0	1	0	0	0	1	0	2	1	2	1	2	1	1	1	2	1	2	8	rs139995124	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:89916781G>T	ENST00000529983.2	-	1	1802	c.1546C>A	c.(1546-1548)Caa>Aaa	p.Q516K	POC1B_ENST00000549035.1_Intron|POC1B-GALNT4_ENST00000547474.1_3'UTR|RP11-734K2.4_ENST00000605233.1_RNA|POC1B-GALNT4_ENST00000548729.1_Missense_Mutation_p.Q513K|POC1B_ENST00000393179.4_Intron|GALNT4_ENST00000413530.1_Missense_Mutation_p.Q344K|POC1B_ENST00000541909.1_Intron|POC1B_ENST00000549504.1_Intron|POC1B_ENST00000313546.3_Intron	NM_003774.4	NP_003765.2	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	516	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						GGACAATTTTGCATTCCCACA	0.358													G|||	11	0.00219649	0.0023	0.0	5008	,	,		19748	0.0		0.007	False		,,,				2504	0.001				p.Q516K		Atlas-SNP	.											.	GALNT4	38	.	0			c.C1546A						PASS	.	G	,LYS/GLN,LYS/GLN,LYS/GLN,	5,3649		0,5,1822	71	67	68		,1537,1030,1546,	5	1	12	dbSNP_134	68	65,8115		0,65,4025	yes	intron,missense,missense,missense,intron	GALNT4,POC1B,POC1B-GALNT4	NM_001199777.1,NM_001199781.1,NM_001199782.1,NM_003774.4,NM_172240.2	,53,53,53,	0,70,5847	TT,TG,GG		0.7946,0.1368,0.5915	,benign,benign,benign,	,513/576,344/407,516/579,	89916781	70,11764	1827	4090	5917	SO:0001583	missense	8693	exon1			AATTTTGCATTCC	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.1546C>A	12.37:g.89916781G>T	ENSP00000436604:p.Gln516Lys	82	0	0		84	46	0.547619	NM_003774	B2R775|B4DMX6|O00208	Missense_Mutation	SNP	ENST00000529983.2	37	CCDS53817.1	9	0.004120879120879121	3	0.006097560975609756	0	0.0	0	0.0	6	0.0079155672823219	G	11.35	1.612993	0.28712	0.001368	0.007946	ENSG00000259075;ENSG00000259075;ENSG00000257594	ENST00000548729;ENST00000413530;ENST00000529983	T;T;T	0.29397	1.57;1.57;1.57	5.93	4.99	0.66335	Ricin B-related lectin (1);Ricin B lectin (3);	.	.	.	.	T	0.11623	0.0283	N	0.10645	0.015	0.39363	D	0.965958	B;B	0.06786	0.0;0.001	B;B	0.09377	0.003;0.004	T	0.08638	-1.0712	9	0.27785	T	0.31	.	12.0779	0.53655	0.0:0.0:0.7004:0.2996	.	513;516	F8VUJ3;Q8N4A0	.;GALT4_HUMAN	K	513;344;516	ENSP00000447852:Q513K;ENSP00000389686:Q344K;ENSP00000436604:Q516K	ENSP00000436604:Q516K	Q	-	1	0	GALNT4;RP11-1109F11.4	88440912	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	6.469000	0.73555	2.814000	0.96858	0.591000	0.81541	CAA	G|0.996;T|0.004	0.004	strong		0.358	GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388973.2	NM_003774		T	89916781	G	T	89916781	3	4	22	1	0	0	0	0	1	0	0	0	6223	1328	46	4	194	4	GALNT4	12	89916781	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1004157	89916781	43935114	2733	5634											
USP44	84101	hgsc.bcm.edu	37	chr12	95927087	95927087	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	cttacaagatcttgtcttctCgctagcagtcatagccagcc	9	12	7	13	1	4	1	1	0	3	1	5	1	4	1	2	0	4	2	2	0	4	5	rs7305024	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:95927087C>G	ENST00000258499.3	-	2	1234	c.946G>C	c.(946-948)Gag>Cag	p.E316Q	USP44_ENST00000537435.2_Missense_Mutation_p.E316Q|USP44_ENST00000552440.1_Missense_Mutation_p.E316Q|USP44_ENST00000393091.2_Missense_Mutation_p.E316Q	NM_001278393.1|NM_032147.2	NP_001265322.1|NP_115523.2	Q9H0E7	UBP44_HUMAN	ubiquitin specific peptidase 44	316	USP.		E -> Q (in dbSNP:rs7305024).		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						CTTGTCTTCTCGCTAGCAGTC	0.368													C|||	251	0.0501198	0.1808	0.0159	5008	,	,		21981	0.0		0.001	False		,,,				2504	0.0				p.E316Q		Atlas-SNP	.											.	USP44	83	.	0			c.G946C						PASS	.	C	GLN/GLU,GLN/GLU	667,3739	282.2+/-276.4	46,575,1582	59	56	57		946,946	5	0.5	12	dbSNP_116	57	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	USP44	NM_001042403.1,NM_032147.2	29,29	46,580,5877	GG,GC,CC		0.0581,15.1384,5.1668	benign,benign	316/713,316/713	95927087	672,12334	2203	4300	6503	SO:0001583	missense	84101	exon2			TCTTCTCGCTAGC	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.946G>C	12.37:g.95927087C>G	ENSP00000258499:p.Glu316Gln	60	0	0		64	31	0.484375	NM_032147	B2RDW3	Missense_Mutation	SNP	ENST00000258499.3	37	CCDS9053.1	103	0.04716117216117216	97	0.19715447154471544	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	C	3.204	-0.163026	0.06502	0.151384	5.81E-4	ENSG00000136014	ENST00000258499;ENST00000393091;ENST00000552440;ENST00000537435	T;T;T;T	0.29655	1.56;1.56;1.56;1.56	4.96	4.96	0.65561	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.473004	0.24200	N	0.040632	T	0.00039	0.0001	N	0.24115	0.695	0.44899	P	0.0020879999999999788	B	0.27264	0.173	B	0.35114	0.196	T	0.27054	-1.0085	9	0.16896	T	0.51	.	18.5826	0.91177	0.0:1.0:0.0:0.0	rs7305024;rs52829293;rs7305024	316	Q9H0E7	UBP44_HUMAN	Q	316	ENSP00000258499:E316Q;ENSP00000376806:E316Q;ENSP00000448670:E316Q;ENSP00000442629:E316Q	ENSP00000258499:E316Q	E	-	1	0	USP44	94451218	1.000000	0.71417	0.477000	0.27303	0.042000	0.13812	2.166000	0.42406	2.457000	0.83068	0.561000	0.74099	GAG	C|0.955;G|0.045	0.045	strong		0.368	USP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408312.1	NM_032147		G	95927087	C	G	95927087	3	3	22	1	0	0	0	0	1	0	0	0	17090	893	31	4	1212	4	USP44	12	95927087	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6010306	95927087	37924808	2734	5635											
USP44	84101	hgsc.bcm.edu	37	chr12	95927172	95927172	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaatgactcaacacctgaagAacagaattcatatagcaagt	19	8	6	8	0	2	4	2	2	0	2	2	4	2	4	1	0	3	1	1	0	8	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:95927172A>G	ENST00000258499.3	-	2	1149	c.861T>C	c.(859-861)gtT>gtC	p.V287V	USP44_ENST00000537435.2_Silent_p.V287V|USP44_ENST00000552440.1_Silent_p.V287V|USP44_ENST00000393091.2_Silent_p.V287V	NM_001278393.1|NM_032147.2	NP_001265322.1|NP_115523.2	Q9H0E7	UBP44_HUMAN	ubiquitin specific peptidase 44	287	USP.				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						ACACCTGAAGAACAGAATTCA	0.378																																					p.V287V		Atlas-SNP	.											.	USP44	83	.	0			c.T861C						PASS	.						77	79	78					12																	95927172		2203	4300	6503	SO:0001819	synonymous_variant	84101	exon2			CTGAAGAACAGAA	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.861T>C	12.37:g.95927172A>G		66	0	0		76	35	0.460526	NM_032147	B2RDW3	Silent	SNP	ENST00000258499.3	37	CCDS9053.1																																																																																			.	.	none		0.378	USP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408312.1	NM_032147		G	95927172	A	G	95927172	2	3	22	1	0	0	0	0	0	0	0	1	17090	233	9	3		3	USP44	12	95927172	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	85	95927172	37924723	2735	5636											
ELK3	2004	hgsc.bcm.edu	37	chr12	96641344	96641344	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagcccttgaacctgtcatcGggctccaagaccaagtctcc	9	8	9	15	1	2	2	1	1	1	1	5	3	3	2	5	1	2	1	5	1	3	1	rs115218295	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:96641344G>A	ENST00000228741.3	+	3	1160	c.834G>A	c.(832-834)tcG>tcA	p.S278S	ELK3_ENST00000552142.1_Intron	NM_005230.2	NP_005221.2	P41970	ELK3_HUMAN	ELK3, ETS-domain protein (SRF accessory protein 2)	278					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)	p.S278S(1)		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)					ACCTGTCATCGGGCTCCAAGA	0.602													G|||	45	0.00898562	0.0333	0.0	5008	,	,		16138	0.0		0.001	False		,,,				2504	0.0				p.S278S		Atlas-SNP	.											.	ELK3	36	.	1	Substitution - coding silent(1)	lung(1)	c.G834A						PASS	.	G		125,4281	90.6+/-129.3	2,121,2080	67	75	72		834	-1.9	0.9	12	dbSNP_132	72	0,8600		0,0,4300	no	coding-synonymous	ELK3	NM_005230.2		2,121,6380	AA,AG,GG		0.0,2.837,0.9611		278/408	96641344	125,12881	2203	4300	6503	SO:0001819	synonymous_variant	2004	exon3			GTCATCGGGCTCC	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.834G>A	12.37:g.96641344G>A		55	0	0		59	32	0.542373	NM_005230	B2R6S6|Q6FG57|Q6GU29|Q9UD17	Silent	SNP	ENST00000228741.3	37	CCDS9060.1																																																																																			G|0.990;A|0.010	0.010	strong		0.602	ELK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408694.1	NM_005230		A	96641344	G	A	96641344	2	1	22	1	0	0	0	0	0	0	0	1	5062	1103	39	1		1	ELK3	12	96641344	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	714172	96641344	37210551	2736	5637											
GAS2L3	283431	hgsc.bcm.edu	37	chr12	101018061	101018061	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atctcacttagctgcacattCaaattcatcctcaaaatgtc	13	13	3	12	0	4	0	4	0	1	0	7	0	5	0	1	0	2	2	1	0	4	3	rs61748063	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:101018061C>T	ENST00000539410.1	+	9	1864	c.1478C>T	c.(1477-1479)tCa>tTa	p.S493L	GAS2L3_ENST00000547754.1_Missense_Mutation_p.S493L|GAS2L3_ENST00000266754.5_Missense_Mutation_p.S493L|GAS2L3_ENST00000537247.1_Missense_Mutation_p.S389L			Q86XJ1	GA2L3_HUMAN	growth arrest-specific 2 like 3	493					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						GCTGCACATTCAAATTCATCC	0.363													C|||	17	0.00339457	0.0008	0.0086	5008	,	,		20148	0.0		0.008	False		,,,				2504	0.002				p.S493L		Atlas-SNP	.											.	GAS2L3	76	.	0			c.C1478T						PASS	.	C	LEU/SER	6,4398	11.4+/-27.6	0,6,2196	61	65	64		1478	-0.2	0	12	dbSNP_129	64	50,8550	32.8+/-85.7	0,50,4250	yes	missense	GAS2L3	NM_174942.1	145	0,56,6446	TT,TC,CC		0.5814,0.1362,0.4306	benign	493/695	101018061	56,12948	2202	4300	6502	SO:0001583	missense	283431	exon10			CACATTCAAATTC	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.1478C>T	12.37:g.101018061C>T	ENSP00000439672:p.Ser493Leu	40	0	0		57	30	0.526316	NM_174942	B2RCN2	Missense_Mutation	SNP	ENST00000539410.1	37	CCDS9079.1	11	0.005036630036630037	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	5	0.006596306068601583	C	0.060	-1.227601	0.01518	0.001362	0.005814	ENSG00000139354	ENST00000266754;ENST00000547754;ENST00000537247;ENST00000539410	T;T;T;T	0.22743	1.96;1.96;1.94;1.96	4.93	-0.166	0.13351	.	1.089570	0.07116	N	0.843066	T	0.06142	0.0159	N	0.02315	-0.6	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.37478	-0.9704	10	0.23302	T	0.38	-1.9276	10.8995	0.47043	0.0:0.4908:0.0:0.5092	rs61748063	493	Q86XJ1	GA2L3_HUMAN	L	493;493;389;493	ENSP00000266754:S493L;ENSP00000448955:S493L;ENSP00000442406:S389L;ENSP00000439672:S493L	ENSP00000266754:S493L	S	+	2	0	GAS2L3	99542192	0.000000	0.05858	0.000000	0.03702	0.198000	0.23893	-0.585000	0.05794	-0.113000	0.11958	-0.793000	0.03317	TCA	C|0.995;T|0.005	0.005	strong		0.363	GAS2L3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409143.1	NM_174942		T	101018061	C	T	101018061	3	4	22	1	0	0	0	0	1	0	0	0	6256	838	29	2	1508	2	GAS2L3	12	101018061	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4376717	101018061	32833834	2737	5638											
SLC5A8	160728	hgsc.bcm.edu	37	chr12	101551065	101551065	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atcagagcagcttcacaaacGagtcccattgctcttgccac	11	9	7	14	1	3	1	2	0	1	1	4	2	4	1	2	0	5	3	2	0	1	3	rs113062899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:101551065G>A	ENST00000536262.2	-	15	2383	c.1825C>T	c.(1825-1827)Cgt>Tgt	p.R609C		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						CTTCACAAACGAGTCCCATTG	0.378													G|||	60	0.0119808	0.0446	0.0014	5008	,	,		19406	0.0		0.0	False		,,,				2504	0.0				p.R609C	GBM(60;420 1056 13605 22380 47675)	Atlas-SNP	.											.	SLC5A8	102	.	0			c.C1825T						PASS	.	G	CYS/ARG	145,4261	100.7+/-139.4	0,145,2058	136	119	125		1825	5.2	1	12	dbSNP_132	125	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SLC5A8	NM_145913.3	180	0,146,6357	AA,AG,GG		0.0116,3.291,1.1226	probably-damaging	609/611	101551065	146,12860	2203	4300	6503	SO:0001583	missense	160728	exon15			ACAAACGAGTCCC	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.1825C>T	12.37:g.101551065G>A	ENSP00000445340:p.Arg609Cys	128	0	0		118	67	0.567797	NM_145913		Missense_Mutation	SNP	ENST00000536262.2	37	CCDS9080.1	27	0.012362637362637362	26	0.052845528455284556	1	0.0027624309392265192	0	0.0	0	0.0	G	15.83	2.949451	0.53186	0.03291	1.16E-4	ENSG00000256870	ENST00000536262	D	0.86230	-2.09	5.15	5.15	0.70609	.	0.710763	0.13338	N	0.395349	T	0.55577	0.1929	L	0.47716	1.5	0.40861	D	0.983839	D	0.56968	0.978	B	0.43623	0.425	T	0.77590	-0.2531	10	0.87932	D	0	.	15.919	0.79544	0.0:0.0:1.0:0.0	.	609	Q8N695	SC5A8_HUMAN	C	609	ENSP00000445340:R609C	ENSP00000445340:R609C	R	-	1	0	SLC5A8	100075196	1.000000	0.71417	1.000000	0.80357	0.510000	0.34073	3.942000	0.56614	2.574000	0.86865	0.655000	0.94253	CGT	G|0.987;A|0.013	0.013	strong		0.378	SLC5A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409401.1	NM_145913		A	101551065	G	A	101551065	3	1	22	1	0	0	0	0	1	0	0	0	14686	1058	37	1	11	1	SLC5A8	12	101551065	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	533004	101551065	32300830	2738	5639											
UTP20	27340	hgsc.bcm.edu	37	chr12	101679569	101679569	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgacaaatgccaatcattcaAtcagttggtgtatcaccaaa	15	11	6	9	0	4	1	4	1	0	0	4	1	4	1	2	1	1	2	2	1	5	3	rs140064475	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:101679569A>G	ENST00000261637.4	+	4	410	c.236A>G	c.(235-237)aAt>aGt	p.N79S		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	79					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						CAATCATTCAATCAGTTGGTG	0.368													A|||	11	0.00219649	0.0083	0.0	5008	,	,		18123	0.0		0.0	False		,,,				2504	0.0				p.N79S		Atlas-SNP	.											.	UTP20	222	.	0			c.A236G						PASS	.	A	SER/ASN	23,4383	30.8+/-60.4	0,23,2180	99	99	99		236	5.6	1	12	dbSNP_134	99	1,8599	1.2+/-3.3	0,1,4299	yes	missense	UTP20	NM_014503.2	46	0,24,6479	GG,GA,AA		0.0116,0.522,0.1845	probably-damaging	79/2786	101679569	24,12982	2203	4300	6503	SO:0001583	missense	27340	exon4			CATTCAATCAGTT	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.236A>G	12.37:g.101679569A>G	ENSP00000261637:p.Asn79Ser	69	0	0		44	25	0.568182	NM_014503	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	37	CCDS9081.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	15.61	2.883689	0.51908	0.00522	1.16E-4	ENSG00000120800	ENST00000261637	T	0.40476	1.03	5.56	5.56	0.83823	.	0.104115	0.64402	D	0.000005	T	0.48132	0.1483	L	0.57536	1.79	0.48040	D	0.999572	D	0.62365	0.991	P	0.58013	0.831	T	0.53215	-0.8470	10	0.46703	T	0.11	-26.0442	15.7176	0.77681	1.0:0.0:0.0:0.0	.	79	O75691	UTP20_HUMAN	S	79	ENSP00000261637:N79S	ENSP00000261637:N79S	N	+	2	0	UTP20	100203700	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.098000	0.76974	2.104000	0.64026	0.528000	0.53228	AAT	A|0.998;G|0.002	0.002	strong		0.368	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		G	101679569	A	G	101679569	3	3	22	1	0	0	0	0	1	0	0	0	17114	101	4	3	250	3	UTP20	12	101679569	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	128504	101679569	32172326	2739	5640											
STAB2	55576	hgsc.bcm.edu	37	chr12	104014294	104014294	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caatggcagaggcagttgtgCtgaaggcatggaaggaaatg	13	7	16	5	0	0	2	0	1	0	1	0	4	0	4	0	5	1	5	0	5	4	1	rs150189813	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:104014294C>T	ENST00000388887.2	+	4	584	c.380C>T	c.(379-381)gCt>gTt	p.A127V		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						GGCAGTTGTGCTGAAGGCATG	0.493													C|||	2	0.000399361	0.0008	0.0014	5008	,	,		19345	0.0		0.0	False		,,,				2504	0.0				p.A127V		Atlas-SNP	.											.	STAB2	370	.	0			c.C380T						PASS	.	C	VAL/ALA	5,4399		0,5,2197	115	93	100		380	1.8	0.1	12	dbSNP_134	100	0,8594		0,0,4297	yes	missense	STAB2	NM_017564.9	64	0,5,6494	TT,TC,CC		0.0,0.1135,0.0385	possibly-damaging	127/2552	104014294	5,12993	2202	4297	6499	SO:0001583	missense	55576	exon4			GTTGTGCTGAAGG	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.380C>T	12.37:g.104014294C>T	ENSP00000373539:p.Ala127Val	195	0	0		209	107	0.511962	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	37	CCDS31888.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	13.25	2.179669	0.38511	0.001135	0.0	ENSG00000136011	ENST00000388887	D	0.83673	-1.75	4.98	1.84	0.25277	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.200082	0.43919	D	0.000512	T	0.71221	0.3314	L	0.33485	1.01	0.18873	N	0.999987	P	0.41041	0.736	B	0.38803	0.282	T	0.59762	-0.7393	10	0.18710	T	0.47	.	11.2145	0.48819	0.5338:0.4662:0.0:0.0	.	127	Q8WWQ8	STAB2_HUMAN	V	127	ENSP00000373539:A127V	ENSP00000373539:A127V	A	+	2	0	STAB2	102538424	0.227000	0.23707	0.136000	0.22124	0.997000	0.91878	0.357000	0.20199	0.122000	0.18314	0.549000	0.68633	GCT	C|1.000;T|0.000	0.000	strong		0.493	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			T	104014294	C	T	104014294	3	4	22	1	0	0	0	0	1	0	0	0	15253	797	28	2	394	2	STAB2	12	104014294	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2334725	104014294	29837601	2740	5641											
STAB2	55576	hgsc.bcm.edu	37	chr12	104089586	104089586	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctccaaacaacaatgccatCgagaattacatcagggagaa	17	6	8	10	1	1	2	1	0	0	2	3	4	2	2	2	1	4	1	2	1	6	1	rs17034395	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:104089586C>T	ENST00000388887.2	+	33	3750	c.3546C>T	c.(3544-3546)atC>atT	p.I1182I		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						ACAATGCCATCGAGAATTACA	0.403													.|||	380	0.0758786	0.2269	0.0231	5008	,	,		24489	0.0		0.0	False		,,,				2504	0.0654				p.I1182I		Atlas-SNP	.											.	STAB2	370	.	0			c.C3546T						PASS	.	C		855,3551	335.5+/-303.9	98,659,1446	112	110	110		3546	-1.1	1	12	dbSNP_123	110	19,8581	12.6+/-44.7	0,19,4281	no	coding-synonymous	STAB2	NM_017564.9		98,678,5727	TT,TC,CC		0.2209,19.4054,6.72		1182/2552	104089586	874,12132	2203	4300	6503	SO:0001819	synonymous_variant	55576	exon33			TGCCATCGAGAAT	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.3546C>T	12.37:g.104089586C>T		142	0	0		123	52	0.422764	NM_017564		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																			C|0.930;T|0.070	0.070	strong		0.403	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			T	104089586	C	T	104089586	2	4	22	1	0	0	0	0	0	0	0	1	15253	874	31	1		1	STAB2	12	104089586	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	75292	104089586	29762309	2741	5642											
RFX4	5992	hgsc.bcm.edu	37	chr12	107114548	107114548	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttcttgtaggtggctgccaaGagacaagggtccttgaagaa	11	10	13	7	0	1	3	0	1	1	2	2	4	2	3	2	3	1	2	2	3	5	4	rs73391388	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:107114548G>A	ENST00000392842.1	+	13	1659	c.1245G>A	c.(1243-1245)aaG>aaA	p.K415K	RP11-482D24.3_ENST00000552415.1_RNA|RFX4_ENST00000229387.5_Silent_p.K321K|RFX4_ENST00000357881.4_Silent_p.K424K|RP11-144F15.1_ENST00000551505.1_Intron	NM_213594.2	NP_998759.1	Q33E94	RFX4_HUMAN	regulatory factor X, 4 (influences HLA class II expression)	415	Necessary for dimerization.				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						TGGCTGCCAAGAGACAAGGGT	0.493													G|||	53	0.0105831	0.0378	0.0043	5008	,	,		20153	0.0		0.0	False		,,,				2504	0.0				p.K424K		Atlas-SNP	.											.	RFX4	218	.	0			c.G1272A						PASS	.	G	,,	175,4231	115.4+/-153.4	2,171,2030	89	81	84		1272,963,1245	5.6	1	12	dbSNP_130	84	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous	RFX4	NM_001206691.1,NM_032491.5,NM_213594.2	,,	2,178,6323	AA,AG,GG		0.0814,3.9719,1.3994	,,	424/745,321/642,415/736	107114548	182,12824	2203	4300	6503	SO:0001819	synonymous_variant	5992	exon13			TGCCAAGAGACAA	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.1245G>A	12.37:g.107114548G>A		165	0	0		156	66	0.423077	NM_001206691	A8K5Y0|B2RDW4|Q33DW6|Q33DW7|Q33E95|Q6YM53|Q8MHQ1|Q8NC78|Q8NDF9|Q8SNA1|Q96S80|Q9BXI0	Silent	SNP	ENST00000392842.1	37	CCDS9106.1																																																																																			G|0.988;A|0.012	0.012	strong		0.493	RFX4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402707.1	NM_032491		A	107114548	G	A	107114548	2	1	22	1	0	0	0	0	0	0	0	1	13280	933	33	2		2	RFX4	12	107114548	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3024962	107114548	26737347	2742	5643											
ACACB	32	hgsc.bcm.edu	37	chr12	109637234	109637234	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attaccatcggcaataagacGtgtgtgtttgagaaggagaa	14	10	12	5	2	0	3	0	1	0	3	1	5	0	3	1	2	1	2	1	2	5	3	rs73398054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:109637234G>T	ENST00000338432.7	+	18	2774	c.2655G>T	c.(2653-2655)acG>acT	p.T885T	ACACB_ENST00000377848.3_Silent_p.T885T|ACACB_ENST00000377854.5_Silent_p.T885T			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	885					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)	GCAATAAGACGTGTGTGTTTG	0.552													G|||	34	0.00678914	0.0234	0.0043	5008	,	,		18076	0.0		0.0	False		,,,				2504	0.0				p.T885T		Atlas-SNP	.											.	ACACB	330	.	0			c.G2655T						PASS	.						146	131	136					12																	109637234		2203	4300	6503	SO:0001819	synonymous_variant	32	exon17			TAAGACGTGTGTG	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.2655G>T	12.37:g.109637234G>T		109	0	0		96	46	0.479167	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Silent	SNP	ENST00000338432.7	37	CCDS31898.1																																																																																			A|0.006;G|0.992;T|0.002	0.002	strong		0.552	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		T	109637234	G	T	109637234	2	4	22	1	0	0	0	0	0	0	0	1	107	1132	40	4		4	ACACB	12	109637234	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2522686	109637234	24214661	2743	5644											
RPL6	6128	hgsc.bcm.edu	37	chr12	112843105	112843105	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtagccctggagctgaggaaTagctttgatttttggtaaaa	11	13	12	5	0	0	2	0	2	0	0	0	4	0	4	1	3	3	4	1	3	5	6	rs141161168	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:112843105T>C	ENST00000424576.2	-	7	975	c.790A>G	c.(790-792)Att>Gtt	p.I264V	RPL6_ENST00000202773.9_Missense_Mutation_p.I264V	NM_001024662.1	NP_001019833.1	Q02878	RL6_HUMAN	ribosomal protein L6	264				AVDSQILPKIKAIPQLQ -> LWTHKFYQKSKLFLSSS (in Ref. 1; CAA49188). {ECO:0000305}.	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)|regulation of transcription, DNA-templated (GO:0006355)|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)	cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			cervix(1)|large_intestine(6)|lung(3)	10						AGCTGAGGAATAGCTTTGATT	0.363													T|||	3	0.000599042	0.0023	0.0	5008	,	,		18604	0.0		0.0	False		,,,				2504	0.0				p.I264V		Atlas-SNP	.											.	RPL6	20	.	0			c.A790G						PASS	.	T	VAL/ILE,VAL/ILE	12,4366		0,12,2177	20	22	22		790,790	-1.2	0	12	dbSNP_134	22	0,8470		0,0,4235	no	missense,missense	RPL6	NM_000970.3,NM_001024662.1	29,29	0,12,6412	CC,CT,TT		0.0,0.2741,0.0934	benign,benign	264/289,264/289	112843105	12,12836	2189	4235	6424	SO:0001583	missense	6128	exon7			GAGGAATAGCTTT	X69391	CCDS9162.1	12q24.13	2014-06-05				ENSG00000089009		"L ribosomal proteins"	10362	protein-coding gene	gene with protein product		603703		TXREB1		8479925, 8457378	Standard	XM_005253920		Approved	TAXREB107, L6	uc001ttv.3	Q02878		ENST00000424576.2:c.790A>G	12.37:g.112843105T>C	ENSP00000403172:p.Ile264Val	90	0	0		80	34	0.425	NM_001024662	Q2M3Q3|Q8WW97	Missense_Mutation	SNP	ENST00000424576.2	37	CCDS9162.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	4.047	0.006419	0.07866	0.002741	0.0	ENSG00000089009	ENST00000202773;ENST00000424576;ENST00000549923	T;T	0.28069	1.63;1.63	5.15	-1.17	0.09648	.	0.242260	0.41294	N	0.000912	T	0.09423	0.0232	N	0.01656	-0.775	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.34054	-0.9844	10	0.10902	T	0.67	.	12.53	0.56109	0.0:0.4627:0.0:0.5373	.	264	Q02878	RL6_HUMAN	V	264;264;204	ENSP00000202773:I264V;ENSP00000403172:I264V	ENSP00000202773:I264V	I	-	1	0	RPL6	111327488	0.025000	0.19082	0.010000	0.14722	0.906000	0.53458	0.202000	0.17295	-0.480000	0.06803	-1.431000	0.01090	ATT	T|1.000;C|0.000	0.000	strong		0.363	RPL6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405422.1			C	112843105	T	C	112843105	3	2	22	1	0	0	0	0	1	0	0	0	13613	1406	49	3	80	3	RPL6	12	112843105	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	3205871	112843105	21008790	2744	5645											
OAS2	4939	hgsc.bcm.edu	37	chr12	113444285	113444285	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcattgatctgtataaatcCtcggacctcccgggaggaga	10	10	10	11	2	2	2	1	1	1	1	5	5	4	4	3	3	0	1	3	3	3	3	rs16942424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:113444285C>T	ENST00000342315.4	+	8	1750	c.1536C>T	c.(1534-1536)tcC>tcT	p.S512S	RP1-71H24.1_ENST00000552784.1_RNA|OAS2_ENST00000392583.2_Silent_p.S512S	NM_016817.2	NP_058197.2	P29728	OAS2_HUMAN	2'-5'-oligoadenylate synthetase 2, 69/71kDa	512	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						TGTATAAATCCTCGGACCTCC	0.522													C|||	172	0.034345	0.1203	0.0173	5008	,	,		16629	0.0		0.001	False		,,,				2504	0.0				p.S512S	Pancreas(199;709 2232 18410 33584 35052)	Atlas-SNP	.											.	OAS2	86	.	0			c.C1536T						PASS	.	C	,	399,4007		18,363,1822	88	88	88		1536,1536	-0.6	0	12	dbSNP_123	88	19,8581		0,19,4281	no	coding-synonymous,coding-synonymous	OAS2	NM_002535.2,NM_016817.2	,	18,382,6103	TT,TC,CC		0.2209,9.0558,3.2139	,	512/688,512/720	113444285	418,12588	2203	4300	6503	SO:0001819	synonymous_variant	4939	exon8			TAAATCCTCGGAC	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.1536C>T	12.37:g.113444285C>T		70	0	0		106	54	0.509434	NM_002535	A8K9T1|Q6PJ33|Q86XX8	Silent	SNP	ENST00000342315.4	37	CCDS31906.1																																																																																			C|0.957;T|0.043	0.043	strong		0.522	OAS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405937.1			T	113444285	C	T	113444285	2	4	22	1	0	0	0	0	0	0	0	1	10809	668	24	2		2	OAS2	12	113444285	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	601180	113444285	20407610	2745	5646											
RBM19	9904	hgsc.bcm.edu	37	chr12	114358449	114358449	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agagctttctgggcttgctcCggcttcctgtattccacaaa	7	13	9	12	1	1	1	0	0	1	1	4	1	4	1	3	2	2	5	3	2	2	5	rs79120696	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:114358449C>T	ENST00000545145.2	-	19	2430	c.2352G>A	c.(2350-2352)ccG>ccA	p.P784P	RBM19_ENST00000392561.3_Silent_p.P784P|RBM19_ENST00000261741.5_Silent_p.P784P	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	784	RRM 5. {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)					GGGCTTGCTCCGGCTTCCTGT	0.562													C|||	384	0.0766773	0.2716	0.0317	5008	,	,		16543	0.0		0.003	False		,,,				2504	0.0				p.P784P		Atlas-SNP	.											.	RBM19	117	.	0			c.G2352A						PASS	.	C	,,	1093,3313	394.4+/-329.3	152,789,1262	237	239	238		2352,2352,2352	-10	0.3	12	dbSNP_131	238	10,8590	5.7+/-21.5	0,10,4290	no	coding-synonymous,coding-synonymous,coding-synonymous	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	,,	152,799,5552	TT,TC,CC		0.1163,24.8071,8.4807	,,	784/961,784/961,784/961	114358449	1103,11903	2203	4300	6503	SO:0001819	synonymous_variant	9904	exon19			TTGCTCCGGCTTC	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.2352G>A	12.37:g.114358449C>T		102	0	0		108	58	0.537037	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Silent	SNP	ENST00000545145.2	37	CCDS9172.1																																																																																			C|0.917;T|0.083	0.083	strong		0.562	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196		T	114358449	C	T	114358449	2	4	22	1	0	0	0	0	0	0	0	1	13136	639	23	1		1	RBM19	12	114358449	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	914164	114358449	19493446	2746	5647											
RBM19	9904	hgsc.bcm.edu	37	chr12	114374887	114374887	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttttcttctgtggggctgTgctggagaagacgccaactg	6	13	13	9	1	2	2	0	0	2	2	2	3	2	2	1	3	2	2	1	3	2	3	rs2290787	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:114374887T>A	ENST00000545145.2	-	16	2071	c.1993A>T	c.(1993-1995)Aca>Tca	p.T665S	RBM19_ENST00000392561.3_Missense_Mutation_p.T665S|RP11-780K2.1_ENST00000550206.1_RNA|RBM19_ENST00000261741.5_Missense_Mutation_p.T665S	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	665			T -> A (in dbSNP:rs2290787). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.		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.T665A(1)		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)					TGTGGGGCTGTGCTGGAGAAG	0.527													C|||	386	0.0770767	0.2731	0.0317	5008	,	,		17578	0.0		0.003	False		,,,				2504	0.0				p.T665S		Atlas-SNP	.											RBM19,NS,carcinoma,0,1	RBM19	117	1	1	Substitution - Missense(1)	stomach(1)	c.A1993T						PASS	.						130	129	129					12																	114374887		2203	4300	6503	SO:0001583	missense	9904	exon16			GGGCTGTGCTGGA	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.1993A>T	12.37:g.114374887T>A	ENSP00000442053:p.Thr665Ser	205	0	0		188	85	0.452128	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	37	CCDS9172.1	127	0.05815018315018315	112	0.22764227642276422	13	0.03591160220994475	0	0.0	2	0.002638522427440633	C	8.267	0.812524	0.16537	.	.	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.05025	3.51;3.51;3.51	4.5	-7.42	0.01388	Nucleotide-binding, alpha-beta plait (1);	0.638273	0.16199	N	0.225012	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.33701	-0.9858	9	0.08599	T	0.76	0.174	2.1166	0.03715	0.1533:0.1255:0.303:0.4182	rs2290787;rs17856103;rs17856172	665	Q9Y4C8	RBM19_HUMAN	S	665	ENSP00000442053:T665S;ENSP00000376344:T665S;ENSP00000261741:T665S	ENSP00000261741:T665S	T	-	1	0	RBM19	112859270	0.076000	0.21285	0.052000	0.19188	0.226000	0.24999	-0.181000	0.09740	-2.257000	0.00695	-1.557000	0.00889	ACA	A|0.076;C|0.019;T|0.905	0.076	strong		0.527	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196		A	114374887	T	A	114374887	3	1	22	1	0	0	0	0	1	0	0	0	13136	1696	59	5	925	5	RBM19	12	114374887	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	16438	114374887	19477008	2747	5648											
RBM19	9904	hgsc.bcm.edu	37	chr12	114386723	114386723	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agccttccggattcggccagGtcctcctcctcttcgttctc	3	13	8	17	3	2	0	0	0	2	0	9	1	6	1	6	3	1	1	6	3	0	4	rs7979406	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:114386723G>A	ENST00000545145.2	-	10	1269	c.1191C>T	c.(1189-1191)gaC>gaT	p.D397D	RBM19_ENST00000392561.3_Silent_p.D397D|RBM19_ENST00000261741.5_Silent_p.D397D	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	397					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)					ATTCGGCCAGGTCCTCCTCCT	0.562													G|||	156	0.0311502	0.1104	0.013	5008	,	,		19228	0.0		0.001	False		,,,				2504	0.0				p.D397D		Atlas-SNP	.											.	RBM19	117	.	0			c.C1191T						PASS	.	G	,,	389,4017	194.0+/-219.0	16,357,1830	180	170	173		1191,1191,1191	4.3	1	12	dbSNP_116	173	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	,,	16,360,6127	AA,AG,GG		0.0349,8.8289,3.014	,,	397/961,397/961,397/961	114386723	392,12614	2203	4300	6503	SO:0001819	synonymous_variant	9904	exon10			GGCCAGGTCCTCC	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.1191C>T	12.37:g.114386723G>A		216	0	0		247	121	0.489879	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Silent	SNP	ENST00000545145.2	37	CCDS9172.1																																																																																			G|0.971;A|0.029	0.029	strong		0.562	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196		A	114386723	G	A	114386723	2	1	22	1	0	0	0	0	0	0	0	1	13136	1252	44	2		2	RBM19	12	114386723	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	11836	114386723	19465172	2748	5649											
TBX3	6926	hgsc.bcm.edu	37	chr12	115118722	115118722	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aatgttgttggtgagtttcaGtttgtggaaagtgacgactt	9	16	13	3	1	1	2	1	2	0	0	1	4	1	3	0	2	0	4	0	2	2	5	rs35069811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:115118722G>A	ENST00000257566.3	-	2	1008	c.619C>T	c.(619-621)Ctg>Ttg	p.L207L	TBX3_ENST00000349155.2_Silent_p.L207L	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	207					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)		GTGAGTTTCAGTTTGTGGAAA	0.463													G|||	73	0.0145767	0.0537	0.0029	5008	,	,		19262	0.0		0.0	False		,,,				2504	0.0				p.L207L		Atlas-SNP	.											.	TBX3	106	.	0			c.C619T						PASS	.	G	,	256,4150	146.9+/-181.5	7,242,1954	147	139	142		619,619	4.9	1	12	dbSNP_126	142	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous	TBX3	NM_005996.3,NM_016569.3	,	7,246,6250	AA,AG,GG		0.0465,5.8103,1.9991	,	207/724,207/744	115118722	260,12746	2203	4300	6503	SO:0001819	synonymous_variant	6926	exon2			GTTTCAGTTTGTG	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.619C>T	12.37:g.115118722G>A		231	0	0		256	118	0.460938	NM_005996	Q8TB20|Q9UKF8	Silent	SNP	ENST00000257566.3	37	CCDS9176.1																																																																																			G|0.979;A|0.021	0.021	strong		0.463	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404947.2	NM_016569, NM_005996		A	115118722	G	A	115118722	2	1	22	1	0	0	0	0	0	0	0	1	15674	1020	36	2		2	TBX3	12	115118722	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	731999	115118722	18733173	2749	5650											
FBXW8	26259	hgsc.bcm.edu	37	chr12	117387465	117387465	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctggagcatgttcctgacAcagttttgtgtgatgtgcat	8	14	12	7	0	0	2	0	2	0	0	1	3	1	3	1	1	3	5	1	1	0	3	rs36021180	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:117387465A>G	ENST00000309909.5	+	4	713	c.631A>G	c.(631-633)Aca>Gca	p.T211A	FBXW8_ENST00000455858.2_Missense_Mutation_p.T145A			Q8N3Y1	FBXW8_HUMAN	F-box and WD repeat domain containing 8	211			T -> A (in dbSNP:rs36021180).		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)		TGTTCCTGACACAGTTTTGTG	0.517													G|||	64	0.0127796	0.0454	0.0029	5008	,	,		24536	0.0		0.002	False		,,,				2504	0.0				p.T211A		Atlas-SNP	.											.	FBXW8	53	.	0			c.A631G						PASS	.	G	ALA/THR,ALA/THR	214,4192	806.9+/-415.9	6,202,1995	331	238	270		433,631	4.1	0.3	12	dbSNP_126	270	33,8567	817.8+/-406.9	0,33,4267	yes	missense,missense	FBXW8	NM_012174.1,NM_153348.2	58,58	6,235,6262	GG,GA,AA		0.3837,4.857,1.8991	benign,benign	145/533,211/599	117387465	247,12759	2203	4300	6503	SO:0001583	missense	26259	exon4			CCTGACACAGTTT	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.631A>G	12.37:g.117387465A>G	ENSP00000310686:p.Thr211Ala	163	0	0		153	85	0.555556	NM_153348	Q9UK95	Missense_Mutation	SNP	ENST00000309909.5	37	CCDS9182.1	26	0.011904761904761904	23	0.046747967479674794	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	0.527	-0.859427	0.02610	0.04857	0.003837	ENSG00000174989	ENST00000309909;ENST00000455858;ENST00000505227	T;T	0.04454	3.62;3.62	5.05	4.09	0.47781	WD40/YVTN repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.116916	0.53938	N	0.000041	T	0.00328	0.0010	N	0.02011	-0.69	0.09310	N	0.999996	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48670	-0.9015	10	0.14656	T	0.56	-3.3319	4.7195	0.12912	0.3949:0.0:0.6051:0.0	rs36021180;rs61748073	211;145	Q8N3Y1;Q8N3Y1-2	FBXW8_HUMAN;.	A	211;145;145	ENSP00000310686:T211A;ENSP00000389144:T145A	ENSP00000310686:T211A	T	+	1	0	FBXW8	115871848	0.960000	0.32886	0.276000	0.24689	0.163000	0.22366	4.018000	0.57174	1.377000	0.46286	-0.227000	0.12334	ACA	A|0.983;G|0.017	0.017	strong		0.517	FBXW8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403561.1	NM_012174		G	117387465	A	G	117387465	3	3	22	1	0	0	0	0	1	0	0	0	5778	159	6	3	645	3	FBXW8	12	117387465	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2268743	117387465	16464430	2750	5651											
NOS1	4842	hgsc.bcm.edu	37	chr12	117685255	117685255	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tcccctcccagttcttccagGagggtgtccacagcgtgtcc	5	10	10	16	1	1	0	0	0	1	0	6	1	6	1	6	2	1	1	6	2	0	2	rs41410247	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:117685255G>A	ENST00000338101.4	-	18	2827	c.2823C>T	c.(2821-2823)ctC>ctT	p.L941L	NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000317775.6_Silent_p.L907L			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)		GTTCTTCCAGGAGGGTGTCCA	0.552													G|||	37	0.00738818	0.0272	0.0014	5008	,	,		16371	0.0		0.0	False		,,,				2504	0.0				p.L941L	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.C2823T						PASS	.	G	,,,	95,3833		0,95,1869	91	91	91		2721,1713,1713,2823	2.7	1	12	dbSNP_127	91	5,8315		0,5,4155	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NOS1	NM_000620.4,NM_001204213.1,NM_001204214.1,NM_001204218.1	,,,	0,100,6024	AA,AG,GG		0.0601,2.4185,0.8165	,,,	907/1435,571/1099,571/1099,941/1469	117685255	100,12148	1964	4160	6124	SO:0001819	synonymous_variant	4842	exon19			TTCCAGGAGGGTG		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.2823C>T	12.37:g.117685255G>A		159	0	0		157	72	0.458599	NM_001204218		Silent	SNP	ENST00000338101.4	37	CCDS55890.1																																																																																			G|0.995;A|0.005	0.005	strong		0.552	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			A	117685255	G	A	117685255	2	1	22	1	0	0	0	0	0	0	0	1	10550	1161	41	2		2	NOS1	12	117685255	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	297790	117685255	16166640	2751	5652											
NOS1	4842	hgsc.bcm.edu	37	chr12	117691490	117691490	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcaaagttgtctctgaggtcGggcccatcgcctgatgattt	7	13	11	10	2	2	3	1	3	1	0	5	3	2	3	2	2	0	1	2	2	1	2	rs9658446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:117691490G>A	ENST00000338101.4	-	17	2707	c.2703C>T	c.(2701-2703)ccC>ccT	p.P901P	NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000317775.6_Silent_p.P867P			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)		CTCTGAGGTCGGGCCCATCGC	0.562													G|||	163	0.0325479	0.0983	0.0202	5008	,	,		18019	0.0		0.002	False		,,,				2504	0.0174				p.P901P	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											NOS1,NS,carcinoma,0,1	NOS1	240	1	0			c.C2703T						PASS	.	G	,,,	340,3958		15,310,1824	90	97	95		2601,1593,1593,2703	-7.8	0.8	12	dbSNP_119	95	26,8488		0,26,4231	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NOS1	NM_000620.4,NM_001204213.1,NM_001204214.1,NM_001204218.1	,,,	15,336,6055	AA,AG,GG		0.3054,7.9107,2.8567	,,,	867/1435,531/1099,531/1099,901/1469	117691490	366,12446	2149	4257	6406	SO:0001819	synonymous_variant	4842	exon18			GAGGTCGGGCCCA		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.2703C>T	12.37:g.117691490G>A		121	0	0		149	51	0.342282	NM_001204218		Silent	SNP	ENST00000338101.4	37	CCDS55890.1																																																																																			G|0.985;A|0.015	0.015	strong		0.562	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			A	117691490	G	A	117691490	2	1	22	1	0	0	0	0	0	0	0	1	10550	1103	39	1		1	NOS1	12	117691490	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6235	117691490	16160405	2752	5653											
WSB2	55884	hgsc.bcm.edu	37	chr12	118474238	118474238	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggcagagtcgggggagaaGtcacaagagacaacactgct	14	4	15	8	1	1	3	1	0	0	3	2	5	1	3	0	3	2	2	0	3	3	0	rs34253698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:118474238G>A	ENST00000315436.3	-	6	879	c.738C>T	c.(736-738)gaC>gaT	p.D246D	WSB2_ENST00000441406.2_Silent_p.D263D|WSB2_ENST00000536738.1_5'UTR|WSB2_ENST00000542304.1_Silent_p.D21D|WSB2_ENST00000535496.1_Silent_p.D248D|WSB2_ENST00000544233.1_Silent_p.D36D	NM_001278557.1|NM_018639.3	NP_001265486.1|NP_061109.1	Q9NYS7	WSB2_HUMAN	WD repeat and SOCS box containing 2	246					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)					CGGGGGAGAAGTCACAAGAGA	0.512													G|||	77	0.0153754	0.056	0.0043	5008	,	,		19879	0.0		0.0	False		,,,				2504	0.0				p.D246D		Atlas-SNP	.											.	WSB2	32	.	0			c.C738T						PASS	.	G		183,4223	117.1+/-155.0	4,175,2024	176	156	163		738	3.8	1	12	dbSNP_126	163	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	WSB2	NM_018639.3		4,178,6321	AA,AG,GG		0.0349,4.1534,1.4301		246/405	118474238	186,12820	2203	4300	6503	SO:0001819	synonymous_variant	55884	exon6			GGAGAAGTCACAA	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.738C>T	12.37:g.118474238G>A		140	0	0		132	59	0.44697	NM_018639	B4DIE6|B4DPV6|Q9NRX9	Silent	SNP	ENST00000315436.3	37	CCDS9186.1																																																																																			G|0.985;A|0.015	0.015	strong		0.512	WSB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401515.1	NM_018639		A	118474238	G	A	118474238	2	1	22	1	0	0	0	0	0	0	0	1	17420	1020	36	2		2	WSB2	12	118474238	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	782748	118474238	15377657	2753	5654											
HSPB8	26353	hgsc.bcm.edu	37	chr12	119631654	119631654	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caggacagccaggaagtcacCtgtacctgagatgccagtac	12	6	11	12	0	1	1	1	1	0	1	1	4	1	3	4	2	4	2	4	2	3	2	rs4628742	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:119631654C>T	ENST00000281938.2	+	3	1253	c.582C>T	c.(580-582)acC>acT	p.T194T		NM_014365.2	NP_055180.1	Q9UJY1	HSPB8_HUMAN	heat shock 22kDa protein 8	194					cell death (GO:0008219)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(9)|skin(1)	14	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AGGAAGTCACCTGTACCTGAG	0.502													C|||	412	0.0822684	0.2867	0.0159	5008	,	,		18743	0.0169		0.001	False		,,,				2504	0.0041				p.T194T		Atlas-SNP	.											.	HSPB8	45	.	0			c.C582T						PASS	.	C		1050,3356	383.5+/-324.9	125,800,1278	89	84	86		582	1.4	1	12	dbSNP_111	86	9,8591	4.3+/-15.6	0,9,4291	no	coding-synonymous	HSPB8	NM_014365.2		125,809,5569	TT,TC,CC		0.1047,23.8311,8.1424		194/197	119631654	1059,11947	2203	4300	6503	SO:0001819	synonymous_variant	26353	exon3			AGTCACCTGTACC	AF191017	CCDS9189.1	12q24.23	2014-09-17	2004-04-23					"Heat shock proteins / HSPB"	30171	protein-coding gene	gene with protein product		608014	"heat shock 27kDa protein 8"			10833516, 11085516	Standard	NM_014365		Approved	H11, E2IG1, HSP22, HspB8	uc001txb.3	Q9UJY1		ENST00000281938.2:c.582C>T	12.37:g.119631654C>T		156	0	0		160	74	0.4625	NM_014365	B2R6A6|Q6FIH3|Q9UKS3	Silent	SNP	ENST00000281938.2	37	CCDS9189.1																																																																																			C|0.917;T|0.083	0.083	strong		0.502	HSPB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401647.1	NM_014365		T	119631654	C	T	119631654	2	4	22	1	0	0	0	0	0	0	0	1	7432	668	24	2		2	HSPB8	12	119631654	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1157416	119631654	14220241	2754	5655											
CIT	11113	hgsc.bcm.edu	37	chr12	120139701	120139701	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttcgtagaatttattggtTccaatgaggatactgtaatt	12	17	8	4	1	0	2	0	1	0	1	2	3	1	3	1	2	1	3	1	2	6	9	rs34140357	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:120139701T>G	ENST00000261833.7	-	41	5293	c.5241A>C	c.(5239-5241)ggA>ggC	p.G1747G	CIT_ENST00000537607.1_5'UTR|CIT_ENST00000392521.2_Silent_p.G1789G	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	1747	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				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)		ATTTATTGGTTCCAATGAGGA	0.512													T|||	252	0.0503195	0.1823	0.0159	5008	,	,		21657	0.0		0.0	False		,,,				2504	0.0				p.G1789G		Atlas-SNP	.											.	CIT	535	.	0			c.A5367C						PASS	.	T	,	639,3767	274.0+/-271.7	50,539,1614	203	195	198		5367,5241	-0.1	1	12	dbSNP_126	198	8,8592	4.3+/-15.6	0,8,4292	no	coding-synonymous,coding-synonymous	CIT	NM_001206999.1,NM_007174.2	,	50,547,5906	GG,GT,TT		0.093,14.503,4.9746	,	1789/2070,1747/2028	120139701	647,12359	2203	4300	6503	SO:0001819	synonymous_variant	11113	exon42			ATTGGTTCCAATG	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.5241A>C	12.37:g.120139701T>G		107	0	0		141	60	0.425532	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Silent	SNP	ENST00000261833.7	37	CCDS9192.1	97	0.044413919413919416	89	0.18089430894308944	8	0.022099447513812154	0	0.0	0	0.0	T	11.11	1.542516	0.27563	0.14503	9.3E-4	ENSG00000122966	ENST00000392520	.	.	.	5.68	-0.123	0.13527	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.14504	-1.0470	3	.	.	.	.	7.4878	0.27443	0.0:0.2091:0.1194:0.6715	rs34140357	.	.	.	A	1360	.	.	E	-	2	0	CIT	118624084	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	1.220000	0.32491	0.060000	0.16281	0.528000	0.53228	GAA	T|0.947;G|0.053	0.053	strong		0.512	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174		G	120139701	T	G	120139701	2	3	22	1	0	0	0	0	0	0	0	1	3440	1770	62	5		5	CIT	12	120139701	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	508047	120139701	13712194	2755	5656											
POP5	51367	hgsc.bcm.edu	37	chr12	121019009	121019009	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	ctgctcagaactcggtcatcGaggcttaggcggcagcgggg	7	7	16	11	4	2	1	2	0	0	1	4	2	2	1	0	6	3	3	0	6	2	1	rs74750729	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:121019009G>C	ENST00000357500.4	-	2	107	c.72C>G	c.(70-72)ctC>ctG	p.L24L	POP5_ENST00000341039.2_Silent_p.L24L|POP5_ENST00000542776.1_5'UTR	NM_015918.3	NP_057002.2	Q969H6	POP5_HUMAN	processing of precursor 5, ribonuclease P/MRP subunit (S. cerevisiae)	24					tRNA processing (GO:0008033)	nucleolar ribonuclease P complex (GO:0005655)	ribonuclease P activity (GO:0004526)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)	7	all_neural(191;0.077)|Medulloblastoma(191;0.0922)					CTCGGTCATCGAGGCTTAGGC	0.672													G|||	8	0.00159744	0.0061	0.0	5008	,	,		16752	0.0		0.0	False		,,,				2504	0.0				p.L24L		Atlas-SNP	.											.	POP5	14	.	0			c.C72G						PASS	.	G	,	43,4363	44.6+/-78.6	0,43,2160	44	46	45		72,72	1.7	1	12	dbSNP_131	45	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	POP5	NM_015918.3,NM_198202.1	,	0,43,6460	CC,CG,GG		0.0,0.9759,0.3306	,	24/164,24/114	121019009	43,12963	2203	4300	6503	SO:0001819	synonymous_variant	51367	exon2			GTCATCGAGGCTT	AJ306296	CCDS9202.1, CCDS9203.1	12q24.31	2012-05-21			ENSG00000167272	ENSG00000167272			17689	protein-coding gene	gene with protein product		609992				11413139	Standard	NM_198202		Approved		uc001tys.3	Q969H6	OTTHUMG00000169023	ENST00000357500.4:c.72C>G	12.37:g.121019009G>C		88	0	0		85	45	0.529412	NM_198202	A6NL80|Q53FS5|Q9Y2Q6	Silent	SNP	ENST00000357500.4	37	CCDS9202.1																																																																																			G|0.998;C|0.002	0.002	strong		0.672	POP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401993.1	NM_015918		C	121019009	G	C	121019009	2	2	22	1	0	0	0	0	0	0	0	1	12262	1045	37	4		4	POP5	12	121019009	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	879308	121019009	12832886	2756	5657											
C12orf43	64897	hgsc.bcm.edu	37	chr12	121442833	121442833	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggagggctgtcgctttcggCggggttggggagactcttcc	3	11	18	9	3	1	1	0	0	1	1	4	3	2	2	1	7	0	3	1	7	0	3	rs34543757	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:121442833C>T	ENST00000288757.3	-	5	447	c.425G>A	c.(424-426)cGc>cAc	p.R142H	C12orf43_ENST00000537817.1_Missense_Mutation_p.R143H|C12orf43_ENST00000536407.2_Intron|C12orf43_ENST00000445832.3_Missense_Mutation_p.R112H|C12orf43_ENST00000539736.1_Missense_Mutation_p.R131H|C12orf43_ENST00000366211.2_Missense_Mutation_p.R100H	NM_022895.1	NP_075046.1	Q96C57	CL043_HUMAN	chromosome 12 open reading frame 43	142										cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TCGCTTTCGGCGGGGTTGGGG	0.527													.|||	31	0.0061901	0.0227	0.0	5008	,	,		13357	0.0		0.0	False		,,,				2504	0.001				p.R142H		Atlas-SNP	.											.	C12orf43	30	.	0			c.G425A						PASS	.	C	HIS/ARG	121,4283		2,117,2083	64	67	66		425	-0.7	0	12	dbSNP_126	66	0,8594		0,0,4297	yes	missense	C12orf43	NM_022895.1	29	2,117,6380	TT,TC,CC		0.0,2.7475,0.9309	benign	142/263	121442833	121,12877	2202	4297	6499	SO:0001583	missense	64897	exon5			TTTCGGCGGGGTT	AK022510	CCDS66486.1, CCDS66487.1	12q24.31	2012-05-30			ENSG00000157895	ENSG00000157895			25719	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_001286195		Approved	FLJ12448	uc001tzh.1	Q96C57	OTTHUMG00000169150	ENST00000288757.3:c.425G>A	12.37:g.121442833C>T	ENSP00000288757:p.Arg142His	84	0	0		100	57	0.57	NM_022895	Q53HF0|Q9H9Z7	Missense_Mutation	SNP	ENST00000288757.3	37	CCDS9210.1	15|15	0.006868131868131868|0.006868131868131868	15|15	0.03048780487804878|0.03048780487804878	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	10.27|10.27	1.304130|1.304130	0.23736|0.23736	0.027475|0.027475	0.0|0.0	ENSG00000157895|ENSG00000157895	ENST00000546272|ENST00000445832;ENST00000288757;ENST00000537817;ENST00000366211;ENST00000539736;ENST00000538296;ENST00000535367	.|T;T;T;T;T	.|0.49432	.|0.81;0.78;0.81;0.84;0.83	5.65|5.65	-0.735|-0.735	0.11137|0.11137	.|.	.|1.534110	.|0.03428	.|N	.|0.207380	T|T	0.11067|0.11067	0.0270|0.0270	N|N	0.21142|0.21142	0.635|0.635	0.09310|0.09310	N|N	1|1	.|B;B;B;B;B	.|0.19817	.|0.017;0.039;0.003;0.017;0.001	.|B;B;B;B;B	.|0.15052	.|0.007;0.012;0.003;0.007;0.002	T|T	0.03514|0.03514	-1.1029|-1.1029	5|10	.|0.17832	.|T	.|0.49	0.9065|0.9065	2.1|2.1	0.03677|0.03677	0.1243:0.427:0.2412:0.2075|0.1243:0.427:0.2412:0.2075	.|.	.|131;100;143;131;142	.|G5EA44;F6TFQ5;F5H7W8;B4DWJ9;Q96C57	.|.;.;.;.;CL043_HUMAN	T|H	95|112;142;143;100;131;79;96	.|ENSP00000409788:R112H;ENSP00000288757:R142H;ENSP00000442224:R143H;ENSP00000437803:R131H;ENSP00000442041:R79H	.|ENSP00000288757:R142H	A|R	-|-	1|2	0|0	C12orf43|C12orf43	119927216|119927216	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	-0.008000|-0.008000	0.12788|0.12788	-0.335000|-0.335000	0.08451|0.08451	-0.158000|-0.158000	0.13435|0.13435	GCC|CGC	C|0.990;G|0.000;T|0.009	0.009	strong		0.527	C12orf43-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022895		T	121442833	C	T	121442833	3	4	22	1	0	0	0	0	1	0	0	0	1691	768	27	1	371	1	C12orf43	12	121442833	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	423824	121442833	12409062	2757	5658											
P2RX7	5027	hgsc.bcm.edu	37	chr12	121622115	121622115	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttgctttttcagagacctgCgatggacttcacagatttgt	8	15	9	9	1	2	2	2	0	0	2	2	5	2	3	1	1	2	1	1	1	0	5	rs28360459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:121622115C>T	ENST00000546057.1	+	13	1441	c.1298C>T	c.(1297-1299)gCg>gTg	p.A433V	P2RX7_ENST00000443520.3_3'UTR|P2RX7_ENST00000328963.5_Missense_Mutation_p.A263V|P2RX7_ENST00000541446.1_Missense_Mutation_p.A144V|P2RX7_ENST00000535250.1_Missense_Mutation_p.A343V	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	433			A -> V (in dbSNP:rs28360459).		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)					CAGAGACCTGCGATGGACTTC	0.453													C|||	177	0.0353435	0.1278	0.0115	5008	,	,		17958	0.0		0.0	False		,,,				2504	0.0				p.A433V		Atlas-SNP	.											.	P2RX7	53	.	0			c.C1298T						PASS	.	C	VAL/ALA	510,3896	235.5+/-248.0	29,452,1722	68	71	70		1298	-5.1	0	12	dbSNP_125	70	6,8594	3.7+/-12.6	0,6,4294	yes	missense	P2RX7	NM_002562.5	64	29,458,6016	TT,TC,CC		0.0698,11.5751,3.9674	benign	433/596	121622115	516,12490	2203	4300	6503	SO:0001583	missense	5027	exon13			GACCTGCGATGGA	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.1298C>T	12.37:g.121622115C>T	ENSP00000442349:p.Ala433Val	37	0	0		28	11	0.392857	NM_002562	A8K2Z0|E7EMK6|F5H6P2|F5H7E8|F8W951|O14991|Q4VKH8|Q4VKH9|Q4VKI0|Q4VKI1|Q4VKI2|Q4VKI3|Q4VKI4|Q7Z771|Q96EV7	Missense_Mutation	SNP	ENST00000546057.1	37	CCDS9213.1	63	0.028846153846153848	58	0.11788617886178862	5	0.013812154696132596	0	0.0	0	0.0	C	2.926	-0.222035	0.06061	0.115751	6.98E-4	ENSG00000089041	ENST00000546057;ENST00000328963;ENST00000535250;ENST00000541446	T;T;T;T	0.05139	4.39;4.0;4.17;3.49	5.21	-5.06	0.02946	.	2.346980	0.01797	N	0.032678	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B;B;B;B	0.14805	0.011;0.001;0.011;0.003	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.42865	-0.9426	9	0.39692	T	0.17	0.4342	1.6799	0.02830	0.4149:0.2708:0.0915:0.2229	rs28360459	263;144;343;433	F8W951;F5H6P2;F5H7E8;Q99572	.;.;.;P2RX7_HUMAN	V	433;263;343;144	ENSP00000442349:A433V;ENSP00000330696:A263V;ENSP00000442572:A343V;ENSP00000437471:A144V	ENSP00000330696:A263V	A	+	2	0	P2RX7	120106498	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-0.486000	0.06513	-0.443000	0.07180	-0.218000	0.12543	GCG	C|0.965;T|0.035	0.035	strong		0.453	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562		T	121622115	C	T	121622115	3	4	22	1	0	0	0	0	1	0	0	0	11354	768	27	1	1348	1	P2RX7	12	121622115	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	179282	121622115	12229780	2758	5659											
P2RX7	5027	hgsc.bcm.edu	37	chr12	121622380	121622380	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagctggtcctgtccagacaCgtcctgcagttcctcctgct	6	11	9	15	1	0	1	0	0	0	1	5	1	5	1	5	1	3	4	5	1	1	1	rs2230913	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:121622380C>G	ENST00000546057.1	+	13	1706	c.1563C>G	c.(1561-1563)caC>caG	p.H521Q	P2RX7_ENST00000443520.3_3'UTR|P2RX7_ENST00000328963.5_Missense_Mutation_p.H351Q|P2RX7_ENST00000541446.1_Missense_Mutation_p.H232Q|P2RX7_ENST00000535250.1_Missense_Mutation_p.H431Q|RP11-340F14.5_ENST00000569999.1_RNA	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	521			H -> Q (in dbSNP:rs2230913).		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)					TGTCCAGACACGTCCTGCAGT	0.627													C|||	223	0.0445288	0.1619	0.013	5008	,	,		17902	0.0		0.0	False		,,,				2504	0.0				p.H521Q		Atlas-SNP	.											.	P2RX7	53	.	0			c.C1563G						PASS	.	C	GLN/HIS	615,3791	246.2+/-254.9	43,529,1631	35	31	32		1563	-10.4	0	12	dbSNP_98	32	7,8593	4.3+/-15.6	0,7,4293	yes	missense	P2RX7	NM_002562.5	24	43,536,5924	GG,GC,CC		0.0814,13.9582,4.7824	benign	521/596	121622380	622,12384	2203	4300	6503	SO:0001583	missense	5027	exon13			CAGACACGTCCTG	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.1563C>G	12.37:g.121622380C>G	ENSP00000442349:p.His521Gln	65	0	0		64	32	0.5	NM_002562	A8K2Z0|E7EMK6|F5H6P2|F5H7E8|F8W951|O14991|Q4VKH8|Q4VKH9|Q4VKI0|Q4VKI1|Q4VKI2|Q4VKI3|Q4VKI4|Q7Z771|Q96EV7	Missense_Mutation	SNP	ENST00000546057.1	37	CCDS9213.1	81	0.03708791208791209	75	0.1524390243902439	6	0.016574585635359115	0	0.0	0	0.0	C	0.024	-1.393088	0.01185	0.139582	8.14E-4	ENSG00000089041	ENST00000546057;ENST00000328963;ENST00000535250;ENST00000541446	T;T;T;T	0.04454	4.5;4.13;4.29;3.62	5.21	-10.4	0.00318	.	2.829390	0.01180	N	0.007078	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B;B;B;B	0.06786	0.001;0.001;0.001;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.40194	-0.9576	9	0.21540	T	0.41	.	3.5355	0.07793	0.0826:0.2354:0.3527:0.3294	rs2230913;rs2230913	351;232;431;521	F8W951;F5H6P2;F5H7E8;Q99572	.;.;.;P2RX7_HUMAN	Q	521;351;431;232	ENSP00000442349:H521Q;ENSP00000330696:H351Q;ENSP00000442572:H431Q;ENSP00000437471:H232Q	ENSP00000330696:H351Q	H	+	3	2	P2RX7	120106763	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-6.209000	0.00076	-4.138000	0.00070	-1.865000	0.00557	CAC	C|0.955;G|0.045;T|0.000	0.045	strong		0.627	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562		G	121622380	C	G	121622380	3	3	22	1	0	0	0	0	1	0	0	0	11354	535	19	4	1613	4	P2RX7	12	121622380	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	265	121622380	12229515	2759	5660											
RNF34	80196	hgsc.bcm.edu	37	chr12	121858078	121858080	+	In_Frame_Del	DEL	GAT	GAT	-																															tcacttcagcaaacacagaaGatgatgatgacgacgatgat																								rs370767127|rs72059744|rs185279212	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAT	GAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:121858078_121858080delGAT	ENST00000392464.2	+	4	736_738	c.667_669delGAT	c.(667-669)gatdel	p.D229del	RNF34_ENST00000361234.5_In_Frame_Del_p.D229del|RNF34_ENST00000555076.1_Intron|RNF34_ENST00000392465.3_In_Frame_Del_p.D230del					ring finger protein 34, E3 ubiquitin protein ligase											breast(1)|large_intestine(1)	2	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000432)|Epithelial(86;0.00233)		AAACACAGAAgatgatgatgacg	0.404														186	0.0371406	0.1339	0.013	5008	,	,		22592	0.0		0.0	False		,,,				2504	0.0				p.223_224del		Pindel,Atlas-Indel	.											.	RNF34	54	.	0			c.669_671del						PASS	.		,	485,3779		29,427,1676					,	-2.2	0.9		dbSNP_130	70	6,8246		0,6,4120	no	coding,coding	RNF34	NM_194271.1,NM_025126.2	,	29,433,5796	A1A1,A1R,RR		0.0727,11.3743,3.923	,	,		491,12025				SO:0001651	inframe_deletion	80196	exon5			.	AF306709, AB084914	CCDS9221.1, CCDS31915.1, CCDS73538.1	12q24.31	2012-02-23	2012-02-23			ENSG00000170633		"RING-type (C3HC4) zinc fingers"	17297	protein-coding gene	gene with protein product		608299	"ring finger protein 34"			12118383	Standard	NM_025126		Approved	RIFF, FLJ21786, RIF	uc001ual.2	Q969K3		ENST00000392464.2:c.667_669delGAT	12.37:g.121858084_121858086delGAT	ENSP00000376257:p.Asp229del	66	0	.		92	35	0.38	NM_194271		In_Frame_Del	DEL	ENST00000392464.2	37																																																																																				GAT|0.969;-|0.031	0.031	strong		0.404	RNF34-005	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000413892.1	NM_194271		-	121858080	GAT	-	121858078	7	5	22	1	0	1	0	1	0	0	0	0	13504	942	33	0	694	0	RNF34	12	121858078	In_Frame_Del	DEL	GAT	TCGA-G8-6324-01A-11D-2210-10	235698	121858078	11993817	2760	5661											
KDM2B	84678	hgsc.bcm.edu	37	chr12	121877739	121877739	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgatagactggtcggtgacGtggttacagtaactgaggtg	9	12	15	5	2	0	4	0	3	0	1	1	4	0	4	0	4	2	2	0	4	3	4	rs35674891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:121877739G>A	ENST00000377071.4	-	22	3822	c.3750C>T	c.(3748-3750)caC>caT	p.H1250H	KDM2B_ENST00000536437.1_Intron|KDM2B_ENST00000542973.1_Silent_p.H618H|KDM2B_ENST00000377069.4_Silent_p.H1181H	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	1250					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						GGTCGGTGACGTGGTTACAGT	0.602													G|||	75	0.014976	0.0567	0.0	5008	,	,		17032	0.0		0.0	False		,,,				2504	0.0				p.H1250H		Atlas-SNP	.											.	KDM2B	218	.	0			c.C3750T						PASS	.	G	,	235,4127		6,223,1952	123	146	138		3543,3750	-0.6	0.6	12	dbSNP_126	138	2,8542		0,2,4270	no	coding-synonymous,coding-synonymous	KDM2B	NM_001005366.1,NM_032590.4	,	6,225,6222	AA,AG,GG		0.0234,5.3874,1.8364	,	1181/1266,1250/1337	121877739	237,12669	2181	4272	6453	SO:0001819	synonymous_variant	84678	exon22			GGTGACGTGGTTA	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.3750C>T	12.37:g.121877739G>A		105	0	0		122	54	0.442623	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Silent	SNP	ENST00000377071.4	37	CCDS41850.1																																																																																			G|0.990;A|0.010	0.010	strong		0.602	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590		A	121877739	G	A	121877739	2	1	22	1	0	0	0	0	0	0	0	1	8134	1136	40	1		1	KDM2B	12	121877739	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	19661	121877739	11974156	2761	5662											
MLXIP	22877	hgsc.bcm.edu	37	chr12	122618417	122618417	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccagccacggttaacttttGtgcaccccaaacctgtatcc	9	10	6	16	1	0	0	0	0	0	0	1	0	1	0	6	1	4	3	6	1	3	4	rs34702867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:122618417G>T	ENST00000319080.7	+	9	1747	c.1615G>T	c.(1615-1617)Gtg>Ttg	p.V539L	MLXIP_ENST00000377037.2_Missense_Mutation_p.V129L|MLXIP_ENST00000538698.1_Missense_Mutation_p.V146L					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)		GTTAACTTTTGTGCACCCCAA	0.607													G|||	194	0.038738	0.1422	0.0086	5008	,	,		14499	0.0		0.0	False		,,,				2504	0.0				p.V539L	Esophageal Squamous(105;787 1493 16200 18566 52466)	Atlas-SNP	.											.	MLXIP	46	.	0			c.G1615T						PASS	.	G	LEU/VAL	448,3490		28,392,1549	22	26	25		1205	4.2	1	12	dbSNP_126	25	6,8264		0,6,4129	yes	missense	MLXIP	NM_014938.3	32	28,398,5678	TT,TG,GG		0.0726,11.3763,3.7189	benign	539/920	122618417	454,11754	1969	4135	6104	SO:0001583	missense	22877	exon9			ACTTTTGTGCACC	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.1615G>T	12.37:g.122618417G>T	ENSP00000312834:p.Val539Leu	55	0	0		38	14	0.368421	NM_014938		Missense_Mutation	SNP	ENST00000319080.7	37		73	0.033424908424908424	70	0.14227642276422764	3	0.008287292817679558	0	0.0	0	0.0	G	14.85	2.657247	0.47467	0.113763	7.26E-4	ENSG00000175727	ENST00000319080;ENST00000538698;ENST00000539039;ENST00000377037	D;D;D	0.84516	-1.86;-1.86;-1.86	5.09	4.19	0.49359	.	0.332806	0.28784	N	0.014156	T	0.02012	0.0063	.	.	.	0.24861	N	0.992344	B;B	0.31318	0.319;0.1	B;B	0.34301	0.179;0.03	T	0.00812	-1.1556	9	0.28530	T	0.3	-11.9952	12.6399	0.56705	0.0813:0.0:0.9187:0.0	rs34702867	539;539	Q9HAP2-3;Q9HAP2	.;MLXIP_HUMAN	L	539;146;146;129	ENSP00000312834:V539L;ENSP00000440769:V146L;ENSP00000366236:V129L	ENSP00000312834:V539L	V	+	1	0	MLXIP	121184370	1.000000	0.71417	0.977000	0.42913	0.967000	0.64934	4.310000	0.59141	1.097000	0.41459	0.655000	0.94253	GTG	G|0.973;T|0.027	0.027	strong		0.607	MLXIP-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401718.2	NM_014938		T	122618417	G	T	122618417	3	4	22	1	0	0	0	0	1	0	0	0	9645	1377	48	4	1649	4	MLXIP	12	122618417	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	740678	122618417	11233478	2762	5663											
LRRC43	254050	hgsc.bcm.edu	37	chr12	122674807	122674807	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acccactggccttggtgcccTactaccgcggcctcaccatc	6	8	8	19	2	1	0	1	0	0	0	2	0	1	0	6	3	3	0	6	3	2	3	rs77473460	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:122674807T>C	ENST00000339777.4	+	5	821	c.793T>C	c.(793-795)Tac>Cac	p.Y265H	LRRC43_ENST00000425921.1_Missense_Mutation_p.Y80H	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	265	LRRCT.									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)		CTTGGTGCCCTACTACCGCGG	0.637													T|||	195	0.0389377	0.1415	0.0101	5008	,	,		20541	0.0		0.001	False		,,,				2504	0.0				p.Y265H		Atlas-SNP	.											.	LRRC43	105	.	0			c.T793C						PASS	.	T	HIS/TYR,HIS/TYR	502,3826		30,442,1692	84	95	92		793,238	-1.6	0.9	12	dbSNP_131	92	4,8530		0,4,4263	yes	missense,missense	LRRC43	NM_001098519.1,NM_152759.4	83,83	30,446,5955	CC,CT,TT		0.0469,11.5989,3.9341	possibly-damaging,possibly-damaging	265/657,80/472	122674807	506,12356	2164	4267	6431	SO:0001583	missense	254050	exon5			GTGCCCTACTACC	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.793T>C	12.37:g.122674807T>C	ENSP00000344233:p.Tyr265His	186	0	0		176	82	0.465909	NM_001098519	Q6ZVT9	Missense_Mutation	SNP	ENST00000339777.4	37	CCDS45001.1	78	0.03571428571428571	75	0.1524390243902439	3	0.008287292817679558	0	0.0	0	0.0	T	9.271	1.045795	0.19748	0.115989	4.69E-4	ENSG00000158113	ENST00000537729;ENST00000339777;ENST00000289014;ENST00000425921	T;T;T	0.23348	1.91;1.91;1.91	5.22	-1.59	0.08453	.	0.926504	0.09255	N	0.827363	T	0.00073	0.0002	N	0.13043	0.29	0.09310	N	1	B	0.18461	0.028	B	0.11329	0.006	T	0.37911	-0.9685	10	0.15499	T	0.54	-14.8888	1.3937	0.02256	0.1943:0.3528:0.2254:0.2275	.	265	Q8N309	LRC43_HUMAN	H	80;265;136;80	ENSP00000438751:Y80H;ENSP00000344233:Y265H;ENSP00000416628:Y80H	ENSP00000289014:Y136H	Y	+	1	0	LRRC43	121240760	0.000000	0.05858	0.934000	0.37439	0.988000	0.76386	0.172000	0.16704	0.039000	0.15632	0.459000	0.35465	TAC	T|0.977;C|0.023	0.023	strong		0.637	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759		C	122674807	T	C	122674807	3	2	22	1	0	0	0	0	1	0	0	0	9010	1522	53	3	811	3	LRRC43	12	122674807	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	56390	122674807	11177088	2763	5664											
B3GNT4	79369	hgsc.bcm.edu	37	chr12	122691058	122691058	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacagtgtctagcgcctctcTgtccctgcctagccgtcacc	5	10	8	18	2	3	0	1	0	2	0	5	0	4	0	5	0	3	0	5	0	2	2	rs35203505	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:122691058T>C	ENST00000324189.4	+	3	616	c.260T>C	c.(259-261)cTg>cCg	p.L87P	B3GNT4_ENST00000535274.1_Missense_Mutation_p.L62P|B3GNT4_ENST00000546192.1_Missense_Mutation_p.L62P|B3GNT4_ENST00000545141.1_Intron	NM_030765.2	NP_110392.1	Q9C0J1	B3GN4_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 4	87			L -> P (in dbSNP:rs35203505).		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)		AGCGCCTCTCTGTCCCTGCCT	0.592													T|||	277	0.0553115	0.1982	0.0202	5008	,	,		16804	0.0		0.001	False		,,,				2504	0.0				p.L87P		Atlas-SNP	.											.	B3GNT4	35	.	0			c.T260C						PASS	.	T	PRO/LEU	794,3612	319.1+/-295.9	77,640,1486	236	227	230		260	-0.7	0.9	12	dbSNP_126	230	7,8593	5.7+/-21.5	0,7,4293	yes	missense	B3GNT4	NM_030765.2	98	77,647,5779	CC,CT,TT		0.0814,18.0209,6.1587	benign	87/379	122691058	801,12205	2203	4300	6503	SO:0001583	missense	79369	exon3			CCTCTCTGTCCCT	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.260T>C	12.37:g.122691058T>C	ENSP00000319636:p.Leu87Pro	194	0	0		187	82	0.438503	NM_030765	Q8N5W4|Q8N934|Q8ND21|Q8WWR5|Q8WY02|Q96QH5	Missense_Mutation	SNP	ENST00000324189.4	37	CCDS9227.1	118	0.05402930402930403	112	0.22764227642276422	6	0.016574585635359115	0	0.0	0	0.0	T	7.052	0.564562	0.13498	0.180209	8.14E-4	ENSG00000176383	ENST00000324189;ENST00000546192;ENST00000535274	T;T;T	0.36878	1.36;1.23;1.23	4.7	-0.663	0.11410	.	0.519308	0.14506	N	0.315425	T	0.00012	0.0000	L	0.40543	1.245	0.51233	P	9.00000000000345E-5	P	0.45283	0.855	B	0.41571	0.36	T	0.15263	-1.0443	9	0.30078	T	0.28	.	1.7591	0.02988	0.1302:0.2171:0.1337:0.519	rs35203505	87	Q9C0J1	B3GN4_HUMAN	P	87;62;62	ENSP00000319636:L87P;ENSP00000438840:L62P;ENSP00000444534:L62P	ENSP00000319636:L87P	L	+	2	0	B3GNT4	121257011	0.000000	0.05858	0.850000	0.33497	0.397000	0.30659	0.008000	0.13197	0.247000	0.21414	0.533000	0.62120	CTG	T|0.944;C|0.056	0.056	strong		0.592	B3GNT4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401595.1	NM_030765		C	122691058	T	C	122691058	3	2	22	1	0	0	0	0	1	0	0	0	1259	1580	55	3	266	3	B3GNT4	12	122691058	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	16251	122691058	11160837	2764	5665											
DIABLO	56616	hgsc.bcm.edu	37	chr12	122692958	122692958	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcaggtaggcctcctgctcCgactcagcccgctcctcccc	4	7	9	21	3	1	0	1	0	0	0	5	1	5	0	7	2	2	4	7	2	1	1	rs35426428	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:122692958C>T	ENST00000443649.3	-	7	1507	c.690G>A	c.(688-690)tcG>tcA	p.S230S	RP11-512M8.5_ENST00000535844.1_3'UTR|DIABLO_ENST00000267169.6_Silent_p.S177S|B3GNT4_ENST00000546192.1_3'UTR|B3GNT4_ENST00000545141.1_Intron|DIABLO_ENST00000353548.6_Silent_p.S186S|DIABLO_ENST00000464942.2_Silent_p.S177S|DIABLO_ENST00000413918.1_Silent_p.S186S	NM_019887.4	NP_063940.1	Q9NR28	DBLOH_HUMAN	diablo, IAP-binding mitochondrial protein	230					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)		CCTCCTGCTCCGACTCAGCCC	0.617													C|||	454	0.090655	0.3283	0.0274	5008	,	,		20976	0.0		0.001	False		,,,				2504	0.0				p.S230S		Atlas-SNP	.											DIABLO,NS,carcinoma,-2,1	DIABLO	16	1	0			c.G690A						PASS	.	C	,	1365,3041	452.8+/-350.1	219,927,1057	113	107	109		690,558	-6.1	0	12	dbSNP_126	109	23,8577	16.0+/-53.3	0,23,4277	no	coding-synonymous,coding-synonymous	DIABLO	NM_019887.4,NM_138929.3	,	219,950,5334	TT,TC,CC		0.2674,30.9805,10.672	,	230/240,186/196	122692958	1388,11618	2203	4300	6503	SO:0001819	synonymous_variant	56616	exon7			CTGCTCCGACTCA	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.690G>A	12.37:g.122692958C>T		130	1	0.00769231		168	168	1	NM_019887	B2RDQ0|Q6W3F3|Q96LV0|Q9BT11|Q9HAV6	Silent	SNP	ENST00000443649.3	37	CCDS9228.1																																																																																			C|0.906;T|0.094	0.094	strong		0.617	DIABLO-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347102.2	NM_019887		T	122692958	C	T	122692958	2	4	22	1	0	0	0	0	0	0	0	1	4519	639	23	1		1	DIABLO	12	122692958	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1900	122692958	11158937	2765	5666											
VPS33A	65082	hgsc.bcm.edu	37	chr12	122720423	122720423	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtctgcggtttcagcaggccGgccttctccaggttgtgtaa	5	12	13	11	2	3	0	1	0	2	0	4	0	3	0	3	4	2	4	3	4	1	4	rs34461198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:122720423G>A	ENST00000267199.4	-	11	1462	c.1350C>T	c.(1348-1350)gcC>gcT	p.A450A	RP11-512M8.5_ENST00000535844.1_Silent_p.A411A	NM_022916.4	NP_075067.2	Q96AX1	VP33A_HUMAN	vacuolar protein sorting 33 homolog A (S. cerevisiae)	450					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)		TCAGCAGGCCGGCCTTCTCCA	0.478													G|||	232	0.0463259	0.1702	0.0086	5008	,	,		18772	0.0		0.001	False		,,,				2504	0.0				p.A450A		Atlas-SNP	.											.	VPS33A	61	.	0			c.C1350T						PASS	.	G		696,3710	291.8+/-281.7	53,590,1560	208	192	197		1350	-11.7	0	12	dbSNP_126	197	17,8583	11.9+/-42.8	0,17,4283	no	coding-synonymous	VPS33A	NM_022916.4		53,607,5843	AA,AG,GG		0.1977,15.7966,5.4821		450/597	122720423	713,12293	2203	4300	6503	SO:0001819	synonymous_variant	65082	exon11			CAGGCCGGCCTTC	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.1350C>T	12.37:g.122720423G>A		240	0	0		253	125	0.494071	NM_022916	Q547V4|Q9H5Q0	Silent	SNP	ENST00000267199.4	37	CCDS9231.1																																																																																			G|0.944;A|0.056	0.056	strong		0.478	VPS33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401607.2			A	122720423	G	A	122720423	2	1	22	1	0	0	0	0	0	0	0	1	17216	1103	39	1		1	VPS33A	12	122720423	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	27465	122720423	11131472	2766	5667											
KNTC1	9735	hgsc.bcm.edu	37	chr12	123089955	123089955	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctatgcccttcaacaaaacCtggtgaagtaagtacttgct	12	11	8	10	0	1	1	1	1	0	0	1	1	1	1	2	1	5	4	2	1	7	5	rs7310898	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:123089955C>T	ENST00000333479.7	+	51	5666	c.5489C>T	c.(5488-5490)cCt>cTt	p.P1830L	KNTC1_ENST00000436959.3_5'UTR|KNTC1_ENST00000537348.1_Missense_Mutation_p.P255L|KNTC1_ENST00000450485.2_Intron	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	1830			P -> L (in dbSNP:rs7310898).		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)		TCAACAAAACCTGGTGAAGTA	0.393													C|||	196	0.0391374	0.143	0.0101	5008	,	,		16684	0.0		0.0	False		,,,				2504	0.0				p.P1830L		Atlas-SNP	.											KNTC1,caecum,carcinoma,0,1	KNTC1	182	1	0			c.C5489T						PASS	.	C	LEU/PRO	433,3323		20,393,1465	57	56	56		5489	3.8	0.1	12	dbSNP_116	56	4,8242		0,4,4119	yes	missense	KNTC1	NM_014708.4	98	20,397,5584	TT,TC,CC		0.0485,11.5282,3.6411	possibly-damaging	1830/2210	123089955	437,11565	1878	4123	6001	SO:0001583	missense	9735	exon51			CAAAACCTGGTGA		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.5489C>T	12.37:g.123089955C>T	ENSP00000328236:p.Pro1830Leu	172	0	0		172	71	0.412791	NM_014708	A7E2C4|B3KSG2	Missense_Mutation	SNP	ENST00000333479.7	37	CCDS45002.1	69	0.03159340659340659	64	0.13008130081300814	5	0.013812154696132596	0	0.0	0	0.0	C	25.8	4.677569	0.88445	0.115282	4.85E-4	ENSG00000184445	ENST00000333479;ENST00000537348;ENST00000546125	T;T;T	0.30182	1.54;1.54;1.54	5.64	3.79	0.43588	RZZ complex, subunit KNTC1/ROD, C-terminal (1);	0.330869	0.36932	N	0.002322	T	0.00328	0.0010	L	0.44542	1.39	0.50813	P	1.0299999999996423E-4	P	0.40534	0.72	P	0.44673	0.457	T	0.09975	-1.0650	9	0.72032	D	0.01	-12.0893	11.1536	0.48473	0.1268:0.806:0.0:0.0672	rs7310898;rs52809397;rs57876510;rs7310898	1830	P50748	KNTC1_HUMAN	L	1830;255;17	ENSP00000328236:P1830L;ENSP00000443622:P255L;ENSP00000439119:P17L	ENSP00000328236:P1830L	P	+	2	0	KNTC1	121655908	0.836000	0.29430	0.093000	0.20910	0.968000	0.65278	3.480000	0.53172	1.372000	0.46190	0.650000	0.86243	CCT	C|0.962;T|0.038	0.038	strong		0.393	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2			T	123089955	C	T	123089955	3	4	22	1	0	0	0	0	1	0	0	0	8437	681	24	2	5687	2	KNTC1	12	123089955	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	369532	123089955	10761940	2767	5668											
HIP1R	9026	hgsc.bcm.edu	37	chr12	123341199	123341199	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaagagcgaccagctggagAagctcaagagggagctggag	14	3	17	7	1	1	4	1	0	0	4	1	8	1	6	1	3	4	3	1	3	3	0	rs7972242	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:123341199A>C	ENST00000253083.4	+	17	1671	c.1546A>C	c.(1546-1548)Aag>Cag	p.K516Q		NM_003959.1	NP_003950.1	O75146	HIP1R_HUMAN	huntingtin interacting protein 1 related	516			K -> Q (in dbSNP:rs7972242).		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)		CCAGCTGGAGAAGCTCAAGAG	0.662													A|||	203	0.0405351	0.146	0.013	5008	,	,		15928	0.0		0.001	False		,,,				2504	0.0				p.K516Q		Atlas-SNP	.											.	HIP1R	68	.	0			c.A1546C						PASS	.	A	GLN/LYS	542,3854		30,482,1686	29	33	32		1546	2.2	1	12	dbSNP_116	32	7,8587		0,7,4290	yes	missense	HIP1R	NM_003959.1	53	30,489,5976	CC,CA,AA		0.0815,12.3294,4.2263	benign	516/1069	123341199	549,12441	2198	4297	6495	SO:0001583	missense	9026	exon17			CTGGAGAAGCTCA	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.1546A>C	12.37:g.123341199A>C	ENSP00000253083:p.Lys516Gln	108	0	0		88	42	0.477273	NM_003959	A6NHQ6|Q6NXG8|Q9UED9	Missense_Mutation	SNP	ENST00000253083.4	37	CCDS31922.1	69	0.03159340659340659	64	0.13008130081300814	5	0.013812154696132596	0	0.0	0	0.0	A	9.125	1.009956	0.19277	0.123294	8.15E-4	ENSG00000130787	ENST00000253083	T	0.14766	2.48	4.77	2.24	0.28232	.	0.103731	0.64402	D	0.000003	T	0.00073	0.0002	N	0.20483	0.58	0.32676	P	0.516181	B;B;B	0.14012	0.0;0.0;0.009	B;B;B	0.09377	0.001;0.004;0.004	T	0.38436	-0.9661	9	0.16420	T	0.52	-44.0738	5.6228	0.17467	0.5893:0.3098:0.101:0.0	rs7972242;rs7972242	516;516;504	O75146;Q6NXG8;B3KQW8	HIP1R_HUMAN;.;.	Q	516	ENSP00000253083:K516Q	ENSP00000253083:K516Q	K	+	1	0	HIP1R	121907152	0.990000	0.36364	0.998000	0.56505	0.681000	0.39784	0.484000	0.22308	0.682000	0.31407	0.459000	0.35465	AAG	A|0.954;C|0.046	0.046	strong		0.662	HIP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400935.1	NM_003959		C	123341199	A	C	123341199	3	2	22	1	0	0	0	0	1	0	0	0	7124	247	9	5	1612	5	HIP1R	12	123341199	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	251244	123341199	10510696	2768	5669											
ARL6IP4	23457	hgsc.bcm.edu	37	chr12	123466304	123466304	+	5'Flank	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caagaggaggaagaagaagaAgaagaggaagaagctgaaga	22	1	16	2	0	0	9	0	1	0	8	0	12	0	12	0	3	1	1	0	3	9	0	rs74758272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:123466304A>G	ENST00000542678.1	-	0	0				RP11-197N18.2_ENST00000540866.2_RNA|ARL6IP4_ENST00000412505.2_Missense_Mutation_p.K97R|ARL6IP4_ENST00000315580.5_Missense_Mutation_p.K239R|ARL6IP4_ENST00000454885.2_Missense_Mutation_p.K105R|ARL6IP4_ENST00000357866.4_Missense_Mutation_p.K108R|ARL6IP4_ENST00000543566.1_Missense_Mutation_p.K220R|ARL6IP4_ENST00000439686.2_Missense_Mutation_p.K108R|ARL6IP4_ENST00000426960.2_Missense_Mutation_p.K97R|ARL6IP4_ENST00000453766.2_Missense_Mutation_p.K231R|ARL6IP4_ENST00000392435.2_Missense_Mutation_p.K220R			Q9NP78	ABCB9_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 9						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)		aagaagaagaagaagaggaag	0.577													A|||	546	0.109026	0.3941	0.0346	5008	,	,		19865	0.0		0.001	False		,,,				2504	0.0				p.K239R	Ovarian(49;786 1333 9175 38236)	Atlas-SNP	.											.	ARL6IP4	14	.	0			c.A716G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	1308,3046		202,904,1071	26	27	27		692,659,659,716	2.6	1	12	dbSNP_131	27	23,8529		0,23,4253	yes	missense,missense,missense,missense	ARL6IP4	NM_001002251.1,NM_001002252.1,NM_016638.2,NM_018694.2	26,26,26,26	202,927,5324	GG,GA,AA		0.2689,30.0413,10.313	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	231/353,220/339,220/342,239/361	123466304	1331,11575	2177	4276	6453	SO:0001631	upstream_gene_variant	51329	exon3			AGAAGAAGAAGAG	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			12.37:g.123466304A>G	Exception_encountered	72	0	0		75	36	0.48	NM_018694	B4E2J0|Q5W9G7|Q769F3|Q769F4|Q96AB1|Q9P208	Missense_Mutation	SNP	ENST00000542678.1	37	CCDS9241.1	193	0.08836996336996338	184	0.37398373983739835	9	0.024861878453038673	0	0.0	0	0.0	A	12.68	2.010868	0.35511	0.300413	0.002689	ENSG00000182196	ENST00000544323;ENST00000543566;ENST00000315580;ENST00000542099;ENST00000392435;ENST00000413381;ENST00000426960;ENST00000453766;ENST00000454885;ENST00000412505;ENST00000439686;ENST00000456762;ENST00000357866	T;T;T;T;T;T;T;T;T;T;T;T;T	0.53857	1.22;0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.69;0.6;0.6;0.69	4.96	2.59	0.31030	.	0.666484	0.15025	N	0.284816	T	0.00012	0.0000	L	0.56769	1.78	0.28457	P	0.9160855999999999	B;B;P;P;P;P	0.39326	0.026;0.021;0.617;0.668;0.467;0.617	B;B;B;B;B;B	0.40444	0.027;0.016;0.221;0.329;0.167;0.221	T	0.34850	-0.9812	9	0.27785	T	0.31	.	4.0754	0.09901	0.6128:0.0:0.2434:0.1437	.	105;231;220;220;239;231	B3V0L1;Q66PJ3-5;Q66PJ3-4;B3V0L0;Q66PJ3;Q66PJ3-2	.;.;.;.;AR6P4_HUMAN;.	R	220;220;239;228;220;108;97;231;105;97;108;98;108	ENSP00000445309:K220R;ENSP00000442718:K220R;ENSP00000313422:K239R;ENSP00000442200:K228R;ENSP00000376230:K220R;ENSP00000441406:K108R;ENSP00000406036:K97R;ENSP00000414847:K231R;ENSP00000396723:K105R;ENSP00000413132:K97R;ENSP00000396365:K108R;ENSP00000391598:K98R;ENSP00000350532:K108R	ENSP00000313422:K239R	K	+	2	0	ARL6IP4	122032257	1.000000	0.71417	0.994000	0.49952	0.062000	0.15995	1.400000	0.34577	0.336000	0.23639	0.397000	0.26171	AAG	A|0.880;G|0.120	0.120	strong		0.577	ABCB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400956.1	NM_019624		G	123466304	A	G	123466304	1	3	22	0	1	0	0	0	0	0	0	0	943	72	3	3		3	ARL6IP4	12	123466304	5'Flank	SNP	A	TCGA-G8-6324-01A-11D-2210-10	125105	123466304	10385591	2769	5670											
CDK2AP1	8099	hgsc.bcm.edu	37	chr12	123749834	123749834	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgatggccagcagctccgcGtatttgctttggggcacctg	6	11	13	11	2	0	1	0	1	0	0	1	1	1	1	3	3	3	5	3	3	1	3	rs76783415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:123749834G>A	ENST00000261692.2	-	3	710	c.189C>T	c.(187-189)taC>taT	p.Y63Y	CDK2AP1_ENST00000535979.1_Silent_p.Y35Y|CDK2AP1_ENST00000544658.1_Silent_p.Y35Y|CDK2AP1_ENST00000538446.1_Silent_p.Y35Y|CDK2AP1_ENST00000542174.1_Silent_p.Y35Y|RP11-282O18.7_ENST00000602352.1_RNA	NM_001270433.1|NM_001270434.1|NM_004642.3	NP_001257362.1|NP_001257363.1|NP_004633.1	O14519	CDKA1_HUMAN	cyclin-dependent kinase 2 associated protein 1	63					cell cycle (GO:0007049)|DNA-dependent DNA replication (GO:0006261)|positive regulation of protein phosphorylation (GO:0001934)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA polymerase binding (GO:0070182)			lung(2)|stomach(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000554)|Epithelial(86;0.00178)		GCAGCTCCGCGTATTTGCTTT	0.582													G|||	152	0.0303514	0.1112	0.0072	5008	,	,		18220	0.0		0.0	False		,,,				2504	0.0				p.Y63Y		Atlas-SNP	.											.	CDK2AP1	8	.	0			c.C189T						PASS	.	G		443,3963	214.1+/-233.5	22,399,1782	137	129	132		189	-7.6	0.1	12	dbSNP_132	132	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	CDK2AP1	NM_004642.2		22,405,6076	AA,AG,GG		0.0698,10.0545,3.4523		63/116	123749834	449,12557	2203	4300	6503	SO:0001819	synonymous_variant	8099	exon3			CTCCGCGTATTTG	AB006077	CCDS9245.1, CCDS58289.1	12q24	2008-11-04	2008-11-04		ENSG00000111328	ENSG00000111328			14002	protein-coding gene	gene with protein product		602198	"CDK2-associated protein 1"			9331572, 9506968	Standard	NM_004642		Approved	DORC1, doc-1, DOC1, ST19, p12DOC-1	uc001ueq.4	O14519	OTTHUMG00000168854	ENST00000261692.2:c.189C>T	12.37:g.123749834G>A		147	0	0		148	77	0.52027	NM_004642	F5GYA4	Silent	SNP	ENST00000261692.2	37	CCDS9245.1																																																																																			G|0.970;A|0.030	0.030	strong		0.582	CDK2AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401387.1	NM_004642		A	123749834	G	A	123749834	2	1	22	1	0	0	0	0	0	0	0	1	3140	1140	40	1		1	CDK2AP1	12	123749834	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	283530	123749834	10102061	2770	5671											
DDX55	57696	hgsc.bcm.edu	37	chr12	124090655	124090655	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	aaaacactcgcttttgtcatCcccatcctggaaattcttct	10	14	4	13	1	3	0	1	0	2	0	6	1	5	1	3	1	1	1	3	1	3	4	rs7973689	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124090655C>T	ENST00000238146.4	+	3	245	c.195C>T	c.(193-195)atC>atT	p.I65I	DDX55_ENST00000538744.1_Silent_p.I65I	NM_020936.1	NP_065987.1	Q8NHQ9	DDX55_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55	65	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					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)		CTTTTGTCATCCCCATCCTGG	0.428													C|||	364	0.0726837	0.2315	0.0202	5008	,	,		20720	0.0		0.0159	False		,,,				2504	0.0286				p.I65I		Atlas-SNP	.											.	DDX55	51	.	0			c.C195T						PASS	.	C		764,3642	308.0+/-290.3	67,630,1506	81	76	77		195	1.6	1	12	dbSNP_116	77	163,8437	74.2+/-136.8	0,163,4137	no	coding-synonymous	DDX55	NM_020936.1		67,793,5643	TT,TC,CC		1.8953,17.34,7.1275		65/601	124090655	927,12079	2203	4300	6503	SO:0001819	synonymous_variant	57696	exon3			TGTCATCCCCATC	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.195C>T	12.37:g.124090655C>T		93	0	0		105	56	0.533333	NM_020936	Q658L6|Q8IYH0|Q9HCH7	Silent	SNP	ENST00000238146.4	37	CCDS9251.1																																																																																			C|0.929;T|0.071	0.071	strong		0.428	DDX55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400616.2			T	124090655	C	T	124090655	2	4	22	1	0	0	0	0	0	0	0	1	4375	845	30	2		2	DDX55	12	124090655	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	340821	124090655	9761240	2771	5672											
DNAH10	196385	hgsc.bcm.edu	37	chr12	124270467	124270467	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtctgccgagtggtcaacCtgcggactttgttcaagtaa	9	11	12	9	2	3	0	2	0	1	0	3	3	3	1	2	2	3	2	2	2	3	3	rs116310078	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124270467C>T	ENST00000409039.3	+	9	1247	c.1222C>T	c.(1222-1224)Ctg>Ttg	p.L408L		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	408	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)		AGTGGTCAACCTGCGGACTTT	0.438													C|||	28	0.00559105	0.0212	0.0	5008	,	,		19731	0.0		0.0	False		,,,				2504	0.0				p.L408L		Atlas-SNP	.											.	DNAH10	888	.	0			c.C1222T						PASS	.	C		76,4330	65.8+/-103.3	0,76,2127	86	77	80		1222	4.4	1	12	dbSNP_132	80	1,8599		0,1,4299	no	coding-synonymous	DNAH10	NM_207437.3		0,77,6426	TT,TC,CC		0.0116,1.7249,0.592		408/4472	124270467	77,12929	2203	4300	6503	SO:0001819	synonymous_variant	196385	exon9			GTCAACCTGCGGA	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.1222C>T	12.37:g.124270467C>T		27	0	0		60	30	0.5	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																			C|0.994;T|0.006	0.006	strong		0.438	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124270467	C	T	124270467	2	4	22	1	0	0	0	0	0	0	0	1	4600	680	24	2		2	DNAH10	12	124270467	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	179812	124270467	9581428	2772	5673											
DNAH10	196385	hgsc.bcm.edu	37	chr12	124288213	124288213	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttctttcttcaaaggtatcGgtgactatataactggttgc	9	17	8	7	1	3	1	1	1	2	0	4	1	3	1	0	3	2	2	0	3	5	8	rs77726895	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124288213G>A	ENST00000409039.3	+	16	2291	c.2266G>A	c.(2266-2268)Ggt>Agt	p.G756S		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	756	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)		CAAAGGTATCGGTGACTATAT	0.428													G|||	78	0.0155751	0.053	0.0115	5008	,	,		19141	0.0		0.0	False		,,,				2504	0.0				p.G756S		Atlas-SNP	.											.	DNAH10	888	.	0			c.G2266A						PASS	.	G	SER/GLY	261,4143	140.4+/-175.9	8,245,1949	37	33	35		2266	2.9	0.1	12	dbSNP_131	35	14,8584	8.4+/-32.0	0,14,4285	yes	missense	DNAH10	NM_207437.3	56	8,259,6234	AA,AG,GG		0.1628,5.9264,2.1151	benign	756/4472	124288213	275,12727	2202	4299	6501	SO:0001583	missense	196385	exon16			GGTATCGGTGACT	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.2266G>A	12.37:g.124288213G>A	ENSP00000386770:p.Gly756Ser	61	0	0		37	23	0.621622	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	20	0.009157509157509158	18	0.036585365853658534	2	0.0055248618784530384	0	0.0	0	0.0	G	0.013	-1.611697	0.00835	0.059264	0.001628	ENSG00000197653	ENST00000409039	T	0.53640	0.61	4.78	2.86	0.33363	Dynein heavy chain, domain-1 (1);	0.636305	0.13044	N	0.418306	T	0.01765	0.0056	N	0.01505	-0.83	0.09310	N	1	B;B;B	0.10296	0.003;0.0;0.0	B;B;B	0.09377	0.004;0.003;0.004	T	0.15925	-1.0420	10	0.08381	T	0.77	.	8.2499	0.31710	0.0747:0.0:0.6468:0.2785	.	756;631;756	Q8IVF4-2;C4IXU6;Q8IVF4	.;.;DYH10_HUMAN	S	756	ENSP00000386770:G756S	ENSP00000386770:G756S	G	+	1	0	DNAH10	122854166	0.000000	0.05858	0.130000	0.21974	0.029000	0.11900	0.209000	0.17435	0.475000	0.27415	0.650000	0.86243	GGT	G|0.980;A|0.020	0.020	strong		0.428	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			A	124288213	G	A	124288213	3	1	22	1	0	0	0	0	1	0	0	0	4600	1116	39	1	2328	1	DNAH10	12	124288213	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	17746	124288213	9563682	2773	5674											
DNAH10	196385	hgsc.bcm.edu	37	chr12	124323011	124323011	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttctggtccagatcatgggTgagaccttaaaagaccccgt	10	10	11	10	1	2	3	1	1	1	3	3	4	3	3	4	2	0	1	4	2	2	2	rs116167096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124323011T>C	ENST00000409039.3	+	28	4582	c.4557T>C	c.(4555-4557)ggT>ggC	p.G1519G		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1519	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)		AGATCATGGGTGAGACCTTAA	0.567													T|||	94	0.01877	0.0688	0.0043	5008	,	,		17334	0.0		0.0	False		,,,				2504	0.0				p.G1519G		Atlas-SNP	.											.	DNAH10	888	.	0			c.T4557C						PASS	.	T		189,3859		4,181,1839	33	34	34		4557	-10.4	0	12	dbSNP_132	34	1,8343		0,1,4171	no	coding-synonymous	DNAH10	NM_207437.3		4,182,6010	CC,CT,TT		0.012,4.669,1.5332		1519/4472	124323011	190,12202	2024	4172	6196	SO:0001819	synonymous_variant	196385	exon28			CATGGGTGAGACC	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.4557T>C	12.37:g.124323011T>C		51	0	0		72	35	0.486111	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																			T|0.983;C|0.017	0.017	strong		0.567	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			C	124323011	T	C	124323011	2	2	22	1	0	0	0	0	0	0	0	1	4600	1683	59	3		3	DNAH10	12	124323011	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	34798	124323011	9528884	2774	5675											
DNAH10	196385	hgsc.bcm.edu	37	chr12	124354954	124354954	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	actttcattttgataacaaaCggaatcaatgggtcccatgg	13	12	8	8	1	2	1	2	1	0	0	3	2	3	2	1	3	2	0	1	3	4	4	rs7977449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124354954C>T	ENST00000409039.3	+	43	7232	c.7207C>T	c.(7207-7209)Cgg>Tgg	p.R2403W		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2403			R -> W (in dbSNP:rs7977449).		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)		TGATAACAAACGGAATCAATG	0.393													C|||	118	0.0235623	0.0295	0.0086	5008	,	,		21920	0.0526		0.007	False		,,,				2504	0.0133				p.R2403W		Atlas-SNP	.											.	DNAH10	888	.	0			c.C7207T						PASS	.	C	TRP/ARG	109,3641		3,103,1769	91	88	89		7207	2.2	0	12	dbSNP_116	89	59,8163		0,59,4052	yes	missense	DNAH10	NM_207437.3	101	3,162,5821	TT,TC,CC		0.7176,2.9067,1.4033	probably-damaging	2403/4472	124354954	168,11804	1875	4111	5986	SO:0001583	missense	196385	exon43			AACAAACGGAATC	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.7207C>T	12.37:g.124354954C>T	ENSP00000386770:p.Arg2403Trp	99	0	0		79	34	0.43038	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	63	0.028846153846153848	19	0.03861788617886179	3	0.008287292817679558	37	0.06468531468531469	4	0.005277044854881266	C	15.02	2.709681	0.48517	0.029067	0.007176	ENSG00000197653	ENST00000409039	T	0.22945	1.93	5.21	2.23	0.28157	.	1.696560	0.05959	U	0.640214	T	0.03434	0.0099	L	0.49778	1.585	0.09310	N	1	P	0.52316	0.952	P	0.44860	0.462	T	0.13255	-1.0516	10	0.66056	D	0.02	.	8.4827	0.33052	0.5085:0.4206:0.0:0.0709	rs7977449;rs7977449	2403	Q8IVF4	DYH10_HUMAN	W	2403	ENSP00000386770:R2403W	ENSP00000386770:R2403W	R	+	1	2	DNAH10	122920907	0.005000	0.15991	0.000000	0.03702	0.001000	0.01503	0.510000	0.22723	0.571000	0.29365	0.655000	0.94253	CGG	C|0.971;T|0.029	0.029	strong		0.393	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124354954	C	T	124354954	3	4	22	1	0	0	0	0	1	0	0	0	4600	527	19	1	7377	1	DNAH10	12	124354954	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	31943	124354954	9496941	2775	5676											
DNAH10	196385	hgsc.bcm.edu	37	chr12	124360032	124360032	+	Silent	SNP	C	C	T																															tcctccatcctgaaaggccaCacctcggtaacttgatttta																								rs11834289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124360032C>T	ENST00000409039.3	+	46	7864	c.7839C>T	c.(7837-7839)caC>caT	p.H2613H		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2613	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(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)		TGAAAGGCCACACCTCGGTAA	0.438													T|||	462	0.0922524	0.2806	0.0418	5008	,	,		17889	0.0506		0.0089	False		,,,				2504	0.002				p.H2613H		Atlas-SNP	.											.	DNAH10	888	.	0			c.C7839T						PASS	.	T		909,2825		110,689,1068	108	100	103		7839	-6.8	0.4	12	dbSNP_120	103	88,8104		1,86,4009	no	coding-synonymous	DNAH10	NM_207437.3		111,775,5077	TT,TC,CC		1.0742,24.3439,8.3599		2613/4472	124360032	997,10929	1867	4096	5963	SO:0001819	synonymous_variant	196385	exon46			AGGCCACACCTCG	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.7839C>T	12.37:g.124360032C>T		91	0	0		101	48	0.475248	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																			C|0.924;T|0.076	0.076	strong		0.438	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124360032	C	T	124360032	2	4	22	1	0	0	0	0	0	0	0	1	4600	477	17	2		2	DNAH10	12	124360032	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	5078	124360032	9491863	2776	5677	67	2									
DNAH10	196385	hgsc.bcm.edu	37	chr12	124360037	124360037	+	Splice_Site	SNP	C	C	T																															catcctgaaaggccacacctCggtaacttgattttaactag																								rs61732737	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124360037C>T	ENST00000409039.3	+	46	7869	c.7844C>T	c.(7843-7845)tCg>tTg	p.S2615L		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2615	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(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)		GGCCACACCTCGGTAACTTGA	0.448													C|||	125	0.0249601	0.034	0.0086	5008	,	,		18069	0.0526		0.007	False		,,,				2504	0.0143				p.S2615L		Atlas-SNP	.											.	DNAH10	888	.	0			c.C7844T						PASS	.	C	LEU/SER	112,3600		3,106,1747	100	93	95		7844	3.3	1	12	dbSNP_129	95	57,8131		0,57,4037	yes	missense-near-splice	DNAH10	NM_207437.3	145	3,163,5784	TT,TC,CC		0.6961,3.0172,1.4202	benign	2615/4472	124360037	169,11731	1856	4094	5950	SO:0001630	splice_region_variant	196385	exon46			ACACCTCGGTAAC	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.7845+1C>T	12.37:g.124360037C>T		88	0	0		103	49	0.475728	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	64	0.029304029304029304	20	0.04065040650406504	3	0.008287292817679558	37	0.06468531468531469	4	0.005277044854881266	C	12.26	1.884048	0.33255	0.030172	0.006961	ENSG00000197653	ENST00000409039	T	0.39787	1.06	5.41	3.3	0.37823	.	2.437090	0.02760	N	0.118428	T	0.05640	0.0148	L	0.41415	1.275	0.80722	D	1	B	0.22080	0.064	B	0.16289	0.015	T	0.03524	-1.1028	10	0.34782	T	0.22	.	10.3793	0.44101	0.1914:0.7324:0.0:0.0762	rs61732737	2615	Q8IVF4	DYH10_HUMAN	L	2615	ENSP00000386770:S2615L	ENSP00000386770:S2615L	S	+	2	0	DNAH10	122925990	0.862000	0.29867	0.998000	0.56505	0.927000	0.56198	0.469000	0.22067	1.425000	0.47237	0.558000	0.71614	TCG	C|0.976;T|0.024	0.024	strong		0.448	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		Missense_Mutation	T	124360037	C	T	124360037	5	4	22	1	0	0	0	0	0	0	1	0	4600	898	31	1	8026	1	DNAH10	12	124360037	Splice_Site	SNP	C	TCGA-G8-6324-01A-11D-2210-10	5	124360037	9491858	2777	5678	67	2									
DNAH10	196385	hgsc.bcm.edu	37	chr12	124401172	124401172	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggcagtttattatcctgggaGacaaggaagtggactatgat	12	11	13	5	0	0	2	0	1	0	1	1	5	1	4	1	4	0	2	1	4	5	4	rs61740383	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124401172G>A	ENST00000409039.3	+	62	10562	c.10537G>A	c.(10537-10539)Gac>Aac	p.D3513N		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3513	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)		TATCCTGGGAGACAAGGAAGT	0.433													G|||	327	0.0652955	0.2322	0.0231	5008	,	,		21713	0.0		0.003	False		,,,				2504	0.001				p.D3513N		Atlas-SNP	.											.	DNAH10	888	.	0			c.G10537A						PASS	.	G	ASN/ASP	688,3042		58,572,1235	71	72	72		10537	4.7	1	12	dbSNP_129	72	38,8150		1,36,4057	yes	missense	DNAH10	NM_207437.3	23	59,608,5292	AA,AG,GG		0.4641,18.445,6.0916	probably-damaging	3513/4472	124401172	726,11192	1865	4094	5959	SO:0001583	missense	196385	exon62			CTGGGAGACAAGG	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.10537G>A	12.37:g.124401172G>A	ENSP00000386770:p.Asp3513Asn	83	0	0		98	52	0.530612	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	113	0.051739926739926737	100	0.2032520325203252	11	0.03038674033149171	0	0.0	2	0.002638522427440633	G	32	5.137071	0.94517	0.18445	0.004641	ENSG00000197653	ENST00000409039	T	0.33654	1.4	4.74	4.74	0.60224	.	0.000000	0.85682	D	0.000000	T	0.00144	0.0004	M	0.90425	3.115	0.09310	P	0.999999878792	D	0.89917	1.0	D	0.87578	0.998	T	0.02471	-1.1154	9	0.87932	D	0	.	17.7267	0.88367	0.0:0.0:1.0:0.0	rs61740383	3513	Q8IVF4	DYH10_HUMAN	N	3513	ENSP00000386770:D3513N	ENSP00000386770:D3513N	D	+	1	0	DNAH10	122967125	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.869000	0.99810	2.177000	0.69029	0.561000	0.74099	GAC	G|0.957;A|0.043	0.043	strong		0.433	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			A	124401172	G	A	124401172	3	1	22	1	0	0	0	0	1	0	0	0	4600	942	33	2	10783	2	DNAH10	12	124401172	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	41135	124401172	9450723	2778	5679											
DNAH10	196385	hgsc.bcm.edu	37	chr12	124409630	124409630	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attcactggagcagtttcccGtccccttgggttacgataac	8	12	9	12	2	1	0	1	0	0	0	3	2	3	1	3	2	3	3	3	2	2	5	rs74845458	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124409630G>T	ENST00000409039.3	+	67	11471	c.11446G>T	c.(11446-11448)Gtc>Ttc	p.V3816F	RP11-380L11.4_ENST00000602952.1_RNA|CCDC92_ENST00000544798.1_Intron	NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3816					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)		GCAGTTTCCCGTCCCCTTGGG	0.473													T|||	327	0.0652955	0.2322	0.0231	5008	,	,		20433	0.0		0.003	False		,,,				2504	0.001				p.V3816F		Atlas-SNP	.											DNAH10_same_name,NS,carcinoma,0,2	DNAH10	888	2	0			c.G11446T						PASS	.	T	PHE/VAL	709,3179		59,591,1294	174	167	170		11446	1.5	0.3	12	dbSNP_131	170	39,8265		1,37,4114	yes	missense	DNAH10	NM_207437.3	50	60,628,5408	TT,TG,GG		0.4697,18.2356,6.1352	benign	3816/4472	124409630	748,11444	1944	4152	6096	SO:0001583	missense	196385	exon67			TTTCCCGTCCCCT	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.11446G>T	12.37:g.124409630G>T	ENSP00000386770:p.Val3816Phe	258	0	0		282	136	0.482269	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	113	0.051739926739926737	100	0.2032520325203252	11	0.03038674033149171	0	0.0	2	0.002638522427440633	T	0.013	-1.642308	0.00799	0.182356	0.004697	ENSG00000197653	ENST00000409039	T	0.09538	2.97	5.45	1.5	0.22942	Dynein heavy chain (1);	0.344630	0.30085	N	0.010460	T	0.00012	0.0000	N	0.00277	-1.72	0.19945	P	0.9999460444	B	0.02656	0.0	B	0.01281	0.0	T	0.40308	-0.9570	9	0.12430	T	0.62	.	2.5158	0.04667	0.11:0.1927:0.1142:0.5831	.	3816	Q8IVF4	DYH10_HUMAN	F	3816	ENSP00000386770:V3816F	ENSP00000386770:V3816F	V	+	1	0	DNAH10	122975583	0.935000	0.31712	0.251000	0.24312	0.009000	0.06853	1.289000	0.33307	0.040000	0.15660	-1.401000	0.01141	GTC	G|0.958;T|0.042	0.042	strong		0.473	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124409630	G	T	124409630	3	4	22	1	0	0	0	0	1	0	0	0	4600	1145	40	4	11712	4	DNAH10	12	124409630	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	8458	124409630	9442265	2779	5680											
DNAH10	196385	hgsc.bcm.edu	37	chr12	124417989	124417989	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agaacggctggccactggacCgctccaccttgttcacacaa	10	7	9	15	2	1	1	1	0	0	1	2	2	2	2	4	3	1	3	4	3	2	2	rs61746561	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124417989C>T	ENST00000409039.3	+	76	13079	c.13054C>T	c.(13054-13056)Cgc>Tgc	p.R4352C	RP11-380L11.3_ENST00000602292.1_RNA|DNAH10OS_ENST00000514254.2_Intron|CCDC92_ENST00000544798.1_Intron	NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	4352					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)		GCCACTGGACCGCTCCACCTT	0.617													C|||	70	0.0139776	0.0507	0.0014	5008	,	,		18672	0.0		0.001	False		,,,				2504	0.001				p.R4352C		Atlas-SNP	.											.	DNAH10	888	.	0			c.C13054T						PASS	.	C	CYS/ARG	149,3855		4,141,1857	40	43	42		13054	5.2	1	12	dbSNP_129	42	7,8303		0,7,4148	yes	missense	DNAH10	NM_207437.3	180	4,148,6005	TT,TC,CC		0.0842,3.7213,1.2669	probably-damaging	4352/4472	124417989	156,12158	2002	4155	6157	SO:0001583	missense	196385	exon76			CTGGACCGCTCCA	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.13054C>T	12.37:g.124417989C>T	ENSP00000386770:p.Arg4352Cys	76	0	0		105	43	0.409524	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	C	34	5.328033	0.95733	0.037213	8.42E-4	ENSG00000197653	ENST00000409039	T	0.09255	3.0	5.18	5.18	0.71444	Dynein heavy chain (1);	0.139800	0.49305	D	0.000149	T	0.11410	0.0278	M	0.83118	2.625	0.80722	D	1	D	0.89917	1.0	D	0.70487	0.969	T	0.02942	-1.1091	10	0.66056	D	0.02	.	18.3051	0.90177	0.0:1.0:0.0:0.0	rs61746561	4352	Q8IVF4	DYH10_HUMAN	C	4352	ENSP00000386770:R4352C	ENSP00000386770:R4352C	R	+	1	0	DNAH10	122983942	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	5.889000	0.69766	2.413000	0.81919	0.561000	0.74099	CGC	C|0.991;T|0.009	0.009	strong		0.617	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124417989	C	T	124417989	3	4	22	1	0	0	0	0	1	0	0	0	4600	652	23	1	13356	1	DNAH10	12	124417989	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	8359	124417989	9433906	2780	5681											
CCDC92	80212	hgsc.bcm.edu	37	chr12	124421764	124421764	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtgcggcttttcgcgggcCgggctgtgctgctcgccgct	0	12	16	13	6	0	0	0	0	0	0	2	0	0	0	2	3	3	5	2	3	0	3	rs34241686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124421764C>T	ENST00000238156.3	-	5	1191	c.837G>A	c.(835-837)ccG>ccA	p.P279P	RP11-380L11.3_ENST00000602292.1_RNA|CCDC92_ENST00000545135.1_Silent_p.P262P|CCDC92_ENST00000545891.1_Silent_p.P262P|DNAH10OS_ENST00000514254.2_5'Flank|CCDC92_ENST00000544798.1_Intron	NM_025140.1	NP_079416.1	Q53HC0	CCD92_HUMAN	coiled-coil domain containing 92	279						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)		TTTCGCGGGCCGGGCTGTGCT	0.701													C|||	27	0.00539137	0.0197	0.0	5008	,	,		12393	0.0		0.001	False		,,,				2504	0.0				p.P279P		Atlas-SNP	.											.	CCDC92	18	.	0			c.G837A						PASS	.	C		54,4342		0,54,2144	18	21	20		837	-9.9	0.1	12	dbSNP_126	20	4,8578		0,4,4287	no	coding-synonymous	CCDC92	NM_025140.1		0,58,6431	TT,TC,CC		0.0466,1.2284,0.4469		279/332	124421764	58,12920	2198	4291	6489	SO:0001819	synonymous_variant	80212	exon5			GCGGGCCGGGCTG	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.837G>A	12.37:g.124421764C>T		13	0	0		22	10	0.454545	NM_025140	B3KNQ0|Q9H697	Silent	SNP	ENST00000238156.3	37	CCDS9256.1																																																																																			C|0.996;T|0.004	0.004	strong		0.701	CCDC92-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400780.2	NM_025140		T	124421764	C	T	124421764	2	4	22	1	0	0	0	0	0	0	0	1	2873	639	23	1		1	CCDC92	12	124421764	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3775	124421764	9430131	2781	5682											
FAM101A	144347	hgsc.bcm.edu	37	chr12	124798797	124798797	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccaggacaaggtcttctatgCgcccgtacccaccgtcacgg	8	7	10	16	4	3	0	1	0	2	0	3	1	3	1	4	3	2	1	4	3	3	3	rs116090335	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124798797C>T	ENST00000389727.3	+	3	377	c.377C>T	c.(376-378)gCg>gTg	p.A126V	FAM101A_ENST00000324038.3_Missense_Mutation_p.A45V|FAM101A_ENST00000546355.1_Missense_Mutation_p.A45V|FAM101A_ENST00000338359.4_Missense_Mutation_p.A45V			Q6ZTI6	F101A_HUMAN	family with sequence similarity 101, member A	126										endometrium(1)|kidney(1)|lung(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;2.38e-05)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-05)|all cancers(50;0.000361)|BRCA - Breast invasive adenocarcinoma(302;0.059)		GTCTTCTATGCGCCCGTACCC	0.622													C|||	9	0.00179712	0.0068	0.0	5008	,	,		18557	0.0		0.0	False		,,,				2504	0.0				p.A45V		Atlas-SNP	.											.	FAM101A	10	.	0			c.C134T						PASS	.	C	VAL/ALA,VAL/ALA	31,4375	37.6+/-69.7	0,31,2172	84	72	76		134,134	0	0.1	12	dbSNP_132	76	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	FAM101A,ZNF664-FAM101A	NM_001204299.1,NM_181709.4	64,64	0,32,6471	TT,TC,CC		0.0116,0.7036,0.246	benign,benign	45/136,45/136	124798797	32,12974	2203	4300	6503	SO:0001583	missense	144347	exon3			TCTATGCGCCCGT		CCDS9258.1	12q24.31	2012-11-30			ENSG00000178882	ENSG00000178882			27051	protein-coding gene	gene with protein product		615927				12477932	Standard	NM_181709		Approved	FLJ44614	uc001ugd.2	Q6ZTI6	OTTHUMG00000168609	ENST00000389727.3:c.377C>T	12.37:g.124798797C>T	ENSP00000374377:p.Ala126Val	114	0	0		144	80	0.555556	NM_181709	A5D8T5	Missense_Mutation	SNP	ENST00000389727.3	37		3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	2.675	-0.276668	0.05679	0.007036	1.16E-4	ENSG00000178882	ENST00000324038;ENST00000541200;ENST00000389727;ENST00000546355;ENST00000338359	.	.	.	4.69	0.0271	0.14153	.	0.566604	0.18703	N	0.133527	T	0.13243	0.0321	N	0.10874	0.06	0.28756	N	0.901148	B	0.13145	0.007	B	0.08055	0.003	T	0.10683	-1.0619	9	0.29301	T	0.29	-0.5442	5.5434	0.17051	0.0:0.3925:0.1872:0.4203	.	126	Q6ZTI6	F101A_HUMAN	V	45;45;126;45;45	.	ENSP00000315626:A45V	A	+	2	0	FAM101A	123364750	0.126000	0.22350	0.078000	0.20375	0.034000	0.12701	0.293000	0.19029	0.085000	0.17107	-1.175000	0.01729	GCG	C|0.998;T|0.002	0.002	strong		0.622	FAM101A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_181709		T	124798797	C	T	124798797	3	4	22	1	0	0	0	0	1	0	0	0	5385	768	27	1	140	1	FAM101A	12	124798797	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	377033	124798797	9053098	2782	5683											
NCOR2	9612	hgsc.bcm.edu	37	chr12	124821705	124821705	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aatgtggcagccgggcgaacGggtgaggaggtggaggtgga	9	5	22	5	3	0	1	0	1	0	0	0	5	0	4	1	8	2	1	1	8	2	0	rs3741512	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124821705G>A	ENST00000405201.1	-	38	5709	c.5709C>T	c.(5707-5709)ccC>ccT	p.P1903P	NCOR2_ENST00000397355.1_Silent_p.P1894P|NCOR2_ENST00000404621.1_Silent_p.P1893P|NCOR2_ENST00000429285.2_Silent_p.P1893P|NCOR2_ENST00000356219.3_Silent_p.P1910P|NCOR2_ENST00000404121.2_Silent_p.P1464P			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1914					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)		CCGGGCGAACGGGTGAGGAGG	0.667													g|||	120	0.0239617	0.0862	0.0086	5008	,	,		14245	0.0		0.0	False		,,,				2504	0.0				p.P1903P		Atlas-SNP	.											.	NCOR2	475	.	0			c.C5709T						PASS	.		,,	227,3647		6,215,1716	12	17	15		5679,5679,5709	-6.6	0.7	12	dbSNP_107	15	2,7984		0,2,3991	no	coding-synonymous,coding-synonymous,coding-synonymous	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	,,	6,217,5707	AA,AG,GG		0.025,5.8596,1.9309	,,	1893/2459,1893/2505,1903/2515	124821705	229,11631	1937	3993	5930	SO:0001819	synonymous_variant	9612	exon40			GCGAACGGGTGAG	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.5709C>T	12.37:g.124821705G>A		252	0	0		269	131	0.486989	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	37	CCDS41858.2	70	0.03205128205128205	67	0.13617886178861788	3	0.008287292817679558	0	0.0	0	0.0	g	6.208	0.406498	0.11754	0.058596	2.5E-4	ENSG00000196498	ENST00000440187	.	.	.	4.36	-6.64	0.01801	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.99999815647	.	.	.	.	.	.	T	0.31613	-0.9937	3	.	.	.	-11.6142	1.0444	0.01566	0.3119:0.1788:0.3193:0.1901	rs3741512	.	.	.	C	138	.	.	R	-	1	0	NCOR2	123387658	0.000000	0.05858	0.747000	0.31113	0.653000	0.38743	-2.100000	0.01345	-0.547000	0.06207	-2.034000	0.00421	CGT	G|0.966;A|0.034	0.034	strong		0.667	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		A	124821705	G	A	124821705	2	1	22	1	0	0	0	0	0	0	0	1	10245	1103	39	1		1	NCOR2	12	124821705	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	22908	124821705	9030190	2783	5684											
NCOR2	9612	hgsc.bcm.edu	37	chr12	124841276	124841276	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcacggggaagggcaggccGgaagtccagcaaggggggtc	9	2	21	9	2	0	0	0	0	0	0	2	2	1	2	2	9	1	3	2	9	3	0	rs200441401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124841276G>A	ENST00000405201.1	-	23	3153	c.3153C>T	c.(3151-3153)tcC>tcT	p.S1051S	NCOR2_ENST00000397355.1_Silent_p.S1042S|NCOR2_ENST00000404621.1_Silent_p.S1041S|NCOR2_ENST00000429285.2_Silent_p.S1041S|NCOR2_ENST00000356219.3_Silent_p.S1058S|NCOR2_ENST00000404121.2_Silent_p.S612S			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1059					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)		AGGGCAGGCCGGAAGTCCAGC	0.677													G|||	5	0.000998403	0.003	0.0	5008	,	,		14484	0.0		0.0	False		,,,				2504	0.001				p.S1051S		Atlas-SNP	.											.	NCOR2	475	.	0			c.C3153T						PASS	.	G	,,	10,3816		0,10,1903	12	17	15		3123,3123,3153	-4.4	0.3	12		15	1,8229		0,1,4114	no	coding-synonymous,coding-synonymous,coding-synonymous	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	,,	0,11,6017	AA,AG,GG		0.0122,0.2614,0.0912	,,	1041/2459,1041/2505,1051/2515	124841276	11,12045	1913	4115	6028	SO:0001819	synonymous_variant	9612	exon25			CAGGCCGGAAGTC	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.3153C>T	12.37:g.124841276G>A		182	0	0		192	94	0.489583	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	37	CCDS41858.2																																																																																			G|1.000;A|0.000	0.000	strong		0.677	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		A	124841276	G	A	124841276	2	1	22	1	0	0	0	0	0	0	0	1	10245	1103	39	1		1	NCOR2	12	124841276	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	19571	124841276	9010619	2784	5685											
NCOR2	9612	hgsc.bcm.edu	37	chr12	124846788	124846788	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtggcggtggggctgggggaGctggcttggtgggagctgcg	2	8	25	6	2	0	0	0	0	0	0	0	2	0	2	0	9	3	4	0	9	0	1	rs11057592	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124846788G>C	ENST00000405201.1	-	22	2984	c.2984C>G	c.(2983-2985)gCt>gGt	p.A995G	NCOR2_ENST00000397355.1_Missense_Mutation_p.A978G|NCOR2_ENST00000404621.1_Missense_Mutation_p.A977G|NCOR2_ENST00000429285.2_Missense_Mutation_p.A977G|NCOR2_ENST00000356219.3_Missense_Mutation_p.A994G|NCOR2_ENST00000404121.2_Missense_Mutation_p.A548G			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	995	Poly-Pro.				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)		GGCTGGGGGAGCTGGCTTGGT	0.682													G|||	117	0.0233626	0.0877	0.0014	5008	,	,		12732	0.0		0.0	False		,,,				2504	0.0				p.A995G		Atlas-SNP	.											.	NCOR2	475	.	0			c.C2984G						PASS	.	G	GLY/ALA,GLY/ALA,GLY/ALA	304,3804		12,280,1762	9	13	12		2930,2930,2984	3	0	12	dbSNP_120	12	4,8366		0,4,4181	yes	missense,missense,missense	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	60,60,60	12,284,5943	CC,CG,GG		0.0478,7.4002,2.4683	possibly-damaging,possibly-damaging,possibly-damaging	977/2459,977/2505,995/2515	124846788	308,12170	2054	4185	6239	SO:0001583	missense	9612	exon24			GGGGGAGCTGGCT	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.2984C>G	12.37:g.124846788G>C	ENSP00000384018:p.Ala995Gly	41	0	0		42	16	0.380952	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	37	CCDS41858.2	47	0.02152014652014652	46	0.09349593495934959	1	0.0027624309392265192	0	0.0	0	0.0	G	8.697	0.908871	0.17833	0.074002	4.78E-4	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285;ENST00000458234	T;T;T;T;T;T;T	0.31510	2.18;2.49;2.22;2.49;2.22;2.48;1.49	4.91	3.02	0.34903	.	0.502628	0.16789	U	0.199466	T	0.00998	0.0033	L	0.44542	1.39	0.09310	N	1	P;P;P	0.51933	0.824;0.824;0.949	B;B;P	0.45881	0.3;0.3;0.496	T	0.02179	-1.1200	10	0.27082	T	0.32	-2.9071	8.1686	0.31241	0.0881:0.1576:0.7543:0.0	rs11057592	977;978;995	C9J0Q5;C9J239;C9JFD3	.;.;.	G	995;977;994;978;994;548;977;995	ENSP00000384018:A995G;ENSP00000384202:A977G;ENSP00000348551:A994G;ENSP00000380513:A978G;ENSP00000385618:A548G;ENSP00000400281:A977G;ENSP00000402808:A995G	ENSP00000348551:A994G	A	-	2	0	NCOR2	123412741	0.024000	0.19004	0.009000	0.14445	0.009000	0.06853	0.963000	0.29293	0.454000	0.26884	0.462000	0.41574	GCT	G|0.973;C|0.027	0.027	strong		0.682	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		C	124846788	G	C	124846788	3	2	22	1	0	0	0	0	1	0	0	0	10245	971	34	4	4688	4	NCOR2	12	124846788	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5512	124846788	9005107	2785	5686											
SCARB1	949	hgsc.bcm.edu	37	chr12	125263039	125263039	+	3'UTR	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtggggctggggggctgtcCgctgggagagtccgggagaa	5	7	22	7	2	0	2	0	0	0	2	2	4	2	2	2	7	0	3	2	7	1	0	rs701103	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:125263039C>T	ENST00000415380.2	-	0	1870				SCARB1_ENST00000339570.5_Missense_Mutation_p.G499R|SCARB1_ENST00000261693.6_3'UTR|SCARB1_ENST00000376788.1_3'UTR			Q8WTV0	SCRB1_HUMAN	scavenger receptor class B, member 1						adhesion of symbiont to host (GO:0044406)|androgen biosynthetic process (GO:0006702)|blood vessel endothelial cell migration (GO:0043534)|cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|detection of lipopolysaccharide (GO:0032497)|endothelial cell proliferation (GO:0001935)|high-density lipoprotein particle clearance (GO:0034384)|high-density lipoprotein particle remodeling (GO:0034375)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|recognition of apoptotic cell (GO:0043654)|regulation of phagocytosis (GO:0050764)|regulation of phosphatidylcholine catabolic process (GO:0010899)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|viral process (GO:0016032)|wound healing (GO:0042060)	caveola (GO:0005901)|cell surface (GO:0009986)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein binding (GO:0034185)|high-density lipoprotein particle binding (GO:0008035)|high-density lipoprotein particle receptor activity (GO:0070506)|lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|prostate(1)	17	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000116)|Epithelial(86;0.000415)|all cancers(50;0.00395)	Phosphatidylserine(DB00144)	GGGGGCTGTCCGCTGGGAGAG	0.692													C|||	305	0.0609026	0.2224	0.0144	5008	,	,		12888	0.0		0.001	False		,,,				2504	0.0				p.G499R		Atlas-SNP	.											.	SCARB1	40	.	0			c.G1495A						PASS	.	C	ARG/GLY,	644,3422		39,566,1428	7	11	10		1495,	1.5	0	12	dbSNP_86	10	16,8256		0,16,4120	yes	missense,utr-3	SCARB1	NM_001082959.1,NM_005505.4	125,	39,582,5548	TT,TC,CC		0.1934,15.8387,5.3493	,	499/507,	125263039	660,11678	2033	4136	6169	SO:0001624	3_prime_UTR_variant	949	exon12			GCTGTCCGCTGGG	Z22555	CCDS9259.1, CCDS45008.1	12q24.32	2008-08-05	2002-09-06	2002-09-06	ENSG00000073060	ENSG00000073060			1664	protein-coding gene	gene with protein product		601040	"CD36 antigen (collagen type I receptor, thrombospondin receptor)-like 1"	CD36L1		7689561	Standard	NM_001082959		Approved	SRB1, CLA-1, CLA1, SR-BI	uc001ugm.4	Q8WTV0	OTTHUMG00000168544	ENST00000415380.2:c.*86G>A	12.37:g.125263039C>T		28	0	0		51	29	0.568627	NM_001082959	F8W8N0|Q14016|Q52LZ5|Q6KFX4	Missense_Mutation	SNP	ENST00000415380.2	37		100	0.045787545787545784	92	0.18699186991869918	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	C	12.90	2.077750	0.36662	0.158387	0.001934	ENSG00000073060	ENST00000339570	T	0.61158	0.13	4.36	1.45	0.22620	.	.	.	.	.	T	0.00073	0.0002	L	0.36672	1.1	0.53688	P	2.4000000000024002E-5	B	0.33135	0.399	B	0.24006	0.05	T	0.03773	-1.1005	8	0.44086	T	0.13	.	4.3702	0.11244	0.0:0.5966:0.1882:0.2152	rs701103;rs747156;rs60594950	499	F8W8N0	.	R	499	ENSP00000343795:G499R	ENSP00000343795:G499R	G	-	1	0	SCARB1	123828992	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.608000	0.05641	-0.010000	0.14271	0.455000	0.32223	GGA	C|0.956;T|0.044	0.044	strong		0.692	SCARB1-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000400165.1	NM_005505		T	125263039	C	T	125263039	1	4	22	0	1	0	0	0	0	0	0	0	13896	661	23	1		1	SCARB1	12	125263039	3'UTR	SNP	C	TCGA-G8-6324-01A-11D-2210-10	416251	125263039	8588856	2786	5687											
TMEM132B	114795	hgsc.bcm.edu	37	chr12	125900104	125900104	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcggcagcaggtgtgaagatAacggcagtgagagtcagcag	12	5	17	7	2	1	3	1	2	0	2	1	4	1	3	0	3	3	4	0	3	2	1	rs143188464	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:125900104A>T	ENST00000299308.3	+	3	980	c.972A>T	c.(970-972)atA>atT	p.I324I		NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	324						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)		GTGTGAAGATAACGGCAGTGA	0.468													A|||	30	0.00599042	0.0219	0.0014	5008	,	,		18015	0.0		0.0	False		,,,				2504	0.0				p.I324I		Atlas-SNP	.											.	TMEM132B	207	.	0			c.A972T						PASS	.	A		118,4212		0,118,2047	77	92	87		972	-11.3	0	12	dbSNP_134	87	1,8527		0,1,4263	no	coding-synonymous	TMEM132B	NM_052907.2		0,119,6310	TT,TA,AA		0.0117,2.7252,0.9255		324/1079	125900104	119,12739	2165	4264	6429	SO:0001819	synonymous_variant	114795	exon3			GAAGATAACGGCA	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.972A>T	12.37:g.125900104A>T		157	0	0		156	81	0.519231	NM_052907	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Silent	SNP	ENST00000299308.3	37	CCDS41859.1																																																																																			A|0.994;T|0.006	0.006	strong		0.468	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907		T	125900104	A	T	125900104	2	4	22	1	0	0	0	0	0	0	0	1	16061	352	13	5		5	TMEM132B	12	125900104	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	637065	125900104	7951791	2787	5688											
GLT1D1	144423	hgsc.bcm.edu	37	chr12	129360518	129360518	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatgcctttgactttgaaaGccgatctgagattgcaaacc	11	11	10	9	1	1	3	0	3	1	1	1	6	1	4	3	1	4	1	3	1	2	3	rs73438369	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:129360518G>A	ENST00000442111.2	+	2	216	c.128G>A	c.(127-129)aGc>aAc	p.S43N	GLT1D1_ENST00000281703.6_Missense_Mutation_p.S43N|GLT1D1_ENST00000537468.1_Missense_Mutation_p.S32N|GLT1D1_ENST00000542193.1_5'UTR			Q96MS3	GL1D1_HUMAN	glycosyltransferase 1 domain containing 1	43					biosynthetic process (GO:0009058)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|prostate(1)|skin(1)|urinary_tract(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.97e-06)|Epithelial(86;3.97e-05)|all cancers(50;0.00019)		GACTTTGAAAGCCGATCTGAG	0.488													G|||	82	0.0163738	0.059	0.0058	5008	,	,		16943	0.0		0.0	False		,,,				2504	0.0				p.S43N		Atlas-SNP	.											.	GLT1D1	48	.	0			c.G128A						PASS	.	G	ASN/SER	227,4179	135.3+/-171.4	3,221,1979	162	164	163		128	4.7	0.1	12	dbSNP_130	163	3,8597	3.7+/-12.6	0,3,4297	yes	missense	GLT1D1	NM_144669.1	46	3,224,6276	AA,AG,GG		0.0349,5.1521,1.7684	probably-damaging	43/267	129360518	230,12776	2203	4300	6503	SO:0001583	missense	144423	exon2			TTGAAAGCCGATC		CCDS9265.1	12q24.32	2013-02-22			ENSG00000151948	ENSG00000151948		"Glycosyltransferase group 1 domain containing"	26483	protein-coding gene	gene with protein product							Standard	NM_144669		Approved	FLJ31978	uc001uhx.1	Q96MS3	OTTHUMG00000168437	ENST00000442111.2:c.128G>A	12.37:g.129360518G>A	ENSP00000394692:p.Ser43Asn	140	0	0		151	72	0.476821	NM_144669	Q86XG8	Missense_Mutation	SNP	ENST00000442111.2	37		31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	G	13.77	2.334875	0.41297	0.051521	3.49E-4	ENSG00000151948	ENST00000442111;ENST00000281703;ENST00000537468	T;T;T	0.79247	-1.25;0.74;0.69	5.54	4.65	0.58169	.	0.144833	0.64402	N	0.000006	T	0.46678	0.1405	M	0.77616	2.38	0.32213	N	0.576306	D;B	0.89917	1.0;0.037	D;B	0.76071	0.987;0.039	T	0.74163	-0.3754	10	0.22706	T	0.39	-25.057	9.1417	0.36908	0.0789:0.1461:0.775:0.0	.	32;43	F5H088;Q96MS3-2	.;.	N	43;43;32	ENSP00000394692:S43N;ENSP00000281703:S43N;ENSP00000438158:S32N	ENSP00000281703:S43N	S	+	2	0	GLT1D1	127926471	0.963000	0.33076	0.145000	0.22337	0.327000	0.28475	1.719000	0.38011	1.320000	0.45209	0.655000	0.94253	AGC	G|0.981;A|0.019	0.019	strong		0.488	GLT1D1-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000399740.1	NM_144669		A	129360518	G	A	129360518	3	1	22	1	0	0	0	0	1	0	0	0	6473	971	34	2	134	2	GLT1D1	12	129360518	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3460414	129360518	4491377	2788	5689											
SFRS8	6433	hgsc.bcm.edu	37	chr12	132237789	132237789	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acccttcctgctggcgtgacCgtgtctaactcccctggagt	5	11	10	15	2	1	1	0	1	1	0	3	2	3	2	5	2	2	1	5	2	1	2	rs202066133		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132237789C>T	ENST00000261674.4	+	8	1344	c.1203C>T	c.(1201-1203)acC>acT	p.T401T	SFSWAP_ENST00000541286.1_Silent_p.T401T	NM_004592.3	NP_004583.2	Q12872	SFSWA_HUMAN	splicing factor, suppressor of white-apricot family	401					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						CTGGCGTGACCGTGTCTAACT	0.637													C|||	1	0.000199681	0.0008	0.0	5008	,	,		16980	0.0		0.0	False		,,,				2504	0.0				p.T401T		Atlas-SNP	.											.	SFSWAP	69	.	0			c.C1203T						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	174	146	156		1203	-2.4	0.9	12		156	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SFSWAP	NM_004592.2		0,4,6499	TT,TC,CC		0.0116,0.0681,0.0308		401/952	132237789	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	6433	exon8			CGTGACCGTGTCT	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.1203C>T	12.37:g.132237789C>T		167	0	0		170	70	0.411765	NM_001261411	B2RN45|B7ZM97|F5H6B8|Q6PJF7	Silent	SNP	ENST00000261674.4	37	CCDS9273.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	7.548	0.662175	0.14645	6.81E-4	1.16E-4	ENSG00000061936	ENST00000537164	.	.	.	5.41	-2.37	0.06643	.	.	.	.	.	T	0.51517	0.1679	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45818	-0.9235	4	.	.	.	-14.7257	7.8087	0.29217	0.0:0.2462:0.2063:0.5475	.	.	.	.	L	41	.	.	P	+	2	0	SFSWAP	130803742	0.647000	0.27304	0.908000	0.35775	0.652000	0.38707	-0.321000	0.08018	-0.413000	0.07507	0.561000	0.74099	CCG	C|1.000;T|0.000	0.000	strong		0.637	SFSWAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399276.1	NM_004592		T	132237789	C	T	132237789	2	4	22	1	0	0	0	0	0	0	0	1	14198	639	23	1		1	SFRS8	12	132237789	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2877271	132237789	1614106	2789	5690											
MMP17	4326	hgsc.bcm.edu	37	chr12	132329666	132329666	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggctctctccctgcaggccCaggaaggacgtgccccacag	7	6	12	16	1	1	0	0	0	1	0	3	2	2	2	4	4	2	2	4	4	1	0	rs36031288	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132329666C>T	ENST00000360564.1	+	7	1074	c.972C>T	c.(970-972)ccC>ccT	p.P324P	MMP17_ENST00000535291.1_Silent_p.P240P|MMP17_ENST00000535004.1_5'Flank|MMP17_ENST00000535182.1_3'UTR	NM_016155.4	NP_057239.4	Q9ULZ9	MMP17_HUMAN	matrix metallopeptidase 17 (membrane-inserted)	324					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)	CCTGCAGGCCCAGGAAGGACG	0.667													C|||	191	0.038139	0.1377	0.0101	5008	,	,		15735	0.0		0.002	False		,,,				2504	0.0				p.P324P		Atlas-SNP	.											.	MMP17	77	.	0			c.C972T						PASS	.	C		485,3921	225.9+/-241.6	31,423,1749	73	70	71		972	-2.7	0.1	12	dbSNP_126	71	6,8594	3.7+/-12.6	0,6,4294	no	coding-synonymous	MMP17	NM_016155.4		31,429,6043	TT,TC,CC		0.0698,11.0077,3.7752		324/604	132329666	491,12515	2203	4300	6503	SO:0001819	synonymous_variant	4326	exon7			CAGGCCCAGGAAG	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.972C>T	12.37:g.132329666C>T		102	0	0		118	58	0.491525	NM_016155	Q14850	Silent	SNP	ENST00000360564.1	37	CCDS31927.1																																																																																			C|0.961;T|0.039	0.039	strong		0.667	MMP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397757.1	NM_016155		T	132329666	C	T	132329666	2	4	22	1	0	0	0	0	0	0	0	1	9665	581	21	2		2	MMP17	12	132329666	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	91877	132329666	1522229	2790	5691											
ULK1	8408	hgsc.bcm.edu	37	chr12	132404101	132404101	+	Silent	SNP	C	C	T																															gccatcgaccagatccgggcCggcaagctctgcctgtcgtc																								rs143340589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132404101C>T	ENST00000321867.4	+	25	3120	c.2769C>T	c.(2767-2769)gcC>gcT	p.A923A	ULK1_ENST00000540647.1_Silent_p.A168A	NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1	923					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)		AGATCCGGGCCGGCAAGCTCT	0.662													C|||	7	0.00139776	0.0053	0.0	5008	,	,		16277	0.0		0.0	False		,,,				2504	0.0				p.A923A		Atlas-SNP	.											.	ULK1	92	.	0			c.C2769T						PASS	.	C		29,4377	34.3+/-65.2	0,29,2174	62	66	65		2769	-4.8	0.9	12	dbSNP_134	65	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	ULK1	NM_003565.2		0,30,6472	TT,TC,CC		0.0116,0.6582,0.2307		923/1051	132404101	30,12974	2203	4299	6502	SO:0001819	synonymous_variant	8408	exon25			CCGGGCCGGCAAG	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.2769C>T	12.37:g.132404101C>T		102	0	0		77	28	0.363636	NM_003565	Q9UQ28	Silent	SNP	ENST00000321867.4	37	CCDS9274.1																																																																																			C|0.998;T|0.002	0.002	strong		0.662	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397769.3			T	132404101	C	T	132404101	2	4	22	1	0	0	0	0	0	0	0	1	16990	639	23	1		1	ULK1	12	132404101	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	74435	132404101	1447794	2791	5692	68	2									
ULK1	8408	hgsc.bcm.edu	37	chr12	132404110	132404110	+	Silent	SNP	C	C	T																															cagatccgggccggcaagctCtgcctgtcgtccactgtgaa																								rs113954208	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132404110C>T	ENST00000321867.4	+	25	3129	c.2778C>T	c.(2776-2778)ctC>ctT	p.L926L	ULK1_ENST00000540647.1_Silent_p.L171L	NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1	926					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)		CCGGCAAGCTCTGCCTGTCGT	0.657													C|||	16	0.00319489	0.0121	0.0	5008	,	,		16514	0.0		0.0	False		,,,				2504	0.0				p.L926L		Atlas-SNP	.											.	ULK1	92	.	0			c.C2778T						PASS	.	C		72,4334	63.5+/-100.7	1,70,2132	63	68	66		2778	1.7	1	12	dbSNP_132	66	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	ULK1	NM_003565.2		1,71,6430	TT,TC,CC		0.0116,1.6341,0.5614		926/1051	132404110	73,12931	2203	4299	6502	SO:0001819	synonymous_variant	8408	exon25			CAAGCTCTGCCTG	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.2778C>T	12.37:g.132404110C>T		90	0	0		69	41	0.594203	NM_003565	Q9UQ28	Silent	SNP	ENST00000321867.4	37	CCDS9274.1																																																																																			C|0.994;T|0.006	0.006	strong		0.657	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397769.3			T	132404110	C	T	132404110	2	4	22	1	0	0	0	0	0	0	0	1	16990	900	32	2		2	ULK1	12	132404110	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	9	132404110	1447785	2792	5693	68	2									
DDX51	317781	hgsc.bcm.edu	37	chr12	132625884	132625884	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acaggggtccgcggggtcctCgctctggaaggcggccgcca	5	5	17	14	5	1	0	0	0	1	0	4	1	3	1	4	7	0	1	4	7	1	0	rs142395492	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132625884C>T	ENST00000397333.3	-	8	1224	c.1186G>A	c.(1186-1188)Gag>Aag	p.E396K		NM_175066.3	NP_778236.2	Q8N8A6	DDX51_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 51	396	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(1)|lung(5)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.59e-08)|Epithelial(86;3.62e-07)|all cancers(50;2.13e-05)		GCGGGGTCCTCGCTCTGGAAG	0.682													C|||	46	0.0091853	0.0318	0.0043	5008	,	,		14725	0.0		0.001	False		,,,				2504	0.0				p.E396K		Atlas-SNP	.											.	DDX51	33	.	0			c.G1186A						PASS	.	C	LYS/GLU	117,3883		6,105,1889	43	54	51		1186	1.9	0	12	dbSNP_134	51	5,8245		0,5,4120	no	missense	DDX51	NM_175066.3	56	6,110,6009	TT,TC,CC		0.0606,2.925,0.9959	benign	396/667	132625884	122,12128	2000	4125	6125	SO:0001583	missense	317781	exon8			GGTCCTCGCTCTG	BC040185	CCDS41865.1	12q24.33	2005-10-12				ENSG00000185163		"DEAD-boxes"	20082	protein-coding gene	gene with protein product							Standard	NM_175066		Approved		uc001ujy.4	Q8N8A6		ENST00000397333.3:c.1186G>A	12.37:g.132625884C>T	ENSP00000380495:p.Glu396Lys	13	0	0		28	18	0.642857	NM_175066	A8MPT9|Q5CZ71|Q8IXK5|Q96ED1	Missense_Mutation	SNP	ENST00000397333.3	37	CCDS41865.1	18	0.008241758241758242	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	11.56	1.674865	0.29783	0.02925	6.06E-4	ENSG00000185163	ENST00000397333	T	0.12255	2.7	4.79	1.92	0.25849	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.770658	0.12492	N	0.464146	T	0.01661	0.0053	N	0.08118	0	0.09310	N	1	B	0.24721	0.11	B	0.20184	0.028	T	0.44221	-0.9342	10	0.14252	T	0.57	-14.9068	5.9048	0.18986	0.0:0.6566:0.1608:0.1826	.	396	Q8N8A6	DDX51_HUMAN	K	396	ENSP00000380495:E396K	ENSP00000380495:E396K	E	-	1	0	DDX51	131191837	0.000000	0.05858	0.005000	0.12908	0.004000	0.04260	0.982000	0.29539	0.438000	0.26450	-0.229000	0.12294	GAG	C|0.992;T|0.008	0.008	strong		0.682	DDX51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398978.1	NM_175066		T	132625884	C	T	132625884	3	4	22	1	0	0	0	0	1	0	0	0	4371	893	31	1	846	1	DDX51	12	132625884	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	221774	132625884	1226011	2793	5694											
DDX51	317781	hgsc.bcm.edu	37	chr12	132628281	132628281	+	Missense_Mutation	SNP	C	C	T																															gaacccccccagcaccaggcCggggaccaggggtccggccg																								rs78871841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132628281C>T	ENST00000397333.3	-	2	516	c.478G>A	c.(478-480)Ggc>Agc	p.G160S	NOC4L_ENST00000330579.1_5'Flank	NM_175066.3	NP_778236.2	Q8N8A6	DDX51_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 51	160					rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(1)|lung(5)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.59e-08)|Epithelial(86;3.62e-07)|all cancers(50;2.13e-05)		AGCACCAGGCCGGGGACCAGG	0.751													c|||	254	0.0507188	0.0802	0.0043	5008	,	,		10953	0.0476		0.0219	False		,,,				2504	0.0767				p.G160S		Atlas-SNP	.											.	DDX51	33	.	0			c.G478A						PASS	.		SER/GLY	138,2788		1,136,1326	3	4	3		478	1.6	0	12	dbSNP_131	3	24,6890		0,24,3433	yes	missense	DDX51	NM_175066.3	56	1,160,4759	TT,TC,CC		0.3471,4.7163,1.6463	benign	160/667	132628281	162,9678	1463	3457	4920	SO:0001583	missense	317781	exon2			CCAGGCCGGGGAC	BC040185	CCDS41865.1	12q24.33	2005-10-12				ENSG00000185163		"DEAD-boxes"	20082	protein-coding gene	gene with protein product							Standard	NM_175066		Approved		uc001ujy.4	Q8N8A6		ENST00000397333.3:c.478G>A	12.37:g.132628281C>T	ENSP00000380495:p.Gly160Ser	8	0	0		16	6	0.375	NM_175066	A8MPT9|Q5CZ71|Q8IXK5|Q96ED1	Missense_Mutation	SNP	ENST00000397333.3	37	CCDS41865.1	82	0.037545787545787544	30	0.06097560975609756	6	0.016574585635359115	26	0.045454545454545456	20	0.026385224274406333	c	0.472	-0.883980	0.02530	0.047163	0.003471	ENSG00000185163	ENST00000397333	T	0.01725	4.67	2.49	1.59	0.23543	.	0.789795	0.11401	U	0.567852	T	0.00178	0.0005	L	0.27053	0.805	0.09310	N	1	B	0.22211	0.066	B	0.09377	0.004	T	0.49504	-0.8933	10	0.13853	T	0.58	-1.4426	5.097	0.14739	0.0:0.8312:0.0:0.1688	.	160	Q8N8A6	DDX51_HUMAN	S	160	ENSP00000380495:G160S	ENSP00000380495:G160S	G	-	1	0	DDX51	131194234	0.000000	0.05858	0.012000	0.15200	0.059000	0.15707	0.104000	0.15313	0.624000	0.30286	0.479000	0.44913	GGC	C|0.962;T|0.038	0.038	strong		0.751	DDX51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398978.1	NM_175066		T	132628281	C	T	132628281	3	4	22	1	0	0	0	0	1	0	0	0	4371	652	23	1	1578	1	DDX51	12	132628281	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2397	132628281	1223614	2794	5695	69	2									
DDX51	317781	hgsc.bcm.edu	37	chr12	132628285	132628285	+	Silent	SNP	G	G	A																															ccccccagcaccaggccgggGaccaggggtccggccgcctc																								rs191101265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132628285G>A	ENST00000397333.3	-	2	512	c.474C>T	c.(472-474)gtC>gtT	p.V158V	NOC4L_ENST00000330579.1_5'Flank	NM_175066.3	NP_778236.2	Q8N8A6	DDX51_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 51	158					rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(1)|lung(5)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.59e-08)|Epithelial(86;3.62e-07)|all cancers(50;2.13e-05)		CCAGGCCGGGGACCAGGGGTC	0.761													g|||	215	0.0429313	0.0492	0.0043	5008	,	,		10654	0.0476		0.0219	False		,,,				2504	0.0787				p.V158V		Atlas-SNP	.											.	DDX51	33	.	0			c.C474T						PASS	.			71,2853		0,71,1391	3	4	3		474	-1.3	0	12		3	17,6853		0,17,3418	no	coding-synonymous	DDX51	NM_175066.3		0,88,4809	AA,AG,GG		0.2475,2.4282,0.8985		158/667	132628285	88,9706	1462	3435	4897	SO:0001819	synonymous_variant	317781	exon2			GCCGGGGACCAGG	BC040185	CCDS41865.1	12q24.33	2005-10-12				ENSG00000185163		"DEAD-boxes"	20082	protein-coding gene	gene with protein product							Standard	NM_175066		Approved		uc001ujy.4	Q8N8A6		ENST00000397333.3:c.474C>T	12.37:g.132628285G>A		8	0	0		16	6	0.375	NM_175066	A8MPT9|Q5CZ71|Q8IXK5|Q96ED1	Silent	SNP	ENST00000397333.3	37	CCDS41865.1																																																																																			G|0.968;A|0.032	0.032	strong		0.761	DDX51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398978.1	NM_175066		A	132628285	G	A	132628285	2	1	22	1	0	0	0	0	0	0	0	1	4371	1161	41	2		2	DDX51	12	132628285	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4	132628285	1223610	2795	5696	69	2									
GALNT9	50614	hgsc.bcm.edu	37	chr12	132681664	132681664	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtggggtcagtgccgtgcGtgtttgatccagtttctgat	5	14	15	7	2	2	2	1	2	1	0	3	2	3	2	2	3	2	2	2	3	0	2	rs111344752	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132681664G>A	ENST00000328957.8	-	11	1799	c.1800C>T	c.(1798-1800)caC>caT	p.H600H	GALNT9_ENST00000541995.1_Silent_p.H234H|GALNT9_ENST00000535228.1_Silent_p.H351H|GALNT9_ENST00000397325.2_Silent_p.H234H	NM_001122636.1	NP_001116108.1	Q9HCQ5	GALT9_HUMAN	polypeptide N-acetylgalactosaminyltransferase 9	600	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)|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)		AGTGCCGTGCGTGTTTGATCC	0.642													g|||	68	0.0135783	0.0499	0.0014	5008	,	,		15532	0.0		0.0	False		,,,				2504	0.001				p.H600H	Colon(186;2147 2752 13553 41466)	Atlas-SNP	.											.	GALNT9	74	.	0			c.C1800T						PASS	.		,	176,3898		3,170,1864	85	100	95		723,702	-6.2	0	12	dbSNP_132	95	0,8376		0,0,4188	no	coding-synonymous,coding-synonymous	GALNT9	NM_001122636.1.dup,NM_021808.3	,	3,170,6052	AA,AG,GG		0.0,4.3201,1.4137	,	241/245,234/238	132681664	176,12274	2037	4188	6225	SO:0001819	synonymous_variant	50614	exon11			CCGTGCGTGTTTG	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.1800C>T	12.37:g.132681664G>A		134	0	0		129	64	0.496124	NM_001122636	Q52LR8|Q6NT54|Q8NFR1	Silent	SNP	ENST00000328957.8	37		20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	g	0.018	-1.482667	0.01027	0.043201	0.0	ENSG00000182870	ENST00000411988	.	.	.	4.45	-6.24	0.02046	.	.	.	.	.	T	0.09905	0.0243	.	.	.	0.30680	N	0.752399	.	.	.	.	.	.	T	0.35375	-0.9791	4	.	.	.	.	8.9918	0.36028	0.5625:0.0:0.3379:0.0995	.	.	.	.	C	373	.	.	R	-	1	0	GALNT9	131247617	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-0.994000	0.03716	-1.273000	0.02424	-1.585000	0.00851	CGC	G|0.990;A|0.010	0.010	strong		0.642	GALNT9-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000402967.1	NM_001122636		A	132681664	G	A	132681664	2	1	22	1	0	0	0	0	0	0	0	1	6228	1136	40	1		1	GALNT9	12	132681664	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	53379	132681664	1170231	2796	5697											
POLE	5426	hgsc.bcm.edu	37	chr12	133201327	133201327	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcagcagccactccagggTctccaggaggtacgacatgc	9	6	12	14	1	1	0	0	0	1	0	3	2	2	1	3	3	5	3	3	3	1	1	rs73481453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:133201327T>A	ENST00000320574.5	-	49	6860	c.6817A>T	c.(6817-6819)Acc>Tcc	p.T2273S	POLE_ENST00000535270.1_Missense_Mutation_p.T2246S	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	2273					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)	CACTCCAGGGTCTCCAGGAGG	0.612								DNA polymerases (catalytic subunits)					T|||	25	0.00499201	0.0189	0.0	5008	,	,		18347	0.0		0.0	False		,,,				2504	0.0				p.T2273S		Atlas-SNP	.											.	POLE	416	.	0			c.A6817T						PASS	.	T	SER/THR	62,4344	58.7+/-95.3	2,58,2143	81	82	82		6817	2.4	1	12	dbSNP_130	82	1,8599	1.2+/-3.3	0,1,4299	yes	missense	POLE	NM_006231.2	58	2,59,6442	AA,AT,TT		0.0116,1.4072,0.4844	benign	2273/2287	133201327	63,12943	2203	4300	6503	SO:0001583	missense	5426	exon49			CCAGGGTCTCCAG		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.6817A>T	12.37:g.133201327T>A	ENSP00000322570:p.Thr2273Ser	169	0	0		154	72	0.467532	NM_006231	Q13533|Q86VH9	Missense_Mutation	SNP	ENST00000320574.5	37	CCDS9278.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	T	16.01	3.000426	0.54147	0.014072	1.16E-4	ENSG00000177084	ENST00000434528;ENST00000320574;ENST00000455752;ENST00000320557;ENST00000535270	T;T;T	0.02944	4.11;4.1;4.11	4.89	2.43	0.29744	.	0.285116	0.38436	N	0.001689	T	0.02193	0.0068	M	0.77103	2.36	0.41149	D	0.98601	B;B	0.12630	0.001;0.006	B;B	0.18263	0.005;0.021	T	0.20405	-1.0276	10	0.59425	D	0.04	.	7.0622	0.25131	0.1316:0.0728:0.0:0.7956	.	2273;483	Q07864;B3KS74	DPOE1_HUMAN;.	S	483;2273;2284;243;2246	ENSP00000322570:T2273S;ENSP00000406383:T2284S;ENSP00000445753:T2246S	ENSP00000322473:T243S	T	-	1	0	POLE	131711400	1.000000	0.71417	0.954000	0.39281	0.840000	0.47671	4.700000	0.61803	0.325000	0.23359	0.459000	0.35465	ACC	T|0.995;A|0.005	0.005	strong		0.612	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231		A	133201327	T	A	133201327	3	1	22	1	0	0	0	0	1	0	0	0	12205	1667	58	5	47	5	POLE	12	133201327	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	519663	133201327	650568	2797	5698											
GOLGA3	2802	hgsc.bcm.edu	37	chr12	133358984	133358984	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttggactgaccgaggcccgtAagcttccctttctcgtgctc	5	12	10	14	3	1	1	0	1	1	0	4	3	2	2	3	2	2	3	3	2	1	4	rs76963006	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:133358984A>G	ENST00000450791.2	-	16	3546	c.3363T>C	c.(3361-3363)ctT>ctC	p.L1121L	GOLGA3_ENST00000204726.3_Silent_p.L1121L|GOLGA3_ENST00000456883.2_Silent_p.L1121L			Q08378	GOGA3_HUMAN	golgin A3	1121					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)		CGAGGCCCGTAAGCTTCCCTT	0.498													A|||	41	0.0081869	0.0303	0.0014	5008	,	,		19000	0.0		0.0	False		,,,				2504	0.0				p.L1121L		Atlas-SNP	.											.	GOLGA3	234	.	0			c.T3363C						PASS	.	A		117,4289	88.7+/-127.4	1,115,2087	216	201	207		3363	-8.6	0	12	dbSNP_132	207	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GOLGA3	NM_005895.3		1,116,6386	GG,GA,AA		0.0116,2.6555,0.9073		1121/1499	133358984	118,12888	2203	4300	6503	SO:0001819	synonymous_variant	2802	exon17			GCCCGTAAGCTTC	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.3363T>C	12.37:g.133358984A>G		234	0	0		201	107	0.532338	NM_005895	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Silent	SNP	ENST00000450791.2	37	CCDS9281.1																																																																																			A|0.990;G|0.010	0.010	strong		0.498	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	NM_005895		G	133358984	A	G	133358984	2	3	22	1	0	0	0	0	0	0	0	1	6562	349	13	3		3	GOLGA3	12	133358984	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	157657	133358984	492911	2798	5699											
GOLGA3	2802	hgsc.bcm.edu	37	chr12	133398638	133398638	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggcccgggggcttcagtgggGcctcggggagagacgagggg	5	4	23	9	3	1	1	1	0	0	1	2	4	1	2	2	9	0	1	2	9	0	1	rs141852501	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:133398638G>A	ENST00000450791.2	-	1	260	c.77C>T	c.(76-78)gCc>gTc	p.A26V	GOLGA3_ENST00000204726.3_Missense_Mutation_p.A26V|GOLGA3_ENST00000537452.1_Missense_Mutation_p.A26V|GOLGA3_ENST00000545875.1_Missense_Mutation_p.A26V|GOLGA3_ENST00000456883.2_Missense_Mutation_p.A26V			Q08378	GOGA3_HUMAN	golgin A3	26	Pro-rich.				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)		CTTCAGTGGGGCCTCGGGGAG	0.647													G|||	8	0.00159744	0.0061	0.0	5008	,	,		14431	0.0		0.0	False		,,,				2504	0.0				p.A26V		Atlas-SNP	.											.	GOLGA3	234	.	0			c.C77T						PASS	.	G	VAL/ALA,VAL/ALA	28,4378	32.6+/-62.9	0,28,2175	44	47	46		77,77	-3.7	0	12	dbSNP_134	46	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	GOLGA3	NM_001172557.1,NM_005895.3	64,64	0,29,6474	AA,AG,GG		0.0116,0.6355,0.223	benign,benign	26/1135,26/1499	133398638	29,12977	2203	4300	6503	SO:0001583	missense	2802	exon2			AGTGGGGCCTCGG	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.77C>T	12.37:g.133398638G>A	ENSP00000410378:p.Ala26Val	112	0	0		111	58	0.522523	NM_001172557	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Missense_Mutation	SNP	ENST00000450791.2	37	CCDS9281.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	G	11.20	1.568083	0.28003	0.006355	1.16E-4	ENSG00000090615	ENST00000204726;ENST00000450791;ENST00000456883;ENST00000537452;ENST00000545875	T;T;T;T;T	0.32988	1.86;1.86;1.86;1.43;1.43	5.4	-3.7	0.04437	.	1.125330	0.06702	N	0.771525	T	0.16896	0.0406	L	0.44542	1.39	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.002;0.001	T	0.33574	-0.9863	10	0.41790	T	0.15	.	7.4989	0.27505	0.069:0.4444:0.3435:0.1431	.	26;26;26	Q08378-4;Q08378-2;Q08378	.;.;GOGA3_HUMAN	V	26	ENSP00000204726:A26V;ENSP00000410378:A26V;ENSP00000409303:A26V;ENSP00000442143:A26V;ENSP00000442603:A26V	ENSP00000204726:A26V	A	-	2	0	GOLGA3	131908711	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.762000	0.04745	-0.565000	0.06061	-2.362000	0.00238	GCC	G|0.997;A|0.003	0.003	strong		0.647	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	NM_005895		A	133398638	G	A	133398638	3	1	22	1	0	0	0	0	1	0	0	0	6562	1203	42	2	4649	2	GOLGA3	12	133398638	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	39654	133398638	453257	2799	5700											
ZDHHC20	253832	hgsc.bcm.edu	37	chr13	21987823	21987823	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgtggtatagataggtaaaGctcttgctgctcttctcaaa	11	14	9	7	0	3	1	1	0	3	1	4	1	3	1	0	2	3	5	0	2	6	6	rs151151710	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:21987823G>A	ENST00000400590.3	-	4	536	c.338C>T	c.(337-339)gCt>gTt	p.A113V	ZDHHC20_ENST00000422251.1_Missense_Mutation_p.A113V|ZDHHC20_ENST00000320220.9_Missense_Mutation_p.A113V|ZDHHC20_ENST00000415724.1_Missense_Mutation_p.A113V|ZDHHC20_ENST00000542645.1_Missense_Mutation_p.A50V|ZDHHC20_ENST00000382466.3_Missense_Mutation_p.A113V|ZDHHC20_ENST00000494731.1_5'UTR			Q5W0Z9	ZDH20_HUMAN	zinc finger, DHHC-type containing 20	113					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)		GATAGGTAAAGCTCTTGCTGC	0.313													G|||	22	0.00439297	0.0159	0.0014	5008	,	,		14776	0.0		0.0	False		,,,				2504	0.0				p.A113V		Atlas-SNP	.											ZDHHC20_ENST00000382466,NS,carcinoma,0,2	ZDHHC20	36	2	0			c.C338T						PASS	.	G	VAL/ALA	66,3544		0,66,1739	117	101	106		338	3.1	1	13	dbSNP_134	106	0,8150		0,0,4075	yes	missense	ZDHHC20	NM_153251.3	64	0,66,5814	AA,AG,GG		0.0,1.8283,0.5612	benign	113/355	21987823	66,11694	1805	4075	5880	SO:0001583	missense	253832	exon4			GGTAAAGCTCTTG	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.338C>T	13.37:g.21987823G>A	ENSP00000383433:p.Ala113Val	58	0	0		51	25	0.490196	NM_153251	A8MTV9|C9JG20|I6L9D4|Q2TB82|Q6NVU8	Missense_Mutation	SNP	ENST00000400590.3	37		13	0.005952380952380952	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	0	0.0	G	10.49	1.365289	0.24684	0.018283	0.0	ENSG00000180776	ENST00000400590;ENST00000320220;ENST00000382466;ENST00000542645;ENST00000415724;ENST00000422251	T;T;T;T;T	0.26373	1.74;1.74;1.74;1.74;1.74	5.59	3.12	0.35913	.	0.330632	0.39834	N	0.001258	T	0.06325	0.0163	N	0.10916	0.065	0.20764	N	0.999855	B;B	0.02656	0.0;0.0	B;B	0.16722	0.016;0.001	T	0.20174	-1.0283	10	0.44086	T	0.13	-10.0193	8.0652	0.30657	0.125:0.0:0.3373:0.5376	.	50;113	B4DRN8;Q5W0Z9-3	.;.	V	113;113;113;50;113;113	ENSP00000383433:A113V;ENSP00000313583:A113V;ENSP00000371905:A113V;ENSP00000443236:A50V;ENSP00000401232:A113V	ENSP00000313583:A113V	A	-	2	0	ZDHHC20	20885823	0.999000	0.42202	0.989000	0.46669	0.681000	0.39784	1.392000	0.34486	0.017000	0.15025	-1.579000	0.00862	GCT	G|0.994;A|0.006	0.006	strong		0.313	ZDHHC20-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000045994.1	NM_153251		A	21987823	G	A	21987823	3	1	22	1	0	0	0	0	1	0	0	0	17626	971	34	2	762	2	ZDHHC20	13	21987823	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10		21987823	93182055	2800	5701											
SGCG	6445	hgsc.bcm.edu	37	chr13	23853547	23853547	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagtttcagatcaactccaaCgacggcaagccactatttac	13	9	6	13	2	2	1	2	0	0	1	3	2	3	1	2	1	4	2	2	1	5	4	rs35628352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:23853547C>T	ENST00000218867.3	+	5	559	c.435C>T	c.(433-435)aaC>aaT	p.N145N	SGCG_ENST00000545013.1_Silent_p.N145N|SGCG_ENST00000537476.1_Silent_p.N145N	NM_000231.2	NP_000222	Q13326	SGCG_HUMAN	sarcoglycan, gamma (35kDa dystrophin-associated glycoprotein)	145					muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188)		all cancers(112;0.00255)|Epithelial(112;0.0129)|OV - Ovarian serous cystadenocarcinoma(117;0.0365)|Lung(94;0.205)		TCAACTCCAACGACGGCAAGC	0.383													C|||	47	0.00938498	0.031	0.0072	5008	,	,		17239	0.0		0.001	False		,,,				2504	0.0				p.N145N		Atlas-SNP	.											.	SGCG	64	.	0			c.C435T						PASS	.	C		130,4276	93.9+/-132.6	2,126,2075	98	90	93		435	-3.5	0.4	13	dbSNP_126	93	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SGCG	NM_000231.2		2,127,6374	TT,TC,CC		0.0116,2.9505,1.0072		145/292	23853547	131,12875	2203	4300	6503	SO:0001819	synonymous_variant	6445	exon5			CTCCAACGACGGC	U34976	CCDS9299.1	13q12-q13	2014-09-17	2002-08-29		ENSG00000102683	ENSG00000102683			10809	protein-coding gene	gene with protein product	"Maghrebian myopathy (autosomal recessive)", "35kD dystrophin-associated glycoprotein", "limb girdle muscular dystrophy 2C (Duchenne-like muscular dystrophy, autosomal recessive)", "gamma sarcoglycan"	608896	"sarcoglycan, gamma (35kD dystrophin-associated glycoprotein)"	DMDA1, MAM, LGMD2C		8968757	Standard	NM_000231		Approved	SCARMD2, DAGA4, SCG3, DMDA, TYPE, A4, MGC130048	uc001uom.2	Q13326	OTTHUMG00000016563	ENST00000218867.3:c.435C>T	13.37:g.23853547C>T		117	0	0		109	59	0.541284	NM_000231	Q32M32|Q5T9J6	Silent	SNP	ENST00000218867.3	37	CCDS9299.1																																																																																			C|0.991;T|0.009	0.009	strong		0.383	SGCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044151.1	NM_000231		T	23853547	C	T	23853547	2	4	22	1	0	0	0	0	0	0	0	1	14218	535	19	1		1	SGCG	13	23853547	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1865724	23853547	91316331	2801	5702											
SACS	26278	hgsc.bcm.edu	37	chr13	23905481	23905481	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtacccaacatattctccCgggtaaaaaacattcattgg	14	10	7	10	1	2	0	1	0	1	0	3	0	2	0	2	3	3	2	2	3	6	6			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:23905481C>T	ENST00000382292.3	-	9	12807	c.12534G>A	c.(12532-12534)ccG>ccA	p.P4178P	SACS_ENST00000382298.3_Silent_p.P4178P|SACS_ENST00000402364.1_Silent_p.P3428P			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	4178					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)		CATATTCTCCCGGGTAAAAAA	0.413																																					p.P4178P		Atlas-SNP	.											.	SACS	871	.	0			c.G12534A						PASS	.						108	113	111					13																	23905481		2203	4300	6503	SO:0001819	synonymous_variant	26278	exon10			TTCTCCCGGGTAA	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.12534G>A	13.37:g.23905481C>T		103	0	0		105	59	0.561905	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2																																																																																			.	.	none		0.413	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		T	23905481	C	T	23905481	2	4	22	1	0	0	0	0	0	0	0	1	13819	639	23	1		1	SACS	13	23905481	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	51934	23905481	91264397	2802	5703											
SACS	26278	hgsc.bcm.edu	37	chr13	23914286	23914286	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgctggaattgatagtagtcTtcatcactaaaggtttttga	11	16	9	5	0	3	2	2	2	1	0	3	3	3	3	0	2	1	3	0	2	5	7			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:23914286T>C	ENST00000382292.3	-	9	4002	c.3729A>G	c.(3727-3729)gaA>gaG	p.E1243E	SACS_ENST00000382298.3_Silent_p.E1243E|SACS_ENST00000402364.1_Silent_p.E493E			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	1243					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)		GATAGTAGTCTTCATCACTAA	0.323																																					p.E1243E		Atlas-SNP	.											.	SACS	871	.	0			c.A3729G						PASS	.						44	43	43					13																	23914286		2202	4300	6502	SO:0001819	synonymous_variant	26278	exon10			GTAGTCTTCATCA	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.3729A>G	13.37:g.23914286T>C		79	0	0		121	62	0.512397	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2																																																																																			.	.	none		0.323	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		C	23914286	T	C	23914286	2	2	22	1	0	0	0	0	0	0	0	1	13819	1606	56	3		3	SACS	13	23914286	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	8805	23914286	91255592	2803	5704											
SACS	26278	hgsc.bcm.edu	37	chr13	23915089	23915089	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcaacatgtttgccagacGaatagtagcttcatcactac	12	13	6	10	1	3	1	3	0	0	1	3	2	3	1	1	0	4	3	1	0	5	6	rs139993038	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:23915089G>T	ENST00000382292.3	-	9	3199	c.2926C>A	c.(2926-2928)Cgt>Agt	p.R976S	SACS_ENST00000382298.3_Missense_Mutation_p.R976S|SACS_ENST00000402364.1_Missense_Mutation_p.R226S			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	976					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)		TTTGCCAGACGAATAGTAGCT	0.348													G|||	8	0.00159744	0.0061	0.0	5008	,	,		20828	0.0		0.0	False		,,,				2504	0.0				p.R976S		Atlas-SNP	.											SACS_ENST00000382298,NS,carcinoma,0,2	SACS	871	2	0			c.C2926A						scavenged	.	G	SER/ARG	27,4379	33.5+/-64.1	0,27,2176	71	70	71		2926	6.1	1	13	dbSNP_134	71	0,8600		0,0,4300	no	missense	SACS	NM_014363.4	110	0,27,6476	TT,TG,GG		0.0,0.6128,0.2076	probably-damaging	976/4580	23915089	27,12979	2203	4300	6503	SO:0001583	missense	26278	exon10			CCAGACGAATAGT	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.2926C>A	13.37:g.23915089G>T	ENSP00000371729:p.Arg976Ser	190	1	0.00526316		183	71	0.387978	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	G	32	5.112212	0.94339	0.006128	0.0	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.87809	-2.14;-2.3;-2.14	6.05	6.05	0.98169	.	0.000000	0.85682	D	0.000000	D	0.82486	0.5047	L	0.34521	1.04	0.80722	D	1	D	0.53312	0.959	P	0.47528	0.549	D	0.85013	0.0907	10	0.56958	D	0.05	.	20.6013	0.99457	0.0:0.0:1.0:0.0	.	976	Q9NZJ4	SACS_HUMAN	S	976;226;976	ENSP00000371729:R976S;ENSP00000385844:R226S;ENSP00000371735:R976S	ENSP00000371729:R976S	R	-	1	0	SACS	22813089	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	9.476000	0.97823	2.878000	0.98634	0.650000	0.86243	CGT	A|0.000;G|0.999;T|0.001	0.001	strong		0.348	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		T	23915089	G	T	23915089	3	4	22	1	0	0	0	0	1	0	0	0	13819	1058	37	4	10817	4	SACS	13	23915089	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	803	23915089	91254789	2804	5705											
SACS	26278	hgsc.bcm.edu	37	chr13	23929189	23929189	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgacaaggggaaatcagagCtcttttccatctccagacgt	11	10	9	11	1	3	3	1	1	2	2	5	4	4	4	2	2	1	1	2	2	2	2	rs190617851		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:23929189C>G	ENST00000382292.3	-	7	1835	c.1562G>C	c.(1561-1563)aGc>aCc	p.S521T	SACS_ENST00000476776.1_5'Flank|SACS_ENST00000382298.3_Missense_Mutation_p.S521T|SACS_ENST00000402364.1_5'UTR			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	521					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)		GAAATCAGAGCTCTTTTCCAT	0.458													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20393	0.0		0.0	False		,,,				2504	0.0				p.S521T		Atlas-SNP	.											.	SACS	871	.	0			c.G1562C						PASS	.	C	THR/SER	1,4405	2.1+/-5.4	0,1,2202	77	85	82		1562	2.3	0	13		82	0,8600		0,0,4300	no	missense	SACS	NM_014363.4	58	0,1,6502	GG,GC,CC		0.0,0.0227,0.0077	benign	521/4580	23929189	1,13005	2203	4300	6503	SO:0001583	missense	26278	exon8			TCAGAGCTCTTTT	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.1562G>C	13.37:g.23929189C>G	ENSP00000371729:p.Ser521Thr	86	0	0		93	44	0.473118	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	1|1	4.578754578754579E-4|4.578754578754579E-4	1|1	0.0020325203252032522|0.0020325203252032522	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	12.48|12.48	1.950654|1.950654	0.34377|0.34377	2.27E-4|2.27E-4	0.0|0.0	ENSG00000151835|ENSG00000151835	ENST00000455470|ENST00000382292;ENST00000382298;ENST00000423156	.|T;T;T	.|0.21191	.|2.02;2.02;2.02	5.48|5.48	2.34|2.34	0.29019|0.29019	.|.	.|0.444341	.|0.27384	.|N	.|0.019604	T|T	0.11495|0.11495	0.0280|0.0280	L|L	0.34521|0.34521	1.04|1.04	0.26264|0.26264	N|N	0.978528|0.978528	.|B;B;B	.|0.31625	.|0.332;0.332;0.0	.|B;B;B	.|0.30572	.|0.075;0.117;0.002	T|T	0.24190|0.24190	-1.0167|-1.0167	5|10	.|0.14656	.|T	.|0.56	.|.	3.6068|3.6068	0.08045|0.08045	0.0:0.2101:0.4786:0.3113|0.0:0.2101:0.4786:0.3113	.|.	.|420;308;521	.|B2REB1;E9PAL4;Q9NZJ4	.|.;.;SACS_HUMAN	D|T	420|521;521;145	.|ENSP00000371729:S521T;ENSP00000371735:S521T;ENSP00000390925:S145T	.|ENSP00000371729:S521T	E|S	-|-	3|2	2|0	SACS|SACS	22827189|22827189	0.968000|0.968000	0.33430|0.33430	0.001000|0.001000	0.08648|0.08648	0.923000|0.923000	0.55619|0.55619	1.379000|1.379000	0.34340|0.34340	0.259000|0.259000	0.21709|0.21709	0.561000|0.561000	0.74099|0.74099	GAG|AGC	C|1.000;G|0.000	0.000	strong		0.458	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		G	23929189	C	G	23929189	3	3	22	1	0	0	0	0	1	0	0	0	13819	797	28	4	12189	4	SACS	13	23929189	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	14100	23929189	91240689	2805	5706											
MIPEP	4285	hgsc.bcm.edu	37	chr13	24463414	24463414	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgcccggcggggcggcagagCtgctgctctggctcccaagc	4	5	16	16	4	1	1	0	0	1	1	2	1	2	1	2	5	4	5	2	5	1	0	rs112735196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:24463414C>A	ENST00000382172.3	-	1	144	c.46G>T	c.(46-48)Gct>Tct	p.A16S	C1QTNF9B_ENST00000556521.1_5'Flank|C1QTNF9B-AS1_ENST00000417034.1_RNA|MIPEP_ENST00000469167.1_5'UTR|C1QTNF9B-AS1_ENST00000435039.2_RNA|C1QTNF9B-AS1_ENST00000382133.4_RNA	NM_005932.3	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase	16					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)		ggcggcAGAGCTGCTGCTCTG	0.692													C|||	24	0.00479233	0.0182	0.0	5008	,	,		11162	0.0		0.0	False		,,,				2504	0.0				p.A16S		Atlas-SNP	.											.	MIPEP	53	.	0			c.G46T						PASS	.						2	3	3					13																	24463414		1592	3189	4781	SO:0001583	missense	4285	exon1			GCAGAGCTGCTGC		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.46G>T	13.37:g.24463414C>A	ENSP00000371607:p.Ala16Ser	4	0	0		18	17	0.944444	NM_005932	Q5JV15|Q5T9Q9|Q96G65	Missense_Mutation	SNP	ENST00000382172.3	37	CCDS9303.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	c	11.93	1.786749	0.31593	.	.	ENSG00000027001	ENST00000382172	T	0.10005	2.92	4.11	2.28	0.28536	.	0.834312	0.10422	N	0.676614	T	0.04363	0.0120	L	0.36672	1.1	0.09310	N	1	B	0.20052	0.041	B	0.17098	0.017	T	0.26849	-1.0091	10	0.59425	D	0.04	-18.1677	7.5781	0.27948	0.0:0.7411:0.1649:0.094	.	16	Q99797	MIPEP_HUMAN	S	16	ENSP00000371607:A16S	ENSP00000371607:A16S	A	-	1	0	MIPEP	23361414	0.002000	0.14202	0.108000	0.21378	0.376000	0.30014	0.683000	0.25349	0.920000	0.36970	0.491000	0.48974	GCT	C|0.994;A|0.006	0.006	strong		0.692	MIPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044169.1			A	24463414	C	A	24463414	3	1	22	1	0	0	0	0	1	0	0	0	9601	797	28	4	2171	4	MIPEP	13	24463414	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	534225	24463414	90706464	2806	5707											
SPATA13	221178	hgsc.bcm.edu	37	chr13	24797333	24797333	+	Intron	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gacgggtgcccaccccgagcGgccccactccatggtcctgg	5	5	13	18	3	0	0	0	0	0	0	2	2	2	0	7	4	2	0	7	4	0	0	rs1220545	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:24797333G>C	ENST00000382095.4	+	2	185				SPATA13_ENST00000424834.2_Missense_Mutation_p.R89P|RP11-307N16.6_ENST00000382141.4_Missense_Mutation_p.R89P|SPATA13_ENST00000382108.3_Missense_Mutation_p.R89P	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)		CACCCCGAGCGGCCCCACTCC	0.607													.|||	15	0.00299521	0.0113	0.0	5008	,	,		18093	0.0		0.0	False		,,,				2504	0.0				p.R89P		Atlas-SNP	.											.	SPATA13	92	.	0			c.G266C						PASS	.	G	PRO/ARG,	25,1359		0,25,667	29	32	31		266,	5.2	1	13	dbSNP_87	31	0,3182		0,0,1591	no	missense,intron	SPATA13	NM_001166271.1,NM_153023.2	103,	0,25,2258	CC,CG,GG		0.0,1.8064,0.5475	benign,	89/1278,	24797333	25,4541	692	1591	2283	SO:0001627	intron_variant	221178	exon2			CCGAGCGGCCCCA	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.-222-26282G>C	13.37:g.24797333G>C		60	0	0		79	50	0.632911	NM_001166271	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Missense_Mutation	SNP	ENST00000382095.4	37	CCDS9305.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	14.69	2.610495	0.46527	0.018064	0.0	ENSG00000182957	ENST00000382108	T	0.81330	-1.48	5.25	5.25	0.73442	.	0.000000	0.39475	U	0.001355	T	0.75280	0.3828	L	0.46157	1.445	0.80722	D	1	.	.	.	.	.	.	T	0.82309	-0.0521	8	0.87932	D	0	.	18.2627	0.90041	0.0:0.0:1.0:0.0	rs1220545	.	.	.	P	89	ENSP00000371542:R89P	ENSP00000371542:R89P	R	+	2	0	SPATA13	23695333	1.000000	0.71417	0.995000	0.50966	0.021000	0.10359	5.152000	0.64882	2.644000	0.89710	0.478000	0.44815	CGG	G|0.997;C|0.003	0.003	strong		0.607	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023		C	24797333	G	C	24797333	1	2	22	0	1	0	0	0	0	0	0	0	15015	1116	39	4		4	SPATA13	13	24797333	Intron	SNP	G	TCGA-G8-6324-01A-11D-2210-10	333919	24797333	90372545	2807	5708											
PARP4	143	hgsc.bcm.edu	37	chr13	25027745	25027745	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgatgaactctgctgccaTggtattgcttgtgatatgct	8	15	10	8	0	1	3	0	3	1	0	1	3	1	3	1	1	5	4	1	1	3	4	rs386769073|rs1130943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:25027745T>C	ENST00000381989.3	-	23	2911	c.2806A>G	c.(2806-2808)Atg>Gtg	p.M936V	PARP4_ENST00000480576.1_5'Flank	NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	936	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.			M -> A (in Ref. 2; AAC62491 and 3; BAA11494). {ECO:0000305}.|M -> T (in Ref. 1; AAD47250). {ECO:0000305}.	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)		TCTGCTGCCATGGTATTGCTT	0.478													N|||	352	0.0702875	0.2262	0.0216	5008	,	,		15989	0.0298		0.001	False		,,,				2504	0.0072				p.M936V		Atlas-SNP	.											PARP4,NS,carcinoma,+2,1	PARP4	142	1	0			c.A2806G						PASS	.	C	VAL/MET	795,3611	743.2+/-411.4	86,623,1494	277	217	237		2806	-3.9	0	13	dbSNP_86	237	14,8586	818.4+/-406.9	0,14,4286	yes	missense	PARP4	NM_006437.3	21	86,637,5780	CC,CT,TT		0.1628,18.0436,6.2202	benign	936/1725	25027745	809,12197	2203	4300	6503	SO:0001583	missense	143	exon23			CTGCCATGGTATT	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.2806A>G	13.37:g.25027745T>C	ENSP00000371419:p.Met936Val	169	0	0		191	95	0.497382	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	84	0.038461538461538464	71	0.1443089430894309	7	0.019337016574585635	6	0.01048951048951049	0	0.0	C	2.522	-0.310435	0.05458	0.180436	0.001628	ENSG00000102699	ENST00000381989	T	0.07567	3.18	4.29	-3.89	0.04193	von Willebrand factor, type A (3);	1.850880	0.02221	N	0.063999	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.41538	-0.9503	9	0.16896	T	0.51	0.2561	6.1523	0.20318	0.1226:0.3669:0.0:0.5105	rs1130943;rs3190390;rs12323011;rs17413359	936	Q9UKK3	PARP4_HUMAN	V	936	ENSP00000371419:M936V	ENSP00000371419:M936V	M	-	1	0	PARP4	23925745	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.131000	0.03238	-1.328000	0.02261	-0.273000	0.10243	ATG	T|0.949;C|0.051	0.051	strong		0.478	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437		C	25027745	T	C	25027745	3	2	22	1	0	0	0	0	1	0	0	0	11472	1464	51	3	2416	3	PARP4	13	25027745	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	230412	25027745	90142133	2808	5709											
RNF17	56163	hgsc.bcm.edu	37	chr13	25374636	25374636	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gacatccagccattagcacaAccatgctcattgaaagacat	15	8	6	12	0	1	2	1	1	0	1	2	3	2	2	3	0	4	2	3	0	3	2	rs35957316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:25374636A>G	ENST00000255324.5	+	13	1774	c.1722A>G	c.(1720-1722)caA>caG	p.Q574Q	RNF17_ENST00000381921.1_Silent_p.Q574Q|RNF17_ENST00000255325.6_Silent_p.Q574Q	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	574					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)		CATTAGCACAACCATGCTCAT	0.358													A|||	244	0.048722	0.1755	0.0159	5008	,	,		18152	0.0		0.001	False		,,,				2504	0.0				p.Q574Q		Atlas-SNP	.											.	RNF17	259	.	0			c.A1722G						PASS	.	A	,	649,3757	277.8+/-273.9	46,557,1600	125	121	123		1722,1722	0.6	0.9	13	dbSNP_126	123	12,8588	8.4+/-32.0	0,12,4288	no	coding-synonymous,coding-synonymous	RNF17	NM_001184993.1,NM_031277.2	,	46,569,5888	GG,GA,AA		0.1395,14.7299,5.0823	,	574/1620,574/1624	25374636	661,12345	2203	4300	6503	SO:0001819	synonymous_variant	56163	exon13			AGCACAACCATGC	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.1722A>G	13.37:g.25374636A>G		80	0	0		87	46	0.528736	NM_001184993	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Silent	SNP	ENST00000255324.5	37	CCDS9308.2																																																																																			A|0.952;G|0.048	0.048	strong		0.358	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994		G	25374636	A	G	25374636	2	3	22	1	0	0	0	0	0	0	0	1	13476	40	2	3		3	RNF17	13	25374636	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	346891	25374636	89795242	2809	5710											
CENPJ	55835	hgsc.bcm.edu	37	chr13	25480616	25480616	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaagtctgtctttaccttgTgtcttattccaccctgtgca	6	16	8	11	0	3	0	0	0	3	0	4	1	4	1	3	1	2	1	3	1	3	5	rs17081368	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:25480616T>A	ENST00000381884.4	-	7	1745	c.1560A>T	c.(1558-1560)acA>acT	p.T520T	CENPJ_ENST00000545981.1_Silent_p.T520T	NM_018451.4	NP_060921.3	Q9HC77	CENPJ_HUMAN	centromere protein J	520					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)		CTTTACCTTGTGTCTTATTCC	0.448													T|||	248	0.0495208	0.1785	0.0159	5008	,	,		17190	0.0		0.001	False		,,,				2504	0.0				p.T520T		Atlas-SNP	.											.	CENPJ	116	.	0			c.A1560T						PASS	.	T		656,3750	274.3+/-271.8	47,562,1594	73	77	76		1560	0.4	0	13	dbSNP_123	76	12,8586	8.4+/-32.0	0,12,4287	no	coding-synonymous	CENPJ	NM_018451.3		47,574,5881	AA,AT,TT		0.1396,14.8888,5.1369		520/1339	25480616	668,12336	2203	4299	6502	SO:0001819	synonymous_variant	55835	exon7			ACCTTGTGTCTTA	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.1560A>T	13.37:g.25480616T>A		88	0	0		118	60	0.508475	NM_018451	Q2KHM6|Q5JPD5|Q5T6R5|Q96KS5|Q9C067	Silent	SNP	ENST00000381884.4	37	CCDS9310.1																																																																																			T|0.950;A|0.050	0.050	strong		0.448	CENPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044209.1	NM_018451		A	25480616	T	A	25480616	2	1	22	1	0	0	0	0	0	0	0	1	3236	1683	59	5		5	CENPJ	13	25480616	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	105980	25480616	89689262	2810	5711											
LNX2	222484	hgsc.bcm.edu	37	chr13	28130473	28130473	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttcccctgcccccagcaacGgtcatgccaagggattcatg	8	8	9	16	1	2	0	2	0	0	0	3	1	3	1	5	2	4	1	5	2	2	2	rs115119970	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:28130473G>A	ENST00000316334.3	-	7	1575	c.1446C>T	c.(1444-1446)acC>acT	p.T482T		NM_153371.3	NP_699202.1	Q8N448	LNX2_HUMAN	ligand of numb-protein X 2	482	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)		CCCCAGCAACGGTCATGCCAA	0.468													G|||	67	0.0133786	0.0446	0.0043	5008	,	,		15881	0.0		0.005	False		,,,				2504	0.0				p.T482T		Atlas-SNP	.											.	LNX2	70	.	0			c.C1446T						PASS	.	G		138,4268	98.9+/-137.6	0,138,2065	114	100	105		1446	-5.4	0.7	13	dbSNP_132	105	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	LNX2	NM_153371.3		0,146,6357	AA,AG,GG		0.093,3.1321,1.1226		482/691	28130473	146,12860	2203	4300	6503	SO:0001819	synonymous_variant	222484	exon7			AGCAACGGTCATG	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.1446C>T	13.37:g.28130473G>A		73	0	0		85	29	0.341176	NM_153371	Q5W0P0|Q6ZMH2|Q96SH4	Silent	SNP	ENST00000316334.3	37	CCDS9323.1																																																																																			G|0.988;A|0.012	0.012	strong		0.468	LNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044302.2			A	28130473	G	A	28130473	2	1	22	1	0	0	0	0	0	0	0	1	8875	1103	39	1		1	LNX2	13	28130473	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2649857	28130473	87039405	2811	5712											
PAN3	255967	hgsc.bcm.edu	37	chr13	28750683	28750683	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctaaatgacagtgccaagccAtattcagcccatggtaagac	14	8	8	11	0	1	2	1	1	0	1	1	2	1	2	3	1	3	1	3	1	5	4	rs142608239	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:28750683A>G	ENST00000380958.3	+	3	758	c.606A>G	c.(604-606)ccA>ccG	p.P202P	PAN3_ENST00000399613.1_Silent_p.P56P	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)		GTGCCAAGCCATATTCAGCCC	0.338													A|||	17	0.00339457	0.0121	0.0014	5008	,	,		18080	0.0		0.0	False		,,,				2504	0.0				p.P202P		Atlas-SNP	.											.	PAN3	123	.	0			c.A606G						PASS	.	A		60,4346	58.7+/-95.3	1,58,2144	125	122	123		606	4.4	1	13	dbSNP_134	123	0,8600		0,0,4300	no	coding-synonymous	PAN3	NM_175854.7		1,58,6444	GG,GA,AA		0.0,1.3618,0.4613		202/888	28750683	60,12946	2203	4300	6503	SO:0001819	synonymous_variant	255967	exon3			CAAGCCATATTCA	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.606A>G	13.37:g.28750683A>G		86	0	0		123	72	0.585366	NM_175854		Silent	SNP	ENST00000380958.3	37	CCDS9329.2																																																																																			A|0.995;G|0.005	0.005	strong		0.338	PAN3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044318.4	NM_175854		G	28750683	A	G	28750683	2	3	22	1	0	0	0	0	0	0	0	1	11424	204	8	3		3	PAN3	13	28750683	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	620210	28750683	86419195	2812	5713											
HMGB1	3146	hgsc.bcm.edu	37	chr13	31037445	31037445	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcataacgggccttgtccgcTtttgccatatcttcaaattt	8	16	6	11	2	3	0	2	0	1	0	4	0	4	0	3	1	2	1	3	1	3	7	rs983723	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:31037445T>C	ENST00000405805.1	-	3	1135	c.195A>G	c.(193-195)aaA>aaG	p.K65K	HMGB1_ENST00000341423.5_Silent_p.K65K|HMGB1_ENST00000399489.1_Silent_p.K65K|HMGB1_ENST00000399494.1_Silent_p.K65K|HMGB1_ENST00000339872.4_Silent_p.K65K|HMGB1_ENST00000326004.4_Silent_p.K65K|HMGB1_ENST00000468384.1_5'Flank			P09429	HMGB1_HUMAN	high mobility group box 1	65					apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|base-excision repair, DNA ligation (GO:0006288)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|dendritic cell chemotaxis (GO:0002407)|DNA ligation involved in DNA repair (GO:0051103)|DNA recombination (GO:0006310)|DNA topological change (GO:0006265)|inflammatory response to antigenic stimulus (GO:0002437)|innate immune response (GO:0045087)|myeloid dendritic cell activation (GO:0001773)|negative regulation of apoptotic cell clearance (GO:2000426)|negative regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0017055)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron projection development (GO:0031175)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|V(D)J recombination (GO:0033151)	cell surface (GO:0009986)|condensed chromosome (GO:0000793)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chemoattractant activity (GO:0042056)|cytokine activity (GO:0005125)|damaged DNA binding (GO:0003684)|DNA binding, bending (GO:0008301)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RAGE receptor binding (GO:0050786)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(1)|ovary(1)	8		Lung SC(185;0.0257)		all cancers(112;0.072)|OV - Ovarian serous cystadenocarcinoma(117;0.177)|Lung(94;0.216)|GBM - Glioblastoma multiforme(144;0.232)		CCTTGTCCGCTTTTGCCATAT	0.368													C|||	399	0.0796725	0.292	0.0159	5008	,	,		19065	0.0		0.002	False		,,,				2504	0.0				p.K65K		Atlas-SNP	.											.	HMGB1	21	.	0			c.A195G						PASS	.	C		996,3410	684.5+/-404.4	121,754,1328	57	64	62		195	3.4	1	13	dbSNP_86	62	7,8593	813.0+/-407.0	0,7,4293	no	coding-synonymous	HMGB1	NM_002128.4		121,761,5621	CC,CT,TT		0.0814,22.6055,7.7118		65/216	31037445	1003,12003	2203	4300	6503	SO:0001819	synonymous_variant	3146	exon3			GTCCGCTTTTGCC	D63874	CCDS9335.1	13q12	2011-07-01	2011-04-05	2002-08-16	ENSG00000189403	ENSG00000189403		"High-mobility group / Canonical"	4983	protein-coding gene	gene with protein product	"high mobility group box 1", "Sulfoglucuronyl carbohydrate binding protein", "Amphoterin", "high mobility group protein 1"	163905	"high-mobility group (nonhistone chromosomal) protein 1", "high-mobility group box 1"	HMG1		8661151, 11279268	Standard	NM_002128		Approved	HMG3, SBP-1, DKFZp686A04236	uc001usx.3	P09429	OTTHUMG00000016670	ENST00000405805.1:c.195A>G	13.37:g.31037445T>C		40	0	0		53	22	0.415094	NM_002128	A5D8W9|Q14321|Q5T7C3|Q6IBE1	Silent	SNP	ENST00000405805.1	37	CCDS9335.1																																																																																			T|0.941;C|0.059	0.059	strong		0.368	HMGB1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303998.2	NM_002128		C	31037445	T	C	31037445	2	2	22	1	0	0	0	0	0	0	0	1	7234	1606	56	3		3	HMGB1	13	31037445	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2286762	31037445	84132433	2813	5714											
N4BP2L2	10443	hgsc.bcm.edu	37	chr13	33110539	33110539	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ttaagagaccattattatgaCcctcataaaatggaacaaat	18	11	5	7	0	1	2	1	1	0	1	1	4	1	3	2	1	1	0	2	1	7	4	rs144941975	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:33110539C>A	ENST00000267068.3	-	2	790	c.626G>T	c.(625-627)gGt>gTt	p.G209V	N4BP2L2_ENST00000399396.3_Intron|N4BP2L2_ENST00000357505.6_Intron|N4BP2L2_ENST00000504114.1_Intron|N4BP2L2_ENST00000446957.2_Missense_Mutation_p.G209V	NM_014887.2	NP_055702.1	Q92802	N42L2_HUMAN	NEDD4 binding protein 2-like 2	209					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)		ATTATTATGACCCTCATAAAA	0.338													C|||	8	0.00159744	0.0053	0.0014	5008	,	,		19947	0.0		0.0	False		,,,				2504	0.0				p.G209V		Atlas-SNP	.											.	N4BP2L2	90	.	0			c.G626T						PASS	.	C	VAL/GLY,	34,4372	37.6+/-69.7	0,34,2169	68	69	68		626,	-3.3	0	13	dbSNP_134	68	0,8600		0,0,4300	yes	missense,intron	N4BP2L2	NM_014887.2,NM_033111.3	109,	0,34,6469	AA,AC,CC		0.0,0.7717,0.2614	,	209/584,	33110539	34,12972	2203	4300	6503	SO:0001583	missense	10443	exon2			TTATGACCCTCAT	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.626G>T	13.37:g.33110539C>A	ENSP00000267068:p.Gly209Val	121	0	0		100	40	0.4	NM_014887	A3KME8	Missense_Mutation	SNP	ENST00000267068.3	37	CCDS9346.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	5.665	0.307323	0.10733	0.007717	0.0	ENSG00000244754	ENST00000446957;ENST00000505213;ENST00000267068	T;T;T	0.42513	0.97;0.97;0.97	5.58	-3.31	0.04988	.	.	.	.	.	T	0.21347	0.0514	L	0.47716	1.5	0.09310	N	1	P;P	0.45902	0.868;0.454	B;B	0.34038	0.174;0.08	T	0.13150	-1.0520	9	0.62326	D	0.03	-15.1664	10.2296	0.43247	0.0:0.2989:0.0999:0.6013	.	209;209	D6R968;Q92802	.;N42L2_HUMAN	V	209	ENSP00000394239:G209V;ENSP00000423362:G209V;ENSP00000267068:G209V	ENSP00000267068:G209V	G	-	2	0	N4BP2L2	32008539	0.000000	0.05858	0.000000	0.03702	0.109000	0.19521	-0.411000	0.07142	-0.881000	0.03992	0.563000	0.77884	GGT	C|0.998;A|0.002	0.002	strong		0.338	N4BP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044421.1	NM_014887		A	33110539	C	A	33110539	3	1	22	1	0	0	0	0	1	0	0	0	10121	507	18	4	3006	4	N4BP2L2	13	33110539	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2073094	33110539	82059339	2814	5715											
N4BP2L2	10443	hgsc.bcm.edu	37	chr13	33110831	33110831	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctatatatctcatcgtctgCggatactaatggaggacgtg	10	12	11	8	3	2	0	1	0	2	0	4	3	2	3	0	3	2	1	0	3	5	5	rs149614093	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:33110831C>T	ENST00000267068.3	-	2	498	c.334G>A	c.(334-336)Gca>Aca	p.A112T	N4BP2L2_ENST00000399396.3_Intron|N4BP2L2_ENST00000357505.6_Intron|N4BP2L2_ENST00000504114.1_Intron|N4BP2L2_ENST00000446957.2_Missense_Mutation_p.A112T	NM_014887.2	NP_055702.1	Q92802	N42L2_HUMAN	NEDD4 binding protein 2-like 2	112					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)		TCATCGTCTGCGGATACTAAT	0.413													T|||	8	0.00159744	0.0053	0.0014	5008	,	,		19703	0.0		0.0	False		,,,				2504	0.0				p.A112T		Atlas-SNP	.											.	N4BP2L2	90	.	0			c.G334A						PASS	.	T	THR/ALA,	35,4371	822.9+/-416.5	0,35,2168	194	193	193		334,	-0.4	0	13	dbSNP_134	193	0,8600		0,0,4300	yes	missense,intron	N4BP2L2	NM_014887.2,NM_033111.3	58,	0,35,6468	TT,TC,CC		0.0,0.7944,0.2691	,	112/584,	33110831	35,12971	2203	4300	6503	SO:0001583	missense	10443	exon2			CGTCTGCGGATAC	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.334G>A	13.37:g.33110831C>T	ENSP00000267068:p.Ala112Thr	184	0	0		192	85	0.442708	NM_014887	A3KME8	Missense_Mutation	SNP	ENST00000267068.3	37	CCDS9346.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	0.982	-0.696861	0.03279	0.007944	0.0	ENSG00000244754	ENST00000446957;ENST00000505213;ENST00000267068	T;T;T	0.41400	1.0;1.0;1.0	5.09	-0.355	0.12587	.	.	.	.	.	T	0.07818	0.0196	N	0.00707	-1.245	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30297	-0.9983	9	0.15499	T	0.54	-16.1287	5.0255	0.14383	0.1598:0.4478:0.0:0.3924	.	112;112	D6R968;Q92802	.;N42L2_HUMAN	T	112	ENSP00000394239:A112T;ENSP00000423362:A112T;ENSP00000267068:A112T	ENSP00000267068:A112T	A	-	1	0	N4BP2L2	32008831	0.005000	0.15991	0.000000	0.03702	0.071000	0.16799	-0.142000	0.10311	-0.249000	0.09569	-0.360000	0.07572	GCA	C|0.998;T|0.002	0.002	strong		0.413	N4BP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044421.1	NM_014887		T	33110831	C	T	33110831	3	4	22	1	0	0	0	0	1	0	0	0	10121	768	27	1	3298	1	N4BP2L2	13	33110831	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	292	33110831	82059047	2815	5716											
STARD13	90627	hgsc.bcm.edu	37	chr13	33684221	33684221	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cagcttcagcgggttcccgtCgcccaccttgggaaagacaa	9	7	11	14	3	1	1	1	0	0	1	3	2	2	2	3	2	2	2	3	2	2	3	rs140868444	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:33684221C>T	ENST00000336934.5	-	12	2952	c.2836G>A	c.(2836-2838)Gac>Aac	p.D946N	STARD13_ENST00000399365.3_Missense_Mutation_p.D828N|STARD13_ENST00000255486.4_Missense_Mutation_p.D938N	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	946	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)		GGGTTCCCGTCGCCCACCTTG	0.547											OREG0022359	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	13	0.00259585	0.0098	0.0	5008	,	,		18177	0.0		0.0	False		,,,				2504	0.0				p.D946N		Atlas-SNP	.											.	STARD13	100	.	0			c.G2836A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP	51,4355	53.6+/-89.4	0,51,2152	36	35	35		2482,2836,2812	5.3	0.9	13	dbSNP_134	35	0,8600		0,0,4300	yes	missense,missense,missense	STARD13	NM_052851.2,NM_178006.3,NM_178007.2	23,23,23	0,51,6452	TT,TC,CC		0.0,1.1575,0.3921	probably-damaging,probably-damaging,probably-damaging	828/996,946/1114,938/1106	33684221	51,12955	2203	4300	6503	SO:0001583	missense	90627	exon12			TCCCGTCGCCCAC	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.2836G>A	13.37:g.33684221C>T	ENSP00000338785:p.Asp946Asn	64	0	0	841	48	14	0.291667	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Missense_Mutation	SNP	ENST00000336934.5	37	CCDS9348.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	35	5.458396	0.96240	0.011575	0.0	ENSG00000133121	ENST00000399365;ENST00000255486;ENST00000336934	T;T;T	0.34859	1.34;1.34;1.34	5.34	5.34	0.76211	Lipid-binding START (3);START-like domain (1);	0.000000	0.85682	D	0.000000	T	0.53690	0.1812	M	0.90650	3.135	0.80722	D	1	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.77004	0.954;0.989;0.982	T	0.71573	-0.4552	10	0.87932	D	0	.	19.4036	0.94640	0.0:1.0:0.0:0.0	.	911;946;938	Q9Y3M8-4;Q9Y3M8;Q9Y3M8-2	.;STA13_HUMAN;.	N	828;938;946	ENSP00000382300:D828N;ENSP00000255486:D938N;ENSP00000338785:D946N	ENSP00000255486:D938N	D	-	1	0	STARD13	32582221	1.000000	0.71417	0.931000	0.37212	0.958000	0.62258	7.689000	0.84165	2.657000	0.90304	0.655000	0.94253	GAC	C|0.996;T|0.004	0.004	strong		0.547	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466		T	33684221	C	T	33684221	3	4	22	1	0	0	0	0	1	0	0	0	15271	884	31	1	517	1	STARD13	13	33684221	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	573390	33684221	81485657	2816	5717											
STARD13	90627	hgsc.bcm.edu	37	chr13	33704346	33704346	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagcgtgtagaggtcgtcCacacgagaccacctgcgact	10	6	12	13	4	0	2	0	0	0	2	2	4	1	2	3	1	3	2	3	1	1	1	rs114088950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:33704346C>T	ENST00000336934.5	-	5	584	c.468G>A	c.(466-468)gtG>gtA	p.V156V	STARD13_ENST00000399365.3_Silent_p.V38V|STARD13_ENST00000255486.4_Silent_p.V148V	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	156					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)		AGAGGTCGTCCACACGAGACC	0.557													C|||	86	0.0171725	0.0492	0.0014	5008	,	,		21153	0.0		0.0	False		,,,				2504	0.0204				p.V156V		Atlas-SNP	.											.	STARD13	100	.	0			c.G468A						PASS	.	C	,,	147,4259	103.8+/-142.4	3,141,2059	82	62	69		114,468,444	5.4	1	13	dbSNP_132	69	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	STARD13	NM_052851.2,NM_178006.3,NM_178007.2	,,	3,142,6358	TT,TC,CC		0.0116,3.3364,1.1379	,,	38/996,156/1114,148/1106	33704346	148,12858	2203	4300	6503	SO:0001819	synonymous_variant	90627	exon5			GTCGTCCACACGA	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.468G>A	13.37:g.33704346C>T		33	0	0		43	18	0.418605	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Silent	SNP	ENST00000336934.5	37	CCDS9348.1																																																																																			C|0.986;T|0.014	0.014	strong		0.557	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466		T	33704346	C	T	33704346	2	4	22	1	0	0	0	0	0	0	0	1	15271	581	21	2		2	STARD13	13	33704346	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	20125	33704346	81465532	2817	5718											
STARD13	90627	hgsc.bcm.edu	37	chr13	33741716	33741716	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aactgagcgtattgcgggaaCccggcagcacggagccagtc	10	5	14	12	4	0	1	0	1	0	0	1	3	0	3	2	3	6	3	2	3	3	2	rs17078661	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:33741716C>T	ENST00000336934.5	-	2	329	c.213G>A	c.(211-213)ggG>ggA	p.G71G	STARD13_ENST00000399365.3_5'UTR|STARD13_ENST00000255486.4_Silent_p.G63G|STARD13_ENST00000487412.1_5'UTR	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	71	SAM.				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)		ATTGCGGGAACCCGGCAGCAC	0.483													C|||	178	0.0355431	0.1301	0.0086	5008	,	,		18769	0.0		0.0	False		,,,				2504	0.0				p.G71G		Atlas-SNP	.											STARD13,NS,carcinoma,-1,1	STARD13	100	1	0			c.G213A						PASS	.	C	,,	558,3848	250.9+/-257.8	30,498,1675	96	93	94		,213,189	-3.2	1	13	dbSNP_123	94	7,8593	5.7+/-21.5	0,7,4293	no	utr-5,coding-synonymous,coding-synonymous	STARD13	NM_052851.2,NM_178006.3,NM_178007.2	,,	30,505,5968	TT,TC,CC		0.0814,12.6645,4.3441	,,	,71/1114,63/1106	33741716	565,12441	2203	4300	6503	SO:0001819	synonymous_variant	90627	exon2			CGGGAACCCGGCA	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.213G>A	13.37:g.33741716C>T		63	0	0		69	33	0.478261	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Silent	SNP	ENST00000336934.5	37	CCDS9348.1																																																																																			C|0.960;T|0.040	0.040	strong		0.483	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466		T	33741716	C	T	33741716	2	4	22	1	0	0	0	0	0	0	0	1	15271	494	18	2		2	STARD13	13	33741716	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	37370	33741716	81428162	2818	5719											
TRPC4	7223	hgsc.bcm.edu	37	chr13	38211046	38211046	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctccttcaagtatcacaaTcttgtggtcacgtaatcttc	9	15	5	12	1	5	0	3	0	2	0	8	0	7	0	2	1	0	2	2	1	4	5	rs731860	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:38211046T>C	ENST00000379705.3	-	11	3785	c.2928A>G	c.(2926-2928)agA>agG	p.R976R	TRPC4_ENST00000358477.2_Silent_p.R892R|TRPC4_ENST00000379681.3_Silent_p.R981R|TRPC4_ENST00000447043.1_Silent_p.R835R|TRPC4_ENST00000379679.1_Silent_p.R803R|TRPC4_ENST00000355779.2_Silent_p.R835R|TRPC4_ENST00000379673.2_Silent_p.R827R|TRPC4_ENST00000338947.5_Silent_p.R803R|TRPC4_ENST00000426868.2_3'UTR			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	976	Binds to ITPR1, ITPR2 and ITPR3.|PDZ-binding domain.				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)		AGTATCACAATCTTGTGGTCA	0.403													T|||	154	0.0307508	0.1112	0.0086	5008	,	,		19821	0.0		0.001	False		,,,				2504	0.0				p.R981R		Atlas-SNP	.											.	TRPC4	389	.	0			c.A2943G						PASS	.	T	,,,,,	428,3978	208.5+/-229.5	24,380,1799	118	111	114		2676,2481,2505,2409,2943,2928	-1.3	0.2	13	dbSNP_86	114	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRPC4	NM_001135955.1,NM_001135956.1,NM_001135957.1,NM_001135958.1,NM_003306.1,NM_016179.2	,,,,,	24,387,6092	CC,CT,TT		0.0814,9.714,3.3446	,,,,,	892/894,827/829,835/837,803/805,981/983,976/978	38211046	435,12571	2203	4300	6503	SO:0001819	synonymous_variant	7223	exon11			TCACAATCTTGTG	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.2928A>G	13.37:g.38211046T>C		102	0	0		112	63	0.5625	NM_003306	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Silent	SNP	ENST00000379705.3	37	CCDS9365.1																																																																																			T|0.959;C|0.041	0.041	strong		0.403	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306		C	38211046	T	C	38211046	2	2	22	1	0	0	0	0	0	0	0	1	16595	1432	50	3		3	TRPC4	13	38211046	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	4469330	38211046	76958832	2819	5720											
FREM2	341640	hgsc.bcm.edu	37	chr13	39263422	39263422	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagagtggcagcagcaggaCataacagagggcaggctgtt	13	5	15	8	0	0	2	0	0	0	2	0	3	0	3	0	4	3	6	0	4	1	2	rs41292751	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:39263422C>T	ENST00000280481.7	+	1	2157	c.1941C>T	c.(1939-1941)gaC>gaT	p.D647D		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	647					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)		AGCAGCAGGACATAACAGAGG	0.532													C|||	61	0.0121805	0.0008	0.0216	5008	,	,		17077	0.0		0.0378	False		,,,				2504	0.0072				p.D647D		Atlas-SNP	.											.	FREM2	385	.	0			c.C1941T						PASS	.	C		43,4363	45.3+/-79.5	0,43,2160	72	66	68		1941	5.1	1	13	dbSNP_127	68	324,8276	114.8+/-174.7	5,314,3981	no	coding-synonymous	FREM2	NM_207361.4		5,357,6141	TT,TC,CC		3.7674,0.9759,2.8218		647/3170	39263422	367,12639	2203	4300	6503	SO:0001819	synonymous_variant	341640	exon1			GCAGGACATAACA	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.1941C>T	13.37:g.39263422C>T		92	0	0		95	49	0.515789	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																			C|0.973;T|0.027	0.027	strong		0.532	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39263422	C	T	39263422	2	4	22	1	0	0	0	0	0	0	0	1	6053	477	17	2		2	FREM2	13	39263422	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1052376	39263422	75906456	2820	5721											
FREM2	341640	hgsc.bcm.edu	37	chr13	39263646	39263646	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atcccagctcacaccactgaGgaagaagtggctgcgctaca	12	6	10	13	1	1	2	1	1	0	1	2	3	2	3	2	2	3	3	2	2	3	1	rs58363253	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:39263646G>A	ENST00000280481.7	+	1	2381	c.2165G>A	c.(2164-2166)aGg>aAg	p.R722K		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	722			R -> K (in dbSNP:rs58363253).		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)		ACACCACTGAGGAAGAAGTGG	0.552													G|||	315	0.0628994	0.208	0.0231	5008	,	,		19051	0.001		0.0089	False		,,,				2504	0.0143				p.R722K		Atlas-SNP	.											.	FREM2	385	.	0			c.G2165A						PASS	.	G	LYS/ARG	745,3661	305.5+/-289.0	68,609,1526	67	64	65		2165	5.1	1	13	dbSNP_129	65	88,8512	49.8+/-109.6	1,86,4213	yes	missense	FREM2	NM_207361.4	26	69,695,5739	AA,AG,GG		1.0233,16.9088,6.4047	benign	722/3170	39263646	833,12173	2203	4300	6503	SO:0001583	missense	341640	exon1			CACTGAGGAAGAA	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.2165G>A	13.37:g.39263646G>A	ENSP00000280481:p.Arg722Lys	97	0	0		127	58	0.456693	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	96	0.04395604395604396	82	0.16666666666666666	9	0.024861878453038673	0	0.0	5	0.006596306068601583	G	11.87	1.768801	0.31320	0.169088	0.010233	ENSG00000150893	ENST00000280481	T	0.28255	1.62	5.97	5.13	0.70059	.	0.088825	0.64402	N	0.000001	T	0.00073	0.0002	L	0.49513	1.565	0.18873	P	0.9999848891	B	0.02656	0.0	B	0.06405	0.002	T	0.12708	-1.0537	9	0.17832	T	0.49	.	14.9829	0.71324	0.0679:0.0:0.932:0.0	rs58363253;rs61734231	722	Q5SZK8	FREM2_HUMAN	K	722	ENSP00000280481:R722K	ENSP00000280481:R722K	R	+	2	0	FREM2	38161646	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.884000	0.48562	1.541000	0.49316	0.655000	0.94253	AGG	G|0.949;A|0.051	0.051	strong		0.552	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		A	39263646	G	A	39263646	3	1	22	1	0	0	0	0	1	0	0	0	6053	1000	35	2	2167	2	FREM2	13	39263646	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	224	39263646	75906232	2821	5722											
FREM2	341640	hgsc.bcm.edu	37	chr13	39264083	39264083	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttgcccatatctctttcactCtcactcaggcacccaaacat	10	12	3	16	0	4	0	3	0	2	0	6	0	4	0	2	1	2	1	2	1	2	3	rs7329939	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:39264083C>G	ENST00000280481.7	+	1	2818	c.2602C>G	c.(2602-2604)Ctc>Gtc	p.L868V		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	868			L -> V (in dbSNP:rs7329939).		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)		CTCTTTCACTCTCACTCAGGC	0.507													C|||	315	0.0628994	0.208	0.0231	5008	,	,		21471	0.001		0.0089	False		,,,				2504	0.0143				p.L868V		Atlas-SNP	.											.	FREM2	385	.	0			c.C2602G						PASS	.	C	VAL/LEU	745,3661	306.3+/-289.4	68,609,1526	101	88	92		2602	5.8	1	13	dbSNP_116	92	88,8512	49.8+/-109.6	1,86,4213	yes	missense	FREM2	NM_207361.4	32	69,695,5739	GG,GC,CC		1.0233,16.9088,6.4047	benign	868/3170	39264083	833,12173	2203	4300	6503	SO:0001583	missense	341640	exon1			TTCACTCTCACTC	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.2602C>G	13.37:g.39264083C>G	ENSP00000280481:p.Leu868Val	112	0	0		114	64	0.561404	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	96	0.04395604395604396	82	0.16666666666666666	9	0.024861878453038673	0	0.0	5	0.006596306068601583	C	10.04	1.240711	0.22711	0.169088	0.010233	ENSG00000150893	ENST00000280481	T	0.43294	0.95	5.8	5.8	0.92144	.	0.062991	0.64402	D	0.000004	T	0.00109	0.0003	N	0.25647	0.755	0.19575	P	0.9999648898	B	0.30824	0.296	B	0.27262	0.078	T	0.03068	-1.1076	9	0.33940	T	0.23	.	20.0609	0.97674	0.0:1.0:0.0:0.0	rs7329939;rs52807873;rs7329939	868	Q5SZK8	FREM2_HUMAN	V	868	ENSP00000280481:L868V	ENSP00000280481:L868V	L	+	1	0	FREM2	38162083	0.038000	0.19896	1.000000	0.80357	0.329000	0.28539	0.383000	0.20651	2.755000	0.94549	0.655000	0.94253	CTC	C|0.947;G|0.053	0.053	strong		0.507	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		G	39264083	C	G	39264083	3	3	22	1	0	0	0	0	1	0	0	0	6053	913	32	4	2604	4	FREM2	13	39264083	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	437	39264083	75905795	2822	5723											
FREM2	341640	hgsc.bcm.edu	37	chr13	39265558	39265558	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagacgaaaacctactggTgcctttgaaaatatcacact	15	9	7	10	1	1	2	1	1	0	1	1	4	1	2	2	1	3	0	2	1	6	3	rs41292757	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:39265558T>A	ENST00000280481.7	+	1	4293	c.4077T>A	c.(4075-4077)ggT>ggA	p.G1359G		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1359					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)		AACCTACTGGTGCCTTTGAAA	0.398													T|||	59	0.0117812	0.0008	0.0216	5008	,	,		21033	0.0		0.0378	False		,,,				2504	0.0051				p.G1359G		Atlas-SNP	.											.	FREM2	385	.	0			c.T4077A						PASS	.	T		43,4363	44.6+/-78.6	0,43,2160	63	64	63		4077	0.2	0.8	13	dbSNP_127	63	324,8276	114.8+/-174.7	5,314,3981	no	coding-synonymous	FREM2	NM_207361.4		5,357,6141	AA,AT,TT		3.7674,0.9759,2.8218		1359/3170	39265558	367,12639	2203	4300	6503	SO:0001819	synonymous_variant	341640	exon1			TACTGGTGCCTTT	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.4077T>A	13.37:g.39265558T>A		101	0	0		128	61	0.476562	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																			T|0.972;A|0.028	0.028	strong		0.398	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		A	39265558	T	A	39265558	2	1	22	1	0	0	0	0	0	0	0	1	6053	1683	59	5		5	FREM2	13	39265558	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1475	39265558	75904320	2823	5724											
LHFP	10186	hgsc.bcm.edu	37	chr13	40175311	40175311	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcagcacaaagaaaagacaGcaaagcccagattactccag	18	3	9	11	0	0	3	0	0	0	3	1	3	1	3	2	1	4	3	2	1	5	1	rs34616166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:40175311G>A	ENST00000379589.3	-	2	505	c.43C>T	c.(43-45)Ctg>Ttg	p.L15L	LHFP_ENST00000495922.1_5'Flank	NM_005780.2	NP_005771.1	Q9Y693	LHFP_HUMAN	lipoma HMGIC fusion partner	15						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)		AGAAAAGACAGCAAAGCCCAG	0.537			T	HMGA2	lipoma								G|||	341	0.0680911	0.2466	0.0159	5008	,	,		20157	0.0		0.004	False		,,,				2504	0.0				p.L15L		Atlas-SNP	.		Dom	yes		13	13q12	10186	lipoma HMGIC fusion partner		M	.	LHFP	31	.	0			c.C43T						PASS	.	G		827,3579	318.0+/-295.4	77,673,1453	66	59	61		43	5.4	1	13	dbSNP_126	61	10,8590	7.1+/-27.0	0,10,4290	no	coding-synonymous	LHFP	NM_005780.2		77,683,5743	AA,AG,GG		0.1163,18.7699,6.4355		15/201	40175311	837,12169	2203	4300	6503	SO:0001819	synonymous_variant	10186	exon2			AAGACAGCAAAGC	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.43C>T	13.37:g.40175311G>A		89	0	0		123	70	0.569106	NM_005780	B2R7M2|Q53FC0|Q96SH5	Silent	SNP	ENST00000379589.3	37	CCDS9369.1																																																																																			G|0.941;A|0.059	0.059	strong		0.537	LHFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044619.1	NM_005780		A	40175311	G	A	40175311	2	1	22	1	0	0	0	0	0	0	0	1	8772	962	34	2		2	LHFP	13	40175311	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	909753	40175311	74994567	2824	5725											
WBP4	11193	hgsc.bcm.edu	37	chr13	41639377	41639377	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gctgcaatggaggcagctgcCctgaaagcataccaagagga	13	5	13	10	0	0	2	0	1	0	1	0	4	0	4	2	3	5	5	2	3	4	1	rs61740513	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:41639377C>T	ENST00000379487.3	+	4	616	c.216C>T	c.(214-216)gcC>gcT	p.A72A	WBP4_ENST00000542082.1_Silent_p.A51A	NM_007187.3	NP_009118.1	O75554	WBP4_HUMAN	WW domain binding protein 4	72					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)		AGGCAGCTGCCCTGAAAGCAT	0.368													C|||	126	0.0251597	0.0908	0.0072	5008	,	,		14418	0.0		0.001	False		,,,				2504	0.0				p.A72A		Atlas-SNP	.											.	WBP4	40	.	0			c.C216T						PASS	.	C		411,3995	201.5+/-224.5	14,383,1806	64	69	67		216	2.8	1	13	dbSNP_129	67	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	WBP4	NM_007187.3		14,385,6104	TT,TC,CC		0.0233,9.3282,3.1755		72/377	41639377	413,12593	2203	4300	6503	SO:0001819	synonymous_variant	11193	exon4			AGCTGCCCTGAAA	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.216C>T	13.37:g.41639377C>T		56	0	0		65	37	0.569231	NM_007187	B7Z4M2|Q32P29	Silent	SNP	ENST00000379487.3	37	CCDS9375.1																																																																																			C|0.967;T|0.033	0.033	strong		0.368	WBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044655.2	NM_007187		T	41639377	C	T	41639377	2	4	22	1	0	0	0	0	0	0	0	1	17276	610	22	2		2	WBP4	13	41639377	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1464066	41639377	73530501	2825	5726											
KBTBD6	89890	hgsc.bcm.edu	37	chr13	41706450	41706450	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccaggcgtcaccacctcgatGgtcacatcacacagcagccg	10	5	9	17	3	3	0	3	0	0	0	4	1	3	0	4	2	2	1	4	2	0	0	rs147388453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:41706450G>C	ENST00000379485.1	-	1	432	c.198C>G	c.(196-198)acC>acG	p.T66T	KBTBD6_ENST00000499385.2_Intron	NM_152903.4	NP_690867.3	Q86V97	KBTB6_HUMAN	kelch repeat and BTB (POZ) domain containing 6	66	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.									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)		CCACCTCGATGGTCACATCAC	0.607													G|||	43	0.00858626	0.031	0.0014	5008	,	,		18622	0.0		0.001	False		,,,				2504	0.0				p.T66T		Atlas-SNP	.											.	KBTBD6	83	.	0			c.C198G						PASS	.	G		152,4254	104.7+/-143.2	0,152,2051	89	89	89		198	3.7	1	13	dbSNP_134	89	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KBTBD6	NM_152903.4		0,153,6350	CC,CG,GG		0.0116,3.4498,1.1764		66/675	41706450	153,12853	2203	4300	6503	SO:0001819	synonymous_variant	89890	exon1			CTCGATGGTCACA	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.198C>G	13.37:g.41706450G>C		101	0	0		71	40	0.56338	NM_152903	Q5T6Y8|Q8N8L0|Q8NDM5|Q96MP6	Silent	SNP	ENST00000379485.1	37	CCDS9376.1																																																																																			G|0.988;C|0.012	0.012	strong		0.607	KBTBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044657.1	NM_152903		C	41706450	G	C	41706450	2	2	22	1	0	0	0	0	0	0	0	1	8006	1335	47	4		4	KBTBD6	13	41706450	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	67073	41706450	73463428	2826	5727											
NAA16	79612	hgsc.bcm.edu	37	chr13	41929296	41929296	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaggtttctataatccaggAacttgttactaattatgaag	14	14	7	6	0	1	1	0	1	1	0	2	2	2	2	1	2	2	2	1	2	7	7	rs17062054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:41929296A>G	ENST00000379406.3	+	10	1355	c.1031A>G	c.(1030-1032)gAa>gGa	p.E344G	RNU6-57P_ENST00000411348.1_RNA|NAA16_ENST00000379367.3_Missense_Mutation_p.E344G|NAA16_ENST00000403412.3_Missense_Mutation_p.E344G	NM_024561.4	NP_078837.3	Q6N069	NAA16_HUMAN	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	344			E -> G (in dbSNP:rs17062054).		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						ATAATCCAGGAACTTGTTACT	0.254													A|||	379	0.0756789	0.2723	0.0259	5008	,	,		14616	0.0		0.001	False		,,,				2504	0.0				p.E344G		Atlas-SNP	.											.	NAA16	74	.	0			c.A1031G						PASS	.	A	GLY/GLU,,GLY/GLU	1062,3342	336.3+/-304.3	129,804,1269	92	103	99		1031,924,1031	5.2	1	13	dbSNP_123	99	17,8567	6.4+/-24.3	0,17,4275	yes	missense,coding-synonymous,missense	NAA16	NM_001110798.1,NM_018527.3,NM_024561.4	98,,98	129,821,5544	GG,GA,AA		0.198,24.1144,8.3077	possibly-damaging,,possibly-damaging	344/430,308/312,344/865	41929296	1079,11909	2202	4292	6494	SO:0001583	missense	79612	exon10			TCCAGGAACTTGT	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.1031A>G	13.37:g.41929296A>G	ENSP00000368716:p.Glu344Gly	33	0	0		36	13	0.361111	NM_001110798	B0QZ59|Q5VSP9|Q6P2D5|Q8N5J3|Q8N870	Missense_Mutation	SNP	ENST00000379406.3	37	CCDS9379.1	122	0.055860805860805864	111	0.22560975609756098	11	0.03038674033149171	0	0.0	0	0.0	A	20.6	4.024646	0.75390	0.241144	0.00198	ENSG00000172766	ENST00000379367;ENST00000379406;ENST00000403412	T;T;T	0.50001	0.76;0.76;0.76	5.23	5.23	0.72850	.	0.074309	0.56097	D	0.000039	T	0.00039	0.0001	.	.	.	0.18873	P	0.9999871049	P;P	0.48640	0.866;0.913	P;P	0.57548	0.61;0.823	T	0.00814	-1.1555	8	0.72032	D	0.01	-14.8273	15.0951	0.72226	1.0:0.0:0.0:0.0	rs17062054;rs52827917;rs59013357;rs17062054	344;344	Q6N069;Q6N069-4	NAA16_HUMAN;.	G	344	ENSP00000368674:E344G;ENSP00000368716:E344G;ENSP00000386103:E344G	ENSP00000368674:E344G	E	+	2	0	NAA16	40827296	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.480000	0.81109	1.980000	0.57719	0.533000	0.62120	GAA	A|0.919;G|0.081	0.081	strong		0.254	NAA16-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044672.2	NM_018527		G	41929296	A	G	41929296	3	3	22	1	0	0	0	0	1	0	0	0	10128	246	9	3	1069	3	NAA16	13	41929296	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	222846	41929296	73240582	2827	5728											
AKAP11	11215	hgsc.bcm.edu	37	chr13	42876996	42876996	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcagtatgccaataggcttGcctaccgatctgttaaatca	12	12	7	10	1	3	0	2	0	1	0	3	1	3	0	3	1	3	3	3	1	6	5	rs114980445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:42876996G>A	ENST00000025301.2	+	8	4289	c.4114G>A	c.(4114-4116)Gcc>Acc	p.A1372T		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	1372					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)		CAATAGGCTTGCCTACCGATC	0.413													G|||	22	0.00439297	0.0144	0.0043	5008	,	,		21346	0.0		0.0	False		,,,				2504	0.0				p.A1372T		Atlas-SNP	.											.	AKAP11	146	.	0			c.G4114A						PASS	.	G	THR/ALA	79,4327	69.8+/-107.6	0,79,2124	88	82	84		4114	6.2	1	13	dbSNP_132	84	1,8599	1.2+/-3.3	0,1,4299	yes	missense	AKAP11	NM_016248.3	58	0,80,6423	AA,AG,GG		0.0116,1.793,0.6151	probably-damaging	1372/1902	42876996	80,12926	2203	4300	6503	SO:0001583	missense	11215	exon8			AGGCTTGCCTACC	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.4114G>A	13.37:g.42876996G>A	ENSP00000025301:p.Ala1372Thr	52	0	0		65	26	0.4	NM_016248	O75124|Q9NUK7	Missense_Mutation	SNP	ENST00000025301.2	37	CCDS9383.1	14	0.00641025641025641	12	0.024390243902439025	2	0.0055248618784530384	0	0.0	0	0.0	G	28.1	4.892258	0.91889	0.01793	1.16E-4	ENSG00000023516	ENST00000025301	T	0.56444	0.46	6.16	6.16	0.99307	.	0.065315	0.64402	D	0.000013	T	0.60287	0.2257	M	0.71581	2.175	0.54753	D	0.999989	D	0.89917	1.0	D	0.72982	0.979	T	0.69194	-0.5209	10	0.87932	D	0	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	1372	Q9UKA4	AKA11_HUMAN	T	1372	ENSP00000025301:A1372T	ENSP00000025301:A1372T	A	+	1	0	AKAP11	41774996	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.096000	0.94182	2.937000	0.99478	0.650000	0.86243	GCC	G|0.992;A|0.008	0.008	strong		0.413	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248		A	42876996	G	A	42876996	3	1	22	1	0	0	0	0	1	0	0	0	447	1319	46	2	4136	2	AKAP11	13	42876996	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	947700	42876996	72292882	2828	5729											
ENOX1	55068	hgsc.bcm.edu	37	chr13	43987003	43987003	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcagccatcatctgaggaagCtcctggggaagctgggtgat	9	8	15	9	0	2	2	1	2	1	0	3	4	3	4	2	4	3	3	2	4	2	0	rs7338624	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:43987003C>G	ENST00000261488.6	-	4	625	c.48G>C	c.(46-48)gaG>gaC	p.E16D	ENOX1_ENST00000412891.1_Missense_Mutation_p.E16D	NM_001242863.1|NM_017993.3	NP_001229792.1|NP_060463.2	Q8TC92	ENOX1_HUMAN	ecto-NOX disulfide-thiol exchanger 1	16			E -> D (in dbSNP:rs7338624). {ECO:0000269|PubMed:19055324}.		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)		TCTGAGGAAGCTCCTGGGGAA	0.498													C|||	242	0.0483227	0.1778	0.0101	5008	,	,		16486	0.0		0.0	False		,,,				2504	0.0				p.E16D		Atlas-SNP	.											.	ENOX1	158	.	0			c.G48C						PASS	.	C	ASP/GLU,ASP/GLU,ASP/GLU	677,3729	286.3+/-278.7	49,579,1575	125	111	116		48,48,48	2.9	0.9	13	dbSNP_116	116	9,8591	5.7+/-21.5	0,9,4291	yes	missense,missense,missense	ENOX1	NM_001127615.1,NM_001242863.1,NM_017993.3	45,45,45	49,588,5866	GG,GC,CC		0.1047,15.3654,5.2745	benign,benign,benign	16/644,16/644,16/644	43987003	686,12320	2203	4300	6503	SO:0001583	missense	55068	exon4			AGGAAGCTCCTGG	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.48G>C	13.37:g.43987003C>G	ENSP00000261488:p.Glu16Asp	96	0	0		93	49	0.526882	NM_017993	A4GU15|A6NMH9|B7Z5K1|Q2TU81|Q5VT11|Q9NWE0	Missense_Mutation	SNP	ENST00000261488.6	37	CCDS9389.1	78	0.03571428571428571	74	0.15040650406504066	4	0.011049723756906077	0	0.0	0	0.0	C	11.61	1.690096	0.29962	0.153654	0.001047	ENSG00000120658	ENST00000261488;ENST00000412891	T;T	0.44083	0.93;0.93	5.91	2.88	0.33553	.	0.688144	0.14119	N	0.340181	T	0.00109	0.0003	N	0.08118	0	0.09310	P	0.99999166027	B	0.02656	0.0	B	0.01281	0.0	T	0.18241	-1.0343	9	0.19590	T	0.45	-0.328	2.7291	0.05222	0.2036:0.4159:0.0:0.3805	rs7338624;rs52798713;rs7338624	16	Q8TC92	ENOX1_HUMAN	D	16	ENSP00000261488:E16D;ENSP00000415054:E16D	ENSP00000261488:E16D	E	-	3	2	ENOX1	42885003	0.996000	0.38824	0.871000	0.34182	0.975000	0.68041	1.058000	0.30504	0.842000	0.35045	0.655000	0.94253	GAG	C|0.955;G|0.045	0.045	strong		0.498	ENOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044717.2	NM_017993		G	43987003	C	G	43987003	3	3	22	1	0	0	0	0	1	0	0	0	5128	796	28	4	1939	4	ENOX1	13	43987003	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1110007	43987003	71182875	2829	5730											
ZC3H13	23091	hgsc.bcm.edu	37	chr13	46584500	46584500	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gacctctgctggtccaacagGggagaagatactgcagatgt	11	8	13	9	0	1	3	0	0	1	3	2	5	2	3	2	3	4	2	2	3	3	1	rs79878411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:46584500G>A	ENST00000242848.4	-	7	1077	c.729C>T	c.(727-729)ccC>ccT	p.P243P	ZC3H13_ENST00000282007.3_Silent_p.P243P|ZC3H13_ENST00000470308.1_5'UTR			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	243							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)		GGTCCAACAGGGGAGAAGATA	0.403													G|||	41	0.0081869	0.031	0.0	5008	,	,		15604	0.0		0.0	False		,,,				2504	0.0				p.P243P	Esophageal Squamous(187;747 2077 11056 31291 44172)	Atlas-SNP	.											.	ZC3H13	197	.	0			c.C729T						PASS	.	G		117,4289	87.8+/-126.4	1,115,2087	107	99	102		729	-1.8	0.5	13	dbSNP_132	102	0,8600		0,0,4300	no	coding-synonymous	ZC3H13	NM_015070.3		1,115,6387	AA,AG,GG		0.0,2.6555,0.8996		243/1565	46584500	117,12889	2203	4300	6503	SO:0001819	synonymous_variant	23091	exon7			CAACAGGGGAGAA	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.729C>T	13.37:g.46584500G>A		115	0	0		162	70	0.432099	NM_015070	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Silent	SNP	ENST00000242848.4	37																																																																																				G|0.990;A|0.010	0.010	strong		0.403	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070		A	46584500	G	A	46584500	2	1	22	1	0	0	0	0	0	0	0	1	17580	1219	43	2		2	ZC3H13	13	46584500	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2597497	46584500	68585378	2830	5731											
C13orf18	80183	hgsc.bcm.edu	37	chr13	46919719	46919719	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caagtgtcccggcacctgctCgaactcctttaatgcactgc	8	10	8	15	2	0	0	0	0	0	0	3	1	2	0	3	1	4	3	3	1	3	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:46919719C>T	ENST00000429979.1	-	13	2252	c.1648G>A	c.(1648-1650)Gag>Aag	p.E550K	KIAA0226L_ENST00000534925.1_Missense_Mutation_p.E415K|KIAA0226L_ENST00000378781.3_3'UTR|KIAA0226L_ENST00000409879.2_Missense_Mutation_p.E393K|KIAA0226L_ENST00000378784.4_Missense_Mutation_p.E483K|KIAA0226L_ENST00000389908.3_Missense_Mutation_p.E550K|KIAA0226L_ENST00000378787.3_Intron|KIAA0226L_ENST00000378797.2_Intron|KIAA0226L_ENST00000322896.6_Missense_Mutation_p.E393K	NM_025113.2	NP_079389.2	Q9H714	K226L_HUMAN	KIAA0226-like	550										NS(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|pancreas(1)	26						GGCACCTGCTCGAACTCCTTT	0.527																																					p.E550K		Atlas-SNP	.											.	KIAA0226L	63	.	0			c.G1648A						PASS	.						43	42	42					13																	46919719		1942	4138	6080	SO:0001583	missense	80183	exon13			CCTGCTCGAACTC	AK025215	CCDS31970.2, CCDS66543.1, CCDS66544.1, CCDS66545.1, CCDS73569.1	13q14.11	2011-08-09	2011-08-09	2011-08-09	ENSG00000102445	ENSG00000102445			20420	protein-coding gene	gene with protein product			"chromosome 13 open reading frame 18"	C13orf18			Standard	NM_001286766		Approved	FLJ21562	uc010acl.3	Q9H714	OTTHUMG00000016868	ENST00000429979.1:c.1648G>A	13.37:g.46919719C>T	ENSP00000396935:p.Glu550Lys	48	0	0		47	25	0.531915	NM_025113	A8KAG9|A8XR19|B3KS87|Q5W051|Q5W053|Q6PJ74|Q6PK94|Q86XH7|Q8N5J6	Missense_Mutation	SNP	ENST00000429979.1	37	CCDS31970.2	.	.	.	.	.	.	.	.	.	.	C	18.22	3.574834	0.65878	.	.	ENSG00000102445	ENST00000429979;ENST00000378784;ENST00000389908;ENST00000409879;ENST00000322896;ENST00000534925	T;T;T;T	0.46819	0.86;0.87;0.86;0.89	5.35	4.51	0.55191	.	.	.	.	.	T	0.41396	0.1157	M	0.77616	2.38	0.80722	D	1	B;B;P;B;B	0.38677	0.231;0.231;0.642;0.251;0.434	B;B;B;B;B	0.33521	0.064;0.064;0.163;0.041;0.165	T	0.35599	-0.9782	9	0.08179	T	0.78	-17.8147	9.4511	0.38727	0.0:0.8394:0.0:0.1606	.	393;393;550;415;483	B7ZBN5;B7Z6E4;Q9H714;A8KAG9;Q9H714-3	.;.;K226L_HUMAN;.;.	K	550;483;550;393;393;415	ENSP00000396935:E550K;ENSP00000368061:E483K;ENSP00000374558:E550K;ENSP00000437501:E415K	ENSP00000315633:E393K	E	-	1	0	KIAA0226L	45817720	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	3.410000	0.52664	1.251000	0.43983	0.655000	0.94253	GAG	.	.	none		0.527	KIAA0226L-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044809.2	NM_025113		T	46919719	C	T	46919719	3	4	22	1	0	0	0	0	1	0	0	0	1722	893	31	1	352	1	C13orf18	13	46919719	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	335219	46919719	68250159	2831	5732											
FNDC3A	22862	hgsc.bcm.edu	37	chr13	49775997	49775997	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tacaaagacttaatgagtcaAcatcctataaattctgtatt	16	14	4	7	0	2	2	1	1	1	1	3	2	3	2	1	0	2	1	1	0	8	7	rs45604939	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:49775997A>G	ENST00000492622.2	+	24	3354	c.3049A>G	c.(3049-3051)Aca>Gca	p.T1017A	FNDC3A_ENST00000398316.3_Missense_Mutation_p.T961A|FNDC3A_ENST00000541916.1_Missense_Mutation_p.T1017A	NM_001079673.1	NP_001073141.1	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	1017	Fibronectin type-III 8. {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)		TAATGAGTCAACATCCTATAA	0.368													A|||	127	0.0253594	0.0008	0.0476	5008	,	,		15155	0.0		0.0676	False		,,,				2504	0.0256				p.T1017A		Atlas-SNP	.											.	FNDC3A	93	.	0			c.A3049G						PASS	.	A	ALA/THR,ALA/THR	52,4354	50.9+/-86.3	0,52,2151	94	95	94		3049,2881	3.7	1	13	dbSNP_127	94	602,7996	158.2+/-211.7	19,564,3716	yes	missense,missense	FNDC3A	NM_001079673.1,NM_014923.3	58,58	19,616,5867	GG,GA,AA		7.0016,1.1802,5.0292	possibly-damaging,possibly-damaging	1017/1199,961/1143	49775997	654,12350	2203	4299	6502	SO:0001583	missense	22862	exon24			GAGTCAACATCCT	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.3049A>G	13.37:g.49775997A>G	ENSP00000417257:p.Thr1017Ala	116	0	0		149	77	0.516779	NM_001079673	B4DYG1|Q5HYC9|Q5JVF8|Q5JVF9|Q6EVH3|Q6EVH4|Q6N020|Q6P9D5|Q6ZME4|Q9H1W1	Missense_Mutation	SNP	ENST00000492622.2	37	CCDS41886.1	68	0.031135531135531136	1	0.0020325203252032522	18	0.049723756906077346	0	0.0	49	0.06464379947229551	A	22.8	4.334633	0.81801	0.011802	0.070016	ENSG00000102531	ENST00000492622;ENST00000337156;ENST00000541916;ENST00000398316	T;T;T	0.61627	0.09;0.09;0.09	6.16	3.66	0.41972	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.079122	0.52532	D	0.000074	T	0.21509	0.0518	M	0.87547	2.89	0.80722	D	1	D;P	0.64830	0.994;0.597	D;P	0.68765	0.96;0.531	T	0.54794	-0.8240	10	0.48119	T	0.1	-24.27	9.0647	0.36455	0.7455:0.1304:0.0:0.1241	rs45604939	961;1017	Q9Y2H6-2;Q9Y2H6	.;FND3A_HUMAN	A	1017;953;1017;961	ENSP00000417257:T1017A;ENSP00000441831:T1017A;ENSP00000381362:T961A	ENSP00000338579:T953A	T	+	1	0	FNDC3A	48673998	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	8.904000	0.92590	0.515000	0.28320	0.528000	0.53228	ACA	A|0.954;G|0.046	0.046	strong		0.368	FNDC3A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354845.2	NM_014923		G	49775997	A	G	49775997	3	3	22	1	0	0	0	0	1	0	0	0	5977	43	2	3	3150	3	FNDC3A	13	49775997	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2856278	49775997	65393881	2832	5733											
ARL11	115761	hgsc.bcm.edu	37	chr13	50205165	50205165	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gctgagcgcggagacagcaaGagatcttgatccagacagag	13	5	14	9	2	1	6	0	2	1	4	2	8	2	6	1	1	2	2	1	1	1	1	rs35835937	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:50205165G>C	ENST00000282026.1	+	2	917	c.582G>C	c.(580-582)aaG>aaC	p.K194N	ARL11_ENST00000490932.1_Intron	NM_138450.5	NP_612459.1	Q969Q4	ARL11_HUMAN	ADP-ribosylation factor-like 11	194					hematopoietic progenitor cell differentiation (GO:0002244)|small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			kidney(1)|large_intestine(4)|ovary(1)	6		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00174)|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;0.119)|Kidney(9;0.169)	GBM - Glioblastoma multiforme(99;1.67e-09)		GAGACAGCAAGAGATCTTGAT	0.522													G|||	38	0.00758786	0.028	0.0014	5008	,	,		20145	0.0		0.0	False		,,,				2504	0.0				p.K194N		Atlas-SNP	.											.	ARL11	26	.	0			c.G582C						PASS	.	G	ASN/LYS	90,4200		1,88,2056	6	6	6		582	0.8	0	13	dbSNP_126	6	0,8320		0,0,4160	yes	missense	ARL11	NM_138450.5	94	1,88,6216	CC,CG,GG		0.0,2.0979,0.7137	benign	194/197	50205165	90,12520	2145	4160	6305	SO:0001583	missense	115761	exon2			CAGCAAGAGATCT	AF441378	CCDS9419.1	13q14.12	2014-05-09			ENSG00000152213	ENSG00000152213		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	24046	protein-coding gene	gene with protein product		609351				12477932	Standard	NM_138450		Approved	ARLTS1, FLJ33930	uc001vdf.2	Q969Q4	OTTHUMG00000016919	ENST00000282026.1:c.582G>C	13.37:g.50205165G>C	ENSP00000282026:p.Lys194Asn	167	0	0		160	91	0.56875	NM_138450		Missense_Mutation	SNP	ENST00000282026.1	37	CCDS9419.1	15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	G	12.80	2.047801	0.36085	0.020979	0.0	ENSG00000152213	ENST00000282026	T	0.61158	0.13	4.85	0.84	0.18912	.	.	.	.	.	T	0.17280	0.0415	N	0.22421	0.69	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.20140	-1.0284	9	0.87932	D	0	.	5.8114	0.18467	0.1723:0.2988:0.5288:0.0	rs35835937	194	Q969Q4	ARL11_HUMAN	N	194	ENSP00000282026:K194N	ENSP00000282026:K194N	K	+	3	2	ARL11	49103166	0.006000	0.16342	0.000000	0.03702	0.014000	0.08584	0.717000	0.25851	0.195000	0.20347	0.561000	0.74099	AAG	G|0.993;C|0.007	0.007	strong		0.522	ARL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044929.2	NM_138450		C	50205165	G	C	50205165	3	2	22	1	0	0	0	0	1	0	0	0	927	933	33	4	584	4	ARL11	13	50205165	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	429168	50205165	64964713	2833	5734											
FAM124A	220108	hgsc.bcm.edu	37	chr13	51855114	51855114	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aaagatgcagcagccactggGcagctcacaaggattccagg	13	5	12	11	0	1	1	1	0	0	1	2	2	2	2	2	3	4	4	2	3	2	1	rs74087446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:51855114G>T	ENST00000322475.8	+	4	1498	c.1363G>T	c.(1363-1365)Gca>Tca	p.A455S	FAM124A_ENST00000280057.6_Missense_Mutation_p.A491S	NM_001242312.1	NP_001229241.1	Q86V42	F124A_HUMAN	family with sequence similarity 124A	455										breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|skin(1)	26		Acute lymphoblastic leukemia(7;0.000334)|Breast(56;0.00156)|Prostate(109;0.00538)|Lung NSC(96;0.0216)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;4.25e-07)		CAGCCACTGGGCAGCTCACAA	0.587													G|||	93	0.0185703	0.0696	0.0014	5008	,	,		18065	0.0		0.0	False		,,,				2504	0.0				p.A491S		Atlas-SNP	.											.	FAM124A	61	.	0			c.G1471T						PASS	.	G	SER/ALA,SER/ALA	315,4091	168.3+/-199.2	15,285,1903	55	54	54		1363,1471	-8.6	0	13	dbSNP_130	54	0,8600		0,0,4300	yes	missense,missense	FAM124A	NM_001242312.1,NM_145019.3	99,99	15,285,6203	TT,TG,GG		0.0,7.1493,2.422	benign,benign	455/547,491/583	51855114	315,12691	2203	4300	6503	SO:0001583	missense	220108	exon5			CACTGGGCAGCTC	AK096364	CCDS9427.1, CCDS55900.1	13q14.3	2006-08-11			ENSG00000150510	ENSG00000150510			26413	protein-coding gene	gene with protein product						12975309	Standard	NM_145019		Approved	FLJ30707	uc001vff.2	Q86V42	OTTHUMG00000016942	ENST00000322475.8:c.1363G>T	13.37:g.51855114G>T	ENSP00000324625:p.Ala455Ser	113	0	0		111	51	0.459459	NM_145019	A2A324|Q8N8P9|Q8NE66|Q96NJ9	Missense_Mutation	SNP	ENST00000322475.8	37	CCDS55900.1	38	0.0173992673992674	37	0.07520325203252033	1	0.0027624309392265192	0	0.0	0	0.0	G	6.025	0.373042	0.11409	0.071493	0.0	ENSG00000150510	ENST00000322475;ENST00000280057	T;T	0.39406	1.13;1.08	5.07	-8.56	0.00904	.	2.466230	0.01371	N	0.012590	T	0.00440	0.0014	N	0.00368	-1.59	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.001;0.002	T	0.13818	-1.0495	10	0.05620	T	0.96	-11.5191	5.727	0.18018	0.0847:0.4204:0.3398:0.1551	.	455;491	Q86V42;Q86V42-2	F124A_HUMAN;.	S	455;491	ENSP00000324625:A455S;ENSP00000280057:A491S	ENSP00000280057:A491S	A	+	1	0	FAM124A	50753115	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.686000	0.05161	-1.642000	0.01521	-0.284000	0.09977	GCA	G|0.975;T|0.026	0.026	strong		0.587	FAM124A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045019.3	NM_145019		T	51855114	G	T	51855114	3	4	22	1	0	0	0	0	1	0	0	0	5430	1203	42	4	1489	4	FAM124A	13	51855114	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1649949	51855114	63314764	2834	5735											
SERPINE3	647174	hgsc.bcm.edu	37	chr13	51936079	51936079	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ataatttatcagtgtctctcTagcaacaagggctcatttgt	11	15	7	8	0	4	0	2	0	2	0	5	0	4	0	0	1	2	2	0	1	5	5	rs74084815	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:51936079T>C	ENST00000521255.1	+	7	1281	c.1221T>C	c.(1219-1221)tcT>tcC	p.S407S	RP11-24B19.3_ENST00000602636.1_RNA|SERPINE3_ENST00000524365.1_Intron|SERPINE3_ENST00000400389.4_Intron|RP11-24B19.4_ENST00000602881.1_RNA	NM_001101320.1	NP_001094790.1	A8MV23	SERP3_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 3	407					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						AGTGTCTCTCTAGCAACAAGG	0.378													T|||	41	0.0081869	0.031	0.0	5008	,	,		16300	0.0		0.0	False		,,,				2504	0.0				p.S407S		Atlas-SNP	.											.	SERPINE3	37	.	0			c.T1221C						PASS	.	T	,,	102,3578		2,98,1740	133	120	124		,1221,	3.2	0.9	13	dbSNP_130	124	0,8172		0,0,4086	no	utr-3,coding-synonymous,utr-3	INTS6,SERPINE3	NM_001039937.1,NM_001101320.1,NM_012141.2	,,	2,98,5826	CC,CT,TT		0.0,2.7717,0.8606	,,	,407/425,	51936079	102,11750	1840	4086	5926	SO:0001819	synonymous_variant	647174	exon7			TCTCTCTAGCAAC	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.1221T>C	13.37:g.51936079T>C		222	1	0.0045045		202	95	0.470297	NM_001101320	B1V8P3	Silent	SNP	ENST00000521255.1	37	CCDS53870.1																																																																																			T|0.992;C|0.008	0.008	strong		0.378	SERPINE3-001	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045021.2	NM_001101320		C	51936079	T	C	51936079	2	2	22	1	0	0	0	0	0	0	0	1	14128	1509	53	3		3	SERPINE3	13	51936079	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	80965	51936079	63233799	2835	5736											
ALG11	440138	hgsc.bcm.edu	37	chr13	52598668	52598668	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactaaaccatattctctcaCtatggaaagttgggaattgc	13	12	7	9	0	2	0	1	0	1	0	3	2	2	2	1	2	2	1	1	2	6	6	rs148434423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:52598668C>A	ENST00000521508.1	+	3	807	c.802C>A	c.(802-804)Cta>Ata	p.L268I	UTP14C_ENST00000521776.2_5'Flank|ALG11_ENST00000523764.1_Intron|ALG11_ENST00000519151.1_3'UTR	NM_001004127.2	NP_001004127.2	Q2TAA5	ALG11_HUMAN	ALG11, alpha-1,2-mannosyltransferase	268					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)		TATTCTCTCACTATGGAAAGT	0.378													C|||	2	0.000399361	0.0015	0.0	5008	,	,		22470	0.0		0.0	False		,,,				2504	0.0				p.L268I		Atlas-SNP	.											.	ALG11	39	.	0			c.C802A						PASS	.	C	ILE/LEU	8,4398	15.5+/-35.6	0,8,2195	120	111	114		802	5.2	1	13	dbSNP_134	114	0,8600		0,0,4300	yes	missense	ALG11	NM_001004127.2	5	0,8,6495	AA,AC,CC		0.0,0.1816,0.0615	possibly-damaging	268/493	52598668	8,12998	2203	4300	6503	SO:0001583	missense	440138	exon3			CTCTCACTATGGA	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.802C>A	13.37:g.52598668C>A	ENSP00000430236:p.Leu268Ile	223	0	0		216	100	0.462963	NM_001004127	A5PLP3|B4DKW9|Q5TAN9|Q6DKI6|Q96FI7	Missense_Mutation	SNP	ENST00000521508.1	37	CCDS31977.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	12.85	2.062733	0.36373	0.001816	0.0	ENSG00000253710	ENST00000521508	T	0.80304	-1.36	6.03	5.19	0.71726	.	0.000000	0.64402	U	0.000002	T	0.81517	0.4839	L	0.50993	1.605	0.80722	D	1	D	0.57571	0.98	P	0.52309	0.695	T	0.78563	-0.2156	10	0.20519	T	0.43	.	15.3059	0.73992	0.0:0.9333:0.0:0.0667	.	268	Q2TAA5	ALG11_HUMAN	I	268	ENSP00000430236:L268I	ENSP00000430236:L268I	L	+	1	2	ALG11	51496669	0.993000	0.37304	0.970000	0.41538	0.930000	0.56654	3.054000	0.49908	1.569000	0.49696	0.557000	0.71058	CTA	C|0.999;A|0.001	0.001	strong		0.378	ALG11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045050.1	NM_001004127		A	52598668	C	A	52598668	3	1	22	1	0	0	0	0	1	0	0	0	513	564	20	4	812	4	ALG11	13	52598668	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	662589	52598668	62571210	2836	5737											
TBC1D4	9882	hgsc.bcm.edu	37	chr13	75861001	75861001	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagcaacaggtcacaattgActagagcatccgcgggcagc	12	6	11	12	2	2	2	2	1	0	1	3	2	3	2	1	2	4	3	1	2	3	2	rs557337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:75861001A>G	ENST00000377636.3	-	21	4170	c.3824T>C	c.(3823-3825)gTc>gCc	p.V1275A	TBC1D4_ENST00000425511.1_Missense_Mutation_p.V439A|TBC1D4_ENST00000431480.2_Missense_Mutation_p.V1267A|TBC1D4_ENST00000377625.2_Missense_Mutation_p.V1212A	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	1275			V -> A (in dbSNP:rs557337). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:19077034, ECO:0000269|PubMed:9628581}.		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)		GTCACAATTGACTAGAGCATC	0.463													G|||	873	0.174321	0.556	0.0778	5008	,	,		16760	0.0		0.0666	False		,,,				2504	0.0174				p.V1275A		Atlas-SNP	.											.	TBC1D4	142	.	0			c.T3824C						PASS	.	G	ALA/VAL	1770,2058		428,914,572	104	107	106		3824	3.9	0	13	dbSNP_83	106	484,7778		13,458,3660	yes	missense	TBC1D4	NM_014832.2	64	441,1372,4232	GG,GA,AA		5.8581,46.2382,18.6435	benign	1275/1299	75861001	2254,9836	1914	4131	6045	SO:0001583	missense	9882	exon21			CAATTGACTAGAG	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.3824T>C	13.37:g.75861001A>G	ENSP00000366863:p.Val1275Ala	312	0	0		333	166	0.498498	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Missense_Mutation	SNP	ENST00000377636.3	37	CCDS41901.1	333	0.15247252747252749	256	0.5203252032520326	32	0.08839779005524862	0	0.0	45	0.059366754617414245	G	0.218	-1.030972	0.02029	0.462382	0.058581	ENSG00000136111	ENST00000377636;ENST00000431480;ENST00000377625;ENST00000425511	T;T;T;T	0.03358	4.23;4.23;4.23;3.96	5.63	3.87	0.44632	.	0.297360	0.28841	N	0.013979	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	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	0.38329	-0.9666	9	0.02654	T	1	-5.6523	10.4567	0.44555	0.2148:0.0:0.7852:0.0	rs557337;rs52811417;rs60191388;rs557337	439;1212;1267;1275	O60343-4;O60343-2;O60343-3;O60343	.;.;.;TBCD4_HUMAN	A	1275;1267;1212;439	ENSP00000366863:V1275A;ENSP00000395986:V1267A;ENSP00000366852:V1212A;ENSP00000390654:V439A	ENSP00000366852:V1212A	V	-	2	0	TBC1D4	74759002	1.000000	0.71417	0.008000	0.14137	0.004000	0.04260	4.134000	0.57990	0.847000	0.35167	-0.119000	0.15052	GTC	A|0.827;G|0.173	0.173	strong		0.463	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832		G	75861001	A	G	75861001	3	3	22	1	0	0	0	0	1	0	0	0	15637	275	10	3	76	3	TBC1D4	13	75861001	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	23262333	75861001	39308877	2837	5738											
LMO7	4008	hgsc.bcm.edu	37	chr13	76195833	76195833	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttttattacaactgctatgAagaaaattaggatatgccat	15	15	6	5	0	0	2	0	1	0	1	0	3	0	3	1	1	4	1	1	1	9	7	rs143470231	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:76195833A>G	ENST00000341547.4	+	1	1264	c.4A>G	c.(4-6)Aag>Gag	p.K2E	LMO7_ENST00000357063.3_Missense_Mutation_p.K2E|RP11-173B14.5_ENST00000568302.1_RNA|LMO7_ENST00000377534.3_Missense_Mutation_p.K2E|RP11-173B14.5_ENST00000568735.1_RNA|RP11-29G8.3_ENST00000563635.1_RNA	NM_005358.5	NP_005349.3	Q8WWI1	LMO7_HUMAN	LIM domain 7	2					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)		AACTGCTATGAAGAAAATTAG	0.363													A|||	57	0.0113818	0.0378	0.0101	5008	,	,		17645	0.0		0.0	False		,,,				2504	0.0				p.K2E		Atlas-SNP	.											LMO7_ENST00000357063,colon,carcinoma,-2,2	LMO7	334	2	0			c.A4G						PASS	.	A	GLU/LYS	168,4238	101.6+/-140.2	4,160,2039	40	38	39		4	1	0.2	13	dbSNP_134	39	0,8600		0,0,4300	yes	missense	LMO7	NM_005358.5	56	4,160,6339	GG,GA,AA		0.0,3.813,1.2917		2/1350	76195833	168,12838	2203	4300	6503	SO:0001583	missense	4008	exon1			GCTATGAAGAAAA	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	ENST00000341547.4:c.4A>G	13.37:g.76195833A>G	ENSP00000342112:p.Lys2Glu	33	0	0		28	13	0.464286	NM_005358	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000341547.4	37	CCDS9454.1	18	0.008241758241758242	16	0.032520325203252036	2	0.0055248618784530384	0	0.0	0	0.0	A	15.96	2.985987	0.53934	0.03813	0.0	ENSG00000136153	ENST00000341547;ENST00000357063;ENST00000377534	T;T;T	0.35048	1.33;1.39;1.44	5.23	1.02	0.19986	.	.	.	.	.	T	0.11707	0.0285	.	.	.	0.09310	N	1	D	0.57257	0.979	P	0.53266	0.722	T	0.11891	-1.0569	8	0.87932	D	0	.	1.7898	0.03049	0.5679:0.1723:0.0937:0.166	.	2	Q8WWI1-3	.	E	2	ENSP00000342112:K2E;ENSP00000349571:K2E;ENSP00000366757:K2E	ENSP00000342112:K2E	K	+	1	0	LMO7	75093834	0.987000	0.35691	0.226000	0.23910	0.335000	0.28730	2.364000	0.44187	0.796000	0.33947	0.460000	0.39030	AAG	A|0.987;G|0.013	0.013	strong		0.363	LMO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045297.1	NM_005358		G	76195833	A	G	76195833	3	3	22	1	0	0	0	0	1	0	0	0	8864	247	9	3	6	3	LMO7	13	76195833	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	334832	76195833	38974045	2838	5739											
NDFIP2	54602	hgsc.bcm.edu	37	chr13	80094993	80094993	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	catcggctatagagcagccaCctacttcaaacccagcaccg	12	6	7	16	2	1	1	1	0	0	1	2	1	1	1	4	1	5	3	4	1	4	4	rs55887763	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:80094993C>T	ENST00000218652.7	+	2	422	c.370C>T	c.(370-372)Cct>Tct	p.P124S	NDFIP2_ENST00000494647.1_3'UTR	NM_001161407.1|NM_019080.2	NP_001154879.1|NP_061953.2	Q9NV92	NFIP2_HUMAN	Nedd4 family interacting protein 2	124			P -> S (in dbSNP:rs55887763).		negative regulation of gene expression (GO:0010629)|negative regulation of protein transport (GO:0051224)|negative regulation of transporter activity (GO:0032410)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)	signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			NS(1)|breast(1)|endometrium(2)|kidney(3)|lung(3)|ovary(2)|prostate(1)|skin(1)	14		Acute lymphoblastic leukemia(28;0.205)		GBM - Glioblastoma multiforme(99;0.0196)		AGAGCAGCCACCTACTTCAAA	0.403													T|||	254	0.0507188	0.1838	0.0101	5008	,	,		15571	0.0		0.004	False		,,,				2504	0.0				p.P124S		Atlas-SNP	.											.	NDFIP2	23	.	0			c.C370T						PASS	.	T	SER/PRO,SER/PRO	641,3765	767.1+/-413.5	43,555,1605	89	82	84		370,370	5.8	0.3	13	dbSNP_129	84	2,8598	819.2+/-406.8	0,2,4298	yes	missense,missense	NDFIP2	NM_001161407.1,NM_019080.2	74,74	43,557,5903	TT,TC,CC		0.0233,14.5483,4.9439	benign,benign	124/317,124/337	80094993	643,12363	2203	4300	6503	SO:0001583	missense	54602	exon2			CAGCCACCTACTT	AB032991	CCDS31998.1	13q22.1	2011-05-18			ENSG00000102471	ENSG00000102471			18537	protein-coding gene	gene with protein product		610041				10574461, 12050153	Standard	NM_019080		Approved	KIAA1165, N4wbp5a	uc001vlf.3	Q9NV92	OTTHUMG00000017136	ENST00000218652.7:c.370C>T	13.37:g.80094993C>T	ENSP00000218652:p.Pro124Ser	110	0	0		117	57	0.487179	NM_019080	Q7Z2H3|Q7Z428|Q8TAR3|Q9ULQ5	Missense_Mutation	SNP	ENST00000218652.7	37	CCDS31998.1	102	0.046703296703296704	99	0.20121951219512196	3	0.008287292817679558	0	0.0	0	0.0	T	1.479	-0.557610	0.03967	0.145483	2.33E-4	ENSG00000102471	ENST00000218652;ENST00000487865	T;T	0.25912	1.78;1.77	5.75	5.75	0.90469	.	0.192068	0.47455	N	0.000229	T	0.00012	0.0000	N	0.00210	-1.845	0.49213	P	2.3799999999996047E-4	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29274	-1.0017	9	0.02654	T	1	-11.3844	11.0315	0.47776	0.0:0.0739:0.0:0.9261	rs55887763;rs58237612	30;124	B4DGY6;Q9NV92	.;NFIP2_HUMAN	S	124;41	ENSP00000218652:P124S;ENSP00000419200:P41S	ENSP00000218652:P124S	P	+	1	0	NDFIP2	78992994	0.995000	0.38212	0.331000	0.25455	0.299000	0.27559	3.411000	0.52672	1.003000	0.39130	-0.254000	0.11334	CCT	C|0.952;T|0.048	0.048	strong		0.403	NDFIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045380.2			T	80094993	C	T	80094993	3	4	22	1	0	0	0	0	1	0	0	0	10255	507	18	2	376	2	NDFIP2	13	80094993	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3899160	80094993	35074885	2839	5740											
ABCC4	10257	hgsc.bcm.edu	37	chr13	95696540	95696540	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cttggatccacatttgccgtCgcttcatcaataatcaatat	11	14	5	11	2	3	0	3	0	0	0	5	1	4	1	2	1	1	1	2	1	4	5	rs11568695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:95696540C>T	ENST00000376887.4	-	28	3723	c.3609G>A	c.(3607-3609)gcG>gcA	p.A1203A	ABCC4_ENST00000412704.1_Silent_p.A1156A	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	1203	ABC transporter 2. {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)	CATTTGCCGTCGCTTCATCAA	0.398													C|||	225	0.0449281	0.1604	0.013	5008	,	,		19815	0.001		0.002	False		,,,				2504	0.001				p.A1203A		Atlas-SNP	.											ABCC4_ENST00000376887,colon,carcinoma,-1,2	ABCC4	248	2	0			c.G3609A						PASS	.	C		644,3762	270.4+/-269.6	52,540,1611	72	64	66		3609	-6.7	0.9	13	dbSNP_126	66	10,8590	7.1+/-27.0	0,10,4290	no	coding-synonymous	ABCC4	NM_005845.3		52,550,5901	TT,TC,CC		0.1163,14.6164,5.0284		1203/1326	95696540	654,12352	2203	4300	6503	SO:0001819	synonymous_variant	10257	exon28			TGCCGTCGCTTCA	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.3609G>A	13.37:g.95696540C>T		127	0	0		111	54	0.486486	NM_005845	A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Silent	SNP	ENST00000376887.4	37	CCDS9474.1																																																																																			C|0.950;T|0.050	0.050	strong		0.398	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045478.2	NM_005845		T	95696540	C	T	95696540	2	4	22	1	0	0	0	0	0	0	0	1	55	871	31	1		1	ABCC4	13	95696540	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	15601547	95696540	19473338	2840	5741											
UGGT2	55757	hgsc.bcm.edu	37	chr13	96508566	96508566	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctagttcatatcggaatccaTactctttagccatgtgagga	11	13	8	9	1	2	1	1	1	1	0	4	3	3	3	2	2	2	1	2	2	5	6	rs35123499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:96508566T>A	ENST00000376747.3	-	34	3924	c.3854A>T	c.(3853-3855)tAt>tTt	p.Y1285F		NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	1285	Glucosyltransferase.		Y -> F (in dbSNP:rs35123499).		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						TCGGAATCCATACTCTTTAGC	0.348													T|||	91	0.0181709	0.0666	0.0029	5008	,	,		15927	0.0		0.001	False		,,,				2504	0.0				p.Y1285F		Atlas-SNP	.											.	UGGT2	127	.	0			c.A3854T						PASS	.	T	PHE/TYR	247,4159	142.7+/-177.9	6,235,1962	112	119	116		3854	5.2	1	13	dbSNP_126	116	0,8600		0,0,4300	yes	missense	UGGT2	NM_020121.3	22	6,235,6262	AA,AT,TT		0.0,5.606,1.8991	probably-damaging	1285/1517	96508566	247,12759	2203	4300	6503	SO:0001583	missense	55757	exon34			AATCCATACTCTT	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.3854A>T	13.37:g.96508566T>A	ENSP00000365938:p.Tyr1285Phe	133	0	0		177	88	0.497175	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	37	CCDS9480.1	31	0.014194139194139194	30	0.06097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	T	25.9	4.680767	0.88542	0.05606	0.0	ENSG00000102595	ENST00000376747	T	0.40756	1.02	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.14614	0.0353	L	0.53671	1.685	0.80722	D	1	D	0.71674	0.998	D	0.80764	0.994	T	0.41106	-0.9527	10	0.87932	D	0	-16.5421	15.0092	0.71536	0.0:0.0:0.0:1.0	rs35123499	1285	Q9NYU1	UGGG2_HUMAN	F	1285	ENSP00000365938:Y1285F	ENSP00000365938:Y1285F	Y	-	2	0	UGGT2	95306567	1.000000	0.71417	0.998000	0.56505	0.950000	0.60333	7.698000	0.84413	1.936000	0.56123	0.533000	0.62120	TAT	T|0.980;A|0.020	0.020	strong		0.348	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121		A	96508566	T	A	96508566	3	1	22	1	0	0	0	0	1	0	0	0	16957	1406	49	5	720	5	UGGT2	13	96508566	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	812026	96508566	18661312	2841	5742											
UGGT2	55757	hgsc.bcm.edu	37	chr13	96648384	96648384	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcctctacagtagtattagTcacagctacattttggaaac	13	13	6	9	0	2	0	1	0	1	0	3	1	3	1	1	1	4	3	1	1	6	7	rs73562939	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:96648384T>C	ENST00000376747.3	-	7	833	c.763A>G	c.(763-765)Act>Gct	p.T255A	UGGT2_ENST00000376714.3_Missense_Mutation_p.T255A|UGGT2_ENST00000467305.1_5'UTR|UGGT2_ENST00000376712.4_Missense_Mutation_p.T255A|UGGT2_ENST00000397618.3_Missense_Mutation_p.T255A	NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	255					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						GTAGTATTAGTCACAGCTACA	0.328													T|||	102	0.0203674	0.0749	0.0029	5008	,	,		18668	0.0		0.001	False		,,,				2504	0.0				p.T255A		Atlas-SNP	.											.	UGGT2	127	.	0			c.A763G						PASS	.	T	ALA/THR	288,4116	158.1+/-190.9	10,268,1924	117	127	124		763	5.8	0.9	13	dbSNP_130	124	0,8598		0,0,4299	yes	missense	UGGT2	NM_020121.3	58	10,268,6223	CC,CT,TT		0.0,6.5395,2.215	benign	255/1517	96648384	288,12714	2202	4299	6501	SO:0001583	missense	55757	exon7			TATTAGTCACAGC	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.763A>G	13.37:g.96648384T>C	ENSP00000365938:p.Thr255Ala	212	0	0		215	98	0.455814	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	37	CCDS9480.1	35	0.016025641025641024	34	0.06910569105691057	1	0.0027624309392265192	0	0.0	0	0.0	T	13.13	2.145554	0.37923	0.065395	0.0	ENSG00000102595	ENST00000376747;ENST00000376714;ENST00000397618;ENST00000376712	T;T	0.29397	1.57;1.57	5.84	5.84	0.93424	.	0.872316	0.10306	N	0.690619	T	0.02970	0.0088	L	0.60845	1.875	0.31130	N	0.707877	P;P;B	0.42692	0.787;0.787;0.004	B;B;B	0.36567	0.228;0.228;0.004	T	0.11966	-1.0566	10	0.87932	D	0	-2.0224	15.19	0.73035	0.0:0.0:0.0:1.0	.	255;255;255	Q2TAA6;E7EMU6;Q9NYU1	.;.;UGGG2_HUMAN	A	255	ENSP00000365938:T255A;ENSP00000380743:T255A	ENSP00000365902:T255A	T	-	1	0	UGGT2	95446385	0.651000	0.27340	0.866000	0.34008	0.846000	0.48090	2.811000	0.47986	2.231000	0.72958	0.397000	0.26171	ACT	T|0.976;C|0.024	0.024	strong		0.328	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121		C	96648384	T	C	96648384	3	2	22	1	0	0	0	0	1	0	0	0	16957	1667	58	3	3919	3	UGGT2	13	96648384	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	139818	96648384	18521494	2842	5743											
PCCA	5095	hgsc.bcm.edu	37	chr13	100992428	100992428	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggacacatgctaaccaagAgtgagaagaaccagttattg	16	7	10	8	0	0	3	0	1	0	3	0	5	0	4	2	1	3	2	2	1	5	3	rs112237881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:100992428A>T	ENST00000376285.1	+	18	1596	c.1558A>T	c.(1558-1560)Agt>Tgt	p.S520C	PCCA_ENST00000376286.4_Missense_Mutation_p.S494C|PCCA_ENST00000376279.3_Missense_Mutation_p.S520C	NM_000282.3	NP_000273.2	P05165	PCCA_HUMAN	propionyl CoA carboxylase, alpha polypeptide	520					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)	GCTAACCAAGAGTGAGAAGAA	0.348													A|||	14	0.00279553	0.0098	0.0014	5008	,	,		20036	0.0		0.0	False		,,,				2504	0.0				p.S520C		Atlas-SNP	.											.	PCCA	59	.	0			c.A1558T						PASS	.	A	CYS/SER,CYS/SER,CYS/SER	18,4388	25.3+/-52.1	0,18,2185	145	133	137		1558,1480,1558	4.1	0	13	dbSNP_132	137	0,8600		0,0,4300	yes	missense,missense,missense	PCCA	NM_000282.3,NM_001127692.2,NM_001178004.1	112,112,112	0,18,6485	TT,TA,AA		0.0,0.4085,0.1384	benign,benign,benign	520/729,494/703,520/682	100992428	18,12988	2203	4300	6503	SO:0001583	missense	5095	exon18			ACCAAGAGTGAGA	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.1558A>T	13.37:g.100992428A>T	ENSP00000365462:p.Ser520Cys	88	0	0		94	43	0.457447	NM_001178004	B4DKY8|B4DPF9|C9JPQ8|Q15979|Q8WXQ7	Missense_Mutation	SNP	ENST00000376285.1	37	CCDS9496.2	6|6	0.0027472527472527475|0.0027472527472527475	5|5	0.01016260162601626|0.01016260162601626	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	A|A	11.63|11.63	1.697151|1.697151	0.30142|0.30142	0.004085|0.004085	0.0|0.0	ENSG00000175198|ENSG00000175198	ENST00000443601|ENST00000376286;ENST00000376279;ENST00000376285;ENST00000424527;ENST00000376254;ENST00000536640	.|D;D;D;D	.|0.97186	.|-4.27;-4.25;-4.28;-1.72	5.3|5.3	4.08|4.08	0.47627|0.47627	.|.	.|1.227710	.|0.05174	.|N	.|0.499995	D|D	0.94165|0.94165	0.8128|0.8128	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.29886	.|0.26;0.221;0.26	.|B;B;B	.|0.41440	.|0.246;0.357;0.246	D|D	0.88437|0.88437	0.3039|0.3039	5|10	.|0.66056	.|D	.|0.02	.|.	11.3631|11.3631	0.49655|0.49655	0.693:0.307:0.0:0.0|0.693:0.307:0.0:0.0	.|.	.|520;494;520	.|C9JPQ8;P05165-2;P05165	.|.;.;PCCA_HUMAN	S|C	111|494;520;520;54;111;16	.|ENSP00000365463:S494C;ENSP00000365456:S520C;ENSP00000365462:S520C;ENSP00000396050:S54C	.|ENSP00000365430:S111C	R|S	+|+	3|1	2|0	PCCA|PCCA	99790429|99790429	0.447000|0.447000	0.25673|0.25673	0.022000|0.022000	0.16811|0.16811	0.327000|0.327000	0.28475|0.28475	1.075000|1.075000	0.30716|0.30716	0.923000|0.923000	0.37045|0.37045	0.528000|0.528000	0.53228|0.53228	AGA|AGT	A|0.997;T|0.003	0.003	strong		0.348	PCCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045627.2			T	100992428	A	T	100992428	3	4	22	1	0	0	0	0	1	0	0	0	11513	304	11	5	1628	5	PCCA	13	100992428	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	4344044	100992428	14177450	2843	5744											
ERCC5	2073	hgsc.bcm.edu	37	chr13	103506690	103506690	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaagagaaaacgacctctatGttttgcctcctttacaagag	13	11	8	9	1	1	2	0	0	1	2	2	5	2	2	3	0	3	1	3	0	6	5	rs4987063	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:103506690G>A	ENST00000355739.4	+	4	1856	c.433G>A	c.(433-435)Gtt>Att	p.V145I	ERCC5_ENST00000535557.1_Missense_Mutation_p.V145I|BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.C570Y	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	145			V -> I (in dbSNP:rs4987063).		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)					CGACCTCTATGTTTTGCCTCC	0.363			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				G|||	35	0.00698882	0.0257	0.0014	5008	,	,		19977	0.0		0.0	False		,,,				2504	0.0				p.V599I		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.G1795A						PASS	.	G	ILE/VAL,ILE/VAL	91,4315	74.7+/-112.8	2,87,2114	123	116	118		1795,433	2.4	0.2	13	dbSNP_111	118	0,8600		0,0,4300	yes	missense,missense	ERCC5,BIVM-ERCC5	NM_001204425.1,NM_000123.3	29,29	2,87,6414	AA,AG,GG		0.0,2.0654,0.6997	benign,benign	599/1641,145/1187	103506690	91,12915	2203	4300	6503	SO:0001583	missense	0	exon12	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	CTCTATGTTTTGC	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.433G>A	13.37:g.103506690G>A	ENSP00000347978:p.Val145Ile	93	0	0		96	35	0.364583	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Missense_Mutation	SNP	ENST00000355739.4	37	CCDS32004.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	G	4.272	0.049520	0.08243	0.020654	0.0	ENSG00000134899	ENST00000418659;ENST00000355739;ENST00000535557	T;T	0.23147	3.49;1.92	6.03	2.39	0.29439	.	0.420080	0.25570	N	0.029763	T	0.07413	0.0187	L	0.28556	0.865	0.26071	N	0.981225	B;B;B	0.22080	0.038;0.064;0.051	B;B;B	0.23275	0.045;0.014;0.01	T	0.18209	-1.0344	10	0.25751	T	0.34	-2.6138	5.2232	0.15379	0.2217:0.0:0.6337:0.1446	rs4987063	145;145;570	B4DSI5;P28715;Q59FZ7	.;ERCC5_HUMAN;.	I	570;145;145	ENSP00000347978:V145I;ENSP00000442117:V145I	ENSP00000347978:V145I	V	+	1	0	ERCC5	102304691	0.999000	0.42202	0.227000	0.23927	0.161000	0.22273	3.038000	0.49783	0.424000	0.26061	-0.136000	0.14681	GTT	G|0.993;A|0.007	0.007	strong		0.363	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1			A	103506690	G	A	103506690	3	1	22	1	0	0	0	0	1	0	0	0	5218	1377	48	2	447	2	ERCC5	13	103506690	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2514262	103506690	11663188	2844	5745											
ERCC5	2073	hgsc.bcm.edu	37	chr13	103514939	103514939	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaacaaatgtcacttgttcaCgtggggactgaagcctttcc	10	11	10	10	1	2	1	2	1	0	0	3	3	3	2	2	2	2	1	2	2	3	3	rs4150316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:103514939C>T	ENST00000355739.4	+	8	2863	c.1440C>T	c.(1438-1440)caC>caT	p.H480H	BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.R906C|ERCC5_ENST00000375954.1_5'Flank	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	480					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)					CACTTGTTCACGTGGGGACTG	0.493			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				C|||	180	0.0359425	0.1331	0.0043	5008	,	,		20640	0.0		0.001	False		,,,				2504	0.0				p.H934H		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.C2802T						PASS	.	C	,	495,3911	228.8+/-243.5	32,431,1740	71	60	64		1440,2802	-10.5	0	13	dbSNP_110	64	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous,coding-synonymous	ERCC5,BIVM-ERCC5	NM_000123.3,NM_001204425.1	,	32,444,6027	TT,TC,CC		0.1512,11.2347,3.9059	,	480/1187,934/1641	103514939	508,12498	2203	4300	6503	SO:0001819	synonymous_variant	0	exon16	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	TGTTCACGTGGGG	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.1440C>T	13.37:g.103514939C>T		111	0	0		120	69	0.575	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Silent	SNP	ENST00000355739.4	37	CCDS32004.1																																																																																			C|0.959;T|0.041	0.041	strong		0.493	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1			T	103514939	C	T	103514939	2	4	22	1	0	0	0	0	0	0	0	1	5218	535	19	1		1	ERCC5	13	103514939	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	8249	103514939	11654939	2845	5746											
ERCC5	2073	hgsc.bcm.edu	37	chr13	103518036	103518036	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggaagtttcattgaagtgcaAagtgtgattagtgatgagga	13	12	14	2	0	1	4	1	4	0	0	1	6	1	6	0	2	1	2	0	2	4	3	rs55686372	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:103518036A>G	ENST00000355739.4	+	9	3397	c.1974A>G	c.(1972-1974)caA>caG	p.Q658Q	BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.K1084E|ERCC5_ENST00000375954.1_5'UTR	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	658					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)					TTGAAGTGCAAAGTGTGATTA	0.413			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				A|||	27	0.00539137	0.0197	0.0014	5008	,	,		18928	0.0		0.0	False		,,,				2504	0.0				p.Q1112Q		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.A3336G						PASS	.	A	,	74,4332	64.1+/-101.4	2,70,2131	33	32	32		1974,3336	-1.4	0.5	13	dbSNP_129	32	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ERCC5,BIVM-ERCC5	NM_000123.3,NM_001204425.1	,	2,70,6431	GG,GA,AA		0.0,1.6795,0.569	,	658/1187,1112/1641	103518036	74,12932	2203	4300	6503	SO:0001819	synonymous_variant	0	exon17	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	AGTGCAAAGTGTG	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.1974A>G	13.37:g.103518036A>G		61	0	0		63	29	0.460317	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Silent	SNP	ENST00000355739.4	37	CCDS32004.1																																																																																			A|0.995;G|0.005	0.005	strong		0.413	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1			G	103518036	A	G	103518036	2	3	22	1	0	0	0	0	0	0	0	1	5218	11	1	3		3	ERCC5	13	103518036	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	3097	103518036	11651842	2846	5747											
ERCC5	2073	hgsc.bcm.edu	37	chr13	103519119	103519119	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	atctggctgtttggagcgcgGcatgtctatagaaacttttt	8	15	11	7	2	2	1	0	0	2	1	2	2	2	2	0	3	2	3	0	3	3	5	rs73573973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:103519119G>A	ENST00000355739.4	+	11	3880	c.2457G>A	c.(2455-2457)cgG>cgA	p.R819R	BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.A1245T|ERCC5_ENST00000375954.1_Silent_p.R52R	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	819	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)					TTGGAGCGCGGCATGTCTATA	0.423			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				G|||	35	0.00698882	0.0257	0.0014	5008	,	,		18124	0.0		0.0	False		,,,				2504	0.0				p.R1273R		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	ERCC5,NS,carcinoma,+2,1	.	.	1	0			c.G3819A						PASS	.	G	,	91,4315	75.2+/-113.4	2,87,2114	57	58	58		2457,3819	3.1	1	13	dbSNP_130	58	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ERCC5,BIVM-ERCC5	NM_000123.3,NM_001204425.1	,	2,87,6414	AA,AG,GG		0.0,2.0654,0.6997	,	819/1187,1273/1641	103519119	91,12915	2203	4300	6503	SO:0001819	synonymous_variant	0	exon19	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	AGCGCGGCATGTC	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.2457G>A	13.37:g.103519119G>A		48	0	0		74	35	0.472973	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Silent	SNP	ENST00000355739.4	37	CCDS32004.1																																																																																			G|0.994;A|0.006	0.006	strong		0.423	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1			A	103519119	G	A	103519119	2	1	22	1	0	0	0	0	0	0	0	1	5218	1190	42	2		2	ERCC5	13	103519119	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1083	103519119	11650759	2847	5748											
ING1	3621	hgsc.bcm.edu	37	chr13	111368023	111368023	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	ctggggcgggccgtgctcttCcgccctgcggtgtggttggt	0	11	18	12	4	1	0	0	0	1	0	2	0	2	0	3	6	2	2	3	6	0	2	rs56682720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:111368023C>G	ENST00000375774.3	+	1	695	c.233C>G	c.(232-234)tCc>tGc	p.S78C	ING1_ENST00000333219.7_Intron|CARS2_ENST00000535398.1_5'Flank|ING1_ENST00000375775.3_Intron|ING1_ENST00000464141.1_Intron|ING1_ENST00000338450.7_Intron	NM_005537.4	NP_005528.3	Q9UK53	ING1_HUMAN	inhibitor of growth family, member 1	78					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)			CCGTGCTCTTCCGCCCTGCGG	0.672													C|||	189	0.0377396	0.1362	0.0101	5008	,	,		13851	0.0		0.002	False		,,,				2504	0.0				p.S78C		Atlas-SNP	.											.	ING1	106	.	0			c.C233G						PASS	.	C	CYS/SER,,,	544,3856		29,486,1685	69	63	65		233,,,	-8.2	0	13	dbSNP_129	65	6,8592		0,6,4293	yes	missense,intron,intron,intron	ING1	NM_005537.3,NM_198217.1,NM_198218.1,NM_198219.1	112,,,	29,492,5978	GG,GC,CC		0.0698,12.3636,4.2314	benign,,,	78/423,,,	111368023	550,12448	2200	4299	6499	SO:0001583	missense	3621	exon1			GCTCTTCCGCCCT		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.233C>G	13.37:g.111368023C>G	ENSP00000364929:p.Ser78Cys	70	0	0		86	42	0.488372	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	37	CCDS9517.1	51	0.023351648351648352	49	0.09959349593495935	2	0.0055248618784530384	0	0.0	0	0.0	C	14.45	2.539810	0.45176	0.123636	6.98E-4	ENSG00000153487	ENST00000375774	T	0.35421	1.31	4.11	-8.22	0.01037	.	.	.	.	.	T	0.00178	0.0005	N	0.08118	0	0.80722	P	0.0	P	0.43352	0.804	B	0.36959	0.237	T	0.15607	-1.0431	8	0.87932	D	0	0.3496	0.192	0.00135	0.2844:0.1541:0.2434:0.318	rs56682720	78	Q9UK53	ING1_HUMAN	C	78	ENSP00000364929:S78C	ENSP00000364929:S78C	S	+	2	0	ING1	110166024	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.050000	0.00628	-2.327000	0.00636	-1.083000	0.02208	TCC	C|0.961;G|0.039	0.039	strong		0.672	ING1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045770.2	NM_005537		G	111368023	C	G	111368023	3	3	22	1	0	0	0	0	1	0	0	0	7744	855	30	4	383	4	ING1	13	111368023	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	7848904	111368023	3801855	2848	5749											
C13orf35	400165	hgsc.bcm.edu	37	chr13	113333809	113333809	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cctgaagatggacccggcagGtctggagggaggcccccgtg	7	5	17	12	2	1	2	0	1	1	1	1	5	1	5	4	6	0	1	4	6	1	0	rs114091399	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:113333809G>A	ENST00000356049.1	+	2	874	c.116G>A	c.(115-117)gGt>gAt	p.G39D		NM_207440.1	NP_997323.1	Q6ZP68	ATPUN_HUMAN		39										breast(1)|lung(2)|ovary(1)|prostate(1)	5	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(43;0.201)			GACCCGGCAGGTCTGGAGGGA	0.602													G|||	71	0.0141773	0.0507	0.0058	5008	,	,		14668	0.0		0.0	False		,,,				2504	0.0				p.G39D		Atlas-SNP	.											.	C13orf35	13	.	0			c.G116A						PASS	.	G	ASP/GLY	194,4212	122.5+/-159.9	3,188,2012	38	40	40		116	-0.7	0	13	dbSNP_132	40	9,8591	7.1+/-27.0	0,9,4291	yes	missense	C13orf35	NM_207440.1	94	3,197,6303	AA,AG,GG		0.1047,4.4031,1.5608	benign	39/122	113333809	203,12803	2203	4300	6503	SO:0001583	missense	400165	exon2			CGGCAGGTCTGGA																												ENST00000356049.1:c.116G>A	13.37:g.113333809G>A	ENSP00000348337:p.Gly39Asp	94	0	0		108	51	0.472222	NM_207440		Missense_Mutation	SNP	ENST00000356049.1	37	CCDS9526.1	25	0.011446886446886446	22	0.044715447154471545	3	0.008287292817679558	0	0.0	0	0.0	G	2.915	-0.224514	0.06061	0.044031	0.001047	ENSG00000197595	ENST00000356049	.	.	.	1.24	-0.688	0.11317	.	.	.	.	.	T	0.03390	0.0098	N	0.08118	0	0.09310	N	1	D	0.54601	0.967	P	0.46629	0.522	T	0.07597	-1.0764	8	0.87932	D	0	.	1.9567	0.03378	0.2212:0.0:0.4635:0.3153	.	39	Q6ZP68	CM035_HUMAN	D	39	.	ENSP00000348337:G39D	G	+	2	0	C13orf35	112381810	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.464000	0.02359	-0.287000	0.09064	-0.372000	0.07161	GGT	G|0.985;A|0.015	0.015	strong		0.602	C13orf35-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000126522.2			A	113333809	G	A	113333809	3	1	22	1	0	0	0	0	1	0	0	0	1731	1261	44	2	118	2	C13orf35	13	113333809	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1965786	113333809	1836069	2849	5750											
MCF2L	23263	hgsc.bcm.edu	37	chr13	113729414	113729414	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccaaagtgccaggagctcCggcacctctgtgaccagttc	8	7	11	15	1	1	1	0	1	1	0	3	2	2	2	5	2	2	3	5	2	1	1	rs74926660	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:113729414C>T	ENST00000375608.3	+	12	1367	c.1309C>T	c.(1309-1311)Cgg>Tgg	p.R437W	MCF2L_ENST00000423482.2_Missense_Mutation_p.R405W|MCF2L_ENST00000434480.2_Missense_Mutation_p.R413W|MCF2L_ENST00000375604.2_Missense_Mutation_p.R464W|MCF2L_ENST00000442652.2_Missense_Mutation_p.R437W|MCF2L_ENST00000397030.1_Missense_Mutation_p.R440W|MCF2L_ENST00000375597.4_Missense_Mutation_p.R405W|MCF2L_ENST00000421756.1_Missense_Mutation_p.R411W|MCF2L_ENST00000535094.2_Missense_Mutation_p.R407W|MCF2L_ENST00000375601.3_Missense_Mutation_p.R411W			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	437					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)				CCAGGAGCTCCGGCACCTCTG	0.667													C|||	67	0.0133786	0.0204	0.0231	5008	,	,		14912	0.0208		0.0	False		,,,				2504	0.0031				p.R407W		Atlas-SNP	.											.	MCF2L	182	.	0			c.C1219T						PASS	.	C	TRP/ARG,TRP/ARG	89,4317	75.2+/-113.4	0,89,2114	60	68	65		1219,1213	4.9	0.9	13	dbSNP_131	65	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	MCF2L	NM_001112732.2,NM_024979.4	101,101	0,91,6412	TT,TC,CC		0.0233,2.02,0.6997	probably-damaging,probably-damaging	407/1126,405/1124	113729414	91,12915	2203	4300	6503	SO:0001583	missense	23263	exon11			GAGCTCCGGCACC	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.1309C>T	13.37:g.113729414C>T	ENSP00000364758:p.Arg437Trp	81	0	0		83	41	0.493976	NM_001112732	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Missense_Mutation	SNP	ENST00000375608.3	37		32|32	0.014652014652014652|0.014652014652014652	14|14	0.028455284552845527|0.028455284552845527	4|4	0.011049723756906077|0.011049723756906077	12|12	0.02097902097902098|0.02097902097902098	2|2	0.002638522427440633|0.002638522427440633	C|C	14.59|14.59	2.580228|2.580228	0.46006|0.46006	0.0202|0.0202	2.33E-4|2.33E-4	ENSG00000126217|ENSG00000126217	ENST00000397017|ENST00000375608;ENST00000442652;ENST00000375604;ENST00000397030;ENST00000535094;ENST00000421756;ENST00000375601;ENST00000434480;ENST00000423482;ENST00000375597;ENST00000440749	.|T;T;T;T;T;T;T;T;T;T	.|0.18016	.|2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24	4.88|4.88	4.88|4.88	0.63580|0.63580	.|.	.|0.622889	.|0.16873	.|N	.|0.196041	T|T	0.19565|0.19565	0.0470|0.0470	M|M	0.77616|0.77616	2.38|2.38	0.09310|0.09310	N|N	0.999999|0.999999	.|D;D;D;D;D;D	.|0.89917	.|0.999;0.996;0.999;1.0;0.985;0.999	.|P;P;P;D;P;D	.|0.70016	.|0.88;0.88;0.888;0.967;0.828;0.954	T|T	0.06180|0.06180	-1.0841|-1.0841	5|10	.|0.87932	.|D	.|0	.|.	13.7445|13.7445	0.62868|0.62868	0.0:0.8458:0.1542:0.0|0.0:0.8458:0.1542:0.0	.|.	.|405;407;464;369;405;437	.|E9PDN8;O15068-9;G5E9A1;E2QRA2;O15068-4;O15068	.|.;.;.;.;.;MCF2L_HUMAN	L|W	67|437;437;464;440;407;411;411;413;405;405;248	.|ENSP00000364758:R437W;ENSP00000401422:R437W;ENSP00000364754:R464W;ENSP00000380225:R440W;ENSP00000440374:R407W;ENSP00000397285:R411W;ENSP00000364751:R411W;ENSP00000407722:R413W;ENSP00000405639:R405W;ENSP00000364747:R405W	.|ENSP00000364747:R405W	P|R	+|+	2|1	0|2	MCF2L|MCF2L	112777415|112777415	0.609000|0.609000	0.26975|0.26975	0.886000|0.886000	0.34754|0.34754	0.181000|0.181000	0.23173|0.23173	1.666000|1.666000	0.37460|0.37460	2.239000|2.239000	0.73571|0.73571	0.561000|0.561000	0.74099|0.74099	CCG|CGG	C|0.990;T|0.010	0.010	strong		0.667	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4			T	113729414	C	T	113729414	3	4	22	1	0	0	0	0	1	0	0	0	9388	643	23	1	1527	1	MCF2L	13	113729414	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	395605	113729414	1440464	2850	5751											
F10	2159	hgsc.bcm.edu	37	chr13	113798236	113798236	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccaggccaccagcagcagcGgggaggcccctgacagcatc	9	2	13	17	1	0	1	0	1	0	0	1	2	0	2	5	4	4	3	5	4	0	0	rs3211783	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:113798236G>A	ENST00000375559.3	+	6	612	c.574G>A	c.(574-576)Ggg>Agg	p.G192R	F10_ENST00000409306.1_Missense_Mutation_p.G192R|F10_ENST00000375551.3_Missense_Mutation_p.G192R	NM_000504.3	NP_000495.1	P00742	FA10_HUMAN	coagulation factor X	192	O-glycosylated at one site.		G -> R (in dbSNP:rs3211783). {ECO:0000269|Ref.3}.		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)	CAGCAGCAGCGGGGAGGCCCC	0.632													G|||	148	0.0295527	0.1089	0.0058	5008	,	,		16770	0.0		0.0	False		,,,				2504	0.0				p.G192R		Atlas-SNP	.											.	F10	53	.	0			c.G574A						PASS	.	G	ARG/GLY	378,4028	188.8+/-215.1	17,344,1842	71	61	64		574	0.6	0	13	dbSNP_105	64	4,8596	3.7+/-12.6	0,4,4296	yes	missense	F10	NM_000504.3	125	17,348,6138	AA,AG,GG		0.0465,8.5792,2.9371	benign	192/489	113798236	382,12624	2203	4300	6503	SO:0001583	missense	2159	exon6			AGCAGCGGGGAGG		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.574G>A	13.37:g.113798236G>A	ENSP00000364709:p.Gly192Arg	47	0	0		59	29	0.491525	NM_000504	Q14340	Missense_Mutation	SNP	ENST00000375559.3	37	CCDS9530.1	46	0.021062271062271064	45	0.09146341463414634	1	0.0027624309392265192	0	0.0	0	0.0	G	6.631	0.484887	0.12641	0.085792	4.65E-4	ENSG00000126218	ENST00000409306;ENST00000375551;ENST00000375559	D;D;D	0.95588	-3.73;-3.75;-2.9	4.72	0.594	0.17485	.	2.606730	0.01382	N	0.012940	T	0.31482	0.0798	L	0.29908	0.895	0.09310	N	1	P;P;P	0.49961	0.93;0.93;0.682	B;B;B	0.34931	0.136;0.192;0.053	T	0.74542	-0.3631	10	0.18276	T	0.48	.	4.0037	0.09592	0.4003:0.1745:0.4252:0.0	rs3211783	192;192;192	B7ZBK1;Q5JVE8;P00742	.;.;FA10_HUMAN	R	192	ENSP00000387092:G192R;ENSP00000364701:G192R;ENSP00000364709:G192R	ENSP00000364701:G192R	G	+	1	0	F10	112846237	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.422000	0.07043	0.081000	0.16988	-0.333000	0.08304	GGG	G|0.973;A|0.027	0.027	strong		0.632	F10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045841.3			A	113798236	G	A	113798236	3	1	22	1	0	0	0	0	1	0	0	0	5338	1116	39	1	596	1	F10	13	113798236	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	68822	113798236	1371642	2851	5752											
FAM70B	348013	hgsc.bcm.edu	37	chr13	114507956	114507956	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacgcaggcttccgcctgacGcccgagcccgtcccgacctg	5	6	11	19	6	0	1	0	1	0	0	2	3	2	1	6	1	2	2	6	1	1	2	rs56032548	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:114507956G>A	ENST00000375353.3	+	8	795	c.768G>A	c.(766-768)acG>acA	p.T256T	TMEM255B_ENST00000467169.1_3'UTR	NM_182614.2	NP_872420.1	Q8WV15	T255B_HUMAN	transmembrane protein 255B	256						integral component of membrane (GO:0016021)											TCCGCCTGACGCCCGAGCCCG	0.672													G|||	355	0.0708866	0.2534	0.0288	5008	,	,		14726	0.0		0.0	False		,,,				2504	0.0				p.T256T		Atlas-SNP	.											.	.	.	.	0			c.G768A						PASS	.	G		962,3442	354.4+/-312.6	113,736,1353	62	60	60		768	-5.7	0	13	dbSNP_129	60	17,8583	12.6+/-44.7	0,17,4283	no	coding-synonymous	FAM70B	NM_182614.2		113,753,5636	AA,AG,GG		0.1977,21.8438,7.5285		256/327	114507956	979,12025	2202	4300	6502	SO:0001819	synonymous_variant	348013	exon8			CCTGACGCCCGAG	BC018995	CCDS45071.1	13q34	2012-11-30	2012-11-30	2012-11-30	ENSG00000184497	ENSG00000184497			28297	protein-coding gene	gene with protein product			"family with sequence similarity 70, member B"	FAM70B		12477932	Standard	NM_182614		Approved	MGC20579	uc001vuh.3	Q8WV15	OTTHUMG00000017398	ENST00000375353.3:c.768G>A	13.37:g.114507956G>A		54	0	0		60	29	0.483333	NM_182614		Silent	SNP	ENST00000375353.3	37	CCDS45071.1																																																																																			G|0.922;A|0.078	0.078	strong		0.672	TMEM255B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045953.4	NM_182614		A	114507956	G	A	114507956	2	1	22	1	0	0	0	0	0	0	0	1	5614	1074	38	1		1	FAM70B	13	114507956	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	709720	114507956	661922	2852	5753											
GAS6	2621	hgsc.bcm.edu	37	chr13	114526504	114526504	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcccaggttgattcagtcccGacgtccagaggggtccgcac	7	8	12	14	3	1	2	1	1	0	1	5	3	5	2	4	3	0	2	4	3	0	2	rs74118435	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:114526504G>A	ENST00000327773.6	-	13	1643	c.1497C>T	c.(1495-1497)gtC>gtT	p.V499V	GAS6_ENST00000355761.4_Silent_p.V445V|GAS6_ENST00000418959.3_Silent_p.V200V|GAS6-AS1_ENST00000458001.1_RNA|GAS6_ENST00000450766.1_Silent_p.V226V|GAS6_ENST00000357389.3_Silent_p.V542V	NM_000820.2	NP_000811.1	Q14393	GAS6_HUMAN	growth arrest-specific 6	542	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				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)				ATTCAGTCCCGACGTCCAGAG	0.627													G|||	111	0.0221645	0.0809	0.0058	5008	,	,		19406	0.0		0.0	False		,,,				2504	0.0				p.V499V		Atlas-SNP	.											.	GAS6	75	.	0			c.C1497T						PASS	.	G	,,	282,4122	157.4+/-190.3	8,266,1928	96	79	85		1497,678,600	-9.1	0	13	dbSNP_130	85	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	GAS6	NM_000820.2,NM_001143945.1,NM_001143946.1	,,	8,269,6225	AA,AG,GG		0.0349,6.4033,2.1916	,,	499/679,226/406,200/380	114526504	285,12719	2202	4300	6502	SO:0001819	synonymous_variant	2621	exon13			AGTCCCGACGTCC		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.1497C>T	13.37:g.114526504G>A		86	0	0		95	54	0.568421	NM_000820	B3KRQ7|B3KVL4|E9PBL7|Q6IMN1|Q7Z7N3	Silent	SNP	ENST00000327773.6	37	CCDS45072.1																																																																																			G|0.971;A|0.029	0.029	strong		0.627	GAS6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045946.2	NM_000820		A	114526504	G	A	114526504	2	1	22	1	0	0	0	0	0	0	0	1	6257	1045	37	1		1	GAS6	13	114526504	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	18548	114526504	643374	2853	5754											
RASA3	22821	hgsc.bcm.edu	37	chr13	114773022	114773022	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccttacccttctttaagcaCgatgggctgctcaacactct	8	13	6	14	1	3	0	1	0	2	0	4	1	4	0	2	1	4	3	2	1	3	4	rs74116414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:114773022C>T	ENST00000334062.7	-	18	1850	c.1729G>A	c.(1729-1731)Gtg>Atg	p.V577M	RASA3_ENST00000389544.4_Missense_Mutation_p.V545M	NM_007368.2	NP_031394.2	Q14644	RASA3_HUMAN	RAS p21 protein activator 3	577	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)			TCTTTAAGCACGATGGGCTGC	0.562													N|||	129	0.0257588	0.0923	0.0101	5008	,	,		20382	0.0		0.0	False		,,,				2504	0.0				p.V577M		Atlas-SNP	.											.	RASA3	83	.	0			c.G1729A						PASS	.	C	MET/VAL	302,4100	162.5+/-194.5	14,274,1913	141	102	115		1729	0.1	1	13	dbSNP_130	115	5,8593	3.7+/-12.6	0,5,4294	yes	missense	RASA3	NM_007368.2	21	14,279,6207	TT,TC,CC		0.0582,6.8605,2.3615	benign	577/835	114773022	307,12693	2201	4299	6500	SO:0001583	missense	22821	exon18			TAAGCACGATGGG		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.1729G>A	13.37:g.114773022C>T	ENSP00000335029:p.Val577Met	47	0	0		48	20	0.416667	NM_007368	A6NL15|F8W6X8|Q8IUY2	Missense_Mutation	SNP	ENST00000334062.7	37	CCDS32016.1	37	0.01694139194139194	35	0.07113821138211382	2	0.0055248618784530384	0	0.0	0	0.0	C	13.21	2.168248	0.38315	0.068605	5.82E-4	ENSG00000185989	ENST00000334062;ENST00000389544	D;D	0.94650	-3.48;-3.48	4.43	0.0618	0.14342	Rho GTPase activation protein (1);Pleckstrin homology-type (1);Pleckstrin homology domain (2);Ras GTPase-activating protein (1);	0.117907	0.56097	D	0.000028	T	0.59293	0.2183	M	0.76170	2.325	0.80722	D	1	B	0.14012	0.009	B	0.35688	0.208	T	0.72232	-0.4353	9	.	.	.	.	3.085	0.06275	0.2028:0.1354:0.5245:0.1373	.	577	Q14644	RASA3_HUMAN	M	577;545	ENSP00000335029:V577M;ENSP00000374195:V545M	.	V	-	1	0	RASA3	113791124	1.000000	0.71417	0.999000	0.59377	0.169000	0.22640	0.524000	0.22940	0.107000	0.17824	-0.928000	0.02712	GTG	C|0.976;T|0.024	0.024	strong		0.562	RASA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045957.2	NM_007368		T	114773022	C	T	114773022	3	4	22	1	0	0	0	0	1	0	0	0	13077	536	19	1	803	1	RASA3	13	114773022	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	246518	114773022	396856	2854	5755											
POTEG	404785	hgsc.bcm.edu	37	chr14	19553494	19553494	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcagaagcaagatgggcaaGtggtgccgccactgcttccc	9	7	12	13	1	1	2	1	0	0	2	2	2	2	2	3	2	3	3	3	2	3	1	rs200256710	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:19553494G>C	ENST00000409832.3	+	1	130	c.78G>C	c.(76-78)aaG>aaC	p.K26N		NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	26										cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	47						AGATGGGCAAGTGGTGCCGCC	0.582																																					p.K26N		Atlas-SNP	.											POTEG,NS,carcinoma,0,1	POTEG	118	1	0			c.G78C						scavenged	.						4	7	6					14																	19553494		1219	2779	3998	SO:0001583	missense	404785	exon1			GGGCAAGTGGTGC		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.78G>C	14.37:g.19553494G>C	ENSP00000386971:p.Lys26Asn	1363	1	0.000733676		2158	285	0.132067	NM_001005356	A1L153|A6NMI9|Q6S5H6|Q6S8J2	Missense_Mutation	SNP	ENST00000409832.3	37	CCDS32018.1	.	.	.	.	.	.	.	.	.	.	g	9.693	1.152413	0.21371	.	.	ENSG00000222036	ENST00000409832	T	0.46819	0.86	.	.	.	.	.	.	.	.	T	0.52025	0.1709	L	0.29908	0.895	0.09310	N	1	D	0.89917	1.0	D	0.83275	0.996	T	0.37934	-0.9684	7	0.87932	D	0	.	.	.	.	.	26	Q6S5H5	POTEG_HUMAN	N	26	ENSP00000386971:K26N	ENSP00000386971:K26N	K	+	3	2	POTEG	18623494	0.003000	0.15002	0.038000	0.18304	0.017000	0.09413	-0.275000	0.08525	0.459000	0.27016	0.152000	0.16155	AAG	G|0.996;A|0.004	.	alt		0.582	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408579.1	NM_001005356		C	19553494	G	C	19553494	3	2	22	1	0	0	0	0	1	0	0	0	12275	1020	36	4	80	4	POTEG	14	19553494	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10		19553494	87796046	2855	5756											
OR4N2	390429	hgsc.bcm.edu	37	chr14	20295972	20295972	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgttgtgatggcctttgaccGctacatcgccatctgccggc	5	12	11	13	3	1	2	0	2	1	0	2	2	1	2	4	2	2	2	4	2	1	3	rs76952476	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20295972G>A	ENST00000315947.1	+	1	365	c.365G>A	c.(364-366)cGc>cAc	p.R122H	OR4N2_ENST00000568211.1_Missense_Mutation_p.R122H	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, 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(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)		GCCTTTGACCGCTACATCGCC	0.507													.|||	121	0.0241613	0.09	0.0029	5008	,	,		28676	0.0		0.0	False		,,,				2504	0.0				p.R122H		Atlas-SNP	.											OR4N2,NS,carcinoma,+1,5	OR4N2	125	5	0			c.G365A						PASS	.	G	HIS/ARG	333,4073		8,317,1878	158	168	165		365	4.5	1	14	dbSNP_131	165	3,8597		0,3,4297	no	missense	OR4N2	NM_001004723.1	29	8,320,6175	AA,AG,GG		0.0349,7.5579,2.5834	probably-damaging	122/308	20295972	336,12670	2203	4300	6503	SO:0001583	missense	390429	exon1			TTGACCGCTACAT		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.365G>A	14.37:g.20295972G>A	ENSP00000319601:p.Arg122His	486	0	0		383	171	0.446475	NM_001004723	Q6IEY9|Q6IFA2	Missense_Mutation	SNP	ENST00000315947.1	37	CCDS32022.1	46	0.021062271062271064	44	0.08943089430894309	2	0.0055248618784530384	0	0.0	0	0.0	.	18.31	3.594861	0.66219	0.075579	3.49E-4	ENSG00000176294	ENST00000557677;ENST00000315947	D;T	0.97161	-4.27;-1.1	4.53	4.53	0.55603	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000113	T	0.66665	0.2812	M	0.90252	3.1	0.36488	D	0.868276	B	0.34103	0.437	B	0.30782	0.12	T	0.83054	-0.0151	10	0.72032	D	0.01	-14.9923	15.1112	0.72359	0.0:0.0:1.0:0.0	.	122	Q8NGD1	OR4N2_HUMAN	H	122	ENSP00000452022:R122H;ENSP00000319601:R122H	ENSP00000319601:R122H	R	+	2	0	OR4N2	19365812	0.992000	0.36948	1.000000	0.80357	0.999000	0.98932	5.956000	0.70315	2.488000	0.83962	0.591000	0.81541	CGC	G|0.977;A|0.023	0.023	strong		0.507	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2			A	20295972	G	A	20295972	3	1	22	1	0	0	0	0	1	0	0	0	11086	1087	38	1	367	1	OR4N2	14	20295972	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	742478	20295972	87053568	2856	5757											
OR4K15	81127	hgsc.bcm.edu	37	chr14	20443751	20443751	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taagtcccttccaaaatcgaTgaatgagacaaatcattctc	15	11	5	10	1	2	2	1	2	1	1	6	4	4	2	2	0	0	0	2	0	5	3	rs139828094	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20443751T>G	ENST00000305051.5	+	1	149	c.74T>G	c.(73-75)aTg>aGg	p.M25R		NM_001005486.1	NP_001005486.1	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K, member 15	25						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)		CCAAAATCGATGAATGAGACA	0.383													T|||	23	0.00459265	0.0174	0.0	5008	,	,		20008	0.0		0.0	False		,,,				2504	0.0				p.M25R		Atlas-SNP	.											.	OR4K15	82	.	0			c.T74G						PASS	.	T	ARG/MET	56,4350		0,56,2147	103	104	103		74	2	1	14	dbSNP_134	103	2,8596		0,2,4297	yes	missense	OR4K15	NM_001005486.1	91	0,58,6444	GG,GT,TT		0.0233,1.271,0.446	probably-damaging	25/349	20443751	58,12946	2203	4299	6502	SO:0001583	missense	81127	exon1			AATCGATGAATGA		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.74T>G	14.37:g.20443751T>G	ENSP00000304077:p.Met25Arg	187	0	0		193	102	0.528497	NM_001005486	B9EIL3|Q6IEZ4	Missense_Mutation	SNP	ENST00000305051.5	37	CCDS32026.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	.	12.07	1.827026	0.32329	0.01271	2.33E-4	ENSG00000169488	ENST00000305051	T	0.01414	4.92	3.26	1.98	0.26296	.	0.000000	0.53938	D	0.000058	T	0.02970	0.0088	M	0.90595	3.13	0.22754	N	0.998776	D	0.63880	0.993	D	0.67382	0.951	T	0.12941	-1.0528	10	0.72032	D	0.01	.	2.5999	0.04864	0.2303:0.1328:0.0:0.6369	.	25	Q8NH41	OR4KF_HUMAN	R	25	ENSP00000304077:M25R	ENSP00000304077:M25R	M	+	2	0	OR4K15	19513591	0.762000	0.28451	0.970000	0.41538	0.716000	0.41182	1.136000	0.31467	1.335000	0.45486	0.383000	0.25322	ATG	T|0.994;G|0.006	0.006	strong		0.383	OR4K15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409883.1			G	20443751	T	G	20443751	3	3	22	1	0	0	0	0	1	0	0	0	11079	1464	51	5	76	5	OR4K15	14	20443751	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	147779	20443751	86905789	2857	5758											
OR4K13	390433	hgsc.bcm.edu	37	chr14	20502779	20502779	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cgaatcaaaggtcacagtcaCcaagatgagcaggtttccta	14	8	9	10	1	3	2	3	1	0	1	4	3	4	2	2	2	1	2	2	2	4	2	rs144683363	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20502779C>T	ENST00000315693.2	-	1	140	c.139G>A	c.(139-141)Gtg>Atg	p.V47M	AL359218.1_ENST00000580563.1_RNA	NM_001004714.1	NP_001004714.1	Q8NH42	OR4KD_HUMAN	olfactory receptor, family 4, subfamily K, member 13	47						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(2)|lung(11)|ovary(3)|skin(4)	24	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		GTCACAGTCACCAAGATGAGC	0.423													C|||	55	0.0109824	0.0393	0.0043	5008	,	,		21594	0.0		0.0	False		,,,				2504	0.0				p.V47M		Atlas-SNP	.											.	OR4K13	68	.	0			c.G139A						PASS	.	C	MET/VAL	178,4228		4,170,2029	109	99	102		139	-1.9	0	14	dbSNP_134	102	1,8599		0,1,4299	yes	missense	OR4K13	NM_001004714.1	21	4,171,6328	TT,TC,CC		0.0116,4.0399,1.3763	possibly-damaging	47/305	20502779	179,12827	2203	4300	6503	SO:0001583	missense	390433	exon1			CAGTCACCAAGAT		CCDS32028.1	14q11.2	2013-09-23			ENSG00000176253	ENSG00000176253		"GPCR / Class A : Olfactory receptors"	15351	protein-coding gene	gene with protein product							Standard	NM_001004714		Approved		uc010tkz.2	Q8NH42	OTTHUMG00000170781	ENST00000315693.2:c.139G>A	14.37:g.20502779C>T	ENSP00000319322:p.Val47Met	107	0	0		86	39	0.453488	NM_001004714	Q6IF13	Missense_Mutation	SNP	ENST00000315693.2	37	CCDS32028.1	27	0.012362637362637362	27	0.054878048780487805	0	0.0	0	0.0	0	0.0	.	10.51	1.369413	0.24771	0.040399	1.16E-4	ENSG00000176253	ENST00000315693	T	0.01113	5.32	3.75	-1.86	0.07760	GPCR, rhodopsin-like superfamily (1);	0.760143	0.10674	U	0.647227	T	0.00241	0.0007	L	0.49571	1.57	0.09310	N	1	B	0.31077	0.307	B	0.22601	0.04	T	0.44682	-0.9312	10	0.52906	T	0.07	.	4.8534	0.13547	0.0:0.3611:0.2819:0.357	.	47	Q8NH42	OR4KD_HUMAN	M	47	ENSP00000319322:V47M	ENSP00000319322:V47M	V	-	1	0	OR4K13	19572619	0.000000	0.05858	0.011000	0.14972	0.005000	0.04900	-0.485000	0.06520	-0.020000	0.14032	-0.335000	0.08231	GTG	C|0.985;T|0.015	0.015	strong		0.423	OR4K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410344.1			T	20502779	C	T	20502779	3	4	22	1	0	0	0	0	1	0	0	0	11077	507	18	2	777	2	OR4K13	14	20502779	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	59028	20502779	86846761	2858	5759											
TEP1	7011	hgsc.bcm.edu	37	chr14	20873695	20873695	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggtcagatgtattgttcAtgtttacttctgagaccaga	9	15	11	6	0	3	3	2	1	1	3	3	4	3	3	1	2	1	3	1	2	2	6	rs148090256	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20873695A>G	ENST00000262715.5	-	4	825	c.785T>C	c.(784-786)aTg>aCg	p.M262T	TEP1_ENST00000556935.1_Missense_Mutation_p.M262T	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	262	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)		TGTATTGTTCATGTTTACTTC	0.463													A|||	33	0.00658946	0.0234	0.0029	5008	,	,		21319	0.0		0.0	False		,,,				2504	0.0				p.M262T		Atlas-SNP	.											TEP1,caecum,carcinoma,0,1	TEP1	224	1	0			c.T785C						PASS	.	A	THR/MET	82,4324	70.3+/-108.2	0,82,2121	116	111	113		785	-2	0	14	dbSNP_134	113	0,8600		0,0,4300	yes	missense	TEP1	NM_007110.4	81	0,82,6421	GG,GA,AA		0.0,1.8611,0.6305	benign	262/2628	20873695	82,12924	2203	4300	6503	SO:0001583	missense	7011	exon4			TTGTTCATGTTTA		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.785T>C	14.37:g.20873695A>G	ENSP00000262715:p.Met262Thr	64	0	0		57	29	0.508772	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	A	5.089	0.202155	0.09652	0.018611	0.0	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935	T;T	0.14144	2.53;2.53	4.07	-1.99	0.07457	TROVE (2);	2.107970	0.01669	N	0.025498	T	0.05044	0.0135	L	0.29908	0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.32534	-0.9903	10	0.49607	T	0.09	15.064	5.3797	0.16183	0.594:0.1384:0.2676:0.0	.	262;262	G3V5X7;Q99973	.;TEP1_HUMAN	T	262	ENSP00000262715:M262T;ENSP00000452574:M262T	ENSP00000262715:M262T	M	-	2	0	TEP1	19943535	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.762000	0.04745	-0.429000	0.07329	0.533000	0.62120	ATG	A|0.994;G|0.006	0.006	strong		0.463	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		G	20873695	A	G	20873695	3	3	22	1	0	0	0	0	1	0	0	0	15774	217	8	3	7306	3	TEP1	14	20873695	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	370916	20873695	86475845	2859	5760											
RNASE4	6038	hgsc.bcm.edu	37	chr14	21167837	21167837	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agatgaactgccatgagggtGtagtgaaggtcacagattgc	12	9	14	6	0	1	5	1	3	0	2	1	5	1	5	1	2	3	1	1	2	3	2	rs59543367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:21167837G>A	ENST00000555835.1	+	2	983	c.307G>A	c.(307-309)Gta>Ata	p.V103I	RNASE4_ENST00000304704.4_Missense_Mutation_p.V103I|AL163636.6_ENST00000553909.1_3'UTR|RNASE4_ENST00000555597.1_Missense_Mutation_p.V103I|RNASE4_ENST00000397995.2_Missense_Mutation_p.V103I|RP11-903H12.3_ENST00000554286.1_RNA	NM_002937.3	NP_002928.1	P34096	RNAS4_HUMAN	ribonuclease, RNase A family, 4	103					cellular response to starvation (GO:0009267)|mRNA cleavage (GO:0006379)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	nucleic acid binding (GO:0003676)|pancreatic ribonuclease activity (GO:0004522)			central_nervous_system(1)|large_intestine(1)|lung(3)|skin(1)	6	all_cancers(95;0.00304)		Epithelial(56;5.13e-07)|all cancers(55;4.73e-06)	GBM - Glioblastoma multiforme(265;0.0133)		CCATGAGGGTGTAGTGAAGGT	0.493													G|||	22	0.00439297	0.0151	0.0029	5008	,	,		22587	0.0		0.0	False		,,,				2504	0.0				p.V103I	Esophageal Squamous(59;1059 1362 26290 51151)	Atlas-SNP	.											.	RNASE4	18	.	0			c.G307A						PASS	.	G	ILE/VAL,ILE/VAL	58,4348	57.4+/-93.9	0,58,2145	154	127	136		307,307	2.9	1	14	dbSNP_129	136	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense	RNASE4	NM_002937.3,NM_194431.1	29,29	0,61,6442	AA,AG,GG		0.0349,1.3164,0.469	benign,benign	103/148,103/148	21167837	61,12945	2203	4300	6503	SO:0001583	missense	6038	exon2			GAGGGTGTAGTGA	U36775	CCDS9555.1	14q11	2014-07-16			ENSG00000258818	ENSG00000258818		"Ribonucleases, RNase A"	10047	protein-coding gene	gene with protein product		601030				7501448	Standard	NM_002937		Approved		uc001vxy.4	P34096	OTTHUMG00000029575	ENST00000555835.1:c.307G>A	14.37:g.21167837G>A	ENSP00000452245:p.Val103Ile	36	0	0		30	22	0.733333	NM_002937		Missense_Mutation	SNP	ENST00000555835.1	37	CCDS9555.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	15.78	2.935052	0.52866	0.013164	3.49E-4	ENSG00000258818;ENSG00000258818;ENSG00000258818;ENSG00000181784;ENSG00000181784;ENSG00000181784	ENST00000555835;ENST00000397995;ENST00000555597;ENST00000398001;ENST00000304704;ENST00000397999	T;T;T;T;T;T	0.72615	-0.67;-0.67;-0.67;-0.67;-0.67;-0.67	5.8	2.92	0.33932	Ribonuclease A, domain (4);	0.325719	0.26453	N	0.024288	T	0.39572	0.1083	L	0.29908	0.895	0.28449	N	0.916432	B	0.06786	0.001	B	0.11329	0.006	T	0.47711	-0.9096	10	0.52906	T	0.07	-2.5954	8.6786	0.34194	0.2536:0.0:0.7464:0.0	rs59543367	103	P34096	RNAS4_HUMAN	I	103	ENSP00000452245:V103I;ENSP00000381081:V103I;ENSP00000451624:V103I;ENSP00000381087:V103I;ENSP00000307096:V103I;ENSP00000381085:V103I	ENSP00000307096:V103I	V	+	1	0	AL163636.2;RNASE4	20237677	0.769000	0.28531	0.998000	0.56505	0.957000	0.61999	1.259000	0.32956	0.886000	0.36113	0.650000	0.86243	GTA	G|0.994;A|0.006	0.006	strong		0.493	RNASE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073729.3			A	21167837	G	A	21167837	3	1	22	1	0	0	0	0	1	0	0	0	13421	1377	48	2	309	2	RNASE4	14	21167837	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	294142	21167837	86181703	2860	5761											
SUPT16H	11198	hgsc.bcm.edu	37	chr14	21841524	21841524	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagttgatttggcataaacAatttcttcatcaacacccac	13	12	5	11	0	3	1	2	1	1	0	3	1	3	1	1	1	2	3	1	1	4	5	rs75576875	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:21841524A>G	ENST00000216297.2	-	2	470	c.132T>C	c.(130-132)atT>atC	p.I44I		NM_007192.3	NP_009123.1	Q9Y5B9	SP16H_HUMAN	suppressor of Ty 16 homolog (S. cerevisiae)	44					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)		TGGCATAAACAATTTCTTCAT	0.378													A|||	80	0.0159744	0.059	0.0029	5008	,	,		18715	0.0		0.0	False		,,,				2504	0.0				p.I44I		Atlas-SNP	.											.	SUPT16H	84	.	0			c.T132C						PASS	.	A		224,4182	134.9+/-171.1	5,214,1984	179	159	166		132	1.9	1	14	dbSNP_132	166	0,8600	1.2+/-3.3	0,0,4300	no	coding-synonymous	SUPT16H	NM_007192.3		5,214,6284	GG,GA,AA		0.0,5.084,1.7223		44/1048	21841524	224,12782	2203	4300	6503	SO:0001819	synonymous_variant	11198	exon2			ATAAACAATTTCT	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.132T>C	14.37:g.21841524A>G		126	0	0		170	84	0.494118	NM_007192	Q6GMT8|Q6P2F1|Q6PJM1|Q9NRX0	Silent	SNP	ENST00000216297.2	37	CCDS9569.1																																																																																			A|0.985;G|0.015	0.015	strong		0.378	SUPT16H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074025.2			G	21841524	A	G	21841524	2	3	22	1	0	0	0	0	0	0	0	1	15411	126	5	3		3	SUPT16H	14	21841524	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	673687	21841524	85508016	2861	5762											
OR10G2	26534	hgsc.bcm.edu	37	chr14	22102315	22102315	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcgtatcttcaggatggcAtggactatgttggcatagga	9	12	14	6	1	2	0	1	0	1	0	2	3	2	3	0	5	1	4	0	5	3	5	rs61753931	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:22102315A>G	ENST00000542433.1	-	1	781	c.684T>C	c.(682-684)caT>caC	p.H228H		NM_001005466.1	NP_001005466.1	Q8NGC3	O10G2_HUMAN	olfactory receptor, family 10, subfamily G, member 2	228						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)		TCAGGATGGCATGGACTATGT	0.532													.|||	70	0.0139776	0.053	0.0	5008	,	,		17587	0.0		0.0	False		,,,				2504	0.0				p.H228H		Atlas-SNP	.											.	OR10G2	35	.	0			c.T684C						PASS	.	A		210,4082		33,144,1969	52	52	52		684	-1.2	0.9	14	dbSNP_129	52	4,8380		1,2,4189	no	coding-synonymous	OR10G2	NM_001005466.1		34,146,6158	GG,GA,AA		0.0477,4.8928,1.6882		228/311	22102315	214,12462	2146	4192	6338	SO:0001819	synonymous_variant	26534	exon1			GATGGCATGGACT		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.684T>C	14.37:g.22102315A>G		375	0	0		356	173	0.485955	NM_001005466	B2RPD0	Silent	SNP	ENST00000542433.1	37	CCDS32047.1																																																																																			A|0.983;G|0.017	0.017	strong		0.532	OR10G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401525.1			G	22102315	A	G	22102315	2	3	22	1	0	0	0	0	0	0	0	1	10908	214	8	3		3	OR10G2	14	22102315	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	260791	22102315	85247225	2862	5763											
JUB	84962	hgsc.bcm.edu	37	chr14	23444247	23444247	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtgaaggggatgccatccaGgcacttgttgcaaacaatgc	11	9	12	9	0	0	1	0	1	0	0	1	2	1	2	2	3	4	3	2	3	3	2	rs10130692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:23444247G>A	ENST00000262713.2	-	5	1681	c.1306C>T	c.(1306-1308)Ctg>Ttg	p.L436L	AJUBA_ENST00000397388.3_Silent_p.L19L|AJUBA_ENST00000361265.4_Silent_p.L436L|RP11-298I3.5_ENST00000555074.1_Intron	NM_032876.4	NP_116265.1	Q96IF1	AJUBA_HUMAN	ajuba LIM protein	436	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				calcium-dependent cell-cell adhesion (GO:0016339)|cellular protein localization (GO:0034613)|focal adhesion assembly (GO:0048041)|G2/M transition of mitotic cell cycle (GO:0000086)|gene silencing by miRNA (GO:0035195)|glycerophospholipid biosynthetic process (GO:0046474)|lamellipodium assembly (GO:0030032)|mitotic cell cycle (GO:0000278)|negative regulation of hippo signaling (GO:0035331)|negative regulation of kinase activity (GO:0033673)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cellular biosynthetic process (GO:0031328)|positive regulation of gene silencing by miRNA (GO:2000637)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein complex assembly (GO:0031334)|regulation of cell migration (GO:0030334)|regulation of cellular response to hypoxia (GO:1900037)|regulation of GTPase activity (GO:0043087)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)|wound healing, spreading of epidermal cells (GO:0035313)	cell-cell junction (GO:0005911)|cytoplasmic mRNA processing body (GO:0000932)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transcription factor complex (GO:0005667)	alpha-catenin binding (GO:0045294)|chromatin binding (GO:0003682)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)										ATGCCATCCAGGCACTTGTTG	0.522													G|||	201	0.0401358	0.1452	0.0101	5008	,	,		22256	0.0		0.002	False		,,,				2504	0.0				p.L436L		Atlas-SNP	.											.	.	.	.	0			c.C1306T						PASS	.	G	,	552,3854	248.7+/-256.4	46,460,1697	150	138	142		1306,55	4.1	1	14	dbSNP_119	142	13,8587	9.1+/-34.3	0,13,4287	no	coding-synonymous,coding-synonymous	JUB	NM_032876.4,NM_198086.1	,	46,473,5984	AA,AG,GG		0.1512,12.5284,4.3441	,	436/539,19/122	23444247	565,12441	2203	4300	6503	SO:0001819	synonymous_variant	84962	exon5			CATCCAGGCACTT	AK025567	CCDS9581.1, CCDS9582.1	14q11.2	2011-11-10	2011-11-10	2011-11-10	ENSG00000129474	ENSG00000129474			20250	protein-coding gene	gene with protein product		609066	"jub, ajuba homolog (Xenopus laevis)"	JUB		10330178	Standard	NM_032876		Approved	MGC15563	uc001whz.3	Q96IF1	OTTHUMG00000028711	ENST00000262713.2:c.1306C>T	14.37:g.23444247G>A		60	0	0		81	49	0.604938	NM_032876	A8MX18|D3DS37	Silent	SNP	ENST00000262713.2	37	CCDS9581.1																																																																																			G|0.955;A|0.045	0.045	strong		0.522	AJUBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071685.2			A	23444247	G	A	23444247	2	1	22	1	0	0	0	0	0	0	0	1	7977	991	35	2		2	JUB	14	23444247	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1341932	23444247	83905293	2863	5764											
ACIN1	22985	hgsc.bcm.edu	37	chr14	23549948	23549948	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgctctgacccttaggtttCtggaaggtgtttcttgatcc	5	16	10	10	0	3	2	0	2	3	0	4	3	4	3	2	3	1	3	2	3	2	4	rs11555803	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:23549948C>T	ENST00000262710.1	-	6	1097	c.770G>A	c.(769-771)aGa>aAa	p.R257K	ACIN1_ENST00000605057.1_Missense_Mutation_p.R199K|ACIN1_ENST00000457657.1_Missense_Mutation_p.R217K|ACIN1_ENST00000555053.1_Missense_Mutation_p.R257K|ACIN1_ENST00000555352.1_5'Flank	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	257	Glu-rich.		R -> K (in dbSNP:rs11555803).		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)		CCTTAGGTTTCTGGAAGGTGT	0.473													C|||	114	0.0227636	0.0825	0.0072	5008	,	,		20266	0.0		0.0	False		,,,				2504	0.0				p.R257K		Atlas-SNP	.											.	ACIN1	147	.	0			c.G770A						PASS	.	C	LYS/ARG,LYS/ARG,LYS/ARG	356,4050	183.6+/-211.2	16,324,1863	175	179	178		770,650,770	5.5	1	14	dbSNP_120	178	8,8592	6.4+/-24.3	0,8,4292	yes	missense,missense,missense	ACIN1	NM_001164814.1,NM_001164815.1,NM_014977.3	26,26,26	16,332,6155	TT,TC,CC		0.093,8.0799,2.7987	probably-damaging,probably-damaging,probably-damaging	257/1329,217/1302,257/1342	23549948	364,12642	2203	4300	6503	SO:0001583	missense	22985	exon6			AGGTTTCTGGAAG	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.770G>A	14.37:g.23549948C>T	ENSP00000262710:p.Arg257Lys	102	0	0		92	48	0.521739	NM_001164814	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Missense_Mutation	SNP	ENST00000262710.1	37	CCDS9587.1	39	0.017857142857142856	38	0.07723577235772358	1	0.0027624309392265192	0	0.0	0	0.0	C	22.9	4.351242	0.82132	0.080799	9.3E-4	ENSG00000100813	ENST00000262710;ENST00000457657;ENST00000555053	T;T;T	0.27890	2.05;1.64;2.04	5.47	5.47	0.80525	.	0.000000	0.43260	D	0.000591	T	0.03178	0.0093	L	0.43152	1.355	0.38624	D	0.951213	D;P	0.53312	0.959;0.932	D;P	0.65684	0.937;0.867	T	0.01039	-1.1472	10	0.17832	T	0.49	-10.3899	14.8326	0.70159	0.0:1.0:0.0:0.0	rs11555803;rs52803485;rs11555803	257;257	G3V3M7;Q9UKV3	.;ACINU_HUMAN	K	257;217;257	ENSP00000262710:R257K;ENSP00000405677:R217K;ENSP00000451328:R257K	ENSP00000262710:R257K	R	-	2	0	ACIN1	22619788	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	3.549000	0.53681	2.569000	0.86673	0.650000	0.86243	AGA	C|0.971;T|0.029	0.029	strong		0.473	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977		T	23549948	C	T	23549948	3	4	22	1	0	0	0	0	1	0	0	0	142	913	32	2	3458	2	ACIN1	14	23549948	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	105701	23549948	83799592	2864	5765											
HOMEZ	57594	hgsc.bcm.edu	37	chr14	23744844	23744844	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttcctcctcctcctcctcCtcttcctcatcatcttctgg	2	17	2	20	0	6	0	2	0	4	0	13	0	13	0	7	1	0	0	7	1	0	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:23744844C>T	ENST00000357460.5	-	2	1757	c.1593G>A	c.(1591-1593)gaG>gaA	p.E531E	HOMEZ_ENST00000431326.2_Silent_p.E533E|HOMEZ_ENST00000561013.1_Silent_p.E533E	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	531	Glu-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|lung(7)	12	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00643)		cctcctcctcctcttcctcat	0.493																																					p.E531E		Atlas-SNP	.											.	HOMEZ	80	.	0			c.G1593A						PASS	.						37	36	36					14																	23744844		2196	4286	6482	SO:0001819	synonymous_variant	57594	exon2			CTCCTCCTCTTCC	AB037864	CCDS45085.1	14q11.2	2011-06-20	2007-02-15	2007-02-15		ENSG00000215271		"Homeoboxes / ZF class"	20164	protein-coding gene	gene with protein product		608119	"KIAA1443"	KIAA1443		12925734	Standard	NM_020834		Approved		uc001wja.2	Q8IX15		ENST00000357460.5:c.1593G>A	14.37:g.23744844C>T		127	0	0		114	7	0.0614035	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	Silent	SNP	ENST00000357460.5	37	CCDS45085.1																																																																																			.	.	none		0.493	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834		T	23744844	C	T	23744844	2	4	22	1	0	0	0	0	0	0	0	1	7290	680	24	2		2	HOMEZ	14	23744844	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	194896	23744844	83604696	2865	5766											
HOMEZ	57594	hgsc.bcm.edu	37	chr14	23745723	23745723	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gtacctatgccatgtgactgGttgggacccctgcctgcctg	5	11	12	13	0	0	1	0	1	0	0	0	2	0	2	6	2	4	2	6	2	2	3	rs11844797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:23745723G>A	ENST00000357460.5	-	2	878	c.714C>T	c.(712-714)aaC>aaT	p.N238N	HOMEZ_ENST00000431326.2_Silent_p.N240N|HOMEZ_ENST00000561013.1_Silent_p.N240N	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	238					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|lung(7)	12	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00643)		CATGTGACTGGTTGGGACCCC	0.532													G|||	250	0.0499201	0.1853	0.0072	5008	,	,		18809	0.0		0.0	False		,,,				2504	0.0				p.N238N		Atlas-SNP	.											.	HOMEZ	80	.	0			c.C714T						PASS	.	G		638,3510		52,534,1488	76	79	78		714	2.2	0	14	dbSNP_120	78	12,8408		1,10,4199	no	coding-synonymous	HOMEZ	NM_020834.2		53,544,5687	AA,AG,GG		0.1425,15.3809,5.1719		238/551	23745723	650,11918	2074	4210	6284	SO:0001819	synonymous_variant	57594	exon2			TGACTGGTTGGGA	AB037864	CCDS45085.1	14q11.2	2011-06-20	2007-02-15	2007-02-15		ENSG00000215271		"Homeoboxes / ZF class"	20164	protein-coding gene	gene with protein product		608119	"KIAA1443"	KIAA1443		12925734	Standard	NM_020834		Approved		uc001wja.2	Q8IX15		ENST00000357460.5:c.714C>T	14.37:g.23745723G>A		155	0	0		134	67	0.5	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	Silent	SNP	ENST00000357460.5	37	CCDS45085.1																																																																																			G|0.948;A|0.052	0.052	strong		0.532	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834		A	23745723	G	A	23745723	2	1	22	1	0	0	0	0	0	0	0	1	7290	1252	44	2		2	HOMEZ	14	23745723	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	879	23745723	83603817	2866	5767											
IL25	64806	hgsc.bcm.edu	37	chr14	23845061	23845061	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtgtttccttagcttgtgTgtgtgtgcggccccgtgtga	2	15	14	10	3	0	1	0	1	0	0	1	1	1	1	4	1	2	2	4	1	1	3	rs149802556	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:23845061T>C	ENST00000329715.2	+	2	764	c.506T>C	c.(505-507)gTg>gCg	p.V169A	CMTM5_ENST00000339180.4_5'Flank|CMTM5_ENST00000342473.4_5'Flank|CMTM5_ENST00000397227.3_5'Flank|CMTM5_ENST00000382809.2_5'Flank|CMTM5_ENST00000359320.3_5'Flank|CMTM5_ENST00000555731.1_5'Flank|IL25_ENST00000397242.2_Missense_Mutation_p.V153A	NM_022789.3	NP_073626.1	Q9H293	IL25_HUMAN	interleukin 25	169					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)		TTAGCTTGTGTGTGTGTGCGG	0.607																																					p.V169A		Atlas-SNP	.											.	IL25	21	.	0			c.T506C						PASS	.	T	ALA/VAL,ALA/VAL	2,4404	4.2+/-10.8	0,2,2201	150	137	141		506,458	4.6	1	14	dbSNP_134	141	0,8600		0,0,4300	no	missense,missense	IL25	NM_022789.3,NM_172314.1	64,64	0,2,6501	CC,CT,TT		0.0,0.0454,0.0154	probably-damaging,probably-damaging	169/178,153/162	23845061	2,13004	2203	4300	6503	SO:0001583	missense	64806	exon2			CTTGTGTGTGTGT	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.506T>C	14.37:g.23845061T>C	ENSP00000328111:p.Val169Ala	254	1	0.00393701		262	105	0.400763	NM_022789	Q2M3F0|Q8IZV3|Q8WXB0	Missense_Mutation	SNP	ENST00000329715.2	37	CCDS9597.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.049273	0.75846	4.54E-4	0.0	ENSG00000166090	ENST00000397242;ENST00000329715	T;T	0.55234	0.53;0.53	4.58	4.58	0.56647	.	0.145674	0.33023	N	0.005361	T	0.57636	0.2067	L	0.44542	1.39	0.30135	N	0.804464	P;D	0.64830	0.64;0.994	B;P	0.59056	0.334;0.851	T	0.58634	-0.7602	10	0.48119	T	0.1	-26.6522	10.2614	0.43430	0.0:0.0:0.0:1.0	.	169;153	Q9H293;Q9H293-2	IL25_HUMAN;.	A	153;169	ENSP00000380417:V153A;ENSP00000328111:V169A	ENSP00000328111:V169A	V	+	2	0	IL25	22914901	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.712000	0.54875	1.947000	0.56498	0.459000	0.35465	GTG	T|1.000;C|0.000	0.000	strong		0.607	IL25-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071789.2			C	23845061	T	C	23845061	3	2	22	1	0	0	0	0	1	0	0	0	7687	1696	59	3	525	3	IL25	14	23845061	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	99338	23845061	83504479	2867	5768											
THTPA	79178	hgsc.bcm.edu	37	chr14	24026174	24026174	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agctcaaatgtcctggagcaGcaggtgtcttaggaccccac	10	8	11	12	0	2	0	1	0	1	0	3	2	3	2	3	3	3	3	3	3	2	1	rs141465409	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24026174G>T	ENST00000288014.6	+	1	944	c.208G>T	c.(208-210)Gca>Tca	p.A70S	THTPA_ENST00000554789.1_Missense_Mutation_p.A70S|THTPA_ENST00000556015.1_Missense_Mutation_p.A70S|THTPA_ENST00000404535.3_Missense_Mutation_p.A70S|THTPA_ENST00000554970.1_Missense_Mutation_p.A70S|RP11-66N24.4_ENST00000555446.1_RNA|RP11-66N24.4_ENST00000556354.1_RNA|RP11-66N24.4_ENST00000553985.1_RNA			Q9BU02	THTPA_HUMAN	thiamine triphosphatase	70	CYTH. {ECO:0000255|PROSITE- ProRule:PRU01044}.				dephosphorylation (GO:0016311)|generation of precursor metabolites and energy (GO:0006091)|small molecule metabolic process (GO:0044281)|thiamine diphosphate metabolic process (GO:0042357)|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)	hydrolase activity (GO:0016787)|magnesium ion binding (GO:0000287)|thiamin-triphosphatase activity (GO:0050333)			large_intestine(1)|prostate(2)	3	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00643)		TCCTGGAGCAGCAGGTGTCTT	0.582													G|||	6	0.00119808	0.0045	0.0	5008	,	,		18740	0.0		0.0	False		,,,				2504	0.0				p.A70S		Atlas-SNP	.											.	THTPA	11	.	0			c.G208T						PASS	.	G	SER/ALA,SER/ALA	5,4401	9.9+/-24.2	0,5,2198	84	71	75		208,208	-2	0	14	dbSNP_134	75	0,8600		0,0,4300	yes	missense,missense	THTPA	NM_001126339.1,NM_024328.3	99,99	0,5,6498	TT,TG,GG		0.0,0.1135,0.0384	benign,benign	70/231,70/231	24026174	5,13001	2203	4300	6503	SO:0001583	missense	79178	exon2			GGAGCAGCAGGTG	AF432862	CCDS32053.1, CCDS58306.1, CCDS58307.1	14q11.2	2011-04-28					3.6.1.28		18987	protein-coding gene	gene with protein product		611612				11827967	Standard	NR_046051		Approved	THTPASE	uc001wkh.5	Q9BU02		ENST00000288014.6:c.208G>T	14.37:g.24026174G>T	ENSP00000288014:p.Ala70Ser	201	0	0		215	115	0.534884	NM_001256321	D3DS50|G3V4J3	Missense_Mutation	SNP	ENST00000288014.6	37	CCDS32053.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	7.575	0.667592	0.14710	0.001135	0.0	ENSG00000157306	ENST00000404535;ENST00000288014;ENST00000557630;ENST00000556015;ENST00000554970;ENST00000554789	T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97	5.91	-1.95	0.07548	CYTH domain (2);CYTH-like domain (1);	1.127190	0.06371	N	0.713610	T	0.24431	0.0592	L	0.41573	1.285	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.12156	0.007;0.003	T	0.22452	-1.0216	10	0.05959	T	0.93	0.0017	1.2016	0.01886	0.2075:0.3314:0.2356:0.2254	.	70;70	G3V4J3;Q9BU02	.;THTPA_HUMAN	S	70	ENSP00000384580:A70S;ENSP00000288014:A70S;ENSP00000452281:A70S;ENSP00000451835:A70S;ENSP00000452465:A70S;ENSP00000450459:A70S	ENSP00000288014:A70S	A	+	1	0	THTPA	23096014	0.000000	0.05858	0.000000	0.03702	0.989000	0.77384	-0.268000	0.08607	-0.725000	0.04901	0.655000	0.94253	GCA	G|0.999;T|0.001	0.001	strong		0.582	THTPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413800.2			T	24026174	G	T	24026174	3	4	22	1	0	0	0	0	1	0	0	0	15896	971	34	4	210	4	THTPA	14	24026174	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	181113	24026174	83323366	2868	5769											
DHRS2	10202	hgsc.bcm.edu	37	chr14	24114483	24114483	+	3'UTR	SNP	T	T	C																															gaggagtgggggcggctgcgTagctgtggtcccaggcccag																								rs7156794	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24114483T>C	ENST00000250383.6	+	0	1340				DHRS2_ENST00000344777.7_Missense_Mutation_p.V292A	NM_005794.3	NP_005785.1	Q13268	DHRS2_HUMAN	dehydrogenase/reductase (SDR family) member 2						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)		GGCGGCTGCGTAGCTGTGGTC	0.602													c|||	572	0.114217	0.4153	0.0303	5008	,	,		17144	0.0		0.002	False		,,,				2504	0.0				p.V292A		Atlas-SNP	.											.	DHRS2	78	.	0			c.T875C						PASS	.		,ALA/VAL	1524,2882	480.3+/-358.8	279,966,958	61	62	61		,875	-2.1	0	14	dbSNP_116	61	19,8581	12.6+/-44.7	0,19,4281	yes	utr-3,missense	DHRS2	NM_005794.3,NM_182908.4	,64	279,985,5239	CC,CT,TT		0.2209,34.5892,11.8638	,benign	,292/301	24114483	1543,11463	2203	4300	6503	SO:0001624	3_prime_UTR_variant	10202	exon9			GCTGCGTAGCTGT		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.*21T>C	14.37:g.24114483T>C		64	0	0		74	41	0.554054	NM_182908	D3DS54|Q53GS4|Q7Z789|Q9H2R2	Missense_Mutation	SNP	ENST00000250383.6	37	CCDS9604.1	198	0.09065934065934066	183	0.3719512195121951	14	0.03867403314917127	0	0.0	1	0.0013192612137203166	t	0.018	-1.479180	0.01035	0.345892	0.002209	ENSG00000100867	ENST00000344777	D	0.82984	-1.67	2.22	-2.14	0.07123	.	2.958940	0.01651	N	0.024553	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.22068	-1.0227	8	0.87932	D	0	.	0.3421	0.00335	0.2015:0.3173:0.1984:0.2828	rs7156794;rs60193895	270	Q13268-2	.	A	292	ENSP00000344674:V292A	ENSP00000344674:V292A	V	+	2	0	DHRS2	23184323	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.227000	0.09126	-0.620000	0.05641	-0.251000	0.11542	GTA	T|0.941;C|0.059	0.059	strong		0.602	DHRS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000071842.2	NM_182908		C	24114483	T	C	24114483	1	2	22	0	1	0	0	0	0	0	0	0	4492	1638	57	3		3	DHRS2	14	24114483	3'UTR	SNP	T	TCGA-G8-6324-01A-11D-2210-10	88309	24114483	83235057	2869	5770	70	2									
DHRS2	10202	hgsc.bcm.edu	37	chr14	24114490	24114490	+	3'UTR	SNP	G	G	A																															gggggcggctgcgtagctgtGgtcccaggcccaggagcctg																								rs7150155	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24114490G>A	ENST00000250383.6	+	0	1347				DHRS2_ENST00000344777.7_Silent_p.V294V	NM_005794.3	NP_005785.1	Q13268	DHRS2_HUMAN	dehydrogenase/reductase (SDR family) member 2						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)		GCGTAGCTGTGGTCCCAGGCC	0.597													g|||	370	0.0738818	0.267	0.0216	5008	,	,		17143	0.0		0.002	False		,,,				2504	0.0				p.V294V		Atlas-SNP	.											DHRS2_ENST00000344777,NS,carcinoma,+1,1	DHRS2	78	1	0			c.G882A						scavenged	.		,	963,3443	362.4+/-316.1	113,737,1353	58	60	59		,882	2.3	0	14	dbSNP_116	59	13,8587	9.1+/-34.3	0,13,4287	no	utr-3,coding-synonymous	DHRS2	NM_005794.3,NM_182908.4	,	113,750,5640	AA,AG,GG		0.1512,21.8566,7.5042	,	,294/301	24114490	976,12030	2203	4300	6503	SO:0001624	3_prime_UTR_variant	10202	exon9			AGCTGTGGTCCCA		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.*28G>A	14.37:g.24114490G>A		61	1	0.0163934		71	39	0.549296	NM_182908	D3DS54|Q53GS4|Q7Z789|Q9H2R2	Silent	SNP	ENST00000250383.6	37	CCDS9604.1																																																																																			G|0.966;A|0.034	0.034	strong		0.597	DHRS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000071842.2	NM_182908		A	24114490	G	A	24114490	1	1	22	0	1	0	0	0	0	0	0	0	4492	1335	47	2		2	DHRS2	14	24114490	3'UTR	SNP	G	TCGA-G8-6324-01A-11D-2210-10	7	24114490	83235050	2870	5771	70	2									
IPO4	79711	hgsc.bcm.edu	37	chr14	24652350	24652350	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcctgcatgtaggatggcacGactcgggccagggcagcctg	7	6	16	12	2	0	0	0	0	0	0	1	2	0	1	3	4	2	4	3	4	1	1	rs377303706		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24652350G>A	ENST00000354464.6	-	23	2429	c.2253C>T	c.(2251-2253)gtC>gtT	p.V751V	RP11-468E2.2_ENST00000561419.1_3'UTR	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4	751					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)		AGGATGGCACGACTCGGGCCA	0.667																																					p.V751V		Atlas-SNP	.											.	IPO4	74	.	0			c.C2253T						PASS	.	C		6,4192		0,6,2093	42	48	46		2253	4	1	14		46	0,8460		0,0,4230	no	coding-synonymous	IPO4	NM_024658.3		0,6,6323	AA,AG,GG		0.0,0.1429,0.0474		751/1082	24652350	6,12652	2099	4230	6329	SO:0001819	synonymous_variant	79711	exon23			TGGCACGACTCGG	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.2253C>T	14.37:g.24652350G>A		138	0	0		136	72	0.529412	NM_024658	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Silent	SNP	ENST00000354464.6	37	CCDS9616.1																																																																																			.	.	weak		0.667	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658		A	24652350	G	A	24652350	2	1	22	1	0	0	0	0	0	0	0	1	7804	1045	37	1		1	IPO4	14	24652350	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	537860	24652350	82697190	2871	5772											
TINF2	26277	hgsc.bcm.edu	37	chr14	24709351	24709351	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgacggagctgcacagagaCggaggacacactgtaggagg	13	4	16	8	2	0	2	0	1	0	1	0	7	0	6	0	5	2	3	0	5	1	1	rs10141326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24709351C>T	ENST00000267415.7	-	8	1481	c.1140G>A	c.(1138-1140)ccG>ccA	p.P380P	TINF2_ENST00000538777.1_3'UTR|TINF2_ENST00000558510.1_5'Flank|TINF2_ENST00000540705.1_Silent_p.P345P|TINF2_ENST00000558566.1_3'UTR|TINF2_ENST00000399423.4_3'UTR	NM_001099274.1	NP_001092744.1	Q9BSI4	TINF2_HUMAN	TERF1 (TRF1)-interacting nuclear factor 2	380					negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of protein ADP-ribosylation (GO:0010836)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of telomere maintenance (GO:0032206)|protein localization to chromosome (GO:0034502)|protein localization to chromosome, telomeric region (GO:0070198)|telomere assembly (GO:0032202)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)	chromosome, telomeric region (GO:0000781)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinucleolar chromocenter (GO:0010370)	telomeric DNA binding (GO:0042162)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|prostate(1)|urinary_tract(1)	7				GBM - Glioblastoma multiforme(265;0.0185)		TGCACAGAGACGGAGGACACA	0.502									Congenital Dyskeratosis;Ataxia Pancytopenia syndrome				T|||	299	0.0597045	0.2209	0.0101	5008	,	,		21880	0.0		0.0	False		,,,				2504	0.0				p.P380P		Atlas-SNP	.											.	TINF2	61	.	0			c.G1140A						PASS	.	T	,	753,3255		77,599,1328	164	172	169		1140,	1.7	0	14	dbSNP_119	169	10,8338		0,10,4164	no	coding-synonymous,utr-3	TINF2	NM_001099274.1,NM_012461.2	,	77,609,5492	TT,TC,CC		0.1198,18.7874,6.1751	,	380/452,	24709351	763,11593	2004	4174	6178	SO:0001819	synonymous_variant	26277	exon8	Familial Cancer Database	Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita;Myelocerebellar disorder	CAGAGACGGAGGA	AF195512	CCDS41936.1, CCDS41937.1	14q12	2008-07-29				ENSG00000092330			11824	protein-coding gene	gene with protein product		604319				10581025, 18252230	Standard	NM_012461		Approved	TIN2	uc001woa.4	Q9BSI4		ENST00000267415.7:c.1140G>A	14.37:g.24709351C>T		125	0	0		123	64	0.520325	NM_001099274	B3W5Q7|Q9H904|Q9UHC2	Silent	SNP	ENST00000267415.7	37	CCDS41936.1																																																																																			C|0.944;T|0.056	0.056	strong		0.502	TINF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415406.2			T	24709351	C	T	24709351	2	4	22	1	0	0	0	0	0	0	0	1	15938	523	19	1		1	TINF2	14	24709351	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	57001	24709351	82640189	2872	5773											
DHRS1	115817	hgsc.bcm.edu	37	chr14	24768220	24768220	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagtgatgtaaactgtggcGcctgctttgcagagctgcaa	9	10	12	10	1	0	2	0	1	0	1	0	2	0	2	2	1	5	5	2	1	3	2	rs150092528		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24768220G>T	ENST00000288111.7	-	2	369	c.93C>A	c.(91-93)ggC>ggA	p.G31G	NOP9_ENST00000267425.3_5'Flank|NOP9_ENST00000396802.3_5'Flank|DHRS1_ENST00000396813.1_Silent_p.G31G	NM_001136050.2	NP_001129522.1	Q96LJ7	DHRS1_HUMAN	dehydrogenase/reductase (SDR family) member 1	31						endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)	oxidoreductase activity (GO:0016491)			cervix(1)|endometrium(1)|large_intestine(2)|lung(2)	6				GBM - Glioblastoma multiforme(265;2.81e-08)|OV - Ovarian serous cystadenocarcinoma(311;0.0442)		AAACTGTGGCGCCTGCTTTGC	0.582																																					p.G31G		Atlas-SNP	.											.	DHRS1	21	.	0			c.C93A						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	67	60	63		93,93	-8.8	0.9	14	dbSNP_134	63	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	DHRS1	NM_001136050.2,NM_138452.2	,	0,1,6502	TT,TG,GG		0.0,0.0227,0.0077	,	31/314,31/314	24768220	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	115817	exon2			TGTGGCGCCTGCT	AK058159	CCDS9623.1	14q11.2	2011-09-14			ENSG00000157379	ENSG00000157379	1.1.-.-	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"	16445	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 19C, member 1"	610410				12153138, 19027726	Standard	NM_138452		Approved	FLJ25430, MGC20204, SDR19C1	uc001wok.3	Q96LJ7	OTTHUMG00000029333	ENST00000288111.7:c.93C>A	14.37:g.24768220G>T		59	0	0		69	25	0.362319	NM_138452	D3DS71|Q8NDG3|Q96B59|Q96CQ5	Silent	SNP	ENST00000288111.7	37	CCDS9623.1																																																																																			G|1.000;T|0.000	0.000	weak		0.582	DHRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073168.4	NM_138452		T	24768220	G	T	24768220	2	4	22	1	0	0	0	0	0	0	0	1	4488	1074	38	4		4	DHRS1	14	24768220	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	58869	24768220	82581320	2873	5774											
C14orf21	161424	hgsc.bcm.edu	37	chr14	24772373	24772373	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttgccctggtgggggcctgtCgcagagttggggcctaccaa	5	9	16	11	1	0	1	0	0	0	1	1	1	0	1	4	5	2	2	4	5	2	3	rs147123517	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24772373C>T	ENST00000267425.3	+	6	1330	c.1237C>T	c.(1237-1239)Cgc>Tgc	p.R413C	NOP9_ENST00000396802.3_Missense_Mutation_p.R413C	NM_174913.1	NP_777573.1	Q86U38	NOP9_HUMAN	NOP9 nucleolar protein	413							poly(A) RNA binding (GO:0044822)										GGGGGCCTGTCGCAGAGTTGG	0.557													C|||	8	0.00159744	0.0	0.0014	5008	,	,		16884	0.0		0.007	False		,,,				2504	0.0				p.R413C		Atlas-SNP	.											.	.	.	.	0			c.C1237T						PASS	.	C	CYS/ARG	4,4402	6.2+/-15.9	0,4,2199	70	71	71		1237	4.2	1	14	dbSNP_134	71	45,8555	30.1+/-81.4	0,45,4255	yes	missense	C14orf21	NM_174913.1	180	0,49,6454	TT,TC,CC		0.5233,0.0908,0.3767	probably-damaging	413/637	24772373	49,12957	2203	4300	6503	SO:0001583	missense	161424	exon6			GCCTGTCGCAGAG		CCDS9624.1, CCDS66616.1	14q12	2012-12-10	2012-12-10	2012-06-06	ENSG00000196943	ENSG00000196943			19826	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 21", "NOP9 nucleolar protein homolog (yeast)"	C14orf21		21653694	Standard	XM_005267385		Approved		uc001wol.1	Q86U38	OTTHUMG00000029342	ENST00000267425.3:c.1237C>T	14.37:g.24772373C>T	ENSP00000267425:p.Arg413Cys	148	0	0		150	70	0.466667	NM_174913	A8MY76|Q8IVF0|Q8TBS6	Missense_Mutation	SNP	ENST00000267425.3	37	CCDS9624.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	18.19	3.567896	0.65651	9.08E-4	0.005233	ENSG00000196943	ENST00000267425;ENST00000396802	T;T	0.32753	1.48;1.44	5.16	4.25	0.50352	.	0.224065	0.38897	N	0.001525	T	0.35189	0.0923	L	0.54323	1.7	0.43536	D	0.995829	D	0.76494	0.999	P	0.59288	0.855	T	0.23013	-1.0200	10	0.52906	T	0.07	-4.9362	11.1833	0.48642	0.4521:0.5479:0.0:0.0	.	413	Q86U38	CN021_HUMAN	C	413	ENSP00000267425:R413C;ENSP00000380020:R413C	ENSP00000267425:R413C	R	+	1	0	C14orf21	23842213	0.869000	0.29996	1.000000	0.80357	0.909000	0.53808	0.630000	0.24553	1.356000	0.45884	0.563000	0.77884	CGC	C|0.996;T|0.004	0.004	strong		0.557	NOP9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073186.2			T	24772373	C	T	24772373	3	4	22	1	0	0	0	0	1	0	0	0	1771	884	31	1	1259	1	C14orf21	14	24772373	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4153	24772373	82577167	2874	5775											
CBLN3	643866	hgsc.bcm.edu	37	chr14	24898135	24898135	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaccaccaggcactccccCtccagcaggacgggctctga	9	4	10	18	1	1	2	0	1	1	1	3	3	3	3	5	3	1	3	5	3	0	0	rs57646536	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24898135C>T	ENST00000267406.6	-	1	596	c.126G>A	c.(124-126)gaG>gaA	p.E42E	CBLN3_ENST00000555436.1_Intron|KHNYN_ENST00000556842.1_5'Flank|KHNYN_ENST00000251343.5_5'Flank|KHNYN_ENST00000553935.1_5'Flank	NM_001039771.2	NP_001034860.1	Q6UW01	CBLN3_HUMAN	cerebellin 3 precursor	42						cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)				central_nervous_system(1)|lung(3)	4				GBM - Glioblastoma multiforme(265;0.00159)		GGCACTCCCCCTCCAGCAGGA	0.716													C|||	296	0.0591054	0.2088	0.0274	5008	,	,		13699	0.0		0.001	False		,,,				2504	0.0				p.E42E		Atlas-SNP	.											.	CBLN3	21	.	0			c.G126A						PASS	.	C		554,3752		31,492,1630	9	11	10		126	1	1	14	dbSNP_129	10	5,8401		0,5,4198	no	coding-synonymous	CBLN3	NM_001039771.2		31,497,5828	TT,TC,CC		0.0595,12.8658,4.3974		42/206	24898135	559,12153	2153	4203	6356	SO:0001819	synonymous_variant	643866	exon1			CTCCCCCTCCAGC	AY359070	CCDS32057.1	14q12	2006-12-13				ENSG00000139899			20146	protein-coding gene	gene with protein product		612978				12975309	Standard	NM_001039771		Approved		uc001wpg.4	Q6UW01		ENST00000267406.6:c.126G>A	14.37:g.24898135C>T		121	0	0		99	50	0.50505	NM_001039771		Silent	SNP	ENST00000267406.6	37	CCDS32057.1																																																																																			C|0.963;T|0.037	0.037	strong		0.716	CBLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412943.1	XM_115232		T	24898135	C	T	24898135	2	4	22	1	0	0	0	0	0	0	0	1	2708	680	24	2		2	CBLN3	14	24898135	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	125762	24898135	82451405	2875	5776											
CMA1	1215	hgsc.bcm.edu	37	chr14	24976605	24976605	+	Frame_Shift_Del	DEL	T	T	-																															cagcacaaagttccgtcttaTaaggaaaccaccacaaaatt																								rs542619483	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24976605delT	ENST00000250378.3	-	2	195	c.166delA	c.(166-168)atafs	p.I56fs	CMA1_ENST00000206446.4_Intron|RP11-80A15.1_ENST00000555109.1_Intron	NM_001836.3	NP_001827.1	P23946	CMA1_HUMAN	chymase 1, mast cell	56	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				angiotensin maturation (GO:0002003)|cellular protein metabolic process (GO:0044267)|cellular response to glucose stimulus (GO:0071333)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|interleukin-1 beta biosynthetic process (GO:0050720)|midbrain development (GO:0030901)|peptide metabolic process (GO:0006518)|positive regulation of angiogenesis (GO:0045766)|regulation of inflammatory response (GO:0050727)	extracellular region (GO:0005576)|intracellular (GO:0005622)	peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			kidney(1)|lung(8)|pancreas(1)|prostate(1)	11				GBM - Glioblastoma multiforme(265;0.0271)		TTCCGTCTTATAAGGAAACCA	0.488													?|T|-|unsure	8	0.00159744	0.0061	0.0	5008	,	,		19307	0.0		0.0	False		,,,				2504	0.0				p.I56fs		Pindel,Atlas-Indel	.											.	CMA1	21	.	0			c.167delT						PASS	.			12,4252		0,12,2120	143	139	140			5	0.2	14		140	0,8254		0,0,4127	no	frameshift	CMA1	NM_001836.2		0,12,6247	A1A1,A1R,RR		0.0,0.2814,0.0959			24976605	12,12506	2203	4300	6503	SO:0001589	frameshift_variant	1215	exon2			.		CCDS9630.1	14q12	2012-08-30			ENSG00000092009	ENSG00000092009	3.4.21.39		2097	protein-coding gene	gene with protein product		118938				8468056	Standard	NM_001836		Approved		uc001wpp.1	P23946	OTTHUMG00000140181	ENST00000250378.3:c.166delA	14.37:g.24976605delT	ENSP00000250378:p.Ile56fs	147	0	.		120	39	0.325	NM_001836	B5BUM8|Q16018|Q3SY36|Q3SY37|Q9UDH5	Frame_Shift_Del	DEL	ENST00000250378.3	37	CCDS9630.1																																																																																			.	.	none		0.488	CMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276535.2			-	24976605	T	-	24976605	7	5	22	1	0	1	0	1	0	0	0	0	3576	1406	49	0	593	0	CMA1	14	24976605	Frame_Shift_Del	DEL	T	TCGA-G8-6324-01A-11D-2210-10	78470	24976605	82372935	2876	5777											
CTSG	1511	hgsc.bcm.edu	37	chr14	25045386	25045386	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gtcactcacctgcctcagccCcagtgggtaggagaaaggcc	9	6	12	14	0	3	1	3	0	0	1	3	2	3	1	5	3	2	1	5	3	2	1	rs61737123	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:25045386C>G	ENST00000216336.2	-	1	80	c.44G>C	c.(43-45)gGg>gCg	p.G15A		NM_001911.2	NP_001902.1	P08311	CATG_HUMAN	cathepsin G	15					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)		TGCCTCAGCCCCAGTGGGTAG	0.527													C|||	68	0.0135783	0.0492	0.0043	5008	,	,		18510	0.0		0.0	False		,,,				2504	0.0				p.G15A		Atlas-SNP	.											.	CTSG	63	.	0			c.G44C						PASS	.	C	ALA/GLY	228,4178	128.6+/-165.4	7,214,1982	63	54	57		44	1.1	0	14	dbSNP_129	57	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CTSG	NM_001911.2	60	7,216,6280	GG,GC,CC		0.0233,5.1748,1.7684	probably-damaging	15/256	25045386	230,12776	2203	4300	6503	SO:0001583	missense	1511	exon1			TCAGCCCCAGTGG	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.44G>C	14.37:g.25045386C>G	ENSP00000216336:p.Gly15Ala	77	0	0		83	37	0.445783	NM_001911	Q6IBJ6|Q9UCA5|Q9UCU6	Missense_Mutation	SNP	ENST00000216336.2	37	CCDS9631.1	22	0.010073260073260074	20	0.04065040650406504	2	0.0055248618784530384	0	0.0	0	0.0	c	11.21	1.572963	0.28092	0.051748	2.33E-4	ENSG00000100448	ENST00000216336	D	0.92752	-3.1	5.29	1.14	0.20703	Peptidase cysteine/serine, trypsin-like (1);	0.801389	0.10545	N	0.662150	T	0.49406	0.1555	L	0.28400	0.85	0.09310	N	1	B	0.25312	0.123	B	0.21360	0.034	T	0.57774	-0.7753	10	0.06236	T	0.91	.	6.4789	0.22051	0.0:0.6773:0.1397:0.1829	rs61737123	15	P08311	CATG_HUMAN	A	15	ENSP00000216336:G15A	ENSP00000216336:G15A	G	-	2	0	CTSG	24115226	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.884000	0.28214	0.309000	0.22966	0.655000	0.94253	GGG	C|0.969;G|0.031	0.031	strong		0.527	CTSG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276536.2	NM_001911		G	25045386	C	G	25045386	3	3	22	1	0	0	0	0	1	0	0	0	4037	623	22	4	743	4	CTSG	14	25045386	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	68781	25045386	82304154	2877	5778											
STRN3	29966	hgsc.bcm.edu	37	chr14	31364948	31364948	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagctaccatagaatggatcAttttacctaaacaaaacata	18	10	5	8	0	1	1	1	0	0	1	1	3	1	2	2	1	5	1	2	1	9	6	rs114922597	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:31364948A>G	ENST00000357479.5	-	17	2340	c.2144T>C	c.(2143-2145)aTg>aCg	p.M715T	STRN3_ENST00000355683.5_Missense_Mutation_p.M631T	NM_001083893.1	NP_001077362.1	Q13033	STRN3_HUMAN	striatin, calmodulin binding protein 3	715					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)		AGAATGGATCATTTTACCTAA	0.333													A|||	40	0.00798722	0.0287	0.0029	5008	,	,		19925	0.0		0.0	False		,,,				2504	0.0				p.M715T		Atlas-SNP	.											.	STRN3	117	.	0			c.T2144C						PASS	.	A	THR/MET,THR/MET	117,4289	89.7+/-128.4	2,113,2088	63	58	60		2144,1892	4.6	1	14	dbSNP_132	60	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	STRN3	NM_001083893.1,NM_014574.3	81,81	2,115,6386	GG,GA,AA		0.0233,2.6555,0.915	benign,benign	715/798,631/714	31364948	119,12887	2203	4300	6503	SO:0001583	missense	29966	exon17			TGGATCATTTTAC		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.2144T>C	14.37:g.31364948A>G	ENSP00000350071:p.Met715Thr	112	0	0		134	54	0.402985	NM_001083893	A2RTX7|A6NHZ7|Q9NRA5	Missense_Mutation	SNP	ENST00000357479.5	37	CCDS41938.1	19	0.0086996336996337	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	A	10.37	1.331773	0.24167	0.026555	2.33E-4	ENSG00000196792	ENST00000355683;ENST00000357479	T;T	0.59502	0.26;0.26	5.77	4.64	0.57946	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.332419	0.39985	N	0.001209	T	0.12518	0.0304	N	0.04090	-0.28	0.37999	D	0.934155	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.11275	-1.0594	10	0.46703	T	0.11	0.4649	7.2945	0.26385	0.7812:0.1462:0.0726:0.0	.	631;715	Q13033-2;Q13033	.;STRN3_HUMAN	T	631;715	ENSP00000347909:M631T;ENSP00000350071:M715T	ENSP00000347909:M631T	M	-	2	0	STRN3	30434699	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.949000	0.49074	2.204000	0.70986	0.383000	0.25322	ATG	A|0.990;G|0.010	0.010	strong		0.333	STRN3-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409713.1	NM_014574		G	31364948	A	G	31364948	3	3	22	1	0	0	0	0	1	0	0	0	15345	217	8	3	257	3	STRN3	14	31364948	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	6319562	31364948	75984592	2878	5779											
CLEC14A	161198	hgsc.bcm.edu	37	chr14	38724043	38724043	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aatatgaagaccacggcagaGgaggagtcgaaagcctgagg	15	4	15	7	2	0	4	0	2	0	2	1	7	0	6	2	4	1	1	2	4	4	1	rs530380827|rs78287081	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:38724043G>A	ENST00000342213.2	-	1	1531	c.1185C>T	c.(1183-1185)tcC>tcT	p.S395S		NM_175060.2	NP_778230.1	Q86T13	CLC14_HUMAN	C-type lectin domain family 14, member A	395						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)		CCACGGCAGAGGAGGAGTCGA	0.502													G|||	44	0.00878594	0.0333	0.0	5008	,	,		19714	0.0		0.0	False		,,,				2504	0.0				p.S395S		Atlas-SNP	.											.	CLEC14A	83	.	0			c.C1185T						PASS	.	G		119,4287	88.2+/-126.9	2,115,2086	52	49	50		1185	-0.7	0.9	14	dbSNP_132	50	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CLEC14A	NM_175060.1		2,116,6385	AA,AG,GG		0.0116,2.7009,0.9227		395/491	38724043	120,12886	2203	4300	6503	SO:0001819	synonymous_variant	161198	exon1			GGCAGAGGAGGAG		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.1185C>T	14.37:g.38724043G>A		72	0	0		76	38	0.5	NM_175060	Q695G9|Q6PWT6|Q8N5V5	Silent	SNP	ENST00000342213.2	37	CCDS9667.1																																																																																			G|0.992;A|0.008	0.008	strong		0.502	CLEC14A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276729.1	NM_175060		A	38724043	G	A	38724043	2	1	22	1	0	0	0	0	0	0	0	1	3501	987	35	2		2	CLEC14A	14	38724043	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	7359095	38724043	68625497	2879	5780											
MIA2	117153	hgsc.bcm.edu	37	chr14	39717002	39717002	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgaagaagatggtggggcAgatgaacatgaacatcctct	15	8	12	6	0	1	6	0	3	1	3	2	6	2	6	1	3	2	1	1	3	5	0	rs17109049	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:39717002A>G	ENST00000280082.3	+	4	1423	c.1224A>G	c.(1222-1224)gcA>gcG	p.A408A	MIA2_ENST00000556784.1_Silent_p.A407A|RP11-407N17.3_ENST00000553728.1_Silent_p.A408A	NM_054024.3	NP_473365.3	Q96PC5	MIA2_HUMAN	melanoma inhibitory activity 2	408					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)		ATGGTGGGGCAGATGAACATG	0.333													A|||	380	0.0758786	0.2769	0.0202	5008	,	,		18395	0.0		0.0	False		,,,				2504	0.0				p.A408A		Atlas-SNP	.											.	MIA2	82	.	0			c.A1224G						PASS	.	A		1093,3313	385.1+/-325.6	116,861,1226	74	79	77		1224	3.1	0	14	dbSNP_123	77	11,8589	7.7+/-29.5	0,11,4289	no	coding-synonymous	MIA2	NM_054024.3		116,872,5515	GG,GA,AA		0.1279,24.8071,8.4884		408/655	39717002	1104,11902	2203	4300	6503	SO:0001819	synonymous_variant	117153	exon4			TGGGGCAGATGAA	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.1224A>G	14.37:g.39717002A>G		41	0	0		46	46	1	NM_054024	A1L4H0|Q9H6C1	Silent	SNP	ENST00000280082.3	37	CCDS9672.1																																																																																			A|0.921;G|0.079	0.079	strong		0.333	MIA2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276768.3	NM_054024		G	39717002	A	G	39717002	2	3	22	1	0	0	0	0	0	0	0	1	9573	175	7	3		3	MIA2	14	39717002	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	992959	39717002	67632538	2880	5781											
CTAGE5	4253	hgsc.bcm.edu	37	chr14	39736693	39736693	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccggggttacccctcaaccGtatttggggctgctcctgga	5	10	12	14	2	1	0	1	0	0	0	2	1	2	1	5	5	3	4	5	5	3	3	rs34909359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:39736693G>T	ENST00000280083.3	+	1	344	c.30G>T	c.(28-30)ccG>ccT	p.P10P	CTAGE5_ENST00000396158.2_Silent_p.P10P|CTAGE5_ENST00000396165.4_Intron|CTAGE5_ENST00000348007.3_Silent_p.P10P|CTAGE5_ENST00000556148.1_5'UTR|RP11-407N17.5_ENST00000605298.1_RNA|RP11-407N17.3_ENST00000553728.1_Intron|RP11-407N17.3_ENST00000603904.1_Intron|CTAGE5_ENST00000341502.5_Silent_p.P10P|CTAGE5_ENST00000341749.3_Intron|RP11-407N17.5_ENST00000553520.1_RNA|CTAGE5_ENST00000557038.1_Intron			O15320	CTGE5_HUMAN	CTAGE family, member 5	10					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)		CCCCTCAACCGTATTTGGGGC	0.662													G|||	100	0.0199681	0.0711	0.0086	5008	,	,		16634	0.0		0.0	False		,,,				2504	0.0				p.P10P		Atlas-SNP	.											.	CTAGE5	75	.	0			c.G30T						PASS	.	G	,,,	285,4121	149.2+/-183.4	6,273,1924	31	33	32		30,,30,	2.4	0	14	dbSNP_126	32	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,intron,coding-synonymous,intron	CTAGE5	NM_005930.3,NM_203354.2,NM_203355.2,NM_203356.2	,,,	6,275,6222	TT,TG,GG		0.0233,6.4685,2.2067	,,,	10/805,,10/762,	39736693	287,12719	2203	4300	6503	SO:0001819	synonymous_variant	4253	exon1			TCAACCGTATTTG	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.30G>T	14.37:g.39736693G>T		74	0	0		73	33	0.452055	NM_001247989	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Silent	SNP	ENST00000280083.3	37	CCDS9674.1																																																																																			G|0.979;T|0.021	0.021	strong		0.662	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930		T	39736693	G	T	39736693	2	4	22	1	0	0	0	0	0	0	0	1	3996	1132	40	4		4	CTAGE5	14	39736693	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	19691	39736693	67612847	2881	5782											
FAM179B	23116	hgsc.bcm.edu	37	chr14	45431636	45431636	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	caaccctgcatggcggctgcCccctccgcgctgcttctgct	3	9	10	19	3	1	0	0	0	1	0	2	0	2	0	4	2	5	5	4	2	1	1	rs141982460	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:45431636C>T	ENST00000361577.3	+	1	226	c.12C>T	c.(10-12)gcC>gcT	p.A4A	KLHL28_ENST00000355081.2_5'Flank|KLHL28_ENST00000396128.4_5'Flank|FAM179B_ENST00000361462.2_Silent_p.A4A|KLHL28_ENST00000553817.1_5'Flank|FAM179B_ENST00000382233.2_Silent_p.A4A	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	4										endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						TGGCGGCTGCCCCCTCCGCGC	0.617													C|||	4	0.000798722	0.003	0.0	5008	,	,		16675	0.0		0.0	False		,,,				2504	0.0				p.A4A		Atlas-SNP	.											.	FAM179B	115	.	0			c.C12T						PASS	.	C		24,4370		0,24,2173	21	24	23		12	0.9	0.3	14	dbSNP_134	23	0,8568		0,0,4284	no	coding-synonymous	FAM179B	NM_015091.2		0,24,6457	TT,TC,CC		0.0,0.5462,0.1852		4/1721	45431636	24,12938	2197	4284	6481	SO:0001819	synonymous_variant	23116	exon1			GGCTGCCCCCTCC	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.12C>T	14.37:g.45431636C>T		51	0	0		60	29	0.483333	NM_015091	Q68D66|Q6PG27	Silent	SNP	ENST00000361577.3	37	CCDS9681.1																																																																																			C|0.998;T|0.002	0.002	strong		0.617	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781		T	45431636	C	T	45431636	2	4	22	1	0	0	0	0	0	0	0	1	5511	610	22	2		2	FAM179B	14	45431636	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	5694943	45431636	61917904	2882	5783											
FAM179B	23116	hgsc.bcm.edu	37	chr14	45473265	45473265	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcttttgttttattacagtGtatgctagcctcaattttgg	8	20	7	6	0	2	0	1	0	1	0	2	0	2	0	1	1	3	3	1	1	5	9	rs17092470	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:45473265G>A	ENST00000361577.3	+	4	2554	c.2340G>A	c.(2338-2340)gtG>gtA	p.V780V	FAM179B_ENST00000361462.2_Splice_Site_p.V780V|KLHL28_ENST00000553817.1_Intron|FAM179B_ENST00000382233.2_Splice_Site_p.V780V	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	780										endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						TTATTACAGTGTATGCTAGCC	0.338													G|||	262	0.0523163	0.1899	0.0159	5008	,	,		17095	0.0		0.0	False		,,,				2504	0.0				p.V780V		Atlas-SNP	.											.	FAM179B	115	.	0			c.G2340A						PASS	.	G		688,3718	284.6+/-277.7	50,588,1565	47	43	44		2340	-0.8	0.1	14	dbSNP_123	44	7,8593	5.0+/-18.6	0,7,4293	yes	coding-synonymous-near-splice	FAM179B	NM_015091.2		50,595,5858	AA,AG,GG		0.0814,15.6151,5.3437		780/1721	45473265	695,12311	2203	4300	6503	SO:0001630	splice_region_variant	23116	exon4			TACAGTGTATGCT	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.2339-1G>A	14.37:g.45473265G>A		27	0	0		37	16	0.432432	NM_015091	Q68D66|Q6PG27	Silent	SNP	ENST00000361577.3	37	CCDS9681.1																																																																																			G|0.948;A|0.052	0.052	strong		0.338	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781	Silent	A	45473265	G	A	45473265	5	1	22	1	0	0	0	0	0	0	1	0	5511	1391	48	2	2354	2	FAM179B	14	45473265	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	41629	45473265	61876275	2883	5784											
C14orf106	55320	hgsc.bcm.edu	37	chr14	45693648	45693648	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtaagtaagtcacgttcatcGcaatcttccttgtttttact	9	17	6	9	2	3	0	2	0	1	0	5	0	4	0	1	0	1	5	1	0	4	8	rs35223850	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:45693648G>A	ENST00000310806.4	-	11	2600	c.2142C>T	c.(2140-2142)tgC>tgT	p.C714C		NM_018353.4	NP_060823.3	Q6P0N0	M18BP_HUMAN	MIS18 binding protein 1	714					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						CACGTTCATCGCAATCTTCCT	0.343													G|||	138	0.0275559	0.0325	0.0159	5008	,	,		19114	0.0		0.0686	False		,,,				2504	0.0153				p.C714C		Atlas-SNP	.											.	MIS18BP1	92	.	0			c.C2142T						PASS	.	G		154,4252	106.5+/-144.9	0,154,2049	69	70	69		2142	0.4	0	14	dbSNP_126	69	517,8083	144.5+/-200.4	17,483,3800	no	coding-synonymous	MIS18BP1	NM_018353.4		17,637,5849	AA,AG,GG		6.0116,3.4952,5.1592		714/1133	45693648	671,12335	2203	4300	6503	SO:0001819	synonymous_variant	55320	exon11			TTCATCGCAATCT	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.2142C>T	14.37:g.45693648G>A		115	0	0		85	42	0.494118	NM_018353	D3DSA7|Q86V14|Q96PY4|Q9NUR5|Q9Y4X9	Silent	SNP	ENST00000310806.4	37	CCDS9684.1																																																																																			G|0.954;A|0.046	0.046	strong		0.343	MIS18BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276795.2			A	45693648	G	A	45693648	2	1	22	1	0	0	0	0	0	0	0	1	1740	1079	38	1		1	C14orf106	14	45693648	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	220383	45693648	61655892	2884	5785											
NID2	22795	hgsc.bcm.edu	37	chr14	52486850	52486850	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaggaaccaggagtattgtaGcaggtagctgcagggtgaca	13	7	15	6	0	0	1	0	1	0	0	0	3	0	3	1	4	4	6	1	4	5	4	rs8007166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:52486850G>A	ENST00000216286.5	-	13	2720	c.2721C>T	c.(2719-2721)tgC>tgT	p.C907C	NID2_ENST00000541773.1_Silent_p.C806C	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	907	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)					GAGTATTGTAGCAGGTAGCTG	0.463													g|||	144	0.028754	0.1051	0.0072	5008	,	,		18243	0.0		0.0	False		,,,				2504	0.0				p.C907C		Atlas-SNP	.											.	NID2	201	.	0			c.C2721T						PASS	.	G		345,4061	181.2+/-209.3	15,315,1873	127	110	115		2721	4.6	1	14	dbSNP_116	115	6,8594	3.7+/-12.6	0,6,4294	no	coding-synonymous	NID2	NM_007361.3		15,321,6167	AA,AG,GG		0.0698,7.8302,2.6988		907/1376	52486850	351,12655	2203	4300	6503	SO:0001819	synonymous_variant	22795	exon13			ATTGTAGCAGGTA	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.2721C>T	14.37:g.52486850G>A		111	0	0		115	60	0.521739	NM_007361	A8K6I7|B4DU19|O43710	Silent	SNP	ENST00000216286.5	37	CCDS9706.1																																																																																			G|0.971;A|0.029	0.029	strong		0.463	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			A	52486850	G	A	52486850	2	1	22	1	0	0	0	0	0	0	0	1	10424	963	34	2		2	NID2	14	52486850	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6793202	52486850	54862690	2885	5786											
NID2	22795	hgsc.bcm.edu	37	chr14	52493996	52493996	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcctccatggtgaacacacCgggcctgcccagcaggagca	9	5	12	15	1	0	1	0	1	0	0	1	2	1	2	5	3	5	2	5	3	1	0	rs28507587	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:52493996C>T	ENST00000216286.5	-	12	2596	c.2597G>A	c.(2596-2598)cGg>cAg	p.R866Q	NID2_ENST00000541773.1_Intron	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	866	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.		R -> Q (in dbSNP:rs28507587).		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)					GTGAACACACCGGGCCTGCCC	0.587													c|||	116	0.0231629	0.0847	0.0058	5008	,	,		19977	0.0		0.0	False		,,,				2504	0.0				p.R866Q		Atlas-SNP	.											NID2,NS,carcinoma,-1,1	NID2	201	1	0			c.G2597A						PASS	.	C	GLN/ARG	293,4113	160.3+/-192.7	12,269,1922	41	37	38		2597	-0.7	1	14	dbSNP_125	38	5,8595	3.0+/-9.4	0,5,4295	yes	missense	NID2	NM_007361.3	43	12,274,6217	TT,TC,CC		0.0581,6.65,2.2913	possibly-damaging	866/1376	52493996	298,12708	2203	4300	6503	SO:0001583	missense	22795	exon12			ACACACCGGGCCT	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.2597G>A	14.37:g.52493996C>T	ENSP00000216286:p.Arg866Gln	70	0	0		107	51	0.476636	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	37	CCDS9706.1	38	0.0173992673992674	35	0.07113821138211382	3	0.008287292817679558	0	0.0	0	0.0	C	9.202	1.028739	0.19512	0.0665	5.81E-4	ENSG00000087303	ENST00000216286;ENST00000316204;ENST00000395707	T	0.71934	-0.61	5.98	-0.687	0.11320	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.509728	0.21782	N	0.069185	T	0.05181	0.0138	L	0.33339	1.005	0.53688	D	0.999977	B;P;B	0.45044	0.012;0.849;0.04	B;B;B	0.26094	0.011;0.066;0.025	T	0.28138	-1.0053	10	0.10902	T	0.67	.	12.2116	0.54383	0.0:0.5941:0.0:0.4059	rs28507587;rs28507587	460;868;866	E7EPP3;Q5CZI2;Q14112	.;.;NID2_HUMAN	Q	866;460;868	ENSP00000216286:R866Q	ENSP00000216286:R866Q	R	-	2	0	NID2	51563746	0.000000	0.05858	0.956000	0.39512	0.155000	0.21991	-1.056000	0.03489	-0.047000	0.13423	-0.222000	0.12452	CGG	C|0.979;T|0.021	0.021	strong		0.587	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			T	52493996	C	T	52493996	3	4	22	1	0	0	0	0	1	0	0	0	10424	652	23	1	1574	1	NID2	14	52493996	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	7146	52493996	54855544	2886	5787											
ERO1L	30001	hgsc.bcm.edu	37	chr14	53133134	53133134	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgacattccatattttccaAgcatctggtcccttgtaacc	10	14	5	12	0	1	1	0	1	1	0	4	1	4	1	4	1	2	2	4	1	3	6	rs34388088	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:53133134A>G	ENST00000395686.3	-	7	811	c.588T>C	c.(586-588)gcT>gcC	p.A196A		NM_014584.1	NP_055399.1	Q96HE7	ERO1A_HUMAN	ERO1-like (S. cerevisiae)	196					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)					ATATTTTCCAAGCATCTGGTC	0.333													A|||	76	0.0151757	0.0537	0.0072	5008	,	,		17663	0.0		0.0	False		,,,				2504	0.0				p.A196A		Atlas-SNP	.											.	ERO1L	35	.	0			c.T588C						PASS	.	A		219,4187	129.4+/-166.1	8,203,1992	79	79	79		588	0.9	1	14	dbSNP_126	79	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	ERO1L	NM_014584.1		8,208,6287	GG,GA,AA		0.0581,4.9705,1.7223		196/469	53133134	224,12782	2203	4300	6503	SO:0001819	synonymous_variant	30001	exon7			TTTCCAAGCATCT	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.588T>C	14.37:g.53133134A>G		230	0	0		199	84	0.422111	NM_014584	A8K9X4|A8MYW1|Q7LD45|Q9P1Q9|Q9UKV6	Silent	SNP	ENST00000395686.3	37	CCDS9709.1																																																																																			A|0.985;G|0.015	0.015	strong		0.333	ERO1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276892.1	NM_014584		G	53133134	A	G	53133134	2	3	22	1	0	0	0	0	0	0	0	1	5241	59	3	3		3	ERO1L	14	53133134	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	639138	53133134	54216406	2887	5788											
FBXO34	55030	hgsc.bcm.edu	37	chr14	55818162	55818162	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgtatctgtggattgtggcCcttcaagagctgatcgttgt	6	15	12	8	1	2	2	1	1	1	1	3	3	2	3	1	2	1	3	1	2	2	4	rs74050979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:55818162C>T	ENST00000313833.4	+	2	1299	c.1054C>T	c.(1054-1056)Cct>Tct	p.P352S	FBXO34_ENST00000440021.1_Missense_Mutation_p.P352S	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	352										breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						GGATTGTGGCCCTTCAAGAGC	0.532													C|||	74	0.0147764	0.053	0.0058	5008	,	,		18923	0.0		0.0	False		,,,				2504	0.0				p.P352S		Atlas-SNP	.											.	FBXO34	61	.	0			c.C1054T						PASS	.	C	SER/PRO,SER/PRO	248,4158	143.8+/-178.8	7,234,1962	118	112	114		1054,1054	1.2	0	14	dbSNP_130	114	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	FBXO34	NM_017943.3,NM_152231.1	74,74	7,237,6259	TT,TC,CC		0.0349,5.6287,1.9299	benign,benign	352/712,352/712	55818162	251,12755	2203	4300	6503	SO:0001583	missense	55030	exon2			TGTGGCCCTTCAA	AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"F-boxes /  "other""	20201	protein-coding gene	gene with protein product		609104	"F-box only protein 34"				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.1054C>T	14.37:g.55818162C>T	ENSP00000313159:p.Pro352Ser	195	0	0		207	90	0.434783	NM_017943	Q2VPB5|Q4VBP5|Q86TY4	Missense_Mutation	SNP	ENST00000313833.4	37	CCDS32086.1	30	0.013736263736263736	28	0.056910569105691054	2	0.0055248618784530384	0	0.0	0	0.0	C	2.024	-0.423983	0.04734	0.056287	3.49E-4	ENSG00000178974	ENST00000313833;ENST00000440021	T;T	0.17528	2.27;2.27	5.29	1.21	0.21127	.	0.444948	0.20885	N	0.083928	T	0.01695	0.0054	M	0.66939	2.045	0.09310	N	1	B	0.10296	0.003	B	0.15484	0.013	T	0.14090	-1.0485	10	0.36615	T	0.2	-19.68	8.4711	0.32986	0.0:0.6402:0.0:0.3598	.	352	Q9NWN3	FBX34_HUMAN	S	352	ENSP00000313159:P352S;ENSP00000394117:P352S	ENSP00000313159:P352S	P	+	1	0	FBXO34	54887915	0.000000	0.05858	0.001000	0.08648	0.034000	0.12701	0.391000	0.20784	0.388000	0.25054	0.650000	0.86243	CCT	C|0.979;T|0.021	0.021	strong		0.532	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1			T	55818162	C	T	55818162	3	4	22	1	0	0	0	0	1	0	0	0	5752	623	22	2	1056	2	FBXO34	14	55818162	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2685028	55818162	51531378	2888	5789											
FBXO34	55030	hgsc.bcm.edu	37	chr14	55818514	55818514	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ggtagacaaagaccagccttCcattttaaactcctgtgaag	13	10	8	10	0	0	3	0	1	0	2	2	3	2	3	4	1	2	1	4	1	5	4	rs59719421	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:55818514C>T	ENST00000313833.4	+	2	1651	c.1406C>T	c.(1405-1407)tCc>tTc	p.S469F	FBXO34_ENST00000440021.1_Missense_Mutation_p.S469F	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	469										breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						GACCAGCCTTCCATTTTAAAC	0.433													C|||	74	0.0147764	0.053	0.0058	5008	,	,		20569	0.0		0.0	False		,,,				2504	0.0				p.S469F		Atlas-SNP	.											.	FBXO34	61	.	0			c.C1406T						PASS	.	C	PHE/SER,PHE/SER	247,4159	143.1+/-178.2	7,233,1963	117	113	114		1406,1406	4.6	0	14	dbSNP_129	114	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	FBXO34	NM_017943.3,NM_152231.1	155,155	7,236,6260	TT,TC,CC		0.0349,5.606,1.9222	possibly-damaging,possibly-damaging	469/712,469/712	55818514	250,12756	2203	4300	6503	SO:0001583	missense	55030	exon2			AGCCTTCCATTTT	AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"F-boxes /  "other""	20201	protein-coding gene	gene with protein product		609104	"F-box only protein 34"				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.1406C>T	14.37:g.55818514C>T	ENSP00000313159:p.Ser469Phe	200	0	0		223	97	0.434978	NM_017943	Q2VPB5|Q4VBP5|Q86TY4	Missense_Mutation	SNP	ENST00000313833.4	37	CCDS32086.1	30	0.013736263736263736	28	0.056910569105691054	2	0.0055248618784530384	0	0.0	0	0.0	C	9.052	0.992345	0.18966	0.05606	3.49E-4	ENSG00000178974	ENST00000313833;ENST00000440021	T;T	0.19938	2.11;2.11	5.48	4.6	0.57074	.	0.393578	0.20036	N	0.100616	T	0.04003	0.0112	L	0.51422	1.61	0.09310	N	1	D	0.53462	0.96	P	0.55965	0.788	T	0.01130	-1.1442	10	0.62326	D	0.03	-11.2954	9.7892	0.40695	0.0:0.7856:0.1416:0.0728	rs59719421	469	Q9NWN3	FBX34_HUMAN	F	469	ENSP00000313159:S469F;ENSP00000394117:S469F	ENSP00000313159:S469F	S	+	2	0	FBXO34	54888267	0.215000	0.23574	0.006000	0.13384	0.072000	0.16883	1.083000	0.30815	1.573000	0.49748	-0.127000	0.14921	TCC	C|0.979;T|0.021	0.021	strong		0.433	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1			T	55818514	C	T	55818514	3	4	22	1	0	0	0	0	1	0	0	0	5752	855	30	2	1408	2	FBXO34	14	55818514	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	352	55818514	51531026	2889	5790											
PELI2	57161	hgsc.bcm.edu	37	chr14	56763743	56763743	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccctgtggacacgtgtgctcGgagaagtctgcaaaatactg	10	9	12	10	2	1	1	0	0	1	1	2	3	1	2	1	2	3	2	1	2	4	1	rs112097284	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:56763743G>T	ENST00000267460.4	+	6	1408	c.1122G>T	c.(1120-1122)tcG>tcT	p.S374S		NM_021255.2	NP_067078.1	Q9HAT8	PELI2_HUMAN	pellino E3 ubiquitin protein ligase family member 2	374					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						ACGTGTGCTCGGAGAAGTCTG	0.547													G|||	114	0.0227636	0.084	0.0043	5008	,	,		20479	0.0		0.0	False		,,,				2504	0.0				p.S374S		Atlas-SNP	.											.	PELI2	55	.	0			c.G1122T						PASS	.	G		307,4099	164.7+/-196.3	15,277,1911	170	147	155		1122	-4	1	14	dbSNP_132	155	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	PELI2	NM_021255.2		15,279,6209	TT,TG,GG		0.0233,6.9678,2.3758		374/421	56763743	309,12697	2203	4300	6503	SO:0001819	synonymous_variant	57161	exon6			GTGCTCGGAGAAG	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.1122G>T	14.37:g.56763743G>T		76	0	0		71	34	0.478873	NM_021255	B2RDY5	Silent	SNP	ENST00000267460.4	37	CCDS9726.1																																																																																			G|0.979;T|0.021	0.021	strong		0.547	PELI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276925.1			T	56763743	G	T	56763743	2	4	22	1	0	0	0	0	0	0	0	1	11731	1103	39	4		4	PELI2	14	56763743	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	945229	56763743	50585797	2890	5791											
DAAM1	23002	hgsc.bcm.edu	37	chr14	59821936	59821936	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtggtgccctcaagcagttgCtggaggtggttttggcattt	5	14	15	7	0	1	0	1	0	0	0	1	1	1	1	1	5	3	5	1	5	1	4	rs61755340	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:59821936C>T	ENST00000395125.1	+	20	2463	c.2440C>T	c.(2440-2442)Ctg>Ttg	p.L814L	DAAM1_ENST00000360909.3_Silent_p.L804L|DAAM1_ENST00000553966.1_Intron|DAAM1_ENST00000351081.1_Silent_p.L814L	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	814	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)		CAAGCAGTTGCTGGAGGTGGT	0.383													C|||	61	0.0121805	0.0446	0.0029	5008	,	,		23182	0.0		0.0	False		,,,				2504	0.0				p.L814L		Atlas-SNP	.											.	DAAM1	95	.	0			c.C2440T						PASS	.	C		90,4316	73.6+/-111.7	1,88,2114	188	176	180		2440	0.6	0.8	14	dbSNP_129	180	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	DAAM1	NM_014992.1		1,92,6410	TT,TC,CC		0.0465,2.0427,0.7227		814/1079	59821936	94,12912	2203	4300	6503	SO:0001819	synonymous_variant	23002	exon20			CAGTTGCTGGAGG	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.2440C>T	14.37:g.59821936C>T		275	0	0		280	126	0.45	NM_014992	Q86U34|Q8N1Z8|Q8TB39	Silent	SNP	ENST00000395125.1	37	CCDS9737.1																																																																																			C|0.993;T|0.007	0.007	strong		0.383	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992		T	59821936	C	T	59821936	2	4	22	1	0	0	0	0	0	0	0	1	4217	796	28	2		2	DAAM1	14	59821936	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3058193	59821936	47527604	2891	5792											
C14orf135	64430	hgsc.bcm.edu	37	chr14	60585282	60585282	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gttcttggtggggtttccccGacctattcagagttggccag	5	13	13	10	1	2	1	1	0	1	1	3	2	3	1	4	4	0	3	4	4	1	6	rs144345462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:60585282G>A	ENST00000406854.1	+	7	2368	c.1814G>A	c.(1813-1815)cGa>cAa	p.R605Q	PCNXL4_ENST00000535349.1_5'UTR|PCNXL4_ENST00000406949.1_Missense_Mutation_p.R371Q|PCNXL4_ENST00000317623.4_Missense_Mutation_p.R371Q|PCNXL4_ENST00000404681.2_Missense_Mutation_p.R605Q			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	605						integral component of membrane (GO:0016021)											GGGTTTCCCCGACCTATTCAG	0.493													G|||	32	0.00638978	0.0242	0.0	5008	,	,		16639	0.0		0.0	False		,,,				2504	0.0				p.R371Q		Atlas-SNP	.											.	.	.	.	0			c.G1112A						PASS	.	G	GLN/ARG	39,4367	42.3+/-75.8	0,39,2164	70	63	65		1112	6.1	1	14	dbSNP_134	65	0,8600		0,0,4300	yes	missense	C14orf135	NM_022495.5	43	0,39,6464	AA,AG,GG		0.0,0.8852,0.2999	probably-damaging	371/939	60585282	39,12967	2203	4300	6503	SO:0001583	missense	64430	exon6			TTCCCCGACCTAT	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.1814G>A	14.37:g.60585282G>A	ENSP00000384801:p.Arg605Gln	294	1	0.00340136		323	148	0.458204	NM_022495	A8MXM2|Q9BQG8|Q9H9F2	Missense_Mutation	SNP	ENST00000406854.1	37		20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	G	36	5.921833	0.97105	0.008852	0.0	ENSG00000126773	ENST00000317623;ENST00000406854;ENST00000406949;ENST00000404681	T;T;T;T	0.57436	0.4;0.43;0.65;0.43	6.07	6.07	0.98685	.	.	.	.	.	T	0.46521	0.1397	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.67304	-0.5704	9	0.87932	D	0	.	20.6439	0.99570	0.0:0.0:1.0:0.0	.	605;371	Q63HM2;B5MC47	CN135_HUMAN;.	Q	371;605;371;605	ENSP00000317396:R371Q;ENSP00000384801:R605Q;ENSP00000385201:R371Q;ENSP00000385713:R605Q	ENSP00000317396:R371Q	R	+	2	0	C14orf135	59655035	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	9.126000	0.94411	2.890000	0.99128	0.650000	0.86243	CGA	G|0.991;A|0.009	0.009	strong		0.493	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495		A	60585282	G	A	60585282	3	1	22	1	0	0	0	0	1	0	0	0	1747	1058	37	1	1130	1	C14orf135	14	60585282	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	763346	60585282	46764258	2892	5793											
TRMT5	145389	hgsc.bcm.edu	37	chr14	61445981	61445981	+	5'Flank	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgaaagacagctgatgatctCgaaggtttaggtgtgcaata	13	11	12	5	1	1	4	0	3	1	1	2	5	1	4	0	2	2	3	0	2	5	3	rs114005374	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:61445981C>T	ENST00000267488.4	+	0	0				TRMT5_ENST00000261249.6_Missense_Mutation_p.R212Q|RP11-193F5.1_ENST00000553946.1_RNA|SLC38A6_ENST00000354886.2_5'Flank|SLC38A6_ENST00000456840.2_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)		p.R212Q(1)		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)		CTGATGATCTCGAAGGTTTAG	0.353													C|||	11	0.00219649	0.0083	0.0	5008	,	,		21341	0.0		0.0	False		,,,				2504	0.0				p.R212Q		Atlas-SNP	.											TRMT5,caecum,carcinoma,0,1	TRMT5	44	1	1	Substitution - Missense(1)	large_intestine(1)	c.G635A						PASS	.	C	GLN/ARG	11,4395	17.9+/-39.9	0,11,2192	99	93	95		635	4.8	1	14	dbSNP_132	95	0,8600		0,0,4300	yes	missense	TRMT5	NM_020810.2	43	0,11,6492	TT,TC,CC		0.0,0.2497,0.0846	probably-damaging	212/510	61445981	11,12995	2203	4300	6503	SO:0001631	upstream_gene_variant	57570	exon2			TGATCTCGAAGGT	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		14.37:g.61445981C>T	Exception_encountered	119	0	0		129	61	0.472868	NM_020810	C9JWA6|Q86SY5	Missense_Mutation	SNP	ENST00000267488.4	37	CCDS9751.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	35	5.439965	0.96168	0.002497	0.0	ENSG00000126814	ENST00000261249	T	0.23754	1.89	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	T	0.51856	0.1699	M	0.91920	3.255	0.58432	D	0.999998	D	0.76494	0.999	D	0.73708	0.981	T	0.65709	-0.6102	10	0.46703	T	0.11	-9.0897	18.1347	0.89614	0.0:1.0:0.0:0.0	.	212	Q32P41	TRM5_HUMAN	Q	212	ENSP00000261249:R212Q	ENSP00000261249:R212Q	R	-	2	0	TRMT5	60515734	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.317000	0.79018	2.489000	0.83994	0.655000	0.94253	CGA	C|0.999;T|0.001	0.001	strong		0.353	SLC38A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276957.1			T	61445981	C	T	61445981	1	4	22	0	1	0	0	0	0	0	0	0	16582	884	31	1		1	TRMT5	14	61445981	5'Flank	SNP	C	TCGA-G8-6324-01A-11D-2210-10	860699	61445981	45903559	2893	5794											
SYNE2	23224	hgsc.bcm.edu	37	chr14	64450479	64450479	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgaacctgccactgatgataAaaaaacaggatcagcccact	16	7	7	11	0	1	3	1	3	0	0	1	4	1	4	3	1	4	0	3	1	5	1	rs78191145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:64450479A>G	ENST00000344113.4	+	18	2238	c.2026A>G	c.(2026-2028)Aaa>Gaa	p.K676E	SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Missense_Mutation_p.K676E|SYNE2_ENST00000358025.3_Missense_Mutation_p.K676E	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	676					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)		ACTGATGATAAAAAAACAGGA	0.303													A|||	31	0.0061901	0.0234	0.0	5008	,	,		14554	0.0		0.0	False		,,,				2504	0.0				p.K676E		Atlas-SNP	.											.	SYNE2	577	.	0			c.A2026G						PASS	.	A	GLU/LYS,GLU/LYS	85,3501		3,79,1711	40	39	39		2026,2026	3	0.1	14	dbSNP_131	39	0,8130		0,0,4065	yes	missense,missense	SYNE2	NM_015180.4,NM_182914.2	56,56	3,79,5776	GG,GA,AA		0.0,2.3703,0.7255	probably-damaging,probably-damaging	676/6886,676/6908	64450479	85,11631	1793	4065	5858	SO:0001583	missense	23224	exon18			ATGATAAAAAAAC	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.2026A>G	14.37:g.64450479A>G	ENSP00000341781:p.Lys676Glu	149	0	0		138	80	0.57971	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	A	10.57	1.387852	0.25031	0.023703	0.0	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	T;T;T	0.57436	0.76;0.76;0.4	5.56	3.05	0.35203	.	0.110909	0.38778	N	0.001580	T	0.24160	0.0585	L	0.44542	1.39	0.20196	N	0.999925	P;P	0.46064	0.798;0.872	B;P	0.45856	0.3;0.495	T	0.16100	-1.0414	10	0.52906	T	0.07	.	11.2166	0.48830	0.565:0.435:0.0:0.0	.	676;676	Q8WXH0;Q8WXH0-2	SYNE2_HUMAN;.	E	676	ENSP00000350719:K676E;ENSP00000341781:K676E;ENSP00000452570:K676E	ENSP00000261678:K676E	K	+	1	0	SYNE2	63520232	0.770000	0.28543	0.119000	0.21687	0.552000	0.35366	1.368000	0.34216	0.909000	0.36697	0.528000	0.53228	AAA	A|0.996;G|0.004	0.004	strong		0.303	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		G	64450479	A	G	64450479	3	3	22	1	0	0	0	0	1	0	0	0	15461	15	1	3	2092	3	SYNE2	14	64450479	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	3004498	64450479	42899061	2894	5795											
SYNE2	23224	hgsc.bcm.edu	37	chr14	64461914	64461914	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	accaagggtctcatcaaagaAcatgaggtacaataaagtgt	17	8	9	7	0	2	2	2	1	1	1	3	2	2	2	1	2	2	1	1	2	7	2	rs34001379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:64461914A>G	ENST00000344113.4	+	23	3146	c.2934A>G	c.(2932-2934)gaA>gaG	p.E978E	SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Silent_p.E978E|SYNE2_ENST00000358025.3_Silent_p.E978E	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	978					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)		TCATCAAAGAACATGAGGTAC	0.318													A|||	32	0.00638978	0.0242	0.0	5008	,	,		18525	0.0		0.0	False		,,,				2504	0.0				p.E978E		Atlas-SNP	.											SYNE2,rectum,carcinoma,+2,1	SYNE2	577	1	0			c.A2934G						PASS	.	A	,	93,3593		3,87,1753	47	46	46		2934,2934	-0.1	1	14	dbSNP_126	46	0,8152		0,0,4076	no	coding-synonymous,coding-synonymous	SYNE2	NM_015180.4,NM_182914.2	,	3,87,5829	GG,GA,AA		0.0,2.5231,0.7856	,	978/6886,978/6908	64461914	93,11745	1843	4076	5919	SO:0001819	synonymous_variant	23224	exon23			CAAAGAACATGAG	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.2934A>G	14.37:g.64461914A>G		171	0	0		158	78	0.493671	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																			A|0.995;G|0.005	0.005	strong		0.318	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		G	64461914	A	G	64461914	2	3	22	1	0	0	0	0	0	0	0	1	15461	40	2	3		3	SYNE2	14	64461914	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	11435	64461914	42887626	2895	5796											
SYNE2	23224	hgsc.bcm.edu	37	chr14	64519053	64519053	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagtgatttaaataataccCtagaggacttacggaatcaa	16	10	8	7	1	1	2	1	1	0	1	1	4	1	4	1	2	2	1	1	2	8	6	rs35960129	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:64519053C>T	ENST00000344113.4	+	48	8634	c.8422C>T	c.(8422-8424)Cta>Tta	p.L2808L	SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Silent_p.L2841L|SYNE2_ENST00000358025.3_Silent_p.L2808L	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2808					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)		AAATAATACCCTAGAGGACTT	0.383													C|||	120	0.0239617	0.087	0.0072	5008	,	,		20674	0.0		0.0	False		,,,				2504	0.0				p.L2808L		Atlas-SNP	.											.	SYNE2	577	.	0			c.C8422T						PASS	.	C	,	260,3436		11,238,1599	73	68	70		8422,8422	4	0.9	14	dbSNP_126	70	0,8182		0,0,4091	no	coding-synonymous,coding-synonymous	SYNE2	NM_015180.4,NM_182914.2	,	11,238,5690	TT,TC,CC		0.0,7.0346,2.1889	,	2808/6886,2808/6908	64519053	260,11618	1848	4091	5939	SO:0001819	synonymous_variant	23224	exon48			AATACCCTAGAGG	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.8422C>T	14.37:g.64519053C>T		85	0	0		114	56	0.491228	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																			C|0.990;T|0.010	0.010	strong		0.383	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		T	64519053	C	T	64519053	2	4	22	1	0	0	0	0	0	0	0	1	15461	680	24	2		2	SYNE2	14	64519053	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	57139	64519053	42830487	2896	5797											
SYNE2	23224	hgsc.bcm.edu	37	chr14	64604634	64604634	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caaaactggaagagcagtggTtgtccctgaacaagaaaatt	16	8	10	7	0	0	3	0	1	0	2	1	4	1	4	1	2	3	2	1	2	7	2	rs8007874	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:64604634T>C	ENST00000344113.4	+	79	14988	c.14776T>C	c.(14776-14778)Ttg>Ctg	p.L4926L	SYNE2_ENST00000394768.2_Silent_p.L1311L|SYNE2_ENST00000357395.3_Silent_p.L1311L|SYNE2_ENST00000554584.1_Silent_p.L4843L|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Silent_p.L1560L|SYNE2_ENST00000358025.3_Silent_p.L4926L	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	4926					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)		AGAGCAGTGGTTGTCCCTGAA	0.512													T|||	228	0.0455272	0.1687	0.0072	5008	,	,		16544	0.0		0.0	False		,,,				2504	0.0				p.L4926L		Atlas-SNP	.											.	SYNE2	577	.	0			c.T14776C						PASS	.	T	,	577,3829	255.5+/-260.7	39,499,1665	83	73	76		14776,14776	-3.5	1	14	dbSNP_116	76	6,8594	3.0+/-9.4	0,6,4294	no	coding-synonymous,coding-synonymous	SYNE2	NM_015180.4,NM_182914.2	,	39,505,5959	CC,CT,TT		0.0698,13.0958,4.4825	,	4926/6886,4926/6908	64604634	583,12423	2203	4300	6503	SO:0001819	synonymous_variant	23224	exon79			CAGTGGTTGTCCC	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.14776T>C	14.37:g.64604634T>C		107	0	0		95	51	0.536842	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																			T|0.941;C|0.059	0.059	strong		0.512	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		C	64604634	T	C	64604634	2	2	22	1	0	0	0	0	0	0	0	1	15461	1722	60	3		3	SYNE2	14	64604634	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	85581	64604634	42744906	2897	5798											
SYNE2	23224	hgsc.bcm.edu	37	chr14	64688335	64688335	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aatctgctgctgtggttagcGagtgccaagaaccggaggca	10	8	14	9	2	1	1	0	0	1	1	1	3	1	2	2	3	5	4	2	3	4	1	rs75079588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:64688335G>A	ENST00000344113.4	+	111	20246	c.20034G>A	c.(20032-20034)gcG>gcA	p.A6678A	SYNE2_ENST00000394768.2_Silent_p.A3063A|SYNE2_ENST00000555022.1_Silent_p.A556A|SYNE2_ENST00000357395.3_Silent_p.A3063A|SYNE2_ENST00000554584.1_Silent_p.A6594A|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000441438.2_Silent_p.A223A|SYNE2_ENST00000555002.1_Silent_p.A3335A|SYNE2_ENST00000358025.3_Silent_p.A6701A|SYNE2_ENST00000554805.1_Silent_p.A461A|SYNE2_ENST00000458046.2_Silent_p.A349A	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	6678					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)	p.A6701A(1)		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)		TGTGGTTAGCGAGTGCCAAGA	0.547													G|||	30	0.00599042	0.0219	0.0014	5008	,	,		18920	0.0		0.0	False		,,,				2504	0.0				p.A6701A		Atlas-SNP	.											SYNE2,NS,carcinoma,0,1	SYNE2	577	1	1	Substitution - coding silent(1)	lung(1)	c.G20103A						PASS	.	G	,,,	88,4318	73.6+/-111.7	1,86,2116	179	174	175		20034,669,1047,20103	-9.2	0	14	dbSNP_131	175	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYNE2	NM_015180.4,NM_182910.2,NM_182913.2,NM_182914.2	,,,	1,87,6415	AA,AG,GG		0.0116,1.9973,0.6843	,,,	6678/6886,223/430,349/557,6701/6908	64688335	89,12917	2203	4300	6503	SO:0001819	synonymous_variant	23224	exon112			GTTAGCGAGTGCC	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.20034G>A	14.37:g.64688335G>A		113	0	0		161	88	0.546584	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																			G|0.994;A|0.006	0.006	strong		0.547	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		A	64688335	G	A	64688335	2	1	22	1	0	0	0	0	0	0	0	1	15461	1045	37	1		1	SYNE2	14	64688335	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	83701	64688335	42661205	2898	5799											
PLEKHH1	57475	hgsc.bcm.edu	37	chr14	68023989	68023989	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atcattgtacttttcaggtgGgtgtcatggaagagaaggta	11	13	13	4	0	3	1	3	0	0	1	3	3	3	2	0	4	1	2	0	4	4	5	rs149253165	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:68023989G>C	ENST00000329153.5	+	4	325	c.193G>C	c.(193-195)Ggt>Cgt	p.G65R		NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	65						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)		TTTTCAGGTGGGTGTCATGGA	0.507													G|||	40	0.00798722	0.028	0.0043	5008	,	,		19812	0.0		0.0	False		,,,				2504	0.0				p.G65R		Atlas-SNP	.											.	PLEKHH1	118	.	0			c.G193C						PASS	.	G	ARG/GLY	87,3815		0,87,1864	74	88	83		193	2.5	1	14	dbSNP_134	83	1,8305		0,1,4152	yes	missense	PLEKHH1	NM_020715.2	125	0,88,6016	CC,CG,GG		0.012,2.2296,0.7208	benign	65/1365	68023989	88,12120	1951	4153	6104	SO:0001583	missense	57475	exon4			CAGGTGGGTGTCA	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.193G>C	14.37:g.68023989G>C	ENSP00000330278:p.Gly65Arg	81	0	0		92	52	0.565217	NM_020715	A6H8X6|Q6PJL4|Q6ZWC7	Missense_Mutation	SNP	ENST00000329153.5	37	CCDS45128.1	16	0.007326007326007326	13	0.026422764227642278	3	0.008287292817679558	0	0.0	0	0.0	G	2.631	-0.286399	0.05605	0.022296	1.2E-4	ENSG00000054690	ENST00000329153	T	0.04083	3.71	5.41	2.47	0.30058	.	0.335067	0.36303	N	0.002673	T	0.00936	0.0031	L	0.28014	0.82	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.42207	-0.9465	10	0.02654	T	1	.	7.9764	0.30157	0.2765:0.0:0.7235:0.0	.	65	Q9ULM0	PKHH1_HUMAN	R	65	ENSP00000330278:G65R	ENSP00000330278:G65R	G	+	1	0	PLEKHH1	67093742	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	0.637000	0.24659	0.349000	0.23975	-0.254000	0.11334	GGT	G|0.993;C|0.007	0.007	strong		0.507	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054		C	68023989	G	C	68023989	3	2	22	1	0	0	0	0	1	0	0	0	12085	1232	43	4	203	4	PLEKHH1	14	68023989	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3335654	68023989	39325551	2899	5800											
VTI1B	10490	hgsc.bcm.edu	37	chr14	68141105	68141105	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gcctcaccggtccccgccgtCcccagcagccgctcgggcac	4	4	11	22	5	1	0	1	0	0	0	4	0	3	0	8	2	2	3	8	2	0	0	rs2234510	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:68141105C>T	ENST00000554659.1	-	1	443	c.102G>A	c.(100-102)ggG>ggA	p.G34G	RP11-1012A1.4_ENST00000554493.1_Intron|RP11-1012A1.4_ENST00000553306.1_Intron	NM_006370.2	NP_006361.1	Q9UEU0	VTI1B_HUMAN	vesicle transport through interaction with t-SNAREs 1B	34					cell proliferation (GO:0008283)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|SNARE complex (GO:0031201)|synaptic vesicle (GO:0008021)	SNARE binding (GO:0000149)			endometrium(1)|large_intestine(2)|stomach(1)|upper_aerodigestive_tract(1)	5				all cancers(60;0.000344)|OV - Ovarian serous cystadenocarcinoma(108;0.00212)|BRCA - Breast invasive adenocarcinoma(234;0.00941)		TCCCCGCCGTCCCCAGCAGCC	0.697													C|||	150	0.0299521	0.1097	0.0072	5008	,	,		8683	0.0		0.0	False		,,,				2504	0.0				p.G34G		Atlas-SNP	.											.	VTI1B	15	.	0			c.G102A						PASS	.	C		347,3945		9,329,1808	8	9	9		102	0.4	0.4	14	dbSNP_98	9	1,8419		0,1,4209	no	coding-synonymous	VTI1B	NM_006370.2		9,330,6017	TT,TC,CC		0.0119,8.0848,2.7376		34/233	68141105	348,12364	2146	4210	6356	SO:0001819	synonymous_variant	10490	exon1			CGCCGTCCCCAGC	AF060902	CCDS9786.1	14q23.3	2012-12-10	2012-12-10		ENSG00000100568	ENSG00000100568			17793	protein-coding gene	gene with protein product		603207	"vesicle transport through interaction with t-SNAREs homolog 1B (yeast)"			9636656, 9446565	Standard	NM_006370		Approved	VTI2	uc001xjt.3	Q9UEU0	OTTHUMG00000171251	ENST00000554659.1:c.102G>A	14.37:g.68141105C>T		24	0	0		63	32	0.507937	NM_006370	O43547|Q96J28	Silent	SNP	ENST00000554659.1	37	CCDS9786.1																																																																																			C|0.973;T|0.027	0.027	strong		0.697	VTI1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412558.2			T	68141105	C	T	68141105	2	4	22	1	0	0	0	0	0	0	0	1	17251	842	30	2		2	VTI1B	14	68141105	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	117116	68141105	39208435	2900	5801											
RAD51L1	5890	hgsc.bcm.edu	37	chr14	68292187	68292187	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttatgtttctttaggactttTtatgtctttccccactggag	6	20	7	8	0	2	0	0	0	2	0	3	2	3	2	2	2	0	1	2	2	3	8	rs114131734	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:68292187T>C	ENST00000487270.1	+	3	139	c.91T>C	c.(91-93)Tta>Cta	p.L31L	RAD51B_ENST00000471583.1_Silent_p.L31L|RAD51B_ENST00000488612.1_Silent_p.L31L|RAD51B_ENST00000390683.3_Silent_p.L31L|RAD51B_ENST00000487861.1_Silent_p.L31L	NM_133509.3	NP_598193.2	O15315	RA51B_HUMAN	RAD51 paralog B	31	Interaction with RAD51C.				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						TTAGGACTTTTTATGTCTTTC	0.383								Direct reversal of damage					T|||	45	0.00898562	0.0325	0.0029	5008	,	,		16807	0.0		0.0	False		,,,				2504	0.0				p.L31L		Atlas-SNP	.											.	RAD51B	80	.	0			c.T91C						PASS	.	T	,,	162,4244	111.6+/-149.8	3,156,2044	118	113	115		91,91,91	0.4	1	14	dbSNP_132	115	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	RAD51B	NM_002877.5,NM_133509.3,NM_133510.3	,,	3,158,6342	CC,CT,TT		0.0233,3.6768,1.261	,,	31/351,31/385,31/351	68292187	164,12842	2203	4300	6503	SO:0001819	synonymous_variant	5890	exon3			GACTTTTTATGTC	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.91T>C	14.37:g.68292187T>C		81	0	0		70	29	0.414286	NM_133509	O60914|O75210|Q3Y4F8|Q6FHX8|Q86SY3|Q86SY4|Q86TR0|Q86U92|Q86U93|Q86U94|Q8N6H4|Q9UPL5	Silent	SNP	ENST00000487270.1	37	CCDS9789.1																																																																																			T|0.991;C|0.009	0.009	strong		0.383	RAD51B-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000349063.1			C	68292187	T	C	68292187	2	2	22	1	0	0	0	0	0	0	0	1	13004	1838	64	3		3	RAD51L1	14	68292187	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	151082	68292187	39057353	2901	5802											
SLC8A3	6547	hgsc.bcm.edu	37	chr14	70512964	70512964	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccaggaagacattgacggcGttgctgcccgtcacgttgcc	7	8	12	14	4	1	2	1	1	0	1	1	3	1	3	3	2	3	3	3	2	1	3	rs144234198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:70512964G>A	ENST00000381269.2	-	8	3237	c.2484C>T	c.(2482-2484)aaC>aaT	p.N828N	SLC8A3_ENST00000528359.1_Silent_p.N826N|SLC8A3_ENST00000533541.1_3'UTR|SLC8A3_ENST00000394330.2_Silent_p.N185N|SLC8A3_ENST00000216568.7_Silent_p.N199N|SLC8A3_ENST00000356921.2_Silent_p.N822N|SLC8A3_ENST00000534137.1_Silent_p.N825N|SLC8A3_ENST00000357887.3_Silent_p.N826N	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 3	828					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)		CATTGACGGCGTTGCTGCCCG	0.602											OREG0022773	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N828N		Atlas-SNP	.											SLC8A3_ENST00000357887,colon,carcinoma,0,2	SLC8A3	234	2	0			c.C2484T						PASS	.	G	,,,,,	1,4405	2.1+/-5.4	0,1,2202	49	43	45		597,2478,2475,2466,555,2484	-3.9	0.9	14	dbSNP_134	45	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC8A3	NM_001130417.1,NM_033262.3,NM_058240.2,NM_182932.1,NM_182936.1,NM_183002.1	,,,,,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	,,,,,	199/299,826/926,825/925,822/922,185/285,828/928	70512964	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	6547	exon8			GACGGCGTTGCTG	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.2484C>T	14.37:g.70512964G>A		94	0	0	1122	148	71	0.47973	NM_183002	Q5K3P6|Q5K3P7|Q8IUE9|Q8IUF0|Q8NFI7|Q96QG1|Q96QG2	Silent	SNP	ENST00000381269.2	37	CCDS35498.1																																																																																			G|1.000;A|0.000	0.000	strong		0.602	SLC8A3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390736.1			A	70512964	G	A	70512964	2	1	22	1	0	0	0	0	0	0	0	1	14723	1136	40	1		1	SLC8A3	14	70512964	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2220777	70512964	36836576	2902	5803											
MAP3K9	4293	hgsc.bcm.edu	37	chr14	71202692	71202692	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcaccccaagtggaaatgTggagattctgatggggtact	11	10	12	8	0	2	2	1	1	1	1	2	4	2	3	2	4	1	1	2	4	3	2	rs78155813	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:71202692T>C	ENST00000554752.2	-	9	1898	c.1899A>G	c.(1897-1899)ccA>ccG	p.P633P	MAP3K9_ENST00000553414.1_Intron|MAP3K9_ENST00000554146.1_Intron|MAP3K9_ENST00000381250.4_Intron|MAP3K9_ENST00000555993.2_Silent_p.P633P	NM_001284230.1	NP_001271159.1	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase 9	633					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)		AGTGGAAATGTGGAGATTCTG	0.453													T|||	59	0.0117812	0.0408	0.0072	5008	,	,		21579	0.0		0.0	False		,,,				2504	0.0				p.P633P	GBM(114;411 1587 13539 28235 50070)	Atlas-SNP	.											.	MAP3K9	109	.	0			c.A1899G						PASS	.	T		85,4321	72.0+/-110.0	1,83,2119	173	148	156		1899	3.2	1	14	dbSNP_132	156	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MAP3K9	NM_033141.2		1,84,6418	CC,CT,TT		0.0116,1.9292,0.6612		633/1119	71202692	86,12920	2203	4300	6503	SO:0001819	synonymous_variant	4293	exon9			GAAATGTGGAGAT	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.1899A>G	14.37:g.71202692T>C		85	0	0		81	44	0.54321	NM_033141	A3KN85|Q0D2G7|Q6EH31|Q9H2N5	Silent	SNP	ENST00000554752.2	37																																																																																				T|0.989;C|0.011	0.011	strong		0.453	MAP3K9-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412550.2			C	71202692	T	C	71202692	2	2	22	1	0	0	0	0	0	0	0	1	9266	1683	59	3		3	MAP3K9	14	71202692	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	689728	71202692	36146848	2903	5804											
PCNX	22990	hgsc.bcm.edu	37	chr14	71514668	71514668	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttttcagagaccatgctgttGgatctcttctttatgtccat	7	18	7	9	0	3	1	1	0	2	1	5	3	4	2	2	1	1	2	2	1	1	6	rs78161372	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:71514668G>C	ENST00000304743.2	+	22	4751	c.4305G>C	c.(4303-4305)ttG>ttC	p.L1435F	PCNX_ENST00000238570.5_Missense_Mutation_p.L1435F|PCNX_ENST00000439984.3_Missense_Mutation_p.L1324F	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1435						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)		CCATGCTGTTGGATCTCTTCT	0.358													G|||	26	0.00519169	0.0174	0.0043	5008	,	,		15956	0.0		0.0	False		,,,				2504	0.0				p.L1435F		Atlas-SNP	.											.	PCNX	198	.	0			c.G4305C						PASS	.	G	PHE/LEU	62,4342	59.3+/-96.0	0,62,2140	129	120	123		4305	3.2	1	14	dbSNP_132	123	0,8598		0,0,4299	yes	missense	PCNX	NM_014982.2	22	0,62,6439	CC,CG,GG		0.0,1.4078,0.4768	possibly-damaging	1435/2342	71514668	62,12940	2202	4299	6501	SO:0001583	missense	22990	exon22			GCTGTTGGATCTC	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.4305G>C	14.37:g.71514668G>C	ENSP00000304192:p.Leu1435Phe	206	0	0		226	102	0.451327	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	37	CCDS9806.1	7|7	0.003205128205128205|0.003205128205128205	6|6	0.012195121951219513|0.012195121951219513	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	G|G	14.02|14.02	2.412251|2.412251	0.42817|0.42817	0.014078|0.014078	0.0|0.0	ENSG00000100731|ENSG00000100731	ENST00000304743;ENST00000238570;ENST00000439984|ENST00000554691	T;T;T|.	0.12147|.	3.14;3.11;2.71|.	5.41|5.41	3.19|3.19	0.36642|0.36642	.|.	0.212294|.	0.41001|.	D|.	0.000979|.	T|T	0.40619|0.40619	0.1124|0.1124	L|L	0.53249|0.53249	1.67|1.67	0.47819|0.47819	D|D	0.999528|0.999528	P;P;P|.	0.50272|.	0.879;0.609;0.933|.	P;B;B|.	0.47573|.	0.55;0.235;0.441|.	T|T	0.45041|0.45041	-0.9288|-0.9288	10|5	0.02654|.	T|.	1|.	.|.	2.1506|2.1506	0.03798|0.03798	0.3175:0.0:0.433:0.2494|0.3175:0.0:0.433:0.2494	.|.	1435;1324;1435|.	Q96RV3-3;B2RTR6;Q96RV3|.	.;.;PCX1_HUMAN|.	F|S	1435;1435;1324|494	ENSP00000304192:L1435F;ENSP00000238570:L1435F;ENSP00000396617:L1324F|.	ENSP00000238570:L1435F|.	L|W	+|+	3|2	2|0	PCNX|PCNX	70584421|70584421	0.927000|0.927000	0.31430|0.31430	0.978000|0.978000	0.43139|0.43139	0.996000|0.996000	0.88848|0.88848	0.071000|0.071000	0.14594|0.14594	1.412000|1.412000	0.46977|0.46977	0.655000|0.655000	0.94253|0.94253	TTG|TGG	G|0.995;C|0.005	0.005	strong		0.358	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		C	71514668	G	C	71514668	3	2	22	1	0	0	0	0	1	0	0	0	11600	1339	47	4	4391	4	PCNX	14	71514668	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	311976	71514668	35834872	2904	5805											
ACOT1	641371	hgsc.bcm.edu	37	chr14	74008304	74008304	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gttttgctgtgatggctctgGcttactataactatgaagac	9	15	10	7	0	1	3	0	2	1	1	1	3	1	3	0	2	3	4	0	2	5	6	rs146335256	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:74008304G>A	ENST00000311148.4	+	2	873	c.565G>A	c.(565-567)Gct>Act	p.A189T	HEATR4_ENST00000553558.1_Intron|HEATR4_ENST00000560393.1_Intron|HEATR4_ENST00000334988.2_Intron|ACOT1_ENST00000557556.1_Missense_Mutation_p.A189T	NM_001037161.1	NP_001032238.1	Q86TX2	ACOT1_HUMAN	acyl-CoA thioesterase 1	189					acyl-CoA metabolic process (GO:0006637)|long-chain fatty acid metabolic process (GO:0001676)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)			endometrium(1)|large_intestine(1)|lung(2)	4				OV - Ovarian serous cystadenocarcinoma(108;1.37e-45)|BRCA - Breast invasive adenocarcinoma(234;0.0033)		GATGGCTCTGGCTTACTATAA	0.527													-|||	78	0.0155751	0.0552	0.0072	5008	,	,		9026	0.0		0.0	False		,,,				2504	0.0				p.A189T		Atlas-SNP	.											.	ACOT1	12	.	0			c.G565A						PASS	.	G	THR/ALA,,	147,3835		36,75,1880	224	174	192		565,,	3.6	1	14	dbSNP_134	192	2,7196		1,0,3598	no	missense,intron,intron	HEATR4,ACOT1	NM_001037161.1,NM_001220484.1,NM_203309.2	58,,	37,75,5478	AA,AG,GG		0.0278,3.6916,1.3327	,,	189/422,,	74008304	149,11031	1991	3599	5590	SO:0001583	missense	641371	exon2			GCTCTGGCTTACT	DQ082754	CCDS32117.1	14q24.3	2013-09-20			ENSG00000184227	ENSG00000184227		"Acyl CoA thioesterases"	33128	protein-coding gene	gene with protein product		614313				16103133, 16940157	Standard	NM_001037161		Approved	ACH2, CTE-1, LACH2		Q86TX2	OTTHUMG00000171607	ENST00000311148.4:c.565G>A	14.37:g.74008304G>A	ENSP00000311224:p.Ala189Thr	241	0	0		258	257	0.996124	NM_001037161	A1L173|Q3I5F9	Missense_Mutation	SNP	ENST00000311148.4	37	CCDS32117.1	21	0.009615384615384616	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	0	0.0	-	15.12	2.737774	0.49045	0.036916	2.78E-4	ENSG00000184227	ENST00000311148;ENST00000557556	T;T	0.42513	0.97;0.97	3.61	3.61	0.41365	.	0.149549	0.64402	D	0.000013	T	0.42743	0.1216	H	0.94345	3.525	0.54753	D	0.999987	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.992	T	0.75634	-0.3250	10	0.87932	D	0	-10.4661	15.853	0.78947	0.0:0.0:1.0:0.0	.	189;189	E9KL42;Q86TX2	.;ACOT1_HUMAN	T	189	ENSP00000311224:A189T;ENSP00000451764:A189T	ENSP00000311224:A189T	A	+	1	0	ACOT1	73078057	1.000000	0.71417	1.000000	0.80357	0.046000	0.14306	5.637000	0.67854	2.022000	0.59522	0.423000	0.28283	GCT	G|0.989;A|0.011	0.011	strong		0.527	ACOT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414432.1	NM_001037161		A	74008304	G	A	74008304	3	1	22	1	0	0	0	0	1	0	0	0	148	1203	42	2	571	2	ACOT1	14	74008304	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2493636	74008304	33341236	2905	5806											
ACOT1	641371	hgsc.bcm.edu	37	chr14	74009937	74009937	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggcgtcaacagaaatcgcAtcaaggtgaccaaagatggc	14	6	12	9	2	2	3	2	1	0	2	3	3	2	3	1	3	1	1	1	3	4	0	rs377598014		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:74009937A>G	ENST00000311148.4	+	3	1152	c.844A>G	c.(844-846)Atc>Gtc	p.I282V	HEATR4_ENST00000553558.1_Intron|HEATR4_ENST00000560393.1_Intron|HEATR4_ENST00000334988.2_Intron|ACOT1_ENST00000557556.1_Missense_Mutation_p.I256V	NM_001037161.1	NP_001032238.1	Q86TX2	ACOT1_HUMAN	acyl-CoA thioesterase 1	282					acyl-CoA metabolic process (GO:0006637)|long-chain fatty acid metabolic process (GO:0001676)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)			endometrium(1)|large_intestine(1)|lung(2)	4				OV - Ovarian serous cystadenocarcinoma(108;1.37e-45)|BRCA - Breast invasive adenocarcinoma(234;0.0033)		CAGAAATCGCATCAAGGTGAC	0.552																																					p.I282V		Atlas-SNP	.											.	ACOT1	12	.	0			c.A844G						PASS	.	A	VAL/ILE,,	1,4395		0,1,2197	84	65	72		844,,	-4.8	0	14		72	0,8584		0,0,4292	no	missense,intron,intron	HEATR4,ACOT1	NM_001037161.1,NM_001220484.1,NM_203309.2	29,,	0,1,6489	GG,GA,AA		0.0,0.0227,0.0077	,,	282/422,,	74009937	1,12979	2198	4292	6490	SO:0001583	missense	641371	exon3			AATCGCATCAAGG	DQ082754	CCDS32117.1	14q24.3	2013-09-20			ENSG00000184227	ENSG00000184227		"Acyl CoA thioesterases"	33128	protein-coding gene	gene with protein product		614313				16103133, 16940157	Standard	NM_001037161		Approved	ACH2, CTE-1, LACH2		Q86TX2	OTTHUMG00000171607	ENST00000311148.4:c.844A>G	14.37:g.74009937A>G	ENSP00000311224:p.Ile282Val	659	0	0		906	319	0.352097	NM_001037161	A1L173|Q3I5F9	Missense_Mutation	SNP	ENST00000311148.4	37	CCDS32117.1	.	.	.	.	.	.	.	.	.	.	-	7.679	0.688575	0.14973	2.27E-4	0.0	ENSG00000184227	ENST00000311148;ENST00000557556	T;T	0.28895	1.59;1.59	4.06	-4.76	0.03229	BAAT/Acyl-CoA thioester hydrolase C-terminal (1);	0.642575	0.16665	N	0.204604	T	0.14830	0.0358	N	0.25789	0.76	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35375	-0.9791	10	0.11794	T	0.64	-8.1147	9.7986	0.40751	0.127:0.2638:0.6092:0.0	.	282	Q86TX2	ACOT1_HUMAN	V	282;256	ENSP00000311224:I282V;ENSP00000451764:I256V	ENSP00000311224:I282V	I	+	1	0	ACOT1	73079690	0.000000	0.05858	0.014000	0.15608	0.043000	0.13939	-2.813000	0.00753	-0.728000	0.04882	0.324000	0.21423	ATC	.	.	weak		0.552	ACOT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414432.1	NM_001037161		G	74009937	A	G	74009937	3	3	22	1	0	0	0	0	1	0	0	0	148	217	8	3	854	3	ACOT1	14	74009937	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1633	74009937	33339603	2906	5807											
ENTPD5	957	hgsc.bcm.edu	37	chr14	74454675	74454675	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccatacaaggtgctggcgCtgacattgatggggcacatg	9	10	13	9	1	0	2	0	2	0	0	1	2	1	2	1	4	2	3	1	4	2	3	rs60372237	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:74454675C>G	ENST00000334696.6	-	4	450	c.131G>C	c.(130-132)aGc>aCc	p.S44T	ENTPD5_ENST00000556242.1_Missense_Mutation_p.S44T|ENTPD5_ENST00000557325.1_Missense_Mutation_p.S44T|ENTPD5_ENST00000554664.1_5'Flank	NM_001249.2	NP_001240.1	O75356	ENTP5_HUMAN	ectonucleoside triphosphate diphosphohydrolase 5	44					'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)		GGTGCTGGCGCTGACATTGAT	0.493													C|||	17	0.00339457	0.0129	0.0	5008	,	,		18640	0.0		0.0	False		,,,				2504	0.0				p.S44T		Atlas-SNP	.											.	ENTPD5	26	.	0			c.G131C						PASS	.	C	THR/SER	21,4385	28.1+/-56.4	0,21,2182	115	100	105		131	5.2	1	14	dbSNP_129	105	0,8600		0,0,4300	yes	missense	ENTPD5	NM_001249.2	58	0,21,6482	GG,GC,CC		0.0,0.4766,0.1615	benign	44/429	74454675	21,12985	2203	4300	6503	SO:0001583	missense	957	exon4			CTGGCGCTGACAT	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.131G>C	14.37:g.74454675C>G	ENSP00000335246:p.Ser44Thr	104	0	0		95	47	0.494737	NM_001249	A1L4C5|Q96RX0	Missense_Mutation	SNP	ENST00000334696.6	37	CCDS9825.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	13.72	2.320324	0.41096	0.004766	0.0	ENSG00000187097	ENST00000557325;ENST00000334696;ENST00000553284;ENST00000556242	T;T;T	0.30714	2.26;2.52;1.52	5.2	5.2	0.72013	.	0.672949	0.15537	N	0.257193	T	0.09291	0.0229	N	0.19112	0.55	0.24994	N	0.991512	B;B	0.22146	0.065;0.053	B;B	0.18561	0.022;0.013	T	0.11446	-1.0587	10	0.13470	T	0.59	-12.6302	10.8164	0.46578	0.0:0.9069:0.0:0.0931	rs60372237	44;44	O75356;G3V4I0	ENTP5_HUMAN;.	T	44	ENSP00000451810:S44T;ENSP00000335246:S44T;ENSP00000451591:S44T	ENSP00000335246:S44T	S	-	2	0	ENTPD5	73524428	0.858000	0.29795	1.000000	0.80357	0.972000	0.66771	1.528000	0.35985	2.708000	0.92522	0.551000	0.68910	AGC	C|0.997;G|0.003	0.003	strong		0.493	ENTPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412637.1	NM_001249		G	74454675	C	G	74454675	3	3	22	1	0	0	0	0	1	0	0	0	5144	797	28	4	1207	4	ENTPD5	14	74454675	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	444738	74454675	32894865	2907	5808											
LTBP2	4053	hgsc.bcm.edu	37	chr14	74973926	74973926	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgtggaagccaggctggcagCccagaacacagcggtaggag	11	4	16	10	1	0	1	0	0	0	1	0	3	0	3	2	5	4	3	2	5	3	1	rs139481866	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:74973926C>A	ENST00000261978.4	-	26	4249	c.3863G>T	c.(3862-3864)gGc>gTc	p.G1288V	LTBP2_ENST00000556690.1_Intron	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	1288	Cys-rich.|EGF-like 14; 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)		AGGCTGGCAGCCCAGAACACA	0.567													C|||	9	0.00179712	0.0053	0.0029	5008	,	,		19539	0.0		0.0	False		,,,				2504	0.0				p.G1288V		Atlas-SNP	.											.	LTBP2	158	.	0			c.G3863T						PASS	.	C	VAL/GLY	20,4386	28.1+/-56.4	0,20,2183	85	80	82		3863	2.4	0.8	14	dbSNP_134	82	0,8600		0,0,4300	yes	missense	LTBP2	NM_000428.2	109	0,20,6483	AA,AC,CC		0.0,0.4539,0.1538	probably-damaging	1288/1822	74973926	20,12986	2203	4300	6503	SO:0001583	missense	4053	exon26			TGGCAGCCCAGAA		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.3863G>T	14.37:g.74973926C>A	ENSP00000261978:p.Gly1288Val	310	0	0		339	178	0.525074	NM_000428	Q99907|Q9NS51	Missense_Mutation	SNP	ENST00000261978.4	37	CCDS9831.1	6	0.0027472527472527475	4	0.008130081300813009	2	0.0055248618784530384	0	0.0	0	0.0	C	14.80	2.643520	0.47258	0.004539	0.0	ENSG00000119681	ENST00000261978	D	0.86694	-2.16	5.22	2.36	0.29203	EGF-like calcium-binding (2);	0.521247	0.16060	N	0.231509	D	0.83147	0.5191	L	0.37630	1.12	0.80722	D	1	D	0.67145	0.996	D	0.66351	0.943	T	0.78610	-0.2137	10	0.30078	T	0.28	.	6.5858	0.22620	0.0:0.6598:0.1289:0.2113	.	1288	Q14767	LTBP2_HUMAN	V	1288	ENSP00000261978:G1288V	ENSP00000261978:G1288V	G	-	2	0	LTBP2	74043679	0.996000	0.38824	0.761000	0.31378	0.370000	0.29829	0.463000	0.21972	0.192000	0.20272	-0.224000	0.12420	GGC	C|0.998;A|0.002	0.002	strong		0.567	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428		A	74973926	C	A	74973926	3	1	22	1	0	0	0	0	1	0	0	0	9083	739	26	4	1646	4	LTBP2	14	74973926	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	519251	74973926	32375614	2908	5809											
POMT2	29954	hgsc.bcm.edu	37	chr14	77786864	77786864	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagggcccaccagccgaccGcctcgaagcgccgtgagccc	7	2	13	19	5	0	1	0	1	0	0	1	3	0	1	7	1	3	1	7	1	1	0	rs8177536	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:77786864G>T	ENST00000261534.4	-	1	363	c.161C>A	c.(160-162)gCg>gAg	p.A54E	GSTZ1_ENST00000556627.1_5'Flank|GSTZ1_ENST00000216465.5_5'Flank|GSTZ1_ENST00000557053.1_5'Flank|GSTZ1_ENST00000349555.3_5'Flank|GSTZ1_ENST00000554279.1_5'Flank|GSTZ1_ENST00000393734.1_5'Flank|GSTZ1_ENST00000557639.1_5'Flank|GSTZ1_ENST00000361389.4_5'Flank	NM_013382.5	NP_037514.2	Q9UKY4	POMT2_HUMAN	protein-O-mannosyltransferase 2	54			A -> E (in dbSNP:rs8177536).			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)		CCAGCCGACCGCCTCGAAGCG	0.711													G|||	162	0.0323482	0.1188	0.0072	5008	,	,		11629	0.0		0.0	False		,,,				2504	0.0				p.A54E		Atlas-SNP	.											.	POMT2	47	.	0			c.C161A						PASS	.	G	GLU/ALA	359,3731		14,331,1700	11	10	10		161	-1.7	0	14	dbSNP_117	10	3,8235		0,3,4116	yes	missense	POMT2	NM_013382.5	107	14,334,5816	TT,TG,GG		0.0364,8.7775,2.9364	benign	54/751	77786864	362,11966	2045	4119	6164	SO:0001583	missense	29954	exon1			CCGACCGCCTCGA	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.161C>A	14.37:g.77786864G>T	ENSP00000261534:p.Ala54Glu	32	0	0		41	27	0.658537	NM_013382	Q9NSG6|Q9P1W0|Q9P1W2	Missense_Mutation	SNP	ENST00000261534.4	37	CCDS9857.1	72	0.03296703296703297	70	0.14227642276422764	2	0.0055248618784530384	0	0.0	0	0.0	G	9.945	1.218430	0.22373	0.087775	3.64E-4	ENSG00000009830	ENST00000261534	T	0.76709	-1.04	5.34	-1.66	0.08265	.	0.721535	0.12751	N	0.442179	T	0.00412	0.0013	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.07271	-1.0781	9	0.02654	T	1	-1.3895	2.5294	0.04699	0.1453:0.2152:0.4208:0.2187	rs8177536;rs8177536	54	Q9UKY4	POMT2_HUMAN	E	54	ENSP00000261534:A54E	ENSP00000261534:A54E	A	-	2	0	POMT2	76856617	0.000000	0.05858	0.041000	0.18516	0.017000	0.09413	-0.222000	0.09190	-0.024000	0.13941	-0.136000	0.14681	GCG	G|0.920;T|0.080	0.080	strong		0.711	POMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414155.1	NM_013382		T	77786864	G	T	77786864	3	4	22	1	0	0	0	0	1	0	0	0	12255	1087	38	4	2175	4	POMT2	14	77786864	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2812938	77786864	29562676	2909	5810											
C14orf174	161394	hgsc.bcm.edu	37	chr14	77843920	77843920	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctaccagcagagatttaccaAgagccacagccagagaccga	15	4	9	13	1	0	3	0	0	0	3	0	6	0	3	5	0	5	1	5	0	3	3	rs61729313	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:77843920A>G	ENST00000216471.4	+	1	445	c.159A>G	c.(157-159)caA>caG	p.Q53Q	TMED8_ENST00000216468.7_5'Flank|SAMD15_ENST00000533095.2_Intron	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	53										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						AGATTTACCAAGAGCCACAGC	0.532													A|||	324	0.0646965	0.2368	0.0159	5008	,	,		18476	0.0		0.0	False		,,,				2504	0.0				p.Q53Q		Atlas-SNP	.											.	SAMD15	60	.	0			c.A159G						PASS	.	A		744,3662	304.4+/-288.4	66,612,1525	68	69	69		159	0.9	0	14	dbSNP_129	69	5,8595	2.2+/-6.3	0,5,4295	no	coding-synonymous	SAMD15	NM_001010860.1		66,617,5820	GG,GA,AA		0.0581,16.8861,5.7589		53/675	77843920	749,12257	2203	4300	6503	SO:0001819	synonymous_variant	161394	exon1			TTACCAAGAGCCA	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.159A>G	14.37:g.77843920A>G		97	0	0		102	54	0.529412	NM_001010860	Q2M3P3	Silent	SNP	ENST00000216471.4	37	CCDS32126.1																																																																																			A|0.932;G|0.068	0.068	strong		0.532	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860		G	77843920	A	G	77843920	2	3	22	1	0	0	0	0	0	0	0	1	1761	69	3	3		3	C14orf174	14	77843920	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	57056	77843920	29505620	2910	5811											
SEL1L	6400	hgsc.bcm.edu	37	chr14	81969158	81969158	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtaatcaccaaataaaagAgcatatgacactctctccag	18	8	5	10	0	2	2	1	1	1	1	4	2	3	2	2	0	1	2	2	0	6	3	rs35377988	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:81969158A>G	ENST00000336735.4	-	6	800	c.684T>C	c.(682-684)gcT>gcC	p.A228A	SEL1L_ENST00000555824.1_Silent_p.A228A	NM_005065.5	NP_005056.3	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like (C. elegans)	228	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)		CAAATAAAAGAGCATATGACA	0.423													A|||	195	0.0389377	0.1437	0.0072	5008	,	,		1526	0.0		0.0	False		,,,				2504	0.0				p.A228A		Atlas-SNP	.											.	SEL1L	67	.	0			c.T684C						PASS	.	A		477,3929	224.6+/-240.7	21,435,1747	185	175	178		684	-1.6	1	14	dbSNP_126	178	0,8600		0,0,4300	no	coding-synonymous	SEL1L	NM_005065.4		21,435,6047	GG,GA,AA		0.0,10.8261,3.6675		228/795	81969158	477,12529	2203	4300	6503	SO:0001819	synonymous_variant	6400	exon6			TAAAAGAGCATAT		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.684T>C	14.37:g.81969158A>G		78	0	0		94	35	0.37234	NM_001244984	Q6UWT6|Q9P1T9|Q9UHK7	Silent	SNP	ENST00000336735.4	37	CCDS9876.1																																																																																			A|0.957;G|0.043	0.043	strong		0.423	SEL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413325.1	NM_005065		G	81969158	A	G	81969158	2	3	22	1	0	0	0	0	0	0	0	1	14025	291	11	3		3	SEL1L	14	81969158	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	4125238	81969158	25380382	2911	5812											
TTC8	123016	hgsc.bcm.edu	37	chr14	89338786	89338786	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctggagatgcggaagggccAcgttgaacaggtcagtgaac	11	6	16	8	2	1	3	1	2	0	1	1	5	1	4	1	4	3	2	1	4	3	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:89338786A>G	ENST00000345383.5	+	12	1391	c.1307A>G	c.(1306-1308)cAc>cGc	p.H436R	TTC8_ENST00000338104.6_Missense_Mutation_p.H462R|TTC8_ENST00000536576.1_Missense_Mutation_p.H207R|TTC8_ENST00000354441.6_Missense_Mutation_p.H181R|TTC8_ENST00000358622.5_Missense_Mutation_p.H248R|TTC8_ENST00000380656.2_Missense_Mutation_p.H446R|TTC8_ENST00000346301.4_Missense_Mutation_p.H406R	NM_198309.2	NP_938051.1	Q8TAM2	TTC8_HUMAN	tetratricopeptide repeat domain 8	472					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						CGGAAGGGCCACGTTGAACAG	0.517																																					p.H446R		Atlas-SNP	.											.	TTC8	42	.	0			c.A1337G						PASS	.						131	110	117					14																	89338786		2203	4300	6503	SO:0001583	missense	123016	exon13			AGGGCCACGTTGA	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.1307A>G	14.37:g.89338786A>G	ENSP00000339486:p.His436Arg	60	0	0		63	24	0.380952	NM_144596	A6NFG2|B3KWA5|Q67B97|Q86SY0|Q86TV9|Q86U26|Q8NDH9|Q96DG8	Missense_Mutation	SNP	ENST00000345383.5	37	CCDS9885.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.85|11.85	1.761724|1.761724	0.31228|0.31228	.|.	.|.	ENSG00000165533|ENSG00000165533	ENST00000345383;ENST00000536576;ENST00000346301;ENST00000338104;ENST00000354441;ENST00000380656;ENST00000358622|ENST00000554686	T;T;T;T;T;T;T|.	0.58797|.	1.0;0.31;1.0;1.0;0.31;1.0;1.0|.	5.59|5.59	5.59|5.59	0.84812|0.84812	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);|.	0.094735|.	0.64402|.	D|.	0.000001|.	T|T	0.30103|0.30103	0.0754|0.0754	N|N	0.02802|0.02802	-0.49|-0.49	0.49798|0.49798	D|D	0.999823|0.999823	B;B;B;B;B|.	0.12013|.	0.005;0.0;0.005;0.0;0.0|.	B;B;B;B;B|.	0.14578|.	0.004;0.004;0.011;0.002;0.002|.	T|T	0.27872|0.27872	-1.0061|-1.0061	10|5	0.27082|.	T|.	0.32|.	-24.1045|-24.1045	11.1717|11.1717	0.48575|0.48575	0.9283:0.0:0.0717:0.0|0.9283:0.0:0.0717:0.0	.|.	181;207;472;416;446|.	Q8TAM2-2;B3KSL8;Q8TAM2;Q8TAM2-3;Q8TAM2-4|.	.;.;TTC8_HUMAN;.;.|.	R|A	436;207;406;462;181;446;248|396	ENSP00000339486:H436R;ENSP00000445067:H207R;ENSP00000298324:H406R;ENSP00000337653:H462R;ENSP00000346427:H181R;ENSP00000370031:H446R;ENSP00000351439:H248R|.	ENSP00000337653:H462R|.	H|T	+|+	2|1	0|0	TTC8|TTC8	88408539|88408539	0.992000|0.992000	0.36948|0.36948	0.930000|0.930000	0.37139|0.37139	0.977000|0.977000	0.68977|0.68977	2.851000|2.851000	0.48302|0.48302	2.254000|2.254000	0.74563|0.74563	0.459000|0.459000	0.35465|0.35465	CAC|ACG	.	.	none		0.517	TTC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410861.1	NM_144596		G	89338786	A	G	89338786	3	3	22	1	0	0	0	0	1	0	0	0	16729	159	6	3	1387	3	TTC8	14	89338786	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	7369628	89338786	18010754	2912	5813											
TTC8	123016	hgsc.bcm.edu	37	chr14	89343670	89343670	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagagaagctatgttgctgcGcagaagtctgaagcagcatt	12	9	12	8	1	1	3	0	1	1	2	1	4	1	3	0	0	5	6	0	0	4	3	rs142073418	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:89343670G>C	ENST00000345383.5	+	14	1518	c.1434G>C	c.(1432-1434)gcG>gcC	p.A478A	TTC8_ENST00000338104.6_Silent_p.A504A|TTC8_ENST00000536576.1_Silent_p.A249A|TTC8_ENST00000354441.6_Silent_p.A223A|TTC8_ENST00000358622.5_Silent_p.A290A|TTC8_ENST00000380656.2_Silent_p.A488A|TTC8_ENST00000346301.4_Silent_p.A448A	NM_198309.2	NP_938051.1	Q8TAM2	TTC8_HUMAN	tetratricopeptide repeat domain 8	514					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						ATGTTGCTGCGCAGAAGTCTG	0.378													G|||	7	0.00139776	0.0008	0.0014	5008	,	,		15836	0.0		0.002	False		,,,				2504	0.0031				p.A488A		Atlas-SNP	.											TTC8,NS,carcinoma,+2,1	TTC8	42	1	0			c.G1464C						PASS	.	G	,,	6,4400	11.4+/-27.6	0,6,2197	81	71	74		1464,1434,1344	-0.1	1	14	dbSNP_134	74	45,8555	27.4+/-76.7	0,45,4255	no	coding-synonymous,coding-synonymous,coding-synonymous	TTC8	NM_144596.2,NM_198309.2,NM_198310.2	,,	0,51,6452	CC,CG,GG		0.5233,0.1362,0.3921	,,	488/516,478/506,448/476	89343670	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	123016	exon15			TGCTGCGCAGAAG	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.1434G>C	14.37:g.89343670G>C		119	0	0		120	54	0.45	NM_144596	A6NFG2|B3KWA5|Q67B97|Q86SY0|Q86TV9|Q86U26|Q8NDH9|Q96DG8	Silent	SNP	ENST00000345383.5	37	CCDS9885.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	8.459	0.854948	0.17106	0.001362	0.005233	ENSG00000165533	ENST00000554686	.	.	.	5.4	-0.12	0.13539	.	.	.	.	.	T	0.34687	0.0906	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.19031	-1.0318	4	.	.	.	-15.2774	2.8711	0.05617	0.4346:0.0675:0.1193:0.3786	.	.	.	.	P	410	.	.	R	+	2	0	TTC8	88413423	0.828000	0.29307	0.998000	0.56505	0.891000	0.51852	-0.119000	0.10676	0.094000	0.17404	-0.384000	0.06662	CGC	G|0.997;C|0.003	0.003	strong		0.378	TTC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410861.1	NM_144596		C	89343670	G	C	89343670	2	2	22	1	0	0	0	0	0	0	0	1	16729	1074	38	4		4	TTC8	14	89343670	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4884	89343670	18005870	2913	5814											
TDP1	55775	hgsc.bcm.edu	37	chr14	90429858	90429858	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaaaatcatggcgctcccGcctgccacaggctcaaagag	11	6	10	14	2	2	2	2	1	0	1	3	2	3	2	3	2	1	2	3	2	3	0	rs28365054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:90429858G>A	ENST00000335725.4	+	3	650	c.400G>A	c.(400-402)Gcc>Acc	p.A134T	TDP1_ENST00000357382.3_5'UTR|TDP1_ENST00000555880.1_Missense_Mutation_p.A134T|TDP1_ENST00000393454.2_Missense_Mutation_p.A134T|TDP1_ENST00000393452.3_Missense_Mutation_p.A134T|TDP1_ENST00000555565.1_Intron	NM_018319.3	NP_060789.2	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	134			A -> T (in dbSNP:rs28365054). {ECO:0000269|Ref.3}.		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)		TGGCGCTCCCGCCTGCCACAG	0.527								Repair of DNA-protein crosslinks					G|||	530	0.105831	0.3336	0.0447	5008	,	,		20317	0.0089		0.0199	False		,,,				2504	0.0297				p.A134T		Atlas-SNP	.											.	TDP1	47	.	0			c.G400A						PASS	.	G	THR/ALA,THR/ALA	1239,3167	411.7+/-335.8	181,877,1145	48	45	46		400,400	-2.6	0	14	dbSNP_126	46	179,8421	80.1+/-142.7	3,173,4124	yes	missense,missense	TDP1	NM_001008744.1,NM_018319.3	58,58	184,1050,5269	AA,AG,GG		2.0814,28.1207,10.9027	benign,benign	134/609,134/609	90429858	1418,11588	2203	4300	6503	SO:0001583	missense	55775	exon3			GCTCCCGCCTGCC	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.400G>A	14.37:g.90429858G>A	ENSP00000337353:p.Ala134Thr	80	0	0		99	54	0.545455	NM_018319	Q2HXX4|Q86TV8|Q96BK7|Q9NZM7|Q9NZM8	Missense_Mutation	SNP	ENST00000335725.4	37	CCDS9888.1	195	0.08928571428571429	155	0.3150406504065041	19	0.052486187845303865	8	0.013986013986013986	13	0.017150395778364115	G	6.023	0.372548	0.11409	0.281207	0.020814	ENSG00000042088	ENST00000393452;ENST00000554180;ENST00000393454;ENST00000553617;ENST00000335725;ENST00000556867;ENST00000553527;ENST00000553989;ENST00000556498;ENST00000555880	T;T;T;T;T;T;T;T;T;T	0.30981	1.51;2.25;1.75;2.22;1.75;1.87;1.87;1.87;1.91;1.52	5.36	-2.62	0.06152	.	1.082140	0.06853	N	0.797624	T	0.00012	0.0000	N	0.13043	0.29	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.09022	0.001;0.001;0.001;0.002	B;B;B;B	0.06405	0.001;0.001;0.002;0.0	T	0.44390	-0.9331	9	0.13108	T	0.6	-10.0622	5.7326	0.18049	0.4341:0.0:0.4386:0.1273	rs28365054;rs35332925;rs28365054	134;134;134;134	G3V2F4;E7EPD8;G3V4W8;Q9NUW8	.;.;.;TYDP1_HUMAN	T	134;134;134;35;134;134;134;134;134;134	ENSP00000377098:A134T;ENSP00000450872:A134T;ENSP00000377099:A134T;ENSP00000450708:A35T;ENSP00000337353:A134T;ENSP00000452279:A134T;ENSP00000451358:A134T;ENSP00000452333:A134T;ENSP00000452183:A134T;ENSP00000450628:A134T	ENSP00000337353:A134T	A	+	1	0	TDP1	89499611	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.012000	0.13287	-0.617000	0.05664	-1.300000	0.01332	GCC	G|0.892;A|0.108	0.108	strong		0.527	TDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411239.1	NM_018319		A	90429858	G	A	90429858	3	1	22	1	0	0	0	0	1	0	0	0	15743	1087	38	1	402	1	TDP1	14	90429858	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1086188	90429858	16919682	2914	5815											
TDP1	55775	hgsc.bcm.edu	37	chr14	90451500	90451500	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatcttattggttcaaccccAggacgctttcaaggaagtca	11	12	8	10	1	4	0	3	0	1	0	4	2	4	2	2	3	1	2	2	3	5	5	rs17126522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:90451500A>G	ENST00000335725.4	+	10	1327	c.1077A>G	c.(1075-1077)ccA>ccG	p.P359P	TDP1_ENST00000357382.3_Silent_p.P120P|TDP1_ENST00000555880.1_Silent_p.P359P|TDP1_ENST00000393454.2_Silent_p.P359P|TDP1_ENST00000393452.3_Silent_p.P359P	NM_018319.3	NP_060789.2	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	359					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)		GTTCAACCCCAGGACGCTTTC	0.284								Repair of DNA-protein crosslinks					A|||	301	0.0601038	0.171	0.0288	5008	,	,		15009	0.0079		0.0179	False		,,,				2504	0.0297				p.P359P		Atlas-SNP	.											.	TDP1	47	.	0			c.A1077G						PASS	.	A	,	597,3809	246.5+/-255.1	44,509,1650	60	58	58		1077,1077	-11.2	0.7	14	dbSNP_123	58	171,8421	79.2+/-141.9	2,167,4127	no	coding-synonymous,coding-synonymous	TDP1	NM_001008744.1,NM_018319.3	,	46,676,5777	GG,GA,AA		1.9902,13.5497,5.9086	,	359/609,359/609	90451500	768,12230	2203	4296	6499	SO:0001819	synonymous_variant	55775	exon10			AACCCCAGGACGC	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.1077A>G	14.37:g.90451500A>G		153	0	0		162	80	0.493827	NM_018319	Q2HXX4|Q86TV8|Q96BK7|Q9NZM7|Q9NZM8	Silent	SNP	ENST00000335725.4	37	CCDS9888.1																																																																																			A|0.938;G|0.062	0.062	strong		0.284	TDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411239.1	NM_018319		G	90451500	A	G	90451500	2	3	22	1	0	0	0	0	0	0	0	1	15743	175	7	3		3	TDP1	14	90451500	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	21642	90451500	16898040	2915	5816											
C14orf159	80017	hgsc.bcm.edu	37	chr14	91666248	91666248	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attcctggaatctcatcaacTggtaagtatggagtactggg	11	12	11	7	0	2	0	2	0	1	0	4	2	3	2	1	4	2	3	1	4	5	4	rs28715808	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:91666248T>C	ENST00000523771.1	+	11	2031	c.1428T>C	c.(1426-1428)acT>acC	p.T476T	C14orf159_ENST00000518868.1_Splice_Site_p.T481T|C14orf159_ENST00000522322.1_Splice_Site_p.T476T|C14orf159_ENST00000521077.2_Splice_Site_p.T481T|C14orf159_ENST00000428926.2_Splice_Site_p.T476T|C14orf159_ENST00000520328.1_Splice_Site_p.T464T|C14orf159_ENST00000523816.1_Splice_Site_p.T476T|C14orf159_ENST00000412671.2_Splice_Site_p.T481T|C14orf159_ENST00000256324.10_Splice_Site_p.T481T|C14orf159_ENST00000525393.2_Splice_Site_p.T352T			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	476						mitochondrion (GO:0005739)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		TCTCATCAACTGGTAAGTATG	0.458													T|||	181	0.0361422	0.1067	0.0346	5008	,	,		22154	0.0		0.0109	False		,,,				2504	0.0051				p.T481T		Atlas-SNP	.											.	C14orf159	57	.	0			c.T1443C						PASS	.	T	,,,,	337,4069	176.9+/-206.0	16,305,1882	151	142	145		1428,1428,1443,1392,1428	-2.7	0.1	14	dbSNP_125	145	117,8483	61.0+/-122.8	0,117,4183	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	C14orf159	NM_001102366.1,NM_001102367.1,NM_001102368.1,NM_001102369.1,NM_024952.6	,,,,	16,422,6065	CC,CT,TT		1.3605,7.6487,3.4907	,,,,	476/617,476/617,481/622,464/565,476/617	91666248	454,12552	2203	4300	6503	SO:0001630	splice_region_variant	80017	exon11			ATCAACTGGTAAG	AK097294	CCDS32141.1, CCDS41979.1, CCDS45150.1, CCDS66693.1, CCDS73677.1	14q32.11	2012-09-26			ENSG00000133943	ENSG00000133943			20498	protein-coding gene	gene with protein product							Standard	NM_001102367		Approved	FLJ39975	uc001xze.2	Q7Z3D6	OTTHUMG00000164980	ENST00000523771.1:c.1429+1T>C	14.37:g.91666248T>C		135	0	0		155	86	0.554839	NM_001102368	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Silent	SNP	ENST00000523771.1	37	CCDS32141.1	60	0.027472527472527472	41	0.08333333333333333	12	0.03314917127071823	0	0.0	7	0.009234828496042216	T	0.894	-0.724442	0.03158	0.076487	0.013605	ENSG00000133943	ENST00000522816	.	.	.	5.1	-2.71	0.05986	.	.	.	.	.	T	0.00967	0.0032	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.22173	-1.0224	3	.	.	.	.	2.29	0.04136	0.3649:0.0777:0.3565:0.2009	rs28715808	.	.	.	P	77	.	.	L	+	2	0	C14orf159	90736001	0.990000	0.36364	0.051000	0.19133	0.053000	0.15095	0.237000	0.17985	-0.360000	0.08138	-0.461000	0.05368	CTG	T|0.967;C|0.033	0.033	strong		0.458	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952	Silent	C	91666248	T	C	91666248	5	2	22	1	0	0	0	0	0	0	1	0	1757	1594	55	3	1477	3	C14orf159	14	91666248	Splice_Site	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1214748	91666248	15683292	2916	5817											
GPR68	8111	hgsc.bcm.edu	37	chr14	91700319	91700319	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggccaacctgcccgtggggAacccgcccgaccctggcgag	7	3	14	17	4	0	0	0	0	0	0	0	3	0	1	6	4	3	0	6	4	2	0	rs151219229	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:91700319A>G	ENST00000531499.2	-	2	1415	c.1076T>C	c.(1075-1077)tTc>tCc	p.F359S	GPR68_ENST00000238699.3_Missense_Mutation_p.F369S|GPR68_ENST00000529300.1_5'Flank|GPR68_ENST00000535815.1_Missense_Mutation_p.F359S			Q15743	OGR1_HUMAN	G protein-coupled receptor 68	359					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)		GCCCGTGGGGAACCCGCCCGA	0.711													G|||	53	0.0105831	0.0393	0.0014	5008	,	,		13610	0.0		0.0	False		,,,				2504	0.0				p.F359S		Atlas-SNP	.											.	GPR68	32	.	0			c.T1076C						PASS	.	G	SER/PHE,SER/PHE	50,3832		0,50,1891	10	13	12		1076,1076	1.6	0	14	dbSNP_134	12	0,7436		0,0,3718	no	missense,missense	GPR68	NM_003485.3,NM_001177676.1	155,155	0,50,5609	GG,GA,AA		0.0,1.288,0.4418	benign,benign	359/366,359/366	91700319	50,11268	1941	3718	5659	SO:0001583	missense	8111	exon2			GTGGGGAACCCGC	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.1076T>C	14.37:g.91700319A>G	ENSP00000434045:p.Phe359Ser	46	0	0		42	11	0.261905	NM_001177676	Q13334|Q4VBB4|Q6IX34	Missense_Mutation	SNP	ENST00000531499.2	37	CCDS9894.2	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	4.035	0.004003	0.07866	0.01288	0.0	ENSG00000119714	ENST00000531499;ENST00000238699;ENST00000535815	T;T;T	0.61040	0.14;0.15;0.14	4.46	1.59	0.23543	.	0.406139	0.19168	N	0.121014	T	0.11324	0.0276	N	0.02539	-0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.16719	-1.0393	10	0.07175	T	0.84	.	4.0511	0.09796	0.2953:0.1741:0.5306:0.0	.	359;359	Q6NWR5;Q15743	.;OGR1_HUMAN	S	359;369;359	ENSP00000434045:F359S;ENSP00000238699:F369S;ENSP00000440797:F359S	ENSP00000238699:F369S	F	-	2	0	GPR68	90770072	.	.	0.005000	0.12908	0.002000	0.02628	.	.	-0.069000	0.12931	-0.227000	0.12334	TTC	A|0.995;G|0.005	0.005	strong		0.711	GPR68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395245.2			G	91700319	A	G	91700319	3	3	22	1	0	0	0	0	1	0	0	0	6715	246	9	3	25	3	GPR68	14	91700319	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	34071	91700319	15649221	2917	5818											
CCDC88C	440193	hgsc.bcm.edu	37	chr14	91739873	91739873	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttttgacggtgggggccacaAagttggtgggcatcttggcc	6	11	16	8	1	1	1	0	1	1	0	1	1	1	1	2	6	0	2	2	6	1	4	rs7145583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:91739873A>G	ENST00000389857.6	-	30	5269	c.5183T>C	c.(5182-5184)tTt>tCt	p.F1728S	CCDC88C_ENST00000331194.7_Missense_Mutation_p.F252S	NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	1728					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)				GGGGGCCACAAAGTTGGTGGG	0.622													A|||	28	0.00559105	0.0189	0.0043	5008	,	,		16431	0.0		0.0	False		,,,				2504	0.0				p.F1728S		Atlas-SNP	.											.	CCDC88C	192	.	0			c.T5183C						PASS	.	A	SER/PHE	63,3873		1,61,1906	29	33	32		5183	3.5	0.8	14	dbSNP_116	32	1,8255		0,1,4127	yes	missense	CCDC88C	NM_001080414.3	155	1,62,6033	GG,GA,AA		0.0121,1.6006,0.5249	benign	1728/2029	91739873	64,12128	1968	4128	6096	SO:0001583	missense	440193	exon30			GCCACAAAGTTGG		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.5183T>C	14.37:g.91739873A>G	ENSP00000374507:p.Phe1728Ser	183	0	0		150	72	0.48	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Missense_Mutation	SNP	ENST00000389857.6	37	CCDS45151.1	7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	A	7.279	0.608712	0.14066	0.016006	1.21E-4	ENSG00000015133	ENST00000389857;ENST00000427583;ENST00000331194	T;T	0.47528	2.39;0.84	4.7	3.52	0.40303	.	0.410931	0.18701	U	0.133580	T	0.25644	0.0624	M	0.64997	1.995	0.27192	N	0.960401	B;B;B	0.32160	0.242;0.231;0.358	B;B;B	0.33042	0.154;0.157;0.157	T	0.17410	-1.0370	10	0.30078	T	0.28	0.4499	6.9029	0.24293	0.6516:0.1293:0.0:0.2191	rs7145583	1728;252;178	Q9P219;Q9P219-2;Q9P219-3	DAPLE_HUMAN;.;.	S	1728;252;252	ENSP00000374507:F1728S;ENSP00000330332:F252S	ENSP00000330332:F252S	F	-	2	0	CCDC88C	90809626	0.999000	0.42202	0.816000	0.32577	0.093000	0.18481	2.620000	0.46410	0.630000	0.30394	0.377000	0.23210	TTT	A|0.997;G|0.003	0.003	strong		0.622	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353		G	91739873	A	G	91739873	3	3	22	1	0	0	0	0	1	0	0	0	2867	14	1	3	907	3	CCDC88C	14	91739873	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	39554	91739873	15609667	2918	5819											
CCDC88C	440193	hgsc.bcm.edu	37	chr14	91744348	91744348	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggggaggccgagcagggcCgcactccgacgtagggaggg	7	3	21	10	4	0	0	0	0	0	0	1	4	1	2	3	6	1	3	3	6	1	1	rs114849211	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:91744348C>T	ENST00000389857.6	-	29	5062	c.4976G>A	c.(4975-4977)cGg>cAg	p.R1659Q	CCDC88C_ENST00000331194.7_Missense_Mutation_p.R183Q	NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	1659					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)	p.R1659Q(2)|p.R183Q(1)		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)				CGAGCAGGGCCGCACTCCGAC	0.677													C|||	52	0.0103834	0.0386	0.0014	5008	,	,		17086	0.0		0.0	False		,,,				2504	0.0				p.R1659Q		Atlas-SNP	.											KIAA1509,caecum,carcinoma,-1,6	CCDC88C	192	6	3	Substitution - Missense(3)	urinary_tract(3)	c.G4976A						PASS	.	C	GLN/ARG	103,3867		0,103,1882	12	15	14		4976	4.5	0.2	14	dbSNP_132	14	1,8315		0,1,4157	yes	missense	CCDC88C	NM_001080414.3	43	0,104,6039	TT,TC,CC		0.012,2.5945,0.8465	probably-damaging	1659/2029	91744348	104,12182	1985	4158	6143	SO:0001583	missense	440193	exon29			CAGGGCCGCACTC		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.4976G>A	14.37:g.91744348C>T	ENSP00000374507:p.Arg1659Gln	77	0	0		103	57	0.553398	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Missense_Mutation	SNP	ENST00000389857.6	37	CCDS45151.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	C	16.75	3.209248	0.58343	0.025945	1.2E-4	ENSG00000015133	ENST00000389857;ENST00000427583;ENST00000331194	T;T	0.55930	2.19;0.49	5.55	4.47	0.54385	.	0.000000	0.47455	U	0.000221	T	0.40423	0.1116	L	0.54323	1.7	0.09310	N	0.999999	D;P;P	0.89917	1.0;0.812;0.812	D;B;B	0.80764	0.994;0.141;0.141	T	0.44757	-0.9307	10	0.72032	D	0.01	-41.3463	9.9503	0.41634	0.0:0.8456:0.0:0.1544	.	1659;183;109	Q9P219;Q9P219-2;Q9P219-3	DAPLE_HUMAN;.;.	Q	1659;183;183	ENSP00000374507:R1659Q;ENSP00000330332:R183Q	ENSP00000330332:R183Q	R	-	2	0	CCDC88C	90814101	0.903000	0.30736	0.169000	0.22859	0.580000	0.36256	2.140000	0.42159	2.608000	0.88229	0.462000	0.41574	CGG	C|0.994;T|0.006	0.006	strong		0.677	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353		T	91744348	C	T	91744348	3	4	22	1	0	0	0	0	1	0	0	0	2867	652	23	1	1118	1	CCDC88C	14	91744348	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4475	91744348	15605192	2919	5820											
CCDC88C	440193	hgsc.bcm.edu	37	chr14	91770308	91770308	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctgcgctctgggaactcagCgtggagttctccacctgccg	5	9	13	14	3	3	0	1	0	2	0	4	2	3	2	3	2	4	3	3	2	1	1	rs112741231	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:91770308C>T	ENST00000389857.6	-	20	3458	c.3372G>A	c.(3370-3372)acG>acA	p.T1124T		NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	1124					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)				GGGAACTCAGCGTGGAGTTCT	0.662													c|||	111	0.0221645	0.0772	0.013	5008	,	,		16262	0.0		0.0	False		,,,				2504	0.0				p.T1124T		Atlas-SNP	.											CCDC88C_ENST00000389857,NS,carcinoma,0,2	CCDC88C	192	2	0			c.G3372A						PASS	.	C		250,3982		8,234,1874	43	49	47		3372	-11	0.2	14	dbSNP_132	47	9,8477		0,9,4234	no	coding-synonymous	CCDC88C	NM_001080414.3		8,243,6108	TT,TC,CC		0.1061,5.9074,2.0365		1124/2029	91770308	259,12459	2116	4243	6359	SO:0001819	synonymous_variant	440193	exon20			ACTCAGCGTGGAG		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.3372G>A	14.37:g.91770308C>T		54	0	0		58	31	0.534483	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Silent	SNP	ENST00000389857.6	37	CCDS45151.1																																																																																			C|0.983;T|0.017	0.017	strong		0.662	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353		T	91770308	C	T	91770308	2	4	22	1	0	0	0	0	0	0	0	1	2867	755	27	1		1	CCDC88C	14	91770308	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	25960	91770308	15579232	2920	5821											
CCDC88C	440193	hgsc.bcm.edu	37	chr14	91805804	91805804	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcctgagtgaggtccacgatCagctgcagccgggcagagag	9	6	15	11	2	1	3	1	2	0	1	3	5	3	3	3	2	3	3	3	2	0	0	rs61220159	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:91805804C>T	ENST00000389857.6	-	8	713	c.627G>A	c.(625-627)ctG>ctA	p.L209L		NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	209					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)				GGTCCACGATCAGCTGCAGCC	0.602													C|||	166	0.033147	0.1188	0.013	5008	,	,		17173	0.0		0.0	False		,,,				2504	0.0				p.L209L		Atlas-SNP	.											.	CCDC88C	192	.	0			c.G627A						PASS	.	C		438,3852		17,404,1724	41	50	47		627	-0.9	1	14	dbSNP_129	47	4,8512		0,4,4254	yes	coding-synonymous	CCDC88C	NM_001080414.3		17,408,5978	TT,TC,CC		0.047,10.2098,3.4515		209/2029	91805804	442,12364	2145	4258	6403	SO:0001819	synonymous_variant	440193	exon8			CACGATCAGCTGC		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.627G>A	14.37:g.91805804C>T		193	0	0		230	124	0.53913	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Silent	SNP	ENST00000389857.6	37	CCDS45151.1																																																																																			C|0.968;T|0.032	0.032	strong		0.602	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353		T	91805804	C	T	91805804	2	4	22	1	0	0	0	0	0	0	0	1	2867	813	29	2		2	CCDC88C	14	91805804	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	35496	91805804	15543736	2921	5822											
TC2N	123036	hgsc.bcm.edu	37	chr14	92264736	92264736	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctttcatctcctgatagagtAattgtatctgaattataaaa	14	16	5	6	0	3	3	1	2	2	1	4	3	3	3	1	0	0	2	1	0	7	7	rs147695092		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:92264736A>G	ENST00000435962.2	-	7	968	c.645T>C	c.(643-645)atT>atC	p.I215I	TC2N_ENST00000556018.1_Silent_p.I215I|TC2N_ENST00000360594.5_Silent_p.I215I|TC2N_ENST00000340892.5_Silent_p.I215I	NM_001128596.1	NP_001122068	Q8N9U0	TAC2N_HUMAN	tandem C2 domains, nuclear	215					regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(5)|skin(1)|upper_aerodigestive_tract(2)	18				COAD - Colon adenocarcinoma(157;0.218)		CTGATAGAGTAATTGTATCTG	0.328													A|||	1	0.000199681	0.0008	0.0	5008	,	,		15932	0.0		0.0	False		,,,				2504	0.0				p.I215I		Atlas-SNP	.											.	TC2N	49	.	0			c.T645C						PASS	.	A	,,	4,4392	8.1+/-20.4	0,4,2194	43	46	45		645,645,645	3.2	1	14	dbSNP_134	45	0,8570		0,0,4285	no	coding-synonymous,coding-synonymous,coding-synonymous	TC2N	NM_001128595.1,NM_001128596.1,NM_152332.4	,,	0,4,6479	GG,GA,AA		0.0,0.091,0.0308	,,	215/491,215/491,215/491	92264736	4,12962	2198	4285	6483	SO:0001819	synonymous_variant	123036	exon7			TAGAGTAATTGTA	AA243837	CCDS9897.1, CCDS73679.1	14q32.12	2007-10-17	2007-08-17	2007-08-17		ENSG00000165929			19859	protein-coding gene	gene with protein product	"C2 calcium-dependent domain containing 1"		"chromosome 14 open reading frame 47", "membrane targeting (tandem) C2 domain containing 1"	C14orf47, MTAC2D1		11526914	Standard	NM_001128596		Approved	FLJ36557, Tac2-N, C2CD1	uc001xzt.4	Q8N9U0		ENST00000435962.2:c.645T>C	14.37:g.92264736A>G		126	0	0		133	74	0.556391	NM_001128596		Silent	SNP	ENST00000435962.2	37	CCDS9897.1																																																																																			A|1.000;G|0.000	0.000	weak		0.328	TC2N-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411778.1	NM_152332		G	92264736	A	G	92264736	2	3	22	1	0	0	0	0	0	0	0	1	15680	358	13	3		3	TC2N	14	92264736	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	458932	92264736	15084804	2922	5823											
TRIP11	9321	hgsc.bcm.edu	37	chr14	92474136	92474136	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caaacttatgtctcttgtagCtgtacttttaattacttcat	10	19	4	8	0	2	0	1	0	1	0	3	0	2	0	0	0	4	3	0	0	6	8	rs372171033		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:92474136C>T	ENST00000267622.4	-	10	1748	c.1375G>A	c.(1375-1377)Gct>Act	p.A459T		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	459					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)		TCTCTTGTAGCTGTACTTTTA	0.303			T	PDGFRB	AML								c|||	1	0.000199681	0.0008	0.0	5008	,	,		19781	0.0		0.0	False		,,,				2504	0.0				p.A459T	Ovarian(84;609 1888 9852 42686)	Atlas-SNP	.		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	.	TRIP11	184	.	0			c.G1375A						PASS	.	C	THR/ALA	5,4399	9.9+/-24.2	0,5,2197	105	97	100		1375	-3.3	0	14		100	0,8598		0,0,4299	no	missense	TRIP11	NM_004239.3	58	0,5,6496	TT,TC,CC		0.0,0.1135,0.0385	benign	459/1980	92474136	5,12997	2202	4299	6501	SO:0001583	missense	9321	exon10			TTGTAGCTGTACT	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.1375G>A	14.37:g.92474136C>T	ENSP00000267622:p.Ala459Thr	127	0	0		83	35	0.421687	NM_004239	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	37	CCDS9899.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	4.257|4.257	0.046773|0.046773	0.08243|0.08243	0.001135|0.001135	0.0|0.0	ENSG00000100815|ENSG00000100815	ENST00000267622;ENST00000542257|ENST00000554357	T|.	0.64438|.	-0.1|.	5.85|5.85	-3.26|-3.26	0.05064|0.05064	.|.	1.114810|.	0.06492|.	N|.	0.734730|.	T|T	0.19846|0.19846	0.0477|0.0477	N|N	0.16656|0.16656	0.425|0.425	0.09310|0.09310	N|N	1|1	B;B|.	0.13594|.	0.003;0.008|.	B;B|.	0.13407|.	0.004;0.009|.	T|T	0.33007|0.33007	-0.9885|-0.9885	10|5	0.14252|.	T|.	0.57|.	.|.	7.9021|7.9021	0.29740|0.29740	0.1338:0.334:0.0:0.5322|0.1338:0.334:0.0:0.5322	.|.	195;459|.	F5H1Z0;Q15643|.	.;TRIPB_HUMAN|.	T|N	459;195|174	ENSP00000267622:A459T|.	ENSP00000267622:A459T|.	A|S	-|-	1|2	0|0	TRIP11|TRIP11	91543889|91543889	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.220000|0.220000	0.24768|0.24768	-0.819000|-0.819000	0.04462|0.04462	-0.445000|-0.445000	0.07159|0.07159	0.561000|0.561000	0.74099|0.74099	GCT|AGC	.	.	weak		0.303	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1			T	92474136	C	T	92474136	3	4	22	1	0	0	0	0	1	0	0	0	16570	797	28	2	4612	2	TRIP11	14	92474136	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	209400	92474136	14875404	2923	5824											
MOAP1	64112	hgsc.bcm.edu	37	chr14	93649552	93649552	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcaggtgaaattaccttccaAtattgcctggagaagggcct	11	11	10	9	0	1	2	1	1	0	1	2	3	2	2	4	3	2	0	4	3	5	4	rs114256363	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:93649552A>G	ENST00000556883.1	-	2	1520	c.1036T>C	c.(1036-1038)Ttg>Ctg	p.L346L	TMEM251_ENST00000283534.4_5'Flank|TMEM251_ENST00000415050.2_5'Flank|MOAP1_ENST00000298894.4_Silent_p.L346L|RP11-371E8.4_ENST00000557574.1_5'Flank			Q96BY2	MOAP1_HUMAN	modulator of apoptosis 1	346					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)		TTACCTTCCAATATTGCCTGG	0.473													A|||	96	0.0191693	0.0696	0.0058	5008	,	,		21495	0.0		0.0	False		,,,				2504	0.0				p.L346L		Atlas-SNP	.											.	MOAP1	32	.	0			c.T1036C						PASS	.	A		233,4173	139.2+/-174.8	8,217,1978	99	90	93		1036	-4.4	0	14	dbSNP_132	93	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MOAP1	NM_022151.4		8,218,6277	GG,GA,AA		0.0116,5.2882,1.7992		346/352	93649552	234,12772	2203	4300	6503	SO:0001819	synonymous_variant	64112	exon3			CTTCCAATATTGC	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.1036T>C	14.37:g.93649552A>G		118	0	0		111	48	0.432432	NM_022151	B2RDF6|Q9H833|Q9HAS1	Silent	SNP	ENST00000556883.1	37	CCDS9908.1																																																																																			A|0.982;G|0.018	0.018	strong		0.473	MOAP1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412685.1			G	93649552	A	G	93649552	2	3	22	1	0	0	0	0	0	0	0	1	9689	98	4	3		3	MOAP1	14	93649552	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1175416	93649552	13699988	2924	5825											
C14orf109	64112	hgsc.bcm.edu	37	chr14	93652734	93652734	+	5'Flank	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagacttacaacaggctggcCttggaacacattcaacagca	14	7	9	11	0	1	1	1	0	0	1	1	3	1	2	1	3	5	2	1	3	4	3	rs61744704	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:93652734C>T	ENST00000556883.1	-	0	0				TMEM251_ENST00000283534.4_Silent_p.A38A|TMEM251_ENST00000415050.2_Silent_p.A76A|MOAP1_ENST00000298894.4_5'Flank|RP11-371E8.4_ENST00000557048.1_Intron|RP11-371E8.4_ENST00000557574.1_Silent_p.A38A			Q96BY2	MOAP1_HUMAN	modulator of apoptosis 1						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)		ACAGGCTGGCCTTGGAACACA	0.478													C|||	20	0.00399361	0.0151	0.0	5008	,	,		18903	0.0		0.0	False		,,,				2504	0.0				p.A76A		Atlas-SNP	.											.	.	.	.	0			c.C228T						PASS	.	C	,	42,3868		0,42,1913	165	163	164		228,114	-0.2	1	14	dbSNP_129	164	0,8292		0,0,4146	no	coding-synonymous,coding-synonymous	C14orf109	NM_001098621.1,NM_015676.1	,	0,42,6059	TT,TC,CC		0.0,1.0742,0.3442	,	76/170,38/132	93652734	42,12160	1955	4146	6101	SO:0001631	upstream_gene_variant	26175	exon2			GCTGGCCTTGGAA	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		14.37:g.93652734C>T	Exception_encountered	246	0	0		263	133	0.505703	NM_001098621	B2RDF6|Q9H833|Q9HAS1	Silent	SNP	ENST00000556883.1	37	CCDS9908.1																																																																																			C|0.997;T|0.003	0.003	strong		0.478	MOAP1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412685.1			T	93652734	C	T	93652734	1	4	22	0	1	0	0	0	0	0	0	0	1741	668	24	2		2	C14orf109	14	93652734	5'Flank	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3182	93652734	13696806	2925	5826											
KIAA1409	57578	hgsc.bcm.edu	37	chr14	94173098	94173098	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaggctattcagaaccacGtgaaccaccacagcctaagg	13	6	8	14	1	1	2	1	1	0	1	2	2	2	2	5	2	3	1	5	2	4	3	rs76642035	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:94173098G>A	ENST00000393151.2	+	50	7756	c.7756G>A	c.(7756-7758)Gtg>Atg	p.V2586M	UNC79_ENST00000256339.4_Missense_Mutation_p.V2409M|UNC79_ENST00000555664.1_Missense_Mutation_p.V2547M|UNC79_ENST00000553484.1_Missense_Mutation_p.V2608M			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	2586					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						TCAGAACCACGTGAACCACCA	0.557													G|||	22	0.00439297	0.0159	0.0014	5008	,	,		17791	0.0		0.0	False		,,,				2504	0.0				p.V2409M		Atlas-SNP	.											.	UNC79	366	.	0			c.G7225A						PASS	.	G	MET/VAL	61,4345	57.4+/-93.9	1,59,2143	69	74	73		7225	5.8	1	14	dbSNP_131	73	0,8600		0,0,4300	yes	missense	UNC79	NM_020818.3	21	1,59,6443	AA,AG,GG		0.0,1.3845,0.469	probably-damaging	2409/2459	94173098	61,12945	2203	4300	6503	SO:0001583	missense	57578	exon50			AACCACGTGAACC	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.7756G>A	14.37:g.94173098G>A	ENSP00000376858:p.Val2586Met	104	0	0		96	48	0.5	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	37		6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	G	23.0	4.363881	0.82353	0.013845	0.0	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.19806	2.12;2.14;2.12;2.12	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.36110	0.0955	L	0.53249	1.67	0.80722	D	1	D	0.76494	0.999	D	0.71656	0.974	T	0.05037	-1.0910	10	0.52906	T	0.07	-21.9581	20.0407	0.97588	0.0:0.0:1.0:0.0	.	2608	C9JQL1	.	M	2409;2547;2608;2586;2608	ENSP00000256339:V2409M;ENSP00000450868:V2547M;ENSP00000451360:V2608M;ENSP00000376858:V2586M	ENSP00000256339:V2409M	V	+	1	0	KIAA1409	93242851	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.869000	0.99810	2.746000	0.94184	0.561000	0.74099	GTG	G|0.996;A|0.004	0.004	strong		0.557	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395		A	94173098	G	A	94173098	3	1	22	1	0	0	0	0	1	0	0	0	8239	1145	40	1	7411	1	KIAA1409	14	94173098	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	520364	94173098	13176442	2926	5827											
PRIMA1	145270	hgsc.bcm.edu	37	chr14	94187816	94187816	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cactgcgttgttcacgtctaCtcctttgttgctctgcgaag	5	15	9	12	3	3	0	1	0	2	0	4	1	4	0	1	0	4	4	1	0	2	5			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:94187816C>G	ENST00000393140.1	-	5	538	c.436G>C	c.(436-438)Gta>Cta	p.V146L	PRIMA1_ENST00000316227.3_3'UTR|PRIMA1_ENST00000393143.1_Missense_Mutation_p.V146L	NM_178013.3	NP_821092.1	Q86XR5	PRIMA_HUMAN	proline rich membrane anchor 1	146					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)		TTCACGTCTACTCCTTTGTTG	0.577																																					p.V146L		Atlas-SNP	.											.	PRIMA1	21	.	0			c.G436C						PASS	.						142	101	115					14																	94187816		2203	4300	6503	SO:0001583	missense	145270	exon5			CGTCTACTCCTTT		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.436G>C	14.37:g.94187816C>G	ENSP00000376848:p.Val146Leu	65	0	0		69	29	0.42029	NM_178013	Q86XR6	Missense_Mutation	SNP	ENST00000393140.1	37	CCDS9912.1	.	.	.	.	.	.	.	.	.	.	C	15.38	2.815771	0.50527	.	.	ENSG00000175785	ENST00000393140;ENST00000393143	.	.	.	4.65	3.72	0.42706	.	0.948209	0.08632	N	0.916915	T	0.45736	0.1357	L	0.27053	0.805	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.36407	-0.9749	9	0.49607	T	0.09	-3.289	10.1546	0.42814	0.1979:0.8021:0.0:0.0	.	146	Q86XR5	PRIMA_HUMAN	L	146	.	ENSP00000376848:V146L	V	-	1	0	PRIMA1	93257569	1.000000	0.71417	0.998000	0.56505	0.070000	0.16714	2.628000	0.46477	2.135000	0.66039	0.591000	0.81541	GTA	.	.	none		0.577	PRIMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280658.1	NM_178013		G	94187816	C	G	94187816	3	3	22	1	0	0	0	0	1	0	0	0	12504	565	20	4	29	4	PRIMA1	14	94187816	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	14718	94187816	13161724	2927	5828											
DDX24	57062	hgsc.bcm.edu	37	chr14	94526812	94526812	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaaggattcgagcaggagcCtgatgcaccagggtgagtgt	10	8	16	7	1	0	3	0	3	0	0	1	6	0	5	2	3	3	2	2	3	1	1	rs11845400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:94526812C>T	ENST00000330836.5	-	5	1676	c.1545G>A	c.(1543-1545)caG>caA	p.Q515Q	DDX24_ENST00000555054.1_Silent_p.Q472Q|DDX24_ENST00000544005.1_Silent_p.Q265Q	NM_020414.3	NP_065147.1	Q9GZR7	DDX24_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 24	515	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)		GAGCAGGAGCCTGATGCACCA	0.473													C|||	202	0.0403355	0.1483	0.0043	5008	,	,		21521	0.0		0.002	False		,,,				2504	0.001				p.Q515Q		Atlas-SNP	.											.	DDX24	82	.	0			c.G1545A						PASS	.	C		558,3848	249.6+/-257.0	33,492,1678	192	177	182		1545	-1.5	1	14	dbSNP_120	182	39,8561	26.3+/-74.7	0,39,4261	no	coding-synonymous	DDX24	NM_020414.3		33,531,5939	TT,TC,CC		0.4535,12.6645,4.5902		515/860	94526812	597,12409	2203	4300	6503	SO:0001819	synonymous_variant	57062	exon5			AGGAGCCTGATGC	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.1545G>A	14.37:g.94526812C>T		197	0	0		228	118	0.517544	NM_020414	E7EMJ4|Q4V9L5	Silent	SNP	ENST00000330836.5	37	CCDS9918.1																																																																																			C|0.952;T|0.048	0.048	strong		0.473	DDX24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412861.1	NM_020414		T	94526812	C	T	94526812	2	4	22	1	0	0	0	0	0	0	0	1	4353	680	24	2		2	DDX24	14	94526812	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	338996	94526812	12822728	2928	5829											
SERPINA1	5265	hgsc.bcm.edu	37	chr14	94844975	94844975	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtcagcacagccttatgcacGgcctggaggggagagaagca	11	5	15	10	1	1	1	1	0	0	1	1	4	1	3	2	4	4	3	2	4	2	1	rs9630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:94844975G>A	ENST00000448921.1	-	7	1640	c.1068C>T	c.(1066-1068)gcC>gcT	p.A356A	SERPINA1_ENST00000355814.4_Silent_p.A356A|SERPINA1_ENST00000393087.4_Silent_p.A356A|SERPINA1_ENST00000449399.3_Silent_p.A356A|SERPINA1_ENST00000393088.4_Silent_p.A356A|SERPINA1_ENST00000437397.1_Silent_p.A356A|SERPINA1_ENST00000440909.1_Silent_p.A356A|SERPINA1_ENST00000404814.4_Silent_p.A356A	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	356					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)		CCTTATGCACGGCCTGGAGGG	0.592													G|||	50	0.00998403	0.0356	0.0043	5008	,	,		19798	0.0		0.0	False		,,,				2504	0.0				p.A356A		Atlas-SNP	.											.	SERPINA1	51	.	0			c.C1068T						PASS	.	G	,,,,,,,,,,	122,4284	90.2+/-128.9	1,120,2082	80	59	66		1068,1068,1068,1068,1068,1068,1068,1068,1068,1068,1068	-9.6	0	14	dbSNP_52	66	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SERPINA1	NM_000295.4,NM_001002235.2,NM_001002236.2,NM_001127700.1,NM_001127701.1,NM_001127702.1,NM_001127703.1,NM_001127704.1,NM_001127705.1,NM_001127706.1,NM_001127707.1	,,,,,,,,,,	1,121,6381	AA,AG,GG		0.0116,2.769,0.9457	,,,,,,,,,,	356/419,356/419,356/419,356/419,356/419,356/419,356/419,356/419,356/419,356/419,356/419	94844975	123,12883	2203	4300	6503	SO:0001819	synonymous_variant	5265	exon7			ATGCACGGCCTGG	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.1068C>T	14.37:g.94844975G>A		154	0	0		168	82	0.488095	NM_001127701	A6PX14|B2RDQ8|Q0PVP5|Q13672|Q53XB8|Q5U0M1|Q7M4R2|Q86U18|Q86U19|Q96BF9|Q96ES1|Q9P1P0|Q9UCE6|Q9UCM3	Silent	SNP	ENST00000448921.1	37	CCDS9925.1																																																																																			G|0.989;A|0.011	0.011	strong		0.592	SERPINA1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317768.2	NM_001002235		A	94844975	G	A	94844975	2	1	22	1	0	0	0	0	0	0	0	1	14101	1103	39	1		1	SERPINA1	14	94844975	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	318163	94844975	12504565	2929	5830											
SERPINA5	5104	hgsc.bcm.edu	37	chr14	95056407	95056407	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agacaagcttcaaccacaaaGgcacccaagagcaagacttc	17	4	7	13	0	1	3	1	0	0	3	2	3	1	3	2	1	3	3	2	1	5	2	rs6114	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:95056407G>C	ENST00000554866.1	+	3	763	c.649G>C	c.(649-651)Ggc>Cgc	p.G217R	RP11-986E7.7_ENST00000553947.1_5'Flank|SERPINA5_ENST00000329597.7_Missense_Mutation_p.G217R|SERPINA5_ENST00000554276.1_Missense_Mutation_p.G217R|SERPINA5_ENST00000553780.1_Missense_Mutation_p.G217R			P05154	IPSP_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5	217			G -> R (in dbSNP:rs6114). {ECO:0000269|PubMed:10391209, ECO:0000269|Ref.6}.		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)	CAACCACAAAGGCACCCAAGA	0.453													G|||	129	0.0257588	0.0923	0.0101	5008	,	,		19756	0.0		0.0	False		,,,				2504	0.0				p.G217R		Atlas-SNP	.											.	SERPINA5	69	.	0			c.G649C						PASS	.	G	ARG/GLY	374,4032	190.5+/-216.4	22,330,1851	71	65	67		649	-2.1	0	14	dbSNP_52	67	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SERPINA5	NM_000624.4	125	22,331,6150	CC,CG,GG		0.0116,8.4884,2.8833	benign	217/407	95056407	375,12631	2203	4300	6503	SO:0001583	missense	5104	exon4			CACAAAGGCACCC	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.649G>C	14.37:g.95056407G>C	ENSP00000451126:p.Gly217Arg	141	0	0		121	50	0.413223	NM_000624	Q07616|Q9UG30	Missense_Mutation	SNP	ENST00000554866.1	37	CCDS9928.1	53	0.024267399267399268	48	0.0975609756097561	5	0.013812154696132596	0	0.0	0	0.0	G	1.396	-0.579550	0.03854	0.084884	1.16E-4	ENSG00000188488	ENST00000553780;ENST00000554760;ENST00000554866;ENST00000329597;ENST00000556775;ENST00000537685;ENST00000438291;ENST00000554276	D;D;D;D;D;D	0.83591	-1.74;-1.74;-1.74;-1.74;-1.74;-1.74	4.63	-2.09	0.07232	Serpin domain (3);	1.511820	0.03611	N	0.234832	T	0.03564	0.0102	N	0.02751	-0.505	0.09310	N	1	B;B	0.18461	0.024;0.028	B;B	0.26864	0.074;0.023	T	0.23226	-1.0194	10	0.33141	T	0.24	.	3.7717	0.08645	0.3912:0.0:0.3351:0.2737	rs6114;rs6114	217;217	G3V5Q9;P05154	.;IPSP_HUMAN	R	217;217;217;217;217;69;141;217	ENSP00000450837:G217R;ENSP00000452469:G217R;ENSP00000451126:G217R;ENSP00000333203:G217R;ENSP00000450745:G217R;ENSP00000451610:G217R	ENSP00000333203:G217R	G	+	1	0	SERPINA5	94126160	0.000000	0.05858	0.000000	0.03702	0.143000	0.21401	-1.700000	0.01905	-0.323000	0.08602	-0.378000	0.06908	GGC	G|0.974;C|0.026	0.026	strong		0.453	SERPINA5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410726.1	NM_000624		C	95056407	G	C	95056407	3	2	22	1	0	0	0	0	1	0	0	0	14107	1000	35	4	655	4	SERPINA5	14	95056407	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	211432	95056407	12293133	2930	5831											
SERPINA5	5104	hgsc.bcm.edu	37	chr14	95058477	95058477	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acaatattcactttcaggtcGgcccgcctgaactctcagag	10	10	8	13	2	3	2	3	1	1	1	5	2	3	2	2	2	1	0	2	2	3	3	rs6117	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:95058477G>A	ENST00000554866.1	+	5	1236	c.1122G>A	c.(1120-1122)tcG>tcA	p.S374S	RP11-986E7.7_ENST00000553947.1_Intron|SERPINA5_ENST00000329597.7_Silent_p.S374S|SERPINA5_ENST00000554276.1_Silent_p.S374S|SERPINA5_ENST00000553780.1_Silent_p.S374S			P05154	IPSP_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5	374		Reactive bond.			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)	CTTTCAGGTCGGCCCGCCTGA	0.557													G|||	199	0.0397364	0.1399	0.0202	5008	,	,		18216	0.0		0.0	False		,,,				2504	0.0				p.S374S		Atlas-SNP	.											.	SERPINA5	69	.	0			c.G1122A						PASS	.	G		562,3844	251.8+/-258.4	41,480,1682	208	214	212		1122	-6.8	0	14	dbSNP_52	212	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	SERPINA5	NM_000624.4		41,487,5975	AA,AG,GG		0.0814,12.7553,4.3749		374/407	95058477	569,12437	2203	4300	6503	SO:0001819	synonymous_variant	5104	exon6			CAGGTCGGCCCGC	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.1122G>A	14.37:g.95058477G>A		126	0	0		124	77	0.620968	NM_000624	Q07616|Q9UG30	Silent	SNP	ENST00000554866.1	37	CCDS9928.1																																																																																			G|0.956;A|0.044	0.044	strong		0.557	SERPINA5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410726.1	NM_000624		A	95058477	G	A	95058477	2	1	22	1	0	0	0	0	0	0	0	1	14107	1103	39	1		1	SERPINA5	14	95058477	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2070	95058477	12291063	2931	5832											
DICER1	23405	hgsc.bcm.edu	37	chr14	95572111	95572111	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcaaatgtcgaggtgtcaaAagattaagtctgtaagaatt	15	13	9	4	1	3	2	2	0	1	2	4	3	3	2	0	1	0	1	0	1	6	4	rs12018992	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:95572111A>C	ENST00000526495.1	-	21	3288	c.2997T>G	c.(2995-2997)ctT>ctG	p.L999L	DICER1_ENST00000393063.1_Silent_p.L999L|DICER1_ENST00000556045.1_5'UTR|DICER1_ENST00000343455.3_Silent_p.L999L|DICER1_ENST00000527414.1_Silent_p.L999L|DICER1_ENST00000541352.1_Silent_p.L999L			Q9UPY3	DICER_HUMAN	dicer 1, ribonuclease type III	999	PAZ. {ECO:0000255|PROSITE- ProRule:PRU00142}.				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)		GAGGTGTCAAAAGATTAAGTC	0.383			"Mis F, N"		"sex cord-stromal tumour, TGCT, embryonal rhadomyosarcoma"	pleuropulmonary blastoma			Familial Multinodular Goiter ;DICER 1 syndrome				A|||	99	0.0197684	0.0711	0.0072	5008	,	,		19488	0.0		0.0	False		,,,				2504	0.0				p.L999L		Atlas-SNP	.	yes	Rec	yes	Familial Pleuropulmonary Blastoma	14	14q32.13	23405	"dicer 1, ribonuclease type III "		"E, M, O"	.	DICER1	181	.	0			c.T2997G						PASS	.	A	,,	252,4154	141.9+/-177.2	11,230,1962	62	62	62		2997,2997,2997	4.2	1	14	dbSNP_120	62	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	DICER1	NM_001195573.1,NM_030621.3,NM_177438.2	,,	11,231,6261	CC,CA,AA		0.0116,5.7195,1.9453	,,	999/1830,999/1923,999/1923	95572111	253,12753	2203	4300	6503	SO:0001819	synonymous_variant	23405	exon20	Familial Cancer Database	Adolescent Multinodular Goiter, incl. Multinodular Euthyroid Goiter & Non-Medullary Thyroid Cancer;incl. Pleuropulmonary Blastoma, Familial ; Cystic Nephroma, Familial	TGTCAAAAGATTA	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.2997T>G	14.37:g.95572111A>C		127	0	0		115	47	0.408696	NM_030621	A7E2D3|B3KRG4|E0AD28|O95943|Q9UQ02	Silent	SNP	ENST00000526495.1	37	CCDS9931.1																																																																																			A|0.977;C|0.023	0.023	strong		0.383	DICER1-004	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387997.1			C	95572111	A	C	95572111	2	2	22	1	0	0	0	0	0	0	0	1	4523	1	1	5		5	DICER1	14	95572111	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	513634	95572111	11777429	2932	5833											
C14orf49	161176	hgsc.bcm.edu	37	chr14	95921722	95921722	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcacgcttaccgagtagcGtctccagtgtgccaccagct	9	8	10	14	3	1	0	0	0	1	0	2	1	1	0	4	0	5	4	4	0	3	2	rs74079986	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:95921722G>A	ENST00000334258.5	-	5	1143	c.1129C>T	c.(1129-1131)Cgc>Tgc	p.R377C	SYNE3_ENST00000557275.1_Missense_Mutation_p.R377C|SYNE3_ENST00000553340.1_Missense_Mutation_p.R377C|SYNE3_ENST00000554873.1_Missense_Mutation_p.R134C	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	377					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						ACCGAGTAGCGTCTCCAGTGT	0.647													G|||	60	0.0119808	0.0439	0.0029	5008	,	,		17289	0.0		0.0	False		,,,				2504	0.0				p.R377C		Atlas-SNP	.											.	SYNE3	130	.	0			c.C1129T						PASS	.	G	CYS/ARG	174,4232	108.6+/-147.0	5,164,2034	29	32	31		1129	3	0.5	14	dbSNP_130	31	1,8597	1.2+/-3.3	0,1,4298	yes	missense	C14orf49	NM_152592.3	180	5,165,6332	AA,AG,GG		0.0116,3.9492,1.3457	possibly-damaging	377/976	95921722	175,12829	2203	4299	6502	SO:0001583	missense	161176	exon5			AGTAGCGTCTCCA	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.1129C>T	14.37:g.95921722G>A	ENSP00000334308:p.Arg377Cys	79	0	0		75	45	0.6	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	37	CCDS9935.1	24	0.01098901098901099	22	0.044715447154471545	2	0.0055248618784530384	0	0.0	0	0.0	G	13.55	2.271639	0.40194	0.039492	1.16E-4	ENSG00000176438	ENST00000334258;ENST00000554873;ENST00000557275;ENST00000553340	T;T;T;T	0.37058	3.5;1.22;3.49;2.9	4.99	2.96	0.34315	.	1.317840	0.05603	N	0.576684	T	0.09730	0.0239	N	0.22421	0.69	0.25690	N	0.985697	D;D;D	0.64830	0.994;0.994;0.989	P;P;B	0.50617	0.646;0.646;0.443	T	0.12502	-1.0545	10	0.66056	D	0.02	-0.0728	5.3201	0.15876	0.1091:0.0:0.5537:0.3371	.	377;377;377	Q6ZMZ3-2;Q6ZMZ3-3;Q6ZMZ3	.;.;SYNE3_HUMAN	C	377;134;377;377	ENSP00000334308:R377C;ENSP00000452154:R134C;ENSP00000450562:R377C;ENSP00000450774:R377C	ENSP00000334308:R377C	R	-	1	0	C14orf49	94991475	0.999000	0.42202	0.468000	0.27192	0.258000	0.26162	3.690000	0.54713	1.110000	0.41699	0.455000	0.32223	CGC	G|0.988;A|0.012	0.012	strong		0.647	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592		A	95921722	G	A	95921722	3	1	22	1	0	0	0	0	1	0	0	0	1778	1145	40	1	1850	1	C14orf49	14	95921722	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	349611	95921722	11427818	2933	5834											
C14orf49	161176	hgsc.bcm.edu	37	chr14	95923644	95923644	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggtactcctcatgctccCgggccacctgctccagcaga	6	8	9	18	1	1	1	1	0	0	1	4	1	4	1	6	2	4	4	6	2	1	1	rs74082143	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:95923644C>T	ENST00000334258.5	-	4	673	c.659G>A	c.(658-660)cGg>cAg	p.R220Q	SYNE3_ENST00000557275.1_Missense_Mutation_p.R220Q|SYNE3_ENST00000553340.1_Missense_Mutation_p.R220Q|SYNE3_ENST00000554873.1_5'Flank	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	220					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						CTCATGCTCCCGGGCCACCTG	0.622													C|||	57	0.0113818	0.0416	0.0029	5008	,	,		15755	0.0		0.0	False		,,,				2504	0.0				p.R220Q		Atlas-SNP	.											.	SYNE3	130	.	0			c.G659A						PASS	.	C	GLN/ARG	164,4242	110.8+/-149.0	4,156,2043	172	146	155		659	-9.7	0.2	14	dbSNP_130	155	1,8599	1.2+/-3.3	0,1,4299	yes	missense	C14orf49	NM_152592.3	43	4,157,6342	TT,TC,CC		0.0116,3.7222,1.2686	benign	220/976	95923644	165,12841	2203	4300	6503	SO:0001583	missense	161176	exon4			TGCTCCCGGGCCA	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.659G>A	14.37:g.95923644C>T	ENSP00000334308:p.Arg220Gln	77	0	0		86	38	0.44186	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	37	CCDS9935.1	24	0.01098901098901099	22	0.044715447154471545	2	0.0055248618784530384	0	0.0	0	0.0	C	8.880	0.951469	0.18431	0.037222	1.16E-4	ENSG00000176438	ENST00000334258;ENST00000557275;ENST00000553340	T;T;T	0.08634	3.67;3.67;3.07	5.59	-9.72	0.00515	.	1.176260	0.06544	N	0.743757	T	0.00784	0.0026	N	0.12471	0.22	0.09310	N	1	B;B;B	0.09022	0.001;0.002;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.46428	-0.9192	10	0.16420	T	0.52	-9.6805	10.7358	0.46124	0.0756:0.1571:0.0:0.7673	.	220;220;220	Q6ZMZ3-2;Q6ZMZ3-3;Q6ZMZ3	.;.;SYNE3_HUMAN	Q	220	ENSP00000334308:R220Q;ENSP00000450562:R220Q;ENSP00000450774:R220Q	ENSP00000334308:R220Q	R	-	2	0	C14orf49	94993397	0.009000	0.17119	0.165000	0.22776	0.027000	0.11550	0.063000	0.14410	-1.210000	0.02627	-0.263000	0.10527	CGG	C|0.989;T|0.011	0.011	strong		0.622	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592		T	95923644	C	T	95923644	3	4	22	1	0	0	0	0	1	0	0	0	1778	652	23	1	2324	1	C14orf49	14	95923644	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1922	95923644	11425896	2934	5835											
EVL	51466	hgsc.bcm.edu	37	chr14	100563868	100563868	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaagtacaatcaggccacGccaaccttccaccagtggcg	11	6	9	15	2	1	1	1	1	0	0	2	1	2	1	5	2	2	1	5	2	4	2	rs35006525	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:100563868G>A	ENST00000402714.2	+	3	829	c.225G>A	c.(223-225)acG>acA	p.T75T	EVL_ENST00000555048.1_3'UTR|EVL_ENST00000392920.3_Silent_p.T77T|EVL_ENST00000544450.2_Silent_p.T81T			Q9UI08	EVL_HUMAN	Enah/Vasp-like	75	WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}.				actin filament organization (GO:0007015)|actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ruffle assembly (GO:1900028)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of stress fiber assembly (GO:0051496)|protein homotetramerization (GO:0051289)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|membrane (GO:0016020)	profilin binding (GO:0005522)|SH3 domain binding (GO:0017124)			cervix(1)|large_intestine(5)|lung(3)|ovary(3)|urinary_tract(2)	14		Melanoma(154;0.152)				ATCAGGCCACGCCAACCTTCC	0.458													G|||	74	0.0147764	0.0545	0.0029	5008	,	,		21124	0.0		0.0	False		,,,				2504	0.0				p.T77T		Atlas-SNP	.											.	EVL	42	.	0			c.G231A						PASS	.	G		217,4189	131.0+/-167.6	6,205,1992	89	81	84		231	-9	0.8	14	dbSNP_126	84	0,8600		0,0,4300	no	coding-synonymous	EVL	NM_016337.2		6,205,6292	AA,AG,GG		0.0,4.9251,1.6685		77/419	100563868	217,12789	2203	4300	6503	SO:0001819	synonymous_variant	51466	exon3			GGCCACGCCAACC	AF112209	CCDS9955.1	14q32.2	2014-08-13			ENSG00000196405	ENSG00000196405			20234	protein-coding gene	gene with protein product						10945997, 10993894	Standard	NM_016337		Approved	RNB6	uc001ygu.3	Q9UI08	OTTHUMG00000171530	ENST00000402714.2:c.225G>A	14.37:g.100563868G>A		77	0	0		93	51	0.548387	NM_016337	A8K105|O95884|Q7Z522|Q8TBV1|Q9UF25|Q9UIC2	Silent	SNP	ENST00000402714.2	37																																																																																				G|0.986;A|0.014	0.014	strong		0.458	EVL-006	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000413958.1			A	100563868	G	A	100563868	2	1	22	1	0	0	0	0	0	0	0	1	5293	1074	38	1		1	EVL	14	100563868	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4640224	100563868	6785672	2935	5836											
DEGS2	123099	hgsc.bcm.edu	37	chr14	100615707	100615707	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agacgcgtgggcacgtccacGtccagcccgtcgccgcccag	6	4	13	18	7	0	1	0	0	0	1	3	1	2	1	5	1	1	1	5	1	0	0	rs113575369	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:100615707G>A	ENST00000305631.5	-	2	998	c.423C>T	c.(421-423)gaC>gaT	p.D141D	DEGS2_ENST00000557117.1_5'UTR|DEGS2_ENST00000553834.1_Intron	NM_206918.2	NP_996801.2			delta(4)-desaturase, sphingolipid 2											breast(1)|lung(6)|skin(1)	8		Melanoma(154;0.212)				GCACGTCCACGTCCAGCCCGT	0.672													G|||	60	0.0119808	0.0431	0.0043	5008	,	,		16559	0.0		0.0	False		,,,				2504	0.0				p.D141D		Atlas-SNP	.											.	DEGS2	25	.	0			c.C423T						PASS	.	G		130,4272	88.7+/-127.4	1,128,2072	29	28	29		423	-1	1	14	dbSNP_132	29	1,8595		0,1,4297	no	coding-synonymous	DEGS2	NM_206918.2		1,129,6369	AA,AG,GG		0.0116,2.9532,1.0078		141/324	100615707	131,12867	2201	4298	6499	SO:0001819	synonymous_variant	123099	exon2			GTCCACGTCCAGC		CCDS9956.1	14q32.2	2013-09-02	2011-12-09	2004-12-14	ENSG00000168350	ENSG00000168350		"Fatty acid desaturases"	20113	protein-coding gene	gene with protein product	"sphingolipid delta(4)-desaturase 2", "dihydroceramide desaturase 2"	610862	"chromosome 14 open reading frame 66", "degenerative spermatocyte homolog 2, lipid desaturase (Drosophila)"	C14orf66			Standard	NM_206918		Approved	DES2, FADS8	uc001ygx.2	Q6QHC5	OTTHUMG00000171537	ENST00000305631.5:c.423C>T	14.37:g.100615707G>A		73	0	0		119	67	0.563025	NM_206918		Silent	SNP	ENST00000305631.5	37	CCDS9956.1																																																																																			G|0.991;A|0.009	0.009	strong		0.672	DEGS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414003.1	NM_206918		A	100615707	G	A	100615707	2	1	22	1	0	0	0	0	0	0	0	1	4425	1136	40	1		1	DEGS2	14	100615707	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	51839	100615707	6733833	2936	5837											
DLK1	8788	hgsc.bcm.edu	37	chr14	101200514	101200514	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagcacggaggcacctgcGtggatgatgagggccgggcc	7	4	18	12	3	0	2	0	2	0	0	0	4	0	4	4	5	2	2	4	5	0	0	rs116078181	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:101200514G>T	ENST00000341267.4	+	5	675	c.433G>T	c.(433-435)Gtg>Ttg	p.V145L	DLK1_ENST00000331224.6_Missense_Mutation_p.V145L	NM_003836.5	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog (Drosophila)	145	EGF-like 4. {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)				AGGCACCTGCGTGGATGATGA	0.652													G|||	93	0.0185703	0.0696	0.0014	5008	,	,		12961	0.0		0.0	False		,,,				2504	0.0				p.V145L		Atlas-SNP	.											.	DLK1	57	.	0			c.G433T						PASS	.	G	LEU/VAL	197,4207		7,183,2012	45	43	44		433	3.2	1	14	dbSNP_132	44	0,8598		0,0,4299	yes	missense	DLK1	NM_003836.5	32	7,183,6311	TT,TG,GG		0.0,4.4732,1.5152	possibly-damaging	145/384	101200514	197,12805	2202	4299	6501	SO:0001583	missense	8788	exon5			ACCTGCGTGGATG	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.433G>T	14.37:g.101200514G>T	ENSP00000340292:p.Val145Leu	126	0	0		89	54	0.606742	NM_003836	P15803|Q96DW5	Missense_Mutation	SNP	ENST00000341267.4	37	CCDS9963.1	37	0.01694139194139194	37	0.07520325203252033	0	0.0	0	0.0	0	0.0	G	15.51	2.856381	0.51376	0.044732	0.0	ENSG00000185559	ENST00000341267;ENST00000331224	T;T	0.71817	-0.6;-0.6	4.1	3.18	0.36537	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.432951	0.20458	N	0.091958	T	0.10981	0.0268	L	0.28776	0.89	0.80722	D	1	D;P	0.67145	0.996;0.926	D;P	0.64595	0.927;0.542	T	0.37820	-0.9689	10	0.30854	T	0.27	.	5.9295	0.19130	0.2969:0.0:0.7031:0.0	.	145;145	P80370-2;P80370	.;DLK1_HUMAN	L	145	ENSP00000340292:V145L;ENSP00000331081:V145L	ENSP00000331081:V145L	V	+	1	0	DLK1	100270267	0.812000	0.29077	0.997000	0.53966	0.813000	0.45954	1.136000	0.31467	1.981000	0.57761	0.491000	0.48974	GTG	G|0.981;T|0.019	0.019	strong		0.652	DLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414389.1			T	101200514	G	T	101200514	3	4	22	1	0	0	0	0	1	0	0	0	4566	1145	40	4	451	4	DLK1	14	101200514	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	584807	101200514	6149026	2937	5838											
DLK1	8788	hgsc.bcm.edu	37	chr14	101200780	101200780	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccaggtgagctacgagtgTctgtgcaagcccgagttcac	9	8	12	12	2	2	1	1	1	1	0	2	3	2	1	2	1	4	3	2	1	2	2	rs2295660	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:101200780T>C	ENST00000341267.4	+	5	941	c.699T>C	c.(697-699)tgT>tgC	p.C233C	DLK1_ENST00000331224.6_Intron	NM_003836.5	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog (Drosophila)	233	EGF-like 6. {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)				GCTACGAGTGTCTGTGCAAGC	0.662													T|||	107	0.0213658	0.0371	0.0058	5008	,	,		15534	0.0506		0.003	False		,,,				2504	0.0				p.C233C		Atlas-SNP	.											.	DLK1	57	.	0			c.T699C						PASS	.	T		104,4300		1,102,2099	38	44	42		699	3.1	1	14	dbSNP_100	42	8,8590		0,8,4291	no	coding-synonymous	DLK1	NM_003836.5		1,110,6390	CC,CT,TT		0.093,2.3615,0.8614		233/384	101200780	112,12890	2202	4299	6501	SO:0001819	synonymous_variant	8788	exon5			CGAGTGTCTGTGC	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.699T>C	14.37:g.101200780T>C		39	0	0		46	15	0.326087	NM_003836	P15803|Q96DW5	Silent	SNP	ENST00000341267.4	37	CCDS9963.1																																																																																			T|0.981;C|0.019	0.019	strong		0.662	DLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414389.1			C	101200780	T	C	101200780	2	2	22	1	0	0	0	0	0	0	0	1	4566	1673	58	3		3	DLK1	14	101200780	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	266	101200780	6148760	2938	5839											
DLK1	8788	hgsc.bcm.edu	37	chr14	101201206	101201206	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atcgacatgaccaccttcagCaaggaggccggcgacgagga	12	4	13	12	4	1	1	1	1	0	0	2	6	1	3	3	4	1	1	3	4	1	1	rs139584149	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:101201206C>T	ENST00000341267.4	+	5	1367	c.1125C>T	c.(1123-1125)agC>agT	p.S375S	DLK1_ENST00000331224.6_Silent_p.S302S|RP11-566J3.4_ENST00000608876.1_lincRNA	NM_003836.5	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog (Drosophila)	375					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)				CCACCTTCAGCAAGGAGGCCG	0.552													C|||	50	0.00998403	0.0371	0.0	5008	,	,		16616	0.0		0.001	False		,,,				2504	0.0				p.S375S		Atlas-SNP	.											.	DLK1	57	.	0			c.C1125T						PASS	.	C		105,4301	82.4+/-120.9	1,103,2099	92	92	92		1125	3.5	0.9	14	dbSNP_134	92	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	DLK1	NM_003836.5		1,107,6395	TT,TC,CC		0.0465,2.3831,0.8381		375/384	101201206	109,12897	2203	4300	6503	SO:0001819	synonymous_variant	8788	exon5			CTTCAGCAAGGAG	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.1125C>T	14.37:g.101201206C>T		30	0	0		26	16	0.615385	NM_003836	P15803|Q96DW5	Silent	SNP	ENST00000341267.4	37	CCDS9963.1																																																																																			C|0.991;T|0.009	0.009	strong		0.552	DLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414389.1			T	101201206	C	T	101201206	2	4	22	1	0	0	0	0	0	0	0	1	4566	709	25	2		2	DLK1	14	101201206	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	426	101201206	6148334	2939	5840											
DLK1	8788	hgsc.bcm.edu	37	chr14	101201219	101201219	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	ccttcagcaaggaggccggcGacgaggagatctaagcagcg	11	4	15	11	4	2	1	1	0	1	1	2	5	2	2	2	4	3	2	2	4	2	2	rs115349979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:101201219G>C	ENST00000341267.4	+	5	1380	c.1138G>C	c.(1138-1140)Gac>Cac	p.D380H	DLK1_ENST00000331224.6_Missense_Mutation_p.D307H|RP11-566J3.4_ENST00000608876.1_lincRNA	NM_003836.5	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog (Drosophila)	380					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)				GGAGGCCGGCGACGAGGAGAT	0.552													G|||	62	0.0123802	0.0469	0.0	5008	,	,		16011	0.0		0.0	False		,,,				2504	0.0				p.D380H		Atlas-SNP	.											DLK1,NS,carcinoma,-2,2	DLK1	57	2	0			c.G1138C						PASS	.	G	HIS/ASP	130,4276	94.8+/-133.5	3,124,2076	85	86	86		1138	0.9	0.2	14	dbSNP_132	86	0,8600		0,0,4300	yes	missense	DLK1	NM_003836.5	81	3,124,6376	CC,CG,GG		0.0,2.9505,0.9995	benign	380/384	101201219	130,12876	2203	4300	6503	SO:0001583	missense	8788	exon5			GCCGGCGACGAGG	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.1138G>C	14.37:g.101201219G>C	ENSP00000340292:p.Asp380His	26	0	0		20	10	0.5	NM_003836	P15803|Q96DW5	Missense_Mutation	SNP	ENST00000341267.4	37	CCDS9963.1	22	0.010073260073260074	22	0.044715447154471545	0	0.0	0	0.0	0	0.0	G	9.764	1.170865	0.21621	0.029505	0.0	ENSG00000185559	ENST00000341267;ENST00000331224	D;D	0.88431	-2.38;-2.32	4.41	0.928	0.19443	.	1.200000	0.06159	N	0.675641	T	0.57844	0.2081	N	0.08118	0	0.09310	N	1	P;P	0.46220	0.874;0.8	P;P	0.54460	0.753;0.571	T	0.69351	-0.5168	10	0.87932	D	0	.	0.6745	0.00864	0.2119:0.1565:0.3728:0.2589	.	307;380	P80370-2;P80370	.;DLK1_HUMAN	H	380;307	ENSP00000340292:D380H;ENSP00000331081:D307H	ENSP00000331081:D307H	D	+	1	0	DLK1	100270972	0.002000	0.14202	0.191000	0.23289	0.049000	0.14656	0.031000	0.13710	0.860000	0.35481	-0.332000	0.08345	GAC	G|0.988;C|0.012	0.012	strong		0.552	DLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414389.1			C	101201219	G	C	101201219	3	2	22	1	0	0	0	0	1	0	0	0	4566	1058	37	4	1156	4	DLK1	14	101201219	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	13	101201219	6148321	2940	5841											
RTL1	388015	hgsc.bcm.edu	37	chr14	101347090	101347090	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtcctcatcaggcagctcttCtagccttgcctgctccctgg	4	12	9	16	0	4	0	2	0	2	0	6	0	6	0	4	2	4	3	4	2	1	3	rs73349352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:101347090C>T	ENST00000534062.1	-	1	4094	c.4036G>A	c.(4036-4038)Gaa>Aaa	p.E1346K	MIR433_ENST00000384837.1_RNA|MIR431_ENST00000385266.1_RNA|MIR127_ENST00000384876.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	1346					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						GGCAGCTCTTCTAGCCTTGCC	0.627													C|||	213	0.0425319	0.1536	0.0144	5008	,	,		14165	0.0		0.0	False		,,,				2504	0.0				p.E1346K		Atlas-SNP	.											.	RTL1	120	.	0			c.G4036A						PASS	.						32	32	32					14																	101347090		692	1591	2283	SO:0001583	missense	388015	exon1			GCTCTTCTAGCCT		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.4036G>A	14.37:g.101347090C>T	ENSP00000435342:p.Glu1346Lys	153	0	0		173	86	0.49711	NM_001134888	E9PKS8	Missense_Mutation	SNP	ENST00000534062.1	37	CCDS53910.1	73	0.033424908424908424	70	0.14227642276422764	3	0.008287292817679558	0	0.0	0	0.0	C	12.39	1.924506	0.34002	.	.	ENSG00000254656	ENST00000534062	T	0.28255	1.62	3.29	0.236	0.15471	.	.	.	.	.	T	0.00144	0.0004	N	0.24115	0.695	0.80722	P	0.0	B	0.34103	0.437	B	0.24541	0.054	T	0.09552	-1.0669	8	0.87932	D	0	.	10.9898	0.47543	0.0:0.4239:0.5761:0.0	.	1346	E9PKS8	.	K	1346	ENSP00000435342:E1346K	ENSP00000435342:E1346K	E	-	1	0	RTL1	100416843	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-0.458000	0.06737	0.044000	0.15775	-0.222000	0.12452	GAA	C|0.966;T|0.034	0.034	strong		0.627	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888		T	101347090	C	T	101347090	3	4	22	1	0	0	0	0	1	0	0	0	13739	922	32	2	44	2	RTL1	14	101347090	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	145871	101347090	6002450	2941	5842											
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102469273	102469273	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaaagcattgggagaataTctggaaagagagcggtcatc	15	7	13	6	1	2	3	1	0	1	3	3	6	2	4	0	3	2	1	0	3	4	2	rs75094258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:102469273T>C	ENST00000360184.4	+	23	5018	c.4854T>C	c.(4852-4854)taT>taC	p.Y1618Y		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	1618	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						TGGGAGAATATCTGGAAAGAG	0.458													T|||	27	0.00539137	0.0197	0.0014	5008	,	,		19492	0.0		0.0	False		,,,				2504	0.0				p.Y1618Y		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.T4854C						PASS	.	T		53,4353	52.9+/-88.7	1,51,2151	70	69	70		4854	4.5	1	14	dbSNP_132	70	0,8600		0,0,4300	no	coding-synonymous	DYNC1H1	NM_001376.4		1,51,6451	CC,CT,TT		0.0,1.2029,0.4075		1618/4647	102469273	53,12953	2203	4300	6503	SO:0001819	synonymous_variant	1778	exon23			AGAATATCTGGAA	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.4854T>C	14.37:g.102469273T>C		92	0	0		79	32	0.405063	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																			T|0.994;C|0.006	0.006	strong		0.458	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		C	102469273	T	C	102469273	2	2	22	1	0	0	0	0	0	0	0	1	4843	1442	50	3		3	DYNC1H1	14	102469273	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1122183	102469273	4880267	2942	5843											
RAGE	5891	hgsc.bcm.edu	37	chr14	102700028	102700028	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagaacacaatacttactgtTtgaacttggtgaggatcttc	12	13	8	8	0	1	3	0	2	1	1	2	4	1	4	0	2	4	1	0	2	5	5	rs34965156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:102700028T>C	ENST00000361847.2	-	8	920	c.689A>G	c.(688-690)aAa>aGa	p.K230R	MOK_ENST00000519058.1_5'UTR|MOK_ENST00000522867.1_5'UTR|MOK_ENST00000524370.1_5'UTR|MOK_ENST00000561150.1_5'UTR|MOK_ENST00000517966.1_5'UTR|MOK_ENST00000522534.1_5'UTR|MOK_ENST00000524214.1_Missense_Mutation_p.K200R|MOK_ENST00000523231.1_5'UTR|MOK_ENST00000193029.6_5'UTR|MOK_ENST00000520266.1_5'UTR|MOK_ENST00000522874.1_Missense_Mutation_p.K229R	NM_014226.1	NP_055041.1	Q9UQ07	MOK_HUMAN	MOK protein kinase	230	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		K -> R (in dbSNP:rs34965156). {ECO:0000269|PubMed:17344846}.		protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)										TACTTACTGTTTGAACTTGGT	0.532													T|||	258	0.0515176	0.1876	0.0115	5008	,	,		19334	0.0		0.002	False		,,,				2504	0.0				p.K230R		Atlas-SNP	.											.	.	.	.	0			c.A689G						PASS	.	T	ARG/LYS	689,3717		61,567,1575	189	147	161		689	5.2	1	14	dbSNP_126	161	17,8583		0,17,4283	yes	missense	MOK	NM_014226.1	26	61,584,5858	CC,CT,TT		0.1977,15.6378,5.4283	benign	230/420	102700028	706,12300	2203	4300	6503	SO:0001583	missense	5891	exon8			TACTGTTTGAACT	AB022694	CCDS9971.1, CCDS61552.1	14q32	2014-04-23	2011-09-06	2011-09-06	ENSG00000080823	ENSG00000080823			9833	protein-coding gene	gene with protein product		605762	"renal tumor antigen"	RAGE		8781117, 10421840	Standard	NM_014226		Approved	RAGE1, STK30	uc001ylm.4	Q9UQ07	OTTHUMG00000164896	ENST00000361847.2:c.689A>G	14.37:g.102700028T>C	ENSP00000355304:p.Lys230Arg	216	0	0		225	113	0.502222	NM_014226	B2R6Z4|B7Z7P6|E7ER76|E7ERR8|Q92790|Q93067	Missense_Mutation	SNP	ENST00000361847.2	37	CCDS9971.1	99	0.04532967032967033	92	0.18699186991869918	5	0.013812154696132596	0	0.0	2	0.002638522427440633	.	14.82	2.649258	0.47362	0.156378	0.001977	ENSG00000080823	ENST00000522874;ENST00000361847;ENST00000524214	T;T;T	0.64803	-0.12;-0.12;-0.12	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);	0.054522	0.64402	D	0.000001	T	0.00073	0.0002	N	0.11313	0.125	0.09310	P	1.0	B;B	0.21225	0.021;0.053	B;B	0.26517	0.044;0.07	T	0.04752	-1.0929	9	0.46703	T	0.11	-1.1389	15.0926	0.72207	0.0:0.0:0.0:1.0	rs34965156	200;230	E7ERR8;Q9UQ07	.;MOK_HUMAN	R	229;230;200	ENSP00000429469:K229R;ENSP00000355304:K230R;ENSP00000428942:K200R	ENSP00000355304:K230R	K	-	2	0	RAGE	101769781	1.000000	0.71417	0.985000	0.45067	0.870000	0.49936	4.211000	0.58507	1.978000	0.57642	0.482000	0.46254	AAA	T|0.940;C|0.060	0.060	strong		0.532	MOK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380848.3			C	102700028	T	C	102700028	3	2	22	1	0	0	0	0	1	0	0	0	13021	1841	64	3	590	3	RAGE	14	102700028	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	230755	102700028	4649512	2943	5844											
AMN	81693	hgsc.bcm.edu	37	chr14	103395212	103395212	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccgagcgcgtgccctgccGccacgacgacgtcttctttc	4	8	11	18	8	2	0	0	0	2	0	3	3	2	0	4	0	3	0	4	0	0	2	rs568801729		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:103395212G>T	ENST00000299155.5	+	5	446	c.413G>T	c.(412-414)cGc>cTc	p.R138L		NM_030943.3	NP_112205.2	Q9BXJ7	AMNLS_HUMAN	amnion associated transmembrane protein	138					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)	GTGCCCTGCCGCCACGACGAC	0.706																																					p.R138L		Atlas-SNP	.											.	AMN	13	.	0			c.G413T						PASS	.						30	28	29					14																	103395212		2203	4297	6500	SO:0001583	missense	81693	exon5			CCTGCCGCCACGA	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.413G>T	14.37:g.103395212G>T	ENSP00000299155:p.Arg138Leu	45	0	0		93	54	0.580645	NM_030943	Q6UX83	Missense_Mutation	SNP	ENST00000299155.5	37	CCDS9977.1	.	.	.	.	.	.	.	.	.	.	G	14.55	2.570223	0.45798	.	.	ENSG00000166126	ENST00000299155;ENST00000541086	D	0.88664	-2.41	4.03	0.969	0.19686	.	0.560105	0.18314	U	0.145003	D	0.84083	0.5394	M	0.61703	1.905	0.26626	N	0.972569	P	0.38020	0.615	B	0.38954	0.286	T	0.76173	-0.3056	10	0.62326	D	0.03	-1.9881	2.5302	0.04701	0.11:0.1861:0.5126:0.1913	.	138	Q9BXJ7	AMNLS_HUMAN	L	138;84	ENSP00000299155:R138L	ENSP00000299155:R138L	R	+	2	0	AMN	102464965	0.003000	0.15002	0.737000	0.30932	0.919000	0.55068	0.296000	0.19083	-0.112000	0.11979	0.306000	0.20318	CGC	.	.	none		0.706	AMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415704.1			T	103395212	G	T	103395212	3	4	22	1	0	0	0	0	1	0	0	0	580	1087	38	4	431	4	AMN	14	103395212	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	695184	103395212	3954328	2944	5845											
CDC42BPB	9578	hgsc.bcm.edu	37	chr14	103406169	103406169	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gtgaggccccgctcctaccgCctctgctgcagtctctcttc	3	11	9	18	2	3	1	0	1	3	0	6	1	4	1	5	1	3	3	5	1	1	2	rs60475222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:103406169C>T	ENST00000361246.2	-	33	4995	c.4707G>A	c.(4705-4707)agG>agA	p.R1569R	RP11-365N19.2_ENST00000560931.1_RNA	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)		GCTCCTACCGCCTCTGCTGCA	0.597													C|||	35	0.00698882	0.0257	0.0014	5008	,	,		19254	0.0		0.0	False		,,,				2504	0.0				p.R1569R		Atlas-SNP	.											.	CDC42BPB	123	.	0			c.G4707A						PASS	.	C		110,4296	86.8+/-125.4	2,106,2095	147	158	155		4707	3.4	1	14	dbSNP_129	155	0,8600		0,0,4300	no	coding-synonymous	CDC42BPB	NM_006035.3		2,106,6395	TT,TC,CC		0.0,2.4966,0.8458		1569/1712	103406169	110,12896	2203	4300	6503	SO:0001819	synonymous_variant	9578	exon33			CTACCGCCTCTGC	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.4707G>A	14.37:g.103406169C>T		163	0	0		216	96	0.444444	NM_006035		Silent	SNP	ENST00000361246.2	37	CCDS9978.1																																																																																			C|0.992;T|0.008	0.008	strong		0.597	CDC42BPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415711.1	NM_006035		T	103406169	C	T	103406169	2	4	22	1	0	0	0	0	0	0	0	1	3075	738	26	2		2	CDC42BPB	14	103406169	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	10957	103406169	3943371	2945	5846											
CDC42BPB	9578	hgsc.bcm.edu	37	chr14	103434985	103434985	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagactttcttctccagctcGgatttgattttggaaatctc	9	16	7	9	1	3	2	0	1	3	1	6	4	3	4	1	2	1	1	1	2	2	5	rs55659700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:103434985G>A	ENST00000361246.2	-	15	2352	c.2064C>T	c.(2062-2064)tcC>tcT	p.S688S		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)		TCTCCAGCTCGGATTTGATTT	0.453													G|||	45	0.00898562	0.0257	0.0159	5008	,	,		19256	0.0		0.0	False		,,,				2504	0.0				p.S688S		Atlas-SNP	.											.	CDC42BPB	123	.	0			c.C2064T						PASS	.	G		111,4295	85.8+/-124.5	2,107,2094	83	90	88		2064	-9.2	0.2	14	dbSNP_129	88	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CDC42BPB	NM_006035.3		2,108,6393	AA,AG,GG		0.0116,2.5193,0.8611		688/1712	103434985	112,12894	2203	4300	6503	SO:0001819	synonymous_variant	9578	exon15			CAGCTCGGATTTG	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.2064C>T	14.37:g.103434985G>A		106	0	0		98	47	0.479592	NM_006035		Silent	SNP	ENST00000361246.2	37	CCDS9978.1																																																																																			G|0.992;A|0.008	0.008	strong		0.453	CDC42BPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415711.1	NM_006035		A	103434985	G	A	103434985	2	1	22	1	0	0	0	0	0	0	0	1	3075	1103	39	1		1	CDC42BPB	14	103434985	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	28816	103434985	3914555	2946	5847											
MARK3	4140	hgsc.bcm.edu	37	chr14	103941392	103941392	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtcagaccagcactgcagatAgtgacctcaaagaagatgga	15	6	11	9	0	2	5	2	1	0	4	2	6	2	6	2	1	2	2	2	1	3	1	rs56305318	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:103941392A>G	ENST00000429436.2	+	13	1837	c.1327A>G	c.(1327-1329)Agt>Ggt	p.S443G	MARK3_ENST00000303622.9_Missense_Mutation_p.S443G|MARK3_ENST00000335102.5_Missense_Mutation_p.S466G|MARK3_ENST00000561071.1_Intron|MARK3_ENST00000216288.7_Missense_Mutation_p.S427G|MARK3_ENST00000416682.2_Missense_Mutation_p.S466G|MARK3_ENST00000440884.3_Missense_Mutation_p.S364G|MARK3_ENST00000553942.1_Missense_Mutation_p.S443G	NM_001128918.1|NM_001128919.1	NP_001122390.1|NP_001122391.1	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	443			S -> G (in dbSNP:rs56305318). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9543386, ECO:0000269|Ref.2}.			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)			CACTGCAGATAGTGACCTCAA	0.448													A|||	242	0.0483227	0.1793	0.0072	5008	,	,		20680	0.0		0.0	False		,,,				2504	0.0				p.S443G		Atlas-SNP	.											.	MARK3	86	.	0			c.A1327G						PASS	.	A	GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER	577,3417		51,475,1471	59	61	60		1327,1327,1279,1090,1327	2	0.8	14	dbSNP_129	60	1,8343		0,1,4171	yes	missense,missense,missense,missense,missense	MARK3	NM_001128918.1,NM_001128919.1,NM_001128920.1,NM_001128921.1,NM_002376.5	56,56,56,56,56	51,476,5642	GG,GA,AA		0.012,14.4467,4.6847	benign,benign,benign,benign,benign	443/754,443/745,427/714,364/660,443/730	103941392	578,11760	1997	4172	6169	SO:0001583	missense	4140	exon13			GCAGATAGTGACC	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.1327A>G	14.37:g.103941392A>G	ENSP00000411397:p.Ser443Gly	86	0	0		85	48	0.564706	NM_001128919	O60219|Q86TT8|Q8TB41|Q8WX83|Q96RG1|Q9UMY9|Q9UN34	Missense_Mutation	SNP	ENST00000429436.2	37	CCDS45165.1	87|87	0.03983516483516483|0.03983516483516483	83|83	0.16869918699186992|0.16869918699186992	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	0|0	0.0|0.0	A|A	12.87|12.87	2.068525|2.068525	0.36470|0.36470	0.144467|0.144467	1.2E-4|1.2E-4	ENSG00000075413|ENSG00000075413	ENST00000554627|ENST00000335102;ENST00000411530;ENST00000440884;ENST00000416682;ENST00000429436;ENST00000303622;ENST00000216288;ENST00000553942	.|T;T;T;T;T;T;T	.|0.55234	.|0.53;0.53;0.53;0.53;0.53;0.53;0.53	5.78|5.78	2.0|2.0	0.26442|0.26442	.|.	.|0.269900	.|0.46758	.|N	.|0.000264	T|T	0.00144|0.00144	0.0004|0.0004	L|L	0.40543|0.40543	1.245|1.245	0.27271|0.27271	P|P	0.9583608|0.9583608	.|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	.|0.10450	.|0.001;0.004;0.001;0.001;0.0;0.005;0.001	T|T	0.07868|0.07868	-1.0750|-1.0750	4|9	.|0.29301	.|T	.|0.29	.|.	9.2811|9.2811	0.37729|0.37729	0.781:0.0:0.219:0.0|0.781:0.0:0.219:0.0	rs56305318;rs61730317|rs56305318;rs61730317	.|450;466;427;443;364;443;443	.|P27448-7;P27448-2;P27448-6;P27448;Q86TT8;P27448-4;P27448-3	.|.;.;.;MARK3_HUMAN;.;.;.	M|G	194|466;92;364;466;443;443;427;443	.|ENSP00000335347:S466G;ENSP00000402104:S364G;ENSP00000408092:S466G;ENSP00000411397:S443G;ENSP00000303698:S443G;ENSP00000216288:S427G;ENSP00000450772:S443G	.|ENSP00000216288:S443G	I|S	+|+	3|1	3|0	MARK3|MARK3	103011145|103011145	0.979000|0.979000	0.34478|0.34478	0.769000|0.769000	0.31535|0.31535	0.720000|0.720000	0.41350|0.41350	1.621000|1.621000	0.36986|0.36986	0.090000|0.090000	0.17273|0.17273	0.533000|0.533000	0.62120|0.62120	ATA|AGT	A|0.958;G|0.042	0.042	strong		0.448	MARK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415144.1	NM_001128918		G	103941392	A	G	103941392	3	3	22	1	0	0	0	0	1	0	0	0	9323	420	15	3	1377	3	MARK3	14	103941392	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	506407	103941392	3408148	2947	5848											
INF2	64423	hgsc.bcm.edu	37	chr14	105180977	105180977	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggacgctgtccacagccgtGgtgccagaccccctgcagca	8	5	12	16	2	0	1	0	0	0	1	1	2	1	2	5	2	4	3	5	2	0	0	rs9672065	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105180977G>A	ENST00000392634.4	+	21	3590	c.3478G>A	c.(3478-3480)Ggt>Agt	p.G1160S	INF2_ENST00000330634.7_Missense_Mutation_p.G1160S	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	inverted formin, FH2 and WH2 domain containing	1160					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)		CCACAGCCGTGGTGCCAGACC	0.652													G|||	110	0.0219649	0.0734	0.0144	5008	,	,		16731	0.0		0.003	False		,,,				2504	0.0				p.G1160S		Atlas-SNP	.											.	INF2	148	.	0			c.G3478A						PASS	.	G	SER/GLY,SER/GLY	221,3991		2,217,1887	38	46	43		3478,3478	-8.5	0	14	dbSNP_119	43	6,8424		0,6,4209	yes	missense,missense	INF2	NM_022489.3,NM_001031714.3	56,56	2,223,6096	AA,AG,GG		0.0712,5.2469,1.7956	benign,benign	1160/1250,1160/1241	105180977	227,12415	2106	4215	6321	SO:0001583	missense	64423	exon21			AGCCGTGGTGCCA	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.3478G>A	14.37:g.105180977G>A	ENSP00000376410:p.Gly1160Ser	44	0	0		39	26	0.666667	NM_022489	Q27J83|Q69YL8|Q6P1X7|Q6PK22|Q86TR7|Q9BRM1|Q9H6N1	Missense_Mutation	SNP	ENST00000392634.4	37	CCDS9989.2	48	0.02197802197802198	44	0.08943089430894309	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	G	2.964	-0.214005	0.06101	0.052469	7.12E-4	ENSG00000203485	ENST00000330634;ENST00000392634	T;T	0.79940	-1.3;-1.32	4.24	-8.47	0.00939	.	1.401710	0.05279	N	0.519086	T	0.02807	0.0084	N	0.02539	-0.55	0.09310	N	0.999998	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.38929	-0.9638	10	0.02654	T	1	.	10.5338	0.44992	0.7803:0.1044:0.1153:0.0	rs9672065	1160;1160	Q27J81-2;Q27J81	.;INF2_HUMAN	S	1160	ENSP00000376406:G1160S;ENSP00000376410:G1160S	ENSP00000252527:G628S	G	+	1	0	INF2	104252022	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.762000	0.01803	-2.735000	0.00382	-0.948000	0.02665	GGT	G|0.978;A|0.022	0.022	strong		0.652	INF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074371.4	NM_022489		A	105180977	G	A	105180977	3	1	22	1	0	0	0	0	1	0	0	0	7743	1348	47	2	3560	2	INF2	14	105180977	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1239585	105180977	2168563	2948	5849											
AKT1	207	hgsc.bcm.edu	37	chr14	105238783	105238783	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggcgtcctcggagcccccGccaagcctgcaggcaggaaa	8	5	13	15	3	0	0	0	0	0	0	2	2	1	2	5	4	3	2	5	4	2	1	rs11555434	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105238783G>A	ENST00000554581.1	-	11	2659	c.1179C>T	c.(1177-1179)ggC>ggT	p.G393G	AKT1_ENST00000402615.2_Silent_p.G393G|AKT1_ENST00000554848.1_Silent_p.G393G|AKT1_ENST00000407796.2_Silent_p.G393G|AKT1_ENST00000544168.1_Silent_p.G331G|AKT1_ENST00000555458.1_Silent_p.G88G|AKT1_ENST00000555528.1_Silent_p.G393G|AKT1_ENST00000349310.3_Silent_p.G393G|AKT1_ENST00000554192.1_Silent_p.G80G|RP11-982M15.2_ENST00000557223.1_RNA|AKT1_ENST00000554585.1_5'UTR			P31749	AKT1_HUMAN	v-akt murine thymoma viral oncogene homolog 1	393	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)	CGGAGCCCCCGCCAAGCCTGC	0.642		1	Mis		"breast, colorectal, ovarian, NSCLC"								g|||	44	0.00878594	0.0325	0.0014	5008	,	,		18738	0.0		0.0	False		,,,				2504	0.0				p.G393G		Atlas-SNP	.		Dom	yes		14	14q32.32	207	v-akt murine thymoma viral oncogene homolog 1		E	.	AKT1	379	.	0			c.C1179T						PASS	.		,,	113,4291	81.4+/-119.9	5,103,2094	65	48	54		1179,1179,1179	-6.1	0.5	14	dbSNP_120	54	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	AKT1	NM_001014431.1,NM_001014432.1,NM_005163.2	,,	5,107,6390	AA,AG,GG		0.0465,2.5658,0.8997	,,	393/481,393/481,393/481	105238783	117,12887	2202	4300	6502	SO:0001819	synonymous_variant	207	exon12			GCCCCCGCCAAGC	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.1179C>T	14.37:g.105238783G>A		103	0	0		130	60	0.461538	NM_005163	B2RAM5|B7Z5R1|Q9BWB6	Silent	SNP	ENST00000554581.1	37	CCDS9994.1																																																																																			G|0.992;A|0.008	0.008	strong		0.642	AKT1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410418.1	NM_005163		A	105238783	G	A	105238783	2	1	22	1	0	0	0	0	0	0	0	1	478	1074	38	1		1	AKT1	14	105238783	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	57806	105238783	2110757	2949	5850											
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105411091	105411091	+	Missense_Mutation	SNP	G	G	A																															ccttgaggtccactttgggcGtctttaaactgggcatctcc																								rs143814844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105411091G>A	ENST00000333244.5	-	7	10816	c.10697C>T	c.(10696-10698)aCg>aTg	p.T3566M	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3566						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)		p.T3566M(1)		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)			CACTTTGGGCGTCTTTAAACT	0.612													.|||	367	0.0732827	0.267	0.0173	5008	,	,		17318	0.0		0.002	False		,,,				2504	0.0				p.T3566M		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	1	Substitution - Missense(1)	prostate(1)	c.C10697T						PASS	.	A	MET/THR	783,2917		107,569,1174	98	113	108		10697	1.6	0	14	dbSNP_134	108	10,8158		0,10,4074	no	missense	AHNAK2	NM_138420.2	81	107,579,5248	AA,AG,GG		0.1224,21.1622,6.6818	benign	3566/5796	105411091	793,11075	1850	4084	5934	SO:0001583	missense	113146	exon7			TTGGGCGTCTTTA	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.10697C>T	14.37:g.105411091G>A	ENSP00000353114:p.Thr3566Met	241	2	0.00829876		257	254	0.988327	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	80	0.03663003663003663	75	0.1524390243902439	5	0.013812154696132596	0	0.0	0	0.0	a	2.924	-0.222471	0.06061	0.211622	0.001224	ENSG00000185567	ENST00000333244	T	0.00745	5.75	4.06	1.63	0.23807	.	1.601890	0.05251	U	0.513995	T	0.00012	0.0000	N	0.00086	-2.195	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39461	-0.9613	9	0.33940	T	0.23	.	4.4622	0.11671	0.5589:0.1614:0.2797:0.0	rs2819442	3566	Q8IVF2	AHNK2_HUMAN	M	3566	ENSP00000353114:T3566M	ENSP00000353114:T3566M	T	-	2	0	AHNAK2	104482136	0.000000	0.05858	0.042000	0.18584	0.008000	0.06430	-0.778000	0.04664	-0.237000	0.09739	-1.140000	0.01884	ACG	G|0.971;A|0.029	0.029	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105411091	G	A	105411091	3	1	22	1	0	0	0	0	1	0	0	0	415	1145	40	1	6694	1	AHNAK2	14	105411091	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	172308	105411091	1938449	2950	5851	71	2	6	29		14	11	7186	N	T_G_C_A	1.596251e-07
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105411096	105411096	+	Missense_Mutation	SNP	T	T	G																															aggtccactttgggcgtcttTaaactgggcatctccacttt																								rs146355838	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105411096T>G	ENST00000333244.5	-	7	10811	c.10692A>C	c.(10690-10692)ttA>ttC	p.L3564F	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3564						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)			TGGGCGTCTTTAAACTGGGCA	0.612													.|||	364	0.0726837	0.2648	0.0173	5008	,	,		17395	0.0		0.002	False		,,,				2504	0.0				p.L3564F		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A10692C						PASS	.	T	PHE/LEU	745,2943		103,539,1202	98	113	108		10692	-0.5	0.1	14	dbSNP_134	108	9,8157		0,9,4074	no	missense	AHNAK2	NM_138420.2	22	103,548,5276	GG,GT,TT		0.1102,20.2007,6.3607	possibly-damaging	3564/5796	105411096	754,11100	1844	4083	5927	SO:0001583	missense	113146	exon7			CGTCTTTAAACTG	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.10692A>C	14.37:g.105411096T>G	ENSP00000353114:p.Leu3564Phe	238	2	0.00840336		254	252	0.992126	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	79	0.036172161172161175	74	0.15040650406504066	5	0.013812154696132596	0	0.0	0	0.0	t	0.125	-1.120104	0.01785	0.202007	0.001102	ENSG00000185567	ENST00000333244	T	0.01034	5.42	3.75	-0.46	0.12175	.	.	.	.	.	T	0.00012	0.0000	N	0.01086	-1.025	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.38373	-0.9664	8	0.39692	T	0.17	.	3.0553	0.06182	0.0902:0.143:0.3249:0.4419	.	3564	Q8IVF2	AHNK2_HUMAN	F	3564	ENSP00000353114:L3564F	ENSP00000353114:L3564F	L	-	3	2	AHNAK2	104482141	0.002000	0.14202	0.063000	0.19743	0.003000	0.03518	-0.991000	0.03728	-0.179000	0.10654	-3.555000	0.00030	TTA	T|0.971;G|0.029	0.029	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		G	105411096	T	G	105411096	3	3	22	1	0	0	0	0	1	0	0	0	415	1751	61	5	6699	5	AHNAK2	14	105411096	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	5	105411096	1938444	2951	5852	71	2	6	29		14	11	7186	N	T_G_C_A	1.596251e-07
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105414316	105414316	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggcagacaccccgaatgacGgcatcttgaacttgggaatt	11	8	12	10	2	1	3	0	2	1	1	1	5	1	4	2	3	1	2	2	3	3	3	rs145541349	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105414316G>A	ENST00000333244.5	-	7	7591	c.7472C>T	c.(7471-7473)cCg>cTg	p.P2491L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2491						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)			CCCGAATGACGGCATCTTGAA	0.612													.|||	100	0.0199681	0.0741	0.0029	5008	,	,		18046	0.0		0.0	False		,,,				2504	0.0				p.P2491L		Atlas-SNP	.											AHNAK2_ENST00000333244,colon,carcinoma,+1,2	AHNAK2	719	2	0			c.C7472T						scavenged	.	G	LEU/PRO	217,3819		11,195,1812	175	202	193		7472	3.7	0.8	14	dbSNP_134	193	0,8354		0,0,4177	no	missense	AHNAK2	NM_138420.2	98	11,195,5989	AA,AG,GG		0.0,5.3766,1.7514	probably-damaging	2491/5796	105414316	217,12173	2018	4177	6195	SO:0001583	missense	113146	exon7			AATGACGGCATCT	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.7472C>T	14.37:g.105414316G>A	ENSP00000353114:p.Pro2491Leu	303	2	0.00660066		259	128	0.494208	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	31	0.014194139194139194	31	0.06300813008130081	0	0.0	0	0.0	0	0.0	g	16.25	3.069305	0.55539	0.053766	0.0	ENSG00000185567	ENST00000333244	T	0.03212	4.01	3.74	3.74	0.42951	.	.	.	.	.	T	0.03011	0.0089	H	0.95328	3.655	0.48632	D	0.999681	D	0.89917	1.0	D	0.97110	1.0	T	0.13469	-1.0508	9	0.42905	T	0.14	.	15.5871	0.76491	0.0:0.0:1.0:0.0	.	2491	Q8IVF2	AHNK2_HUMAN	L	2491	ENSP00000353114:P2491L	ENSP00000353114:P2491L	P	-	2	0	AHNAK2	104485361	0.998000	0.40836	0.839000	0.33178	0.181000	0.23173	3.089000	0.50183	1.642000	0.50584	0.485000	0.47835	CCG	G|0.988;A|0.012	0.012	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105414316	G	A	105414316	3	1	22	1	0	0	0	0	1	0	0	0	415	1116	39	1	9919	1	AHNAK2	14	105414316	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3220	105414316	1935224	2952	5853			6	29		14	11	7186	N	T_G_C_A	1.596251e-07
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105414559	105414559	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgagatctactttgggcatcTtgaaactgggcatctgcagc	9	12	11	9	0	3	2	0	2	3	1	3	3	3	2	0	2	4	3	0	2	2	3	rs11845746	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105414559T>C	ENST00000333244.5	-	7	7348	c.7229A>G	c.(7228-7230)aAg>aGg	p.K2410R	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2410			K -> R (in dbSNP:rs11845746).			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)			TTTGGGCATCTTGAAACTGGG	0.627													.|||	283	0.0565096	0.2073	0.0115	5008	,	,		17440	0.0		0.001	False		,,,				2504	0.0				p.K2410R		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A7229G						PASS	.	T	ARG/LYS	591,3093		71,449,1322	130	145	140		7229	2.9	0.5	14	dbSNP_120	140	5,8187		0,5,4091	no	missense	AHNAK2	NM_138420.2	26	71,454,5413	CC,CT,TT		0.061,16.0423,5.0185	probably-damaging	2410/5796	105414559	596,11280	1842	4096	5938	SO:0001583	missense	113146	exon7			GGCATCTTGAAAC	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.7229A>G	14.37:g.105414559T>C	ENSP00000353114:p.Lys2410Arg	208	0	0		240	236	0.983333	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	86	0.039377289377289376	82	0.16666666666666666	4	0.011049723756906077	0	0.0	0	0.0	-	12.77	2.037786	0.35989	0.160423	6.1E-4	ENSG00000185567	ENST00000333244	T	0.01265	5.08	4.08	2.93	0.34026	.	.	.	.	.	T	0.00039	0.0001	M	0.90759	3.145	0.49915	P	1.6599999999999948E-4	D	0.69078	0.997	D	0.77004	0.989	T	0.11767	-1.0574	8	0.39692	T	0.17	.	7.5349	0.27704	0.0:0.181:0.0:0.819	rs11845746;rs34729166;rs52811002;rs11845746	2410	Q8IVF2	AHNK2_HUMAN	R	2410	ENSP00000353114:K2410R	ENSP00000353114:K2410R	K	-	2	0	AHNAK2	104485604	0.002000	0.14202	0.526000	0.27913	0.064000	0.16182	0.833000	0.27504	0.468000	0.27243	0.397000	0.26171	AAG	T|0.967;C|0.033	0.033	strong		0.627	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		C	105414559	T	C	105414559	3	2	22	1	0	0	0	0	1	0	0	0	415	1609	56	3	10162	3	AHNAK2	14	105414559	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	243	105414559	1934981	2953	5854			6	29		14	11	7186	N	T_G_C_A	1.596251e-07
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105415899	105415899	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agccgcgcaccatccagcttAgccttctgggcctggacatc	7	8	10	16	2	1	0	0	0	1	0	3	1	2	1	5	2	3	2	5	2	1	2	rs11850869	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105415899A>G	ENST00000333244.5	-	7	6008	c.5889T>C	c.(5887-5889)gcT>gcC	p.A1963A	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1963						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)			CATCCAGCTTAGCCTTCTGGG	0.597													.|||	339	0.0676917	0.2315	0.013	5008	,	,		18512	0.0218		0.001	False		,,,				2504	0.001				p.A1963A		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T5889C						PASS	.	G		716,3310		132,452,1429	142	155	151		5889	-2.9	0	14	dbSNP_120	151	7,8261		1,5,4128	no	coding-synonymous	AHNAK2	NM_138420.2		133,457,5557	GG,GA,AA		0.0847,17.7844,5.8809		1963/5796	105415899	723,11571	2013	4134	6147	SO:0001819	synonymous_variant	113146	exon7			CAGCTTAGCCTTC	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.5889T>C	14.37:g.105415899A>G		276	0	0		296	294	0.993243	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.965;G|0.035	0.035	strong		0.597	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		G	105415899	A	G	105415899	2	3	22	1	0	0	0	0	0	0	0	1	415	407	15	3		3	AHNAK2	14	105415899	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1340	105415899	1933641	2954	5855			6	29		14	11	7186	N	T_G_C_A	1.596251e-07
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105416344	105416344	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctgtctttggcagtcacaTccttgtcggccagggacagg	6	11	13	11	1	2	0	1	0	1	0	4	1	3	1	2	4	1	2	2	4	0	2	rs368838079		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105416344T>G	ENST00000333244.5	-	7	5563	c.5444A>C	c.(5443-5445)gAt>gCt	p.D1815A	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1815						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)			GGCAGTCACATCCTTGTCGGC	0.612																																					p.D1815A		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A5444C						PASS	.	T	ALA/ASP	15,3901		2,11,1945	157	191	180		5444	0.1	0	14		180	0,8254		0,0,4127	no	missense	AHNAK2	NM_138420.2	126	2,11,6072	GG,GT,TT		0.0,0.383,0.1233	benign	1815/5796	105416344	15,12155	1958	4127	6085	SO:0001583	missense	113146	exon7			GTCACATCCTTGT	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.5444A>C	14.37:g.105416344T>G	ENSP00000353114:p.Asp1815Ala	290	0	0		301	16	0.0531561	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	t	13.76	2.332517	0.41297	0.00383	0.0	ENSG00000185567	ENST00000333244	T	0.01947	4.54	4.3	0.0484	0.14285	.	.	.	.	.	T	0.04861	0.0131	M	0.92317	3.295	0.09310	N	1	B	0.33637	0.42	B	0.25506	0.061	T	0.18524	-1.0334	9	0.34782	T	0.22	-8.5499	7.3574	0.26727	0.0:0.0901:0.4093:0.5005	.	1815	Q8IVF2	AHNK2_HUMAN	A	1815	ENSP00000353114:D1815A	ENSP00000353114:D1815A	D	-	2	0	AHNAK2	104487389	0.291000	0.24352	0.004000	0.12327	0.019000	0.09904	2.523000	0.45580	0.079000	0.16929	0.374000	0.22700	GAT	.	.	weak		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		G	105416344	T	G	105416344	3	3	22	1	0	0	0	0	1	0	0	0	415	1435	50	5	11947	5	AHNAK2	14	105416344	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	445	105416344	1933196	2955	5856			6	29		14	11	7186	N	T_G_C_A	1.596251e-07
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105416775	105416775	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgatggacttgcctggggcCgacaccccaaatgatggcat	9	8	12	12	2	0	1	0	1	0	0	1	4	0	2	4	4	1	1	4	4	1	1	rs60880494	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105416775C>A	ENST00000333244.5	-	7	5132	c.5013G>T	c.(5011-5013)tcG>tcT	p.S1671S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1671						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)			TGCCTGGGGCCGACACCCCAA	0.602													.|||	107	0.0213658	0.0613	0.0058	5008	,	,		17088	0.005		0.001	False		,,,				2504	0.0164				p.S1671S		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G5013T						PASS	.	T		136,3744		13,110,1817	190	222	212		5013	-5.7	0	14	dbSNP_129	212	15,8193		2,11,4091	no	coding-synonymous	AHNAK2	NM_138420.2		15,121,5908	AA,AC,CC		0.1827,3.5052,1.2492		1671/5796	105416775	151,11937	1940	4104	6044	SO:0001819	synonymous_variant	113146	exon7			TGGGGCCGACACC	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.5013G>T	14.37:g.105416775C>A		316	0	0		213	82	0.384977	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.015;C|0.985	0.015	strong		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105416775	C	A	105416775	2	1	22	1	0	0	0	0	0	0	0	1	415	639	23	4		4	AHNAK2	14	105416775	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	431	105416775	1932765	2956	5857			6	29		14	11	7186	N	T_G_C_A	1.596251e-07
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105417286	105417286	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggcagacaccccgaacgacGgcatcttgaacttgggcatt	10	7	12	12	3	1	2	0	1	1	1	1	4	1	2	2	3	2	3	2	3	2	3	rs149840830	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105417286G>A	ENST00000333244.5	-	7	4621	c.4502C>T	c.(4501-4503)cCg>cTg	p.P1501L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1501						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)			CCCGAACGACGGCATCTTGAA	0.607													.|||	272	0.0543131	0.2027	0.0058	5008	,	,		14935	0.0		0.0	False		,,,				2504	0.0				p.P1501L		Atlas-SNP	.											AHNAK2_ENST00000333244,colon,carcinoma,0,1	AHNAK2	719	1	0			c.C4502T						PASS	.	G	LEU/PRO	600,3288		124,352,1468	194	134	153		4502	4.2	0.9	14	dbSNP_134	153	13,8061		4,5,4028	no	missense	AHNAK2	NM_138420.2	98	128,357,5496	AA,AG,GG		0.161,15.4321,5.1246	probably-damaging	1501/5796	105417286	613,11349	1944	4037	5981	SO:0001583	missense	113146	exon7			AACGACGGCATCT	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.4502C>T	14.37:g.105417286G>A	ENSP00000353114:p.Pro1501Leu	370	0	0		355	337	0.949296	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	92	0.04212454212454213	90	0.18292682926829268	2	0.0055248618784530384	0	0.0	0	0.0	g	14.95	2.687349	0.48097	0.154321	0.00161	ENSG00000185567	ENST00000333244	T	0.03065	4.06	4.16	4.16	0.48862	.	.	.	.	.	T	0.00073	0.0002	H	0.95043	3.615	0.27144	P	0.9615793	D	0.89917	1.0	D	0.91635	0.999	T	0.05305	-1.0893	8	0.87932	D	0	-29.3229	16.1243	0.81382	0.0:0.0:1.0:0.0	.	1501	Q8IVF2	AHNK2_HUMAN	L	1501	ENSP00000353114:P1501L	ENSP00000353114:P1501L	P	-	2	0	AHNAK2	104488331	0.035000	0.19736	0.884000	0.34674	0.008000	0.06430	0.923000	0.28757	1.867000	0.54127	0.485000	0.47835	CCG	G|0.966;A|0.034	0.034	strong		0.607	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105417286	G	A	105417286	3	1	22	1	0	0	0	0	1	0	0	0	415	1116	39	1	12889	1	AHNAK2	14	105417286	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	511	105417286	1932254	2957	5858			6	29		14	11	7186	N	T_G_C_A	1.596251e-07
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105417503	105417503	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gcccttgatgtctatttcagGgcccttgaggtccactttgg	5	14	11	11	0	2	2	1	2	1	0	3	2	3	2	3	3	0	0	3	3	1	5	rs146582718	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105417503G>T	ENST00000333244.5	-	7	4404	c.4285C>A	c.(4285-4287)Cct>Act	p.P1429T	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1429						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)			TCTATTTCAGGGCCCTTGAGG	0.612													.|||	321	0.0640974	0.2307	0.0159	5008	,	,		12778	0.0		0.005	False		,,,				2504	0.0				p.P1429T		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C4285A						PASS	.	G	THR/PRO	721,2755		187,347,1204	98	74	83		4285	3.9	0.1	14	dbSNP_134	83	22,5768		3,16,2876	no	missense	AHNAK2	NM_138420.2	38	190,363,4080	TT,TG,GG		0.38,20.7422,8.0186	probably-damaging	1429/5796	105417503	743,8523	1738	2895	4633	SO:0001583	missense	113146	exon7			TTTCAGGGCCCTT	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.4285C>A	14.37:g.105417503G>T	ENSP00000353114:p.Pro1429Thr	389	0	0		411	406	0.987835	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	102	0.046703296703296704	99	0.20121951219512196	3	0.008287292817679558	0	0.0	0	0.0	g	11.78	1.742050	0.30865	0.207422	0.0038	ENSG00000185567	ENST00000333244	T	0.02656	4.21	3.87	3.87	0.44632	.	.	.	.	.	T	0.00012	0.0000	M	0.93328	3.405	0.38700	P	0.047036999999999995	D	0.89917	1.0	D	0.77557	0.99	T	0.06607	-1.0817	8	0.40728	T	0.16	-26.1992	9.0134	0.36155	0.1094:0.0:0.8906:0.0	.	1429	Q8IVF2	AHNK2_HUMAN	T	1429	ENSP00000353114:P1429T	ENSP00000353114:P1429T	P	-	1	0	AHNAK2	104488548	0.998000	0.40836	0.081000	0.20488	0.012000	0.07955	2.751000	0.47508	1.727000	0.51537	0.306000	0.20318	CCT	G|0.962;T|0.038	0.038	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		T	105417503	G	T	105417503	3	4	22	1	0	0	0	0	1	0	0	0	415	1232	43	4	13106	4	AHNAK2	14	105417503	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	217	105417503	1932037	2958	5859			6	29		14	11	7186	N	T_G_C_A	1.596251e-07
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105417731	105417731	+	Missense_Mutation	SNP	G	G	C																															ctccaccttgggtgcagacaGgtccacggaggcctcaatgg																								rs199870471	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105417731G>C	ENST00000333244.5	-	7	4176	c.4057C>G	c.(4057-4059)Ctg>Gtg	p.L1353V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1353						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)			GGTGCAGACAGGTCCACGGAG	0.597													.|||	284	0.0567093	0.0113	0.1311	5008	,	,		13717	0.0129		0.1153	False		,,,				2504	0.0501				p.L1353V		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C4057G						PASS	.						125	106	114					14																	105417731		1812	2876	4688	SO:0001583	missense	113146	exon7			CAGACAGGTCCAC	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.4057C>G	14.37:g.105417731G>C	ENSP00000353114:p.Leu1353Val	364	0	0		261	108	0.413793	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	-	0.008	-1.901985	0.00517	.	.	ENSG00000185567	ENST00000333244	T	0.01933	4.55	4.27	0.17	0.15021	.	.	.	.	.	T	0.00784	0.0026	N	0.01529	-0.815	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46721	-0.9171	9	0.02654	T	1	-1.5949	5.7398	0.18087	0.0:0.3359:0.4011:0.263	.	1353	Q8IVF2	AHNK2_HUMAN	V	1353	ENSP00000353114:L1353V	ENSP00000353114:L1353V	L	-	1	2	AHNAK2	104488776	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.272000	0.01165	-0.259000	0.09432	-1.901000	0.00528	CTG	.	.	weak		0.597	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		C	105417731	G	C	105417731	3	2	22	1	0	0	0	0	1	0	0	0	415	991	35	4	13334	4	AHNAK2	14	105417731	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	228	105417731	1931809	2959	5860	72	3	6	29		14	11	7186	N	T_G_C_A	1.596251e-07
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105417732	105417732	+	Silent	SNP	G	G	A																															tccaccttgggtgcagacagGtccacggaggcctcaatgga																								rs190986194	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105417732G>A	ENST00000333244.5	-	7	4175	c.4056C>T	c.(4054-4056)gaC>gaT	p.D1352D	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1352						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)			GTGCAGACAGGTCCACGGAGG	0.597													.|||	283	0.0565096	0.0113	0.1297	5008	,	,		13768	0.0129		0.1153	False		,,,				2504	0.0501				p.D1352D		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C4056T						PASS	.						126	107	114					14																	105417732		1812	2877	4689	SO:0001819	synonymous_variant	113146	exon7			AGACAGGTCCACG	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.4056C>T	14.37:g.105417732G>A		363	0	0		258	105	0.406977	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			G|0.914;A|0.086	0.086	strong		0.597	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105417732	G	A	105417732	2	1	22	1	0	0	0	0	0	0	0	1	415	1252	44	2		2	AHNAK2	14	105417732	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1	105417732	1931808	2960	5861	72	3	6	29		14	11	7186	N	T_G_C_A	1.596251e-07
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105417738	105417738	+	Silent	SNP	G	G	C																															ttgggtgcagacaggtccacGgaggcctcaatggacttgcc																								rs536679222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105417738G>C	ENST00000333244.5	-	7	4169	c.4050C>G	c.(4048-4050)tcC>tcG	p.S1350S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1350						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)			ACAGGTCCACGGAGGCCTCAA	0.592													.|||	371	0.0740815	0.0136	0.1398	5008	,	,		14224	0.0119		0.1571	False		,,,				2504	0.0879				p.S1350S		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C4050G						PASS	.						129	111	118					14																	105417738		1816	2913	4729	SO:0001819	synonymous_variant	113146	exon7			GTCCACGGAGGCC	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.4050C>G	14.37:g.105417738G>C		371	0	0		265	107	0.403774	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			.	.	none		0.592	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		C	105417738	G	C	105417738	2	2	22	1	0	0	0	0	0	0	0	1	415	1103	39	4		4	AHNAK2	14	105417738	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6	105417738	1931802	2961	5862	72	3	6	29		14	11	7186	N	T_G_C_A	1.596251e-07
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105417777	105417777	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctggggcagacaccccgaaCgacggcatcttgaacttggg	9	6	13	13	3	1	2	0	1	1	1	1	4	1	2	3	4	2	2	3	4	2	2	rs1960092	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105417777C>T	ENST00000333244.5	-	7	4130	c.4011G>A	c.(4009-4011)tcG>tcA	p.S1337S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1337						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)			ACACCCCGAACGACGGCATCT	0.612													.|||	385	0.076877	0.2693	0.0173	5008	,	,		14219	0.0079		0.007	False		,,,				2504	0.002				p.S1337S		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G4011A						PASS	.	G		843,2819		207,429,1195	147	129	135		4011	-2.5	0	14	dbSNP_92	135	21,6593		3,15,3289	no	coding-synonymous	AHNAK2	NM_138420.2		210,444,4484	TT,TC,CC		0.3175,23.0202,8.4079		1337/5796	105417777	864,9412	1831	3307	5138	SO:0001819	synonymous_variant	113146	exon7			CCCGAACGACGGC	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.4011G>A	14.37:g.105417777C>T		374	0	0		255	254	0.996078	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			C|0.959;T|0.041	0.041	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		T	105417777	C	T	105417777	2	4	22	1	0	0	0	0	0	0	0	1	415	523	19	1		1	AHNAK2	14	105417777	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	39	105417777	1931763	2962	5863			6	29		14	11	7186	N	T_G_C_A	1.596251e-07
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105418276	105418276	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggctgacgccccgaacgatGgcatcttgaacttgggcatt	8	9	13	11	3	1	2	0	2	1	0	1	4	1	2	2	3	2	3	2	3	2	3	rs35374867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105418276G>A	ENST00000333244.5	-	7	3631	c.3512C>T	c.(3511-3513)cCa>cTa	p.P1171L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1171						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)			CCCGAACGATGGCATCTTGAA	0.617													.|||	175	0.0349441	0.1286	0.0058	5008	,	,		18260	0.0		0.001	False		,,,				2504	0.0				p.P1171L		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C3512T						PASS	.	G	LEU/PRO	399,3475		46,307,1584	189	192	191		3512	4.4	1	14	dbSNP_126	191	5,8237		0,5,4116	no	missense	AHNAK2	NM_138420.2	98	46,312,5700	AA,AG,GG		0.0607,10.2994,3.3344	benign	1171/5796	105418276	404,11712	1937	4121	6058	SO:0001583	missense	113146	exon7			AACGATGGCATCT	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.3512C>T	14.37:g.105418276G>A	ENSP00000353114:p.Pro1171Leu	285	0	0		303	140	0.462046	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	60	0.027472527472527472	57	0.11585365853658537	3	0.008287292817679558	0	0.0	0	0.0	g	19.11	3.763478	0.69763	0.102994	6.07E-4	ENSG00000185567	ENST00000333244	T	0.05717	3.4	4.4	4.4	0.53042	.	.	.	.	.	T	0.00552	0.0018	H	0.95712	3.71	0.49483	D	0.999799	D	0.89917	1.0	D	0.91635	0.999	T	0.06826	-1.0805	9	0.72032	D	0.01	-13.4451	16.6046	0.84825	0.0:0.0:1.0:0.0	.	1171	Q8IVF2	AHNK2_HUMAN	L	1171	ENSP00000353114:P1171L	ENSP00000353114:P1171L	P	-	2	0	AHNAK2	104489321	1.000000	0.71417	0.967000	0.41034	0.114000	0.19823	5.979000	0.70508	1.998000	0.58463	0.491000	0.48974	CCA	G|0.978;A|0.022	0.022	strong		0.617	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105418276	G	A	105418276	3	1	22	1	0	0	0	0	1	0	0	0	415	1348	47	2	13879	2	AHNAK2	14	105418276	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	499	105418276	1931264	2963	5864			6	29		14	11	7186	N	T_G_C_A	1.596251e-07
JAG2	3714	hgsc.bcm.edu	37	chr14	105622157	105622157	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgtagtggccgaaaaagtcGttgcggggccggcagaactt	9	8	16	8	4	0	1	0	0	0	1	1	2	0	1	2	4	2	3	2	4	4	3	rs61750261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105622157G>A	ENST00000331782.3	-	4	1048	c.645C>T	c.(643-645)aaC>aaT	p.N215N	JAG2_ENST00000347004.2_Silent_p.N215N|RP11-44N21.4_ENST00000548203.1_RNA	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	215	DSL. {ECO:0000255|PROSITE- ProRule:PRU00377}.				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)		CGAAAAAGTCGTTGCGGGGCC	0.637													G|||	147	0.029353	0.1074	0.0072	5008	,	,		16759	0.0		0.0	False		,,,				2504	0.0				p.N215N		Atlas-SNP	.											.	JAG2	69	.	0			c.C645T						PASS	.	G	,	361,4031	179.7+/-208.2	15,331,1850	85	62	70		645,645	-3.3	1	14	dbSNP_129	70	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous,coding-synonymous	JAG2	NM_002226.3,NM_145159.1	,	15,332,6146	AA,AG,GG		0.0116,8.2195,2.7876	,	215/1239,215/1201	105622157	362,12624	2196	4297	6493	SO:0001819	synonymous_variant	3714	exon4			AAAGTCGTTGCGG	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.645C>T	14.37:g.105622157G>A		161	0	0		153	68	0.444444	NM_145159	Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Silent	SNP	ENST00000331782.3	37	CCDS9998.1																																																																																			G|0.974;A|0.026	0.026	strong		0.637	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2			A	105622157	G	A	105622157	2	1	22	1	0	0	0	0	0	0	0	1	7944	1136	40	1		1	JAG2	14	105622157	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	203881	105622157	1727383	2964	5865											
PACS2	23241	hgsc.bcm.edu	37	chr14	105821457	105821457	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagcgcagaaagcgctacaaGaacagaaccatcctgggcta	15	4	10	12	2	0	3	0	0	0	3	1	3	1	3	2	1	5	3	2	1	6	2	rs61738367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105821457G>A	ENST00000325438.8	+	4	870	c.366G>A	c.(364-366)aaG>aaA	p.K122K	PACS2_ENST00000430725.2_Silent_p.K55K|PACS2_ENST00000447393.1_Silent_p.K122K|PACS2_ENST00000458164.2_Silent_p.K122K|PACS2_ENST00000547217.1_Silent_p.K92K			Q86VP3	PACS2_HUMAN	phosphofurin acidic cluster sorting protein 2	122					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)		AGCGCTACAAGAACAGAACCA	0.602													G|||	56	0.0111821	0.0416	0.0	5008	,	,		19971	0.0		0.001	False		,,,				2504	0.0				p.K122K		Atlas-SNP	.											.	PACS2	75	.	0			c.G366A						PASS	.	G	,	200,4206	123.3+/-160.7	7,186,2010	78	64	69		366,366	-3.3	0.9	14	dbSNP_129	69	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	PACS2	NM_001100913.2,NM_015197.3	,	7,187,6309	AA,AG,GG		0.0116,4.5393,1.5454	,	122/894,122/890	105821457	201,12805	2203	4300	6503	SO:0001819	synonymous_variant	23241	exon4			CTACAAGAACAGA	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.366G>A	14.37:g.105821457G>A		105	0	0		97	48	0.494845	NM_001100913	A2VDJ9|G8JLK3|O60342|Q6P191|Q96FL7	Silent	SNP	ENST00000325438.8	37	CCDS32168.1																																																																																			G|0.986;A|0.014	0.014	strong		0.602	PACS2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000409209.1	XM_377355		A	105821457	G	A	105821457	2	1	22	1	0	0	0	0	0	0	0	1	11382	933	33	2		2	PACS2	14	105821457	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	199300	105821457	1528083	2965	5866											
MTA1	9112	hgsc.bcm.edu	37	chr14	105931109	105931109	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acgacgaagctgacgcggatCgcccggcgcctgtgccgtga	7	5	15	14	8	0	2	0	2	0	0	1	5	0	3	3	2	2	1	3	2	1	0	rs36015555	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105931109C>T	ENST00000331320.7	+	15	1657	c.1443C>T	c.(1441-1443)atC>atT	p.I481I	MTA1_ENST00000406191.1_Silent_p.I481I|MTA1_ENST00000405646.1_Silent_p.I464I|MTA1_ENST00000435036.2_Silent_p.I17I	NM_001203258.1|NM_004689.3	NP_001190187.1|NP_004680.2	Q13330	MTA1_HUMAN	metastasis associated 1	481					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)		TGACGCGGATCGCCCGGCGCC	0.672													C|||	257	0.0513179	0.1884	0.0115	5008	,	,		16374	0.0		0.0	False		,,,				2504	0.0				p.I481I		Atlas-SNP	.											.	MTA1	61	.	0			c.C1443T						PASS	.	C	,	712,3684		67,578,1553	32	28	29		,1443	-1.1	0.9	14	dbSNP_126	29	7,8587		0,7,4290	no	utr-3,coding-synonymous	MTA1	NM_001203258.1,NM_004689.3	,	67,585,5843	TT,TC,CC		0.0815,16.1965,5.535	,	,481/716	105931109	719,12271	2198	4297	6495	SO:0001819	synonymous_variant	9112	exon15			GCGGATCGCCCGG	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.1443C>T	14.37:g.105931109C>T		42	0	0		60	39	0.65	NM_004689	A5PLK4|Q86SW2|Q8NFI8|Q96GI8	Silent	SNP	ENST00000331320.7	37	CCDS32169.1																																																																																			C|0.947;T|0.053	0.053	strong		0.672	MTA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317849.15			T	105931109	C	T	105931109	2	4	22	1	0	0	0	0	0	0	0	1	9917	874	31	1		1	MTA1	14	105931109	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	109652	105931109	1418431	2966	5867											
C14orf80	283643	hgsc.bcm.edu	37	chr14	105957446	105957446	+	5'Flank	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagtgattggatgcatgtccGgccagcgcggtgattgggta	7	10	16	8	3	0	2	0	2	0	0	1	3	1	3	2	4	2	2	2	4	1	3	rs76864584	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105957446G>A	ENST00000392523.4	+	0	0				C14orf80_ENST00000329886.7_Missense_Mutation_p.G3S|C14orf80_ENST00000551054.1_3'UTR|C14orf80_ENST00000392527.1_Missense_Mutation_p.G3S|CRIP1_ENST00000551180.1_3'UTR|C14orf80_ENST00000334656.7_Missense_Mutation_p.G3S|C14orf80_ENST00000392522.3_5'Flank|C14orf80_ENST00000354560.6_5'Flank|C14orf80_ENST00000450383.1_5'Flank			Q86SX3	CN080_HUMAN	chromosome 14 open reading frame 80											central_nervous_system(1)	1		Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0188)	Epithelial(152;0.239)		ATGCATGTCCGGCCAGCGCGG	0.627													G|||	273	0.0545128	0.202	0.0086	5008	,	,		12847	0.0		0.0	False		,,,				2504	0.0				p.G3S		Atlas-SNP	.											.	C14orf80	19	.	0			c.G7A						PASS	.						115	102	106					14																	105957446		692	1591	2283	SO:0001631	upstream_gene_variant	283643	exon2			ATGTCCGGCCAGC		CCDS45180.1, CCDS45181.1, CCDS45182.1, CCDS55955.1	14q32.33	2012-09-25			ENSG00000185347	ENSG00000185347			20127	protein-coding gene	gene with protein product							Standard	NM_001134875		Approved		uc001yrn.3	Q86SX3	OTTHUMG00000170426		14.37:g.105957446G>A	Exception_encountered	117	0	0		168	91	0.541667	NM_001134877	B5MDG3|E9PAQ4|Q86TT3|Q86TT4|Q86TT5|Q96B41|Q9H7H4	Missense_Mutation	SNP	ENST00000392523.4	37		96	0.04395604395604396	91	0.18495934959349594	5	0.013812154696132596	0	0.0	0	0.0	G	12.89	2.073301	0.36566	.	.	ENSG00000185347	ENST00000329886;ENST00000427614;ENST00000455454;ENST00000432805;ENST00000392527;ENST00000443229;ENST00000334656	.	.	.	1.43	0.424	0.16468	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	D;D	0.62365	0.991;0.991	P;P	0.45610	0.487;0.487	T	0.17471	-1.0368	7	0.87932	D	0	.	6.8588	0.24056	0.0:0.0:0.7222:0.2778	.	3;3	B5MDG3;Q86SX3-3	.;.	S	3	.	ENSP00000333010:G3S	G	+	1	0	C14orf80	105028491	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.549000	0.02182	-0.096000	0.12329	-0.708000	0.03648	GGC	G|0.956;A|0.044	0.044	strong		0.627	C14orf80-017	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409090.1	NM_001134875		A	105957446	G	A	105957446	1	1	22	0	1	0	0	0	0	0	0	0	1783	1116	39	1		1	C14orf80	14	105957446	5'Flank	SNP	G	TCGA-G8-6324-01A-11D-2210-10	26337	105957446	1392094	2967	5868											
C14orf80	283643	hgsc.bcm.edu	37	chr14	105958010	105958010	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgctctcgccactccctgcgGgcaacgccttggcatcgctc	4	9	10	18	4	1	0	0	0	1	0	5	0	2	0	3	2	3	4	3	2	1	1	rs587675709	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105958010G>T	ENST00000392523.4	+	2	320	c.199G>T	c.(199-201)Ggc>Tgc	p.G67C	C14orf80_ENST00000329886.7_Missense_Mutation_p.G28C|C14orf80_ENST00000551054.1_3'UTR|C14orf80_ENST00000392527.1_Missense_Mutation_p.G26C|C14orf80_ENST00000334656.7_Missense_Mutation_p.G26C|C14orf80_ENST00000392522.3_Missense_Mutation_p.G67C|C14orf80_ENST00000354560.6_Missense_Mutation_p.G67C|C14orf80_ENST00000450383.1_5'UTR			Q86SX3	CN080_HUMAN	chromosome 14 open reading frame 80	67										central_nervous_system(1)	1		Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0188)	Epithelial(152;0.239)		ACTCCCTGCGGGCAACGCCTT	0.692													G|||	4	0.000798722	0.003	0.0	5008	,	,		10467	0.0		0.0	False		,,,				2504	0.0				p.G67C		Atlas-SNP	.											.	C14orf80	19	.	0			c.G199T						PASS	.						12	13	13					14																	105958010		692	1587	2279	SO:0001583	missense	283643	exon2			CCTGCGGGCAACG		CCDS45180.1, CCDS45181.1, CCDS45182.1, CCDS55955.1	14q32.33	2012-09-25			ENSG00000185347	ENSG00000185347			20127	protein-coding gene	gene with protein product							Standard	NM_001134875		Approved		uc001yrn.3	Q86SX3	OTTHUMG00000170426	ENST00000392523.4:c.199G>T	14.37:g.105958010G>T	ENSP00000376308:p.Gly67Cys	147	0	0		154	77	0.5	NM_001134876	B5MDG3|E9PAQ4|Q86TT3|Q86TT4|Q86TT5|Q96B41|Q9H7H4	Missense_Mutation	SNP	ENST00000392523.4	37		.	.	.	.	.	.	.	.	.	.	G	17.21	3.331819	0.60853	.	.	ENSG00000185347	ENST00000329886;ENST00000427614;ENST00000455454;ENST00000432805;ENST00000392527;ENST00000443229;ENST00000334656;ENST00000392522;ENST00000392523;ENST00000354560;ENST00000548920	.	.	.	5.35	-5.54	0.02544	.	2.792540	0.01787	N	0.032086	T	0.22820	0.0551	L	0.40543	1.245	0.09310	N	1	B;P;B;P;B	0.50272	0.002;0.933;0.007;0.932;0.015	B;B;B;B;B	0.43445	0.002;0.394;0.002;0.42;0.009	T	0.37407	-0.9707	9	0.48119	T	0.1	-2.1135	2.1586	0.03819	0.2184:0.4083:0.1687:0.2046	.	67;67;67;26;28	Q86SX3-2;E9PAQ4;Q86SX3;B5MDG3;Q86SX3-3	.;.;CN080_HUMAN;.;.	C	28;26;26;26;26;26;26;67;67;67;67	.	ENSP00000333010:G28C	G	+	1	0	C14orf80	105029055	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.058000	0.11750	-0.676000	0.05238	0.561000	0.74099	GGC	.	.	none		0.692	C14orf80-017	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409090.1	NM_001134875		T	105958010	G	T	105958010	3	4	22	1	0	0	0	0	1	0	0	0	1783	1232	43	4	233	4	C14orf80	14	105958010	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	564	105958010	1391530	2968	5869											
C15orf2	23742	hgsc.bcm.edu	37	chr15	24922407	24922407	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tccctaactctcctctggctCttcctgctgaccttgttccc	3	15	5	18	0	3	1	0	1	3	0	7	1	6	1	5	1	2	3	5	1	1	4	rs79339610	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:24922407C>T	ENST00000329468.2	+	1	1867	c.1393C>T	c.(1393-1395)Ctt>Ttt	p.L465F		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	465	Pro-rich.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											TCCTCTGGCTCTTCCTGCTGA	0.502													C|||	18	0.00359425	0.0121	0.0	5008	,	,		20216	0.0		0.002	False		,,,				2504	0.0				p.L465F		Atlas-SNP	.											C15orf2,colon,carcinoma,0,1	.	.	1	0			c.C1393T						PASS	.	C	PHE/LEU	56,4350		1,54,2148	191	185	187		1393	-4.1	0	15	dbSNP_131	187	1,8599		0,1,4299	yes	missense	C15orf2	NM_018958.2	22	1,55,6447	TT,TC,CC		0.0116,1.271,0.4383	probably-damaging	465/1157	24922407	57,12949	2203	4300	6503	SO:0001583	missense	23742	exon1			CTGGCTCTTCCTG	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.1393C>T	15.37:g.24922407C>T	ENSP00000333735:p.Leu465Phe	99	0	0		107	41	0.383178	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	37	CCDS10015.1	6	0.0027472527472527475	5	0.01016260162601626	0	0.0	0	0.0	1	0.0013192612137203166	.	12.35	1.912039	0.33721	0.01271	1.16E-4	ENSG00000185823	ENST00000329468	T	0.10860	2.83	2.07	-4.13	0.03904	.	2.992630	0.01188	N	0.007259	T	0.04952	0.0133	L	0.29908	0.895	0.09310	N	1	B	0.31383	0.321	B	0.31614	0.133	T	0.14615	-1.0466	10	0.24483	T	0.36	.	2.191	0.03899	0.2812:0.1844:0.4144:0.12	.	465	Q9NZP6	CO002_HUMAN	F	465	ENSP00000333735:L465F	ENSP00000333735:L465F	L	+	1	0	C15orf2	22473500	0.000000	0.05858	0.000000	0.03702	0.366000	0.29705	-2.799000	0.00762	-2.586000	0.00459	0.313000	0.20887	CTT	C|0.996;T|0.004	0.004	strong		0.502	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		T	24922407	C	T	24922407	3	4	22	1	0	0	0	0	1	0	0	0	1786	913	32	2	1395	2	C15orf2	15	24922407	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10		24922407	77608985	2969	5870											
UBE3A	7337	hgsc.bcm.edu	37	chr15	25616844	25616844	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccggaagctctgtaccaaTgcctcagcactagaaaaaac	14	8	7	12	1	2	1	1	0	1	1	3	2	3	2	3	1	5	3	3	1	7	3	rs28528079	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:25616844T>A	ENST00000397954.2	-	4	485	c.486A>T	c.(484-486)gcA>gcT	p.A162A	SNHG14_ENST00000554726.1_RNA|UBE3A_ENST00000566215.1_Silent_p.A139A|UBE3A_ENST00000428984.2_Silent_p.A139A|UBE3A_ENST00000438097.1_Silent_p.A139A|UBE3A_ENST00000232165.3_Silent_p.A159A			Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A	162					androgen receptor signaling pathway (GO:0030521)|brain development (GO:0007420)|ovarian follicle development (GO:0001541)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland growth (GO:0060736)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|proteolysis (GO:0006508)|sperm entry (GO:0035037)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	38		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)		TCTGTACCAATGCCTCAGCAC	0.363													T|||	167	0.0333466	0.1172	0.0144	5008	,	,		19091	0.0		0.001	False		,,,				2504	0.001				p.A162A		Atlas-SNP	.											.	UBE3A	109	.	0			c.A486T						PASS	.	T	,,	406,4000	196.0+/-220.5	19,368,1816	104	106	105		486,417,477	-0.7	1	15	dbSNP_125	105	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	UBE3A	NM_000462.3,NM_130838.1,NM_130839.2	,,	19,369,6115	AA,AT,TT		0.0116,9.2147,3.1293	,,	162/876,139/853,159/873	25616844	407,12599	2203	4300	6503	SO:0001819	synonymous_variant	7337	exon7			TACCAATGCCTCA	AF002224	CCDS32177.1, CCDS45191.1, CCDS45192.1	15q11.2	2014-09-17	2008-07-31		ENSG00000114062	ENSG00000114062	6.3.2.19		12496	protein-coding gene	gene with protein product	"Angelman syndrome"	601623	"human papilloma virus E6-associated protein"	EPVE6AP, HPVE6A		8221889	Standard	NM_130838		Approved	AS, ANCR, E6-AP, FLJ26981	uc001zas.3	Q05086		ENST00000397954.2:c.486A>T	15.37:g.25616844T>A		295	0	0		341	169	0.495601	NM_000462	A8K8Z9|P78355|Q93066|Q9UEP4|Q9UEP5|Q9UEP6|Q9UEP7|Q9UEP8|Q9UEP9	Silent	SNP	ENST00000397954.2	37	CCDS45192.1																																																																																			T|0.958;A|0.042	0.042	strong		0.363	UBE3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000434203.1	NM_000462		A	25616844	T	A	25616844	2	1	22	1	0	0	0	0	0	0	0	1	16894	1451	51	5		5	UBE3A	15	25616844	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	694437	25616844	76914548	2970	5871											
ATP10A	57194	hgsc.bcm.edu	37	chr15	25928508	25928508	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggcacatccctgtccagcacCccagtcacgagcgggggaag	9	4	13	15	2	1	0	1	0	0	0	3	2	3	1	4	3	2	2	4	3	1	0	rs142960034	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:25928508C>T	ENST00000356865.6	-	17	3528	c.3417G>A	c.(3415-3417)ggG>ggA	p.G1139G		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	1139					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)		TGTCCAGCACCCCAGTCACGA	0.537													C|||	19	0.00379393	0.0144	0.0	5008	,	,		17004	0.0		0.0	False		,,,				2504	0.0				p.G1139G		Atlas-SNP	.											.	ATP10A	270	.	0			c.G3417A						PASS	.	C		63,4343	59.3+/-96.0	0,63,2140	75	66	69		3417	2.5	1	15	dbSNP_134	69	0,8600		0,0,4300	no	coding-synonymous	ATP10A	NM_024490.3		0,63,6440	TT,TC,CC		0.0,1.4299,0.4844		1139/1500	25928508	63,12943	2203	4300	6503	SO:0001819	synonymous_variant	57194	exon17			CAGCACCCCAGTC	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.3417G>A	15.37:g.25928508C>T		142	0	0		148	73	0.493243	NM_024490	Q4G0S9|Q969I4	Silent	SNP	ENST00000356865.6	37	CCDS32178.1																																																																																			C|0.996;T|0.004	0.004	strong		0.537	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		T	25928508	C	T	25928508	2	4	22	1	0	0	0	0	0	0	0	1	1116	610	22	2		2	ATP10A	15	25928508	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	311664	25928508	76602884	2971	5872											
ATP10A	57194	hgsc.bcm.edu	37	chr15	25959298	25959298	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccaggctcccgatgctgcTgcagcctgaggtcaggcagc	6	6	15	14	1	1	1	1	1	0	0	2	2	2	1	3	4	5	5	3	4	0	0	rs141928852	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:25959298T>C	ENST00000356865.6	-	10	1978	c.1867A>G	c.(1867-1869)Agc>Ggc	p.S623G		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	623					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)		CCGATGCTGCTGCAGCCTGAG	0.617													T|||	18	0.00359425	0.0136	0.0	5008	,	,		14466	0.0		0.0	False		,,,				2504	0.0				p.S623G		Atlas-SNP	.											.	ATP10A	270	.	0			c.A1867G						PASS	.	T	GLY/SER	50,4356	43.8+/-77.6	0,50,2153	44	49	47		1867	0.6	1	15	dbSNP_134	47	0,8600		0,0,4300	yes	missense	ATP10A	NM_024490.3	56	0,50,6453	CC,CT,TT		0.0,1.1348,0.3844	benign	623/1500	25959298	50,12956	2203	4300	6503	SO:0001583	missense	57194	exon10			TGCTGCTGCAGCC	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.1867A>G	15.37:g.25959298T>C	ENSP00000349325:p.Ser623Gly	58	0	0		70	30	0.428571	NM_024490	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	T	11.14	1.550168	0.27652	0.011348	0.0	ENSG00000206190	ENST00000356865	T	0.11604	2.76	4.21	0.576	0.17380	HAD-like domain (1);	0.310582	0.37761	N	0.001944	T	0.04907	0.0132	L	0.35723	1.085	0.41036	D	0.985193	B	0.17038	0.02	B	0.20384	0.029	T	0.34527	-0.9825	10	0.28530	T	0.3	-9.6357	5.3687	0.16127	0.0:0.1605:0.149:0.6905	.	623	O60312	AT10A_HUMAN	G	623	ENSP00000349325:S623G	ENSP00000349325:S623G	S	-	1	0	ATP10A	23510391	1.000000	0.71417	0.952000	0.39060	0.450000	0.32258	3.499000	0.53310	-0.061000	0.13110	0.533000	0.62120	AGC	T|0.997;C|0.003	0.003	strong		0.617	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		C	25959298	T	C	25959298	3	2	22	1	0	0	0	0	1	0	0	0	1116	1580	55	3	2680	3	ATP10A	15	25959298	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	30790	25959298	76572094	2972	5873											
ATP10A	57194	hgsc.bcm.edu	37	chr15	25962057	25962057	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagcagctttgggtcgggCgtgatatccttctcctggga	5	12	13	11	2	1	1	0	1	1	0	5	2	3	2	3	3	2	2	3	3	1	3	rs115618637	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:25962057C>T	ENST00000356865.6	-	9	1707	c.1596G>A	c.(1594-1596)acG>acA	p.T532T		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	532			T -> M (in dbSNP:rs2066703).		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)		TTGGGTCGGGCGTGATATCCT	0.577													C|||	11	0.00219649	0.0083	0.0	5008	,	,		15659	0.0		0.0	False		,,,				2504	0.0				p.T532T		Atlas-SNP	.											.	ATP10A	270	.	0			c.G1596A						PASS	.	C		36,4370	40.0+/-72.8	0,36,2167	85	63	71		1596	-10.8	0.2	15	dbSNP_132	71	0,8600		0,0,4300	no	coding-synonymous	ATP10A	NM_024490.3		0,36,6467	TT,TC,CC		0.0,0.8171,0.2768		532/1500	25962057	36,12970	2203	4300	6503	SO:0001819	synonymous_variant	57194	exon9			GTCGGGCGTGATA	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.1596G>A	15.37:g.25962057C>T		82	0	0		113	47	0.415929	NM_024490	Q4G0S9|Q969I4	Silent	SNP	ENST00000356865.6	37	CCDS32178.1																																																																																			C|0.998;T|0.002	0.002	strong		0.577	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		T	25962057	C	T	25962057	2	4	22	1	0	0	0	0	0	0	0	1	1116	755	27	1		1	ATP10A	15	25962057	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2759	25962057	76569335	2973	5874											
ATP10A	57194	hgsc.bcm.edu	37	chr15	25963484	25963484	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gccgcgctgggacaccgagcCccctctgggcaccacctcct	5	5	11	20	3	1	0	0	0	1	0	2	2	2	1	7	2	1	2	7	2	0	0	rs116055743	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:25963484C>T	ENST00000356865.6	-	8	1537	c.1426G>A	c.(1426-1428)Ggc>Agc	p.G476S		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	476					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)		GACACCGAGCCCCCTCTGGGC	0.706													C|||	24	0.00479233	0.0182	0.0	5008	,	,		14866	0.0		0.0	False		,,,				2504	0.0				p.G476S		Atlas-SNP	.											.	ATP10A	270	.	0			c.G1426A						PASS	.	C	SER/GLY	84,4314		0,84,2115	29	25	26		1426	0.9	0	15	dbSNP_132	26	0,8594		0,0,4297	yes	missense	ATP10A	NM_024490.3	56	0,84,6412	TT,TC,CC		0.0,1.91,0.6466	benign	476/1500	25963484	84,12908	2199	4297	6496	SO:0001583	missense	57194	exon8			CCGAGCCCCCTCT	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.1426G>A	15.37:g.25963484C>T	ENSP00000349325:p.Gly476Ser	136	0	0		126	65	0.515873	NM_024490	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	9.534	1.111487	0.20714	0.0191	0.0	ENSG00000206190	ENST00000356865	T	0.64991	-0.13	5.14	0.881	0.19166	HAD-like domain (1);	0.228496	0.44688	N	0.000436	T	0.29684	0.0741	L	0.46741	1.465	0.19300	N	0.999978	B	0.10296	0.003	B	0.11329	0.006	T	0.24261	-1.0165	10	0.07030	T	0.85	-7.1028	8.7017	0.34329	0.0:0.6623:0.0:0.3377	.	476	O60312	AT10A_HUMAN	S	476	ENSP00000349325:G476S	ENSP00000349325:G476S	G	-	1	0	ATP10A	23514577	0.382000	0.25148	0.000000	0.03702	0.225000	0.24961	2.423000	0.44705	-0.104000	0.12154	0.655000	0.94253	GGC	C|0.994;T|0.006	0.006	strong		0.706	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490		T	25963484	C	T	25963484	3	4	22	1	0	0	0	0	1	0	0	0	1116	623	22	2	3129	2	ATP10A	15	25963484	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1427	25963484	76567908	2974	5875											
GABRG3	2567	hgsc.bcm.edu	37	chr15	27222266	27222266	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcaacaagttgctaagagaAtatgataaaaagctgaggcc	17	8	9	7	0	1	3	1	2	0	1	1	4	1	3	1	1	3	3	1	1	8	4	rs35752220	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:27222266A>G	ENST00000333743.6	+	2	425	c.171A>G	c.(169-171)gaA>gaG	p.E57E	GABRG3_ENST00000555083.1_Silent_p.E57E	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	57					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)	TGCTAAGAGAATATGATAAAA	0.348													A|||	182	0.0363419	0.1316	0.0101	5008	,	,		19188	0.0		0.001	False		,,,				2504	0.0				p.E57E	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											.	GABRG3	115	.	0			c.A171G						PASS	.	A		345,3291		16,313,1489	99	99	99		171	3	1	15	dbSNP_126	99	3,8149		0,3,4073	no	coding-synonymous	GABRG3	NM_033223.4		16,316,5562	GG,GA,AA		0.0368,9.4884,2.9522		57/468	27222266	348,11440	1818	4076	5894	SO:0001819	synonymous_variant	2567	exon2			AAGAGAATATGAT		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.171A>G	15.37:g.27222266A>G		105	0	0		122	53	0.434426	NM_001270873	G3V594|Q9HD46|Q9NYT2	Silent	SNP	ENST00000333743.6	37	CCDS45195.1																																																																																			A|0.970;G|0.030	0.030	strong		0.348	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2			G	27222266	A	G	27222266	2	3	22	1	0	0	0	0	0	0	0	1	6181	98	4	3		3	GABRG3	15	27222266	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1258782	27222266	75309126	2975	5876											
GABRG3	2567	hgsc.bcm.edu	37	chr15	27777751	27777751	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttgttgcttgcagaactaTtccctcctggacatgaggcc	7	14	9	11	0	0	2	0	1	0	1	2	3	2	3	3	2	3	3	3	2	2	6	rs16950126	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:27777751T>C	ENST00000333743.6	+	10	1382	c.1128T>C	c.(1126-1128)taT>taC	p.Y376Y	RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	376					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)	TGCAGAACTATTCCCTCCTGG	0.423													T|||	316	0.063099	0.2216	0.0274	5008	,	,		19532	0.0		0.004	False		,,,				2504	0.0				p.Y376Y	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											.	GABRG3	115	.	0			c.T1128C						PASS	.	T		648,3304		48,552,1376	91	88	89		1128	-7.8	0.7	15	dbSNP_123	89	8,8332		0,8,4162	no	coding-synonymous	GABRG3	NM_033223.4		48,560,5538	CC,CT,TT		0.0959,16.3968,5.3368		376/468	27777751	656,11636	1976	4170	6146	SO:0001819	synonymous_variant	2567	exon10			GAACTATTCCCTC		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.1128T>C	15.37:g.27777751T>C		99	0	0		147	75	0.510204	NM_033223	G3V594|Q9HD46|Q9NYT2	Silent	SNP	ENST00000333743.6	37	CCDS45195.1																																																																																			T|0.932;C|0.068	0.068	strong		0.423	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2			C	27777751	T	C	27777751	2	2	22	1	0	0	0	0	0	0	0	1	6181	1500	52	3		3	GABRG3	15	27777751	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	555485	27777751	74753641	2976	5877											
HERC2	8924	hgsc.bcm.edu	37	chr15	28389880	28389880	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagccattcacagacccatcGctgatgaacttccactttaa	12	10	5	14	1	1	3	1	2	0	1	3	3	2	3	3	0	2	1	3	0	2	4	rs1133496	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:28389880G>A	ENST00000261609.7	-	72	11187	c.11079C>T	c.(11077-11079)agC>agT	p.S3693S		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)		CAGACCCATCGCTGATGAACT	0.592													G|||	434	0.0866613	0.3132	0.0274	5008	,	,		20257	0.0		0.001	False		,,,				2504	0.0				p.S3693S		Atlas-SNP	.											.	HERC2	501	.	0			c.C11079T						PASS	.	G		1171,3235	414.6+/-336.9	156,859,1188	106	86	93		11079	-2.7	1	15	dbSNP_86	93	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	HERC2	NM_004667.4		156,863,5484	AA,AG,GG		0.0465,26.5774,9.0343		3693/4835	28389880	1175,11831	2203	4300	6503	SO:0001819	synonymous_variant	8924	exon72			CCCATCGCTGATG	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.11079C>T	15.37:g.28389880G>A		129	0	0		145	73	0.503448	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			G|0.916;A|0.084	0.084	strong		0.592	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		A	28389880	G	A	28389880	2	1	22	1	0	0	0	0	0	0	0	1	7067	1078	38	1		1	HERC2	15	28389880	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	612129	28389880	74141512	2977	5878											
HERC2	8924	hgsc.bcm.edu	37	chr15	28424100	28424100	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atctgccgtgggatgggcacCgtcccgctggaaatgcccag	7	7	14	13	3	1	0	0	0	1	0	2	2	2	2	4	3	2	2	4	3	1	0	rs9806328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:28424100C>T	ENST00000261609.7	-	59	9204	c.9096G>A	c.(9094-9096)acG>acA	p.T3032T		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)		GGATGGGCACCGTCCCGCTGG	0.612													C|||	716	0.142971	0.5166	0.0375	5008	,	,		11324	0.004		0.001	False		,,,				2504	0.002				p.T3032T		Atlas-SNP	.											.	HERC2	501	.	0			c.G9096A						PASS	.	C		1921,2485	549.9+/-377.9	410,1101,692	82	84	83		9096	-11.2	0.1	15	dbSNP_119	83	7,8593	4.3+/-15.6	0,7,4293	no	coding-synonymous	HERC2	NM_004667.4		410,1108,4985	TT,TC,CC		0.0814,43.5996,14.8239		3032/4835	28424100	1928,11078	2203	4300	6503	SO:0001819	synonymous_variant	8924	exon59			GGGCACCGTCCCG	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.9096G>A	15.37:g.28424100C>T		76	0	0		92	37	0.402174	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			C|0.864;T|0.136	0.136	strong		0.612	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		T	28424100	C	T	28424100	2	4	22	1	0	0	0	0	0	0	0	1	7067	639	23	1		1	HERC2	15	28424100	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	34220	28424100	74107292	2978	5879											
APBA2	321	hgsc.bcm.edu	37	chr15	29398914	29398914	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggccaacatgatgaatggCggcccggctgcccgctcggg	6	6	15	14	4	0	2	0	2	0	0	1	2	0	2	3	5	2	2	3	5	2	0	rs8032178	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:29398914C>T	ENST00000558402.1	+	13	2408	c.1809C>T	c.(1807-1809)ggC>ggT	p.G603G	APBA2_ENST00000558259.1_Silent_p.G603G|APBA2_ENST00000561069.1_Silent_p.G603G|APBA2_ENST00000558330.1_Silent_p.G591G|APBA2_ENST00000411764.1_Silent_p.G591G			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	603	PDZ 1. {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)		TGATGAATGGCGGCCCGGCTG	0.662													C|||	295	0.0589058	0.2118	0.0202	5008	,	,		13171	0.001		0.0	False		,,,				2504	0.0				p.G603G		Atlas-SNP	.											.	APBA2	132	.	0			c.C1809T						PASS	.	C	,	801,3605	312.2+/-292.5	71,659,1473	48	49	49		1773,1809	-8.4	0.4	15	dbSNP_116	49	3,8593	3.0+/-9.4	0,3,4295	no	coding-synonymous,coding-synonymous	APBA2	NM_001130414.1,NM_005503.3	,	71,662,5768	TT,TC,CC		0.0349,18.1798,6.1837	,	591/738,603/750	29398914	804,12198	2203	4298	6501	SO:0001819	synonymous_variant	321	exon11			GAATGGCGGCCCG	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.1809C>T	15.37:g.29398914C>T		231	0	0		222	107	0.481982	NM_005503	E9PGI4|O60571|Q5XKC0	Silent	SNP	ENST00000558402.1	37	CCDS10022.1																																																																																			C|0.932;T|0.068	0.068	strong		0.662	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503		T	29398914	C	T	29398914	2	4	22	1	0	0	0	0	0	0	0	1	757	755	27	1		1	APBA2	15	29398914	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	974814	29398914	73132478	2979	5880											
NDNL2	56160	hgsc.bcm.edu	37	chr15	29561467	29561467	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgaggatgtaagtgttgctcTtgggttcaagttccaccagc	8	13	12	8	0	2	1	1	1	1	0	3	2	3	2	2	2	2	5	2	2	2	5			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:29561467T>G	ENST00000332303.4	-	1	566	c.443A>C	c.(442-444)aAg>aCg	p.K148T	FAM189A1_ENST00000261275.4_Intron	NM_138704.3	NP_619649.1	Q96MG7	MAGG1_HUMAN	necdin-like 2	148	Interaction with NSMCE1.|MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)|regulation of growth (GO:0040008)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Smc5-Smc6 complex (GO:0030915)				breast(3)|large_intestine(2)|lung(3)	8		all_lung(180;4.69e-11)|Breast(32;0.0013)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00736)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		AGTGTTGCTCTTGGGTTCAAG	0.582																																					p.K148T		Atlas-SNP	.											.	NDNL2	19	.	0			c.A443C						PASS	.						81	74	76					15																	29561467		2203	4300	6503	SO:0001583	missense	56160	exon1			TTGCTCTTGGGTT	AF490510	CCDS10023.1	15q13.1	2008-02-01			ENSG00000185115	ENSG00000185115			7677	protein-coding gene	gene with protein product		608243				18086888	Standard	NM_138704		Approved	HCA4, MAGEG1, MAGEL3, NSE3, NSMCE3	uc001zco.3	Q96MG7	OTTHUMG00000129261	ENST00000332303.4:c.443A>C	15.37:g.29561467T>G	ENSP00000330694:p.Lys148Thr	111	0	0		116	58	0.5	NM_138704	Q8IW16|Q8TEI6|Q9H214	Missense_Mutation	SNP	ENST00000332303.4	37	CCDS10023.1	.	.	.	.	.	.	.	.	.	.	T	16.86	3.238898	0.58995	.	.	ENSG00000185115	ENST00000332303	T	0.05717	3.4	3.91	-1.44	0.08856	.	0.124104	0.52532	U	0.000070	T	0.03305	0.0096	N	0.20807	0.61	0.09310	N	0.999997	P	0.36712	0.566	B	0.42959	0.403	T	0.35051	-0.9804	10	0.02654	T	1	.	4.0573	0.09823	0.0:0.3563:0.1937:0.45	.	148	Q96MG7	MAGG1_HUMAN	T	148	ENSP00000330694:K148T	ENSP00000330694:K148T	K	-	2	0	NDNL2	27348759	1.000000	0.71417	0.007000	0.13788	0.969000	0.65631	0.975000	0.29449	-0.271000	0.09272	0.460000	0.39030	AAG	.	.	none		0.582	NDNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251370.1	NM_138704		G	29561467	T	G	29561467	3	3	22	1	0	0	0	0	1	0	0	0	10257	1609	56	5	475	5	NDNL2	15	29561467	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	162553	29561467	72969925	2980	5881											
TJP1	7082	hgsc.bcm.edu	37	chr15	30012209	30012209	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggtaagggactggagatgaAgcttctgctttctgtgaagt	10	12	14	5	0	2	3	0	2	2	1	2	5	2	4	0	3	2	3	0	3	3	3	rs376115263		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:30012209A>C	ENST00000346128.6	-	20	3249	c.2775T>G	c.(2773-2775)gcT>gcG	p.A925A	TJP1_ENST00000400011.2_Intron|TJP1_ENST00000356107.6_Silent_p.A925A|TJP1_ENST00000545208.2_Intron	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	925					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)		CTGGAGATGAAGCTTCTGCTT	0.353																																					p.A925A	Melanoma(77;681 1843 6309 6570)	Atlas-SNP	.											.	TJP1	140	.	0			c.T2775G						PASS	.	A	,	3,3687		0,3,1842	125	115	118		2775,	4.2	1	15		118	0,8186		0,0,4093	no	coding-synonymous,intron	TJP1	NM_003257.3,NM_175610.2	,	0,3,5935	CC,CA,AA		0.0,0.0813,0.0253	,	925/1749,	30012209	3,11873	1845	4093	5938	SO:0001819	synonymous_variant	7082	exon20			AGATGAAGCTTCT		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.2775T>G	15.37:g.30012209A>C		80	0	0		86	41	0.476744	NM_003257	B4E3K1|Q2NKP3|Q4ZGJ6	Silent	SNP	ENST00000346128.6	37	CCDS42007.1																																																																																			.	.	weak		0.353	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		C	30012209	A	C	30012209	2	2	22	1	0	0	0	0	0	0	0	1	15944	59	3	5		5	TJP1	15	30012209	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	450742	30012209	72519183	2981	5882											
MTMR15	22909	hgsc.bcm.edu	37	chr15	31196984	31196984	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gttttaacaatgcaccacctGctaaacttgcctgccccgtt	9	12	6	14	1	0	0	0	0	0	0	0	0	0	0	5	0	6	4	5	0	4	5			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:31196984G>A	ENST00000362065.4	+	2	409	c.118G>A	c.(118-120)Gct>Act	p.A40T	FAN1_ENST00000565466.1_Missense_Mutation_p.A40T|FAN1_ENST00000561607.1_Missense_Mutation_p.A40T|FAN1_ENST00000561594.1_Missense_Mutation_p.A40T	NM_014967.4	NP_055782.3	Q9Y2M0	FAN1_HUMAN	FANCD2/FANCI-associated nuclease 1	40					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						TGCACCACCTGCTAAACTTGC	0.398								Direct reversal of damage																													p.A40T		Atlas-SNP	.											.	FAN1	77	.	0			c.G118A						PASS	.						74	76	75					15																	31196984		2202	4300	6502	SO:0001583	missense	22909	exon2			CCACCTGCTAAAC		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.118G>A	15.37:g.31196984G>A	ENSP00000354497:p.Ala40Thr	134	0	0		135	67	0.496296	NM_001146095	A8K4M2|Q86WU8	Missense_Mutation	SNP	ENST00000362065.4	37	CCDS32186.1	.	.	.	.	.	.	.	.	.	.	g	21.9	4.222546	0.79464	.	.	ENSG00000198690	ENST00000362065	D	0.82711	-1.64	5.28	3.31	0.37934	.	0.247400	0.41097	D	0.000947	D	0.88749	0.6521	M	0.66939	2.045	0.39089	D	0.961052	D;D	0.89917	0.986;1.0	P;D	0.72982	0.738;0.979	D	0.89320	0.3639	10	0.72032	D	0.01	-9.7976	12.0726	0.53626	0.0:0.1314:0.7318:0.1368	.	40;40	Q9Y2M0;Q9Y2M0-2	FAN1_HUMAN;.	T	40	ENSP00000354497:A40T	ENSP00000354497:A40T	A	+	1	0	FAN1	28984276	0.538000	0.26394	0.288000	0.24862	0.886000	0.51366	2.025000	0.41059	0.662000	0.31006	0.555000	0.69702	GCT	.	.	none		0.398	FAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430740.1	NM_014967		A	31196984	G	A	31196984	3	1	22	1	0	0	0	0	1	0	0	0	9952	1319	46	2	120	2	MTMR15	15	31196984	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1184775	31196984	71334408	2982	5883											
TRPM1	4308	hgsc.bcm.edu	37	chr15	31294773	31294773	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ttgaaatcccaatatctggaCctaattttgactcttcagcg	11	14	6	10	1	3	2	1	2	2	0	4	3	4	3	2	1	1	0	2	1	4	6			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:31294773C>T	ENST00000256552.6	-	28	4277	c.4130G>A	c.(4129-4131)gGt>gAt	p.G1377D	RP11-348B17.1_ENST00000561299.1_RNA|TRPM1_ENST00000542188.1_Missense_Mutation_p.G1394D|TRPM1_ENST00000397795.2_Missense_Mutation_p.G1355D	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)		AATATCTGGACCTAATTTTGA	0.393																																					p.G1394D		Atlas-SNP	.											.	TRPM1	183	.	0			c.G4181A						PASS	.						160	153	155					15																	31294773		1917	4138	6055	SO:0001583	missense	4308	exon27			TCTGGACCTAATT	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.4130G>A	15.37:g.31294773C>T	ENSP00000256552:p.Gly1377Asp	74	0	0		88	38	0.431818	NM_001252020		Missense_Mutation	SNP	ENST00000256552.6	37	CCDS58346.1	.	.	.	.	.	.	.	.	.	.	C	4.656	0.121910	0.08931	.	.	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	T;T;T	0.52526	0.67;0.66;0.68	4.81	2.63	0.31362	.	0.300372	0.27851	N	0.017600	T	0.26919	0.0659	N	0.17082	0.46	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.002;0.003	T	0.10132	-1.0643	10	0.52906	T	0.07	-6.7074	5.797	0.18392	0.1392:0.6449:0.1355:0.0804	.	1349;1355	Q7Z4N2-3;Q7Z4N2	.;TRPM1_HUMAN	D	1355;1394;1377;1355	ENSP00000380897:G1355D;ENSP00000437849:G1394D;ENSP00000256552:G1377D	ENSP00000256552:G1377D	G	-	2	0	TRPM1	29082065	0.035000	0.19736	0.093000	0.20910	0.043000	0.13939	0.395000	0.20850	2.201000	0.70794	0.650000	0.86243	GGT	.	.	none		0.393	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420		T	31294773	C	T	31294773	3	4	22	1	0	0	0	0	1	0	0	0	16600	507	18	2	751	2	TRPM1	15	31294773	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	97789	31294773	71236619	2983	5884											
TRPM1	4308	hgsc.bcm.edu	37	chr15	31323360	31323360	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagtacagcatgtcgatcaTctgagtaaggagaacatttg	15	10	10	6	1	2	2	1	1	1	1	3	4	2	2	0	1	3	3	0	1	4	3	rs181499296	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:31323360T>G	ENST00000256552.6	-	23	3100	c.2953A>C	c.(2953-2955)Atg>Ctg	p.M985L	RP11-348B17.1_ENST00000561299.1_RNA|RP11-348B17.1_ENST00000558755.1_RNA|TRPM1_ENST00000542188.1_Splice_Site_p.M1002L|TRPM1_ENST00000397795.2_Splice_Site_p.M963L	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)		ATGTCGATCATCTGAGTAAGG	0.493													T|||	4	0.000798722	0.0023	0.0014	5008	,	,		22528	0.0		0.0	False		,,,				2504	0.0				p.M1002L		Atlas-SNP	.											.	TRPM1	183	.	0			c.A3004C						PASS	.	T	LEU/MET	8,4150		0,8,2071	68	66	66		2887	5.9	1	15		66	0,8476		0,0,4238	yes	missense-near-splice	TRPM1	NM_002420.4	15	0,8,6309	GG,GT,TT		0.0,0.1924,0.0633	possibly-damaging	963/1604	31323360	8,12626	2079	4238	6317	SO:0001630	splice_region_variant	4308	exon22			CGATCATCTGAGT	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.2953-1A>C	15.37:g.31323360T>G		74	0	0		126	46	0.365079	NM_001252020		Missense_Mutation	SNP	ENST00000256552.6	37	CCDS58346.1	2	9.157509157509158E-4	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	T	21.6	4.177858	0.78564	0.001924	0.0	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	T;T;T	0.73363	-0.74;-0.74;-0.74	5.92	5.92	0.95590	Ion transport (1);	0.000000	0.85682	D	0.000000	T	0.79718	0.4494	L	0.33485	1.01	0.58432	D	0.999997	D;D	0.59767	0.986;0.983	P;D	0.64687	0.8;0.928	T	0.81803	-0.0765	10	0.72032	D	0.01	-46.9433	16.371	0.83361	0.0:0.0:0.0:1.0	.	957;963	Q7Z4N2-3;Q7Z4N2	.;TRPM1_HUMAN	L	963;1002;985;963	ENSP00000380897:M963L;ENSP00000437849:M1002L;ENSP00000256552:M985L	ENSP00000256552:M985L	M	-	1	0	TRPM1	29110652	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	6.296000	0.72751	2.267000	0.75376	0.477000	0.44152	ATG	T|0.999;G|0.001	0.001	strong		0.493	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420	Missense_Mutation	G	31323360	T	G	31323360	5	3	22	1	0	0	0	0	0	0	1	0	16600	1449	50	5	1948	5	TRPM1	15	31323360	Splice_Site	SNP	T	TCGA-G8-6324-01A-11D-2210-10	28587	31323360	71208032	2984	5885											
RYR3	6263	hgsc.bcm.edu	37	chr15	34030767	34030767	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	acggagaagcttttctggggGatttttgactcgctctccca	7	13	11	10	2	2	2	0	1	2	1	4	4	2	3	1	3	1	2	1	3	1	4	rs115185294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:34030767G>T	ENST00000389232.4	+	50	7702	c.7632G>T	c.(7630-7632)ggG>ggT	p.G2544G	RYR3_ENST00000415757.3_Silent_p.G2544G	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	2544	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)		TTTTCTGGGGGATTTTTGACT	0.473											OREG0023032	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	36	0.0071885	0.025	0.0043	5008	,	,		18919	0.0		0.0	False		,,,				2504	0.0				p.G2544G		Atlas-SNP	.											.	RYR3	760	.	0			c.G7632T						PASS	.	G		61,3703		1,59,1822	96	104	102		7632	0.4	1	15	dbSNP_132	102	1,8205		0,1,4102	no	coding-synonymous	RYR3	NM_001036.3		1,60,5924	TT,TG,GG		0.0122,1.6206,0.518		2544/4871	34030767	62,11908	1882	4103	5985	SO:0001819	synonymous_variant	6263	exon50			CTGGGGGATTTTT		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.7632G>T	15.37:g.34030767G>T		65	0	0	844	59	25	0.423729	NM_001243996	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			G|0.994;T|0.006	0.006	strong		0.473	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	34030767	G	T	34030767	2	4	22	1	0	0	0	0	0	0	0	1	13785	1161	41	4		4	RYR3	15	34030767	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2707407	34030767	68500625	2985	5886											
RYR3	6263	hgsc.bcm.edu	37	chr15	34105084	34105084	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctgatgacccagctgtaaaAtggcaactgaacctctacaa	14	9	7	11	0	2	3	0	3	2	0	2	3	2	3	2	1	4	3	2	1	6	2	rs16958093	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:34105084A>G	ENST00000389232.4	+	73	10348	c.10278A>G	c.(10276-10278)aaA>aaG	p.K3426K	RYR3_ENST00000415757.3_Silent_p.K3421K	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3426					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)		CAGCTGTAAAATGGCAACTGA	0.428													A|||	198	0.0395367	0.1362	0.0101	5008	,	,		21062	0.006		0.0	False		,,,				2504	0.0051				p.K3426K		Atlas-SNP	.											.	RYR3	760	.	0			c.A10278G						PASS	.	A		360,3396		26,308,1544	88	85	86		10278	0.6	1	15	dbSNP_123	86	4,8238		0,4,4117	no	coding-synonymous	RYR3	NM_001036.3		26,312,5661	GG,GA,AA		0.0485,9.5847,3.0338		3426/4871	34105084	364,11634	1878	4121	5999	SO:0001819	synonymous_variant	6263	exon73			TGTAAAATGGCAA		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.10278A>G	15.37:g.34105084A>G		68	0	0		77	35	0.454545	NM_001036	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			A|0.955;G|0.045	0.045	strong		0.428	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			G	34105084	A	G	34105084	2	3	22	1	0	0	0	0	0	0	0	1	13785	98	4	3		3	RYR3	15	34105084	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	74317	34105084	68426308	2986	5887											
RYR3	6263	hgsc.bcm.edu	37	chr15	34111969	34111969	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttccagcaaattggaagaCgaccctttgtacacctccta	11	11	6	13	1	0	1	0	0	0	1	2	3	2	2	4	1	2	2	4	1	4	5	rs58745096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:34111969C>T	ENST00000389232.4	+	77	10789	c.10719C>T	c.(10717-10719)gaC>gaT	p.D3573D	RYR3_ENST00000415757.3_Silent_p.D3568D	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3573					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)		AATTGGAAGACGACCCTTTGT	0.338													C|||	91	0.0181709	0.0666	0.0029	5008	,	,		14784	0.0		0.001	False		,,,				2504	0.0				p.D3573D		Atlas-SNP	.											RYR3,NS,carcinoma,0,1	RYR3	760	1	0			c.C10719T						PASS	.	C		163,3477		5,153,1662	318	297	303		10719	-6.1	0.9	15	dbSNP_129	303	2,8170		0,2,4084	no	coding-synonymous	RYR3	NM_001036.3		5,155,5746	TT,TC,CC		0.0245,4.478,1.3969		3573/4871	34111969	165,11647	1820	4086	5906	SO:0001819	synonymous_variant	6263	exon77			GGAAGACGACCCT		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.10719C>T	15.37:g.34111969C>T		168	0	0		174	87	0.5	NM_001036	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			C|0.984;T|0.016	0.016	strong		0.338	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	34111969	C	T	34111969	2	4	22	1	0	0	0	0	0	0	0	1	13785	535	19	1		1	RYR3	15	34111969	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6885	34111969	68419423	2987	5888											
GOLGA8B	440270	hgsc.bcm.edu	37	chr15	34825091	34825091	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgactgatttttatggaccTcgagttcaggactgctgctt	7	15	10	9	2	1	1	1	1	0	0	3	5	1	3	1	2	2	3	1	2	1	5	rs200439797		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:34825091T>A	ENST00000342314.5	-	3	338	c.241A>T	c.(241-243)Agg>Tgg	p.R81W	GOLGA8B_ENST00000267731.7_Missense_Mutation_p.R81W|GOLGA8A_ENST00000543376.1_Intron|GOLGA8B_ENST00000438958.2_Missense_Mutation_p.R111W	NM_001023567.4	NP_001018861.3	A8MQT2	GOG8B_HUMAN	golgin A8 family, member B	81						Golgi apparatus (GO:0005794)|membrane (GO:0016020)				endometrium(1)	1		all_lung(180;2.78e-08)		all cancers(64;8.27e-19)|GBM - Glioblastoma multiforme(113;6.98e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		TTTATGGACCTCGAGTTCAGG	0.552																																					p.R81W		Atlas-SNP	.											GOLGA8B_ENST00000267731,right_upper_lobe,carcinoma,+1,2	GOLGA8B	7	2	0			c.A241T						scavenged	.						34	19	24					15																	34825091		686	1359	2045	SO:0001583	missense	440270	exon3			TGGACCTCGAGTT	AF164622	CCDS45211.1	15q14	2011-10-25	2010-02-12		ENSG00000215252	ENSG00000215252			31973	protein-coding gene	gene with protein product		609619	"golgi autoantigen, golgin subfamily a, 8B"				Standard	NM_001023567		Approved		uc001ziq.3	A8MQT2	OTTHUMG00000129549	ENST00000342314.5:c.241A>T	15.37:g.34825091T>A	ENSP00000343064:p.Arg81Trp	1385	0	0		1873	467	0.249333	NM_001023567	A6NLZ2|O94937|Q2M3S9|Q9NZG8|Q9NZW0|Q9NZW3	Missense_Mutation	SNP	ENST00000342314.5	37	CCDS45211.1	.	.	.	.	.	.	.	.	.	.	t	13.59	2.284070	0.40394	.	.	ENSG00000215252	ENST00000342314;ENST00000267731;ENST00000438958	T;T;T	0.22743	1.94;1.94;2.5	1.55	0.322	0.15888	.	.	.	.	.	T	0.34745	0.0908	M	0.66939	2.045	0.21355	N	0.999712	D	0.67145	0.996	D	0.64687	0.928	T	0.13575	-1.0504	9	0.66056	D	0.02	.	3.6826	0.08316	0.3389:0.0:0.0:0.6611	.	81	A8MQT2	GOG8B_HUMAN	W	81;81;111	ENSP00000343064:R81W;ENSP00000267731:R81W;ENSP00000400063:R111W	ENSP00000267731:R81W	R	-	1	2	GOLGA8B	32612383	1.000000	0.71417	0.371000	0.25978	0.004000	0.04260	4.296000	0.59055	0.067000	0.16545	-1.078000	0.02229	AGG	T|0.998;A|0.002	0.002	weak		0.552	GOLGA8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251739.2	NM_001023567		A	34825091	T	A	34825091	3	1	22	1	0	0	0	0	1	0	0	0	6572	1550	54	5	1626	5	GOLGA8B	15	34825091	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	713122	34825091	67706301	2988	5889											
ZNF770	54989	hgsc.bcm.edu	37	chr15	35273867	35273867	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gacagggttgcccggtgctaCcaggaataaaatcctgtgac	11	8	12	10	1	0	1	0	1	0	0	1	3	1	2	3	3	3	2	3	3	4	3	rs141323293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:35273867C>A	ENST00000356321.4	-	3	2113	c.1769G>T	c.(1768-1770)gGt>gTt	p.G590V		NM_014106.3	NP_054825.2	Q6IQ21	ZN770_HUMAN	zinc finger protein 770	590					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)		CCCGGTGCTACCAGGAATAAA	0.438													C|||	3	0.000599042	0.0023	0.0	5008	,	,		19415	0.0		0.0	False		,,,				2504	0.0				p.G590V		Atlas-SNP	.											.	ZNF770	64	.	0			c.G1769T						PASS	.	C	VAL/GLY	45,4357	46.7+/-81.2	0,45,2156	117	119	118		1769	-0.4	0	15	dbSNP_134	118	0,8596		0,0,4298	no	missense	ZNF770	NM_014106.3	109	0,45,6454	AA,AC,CC		0.0,1.0223,0.3462	possibly-damaging	590/692	35273867	45,12953	2201	4298	6499	SO:0001583	missense	54989	exon3			GTGCTACCAGGAA	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.1769G>T	15.37:g.35273867C>A	ENSP00000348673:p.Gly590Val	60	0	0		48	22	0.458333	NM_014106	Q6ZMZ6|Q9NWV2	Missense_Mutation	SNP	ENST00000356321.4	37	CCDS10042.1	.	.	.	.	.	.	.	.	.	.	C	0.324	-0.960173	0.02267	0.010223	0.0	ENSG00000198146	ENST00000356321	T	0.10288	2.89	5.24	-0.357	0.12579	.	0.716901	0.12735	N	0.443539	T	0.03434	0.0099	N	0.14661	0.345	0.21020	N	0.999802	B	0.16396	0.017	B	0.15052	0.012	T	0.39014	-0.9634	10	0.33141	T	0.24	-0.2229	4.5334	0.12017	0.1656:0.3386:0.0:0.4958	.	590	Q6IQ21	ZN770_HUMAN	V	590	ENSP00000348673:G590V	ENSP00000348673:G590V	G	-	2	0	ZNF770	33061159	0.039000	0.19947	0.021000	0.16686	0.125000	0.20455	0.555000	0.23422	0.090000	0.17273	0.467000	0.42956	GGT	C|0.996;A|0.004	0.004	strong		0.438	ZNF770-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251896.2	NM_014106		A	35273867	C	A	35273867	3	1	22	1	0	0	0	0	1	0	0	0	18158	507	18	4	310	4	ZNF770	15	35273867	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	448776	35273867	67257525	2989	5890											
ATPBD4	89978	hgsc.bcm.edu	37	chr15	35830665	35830665	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	agctatccagttcatcagacCccactgcaacaattaaaatg	15	9	5	12	0	2	1	2	0	0	1	3	1	3	1	3	0	3	3	3	0	5	3	rs34907758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:35830665C>T	ENST00000256538.4	-	3	148	c.122G>A	c.(121-123)gGg>gAg	p.G41E	DPH6_ENST00000440392.2_Missense_Mutation_p.G41E	NM_080650.3	NP_542381.1	Q7L8W6	DPH6_HUMAN	diphthamine biosynthesis 6	41			G -> E (in dbSNP:rs34907758).		peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)		ATP binding (GO:0005524)|diphthine-ammonia ligase activity (GO:0017178)										TTCATCAGACCCCACTGCAAC	0.433													C|||	152	0.0303514	0.1097	0.0101	5008	,	,		17189	0.0		0.0	False		,,,				2504	0.0				p.G41E		Atlas-SNP	.											.	ATPBD4	30	.	0			c.G122A						PASS	.	C	GLU/GLY,GLU/GLY	311,4091	161.4+/-193.6	13,285,1903	73	62	66		122,122	2.9	1	15	dbSNP_126	66	5,8589	3.7+/-12.6	0,5,4292	no	missense,missense	ATPBD4	NM_001141972.1,NM_080650.3	98,98	13,290,6195	TT,TC,CC		0.0582,7.065,2.4315	benign,benign	41/166,41/268	35830665	316,12680	2201	4297	6498	SO:0001583	missense	89978	exon3			TCAGACCCCACTG		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.122G>A	15.37:g.35830665C>T	ENSP00000256538:p.Gly41Glu	117	0	0		103	49	0.475728	NM_001141972	B3KWG1|Q96HJ6	Missense_Mutation	SNP	ENST00000256538.4	37	CCDS10043.1	50	0.022893772893772892	44	0.08943089430894309	6	0.016574585635359115	0	0.0	0	0.0	C	8.198	0.797575	0.16327	0.07065	5.82E-4	ENSG00000134146	ENST00000256538;ENST00000440392	T;T	0.42900	1.54;0.96	5.8	2.88	0.33553	Domain of unknown function DUF71, ATP-binding domain (2);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.676327	0.14999	N	0.286217	T	0.00524	0.0017	N	0.02708	-0.52	0.22851	N	0.998659	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.20638	-1.0269	10	0.02654	T	1	-0.1968	7.3765	0.26831	0.0:0.5948:0.0:0.4052	rs34907758	41;41	B3KWG1;Q7L8W6	.;ATBD4_HUMAN	E	41	ENSP00000256538:G41E;ENSP00000406976:G41E	ENSP00000256538:G41E	G	-	2	0	ATPBD4	33617957	0.000000	0.05858	0.998000	0.56505	0.692000	0.40212	-0.022000	0.12480	0.362000	0.24319	-0.142000	0.14014	GGG	C|0.972;T|0.028	0.028	strong		0.433	DPH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251973.1	NM_080650		T	35830665	C	T	35830665	3	4	22	1	0	0	0	0	1	0	0	0	1202	623	22	2	899	2	ATPBD4	15	35830665	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	556798	35830665	66700727	2990	5891											
C15orf54	400360	hgsc.bcm.edu	37	chr15	39544809	39544809	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgctgctgacaggggagagaGgggacattttggagtccaaa	11	8	16	6	0	0	2	0	1	0	1	1	6	1	5	1	5	2	2	1	5	1	2	rs115130297	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:39544809G>C	ENST00000318578.3	+	2	841	c.473G>C	c.(472-474)aGg>aCg	p.R158T	RP11-624L4.1_ENST00000560484.1_RNA|RP11-624L4.1_ENST00000558209.1_RNA|RP11-624L4.1_ENST00000561058.1_RNA|C15orf54_ENST00000561223.1_Missense_Mutation_p.R158T	NM_207445.2	NP_997328.1	Q8N8G6	CO054_HUMAN	chromosome 15 open reading frame 54	158										NS(1)|haematopoietic_and_lymphoid_tissue(2)|lung(2)	5		all_cancers(109;5.39e-14)|all_epithelial(112;3.14e-12)|Lung NSC(122;9.74e-10)|all_lung(180;2.23e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)		GBM - Glioblastoma multiforme(113;1.19e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0706)		AGGGGAGAGAGGGGACATTTT	0.448													G|||	16	0.00319489	0.0121	0.0	5008	,	,		21387	0.0		0.0	False		,,,				2504	0.0				p.R158T		Atlas-SNP	.											.	C15orf54	18	.	0			c.G473C						PASS	.	G	THR/ARG	28,4372	34.3+/-65.2	0,28,2172	98	84	88		473	0.3	0	15	dbSNP_132	88	0,8594		0,0,4297	yes	missense	C15orf54	NM_207445.2	71	0,28,6469	CC,CG,GG		0.0,0.6364,0.2155	benign	158/184	39544809	28,12966	2200	4297	6497	SO:0001583	missense	400360	exon2			GAGAGAGGGGACA		CCDS10049.1	15q14	2014-09-10			ENSG00000175746	ENSG00000175746			33797	protein-coding gene	gene with protein product							Standard	NM_207445		Approved	FLJ39531	uc001zkg.2	Q8N8G6	OTTHUMG00000129843	ENST00000318578.3:c.473G>C	15.37:g.39544809G>C	ENSP00000323686:p.Arg158Thr	145	0	0		165	88	0.533333	NM_207445	B7ZVZ9	Missense_Mutation	SNP	ENST00000318578.3	37	CCDS10049.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	G	4.682	0.126814	0.08931	0.006364	0.0	ENSG00000175746	ENST00000318578	T	0.39406	1.08	3.57	0.297	0.15762	.	.	.	.	.	T	0.09247	0.0228	N	0.08118	0	0.09310	N	1	B	0.25312	0.123	B	0.16289	0.015	T	0.15235	-1.0444	9	0.87932	D	0	.	2.1381	0.03768	0.1165:0.1939:0.4906:0.199	.	158	Q8N8G6	CO054_HUMAN	T	158	ENSP00000323686:R158T	ENSP00000323686:R158T	R	+	2	0	C15orf54	37332101	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.520000	0.06252	-0.036000	0.13669	0.609000	0.83330	AGG	G|0.997;C|0.003	0.003	strong		0.448	C15orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252083.1	NM_207445		C	39544809	G	C	39544809	3	2	22	1	0	0	0	0	1	0	0	0	1804	1000	35	4	475	4	C15orf54	15	39544809	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3714144	39544809	62986583	2991	5892											
THBS1	7057	hgsc.bcm.edu	37	chr15	39874092	39874092	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggactaggcgtcctgttcCtgatgcatgtgtgtggcacc	5	11	15	10	1	0	1	0	1	0	0	2	2	2	2	3	4	1	3	3	4	1	2	rs35248254	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:39874092C>T	ENST00000260356.5	+	2	199	c.34C>T	c.(34-36)Ctg>Ttg	p.L12L		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	12					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)		CGTCCTGTTCCTGATGCATGT	0.592											OREG0023050	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	78	0.0155751	0.0552	0.0072	5008	,	,		18818	0.0		0.0	False		,,,				2504	0.0				p.L12L		Atlas-SNP	.											.	THBS1	106	.	0			c.C34T						PASS	.	C		165,4235	110.4+/-148.6	3,159,2038	121	101	108		34	4	1	15	dbSNP_126	108	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous	THBS1	NM_003246.2		3,160,6334	TT,TC,CC		0.0116,3.75,1.2775		12/1171	39874092	166,12828	2200	4297	6497	SO:0001819	synonymous_variant	7057	exon2			CTGTTCCTGATGC		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.34C>T	15.37:g.39874092C>T		128	0	0	889	125	57	0.456	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	37	CCDS32194.1																																																																																			C|0.985;T|0.015	0.015	strong		0.592	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		T	39874092	C	T	39874092	2	4	22	1	0	0	0	0	0	0	0	1	15868	680	24	2		2	THBS1	15	39874092	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	329283	39874092	62657300	2992	5893											
THBS1	7057	hgsc.bcm.edu	37	chr15	39874396	39874396	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctctcctgtctaacagagTctggcggagacaacagcgtg	9	10	11	11	2	3	2	0	0	3	2	5	3	4	2	1	2	3	0	1	2	2	2	rs41515347	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:39874396T>G	ENST00000260356.5	+	3	235	c.70T>G	c.(70-72)Tct>Gct	p.S24A		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	24			S -> A (in dbSNP:rs41515347).		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)		TCTAACAGAGTCTGGCGGAGA	0.597													T|||	183	0.0365415	0.1241	0.0101	5008	,	,		18737	0.0099		0.001	False		,,,				2504	0.001				p.S24A		Atlas-SNP	.											.	THBS1	106	.	0			c.T70G						PASS	.	T	ALA/SER	457,3939	207.2+/-228.6	28,401,1769	36	39	38		70	4	1	15	dbSNP_127	38	7,8579	5.7+/-21.5	0,7,4286	yes	missense	THBS1	NM_003246.2	99	28,408,6055	GG,GT,TT		0.0815,10.3958,3.5742	benign	24/1171	39874396	464,12518	2198	4293	6491	SO:0001583	missense	7057	exon3			ACAGAGTCTGGCG		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.70T>G	15.37:g.39874396T>G	ENSP00000260356:p.Ser24Ala	76	0	0		94	41	0.43617	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	37	CCDS32194.1	73	0.033424908424908424	62	0.12601626016260162	5	0.013812154696132596	5	0.008741258741258742	1	0.0013192612137203166	T	17.25	3.342644	0.61073	0.103958	8.15E-4	ENSG00000137801	ENST00000260356;ENST00000397591	T;T	0.78003	-1.14;0.73	5.17	4.02	0.46733	Laminin G, thrombospondin-type, N-terminal (1);	0.000000	0.35708	N	0.003030	T	0.02727	0.0082	N	0.22421	0.69	0.32910	D	0.514417	D	0.58268	0.982	D	0.67548	0.952	T	0.52586	-0.8556	10	0.34782	T	0.22	-12.2229	11.4375	0.50076	0.0:0.0:0.1511:0.8489	rs41515347;rs61731227	24	P07996	TSP1_HUMAN	A	24	ENSP00000260356:S24A;ENSP00000380720:S24A	ENSP00000260356:S24A	S	+	1	0	THBS1	37661688	1.000000	0.71417	0.993000	0.49108	0.712000	0.41017	5.745000	0.68672	0.947000	0.37659	0.460000	0.39030	TCT	T|0.969;G|0.031	0.031	strong		0.597	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		G	39874396	T	G	39874396	3	3	22	1	0	0	0	0	1	0	0	0	15868	1667	58	5	76	5	THBS1	15	39874396	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	304	39874396	62656996	2993	5894											
GPR176	11245	hgsc.bcm.edu	37	chr15	40094431	40094431	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatcagatattttcctctcCagtggatagaggactgagta	11	12	10	8	0	2	3	1	1	1	2	4	5	3	5	2	2	0	2	2	2	3	5	rs76578471	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:40094431C>T	ENST00000561100.1	-	3	1315	c.450G>A	c.(448-450)ctG>ctA	p.L150L	GPR176_ENST00000299092.3_Silent_p.L149L|GPR176_ENST00000543580.1_Silent_p.L105L|RP11-37C7.1_ENST00000558616.1_RNA|GPR176_ENST00000560729.1_5'UTR	NM_007223.1	NP_009154.1	Q14439	GP176_HUMAN	G protein-coupled receptor 176	150					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)		TTTTCCTCTCCAGTGGATAGA	0.438											OREG0023053	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	67	0.0133786	0.0477	0.0058	5008	,	,		21801	0.0		0.0	False		,,,				2504	0.0				p.L150L		Atlas-SNP	.											.	GPR176	41	.	0			c.G450A						PASS	.	C		112,4294	86.3+/-125.0	0,112,2091	70	61	64		450	4.8	1	15	dbSNP_132	64	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GPR176	NM_007223.1		0,113,6390	TT,TC,CC		0.0116,2.542,0.8688		150/516	40094431	113,12893	2203	4300	6503	SO:0001819	synonymous_variant	11245	exon3			CCTCTCCAGTGGA	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.450G>A	15.37:g.40094431C>T		39	0	0	890	47	21	0.446809	NM_007223	Q6NXF6	Silent	SNP	ENST00000561100.1	37	CCDS10051.1																																																																																			C|0.989;T|0.011	0.011	strong		0.438	GPR176-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252117.2	NM_007223		T	40094431	C	T	40094431	2	4	22	1	0	0	0	0	0	0	0	1	6681	581	21	2		2	GPR176	15	40094431	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	220035	40094431	62436961	2994	5895											
BUB1B	701	hgsc.bcm.edu	37	chr15	40453430	40453430	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caggaatgcaggatggcggcGgtgaagaaggaagggggtgc	11	4	21	5	2	0	2	0	1	0	1	0	5	0	5	0	8	2	1	0	8	4	0	rs7168394	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:40453430G>T	ENST00000287598.6	+	1	204	c.9G>T	c.(7-9)gcG>gcT	p.A3A	BUB1B_ENST00000560120.1_3'UTR|BUB1B_ENST00000412359.3_Silent_p.A3A	NM_001211.5	NP_001202	O60566	BUB1B_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase B	3					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)		GGATGGCGGCGGTGAAGAAGG	0.637			"Mis, N, F, S"			rhabdomyosarcoma			Mosaic Variegated Aneuploidy Syndrome				G|||	335	0.066893	0.2458	0.0144	5008	,	,		17894	0.0		0.0	False		,,,				2504	0.0				p.A3A		Atlas-SNP	.	yes	Rec		Mosaic variegated aneuploidy	15	15q15	701	BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)		M	.	BUB1B	71	.	0			c.G9T						PASS	.	G		761,3645	297.3+/-284.7	70,621,1512	66	54	58		9	1.1	0	15	dbSNP_116	58	18,8582	12.6+/-44.7	0,18,4282	no	coding-synonymous	BUB1B	NM_001211.5		70,639,5794	TT,TG,GG		0.2093,17.2719,5.9895		3/1051	40453430	779,12227	2203	4300	6503	SO:0001819	synonymous_variant	701	exon1	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	GGCGGCGGTGAAG	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.9G>T	15.37:g.40453430G>T		126	0	0		136	74	0.544118	NM_001211	B2R6U0|B4DL09|B4DLG3|O60501|O60627|O60758|O75389|Q59HH6|Q8WV50|Q96KM4	Silent	SNP	ENST00000287598.6	37	CCDS10053.1																																																																																			G|0.922;T|0.078	0.078	strong		0.637	BUB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252122.4			T	40453430	G	T	40453430	2	4	22	1	0	0	0	0	0	0	0	1	1573	1103	39	4		4	BUB1B	15	40453430	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	358999	40453430	62077962	2995	5896											
BUB1B	701	hgsc.bcm.edu	37	chr15	40498503	40498503	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgccagagcagctcgttttgTatccactccttttcatgaga	8	14	8	11	1	1	2	1	1	0	2	4	3	3	2	3	0	3	4	3	0	1	5	rs1801528	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:40498503T>C	ENST00000287598.6	+	15	2048	c.1853T>C	c.(1852-1854)gTa>gCa	p.V618A	BUB1B_ENST00000412359.3_Missense_Mutation_p.V632A	NM_001211.5	NP_001202	O60566	BUB1B_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase B	618			V -> A (in colorectal cancer; dbSNP:rs1801528). {ECO:0000269|PubMed:10366450, ECO:0000269|PubMed:17344846}.		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)		GCTCGTTTTGTATCCACTCCT	0.448			"Mis, N, F, S"			rhabdomyosarcoma			Mosaic Variegated Aneuploidy Syndrome				T|||	465	0.0928514	0.3389	0.0245	5008	,	,		19876	0.0		0.0	False		,,,				2504	0.0				p.V618A		Atlas-SNP	.	yes	Rec		Mosaic variegated aneuploidy	15	15q15	701	BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)		M	BUB1B,NS,carcinoma,+1,1	BUB1B	71	1	0			c.T1853C						PASS	.	T	ALA/VAL	1117,3289	402.2+/-332.3	135,847,1221	95	96	96		1853	-0.5	1	15	dbSNP_89	96	18,8582	13.3+/-46.6	0,18,4282	yes	missense	BUB1B	NM_001211.5	64	135,865,5503	CC,CT,TT		0.2093,25.3518,8.7267	benign	618/1051	40498503	1135,11871	2203	4300	6503	SO:0001583	missense	701	exon15	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	GTTTTGTATCCAC	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.1853T>C	15.37:g.40498503T>C	ENSP00000287598:p.Val618Ala	167	0	0		176	86	0.488636	NM_001211	B2R6U0|B4DL09|B4DLG3|O60501|O60627|O60758|O75389|Q59HH6|Q8WV50|Q96KM4	Missense_Mutation	SNP	ENST00000287598.6	37	CCDS10053.1	179	0.08195970695970696	169	0.3434959349593496	9	0.024861878453038673	0	0.0	1	0.0013192612137203166	T	5.086	0.201529	0.09652	0.253518	0.002093	ENSG00000156970	ENST00000287598;ENST00000412359	T;T	0.11277	2.79;2.8	5.51	-0.494	0.12034	.	0.391035	0.23252	N	0.050240	T	0.00012	0.0000	N	0.01874	-0.695	0.44409	P	0.0026760000000000117	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48490	-0.9031	9	0.02654	T	1	-0.8963	13.1761	0.59629	0.0:0.7666:0.0:0.2334	rs1801528;rs52836029	632;618	O60566-3;O60566	.;BUB1B_HUMAN	A	618;632	ENSP00000287598:V618A;ENSP00000398470:V632A	ENSP00000287598:V618A	V	+	2	0	BUB1B	38285795	0.999000	0.42202	0.961000	0.40146	0.990000	0.78478	0.726000	0.25984	-0.099000	0.12263	0.482000	0.46254	GTA	T|0.917;C|0.083	0.083	strong		0.448	BUB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252122.4			C	40498503	T	C	40498503	3	2	22	1	0	0	0	0	1	0	0	0	1573	1638	57	3	1911	3	BUB1B	15	40498503	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	45073	40498503	62032889	2996	5897											
BUB1B	701	hgsc.bcm.edu	37	chr15	40512906	40512906	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttccaaagtcacctgaacaaAgccttatggaaggtagggaa	15	8	10	8	0	1	1	1	1	0	0	2	3	2	3	3	3	2	1	3	3	7	3	rs35611758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:40512906A>G	ENST00000287598.6	+	23	3294	c.3099A>G	c.(3097-3099)aaA>aaG	p.K1033K	PAK6_ENST00000453867.1_Intron|BUB1B_ENST00000412359.3_Silent_p.K1047K|PAK6_ENST00000441369.1_Intron|RP11-133K1.2_ENST00000558658.1_Intron	NM_001211.5	NP_001202	O60566	BUB1B_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase B	1033	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)		ACCTGAACAAAGCCTTATGGA	0.468			"Mis, N, F, S"			rhabdomyosarcoma			Mosaic Variegated Aneuploidy Syndrome				A|||	480	0.0958466	0.3502	0.0245	5008	,	,		19233	0.0		0.0	False		,,,				2504	0.0				p.K1033K		Atlas-SNP	.	yes	Rec		Mosaic variegated aneuploidy	15	15q15	701	BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)		M	.	BUB1B	71	.	0			c.A3099G						PASS	.	A	,,	1160,3246	411.9+/-335.9	151,858,1194	139	133	135		,,3099	5.3	1	15	dbSNP_126	135	18,8582	13.3+/-46.6	0,18,4282	no	intron,intron,coding-synonymous	BUB1B,PAK6	NM_001128628.1,NM_001128629.1,NM_001211.5	,,	151,876,5476	GG,GA,AA		0.2093,26.3277,9.0574	,,	,,1033/1051	40512906	1178,11828	2203	4300	6503	SO:0001819	synonymous_variant	701	exon23	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	GAACAAAGCCTTA	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.3099A>G	15.37:g.40512906A>G		151	0	0		137	73	0.532847	NM_001211	B2R6U0|B4DL09|B4DLG3|O60501|O60627|O60758|O75389|Q59HH6|Q8WV50|Q96KM4	Silent	SNP	ENST00000287598.6	37	CCDS10053.1																																																																																			A|0.915;G|0.085	0.085	strong		0.468	BUB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252122.4			G	40512906	A	G	40512906	2	3	22	1	0	0	0	0	0	0	0	1	1573	69	3	3		3	BUB1B	15	40512906	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	14403	40512906	62018486	2997	5898											
CASC5	57082	hgsc.bcm.edu	37	chr15	40916272	40916272	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcctgtacattggaaaaagcGcaagttgaaagctgtcagtt	13	10	11	7	1	1	1	1	1	0	0	1	2	1	2	1	1	3	5	1	1	5	4	rs34758606	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:40916272G>A	ENST00000346991.5	+	11	4278	c.3888G>A	c.(3886-3888)gcG>gcA	p.A1296A	CASC5_ENST00000399668.2_Silent_p.A1270A			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	1296					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)		TGGAAAAAGCGCAAGTTGAAA	0.363													G|||	68	0.0135783	0.0484	0.0058	5008	,	,		20456	0.0		0.0	False		,,,				2504	0.0				p.A1296A		Atlas-SNP	.											.	CASC5	269	.	0			c.G3888A						PASS	.	G	,	134,3578		6,122,1728	87	81	83		3810,3888	-4.3	0	15	dbSNP_126	83	1,8199		0,1,4099	no	coding-synonymous,coding-synonymous	CASC5	NM_144508.3,NM_170589.3	,	6,123,5827	AA,AG,GG		0.0122,3.6099,1.1333	,	1270/2317,1296/2343	40916272	135,11777	1856	4100	5956	SO:0001819	synonymous_variant	57082	exon11			AAAAGCGCAAGTT	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.3888G>A	15.37:g.40916272G>A		75	0	0		98	55	0.561224	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Silent	SNP	ENST00000346991.5	37	CCDS42023.1																																																																																			G|0.991;A|0.009	0.009	strong		0.363	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508		A	40916272	G	A	40916272	2	1	22	1	0	0	0	0	0	0	0	1	2665	1074	38	1		1	CASC5	15	40916272	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	403366	40916272	61615120	2998	5899											
DNAJC17	55192	hgsc.bcm.edu	37	chr15	41068409	41068409	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgcacctctcaacctctggtCacgctcctggcgtatctgct	5	12	8	16	2	4	0	2	0	3	0	6	0	5	0	3	2	3	4	3	2	2	1	rs73398528	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:41068409C>T	ENST00000220496.4	-	6	493	c.463G>A	c.(463-465)Gac>Aac	p.D155N		NM_018163.2	NP_060633.1	Q9NVM6	DJC17_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 17	155					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)		AACCTCTGGTCACGCTCCTGG	0.622													C|||	294	0.0587061	0.2141	0.0144	5008	,	,		16797	0.001		0.0	False		,,,				2504	0.0				p.D155N		Atlas-SNP	.											.	DNAJC17	18	.	0			c.G463A						PASS	.	C	ASN/ASP	781,3625	315.2+/-294.0	55,671,1477	104	84	91		463	4.4	0.3	15	dbSNP_130	91	3,8597	2.2+/-6.3	0,3,4297	yes	missense	DNAJC17	NM_018163.2	23	55,674,5774	TT,TC,CC		0.0349,17.7258,6.028	benign	155/305	41068409	784,12222	2203	4300	6503	SO:0001583	missense	55192	exon6			TCTGGTCACGCTC	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.463G>A	15.37:g.41068409C>T	ENSP00000220496:p.Asp155Asn	88	0	0		103	46	0.446602	NM_018163		Missense_Mutation	SNP	ENST00000220496.4	37	CCDS10065.1	103	0.04716117216117216	95	0.19308943089430894	7	0.019337016574585635	1	0.0017482517482517483	0	0.0	C	6.900	0.535565	0.13188	0.177258	3.49E-4	ENSG00000104129	ENST00000220496	T	0.18338	2.22	4.41	4.41	0.53225	.	0.289804	0.36444	N	0.002600	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.38394	-0.9663	9	0.21540	T	0.41	.	13.7416	0.62852	0.0:0.8449:0.1551:0.0	.	155	Q9NVM6	DJC17_HUMAN	N	155	ENSP00000220496:D155N	ENSP00000220496:D155N	D	-	1	0	DNAJC17	38855701	0.959000	0.32827	0.332000	0.25469	0.105000	0.19272	3.571000	0.53841	2.300000	0.77407	0.561000	0.74099	GAC	C|0.947;T|0.053	0.053	strong		0.622	DNAJC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252356.2	NM_018163		T	41068409	C	T	41068409	3	4	22	1	0	0	0	0	1	0	0	0	4638	826	29	2	475	2	DNAJC17	15	41068409	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	152137	41068409	61462983	2999	5900											
ZFYVE19	84936	hgsc.bcm.edu	37	chr15	41105979	41105979	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagagcaggcttctcgaccCtggacgcaaccccgcggggc	7	4	14	16	4	1	1	0	0	1	1	2	3	1	2	3	4	2	4	3	4	1	1	rs116749518	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:41105979C>G	ENST00000355341.4	+	9	1680	c.1179C>G	c.(1177-1179)ccC>ccG	p.P393P	ZFYVE19_ENST00000570108.1_Silent_p.P370P|ZFYVE19_ENST00000299173.10_Silent_p.P325P|ZFYVE19_ENST00000564258.1_Silent_p.P218P|ZFYVE19_ENST00000336455.5_Silent_p.P383P	NM_001077268.1	NP_001070736.1	Q96K21	ANCHR_HUMAN	zinc finger, FYVE domain containing 19	393					abscission (GO:0009838)|cell division (GO:0051301)|cytokinesis checkpoint (GO:0031565)|negative regulation of cytokinesis (GO:0032466)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|midbody (GO:0030496)	phosphatidylinositol-3-phosphate binding (GO:0032266)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	9		all_cancers(109;3.31e-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;2.76e-05)|COAD - Colon adenocarcinoma(120;0.151)|BRCA - Breast invasive adenocarcinoma(123;0.164)		CTTCTCGACCCTGGACGCAAC	0.612													C|||	18	0.00359425	0.0136	0.0	5008	,	,		18843	0.0		0.0	False		,,,				2504	0.0				p.P393P		Atlas-SNP	.											.	ZFYVE19	31	.	0			c.C1179G						PASS	.	C		33,3971		1,31,1970	49	54	52		1179	1.1	0	15	dbSNP_132	52	1,8315		0,1,4157	no	coding-synonymous	ZFYVE19	NM_001077268.1		1,32,6127	GG,GC,CC		0.012,0.8242,0.276		393/472	41105979	34,12286	2002	4158	6160	SO:0001819	synonymous_variant	84936	exon9			TCGACCCTGGACG	AK027746	CCDS42025.1, CCDS58353.1, CCDS58354.1, CCDS58355.1	15q14	2008-05-02				ENSG00000166140		"Zinc fingers, FYVE domain containing"	20758	protein-coding gene	gene with protein product							Standard	NM_001077268		Approved	FLJ14840	uc031qrk.1	Q96K21		ENST00000355341.4:c.1179C>G	15.37:g.41105979C>G		90	0	0		100	51	0.51	NM_001077268	B3KVB2|C9JNF4|H3BUF9|Q86WC2|Q8WU96	Silent	SNP	ENST00000355341.4	37	CCDS42025.1																																																																																			C|0.997;G|0.003	0.003	strong		0.612	ZFYVE19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418996.1	NM_032850		G	41105979	C	G	41105979	2	3	22	1	0	0	0	0	0	0	0	1	17680	668	24	4		4	ZFYVE19	15	41105979	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	37570	41105979	61425413	3000	5901											
RPAP1	26015	hgsc.bcm.edu	37	chr15	41815063	41815063	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgagccagccagactgagaCgggggcagcctcccgagcag	9	3	15	14	2	0	3	0	2	0	2	1	5	1	3	4	2	4	2	4	2	0	0	rs61748721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:41815063C>T	ENST00000304330.4	-	19	2758	c.2642G>A	c.(2641-2643)cGt>cAt	p.R881H	RPAP1_ENST00000561603.1_Missense_Mutation_p.R881H	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	881	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)		CAGACTGAGACGGGGGCAGCC	0.632													C|||	177	0.0353435	0.1324	0.0029	5008	,	,		16841	0.0		0.0	False		,,,				2504	0.0				p.R881H		Atlas-SNP	.											.	RPAP1	111	.	0			c.G2642A						PASS	.	C	HIS/ARG	531,3875	241.5+/-251.9	29,473,1701	56	50	52		2642	-1.3	0	15	dbSNP_129	52	3,8597	2.2+/-6.3	0,3,4297	yes	missense	RPAP1	NM_015540.2	29	29,476,5998	TT,TC,CC		0.0349,12.0517,4.1058	benign	881/1394	41815063	534,12472	2203	4300	6503	SO:0001583	missense	26015	exon19			CTGAGACGGGGGC	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.2642G>A	15.37:g.41815063C>T	ENSP00000306123:p.Arg881His	44	0	0		51	29	0.568627	NM_015540	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Missense_Mutation	SNP	ENST00000304330.4	37	CCDS10079.1	60	0.027472527472527472	59	0.11991869918699187	1	0.0027624309392265192	0	0.0	0	0.0	C	10.52	1.373816	0.24857	0.120517	3.49E-4	ENSG00000103932	ENST00000304330	T	0.11930	2.73	5.27	-1.3	0.09259	.	0.689147	0.15432	N	0.262677	T	0.00109	0.0003	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36986	-0.9725	10	0.41790	T	0.15	-23.5071	5.7717	0.18257	0.0626:0.3333:0.3812:0.2229	.	881	Q9BWH6	RPAP1_HUMAN	H	881	ENSP00000306123:R881H	ENSP00000306123:R881H	R	-	2	0	RPAP1	39602355	0.005000	0.15991	0.000000	0.03702	0.660000	0.38997	0.344000	0.19962	-0.381000	0.07882	-1.067000	0.02272	CGT	C|0.958;T|0.042	0.042	strong		0.632	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540		T	41815063	C	T	41815063	3	4	22	1	0	0	0	0	1	0	0	0	13556	536	19	1	1567	1	RPAP1	15	41815063	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	709084	41815063	60716329	3001	5902											
MGA	23269	hgsc.bcm.edu	37	chr15	42019421	42019421	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcctgttcgacattacccAttatgggtaaaagtagaagg	13	10	10	8	1	0	1	0	0	0	1	1	2	0	1	2	2	2	3	2	2	6	5	rs61736067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42019421A>G	ENST00000570161.1	+	9	3474	c.3474A>G	c.(3472-3474)ccA>ccG	p.P1158P	MGA_ENST00000545763.1_Silent_p.P1158P|MGA_ENST00000219905.7_Silent_p.P1158P|MGA_ENST00000389936.4_Silent_p.P1158P|MGA_ENST00000566586.1_Silent_p.P1158P			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)	GACATTACCCATTATGGGTAA	0.408													A|||	80	0.0159744	0.0582	0.0029	5008	,	,		18915	0.0		0.001	False		,,,				2504	0.0				p.P1158P		Atlas-SNP	.											.	MGA	264	.	0			c.A3474G						PASS	.	A	,	166,3584		7,152,1716	86	79	81		3474,3474	0.6	1	15	dbSNP_129	81	3,8199		0,3,4098	no	coding-synonymous,coding-synonymous	MGA	NM_001080541.2,NM_001164273.1	,	7,155,5814	GG,GA,AA		0.0366,4.4267,1.414	,	1158/2857,1158/3066	42019421	169,11783	1875	4101	5976	SO:0001819	synonymous_variant	23269	exon10			TTACCCATTATGG	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.3474A>G	15.37:g.42019421A>G		97	0	0		87	41	0.471264	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000570161.1	37	CCDS55959.1																																																																																			A|0.988;G|0.012	0.012	strong		0.408	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		G	42019421	A	G	42019421	2	3	22	1	0	0	0	0	0	0	0	1	9549	204	8	3		3	MGA	15	42019421	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	204358	42019421	60511971	3002	5903											
JMJD7-PLA2G4B	100137049	hgsc.bcm.edu	37	chr15	42137201	42137201	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggagctggccgagcgtgcccGcttgggctacccaagctgct	5	7	15	14	3	0	0	0	0	0	0	0	2	0	1	3	3	6	5	3	3	2	2	rs34807597	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42137201G>A	ENST00000452633.1	+	14	1524	c.1172G>A	c.(1171-1173)cGc>cAc	p.R391H	PLA2G4B_ENST00000542534.2_Missense_Mutation_p.R622H|PLA2G4B_ENST00000458483.1_Missense_Mutation_p.R391H|JMJD7-PLA2G4B_ENST00000382448.4_Missense_Mutation_p.R622H|JMJD7-PLA2G4B_ENST00000342159.4_Missense_Mutation_p.R622H			P0C869	PA24B_HUMAN	phospholipase A2, group IVB (cytosolic)	391	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.		R -> H (in dbSNP:rs34807597).		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|arachidonic acid metabolic process (GO:0019369)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|parturition (GO:0007567)|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)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|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)						all_cancers(109;1.84e-13)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		all cancers(2;1.08e-30)|Epithelial(2;1.43e-22)|OV - Ovarian serous cystadenocarcinoma(18;1.13e-17)|GBM - Glioblastoma multiforme(94;9.77e-07)|Colorectal(2;0.0129)|COAD - Colon adenocarcinoma(120;0.0371)		GAGCGTGCCCGCTTGGGCTAC	0.672													G|||	77	0.0153754	0.0552	0.0043	5008	,	,		15685	0.0		0.001	False		,,,				2504	0.0				p.R622H		Atlas-SNP	.											.	JMJD7-PLA2G4B	90	.	0			c.G1865A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG	189,4209		7,175,2017	16	17	17		1172,1865,1865	-1.9	0.4	15	dbSNP_126	17	3,8581		0,3,4289	yes	missense,missense,missense	JMJD7-PLA2G4B,PLA2G4B	NM_001114633.1,NM_001198588.1,NM_005090.3	29,29,29	7,178,6306	AA,AG,GG		0.0349,4.2974,1.479	benign,benign,benign	391/782,622/894,622/1013	42137201	192,12790	2199	4292	6491	SO:0001583	missense	8681	exon18			GTGCCCGCTTGGG	AF065215	CCDS45241.1	15q11.2-q21.3	2010-08-17			ENSG00000243708	ENSG00000243708	3.1.1.4		9036	protein-coding gene	gene with protein product		606088				9705332	Standard	NM_001114633		Approved	cPLA2-beta, HsT16992		P0C869	OTTHUMG00000156809	ENST00000452633.1:c.1172G>A	15.37:g.42137201G>A	ENSP00000396045:p.Arg391His	65	0	0		79	36	0.455696	NM_005090	B4DRT9|O95712|Q19KD5|Q19KD6|Q59GF9|Q8TB10|Q9UKV7	Missense_Mutation	SNP	ENST00000452633.1	37	CCDS45241.1	25	0.011446886446886446	22	0.044715447154471545	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	.	10.30	1.310981	0.23821	0.042974	3.49E-4	ENSG00000168970;ENSG00000168970;ENSG00000168970;ENSG00000243708	ENST00000382448;ENST00000342159;ENST00000458483;ENST00000452633	T;T;T;T	0.04603	3.59;3.59;3.59;3.59	5.51	-1.88	0.07713	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.492693	0.18810	N	0.130531	T	0.01156	0.0038	M	0.65498	2.005	0.09310	N	1	B;B;B;B	0.13594	0.008;0.0;0.003;0.003	B;B;B;B	0.12156	0.007;0.0;0.002;0.001	T	0.30001	-0.9993	10	0.62326	D	0.03	-2.658	5.6051	0.17374	0.6081:0.0:0.2403:0.1516	rs34807597	391;622;92;622	P0C869;P0C869-7;P0C869-4;P0C869-6	PA24B_HUMAN;.;.;.	H	622;622;391;391	ENSP00000371886:R622H;ENSP00000342785:R622H;ENSP00000416610:R391H;ENSP00000396045:R391H	ENSP00000342785:R622H	R	+	2	0	JMJD7-PLA2G4B;PLA2G4B	39924493	0.002000	0.14202	0.381000	0.26106	0.055000	0.15305	0.861000	0.27885	-0.138000	0.11434	0.561000	0.74099	CGC	G|0.984;A|0.016	0.016	strong		0.672	PLA2G4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345969.1	NM_001114633		A	42137201	G	A	42137201	3	1	22	1	0	0	0	0	1	0	0	0	7964	1087	38	1	1935	1	JMJD7-PLA2G4B	15	42137201	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	117780	42137201	60394191	3003	5904											
JMJD7-PLA2G4B	100137049	hgsc.bcm.edu	37	chr15	42138572	42138572	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagcatcctcacttctccaCatggaaaggtacctgcttct	9	12	6	14	0	4	0	2	0	2	0	6	1	5	1	3	2	3	3	3	2	2	3	rs36126315	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42138572C>T	ENST00000452633.1	+	18	2124	c.1772C>T	c.(1771-1773)aCa>aTa	p.T591I	PLA2G4B_ENST00000542534.2_Missense_Mutation_p.T822I|PLA2G4B_ENST00000458483.1_Missense_Mutation_p.T591I|JMJD7-PLA2G4B_ENST00000382448.4_Missense_Mutation_p.T822I|JMJD7-PLA2G4B_ENST00000342159.4_Missense_Mutation_p.T822I			P0C869	PA24B_HUMAN	phospholipase A2, group IVB (cytosolic)	591	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.		T -> I (in dbSNP:rs36126315).		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|arachidonic acid metabolic process (GO:0019369)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|parturition (GO:0007567)|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)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|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)						all_cancers(109;1.84e-13)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		all cancers(2;1.08e-30)|Epithelial(2;1.43e-22)|OV - Ovarian serous cystadenocarcinoma(18;1.13e-17)|GBM - Glioblastoma multiforme(94;9.77e-07)|Colorectal(2;0.0129)|COAD - Colon adenocarcinoma(120;0.0371)		CACTTCTCCACATGGAAAGGT	0.547													C|||	76	0.0151757	0.0552	0.0029	5008	,	,		20192	0.0		0.001	False		,,,				2504	0.0				p.T822I		Atlas-SNP	.											.	JMJD7-PLA2G4B	90	.	0			c.C2465T						PASS	.	C	ILE/THR,ILE/THR,ILE/THR	194,4212		8,178,2017	99	97	98		1772,2465,2465	3	0.6	15	dbSNP_126	98	3,8597		0,3,4297	yes	missense,missense,missense	JMJD7-PLA2G4B,PLA2G4B	NM_001114633.1,NM_001198588.1,NM_005090.3	89,89,89	8,181,6314	TT,TC,CC		0.0349,4.4031,1.5147	benign,benign,benign	591/782,822/894,822/1013	42138572	197,12809	2203	4300	6503	SO:0001583	missense	8681	exon22			TCTCCACATGGAA	AF065215	CCDS45241.1	15q11.2-q21.3	2010-08-17			ENSG00000243708	ENSG00000243708	3.1.1.4		9036	protein-coding gene	gene with protein product		606088				9705332	Standard	NM_001114633		Approved	cPLA2-beta, HsT16992		P0C869	OTTHUMG00000156809	ENST00000452633.1:c.1772C>T	15.37:g.42138572C>T	ENSP00000396045:p.Thr591Ile	114	0	0		112	55	0.491071	NM_005090	B4DRT9|O95712|Q19KD5|Q19KD6|Q59GF9|Q8TB10|Q9UKV7	Missense_Mutation	SNP	ENST00000452633.1	37	CCDS45241.1	24	0.01098901098901099	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	.	15.97	2.990575	0.54041	0.044031	3.49E-4	ENSG00000168970;ENSG00000168970;ENSG00000168970;ENSG00000243708	ENST00000382448;ENST00000342159;ENST00000458483;ENST00000452633	T;T;T;T	0.12984	2.63;2.63;2.63;2.63	4.96	3.05	0.35203	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	1.072970	0.07218	N	0.860326	T	0.04452	0.0122	L	0.49778	1.585	0.23454	N	0.997645	P;B;B	0.45283	0.855;0.078;0.178	P;B;B	0.47470	0.548;0.055;0.086	T	0.16928	-1.0386	10	0.40728	T	0.16	-4.9065	7.2416	0.26100	0.0:0.6949:0.144:0.1611	rs36126315	591;822;822	P0C869;P0C869-7;P0C869-6	PA24B_HUMAN;.;.	I	822;822;591;591	ENSP00000371886:T822I;ENSP00000342785:T822I;ENSP00000416610:T591I;ENSP00000396045:T591I	ENSP00000342785:T822I	T	+	2	0	JMJD7-PLA2G4B;PLA2G4B	39925864	0.227000	0.23707	0.645000	0.29479	0.900000	0.52787	0.800000	0.27042	0.727000	0.32360	0.655000	0.94253	ACA	C|0.985;T|0.015	0.015	strong		0.547	PLA2G4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345969.1	NM_001114633		T	42138572	C	T	42138572	3	4	22	1	0	0	0	0	1	0	0	0	7964	478	17	2	2551	2	JMJD7-PLA2G4B	15	42138572	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1371	42138572	60392820	3004	5905											
JMJD7-PLA2G4B	100137049	hgsc.bcm.edu	37	chr15	42139875	42139875	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggacacccgaggaggcggcAgctggggaggtgaacctgtc	8	4	18	11	3	0	1	0	1	0	0	1	5	0	4	2	7	2	2	2	7	1	0	rs34424865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42139875A>G	ENST00000452633.1	+	21	2515	c.2163A>G	c.(2161-2163)gcA>gcG	p.A721A	PLA2G4B_ENST00000542534.2_Silent_p.A952A|PLA2G4B_ENST00000458483.1_Silent_p.A721A|JMJD7-PLA2G4B_ENST00000382448.4_Silent_p.A952A|JMJD7-PLA2G4B_ENST00000342159.4_Missense_Mutation_p.Q890R			P0C869	PA24B_HUMAN	phospholipase A2, group IVB (cytosolic)	721	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|arachidonic acid metabolic process (GO:0019369)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|parturition (GO:0007567)|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)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|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)						all_cancers(109;1.84e-13)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		all cancers(2;1.08e-30)|Epithelial(2;1.43e-22)|OV - Ovarian serous cystadenocarcinoma(18;1.13e-17)|GBM - Glioblastoma multiforme(94;9.77e-07)|Colorectal(2;0.0129)|COAD - Colon adenocarcinoma(120;0.0371)		AGGAGGCGGCAGCTGGGGAGG	0.617													a|||	78	0.0155751	0.0567	0.0029	5008	,	,		17421	0.0		0.001	False		,,,				2504	0.0				p.Q890R		Atlas-SNP	.											.	JMJD7-PLA2G4B	90	.	0			c.A2669G						PASS	.	A	,ARG/GLN,	196,4210		8,180,2015	74	66	69		2163,2669,2856	-9.6	0	15	dbSNP_126	69	3,8597		0,3,4297	yes	coding-synonymous,missense,coding-synonymous	JMJD7-PLA2G4B,PLA2G4B	NM_001114633.1,NM_001198588.1,NM_005090.3	,43,	8,183,6312	GG,GA,AA		0.0349,4.4485,1.5301	,,	721/782,890/894,952/1013	42139875	199,12807	2203	4300	6503	SO:0001819	synonymous_variant	8681	exon24			GGCGGCAGCTGGG	AF065215	CCDS45241.1	15q11.2-q21.3	2010-08-17			ENSG00000243708	ENSG00000243708	3.1.1.4		9036	protein-coding gene	gene with protein product		606088				9705332	Standard	NM_001114633		Approved	cPLA2-beta, HsT16992		P0C869	OTTHUMG00000156809	ENST00000452633.1:c.2163A>G	15.37:g.42139875A>G		92	0	0		91	49	0.538462	NM_001198588	B4DRT9|O95712|Q19KD5|Q19KD6|Q59GF9|Q8TB10|Q9UKV7	Missense_Mutation	SNP	ENST00000452633.1	37	CCDS45241.1	26	0.011904761904761904	24	0.04878048780487805	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	.	5.025	0.190237	0.09547	0.044485	3.49E-4	ENSG00000168970	ENST00000342159	T	0.01484	4.84	4.77	-9.55	0.00569	.	.	.	.	.	T	0.00241	0.0007	.	.	.	0.09310	N	0.999995	B	0.02656	0.0	B	0.01281	0.0	T	0.47249	-0.9132	8	0.87932	D	0	-0.1604	2.4723	0.04567	0.2543:0.1668:0.4127:0.1662	rs34424865	890	P0C869-7	.	R	890	ENSP00000342785:Q890R	ENSP00000342785:Q890R	Q	+	2	0	JMJD7-PLA2G4B	39927167	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-4.099000	0.00295	-2.603000	0.00450	-2.852000	0.00102	CAG	A|0.984;G|0.016	0.016	strong		0.617	PLA2G4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345969.1	NM_001114633		G	42139875	A	G	42139875	2	3	22	1	0	0	0	0	0	0	0	1	7964	175	7	3		3	JMJD7-PLA2G4B	15	42139875	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1303	42139875	60391517	3005	5906											
SPTBN5	51332	hgsc.bcm.edu	37	chr15	42179424	42179424	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccccaccttagtgagtctcCtctggacagtctgcccctga	6	10	8	17	0	3	2	0	2	3	0	4	3	3	3	6	1	1	0	6	1	1	1	rs890499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42179424C>T	ENST00000320955.6	-	6	1102	c.875G>A	c.(874-876)aGg>aAg	p.R292K		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	292					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)		AGTGAGTCTCCTCTGGACAGT	0.612													C|||	306	0.0611022	0.2239	0.013	5008	,	,		19925	0.0		0.001	False		,,,				2504	0.0				p.R257K		Atlas-SNP	.											.	SPTBN5	171	.	0			c.G770A						PASS	.	C	LYS/ARG	563,2887		35,493,1197	25	33	30		770	1.1	0.8	15	dbSNP_86	30	9,6849		0,9,3420	yes	missense	SPTBN5	NM_016642.2	26	35,502,4617	TT,TC,CC		0.1312,16.3188,5.5491	possibly-damaging	257/3640	42179424	572,9736	1725	3429	5154	SO:0001583	missense	51332	exon6			AGTCTCCTCTGGA	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.875G>A	15.37:g.42179424C>T	ENSP00000317790:p.Arg292Lys	231	0	0		274	140	0.510949	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		106	0.048534798534798536	103	0.20934959349593496	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	C	5.966	0.362219	0.11296	0.163188	0.001312	ENSG00000137877	ENST00000320955	T	0.69806	-0.43	4.49	1.08	0.20341	.	0.076889	0.48286	D	0.000197	T	0.00039	0.0001	N	0.05383	-0.06	0.43540	P	0.00416099999999997	P	0.35612	0.512	B	0.24541	0.054	T	0.22906	-1.0203	9	0.02654	T	1	.	5.7068	0.17913	0.0:0.3579:0.0:0.6421	rs890499;rs1704358;rs890499	292	Q9NRC6	SPTN5_HUMAN	K	292	ENSP00000317790:R292K	ENSP00000317790:R292K	R	-	2	0	SPTBN5	39966716	0.982000	0.34865	0.797000	0.32132	0.954000	0.61252	0.676000	0.25247	0.357000	0.24183	0.591000	0.81541	AGG	C|0.929;T|0.071	0.071	strong		0.612	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		T	42179424	C	T	42179424	3	4	22	1	0	0	0	0	1	0	0	0	15137	681	24	2	10401	2	SPTBN5	15	42179424	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	39549	42179424	60351968	3006	5907											
PLA2G4E	123745	hgsc.bcm.edu	37	chr15	42289456	42289456	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ccgcacgtccagtgtctcagGgctggagggagagaggaccc	8	5	16	12	2	1	1	1	0	1	1	3	5	2	4	3	4	0	2	3	4	0	0	rs79040960	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42289456G>C	ENST00000399518.3	-	11	1462	c.976C>G	c.(976-978)Cct>Gct	p.P326A	PLA2G4E_ENST00000413860.2_Splice_Site_p.P297A|CTD-2382E5.1_ENST00000499478.2_RNA	NM_001206670.1	NP_001193599.1	Q3MJ16	PA24E_HUMAN	phospholipase A2, group IVE	314	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)		AGTGTCTCAGGGCTGGAGGGA	0.607													G|||	125	0.0249601	0.0885	0.0115	5008	,	,		19005	0.0		0.0	False		,,,				2504	0.0				p.P326A		Atlas-SNP	.											.	PLA2G4E	60	.	0			c.C976G						PASS	.	G	ALA/PRO	214,3522		2,210,1656	11	14	13		976	-0.7	0.2	15	dbSNP_131	13	2,7470		0,2,3734	yes	missense-near-splice	PLA2G4E	NM_001206670.1	27	2,212,5390	CC,CG,GG		0.0268,5.7281,1.9272	benign	326/869	42289456	216,10992	1868	3736	5604	SO:0001630	splice_region_variant	123745	exon11			TCTCAGGGCTGGA		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.975-1C>G	15.37:g.42289456G>C		125	0	0		106	53	0.5	NM_001206670	Q6ZSC0	Missense_Mutation	SNP	ENST00000399518.3	37	CCDS55962.1	33	0.01510989010989011	31	0.06300813008130081	2	0.0055248618784530384	0	0.0	0	0.0	G	12.97	2.097162	0.37048	0.057281	2.68E-4	ENSG00000188089	ENST00000399518;ENST00000413860	T;T	0.01599	4.86;4.74	5.68	-0.726	0.11170	.	0.499688	0.17527	U	0.171007	T	0.00356	0.0011	M	0.72118	2.19	0.22656	N	0.998886	B	0.32731	0.382	B	0.32677	0.15	T	0.37033	-0.9723	10	0.51188	T	0.08	-4.1952	10.0101	0.41981	0.4735:0.0:0.5265:0.0	.	297	C9JK77	.	A	326;297	ENSP00000382434:P326A;ENSP00000413897:P297A	ENSP00000382434:P326A	P	-	1	0	PLA2G4E	40076748	0.130000	0.22417	0.193000	0.23327	0.022000	0.10575	-0.429000	0.06982	0.048000	0.15891	-0.251000	0.11542	CCT	G|0.982;C|0.018	0.018	strong		0.607	PLA2G4E-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252738.2	NM_198442	Missense_Mutation	C	42289456	G	C	42289456	5	2	22	1	0	0	0	0	0	0	1	0	12014	1246	43	4	1670	4	PLA2G4E	15	42289456	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	110032	42289456	60241936	3007	5908											
PLA2G4F	255189	hgsc.bcm.edu	37	chr15	42434905	42434905	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggcagtacttctctgtcatcTtcaagacctgagcaggagca	10	10	10	11	0	4	2	2	1	2	1	5	3	4	3	1	2	3	4	1	2	2	3	rs144100358	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42434905T>C	ENST00000382396.4	-	19	2236	c.2150A>G	c.(2149-2151)aAg>aGg	p.K717R	PLA2G4F_ENST00000397272.3_Missense_Mutation_p.K719R			Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	717	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)		CTCTGTCATCTTCAAGACCTG	0.607													T|||	38	0.00758786	0.028	0.0014	5008	,	,		15524	0.0		0.0	False		,,,				2504	0.0				p.K717R		Atlas-SNP	.											.	PLA2G4F	75	.	0			c.A2150G						PASS	.	T	ARG/LYS	97,4309	78.3+/-116.7	5,87,2111	70	58	62		2150	3.5	1	15	dbSNP_134	62	1,8597	1.2+/-3.3	0,1,4298	yes	missense	PLA2G4F	NM_213600.3	26	5,88,6409	CC,CT,TT		0.0116,2.2015,0.7536	benign	717/850	42434905	98,12906	2203	4299	6502	SO:0001583	missense	255189	exon19			GTCATCTTCAAGA		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.2150A>G	15.37:g.42434905T>C	ENSP00000371833:p.Lys717Arg	97	0	0		114	67	0.587719	NM_213600	Q6ZMC8	Missense_Mutation	SNP	ENST00000382396.4	37	CCDS32204.1	15	0.006868131868131868	14	0.028455284552845527	1	0.0027624309392265192	0	0.0	0	0.0	T	11.00	1.510289	0.27036	0.022015	1.16E-4	ENSG00000168907	ENST00000290497;ENST00000397272;ENST00000382396;ENST00000443825	T;T	0.11821	2.74;2.74	4.69	3.53	0.40419	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	0.502059	0.18373	N	0.143181	T	0.02304	0.0071	N	0.12887	0.27	0.23611	N	0.997295	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.08055	0.001;0.003;0.001	T	0.32052	-0.9921	10	0.30854	T	0.27	-12.5606	10.4046	0.44249	0.0:0.0796:0.0:0.9204	.	504;719;717	A2RRC4;C9J281;Q68DD2	.;.;PA24F_HUMAN	R	713;719;717;717	ENSP00000380442:K719R;ENSP00000371833:K717R	ENSP00000290497:K713R	K	-	2	0	PLA2G4F	40222197	0.787000	0.28750	0.998000	0.56505	0.446000	0.32137	3.246000	0.51414	0.908000	0.36671	0.482000	0.46254	AAG	T|0.992;C|0.008	0.008	strong		0.607	PLA2G4F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000420463.1	NM_213600		C	42434905	T	C	42434905	3	2	22	1	0	0	0	0	1	0	0	0	12015	1609	56	3	407	3	PLA2G4F	15	42434905	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	145449	42434905	60096487	3008	5909											
PLA2G4F	255189	hgsc.bcm.edu	37	chr15	42438380	42438380	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ttgacactggtgtaaatgggGtaagggttctgaccctggcg	8	11	15	7	1	1	2	0	2	1	0	1	2	1	2	1	5	0	3	1	5	3	4	rs80108792	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42438380G>A	ENST00000382396.4	-	14	1565	c.1479C>T	c.(1477-1479)taC>taT	p.Y493Y	PLA2G4F_ENST00000397272.3_Silent_p.Y495Y			Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	493	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)		TGTAAATGGGGTAAGGGTTCT	0.582													G|||	69	0.013778	0.0507	0.0014	5008	,	,		20601	0.0		0.001	False		,,,				2504	0.0				p.Y493Y		Atlas-SNP	.											.	PLA2G4F	75	.	0			c.C1479T						PASS	.	G		155,4251	105.6+/-144.1	4,147,2052	100	89	92		1479	-2	1	15	dbSNP_132	92	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	PLA2G4F	NM_213600.3		4,148,6350	AA,AG,GG		0.0116,3.5179,1.1996		493/850	42438380	156,12848	2203	4299	6502	SO:0001819	synonymous_variant	255189	exon14			AATGGGGTAAGGG		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.1479C>T	15.37:g.42438380G>A		109	0	0		90	47	0.522222	NM_213600	Q6ZMC8	Silent	SNP	ENST00000382396.4	37	CCDS32204.1																																																																																			G|0.988;A|0.012	0.012	strong		0.582	PLA2G4F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000420463.1	NM_213600		A	42438380	G	A	42438380	2	1	22	1	0	0	0	0	0	0	0	1	12015	1256	44	2		2	PLA2G4F	15	42438380	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3475	42438380	60093012	3009	5910											
GANC	2595	hgsc.bcm.edu	37	chr15	42585099	42585099	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatactttgagcatctacagAttcttcacaaacaaaggtat	15	13	5	8	0	3	2	1	1	2	1	3	2	3	2	0	1	4	2	0	1	6	7	rs16973015	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42585099A>G	ENST00000318010.8	+	5	736	c.496A>G	c.(496-498)Att>Gtt	p.I166V	GANC_ENST00000566442.1_Missense_Mutation_p.I166V	NM_198141.2	NP_937784.2	Q8TET4	GANC_HUMAN	glucosidase, alpha; neutral C	166			I -> V (in dbSNP:rs16973015).		carbohydrate metabolic process (GO:0005975)		alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|maltose alpha-glucosidase activity (GO:0032450)			breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		all_cancers(109;3.08e-16)|all_epithelial(112;7.48e-15)|Lung NSC(122;3.08e-09)|all_lung(180;1.48e-08)|Melanoma(134;0.0574)|Colorectal(260;0.153)		GBM - Glioblastoma multiforme(94;1.06e-06)	Miglitol(DB00491)	GCATCTACAGATTCTTCACAA	0.363													A|||	64	0.0127796	0.0212	0.0058	5008	,	,		20822	0.0		0.008	False		,,,				2504	0.0245				p.I166V		Atlas-SNP	.											.	GANC	57	.	0			c.A496G						PASS	.	A	VAL/ILE	63,4343	59.9+/-96.7	0,63,2140	128	123	125		496	0.4	0.9	15	dbSNP_123	125	39,8559	26.8+/-75.7	0,39,4260	yes	missense	GANC	NM_198141.2	29	0,102,6400	GG,GA,AA		0.4536,1.4299,0.7844	benign	166/915	42585099	102,12902	2203	4299	6502	SO:0001583	missense	2595	exon5			CTACAGATTCTTC	AF545045	CCDS10084.1	15q15.2	2012-10-02			ENSG00000214013	ENSG00000214013	3.2.1.20		4139	protein-coding gene	gene with protein product		104180				6995030, 12370436	Standard	NM_198141		Approved		uc001zpi.3	Q8TET4	OTTHUMG00000130487	ENST00000318010.8:c.496A>G	15.37:g.42585099A>G	ENSP00000326227:p.Ile166Val	177	0	0		170	99	0.582353	NM_198141	Q52LQ4|Q8IWZ0|Q8IZM4|Q8IZM5	Missense_Mutation	SNP	ENST00000318010.8	37	CCDS10084.1	22	0.010073260073260074	13	0.026422764227642278	4	0.011049723756906077	0	0.0	5	0.006596306068601583	A	2.471	-0.321955	0.05386	0.014299	0.004536	ENSG00000214013	ENST00000318010	T	0.15487	2.42	5.27	0.387	0.16259	Glycoside hydrolase-type carbohydrate-binding (1);	1.002620	0.08037	N	0.994447	T	0.02342	0.0072	N	0.08118	0	0.19575	N	0.999961	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40553	-0.9557	10	0.25106	T	0.35	-0.2169	5.5278	0.16967	0.4019:0.2069:0.3911:0.0	rs16973015;rs52796001;rs16973015	166;166	Q8TET4;Q2M2A3	GANC_HUMAN;.	V	166	ENSP00000326227:I166V	ENSP00000326227:I166V	I	+	1	0	GANC	40372391	0.078000	0.21339	0.939000	0.37840	0.098000	0.18820	0.247000	0.18179	-0.089000	0.12484	0.528000	0.53228	ATT	A|0.989;G|0.011	0.011	strong		0.363	GANC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252887.2	NM_198141		G	42585099	A	G	42585099	3	3	22	1	0	0	0	0	1	0	0	0	6242	333	12	3	514	3	GANC	15	42585099	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	146719	42585099	59946293	3010	5911											
GANC	2595	hgsc.bcm.edu	37	chr15	42644235	42644235	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcttgctatttagatggtaaAgatcagcctgtggcttttac	9	16	9	7	0	2	2	1	0	1	2	2	2	2	2	1	2	3	3	1	2	5	7	rs145163630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42644235A>G	ENST00000318010.8	+	24	2883	c.2643A>G	c.(2641-2643)aaA>aaG	p.K881K	CAPN3_ENST00000356316.3_5'UTR|RP11-164J13.1_ENST00000495723.1_RNA	NM_198141.2	NP_937784.2	Q8TET4	GANC_HUMAN	glucosidase, alpha; neutral C	881					carbohydrate metabolic process (GO:0005975)		alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|maltose alpha-glucosidase activity (GO:0032450)			breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		all_cancers(109;3.08e-16)|all_epithelial(112;7.48e-15)|Lung NSC(122;3.08e-09)|all_lung(180;1.48e-08)|Melanoma(134;0.0574)|Colorectal(260;0.153)		GBM - Glioblastoma multiforme(94;1.06e-06)	Miglitol(DB00491)	TAGATGGTAAAGATCAGCCTG	0.408													A|||	2	0.000399361	0.0015	0.0	5008	,	,		19780	0.0		0.0	False		,,,				2504	0.0				p.K881K		Atlas-SNP	.											.	GANC	57	.	0			c.A2643G						PASS	.	A		12,4394	16.8+/-37.8	0,12,2191	134	117	123		2643	1.8	0.2	15	dbSNP_134	123	0,8598		0,0,4299	no	coding-synonymous	GANC	NM_198141.2		0,12,6490	GG,GA,AA		0.0,0.2724,0.0923		881/915	42644235	12,12992	2203	4299	6502	SO:0001819	synonymous_variant	2595	exon24			TGGTAAAGATCAG	AF545045	CCDS10084.1	15q15.2	2012-10-02			ENSG00000214013	ENSG00000214013	3.2.1.20		4139	protein-coding gene	gene with protein product		104180				6995030, 12370436	Standard	NM_198141		Approved		uc001zpi.3	Q8TET4	OTTHUMG00000130487	ENST00000318010.8:c.2643A>G	15.37:g.42644235A>G		141	0	0		192	85	0.442708	NM_198141	Q52LQ4|Q8IWZ0|Q8IZM4|Q8IZM5	Silent	SNP	ENST00000318010.8	37	CCDS10084.1																																																																																			A|0.999;G|0.001	0.001	strong		0.408	GANC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252887.2	NM_198141		G	42644235	A	G	42644235	2	3	22	1	0	0	0	0	0	0	0	1	6242	69	3	3		3	GANC	15	42644235	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	59136	42644235	59887157	3011	5912											
CAPN3	825	hgsc.bcm.edu	37	chr15	42680058	42680058	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccgcaatgagttctggagTgctctgctggagaaggctta	9	10	13	9	1	2	2	0	1	2	1	2	4	2	3	1	3	2	5	1	3	3	2	rs17593	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42680058T>C	ENST00000397163.3	+	4	825	c.606T>C	c.(604-606)agT>agC	p.S202S	CAPN3_ENST00000349748.3_Silent_p.S202S|CAPN3_ENST00000356316.3_Silent_p.S115S|CAPN3_ENST00000357568.3_Silent_p.S202S|CAPN3_ENST00000318023.7_Silent_p.S202S|RP11-164J13.1_ENST00000495723.1_RNA	NM_000070.2	NP_000061.1	P20807	CAN3_HUMAN	calpain 3, (p94)	202	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.		Missing (in LGMD2A). {ECO:0000269|PubMed:9452114}.		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)		AGTTCTGGAGTGCTCTGCTGG	0.498													C|||	321	0.0640974	0.2095	0.0159	5008	,	,		22401	0.0		0.0089	False		,,,				2504	0.0245				p.S202S		Atlas-SNP	.											.	CAPN3	172	.	0			c.T606C						PASS	.	C	,,	698,3708	761.2+/-413.0	49,600,1554	192	164	174		606,606,606	-4.9	0.8	15	dbSNP_63	174	38,8560	817.5+/-406.9	0,38,4261	no	coding-synonymous,coding-synonymous,coding-synonymous	CAPN3	NM_000070.2,NM_024344.1,NM_173087.1	,,	49,638,5815	CC,CT,TT		0.442,15.842,5.6598	,,	202/822,202/816,202/730	42680058	736,12268	2203	4299	6502	SO:0001819	synonymous_variant	825	exon4			CTGGAGTGCTCTG	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.606T>C	15.37:g.42680058T>C		159	1	0.00628931		163	163	1	NM_000070	A6H8K6|Q7L4R0|Q9BQC8|Q9BTU4|Q9Y5S6|Q9Y5S7	Silent	SNP	ENST00000397163.3	37	CCDS45245.1																																																																																			T|0.944;C|0.056	0.056	strong		0.498	CAPN3-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421075.1			C	42680058	T	C	42680058	2	2	22	1	0	0	0	0	0	0	0	1	2630	1693	59	3		3	CAPN3	15	42680058	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	35823	42680058	59851334	3012	5913											
CDAN1	146059	hgsc.bcm.edu	37	chr15	43028207	43028207	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	attgggggtgaggtgaagcaGgtcttgggcttggagagtga	8	10	20	3	0	1	4	0	3	1	1	1	5	1	4	0	6	1	2	0	6	1	3	rs143391538	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:43028207G>C	ENST00000356231.3	-	3	662	c.639C>G	c.(637-639)acC>acG	p.T213T		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	213					chromatin assembly (GO:0031497)|chromatin organization (GO:0006325)|negative regulation of DNA replication (GO:0008156)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	24		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		AGGTGAAGCAGGTCTTGGGCT	0.592													G|||	10	0.00199681	0.0076	0.0	5008	,	,		16376	0.0		0.0	False		,,,				2504	0.0				p.T213T		Atlas-SNP	.											.	CDAN1	70	.	0			c.C639G						PASS	.	G		15,4391	22.3+/-47.3	0,15,2188	107	124	118		639	-0.6	1	15	dbSNP_134	118	0,8598		0,0,4299	no	coding-synonymous	CDAN1	NM_138477.2		0,15,6487	CC,CG,GG		0.0,0.3404,0.1153		213/1228	43028207	15,12989	2203	4299	6502	SO:0001819	synonymous_variant	146059	exon3			GAAGCAGGTCTTG	AF525398	CCDS32209.1	15q15.2	2012-04-25	2012-04-25			ENSG00000140326			1713	protein-coding gene	gene with protein product		607465	"congenital dyserythropoietic anemia, type I"			8634422, 12434312	Standard	XM_005254177		Approved	CDA-I, CDAI	uc001zql.3	Q8IWY9		ENST00000356231.3:c.639C>G	15.37:g.43028207G>C		184	0	0		166	83	0.5	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Silent	SNP	ENST00000356231.3	37	CCDS32209.1																																																																																			G|0.998;C|0.002	0.002	strong		0.592	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300		C	43028207	G	C	43028207	2	2	22	1	0	0	0	0	0	0	0	1	3056	987	35	4		4	CDAN1	15	43028207	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	348149	43028207	59503185	3013	5914											
ZSCAN29	146050	hgsc.bcm.edu	37	chr15	43658416	43658418	+	In_Frame_Del	DEL	CCT	CCT	-																															agccacagcctcttctgctcCctcctcatgctgccagcccc																								rs377169169|rs151154169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:43658416_43658418delCCT	ENST00000396976.2	-	3	1246_1248	c.1112_1114delAGG	c.(1111-1116)gaggga>gga	p.E371del	ZSCAN29_ENST00000568898.1_Intron|ZSCAN29_ENST00000562072.1_In_Frame_Del_p.E370del|ZSCAN29_ENST00000396972.1_Intron	NM_152455.3	NP_689668.3	Q8IWY8	ZSC29_HUMAN	zinc finger and SCAN domain containing 29	371					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)		TCTTCTGCTCCCTCCTCATGCTG	0.601														118	0.0235623	0.0855	0.0058	5008	,	,		18099	0.0		0.001	False		,,,				2504	0.0				p.371_372del		Pindel,Atlas-Indel	.											.	ZSCAN29	57	.	0			c.1113_1115del						PASS	.			330,3934		28,274,1830						-9	0		dbSNP_119	68	3,8251		0,3,4124	no	coding	ZSCAN29	NM_152455.3		28,277,5954	A1A1,A1R,RR		0.0363,7.7392,2.6602				333,12185				SO:0001651	inframe_deletion	146050	exon3			.	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.1112_1114delAGG	15.37:g.43658419_43658421delCCT	ENSP00000380174:p.Glu371del	61	0	.		74	25	0.338	NM_152455	B3KVB9|Q32M75|Q32M76|Q8NA40	In_Frame_Del	DEL	ENST00000396976.2	37	CCDS10095.2																																																																																			CCT|0.977;-|0.023	0.023	strong		0.601	ZSCAN29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253278.1	NM_152455		-	43658418	CCT	-	43658416	7	5	22	1	0	1	0	1	0	0	0	0	18251	632	22	0	1456	0	ZSCAN29	15	43658416	In_Frame_Del	DEL	CCT	TCGA-G8-6324-01A-11D-2210-10	630209	43658416	58872976	3014	5915											
C15orf43	145645	hgsc.bcm.edu	37	chr15	45250685	45250685	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggctttgggtcatttcatTcttcctcctgcgtgcctgca	3	16	10	12	1	3	0	2	0	1	0	5	0	5	0	3	2	3	2	3	2	0	4	rs147135555	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:45250685T>G	ENST00000340827.3	+	3	278	c.261T>G	c.(259-261)atT>atG	p.I87M		NM_152448.2	NP_689661.1	Q8NHR7	CO043_HUMAN	chromosome 15 open reading frame 43	87										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)		GTCATTTCATTCTTCCTCCTG	0.408													T|||	18	0.00359425	0.0136	0.0	5008	,	,		18466	0.0		0.0	False		,,,				2504	0.0				p.I87M		Atlas-SNP	.											.	C15orf43	19	.	0			c.T261G						PASS	.	T	MET/ILE	52,4344	52.3+/-87.9	1,50,2147	79	74	75		261	-2.2	1	15	dbSNP_134	75	0,8596		0,0,4298	yes	missense	C15orf43	NM_152448.1	10	1,50,6445	GG,GT,TT		0.0,1.1829,0.4002	benign	87/221	45250685	52,12940	2198	4298	6496	SO:0001583	missense	145645	exon3			TTTCATTCTTCCT	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.261T>G	15.37:g.45250685T>G	ENSP00000340644:p.Ile87Met	98	0	0		132	63	0.477273	NM_152448		Missense_Mutation	SNP	ENST00000340827.3	37	CCDS10115.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	t	12.26	1.883358	0.33255	0.011829	0.0	ENSG00000167014	ENST00000340827	T	0.55234	0.53	4.45	-2.18	0.07037	.	0.349419	0.23496	N	0.047553	T	0.21881	0.0527	N	0.19112	0.55	0.22185	N	0.999309	B	0.15141	0.012	B	0.13407	0.009	T	0.08513	-1.0718	10	0.52906	T	0.07	.	5.0719	0.14611	0.0:0.4003:0.1728:0.4268	.	87	Q8NHR7	CO043_HUMAN	M	87	ENSP00000340644:I87M	ENSP00000340644:I87M	I	+	3	3	C15orf43	43037977	0.971000	0.33674	0.971000	0.41717	0.977000	0.68977	0.016000	0.13377	-0.254000	0.09500	0.523000	0.50628	ATT	T|0.997;G|0.003	0.003	strong		0.408	C15orf43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254032.1	NM_152448		G	45250685	T	G	45250685	3	3	22	1	0	0	0	0	1	0	0	0	1799	1771	62	5	271	5	C15orf43	15	45250685	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1592269	45250685	57280707	3015	5916											
DUOX2	50506	hgsc.bcm.edu	37	chr15	45392382	45392382	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaagcctcgctgcatcttcTcttgcagcgcctctgtgtac	5	12	10	14	2	3	0	0	0	3	0	5	1	3	1	2	1	5	4	2	1	2	3	rs79393107	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:45392382T>C	ENST00000603300.1	-	24	3252	c.3050A>G	c.(3049-3051)gAg>gGg	p.E1017G	DUOX2_ENST00000389039.6_Missense_Mutation_p.E1017G	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	1017	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)		CTGCATCTTCTCTTGCAGCGC	0.602													T|||	183	0.0365415	0.1293	0.0173	5008	,	,		20832	0.0		0.0	False		,,,				2504	0.0				p.E1017G		Atlas-SNP	.											.	DUOX2	137	.	0			c.A3050G						PASS	.	T	GLY/GLU	524,3872	240.6+/-251.3	40,444,1714	78	68	72		3050	5.4	1	15	dbSNP_131	72	3,8593	3.0+/-9.4	0,3,4295	yes	missense	DUOX2	NM_014080.4	98	40,447,6009	CC,CT,TT		0.0349,11.9199,4.0563	probably-damaging	1017/1549	45392382	527,12465	2198	4298	6496	SO:0001583	missense	50506	exon24			ATCTTCTCTTGCA	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.3050A>G	15.37:g.45392382T>C	ENSP00000475084:p.Glu1017Gly	95	0	0		79	31	0.392405	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Missense_Mutation	SNP	ENST00000603300.1	37	CCDS10117.1	58	0.026556776556776556	51	0.10365853658536585	7	0.019337016574585635	0	0.0	0	0.0	T	25.5	4.644005	0.87859	0.119199	3.49E-4	ENSG00000140279	ENST00000389039	.	.	.	5.45	5.45	0.79879	.	0.105054	0.64402	D	0.000003	T	0.02727	0.0082	M	0.76328	2.33	0.58432	D	0.999998	D	0.52996	0.957	P	0.52823	0.71	T	0.06698	-1.0812	9	0.34782	T	0.22	-29.5989	14.7059	0.69189	0.0:0.0:0.0:1.0	.	1017	Q9NRD8	DUOX2_HUMAN	G	1017	.	ENSP00000373691:E1017G	E	-	2	0	DUOX2	43179674	1.000000	0.71417	1.000000	0.80357	0.779000	0.44077	3.726000	0.54977	2.080000	0.62538	0.460000	0.39030	GAG	T|0.960;C|0.040	0.040	strong		0.602	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080		C	45392382	T	C	45392382	3	2	22	1	0	0	0	0	1	0	0	0	4803	1551	54	3	1640	3	DUOX2	15	45392382	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	141697	45392382	57139010	3016	5917											
DUOX1	53905	hgsc.bcm.edu	37	chr15	45427345	45427345	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgagcgtggaaactcccggCtgccccgccgagttcctcaa	7	7	12	15	4	1	1	1	1	0	0	3	3	3	2	5	2	3	2	5	2	2	1	rs78022423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:45427345C>T	ENST00000321429.4	+	6	758	c.351C>T	c.(349-351)ggC>ggT	p.G117G	DUOX1_ENST00000389037.3_Silent_p.G117G	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	117	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)		AAACTCCCGGCTGCCCCGCCG	0.647													C|||	111	0.0221645	0.0809	0.0058	5008	,	,		15061	0.0		0.0	False		,,,				2504	0.0				p.G117G		Atlas-SNP	.											.	DUOX1	125	.	0			c.C351T						PASS	.	C	,	295,4099	160.0+/-192.4	11,273,1913	48	48	48		351,351	2.1	1	15	dbSNP_131	48	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous	DUOX1	NM_017434.3,NM_175940.1	,	11,273,6211	TT,TC,CC		0.0,6.7137,2.271	,	117/1552,117/1552	45427345	295,12695	2197	4298	6495	SO:0001819	synonymous_variant	53905	exon6			TCCCGGCTGCCCC	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.351C>T	15.37:g.45427345C>T		170	0	0		206	95	0.461165	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Silent	SNP	ENST00000321429.4	37	CCDS32221.1																																																																																			C|0.976;T|0.024	0.024	strong		0.647	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434		T	45427345	C	T	45427345	2	4	22	1	0	0	0	0	0	0	0	1	4802	784	28	2		2	DUOX1	15	45427345	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	34963	45427345	57104047	3017	5918											
DUOX1	53905	hgsc.bcm.edu	37	chr15	45444572	45444572	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggcacagcagccagcatctcTttcatgttctcctacatctt	8	13	6	14	0	4	0	1	0	3	0	6	0	4	0	2	1	4	4	2	1	1	4	rs114272662	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:45444572T>C	ENST00000321429.4	+	26	3689	c.3282T>C	c.(3280-3282)tcT>tcC	p.S1094S	CTD-2651B20.1_ENST00000558039.1_lincRNA|DUOX1_ENST00000389037.3_Silent_p.S1094S|DUOX1_ENST00000561166.1_Silent_p.S740S	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	1094	Ferric oxidoreductase.|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)		CCAGCATCTCTTTCATGTTCT	0.602													T|||	137	0.0273562	0.0976	0.0086	5008	,	,		20873	0.0		0.002	False		,,,				2504	0.0				p.S1094S		Atlas-SNP	.											.	DUOX1	125	.	0			c.T3282C						PASS	.	T	,	415,3981	202.1+/-225.0	17,381,1800	212	155	174		3282,3282	2.2	1	15	dbSNP_132	174	7,8589	5.0+/-18.6	0,7,4291	no	coding-synonymous,coding-synonymous	DUOX1	NM_017434.3,NM_175940.1	,	17,388,6091	CC,CT,TT		0.0814,9.4404,3.2482	,	1094/1552,1094/1552	45444572	422,12570	2198	4298	6496	SO:0001819	synonymous_variant	53905	exon26			CATCTCTTTCATG	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.3282T>C	15.37:g.45444572T>C		194	1	0.00515464		219	116	0.52968	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Silent	SNP	ENST00000321429.4	37	CCDS32221.1																																																																																			T|0.968;C|0.032	0.032	strong		0.602	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434		C	45444572	T	C	45444572	2	2	22	1	0	0	0	0	0	0	0	1	4802	1596	56	3		3	DUOX1	15	45444572	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	17227	45444572	57086820	3018	5919											
SLC28A2	9153	hgsc.bcm.edu	37	chr15	45556163	45556163	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagagcagctgatccccttTgcaggaatctgcatgttcat	9	11	9	12	0	2	2	1	1	1	1	3	3	3	3	3	1	4	5	3	1	1	2	rs8023604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:45556163T>C	ENST00000347644.3	+	6	596	c.531T>C	c.(529-531)ttT>ttC	p.F177F	CTD-2651B20.3_ENST00000560344.1_RNA|CTD-2651B20.3_ENST00000561404.1_RNA	NM_004212.3	NP_004203.2	O43868	S28A2_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 2	177					nucleobase-containing compound metabolic process (GO:0006139)|purine nucleoside transmembrane transport (GO:0015860)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside:sodium symporter activity (GO:0005415)|purine nucleoside transmembrane transporter activity (GO:0015211)			NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(4)|skin(1)	26		all_cancers(109;8.53e-07)|all_epithelial(112;1.39e-05)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.77e-16)|GBM - Glioblastoma multiforme(94;2.71e-06)	Mercaptopurine(DB01033)	TGATCCCCTTTGCAGGAATCT	0.507													C|||	866	0.172923	0.5734	0.0533	5008	,	,		19479	0.0		0.002	False		,,,				2504	0.0706				p.F177F	NSCLC(92;493 1501 26361 28917 47116)	Atlas-SNP	.											.	SLC28A2	64	.	0			c.T531C						PASS	.	C		2273,2123	578.0+/-384.6	611,1051,536	196	159	171		531	-6.4	0.5	15	dbSNP_116	171	13,8583	818.5+/-406.9	0,13,4285	no	coding-synonymous	SLC28A2	NM_004212.3		611,1064,4821	CC,CT,TT		0.1512,48.2939,17.5954		177/659	45556163	2286,10706	2198	4298	6496	SO:0001819	synonymous_variant	9153	exon6			CCCCTTTGCAGGA	U84392	CCDS10121.1	15q15	2013-07-17	2013-07-17		ENSG00000137860	ENSG00000137860		"Solute carriers"	11002	protein-coding gene	gene with protein product		606208	"solute carrier family 28 (sodium-coupled nucleoside transporter), member 2"			9435697	Standard	NM_004212		Approved	CNT2, SPNT1, HCNT2, HsT17153	uc001zva.2	O43868	OTTHUMG00000131426	ENST00000347644.3:c.531T>C	15.37:g.45556163T>C		189	0	0		177	82	0.463277	NM_004212	A8K7F9|O43239|Q52LZ0	Silent	SNP	ENST00000347644.3	37	CCDS10121.1																																																																																			T|0.841;C|0.159	0.159	strong		0.507	SLC28A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254219.2	NM_004212		C	45556163	T	C	45556163	2	2	22	1	0	0	0	0	0	0	0	1	14547	1809	63	3		3	SLC28A2	15	45556163	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	111591	45556163	56975229	3019	5920											
SPATA5L1	79029	hgsc.bcm.edu	37	chr15	45695612	45695612	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggcccaggtgttgacgctgCtggacggcgccagtggggac	5	7	18	11	3	0	1	0	1	0	0	0	3	0	3	2	6	1	3	2	6	0	1	rs1346265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:45695612C>T	ENST00000305560.6	+	1	1084	c.985C>T	c.(985-987)Ctg>Ttg	p.L329L	SPATA5L1_ENST00000559860.1_Silent_p.L329L|GATM_ENST00000458245.5_5'Flank	NM_024063.2	NP_076968.2	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	329						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)		GTTGACGCTGCTGGACGGCGC	0.687													C|||	803	0.160343	0.528	0.0476	5008	,	,		14072	0.0079		0.002	False		,,,				2504	0.0634				p.L329L		Atlas-SNP	.											.	SPATA5L1	40	.	0			c.C985T						PASS	.	C		1987,2399		467,1053,673	21	26	24		985	1.4	1	15	dbSNP_88	24	12,8564		0,12,4276	no	coding-synonymous	SPATA5L1	NM_024063.2		467,1065,4949	TT,TC,CC		0.1399,45.3032,15.422		329/754	45695612	1999,10963	2193	4288	6481	SO:0001819	synonymous_variant	79029	exon1			ACGCTGCTGGACG	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.985C>T	15.37:g.45695612C>T		62	0	0		79	35	0.443038	NM_024063	C9JHR5|Q9H8W7|Q9HA41	Silent	SNP	ENST00000305560.6	37	CCDS10123.1																																																																																			C|0.860;T|0.140	0.140	strong		0.687	SPATA5L1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254218.1	NM_024063		T	45695612	C	T	45695612	2	4	22	1	0	0	0	0	0	0	0	1	15027	796	28	2		2	SPATA5L1	15	45695612	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	139449	45695612	56835780	3020	5921											
FBN1	2200	hgsc.bcm.edu	37	chr15	48734008	48734008	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttactgcatgtgcccagggCacaaatttctggctcttcga	8	12	10	11	1	2	0	0	0	2	0	3	1	2	0	1	2	3	4	1	2	2	3	rs113577372	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:48734008C>A	ENST00000316623.5	-	50	6528	c.6073G>T	c.(6073-6075)Gcc>Tcc	p.A2025S		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	2025	EGF-like 35; 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)		GTGCCCAGGGCACAAATTTCT	0.448													C|||	10	0.00199681	0.0076	0.0	5008	,	,		19650	0.0		0.0	False		,,,				2504	0.0				p.A2025S		Atlas-SNP	.											.	FBN1	310	.	0			c.G6073T						PASS	.	C	SER/ALA	21,4375	29.0+/-57.7	0,21,2177	137	135	136		6073	5.9	1	15	dbSNP_132	136	0,8592		0,0,4296	yes	missense	FBN1	NM_000138.4	99	0,21,6473	AA,AC,CC		0.0,0.4777,0.1617	possibly-damaging	2025/2872	48734008	21,12967	2198	4296	6494	SO:0001583	missense	2200	exon50			CCAGGGCACAAAT	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.6073G>T	15.37:g.48734008C>A	ENSP00000325527:p.Ala2025Ser	59	0	0		68	34	0.5	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	37	CCDS32232.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	C	12.59	1.982249	0.34942	0.004777	0.0	ENSG00000166147	ENST00000316623;ENST00000389087;ENST00000544030	D	0.91996	-2.95	5.94	5.94	0.96194	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.098253	0.64402	D	0.000001	T	0.77552	0.4147	N	0.01800	-0.715	0.80722	D	1	B	0.25850	0.136	B	0.29942	0.109	T	0.76753	-0.2843	10	0.17832	T	0.49	.	19.9452	0.97179	0.0:1.0:0.0:0.0	.	2025	P35555	FBN1_HUMAN	S	2025;593;915	ENSP00000325527:A2025S	ENSP00000325527:A2025S	A	-	1	0	FBN1	46521300	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.864000	0.39469	2.807000	0.96579	0.650000	0.86243	GCC	C|0.998;A|0.002	0.002	strong		0.448	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1			A	48734008	C	A	48734008	3	1	22	1	0	0	0	0	1	0	0	0	5710	710	25	4	2610	4	FBN1	15	48734008	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3038396	48734008	53797384	3021	5922											
GALK2	2585	hgsc.bcm.edu	37	chr15	49574223	49574223	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgccaagagtgagcgttacAttggcactgaaggaggaggc	11	7	16	7	1	0	3	0	2	0	1	0	5	0	5	1	4	3	2	1	4	3	2	rs35507772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:49574223A>G	ENST00000560031.1	+	6	851	c.544A>G	c.(544-546)Att>Gtt	p.I182V	GALK2_ENST00000561014.1_3'UTR|GALK2_ENST00000559454.1_Missense_Mutation_p.I158V|GALK2_ENST00000327171.3_Missense_Mutation_p.I171V|GALK2_ENST00000544523.1_Missense_Mutation_p.I158V|GALK2_ENST00000396509.2_Missense_Mutation_p.I158V|GALK2_ENST00000543495.1_Missense_Mutation_p.I53V			Q01415	GALK2_HUMAN	galactokinase 2	182			I -> V (in dbSNP:rs35507772).		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)		TGAGCGTTACATTGGCACTGA	0.418													A|||	31	0.0061901	0.0227	0.0014	5008	,	,		20552	0.0		0.0	False		,,,				2504	0.0				p.I182V		Atlas-SNP	.											.	GALK2	78	.	0			c.A544G						PASS	.	A	VAL/ILE,VAL/ILE	85,4307	72.0+/-110.0	0,85,2111	132	124	126		511,544	5.8	1	15	dbSNP_126	126	0,8590		0,0,4295	yes	missense,missense	GALK2	NM_001001556.1,NM_002044.2	29,29	0,85,6406	GG,GA,AA		0.0,1.9353,0.6548	benign,benign	171/448,182/459	49574223	85,12897	2196	4295	6491	SO:0001583	missense	2585	exon6			CGTTACATTGGCA		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.544A>G	15.37:g.49574223A>G	ENSP00000453129:p.Ile182Val	133	0	0		134	75	0.559702	NM_002044	Q7Z4Q4	Missense_Mutation	SNP	ENST00000560031.1	37	CCDS42034.1	18	0.008241758241758242	17	0.034552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	A	17.89	3.500334	0.64298	0.019353	0.0	ENSG00000156958	ENST00000327171;ENST00000396509;ENST00000543495;ENST00000544523	D;D;D	0.86562	-2.14;-2.14;-2.14	5.79	5.79	0.91817	Ribosomal protein S5 domain 2-type fold (1);GHMP kinase (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);	0.043082	0.85682	D	0.000000	T	0.62245	0.2412	N	0.11870	0.19	0.80722	D	1	B;B	0.32382	0.368;0.174	B;B	0.42062	0.374;0.213	T	0.72047	-0.4408	10	0.15499	T	0.54	-14.2408	16.1193	0.81336	1.0:0.0:0.0:0.0	rs35507772	182;171	Q01415;Q7Z4Q4	GALK2_HUMAN;.	V	171;182;53;158	ENSP00000316632:I171V;ENSP00000443220:I53V;ENSP00000440312:I158V	ENSP00000316632:I171V	I	+	1	0	GALK2	47361515	1.000000	0.71417	0.999000	0.59377	0.968000	0.65278	5.983000	0.70540	2.201000	0.70794	0.533000	0.62120	ATT	A|0.992;G|0.008	0.008	strong		0.418	GALK2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417854.1			G	49574223	A	G	49574223	3	3	22	1	0	0	0	0	1	0	0	0	6212	217	8	3	590	3	GALK2	15	49574223	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	840215	49574223	52957169	3022	5923											
HDC	3067	hgsc.bcm.edu	37	chr15	50534789	50534789	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atctggggcctcttctgaaaAgcagtcatcaactgggtcca	10	10	10	11	0	5	1	2	1	3	0	6	1	6	1	2	3	2	1	2	3	3	1	rs16963486	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:50534789A>G	ENST00000267845.3	-	12	2059	c.1657T>C	c.(1657-1659)Ttt>Ctt	p.F553L	HDC_ENST00000543581.1_Missense_Mutation_p.F520L|RN7SL494P_ENST00000461517.2_RNA	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)		TCTTCTGAAAAGCAGTCATCA	0.537													A|||	105	0.0209665	0.0764	0.0058	5008	,	,		20285	0.0		0.0	False		,,,				2504	0.0				p.F553L	GBM(95;1627 1936 6910 9570)	Atlas-SNP	.											.	HDC	86	.	0			c.T1657C						PASS	.	A	LEU/PHE	319,4073	168.3+/-199.2	11,297,1888	87	88	88		1657	5.7	1	15	dbSNP_123	88	1,8589	1.2+/-3.3	0,1,4294	yes	missense	HDC	NM_002112.3	22	11,298,6182	GG,GA,AA		0.0116,7.2632,2.465	probably-damaging	553/663	50534789	320,12662	2196	4295	6491	SO:0001583	missense	3067	exon12			CTGAAAAGCAGTC		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.1657T>C	15.37:g.50534789A>G	ENSP00000267845:p.Phe553Leu	135	0	0		123	65	0.528455	NM_002112		Missense_Mutation	SNP	ENST00000267845.3	37	CCDS10134.1	44	0.020146520146520148	41	0.08333333333333333	3	0.008287292817679558	0	0.0	0	0.0	A	17.30	3.353885	0.61293	0.072632	1.16E-4	ENSG00000140287	ENST00000267845;ENST00000543581	T;T	0.14144	2.92;2.53	5.73	5.73	0.89815	.	0.365309	0.23805	N	0.044383	T	0.01061	0.0035	L	0.34521	1.04	0.43444	D	0.99562	D;D	0.67145	0.996;0.976	P;B	0.54759	0.76;0.446	T	0.00294	-1.1840	10	0.54805	T	0.06	-19.7657	16.0115	0.80406	1.0:0.0:0.0:0.0	rs16963486;rs52824591;rs16963486	520;553	B7ZM01;P19113	.;DCHS_HUMAN	L	553;520	ENSP00000267845:F553L;ENSP00000440252:F520L	ENSP00000267845:F553L	F	-	1	0	HDC	48322081	1.000000	0.71417	0.999000	0.59377	0.039000	0.13416	6.778000	0.75043	2.187000	0.69744	0.460000	0.39030	TTT	A|0.975;G|0.025	0.025	strong		0.537	HDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254540.1			G	50534789	A	G	50534789	3	3	22	1	0	0	0	0	1	0	0	0	7024	72	3	3	335	3	HDC	15	50534789	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	960566	50534789	51996603	3023	5924											
USP50	373509	hgsc.bcm.edu	37	chr15	50836846	50836846	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	accagcggcaagatgctgcaGagacactgtgagatggcatt	12	7	13	9	1	0	3	0	1	0	3	0	5	0	3	1	2	3	4	1	2	1	1	rs114737323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:50836846G>C	ENST00000532404.1	-	2	359	c.186C>G	c.(184-186)ctC>ctG	p.L62L	USP50_ENST00000530218.1_Intron	NM_203494.4	NP_987090.2	Q70EL3	UBP50_HUMAN	ubiquitin specific peptidase 50	62	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)		AGATGCTGCAGAGACACTGTG	0.537													G|||	166	0.033147	0.121	0.0086	5008	,	,		16271	0.0		0.0	False		,,,				2504	0.0				p.L62L		Atlas-SNP	.											.	USP50	24	.	0			c.C186G						PASS	.	G		364,3704		20,324,1690	55	58	57		186	1.7	1	15	dbSNP_132	57	2,8376		0,2,4187	no	coding-synonymous	USP50	NM_203494.4		20,326,5877	CC,CG,GG		0.0239,8.9479,2.9407		62/335	50836846	366,12080	2034	4189	6223	SO:0001819	synonymous_variant	373509	exon2			GCTGCAGAGACAC	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.186C>G	15.37:g.50836846G>C		53	0	0		86	43	0.5	NM_203494	E9PP86	Silent	SNP	ENST00000532404.1	37	CCDS53944.1																																																																																			G|0.957;C|0.043	0.043	strong		0.537	USP50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395249.1			C	50836846	G	C	50836846	2	2	22	1	0	0	0	0	0	0	0	1	17097	929	33	4		4	USP50	15	50836846	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	302057	50836846	51694546	3024	5925											
SPPL2A	84888	hgsc.bcm.edu	37	chr15	51023216	51023216	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	acatcatagaggaggagaagGcctagaagtatcacacatga	17	6	11	7	0	2	4	2	1	0	3	2	6	2	5	1	3	0	1	1	3	5	3	rs76947817	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:51023216G>C	ENST00000261854.5	-	10	1309	c.1035C>G	c.(1033-1035)ggC>ggG	p.G345G		NM_032802.3	NP_116191.2	Q8TCT8	SPP2A_HUMAN	signal peptide peptidase like 2A	345					membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|regulation of immune response (GO:0050776)	extracellular vesicular exosome (GO:0070062)|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)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15				all cancers(107;0.000712)|GBM - Glioblastoma multiforme(94;0.00314)		GGAGGAGAAGGCCTAGAAGTA	0.313													G|||	86	0.0171725	0.0635	0.0029	5008	,	,		15019	0.0		0.0	False		,,,				2504	0.0				p.G345G	Melanoma(50;790 1209 4069 22965 33125)	Atlas-SNP	.											.	SPPL2A	26	.	0			c.C1035G						PASS	.	G		240,4152	134.5+/-170.7	6,228,1962	64	60	61		1035	1.6	1	15	dbSNP_131	61	1,8575	1.2+/-3.3	0,1,4287	no	coding-synonymous	SPPL2A	NM_032802.3		6,229,6249	CC,CG,GG		0.0117,5.4645,1.8584		345/521	51023216	241,12727	2196	4288	6484	SO:0001819	synonymous_variant	84888	exon10			GAGAAGGCCTAGA		CCDS10138.1	15q21.2	2012-02-21			ENSG00000138600	ENSG00000138600			30227	protein-coding gene	gene with protein product	"intramembrane protease 3", "presenilin-like protein 2"	608238				12077416, 12139484	Standard	NM_032802		Approved	IMP3, PSL2	uc001zyv.3	Q8TCT8	OTTHUMG00000131647	ENST00000261854.5:c.1035C>G	15.37:g.51023216G>C		220	0	0		214	104	0.485981	NM_032802	B2RDS0|Q8TAW1|Q96SZ8	Silent	SNP	ENST00000261854.5	37	CCDS10138.1																																																																																			G|0.977;C|0.023	0.023	strong		0.313	SPPL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254543.3	NM_032802		C	51023216	G	C	51023216	2	2	22	1	0	0	0	0	0	0	0	1	15103	1190	42	4		4	SPPL2A	15	51023216	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	186370	51023216	51508176	3025	5926											
AP4E1	23431	hgsc.bcm.edu	37	chr15	51233881	51233881	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggactgaaggctcttacctAtgttatccaacaggatccta	12	11	8	10	0	1	1	0	1	1	0	3	3	3	3	3	3	2	2	3	3	6	4	rs58909326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:51233881A>G	ENST00000261842.5	+	10	1191	c.1085A>G	c.(1084-1086)tAt>tGt	p.Y362C	AP4E1_ENST00000560508.1_Missense_Mutation_p.Y287C	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	362					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)		GCTCTTACCTATGTTATCCAA	0.353													A|||	72	0.014377	0.053	0.0029	5008	,	,		16104	0.0		0.0	False		,,,				2504	0.0				p.Y362C		Atlas-SNP	.											.	AP4E1	78	.	0			c.A1085G						PASS	.	A	CYS/TYR	216,4176	131.8+/-168.3	5,206,1985	147	137	141		1085	4.9	1	15	dbSNP_129	141	2,8586	2.2+/-6.3	0,2,4292	yes	missense	AP4E1	NM_007347.3	194	5,208,6277	GG,GA,AA		0.0233,4.918,1.6795	benign	362/1138	51233881	218,12762	2196	4294	6490	SO:0001583	missense	23431	exon10			TTACCTATGTTAT	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.1085A>G	15.37:g.51233881A>G	ENSP00000261842:p.Tyr362Cys	114	0	0		128	62	0.484375	NM_007347	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Missense_Mutation	SNP	ENST00000261842.5	37	CCDS32240.1	35	0.016025641025641024	35	0.07113821138211382	0	0.0	0	0.0	0	0.0	A	11.86	1.763436	0.31228	0.04918	2.33E-4	ENSG00000081014	ENST00000261842	T	0.25414	1.8	6.04	4.93	0.64822	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.061436	0.64402	D	0.000002	T	0.01029	0.0034	N	0.16098	0.37	0.58432	D	0.999997	B	0.22800	0.075	B	0.21917	0.037	T	0.10823	-1.0613	10	0.37606	T	0.19	-17.2068	9.7604	0.40528	0.8689:0.0:0.1311:0.0	rs58909326	362	Q9UPM8	AP4E1_HUMAN	C	362	ENSP00000261842:Y362C	ENSP00000261842:Y362C	Y	+	2	0	AP4E1	49021173	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	4.930000	0.63462	2.317000	0.78254	0.460000	0.39030	TAT	A|0.982;G|0.018	0.018	strong		0.353	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1			G	51233881	A	G	51233881	3	3	22	1	0	0	0	0	1	0	0	0	752	449	16	3	1123	3	AP4E1	15	51233881	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	210665	51233881	51297511	3026	5927											
MYO5C	55930	hgsc.bcm.edu	37	chr15	52553259	52553259	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attttgcgattgcacagccaCtgagcaactctgccactctc	9	11	7	14	1	2	1	0	1	2	0	3	2	2	1	2	0	6	2	2	0	1	3	rs200784696		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:52553259C>G	ENST00000261839.7	-	10	1274	c.1113G>C	c.(1111-1113)caG>caC	p.Q371H	MYO5C_ENST00000541028.1_5'UTR|MYO5C_ENST00000443683.2_Missense_Mutation_p.Q314H	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	371	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)		TGCACAGCCACTGAGCAACTC	0.557													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19769	0.0		0.0	False		,,,				2504	0.0				p.Q371H		Atlas-SNP	.											.	MYO5C	162	.	0			c.G1113C						PASS	.	C	HIS/GLN	2,4080		0,2,2039	67	71	70		1113	4.6	1	15		70	0,8416		0,0,4208	yes	missense	MYO5C	NM_018728.3	24	0,2,6247	GG,GC,CC		0.0,0.049,0.016	benign	371/1743	52553259	2,12496	2041	4208	6249	SO:0001583	missense	55930	exon10			CAGCCACTGAGCA	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.1113G>C	15.37:g.52553259C>G	ENSP00000261839:p.Gln371His	56	0	0		66	29	0.439394	NM_018728	Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	37	CCDS42036.1	.	.	.	.	.	.	.	.	.	.	C	6.117	0.389752	0.11581	4.9E-4	0.0	ENSG00000128833	ENST00000261839;ENST00000443683	D;D	0.95238	-3.65;-2.21	5.51	4.59	0.56863	Myosin head, motor domain (2);	0.190704	0.47852	D	0.000217	D	0.87047	0.6080	N	0.05050	-0.12	0.47737	D	0.999502	B	0.09022	0.002	B	0.11329	0.006	T	0.81245	-0.1020	10	0.23302	T	0.38	.	16.3026	0.82830	0.0:0.8673:0.1327:0.0	.	371	Q9NQX4	MYO5C_HUMAN	H	371;314	ENSP00000261839:Q371H;ENSP00000410582:Q314H	ENSP00000261839:Q371H	Q	-	3	2	MYO5C	50340551	1.000000	0.71417	0.999000	0.59377	0.071000	0.16799	0.860000	0.27871	1.325000	0.45301	-0.175000	0.13238	CAG	.	.	weak		0.557	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728		G	52553259	C	G	52553259	3	3	22	1	0	0	0	0	1	0	0	0	10089	564	20	4	4243	4	MYO5C	15	52553259	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1319378	52553259	49978133	3027	5928											
KIAA1370	56204	hgsc.bcm.edu	37	chr15	52901109	52901109	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgaagattgccaaagaattTtggattatagttctcattta	13	16	7	5	0	1	3	1	1	1	2	2	4	1	4	1	1	1	1	1	1	6	8	rs61731676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:52901109T>C	ENST00000261844.7	-	6	2154	c.2002A>G	c.(2002-2004)Aaa>Gaa	p.K668E	FAM214A_ENST00000546305.2_Missense_Mutation_p.K675E	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	668																	CCAAAGAATTTTGGATTATAG	0.269													T|||	98	0.0195687	0.0726	0.0029	5008	,	,		17454	0.0		0.0	False		,,,				2504	0.0				p.K668E		Atlas-SNP	.											.	.	.	.	0			c.A2002G						PASS	.	T	GLU/LYS	195,3367		6,183,1592	51	47	48		2002	5.2	0.2	15	dbSNP_129	48	1,8081		0,1,4040	yes	missense	KIAA1370	NM_019600.2	56	6,184,5632	CC,CT,TT		0.0124,5.4745,1.6833	benign	668/1077	52901109	196,11448	1781	4041	5822	SO:0001583	missense	56204	exon6			AGAATTTTGGATT	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.2002A>G	15.37:g.52901109T>C	ENSP00000261844:p.Lys668Glu	55	0	0		83	38	0.457831	NM_019600	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Missense_Mutation	SNP	ENST00000261844.7	37	CCDS45263.1	35	0.016025641025641024	34	0.06910569105691057	1	0.0027624309392265192	0	0.0	0	0.0	T	0	-2.662882	0.00107	0.054745	1.24E-4	ENSG00000047346	ENST00000261844;ENST00000399202;ENST00000534964;ENST00000546305	T;T;T	0.29397	1.65;1.57;1.65	6.16	5.24	0.73138	.	0.435251	0.24628	N	0.036918	T	0.00524	0.0017	N	0.00368	-1.59	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.21314	-1.0249	10	0.02654	T	1	.	11.867	0.52499	0.0:0.859:0.0:0.141	.	675;668	F5H8G0;Q32MH5	.;K1370_HUMAN	E	668;668;667;675	ENSP00000261844:K668E;ENSP00000382153:K668E;ENSP00000443598:K675E	ENSP00000261844:K668E	K	-	1	0	KIAA1370	50688401	0.012000	0.17670	0.195000	0.23364	0.037000	0.13140	1.798000	0.38814	1.598000	0.50083	-0.248000	0.11899	AAA	T|0.982;C|0.018	0.018	strong		0.269	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600		C	52901109	T	C	52901109	3	2	22	1	0	0	0	0	1	0	0	0	8235	1850	64	3	1260	3	KIAA1370	15	52901109	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	347850	52901109	49630283	3028	5929											
KIAA1370	56204	hgsc.bcm.edu	37	chr15	52901887	52901887	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttttcttgtgaaacccggaaAagttttgaatggagtgaact	12	14	10	5	1	1	3	0	3	1	0	1	5	1	5	1	2	2	1	1	2	5	5	rs75512966	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:52901887A>G	ENST00000261844.7	-	6	1376	c.1224T>C	c.(1222-1224)ctT>ctC	p.L408L	FAM214A_ENST00000546305.2_Silent_p.L415L	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	408																	AAACCCGGAAAAGTTTTGAAT	0.403													A|||	99	0.0197684	0.0734	0.0029	5008	,	,		19310	0.0		0.0	False		,,,				2504	0.0				p.L408L		Atlas-SNP	.											.	.	.	.	0			c.T1224C						PASS	.	A		198,3438		6,186,1626	60	56	57		1224	0.5	0	15	dbSNP_132	57	1,8143		0,1,4071	no	coding-synonymous	KIAA1370	NM_019600.2		6,187,5697	GG,GA,AA		0.0123,5.4455,1.6893		408/1077	52901887	199,11581	1818	4072	5890	SO:0001819	synonymous_variant	56204	exon6			CCGGAAAAGTTTT	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.1224T>C	15.37:g.52901887A>G		47	0	0		58	29	0.5	NM_019600	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Silent	SNP	ENST00000261844.7	37	CCDS45263.1																																																																																			A|0.981;G|0.019	0.019	strong		0.403	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600		G	52901887	A	G	52901887	2	3	22	1	0	0	0	0	0	0	0	1	8235	1	1	3		3	KIAA1370	15	52901887	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	778	52901887	49629505	3029	5930											
WDR72	256764	hgsc.bcm.edu	37	chr15	53997415	53997415	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tatcttgaagagtccaggtgGcagttactggtatctctaaa	11	13	10	7	0	2	2	0	1	2	1	4	2	3	2	1	3	1	3	1	3	6	5	rs142505794		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:53997415G>T	ENST00000396328.1	-	11	1357	c.1118C>A	c.(1117-1119)gCc>gAc	p.A373D	WDR72_ENST00000559418.1_Missense_Mutation_p.A383D|WDR72_ENST00000557913.1_Missense_Mutation_p.A370D|WDR72_ENST00000360509.5_Missense_Mutation_p.A373D	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	373										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)		AGTCCAGGTGGCAGTTACTGG	0.358																																					p.A373D		Atlas-SNP	.											.	WDR72	177	.	0			c.C1118A						PASS	.	G	ASP/ALA	1,4387	2.1+/-5.4	0,1,2193	61	62	61		1118	4.8	1	15	dbSNP_134	61	0,8586		0,0,4293	no	missense	WDR72	NM_182758.2	126	0,1,6486	TT,TG,GG		0.0,0.0228,0.0077	benign	373/1103	53997415	1,12973	2194	4293	6487	SO:0001583	missense	256764	exon11			CAGGTGGCAGTTA	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.1118C>A	15.37:g.53997415G>T	ENSP00000379619:p.Ala373Asp	34	0	0		38	23	0.605263	NM_182758	Q7Z3I3|Q8N8X2	Missense_Mutation	SNP	ENST00000396328.1	37	CCDS10151.1	.	.	.	.	.	.	.	.	.	.	G	13.53	2.265633	0.40095	2.28E-4	0.0	ENSG00000166415	ENST00000396328;ENST00000360509	T;T	0.52295	0.67;0.67	5.75	4.84	0.62591	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.281989	0.35262	N	0.003332	T	0.33876	0.0878	N	0.14661	0.345	0.24960	N	0.991737	B	0.21606	0.058	B	0.18561	0.022	T	0.31641	-0.9936	10	0.59425	D	0.04	.	15.9329	0.79679	0.0:0.1353:0.8647:0.0	.	373	Q3MJ13	WDR72_HUMAN	D	373	ENSP00000379619:A373D;ENSP00000353699:A373D	ENSP00000353699:A373D	A	-	2	0	WDR72	51784707	0.988000	0.35896	0.997000	0.53966	0.830000	0.47004	3.442000	0.52900	1.434000	0.47414	0.460000	0.39030	GCC	G|1.000;T|0.000	0.000	weak		0.358	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758		T	53997415	G	T	53997415	3	4	22	1	0	0	0	0	1	0	0	0	17337	1203	42	4	2230	4	WDR72	15	53997415	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1095528	53997415	48533977	3030	5931											
PIGB	9488	hgsc.bcm.edu	37	chr15	55647617	55647617	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaagggaaattcaacatgaAgatgaaattctgaactttcc	18	10	7	6	0	2	4	1	3	1	1	3	5	3	5	1	1	2	0	1	1	7	3	rs2444042	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:55647617A>C	ENST00000164305.5	+	12	1943	c.1652A>C	c.(1651-1653)aAg>aCg	p.K551T	DYX1C1-CCPG1_ENST00000565113.1_RNA|CCPG1_ENST00000310958.6_3'UTR|PIGB_ENST00000539642.1_Missense_Mutation_p.K356T|CCPG1_ENST00000442196.3_3'UTR	NM_004855.4	NP_004846.4	Q92521	PIGB_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class B	551			K -> T (in dbSNP:rs2444042).		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)		TTCAACATGAAGATGAAATTC	0.368													A|||	96	0.0191693	0.0719	0.0014	5008	,	,		17374	0.0		0.0	False		,,,				2504	0.0				p.K551T		Atlas-SNP	.											.	PIGB	36	.	0			c.A1652C						PASS	.	A	,,,THR/LYS,	239,3401		7,225,1588	89	89	89		,,,1652,	3.4	0.3	15	dbSNP_100	89	2,8126		0,2,4062	yes	utr-3,utr-3,utr-3,missense,utr-3	CCPG1,PIGB	NM_001204450.1,NM_001204451.1,NM_004748.4,NM_004855.4,NM_020739.3	,,,78,	7,227,5650	CC,CA,AA		0.0246,6.5659,2.0479	,,,benign,	,,,551/555,	55647617	241,11527	1820	4064	5884	SO:0001583	missense	9488	exon12			ACATGAAGATGAA	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.1652A>C	15.37:g.55647617A>C	ENSP00000164305:p.Lys551Thr	94	0	0		103	47	0.456311	NM_004855	Q53FF9|Q8WVN7	Missense_Mutation	SNP	ENST00000164305.5	37		32	0.014652014652014652	31	0.06300813008130081	1	0.0027624309392265192	0	0.0	0	0.0	A	7.554	0.663207	0.14710	0.065659	2.46E-4	ENSG00000069943	ENST00000164305;ENST00000539642	T;T	0.59638	0.51;0.25	5.67	3.39	0.38822	.	3.113960	0.00954	N	0.003003	T	0.03827	0.0108	N	0.03608	-0.345	0.80722	D	1	B	0.31318	0.319	B	0.30029	0.11	T	0.02668	-1.1126	10	0.66056	D	0.02	9.0326	8.6085	0.33789	0.8432:0.0:0.1568:0.0	rs2444042;rs52826750;rs2444042	551	Q92521	PIGB_HUMAN	T	551;356	ENSP00000164305:K551T;ENSP00000438963:K356T	ENSP00000164305:K551T	K	+	2	0	PIGB	53434909	0.999000	0.42202	0.263000	0.24496	0.257000	0.26127	1.168000	0.31859	0.452000	0.26830	0.482000	0.46254	AAG	A|0.977;C|0.023	0.023	strong		0.368	PIGB-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000419687.1	NM_004855		C	55647617	A	C	55647617	3	2	22	1	0	0	0	0	1	0	0	0	11894	72	3	5	1698	5	PIGB	15	55647617	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1650202	55647617	46883775	3031	5932											
DYX1C1	161582	hgsc.bcm.edu	37	chr15	55790053	55790053	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caaataaaaatggaggaaagTtgacctatgcagaagggtga	18	7	12	4	0	0	3	0	2	0	1	0	5	0	5	1	3	1	2	1	3	7	3	rs61733359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:55790053T>C	ENST00000321149.3	-	3	495	c.128A>G	c.(127-129)aAc>aGc	p.N43S	DYX1C1_ENST00000348518.3_Missense_Mutation_p.N43S|DYX1C1_ENST00000457155.2_Missense_Mutation_p.N43S|DYX1C1-CCPG1_ENST00000565113.1_RNA|DYX1C1_ENST00000380679.1_Missense_Mutation_p.N43S|DYX1C1_ENST00000448430.2_Missense_Mutation_p.N43S	NM_130810.3	NP_570722.2	Q8WXU2	DYXC1_HUMAN	dyslexia susceptibility 1 candidate 1	43	CS. {ECO:0000255|PROSITE- ProRule:PRU00547}.|Mediates interaction with ESR1 and STUB1.				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)		TGGAGGAAAGTTGACCTATGC	0.363													T|||	15	0.00299521	0.0106	0.0014	5008	,	,		17266	0.0		0.0	False		,,,				2504	0.0				p.N43S		Atlas-SNP	.											.	DYX1C1	54	.	0			c.A128G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN	59,4327	55.5+/-91.7	0,59,2134	81	81	81		128,128,128	3.6	1	15	dbSNP_129	81	1,8583		0,1,4291	yes	missense,missense,missense	DYX1C1	NM_001033559.2,NM_001033560.1,NM_130810.3	46,46,46	0,60,6425	CC,CT,TT		0.0116,1.3452,0.4626	benign,benign,benign	43/377,43/382,43/421	55790053	60,12910	2193	4292	6485	SO:0001583	missense	161582	exon3			GGAAAGTTGACCT		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.128A>G	15.37:g.55790053T>C	ENSP00000323275:p.Asn43Ser	50	0	0		37	19	0.513514	NM_001033560	Q6P5Y9|Q8N1S6	Missense_Mutation	SNP	ENST00000321149.3	37	CCDS10154.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	T	15.43	2.830177	0.50845	0.013452	1.16E-4	ENSG00000256061	ENST00000420792;ENST00000448430;ENST00000380679;ENST00000457155;ENST00000321149;ENST00000348518	T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59	4.72	3.56	0.40772	CS-like domain (1);CS domain (1);HSP20-like chaperone (1);	0.272597	0.33610	U	0.004729	T	0.10723	0.0262	N	0.17872	0.535	0.30138	N	0.804168	B;B;B	0.32526	0.057;0.119;0.374	B;B;B	0.34138	0.082;0.078;0.176	T	0.16958	-1.0385	10	0.02654	T	1	.	7.8669	0.29543	0.0:0.1574:0.0:0.8426	.	43;43;43	Q8WXU2-3;Q8WXU2;Q8WXU2-2	.;DYXC1_HUMAN;.	S	43	ENSP00000403412:N43S;ENSP00000370054:N43S;ENSP00000402640:N43S;ENSP00000323275:N43S;ENSP00000299561:N43S	ENSP00000323275:N43S	N	-	2	0	DYX1C1	53577345	1.000000	0.71417	0.980000	0.43619	0.984000	0.73092	1.407000	0.34657	1.984000	0.57885	0.459000	0.35465	AAC	T|0.995;C|0.005	0.005	strong		0.363	DYX1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254976.1	NM_130810		C	55790053	T	C	55790053	3	2	22	1	0	0	0	0	1	0	0	0	4864	1725	60	3	1269	3	DYX1C1	15	55790053	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	142436	55790053	46741339	3032	5933											
DYX1C1	161582	hgsc.bcm.edu	37	chr15	55790414	55790414	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgcattcttaccttcagataGttttccgtgcagaacacgtc	9	14	7	11	2	2	2	1	0	1	2	4	2	3	2	2	0	4	3	2	0	3	6	rs16976354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:55790414G>T	ENST00000321149.3	-	2	481	c.114C>A	c.(112-114)aaC>aaA	p.N38K	DYX1C1_ENST00000348518.3_Missense_Mutation_p.N38K|DYX1C1_ENST00000457155.2_Missense_Mutation_p.N38K|DYX1C1-CCPG1_ENST00000565113.1_RNA|DYX1C1_ENST00000380679.1_Missense_Mutation_p.N38K|DYX1C1_ENST00000448430.2_Missense_Mutation_p.N38K	NM_130810.3	NP_570722.2	Q8WXU2	DYXC1_HUMAN	dyslexia susceptibility 1 candidate 1	38	CS. {ECO:0000255|PROSITE- ProRule:PRU00547}.|Mediates interaction with ESR1 and STUB1.		N -> K (in dbSNP:rs16976354).		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)		CCTTCAGATAGTTTTCCGTGC	0.562													G|||	311	0.0621006	0.2262	0.0159	5008	,	,		16045	0.0		0.001	False		,,,				2504	0.0				p.N38K		Atlas-SNP	.											.	DYX1C1	54	.	0			c.C114A						PASS	.	G	LYS/ASN,LYS/ASN,LYS/ASN	849,3537	325.3+/-299.0	72,705,1416	45	42	43		114,114,114	-1.6	0.1	15	dbSNP_123	43	0,8582		0,0,4291	yes	missense,missense,missense	DYX1C1	NM_001033559.2,NM_001033560.1,NM_130810.3	94,94,94	72,705,5707	TT,TG,GG		0.0,19.357,6.5469	benign,benign,benign	38/377,38/382,38/421	55790414	849,12119	2193	4291	6484	SO:0001583	missense	161582	exon2			CAGATAGTTTTCC		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.114C>A	15.37:g.55790414G>T	ENSP00000323275:p.Asn38Lys	110	0	0		132	53	0.401515	NM_001033560	Q6P5Y9|Q8N1S6	Missense_Mutation	SNP	ENST00000321149.3	37	CCDS10154.1	103	0.04716117216117216	97	0.19715447154471544	6	0.016574585635359115	0	0.0	0	0.0	G	12.94	2.089312	0.36855	0.19357	0.0	ENSG00000256061	ENST00000420792;ENST00000448430;ENST00000380679;ENST00000457155;ENST00000321149;ENST00000348518	T;T;T;T;T	0.12984	2.63;2.63;2.63;2.63;2.63	4.82	-1.59	0.08453	CS-like domain (1);CS domain (1);HSP20-like chaperone (1);	1.338300	0.05207	U	0.506081	T	0.00012	0.0000	L	0.41573	1.285	0.58432	P	9.000000000036756E-6	B;B;P	0.44044	0.307;0.109;0.825	B;B;B	0.39217	0.117;0.122;0.294	T	0.26224	-1.0109	9	0.07813	T	0.8	.	5.7047	0.17901	0.459:0.2611:0.2799:0.0	rs16976354;rs52829594;rs58871707;rs16976354	38;38;38	Q8WXU2-3;Q8WXU2;Q8WXU2-2	.;DYXC1_HUMAN;.	K	38	ENSP00000403412:N38K;ENSP00000370054:N38K;ENSP00000402640:N38K;ENSP00000323275:N38K;ENSP00000299561:N38K	ENSP00000323275:N38K	N	-	3	2	DYX1C1	53577706	0.085000	0.21516	0.131000	0.22000	0.920000	0.55202	0.021000	0.13489	0.043000	0.15746	0.655000	0.94253	AAC	G|0.928;T|0.072	0.072	strong		0.562	DYX1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254976.1	NM_130810		T	55790414	G	T	55790414	3	4	22	1	0	0	0	0	1	0	0	0	4864	1020	36	4	1287	4	DYX1C1	15	55790414	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	361	55790414	46740978	3033	5934											
RFX7	64864	hgsc.bcm.edu	37	chr15	56387421	56387421	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gattcctgtatctggctatgTagctgctggctatatgtgtc	6	16	11	8	0	1	0	0	0	1	0	3	1	2	0	1	2	2	6	1	2	5	6	rs34255389	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:56387421T>C	ENST00000559447.2	-	9	2485	c.2214A>G	c.(2212-2214)ctA>ctG	p.L738L	RFX7_ENST00000317318.6_Silent_p.L835L|RFX7_ENST00000422057.1_Silent_p.L738L|RFX7_ENST00000423270.1_Silent_p.L835L			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	738					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						TCTGGCTATGTAGCTGCTGGC	0.393													T|||	16	0.00319489	0.0113	0.0014	5008	,	,		20635	0.0		0.0	False		,,,				2504	0.0				p.L835L		Atlas-SNP	.											.	RFX7	170	.	0			c.A2505G						PASS	.	T		40,3758		0,40,1859	115	113	114		2505	-10.9	0	15	dbSNP_126	114	0,8254		0,0,4127	no	coding-synonymous	RFX7	NM_022841.5		0,40,5986	CC,CT,TT		0.0,1.0532,0.3319		835/1461	56387421	40,12012	1899	4127	6026	SO:0001819	synonymous_variant	64864	exon9			GCTATGTAGCTGC			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.2214A>G	15.37:g.56387421T>C		137	0	0		172	82	0.476744	NM_022841	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Silent	SNP	ENST00000559447.2	37																																																																																				T|0.996;C|0.004	0.004	strong		0.393	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841		C	56387421	T	C	56387421	2	2	22	1	0	0	0	0	0	0	0	1	13283	1625	57	3		3	RFX7	15	56387421	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	597007	56387421	46143971	3034	5935											
RFX7	64864	hgsc.bcm.edu	37	chr15	56387581	56387581	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aatctttagtgatttgttgcCatccatttggattaaagctg	10	17	8	6	0	1	1	0	1	1	0	2	2	2	2	2	1	2	2	2	1	4	6			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:56387581C>T	ENST00000559447.2	-	9	2325	c.2054G>A	c.(2053-2055)tGg>tAg	p.W685*	RFX7_ENST00000317318.6_Nonsense_Mutation_p.W782*|RFX7_ENST00000422057.1_Nonsense_Mutation_p.W685*|RFX7_ENST00000423270.1_Nonsense_Mutation_p.W782*			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	685					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.W685*(1)|p.W782*(1)		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						GATTTGTTGCCATCCATTTGG	0.378																																					p.W782X		Atlas-SNP	.											RFX7_ENST00000423270,NS,lymphoid_neoplasm,0,2	RFX7	170	2	2	Substitution - Nonsense(2)	haematopoietic_and_lymphoid_tissue(2)	c.G2345A						PASS	.						124	116	118					15																	56387581		1850	4096	5946	SO:0001587	stop_gained	64864	exon9			TGTTGCCATCCAT			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.2054G>A	15.37:g.56387581C>T	ENSP00000453281:p.Trp685*	79	0	0		95	27	0.284211	NM_022841	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Nonsense_Mutation	SNP	ENST00000559447.2	37		.	.	.	.	.	.	.	.	.	.	C	30	5.054224	0.93793	.	.	ENSG00000181827	ENST00000422057;ENST00000317318;ENST00000423270	.	.	.	5.44	4.32	0.51571	.	0.000000	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.19147	T	0.46	-4.9265	14.1694	0.65500	0.0:0.9149:0.0:0.0851	.	.	.	.	X	685;782;782	.	ENSP00000313299:W782X	W	-	2	0	RFX7	54174873	1.000000	0.71417	1.000000	0.80357	0.825000	0.46686	5.485000	0.66850	2.531000	0.85337	0.563000	0.77884	TGG	.	.	none		0.378	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841		T	56387581	C	T	56387581	4	4	22	1	0	0	0	0	0	1	0	0	13283	595	21	2	2041	2	RFX7	15	56387581	Nonsense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	160	56387581	46143811	3035	5936											
TCF12	6938	hgsc.bcm.edu	37	chr15	57384061	57384061	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccatgaaggcttgtccccAacacctttcatgaactcaaa	12	9	6	14	0	2	2	2	2	0	0	3	2	3	2	4	1	2	1	4	1	4	2	rs34560099	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:57384061A>G	ENST00000267811.5	+	5	601	c.297A>G	c.(295-297)ccA>ccG	p.P99P	TCF12_ENST00000557843.1_Silent_p.P99P|TCF12_ENST00000333725.5_Silent_p.P99P|TCF12_ENST00000452095.2_Silent_p.P95P|TCF12_ENST00000438423.2_Silent_p.P99P	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN	transcription factor 12	99					immune response (GO:0006955)|muscle organ development (GO:0007517)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)		TCF12/NR4A3(2)	breast(2)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	36		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		GCTTGTCCCCAACACCTTTCA	0.423			T	TEC	extraskeletal myxoid chondrosarcoma								A|||	237	0.0473243	0.1626	0.0216	5008	,	,		18239	0.0		0.007	False		,,,				2504	0.0				p.P99P		Atlas-SNP	.		Dom	yes		15	15q21	6938	"transcription factor 12 (HTF4, helix-loop-helix transcription factors 4)"		M	.	TCF12	242	.	0			c.A297G						PASS	.	A	,,,	551,3833	247.8+/-255.9	35,481,1676	109	107	108		297,297,297,297	4.6	1	15	dbSNP_126	108	37,8547	25.1+/-72.6	1,35,4256	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TCF12	NM_003205.3,NM_207036.1,NM_207037.1,NM_207038.1	,,,	36,516,5932	GG,GA,AA		0.431,12.5684,4.5342	,,,	99/683,99/707,99/707,99/683	57384061	588,12380	2192	4292	6484	SO:0001819	synonymous_variant	6938	exon5			GTCCCCAACACCT	BC050556	CCDS10159.1, CCDS10160.1, CCDS42042.1	15q21	2013-05-21	2008-07-31		ENSG00000140262	ENSG00000140262		"Basic helix-loop-helix proteins"	11623	protein-coding gene	gene with protein product	"helix-loop-helix transcription factor 4"	600480				1886779	Standard	NM_003205		Approved	HEB, HTF4, HsT17266, bHLHb20	uc002aeb.3	Q99081	OTTHUMG00000132047	ENST00000267811.5:c.297A>G	15.37:g.57384061A>G		90	0	0		91	33	0.362637	NM_207036	Q7Z3D9|Q86TC1|Q86VM2	Silent	SNP	ENST00000267811.5	37	CCDS10159.1																																																																																			A|0.959;G|0.041	0.041	strong		0.423	TCF12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255069.3	NM_003205		G	57384061	A	G	57384061	2	3	22	1	0	0	0	0	0	0	0	1	15702	117	5	3		3	TCF12	15	57384061	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	996480	57384061	45147331	3036	5937											
GCOM1	100820829	hgsc.bcm.edu	37	chr15	57925873	57925873	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aaaaagatgcaagcagcagaGatcagcctagaggagaaaga	20	3	12	6	0	1	5	1	0	0	5	1	7	1	5	1	1	4	3	1	1	5	1	rs148672365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:57925873G>C	ENST00000267853.5	+	8	961	c.867G>C	c.(865-867)gaG>gaC	p.E289D	GCOM1_ENST00000380561.2_Missense_Mutation_p.E258D|POLR2M_ENST00000380563.2_5'UTR|GCOM1_ENST00000587652.1_Missense_Mutation_p.E289D|GCOM1_ENST00000396180.1_Missense_Mutation_p.E258D|GCOM1_ENST00000572390.1_Missense_Mutation_p.E289D|GCOM1_ENST00000380568.3_Missense_Mutation_p.E289D|GCOM1_ENST00000380560.2_Missense_Mutation_p.E220D|GCOM1_ENST00000380569.2_Missense_Mutation_p.E289D|GCOM1_ENST00000574161.1_Missense_Mutation_p.E289D|MYZAP_ENST00000380565.4_Missense_Mutation_p.E289D			P0CAP1	MYZAP_HUMAN	myocardial zonula adherens protein	289					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)											AAGCAGCAGAGATCAGCCTAG	0.478													G|||	20	0.00399361	0.0144	0.0014	5008	,	,		18055	0.0		0.0	False		,,,				2504	0.0				p.E289D		Atlas-SNP	.											.	GCOM1	66	.	0			c.G867C						PASS	.	G	ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU	70,4314	64.7+/-102.0	0,70,2122	128	127	128		867,867,867,867	3.5	1	15	dbSNP_134	128	0,8584		0,0,4292	yes	missense,missense,missense,missense	GCOM1	NM_001018090.3,NM_001018091.3,NM_001018100.3,NM_152451.6	45,45,45,45	0,70,6414	CC,CG,GG		0.0,1.5967,0.5398	probably-damaging,probably-damaging,probably-damaging,probably-damaging	289/551,289/446,289/467,289/439	57925873	70,12898	2192	4292	6484	SO:0001583	missense	145781	exon8			AGCAGAGATCAGC	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.867G>C	15.37:g.57925873G>C	ENSP00000267853:p.Glu289Asp	170	0	0		162	79	0.487654	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	37	CCDS10162.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	G	18.62	3.663734	0.67700	0.015967	0.0	ENSG00000137878	ENST00000380569;ENST00000380561;ENST00000396180;ENST00000380560;ENST00000267853;ENST00000380565;ENST00000380568;ENST00000461709	T;T;T;T;T;T;T;T	0.33438	1.41;1.41;1.41;1.41;1.41;1.41;1.41;1.41	5.68	3.46	0.39613	.	0.000000	0.85682	D	0.000000	T	0.37019	0.0988	M	0.75615	2.305	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;0.999;1.0	D;D;D;D	0.87578	0.995;0.993;0.995;0.998	T	0.51911	-0.8645	10	0.62326	D	0.03	-34.0747	12.4064	0.55443	0.1663:0.0:0.8337:0.0	.	289;289;289;289	P0CAP1-2;P0CAP1-11;P0CAP1-4;P0CAP1	.;.;.;GCOM1_HUMAN	D	289;258;258;220;289;289;289;4	ENSP00000369943:E289D;ENSP00000369935:E258D;ENSP00000379483:E258D;ENSP00000369933:E220D;ENSP00000267853:E289D;ENSP00000369939:E289D;ENSP00000369942:E289D;ENSP00000431396:E4D	ENSP00000267853:E289D	E	+	3	2	GCOM1	55713165	1.000000	0.71417	0.998000	0.56505	0.916000	0.54674	1.551000	0.36233	1.394000	0.46624	0.563000	0.77884	GAG	G|0.994;C|0.006	0.006	strong		0.478	MYZAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255716.2	NM_001018100		C	57925873	G	C	57925873	3	2	22	1	0	0	0	0	1	0	0	0	6312	933	33	4	897	4	GCOM1	15	57925873	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	541812	57925873	44605519	3037	5938											
CCNB2	9133	hgsc.bcm.edu	37	chr15	59406674	59406674	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacacctgaggatgtctccaTgaaggaagagaatctctgcc	12	8	10	11	0	2	3	0	2	2	1	4	6	2	5	3	2	1	0	3	2	3	0	rs16941036	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:59406674T>C	ENST00000288207.2	+	4	490	c.299T>C	c.(298-300)aTg>aCg	p.M100T	CCNB2_ENST00000559622.1_Missense_Mutation_p.M19T	NM_004701.3	NP_004692.1	O95067	CCNB2_HUMAN	cyclin B2	100			M -> T (in dbSNP:rs16941036). {ECO:0000269|Ref.5}.		G2/M transition of mitotic cell cycle (GO:0000086)|growth (GO:0040007)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)	centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)				kidney(4)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	9						GATGTCTCCATGAAGGAAGAG	0.473													T|||	17	0.00339457	0.0121	0.0014	5008	,	,		20124	0.0		0.0	False		,,,				2504	0.0				p.M100T		Atlas-SNP	.											.	CCNB2	23	.	0			c.T299C						PASS	.	T	THR/MET	72,4310	64.1+/-101.4	0,72,2119	92	85	87		299	4.2	1	15	dbSNP_123	87	1,8581	1.2+/-3.3	0,1,4290	yes	missense	CCNB2	NM_004701.3	81	0,73,6409	CC,CT,TT		0.0117,1.6431,0.5631	benign	100/399	59406674	73,12891	2191	4291	6482	SO:0001583	missense	9133	exon4			TCTCCATGAAGGA	AF002822	CCDS10170.1	15q21.3	2004-01-19			ENSG00000157456	ENSG00000157456			1580	protein-coding gene	gene with protein product		602755					Standard	NM_004701		Approved	HsT17299	uc002afz.3	O95067	OTTHUMG00000132715	ENST00000288207.2:c.299T>C	15.37:g.59406674T>C	ENSP00000288207:p.Met100Thr	102	0	0		126	61	0.484127	NM_004701	B3KM93|Q6FI99	Missense_Mutation	SNP	ENST00000288207.2	37	CCDS10170.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	T	8.119	0.780523	0.16120	0.016431	1.17E-4	ENSG00000157456	ENST00000288207	T	0.13538	2.58	5.3	4.17	0.49024	.	0.590246	0.19354	N	0.116311	T	0.08133	0.0203	M	0.75777	2.31	0.43457	D	0.995659	B;B	0.19935	0.017;0.04	B;B	0.20384	0.029;0.029	T	0.03524	-1.1028	10	0.13853	T	0.58	.	10.3592	0.43982	0.0:0.0774:0.0:0.9226	rs16941036;rs52827002;rs16941036	100;100	Q53HG9;O95067	.;CCNB2_HUMAN	T	100	ENSP00000288207:M100T	ENSP00000288207:M100T	M	+	2	0	CCNB2	57193966	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.612000	0.46343	0.862000	0.35528	0.459000	0.35465	ATG	T|0.994;C|0.006	0.006	strong		0.473	CCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256016.1	NM_004701		C	59406674	T	C	59406674	3	2	22	1	0	0	0	0	1	0	0	0	2915	1464	51	3	313	3	CCNB2	15	59406674	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1480801	59406674	43124718	3038	5939											
CSNK1G1	53944	hgsc.bcm.edu	37	chr15	64592522	64592522	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataaccaagtgcttacctaaTctgagctctccgaagttccc	11	11	6	13	1	2	1	0	1	2	0	4	2	3	1	4	0	4	3	4	0	5	4	rs7163558	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:64592522T>C	ENST00000303052.7	-	2	600	c.177A>G	c.(175-177)agA>agG	p.R59R	CSNK1G1_ENST00000607537.1_Silent_p.R59R|CTD-2116N17.1_ENST00000558783.1_5'Flank|CSNK1G1_ENST00000303032.6_Silent_p.R59R|CTD-2116N17.1_ENST00000606793.1_5'UTR	NM_022048.3	NP_071331.2	Q9HCP0	KC1G1_HUMAN	casein kinase 1, gamma 1	59	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						GCTTACCTAATCTGAGCTCTC	0.448													T|||	153	0.0305511	0.115	0.0014	5008	,	,		19957	0.0		0.0	False		,,,				2504	0.0				p.R59R		Atlas-SNP	.											.	CSNK1G1	56	.	0			c.A177G						PASS	.	T		401,4005	199.1+/-222.7	18,365,1820	253	243	246		177	5.4	1	15	dbSNP_116	246	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	CSNK1G1	NM_022048.3		18,372,6113	CC,CT,TT		0.0814,9.1012,3.137		59/423	64592522	408,12598	2203	4300	6503	SO:0001819	synonymous_variant	53944	exon2			ACCTAATCTGAGC	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.177A>G	15.37:g.64592522T>C		147	0	0		190	91	0.478947	NM_022048	Q5JPH1|Q96AE9|Q9HCP1	Silent	SNP	ENST00000303052.7	37	CCDS10192.2																																																																																			T|0.968;C|0.032	0.032	strong		0.448	CSNK1G1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256605.1	NM_022048		C	64592522	T	C	64592522	2	2	22	1	0	0	0	0	0	0	0	1	3956	1432	50	3		3	CSNK1G1	15	64592522	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	5185848	64592522	37938870	3039	5940											
PIF1	80119	hgsc.bcm.edu	37	chr15	65108939	65108939	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaacacacggcccagagaaAtctccacacaatccagggtc	15	4	7	15	1	1	1	0	0	1	1	4	2	2	1	3	2	1	0	3	2	3	0	rs138069301		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65108939A>G	ENST00000268043.4	-	12	1794	c.1700T>C	c.(1699-1701)aTt>aCt	p.I567T	PIF1_ENST00000333425.6_Missense_Mutation_p.I567T|PIF1_ENST00000559239.1_Missense_Mutation_p.I567T					PIF1 5'-to-3' DNA helicase											kidney(1)|lung(1)	2						GCCCAGAGAAATCTCCACACA	0.612																																					p.I567T		Atlas-SNP	.											.	PIF1	43	.	0			c.T1700C						PASS	.	A	THR/ILE	1,4399		0,1,2199	42	38	39		1700	5.7	1	15	dbSNP_134	39	0,8592		0,0,4296	no	missense	PIF1	NM_025049.2	89	0,1,6495	GG,GA,AA		0.0,0.0227,0.0077	possibly-damaging	567/642	65108939	1,12991	2200	4296	6496	SO:0001583	missense	80119	exon12			AGAGAAATCTCCA	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.1700T>C	15.37:g.65108939A>G	ENSP00000268043:p.Ile567Thr	175	0	0		174	84	0.482759	NM_025049		Missense_Mutation	SNP	ENST00000268043.4	37	CCDS10195.2	.	.	.	.	.	.	.	.	.	.	A	19.18	3.777475	0.70107	2.27E-4	0.0	ENSG00000140451	ENST00000268043;ENST00000333425	T;T	0.48836	0.8;0.8	5.73	5.73	0.89815	.	0.045148	0.85682	D	0.000000	T	0.64000	0.2559	M	0.75085	2.285	0.80722	D	1	P	0.51653	0.947	P	0.56751	0.805	T	0.68573	-0.5373	10	0.87932	D	0	-13.5461	13.9753	0.64268	1.0:0.0:0.0:0.0	.	567	Q9H611	PIF1_HUMAN	T	567	ENSP00000268043:I567T;ENSP00000328174:I567T	ENSP00000268043:I567T	I	-	2	0	PIF1	62895992	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.272000	0.95707	2.186000	0.69663	0.533000	0.62120	ATT	A|1.000;G|0.000	0.000	weak		0.612	PIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256533.1	NM_025049		G	65108939	A	G	65108939	3	3	22	1	0	0	0	0	1	0	0	0	11892	101	4	3	233	3	PIF1	15	65108939	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	516417	65108939	37422453	3040	5941											
PIF1	80119	hgsc.bcm.edu	37	chr15	65112116	65112116	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggtgcagagcctcgtggcCacaatcccatctcgccccac	7	7	10	17	2	1	1	0	0	1	1	4	1	2	1	5	2	2	1	5	2	1	0	rs145376177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65112116C>T	ENST00000268043.4	-	8	1357	c.1263G>A	c.(1261-1263)gtG>gtA	p.V421V	PIF1_ENST00000333425.6_Silent_p.V421V|PIF1_ENST00000559239.1_Silent_p.V421V					PIF1 5'-to-3' DNA helicase											kidney(1)|lung(1)	2						GCCTCGTGGCCACAATCCCAT	0.652													C|||	2	0.000399361	0.0	0.0	5008	,	,		18557	0.002		0.0	False		,,,				2504	0.0				p.V421V		Atlas-SNP	.											.	PIF1	43	.	0			c.G1263A						PASS	.	C		1,4403	2.1+/-5.4	0,1,2201	81	72	75		1263	4.7	1	15	dbSNP_134	75	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	PIF1	NM_025049.2		0,2,6499	TT,TC,CC		0.0116,0.0227,0.0154		421/642	65112116	2,13000	2202	4299	6501	SO:0001819	synonymous_variant	80119	exon8			CGTGGCCACAATC	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.1263G>A	15.37:g.65112116C>T		71	0	0		90	45	0.5	NM_025049		Silent	SNP	ENST00000268043.4	37	CCDS10195.2																																																																																			C|1.000;T|0.000	0.000	weak		0.652	PIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256533.1	NM_025049		T	65112116	C	T	65112116	2	4	22	1	0	0	0	0	0	0	0	1	11892	581	21	2		2	PIF1	15	65112116	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3177	65112116	37419276	3041	5942											
CILP	8483	hgsc.bcm.edu	37	chr15	65496624	65496624	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	acctgccctcacaaactctgCcttgatggtggctgccttca	7	11	8	15	0	3	1	2	1	1	0	3	1	3	1	4	2	4	1	4	2	1	2	rs140625947	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65496624C>G	ENST00000261883.4	-	6	1067	c.901G>C	c.(901-903)Gca>Cca	p.A301P		NM_003613.3	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	301					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						ACAAACTCTGCCTTGATGGTG	0.473													C|||	13	0.00259585	0.0008	0.0	5008	,	,		20367	0.0119		0.0	False		,,,				2504	0.0				p.A301P		Atlas-SNP	.											.	CILP	124	.	0			c.G901C						PASS	.	C	PRO/ALA	4,4398	8.1+/-20.4	0,4,2197	83	82	83		901	5.6	0.8	15	dbSNP_134	83	0,8598		0,0,4299	yes	missense	CILP	NM_003613.3	27	0,4,6496	GG,GC,CC		0.0,0.0909,0.0308	possibly-damaging	301/1185	65496624	4,12996	2201	4299	6500	SO:0001583	missense	8483	exon6			ACTCTGCCTTGAT	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.901G>C	15.37:g.65496624C>G	ENSP00000261883:p.Ala301Pro	137	0	0		164	75	0.457317	NM_003613	B2R8F7|Q6UW99|Q8IYI5	Missense_Mutation	SNP	ENST00000261883.4	37	CCDS10203.1	7	0.003205128205128205	1	0.0020325203252032522	0	0.0	6	0.01048951048951049	0	0.0	C	18.99	3.738884	0.69304	9.09E-4	0.0	ENSG00000138615	ENST00000261883	T	0.40476	1.03	5.63	5.63	0.86233	.	0.163750	0.52532	D	0.000061	T	0.37019	0.0988	L	0.50333	1.59	0.43058	D	0.994673	P	0.50943	0.94	B	0.44044	0.439	T	0.44862	-0.9300	10	0.72032	D	0.01	-27.6493	18.6742	0.91523	0.0:1.0:0.0:0.0	.	301	O75339	CILP1_HUMAN	P	301	ENSP00000261883:A301P	ENSP00000261883:A301P	A	-	1	0	CILP	63283677	0.983000	0.35010	0.798000	0.32154	0.651000	0.38670	2.711000	0.47177	2.659000	0.90383	0.563000	0.77884	GCA	C|0.999;G|0.001	0.001	strong		0.473	CILP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256829.1	NM_003613		G	65496624	C	G	65496624	3	3	22	1	0	0	0	0	1	0	0	0	3431	739	26	4	2669	4	CILP	15	65496624	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	384508	65496624	37034768	3042	5943											
IGDCC4	57722	hgsc.bcm.edu	37	chr15	65681648	65681648	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagggtggagcgctccaccAcagagccgaaaggcccatcc	10	3	13	15	2	0	1	0	0	0	1	2	3	2	2	5	3	2	2	5	3	1	0	rs144676391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65681648A>G	ENST00000352385.2	-	14	2719	c.2510T>C	c.(2509-2511)gTg>gCg	p.V837A		NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	837	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.					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						GCGCTCCACCACAGAGCCGAA	0.572													A|||	21	0.00419329	0.0159	0.0	5008	,	,		16119	0.0		0.0	False		,,,				2504	0.0				p.V837A		Atlas-SNP	.											.	IGDCC4	95	.	0			c.T2510C						PASS	.	A	ALA/VAL	46,4356	48.2+/-83.0	0,46,2155	82	63	69		2510	4.3	1	15	dbSNP_134	69	0,8598		0,0,4299	yes	missense	IGDCC4	NM_020962.1	64	0,46,6454	GG,GA,AA		0.0,1.045,0.3538	benign	837/1251	65681648	46,12954	2201	4299	6500	SO:0001583	missense	57722	exon14			TCCACCACAGAGC		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.2510T>C	15.37:g.65681648A>G	ENSP00000319623:p.Val837Ala	79	0	0		50	18	0.36	NM_020962	Q9HCE4	Missense_Mutation	SNP	ENST00000352385.2	37	CCDS10206.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	A	13.90	2.373757	0.42105	0.01045	0.0	ENSG00000103742	ENST00000352385;ENST00000356152	T	0.54279	0.58	5.37	4.26	0.50523	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.256570	0.38058	N	0.001833	T	0.18676	0.0448	N	0.13098	0.295	0.30508	N	0.76971	B	0.23377	0.084	B	0.17722	0.019	T	0.15925	-1.0420	10	0.35671	T	0.21	-20.1912	10.6197	0.45472	0.9248:0.0:0.0752:0.0	.	837	Q8TDY8	IGDC4_HUMAN	A	837;566	ENSP00000319623:V837A	ENSP00000319623:V837A	V	-	2	0	IGDCC4	63468701	1.000000	0.71417	0.996000	0.52242	0.975000	0.68041	5.865000	0.69583	2.043000	0.60533	0.454000	0.30748	GTG	A|0.995;G|0.005	0.005	strong		0.572	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962		G	65681648	A	G	65681648	3	3	22	1	0	0	0	0	1	0	0	0	7578	159	6	3	1270	3	IGDCC4	15	65681648	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	185024	65681648	36849744	3043	5944											
DPP8	54878	hgsc.bcm.edu	37	chr15	65793060	65793060	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aattccgactgttccaatgcGttttctttctcttaatagtt	8	19	5	9	2	2	0	0	0	2	0	5	1	4	0	2	0	1	3	2	0	4	8			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65793060G>A	ENST00000341861.5	-	4	2058	c.478C>T	c.(478-480)Cgc>Tgc	p.R160C	DPP8_ENST00000339244.5_Missense_Mutation_p.R160C|DPP8_ENST00000300141.6_Missense_Mutation_p.R144C|Y_RNA_ENST00000516408.1_RNA|DPP8_ENST00000321147.6_Missense_Mutation_p.R160C|DPP8_ENST00000321118.7_Missense_Mutation_p.R160C|DPP8_ENST00000358939.4_Missense_Mutation_p.R144C|DPP8_ENST00000559233.1_Missense_Mutation_p.R160C	NM_197960.2	NP_932064.1	Q6V1X1	DPP8_HUMAN	dipeptidyl-peptidase 8	160					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						GTTCCAATGCGTTTTCTTTCT	0.393																																					p.R160C		Atlas-SNP	.											DPP8,colon,carcinoma,+1,1	DPP8	78	1	0			c.C478T						PASS	.						204	196	199					15																	65793060		2201	4299	6500	SO:0001583	missense	54878	exon5			CAATGCGTTTTCT	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.478C>T	15.37:g.65793060G>A	ENSP00000339208:p.Arg160Cys	190	0	0		179	62	0.346369	NM_197960	Q7Z4C8|Q7Z4D3|Q7Z4E1|Q8IWG7|Q8NEM5|Q96JX1|Q9HBM2|Q9HBM3|Q9HBM4|Q9HBM5|Q9NXF4	Missense_Mutation	SNP	ENST00000341861.5	37	CCDS10207.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.943085	0.92526	.	.	ENSG00000074603	ENST00000341861;ENST00000358939;ENST00000300141;ENST00000321147;ENST00000321118;ENST00000339244;ENST00000395652	T;T;T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5;1.5;1.5	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.58864	0.2152	M	0.72479	2.2	0.40608	D	0.981643	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.996;1.0;1.0	T	0.60047	-0.7339	10	0.87932	D	0	-17.8264	20.2885	0.98538	0.0:0.0:1.0:0.0	.	144;144;160;160	Q6V1X1-3;Q6V1X1-4;Q6V1X1-2;Q6V1X1	.;.;.;DPP8_HUMAN	C	160;144;144;160;160;160;160	ENSP00000339208:R160C;ENSP00000351817:R144C;ENSP00000300141:R144C;ENSP00000318111:R160C;ENSP00000316373:R160C;ENSP00000341230:R160C;ENSP00000379013:R160C	ENSP00000300141:R144C	R	-	1	0	DPP8	63580113	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.896000	0.87350	2.791000	0.96007	0.650000	0.86243	CGC	.	.	none		0.393	DPP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256847.1	NM_017743		A	65793060	G	A	65793060	3	1	22	1	0	0	0	0	1	0	0	0	4734	1145	40	1	2286	1	DPP8	15	65793060	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	111412	65793060	36738332	3044	5945											
MAP2K1	5604	hgsc.bcm.edu	37	chr15	66779597	66779597	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacagccgacctcccatggcAatttttgagttgttggatta	9	13	10	9	1	0	1	0	1	0	0	1	4	1	2	3	2	1	3	3	2	2	5	rs146869577	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:66779597A>T	ENST00000307102.5	+	8	1458	c.927A>T	c.(925-927)gcA>gcT	p.A309A	CTD-3185P2.1_ENST00000565387.1_RNA|MAP2K1_ENST00000566326.1_Silent_p.A133A|CTD-3185P2.2_ENST00000602360.1_RNA	NM_002755.3	NP_002746.1	Q02750	MP2K1_HUMAN	mitogen-activated protein kinase kinase 1	309	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cellular senescence (GO:0090398)|chemotaxis (GO:0006935)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|Golgi inheritance (GO:0048313)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|keratinocyte differentiation (GO:0030216)|labyrinthine layer development (GO:0060711)|MAPK cascade (GO:0000165)|melanosome transport (GO:0032402)|mitotic nuclear division (GO:0007067)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell proliferation (GO:0008285)|negative regulation of homotypic cell-cell adhesion (GO:0034111)|neurotrophin TRK receptor signaling pathway (GO:0048011)|placenta blood vessel development (GO:0060674)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|protein heterooligomerization (GO:0051291)|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)|regulation of vascular smooth muscle contraction (GO:0003056)|response to axon injury (GO:0048678)|response to glucocorticoid (GO:0051384)|response to oxidative stress (GO:0006979)|signal transduction (GO:0007165)|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)|vesicle transport along microtubule (GO:0047496)	cell cortex (GO:0005938)|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)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase activity (GO:0004672)|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)|receptor signaling protein tyrosine phosphatase activity (GO:0004728)			endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(8)|urinary_tract(1)	20					Bosutinib(DB06616)|Trametinib(DB08911)	CTCCCATGGCAATTTTTGAGT	0.393													A|||	25	0.00499201	0.0182	0.0014	5008	,	,		20753	0.0		0.0	False		,,,				2504	0.0				p.A309A		Atlas-SNP	.											.	MAP2K1	115	.	0			c.A927T						PASS	.	A		61,4341	58.1+/-94.6	0,61,2140	141	130	134		927	-5.7	1	15	dbSNP_134	134	0,8598		0,0,4299	no	coding-synonymous	MAP2K1	NM_002755.3		0,61,6439	TT,TA,AA		0.0,1.3857,0.4692		309/394	66779597	61,12939	2201	4299	6500	SO:0001819	synonymous_variant	5604	exon8			CATGGCAATTTTT	L11284	CCDS10216.1	15q22.1-q22.33	2014-09-17			ENSG00000169032	ENSG00000169032	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6840	protein-coding gene	gene with protein product		176872		PRKMK1		9465908, 8388392	Standard	NM_002755		Approved	MEK1, MAPKK1	uc010bhq.3	Q02750	OTTHUMG00000133196	ENST00000307102.5:c.927A>T	15.37:g.66779597A>T		133	0	0		115	51	0.443478	NM_002755		Silent	SNP	ENST00000307102.5	37	CCDS10216.1																																																																																			A|0.995;T|0.005	0.005	strong		0.393	MAP2K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256906.4			T	66779597	A	T	66779597	2	4	22	1	0	0	0	0	0	0	0	1	9245	117	5	5		5	MAP2K1	15	66779597	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	986537	66779597	35751795	3045	5946											
ITGA11	22801	hgsc.bcm.edu	37	chr15	68603345	68603345	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactcaccagctgtggagcaCgacgcaagtcttcctccact	9	8	8	16	2	2	0	1	0	1	0	4	2	4	1	3	1	2	3	3	1	1	1	rs146663204	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:68603345C>T	ENST00000315757.7	-	26	3247	c.3161G>A	c.(3160-3162)cGt>cAt	p.R1054H	ITGA11_ENST00000423218.2_Missense_Mutation_p.R1055H	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	1054					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						CTGTGGAGCACGACGCAAGTC	0.607													C|||	22	0.00439297	0.0166	0.0	5008	,	,		17947	0.0		0.0	False		,,,				2504	0.0				p.R1054H		Atlas-SNP	.											.	ITGA11	110	.	0			c.G3161A						PASS	.	C	HIS/ARG	64,4062		1,62,2000	37	38	38		3161	-0.7	0	15	dbSNP_134	38	0,8378		0,0,4189	yes	missense	ITGA11	NM_001004439.1	29	1,62,6189	TT,TC,CC		0.0,1.5511,0.5118	benign	1054/1189	68603345	64,12440	2063	4189	6252	SO:0001583	missense	22801	exon26			GGAGCACGACGCA	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.3161G>A	15.37:g.68603345C>T	ENSP00000327290:p.Arg1054His	76	0	0		88	33	0.375	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	37	CCDS45291.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	0.254	-1.004438	0.02112	0.015511	0.0	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000535491	T;T	0.51325	0.71;0.8	4.72	-0.744	0.11101	.	0.394401	0.31051	N	0.008356	T	0.11024	0.0269	N	0.05383	-0.06	0.09310	N	0.99999	B;B	0.11235	0.0;0.004	B;B	0.08055	0.002;0.003	T	0.13522	-1.0506	10	0.23891	T	0.37	.	8.4623	0.32936	0.0:0.5066:0.0:0.4934	.	1054;1054	A8K8T0;Q9UKX5	.;ITA11_HUMAN	H	1054;1055;689	ENSP00000327290:R1054H;ENSP00000403392:R1055H	ENSP00000327290:R1054H	R	-	2	0	ITGA11	66390399	0.024000	0.19004	0.024000	0.17045	0.267000	0.26476	0.065000	0.14466	0.021000	0.15133	0.655000	0.94253	CGT	C|0.997;T|0.003	0.003	strong		0.607	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211		T	68603345	C	T	68603345	3	4	22	1	0	0	0	0	1	0	0	0	7883	536	19	1	425	1	ITGA11	15	68603345	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1823748	68603345	33928047	3046	5947											
ITGA11	22801	hgsc.bcm.edu	37	chr15	68631920	68631920	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggaatgaccttcccggcactCgtctcctttagcacagctcc	7	10	8	16	2	1	1	0	1	1	0	5	2	3	2	4	2	2	3	4	2	2	3	rs9302249	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:68631920C>T	ENST00000315757.7	-	11	1280	c.1194G>A	c.(1192-1194)acG>acA	p.T398T	ITGA11_ENST00000423218.2_Silent_p.T398T	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	398					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						TCCCGGCACTCGTCTCCTTTA	0.582													C|||	302	0.0603035	0.2201	0.013	5008	,	,		17677	0.0		0.001	False		,,,				2504	0.001				p.T398T		Atlas-SNP	.											ITGA11,colon,carcinoma,-1,1	ITGA11	110	1	0			c.G1194A						PASS	.	C		666,3374		51,564,1405	69	75	73		1194	-3.1	0.2	15	dbSNP_119	73	4,8346		0,4,4171	no	coding-synonymous	ITGA11	NM_001004439.1		51,568,5576	TT,TC,CC		0.0479,16.4851,5.4076		398/1189	68631920	670,11720	2020	4175	6195	SO:0001819	synonymous_variant	22801	exon11			GGCACTCGTCTCC	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.1194G>A	15.37:g.68631920C>T		56	0	0		78	32	0.410256	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Silent	SNP	ENST00000315757.7	37	CCDS45291.1																																																																																			C|0.956;T|0.044	0.044	strong		0.582	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211		T	68631920	C	T	68631920	2	4	22	1	0	0	0	0	0	0	0	1	7883	871	31	1		1	ITGA11	15	68631920	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	28575	68631920	33899472	3047	5948											
ITGA11	22801	hgsc.bcm.edu	37	chr15	68650913	68650913	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acaatgacgatgtccatgtaGgtctggcaccctggaaagtg	11	9	12	9	1	1	1	0	1	1	0	2	3	2	2	2	3	0	2	2	3	3	1	rs61729771	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:68650913G>A	ENST00000315757.7	-	6	569	c.483C>T	c.(481-483)acC>acT	p.T161T	ITGA11_ENST00000423218.2_Silent_p.T161T|ITGA11_ENST00000562826.1_5'UTR	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	161					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						TGTCCATGTAGGTCTGGCACC	0.483													G|||	259	0.0517173	0.1853	0.0202	5008	,	,		22319	0.0		0.0	False		,,,				2504	0.0				p.T161T		Atlas-SNP	.											.	ITGA11	110	.	0			c.C483T						PASS	.	G		686,3688	269.5+/-269.1	42,602,1543	73	75	74		483	2.1	1	15	dbSNP_129	74	4,8592	3.7+/-12.6	0,4,4294	no	coding-synonymous	ITGA11	NM_001004439.1		42,606,5837	AA,AG,GG		0.0465,15.6836,5.32		161/1189	68650913	690,12280	2187	4298	6485	SO:0001819	synonymous_variant	22801	exon6			CATGTAGGTCTGG	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.483C>T	15.37:g.68650913G>A		74	0	0		75	74	0.986667	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Silent	SNP	ENST00000315757.7	37	CCDS45291.1																																																																																			G|0.956;A|0.044	0.044	strong		0.483	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211		A	68650913	G	A	68650913	2	1	22	1	0	0	0	0	0	0	0	1	7883	987	35	2		2	ITGA11	15	68650913	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	18993	68650913	33880479	3048	5949											
GLCE	26035	hgsc.bcm.edu	37	chr15	69561181	69561181	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtttctatctgagcagcaTggagttaaagctgtgtttat	11	15	10	5	0	2	1	0	1	2	0	2	2	2	2	0	1	3	6	0	1	5	5	rs56045514	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:69561181T>C	ENST00000261858.2	+	5	1680	c.1452T>C	c.(1450-1452)caT>caC	p.H484H	GLCE_ENST00000559420.2_Silent_p.H420H	NM_015554.1	NP_056369.1	O94923	GLCE_HUMAN	glucuronic acid epimerase	484					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						CTGAGCAGCATGGAGTTAAAG	0.353													T|||	323	0.0644968	0.2383	0.0086	5008	,	,		21803	0.0		0.002	False		,,,				2504	0.0				p.H484H		Atlas-SNP	.											.	GLCE	48	.	0			c.T1452C						PASS	.	T		685,3715	279.6+/-274.9	68,549,1583	58	65	62		1452	-6.6	0.8	15	dbSNP_129	62	5,8591	3.7+/-12.6	0,5,4293	no	coding-synonymous	GLCE	NM_015554.1		68,554,5876	CC,CT,TT		0.0582,15.5682,5.3093		484/618	69561181	690,12306	2200	4298	6498	SO:0001819	synonymous_variant	26035	exon5			GCAGCATGGAGTT	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.1452T>C	15.37:g.69561181T>C		60	0	0		62	35	0.564516	NM_015554	Q6GUQ2	Silent	SNP	ENST00000261858.2	37	CCDS32277.1																																																																																			T|0.951;C|0.049	0.049	strong		0.353	GLCE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015554		C	69561181	T	C	69561181	2	2	22	1	0	0	0	0	0	0	0	1	6440	1461	51	3		3	GLCE	15	69561181	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	910268	69561181	32970211	3049	5950											
KIF23	9493	hgsc.bcm.edu	37	chr15	69714347	69714347	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaggtcttctttttacataTggtgtgacgggaagtggaaa	10	14	13	4	1	2	1	0	1	2	0	2	3	2	3	0	4	1	1	0	4	5	6	rs34969957	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:69714347T>C	ENST00000260363.4	+	5	450	c.333T>C	c.(331-333)taT>taC	p.Y111Y	KIF23_ENST00000558585.1_5'Flank|KIF23_ENST00000559279.1_Silent_p.Y111Y|KIF23_ENST00000537891.1_5'Flank|KIF23_ENST00000395392.2_Silent_p.Y111Y|KIF23_ENST00000352331.4_Silent_p.Y111Y	NM_138555.2	NP_612565.1	Q02241	KIF23_HUMAN	kinesin family member 23	111	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)|cytokinesis (GO:0000910)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle elongation (GO:0000022)|positive regulation of cytokinesis (GO:0032467)|spindle midzone assembly involved in mitosis (GO:0051256)	centralspindlin complex (GO:0097149)|centrosome (GO:0005813)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercellular bridge (GO:0045171)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(6)|prostate(2)|skin(1)	21						TTTTTACATATGGTGTGACGG	0.408													T|||	60	0.0119808	0.0401	0.0043	5008	,	,		17202	0.0		0.003	False		,,,				2504	0.001				p.Y111Y		Atlas-SNP	.											.	KIF23	57	.	0			c.T333C						PASS	.	T	,	162,4236	110.8+/-149.0	4,154,2041	110	88	96		333,333	-0.3	1	15	dbSNP_126	96	6,8590	5.0+/-18.6	0,6,4292	no	coding-synonymous,coding-synonymous	KIF23	NM_004856.5,NM_138555.2	,	4,160,6333	CC,CT,TT		0.0698,3.6835,1.2929	,	111/857,111/961	69714347	168,12826	2199	4298	6497	SO:0001819	synonymous_variant	9493	exon5			TACATATGGTGTG	X67155	CCDS32278.1, CCDS32279.1	15q23	2008-03-03	2003-01-13	2003-01-17		ENSG00000137807		"Kinesins"	6392	protein-coding gene	gene with protein product		605064	"kinesin-like 5 (mitotic kinesin-like protein 1)"	KNSL5		1406973	Standard	NM_138555		Approved	MKLP1, MKLP-1	uc002asb.3	Q02241		ENST00000260363.4:c.333T>C	15.37:g.69714347T>C		175	0	0		180	90	0.5	NM_138555	Q8WVP0	Silent	SNP	ENST00000260363.4	37	CCDS32278.1																																																																																			T|0.985;C|0.015	0.015	strong		0.408	KIF23-201	KNOWN	basic|CCDS	protein_coding	protein_coding				C	69714347	T	C	69714347	2	2	22	1	0	0	0	0	0	0	0	1	8300	1471	51	3		3	KIF23	15	69714347	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	153166	69714347	32817045	3050	5951											
UACA	55075	hgsc.bcm.edu	37	chr15	70957106	70957106	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taggtgagttgggaaaggccAttgagtgcctgttttaatct	9	14	13	5	0	1	2	0	2	1	0	1	3	1	3	2	3	1	2	2	3	3	5	rs78551559	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:70957106A>G	ENST00000322954.6	-	17	4193	c.4008T>C	c.(4006-4008)aaT>aaC	p.N1336N	UACA_ENST00000379983.2_Silent_p.N1323N|UACA_ENST00000560441.1_Silent_p.N1321N|UACA_ENST00000539319.1_Silent_p.N1227N	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	1336					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						GGGAAAGGCCATTGAGTGCCT	0.413													A|||	83	0.0165735	0.0605	0.0043	5008	,	,		17428	0.0		0.0	False		,,,				2504	0.0				p.N1336N		Atlas-SNP	.											.	UACA	235	.	0			c.T4008C						PASS	.	A	,	203,4195	126.6+/-163.6	3,197,1999	150	127	135		3969,4008	-4.9	0	15	dbSNP_132	135	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous,coding-synonymous	UACA	NM_001008224.1,NM_018003.2	,	3,198,6296	GG,GA,AA		0.0116,4.6157,1.57	,	1323/1404,1336/1417	70957106	204,12790	2199	4298	6497	SO:0001819	synonymous_variant	55075	exon17			AAGGCCATTGAGT	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.4008T>C	15.37:g.70957106A>G		203	0	0		203	101	0.497537	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Silent	SNP	ENST00000322954.6	37	CCDS10235.1																																																																																			A|0.983;G|0.017	0.017	strong		0.413	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			G	70957106	A	G	70957106	2	3	22	1	0	0	0	0	0	0	0	1	16839	214	8	3		3	UACA	15	70957106	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1242759	70957106	31574286	3051	5952											
UACA	55075	hgsc.bcm.edu	37	chr15	70959576	70959576	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aacaattgatgcagtttggtCactgtctgctgctctttctc	7	16	8	10	0	4	1	1	1	3	0	5	1	4	1	0	1	4	4	0	1	2	3	rs61746327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:70959576C>T	ENST00000322954.6	-	16	3632	c.3447G>A	c.(3445-3447)gtG>gtA	p.V1149V	UACA_ENST00000379983.2_Silent_p.V1136V|UACA_ENST00000560441.1_Silent_p.V1134V|UACA_ENST00000539319.1_Silent_p.V1040V	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	1149					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						GCAGTTTGGTCACTGTCTGCT	0.393													C|||	49	0.00978435	0.0356	0.0029	5008	,	,		20629	0.0		0.0	False		,,,				2504	0.0				p.V1149V		Atlas-SNP	.											.	UACA	235	.	0			c.G3447A						PASS	.	C	,	148,4250	100.7+/-139.4	1,146,2052	179	178	179		3408,3447	4.7	0.8	15	dbSNP_129	179	0,8594		0,0,4297	no	coding-synonymous,coding-synonymous	UACA	NM_001008224.1,NM_018003.2	,	1,146,6349	TT,TC,CC		0.0,3.3652,1.1392	,	1136/1404,1149/1417	70959576	148,12844	2199	4297	6496	SO:0001819	synonymous_variant	55075	exon16			TTTGGTCACTGTC	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.3447G>A	15.37:g.70959576C>T		149	0	0		161	68	0.42236	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Silent	SNP	ENST00000322954.6	37	CCDS10235.1																																																																																			C|0.989;T|0.011	0.011	strong		0.393	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			T	70959576	C	T	70959576	2	4	22	1	0	0	0	0	0	0	0	1	16839	813	29	2		2	UACA	15	70959576	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2470	70959576	31571816	3052	5953											
UACA	55075	hgsc.bcm.edu	37	chr15	70960422	70960422	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcattcagtgtcattttaacCtcttcatgggttttaactgg	8	18	7	8	0	5	0	4	0	1	0	5	0	5	0	1	2	2	1	1	2	2	6	rs61742861	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:70960422C>T	ENST00000322954.6	-	16	2786	c.2601G>A	c.(2599-2601)gaG>gaA	p.E867E	UACA_ENST00000379983.2_Silent_p.E854E|UACA_ENST00000560441.1_Silent_p.E852E|UACA_ENST00000539319.1_Silent_p.E758E	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	867					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						TCATTTTAACCTCTTCATGGG	0.333													C|||	75	0.014976	0.0552	0.0029	5008	,	,		19447	0.0		0.0	False		,,,				2504	0.0				p.E867E		Atlas-SNP	.											.	UACA	235	.	0			c.G2601A						PASS	.	C	,	195,4201	120.0+/-157.7	3,189,2006	96	90	92		2562,2601	2.6	0.6	15	dbSNP_129	92	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous,coding-synonymous	UACA	NM_001008224.1,NM_018003.2	,	3,190,6303	TT,TC,CC		0.0116,4.4359,1.5086	,	854/1404,867/1417	70960422	196,12796	2198	4298	6496	SO:0001819	synonymous_variant	55075	exon16			TTTAACCTCTTCA	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.2601G>A	15.37:g.70960422C>T		140	0	0		108	56	0.518519	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Silent	SNP	ENST00000322954.6	37	CCDS10235.1																																																																																			C|0.985;T|0.015	0.015	strong		0.333	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			T	70960422	C	T	70960422	2	4	22	1	0	0	0	0	0	0	0	1	16839	680	24	2		2	UACA	15	70960422	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	846	70960422	31570970	3053	5954											
UACA	55075	hgsc.bcm.edu	37	chr15	70968850	70968850	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acctcaaaatatttaaatctAtttttcagagcctcaatagt	15	15	3	8	0	4	1	3	0	1	1	4	1	4	1	2	0	1	0	2	0	8	7	rs61741196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:70968850A>G	ENST00000322954.6	-	13	1298	c.1113T>C	c.(1111-1113)aaT>aaC	p.N371N	UACA_ENST00000379983.2_Silent_p.N358N|UACA_ENST00000560441.1_Silent_p.N358N|UACA_ENST00000539319.1_Silent_p.N262N	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	371					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						ATTTAAATCTATTTTTCAGAG	0.318													A|||	49	0.00978435	0.0356	0.0029	5008	,	,		16930	0.0		0.0	False		,,,				2504	0.0				p.N371N		Atlas-SNP	.											.	UACA	235	.	0			c.T1113C						PASS	.	A	,	142,4254	98.0+/-136.7	1,140,2057	61	63	62		1074,1113	-5.5	0.7	15	dbSNP_129	62	0,8584		0,0,4292	no	coding-synonymous,coding-synonymous	UACA	NM_001008224.1,NM_018003.2	,	1,140,6349	GG,GA,AA		0.0,3.2302,1.094	,	358/1404,371/1417	70968850	142,12838	2198	4292	6490	SO:0001819	synonymous_variant	55075	exon13			AAATCTATTTTTC	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.1113T>C	15.37:g.70968850A>G		50	0	0		52	30	0.576923	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Silent	SNP	ENST00000322954.6	37	CCDS10235.1																																																																																			A|0.989;G|0.011	0.011	strong		0.318	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			G	70968850	A	G	70968850	2	3	22	1	0	0	0	0	0	0	0	1	16839	446	16	3		3	UACA	15	70968850	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	8428	70968850	31562542	3054	5955											
LARP6	55323	hgsc.bcm.edu	37	chr15	71128691	71128691	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccagcttgttcctcctcacGtgttttagcaaaaaggcgtc	8	12	8	13	2	1	0	1	0	0	0	4	0	3	0	3	1	2	4	3	1	3	4	rs78188777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:71128691G>A	ENST00000299213.8	-	2	424	c.354C>T	c.(352-354)caC>caT	p.H118H		NM_018357.2	NP_060827.2	Q9BRS8	LARP6_HUMAN	La ribonucleoprotein domain family, member 6	118	HTH La-type RNA-binding. {ECO:0000255|PROSITE-ProRule:PRU00332}.				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						TCCTCCTCACGTGTTTTAGCA	0.453													G|||	79	0.0157748	0.0567	0.0058	5008	,	,		20033	0.0		0.0	False		,,,				2504	0.0				p.H118H		Atlas-SNP	.											.	LARP6	43	.	0			c.C354T						PASS	.	G		219,4179	132.1+/-168.6	5,209,1985	124	123	123		354	-3.1	1	15	dbSNP_132	123	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous	LARP6	NM_018357.2		5,210,6281	AA,AG,GG		0.0116,4.9795,1.6933		118/492	71128691	220,12772	2199	4297	6496	SO:0001819	synonymous_variant	55323	exon2			CCTCACGTGTTTT	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.354C>T	15.37:g.71128691G>A		250	0	0		206	93	0.451456	NM_018357	Q5XKE4|Q8N3N2|Q9NUR0	Silent	SNP	ENST00000299213.8	37	CCDS32281.1																																																																																			G|0.984;A|0.016	0.016	strong		0.453	LARP6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417197.2	NM_018357		A	71128691	G	A	71128691	2	1	22	1	0	0	0	0	0	0	0	1	8641	1136	40	1		1	LARP6	15	71128691	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	159841	71128691	31402701	3055	5956											
HCN4	10021	hgsc.bcm.edu	37	chr15	73617723	73617723	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cggtgctcgtagtagtcgtgGatgcgctgccgggtgtcggg	3	10	19	9	6	0	0	0	0	0	0	3	1	0	1	1	4	3	4	1	4	2	2	rs141966309	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:73617723G>T	ENST00000261917.3	-	5	2646	c.1653C>A	c.(1651-1653)atC>atA	p.I551I		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	551					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)		AGTAGTCGTGGATGCGCTGCC	0.647													g|||	7	0.00139776	0.0053	0.0	5008	,	,		16066	0.0		0.0	False		,,,				2504	0.0				p.I551I		Atlas-SNP	.											.	HCN4	150	.	0			c.C1653A						PASS	.	G		23,4373	30.8+/-60.4	1,21,2176	107	111	110		1653	3.3	1	15	dbSNP_134	110	0,8594		0,0,4297	no	coding-synonymous	HCN4	NM_005477.2		1,21,6473	TT,TG,GG		0.0,0.5232,0.1771		551/1204	73617723	23,12967	2198	4297	6495	SO:0001819	synonymous_variant	10021	exon5			GTCGTGGATGCGC	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.1653C>A	15.37:g.73617723G>T		217	0	0		196	94	0.479592	NM_005477	Q9UMQ7	Silent	SNP	ENST00000261917.3	37	CCDS10248.1																																																																																			G|0.998;T|0.002	0.002	strong		0.647	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477		T	73617723	G	T	73617723	2	4	22	1	0	0	0	0	0	0	0	1	7008	1164	41	4		4	HCN4	15	73617723	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2489032	73617723	28913669	3056	5957											
NPTN	27020	hgsc.bcm.edu	37	chr15	73862606	73862606	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtggggccaggtggctccgCaccctgaggacagtgacaac	9	5	15	12	1	0	2	0	2	0	0	1	3	1	3	3	5	1	2	3	5	1	0	rs35100473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:73862606C>T	ENST00000345330.4	-	6	1196	c.999G>A	c.(997-999)gtG>gtA	p.V333V	NPTN_ENST00000564551.1_5'Flank|NPTN_ENST00000351217.6_Silent_p.V217V|NPTN_ENST00000563691.1_Silent_p.V333V|NPTN_ENST00000545878.1_Silent_p.V333V|NPTN_ENST00000542234.1_Silent_p.V128V|NPTN_ENST00000287226.8_Missense_Mutation_p.C317Y|NPTN_ENST00000562924.1_Silent_p.V217V	NM_001161363.1|NM_012428.3	NP_001154835.1|NP_036560.1	Q9Y639	NPTN_HUMAN	neuroplastin	333					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						GGTGGCTCCGCACCCTGAGGA	0.522													C|||	57	0.0113818	0.0393	0.0043	5008	,	,		16485	0.0		0.002	False		,,,				2504	0.0				p.V333V	Pancreas(101;1519 1568 9459 19537 41286)|Esophageal Squamous(143;1278 1787 35254 36835 44843)	Atlas-SNP	.											.	NPTN	35	.	0			c.G999A						PASS	.	C	,,,	139,4257	100.3+/-138.9	3,133,2062	80	75	76		999,651,999,651	0.3	1	15	dbSNP_126	76	0,8594		0,0,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NPTN	NM_001161363.1,NM_001161364.1,NM_012428.3,NM_017455.3	,,,	3,133,6359	TT,TC,CC		0.0,3.162,1.0701	,,,	333/395,217/279,333/399,217/283	73862606	139,12851	2198	4297	6495	SO:0001819	synonymous_variant	27020	exon6			GCTCCGCACCCTG	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.999G>A	15.37:g.73862606C>T		160	0	0		187	103	0.550802	NM_001161363	B2RAL7|B7Z4D3|B7ZLL2|Q17R52|Q59EJ9|Q6NVX7|Q9Y640	Silent	SNP	ENST00000345330.4	37	CCDS10249.1	21	0.009615384615384616	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	16.12	3.034197	0.54896	0.03162	0.0	ENSG00000156642	ENST00000287226	T	0.67171	-0.25	5.6	0.321	0.15883	.	.	.	.	.	T	0.33411	0.0862	.	.	.	0.52501	D	0.999955	.	.	.	.	.	.	T	0.54516	-0.8282	6	0.87932	D	0	.	3.2099	0.06678	0.1208:0.4314:0.1233:0.3246	rs35100473	.	.	.	Y	317	ENSP00000287226:C317Y	ENSP00000287226:C317Y	C	-	2	0	NPTN	71649659	0.657000	0.27393	1.000000	0.80357	0.994000	0.84299	-0.201000	0.09464	0.055000	0.16094	-0.345000	0.07892	TGC	C|0.988;G|0.000;T|0.012	0.012	strong		0.522	NPTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268980.1	NM_012428		T	73862606	C	T	73862606	2	4	22	1	0	0	0	0	0	0	0	1	10610	697	25	2		2	NPTN	15	73862606	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	244883	73862606	28668786	3057	5958											
CYP1A2	1544	hgsc.bcm.edu	37	chr15	75043592	75043592	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagaaggggcctagagccagCggcaacctcatcccacagga	13	3	12	13	1	1	2	1	0	0	2	2	3	2	3	4	4	3	1	4	4	4	1	rs17861157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:75043592C>A	ENST00000343932.4	+	3	957	c.894C>A	c.(892-894)agC>agA	p.S298R		NM_000761.3	NP_000752.2	P05177	CP1A2_HUMAN	cytochrome P450, family 1, subfamily A, polypeptide 2	298			S -> R (in dbSNP:rs17861157). {ECO:0000269|PubMed:15469410}.		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)"	CTAGAGCCAGCGGCAACCTCA	0.562													C|||	120	0.0239617	0.0893	0.0029	5008	,	,		21893	0.0		0.0	False		,,,				2504	0.0				p.S298R		Atlas-SNP	.											.	CYP1A2	70	.	0			c.C894A						PASS	.	C	ARG/SER	308,4086	164.7+/-196.3	7,294,1896	138	110	120		894	-9.7	0	15	dbSNP_123	120	2,8590	2.2+/-6.3	0,2,4294	yes	missense	CYP1A2	NM_000761.3	110	7,296,6190	AA,AC,CC		0.0233,7.0096,2.3872	benign	298/517	75043592	310,12676	2197	4296	6493	SO:0001583	missense	1544	exon3			AGCCAGCGGCAAC	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.894C>A	15.37:g.75043592C>A	ENSP00000342007:p.Ser298Arg	111	1	0.00900901		119	119	1	NM_000761	Q16754|Q6NWU5|Q9BXX7|Q9UK49	Missense_Mutation	SNP	ENST00000343932.4	37	CCDS32293.1	41	0.018772893772893772	41	0.08333333333333333	0	0.0	0	0.0	0	0.0	C	12.56	1.975261	0.34848	0.070096	2.33E-4	ENSG00000140505	ENST00000343932	T	0.79653	-1.29	4.85	-9.7	0.00521	.	0.549195	0.21605	N	0.071895	T	0.06962	0.0177	L	0.27053	0.805	0.09310	N	1	B	0.31174	0.311	B	0.28784	0.094	T	0.38112	-0.9676	10	0.59425	D	0.04	.	8.7855	0.34818	0.0:0.2777:0.1818:0.5405	rs17861157;rs56991650	298	P05177-2	.	R	298	ENSP00000342007:S298R	ENSP00000342007:S298R	S	+	3	2	CYP1A2	72830645	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-4.224000	0.00271	-3.301000	0.00192	-0.369000	0.07265	AGC	C|0.973;A|0.027	0.027	strong		0.562	CYP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421263.2	NM_000761		A	75043592	C	A	75043592	3	1	22	1	0	0	0	0	1	0	0	0	4152	767	27	4	900	4	CYP1A2	15	75043592	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1180986	75043592	27487800	3058	5959											
LMAN1L	79748	hgsc.bcm.edu	37	chr15	75111530	75111530	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cctcactcccagtgatccagGtgagttctgtgtggatgtgg	6	12	13	10	0	2	2	1	2	1	0	4	3	4	3	3	3	0	1	3	3	0	1	rs62621375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:75111530G>A	ENST00000309664.5	+	6	774	c.635G>A	c.(634-636)gGt>gAt	p.G212D	LMAN1L_ENST00000379709.3_Missense_Mutation_p.G212D|RP11-414J4.2_ENST00000564823.1_RNA	NM_021819.2	NP_068591.2	Q9HAT1	LMA1L_HUMAN	lectin, mannose-binding, 1 like	212	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						AGTGATCCAGGTGAGTTCTGT	0.612													A|||	374	0.0746805	0.2723	0.0144	5008	,	,		19129	0.001		0.003	False		,,,				2504	0.0				p.G212D		Atlas-SNP	.											.	LMAN1L	43	.	0			c.G635A						PASS	.	A	ASP/GLY	1009,3385	728.8+/-410.0	126,757,1314	207	185	193		635	5.7	0	15	dbSNP_129	193	6,8586	818.6+/-406.8	0,6,4290	yes	missense	LMAN1L	NM_021819.2	94	126,763,5604	AA,AG,GG		0.0698,22.9631,7.8161	benign	212/527	75111530	1015,11971	2197	4296	6493	SO:0001583	missense	79748	exon6			ATCCAGGTGAGTT	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.635G>A	15.37:g.75111530G>A	ENSP00000310431:p.Gly212Asp	236	0	0		225	224	0.995556	NM_021819	Q6UWN2	Missense_Mutation	SNP	ENST00000309664.5	37	CCDS10270.1	151	0.06913919413919414	143	0.29065040650406504	5	0.013812154696132596	1	0.0017482517482517483	2	0.002638522427440633	A	4.989	0.183651	0.09495	0.229631	6.98E-4	ENSG00000140506	ENST00000309664;ENST00000456603;ENST00000379709	T;T	0.63255	-0.03;-0.03	5.67	5.67	0.87782	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.744014	0.12971	N	0.424120	T	0.00012	0.0000	N	0.00072	-2.265	0.80722	P	0.0	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	0.20174	-1.0283	8	.	.	.	.	8.6109	0.33801	0.9131:0.0:0.0869:0.0	rs62621375	104;212;140;212	B4DGW5;Q9HAT1-3;B4DU67;Q9HAT1	.;.;.;LMA1L_HUMAN	D	212;104;212	ENSP00000310431:G212D;ENSP00000369031:G212D	.	G	+	2	0	LMAN1L	72898583	0.706000	0.27856	0.008000	0.14137	0.095000	0.18619	2.764000	0.47613	0.987000	0.38709	-0.332000	0.08345	GGT	G|0.924;A|0.076	0.076	strong		0.612	LMAN1L-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286397.4			A	75111530	G	A	75111530	3	1	22	1	0	0	0	0	1	0	0	0	8846	1261	44	2	657	2	LMAN1L	15	75111530	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	67938	75111530	27419862	3059	5960											
SCAMP5	192683	hgsc.bcm.edu	37	chr15	75305058	75305058	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccattgcccaaattcatcccGctgaagccatgtttctacca	10	11	5	15	1	2	1	1	1	1	0	3	1	3	1	5	0	3	2	5	0	3	4	rs60910940	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:75305058G>T	ENST00000361900.6	+	4	255	c.48G>T	c.(46-48)ccG>ccT	p.P16P	SCAMP5_ENST00000545456.1_5'UTR|SCAMP5_ENST00000425597.3_Silent_p.P16P|SCAMP5_ENST00000562212.1_Silent_p.P16P|SCAMP5_ENST00000565923.1_3'UTR	NM_001178111.1	NP_001171582.1	Q8TAC9	SCAM5_HUMAN	secretory carrier membrane protein 5	16					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						AATTCATCCCGCTGAAGCCAT	0.507													G|||	168	0.0335463	0.1241	0.0043	5008	,	,		19935	0.0		0.001	False		,,,				2504	0.0				p.P16P		Atlas-SNP	.											.	SCAMP5	34	.	0			c.G48T						PASS	.	G	,,	388,3722		14,360,1681	97	102	101		48,48,48	-10.7	0.4	15	dbSNP_129	101	3,8399		0,3,4198	no	coding-synonymous,coding-synonymous,coding-synonymous	SCAMP5	NM_001178111.1,NM_001178112.1,NM_138967.3	,,	14,363,5879	TT,TG,GG		0.0357,9.4404,3.125	,,	16/236,16/236,16/236	75305058	391,12121	2055	4201	6256	SO:0001819	synonymous_variant	192683	exon4			CATCCCGCTGAAG	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.48G>T	15.37:g.75305058G>T		164	1	0.00609756		167	167	1	NM_001178111	B3KPJ7|B7Z762|D3DW71|Q8N3M4	Silent	SNP	ENST00000361900.6	37	CCDS45306.1																																																																																			G|0.966;T|0.034	0.034	strong		0.507	SCAMP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420015.2	NM_138967		T	75305058	G	T	75305058	2	4	22	1	0	0	0	0	0	0	0	1	13889	1074	38	4		4	SCAMP5	15	75305058	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	193528	75305058	27226334	3060	5961											
FBXO22	26263	hgsc.bcm.edu	37	chr15	76205550	76205550	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttttttctttgcagaatgttCgcatcttaccacatacagtt	9	18	5	9	1	2	1	0	0	2	1	3	1	2	1	1	0	3	4	1	0	3	8			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:76205550C>T	ENST00000308275.3	+	3	391	c.286C>T	c.(286-288)Cgc>Tgc	p.R96C	FBXO22_ENST00000453211.2_Missense_Mutation_p.R96C|FBXO22_ENST00000540507.1_5'UTR	NM_147188.2	NP_671717.1	Q8NEZ5	FBX22_HUMAN	F-box protein 22	96					cellular protein modification process (GO:0006464)|cellular response to starvation (GO:0009267)|nucleocytoplasmic transport (GO:0006913)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein polyubiquitination (GO:0000209)|regulation of skeletal muscle fiber development (GO:0048742)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						GCAGAATGTTCGCATCTTACC	0.383																																					p.R96C		Atlas-SNP	.											FBXO22_ENST00000453211,NS,carcinoma,0,3	FBXO22	60	3	0			c.C286T						PASS	.						65	69	68					15																	76205550		2197	4294	6491	SO:0001583	missense	26263	exon3			AATGTTCGCATCT	AF174602	CCDS10287.1, CCDS45310.1	15q23	2008-10-03	2004-06-15		ENSG00000167196	ENSG00000167196		"F-boxes /  "other""	13593	protein-coding gene	gene with protein product	"FIST domain containing 1"	609096	"F-box only protein 22"			10531035, 10531037, 17855421	Standard	NM_147188		Approved	FBX22, FISTC1	uc002bbk.3	Q8NEZ5	OTTHUMG00000142841	ENST00000308275.3:c.286C>T	15.37:g.76205550C>T	ENSP00000307833:p.Arg96Cys	16	0	0		20	11	0.55	NM_012170	Q0D2P8|Q6PIL5|Q8IXW3|Q9H824|Q9UKC0	Missense_Mutation	SNP	ENST00000308275.3	37	CCDS10287.1	.	.	.	.	.	.	.	.	.	.	C	15.09	2.729883	0.48833	.	.	ENSG00000167196	ENST00000308275;ENST00000453211	.	.	.	5.95	5.95	0.96441	.	0.409490	0.29676	N	0.011486	T	0.39937	0.1097	N	0.08118	0	0.80722	D	1	P;D	0.57571	0.916;0.98	B;P	0.46049	0.23;0.502	T	0.37663	-0.9696	9	0.39692	T	0.17	-3.1292	17.1124	0.86679	0.0:1.0:0.0:0.0	.	96;96	Q8NEZ5;Q8NEZ5-3	FBX22_HUMAN;.	C	96	.	ENSP00000307833:R96C	R	+	1	0	FBXO22	73992605	0.995000	0.38212	0.523000	0.27875	0.842000	0.47809	2.942000	0.49018	2.824000	0.97209	0.655000	0.94253	CGC	.	.	none		0.383	FBXO22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286477.2	NM_147188		T	76205550	C	T	76205550	3	4	22	1	0	0	0	0	1	0	0	0	5742	884	31	1	296	1	FBXO22	15	76205550	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	900492	76205550	26325842	3061	5962											
ADAMTS7	11173	hgsc.bcm.edu	37	chr15	79065509	79065509	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cacaccacagcggtcctccaTagcaccggagtcaatctcga	11	6	8	16	3	2	0	1	0	1	0	5	2	4	1	4	2	2	1	4	2	2	1	rs146076001	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:79065509T>C	ENST00000388820.4	-	14	2257	c.2047A>G	c.(2047-2049)Atg>Gtg	p.M683V	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	683	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						CGGTCCTCCATAGCACCGGAG	0.677													T|||	3	0.000599042	0.0023	0.0	5008	,	,		9782	0.0		0.0	False		,,,				2504	0.0				p.M683V		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.A2047G						PASS	.	T	VAL/MET	3,4287		0,3,2142	15	14	15		2047	-4.2	0.1	15	dbSNP_134	15	0,8154		0,0,4077	no	missense	ADAMTS7	NM_014272.3	21	0,3,6219	CC,CT,TT		0.0,0.0699,0.0241	benign	683/1687	79065509	3,12441	2145	4077	6222	SO:0001583	missense	11173	exon14			CCTCCATAGCACC	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.2047A>G	15.37:g.79065509T>C	ENSP00000373472:p.Met683Val	461	1	0.0021692		783	340	0.434227	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	37	CCDS32303.1	.	.	.	.	.	.	.	.	.	.	T	0.018	-1.480661	0.01027	6.99E-4	0.0	ENSG00000136378	ENST00000388820	T	0.68025	-0.3	3.75	-4.16	0.03869	.	0.686315	0.12999	N	0.421839	T	0.22282	0.0537	N	0.00347	-1.61	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43621	-0.9380	10	0.02654	T	1	.	10.8048	0.46512	0.0:0.4278:0.0:0.5722	.	683;683	A8MQ00;Q9UKP4	.;ATS7_HUMAN	V	683	ENSP00000373472:M683V	ENSP00000373472:M683V	M	-	1	0	ADAMTS7	76852564	0.000000	0.05858	0.065000	0.19835	0.592000	0.36648	0.103000	0.15292	-0.746000	0.04766	0.386000	0.25728	ATG	T|1.000;C|0.000	0.000	weak		0.677	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272		C	79065509	T	C	79065509	3	2	22	1	0	0	0	0	1	0	0	0	271	1406	49	3	3057	3	ADAMTS7	15	79065509	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2859959	79065509	23465883	3062	5963											
BCL2A1	597	hgsc.bcm.edu	37	chr15	80263111	80263111	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccgcaacaaaatatgaaatCtccttataggtatccacatc	15	11	4	11	1	1	1	0	1	1	0	5	1	3	1	3	1	1	2	3	1	8	4	rs34080999	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:80263111C>A	ENST00000267953.3	-	1	677	c.351G>T	c.(349-351)gaG>gaT	p.E117D	BCL2A1_ENST00000335661.6_Missense_Mutation_p.E117D	NM_004049.3	NP_004040.1	Q16548	B2LA1_HUMAN	BCL2-related protein A1	117			E -> D (in dbSNP:rs34080999).		extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)	mitochondrial outer membrane (GO:0005741)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	12						AATATGAAATCTCCTTATAGG	0.383													C|||	191	0.038139	0.1384	0.0086	5008	,	,		17180	0.0		0.002	False		,,,				2504	0.0				p.E117D		Atlas-SNP	.											.	BCL2A1	28	.	0			c.G351T						PASS	.	C	ASP/GLU,ASP/GLU	472,3934	219.1+/-236.9	26,420,1757	118	125	123		351,351	-5	0	15	dbSNP_126	123	7,8593	6.4+/-24.3	0,7,4293	yes	missense,missense	BCL2A1	NM_001114735.1,NM_004049.3	45,45	26,427,6050	AA,AC,CC		0.0814,10.7127,3.6829	benign,benign	117/164,117/176	80263111	479,12527	2203	4300	6503	SO:0001583	missense	597	exon1			TGAAATCTCCTTA		CCDS10312.1, CCDS45322.1	15q24.3	2014-05-20			ENSG00000140379	ENSG00000140379			991	protein-coding gene	gene with protein product		601056		HBPA1		8589678, 12771180	Standard	NM_004049		Approved	GRS, BFL1, BCL2L5, ACC-1, ACC-2	uc002bfc.4	Q16548	OTTHUMG00000144173	ENST00000267953.3:c.351G>T	15.37:g.80263111C>A	ENSP00000267953:p.Glu117Asp	244	0	0		224	105	0.46875	NM_001114735	Q6FGZ4|Q6FH19|Q86W13|Q99524	Missense_Mutation	SNP	ENST00000267953.3	37	CCDS10312.1	55	0.025183150183150184	50	0.1016260162601626	5	0.013812154696132596	0	0.0	0	0.0	C	11.44	1.639200	0.29157	0.107127	8.14E-4	ENSG00000140379	ENST00000267953;ENST00000335661	T;T	0.11604	2.76;2.76	4.98	-5.04	0.02964	Apoptosis regulator, Bcl2-like (1);Apoptosis regulator, Bcl-2, BH (3);	1.167600	0.06235	N	0.689282	T	0.00144	0.0004	N	0.21448	0.665	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.44742	-0.9308	10	0.15499	T	0.54	-25.672	8.3287	0.32173	0.0:0.3478:0.4258:0.2264	rs34080999	117;117	Q86W13;Q16548	.;B2LA1_HUMAN	D	117	ENSP00000267953:E117D;ENSP00000335250:E117D	ENSP00000267953:E117D	E	-	3	2	BCL2A1	78050166	0.457000	0.25752	0.000000	0.03702	0.018000	0.09664	-0.218000	0.09240	-0.861000	0.04094	0.655000	0.94253	GAG	C|0.968;A|0.032	0.032	strong		0.383	BCL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291372.1	NM_004049		A	80263111	C	A	80263111	3	1	22	1	0	0	0	0	1	0	0	0	1366	912	32	4	244	4	BCL2A1	15	80263111	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1197602	80263111	22268281	3063	5964											
FAH	2184	hgsc.bcm.edu	37	chr15	80460421	80460421	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ttaccagtgggctaccatggCcgtgcctcctctgtcgtggt	4	12	12	13	2	1	0	0	0	1	0	3	0	2	0	5	3	3	1	5	3	2	2	rs116272698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:80460421C>T	ENST00000407106.1	+	7	638	c.483C>T	c.(481-483)ggC>ggT	p.G161G	FAH_ENST00000558627.1_3'UTR|FAH_ENST00000539156.1_Silent_p.G91G|FAH_ENST00000561421.1_Silent_p.G161G|RP11-2E17.2_ENST00000568836.1_lincRNA|FAH_ENST00000261755.5_Silent_p.G161G			P16930	FAAA_HUMAN	fumarylacetoacetate hydrolase (fumarylacetoacetase)	161					arginine catabolic process (GO:0006527)|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)	fumarylacetoacetase activity (GO:0004334)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GCTACCATGGCCGTGCCTCCT	0.522									Tyrosinemia, type 1				C|||	45	0.00898562	0.0318	0.0043	5008	,	,		19054	0.0		0.0	False		,,,				2504	0.0				p.G161G		Atlas-SNP	.											.	FAH	36	.	0			c.C483T						PASS	.	C		124,4282	91.1+/-129.8	0,124,2079	116	93	101		483	-0.1	1	15	dbSNP_132	101	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FAH	NM_000137.2		0,125,6378	TT,TC,CC		0.0116,2.8143,0.9611		161/420	80460421	125,12881	2203	4300	6503	SO:0001819	synonymous_variant	2184	exon6	Familial Cancer Database	Fumarylacetoacetase Deficiency, Hepatorenal Tyrosinemia, Hereditary Tyrosinemia 1, HT1	CCATGGCCGTGCC	M55150	CCDS10314.1	15q25.1	2012-08-30			ENSG00000103876	ENSG00000103876	3.7.1.2		3579	protein-coding gene	gene with protein product		613871				1998338, 2336361	Standard	NM_000137		Approved		uc002bfm.2	P16930	OTTHUMG00000144187	ENST00000407106.1:c.483C>T	15.37:g.80460421C>T		215	0	0		220	105	0.477273	NM_000137	B2R9X1|D3DW95|Q53XA7	Silent	SNP	ENST00000407106.1	37	CCDS10314.1																																																																																			C|0.990;T|0.010	0.010	strong		0.522	FAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291392.2			T	80460421	C	T	80460421	2	4	22	1	0	0	0	0	0	0	0	1	5376	726	26	2		2	FAH	15	80460421	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	197310	80460421	22070971	3064	5965											
ARNT2	9915	hgsc.bcm.edu	37	chr15	80843578	80843578	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagacgctgatgtgggacaaGgcagtaaatattgcctcgtg	12	9	13	7	2	0	2	0	1	0	1	1	3	0	3	1	2	1	3	1	2	5	3	rs150765047	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:80843578G>A	ENST00000303329.4	+	9	1081	c.916G>A	c.(916-918)Ggc>Agc	p.G306S	ARNT2_ENST00000527771.1_Missense_Mutation_p.G295S|ARNT2_ENST00000533983.1_Missense_Mutation_p.G295S	NM_014862.3	NP_055677.3	Q9HBZ2	ARNT2_HUMAN	aryl-hydrocarbon receptor nuclear translocator 2	306					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)			TGTGGGACAAGGCAGTAAATA	0.413													G|||	10	0.00199681	0.0076	0.0	5008	,	,		22886	0.0		0.0	False		,,,				2504	0.0				p.G306S		Atlas-SNP	.											.	ARNT2	88	.	0			c.G916A						PASS	.	G	SER/GLY	23,4383	29.9+/-59.1	0,23,2180	128	117	121		916	4	1	15	dbSNP_134	121	0,8600		0,0,4300	yes	missense	ARNT2	NM_014862.3	56	0,23,6480	AA,AG,GG		0.0,0.522,0.1768	benign	306/718	80843578	23,12983	2203	4300	6503	SO:0001583	missense	9915	exon9			GGACAAGGCAGTA	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.916G>A	15.37:g.80843578G>A	ENSP00000307479:p.Gly306Ser	26	0	0		38	23	0.605263	NM_014862	B4DIS7|O15024|Q8IYC2	Missense_Mutation	SNP	ENST00000303329.4	37	CCDS32307.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	15.74	2.923805	0.52653	0.00522	0.0	ENSG00000172379	ENST00000360062;ENST00000303329;ENST00000540859	T	0.06142	3.34	4.9	3.98	0.46160	.	0.412872	0.25801	N	0.028211	T	0.03095	0.0091	N	0.16656	0.425	0.54753	D	0.999984	B	0.15719	0.014	B	0.17722	0.019	T	0.43163	-0.9408	10	0.18276	T	0.48	.	13.4258	0.61024	0.0763:0.0:0.9237:0.0	.	306	Q9HBZ2	ARNT2_HUMAN	S	295;306;306	ENSP00000307479:G306S	ENSP00000307479:G306S	G	+	1	0	ARNT2	78630633	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	4.471000	0.60182	1.060000	0.40578	0.655000	0.94253	GGC	G|0.999;A|0.001	0.001	strong		0.413	ARNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384389.2			A	80843578	G	A	80843578	3	1	22	1	0	0	0	0	1	0	0	0	966	1000	35	2	950	2	ARNT2	15	80843578	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	383157	80843578	21687814	3065	5966											
KIAA1199	57214	hgsc.bcm.edu	37	chr15	81172064	81172064	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctacctcttcaggcaagctGgtcattaaagaccacgacga	12	8	9	12	2	3	1	2	0	1	1	3	3	3	1	2	2	2	3	2	2	4	3	rs35541581	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:81172064G>A	ENST00000394685.3	+	5	668	c.249G>A	c.(247-249)ctG>ctA	p.L83L	KIAA1199_ENST00000220244.3_Silent_p.L83L|KIAA1199_ENST00000356249.5_Silent_p.L83L			Q8WUJ3	CEMIP_HUMAN		83	G8. {ECO:0000255|PROSITE- ProRule:PRU00817}.				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						CAGGCAAGCTGGTCATTAAAG	0.527													A|||	357	0.0712859	0.2481	0.0389	5008	,	,		19880	0.0		0.002	False		,,,				2504	0.0				p.L83L		Atlas-SNP	.											.	KIAA1199	118	.	0			c.G249A						PASS	.	A		941,3465	736.2+/-410.7	102,737,1364	78	70	73		249	-12.1	0	15	dbSNP_126	73	29,8571	817.9+/-406.9	0,29,4271	no	coding-synonymous	KIAA1199	NM_018689.1		102,766,5635	AA,AG,GG		0.3372,21.3572,7.4581		83/1362	81172064	970,12036	2203	4300	6503	SO:0001819	synonymous_variant	57214	exon4			CAAGCTGGTCATT																												ENST00000394685.3:c.249G>A	15.37:g.81172064G>A		112	0	0		125	62	0.496	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Silent	SNP	ENST00000394685.3	37	CCDS10315.1																																																																																			G|0.928;A|0.072	0.072	strong		0.527	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1			A	81172064	G	A	81172064	2	1	22	1	0	0	0	0	0	0	0	1	8222	1335	47	2		2	KIAA1199	15	81172064	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	328486	81172064	21359328	3066	5967											
KIAA1199	57214	hgsc.bcm.edu	37	chr15	81217024	81217024	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tctgccaaggacaagcggccGttcctctcaatcatctctgc	8	10	8	15	2	4	0	2	0	3	0	7	1	5	1	3	2	3	1	3	2	3	1	rs28566789	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:81217024G>A	ENST00000394685.3	+	18	2684	c.2265G>A	c.(2263-2265)ccG>ccA	p.P755P	KIAA1199_ENST00000220244.3_Silent_p.P755P|RP11-351M8.2_ENST00000560873.1_RNA|KIAA1199_ENST00000356249.5_Silent_p.P755P			Q8WUJ3	CEMIP_HUMAN		755					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						ACAAGCGGCCGTTCCTCTCAA	0.532													G|||	139	0.0277556	0.0998	0.0086	5008	,	,		19966	0.0		0.001	False		,,,				2504	0.0				p.P755P		Atlas-SNP	.											.	KIAA1199	118	.	0			c.G2265A						PASS	.	G		341,4065	178.3+/-207.1	17,307,1879	123	101	108		2265	-0.2	1	15	dbSNP_125	108	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	KIAA1199	NM_018689.1		17,309,6177	AA,AG,GG		0.0233,7.7394,2.6372		755/1362	81217024	343,12663	2203	4300	6503	SO:0001819	synonymous_variant	57214	exon17			GCGGCCGTTCCTC																												ENST00000394685.3:c.2265G>A	15.37:g.81217024G>A		184	0	0		196	92	0.469388	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Silent	SNP	ENST00000394685.3	37	CCDS10315.1																																																																																			G|0.973;A|0.027	0.027	strong		0.532	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1			A	81217024	G	A	81217024	2	1	22	1	0	0	0	0	0	0	0	1	8222	1132	40	1		1	KIAA1199	15	81217024	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	44960	81217024	21314368	3067	5968											
IL16	3603	hgsc.bcm.edu	37	chr15	81589340	81589340	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agaagccctagtgcctctgcCggctgcccaggacctggtat	7	8	12	14	1	1	1	0	0	1	1	1	2	1	2	5	3	4	2	5	3	3	2	rs201624502	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:81589340C>T	ENST00000302987.4	+	12	1974	c.1974C>T	c.(1972-1974)gcC>gcT	p.A658A	IL16_ENST00000560230.1_3'UTR|IL16_ENST00000394652.2_5'UTR|IL16_ENST00000394660.2_Silent_p.A658A			Q14005	IL16_HUMAN	interleukin 16	658					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						GTGCCTCTGCCGGCTGCCCAG	0.592													C|||	6	0.00119808	0.0045	0.0	5008	,	,		18755	0.0		0.0	False		,,,				2504	0.0				p.A658A		Atlas-SNP	.											.	IL16	254	.	0			c.C1974T						PASS	.	C	,,	8,3906		0,8,1949	34	39	37		1974,,1974	-3.6	0	15		37	0,8326		0,0,4163	no	coding-synonymous,utr-5,coding-synonymous	IL16	NM_001172128.1,NM_004513.5,NM_172217.3	,,	0,8,6112	TT,TC,CC		0.0,0.2044,0.0654	,,	658/1332,,658/1333	81589340	8,12232	1957	4163	6120	SO:0001819	synonymous_variant	3603	exon13			CTCTGCCGGCTGC	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.1974C>T	15.37:g.81589340C>T		176	0	0		173	89	0.514451	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Silent	SNP	ENST00000302987.4	37	CCDS42069.1																																																																																			C|0.999;T|0.001	0.001	strong		0.592	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217		T	81589340	C	T	81589340	2	4	22	1	0	0	0	0	0	0	0	1	7642	639	23	1		1	IL16	15	81589340	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	372316	81589340	20942052	3068	5969											
IL16	3603	hgsc.bcm.edu	37	chr15	81592384	81592384	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcctgagcaagtactgtcctCggggtcccctgcagcctccg	5	8	12	16	2	0	1	0	1	0	0	4	1	3	1	6	2	4	3	6	2	2	1	rs17875513	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:81592384C>T	ENST00000302987.4	+	13	2717	c.2717C>T	c.(2716-2718)tCg>tTg	p.S906L	IL16_ENST00000560230.1_3'UTR|IL16_ENST00000394652.2_Missense_Mutation_p.S205L|IL16_ENST00000394660.2_Missense_Mutation_p.S906L			Q14005	IL16_HUMAN	interleukin 16	906			S -> L (in dbSNP:rs17875513). {ECO:0000269|Ref.8}.		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						GTACTGTCCTCGGGGTCCCCT	0.642													C|||	215	0.0429313	0.1536	0.0115	5008	,	,		11772	0.0		0.004	False		,,,				2504	0.0				p.S906L		Atlas-SNP	.											.	IL16	254	.	0			c.C2717T						PASS	.	C	LEU/SER,LEU/SER,LEU/SER	558,3836		38,482,1677	44	49	47		2717,614,2717	-9.7	0	15	dbSNP_124	47	28,8572		0,28,4272	yes	missense,missense,missense	IL16	NM_001172128.1,NM_004513.5,NM_172217.3	145,145,145	38,510,5949	TT,TC,CC		0.3256,12.6991,4.5098	benign,benign,benign	906/1332,205/632,906/1333	81592384	586,12408	2197	4300	6497	SO:0001583	missense	3603	exon14			TGTCCTCGGGGTC	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.2717C>T	15.37:g.81592384C>T	ENSP00000302935:p.Ser906Leu	58	0	0		50	21	0.42	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Missense_Mutation	SNP	ENST00000302987.4	37	CCDS42069.1	82	0.037545787545787544	76	0.15447154471544716	4	0.011049723756906077	0	0.0	2	0.002638522427440633	C	8.558	0.877168	0.17395	0.126991	0.003256	ENSG00000172349	ENST00000394660;ENST00000355368;ENST00000302987;ENST00000329842;ENST00000394653;ENST00000394652;ENST00000394656	T;T;T	0.10763	2.84;2.84;3.43	4.85	-9.71	0.00518	.	1.594110	0.03725	N	0.252561	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	B;B;B;B;B;B	0.14438	0.001;0.01;0.0;0.001;0.0;0.001	B;B;B;B;B;B	0.04013	0.001;0.001;0.0;0.001;0.001;0.001	T	0.30208	-0.9986	9	0.30078	T	0.28	.	8.1212	0.30971	0.0709:0.1747:0.5288:0.2256	rs17875513	738;399;443;296;906;906	F8W7Z5;Q6ZTT5;B7Z8M3;B3KY62;Q14005;Q14005-2	.;.;.;.;IL16_HUMAN;.	L	906;738;906;443;296;205;205	ENSP00000378155:S906L;ENSP00000302935:S906L;ENSP00000378147:S205L	ENSP00000302935:S906L	S	+	2	0	IL16	79379439	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.830000	0.00744	-1.944000	0.01038	-1.710000	0.00715	TCG	C|0.955;T|0.045	0.045	strong		0.642	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217		T	81592384	C	T	81592384	3	4	22	1	0	0	0	0	1	0	0	0	7642	893	31	1	2767	1	IL16	15	81592384	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3044	81592384	20939008	3069	5970											
TMC3	342125	hgsc.bcm.edu	37	chr15	81625028	81625028	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aattccgggatcgtggctttCtgggcacataggctggcctc	6	11	13	11	2	1	0	0	0	1	0	4	1	2	1	2	5	0	3	2	5	2	3	rs8031046	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:81625028C>T	ENST00000359440.5	-	22	3170	c.3035G>A	c.(3034-3036)aGa>aAa	p.R1012K	RP11-761I4.3_ENST00000560851.1_RNA|TMC3_ENST00000558726.1_Missense_Mutation_p.R1013K|RP11-761I4.3_ENST00000560973.1_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						TCGTGGCTTTCTGGGCACATA	0.582													T|||	836	0.166933	0.4728	0.062	5008	,	,		16882	0.0952		0.0517	False		,,,				2504	0.0204				p.R1012K		Atlas-SNP	.											.	TMC3	112	.	0			c.G3035A						PASS	.	T	LYS/ARG	1592,2362		345,902,730	35	40	39		3035	-9	0	15	dbSNP_116	39	440,7886		12,416,3735	yes	missense	TMC3	NM_001080532.1	26	357,1318,4465	TT,TC,CC		5.2847,40.263,16.5472	benign	1012/1101	81625028	2032,10248	1977	4163	6140	SO:0001583	missense	342125	exon22			GGCTTTCTGGGCA	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.3035G>A	15.37:g.81625028C>T	ENSP00000352413:p.Arg1012Lys	158	0	0		168	93	0.553571	NM_001080532		Missense_Mutation	SNP	ENST00000359440.5	37	CCDS45324.1	363	0.1662087912087912	240	0.4878048780487805	25	0.06906077348066299	61	0.10664335664335664	37	0.048812664907651716	T	4.161	0.028403	0.08054	0.40263	0.052847	ENSG00000188869	ENST00000359440	T	0.62232	0.04	5.42	-9.03	0.00737	.	0.406919	0.19362	N	0.116103	T	0.00012	0.0000	N	0.01742	-0.745	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31916	-0.9926	9	0.02654	T	1	-0.4035	21.2883	0.99950	0.0:0.656:0.0:0.344	rs8031046;rs52825478;rs59441739;rs8031046	1012	Q7Z5M5	TMC3_HUMAN	K	1012	ENSP00000352413:R1012K	ENSP00000352413:R1012K	R	-	2	0	TMC3	79412083	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-0.956000	0.03865	-2.591000	0.00456	-1.213000	0.01624	AGA	C|0.811;T|0.189	0.189	strong		0.582	TMC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417795.3	NM_181841		T	81625028	C	T	81625028	3	4	22	1	0	0	0	0	1	0	0	0	16001	913	32	2	271	2	TMC3	15	81625028	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	32644	81625028	20906364	3070	5971											
TMC3	342125	hgsc.bcm.edu	37	chr15	81641872	81641872	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aatgaggtcaaaggctgatgGtgctatcatggtgacgaggg	11	9	16	5	1	2	3	2	3	0	0	2	4	2	3	0	5	1	2	0	5	3	1	rs61740148	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:81641872G>T	ENST00000359440.5	-	11	1255	c.1120C>A	c.(1120-1122)Cca>Aca	p.P374T	RP11-761I4.3_ENST00000560851.1_RNA|TMC3_ENST00000558726.1_Missense_Mutation_p.P375T|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						AAGGCTGATGGTGCTATCATG	0.577													G|||	58	0.0115815	0.0408	0.0058	5008	,	,		16696	0.0		0.0	False		,,,				2504	0.0				p.P374T		Atlas-SNP	.											.	TMC3	112	.	0			c.C1120A						PASS	.	G	THR/PRO	172,4164		3,166,1999	107	111	110		1120	5	0.6	15	dbSNP_129	110	1,8523		0,1,4261	yes	missense	TMC3	NM_001080532.1	38	3,167,6260	TT,TG,GG		0.0117,3.9668,1.3453	probably-damaging	374/1101	81641872	173,12687	2168	4262	6430	SO:0001583	missense	342125	exon11			CTGATGGTGCTAT	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.1120C>A	15.37:g.81641872G>T	ENSP00000352413:p.Pro374Thr	218	0	0		211	99	0.469194	NM_001080532		Missense_Mutation	SNP	ENST00000359440.5	37	CCDS45324.1	20	0.009157509157509158	18	0.036585365853658534	2	0.0055248618784530384	0	0.0	0	0.0	G	16.89	3.247828	0.59103	0.039668	1.17E-4	ENSG00000188869	ENST00000359440	D	0.91237	-2.81	5.02	5.02	0.67125	.	0.129405	0.53938	D	0.000052	D	0.87466	0.6184	M	0.85041	2.73	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.89179	0.3542	10	0.87932	D	0	-13.1745	18.3718	0.90409	0.0:0.0:1.0:0.0	.	374;374	Q7Z5M5-2;Q7Z5M5	.;TMC3_HUMAN	T	374	ENSP00000352413:P374T	ENSP00000352413:P374T	P	-	1	0	TMC3	79428927	1.000000	0.71417	0.619000	0.29118	0.082000	0.17680	9.398000	0.97281	2.322000	0.78497	0.655000	0.94253	CCA	G|0.990;T|0.010	0.010	strong		0.577	TMC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417795.3	NM_181841		T	81641872	G	T	81641872	3	4	22	1	0	0	0	0	1	0	0	0	16001	1261	44	4	2230	4	TMC3	15	81641872	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	16844	81641872	20889520	3071	5972											
C15orf40	123207	hgsc.bcm.edu	37	chr15	83673653	83673653	+	3'UTR	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatctagaaaaactgcattcAacaagtagtccaaggatttg	17	10	7	7	0	2	1	1	0	1	1	3	2	3	2	1	1	3	2	1	1	8	4	rs74028206	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:83673653A>C	ENST00000513601.2	-	0	1165				C15orf40_ENST00000304177.5_3'UTR|RP11-382A20.5_ENST00000566841.1_RNA|C15orf40_ENST00000451195.3_Intron|C15orf40_ENST00000538348.2_Intron			Q8WUR7	CO040_HUMAN	chromosome 15 open reading frame 40											large_intestine(3)|lung(2)|skin(1)	6						AACTGCATTCAACAAGTagtc	0.393													A|||	66	0.0131789	0.0386	0.0173	5008	,	,		15049	0.0		0.003	False		,,,				2504	0.0				p.V146V		Atlas-SNP	.											.	C15orf40	18	.	0			c.T438G						PASS	.	A	,,,	38,1346		1,36,655	112	100	104		438,,,	1.1	0	15	dbSNP_130	104	0,3182		0,0,1591	no	coding-synonymous,intron,intron,utr-3	C15orf40	NM_001160114.1,NM_001160115.1,NM_001160116.1,NM_144597.2	,,,	1,36,2246	CC,CA,AA		0.0,2.7457,0.8322	,,,	146/154,,,	83673653	38,4528	692	1591	2283	SO:0001624	3_prime_UTR_variant	123207	exon4			GCATTCAACAAGT	BC019820	CCDS32312.1, CCDS32312.2, CCDS53968.1, CCDS53969.1	15q25.2	2012-05-30			ENSG00000169609	ENSG00000169609			28443	protein-coding gene	gene with protein product							Standard	NM_144597		Approved	MGC29937	uc010uoo.1	Q8WUR7	OTTHUMG00000160473	ENST00000513601.2:c.*696T>G	15.37:g.83673653A>C		122	0	0		101	53	0.524752	NM_001160114	A6NIC9|B2R5E7|F5GX92|F8WD31|G5EA00	Silent	SNP	ENST00000513601.2	37	CCDS32312.2																																																																																			A|0.985;C|0.015	0.015	strong		0.393	C15orf40-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360737.2	NM_144597		C	83673653	A	C	83673653	1	2	22	0	1	0	0	0	0	0	0	0	1796	117	5	5		5	C15orf40	15	83673653	3'UTR	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2031781	83673653	18857739	3072	5973											
C15orf40	123207	hgsc.bcm.edu	37	chr15	83680313	83680313	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccgagcggagccccgagtaTtgggtgttgcccgaaggtgc	6	7	17	11	4	0	0	0	0	0	0	0	4	0	1	4	3	4	2	4	3	2	3	rs114478510	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:83680313T>G	ENST00000513601.2	-	1	54	c.47A>C	c.(46-48)aAt>aCt	p.N16T	C15orf40_ENST00000565712.1_Missense_Mutation_p.N16T|C15orf40_ENST00000304177.5_5'UTR|RP11-382A20.5_ENST00000566841.1_RNA|C15orf40_ENST00000451195.3_Missense_Mutation_p.N16T|C15orf40_ENST00000538348.2_Missense_Mutation_p.N16T|RP11-382A20.7_ENST00000570202.1_RNA			Q8WUR7	CO040_HUMAN	chromosome 15 open reading frame 40	16										large_intestine(3)|lung(2)|skin(1)	6						GCCCCGAGTATTGGGTGTTGC	0.692											OREG0023391	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	50	0.00998403	0.028	0.0144	5008	,	,		14631	0.0		0.003	False		,,,				2504	0.0				p.N16T		Atlas-SNP	.											.	C15orf40	18	.	0			c.A47C						PASS	.	T	THR/ASN,THR/ASN,THR/ASN,THR/ASN,THR/ASN	69,4335		0,69,2133	21	22	22		47,47,47,47,47	1.6	0	15	dbSNP_132	22	5,8595		0,5,4295	yes	missense,missense,missense,missense,missense	C15orf40	NM_144597.2,NM_001160116.1,NM_001160115.1,NM_001160114.1,NM_001160113.1	65,65,65,65,65	0,74,6428	GG,GT,TT		0.0581,1.5668,0.5691	benign,benign,benign,benign,benign	16/154,16/150,16/168,16/154,16/168	83680313	74,12930	2202	4300	6502	SO:0001583	missense	123207	exon1			CGAGTATTGGGTG	BC019820	CCDS32312.1, CCDS32312.2, CCDS53968.1, CCDS53969.1	15q25.2	2012-05-30			ENSG00000169609	ENSG00000169609			28443	protein-coding gene	gene with protein product							Standard	NM_144597		Approved	MGC29937	uc010uoo.1	Q8WUR7	OTTHUMG00000160473	ENST00000513601.2:c.47A>C	15.37:g.83680313T>G	ENSP00000424666:p.Asn16Thr	37	0	0	1223	30	9	0.3	NM_001160116	A6NIC9|B2R5E7|F5GX92|F8WD31|G5EA00	Missense_Mutation	SNP	ENST00000513601.2	37	CCDS32312.2	24	0.01098901098901099	16	0.032520325203252036	6	0.016574585635359115	0	0.0	2	0.002638522427440633	T	9.731	1.162258	0.21538	0.015668	5.81E-4	ENSG00000169609	ENST00000538348;ENST00000451195;ENST00000513601	.	.	.	3.61	1.58	0.23477	.	.	.	.	.	T	0.05823	0.0152	N	0.08118	0	0.20764	N	0.99985	B;B;B	0.17038	0.02;0.02;0.008	B;B;B	0.11329	0.006;0.006;0.006	T	0.15350	-1.0440	8	0.42905	T	0.14	.	5.5455	0.17061	0.0:0.7421:0.0:0.2579	.	16;16;16	F8WD31;F5GX92;G5EA00	.;.;.	T	16	.	ENSP00000403987:N16T	N	-	2	0	C15orf40	81471317	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.131000	0.10482	0.499000	0.27970	-0.624000	0.04008	AAT	T|0.992;G|0.008	0.008	strong		0.692	C15orf40-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360737.2	NM_144597		G	83680313	T	G	83680313	3	3	22	1	0	0	0	0	1	0	0	0	1796	1493	52	5	902	5	C15orf40	15	83680313	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	6660	83680313	18851079	3073	5974											
BTBD1	53339	hgsc.bcm.edu	37	chr15	83725291	83725291	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atttgaacttcatctgaataTagaaatctggaaaacaattg	17	13	6	5	0	3	3	1	2	2	1	3	4	3	4	0	1	2	0	0	1	8	5			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:83725291T>A	ENST00000261721.4	-	2	610	c.408A>T	c.(406-408)ctA>ctT	p.L136L	RP11-382A20.6_ENST00000568441.1_RNA|BTBD1_ENST00000379403.2_Silent_p.L136L|RP11-382A20.5_ENST00000566841.1_RNA|RP11-382A20.7_ENST00000570202.1_RNA	NM_001011885.1|NM_025238.3	NP_001011885.1|NP_079514.1	Q9H0C5	BTBD1_HUMAN	BTB (POZ) domain containing 1	136	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				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)		CATCTGAATATAGAAATCTGG	0.358																																					p.L136L		Atlas-SNP	.											BTBD1,NS,carcinoma,-2,1	BTBD1	32	1	0			c.A408T						PASS	.						87	83	84					15																	83725291		2203	4300	6503	SO:0001819	synonymous_variant	53339	exon2			TGAATATAGAAAT	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.408A>T	15.37:g.83725291T>A		69	0	0		87	35	0.402299	NM_025238	A6NMI8|Q9BX71|Q9NWN4	Silent	SNP	ENST00000261721.4	37	CCDS10322.1																																																																																			.	.	none		0.358	BTBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304008.1			A	83725291	T	A	83725291	2	1	22	1	0	0	0	0	0	0	0	1	1539	1393	49	5		5	BTBD1	15	83725291	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	44978	83725291	18806101	3074	5975											
ADAMTSL3	57188	hgsc.bcm.edu	37	chr15	84683428	84683428	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaacctacgtctgcatagccAccaatgctcttggaaaggca	12	8	9	12	1	2	0	0	0	2	0	2	2	2	1	3	2	5	3	3	2	5	3	rs17158450	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:84683428A>G	ENST00000286744.5	+	24	4332	c.4108A>G	c.(4108-4110)Acc>Gcc	p.T1370A	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.T1370A	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	1370	Ig-like C2-type 3.		T -> A (in dbSNP:rs17158450).			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)			CTGCATAGCCACCAATGCTCT	0.443													A|||	240	0.0479233	0.1717	0.0187	5008	,	,		20971	0.0		0.0	False		,,,				2504	0.0				p.T1370A		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.A4108G						PASS	.	A	ALA/THR	680,3726	286.6+/-278.8	50,580,1573	134	125	128		4108	2.7	1	15	dbSNP_123	128	7,8591	6.4+/-24.3	0,7,4292	yes	missense	ADAMTSL3	NM_207517.2	58	50,587,5865	GG,GA,AA		0.0814,15.4335,5.283	benign	1370/1692	84683428	687,12317	2203	4299	6502	SO:0001583	missense	57188	exon24			ATAGCCACCAATG	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.4108A>G	15.37:g.84683428A>G	ENSP00000286744:p.Thr1370Ala	122	0	0		159	63	0.396226	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	94	0.04304029304029304	86	0.17479674796747968	8	0.022099447513812154	0	0.0	0	0.0	A	2.759	-0.258227	0.05791	0.154335	8.14E-4	ENSG00000156218	ENST00000286744	T	0.68903	-0.36	5.03	2.73	0.32206	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.188900	0.26149	N	0.026056	T	0.00210	0.0006	L	0.46741	1.465	0.30564	P	0.7641979999999999	B;B	0.17465	0.002;0.022	B;B	0.19946	0.01;0.027	T	0.06991	-1.0796	9	0.10111	T	0.7	.	8.0282	0.30448	0.7665:0.0:0.2335:0.0	rs17158450;rs52789838;rs17158450	1370;1370	P82987-2;P82987	.;ATL3_HUMAN	A	1370	ENSP00000286744:T1370A	ENSP00000286744:T1370A	T	+	1	0	ADAMTSL3	82474432	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.012000	0.29924	0.760000	0.33108	0.454000	0.30748	ACC	A|0.943;G|0.057	0.057	strong		0.443	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517		G	84683428	A	G	84683428	3	3	22	1	0	0	0	0	1	0	0	0	276	159	6	3	4198	3	ADAMTSL3	15	84683428	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	958137	84683428	17847964	3075	5976											
ZSCAN2	54993	hgsc.bcm.edu	37	chr15	85164530	85164530	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacgaatgtaaagaatgcggCgaaagctttagttacaactc	15	10	9	7	3	0	1	0	0	0	1	1	3	0	1	0	1	5	3	0	1	9	5	rs115131715	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:85164530C>T	ENST00000448803.2	+	3	1396	c.1104C>T	c.(1102-1104)ggC>ggT	p.G368G	ZSCAN2_ENST00000541040.1_Intron|ZSCAN2_ENST00000485222.2_Intron|ZSCAN2_ENST00000538076.1_Intron|ZSCAN2_ENST00000358472.3_Silent_p.G218G|ZSCAN2_ENST00000327179.6_Silent_p.G367G|ZSCAN2_ENST00000546148.1_Silent_p.G368G	NM_181877.3	NP_870992.2	Q7Z7L9	ZSCA2_HUMAN	zinc finger and SCAN domain containing 2	368					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)		AAGAATGCGGCGAAAGCTTTA	0.502													C|||	49	0.00978435	0.0363	0.0014	5008	,	,		18077	0.0		0.0	False		,,,				2504	0.0				p.G368G		Atlas-SNP	.											.	ZSCAN2	43	.	0			c.C1104T						PASS	.	C		132,4274	96.2+/-134.9	3,126,2074	132	137	135		1104	-6.7	0.8	15	dbSNP_132	135	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	ZSCAN2	NM_181877.3		3,127,6372	TT,TC,CC		0.0116,2.9959,1.0228		368/615	85164530	133,12871	2203	4299	6502	SO:0001819	synonymous_variant	54993	exon3			ATGCGGCGAAAGC	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.1104C>T	15.37:g.85164530C>T		79	0	0		61	35	0.57377	NM_181877	A6NG83|B2RMQ9|Q6ZQY9|Q9NWU4	Silent	SNP	ENST00000448803.2	37	CCDS10329.2																																																																																			C|0.988;T|0.012	0.012	strong		0.502	ZSCAN2-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396956.1	NM_017894		T	85164530	C	T	85164530	2	4	22	1	0	0	0	0	0	0	0	1	18246	755	27	1		1	ZSCAN2	15	85164530	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	481102	85164530	17366862	3076	5977											
ZNF592	9640	hgsc.bcm.edu	37	chr15	85326315	85326315	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaagtcagagccattacccAccttcaaccagttcagtcca	12	8	5	16	0	3	1	3	0	0	1	4	1	4	1	6	0	3	1	6	0	3	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:85326315A>C	ENST00000560079.2	+	4	697	c.409A>C	c.(409-411)Acc>Ccc	p.T137P	ZNF592_ENST00000299927.3_Missense_Mutation_p.T137P	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	137					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)			GCCATTACCCACCTTCAACCA	0.478																																					p.T137P		Atlas-SNP	.											.	ZNF592	95	.	0			c.A409C						PASS	.						99	105	103					15																	85326315		2203	4299	6502	SO:0001583	missense	9640	exon4			TTACCCACCTTCA	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.409A>C	15.37:g.85326315A>C	ENSP00000452877:p.Thr137Pro	80	0	0		62	29	0.467742	NM_014630	Q2M1T2|Q504Y9	Missense_Mutation	SNP	ENST00000560079.2	37	CCDS32317.1	.	.	.	.	.	.	.	.	.	.	A	16.70	3.196504	0.58126	.	.	ENSG00000166716	ENST00000299927	T	0.00640	6.03	6.06	6.06	0.98353	.	0.249606	0.46145	D	0.000302	T	0.02156	0.0067	L	0.48642	1.525	0.43852	D	0.99644	D	0.65815	0.995	D	0.63381	0.914	T	0.64580	-0.6374	10	0.72032	D	0.01	-20.196	14.5614	0.68140	1.0:0.0:0.0:0.0	.	137	Q92610	ZN592_HUMAN	P	137	ENSP00000299927:T137P	ENSP00000299927:T137P	T	+	1	0	ZNF592	83127319	0.986000	0.35501	0.998000	0.56505	0.999000	0.98932	3.000000	0.49481	2.324000	0.78689	0.533000	0.62120	ACC	.	.	none		0.478	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2	NM_014630		C	85326315	A	C	85326315	3	2	22	1	0	0	0	0	1	0	0	0	18037	159	6	5	411	5	ZNF592	15	85326315	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	161785	85326315	17205077	3077	5978											
ALPK3	57538	hgsc.bcm.edu	37	chr15	85403104	85403104	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tccacaatgagcacggctcgGcctccaccgacttctgcctc	7	8	8	18	3	1	1	0	1	1	0	5	2	3	1	5	2	2	2	5	2	1	1	rs114686452	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:85403104G>A	ENST00000258888.5	+	8	4836	c.4669G>A	c.(4669-4671)Gcc>Acc	p.A1557T		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1557	Ig-like 2.		A -> D (in dbSNP:rs34775428). {ECO:0000269|PubMed:17344846}.		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)			GCACGGCTCGGCCTCCACCGA	0.687													G|||	11	0.00219649	0.0083	0.0	5008	,	,		16937	0.0		0.0	False		,,,				2504	0.0				p.A1557T		Atlas-SNP	.											.	ALPK3	289	.	0			c.G4669A						PASS	.	G	THR/ALA	17,4389	24.3+/-50.5	0,17,2186	57	55	55		4669	3.6	0.6	15	dbSNP_132	55	0,8598		0,0,4299	yes	missense	ALPK3	NM_020778.4	58	0,17,6485	AA,AG,GG		0.0,0.3858,0.1307	possibly-damaging	1557/1908	85403104	17,12987	2203	4299	6502	SO:0001583	missense	57538	exon8			GGCTCGGCCTCCA	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.4669G>A	15.37:g.85403104G>A	ENSP00000258888:p.Ala1557Thr	102	0	0		103	46	0.446602	NM_020778	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	37	CCDS10333.1	4	0.0018315018315018315	3	0.006097560975609756	0	0.0	0	0.0	1	0.0013192612137203166	G	22.4	4.289118	0.80914	0.003858	0.0	ENSG00000136383	ENST00000258888	T	0.06687	3.27	5.52	3.62	0.41486	Immunoglobulin-like (1);Protein kinase-like domain (1);Immunoglobulin-like fold (1);	0.331817	0.30383	N	0.009744	T	0.07863	0.0197	L	0.34521	1.04	0.26266	N	0.978497	D	0.60575	0.988	P	0.54590	0.756	T	0.12344	-1.0551	10	0.27082	T	0.32	-10.6766	9.2405	0.37493	0.0811:0.1467:0.7721:0.0	.	1557	Q96L96	ALPK3_HUMAN	T	1557	ENSP00000258888:A1557T	ENSP00000258888:A1557T	A	+	1	0	ALPK3	83204108	1.000000	0.71417	0.556000	0.28293	0.972000	0.66771	3.919000	0.56439	0.680000	0.31366	0.563000	0.77884	GCC	G|0.998;A|0.002	0.002	strong		0.687	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778		A	85403104	G	A	85403104	3	1	22	1	0	0	0	0	1	0	0	0	546	1203	42	2	4699	2	ALPK3	15	85403104	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	76789	85403104	17128288	3078	5979											
SLC28A1	9154	hgsc.bcm.edu	37	chr15	85448796	85448796	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggagggccgtgtcttggggActtggactgcagtttgtact	5	13	16	7	1	1	0	0	0	1	0	1	3	1	3	1	5	2	3	1	5	1	4	rs8187755	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:85448796A>T	ENST00000286749.3	+	7	720	c.630A>T	c.(628-630)ggA>ggT	p.G210G	SLC28A1_ENST00000537703.1_Silent_p.G132G|SLC28A1_ENST00000394573.1_Silent_p.G210G|SLC28A1_ENST00000537624.1_Silent_p.G210G|SLC28A1_ENST00000537216.1_Silent_p.G210G|SLC28A1_ENST00000538177.1_Silent_p.G210G			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	210					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)	TGTCTTGGGGACTTGGACTGC	0.587													A|||	156	0.0311502	0.1142	0.0072	5008	,	,		19535	0.0		0.0	False		,,,				2504	0.0				p.G210G		Atlas-SNP	.											SLC28A1_ENST00000537624,NS,carcinoma,+1,2	SLC28A1	118	2	0			c.A630T						scavenged	.	A		404,4002	200.8+/-224.0	20,364,1819	215	172	186		630	1.1	1	15	dbSNP_123	186	3,8595	2.2+/-6.3	0,3,4296	no	coding-synonymous	SLC28A1	NM_004213.3		20,367,6115	TT,TA,AA		0.0349,9.1693,3.1298		210/650	85448796	407,12597	2203	4299	6502	SO:0001819	synonymous_variant	9154	exon8			TTGGGGACTTGGA	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.630A>T	15.37:g.85448796A>T		182	1	0.00549451		198	74	0.373737	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Silent	SNP	ENST00000286749.3	37	CCDS10334.1																																																																																			A|0.973;T|0.027	0.027	strong		0.587	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2			T	85448796	A	T	85448796	2	4	22	1	0	0	0	0	0	0	0	1	14546	262	10	5		5	SLC28A1	15	85448796	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	45692	85448796	17082596	3079	5980											
SLC28A1	9154	hgsc.bcm.edu	37	chr15	85478573	85478573	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcatctgctcctacatcctgCggcctgtagccttcttgatg	5	14	8	14	1	3	1	1	1	2	0	5	1	5	1	4	1	4	2	4	1	2	4	rs8187779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:85478573C>A	ENST00000286749.3	+	14	1495	c.1405C>A	c.(1405-1407)Cgg>Agg	p.R469R	SLC28A1_ENST00000394573.1_Silent_p.R469R|SLC28A1_ENST00000537624.1_Silent_p.R469R|SLC28A1_ENST00000537216.1_Silent_p.R469R|SLC28A1_ENST00000538177.1_Intron			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	469					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)	CTACATCCTGCGGCCTGTAGC	0.607													C|||	34	0.00678914	0.0227	0.0043	5008	,	,		20483	0.0		0.001	False		,,,				2504	0.0				p.R469R		Atlas-SNP	.											SLC28A1,colon,carcinoma,-1,1	SLC28A1	118	1	0			c.C1405A						scavenged	.	C		79,4327	68.7+/-106.4	2,75,2126	110	88	95		1405	2.2	1	15	dbSNP_123	95	4,8594	3.7+/-12.6	0,4,4295	no	coding-synonymous	SLC28A1	NM_004213.3		2,79,6421	AA,AC,CC		0.0465,1.793,0.6383		469/650	85478573	83,12921	2203	4299	6502	SO:0001819	synonymous_variant	9154	exon15			ATCCTGCGGCCTG	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.1405C>A	15.37:g.85478573C>A		174	1	0.00574713		142	77	0.542253	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Silent	SNP	ENST00000286749.3	37	CCDS10334.1																																																																																			C|0.995;A|0.005	0.005	strong		0.607	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2			A	85478573	C	A	85478573	2	1	22	1	0	0	0	0	0	0	0	1	14546	759	27	4		4	SLC28A1	15	85478573	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	29777	85478573	17052819	3080	5981											
NTRK3	4916	hgsc.bcm.edu	37	chr15	88576215	88576215	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacgagggcgtggtgatgccGtggttgatgtggtgcagtgg	5	10	21	5	3	0	2	0	2	0	0	0	4	0	2	1	5	2	2	1	5	0	1	rs2229909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:88576215G>A	ENST00000360948.2	-	13	1619	c.1458C>T	c.(1456-1458)caC>caT	p.H486H	NTRK3_ENST00000557856.1_Silent_p.H478H|NTRK3_ENST00000542733.2_Silent_p.H388H|NTRK3_ENST00000558676.1_Silent_p.H478H|NTRK3_ENST00000317501.3_Silent_p.H486H|NTRK3_ENST00000558306.1_5'UTR|NTRK3_ENST00000357724.2_Silent_p.H478H|NTRK3_ENST00000355254.2_Silent_p.H486H|NTRK3_ENST00000540489.2_Silent_p.H486H|NTRK3_ENST00000394480.2_Silent_p.H486H	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	486					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)			TGGTGATGCCGTGGTTGATGT	0.607			T	ETV6	"congenital fibrosarcoma, Secretory breast "					TSP Lung(13;0.10)			G|||	143	0.0285543	0.1051	0.0058	5008	,	,		10706	0.0		0.0	False		,,,				2504	0.0				p.H486H		Atlas-SNP	.		Dom	yes		15	15q25	4916	"neurotrophic tyrosine kinase, receptor, type 3"		"E, M"	NTRK3_ENST00000360948,NS,carcinoma,0,3	NTRK3	587	3	0			c.C1458T						PASS	.	G	,,	457,3945	216.4+/-235.1	27,403,1771	97	61	73		1458,1458,1458	-4.4	1	15	dbSNP_129	73	2,8596	3.0+/-9.4	0,2,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	NTRK3	NM_001007156.2,NM_001012338.2,NM_002530.3	,,	27,405,6068	AA,AG,GG		0.0233,10.3816,3.5308	,,	486/613,486/840,486/826	88576215	459,12541	2201	4299	6500	SO:0001819	synonymous_variant	4916	exon14			GATGCCGTGGTTG	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.1458C>T	15.37:g.88576215G>A		98	0	0		97	47	0.484536	NM_001012338	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Silent	SNP	ENST00000360948.2	37	CCDS32322.1																																																																																			G|0.962;A|0.038	0.038	strong		0.607	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding				A	88576215	G	A	88576215	2	1	22	1	0	0	0	0	0	0	0	1	10717	1136	40	1		1	NTRK3	15	88576215	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3097642	88576215	13955177	3081	5982											
MRPL46	26589	hgsc.bcm.edu	37	chr15	89002888	89002888	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aacttgggccaggtattttgGtttcaaatagtcacccagct	10	13	9	9	0	2	0	2	0	0	0	2	0	2	0	2	3	2	3	2	3	4	6	rs146290179		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:89002888G>T	ENST00000312475.4	-	4	837	c.796C>A	c.(796-798)Cca>Aca	p.P266T	MRPL46_ENST00000559538.1_5'UTR	NM_022163.3	NP_071446.2	Q9H2W6	RM46_HUMAN	mitochondrial ribosomal protein L46	266						mitochondrion (GO:0005739)|ribosome (GO:0005840)	hydrolase activity (GO:0016787)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)	5	Lung NSC(78;0.203)		BRCA - Breast invasive adenocarcinoma(143;0.188)			AGGTATTTTGGTTTCAAATAG	0.502																																					p.P266T		Atlas-SNP	.											.	MRPL46	13	.	0			c.C796A						PASS	.	G	THR/PRO	2,4400	4.2+/-10.8	0,2,2199	119	101	107		796	6	0.5	15	dbSNP_134	107	0,8598		0,0,4299	no	missense	MRPL46	NM_022163.3	38	0,2,6498	TT,TG,GG		0.0,0.0454,0.0154	possibly-damaging	266/280	89002888	2,12998	2201	4299	6500	SO:0001583	missense	26589	exon4			ATTTTGGTTTCAA	AF210056	CCDS10341.1	15q25.3	2012-10-08	2001-12-10	2001-12-14	ENSG00000259494	ENSG00000259494		"Mitochondrial ribosomal proteins / large subunits"	1192	protein-coding gene	gene with protein product		611851	"chromosome 15 open reading frame 4"	C15orf4		11761714, 11551941	Standard	NM_022163		Approved	LIECG2, P2ECSL	uc002bmj.2	Q9H2W6	OTTHUMG00000148683	ENST00000312475.4:c.796C>A	15.37:g.89002888G>T	ENSP00000312311:p.Pro266Thr	114	0	0		122	53	0.434426	NM_022163	B2RD75|Q9HBU8	Missense_Mutation	SNP	ENST00000312475.4	37	CCDS10341.1	.	.	.	.	.	.	.	.	.	.	G	17.01	3.278489	0.59758	4.54E-4	0.0	ENSG00000173867	ENST00000312475	T	0.48201	0.82	5.98	5.98	0.97165	.	0.102208	0.64402	D	0.000002	T	0.47967	0.1474	M	0.62154	1.92	0.58432	D	0.999993	P	0.51653	0.947	B	0.43916	0.436	T	0.44697	-0.9311	10	0.36615	T	0.2	.	12.628	0.56640	0.0824:0.0:0.9176:0.0	.	266	Q9H2W6	RM46_HUMAN	T	266	ENSP00000312311:P266T	ENSP00000312311:P266T	P	-	1	0	MRPL46	86803892	1.000000	0.71417	0.508000	0.27688	0.542000	0.35054	4.395000	0.59678	2.835000	0.97688	0.650000	0.86243	CCA	G|1.000;T|0.000	0.000	weak		0.502	MRPL46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309073.1	NM_022163		T	89002888	G	T	89002888	3	4	22	1	0	0	0	0	1	0	0	0	9819	1261	44	4	47	4	MRPL46	15	89002888	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	426673	89002888	13528504	3082	5983											
ABHD2	11057	hgsc.bcm.edu	37	chr15	89738475	89738475	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagaaacgagagaacgtcAtgtttgtgctgcctctgcat	11	10	11	9	2	2	2	1	0	1	2	2	5	2	2	1	0	5	3	1	0	2	1	rs147106119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:89738475A>C	ENST00000352732.5	+	11	1619	c.1099A>C	c.(1099-1101)Atg>Ctg	p.M367L	ABHD2_ENST00000355100.3_Missense_Mutation_p.M367L|ABHD2_ENST00000565973.1_Missense_Mutation_p.M367L	NM_152924.4	NP_690888.1	P08910	ABHD2_HUMAN	abhydrolase domain containing 2	367					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)					AGAGAACGTCATGTTTGTGCT	0.557													A|||	5	0.000998403	0.0038	0.0	5008	,	,		20328	0.0		0.0	False		,,,				2504	0.0				p.M367L	Colon(11;252 417 24570 33239 41878)	Atlas-SNP	.											.	ABHD2	55	.	0			c.A1099C						PASS	.	A	LEU/MET,LEU/MET	16,4384	23.3+/-48.9	0,16,2184	142	124	130		1099,1099	4.6	1	15	dbSNP_134	130	0,8598		0,0,4299	yes	missense,missense	ABHD2	NM_007011.7,NM_152924.4	15,15	0,16,6483	CC,CA,AA		0.0,0.3636,0.1231	benign,benign	367/426,367/426	89738475	16,12982	2200	4299	6499	SO:0001583	missense	11057	exon15			AACGTCATGTTTG	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.1099A>C	15.37:g.89738475A>C	ENSP00000268129:p.Met367Leu	115	0	0		115	55	0.478261	NM_007011	Q53G48|Q53GU0|Q5FVD9|Q8TC79	Missense_Mutation	SNP	ENST00000352732.5	37	CCDS10348.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	5.968	0.362642	0.11296	0.003636	0.0	ENSG00000140526	ENST00000352732;ENST00000355100	T;T	0.60299	0.2;0.2	5.75	4.6	0.57074	Alpha/beta hydrolase fold-1 (1);	0.166180	0.64402	D	0.000008	T	0.34019	0.0883	N	0.16307	0.4	0.41422	D	0.987801	B	0.10296	0.003	B	0.15052	0.012	T	0.10847	-1.0612	10	0.08179	T	0.78	-14.589	6.6357	0.22881	0.7918:0.0:0.0709:0.1373	.	367	P08910	ABHD2_HUMAN	L	367	ENSP00000268129:M367L;ENSP00000347217:M367L	ENSP00000268129:M367L	M	+	1	0	ABHD2	87539479	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.877000	0.63086	0.974000	0.38366	0.533000	0.62120	ATG	A|0.999;C|0.001	0.001	strong		0.557	ABHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309074.2			C	89738475	A	C	89738475	3	2	22	1	0	0	0	0	1	0	0	0	82	217	8	5	1133	5	ABHD2	15	89738475	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	735587	89738475	12792917	3083	5984											
RLBP1	6017	hgsc.bcm.edu	37	chr15	89762198	89762198	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaggacagggtacttaccccTtctgacatgttgcctatgga	9	11	11	10	0	1	1	0	1	1	0	1	4	1	3	3	3	3	2	3	3	3	5	rs146844731	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:89762198T>G	ENST00000268125.5	-	3	448	c.9A>C	c.(7-9)gaA>gaC	p.E3D		NM_000326.4	NP_000317.1	P12271	RLBP1_HUMAN	retinaldehyde binding protein 1	3					phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	cell body (GO:0044297)|cytosol (GO:0005829)	11-cis retinal binding (GO:0005502)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(1)|prostate(1)|skin(1)	18	Lung NSC(78;0.0472)|all_lung(78;0.089)				Vitamin A(DB00162)	TACTTACCCCTTCTGACATGT	0.542													T|||	10	0.00199681	0.0076	0.0	5008	,	,		19219	0.0		0.0	False		,,,				2504	0.0				p.E3D		Atlas-SNP	.											RLBP1,NS,carcinoma,-2,1	RLBP1	34	1	0			c.A9C						PASS	.	T	ASP/GLU	26,4374	32.6+/-62.9	0,26,2174	146	125	132		9	-3.2	1	15	dbSNP_134	132	0,8598		0,0,4299	yes	missense	RLBP1	NM_000326.4	45	0,26,6473	GG,GT,TT		0.0,0.5909,0.2	benign	3/318	89762198	26,12972	2200	4299	6499	SO:0001583	missense	6017	exon3			TACCCCTTCTGAC	BC004199	CCDS32324.1	15q26.1	2007-07-16	2001-11-28			ENSG00000140522			10024	protein-coding gene	gene with protein product		180090	"retinaldehyde-binding protein 1"			1733864, 9326942	Standard	NM_000326		Approved	CRALBP	uc002bnl.3	P12271		ENST00000268125.5:c.9A>C	15.37:g.89762198T>G	ENSP00000268125:p.Glu3Asp	76	0	0		63	38	0.603175	NM_000326	B2R667	Missense_Mutation	SNP	ENST00000268125.5	37	CCDS32324.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	T	9.490	1.100449	0.20552	0.005909	0.0	ENSG00000140522	ENST00000268125	T	0.79141	-1.24	5.17	-3.21	0.05140	.	0.467603	0.23298	N	0.049703	T	0.42359	0.1199	N	0.14661	0.345	0.26969	N	0.965636	B	0.02656	0.0	B	0.01281	0.0	T	0.30001	-0.9993	10	0.16420	T	0.52	-10.8678	5.1979	0.15249	0.0:0.2661:0.2778:0.4561	.	3	P12271	RLBP1_HUMAN	D	3	ENSP00000268125:E3D	ENSP00000268125:E3D	E	-	3	2	RLBP1	87563202	0.925000	0.31364	0.968000	0.41197	0.138000	0.21146	-0.148000	0.10219	-0.417000	0.07461	-1.276000	0.01395	GAA	T|0.998;G|0.002	0.002	strong		0.542	RLBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421135.1	NM_000326		G	89762198	T	G	89762198	3	3	22	1	0	0	0	0	1	0	0	0	13403	1606	56	5	972	5	RLBP1	15	89762198	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	23723	89762198	12769194	3084	5985											
FANCI	55215	hgsc.bcm.edu	37	chr15	89849413	89849413	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	atgtacaccacacttacagcCcttgtcagatatgtgagtat	12	12	7	10	0	1	2	1	1	0	1	1	2	1	2	2	0	3	2	2	0	4	5	rs114810692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:89849413C>A	ENST00000310775.7	+	32	3611	c.3525C>A	c.(3523-3525)gcC>gcA	p.A1175A	FANCI_ENST00000300027.8_Silent_p.A1115A	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	1175					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)					CACTTACAGCCCTTGTCAGAT	0.512								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				C|||	33	0.00658946	0.0242	0.0014	5008	,	,		19687	0.0		0.0	False		,,,				2504	0.0				p.A1175A		Atlas-SNP	.											.	FANCI	129	.	0			c.C3525A						PASS	.	C	,	75,4325	66.4+/-103.9	0,75,2125	109	96	100		3525,3345	-10.8	0.6	15	dbSNP_132	100	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous,coding-synonymous	FANCI	NM_001113378.1,NM_018193.2	,	0,76,6423	AA,AC,CC		0.0116,1.7045,0.5847	,	1175/1329,1115/1269	89849413	76,12922	2200	4299	6499	SO:0001819	synonymous_variant	55215	exon32	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TACAGCCCTTGTC	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.3525C>A	15.37:g.89849413C>A		66	0	0		68	32	0.470588	NM_001113378	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Silent	SNP	ENST00000310775.7	37	CCDS45346.1																																																																																			C|0.994;A|0.006	0.006	strong		0.512	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193		A	89849413	C	A	89849413	2	1	22	1	0	0	0	0	0	0	0	1	5677	610	22	4		4	FANCI	15	89849413	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	87215	89849413	12681979	3085	5986											
C15orf42	90381	hgsc.bcm.edu	37	chr15	90145118	90145118	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcaccacttctttctgtgccTtttttgtcaagtgctcgtag	5	18	7	11	1	4	0	2	0	2	0	5	0	4	0	2	0	2	2	2	0	2	6	rs202042800		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90145118T>A	ENST00000268138.7	+	12	2583	c.2478T>A	c.(2476-2478)ccT>ccA	p.P826P	TICRR_ENST00000560985.1_Silent_p.P825P			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	826					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)										TTTCTGTGCCTTTTTTGTCAA	0.458													T|||	1	0.000199681	0.0008	0.0	5008	,	,		19991	0.0		0.0	False		,,,				2504	0.0				p.P826P		Atlas-SNP	.											.	.	.	.	0			c.T2478A						PASS	.	T		5,3841		0,5,1918	137	125	129		2478	0.3	0.1	15		129	0,8276		0,0,4138	no	coding-synonymous	C15orf42	NM_152259.3		0,5,6056	AA,AT,TT		0.0,0.13,0.0412		826/1911	90145118	5,12117	1923	4138	6061	SO:0001819	synonymous_variant	90381	exon12			TGTGCCTTTTTTG	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.2478T>A	15.37:g.90145118T>A		80	0	0		74	36	0.486486	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Silent	SNP	ENST00000268138.7	37	CCDS10352.2																																																																																			T|1.000;A|0.000	0.000	strong		0.458	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259		A	90145118	T	A	90145118	2	1	22	1	0	0	0	0	0	0	0	1	1798	1596	56	5		5	C15orf42	15	90145118	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	295705	90145118	12386274	3086	5987											
C15orf42	90381	hgsc.bcm.edu	37	chr15	90164769	90164769	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actttggattcggaggtaccTgcagcttaccaggtataatg	10	12	11	8	1	0	0	0	0	0	0	1	2	0	2	2	4	4	4	2	4	4	6	rs75934760	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90164769T>C	ENST00000268138.7	+	19	3405	c.3300T>C	c.(3298-3300)ccT>ccC	p.P1100P	TICRR_ENST00000560985.1_Silent_p.P1099P|KIF7_ENST00000558928.1_Intron			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	1100					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)										CGGAGGTACCTGCAGCTTACC	0.428													T|||	221	0.0441294	0.1558	0.0216	5008	,	,		19124	0.0		0.0	False		,,,				2504	0.0				p.P1100P		Atlas-SNP	.											.	.	.	.	0			c.T3300C						PASS	.	T		445,3261		33,379,1441	55	54	54		3300	1.5	0	15	dbSNP_132	54	6,8188		0,6,4091	no	coding-synonymous	C15orf42	NM_152259.3		33,385,5532	CC,CT,TT		0.0732,12.0076,3.7899		1100/1911	90164769	451,11449	1853	4097	5950	SO:0001819	synonymous_variant	90381	exon19			GGTACCTGCAGCT	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.3300T>C	15.37:g.90164769T>C		70	0	0		55	26	0.472727	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Silent	SNP	ENST00000268138.7	37	CCDS10352.2																																																																																			T|0.973;C|0.027	0.027	strong		0.428	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259		C	90164769	T	C	90164769	2	2	22	1	0	0	0	0	0	0	0	1	1798	1567	55	3		3	C15orf42	15	90164769	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	19651	90164769	12366623	3087	5988											
C15orf42	90381	hgsc.bcm.edu	37	chr15	90167610	90167610	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgcatctctctcctgccctGttccctcaactccccctgaa	5	12	4	20	0	3	1	1	1	2	0	7	1	5	1	5	0	3	2	5	0	2	1	rs115865608	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90167610G>T	ENST00000268138.7	+	20	4174	c.4069G>T	c.(4069-4071)Gtt>Ttt	p.V1357F	TICRR_ENST00000560985.1_Missense_Mutation_p.V1356F|KIF7_ENST00000558928.1_Intron			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	1357	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)										CTCCTGCCCTGTTCCCTCAAC	0.517													G|||	15	0.00299521	0.0098	0.0029	5008	,	,		20300	0.0		0.0	False		,,,				2504	0.0				p.V1357F		Atlas-SNP	.											.	.	.	.	0			c.G4069T						PASS	.	G	PHE/VAL	47,4353	48.9+/-83.8	1,45,2154	129	129	129		4069	0.1	0	15	dbSNP_132	129	0,8598		0,0,4299	yes	missense	C15orf42	NM_152259.3	50	1,45,6453	TT,TG,GG		0.0,1.0682,0.3616	possibly-damaging	1357/1911	90167610	47,12951	2200	4299	6499	SO:0001583	missense	90381	exon20			TGCCCTGTTCCCT	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.4069G>T	15.37:g.90167610G>T	ENSP00000268138:p.Val1357Phe	63	0	0		60	34	0.566667	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Missense_Mutation	SNP	ENST00000268138.7	37	CCDS10352.2	3	0.0013736263736263737	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	0	0.0	G	8.278	0.814810	0.16607	0.010682	0.0	ENSG00000140534	ENST00000268138	T	0.08984	3.03	4.59	0.12	0.14691	.	1.919780	0.02660	N	0.107408	T	0.09598	0.0236	L	0.50333	1.59	0.09310	N	1	P	0.43701	0.815	P	0.46389	0.515	T	0.26883	-1.0090	10	0.40728	T	0.16	0.4344	7.2402	0.26092	0.2249:0.1216:0.6535:0.0	.	1357	Q7Z2Z1	TICRR_HUMAN	F	1357	ENSP00000268138:V1357F	ENSP00000268138:V1357F	V	+	1	0	C15orf42	87968614	0.003000	0.15002	0.002000	0.10522	0.216000	0.24613	0.321000	0.19558	0.118000	0.18165	-0.140000	0.14226	GTT	G|0.996;T|0.004	0.004	strong		0.517	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259		T	90167610	G	T	90167610	3	4	22	1	0	0	0	0	1	0	0	0	1798	1377	48	4	4147	4	C15orf42	15	90167610	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2841	90167610	12363782	3088	5989											
KIF7	374654	hgsc.bcm.edu	37	chr15	90192363	90192363	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcttgagcaccctctctgaGcccgccaggtccacgaagtg	7	8	11	15	2	2	2	0	2	2	0	4	3	3	2	4	1	2	1	4	1	1	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90192363G>A	ENST00000394412.3	-	4	841	c.765C>T	c.(763-765)ggC>ggT	p.G255G		NM_198525.2	NP_940927.2	Q2M1P5	KIF7_HUMAN	kinesin family member 7	255	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				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)			CCCTCTCTGAGCCCGCCAGGT	0.711																																					p.G255G		Atlas-SNP	.											.	KIF7	130	.	0			c.C765T						PASS	.						9	13	12					15																	90192363		684	1585	2269	SO:0001819	synonymous_variant	374654	exon4			CTCTGAGCCCGCC	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.765C>T	15.37:g.90192363G>A		48	0	0		57	32	0.561404	NM_198525	Q3SXY0|Q6UXE9|Q8IW72	Silent	SNP	ENST00000394412.3	37	CCDS32325.2																																																																																			.	.	none		0.711	KIF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347782.1	NM_198525		A	90192363	G	A	90192363	2	1	22	1	0	0	0	0	0	0	0	1	8318	958	34	2		2	KIF7	15	90192363	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	24753	90192363	12339029	3089	5990											
KIF7	374654	hgsc.bcm.edu	37	chr15	90196113	90196113	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcgaactcgcagggcaacccGcactggggcctcctcagccc	7	5	11	18	3	1	0	1	0	0	0	4	1	2	0	4	3	3	3	4	3	2	0	rs141865394	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90196113G>A	ENST00000394412.3	-	2	125	c.49C>T	c.(49-51)Cgg>Tgg	p.R17W		NM_198525.2	NP_940927.2	Q2M1P5	KIF7_HUMAN	kinesin family member 7	17	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				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)			AGGGCAACCCGCACTGGGGCC	0.687													G|||	26	0.00519169	0.0174	0.0029	5008	,	,		15541	0.001		0.0	False		,,,				2504	0.0				p.R17W		Atlas-SNP	.											.	KIF7	130	.	0			c.C49T						PASS	.						12	17	16					15																	90196113		688	1589	2277	SO:0001583	missense	374654	exon2			CAACCCGCACTGG	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.49C>T	15.37:g.90196113G>A	ENSP00000377934:p.Arg17Trp	90	0	0		100	54	0.54	NM_198525	Q3SXY0|Q6UXE9|Q8IW72	Missense_Mutation	SNP	ENST00000394412.3	37	CCDS32325.2	13	0.005952380952380952	10	0.02032520325203252	2	0.0055248618784530384	1	0.0017482517482517483	0	0.0	G	12.35	1.912773	0.33721	.	.	ENSG00000166813	ENST00000394412	T	0.74526	-0.85	4.66	2.23	0.28157	Kinesin, motor domain (3);	.	.	.	.	T	0.80597	0.4653	H	0.96048	3.76	0.35264	D	0.779872	D	0.76494	0.999	P	0.59424	0.857	D	0.89286	0.3615	9	0.87932	D	0	.	12.8485	0.57844	0.0:0.0:0.5816:0.4184	.	17	Q2M1P5	KIF7_HUMAN	W	17	ENSP00000377934:R17W	ENSP00000377934:R17W	R	-	1	2	KIF7	87997117	0.008000	0.16893	0.921000	0.36526	0.005000	0.04900	0.750000	0.26334	0.144000	0.18951	-0.262000	0.10625	CGG	G|0.994;A|0.006	0.006	strong		0.687	KIF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347782.1	NM_198525		A	90196113	G	A	90196113	3	1	22	1	0	0	0	0	1	0	0	0	8318	1086	38	1	4054	1	KIF7	15	90196113	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3750	90196113	12335279	3090	5991											
WDR93	56964	hgsc.bcm.edu	37	chr15	90274756	90274756	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcctacctggtgctggcctgCgaggatggtgtgctcacgct	4	11	14	12	2	1	0	1	0	0	0	2	2	2	1	3	4	4	3	3	4	1	1	rs35502270	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90274756C>T	ENST00000268130.7	+	12	1394	c.1293C>T	c.(1291-1293)tgC>tgT	p.C431C	WDR93_ENST00000560294.1_Silent_p.C431C|WDR93_ENST00000444934.2_Silent_p.C148C	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	431					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)			TGCTGGCCTGCGAGGATGGTG	0.617													C|||	134	0.0267572	0.0998	0.0029	5008	,	,		18890	0.0		0.0	False		,,,				2504	0.0				p.C431C		Atlas-SNP	.											.	WDR93	63	.	0			c.C1293T						PASS	.	C		363,4037	184.7+/-212.0	14,335,1851	208	181	190		1293	-4.6	0.9	15	dbSNP_126	190	3,8595	3.0+/-9.4	0,3,4296	no	coding-synonymous	WDR93	NM_020212.1		14,338,6147	TT,TC,CC		0.0349,8.25,2.8158		431/687	90274756	366,12632	2200	4299	6499	SO:0001819	synonymous_variant	56964	exon12			GGCCTGCGAGGAT		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.1293C>T	15.37:g.90274756C>T		131	0	0		147	72	0.489796	NM_020212	Q8N7Y8|Q9NP89	Silent	SNP	ENST00000268130.7	37	CCDS32326.1																																																																																			C|0.973;T|0.027	0.027	strong		0.617	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212		T	90274756	C	T	90274756	2	4	22	1	0	0	0	0	0	0	0	1	17355	776	27	1		1	WDR93	15	90274756	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	78643	90274756	12256636	3091	5992											
WDR93	56964	hgsc.bcm.edu	37	chr15	90281381	90281381	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaaaatatctcaaaaaattgTaccattcctcaaagggactt	17	11	5	8	0	2	0	2	0	1	0	4	2	3	1	2	1	1	1	2	1	8	5	rs35017767	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90281381T>C	ENST00000268130.7	+	16	1976	c.1875T>C	c.(1873-1875)tgT>tgC	p.C625C	WDR93_ENST00000560294.1_Silent_p.C597C|WDR93_ENST00000444934.2_Silent_p.C342C	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	625					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)			CAAAAAATTGTACCATTCCTC	0.453													C|||	235	0.0469249	0.1755	0.0043	5008	,	,		17775	0.0		0.0	False		,,,				2504	0.0				p.C625C		Atlas-SNP	.											.	WDR93	63	.	0			c.T1875C						PASS	.	C		662,3738	763.7+/-413.2	44,574,1582	232	238	236		1875	-1.2	0	15	dbSNP_126	236	6,8592	818.8+/-406.8	0,6,4293	no	coding-synonymous	WDR93	NM_020212.1		44,580,5875	CC,CT,TT		0.0698,15.0455,5.1393		625/687	90281381	668,12330	2200	4299	6499	SO:0001819	synonymous_variant	56964	exon16			AAATTGTACCATT		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.1875T>C	15.37:g.90281381T>C		151	0	0		153	90	0.588235	NM_020212	Q8N7Y8|Q9NP89	Silent	SNP	ENST00000268130.7	37	CCDS32326.1																																																																																			T|0.955;C|0.045	0.045	strong		0.453	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212		C	90281381	T	C	90281381	2	2	22	1	0	0	0	0	0	0	0	1	17355	1644	57	3		3	WDR93	15	90281381	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	6625	90281381	12250011	3092	5993											
WDR93	56964	hgsc.bcm.edu	37	chr15	90281452	90281452	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	actggagaagagatgtgagcGtttcctccagaagaggtaaa	14	8	13	6	1	0	5	0	1	0	4	2	7	2	5	2	2	1	2	2	2	4	2	rs35389334	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90281452G>A	ENST00000268130.7	+	16	2047	c.1946G>A	c.(1945-1947)cGt>cAt	p.R649H	WDR93_ENST00000560294.1_Missense_Mutation_p.R621H|WDR93_ENST00000444934.2_Missense_Mutation_p.R366H	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	649					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)			AGATGTGAGCGTTTCCTCCAG	0.473													G|||	102	0.0203674	0.0756	0.0029	5008	,	,		17358	0.0		0.0	False		,,,				2504	0.0				p.R649H		Atlas-SNP	.											WDR93,colon,carcinoma,+1,1	WDR93	63	1	0			c.G1946A						PASS	.	G	HIS/ARG	251,4149	143.8+/-178.8	7,237,1956	165	167	166		1946	-10.5	0	15	dbSNP_126	166	2,8596	2.2+/-6.3	0,2,4297	yes	missense	WDR93	NM_020212.1	29	7,239,6253	AA,AG,GG		0.0233,5.7045,1.9465	possibly-damaging	649/687	90281452	253,12745	2200	4299	6499	SO:0001583	missense	56964	exon16			GTGAGCGTTTCCT		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.1946G>A	15.37:g.90281452G>A	ENSP00000268130:p.Arg649His	105	0	0		130	72	0.553846	NM_020212	Q8N7Y8|Q9NP89	Missense_Mutation	SNP	ENST00000268130.7	37	CCDS32326.1	52	0.023809523809523808	50	0.1016260162601626	2	0.0055248618784530384	0	0.0	0	0.0	G	11.54	1.670012	0.29693	0.057045	2.33E-4	ENSG00000140527	ENST00000268130;ENST00000444934	T;T	0.43294	1.95;0.95	5.27	-10.5	0.00291	.	3.609450	0.00520	N	0.000193	T	0.00608	0.0020	N	0.22421	0.69	0.09310	N	1	P;P	0.50943	0.859;0.94	B;B	0.41571	0.276;0.36	T	0.38520	-0.9657	10	0.40728	T	0.16	3.3554	5.7049	0.17903	0.3798:0.0:0.2483:0.3718	rs35389334	621;649	Q6P2C0-2;Q6P2C0	.;WDR93_HUMAN	H	649;366	ENSP00000268130:R649H;ENSP00000403871:R366H	ENSP00000268130:R649H	R	+	2	0	WDR93	88082456	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.725000	0.00808	-2.790000	0.00356	-0.156000	0.13503	CGT	G|0.977;A|0.023	0.023	strong		0.473	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212		A	90281452	G	A	90281452	3	1	22	1	0	0	0	0	1	0	0	0	17355	1145	40	1	2004	1	WDR93	15	90281452	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	71	90281452	12249940	3093	5994											
MESP2	145873	hgsc.bcm.edu	37	chr15	90320000	90320000	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatcggccacctatcggccGtgctgggtctcagcgaggag	7	7	14	13	4	1	0	1	0	1	0	4	2	1	1	3	4	2	1	3	4	1	1	rs28462216	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90320000G>A	ENST00000341735.3	+	1	412	c.412G>A	c.(412-414)Gtg>Atg	p.V138M	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	138			V -> M (in dbSNP:rs28462216).		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)			CCTATCGGCCGTGCTGGGTCT	0.736													G|||	393	0.0784744	0.2572	0.0216	5008	,	,		13798	0.0		0.002	False		,,,				2504	0.0368				p.V138M		Atlas-SNP	.											.	MESP2	20	.	0			c.G412A						PASS	.	G	MET/VAL	771,3403		58,655,1374	7	9	8		412	1.8	1	15	dbSNP_125	8	5,8363		0,5,4179	no	missense	MESP2	NM_001039958.1	21	58,660,5553	AA,AG,GG		0.0598,18.4715,6.1872	benign	138/398	90320000	776,11766	2087	4184	6271	SO:0001583	missense	145873	exon1			TCGGCCGTGCTGG		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.412G>A	15.37:g.90320000G>A	ENSP00000342392:p.Val138Met	36	0	0		42	42	1	NM_001039958	Q7RTU2	Missense_Mutation	SNP	ENST00000341735.3	37	CCDS42078.1	130	0.05952380952380952	121	0.2459349593495935	8	0.022099447513812154	0	0.0	1	0.0013192612137203166	G	13.92	2.380200	0.42207	0.184715	5.98E-4	ENSG00000188095	ENST00000341735	D	0.88509	-2.39	3.89	1.76	0.24704	Helix-loop-helix DNA-binding (3);	.	.	.	.	T	0.00109	0.0003	L	0.55481	1.735	0.47905	P	4.5799999999995844E-4	D	0.63880	0.993	P	0.49528	0.614	T	0.00146	-1.1991	8	0.51188	T	0.08	-6.0463	11.5389	0.50655	0.0:0.6191:0.3809:0.0	rs28462216;rs60624982	138	Q0VG99	MESP2_HUMAN	M	138	ENSP00000342392:V138M	ENSP00000342392:V138M	V	+	1	0	MESP2	88121004	0.564000	0.26602	1.000000	0.80357	0.565000	0.35776	0.973000	0.29422	0.785000	0.33685	0.313000	0.20887	GTG	G|0.940;A|0.060	0.060	strong		0.736	MESP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416421.1	XM_085261		A	90320000	G	A	90320000	3	1	22	1	0	0	0	0	1	0	0	0	9492	1145	40	1	414	1	MESP2	15	90320000	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	38548	90320000	12211392	3094	5995											
SEMA4B	10519	hgsc.bcm.edu	37	chr15	90771787	90771787	+	IGR	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcagagaagaggccactcaGcatccaagacagcttcgtgg	12	6	12	11	1	2	3	2	0	0	3	4	4	3	3	2	2	2	2	2	2	2	1	rs16944065	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90771787G>A	ENST00000328649.6	-	0	1247				SEMA4B_ENST00000332496.6_Missense_Mutation_p.S809N|SEMA4B_ENST00000379122.3_Intron|SEMA4B_ENST00000411539.2_Missense_Mutation_p.S809N	NM_006384.3	NP_006375.2	Q99828	CIB1_HUMAN	calcium and integrin binding 1 (calmyrin)						angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell division (GO:0051301)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to growth factor stimulus (GO:0071363)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to tumor necrosis factor (GO:0071356)|cytoplasmic microtubule organization (GO:0031122)|double-strand break repair (GO:0006302)|endomitotic cell cycle (GO:0007113)|extrinsic apoptotic signaling pathway (GO:0097191)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of megakaryocyte differentiation (GO:0045653)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|platelet formation (GO:0030220)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell growth (GO:0030307)|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-matrix adhesion (GO:0001954)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of male germ cell proliferation (GO:2000256)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of cell division (GO:0051302)|regulation of cell proliferation (GO:0042127)|response to ischemia (GO:0002931)|spermatid development (GO:0007286)|thrombopoietin-mediated signaling pathway (GO:0038163)	cell periphery (GO:0071944)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|protein anchor (GO:0043495)|Ras GTPase binding (GO:0017016)			lung(1)|prostate(1)	2	Melanoma(11;0.00551)|Lung NSC(78;0.0141)|all_lung(78;0.0303)		BRCA - Breast invasive adenocarcinoma(143;0.00269)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217)			AGGCCACTCAGCATCCAAGAC	0.652													G|||	47	0.00938498	0.0348	0.0014	5008	,	,		16568	0.0		0.0	False		,,,				2504	0.0				p.S809N		Atlas-SNP	.											.	SEMA4B	51	.	0			c.G2426A						PASS	.	G	ASN/SER,ASN/SER	156,3862		0,156,1853	29	34	32		2426,2426	4.8	1	15	dbSNP_123	32	3,8309		0,3,4153	yes	missense,missense	SEMA4B	NM_020210.3,NM_198925.2	46,46	0,159,6006	AA,AG,GG		0.0361,3.8825,1.2895	benign,benign	809/838,809/838	90771787	159,12171	2009	4156	6165	SO:0001628	intergenic_variant	10509	exon15			CACTCAGCATCCA	U82226	CCDS10360.1, CCDS73781.1	15q25.3-q26	2013-01-10			ENSG00000185043	ENSG00000185043		"EF-hand domain containing"	16920	protein-coding gene	gene with protein product		602293				9030514, 10826701	Standard	NM_006384		Approved	SIP2-28, CALMYRIN, CIB, KIP	uc031qtq.1	Q99828	OTTHUMG00000149808		15.37:g.90771787G>A		58	0	0		70	30	0.428571	NM_020210	B5BU40|H6WJF3|O00693|O00735|Q6IB49|Q96J54|Q99971	Missense_Mutation	SNP	ENST00000328649.6	37	CCDS10360.1	45	0.020604395604395604	23	0.046747967479674794	4	0.011049723756906077	6	0.01048951048951049	12	0.0158311345646438	G	12.52	1.963517	0.34659	0.038825	3.61E-4	ENSG00000185033	ENST00000332496;ENST00000411539	T;T	0.21543	2.0;2.0	4.75	4.75	0.60458	.	0.102022	0.64402	D	0.000003	T	0.01558	0.0050	N	0.11560	0.145	0.80722	D	1	B;B	0.26120	0.142;0.072	B;B	0.23018	0.043;0.031	T	0.20140	-1.0284	10	0.34782	T	0.22	.	10.5938	0.45325	0.0988:0.0:0.9012:0.0	rs16944065;rs16944065	809;804	Q2NL81;Q9NPR2	.;SEM4B_HUMAN	N	809	ENSP00000332204:S809N;ENSP00000394720:S809N	ENSP00000332204:S809N	S	+	2	0	SEMA4B	88572791	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	3.820000	0.55693	2.624000	0.88883	0.561000	0.74099	AGC	G|0.979;A|0.021	0.021	strong		0.652	CIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313419.1			A	90771787	G	A	90771787	1	1	22	0	1	0	0	0	0	0	0	0	14047	971	34	2		2	SEMA4B	15	90771787	IGR	SNP	G	TCGA-G8-6324-01A-11D-2210-10	451787	90771787	11759605	3095	5996											
C15orf58	390637	hgsc.bcm.edu	37	chr15	90784862	90784862	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aagcgagcccctggaccctgGaggccatttgcatctgctcc	7	8	11	15	1	1	0	0	0	1	0	2	3	2	2	5	3	4	2	5	3	1	1	rs75296384	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90784862G>A	ENST00000558017.1	+	4	1142	c.722G>A	c.(721-723)gGa>gAa	p.G241E	GDPGP1_ENST00000329600.6_Missense_Mutation_p.G241E	NM_001013657.2	NP_001013679.2	Q6ZNW5	GDPP1_HUMAN	GDP-D-glucose phosphorylase 1	241					glucose metabolic process (GO:0006006)	cytoplasm (GO:0005737)	GDP-D-glucose phosphorylase activity (GO:0080048)|guanyl-nucleotide exchange factor activity (GO:0005085)|hydrolase activity (GO:0016787)|nucleotide binding (GO:0000166)|nucleotidyltransferase activity (GO:0016779)										CTGGACCCTGGAGGCCATTTG	0.617													G|||	174	0.0347444	0.1248	0.013	5008	,	,		17261	0.0		0.0	False		,,,				2504	0.0				p.G241E		Atlas-SNP	.											.	.	.	.	0			c.G722A						PASS	.	G	GLU/GLY	608,3790	264.4+/-266.0	41,526,1632	47	43	45		722	-2.9	0	15	dbSNP_131	45	9,8587	7.1+/-27.0	0,9,4289	yes	missense	C15orf58	NM_001013657.2	98	41,535,5921	AA,AG,GG		0.1047,13.8245,4.7483	benign	241/386	90784862	617,12377	2199	4298	6497	SO:0001583	missense	390637	exon4			ACCCTGGAGGCCA		CCDS32327.1	15q26.1	2012-05-04	2012-05-04	2012-05-04	ENSG00000183208	ENSG00000183208	2.7.7.78		34360	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 58"	C15orf58		21507950	Standard	NM_001013657		Approved		uc002bpc.3	Q6ZNW5		ENST00000558017.1:c.722G>A	15.37:g.90784862G>A	ENSP00000452793:p.Gly241Glu	48	0	0		50	18	0.36	NM_001013657		Missense_Mutation	SNP	ENST00000558017.1	37	CCDS32327.1	64	0.029304029304029304	57	0.11585365853658537	7	0.019337016574585635	0	0.0	0	0.0	G	0.008	-1.878262	0.00537	0.138245	0.001047	ENSG00000183208	ENST00000329600	T	0.25579	1.79	5.95	-2.86	0.05717	.	1.014510	0.07864	N	0.966806	T	0.00109	0.0003	L	0.35341	1.055	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.34229	-0.9837	10	0.10902	T	0.67	0.0023	2.465	0.04550	0.4479:0.2093:0.2364:0.1065	.	241	Q6ZNW5	VTC2_HUMAN	E	241	ENSP00000368405:G241E	ENSP00000368405:G241E	G	+	2	0	C15orf58	88585866	0.000000	0.05858	0.000000	0.03702	0.142000	0.21351	0.507000	0.22675	-0.510000	0.06523	-0.150000	0.13652	GGA	G|0.962;A|0.038	0.038	strong		0.617	GDPGP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416973.1	NM_001013657		A	90784862	G	A	90784862	3	1	22	1	0	0	0	0	1	0	0	0	1808	1174	41	2	724	2	C15orf58	15	90784862	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	13075	90784862	11746530	3096	5997											
FURIN	5045	hgsc.bcm.edu	37	chr15	91419098	91419098	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcgcatccctggaggcccagCggtggccaacagtgtggcac	7	5	15	14	2	0	0	0	0	0	0	1	1	1	1	3	5	2	2	3	5	1	0	rs16944971	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:91419098C>T	ENST00000268171.3	+	2	407	c.128C>T	c.(127-129)gCg>gTg	p.A43V		NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	43			A -> V (in dbSNP:rs16944971).		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)			GGAGGCCCAGCGGTGGCCAAC	0.622													C|||	143	0.0285543	0.0938	0.0173	5008	,	,		18737	0.0		0.007	False		,,,				2504	0.0				p.A43V		Atlas-SNP	.											.	FURIN	85	.	0			c.C128T						PASS	.	C	VAL/ALA	340,4048		9,322,1863	54	39	44		128	3.8	0	15	dbSNP_123	44	30,8546		0,30,4258	yes	missense	FURIN	NM_002569.2	64	9,352,6121	TT,TC,CC		0.3498,7.7484,2.8541	benign	43/795	91419098	370,12594	2194	4288	6482	SO:0001583	missense	5045	exon2			GCCCAGCGGTGGC	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.128C>T	15.37:g.91419098C>T	ENSP00000268171:p.Ala43Val	59	0	0		57	57	1	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Missense_Mutation	SNP	ENST00000268171.3	37	CCDS10364.1	52	0.023809523809523808	38	0.07723577235772358	11	0.03038674033149171	0	0.0	3	0.00395778364116095	C	3.280	-0.147217	0.06627	0.077484	0.003498	ENSG00000140564	ENST00000268171	T	0.31510	1.49	4.77	3.85	0.44370	Proteinase inhibitor, propeptide (1);	0.284147	0.31963	N	0.006784	T	0.00936	0.0031	L	0.35487	1.065	0.09310	N	1	B	0.14438	0.01	B	0.12156	0.007	T	0.09443	-1.0674	10	0.32370	T	0.25	-14.4547	4.2077	0.10497	0.2574:0.5633:0.0:0.1793	rs16944971;rs16944971	43	P09958	FURIN_HUMAN	V	43	ENSP00000268171:A43V	ENSP00000268171:A43V	A	+	2	0	FURIN	89220102	0.000000	0.05858	0.004000	0.12327	0.036000	0.12997	0.595000	0.24029	1.257000	0.44085	0.555000	0.69702	GCG	C|0.968;T|0.032	0.032	strong		0.622	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569		T	91419098	C	T	91419098	3	4	22	1	0	0	0	0	1	0	0	0	6107	768	27	1	130	1	FURIN	15	91419098	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	634236	91419098	11112294	3097	5998											
FES	2242	hgsc.bcm.edu	37	chr15	91434277	91434277	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgagcagctgtggtaccaCggggccatcccgagggcaga	9	5	15	12	2	0	2	0	1	0	1	1	3	1	2	3	4	3	4	3	4	1	1	rs2229074	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:91434277C>T	ENST00000328850.3	+	11	1528	c.1386C>T	c.(1384-1386)caC>caT	p.H462H	FES_ENST00000450438.2_Intron|FES_ENST00000444422.2_Intron|FES_ENST00000394300.3_Silent_p.H404H|FES_ENST00000414248.2_Intron|FES_ENST00000394302.1_Intron	NM_002005.3	NP_001996.1	P07332	FES_HUMAN	FES proto-oncogene, tyrosine kinase	462	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)			TGTGGTACCACGGGGCCATCC	0.647													C|||	297	0.0593051	0.2126	0.0202	5008	,	,		18427	0.0		0.002	False		,,,				2504	0.0				p.H462H		Atlas-SNP	.											.	FES	102	.	0			c.C1386T						PASS	.	C	,,,	799,3595		75,649,1473	58	49	52		1212,,,1386	-8	0.8	15	dbSNP_98	52	9,8581		0,9,4286	no	coding-synonymous,intron,intron,coding-synonymous	FES	NM_001143783.1,NM_001143784.1,NM_001143785.1,NM_002005.3	,,,	75,658,5759	TT,TC,CC		0.1048,18.1839,6.223	,,,	404/765,,,462/823	91434277	808,12176	2197	4295	6492	SO:0001819	synonymous_variant	2242	exon11			GTACCACGGGGCC	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.1386C>T	15.37:g.91434277C>T		75	0	0		100	98	0.98	NM_002005	B2R6E6|B4DUD0|E9PC94|E9PC95|Q2VXS7|Q2VXS8|Q2VXT0|Q6GTU5	Silent	SNP	ENST00000328850.3	37	CCDS10365.1																																																																																			C|0.935;T|0.065	0.065	strong		0.647	FES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313497.1	NM_002005		T	91434277	C	T	91434277	2	4	22	1	0	0	0	0	0	0	0	1	5828	535	19	1		1	FES	15	91434277	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	15179	91434277	11097115	3098	5999											
FES	2242	hgsc.bcm.edu	37	chr15	91436965	91436965	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggatgtcccgagaggaagcCgatggggtctatgcagcctc	8	7	16	10	2	1	1	0	0	1	1	3	5	2	3	3	4	3	1	3	4	2	1	rs2227989	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:91436965C>T	ENST00000328850.3	+	17	2269	c.2127C>T	c.(2125-2127)gcC>gcT	p.A709A	FES_ENST00000450438.2_Silent_p.A581A|FES_ENST00000444422.2_Silent_p.A639A|FES_ENST00000394300.3_Silent_p.A651A|FES_ENST00000414248.2_Silent_p.A581A|FES_ENST00000394302.1_Silent_p.A568A	NM_002005.3	NP_001996.1	P07332	FES_HUMAN	FES proto-oncogene, tyrosine kinase	709	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)			GAGAGGAAGCCGATGGGGTCT	0.597													T|||	396	0.0790735	0.2829	0.0274	5008	,	,		19349	0.0		0.003	False		,,,				2504	0.0				p.A709A		Atlas-SNP	.											.	FES	102	.	0			c.C2127T						PASS	.	T	,,,	1132,3264	713.0+/-408.2	156,820,1222	69	77	74		1953,1917,1743,2127	-10.7	0.1	15	dbSNP_98	74	15,8581	816.6+/-406.9	0,15,4283	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FES	NM_001143783.1,NM_001143784.1,NM_001143785.1,NM_002005.3	,,,	156,835,5505	TT,TC,CC		0.1745,25.7507,8.8285	,,,	651/765,639/753,581/695,709/823	91436965	1147,11845	2198	4298	6496	SO:0001819	synonymous_variant	2242	exon17			GGAAGCCGATGGG	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.2127C>T	15.37:g.91436965C>T		104	1	0.00961538		70	70	1	NM_002005	B2R6E6|B4DUD0|E9PC94|E9PC95|Q2VXS7|Q2VXS8|Q2VXT0|Q6GTU5	Silent	SNP	ENST00000328850.3	37	CCDS10365.1																																																																																			C|0.910;T|0.090	0.090	strong		0.597	FES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313497.1	NM_002005		T	91436965	C	T	91436965	2	4	22	1	0	0	0	0	0	0	0	1	5828	639	23	1		1	FES	15	91436965	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2688	91436965	11094427	3099	6000											
UNC45A	55898	hgsc.bcm.edu	37	chr15	91485730	91485730	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatcctgggcgtggaaagcCaggctgtgtccctggctgcc	5	8	14	14	1	0	0	0	0	0	0	2	1	2	1	5	4	2	2	5	4	1	0	rs115978927	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:91485730C>G	ENST00000418476.2	+	7	791	c.751C>G	c.(751-753)Cag>Gag	p.Q251E	UNC45A_ENST00000553671.2_Intron|UNC45A_ENST00000394275.2_Missense_Mutation_p.Q236E	NM_018671.3	NP_061141.2	Q9H3U1	UN45A_HUMAN	unc-45 homolog A (C. elegans)	251					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)			CGTGGAAAGCCAGGCTGTGTC	0.557													C|||	48	0.00958466	0.0325	0.0072	5008	,	,		19205	0.0		0.0	False		,,,				2504	0.0				p.Q251E		Atlas-SNP	.											.	UNC45A	57	.	0			c.C751G						PASS	.	C	GLU/GLN,GLU/GLN	99,4297	79.3+/-117.8	1,97,2100	118	109	112		706,751	4.6	1	15	dbSNP_132	112	1,8595	1.2+/-3.3	0,1,4297	yes	missense,missense	UNC45A	NM_001039675.1,NM_018671.3	29,29	1,98,6397	GG,GC,CC		0.0116,2.252,0.7697	benign,benign	236/930,251/945	91485730	100,12892	2198	4298	6496	SO:0001583	missense	55898	exon7			GAAAGCCAGGCTG		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.751C>G	15.37:g.91485730C>G	ENSP00000407487:p.Gln251Glu	100	0	0		85	38	0.447059	NM_018671	A8K6F7|Q7L3Y6|Q9H3U8|Q9NSE8|Q9NSE9	Missense_Mutation	SNP	ENST00000418476.2	37	CCDS10367.1	14	0.00641025641025641	12	0.024390243902439025	2	0.0055248618784530384	0	0.0	0	0.0	C	3.104	-0.184173	0.06340	0.02252	1.16E-4	ENSG00000140553	ENST00000394275;ENST00000418476	T;T	0.44482	0.92;0.92	5.5	4.56	0.56223	Armadillo-like helical (1);Armadillo-type fold (1);	0.329961	0.31051	N	0.008356	T	0.06872	0.0175	N	0.01109	-1.01	0.28195	N	0.927606	B;B;B;B	0.12630	0.004;0.006;0.0;0.0	B;B;B;B	0.08055	0.002;0.003;0.001;0.001	T	0.12708	-1.0537	10	0.02654	T	1	-19.8406	13.9263	0.63964	0.0:0.6338:0.3662:0.0	.	251;243;251;236	B4DZL0;B4DLE6;Q9H3U1;A8K6F7	.;.;UN45A_HUMAN;.	E	236;251	ENSP00000377816:Q236E;ENSP00000407487:Q251E	ENSP00000377816:Q236E	Q	+	1	0	UNC45A	89286734	0.984000	0.35163	1.000000	0.80357	0.929000	0.56500	3.726000	0.54977	1.405000	0.46838	0.558000	0.71614	CAG	C|0.991;G|0.009	0.009	strong		0.557	UNC45A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280406.2	NM_018671		G	91485730	C	G	91485730	3	3	22	1	0	0	0	0	1	0	0	0	17003	595	21	4	777	4	UNC45A	15	91485730	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	48765	91485730	11045662	3100	6001											
VPS33B	26276	hgsc.bcm.edu	37	chr15	91550232	91550232	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccttcggcccttggtttcGccatcctcctcctcctccag	2	12	8	19	2	0	0	0	0	0	0	7	0	5	0	8	3	0	1	8	3	0	3	rs59648701	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:91550232G>A	ENST00000333371.3	-	9	1001	c.648C>T	c.(646-648)ggC>ggT	p.G216G	VPS33B_ENST00000535906.1_Silent_p.G189G|VPS33B_ENST00000535843.1_Silent_p.G125G	NM_018668.3	NP_061138.3	Q9H267	VP33B_HUMAN	vacuolar protein sorting 33 homolog B (yeast)	216					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)					CCTTGGTTTCGCCATCCTCCT	0.527													G|||	120	0.0239617	0.0809	0.0144	5008	,	,		19376	0.0		0.003	False		,,,				2504	0.0				p.G216G		Atlas-SNP	.											.	VPS33B	42	.	0			c.C648T						PASS	.	G		294,4102	161.4+/-193.6	7,280,1911	114	118	117		648	-1.7	1	15	dbSNP_129	117	8,8588	7.1+/-27.0	0,8,4290	no	coding-synonymous	VPS33B	NM_018668.3		7,288,6201	AA,AG,GG		0.0931,6.6879,2.3245		216/618	91550232	302,12690	2198	4298	6496	SO:0001819	synonymous_variant	26276	exon9			GGTTTCGCCATCC	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.648C>T	15.37:g.91550232G>A		14	0	0		33	32	0.969697	NM_018668	B3KQF6|Q96K14|Q9NRP6|Q9NSF3	Silent	SNP	ENST00000333371.3	37	CCDS10369.1																																																																																			G|0.978;A|0.022	0.022	strong		0.527	VPS33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313496.1	NM_018668		A	91550232	G	A	91550232	2	1	22	1	0	0	0	0	0	0	0	1	17217	1074	38	1		1	VPS33B	15	91550232	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	64502	91550232	10981160	3101	6002											
RGMA	56963	hgsc.bcm.edu	37	chr15	93588657	93588657	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaggtagagaccctggctGtcccagtcctccacagcatt	9	8	10	14	0	0	2	0	0	0	2	3	3	3	2	4	2	1	3	4	2	1	2	rs61733836	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:93588657G>A	ENST00000329082.7	-	4	1195	c.924C>T	c.(922-924)gaC>gaT	p.D308D	RGMA_ENST00000538818.1_Silent_p.D199D|RGMA_ENST00000557301.1_Silent_p.D316D|RGMA_ENST00000425933.2_Silent_p.D292D|RGMA_ENST00000542321.2_Silent_p.D292D|RGMA_ENST00000543599.1_Silent_p.D292D|RGMA_ENST00000557420.1_3'UTR|RGMA_ENST00000556658.1_Silent_p.D199D	NM_020211.2	NP_064596	Q96B86	RGMA_HUMAN	repulsive guidance molecule family member a	308					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)			GACCCTGGCTGTCCCAGTCCT	0.647													G|||	30	0.00599042	0.0212	0.0029	5008	,	,		18464	0.0		0.0	False		,,,				2504	0.0				p.D316D		Atlas-SNP	.											.	RGMA	49	.	0			c.C948T						PASS	.	G	,,,,,	93,4121		3,87,2017	27	34	32		948,876,876,876,876,924	4.8	1	15	dbSNP_129	32	0,8432		0,0,4216	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RGMA	NM_001166283.1,NM_001166286.1,NM_001166287.1,NM_001166288.1,NM_001166289.1,NM_020211.2	,,,,,	3,87,6233	AA,AG,GG		0.0,2.2069,0.7354	,,,,,	316/459,292/435,292/435,292/435,292/435,308/451	93588657	93,12553	2107	4216	6323	SO:0001819	synonymous_variant	56963	exon4			CTGGCTGTCCCAG	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.924C>T	15.37:g.93588657G>A		77	0	0		84	38	0.452381	NM_001166283	B2RTW1|B7Z5S8|F5GXQ7|F5GZU6|G3V518|Q0JV97|Q8NC80|Q9H0E6|Q9NPM3	Silent	SNP	ENST00000329082.7	37	CCDS45357.1																																																																																			G|0.994;A|0.006	0.006	strong		0.647	RGMA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415091.1	NM_020211		A	93588657	G	A	93588657	2	1	22	1	0	0	0	0	0	0	0	1	13295	1368	48	2		2	RGMA	15	93588657	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2038425	93588657	8942735	3102	6003											
MCTP2	55784	hgsc.bcm.edu	37	chr15	94858808	94858808	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aacctccccagcccttttgcGtacctcctcaccatacacct	8	10	3	20	1	1	0	1	0	0	0	3	0	3	0	8	0	5	1	8	0	3	4	rs146431277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:94858808G>A	ENST00000357742.4	+	3	579	c.579G>A	c.(577-579)gcG>gcA	p.A193A	MCTP2_ENST00000331706.4_5'UTR|MCTP2_ENST00000451018.3_Silent_p.A193A|MCTP2_ENST00000543482.1_Silent_p.A193A	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	193	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)			GCCCTTTTGCGTACCTCCTCA	0.547													g|||	8	0.00159744	0.0053	0.0	5008	,	,		17286	0.0		0.0	False		,,,				2504	0.001				p.A193A		Atlas-SNP	.											MCTP2,NS,adenoma,0,1	MCTP2	122	1	0			c.G579A						PASS	.	A	,	28,4366	34.3+/-65.2	0,28,2169	150	121	131		579,579	-12.1	0	15	dbSNP_134	131	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous,coding-synonymous	MCTP2	NM_001159643.1,NM_018349.3	,	0,29,6466	AA,AG,GG		0.0116,0.6372,0.2232	,	193/824,193/879	94858808	29,12961	2197	4298	6495	SO:0001819	synonymous_variant	55784	exon3			TTTTGCGTACCTC	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.579G>A	15.37:g.94858808G>A		191	0	0		203	105	0.517241	NM_001159643	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Silent	SNP	ENST00000357742.4	37	CCDS32338.1																																																																																			G|0.998;A|0.002	0.002	strong		0.547	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349		A	94858808	G	A	94858808	2	1	22	1	0	0	0	0	0	0	0	1	9410	1132	40	1		1	MCTP2	15	94858808	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1270151	94858808	7672584	3103	6004											
PGPEP1L	145814	hgsc.bcm.edu	37	chr15	99512877	99512877	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccatgcccacatgcacgaCgagctgtgtgaacgggtaac	10	7	12	12	3	0	1	0	1	0	0	1	3	1	1	2	1	5	3	2	1	2	1	rs78254881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:99512877C>T	ENST00000378919.6	-	4	353	c.148G>A	c.(148-150)Gtc>Atc	p.V50I	RP11-654A16.3_ENST00000559468.1_RNA|PGPEP1L_ENST00000535714.1_5'UTR	NM_001102612.2	NP_001096082.2	A6NFU8	PGPIL_HUMAN	pyroglutamyl-peptidase I-like	50							cysteine-type peptidase activity (GO:0008234)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(2)|skin(1)|stomach(1)	14						ACATGCACGACGAGCTGTGTG	0.602													C|||	66	0.0131789	0.0469	0.0058	5008	,	,		16700	0.0		0.0	False		,,,				2504	0.0				p.V50I		Atlas-SNP	.											.	PGPEP1L	26	.	0			c.G148A						PASS	.	C	ILE/VAL,	145,4113		4,137,1988	77	82	80		148,	0.1	0.1	15	dbSNP_131	80	5,8489		0,5,4242	yes	missense,utr-5	PGPEP1L	NM_001102612.2,NM_001167902.1	29,	4,142,6230	TT,TC,CC		0.0589,3.4054,1.1763	benign,	50/197,	99512877	150,12602	2129	4247	6376	SO:0001583	missense	145814	exon4			GCACGACGAGCTG		CCDS53977.1, CCDS58400.1	15q26.3	2010-02-16			ENSG00000183571	ENSG00000183571			27080	protein-coding gene	gene with protein product							Standard	NM_001102612		Approved		uc002bum.3	A6NFU8		ENST00000378919.6:c.148G>A	15.37:g.99512877C>T	ENSP00000368199:p.Val50Ile	71	0	0		74	39	0.527027	NM_001102612	H0YF86	Missense_Mutation	SNP	ENST00000378919.6	37	CCDS53977.1	25	0.011446886446886446	20	0.04065040650406504	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	C	4.380	0.070062	0.08436	0.034054	5.89E-4	ENSG00000183571	ENST00000378919;ENST00000535714	T	0.54279	0.58	4.36	0.0993	0.14502	.	.	.	.	.	T	0.11024	0.0269	L	0.41573	1.285	0.09310	N	1	B	0.22346	0.068	B	0.18561	0.022	T	0.12502	-1.0545	9	0.40728	T	0.16	-23.075	3.4626	0.07539	0.1898:0.3126:0.0:0.4976	.	50	A6NFU8	PGPIL_HUMAN	I	50;43	ENSP00000368199:V50I	ENSP00000368199:V50I	V	-	1	0	PGPEP1L	97330400	0.000000	0.05858	0.065000	0.19835	0.005000	0.04900	0.029000	0.13666	0.141000	0.18875	-0.827000	0.03088	GTC	C|0.986;T|0.014	0.014	strong		0.602	PGPEP1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415703.1	NM_001102612.2		T	99512877	C	T	99512877	3	4	22	1	0	0	0	0	1	0	0	0	11813	536	19	1	450	1	PGPEP1L	15	99512877	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4654069	99512877	3018515	3104	6005											
LRRK1	79705	hgsc.bcm.edu	37	chr15	101606084	101606084	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctgagggggactccatcgcGgacgtgagcatcatgtacag	9	7	14	11	3	1	2	1	2	0	0	3	4	2	4	2	3	2	2	2	3	1	1	rs116529941	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:101606084G>A	ENST00000388948.3	+	32	5801	c.5442G>A	c.(5440-5442)gcG>gcA	p.A1814A	RP11-505E24.2_ENST00000559857.1_RNA|LRRK1_ENST00000284395.5_Silent_p.A1811A|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)			ACTCCATCGCGGACGTGAGCA	0.622													G|||	6	0.00119808	0.0045	0.0	5008	,	,		17606	0.0		0.0	False		,,,				2504	0.0				p.A1814A		Atlas-SNP	.											.	LRRK1	310	.	0			c.G5442A						PASS	.	G		10,4162		0,10,2076	61	69	66		5442	-11	0	15	dbSNP_132	66	0,8430		0,0,4215	no	coding-synonymous	LRRK1	NM_024652.3		0,10,6291	AA,AG,GG		0.0,0.2397,0.0794		1814/2016	101606084	10,12592	2086	4215	6301	SO:0001819	synonymous_variant	79705	exon32			CATCGCGGACGTG	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.5442G>A	15.37:g.101606084G>A		111	0	0		136	75	0.551471	NM_024652		Silent	SNP	ENST00000388948.3	37	CCDS42086.1																																																																																			G|0.997;A|0.003	0.003	strong		0.622	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		A	101606084	G	A	101606084	2	1	22	1	0	0	0	0	0	0	0	1	9041	1103	39	1		1	LRRK1	15	101606084	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2093207	101606084	925308	3105	6006											
SNRPA1	6627	hgsc.bcm.edu	37	chr15	101835306	101835306	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	acgcccccggactcaccccgGaggtccagctcccggtcgcg	5	4	12	20	6	1	0	1	0	0	0	4	2	3	2	6	4	1	1	6	4	0	0	rs61738984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:101835306G>C	ENST00000254193.6	-	1	150	c.78C>G	c.(76-78)ctC>ctG	p.L26L	SNRPA1_ENST00000560856.1_5'UTR|RP11-299G20.2_ENST00000558838.1_RNA	NM_003090.2	NP_003081.2	P09661	RU2A_HUMAN	small nuclear ribonucleoprotein polypeptide A'	26					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)			ACTCACCCCGGAGGTCCAGCT	0.721													G|||	442	0.0882588	0.2829	0.0749	5008	,	,		11636	0.001		0.007	False		,,,				2504	0.0082				p.L26L		Atlas-SNP	.											.	SNRPA1	11	.	0			c.C78G						PASS	.	G		774,3286		49,676,1305	5	5	5		78	-8.1	0.2	15	dbSNP_129	5	29,7973		1,27,3973	no	coding-synonymous	SNRPA1	NM_003090.2		50,703,5278	CC,CG,GG		0.3624,19.064,6.6573		26/256	101835306	803,11259	2030	4001	6031	SO:0001819	synonymous_variant	6627	exon1			ACCCCGGAGGTCC	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.78C>G	15.37:g.101835306G>C		36	0	0		47	21	0.446809	NM_003090	B2R5I6|Q8TBD2	Silent	SNP	ENST00000254193.6	37	CCDS10391.1																																																																																			G|0.906;C|0.094	0.094	strong		0.721	SNRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313621.2	NM_003090		C	101835306	G	C	101835306	2	2	22	1	0	0	0	0	0	0	0	1	14875	1161	41	4		4	SNRPA1	15	101835306	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	229222	101835306	696086	3106	6007											
OR4F6	390648	hgsc.bcm.edu	37	chr15	102346030	102346030	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttttctcagtgttctatgtGtcaagcctgatgggaaatct	8	17	9	7	0	4	1	2	1	3	0	5	2	4	2	1	1	1	1	1	1	3	4	rs401632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:102346030G>A	ENST00000328882.4	+	1	129	c.108G>A	c.(106-108)gtG>gtA	p.V36V		NM_001005326.1	NP_001005326.1	Q8NGB9	OR4F6_HUMAN	olfactory receptor, family 4, subfamily F, member 6	36						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)			TGTTCTATGTGTCAAGCCTGA	0.498													g|||	235	0.0469249	0.1732	0.0086	5008	,	,		20248	0.0		0.0	False		,,,				2504	0.0				p.V36V		Atlas-SNP	.											.	OR4F6	45	.	0			c.G108A						PASS	.	G		769,3637		68,633,1502	254	233	240		108	0.4	0.1	15	dbSNP_80	240	23,8577		0,23,4277	no	coding-synonymous	OR4F6	NM_001005326.1		68,656,5779	AA,AG,GG		0.2674,17.4535,6.0895		36/313	102346030	792,12214	2203	4300	6503	SO:0001819	synonymous_variant	390648	exon1			CTATGTGTCAAGC	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.108G>A	15.37:g.102346030G>A		267	1	0.00374532		279	135	0.483871	NM_001005326	B9EH28|Q6IF95	Silent	SNP	ENST00000328882.4	37	CCDS32341.1																																																																																			G|0.944;A|0.056	0.056	strong		0.498	OR4F6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417593.1			A	102346030	G	A	102346030	2	1	22	1	0	0	0	0	0	0	0	1	11075	1364	48	2		2	OR4F6	15	102346030	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	510724	102346030	185362	3107	6008											
RHBDF1	64285	hgsc.bcm.edu	37	chr16	113027	113027	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccaccgactctcgcttgcGccgccgcgggagccggtgga	4	5	16	16	7	1	0	0	0	1	0	2	3	1	2	5	4	2	1	5	4	0	1	rs78541046	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:113027G>A	ENST00000262316.6	-	5	758	c.616C>T	c.(616-618)Cgc>Tgc	p.R206C	RHBDF1_ENST00000454039.2_Missense_Mutation_p.R206C	NM_022450.3	NP_071895.3	Q96CC6	RHDF1_HUMAN	rhomboid 5 homolog 1 (Drosophila)	206					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)				TCTCGCTTGCGCCGCCGCGGG	0.701													G|||	19	0.00379393	0.0144	0.0	5008	,	,		13623	0.0		0.0	False		,,,				2504	0.0				p.R206C		Atlas-SNP	.											.	RHBDF1	54	.	0			c.C616T						PASS	.	G	CYS/ARG	46,4332		1,44,2144	27	32	30		616	5.1	1	16	dbSNP_131	30	0,8578		0,0,4289	yes	missense	RHBDF1	NM_022450.3	180	1,44,6433	AA,AG,GG		0.0,1.0507,0.355	probably-damaging	206/856	113027	46,12910	2189	4289	6478	SO:0001583	missense	64285	exon5			GCTTGCGCCGCCG	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.616C>T	16.37:g.113027G>A	ENSP00000262316:p.Arg206Cys	96	0	0		140	80	0.571429	NM_022450	Q04842|Q1W6H2|Q4TT59|Q96S34|Q9H6E1	Missense_Mutation	SNP	ENST00000262316.6	37	CCDS32344.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	.	24.2	4.509855	0.85282	0.010507	0.0	ENSG00000007384	ENST00000262316;ENST00000454039	T;T	0.80304	-1.36;-1.36	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	D	0.86406	0.5925	M	0.74258	2.255	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.994;0.998;0.999	D	0.88684	0.3204	10	0.62326	D	0.03	-33.0545	17.4836	0.87682	0.0:0.0:1.0:0.0	.	206;229;206	F5GWL4;B4E3Q0;Q96CC6	.;.;RHDF1_HUMAN	C	206	ENSP00000262316:R206C;ENSP00000392133:R206C	ENSP00000262316:R206C	R	-	1	0	RHBDF1	53027	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.266000	0.65525	2.354000	0.79902	0.462000	0.41574	CGC	G|0.996;A|0.004	0.004	strong		0.701	RHBDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134178.2	NM_022450		A	113027	G	A	113027	3	1	22	1	0	0	0	0	1	0	0	0	13334	1087	38	1	2007	1	RHBDF1	16	113027	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10		113027	90241726	3108	6009											
MRPL28	10573	hgsc.bcm.edu	37	chr16	417691	417691	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtggtcactggccactggctCtcttctgcaccaccgccggc	4	9	11	17	2	3	0	1	0	2	0	4	0	3	0	4	4	1	2	4	4	0	1	rs114486517	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:417691C>G	ENST00000199706.8	-	6	790	c.755G>C	c.(754-756)aGa>aCa	p.R252T	MRPL28_ENST00000389675.2_Missense_Mutation_p.R252T|MRPL28_ENST00000429738.1_Intron	NM_006428.4	NP_006419.2	Q13084	RM28_HUMAN	mitochondrial ribosomal protein L28	252				R -> T (in Ref. 6; AAC50181). {ECO:0000305}.	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)				GCCACTGGCTCTCTTCTGCAC	0.617													C|||	327	0.0652955	0.2194	0.0303	5008	,	,		18217	0.0		0.008	False		,,,				2504	0.0082				p.R252T		Atlas-SNP	.											.	MRPL28	15	.	0			c.G755C						PASS	.	C	THR/ARG	811,3595	316.1+/-294.4	77,657,1469	53	48	50		755	-3	0	16	dbSNP_132	50	57,8543	33.3+/-86.6	1,55,4244	yes	missense	MRPL28	NM_006428.4	71	78,712,5713	GG,GC,CC		0.6628,18.4067,6.6738	benign	252/257	417691	868,12138	2203	4300	6503	SO:0001583	missense	10573	exon6			CTGGCTCTCTTCT	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.755G>C	16.37:g.417691C>G	ENSP00000199706:p.Arg252Thr	119	0	0		134	69	0.514925	NM_006428	B2RCM4|D3DU46|Q4TT39|Q96S26|Q9BQD8|Q9BR04	Missense_Mutation	SNP	ENST00000199706.8	37	CCDS32349.1	109	0.04990842490842491	98	0.1991869918699187	9	0.024861878453038673	0	0.0	2	0.002638522427440633	C	8.839	0.941748	0.18281	0.184067	0.006628	ENSG00000086504	ENST00000397735;ENST00000199706;ENST00000397734;ENST00000389675	T;T	0.23950	1.88;1.88	4.86	-2.96	0.05547	.	0.400839	0.27000	N	0.021425	T	0.00012	0.0000	L	0.31294	0.92	0.80722	P	0.0	B;B	0.22003	0.063;0.063	B;B	0.15484	0.013;0.013	T	0.23940	-1.0174	9	0.49607	T	0.09	-0.0185	4.4593	0.11659	0.0:0.2928:0.309:0.3982	.	252;252	Q13084;Q4TT38	RM28_HUMAN;.	T	252	ENSP00000199706:R252T;ENSP00000374326:R252T	ENSP00000199706:R252T	R	-	2	0	MRPL28	357692	0.007000	0.16637	0.004000	0.12327	0.779000	0.44077	-0.411000	0.07142	-0.118000	0.11851	0.637000	0.83480	AGA	C|0.937;G|0.063	0.063	strong		0.617	MRPL28-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139285.2			G	417691	C	G	417691	3	3	22	1	0	0	0	0	1	0	0	0	9801	913	32	4	19	4	MRPL28	16	417691	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	304664	417691	89937062	3109	6010											
MSLN	10232	hgsc.bcm.edu	37	chr16	815593	815593	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctgcccgtgctgggccaGcccatcatccgcagcatccc	5	7	10	19	2	1	0	1	0	0	0	3	0	3	0	5	1	5	4	5	1	0	0	rs115279916	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:815593G>C	ENST00000382862.3	+	9	866	c.771G>C	c.(769-771)caG>caC	p.Q257H	MSLN_ENST00000566549.1_Missense_Mutation_p.Q257H|MSLN_ENST00000563941.1_Missense_Mutation_p.Q257H|MSLN_ENST00000545450.2_Missense_Mutation_p.Q257H	NM_013404.4	NP_037536.2	Q13421	MSLN_HUMAN	mesothelin	257					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)				TGCTGGGCCAGCCCATCATCC	0.706													G|||	81	0.0161741	0.059	0.0043	5008	,	,		14281	0.0		0.0	False		,,,				2504	0.0				p.Q257H		Atlas-SNP	.											.	MSLN	109	.	0			c.G771C						PASS	.	G	HIS/GLN,HIS/GLN,HIS/GLN	207,4145	119.2+/-156.9	5,197,1974	31	32	32		771,771,771	1	0	16	dbSNP_132	32	1,8569	1.2+/-3.3	0,1,4284	yes	missense,missense,missense	MSLN	NM_001177355.1,NM_005823.5,NM_013404.4	24,24,24	5,198,6258	CC,CG,GG		0.0117,4.7564,1.6097	benign,benign,benign	257/623,257/623,257/631	815593	208,12714	2176	4285	6461	SO:0001583	missense	10232	exon10			GGGCCAGCCCATC	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.771G>C	16.37:g.815593G>C	ENSP00000372313:p.Gln257His	60	0	0		117	65	0.555556	NM_005823	D3DU65|Q14859|Q4VQD5|Q96GR6|Q96KJ5|Q9BR17|Q9BTR2|Q9UCB2|Q9UK57	Missense_Mutation	SNP	ENST00000382862.3	37	CCDS32356.1	24	0.01098901098901099	22	0.044715447154471545	2	0.0055248618784530384	0	0.0	0	0.0	G	2.785	-0.252545	0.05829	0.047564	1.17E-4	ENSG00000102854	ENST00000446427;ENST00000445361;ENST00000545450;ENST00000382862	T;T	0.12569	2.67;2.67	3.03	1.03	0.20045	.	1.781050	0.03402	N	0.203448	T	0.01489	0.0048	N	0.25647	0.755	0.09310	N	1	B;B;B;B	0.15141	0.007;0.008;0.012;0.007	B;B;B;B	0.12156	0.004;0.007;0.007;0.004	T	0.30119	-0.9989	10	0.39692	T	0.17	-0.1169	4.9829	0.14175	0.2994:0.0:0.7006:0.0	.	256;257;257;257	Q13421-4;Q13421;Q13421-2;Q13421-3	.;MSLN_HUMAN;.;.	H	257	ENSP00000442965:Q257H;ENSP00000372313:Q257H	ENSP00000372313:Q257H	Q	+	3	2	MSLN	755594	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.687000	0.25407	0.060000	0.16281	-0.271000	0.10264	CAG	G|0.985;C|0.015	0.015	strong		0.706	MSLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109253.2			C	815593	G	C	815593	3	2	22	1	0	0	0	0	1	0	0	0	9890	962	34	4	801	4	MSLN	16	815593	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	397902	815593	89539160	3110	6011											
MSLN	10232	hgsc.bcm.edu	37	chr16	816973	816973	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccttgctttccagaacatgAacgggtccgaatacttcgtg	9	11	10	11	3	0	2	0	1	0	1	3	3	2	2	3	1	4	1	3	1	4	4	rs35317722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:816973A>G	ENST00000382862.3	+	14	1581	c.1486A>G	c.(1486-1488)Aac>Gac	p.N496D	MSLN_ENST00000566549.1_Missense_Mutation_p.N488D|MSLN_ENST00000563941.1_Missense_Mutation_p.N488D|MSLN_ENST00000545450.2_Missense_Mutation_p.N488D	NM_013404.4	NP_037536.2	Q13421	MSLN_HUMAN	mesothelin	496					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)				CCAGAACATGAACGGGTCCGA	0.627													A|||	151	0.0301518	0.1104	0.0072	5008	,	,		18480	0.0		0.0	False		,,,				2504	0.0				p.N496D		Atlas-SNP	.											.	MSLN	109	.	0			c.A1486G						PASS	.	A	ASP/ASN,ASP/ASN,ASP/ASN	341,4039	175.5+/-204.9	19,303,1868	79	80	79		1462,1462,1486	-0.5	0	16	dbSNP_126	79	3,8581	3.0+/-9.4	0,3,4289	yes	missense,missense,missense	MSLN	NM_001177355.1,NM_005823.5,NM_013404.4	23,23,23	19,306,6157	GG,GA,AA		0.0349,7.7854,2.6535	benign,benign,benign	488/623,488/623,496/631	816973	344,12620	2190	4292	6482	SO:0001583	missense	10232	exon14			AACATGAACGGGT	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.1486A>G	16.37:g.816973A>G	ENSP00000372313:p.Asn496Asp	58	0	0		77	38	0.493506	NM_013404	D3DU65|Q14859|Q4VQD5|Q96GR6|Q96KJ5|Q9BR17|Q9BTR2|Q9UCB2|Q9UK57	Missense_Mutation	SNP	ENST00000382862.3	37	CCDS32356.1	66	0.03021978021978022	63	0.12804878048780488	3	0.008287292817679558	0	0.0	0	0.0	A	5.121	0.207947	0.09704	0.077854	3.49E-4	ENSG00000102854	ENST00000446427;ENST00000445361;ENST00000545450;ENST00000382862	T;T	0.12039	2.72;2.72	5.13	-0.498	0.12019	.	0.811867	0.11375	N	0.570445	T	0.00073	0.0002	N	0.19112	0.55	0.09310	N	1	B;B;B;B	0.15719	0.004;0.009;0.014;0.004	B;B;B;B	0.13407	0.005;0.009;0.005;0.005	T	0.44620	-0.9316	10	0.11485	T	0.65	-15.2008	5.1406	0.14957	0.4492:0.2783:0.0:0.2724	rs35317722	487;496;488;488	Q13421-4;Q13421;Q13421-2;Q13421-3	.;MSLN_HUMAN;.;.	D	496;488;488;496	ENSP00000442965:N488D;ENSP00000372313:N496D	ENSP00000372313:N496D	N	+	1	0	MSLN	756974	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.121000	0.15667	0.222000	0.20900	0.443000	0.29094	AAC	A|0.970;G|0.030	0.030	strong		0.627	MSLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109253.2			G	816973	A	G	816973	3	3	22	1	0	0	0	0	1	0	0	0	9890	246	9	3	1536	3	MSLN	16	816973	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1380	816973	89537780	3111	6012											
RPUSD1	113000	hgsc.bcm.edu	37	chr16	836111	836111	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gcccctatcctcggggtcagGgtcgggggtggcccgtaagg	4	7	18	12	3	1	0	1	0	0	0	4	0	2	0	4	7	0	1	4	7	2	2	rs112366818	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:836111G>T	ENST00000561734.1	-	5	1021	c.778C>A	c.(778-780)Cct>Act	p.P260T	RPUSD1_ENST00000565809.1_3'UTR|CHTF18_ENST00000455171.2_5'Flank|RPUSD1_ENST00000007264.2_Missense_Mutation_p.P260T|RPUSD1_ENST00000567114.1_Missense_Mutation_p.P131T|MSLNL_ENST00000442466.1_5'Flank|CHTF18_ENST00000317063.6_5'Flank|CHTF18_ENST00000262315.9_5'Flank			Q9UJJ7	RUSD1_HUMAN	RNA pseudouridylate synthase domain containing 1	260	Pro-rich.				pseudouridine synthesis (GO:0001522)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			endometrium(3)|lung(2)|skin(2)	7		Hepatocellular(780;0.00335)				TCGGGGTCAGGGTCGGGGGTG	0.721													G|||	227	0.0453275	0.1641	0.0115	5008	,	,		13109	0.0		0.002	False		,,,				2504	0.0				p.P260T		Atlas-SNP	.											.	RPUSD1	19	.	0			c.C778A						PASS	.	G	THR/PRO	471,3899		25,421,1739	18	24	22		778	4.2	1	16	dbSNP_132	22	3,8555		0,3,4276	yes	missense	RPUSD1	NM_058192.2	38	25,424,6015	TT,TG,GG		0.0351,10.778,3.6665	possibly-damaging	260/313	836111	474,12454	2185	4279	6464	SO:0001583	missense	113000	exon6			GGTCAGGGTCGGG	AE006465	CCDS10426.1	16p13.3	2013-02-11	2005-01-31	2005-01-31	ENSG00000007376	ENSG00000007376		"RNA pseudouridylate synthase domain containing"	14173	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 40"	C16orf40			Standard	NM_058192		Approved	RLUCL, MGC19600	uc002ckb.3	Q9UJJ7	OTTHUMG00000047840	ENST00000561734.1:c.778C>A	16.37:g.836111G>T	ENSP00000455026:p.Pro260Thr	59	0	0		72	71	0.986111	NM_058192	D3DU66	Missense_Mutation	SNP	ENST00000561734.1	37	CCDS10426.1	79	0.036172161172161175	75	0.1524390243902439	4	0.011049723756906077	0	0.0	0	0.0	G	10.09	1.256160	0.22965	0.10778	3.51E-4	ENSG00000007376	ENST00000007264	T	0.16743	2.32	4.21	4.21	0.49690	.	0.832292	0.11055	N	0.604570	T	0.00109	0.0003	L	0.44542	1.39	0.20703	N	0.999863	P	0.52316	0.952	P	0.45998	0.5	T	0.08554	-1.0716	10	0.72032	D	0.01	-9.908	12.1354	0.53968	0.0:0.0:1.0:0.0	.	260	Q9UJJ7	RUSD1_HUMAN	T	260	ENSP00000007264:P260T	ENSP00000007264:P260T	P	-	1	0	RPUSD1	776112	0.991000	0.36638	0.987000	0.45799	0.161000	0.22273	2.137000	0.42130	1.920000	0.55613	0.456000	0.33151	CCT	G|0.962;T|0.038	0.038	strong		0.721	RPUSD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420620.1	NM_058192		T	836111	G	T	836111	3	4	22	1	0	0	0	0	1	0	0	0	13681	1232	43	4	164	4	RPUSD1	16	836111	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	19138	836111	89518642	3112	6013											
CHTF18	63922	hgsc.bcm.edu	37	chr16	842972	842972	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccttctccaccaggtctccCtgcggcagggcatgagggcc	5	7	12	17	1	2	1	0	1	2	0	4	1	2	1	5	4	1	2	5	4	0	1	rs534605273		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:842972C>G	ENST00000262315.9	+	13	1642	c.1579C>G	c.(1579-1581)Ctg>Gtg	p.L527V	CHTF18_ENST00000455171.2_Missense_Mutation_p.L555V|CHTF18_ENST00000317063.6_Intron	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	527					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)				CCAGGTCTCCCTGCGGCAGGG	0.657													c|||	1	0.000199681	0.0008	0.0	5008	,	,		14564	0.0		0.0	False		,,,				2504	0.0				p.L527V		Atlas-SNP	.											.	CHTF18	52	.	0			c.C1579G						PASS	.						9	12	11					16																	842972		1892	4037	5929	SO:0001583	missense	63922	exon13			GTCTCCCTGCGGC	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.1579C>G	16.37:g.842972C>G	ENSP00000262315:p.Leu527Val	63	0	0		102	50	0.490196	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Missense_Mutation	SNP	ENST00000262315.9	37	CCDS45371.1	.	.	.	.	.	.	.	.	.	.	c	2.016	-0.425888	0.04701	.	.	ENSG00000127586	ENST00000455171;ENST00000262315	T;T	0.17370	2.28;2.28	4.9	0.103	0.14526	.	.	.	.	.	T	0.09949	0.0244	L	0.38838	1.175	0.25065	N	0.991037	B;B	0.29909	0.261;0.172	B;B	0.26202	0.067;0.03	T	0.31251	-0.9950	9	0.31617	T	0.26	.	1.2554	0.01990	0.1656:0.3096:0.3219:0.2029	.	555;527	Q8WVB6-2;Q8WVB6	.;CTF18_HUMAN	V	555;527	ENSP00000406252:L555V;ENSP00000262315:L527V	ENSP00000262315:L527V	L	+	1	2	CHTF18	782973	0.000000	0.05858	0.502000	0.27614	0.443000	0.32047	-0.035000	0.12205	0.474000	0.27392	0.556000	0.70494	CTG	.	.	none		0.657	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092		G	842972	C	G	842972	3	3	22	1	0	0	0	0	1	0	0	0	3416	680	24	4	1629	4	CHTF18	16	842972	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6861	842972	89511781	3113	6014											
CHTF18	63922	hgsc.bcm.edu	37	chr16	846012	846012	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agcctggtgggcacgatgctCgcttacagcctgacctaccg	7	8	12	14	3	0	1	0	1	0	0	1	2	0	1	4	2	5	3	4	2	2	2	rs114461038	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:846012C>T	ENST00000262315.9	+	18	2454	c.2391C>T	c.(2389-2391)ctC>ctT	p.L797L	CHTF18_ENST00000455171.2_Silent_p.L825L|CHTF18_ENST00000317063.6_Silent_p.L1006L	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	797					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)				GCACGATGCTCGCTTACAGCC	0.642													c|||	89	0.0177716	0.0643	0.0058	5008	,	,		14732	0.0		0.0	False		,,,				2504	0.0				p.L797L		Atlas-SNP	.											.	CHTF18	52	.	0			c.C2391T						PASS	.			175,4107		8,159,1974	29	36	34		2391	-8.6	0.6	16	dbSNP_132	34	3,8505		0,3,4251	no	coding-synonymous	CHTF18	NM_022092.2		8,162,6225	TT,TC,CC		0.0353,4.0869,1.3917		797/976	846012	178,12612	2141	4254	6395	SO:0001819	synonymous_variant	63922	exon18			GATGCTCGCTTAC	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.2391C>T	16.37:g.846012C>T		92	0	0		90	40	0.444444	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Silent	SNP	ENST00000262315.9	37	CCDS45371.1																																																																																			C|0.979;T|0.021	0.021	strong		0.642	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092		T	846012	C	T	846012	2	4	22	1	0	0	0	0	0	0	0	1	3416	871	31	1		1	CHTF18	16	846012	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3040	846012	89508741	3114	6015											
PRR25	388199	hgsc.bcm.edu	37	chr16	855732	855732	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cccaaccagctcaggaacagCgcagccgctcgcaaatgcag	12	3	10	16	3	1	0	1	0	0	0	2	1	1	1	3	1	6	5	3	1	3	0	rs115484509	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:855732C>T	ENST00000301698.1	+	1	290	c.290C>T	c.(289-291)gCg>gTg	p.A97V		NM_001013638.1	NP_001013660.1	Q96S07	PRR25_HUMAN	proline rich 25	97										large_intestine(1)|lung(1)|skin(1)	3						TCAGGAACAGCGCAGCCGCTC	0.652													C|||	129	0.0257588	0.0938	0.0072	5008	,	,		17511	0.0		0.0	False		,,,				2504	0.0				p.A97V		Atlas-SNP	.											PRR25,NS,carcinoma,+1,1	PRR25	27	1	0			c.C290T						PASS	.	C	VAL/ALA	307,3571		16,275,1648	21	28	26		290	-0.5	0	16	dbSNP_132	26	1,8279		0,1,4139	yes	missense	PRR25	NM_001013638.1	64	16,276,5787	TT,TC,CC		0.0121,7.9165,2.5333	possibly-damaging	97/403	855732	308,11850	1939	4140	6079	SO:0001583	missense	388199	exon1			GAACAGCGCAGCC	BC156145	CCDS45372.1	16p13.3	2009-09-11			ENSG00000167945	ENSG00000167945			37230	protein-coding gene	gene with protein product						11157797	Standard	NM_001013638		Approved	gs64	uc010uut.2	Q96S07		ENST00000301698.1:c.290C>T	16.37:g.855732C>T	ENSP00000301698:p.Ala97Val	53	0	0		68	68	1	NM_001013638		Missense_Mutation	SNP	ENST00000301698.1	37	CCDS45372.1	44	0.020146520146520148	41	0.08333333333333333	3	0.008287292817679558	0	0.0	0	0.0	C	8.111	0.778895	0.16120	0.079165	1.21E-4	ENSG00000167945	ENST00000301698	T	0.38401	1.14	0.701	-0.467	0.12150	.	.	.	.	.	T	0.00815	0.0027	N	0.19112	0.55	0.09310	N	1	P	0.39964	0.697	B	0.29440	0.102	T	0.07121	-1.0789	8	0.87932	D	0	.	.	.	.	.	97	Q96S07	PRR25_HUMAN	V	97	ENSP00000301698:A97V	ENSP00000301698:A97V	A	+	2	0	PRR25	795733	0.000000	0.05858	0.013000	0.15412	0.030000	0.12068	-0.594000	0.05733	-0.199000	0.10317	0.313000	0.20887	GCG	C|0.977;T|0.023	0.023	strong		0.652	PRR25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440563.1	NM_001013638		T	855732	C	T	855732	3	4	22	1	0	0	0	0	1	0	0	0	12609	768	27	1	292	1	PRR25	16	855732	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	9720	855732	89499021	3115	6016											
SSTR5	6755	hgsc.bcm.edu	37	chr16	1128901	1128901	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcccagcctccacgcccagCtggaacgcctcctccccggg	5	6	9	21	3	0	0	0	0	0	0	4	1	4	1	8	2	3	1	8	2	1	1	rs35128939	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1128901C>T	ENST00000293897.4	+	1	121	c.33C>T	c.(31-33)agC>agT	p.S11S	SSTR5-AS1_ENST00000569832.1_RNA|SSTR5_ENST00000397547.2_Silent_p.S11S|SSTR5_ENST00000562758.1_Silent_p.S11S	NM_001053.3	NP_001044.1	P35346	SSR5_HUMAN	somatostatin receptor 5	11					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)	CCACGCCCAGCTGGAACGCCT	0.731													C|||	17	0.00339457	0.0121	0.0014	5008	,	,		13446	0.0		0.0	False		,,,				2504	0.0				p.S11S		Atlas-SNP	.											.	SSTR5	36	.	0			c.C33T						PASS	.	C	,	44,4262		0,44,2109	10	11	11		33,33	3.8	1	16	dbSNP_126	11	0,8488		0,0,4244	no	coding-synonymous,coding-synonymous	SSTR5	NM_001053.3,NM_001172560.1	,	0,44,6353	TT,TC,CC		0.0,1.0218,0.3439	,	11/365,11/365	1128901	44,12750	2153	4244	6397	SO:0001819	synonymous_variant	6755	exon2			GCCCAGCTGGAAC	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.33C>T	16.37:g.1128901C>T		24	0	0		24	5	0.208333	NM_001172560	P34988|Q541E0|Q9UJI5	Silent	SNP	ENST00000293897.4	37	CCDS10429.1																																																																																			C|0.997;T|0.003	0.003	strong		0.731	SSTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420836.1			T	1128901	C	T	1128901	2	4	22	1	0	0	0	0	0	0	0	1	15216	796	28	2		2	SSTR5	16	1128901	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	273169	1128901	89225852	3116	6017											
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1245062	1245062	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggacgttgagtgcggctcCgagcgctgcaacatcctgga	8	7	15	11	4	0	1	0	1	0	0	2	5	2	3	2	3	4	4	2	3	1	1	rs59794024	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1245062C>T	ENST00000348261.5	+	3	638	c.390C>T	c.(388-390)tcC>tcT	p.S130S	CACNA1H_ENST00000565831.1_Silent_p.S130S|CACNA1H_ENST00000358590.4_Silent_p.S130S	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	130					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)	AGTGCGGCTCCGAGCGCTGCA	0.647											OREG0023543	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	c|||	215	0.0429313	0.1551	0.0144	5008	,	,		8995	0.0		0.0	False		,,,				2504	0.0				p.S130S		Atlas-SNP	.											.	CACNA1H	317	.	0			c.C390T						PASS	.		,	470,3718		28,414,1652	79	86	84		390,390	-9	0.7	16	dbSNP_129	84	3,8407		0,3,4202	no	coding-synonymous,coding-synonymous	CACNA1H	NM_001005407.1,NM_021098.2	,	28,417,5854	TT,TC,CC		0.0357,11.2225,3.7546	,	130/2348,130/2354	1245062	473,12125	2094	4205	6299	SO:0001819	synonymous_variant	8912	exon3			CGGCTCCGAGCGC	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.390C>T	16.37:g.1245062C>T		80	0	0	594	77	34	0.441558	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	37	CCDS45375.1																																																																																			C|0.967;T|0.033	0.033	strong		0.647	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		T	1245062	C	T	1245062	2	4	22	1	0	0	0	0	0	0	0	1	2547	639	23	1		1	CACNA1H	16	1245062	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	116161	1245062	89109691	3117	6018											
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1255206	1255206	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgaagctgctggcctgcggCcctctgggctacatccggaa	6	8	13	14	2	1	1	0	1	1	0	2	2	2	2	3	4	4	3	3	4	3	1	rs28365123	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1255206C>T	ENST00000348261.5	+	11	2792	c.2544C>T	c.(2542-2544)ggC>ggT	p.G848G	RP11-616M22.3_ENST00000564700.1_RNA|CACNA1H_ENST00000565831.1_Silent_p.G848G|CACNA1H_ENST00000358590.4_Silent_p.G848G	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	848			G -> S (in ECA6). {ECO:0000269|PubMed:12891677}.		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)	TGGCCTGCGGCCCTCTGGGCT	0.612													c|||	290	0.0579073	0.2057	0.0216	5008	,	,		14068	0.0		0.003	False		,,,				2504	0.0				p.G848G		Atlas-SNP	.											.	CACNA1H	317	.	0			c.C2544T						PASS	.		,	677,3501		66,545,1478	74	79	77		2544,2544	1.9	0.9	16	dbSNP_126	77	5,8423		0,5,4209	no	coding-synonymous,coding-synonymous	CACNA1H	NM_001005407.1,NM_021098.2	,	66,550,5687	TT,TC,CC		0.0593,16.2039,5.4101	,	848/2348,848/2354	1255206	682,11924	2089	4214	6303	SO:0001819	synonymous_variant	8912	exon11			CTGCGGCCCTCTG	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.2544C>T	16.37:g.1255206C>T		67	0	0		65	38	0.584615	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	37	CCDS45375.1																																																																																			C|0.953;T|0.047	0.047	strong		0.612	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		T	1255206	C	T	1255206	2	4	22	1	0	0	0	0	0	0	0	1	2547	726	26	2		2	CACNA1H	16	1255206	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	10144	1255206	89099547	3118	6019											
BAIAP3	8938	hgsc.bcm.edu	37	chr16	1391362	1391362	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccacgcgggagccccgtgcAcagaaggagcagcgcttcgg	8	3	16	14	5	0	1	0	0	0	1	1	3	0	3	3	3	4	3	3	3	1	1	rs75271587	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1391362A>G	ENST00000324385.5	+	8	866	c.708A>G	c.(706-708)gcA>gcG	p.A236A	BAIAP3_ENST00000421665.2_Silent_p.A201A|BAIAP3_ENST00000426824.3_Silent_p.A201A|BAIAP3_ENST00000568887.1_Silent_p.A173A|BAIAP3_ENST00000397489.1_Silent_p.A218A|BAIAP3_ENST00000397488.2_Silent_p.A218A|BAIAP3_ENST00000562208.1_Silent_p.A178A	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	236	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				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)				AGCCCCGTGCACAGAAGGAGC	0.682													G|||	52	0.0103834	0.0386	0.0014	5008	,	,		17448	0.0		0.0	False		,,,				2504	0.0				p.A236A		Atlas-SNP	.											.	BAIAP3	88	.	0			c.A708G						PASS	.	G	,,,,	126,4260		1,124,2068	37	36	36		603,603,534,519,708	-5.2	0	16	dbSNP_131	36	0,8590		0,0,4295	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BAIAP3	NM_001199096.1,NM_001199097.1,NM_001199098.1,NM_001199099.1,NM_003933.4	,,,,	1,124,6363	GG,GA,AA		0.0,2.8728,0.971	,,,,	201/1117,201/1153,178/1130,173/1125,236/1188	1391362	126,12850	2193	4295	6488	SO:0001819	synonymous_variant	8938	exon8			CCGTGCACAGAAG	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.708A>G	16.37:g.1391362A>G		74	0	0		53	24	0.45283	NM_003933	A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Silent	SNP	ENST00000324385.5	37	CCDS10434.1																																																																																			A|0.988;G|0.012	0.012	strong		0.682	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3			G	1391362	A	G	1391362	2	3	22	1	0	0	0	0	0	0	0	1	1304	146	6	3		3	BAIAP3	16	1391362	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	136156	1391362	88963391	3119	6020											
BAIAP3	8938	hgsc.bcm.edu	37	chr16	1391419	1391419	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcgcggtggacccctgccTgccaagtgcatccaggtcac	8	6	12	15	2	1	0	1	0	0	0	2	1	2	1	5	3	4	1	5	3	2	0	rs73485660	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1391419T>C	ENST00000324385.5	+	8	923	c.765T>C	c.(763-765)ccT>ccC	p.P255P	BAIAP3_ENST00000421665.2_Silent_p.P220P|BAIAP3_ENST00000426824.3_Silent_p.P220P|BAIAP3_ENST00000568887.1_Silent_p.P192P|BAIAP3_ENST00000397489.1_Silent_p.P237P|BAIAP3_ENST00000397488.2_Silent_p.P237P|BAIAP3_ENST00000562208.1_Silent_p.P197P	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	255	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				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)				GACCCCTGCCTGCCAAGTGCA	0.677													C|||	42	0.00838658	0.031	0.0014	5008	,	,		17741	0.0		0.0	False		,,,				2504	0.0				p.P255P		Atlas-SNP	.											.	BAIAP3	88	.	0			c.T765C						PASS	.	C	,,,,	113,4283		0,113,2085	61	56	58		660,660,591,576,765	-9.4	0.1	16	dbSNP_130	58	0,8594		0,0,4297	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BAIAP3	NM_001199096.1,NM_001199097.1,NM_001199098.1,NM_001199099.1,NM_003933.4	,,,,	0,113,6382	CC,CT,TT		0.0,2.5705,0.8699	,,,,	220/1117,220/1153,197/1130,192/1125,255/1188	1391419	113,12877	2198	4297	6495	SO:0001819	synonymous_variant	8938	exon8			CCTGCCTGCCAAG	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.765T>C	16.37:g.1391419T>C		124	0	0		126	65	0.515873	NM_003933	A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Silent	SNP	ENST00000324385.5	37	CCDS10434.1																																																																																			T|0.989;C|0.011	0.011	strong		0.677	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3			C	1391419	T	C	1391419	2	2	22	1	0	0	0	0	0	0	0	1	1304	1567	55	3		3	BAIAP3	16	1391419	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	57	1391419	88963334	3120	6021											
PTX4	390667	hgsc.bcm.edu	37	chr16	1536047	1536047	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcgggaactctttcccgaTggcaaggtttgcaacttccc	7	12	10	12	2	1	0	0	0	1	0	4	2	3	1	2	3	3	3	2	3	3	3	rs59554810	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1536047T>C	ENST00000447419.2	-	3	1355	c.1330A>G	c.(1330-1332)Atc>Gtc	p.I444V	PTX4_ENST00000293922.1_Missense_Mutation_p.I439V|PTX4_ENST00000440447.2_3'UTR			Q96A99	PTX4_HUMAN	pentraxin 4, long	444	Pentaxin.		I -> V (in dbSNP:rs59554810).			extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						TCTTTCCCGATGGCAAGGTTT	0.632													T|||	277	0.0553115	0.1974	0.0231	5008	,	,		16980	0.0		0.0	False		,,,				2504	0.0				p.I439V		Atlas-SNP	.											.	PTX4	46	.	0			c.A1315G						PASS	.	T	VAL/ILE	834,3564	328.8+/-300.7	75,684,1440	69	68	68		1315	1.5	0	16	dbSNP_129	68	3,8597	2.2+/-6.3	0,3,4297	yes	missense	PTX4	NM_001013658.1	29	75,687,5737	CC,CT,TT		0.0349,18.9632,6.4395	benign	439/474	1536047	837,12161	2199	4300	6499	SO:0001583	missense	390667	exon3			TCCCGATGGCAAG		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"chromosome 16 open reading frame 38"	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.1330A>G	16.37:g.1536047T>C	ENSP00000445277:p.Ile444Val	56	0	0		46	23	0.5	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		110	0.05036630036630037	99	0.20121951219512196	11	0.03038674033149171	0	0.0	0	0.0	T	10.44	1.351103	0.24512	0.189632	3.49E-4	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.62788	0.0;0.0	5.21	1.54	0.23209	.	3.825800	0.00481	N	0.000131	T	0.00073	0.0002	N	0.22421	0.69	0.80722	P	0.0	B	0.17465	0.022	B	0.21917	0.037	T	0.03354	-1.1045	9	0.29301	T	0.29	.	2.6395	0.04967	0.1515:0.0841:0.1477:0.6167	rs59554810	439	Q96A99-2	.	V	444;439	ENSP00000445277:I444V;ENSP00000293922:I439V	ENSP00000293922:I439V	I	-	1	0	PTX4	1476048	0.001000	0.12720	0.002000	0.10522	0.006000	0.05464	0.387000	0.20718	-0.013000	0.14199	-0.376000	0.06991	ATC	T|0.942;C|0.058	0.058	strong		0.632	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658		C	1536047	T	C	1536047	3	2	22	1	0	0	0	0	1	0	0	0	12838	1464	51	3	109	3	PTX4	16	1536047	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	144628	1536047	88818706	3121	6022			7	30		6	4	311	N	T_G_C	1.446331e-05
PTX4	390667	hgsc.bcm.edu	37	chr16	1536114	1536114	+	Silent	SNP	C	C	A																															gccaagccagacatgctcccCacgaaggcctcggagctgtc																								rs79788206	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1536114C>A	ENST00000447419.2	-	3	1288	c.1263G>T	c.(1261-1263)gtG>gtT	p.V421V	PTX4_ENST00000293922.1_Silent_p.V416V|PTX4_ENST00000440447.2_3'UTR			Q96A99	PTX4_HUMAN	pentraxin 4, long	421	Pentaxin.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						ACATGCTCCCCACGAAGGCCT	0.637													C|||	88	0.0175719	0.0635	0.0058	5008	,	,		17747	0.0		0.0	False		,,,				2504	0.0				p.V416V		Atlas-SNP	.											.	PTX4	46	.	0			c.G1248T						PASS	.	C		286,4112	139.6+/-175.2	5,276,1918	67	65	66		1248	4.2	1	16	dbSNP_131	66	0,8600		0,0,4300	no	coding-synonymous	PTX4	NM_001013658.1		5,276,6218	AA,AC,CC		0.0,6.503,2.2003		416/474	1536114	286,12712	2199	4300	6499	SO:0001819	synonymous_variant	390667	exon3			GCTCCCCACGAAG		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"chromosome 16 open reading frame 38"	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.1263G>T	16.37:g.1536114C>A		76	0	0		83	37	0.445783	NM_001013658		Silent	SNP	ENST00000447419.2	37																																																																																				C|0.976;A|0.024	0.024	strong		0.637	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658		A	1536114	C	A	1536114	2	1	22	1	0	0	0	0	0	0	0	1	12838	581	21	4		4	PTX4	16	1536114	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	67	1536114	88818639	3122	6023	73	2	7	30		6	4	311	N	T_G_C	1.446331e-05
PTX4	390667	hgsc.bcm.edu	37	chr16	1536117	1536117	+	Silent	SNP	G	G	A																															aagccagacatgctccccacGaaggcctcggagctgtcgaa																								rs58192896	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1536117G>A	ENST00000447419.2	-	3	1285	c.1260C>T	c.(1258-1260)ttC>ttT	p.F420F	PTX4_ENST00000293922.1_Silent_p.F415F|PTX4_ENST00000440447.2_3'UTR			Q96A99	PTX4_HUMAN	pentraxin 4, long	420	Pentaxin.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						TGCTCCCCACGAAGGCCTCGG	0.647													G|||	277	0.0553115	0.1974	0.0231	5008	,	,		17589	0.0		0.0	False		,,,				2504	0.0				p.F415F		Atlas-SNP	.											.	PTX4	46	.	0			c.C1245T						PASS	.	G		831,3567	324.8+/-298.8	76,679,1444	65	62	63		1245	-10.4	0.5	16	dbSNP_129	63	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	PTX4	NM_001013658.1		76,682,5741	AA,AG,GG		0.0349,18.895,6.4164		415/474	1536117	834,12164	2199	4300	6499	SO:0001819	synonymous_variant	390667	exon3			CCCCACGAAGGCC		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"chromosome 16 open reading frame 38"	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.1260C>T	16.37:g.1536117G>A		73	0	0		79	36	0.455696	NM_001013658		Silent	SNP	ENST00000447419.2	37																																																																																				G|0.941;A|0.059	0.059	strong		0.647	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658		A	1536117	G	A	1536117	2	1	22	1	0	0	0	0	0	0	0	1	12838	1049	37	1		1	PTX4	16	1536117	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3	1536117	88818636	3123	6024	73	2	7	30		6	4	311	N	T_G_C	1.446331e-05
PTX4	390667	hgsc.bcm.edu	37	chr16	1536138	1536138	+	Silent	SNP	T	T	C																															aaggcctcggagctgtcgaaTccgccccccacgctgtcttg																								rs386787711|rs114122805	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1536138T>C	ENST00000447419.2	-	3	1264	c.1239A>G	c.(1237-1239)ggA>ggG	p.G413G	PTX4_ENST00000293922.1_Silent_p.G408G|PTX4_ENST00000440447.2_3'UTR			Q96A99	PTX4_HUMAN	pentraxin 4, long	413	Pentaxin.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						AGCTGTCGAATCCGCCCCCCA	0.662													T|||	87	0.0173722	0.0643	0.0029	5008	,	,		16736	0.0		0.0	False		,,,				2504	0.0				p.G408G		Atlas-SNP	.											.	PTX4	46	.	0			c.A1224G						PASS	.						59	56	57					16																	1536138		2199	4300	6499	SO:0001819	synonymous_variant	390667	exon3			GTCGAATCCGCCC		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"chromosome 16 open reading frame 38"	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.1239A>G	16.37:g.1536138T>C		66	0	0		77	41	0.532468	NM_001013658		Silent	SNP	ENST00000447419.2	37																																																																																				T|0.980;C|0.020	0.020	strong		0.662	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658		C	1536138	T	C	1536138	2	2	22	1	0	0	0	0	0	0	0	1	12838	1422	50	3		3	PTX4	16	1536138	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	21	1536138	88818615	3124	6025	74	2	7	30		6	4	311	N	T_G_C	1.446331e-05
PTX4	390667	hgsc.bcm.edu	37	chr16	1536140	1536140	+	Missense_Mutation	SNP	C	C	T																															ggcctcggagctgtcgaatcCgccccccacgctgtcttgtt																								rs386787711|rs79505704	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1536140C>T	ENST00000447419.2	-	3	1262	c.1237G>A	c.(1237-1239)Gga>Aga	p.G413R	PTX4_ENST00000293922.1_Missense_Mutation_p.G408R|PTX4_ENST00000440447.2_3'UTR			Q96A99	PTX4_HUMAN	pentraxin 4, long	413	Pentaxin.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						CTGTCGAATCCGCCCCCCACG	0.662													C|||	87	0.0173722	0.0643	0.0029	5008	,	,		16723	0.0		0.0	False		,,,				2504	0.0				p.G408R		Atlas-SNP	.											.	PTX4	46	.	0			c.G1222A						PASS	.						57	55	55					16																	1536140		2199	4300	6499	SO:0001583	missense	390667	exon3			CGAATCCGCCCCC		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"chromosome 16 open reading frame 38"	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.1237G>A	16.37:g.1536140C>T	ENSP00000445277:p.Gly413Arg	65	0	0		75	40	0.533333	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		43	0.019688644688644688	41	0.08333333333333333	2	0.0055248618784530384	0	0.0	0	0.0	C	13.11	2.138909	0.37728	.	.	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.65364	-0.15;-0.15	5.45	3.39	0.38822	.	0.128923	0.51477	D	0.000092	T	0.09202	0.0227	M	0.63428	1.95	0.09310	N	0.999999	D	0.56287	0.975	P	0.55011	0.766	T	0.10382	-1.0632	10	0.18710	T	0.47	.	8.671	0.34149	0.0:0.7615:0.1535:0.085	.	408	Q96A99-2	.	R	413;408	ENSP00000445277:G413R;ENSP00000293922:G408R	ENSP00000293922:G408R	G	-	1	0	PTX4	1476141	0.000000	0.05858	0.048000	0.18961	0.000000	0.00434	0.922000	0.28734	1.318000	0.45170	-0.251000	0.11542	GGA	C|0.987;T|0.013	0.013	strong		0.662	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658		T	1536140	C	T	1536140	3	4	22	1	0	0	0	0	1	0	0	0	12838	661	23	1	202	1	PTX4	16	1536140	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2	1536140	88818613	3125	6026	74	2	7	30		6	4	311	N	T_G_C	1.446331e-05
PTX4	390667	hgsc.bcm.edu	37	chr16	1536357	1536357	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aaggccgggtccccgatcacGaagtggatggatccgggcag	9	5	16	11	4	1	0	1	0	0	0	3	4	3	2	4	5	0	1	4	5	2	0	rs112226694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1536357G>A	ENST00000447419.2	-	3	1045	c.1020C>T	c.(1018-1020)ttC>ttT	p.F340F	PTX4_ENST00000293922.1_Silent_p.F335F|PTX4_ENST00000440447.2_Missense_Mutation_p.S192L			Q96A99	PTX4_HUMAN	pentraxin 4, long	340	Pentaxin.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						CCCCGATCACGAAGTGGATGG	0.662													G|||	88	0.0175719	0.0651	0.0029	5008	,	,		16575	0.0		0.0	False		,,,				2504	0.0				p.F335F		Atlas-SNP	.											.	PTX4	46	.	0			c.C1005T						PASS	.	G		251,4147	138.8+/-174.5	4,243,1952	42	50	47		1005	-11.2	0.2	16	dbSNP_132	47	0,8600		0,0,4300	no	coding-synonymous	PTX4	NM_001013658.1		4,243,6252	AA,AG,GG		0.0,5.7071,1.9311		335/474	1536357	251,12747	2199	4300	6499	SO:0001819	synonymous_variant	390667	exon3			GATCACGAAGTGG		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"chromosome 16 open reading frame 38"	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.1020C>T	16.37:g.1536357G>A		99	0	0		76	37	0.486842	NM_001013658		Silent	SNP	ENST00000447419.2	37																																																																																				G|0.979;A|0.021	0.021	strong		0.662	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658		A	1536357	G	A	1536357	2	1	22	1	0	0	0	0	0	0	0	1	12838	1049	37	1		1	PTX4	16	1536357	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	217	1536357	88818396	3126	6027			7	30		6	4	311	N	T_G_C	1.446331e-05
TELO2	9894	hgsc.bcm.edu	37	chr16	1552107	1552107	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagctgaagagcagcaaggCtcctgcctacgtccgggact	10	6	13	12	2	0	3	0	1	0	2	2	4	2	4	3	2	5	4	3	2	3	1	rs58099766	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1552107C>T	ENST00000262319.6	+	12	1811	c.1532C>T	c.(1531-1533)gCt>gTt	p.A511V	TELO2_ENST00000564507.1_3'UTR	NM_016111.3	NP_057195.2	Q9Y4R8	TELO2_HUMAN	telomere maintenance 2	511			A -> V (in dbSNP:rs58099766).		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)				AGCAGCAAGGCTCCTGCCTAC	0.632													C|||	115	0.0229633	0.0847	0.0043	5008	,	,		15233	0.0		0.0	False		,,,				2504	0.0				p.A511V		Atlas-SNP	.											.	TELO2	44	.	0			c.C1532T						PASS	.	C	VAL/ALA	328,4070	172.7+/-202.6	14,300,1885	67	64	65		1532	0.3	0.1	16	dbSNP_129	65	1,8599		0,1,4299	yes	missense	TELO2	NM_016111.3	64	14,301,6184	TT,TC,CC		0.0116,7.4579,2.5312	benign	511/838	1552107	329,12669	2199	4300	6499	SO:0001583	missense	9894	exon12			GCAAGGCTCCTGC	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.1532C>T	16.37:g.1552107C>T	ENSP00000262319:p.Ala511Val	63	0	0		68	36	0.529412	NM_016111	D3DU73|O75168|Q7LDV4|Q9BR21	Missense_Mutation	SNP	ENST00000262319.6	37	CCDS32363.1	48	0.02197802197802198	46	0.09349593495934959	2	0.0055248618784530384	0	0.0	0	0.0	C	10.54	1.379287	0.24944	0.074579	1.16E-4	ENSG00000100726	ENST00000437914;ENST00000262319	T	0.16743	2.32	5.67	0.301	0.15781	Telomere length regulation protein, conserved domain (1);	0.329093	0.36200	N	0.002734	T	0.00608	0.0020	M	0.76838	2.35	0.30705	N	0.749924	B	0.22800	0.075	B	0.24848	0.056	T	0.07309	-1.0779	10	0.29301	T	0.29	-4.6319	5.3866	0.16222	0.135:0.5696:0.0:0.2954	rs58099766	511	Q9Y4R8	TELO2_HUMAN	V	125;511	ENSP00000262319:A511V	ENSP00000262319:A511V	A	+	2	0	TELO2	1492108	0.983000	0.35010	0.139000	0.22197	0.033000	0.12548	2.614000	0.46359	0.055000	0.16094	0.655000	0.94253	GCT	C|0.972;T|0.028	0.028	strong		0.632	TELO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103602.2	NM_016111		T	1552107	C	T	1552107	3	4	22	1	0	0	0	0	1	0	0	0	15772	797	28	2	1574	2	TELO2	16	1552107	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	15750	1552107	88802646	3127	6028											
TMEM204	79652	hgsc.bcm.edu	37	chr16	1584294	1584294	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcgatgaccgtgcagagactCgtggccgcggccgtgctggt	5	7	17	12	6	0	2	0	1	0	1	1	4	0	2	3	3	2	2	3	3	0	0	rs79579867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1584294C>T	ENST00000566264.1	+	1	721	c.18C>T	c.(16-18)ctC>ctT	p.L6L	IFT140_ENST00000426508.2_Intron|TMEM204_ENST00000253934.5_Silent_p.L6L|IFT140_ENST00000361339.5_5'Flank	NM_024600.5	NP_078876.2	Q9BSN7	TM204_HUMAN	transmembrane protein 204	6					lymph vessel development (GO:0001945)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|response to stress (GO:0006950)|smooth muscle cell differentiation (GO:0051145)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|cervix(1)|endometrium(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	11		Hepatocellular(780;0.219)				TGCAGAGACTCGTGGCCGCGG	0.672													C|||	103	0.0205671	0.0764	0.0029	5008	,	,		15087	0.0		0.0	False		,,,				2504	0.0				p.L6L		Atlas-SNP	.											.	TMEM204	29	.	0			c.C18T						PASS	.	C	,	263,3993		4,255,1869	32	39	37		,18	-10.6	0.1	16	dbSNP_131	37	2,8484		0,2,4241	no	intron,coding-synonymous	IFT140,TMEM204	NM_014714.3,NM_024600.4	,	4,257,6110	TT,TC,CC		0.0236,6.1795,2.0797	,	,6/227	1584294	265,12477	2128	4243	6371	SO:0001819	synonymous_variant	79652	exon1			GAGACTCGTGGCC		CCDS42098.1	16p13.3	2008-02-05	2008-01-08	2008-01-08		ENSG00000131634			14158	protein-coding gene	gene with protein product		611002	"chromosome 16 open reading frame 30"	C16orf30			Standard	NM_024600		Approved	FLJ20898	uc002cmc.3	Q9BSN7		ENST00000566264.1:c.18C>T	16.37:g.1584294C>T		182	0	0		202	98	0.485149	NM_024600	D3DU76|Q3KRC1|Q9H7G5	Silent	SNP	ENST00000566264.1	37	CCDS42098.1																																																																																			C|0.979;T|0.021	0.021	strong		0.672	TMEM204-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432610.1	NM_024600		T	1584294	C	T	1584294	2	4	22	1	0	0	0	0	0	0	0	1	16144	871	31	1		1	TMEM204	16	1584294	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	32187	1584294	88770459	3128	6029											
IFT140	9742	hgsc.bcm.edu	37	chr16	1618306	1618306	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagggaccagctccgccaggCtcctgcagctacagtgtgct	7	7	12	15	1	0	0	0	0	0	0	2	1	2	1	4	2	5	5	4	2	1	1	rs8050974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1618306C>T	ENST00000426508.2	-	15	2045	c.1682G>A	c.(1681-1683)aGc>aAc	p.S561N	IFT140_ENST00000439987.2_5'UTR	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	561			S -> N (in dbSNP:rs8050974).		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)				CTCCGCCAGGCTCCTGCAGCT	0.662													C|||	128	0.0255591	0.0953	0.0029	5008	,	,		18208	0.0		0.0	False		,,,				2504	0.0				p.S561N		Atlas-SNP	.											.	IFT140	128	.	0			c.G1682A						PASS	.	C	ASN/SER	393,4005	193.0+/-218.2	17,359,1823	71	51	58		1682	-4.9	0.9	16	dbSNP_116	58	2,8598	1.2+/-3.3	0,2,4298	yes	missense	IFT140	NM_014714.3	46	17,361,6121	TT,TC,CC		0.0233,8.9359,3.0389	benign	561/1463	1618306	395,12603	2199	4300	6499	SO:0001583	missense	9742	exon15			GCCAGGCTCCTGC	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.1682G>A	16.37:g.1618306C>T	ENSP00000406012:p.Ser561Asn	98	0	0		125	59	0.472	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Missense_Mutation	SNP	ENST00000426508.2	37	CCDS10439.1	55	0.025183150183150184	54	0.10975609756097561	1	0.0027624309392265192	0	0.0	0	0.0	C	0.085	-1.177507	0.01633	0.089359	2.33E-4	ENSG00000187535	ENST00000397417;ENST00000426508;ENST00000439987	T	0.70516	-0.49	5.79	-4.95	0.03048	.	0.370546	0.32357	N	0.006210	T	0.00724	0.0024	N	0.02854	-0.475	0.09310	N	0.999996	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.07947	-1.0746	10	0.10902	T	0.67	.	10.6786	0.45799	0.0:0.453:0.0951:0.4519	rs8050974;rs8050974	561;286	Q96RY7;B4DR58	IF140_HUMAN;.	N	561	ENSP00000406012:S561N	ENSP00000380562:S561N	S	-	2	0	IFT140	1558307	0.997000	0.39634	0.855000	0.33649	0.090000	0.18270	0.272000	0.18644	-1.081000	0.03105	-1.110000	0.02074	AGC	C|0.964;T|0.036	0.036	strong		0.662	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714		T	1618306	C	T	1618306	3	4	22	1	0	0	0	0	1	0	0	0	7565	797	28	2	2774	2	IFT140	16	1618306	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	34012	1618306	88736447	3129	6030											
IFT140	9742	hgsc.bcm.edu	37	chr16	1634225	1634225	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cctcggcagtcaccttggtgGcaaacactccactgatgtgc	8	9	10	14	1	1	1	1	1	0	0	3	1	2	1	3	3	2	2	3	3	1	1	rs8060532	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1634225G>A	ENST00000426508.2	-	11	1715	c.1352C>T	c.(1351-1353)gCc>gTc	p.A451V	IFT140_ENST00000439987.2_5'UTR|LA16c-395F10.2_ENST00000563162.1_RNA	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	451			A -> V (in dbSNP:rs8060532).		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)				CACCTTGGTGGCAAACACTCC	0.632													G|||	129	0.0257588	0.0961	0.0029	5008	,	,		17110	0.0		0.0	False		,,,				2504	0.0				p.A451V		Atlas-SNP	.											.	IFT140	128	.	0			c.C1352T						PASS	.	G	VAL/ALA	393,4005	194.0+/-219.0	19,355,1825	41	34	36		1352	1.4	0.6	16	dbSNP_116	36	2,8598	1.2+/-3.3	0,2,4298	yes	missense	IFT140	NM_014714.3	64	19,357,6123	AA,AG,GG		0.0233,8.9359,3.0389	benign	451/1463	1634225	395,12603	2199	4300	6499	SO:0001583	missense	9742	exon11			TTGGTGGCAAACA	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.1352C>T	16.37:g.1634225G>A	ENSP00000406012:p.Ala451Val	41	0	0		43	24	0.55814	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Missense_Mutation	SNP	ENST00000426508.2	37	CCDS10439.1	55	0.025183150183150184	54	0.10975609756097561	1	0.0027624309392265192	0	0.0	0	0.0	G	0.024	-1.389209	0.01185	0.089359	2.33E-4	ENSG00000187535	ENST00000397417;ENST00000426508;ENST00000439987	T	0.58210	0.35	5.51	1.37	0.22104	.	0.719273	0.14508	N	0.315333	T	0.00754	0.0025	L	0.43923	1.385	0.26845	N	0.968287	B;B	0.18461	0.009;0.028	B;B	0.21360	0.007;0.034	T	0.08973	-1.0696	10	0.02654	T	1	.	8.7453	0.34583	0.3607:0.0:0.6392:0.0	rs8060532;rs8060532	451;176	Q96RY7;B4DR58	IF140_HUMAN;.	V	451	ENSP00000406012:A451V	ENSP00000380562:A451V	A	-	2	0	IFT140	1574226	1.000000	0.71417	0.621000	0.29145	0.082000	0.17680	4.038000	0.57318	0.105000	0.17753	-0.150000	0.13652	GCC	G|0.969;A|0.031	0.031	strong		0.632	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714		A	1634225	G	A	1634225	3	1	22	1	0	0	0	0	1	0	0	0	7565	1203	42	2	3120	2	IFT140	16	1634225	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	15919	1634225	88720528	3130	6031											
IFT140	9742	hgsc.bcm.edu	37	chr16	1637998	1637998	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aatcaaagcgatgtctgcccGgcggccggttttcccgctca	7	9	11	14	5	3	0	2	0	1	0	4	1	4	0	3	3	2	2	3	3	2	2	rs8058674	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1637998G>A	ENST00000426508.2	-	8	1201	c.838C>T	c.(838-840)Cgg>Tgg	p.R280W	IFT140_ENST00000439987.2_5'UTR|LA16c-395F10.2_ENST00000563162.1_RNA	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	280			R -> Q (in dbSNP:rs35404373).		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)				ATGTCTGCCCGGCGGCCGGTT	0.622													G|||	98	0.0195687	0.0734	0.0014	5008	,	,		16114	0.0		0.0	False		,,,				2504	0.0				p.R280W		Atlas-SNP	.											.	IFT140	128	.	0			c.C838T						PASS	.	G	TRP/ARG	276,4122	153.7+/-187.2	7,262,1930	43	37	39		838	3.2	0	16	dbSNP_116	39	1,8599	1.2+/-3.3	0,1,4299	no	missense	IFT140	NM_014714.3	101	7,263,6229	AA,AG,GG		0.0116,6.2756,2.1311	probably-damaging	280/1463	1637998	277,12721	2199	4300	6499	SO:0001583	missense	9742	exon8			CTGCCCGGCGGCC	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.838C>T	16.37:g.1637998G>A	ENSP00000406012:p.Arg280Trp	103	0	0		94	50	0.531915	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Missense_Mutation	SNP	ENST00000426508.2	37	CCDS10439.1	37	0.01694139194139194	36	0.07317073170731707	1	0.0027624309392265192	0	0.0	0	0.0	G	11.60	1.686901	0.29962	0.062756	1.16E-4	ENSG00000187535	ENST00000397417;ENST00000426508;ENST00000439987	T	0.30448	1.53	5.32	3.15	0.36227	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.748429	0.13091	N	0.414548	T	0.01976	0.0062	L	0.60455	1.87	0.09310	N	1	D	0.60160	0.987	B	0.42653	0.394	T	0.15809	-1.0424	10	0.54805	T	0.06	.	2.9009	0.05705	0.3065:0.2411:0.4525:0.0	rs8058674	280	Q96RY7	IF140_HUMAN	W	280	ENSP00000406012:R280W	ENSP00000380562:R280W	R	-	1	2	IFT140	1577999	0.021000	0.18746	0.008000	0.14137	0.002000	0.02628	1.743000	0.38258	1.241000	0.43820	-0.136000	0.14681	CGG	G|0.978;A|0.022	0.022	strong		0.622	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714		A	1637998	G	A	1637998	3	1	22	1	0	0	0	0	1	0	0	0	7565	1115	39	1	3646	1	IFT140	16	1637998	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3773	1637998	88716755	3131	6032											
CRAMP1L	57585	hgsc.bcm.edu	37	chr16	1706480	1706480	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcaggacctcattgtcccCgagcagtgccgctgtgcgga	6	9	13	13	3	2	0	2	0	0	0	3	3	3	2	4	2	3	2	4	2	0	1	rs80154657	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1706480C>G	ENST00000397412.3	+	10	1821	c.1722C>G	c.(1720-1722)ccC>ccG	p.P574P	CRAMP1L_ENST00000262317.4_Intron|CRAMP1L_ENST00000436138.3_Silent_p.P571P|CRAMP1L_ENST00000293925.5_Silent_p.P574P|LA16c-431H6.6_ENST00000454337.1_Intron			Q96RY5	CRML_HUMAN	Crm, cramped-like (Drosophila)	574						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						TCATTGTCCCCGAGCAGTGCC	0.677													C|||	98	0.0195687	0.0726	0.0029	5008	,	,		15682	0.0		0.0	False		,,,				2504	0.0				p.P574P		Atlas-SNP	.											.	CRAMP1L	60	.	0			c.C1722G						PASS	.	C		168,3706		3,162,1772	15	16	16		1722	-10	0	16	dbSNP_132	16	1,8121		0,1,4060	no	coding-synonymous	CRAMP1L	NM_020825.3		3,163,5832	GG,GC,CC		0.0123,4.3366,1.4088		574/1270	1706480	169,11827	1937	4061	5998	SO:0001819	synonymous_variant	57585	exon9			TGTCCCCGAGCAG	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.1722C>G	16.37:g.1706480C>G		30	0	0		24	9	0.375	NM_020825	A8MZL1|B1AJY1|Q8NDN1|Q9P2C1	Silent	SNP	ENST00000397412.3	37	CCDS10440.2																																																																																			C|0.979;G|0.021	0.021	strong		0.677	CRAMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157297.4			G	1706480	C	G	1706480	2	3	22	1	0	0	0	0	0	0	0	1	3848	639	23	4		4	CRAMP1L	16	1706480	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	68482	1706480	88648273	3132	6033											
NUBP2	3483	hgsc.bcm.edu	37	chr16	1838050	1838050	+	IGR	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttcacctgcccacactgcAcggtgagtcccgggggttgc	5	8	13	15	2	1	1	1	1	0	0	2	1	2	1	3	3	3	3	3	3	0	2	rs57822546	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1838050A>G	ENST00000215539.3	-	0	2116				NUBP2_ENST00000565134.1_Missense_Mutation_p.T200A|NUBP2_ENST00000565987.1_Missense_Mutation_p.T140A|NUBP2_ENST00000568706.1_Missense_Mutation_p.T59A|NUBP2_ENST00000262302.9_Missense_Mutation_p.T200A|NUBP2_ENST00000543305.1_Missense_Mutation_p.T59A			P35858	ALS_HUMAN	insulin-like growth factor binding protein, acid labile subunit						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						CCCACACTGCACGGTGAGTCC	0.662													A|||	461	0.0920527	0.3359	0.0216	5008	,	,		15389	0.0		0.002	False		,,,				2504	0.0				p.T200A		Atlas-SNP	.											.	NUBP2	25	.	0			c.A598G						PASS	.	G	ALA/THR	1287,3109	430.4+/-342.5	179,929,1090	64	66	65		598	-9	0	16	dbSNP_129	65	8,8592	5.7+/-21.5	0,8,4292	yes	missense	NUBP2	NM_012225.2	58	179,937,5382	GG,GA,AA		0.093,29.2766,9.9646	benign	200/272	1838050	1295,11701	2198	4300	6498	SO:0001628	intergenic_variant	10101	exon5			CACTGCACGGTGA	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		16.37:g.1838050A>G		78	0	0		80	36	0.45	NM_012225	B4DZY8|E9PGU3	Missense_Mutation	SNP	ENST00000215539.3	37	CCDS10446.1	165	0.07554945054945054	156	0.3170731707317073	9	0.024861878453038673	0	0.0	0	0.0	A	7.896	0.733364	0.15574	0.292766	9.3E-4	ENSG00000095906	ENST00000262302;ENST00000543305	T;T	0.40476	1.03;1.61	4.6	-9.03	0.00737	.	0.551776	0.20420	N	0.092691	T	0.00012	0.0000	N	0.03253	-0.375	0.80722	P	0.0	B	0.02656	0.0	B	0.09377	0.004	T	0.22941	-1.0202	9	0.14252	T	0.57	-10.367	2.1262	0.03739	0.2373:0.079:0.3155:0.3683	rs57822546;rs61739604	200	Q9Y5Y2	NUBP2_HUMAN	A	200;59	ENSP00000262302:T200A;ENSP00000437763:T59A	ENSP00000262302:T200A	T	+	1	0	NUBP2	1778051	0.000000	0.05858	0.004000	0.12327	0.013000	0.08279	-0.292000	0.08332	-1.796000	0.01253	-2.629000	0.00154	ACG	A|0.895;G|0.105	0.105	strong		0.662	IGFALS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250509.2			G	1838050	A	G	1838050	1	3	22	0	1	0	0	0	0	0	0	0	10725	159	6	3		3	NUBP2	16	1838050	IGR	SNP	A	TCGA-G8-6324-01A-11D-2210-10	131570	1838050	88516703	3133	6034											
IGFALS	3483	hgsc.bcm.edu	37	chr16	1840777	1840777	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gttctgcagggcgaagtcccGcagcgccttgagagggcagc	7	6	16	12	3	1	1	0	1	1	1	2	3	2	1	2	2	3	4	2	2	1	2	rs9282731	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1840777G>A	ENST00000215539.3	-	2	1752	c.1642C>T	c.(1642-1644)Cgg>Tgg	p.R548W	IGFALS_ENST00000415638.3_Missense_Mutation_p.R586W			P35858	ALS_HUMAN	insulin-like growth factor binding protein, acid labile subunit	548	LRRCT.		R -> W (in dbSNP:rs9282731).		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						GCGAAGTCCCGCAGCGCCTTG	0.667													G|||	458	0.0914537	0.2837	0.0159	5008	,	,		13459	0.003		0.004	False		,,,				2504	0.0665				p.R586W		Atlas-SNP	.											.	IGFALS	29	.	0			c.C1756T						PASS	.	G	TRP/ARG,TRP/ARG	1035,3305		125,785,1260	21	18	19		1756,1642	-2.2	0	16	dbSNP_118	19	14,8548		0,14,4267	yes	missense,missense	IGFALS	NM_001146006.1,NM_004970.2	101,101	125,799,5527	AA,AG,GG		0.1635,23.8479,8.1305	probably-damaging,probably-damaging	586/644,548/606	1840777	1049,11853	2170	4281	6451	SO:0001583	missense	3483	exon2			AGTCCCGCAGCGC	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.1642C>T	16.37:g.1840777G>A	ENSP00000215539:p.Arg548Trp	103	0	0		109	61	0.559633	NM_001146006	B4DZY8|E9PGU3	Missense_Mutation	SNP	ENST00000215539.3	37	CCDS10446.1	124	0.056776556776556776	117	0.23780487804878048	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	G	12.57	1.976387	0.34848	0.238479	0.001635	ENSG00000099769	ENST00000215539;ENST00000415638	T;T	0.25749	1.78;1.78	4.54	-2.24	0.06909	Cysteine-rich flanking region, C-terminal (1);	0.186351	0.45361	N	0.000368	T	0.00012	0.0000	L	0.53780	1.695	0.09310	P	0.9999999850705	B;B	0.33135	0.399;0.399	B;B	0.23275	0.045;0.045	T	0.27571	-1.0070	9	0.40728	T	0.16	.	6.0748	0.19909	0.1844:0.0:0.5355:0.2801	rs9282731;rs9282731	586;548	E9PGU3;P35858	.;ALS_HUMAN	W	548;586	ENSP00000215539:R548W;ENSP00000416683:R586W	ENSP00000215539:R548W	R	-	1	2	IGFALS	1780778	0.001000	0.12720	0.006000	0.13384	0.033000	0.12548	-0.195000	0.09546	-0.354000	0.08212	-0.219000	0.12488	CGG	G|0.909;A|0.091	0.091	strong		0.667	IGFALS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250509.2			A	1840777	G	A	1840777	3	1	22	1	0	0	0	0	1	0	0	0	7586	1086	38	1	179	1	IGFALS	16	1840777	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2727	1840777	88513976	3134	6035											
IGFALS	3483	hgsc.bcm.edu	37	chr16	1842454	1842454	+	Intron	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaggagggctctgcccgagtGagcctgataccagcacagcc	9	5	14	13	1	1	2	0	2	1	0	1	5	1	3	4	2	5	2	4	2	1	1	rs34680334	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1842454G>A	ENST00000215539.3	-	2	127				IGFALS_ENST00000415638.3_Missense_Mutation_p.H27Y|IGFALS_ENST00000568221.1_Intron			P35858	ALS_HUMAN	insulin-like growth factor binding protein, acid labile subunit						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						CTGCCCGAGTGAGCCTGATAC	0.701													G|||	347	0.0692891	0.2511	0.0187	5008	,	,		12605	0.0		0.002	False		,,,				2504	0.0				p.H27Y		Atlas-SNP	.											.	IGFALS	29	.	0			c.C79T						PASS	.	G	,TYR/HIS	325,1837		9,307,765	2	4	3		,79	-1.3	0	16	dbSNP_126	3	3,3869		0,3,1933	yes	intron,missense	IGFALS	NM_004970.2,NM_001146006.1	,83	9,310,2698	AA,AG,GG		0.0775,15.0324,5.4359	,benign	,27/644	1842454	328,5706	1081	1936	3017	SO:0001627	intron_variant	3483	exon2			CCGAGTGAGCCTG	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.17-52C>T	16.37:g.1842454G>A		11	0	0		13	9	0.692308	NM_001146006	B4DZY8|E9PGU3	Missense_Mutation	SNP	ENST00000215539.3	37	CCDS10446.1	114	0.0521978021978022	105	0.21341463414634146	7	0.019337016574585635	2	0.0034965034965034965	0	0.0	G	8.995	0.978678	0.18812	0.150324	7.75E-4	ENSG00000099769	ENST00000415638	T	0.54071	0.59	1.11	-1.27	0.09347	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.33266	0.404	B	0.18263	0.021	T	0.11717	-1.0576	8	0.66056	D	0.02	.	1.1011	0.01684	0.1624:0.2175:0.4:0.22	rs34680334	27	E9PGU3	.	Y	27	ENSP00000416683:H27Y	ENSP00000416683:H27Y	H	-	1	0	IGFALS	1782455	0.002000	0.14202	0.000000	0.03702	0.043000	0.13939	0.803000	0.27083	-0.428000	0.07339	0.549000	0.68633	CAC	G|0.947;A|0.053	0.053	strong		0.701	IGFALS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250509.2			A	1842454	G	A	1842454	1	1	22	0	1	0	0	0	0	0	0	0	7586	1290	45	2		2	IGFALS	16	1842454	Intron	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1677	1842454	88512299	3135	6036											
HAGH	3029	hgsc.bcm.edu	37	chr16	1869907	1869907	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcactccttacctgcagtgtGgacaggtgagtgatcttgtg	7	13	12	9	0	2	2	1	2	1	0	3	3	3	3	2	2	2	1	2	2	1	2	rs17849371	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1869907G>A	ENST00000397356.3	-	4	829	c.423C>T	c.(421-423)tcC>tcT	p.S141S	HAGH_ENST00000566709.1_Silent_p.S93S|HAGH_ENST00000455446.2_Silent_p.S141S|HAGH_ENST00000397353.2_Silent_p.S93S	NM_005326.4	NP_005317.2	Q16775	GLO2_HUMAN	hydroxyacylglutathione hydrolase	141					glutathione biosynthetic process (GO:0006750)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxyacylglutathione hydrolase activity (GO:0004416)|zinc ion binding (GO:0008270)			kidney(2)|lung(1)|ovary(1)|skin(1)	5		Hepatocellular(780;0.00335)			Glutathione(DB00143)	CCTGCAGTGTGGACAGGTGAG	0.627													G|||	218	0.0435304	0.1528	0.0173	5008	,	,		16762	0.0		0.004	False		,,,				2504	0.0				p.S141S	Pancreas(55;1048 1176 25227 40124 41333)	Atlas-SNP	.											.	HAGH	20	.	0			c.C423T						PASS	.	G	,	574,3824	251.5+/-258.2	41,492,1666	104	82	90		279,423	-1.1	0.5	16	dbSNP_123	90	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous,coding-synonymous	HAGH	NM_001040427.1,NM_005326.4	,	41,499,5959	AA,AG,GG		0.0814,13.0514,4.4699	,	93/261,141/309	1869907	581,12417	2199	4300	6499	SO:0001819	synonymous_variant	3029	exon4			CAGTGTGGACAGG	X90999	CCDS32366.1, CCDS10447.2, CCDS66900.1	16p13.3	2012-10-02	2003-11-04		ENSG00000063854	ENSG00000063854	3.1.2.6		4805	protein-coding gene	gene with protein product		138760	"hydroxyacyl glutathione hydrolase"			3025077, 7327557	Standard	NM_001286249		Approved	GLO2, GLXII, HAGH1	uc002cna.3	Q16775	OTTHUMG00000128662	ENST00000397356.3:c.423C>T	16.37:g.1869907G>A		84	0	0		78	28	0.358974	NM_005326	A8K290|B4DP33|B4DRA7|E7EN93	Silent	SNP	ENST00000397356.3	37	CCDS10447.2																																																																																			G|0.958;A|0.042	0.042	strong		0.627	HAGH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250548.2	NM_005326		A	1869907	G	A	1869907	2	1	22	1	0	0	0	0	0	0	0	1	6954	1335	47	2		2	HAGH	16	1869907	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	27453	1869907	88484846	3136	6037											
RNF151	146310	hgsc.bcm.edu	37	chr16	2018580	2018580	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgggaccctggcagagcaccGgcagcattgccagcaagggt	9	5	15	12	1	0	1	0	0	0	1	0	2	0	2	3	4	4	5	3	4	1	1	rs62038784	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2018580G>A	ENST00000569714.1	+	4	400	c.392G>A	c.(391-393)cGg>cAg	p.R131Q	RNF151_ENST00000321392.3_Missense_Mutation_p.R130Q|RNF151_ENST00000569210.2_3'UTR	NM_174903.4	NP_777563.2	Q2KHN1	RN151_HUMAN	ring finger protein 151	131					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						GCAGAGCACCGGCAGCATTGC	0.706													G|||	204	0.0407348	0.118	0.0159	5008	,	,		15035	0.0069		0.0179	False		,,,				2504	0.0123				p.R131Q		Atlas-SNP	.											.	RNF151	12	.	0			c.G392A						PASS	.	G	GLN/ARG	323,3615		11,301,1657	10	10	10		392	-6.3	0	16	dbSNP_129	10	101,8157		1,99,4029	no	missense	RNF151	NM_174903.4	43	12,400,5686	AA,AG,GG		1.2231,8.2021,3.4765	benign	131/246	2018580	424,11772	1969	4129	6098	SO:0001583	missense	146310	exon4			AGCACCGGCAGCA	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.392G>A	16.37:g.2018580G>A	ENSP00000456566:p.Arg131Gln	73	0	0		77	44	0.571429	NM_174903	Q8NHS5	Missense_Mutation	SNP	ENST00000569714.1	37	CCDS58405.1	67	0.030677655677655676	49	0.09959349593495935	6	0.016574585635359115	4	0.006993006993006993	8	0.010554089709762533	g	1.782	-0.481785	0.04383	0.082021	0.012231	ENSG00000179580	ENST00000321392	T	0.29142	1.58	5.25	-6.3	0.02007	Zinc finger, TRAF-type (1);TRAF-like (1);Zinc finger, SIAH-type (1);	0.679770	0.13596	N	0.376216	T	0.00384	0.0012	L	0.33485	1.01	0.09310	N	1	B	0.22683	0.073	B	0.16289	0.015	T	0.22138	-1.0225	10	0.12430	T	0.62	-5.4708	7.1367	0.25533	0.5424:0.0:0.3431:0.1145	rs62038784	131	Q2KHN1	RN151_HUMAN	Q	130	ENSP00000325794:R130Q	ENSP00000325794:R130Q	R	+	2	0	RNF151	1958581	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.062000	0.11674	-1.696000	0.01421	-1.119000	0.02030	CGG	G|0.970;A|0.030	0.030	strong		0.706	RNF151-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434030.1	NM_174903		A	2018580	G	A	2018580	3	1	22	1	0	0	0	0	1	0	0	0	13467	1116	39	1	406	1	RNF151	16	2018580	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	148673	2018580	88336173	3137	6038											
NOXO1	124056	hgsc.bcm.edu	37	chr16	2030029	2030029	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgcagcagcacgtccaggctCtcctgggcctgcgcctgaaa	7	6	12	16	3	1	1	0	1	1	0	3	1	2	1	4	2	3	4	4	2	1	0	rs34358073	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2030029C>T	ENST00000397280.4	-	5	573	c.570G>A	c.(568-570)gaG>gaA	p.E190E	NOXO1_ENST00000566005.1_Silent_p.E189E|NOXO1_ENST00000356120.4_Silent_p.E185E|AC005606.1_ENST00000598236.1_5'Flank|NOXO1_ENST00000354249.4_Silent_p.E184E|TBL3_ENST00000568546.1_3'UTR			Q8NFA2	NOXO1_HUMAN	NADPH oxidase organizer 1	190	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				extracellular matrix disassembly (GO:0022617)|regulation of hydrogen peroxide metabolic process (GO:0010310)|regulation of respiratory burst (GO:0060263)|superoxide metabolic process (GO:0006801)	NADPH oxidase complex (GO:0043020)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)|phospholipid binding (GO:0005543)|superoxide-generating NADPH oxidase activator activity (GO:0016176)			lung(2)	2					Ecabet(DB05265)	CGTCCAGGCTCTCCTGGGCCT	0.652													C|||	194	0.038738	0.1415	0.0086	5008	,	,		16170	0.0		0.001	False		,,,				2504	0.0				p.E190E	Pancreas(104;2811 2841 4129)|Esophageal Squamous(25;910 1225 43728)	Atlas-SNP	.											.	NOXO1	13	.	0			c.G570A						PASS	.	C	,,	442,3932		20,402,1765	15	20	18		552,555,570	-0.2	0	16	dbSNP_126	18	3,8593		0,3,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	NOXO1	NM_144603.2,NM_172167.1,NM_172168.1	,,	20,405,6060	TT,TC,CC		0.0349,10.1052,3.431	,,	184/371,185/372,190/377	2030029	445,12525	2187	4298	6485	SO:0001819	synonymous_variant	124056	exon5			CAGGCTCTCCTGG	AF532985	CCDS10454.1, CCDS10455.1, CCDS42101.1, CCDS58406.1	16p13.3	2008-02-05			ENSG00000196408	ENSG00000196408			19404	protein-coding gene	gene with protein product		611256					Standard	NM_144603		Approved	P41NOXA, P41NOXB, P41NOXC, SH3PXD5, SNX28	uc002cnx.4	Q8NFA2	OTTHUMG00000128707	ENST00000397280.4:c.570G>A	16.37:g.2030029C>T		74	0	0		82	46	0.560976	NM_172168	Q86YM1|Q8NFA3|Q96B73	Silent	SNP	ENST00000397280.4	37	CCDS42101.1																																																																																			C|0.966;T|0.034	0.034	strong		0.652	NOXO1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250612.1			T	2030029	C	T	2030029	2	4	22	1	0	0	0	0	0	0	0	1	10570	912	32	2		2	NOXO1	16	2030029	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	11449	2030029	88324724	3138	6039											
SYNGR3	9143	hgsc.bcm.edu	37	chr16	2042086	2042086	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acgcgggcgcctgccgcttcGgcgtcgcgctgggcctcgga	2	6	17	16	9	0	0	0	0	0	0	3	1	0	1	3	4	1	2	3	4	0	1	rs199784173	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2042086G>A	ENST00000248121.2	+	2	369	c.211G>A	c.(211-213)Ggc>Agc	p.G71S	SYNGR3_ENST00000562045.1_5'UTR	NM_004209.5	NP_004200.2	O43761	SNG3_HUMAN	synaptogyrin 3	71	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				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						CTGCCGCTTCGGCGTCGCGCT	0.716													G|||	18	0.00359425	0.0113	0.0043	5008	,	,		8658	0.0		0.0	False		,,,				2504	0.0				p.G71S		Atlas-SNP	.											.	SYNGR3	10	.	0			c.G211A						PASS	.	G	SER/GLY	21,3953		0,21,1966	6	6	6		211	4.2	1	16		6	0,8028		0,0,4014	no	missense	SYNGR3	NM_004209.5	56	0,21,5980	AA,AG,GG		0.0,0.5284,0.175	probably-damaging	71/230	2042086	21,11981	1987	4014	6001	SO:0001583	missense	9143	exon2			CGCTTCGGCGTCG	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.211G>A	16.37:g.2042086G>A	ENSP00000248121:p.Gly71Ser	5	0	0		11	10	0.909091	NM_004209	B2R9S0	Missense_Mutation	SNP	ENST00000248121.2	37	CCDS10456.1	13	0.005952380952380952	11	0.022357723577235773	1	0.0027624309392265192	1	0.0017482517482517483	0	0.0	g	23.6	4.432249	0.83776	0.005284	0.0	ENSG00000127561	ENST00000248121;ENST00000320633	T	0.24908	1.83	4.2	4.2	0.49525	Marvel (1);MARVEL-like domain (1);	0.056575	0.64402	D	0.000001	T	0.31575	0.0801	M	0.66378	2.025	0.80722	D	1	D	0.89917	1.0	D	0.68621	0.959	T	0.40590	-0.9555	10	0.62326	D	0.03	.	15.6377	0.76966	0.0:0.0:1.0:0.0	.	71	O43761	SNG3_HUMAN	S	71	ENSP00000248121:G71S	ENSP00000248121:G71S	G	+	1	0	SYNGR3	1982087	1.000000	0.71417	1.000000	0.80357	0.135000	0.20990	9.184000	0.94893	2.340000	0.79590	0.561000	0.74099	GGC	G|0.994;A|0.006	0.006	strong		0.716	SYNGR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250616.1			A	2042086	G	A	2042086	3	1	22	1	0	0	0	0	1	0	0	0	15465	1116	39	1	217	1	SYNGR3	16	2042086	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	12057	2042086	88312667	3139	6040											
ZNF598	90850	hgsc.bcm.edu	37	chr16	2050151	2050151	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatggcgtacggcagcgccaAccccacagggcccggggttg	7	4	16	14	4	0	0	0	0	0	0	0	1	0	0	4	5	3	3	4	5	2	2	rs114023844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2050151A>G	ENST00000563630.1	-	9	1476	c.1234T>C	c.(1234-1236)Ttg>Ctg	p.L412L	ZNF598_ENST00000562103.1_Silent_p.L412L|ZNF598_ENST00000431526.1_Silent_p.L467L|AC005606.15_ENST00000567515.1_lincRNA			Q86UK7	ZN598_HUMAN	zinc finger protein 598	467							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						GGCAGCGCCAACCCCACAGGG	0.687													A|||	137	0.0273562	0.0998	0.0072	5008	,	,		16236	0.0		0.0	False		,,,				2504	0.0				p.L467L		Atlas-SNP	.											.	ZNF598	55	.	0			c.T1399C						PASS	.	A		210,3608		6,198,1705	22	26	25		1401	-6.5	0	16	dbSNP_132	25	0,8050		0,0,4025	no	coding-synonymous	ZNF598	NM_178167.2		6,198,5730	GG,GA,AA		0.0,5.5003,1.7695		467/905	2050151	210,11658	1909	4025	5934	SO:0001819	synonymous_variant	90850	exon11			GCGCCAACCCCAC	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.1234T>C	16.37:g.2050151A>G		35	0	0		43	19	0.44186	NM_178167	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Silent	SNP	ENST00000563630.1	37																																																																																				A|0.978;G|0.022	0.022	strong		0.687	ZNF598-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000434439.1	NM_178167		G	2050151	A	G	2050151	2	3	22	1	0	0	0	0	0	0	0	1	18043	40	2	3		3	ZNF598	16	2050151	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	8065	2050151	88304602	3140	6041											
PKD1	5310	hgsc.bcm.edu	37	chr16	2152850	2152850	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggtgtagggccggtggtcAgcaccctggagtgactctgg	7	8	17	9	1	2	1	1	1	1	0	2	2	2	2	2	6	1	2	2	6	2	1	rs9926309	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2152850A>G	ENST00000262304.4	-	24	9121	c.8913T>C	c.(8911-8913)gcT>gcC	p.A2971A	PKD1_ENST00000561991.1_5'Flank|PKD1_ENST00000423118.1_Silent_p.A2971A	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	2971					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						GCCGGTGGTCAGCACCCTGGA	0.642													g|||	190	0.0379393	0.1369	0.0115	5008	,	,		11693	0.001		0.0	False		,,,				2504	0.0				p.A2971A		Atlas-SNP	.											.	PKD1	184	.	0			c.T8913C						PASS	.	G	,	394,3996	767.2+/-413.5	22,350,1823	62	72	69		8913,8913	-9.1	0	16	dbSNP_119	69	5,8575	816.3+/-406.9	0,5,4285	no	coding-synonymous,coding-synonymous	PKD1	NM_000296.3,NM_001009944.2	,	22,355,6108	GG,GA,AA		0.0583,8.9749,3.0763	,	2971/4303,2971/4304	2152850	399,12571	2195	4290	6485	SO:0001819	synonymous_variant	5310	exon24			GTGGTCAGCACCC	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.8913T>C	16.37:g.2152850A>G		80	0	0		68	24	0.352941	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1	49	0.022435897435897436	45	0.09146341463414634	4	0.011049723756906077	0	0.0	0	0.0	G	0.702	-0.790596	0.02884	0.089749	5.83E-4	ENSG00000008710	ENST00000382481	.	.	.	4.55	-9.1	0.00714	.	.	.	.	.	T	0.04137	0.0115	.	.	.	0.58432	D	0.999995	.	.	.	.	.	.	T	0.65701	-0.6104	5	0.87932	D	0	.	9.2021	0.37265	0.2909:0.5516:0.0851:0.0724	rs9926309	.	.	.	P	1209	.	ENSP00000371921:L1209P	L	-	2	0	PKD1	2092851	0.000000	0.05858	0.001000	0.08648	0.014000	0.08584	-2.024000	0.01436	-1.933000	0.01052	-1.087000	0.02190	CTG	A|0.976;G|0.024	0.024	strong		0.642	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			G	2152850	A	G	2152850	2	3	22	1	0	0	0	0	0	0	0	1	11972	175	7	3		3	PKD1	16	2152850	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	102699	2152850	88201903	3141	6042											
PKD1	5310	hgsc.bcm.edu	37	chr16	2156153	2156153	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	caccacggccaggcccacctCgaagtgtggcctgaaacccg	9	4	11	17	3	0	1	0	1	0	0	1	2	0	1	6	3	1	0	6	3	2	0	rs28369051	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2156153C>G	ENST00000262304.4	-	19	7850	c.7642G>C	c.(7642-7644)Gag>Cag	p.E2548Q	PKD1_ENST00000561991.1_5'UTR|PKD1_ENST00000423118.1_Missense_Mutation_p.E2548Q	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	2548	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.		E -> Q (in dbSNP:rs28369051). {ECO:0000269|PubMed:10577909}.		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						AGGCCCACCTCGAAGTGTGGC	0.701													c|||	192	0.0383387	0.1392	0.0115	5008	,	,		16164	0.0		0.0	False		,,,				2504	0.0				p.E2548Q		Atlas-SNP	.											.	PKD1	184	.	0			c.G7642C						PASS	.		GLN/GLU,GLN/GLU	303,3739		5,293,1723	5	8	7		7642,7642	-4	0	16	dbSNP_125	7	2,8128		0,2,4063	no	missense,missense	PKD1	NM_000296.3,NM_001009944.2	29,29	5,295,5786	GG,GC,CC		0.0246,7.4963,2.5058	benign,benign	2548/4303,2548/4304	2156153	305,11867	2021	4065	6086	SO:0001583	missense	5310	exon19			CCACCTCGAAGTG	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.7642G>C	16.37:g.2156153C>G	ENSP00000262304:p.Glu2548Gln	223	0	0		296	138	0.466216	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	79	0.036172161172161175	74	0.15040650406504066	5	0.013812154696132596	0	0.0	0	0.0	c	2.890	-0.229927	0.06022	0.074963	2.46E-4	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101;ENST00000382481	T;T	0.68624	-0.34;-0.34	5.14	-4.01	0.04045	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);Polycystin cation channel (1);	1.060040	0.07309	N	0.875540	T	0.00178	0.0005	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.21688	0.059;0.053	B;B	0.20384	0.012;0.029	T	0.04090	-1.0978	9	0.13108	T	0.6	.	6.7917	0.23703	0.0891:0.3434:0.4431:0.1245	rs28369051	2548;2548	P98161-3;P98161	.;PKD1_HUMAN	Q	2548;2548;1899;827	ENSP00000262304:E2548Q;ENSP00000399501:E2548Q	ENSP00000262304:E2548Q	E	-	1	0	PKD1	2096154	0.000000	0.05858	0.001000	0.08648	0.967000	0.64934	-2.425000	0.01028	-0.502000	0.06596	0.544000	0.68410	GAG	C|0.972;G|0.028	0.028	strong		0.701	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			G	2156153	C	G	2156153	3	3	22	1	0	0	0	0	1	0	0	0	11972	893	31	4	5381	4	PKD1	16	2156153	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3303	2156153	88198600	3142	6043											
PKD1	5310	hgsc.bcm.edu	37	chr16	2162810	2162810	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggaaggccacctccacggccGagtccaccagcacgcccgcc	8	2	11	20	4	0	0	0	0	0	0	2	2	2	1	8	3	1	1	8	3	1	0	rs147910505	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2162810G>A	ENST00000262304.4	-	13	3348	c.3140C>T	c.(3139-3141)tCg>tTg	p.S1047L	PKD1_ENST00000423118.1_Missense_Mutation_p.S1047L|RP11-304L19.4_ENST00000568795.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1047	PKD 5. {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						CTCCACGGCCGAGTCCACCAG	0.682													g|||	5	0.000998403	0.003	0.0014	5008	,	,		9360	0.0		0.0	False		,,,				2504	0.0				p.S1047L		Atlas-SNP	.											.	PKD1	184	.	0			c.C3140T	GRCh37	CM074435	PKD1	M	rs147910505	PASS	.	G	LEU/SER,LEU/SER	16,4376	22.3+/-47.3	0,16,2180	50	53	52		3140,3140	5	1	16	dbSNP_134	52	0,8586		0,0,4293	no	missense,missense	PKD1	NM_000296.3,NM_001009944.2	145,145	0,16,6473	AA,AG,GG		0.0,0.3643,0.1233	possibly-damaging,possibly-damaging	1047/4303,1047/4304	2162810	16,12962	2196	4293	6489	SO:0001583	missense	5310	exon13			ACGGCCGAGTCCA	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.3140C>T	16.37:g.2162810G>A	ENSP00000262304:p.Ser1047Leu	27	0	0		26	11	0.423077	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	.	.	.	.	.	.	.	.	.	.	g	15.48	2.845291	0.51164	0.003643	0.0	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.62105	0.05;0.05	4.99	4.99	0.66335	PKD/Chitinase domain (1);Polycystin cation channel (1);PKD domain (2);	0.207794	0.41500	D	0.000864	T	0.74261	0.3693	M	0.68952	2.095	0.40941	D	0.984461	D;D	0.89917	1.0;0.997	D;D	0.91635	0.999;0.915	T	0.70506	-0.4853	10	0.02654	T	1	.	18.2979	0.90153	0.0:0.0:1.0:0.0	.	1047;1047	P98161-3;P98161	.;PKD1_HUMAN	L	1047;1047;762	ENSP00000262304:S1047L;ENSP00000399501:S1047L	ENSP00000262304:S1047L	S	-	2	0	PKD1	2102811	1.000000	0.71417	0.969000	0.41365	0.444000	0.32077	5.507000	0.66999	2.321000	0.78463	0.645000	0.84053	TCG	G|0.999;A|0.001	0.001	strong		0.682	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			A	2162810	G	A	2162810	3	1	22	1	0	0	0	0	1	0	0	0	11972	1059	37	1	9907	1	PKD1	16	2162810	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6657	2162810	88191943	3143	6044											
PKD1	5310	hgsc.bcm.edu	37	chr16	2166538	2166538	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggggccgactacctccacggGctcgtgcggggctgagaggc	5	5	18	13	4	0	1	0	1	0	1	2	3	1	1	3	6	2	2	3	6	1	1	rs149022148	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2166538G>A	ENST00000262304.4	-	8	1922	c.1714C>T	c.(1714-1716)Ccc>Tcc	p.P572S	RP11-304L19.2_ENST00000562027.1_RNA|PKD1_ENST00000423118.1_Missense_Mutation_p.P572S	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	572			P -> S (in dbSNP:rs149022148). {ECO:0000269|PubMed:11967008}.		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						ACCTCCACGGGCTCGTGCGGG	0.682													g|||	204	0.0407348	0.1467	0.0144	5008	,	,		12972	0.0		0.0	False		,,,				2504	0.0				p.P572S		Atlas-SNP	.											PKD1,caecum,carcinoma,0,1	PKD1	184	1	0			c.C1714T						PASS	.	G	SER/PRO,SER/PRO	422,3878		16,390,1744	7	8	7		1714,1714	1.8	0	16	dbSNP_134	7	4,8436		0,4,4216	no	missense,missense	PKD1	NM_000296.3,NM_001009944.2	74,74	16,394,5960	AA,AG,GG		0.0474,9.814,3.3438	benign,benign	572/4303,572/4304	2166538	426,12314	2150	4220	6370	SO:0001583	missense	5310	exon8			CCACGGGCTCGTG	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.1714C>T	16.37:g.2166538G>A	ENSP00000262304:p.Pro572Ser	104	0	0		85	45	0.529412	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	86	0.039377289377289376	81	0.16463414634146342	5	0.013812154696132596	0	0.0	0	0.0	G	8.927	0.962500	0.18583	0.09814	4.74E-4	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.34472	1.36;1.36	4.27	1.83	0.25207	Polycystin cation channel (1);	0.410377	0.23245	N	0.050320	T	0.00109	0.0003	L	0.60455	1.87	0.80722	P	0.0	B;B	0.33171	0.4;0.179	B;B	0.30855	0.121;0.057	T	0.10941	-1.0608	9	0.11182	T	0.66	.	7.8856	0.29648	0.0:0.2683:0.5323:0.1994	.	572;572	P98161-3;P98161	.;PKD1_HUMAN	S	572;572;505	ENSP00000262304:P572S;ENSP00000399501:P572S	ENSP00000262304:P572S	P	-	1	0	PKD1	2106539	0.000000	0.05858	0.004000	0.12327	0.034000	0.12701	0.309000	0.19332	0.907000	0.36646	0.555000	0.69702	CCC	G|0.961;A|0.039	0.039	strong		0.682	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			A	2166538	G	A	2166538	3	1	22	1	0	0	0	0	1	0	0	0	11972	1203	42	2	11353	2	PKD1	16	2166538	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3728	2166538	88188215	3144	6045											
C16orf79	283870	hgsc.bcm.edu	37	chr16	2259673	2259673	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagcagctcctgggtgtggTgggtgtcctggctggggacc	3	9	18	11	0	0	0	0	0	0	0	2	1	2	1	4	6	2	3	4	6	0	0	rs144886139	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2259673T>C	ENST00000562360.1	-	5	472	c.473A>G	c.(472-474)cAc>cGc	p.H158R	BRICD5_ENST00000328540.3_Missense_Mutation_p.H158R|RP11-304L19.8_ENST00000561544.1_lincRNA			Q6PL45	BRID5_HUMAN	BRICHOS domain containing 5	158	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.					integral component of membrane (GO:0016021)											CTGGGTGTGGTGGGTGTCCTG	0.687													T|||	42	0.00838658	0.031	0.0014	5008	,	,		14172	0.0		0.0	False		,,,				2504	0.0				p.H158R		Atlas-SNP	.											C16orf79,NS,carcinoma,+1,1	.	.	1	0			c.A473G						PASS	.	T	ARG/HIS	108,4288	77.3+/-115.6	1,106,2091	55	68	64		473	-1.1	0	16	dbSNP_134	64	2,8598	1.2+/-3.3	0,2,4298	yes	missense	C16orf79	NM_182563.3	29	1,108,6389	CC,CT,TT		0.0233,2.4568,0.8464	benign	158/229	2259673	110,12886	2198	4300	6498	SO:0001583	missense	283870	exon5			GTGTGGTGGGTGT	BC039154	CCDS10463.1	16p13.3	2012-10-10	2012-10-10	2012-10-10	ENSG00000182685	ENSG00000182685		"BRICHOS domain containing"	28309	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 79"	C16orf79		12477932	Standard	NM_182563		Approved	MGC21830	uc002cpi.2	Q6PL45	OTTHUMG00000128831	ENST00000562360.1:c.473A>G	16.37:g.2259673T>C	ENSP00000455052:p.His158Arg	91	0	0		85	42	0.494118	NM_182563	C9J7K2|Q8IXU9	Missense_Mutation	SNP	ENST00000562360.1	37	CCDS10463.1	18	0.008241758241758242	17	0.034552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	T	6.160	0.397772	0.11696	0.024568	2.33E-4	ENSG00000182685	ENST00000328540	T	0.77877	-1.13	5.82	-1.09	0.09904	BRICHOS (2);	0.980375	0.08392	N	0.952853	T	0.27765	0.0683	.	.	.	0.09310	N	0.999999	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.19614	-1.0300	9	0.07813	T	0.8	-22.7577	5.497	0.16807	0.0:0.3998:0.2833:0.3169	.	158;158	Q6PL45;Q6PL45-2	CP079_HUMAN;.	R	158	ENSP00000332389:H158R	ENSP00000332389:H158R	H	-	2	0	C16orf79	2199674	0.000000	0.05858	0.002000	0.10522	0.081000	0.17604	0.005000	0.13129	-0.143000	0.11334	0.459000	0.35465	CAC	T|0.993;C|0.007	0.007	strong		0.687	BRICD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435091.1	NM_182563		C	2259673	T	C	2259673	3	2	22	1	0	0	0	0	1	0	0	0	1838	1696	59	3	221	3	C16orf79	16	2259673	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	93135	2259673	88095080	3145	6046											
E4F1	1877	hgsc.bcm.edu	37	chr16	2273676	2273676	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggcagaagcccaggccgaagCcgggcgggaagcgggcgagg	9	0	21	11	5	0	1	0	0	0	1	0	4	0	2	3	6	3	1	3	6	3	0	rs200831818	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2273676C>A	ENST00000301727.4	+	1	110	c.62C>A	c.(61-63)gCc>gAc	p.A21D	E4F1_ENST00000565090.1_Missense_Mutation_p.A21D|E4F1_ENST00000564139.1_Missense_Mutation_p.A21D	NM_004424.3	NP_004415.2	Q66K89	E4F1_HUMAN	E4F transcription factor 1	21					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|mitotic cell cycle arrest (GO:0071850)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|regulation of cell cycle process (GO:0010564)|regulation of growth (GO:0040008)|regulation of mitotic cell cycle, embryonic (GO:0009794)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	cAMP response element binding (GO:0035497)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|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 coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			ovary(1)	1						CAGGCCGAAGCCGGGCGGGAA	0.711													C|||	11	0.00219649	0.0076	0.0014	5008	,	,		11713	0.0		0.0	False		,,,				2504	0.0				p.A21D		Atlas-SNP	.											.	E4F1	53	.	0			c.C62A						PASS	.	C	ASP/ALA	26,4326		0,26,2150	12	16	15		62	4.7	1	16		15	0,8536		0,0,4268	yes	missense	E4F1	NM_004424.3	126	0,26,6418	AA,AC,CC		0.0,0.5974,0.2017	probably-damaging	21/785	2273676	26,12862	2176	4268	6444	SO:0001583	missense	1877	exon1			CCGAAGCCGGGCG	U87269	CCDS32370.1, CCDS73809.1, CCDS73810.1	16p13.3	2013-01-08				ENSG00000167967		"Zinc fingers, C2H2-type"	3121	protein-coding gene	gene with protein product		603022				9763670, 8828041	Standard	XM_005255155		Approved	E4F	uc002cpm.3	Q66K89		ENST00000301727.4:c.62C>A	16.37:g.2273676C>A	ENSP00000301727:p.Ala21Asp	8	0	0		20	12	0.6	NM_004424	A8K2R4|O00146	Missense_Mutation	SNP	ENST00000301727.4	37	CCDS32370.1	.	.	.	.	.	.	.	.	.	.	C	10.88	1.476414	0.26511	0.005974	0.0	ENSG00000167967	ENST00000301727	T	0.09723	2.95	4.68	4.68	0.58851	.	0.718111	0.13054	N	0.417418	T	0.11537	0.0281	N	0.14661	0.345	0.44523	D	0.997474	D;D;D	0.64830	0.985;0.994;0.985	P;P;P	0.57911	0.767;0.829;0.767	T	0.18241	-1.0343	10	0.59425	D	0.04	-23.6911	16.3289	0.83001	0.0:1.0:0.0:0.0	.	17;21;21	E9PFZ8;E7EMF7;Q66K89	.;.;E4F1_HUMAN	D	21	ENSP00000301727:A21D	ENSP00000301727:A21D	A	+	2	0	E4F1	2213677	1.000000	0.71417	1.000000	0.80357	0.858000	0.48976	1.236000	0.32683	2.425000	0.82216	0.655000	0.94253	GCC	.	.	weak		0.711	E4F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435225.1	NM_004424		A	2273676	C	A	2273676	3	1	22	1	0	0	0	0	1	0	0	0	4876	739	26	4	64	4	E4F1	16	2273676	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	14003	2273676	88081077	3146	6047											
ABCA3	21	hgsc.bcm.edu	37	chr16	2373687	2373687	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgaaccgtaggtgatatttCacctgtggaaacaaagagaa	15	9	10	7	1	1	3	1	2	0	1	1	5	1	4	2	2	2	1	2	2	6	3	rs74002800	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2373687C>T	ENST00000301732.5	-	7	1150	c.450G>A	c.(448-450)gtG>gtA	p.V150V	ABCA3_ENST00000567910.1_Silent_p.V150V|ABCA3_ENST00000382381.3_Silent_p.V150V	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	150					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)	GGTGATATTTCACCTGTGGAA	0.517													C|||	172	0.034345	0.1218	0.0159	5008	,	,		18945	0.0		0.0	False		,,,				2504	0.0				p.V150V		Atlas-SNP	.											.	ABCA3	176	.	0			c.G450A						PASS	.	C		498,3898	228.8+/-243.5	29,440,1729	170	192	185		450	0.9	0.9	16	dbSNP_130	185	6,8594	3.7+/-12.6	0,6,4294	no	coding-synonymous	ABCA3	NM_001089.2		29,446,6023	TT,TC,CC		0.0698,11.3285,3.8781		150/1705	2373687	504,12492	2198	4300	6498	SO:0001819	synonymous_variant	21	exon7			ATATTTCACCTGT	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.450G>A	16.37:g.2373687C>T		111	0	0		126	46	0.365079	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Silent	SNP	ENST00000301732.5	37	CCDS10466.1																																																																																			C|0.963;T|0.037	0.037	strong		0.517	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089		T	2373687	C	T	2373687	2	4	22	1	0	0	0	0	0	0	0	1	33	813	29	2		2	ABCA3	16	2373687	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	100011	2373687	87981066	3147	6048											
TBC1D24	57465	hgsc.bcm.edu	37	chr16	2546356	2546356	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctgccgcacggtcacgccTgacgccagcgtgtacagcga	7	5	12	17	6	1	1	1	1	0	0	1	2	1	1	4	1	4	2	4	1	1	1	rs13339237	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2546356T>C	ENST00000293970.5	+	2	340	c.207T>C	c.(205-207)ccT>ccC	p.P69P	TBC1D24_ENST00000567020.1_Silent_p.P69P|TBC1D24_ENST00000434757.2_Silent_p.P69P|RP11-20I23.1_ENST00000564543.1_Silent_p.P69P	NM_001199107.1	NP_001186036.1	Q9ULP9	TBC24_HUMAN	TBC1 domain family, member 24	69	Rab-GAP TBC.				neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|terminal bouton (GO:0043195)	Rab GTPase activator activity (GO:0005097)			endometrium(2)|kidney(4)|large_intestine(3)|lung(4)	13						CGGTCACGCCTGACGCCAGCG	0.672													C|||	326	0.0650958	0.2322	0.0231	5008	,	,		18489	0.0		0.003	False		,,,				2504	0.0				p.P69P		Atlas-SNP	.											.	TBC1D24	35	.	0			c.T207C						PASS	.	C	,	748,3566		62,624,1471	45	55	52		207,207	-11.2	0	16	dbSNP_121	52	18,8500		0,18,4241	no	coding-synonymous,coding-synonymous	TBC1D24	NM_001199107.1,NM_020705.2	,	62,642,5712	CC,CT,TT		0.2113,17.3389,5.9695	,	69/560,69/554	2546356	766,12066	2157	4259	6416	SO:0001819	synonymous_variant	57465	exon2			CACGCCTGACGCC	AB032997	CCDS42107.1, CCDS55980.1	16p13.3	2014-05-07				ENSG00000162065			29203	protein-coding gene	gene with protein product	"TBC/LysM-associated domain containing 6"	613577	"deafness, autosomal recessive 86"	DFNB86		10574461, 24387994, 24729539	Standard	NM_001199107		Approved	KIAA1171, TLDC6, DFNA65	uc002cql.3	Q9ULP9		ENST00000293970.5:c.207T>C	16.37:g.2546356T>C		116	1	0.00862069		105	105	1	NM_001199107	A0JNW3|B9A6M6|Q2KJ08	Silent	SNP	ENST00000293970.5	37	CCDS55980.1																																																																																			T|0.941;C|0.059	0.059	strong		0.672	TBC1D24-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000435637.1	NM_020705		C	2546356	T	C	2546356	2	2	22	1	0	0	0	0	0	0	0	1	15629	1567	55	3		3	TBC1D24	16	2546356	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	172669	2546356	87808397	3148	6049											
AMDHD2	51005	hgsc.bcm.edu	37	chr16	2578131	2578131	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gccaccttcatcacccacctCttcaacgccatgctgcctgt	7	10	5	19	1	4	0	3	0	1	0	4	0	4	0	6	0	3	1	6	0	1	2	rs35816046	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2578131C>G	ENST00000293971.6	+	6	793	c.699C>G	c.(697-699)ctC>ctG	p.L233L	AMDHD2_ENST00000565570.1_Intron|AMDHD2_ENST00000413459.3_Silent_p.L233L|CEMP1_ENST00000382350.1_Intron|AMDHD2_ENST00000302956.4_Silent_p.L233L	NM_015944.3	NP_057028.2	Q9Y303	NAGA_HUMAN	amidohydrolase domain containing 2	233					carbohydrate metabolic process (GO:0005975)|N-acetylglucosamine metabolic process (GO:0006044)|N-acetylneuraminate catabolic process (GO:0019262)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|N-acetylglucosamine-6-phosphate deacetylase activity (GO:0008448)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(3)|skin(2)|urinary_tract(2)	19						TCACCCACCTCTTCAACGCCA	0.667													C|||	109	0.0217652	0.0802	0.0043	5008	,	,		13645	0.0		0.0	False		,,,				2504	0.0				p.L233L		Atlas-SNP	.											.	AMDHD2	33	.	0			c.C699G						PASS	.	C	,	285,4111	155.5+/-188.7	9,267,1922	74	76	75		699,699	5.4	1	16	dbSNP_126	75	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	AMDHD2	NM_001145815.1,NM_015944.3	,	9,269,6220	GG,GC,CC		0.0233,6.4832,2.2084	,	233/595,233/440	2578131	287,12709	2198	4300	6498	SO:0001819	synonymous_variant	51005	exon6			CCACCTCTTCAAC	AF132948	CCDS10471.1, CCDS53984.1	16p13.3	2008-02-05			ENSG00000162066	ENSG00000162066			24262	protein-coding gene	gene with protein product						10810093	Standard	NM_001145815		Approved	CGI-14	uc010uwc.2	Q9Y303	OTTHUMG00000128866	ENST00000293971.6:c.699C>G	16.37:g.2578131C>G		84	0	0		98	37	0.377551	NM_001145815	B4DL77|Q8WV54	Silent	SNP	ENST00000293971.6	37																																																																																				G|0.019;C|0.981	0.019	strong		0.667	AMDHD2-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000435652.1	NM_015944		G	2578131	C	G	2578131	2	3	22	1	0	0	0	0	0	0	0	1	568	900	32	4		4	AMDHD2	16	2578131	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	31775	2578131	87776622	3149	6050											
PRSS27	83886	hgsc.bcm.edu	37	chr16	2762637	2762637	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtctcacttctggccgcccAacctcgctggctggaactgc	5	9	11	16	2	2	0	1	0	2	0	4	1	2	1	3	4	3	2	3	4	2	1	rs61734617	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2762637A>G	ENST00000302641.3	-	6	911	c.857T>C	c.(856-858)tTg>tCg	p.L286S	AC092117.1_ENST00000410123.1_RNA	NM_031948.3	NP_114154.1	Q9BQR3	PRS27_HUMAN	protease, serine 27	286						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						CTGGCCGCCCAACCTCGCTGG	0.662													g|||	240	0.0479233	0.174	0.0101	5008	,	,		14544	0.0		0.003	False		,,,				2504	0.0				p.L286S		Atlas-SNP	.											.	PRSS27	20	.	0			c.T857C						PASS	.	G	SER/LEU	609,3777		37,535,1621	42	37	38		857	-2	0	16	dbSNP_129	38	4,8592		0,4,4294	yes	missense	PRSS27	NM_031948.3	145	37,539,5915	GG,GA,AA		0.0465,13.8851,4.7219	benign	286/291	2762637	613,12369	2193	4298	6491	SO:0001583	missense	83886	exon6			CCGCCCAACCTCG	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.857T>C	16.37:g.2762637A>G	ENSP00000306390:p.Leu286Ser	164	0	0		171	82	0.479532	NM_031948		Missense_Mutation	SNP	ENST00000302641.3	37	CCDS10476.1	93	0.042582417582417584	90	0.18292682926829268	3	0.008287292817679558	0	0.0	0	0.0	.	2.610	-0.290913	0.05568	0.138851	4.65E-4	ENSG00000172382	ENST00000302641;ENST00000543965	D	0.88586	-2.4	4.96	-2.0	0.07433	.	5.046650	0.00575	N	0.000311	T	0.00412	0.0013	N	0.19112	0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.50676	-0.8800	9	0.06625	T	0.88	.	2.0974	0.03671	0.3642:0.1178:0.3973:0.1207	.	286;250	Q9BQR3;B3KP25	PRS27_HUMAN;.	S	286;250	ENSP00000306390:L286S	ENSP00000306390:L286S	L	-	2	0	PRSS27	2702638	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.040000	0.13905	-1.081000	0.03105	-1.147000	0.01851	TTG	A|0.948;G|0.052	0.052	strong		0.662	PRSS27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250908.1	NM_031948		G	2762637	A	G	2762637	3	3	22	1	0	0	0	0	1	0	0	0	12633	131	5	3	19	3	PRSS27	16	2762637	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	184506	2762637	87592116	3150	6051											
SRRM2	23524	hgsc.bcm.edu	37	chr16	2813177	2813177	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	acctgaccctgagttgaaatCtaggaccccttctagacata	12	10	7	12	0	2	4	0	3	2	1	2	5	2	5	4	1	0	1	4	1	4	5	rs17136053	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2813177C>G	ENST00000301740.8	+	11	3197	c.2648C>G	c.(2647-2649)tCt>tGt	p.S883C		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	883	Ser-rich.		S -> C (in dbSNP:rs17136053).		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						GAGTTGAAATCTAGGACCCCT	0.517													C|||	127	0.0253594	0.0923	0.0072	5008	,	,		19890	0.0		0.0	False		,,,				2504	0.0				p.S883C		Atlas-SNP	.											.	SRRM2	263	.	0			c.C2648G						PASS	.	C	CYS/SER	373,4023	189.5+/-215.6	16,341,1841	82	74	77		2648	2.2	0.7	16	dbSNP_123	77	2,8598	2.2+/-6.3	0,2,4298	yes	missense	SRRM2	NM_016333.3	112	16,343,6139	GG,GC,CC		0.0233,8.485,2.8855	possibly-damaging	883/2753	2813177	375,12621	2198	4300	6498	SO:0001583	missense	23524	exon11			TGAAATCTAGGAC	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.2648C>G	16.37:g.2813177C>G	ENSP00000301740:p.Ser883Cys	47	0	0		49	21	0.428571	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	37	CCDS32373.1	56	0.02564102564102564	53	0.10772357723577236	3	0.008287292817679558	0	0.0	0	0.0	C	4.788	0.146546	0.09134	0.08485	2.33E-4	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933;ENST00000426305	T	0.31247	1.5	5.37	2.21	0.28008	.	0.094270	0.47852	N	0.000215	T	0.00524	0.0017	L	0.58101	1.795	0.28061	N	0.932955	B	0.09022	0.002	B	0.04013	0.001	T	0.05354	-1.0890	10	0.59425	D	0.04	-0.8628	8.8449	0.35164	0.0:0.6364:0.2835:0.0801	rs17136053;rs52826498;rs17136053	883	Q9UQ35	SRRM2_HUMAN	C	883;883;135;848	ENSP00000301740:S883C	ENSP00000301740:S883C	S	+	2	0	SRRM2	2753178	0.942000	0.31987	0.690000	0.30148	0.967000	0.64934	1.873000	0.39558	0.215000	0.20761	0.650000	0.86243	TCT	C|0.969;G|0.031	0.031	strong		0.517	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			G	2813177	C	G	2813177	3	3	22	1	0	0	0	0	1	0	0	0	15184	913	32	4	2686	4	SRRM2	16	2813177	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	50540	2813177	87541576	3151	6052											
KREMEN2	79412	hgsc.bcm.edu	37	chr16	3016716	3016716	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggcccggggacgcctggcccCcgccaccgactgtgaccaga	6	3	14	18	4	0	2	0	1	0	1	0	4	0	3	7	4	0	0	7	4	0	0	rs111311295	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3016716C>G	ENST00000303746.5	+	5	1137	c.560C>G	c.(559-561)cCc>cGc	p.P187R	PAQR4_ENST00000572687.1_5'Flank|PKMYT1_ENST00000571102.1_5'Flank|KREMEN2_ENST00000575769.1_Missense_Mutation_p.P187R|PAQR4_ENST00000576565.1_5'Flank|KREMEN2_ENST00000571007.1_Intron|PAQR4_ENST00000293978.8_5'Flank|KREMEN2_ENST00000572045.1_Missense_Mutation_p.P187R|KREMEN2_ENST00000575885.1_Intron|KREMEN2_ENST00000319500.6_Missense_Mutation_p.P187R|PAQR4_ENST00000318782.8_5'Flank			Q8NCW0	KREM2_HUMAN	kringle containing transmembrane protein 2	187	WSC. {ECO:0000255|PROSITE- ProRule:PRU00558, ECO:0000305}.			Missing (in Ref. 2; BAC11365). {ECO:0000305}.	Wnt signaling pathway (GO:0016055)	integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(1)|large_intestine(1)	4						CGCCTGGCCCCCGCCACCGAC	0.692																																					p.P187R		Atlas-SNP	.											.	KREMEN2	13	.	0			c.C560G						PASS	.	C	ARG/PRO,ARG/PRO	14,4368		0,14,2177	19	24	22		560,560	2.9	0	16	dbSNP_132	22	0,8584		0,0,4292	yes	missense,missense	KREMEN2	NM_024507.2,NM_172229.1	103,103	0,14,6469	GG,GC,CC		0.0,0.3195,0.108	probably-damaging,probably-damaging	187/421,187/463	3016716	14,12952	2191	4292	6483	SO:0001583	missense	79412	exon5			TGGCCCCCGCCAC	BC003533	CCDS10483.1, CCDS10484.1, CCDS58412.1, CCDS58413.1	16p13.11	2008-08-04			ENSG00000131650	ENSG00000131650			18797	protein-coding gene	gene with protein product		609899				12050670	Standard	NM_172229		Approved	MGC10791, KRM2	uc002csg.3	Q8NCW0	OTTHUMG00000128976	ENST00000303746.5:c.560C>G	16.37:g.3016716C>G	ENSP00000304422:p.Pro187Arg	120	0	0		124	60	0.483871	NM_024507	B4DXF6|I3L2S2|Q8N2J4|Q8NCW1|Q96GL8|Q9BTP9	Missense_Mutation	SNP	ENST00000303746.5	37	CCDS10483.1	.	.	.	.	.	.	.	.	.	.	C	14.59	2.579580	0.46006	0.003195	0.0	ENSG00000131650	ENST00000303746;ENST00000319500	T;T	0.54071	0.59;0.59	4.91	2.92	0.33932	Carbohydrate-binding WSC (2);	0.151142	0.30732	N	0.008999	T	0.57242	0.2040	M	0.78285	2.405	0.30519	N	0.768604	P;P;P;P	0.37101	0.527;0.527;0.527;0.582	B;B;B;P	0.46299	0.377;0.377;0.377;0.511	T	0.60151	-0.7319	10	0.49607	T	0.09	.	5.5586	0.17131	0.0:0.6523:0.1625:0.1852	.	187;187;187;187	Q8NCW0-2;Q8NCW0-4;Q8NCW0-3;Q8NCW0	.;.;.;KREM2_HUMAN	R	187	ENSP00000304422:P187R;ENSP00000322079:P187R	ENSP00000304422:P187R	P	+	2	0	KREMEN2	2956717	0.083000	0.21467	0.035000	0.18076	0.983000	0.72400	1.656000	0.37355	1.066000	0.40716	0.456000	0.33151	CCC	C|0.999;G|0.001	0.001	strong		0.692	KREMEN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250964.2	NM_145347		G	3016716	C	G	3016716	3	3	22	1	0	0	0	0	1	0	0	0	8452	623	22	4	578	4	KREMEN2	16	3016716	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	203539	3016716	87338037	3152	6053											
PKMYT1	9088	hgsc.bcm.edu	37	chr16	3023185	3023185	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggaggtgctccccacagtccGggccaggacagcctcagggg	7	4	16	14	1	1	0	1	0	0	0	3	2	3	2	5	6	2	1	5	6	0	0	rs150931982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3023185G>A	ENST00000262300.8	-	8	1850	c.1342C>T	c.(1342-1344)Cgg>Tgg	p.R448W	PKMYT1_ENST00000574385.1_Missense_Mutation_p.R439W|PAQR4_ENST00000572687.1_3'UTR|PKMYT1_ENST00000431515.2_Missense_Mutation_p.R448W|PKMYT1_ENST00000573944.1_Missense_Mutation_p.R439W|PAQR4_ENST00000318782.8_3'UTR|PKMYT1_ENST00000571102.1_5'Flank|PAQR4_ENST00000293978.8_3'UTR|PKMYT1_ENST00000574730.1_Missense_Mutation_p.R379W|PKMYT1_ENST00000440027.2_Silent_p.P460P	NM_001258450.1|NM_004203.4|NM_182687.2	NP_001245379.1|NP_004194.3|NP_872629.1	Q99640	PMYT1_HUMAN	protein kinase, membrane associated tyrosine/threonine 1	448	Interaction with CDC2-CCNB1.|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)			NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	10						CCCACAGTCCGGGCCAGGACA	0.657													G|||	17	0.00339457	0.0129	0.0	5008	,	,		15724	0.0		0.0	False		,,,				2504	0.0				p.R448W		Atlas-SNP	.											.	PKMYT1	23	.	0			c.C1342T						PASS	.	G	TRP/ARG,,	34,4316		0,34,2141	28	27	28		1342,,1380	2.5	0.8	16	dbSNP_134	28	0,8560		0,0,4280	yes	missense,utr-3,coding-synonymous	PKMYT1,PAQR4	NM_004203.4,NM_152341.3,NM_182687.2	101,,	0,34,6421	AA,AG,GG		0.0,0.7816,0.2634	probably-damaging,,	448/500,,460/481	3023185	34,12876	2175	4280	6455	SO:0001583	missense	9088	exon8			CAGTCCGGGCCAG	AK097642	CCDS10486.1, CCDS45391.1, CCDS58414.1, CCDS58415.1	16p13.3	2014-06-13			ENSG00000127564	ENSG00000127564			29650	protein-coding gene	gene with protein product	"membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase", "protein phosphatase 1, regulatory subunit 126"	602474				9001210, 12606722	Standard	NM_004203		Approved	MYT1, PPP1R126	uc002csn.3	Q99640	OTTHUMG00000128975	ENST00000262300.8:c.1342C>T	16.37:g.3023185G>A	ENSP00000262300:p.Arg448Trp	65	0	0		108	48	0.444444	NM_004203	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000262300.8	37	CCDS10486.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	13.73	2.324957	0.41197	0.007816	0.0	ENSG00000127564	ENST00000431515;ENST00000262300;ENST00000402679	T;T	0.62941	-0.01;0.15	4.75	2.47	0.30058	.	0.463681	0.22806	N	0.055404	T	0.41719	0.1171	L	0.32530	0.975	0.80722	D	1	D;D	0.60575	0.988;0.988	P;P	0.52424	0.698;0.698	T	0.53514	-0.8428	10	0.59425	D	0.04	-16.2832	9.4789	0.38889	0.0:0.0:0.6461:0.3539	.	379;448	B4DXD4;Q99640	.;PMYT1_HUMAN	W	448	ENSP00000392855:R448W;ENSP00000262300:R448W	ENSP00000262300:R448W	R	-	1	2	PKMYT1	2963186	0.954000	0.32549	0.808000	0.32385	0.023000	0.10783	1.549000	0.36212	1.104000	0.41587	0.655000	0.94253	CGG	G|0.995;A|0.005	0.005	strong		0.657	PKMYT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250963.2	NM_004203		A	3023185	G	A	3023185	3	1	22	1	0	0	0	0	1	0	0	0	11987	1115	39	1	165	1	PKMYT1	16	3023185	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6469	3023185	87331568	3153	6054											
PKMYT1	9088	hgsc.bcm.edu	37	chr16	3026956	3026956	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgcgtggcggaagtaggcTgggactgggatgggggtgcc	5	8	21	7	2	1	0	0	0	1	0	1	3	1	3	1	7	2	2	1	7	2	1	rs4149786	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3026956T>C	ENST00000262300.8	-	3	595	c.87A>G	c.(85-87)ccA>ccG	p.P29P	PKMYT1_ENST00000574385.1_Silent_p.P20P|PKMYT1_ENST00000431515.2_Silent_p.P29P|PKMYT1_ENST00000573944.1_Silent_p.P20P|PKMYT1_ENST00000574730.1_Intron|PKMYT1_ENST00000440027.2_Silent_p.P29P	NM_001258450.1|NM_004203.4|NM_182687.2	NP_001245379.1|NP_004194.3|NP_872629.1	Q99640	PMYT1_HUMAN	protein kinase, membrane associated tyrosine/threonine 1	29	Pro-rich.				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)			NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	10						GGAAGTAGGCTGGGACTGGGA	0.692													C|||	5	0.000998403	0.0	0.0	5008	,	,		16125	0.0		0.0	False		,,,				2504	0.0051				p.P29P		Atlas-SNP	.											.	PKMYT1	23	.	0			c.A87G						PASS	.	C	,	10,4286		0,10,2138	12	15	14		87,87	-3.7	1	16	dbSNP_110	14	0,8510		0,0,4255	no	coding-synonymous,coding-synonymous	PKMYT1	NM_004203.4,NM_182687.2	,	0,10,6393	CC,CT,TT		0.0,0.2328,0.0781	,	29/500,29/481	3026956	10,12796	2148	4255	6403	SO:0001819	synonymous_variant	9088	exon3			GTAGGCTGGGACT	AK097642	CCDS10486.1, CCDS45391.1, CCDS58414.1, CCDS58415.1	16p13.3	2014-06-13			ENSG00000127564	ENSG00000127564			29650	protein-coding gene	gene with protein product	"membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase", "protein phosphatase 1, regulatory subunit 126"	602474				9001210, 12606722	Standard	NM_004203		Approved	MYT1, PPP1R126	uc002csn.3	Q99640	OTTHUMG00000128975	ENST00000262300.8:c.87A>G	16.37:g.3026956T>C		76	0	0		65	21	0.323077	NM_182687	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Silent	SNP	ENST00000262300.8	37	CCDS10486.1																																																																																			T|0.993;C|0.007	0.007	strong		0.692	PKMYT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250963.2	NM_004203		C	3026956	T	C	3026956	2	2	22	1	0	0	0	0	0	0	0	1	11987	1567	55	3		3	PKMYT1	16	3026956	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	3771	3026956	87327797	3154	6055											
ZSCAN10	84891	hgsc.bcm.edu	37	chr16	3140601	3140601	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccaggcagcccctttgggCtcttcttgtttaaattcctc	5	14	9	13	0	2	0	0	0	2	0	4	0	3	0	4	3	1	3	4	3	2	6	rs140690870	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3140601C>T	ENST00000252463.2	-	5	756	c.669G>A	c.(667-669)gaG>gaA	p.E223E	ZSCAN10_ENST00000538082.2_Silent_p.E141E|ZSCAN10_ENST00000572548.1_3'UTR|ZSCAN10_ENST00000575108.1_5'UTR	NM_032805.1	NP_116194.1	Q96SZ4	ZSC10_HUMAN	zinc finger and SCAN domain containing 10	223					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						CCCCTTTGGGCTCTTCTTGTT	0.592													C|||	25	0.00499201	0.0182	0.0014	5008	,	,		15976	0.0		0.0	False		,,,				2504	0.0				p.E223E		Atlas-SNP	.											.	ZSCAN10	63	.	0			c.G669A						PASS	.	C		77,4279		1,75,2102	33	36	35		669	-6	0	16	dbSNP_134	35	0,8496		0,0,4248	no	coding-synonymous	ZSCAN10	NM_032805.1		1,75,6350	TT,TC,CC		0.0,1.7677,0.5991		223/726	3140601	77,12775	2178	4248	6426	SO:0001819	synonymous_variant	84891	exon5			TTTGGGCTCTTCT	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.669G>A	16.37:g.3140601C>T		41	0	0		30	11	0.366667	NM_032805	B3KQD3|H0YFS6|Q1WWM2	Silent	SNP	ENST00000252463.2	37	CCDS10493.1																																																																																			C|0.991;T|0.009	0.009	strong		0.592	ZSCAN10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437124.2	NM_032805		T	3140601	C	T	3140601	2	4	22	1	0	0	0	0	0	0	0	1	18242	796	28	2		2	ZSCAN10	16	3140601	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	113645	3140601	87214152	3155	6056											
ZNF205	7755	hgsc.bcm.edu	37	chr16	3169321	3169321	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccttgggaatgtgaagccCttcagaaccagggcagggag	10	6	15	10	0	1	2	1	1	0	1	1	4	1	4	3	3	2	1	3	3	3	2	rs59049520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3169321C>T	ENST00000382192.3	+	7	865	c.660C>T	c.(658-660)ccC>ccT	p.P220P	RP11-473M20.14_ENST00000575139.1_RNA|ZNF205_ENST00000219091.4_Silent_p.P220P|RP11-473M20.14_ENST00000576490.1_RNA	NM_001278158.1|NM_003456.2	NP_001265087.1|NP_003447.2	O95201	ZN205_HUMAN	zinc finger protein 205	220					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						ATGTGAAGCCCTTCAGAACCA	0.657													C|||	281	0.0561102	0.2065	0.0101	5008	,	,		15886	0.0		0.001	False		,,,				2504	0.0				p.P220P		Atlas-SNP	.											.	ZNF205	42	.	0			c.C660T						PASS	.	C	,	701,3651		60,581,1535	41	37	38		660,660	1.8	0.2	16	dbSNP_129	38	8,8474		0,8,4233	no	coding-synonymous,coding-synonymous	ZNF205	NM_001042428.1,NM_003456.2	,	60,589,5768	TT,TC,CC		0.0943,16.1075,5.5244	,	220/555,220/555	3169321	709,12125	2176	4241	6417	SO:0001819	synonymous_variant	7755	exon7			GAAGCCCTTCAGA	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.660C>T	16.37:g.3169321C>T		88	0	0		83	52	0.626506	NM_003456	A8MZK0|D3DUB4|Q9BU95	Silent	SNP	ENST00000382192.3	37	CCDS10494.2																																																																																			C|0.944;T|0.056	0.056	strong		0.657	ZNF205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309057.1	NM_003456		T	3169321	C	T	3169321	2	4	22	1	0	0	0	0	0	0	0	1	17779	668	24	2		2	ZNF205	16	3169321	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	28720	3169321	87185432	3156	6057											
ZNF213	7760	hgsc.bcm.edu	37	chr16	3188789	3188789	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gagggtcgtcccggagagacGacggacacctgctttgtctc	7	8	14	12	4	1	1	0	0	1	1	4	6	2	3	2	3	1	1	2	3	0	1	rs35931391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3188789G>A	ENST00000396878.3	+	4	1042	c.567G>A	c.(565-567)acG>acA	p.T189T	ZNF213_ENST00000574902.1_Silent_p.T189T|ZNF213_ENST00000576416.1_Silent_p.T189T|ZNF213_ENST00000416391.2_Intron	NM_001134655.1|NM_004220.2	NP_001128127.1|NP_004211.1	O14771	ZN213_HUMAN	zinc finger protein 213	189					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)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	16						CCGGAGAGACGACGGACACCT	0.542													G|||	274	0.0547125	0.2012	0.0101	5008	,	,		19201	0.0		0.001	False		,,,				2504	0.0				p.T189T		Atlas-SNP	.											.	ZNF213	36	.	0			c.G567A						PASS	.	G	,	709,3685	297.6+/-284.8	61,587,1549	66	63	64		567,567	-10.3	0	16	dbSNP_126	64	9,8591	6.4+/-24.3	0,9,4291	no	coding-synonymous,coding-synonymous	ZNF213	NM_001134655.1,NM_004220.2	,	61,596,5840	AA,AG,GG		0.1047,16.1356,5.5256	,	189/460,189/460	3188789	718,12276	2197	4300	6497	SO:0001819	synonymous_variant	7760	exon4			AGAGACGACGGAC	AF017433	CCDS10495.1	16p13.3	2014-05-13	2007-02-20	2007-02-20	ENSG00000085644	ENSG00000085644		"Zinc fingers, C2H2-type", "-", "-", "-"	13005	protein-coding gene	gene with protein product		608387				9653642, 10023065	Standard	NM_004220		Approved	CR53, ZKSCAN21, ZSCAN53	uc010uws.2	O14771	OTTHUMG00000177519	ENST00000396878.3:c.567G>A	16.37:g.3188789G>A		95	0	0		112	62	0.553571	NM_004220	A8K1B9|B4DMG6|Q96IS1	Silent	SNP	ENST00000396878.3	37	CCDS10495.1																																																																																			G|0.949;A|0.051	0.051	strong		0.542	ZNF213-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437334.1	NM_004220		A	3188789	G	A	3188789	2	1	22	1	0	0	0	0	0	0	0	1	17784	1045	37	1		1	ZNF213	16	3188789	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	19468	3188789	87165964	3157	6058											
ZNF213	7760	hgsc.bcm.edu	37	chr16	3190767	3190767	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgccaggccagacaggcagcGacgtgactgtgtcctggagc	8	6	15	12	2	0	2	0	1	0	1	1	4	1	3	3	3	3	1	3	3	0	0	rs143851164		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3190767G>A	ENST00000396878.3	+	6	1274	c.799G>A	c.(799-801)Gac>Aac	p.D267N	ZNF213_ENST00000574902.1_Missense_Mutation_p.D267N|ZNF213_ENST00000576416.1_Missense_Mutation_p.D267N|ZNF213_ENST00000416391.2_Missense_Mutation_p.D109N	NM_001134655.1|NM_004220.2	NP_001128127.1|NP_004211.1	O14771	ZN213_HUMAN	zinc finger protein 213	267	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	16						GACAGGCAGCGACGTGACTGT	0.692																																					p.D267N		Atlas-SNP	.											.	ZNF213	36	.	0			c.G799A						PASS	.	G	ASN/ASP,ASN/ASP	1,4387		0,1,2193	34	38	37		799,799	-0.4	0	16	dbSNP_134	37	0,8598		0,0,4299	no	missense,missense	ZNF213	NM_001134655.1,NM_004220.2	23,23	0,1,6492	AA,AG,GG		0.0,0.0228,0.0077	benign,benign	267/460,267/460	3190767	1,12985	2194	4299	6493	SO:0001583	missense	7760	exon6			GGCAGCGACGTGA	AF017433	CCDS10495.1	16p13.3	2014-05-13	2007-02-20	2007-02-20	ENSG00000085644	ENSG00000085644		"Zinc fingers, C2H2-type", "-", "-", "-"	13005	protein-coding gene	gene with protein product		608387				9653642, 10023065	Standard	NM_004220		Approved	CR53, ZKSCAN21, ZSCAN53	uc010uws.2	O14771	OTTHUMG00000177519	ENST00000396878.3:c.799G>A	16.37:g.3190767G>A	ENSP00000380087:p.Asp267Asn	33	0	0		33	20	0.606061	NM_004220	A8K1B9|B4DMG6|Q96IS1	Missense_Mutation	SNP	ENST00000396878.3	37	CCDS10495.1	.	.	.	.	.	.	.	.	.	.	G	10.65	1.409959	0.25465	2.28E-4	0.0	ENSG00000085644	ENST00000396878;ENST00000416391	T;T	0.05319	3.46;3.46	4.23	-0.444	0.12245	Krueppel-associated box (1);	1.158390	0.06689	N	0.769413	T	0.03348	0.0097	N	0.08118	0	0.09310	N	1	B	0.13594	0.008	B	0.10450	0.005	T	0.44907	-0.9297	10	0.52906	T	0.07	.	3.1334	0.06431	0.099:0.3134:0.4223:0.1652	.	267	O14771	ZN213_HUMAN	N	267;109	ENSP00000380087:D267N;ENSP00000403892:D109N	ENSP00000380087:D267N	D	+	1	0	ZNF213	3130768	0.000000	0.05858	0.000000	0.03702	0.242000	0.25591	-0.566000	0.05922	-0.371000	0.08004	-1.048000	0.02349	GAC	G|1.000;A|0.000	0.000	weak		0.692	ZNF213-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437334.1	NM_004220		A	3190767	G	A	3190767	3	1	22	1	0	0	0	0	1	0	0	0	17784	1058	37	1	817	1	ZNF213	16	3190767	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1978	3190767	87163986	3158	6059											
OR1F1	4992	hgsc.bcm.edu	37	chr16	3254622	3254622	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctatgaccactttgtcgccGtgtgccaccccttacattac	7	12	6	16	2	0	1	0	1	0	0	1	1	0	1	6	0	3	0	6	0	3	4	rs8045183	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3254622G>A	ENST00000304646.2	+	1	376	c.376G>A	c.(376-378)Gtg>Atg	p.V126M	AJ003147.9_ENST00000576468.1_RNA	NM_012360.1	NP_036492.1	O43749	OR1F1_HUMAN	olfactory receptor, family 1, subfamily F, member 1	126			V -> M (in dbSNP:rs8045183).		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						CTTTGTCGCCGTGTGCCACCC	0.502													g|||	159	0.0317492	0.115	0.0086	5008	,	,		24960	0.0		0.001	False		,,,				2504	0.0				p.V126M		Atlas-SNP	.											.	OR1F1	36	.	0			c.G376A						PASS	.	A	MET/VAL	402,3992	199.4+/-223.0	11,380,1806	220	175	190		376	-6.7	0	16	dbSNP_116	190	7,8593	5.7+/-21.5	0,7,4293	no	missense	OR1F1	NM_012360.1	21	11,387,6099	AA,AG,GG		0.0814,9.1488,3.1476	possibly-damaging	126/313	3254622	409,12585	2197	4300	6497	SO:0001583	missense	4992	exon1			GTCGCCGTGTGCC	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.376G>A	16.37:g.3254622G>A	ENSP00000305424:p.Val126Met	243	1	0.00411523		250	126	0.504	NM_012360	O15246|Q6IFL5	Missense_Mutation	SNP	ENST00000304646.2	37	CCDS10496.1	68	0.031135531135531136	65	0.13211382113821138	3	0.008287292817679558	0	0.0	0	0.0	G	13.94	2.388405	0.42308	0.091488	8.14E-4	ENSG00000168124	ENST00000304646	T	0.49432	0.78	5.27	-6.68	0.01778	GPCR, rhodopsin-like superfamily (1);	0.893841	0.09289	N	0.822529	T	0.00695	0.0023	M	0.72118	2.19	0.80722	P	0.0	D	0.55800	0.973	P	0.51135	0.66	T	0.48714	-0.9011	9	0.87932	D	0	.	10.8187	0.46591	0.7188:0.1085:0.1727:0.0	rs8045183;rs52799876;rs8045183	126	O43749	OR1F1_HUMAN	M	126	ENSP00000305424:V126M	ENSP00000305424:V126M	V	+	1	0	OR1F1	3194623	0.418000	0.25440	0.000000	0.03702	0.630000	0.37929	0.957000	0.29215	-1.050000	0.03230	0.393000	0.25936	GTG	G|0.966;A|0.034	0.034	strong		0.502	OR1F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206985.1			A	3254622	G	A	3254622	3	1	22	1	0	0	0	0	1	0	0	0	10965	1145	40	1	378	1	OR1F1	16	3254622	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	63855	3254622	87100131	3159	6060											
ZNF200	7752	hgsc.bcm.edu	37	chr16	3282468	3282468	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcatcttccttctctgacGtgagttgttgagtaggatcc	6	16	10	9	1	3	3	1	3	2	0	6	4	5	4	2	1	0	3	2	1	1	5	rs9302870	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3282468G>A	ENST00000431561.3	-	4	1031	c.419C>T	c.(418-420)aCg>aTg	p.T140M	ZNF200_ENST00000396871.4_Missense_Mutation_p.T140M|ZNF200_ENST00000396870.4_Missense_Mutation_p.T140M|ZNF200_ENST00000575948.1_Missense_Mutation_p.T140M|ZNF200_ENST00000414144.2_Missense_Mutation_p.T140M|ZNF200_ENST00000396868.3_Missense_Mutation_p.T139M	NM_001145447.1|NM_003454.3	NP_001138919.1|NP_003445.2	P98182	ZN200_HUMAN	zinc finger protein 200	140			T -> M (in dbSNP:rs9302870).		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(2)|kidney(2)|large_intestine(4)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	17						CTTCTCTGACGTGAGTTGTTG	0.463													G|||	346	0.0690895	0.2504	0.0173	5008	,	,		21841	0.0		0.003	False		,,,				2504	0.0				p.T140M		Atlas-SNP	.											.	ZNF200	36	.	0			c.C419T						PASS	.	G	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	817,3577	326.7+/-299.7	77,663,1457	237	211	220		419,419,419,419,416,419	2.7	0.6	16	dbSNP_119	220	10,8590	7.1+/-27.0	0,10,4290	yes	missense,missense,missense,missense,missense,missense	ZNF200	NM_001145446.1,NM_001145447.1,NM_001145448.1,NM_003454.3,NM_198087.2,NM_198088.2	81,81,81,81,81,81	77,673,5747	AA,AG,GG		0.1163,18.5935,6.3645	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	140/395,140/395,140/395,140/396,139/395,140/396	3282468	827,12167	2197	4300	6497	SO:0001583	missense	7752	exon4			TCTGACGTGAGTT	AF060866	CCDS10497.1, CCDS42112.1, CCDS45395.1	16p13.3	2013-01-08			ENSG00000010539	ENSG00000010539		"Zinc fingers, C2H2-type"	12993	protein-coding gene	gene with protein product		603231				9288094, 9787081	Standard	NM_003454		Approved		uc002cuk.2	P98182	OTTHUMG00000129317	ENST00000431561.3:c.419C>T	16.37:g.3282468G>A	ENSP00000395723:p.Thr140Met	98	0	0		128	68	0.53125	NM_003454	D3DUB7|D3DUB8|O15361|Q5XKM5|Q7Z5V1	Missense_Mutation	SNP	ENST00000431561.3	37	CCDS10497.1	139	0.06364468864468864	133	0.2703252032520325	6	0.016574585635359115	0	0.0	0	0.0	G	12.60	1.986342	0.35036	0.185935	0.001163	ENSG00000010539	ENST00000396870;ENST00000396868;ENST00000396871;ENST00000414144;ENST00000431561	T;T;T;T;T	0.06449	3.3;3.33;3.3;3.39;3.39	4.84	2.73	0.32206	.	0.395014	0.18653	N	0.134956	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	P;P;P	0.42039	0.658;0.658;0.769	B;B;B	0.43082	0.23;0.23;0.407	T	0.49273	-0.8957	9	0.62326	D	0.03	-13.3741	8.5959	0.33714	0.2043:0.0:0.7957:0.0	rs9302870;rs9302870	140;140;139	D3DUB7;P98182;P98182-2	.;ZN200_HUMAN;.	M	140;139;140;140;140	ENSP00000380079:T140M;ENSP00000380077:T139M;ENSP00000380080:T140M;ENSP00000405786:T140M;ENSP00000395723:T140M	ENSP00000380077:T139M	T	-	2	0	ZNF200	3222469	0.179000	0.23135	0.574000	0.28523	0.226000	0.24999	0.021000	0.13489	1.257000	0.44085	0.555000	0.69702	ACG	G|0.914;A|0.086	0.086	strong		0.463	ZNF200-005	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000437545.1			A	3282468	G	A	3282468	3	1	22	1	0	0	0	0	1	0	0	0	17777	1145	40	1	776	1	ZNF200	16	3282468	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	27846	3282468	87072285	3160	6061											
TIGD7	91151	hgsc.bcm.edu	37	chr16	3349300	3349300	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ttcatctccatttaaccacaCcctatcatcatccaacttag	12	13	1	15	0	4	0	3	0	1	0	6	0	5	0	4	0	2	0	4	0	4	5	rs151295470		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3349300C>G	ENST00000396862.1	-	2	3143	c.1315G>C	c.(1315-1317)Gtg>Ctg	p.V439L	TIGD7_ENST00000574598.1_5'Flank|TIGD7_ENST00000268674.2_Missense_Mutation_p.V439L	NM_033208.3	NP_149985.2	Q6NT04	TIGD7_HUMAN	tigger transposable element derived 7	439						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	12						TTTAACCACACCCTATCATCA	0.383																																					p.V439L		Atlas-SNP	.											.	TIGD7	41	.	0			c.G1315C						PASS	.	C	LEU/VAL	3,4391	6.2+/-15.9	0,3,2194	162	174	170		1315	-0.7	0	16	dbSNP_134	170	0,8600		0,0,4300	yes	missense	TIGD7	NM_033208.3	32	0,3,6494	GG,GC,CC		0.0,0.0683,0.0231	possibly-damaging	439/550	3349300	3,12991	2197	4300	6497	SO:0001583	missense	91151	exon2			ACCACACCCTATC	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.1315G>C	16.37:g.3349300C>G	ENSP00000380071:p.Val439Leu	264	0	0		300	142	0.473333	NM_033208	Q9BXZ0	Missense_Mutation	SNP	ENST00000396862.1	37	CCDS10500.1	.	.	.	.	.	.	.	.	.	.	C	0.050	-1.253366	0.01457	6.83E-4	0.0	ENSG00000140993	ENST00000426381;ENST00000396862;ENST00000268674	T;T	0.31510	1.49;1.49	4.88	-0.699	0.11277	.	1.396770	0.05259	U	0.515337	T	0.19327	0.0464	N	0.19112	0.55	0.09310	N	1	B	0.13145	0.007	B	0.09377	0.004	T	0.26503	-1.0101	10	0.26408	T	0.33	.	7.8653	0.29533	0.0:0.5056:0.0:0.4944	.	439	Q6NT04	TIGD7_HUMAN	L	439	ENSP00000380071:V439L;ENSP00000268674:V439L	ENSP00000268674:V439L	V	-	1	0	TIGD7	3289301	0.005000	0.15991	0.001000	0.08648	0.291000	0.27294	-0.189000	0.09629	-0.110000	0.12022	-0.150000	0.13652	GTG	C|1.000;G|0.000	0.000	weak		0.383	TIGD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251465.1	NM_033208		G	3349300	C	G	3349300	3	3	22	1	0	0	0	0	1	0	0	0	15916	507	18	4	338	4	TIGD7	16	3349300	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	66832	3349300	87005453	3161	6062											
ZNF597	146434	hgsc.bcm.edu	37	chr16	3486736	3486736	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatcgctgcagcgttcagaGtcctcgtcgtggctcttctc	4	13	10	14	4	4	1	2	0	2	1	9	1	5	1	1	1	2	4	1	1	0	2	rs34461484	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3486736G>A	ENST00000301744.4	-	4	1198	c.963C>T	c.(961-963)gaC>gaT	p.D321D		NM_152457.1	NP_689670.1	Q96LX8	ZN597_HUMAN	zinc finger protein 597	321					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						AGCGTTCAGAGTCCTCGTCGT	0.488													G|||	102	0.0203674	0.0726	0.0072	5008	,	,		20540	0.0		0.001	False		,,,				2504	0.0				p.D321D		Atlas-SNP	.											.	ZNF597	41	.	0			c.C963T						PASS	.	G		239,4155	141.9+/-177.2	4,231,1962	70	66	67		963	-7.5	0	16	dbSNP_126	67	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	ZNF597	NM_152457.1		4,236,6257	AA,AG,GG		0.0581,5.4392,1.8778		321/425	3486736	244,12750	2197	4300	6497	SO:0001819	synonymous_variant	146434	exon4			TTCAGAGTCCTCG	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.963C>T	16.37:g.3486736G>A		43	0	0		50	24	0.48	NM_152457		Silent	SNP	ENST00000301744.4	37	CCDS10505.1																																																																																			G|0.985;A|0.015	0.015	strong		0.488	ZNF597-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251511.2	NM_152457		A	3486736	G	A	3486736	2	1	22	1	0	0	0	0	0	0	0	1	18042	1020	36	2		2	ZNF597	16	3486736	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	137436	3486736	86868017	3162	6063											
CLUAP1	23059	hgsc.bcm.edu	37	chr16	3554799	3554799	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtacacccaattttggactTgtatctgaagtgcttctctg	8	15	8	10	1	2	1	0	1	2	0	3	2	2	2	1	1	2	3	1	1	4	6	rs34672214	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3554799T>C	ENST00000576634.1	+	2	246	c.102T>C	c.(100-102)ctT>ctC	p.L34L	CLUAP1_ENST00000571025.1_Silent_p.L34L|CLUAP1_ENST00000341633.5_Silent_p.L34L|CLUAP1_ENST00000417763.2_5'UTR|LA16c-306E5.3_ENST00000574423.2_RNA	NM_015041.2	NP_055856.1	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1	34					cilium assembly (GO:0042384)	centrosome (GO:0005813)|cilium (GO:0005929)|intracellular membrane-bounded organelle (GO:0043231)|intraciliary transport particle B (GO:0030992)|nucleus (GO:0005634)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(2)	16						ATTTTGGACTTGTATCTGAAG	0.383													T|||	283	0.0565096	0.115	0.0331	5008	,	,		19316	0.0556		0.0159	False		,,,				2504	0.0368				p.L34L		Atlas-SNP	.											.	CLUAP1	32	.	0			c.T102C						PASS	.	T		427,3967	207.5+/-228.8	19,389,1789	111	109	110		102	3.1	1	16	dbSNP_126	110	138,8462	69.0+/-131.5	0,138,4162	no	coding-synonymous	CLUAP1	NM_015041.1		19,527,5951	CC,CT,TT		1.6047,9.7178,4.3482		34/414	3554799	565,12429	2197	4300	6497	SO:0001819	synonymous_variant	23059	exon2			TGGACTTGTATCT	BC017070	CCDS32381.1, CCDS45398.1	16p13.3	2014-07-18				ENSG00000103351		"Intraflagellar transport homologs"	19009	protein-coding gene	gene with protein product	"flagellar associated protein 22, qilin-like protein, homolog (Chlamydomonas)", "cilia and flagella associated protein 22"					15480429, 9734811, 19253336	Standard	NM_015041		Approved	FLJ13297, KIAA0643, FAP22, CFAP22	uc002cvk.2	Q96AJ1		ENST00000576634.1:c.102T>C	16.37:g.3554799T>C		243	0	0		192	84	0.4375	NM_015041	O75138|Q65ZA3|Q9H8R4|Q9H8T1	Silent	SNP	ENST00000576634.1	37	CCDS32381.1																																																																																			T|0.955;C|0.045	0.045	strong		0.383	CLUAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437883.2	NM_024793		C	3554799	T	C	3554799	2	2	22	1	0	0	0	0	0	0	0	1	3571	1799	63	3		3	CLUAP1	16	3554799	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	68063	3554799	86799954	3163	6064											
CLUAP1	23059	hgsc.bcm.edu	37	chr16	3556398	3556398	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	accgagttttcttcattaagGcaattgcccagttcatggtt	9	15	8	9	1	3	0	2	0	1	0	3	1	3	0	2	2	1	4	2	2	2	7	rs34115694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3556398G>T	ENST00000576634.1	+	3	346	c.202G>T	c.(202-204)Gca>Tca	p.A68S	CLUAP1_ENST00000571025.1_Missense_Mutation_p.A68S|CLUAP1_ENST00000341633.5_Missense_Mutation_p.A68S|CLUAP1_ENST00000417763.2_5'UTR|LA16c-306E5.3_ENST00000574423.2_RNA	NM_015041.2	NP_055856.1	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1	68			A -> S (in dbSNP:rs34115694).		cilium assembly (GO:0042384)	centrosome (GO:0005813)|cilium (GO:0005929)|intracellular membrane-bounded organelle (GO:0043231)|intraciliary transport particle B (GO:0030992)|nucleus (GO:0005634)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(2)	16						CTTCATTAAGGCAATTGCCCA	0.438													G|||	130	0.0259585	0.0968	0.0029	5008	,	,		18976	0.0		0.0	False		,,,				2504	0.0				p.A68S		Atlas-SNP	.											.	CLUAP1	32	.	0			c.G202T						PASS	.	G	SER/ALA	337,4057	178.7+/-207.4	8,321,1868	158	139	146		202	5.5	1	16	dbSNP_126	146	3,8597	3.0+/-9.4	0,3,4297	yes	missense	CLUAP1	NM_015041.1	99	8,324,6165	TT,TG,GG		0.0349,7.6695,2.6166	benign	68/414	3556398	340,12654	2197	4300	6497	SO:0001583	missense	23059	exon3			ATTAAGGCAATTG	BC017070	CCDS32381.1, CCDS45398.1	16p13.3	2014-07-18				ENSG00000103351		"Intraflagellar transport homologs"	19009	protein-coding gene	gene with protein product	"flagellar associated protein 22, qilin-like protein, homolog (Chlamydomonas)", "cilia and flagella associated protein 22"					15480429, 9734811, 19253336	Standard	NM_015041		Approved	FLJ13297, KIAA0643, FAP22, CFAP22	uc002cvk.2	Q96AJ1		ENST00000576634.1:c.202G>T	16.37:g.3556398G>T	ENSP00000460850:p.Ala68Ser	98	0	0		101	63	0.623762	NM_015041	O75138|Q65ZA3|Q9H8R4|Q9H8T1	Missense_Mutation	SNP	ENST00000576634.1	37	CCDS32381.1	60	0.027472527472527472	59	0.11991869918699187	1	0.0027624309392265192	0	0.0	0	0.0	G	16.19	3.053615	0.55218	0.076695	3.49E-4	ENSG00000103351	ENST00000341633	T	0.43688	0.94	5.49	5.49	0.81192	.	0.046661	0.85682	D	0.000000	T	0.00384	0.0012	N	0.11789	0.175	0.80722	D	1	P	0.39903	0.694	B	0.39339	0.297	T	0.03969	-1.0988	10	0.12766	T	0.61	-16.0476	17.213	0.86935	0.0:0.0:1.0:0.0	rs34115694	68	Q96AJ1	CLUA1_HUMAN	S	68	ENSP00000344392:A68S	ENSP00000344392:A68S	A	+	1	0	CLUAP1	3496399	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.503000	0.81632	2.745000	0.94114	0.557000	0.71058	GCA	G|0.974;T|0.026	0.026	strong		0.438	CLUAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437883.2	NM_024793		T	3556398	G	T	3556398	3	4	22	1	0	0	0	0	1	0	0	0	3571	1203	42	4	212	4	CLUAP1	16	3556398	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1599	3556398	86798355	3164	6065											
CLUAP1	23059	hgsc.bcm.edu	37	chr16	3576475	3576475	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaagagaagcgcctgctcAagagtggaagtaaggctggg	13	5	17	6	1	1	2	1	0	0	2	1	5	1	4	1	4	2	3	1	4	5	1	rs35603863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3576475A>C	ENST00000576634.1	+	9	1063	c.919A>C	c.(919-921)Aag>Cag	p.K307Q	CLUAP1_ENST00000572600.1_Missense_Mutation_p.K141Q|CLUAP1_ENST00000571025.1_Missense_Mutation_p.K307Q|CLUAP1_ENST00000341633.5_Missense_Mutation_p.K307Q|CLUAP1_ENST00000417763.2_Missense_Mutation_p.K141Q|CLUAP1_ENST00000445795.2_Missense_Mutation_p.K66Q	NM_015041.2	NP_055856.1	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1	307					cilium assembly (GO:0042384)	centrosome (GO:0005813)|cilium (GO:0005929)|intracellular membrane-bounded organelle (GO:0043231)|intraciliary transport particle B (GO:0030992)|nucleus (GO:0005634)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(2)	16						GCGCCTGCTCAAGAGTGGAAG	0.418													A|||	78	0.0155751	0.056	0.0058	5008	,	,		15679	0.0		0.0	False		,,,				2504	0.0				p.K307Q		Atlas-SNP	.											.	CLUAP1	32	.	0			c.A919C						PASS	.	A	GLN/LYS,GLN/LYS	223,4171	127.0+/-164.0	5,213,1979	53	52	52		919,421	4.3	1	16	dbSNP_126	52	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	CLUAP1	NM_015041.1,NM_024793.1	53,53	5,214,6278	CC,CA,AA		0.0116,5.0751,1.7239	benign,benign	307/414,141/248	3576475	224,12770	2197	4300	6497	SO:0001583	missense	23059	exon9			CTGCTCAAGAGTG	BC017070	CCDS32381.1, CCDS45398.1	16p13.3	2014-07-18				ENSG00000103351		"Intraflagellar transport homologs"	19009	protein-coding gene	gene with protein product	"flagellar associated protein 22, qilin-like protein, homolog (Chlamydomonas)", "cilia and flagella associated protein 22"					15480429, 9734811, 19253336	Standard	NM_015041		Approved	FLJ13297, KIAA0643, FAP22, CFAP22	uc002cvk.2	Q96AJ1		ENST00000576634.1:c.919A>C	16.37:g.3576475A>C	ENSP00000460850:p.Lys307Gln	97	0	0		107	55	0.514019	NM_015041	O75138|Q65ZA3|Q9H8R4|Q9H8T1	Missense_Mutation	SNP	ENST00000576634.1	37	CCDS32381.1	27	0.012362637362637362	26	0.052845528455284556	1	0.0027624309392265192	0	0.0	0	0.0	A	11.85	1.761898	0.31228	0.050751	1.16E-4	ENSG00000103351	ENST00000341633;ENST00000417763;ENST00000445795	T;T;T	0.47869	1.55;0.83;0.84	5.41	4.3	0.51218	.	0.180820	0.64402	D	0.000017	T	0.09905	0.0243	M	0.64997	1.995	0.42629	D	0.993376	P;P;P	0.46706	0.813;0.498;0.883	B;B;B	0.41860	0.368;0.202;0.255	T	0.05683	-1.0870	10	0.14252	T	0.57	-26.918	10.7228	0.46050	0.8398:0.1602:0.0:0.0	rs35603863	141;307;66	Q96AJ1-2;Q96AJ1;B4DFY1	.;CLUA1_HUMAN;.	Q	307;141;66	ENSP00000344392:K307Q;ENSP00000388642:K141Q;ENSP00000397710:K66Q	ENSP00000344392:K307Q	K	+	1	0	CLUAP1	3516476	1.000000	0.71417	0.972000	0.41901	0.260000	0.26232	5.607000	0.67648	0.877000	0.35895	0.523000	0.50628	AAG	A|0.981;C|0.019	0.019	strong		0.418	CLUAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437883.2	NM_024793		C	3576475	A	C	3576475	3	2	22	1	0	0	0	0	1	0	0	0	3571	131	5	5	953	5	CLUAP1	16	3576475	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	20077	3576475	86778278	3165	6066											
NLRC3	197358	hgsc.bcm.edu	37	chr16	3599220	3599220	+	RNA	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cgggactgatggagttttctCgaaggctgaaaaaaaaggaa	15	8	13	5	2	1	2	0	2	1	0	2	6	1	5	0	4	0	2	0	4	6	2	rs373104014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3599220C>T	ENST00000301749.7	-	0	2930				NLRC3_ENST00000603507.1_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000448023.2_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GGAGTTTTCTCGAAGGCTGAA	0.562													C|||	11	0.00219649	0.0083	0.0	5008	,	,		19418	0.0		0.0	False		,,,				2504	0.0				p.R842Q		Atlas-SNP	.											.	NLRC3	103	.	0			c.G2525A						PASS	.	C	GLN/ARG	10,3958		0,10,1974	36	37	37		2526	4.9	0.6	16		37	0,8318		0,0,4159	no	missense	NLRC3	NM_178844.2	43	0,10,6133	TT,TC,CC		0.0,0.252,0.0814	probably-damaging	842/1066	3599220	10,12276	1984	4159	6143			197358	exon14			TTTTCTCGAAGGC	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"Nucleotide-binding domain and leucine rich repeat containing"	29889	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3", "NOD-like receptor C3"	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3599220C>T		103	0	0		99	43	0.434343	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	37		.	.	.	.	.	.	.	.	.	.	C	18.58	3.655008	0.67472	0.00252	0.0	ENSG00000167984	ENST00000301749;ENST00000359128;ENST00000448023	T;T;T	0.54071	0.59;0.6;0.59	4.95	4.95	0.65309	.	0.000000	0.64402	D	0.000001	T	0.52370	0.1730	N	0.13003	0.285	0.23227	N	0.998083	D;D	0.69078	0.997;0.961	D;P	0.76071	0.987;0.818	T	0.45542	-0.9254	10	0.15499	T	0.54	.	13.7484	0.62890	0.0:1.0:0.0:0.0	.	842;888	Q7RTR2;C9JLH9	NLRC3_HUMAN;.	Q	842;841;888	ENSP00000301749:R842Q;ENSP00000352039:R841Q;ENSP00000414415:R888Q	ENSP00000301749:R842Q	R	-	2	0	NLRC3	3539221	1.000000	0.71417	0.612000	0.29024	0.688000	0.40055	4.089000	0.57685	2.313000	0.78055	0.558000	0.71614	CGA	.	.	weak		0.562	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844		T	3599220	C	T	3599220	1	4	22	0	1	0	0	0	0	0	0	0	10477	884	31	1		1	NLRC3	16	3599220	RNA	SNP	C	TCGA-G8-6324-01A-11D-2210-10	22745	3599220	86755533	3166	6067											
NLRC3	197358	hgsc.bcm.edu	37	chr16	3606947	3606947	+	RNA	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcggttgatcttcaaagcGtctgccagcgccttggcccc	5	10	12	14	3	3	1	1	1	2	0	3	1	3	1	4	2	4	1	4	2	1	3	rs116349864	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3606947G>T	ENST00000301749.7	-	0	2553				NLRC3_ENST00000603507.1_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000448023.2_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TCTTCAAAGCGTCTGCCAGCG	0.582													g|||	78	0.0155751	0.056	0.0058	5008	,	,		18998	0.0		0.0	False		,,,				2504	0.0				p.D716E		Atlas-SNP	.											.	NLRC3	103	.	0			c.C2148A						PASS	.	A	GLU/ASP	187,3749		5,177,1786	78	87	84		2148	-7	0.6	16	dbSNP_132	84	1,8305		0,1,4152	yes	missense	NLRC3	NM_178844.2	45	5,178,5938	TT,TG,GG		0.012,4.751,1.5357	benign	716/1066	3606947	188,12054	1968	4153	6121			197358	exon8			CAAAGCGTCTGCC	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"Nucleotide-binding domain and leucine rich repeat containing"	29889	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3", "NOD-like receptor C3"	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3606947G>T		108	0	0		90	46	0.511111	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	37		26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	g	13.03	2.114951	0.37339	0.04751	1.2E-4	ENSG00000167984	ENST00000419350;ENST00000301749;ENST00000359128;ENST00000448023	T;T;T	0.50548	0.74;0.74;0.74	5.37	-6.97	0.01616	.	0.127878	0.52532	N	0.000077	T	0.04318	0.0119	.	.	.	0.20563	N	0.999887	B	0.28026	0.198	B	0.34138	0.176	T	0.15780	-1.0425	9	0.18276	T	0.48	.	7.4907	0.27460	0.6283:0.0:0.1808:0.1909	.	763	C9JLH9	.	E	716;716;716;763	ENSP00000301749:D716E;ENSP00000352039:D716E;ENSP00000414415:D763E	ENSP00000301749:D716E	D	-	3	2	NLRC3	3546948	0.002000	0.14202	0.606000	0.28943	0.419000	0.31324	-1.356000	0.02609	-1.733000	0.01357	-2.239000	0.00288	GAC	G|0.985;T|0.015	0.015	strong		0.582	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844		T	3606947	G	T	3606947	1	4	22	0	1	0	0	0	0	0	0	0	10477	1136	40	4		4	NLRC3	16	3606947	RNA	SNP	G	TCGA-G8-6324-01A-11D-2210-10	7727	3606947	86747806	3167	6068											
NLRC3	197358	hgsc.bcm.edu	37	chr16	3613239	3613239	+	RNA	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcatgcaggcagtgcaacaCgttgatggcccgtgcacaga	10	7	12	12	2	1	2	1	1	0	1	1	2	1	2	1	2	4	5	1	2	1	1	rs8057436	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3613239C>T	ENST00000301749.7	-	0	2104				NLRC3_ENST00000324659.8_RNA|NLRC3_ENST00000603507.1_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000448023.2_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CAGTGCAACACGTTGATGGCC	0.706													C|||	189	0.0377396	0.1331	0.0144	5008	,	,		16561	0.0		0.001	False		,,,				2504	0.002				p.V567M		Atlas-SNP	.											.	NLRC3	103	.	0			c.G1699A						PASS	.	C	MET/VAL	433,3803		13,407,1698	12	15	14		1699	-7.5	0	16	dbSNP_116	14	27,8409		0,27,4191	yes	missense	NLRC3	NM_178844.2	21	13,434,5889	TT,TC,CC		0.3201,10.2219,3.6301	benign	567/1066	3613239	460,12212	2118	4218	6336			197358	exon5			GCAACACGTTGAT	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"Nucleotide-binding domain and leucine rich repeat containing"	29889	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3", "NOD-like receptor C3"	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3613239C>T		24	0	0		32	20	0.625	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	37		69	0.03159340659340659	61	0.12398373983739837	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	C	2.395	-0.338967	0.05243	0.102219	0.003201	ENSG00000167984	ENST00000419350;ENST00000301749;ENST00000359128;ENST00000448023;ENST00000324659	D;D;D;D	0.85556	-2.0;-2.0;-2.0;-2.0	5.1	-7.47	0.01365	.	0.710025	0.13675	N	0.370619	T	0.03011	0.0089	.	.	.	0.09310	N	1	B	0.23650	0.089	B	0.20577	0.03	T	0.23691	-1.0181	9	0.46703	T	0.11	.	11.4138	0.49941	0.0:0.2375:0.0978:0.6647	rs8057436;rs8057436	614	C9JLH9	.	M	567;567;567;614;549	ENSP00000301749:V567M;ENSP00000352039:V567M;ENSP00000414415:V614M;ENSP00000323897:V549M	ENSP00000301749:V567M	V	-	1	0	NLRC3	3553240	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.154000	0.00580	-1.430000	0.01985	-0.812000	0.03155	GTG	C|0.969;T|0.031	0.031	strong		0.706	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844		T	3613239	C	T	3613239	1	4	22	0	1	0	0	0	0	0	0	0	10477	536	19	1		1	NLRC3	16	3613239	RNA	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6292	3613239	86741514	3168	6069											
NLRC3	197358	hgsc.bcm.edu	37	chr16	3613690	3613690	+	RNA	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aacgccttcatgtcttgctcGtaaaacacgtatttcttctt	9	16	5	11	3	4	0	1	0	3	0	5	0	4	0	1	0	3	3	1	0	4	7	rs144685315	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3613690G>A	ENST00000301749.7	-	0	1653				NLRC3_ENST00000324659.8_RNA|NLRC3_ENST00000603507.1_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000448023.2_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TGTCTTGCTCGTAAAACACGT	0.602													G|||	11	0.00219649	0.0083	0.0	5008	,	,		20370	0.0		0.0	False		,,,				2504	0.0				p.Y416Y		Atlas-SNP	.											.	NLRC3	103	.	0			c.C1248T						PASS	.	G		28,4006		0,28,1989	62	62	62		1248	-6.6	0.9	16	dbSNP_134	62	0,8352		0,0,4176	no	coding-synonymous	NLRC3	NM_178844.2		0,28,6165	AA,AG,GG		0.0,0.6941,0.2261		416/1066	3613690	28,12358	2017	4176	6193			197358	exon5			TTGCTCGTAAAAC	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"Nucleotide-binding domain and leucine rich repeat containing"	29889	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3", "NOD-like receptor C3"	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3613690G>A		91	0	0		93	46	0.494624	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Silent	SNP	ENST00000301749.7	37																																																																																				G|0.999;A|0.001	0.001	strong		0.602	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844		A	3613690	G	A	3613690	1	1	22	0	1	0	0	0	0	0	0	0	10477	1140	40	1		1	NLRC3	16	3613690	RNA	SNP	G	TCGA-G8-6324-01A-11D-2210-10	451	3613690	86741063	3169	6070											
BTBD12	84464	hgsc.bcm.edu	37	chr16	3640893	3640893	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cttctcccaggtggtggcggCctcatctcttcctggctcca	3	12	10	16	1	3	0	1	0	2	0	7	0	5	0	4	5	0	1	4	5	0	2	rs79448721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3640893C>A	ENST00000294008.3	-	12	3386	c.2746G>T	c.(2746-2748)Gcc>Tcc	p.A916S		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	916	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						GTGGTGGCGGCCTCATCTCTT	0.657								Direct reversal of damage					C|||	53	0.0105831	0.0393	0.0014	5008	,	,		15331	0.0		0.0	False		,,,				2504	0.0				p.A916S		Atlas-SNP	.											.	SLX4	173	.	0			c.G2746T						PASS	.	C	SER/ALA	146,4248	101.2+/-139.8	3,140,2054	88	89	88		2746	-4.9	0	16	dbSNP_131	88	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SLX4	NM_032444.2	99	3,141,6353	AA,AC,CC		0.0116,3.3227,1.1313	benign	916/1835	3640893	147,12847	2197	4300	6497	SO:0001583	missense	84464	exon12			TGGCGGCCTCATC	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.2746G>T	16.37:g.3640893C>A	ENSP00000294008:p.Ala916Ser	308	0	0		343	168	0.489796	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	18	0.008241758241758242	17	0.034552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	C	6.127	0.391716	0.11581	0.033227	1.16E-4	ENSG00000188827	ENST00000294008	T	0.01139	5.28	5.04	-4.9	0.03094	.	1.567630	0.03656	N	0.241881	T	0.00412	0.0013	L	0.43152	1.355	0.09310	N	1	B	0.14438	0.01	B	0.11329	0.006	T	0.48525	-0.9028	10	0.09843	T	0.71	.	3.8877	0.09105	0.3555:0.2957:0.0:0.3488	.	916	Q8IY92	SLX4_HUMAN	S	916	ENSP00000294008:A916S	ENSP00000294008:A916S	A	-	1	0	SLX4	3580894	0.004000	0.15560	0.000000	0.03702	0.009000	0.06853	-0.251000	0.08818	-1.230000	0.02561	0.561000	0.74099	GCC	C|0.990;A|0.010	0.010	strong		0.657	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444		A	3640893	C	A	3640893	3	1	22	1	0	0	0	0	1	0	0	0	1542	739	26	4	2774	4	BTBD12	16	3640893	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	27203	3640893	86713860	3170	6071											
DNASE1	1773	hgsc.bcm.edu	37	chr16	3707262	3707262	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtggtcatccatccgcctGtggacaagccccaccttcca	8	8	8	17	1	1	0	1	0	0	0	4	1	4	1	7	2	1	0	7	2	1	1	rs8176920	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3707262G>A	ENST00000246949.5	+	7	3833	c.624G>A	c.(622-624)ctG>ctA	p.L208L	DNASE1_ENST00000407479.1_Silent_p.L208L|DNASE1_ENST00000414110.2_Silent_p.L91L	NM_005223.3	NP_005214.2	P24855	DNAS1_HUMAN	deoxyribonuclease I	208					apoptotic process (GO:0006915)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	deoxyribonuclease I activity (GO:0004530)			lung(1)	1		Ovarian(90;0.0261)		Kidney(780;0.0556)		CCATCCGCCTGTGGACAAGCC	0.617													G|||	160	0.0319489	0.1195	0.0029	5008	,	,		18167	0.0		0.0	False		,,,				2504	0.0				p.L208L		Atlas-SNP	.											.	DNASE1	16	.	0			c.G624A						PASS	.	G		370,4024	189.9+/-215.9	14,342,1841	86	69	75		624	1.8	1	16	dbSNP_117	75	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	DNASE1	NM_005223.3		14,345,6138	AA,AG,GG		0.0349,8.4206,2.8706		208/283	3707262	373,12621	2197	4300	6497	SO:0001819	synonymous_variant	1773	exon7			CCGCCTGTGGACA		CCDS10507.1	16p13.3	2008-02-05			ENSG00000213918	ENSG00000213918	3.1.21.1		2956	protein-coding gene	gene with protein product		125505		DNL1		2349940	Standard	XM_005255148		Approved		uc002cvr.3	P24855	OTTHUMG00000129426	ENST00000246949.5:c.624G>A	16.37:g.3707262G>A		120	0	0		115	115	1	NM_005223	B4DV35|Q14UU9|Q14UV0	Silent	SNP	ENST00000246949.5	37	CCDS10507.1																																																																																			G|0.970;A|0.030	0.030	strong		0.617	DNASE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251585.2			A	3707262	G	A	3707262	2	1	22	1	0	0	0	0	0	0	0	1	4662	1364	48	2		2	DNASE1	16	3707262	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	66369	3707262	86647491	3171	6072											
ADCY9	115	hgsc.bcm.edu	37	chr16	4043415	4043415	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcttgttaccttggtgcTgtttttatgctcgtcttggc	3	19	11	8	1	1	1	0	1	1	0	2	1	1	1	1	2	4	5	1	2	2	7	rs113187435	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4043415T>C	ENST00000294016.3	-	4	2519	c.1981A>G	c.(1981-1983)Agc>Ggc	p.S661G	ADCY9_ENST00000571889.1_5'UTR	NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	661					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						ACCTTGGTGCTGTTTTTATGC	0.532													T|||	37	0.00738818	0.0272	0.0014	5008	,	,		19275	0.0		0.0	False		,,,				2504	0.0				p.S661G		Atlas-SNP	.											.	ADCY9	151	.	0			c.A1981G						PASS	.	T	GLY/SER	111,4283	85.8+/-124.5	1,109,2087	235	202	213		1981	4.2	0.8	16	dbSNP_132	213	0,8600		0,0,4300	yes	missense	ADCY9	NM_001116.3	56	1,109,6387	CC,CT,TT		0.0,2.5262,0.8542	benign	661/1354	4043415	111,12883	2197	4300	6497	SO:0001583	missense	115	exon4			TGGTGCTGTTTTT	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.1981A>G	16.37:g.4043415T>C	ENSP00000294016:p.Ser661Gly	269	0	0		245	116	0.473469	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Missense_Mutation	SNP	ENST00000294016.3	37	CCDS32382.1	9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	T	11.87	1.769081	0.31320	0.025262	0.0	ENSG00000162104	ENST00000294016	D	0.84070	-1.8	5.36	4.24	0.50183	.	0.368925	0.31884	N	0.006919	T	0.43366	0.1244	N	0.14661	0.345	0.31169	N	0.703441	B	0.02656	0.0	B	0.01281	0.0	T	0.54977	-0.8212	10	0.28530	T	0.3	.	8.1862	0.31341	0.0:0.1581:0.0:0.8419	.	661	O60503	ADCY9_HUMAN	G	661	ENSP00000294016:S661G	ENSP00000294016:S661G	S	-	1	0	ADCY9	3983416	1.000000	0.71417	0.842000	0.33263	0.993000	0.82548	1.848000	0.39309	0.845000	0.35118	0.445000	0.29226	AGC	T|0.991;C|0.009	0.009	strong		0.532	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1			C	4043415	T	C	4043415	3	2	22	1	0	0	0	0	1	0	0	0	301	1580	55	3	2112	3	ADCY9	16	4043415	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	336153	4043415	86311338	3172	6073											
SRL	6345	hgsc.bcm.edu	37	chr16	4245656	4245656	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aatgccaatcagcttctctaGgaaattctggccaaacttct	12	12	6	11	0	4	0	1	0	3	0	5	1	4	1	2	2	3	1	2	2	5	4	rs76988584	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4245656G>A	ENST00000399609.3	-	5	520	c.508C>T	c.(508-510)Cta>Tta	p.L170L	SRL_ENST00000537996.1_Silent_p.L128L	NM_001098814.1	NP_001092284.1	Q86TD4	SRCA_HUMAN	sarcalumenin	629	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						AGCTTCTCTAGGAAATTCTGG	0.522													G|||	95	0.0189696	0.0703	0.0029	5008	,	,		18443	0.0		0.0	False		,,,				2504	0.0				p.L170L		Atlas-SNP	.											.	SRL	56	.	0			c.C508T						PASS	.	G		177,3613		5,167,1723	102	102	102		508	4.1	1	16	dbSNP_131	102	1,8253		0,1,4126	no	coding-synonymous	SRL	NM_001098814.1		5,168,5849	AA,AG,GG		0.0121,4.6702,1.4779		170/474	4245656	178,11866	1895	4127	6022	SO:0001819	synonymous_variant	6345	exon5			TCTCTAGGAAATT	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.508C>T	16.37:g.4245656G>A		220	0	0		248	118	0.475806	NM_001098814		Silent	SNP	ENST00000399609.3	37	CCDS42113.1																																																																																			G|0.992;A|0.008	0.008	strong		0.522	SRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438087.1	XM_064152		A	4245656	G	A	4245656	2	1	22	1	0	0	0	0	0	0	0	1	15165	991	35	2		2	SRL	16	4245656	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	202241	4245656	86109097	3173	6074											
VASN	114990	hgsc.bcm.edu	37	chr16	4431880	4431880	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgccacttcccgcccaagaaCgctggccggctgctcctgga	6	7	11	17	3	0	1	0	0	0	1	2	2	2	2	5	3	3	3	5	3	2	1	rs13333950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4431880C>T	ENST00000304735.3	+	2	1157	c.1002C>T	c.(1000-1002)aaC>aaT	p.N334N	CORO7_ENST00000423908.2_Intron|CORO7_ENST00000539968.1_Intron|CORO7_ENST00000251166.4_Intron|CORO7-PAM16_ENST00000572467.1_Intron|CORO7_ENST00000537233.2_Intron|CORO7_ENST00000574025.1_Intron	NM_138440.2	NP_612449.2	Q6EMK4	VASN_HUMAN	vasorin	334	LRRCT.				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						CGCCCAAGAACGCTGGCCGGC	0.692													C|||	177	0.0353435	0.1309	0.0058	5008	,	,		14062	0.0		0.0	False		,,,				2504	0.0				p.N334N		Atlas-SNP	.											.	VASN	21	.	0			c.C1002T						PASS	.	C	,,,,	532,3842		38,456,1693	19	22	21		,,,,1002	-11.3	0.1	16	dbSNP_121	21	1,8583		0,1,4291	no	intron,intron,intron,intron,coding-synonymous	CORO7,VASN,CORO7-PAM16	NM_001201472.1,NM_001201473.1,NM_001201479.1,NM_024535.4,NM_138440.2	,,,,	38,457,5984	TT,TC,CC		0.0116,12.1628,4.1133	,,,,	,,,,334/674	4431880	533,12425	2187	4292	6479	SO:0001819	synonymous_variant	114990	exon2			CAAGAACGCTGGC	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.1002C>T	16.37:g.4431880C>T		45	0	0		58	31	0.534483	NM_138440	Q6UXL4|Q6UXL5|Q96CX1	Silent	SNP	ENST00000304735.3	37	CCDS10514.1																																																																																			C|0.962;T|0.038	0.038	strong		0.692	VASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251632.1	NM_138440		T	4431880	C	T	4431880	2	4	22	1	0	0	0	0	0	0	0	1	17142	535	19	1		1	VASN	16	4431880	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	186224	4431880	85922873	3174	6075											
C16orf71	146562	hgsc.bcm.edu	37	chr16	4790304	4790304	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttcttgggatggccgaggagCcccccaggtggctggaaggc	6	7	17	11	1	1	0	0	0	1	0	1	4	1	3	4	7	1	1	4	7	1	2	rs527269249|rs17137230	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4790304C>T	ENST00000299320.5	+	4	905	c.427C>T	c.(427-429)Ccc>Tcc	p.P143S	C16orf71_ENST00000590191.1_Missense_Mutation_p.P157S|RP11-127I20.7_ENST00000588099.1_RNA	NM_139170.2	NP_631909.2	Q8IYS4	CP071_HUMAN	chromosome 16 open reading frame 71	143			P -> S (in dbSNP:rs17137230).							breast(1)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(1)	11						GGCCGAGGAGCCCCCCAGGTG	0.597													A|||	66	0.0131789	0.0469	0.0058	5008	,	,		15525	0.0		0.0	False		,,,				2504	0.0				p.P143S		Atlas-SNP	.											.	C16orf71	46	.	0			c.C427T						PASS	.	A	SER/PRO	250,4144		11,228,1958	67	74	72		427	3	0.2	16	dbSNP_123	72	3,8597		0,3,4297	yes	missense	C16orf71	NM_139170.2	74	11,231,6255	TT,TC,CC		0.0349,5.6896,1.9471	benign	143/521	4790304	253,12741	2197	4300	6497	SO:0001583	missense	146562	exon4			GAGGAGCCCCCCA	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.427C>T	16.37:g.4790304C>T	ENSP00000299320:p.Pro143Ser	156	0	0		192	103	0.536458	NM_139170	Q8NCV0	Missense_Mutation	SNP	ENST00000299320.5	37	CCDS10521.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	A	14.78	2.636363	0.47049	0.056896	3.49E-4	ENSG00000166246	ENST00000299320	T	0.08807	3.05	4.05	2.95	0.34219	.	0.488693	0.16973	N	0.192010	T	0.00412	0.0013	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46470	-0.9189	10	0.23891	T	0.37	-3.9933	3.8797	0.09072	0.6631:0.2192:0.1178:0.0	rs17137230;rs52805275;rs17137230	143	Q8IYS4	CP071_HUMAN	S	143	ENSP00000299320:P143S	ENSP00000299320:P143S	P	+	1	0	C16orf71	4730305	0.001000	0.12720	0.189000	0.23252	0.035000	0.12851	0.195000	0.17155	0.253000	0.21552	-0.559000	0.04183	CCC	C|0.980;T|0.020	0.020	strong		0.597	C16orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251644.1	NM_139170		T	4790304	C	T	4790304	3	4	22	1	0	0	0	0	1	0	0	0	1832	739	26	2	437	2	C16orf71	16	4790304	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	358424	4790304	85564449	3175	6076											
ZNF500	26048	hgsc.bcm.edu	37	chr16	4810583	4810583	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccacgtcctccaagttcaCgggcacctgccagaacgcac	10	5	9	17	3	1	1	1	0	0	1	3	1	3	1	5	1	3	3	5	1	2	1	rs151148153	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4810583C>T	ENST00000219478.6	-	5	969	c.670G>A	c.(670-672)Gtg>Atg	p.V224M	ZNF500_ENST00000545009.1_Missense_Mutation_p.V224M			O60304	ZN500_HUMAN	zinc finger protein 500	224	KRAB.				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						TCCAAGTTCACGGGCACCTGC	0.632													C|||	11	0.00219649	0.0076	0.0014	5008	,	,		20443	0.0		0.0	False		,,,				2504	0.0				p.V224M		Atlas-SNP	.											.	ZNF500	45	.	0			c.G670A						PASS	.	C	MET/VAL	65,4329	61.1+/-98.1	0,65,2132	96	79	85		670	3.2	0.1	16	dbSNP_134	85	6,8594	5.0+/-18.6	0,6,4294	yes	missense	ZNF500	NM_021646.1	21	0,71,6426	TT,TC,CC		0.0698,1.4793,0.5464	possibly-damaging	224/481	4810583	71,12923	2197	4300	6497	SO:0001583	missense	26048	exon5			AGTTCACGGGCAC	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.670G>A	16.37:g.4810583C>T	ENSP00000219478:p.Val224Met	103	0	0		108	45	0.416667	NM_021646	A8K6X7|B4DNN9|Q0VAL2|Q96CQ8|Q9BTG0	Missense_Mutation	SNP	ENST00000219478.6	37	CCDS32383.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	C	14.40	2.524884	0.44969	0.014793	6.98E-4	ENSG00000103199	ENST00000545009;ENST00000219478	T;T	0.05925	3.37;3.37	3.16	3.16	0.36331	Krueppel-associated box (3);	.	.	.	.	T	0.11495	0.0280	L	0.51853	1.615	0.21445	N	0.99968	D;D	0.76494	0.995;0.999	P;P	0.61874	0.82;0.895	T	0.04165	-1.0972	9	0.48119	T	0.1	.	12.1628	0.54113	0.0:1.0:0.0:0.0	.	224;224	B4DNN9;O60304	.;ZN500_HUMAN	M	224	ENSP00000445714:V224M;ENSP00000219478:V224M	ENSP00000219478:V224M	V	-	1	0	ZNF500	4750584	0.000000	0.05858	0.066000	0.19879	0.003000	0.03518	0.802000	0.27069	1.785000	0.52413	0.655000	0.94253	GTG	C|0.995;T|0.005	0.005	strong		0.632	ZNF500-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432461.1	XM_085507		T	4810583	C	T	4810583	3	4	22	1	0	0	0	0	1	0	0	0	17963	536	19	1	780	1	ZNF500	16	4810583	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	20279	4810583	85544170	3176	6077											
ROGDI	79641	hgsc.bcm.edu	37	chr16	4847976	4847976	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atgcagcaccgcgcccccagCtgggcggaagttctagggag	8	5	15	13	3	1	0	0	0	1	0	1	2	1	2	3	3	3	4	3	3	2	2	rs546063670	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4847976C>T	ENST00000322048.7	-	9	1036	c.658G>A	c.(658-660)Gct>Act	p.A220T	RP11-127I20.5_ENST00000592465.1_RNA|ROGDI_ENST00000586336.1_5'UTR	NM_024589.2	NP_078865.1	Q9GZN7	ROGDI_HUMAN	rogdi homolog (Drosophila)	220					hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)	intracellular (GO:0005622)|nucleus (GO:0005634)				endometrium(2)|lung(1)|ovary(1)|skin(1)	5						GCGCCCCCAGCTGGGCGGAAG	0.701													C|||	2	0.000399361	0.0015	0.0	5008	,	,		17557	0.0		0.0	False		,,,				2504	0.0				p.A220T		Atlas-SNP	.											.	ROGDI	11	.	0			c.G658A						PASS	.						27	29	28					16																	4847976		2197	4299	6496	SO:0001583	missense	79641	exon9			CCCCAGCTGGGCG	AK026039	CCDS10523.1	16p13.3	2014-09-17			ENSG00000067836	ENSG00000067836			29478	protein-coding gene	gene with protein product		614574				11230166	Standard	NM_024589		Approved	FLJ22386	uc002cxv.4	Q9GZN7	OTTHUMG00000129479	ENST00000322048.7:c.658G>A	16.37:g.4847976C>T	ENSP00000322832:p.Ala220Thr	134	0	0		148	87	0.587838	NM_024589	Q6IA00	Missense_Mutation	SNP	ENST00000322048.7	37	CCDS10523.1	.	.	.	.	.	.	.	.	.	.	C	10.60	1.396518	0.25205	.	.	ENSG00000067836	ENST00000322048	T	0.42900	0.96	5.11	0.509	0.16977	.	0.114933	0.64402	D	0.000019	T	0.23249	0.0562	N	0.22421	0.69	0.28464	N	0.915729	B	0.13145	0.007	B	0.19148	0.024	T	0.18555	-1.0333	10	0.18276	T	0.48	-10.8216	7.925	0.29870	0.5389:0.3846:0.0:0.0765	.	220	Q9GZN7	ROGDI_HUMAN	T	220	ENSP00000322832:A220T	ENSP00000322832:A220T	A	-	1	0	ROGDI	4787977	0.000000	0.05858	0.178000	0.23040	0.322000	0.28314	-0.231000	0.09069	0.147000	0.19030	0.561000	0.74099	GCT	.	.	none		0.701	ROGDI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251643.3	NM_024589		T	4847976	C	T	4847976	3	4	22	1	0	0	0	0	1	0	0	0	13535	797	28	2	217	2	ROGDI	16	4847976	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	37393	4847976	85506777	3177	6078											
ROGDI	79641	hgsc.bcm.edu	37	chr16	4849726	4849726	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gtcttgaactggtagctctgGtcccggctggtaagcaggta	7	11	14	9	1	2	1	0	1	2	0	3	1	3	1	1	5	3	6	1	5	4	4	rs143095485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4849726G>C	ENST00000322048.7	-	6	771	c.393C>G	c.(391-393)gaC>gaG	p.D131E	ROGDI_ENST00000586336.1_5'UTR	NM_024589.2	NP_078865.1	Q9GZN7	ROGDI_HUMAN	rogdi homolog (Drosophila)	131					hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)	intracellular (GO:0005622)|nucleus (GO:0005634)				endometrium(2)|lung(1)|ovary(1)|skin(1)	5						GGTAGCTCTGGTCCCGGCTGG	0.602													G|||	88	0.0175719	0.0643	0.0043	5008	,	,		12956	0.0		0.0	False		,,,				2504	0.0				p.D131E		Atlas-SNP	.											.	ROGDI	11	.	0			c.C393G						PASS	.	G	GLU/ASP	269,4125	152.5+/-186.2	5,259,1933	99	79	86		393	-9.8	0.4	16	dbSNP_134	86	0,8600		0,0,4300	yes	missense	ROGDI	NM_024589.1	45	5,259,6233	CC,CG,GG		0.0,6.122,2.0702	benign	131/288	4849726	269,12725	2197	4300	6497	SO:0001583	missense	79641	exon6			GCTCTGGTCCCGG	AK026039	CCDS10523.1	16p13.3	2014-09-17			ENSG00000067836	ENSG00000067836			29478	protein-coding gene	gene with protein product		614574				11230166	Standard	NM_024589		Approved	FLJ22386	uc002cxv.4	Q9GZN7	OTTHUMG00000129479	ENST00000322048.7:c.393C>G	16.37:g.4849726G>C	ENSP00000322832:p.Asp131Glu	119	0	0		129	59	0.457364	NM_024589	Q6IA00	Missense_Mutation	SNP	ENST00000322048.7	37	CCDS10523.1	21	0.009615384615384616	21	0.042682926829268296	0	0.0	0	0.0	0	0.0	G	6.305	0.424431	0.11928	0.06122	0.0	ENSG00000067836	ENST00000322048	T	0.41065	1.01	4.91	-9.82	0.00484	.	0.057101	0.64402	D	0.000002	T	0.01870	0.0059	L	0.39020	1.185	0.32051	N	0.596972	B	0.10296	0.003	B	0.14023	0.01	T	0.11227	-1.0596	10	0.17369	T	0.5	1.2912	4.1989	0.10457	0.1965:0.3057:0.4049:0.0929	.	131	Q9GZN7	ROGDI_HUMAN	E	131	ENSP00000322832:D131E	ENSP00000322832:D131E	D	-	3	2	ROGDI	4789727	0.003000	0.15002	0.407000	0.26434	0.258000	0.26162	-0.702000	0.05069	-2.194000	0.00753	-0.254000	0.11334	GAC	G|0.980;C|0.020	0.020	strong		0.602	ROGDI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251643.3	NM_024589		C	4849726	G	C	4849726	3	2	22	1	0	0	0	0	1	0	0	0	13535	1252	44	4	494	4	ROGDI	16	4849726	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1750	4849726	85505027	3178	6079											
PPL	5493	hgsc.bcm.edu	37	chr16	4935257	4935257	+	Silent	SNP	G	G	A																															tcgtcctcatattggcgggtGagatcgctgacctccctctc																								rs571194570	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4935257G>A	ENST00000345988.2	-	22	3488	c.3399C>T	c.(3397-3399)ctC>ctT	p.L1133L	PPL_ENST00000590782.2_Silent_p.L1131L	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1133					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						ATTGGCGGGTGAGATCGCTGA	0.627													G|||	13	0.00259585	0.0091	0.0014	5008	,	,		12926	0.0		0.0	False		,,,				2504	0.0				p.L1133L		Atlas-SNP	.											.	PPL	168	.	0			c.C3399T						PASS	.						79	71	74					16																	4935257		2197	4300	6497	SO:0001819	synonymous_variant	5493	exon22			GCGGGTGAGATCG	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.3399C>T	16.37:g.4935257G>A		152	0	0		135	48	0.355556	NM_002705	O60314|O60454|Q14C98	Silent	SNP	ENST00000345988.2	37	CCDS10526.1																																																																																			.	.	none		0.627	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705		A	4935257	G	A	4935257	2	1	22	1	0	0	0	0	0	0	0	1	12346	1277	45	2		2	PPL	16	4935257	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	85531	4935257	85419496	3179	6080	75	2									
PPL	5493	hgsc.bcm.edu	37	chr16	4935258	4935258	+	Missense_Mutation	SNP	A	A	T																															cgtcctcatattggcgggtgAgatcgctgacctccctctcg																								rs145318499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4935258A>T	ENST00000345988.2	-	22	3487	c.3398T>A	c.(3397-3399)cTc>cAc	p.L1133H	PPL_ENST00000590782.2_Missense_Mutation_p.L1131H	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1133					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						TTGGCGGGTGAGATCGCTGAC	0.627													A|||	13	0.00259585	0.0091	0.0014	5008	,	,		12714	0.0		0.0	False		,,,				2504	0.0				p.L1133H		Atlas-SNP	.											.	PPL	168	.	0			c.T3398A						PASS	.						79	71	74					16																	4935258		2197	4300	6497	SO:0001583	missense	5493	exon22			CGGGTGAGATCGC	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.3398T>A	16.37:g.4935258A>T	ENSP00000340510:p.Leu1133His	151	0	0		149	54	0.362416	NM_002705	O60314|O60454|Q14C98	Missense_Mutation	SNP	ENST00000345988.2	37	CCDS10526.1	.	.	.	.	.	.	.	.	.	.	A	15.98	2.992856	0.54041	.	.	ENSG00000118898	ENST00000345988	T	0.43688	0.94	5.17	5.17	0.71159	.	0.000000	0.64402	D	0.000001	T	0.66626	0.2808	M	0.80746	2.51	0.49130	D	0.99975	D	0.89917	1.0	D	0.91635	0.999	T	0.72327	-0.4327	10	0.87932	D	0	.	15.0069	0.71519	1.0:0.0:0.0:0.0	.	1133	O60437	PEPL_HUMAN	H	1133	ENSP00000340510:L1133H	ENSP00000340510:L1133H	L	-	2	0	PPL	4875259	1.000000	0.71417	0.064000	0.19789	0.868000	0.49771	9.292000	0.96076	1.967000	0.57214	0.459000	0.35465	CTC	.	.	weak		0.627	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705		T	4935258	A	T	4935258	3	4	22	1	0	0	0	0	1	0	0	0	12346	304	11	5	1876	5	PPL	16	4935258	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1	4935258	85419495	3180	6081	75	2									
PPL	5493	hgsc.bcm.edu	37	chr16	4952511	4952511	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gcgcaggttggtcacacgctCcttcagctggcggatactga	7	9	13	12	3	2	1	2	1	0	0	3	2	3	2	1	4	2	4	1	4	1	3	rs115478590	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4952511C>T	ENST00000345988.2	-	4	423	c.334G>A	c.(334-336)Gag>Aag	p.E112K	PPL_ENST00000590782.2_Missense_Mutation_p.E112K	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	112					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						GTCACACGCTCCTTCAGCTGG	0.637													C|||	16	0.00319489	0.0113	0.0014	5008	,	,		18020	0.0		0.0	False		,,,				2504	0.0				p.E112K		Atlas-SNP	.											.	PPL	168	.	0			c.G334A						PASS	.	C	LYS/GLU	47,4347	48.9+/-83.8	0,47,2150	129	94	106		334	5	1	16	dbSNP_132	106	0,8600		0,0,4300	yes	missense	PPL	NM_002705.4	56	0,47,6450	TT,TC,CC		0.0,1.0696,0.3617	probably-damaging	112/1757	4952511	47,12947	2197	4300	6497	SO:0001583	missense	5493	exon4			CACGCTCCTTCAG	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.334G>A	16.37:g.4952511C>T	ENSP00000340510:p.Glu112Lys	128	0	0		160	90	0.5625	NM_002705	O60314|O60454|Q14C98	Missense_Mutation	SNP	ENST00000345988.2	37	CCDS10526.1	10	0.004578754578754579	8	0.016260162601626018	2	0.0055248618784530384	0	0.0	0	0.0	C	25.4	4.631767	0.87660	0.010696	0.0	ENSG00000118898	ENST00000345988	T	0.36520	1.25	4.98	4.98	0.66077	.	0.126906	0.52532	D	0.000078	T	0.43523	0.1251	M	0.69823	2.125	0.45528	D	0.998484	D	0.69078	0.997	D	0.75020	0.985	T	0.58629	-0.7603	10	0.72032	D	0.01	.	16.4235	0.83790	0.0:1.0:0.0:0.0	.	112	O60437	PEPL_HUMAN	K	112	ENSP00000340510:E112K	ENSP00000340510:E112K	E	-	1	0	PPL	4892512	1.000000	0.71417	1.000000	0.80357	0.645000	0.38454	5.290000	0.65661	2.311000	0.77944	0.650000	0.86243	GAG	C|0.996;T|0.004	0.004	strong		0.637	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705		T	4952511	C	T	4952511	3	4	22	1	0	0	0	0	1	0	0	0	12346	864	30	2	5012	2	PPL	16	4952511	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	17253	4952511	85402242	3181	6082											
SEC14L5	9717	hgsc.bcm.edu	37	chr16	5050678	5050678	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ggccgccccctctacatcctCcgcctgggccagatggacac	6	6	10	19	2	1	1	0	0	1	1	3	2	3	2	7	3	1	0	7	3	1	1	rs61745575	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:5050678C>T	ENST00000251170.7	+	9	1173	c.993C>T	c.(991-993)ctC>ctT	p.L331L		NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN	SEC14-like 5 (S. cerevisiae)	331	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						TCTACATCCTCCGCCTGGGCC	0.632													C|||	132	0.0263578	0.0923	0.0115	5008	,	,		16872	0.0		0.002	False		,,,				2504	0.0				p.L331L		Atlas-SNP	.											SEC14L5,NS,carcinoma,+2,1	SEC14L5	79	1	0			c.C993T						PASS	.	C		191,3593		4,183,1705	11	12	12		993	1.2	1	16	dbSNP_129	12	2,7978		0,2,3988	no	coding-synonymous	SEC14L5	NM_014692.1		4,185,5693	TT,TC,CC		0.0251,5.0476,1.6406		331/697	5050678	193,11571	1892	3990	5882	SO:0001819	synonymous_variant	9717	exon9			CATCCTCCGCCTG	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.993C>T	16.37:g.5050678C>T		125	0	0		104	50	0.480769	NM_014692		Silent	SNP	ENST00000251170.7	37	CCDS45403.1																																																																																			C|0.975;T|0.025	0.025	strong		0.632	SEC14L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434379.1			T	5050678	C	T	5050678	2	4	22	1	0	0	0	0	0	0	0	1	14000	842	30	2		2	SEC14L5	16	5050678	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	98167	5050678	85304075	3182	6083											
SEC14L5	9717	hgsc.bcm.edu	37	chr16	5061191	5061191	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagcctcccgggtgtggaCgatgtcctgacggctctgca	5	9	14	13	3	1	1	0	1	1	0	3	3	3	2	3	3	3	3	3	3	0	0	rs8055468	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:5061191C>T	ENST00000251170.7	+	15	2076	c.1896C>T	c.(1894-1896)gaC>gaT	p.D632D	RP11-165E7.1_ENST00000588778.1_RNA	NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN	SEC14-like 5 (S. cerevisiae)	632	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.					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						CGGGTGTGGACGATGTCCTGA	0.652													C|||	159	0.0317492	0.1135	0.0115	5008	,	,		16324	0.001		0.0	False		,,,				2504	0.0				p.D632D		Atlas-SNP	.											.	SEC14L5	79	.	0			c.C1896T						PASS	.	C		368,3642		19,330,1656	25	29	28		1896	-5.6	0	16	dbSNP_116	28	7,8319		0,7,4156	no	coding-synonymous	SEC14L5	NM_014692.1		19,337,5812	TT,TC,CC		0.0841,9.1771,3.0399		632/697	5061191	375,11961	2005	4163	6168	SO:0001819	synonymous_variant	9717	exon15			TGTGGACGATGTC	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.1896C>T	16.37:g.5061191C>T		140	0	0		146	69	0.472603	NM_014692		Silent	SNP	ENST00000251170.7	37	CCDS45403.1																																																																																			C|0.968;T|0.032	0.032	strong		0.652	SEC14L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434379.1			T	5061191	C	T	5061191	2	4	22	1	0	0	0	0	0	0	0	1	14000	535	19	1		1	SEC14L5	16	5061191	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	10513	5061191	85293562	3183	6084											
C16orf89	146556	hgsc.bcm.edu	37	chr16	5115811	5115811	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggatcaggtctgcaatggtGgctttactttcagcagtgtc	8	13	12	8	0	3	0	2	0	1	0	4	1	3	1	0	4	3	3	0	4	2	3	rs35751409	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:5115811G>A	ENST00000315997.5	-	1	300	c.99C>T	c.(97-99)gcC>gcT	p.A33A	C16orf89_ENST00000422873.1_Silent_p.A71A|C16orf89_ENST00000350219.4_Silent_p.A71A|C16orf89_ENST00000474471.3_Silent_p.A33A|ALG1_ENST00000588623.1_Intron|C16orf89_ENST00000472572.3_Silent_p.A33A	NM_152459.4	NP_689672.4	Q6UX73	CP089_HUMAN	chromosome 16 open reading frame 89	33						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						CTGCAATGGTGGCTTTACTTT	0.602													G|||	35	0.00698882	0.0265	0.0	5008	,	,		19948	0.0		0.0	False		,,,				2504	0.0				p.A33A		Atlas-SNP	.											.	C16orf89	64	.	0			c.C99T						PASS	.	G	,	111,4137		1,109,2014	61	66	64		99,99	-0.5	0.5	16	dbSNP_126	64	0,8502		0,0,4251	no	coding-synonymous,coding-synonymous	C16orf89	NM_001098514.2,NM_152459.4	,	1,109,6265	AA,AG,GG		0.0,2.613,0.8706	,	33/362,33/403	5115811	111,12639	2124	4251	6375	SO:0001819	synonymous_variant	146556	exon1			AATGGTGGCTTTA		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.99C>T	16.37:g.5115811G>A		127	0	0		143	61	0.426573	NM_001098514	B4DUM5|Q8N2I3|Q8N4T1	Silent	SNP	ENST00000315997.5	37	CCDS42116.2																																																																																			G|0.990;A|0.010	0.010	strong		0.602	C16orf89-001	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354524.1	NM_152459		A	5115811	G	A	5115811	2	1	22	1	0	0	0	0	0	0	0	1	1844	1335	47	2		2	C16orf89	16	5115811	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	54620	5115811	85238942	3184	6085											
ATF7IP2	80063	hgsc.bcm.edu	37	chr16	10527404	10527404	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cattatcaaaagaagaggatGttttcagaaaacgaggaaaa	20	8	9	4	1	2	3	2	0	0	3	2	6	2	5	0	2	1	1	0	2	8	3	rs141089693	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:10527404G>A	ENST00000396560.2	+	4	1085	c.858G>A	c.(856-858)atG>atA	p.M286I	ATF7IP2_ENST00000543967.1_Intron|ATF7IP2_ENST00000396559.1_Missense_Mutation_p.M286I|ATF7IP2_ENST00000356427.2_Missense_Mutation_p.M286I|ATF7IP2_ENST00000324570.5_Missense_Mutation_p.M286I	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	286					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				large_intestine(3)	3						AGAAGAGGATGTTTTCAGAAA	0.338													G|||	5	0.000998403	0.0038	0.0	5008	,	,		21095	0.0		0.0	False		,,,				2504	0.0				p.M286I		Atlas-SNP	.											.	ATF7IP2	40	.	0			c.G858A						PASS	.	G	ILE/MET	30,4362	32.6+/-62.9	1,28,2167	54	56	55		858	1.8	1	16	dbSNP_134	55	0,8598		0,0,4299	yes	missense	ATF7IP2	NM_024997.2	10	1,28,6466	AA,AG,GG		0.0,0.6831,0.2309	possibly-damaging	286/683	10527404	30,12960	2196	4299	6495	SO:0001583	missense	80063	exon4			GAGGATGTTTTCA	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.858G>A	16.37:g.10527404G>A	ENSP00000379808:p.Met286Ile	152	0	0		159	81	0.509434	NM_024997	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	Missense_Mutation	SNP	ENST00000396560.2	37	CCDS10540.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	13.62	2.292811	0.40594	0.006831	0.0	ENSG00000166669	ENST00000396559;ENST00000396560;ENST00000535850;ENST00000356427;ENST00000324570	T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93	5.02	1.79	0.24919	.	0.492757	0.20948	N	0.082817	T	0.25269	0.0614	L	0.55481	1.735	0.21822	N	0.999525	B;B	0.27656	0.184;0.161	B;B	0.29353	0.101;0.053	T	0.13522	-1.0506	10	0.33940	T	0.23	-6.0402	5.1577	0.15044	0.1856:0.0:0.6499:0.1645	.	286;286	Q5U623-2;Q5U623	.;MCAF2_HUMAN	I	286	ENSP00000379807:M286I;ENSP00000379808:M286I;ENSP00000440791:M286I;ENSP00000348799:M286I;ENSP00000322811:M286I	ENSP00000322811:M286I	M	+	3	0	ATF7IP2	10434905	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	1.462000	0.35266	0.648000	0.30732	-0.145000	0.13849	ATG	G|0.999;A|0.001	0.001	strong		0.338	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997		A	10527404	G	A	10527404	3	1	22	1	0	0	0	0	1	0	0	0	1088	1377	48	2	864	2	ATF7IP2	16	10527404	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5411593	10527404	79827349	3185	6086											
TEKT5	146279	hgsc.bcm.edu	37	chr16	10769873	10769873	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcacctcagagatgcgggcGttgaaggccaggttggtgtc	7	9	16	9	2	2	2	2	1	0	1	3	3	2	2	2	4	1	2	2	4	1	2	rs115325161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:10769873G>A	ENST00000283025.2	-	5	1100	c.1029C>T	c.(1027-1029)aaC>aaT	p.N343N		NM_144674.1	NP_653275.1	Q96M29	TEKT5_HUMAN	tektin 5	343						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						AGATGCGGGCGTTGAAGGCCA	0.602													A|||	25	0.00499201	0.0174	0.0029	5008	,	,		21091	0.0		0.0	False		,,,				2504	0.0				p.N343N		Atlas-SNP	.											.	TEKT5	66	.	0			c.C1029T						PASS	.	A		72,4322	818.8+/-416.3	1,70,2126	153	126	135		1029	-3.3	0.1	16	dbSNP_132	135	0,8600		0,0,4300	no	coding-synonymous	TEKT5	NM_144674.1		1,70,6426	AA,AG,GG		0.0,1.6386,0.5541		343/486	10769873	72,12922	2197	4300	6497	SO:0001819	synonymous_variant	146279	exon5			GCGGGCGTTGAAG		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.1029C>T	16.37:g.10769873G>A		86	0	0		101	56	0.554455	NM_144674	A1L3Z3	Silent	SNP	ENST00000283025.2	37	CCDS10542.1																																																																																			G|0.995;A|0.005	0.005	strong		0.602	TEKT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251963.1	NM_144674		A	10769873	G	A	10769873	2	1	22	1	0	0	0	0	0	0	0	1	15771	1136	40	1		1	TEKT5	16	10769873	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	242469	10769873	79584880	3186	6087											
CLEC16A	23274	hgsc.bcm.edu	37	chr16	11114174	11114174	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acctgctctgagagcacgcaAtggagcaggtagctgcccga	10	6	13	12	2	1	1	0	1	1	1	1	4	1	2	2	2	5	6	2	2	2	1	rs61741309	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:11114174A>G	ENST00000409790.1	+	12	1658	c.1428A>G	c.(1426-1428)caA>caG	p.Q476Q	CLEC16A_ENST00000409552.3_Silent_p.Q458Q	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						AGAGCACGCAATGGAGCAGGT	0.632													A|||	245	0.0489217	0.18	0.0101	5008	,	,		21149	0.0		0.0	False		,,,				2504	0.0				p.Q476Q		Atlas-SNP	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.A1428G						PASS	.	A		489,3493		31,427,1533	16	19	18		1428	4.4	1	16	dbSNP_129	18	4,8358		0,4,4177	no	coding-synonymous	CLEC16A	NM_015226.2		31,431,5710	GG,GA,AA		0.0478,12.2803,3.9938		476/1054	11114174	493,11851	1991	4181	6172	SO:0001819	synonymous_variant	23274	exon11			CACGCAATGGAGC	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.1428A>G	16.37:g.11114174A>G		74	0	0		116	60	0.517241	NM_015226		Silent	SNP	ENST00000409790.1	37	CCDS45409.1																																																																																			A|0.962;G|0.038	0.038	strong		0.632	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226		G	11114174	A	G	11114174	2	3	22	1	0	0	0	0	0	0	0	1	3502	98	4	3		3	CLEC16A	16	11114174	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	344301	11114174	79240579	3187	6088											
CLEC16A	23274	hgsc.bcm.edu	37	chr16	11133642	11133642	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaaaaattagagcgaatccaGctccccgtgccaaatgcggc	13	6	10	12	3	0	1	0	0	0	1	2	3	2	1	4	1	4	1	4	1	5	1	rs61740101	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:11133642G>A	ENST00000409790.1	+	14	1799	c.1569G>A	c.(1567-1569)caG>caA	p.Q523Q	CLEC16A_ENST00000465491.1_3'UTR|CLEC16A_ENST00000409552.3_Silent_p.Q505Q	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						AGCGAATCCAGCTCCCCGTGC	0.547													G|||	64	0.0127796	0.0477	0.0014	5008	,	,		18325	0.0		0.0	False		,,,				2504	0.0				p.Q523Q		Atlas-SNP	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.G1569A						PASS	.	G		137,3891		6,125,1883	51	55	54		1569	3.3	1	16	dbSNP_129	54	0,8358		0,0,4179	no	coding-synonymous	CLEC16A	NM_015226.2		6,125,6062	AA,AG,GG		0.0,3.4012,1.1061		523/1054	11133642	137,12249	2014	4179	6193	SO:0001819	synonymous_variant	23274	exon13			AATCCAGCTCCCC	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.1569G>A	16.37:g.11133642G>A		89	0	0		93	46	0.494624	NM_015226		Silent	SNP	ENST00000409790.1	37	CCDS45409.1																																																																																			G|0.989;A|0.011	0.011	strong		0.547	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226		A	11133642	G	A	11133642	2	1	22	1	0	0	0	0	0	0	0	1	3502	962	34	2		2	CLEC16A	16	11133642	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	19468	11133642	79221111	3188	6089											
CLEC16A	23274	hgsc.bcm.edu	37	chr16	11133681	11133681	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gccgagaagaccacctacaaCcacccgctagctgaaagact	14	4	8	15	2	0	4	0	1	0	3	0	5	0	4	5	0	3	2	5	0	5	2	rs61740118	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:11133681C>T	ENST00000409790.1	+	14	1838	c.1608C>T	c.(1606-1608)aaC>aaT	p.N536N	CLEC16A_ENST00000465491.1_3'UTR|CLEC16A_ENST00000409552.3_Silent_p.N518N	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						CCACCTACAACCACCCGCTAG	0.552													C|||	64	0.0127796	0.0477	0.0014	5008	,	,		18259	0.0		0.0	False		,,,				2504	0.0				p.N536N		Atlas-SNP	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.C1608T						PASS	.	C		139,3971		5,129,1921	57	61	59		1608	4.3	1	16	dbSNP_129	59	0,8386		0,0,4193	no	coding-synonymous	CLEC16A	NM_015226.2		5,129,6114	TT,TC,CC		0.0,3.382,1.1124		536/1054	11133681	139,12357	2055	4193	6248	SO:0001819	synonymous_variant	23274	exon13			CTACAACCACCCG	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.1608C>T	16.37:g.11133681C>T		99	0	0		97	44	0.453608	NM_015226		Silent	SNP	ENST00000409790.1	37	CCDS45409.1																																																																																			C|0.989;T|0.011	0.011	strong		0.552	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226		T	11133681	C	T	11133681	2	4	22	1	0	0	0	0	0	0	0	1	3502	506	18	2		2	CLEC16A	16	11133681	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	39	11133681	79221072	3189	6090											
CLEC16A	23274	hgsc.bcm.edu	37	chr16	11272227	11272227	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaactgcctaagcctcacCttcctgaccagttggtaatc	10	10	7	14	0	1	2	1	1	0	1	3	2	2	2	5	1	3	2	5	1	3	4	rs61744103	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:11272227C>T	ENST00000409790.1	+	24	3072	c.2842C>T	c.(2842-2844)Ctt>Ttt	p.L948F	CLEC16A_ENST00000381822.2_Missense_Mutation_p.L35F	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						TAAGCCTCACCTTCCTGACCA	0.592													C|||	90	0.0179712	0.0658	0.0043	5008	,	,		6774	0.0		0.0	False		,,,				2504	0.0				p.L948F		Atlas-SNP	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.C2842T						PASS	.	C	PHE/LEU	177,4103		3,171,1966	100	111	107		2842	2	0.9	16	dbSNP_129	107	1,8491		0,1,4245	yes	missense	CLEC16A	NM_015226.2	22	3,172,6211	TT,TC,CC		0.0118,4.1355,1.3937	benign	948/1054	11272227	178,12594	2140	4246	6386	SO:0001583	missense	23274	exon23			CCTCACCTTCCTG	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.2842C>T	16.37:g.11272227C>T	ENSP00000387122:p.Leu948Phe	73	0	0		77	46	0.597403	NM_015226		Missense_Mutation	SNP	ENST00000409790.1	37	CCDS45409.1	20	0.009157509157509158	18	0.036585365853658534	2	0.0055248618784530384	0	0.0	0	0.0	C	10.65	1.409444	0.25378	0.041355	1.18E-4	ENSG00000038532	ENST00000409790;ENST00000542102;ENST00000381822	T	0.50548	0.74	4.13	2.02	0.26589	.	1.046110	0.07487	N	0.904880	T	0.11879	0.0289	N	0.03608	-0.345	0.09310	N	1	D;B	0.69078	0.997;0.0	D;B	0.63283	0.913;0.0	T	0.21895	-1.0232	10	0.32370	T	0.25	-2.4515	5.4981	0.16813	0.3727:0.5235:0.0:0.1038	rs61744103	35;948	Q2KHT3-3;Q2KHT3	.;CL16A_HUMAN	F	948;948;35	ENSP00000387122:L948F	ENSP00000371244:L35F	L	+	1	0	CLEC16A	11179728	0.120000	0.22244	0.917000	0.36280	0.855000	0.48748	0.314000	0.19432	0.815000	0.34398	0.563000	0.77884	CTT	C|0.991;T|0.009	0.009	strong		0.592	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226		T	11272227	C	T	11272227	3	4	22	1	0	0	0	0	1	0	0	0	3502	681	24	2	2932	2	CLEC16A	16	11272227	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	138546	11272227	79082526	3190	6091											
TXNDC11	51061	hgsc.bcm.edu	37	chr16	11773261	11773261	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atcttgagccacgtgttctcGgtaaggaggttttctgaggc	7	13	13	8	2	3	2	0	2	3	0	4	3	3	3	1	4	1	3	1	4	1	5	rs8191350	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:11773261G>C	ENST00000356957.3	-	13	2855	c.2748C>G	c.(2746-2748)acC>acG	p.T916T	TXNDC11_ENST00000283033.5_Silent_p.T889T|TXNDC11_ENST00000570917.1_5'UTR			Q6PKC3	TXD11_HUMAN	thioredoxin domain containing 11	916					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						ACGTGTTCTCGGTAAGGAGGT	0.617													G|||	117	0.0233626	0.087	0.0029	5008	,	,		17720	0.0		0.0	False		,,,				2504	0.0				p.T889T		Atlas-SNP	.											.	TXNDC11	75	.	0			c.C2667G						PASS	.	G		362,4032	181.2+/-209.3	18,326,1853	61	60	61		2667	-11.3	0	16	dbSNP_117	61	4,8596	2.2+/-6.3	0,4,4296	no	coding-synonymous	TXNDC11	NM_015914.5		18,330,6149	CC,CG,GG		0.0465,8.2385,2.8167		889/959	11773261	366,12628	2197	4300	6497	SO:0001819	synonymous_variant	51061	exon12			GTTCTCGGTAAGG	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.2748C>G	16.37:g.11773261G>C		101	0	0		119	53	0.445378	NM_015914	O95887|Q6PJA6|Q8N2Q4|Q96K45|Q96K53	Silent	SNP	ENST00000356957.3	37																																																																																				G|0.970;C|0.030	0.030	strong		0.617	TXNDC11-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000437057.1	NM_015914		C	11773261	G	C	11773261	2	2	22	1	0	0	0	0	0	0	0	1	16807	1103	39	4		4	TXNDC11	16	11773261	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	501034	11773261	78581492	3191	6092											
CPPED1	55313	hgsc.bcm.edu	37	chr16	12798724	12798724	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgaggaccaggaacaggaCgcccccgacccagaagctga	12	3	13	13	2	0	3	0	2	0	1	0	7	0	6	4	3	2	2	4	3	2	1	rs145004672	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:12798724C>T	ENST00000381774.4	-	3	712	c.472G>A	c.(472-474)Gtc>Atc	p.V158I	CPPED1_ENST00000261660.4_Intron|CPPED1_ENST00000433677.2_Intron	NM_018340.2	NP_060810.2	Q9BRF8	CPPED_HUMAN	calcineurin-like phosphoesterase domain containing 1	158	Catalytic.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)	p.V158I(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|urinary_tract(1)	18						AGGAACAGGACGCCCCCGACC	0.612													C|||	42	0.00838658	0.0272	0.0029	5008	,	,		17716	0.003		0.0	False		,,,				2504	0.001				p.V158I		Atlas-SNP	.											CPPED1,rectum,carcinoma,0,1	CPPED1	41	1	1	Substitution - Missense(1)	large_intestine(1)	c.G472A						scavenged	.	C	,ILE/VAL	69,3929		1,67,1931	57	62	60		,472	4.4	0.8	16	dbSNP_134	60	1,8319		0,1,4159	yes	intron,missense	CPPED1	NM_001099455.1,NM_018340.2	,29	1,68,6090	TT,TC,CC		0.012,1.7259,0.5683	,possibly-damaging	,158/315	12798724	70,12248	1999	4160	6159	SO:0001583	missense	55313	exon3			ACAGGACGCCCCC	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.472G>A	16.37:g.12798724C>T	ENSP00000371193:p.Val158Ile	94	1	0.0106383		83	45	0.542169	NM_018340	B4DQ68|Q6MZY9|Q9H9M9|Q9NUT6	Missense_Mutation	SNP	ENST00000381774.4	37	CCDS42120.1	27	0.012362637362637362	23	0.046747967479674794	1	0.0027624309392265192	3	0.005244755244755245	0	0.0	C	16.61	3.171078	0.57584	0.017259	1.2E-4	ENSG00000103381	ENST00000381774	T	0.72505	-0.66	5.32	4.37	0.52481	Metallophosphoesterase domain (1);	0.053983	0.64402	D	0.000001	T	0.29882	0.0747	M	0.67397	2.05	0.80722	D	1	P	0.47191	0.891	B	0.43194	0.411	T	0.56165	-0.8024	10	0.46703	T	0.11	-31.751	12.0777	0.53653	0.0:0.9163:0.0:0.0837	.	158	Q9BRF8	CPPED_HUMAN	I	158	ENSP00000371193:V158I	ENSP00000371193:V158I	V	-	1	0	CPPED1	12706225	0.998000	0.40836	0.840000	0.33206	0.315000	0.28087	3.848000	0.55903	1.256000	0.44068	-0.128000	0.14901	GTC	C|0.988;T|0.012	0.012	strong		0.612	CPPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395795.2	NM_018340		T	12798724	C	T	12798724	3	4	22	1	0	0	0	0	1	0	0	0	3824	536	19	1	480	1	CPPED1	16	12798724	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1025463	12798724	77556029	3192	6093											
ERCC4	2072	hgsc.bcm.edu	37	chr16	14031695	14031695	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctttgcggaaagaaaaggaAgcttttgaaaaactcataag	17	9	10	5	1	1	2	1	1	0	1	1	4	1	4	0	2	3	2	0	2	7	4	rs2020958	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:14031695A>G	ENST00000311895.7	+	9	1893	c.1884A>G	c.(1882-1884)gaA>gaG	p.E628E	CTD-2135D7.2_ENST00000570663.1_RNA|CTD-2135D7.2_ENST00000575137.1_RNA	NM_005236.2	NP_005227.1	Q92889	XPF_HUMAN	excision repair cross-complementation group 4	628					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						AAGAAAAGGAAGCTTTTGAAA	0.393			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				A|||	77	0.0153754	0.0582	0.0	5008	,	,		16132	0.0		0.0	False		,,,				2504	0.0				p.E628E		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.A1884G						PASS	.	A		170,4224	105.2+/-143.6	3,164,2030	76	75	75		1884	4.2	1	16	dbSNP_94	75	0,8600		0,0,4300	no	coding-synonymous	ERCC4	NM_005236.2		3,164,6330	GG,GA,AA		0.0,3.8689,1.3083		628/917	14031695	170,12824	2197	4300	6497	SO:0001819	synonymous_variant	2072	exon9	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	AAAGGAAGCTTTT	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.1884A>G	16.37:g.14031695A>G		70	0	0		81	41	0.506173	NM_005236	A5PKV6|A8K111|O00140|Q8TD83	Silent	SNP	ENST00000311895.7	37	CCDS32390.1																																																																																			A|0.982;G|0.018	0.018	strong		0.393	ERCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109634.2	NM_005236		G	14031695	A	G	14031695	2	3	22	1	0	0	0	0	0	0	0	1	5217	69	3	3		3	ERCC4	16	14031695	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1232971	14031695	76323058	3193	6094											
ERCC4	2072	hgsc.bcm.edu	37	chr16	14038659	14038659	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctagtaagaggcacagcaTctgcagatgtttccactgac	12	9	9	11	0	1	3	0	1	1	2	2	3	2	3	2	1	2	5	2	1	2	3	rs2020955	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:14038659T>C	ENST00000311895.7	+	10	1993	c.1984T>C	c.(1984-1986)Tct>Cct	p.S662P		NM_005236.2	NP_005227.1	Q92889	XPF_HUMAN	excision repair cross-complementation group 4	662	Nuclease.		S -> P (in dbSNP:rs2020955). {ECO:0000269|Ref.2}.		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						AGGCACAGCATCTGCAGATGT	0.488			"Mis, N, F"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				T|||	306	0.0611022	0.2209	0.0187	5008	,	,		19375	0.0		0.001	False		,,,				2504	0.0				p.S662P		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.T1984C						PASS	.	T	PRO/SER	845,3549	335.7+/-304.0	79,687,1431	103	93	97		1984	0.9	0	16	dbSNP_94	97	11,8589	8.4+/-32.0	0,11,4289	yes	missense	ERCC4	NM_005236.2	74	79,698,5720	CC,CT,TT		0.1279,19.2308,6.5877	benign	662/917	14038659	856,12138	2197	4300	6497	SO:0001583	missense	2072	exon10	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	ACAGCATCTGCAG	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.1984T>C	16.37:g.14038659T>C	ENSP00000310520:p.Ser662Pro	168	0	0		133	61	0.458647	NM_005236	A5PKV6|A8K111|O00140|Q8TD83	Missense_Mutation	SNP	ENST00000311895.7	37	CCDS32390.1	106	0.048534798534798536	100	0.2032520325203252	6	0.016574585635359115	0	0.0	0	0.0	T	8.372	0.835596	0.16820	0.192308	0.001279	ENSG00000175595	ENST00000311895;ENST00000389138	T	0.62105	0.05	5.8	0.884	0.19182	.	0.401079	0.30732	N	0.008982	T	0.00039	0.0001	N	0.05414	-0.055	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.06162	-1.0842	9	0.27082	T	0.32	-7.9859	1.9232	0.03312	0.1348:0.1162:0.2951:0.4539	rs2020955;rs2020955	662	Q92889	XPF_HUMAN	P	662;650	ENSP00000310520:S662P	ENSP00000310520:S662P	S	+	1	0	ERCC4	13946160	0.014000	0.17966	0.001000	0.08648	0.041000	0.13682	0.464000	0.21988	0.084000	0.17077	0.533000	0.62120	TCT	T|0.934;C|0.066	0.066	strong		0.488	ERCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109634.2	NM_005236		C	14038659	T	C	14038659	3	2	22	1	0	0	0	0	1	0	0	0	5217	1435	50	3	2022	3	ERCC4	16	14038659	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	6964	14038659	76316094	3194	6095											
MYH11	4629	hgsc.bcm.edu	37	chr16	15841534	15841534	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggacgccagttcggaagaaGattttgctctgccctatcct	9	11	10	11	2	1	2	0	0	1	2	3	4	2	4	3	2	2	2	3	2	3	4			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:15841534G>T	ENST00000300036.5	-	19	2413	c.2304C>A	c.(2302-2304)atC>atA	p.I768I	MYH11_ENST00000452625.2_Silent_p.I775I|MYH11_ENST00000396324.3_Silent_p.I775I|MYH11_ENST00000576790.2_Silent_p.I768I	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	768	Actin-binding. {ECO:0000250}.|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						TTCGGAAGAAGATTTTGCTCT	0.512			T	CBFB	AML																																p.I775I		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	.	MYH11	520	.	0			c.C2325A						PASS	.						97	93	94					16																	15841534		2197	4300	6497	SO:0001819	synonymous_variant	4629	exon20			GAAGAAGATTTTG	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.2304C>A	16.37:g.15841534G>T		110	0	0		96	55	0.572917	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																			.	.	none		0.512	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		T	15841534	G	T	15841534	2	4	22	1	0	0	0	0	0	0	0	1	10040	932	33	4		4	MYH11	16	15841534	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1802875	15841534	74513219	3195	6096											
MYH11	4629	hgsc.bcm.edu	37	chr16	15931975	15931975	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tccttaatgctggctgcctcGaagccctgcttctccgaggg	5	11	11	14	2	1	0	0	0	1	0	4	2	2	0	4	2	4	3	4	2	2	2	rs28570191|rs587781074	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:15931975G>A	ENST00000300036.5	-	2	244	c.135C>T	c.(133-135)ttC>ttT	p.F45F	MYH11_ENST00000452625.2_Silent_p.F45F|MYH11_ENST00000396324.3_Silent_p.F45F|MYH11_ENST00000576790.2_Silent_p.F45F	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	45					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						TGGCTGCCTCGAAGCCCTGCT	0.562			T	CBFB	AML								G|||	220	0.0439297	0.1543	0.0231	5008	,	,		18928	0.0		0.0	False		,,,				2504	0.0				p.F45F		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	.	MYH11	520	.	0			c.C135T						PASS	.	G	,,,	591,3803	261.9+/-264.6	42,507,1648	166	156	159		135,135,135,135	-0.4	1	16	dbSNP_125	159	17,8583	11.9+/-42.8	0,17,4283	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MYH11	NM_001040113.1,NM_001040114.1,NM_002474.2,NM_022844.2	,,,	42,524,5931	AA,AG,GG		0.1977,13.4502,4.6791	,,,	45/1946,45/1980,45/1973,45/1939	15931975	608,12386	2197	4300	6497	SO:0001819	synonymous_variant	4629	exon2			TGCCTCGAAGCCC	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.135C>T	16.37:g.15931975G>A		87	0	0		98	58	0.591837	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																			G|0.951;A|0.049	0.049	strong		0.562	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		A	15931975	G	A	15931975	2	1	22	1	0	0	0	0	0	0	0	1	10040	1049	37	1		1	MYH11	16	15931975	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	90441	15931975	74422778	3196	6097											
ABCC1	4363	hgsc.bcm.edu	37	chr16	16184366	16184366	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgggctcctaccaggagctGctggctcgagacggcgcctt	6	8	14	13	3	0	1	0	0	0	1	2	3	1	2	3	4	3	4	3	4	1	2	rs28364004	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:16184366G>T	ENST00000399410.3	+	19	2740	c.2565G>T	c.(2563-2565)ctG>ctT	p.L855L	ABCC1_ENST00000399408.2_Silent_p.L855L|ABCC1_ENST00000351154.5_Silent_p.L796L|ABCC1_ENST00000345148.5_Silent_p.L855L|ABCC1_ENST00000349029.5_Silent_p.L740L|ABCC1_ENST00000346370.5_Silent_p.L799L	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	855	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)	ACCAGGAGCTGCTGGCTCGAG	0.607													G|||	24	0.00479233	0.0136	0.0072	5008	,	,		19519	0.0		0.001	False		,,,				2504	0.0				p.L855L		Atlas-SNP	.											.	ABCC1	156	.	0			c.G2565T						PASS	.	G	,,,,	40,4072		0,40,2016	34	36	36		2565,2388,2397,2220,2565	3.3	1	16	dbSNP_126	36	7,8397		0,7,4195	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ABCC1	NM_004996.3,NM_019862.2,NM_019898.2,NM_019899.2,NM_019900.2	,,,,	0,47,6211	TT,TG,GG		0.0833,0.9728,0.3755	,,,,	855/1532,796/1473,799/1476,740/1417,855/1467	16184366	47,12469	2056	4202	6258	SO:0001819	synonymous_variant	4363	exon19			GGAGCTGCTGGCT	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.2565G>T	16.37:g.16184366G>T		66	0	0		72	31	0.430556	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Silent	SNP	ENST00000399410.3	37	CCDS42122.1																																																																																			G|0.983;T|0.017	0.017	strong		0.607	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996		T	16184366	G	T	16184366	2	4	22	1	0	0	0	0	0	0	0	1	49	1306	46	4		4	ABCC1	16	16184366	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	252391	16184366	74170387	3197	6098											
ABCC1	4363	hgsc.bcm.edu	37	chr16	16230427	16230427	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tggacgtccctggagctggcCcacctgaaggacttcgtgtc	6	9	13	13	2	0	1	0	1	0	0	3	4	1	4	3	4	1	1	3	4	1	1	rs34526519	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:16230427C>T	ENST00000399410.3	+	29	4393	c.4218C>T	c.(4216-4218)gcC>gcT	p.A1406A	ABCC1_ENST00000399408.2_Silent_p.A1416A|ABCC1_ENST00000351154.5_Silent_p.A1347A|ABCC1_ENST00000345148.5_Silent_p.A1406A|ABCC1_ENST00000349029.5_Silent_p.A1291A|ABCC1_ENST00000346370.5_Silent_p.A1350A	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	1406	ABC transporter 2. {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)	TGGAGCTGGCCCACCTGAAGG	0.562													C|||	28	0.00559105	0.0166	0.0058	5008	,	,		18552	0.0		0.002	False		,,,				2504	0.0				p.A1406A		Atlas-SNP	.											.	ABCC1	156	.	0			c.C4218T						PASS	.	C	,,,,	64,3882		0,64,1909	51	52	52		4218,4041,4050,3873,4218	-12.1	0.2	16	dbSNP_126	52	6,8310		0,6,4152	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ABCC1	NM_004996.3,NM_019862.2,NM_019898.2,NM_019899.2,NM_019900.2	,,,,	0,70,6061	TT,TC,CC		0.0722,1.6219,0.5709	,,,,	1406/1532,1347/1473,1350/1476,1291/1417,1406/1467	16230427	70,12192	1973	4158	6131	SO:0001819	synonymous_variant	4363	exon29			GCTGGCCCACCTG	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.4218C>T	16.37:g.16230427C>T		88	0	0		118	54	0.457627	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Silent	SNP	ENST00000399410.3	37	CCDS42122.1																																																																																			C|0.994;T|0.006	0.006	strong		0.562	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996		T	16230427	C	T	16230427	2	4	22	1	0	0	0	0	0	0	0	1	49	610	22	2		2	ABCC1	16	16230427	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	46061	16230427	74124326	3198	6099											
ABCC6	368	hgsc.bcm.edu	37	chr16	16248791	16248791	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccacgtgggcaatggggaccCcgtcgatccagatcccaccc	8	5	11	17	3	0	1	0	0	0	1	3	3	2	2	6	3	0	1	6	3	1	0	rs57695665	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:16248791C>T	ENST00000205557.7	-	28	4009	c.3980G>A	c.(3979-3981)gGg>gAg	p.G1327E		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1327	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)	AATGGGGACCCCGTCGATCCA	0.672													C|||	27	0.00539137	0.0197	0.0014	5008	,	,		16551	0.0		0.0	False		,,,				2504	0.0				p.G1327E		Atlas-SNP	.											.	ABCC6	110	.	0			c.G3980A						PASS	.	C	GLU/GLY	51,4343		0,51,2146	29	25	26		3980	3.6	1	16	dbSNP_129	26	1,8597		0,1,4298	yes	missense	ABCC6	NM_001171.5	98	0,52,6444	TT,TC,CC		0.0116,1.1607,0.4002	probably-damaging	1327/1504	16248791	52,12940	2197	4299	6496	SO:0001583	missense	368	exon28			GGGACCCCGTCGA	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.3980G>A	16.37:g.16248791C>T	ENSP00000205557:p.Gly1327Glu	115	0	0		108	58	0.537037	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	CCDS10568.1	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	C	18.13	3.554991	0.65425	0.011607	1.16E-4	ENSG00000091262	ENST00000205557;ENST00000205558	D	0.92149	-2.98	4.53	3.57	0.40892	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.47852	U	0.000212	D	0.90232	0.6946	M	0.84773	2.715	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90118	0.4197	10	0.62326	D	0.03	.	12.2401	0.54538	0.0:0.9153:0.0:0.0847	rs57695665	1327;1327	O95255;A8Y988	MRP6_HUMAN;.	E	1327;265	ENSP00000205557:G1327E	ENSP00000205557:G1327E	G	-	2	0	ABCC6	16156292	0.891000	0.30450	0.957000	0.39632	0.594000	0.36715	2.702000	0.47102	0.901000	0.36495	0.465000	0.42564	GGG	C|0.994;T|0.006	0.006	strong		0.672	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2			T	16248791	C	T	16248791	3	4	22	1	0	0	0	0	1	0	0	0	57	623	22	2	547	2	ABCC6	16	16248791	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	18364	16248791	74105962	3199	6100											
ABCC6	368	hgsc.bcm.edu	37	chr16	16259497	16259497	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tacctgaaacccagcgtagaGgagaaacagtggcaggatgg	14	5	14	8	1	0	3	0	1	0	2	0	5	0	4	2	4	4	2	2	4	4	2	rs60707953	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:16259497G>T	ENST00000205557.7	-	23	3318	c.3289C>A	c.(3289-3291)Ctc>Atc	p.L1097I		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1097	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.		L -> I (in dbSNP:rs60707953).		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)	CCAGCGTAGAGGAGAAACAGT	0.612													G|||	38	0.00758786	0.0242	0.0058	5008	,	,		17411	0.0		0.002	False		,,,				2504	0.0				p.L1097I		Atlas-SNP	.											.	ABCC6	110	.	0			c.C3289A						PASS	.	G	ILE/LEU	94,4300	71.4+/-109.4	1,92,2104	58	51	54		3289	-0.2	0.9	16	dbSNP_129	54	7,8591	4.3+/-15.6	0,7,4292	yes	missense	ABCC6	NM_001171.5	5	1,99,6396	TT,TG,GG		0.0814,2.1393,0.7774	benign	1097/1504	16259497	101,12891	2197	4299	6496	SO:0001583	missense	368	exon23			CGTAGAGGAGAAA	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.3289C>A	16.37:g.16259497G>T	ENSP00000205557:p.Leu1097Ile	88	0	0		84	38	0.452381	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	CCDS10568.1	14	0.00641025641025641	13	0.026422764227642278	1	0.0027624309392265192	0	0.0	0	0.0	G	8.586	0.883526	0.17467	0.021393	8.14E-4	ENSG00000091262	ENST00000205557	D	0.89681	-2.55	5.38	-0.254	0.12992	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.180137	0.27482	U	0.019165	T	0.63367	0.2505	L	0.33710	1.025	0.80722	D	1	D	0.53619	0.961	P	0.48089	0.566	T	0.68205	-0.5470	10	0.20519	T	0.43	.	5.9149	0.19050	0.3303:0.2203:0.4494:0.0	rs60707953;rs61731991	1097	O95255	MRP6_HUMAN	I	1097	ENSP00000205557:L1097I	ENSP00000205557:L1097I	L	-	1	0	ABCC6	16166998	0.280000	0.24249	0.932000	0.37286	0.098000	0.18820	0.223000	0.17719	0.247000	0.21414	0.561000	0.74099	CTC	G|0.992;T|0.008	0.008	strong		0.612	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2			T	16259497	G	T	16259497	3	4	22	1	0	0	0	0	1	0	0	0	57	1000	35	4	1258	4	ABCC6	16	16259497	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	10706	16259497	74095256	3200	6101											
XYLT1	64131	hgsc.bcm.edu	37	chr16	17353090	17353090	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cgtggctgctgttggctgcgGctctgtccccgggaggcagc	2	9	17	13	3	1	0	0	0	1	0	2	1	2	1	2	5	3	6	2	5	0	1	rs113276942	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:17353090G>C	ENST00000261381.6	-	3	752	c.668C>G	c.(667-669)gCc>gGc	p.A223G		NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	223					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						GTTGGCTGCGGCTCTGTCCCC	0.592													G|||	265	0.0529153	0.1914	0.0173	5008	,	,		17039	0.0		0.0	False		,,,				2504	0.0				p.A223G		Atlas-SNP	.											XYLT1,NS,carcinoma,+1,1	XYLT1	147	1	0			c.C668G						PASS	.	G	GLY/ALA	697,3697	288.1+/-279.7	67,563,1567	106	117	113		668	4.5	0	16	dbSNP_132	113	19,8581	11.2+/-40.8	0,19,4281	yes	missense	XYLT1	NM_022166.3	60	67,582,5848	CC,CG,GG		0.2209,15.8625,5.5102	benign	223/960	17353090	716,12278	2197	4300	6497	SO:0001583	missense	64131	exon3			GCTGCGGCTCTGT	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.668C>G	16.37:g.17353090G>C	ENSP00000261381:p.Ala223Gly	143	0	0		197	110	0.558376	NM_022166	Q9H1B6	Missense_Mutation	SNP	ENST00000261381.6	37	CCDS10569.1	89	0.04075091575091575	81	0.16463414634146342	8	0.022099447513812154	0	0.0	0	0.0	G	9.870	1.198774	0.22121	0.158625	0.002209	ENSG00000103489	ENST00000261381	T	0.04809	3.55	5.43	4.47	0.54385	.	0.429861	0.27500	N	0.019098	T	0.00039	0.0001	L	0.44542	1.39	0.09310	N	1	B	0.32245	0.361	B	0.19148	0.024	T	0.49021	-0.8982	10	0.31617	T	0.26	-19.7884	11.4244	0.50001	0.1501:0.0:0.8499:0.0	.	223	Q86Y38	XYLT1_HUMAN	G	223	ENSP00000261381:A223G	ENSP00000261381:A223G	A	-	2	0	XYLT1	17260591	0.015000	0.18098	0.011000	0.14972	0.446000	0.32137	1.886000	0.39688	1.296000	0.44742	0.655000	0.94253	GCC	G|0.950;C|0.050	0.050	strong		0.592	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166		C	17353090	G	C	17353090	3	2	22	1	0	0	0	0	1	0	0	0	17478	1203	42	4	2251	4	XYLT1	16	17353090	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1093593	17353090	73001663	3201	6102											
ITPRIPL2	162073	hgsc.bcm.edu	37	chr16	19126492	19126492	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaccctttgctgatgccttcTgcgtggatgtgcgcgggcgg	4	11	15	11	4	1	1	0	1	1	0	1	2	1	2	2	3	5	1	2	3	1	2	rs8051801	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:19126492T>A	ENST00000381440.3	+	1	1239	c.709T>A	c.(709-711)Tgc>Agc	p.C237S	CTD-2349B8.1_ENST00000564808.2_Intron	NM_001034841.3	NP_001030013.1	Q3MIP1	IPIL2_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein-like 2	237			C -> S (in dbSNP:rs8051801).			integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						TGATGCCTTCTGCGTGGATGT	0.657											OREG0023657	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	43	0.00858626	0.0325	0.0	5008	,	,		17049	0.0		0.0	False		,,,				2504	0.0				p.C237S		Atlas-SNP	.											.	ITPRIPL2	40	.	0			c.T709A						PASS	.	T	SER/CYS	146,4248	100.7+/-139.4	3,140,2054	74	78	77		709	4.7	1	16	dbSNP_116	77	0,8600		0,0,4300	yes	missense	ITPRIPL2	NM_001034841.3	112	3,140,6354	AA,AT,TT		0.0,3.3227,1.1236	probably-damaging	237/536	19126492	146,12848	2197	4300	6497	SO:0001583	missense	162073	exon1			GCCTTCTGCGTGG		CCDS32395.1	16p12.3	2011-04-28	2011-04-28		ENSG00000205730	ENSG00000205730			27257	protein-coding gene	gene with protein product			"inositol 1,4,5-triphosphate receptor interacting protein-like 2"				Standard	NM_001034841		Approved	FLJ22994, MGC126798, MGC126800, LOC162073	uc002dfu.4	Q3MIP1		ENST00000381440.3:c.709T>A	16.37:g.19126492T>A	ENSP00000370849:p.Cys237Ser	86	0	0	730	85	36	0.423529	NM_001034841		Missense_Mutation	SNP	ENST00000381440.3	37	CCDS32395.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	T	22.2	4.253591	0.80135	0.033227	0.0	ENSG00000205730	ENST00000381440	T	0.16597	2.33	4.71	4.71	0.59529	.	0.382932	0.21183	U	0.078791	T	0.10895	0.0266	L	0.27053	0.805	0.46521	D	0.999086	D	0.71674	0.998	D	0.78314	0.991	T	0.01452	-1.1351	10	0.72032	D	0.01	-13.7638	13.3495	0.60593	0.0:0.0:0.0:1.0	rs8051801;rs8051801	237	Q3MIP1	IPIL2_HUMAN	S	237	ENSP00000370849:C237S	ENSP00000370849:C237S	C	+	1	0	ITPRIPL2	19033993	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.264000	0.58859	1.743000	0.51761	0.533000	0.62120	TGC	T|0.989;A|0.011	0.011	strong		0.657	ITPRIPL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435827.3	NM_001034841		A	19126492	T	A	19126492	3	1	22	1	0	0	0	0	1	0	0	0	7934	1580	55	5	711	5	ITPRIPL2	16	19126492	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1773402	19126492	71228261	3202	6103											
ITPRIPL2	162073	hgsc.bcm.edu	37	chr16	19126578	19126578	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcagcgctccttggccacTgtgcgttacagcctggaggg	5	9	14	13	2	0	0	0	0	0	0	1	1	1	1	3	3	5	3	3	3	1	2	rs114869688	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:19126578T>C	ENST00000381440.3	+	1	1325	c.795T>C	c.(793-795)acT>acC	p.T265T	CTD-2349B8.1_ENST00000564808.2_Intron	NM_001034841.3	NP_001030013.1	Q3MIP1	IPIL2_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein-like 2	265						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						CCTTGGCCACTGTGCGTTACA	0.642											OREG0023657	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	16	0.00319489	0.0121	0.0	5008	,	,		17325	0.0		0.0	False		,,,				2504	0.0				p.T265T		Atlas-SNP	.											ITPRIPL2,colon,carcinoma,+1,1	ITPRIPL2	40	1	0			c.T795C						PASS	.	T		72,4322	63.5+/-100.7	0,72,2125	94	95	95		795	-9.6	0.3	16	dbSNP_132	95	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ITPRIPL2	NM_001034841.3		0,73,6424	CC,CT,TT		0.0116,1.6386,0.5618		265/536	19126578	73,12921	2197	4300	6497	SO:0001819	synonymous_variant	162073	exon1			GGCCACTGTGCGT		CCDS32395.1	16p12.3	2011-04-28	2011-04-28		ENSG00000205730	ENSG00000205730			27257	protein-coding gene	gene with protein product			"inositol 1,4,5-triphosphate receptor interacting protein-like 2"				Standard	NM_001034841		Approved	FLJ22994, MGC126798, MGC126800, LOC162073	uc002dfu.4	Q3MIP1		ENST00000381440.3:c.795T>C	16.37:g.19126578T>C		106	0	0	730	88	38	0.431818	NM_001034841		Silent	SNP	ENST00000381440.3	37	CCDS32395.1																																																																																			T|0.995;C|0.005	0.005	strong		0.642	ITPRIPL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435827.3	NM_001034841		C	19126578	T	C	19126578	2	2	22	1	0	0	0	0	0	0	0	1	7934	1567	55	3		3	ITPRIPL2	16	19126578	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	86	19126578	71228175	3203	6104											
C16orf62	57020	hgsc.bcm.edu	37	chr16	19590444	19590444	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggaggagctggatgacttTgaggaggtgagcaagtcatt	10	10	16	5	0	1	3	1	3	0	0	1	7	1	7	0	5	2	2	0	5	1	2	rs11866050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:19590444T>C	ENST00000251143.5	+	6	516	c.504T>C	c.(502-504)ttT>ttC	p.F168F	C16orf62_ENST00000448695.1_Silent_p.F46F|C16orf62_ENST00000543152.1_5'UTR|C16orf62_ENST00000542263.1_Silent_p.F257F|C16orf62_ENST00000438132.3_Silent_p.F257F|C16orf62_ENST00000417362.2_Silent_p.F168F|C16orf62_ENST00000538853.1_3'UTR			Q7Z3J2	CP062_HUMAN	chromosome 16 open reading frame 62	168				F -> S (in Ref. 3; CAH10399). {ECO:0000305}.		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						TGGATGACTTTGAGGAGGTGA	0.502													T|||	359	0.0716853	0.2057	0.0144	5008	,	,		18705	0.0337		0.0209	False		,,,				2504	0.0225				p.F257F		Atlas-SNP	.											.	C16orf62	164	.	0			c.T771C						PASS	.	T		633,3761	272.8+/-271.0	34,565,1598	94	83	87		771	-1.1	1	16	dbSNP_120	87	152,8448	72.3+/-134.9	0,152,4148	no	coding-synonymous	C16orf62	NM_020314.5		34,717,5746	CC,CT,TT		1.7674,14.406,6.0412		257/1053	19590444	785,12209	2197	4300	6497	SO:0001819	synonymous_variant	57020	exon6			TGACTTTGAGGAG		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.504T>C	16.37:g.19590444T>C		95	0	0		108	61	0.564815	NM_020314	A8K2M1|O43329|Q69YI1|Q6PDA0|Q7L371|Q86W66|Q8WXA5|Q9H0L7|Q9H7C8	Silent	SNP	ENST00000251143.5	37																																																																																				T|0.937;C|0.063	0.063	strong		0.502	C16orf62-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_020314		C	19590444	T	C	19590444	2	2	22	1	0	0	0	0	0	0	0	1	1827	1809	63	3		3	C16orf62	16	19590444	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	463866	19590444	70764309	3204	6105											
C16orf88	400506	hgsc.bcm.edu	37	chr16	19726124	19726124	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcaggttctacatgctcctcGcaaagggtgctgacaccctt	8	11	9	13	1	2	1	1	1	1	0	4	1	3	1	2	2	3	4	2	2	2	3	rs58543897	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:19726124G>A	ENST00000219837.7	-	2	312	c.234C>T	c.(232-234)tgC>tgT	p.C78C	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	78	Lys-rich.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)										CATGCTCCTCGCAAAGGGTGC	0.542													G|||	271	0.0541134	0.1906	0.0245	5008	,	,		18472	0.0		0.002	False		,,,				2504	0.0				p.C78C		Atlas-SNP	.											.	C16orf88	41	.	0			c.C234T						PASS	.	G		700,3352		55,590,1381	65	64	64		234	-9.2	0	16	dbSNP_129	64	22,8366		0,22,4172	no	coding-synonymous	C16orf88	NM_001012991.2		55,612,5553	AA,AG,GG		0.2623,17.2754,5.8039		78/459	19726124	722,11718	2026	4194	6220	SO:0001819	synonymous_variant	400506	exon2			CTCCTCGCAAAGG	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.234C>T	16.37:g.19726124G>A		91	0	0		107	54	0.504673	NM_001012991	O43328|Q5FWF3	Silent	SNP	ENST00000219837.7	37	CCDS42127.1																																																																																			G|0.972;A|0.028	0.028	strong		0.542	KNOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435993.2	NM_001012991		A	19726124	G	A	19726124	2	1	22	1	0	0	0	0	0	0	0	1	1843	1079	38	1		1	C16orf88	16	19726124	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	135680	19726124	70628629	3205	6106											
ACSM2A	123876	hgsc.bcm.edu	37	chr16	20471487	20471487	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgcaccctgtggggtactcaGatgtccagccgcactctcta	7	10	10	14	1	2	1	1	0	1	1	4	1	3	1	3	2	3	3	3	2	2	2	rs137947890	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:20471487G>C	ENST00000573854.1	+	2	165	c.51G>C	c.(49-51)caG>caC	p.Q17H	ACSM2A_ENST00000575690.1_Missense_Mutation_p.Q17H|ACSM2A_ENST00000396104.2_Missense_Mutation_p.Q17H|ACSM2A_ENST00000417235.2_Intron|ACSM2A_ENST00000424070.1_Missense_Mutation_p.Q17H|ACSM2A_ENST00000219054.6_Missense_Mutation_p.Q17H|ACSM2A_ENST00000536134.1_5'UTR|ACSM2A_ENST00000575558.1_Intron	NM_001010845.2	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member 2A	17					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						GGGGTACTCAGATGTCCAGCC	0.493													G|||	85	0.0169728	0.0635	0.0014	5008	,	,		18245	0.0		0.0	False		,,,				2504	0.0				p.Q17H		Atlas-SNP	.											.	ACSM2A	120	.	0			c.G51C						PASS	.	G	HIS/GLN	220,4186	133.7+/-170.0	8,204,1991	46	48	47		51	1	0	16	dbSNP_134	47	5,8589	4.3+/-15.6	0,5,4292	no	missense	ACSM2A	NM_001010845.2	24	8,209,6283	CC,CG,GG		0.0582,4.9932,1.7308	benign	17/578	20471487	225,12775	2203	4297	6500	SO:0001583	missense	123876	exon3			TACTCAGATGTCC	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.51G>C	16.37:g.20471487G>C	ENSP00000459451:p.Gln17His	124	0	0		120	68	0.566667	NM_001010845	B3KTT9|O75202	Missense_Mutation	SNP	ENST00000573854.1	37	CCDS32401.1	30	0.013736263736263736	29	0.05894308943089431	0	0.0	0	0.0	1	0.0013192612137203166	G	7.282	0.609329	0.14066	0.049932	5.82E-4	ENSG00000183747	ENST00000219054;ENST00000424070;ENST00000396104	T;T;T	0.43688	0.94;2.24;0.94	3.28	1.03	0.20045	.	0.746597	0.11304	N	0.577908	T	0.02380	0.0073	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.15407	-1.0438	10	0.14252	T	0.57	-4.0391	5.9796	0.19399	0.1217:0.1954:0.6829:0.0	.	17	Q08AH3	ACS2A_HUMAN	H	17	ENSP00000219054:Q17H;ENSP00000394904:Q17H;ENSP00000379411:Q17H	ENSP00000219054:Q17H	Q	+	3	2	ACSM2A	20378988	0.000000	0.05858	0.001000	0.08648	0.661000	0.39034	0.388000	0.20735	0.709000	0.31976	0.454000	0.30748	CAG	.	.	weak		0.493	ACSM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436764.1	NM_001010845		C	20471487	G	C	20471487	3	2	22	1	0	0	0	0	1	0	0	0	183	933	33	4	53	4	ACSM2A	16	20471487	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	745363	20471487	69883266	3206	6107											
ACSM2A	123876	hgsc.bcm.edu	37	chr16	20476974	20476974	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgggagcctgtggcctgcagCgtggggatcgtgtggcagtg	4	8	20	9	3	0	0	0	0	0	0	1	2	0	2	2	5	3	2	2	5	0	0	rs13332099	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:20476974C>T	ENST00000573854.1	+	3	427	c.313C>T	c.(313-315)Cgt>Tgt	p.R105C	ACSM2A_ENST00000575690.1_Missense_Mutation_p.R105C|ACSM2A_ENST00000396104.2_Missense_Mutation_p.R105C|ACSM2A_ENST00000417235.2_Missense_Mutation_p.R26C|ACSM2A_ENST00000424070.1_Missense_Mutation_p.R105C|ACSM2A_ENST00000219054.6_Missense_Mutation_p.R105C|ACSM2A_ENST00000536134.1_5'UTR|ACSM2A_ENST00000575558.1_3'UTR	NM_001010845.2	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member 2A	105					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)	p.R105G(1)		breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(34)|ovary(1)|skin(6)|stomach(1)	51						TGGCCTGCAGCGTGGGGATCG	0.577													C|||	31	0.0061901	0.0212	0.0029	5008	,	,		20999	0.0		0.0	False		,,,				2504	0.001				p.R105C		Atlas-SNP	.											ACSM2A,NS,carcinoma,-2,1	ACSM2A	120	1	1	Substitution - Missense(1)	lung(1)	c.C313T						PASS	.	C	CYS/ARG	79,4327	68.1+/-105.8	1,77,2125	121	101	108		313	2.8	1	16	dbSNP_121	108	0,8600		0,0,4300	no	missense	ACSM2A	NM_001010845.2	180	1,77,6425	TT,TC,CC		0.0,1.793,0.6074	benign	105/578	20476974	79,12927	2203	4300	6503	SO:0001583	missense	123876	exon4			CTGCAGCGTGGGG	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.313C>T	16.37:g.20476974C>T	ENSP00000459451:p.Arg105Cys	502	0	0		521	179	0.34357	NM_001010845	B3KTT9|O75202	Missense_Mutation	SNP	ENST00000573854.1	37	CCDS32401.1	14	0.00641025641025641	13	0.026422764227642278	1	0.0027624309392265192	0	0.0	0	0.0	C	11.81	1.750666	0.31046	0.01793	0.0	ENSG00000183747	ENST00000417235;ENST00000219054;ENST00000424070;ENST00000396104	T;T;T;T	0.52295	0.67;0.67;0.67;0.67	3.76	2.79	0.32731	AMP-dependent synthetase/ligase (1);	0.189594	0.27262	N	0.020171	T	0.19967	0.0480	M	0.84326	2.69	0.30993	N	0.721168	P;P	0.37636	0.485;0.603	B;B	0.28916	0.096;0.096	T	0.46569	-0.9182	10	0.56958	D	0.05	-6.0087	6.554	0.22450	0.1772:0.7202:0.0:0.1026	rs13332099	26;105	B7Z8R0;Q08AH3	.;ACS2A_HUMAN	C	26;105;105;105	ENSP00000392169:R26C;ENSP00000219054:R105C;ENSP00000394904:R105C;ENSP00000379411:R105C	ENSP00000219054:R105C	R	+	1	0	ACSM2A	20384475	0.515000	0.26210	0.989000	0.46669	0.734000	0.41952	1.158000	0.31737	0.694000	0.31654	0.298000	0.19748	CGT	C|0.993;T|0.007	0.007	strong		0.577	ACSM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436764.1	NM_001010845		T	20476974	C	T	20476974	3	4	22	1	0	0	0	0	1	0	0	0	183	768	27	1	319	1	ACSM2A	16	20476974	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	5487	20476974	69877779	3207	6108											
ERI2	112479	hgsc.bcm.edu	37	chr16	20809240	20809240	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acaacattttctgttttcttGgtatttcccgatagggcaac	9	16	7	9	1	2	0	0	0	2	0	3	1	3	0	1	2	2	3	1	2	4	8	rs61746707	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:20809240G>T	ENST00000357967.4	-	9	1924	c.1882C>A	c.(1882-1884)Caa>Aaa	p.Q628K	ERI2_ENST00000569729.1_3'UTR|ERI2_ENST00000563117.1_Missense_Mutation_p.Q535K|ERI2_ENST00000300005.3_Intron|ERI2_ENST00000389345.5_Missense_Mutation_p.Q363K|ERI2_ENST00000564349.1_Missense_Mutation_p.Q535K	NM_001142725.1	NP_001136197.1	A8K979	ERI2_HUMAN	ERI1 exoribonuclease family member 2	628							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						CTGTTTTCTTGGTATTTCCCG	0.413													G|||	74	0.0147764	0.0545	0.0014	5008	,	,		17542	0.0		0.001	False		,,,				2504	0.0				p.Q628K		Atlas-SNP	.											.	ERI2	50	.	0			c.C1882A						PASS	.	G	LYS/GLN,	53,1331		1,51,640	115	94	100		1882,	3.4	1	16	dbSNP_129	100	0,3182		0,0,1591	no	missense,intron	ERI2	NM_001142725.1,NM_080663.2	53,	1,51,2231	TT,TG,GG		0.0,3.8295,1.1608	benign,	628/692,	20809240	53,4513	692	1591	2283	SO:0001583	missense	112479	exon9			TTTCTTGGTATTT	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.1882C>A	16.37:g.20809240G>T	ENSP00000350651:p.Gln628Lys	189	0	0		248	114	0.459677	NM_001142725	Q6ZSJ2|Q96FR9|Q9P224|Q9Y6V3	Missense_Mutation	SNP	ENST00000357967.4	37	CCDS45436.1	28	0.01282051282051282	28	0.056910569105691054	0	0.0	0	0.0	0	0.0	G	9.624	1.134740	0.21123	0.038295	0.0	ENSG00000196678	ENST00000357967;ENST00000389345	T;T	0.18338	2.26;2.22	5.57	3.44	0.39384	Zinc finger, GRF-type (1);	0.400221	0.26349	N	0.024900	T	0.01029	0.0034	N	0.25245	0.725	0.23204	N	0.99813	B	0.17465	0.022	B	0.15052	0.012	T	0.21586	-1.0241	10	0.33940	T	0.23	-3.6176	8.303	0.32025	0.0:0.2738:0.4857:0.2405	.	628	A8K979	ERI2_HUMAN	K	628;363	ENSP00000350651:Q628K;ENSP00000373996:Q363K	ENSP00000350651:Q628K	Q	-	1	0	ERI2	20716741	0.998000	0.40836	1.000000	0.80357	0.562000	0.35680	2.069000	0.41481	1.450000	0.47717	0.591000	0.81541	CAA	G|0.987;T|0.013	0.013	strong		0.413	ERI2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_080663		T	20809240	G	T	20809240	3	4	22	1	0	0	0	0	1	0	0	0	5230	1357	47	4	464	4	ERI2	16	20809240	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	332266	20809240	69545513	3208	6109											
DNAH3	55567	hgsc.bcm.edu	37	chr16	20996868	20996868	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggacatgggggccttgctgAtgttgttgaattcttccaga	7	13	14	7	0	1	3	0	2	1	1	2	4	2	4	2	3	1	3	2	3	1	5	rs34179606	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:20996868A>T	ENST00000261383.3	-	48	7195	c.7196T>A	c.(7195-7197)aTc>aAc	p.I2399N	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	2399	AAA 4. {ECO:0000250}.		I -> N (in dbSNP:rs34179606).		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)		GGCCTTGCTGATGTTGTTGAA	0.488													A|||	67	0.0133786	0.0507	0.0	5008	,	,		20170	0.0		0.0	False		,,,				2504	0.0				p.I2399N		Atlas-SNP	.											.	DNAH3	1142	.	0			c.T7196A						PASS	.	A	ASN/ILE	139,4263	98.9+/-137.6	2,135,2064	142	122	129		7196	4.8	1	16	dbSNP_126	129	3,8597	3.0+/-9.4	0,3,4297	yes	missense	DNAH3	NM_017539.1	149	2,138,6361	TT,TA,AA		0.0349,3.1577,1.0921	benign	2399/4117	20996868	142,12860	2201	4300	6501	SO:0001583	missense	55567	exon48			TTGCTGATGTTGT	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.7196T>A	16.37:g.20996868A>T	ENSP00000261383:p.Ile2399Asn	79	0	0		66	35	0.530303	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	A	12.96	2.093349	0.36952	0.031577	3.49E-4	ENSG00000158486	ENST00000261383	T	0.22945	1.93	4.79	4.79	0.61399	.	0.272346	0.29438	N	0.012143	T	0.06645	0.0170	L	0.48174	1.505	0.80722	D	1	P	0.39480	0.675	B	0.42343	0.384	T	0.00920	-1.1514	10	0.39692	T	0.17	.	10.7686	0.46308	0.9222:0.0:0.0778:0.0	rs34179606	2399	Q8TD57	DYH3_HUMAN	N	2399	ENSP00000261383:I2399N	ENSP00000261383:I2399N	I	-	2	0	DNAH3	20904369	0.994000	0.37717	0.975000	0.42487	0.937000	0.57800	2.961000	0.49168	1.930000	0.55929	0.533000	0.62120	ATC	A|0.989;T|0.011	0.011	strong		0.488	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		T	20996868	A	T	20996868	3	4	22	1	0	0	0	0	1	0	0	0	4605	333	12	5	5213	5	DNAH3	16	20996868	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	187628	20996868	69357885	3209	6110											
DNAH3	55567	hgsc.bcm.edu	37	chr16	21042391	21042391	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttattgtcatccagaacagtGttcatattttcaatccaaat	13	16	4	8	0	3	1	3	0	0	1	5	1	5	1	2	0	1	1	2	0	5	6	rs114086288	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:21042391G>A	ENST00000261383.3	-	37	5414	c.5415C>T	c.(5413-5415)aaC>aaT	p.N1805N	DNAH3_ENST00000415178.1_Silent_p.N1805N	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1805	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)|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)		CCAGAACAGTGTTCATATTTT	0.378													G|||	55	0.0109824	0.0401	0.0014	5008	,	,		20518	0.0		0.001	False		,,,				2504	0.0				p.N1805N		Atlas-SNP	.											.	DNAH3	1142	.	0			c.C5415T						PASS	.	G		133,4269	96.7+/-135.4	3,127,2071	103	96	98		5415	4.7	1	16	dbSNP_132	98	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DNAH3	NM_017539.1		3,128,6370	AA,AG,GG		0.0116,3.0214,1.0306		1805/4117	21042391	134,12868	2201	4300	6501	SO:0001819	synonymous_variant	55567	exon37			AACAGTGTTCATA	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.5415C>T	16.37:g.21042391G>A		114	0	0		103	55	0.533981	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	37	CCDS10594.1																																																																																			G|0.989;A|0.011	0.011	strong		0.378	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		A	21042391	G	A	21042391	2	1	22	1	0	0	0	0	0	0	0	1	4605	1368	48	2		2	DNAH3	16	21042391	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	45523	21042391	69312362	3210	6111											
DNAH3	55567	hgsc.bcm.edu	37	chr16	21049286	21049286	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcacaggcggtaggtcgcaaCgatcttctgggcgagactag	9	7	15	10	4	2	1	0	0	2	1	3	3	2	1	0	4	1	3	0	4	3	3	rs16970832	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:21049286C>T	ENST00000261383.3	-	34	4746	c.4747G>A	c.(4747-4749)Gtt>Att	p.V1583I	DNAH3_ENST00000415178.1_Missense_Mutation_p.V1583I	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1583	AAA 1. {ECO:0000250}.		V -> I (in dbSNP:rs16970832).		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)		TAGGTCGCAACGATCTTCTGG	0.547													C|||	248	0.0495208	0.1808	0.0101	5008	,	,		21358	0.0		0.002	False		,,,				2504	0.0				p.V1583I		Atlas-SNP	.											.	DNAH3	1142	.	0			c.G4747A						PASS	.	C	ILE/VAL	675,3727	286.9+/-279.0	56,563,1582	88	66	74		4747	5.8	1	16	dbSNP_123	74	7,8593	3.7+/-12.6	0,7,4293	yes	missense	DNAH3	NM_017539.1	29	56,570,5875	TT,TC,CC		0.0814,15.3339,5.2453	probably-damaging	1583/4117	21049286	682,12320	2201	4300	6501	SO:0001583	missense	55567	exon34			TCGCAACGATCTT	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.4747G>A	16.37:g.21049286C>T	ENSP00000261383:p.Val1583Ile	88	0	0		96	60	0.625	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	79	0.036172161172161175	77	0.1565040650406504	2	0.0055248618784530384	0	0.0	0	0.0	C	32	5.164216	0.94727	0.153339	8.14E-4	ENSG00000158486	ENST00000261383;ENST00000415178	T;T	0.06608	3.28;3.28	5.76	5.76	0.90799	.	0.000000	0.64402	D	0.000001	T	0.00109	0.0003	M	0.82056	2.57	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.00076	-1.2118	10	0.36615	T	0.2	.	19.9616	0.97254	0.0:1.0:0.0:0.0	rs16970832;rs56565035;rs16970832	1583	Q8TD57	DYH3_HUMAN	I	1583	ENSP00000261383:V1583I;ENSP00000394245:V1583I	ENSP00000261383:V1583I	V	-	1	0	DNAH3	20956787	1.000000	0.71417	0.998000	0.56505	0.731000	0.41821	7.764000	0.85297	2.724000	0.93272	0.561000	0.74099	GTT	C|0.944;T|0.056	0.056	strong		0.547	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		T	21049286	C	T	21049286	3	4	22	1	0	0	0	0	1	0	0	0	4605	536	19	1	7718	1	DNAH3	16	21049286	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6895	21049286	69305467	3211	6112											
HS3ST2	9956	hgsc.bcm.edu	37	chr16	22826321	22826321	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaggggggcacccgggccgtGctggagtttatccgagtaca	8	7	16	10	3	0	0	0	0	0	0	1	2	1	1	3	5	2	4	3	5	3	3	rs111703383	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:22826321G>A	ENST00000261374.3	+	1	824	c.390G>A	c.(388-390)gtG>gtA	p.V130V		NM_006043.1	NP_006034.1	Q9Y278	HS3S2_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 2	130					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)		CCCGGGCCGTGCTGGAGTTTA	0.637													G|||	271	0.0541134	0.1959	0.0173	5008	,	,		13590	0.0		0.0	False		,,,				2504	0.0				p.V130V		Atlas-SNP	.											.	HS3ST2	59	.	0			c.G390A						PASS	.	G		724,3626		47,630,1498	15	19	17		390	4.1	1	16	dbSNP_132	17	4,8560		0,4,4278	no	coding-synonymous	HS3ST2	NM_006043.1		47,634,5776	AA,AG,GG		0.0467,16.6437,5.6373		130/368	22826321	728,12186	2175	4282	6457	SO:0001819	synonymous_variant	9956	exon1			GGCCGTGCTGGAG	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.390G>A	16.37:g.22826321G>A		106	0	0		94	94	1	NM_006043	Q52LZ1	Silent	SNP	ENST00000261374.3	37	CCDS10606.1																																																																																			G|0.949;A|0.051	0.051	strong		0.637	HS3ST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211598.1	NM_006043		A	22826321	G	A	22826321	2	1	22	1	0	0	0	0	0	0	0	1	7373	1306	46	2		2	HS3ST2	16	22826321	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1777035	22826321	67528432	3212	6113											
COG7	91949	hgsc.bcm.edu	37	chr16	23403744	23403744	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagagtgtgggctcagctcAgggatctgtaggatcgcatc	8	9	15	9	1	3	1	2	0	1	1	5	3	3	3	0	3	1	5	0	3	1	1	rs8057712	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:23403744A>G	ENST00000307149.5	-	16	2288	c.2103T>C	c.(2101-2103)ccT>ccC	p.P701P	COG7_ENST00000569635.1_Intron	NM_153603.3	NP_705831.1	P83436	COG7_HUMAN	component of oligomeric golgi complex 7	701					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)		GGCTCAGCTCAGGGATCTGTA	0.597													G|||	540	0.107827	0.2625	0.1268	5008	,	,		18783	0.0169		0.0258	False		,,,				2504	0.0634				p.P701P		Atlas-SNP	.											COG7,NS,malignant_melanoma,-2,1	COG7	62	1	0			c.T2103C						PASS	.	G		947,3447	733.6+/-410.5	98,751,1348	107	92	97		2103	-11	0.3	16	dbSNP_116	97	254,8346	807.9+/-407.2	4,246,4050	no	coding-synonymous	COG7	NM_153603.3		102,997,5398	GG,GA,AA		2.9535,21.5521,9.2427		701/771	23403744	1201,11793	2197	4300	6497	SO:0001819	synonymous_variant	91949	exon16			CAGCTCAGGGATC	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.2103T>C	16.37:g.23403744A>G		127	0	0		132	59	0.44697	NM_153603	Q6UWU7	Silent	SNP	ENST00000307149.5	37	CCDS10610.1																																																																																			A|0.910;G|0.090	0.090	strong		0.597	COG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211625.1			G	23403744	A	G	23403744	2	3	22	1	0	0	0	0	0	0	0	1	3665	175	7	3		3	COG7	16	23403744	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	577423	23403744	66951009	3213	6114											
COG7	91949	hgsc.bcm.edu	37	chr16	23409440	23409440	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggtttctccgatgccagccGtattccagctctaagggtgg	6	11	13	11	2	2	0	0	0	2	0	4	1	3	0	4	3	3	3	4	3	2	4	rs16940094	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:23409440G>A	ENST00000307149.5	-	14	1999	c.1814C>T	c.(1813-1815)aCg>aTg	p.T605M		NM_153603.3	NP_705831.1	P83436	COG7_HUMAN	component of oligomeric golgi complex 7	605			T -> M (in dbSNP:rs16940094).		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)		GATGCCAGCCGTATTCCAGCT	0.532													G|||	441	0.0880591	0.1861	0.1239	5008	,	,		19099	0.0169		0.0258	False		,,,				2504	0.0675				p.T605M		Atlas-SNP	.											.	COG7	62	.	0			c.C1814T						PASS	.	G	MET/THR	681,3713	286.9+/-279.0	50,581,1566	122	98	106		1814	3.7	0.7	16	dbSNP_123	106	257,8343	101.4+/-162.7	4,249,4047	yes	missense	COG7	NM_153603.3	81	54,830,5613	AA,AG,GG		2.9884,15.4984,7.2187	possibly-damaging	605/771	23409440	938,12056	2197	4300	6497	SO:0001583	missense	91949	exon14			CCAGCCGTATTCC	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.1814C>T	16.37:g.23409440G>A	ENSP00000305442:p.Thr605Met	125	0	0		150	87	0.58	NM_153603	Q6UWU7	Missense_Mutation	SNP	ENST00000307149.5	37	CCDS10610.1	136	0.06227106227106227	79	0.16056910569105692	28	0.07734806629834254	11	0.019230769230769232	18	0.023746701846965697	G	13.05	2.121490	0.37436	0.154984	0.029884	ENSG00000168434	ENST00000307149	T	0.44881	0.91	5.6	3.67	0.42095	.	0.270197	0.42682	N	0.000671	T	0.00178	0.0005	N	0.24115	0.695	0.34894	P	0.254186	D	0.57571	0.98	P	0.52109	0.69	T	0.05632	-1.0873	9	0.42905	T	0.14	-15.5303	10.0248	0.42066	0.1547:0.0:0.8453:0.0	rs16940094;rs16940094	605	P83436	COG7_HUMAN	M	605	ENSP00000305442:T605M	ENSP00000305442:T605M	T	-	2	0	COG7	23316941	1.000000	0.71417	0.745000	0.31077	0.194000	0.23727	5.583000	0.67484	0.747000	0.32809	-0.742000	0.03525	ACG	G|0.931;A|0.069	0.069	strong		0.532	COG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211625.1			A	23409440	G	A	23409440	3	1	22	1	0	0	0	0	1	0	0	0	3665	1145	40	1	514	1	COG7	16	23409440	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5696	23409440	66945313	3214	6115											
ERN2	10595	hgsc.bcm.edu	37	chr16	23721865	23721865	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtacattggtccttcgatgaCgggatctgcagggacaggga	9	9	15	8	2	1	1	0	1	1	0	3	5	2	4	1	4	2	2	1	4	1	3	rs9932495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:23721865C>T	ENST00000457008.2	-	3	243	c.205G>A	c.(205-207)Gtc>Atc	p.V69I	CTD-2385L22.1_ENST00000563611.1_RNA|ERN2_ENST00000256797.4_Missense_Mutation_p.V117I					endoplasmic reticulum to nucleus signaling 2											large_intestine(2)|lung(2)|ovary(2)	6				GBM - Glioblastoma multiforme(48;0.0156)		CCTTCGATGACGGGATCTGCA	0.507													C|||	104	0.0207668	0.0756	0.0014	5008	,	,		21483	0.0		0.001	False		,,,				2504	0.002				p.V117I		Atlas-SNP	.											.	ERN2	131	.	0			c.G349A						PASS	.	C	ILE/VAL	242,4152	141.1+/-176.5	7,228,1962	206	200	202		349	-3.1	0.4	16	dbSNP_119	202	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ERN2	NM_033266.3	29	7,229,6261	TT,TC,CC		0.0116,5.5075,1.8701	benign	117/975	23721865	243,12751	2197	4300	6497	SO:0001583	missense	10595	exon3			CGATGACGGGATC	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.205G>A	16.37:g.23721865C>T	ENSP00000413812:p.Val69Ile	156	0	0		99	51	0.515152	NM_033266		Missense_Mutation	SNP	ENST00000457008.2	37		31	0.014194139194139194	30	0.06097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	C	5.726	0.318420	0.10845	0.055075	1.16E-4	ENSG00000134398	ENST00000256797;ENST00000457008	T;T	0.21361	2.01;2.01	4.91	-3.07	0.05363	.	0.439897	0.27147	N	0.020713	T	0.00724	0.0024	N	0.05574	-0.02	0.25356	N	0.988828	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.28073	-1.0055	10	0.19147	T	0.46	.	6.6045	0.22718	0.0:0.4318:0.2707:0.2975	rs9932495;rs52791098;rs9932495	69;69	E7ETG2;A5YM65	.;.	I	117;69	ENSP00000256797:V117I;ENSP00000413812:V69I	ENSP00000256797:V117I	V	-	1	0	ERN2	23629366	0.991000	0.36638	0.383000	0.26132	0.543000	0.35085	0.246000	0.18160	-0.855000	0.04125	-0.379000	0.06801	GTC	C|0.981;T|0.019	0.019	strong		0.507	ERN2-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000434886.1			T	23721865	C	T	23721865	3	4	22	1	0	0	0	0	1	0	0	0	5240	536	19	1	2655	1	ERN2	16	23721865	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	312425	23721865	66632888	3215	6116											
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24788401	24788402	+	In_Frame_Ins	INS	-	-	GCA																															cagcagcaacagcagcagccINSgcagcagcagcagccacagc																								rs112426081|rs575176088	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:24788401_24788402insGCA	ENST00000395799.3	+	5	440_441	c.311_312insGCA	c.(310-315)ccgcag>ccGCAgcag	p.108_109insQ	TNRC6A_ENST00000315183.7_In_Frame_Ins_p.108_109insQ	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	108	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)		cagcagcagccgcagcagcagc	0.589														11	0.00219649	0.0083	0.0	5008	,	,		10840	0.0		0.0	False		,,,				2504	0.0				p.P104delinsPQ		Atlas-Indel	.											TNRC6A,NS,carcinoma,0,1	TNRC6A	171	1	0			c.311_312insGCA						PASS	.			43,3543		6,31,1756						-2.9	0		dbSNP_132	22	8,7216		1,6,3605	no	coding	TNRC6A	NM_014494.2		7,37,5361	A1A1,A1R,RR		0.1107,1.1991,0.4718				51,10759				SO:0001652	inframe_insertion	27327	exon5			.	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.321_323dupGCA	16.37:g.24788408_24788410dupGCA	ENSP00000379144:p.Gln111_Gln112dup	48	0	0		55	11	0.2	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	In_Frame_Ins	INS	ENST00000395799.3	37	CCDS10624.2																																																																																			-|0.500;GCA|0.500	0.500	weak		0.589	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		GCA	24788402	-	GCA	24788401	7	5	22	1	0	1	1	0	0	0	0	0	16355	652	23	0	329	0	TNRC6A	16	24788401	In_Frame_Ins	INS	-	TCGA-G8-6324-01A-11D-2210-10	1066536	24788401	65566352	3216	6117											
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24802204	24802204	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaggggaacgaaagactgaCaatgggacagaggcctgggg	14	3	18	6	1	0	4	0	1	0	3	0	7	0	6	1	6	1	0	1	6	3	0	rs113288384		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:24802204C>T	ENST00000395799.3	+	6	2370	c.2241C>T	c.(2239-2241)gaC>gaT	p.D747D	TNRC6A_ENST00000315183.7_Silent_p.D747D	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	747	Interaction with argonaute family proteins.|Sufficient for interaction with AGO1 and AGO4.|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)		GAAAGACTGACAATGGGACAG	0.473													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20045	0.0		0.0	False		,,,				2504	0.0				p.D747D		Atlas-SNP	.											.	TNRC6A	171	.	0			c.C2241T						PASS	.	C		2,4392	4.2+/-10.8	0,2,2195	53	55	55		2241	3.9	1	16	dbSNP_132	55	0,8600		0,0,4300	no	coding-synonymous	TNRC6A	NM_014494.2		0,2,6495	TT,TC,CC		0.0,0.0455,0.0154		747/1963	24802204	2,12992	2197	4300	6497	SO:0001819	synonymous_variant	27327	exon6			GACTGACAATGGG	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.2241C>T	16.37:g.24802204C>T		49	0	0		52	26	0.5	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Silent	SNP	ENST00000395799.3	37	CCDS10624.2																																																																																			C|0.999;T|0.001	0.001	strong		0.473	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		T	24802204	C	T	24802204	2	4	22	1	0	0	0	0	0	0	0	1	16355	477	17	2		2	TNRC6A	16	24802204	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	13803	24802204	65552549	3217	6118											
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24802245	24802245	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagctctgcaacacagacttTtaactcaggggcatgtatag	13	10	9	9	0	2	1	1	0	1	1	2	1	2	1	0	2	4	4	0	2	5	4	rs112027699		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:24802245T>G	ENST00000395799.3	+	6	2411	c.2282T>G	c.(2281-2283)tTt>tGt	p.F761C	TNRC6A_ENST00000315183.7_Missense_Mutation_p.F761C	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	761	Interaction with argonaute family proteins.|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)		ACACAGACTTTTAACTCAGGG	0.488													T|||	1	0.000199681	0.0008	0.0	5008	,	,		19808	0.0		0.0	False		,,,				2504	0.0				p.F761C		Atlas-SNP	.											.	TNRC6A	171	.	0			c.T2282G						PASS	.	T	CYS/PHE	2,4390	2.1+/-5.4	0,2,2194	46	51	50		2282	4.7	1	16	dbSNP_132	50	0,8600		0,0,4300	no	missense	TNRC6A	NM_014494.2	205	0,2,6494	GG,GT,TT		0.0,0.0455,0.0154	benign	761/1963	24802245	2,12990	2196	4300	6496	SO:0001583	missense	27327	exon6			AGACTTTTAACTC	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.2282T>G	16.37:g.24802245T>G	ENSP00000379144:p.Phe761Cys	45	0	0		50	24	0.48	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	37	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	T	9.930	1.214512	0.22289	4.55E-4	0.0	ENSG00000090905	ENST00000315183;ENST00000395799	T;T	0.11495	2.77;2.78	5.82	4.71	0.59529	.	0.329999	0.31859	N	0.006945	T	0.05410	0.0143	N	0.08118	0	0.80722	D	1	P;P;P	0.45078	0.687;0.681;0.85	B;B;B	0.42282	0.382;0.181;0.258	T	0.24440	-1.0160	10	0.56958	D	0.05	-1.2962	3.6846	0.08323	0.0:0.2795:0.0:0.7205	.	508;761;761	Q8NDV7-2;Q8NDV7-6;Q8NDV7	.;.;TNR6A_HUMAN	C	761	ENSP00000326900:F761C;ENSP00000379144:F761C	ENSP00000326900:F761C	F	+	2	0	TNRC6A	24709746	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.281000	0.33214	2.225000	0.72522	0.460000	0.39030	TTT	T|0.999;G|0.001	0.001	strong		0.488	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		G	24802245	T	G	24802245	3	3	22	1	0	0	0	0	1	0	0	0	16355	1841	64	5	2304	5	TNRC6A	16	24802245	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	41	24802245	65552508	3218	6119											
ARHGAP17	55114	hgsc.bcm.edu	37	chr16	24942272	24942272	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtggctgtgcagtttcagggTtaccccctgccagggtctga	5	11	14	11	0	2	1	1	1	1	0	2	1	2	1	3	3	3	4	3	3	1	2	rs111463480	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:24942272T>A	ENST00000289968.6	-	19	2417	c.2348A>T	c.(2347-2349)aAc>aTc	p.N783I	ARHGAP17_ENST00000441763.2_3'UTR|ARHGAP17_ENST00000303665.5_Missense_Mutation_p.N705I	NM_001006634.1	NP_001006635.1	Q68EM7	RHG17_HUMAN	Rho GTPase activating protein 17	783	Pro-rich.				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)		AGTTTCAGGGTTACCCCCTGC	0.632													T|||	3	0.000599042	0.0023	0.0	5008	,	,		14279	0.0		0.0	False		,,,				2504	0.0				p.N783I		Atlas-SNP	.											.	ARHGAP17	138	.	0			c.A2348T						PASS	.	T	ILE/ASN,ILE/ASN	1,4393	2.1+/-5.4	0,1,2196	71	80	77		2348,2114	5.1	0.6	16	dbSNP_132	77	0,8600		0,0,4300	no	missense,missense	ARHGAP17	NM_001006634.1,NM_018054.4	149,149	0,1,6496	AA,AT,TT		0.0,0.0228,0.0077	possibly-damaging,possibly-damaging	783/882,705/804	24942272	1,12993	2197	4300	6497	SO:0001583	missense	55114	exon19			TCAGGGTTACCCC	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.2348A>T	16.37:g.24942272T>A	ENSP00000289968:p.Asn783Ile	161	0	0		179	76	0.424581	NM_001006634	A8K6M6|Q6ZUS4|Q7Z2F2|Q8NDG2|Q96KS2|Q96KS3|Q96SS8|Q9BVF6|Q9H8U5|Q9NW54	Missense_Mutation	SNP	ENST00000289968.6	37	CCDS32409.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	T	12.57	1.977941	0.34942	2.28E-4	0.0	ENSG00000140750	ENST00000289968;ENST00000303665;ENST00000455311	T;T	0.21361	2.01;2.06	5.13	5.13	0.70059	.	0.588411	0.14194	N	0.335149	T	0.34658	0.0905	L	0.44542	1.39	0.80722	D	1	B;B;D;P;P	0.64830	0.343;0.232;0.994;0.736;0.729	B;B;P;B;B	0.59703	0.134;0.063;0.862;0.205;0.372	T	0.02294	-1.1181	10	0.52906	T	0.07	.	12.8937	0.58087	0.0:0.0:0.0:1.0	.	705;783;316;616;344	Q68EM7-2;Q68EM7;Q68EM7-7;B4DWE9;B4DVF3	.;RHG17_HUMAN;.;.;.	I	783;705;783	ENSP00000289968:N783I;ENSP00000303130:N705I	ENSP00000289968:N783I	N	-	2	0	ARHGAP17	24849773	0.994000	0.37717	0.604000	0.28916	0.012000	0.07955	1.696000	0.37773	1.923000	0.55706	0.528000	0.53228	AAC	T|0.999;A|0.001	0.001	strong		0.632	ARHGAP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436548.3	NM_018054		A	24942272	T	A	24942272	3	1	22	1	0	0	0	0	1	0	0	0	867	1725	60	5	305	5	ARHGAP17	16	24942272	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	140027	24942272	65412481	3219	6120											
ARHGAP17	55114	hgsc.bcm.edu	37	chr16	24965975	24965975	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgacacaggcttcaatgggCagcgcaatctcgcgcccgct	9	7	11	14	4	2	1	1	1	1	0	3	1	2	1	1	2	1	4	1	2	2	1	rs111986765	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:24965975C>G	ENST00000289968.6	-	10	870	c.801G>C	c.(799-801)ctG>ctC	p.L267L	ARHGAP17_ENST00000441763.2_3'UTR|ARHGAP17_ENST00000303665.5_Silent_p.L267L|ARHGAP17_ENST00000575975.1_5'Flank	NM_001006634.1	NP_001006635.1	Q68EM7	RHG17_HUMAN	Rho GTPase activating protein 17	267	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)		CTTCAATGGGCAGCGCAATCT	0.542													C|||	2	0.000399361	0.0015	0.0	5008	,	,		18487	0.0		0.0	False		,,,				2504	0.0				p.L267L		Atlas-SNP	.											.	ARHGAP17	138	.	0			c.G801C						PASS	.	C	,	1,4393	2.1+/-5.4	0,1,2196	138	132	134		801,801	-10.4	0.1	16	dbSNP_132	134	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ARHGAP17	NM_001006634.1,NM_018054.4	,	0,1,6496	GG,GC,CC		0.0,0.0228,0.0077	,	267/882,267/804	24965975	1,12993	2197	4300	6497	SO:0001819	synonymous_variant	55114	exon10			AATGGGCAGCGCA	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.801G>C	16.37:g.24965975C>G		91	0	0		87	43	0.494253	NM_001006634	A8K6M6|Q6ZUS4|Q7Z2F2|Q8NDG2|Q96KS2|Q96KS3|Q96SS8|Q9BVF6|Q9H8U5|Q9NW54	Silent	SNP	ENST00000289968.6	37	CCDS32409.1																																																																																			C|0.999;G|0.001	0.001	strong		0.542	ARHGAP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436548.3	NM_018054		G	24965975	C	G	24965975	2	3	22	1	0	0	0	0	0	0	0	1	867	697	25	4		4	ARHGAP17	16	24965975	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	23703	24965975	65388778	3220	6121											
AQP8	343	hgsc.bcm.edu	37	chr16	25228566	25228566	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aatgacaaggccagggagccGagcgtgggtggcaggtggcg	9	4	20	8	3	0	1	0	1	0	0	0	3	0	2	2	6	2	1	2	6	2	0	rs139992979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:25228566G>A	ENST00000219660.5	+	2	185	c.60G>A	c.(58-60)ccG>ccA	p.P20P	AQP8_ENST00000566125.1_Silent_p.P14P	NM_001169.2	NP_001160.2	O94778	AQP8_HUMAN	aquaporin 8	20					canalicular bile acid transport (GO:0015722)|cellular response to cAMP (GO:0071320)|transmembrane transport (GO:0055085)|transport (GO:0006810)|water transport (GO:0006833)	apical part of cell (GO:0045177)|integral component of plasma membrane (GO:0005887)|intracellular canaliculus (GO:0046691)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	water channel activity (GO:0015250)			NS(1)|breast(1)|large_intestine(3)|lung(8)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)	16				GBM - Glioblastoma multiforme(48;0.044)		CCAGGGAGCCGAGCGTGGGTG	0.577													G|||	50	0.00998403	0.031	0.0115	5008	,	,		18800	0.0		0.001	False		,,,				2504	0.0				p.P20P		Atlas-SNP	.											.	AQP8	75	.	0			c.G60A						PASS	.	G		105,4289	82.4+/-120.9	2,101,2094	190	187	188		60	-9.9	0	16	dbSNP_134	188	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	AQP8	NM_001169.2		2,106,6389	AA,AG,GG		0.0581,2.3896,0.8465		20/262	25228566	110,12884	2197	4300	6497	SO:0001819	synonymous_variant	343	exon2			GGAGCCGAGCGTG	BC040630	CCDS10626.1	16p12	2008-02-05			ENSG00000103375	ENSG00000103375		"Ion channels / Aquaporins"	642	protein-coding gene	gene with protein product		603750				9806845, 10393433	Standard	NM_001169		Approved		uc002doc.3	O94778	OTTHUMG00000097013	ENST00000219660.5:c.60G>A	16.37:g.25228566G>A		233	0	0		238	111	0.466387	NM_001169	Q8IUU3|Q9UIA4	Silent	SNP	ENST00000219660.5	37	CCDS10626.1																																																																																			G|0.993;A|0.007	0.007	strong		0.577	AQP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214102.2	NM_001169		A	25228566	G	A	25228566	2	1	22	1	0	0	0	0	0	0	0	1	832	1045	37	1		1	AQP8	16	25228566	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	262591	25228566	65126187	3221	6122											
ZKSCAN2	342357	hgsc.bcm.edu	37	chr16	25266547	25266547	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattcttgggtaagggccgaCgttctcgctttcggttcagc	5	13	12	11	4	3	0	1	0	2	0	5	1	3	0	1	3	1	4	1	3	1	6	rs113273135	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:25266547C>A	ENST00000328086.7	-	2	1369	c.566G>T	c.(565-567)cGt>cTt	p.R189L		NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	189					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)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	36				GBM - Glioblastoma multiforme(48;0.0378)		TAAGGGCCGACGTTCTCGCTT	0.602													C|||	70	0.0139776	0.0477	0.0072	5008	,	,		17212	0.0		0.002	False		,,,				2504	0.0				p.R189L		Atlas-SNP	.											ZKSCAN2,NS,carcinoma,-1,1	ZKSCAN2	90	1	0			c.G566T						PASS	.	C	LEU/ARG	136,4258	98.0+/-136.7	2,132,2063	114	99	104		566	-5.2	0	16	dbSNP_132	104	8,8592	5.0+/-18.6	1,6,4293	yes	missense	ZKSCAN2	NM_001012981.4	102	3,138,6356	AA,AC,CC		0.093,3.0951,1.1082	benign	189/968	25266547	144,12850	2197	4300	6497	SO:0001583	missense	342357	exon2			GGCCGACGTTCTC	AK026852	CCDS32410.1	16p12.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000155592		"Zinc fingers, C2H2-type", "-", "-", "-"	25677	protein-coding gene	gene with protein product			"zinc finger protein 694"	ZNF694			Standard	NM_001012981		Approved	FLJ23199, ZSCAN34	uc002dod.4	Q63HK3		ENST00000328086.7:c.566G>T	16.37:g.25266547C>A	ENSP00000331626:p.Arg189Leu	92	0	0		101	58	0.574257	NM_001012981	A1L3B4|Q6ZN77	Missense_Mutation	SNP	ENST00000328086.7	37	CCDS32410.1	24	0.01098901098901099	19	0.03861788617886179	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	C	0.541	-0.853648	0.02630	0.030951	9.3E-4	ENSG00000155592	ENST00000328086;ENST00000536768	T	0.14144	2.53	5.3	-5.17	0.02849	.	1.318600	0.04683	N	0.412758	T	0.00608	0.0020	N	0.00621	-1.32	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.36456	-0.9747	10	0.12766	T	0.61	0.0	0.7766	0.01033	0.3527:0.1598:0.1131:0.3743	.	189;189	Q63HK3-2;Q63HK3	.;ZKSC2_HUMAN	L	189	ENSP00000331626:R189L	ENSP00000331626:R189L	R	-	2	0	ZKSCAN2	25174048	0.000000	0.05858	0.000000	0.03702	0.100000	0.18952	-0.679000	0.05203	-0.480000	0.06803	-1.467000	0.01014	CGT	C|0.991;A|0.009	0.009	strong		0.602	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981		A	25266547	C	A	25266547	3	1	22	1	0	0	0	0	1	0	0	0	17702	536	19	4	2361	4	ZKSCAN2	16	25266547	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	37981	25266547	65088206	3222	6123											
IL4R	3566	hgsc.bcm.edu	37	chr16	27356271	27356271	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatgacgtggtcagtgcggaTaactatacactggacctgtg	10	10	13	8	2	1	1	1	1	0	0	1	4	1	3	1	3	3	0	1	3	3	3	rs112497527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27356271T>C	ENST00000395762.2	+	5	550	c.291T>C	c.(289-291)gaT>gaC	p.D97D	IL4R_ENST00000170630.2_Silent_p.D97D|IL4R_ENST00000543915.2_Silent_p.D97D|IL4R_ENST00000380922.3_Silent_p.D82D|IL4R_ENST00000449195.1_Silent_p.D97D	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	97		Major IL4 binding determinant.			defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|ovulation (GO:0030728)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|production of molecular mediator involved in inflammatory response (GO:0002532)|regulation of cell proliferation (GO:0042127)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	interleukin-4 receptor activity (GO:0004913)|receptor signaling protein activity (GO:0005057)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	33						TCAGTGCGGATAACTATACAC	0.642													C|||	66	0.0131789	0.0469	0.0058	5008	,	,		14225	0.0		0.0	False		,,,				2504	0.0				p.D97D		Atlas-SNP	.											.	IL4R	70	.	0			c.T291C						PASS	.	C	,	198,4196	807.2+/-415.9	3,192,2002	108	92	98		291,291	2.4	0	16	dbSNP_132	98	2,8598	819.2+/-406.8	0,2,4298	no	coding-synonymous,coding-synonymous	IL4R	NM_000418.2,NM_001008699.1	,	3,194,6300	CC,CT,TT		0.0233,4.5061,1.5392	,	97/826,97/228	27356271	200,12794	2197	4300	6497	SO:0001819	synonymous_variant	3566	exon5			TGCGGATAACTAT	X52425	CCDS10629.1, CCDS58441.1	16p12.1-p11.2	2008-05-14			ENSG00000077238	ENSG00000077238		"Interleukins and interleukin receptors", "CD molecules"	6015	protein-coding gene	gene with protein product		147781				1679753	Standard	NM_000418		Approved	CD124	uc010bxy.4	P24394	OTTHUMG00000097015	ENST00000395762.2:c.291T>C	16.37:g.27356271T>C		127	0	0		111	50	0.45045	NM_000418	B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Silent	SNP	ENST00000395762.2	37	CCDS10629.1																																																																																			T|0.988;C|0.012	0.012	strong		0.642	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4			C	27356271	T	C	27356271	2	2	22	1	0	0	0	0	0	0	0	1	7707	1403	49	3		3	IL4R	16	27356271	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2089724	27356271	62998482	3223	6124											
IL21R	50615	hgsc.bcm.edu	37	chr16	27460437	27460437	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggcgggctcacccctggccGgcctggatatggacacgttt	6	8	14	13	3	1	0	1	0	0	0	1	2	1	2	4	6	0	2	4	6	1	2	rs3093386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27460437G>A	ENST00000337929.3	+	9	1923	c.1450G>A	c.(1450-1452)Ggc>Agc	p.G484S	IL21R-AS1_ENST00000563191.1_RNA|IL21R_ENST00000564089.1_Missense_Mutation_p.G484S|IL21R_ENST00000395754.4_Missense_Mutation_p.G484S|IL21R_ENST00000395755.1_Missense_Mutation_p.G484S	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	484			G -> S (in dbSNP:rs3093386). {ECO:0000269|Ref.4}.		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						ACCCCTGGCCGGCCTGGATAT	0.677			T	BCL6	NHL								G|||	180	0.0359425	0.1324	0.0058	5008	,	,		18816	0.0		0.001	False		,,,				2504	0.0				p.G506S		Atlas-SNP	.		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	.	IL21R	95	.	0			c.G1516A						PASS	.	G	SER/GLY,SER/GLY,SER/GLY	415,3979		26,363,1808	42	39	40		1450,1450,1516	2.6	0.9	16	dbSNP_103	40	3,8597		0,3,4297	yes	missense,missense,missense	IL21R	NM_021798.3,NM_181078.2,NM_181079.4	56,56,56	26,366,6105	AA,AG,GG		0.0349,9.4447,3.2169	benign,benign,benign	484/539,484/539,506/561	27460437	418,12576	2197	4300	6497	SO:0001583	missense	50615	exon10			CTGGCCGGCCTGG	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.1450G>A	16.37:g.27460437G>A	ENSP00000338010:p.Gly484Ser	103	0	0		112	58	0.517857	NM_181079	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Missense_Mutation	SNP	ENST00000337929.3	37	CCDS10630.1	64	0.029304029304029304	59	0.11991869918699187	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	14.35	2.509511	0.44660	0.094447	3.49E-4	ENSG00000103522	ENST00000337929;ENST00000395755;ENST00000395754	T;T;T	0.15952	2.38;2.38;2.38	4.9	2.64	0.31445	.	0.231408	0.37437	N	0.002082	T	0.00144	0.0004	L	0.50919	1.6	0.29586	N	0.848826	P	0.42357	0.777	B	0.30179	0.112	T	0.16512	-1.0400	10	0.15952	T	0.53	-30.5288	4.0671	0.09866	0.124:0.0:0.6404:0.2356	rs3093386;rs61328560;rs3093386	484	Q9HBE5	IL21R_HUMAN	S	484	ENSP00000338010:G484S;ENSP00000379104:G484S;ENSP00000379103:G484S	ENSP00000338010:G484S	G	+	1	0	IL21R	27367938	0.055000	0.20627	0.916000	0.36221	0.741000	0.42261	0.087000	0.14958	2.271000	0.75665	0.561000	0.74099	GGC	G|0.962;A|0.038	0.038	strong		0.677	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078		A	27460437	G	A	27460437	3	1	22	1	0	0	0	0	1	0	0	0	7680	1116	39	1	1480	1	IL21R	16	27460437	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	104166	27460437	62894316	3224	6125											
KIAA0556	23247	hgsc.bcm.edu	37	chr16	27689137	27689137	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtatgactctattgaggaaGacatactctctgagcctgag	12	11	10	8	0	2	5	0	4	2	1	3	6	2	6	1	1	2	1	1	1	4	4	rs147094899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27689137G>T	ENST00000261588.4	+	7	647	c.628G>T	c.(628-630)Gac>Tac	p.D210Y	KIAA0556_ENST00000567894.1_3'UTR|CTD-2049O4.1_ENST00000564893.1_RNA	NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	210						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						TATTGAGGAAGACATACTCTC	0.507													G|||	40	0.00798722	0.028	0.0014	5008	,	,		16870	0.001		0.001	False		,,,				2504	0.0				p.D210Y		Atlas-SNP	.											.	KIAA0556	348	.	0			c.G628T						PASS	.	G	TYR/ASP	81,4313	71.4+/-109.4	0,81,2116	65	59	61		628	4.5	1	16	dbSNP_134	61	1,8599	1.2+/-3.3	0,1,4299	yes	missense	KIAA0556	NM_015202.2	160	0,82,6415	TT,TG,GG		0.0116,1.8434,0.6311	benign	210/1619	27689137	82,12912	2197	4300	6497	SO:0001583	missense	23247	exon7			GAGGAAGACATAC	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.628G>T	16.37:g.27689137G>T	ENSP00000261588:p.Asp210Tyr	89	0	0		124	54	0.435484	NM_015202	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	37	CCDS32415.1	12	0.005494505494505495	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	13.62	2.290322	0.40494	0.018434	1.16E-4	ENSG00000047578	ENST00000261588;ENST00000327217	T	0.49432	0.78	5.48	4.53	0.55603	.	0.296062	0.32175	N	0.006462	T	0.43612	0.1255	L	0.54323	1.7	0.36190	D	0.850035	D;D	0.76494	0.999;0.979	D;P	0.66497	0.944;0.81	T	0.65014	-0.6271	10	0.87932	D	0	-4.2839	10.458	0.44561	0.09:0.0:0.91:0.0	.	118;210	Q8N803;O60303	.;K0556_HUMAN	Y	210;117	ENSP00000261588:D210Y	ENSP00000261588:D210Y	D	+	1	0	KIAA0556	27596638	1.000000	0.71417	0.973000	0.42090	0.021000	0.10359	3.790000	0.55461	1.320000	0.45209	-0.137000	0.14449	GAC	G|0.993;T|0.007	0.007	strong		0.507	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202		T	27689137	G	T	27689137	3	4	22	1	0	0	0	0	1	0	0	0	8192	942	33	4	654	4	KIAA0556	16	27689137	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	228700	27689137	62665616	3225	6126											
KIAA0556	23247	hgsc.bcm.edu	37	chr16	27709812	27709812	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aaggccgagcagccagccagCccactgcaggtgcgctccgg	8	3	14	16	3	0	0	0	0	0	0	1	1	1	0	5	3	6	3	5	3	1	0	rs61740294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27709812C>T	ENST00000261588.4	+	9	1123	c.1104C>T	c.(1102-1104)agC>agT	p.S368S	KIAA0556_ENST00000567894.1_3'UTR|CTD-2049O4.1_ENST00000564893.1_RNA	NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	368						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						AGCCAGCCAGCCCACTGCAGG	0.637													C|||	81	0.0161741	0.0575	0.0072	5008	,	,		17048	0.0		0.0	False		,,,				2504	0.0				p.S368S		Atlas-SNP	.											.	KIAA0556	348	.	0			c.C1104T						PASS	.	C		254,4140		7,240,1950	20	21	21		1104	1.3	0.2	16	dbSNP_129	21	0,8600		0,0,4300	no	coding-synonymous	KIAA0556	NM_015202.2		7,240,6250	TT,TC,CC		0.0,5.7806,1.9547		368/1619	27709812	254,12740	2197	4300	6497	SO:0001819	synonymous_variant	23247	exon9			AGCCAGCCCACTG	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.1104C>T	16.37:g.27709812C>T		29	0	0		42	18	0.428571	NM_015202	A7E2C2	Silent	SNP	ENST00000261588.4	37	CCDS32415.1																																																																																			C|0.978;T|0.022	0.022	strong		0.637	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202		T	27709812	C	T	27709812	2	4	22	1	0	0	0	0	0	0	0	1	8192	738	26	2		2	KIAA0556	16	27709812	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	20675	27709812	62644941	3226	6127											
SULT1A1	6817	hgsc.bcm.edu	37	chr16	28617413	28617413	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggagatgctgtggtccatgaActcctgggggacggtggtgt	6	10	18	7	1	0	2	0	1	0	1	2	4	2	3	2	6	2	1	2	6	1	0	rs28374453		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:28617413A>G	ENST00000395607.1	-	7	1012	c.739T>C	c.(739-741)Ttc>Ctc	p.F247L	SULT1A1_ENST00000350842.4_Missense_Mutation_p.F169L|SULT1A1_ENST00000314752.7_Missense_Mutation_p.F247L|SULT1A1_ENST00000569554.1_Missense_Mutation_p.F247L|SULT1A1_ENST00000395609.1_Missense_Mutation_p.F247L	NM_177530.2|NM_177534.2	NP_803566.1|NP_803878.1	P50225	ST1A1_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 1	247					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|estrogen metabolic process (GO:0008210)|flavonoid metabolic process (GO:0009812)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|flavonol 3-sulfotransferase activity (GO:0047894)|steroid sulfotransferase activity (GO:0050294)|sulfotransferase activity (GO:0008146)	p.F247L(5)|p.F169L(5)		endometrium(2)|kidney(7)|large_intestine(2)|lung(2)|ovary(1)|stomach(2)	16					Acetaminophen(DB00316)|Tamoxifen(DB00675)	TGGTCCATGAACTCCTGGGGG	0.607																																					p.F247L		Atlas-SNP	.											SULT1A1_ENST00000350842,NS,carcinoma,0,10	SULT1A1	53	10	10	Substitution - Missense(10)	kidney(10)	c.T739C						scavenged	.						264	206	226					16																	28617413		2197	4300	6497	SO:0001583	missense	6817	exon6			CCATGAACTCCTG	U52852	CCDS10637.1, CCDS32420.1	16p12.1	2008-02-05			ENSG00000196502	ENSG00000196502	2.8.2.1	"Sulfotransferases, cytosolic"	11453	protein-coding gene	gene with protein product		171150		STP, STP1		8288252, 8912648	Standard	NM_177534		Approved	P-PST	uc002dqj.3	P50225	OTTHUMG00000131765	ENST00000395607.1:c.739T>C	16.37:g.28617413A>G	ENSP00000378971:p.Phe247Leu	516	0	0		271	83	0.306273	NM_177534	Q2NL71|Q86U58|Q92818|Q9BVU6|Q9UGG7	Missense_Mutation	SNP	ENST00000395607.1	37	CCDS32420.1	56	0.02564102564102564	29	0.05894308943089431	5	0.013812154696132596	1	0.0017482517482517483	21	0.027704485488126648	a	7.042	0.562645	0.13498	.	.	ENSG00000196502	ENST00000314752;ENST00000350842;ENST00000395609;ENST00000395607	T;T;T;T	0.01548	4.78;4.78;4.78;4.78	2.17	-4.34	0.03666	Sulfotransferase domain (1);	0.865026	0.10074	N	0.719350	T	0.00144	0.0004	N	0.12920	0.275	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	0.46414	-0.9193	10	0.22109	T	0.4	.	1.793	0.03056	0.1608:0.4101:0.2253:0.2039	rs28374453	199;169;247	Q59GG0;P50225-2;P50225	.;.;ST1A1_HUMAN	L	247;169;247;247	ENSP00000321988:F247L;ENSP00000329399:F169L;ENSP00000378972:F247L;ENSP00000378971:F247L	ENSP00000321988:F247L	F	-	1	0	SULT1A1	28524914	0.000000	0.05858	0.001000	0.08648	0.047000	0.14425	-3.681000	0.00394	-1.249000	0.02500	0.248000	0.18094	TTC	A|0.974;G|0.026	0.026	strong		0.607	SULT1A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254694.2	NM_001055		G	28617413	A	G	28617413	3	3	22	1	0	0	0	0	1	0	0	0	15387	43	2	3	156	3	SULT1A1	16	28617413	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	907601	28617413	61737340	3227	6128											
MVP	9961	hgsc.bcm.edu	37	chr16	29841950	29841950	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagaacagcaacgtgtcccGtgtggaggtcgggccaaaga	11	5	14	11	3	0	2	0	0	0	2	2	3	1	3	3	3	3	1	3	3	3	0	rs142997389	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:29841950G>A	ENST00000357402.5	+	2	218	c.80G>A	c.(79-81)cGt>cAt	p.R27H	MVP_ENST00000566554.1_3'UTR|MVP_ENST00000452209.2_Missense_Mutation_p.V11M|MVP_ENST00000395353.1_Missense_Mutation_p.R27H	NM_005115.4|NM_017458.3	NP_005106.2|NP_059447.2	Q14764	MVP_HUMAN	major vault protein	27					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						AACGTGTCCCGTGTGGAGGTC	0.597													G|||	40	0.00798722	0.0287	0.0029	5008	,	,		15564	0.0		0.0	False		,,,				2504	0.0				p.R27H		Atlas-SNP	.											.	MVP	80	.	0			c.G80A						PASS	.	G	HIS/ARG,HIS/ARG	112,4282	88.2+/-126.9	0,112,2085	135	97	110		80,80	0.5	0.2	16	dbSNP_134	110	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	MVP	NM_005115.4,NM_017458.3	29,29	0,114,6383	AA,AG,GG		0.0233,2.5489,0.8773	benign,benign	27/894,27/894	29841950	114,12880	2197	4300	6497	SO:0001583	missense	9961	exon2			TGTCCCGTGTGGA	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.80G>A	16.37:g.29841950G>A	ENSP00000349977:p.Arg27His	132	0	0		123	52	0.422764	NM_017458	Q96BG4|Q9BPW6|Q9BQT1|Q9UBD1	Missense_Mutation	SNP	ENST00000357402.5	37	CCDS10656.1	12|12	0.005494505494505495|0.005494505494505495	12|12	0.024390243902439025|0.024390243902439025	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	14.62|14.62	2.588764|2.588764	0.46110|0.46110	0.025489|0.025489	2.33E-4|2.33E-4	ENSG00000013364|ENSG00000013364	ENST00000357402;ENST00000395353|ENST00000452209	T;T|.	0.33865|.	1.39;1.39|.	5.82|5.82	0.469|0.469	0.16741|0.16741	.|.	0.109460|.	0.64402|.	N|.	0.000005|.	T|T	0.35998|0.35998	0.0951|0.0951	M|M	0.85197|0.85197	2.74|2.74	0.21675|0.21675	N|N	0.999591|0.999591	B|.	0.28400|.	0.21|.	B|.	0.27500|.	0.08|.	T|T	0.47509|0.47509	-0.9112|-0.9112	10|6	0.48119|0.87932	T|D	0.1|0	-4.9453|-4.9453	9.041|9.041	0.36319|0.36319	0.3672:0.0:0.6328:0.0|0.3672:0.0:0.6328:0.0	.|.	27|.	Q14764|.	MVP_HUMAN|.	H|M	27|11	ENSP00000349977:R27H;ENSP00000378760:R27H|.	ENSP00000349977:R27H|ENSP00000387916:V11M	R|V	+|+	2|1	0|0	MVP|MVP	29749451|29749451	0.915000|0.915000	0.31059|0.31059	0.191000|0.191000	0.23289|0.23289	0.606000|0.606000	0.37113|0.37113	1.270000|1.270000	0.33086|0.33086	0.110000|0.110000	0.17919|0.17919	-0.224000|-0.224000	0.12420|0.12420	CGT|GTG	G|0.991;A|0.009	0.009	strong		0.597	MVP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109711.3	NM_005115		A	29841950	G	A	29841950	3	1	22	1	0	0	0	0	1	0	0	0	10005	1145	40	1	82	1	MVP	16	29841950	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1224537	29841950	60512803	3228	6129											
MVP	9961	hgsc.bcm.edu	37	chr16	29856082	29856082	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tcccccaaaacgggctggtgGtcagcagtgtggacgtgcag	8	7	15	11	2	1	0	1	0	0	0	2	1	2	1	2	4	3	3	2	4	2	0	rs35916172	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:29856082G>A	ENST00000357402.5	+	11	2041	c.1903G>A	c.(1903-1905)Gtc>Atc	p.V635I	MVP_ENST00000395353.1_Missense_Mutation_p.V635I	NM_005115.4|NM_017458.3	NP_005106.2|NP_059447.2	Q14764	MVP_HUMAN	major vault protein	635			V -> I (in dbSNP:rs35916172).		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						CGGGCTGGTGGTCAGCAGTGT	0.647													G|||	63	0.0125799	0.0439	0.0058	5008	,	,		16638	0.0		0.001	False		,,,				2504	0.0				p.V635I		Atlas-SNP	.											.	MVP	80	.	0			c.G1903A						PASS	.	G	ILE/VAL,ILE/VAL	151,4243	106.0+/-144.5	0,151,2046	80	81	81		1903,1903	5	1	16	dbSNP_126	81	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	MVP	NM_005115.4,NM_017458.3	29,29	0,152,6345	AA,AG,GG		0.0116,3.4365,1.1698	benign,benign	635/894,635/894	29856082	152,12842	2197	4300	6497	SO:0001583	missense	9961	exon11			CTGGTGGTCAGCA	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.1903G>A	16.37:g.29856082G>A	ENSP00000349977:p.Val635Ile	55	0	0		51	25	0.490196	NM_017458	Q96BG4|Q9BPW6|Q9BQT1|Q9UBD1	Missense_Mutation	SNP	ENST00000357402.5	37	CCDS10656.1	17	0.007783882783882784	16	0.032520325203252036	0	0.0	0	0.0	1	0.0013192612137203166	G	7.470	0.646386	0.14451	0.034365	1.16E-4	ENSG00000013364	ENST00000357402;ENST00000395353	T;T	0.39406	1.08;1.08	5.91	4.96	0.65561	Shoulder domain (1);	0.103708	0.64402	N	0.000003	T	0.08980	0.0222	N	0.20881	0.62	0.80722	D	1	B	0.18610	0.029	B	0.25140	0.058	T	0.04664	-1.0935	10	0.02654	T	1	-17.7157	9.1044	0.36689	0.1639:0.0:0.836:0.0	rs35916172;rs35916172	635	Q14764	MVP_HUMAN	I	635	ENSP00000349977:V635I;ENSP00000378760:V635I	ENSP00000349977:V635I	V	+	1	0	MVP	29763583	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	3.270000	0.51600	1.513000	0.48852	0.655000	0.94253	GTC	G|0.985;A|0.015	0.015	strong		0.647	MVP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109711.3	NM_005115		A	29856082	G	A	29856082	3	1	22	1	0	0	0	0	1	0	0	0	10005	1261	44	2	1941	2	MVP	16	29856082	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	14132	29856082	60498671	3229	6130											
ITGAL	3683	hgsc.bcm.edu	37	chr16	30495496	30495496	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacaaatttgcatcaaaaccCgcgagcgagtttgtgaaaat	15	9	8	9	3	1	1	1	1	0	0	1	3	1	1	1	0	3	2	1	0	5	2	rs7191097	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:30495496C>T	ENST00000356798.6	+	9	1098	c.918C>T	c.(916-918)ccC>ccT	p.P306P	RP11-297C4.3_ENST00000562525.1_RNA|RP11-297C4.2_ENST00000569459.1_RNA|ITGAL_ENST00000433423.2_Intron|ITGAL_ENST00000358164.5_Silent_p.P223P|RNU7-61P_ENST00000515897.1_RNA	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	306	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)	CATCAAAACCCGCGAGCGAGT	0.468													C|||	423	0.0844649	0.3086	0.0159	5008	,	,		18600	0.0		0.004	False		,,,				2504	0.0				p.P306P	NSCLC(110;1462 1641 3311 33990 49495)	Atlas-SNP	.											.	ITGAL	149	.	0			c.C918T						PASS	.	C	,	1274,3120	434.7+/-344.0	192,890,1115	110	112	111		669,918	-3.8	0	16	dbSNP_116	111	27,8573	17.9+/-57.8	1,25,4274	no	coding-synonymous,coding-synonymous	ITGAL	NM_001114380.1,NM_002209.2	,	193,915,5389	TT,TC,CC		0.314,28.9941,10.0123	,	223/1087,306/1171	30495496	1301,11693	2197	4300	6497	SO:0001819	synonymous_variant	3683	exon9			AAAACCCGCGAGC		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.918C>T	16.37:g.30495496C>T		63	0	0		61	61	1	NM_002209	O43746|Q45H73|Q96HB1|Q9UBC8	Silent	SNP	ENST00000356798.6	37	CCDS32433.1																																																																																			C|0.900;T|0.100	0.100	strong		0.468	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2			T	30495496	C	T	30495496	2	4	22	1	0	0	0	0	0	0	0	1	7895	639	23	1		1	ITGAL	16	30495496	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	639414	30495496	59859257	3230	6131											
ZNF689	115509	hgsc.bcm.edu	37	chr16	30616317	30616317	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcactggtggggtttttcAcctgtgtgtgtggtccggtg	2	14	18	7	1	1	0	1	0	0	0	2	0	2	0	2	6	0	2	2	6	0	2	rs34007971	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:30616317A>G	ENST00000287461.3	-	3	1108	c.771T>C	c.(769-771)ggT>ggC	p.G257G	ZNF689_ENST00000566673.1_5'UTR|RP11-146F11.5_ENST00000563540.1_RNA	NM_138447.1	NP_612456.1	Q96CS4	ZN689_HUMAN	zinc finger protein 689	257					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)			GGGGTTTTTCACCTGTGTGTG	0.602													G|||	360	0.071885	0.2595	0.0187	5008	,	,		16142	0.0		0.003	False		,,,				2504	0.001				p.G257G		Atlas-SNP	.											.	ZNF689	48	.	0			c.T771C						PASS	.	G		1032,3362	725.7+/-409.6	123,786,1288	86	80	82		771	-8.2	0.1	16	dbSNP_126	82	33,8567	817.8+/-406.9	1,31,4268	no	coding-synonymous	ZNF689	NM_138447.1		124,817,5556	GG,GA,AA		0.3837,23.4866,8.1961		257/501	30616317	1065,11929	2197	4300	6497	SO:0001819	synonymous_variant	115509	exon3			TTTTTCACCTGTG	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.771T>C	16.37:g.30616317A>G		62	0	0		90	47	0.522222	NM_138447	Q658J5	Silent	SNP	ENST00000287461.3	37	CCDS10686.1																																																																																			A|0.917;G|0.083	0.083	strong		0.602	ZNF689-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255552.1	NM_138447		G	30616317	A	G	30616317	2	3	22	1	0	0	0	0	0	0	0	1	18109	146	6	3		3	ZNF689	16	30616317	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	120821	30616317	59738436	3231	6132											
ZNF689	115509	hgsc.bcm.edu	37	chr16	30616488	30616488	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caaacataggggcactcgccGgagtgtgcccgccggtgact	8	6	14	13	4	0	1	0	1	0	0	1	2	0	2	3	4	2	1	3	4	2	1	rs9937653	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:30616488G>A	ENST00000287461.3	-	3	937	c.600C>T	c.(598-600)tcC>tcT	p.S200S	ZNF689_ENST00000566673.1_5'UTR|RP11-146F11.5_ENST00000563540.1_RNA	NM_138447.1	NP_612456.1	Q96CS4	ZN689_HUMAN	zinc finger protein 689	200					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)			GGCACTCGCCGGAGTGTGCCC	0.577													G|||	155	0.0309505	0.1135	0.0072	5008	,	,		14868	0.0		0.0	False		,,,				2504	0.0				p.S200S		Atlas-SNP	.											.	ZNF689	48	.	0			c.C600T						PASS	.	G		371,4023	190.2+/-216.2	14,343,1840	65	65	65		600	-9.9	0.1	16	dbSNP_119	65	4,8596	2.2+/-6.3	0,4,4296	no	coding-synonymous	ZNF689	NM_138447.1		14,347,6136	AA,AG,GG		0.0465,8.4433,2.8859		200/501	30616488	375,12619	2197	4300	6497	SO:0001819	synonymous_variant	115509	exon3			CTCGCCGGAGTGT	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.600C>T	16.37:g.30616488G>A		125	0	0		120	51	0.425	NM_138447	Q658J5	Silent	SNP	ENST00000287461.3	37	CCDS10686.1																																																																																			G|0.972;A|0.028	0.028	strong		0.577	ZNF689-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255552.1	NM_138447		A	30616488	G	A	30616488	2	1	22	1	0	0	0	0	0	0	0	1	18109	1103	39	1		1	ZNF689	16	30616488	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	171	30616488	59738265	3232	6133											
SRCAP	10847	hgsc.bcm.edu	37	chr16	30748715	30748715	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ccactccagcttcagctccgGctgcaattcctgcccttgtt	5	12	7	17	1	1	0	1	0	0	0	4	0	4	0	5	1	4	5	5	1	1	4	rs144295177		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:30748715G>A	ENST00000262518.4	+	34	7739	c.7354G>A	c.(7354-7356)Gct>Act	p.A2452T	SRCAP_ENST00000395059.2_Missense_Mutation_p.A2390T|SRCAP_ENST00000344771.4_Missense_Mutation_p.A2294T	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	2452	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)			ttcagctccggctgcaattcc	0.587																																					p.A2452T		Atlas-SNP	.											.	SRCAP	298	.	0			c.G7354A						PASS	.	G	THR/ALA	3,4389	6.2+/-15.9	0,3,2193	124	89	101		7354	1.9	0.2	16	dbSNP_134	101	0,8596		0,0,4298	yes	missense	SRCAP	NM_006662.2	58	0,3,6491	AA,AG,GG		0.0,0.0683,0.0231	benign	2452/3231	30748715	3,12985	2196	4298	6494	SO:0001583	missense	10847	exon34			GCTCCGGCTGCAA	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.7354G>A	16.37:g.30748715G>A	ENSP00000262518:p.Ala2452Thr	144	0	0		149	78	0.52349	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	37	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	G	8.548	0.874873	0.17395	6.83E-4	0.0	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.91521	-2.85;-2.85;-2.86	3.9	1.89	0.25635	.	.	.	.	.	T	0.77164	0.4090	N	0.08118	0	0.19575	N	0.999965	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.61441	-0.7062	9	0.17369	T	0.5	2.0848	6.8859	0.24199	0.1034:0.1777:0.7189:0.0	.	2390;2452	Q6ZRS2-2;Q6ZRS2	.;SRCAP_HUMAN	T	2452;2390;2294	ENSP00000262518:A2452T;ENSP00000378499:A2390T;ENSP00000343042:A2294T	ENSP00000262518:A2452T	A	+	1	0	SRCAP	30656216	0.830000	0.29337	0.206000	0.23566	0.629000	0.37895	1.913000	0.39956	0.317000	0.23160	0.306000	0.20318	GCT	G|1.000;A|0.000	0.000	weak		0.587	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		A	30748715	G	A	30748715	3	1	22	1	0	0	0	0	1	0	0	0	15150	1203	42	2	7480	2	SRCAP	16	30748715	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	132227	30748715	59606038	3233	6134											
CTF1	1489	hgsc.bcm.edu	37	chr16	30910830	30910830	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcgcacctcctcaccaaataCgctgagcagctgctccagga	10	6	9	16	2	1	1	1	1	0	0	3	2	3	2	4	1	4	5	4	1	2	1	rs8059269	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:30910830C>T	ENST00000279804.2	+	2	157	c.120C>T	c.(118-120)taC>taT	p.Y40Y	CTF1_ENST00000395019.3_Silent_p.Y39Y	NM_001142544.1|NM_001330.3	NP_001136016.1|NP_001321.1	Q16619	CTF1_HUMAN	cardiotrophin 1	40					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|leukemia inhibitory factor signaling pathway (GO:0048861)|muscle organ development (GO:0007517)|nervous system development (GO:0007399)|neuron development (GO:0048666)|positive regulation of cell proliferation (GO:0008284)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	leukemia inhibitory factor receptor binding (GO:0005146)			large_intestine(1)|urinary_tract(1)	2			Colorectal(24;0.198)			TCACCAAATACGCTGAGCAGC	0.592													C|||	143	0.0285543	0.1051	0.0058	5008	,	,		11807	0.0		0.0	False		,,,				2504	0.0				p.Y40Y		Atlas-SNP	.											.	CTF1	3	.	0			c.C120T						PASS	.	C	,	349,4045	180.5+/-208.7	14,321,1862	67	61	63		117,120	-0.7	1	16	dbSNP_116	63	4,8596	2.2+/-6.3	0,4,4296	no	coding-synonymous,coding-synonymous	CTF1	NM_001142544.1,NM_001330.3	,	14,325,6158	TT,TC,CC		0.0465,7.9426,2.7166	,	39/201,40/202	30910830	353,12641	2197	4300	6497	SO:0001819	synonymous_variant	1489	exon2			CAAATACGCTGAG	U43030	CCDS10694.1, CCDS45464.1	16p11.2	2014-09-17			ENSG00000150281	ENSG00000150281			2499	protein-coding gene	gene with protein product		600435				8833032	Standard	NM_001330		Approved	CT-1, CT1	uc002dzw.3	Q16619	OTTHUMG00000132413	ENST00000279804.2:c.120C>T	16.37:g.30910830C>T		194	0	0		188	83	0.441489	NM_001330	A8MVX4|Q5U5Y7	Silent	SNP	ENST00000279804.2	37	CCDS10694.1																																																																																			C|0.965;T|0.035	0.035	strong		0.592	CTF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255550.1	NM_001330		T	30910830	C	T	30910830	2	4	22	1	0	0	0	0	0	0	0	1	4009	547	19	1		1	CTF1	16	30910830	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	162115	30910830	59443923	3234	6135											
SETD1A	9739	hgsc.bcm.edu	37	chr16	30978324	30978324	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcgggggcactacgggcatCgaggctttcgcctttgggtc	5	9	16	11	4	0	0	0	0	0	0	3	1	0	0	1	5	2	3	1	5	1	3	rs11866157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:30978324C>A	ENST00000262519.8	+	9	3311	c.2625C>A	c.(2623-2625)atC>atA	p.I875I		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	875					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						CTACGGGCATCGAGGCTTTCG	0.607													C|||	150	0.0299521	0.1104	0.0058	5008	,	,		14627	0.0		0.0	False		,,,				2504	0.0				p.I875I		Atlas-SNP	.											.	SETD1A	143	.	0			c.C2625A						PASS	.	C		357,4037		14,329,1854	30	27	28		2625	-7.1	0.9	16	dbSNP_120	28	4,8594		0,4,4295	no	coding-synonymous	SETD1A	NM_014712.1		14,333,6149	AA,AC,CC		0.0465,8.1247,2.7786		875/1708	30978324	361,12631	2197	4299	6496	SO:0001819	synonymous_variant	9739	exon9			GGGCATCGAGGCT	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.2625C>A	16.37:g.30978324C>A		81	0	0		100	54	0.54	NM_014712	A6NP62|Q6PIF3|Q8TAJ6	Silent	SNP	ENST00000262519.8	37	CCDS32435.1																																																																																			C|0.968;A|0.032	0.032	strong		0.607	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712		A	30978324	C	A	30978324	2	1	22	1	0	0	0	0	0	0	0	1	14145	874	31	4		4	SETD1A	16	30978324	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	67494	30978324	59376429	3235	6136											
ZNF668	79759	hgsc.bcm.edu	37	chr16	31073244	31073244	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcacattgcaggcacttgaaCggccggtcgcctgtgtgcac	7	9	12	13	3	1	1	1	1	0	0	2	1	1	1	2	3	3	3	2	3	1	2	rs34831291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31073244C>A	ENST00000538906.1	-	3	1789	c.1005G>T	c.(1003-1005)ccG>ccT	p.P335P	ZNF668_ENST00000417110.2_Missense_Mutation_p.N144K|ZNF668_ENST00000539836.3_Silent_p.P358P|ZNF668_ENST00000564456.1_5'Flank|ZNF668_ENST00000535577.1_Silent_p.P335P|ZNF668_ENST00000426488.2_Silent_p.P358P|ZNF668_ENST00000300849.4_Silent_p.P335P|ZNF668_ENST00000394983.2_Silent_p.P335P	NM_001172668.1	NP_001166139	Q96K58	ZN668_HUMAN	zinc finger protein 668	335					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						GGCACTTGAACGGCCGGTCGC	0.652													C|||	36	0.0071885	0.0242	0.0058	5008	,	,		15280	0.0		0.0	False		,,,				2504	0.0				p.P358P	Colon(181;1111 1980 5060 10512 25785)	Atlas-SNP	.											.	ZNF668	121	.	0			c.G1074T						PASS	.	C	,,,	133,4259		3,127,2066	35	37	36		1005,1074,1005,1005	-11.3	0.5	16	dbSNP_126	36	1,8591		0,1,4295	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF668	NM_001172668.1,NM_001172669.1,NM_001172670.1,NM_024706.4	,,,	3,128,6361	AA,AC,CC		0.0116,3.0282,1.032	,,,	335/620,358/643,335/620,335/620	31073244	134,12850	2196	4296	6492	SO:0001819	synonymous_variant	79759	exon4			CTTGAACGGCCGG		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.1005G>T	16.37:g.31073244C>A		53	0	0		53	25	0.471698	NM_001172669	C9JHH8|F5H7E7|Q59EV1|Q8N669|Q9H8L4	Silent	SNP	ENST00000538906.1	37	CCDS10701.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	C	3.701	-0.061523	0.07317	0.030282	1.16E-4	ENSG00000232748	ENST00000417110	.	.	.	5.63	-11.3	0.00108	.	.	.	.	.	T	0.27594	0.0678	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.66356	-0.5944	5	0.87932	D	0	-27.0566	5.6564	0.17644	0.17:0.1581:0.4906:0.1812	rs34831291	.	.	.	K	144	.	ENSP00000391989:N144K	N	+	3	2	AC135050.1	30980745	0.000000	0.05858	0.522000	0.27862	0.356000	0.29392	-5.729000	0.00102	-1.861000	0.01153	-1.119000	0.02030	AAC	C|0.990;A|0.010	0.010	strong		0.652	ZNF668-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108516.2	NM_024706		A	31073244	C	A	31073244	2	1	22	1	0	0	0	0	0	0	0	1	18090	523	19	4		4	ZNF668	16	31073244	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	94920	31073244	59281509	3236	6137											
ZNF668	79759	hgsc.bcm.edu	37	chr16	31075364	31075364	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggcagtgcgcacagcggaaGggcagttcgccagcgtgcga	8	4	18	11	5	0	0	0	0	0	0	1	2	0	1	1	3	4	4	1	3	1	1	rs34889904	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31075364G>A	ENST00000538906.1	-	2	1201	c.417C>T	c.(415-417)ccC>ccT	p.P139P	ZNF668_ENST00000539836.3_Silent_p.P162P|ZNF668_ENST00000564456.1_5'Flank|ZNF668_ENST00000535577.1_Silent_p.P139P|ZNF668_ENST00000426488.2_Silent_p.P162P|ZNF668_ENST00000300849.4_Silent_p.P139P|AC135050.5_ENST00000568708.1_RNA|ZNF668_ENST00000394983.2_Silent_p.P139P	NM_001172668.1	NP_001166139	Q96K58	ZN668_HUMAN	zinc finger protein 668	139					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						CACAGCGGAAGGGCAGTTCGC	0.697													G|||	38	0.00758786	0.0257	0.0058	5008	,	,		17086	0.0		0.0	False		,,,				2504	0.0				p.P162P	Colon(181;1111 1980 5060 10512 25785)	Atlas-SNP	.											.	ZNF668	121	.	0			c.C486T						PASS	.	G	,,,	135,4259	84.8+/-123.5	4,127,2066	26	23	24		417,486,417,417	-0.6	1	16	dbSNP_126	24	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF668	NM_001172668.1,NM_001172669.1,NM_001172670.1,NM_024706.4	,,,	4,128,6363	AA,AG,GG		0.0116,3.0724,1.047	,,,	139/620,162/643,139/620,139/620	31075364	136,12854	2197	4298	6495	SO:0001819	synonymous_variant	79759	exon3			GCGGAAGGGCAGT		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.417C>T	16.37:g.31075364G>A		38	0	0		60	29	0.483333	NM_001172669	C9JHH8|F5H7E7|Q59EV1|Q8N669|Q9H8L4	Silent	SNP	ENST00000538906.1	37	CCDS10701.1																																																																																			G|0.990;A|0.010	0.010	strong		0.697	ZNF668-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108516.2	NM_024706		A	31075364	G	A	31075364	2	1	22	1	0	0	0	0	0	0	0	1	18090	987	35	2		2	ZNF668	16	31075364	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2120	31075364	59279389	3237	6138											
ZNF668	79759	hgsc.bcm.edu	37	chr16	31075439	31075439	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aagcggcggccgcactcgggGcacggaaagggcttctcccc	7	4	15	15	5	1	0	0	0	1	0	3	1	1	1	3	6	1	3	3	6	2	1	rs34107331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31075439G>A	ENST00000538906.1	-	2	1126	c.342C>T	c.(340-342)tgC>tgT	p.C114C	ZNF668_ENST00000539836.3_Silent_p.C137C|ZNF668_ENST00000564456.1_5'Flank|ZNF668_ENST00000535577.1_Silent_p.C114C|ZNF668_ENST00000426488.2_Silent_p.C137C|ZNF668_ENST00000300849.4_Silent_p.C114C|AC135050.5_ENST00000568708.1_RNA|ZNF668_ENST00000394983.2_Silent_p.C114C	NM_001172668.1	NP_001166139	Q96K58	ZN668_HUMAN	zinc finger protein 668	114					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						CGCACTCGGGGCACGGAAAGG	0.706													G|||	38	0.00758786	0.0257	0.0058	5008	,	,		14213	0.0		0.0	False		,,,				2504	0.0				p.C137C	Colon(181;1111 1980 5060 10512 25785)	Atlas-SNP	.											.	ZNF668	121	.	0			c.C411T						PASS	.	G	,,,	130,4260		2,126,2067	22	23	23		342,411,342,342	0.9	1	16	dbSNP_126	23	1,8595		0,1,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF668	NM_001172668.1,NM_001172669.1,NM_001172670.1,NM_024706.4	,,,	2,127,6364	AA,AG,GG		0.0116,2.9613,1.0088	,,,	114/620,137/643,114/620,114/620	31075439	131,12855	2195	4298	6493	SO:0001819	synonymous_variant	79759	exon3			CTCGGGGCACGGA		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.342C>T	16.37:g.31075439G>A		7	0	0		14	7	0.5	NM_001172669	C9JHH8|F5H7E7|Q59EV1|Q8N669|Q9H8L4	Silent	SNP	ENST00000538906.1	37	CCDS10701.1																																																																																			G|0.990;A|0.010	0.010	strong		0.706	ZNF668-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108516.2	NM_024706		A	31075439	G	A	31075439	2	1	22	1	0	0	0	0	0	0	0	1	18090	1195	42	2		2	ZNF668	16	31075439	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	75	31075439	59279314	3238	6139											
ZNF646	9726	hgsc.bcm.edu	37	chr16	31092629	31092629	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgtggagagagccaggggaGgacaagcggtgacgtccatg	10	5	19	7	2	0	2	0	1	0	1	1	6	1	5	2	5	2	0	2	5	1	0	rs370035952		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31092629G>A	ENST00000394979.2	+	1	5407	c.4984G>A	c.(4984-4986)Gga>Aga	p.G1662R	ZNF646_ENST00000300850.5_Missense_Mutation_p.G1662R			O15015	ZN646_HUMAN	zinc finger protein 646	1662					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						AGCCAGGGGAGGACAAGCGGT	0.662																																					p.G1662R		Atlas-SNP	.											.	ZNF646	133	.	0			c.G4984A						PASS	.	G	ARG/GLY	1,4393	2.1+/-5.4	0,1,2196	63	73	70		4984	2.8	0	16		70	0,8598		0,0,4299	no	missense	ZNF646	NM_014699.3	125	0,1,6495	AA,AG,GG		0.0,0.0228,0.0077	benign	1662/1833	31092629	1,12991	2197	4299	6496	SO:0001583	missense	9726	exon2			AGGGGAGGACAAG	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.4984G>A	16.37:g.31092629G>A	ENSP00000378429:p.Gly1662Arg	141	0	0		144	83	0.576389	NM_014699	Q8IVD8	Missense_Mutation	SNP	ENST00000394979.2	37		.	.	.	.	.	.	.	.	.	.	G	5.858	0.342448	0.11069	2.28E-4	0.0	ENSG00000167395	ENST00000300850;ENST00000394979	T;T	0.09445	2.98;3.04	5.8	2.76	0.32466	.	.	.	.	.	T	0.07007	0.0178	L	0.29908	0.895	0.09310	N	1	B	0.15930	0.015	B	0.16289	0.015	T	0.40831	-0.9542	9	0.20519	T	0.43	-7.682	4.3737	0.11260	0.2498:0.1703:0.5798:0.0	.	1662	O15015-2	.	R	1662	ENSP00000300850:G1662R;ENSP00000378429:G1662R	ENSP00000300850:G1662R	G	+	1	0	ZNF646	31000130	0.133000	0.22466	0.003000	0.11579	0.061000	0.15899	1.546000	0.36179	0.783000	0.33636	0.655000	0.94253	GGA	.	.	weak		0.662	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699		A	31092629	G	A	31092629	3	1	22	1	0	0	0	0	1	0	0	0	18077	1001	35	2	4986	2	ZNF646	16	31092629	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	17190	31092629	59262124	3239	6140											
PRSS36	146547	hgsc.bcm.edu	37	chr16	31151622	31151622	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caggcccctgtacctcacacCtgttctcctgcccctctgca	5	10	6	20	0	3	0	1	0	2	0	4	0	3	0	7	1	3	3	7	1	1	2	rs61729752	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31151622C>T	ENST00000268281.4	-	14	2340	c.2282G>A	c.(2281-2283)aGg>aAg	p.R761K	PRSS36_ENST00000418068.2_Intron|PRSS36_ENST00000569305.1_Missense_Mutation_p.R756K	NM_001258290.1|NM_173502.4	NP_001245219.1|NP_775773.2	Q5K4E3	POLS2_HUMAN	protease, serine, 36	761	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						TACCTCACACCTGTTCTCCTG	0.537													c|||	78	0.0155751	0.0545	0.0086	5008	,	,		17560	0.0		0.0	False		,,,				2504	0.0				p.R761K		Atlas-SNP	.											.	PRSS36	50	.	0			c.G2282A						PASS	.		LYS/ARG	237,4157	139.6+/-175.2	8,221,1968	57	54	55		2282	2.9	1	16	dbSNP_129	55	1,8599	1.2+/-3.3	0,1,4299	yes	missense	PRSS36	NM_173502.3	26	8,222,6267	TT,TC,CC		0.0116,5.3937,1.8316	benign	761/856	31151622	238,12756	2197	4300	6497	SO:0001583	missense	146547	exon14			TCACACCTGTTCT	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.2282G>A	16.37:g.31151622C>T	ENSP00000268281:p.Arg761Lys	93	0	0		96	50	0.520833	NM_173502	A8K2P5|B4DW80|B7ZMK8|E7EX56|Q8NBY4	Missense_Mutation	SNP	ENST00000268281.4	37	CCDS32436.1	31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	C	10.18	1.279325	0.23307	0.053937	1.16E-4	ENSG00000178226	ENST00000268281	T	0.58940	0.3	4.92	2.86	0.33363	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.07818	0.0196	L	0.40543	1.245	0.21740	N	0.99957	B;B	0.09022	0.002;0.002	B;B	0.12156	0.007;0.007	T	0.12967	-1.0527	9	0.59425	D	0.04	.	6.1003	0.20043	0.0:0.7536:0.0:0.2464	.	756;761	B7ZMK8;Q5K4E3	.;POLS2_HUMAN	K	761	ENSP00000268281:R761K	ENSP00000268281:R761K	R	-	2	0	PRSS36	31059123	0.001000	0.12720	1.000000	0.80357	0.981000	0.71138	-0.769000	0.04710	1.125000	0.41998	0.555000	0.69702	AGG	C|0.982;T|0.018	0.018	strong		0.537	PRSS36-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433542.1	NM_173502		T	31151622	C	T	31151622	3	4	22	1	0	0	0	0	1	0	0	0	12637	681	24	2	293	2	PRSS36	16	31151622	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	58993	31151622	59203131	3240	6141											
PRSS36	146547	hgsc.bcm.edu	37	chr16	31151927	31151927	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggctccacccgggagctcaGctccaggagggccagggggg	6	3	19	13	1	1	0	1	0	0	0	3	2	3	2	4	7	2	3	4	7	0	0	rs61976958	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31151927G>A	ENST00000268281.4	-	13	2111	c.2053C>T	c.(2053-2055)Ctg>Ttg	p.L685L	PRSS36_ENST00000418068.2_Intron|PRSS36_ENST00000569305.1_Silent_p.L680L	NM_001258290.1|NM_173502.4	NP_001245219.1|NP_775773.2	Q5K4E3	POLS2_HUMAN	protease, serine, 36	685	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						CGGGAGCTCAGCTCCAGGAGG	0.706													G|||	78	0.0155751	0.0545	0.0086	5008	,	,		15742	0.0		0.0	False		,,,				2504	0.0				p.L685L		Atlas-SNP	.											.	PRSS36	50	.	0			c.C2053T						PASS	.	G		227,4155		8,211,1972	14	19	17		2053	2.7	1	16	dbSNP_129	17	1,8573		0,1,4286	no	coding-synonymous	PRSS36	NM_173502.3		8,212,6258	AA,AG,GG		0.0117,5.1803,1.7598		685/856	31151927	228,12728	2191	4287	6478	SO:0001819	synonymous_variant	146547	exon13			AGCTCAGCTCCAG	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.2053C>T	16.37:g.31151927G>A		75	0	0		69	28	0.405797	NM_173502	A8K2P5|B4DW80|B7ZMK8|E7EX56|Q8NBY4	Silent	SNP	ENST00000268281.4	37	CCDS32436.1																																																																																			G|0.983;A|0.017	0.017	strong		0.706	PRSS36-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433542.1	NM_173502		A	31151927	G	A	31151927	2	1	22	1	0	0	0	0	0	0	0	1	12637	962	34	2		2	PRSS36	16	31151927	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	305	31151927	59202826	3241	6142											
FUS	2521	hgsc.bcm.edu	37	chr16	31193948	31193948	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	acggacacttcaggctatggCcagagcagctattcttctta	10	11	9	11	1	3	1	1	0	2	1	3	2	3	2	1	3	2	3	1	3	3	6	rs61733962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31193948C>T	ENST00000254108.7	+	3	258	c.153C>T	c.(151-153)ggC>ggT	p.G51G	RP11-388M20.6_ENST00000564743.1_RNA|FUS_ENST00000568685.1_Silent_p.G51G|FUS_ENST00000380244.3_Silent_p.G51G	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	51	Gln/Gly/Ser/Tyr-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)		CAGGCTATGGCCAGAGCAGCT	0.522			T	"DDIT3, ERG, FEV, ATF1, CREB3L2, CREB3L1"	"liposarcoma, AML, Ewing sarcoma, angiomatoid fibrous histiocytoma, fibromyxoid sarcoma"								C|||	169	0.033746	0.1097	0.0187	5008	,	,		19819	0.0		0.005	False		,,,				2504	0.0061				p.G51G		Atlas-SNP	.		Dom	yes		16	16p11.2	2521	"fusion, derived from t(12;16) malignant liposarcoma"		"M, L"	.	FUS	52	.	0			c.C153T						PASS	.	C	,,	427,3967	210.8+/-231.2	24,379,1794	100	95	97		153,153,153	1.4	1	16	dbSNP_129	97	30,8570	20.4+/-63.3	0,30,4270	no	coding-synonymous,coding-synonymous,coding-synonymous	FUS	NM_001170634.1,NM_001170937.1,NM_004960.3	,,	24,409,6064	TT,TC,CC		0.3488,9.7178,3.517	,,	51/526,51/523,51/527	31193948	457,12537	2197	4300	6497	SO:0001819	synonymous_variant	2521	exon3			CTATGGCCAGAGC	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.153C>T	16.37:g.31193948C>T		193	0	0		183	94	0.513661	NM_001170634	Q9H4A8	Silent	SNP	ENST00000254108.7	37	CCDS10707.1																																																																																			C|0.965;T|0.035	0.035	strong		0.522	FUS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255526.2	NM_004960		T	31193948	C	T	31193948	2	4	22	1	0	0	0	0	0	0	0	1	6108	726	26	2		2	FUS	16	31193948	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	42021	31193948	59160805	3242	6143											
TRIM72	493829	hgsc.bcm.edu	37	chr16	31235548	31235548	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agctctgcgcacccgagcctGgtggtgtcttcctctggccg	3	10	13	15	3	3	0	0	0	3	0	4	1	4	0	4	3	3	2	4	3	0	1	rs58585879	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31235548G>C	ENST00000322122.3	+	7	1190	c.906G>C	c.(904-906)ctG>ctC	p.L302L	RP11-388M20.9_ENST00000576745.1_lincRNA	NM_001008274.3	NP_001008275.2			tripartite motif containing 72, E3 ubiquitin protein ligase											breast(1)|endometrium(2)|large_intestine(2)|lung(9)|skin(1)	15						ACCCGAGCCTGGTGGTGTCTT	0.677													G|||	154	0.0307508	0.1067	0.0086	5008	,	,		12224	0.0		0.002	False		,,,				2504	0.0051				p.L302L		Atlas-SNP	.											.	TRIM72	32	.	0			c.G906C						PASS	.	G		414,3970		20,374,1798	22	23	23		906	2.3	1	16	dbSNP_129	23	6,8568		0,6,4281	no	coding-synonymous	TRIM72	NM_001008274.3		20,380,6079	CC,CG,GG		0.07,9.4434,3.2412		302/478	31235548	420,12538	2192	4287	6479	SO:0001819	synonymous_variant	493829	exon7			GAGCCTGGTGGTG	AK090695	CCDS32437.1	16p11.2	2014-02-10	2014-02-10					"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	32671	protein-coding gene	gene with protein product	"mitsugumin 53"	613288	"tripartite motif-containing 72", "tripartite motif containing 72"			20399744, 23354051	Standard	NM_001008274		Approved	MG53	uc002ebn.2	Q6ZMU5		ENST00000322122.3:c.906G>C	16.37:g.31235548G>C		25	0	0		33	10	0.30303	NM_001008274		Silent	SNP	ENST00000322122.3	37	CCDS32437.1																																																																																			G|0.966;C|0.034	0.034	strong		0.677	TRIM72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433567.1	NM_001008274		C	31235548	G	C	31235548	2	2	22	1	0	0	0	0	0	0	0	1	16560	1335	47	4		4	TRIM72	16	31235548	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	41600	31235548	59119205	3243	6144											
ITGAX	3687	hgsc.bcm.edu	37	chr16	31382464	31382464	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tttgggcaggcactgagcggGggtcaagacctcacccagga	9	6	15	11	1	2	2	2	1	0	1	2	3	2	3	2	5	1	2	2	5	1	1	rs2230426	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31382464G>C	ENST00000268296.4	+	15	1891	c.1770G>C	c.(1768-1770)ggG>ggC	p.G590G	ITGAX_ENST00000562522.1_Silent_p.G590G	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	590					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						CACTGAGCGGGGGTCAAGACC	0.637													G|||	223	0.0445288	0.1619	0.0115	5008	,	,		17382	0.0		0.001	False		,,,				2504	0.0				p.G590G		Atlas-SNP	.											.	ITGAX	198	.	0			c.G1770C						PASS	.	G		552,3842	239.0+/-250.2	39,474,1684	60	66	64		1770	2.3	1	16	dbSNP_98	64	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	ITGAX	NM_000887.3		39,479,5979	CC,CG,GG		0.0581,12.5626,4.2866		590/1164	31382464	557,12437	2197	4300	6497	SO:0001819	synonymous_variant	3687	exon15			GAGCGGGGGTCAA	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.1770G>C	16.37:g.31382464G>C		68	0	0		77	36	0.467532	NM_000887	Q8IVA6	Silent	SNP	ENST00000268296.4	37	CCDS10711.1																																																																																			G|0.961;C|0.039	0.039	strong		0.637	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887		C	31382464	G	C	31382464	2	2	22	1	0	0	0	0	0	0	0	1	7898	1219	43	4		4	ITGAX	16	31382464	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	146916	31382464	58972289	3244	6145											
ITGAD	3681	hgsc.bcm.edu	37	chr16	31422071	31422071	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctcaggttactccaccgagCtagccctgtggaagggggta	8	8	13	12	1	1	0	1	0	0	0	2	2	2	1	4	4	3	3	4	4	4	3	rs142278416	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31422071C>G	ENST00000389202.2	+	12	1277	c.1228C>G	c.(1228-1230)Cta>Gta	p.L410V		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	410					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						CTCCACCGAGCTAGCCCTGTG	0.667													c|||	38	0.00758786	0.0265	0.0043	5008	,	,		7588	0.0		0.0	False		,,,				2504	0.0				p.L410V		Atlas-SNP	.											.	ITGAD	154	.	0			c.C1228G						PASS	.	C	VAL/LEU	110,4284		2,106,2089	28	30	29		1228	1	0	16	dbSNP_134	29	1,8597		0,1,4298	yes	missense	ITGAD	NM_005353.2	32	2,107,6387	GG,GC,CC		0.0116,2.5034,0.8544	benign	410/1162	31422071	111,12881	2197	4299	6496	SO:0001583	missense	3681	exon12			ACCGAGCTAGCCC	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.1228C>G	16.37:g.31422071C>G	ENSP00000373854:p.Leu410Val	209	0	0		190	89	0.468421	NM_005353	Q15575|Q15576	Missense_Mutation	SNP	ENST00000389202.2	37	CCDS32438.1	14	0.00641025641025641	13	0.026422764227642278	1	0.0027624309392265192	0	0.0	0	0.0	c	0.001	-2.980833	0.00046	0.025034	1.16E-4	ENSG00000156886	ENST00000444228;ENST00000389202	T	0.15139	2.45	4.4	1.04	0.20106	.	.	.	.	.	T	0.01387	0.0045	N	0.01446	-0.86	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.001	T	0.40232	-0.9574	9	0.02654	T	1	.	7.4596	0.27287	0.0:0.3542:0.5324:0.1134	.	426;410	Q59H14;Q13349	.;ITAD_HUMAN	V	426;410	ENSP00000373854:L410V	ENSP00000373854:L410V	L	+	1	2	ITGAD	31329572	0.949000	0.32298	0.037000	0.18230	0.014000	0.08584	-0.348000	0.07740	0.286000	0.22352	0.197000	0.17608	CTA	C|0.991;G|0.009	0.009	strong		0.667	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353		G	31422071	C	G	31422071	3	3	22	1	0	0	0	0	1	0	0	0	7893	796	28	4	1274	4	ITGAD	16	31422071	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	39607	31422071	58932682	3245	6146											
ITGAD	3681	hgsc.bcm.edu	37	chr16	31422531	31422531	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgtccgtgtgtcccttgccTaggggggtgagtggctgatg	3	12	18	8	1	0	2	0	2	0	0	2	2	2	2	3	4	1	1	3	4	1	2	rs368058587		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31422531T>C	ENST00000389202.2	+	13	1540	c.1491T>C	c.(1489-1491)ccT>ccC	p.P497P		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	497					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						GTCCCTTGCCTAGGGGGGTGA	0.627													t|||	1	0.000199681	0.0008	0.0	5008	,	,		15986	0.0		0.0	False		,,,				2504	0.0				p.P497P		Atlas-SNP	.											.	ITGAD	154	.	0			c.T1491C						PASS	.	T		2,4392	4.2+/-10.8	0,2,2195	82	79	80		1491	0.8	0.1	16		80	0,8600		0,0,4300	no	coding-synonymous	ITGAD	NM_005353.2		0,2,6495	CC,CT,TT		0.0,0.0455,0.0154		497/1162	31422531	2,12992	2197	4300	6497	SO:0001819	synonymous_variant	3681	exon13			CTTGCCTAGGGGG	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.1491T>C	16.37:g.31422531T>C		179	0	0		229	104	0.454148	NM_005353	Q15575|Q15576	Silent	SNP	ENST00000389202.2	37	CCDS32438.1																																																																																			.	.	weak		0.627	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353		C	31422531	T	C	31422531	2	2	22	1	0	0	0	0	0	0	0	1	7893	1509	53	3		3	ITGAD	16	31422531	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	460	31422531	58932222	3246	6147											
ITGAD	3681	hgsc.bcm.edu	37	chr16	31429479	31429479	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctaagaagcagccgctgcagTgtcaaccaccccatcttcca	11	7	7	16	1	2	1	1	0	1	1	3	1	3	1	5	0	4	3	5	0	3	2	rs78517822	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31429479T>C	ENST00000389202.2	+	21	2632	c.2583T>C	c.(2581-2583)agT>agC	p.S861S		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	861					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						GCCGCTGCAGTGTCAACCACC	0.572													c|||	265	0.0529153	0.1906	0.0173	5008	,	,		17653	0.0		0.001	False		,,,				2504	0.0				p.S861S		Atlas-SNP	.											.	ITGAD	154	.	0			c.T2583C						PASS	.	C		752,3642	754.3+/-412.4	67,618,1512	140	132	135		2583	4.1	0.8	16	dbSNP_132	135	12,8588	818.8+/-406.8	0,12,4288	no	coding-synonymous	ITGAD	NM_005353.2		67,630,5800	CC,CT,TT		0.1395,17.1142,5.8796		861/1162	31429479	764,12230	2197	4300	6497	SO:0001819	synonymous_variant	3681	exon21			CTGCAGTGTCAAC	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.2583T>C	16.37:g.31429479T>C		225	0	0		205	96	0.468293	NM_005353	Q15575|Q15576	Silent	SNP	ENST00000389202.2	37	CCDS32438.1																																																																																			T|0.947;C|0.053	0.053	strong		0.572	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353		C	31429479	T	C	31429479	2	2	22	1	0	0	0	0	0	0	0	1	7893	1693	59	3		3	ITGAD	16	31429479	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	6948	31429479	58925274	3247	6148											
ARMC5	79798	hgsc.bcm.edu	37	chr16	31477442	31477442	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcttctggagcagggtggTctccggctcctccttgcggc	2	11	14	14	2	2	0	0	0	2	0	5	1	4	1	3	5	3	3	3	5	0	2	rs116201073	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31477442T>C	ENST00000563544.1	+	7	2586	c.2040T>C	c.(2038-2040)ggT>ggC	p.G680G	ARMC5_ENST00000412665.2_Silent_p.G324G|ARMC5_ENST00000457010.2_3'UTR|ARMC5_ENST00000268314.4_Silent_p.G680G|ARMC5_ENST00000538189.1_Silent_p.G712G|ARMC5_ENST00000408912.3_Silent_p.G775G			Q96C12	ARMC5_HUMAN	armadillo repeat containing 5	680										central_nervous_system(1)|endometrium(4)|large_intestine(3)|liver(2)|lung(12)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						AGCAGGGTGGTCTCCGGCTCC	0.647													C|||	122	0.024361	0.0893	0.0058	5008	,	,		15259	0.0		0.0	False		,,,				2504	0.0				p.G680G		Atlas-SNP	.											ARMC5,NS,carcinoma,0,1	ARMC5	94	1	0			c.T2040C						scavenged	.	C	,	253,3943		8,237,1853	31	36	34		2040,	3	1	16	dbSNP_132	34	1,8425		0,1,4212	no	coding-synonymous,utr-3	ARMC5	NM_001105247.1,NM_024742.2	,	8,238,6065	CC,CT,TT		0.0119,6.0296,2.0124	,	680/936,	31477442	254,12368	2098	4213	6311	SO:0001819	synonymous_variant	79798	exon6			GGGTGGTCTCCGG	AY217348	CCDS42155.1, CCDS45472.1, CCDS73874.1	16p11	2013-02-14			ENSG00000140691	ENSG00000140691		"Armadillo repeat containing"	25781	protein-coding gene	gene with protein product		615549					Standard	NM_024742		Approved	FLJ13063	uc002ecc.3	Q96C12	OTTHUMG00000176618	ENST00000563544.1:c.2040T>C	16.37:g.31477442T>C		56	1	0.0178571		55	55	1	NM_001105247	Q86WM9|Q9H7P8|Q9H925	Silent	SNP	ENST00000563544.1	37	CCDS45472.1																																																																																			T|0.974;C|0.026	0.026	strong		0.647	ARMC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432847.1	NM_024742		C	31477442	T	C	31477442	2	2	22	1	0	0	0	0	0	0	0	1	954	1654	58	3		3	ARMC5	16	31477442	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	47963	31477442	58877311	3248	6149											
ARMC5	79798	hgsc.bcm.edu	37	chr16	31477795	31477795	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cctgcgaggtctgtcgcctgGtgcagcctggcctgtcctgc	2	10	14	15	2	1	0	0	0	1	0	3	1	2	0	5	3	4	1	5	3	0	0	rs115611533	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31477795G>C	ENST00000563544.1	+	7	2939	c.2393G>C	c.(2392-2394)gGt>gCt	p.G798A	ARMC5_ENST00000412665.2_Missense_Mutation_p.G442A|ARMC5_ENST00000457010.2_3'UTR|ARMC5_ENST00000268314.4_Missense_Mutation_p.G798A|ARMC5_ENST00000538189.1_Missense_Mutation_p.G830A|ARMC5_ENST00000408912.3_Missense_Mutation_p.G893A			Q96C12	ARMC5_HUMAN	armadillo repeat containing 5	798	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.									central_nervous_system(1)|endometrium(4)|large_intestine(3)|liver(2)|lung(12)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						CTGTCGCCTGGTGCAGCCTGG	0.687													g|||	41	0.0081869	0.0287	0.0043	5008	,	,		16435	0.0		0.0	False		,,,				2504	0.0				p.G798A		Atlas-SNP	.											.	ARMC5	94	.	0			c.G2393C						PASS	.		ALA/GLY,	94,3996		2,90,1953	29	35	33		2393,	4.7	0.3	16	dbSNP_132	33	1,8347		0,1,4173	yes	missense,utr-3	ARMC5	NM_001105247.1,NM_024742.2	60,	2,91,6126	CC,CG,GG		0.012,2.2983,0.7638	benign,	798/936,	31477795	95,12343	2045	4174	6219	SO:0001583	missense	79798	exon6			CGCCTGGTGCAGC	AY217348	CCDS42155.1, CCDS45472.1, CCDS73874.1	16p11	2013-02-14			ENSG00000140691	ENSG00000140691		"Armadillo repeat containing"	25781	protein-coding gene	gene with protein product		615549					Standard	NM_024742		Approved	FLJ13063	uc002ecc.3	Q96C12	OTTHUMG00000176618	ENST00000563544.1:c.2393G>C	16.37:g.31477795G>C	ENSP00000456877:p.Gly798Ala	35	0	0		50	26	0.52	NM_001105247	Q86WM9|Q9H7P8|Q9H925	Missense_Mutation	SNP	ENST00000563544.1	37	CCDS45472.1	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	g	0.136	-1.108013	0.01813	0.022983	1.2E-4	ENSG00000140691	ENST00000408912;ENST00000538189;ENST00000268314;ENST00000412665	T;T;T;T	0.70045	-0.45;-0.45;-0.45;-0.45	5.64	4.69	0.59074	BTB/POZ-like (1);BTB/POZ fold (1);	0.393509	0.28549	N	0.014953	T	0.22244	0.0536	N	0.13235	0.315	0.09310	N	1	B;B;B;B	0.22800	0.031;0.031;0.075;0.015	B;B;B;B	0.20184	0.028;0.028;0.017;0.012	T	0.07214	-1.0784	10	0.10377	T	0.69	-26.6313	12.3369	0.55073	0.0816:0.0:0.9184:0.0	.	830;830;893;798	B4DH27;F5H156;B4DIU9;Q96C12	.;.;.;ARMC5_HUMAN	A	893;830;798;442	ENSP00000386125:G893A;ENSP00000443995:G830A;ENSP00000268314:G798A;ENSP00000400183:G442A	ENSP00000268314:G798A	G	+	2	0	ARMC5	31385296	0.704000	0.27836	0.271000	0.24616	0.056000	0.15407	4.288000	0.59007	1.389000	0.46526	0.546000	0.68486	GGT	G|0.992;C|0.008	0.008	strong		0.687	ARMC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432847.1	NM_024742		C	31477795	G	C	31477795	3	2	22	1	0	0	0	0	1	0	0	0	954	1261	44	4	2729	4	ARMC5	16	31477795	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	353	31477795	58876958	3249	6150											
SLC5A2	6524	hgsc.bcm.edu	37	chr16	31501642	31501642	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccctcagagccccaggcccCggcaccaagcctcttccgcc	6	5	8	22	2	2	1	1	0	1	1	4	1	4	1	9	2	2	1	9	2	1	1	rs61746400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31501642C>T	ENST00000330498.3	+	14	1824	c.1805C>T	c.(1804-1806)cCg>cTg	p.P602L	C16orf58_ENST00000567994.1_3'UTR|SLC5A2_ENST00000564197.1_Intron|C16orf58_ENST00000327237.2_3'UTR|AC026471.6_ENST00000565137.1_RNA|C16orf58_ENST00000570164.1_3'UTR	NM_003041.3	NP_003032.1	P31639	SC5A2_HUMAN	solute carrier family 5 (sodium/glucose cotransporter), member 2	602					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-affinity glucose:sodium symporter activity (GO:0005362)			endometrium(2)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	25					Canagliflozin(DB08907)|Dapagliflozin(DB06292)	CCCCAGGCCCCGGCACCAAGC	0.632													c|||	44	0.00878594	0.0325	0.0014	5008	,	,		16541	0.0		0.0	False		,,,				2504	0.0				p.P602L		Atlas-SNP	.											.	SLC5A2	58	.	0			c.C1805T						PASS	.	T	LEU/PRO,	75,4319		2,71,2124	16	18	18		1805,	-0.1	0	16	dbSNP_129	18	0,8600		0,0,4300	yes	missense,utr-3	SLC5A2,C16orf58	NM_003041.3,NM_022744.2	98,	2,71,6424	TT,TC,CC		0.0,1.7069,0.5772	benign,	602/673,	31501642	75,12919	2197	4300	6497	SO:0001583	missense	6524	exon14			AGGCCCCGGCACC		CCDS10714.1	16p11.2	2013-05-22			ENSG00000140675	ENSG00000140675		"Solute carriers"	11037	protein-coding gene	gene with protein product		182381		SGLT2		8244402	Standard	NM_003041		Approved		uc002ecf.4	P31639	OTTHUMG00000176620	ENST00000330498.3:c.1805C>T	16.37:g.31501642C>T	ENSP00000327943:p.Pro602Leu	84	0	0		75	31	0.413333	NM_003041	A2RRD2	Missense_Mutation	SNP	ENST00000330498.3	37	CCDS10714.1	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	c	3.253	-0.152863	0.06585	0.017069	0.0	ENSG00000140675	ENST00000330498	D	0.91740	-2.9	5.22	-0.0727	0.13738	.	1.172050	0.06093	N	0.663966	T	0.68118	0.2966	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.65903	-0.6055	10	0.49607	T	0.09	.	8.1774	0.31289	0.0:0.5827:0.0:0.4173	rs61746400	602	P31639	SC5A2_HUMAN	L	602	ENSP00000327943:P602L	ENSP00000327943:P602L	P	+	2	0	SLC5A2	31409143	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.493000	0.22451	-0.230000	0.09840	-0.993000	0.02533	CCG	C|0.992;T|0.008	0.008	strong		0.632	SLC5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255627.2			T	31501642	C	T	31501642	3	4	22	1	0	0	0	0	1	0	0	0	14680	652	23	1	1859	1	SLC5A2	16	31501642	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	23847	31501642	58853111	3250	6151											
C16orf58	64755	hgsc.bcm.edu	37	chr16	31505252	31505252	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agccccgccaggttcaccagCgtctcctggaaaatggcaga	10	6	11	14	2	2	1	1	0	1	1	3	2	2	2	5	3	2	2	5	3	2	1	rs34231527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31505252C>T	ENST00000327237.2	-	7	747	c.708G>A	c.(706-708)acG>acA	p.T236T	C16orf58_ENST00000567994.1_Silent_p.T191T|C16orf58_ENST00000430477.2_Silent_p.T94T|C16orf58_ENST00000570164.1_Silent_p.T236T			Q96GQ5	RUS1_HUMAN	chromosome 16 open reading frame 58	236						integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)	14						GGTTCACCAGCGTCTCCTGGA	0.622													C|||	36	0.0071885	0.025	0.0043	5008	,	,		16051	0.0		0.0	False		,,,				2504	0.0				p.S236S		Atlas-SNP	.											.	C16orf58	28	.	0			c.C708A						PASS	.	C		101,4291	76.8+/-115.0	1,99,2096	34	36	36		708	-6.7	0.8	16	dbSNP_126	36	1,8599	1.2+/-3.3	0,1,4299	yes	coding-synonymous	C16orf58	NM_022744.2		1,100,6395	TT,TC,CC		0.0116,2.2996,0.7851		236/469	31505252	102,12890	2196	4300	6496	SO:0001819	synonymous_variant	64755	exon7			CACCAGCGTCTCC	AK023930	CCDS10715.1	16p11.2	2013-03-04			ENSG00000140688	ENSG00000140688			25848	protein-coding gene	gene with protein product							Standard	NM_022744		Approved	FLJ13868	uc002eci.3	Q96GQ5	OTTHUMG00000132466	ENST00000327237.2:c.708G>A	16.37:g.31505252C>T		78	0	0		124	63	0.508065	NM_022744	Q53GL8|Q8NAJ4|Q9BVY3|Q9H887	Silent	SNP	ENST00000327237.2	37	CCDS10715.1																																																																																			C|0.991;T|0.009	0.009	strong		0.622	C16orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255629.2	NM_022744		T	31505252	C	T	31505252	2	4	22	1	0	0	0	0	0	0	0	1	1824	755	27	1		1	C16orf58	16	31505252	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3610	31505252	58849501	3251	6152											
C16orf58	64755	hgsc.bcm.edu	37	chr16	31519174	31519174	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	agactgcctgggtggctaggGagccggagaggctggaagca	9	5	19	8	1	0	2	0	0	0	2	0	5	0	4	2	6	3	3	2	6	2	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31519174G>C	ENST00000327237.2	-	2	365	c.326C>G	c.(325-327)tCc>tGc	p.S109C	C16orf58_ENST00000567994.1_Missense_Mutation_p.S64C|C16orf58_ENST00000430477.2_Intron|C16orf58_ENST00000570164.1_Missense_Mutation_p.S109C|RP11-452L6.7_ENST00000569782.1_RNA			Q96GQ5	RUS1_HUMAN	chromosome 16 open reading frame 58	109						integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)	14						GGTGGCTAGGGAGCCGGAGAG	0.587																																					p.G109G		Atlas-SNP	.											.	C16orf58	28	.	0			c.G326G						PASS	.						32	27	29					16																	31519174		2189	4291	6480	SO:0001583	missense	64755	exon2			GCTAGGGAGCCGG	AK023930	CCDS10715.1	16p11.2	2013-03-04			ENSG00000140688	ENSG00000140688			25848	protein-coding gene	gene with protein product							Standard	NM_022744		Approved	FLJ13868	uc002eci.3	Q96GQ5	OTTHUMG00000132466	ENST00000327237.2:c.326C>G	16.37:g.31519174G>C	ENSP00000317579:p.Ser109Cys	64	0	0		99	51	0.515152	NM_022744	Q53GL8|Q8NAJ4|Q9BVY3|Q9H887	Silent	SNP	ENST00000327237.2	37	CCDS10715.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.018996	0.93462	.	.	ENSG00000140688	ENST00000327237;ENST00000452223;ENST00000541442	T	0.43294	0.95	5.45	5.45	0.79879	.	0.158717	0.56097	D	0.000026	T	0.59905	0.2228	M	0.74881	2.28	0.80722	D	1	P	0.45531	0.86	P	0.55667	0.781	T	0.62817	-0.6774	10	0.66056	D	0.02	-3.0354	14.7866	0.69808	0.0:0.0:1.0:0.0	.	109	Q96GQ5	CP058_HUMAN	C	109;63;109	ENSP00000317579:S109C	ENSP00000317579:S109C	S	-	2	0	C16orf58	31426675	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.068000	0.76748	2.559000	0.86315	0.655000	0.94253	TCC	.	.	none		0.587	C16orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255629.2	NM_022744		C	31519174	G	C	31519174	3	2	22	1	0	0	0	0	1	0	0	0	1824	1174	41	4	1128	4	C16orf58	16	31519174	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	13922	31519174	58835579	3252	6153											
ABCC12	94160	hgsc.bcm.edu	37	chr16	48145742	48145742	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgcatagcgccctctctccTccattaactccttgtgggtt	5	15	7	14	1	1	0	0	0	1	0	5	0	4	0	4	1	3	2	4	1	2	5	rs34135219	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:48145742T>A	ENST00000311303.3	-	14	2414	c.2069A>T	c.(2068-2070)gAg>gTg	p.E690V	ABCC12_ENST00000416054.1_3'UTR|ABCC12_ENST00000448542.1_Missense_Mutation_p.E690V	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	690	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.		E -> V (in dbSNP:rs34135219).			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)				CCCTCTCTCCTCCATTAACTC	0.458													T|||	249	0.0497204	0.1399	0.0159	5008	,	,		20912	0.0149		0.003	False		,,,				2504	0.0358				p.E690V		Atlas-SNP	.											.	ABCC12	190	.	0			c.A2069T						PASS	.	T	VAL/GLU	506,3896	237.7+/-249.4	28,450,1723	160	150	154		2069	3.1	1	16	dbSNP_126	154	33,8567	21.6+/-65.8	0,33,4267	yes	missense	ABCC12	NM_033226.2	121	28,483,5990	AA,AT,TT		0.3837,11.4948,4.1455	benign	690/1360	48145742	539,12463	2201	4300	6501	SO:0001583	missense	94160	exon14			CTCTCCTCCATTA	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.2069A>T	16.37:g.48145742T>A	ENSP00000311030:p.Glu690Val	224	0	0		235	118	0.502128	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Missense_Mutation	SNP	ENST00000311303.3	37	CCDS10730.1	71	0.03250915750915751	62	0.12601626016260162	6	0.016574585635359115	3	0.005244755244755245	0	0.0	T	12.35	1.912301	0.33721	0.114948	0.003837	ENSG00000140798	ENST00000311303;ENST00000448542;ENST00000449939	T;T	0.68331	-0.32;-0.32	5.56	3.08	0.35506	ABC transporter-like (1);	0.429810	0.26623	N	0.023346	T	0.00936	0.0031	L	0.55213	1.73	0.58432	D	0.999997	B	0.19445	0.036	B	0.22880	0.042	T	0.03060	-1.1077	10	0.45353	T	0.12	.	7.8142	0.29249	0.1333:0.0777:0.0:0.789	rs34135219;rs58143374	690	Q96J65	MRP9_HUMAN	V	690;690;632	ENSP00000311030:E690V;ENSP00000401855:E690V	ENSP00000311030:E690V	E	-	2	0	ABCC12	46703243	0.815000	0.29118	1.000000	0.80357	0.501000	0.33797	1.779000	0.38624	0.951000	0.37770	0.459000	0.35465	GAG	T|0.963;A|0.037	0.037	strong		0.458	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226		A	48145742	T	A	48145742	3	1	22	1	0	0	0	0	1	0	0	0	52	1551	54	5	2074	5	ABCC12	16	48145742	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	16626568	48145742	42209011	3253	6154											
ABCC12	94160	hgsc.bcm.edu	37	chr16	48174766	48174766	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaagggctatgcacagtccAatgccaacccagactttccc	13	7	7	14	0	0	1	0	0	0	1	2	1	2	1	4	1	3	2	4	1	5	2	rs16945872	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:48174766A>G	ENST00000311303.3	-	4	834	c.489T>C	c.(487-489)atT>atC	p.I163I	ABCC12_ENST00000416054.1_Silent_p.I163I|ABCC12_ENST00000448542.1_Silent_p.I163I	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	163	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)				TGCACAGTCCAATGCCAACCC	0.537													a|||	189	0.0377396	0.1399	0.0058	5008	,	,		19380	0.0		0.0	False		,,,				2504	0.0				p.I163I		Atlas-SNP	.											.	ABCC12	190	.	0			c.T489C						PASS	.	A		477,3925	225.9+/-241.6	24,429,1748	98	96	97		489	-2.6	0	16	dbSNP_123	97	7,8593	4.3+/-15.6	0,7,4293	no	coding-synonymous	ABCC12	NM_033226.2		24,436,6041	GG,GA,AA		0.0814,10.836,3.7225		163/1360	48174766	484,12518	2201	4300	6501	SO:0001819	synonymous_variant	94160	exon4			CAGTCCAATGCCA	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.489T>C	16.37:g.48174766A>G		94	0	0		103	47	0.456311	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Silent	SNP	ENST00000311303.3	37	CCDS10730.1																																																																																			A|0.955;G|0.045	0.045	strong		0.537	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226		G	48174766	A	G	48174766	2	3	22	1	0	0	0	0	0	0	0	1	52	126	5	3		3	ABCC12	16	48174766	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	29024	48174766	42179987	3254	6155											
ABCC12	94160	hgsc.bcm.edu	37	chr16	48180311	48180311	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcgctggtccagatctgagaTaaggtagggtccttcaccca	9	10	11	11	1	2	2	1	1	1	2	5	3	4	2	3	3	0	2	3	3	2	3	rs16945901	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:48180311T>G	ENST00000311303.3	-	1	370	c.25A>C	c.(25-27)Atc>Ctc	p.I9L	ABCC12_ENST00000416054.1_Missense_Mutation_p.I9L|ABCC12_ENST00000448542.1_Missense_Mutation_p.I9L	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	9			I -> L (in dbSNP:rs16945901).			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)				AGATCTGAGATAAGGTAGGGT	0.552													T|||	189	0.0377396	0.1399	0.0058	5008	,	,		20637	0.0		0.0	False		,,,				2504	0.0				p.I9L		Atlas-SNP	.											.	ABCC12	190	.	0			c.A25C						PASS	.	T	LEU/ILE	477,3925	225.9+/-241.6	24,429,1748	108	96	100		25	5.4	1	16	dbSNP_123	100	7,8593	4.3+/-15.6	0,7,4293	yes	missense	ABCC12	NM_033226.2	5	24,436,6041	GG,GT,TT		0.0814,10.836,3.7225	possibly-damaging	9/1360	48180311	484,12518	2201	4300	6501	SO:0001583	missense	94160	exon1			CTGAGATAAGGTA	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.25A>C	16.37:g.48180311T>G	ENSP00000311030:p.Ile9Leu	133	0	0		128	63	0.492188	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Missense_Mutation	SNP	ENST00000311303.3	37	CCDS10730.1	74	0.03388278388278388	72	0.14634146341463414	2	0.0055248618784530384	0	0.0	0	0.0	T	17.20	3.327928	0.60743	0.10836	8.14E-4	ENSG00000140798	ENST00000311303;ENST00000448542;ENST00000449939;ENST00000416054;ENST00000527640	D;D;D;D	0.92911	-2.8;-3.04;-3.13;-2.66	5.41	5.41	0.78517	.	0.208161	0.39687	N	0.001292	T	0.01976	0.0062	N	0.25144	0.715	0.34860	P	0.257501	B;B	0.21821	0.061;0.007	B;B	0.16289	0.015;0.003	T	0.56914	-0.7900	9	0.02654	T	1	.	11.8356	0.52321	0.0:0.0:0.0:1.0	rs16945901;rs59437921;rs16945901	9;9	Q96J65-2;Q96J65	.;MRP9_HUMAN	L	9	ENSP00000311030:I9L;ENSP00000401855:I9L;ENSP00000413046:I9L;ENSP00000436647:I9L	ENSP00000311030:I9L	I	-	1	0	ABCC12	46737812	0.989000	0.36119	0.994000	0.49952	0.960000	0.62799	1.976000	0.40579	2.022000	0.59522	0.496000	0.49642	ATC	T|0.955;G|0.045	0.045	strong		0.552	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226		G	48180311	T	G	48180311	3	3	22	1	0	0	0	0	1	0	0	0	52	1406	49	5	4170	5	ABCC12	16	48180311	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	5545	48180311	42174442	3255	6156											
ABCC11	85320	hgsc.bcm.edu	37	chr16	48234214	48234214	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtgggtcaccaggacgacCgtcttccccctgagtgtctt	5	11	12	13	2	3	1	1	1	2	0	4	3	4	2	4	3	0	0	4	3	0	2	rs61745566	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:48234214C>T	ENST00000394747.1	-	14	2404	c.2055G>A	c.(2053-2055)acG>acA	p.T685T	ABCC11_ENST00000394748.1_Silent_p.T685T|ABCC11_ENST00000356608.2_Silent_p.T685T|ABCC11_ENST00000353782.5_Silent_p.T685T|ABCC11_ENST00000537808.1_Silent_p.T685T	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	685	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)	CCAGGACGACCGTCTTCCCCC	0.552													C|||	108	0.0215655	0.0787	0.0043	5008	,	,		17717	0.0		0.0	False		,,,				2504	0.001				p.T685T		Atlas-SNP	.											.	ABCC11	177	.	0			c.G2055A						PASS	.	C	,,	233,4169	140.0+/-175.5	7,219,1975	114	98	104		2055,2055,2055	-11.4	0	16	dbSNP_129	104	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	ABCC11	NM_032583.3,NM_033151.3,NM_145186.2	,,	7,224,6270	TT,TC,CC		0.0581,5.293,1.8305	,,	685/1383,685/1383,685/1345	48234214	238,12764	2201	4300	6501	SO:0001819	synonymous_variant	85320	exon14			GACGACCGTCTTC	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.2055G>A	16.37:g.48234214C>T		62	0	0		61	27	0.442623	NM_033151	Q8TDJ0|Q96JA6|Q9BX80	Silent	SNP	ENST00000394747.1	37	CCDS10732.1																																																																																			C|0.980;T|0.020	0.020	strong		0.552	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583		T	48234214	C	T	48234214	2	4	22	1	0	0	0	0	0	0	0	1	51	639	23	1		1	ABCC11	16	48234214	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	53903	48234214	42120539	3256	6157											
ABCC11	85320	hgsc.bcm.edu	37	chr16	48234381	48234381	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccagagaggttgaggccccGctctccaatctgcagacagg	9	6	12	14	1	2	3	0	1	2	2	3	4	2	3	4	3	1	3	4	3	1	1	rs41282045	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:48234381G>A	ENST00000394747.1	-	14	2237	c.1888C>T	c.(1888-1890)Cgg>Tgg	p.R630W	ABCC11_ENST00000394748.1_Missense_Mutation_p.R630W|ABCC11_ENST00000356608.2_Missense_Mutation_p.R630W|ABCC11_ENST00000353782.5_Missense_Mutation_p.R630W|ABCC11_ENST00000537808.1_Missense_Mutation_p.R630W	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	630	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)	TTGAGGCCCCGCTCTCCAATC	0.597													G|||	13	0.00259585	0.003	0.0043	5008	,	,		18082	0.0		0.004	False		,,,				2504	0.002				p.R630W		Atlas-SNP	.											.	ABCC11	177	.	0			c.C1888T						PASS	.	G	TRP/ARG,TRP/ARG,TRP/ARG	12,4390	19.1+/-41.9	0,12,2189	46	38	41		1888,1888,1888	1.2	1	16	dbSNP_127	41	61,8539	37.8+/-93.5	0,61,4239	yes	missense,missense,missense	ABCC11	NM_032583.3,NM_033151.3,NM_145186.2	101,101,101	0,73,6428	AA,AG,GG		0.7093,0.2726,0.5615	probably-damaging,probably-damaging,probably-damaging	630/1383,630/1383,630/1345	48234381	73,12929	2201	4300	6501	SO:0001583	missense	85320	exon14			GGCCCCGCTCTCC	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.1888C>T	16.37:g.48234381G>A	ENSP00000378230:p.Arg630Trp	50	0	0		48	24	0.5	NM_033151	Q8TDJ0|Q96JA6|Q9BX80	Missense_Mutation	SNP	ENST00000394747.1	37	CCDS10732.1	6	0.0027472527472527475	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	20.3	3.968770	0.74131	0.002726	0.007093	ENSG00000121270	ENST00000353782;ENST00000356608;ENST00000394748;ENST00000394747;ENST00000537808	D;D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53;-1.53	5.61	1.19	0.21007	ABC transporter, transmembrane domain, type 1 (1);ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.067924	0.64402	N	0.000016	D	0.85375	0.5682	M	0.91561	3.22	0.80722	D	1	B;D	0.89917	0.333;1.0	B;D	0.97110	0.061;1.0	D	0.83707	0.0185	10	0.87932	D	0	-11.3458	4.1375	0.10178	0.1727:0.0:0.5052:0.3221	rs41282045	630;630	Q96J66-2;Q96J66	.;ABCCB_HUMAN	W	630	ENSP00000311326:R630W;ENSP00000349017:R630W;ENSP00000378231:R630W;ENSP00000378230:R630W;ENSP00000438530:R630W	ENSP00000311326:R630W	R	-	1	2	ABCC11	46791882	0.945000	0.32115	0.999000	0.59377	0.784000	0.44337	0.691000	0.25467	0.316000	0.23135	0.655000	0.94253	CGG	G|0.996;A|0.004	0.004	strong		0.597	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583		A	48234381	G	A	48234381	3	1	22	1	0	0	0	0	1	0	0	0	51	1086	38	1	2324	1	ABCC11	16	48234381	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	167	48234381	42120372	3257	6158											
ABCC11	85320	hgsc.bcm.edu	37	chr16	48250031	48250031	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagaaagacattaccgccagTgggaaaaccaggagatagca	17	4	12	8	1	0	3	0	0	0	3	0	6	0	4	3	2	3	1	3	2	5	2	rs11860868	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:48250031T>C	ENST00000394747.1	-	6	1294	c.945A>G	c.(943-945)ccA>ccG	p.P315P	ABCC11_ENST00000394748.1_Silent_p.P315P|ABCC11_ENST00000356608.2_Silent_p.P315P|ABCC11_ENST00000353782.5_Silent_p.P315P|ABCC11_ENST00000537808.1_Silent_p.P315P	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	315	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				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)	TTACCGCCAGTGGGAAAACCA	0.473													C|||	295	0.0589058	0.2156	0.013	5008	,	,		21846	0.0		0.001	False		,,,				2504	0.0				p.P315P		Atlas-SNP	.											.	ABCC11	177	.	0			c.A945G						PASS	.	C	,,	768,3634	752.7+/-412.3	65,638,1498	128	132	130		945,945,945	-6.8	0	16	dbSNP_120	130	4,8596	819.1+/-406.8	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	ABCC11	NM_032583.3,NM_033151.3,NM_145186.2	,,	65,642,5794	CC,CT,TT		0.0465,17.4466,5.9375	,,	315/1383,315/1383,315/1345	48250031	772,12230	2201	4300	6501	SO:0001819	synonymous_variant	85320	exon6			CGCCAGTGGGAAA	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.945A>G	16.37:g.48250031T>C		31	0	0		55	27	0.490909	NM_033151	Q8TDJ0|Q96JA6|Q9BX80	Silent	SNP	ENST00000394747.1	37	CCDS10732.1																																																																																			T|0.927;C|0.073	0.073	strong		0.473	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583		C	48250031	T	C	48250031	2	2	22	1	0	0	0	0	0	0	0	1	51	1683	59	3		3	ABCC11	16	48250031	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	15650	48250031	42104722	3258	6159											
ADCY7	113	hgsc.bcm.edu	37	chr16	50344627	50344627	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgcagctgtgtcctgggcttCatcgcctgctcggtcttcct	2	14	11	14	2	2	0	1	0	1	0	6	0	4	0	3	2	3	4	3	2	0	2	rs140505854	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:50344627C>T	ENST00000394697.2	+	19	2530	c.2190C>T	c.(2188-2190)ttC>ttT	p.F730F	ADCY7_ENST00000254235.3_Silent_p.F730F			P51828	ADCY7_HUMAN	adenylate cyclase 7	730					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)		TCCTGGGCTTCATCGCCTGCT	0.617													C|||	2	0.000399361	0.0015	0.0	5008	,	,		18686	0.0		0.0	False		,,,				2504	0.0				p.F730F		Atlas-SNP	.											.	ADCY7	90	.	0			c.C2190T						PASS	.	C		4,4392	8.1+/-20.4	0,4,2194	107	78	88		2190	1.1	0.2	16	dbSNP_134	88	0,8600		0,0,4300	no	coding-synonymous	ADCY7	NM_001114.3		0,4,6494	TT,TC,CC		0.0,0.091,0.0308		730/1081	50344627	4,12992	2198	4300	6498	SO:0001819	synonymous_variant	113	exon18			GGGCTTCATCGCC	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.2190C>T	16.37:g.50344627C>T		127	0	0		142	71	0.5	NM_001114	A0AVA6	Silent	SNP	ENST00000394697.2	37	CCDS10741.1																																																																																			C|1.000;T|0.000	0.000	weak		0.617	ADCY7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256877.3			T	50344627	C	T	50344627	2	4	22	1	0	0	0	0	0	0	0	1	299	825	29	2		2	ADCY7	16	50344627	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2094596	50344627	40010126	3259	6160											
BRD7	29117	hgsc.bcm.edu	37	chr16	50368626	50368626	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cccaaagatcttttacttttTattttctttgctgggactct	7	20	5	9	0	3	1	0	0	3	1	3	2	3	2	1	1	2	1	1	1	3	8			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:50368626T>C	ENST00000394688.3	-	7	1042	c.883A>G	c.(883-885)Aaa>Gaa	p.K295E	BRD7_ENST00000394689.2_Missense_Mutation_p.K295E			Q9NPI1	BRD7_HUMAN	bromodomain containing 7	295					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)				TTTTACTTTTTATTTTCTTTG	0.488																																					p.K295E		Atlas-SNP	.											.	BRD7	61	.	0			c.A883G						PASS	.						95	110	105					16																	50368626		2192	4296	6488	SO:0001583	missense	29117	exon7			ACTTTTTATTTTC	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.883A>G	16.37:g.50368626T>C	ENSP00000378180:p.Lys295Glu	71	0	0		84	8	0.0952381	NM_013263	Q4VC09|Q8N2L9|Q96KA4|Q9BV48|Q9UH59	Missense_Mutation	SNP	ENST00000394688.3	37	CCDS10742.1	.	.	.	.	.	.	.	.	.	.	T	12.84	2.058696	0.36277	.	.	ENSG00000166164	ENST00000394688;ENST00000394689	T;T	0.52754	0.65;0.65	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.49321	0.1550	M	0.67953	2.075	0.47374	D	0.999409	B;B	0.27910	0.193;0.161	B;B	0.31442	0.13;0.079	T	0.45891	-0.9230	10	0.34782	T	0.22	.	14.6369	0.68696	0.0:0.0:0.0:1.0	.	295;295	Q9NPI1;Q9NPI1-2	BRD7_HUMAN;.	E	295	ENSP00000378180:K295E;ENSP00000378181:K295E	ENSP00000378180:K295E	K	-	1	0	BRD7	48926127	1.000000	0.71417	0.995000	0.50966	0.266000	0.26442	4.022000	0.57203	2.254000	0.74563	0.528000	0.53228	AAA	.	.	none		0.488	BRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256874.3	NM_013263		C	50368626	T	C	50368626	3	2	22	1	0	0	0	0	1	0	0	0	1507	1763	61	3	1119	3	BRD7	16	50368626	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	23999	50368626	39986127	3260	6161											
BRD7	29117	hgsc.bcm.edu	37	chr16	50368670	50368670	+	Missense_Mutation	SNP	C	C	A																															aggcgtgtgcttcggcatctCcagagtcctctctctctctc																								rs113038433	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:50368670C>A	ENST00000394688.3	-	7	998	c.839G>T	c.(838-840)gGa>gTa	p.G280V	BRD7_ENST00000394689.2_Missense_Mutation_p.G280V			Q9NPI1	BRD7_HUMAN	bromodomain containing 7	280					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)				TTCGGCATCTCCAGAGTCCTC	0.473													C|||	60	0.0119808	0.0431	0.0043	5008	,	,		17122	0.0		0.0	False		,,,				2504	0.0				p.G280V		Atlas-SNP	.											.	BRD7	61	.	0			c.G839T						PASS	.	C	VAL/GLY,VAL/GLY	129,4267	94.4+/-133.1	1,127,2070	138	142	141		839,839	4.4	0.4	16	dbSNP_132	141	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	BRD7	NM_001173984.2,NM_013263.4	109,109	1,128,6369	AA,AC,CC		0.0116,2.9345,1.0003	benign,benign	280/653,280/652	50368670	130,12866	2198	4300	6498	SO:0001583	missense	29117	exon7			GCATCTCCAGAGT	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.839G>T	16.37:g.50368670C>A	ENSP00000378180:p.Gly280Val	136	0	0		192	59	0.307292	NM_013263	Q4VC09|Q8N2L9|Q96KA4|Q9BV48|Q9UH59	Missense_Mutation	SNP	ENST00000394688.3	37	CCDS10742.1	25	0.011446886446886446	24	0.04878048780487805	1	0.0027624309392265192	0	0.0	0	0.0	C	10.22	1.289343	0.23478	0.029345	1.16E-4	ENSG00000166164	ENST00000394688;ENST00000394689	T;T	0.30448	1.54;1.53	5.47	4.41	0.53225	.	0.486780	0.23583	N	0.046637	T	0.02193	0.0068	N	0.08118	0	0.24366	N	0.994853	B;B	0.06786	0.0;0.001	B;B	0.09377	0.002;0.004	T	0.07121	-1.0789	10	0.27082	T	0.32	-13.1079	10.8718	0.46887	0.3081:0.6919:0.0:0.0	.	280;280	Q9NPI1;Q9NPI1-2	BRD7_HUMAN;.	V	280	ENSP00000378180:G280V;ENSP00000378181:G280V	ENSP00000378180:G280V	G	-	2	0	BRD7	48926171	0.945000	0.32115	0.424000	0.26647	0.782000	0.44232	2.285000	0.43487	2.733000	0.93635	0.650000	0.86243	GGA	C|0.988;A|0.012	0.012	strong		0.473	BRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256874.3	NM_013263		A	50368670	C	A	50368670	3	1	22	1	0	0	0	0	1	0	0	0	1507	855	30	4	1163	4	BRD7	16	50368670	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	44	50368670	39986083	3261	6162	76	2									
BRD7	29117	hgsc.bcm.edu	37	chr16	50368671	50368671	+	Missense_Mutation	SNP	C	C	G																															ggcgtgtgcttcggcatctcCagagtcctctctctctctct																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:50368671C>G	ENST00000394688.3	-	7	997	c.838G>C	c.(838-840)Gga>Cga	p.G280R	BRD7_ENST00000394689.2_Missense_Mutation_p.G280R			Q9NPI1	BRD7_HUMAN	bromodomain containing 7	280					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)				TCGGCATCTCCAGAGTCCTCT	0.473																																					p.G280R		Atlas-SNP	.											.	BRD7	61	.	0			c.G838C						PASS	.						138	142	141					16																	50368671		2198	4300	6498	SO:0001583	missense	29117	exon7			CATCTCCAGAGTC	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.838G>C	16.37:g.50368671C>G	ENSP00000378180:p.Gly280Arg	136	0	0		194	58	0.298969	NM_013263	Q4VC09|Q8N2L9|Q96KA4|Q9BV48|Q9UH59	Missense_Mutation	SNP	ENST00000394688.3	37	CCDS10742.1	.	.	.	.	.	.	.	.	.	.	C	8.023	0.760146	0.15846	.	.	ENSG00000166164	ENST00000394688;ENST00000394689	T;T	0.30981	1.51;1.51	5.47	3.42	0.39159	.	0.486780	0.23583	N	0.046637	T	0.18173	0.0436	L	0.29908	0.895	0.09310	N	1	B;P	0.35923	0.393;0.528	B;B	0.37943	0.133;0.261	T	0.10636	-1.0621	10	0.14252	T	0.57	-13.1079	5.4568	0.16594	0.1802:0.6543:0.0:0.1655	.	280;280	Q9NPI1;Q9NPI1-2	BRD7_HUMAN;.	R	280	ENSP00000378180:G280R;ENSP00000378181:G280R	ENSP00000378180:G280R	G	-	1	0	BRD7	48926172	0.849000	0.29639	0.418000	0.26571	0.791000	0.44710	1.471000	0.35365	2.733000	0.93635	0.650000	0.86243	GGA	.	.	none		0.473	BRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256874.3	NM_013263		G	50368671	C	G	50368671	3	3	22	1	0	0	0	0	1	0	0	0	1507	603	21	4	1164	4	BRD7	16	50368671	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1	50368671	39986082	3262	6163	76	2									
SNX20	124460	hgsc.bcm.edu	37	chr16	50709792	50709792	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtactgctgaagctcccgCgtggtcatgctggagttgga	7	10	14	10	2	1	1	1	1	0	0	2	3	2	3	1	3	4	5	1	3	2	2	rs35435054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:50709792C>T	ENST00000330943.4	-	3	342	c.171G>A	c.(169-171)acG>acA	p.T57T	SNX20_ENST00000423026.2_Silent_p.T57T|SNX20_ENST00000300590.3_Silent_p.T57T	NM_182854.2	NP_878274.1	Q7Z614	SNX20_HUMAN	sorting nexin 20	57					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						GAAGCTCCCGCGTGGTCATGC	0.552													C|||	70	0.0139776	0.0499	0.0043	5008	,	,		21120	0.0		0.001	False		,,,				2504	0.0				p.T57T		Atlas-SNP	.											SNX20_ENST00000300590,NS,carcinoma,-1,2	SNX20	50	2	0			c.G171A						PASS	.	C	,,	220,4176	132.1+/-168.6	5,210,1983	103	92	96		171,171,171	-11.3	0.1	16	dbSNP_126	96	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	SNX20	NM_001144972.1,NM_153337.2,NM_182854.2	,,	5,211,6282	TT,TC,CC		0.0116,5.0045,1.7005	,,	57/103,57/130,57/317	50709792	221,12775	2198	4300	6498	SO:0001819	synonymous_variant	124460	exon3			CTCCCGCGTGGTC	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.171G>A	16.37:g.50709792C>T		66	0	0		80	34	0.425	NM_001144972	A8K9D5|Q08E98|Q6P4H2|Q8IV59	Silent	SNP	ENST00000330943.4	37	CCDS10745.1																																																																																			C|0.981;T|0.019	0.019	strong		0.552	SNX20-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256879.2	NM_153337		T	50709792	C	T	50709792	2	4	22	1	0	0	0	0	0	0	0	1	14907	755	27	1		1	SNX20	16	50709792	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	341121	50709792	39644961	3263	6164											
NOD2	64127	hgsc.bcm.edu	37	chr16	50746191	50746191	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctttgtgctgcagcacctccGgcggcccgtggccctgcagc	3	8	13	17	3	0	0	0	0	0	0	1	0	1	0	4	3	5	4	4	3	0	1	rs5743279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:50746191G>A	ENST00000300589.2	+	4	2474	c.2369G>A	c.(2368-2370)cGg>cAg	p.R790Q	RP11-327F22.6_ENST00000602304.1_RNA	NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	790			R -> Q (in dbSNP:rs5743279).		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)	p.R790L(1)		cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				CAGCACCTCCGGCGGCCCGTG	0.607													G|||	51	0.0101837	0.0371	0.0029	5008	,	,		21469	0.0		0.0	False		,,,				2504	0.0				p.R790Q		Atlas-SNP	.											NOD2,colon,carcinoma,+1,2	NOD2	118	2	1	Substitution - Missense(1)	lung(1)	c.G2369A						PASS	.	G	GLN/ARG	149,4247	101.2+/-139.8	2,145,2051	95	88	90		2369	-0.2	1	16	dbSNP_114	90	1,8599	1.2+/-3.3	0,1,4299	yes	missense	NOD2	NM_022162.1	43	2,146,6350	AA,AG,GG		0.0116,3.3894,1.1542	benign	790/1041	50746191	150,12846	2198	4300	6498	SO:0001583	missense	64127	exon4			ACCTCCGGCGGCC	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.2369G>A	16.37:g.50746191G>A	ENSP00000300589:p.Arg790Gln	102	0	0		125	67	0.536	NM_022162	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Missense_Mutation	SNP	ENST00000300589.2	37	CCDS10746.1	14	0.00641025641025641	13	0.026422764227642278	1	0.0027624309392265192	0	0.0	0	0.0	G	0.038	-1.298744	0.01364	0.033894	1.16E-4	ENSG00000167207	ENST00000526417;ENST00000300589	T	0.51817	0.69	5.3	-0.17	0.13335	.	0.234851	0.28983	N	0.013509	T	0.09774	0.0240	N	0.21194	0.64	0.09310	N	1	B;B;B	0.27166	0.002;0.17;0.039	B;B;B	0.19391	0.001;0.025;0.003	T	0.10042	-1.0647	10	0.20519	T	0.43	.	8.9611	0.35847	0.5027:0.0:0.4973:0.0	rs5743279;rs5743279	574;763;790	D6CHF9;Q9HC29-2;Q9HC29	.;.;NOD2_HUMAN	Q	763;790	ENSP00000300589:R790Q	ENSP00000300589:R790Q	R	+	2	0	NOD2	49303692	0.000000	0.05858	0.988000	0.46212	0.065000	0.16274	0.196000	0.17176	0.076000	0.16826	-0.254000	0.11334	CGG	G|0.989;A|0.011	0.011	strong		0.607	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162		A	50746191	G	A	50746191	3	1	22	1	0	0	0	0	1	0	0	0	10526	1116	39	1	2383	1	NOD2	16	50746191	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	36399	50746191	39608562	3264	6165											
CYLD	1540	hgsc.bcm.edu	37	chr16	50783696	50783696	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgcttcttcaagaatgcagCgttacagacaaacaaacaca	16	9	6	10	1	2	2	1	0	1	2	2	2	2	2	0	0	6	3	0	0	5	4	rs34564491	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:50783696C>T	ENST00000427738.3	+	2	292	c.87C>T	c.(85-87)agC>agT	p.S29S	CYLD_ENST00000566206.1_Silent_p.S29S|CYLD_ENST00000569418.1_Silent_p.S29S|CYLD_ENST00000398568.2_Silent_p.S29S|CYLD_ENST00000564326.1_Silent_p.S29S|CYLD_ENST00000540145.1_Silent_p.S29S|CYLD_ENST00000311559.9_Silent_p.S29S|CYLD_ENST00000568704.2_Silent_p.S29S			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	29					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)				AAGAATGCAGCGTTACAGACA	0.408			"Mis, N, F, S"		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis				C|||	63	0.0125799	0.0446	0.0058	5008	,	,		18761	0.0		0.0	False		,,,				2504	0.0				p.S29S		Atlas-SNP	.	yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	.	CYLD	150	.	0			c.C87T						PASS	.	C	,,	145,3565		2,141,1712	83	79	80		87,87,87	2	1	16	dbSNP_126	80	1,8179		0,1,4089	no	coding-synonymous,coding-synonymous,coding-synonymous	CYLD	NM_001042355.1,NM_001042412.1,NM_015247.2	,,	2,142,5801	TT,TC,CC		0.0122,3.9084,1.2279	,,	29/954,29/954,29/957	50783696	146,11744	1855	4090	5945	SO:0001819	synonymous_variant	1540	exon3	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	ATGCAGCGTTACA	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.87C>T	16.37:g.50783696C>T		50	0	0		60	26	0.433333	NM_001042355	O94934|Q7L3N6|Q96EH0|Q9NZX9	Silent	SNP	ENST00000427738.3	37	CCDS45482.1																																																																																			C|0.991;T|0.009	0.009	strong		0.408	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2			T	50783696	C	T	50783696	2	4	22	1	0	0	0	0	0	0	0	1	4145	767	27	1		1	CYLD	16	50783696	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	37505	50783696	39571057	3265	6166											
SALL1	6299	hgsc.bcm.edu	37	chr16	51173823	51173823	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttcgtgaacttcttctggcaGatggggcaggaatgctggac	8	11	14	8	1	2	2	0	1	2	1	3	4	2	4	0	5	2	3	0	5	2	3	rs61740811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:51173823G>A	ENST00000251020.4	-	2	2343	c.2310C>T	c.(2308-2310)atC>atT	p.I770I	SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_Silent_p.I673I|SALL1_ENST00000541611.1_Intron	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	770					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)			TCTTCTGGCAGATGGGGCAGG	0.567													G|||	201	0.0401358	0.1392	0.0231	5008	,	,		19398	0.0		0.001	False		,,,				2504	0.0				p.I770I	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.C2310T						PASS	.	G	,	539,3857	246.8+/-255.3	25,489,1684	86	90	89		2019,2310	4.2	1	16	dbSNP_129	89	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous	SALL1	NM_001127892.1,NM_002968.2	,	25,493,5980	AA,AG,GG		0.0465,12.2611,4.1782	,	673/1228,770/1325	51173823	543,12453	2198	4300	6498	SO:0001819	synonymous_variant	6299	exon2			CTGGCAGATGGGG	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.2310C>T	16.37:g.51173823G>A		221	0	0		228	114	0.5	NM_002968	Q99881|Q9NSC3|Q9P1R0	Silent	SNP	ENST00000251020.4	37	CCDS10747.1																																																																																			G|0.957;A|0.043	0.043	strong		0.567	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		A	51173823	G	A	51173823	2	1	22	1	0	0	0	0	0	0	0	1	13825	932	33	2		2	SALL1	16	51173823	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	390127	51173823	39180930	3266	6167											
TOX3	27324	hgsc.bcm.edu	37	chr16	52484317	52484317	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaattcaaccccaactgggCgctgagctgagactggttga	11	8	11	11	1	1	3	1	3	0	1	1	4	1	3	2	2	3	3	2	2	3	2	rs114182621	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:52484317C>T	ENST00000219746.9	-	4	834	c.550G>A	c.(550-552)Gcc>Acc	p.A184T	TOX3_ENST00000407228.3_Missense_Mutation_p.A179T	NM_001080430.2	NP_001073899.2	O15405	TOX3_HUMAN	TOX high mobility group box family member 3	184					apoptotic process (GO:0006915)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|estrogen response element binding (GO:0034056)|phosphoprotein binding (GO:0051219)|protein homodimerization activity (GO:0042803)			NS(2)|endometrium(6)|kidney(1)|lung(8)|prostate(3)|stomach(3)|upper_aerodigestive_tract(1)	24						CCCAACTGGGCGCTGAGCTGA	0.582													C|||	28	0.00559105	0.0189	0.0029	5008	,	,		17831	0.001		0.0	False		,,,				2504	0.0				p.A184T		Atlas-SNP	.											.	TOX3	121	.	0			c.G550A						PASS	.	C	THR/ALA,THR/ALA	74,4182		2,70,2056	150	158	155		550,535	3.8	1	16	dbSNP_132	155	0,8480		0,0,4240	yes	missense,missense	TOX3	NM_001080430.2,NM_001146188.1	58,58	2,70,6296	TT,TC,CC		0.0,1.7387,0.581	probably-damaging,probably-damaging	184/577,179/572	52484317	74,12662	2128	4240	6368	SO:0001583	missense	27324	exon4			ACTGGGCGCTGAG	U80736	CCDS54008.1, CCDS54009.1	16q12.1	2008-02-05	2007-03-20	2007-03-20		ENSG00000103460		"Trinucleotide (CAG) repeat containing"	11972	protein-coding gene	gene with protein product		611416	"trinucleotide repeat containing 9"	TNRC9		9225980	Standard	NM_001080430		Approved	CAGF9	uc002egw.2	O15405		ENST00000219746.9:c.550G>A	16.37:g.52484317C>T	ENSP00000219746:p.Ala184Thr	118	0	0		140	70	0.5	NM_001080430	B4DRD0|B5MCW4	Missense_Mutation	SNP	ENST00000219746.9	37	CCDS54009.1	15	0.006868131868131868	13	0.026422764227642278	1	0.0027624309392265192	1	0.0017482517482517483	0	0.0	C	13.54	2.267516	0.40095	0.017387	0.0	ENSG00000103460	ENST00000219746;ENST00000407228	T;T	0.11495	2.77;2.77	5.71	3.77	0.43336	.	0.129794	0.49916	D	0.000134	T	0.04588	0.0125	M	0.68593	2.085	0.45025	D	0.998041	B;B	0.17268	0.008;0.021	B;B	0.06405	0.002;0.002	T	0.02411	-1.1163	10	0.72032	D	0.01	.	11.9513	0.52956	0.0:0.8601:0.0:0.1399	.	179;184	B4DRD0;O15405	.;TOX3_HUMAN	T	184;179	ENSP00000219746:A184T;ENSP00000385705:A179T	ENSP00000219746:A184T	A	-	1	0	TOX3	51041818	1.000000	0.71417	0.992000	0.48379	0.014000	0.08584	3.357000	0.52277	0.763000	0.33175	0.563000	0.77884	GCC	C|0.992;T|0.008	0.008	strong		0.582	TOX3-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000422534.1	XM_049037		T	52484317	C	T	52484317	3	4	22	1	0	0	0	0	1	0	0	0	16394	768	27	1	1196	1	TOX3	16	52484317	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1310494	52484317	37870436	3267	6168											
AKTIP	64400	hgsc.bcm.edu	37	chr16	53526366	53526366	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctttactgaaaggctgtacTgagccaggctttacccatga	10	12	9	10	0	1	3	0	3	1	0	1	3	1	3	2	2	4	3	2	2	4	5	rs16952272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:53526366T>C	ENST00000394657.7	-	10	1011	c.837A>G	c.(835-837)tcA>tcG	p.S279S	AKTIP_ENST00000570004.1_Silent_p.S279S|AKTIP_ENST00000300245.4_Silent_p.S280S	NM_001012398.1|NM_022476.2	NP_001012398.1|NP_071921.1	Q9H8T0	AKTIP_HUMAN	AKT interacting protein	279					apoptotic process (GO:0006915)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|protein transport (GO:0015031)	FHF complex (GO:0070695)|plasma membrane (GO:0005886)	acid-amino acid ligase activity (GO:0016881)			large_intestine(1)|lung(2)|prostate(2)	5		all_cancers(37;0.14)				AAGGCTGTACTGAGCCAGGCT	0.433													T|||	36	0.0071885	0.025	0.0029	5008	,	,		20673	0.0		0.001	False		,,,				2504	0.0				p.S279S		Atlas-SNP	.											.	AKTIP	16	.	0			c.A837G						PASS	.	T	,	119,4277	89.2+/-127.9	2,115,2081	115	112	113		837,837	1.3	1	16	dbSNP_123	113	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	AKTIP	NM_001012398.1,NM_022476.2	,	2,116,6380	CC,CT,TT		0.0116,2.707,0.9234	,	279/293,279/293	53526366	120,12876	2198	4300	6498	SO:0001819	synonymous_variant	64400	exon10			CTGTACTGAGCCA	AK023320	CCDS10749.1	16q12.2	2010-01-14	2007-01-16	2007-01-16	ENSG00000166971	ENSG00000166971		"Ubiquitin-conjugating enzymes E2"	16710	protein-coding gene	gene with protein product		608483	"fused toes (mouse) homolog", "fused toes homolog (mouse)"	FTS		7818539, 8626685	Standard	XM_005256094		Approved	FLJ13258	uc002ehl.3	Q9H8T0	OTTHUMG00000133199	ENST00000394657.7:c.837A>G	16.37:g.53526366T>C		180	0	0		184	87	0.472826	NM_022476	Q503B1|Q53H38	Silent	SNP	ENST00000394657.7	37	CCDS10749.1																																																																																			T|0.990;C|0.010	0.010	strong		0.433	AKTIP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256909.4	NM_022476		C	53526366	T	C	53526366	2	2	22	1	0	0	0	0	0	0	0	1	482	1567	55	3		3	AKTIP	16	53526366	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1042049	53526366	36828387	3268	6169											
FTO	79068	hgsc.bcm.edu	37	chr16	53922838	53922838	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acccatggctcaactggaagCactgtggaagaagatggagg	13	6	14	8	0	1	2	1	0	0	2	1	5	1	5	1	5	2	2	1	5	4	0	rs16952624	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:53922838C>T	ENST00000471389.1	+	7	1436	c.1214C>T	c.(1213-1215)gCa>gTa	p.A405V	FTO_ENST00000431610.2_Missense_Mutation_p.A6V|FTO_ENST00000394647.3_Missense_Mutation_p.A109V|FTO_ENST00000460382.1_Missense_Mutation_p.A6V	NM_001080432.2	NP_001073901.1	Q9C0B1	FTO_HUMAN	fat mass and obesity associated	405			A -> V (in dbSNP:rs16952624).		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						CAACTGGAAGCACTGTGGAAG	0.502													C|||	37	0.00738818	0.0272	0.0014	5008	,	,		18970	0.0		0.0	False		,,,				2504	0.0				p.A405V		Atlas-SNP	.											FTO,NS,carcinoma,-1,1	FTO	51	1	0			c.C1214T						PASS	.	C	VAL/ALA	124,4272	93.0+/-131.7	4,116,2078	287	257	267		1214	-3.4	0	16	dbSNP_123	267	0,8600		0,0,4300	yes	missense	FTO	NM_001080432.2	64	4,116,6378	TT,TC,CC		0.0,2.8207,0.9541	benign	405/506	53922838	124,12872	2198	4300	6498	SO:0001583	missense	79068	exon7			TGGAAGCACTGTG	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.1214C>T	16.37:g.53922838C>T	ENSP00000418823:p.Ala405Val	299	0	0		326	156	0.478528	NM_001080432	A2RUH1|B2RNS0|Q0P676|Q7Z785	Missense_Mutation	SNP	ENST00000471389.1	37	CCDS32448.1	21	0.009615384615384616	20	0.04065040650406504	1	0.0027624309392265192	0	0.0	0	0.0	C	8.234	0.805364	0.16467	0.028207	0.0	ENSG00000140718	ENST00000471389;ENST00000394647;ENST00000431610;ENST00000460382;ENST00000476894	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.84	-3.41	0.04839	Alpha-ketoglutarate-dependent dioxygenase FTO, C-terminal (1);	0.513654	0.22753	N	0.056043	T	0.04724	0.0128	N	0.14661	0.345	0.09310	N	0.999998	B	0.18013	0.025	B	0.18871	0.023	T	0.06552	-1.0820	10	0.46703	T	0.11	-3.9788	7.7201	0.28727	0.3262:0.2045:0.4693:0.0	rs16952624;rs52815989;rs16952624	405	Q9C0B1	FTO_HUMAN	V	405;109;6;6;6	ENSP00000418823:A405V;ENSP00000378142:A109V;ENSP00000415636:A6V;ENSP00000417422:A6V	ENSP00000378142:A109V	A	+	2	0	FTO	52480339	0.643000	0.27269	0.004000	0.12327	0.166000	0.22503	0.621000	0.24418	-0.639000	0.05502	-0.275000	0.10095	GCA	C|0.988;T|0.012	0.012	strong		0.502	FTO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352196.1	NM_001080432		T	53922838	C	T	53922838	3	4	22	1	0	0	0	0	1	0	0	0	6094	710	25	2	1240	2	FTO	16	53922838	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	396472	53922838	36431915	3269	6170											
CES7	221223	hgsc.bcm.edu	37	chr16	55883667	55883667	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtgccgaaactcatagaagTagacaggtgcaccagcatct	13	7	11	10	1	2	2	1	0	1	2	2	3	2	2	2	2	4	3	2	2	4	2	rs545527146		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:55883667T>C	ENST00000290567.9	-	11	1413	c.1292A>G	c.(1291-1293)tAc>tGc	p.Y431C	CES5A_ENST00000319165.9_Intron|CES5A_ENST00000541580.1_5'UTR|CES5A_ENST00000520435.1_Missense_Mutation_p.Y401C|CES5A_ENST00000518005.1_Missense_Mutation_p.Y325C|CES5A_ENST00000521992.1_Missense_Mutation_p.Y460C	NM_001143685.1	NP_001137157.1	Q6NT32	EST5A_HUMAN	carboxylesterase 5A	431						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						CTCATAGAAGTAGACAGGTGC	0.557																																					p.Y460C		Atlas-SNP	.											.	CES5A	206	.	0			c.A1379G						PASS	.						77	68	71					16																	55883667		1568	3582	5150	SO:0001583	missense	221223	exon12			TAGAAGTAGACAG	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.1292A>G	16.37:g.55883667T>C	ENSP00000290567:p.Tyr431Cys	58	0	0		54	31	0.574074	NM_001190158	B7Z252|B7ZLB6|Q8NBC8|Q96DN9	Missense_Mutation	SNP	ENST00000290567.9	37	CCDS45490.1	.	.	.	.	.	.	.	.	.	.	.	15.85	2.955162	0.53293	.	.	ENSG00000159398	ENST00000521992;ENST00000518005;ENST00000290567;ENST00000520435;ENST00000541580	T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07	5.03	5.03	0.67393	Carboxylesterase, type B (1);	0.181974	0.27084	N	0.021018	D	0.92665	0.7669	H	0.98802	4.335	0.49483	D	0.999795	D	0.89917	1.0	D	0.91635	0.999	D	0.95007	0.8148	10	0.87932	D	0	.	13.3257	0.60459	0.0:0.0:0.0:1.0	.	431	Q6NT32	EST5A_HUMAN	C	460;325;431;401;211	ENSP00000428864:Y460C;ENSP00000428571:Y325C;ENSP00000290567:Y431C;ENSP00000428887:Y401C	ENSP00000290567:Y431C	Y	-	2	0	CES5A	54441168	1.000000	0.71417	0.999000	0.59377	0.526000	0.34562	4.597000	0.61062	2.194000	0.70268	0.379000	0.24179	TAC	.	.	none		0.557	CES5A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256975.3	NM_145024		C	55883667	T	C	55883667	3	2	22	1	0	0	0	0	1	0	0	0	3274	1638	57	3	447	3	CES7	16	55883667	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1960829	55883667	34471086	3270	6171											
OGFOD1	55239	hgsc.bcm.edu	37	chr16	56496469	56496469	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aattctgtttgaagatttccGgtcctggctttctgatattt	7	19	8	7	1	2	3	0	2	2	1	4	3	4	3	2	2	0	2	2	2	3	6	rs147797412	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:56496469G>A	ENST00000566157.1	+	4	494	c.371G>A	c.(370-372)cGg>cAg	p.R124Q	OGFOD1_ENST00000565209.1_3'UTR|OGFOD1_ENST00000568397.1_Missense_Mutation_p.R124Q	NM_018233.3	NP_060703.3	Q8N543	OGFD1_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 1	124					cell proliferation (GO:0008283)|peptidyl-proline hydroxylation (GO:0019511)|protein hydroxylation (GO:0018126)|regulation of translational termination (GO:0006449)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|peptidyl-proline 3-dioxygenase activity (GO:0031544)|peptidyl-proline dioxygenase activity (GO:0031543)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	8					Vitamin C(DB00126)	GAAGATTTCCGGTCCTGGCTT	0.393													G|||	5	0.000998403	0.0008	0.0029	5008	,	,		19961	0.0		0.0	False		,,,				2504	0.002				p.R124Q		Atlas-SNP	.											.	OGFOD1	31	.	0			c.G371A						PASS	.	G	GLN/ARG	4,4392	8.1+/-20.4	0,4,2194	80	77	78		371	5.6	1	16	dbSNP_134	78	0,8600		0,0,4300	yes	missense	OGFOD1	NM_018233.3	43	0,4,6494	AA,AG,GG		0.0,0.091,0.0308	possibly-damaging	124/543	56496469	4,12992	2198	4300	6498	SO:0001583	missense	55239	exon4			ATTTCCGGTCCTG	BC032919	CCDS10761.2	16q12.2	2010-11-23			ENSG00000087263	ENSG00000087263			25585	protein-coding gene	gene with protein product	"TPA1, termination and polyadenylation 1, homolog (S. cerevisiae)"	615857				10997877	Standard	NM_018233		Approved	KIAA1612, FLJ10826, TPA1	uc002ejb.3	Q8N543	OTTHUMG00000133237	ENST00000566157.1:c.371G>A	16.37:g.56496469G>A	ENSP00000457258:p.Arg124Gln	95	0	0		56	27	0.482143	NM_018233	H3BUQ2|Q9H7U5|Q9H9J9|Q9HA87|Q9HCG0|Q9NVB6	Missense_Mutation	SNP	ENST00000566157.1	37	CCDS10761.2	.	.	.	.	.	.	.	.	.	.	G	23.9	4.474261	0.84640	9.1E-4	0.0	ENSG00000087263	ENST00000336111	.	.	.	5.61	5.61	0.85477	Prolyl 4-hydroxylase, alpha subunit (1);	0.000000	0.85682	D	0.000000	T	0.59582	0.2204	M	0.79258	2.445	0.80722	D	1	D	0.58268	0.982	B	0.41510	0.359	T	0.67616	-0.5625	9	0.59425	D	0.04	-17.5224	13.8776	0.63662	0.0748:0.0:0.9252:0.0	.	124	Q8N543	OGFD1_HUMAN	Q	124	.	ENSP00000337196:R124Q	R	+	2	0	OGFOD1	55053970	1.000000	0.71417	0.989000	0.46669	0.997000	0.91878	6.847000	0.75404	2.658000	0.90341	0.585000	0.79938	CGG	G|1.000;A|0.000	0.000	weak		0.393	OGFOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256976.3	NM_018233		A	56496469	G	A	56496469	3	1	22	1	0	0	0	0	1	0	0	0	10850	1116	39	1	385	1	OGFOD1	16	56496469	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	612802	56496469	33858284	3271	6172											
SLC12A3	6559	hgsc.bcm.edu	37	chr16	56919216	56919216	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtacaggctggctcctacaAcctggccctcagctactcgg	7	8	11	15	1	1	0	1	0	0	0	3	0	2	0	3	5	5	4	3	5	4	3	rs61746763	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:56919216A>G	ENST00000563236.1	+	15	1890	c.1865A>G	c.(1864-1866)aAc>aGc	p.N622S	SLC12A3_ENST00000566786.1_Missense_Mutation_p.N621S|SLC12A3_ENST00000438926.2_Missense_Mutation_p.N622S|SLC12A3_ENST00000262502.5_Missense_Mutation_p.N621S			P55017	S12A3_HUMAN	solute carrier family 12 (sodium/chloride transporter), member 3	622					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)	GGCTCCTACAACCTGGCCCTC	0.597													A|||	84	0.0167732	0.0598	0.0058	5008	,	,		19315	0.0		0.001	False		,,,				2504	0.0				p.N622S		Atlas-SNP	.											.	SLC12A3	99	.	0			c.A1865G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN	155,4165		1,153,2006	80	62	68		1865,1862,1865	5.4	1	16	dbSNP_129	68	15,8429		0,15,4207	yes	missense,missense,missense	SLC12A3	NM_000339.2,NM_001126107.1,NM_001126108.1	46,46,46	1,168,6213	GG,GA,AA		0.1776,3.588,1.3319	benign,benign,benign	622/1031,621/1030,622/1022	56919216	170,12594	2160	4222	6382	SO:0001583	missense	6559	exon15			CCTACAACCTGGC		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.1865A>G	16.37:g.56919216A>G	ENSP00000456149:p.Asn622Ser	70	0	0		50	20	0.4	NM_001126108	A8MSJ2|C9JNN9	Missense_Mutation	SNP	ENST00000563236.1	37	CCDS58464.1	39	0.017857142857142856	37	0.07520325203252033	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	A	12.22	1.872882	0.33069	0.03588	0.001776	ENSG00000070915	ENST00000438926;ENST00000262502	.	.	.	5.4	5.4	0.78164	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	T	0.06826	0.0174	L	0.37561	1.115	0.80722	D	1	B;P;B	0.36110	0.048;0.537;0.343	B;P;B	0.50049	0.039;0.629;0.343	T	0.11446	-1.0587	9	0.11794	T	0.64	.	15.1083	0.72336	1.0:0.0:0.0:0.0	rs61746763	621;622;622	P55017-3;P55017;P55017-2	.;S12A3_HUMAN;.	S	621;622	.	ENSP00000262502:N622S	N	+	2	0	SLC12A3	55476717	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.253000	0.78320	2.048000	0.60808	0.533000	0.62120	AAC	A|0.981;G|0.019	0.019	strong		0.597	SLC12A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432337.1			G	56919216	A	G	56919216	3	3	22	1	0	0	0	0	1	0	0	0	14399	43	2	3	1923	3	SLC12A3	16	56919216	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	422747	56919216	33435537	3272	6173											
CETP	1071	hgsc.bcm.edu	37	chr16	57003846	57003846	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctgtgactctggtagagtgCggaccgatgcccctgactgc	6	9	13	13	2	1	3	0	2	1	1	1	5	1	4	4	2	3	1	4	2	1	1	rs34716057	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57003846C>T	ENST00000566128.1	+	5	532	c.265C>T	c.(265-267)Cgg>Tgg	p.R89W	CETP_ENST00000200676.3_Missense_Mutation_p.R154W|CETP_ENST00000569082.1_3'UTR|CETP_ENST00000379780.2_Missense_Mutation_p.R154W					cholesteryl ester transfer protein, plasma											NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(4)|skin(3)	23						TGGTAGAGTGCGGACCGATGC	0.597													C|||	41	0.0081869	0.0295	0.0029	5008	,	,		19510	0.0		0.0	False		,,,				2504	0.0				p.R154W		Atlas-SNP	.											.	CETP	50	.	0			c.C460T						PASS	.	C	TRP/ARG	116,4280	88.7+/-127.4	3,110,2085	133	80	98		460	-2.7	0	16	dbSNP_126	98	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CETP	NM_000078.2	101	3,112,6383	TT,TC,CC		0.0233,2.6388,0.908	probably-damaging	154/494	57003846	118,12878	2198	4300	6498	SO:0001583	missense	1071	exon5			AGAGTGCGGACCG	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.265C>T	16.37:g.57003846C>T	ENSP00000456276:p.Arg89Trp	136	0	0		139	72	0.517986	NM_000078		Missense_Mutation	SNP	ENST00000566128.1	37		17	0.007783882783882784	17	0.034552845528455285	0	0.0	0	0.0	0	0.0	C	9.523	1.108810	0.20714	0.026388	2.33E-4	ENSG00000087237	ENST00000200676;ENST00000379780	T;T	0.06768	3.26;3.26	4.05	-2.74	0.05932	Lipid-binding serum glycoprotein, N-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.824610	0.10339	U	0.686590	T	0.01730	0.0055	N	0.12182	0.205	0.09310	N	1	D;B	0.71674	0.998;0.066	P;B	0.50754	0.649;0.021	T	0.18935	-1.0321	10	0.66056	D	0.02	-16.4666	2.4134	0.04430	0.1231:0.3542:0.3268:0.1959	rs34716057;rs35242580;rs59039225	154;154	P11597-2;P11597	.;CETP_HUMAN	W	154	ENSP00000200676:R154W;ENSP00000369106:R154W	ENSP00000200676:R154W	R	+	1	2	CETP	55561347	0.074000	0.21230	0.000000	0.03702	0.001000	0.01503	0.020000	0.13466	-0.956000	0.03631	-1.961000	0.00478	CGG	C|0.992;T|0.008	0.008	strong		0.597	CETP-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432305.1	NM_000078		T	57003846	C	T	57003846	3	4	22	1	0	0	0	0	1	0	0	0	3279	759	27	1	478	1	CETP	16	57003846	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	84630	57003846	33350907	3273	6174											
CETP	1071	hgsc.bcm.edu	37	chr16	57017279	57017279	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctcatgaacagcaaaggcGtgagcctcttcgacatcatc	11	8	8	14	2	3	2	2	2	1	0	5	3	3	2	2	1	3	1	2	1	2	1	rs2228667	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57017279G>A	ENST00000566128.1	+	15	1435	c.1168G>A	c.(1168-1170)Gtg>Atg	p.V390M	CETP_ENST00000200676.3_Missense_Mutation_p.V455M|CETP_ENST00000379780.2_Missense_Mutation_p.V395M					cholesteryl ester transfer protein, plasma											NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(4)|skin(3)	23						CAGCAAAGGCGTGAGCCTCTT	0.607																																					p.V455M		Atlas-SNP	.											CETP,NS,carcinoma,-1,1	CETP	50	1	0			c.G1363A						PASS	.		MET/VAL	3,4393		0,3,2195	103	95	98		1363	3.2	1	16	dbSNP_98	98	0,8600		0,0,4300	no	missense	CETP	NM_000078.2	21	0,3,6495	AA,AG,GG		0.0,0.0682,0.0231	benign	455/494	57017279	3,12993	2198	4300	6498	SO:0001583	missense	1071	exon15			AAAGGCGTGAGCC	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.1168G>A	16.37:g.57017279G>A	ENSP00000456276:p.Val390Met	107	0	0		95	49	0.515789	NM_000078		Missense_Mutation	SNP	ENST00000566128.1	37		.	.	.	.	.	.	.	.	.	.	c	14.33	2.503998	0.44558	6.82E-4	0.0	ENSG00000087237	ENST00000200676;ENST00000379780	T;T	0.11712	2.75;2.75	3.16	3.16	0.36331	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.497607	0.16291	U	0.220905	T	0.04272	0.0118	N	0.08118	0	0.24408	N	0.994677	B;P	0.44380	0.049;0.834	B;B	0.30029	0.026;0.11	T	0.31833	-0.9929	10	0.66056	D	0.02	0.0425	8.4085	0.32629	0.0:0.7577:0.2423:0.0	rs2228667	395;455	P11597-2;P11597	.;CETP_HUMAN	M	455;395	ENSP00000200676:V455M;ENSP00000369106:V395M	ENSP00000200676:V455M	V	+	1	0	CETP	55574780	0.996000	0.38824	1.000000	0.80357	0.010000	0.07245	0.994000	0.29693	0.668000	0.31126	-0.225000	0.12378	GTG	A|0.002;G|0.998	0.002	strong		0.607	CETP-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432305.1	NM_000078		A	57017279	G	A	57017279	3	1	22	1	0	0	0	0	1	0	0	0	3279	1145	40	1	1421	1	CETP	16	57017279	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	13433	57017279	33337474	3274	6175											
NLRC5	84166	hgsc.bcm.edu	37	chr16	57060136	57060136	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgaccacgccccaggccaGtctgtggccctcctgcccaa	6	6	9	20	1	1	1	0	1	1	0	2	1	2	1	8	2	1	0	8	2	1	0	rs149735722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57060136G>T	ENST00000262510.6	+	6	1506	c.1281G>T	c.(1279-1281)caG>caT	p.Q427H	NLRC5_ENST00000436936.1_Missense_Mutation_p.Q427H|NLRC5_ENST00000539144.1_Missense_Mutation_p.Q427H|NLRC5_ENST00000308149.7_Missense_Mutation_p.Q427H	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	427	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)				CCCCAGGCCAGTCTGTGGCCC	0.632													G|||	13	0.00259585	0.0098	0.0	5008	,	,		19350	0.0		0.0	False		,,,				2504	0.0				p.Q427H		Atlas-SNP	.											NLRC5,NS,carcinoma,+1,1	NLRC5	186	1	0			c.G1281T						scavenged	.	G	HIS/GLN	16,4380	22.3+/-47.3	0,16,2182	67	67	67		1281	1.6	0.8	16	dbSNP_134	67	0,8600		0,0,4300	yes	missense	NLRC5	NM_032206.3	24	0,16,6482	TT,TG,GG		0.0,0.364,0.1231	probably-damaging	427/1867	57060136	16,12980	2198	4300	6498	SO:0001583	missense	84166	exon5			AGGCCAGTCTGTG	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.1281G>T	16.37:g.57060136G>T	ENSP00000262510:p.Gln427His	44	1	0.0227273		46	19	0.413043	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Missense_Mutation	SNP	ENST00000262510.6	37	CCDS10773.1	3|3	0.0013736263736263737|0.0013736263736263737	3|3	0.006097560975609756|0.006097560975609756	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	8.532|8.532	0.871284|0.871284	0.17322|0.17322	0.00364|0.00364	0.0|0.0	ENSG00000140853|ENSG00000140853	ENST00000262510;ENST00000308149;ENST00000436936;ENST00000539144|ENST00000538805	T;T;T;T|.	0.75477|.	-0.75;-0.77;-0.94;-0.77|.	5.21|5.21	1.62|1.62	0.23740|0.23740	.|.	0.000000|.	0.32819|.	N|.	0.005615|.	T|T	0.42832|0.42832	0.1220|0.1220	L|L	0.60455|0.60455	1.87|1.87	0.09310|0.09310	N|N	1|1	P;B;B;B|.	0.42518|.	0.782;0.204;0.191;0.157|.	B;B;B;B|.	0.39339|.	0.297;0.056;0.112;0.122|.	T|T	0.37686|0.37686	-0.9695|-0.9695	10|5	0.44086|.	T|.	0.13|.	.|.	11.318|11.318	0.49403|0.49403	0.2425:0.0:0.7575:0.0|0.2425:0.0:0.7575:0.0	.|.	427;427;427;427|.	Q86WI3-5;Q86WI3-4;Q86WI3-6;Q86WI3|.	.;.;.;NLRC5_HUMAN|.	H|F	427|180	ENSP00000262510:Q427H;ENSP00000308886:Q427H;ENSP00000389739:Q427H;ENSP00000441727:Q427H|.	ENSP00000262510:Q427H|.	Q|V	+|+	3|1	2|0	NLRC5|NLRC5	55617637|55617637	0.142000|0.142000	0.22610|0.22610	0.826000|0.826000	0.32828|0.32828	0.189000|0.189000	0.23516|0.23516	0.756000|0.756000	0.26419|0.26419	0.568000|0.568000	0.29311|0.29311	0.561000|0.561000	0.74099|0.74099	CAG|GTC	G|0.998;T|0.002	0.002	strong		0.632	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206		T	57060136	G	T	57060136	3	4	22	1	0	0	0	0	1	0	0	0	10479	1020	36	4	1295	4	NLRC5	16	57060136	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	42857	57060136	33294617	3275	6176											
NLRC5	84166	hgsc.bcm.edu	37	chr16	57071167	57071167	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgctgagggccgtgagtgcGtgctggaccctggcagagct	5	8	18	10	2	0	3	0	2	0	1	0	4	0	4	2	3	4	4	2	3	0	0	rs137919442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57071167G>A	ENST00000262510.6	+	15	2997	c.2772G>A	c.(2770-2772)gcG>gcA	p.A924A	NLRC5_ENST00000436936.1_Silent_p.A924A|NLRC5_ENST00000539144.1_Silent_p.A924A|NLRC5_ENST00000308149.7_Silent_p.A924A	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	924					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)				CCGTGAGTGCGTGCTGGACCC	0.622													G|||	14	0.00279553	0.0106	0.0	5008	,	,		18115	0.0		0.0	False		,,,				2504	0.0				p.A924A		Atlas-SNP	.											.	NLRC5	186	.	0			c.G2772A						PASS	.	G		20,4376	26.2+/-53.5	0,20,2178	119	103	108		2772	-6.2	0	16	dbSNP_134	108	0,8600		0,0,4300	no	coding-synonymous	NLRC5	NM_032206.3		0,20,6478	AA,AG,GG		0.0,0.455,0.1539		924/1867	57071167	20,12976	2198	4300	6498	SO:0001819	synonymous_variant	84166	exon14			GAGTGCGTGCTGG	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.2772G>A	16.37:g.57071167G>A		62	0	0		67	23	0.343284	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Silent	SNP	ENST00000262510.6	37	CCDS10773.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	g	3.650	-0.071627	0.07228	0.00455	0.0	ENSG00000140853	ENST00000538805	.	.	.	3.5	-6.21	0.02065	.	.	.	.	.	T	0.19685	0.0473	.	.	.	0.19300	N	0.99997	.	.	.	.	.	.	T	0.25950	-1.0117	4	.	.	.	.	7.5874	0.28002	0.4148:0.309:0.2761:0.0	.	.	.	.	M	677	.	.	V	+	1	0	NLRC5	55628668	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.843000	0.00736	-1.778000	0.01282	-1.694000	0.00725	GTG	G|0.998;A|0.002	0.002	strong		0.622	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206		A	57071167	G	A	57071167	2	1	22	1	0	0	0	0	0	0	0	1	10479	1132	40	1		1	NLRC5	16	57071167	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	11031	57071167	33283586	3276	6177											
CPNE2	221184	hgsc.bcm.edu	37	chr16	57144689	57144689	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagtgggggtgccccagcagCgggggcagcccccatgggcc	5	3	18	15	1	0	0	0	0	0	0	0	0	0	0	5	5	4	2	5	5	0	0	rs141954860		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57144689C>T	ENST00000535318.2	+	3	396	c.35C>T	c.(34-36)gCg>gTg	p.A12V	CPNE2_ENST00000290776.8_Missense_Mutation_p.A12V|CPNE2_ENST00000565874.1_Missense_Mutation_p.A12V|CPNE2_ENST00000537605.1_5'UTR			Q96FN4	CPNE2_HUMAN	copine II	12	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)				GCCCCAGCAGCGGGGGCAGCC	0.642													c|||	1	0.000199681	0.0008	0.0	5008	,	,		13191	0.0		0.0	False		,,,				2504	0.0				p.A12V		Atlas-SNP	.											.	CPNE2	48	.	0			c.C35T						PASS	.	C	VAL/ALA	0,4394		0,0,2197	28	27	28		35	-2	0	16	dbSNP_134	28	6,8592		0,6,4293	no	missense	CPNE2	NM_152727.5	64	0,6,6490	TT,TC,CC		0.0698,0.0,0.0462	benign	12/549	57144689	6,12986	2197	4299	6496	SO:0001583	missense	221184	exon2			CAGCAGCGGGGGC		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.35C>T	16.37:g.57144689C>T	ENSP00000439018:p.Ala12Val	114	0	0		123	66	0.536585	NM_152727	Q68D19|Q719H8|Q86XP9	Missense_Mutation	SNP	ENST00000535318.2	37	CCDS10774.1	.	.	.	.	.	.	.	.	.	.	C	13.92	2.381069	0.42207	0.0	6.98E-4	ENSG00000140848	ENST00000290776;ENST00000535318	T;T	0.05319	3.46;3.46	5.08	-1.97	0.07503	C2 calcium/lipid-binding domain, CaLB (1);	1.227400	0.05504	N	0.558977	T	0.04861	0.0131	N	0.24115	0.695	0.09310	N	0.999999	B;B	0.13145	0.007;0.001	B;B	0.04013	0.001;0.001	T	0.45056	-0.9287	10	0.33141	T	0.24	-14.5631	7.8677	0.29547	0.0:0.5348:0.2084:0.2568	.	12;12	A8K8A4;Q96FN4	.;CPNE2_HUMAN	V	12	ENSP00000290776:A12V;ENSP00000439018:A12V	ENSP00000290776:A12V	A	+	2	0	CPNE2	55702190	0.000000	0.05858	0.000000	0.03702	0.234000	0.25298	-0.045000	0.12003	-0.152000	0.11156	-0.201000	0.12746	GCG	C|0.999;T|0.001	0.001	strong		0.642	CPNE2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432986.2	NM_152727		T	57144689	C	T	57144689	3	4	22	1	0	0	0	0	1	0	0	0	3814	768	27	1	37	1	CPNE2	16	57144689	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	73522	57144689	33210064	3277	6178											
CIAPIN1	57019	hgsc.bcm.edu	37	chr16	57468110	57468110	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgtacttcctcaggggttagGggctcccgctgcagctagaa	7	10	13	11	1	1	1	1	0	0	1	3	1	3	1	2	4	3	6	2	4	4	4	rs77773186	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57468110G>A	ENST00000569979.1	-	4	448	c.402C>T	c.(400-402)ccC>ccT	p.P134P	CIAPIN1_ENST00000568940.1_Silent_p.P134P|CIAPIN1_ENST00000394391.4_Silent_p.P134P|CIAPIN1_ENST00000569370.1_Silent_p.P134P|CIAPIN1_ENST00000567518.1_Silent_p.P121P|CIAPIN1_ENST00000569246.1_5'UTR|CIAPIN1_ENST00000565961.1_Silent_p.P107P					cytokine induced apoptosis inhibitor 1											cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	10						CAGGGGTTAGGGGCTCCCGCT	0.443													G|||	24	0.00479233	0.0182	0.0	5008	,	,		20722	0.0		0.0	False		,,,				2504	0.0				p.P134P		Atlas-SNP	.											.	CIAPIN1	17	.	0			c.C402T						PASS	.	G		40,3776		0,40,1868	108	102	104		402	2.2	0.1	16	dbSNP_131	104	1,8231		0,1,4115	no	coding-synonymous	CIAPIN1	NM_020313.2		0,41,5983	AA,AG,GG		0.0121,1.0482,0.3403		134/313	57468110	41,12007	1908	4116	6024	SO:0001819	synonymous_variant	57019	exon5			GGTTAGGGGCTCC	AF248964	CCDS10781.2	16q21	2012-09-20			ENSG00000005194	ENSG00000005194			28050	protein-coding gene	gene with protein product		608943				10493829, 11230166	Standard	XM_005256061		Approved	Anamorsin	uc002ell.1	Q6FI81	OTTHUMG00000133457	ENST00000569979.1:c.402C>T	16.37:g.57468110G>A		122	0	0		96	56	0.583333	NM_020313		Silent	SNP	ENST00000569979.1	37																																																																																				G|0.993;A|0.007	0.007	strong		0.443	CIAPIN1-010	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432580.1	NM_020313		A	57468110	G	A	57468110	2	1	22	1	0	0	0	0	0	0	0	1	3421	1219	43	2		2	CIAPIN1	16	57468110	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	323421	57468110	32886643	3278	6179											
CIAPIN1	57019	hgsc.bcm.edu	37	chr16	57474740	57474740	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggccctcattgccggttaacGcttgaagcttatccaccaga	9	10	9	13	2	1	2	1	1	0	1	2	2	2	2	4	2	3	3	4	2	3	4	rs11557672	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57474740G>T	ENST00000569979.1	-	1	147	c.101C>A	c.(100-102)gCg>gAg	p.A34E	CIAPIN1_ENST00000568940.1_Missense_Mutation_p.A34E|CIAPIN1_ENST00000394391.4_Missense_Mutation_p.A34E|CIAPIN1_ENST00000569370.1_Missense_Mutation_p.A34E|CIAPIN1_ENST00000567518.1_Missense_Mutation_p.A34E|CIAPIN1_ENST00000569246.1_5'UTR|CIAPIN1_ENST00000565961.1_Missense_Mutation_p.A34E					cytokine induced apoptosis inhibitor 1											cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	10						GCCGGTTAACGCTTGAAGCTT	0.522													G|||	73	0.0145767	0.0499	0.0086	5008	,	,		18615	0.0		0.001	False		,,,				2504	0.0				p.A34E		Atlas-SNP	.											.	CIAPIN1	17	.	0			c.C101A						PASS	.	G	GLU/ALA	142,3808		2,138,1835	86	84	85		101	-10	0	16	dbSNP_120	85	3,8331		0,3,4164	no	missense	CIAPIN1	NM_020313.2	107	2,141,5999	TT,TG,GG		0.036,3.5949,1.1804	benign	34/313	57474740	145,12139	1975	4167	6142	SO:0001583	missense	57019	exon2			GTTAACGCTTGAA	AF248964	CCDS10781.2	16q21	2012-09-20			ENSG00000005194	ENSG00000005194			28050	protein-coding gene	gene with protein product		608943				10493829, 11230166	Standard	XM_005256061		Approved	Anamorsin	uc002ell.1	Q6FI81	OTTHUMG00000133457	ENST00000569979.1:c.101C>A	16.37:g.57474740G>T	ENSP00000458000:p.Ala34Glu	117	0	0		138	56	0.405797	NM_020313		Missense_Mutation	SNP	ENST00000569979.1	37		31	0.014194139194139194	26	0.052845528455284556	5	0.013812154696132596	0	0.0	0	0.0	G	4.538	0.099964	0.08681	0.035949	3.6E-4	ENSG00000005194	ENST00000394391	T	0.28666	1.6	4.98	-9.96	0.00443	.	1.395360	0.05048	N	0.477654	T	0.01976	0.0062	L	0.33753	1.03	0.09310	N	1	B;B;B	0.10296	0.001;0.003;0.0	B;B;B	0.08055	0.002;0.003;0.001	T	0.18935	-1.0321	10	0.05959	T	0.93	1.2775	3.7895	0.08715	0.0939:0.1347:0.3108:0.4606	rs11557672;rs16957069;rs11557672	34;34;34	B4DHB9;Q6FI81-3;Q6FI81	.;.;CPIN1_HUMAN	E	34	ENSP00000377914:A34E	ENSP00000377914:A34E	A	-	2	0	CIAPIN1	56032241	0.000000	0.05858	0.009000	0.14445	0.950000	0.60333	-1.034000	0.03567	-2.690000	0.00404	-0.295000	0.09555	GCG	G|0.975;T|0.025	0.025	strong		0.522	CIAPIN1-010	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432580.1	NM_020313		T	57474740	G	T	57474740	3	4	22	1	0	0	0	0	1	0	0	0	3421	1087	38	4	869	4	CIAPIN1	16	57474740	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6630	57474740	32880013	3279	6180											
CNGB1	1258	hgsc.bcm.edu	37	chr16	57935443	57935443	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaggtgtacctgaaagagtgCgactttgctaacgatgttgt	11	12	12	6	2	0	2	0	1	0	1	0	4	0	2	1	1	4	3	1	1	4	4	rs16942445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57935443C>A	ENST00000251102.8	-	28	2941	c.2881G>T	c.(2881-2883)Gca>Tca	p.A961S	CNGB1_ENST00000564448.1_Missense_Mutation_p.A955S	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	961			A -> S (in dbSNP:rs16942445).		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						TGAAAGAGTGCGACTTTGCTA	0.537													C|||	193	0.0385383	0.1384	0.0086	5008	,	,		22586	0.0		0.004	False		,,,				2504	0.0				p.A961S	Colon(156;1293 1853 16336 28962 38659)	Atlas-SNP	.											.	CNGB1	105	.	0			c.G2881T						PASS	.	C	SER/ALA	387,3743		19,349,1697	111	114	113		2881	3.9	1	16	dbSNP_123	113	5,8409		0,5,4202	yes	missense	CNGB1	NM_001297.4	99	19,354,5899	AA,AC,CC		0.0594,9.3705,3.125	benign	961/1252	57935443	392,12152	2065	4207	6272	SO:0001583	missense	1258	exon28			AGAGTGCGACTTT	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.2881G>T	16.37:g.57935443C>A	ENSP00000251102:p.Ala961Ser	97	0	0		93	46	0.494624	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Missense_Mutation	SNP	ENST00000251102.8	37	CCDS42169.1	63	0.028846153846153848	59	0.11991869918699187	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	8.424	0.846959	0.17034	0.093705	5.94E-4	ENSG00000070729	ENST00000251102	D	0.96427	-4.01	4.8	3.86	0.44501	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);	0.070612	0.56097	D	0.000026	T	0.17450	0.0419	L	0.28556	0.865	0.80722	D	1	B;B	0.23540	0.087;0.082	B;B	0.28784	0.041;0.094	T	0.62955	-0.6744	10	0.14252	T	0.57	.	8.8322	0.35091	0.0:0.8291:0.0:0.1709	rs16942445;rs52812859;rs16942445	333;961	Q14028-2;Q14028	.;CNGB1_HUMAN	S	961	ENSP00000251102:A961S	ENSP00000251102:A961S	A	-	1	0	CNGB1	56492944	1.000000	0.71417	0.996000	0.52242	0.031000	0.12232	2.124000	0.42006	1.028000	0.39785	-0.215000	0.12644	GCA	C|0.957;A|0.043	0.043	strong		0.537	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297		A	57935443	C	A	57935443	3	1	22	1	0	0	0	0	1	0	0	0	3602	768	27	4	898	4	CNGB1	16	57935443	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	460703	57935443	32419310	3280	6181											
ZNF319	57567	hgsc.bcm.edu	37	chr16	58031996	58031996	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgttgtgggggctgcaggccGgggtctggctgcaggaggat	4	9	21	7	1	1	0	0	0	1	0	1	2	1	2	1	8	2	5	1	8	0	1	rs115738968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:58031996G>A	ENST00000299237.2	-	2	796	c.174C>T	c.(172-174)ccC>ccT	p.P58P	USB1_ENST00000561743.1_5'Flank	NM_020807.1	NP_065858.1	Q9P2F9	ZN319_HUMAN	zinc finger protein 319	58	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)			large_intestine(2)|lung(4)|ovary(1)|urinary_tract(1)	8						GCTGCAGGCCGGGGTCTGGCT	0.701													G|||	42	0.00838658	0.0272	0.0058	5008	,	,		16696	0.0		0.002	False		,,,				2504	0.0				p.P58P		Atlas-SNP	.											.	ZNF319	42	.	0			c.C174T						PASS	.	G		102,4294	79.3+/-117.8	4,94,2100	33	36	35		174	-10.4	0	16	dbSNP_132	35	19,8577	13.3+/-46.6	0,19,4279	no	coding-synonymous	ZNF319	NM_020807.1		4,113,6379	AA,AG,GG		0.221,2.3203,0.9313		58/583	58031996	121,12871	2198	4298	6496	SO:0001819	synonymous_variant	57567	exon2			CAGGCCGGGGTCT	AB037809	CCDS32462.1	16q21	2013-01-08				ENSG00000166188		"Zinc fingers, C2H2-type"	13644	protein-coding gene	gene with protein product						10718198, 11161788	Standard	XM_005256069		Approved	KIAA1388, Zfp319	uc002emx.1	Q9P2F9		ENST00000299237.2:c.174C>T	16.37:g.58031996G>A		49	0	0		34	18	0.529412	NM_020807	Q52LH8	Silent	SNP	ENST00000299237.2	37	CCDS32462.1																																																																																			G|0.992;A|0.008	0.008	strong		0.701	ZNF319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430317.1			A	58031996	G	A	58031996	2	1	22	1	0	0	0	0	0	0	0	1	17852	1103	39	1		1	ZNF319	16	58031996	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	96553	58031996	32322757	3281	6182											
MMP15	4324	hgsc.bcm.edu	37	chr16	58079268	58079268	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gctctgcgtcctgggcctcaCctacgcgctggtgcagatgc	4	9	13	15	3	2	1	1	0	1	1	3	1	3	1	3	2	4	3	3	2	1	1	rs141377329	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:58079268C>T	ENST00000219271.3	+	10	2713	c.1928C>T	c.(1927-1929)aCc>aTc	p.T643I		NM_002428.2	NP_002419.1	P51511	MMP15_HUMAN	matrix metallopeptidase 15 (membrane-inserted)	643					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)	CTGGGCCTCACCTACGCGCTG	0.662													C|||	14	0.00279553	0.0098	0.0014	5008	,	,		14760	0.0		0.0	False		,,,				2504	0.0				p.T643I		Atlas-SNP	.											.	MMP15	58	.	0			c.C1928T						PASS	.	C	ILE/THR	39,4355		0,39,2158	124	127	126		1928	3.6	0	16	dbSNP_134	126	1,8595		0,1,4297	yes	missense	MMP15	NM_002428.2	89	0,40,6455	TT,TC,CC		0.0116,0.8876,0.3079	benign	643/670	58079268	40,12950	2197	4298	6495	SO:0001583	missense	4324	exon10			GCCTCACCTACGC	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.1928C>T	16.37:g.58079268C>T	ENSP00000219271:p.Thr643Ile	77	0	0		90	51	0.566667	NM_002428	A0A2U6|Q14111	Missense_Mutation	SNP	ENST00000219271.3	37	CCDS10792.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	C	2.732	-0.264139	0.05754	0.008876	1.16E-4	ENSG00000102996	ENST00000219271	T	0.25579	1.79	4.65	3.62	0.41486	Peptidase M10A, matrix metallopeptidase, C-terminal (1);	0.337903	0.33772	N	0.004578	T	0.02970	0.0088	N	0.00186	-1.895	0.26149	N	0.980165	B	0.06786	0.001	B	0.06405	0.002	T	0.40194	-0.9576	10	0.10902	T	0.67	.	5.4497	0.16556	0.0:0.7809:0.0:0.2191	.	643	P51511	MMP15_HUMAN	I	643	ENSP00000219271:T643I	ENSP00000219271:T643I	T	+	2	0	MMP15	56636769	0.999000	0.42202	0.018000	0.16275	0.093000	0.18481	2.919000	0.48836	2.418000	0.82041	0.555000	0.69702	ACC	C|0.997;T|0.003	0.003	strong		0.662	MMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257342.1	NM_002428		T	58079268	C	T	58079268	3	4	22	1	0	0	0	0	1	0	0	0	9663	507	18	2	1966	2	MMP15	16	58079268	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	47272	58079268	32275485	3282	6183											
CBFB	865	hgsc.bcm.edu	37	chr16	67116169	67116169	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggctcggagaaggacacgCgaatttgaagatagagacag	15	5	15	6	3	0	4	0	1	0	3	1	9	0	5	0	3	0	1	0	3	4	2	rs78053453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67116169C>T	ENST00000290858.6	+	5	714	c.453C>T	c.(451-453)cgC>cgT	p.R151R	CBFB_ENST00000561924.2_Silent_p.R51R|CBFB_ENST00000412916.2_Silent_p.R151R	NM_001755.2|NM_022845.2	NP_001746.1|NP_074036.1	Q13951	PEBB_HUMAN	core-binding factor, beta subunit	151					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)		GAAGGACACGCGAATTTGAAG	0.433			T	MYH11	AML								C|||	358	0.0714856	0.1853	0.0115	5008	,	,		12709	0.0377		0.002	False		,,,				2504	0.0665				p.R151R		Atlas-SNP	.		Dom	yes		16	16q22	865	"core-binding factor, beta subunit"		L	CBFB_ENST00000412916,NS,carcinoma,+1,2	CBFB	52	2	0			c.C453T						PASS	.	C	,	664,3736	281.9+/-276.2	46,572,1582	98	90	93		453,453	0.1	1	16	dbSNP_132	93	10,8590	5.7+/-21.5	0,10,4290	no	coding-synonymous,coding-synonymous	CBFB	NM_001755.2,NM_022845.2	,	46,582,5872	TT,TC,CC		0.1163,15.0909,5.1846	,	151/183,151/188	67116169	674,12326	2200	4300	6500	SO:0001819	synonymous_variant	865	exon5			GACACGCGAATTT	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.453C>T	16.37:g.67116169C>T		80	0	0		88	38	0.431818	NM_022845	A8K347|Q13124|Q9HCT2	Silent	SNP	ENST00000290858.6	37	CCDS10827.1																																																																																			C|0.951;T|0.049	0.049	strong		0.433	CBFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268843.2	NM_001755		T	67116169	C	T	67116169	2	4	22	1	0	0	0	0	0	0	0	1	2701	755	27	1		1	CBFB	16	67116169	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	9036901	67116169	23238584	3283	6184											
KIAA0895L	653319	hgsc.bcm.edu	37	chr16	67210855	67210855	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agcaccccatggggccgcagGtggtccacatcctcatagga	9	6	12	14	1	1	0	1	0	0	0	3	1	3	1	5	5	1	2	5	5	1	1	rs61733789	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67210855G>C	ENST00000290881.7	-	8	2201	c.1275C>G	c.(1273-1275)caC>caG	p.H425Q	KIAA0895L_ENST00000561621.1_3'UTR|KIAA0895L_ENST00000563831.2_5'UTR|KIAA0895L_ENST00000563902.1_Missense_Mutation_p.H425Q			Q68EN5	K895L_HUMAN	KIAA0895-like	425										breast(2)|endometrium(5)|kidney(2)|large_intestine(3)|lung(2)|prostate(2)|skin(1)	17						GGGGCCGCAGGTGGTCCACAT	0.627													G|||	334	0.0666933	0.1929	0.0086	5008	,	,		17791	0.003		0.003	False		,,,				2504	0.0685				p.H425Q		Atlas-SNP	.											.	KIAA0895L	32	.	0			c.C1275G						PASS	.	G	GLN/HIS	589,3435		38,513,1461	61	66	64		1275	-3.4	1	16	dbSNP_129	64	8,8370		0,8,4181	yes	missense	KIAA0895L	NM_001040715.1	24	38,521,5642	CC,CG,GG		0.0955,14.6372,4.8137	benign	425/472	67210855	597,11805	2012	4189	6201	SO:0001583	missense	653319	exon7			CCGCAGGTGGTCC	AK092303	CCDS42177.1	16q22.1	2008-11-27				ENSG00000196123			34408	protein-coding gene	gene with protein product							Standard	NM_001040715		Approved	LOC653319	uc002ert.3	Q68EN5		ENST00000290881.7:c.1275C>G	16.37:g.67210855G>C	ENSP00000290881:p.His425Gln	99	0	0		94	49	0.521277	NM_001040715	A2VCS8|Q8N3H9|Q8NAQ5|Q96IE5	Missense_Mutation	SNP	ENST00000290881.7	37	CCDS42177.1	101	0.04624542124542125	95	0.19308943089430894	4	0.011049723756906077	2	0.0034965034965034965	0	0.0	G	11.37	1.618724	0.28801	0.146372	9.55E-4	ENSG00000196123	ENST00000290881	.	.	.	4.59	-3.36	0.04913	.	0.520084	0.22311	N	0.061738	T	0.00012	0.0000	N	0.11560	0.145	0.43271	P	0.004773000000000027	B;B	0.10296	0.001;0.003	B;B	0.11329	0.006;0.005	T	0.23868	-1.0176	8	0.17369	T	0.5	-13.5417	1.6114	0.02694	0.2829:0.364:0.2227:0.1304	rs61733789	425;270	Q68EN5;Q68EN5-3	K895L_HUMAN;.	Q	425	.	ENSP00000290881:H425Q	H	-	3	2	KIAA0895L	65768356	0.060000	0.20803	0.971000	0.41717	0.993000	0.82548	-0.536000	0.06135	-0.345000	0.08325	0.555000	0.69702	CAC	G|0.923;C|0.077	0.077	strong		0.627	KIAA0895L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421193.4	NM_001040715		C	67210855	G	C	67210855	3	2	22	1	0	0	0	0	1	0	0	0	8207	1252	44	4	144	4	KIAA0895L	16	67210855	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	94686	67210855	23143898	3284	6185											
EXOC3L	283849	hgsc.bcm.edu	37	chr16	67221494	67221494	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtctccacctccgccacaCgcacagcagccaccaacagg	11	3	7	20	2	1	0	0	0	1	0	3	0	2	0	6	1	3	2	6	1	1	0	rs79820293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67221494C>T	ENST00000314586.6	-	5	914	c.674G>A	c.(673-675)cGt>cAt	p.R225H	EXOC3L1_ENST00000562887.1_Intron	NM_178516.3	NP_848611.2	Q86VI1	EX3L1_HUMAN	exocyst complex component 3-like 1	225	Mediates interaction with EXOC2, EXOC4 and EXOC5. {ECO:0000250}.				exocytosis (GO:0006887)|peptide hormone secretion (GO:0030072)	exocyst (GO:0000145)|secretory granule (GO:0030141)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	21						CTCCGCCACACGCACAGCAGC	0.687													C|||	107	0.0213658	0.0772	0.0043	5008	,	,		16224	0.0		0.002	False		,,,				2504	0.0				p.R225H		Atlas-SNP	.											.	EXOC3L1	52	.	0			c.G674A						PASS	.	C	HIS/ARG	242,4152		8,226,1963	28	33	32		674	5.8	1	16	dbSNP_131	32	1,8597		0,1,4298	yes	missense	EXOC3L1	NM_178516.3	29	8,227,6261	TT,TC,CC		0.0116,5.5075,1.8704	probably-damaging	225/747	67221494	243,12749	2197	4299	6496	SO:0001583	missense	283849	exon5			GCCACACGCACAG	AK092858	CCDS10832.1	16q22.1	2011-01-31	2011-01-31	2011-01-31	ENSG00000179044	ENSG00000179044			27540	protein-coding gene	gene with protein product		614117	"exocyst complex component 3-like"	EXOC3L		12477932	Standard	NM_178516		Approved	FLJ35539, FLJ35587	uc002erx.1	Q86VI1	OTTHUMG00000137508	ENST00000314586.6:c.674G>A	16.37:g.67221494C>T	ENSP00000325674:p.Arg225His	63	0	0		75	30	0.4	NM_178516	A8K7I9|Q8NAD2|Q8TEN2	Missense_Mutation	SNP	ENST00000314586.6	37	CCDS10832.1	49	0.022435897435897436	47	0.09552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	C	26.0	4.691637	0.88735	0.055075	1.16E-4	ENSG00000179044	ENST00000314586;ENST00000545725;ENST00000314553	T;T	0.34472	3.05;1.36	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.03695	0.0105	M	0.74881	2.28	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.996;0.998;0.999	T	0.04454	-1.0950	10	0.59425	D	0.04	-11.3738	18.7162	0.91677	0.0:1.0:0.0:0.0	.	164;164;225	F5H4W1;B7Z6U0;Q86VI1	.;.;EX3L1_HUMAN	H	225;164;169	ENSP00000325674:R225H;ENSP00000439910:R164H	ENSP00000325008:R169H	R	-	2	0	EXOC3L1	65778995	0.997000	0.39634	1.000000	0.80357	0.982000	0.71751	4.142000	0.58044	2.763000	0.94921	0.650000	0.86243	CGT	C|0.978;T|0.022	0.022	strong		0.687	EXOC3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268827.2	NM_178516		T	67221494	C	T	67221494	3	4	22	1	0	0	0	0	1	0	0	0	5306	536	19	1	1606	1	EXOC3L	16	67221494	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	10639	67221494	23133259	3285	6186											
E2F4	1874	hgsc.bcm.edu	37	chr16	67229827	67229827	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcagcagcagcagcagcagCagcagcaacagtaacagcag	16	1	12	12	0	0	0	0	0	0	0	0	0	0	0	0	0	12	11	0	0	2	1	rs3730404	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67229827C>T	ENST00000379378.3	+	7	1010	c.951C>T	c.(949-951)agC>agT	p.S317S		NM_001950.3	NP_001941.2	Q16254	E2F4_HUMAN	E2F transcription factor 4, p107/p130-binding	317	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)		gcagcagcagcagcagcaaca	0.612													C|||	311	0.0621006	0.1762	0.0086	5008	,	,		18005	0.003		0.003	False		,,,				2504	0.0675				p.S317S		Atlas-SNP	.											.	E2F4	25	.	0			c.C951T						PASS	.	-		587,3809	256.1+/-261.0	39,509,1650	47	50	49		951	0.5	1	16	dbSNP_107	49	7,8591	3.7+/-12.6	0,7,4292	no	coding-synonymous	E2F4	NM_001950.3		39,516,5942	TT,TC,CC		0.0814,13.353,4.5713		317/414	67229827	594,12400	2198	4299	6497	SO:0001819	synonymous_variant	1874	exon7			CAGCAGCAGCAGC	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.951C>T	16.37:g.67229827C>T		118	0	0		115	63	0.547826	NM_001950	A6NGR8|B5BU56|Q12991|Q15328	Silent	SNP	ENST00000379378.3	37	CCDS32464.1																																																																																			C|0.949;T|0.051	0.051	strong		0.612	E2F4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421565.1	NM_001950		T	67229827	C	T	67229827	2	4	22	1	0	0	0	0	0	0	0	1	4871	709	25	2		2	E2F4	16	67229827	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	8333	67229827	23124926	3286	6187											
FHOD1	29109	hgsc.bcm.edu	37	chr16	67266065	67266065	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcgcttggggtccagcacTgtggtcattgtccggcggcc	3	10	15	13	3	1	0	1	0	0	0	3	0	3	0	3	5	2	2	3	5	0	2	rs34888644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67266065T>C	ENST00000258201.4	-	14	2326	c.2079A>G	c.(2077-2079)acA>acG	p.T693T		NM_013241.2	NP_037373.2	Q9Y613	FHOD1_HUMAN	formin homology 2 domain containing 1	693	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.|Interaction with ROCK1.				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)		GGTCCAGCACTGTGGTCATTG	0.582													T|||	375	0.0748802	0.2201	0.013	5008	,	,		18790	0.003		0.003	False		,,,				2504	0.0706				p.T693T		Atlas-SNP	.											.	FHOD1	86	.	0			c.A2079G						PASS	.	T		797,3599	319.1+/-295.9	76,645,1477	147	122	131		2079	-0.9	1	16	dbSNP_126	131	8,8592	3.7+/-12.6	0,8,4292	no	coding-synonymous	FHOD1	NM_013241.2		76,653,5769	CC,CT,TT		0.093,18.1301,6.1942		693/1165	67266065	805,12191	2198	4300	6498	SO:0001819	synonymous_variant	29109	exon14			CAGCACTGTGGTC	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.2079A>G	16.37:g.67266065T>C		418	1	0.00239234		452	223	0.493363	NM_013241	Q59F76|Q6Y1F2|Q76MS8|Q8N521	Silent	SNP	ENST00000258201.4	37	CCDS10834.1																																																																																			T|0.919;C|0.081	0.081	strong		0.582	FHOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268844.2			C	67266065	T	C	67266065	2	2	22	1	0	0	0	0	0	0	0	1	5890	1567	55	3		3	FHOD1	16	67266065	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	36238	67266065	23088688	3287	6188											
ZDHHC1	29800	hgsc.bcm.edu	37	chr16	67440289	67440289	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgctgggctgtgccggtgcCgtccacacactcttctcagg	4	9	12	16	3	2	0	1	0	2	0	4	0	3	0	4	3	2	2	4	3	0	1	rs8058306	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67440289C>T	ENST00000348579.2	-	3	407	c.66G>A	c.(64-66)acG>acA	p.T22T		NM_013304.2	NP_037436.1	Q8WTX9	ZDHC1_HUMAN	zinc finger, DHHC-type containing 1	22					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)		GTGCCGGTGCCGTCCACACAC	0.622													C|||	361	0.0720847	0.205	0.013	5008	,	,		17815	0.003		0.003	False		,,,				2504	0.0767				p.T22T		Atlas-SNP	.											.	ZDHHC1	28	.	0			c.G66A						PASS	.	C		710,3678		52,606,1536	26	23	24		66	-9.3	0.1	16	dbSNP_116	24	11,8577		0,11,4283	no	coding-synonymous	ZDHHC1	NM_013304.2		52,617,5819	TT,TC,CC		0.1281,16.1805,5.5564		22/486	67440289	721,12255	2194	4294	6488	SO:0001819	synonymous_variant	29800	exon3			CGGTGCCGTCCAC	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.66G>A	16.37:g.67440289C>T		138	0	0		161	71	0.440994	NM_013304	O15461	Silent	SNP	ENST00000348579.2	37	CCDS10836.1																																																																																			C|0.924;T|0.076	0.076	strong		0.622	ZDHHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268845.1	NM_013304		T	67440289	C	T	67440289	2	4	22	1	0	0	0	0	0	0	0	1	17615	639	23	1		1	ZDHHC1	16	67440289	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	174224	67440289	22914464	3288	6189											
NFATC3	4775	hgsc.bcm.edu	37	chr16	68224786	68224786	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gattcagggtgttcacatgaCagtgtactgtcaggacagag	11	10	13	7	0	3	2	3	1	0	1	3	4	3	3	0	2	1	2	0	2	1	3	rs77352556	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:68224786C>G	ENST00000346183.3	+	9	2238	c.2214C>G	c.(2212-2214)gaC>gaG	p.D738E	SNORA48_ENST00000391143.1_RNA|NFATC3_ENST00000329524.4_Missense_Mutation_p.D738E|NFATC3_ENST00000349223.5_Missense_Mutation_p.D738E|NFATC3_ENST00000535127.2_3'UTR|NFATC3_ENST00000575270.1_Missense_Mutation_p.D738E	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3	738					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)		GTTCACATGACAGTGTACTGT	0.478													C|||	46	0.0091853	0.0333	0.0029	5008	,	,		21238	0.0		0.0	False		,,,				2504	0.0				p.D738E		Atlas-SNP	.											.	NFATC3	190	.	0			c.C2214G						PASS	.	C	GLU/ASP,GLU/ASP,GLU/ASP	88,4308	74.1+/-112.3	2,84,2112	109	92	97		2214,2214,2214	-1.8	0.9	16	dbSNP_131	97	0,8600		0,0,4300	yes	missense,missense,missense	NFATC3	NM_004555.3,NM_173163.2,NM_173165.2	45,45,45	2,84,6412	GG,GC,CC		0.0,2.0018,0.6771	benign,benign,benign	738/1069,738/1066,738/1076	68224786	88,12908	2198	4300	6498	SO:0001583	missense	4775	exon9			ACATGACAGTGTA	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.2214C>G	16.37:g.68224786C>G	ENSP00000300659:p.Asp738Glu	200	0	0		231	128	0.554113	NM_173163	O75211|Q14516|Q99840|Q99841|Q99842	Missense_Mutation	SNP	ENST00000346183.3	37	CCDS10860.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	C	9.959	1.222209	0.22457	0.020018	0.0	ENSG00000072736	ENST00000349223;ENST00000346183;ENST00000329524;ENST00000535127	T;T;T	0.11604	2.76;2.76;2.76	5.55	-1.84	0.07809	.	1.004540	0.07995	N	0.987827	T	0.01353	0.0044	M	0.65975	2.015	0.38233	D	0.941091	B;B;B;B	0.13145	0.001;0.006;0.007;0.001	B;B;B;B	0.16289	0.004;0.015;0.007;0.004	T	0.46062	-0.9218	10	0.06099	T	0.92	-3.3363	6.3098	0.21159	0.0:0.2985:0.3225:0.379	.	738;738;738;738	Q12968;Q12968-3;B5B2S0;B5B2S2	NFAC3_HUMAN;.;.;.	E	738;738;738;259	ENSP00000264008:D738E;ENSP00000300659:D738E;ENSP00000331324:D738E	ENSP00000331324:D738E	D	+	3	2	NFATC3	66782287	0.992000	0.36948	0.876000	0.34364	0.316000	0.28119	0.366000	0.20365	-0.220000	0.09988	0.557000	0.71058	GAC	C|0.991;G|0.009	0.009	strong		0.478	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555		G	68224786	C	G	68224786	3	3	22	1	0	0	0	0	1	0	0	0	10373	477	17	4	2248	4	NFATC3	16	68224786	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	784497	68224786	22129967	3289	6190											
NFATC3	4775	hgsc.bcm.edu	37	chr16	68225197	68225197	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	acacctcattctgtgcatacCctgcctcatctgcaatcaat	10	12	4	15	0	5	0	3	0	2	0	5	0	5	0	3	0	4	2	3	0	3	2	rs140991156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:68225197C>T	ENST00000346183.3	+	9	2649	c.2625C>T	c.(2623-2625)acC>acT	p.T875T	SNORA48_ENST00000391143.1_RNA|NFATC3_ENST00000329524.4_Silent_p.T875T|NFATC3_ENST00000349223.5_Silent_p.T875T|NFATC3_ENST00000535127.2_3'UTR|NFATC3_ENST00000575270.1_Silent_p.T875T	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3	875					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)		CTGTGCATACCCTGCCTCATC	0.443																																					p.T875T		Atlas-SNP	.											.	NFATC3	190	.	0			c.C2625T						PASS	.	C	,,	4,4392	8.1+/-20.4	0,4,2194	199	181	187		2625,2625,2625	-1.8	0.4	16	dbSNP_134	187	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	NFATC3	NM_004555.3,NM_173163.2,NM_173165.2	,,	0,4,6494	TT,TC,CC		0.0,0.091,0.0308	,,	875/1069,875/1066,875/1076	68225197	4,12992	2198	4300	6498	SO:0001819	synonymous_variant	4775	exon9			GCATACCCTGCCT	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.2625C>T	16.37:g.68225197C>T		243	1	0.00411523		251	125	0.498008	NM_173163	O75211|Q14516|Q99840|Q99841|Q99842	Silent	SNP	ENST00000346183.3	37	CCDS10860.1																																																																																			C|1.000;T|0.000	0.000	strong		0.443	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555		T	68225197	C	T	68225197	2	4	22	1	0	0	0	0	0	0	0	1	10373	610	22	2		2	NFATC3	16	68225197	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	411	68225197	22129556	3290	6191											
CIRH1A	84916	hgsc.bcm.edu	37	chr16	69191012	69191012	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caaaatgccagcattccttcGctctgcccttcagattttgt	8	14	6	13	1	2	1	1	0	1	1	4	1	3	1	3	0	3	2	3	0	2	5	rs8056684	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:69191012G>A	ENST00000314423.7	+	12	1490	c.1313G>A	c.(1312-1314)cGc>cAc	p.R438H	CIRH1A_ENST00000563094.1_Missense_Mutation_p.R438H|CIRH1A_ENST00000352319.4_Intron			Q969X6	CIR1A_HUMAN	cirrhosis, autosomal recessive 1A (cirhin)	438			R -> H (in dbSNP:rs8056684).		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)		GCATTCCTTCGCTCTGCCCTT	0.443													G|||	28	0.00559105	0.0204	0.0014	5008	,	,		19933	0.0		0.0	False		,,,				2504	0.0				p.R438H	Melanoma(69;1156 1278 4951 8715 52012)	Atlas-SNP	.											.	CIRH1A	48	.	0			c.G1313A						PASS	.	G	HIS/ARG	91,4305	75.2+/-113.4	1,89,2108	97	89	92		1313	0.4	1	16	dbSNP_116	92	0,8600		0,0,4300	yes	missense	CIRH1A	NM_032830.2	29	1,89,6408	AA,AG,GG		0.0,2.0701,0.7002	benign	438/687	69191012	91,12905	2198	4300	6498	SO:0001583	missense	84916	exon12			TCCTTCGCTCTGC	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.1313G>A	16.37:g.69191012G>A	ENSP00000327179:p.Arg438His	111	0	0		155	69	0.445161	NM_032830	Q8NCD9|Q8TF14|Q96SP0|Q96SR9|Q96SZ9|Q96T13|Q9BWK6	Missense_Mutation	SNP	ENST00000314423.7	37	CCDS10872.1	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	G	11.42	1.632635	0.29068	0.020701	0.0	ENSG00000141076	ENST00000314423	T	0.29917	1.55	5.63	0.418	0.16429	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	0.577687	0.20003	N	0.101285	T	0.04092	0.0114	N	0.04959	-0.14	0.22389	N	0.999142	B;B	0.10296	0.0;0.003	B;B	0.01281	0.0;0.0	T	0.18903	-1.0322	10	0.38643	T	0.18	.	7.8446	0.29419	0.5019:0.0:0.4981:0.0	rs8056684;rs52807145;rs8056684	438;438	Q969X6;Q969X6-3	CIR1A_HUMAN;.	H	438	ENSP00000327179:R438H	ENSP00000327179:R438H	R	+	2	0	CIRH1A	67748513	0.806000	0.28996	0.991000	0.47740	0.870000	0.49936	0.011000	0.13264	0.341000	0.23771	0.455000	0.32223	CGC	G|0.990;A|0.010	0.010	strong		0.443	CIRH1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268950.2	NM_032830		A	69191012	G	A	69191012	3	1	22	1	0	0	0	0	1	0	0	0	3436	1087	38	1	1355	1	CIRH1A	16	69191012	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	965815	69191012	21163741	3291	6192											
TERF2	7014	hgsc.bcm.edu	37	chr16	69401085	69401085	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcatcattccaatggtggttGgaggattccgtagctgcctg	7	13	12	9	1	2	0	2	0	0	0	4	2	4	2	3	4	2	3	3	4	2	4	rs34014829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:69401085G>T	ENST00000254942.3	-	7	981	c.965C>A	c.(964-966)cCa>cAa	p.P322Q	TERF2_ENST00000569611.2_5'Flank|TERF2_ENST00000603068.1_Missense_Mutation_p.P280Q	NM_005652.3	NP_005643.2	Q15554	TERF2_HUMAN	telomeric repeat binding factor 2	322					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)				AATGGTGGTTGGAGGATTCCG	0.453													G|||	28	0.00559105	0.0204	0.0014	5008	,	,		18068	0.0		0.0	False		,,,				2504	0.0				p.P322Q	Ovarian(13;63 524 30420 31710 34037)	Atlas-SNP	.											.	TERF2	24	.	0			c.C965A						PASS	.	G	GLN/PRO	80,4316	68.1+/-105.8	1,78,2119	49	50	49		839	6.2	1	16	dbSNP_126	49	0,8600		0,0,4300	yes	missense	TERF2	NM_005652.3	76	1,78,6419	TT,TG,GG		0.0,1.8198,0.6156	probably-damaging	280/501	69401085	80,12916	2198	4300	6498	SO:0001583	missense	7014	exon7			GTGGTTGGAGGAT		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.965C>A	16.37:g.69401085G>T	ENSP00000254942:p.Pro322Gln	69	0	0		74	36	0.486486	NM_005652		Missense_Mutation	SNP	ENST00000254942.3	37		15	0.006868131868131868	14	0.028455284552845527	1	0.0027624309392265192	0	0.0	0	0.0	G	19.48	3.834956	0.71373	0.018198	0.0	ENSG00000132604	ENST00000254942	.	.	.	6.17	6.17	0.99709	.	0.265458	0.37761	N	0.001941	T	0.53270	0.1786	L	0.53249	1.67	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.62101	-0.6925	9	0.31617	T	0.26	-7.4119	16.3795	0.83443	0.0:0.0:1.0:0.0	rs34014829	280	Q15554	TERF2_HUMAN	Q	280	.	ENSP00000254942:P280Q	P	-	2	0	TERF2	67958586	1.000000	0.71417	0.998000	0.56505	0.894000	0.52154	3.792000	0.55476	2.941000	0.99782	0.655000	0.94253	CCA	G|0.991;T|0.009	0.009	strong		0.453	TERF2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000268944.2			T	69401085	G	T	69401085	3	4	22	1	0	0	0	0	1	0	0	0	15777	1348	47	4	679	4	TERF2	16	69401085	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	210073	69401085	20953668	3292	6193											
CYB5B	80777	hgsc.bcm.edu	37	chr16	69458746	69458746	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgagtctacgatgtcaccCgcttcctcaacgaggtgggg	7	8	14	12	4	3	0	2	0	1	0	4	3	4	0	2	4	2	1	2	4	2	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:69458746C>T	ENST00000512062.1	+	1	319	c.148C>T	c.(148-150)Cgc>Tgc	p.R50C	CYB5B_ENST00000561792.1_Missense_Mutation_p.R50C|CYB5B_ENST00000307892.8_Missense_Mutation_p.R54C|CYB5B_ENST00000515314.1_Missense_Mutation_p.R50C			O43169	CYB5B_HUMAN	cytochrome b5 type B (outer mitochondrial membrane)	50	Cytochrome b5 heme-binding. {ECO:0000255|PROSITE-ProRule:PRU00279}.				oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	heme binding (GO:0020037)|metal ion binding (GO:0046872)			endometrium(3)|kidney(3)|lung(2)	8		Ovarian(137;0.101)				CGATGTCACCCGCTTCCTCAA	0.592																																					p.R54C		Atlas-SNP	.											.	CYB5B	12	.	0			c.C160T						PASS	.						52	53	53					16																	69458746		2066	4196	6262	SO:0001583	missense	80777	exon1			GTCACCCGCTTCC		CCDS10880.2	16q22.1	2006-02-02			ENSG00000103018	ENSG00000103018			24374	protein-coding gene	gene with protein product		611964				11867265, 14733950	Standard	NM_030579		Approved	CYB5-M	uc002exg.1	O43169	OTTHUMG00000133020	ENST00000512062.1:c.148C>T	16.37:g.69458746C>T	ENSP00000423679:p.Arg50Cys	67	0	0		89	4	0.0449438	NM_030579	A8K6B1|Q96CC3|Q9BT35	Missense_Mutation	SNP	ENST00000512062.1	37		.	.	.	.	.	.	.	.	.	.	C	16.35	3.099759	0.56183	.	.	ENSG00000103018	ENST00000512062;ENST00000307892;ENST00000515314	T;T;T	0.77229	-1.08;-1.08;-1.08	5.88	2.86	0.33363	Cytochrome b5 (5);	0.620650	0.18955	N	0.126564	T	0.62344	0.2420	N	0.26092	0.79	0.58432	D	0.999999	B;B;B	0.30584	0.286;0.047;0.004	B;B;B	0.28638	0.092;0.012;0.005	T	0.57843	-0.7741	10	0.87932	D	0	-12.3637	6.394	0.21603	0.1369:0.6613:0.1316:0.0702	.	50;50;50	D6RFH4;O43169;Q5HYD9	.;CYB5B_HUMAN;.	C	50;54;50	ENSP00000423679:R50C;ENSP00000308430:R54C;ENSP00000421492:R50C	ENSP00000308430:R54C	R	+	1	0	CYB5B	68016247	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	1.771000	0.38542	0.382000	0.24878	0.655000	0.94253	CGC	.	.	none		0.592	CYB5B-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256606.2	NM_030579		T	69458746	C	T	69458746	3	4	22	1	0	0	0	0	1	0	0	0	4125	652	23	1	162	1	CYB5B	16	69458746	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	57661	69458746	20896007	3293	6194											
FUK	197258	hgsc.bcm.edu	37	chr16	70508544	70508544	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacagagcaggtggaactgcCgggacctgggcagtgggtgg	8	5	19	9	1	0	1	0	0	0	1	0	3	0	3	2	6	3	2	2	6	1	0	rs17883716	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:70508544C>T	ENST00000288078.6	+	17	2334	c.2102C>T	c.(2101-2103)cCg>cTg	p.P701L	FUK_ENST00000571514.1_Missense_Mutation_p.P192L|FUK_ENST00000378912.2_Missense_Mutation_p.P733L	NM_145059.2	NP_659496.2	Q8N0W3	FUK_HUMAN	fucokinase	701			P -> L (in dbSNP:rs17883716). {ECO:0000269|Ref.3}.			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)				GTGGAACTGCCGGGACCTGGG	0.657													C|||	2	0.000399361	0.0	0.0	5008	,	,		17514	0.0		0.002	False		,,,				2504	0.0				p.P701L		Atlas-SNP	.											.	FUK	72	.	0			c.C2102T						PASS	.	C	LEU/PRO	3,4111		0,3,2054	34	43	40		2102	3.7	0.9	16	dbSNP_124	40	25,8379		0,25,4177	yes	missense	FUK	NM_145059.2	98	0,28,6231	TT,TC,CC		0.2975,0.0729,0.2237	possibly-damaging	701/1085	70508544	28,12490	2057	4202	6259	SO:0001583	missense	197258	exon17			AACTGCCGGGACC		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	ENST00000288078.6:c.2102C>T	16.37:g.70508544C>T	ENSP00000288078:p.Pro701Leu	93	0	0		96	47	0.489583	NM_145059	Q5PSM3|Q5XKL6|Q6ZRA0|Q96MT9	Missense_Mutation	SNP	ENST00000288078.6	37	CCDS10891.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	16.20	3.054738	0.55325	7.29E-4	0.002975	ENSG00000157353	ENST00000288078;ENST00000378912;ENST00000538525	T;T	0.08634	3.12;3.07	5.77	3.72	0.42706	.	0.176184	0.50627	N	0.000110	T	0.09468	0.0233	M	0.66939	2.045	0.80722	D	1	P;P;P	0.52692	0.579;0.955;0.955	B;B;B	0.42087	0.072;0.375;0.267	T	0.27365	-1.0076	10	0.12766	T	0.61	-16.2145	9.0313	0.36260	0.146:0.7799:0.0:0.0741	rs17883716;rs17883716	733;607;701	Q8N0W3-2;B2RDL5;Q8N0W3	.;.;FUK_HUMAN	L	701;733;15	ENSP00000288078:P701L;ENSP00000368192:P733L	ENSP00000288078:P701L	P	+	2	0	FUK	69066045	0.990000	0.36364	0.878000	0.34440	0.674000	0.39518	2.878000	0.48515	1.463000	0.47967	-0.140000	0.14226	CCG	C|0.995;T|0.005	0.005	strong		0.657	FUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157291.2	NM_145059		T	70508544	C	T	70508544	3	4	22	1	0	0	0	0	1	0	0	0	6104	652	23	1	2164	1	FUK	16	70508544	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1049798	70508544	19846209	3294	6195											
HYDIN	54768	hgsc.bcm.edu	37	chr16	70841703	70841703	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgatgatggagaaggtcaccAtgtgatagaagacattcttg	13	10	12	6	1	2	5	1	2	1	3	2	7	2	5	1	2	0	0	1	2	3	3	rs116730273	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:70841703A>G	ENST00000393567.2	-	86	15296	c.15146T>C	c.(15145-15147)aTg>aCg	p.M5049T		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	5049					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)				GAAGGTCACCATGTGATAGAA	0.527													A|||	27	0.00539137	0.0197	0.0014	5008	,	,		21437	0.0		0.0	False		,,,				2504	0.0				p.M5049T		Atlas-SNP	.											.	HYDIN	788	.	0			c.T15146C						PASS	.	A	THR/MET	39,4047		0,39,2004	124	127	126		15143	3.1	0	16	dbSNP_132	126	0,8402		0,0,4201	yes	missense	HYDIN	NM_032821.2	81	0,39,6205	GG,GA,AA		0.0,0.9545,0.3123	benign	5048/5121	70841703	39,12449	2043	4201	6244	SO:0001583	missense	54768	exon86			GTCACCATGTGAT	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.15146T>C	16.37:g.70841703A>G	ENSP00000377197:p.Met5049Thr	273	0	0		310	142	0.458065	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	A	0.004	-2.378729	0.00205	0.009545	0.0	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.00705	5.81	6.16	3.06	0.35304	.	7.165540	0.02602	N	0.101146	T	0.00178	0.0005	N	0.00142	-2.005	0.23645	N	0.997212	B	0.09022	0.002	B	0.01281	0.0	T	0.41875	-0.9484	10	0.02654	T	1	.	8.741	0.34558	0.1238:0.0:0.7538:0.1223	.	5048	F8WD23	.	T	5049;5048	ENSP00000377197:M5049T	ENSP00000313052:M5048T	M	-	2	0	HYDIN	69399204	0.030000	0.19436	0.001000	0.08648	0.002000	0.02628	2.046000	0.41260	0.921000	0.36994	-0.924000	0.02725	ATG	A|0.994;G|0.006	0.006	strong		0.527	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			G	70841703	A	G	70841703	3	3	22	1	0	0	0	0	1	0	0	0	7476	217	8	3	223	3	HYDIN	16	70841703	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	333159	70841703	19513050	3295	6196											
HYDIN	54768	hgsc.bcm.edu	37	chr16	70954682	70954682	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagcttctccaggcgctcccGctccgccttctccctctcca	3	10	6	22	3	3	0	0	0	3	0	8	0	5	0	6	1	1	3	6	1	0	2	rs143849088	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:70954682G>A	ENST00000393567.2	-	46	7747	c.7597C>T	c.(7597-7599)Cgg>Tgg	p.R2533W		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2533					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)				aggcgctcccgctccgccttc	0.697													G|||	17	0.00339457	0.0129	0.0	5008	,	,		19002	0.0		0.0	False		,,,				2504	0.0				p.R2533W		Atlas-SNP	.											.	HYDIN	788	.	0			c.C7597T						PASS	.	G	TRP/ARG	28,3858		0,28,1915	20	21	21		7594	-0.8	1	16	dbSNP_134	21	0,8242		0,0,4121	yes	missense	HYDIN	NM_032821.2	101	0,28,6036	AA,AG,GG		0.0,0.7205,0.2309	probably-damaging	2532/5121	70954682	28,12100	1943	4121	6064	SO:0001583	missense	54768	exon46			GCTCCCGCTCCGC	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.7597C>T	16.37:g.70954682G>A	ENSP00000377197:p.Arg2533Trp	82	0	0		88	43	0.488636	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	18.32	3.597425	0.66332	0.007205	0.0	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.01178	5.22	5.89	-0.796	0.10912	.	0.000000	0.33834	U	0.004514	T	0.01061	0.0035	N	0.14661	0.345	0.25478	N	0.987764	D	0.89917	1.0	D	0.72338	0.977	T	0.38134	-0.9675	10	0.72032	D	0.01	.	13.9873	0.64343	0.1005:0.0:0.6814:0.2181	.	2532	F8WD23	.	W	2533;2532	ENSP00000377197:R2533W	ENSP00000313052:R2532W	R	-	1	2	HYDIN	69512183	0.996000	0.38824	0.984000	0.44739	0.832000	0.47134	0.126000	0.15769	-0.426000	0.07360	-1.296000	0.01341	CGG	G|0.996;A|0.004	0.004	strong		0.697	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			A	70954682	G	A	70954682	3	1	22	1	0	0	0	0	1	0	0	0	7476	1086	38	1	7932	1	HYDIN	16	70954682	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	112979	70954682	19400071	3296	6197											
HYDIN	54768	hgsc.bcm.edu	37	chr16	71007312	71007312	+	Frame_Shift_Del	DEL	G	G	-																															ggatccaagactccagaaatGggctggatttcgaagatccg																								rs373616607		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:71007312delG	ENST00000393567.2	-	35	5463	c.5313delC	c.(5311-5313)cccfs	p.P1771fs		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	1771					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)				CTCCAGAAATGGGCTGGATTT	0.403																																					p.I1772fs		Pindel,Atlas-Indel	.											.	HYDIN	788	.	0			c.5314delA						PASS	.						1	1	1					16																	71007312		454	1000	1454	SO:0001589	frameshift_variant	54768	exon35			.	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.5313delC	16.37:g.71007312delG	ENSP00000377197:p.Pro1771fs	101	0	.		140	25	0.179	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Frame_Shift_Del	DEL	ENST00000393567.2	37	CCDS59269.1																																																																																			.	.	weak		0.403	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			-	71007312	G	-	71007312	7	5	22	1	0	1	0	1	0	0	0	0	7476	1335	47	0	10260	0	HYDIN	16	71007312	Frame_Shift_Del	DEL	G	TCGA-G8-6324-01A-11D-2210-10	52630	71007312	19347441	3297	6198											
HYDIN	54768	hgsc.bcm.edu	37	chr16	71009054	71009054	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcacttggccagtttgcggCgactccgatggctgaagcag	7	9	13	12	3	1	1	1	1	0	0	2	3	2	1	2	3	2	3	2	3	1	2	rs201855097	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:71009054C>T	ENST00000393567.2	-	31	4907	c.4757G>A	c.(4756-4758)cGc>cAc	p.R1586H		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	1586					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)				CAGTTTGCGGCGACTCCGATG	0.512													C|||	27	0.00539137	0.0144	0.0029	5008	,	,		20704	0.001		0.005	False		,,,				2504	0.0				p.R1586H		Atlas-SNP	.											LOC652153,NS,carcinoma,-1,2	HYDIN	788	2	0			c.G4757A						scavenged	.						2	2	2					16																	71009054		1187	2725	3912	SO:0001583	missense	54768	exon31			TTGCGGCGACTCC	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.4757G>A	16.37:g.71009054C>T	ENSP00000377197:p.Arg1586His	151	0	0		170	45	0.264706	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	C	10.57	1.388546	0.25118	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.00966	5.49	4.61	-0.89	0.10577	.	0.499604	0.14321	U	0.326982	T	0.01189	0.0039	M	0.66939	2.045	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.42344	-0.9457	10	0.42905	T	0.14	.	3.7169	0.08441	0.1643:0.4632:0.0:0.3725	.	1585	F8WD23	.	H	1586;1585	ENSP00000377197:R1586H	ENSP00000313052:R1585H	R	-	2	0	HYDIN	69566555	0.002000	0.14202	0.000000	0.03702	0.007000	0.05969	0.261000	0.18442	-0.186000	0.10533	-0.444000	0.05651	CGC	C|0.999;T|0.001	0.001	weak		0.512	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			T	71009054	C	T	71009054	3	4	22	1	0	0	0	0	1	0	0	0	7476	768	27	1	10832	1	HYDIN	16	71009054	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1742	71009054	19345699	3298	6199											
HYDIN	54768	hgsc.bcm.edu	37	chr16	71101206	71101206	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcaataccttgctgtaattaAgagcgccagcacctcttctc	10	11	7	13	1	2	1	0	0	2	1	3	1	2	1	3	0	4	4	3	0	4	5	rs11866903	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:71101206A>G	ENST00000393567.2	-	15	2212	c.2062T>C	c.(2062-2064)Tta>Cta	p.L688L	HYDIN_ENST00000288168.10_Silent_p.L705L|HYDIN_ENST00000393550.2_Silent_p.L703L|HYDIN_ENST00000448089.2_Silent_p.L688L|HYDIN_ENST00000541601.1_Silent_p.L705L|HYDIN_ENST00000538248.1_Silent_p.L715L|HYDIN_ENST00000321489.5_Silent_p.L688L|HYDIN_ENST00000448691.1_Silent_p.L688L|HYDIN_ENST00000543639.1_5'Flank	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	688					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)				GCTGTAATTAAGAGCGCCAGC	0.562													A|||	378	0.0754792	0.2769	0.013	5008	,	,		18119	0.001		0.001	False		,,,				2504	0.001				p.L715L		Atlas-SNP	.											.	HYDIN	788	.	0			c.T2143C						PASS	.	A	,,,	969,3427	361.6+/-315.8	118,733,1347	68	59	62		2143,2113,2062,2062	0	1	16	dbSNP_120	62	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HYDIN	NM_001198542.1,NM_001198543.1,NM_017558.3,NM_032821.2	,,,	118,737,5643	GG,GA,AA		0.0465,22.0428,7.4869	,,,	715/951,705/941,688/1018,688/5121	71101206	973,12023	2198	4300	6498	SO:0001819	synonymous_variant	54768	exon15			TAATTAAGAGCGC	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.2062T>C	16.37:g.71101206A>G		70	0	0		54	22	0.407407	NM_001198542	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Silent	SNP	ENST00000393567.2	37	CCDS59269.1																																																																																			A|0.919;G|0.081	0.081	strong		0.562	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			G	71101206	A	G	71101206	2	3	22	1	0	0	0	0	0	0	0	1	7476	69	3	3		3	HYDIN	16	71101206	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	92152	71101206	19253547	3299	6200											
FTSJD1	55783	hgsc.bcm.edu	37	chr16	71317567	71317567	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctctctctttgaataatgaAatgcaaatgccttttagcaa	13	15	5	8	0	2	2	0	2	2	0	4	2	2	2	1	0	3	2	1	0	6	4	rs16970857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:71317567A>G	ENST00000338099.5	-	3	2593	c.2257T>C	c.(2257-2259)Ttc>Ctc	p.F753L	CMTR2_ENST00000434935.2_Missense_Mutation_p.F753L			Q8IYT2	CMTR2_HUMAN	cap methyltransferase 2	753			F -> L (in dbSNP:rs16970857).		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)										TGAATAATGAAATGCAAATGC	0.368													A|||	159	0.0317492	0.1165	0.0072	5008	,	,		19301	0.0		0.0	False		,,,				2504	0.0				p.F753L		Atlas-SNP	.											.	FTSJD1	70	.	0			c.T2257C						PASS	.	A	LEU/PHE,LEU/PHE	481,3915	216.8+/-235.3	32,417,1749	41	44	43		2257,2257	3.6	1	16	dbSNP_123	43	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense	FTSJD1	NM_001099642.1,NM_018348.5	22,22	32,420,6046	GG,GA,AA		0.0349,10.9418,3.7242	benign,benign	753/771,753/771	71317567	484,12512	2198	4300	6498	SO:0001583	missense	55783	exon3			TAATGAAATGCAA	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.2257T>C	16.37:g.71317567A>G	ENSP00000337512:p.Phe753Leu	178	0	0		180	88	0.488889	NM_018348	B2RCD5|D3DWS1|Q8NE77|Q8NFR5|Q9H8Z4|Q9NUS3|Q9NXF5	Missense_Mutation	SNP	ENST00000338099.5	37	CCDS10898.1	44	0.020146520146520148	42	0.08536585365853659	2	0.0055248618784530384	0	0.0	0	0.0	A	4.716	0.133141	0.09032	0.109418	3.49E-4	ENSG00000180917	ENST00000338099;ENST00000434935	T;T	0.09445	2.98;2.98	5.8	3.58	0.41010	.	0.463445	0.21366	N	0.075705	T	0.00073	0.0002	N	0.01168	-0.975	0.21499	N	0.99967	B	0.02656	0.0	B	0.01281	0.0	T	0.45600	-0.9250	10	0.02654	T	1	-21.5732	6.5334	0.22339	0.7212:0.147:0.1318:0.0	rs16970857;rs52837568;rs16970857	753	Q8IYT2	FTSJ1_HUMAN	L	753	ENSP00000337512:F753L;ENSP00000411148:F753L	ENSP00000337512:F753L	F	-	1	0	FTSJD1	69875068	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	0.876000	0.28092	1.020000	0.39573	0.477000	0.44152	TTC	A|0.964;G|0.036	0.036	strong		0.368	CMTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268984.2	NM_018348		G	71317567	A	G	71317567	3	3	22	1	0	0	0	0	1	0	0	0	6098	14	1	3	59	3	FTSJD1	16	71317567	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	216361	71317567	19037186	3300	6201											
TAT	6898	hgsc.bcm.edu	37	chr16	71602665	71602665	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcaactaaccgctccgtgaaCtccacatcgttctcaaattc	11	10	5	15	3	1	1	1	1	1	0	6	1	3	1	3	0	3	3	3	0	4	3	rs16973331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:71602665C>T	ENST00000355962.4	-	11	1306	c.1173G>A	c.(1171-1173)gaG>gaA	p.E391E	RP11-432I5.1_ENST00000561529.1_RNA	NM_000353.2	NP_000344.1	P17735	ATTY_HUMAN	tyrosine aminotransferase	391					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)	GCTCCGTGAACTCCACATCGT	0.522													C|||	189	0.0377396	0.1377	0.0101	5008	,	,		16730	0.0		0.0	False		,,,				2504	0.0				p.E391E	Melanoma(198;542 2142 10292 21661 50033)|Esophageal Squamous(48;487 1013 5572 44395 52594)	Atlas-SNP	.											.	TAT	80	.	0			c.G1173A						PASS	.	C		561,3835	250.9+/-257.8	44,473,1681	84	70	75		1173	-0.3	1	16	dbSNP_123	75	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous	TAT	NM_000353.2		44,478,5976	TT,TC,CC		0.0581,12.7616,4.3552		391/455	71602665	566,12430	2198	4300	6498	SO:0001819	synonymous_variant	6898	exon11			CGTGAACTCCACA		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.1173G>A	16.37:g.71602665C>T		118	0	0		134	63	0.470149	NM_000353	B2R8I1|D3DWS2	Silent	SNP	ENST00000355962.4	37	CCDS10903.1																																																																																			C|0.958;T|0.042	0.042	strong		0.522	TAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268989.1			T	71602665	C	T	71602665	2	4	22	1	0	0	0	0	0	0	0	1	15605	564	20	2		2	TAT	16	71602665	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	285098	71602665	18752088	3301	6202											
ZFHX3	463	hgsc.bcm.edu	37	chr16	72831357	72831358	+	In_Frame_Ins	INS	-	-	TTG																															gcctgggccagcgtttgtgcINSttgttgttgttgttgttgtt																								rs568545014|rs34918837|rs552138038|rs372909378	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:72831357_72831358insTTG	ENST00000268489.5	-	9	5895_5896	c.5223_5224insCAA	c.(5221-5226)caagca>caaCAAgca	p.1741_1742insQ	ZFHX3_ENST00000397992.5_In_Frame_Ins_p.827_828insQ	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	1741	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)				AGCGTTTGTGCttgttgttgtt	0.53														242	0.0483227	0.1755	0.0115	5008	,	,		29749	0.002		0.0	False		,,,				2504	0.0				p.A1742delinsQA		Atlas-Indel	.											.	ZFHX3	404	.	0			c.5224_5225insCAA						PASS	.																																			SO:0001652	inframe_insertion	463	exon9			.	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.5221_5223dupCAA	16.37:g.72831364_72831366dupTTG	ENSP00000268489:p.Gln1742_Gln1743dup	198	0	0		184	51	0.277174	NM_006885	D3DWS8|O15101|Q13719	In_Frame_Ins	INS	ENST00000268489.5	37	CCDS10908.1																																																																																			.	.	weak		0.53	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		TTG	72831358	-	TTG	72831357	7	5	22	1	0	1	1	0	0	0	0	0	17649	797	28	0	5895	0	ZFHX3	16	72831357	In_Frame_Ins	INS	-	TCGA-G8-6324-01A-11D-2210-10	1228692	72831357	17523396	3302	6203											
RFWD3	55159	hgsc.bcm.edu	37	chr16	74664698	74664698	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctggctttctgagctactaActcctgcacatgactgctcg	7	12	8	14	1	1	2	0	2	1	0	3	2	2	2	2	1	5	4	2	1	2	3	rs78796563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:74664698A>G	ENST00000361070.4	-	10	1832	c.1735T>C	c.(1735-1737)Tta>Cta	p.L579L	RFWD3_ENST00000571750.1_Silent_p.L579L	NM_018124.3	NP_060594.3	Q6PCD5	RFWD3_HUMAN	ring finger and WD repeat domain 3	579					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)	p.L579L(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	26						TGAGCTACTAACTCCTGCACA	0.473													A|||	67	0.0133786	0.0023	0.0259	5008	,	,		18719	0.0		0.0288	False		,,,				2504	0.0174				p.L579L		Atlas-SNP	.											RFWD3,NS,carcinoma,0,1	RFWD3	49	1	1	Substitution - coding silent(1)	lung(1)	c.T1735C						scavenged	.	A		28,4368	32.6+/-62.9	1,26,2171	94	70	78		1735	3.5	0.3	16	dbSNP_132	78	267,8333	102.3+/-163.5	4,259,4037	no	coding-synonymous	RFWD3	NM_018124.3		5,285,6208	GG,GA,AA		3.1047,0.6369,2.2699		579/775	74664698	295,12701	2198	4300	6498	SO:0001819	synonymous_variant	55159	exon10			CTACTAACTCCTG	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.1735T>C	16.37:g.74664698A>G		86	1	0.0116279		75	44	0.586667	NM_018124	A8K585|B2RE35|D3DUJ8|Q5XKR3|Q9H9Q3|Q9NVT4	Silent	SNP	ENST00000361070.4	37	CCDS32486.1																																																																																			A|0.981;G|0.019	0.019	strong		0.473	RFWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436506.2	NM_018124		G	74664698	A	G	74664698	2	3	22	1	0	0	0	0	0	0	0	1	13276	40	2	3		3	RFWD3	16	74664698	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1833341	74664698	15690055	3303	6204											
MLKL	197259	hgsc.bcm.edu	37	chr16	74709233	74709233	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	caacctcaccactggctgagCcagtcttcacattcttcacc	9	10	5	17	0	5	1	3	1	2	0	5	1	5	1	4	1	2	1	4	1	1	3	rs144526386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:74709233C>A	ENST00000306247.7	-	4	944	c.605G>T	c.(604-606)gGc>gTc	p.G202V	MLKL_ENST00000308807.7_Intron	NM_001142497.1	NP_001135969.1			mixed lineage kinase domain-like											breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(6)|skin(1)|stomach(2)	19						ACTGGCTGAGCCAGTCTTCAC	0.493													C|||	51	0.0101837	0.0023	0.0144	5008	,	,		19105	0.0		0.0209	False		,,,				2504	0.0174				p.G202V		Atlas-SNP	.											.	MLKL	51	.	0			c.G605T						PASS	.	C	VAL/GLY,	17,4379	23.3+/-48.9	0,17,2181	113	108	110		605,	-1	0	16	dbSNP_134	110	162,8438	76.3+/-139.0	2,158,4140	yes	missense,intron	MLKL	NM_001142497.1,NM_152649.2	109,	2,175,6321	AA,AC,CC		1.8837,0.3867,1.3773	,	202/264,	74709233	179,12817	2198	4300	6498	SO:0001583	missense	197259	exon4			GCTGAGCCAGTCT	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		ENST00000306247.7:c.605G>T	16.37:g.74709233C>A	ENSP00000303118:p.Gly202Val	103	0	0		93	49	0.526882	NM_001142497		Missense_Mutation	SNP	ENST00000306247.7	37	CCDS45528.1	23	0.010531135531135532	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	15	0.01978891820580475	C	8.923	0.961462	0.18583	0.003867	0.018837	ENSG00000168404	ENST00000306247	T	0.12147	2.71	4.96	-1.05	0.10036	.	.	.	.	.	T	0.14313	0.0346	.	.	.	0.09310	N	1	D	0.67145	0.996	D	0.65573	0.936	T	0.07501	-1.0769	8	0.48119	T	0.1	.	8.2986	0.32001	0.0:0.4852:0.0:0.5148	.	202	Q8NB16-2	.	V	202	ENSP00000303118:G202V	ENSP00000303118:G202V	G	-	2	0	MLKL	73266734	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	-0.620000	0.05565	-0.228000	0.09869	-0.374000	0.07098	GGC	C|0.986;A|0.014	0.014	strong		0.493	MLKL-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000436402.1	NM_152649		A	74709233	C	A	74709233	3	1	22	1	0	0	0	0	1	0	0	0	9628	739	26	4	198	4	MLKL	16	74709233	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	44535	74709233	15645520	3304	6205											
WDR59	79726	hgsc.bcm.edu	37	chr16	74943471	74943471	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggtacgacccgtaagccgTggtcacccgcgcaaacgtcg	8	6	12	15	7	1	0	1	0	0	0	2	1	1	0	3	2	3	3	3	2	3	2	rs61734551	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:74943471T>C	ENST00000262144.6	-	16	1700	c.1570A>G	c.(1570-1572)Acg>Gcg	p.T524A		NM_030581.3	NP_085058.3	Q6PJI9	WDR59_HUMAN	WD repeat domain 59	524										breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)	27						CCGTAAGCCGTGGTCACCCGC	0.547													T|||	66	0.0131789	0.0484	0.0029	5008	,	,		16262	0.0		0.0	False		,,,				2504	0.0				p.T524A		Atlas-SNP	.											.	WDR59	66	.	0			c.A1570G						PASS	.	T	ALA/THR	124,4272	92.5+/-131.2	0,124,2074	89	95	93		1570	4.8	1	16	dbSNP_129	93	2,8598	2.2+/-6.3	0,2,4298	yes	missense	WDR59	NM_030581.3	58	0,126,6372	CC,CT,TT		0.0233,2.8207,0.9695	benign	524/975	74943471	126,12870	2198	4300	6498	SO:0001583	missense	79726	exon16			AAGCCGTGGTCAC	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.1570A>G	16.37:g.74943471T>C	ENSP00000262144:p.Thr524Ala	43	0	0		44	21	0.477273	NM_030581	B3KRC3|Q71RE7|Q96PW5|Q9BSW6|Q9HA43	Missense_Mutation	SNP	ENST00000262144.6	37	CCDS32488.1	20	0.009157509157509158	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	0	0.0	T	10.57	1.388491	0.25118	0.028207	2.33E-4	ENSG00000103091	ENST00000262144	T	0.67698	-0.28	5.86	4.76	0.60689	.	0.137136	0.64402	D	0.000005	T	0.14313	0.0346	N	0.08118	0	0.34596	D	0.715995	B	0.12013	0.005	B	0.14023	0.01	T	0.30794	-0.9966	10	0.08381	T	0.77	-12.4732	13.1941	0.59728	0.0:0.0:0.1332:0.8668	.	524	Q6PJI9	WDR59_HUMAN	A	524	ENSP00000262144:T524A	ENSP00000262144:T524A	T	-	1	0	WDR59	73500972	1.000000	0.71417	0.997000	0.53966	0.015000	0.08874	5.542000	0.67218	1.129000	0.42072	-0.323000	0.08544	ACG	T|0.988;C|0.012	0.012	strong		0.547	WDR59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410601.3	NM_030581		C	74943471	T	C	74943471	3	2	22	1	0	0	0	0	1	0	0	0	17323	1696	59	3	1398	3	WDR59	16	74943471	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	234238	74943471	15411282	3305	6206											
BCAR1	9564	hgsc.bcm.edu	37	chr16	75269730	75269730	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	catacacgtcctcggccggcGgggagtctggagggggcgca	6	5	18	12	5	1	0	0	0	1	0	3	2	2	2	2	7	1	1	2	7	1	1	rs61729593	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:75269730G>A	ENST00000162330.5	-	5	1193	c.1067C>T	c.(1066-1068)cCg>cTg	p.P356L	BCAR1_ENST00000535626.2_Missense_Mutation_p.P208L|BCAR1_ENST00000566982.1_5'UTR|BCAR1_ENST00000420641.3_Missense_Mutation_p.P374L|BCAR1_ENST00000538440.2_Missense_Mutation_p.P356L|BCAR1_ENST00000393422.2_Missense_Mutation_p.P374L|BCAR1_ENST00000393420.6_Missense_Mutation_p.P374L|BCAR1_ENST00000418647.3_Missense_Mutation_p.P402L|BCAR1_ENST00000546196.1_Missense_Mutation_p.P327L|BCAR1_ENST00000542031.2_Missense_Mutation_p.P354L	NM_001170717.1|NM_014567.3	NP_001164188.1|NP_055382.2	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	356	Substrate for kinases. {ECO:0000250}.				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)		CTCGGCCGGCGGGGAGTCTGG	0.716													G|||	36	0.0071885	0.0257	0.0029	5008	,	,		14012	0.0		0.0	False		,,,				2504	0.0				p.P402L		Atlas-SNP	.											.	BCAR1	184	.	0			c.C1205T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	38,4262		0,38,2112	7	8	8		1205,1121,1121,1121,1067,1061,623,437,1067	3.3	0.3	16	dbSNP_129	8	2,8398		0,2,4198	no	missense,missense,missense,missense,missense,missense,missense,missense,missense	BCAR1	NM_001170714.1,NM_001170715.1,NM_001170716.1,NM_001170717.1,NM_001170718.1,NM_001170719.1,NM_001170720.1,NM_001170721.1,NM_014567.3	98,98,98,98,98,98,98,98,98	0,40,6310	AA,AG,GG		0.0238,0.8837,0.315	benign,benign,benign,benign,benign,benign,benign,benign,benign	402/917,374/889,374/889,374/889,356/871,354/869,208/723,146/661,356/871	75269730	40,12660	2150	4200	6350	SO:0001583	missense	9564	exon6			GCCGGCGGGGAGT	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.1067C>T	16.37:g.75269730G>A	ENSP00000162330:p.Pro356Leu	22	0	0		33	15	0.454545	NM_001170714	B3KWD7|B4DEV4|B4DGB5|B4DIW5|B7Z7X7|E9PCL5|E9PCV2|F5GXA2|F5GXV6|F5H7Z0|F8WA69|Q6QEF7	Missense_Mutation	SNP	ENST00000162330.5	37	CCDS10915.1	19	0.0086996336996337	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	G	8.927	0.962569	0.18583	0.008837	2.38E-4	ENSG00000050820	ENST00000162330;ENST00000393422;ENST00000420641;ENST00000538440;ENST00000418647;ENST00000535626;ENST00000393420;ENST00000542031;ENST00000546196	T;T;T;T;T;T;T;T;T	0.41065	1.12;1.66;1.47;1.23;1.4;1.01;1.3;1.13;2.9	4.29	3.29	0.37713	.	0.858926	0.10058	N	0.721285	T	0.14399	0.0348	L	0.47716	1.5	0.29586	N	0.848804	B;B;B;B;B;B;B;B;B	0.10296	0.001;0.003;0.002;0.001;0.002;0.0;0.0;0.001;0.0	B;B;B;B;B;B;B;B;B	0.09377	0.0;0.004;0.001;0.002;0.001;0.0;0.002;0.001;0.001	T	0.18555	-1.0333	10	0.21014	T	0.42	-13.6226	9.512	0.39082	0.113:0.0:0.887:0.0	.	374;208;402;354;374;374;356;356;146	B4DIW5;F5GXV6;E9PCL5;F5GXA2;F8WA69;E9PCV2;F5H7Z0;P56945;B3KWE2	.;.;.;.;.;.;.;BCAR1_HUMAN;.	L	356;374;374;356;402;208;374;354;327	ENSP00000162330:P356L;ENSP00000377074:P374L;ENSP00000392708:P374L;ENSP00000443841:P356L;ENSP00000391669:P402L;ENSP00000440370:P208L;ENSP00000377072:P374L;ENSP00000440415:P354L;ENSP00000442161:P327L	ENSP00000162330:P356L	P	-	2	0	BCAR1	73827231	0.006000	0.16342	0.262000	0.24481	0.052000	0.14988	1.241000	0.32743	0.871000	0.35750	0.558000	0.71614	CCG	G|0.991;A|0.009	0.009	strong		0.716	BCAR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269017.1	NM_014567		A	75269730	G	A	75269730	3	1	22	1	0	0	0	0	1	0	0	0	1348	1116	39	1	1557	1	BCAR1	16	75269730	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	326259	75269730	15085023	3306	6207											
CHST5	23563	hgsc.bcm.edu	37	chr16	75563352	75563352	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagggtcaggccggtgaaggCgtagagtgcgcggatctctg	7	7	19	8	4	2	2	1	1	1	1	3	4	2	3	1	5	1	1	1	5	2	1	rs7206332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:75563352C>T	ENST00000336257.3	-	3	2325	c.931G>A	c.(931-933)Gcc>Acc	p.A311T	CHST5_ENST00000541075.1_Missense_Mutation_p.A317T|RP11-77K12.7_ENST00000460606.1_3'UTR	NM_024533.4	NP_078809.2	Q9GZS9	CHST5_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5	311			A -> T (in dbSNP:rs7206332).		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						CCGGTGAAGGCGTAGAGTGCG	0.677													C|||	124	0.0247604	0.0908	0.0058	5008	,	,		15530	0.0		0.0	False		,,,				2504	0.0				p.A311T		Atlas-SNP	.											CHST5,middle_lobe,carcinoma,+1,1	CHST5	47	1	0			c.G931A						PASS	.	C	THR/ALA	322,4070	164.0+/-195.7	15,292,1889	67	68	67		931	2.8	1	16	dbSNP_116	67	13,8587	7.7+/-29.5	0,13,4287	yes	missense	CHST5	NM_024533.4	58	15,305,6176	TT,TC,CC		0.1512,7.3315,2.5785	benign	311/412	75563352	335,12657	2196	4300	6496	SO:0001583	missense	23563	exon3			TGAAGGCGTAGAG	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.931G>A	16.37:g.75563352C>T	ENSP00000338783:p.Ala311Thr	58	0	0		55	27	0.490909	NM_024533	B2RV23|Q7LCN3|Q9UBY3	Missense_Mutation	SNP	ENST00000336257.3	37	CCDS10919.1	36	0.016483516483516484	32	0.06504065040650407	4	0.011049723756906077	0	0.0	0	0.0	C	6.674	0.492920	0.12702	0.073315	0.001512	ENSG00000135702	ENST00000336257;ENST00000541075	T;T	0.23950	1.88;1.88	2.84	2.84	0.33178	Sulfotransferase domain (1);	0.322809	0.31495	N	0.007547	T	0.01092	0.0036	L	0.29908	0.895	0.26382	N	0.976729	B;B	0.22851	0.062;0.076	B;B	0.22753	0.024;0.041	T	0.11567	-1.0582	10	0.25751	T	0.34	.	7.8661	0.29539	0.0:0.8684:0.0:0.1316	rs7206332;rs57580922;rs7206332	317;311	Q9GZS9-2;Q9GZS9	.;CHST5_HUMAN	T	311;317	ENSP00000338783:A311T;ENSP00000441220:A317T	ENSP00000338783:A311T	A	-	1	0	CHST5	74120853	0.000000	0.05858	0.995000	0.50966	0.142000	0.21351	0.279000	0.18771	1.583000	0.49898	0.313000	0.20887	GCC	C|0.974;T|0.026	0.026	strong		0.677	CHST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269025.2	NM_012126		T	75563352	C	T	75563352	3	4	22	1	0	0	0	0	1	0	0	0	3409	768	27	1	308	1	CHST5	16	75563352	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	293622	75563352	14791401	3307	6208											
CHST5	23563	hgsc.bcm.edu	37	chr16	75564172	75564172	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaggcaggtggtctgtgcCaggaggagcactgtcactgt	8	8	17	8	0	2	0	1	0	1	0	2	3	2	3	1	6	2	2	1	6	0	0	rs74355367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:75564172C>G	ENST00000336257.3	-	3	1505	c.111G>C	c.(109-111)ctG>ctC	p.L37L	CHST5_ENST00000541075.1_Silent_p.L43L|RP11-77K12.7_ENST00000460606.1_3'UTR	NM_024533.4	NP_078809.2	Q9GZS9	CHST5_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5	37					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						TGGTCTGTGCCAGGAGGAGCA	0.672													C|||	193	0.0385383	0.1422	0.0072	5008	,	,		17477	0.0		0.0	False		,,,				2504	0.0				p.L37L		Atlas-SNP	.											.	CHST5	47	.	0			c.G111C						PASS	.	C		537,3859	225.9+/-241.6	27,483,1688	32	28	29		111	1.1	1	16	dbSNP_131	29	16,8582	9.1+/-34.3	0,16,4283	no	coding-synonymous	CHST5	NM_024533.4		27,499,5971	GG,GC,CC		0.1861,12.2157,4.2558		37/412	75564172	553,12441	2198	4299	6497	SO:0001819	synonymous_variant	23563	exon3			CTGTGCCAGGAGG	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.111G>C	16.37:g.75564172C>G		95	0	0		114	52	0.45614	NM_024533	B2RV23|Q7LCN3|Q9UBY3	Silent	SNP	ENST00000336257.3	37	CCDS10919.1																																																																																			C|0.955;G|0.045	0.045	strong		0.672	CHST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269025.2	NM_012126		G	75564172	C	G	75564172	2	3	22	1	0	0	0	0	0	0	0	1	3409	581	21	4		4	CHST5	16	75564172	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	820	75564172	14790581	3308	6209											
WWOX	51741	hgsc.bcm.edu	37	chr16	78458807	78458807	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gcaacgcagcaacttttgctCtaccctggagtctcaccaaa	11	9	7	14	1	2	0	1	0	2	0	3	1	2	1	2	1	5	4	2	1	4	3	rs7201683	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:78458807C>G	ENST00000566780.1	+	7	1012	c.646C>G	c.(646-648)Cta>Gta	p.L216V	WWOX_ENST00000539474.2_Intron|WWOX_ENST00000402655.2_Intron|WWOX_ENST00000408984.3_Missense_Mutation_p.L216V|WWOX_ENST00000406884.2_Intron	NM_016373.2	NP_057457.1	Q9NZC7	WWOX_HUMAN	WW domain containing oxidoreductase	216	Interaction with MAPT. {ECO:0000250}.|Mediates targeting to the mitochondria. {ECO:0000250}.		L -> V (in dbSNP:rs7201683).		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)		AACTTTTGCTCTACCCTGGAG	0.468													C|||	197	0.0393371	0.1218	0.0202	5008	,	,		19087	0.0		0.0089	False		,,,				2504	0.0133				p.L216V		Atlas-SNP	.											.	WWOX	98	.	0			c.C646G						PASS	.	C	VAL/LEU	370,3528		15,340,1594	281	282	282		646	1.1	0	16	dbSNP_116	282	102,8180		1,100,4040	yes	missense	WWOX	NM_016373.2	32	16,440,5634	GG,GC,CC		1.2316,9.492,3.8752	possibly-damaging	216/415	78458807	472,11708	1949	4141	6090	SO:0001583	missense	51741	exon7			TTTGCTCTACCCT	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.646C>G	16.37:g.78458807C>G	ENSP00000457230:p.Leu216Val	176	0	0		196	100	0.510204	NM_016373	A8K323|Q5MYT5|Q96KM3|Q96RF2|Q9BTT8|Q9NPC9|Q9NRF4|Q9NRF5|Q9NRF6|Q9NRK1|Q9NZC5	Missense_Mutation	SNP	ENST00000566780.1	37	CCDS42196.1	79	0.036172161172161175	64	0.13008130081300814	9	0.024861878453038673	0	0.0	6	0.0079155672823219	C	0.015	-1.539831	0.00934	0.09492	0.012316	ENSG00000186153	ENST00000408984;ENST00000299644	T	0.21191	2.02	5.66	1.14	0.20703	NAD(P)-binding domain (1);	0.170005	0.43416	D	0.000569	T	0.00109	0.0003	N	0.16016	0.355	0.80722	P	0.0	B	0.14805	0.011	B	0.22601	0.04	T	0.23691	-1.0181	9	0.40728	T	0.16	.	8.0658	0.30659	0.0:0.5003:0.1647:0.335	rs7201683;rs52793545;rs7201683	216	Q9NZC7	WWOX_HUMAN	V	216;59	ENSP00000386161:L216V	ENSP00000299644:L59V	L	+	1	2	WWOX	77016308	0.006000	0.16342	0.043000	0.18650	0.121000	0.20230	0.216000	0.17585	-0.215000	0.10063	-0.797000	0.03246	CTA	C|0.956;G|0.044	0.044	strong		0.468	WWOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434328.1			G	78458807	C	G	78458807	3	3	22	1	0	0	0	0	1	0	0	0	17429	912	32	4	734	4	WWOX	16	78458807	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2894635	78458807	11895946	3309	6210											
CDYL2	124359	hgsc.bcm.edu	37	chr16	80642076	80642076	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aagacctgcgacaccagcccCctgctgcaggcctcctgggc	7	5	11	18	1	0	1	0	0	0	1	1	2	1	1	6	2	4	2	6	2	1	0	rs117351184	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:80642076C>T	ENST00000570137.2	-	6	1430	c.1275G>A	c.(1273-1275)agG>agA	p.R425R	CDYL2_ENST00000563890.1_Silent_p.R426R|CDYL2_ENST00000562812.1_Silent_p.R426R|CDYL2_ENST00000566173.1_Silent_p.R426R	NM_152342.2	NP_689555.2	Q8N8U2	CDYL2_HUMAN	chromodomain protein, Y-like 2	425						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	21						ACACCAGCCCCCTGCTGCAGG	0.617													C|||	27	0.00539137	0.0	0.0029	5008	,	,		6251	0.0		0.0239	False		,,,				2504	0.001				p.R425R		Atlas-SNP	.											.	CDYL2	66	.	0			c.G1275A						PASS	.	C		15,4385		0,15,2185	36	26	30		1275	-5.3	0.9	16	dbSNP_132	30	120,8478		0,120,4179	no	coding-synonymous	CDYL2	NM_152342.2		0,135,6364	TT,TC,CC		1.3957,0.3409,1.0386		425/507	80642076	135,12863	2200	4299	6499	SO:0001819	synonymous_variant	124359	exon6			CAGCCCCCTGCTG	AK096185	CCDS32493.1	16q23.2	2008-02-05	2003-09-12			ENSG00000166446			23030	protein-coding gene	gene with protein product			"chromodomain Y-like protein 2"			12837688	Standard	NM_152342		Approved	FLJ38866	uc002ffs.3	Q8N8U2		ENST00000570137.2:c.1275G>A	16.37:g.80642076C>T		117	0	0		130	59	0.453846	NM_152342	Q7Z5I8	Silent	SNP	ENST00000570137.2	37	CCDS32493.1																																																																																			C|0.990;T|0.010	0.010	strong		0.617	CDYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434727.2	NM_152342		T	80642076	C	T	80642076	2	4	22	1	0	0	0	0	0	0	0	1	3188	622	22	2		2	CDYL2	16	80642076	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2183269	80642076	9712677	3310	6211											
PKD1L2	114780	hgsc.bcm.edu	37	chr16	81208348	81208348	+	RNA	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtctgacgtctatgctcaGtgactgtcctgagccctggc	5	12	11	13	1	3	3	1	3	2	0	4	3	4	3	2	1	2	1	2	1	1	1	rs745211	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:81208348G>T	ENST00000527937.1	-	0	636				PKD1L2_ENST00000533478.1_RNA|PKD1L2_ENST00000337114.4_RNA|PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000531391.1_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						TCTATGCTCAGTGACTGTCCT	0.622													G|||	336	0.0670927	0.2443	0.0187	5008	,	,		18559	0.0		0.0	False		,,,				2504	0.0				p.L919M		Atlas-SNP	.											.	PKD1L2	361	.	0			c.C2755A						PASS	.	G	MET/LEU,MET/LEU	897,3165		103,691,1237	55	54	54		2755,2755	4.3	0	16	dbSNP_86	54	8,8374		0,8,4183	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	15,15	103,699,5420	TT,TG,GG		0.0954,22.0827,7.2726	probably-damaging,probably-damaging	919/992,919/2460	81208348	905,11539	2031	4191	6222			114780	exon16			TGCTCAGTGACTG	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		16.37:g.81208348G>T		115	0	0		118	67	0.567797	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000527937.1	37		139|139	0.06364468864468864|0.06364468864468864	134|134	0.27235772357723576|0.27235772357723576	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	0|0	0.0|0.0	G|G	15.20|15.20	2.762411|2.762411	0.49468|0.49468	0.220827|0.220827	9.54E-4|9.54E-4	ENSG00000166473|ENSG00000166473	ENST00000531391;ENST00000337114;ENST00000527937|ENST00000526632	T;T;T|.	0.34667|.	2.35;4.96;1.35|.	4.33|4.33	4.33|4.33	0.51752|0.51752	Egg jelly receptor, REJ-like (1);|.	1.304660|.	0.05138|.	N|.	0.493678|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	D;D;B|.	0.89917|.	0.999;1.0;0.329|.	D;D;B|.	0.74348|.	0.967;0.983;0.077|.	T|T	0.03086|0.03086	-1.1074|-1.1074	8|3	0.87932|.	D|.	0|.	-5.2934|-5.2934	14.1184|14.1184	0.65169|0.65169	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs745211;rs52837063;rs745211|rs745211;rs52837063;rs745211	175;919;919|.	Q7Z442-6;Q7Z442-3;Q7Z442|.	.;.;PK1L2_HUMAN|.	M|N	234;919;175|446	ENSP00000436309:L234M;ENSP00000337397:L919M;ENSP00000432818:L175M|.	ENSP00000337397:L919M|.	L|T	-|-	1|2	2|0	PKD1L2|PKD1L2	79765849|79765849	0.108000|0.108000	0.22018|0.22018	0.003000|0.003000	0.11579|0.11579	0.003000|0.003000	0.03518|0.03518	3.794000|3.794000	0.55492|0.55492	2.116000|2.116000	0.64780|0.64780	0.555000|0.555000	0.69702|0.69702	CTG|ACT	G|0.924;T|0.076	0.076	strong		0.622	PKD1L2-007	KNOWN	basic|exp_conf	protein_coding	polymorphic_pseudogene	OTTHUMT00000387978.1			T	81208348	G	T	81208348	1	4	22	0	1	0	0	0	0	0	0	0	11974	1020	36	4		4	PKD1L2	16	81208348	RNA	SNP	G	TCGA-G8-6324-01A-11D-2210-10	566272	81208348	9146405	3311	6212											
PKD1L2	114780	hgsc.bcm.edu	37	chr16	81208473	81208473	+	RNA	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tggggattttctctgacacgGcagcctggaatgctacatcc	8	11	11	11	1	1	1	0	1	1	0	3	3	2	3	2	4	3	2	2	4	2	3	rs115666278	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:81208473G>T	ENST00000527937.1	-	0	511				PKD1L2_ENST00000533478.1_RNA|PKD1L2_ENST00000337114.4_RNA|PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000531391.1_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						CTCTGACACGGCAGCCTGGAA	0.557													G|||	302	0.0603035	0.2186	0.0187	5008	,	,		19807	0.0		0.0	False		,,,				2504	0.0				p.A877D		Atlas-SNP	.											.	PKD1L2	361	.	0			c.C2630A						PASS	.	G	ASP/ALA,ASP/ALA	829,3309		91,647,1331	66	64	65		2630,2630	-1.8	0	16	dbSNP_132	65	8,8426		0,8,4209	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	126,126	91,655,5540	TT,TG,GG		0.0949,20.0338,6.6577	possibly-damaging,possibly-damaging	877/992,877/2460	81208473	837,11735	2069	4217	6286			114780	exon16			GACACGGCAGCCT	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		16.37:g.81208473G>T		84	0	0		90	43	0.477778	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000527937.1	37		126|126	0.057692307692307696|0.057692307692307696	121|121	0.2459349593495935|0.2459349593495935	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	0|0	0.0|0.0	G|G	13.39|13.39	2.221594|2.221594	0.39300|0.39300	0.200338|0.200338	9.49E-4|9.49E-4	ENSG00000166473|ENSG00000166473	ENST00000531391;ENST00000337114;ENST00000527937|ENST00000526632	T;T;T|.	0.57107|.	0.42;0.42;0.42|.	4.55|4.55	-1.81|-1.81	0.07882|0.07882	Egg jelly receptor, REJ-like (1);|.	1.422600|.	0.04339|.	N|.	0.353783|.	T|.	0.00012|.	0.0000|.	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	P;P;B|.	0.37636|.	0.513;0.603;0.009|.	B;B;B|.	0.40009|.	0.299;0.316;0.009|.	T|.	0.29458|.	-1.0011|.	8|.	0.66056|.	D|.	0.02|.	-0.6932|-0.6932	8.1615|8.1615	0.31201|0.31201	0.6442:0.0:0.3558:0.0|0.6442:0.0:0.3558:0.0	.|.	133;877;877|.	Q7Z442-6;Q7Z442-3;Q7Z442|.	.;.;PK1L2_HUMAN|.	D|X	192;877;133|404	ENSP00000436309:A192D;ENSP00000337397:A877D;ENSP00000432818:A133D|.	ENSP00000337397:A877D|.	A|C	-|-	2|3	0|2	PKD1L2|PKD1L2	79765974|79765974	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.081000|0.081000	0.17604|0.17604	0.031000|0.031000	0.13710|0.13710	-0.115000|-0.115000	0.11915|0.11915	0.555000|0.555000	0.69702|0.69702	GCC|TGC	G|0.963;T|0.037	0.037	strong		0.557	PKD1L2-007	KNOWN	basic|exp_conf	protein_coding	polymorphic_pseudogene	OTTHUMT00000387978.1			T	81208473	G	T	81208473	1	4	22	0	1	0	0	0	0	0	0	0	11974	1203	42	4		4	PKD1L2	16	81208473	RNA	SNP	G	TCGA-G8-6324-01A-11D-2210-10	125	81208473	9146280	3312	6213											
PKD1L2	114780	hgsc.bcm.edu	37	chr16	81232426	81232426	+	RNA	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taggtcctgtccaagctccaAatggtcagaagcccaggagg	11	7	12	11	0	1	1	1	0	0	1	4	2	4	2	4	4	2	1	4	4	4	1	rs9934856	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:81232426A>C	ENST00000525539.1	-	0	1383				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						CCAAGCTCCAAATGGTCAGAA	0.557													A|||	101	0.0201677	0.0734	0.0058	5008	,	,		20314	0.0		0.0	False		,,,				2504	0.0				p.L462V		Atlas-SNP	.											.	PKD1L2	361	.	0			c.T1384G						PASS	.	A	VAL/LEU,VAL/LEU	224,3784		6,212,1786	128	131	130		1384,1384	-7.3	0	16	dbSNP_119	130	0,8340		0,0,4170	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	32,32	6,212,5956	CC,CA,AA		0.0,5.5888,1.8141	benign,benign	462/992,462/2460	81232426	224,12124	2004	4170	6174			114780	exon7			GCTCCAAATGGTC	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		16.37:g.81232426A>C		245	0	0		203	111	0.546798	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	A	2.456	-0.325238	0.05350	0.055888	0.0	ENSG00000166473	ENST00000337114	T	0.01304	5.03	4.77	-7.3	0.01446	Egg jelly receptor, REJ-like (1);	0.379301	0.24776	N	0.035687	T	0.00144	0.0004	.	.	.	0.09310	N	1	B;B	0.15473	0.013;0.001	B;B	0.19666	0.026;0.002	T	0.44498	-0.9324	9	0.23302	T	0.38	-1.4298	11.0124	0.47669	0.1809:0.5054:0.3137:0.0	rs9934856;rs52821211;rs56414767;rs9934856	462;462	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	V	462	ENSP00000337397:L462V	ENSP00000337397:L462V	L	-	1	2	PKD1L2	79789927	0.000000	0.05858	0.001000	0.08648	0.041000	0.13682	-0.318000	0.08050	-1.278000	0.02408	-1.249000	0.01516	TTG	A|0.984;C|0.016;G|0.000	0.016	strong		0.557	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2			C	81232426	A	C	81232426	1	2	22	0	1	0	0	0	0	0	0	0	11974	11	1	5		5	PKD1L2	16	81232426	RNA	SNP	A	TCGA-G8-6324-01A-11D-2210-10	23953	81232426	9122327	3313	6214											
PKD1L2	114780	hgsc.bcm.edu	37	chr16	81242184	81242184	+	RNA	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatctgctgccacctggcaTgactgtagctcctggcactg	6	11	10	14	0	2	1	1	1	1	0	3	1	3	1	3	2	3	5	3	2	1	1	rs9927930	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:81242184T>C	ENST00000525539.1	-	0	671				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						CCACCTGGCATGACTGTAGCT	0.562													T|||	184	0.0367412	0.1339	0.0101	5008	,	,		20552	0.0		0.0	False		,,,				2504	0.0				p.S224S		Atlas-SNP	.											.	PKD1L2	361	.	0			c.A672G						PASS	.	T	,	433,3807		22,389,1709	75	73	74		672,672	-8.6	0.6	16	dbSNP_119	74	3,8453		0,3,4225	no	coding-synonymous,coding-synonymous	PKD1L2	NM_001076780.1,NM_052892.3	,	22,392,5934	CC,CT,TT		0.0355,10.2123,3.4342	,	224/992,224/2460	81242184	436,12260	2120	4228	6348			114780	exon4			CTGGCATGACTGT	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		16.37:g.81242184T>C		37	0	0		47	21	0.446809	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Silent	SNP	ENST00000525539.1	37																																																																																				T|0.951;C|0.049	0.049	strong		0.562	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2			C	81242184	T	C	81242184	1	2	22	0	1	0	0	0	0	0	0	0	11974	1451	51	3		3	PKD1L2	16	81242184	RNA	SNP	T	TCGA-G8-6324-01A-11D-2210-10	9758	81242184	9112569	3314	6215											
PLCG2	5336	hgsc.bcm.edu	37	chr16	81960783	81960783	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcgaggagctagaaaagcaGgtgagtccccctcttcgatc	10	9	11	11	2	1	2	0	1	1	1	5	5	2	3	2	2	2	2	2	2	3	3	rs115583707	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:81960783G>A	ENST00000359376.3	+	23	2728	c.2514G>A	c.(2512-2514)caG>caA	p.Q838Q		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	838					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						TAGAAAAGCAGGTGAGTCCCC	0.512													G|||	54	0.0107827	0.0356	0.0101	5008	,	,		20557	0.0		0.0	False		,,,				2504	0.0				p.Q838Q		Atlas-SNP	.											.	PLCG2	276	.	0			c.G2514A						PASS	.	G		149,3837		3,143,1847	109	107	107		2514	5.3	1	16	dbSNP_132	107	1,8337		0,1,4168	yes	coding-synonymous-near-splice	PLCG2	NM_002661.3		3,144,6015	AA,AG,GG		0.012,3.7381,1.2171		838/1266	81960783	150,12174	1993	4169	6162	SO:0001630	splice_region_variant	5336	exon23			AAAGCAGGTGAGT		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.2514+1G>A	16.37:g.81960783G>A		81	0	0		74	39	0.527027	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Silent	SNP	ENST00000359376.3	37	CCDS42204.1																																																																																			G|0.984;A|0.016	0.016	strong		0.512	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1		Silent	A	81960783	G	A	81960783	5	1	22	1	0	0	0	0	0	0	1	0	12045	1014	35	2	2600	2	PLCG2	16	81960783	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	718599	81960783	8393970	3315	6216											
CDH13	1012	hgsc.bcm.edu	37	chr16	83378487	83378487	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctatttgtggagaccactgaTgtcaatggcaaaactctcga	12	11	9	9	1	2	2	1	1	1	1	3	4	2	2	1	2	1	1	1	2	4	2	rs145120824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:83378487T>C	ENST00000566620.1	+	6	947	c.657T>C	c.(655-657)gaT>gaC	p.D219D	CDH13_ENST00000428848.3_Silent_p.D180D|CDH13_ENST00000268613.10_Silent_p.D266D|CDH13_ENST00000569454.1_3'UTR	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	219	Cadherin 1. {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)		AGACCACTGATGTCAATGGCA	0.438													T|||	21	0.00419329	0.0144	0.0029	5008	,	,		19418	0.0		0.0	False		,,,				2504	0.0				p.D266D		Atlas-SNP	.											.	CDH13	97	.	0			c.T798C						PASS	.	T	,,,	47,3655		0,47,1804	78	80	79		798,540,,657	3.5	0.8	16	dbSNP_134	79	0,8178		0,0,4089	no	coding-synonymous,coding-synonymous,utr-5,coding-synonymous	CDH13	NM_001220488.1,NM_001220489.1,NM_001220490.1,NM_001257.4	,,,	0,47,5893	CC,CT,TT		0.0,1.2696,0.3956	,,,	266/761,180/675,,219/714	83378487	47,11833	1851	4089	5940	SO:0001819	synonymous_variant	1012	exon7			CACTGATGTCAAT	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.657T>C	16.37:g.83378487T>C		126	0	0		120	48	0.4	NM_001220488	A8W476|A8W477|B7Z590|C9JRI6|J3KN62|Q6GTW4|Q8TBX3	Silent	SNP	ENST00000566620.1	37	CCDS58486.1																																																																																			T|0.996;C|0.004	0.004	strong		0.438	CDH13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432917.1	NM_001257		C	83378487	T	C	83378487	2	2	22	1	0	0	0	0	0	0	0	1	3101	1461	51	3		3	CDH13	16	83378487	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1417704	83378487	6976266	3316	6217											
NECAB2	54550	hgsc.bcm.edu	37	chr16	84027966	84027966	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctggtgtggaagccccactcCcgcctctgcccccaaccaca	7	6	8	20	1	1	0	0	0	1	0	2	1	2	1	7	2	3	0	7	2	2	0	rs79514285	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84027966C>T	ENST00000305202.4	+	7	673	c.656C>T	c.(655-657)cCc>cTc	p.P219L	NECAB2_ENST00000567703.1_3'UTR|NECAB2_ENST00000565691.1_Missense_Mutation_p.P136L	NM_019065.2	NP_061938.2	Q7Z6G3	NECA2_HUMAN	N-terminal EF-hand calcium binding protein 2	219						cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	19						AGCCCCACTCCCGCCTCTGCC	0.617													C|||	12	0.00239617	0.0083	0.0014	5008	,	,		16456	0.0		0.0	False		,,,				2504	0.0				p.P219L		Atlas-SNP	.											.	NECAB2	36	.	0			c.C656T						PASS	.	C	LEU/PRO	49,4351	50.2+/-85.5	0,49,2151	56	55	55		656	2.6	0	16	dbSNP_131	55	1,8599	1.2+/-3.3	0,1,4299	yes	missense	NECAB2	NM_019065.2	98	0,50,6450	TT,TC,CC		0.0116,1.1136,0.3846	possibly-damaging	219/387	84027966	50,12950	2200	4300	6500	SO:0001583	missense	54550	exon7			CCACTCCCGCCTC	AY299331	CCDS10940.1	16q23.3-q24.1	2013-01-10	2007-12-06	2007-12-06	ENSG00000103154	ENSG00000103154		"N-terminal EF-hand calcium binding proteins", "EF-hand domain containing"	23746	protein-coding gene	gene with protein product			"EF-hand calcium binding protein 2"	EFCBP2		12044471	Standard	NM_019065		Approved		uc002fhd.3	Q7Z6G3	OTTHUMG00000137636	ENST00000305202.4:c.656C>T	16.37:g.84027966C>T	ENSP00000307449:p.Pro219Leu	100	0	0		99	50	0.50505	NM_019065	A2RRG3|O75547|Q6ZSK0	Missense_Mutation	SNP	ENST00000305202.4	37	CCDS10940.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	6.435	0.448444	0.12223	0.011136	1.16E-4	ENSG00000103154	ENST00000305202	T	0.18338	2.22	4.58	2.62	0.31277	.	0.326488	0.32868	N	0.005554	T	0.09598	0.0236	L	0.44542	1.39	0.09310	N	0.999999	B	0.06786	0.001	B	0.06405	0.002	T	0.27773	-1.0064	10	0.21540	T	0.41	-9.3808	10.4175	0.44331	0.0:0.7817:0.1375:0.0809	.	219	Q7Z6G3	NECA2_HUMAN	L	219	ENSP00000307449:P219L	ENSP00000307449:P219L	P	+	2	0	NECAB2	82585467	0.004000	0.15560	0.000000	0.03702	0.000000	0.00434	1.654000	0.37334	0.128000	0.18479	-1.872000	0.00552	CCC	C|0.996;T|0.004	0.004	strong		0.617	NECAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269077.2	NM_019065		T	84027966	C	T	84027966	3	4	22	1	0	0	0	0	1	0	0	0	10314	623	22	2	682	2	NECAB2	16	84027966	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	649479	84027966	6326787	3317	6218											
SLC38A8	146167	hgsc.bcm.edu	37	chr16	84050218	84050218	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcgccatggcgagcgtcacGgtgacccacaggatggtcag	9	5	15	12	4	2	1	2	1	0	0	2	3	2	2	2	4	2	0	2	4	0	0	rs13334006	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84050218G>A	ENST00000299709.3	-	8	1067	c.1068C>T	c.(1066-1068)acC>acT	p.T356T		NM_001080442.1	NP_001073911.1	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8	356					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						CGAGCGTCACGGTGACCCACA	0.627													G|||	295	0.0589058	0.2156	0.0144	5008	,	,		20259	0.0		0.0	False		,,,				2504	0.0				p.T356T		Atlas-SNP	.											.	SLC38A8	60	.	0			c.C1068T						PASS	.	G		822,3578	326.1+/-299.4	78,666,1456	74	67	69		1068	-7.5	0	16	dbSNP_121	69	12,8588	7.7+/-29.5	0,12,4288	no	coding-synonymous	SLC38A8	NM_001080442.1		78,678,5744	AA,AG,GG		0.1395,18.6818,6.4154		356/436	84050218	834,12166	2200	4300	6500	SO:0001819	synonymous_variant	146167	exon8			CGTCACGGTGACC		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.1068C>T	16.37:g.84050218G>A		46	0	0		36	21	0.583333	NM_001080442		Silent	SNP	ENST00000299709.3	37	CCDS32495.1																																																																																			G|0.939;A|0.061	0.061	strong		0.627	SLC38A8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432623.1	NM_001080442		A	84050218	G	A	84050218	2	1	22	1	0	0	0	0	0	0	0	1	14625	1103	39	1		1	SLC38A8	16	84050218	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	22252	84050218	6304535	3318	6219											
SLC38A8	146167	hgsc.bcm.edu	37	chr16	84056442	84056442	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	cagacaccagggcccagtggGagaggctccgtttgcgcatg	8	6	15	12	2	0	2	0	0	0	2	1	3	1	2	3	3	1	3	3	3	0	1	rs11861325	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84056442G>C	ENST00000299709.3	-	6	742	c.743C>G	c.(742-744)tCc>tGc	p.S248C		NM_001080442.1	NP_001073911.1	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8	248					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						GGCCCAGTGGGAGAGGCTCCG	0.617													G|||	179	0.0357428	0.1271	0.0115	5008	,	,		17454	0.0		0.001	False		,,,				2504	0.002				p.S248C		Atlas-SNP	.											.	SLC38A8	60	.	0			c.C743G						PASS	.	G	CYS/SER	463,3937	217.1+/-235.6	27,409,1764	84	67	73		743	1	0	16	dbSNP_120	73	4,8596	3.0+/-9.4	0,4,4296	yes	missense	SLC38A8	NM_001080442.1	112	27,413,6060	CC,CG,GG		0.0465,10.5227,3.5923	probably-damaging	248/436	84056442	467,12533	2200	4300	6500	SO:0001583	missense	146167	exon6			CAGTGGGAGAGGC		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.743C>G	16.37:g.84056442G>C	ENSP00000299709:p.Ser248Cys	71	0	0		79	37	0.468354	NM_001080442		Missense_Mutation	SNP	ENST00000299709.3	37	CCDS32495.1	71	0.03250915750915751	65	0.13211382113821138	6	0.016574585635359115	0	0.0	0	0.0	G	9.359	1.067547	0.20067	0.105227	4.65E-4	ENSG00000166558	ENST00000299709	T	0.02421	4.3	5.37	0.968	0.19680	.	0.403682	0.28322	N	0.015761	T	0.00109	0.0003	M	0.67953	2.075	0.43114	D	0.994829	D	0.65815	0.995	P	0.61800	0.894	T	0.12344	-1.0551	10	0.62326	D	0.03	.	10.254	0.43385	0.0736:0.4038:0.5226:0.0	rs11861325	248	A6NNN8	S38A8_HUMAN	C	248	ENSP00000299709:S248C	ENSP00000299709:S248C	S	-	2	0	SLC38A8	82613943	0.961000	0.32948	0.019000	0.16419	0.034000	0.12701	4.054000	0.57434	-0.033000	0.13736	0.549000	0.68633	TCC	G|0.961;C|0.039	0.039	strong		0.617	SLC38A8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432623.1	NM_001080442		C	84056442	G	C	84056442	3	2	22	1	0	0	0	0	1	0	0	0	14625	1174	41	4	584	4	SLC38A8	16	84056442	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6224	84056442	6298311	3319	6220											
MBTPS1	8720	hgsc.bcm.edu	37	chr16	84097021	84097021	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aatggggacgttttcaacaaCtgctgtttcctgctttaaaa	11	14	8	8	1	1	0	1	0	0	0	2	1	2	1	1	2	4	4	1	2	5	5	rs35417190	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84097021C>G	ENST00000343411.3	-	19	2956	c.2461G>C	c.(2461-2463)Gtt>Ctt	p.V821L		NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	821					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						TTTTCAACAACTGCTGTTTCC	0.438											OREG0023981	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	15	0.00299521	0.0091	0.0043	5008	,	,		17016	0.0		0.0	False		,,,				2504	0.0				p.V821L		Atlas-SNP	.											.	MBTPS1	85	.	0			c.G2461C						PASS	.	C	LEU/VAL	40,4360	43.8+/-77.6	0,40,2160	78	75	76		2461	2.4	0.1	16	dbSNP_126	76	0,8600		0,0,4300	yes	missense	MBTPS1	NM_003791.2	32	0,40,6460	GG,GC,CC		0.0,0.9091,0.3077	benign	821/1053	84097021	40,12960	2200	4300	6500	SO:0001583	missense	8720	exon19			CAACAACTGCTGT	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.2461G>C	16.37:g.84097021C>G	ENSP00000344223:p.Val821Leu	123	0	0	1226	120	53	0.441667	NM_003791	A8K6V8|Q24JQ2|Q9UF67	Missense_Mutation	SNP	ENST00000343411.3	37	CCDS10941.1	3	0.0013736263736263737	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	C	10.63	1.403350	0.25291	0.009091	0.0	ENSG00000140943	ENST00000343411;ENST00000347334	T	0.30182	1.54	5.44	2.36	0.29203	.	0.294067	0.37261	N	0.002176	T	0.10465	0.0256	N	0.16656	0.425	0.40773	D	0.983105	B	0.02656	0.0	B	0.04013	0.001	T	0.10730	-1.0617	10	0.25106	T	0.35	-6.6213	4.5503	0.12108	0.2657:0.5222:0.0:0.2121	rs35417190	821	Q14703	MBTP1_HUMAN	L	821;266	ENSP00000344223:V821L	ENSP00000344223:V821L	V	-	1	0	MBTPS1	82654522	0.002000	0.14202	0.082000	0.20525	0.989000	0.77384	0.019000	0.13444	0.335000	0.23614	0.491000	0.48974	GTT	C|0.997;G|0.003	0.003	strong		0.438	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269080.2	NM_003791		G	84097021	C	G	84097021	3	3	22	1	0	0	0	0	1	0	0	0	9370	565	20	4	717	4	MBTPS1	16	84097021	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	40579	84097021	6257732	3320	6221											
KCNG4	93107	hgsc.bcm.edu	37	chr16	84270650	84270650	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctcctcgatgccccagtaggCcagctcctcctggaaggaca	8	7	10	16	1	0	0	0	0	0	0	4	3	3	2	6	3	2	2	6	3	2	1	rs61743417	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84270650C>T	ENST00000308251.4	-	2	510	c.442G>A	c.(442-444)Gcc>Acc	p.A148T	KCNG4_ENST00000568181.1_Missense_Mutation_p.A148T	NM_172347.2	NP_758857.1	Q8TDN1	KCNG4_HUMAN	potassium voltage-gated channel, subfamily G, member 4	148					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)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	31						CCCCAGTAGGCCAGCTCCTCC	0.667													C|||	149	0.0297524	0.1097	0.0058	5008	,	,		16764	0.0		0.0	False		,,,				2504	0.0				p.A148T		Atlas-SNP	.											KCNG4,NS,carcinoma,0,1	KCNG4	71	1	0			c.G442A						PASS	.	C	THR/ALA	380,4020	191.6+/-217.2	19,342,1839	42	43	42		442	-1	0.6	16	dbSNP_129	42	0,8600		0,0,4300	yes	missense	KCNG4	NM_172347.2	58	19,342,6139	TT,TC,CC		0.0,8.6364,2.9231	benign	148/520	84270650	380,12620	2200	4300	6500	SO:0001583	missense	93107	exon2			AGTAGGCCAGCTC	AF348984	CCDS10945.1	16q24.1	2011-07-05			ENSG00000168418	ENSG00000168418		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	19697	protein-coding gene	gene with protein product		607603				12060745, 16382104	Standard	NM_172347		Approved	Kv6.4	uc010voc.2	Q8TDN1	OTTHUMG00000137638	ENST00000308251.4:c.442G>A	16.37:g.84270650C>T	ENSP00000312129:p.Ala148Thr	126	0	0		142	59	0.415493	NM_172347	Q96H24	Missense_Mutation	SNP	ENST00000308251.4	37	CCDS10945.1	48	0.02197802197802198	47	0.09552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	C	4.103	0.017220	0.07959	0.086364	0.0	ENSG00000168418	ENST00000308251	T	0.76709	-1.04	5.11	-1.05	0.10036	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.951541	0.08816	N	0.889546	T	0.02727	0.0082	N	0.11818	0.18	0.09310	N	0.999999	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.001	T	0.01215	-1.1416	10	0.16896	T	0.51	.	9.62	0.39716	0.0:0.3441:0.0:0.6559	.	148;148	Q8TDN1;Q8TDN1-2	KCNG4_HUMAN;.	T	148	ENSP00000312129:A148T	ENSP00000312129:A148T	A	-	1	0	KCNG4	82828151	0.000000	0.05858	0.631000	0.29282	0.993000	0.82548	-0.583000	0.05807	-0.538000	0.06281	-0.275000	0.10095	GCC	C|0.971;T|0.029	0.029	strong		0.667	KCNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269079.2	NM_172347		T	84270650	C	T	84270650	3	4	22	1	0	0	0	0	1	0	0	0	8039	739	26	2	1123	2	KCNG4	16	84270650	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	173629	84270650	6084103	3321	6222											
ATP2C2	9914	hgsc.bcm.edu	37	chr16	84497336	84497337	+	Stop_Codon_Ins	INS	-	-	AGTGGA																															gatgcaccctgaagatgtgtINSagtggaccgcactccgcggc																								rs149491518|rs568403499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84497336_84497337insAGTGGA	ENST00000262429.4	+	0	2928_2929				RP11-517C16.2_ENST00000565700.1_RNA|ATP2C2_ENST00000420010.2_3'UTR|ATP2C2_ENST00000416219.2_Stop_Codon_Ins	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						TGAAGATGTGTAGTGGACCGCA	0.54														67	0.0133786	0.0499	0.0014	5008	,	,		19122	0.0		0.0	False		,,,				2504	0.0				p.X947delinsX		Pindel,Atlas-Indel	.											.	ATP2C2	75	.	0			c.2839_2840insAGTGGA						PASS	.			151,3647		1,149,1749						3.1	0		dbSNP_134	118	1,7939		0,1,3969	no	coding	ATP2C2	NM_014861.2		1,150,5718	A1A1,A1R,RR		0.0126,3.9758,1.2949				152,11586				SO:0001567	stop_retained_variant	9914	exon27			.	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.2839_2844dupAGTGGA	16.37:g.84497337_84497342dupAGTGGA		146	0	.		120	26	0.217	NM_014861	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	In_Frame_Ins	INS	ENST00000262429.4	37	CCDS42207.1																																																																																			-|0.987;AGTGGA|0.013	0.013	strong		0.54	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861		AGTGGA	84497337	-	AGTGGA	84497336	7	5	22	1	0	1	1	0	0	0	0	0	1144	1651	57	0	2945	0	ATP2C2	16	84497336	Stop_Codon_Ins	INS	-	TCGA-G8-6324-01A-11D-2210-10	226686	84497336	5857417	3322	6223											
KIAA1609	57707	hgsc.bcm.edu	37	chr16	84520496	84520496	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgccctggtccacttgacgCtcagggaccagggtagtcag	7	8	13	13	1	2	1	2	1	0	0	3	2	3	2	3	3	1	2	3	3	1	2	rs34244563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84520496C>G	ENST00000343629.6	-	5	881	c.699G>C	c.(697-699)gaG>gaC	p.E233D	TLDC1_ENST00000561807.1_5'Flank|TLDC1_ENST00000535580.1_Missense_Mutation_p.E206D	NM_020947.3	NP_065998.3	Q6P9B6	TLDC1_HUMAN	TBC/LysM-associated domain containing 1	233			E -> D (in dbSNP:rs34244563).			lysosomal membrane (GO:0005765)											CCACTTGACGCTCAGGGACCA	0.572													C|||	55	0.0109824	0.0401	0.0014	5008	,	,		21248	0.0		0.001	False		,,,				2504	0.0				p.E233D		Atlas-SNP	.											.	KIAA1609	39	.	0			c.G699C						PASS	.	C	ASP/GLU	128,4272	91.6+/-130.3	3,122,2075	45	44	44		699	5	0.4	16	dbSNP_126	44	3,8597	3.0+/-9.4	0,3,4297	yes	missense	KIAA1609	NM_020947.3	45	3,125,6372	GG,GC,CC		0.0349,2.9091,1.0077	possibly-damaging	233/457	84520496	131,12869	2200	4300	6500	SO:0001583	missense	57707	exon5			TTGACGCTCAGGG	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.699G>C	16.37:g.84520496C>G	ENSP00000343635:p.Glu233Asp	149	0	0		145	72	0.496552	NM_020947	Q8IZ64|Q9HCG3|Q9NTE8	Missense_Mutation	SNP	ENST00000343629.6	37	CCDS32498.1	27	0.012362637362637362	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	9.308	1.054856	0.19907	0.029091	3.49E-4	ENSG00000140950	ENST00000343629;ENST00000535580	T;T	0.10668	3.03;2.85	4.98	4.98	0.66077	.	0.749691	0.13046	N	0.418157	T	0.01905	0.0060	M	0.67953	2.075	0.25363	N	0.988763	P;B	0.51933	0.949;0.251	B;B	0.43301	0.415;0.051	T	0.19128	-1.0315	10	0.22706	T	0.39	-28.8132	7.464	0.27312	0.0:0.725:0.1841:0.0909	rs34244563	206;233	F5GWS3;Q6P9B6	.;K1609_HUMAN	D	233;206	ENSP00000343635:E233D;ENSP00000441997:E206D	ENSP00000343635:E233D	E	-	3	2	KIAA1609	83077997	0.971000	0.33674	0.403000	0.26384	0.015000	0.08874	1.112000	0.31172	2.295000	0.77249	0.563000	0.77884	GAG	C|0.989;G|0.011	0.011	strong		0.572	TLDC1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433421.1	NM_020947		G	84520496	C	G	84520496	3	3	22	1	0	0	0	0	1	0	0	0	8256	796	28	4	687	4	KIAA1609	16	84520496	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	23160	84520496	5834257	3323	6224											
KIAA1609	57707	hgsc.bcm.edu	37	chr16	84529358	84529360	+	In_Frame_Del	DEL	CTC	CTC	-																															ttcataatcatgagactcttCtcctcggagtttcctttcaa																								rs200260198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84529358_84529360delCTC	ENST00000343629.6	-	3	495_497	c.313_315delGAG	c.(313-315)gagdel	p.E105del	TLDC1_ENST00000561807.1_5'UTR|TLDC1_ENST00000535580.1_In_Frame_Del_p.E78del|RP11-517C16.4_ENST00000568771.1_RNA	NM_020947.3	NP_065998.3	Q6P9B6	TLDC1_HUMAN	TBC/LysM-associated domain containing 1	105						lysosomal membrane (GO:0005765)											TGAGACTCTTCTCCTCGGAGTTT	0.542														32	0.00638978	0.0219	0.0029	5008	,	,		19194	0.0		0.001	False		,,,				2504	0.0				p.105_106del		Pindel,Atlas-Indel	.											.	KIAA1609	39	.	0			c.314_316del						PASS	.			120,4144		5,110,2017						4.2	0.9			119	32,8222		12,8,4107	no	coding	KIAA1609	NM_020947.3		17,118,6124	A1A1,A1R,RR		0.3877,2.8143,1.2143				152,12366				SO:0001651	inframe_deletion	57707	exon3			.	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.313_315delGAG	16.37:g.84529361_84529363delCTC	ENSP00000343635:p.Glu105del	226	0	.		184	53	0.288	NM_020947	Q8IZ64|Q9HCG3|Q9NTE8	In_Frame_Del	DEL	ENST00000343629.6	37	CCDS32498.1																																																																																			CTC|0.994;-|0.006	0.006	strong		0.542	TLDC1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433421.1	NM_020947		-	84529360	CTC	-	84529358	7	5	22	1	0	1	0	1	0	0	0	0	8256	912	32	0	1079	0	KIAA1609	16	84529358	In_Frame_Del	DEL	CTC	TCGA-G8-6324-01A-11D-2210-10	8862	84529358	5825395	3324	6225											
COTL1	23406	hgsc.bcm.edu	37	chr16	84651452	84651452	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaaagttcctaccagatgacGgccgagccgtcgtcgcgcac	10	6	11	14	6	0	2	0	1	0	1	3	3	1	2	4	1	2	2	4	1	3	2	rs144159131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84651452G>C	ENST00000262428.4	-	1	231	c.69C>G	c.(67-69)gcC>gcG	p.A23A	COTL1_ENST00000564057.1_5'UTR	NM_021149.2	NP_066972.1	Q14019	COTL1_HUMAN	coactosin-like F-actin binding protein 1	23	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						ACCAGATGACGGCCGAGCCGT	0.706													g|||	3	0.000599042	0.0015	0.0	5008	,	,		7761	0.0		0.0	False		,,,				2504	0.001				p.A23A		Atlas-SNP	.											.	COTL1	17	.	0			c.C69G						PASS	.			4,4354		0,4,2175	19	15	16		69	-5.9	1	16	dbSNP_134	16	0,8534		0,0,4267	no	coding-synonymous	COTL1	NM_021149.2		0,4,6442	CC,CG,GG		0.0,0.0918,0.031		23/143	84651452	4,12888	2179	4267	6446	SO:0001819	synonymous_variant	23406	exon1			GATGACGGCCGAG	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.69C>G	16.37:g.84651452G>C		22	0	0		35	16	0.457143	NM_021149	B2RDU3|D3DUL9|Q86XM5	Silent	SNP	ENST00000262428.4	37	CCDS10947.1																																																																																			G|0.999;C|0.001	0.001	strong		0.706	COTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269075.1	NM_021149		C	84651452	G	C	84651452	2	2	22	1	0	0	0	0	0	0	0	1	3763	1103	39	4		4	COTL1	16	84651452	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	122094	84651452	5703301	3325	6226											
KLHL36	79786	hgsc.bcm.edu	37	chr16	84691256	84691256	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aacaacctggcggcccagccCgtcatgcagaccaagcgcac	11	3	10	17	3	1	1	1	0	0	1	1	1	1	1	4	2	5	2	4	2	3	0	rs12102528	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84691256C>T	ENST00000564996.1	+	3	984	c.843C>T	c.(841-843)ccC>ccT	p.P281P	KLHL36_ENST00000258157.5_Silent_p.P281P	NM_024731.2	NP_079007.2	Q8N4N3	KLH36_HUMAN	kelch-like family member 36	281					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						CGGCCCAGCCCGTCATGCAGA	0.677													C|||	79	0.0157748	0.0567	0.0058	5008	,	,		17332	0.0		0.0	False		,,,				2504	0.0				p.P281P		Atlas-SNP	.											.	KLHL36	51	.	0			c.C843T						PASS	.	C		208,4182		6,196,1993	29	28	28		843	-3.6	1	16	dbSNP_120	28	1,8595		0,1,4297	no	coding-synonymous	KLHL36	NM_024731.2		6,197,6290	TT,TC,CC		0.0116,4.738,1.6094		281/617	84691256	209,12777	2195	4298	6493	SO:0001819	synonymous_variant	79786	exon3			CCAGCCCGTCATG	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.843C>T	16.37:g.84691256C>T		45	0	0		59	23	0.38983	NM_024731	Q8N5G6|Q9H9U6	Silent	SNP	ENST00000564996.1	37	CCDS10948.1																																																																																			C|0.984;T|0.016	0.016	strong		0.677	KLHL36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269084.2			T	84691256	C	T	84691256	2	4	22	1	0	0	0	0	0	0	0	1	8398	639	23	1		1	KLHL36	16	84691256	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	39804	84691256	5663497	3326	6227											
USP10	9100	hgsc.bcm.edu	37	chr16	84778261	84778261	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caagaatatcagagaattgaGtttggtgtcgatgaagtcat	14	12	11	4	1	2	4	2	2	0	2	3	6	2	4	0	1	0	1	0	1	5	3	rs77170713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84778261G>A	ENST00000219473.7	+	4	287	c.174G>A	c.(172-174)gaG>gaA	p.E58E	USP10_ENST00000562743.1_3'UTR|USP10_ENST00000570191.1_Silent_p.E62E	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	58	Interaction with p53/TP53.				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						AGAGAATTGAGTTTGGTGTCG	0.403													G|||	27	0.00539137	0.0204	0.0	5008	,	,		16411	0.0		0.0	False		,,,				2504	0.0				p.E62E		Atlas-SNP	.											.	USP10	51	.	0			c.G186A						PASS	.	G		55,3637		0,55,1791	45	43	43		174	-3	1	16	dbSNP_131	43	1,8163		0,1,4081	no	coding-synonymous	USP10	NM_005153.2		0,56,5872	AA,AG,GG		0.0122,1.4897,0.4723		58/799	84778261	56,11800	1846	4082	5928	SO:0001819	synonymous_variant	9100	exon5			AATTGAGTTTGGT	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.174G>A	16.37:g.84778261G>A		119	0	0		145	77	0.531034	NM_001272075	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Silent	SNP	ENST00000219473.7	37	CCDS45537.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	12.78	2.039111	0.35989	0.014897	1.22E-4	ENSG00000103194	ENST00000540269	.	.	.	5.06	-3.04	0.05412	.	.	.	.	.	T	0.59609	0.2206	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.67538	-0.5645	5	0.66056	D	0.02	-22.7486	11.4442	0.50114	0.7447:0.0:0.2553:0.0	.	.	.	.	N	38	.	ENSP00000445589:S38N	S	+	2	0	USP10	83335762	1.000000	0.71417	0.969000	0.41365	0.892000	0.51952	0.653000	0.24902	-0.665000	0.05317	-0.339000	0.08088	AGT	G|0.997;A|0.003	0.003	strong		0.403	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1			A	84778261	G	A	84778261	2	1	22	1	0	0	0	0	0	0	0	1	17056	1020	36	2		2	USP10	16	84778261	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	87005	84778261	5576492	3327	6228											
ZDHHC7	55625	hgsc.bcm.edu	37	chr16	85011548	85011548	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accagtccactgccctcggaCacaggagatgaactgaaatc	13	6	9	13	1	0	3	0	2	0	1	3	5	1	4	3	2	2	0	3	2	2	0	rs13334011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:85011548C>T	ENST00000313732.4	-	6	953	c.601G>A	c.(601-603)Gtc>Atc	p.V201I	ZDHHC7_ENST00000569488.1_5'UTR|ZDHHC7_ENST00000564466.1_Missense_Mutation_p.V238I	NM_017740.2	NP_060210.2	Q9NXF8	ZDHC7_HUMAN	zinc finger, DHHC-type containing 7	201			V -> I (in dbSNP:rs13334011).		peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein palmitoylation (GO:0018345)	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)			large_intestine(6)|lung(4)	10						TGCCCTCGGACACAGGAGATG	0.443													C|||	134	0.0267572	0.0968	0.0086	5008	,	,		19553	0.0		0.0	False		,,,				2504	0.0				p.V238I		Atlas-SNP	.											.	ZDHHC7	55	.	0			c.G712A						PASS	.	C	ILE/VAL,ILE/VAL	332,4066	175.1+/-204.6	13,306,1880	138	130	133		712,601	5.2	1	16	dbSNP_121	133	7,8593	5.0+/-18.6	0,7,4293	yes	missense,missense	ZDHHC7	NM_001145548.1,NM_017740.2	29,29	13,313,6173	TT,TC,CC		0.0814,7.5489,2.6081	benign,benign	238/346,201/309	85011548	339,12659	2199	4300	6499	SO:0001583	missense	55625	exon7			CTCGGACACAGGA	AK000286	CCDS10950.1, CCDS45538.1	16q23.1	2010-02-09			ENSG00000153786	ENSG00000153786		"Zinc fingers, DHHC-type"	18459	protein-coding gene	gene with protein product	"Sertoli cell gene with zinc finger domain-&#946;"	614604					Standard	NM_017740		Approved	FLJ10792, ZNF370, FLJ20279, SERZ-B, SERZ1	uc002fiq.2	Q9NXF8	OTTHUMG00000137645	ENST00000313732.4:c.601G>A	16.37:g.85011548C>T	ENSP00000315604:p.Val201Ile	181	0	0		187	91	0.486631	NM_001145548	D3DUM1|Q8WV42|Q9NVD8	Missense_Mutation	SNP	ENST00000313732.4	37	CCDS10950.1	52	0.023809523809523808	50	0.1016260162601626	2	0.0055248618784530384	0	0.0	0	0.0	C	11.97	1.796547	0.31777	0.075489	8.14E-4	ENSG00000153786	ENST00000313732;ENST00000344861	T;T	0.39229	1.09;1.09	5.21	5.21	0.72293	.	0.056982	0.64402	D	0.000001	T	0.00845	0.0028	N	0.17631	0.505	0.58432	D	0.999999	B;B	0.12630	0.006;0.004	B;B	0.17979	0.02;0.02	T	0.01652	-1.1303	10	0.26408	T	0.33	-23.2644	17.7601	0.88462	0.0:1.0:0.0:0.0	rs13334011;rs56605352;rs13334011	238;201	Q9NXF8-2;Q9NXF8	.;ZDHC7_HUMAN	I	201;238	ENSP00000315604:V201I;ENSP00000341681:V238I	ENSP00000315604:V201I	V	-	1	0	ZDHHC7	83569049	1.000000	0.71417	0.995000	0.50966	0.805000	0.45488	3.515000	0.53429	2.428000	0.82296	0.561000	0.74099	GTC	C|0.962;T|0.038	0.038	strong		0.443	ZDHHC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269087.1	NM_017740		T	85011548	C	T	85011548	3	4	22	1	0	0	0	0	1	0	0	0	17635	478	17	2	337	2	ZDHHC7	16	85011548	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	233287	85011548	5343205	3328	6229											
KIAA0182	23199	hgsc.bcm.edu	37	chr16	85690900	85690900	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagagaagctgaaggatgccGgcctgcaggcgcccaagccc	10	3	14	14	2	0	2	0	1	0	1	0	4	0	3	4	3	4	2	4	3	3	0	rs35446008	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:85690900G>A	ENST00000253458.7	+	8	1506	c.1330G>A	c.(1330-1332)Ggc>Agc	p.G444S	GSE1_ENST00000393243.1_Missense_Mutation_p.G371S|RN7SL381P_ENST00000577658.1_RNA|GSE1_ENST00000405402.2_Missense_Mutation_p.G340S	NM_014615.2	NP_055430.1	Q14687	GSE1_HUMAN	Gse1 coiled-coil protein	444				G -> S (in Ref. 1; BAA11499). {ECO:0000305}.													GAAGGATGCCGGCCTGCAGGC	0.642													G|||	67	0.0133786	0.0484	0.0043	5008	,	,		16388	0.0		0.0	False		,,,				2504	0.0				p.G444S		Atlas-SNP	.											.	.	.	.	0			c.G1330A						PASS	.	G	SER/GLY,SER/GLY	180,4216	110.4+/-148.6	4,172,2022	51	51	51		1018,1330	4	0.9	16	dbSNP_126	51	1,8597	1.2+/-3.3	0,1,4298	yes	missense,missense	KIAA0182	NM_001134473.1,NM_014615.2	56,56	4,173,6320	AA,AG,GG		0.0116,4.0946,1.393	benign,benign	340/1114,444/1218	85690900	181,12813	2198	4299	6497	SO:0001583	missense	23199	exon8			GATGCCGGCCTGC	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.1330G>A	16.37:g.85690900G>A	ENSP00000253458:p.Gly444Ser	101	0	0		92	46	0.5	NM_014615	D3DUM4|Q8IY61|Q96GA4|Q9BW09	Missense_Mutation	SNP	ENST00000253458.7	37	CCDS10952.1	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	G	8.046	0.765024	0.15914	0.040946	1.16E-4	ENSG00000131149	ENST00000405402;ENST00000253458;ENST00000393243	T;T;T	0.30981	1.51;1.51;1.51	5.07	4.04	0.47022	.	0.488693	0.24152	N	0.041074	T	0.02083	0.0065	N	0.01705	-0.755	0.22457	N	0.999083	B;B	0.32203	0.325;0.36	B;B	0.21151	0.033;0.027	T	0.14227	-1.0480	10	0.18276	T	0.48	-34.1225	12.2615	0.54652	0.0:0.0:0.702:0.298	rs35446008	371;444	Q14687-3;Q14687	.;GSE1_HUMAN	S	340;444;371	ENSP00000384839:G340S;ENSP00000253458:G444S;ENSP00000376934:G371S	ENSP00000253458:G444S	G	+	1	0	KIAA0182	84248401	0.732000	0.28121	0.941000	0.38009	0.471000	0.32888	1.422000	0.34826	2.367000	0.80283	0.561000	0.74099	GGC	G|0.985;A|0.015	0.015	strong		0.642	GSE1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325527.1	NM_014615		A	85690900	G	A	85690900	3	1	22	1	0	0	0	0	1	0	0	0	8168	1116	39	1	1360	1	KIAA0182	16	85690900	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	679352	85690900	4663853	3329	6230											
KIAA0182	23199	hgsc.bcm.edu	37	chr16	85695298	85695298	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gcctacatctatgatgagttCctgcagcagcgccggaggct	8	9	12	12	2	1	2	0	2	1	0	2	3	2	3	3	2	4	4	3	2	2	3	rs61737039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:85695298C>T	ENST00000253458.7	+	9	2363	c.2187C>T	c.(2185-2187)ttC>ttT	p.F729F	GSE1_ENST00000393243.1_Silent_p.F656F|RN7SL381P_ENST00000577658.1_RNA|GSE1_ENST00000405402.2_Silent_p.F625F	NM_014615.2	NP_055430.1	Q14687	GSE1_HUMAN	Gse1 coiled-coil protein	729																	ATGATGAGTTCCTGCAGCAGC	0.716													C|||	66	0.0131789	0.0469	0.0043	5008	,	,		14613	0.0		0.001	False		,,,				2504	0.0				p.F729F		Atlas-SNP	.											.	.	.	.	0			c.C2187T						PASS	.	C	,	139,4221		2,135,2043	11	14	13		1875,2187	-1.5	1	16	dbSNP_129	13	3,8533		0,3,4265	no	coding-synonymous,coding-synonymous	KIAA0182	NM_001134473.1,NM_014615.2	,	2,138,6308	TT,TC,CC		0.0351,3.1881,1.1011	,	625/1114,729/1218	85695298	142,12754	2180	4268	6448	SO:0001819	synonymous_variant	23199	exon9			TGAGTTCCTGCAG	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.2187C>T	16.37:g.85695298C>T		125	0	0		126	61	0.484127	NM_014615	D3DUM4|Q8IY61|Q96GA4|Q9BW09	Silent	SNP	ENST00000253458.7	37	CCDS10952.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	C	5.452	0.268528	0.10349	0.031881	3.51E-4	ENSG00000131149	ENST00000412692	.	.	.	4.88	-1.45	0.08828	.	.	.	.	.	T	0.17238	0.0414	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31052	-0.9957	4	.	.	.	-10.3922	10.1383	0.42719	0.0:0.4732:0.0:0.5268	rs61737039	.	.	.	F	536	.	.	S	+	2	0	KIAA0182	84252799	0.988000	0.35896	0.990000	0.47175	0.473000	0.32948	0.303000	0.19210	-0.171000	0.10797	-0.291000	0.09656	TCC	C|0.988;T|0.012	0.012	strong		0.716	GSE1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325527.1	NM_014615		T	85695298	C	T	85695298	2	4	22	1	0	0	0	0	0	0	0	1	8168	854	30	2		2	KIAA0182	16	85695298	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4398	85695298	4659455	3330	6231											
JPH3	57338	hgsc.bcm.edu	37	chr16	87717863	87717863	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctccccttccttccagcacCgggaaaacggtgagtctcgc	7	9	9	16	3	2	1	0	1	2	0	6	2	4	2	5	2	2	1	5	2	2	2	rs138328691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:87717863C>T	ENST00000284262.2	+	3	1518	c.1276C>T	c.(1276-1278)Cgg>Tgg	p.R426W	JPH3_ENST00000563609.1_3'UTR	NM_020655.2	NP_065706.2	Q8WXH2	JPH3_HUMAN	junctophilin 3	426					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)		CTTCCAGCACCGGGAAAACGG	0.647																																					p.R426W		Atlas-SNP	.											JPH3,NS,carcinoma,-2,1	JPH3	95	1	0			c.C1276T						PASS	.	C	TRP/ARG	4,4392	6.2+/-15.9	0,4,2194	73	60	64		1276	-4.8	0.9	16	dbSNP_134	64	0,8600		0,0,4300	yes	missense	JPH3	NM_020655.2	101	0,4,6494	TT,TC,CC		0.0,0.091,0.0308	probably-damaging	426/749	87717863	4,12992	2198	4300	6498	SO:0001583	missense	57338	exon3			CAGCACCGGGAAA	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.1276C>T	16.37:g.87717863C>T	ENSP00000284262:p.Arg426Trp	192	0	0		218	121	0.555046	NM_020655	D3DUN2|Q8N471|Q9HDC3|Q9HDC4	Missense_Mutation	SNP	ENST00000284262.2	37	CCDS10962.1	.	.	.	.	.	.	.	.	.	.	C	18.52	3.641510	0.67244	9.1E-4	0.0	ENSG00000154118	ENST00000537256;ENST00000284262	T	0.49720	0.77	4.64	-4.8	0.03190	.	0.326711	0.28371	N	0.015584	T	0.51517	0.1679	L	0.50333	1.59	0.43617	D	0.995991	D	0.76494	0.999	P	0.55871	0.786	T	0.57797	-0.7749	10	0.56958	D	0.05	.	16.5936	0.84789	0.5065:0.4935:0.0:0.0	.	426	Q8WXH2	JPH3_HUMAN	W	289;426	ENSP00000284262:R426W	ENSP00000284262:R426W	R	+	1	2	JPH3	86275364	0.404000	0.25328	0.947000	0.38551	0.966000	0.64601	-0.364000	0.07583	-1.153000	0.02829	-0.181000	0.13052	CGG	C|0.999;T|0.001	0.001	strong		0.647	JPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269108.2			T	87717863	C	T	87717863	3	4	22	1	0	0	0	0	1	0	0	0	7971	643	23	1	1286	1	JPH3	16	87717863	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2022565	87717863	2636890	3331	6232											
KLHDC4	54758	hgsc.bcm.edu	37	chr16	87743072	87743072	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggcctcctcaaggctgtcttCgtcctcagaccggggctgcc	4	9	12	16	2	3	1	2	0	1	1	6	1	5	1	5	4	1	2	5	4	1	1	rs61735154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:87743072C>T	ENST00000270583.5	-	10	1304	c.1246G>A	c.(1246-1248)Gaa>Aaa	p.E416K	KLHDC4_ENST00000347925.5_Missense_Mutation_p.E385K|KLHDC4_ENST00000566349.1_5'UTR|KLHDC4_ENST00000353170.5_Missense_Mutation_p.E359K	NM_017566.3	NP_060036.2	Q8TBB5	KLDC4_HUMAN	kelch domain containing 4	416										breast(2)|endometrium(3)|lung(10)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(2)	21				BRCA - Breast invasive adenocarcinoma(80;0.0283)		AGGCTGTCTTCGTCCTCAGAC	0.677													C|||	101	0.0201677	0.0726	0.0072	5008	,	,		12720	0.0		0.0	False		,,,				2504	0.0				p.E416K		Atlas-SNP	.											.	KLHDC4	45	.	0			c.G1246A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU	239,4155	133.7+/-170.0	4,231,1962	37	39	38		1075,1153,1246	5.3	0.2	16	dbSNP_129	38	0,8598		0,0,4299	no	missense,missense,missense	KLHDC4	NM_001184854.1,NM_001184856.1,NM_017566.3	56,56,56	4,231,6261	TT,TC,CC		0.0,5.4392,1.8396	benign,benign,benign	359/464,385/490,416/521	87743072	239,12753	2197	4299	6496	SO:0001583	missense	54758	exon10			TGTCTTCGTCCTC	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.1246G>A	16.37:g.87743072C>T	ENSP00000270583:p.Glu416Lys	34	0	0		62	32	0.516129	NM_017566	D3DUN3|D3DUN4|D3DUN5|Q96F29|Q9BVN3	Missense_Mutation	SNP	ENST00000270583.5	37	CCDS10963.1	41	0.018772893772893772	36	0.07317073170731707	5	0.013812154696132596	0	0.0	0	0.0	C	14.89	2.668986	0.47677	0.054392	0.0	ENSG00000104731	ENST00000270583;ENST00000347925;ENST00000353170	T;T;T	0.08807	3.83;3.05;3.59	5.27	5.27	0.74061	.	0.518149	0.21288	N	0.077021	T	0.00936	0.0031	M	0.69823	2.125	0.80722	D	1	B;D;D	0.57571	0.145;0.98;0.967	B;P;B	0.45449	0.04;0.481;0.229	T	0.27088	-1.0084	10	0.06757	T	0.87	-0.0563	17.8669	0.88797	0.0:1.0:0.0:0.0	.	359;385;416	Q8TBB5-2;Q8TBB5-3;Q8TBB5	.;.;KLDC4_HUMAN	K	416;385;359	ENSP00000270583:E416K;ENSP00000325717:E385K;ENSP00000262530:E359K	ENSP00000270583:E416K	E	-	1	0	KLHDC4	86300573	1.000000	0.71417	0.217000	0.23759	0.110000	0.19582	5.604000	0.67626	2.467000	0.83353	0.313000	0.20887	GAA	C|0.978;T|0.022	0.022	strong		0.677	KLHDC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269109.2	NM_017566		T	87743072	C	T	87743072	3	4	22	1	0	0	0	0	1	0	0	0	8367	893	31	1	324	1	KLHDC4	16	87743072	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	25209	87743072	2611681	3332	6233											
ZC3H18	124245	hgsc.bcm.edu	37	chr16	88643806	88643806	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatgagctgagccggggccCgaccagctccccctgcgagg	7	4	15	15	3	0	2	0	2	0	0	1	5	1	2	5	3	4	2	5	3	1	0	rs114866066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88643806C>G	ENST00000301011.5	+	2	475	c.275C>G	c.(274-276)cCg>cGg	p.P92R	ZC3H18_ENST00000452588.2_Missense_Mutation_p.P92R	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	92						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)		AGCCGGGGCCCGACCAGCTCC	0.622													C|||	5	0.000998403	0.0038	0.0	5008	,	,		18131	0.0		0.0	False		,,,				2504	0.0				p.P92R	Ovarian(121;375 2276 20373 38669)	Atlas-SNP	.											.	ZC3H18	90	.	0			c.C275G						PASS	.	C	ARG/PRO	22,4372	27.2+/-55.0	0,22,2175	29	33	32		275	3.4	0.8	16	dbSNP_132	32	0,8600		0,0,4300	yes	missense	ZC3H18	NM_144604.3	103	0,22,6475	GG,GC,CC		0.0,0.5007,0.1693	benign	92/954	88643806	22,12972	2197	4300	6497	SO:0001583	missense	124245	exon2			GGGGCCCGACCAG	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.275C>G	16.37:g.88643806C>G	ENSP00000301011:p.Pro92Arg	43	0	0		31	18	0.580645	NM_144604	Q96DG4|Q96MP7	Missense_Mutation	SNP	ENST00000301011.5	37	CCDS10967.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	6.042	0.376025	0.11466	0.005007	0.0	ENSG00000158545	ENST00000301011;ENST00000289509;ENST00000452588	T;T	0.30448	1.53;1.56	5.57	3.36	0.38483	.	0.366727	0.28908	N	0.013743	T	0.13243	0.0321	L	0.36672	1.1	0.09310	N	1	B;B	0.27416	0.178;0.178	B;B	0.28916	0.096;0.096	T	0.11179	-1.0598	10	0.18276	T	0.48	-21.7543	2.9583	0.05884	0.5017:0.3387:0.0:0.1595	.	92;92	E7ERS3;Q86VM9	.;ZCH18_HUMAN	R	92	ENSP00000301011:P92R;ENSP00000416951:P92R	ENSP00000289509:P92R	P	+	2	0	ZC3H18	87171307	0.247000	0.23920	0.778000	0.31720	0.046000	0.14306	0.728000	0.26013	1.310000	0.45006	0.561000	0.74099	CCG	C|0.999;G|0.001	0.001	strong		0.622	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1	NM_144604		G	88643806	C	G	88643806	3	3	22	1	0	0	0	0	1	0	0	0	17583	652	23	4	277	4	ZC3H18	16	88643806	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	900734	88643806	1710947	3333	6234											
CYBA	1535	hgsc.bcm.edu	37	chr16	88713213	88713213	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcctggtaaagggcccgaaCagcttcaccacggcggtcat	9	8	11	13	3	2	0	2	0	0	0	3	1	3	0	3	4	2	2	3	4	3	3	rs2228472	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88713213C>G	ENST00000261623.3	-	4	375	c.237G>C	c.(235-237)ctG>ctC	p.L79L	CYBA_ENST00000567174.1_Silent_p.L79L|CYBA_ENST00000561972.1_5'Flank|CYBA_ENST00000569359.1_Silent_p.L79L	NM_000101.3	NP_000092.2	P13498	CY24A_HUMAN	cytochrome b-245, alpha polypeptide	79					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)	AGGGCCCGAACAGCTTCACCA	0.652													C|||	227	0.0453275	0.1672	0.0086	5008	,	,		15785	0.0		0.0	False		,,,				2504	0.0				p.L79L		Atlas-SNP	.											.	CYBA	12	.	0			c.G237C						PASS	.	C		627,3769	269.8+/-269.2	48,531,1619	81	91	87		237	0.7	0.3	16	dbSNP_98	87	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	CYBA	NM_000101.2		48,536,5914	GG,GC,CC		0.0581,14.263,4.863		79/196	88713213	632,12364	2198	4300	6498	SO:0001819	synonymous_variant	1535	exon4			CCCGAACAGCTTC		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.237G>C	16.37:g.88713213C>G		65	0	0		67	36	0.537313	NM_000101	Q14090|Q9BR72	Silent	SNP	ENST00000261623.3	37	CCDS32504.1																																																																																			C|0.949;G|0.051	0.051	strong		0.652	CYBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422765.1	NM_000101		G	88713213	C	G	88713213	2	3	22	1	0	0	0	0	0	0	0	1	4133	465	17	4		4	CYBA	16	88713213	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	69407	88713213	1641540	3334	6235											
CTU2	9780	hgsc.bcm.edu	37	chr16	88780603	88780603	+	IGR	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ttcatcctcaggctgcagacCcagttcccctccactgtcag	7	10	7	17	0	3	1	3	0	0	1	6	1	6	1	5	1	1	3	5	1	0	2	rs73262673	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88780603C>G	ENST00000301015.9	-	0	8072				CTU2_ENST00000378384.3_Silent_p.T268T|MIR4722_ENST00000578292.1_RNA|CTU2_ENST00000567949.1_Silent_p.T426T|CTU2_ENST00000453996.2_Silent_p.T355T|CTU2_ENST00000312060.5_Silent_p.T355T	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						GGCTGCAGACCCAGTTCCCCT	0.632													C|||	245	0.0489217	0.177	0.0159	5008	,	,		16241	0.0		0.0	False		,,,				2504	0.0				p.T355T		Atlas-SNP	.											.	CTU2	66	.	0			c.C1065G						PASS	.	C	,	604,3774	262.8+/-265.1	38,528,1623	84	76	79		1065,1065	0.1	1	16	dbSNP_130	79	5,8587	4.3+/-15.6	0,5,4291	no	coding-synonymous,coding-synonymous	CTU2	NM_001012759.1,NM_001012762.1	,	38,533,5914	GG,GC,CC		0.0582,13.7963,4.6955	,	355/516,355/486	88780603	609,12361	2189	4296	6485	SO:0001628	intergenic_variant	348180	exon10			GCAGACCCAGTTC	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		16.37:g.88780603C>G		145	0	0		93	41	0.44086	NM_001012759	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	37	CCDS54058.1																																																																																			C|0.960;G|0.040	0.040	strong		0.632	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745		G	88780603	C	G	88780603	1	3	22	0	1	0	0	0	0	0	0	0	4050	610	22	4		4	CTU2	16	88780603	IGR	SNP	C	TCGA-G8-6324-01A-11D-2210-10	67390	88780603	1574150	3335	6236											
CDT1	353	hgsc.bcm.edu	37	chr16	88874545	88874545	+	IGR	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaaatggagaagcacctgctGctcctctccgagctgctgcc	8	8	11	14	1	1	1	0	0	1	1	3	4	2	1	4	1	6	5	4	1	2	0	rs3218720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88874545G>T	ENST00000378364.3	-	0	947				CDT1_ENST00000301019.4_Silent_p.L500L	NM_000485.2	NP_000476.1	P07741	APT_HUMAN	adenine phosphoribosyltransferase						adenine salvage (GO:0006168)|AMP salvage (GO:0044209)|cellular response to insulin stimulus (GO:0032869)|grooming behavior (GO:0007625)|lactation (GO:0007595)|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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	adenine binding (GO:0002055)|adenine phosphoribosyltransferase activity (GO:0003999)|AMP binding (GO:0016208)			cervix(1)|endometrium(1)|liver(1)	3				BRCA - Breast invasive adenocarcinoma(80;0.0477)	Adenine(DB00173)|Adenosine monophosphate(DB00131)	AGCACCTGCTGCTCCTCTCCG	0.662													G|||	217	0.0433307	0.1581	0.0115	5008	,	,		18032	0.0		0.0	False		,,,				2504	0.0				p.L500L		Atlas-SNP	.											.	CDT1	30	.	0			c.G1500T						PASS	.	G		651,3741		50,551,1595	42	31	35		1500	2.8	0.1	16	dbSNP_106	35	6,8592		0,6,4293	no	coding-synonymous	CDT1	NM_030928.3		50,557,5888	TT,TG,GG		0.0698,14.8224,5.0577		500/547	88874545	657,12333	2196	4299	6495	SO:0001628	intergenic_variant	81620	exon10			CCTGCTGCTCCTC		CCDS32511.1, CCDS45546.1	16q24	2012-10-02				ENSG00000198931	2.4.2.7		626	protein-coding gene	gene with protein product		102600					Standard	NM_000485		Approved		uc002flv.3	P07741			16.37:g.88874545G>T		131	0	0		121	118	0.975207	NM_030928	G5E9J2|Q3KP55|Q68DF9	Silent	SNP	ENST00000378364.3	37	CCDS32511.1																																																																																			G|0.953;T|0.047	0.047	strong		0.662	APRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430000.2	NM_000485		T	88874545	G	T	88874545	1	4	22	0	1	0	0	0	0	0	0	0	3182	1306	46	4		4	CDT1	16	88874545	IGR	SNP	G	TCGA-G8-6324-01A-11D-2210-10	93942	88874545	1480208	3336	6237											
SPG7	6687	hgsc.bcm.edu	37	chr16	89623301	89623301	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctgttctttctagctggcaAacgcccttctggaaaaggaa	10	11	9	11	1	3	0	0	0	3	0	3	2	3	2	2	3	2	3	2	3	5	4	rs35749032	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89623301A>G	ENST00000268704.2	+	17	2203	c.2188A>G	c.(2188-2190)Aac>Gac	p.N730D	SPG7_ENST00000565891.1_3'UTR	NM_003119.2	NP_003110.1	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 (pure and complicated autosomal recessive)	730			N -> D (in dbSNP:rs35749032). {ECO:0000269|PubMed:16534102}.		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)		CTAGCTGGCAAACGCCCTTCT	0.562													A|||	85	0.0169728	0.062	0.0043	5008	,	,		19441	0.0		0.0	False		,,,				2504	0.0				p.N730D		Atlas-SNP	.											.	SPG7	75	.	0			c.A2188G						PASS	.	A	ASP/ASN	203,4193	123.3+/-160.7	7,189,2002	111	110	110		2188	4.5	0	16	dbSNP_126	110	1,8595		0,1,4297	yes	missense	SPG7	NM_003119.2	23	7,190,6299	GG,GA,AA		0.0116,4.6178,1.5702	benign	730/796	89623301	204,12788	2198	4298	6496	SO:0001583	missense	6687	exon17			CTGGCAAACGCCC	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.2188A>G	16.37:g.89623301A>G	ENSP00000268704:p.Asn730Asp	91	0	0		93	45	0.483871	NM_003119	O75756|Q2TB70|Q58F00|Q96IB0	Missense_Mutation	SNP	ENST00000268704.2	37	CCDS10977.1	30	0.013736263736263736	29	0.05894308943089431	1	0.0027624309392265192	0	0.0	0	0.0	A	7.955	0.745801	0.15710	0.046178	1.16E-4	ENSG00000197912	ENST00000268704	D	0.84370	-1.84	5.59	4.49	0.54785	Peptidase M41 (1);Peptidase M41, FtsH (2);	0.304067	0.39687	N	0.001298	T	0.25121	0.0610	N	0.12746	0.255	0.36713	D	0.880754	B	0.06786	0.001	B	0.09377	0.004	T	0.55250	-0.8170	10	0.36615	T	0.2	-6.0E-4	10.7824	0.46386	0.9228:0.0:0.0772:0.0	rs35749032	730	Q9UQ90	SPG7_HUMAN	D	730	ENSP00000268704:N730D	ENSP00000268704:N730D	N	+	1	0	SPG7	88150802	0.057000	0.20700	0.002000	0.10522	0.321000	0.28281	1.649000	0.37281	0.925000	0.37094	0.460000	0.39030	AAC	A|0.982;G|0.018	0.018	strong		0.562	SPG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269921.2	NM_003119		G	89623301	A	G	89623301	3	3	22	1	0	0	0	0	1	0	0	0	15059	14	1	3	2404	3	SPG7	16	89623301	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	748756	89623301	731452	3337	6238											
CPNE7	27132	hgsc.bcm.edu	37	chr16	89645345	89645345	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctggacactgcgctaagcaCttcctgtgctgcacggaatc	8	9	11	13	2	0	0	0	0	0	0	2	2	1	2	1	2	4	5	1	2	2	2	rs9944362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89645345C>A	ENST00000268720.5	+	3	568	c.438C>A	c.(436-438)caC>caA	p.H146Q	CPNE7_ENST00000319518.8_Intron	NM_014427.4	NP_055242.1	Q9UBL6	CPNE7_HUMAN	copine VII	146					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)		GCGCTAAGCACTTCCTGTGCT	0.552													C|||	24	0.00479233	0.0174	0.0014	5008	,	,		16713	0.0		0.0	False		,,,				2504	0.0				p.H146Q		Atlas-SNP	.											.	CPNE7	56	.	0			c.C438A						PASS	.	C	GLN/HIS,	41,4355	46.0+/-80.4	1,39,2158	133	112	119		438,	-0.7	0	16	dbSNP_119	119	1,8599	1.2+/-3.3	0,1,4299	yes	missense,intron	CPNE7	NM_014427.4,NM_153636.2	24,	1,40,6457	AA,AC,CC		0.0116,0.9327,0.3232	,	146/634,	89645345	42,12954	2198	4300	6498	SO:0001583	missense	27132	exon3			TAAGCACTTCCTG	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.438C>A	16.37:g.89645345C>A	ENSP00000268720:p.His146Gln	78	0	0		100	58	0.58	NM_014427		Missense_Mutation	SNP	ENST00000268720.5	37	CCDS10980.1	4	0.0018315018315018315	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	C	0.672	-0.801433	0.02841	0.009327	1.16E-4	ENSG00000178773	ENST00000268720	T	0.13089	2.62	0.471	-0.661	0.11417	C2 calcium/lipid-binding domain, CaLB (1);	432.516000	0.00520	U	0.000184	T	0.07324	0.0185	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21965	-1.0230	9	0.15066	T	0.55	.	.	.	.	rs9944362	146	Q9UBL6	CPNE7_HUMAN	Q	146	ENSP00000268720:H146Q	ENSP00000268720:H146Q	H	+	3	2	CPNE7	88172846	0.003000	0.15002	0.001000	0.08648	0.006000	0.05464	0.396000	0.20867	-0.368000	0.08040	0.205000	0.17691	CAC	C|0.998;A|0.002	0.002	strong		0.552	CPNE7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269929.2			A	89645345	C	A	89645345	3	1	22	1	0	0	0	0	1	0	0	0	3819	564	20	4	448	4	CPNE7	16	89645345	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	22044	89645345	709408	3338	6239											
CPNE7	27132	hgsc.bcm.edu	37	chr16	89645360	89645360	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagcacttcctgtgctgcacGgaatcctcacaccttgccag	9	9	8	15	1	1	0	1	0	0	0	3	1	3	1	4	1	4	3	4	1	2	2	rs149812493	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89645360G>A	ENST00000268720.5	+	3	583	c.453G>A	c.(451-453)acG>acA	p.T151T	CPNE7_ENST00000319518.8_Intron	NM_014427.4	NP_055242.1	Q9UBL6	CPNE7_HUMAN	copine VII	151					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)		TGTGCTGCACGGAATCCTCAC	0.542													G|||	42	0.00838658	0.031	0.0014	5008	,	,		16677	0.0		0.0	False		,,,				2504	0.0				p.T151T		Atlas-SNP	.											.	CPNE7	56	.	0			c.G453A						PASS	.	G	,	132,4264	95.3+/-134.0	2,128,2068	115	98	104		453,	-0.3	0	16	dbSNP_134	104	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,intron	CPNE7	NM_014427.4,NM_153636.2	,	2,129,6367	AA,AG,GG		0.0116,3.0027,1.0234	,	151/634,	89645360	133,12863	2198	4300	6498	SO:0001819	synonymous_variant	27132	exon3			CTGCACGGAATCC	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.453G>A	16.37:g.89645360G>A		72	0	0		86	37	0.430233	NM_014427		Silent	SNP	ENST00000268720.5	37	CCDS10980.1																																																																																			G|0.988;A|0.012	0.012	strong		0.542	CPNE7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269929.2			A	89645360	G	A	89645360	2	1	22	1	0	0	0	0	0	0	0	1	3819	1103	39	1		1	CPNE7	16	89645360	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	15	89645360	709393	3339	6240											
CPNE7	27132	hgsc.bcm.edu	37	chr16	89655120	89655120	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgcctccaatggagacccgcGgaacagctgctccctgcact	8	6	10	17	3	0	1	0	0	0	1	2	3	2	2	4	2	4	3	4	2	2	0	rs28568523	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89655120G>A	ENST00000268720.5	+	12	1320	c.1190G>A	c.(1189-1191)cGg>cAg	p.R397Q	CPNE7_ENST00000319518.8_Missense_Mutation_p.R322Q	NM_014427.4	NP_055242.1	Q9UBL6	CPNE7_HUMAN	copine VII	397	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.		R -> Q (in dbSNP:rs28568523).		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)		GGAGACCCGCGGAACAGCTGC	0.647													G|||	28	0.00559105	0.0144	0.0	5008	,	,		15442	0.002		0.007	False		,,,				2504	0.0				p.R397Q		Atlas-SNP	.											.	CPNE7	56	.	0			c.G1190A						PASS	.	G	GLN/ARG,GLN/ARG	43,4353	46.7+/-81.2	0,43,2155	129	98	108		1190,965	3.8	0.8	16	dbSNP_125	108	51,8549	33.3+/-86.6	0,51,4249	yes	missense,missense	CPNE7	NM_014427.4,NM_153636.2	43,43	0,94,6404	AA,AG,GG		0.593,0.9782,0.7233	probably-damaging,probably-damaging	397/634,322/559	89655120	94,12902	2198	4300	6498	SO:0001583	missense	27132	exon12			ACCCGCGGAACAG	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.1190G>A	16.37:g.89655120G>A	ENSP00000268720:p.Arg397Gln	66	0	0		58	41	0.706897	NM_014427		Missense_Mutation	SNP	ENST00000268720.5	37	CCDS10980.1	10	0.004578754578754579	3	0.006097560975609756	0	0.0	1	0.0017482517482517483	6	0.0079155672823219	G	18.57	3.653381	0.67472	0.009782	0.00593	ENSG00000178773	ENST00000319518;ENST00000268720;ENST00000529800	T;T;T	0.18174	2.45;2.41;2.23	3.75	3.75	0.43078	von Willebrand factor, type A (2);	0.000000	0.85682	D	0.000000	T	0.18130	0.0435	M	0.64676	1.99	0.49798	D	0.999823	P;P	0.52316	0.907;0.952	P;B	0.46299	0.511;0.259	T	0.06481	-1.0824	10	0.49607	T	0.09	-8.211	15.5036	0.75719	0.0:0.0:1.0:0.0	rs28568523;rs28568523	322;397	Q9UBL6-2;Q9UBL6	.;CPNE7_HUMAN	Q	322;397;42	ENSP00000317374:R322Q;ENSP00000268720:R397Q;ENSP00000435876:R42Q	ENSP00000268720:R397Q	R	+	2	0	CPNE7	88182621	0.993000	0.37304	0.844000	0.33320	0.161000	0.22273	7.195000	0.77798	1.776000	0.52262	0.313000	0.20887	CGG	G|0.992;A|0.008	0.008	strong		0.647	CPNE7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269929.2			A	89655120	G	A	89655120	3	1	22	1	0	0	0	0	1	0	0	0	3819	1116	39	1	1236	1	CPNE7	16	89655120	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	9760	89655120	699633	3340	6241											
C16orf7	9605	hgsc.bcm.edu	37	chr16	89778919	89778919	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttctccatcatctgccgctgTagagagagggtctggggggg	6	10	16	9	1	4	2	1	0	3	2	5	3	4	2	2	4	1	2	2	4	1	2	rs139626173	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89778919T>C	ENST00000389386.3	-	6	679	c.555A>G	c.(553-555)ctA>ctG	p.L185L	VPS9D1_ENST00000565452.1_5'Flank|VPS9D1-AS1_ENST00000562866.1_RNA|VPS9D1_ENST00000561976.1_Silent_p.L115L	NM_004913.2	NP_004904.2	Q9Y2B5	VP9D1_HUMAN	VPS9 domain containing 1	185					ATP synthesis coupled proton transport (GO:0015986)		GTPase activator activity (GO:0005096)|transporter activity (GO:0005215)										TCTGCCGCTGTAGAGAGAGGG	0.662													t|||	80	0.0159744	0.0575	0.0058	5008	,	,		12775	0.0		0.0	False		,,,				2504	0.0				p.L185L		Atlas-SNP	.											.	.	.	.	0			c.A555G						PASS	.			191,3575		3,185,1695	49	56	54		555	0.6	1	16	dbSNP_134	54	4,8210		0,4,4103	no	coding-synonymous	C16orf7	NM_004913.2		3,189,5798	CC,CT,TT		0.0487,5.0717,1.6277		185/632	89778919	195,11785	1883	4107	5990	SO:0001819	synonymous_variant	9605	exon6			CCGCTGTAGAGAG	AB018551	CCDS42220.1	16q24.3	2012-10-09	2012-10-09	2012-10-09	ENSG00000075399	ENSG00000075399			13526	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 7"	C16orf7		10231027	Standard	NM_004913		Approved	ATP-BL	uc002fom.1	Q9Y2B5	OTTHUMG00000173219	ENST00000389386.3:c.555A>G	16.37:g.89778919T>C		42	0	0		38	27	0.710526	NM_004913		Silent	SNP	ENST00000389386.3	37	CCDS42220.1																																																																																			T|0.989;C|0.011	0.011	strong		0.662	VPS9D1-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422508.1	NM_004913		C	89778919	T	C	89778919	2	2	22	1	0	0	0	0	0	0	0	1	1830	1625	57	3		3	C16orf7	16	89778919	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	123799	89778919	575834	3341	6242											
ZNF276	92822	hgsc.bcm.edu	37	chr16	89790020	89790020	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgagaccaagaccctgccCagcacggatgtggcccagcc	9	4	12	16	1	0	2	0	1	0	2	0	4	0	3	5	2	3	2	5	2	1	0	rs34629175	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89790020C>T	ENST00000443381.2	+	4	1006	c.909C>T	c.(907-909)ccC>ccT	p.P303P	ZNF276_ENST00000568064.1_Missense_Mutation_p.P222L|ZNF276_ENST00000446326.2_Missense_Mutation_p.P100L|ZNF276_ENST00000289816.5_Silent_p.P228P|VPS9D1_ENST00000389386.3_5'Flank	NM_001113525.1	NP_001106997.1	Q8N554	ZN276_HUMAN	zinc finger protein 276	303					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)		AGACCCTGCCCAGCACGGATG	0.697													C|||	131	0.0261581	0.0968	0.0043	5008	,	,		17634	0.0		0.0	False		,,,				2504	0.0				p.P303P		Atlas-SNP	.											.	ZNF276	70	.	0			c.C909T						PASS	.	C	,	354,4038		12,330,1854	30	37	34		909,684	2.4	0.1	16	dbSNP_126	34	1,8587		0,1,4293	no	coding-synonymous,coding-synonymous	ZNF276	NM_001113525.1,NM_152287.3	,	12,331,6147	TT,TC,CC		0.0116,8.0601,2.735	,	303/615,228/540	89790020	355,12625	2196	4294	6490	SO:0001819	synonymous_variant	92822	exon4			CCTGCCCAGCACG	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.909C>T	16.37:g.89790020C>T		107	0	0		123	66	0.536585	NM_001113525	Q0VGA1|Q2TBE8|Q3B7H7	Silent	SNP	ENST00000443381.2	37	CCDS45554.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	C	2.587	-0.296169	0.05532	0.080601	1.16E-4	ENSG00000158805	ENST00000446326	T	0.13307	2.6	5.66	2.44	0.29823	.	0.247400	0.40818	N	0.001014	T	0.00468	0.0015	.	.	.	0.24132	N	0.995761	B	0.11235	0.004	B	0.08055	0.003	T	0.30765	-0.9967	9	0.56958	D	0.05	-22.5813	5.0473	0.14490	0.0:0.5552:0.1597:0.2851	rs34629175	100	A8K186	.	L	100	ENSP00000415999:P100L	ENSP00000415999:P100L	P	+	2	0	ZNF276	88317521	0.001000	0.12720	0.110000	0.21437	0.015000	0.08874	0.109000	0.15417	0.240000	0.21263	-0.367000	0.07326	CCA	C|0.976;T|0.024	0.024	strong		0.697	ZNF276-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422517.1	NM_152287		T	89790020	C	T	89790020	2	4	22	1	0	0	0	0	0	0	0	1	17826	581	21	2		2	ZNF276	16	89790020	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	11101	89790020	564733	3342	6243											
FANCA	2175	hgsc.bcm.edu	37	chr16	89839752	89839752	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgagctgtcccaggggctcCtcagcagagttgggttctgc	5	10	15	11	0	2	2	1	1	1	1	4	2	4	2	2	3	3	5	2	3	0	2	rs17232917	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89839752C>T	ENST00000389301.3	-	22	1971	c.1941G>A	c.(1939-1941)gaG>gaA	p.E647E	FANCA_ENST00000568369.1_Silent_p.E647E|FANCA_ENST00000567284.2_5'UTR	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	647					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)		CCAGGGGCTCCTCAGCAGAGT	0.562			"D, Mis, N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				C|||	191	0.038139	0.1407	0.0072	5008	,	,		17401	0.0		0.0	False		,,,				2504	0.0				p.E647E		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"Fanconi anemia, complementation group A"		L	.	FANCA	99	.	0			c.G1941A						PASS	.	C		425,3647		19,387,1630	32	27	29		1941	-9.1	0	16	dbSNP_123	29	1,7893		0,1,3946	no	coding-synonymous	FANCA	NM_000135.2		19,388,5576	TT,TC,CC		0.0127,10.4371,3.5601		647/1456	89839752	426,11540	2036	3947	5983	SO:0001819	synonymous_variant	2175	exon22	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GGGCTCCTCAGCA	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.1941G>A	16.37:g.89839752C>T		90	0	0		94	52	0.553191	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Silent	SNP	ENST00000389301.3	37	CCDS32515.1																																																																																			C|0.960;T|0.040	0.040	strong		0.562	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1			T	89839752	C	T	89839752	2	4	22	1	0	0	0	0	0	0	0	1	5670	680	24	2		2	FANCA	16	89839752	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	49732	89839752	515001	3343	6244											
FANCA	2175	hgsc.bcm.edu	37	chr16	89857880	89857880	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcctggcgcacaaccaggaaCgcagtgaccatgctgtccag	10	5	12	14	2	0	1	0	1	0	0	1	2	1	2	4	2	3	3	4	2	2	0	rs1800332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89857880C>T	ENST00000389301.3	-	14	1320	c.1290G>A	c.(1288-1290)gcG>gcA	p.A430A	FANCA_ENST00000568369.1_Silent_p.A430A	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	430					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)		CAACCAGGAACGCAGTGACCA	0.557			"D, Mis, N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				C|||	163	0.0325479	0.1195	0.0072	5008	,	,		20326	0.0		0.0	False		,,,				2504	0.0				p.A430A		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"Fanconi anemia, complementation group A"		L	FANCA,NS,lymphoid_neoplasm,-1,1	FANCA	99	1	0			c.G1290A						PASS	.	C		453,3943	217.1+/-235.6	20,413,1765	63	51	55		1290	-10.9	0	16	dbSNP_89	55	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	FANCA	NM_000135.2		20,415,6063	TT,TC,CC		0.0233,10.3048,3.5011		430/1456	89857880	455,12541	2198	4300	6498	SO:0001819	synonymous_variant	2175	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CAGGAACGCAGTG	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.1290G>A	16.37:g.89857880C>T		86	0	0		96	37	0.385417	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Silent	SNP	ENST00000389301.3	37	CCDS32515.1																																																																																			C|0.967;T|0.033	0.033	strong		0.557	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1			T	89857880	C	T	89857880	2	4	22	1	0	0	0	0	0	0	0	1	5670	523	19	1		1	FANCA	16	89857880	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	18128	89857880	496873	3344	6245											
FANCA	2175	hgsc.bcm.edu	37	chr16	89874756	89874756	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtacgtgaagatgccacaccGcttcaagcaacaaagaactc	15	6	8	12	2	1	3	1	1	0	2	2	3	1	3	2	0	5	3	2	0	6	2	rs17232246	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89874756G>A	ENST00000389301.3	-	6	572	c.542C>T	c.(541-543)gCg>gTg	p.A181V	FANCA_ENST00000389302.3_Missense_Mutation_p.A181V|FANCA_ENST00000568369.1_Missense_Mutation_p.A181V|FANCA_ENST00000534992.1_Missense_Mutation_p.A181V|FANCA_ENST00000543736.1_Missense_Mutation_p.A149V|FANCA_ENST00000563673.1_Missense_Mutation_p.A181V	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	181			A -> V (in FA; dbSNP:rs17232246).		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)		ATGCCACACCGCTTCAAGCAA	0.398			"D, Mis, N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				G|||	267	0.0533147	0.1959	0.0115	5008	,	,		18304	0.0		0.0	False		,,,				2504	0.0				p.A181V		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"Fanconi anemia, complementation group A"		L	.	FANCA	99	.	0			c.C542T						PASS	.	G	VAL/ALA,VAL/ALA	738,3658	304.9+/-288.7	64,610,1524	137	129	131		542,542	2.8	0.3	16	dbSNP_123	131	4,8596	2.2+/-6.3	0,4,4296	yes	missense,missense	FANCA	NM_000135.2,NM_001018112.1	64,64	64,614,5820	AA,AG,GG		0.0465,16.788,5.7094	benign,benign	181/1456,181/298	89874756	742,12254	2198	4300	6498	SO:0001583	missense	2175	exon6	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CACACCGCTTCAA	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.542C>T	16.37:g.89874756G>A	ENSP00000373952:p.Ala181Val	172	0	0		194	87	0.448454	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	65	0.02976190476190476	61	0.12398373983739837	4	0.011049723756906077	0	0.0	0	0.0	G	7.667	0.686109	0.14973	0.16788	4.65E-4	ENSG00000187741	ENST00000389301;ENST00000389302;ENST00000534992;ENST00000543736	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	4.77	2.81	0.32909	.	0.147328	0.30879	N	0.008682	T	0.00109	0.0003	L	0.58669	1.825	0.32276	N	0.568249	P;B;B;B;B;P	0.48230	0.907;0.241;0.06;0.06;0.06;0.907	B;B;B;B;B;B	0.33295	0.161;0.064;0.012;0.019;0.012;0.161	T	0.04165	-1.0972	10	0.38643	T	0.18	-6.3506	9.5774	0.39465	0.1724:0.0:0.8276:0.0	rs17232246	181;149;181;181;181;181	B4DRI7;Q0VAP4;A0PJU8;F5H8D5;O15360-2;O15360	.;.;.;.;.;FANCA_HUMAN	V	181;181;181;149	ENSP00000373952:A181V;ENSP00000373953:A181V;ENSP00000443675:A181V;ENSP00000443409:A149V	ENSP00000373952:A181V	A	-	2	0	FANCA	88402257	0.730000	0.28100	0.335000	0.25508	0.047000	0.14425	0.788000	0.26872	0.517000	0.28361	-0.924000	0.02725	GCG	G|0.950;A|0.050	0.050	strong		0.398	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1			A	89874756	G	A	89874756	3	1	22	1	0	0	0	0	1	0	0	0	5670	1087	38	1	3982	1	FANCA	16	89874756	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	16876	89874756	479997	3345	6246											
SPIRE2	84501	hgsc.bcm.edu	37	chr16	89927102	89927102	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcccccaggtacctgtcccGcgagtgtctctgaccccagc	5	8	9	19	2	1	1	0	1	1	0	4	2	3	1	6	1	2	1	6	1	1	1	rs28478911		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89927102G>A	ENST00000378247.3	+	10	1517	c.1474G>A	c.(1474-1476)Gcg>Acg	p.A492T	SPIRE2_ENST00000393062.2_Missense_Mutation_p.A492T	NM_032451.1	NP_115827.1	Q8WWL2	SPIR2_HUMAN	spire-type actin nucleation factor 2	492					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)		TACCTGTCCCGCGAGTGTCTC	0.642											OREG0024056	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0.0008	0.0	5008	,	,		14998	0.0		0.0	False		,,,				2504	0.0				p.A492T		Atlas-SNP	.											SPIRE2,colon,carcinoma,-1,1	SPIRE2	63	1	0			c.G1474A						PASS	.	G	THR/ALA	3,4371		0,3,2184	29	28	28		1474	1.9	0	16	dbSNP_125	28	0,8572		0,0,4286	no	missense	SPIRE2	NM_032451.1	58	0,3,6470	AA,AG,GG		0.0,0.0686,0.0232	benign	492/715	89927102	3,12943	2187	4286	6473	SO:0001583	missense	84501	exon10			TGTCCCGCGAGTG	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.1474G>A	16.37:g.89927102G>A	ENSP00000367494:p.Ala492Thr	67	0	0	1271	76	41	0.539474	NM_032451	A4QPB1|Q2TA98|Q6P433|Q8ND47|Q96JJ5	Missense_Mutation	SNP	ENST00000378247.3	37	CCDS32516.1	.	.	.	.	.	.	.	.	.	.	G	6.872	0.530358	0.13127	6.86E-4	0.0	ENSG00000204991	ENST00000378247;ENST00000393062	T;T	0.43688	0.95;0.94	5.08	1.87	0.25490	.	0.915637	0.09208	N	0.833668	T	0.25382	0.0617	N	0.22421	0.69	0.09310	N	0.999999	B;B;B;B	0.15719	0.001;0.014;0.008;0.001	B;B;B;B	0.10450	0.001;0.005;0.002;0.001	T	0.27571	-1.0070	10	0.15066	T	0.55	-9.4382	6.2595	0.20891	0.1685:0.1545:0.6769:0.0	rs28478911	359;492;444;492	Q8WWL2-4;Q8WWL2-2;Q8WWL2-3;Q8WWL2	.;.;.;SPIR2_HUMAN	T	492	ENSP00000367494:A492T;ENSP00000376782:A492T	ENSP00000367494:A492T	A	+	1	0	SPIRE2	88454603	0.002000	0.14202	0.001000	0.08648	0.000000	0.00434	1.200000	0.32247	0.668000	0.31126	-0.794000	0.03295	GCG	G|1.000;|0.000	.	weak		0.642	SPIRE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421843.1	XM_047462		A	89927102	G	A	89927102	3	1	22	1	0	0	0	0	1	0	0	0	15087	1087	38	1	1512	1	SPIRE2	16	89927102	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	52346	89927102	427651	3346	6247											
MC1R	4157	hgsc.bcm.edu	37	chr16	89985984	89985984	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgctggaggccggtgcactGgtggcccgggctgcggtgct	2	8	19	12	3	0	0	0	0	0	0	0	1	0	1	2	7	4	4	2	7	0	0	rs3212364	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89985984G>A	ENST00000555147.1	+	1	1698	c.318G>A	c.(316-318)ctG>ctA	p.L106L	RP11-566K11.4_ENST00000554623.1_RNA|MC1R_ENST00000555427.1_Silent_p.L106L|TUBB3_ENST00000556922.1_Silent_p.L106L|RP11-566K11.7_ENST00000570217.1_RNA|TUBB3_ENST00000554444.1_5'Flank	NM_002386.3	NP_002377.4	Q01726	MSHR_HUMAN	melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor)	106					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|intracellular signal transduction (GO:0035556)|melanin biosynthetic process (GO:0042438)|multicellular organismal development (GO:0007275)|negative regulation of tumor necrosis factor production (GO:0032720)|pigmentation (GO:0043473)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sensory perception of pain (GO:0019233)|UV protection (GO:0009650)|UV-damage excision repair (GO:0070914)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled peptide receptor activity (GO:0008528)|melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|ubiquitin protein ligase binding (GO:0031625)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	11		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)		CCGGTGCACTGGTGGCCCGGG	0.647									Melanoma, Familial Clustering of				G|||	56	0.0111821	0.0401	0.0043	5008	,	,		18870	0.0		0.0	False		,,,				2504	0.0				p.L106L		Atlas-SNP	.											.	MC1R	20	.	0			c.G318A						PASS	.	G		179,4203		4,171,2016	42	51	48		318	4.8	0.2	16	dbSNP_106	48	2,8582		0,2,4290	no	coding-synonymous	MC1R	NM_002386.3		4,173,6306	AA,AG,GG		0.0233,4.0849,1.396		106/318	89985984	181,12785	2191	4292	6483	SO:0001819	synonymous_variant	4157	exon1	Familial Cancer Database		TGCACTGGTGGCC		CCDS56011.1	16q24.3	2012-10-05			ENSG00000258839	ENSG00000258839		"GPCR / Class A : Melanocortin receptors"	6929	protein-coding gene	gene with protein product		155555				8458079	Standard	NM_002386		Approved	MSH-R		Q01726		ENST00000555147.1:c.318G>A	16.37:g.89985984G>A		62	0	0		83	35	0.421687	NM_002386	Q66K38|Q6UR93|Q8WWX6|Q8WWX7|Q96I33|Q96RU4|Q9UBF7|Q9UN58|Q9UN59|Q9UN60|Q9UN61|Q9UN62	Silent	SNP	ENST00000555147.1	37	CCDS56011.1																																																																																			G|0.991;A|0.009	0.009	strong		0.647	MC1R-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412014.1	NM_002386		A	89985984	G	A	89985984	2	1	22	1	0	0	0	0	0	0	0	1	9372	1335	47	2		2	MC1R	16	89985984	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	58882	89985984	368769	3347	6248											
MC1R	4157	hgsc.bcm.edu	37	chr16	89986566	89986566	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gaccccctcatctacgccttCcacagccaggagctccgcag	8	6	8	19	2	2	0	1	0	1	0	4	2	4	1	6	1	3	2	6	1	1	2	rs3212367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89986566C>T	ENST00000555147.1	+	1	2280	c.900C>T	c.(898-900)ttC>ttT	p.F300F	RP11-566K11.4_ENST00000554623.1_RNA|MC1R_ENST00000555427.1_Silent_p.F300F|TUBB3_ENST00000556922.1_Silent_p.F300F|RP11-566K11.7_ENST00000570217.1_RNA|TUBB3_ENST00000554444.1_5'Flank	NM_002386.3	NP_002377.4	Q01726	MSHR_HUMAN	melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor)	300					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|intracellular signal transduction (GO:0035556)|melanin biosynthetic process (GO:0042438)|multicellular organismal development (GO:0007275)|negative regulation of tumor necrosis factor production (GO:0032720)|pigmentation (GO:0043473)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sensory perception of pain (GO:0019233)|UV protection (GO:0009650)|UV-damage excision repair (GO:0070914)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled peptide receptor activity (GO:0008528)|melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|ubiquitin protein ligase binding (GO:0031625)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	11		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)		TCTACGCCTTCCACAGCCAGG	0.612									Melanoma, Familial Clustering of				C|||	98	0.0195687	0.0711	0.0058	5008	,	,		20124	0.0		0.0	False		,,,				2504	0.0				p.F300F		Atlas-SNP	.											.	MC1R	20	.	0			c.C900T						PASS	.	C		201,3963		2,197,1883	62	66	64		900	3.3	1	16	dbSNP_106	64	5,8459		0,5,4227	no	coding-synonymous	MC1R	NM_002386.3		2,202,6110	TT,TC,CC		0.0591,4.8271,1.6313		300/318	89986566	206,12422	2082	4232	6314	SO:0001819	synonymous_variant	4157	exon1	Familial Cancer Database		CGCCTTCCACAGC		CCDS56011.1	16q24.3	2012-10-05			ENSG00000258839	ENSG00000258839		"GPCR / Class A : Melanocortin receptors"	6929	protein-coding gene	gene with protein product		155555				8458079	Standard	NM_002386		Approved	MSH-R		Q01726		ENST00000555147.1:c.900C>T	16.37:g.89986566C>T		163	0	0		162	75	0.462963	NM_002386	Q66K38|Q6UR93|Q8WWX6|Q8WWX7|Q96I33|Q96RU4|Q9UBF7|Q9UN58|Q9UN59|Q9UN60|Q9UN61|Q9UN62	Silent	SNP	ENST00000555147.1	37	CCDS56011.1																																																																																			C|0.978;T|0.022	0.022	strong		0.612	MC1R-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412014.1	NM_002386		T	89986566	C	T	89986566	2	4	22	1	0	0	0	0	0	0	0	1	9372	854	30	2		2	MC1R	16	89986566	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	582	89986566	368187	3348	6249											
DEF8	54849	hgsc.bcm.edu	37	chr16	90032296	90032296	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tactacgacaactccaccacTtgtcccaagtgtgcccggct	9	9	7	16	2	0	0	0	0	0	0	2	1	2	0	4	1	4	1	4	1	4	3	rs11861894	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:90032296T>G	ENST00000268676.7	+	13	1553	c.1464T>G	c.(1462-1464)acT>acG	p.T488T	DEF8_ENST00000567874.1_Silent_p.T367T|DEF8_ENST00000569453.1_Silent_p.T427T|DEF8_ENST00000563594.1_Silent_p.T427T|DEF8_ENST00000570182.1_Silent_p.T417T|DEF8_ENST00000563795.1_Silent_p.T410T	NM_207514.2	NP_997397.1	Q6ZN54	DEFI8_HUMAN	differentially expressed in FDCP 8 homolog (mouse)	488					intracellular signal transduction (GO:0035556)		zinc ion binding (GO:0008270)			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)		ACTCCACCACTTGTCCCAAGT	0.627													G|||	806	0.160942	0.4599	0.0591	5008	,	,		17453	0.0089		0.0258	False		,,,				2504	0.1247				p.T488T		Atlas-SNP	.											.	DEF8	28	.	0			c.T1464G						PASS	.	G	,,,,,	1762,2634	642.8+/-397.7	346,1070,782	51	43	46		1251,1101,1281,1230,1281,1464	-6.2	0.6	16	dbSNP_120	46	253,8347	806.5+/-407.2	4,245,4051	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DEF8	NM_001242816.1,NM_001242817.1,NM_001242818.1,NM_001242819.1,NM_001242820.1,NM_207514.2	,,,,,	350,1315,4833	GG,GT,TT		2.9419,40.0819,15.5048	,,,,,	417/442,367/392,427/452,410/435,427/452,488/513	90032296	2015,10981	2198	4300	6498	SO:0001819	synonymous_variant	54849	exon13			CACCACTTGTCCC	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.1464T>G	16.37:g.90032296T>G		122	0	0		109	63	0.577982	NM_207514	B3KT65|B4DK62|B4E0S9|B7Z3H6|H3BUG7|Q8N8N3|Q9NXL0	Silent	SNP	ENST00000268676.7	37	CCDS10989.1																																																																																			T|0.861;G|0.139	0.139	strong		0.627	DEF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000272878.1	NM_207514		G	90032296	T	G	90032296	2	3	22	1	0	0	0	0	0	0	0	1	4389	1596	56	5		5	DEF8	16	90032296	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	45730	90032296	322457	3349	6250											
GEMIN4	50628	hgsc.bcm.edu	37	chr17	648916	648916	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcttacagatctcaaaaagTgtggctggcacttcacactt	12	11	8	10	0	2	1	2	0	1	1	3	1	2	1	0	2	2	3	0	2	3	3	rs12942598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:648916T>C	ENST00000319004.5	-	2	2485	c.2367A>G	c.(2365-2367)acA>acG	p.T789T	GEMIN4_ENST00000576778.1_Silent_p.T778T	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	789					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		TCTCAAAAAGTGTGGCTGGCA	0.587													T|||	74	0.0147764	0.0008	0.0331	5008	,	,		19967	0.0		0.0398	False		,,,				2504	0.0102				p.T789T		Atlas-SNP	.											.	GEMIN4	116	.	0			c.A2367G						PASS	.	T		28,3812		0,28,1892	16	17	17		2367	-5.6	1	17	dbSNP_121	17	360,7860		8,344,3758	no	coding-synonymous	GEMIN4	NM_015721.2		8,372,5650	CC,CT,TT		4.3796,0.7292,3.2172		789/1059	648916	388,11672	1920	4110	6030	SO:0001819	synonymous_variant	50628	exon2			AAAAAGTGTGGCT	AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"HCC-associated protein 1", "component of gems 4"	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.2367A>G	17.37:g.648916T>C		80	0	0		98	38	0.387755	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Silent	SNP	ENST00000319004.5	37	CCDS45559.1																																																																																			T|0.974;C|0.026	0.026	strong		0.587	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721		C	648916	T	C	648916	2	2	22	1	0	0	0	0	0	0	0	1	6338	1683	59	3		3	GEMIN4	17	648916	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10		648916	80546294	3350	6251											
GEMIN4	50628	hgsc.bcm.edu	37	chr17	649164	649164	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgccagtatttgctgaagcGgtccaagagctggcacaagc	10	8	12	11	1	0	2	0	1	0	1	1	2	1	2	2	2	5	4	2	2	4	2	rs34519093	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:649164G>A	ENST00000319004.5	-	2	2237	c.2119C>T	c.(2119-2121)Cgc>Tgc	p.R707C	GEMIN4_ENST00000576778.1_Missense_Mutation_p.R696C	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	707					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		TTGCTGAAGCGGTCCAAGAGC	0.542													T|||	116	0.0231629	0.0832	0.0058	5008	,	,		19134	0.0		0.002	False		,,,				2504	0.0				p.R707C		Atlas-SNP	.											.	GEMIN4	116	.	0			c.C2119T						PASS	.	T	CYS/ARG	263,3613		6,251,1681	28	29	29		2119	-6.4	0	17	dbSNP_126	29	4,8282		0,4,4139	yes	missense	GEMIN4	NM_015721.2	180	6,255,5820	AA,AG,GG		0.0483,6.7853,2.1954	benign	707/1059	649164	267,11895	1938	4143	6081	SO:0001583	missense	50628	exon2			TGAAGCGGTCCAA	AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"HCC-associated protein 1", "component of gems 4"	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.2119C>T	17.37:g.649164G>A	ENSP00000321706:p.Arg707Cys	46	0	0		35	22	0.628571	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Missense_Mutation	SNP	ENST00000319004.5	37	CCDS45559.1	50	0.022893772893772892	46	0.09349593495934959	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	T	8.559	0.877352	0.17395	0.067853	4.83E-4	ENSG00000179409	ENST00000319004	T	0.05855	3.38	5.56	-6.42	0.01932	.	0.696678	0.15313	N	0.268978	T	0.00109	0.0003	N	0.02011	-0.69	0.25173	N	0.990269	B	0.02656	0.0	B	0.01281	0.0	T	0.37454	-0.9705	10	0.48119	T	0.1	-0.0898	4.5907	0.12306	0.2625:0.4379:0.0738:0.2258	rs34519093	707	P57678	GEMI4_HUMAN	C	707	ENSP00000321706:R707C	ENSP00000321706:R707C	R	-	1	0	GEMIN4	595914	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.501000	0.02281	-2.443000	0.00548	-3.149000	0.00058	CGC	G|0.978;A|0.022	0.022	strong		0.542	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721		A	649164	G	A	649164	3	1	22	1	0	0	0	0	1	0	0	0	6338	1116	39	1	1061	1	GEMIN4	17	649164	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	248	649164	80546046	3351	6252											
GEMIN4	50628	hgsc.bcm.edu	37	chr17	650371	650371	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcactggggagtttggccagCgaggtcaggctgacatcccg	7	8	15	11	2	2	1	2	1	0	0	3	3	3	2	2	5	1	2	2	5	0	1	rs61735317	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:650371C>T	ENST00000319004.5	-	2	1030	c.912G>A	c.(910-912)tcG>tcA	p.S304S	GEMIN4_ENST00000437269.1_3'UTR|GEMIN4_ENST00000576778.1_Silent_p.S293S	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	304					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		GTTTGGCCAGCGAGGTCAGGC	0.627													C|||	116	0.0231629	0.0832	0.0058	5008	,	,		20285	0.0		0.002	False		,,,				2504	0.0				p.S304S		Atlas-SNP	.											.	GEMIN4	116	.	0			c.G912A						PASS	.	C		280,3980		7,266,1857	116	127	124		912	-11.3	0.1	17	dbSNP_129	124	4,8464		0,4,4230	no	coding-synonymous	GEMIN4	NM_015721.2		7,270,6087	TT,TC,CC		0.0472,6.5728,2.2313		304/1059	650371	284,12444	2130	4234	6364	SO:0001819	synonymous_variant	50628	exon2			GGCCAGCGAGGTC	AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"HCC-associated protein 1", "component of gems 4"	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.912G>A	17.37:g.650371C>T		100	0	0		118	66	0.559322	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Silent	SNP	ENST00000319004.5	37	CCDS45559.1																																																																																			C|0.978;T|0.022	0.022	strong		0.627	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721		T	650371	C	T	650371	2	4	22	1	0	0	0	0	0	0	0	1	6338	755	27	1		1	GEMIN4	17	650371	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1207	650371	80544839	3352	6253											
NXN	64359	hgsc.bcm.edu	37	chr17	706933	706933	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgcactcacctccccggctaCgaagaacagaaggggtgcct	10	5	11	15	3	1	2	1	0	0	2	2	3	2	2	4	3	3	2	4	3	4	1	rs61731770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:706933C>T	ENST00000336868.3	-	7	1205	c.1114G>A	c.(1114-1116)Gta>Ata	p.V372I	NXN_ENST00000575801.1_Missense_Mutation_p.V264I|NXN_ENST00000538650.1_Missense_Mutation_p.V63I|NXN_ENST00000537628.2_Missense_Mutation_p.V123I	NM_022463.4	NP_071908.2	Q6DKJ4	NXN_HUMAN	nucleoredoxin	372				V -> I (in Ref. 4; AAH73845). {ECO:0000305}.	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)		TCCCCGGCTACGAAGAACAGA	0.602													c|||	110	0.0219649	0.0787	0.0043	5008	,	,		17906	0.0		0.003	False		,,,				2504	0.0				p.V372I		Atlas-SNP	.											.	NXN	32	.	0			c.G1114A						PASS	.	C	ILE/VAL,ILE/VAL	328,4078	173.4+/-203.2	20,288,1895	102	100	101		790,1114	5.3	1	17	dbSNP_129	101	11,8589	8.4+/-32.0	0,11,4289	yes	missense,missense	NXN	NM_001205319.1,NM_022463.4	29,29	20,299,6184	TT,TC,CC		0.1279,7.4444,2.6065	benign,benign	264/328,372/436	706933	339,12667	2203	4300	6503	SO:0001583	missense	64359	exon7			CGGCTACGAAGAA		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.1114G>A	17.37:g.706933C>T	ENSP00000337443:p.Val372Ile	93	0	0		88	52	0.590909	NM_022463	B4DXQ0|D3DTH2|Q3SWW6|Q6P3U6|Q7L4C6|Q9H9Q1	Missense_Mutation	SNP	ENST00000336868.3	37	CCDS10998.1	42	0.019230769230769232	39	0.07926829268292683	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	C	13.45	2.239485	0.39598	0.074444	0.001279	ENSG00000167693	ENST00000336868;ENST00000538650;ENST00000537628	T;T	0.28454	1.61;2.57	5.26	5.26	0.73747	Thioredoxin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.02727	0.0082	L	0.28274	0.84	0.58432	D	0.999996	D;D;D	0.76494	0.999;0.981;0.992	D;P;P	0.74674	0.984;0.899;0.834	T	0.00883	-1.1528	10	0.15952	T	0.53	-19.0247	17.8205	0.88649	0.0:1.0:0.0:0.0	.	264;63;372	B4DXQ0;B4DNN6;Q6DKJ4	.;.;NXN_HUMAN	I	372;63;264	ENSP00000337443:V372I;ENSP00000445087:V63I	ENSP00000337443:V372I	V	-	1	0	NXN	653683	1.000000	0.71417	0.983000	0.44433	0.246000	0.25737	4.470000	0.60175	2.635000	0.89317	0.655000	0.94253	GTA	C|0.977;T|0.023	0.023	strong		0.602	NXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206669.1			T	706933	C	T	706933	3	4	22	1	0	0	0	0	1	0	0	0	10796	536	19	1	201	1	NXN	17	706933	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	56562	706933	80488277	3353	6254											
SLC43A2	124935	hgsc.bcm.edu	37	chr17	1494660	1494660	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgctccttggcactcctcatGgagctgcccacactcaggcg	6	9	10	16	1	2	0	2	0	0	0	4	1	4	1	3	3	3	3	3	3	0	1	rs73976240	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1494660G>A	ENST00000301335.5	-	8	922	c.834C>T	c.(832-834)tcC>tcT	p.S278S	SLC43A2_ENST00000412517.3_Silent_p.S141S|SLC43A2_ENST00000574274.1_5'UTR|SLC43A2_ENST00000571650.1_Silent_p.S278S|SLC43A2_ENST00000382147.4_Silent_p.S278S	NM_001284498.1|NM_001284499.1	NP_001271427.1|NP_001271428.1	Q8N370	LAT4_HUMAN	solute carrier family 43 (amino acid system L transporter), member 2	278					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-amino acid transmembrane transporter activity (GO:0015179)			endometrium(4)|large_intestine(4)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0883)		CACTCCTCATGGAGCTGCCCA	0.622													G|||	129	0.0257588	0.0961	0.0029	5008	,	,		10550	0.0		0.0	False		,,,				2504	0.0				p.S278S		Atlas-SNP	.											.	SLC43A2	37	.	0			c.C834T						PASS	.	G		311,4095	167.3+/-198.3	13,285,1905	76	70	72		834	5.1	1	17	dbSNP_130	72	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	SLC43A2	NM_152346.1		13,288,6202	AA,AG,GG		0.0349,7.0586,2.4143		278/570	1494660	314,12692	2203	4300	6503	SO:0001819	synonymous_variant	124935	exon8			CCTCATGGAGCTG	BC027923	CCDS11006.1, CCDS67107.1, CCDS67108.1	17p13.3	2013-07-17	2013-07-17		ENSG00000167703	ENSG00000167703		"Solute carriers"	23087	protein-coding gene	gene with protein product		610791				23268354	Standard	NM_001284498		Approved	MGC34680	uc002fsv.3	Q8N370	OTTHUMG00000090345	ENST00000301335.5:c.834C>T	17.37:g.1494660G>A		74	0	0		83	48	0.578313	NM_152346	B7Z6X9|C9JNU8|D3DTH9|Q5CD75|Q6IPM1|Q8NBX1|Q8NC21|Q8WZ00	Silent	SNP	ENST00000301335.5	37	CCDS11006.1																																																																																			G|0.971;A|0.029	0.029	strong		0.622	SLC43A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206717.4	NM_152346		A	1494660	G	A	1494660	2	1	22	1	0	0	0	0	0	0	0	1	14648	1335	47	2		2	SLC43A2	17	1494660	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	787727	1494660	79700550	3354	6255											
SCARF1	8578	hgsc.bcm.edu	37	chr17	1538561	1538561	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggccaccaagtgggggccGccggtggccagtggctgaat	6	5	17	13	3	0	1	0	1	0	0	0	1	0	1	6	6	0	1	6	6	2	0	rs8072430	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1538561G>A	ENST00000263071.4	-	11	2033	c.1984C>T	c.(1984-1986)Cgg>Tgg	p.R662W	SCARF1_ENST00000348987.3_Missense_Mutation_p.R576W|SCARF1_ENST00000571272.1_3'UTR	NM_003693.2|NM_145350.1	NP_003684.2|NP_663325.1	Q14162	SREC_HUMAN	scavenger receptor class F, member 1	662	Gly-rich.		R -> W (in dbSNP:rs8072430). {ECO:0000269|PubMed:8590280, ECO:0000269|PubMed:9395444}.		cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|dendrite development (GO:0016358)|neuron remodeling (GO:0016322)|positive regulation of axon regeneration (GO:0048680)|positive regulation of neuron projection development (GO:0010976)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(3)|kidney(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		AGTGGGGGCCGCCGGTGGCCA	0.682													G|||	105	0.0209665	0.0764	0.0058	5008	,	,		13011	0.0		0.0	False		,,,				2504	0.0				p.R662W		Atlas-SNP	.											.	SCARF1	46	.	0			c.C1984T						PASS	.	G	TRP/ARG,,TRP/ARG	237,3973		10,217,1878	15	17	17		1984,,1726	1.2	0	17	dbSNP_116	17	3,8223		0,3,4110	yes	missense,utr-3,missense	SCARF1	NM_003693.2,NM_145350.1,NM_145352.2	101,,101	10,220,5988	AA,AG,GG		0.0365,5.6295,1.9299	probably-damaging,,probably-damaging	662/831,,576/745	1538561	240,12196	2105	4113	6218	SO:0001583	missense	8578	exon11			GGGGCCGCCGGTG	D63483	CCDS11007.1, CCDS45564.1	17p13.3	2008-07-18			ENSG00000074660	ENSG00000074660			16820	protein-coding gene	gene with protein product	"scavenger receptor expressed by endothelial cells", "acetyl LDL receptor"	607873				9395444, 8590280	Standard	NM_003693		Approved	SREC, KIAA0149	uc002fsz.2	Q14162	OTTHUMG00000090555	ENST00000263071.4:c.1984C>T	17.37:g.1538561G>A	ENSP00000263071:p.Arg662Trp	53	0	0		68	25	0.367647	NM_003693	A8MQ05|O43701|Q8NHD2|Q8NHD3|Q8NHD4|Q8NHD5	Missense_Mutation	SNP	ENST00000263071.4	37	CCDS11007.1	36	0.016483516483516484	34	0.06910569105691057	2	0.0055248618784530384	0	0.0	0	0.0	G	11.44	1.639770	0.29157	0.056295	3.65E-4	ENSG00000074660	ENST00000263071;ENST00000348987	T;T	0.35973	1.28;1.28	5.0	1.23	0.21249	.	1.186410	0.06503	N	0.736688	T	0.07908	0.0198	M	0.62723	1.935	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.72075	0.942;0.976	T	0.04930	-1.0917	10	0.72032	D	0.01	-0.2214	6.3298	0.21264	0.1799:0.0:0.5964:0.2237	rs8072430;rs8072430	576;662	Q14162-2;Q14162	.;SREC_HUMAN	W	662;576	ENSP00000263071:R662W;ENSP00000323964:R576W	ENSP00000263071:R662W	R	-	1	2	SCARF1	1485311	0.001000	0.12720	0.008000	0.14137	0.014000	0.08584	0.529000	0.23019	0.433000	0.26313	-0.377000	0.06932	CGG	G|0.979;A|0.021	0.021	strong		0.682	SCARF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207081.4	NM_003693		A	1538561	G	A	1538561	3	1	22	1	0	0	0	0	1	0	0	0	13898	1086	38	1	512	1	SCARF1	17	1538561	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	43901	1538561	79656649	3355	6256											
RTN4RL1	146760	hgsc.bcm.edu	37	chr17	1840079	1840079	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggcttcctgtggccgggcCgggggccgtgcgggtggccc	0	6	20	15	5	0	0	0	0	0	0	1	0	1	0	6	7	1	1	6	7	0	1	rs143202933	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1840079C>T	ENST00000331238.6	-	2	1516	c.1037G>A	c.(1036-1038)cGg>cAg	p.R346Q		NM_178568.2	NP_848663.1			reticulon 4 receptor-like 1											breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|prostate(2)|skin(1)	11						GTGGCCGGGCCGGGGGCCGTG	0.687													C|||	14	0.00279553	0.0	0.0014	5008	,	,		13824	0.0		0.007	False		,,,				2504	0.0061				p.R346Q	GBM(68;949 1139 14865 32798 38342)	Atlas-SNP	.											.	RTN4RL1	21	.	0			c.G1037A						PASS	.	C	GLN/ARG	2,3884		0,2,1941	16	19	18		1037	4.2	0.9	17	dbSNP_134	18	25,8203		0,25,4089	yes	missense	RTN4RL1	NM_178568.2	43	0,27,6030	TT,TC,CC		0.3038,0.0515,0.2229	benign	346/442	1840079	27,12087	1943	4114	6057	SO:0001583	missense	146760	exon2			CCGGGCCGGGGGC	AF532859	CCDS45569.1	17p13.3	2008-02-05				ENSG00000185924			21329	protein-coding gene	gene with protein product	"nogo-66 receptor homolog 2"	610461					Standard	NM_178568		Approved	NGRH2, NgR3, DKFZp547J144	uc002ftp.3	Q86UN2		ENST00000331238.6:c.1037G>A	17.37:g.1840079C>T	ENSP00000330631:p.Arg346Gln	129	0	0		158	71	0.449367	NM_178568		Missense_Mutation	SNP	ENST00000331238.6	37	CCDS45569.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	6.698	0.497343	0.12762	5.15E-4	0.003038	ENSG00000185924	ENST00000331238	T	0.61980	0.06	4.17	4.17	0.49024	.	0.000000	0.33670	N	0.004666	T	0.57989	0.2091	L	0.54323	1.7	0.44042	D	0.996779	D	0.63880	0.993	P	0.53146	0.719	T	0.60601	-0.7231	10	0.12103	T	0.63	.	16.5187	0.84308	0.0:1.0:0.0:0.0	.	346	Q86UN2	R4RL1_HUMAN	Q	346	ENSP00000330631:R346Q	ENSP00000330631:R346Q	R	-	2	0	RTN4RL1	1786829	0.997000	0.39634	0.889000	0.34880	0.009000	0.06853	2.063000	0.41423	1.883000	0.54544	0.549000	0.68633	CGG	C|0.997;T|0.003	0.003	strong		0.687	RTN4RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450155.2	NM_178568		T	1840079	C	T	1840079	3	4	22	1	0	0	0	0	1	0	0	0	13746	652	23	1	292	1	RTN4RL1	17	1840079	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	301518	1840079	79355131	3356	6257											
DPH1	1801	hgsc.bcm.edu	37	chr17	1943525	1943525	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttccaggtatgacccatatAgcaaagtcctatccagagaa	14	10	7	10	0	0	2	0	1	0	1	3	3	3	2	4	1	1	2	4	1	6	5	rs200693145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1943525A>G	ENST00000263083.6	+	8	823	c.778A>G	c.(778-780)Agc>Ggc	p.S260G	RP11-667K14.4_ENST00000572404.1_RNA|DPH1_ENST00000570477.1_Missense_Mutation_p.S180G|OVCA2_ENST00000572195.1_5'Flank	NM_001383.3	NP_001374.3	Q9BZG8	DPH1_HUMAN	diphthamide biosynthesis 1	260					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						TGACCCATATAGCAAAGTCCT	0.557													A|||	6	0.00119808	0.0045	0.0	5008	,	,		19386	0.0		0.0	False		,,,				2504	0.0				p.S260G		Atlas-SNP	.											.	DPH1	32	.	0			c.A778G						PASS	.	A	GLY/SER	13,4155		0,13,2071	86	87	87		778	4	1	17		87	0,8422		0,0,4211	yes	missense	DPH1	NM_001383.3	56	0,13,6282	GG,GA,AA		0.0,0.3119,0.1033	benign	260/444	1943525	13,12577	2084	4211	6295	SO:0001583	missense	1801	exon8			CCATATAGCAAAG	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.778A>G	17.37:g.1943525A>G	ENSP00000263083:p.Ser260Gly	55	0	0		51	34	0.666667	NM_001383	D3DTI3|Q16439|Q4VBA2|Q9BTW7|Q9UCY0	Missense_Mutation	SNP	ENST00000263083.6	37	CCDS42228.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	10.42	1.346368	0.24426	0.003119	0.0	ENSG00000108963	ENST00000263083	T	0.49720	0.77	5.15	4.03	0.46877	.	0.040549	0.85682	N	0.000000	T	0.48241	0.1489	M	0.74647	2.275	0.50467	D	0.999871	B;B;B	0.14805	0.011;0.011;0.003	B;B;B	0.23852	0.049;0.049;0.033	T	0.43410	-0.9393	10	0.46703	T	0.11	-13.6359	10.1501	0.42788	0.9183:0.0:0.0817:0.0	.	270;270;260	E7ENH3;B4DNK0;Q9BZG8	.;.;DPH1_HUMAN	G	260	ENSP00000263083:S260G	ENSP00000263083:S260G	S	+	1	0	DPH1	1890275	1.000000	0.71417	0.990000	0.47175	0.054000	0.15201	4.836000	0.62789	0.748000	0.32831	0.459000	0.35465	AGC	A|1.000;G|0.000	0.000	strong		0.557	DPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438660.1	NM_001383		G	1943525	A	G	1943525	3	3	22	1	0	0	0	0	1	0	0	0	4721	420	15	3	808	3	DPH1	17	1943525	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	103446	1943525	79251685	3357	6258											
SMG6	23293	hgsc.bcm.edu	37	chr17	2203462	2203462	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttctatctcagccctgtcTggtttattcgcaacttcctc	5	18	5	13	1	3	0	1	0	3	0	7	0	4	0	2	1	2	2	2	1	3	7	rs140746531	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:2203462T>C	ENST00000263073.6	-	2	635	c.585A>G	c.(583-585)ccA>ccG	p.P195P	SMG6_ENST00000544865.1_Silent_p.P164P	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	195	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						CAGCCCTGTCTGGTTTATTCG	0.512													T|||	3	0.000599042	0.0023	0.0	5008	,	,		17852	0.0		0.0	False		,,,				2504	0.0				p.P195P	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.A585G						PASS	.	T	,	6,4400	12.9+/-30.5	0,6,2197	249	270	263		492,585	0.1	0.3	17	dbSNP_134	263	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SMG6	NM_001170957.1,NM_017575.4	,	0,6,6497	CC,CT,TT		0.0,0.1362,0.0461	,	164/1389,195/1420	2203462	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	23293	exon2			CCTGTCTGGTTTA	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.585A>G	17.37:g.2203462T>C		73	0	0		97	49	0.505155	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Silent	SNP	ENST00000263073.6	37	CCDS11016.1																																																																																			T|1.000;C|0.000	0.000	strong		0.512	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3			C	2203462	T	C	2203462	2	2	22	1	0	0	0	0	0	0	0	1	14812	1567	55	3		3	SMG6	17	2203462	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	259937	2203462	78991748	3358	6259											
KIAA0664	23277	hgsc.bcm.edu	37	chr17	2604698	2604698	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgtgtggacgcggtgatgctGacttgccggtcctcggctgt	3	11	16	11	5	0	2	0	2	0	0	2	3	1	3	2	4	2	2	2	4	0	1	rs115717445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:2604698G>A	ENST00000570628.2	-	6	852	c.747C>T	c.(745-747)gtC>gtT	p.V249V	CLUH_ENST00000538975.1_Silent_p.V249V|CLUH_ENST00000435359.1_Silent_p.V249V			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	249					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)											CGGTGATGCTGACTTGCCGGT	0.632													G|||	21	0.00419329	0.0159	0.0	5008	,	,		14270	0.0		0.0	False		,,,				2504	0.0				p.V249V		Atlas-SNP	.											.	.	.	.	0			c.C747T						PASS	.	G		48,4218		0,48,2085	27	34	32		747	1.3	1	17	dbSNP_132	32	0,8468		0,0,4234	yes	coding-synonymous	KIAA0664	NM_015229.3		0,48,6319	AA,AG,GG		0.0,1.1252,0.3769		249/1310	2604698	48,12686	2133	4234	6367	SO:0001819	synonymous_variant	23277	exon6			GATGCTGACTTGC	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.747C>T	17.37:g.2604698G>A		95	0	0		87	53	0.609195	NM_015229	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Silent	SNP	ENST00000570628.2	37	CCDS45572.1																																																																																			G|0.993;A|0.007	0.007	strong		0.632	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229		A	2604698	G	A	2604698	2	1	22	1	0	0	0	0	0	0	0	1	8198	1277	45	2		2	KIAA0664	17	2604698	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	401236	2604698	78590512	3359	6260											
RAP1GAP2	23108	hgsc.bcm.edu	37	chr17	2911352	2911352	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaccttcacgatgagctccaCgcccacacacaggccatgct	11	6	7	17	2	1	1	1	1	0	0	2	2	2	1	4	1	3	2	4	1	1	1	rs36016465	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:2911352C>T	ENST00000254695.8	+	17	1497	c.1407C>T	c.(1405-1407)caC>caT	p.H469H	RAP1GAP2_ENST00000542807.1_Silent_p.H469H|RAP1GAP2_ENST00000366401.4_Silent_p.H454H|RAP1GAP2_ENST00000540393.2_Silent_p.H450H	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	469					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						ATGAGCTCCACGCCCACACAC	0.597													C|||	77	0.0153754	0.056	0.0029	5008	,	,		18125	0.0		0.001	False		,,,				2504	0.0				p.H469H		Atlas-SNP	.											.	RAP1GAP2	90	.	0			c.C1407T						PASS	.	C	,	139,3993		2,135,1929	63	69	67		1362,1407	-9.6	0	17	dbSNP_126	67	2,8384		0,2,4191	no	coding-synonymous,coding-synonymous	RAP1GAP2	NM_001100398.1,NM_015085.4	,	2,137,6120	TT,TC,CC		0.0238,3.364,1.1264	,	454/716,469/731	2911352	141,12377	2066	4193	6259	SO:0001819	synonymous_variant	23108	exon17			GCTCCACGCCCAC	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.1407C>T	17.37:g.2911352C>T		74	0	0		128	72	0.5625	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Silent	SNP	ENST00000254695.8	37	CCDS45573.1																																																																																			C|0.988;T|0.012	0.012	strong		0.597	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2			T	2911352	C	T	2911352	2	4	22	1	0	0	0	0	0	0	0	1	13053	535	19	1		1	RAP1GAP2	17	2911352	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	306654	2911352	78283858	3360	6261											
OR3A2	4995	hgsc.bcm.edu	37	chr17	3181677	3181677	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgggaggtcacagtagaagtGattgacctcattggggccac	10	9	14	8	0	2	3	2	2	0	1	2	4	2	4	2	4	0	1	2	4	2	3	rs73977611	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3181677G>C	ENST00000408891.2	-	1	591	c.553C>G	c.(553-555)Cac>Gac	p.H185D	RP11-64J4.2_ENST00000573491.1_RNA	NM_002551.3	NP_002542.3	P47893	OR3A2_HUMAN	olfactory receptor, family 3, subfamily A, member 2	185					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)			ovary(1)	1						CAGTAGAAGTGATTGACCTCA	0.562													G|||	81	0.0161741	0.0575	0.0072	5008	,	,		21392	0.0		0.0	False		,,,				2504	0.0				p.H185D	GBM(166;478 2018 3875 5042 31983)|Esophageal Squamous(77;407 1232 1405 14297 15272)	Atlas-SNP	.											.	OR3A2	36	.	0			c.C553G						PASS	.	G	ASP/HIS	188,4216	120.8+/-158.4	4,180,2018	71	59	63		553	2.8	1	17	dbSNP_130	63	1,8559		0,1,4279	no	missense	OR3A2	NM_002551.3	81	4,181,6297	CC,CG,GG		0.0117,4.2688,1.4579	probably-damaging	185/322	3181677	189,12775	2202	4280	6482	SO:0001583	missense	4995	exon1			AGAAGTGATTGAC	U04713	CCDS42233.1	17p13.3	2012-08-09				ENSG00000221882		"GPCR / Class A : Olfactory receptors"	8283	protein-coding gene	gene with protein product						8921386, 10673334	Standard	NM_002551		Approved	OLFRA04, OR228, OR17-228	uc002fvg.3	P47893		ENST00000408891.2:c.553C>G	17.37:g.3181677G>C	ENSP00000386180:p.His185Asp	274	1	0.00364964		295	140	0.474576	NM_002551	Q6IFM3|Q9P1Q3	Missense_Mutation	SNP	ENST00000408891.2	37	CCDS42233.1	28	0.01282051282051282	24	0.04878048780487805	4	0.011049723756906077	0	0.0	0	0.0	G	15.06	2.721441	0.48728	0.042688	1.17E-4	ENSG00000221882	ENST00000408891	T	0.00174	8.62	4.9	2.85	0.33270	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000069	T	0.00144	0.0004	M	0.90425	3.115	0.31106	N	0.710527	D	0.59357	0.985	D	0.68039	0.955	T	0.03335	-1.1047	10	0.87932	D	0	-23.7752	13.1298	0.59375	0.0:0.0:0.7099:0.2901	.	185	P47893	OR3A2_HUMAN	D	185	ENSP00000386180:H185D	ENSP00000386180:H185D	H	-	1	0	OR3A2	3128427	0.630000	0.27155	0.983000	0.44433	0.377000	0.30045	1.081000	0.30791	0.745000	0.32763	0.561000	0.74099	CAC	G|0.991;C|0.009	0.009	strong		0.562	OR3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438370.1			C	3181677	G	C	3181677	3	2	22	1	0	0	0	0	1	0	0	0	11047	1290	45	4	416	4	OR3A2	17	3181677	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	270325	3181677	78013533	3361	6262											
OR3A1	4994	hgsc.bcm.edu	37	chr17	3195603	3195603	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccacagggaactgcacgctTgcgggacaggagacgactca	11	4	13	13	3	1	1	1	0	0	1	1	5	1	3	1	3	3	2	1	3	1	1	rs7218125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3195603T>A	ENST00000323404.1	-	1	273	c.274A>T	c.(274-276)Aag>Tag	p.K92*	RP11-64J4.2_ENST00000573491.1_RNA	NM_002550.2	NP_002541.2	P47881	OR3A1_HUMAN	olfactory receptor, family 3, subfamily A, member 1	92					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						ACTGCACGCTTGCGGGACAGG	0.567													.|||	111	0.0221645	0.0779	0.0101	5008	,	,		18657	0.0		0.001	False		,,,				2504	0.0				p.K92X	GBM(20;287 516 18743 28660 36594)	Atlas-SNP	.											.	OR3A1	46	.	0			c.A274T						PASS	.	T	stop/LYS	278,4128	155.5+/-188.7	10,258,1935	82	67	72		274	3	0.1	17	dbSNP_116	72	3,8597	2.2+/-6.3	0,3,4297	yes	stop-gained	OR3A1	NM_002550.2		10,261,6232	AA,AT,TT		0.0349,6.3096,2.1605		92/316	3195603	281,12725	2203	4300	6503	SO:0001587	stop_gained	4994	exon1			CACGCTTGCGGGA	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.274A>T	17.37:g.3195603T>A	ENSP00000313803:p.Lys92*	254	0	0		277	148	0.534296	NM_002550	Q4VB06|Q6IFM4	Nonsense_Mutation	SNP	ENST00000323404.1	37	CCDS11023.1	37	0.01694139194139194	31	0.06300813008130081	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	T	10.77	1.444920	0.25987	0.063096	3.49E-4	ENSG00000180090	ENST00000323404	.	.	.	5.31	3.01	0.34805	.	0.663946	0.13864	N	0.357451	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.6046	7.6409	0.28292	0.0:0.0758:0.1405:0.7836	rs7218125;rs16952824;rs7218125	.	.	.	X	92	.	ENSP00000313803:K92X	K	-	1	0	OR3A1	3142353	0.000000	0.05858	0.097000	0.21041	0.002000	0.02628	0.063000	0.14410	1.003000	0.39130	0.528000	0.53228	AAG	T|0.972;A|0.028	0.028	strong		0.567	OR3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207302.2			A	3195603	T	A	3195603	4	1	22	1	0	0	0	0	0	1	0	0	11046	1821	63	5	677	5	OR3A1	17	3195603	Nonsense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	13926	3195603	77999607	3362	6263											
OR1E1	8387	hgsc.bcm.edu	37	chr17	3301246	3301246	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgtgtaacatggcatggaaGgtggtcagcacccaggacag	11	7	15	8	0	1	0	1	0	0	0	1	2	1	2	1	5	2	3	1	5	2	1	rs11078447	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3301246G>A	ENST00000322608.2	-	1	458	c.459C>T	c.(457-459)acC>acT	p.T153T		NM_003553.2	NP_003544.2	P30953	OR1E1_HUMAN	olfactory receptor, family 1, subfamily E, member 1	153					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)|large_intestine(2)|lung(5)	10						TGGCATGGAAGGTGGTCAGCA	0.542													G|||	110	0.0219649	0.0772	0.0115	5008	,	,		22193	0.0		0.0	False		,,,				2504	0.0				p.T153T		Atlas-SNP	.											.	OR1E1	37	.	0			c.C459T						PASS	.	G		240,4166	140.8+/-176.2	5,230,1968	77	61	66		459	-9.4	0	17	dbSNP_120	66	2,8598		0,2,4298	no	coding-synonymous	OR1E1	NM_003553.2		5,232,6266	AA,AG,GG		0.0233,5.4471,1.8607		153/315	3301246	242,12764	2203	4300	6503	SO:0001819	synonymous_variant	8387	exon1			ATGGAAGGTGGTC	U04642	CCDS11024.1	17p13.3	2012-08-09			ENSG00000180016	ENSG00000180016		"GPCR / Class A : Olfactory receptors"	8189	protein-coding gene	gene with protein product				OR1E9P, OR1E5, OR1E6		8004088, 1370859	Standard	NM_003553		Approved	OR17-2, HGM071, OR17-32, OR13-66	uc002fvj.1	P30953	OTTHUMG00000090643	ENST00000322608.2:c.459C>T	17.37:g.3301246G>A		200	0	0		243	121	0.497942	NM_003553	O43884|P47882|P47885|Q6IFA9|Q6IFM5|Q9UBJ1|Q9UM60	Silent	SNP	ENST00000322608.2	37	CCDS11024.1																																																																																			G|0.983;A|0.017	0.017	strong		0.542	OR1E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207303.1	NM_003553		A	3301246	G	A	3301246	2	1	22	1	0	0	0	0	0	0	0	1	10963	987	35	2		2	OR1E1	17	3301246	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	105643	3301246	77893964	3363	6264											
OR1E2	8388	hgsc.bcm.edu	37	chr17	3336697	3336697	+	Missense_Mutation	SNP	G	G	A																															cacggagagacagagcatggGgctcatgatggcggtgtagt																								rs77501388	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3336697G>A	ENST00000248384.1	-	1	438	c.439C>T	c.(439-441)Ccc>Tcc	p.P147S		NM_003554.1	NP_003545.1	P47887	OR1E2_HUMAN	olfactory receptor, family 1, subfamily E, member 2	147					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						CAGAGCATGGGGCTCATGATG	0.567													G|||	120	0.0239617	0.0885	0.0043	5008	,	,		19503	0.0		0.0	False		,,,				2504	0.0				p.P147S		Atlas-SNP	.											OR1E2,right_upper_lobe,carcinoma,+1,1	OR1E2	25	1	0			c.C439T						PASS	.																																			SO:0001583	missense	8388	exon1			GCATGGGGCTCAT	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.439C>T	17.37:g.3336697G>A	ENSP00000248384:p.Pro147Ser	221	0	0		230	98	0.426087	NM_003554	O43877|O95632|Q0VAD5|Q0VAD6|Q9UL13	Missense_Mutation	SNP	ENST00000248384.1	37	CCDS11026.1	45	0.020604395604395604	45	0.09146341463414634	0	0.0	0	0.0	0	0.0	G	9.675	1.147752	0.21288	.	.	ENSG00000127780	ENST00000248384;ENST00000454364	T	0.05649	3.41	5.47	4.51	0.55191	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000009	T	0.00144	0.0004	N	0.08118	0	0.09310	N	0.999998	B	0.31077	0.307	B	0.27608	0.081	T	0.45862	-0.9232	10	0.62326	D	0.03	.	6.8412	0.23963	0.0829:0.0:0.6588:0.2582	.	147	P47887	OR1E2_HUMAN	S	147;137	ENSP00000248384:P147S	ENSP00000248384:P147S	P	-	1	0	OR1E2	3283447	0.000000	0.05858	0.943000	0.38184	0.313000	0.28021	-0.200000	0.09478	1.550000	0.49438	0.650000	0.86243	CCC	G|0.987;A|0.013	0.013	strong		0.567	OR1E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207311.1			A	3336697	G	A	3336697	3	1	22	1	0	0	0	0	1	0	0	0	10964	1232	43	2	535	2	OR1E2	17	3336697	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	35451	3336697	77858513	3364	6265	77	2									
OR1E2	8388	hgsc.bcm.edu	37	chr17	3336699	3336699	+	Missense_Mutation	SNP	C	C	G																															cggagagacagagcatggggCtcatgatggcggtgtagtgc																								rs78339092	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3336699C>G	ENST00000248384.1	-	1	436	c.437G>C	c.(436-438)aGc>aCc	p.S146T		NM_003554.1	NP_003545.1	P47887	OR1E2_HUMAN	olfactory receptor, family 1, subfamily E, member 2	146					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						GAGCATGGGGCTCATGATGGC	0.562													C|||	120	0.0239617	0.0885	0.0043	5008	,	,		19338	0.0		0.0	False		,,,				2504	0.0				p.S146T		Atlas-SNP	.											OR1E2,right_upper_lobe,carcinoma,+1,1	OR1E2	25	1	0			c.G437C						PASS	.																																			SO:0001583	missense	8388	exon1			ATGGGGCTCATGA	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.437G>C	17.37:g.3336699C>G	ENSP00000248384:p.Ser146Thr	225	0	0		228	96	0.421053	NM_003554	O43877|O95632|Q0VAD5|Q0VAD6|Q9UL13	Missense_Mutation	SNP	ENST00000248384.1	37	CCDS11026.1	45	0.020604395604395604	45	0.09146341463414634	0	0.0	0	0.0	0	0.0	C	7.609	0.674467	0.14841	.	.	ENSG00000127780	ENST00000248384;ENST00000454364	T	0.03717	3.83	5.47	2.44	0.29823	GPCR, rhodopsin-like superfamily (1);	0.148993	0.48286	N	0.000187	T	0.00109	0.0003	N	0.08118	0	0.25052	N	0.99113	B	0.21225	0.053	B	0.26693	0.072	T	0.49495	-0.8934	10	0.33940	T	0.23	.	9.9959	0.41898	0.0:0.7793:0.0:0.2207	.	146	P47887	OR1E2_HUMAN	T	146;136	ENSP00000248384:S146T	ENSP00000248384:S146T	S	-	2	0	OR1E2	3283449	0.000000	0.05858	0.958000	0.39756	0.329000	0.28539	-0.448000	0.06820	0.439000	0.26476	0.650000	0.86243	AGC	C|0.987;G|0.013	0.013	strong		0.562	OR1E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207311.1			G	3336699	C	G	3336699	3	3	22	1	0	0	0	0	1	0	0	0	10964	797	28	4	537	4	OR1E2	17	3336699	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2	3336699	77858511	3365	6266	77	2									
OR1E2	8388	hgsc.bcm.edu	37	chr17	3336723	3336723	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatggcggtgtagtgcaggAggaagcagatggcggtgtag	9	8	20	4	2	0	2	0	1	0	1	0	4	0	4	0	6	2	4	0	6	3	2	rs73296096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3336723A>G	ENST00000248384.1	-	1	412	c.413T>C	c.(412-414)cTc>cCc	p.L138P		NM_003554.1	NP_003545.1	P47887	OR1E2_HUMAN	olfactory receptor, family 1, subfamily E, member 2	138					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						GTAGTGCAGGAGGAAGCAGAT	0.552													G|||	153	0.0305511	0.1112	0.0072	5008	,	,		19727	0.0		0.001	False		,,,				2504	0.0				p.L138P		Atlas-SNP	.											.	OR1E2	25	.	0			c.T413C						PASS	.	-	PRO/LEU	356,4050	793.7+/-415.2	24,308,1871	90	75	80		413		1	17	dbSNP_130	80	2,8598	819.2+/-406.8	0,2,4298	yes	missense	OR1E2	NM_003554.1	98	24,310,6169	GG,GA,AA		0.0233,8.0799,2.7526		138/324	3336723	358,12648	2203	4300	6503	SO:0001583	missense	8388	exon1			TGCAGGAGGAAGC	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.413T>C	17.37:g.3336723A>G	ENSP00000248384:p.Leu138Pro	214	0	0		223	98	0.439462	NM_003554	O43877|O95632|Q0VAD5|Q0VAD6|Q9UL13	Missense_Mutation	SNP	ENST00000248384.1	37	CCDS11026.1	49	0.022435897435897436	49	0.09959349593495935	0	0.0	0	0.0	0	0.0	G	2.920	-0.223476	0.06061	0.080799	2.33E-4	ENSG00000127780	ENST00000248384	T	0.02890	4.12	.	.	.	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00073	0.0002	N	0.08118	0	0.25307	N	0.989232	.	.	.	.	.	.	T	0.50825	-0.8782	5	0.72032	D	0.01	.	.	.	.	.	138	P47887	OR1E2_HUMAN	P	138	ENSP00000248384:L138P	ENSP00000248384:L138P	L	-	2	0	OR1E2	3283473	.	.	0.977000	0.42913	0.222000	0.24845	.	.	0.000000	0.14550	0.000000	0.15137	CTC	A|0.975;G|0.025	0.025	strong		0.552	OR1E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207311.1			G	3336723	A	G	3336723	3	3	22	1	0	0	0	0	1	0	0	0	10964	304	11	3	561	3	OR1E2	17	3336723	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	24	3336723	77858487	3366	6267											
GSG2	83903	hgsc.bcm.edu	37	chr17	3627619	3627619	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagaagtgcagcacaccctgCggcccgctccgacttccgcc	7	5	10	19	4	0	1	0	0	0	1	2	2	2	1	5	1	3	3	5	1	1	1	rs1185511	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3627619C>T	ENST00000325418.4	+	1	409	c.390C>T	c.(388-390)tgC>tgT	p.C130C	CTD-3195I5.3_ENST00000571741.1_RNA|ITGAE_ENST00000571185.1_5'UTR|ITGAE_ENST00000263087.4_Intron	NM_031965.2	NP_114171.2	Q8TF76	HASP_HUMAN	germ cell associated 2 (haspin)	130					histone H3-T3 phosphorylation involved in chromosome passenger complex localization to kinetochore (GO:2000751)|intracellular signal transduction (GO:0035556)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|protein localization to chromosome, centromeric region (GO:0071459)|protein phosphorylation (GO:0006468)|regulation of spindle checkpoint (GO:0090231)	centrosome (GO:0005813)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|histone kinase activity (H3-T3 specific) (GO:0072354)|protein kinase activity (GO:0004672)										GCACACCCTGCGGCCCGCTCC	0.731													C|||	804	0.160543	0.587	0.0403	5008	,	,		12752	0.0		0.0	False		,,,				2504	0.0				p.C130C		Atlas-SNP	.											.	GSG2	48	.	0			c.C390T						PASS	.	C	,	1822,2460		390,1042,709	6	8	8		,390	4.4	0.7	17	dbSNP_87	8	25,8313		0,25,4144	no	intron,coding-synonymous	ITGAE,GSG2	NM_002208.4,NM_031965.2	,	390,1067,4853	TT,TC,CC		0.2998,42.5502,14.6355	,	,130/799	3627619	1847,10773	2141	4169	6310	SO:0001819	synonymous_variant	83903	exon1			ACCCTGCGGCCCG	AB039834	CCDS11036.1	17p13	2005-01-19			ENSG00000177602	ENSG00000177602			19682	protein-coding gene	gene with protein product		609240					Standard	NM_031965		Approved	haspin	uc002fwp.3	Q8TF76	OTTHUMG00000090703	ENST00000325418.4:c.390C>T	17.37:g.3627619C>T		0	0	.		7	5	0.714286	NM_031965	Q5U5K3|Q96MN1|Q9BXS7	Silent	SNP	ENST00000325418.4	37	CCDS11036.1																																																																																			C|0.779;T|0.221	0.221	strong		0.731	GSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207391.1	NM_031965		T	3627619	C	T	3627619	2	4	22	1	0	0	0	0	0	0	0	1	6831	776	27	1		1	GSG2	17	3627619	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	290896	3627619	77567591	3367	6268											
C17orf85	55421	hgsc.bcm.edu	37	chr17	3728315	3728315	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatcgtttcttaacaaagaCtcctcttctacctgagacaa	13	12	5	11	1	3	3	0	1	3	3	5	4	4	3	2	0	2	1	2	0	4	4	rs218719	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3728315C>T	ENST00000389005.4	-	7	744	c.717G>A	c.(715-717)gaG>gaA	p.E239E	C17orf85_ENST00000577169.1_5'UTR|C17orf85_ENST00000158149.3_5'UTR	NM_001114118.2	NP_001107590.1	Q53F19	CQ085_HUMAN	chromosome 17 open reading frame 85	239							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (3;0.0725)		TTAACAAAGACTCCTCTTCTA	0.308													C|||	249	0.0497204	0.1808	0.0115	5008	,	,		17016	0.001		0.0	False		,,,				2504	0.001				p.E239E		Atlas-SNP	.											.	C17orf85	66	.	0			c.G717A						PASS	.	C	,	179,1205		16,147,529	120	94	102		717,	-1.8	1	17	dbSNP_79	102	2,3172		0,2,1585	no	coding-synonymous,utr-5	C17orf85	NM_001114118.1,NM_018553.3	,	16,149,2114	TT,TC,CC		0.063,12.9335,3.971	,	239/621,	3728315	181,4377	692	1587	2279	SO:0001819	synonymous_variant	55421	exon7			CAAAGACTCCTCT		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.717G>A	17.37:g.3728315C>T		30	0	0		27	11	0.407407	NM_001114118	B3KWG7|Q7L406|Q96FK1|Q9NXZ4	Silent	SNP	ENST00000389005.4	37	CCDS45578.1																																																																																			C|0.932;T|0.068	0.068	strong		0.308	C17orf85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438385.1	NM_018553		T	3728315	C	T	3728315	2	4	22	1	0	0	0	0	0	0	0	1	1890	564	20	2		2	C17orf85	17	3728315	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	100696	3728315	77466895	3368	6269											
CAMKK1	84254	hgsc.bcm.edu	37	chr17	3786456	3786456	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgggcagcctgggaccctctCgggggagggcgacctgtgac	5	6	18	12	2	1	1	0	1	1	0	2	4	1	3	3	5	1	1	3	5	0	0	rs737362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3786456C>T	ENST00000348335.2	-	6	676	c.528G>A	c.(526-528)ccG>ccA	p.P176P	CAMKK1_ENST00000158166.5_Silent_p.P176P|CAMKK1_ENST00000381769.2_Silent_p.P203P|CAMKK1_ENST00000381771.2_Silent_p.P176P	NM_032294.2	NP_115670.1	Q8N5S9	KKCC1_HUMAN	calcium/calmodulin-dependent protein kinase kinase 1, alpha	176	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|RP domain.				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)		GGGACCCTCTCGGGGGAGGGC	0.627													C|||	289	0.0577077	0.2118	0.0101	5008	,	,		19719	0.0		0.002	False		,,,				2504	0.0				p.P176P		Atlas-SNP	.											.	CAMKK1	70	.	0			c.G528A						PASS	.	C	,,	836,3570	328.5+/-300.6	77,682,1444	61	60	60		528,528,528	-10.9	0	17	dbSNP_86	60	9,8591	6.4+/-24.3	0,9,4291	no	coding-synonymous,coding-synonymous,coding-synonymous	CAMKK1	NM_032294.2,NM_172206.1,NM_172207.2	,,	77,691,5735	TT,TC,CC		0.1047,18.9741,6.497	,,	176/506,176/506,176/521	3786456	845,12161	2203	4300	6503	SO:0001819	synonymous_variant	84254	exon6			CCCTCTCGGGGGA	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.528G>A	17.37:g.3786456C>T		43	0	0		42	18	0.428571	NM_032294	Q9BQH3	Silent	SNP	ENST00000348335.2	37	CCDS11038.1																																																																																			C|0.934;T|0.066	0.066	strong		0.627	CAMKK1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207456.1	NM_032294, NM_172206, NM_172207		T	3786456	C	T	3786456	2	4	22	1	0	0	0	0	0	0	0	1	2608	871	31	1		1	CAMKK1	17	3786456	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	58141	3786456	77408754	3369	6270											
ATP2A3	489	hgsc.bcm.edu	37	chr17	3850910	3850910	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgaagtagtagacagcgccAcgcagccaggagccaccgtg	11	5	13	12	3	0	2	0	1	0	1	0	3	0	3	4	1	3	3	4	1	3	3	rs55837933	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3850910A>G	ENST00000352011.3	-	8	924	c.870T>C	c.(868-870)cgT>cgC	p.R290R	ATP2A3_ENST00000397035.3_Silent_p.R290R|ATP2A3_ENST00000397041.3_Silent_p.R290R|ATP2A3_ENST00000397043.3_Silent_p.R290R|ATP2A3_ENST00000309890.7_Silent_p.R290R|ATP2A3_ENST00000397039.1_5'UTR|ATP2A3_ENST00000359983.3_Silent_p.R290R			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	290					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)		AGACAGCGCCACGCAGCCAGG	0.677													G|||	356	0.0710863	0.2564	0.0245	5008	,	,		16011	0.0		0.0	False		,,,				2504	0.0				p.R290R	GBM(32;29 774 15719 37967)	Atlas-SNP	.											.	ATP2A3	148	.	0			c.T870C						PASS	.	G	,,,,,,	1054,3350		133,788,1281	28	31	30		870,870,870,870,870,870,870	-7.5	0.1	17	dbSNP_129	30	5,8591		0,5,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ATP2A3	NM_005173.3,NM_174953.2,NM_174954.2,NM_174955.2,NM_174956.2,NM_174957.2,NM_174958.2	,,,,,,	133,793,5574	GG,GA,AA		0.0582,23.9328,8.1462	,,,,,,	290/1000,290/1053,290/1045,290/1044,290/1030,290/999,290/1030	3850910	1059,11941	2202	4298	6500	SO:0001819	synonymous_variant	489	exon8			AGCGCCACGCAGC		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.870T>C	17.37:g.3850910A>G		38	0	0		43	26	0.604651	NM_174956	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Silent	SNP	ENST00000352011.3	37	CCDS11041.1																																																																																			A|0.928;G|0.072	0.072	strong		0.677	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953		G	3850910	A	G	3850910	2	3	22	1	0	0	0	0	0	0	0	1	1138	146	6	3		3	ATP2A3	17	3850910	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	64454	3850910	77344300	3370	6271											
SPNS3	201305	hgsc.bcm.edu	37	chr17	4351534	4351534	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggggagctgccgagacacagGgggagggggccgtgggaggc	7	2	24	8	2	0	1	0	0	0	1	0	5	0	4	2	8	2	1	2	8	0	0	rs61740736	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4351534G>C	ENST00000355530.2	+	6	986	c.706G>C	c.(706-708)Ggg>Cgg	p.G236R	SPNS3_ENST00000333476.2_Missense_Mutation_p.G109R|SPNS3_ENST00000576069.1_3'UTR	NM_182538.4	NP_872344.3	Q6ZMD2	SPNS3_HUMAN	spinster homolog 3 (Drosophila)	236					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				NS(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(6)|stomach(2)	28						CGAGACACAGGGGGAGGGGGC	0.637													G|||	77	0.0153754	0.0552	0.0058	5008	,	,		17510	0.0		0.0	False		,,,				2504	0.0				p.G236R		Atlas-SNP	.											.	SPNS3	52	.	0			c.G706C						PASS	.	G	ARG/GLY	160,4246	104.3+/-142.8	3,154,2046	33	31	32		706	1.9	0.2	17	dbSNP_129	32	0,8600		0,0,4300	yes	missense	SPNS3	NM_182538.4	125	3,154,6346	CC,CG,GG		0.0,3.6314,1.2302	benign	236/513	4351534	160,12846	2203	4300	6503	SO:0001583	missense	201305	exon6			ACACAGGGGGAGG		CCDS11045.1	17p13.2	2014-08-12			ENSG00000182557	ENSG00000182557			28433	protein-coding gene	gene with protein product		611701					Standard	NM_182538		Approved	MGC29671	uc002fxt.3	Q6ZMD2	OTTHUMG00000177737	ENST00000355530.2:c.706G>C	17.37:g.4351534G>C	ENSP00000347721:p.Gly236Arg	95	0	0		103	43	0.417476	NM_182538	Q8IZ31	Missense_Mutation	SNP	ENST00000355530.2	37	CCDS11045.1	28	0.01282051282051282	25	0.0508130081300813	3	0.008287292817679558	0	0.0	0	0.0	G	3.051	-0.195356	0.06259	0.036314	0.0	ENSG00000182557	ENST00000355530;ENST00000333476	T;T	0.58797	0.31;0.31	5.42	1.9	0.25705	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.357041	0.32343	N	0.006225	T	0.05960	0.0155	N	0.17312	0.475	0.09310	N	0.999999	B;B	0.15141	0.001;0.012	B;B	0.23852	0.002;0.049	T	0.04153	-1.0973	10	0.11485	T	0.65	-3.8842	3.2294	0.06744	0.3204:0.0:0.4977:0.1819	rs61740736	109;236	Q6ZMD2-2;Q6ZMD2	.;SPNS3_HUMAN	R	236;109	ENSP00000347721:G236R;ENSP00000333207:G109R	ENSP00000333207:G109R	G	+	1	0	SPNS3	4298283	0.202000	0.23423	0.212000	0.23672	0.006000	0.05464	0.900000	0.28431	0.794000	0.33899	-0.217000	0.12591	GGG	G|0.989;C|0.011	0.011	strong		0.637	SPNS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438793.1	NM_182538		C	4351534	G	C	4351534	3	2	22	1	0	0	0	0	1	0	0	0	15091	1232	43	4	728	4	SPNS3	17	4351534	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	500624	4351534	76843676	3371	6272											
MYBBP1A	10514	hgsc.bcm.edu	37	chr17	4448324	4448324	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccacctcccccactcaccagCgccttcccagcctgcagcac	7	5	5	24	1	1	0	1	0	0	0	3	0	3	0	8	0	4	2	8	0	0	1	rs9910964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4448324C>T	ENST00000254718.4	-	17	2613	c.2307G>A	c.(2305-2307)gcG>gcA	p.A769A	MYBBP1A_ENST00000381556.2_Silent_p.A769A			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	769	Glu-rich.				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						CACTCACCAGCGCCTTCCCAG	0.711													C|||	363	0.072484	0.2572	0.0231	5008	,	,		4471	0.0		0.007	False		,,,				2504	0.0				p.A769A		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.G2307A						PASS	.	C	,	821,3251		77,667,1292	88	62	71		2307,2307	-1.9	1	17	dbSNP_119	71	16,7960		0,16,3972	yes	coding-synonymous,coding-synonymous	MYBBP1A	NM_001105538.1,NM_014520.3	,	77,683,5264	TT,TC,CC		0.2006,20.1621,6.9472	,	769/1333,769/1329	4448324	837,11211	2036	3988	6024	SO:0001819	synonymous_variant	10514	exon17			CACCAGCGCCTTC	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.2307G>A	17.37:g.4448324C>T		62	0	0		62	31	0.5	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Silent	SNP	ENST00000254718.4	37	CCDS11046.1																																																																																			C|0.916;T|0.084	0.084	strong		0.711	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520		T	4448324	C	T	4448324	2	4	22	1	0	0	0	0	0	0	0	1	10017	755	27	1		1	MYBBP1A	17	4448324	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	96790	4448324	76746886	3372	6273											
MYBBP1A	10514	hgsc.bcm.edu	37	chr17	4458536	4458536	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aactcgcgactgtgcttcaaTaggccatagcggtcggcagg	9	8	13	11	4	1	0	1	0	0	0	3	1	1	0	1	4	3	2	1	4	4	3	rs144321472	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4458536T>C	ENST00000254718.4	-	1	390	c.84A>G	c.(82-84)ctA>ctG	p.L28L	MYBBP1A_ENST00000381556.2_Silent_p.L28L			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	28	Interaction with MYB. {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						TGTGCTTCAATAGGCCATAGC	0.637													C|||	34	0.00678914	0.0234	0.0043	5008	,	,		16162	0.0		0.0	False		,,,				2504	0.0				p.L28L		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.A84G						PASS	.	C	,	77,4327	780.9+/-414.5	1,75,2126	24	25	25		84,84	0.6	0.1	17	dbSNP_134	25	2,8596	790.5+/-407.6	0,2,4297	no	coding-synonymous,coding-synonymous	MYBBP1A	NM_001105538.1,NM_014520.3	,	1,77,6423	CC,CT,TT		0.0233,1.7484,0.6076	,	28/1333,28/1329	4458536	79,12923	2202	4299	6501	SO:0001819	synonymous_variant	10514	exon1			CTTCAATAGGCCA	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.84A>G	17.37:g.4458536T>C		59	0	0		64	39	0.609375	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Silent	SNP	ENST00000254718.4	37	CCDS11046.1																																																																																			T|0.995;C|0.005	0.005	strong		0.637	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520		C	4458536	T	C	4458536	2	2	22	1	0	0	0	0	0	0	0	1	10017	1393	49	3		3	MYBBP1A	17	4458536	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	10212	4458536	76736674	3373	6274											
SMTNL2	342527	hgsc.bcm.edu	37	chr17	4497137	4497137	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaagaattcctctttcacgTggtctgtgccaagctctggc	8	12	10	11	1	4	2	1	0	3	2	5	2	5	2	2	2	2	1	2	2	3	2	rs9916524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4497137T>C	ENST00000389313.4	+	4	818	c.751T>C	c.(751-753)Tgg>Cgg	p.W251R	SMTNL2_ENST00000338859.4_Missense_Mutation_p.W107R	NM_001114974.1	NP_001108446.1	Q2TAL5	SMTL2_HUMAN	smoothelin-like 2	251			W -> R (in dbSNP:rs9916524).							breast(1)|endometrium(9)|kidney(1)|lung(1)|skin(1)	13				READ - Rectum adenocarcinoma(115;0.0325)		CTCTTTCACGTGGTCTGTGCC	0.592													C|||	229	0.0457268	0.1399	0.0159	5008	,	,		18798	0.0		0.008	False		,,,				2504	0.0256				p.W251R		Atlas-SNP	.											.	SMTNL2	57	.	0			c.T751C						PASS	.	C	ARG/TRP,ARG/TRP	520,3886	776.1+/-414.1	26,468,1709	76	69	72		751,319	-0.1	0	17	dbSNP_119	72	10,8590	818.7+/-406.8	0,10,4290	yes	missense,missense	SMTNL2	NM_001114974.1,NM_198501.2	101,101	26,478,5999	CC,CT,TT		0.1163,11.8021,4.075	benign,benign	251/462,107/318	4497137	530,12476	2203	4300	6503	SO:0001583	missense	342527	exon4			TTCACGTGGTCTG	AK124452	CCDS11048.1, CCDS45583.1	17p13.2	2006-04-26			ENSG00000188176	ENSG00000188176			24764	protein-coding gene	gene with protein product							Standard	NM_001114974		Approved	FLJ42461	uc002fyf.1	Q2TAL5	OTTHUMG00000132938	ENST00000389313.4:c.751T>C	17.37:g.4497137T>C	ENSP00000373964:p.Trp251Arg	129	0	0		118	45	0.381356	NM_001114974	Q6ZVK6	Missense_Mutation	SNP	ENST00000389313.4	37	CCDS45583.1	93	0.042582417582417584	84	0.17073170731707318	4	0.011049723756906077	0	0.0	5	0.006596306068601583	C	0.021	-1.428801	0.01117	0.118021	0.001163	ENSG00000188176	ENST00000338859;ENST00000389313	T;T	0.80994	-1.41;-1.44	4.45	-0.126	0.13515	.	.	.	.	.	T	0.00178	0.0005	N	0.02142	-0.665	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.01814	-1.1268	9	0.02654	T	1	-20.7736	3.6672	0.08260	0.4915:0.3015:0.0:0.207	rs9916524;rs52797495;rs56667747;rs9916524	251	Q2TAL5	SMTL2_HUMAN	R	107;251	ENSP00000345143:W107R;ENSP00000373964:W251R	ENSP00000345143:W107R	W	+	1	0	SMTNL2	4443886	0.000000	0.05858	0.018000	0.16275	0.001000	0.01503	-2.881000	0.00715	-0.161000	0.10983	-1.043000	0.02367	TGG	T|0.951;C|0.049	0.049	strong		0.592	SMTNL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439129.1	NM_198501		C	4497137	T	C	4497137	3	2	22	1	0	0	0	0	1	0	0	0	14831	1696	59	3	765	3	SMTNL2	17	4497137	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	38601	4497137	76698073	3374	6275											
ALOX15	246	hgsc.bcm.edu	37	chr17	4539171	4539171	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggagctggaagtcagagctGcgcacccagcatttggccag	9	7	14	11	1	1	1	1	0	0	1	1	3	1	3	2	3	4	4	2	3	1	1	rs11568113	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4539171G>T	ENST00000570836.1	-	9	1140	c.1044C>A	c.(1042-1044)cgC>cgA	p.R348R	ALOX15_ENST00000574640.1_Silent_p.R309R|ALOX15_ENST00000545513.1_Silent_p.R370R|ALOX15_ENST00000293761.3_Silent_p.R348R			P16050	LOX15_HUMAN	arachidonate 15-lipoxygenase	348	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				apoptotic cell clearance (GO:0043277)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|cellular response to calcium ion (GO:0071277)|cellular response to interleukin-13 (GO:0035963)|hepoxilin biosynthetic process (GO:0051122)|inflammatory response (GO:0006954)|leukotriene metabolic process (GO:0006691)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxygenase pathway (GO:0019372)|negative regulation of adaptive immune response (GO:0002820)|ossification (GO:0001503)|phosphatidylethanolamine biosynthetic process (GO:0006646)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of engulfment of apoptotic cell (GO:1901074)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|lipid particle (GO:0005811)|membrane (GO:0016020)|plasma membrane (GO:0005886)	arachidonate 12-lipoxygenase activity (GO:0004052)|arachidonate 15-lipoxygenase activity (GO:0050473)|eoxin A4 synthase activity (GO:0097260)|iron ion binding (GO:0005506)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(5)	20				READ - Rectum adenocarcinoma(115;0.0327)		AGTCAGAGCTGCGCACCCAGC	0.602													G|||	93	0.0185703	0.0681	0.0043	5008	,	,		20183	0.0		0.0	False		,,,				2504	0.0				p.R348R		Atlas-SNP	.											.	ALOX15	70	.	0			c.C1044A						PASS	.	G		314,4092	169.1+/-199.8	15,284,1904	68	70	69		1044	-7.4	0.6	17	dbSNP_120	69	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	ALOX15	NM_001140.3		15,286,6202	TT,TG,GG		0.0233,7.1266,2.4296		348/663	4539171	316,12690	2203	4300	6503	SO:0001819	synonymous_variant	246	exon8			AGAGCTGCGCACC	M23892	CCDS11049.1	17p13.3	2010-09-24			ENSG00000161905	ENSG00000161905	1.13.11.33	"Arachidonate lipoxygenases"	433	protein-coding gene	gene with protein product		152392				1570320	Standard	NM_001140		Approved	15-LOX-1	uc002fyh.3	P16050	OTTHUMG00000090746	ENST00000570836.1:c.1044C>A	17.37:g.4539171G>T		160	0	0		150	77	0.513333	NM_001140	A8K2P4|B7ZA11|Q8N6R7|Q99657	Silent	SNP	ENST00000570836.1	37	CCDS11049.1																																																																																			G|0.973;T|0.027	0.027	strong		0.602	ALOX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207487.2			T	4539171	G	T	4539171	2	4	22	1	0	0	0	0	0	0	0	1	538	1306	46	4		4	ALOX15	17	4539171	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	42034	4539171	76656039	3375	6276											
PELP1	27043	hgsc.bcm.edu	37	chr17	4576623	4576623	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggtgggcagcgaggagacggGgccagcagcagcgccagcag	9	1	20	11	3	0	1	0	0	0	1	0	3	0	1	2	5	5	4	2	5	0	0	rs191748391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4576623G>A	ENST00000574876.1	-	15	1784	c.1767C>T	c.(1765-1767)gcC>gcT	p.A589A	PELP1_ENST00000436683.2_Silent_p.A442A|AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000269230.7_Intron|PELP1_ENST00000301396.4_Silent_p.A733A|PELP1_ENST00000572293.1_Silent_p.A639A			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	589					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						GAGGAGACGGGGCCAGCAGCA	0.647													G|||	4	0.000798722	0.003	0.0	5008	,	,		16322	0.0		0.0	False		,,,				2504	0.0				p.A589A		Atlas-SNP	.											.	PELP1	102	.	0			c.C1767T						PASS	.	G		8,4302		0,8,2147	18	30	26		1767	-11.1	0	17		26	0,8548		0,0,4274	no	coding-synonymous	PELP1	NM_014389.2		0,8,6421	AA,AG,GG		0.0,0.1856,0.0622		589/1131	4576623	8,12850	2155	4274	6429	SO:0001819	synonymous_variant	27043	exon15			AGACGGGGCCAGC		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.1767C>T	17.37:g.4576623G>A		161	0	0		194	97	0.5	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Silent	SNP	ENST00000574876.1	37	CCDS58503.1																																																																																			G|0.999;A|0.001	0.001	strong		0.647	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389		A	4576623	G	A	4576623	2	1	22	1	0	0	0	0	0	0	0	1	11734	1219	43	2		2	PELP1	17	4576623	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	37452	4576623	76618587	3376	6277											
PELP1	27043	hgsc.bcm.edu	37	chr17	4586220	4586220	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctcaggacagccacggccaGctccattgtggcaggcgggt	7	6	14	14	2	1	0	1	0	0	0	2	1	2	1	4	5	2	2	4	5	0	1	rs35109567	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4586220G>A	ENST00000574876.1	-	4	465	c.448C>T	c.(448-450)Ctg>Ttg	p.L150L	PELP1_ENST00000436683.2_Silent_p.L3L|AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000269230.7_Silent_p.L150L|PELP1_ENST00000301396.4_Silent_p.L150L|PELP1_ENST00000572293.1_Silent_p.L200L|PELP1_ENST00000570823.1_5'Flank			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	150					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						GCCACGGCCAGCTCCATTGTG	0.557													g|||	138	0.0275559	0.1014	0.0058	5008	,	,		16714	0.0		0.0	False		,,,				2504	0.0				p.L150L		Atlas-SNP	.											.	PELP1	102	.	0			c.C448T						PASS	.			338,3568		15,308,1630	24	28	27		448	-3.3	1	17	dbSNP_126	27	5,8279		0,5,4137	no	coding-synonymous	PELP1	NM_014389.2		15,313,5767	AA,AG,GG		0.0604,8.6534,2.8138		150/1131	4586220	343,11847	1953	4142	6095	SO:0001819	synonymous_variant	27043	exon4			CGGCCAGCTCCAT		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.448C>T	17.37:g.4586220G>A		185	0	0		176	84	0.477273	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Silent	SNP	ENST00000574876.1	37	CCDS58503.1																																																																																			G|0.974;A|0.026	0.026	strong		0.557	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389		A	4586220	G	A	4586220	2	1	22	1	0	0	0	0	0	0	0	1	11734	962	34	2		2	PELP1	17	4586220	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	9597	4586220	76608990	3377	6278											
SPAG7	9552	hgsc.bcm.edu	37	chr17	4863540	4863540	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccctttacctttttgaagaTcatgacatagcgacagtcat	11	13	7	10	1	2	3	2	2	0	1	2	4	2	3	2	0	2	0	2	0	3	5	rs73343382	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4863540T>C	ENST00000206020.3	-	4	383	c.316A>G	c.(316-318)Atc>Gtc	p.I106V	SPAG7_ENST00000575142.1_Missense_Mutation_p.I95V|SPAG7_ENST00000573366.1_Missense_Mutation_p.I55V	NM_004890.2	NP_004881.2	O75391	SPAG7_HUMAN	sperm associated antigen 7	106	R3H. {ECO:0000255|PROSITE- ProRule:PRU00382}.					nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			central_nervous_system(1)|endometrium(1)|kidney(2)|lung(3)|ovary(2)|urinary_tract(1)	10						TTTTTGAAGATCATGACATAG	0.488													T|||	154	0.0307508	0.1127	0.0058	5008	,	,		19237	0.0		0.001	False		,,,				2504	0.0				p.I106V		Atlas-SNP	.											.	SPAG7	22	.	0			c.A316G						PASS	.	T	VAL/ILE	363,3671		20,323,1674	75	79	78		316	5.3	1	17	dbSNP_130	78	4,8376		0,4,4186	yes	missense	SPAG7	NM_004890.2	29	20,327,5860	CC,CT,TT		0.0477,8.9985,2.9563	benign	106/228	4863540	367,12047	2017	4190	6207	SO:0001583	missense	9552	exon4			TGAAGATCATGAC	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.316A>G	17.37:g.4863540T>C	ENSP00000206020:p.Ile106Val	197	0	0		183	95	0.519126	NM_004890	Q96EU5	Missense_Mutation	SNP	ENST00000206020.3	37	CCDS42240.1	46	0.021062271062271064	44	0.08943089430894309	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	0.871	-0.732127	0.03135	0.089985	4.77E-4	ENSG00000091640	ENST00000206020	T	0.43688	0.94	5.3	5.3	0.74995	Single-stranded nucleic acid binding R3H (3);	0.117351	0.56097	D	0.000028	T	0.00967	0.0032	N	0.25789	0.76	0.41244	D	0.986669	B	0.10296	0.003	B	0.12837	0.008	T	0.02610	-1.1134	10	0.02654	T	1	-4.764	13.2379	0.59979	0.0:0.0:0.0:1.0	.	106	O75391	SPAG7_HUMAN	V	106	ENSP00000206020:I106V	ENSP00000206020:I106V	I	-	1	0	SPAG7	4804263	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.809000	0.38922	2.225000	0.72522	0.533000	0.62120	ATC	T|0.978;C|0.022	0.022	strong		0.488	SPAG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438747.1	NM_004890		C	4863540	T	C	4863540	3	2	22	1	0	0	0	0	1	0	0	0	14998	1435	50	3	383	3	SPAG7	17	4863540	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	277320	4863540	76331670	3378	6279											
SPAG7	9552	hgsc.bcm.edu	37	chr17	4863574	4863574	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagtcatcatcttccccaaaGgagaaggatgtcaggccagc	12	7	10	12	0	4	1	3	0	1	1	5	3	5	2	3	3	1	0	3	3	2	1	rs73343383	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4863574G>A	ENST00000206020.3	-	4	349	c.282C>T	c.(280-282)tcC>tcT	p.S94S	SPAG7_ENST00000575142.1_Silent_p.S83S|SPAG7_ENST00000573366.1_Silent_p.S43S	NM_004890.2	NP_004881.2	O75391	SPAG7_HUMAN	sperm associated antigen 7	94	R3H. {ECO:0000255|PROSITE- ProRule:PRU00382}.					nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			central_nervous_system(1)|endometrium(1)|kidney(2)|lung(3)|ovary(2)|urinary_tract(1)	10						CTTCCCCAAAGGAGAAGGATG	0.537													G|||	149	0.0297524	0.1089	0.0058	5008	,	,		18290	0.0		0.001	False		,,,				2504	0.0				p.S94S		Atlas-SNP	.											.	SPAG7	22	.	0			c.C282T						PASS	.	G		347,3719		20,307,1706	63	66	65		282	2.2	1	17	dbSNP_130	65	4,8392		0,4,4194	no	coding-synonymous	SPAG7	NM_004890.2		20,311,5900	AA,AG,GG		0.0476,8.5342,2.8166		94/228	4863574	351,12111	2033	4198	6231	SO:0001819	synonymous_variant	9552	exon4			CCCAAAGGAGAAG	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.282C>T	17.37:g.4863574G>A		163	0	0		127	67	0.527559	NM_004890	Q96EU5	Silent	SNP	ENST00000206020.3	37	CCDS42240.1																																																																																			G|0.978;A|0.022	0.022	strong		0.537	SPAG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438747.1	NM_004890		A	4863574	G	A	4863574	2	1	22	1	0	0	0	0	0	0	0	1	14998	987	35	2		2	SPAG7	17	4863574	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	34	4863574	76331636	3379	6280											
KIF1C	10749	hgsc.bcm.edu	37	chr17	4918122	4918122	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccggagcatcccccagccAgatggagaaggtaatggctg	10	7	13	11	1	0	2	0	0	0	2	2	4	2	3	4	4	2	3	4	4	2	2	rs57144955	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4918122A>G	ENST00000320785.5	+	18	2013	c.1656A>G	c.(1654-1656)ccA>ccG	p.P552P	KIF1C_ENST00000573815.1_3'UTR	NM_006612.5	NP_006603.2	O43896	KIF1C_HUMAN	kinesin family member 1C	552	FHA.				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						TCCCCCAGCCAGATGGAGAAG	0.587													A|||	170	0.0339457	0.1225	0.0101	5008	,	,		19813	0.0		0.001	False		,,,				2504	0.0				p.P552P	Melanoma(96;1023 1447 10250 19259 33730)	Atlas-SNP	.											.	KIF1C	70	.	0			c.A1656G						PASS	.	A		454,3952		26,402,1775	41	29	33		1656	-9.6	0.1	17	dbSNP_129	33	4,8594		0,4,4295	no	coding-synonymous	KIF1C	NM_006612.5		26,406,6070	GG,GA,AA		0.0465,10.3041,3.522		552/1104	4918122	458,12546	2203	4299	6502	SO:0001819	synonymous_variant	10749	exon18			CCAGCCAGATGGA	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.1656A>G	17.37:g.4918122A>G		76	0	0		63	30	0.47619	NM_006612	D3DTL6|O75186|Q5U618	Silent	SNP	ENST00000320785.5	37	CCDS11065.1																																																																																			A|0.964;G|0.036	0.036	strong		0.587	KIF1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216916.1			G	4918122	A	G	4918122	2	3	22	1	0	0	0	0	0	0	0	1	8294	175	7	3		3	KIF1C	17	4918122	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	54548	4918122	76277088	3380	6281											
KIF1C	10749	hgsc.bcm.edu	37	chr17	4925674	4925674	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccctggctgacttccgccaCgggcgggctgagattgaggc	5	7	16	13	3	0	3	0	3	0	1	1	4	1	3	3	4	0	2	3	4	0	2	rs73345356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4925674C>T	ENST00000320785.5	+	22	2655	c.2298C>T	c.(2296-2298)caC>caT	p.H766H	AC109333.10_ENST00000438266.1_RNA	NM_006612.5	NP_006603.2	O43896	KIF1C_HUMAN	kinesin family member 1C	766					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						ACTTCCGCCACGGGCGGGCTG	0.677													C|||	167	0.0333466	0.1188	0.0115	5008	,	,		17324	0.0		0.002	False		,,,				2504	0.0				p.H766H	Melanoma(96;1023 1447 10250 19259 33730)	Atlas-SNP	.											KIF1C,colon,carcinoma,0,1	KIF1C	70	1	0			c.C2298T						PASS	.	C		432,3962		26,380,1791	19	18	19		2298	-1.4	1	17	dbSNP_130	19	16,8566		0,16,4275	no	coding-synonymous	KIF1C	NM_006612.5		26,396,6066	TT,TC,CC		0.1864,9.8316,3.4525		766/1104	4925674	448,12528	2197	4291	6488	SO:0001819	synonymous_variant	10749	exon22			CCGCCACGGGCGG	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.2298C>T	17.37:g.4925674C>T		94	0	0		80	42	0.525	NM_006612	D3DTL6|O75186|Q5U618	Silent	SNP	ENST00000320785.5	37	CCDS11065.1																																																																																			C|0.964;T|0.036	0.036	strong		0.677	KIF1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216916.1			T	4925674	C	T	4925674	2	4	22	1	0	0	0	0	0	0	0	1	8294	535	19	1		1	KIF1C	17	4925674	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	7552	4925674	76269536	3381	6282											
USP6	9098	hgsc.bcm.edu	37	chr17	5039138	5039138	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agggacctgagccacatcacCgccttgttcctcctttatct	7	12	7	15	1	2	1	1	1	1	0	4	2	4	2	6	1	1	1	6	1	1	4	rs3213878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5039138C>T	ENST00000574788.1	+	17	2809	c.579C>T	c.(577-579)acC>acT	p.T193T	USP6_ENST00000304328.5_5'UTR|USP6_ENST00000250066.6_Silent_p.T193T|USP6_ENST00000332776.4_Silent_p.T193T			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	193	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				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						GCCACATCACCGCCTTGTTCC	0.607			T	"COL1A1, CDH11, ZNF9, OMD"	aneurysmal bone cysts								C|||	490	0.0978435	0.1853	0.0375	5008	,	,		20475	0.0774		0.1143	False		,,,				2504	0.0266				p.T193T		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	.	USP6	213	.	0			c.C579T						PASS	.	C		682,3724	287.2+/-279.2	60,562,1581	126	110	115		579	-1.7	0.2	17	dbSNP_106	115	949,7651	208.0+/-249.6	52,845,3403	no	coding-synonymous	USP6	NM_004505.2		112,1407,4984	TT,TC,CC		11.0349,15.4789,12.5404		193/1407	5039138	1631,11375	2203	4300	6503	SO:0001819	synonymous_variant	9098	exon9			CATCACCGCCTTG	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.579C>T	17.37:g.5039138C>T		14	0	0		21	10	0.47619	NM_004505	Q15634|Q86WP6|Q8IWT4	Silent	SNP	ENST00000574788.1	37	CCDS11069.2																																																																																			C|0.883;T|0.117	0.117	strong		0.607	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505		T	5039138	C	T	5039138	2	4	22	1	0	0	0	0	0	0	0	1	17101	639	23	1		1	USP6	17	5039138	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	113464	5039138	76156072	3382	6283											
ZNF594	84622	hgsc.bcm.edu	37	chr17	5085245	5085245	+	Silent	SNP	G	G	A																															agatctgagctgccctggaaGgtcctactacactgattaca																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5085245G>A	ENST00000399604.4	-	1	2447	c.2307C>T	c.(2305-2307)acC>acT	p.T769T	ZNF594_ENST00000575779.1_Silent_p.T769T			Q96JF6	ZN594_HUMAN	zinc finger protein 594	769					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						TGCCCTGGAAGGTCCTACTAC	0.413																																					p.T769T		Atlas-SNP	.											.	ZNF594	89	.	0			c.C2307T						PASS	.						205	206	206					17																	5085245		1989	4182	6171	SO:0001819	synonymous_variant	84622	exon2			CTGGAAGGTCCTA	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.2307C>T	17.37:g.5085245G>A		154	0	0		100	18	0.18	NM_032530	Q6RFS0	Silent	SNP	ENST00000399604.4	37	CCDS42241.1																																																																																			.	.	none		0.413	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737		A	5085245	G	A	5085245	2	1	22	1	0	0	0	0	0	0	0	1	18039	987	35	2		2	ZNF594	17	5085245	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	46107	5085245	76109965	3383	6284	78	2									
ZNF594	84622	hgsc.bcm.edu	37	chr17	5085247	5085247	+	Missense_Mutation	SNP	T	T	C																															atctgagctgccctggaaggTcctactacactgattacacc																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5085247T>C	ENST00000399604.4	-	1	2445	c.2305A>G	c.(2305-2307)Acc>Gcc	p.T769A	ZNF594_ENST00000575779.1_Missense_Mutation_p.T769A			Q96JF6	ZN594_HUMAN	zinc finger protein 594	769					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						CCCTGGAAGGTCCTACTACAC	0.413																																					p.T769A		Atlas-SNP	.											.	ZNF594	89	.	0			c.A2305G						PASS	.						207	208	208					17																	5085247		1990	4182	6172	SO:0001583	missense	84622	exon2			GGAAGGTCCTACT	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.2305A>G	17.37:g.5085247T>C	ENSP00000382513:p.Thr769Ala	155	0	0		98	16	0.163265	NM_032530	Q6RFS0	Missense_Mutation	SNP	ENST00000399604.4	37	CCDS42241.1	.	.	.	.	.	.	.	.	.	.	T	0.005	-2.220840	0.00286	.	.	ENSG00000180626	ENST00000399604	T	0.14022	2.54	0.98	-0.251	0.13003	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04907	0.0132	N	0.12831	0.26	0.09310	N	1	B	0.18310	0.027	B	0.04013	0.001	T	0.42616	-0.9441	9	0.02654	T	1	.	4.0333	0.09719	0.0:0.2705:0.0:0.7295	.	769	Q96JF6	ZN594_HUMAN	A	769	ENSP00000382513:T769A	ENSP00000382513:T769A	T	-	1	0	ZNF594	5025971	0.000000	0.05858	0.002000	0.10522	0.239000	0.25481	-1.239000	0.02916	0.413000	0.25759	0.240000	0.17902	ACC	.	.	none		0.413	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737		C	5085247	T	C	5085247	3	2	22	1	0	0	0	0	1	0	0	0	18039	1667	58	3	122	3	ZNF594	17	5085247	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2	5085247	76109963	3384	6285	78	2									
ZNF594	84622	hgsc.bcm.edu	37	chr17	5085806	5085806	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gttacctgatgtctgatgagGtctgagctgccctggaaagc	8	11	13	9	0	2	4	0	4	2	0	2	5	2	5	2	2	4	2	2	2	2	1	rs114624606	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5085806G>A	ENST00000399604.4	-	1	1886	c.1746C>T	c.(1744-1746)gaC>gaT	p.D582D	ZNF594_ENST00000575779.1_Silent_p.D582D			Q96JF6	ZN594_HUMAN	zinc finger protein 594	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)			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						GTCTGATGAGGTCTGAGCTGC	0.453																																					p.D582D		Atlas-SNP	.											.	ZNF594	89	.	0			c.C1746T						PASS	.	G		95,3919		4,87,1916	149	144	145		1746	-2.1	0	17	dbSNP_132	145	1,8411		0,1,4205	no	coding-synonymous	ZNF594	NM_032530.1		4,88,6121	AA,AG,GG		0.0119,2.3667,0.7726		582/808	5085806	96,12330	2007	4206	6213	SO:0001819	synonymous_variant	84622	exon2			GATGAGGTCTGAG	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.1746C>T	17.37:g.5085806G>A		124	0	0		112	47	0.419643	NM_032530	Q6RFS0	Silent	SNP	ENST00000399604.4	37	CCDS42241.1																																																																																			G|0.990;A|0.010	0.010	strong		0.453	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737		A	5085806	G	A	5085806	2	1	22	1	0	0	0	0	0	0	0	1	18039	1252	44	2		2	ZNF594	17	5085806	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	559	5085806	76109404	3385	6286											
ZNF594	84622	hgsc.bcm.edu	37	chr17	5085878	5085879	+	Frame_Shift_Del	DEL	CT	CT	-																															gcttcctggtgaattttctgCtctcccctaagctcctcatc																								rs146837771	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5085878_5085879delCT	ENST00000399604.4	-	1	1813_1814	c.1673_1674delAG	c.(1672-1674)gagfs	p.E558fs	ZNF594_ENST00000575779.1_Frame_Shift_Del_p.E558fs			Q96JF6	ZN594_HUMAN	zinc finger protein 594	558					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						GAATTTTCTGCTCTCCCCTAAG	0.47														55	0.0109824	0.0378	0.0029	5008	,	,		21001	0.0		0.003	False		,,,				2504	0.0				p.558_559del		Pindel,Atlas-Indel	.											.	ZNF594	89	.	0			c.1674_1675del						PASS	.			154,3700		12,130,1785						-0.1	0		dbSNP_134	128	1,8047		0,1,4023	no	frameshift	ZNF594	NM_032530.1		12,131,5808	A1A1,A1R,RR		0.0124,3.9958,1.3023				155,11747				SO:0001589	frameshift_variant	84622	exon2			.	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.1673_1674delAG	17.37:g.5085880_5085881delCT	ENSP00000382513:p.Glu558fs	120	0	.		117	33	0.282	NM_032530	Q6RFS0	Frame_Shift_Del	DEL	ENST00000399604.4	37	CCDS42241.1																																																																																			CT|0.987;-|0.013	0.013	strong		0.47	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737		-	5085879	CT	-	5085878	7	5	22	1	0	1	0	1	0	0	0	0	18039	796	28	0	753	0	ZNF594	17	5085878	Frame_Shift_Del	DEL	CT	TCGA-G8-6324-01A-11D-2210-10	72	5085878	76109332	3386	6287											
NUP88	4927	hgsc.bcm.edu	37	chr17	5291126	5291126	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatctcctcctttgccaagTcctgtttgagaatgtactgc	8	14	8	11	0	1	1	0	1	1	1	4	3	3	1	4	0	3	2	4	0	4	3	rs149760662	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5291126T>C	ENST00000573584.1	-	12	2251	c.1742A>G	c.(1741-1743)gAc>gGc	p.D581G	NUP88_ENST00000573169.1_5'Flank	NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	581					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						CTTTGCCAAGTCCTGTTTGAG	0.522													T|||	5	0.000998403	0.0	0.0014	5008	,	,		15835	0.0		0.003	False		,,,				2504	0.001				p.D581G		Atlas-SNP	.											.	NUP88	47	.	0			c.A1742G						PASS	.	T	GLY/ASP	6,4400	11.4+/-27.6	0,6,2197	96	96	96		1742	4.8	1	17	dbSNP_134	96	44,8556	27.9+/-77.7	0,44,4256	yes	missense	NUP88	NM_002532.4	94	0,50,6453	CC,CT,TT		0.5116,0.1362,0.3844	benign	581/742	5291126	50,12956	2203	4300	6503	SO:0001583	missense	4927	exon12			GCCAAGTCCTGTT	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.1742A>G	17.37:g.5291126T>C	ENSP00000458954:p.Asp581Gly	86	0	0		119	61	0.512605	NM_002532	D3DTM2|Q9BWE5	Missense_Mutation	SNP	ENST00000573584.1	37	CCDS11070.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	T	19.11	3.764327	0.69878	0.001362	0.005116	ENSG00000108559	ENST00000225696;ENST00000543132	.	.	.	4.76	4.76	0.60689	.	0.047661	0.85682	D	0.000000	T	0.48822	0.1521	L	0.38838	1.175	0.52501	D	0.999951	P;B	0.52692	0.955;0.046	P;B	0.51615	0.675;0.04	T	0.51196	-0.8736	9	0.32370	T	0.25	-20.571	13.9189	0.63919	0.0:0.0:0.0:1.0	.	466;581	B4DP20;Q99567	.;NUP88_HUMAN	G	581;466	.	ENSP00000225696:D581G	D	-	2	0	NUP88	5231850	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.299000	0.65716	2.137000	0.66172	0.454000	0.30748	GAC	T|0.998;C|0.002	0.002	strong		0.522	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532		C	5291126	T	C	5291126	3	2	22	1	0	0	0	0	1	0	0	0	10780	1667	58	3	507	3	NUP88	17	5291126	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	205248	5291126	75904084	3387	6288											
BCL6B	255877	hgsc.bcm.edu	37	chr17	6930927	6930927	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagtgcactaccacattctcGgggggccctagctgagcgca	9	7	12	13	2	1	1	0	1	1	0	2	1	1	1	2	3	4	3	2	3	3	3	rs201522060	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:6930927G>A	ENST00000293805.5	+	9	1521	c.1429G>A	c.(1429-1431)Ggg>Agg	p.G477R		NM_181844.3	NP_862827	Q8N143	BCL6B_HUMAN	B-cell CLL/lymphoma 6, member B	477					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			skin(1)	1						CCACATTCTCGGGGGGCCCTA	0.627													G|||	7	0.00139776	0.0045	0.0014	5008	,	,		17141	0.0		0.0	False		,,,				2504	0.0				p.G477R		Atlas-SNP	.											.	BCL6B	85	.	0			c.G1429A						PASS	.	G	ARG/GLY	15,3949		0,15,1967	49	54	53		1429	5.5	1	17		53	1,8327		0,1,4163	yes	missense	BCL6B	NM_181844.3	125	0,16,6130	AA,AG,GG		0.012,0.3784,0.1302	probably-damaging	477/480	6930927	16,12276	1982	4164	6146	SO:0001583	missense	255877	exon9			ATTCTCGGGGGGC	AI672318	CCDS42248.1	17p13.1	2014-06-10	2010-04-14		ENSG00000161940	ENSG00000161940		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	1002	protein-coding gene	gene with protein product		608992	"zinc finger protein 62", "B-cell CLL/lymphoma 6, member B (zinc finger protein)"	ZNF62		9632807	Standard	NM_181844		Approved	ZBTB28, BAZF	uc010clt.1	Q8N143	OTTHUMG00000177882	ENST00000293805.5:c.1429G>A	17.37:g.6930927G>A	ENSP00000293805:p.Gly477Arg	65	0	0		86	44	0.511628	NM_181844	Q6PCB4	Missense_Mutation	SNP	ENST00000293805.5	37	CCDS42248.1	.	.	.	.	.	.	.	.	.	.	G	14.52	2.560429	0.45590	0.003784	1.2E-4	ENSG00000161940	ENST00000293805	T	0.07114	3.22	5.47	5.47	0.80525	.	0.340325	0.32161	N	0.006486	T	0.08133	0.0203	L	0.29908	0.895	0.38463	D	0.94726	B	0.22541	0.071	B	0.14578	0.011	T	0.15636	-1.0430	10	0.51188	T	0.08	.	14.8178	0.70048	0.0:0.0:1.0:0.0	.	477	Q8N143	BCL6B_HUMAN	R	477	ENSP00000293805:G477R	ENSP00000293805:G477R	G	+	1	0	BCL6B	6871651	0.978000	0.34361	0.999000	0.59377	0.849000	0.48306	4.025000	0.57225	2.584000	0.87258	0.462000	0.41574	GGG	.	.	weak		0.627	BCL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439455.2	NM_181844		A	6930927	G	A	6930927	3	1	22	1	0	0	0	0	1	0	0	0	1377	1116	39	1	1459	1	BCL6B	17	6930927	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1639801	6930927	74264283	3388	6289											
NEURL4	84461	hgsc.bcm.edu	37	chr17	7221454	7221454	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagctctttagaggactagcGgcaggtggtggaccccagca	9	7	14	11	1	1	1	0	0	1	1	1	3	1	3	2	5	3	3	2	5	2	3	rs73239601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7221454G>A	ENST00000399464.2	-	25	4005	c.3990C>T	c.(3988-3990)gcC>gcT	p.A1330A	RP11-542C16.2_ENST00000575474.1_Missense_Mutation_p.P144L|NEURL4_ENST00000574120.1_5'UTR|GPS2_ENST00000389167.5_5'Flank|GPS2_ENST00000380728.2_5'Flank|NEURL4_ENST00000315614.7_Silent_p.A1328A|NEURL4_ENST00000570460.1_Silent_p.A1306A|GPS2_ENST00000391950.3_5'Flank	NM_032442.2	NP_115818.2	Q96JN8	NEUL4_HUMAN	neuralized E3 ubiquitin protein ligase 4	1330						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						GAGGACTAGCGGCAGGTGGTG	0.592													G|||	5	0.000998403	0.0038	0.0	5008	,	,		18299	0.0		0.0	False		,,,				2504	0.0				p.A1330A		Atlas-SNP	.											.	NEURL4	192	.	0			c.C3990T						PASS	.	G	,	22,4102		0,22,2040	82	93	89		3984,3990	1.4	0.1	17	dbSNP_130	89	1,8389		0,1,4194	no	coding-synonymous,coding-synonymous	NEURL4	NM_001005408.1,NM_032442.2	,	0,23,6234	AA,AG,GG		0.0119,0.5335,0.1838	,	1328/1561,1330/1563	7221454	23,12491	2062	4195	6257	SO:0001819	synonymous_variant	84461	exon25			ACTAGCGGCAGGT		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.3990C>T	17.37:g.7221454G>A		97	0	0		87	43	0.494253	NM_032442	Q6GPI8|Q96IU9|Q9H0B0	Silent	SNP	ENST00000399464.2	37	CCDS42251.1																																																																																			G|0.999;A|0.001	0.001	strong		0.592	NEURL4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255434.2	NM_032442		A	7221454	G	A	7221454	2	1	22	1	0	0	0	0	0	0	0	1	10356	1103	39	1		1	NEURL4	17	7221454	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	290527	7221454	73973756	3389	6290											
NEURL4	84461	hgsc.bcm.edu	37	chr17	7226082	7226082	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgcagtgggaaggacttctcGgtggcagtgttgctggtcgc	5	11	17	8	2	1	0	0	0	1	0	3	2	1	2	0	5	2	4	0	5	1	2	rs116452797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7226082G>A	ENST00000399464.2	-	16	2712	c.2697C>T	c.(2695-2697)acC>acT	p.T899T	NEURL4_ENST00000315614.7_Silent_p.T897T|NEURL4_ENST00000570460.1_Silent_p.T875T	NM_032442.2	NP_115818.2	Q96JN8	NEUL4_HUMAN	neuralized E3 ubiquitin protein ligase 4	899						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						AGGACTTCTCGGTGGCAGTGT	0.622													G|||	2	0.000399361	0.0015	0.0	5008	,	,		21184	0.0		0.0	False		,,,				2504	0.0				p.T899T		Atlas-SNP	.											.	NEURL4	192	.	0			c.C2697T						PASS	.	G	,	6,4132		0,6,2063	159	171	167		2691,2697	-4.8	1	17	dbSNP_132	167	0,8428		0,0,4214	no	coding-synonymous,coding-synonymous	NEURL4	NM_001005408.1,NM_032442.2	,	0,6,6277	AA,AG,GG		0.0,0.145,0.0477	,	897/1561,899/1563	7226082	6,12560	2069	4214	6283	SO:0001819	synonymous_variant	84461	exon16			CTTCTCGGTGGCA		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.2697C>T	17.37:g.7226082G>A		72	0	0		100	52	0.52	NM_032442	Q6GPI8|Q96IU9|Q9H0B0	Silent	SNP	ENST00000399464.2	37	CCDS42251.1																																																																																			G|0.999;A|0.001	0.001	strong		0.622	NEURL4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255434.2	NM_032442		A	7226082	G	A	7226082	2	1	22	1	0	0	0	0	0	0	0	1	10356	1103	39	1		1	NEURL4	17	7226082	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4628	7226082	73969128	3390	6291											
SPEM1	374768	hgsc.bcm.edu	37	chr17	7324340	7324340	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcaccgccatcgccgtcgaGgctctcccacacgctgtgct	5	8	9	19	5	2	0	1	0	1	0	5	1	2	0	4	1	1	3	4	1	0	0	rs61741352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7324340G>A	ENST00000323675.3	+	3	371	c.346G>A	c.(346-348)Ggc>Agc	p.G116S	RP11-104H15.7_ENST00000575310.1_RNA	NM_199339.2	NP_955371.2	Q8N4L4	SPEM1_HUMAN	spermatid maturation 1	116					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)				TCGCCGTCGAGGCTCTCCCAC	0.602													G|||	229	0.0457268	0.1672	0.0115	5008	,	,		18927	0.0		0.0	False		,,,				2504	0.0				p.G116S		Atlas-SNP	.											.	SPEM1	41	.	0			c.G346A						PASS	.	G	SER/GLY	547,3757		37,473,1642	70	76	74		346	2.7	0	17	dbSNP_129	74	3,8483		0,3,4240	yes	missense	SPEM1	NM_199339.2	56	37,476,5882	AA,AG,GG		0.0354,12.7091,4.3002	possibly-damaging	116/310	7324340	550,12240	2152	4243	6395	SO:0001583	missense	374768	exon3			CGTCGAGGCTCTC	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.346G>A	17.37:g.7324340G>A	ENSP00000315554:p.Gly116Ser	134	0	0		165	74	0.448485	NM_199339		Missense_Mutation	SNP	ENST00000323675.3	37	CCDS42254.1	83	0.038003663003663	78	0.15853658536585366	5	0.013812154696132596	0	0.0	0	0.0	G	10.79	1.449713	0.26074	0.127091	3.54E-4	ENSG00000181323	ENST00000323383;ENST00000323675	.	.	.	4.7	2.67	0.31697	.	1.055190	0.07527	N	0.911526	T	0.00109	0.0003	L	0.32530	0.975	0.09310	N	1	B	0.32829	0.386	B	0.31101	0.124	T	0.12528	-1.0544	9	0.46703	T	0.11	-0.4131	6.202	0.20581	0.1006:0.1883:0.7111:0.0	rs61741352	116	Q8N4L4	SPEM1_HUMAN	S	65;116	.	ENSP00000315511:G65S	G	+	1	0	SPEM1	7265064	0.004000	0.15560	0.001000	0.08648	0.146000	0.21551	1.315000	0.33608	0.566000	0.29273	0.655000	0.94253	GGC	G|0.962;A|0.038	0.038	strong		0.602	SPEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440932.1	NM_199339		A	7324340	G	A	7324340	3	1	22	1	0	0	0	0	1	0	0	0	15052	1000	35	2	356	2	SPEM1	17	7324340	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	98258	7324340	73870870	3391	6292											
SPEM1	374768	hgsc.bcm.edu	37	chr17	7324588	7324588	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acaggcatatggtccgagctGggcctaagggcctatgtgta	9	9	14	9	1	0	0	0	0	0	0	1	1	1	0	3	4	1	3	3	4	4	4	rs78583740	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7324588G>A	ENST00000323675.3	+	3	619	c.594G>A	c.(592-594)ctG>ctA	p.L198L	RP11-104H15.7_ENST00000575310.1_RNA	NM_199339.2	NP_955371.2	Q8N4L4	SPEM1_HUMAN	spermatid maturation 1	198					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)				GGTCCGAGCTGGGCCTAAGGG	0.632													G|||	241	0.048123	0.1762	0.0115	5008	,	,		17257	0.0		0.0	False		,,,				2504	0.0				p.L198L		Atlas-SNP	.											.	SPEM1	41	.	0			c.G594A						PASS	.	G		512,3372		36,440,1466	50	55	53		594	4.8	0.5	17	dbSNP_132	53	3,8221		0,3,4109	no	coding-synonymous	SPEM1	NM_199339.2		36,443,5575	AA,AG,GG		0.0365,13.1823,4.2534		198/310	7324588	515,11593	1942	4112	6054	SO:0001819	synonymous_variant	374768	exon3			CGAGCTGGGCCTA	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.594G>A	17.37:g.7324588G>A		70	0	0		98	52	0.530612	NM_199339		Silent	SNP	ENST00000323675.3	37	CCDS42254.1																																																																																			G|0.961;A|0.039	0.039	strong		0.632	SPEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440932.1	NM_199339		A	7324588	G	A	7324588	2	1	22	1	0	0	0	0	0	0	0	1	15052	1335	47	2		2	SPEM1	17	7324588	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	248	7324588	73870622	3392	6293											
C17orf74	201243	hgsc.bcm.edu	37	chr17	7330437	7330437	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccttgggctacagctcccAggacccccgtgaggtgcggc	6	6	13	16	2	0	1	0	1	0	0	1	2	1	2	4	4	3	2	4	4	1	2	rs3892554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7330437A>G	ENST00000333870.3	+	3	1201	c.1127A>G	c.(1126-1128)cAg>cGg	p.Q376R	RP11-104H15.7_ENST00000575310.1_RNA|C17orf74_ENST00000574034.1_3'UTR	NM_175734.4	NP_783861.3	Q0P670	CQ074_HUMAN	chromosome 17 open reading frame 74	376			Q -> R (in dbSNP:rs3892554).			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)				TACAGCTCCCAGGACCCCCGT	0.677													G|||	275	0.0549121	0.1997	0.0144	5008	,	,		15995	0.0		0.001	False		,,,				2504	0.0				p.Q376R		Atlas-SNP	.											.	C17orf74	56	.	0			c.A1127G						PASS	.	G	ARG/GLN	610,3590		52,506,1542	26	33	31		1127	3.8	0.9	17	dbSNP_108	31	6,8406		0,6,4200	yes	missense	C17orf74	NM_175734.4	43	52,512,5742	GG,GA,AA		0.0713,14.5238,4.8842	benign	376/502	7330437	616,11996	2100	4206	6306	SO:0001583	missense	201243	exon3			GCTCCCAGGACCC	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.1127A>G	17.37:g.7330437A>G	ENSP00000328061:p.Gln376Arg	68	0	0		67	30	0.447761	NM_175734		Missense_Mutation	SNP	ENST00000333870.3	37	CCDS42255.1	94	0.04304029304029304	89	0.18089430894308944	5	0.013812154696132596	0	0.0	0	0.0	G	0.011	-1.711549	0.00712	0.145238	7.13E-4	ENSG00000184560	ENST00000333870	T	0.21734	1.99	4.81	3.84	0.44239	.	0.000000	0.40144	N	0.001179	T	0.00012	0.0000	N	0.02247	-0.625	0.09310	P	0.9999999828706	B	0.02656	0.0	B	0.01281	0.0	T	0.37776	-0.9691	9	0.02654	T	1	-11.9907	8.1233	0.30984	0.1913:0.0:0.8087:0.0	rs3892554;rs4069866;rs3892554	376	Q0P670	CQ074_HUMAN	R	376	ENSP00000328061:Q376R	ENSP00000328061:Q376R	Q	+	2	0	C17orf74	7271161	0.809000	0.29036	0.909000	0.35828	0.004000	0.04260	0.841000	0.27613	0.574000	0.29417	-1.383000	0.01170	CAG	A|0.955;G|0.045	0.045	strong		0.677	C17orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440933.2	NM_175734		G	7330437	A	G	7330437	3	3	22	1	0	0	0	0	1	0	0	0	1881	188	7	3	1137	3	C17orf74	17	7330437	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	5849	7330437	73864773	3393	6294											
TMEM102	284114	hgsc.bcm.edu	37	chr17	7339903	7339903	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctacgtcactgagcacgaggCgccggtgtctttggaaaaat	10	9	12	10	4	2	1	1	1	1	0	2	3	2	2	1	3	2	1	1	3	3	2	rs76805816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7339903C>G	ENST00000323206.1	+	3	878	c.605C>G	c.(604-606)gCg>gGg	p.A202G	FGF11_ENST00000293829.4_5'Flank|FGF11_ENST00000575235.1_5'Flank|RP11-104H15.9_ENST00000570444.1_RNA|RP11-104H15.8_ENST00000576615.1_RNA|RP11-104H15.7_ENST00000575310.1_RNA|RP11-104H15.10_ENST00000575331.1_RNA|TMEM102_ENST00000396568.1_Missense_Mutation_p.A202G	NM_178518.2	NP_848613.1	Q8N9M5	TM102_HUMAN	transmembrane protein 102	202					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)				GAGCACGAGGCGCCGGTGTCT	0.557													C|||	179	0.0357428	0.1286	0.0115	5008	,	,		18254	0.0		0.001	False		,,,				2504	0.0				p.A202G		Atlas-SNP	.											.	TMEM102	11	.	0			c.C605G						PASS	.	C	GLY/ALA	481,3925	224.3+/-240.5	32,417,1754	90	92	91		605	3.2	0	17	dbSNP_132	91	2,8598	2.2+/-6.3	0,2,4298	yes	missense	TMEM102	NM_178518.2	60	32,419,6052	GG,GC,CC		0.0233,10.9169,3.7137	possibly-damaging	202/509	7339903	483,12523	2203	4300	6503	SO:0001583	missense	284114	exon3			ACGAGGCGCCGGT	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.605C>G	17.37:g.7339903C>G	ENSP00000315387:p.Ala202Gly	89	0	0		131	62	0.473282	NM_178518	D3DTP8	Missense_Mutation	SNP	ENST00000323206.1	37	CCDS11104.1	64	0.029304029304029304	59	0.11991869918699187	5	0.013812154696132596	0	0.0	0	0.0	C	9.073	0.997424	0.19043	0.109169	2.33E-4	ENSG00000181284	ENST00000323206;ENST00000396568	T;T	0.44482	0.92;0.92	5.36	3.25	0.37280	.	1.011090	0.07935	N	0.978275	T	0.00384	0.0012	N	0.14661	0.345	0.09310	N	1	B	0.20887	0.049	B	0.20384	0.029	T	0.05162	-1.0902	10	0.49607	T	0.09	-0.6557	6.9622	0.24603	0.0:0.7316:0.1752:0.0931	.	202	Q8N9M5	TM102_HUMAN	G	202	ENSP00000315387:A202G;ENSP00000379815:A202G	ENSP00000315387:A202G	A	+	2	0	TMEM102	7280627	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	-0.442000	0.06871	1.399000	0.46721	0.655000	0.94253	GCG	C|0.967;G|0.033	0.033	strong		0.557	TMEM102-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256405.1	NM_178518		G	7339903	C	G	7339903	3	3	22	1	0	0	0	0	1	0	0	0	16032	768	27	4	611	4	TMEM102	17	7339903	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	9466	7339903	73855307	3394	6295											
ZBTB4	57659	hgsc.bcm.edu	37	chr17	7365289	7365289	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgcccttctgggttctctcAacccctgccctttccccttc	2	14	5	20	1	3	0	1	0	2	0	7	0	4	0	6	1	2	1	6	1	1	4	rs114898274	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7365289A>T	ENST00000311403.4	-	4	3351	c.3012T>A	c.(3010-3012)gtT>gtA	p.V1004V	ZBTB4_ENST00000380599.4_Silent_p.V1004V	NM_020899.3	NP_065950.2	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4	1004					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)		GGGTTCTCTCAACCCCTGCCC	0.617													A|||	41	0.0081869	0.0287	0.0043	5008	,	,		14891	0.0		0.0	False		,,,				2504	0.0				p.V1004V		Atlas-SNP	.											.	ZBTB4	163	.	0			c.T3012A						PASS	.	A	,	88,4318	74.1+/-112.3	1,86,2116	58	64	62		3012,3012	0.3	1	17	dbSNP_132	62	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous,coding-synonymous	ZBTB4	NM_001128833.1,NM_020899.3	,	1,92,6410	TT,TA,AA		0.0698,1.9973,0.7227	,	1004/1014,1004/1014	7365289	94,12912	2203	4300	6503	SO:0001819	synonymous_variant	57659	exon4			TCTCTCAACCCCT	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.3012T>A	17.37:g.7365289A>T		110	0	0		93	40	0.430108	NM_001128833	B3KVL6|Q7Z697|Q86XJ4|Q8N4V8	Silent	SNP	ENST00000311403.4	37	CCDS11107.1																																																																																			A|0.992;T|0.008	0.008	strong		0.617	ZBTB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226940.2	NM_020899		T	7365289	A	T	7365289	2	4	22	1	0	0	0	0	0	0	0	1	17556	117	5	5		5	ZBTB4	17	7365289	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	25386	7365289	73829921	3395	6296											
AMAC1L3	643664	hgsc.bcm.edu	37	chr17	7385661	7385661	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagcattggatgtgcctacAgtgcggttcaggtggtgccc	6	11	14	10	1	2	0	2	0	0	0	2	1	2	1	2	4	5	2	2	4	1	3	rs192630658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7385661A>G	ENST00000412468.2	+	2	473	c.358A>G	c.(358-360)Agt>Ggt	p.S120G	ZBTB4_ENST00000311403.4_Intron|ZBTB4_ENST00000380599.4_5'Flank|POLR2A_ENST00000322644.6_5'Flank|POLR2A_ENST00000572844.1_5'Flank	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	120	EamA 1.					integral component of membrane (GO:0016021)											ATGTGCCTACAGTGCGGTTCA	0.617													A|||	183	0.0365415	0.1309	0.013	5008	,	,		18822	0.0		0.001	False		,,,				2504	0.0				p.S120G		Atlas-SNP	.											.	.	.	.	0			c.A358G						PASS	.	A	GLY/SER,	467,3939	220.4+/-237.8	34,399,1770	139	139	139		358,	4.2	1	17		139	4,8596	3.7+/-12.6	0,4,4296	no	missense,intron	ZBTB4,SLC35G6	NM_001102614.1,NM_020899.3	56,	34,403,6066	GG,GA,AA		0.0465,10.5992,3.6214	possibly-damaging,	120/339,	7385661	471,12535	2203	4300	6503	SO:0001583	missense	643664	exon2			GCCTACAGTGCGG		CCDS45603.1	17p13.1	2013-05-22	2011-08-03	2011-08-03		ENSG00000259224		"Solute carriers"	31351	protein-coding gene	gene with protein product			"transmembrane protein 21B", "acyl-malonyl condensing enzyme 1-like 3"	TMEM21B, AMAC1L3			Standard	NM_001102614		Approved		uc010cmj.1	P0C7Q6		ENST00000412468.2:c.358A>G	17.37:g.7385661A>G	ENSP00000396523:p.Ser120Gly	214	1	0.0046729		220	119	0.540909	NM_001102614		Missense_Mutation	SNP	ENST00000412468.2	37	CCDS45603.1	63	0.028846153846153848	57	0.11585365853658537	5	0.013812154696132596	1	0.0017482517482517483	0	0.0	A	14.87	2.665416	0.47677	0.105992	4.65E-4	ENSG00000181222	ENST00000412468	T	0.52057	0.68	4.19	4.19	0.49359	.	.	.	.	.	T	0.00524	0.0017	N	0.24115	0.695	0.43740	D	0.996233	B	0.27286	0.174	B	0.33846	0.171	T	0.01925	-1.1246	9	0.27082	T	0.32	-4.3505	12.5602	0.56277	1.0:0.0:0.0:0.0	.	120	P0C7Q6	S35G6_HUMAN	G	120	ENSP00000396523:S120G	ENSP00000396523:S120G	S	+	1	0	SLC35G6	7326385	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	4.149000	0.58091	1.671000	0.50874	0.460000	0.39030	AGT	A|0.977;G|0.023	0.023	strong		0.617	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614		G	7385661	A	G	7385661	3	3	22	1	0	0	0	0	1	0	0	0	561	188	7	3	364	3	AMAC1L3	17	7385661	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	20372	7385661	73809549	3396	6297											
AMAC1L3	643664	hgsc.bcm.edu	37	chr17	7385774	7385774	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agccagggtctcagtggctaCgactggtgtggactgttggg	6	10	17	8	1	1	0	1	0	1	0	2	2	1	1	1	5	2	2	1	5	1	2	rs201649944	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7385774C>T	ENST00000412468.2	+	2	586	c.471C>T	c.(469-471)taC>taT	p.Y157Y	ZBTB4_ENST00000311403.4_Intron|ZBTB4_ENST00000380599.4_5'Flank|POLR2A_ENST00000322644.6_5'Flank|POLR2A_ENST00000572844.1_5'Flank	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	157	EamA 1.					integral component of membrane (GO:0016021)											TCAGTGGCTACGACTGGTGTG	0.602													c|||	3	0.000599042	0.0023	0.0	5008	,	,		20504	0.0		0.0	False		,,,				2504	0.0				p.Y157Y		Atlas-SNP	.											.	.	.	.	0			c.C471T						PASS	.	T	,	8,4398	14.3+/-33.2	0,8,2195	182	174	176		471,	-5.2	0.9	17		176	0,8600		0,0,4300	no	coding-synonymous,intron	ZBTB4,SLC35G6	NM_001102614.1,NM_020899.3	,	0,8,6495	TT,TC,CC		0.0,0.1816,0.0615	,	157/339,	7385774	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	643664	exon2			TGGCTACGACTGG		CCDS45603.1	17p13.1	2013-05-22	2011-08-03	2011-08-03		ENSG00000259224		"Solute carriers"	31351	protein-coding gene	gene with protein product			"transmembrane protein 21B", "acyl-malonyl condensing enzyme 1-like 3"	TMEM21B, AMAC1L3			Standard	NM_001102614		Approved		uc010cmj.1	P0C7Q6		ENST00000412468.2:c.471C>T	17.37:g.7385774C>T		235	1	0.00425532		235	120	0.510638	NM_001102614		Silent	SNP	ENST00000412468.2	37	CCDS45603.1																																																																																			C|0.999;T|0.001	0.001	weak		0.602	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614		T	7385774	C	T	7385774	2	4	22	1	0	0	0	0	0	0	0	1	561	547	19	1		1	AMAC1L3	17	7385774	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	113	7385774	73809436	3397	6298											
POLR2A	5430	hgsc.bcm.edu	37	chr17	7412349	7412349	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaccccaacccccagagcacGgtggtggcagaggatcagga	11	3	14	13	1	1	2	1	0	0	2	1	5	1	4	4	5	2	2	4	5	1	0	rs2228134	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7412349G>A	ENST00000322644.6	+	21	3951	c.3552G>A	c.(3550-3552)acG>acA	p.T1184T		NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	1184					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)				CCCAGAGCACGGTGGTGGCAG	0.547													G|||	380	0.0758786	0.2655	0.0288	5008	,	,		17738	0.0		0.001	False		,,,				2504	0.0082				p.T1184T		Atlas-SNP	.											POLR2A,colon,carcinoma,+1,1	POLR2A	157	1	0			c.G3552A						PASS	.	G		993,3413	370.3+/-319.5	115,763,1325	141	108	119		3552	-11	0	17	dbSNP_98	119	13,8587	9.1+/-34.3	0,13,4287	no	coding-synonymous	POLR2A	NM_000937.4		115,776,5612	AA,AG,GG		0.1512,22.5374,7.7349		1184/1971	7412349	1006,12000	2203	4300	6503	SO:0001819	synonymous_variant	5430	exon21			GAGCACGGTGGTG			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.3552G>A	17.37:g.7412349G>A		262	1	0.00381679		251	135	0.537849	NM_000937	A6NN93|B9EH88|Q6NX41	Silent	SNP	ENST00000322644.6	37	CCDS32548.1																																																																																			G|0.935;A|0.065	0.065	strong		0.547	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937		A	7412349	G	A	7412349	2	1	22	1	0	0	0	0	0	0	0	1	12223	1103	39	1		1	POLR2A	17	7412349	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	26575	7412349	73782861	3398	6299											
TNFSF12	8742	hgsc.bcm.edu	37	chr17	7460514	7460514	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggaattctcagccactgcGgcgagttccctcgggcccca	7	7	12	15	3	1	0	1	0	1	0	4	3	2	1	4	3	2	1	4	3	1	2	rs143039184	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7460514G>A	ENST00000293825.6	+	7	860	c.597G>A	c.(595-597)gcG>gcA	p.A199A	TNFSF13_ENST00000380535.4_5'Flank|TNFSF13_ENST00000396542.1_5'Flank|TNFSF12-TNFSF13_ENST00000293826.4_Intron|TNFSF12_ENST00000462811.1_3'UTR|TNFSF13_ENST00000396545.4_5'Flank|TNFSF13_ENST00000483039.1_5'Flank|TNFSF13_ENST00000338784.4_5'Flank|TNFSF12_ENST00000557233.1_Intron|TNFSF13_ENST00000349228.4_5'Flank	NM_003809.2	NP_003800.1	O43508	TNF12_HUMAN	tumor necrosis factor (ligand) superfamily, member 12	199					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|endothelial cell migration (GO:0043542)|immune response (GO:0006955)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	cytokine activity (GO:0005125)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|large_intestine(5)|prostate(2)	11		Prostate(122;0.157)				CAGCCACTGCGGCGAGTTCCC	0.667													G|||	7	0.00139776	0.003	0.0043	5008	,	,		13746	0.0		0.0	False		,,,				2504	0.0				p.A199A		Atlas-SNP	.											.	TNFSF12	20	.	0			c.G597A						PASS	.	G	,	14,4392	21.2+/-45.6	0,14,2189	83	65	71		597,	-7.7	0	17	dbSNP_134	71	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,intron	TNFSF12,TNFSF12-TNFSF13	NM_003809.2,NM_172089.3	,	0,18,6485	AA,AG,GG		0.0465,0.3177,0.1384	,	199/250,	7460514	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	8742	exon7			CACTGCGGCGAGT	AF030099	CCDS11109.1	17p13.1	2008-02-01			ENSG00000239697	ENSG00000239697		"Tumor necrosis factor (ligand) superfamily"	11927	protein-coding gene	gene with protein product		602695				9405449, 9560343	Standard	NM_003809		Approved	TWEAK, DR3LG, APO3L		O43508	OTTHUMG00000108148	ENST00000293825.6:c.597G>A	17.37:g.7460514G>A		87	0	0		84	45	0.535714	NM_003809	Q8IZK7|Q8WUZ7	Silent	SNP	ENST00000293825.6	37	CCDS11109.1																																																																																			G|0.999;A|0.001	0.001	strong		0.667	TNFSF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226951.2	NM_003809		A	7460514	G	A	7460514	2	1	22	1	0	0	0	0	0	0	0	1	16318	1103	39	1		1	TNFSF12	17	7460514	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	48165	7460514	73734696	3399	6300											
DNAH2	146754	hgsc.bcm.edu	37	chr17	7722048	7722048	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcactggtcatcaacatcGcggctggtaaaaggaagctc	12	8	10	11	2	3	0	3	0	0	0	5	1	3	1	0	4	2	3	0	4	4	1	rs61743907	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7722048G>A	ENST00000572933.1	+	70	12084	c.10624G>A	c.(10624-10626)Gcg>Acg	p.A3542T	DNAH2_ENST00000389173.2_Missense_Mutation_p.A3542T			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	3542	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)				CATCAACATCGCGGCTGGTAA	0.642													G|||	52	0.0103834	0.0363	0.0058	5008	,	,		20147	0.0		0.0	False		,,,				2504	0.0				p.A3542T		Atlas-SNP	.											.	DNAH2	498	.	0			c.G10624A						PASS	.	G	THR/ALA	146,4260	102.5+/-141.1	2,142,2059	119	107	111		10624	3.4	0.1	17	dbSNP_129	111	0,8600		0,0,4300	yes	missense	DNAH2	NM_020877.2	58	2,142,6359	AA,AG,GG		0.0,3.3137,1.1226	probably-damaging	3542/4428	7722048	146,12860	2203	4300	6503	SO:0001583	missense	146754	exon69			AACATCGCGGCTG	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.10624G>A	17.37:g.7722048G>A	ENSP00000458355:p.Ala3542Thr	92	0	0		101	50	0.49505	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	CCDS32551.1	16	0.007326007326007326	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	0	0.0	G	21.0	4.082529	0.76528	0.033137	0.0	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.22134	1.97	4.34	3.38	0.38709	.	0.000000	0.85682	D	0.000000	T	0.09468	0.0233	M	0.65498	2.005	0.80722	D	1	P;P	0.42735	0.749;0.788	B;P	0.44422	0.321;0.449	T	0.01702	-1.1292	10	0.22706	T	0.39	.	11.1468	0.48434	0.0914:0.0:0.9086:0.0	rs61743907	3503;3542	Q9P225-2;Q9P225	.;DYH2_HUMAN	T	3503;3542	ENSP00000373825:A3542T	ENSP00000353818:A3503T	A	+	1	0	DNAH2	7662773	1.000000	0.71417	0.117000	0.21633	0.933000	0.57130	5.115000	0.64655	1.045000	0.40225	0.563000	0.77884	GCG	G|0.989;A|0.011	0.011	strong		0.642	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		A	7722048	G	A	7722048	3	1	22	1	0	0	0	0	1	0	0	0	4604	1087	38	1	10898	1	DNAH2	17	7722048	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	261534	7722048	73473162	3400	6301											
CHD3	1107	hgsc.bcm.edu	37	chr17	7792326	7792326	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctcctgtgtgatgaaggCggcagacactgtgatcctgt	7	13	12	9	1	1	4	0	3	1	1	3	4	2	4	2	2	0	1	2	2	1	1	rs931543	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7792326C>T	ENST00000330494.7	+	1	158	c.8C>T	c.(7-9)gCg>gTg	p.A3V	CHD3_ENST00000380358.4_Intron|CHD3_ENST00000358181.4_Missense_Mutation_p.A3V	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	3			A -> V (in dbSNP:rs931543).		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)				GTGATGAAGGCGGCAGACACT	0.468													T|||	392	0.0782748	0.2179	0.062	5008	,	,		18301	0.0278		0.0239	False		,,,				2504	0.0092				p.A3V		Atlas-SNP	.											.	CHD3	169	.	0			c.C8T						PASS	.	T	,VAL/ALA,VAL/ALA	865,3541		76,713,1414	151	155	154		,8,8	1.3	0.4	17	dbSNP_86	154	223,8377		4,215,4081	yes	intron,missense,missense	CHD3	NM_001005271.2,NM_001005273.2,NM_005852.3	,64,64	80,928,5495	TT,TC,CC		2.593,19.6323,8.3654	,,	,3/2001,3/1967	7792326	1088,11918	2203	4300	6503	SO:0001583	missense	1107	exon1			TGAAGGCGGCAGA	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.8C>T	17.37:g.7792326C>T	ENSP00000332628:p.Ala3Val	102	0	0		100	47	0.47	NM_001005273	D3DTQ9|E9PG89|Q9Y4I0	Missense_Mutation	SNP	ENST00000330494.7	37	CCDS32554.1	167	0.07646520146520147	105	0.21341463414634146	21	0.058011049723756904	23	0.04020979020979021	18	0.023746701846965697	N	14.54	2.564799	0.45694	0.196323	0.02593	ENSG00000170004	ENST00000358181;ENST00000330494	D;D	0.89552	-2.53;-2.53	3.7	1.29	0.21616	.	.	.	.	.	T	0.00144	0.0004	N	0.08118	0	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.03394	-1.1041	8	0.16896	T	0.51	.	5.2159	0.15342	0.3615:0.5187:0.1197:0.0	rs931543;rs58342197;rs931543	3;3	Q12873-2;Q12873	.;CHD3_HUMAN	V	3	ENSP00000350907:A3V;ENSP00000332628:A3V	ENSP00000332628:A3V	A	+	2	0	CHD3	7733051	0.033000	0.19621	0.446000	0.26920	0.797000	0.45037	0.104000	0.15313	0.096000	0.17463	-0.398000	0.06409	GCG	C|0.915;T|0.085	0.085	strong		0.468	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273		T	7792326	C	T	7792326	3	4	22	1	0	0	0	0	1	0	0	0	3328	768	27	1	291	1	CHD3	17	7792326	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	70278	7792326	73402884	3401	6302											
ALOX15B	247	hgsc.bcm.edu	37	chr17	7942785	7942785	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	acaaggcgcccccagtgctgCccctgctggggcccctggcc	4	5	13	19	1	0	0	0	0	0	0	0	0	0	0	7	4	3	2	7	4	1	0	rs78230493	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7942785C>G	ENST00000380183.4	+	2	368	c.229C>G	c.(229-231)Ccc>Gcc	p.P77A	ALOX15B_ENST00000380173.2_Missense_Mutation_p.P77A|ALOX15B_ENST00000572022.1_Missense_Mutation_p.P77A|ALOX15B_ENST00000573359.1_Missense_Mutation_p.P77A	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	77	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				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						CCCAGTGCTGCCCCTGCTGGG	0.692													C|||	175	0.0349441	0.1241	0.0144	5008	,	,		9830	0.0		0.001	False		,,,				2504	0.0				p.P77A		Atlas-SNP	.											.	ALOX15B	66	.	0			c.C229G						PASS	.	C	ALA/PRO,ALA/PRO,ALA/PRO	282,4080		13,256,1912	8	9	9		229,229,229	-0.4	0	17	dbSNP_131	9	3,8557		0,3,4277	no	missense,missense,missense	ALOX15B	NM_001039130.1,NM_001039131.1,NM_001141.2	27,27,27	13,259,6189	GG,GC,CC		0.035,6.4649,2.2055	possibly-damaging,possibly-damaging,possibly-damaging	77/648,77/603,77/677	7942785	285,12637	2181	4280	6461	SO:0001583	missense	247	exon2			GTGCTGCCCCTGC	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.229C>G	17.37:g.7942785C>G	ENSP00000369530:p.Pro77Ala	29	0	0		22	15	0.681818	NM_001141	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Missense_Mutation	SNP	ENST00000380183.4	37	CCDS11128.1	69	0.03159340659340659	64	0.13008130081300814	5	0.013812154696132596	0	0.0	0	0.0	C	10.09	1.253985	0.22965	0.064649	3.5E-4	ENSG00000179593	ENST00000380173;ENST00000339694;ENST00000380183	T;T	0.20738	2.05;2.05	4.15	-0.36	0.12568	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	2.042930	0.02987	N	0.146355	T	0.00144	0.0004	N	0.08118	0	0.09310	N	1	B;B;B;B	0.22800	0.075;0.061;0.061;0.075	B;B;B;B	0.29524	0.071;0.043;0.043;0.103	T	0.31806	-0.9930	10	0.40728	T	0.16	-4.4415	7.6122	0.28137	0.0:0.6248:0.0:0.3752	.	77;77;77;77	B4DNW8;O15296-2;O15296-4;O15296	.;.;.;LX15B_HUMAN	A	77	ENSP00000369520:P77A;ENSP00000369530:P77A	ENSP00000344337:P77A	P	+	1	0	ALOX15B	7883510	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-0.527000	0.06200	-0.237000	0.09739	0.591000	0.81541	CCC	C|0.966;G|0.034	0.034	strong		0.692	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2			G	7942785	C	G	7942785	3	3	22	1	0	0	0	0	1	0	0	0	539	739	26	4	235	4	ALOX15B	17	7942785	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	150459	7942785	73252425	3402	6303											
C17orf68	80169	hgsc.bcm.edu	37	chr17	8135446	8135446	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggtggggtccctctgggccGgtgggatctgtctgaggtgt	3	11	19	8	1	3	1	0	1	3	0	4	2	4	2	2	7	0	0	2	7	0	0	rs3027235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:8135446G>A	ENST00000315684.8	-	13	2167	c.2160C>T	c.(2158-2160)acC>acT	p.T720T		NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	720					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						CCTCTGGGCCGGTGGGATCTG	0.577													G|||	217	0.0433307	0.087	0.1009	5008	,	,		17092	0.0099		0.0139	False		,,,				2504	0.0082				p.T720T		Atlas-SNP	.											.	CTC1	75	.	0			c.C2160T						PASS	.	G		260,3684		9,242,1721	21	22	22		2160	2.3	0	17	dbSNP_102	22	124,8160		3,118,4021	no	coding-synonymous	CTC1	NM_025099.5		12,360,5742	AA,AG,GG		1.4969,6.5923,3.1403		720/1218	8135446	384,11844	1972	4142	6114	SO:0001819	synonymous_variant	80169	exon13			TGGGCCGGTGGGA	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.2160C>T	17.37:g.8135446G>A		53	0	0		92	41	0.445652	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Silent	SNP	ENST00000315684.8	37	CCDS42259.1																																																																																			G|0.964;A|0.036	0.036	strong		0.577	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099		A	8135446	G	A	8135446	2	1	22	1	0	0	0	0	0	0	0	1	1878	1103	39	1		1	C17orf68	17	8135446	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	192661	8135446	73059764	3403	6304											
C17orf68	80169	hgsc.bcm.edu	37	chr17	8141779	8141779	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcactcttgttccaagtcTgccgataggtctgttagtgt	6	15	10	10	1	3	0	0	0	3	0	4	1	4	0	2	1	2	3	2	1	3	4	rs73244859	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:8141779T>C	ENST00000315684.8	-	3	373	c.366A>G	c.(364-366)gcA>gcG	p.A122A	CTC1_ENST00000581671.1_5'UTR	NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	122					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						GTTCCAAGTCTGCCGATAGGT	0.547													C|||	111	0.0221645	0.0787	0.0	5008	,	,		19305	0.003		0.001	False		,,,				2504	0.0031				p.A122A		Atlas-SNP	.											.	CTC1	75	.	0			c.A366G						PASS	.	C		248,3754		8,232,1761	125	125	125		366	1.5	0	17	dbSNP_130	125	0,8334		0,0,4167	no	coding-synonymous	CTC1	NM_025099.5		8,232,5928	CC,CT,TT		0.0,6.1969,2.0104		122/1218	8141779	248,12088	2001	4167	6168	SO:0001819	synonymous_variant	80169	exon3			CAAGTCTGCCGAT	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.366A>G	17.37:g.8141779T>C		208	0	0		201	102	0.507463	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Silent	SNP	ENST00000315684.8	37	CCDS42259.1																																																																																			T|0.984;C|0.016	0.016	strong		0.547	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099		C	8141779	T	C	8141779	2	2	22	1	0	0	0	0	0	0	0	1	1878	1567	55	3		3	C17orf68	17	8141779	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	6333	8141779	73053431	3404	6305											
PFAS	5198	hgsc.bcm.edu	37	chr17	8172141	8172141	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctgcgagggatggagggcGccgtgctgcccgtgtggagt	4	8	20	9	4	0	0	0	0	0	0	0	4	0	3	2	4	4	2	2	4	0	0	rs73975814	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:8172141G>A	ENST00000314666.6	+	27	3806	c.3673G>A	c.(3673-3675)Gcc>Acc	p.A1225T	PFAS_ENST00000545834.1_Missense_Mutation_p.A801T	NM_012393.2	NP_036525.1	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	1225	Glutamine amidotransferase type-1.				'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)	GATGGAGGGCGCCGTGCTGCC	0.697													G|||	46	0.0091853	0.0333	0.0	5008	,	,		14129	0.001		0.0	False		,,,				2504	0.001				p.A1225T		Atlas-SNP	.											.	PFAS	91	.	0			c.G3673A						PASS	.	G	THR/ALA	73,4329		0,73,2128	33	37	36		3673	4.4	0	17	dbSNP_130	36	0,8592		0,0,4296	no	missense	PFAS	NM_012393.2	58	0,73,6424	AA,AG,GG		0.0,1.6583,0.5618	benign	1225/1339	8172141	73,12921	2201	4296	6497	SO:0001583	missense	5198	exon27			GAGGGCGCCGTGC	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.3673G>A	17.37:g.8172141G>A	ENSP00000313490:p.Ala1225Thr	17	0	0		18	10	0.555556	NM_012393	A6H8V8	Missense_Mutation	SNP	ENST00000314666.6	37	CCDS11136.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	13.30	2.195407	0.38806	0.016583	0.0	ENSG00000178921	ENST00000545834;ENST00000314666;ENST00000546020	T;T	0.29397	1.57;2.3	5.41	4.41	0.53225	Glutamine amidotransferase type 1 (1);	0.192639	0.45606	D	0.000358	T	0.08670	0.0215	N	0.10685	0.025	0.09310	N	1	B;B	0.30439	0.279;0.279	B;B	0.31390	0.129;0.129	T	0.14504	-1.0470	10	0.87932	D	0	-12.0495	10.9394	0.47264	0.0:0.0:0.6471:0.3529	.	1225;1225	A8K8N7;O15067	.;PUR4_HUMAN	T	801;1225;634	ENSP00000441706:A801T;ENSP00000313490:A1225T	ENSP00000313490:A1225T	A	+	1	0	PFAS	8112866	0.998000	0.40836	0.033000	0.17914	0.848000	0.48234	3.977000	0.56874	1.220000	0.43490	0.563000	0.77884	GCC	G|0.994;A|0.006	0.006	strong		0.697	PFAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226994.2			A	8172141	G	A	8172141	3	1	22	1	0	0	0	0	1	0	0	0	11763	1087	38	1	3775	1	PFAS	17	8172141	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	30362	8172141	73023069	3405	6306											
KRBA2	124751	hgsc.bcm.edu	37	chr17	8273246	8273246	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acacagagtcagatataagaCaataacttctttggtgacat	16	11	7	7	0	2	4	1	1	1	3	2	4	2	4	0	1	1	0	0	1	4	5			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:8273246C>T	ENST00000331336.2	-	2	690	c.685G>A	c.(685-687)Gtc>Atc	p.V229I	RP11-849F2.5_ENST00000583963.1_RNA|RP11-849F2.7_ENST00000582471.1_3'UTR|RP11-849F2.5_ENST00000580537.1_RNA|KRBA2_ENST00000396267.1_Missense_Mutation_p.V147I	NM_213597.2	NP_998762.1	Q6ZNG9	KRBA2_HUMAN	KRAB-A domain containing 2	229					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						AGATATAAGACAATAACTTCT	0.453																																					p.V229I		Atlas-SNP	.											.	KRBA2	34	.	0			c.G685A						PASS	.						126	121	123					17																	8273246		2203	4300	6503	SO:0001583	missense	124751	exon2			ATAAGACAATAAC	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.685G>A	17.37:g.8273246C>T	ENSP00000328017:p.Val229Ile	259	0	0		225	61	0.271111	NM_213597	Q8IYY0	Missense_Mutation	SNP	ENST00000331336.2	37	CCDS11141.1	.	.	.	.	.	.	.	.	.	.	C	12.40	1.926066	0.34002	.	.	ENSG00000184619	ENST00000396267;ENST00000331336	T;T	0.23348	1.93;1.91	2.64	2.64	0.31445	.	.	.	.	.	T	0.13329	0.0323	N	0.08118	0	0.22982	N	0.998471	B	0.23490	0.086	B	0.22601	0.04	T	0.15350	-1.0440	9	0.48119	T	0.1	.	8.9489	0.35776	0.0:1.0:0.0:0.0	.	229	Q6ZNG9	KRBA2_HUMAN	I	147;229	ENSP00000379565:V147I;ENSP00000328017:V229I	ENSP00000328017:V229I	V	-	1	0	KRBA2	8213971	0.997000	0.39634	1.000000	0.80357	0.992000	0.81027	1.587000	0.36622	1.804000	0.52760	0.650000	0.86243	GTC	.	.	none		0.453	KRBA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256338.1	NM_213597		T	8273246	C	T	8273246	3	4	22	1	0	0	0	0	1	0	0	0	8449	478	17	2	797	2	KRBA2	17	8273246	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	101105	8273246	72921964	3406	6307											
MFSD6L	162387	hgsc.bcm.edu	37	chr17	8701701	8701701	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acggaccccaaggagaggatAaaagtccgccgcaacgcctc	13	3	11	14	4	0	1	0	0	0	1	2	4	1	3	5	3	1	1	5	3	4	1	rs16957601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:8701701A>G	ENST00000329805.4	-	1	966	c.738T>C	c.(736-738)ttT>ttC	p.F246F		NM_152599.3	NP_689812.3	Q8IWD5	MFS6L_HUMAN	major facilitator superfamily domain containing 6-like	246						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(7)|skin(4)	17						AGGAGAGGATAAAAGTCCGCC	0.582													G|||	141	0.028155	0.1021	0.0072	5008	,	,		17572	0.0		0.001	False		,,,				2504	0.0				p.F246F		Atlas-SNP	.											.	MFSD6L	46	.	0			c.T738C						PASS	.	G		349,4057	788.5+/-414.9	14,321,1868	56	63	60		738	2.8	1	17	dbSNP_123	60	2,8598	812.0+/-407.1	0,2,4298	no	coding-synonymous	MFSD6L	NM_152599.3		14,323,6166	GG,GA,AA		0.0233,7.921,2.6988		246/587	8701701	351,12655	2203	4300	6503	SO:0001819	synonymous_variant	162387	exon1			GAGGATAAAAGTC	AK093092	CCDS11146.1	17p13.1	2014-05-30			ENSG00000185156	ENSG00000185156			26656	protein-coding gene	gene with protein product							Standard	NM_152599		Approved	FLJ35773	uc002glp.2	Q8IWD5	OTTHUMG00000178584	ENST00000329805.4:c.738T>C	17.37:g.8701701A>G		15	0	0		12	9	0.75	NM_152599	Q6YL34|Q8NA76	Silent	SNP	ENST00000329805.4	37	CCDS11146.1																																																																																			A|0.974;G|0.026	0.026	strong		0.582	MFSD6L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442554.1	NM_152599		G	8701701	A	G	8701701	2	3	22	1	0	0	0	0	0	0	0	1	9545	359	13	3		3	MFSD6L	17	8701701	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	428455	8701701	72493509	3407	6308											
MYH8	4626	hgsc.bcm.edu	37	chr17	10312792	10312792	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctttgaccaccttgggcttCtggaagttggcagacttgcc	6	12	11	12	0	1	2	0	1	1	1	1	3	1	3	4	3	1	3	4	3	1	5	rs73275411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:10312792C>T	ENST00000403437.2	-	16	1795	c.1701G>A	c.(1699-1701)caG>caA	p.Q567Q	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	567	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						CCTTGGGCTTCTGGAAGTTGG	0.517									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling				C|||	88	0.0175719	0.0666	0.0	5008	,	,		18938	0.0		0.0	False		,,,				2504	0.0				p.Q567Q		Atlas-SNP	.											.	MYH8	346	.	0			c.G1701A						PASS	.	C		288,4118	158.5+/-191.2	12,264,1927	119	118	118		1701	3.3	1	17	dbSNP_131	118	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MYH8	NM_002472.2		12,265,6226	TT,TC,CC		0.0116,6.5365,2.2221		567/1938	10312792	289,12717	2203	4300	6503	SO:0001819	synonymous_variant	4626	exon16	Familial Cancer Database	Carney Complex Variant	GGGCTTCTGGAAG		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.1701G>A	17.37:g.10312792C>T		316	0	0		251	134	0.533865	NM_002472	Q14910	Silent	SNP	ENST00000403437.2	37	CCDS11153.1																																																																																			C|0.976;T|0.024	0.024	strong		0.517	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472		T	10312792	C	T	10312792	2	4	22	1	0	0	0	0	0	0	0	1	10050	912	32	2		2	MYH8	17	10312792	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1611091	10312792	70882418	3408	6309											
MYH4	4622	hgsc.bcm.edu	37	chr17	10354747	10354747	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	taagctggtcctctagggtgCggcacattttctcaaagttt	8	14	10	9	1	2	0	1	0	2	0	4	0	3	0	1	3	2	3	1	3	3	5	rs200121484		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:10354747C>T	ENST00000255381.2	-	28	3871	c.3761G>A	c.(3760-3762)cGc>cAc	p.R1254H	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	1254					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)	p.R1254H(1)		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						CTCTAGGGTGCGGCACATTTT	0.418													C|||	1	0.000199681	0.0008	0.0	5008	,	,		11762	0.0		0.0	False		,,,				2504	0.0				p.R1254H		Atlas-SNP	.											MYH4,caecum,carcinoma,0,1	MYH4	349	1	1	Substitution - Missense(1)	large_intestine(1)	c.G3761A						PASS	.	C	HIS/ARG	5,4401	9.9+/-24.2	0,5,2198	159	139	146		3761	3.6	1	17		146	0,8600		0,0,4300	yes	missense	MYH4	NM_017533.2	29	0,5,6498	TT,TC,CC		0.0,0.1135,0.0384	probably-damaging	1254/1940	10354747	5,13001	2203	4300	6503	SO:0001583	missense	4622	exon28			AGGGTGCGGCACA		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.3761G>A	17.37:g.10354747C>T	ENSP00000255381:p.Arg1254His	198	0	0		202	99	0.490099	NM_017533		Missense_Mutation	SNP	ENST00000255381.2	37	CCDS11154.1	.	.	.	.	.	.	.	.	.	.	C	17.94	3.511257	0.64522	0.001135	0.0	ENSG00000141048	ENST00000255381	T	0.78924	-1.22	5.62	3.64	0.41730	Myosin tail (1);	0.000000	0.37219	U	0.002181	T	0.76300	0.3968	M	0.65975	2.015	0.44359	D	0.997257	B	0.18863	0.031	B	0.26770	0.073	T	0.73688	-0.3904	10	0.59425	D	0.04	.	12.8771	0.57996	0.0:0.8666:0.0:0.1334	.	1254	Q9Y623	MYH4_HUMAN	H	1254	ENSP00000255381:R1254H	ENSP00000255381:R1254H	R	-	2	0	MYH4	10295472	0.952000	0.32445	0.963000	0.40424	0.878000	0.50629	2.224000	0.42945	0.845000	0.35118	0.655000	0.94253	CGC	.	.	weak		0.418	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533		T	10354747	C	T	10354747	3	4	22	1	0	0	0	0	1	0	0	0	10046	768	27	1	2110	1	MYH4	17	10354747	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	41955	10354747	70840463	3409	6310											
MYH1	4619	hgsc.bcm.edu	37	chr17	10404766	10404766	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cgctgcttctctgctttggcCcgggaggcccgctctgcctc	1	11	12	17	3	2	0	0	0	2	0	4	1	2	1	3	3	3	4	3	3	0	2	rs61730793	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:10404766C>T	ENST00000226207.5	-	27	3493	c.3399G>A	c.(3397-3399)cgG>cgA	p.R1133R	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	1133					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						CTGCTTTGGCCCGGGAGGCCC	0.572													C|||	31	0.0061901	0.0227	0.0014	5008	,	,		16908	0.0		0.0	False		,,,				2504	0.0				p.R1133R		Atlas-SNP	.											.	MYH1	403	.	0			c.G3399A						PASS	.	C		90,4316		1,88,2114	40	45	44		3399	3.3	1	17	dbSNP_129	44	0,8588		0,0,4294	no	coding-synonymous	MYH1	NM_005963.3		1,88,6408	TT,TC,CC		0.0,2.0427,0.6926		1133/1940	10404766	90,12904	2203	4294	6497	SO:0001819	synonymous_variant	4619	exon27			TTTGGCCCGGGAG		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.3399G>A	17.37:g.10404766C>T		144	0	0		160	86	0.5375	NM_005963	Q14CA4|Q9Y622	Silent	SNP	ENST00000226207.5	37	CCDS11155.1																																																																																			C|0.994;T|0.006	0.006	strong		0.572	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		T	10404766	C	T	10404766	2	4	22	1	0	0	0	0	0	0	0	1	10038	610	22	2		2	MYH1	17	10404766	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	50019	10404766	70790444	3410	6311											
SCO1	6341	hgsc.bcm.edu	37	chr17	10595250	10595250	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtcaatgctgatgaaaagTggagttagatctggcagagt	12	10	15	4	0	2	4	1	2	1	2	2	5	2	5	0	3	1	3	0	3	4	1	rs2271228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:10595250T>C	ENST00000255390.5	-	4	654	c.594A>G	c.(592-594)ccA>ccG	p.P198P	SCO1_ENST00000577427.1_Silent_p.P167P|SCO1_ENST00000582053.1_5'Flank	NM_004589.2	NP_004580.1	O75880	SCO1_HUMAN	SCO1 cytochrome c oxidase assembly protein	198					cellular copper ion homeostasis (GO:0006878)|copper ion transport (GO:0006825)|generation of precursor metabolites and energy (GO:0006091)|respiratory chain complex IV assembly (GO:0008535)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|myofibril (GO:0030016)	copper ion binding (GO:0005507)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|urinary_tract(1)	10						TGATGAAAAGTGGAGTTAGAT	0.358													T|||	249	0.0497204	0.1679	0.0072	5008	,	,		21532	0.0169		0.003	False		,,,				2504	0.002				p.P198P	Melanoma(128;591 1731 19711 31891 44645)	Atlas-SNP	.											SCO1,NS,carcinoma,-1,1	SCO1	24	1	0			c.A594G						scavenged	.	T		567,3839	253.4+/-259.3	36,495,1672	112	109	110		594	-2.1	1	17	dbSNP_100	110	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	SCO1	NM_004589.2		36,500,5967	CC,CT,TT		0.0581,12.8688,4.398		198/302	10595250	572,12434	2203	4300	6503	SO:0001819	synonymous_variant	6341	exon4			GAAAAGTGGAGTT	AF026852	CCDS11158.1	17p13.1	2012-10-15	2012-10-15		ENSG00000133028	ENSG00000133028		"Mitochondrial respiratory chain complex assembly factors"	10603	protein-coding gene	gene with protein product		603644	"SCO (cytochrome oxidase deficient, yeast) homolog 1", "SCO cytochrome oxidase deficient homolog 1 (yeast)"	SCOD1		9878253	Standard	NM_004589		Approved		uc002gmr.4	O75880	OTTHUMG00000130364	ENST00000255390.5:c.594A>G	17.37:g.10595250T>C		124	1	0.00806452		143	59	0.412587	NM_004589	B2RDM0	Silent	SNP	ENST00000255390.5	37	CCDS11158.1																																																																																			T|0.961;C|0.039	0.039	strong		0.358	SCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252729.2	NM_004589		C	10595250	T	C	10595250	2	2	22	1	0	0	0	0	0	0	0	1	13946	1683	59	3		3	SCO1	17	10595250	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	190484	10595250	70599960	3411	6312											
SCO1	6341	hgsc.bcm.edu	37	chr17	10600653	10600653	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggttcccaggcaatagccagGgcgccccgaggcacgccacg	8	3	14	16	4	0	0	0	0	0	0	1	1	1	0	5	4	1	3	5	4	2	2	rs1802083	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:10600653G>A	ENST00000255390.5	-	1	232	c.172C>T	c.(172-174)Cct>Tct	p.P58S	SCO1_ENST00000577427.1_Missense_Mutation_p.P58S|ADPRM_ENST00000379774.4_5'Flank|SCO1_ENST00000582053.1_Intron	NM_004589.2	NP_004580.1	O75880	SCO1_HUMAN	SCO1 cytochrome c oxidase assembly protein	58			P -> S (in dbSNP:rs1802083).		cellular copper ion homeostasis (GO:0006878)|copper ion transport (GO:0006825)|generation of precursor metabolites and energy (GO:0006091)|respiratory chain complex IV assembly (GO:0008535)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|myofibril (GO:0030016)	copper ion binding (GO:0005507)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|urinary_tract(1)	10						CAATAGCCAGGGCGCCCCGAG	0.726													G|||	309	0.0617013	0.2216	0.0159	5008	,	,		10465	0.0		0.005	False		,,,				2504	0.0				p.P58S	Melanoma(128;591 1731 19711 31891 44645)	Atlas-SNP	.											.	SCO1	24	.	0			c.C172T						PASS	.	G	SER/PRO	629,3663		35,559,1552	6	7	7		172	1.7	0	17	dbSNP_89	7	11,8423		0,11,4206	no	missense	SCO1	NM_004589.2	74	35,570,5758	AA,AG,GG		0.1304,14.6552,5.0291	benign	58/302	10600653	640,12086	2146	4217	6363	SO:0001583	missense	6341	exon1			AGCCAGGGCGCCC	AF026852	CCDS11158.1	17p13.1	2012-10-15	2012-10-15		ENSG00000133028	ENSG00000133028		"Mitochondrial respiratory chain complex assembly factors"	10603	protein-coding gene	gene with protein product		603644	"SCO (cytochrome oxidase deficient, yeast) homolog 1", "SCO cytochrome oxidase deficient homolog 1 (yeast)"	SCOD1		9878253	Standard	NM_004589		Approved		uc002gmr.4	O75880	OTTHUMG00000130364	ENST00000255390.5:c.172C>T	17.37:g.10600653G>A	ENSP00000255390:p.Pro58Ser	29	0	0		43	21	0.488372	NM_004589	B2RDM0	Missense_Mutation	SNP	ENST00000255390.5	37	CCDS11158.1	110	0.05036630036630037	99	0.20121951219512196	9	0.024861878453038673	0	0.0	2	0.002638522427440633	G	10.34	1.324239	0.24080	0.146552	0.001304	ENSG00000133028	ENST00000255390;ENST00000396047	D	0.84873	-1.91	3.87	1.72	0.24424	.	0.533478	0.16696	N	0.203334	T	0.00178	0.0005	N	0.14661	0.345	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.03184	-1.1063	9	0.12430	T	0.62	-1.1139	10.6528	0.45657	0.0:0.4881:0.5119:0.0	rs1802083	58;58	A8MY34;O75880	.;SCO1_HUMAN	S	58	ENSP00000255390:P58S	ENSP00000255390:P58S	P	-	1	0	SCO1	10541378	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.044000	0.03532	0.504000	0.28082	-0.171000	0.13296	CCT	G|0.948;A|0.052	0.052	strong		0.726	SCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252729.2	NM_004589		A	10600653	G	A	10600653	3	1	22	1	0	0	0	0	1	0	0	0	13946	1232	43	2	757	2	SCO1	17	10600653	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5403	10600653	70594557	3412	6313											
DNAH9	1770	hgsc.bcm.edu	37	chr17	11532787	11532787	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgggaaaggtggagttcagCggcgtcagagggaatgctct	9	8	17	7	2	3	1	2	0	1	1	3	4	3	4	0	5	2	2	0	5	2	1	rs73290804	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11532787C>T	ENST00000262442.4	+	7	1472	c.1404C>T	c.(1402-1404)agC>agT	p.S468S	DNAH9_ENST00000454412.2_Silent_p.S468S	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	468	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)		TGGAGTTCAGCGGCGTCAGAG	0.478													C|||	100	0.0199681	0.0726	0.0043	5008	,	,		15848	0.001		0.0	False		,,,				2504	0.0				p.S468S		Atlas-SNP	.											.	DNAH9	695	.	0			c.C1404T						PASS	.	C		272,4134	155.2+/-188.4	10,252,1941	100	98	99		1404	-0.7	1	17	dbSNP_130	99	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	DNAH9	NM_001372.3		10,254,6239	TT,TC,CC		0.0233,6.1734,2.1067		468/4487	11532787	274,12732	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon7			GTTCAGCGGCGTC	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.1404C>T	17.37:g.11532787C>T		132	0	0		159	78	0.490566	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			C|0.978;T|0.022	0.022	strong		0.478	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11532787	C	T	11532787	2	4	22	1	0	0	0	0	0	0	0	1	4610	767	27	1		1	DNAH9	17	11532787	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	932134	11532787	69662423	3413	6314											
DNAH9	1770	hgsc.bcm.edu	37	chr17	11540079	11540079	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggatgatctacagtcagcaCgtccaggaggaagcagaact	14	6	12	9	1	2	2	1	1	1	1	3	5	3	5	1	3	4	2	1	3	3	1	rs8065057	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11540079C>T	ENST00000262442.4	+	9	1832	c.1764C>T	c.(1762-1764)caC>caT	p.H588H	DNAH9_ENST00000454412.2_Silent_p.H588H	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	588	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)		ACAGTCAGCACGTCCAGGAGG	0.438													T|||	54	0.0107827	0.0393	0.0029	5008	,	,		22057	0.0		0.0	False		,,,				2504	0.0				p.H588H		Atlas-SNP	.											.	DNAH9	695	.	0			c.C1764T						PASS	.	T		210,4196	807.3+/-415.9	3,204,1996	145	138	140		1764	-0.4	0.6	17	dbSNP_116	140	2,8598	819.2+/-406.8	0,2,4298	no	coding-synonymous	DNAH9	NM_001372.3		3,206,6294	TT,TC,CC		0.0233,4.7662,1.63		588/4487	11540079	212,12794	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon9			TCAGCACGTCCAG	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.1764C>T	17.37:g.11540079C>T		77	0	0		93	36	0.387097	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			C|0.984;T|0.016	0.016	strong		0.438	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11540079	C	T	11540079	2	4	22	1	0	0	0	0	0	0	0	1	4610	535	19	1		1	DNAH9	17	11540079	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	7292	11540079	69655131	3414	6315											
DNAH9	1770	hgsc.bcm.edu	37	chr17	11550413	11550413	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagacaagactttatgaggaTtggtgccggacagtatcaga	13	9	13	6	1	1	4	1	1	0	3	1	7	1	6	1	3	1	1	1	3	3	4	rs61745426	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11550413T>C	ENST00000262442.4	+	12	2063	c.1995T>C	c.(1993-1995)gaT>gaC	p.D665D	DNAH9_ENST00000454412.2_Silent_p.D665D	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	665	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)		TTTATGAGGATTGGTGCCGGA	0.488													T|||	59	0.0117812	0.0431	0.0029	5008	,	,		16804	0.0		0.0	False		,,,				2504	0.0				p.D665D		Atlas-SNP	.											.	DNAH9	695	.	0			c.T1995C						PASS	.	T		162,4244	110.8+/-149.0	6,150,2047	151	128	136		1995	-0.4	1	17	dbSNP_129	136	1,8599		0,1,4299	no	coding-synonymous	DNAH9	NM_001372.3		6,151,6346	CC,CT,TT		0.0116,3.6768,1.2533		665/4487	11550413	163,12843	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon12			TGAGGATTGGTGC	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.1995T>C	17.37:g.11550413T>C		129	0	0		131	59	0.450382	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			T|0.988;C|0.012	0.012	strong		0.488	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		C	11550413	T	C	11550413	2	2	22	1	0	0	0	0	0	0	0	1	4610	1490	52	3		3	DNAH9	17	11550413	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	10334	11550413	69644797	3415	6316											
DNAH9	1770	hgsc.bcm.edu	37	chr17	11583192	11583192	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accttatggctgttaaagaaCggcagagtaacactgatgag	14	9	11	7	1	0	4	0	2	0	2	0	4	0	4	1	2	2	4	1	2	5	3	rs8070501	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11583192C>T	ENST00000262442.4	+	18	3540	c.3472C>T	c.(3472-3474)Cgg>Tgg	p.R1158W	DNAH9_ENST00000454412.2_Missense_Mutation_p.R1158W	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	1158	Stem. {ECO:0000250}.		R -> W (in dbSNP:rs8070501).		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)		TGTTAAAGAACGGCAGAGTAA	0.408													C|||	57	0.0113818	0.0408	0.0029	5008	,	,		18781	0.001		0.0	False		,,,				2504	0.0				p.R1158W		Atlas-SNP	.											DNAH9,rectum,carcinoma,0,1	DNAH9	695	1	0			c.C3472T						PASS	.	C	TRP/ARG	164,4242	111.6+/-149.8	6,152,2045	136	129	132		3472	2.5	0.9	17	dbSNP_116	132	2,8598	1.2+/-3.3	0,2,4298	yes	missense	DNAH9	NM_001372.3	101	6,154,6343	TT,TC,CC		0.0233,3.7222,1.2763	probably-damaging	1158/4487	11583192	166,12840	2203	4300	6503	SO:0001583	missense	1770	exon18			AAAGAACGGCAGA	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.3472C>T	17.37:g.11583192C>T	ENSP00000262442:p.Arg1158Trp	90	0	0		99	50	0.50505	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	C	14.02	2.409862	0.42715	0.037222	2.33E-4	ENSG00000007174	ENST00000262442;ENST00000454412	T;T	0.25414	1.8;1.8	5.69	2.5	0.30297	.	0.257159	0.32343	N	0.006221	T	0.25717	0.0626	M	0.89840	3.065	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.60865	-0.7178	10	0.87932	D	0	.	16.2874	0.82727	0.6259:0.3741:0.0:0.0	rs8070501;rs52812603;rs56633662;rs8070501	1158	Q9NYC9	DYH9_HUMAN	W	1158	ENSP00000262442:R1158W;ENSP00000414874:R1158W	ENSP00000262442:R1158W	R	+	1	2	DNAH9	11523917	0.585000	0.26774	0.926000	0.36857	0.245000	0.25701	0.963000	0.29293	0.294000	0.22547	0.650000	0.86243	CGG	C|0.988;T|0.012	0.012	strong		0.408	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11583192	C	T	11583192	3	4	22	1	0	0	0	0	1	0	0	0	4610	527	19	1	3542	1	DNAH9	17	11583192	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	32779	11583192	69612018	3416	6317											
DNAH9	1770	hgsc.bcm.edu	37	chr17	11583245	11583245	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttaaagcagactattgaattGctgaagacctatgaacaaga	17	10	8	6	0	0	6	0	3	0	3	0	6	0	6	1	0	3	2	1	0	8	5	rs8070788	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11583245G>A	ENST00000262442.4	+	18	3593	c.3525G>A	c.(3523-3525)ttG>ttA	p.L1175L	DNAH9_ENST00000454412.2_Silent_p.L1175L	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	1175	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)		CTATTGAATTGCTGAAGACCT	0.398													G|||	56	0.0111821	0.0408	0.0029	5008	,	,		19789	0.0		0.0	False		,,,				2504	0.0				p.L1175L		Atlas-SNP	.											.	DNAH9	695	.	0			c.G3525A						PASS	.	G		163,4243	111.2+/-149.4	6,151,2046	115	110	112		3525	4.6	1	17	dbSNP_116	112	1,8599		0,1,4299	no	coding-synonymous	DNAH9	NM_001372.3		6,152,6345	AA,AG,GG		0.0116,3.6995,1.261		1175/4487	11583245	164,12842	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon18			TGAATTGCTGAAG	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.3525G>A	17.37:g.11583245G>A		82	0	0		80	37	0.4625	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			G|0.988;A|0.012	0.012	strong		0.398	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		A	11583245	G	A	11583245	2	1	22	1	0	0	0	0	0	0	0	1	4610	1310	46	2		2	DNAH9	17	11583245	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	53	11583245	69611965	3417	6318											
DNAH9	1770	hgsc.bcm.edu	37	chr17	11592928	11592928	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atgctggatgccaggcacatCgagatccagcagatggaatc	12	7	12	10	1	0	2	0	0	0	2	3	5	1	4	2	3	3	3	2	3	1	0	rs35922062	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11592928C>T	ENST00000262442.4	+	20	3857	c.3789C>T	c.(3787-3789)atC>atT	p.I1263I	DNAH9_ENST00000454412.2_Silent_p.I1263I	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	1263	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)		CCAGGCACATCGAGATCCAGC	0.493													c|||	58	0.0115815	0.0424	0.0029	5008	,	,		19643	0.0		0.0	False		,,,				2504	0.0				p.I1263I		Atlas-SNP	.											.	DNAH9	695	.	0			c.C3789T						PASS	.	T		164,4242	111.6+/-149.8	6,152,2045	115	106	109		3789	-11.2	0	17	dbSNP_126	109	1,8599		0,1,4299	no	coding-synonymous	DNAH9	NM_001372.3		6,153,6344	TT,TC,CC		0.0116,3.7222,1.2686		1263/4487	11592928	165,12841	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon20			GCACATCGAGATC	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.3789C>T	17.37:g.11592928C>T		75	0	0		88	46	0.522727	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			C|0.988;T|0.012	0.012	strong		0.493	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11592928	C	T	11592928	2	4	22	1	0	0	0	0	0	0	0	1	4610	874	31	1		1	DNAH9	17	11592928	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	9683	11592928	69602282	3418	6319											
DNAH9	1770	hgsc.bcm.edu	37	chr17	11622729	11622729	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcaggcacaggcaagacCgagaccaccaaggacctggg	12	2	13	14	1	0	2	0	0	0	2	0	4	0	3	5	4	1	3	5	4	2	0	rs61739488	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11622729C>T	ENST00000262442.4	+	27	5699	c.5631C>T	c.(5629-5631)acC>acT	p.T1877T	DNAH9_ENST00000454412.2_Silent_p.T1877T	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	1877	AAA 1. {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)		CAGGCAAGACCGAGACCACCA	0.607													c|||	256	0.0511182	0.1861	0.0115	5008	,	,		16870	0.0		0.001	False		,,,				2504	0.001				p.T1877T		Atlas-SNP	.											.	DNAH9	695	.	0			c.C5631T						PASS	.	G		706,3700	294.1+/-283.0	52,602,1549	92	79	83		5631	-10.4	0	17	dbSNP_129	83	7,8593	4.3+/-15.6	0,7,4293	no	coding-synonymous	DNAH9	NM_001372.3		52,609,5842	TT,TC,CC		0.0814,16.0236,5.4821		1877/4487	11622729	713,12293	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon27			CAAGACCGAGACC	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.5631C>T	17.37:g.11622729C>T		114	0	0		106	47	0.443396	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			C|0.950;T|0.050	0.050	strong		0.607	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11622729	C	T	11622729	2	4	22	1	0	0	0	0	0	0	0	1	4610	639	23	1		1	DNAH9	17	11622729	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	29801	11622729	69572481	3419	6320											
DNAH9	1770	hgsc.bcm.edu	37	chr17	11687721	11687721	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagctcggaaacttcccggcGtccctgcagaaatccatccc	10	7	8	16	3	0	1	0	0	0	1	5	2	4	2	4	2	3	2	4	2	3	1	rs16945337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11687721G>A	ENST00000262442.4	+	41	7994	c.7926G>A	c.(7924-7926)gcG>gcA	p.A2642A	DNAH9_ENST00000454412.2_Silent_p.A2642A	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2642	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)		ACTTCCCGGCGTCCCTGCAGA	0.542													G|||	239	0.0477236	0.0877	0.0058	5008	,	,		17425	0.002		0.0348	False		,,,				2504	0.0838				p.A2642A		Atlas-SNP	.											DNAH9,NS,carcinoma,+1,1	DNAH9	695	1	0			c.G7926A						PASS	.	G		358,4048	185.0+/-212.2	14,330,1859	177	169	172		7926	-2.6	0	17	dbSNP_123	172	195,8405	86.1+/-148.5	0,195,4105	no	coding-synonymous	DNAH9	NM_001372.3		14,525,5964	AA,AG,GG		2.2674,8.1253,4.2519		2642/4487	11687721	553,12453	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon41			CCCGGCGTCCCTG	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.7926G>A	17.37:g.11687721G>A		200	0	0		192	91	0.473958	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			G|0.956;A|0.044	0.044	strong		0.542	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		A	11687721	G	A	11687721	2	1	22	1	0	0	0	0	0	0	0	1	4610	1132	40	1		1	DNAH9	17	11687721	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	64992	11687721	69507489	3420	6321											
HS3ST3B1	9953	hgsc.bcm.edu	37	chr17	14248345	14248345	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgtttgcttgcgtttctcagGgacctgatgcccagaaccct	6	13	10	12	1	1	2	1	1	1	1	2	3	1	3	3	1	4	3	3	1	1	3	rs77608217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:14248345G>A	ENST00000360954.2	+	2	991	c.555G>A	c.(553-555)cgG>cgA	p.R185R		NM_006041.1	NP_006032.1	Q9Y662	HS3SB_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 3B1	185					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)|[heparan sulfate]-glucosamine 3-sulfotransferase 3 activity (GO:0033872)			large_intestine(3)|lung(3)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (92;0.0887)		CGTTTCTCAGGGACCTGATGC	0.577													G|||	17	0.00339457	0.0129	0.0	5008	,	,		17223	0.0		0.0	False		,,,				2504	0.0				p.R185R		Atlas-SNP	.											.	HS3ST3B1	19	.	0			c.G555A						PASS	.	G		70,4336	62.9+/-100.1	1,68,2134	61	63	63		555	2.6	1	17	dbSNP_131	63	0,8600		0,0,4300	yes	coding-synonymous-near-splice	HS3ST3B1	NM_006041.1		1,68,6434	AA,AG,GG		0.0,1.5887,0.5382		185/391	14248345	70,12936	2203	4300	6503	SO:0001630	splice_region_variant	9953	exon2			TCTCAGGGACCTG	AF105377	CCDS11167.1	17p12	2007-04-02			ENSG00000125430	ENSG00000125430	2.8.2.23	"Sulfotransferases, membrane-bound"	5198	protein-coding gene	gene with protein product		604058				9988767	Standard	NM_006041		Approved	3OST3B1, 30ST3B1	uc002goh.1	Q9Y662	OTTHUMG00000058810	ENST00000360954.2:c.555-1G>A	17.37:g.14248345G>A		241	0	0		290	148	0.510345	NM_006041	B3KN58|D3DTS6	Silent	SNP	ENST00000360954.2	37	CCDS11167.1																																																																																			G|0.995;A|0.005	0.005	strong		0.577	HS3ST3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129998.1	NM_006041	Silent	A	14248345	G	A	14248345	5	1	22	1	0	0	0	0	0	0	1	0	7375	1246	43	2	561	2	HS3ST3B1	17	14248345	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2560624	14248345	66946865	3421	6322											
TEKT3	64518	hgsc.bcm.edu	37	chr17	15217535	15217535	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttccagctcatgctgggaCgctctgttggctctgcaata	6	14	10	11	1	3	0	1	0	2	0	4	1	4	1	1	2	3	6	1	2	2	4	rs144456077	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:15217535C>T	ENST00000395930.1	-	6	933	c.747G>A	c.(745-747)gcG>gcA	p.A249A	TEKT3_ENST00000338696.2_Silent_p.A249A|RNU6-799P_ENST00000363567.1_RNA	NM_031898.2	NP_114104.1	Q9BXF9	TEKT3_HUMAN	tektin 3	249					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)		CATGCTGGGACGCTCTGTTGG	0.547													C|||	20	0.00399361	0.0151	0.0	5008	,	,		21690	0.0		0.0	False		,,,				2504	0.0				p.A249A		Atlas-SNP	.											TEKT3,NS,adenocarcinoma,0,1	TEKT3	64	1	0			c.G747A						PASS	.	C		47,4359	49.6+/-84.7	0,47,2156	174	111	132		747	-10.9	0	17	dbSNP_134	132	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	TEKT3	NM_031898.2		0,51,6452	TT,TC,CC		0.0465,1.0667,0.3921		249/491	15217535	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	64518	exon6			CTGGGACGCTCTG	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.747G>A	17.37:g.15217535C>T		286	0	0		312	159	0.509615	NM_031898	B2RAS7|D3DTT0|Q8N5R5|Q96M48	Silent	SNP	ENST00000395930.1	37	CCDS11169.1																																																																																			C|0.996;T|0.004	0.004	strong		0.547	TEKT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130385.2	NM_031898		T	15217535	C	T	15217535	2	4	22	1	0	0	0	0	0	0	0	1	15769	523	19	1		1	TEKT3	17	15217535	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	969190	15217535	65977675	3422	6323											
TRIM16	10626	hgsc.bcm.edu	37	chr17	15532430	15532430	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tagggatgctcccagggcgtGgtgttggtgaccttgcggtt	4	12	17	8	2	0	1	0	1	0	0	1	2	1	2	2	5	2	3	2	5	1	4	rs7225221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:15532430G>A	ENST00000578237.1	-	11	2049	c.1194C>T	c.(1192-1194)acC>acT	p.T398T	RP11-385D13.1_ENST00000455584.2_Silent_p.T398T|TRIM16_ENST00000416464.2_Silent_p.T268T|TRIM16_ENST00000579219.1_Missense_Mutation_p.P95L|TRIM16_ENST00000577886.1_Silent_p.T182T|TRIM16_ENST00000336708.7_Silent_p.T398T			O95361	TRI16_HUMAN	tripartite motif containing 16	398	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				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)		CCCAGGGCGTGGTGTTGGTGA	0.587													G|||	309	0.0617013	0.2269	0.0115	5008	,	,		19836	0.0		0.001	False		,,,				2504	0.0				p.T398T		Atlas-SNP	.											.	TRIM16	45	.	0			c.C1194T						PASS	.	G		746,3660		67,612,1524	44	42	43		1194	-1.7	0.8	17	dbSNP_116	43	5,8587		0,5,4291	no	coding-synonymous	TRIM16	NM_006470.3		67,617,5815	AA,AG,GG		0.0582,16.9315,5.7778		398/565	15532430	751,12247	2203	4296	6499	SO:0001819	synonymous_variant	10626	exon9			GGGCGTGGTGTTG	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.1194C>T	17.37:g.15532430G>A		269	0	0		324	142	0.438272	NM_006470	Q6IAL8|Q7Z6I2|Q96BE8|Q96J43	Silent	SNP	ENST00000578237.1	37	CCDS11171.1	87	0.03983516483516483	83	0.16869918699186992	4	0.011049723756906077	0	0.0	0	0.0	.	12.03	1.816778	0.32145	0.169315	5.82E-4	ENSG00000251537	ENST00000455584	.	.	.	4.53	-1.68	0.08212	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.9999999999999986	.	.	.	.	.	.	T	0.23726	-1.0180	3	.	.	.	.	5.0704	0.14604	0.0891:0.4085:0.378:0.1244	rs7225221	.	.	.	L	413	.	.	P	-	2	0	RP11-385D13.1	15473155	0.983000	0.35010	0.789000	0.31954	0.992000	0.81027	0.170000	0.16663	0.096000	0.17463	0.650000	0.86243	CCA	G|0.953;A|0.047	0.047	strong		0.587	TRIM16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130700.2	NM_006470		A	15532430	G	A	15532430	2	1	22	1	0	0	0	0	0	0	0	1	16506	1335	47	2		2	TRIM16	17	15532430	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	314895	15532430	65662780	3423	6324											
TRIM16	10626	hgsc.bcm.edu	37	chr17	15546132	15546133	+	Splice_Site	INS	-	-	A																															ggtgcactggagttcagcctINSaaaagtggaaagcagagaat																								rs577610193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:15546132_15546133insA	ENST00000578237.1	-	7	1375		c.e7-2		RP11-385D13.1_ENST00000455584.2_Splice_Site|TRIM16_ENST00000416464.2_Splice_Site|TRIM16_ENST00000579219.1_5'UTR|TRIM16_ENST00000577886.1_5'UTR|TRIM16_ENST00000336708.7_Splice_Site|TRIM16_ENST00000581224.1_Splice_Site			O95361	TRI16_HUMAN	tripartite motif containing 16						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)		GAGTTCAGCCTAAAAGTGGAAA	0.515													AAAAA|AAAA|AAAAA|deletion	377	0.0752796	0.2511	0.0173	5008	,	,		20717	0.0		0.0099	False		,,,				2504	0.0235				.		Atlas-Indel	.											.	TRIM16	45	.	0			c.520-2->T						PASS	.			457,1595		140,177,709						3.8	0.9			2	44,3468		15,14,1727	no	splice-3	TRIM16	NM_006470.3		155,191,2436	A1A1,A1R,RR		1.2528,22.271,9.0043				501,5063				SO:0001630	splice_region_variant	10626	exon6			.	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.520-2->T	17.37:g.15546136_15546136dupA		335	0	0		402	88	0.218905	NM_006470	Q6IAL8|Q7Z6I2|Q96BE8|Q96J43	Splice_Site	INS	ENST00000578237.1	37	CCDS11171.1																																																																																			.	.	none		0.515	TRIM16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130700.2	NM_006470	Intron	A	15546133	-	A	15546132	8	5	22	1	0	1	1	0	0	0	1	0	16506	1536	53	0	1196	0	TRIM16	17	15546132	Splice_Site	INS	-	TCGA-G8-6324-01A-11D-2210-10	13702	15546132	65649078	3424	6325											
ZNF286A	57335	hgsc.bcm.edu	37	chr17	15604508	15604508	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatttccaagagaagagcaCagaagagggagaagtggctg	15	5	14	7	0	0	5	0	0	0	5	1	7	1	5	2	2	1	2	2	2	4	1	rs144115902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:15604508C>G	ENST00000464847.2	+	2	633	c.80C>G	c.(79-81)aCa>aGa	p.T27R	ZNF286A_ENST00000395893.2_Missense_Mutation_p.T27R|ZNF286A_ENST00000580259.1_Missense_Mutation_p.T27R|ZNF286A_ENST00000472486.1_Missense_Mutation_p.T17R|ZNF286A_ENST00000585194.1_Missense_Mutation_p.T27R|ZNF286A_ENST00000581529.1_Missense_Mutation_p.T17R|ZNF286A_ENST00000421016.1_Missense_Mutation_p.T27R|ZNF286A_ENST00000585171.1_3'UTR|ZNF286A_ENST00000583566.1_Missense_Mutation_p.T27R|ZNF286A_ENST00000413242.2_Missense_Mutation_p.T27R|ZNF286A_ENST00000593105.1_Missense_Mutation_p.T17R|ZNF286A_ENST00000395894.2_Missense_Mutation_p.T27R			Q9HBT8	Z286A_HUMAN	zinc finger protein 286A	27					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)		GAGAAGAGCACAGAAGAGGGA	0.478													C|||	121	0.0241613	0.0855	0.0115	5008	,	,		21616	0.0		0.0	False		,,,				2504	0.0				p.T27R		Atlas-SNP	.											.	ZNF286A	58	.	0			c.C80G						PASS	.	C	ARG/THR,ARG/THR	334,4072		6,322,1875	220	201	207		80,80	4.3	0.8	17	dbSNP_134	207	4,8592		0,4,4294	no	missense,missense	ZNF286A	NM_001130842.1,NM_020652.2	71,71	6,326,6169	GG,GC,CC		0.0465,7.5806,2.5996	benign,benign	27/522,27/522	15604508	338,12664	2203	4298	6501	SO:0001583	missense	57335	exon3			AGAGCACAGAAGA	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.80C>G	17.37:g.15604508C>G	ENSP00000464218:p.Thr27Arg	263	0	0		222	110	0.495495	NM_020652	B4DKF9|Q96JF3	Missense_Mutation	SNP	ENST00000464847.2	37	CCDS11172.1	49	0.022435897435897436	41	0.08333333333333333	6	0.016574585635359115	0	0.0	2	0.002638522427440633	.	12.15	1.851494	0.32699	0.075806	4.65E-4	ENSG00000187607	ENST00000421016;ENST00000412988;ENST00000395894;ENST00000395893	T;T;T;T	0.07327	3.55;3.2;5.46;5.59	4.3	4.3	0.51218	.	1.408720	0.05359	N	0.533364	T	0.00384	0.0012	N	0.14661	0.345	0.26812	N	0.968979	B	0.19583	0.037	B	0.20955	0.032	T	0.25152	-1.0140	10	0.14252	T	0.57	-0.6478	12.9853	0.58588	0.0:1.0:0.0:0.0	.	27	Q9HBT8	Z286A_HUMAN	R	27;17;27;27	ENSP00000397163:T27R;ENSP00000408168:T17R;ENSP00000379231:T27R;ENSP00000379230:T27R	ENSP00000435872:T27R	T	+	2	0	ZNF286A	15545233	0.001000	0.12720	0.848000	0.33437	0.905000	0.53344	0.004000	0.13106	2.320000	0.78422	0.555000	0.69702	ACA	C|0.978;G|0.022	0.022	strong		0.478	ZNF286A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130696.4	NM_020652		G	15604508	C	G	15604508	3	3	22	1	0	0	0	0	1	0	0	0	17838	478	17	4	86	4	ZNF286A	17	15604508	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	58376	15604508	65590702	3425	6326											
NCOR1	9611	hgsc.bcm.edu	37	chr17	15968887	15968887	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgcaagttcacttgcatctgTtgtgaggtaatgtaatcatt	10	15	9	7	1	3	1	2	1	1	0	3	1	3	1	0	1	1	6	0	1	3	6	rs7210057	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:15968887T>C	ENST00000268712.3	-	33	5120	c.4863A>G	c.(4861-4863)caA>caG	p.Q1621Q	NCOR1_ENST00000395857.3_Silent_p.Q205Q|NCOR1_ENST00000395851.1_Silent_p.Q1637Q	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1621	Interaction with C1D. {ECO:0000250}.|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)		CTTGCATCTGTTGTGAGGTAA	0.483													T|||	96	0.0191693	0.0666	0.0115	5008	,	,		19833	0.0		0.0	False		,,,				2504	0.0				p.Q1637Q		Atlas-SNP	.											.	NCOR1	240	.	0			c.A4911G						PASS	.	T	,	229,4177	137.3+/-173.1	5,219,1979	192	167	175		4911,4863	0.8	1	17	dbSNP_116	175	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous	NCOR1	NM_001190440.1,NM_006311.3	,	5,222,6276	CC,CT,TT		0.0349,5.1975,1.7838	,	1637/2338,1621/2441	15968887	232,12774	2203	4300	6503	SO:0001819	synonymous_variant	9611	exon32			CATCTGTTGTGAG	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.4863A>G	17.37:g.15968887T>C		299	1	0.00334448		314	150	0.477707	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Silent	SNP	ENST00000268712.3	37	CCDS11175.1																																																																																			T|0.979;C|0.021	0.021	strong		0.483	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		C	15968887	T	C	15968887	2	2	22	1	0	0	0	0	0	0	0	1	10244	1722	60	3		3	NCOR1	17	15968887	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	364379	15968887	65226323	3426	6327											
NCOR1	9611	hgsc.bcm.edu	37	chr17	16001756	16001756	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggttttaacggagatgagacGagtatagatccagtggggtt	11	11	15	4	2	0	3	0	1	0	3	1	6	1	3	1	4	1	3	1	4	3	5	rs79413281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:16001756G>A	ENST00000268712.3	-	21	3002	c.2745C>T	c.(2743-2745)ctC>ctT	p.L915L	NCOR1_ENST00000395848.1_Silent_p.L822L|NCOR1_ENST00000395851.1_Silent_p.L931L|RNU6-314P_ENST00000516574.1_RNA	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	915					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)		GAGATGAGACGAGTATAGATC	0.378													a|||	109	0.0217652	0.0764	0.0115	5008	,	,		17847	0.0		0.0	False		,,,				2504	0.0				p.L931L		Atlas-SNP	.											.	NCOR1	240	.	0			c.C2793T						PASS	.	A	,,	262,4144	802.4+/-415.7	7,248,1948	87	87	87		2466,2793,2745	-5.2	0.8	17	dbSNP_132	87	4,8596	819.1+/-406.8	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	NCOR1	NM_001190438.1,NM_001190440.1,NM_006311.3	,,	7,252,6244	AA,AG,GG		0.0465,5.9464,2.0452	,,	822/915,931/2338,915/2441	16001756	266,12740	2203	4300	6503	SO:0001819	synonymous_variant	9611	exon20			TGAGACGAGTATA	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.2745C>T	17.37:g.16001756G>A		130	0	0		119	51	0.428571	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Silent	SNP	ENST00000268712.3	37	CCDS11175.1																																																																																			G|0.981;A|0.019	0.019	strong		0.378	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		A	16001756	G	A	16001756	2	1	22	1	0	0	0	0	0	0	0	1	10244	1045	37	1		1	NCOR1	17	16001756	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	32869	16001756	65193454	3427	6328											
TNFRSF13B	23495	hgsc.bcm.edu	37	chr17	16843708	16843708	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggagcagggatcccccctcTtcttgaggaagcaggccacc	9	6	12	14	0	2	1	0	1	2	0	3	4	3	4	5	4	2	2	5	4	1	2	rs74811083|rs376630110	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:16843708T>A	ENST00000261652.2	-	4	575	c.563A>T	c.(562-564)aAg>aTg	p.K188M	TNFRSF13B_ENST00000437538.2_Missense_Mutation_p.K142M|TNFRSF13B_ENST00000583789.1_Missense_Mutation_p.K142M|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	188					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						ATCCCCCCTCTTCTTGAGGAA	0.647									IgA Deficiency, Selective				.|||	74	0.0147764	0.053	0.0058	5008	,	,		15377	0.0		0.0	False		,,,				2504	0.0				p.K188M		Atlas-SNP	.											.	TNFRSF13B	34	.	0			c.A563T						PASS	.	T	MET/LYS	217,4189	132.1+/-168.6	3,211,1989	73	74	74		563	2.4	0.8	17	dbSNP_131	74	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TNFRSF13B	NM_012452.2	95	3,212,6288	AA,AT,TT		0.0116,4.9251,1.6761	benign	188/294	16843708	218,12788	2203	4300	6503	SO:0001583	missense	23495	exon4	Familial Cancer Database	IGAD1, IGAD2	CCCCTCTTCTTGA	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.563A>T	17.37:g.16843708T>A	ENSP00000261652:p.Lys188Met	74	0	0		94	58	0.617021	NM_012452	B2R8B0|B7Z6V8|Q32LX4|Q7Z6F5	Missense_Mutation	SNP	ENST00000261652.2	37	CCDS11181.1	25	0.011446886446886446	22	0.044715447154471545	3	0.008287292817679558	0	0.0	0	0.0	t	3.080	-0.189246	0.06299	0.049251	1.16E-4	ENSG00000240505	ENST00000437538;ENST00000261652	D;D	0.94417	-3.42;-3.38	3.43	2.43	0.29744	.	0.227067	0.28778	N	0.014167	T	0.70527	0.3234	L	0.39898	1.24	0.28171	N	0.928553	P;P	0.49447	0.924;0.875	P;B	0.47981	0.563;0.36	T	0.77109	-0.2709	10	0.87932	D	0	-20.7502	6.3592	0.21419	0.0:0.8441:0.0:0.1559	.	142;188	O14836-2;O14836	.;TR13B_HUMAN	M	142;188	ENSP00000413453:K142M;ENSP00000261652:K188M	ENSP00000261652:K188M	K	-	2	0	TNFRSF13B	16784433	0.992000	0.36948	0.846000	0.33378	0.143000	0.21401	0.653000	0.24902	0.520000	0.28426	-0.477000	0.04895	AAG	T|0.985;A|0.015	0.015	strong		0.647	TNFRSF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131474.2			A	16843708	T	A	16843708	3	1	22	1	0	0	0	0	1	0	0	0	16302	1609	56	5	326	5	TNFRSF13B	17	16843708	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	841952	16843708	64351502	3428	6329											
MPRIP	23164	hgsc.bcm.edu	37	chr17	17030129	17030129	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	attctgacgcctgagaaggaGcatttcatccgggcggagac	10	8	13	10	3	2	3	1	2	1	2	3	6	3	4	2	3	1	1	2	3	1	2	rs140002644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:17030129G>A	ENST00000341712.4	+	4	381	c.381G>A	c.(379-381)gaG>gaA	p.E127E	MPRIP_ENST00000395811.5_Silent_p.E127E|MPRIP_ENST00000444976.1_Silent_p.E127E|MPRIP_ENST00000395804.3_Silent_p.E127E			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	127	Interaction with F-actin. {ECO:0000250}.|PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.					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						CTGAGAAGGAGCATTTCATCC	0.587													G|||	3	0.000599042	0.0023	0.0	5008	,	,		20330	0.0		0.0	False		,,,				2504	0.0				p.E127E		Atlas-SNP	.											.	MPRIP	87	.	0			c.G381A						PASS	.	G	,	21,4385	28.1+/-56.4	0,21,2182	92	89	90		381,381	3.4	1	17	dbSNP_134	90	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	MPRIP	NM_015134.3,NM_201274.3	,	0,21,6482	AA,AG,GG		0.0,0.4766,0.1615	,	127/1039,127/1026	17030129	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	23164	exon4			GAAGGAGCATTTC	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.381G>A	17.37:g.17030129G>A		160	0	0		136	52	0.382353	NM_015134	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Silent	SNP	ENST00000341712.4	37	CCDS32578.1																																																																																			G|0.998;A|0.002	0.002	strong		0.587	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134		A	17030129	G	A	17030129	2	1	22	1	0	0	0	0	0	0	0	1	9752	962	34	2		2	MPRIP	17	17030129	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	186421	17030129	64165081	3429	6330											
RAI1	10743	hgsc.bcm.edu	37	chr17	17696526	17696526	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agcaaggccctgcccacacaGcaaggcctgcaggggaggcc	10	2	14	15	0	0	0	0	0	0	0	0	1	0	1	4	5	4	3	4	5	2	0	rs61999281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:17696526G>A	ENST00000353383.1	+	3	733	c.264G>A	c.(262-264)caG>caA	p.Q88Q	RAI1_ENST00000261641.6_Silent_p.Q88Q	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	88					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)		TGCCCACACAGCAAGGCCTGC	0.687													G|||	105	0.0209665	0.0749	0.0086	5008	,	,		12762	0.0		0.0	False		,,,				2504	0.0				p.Q88Q		Atlas-SNP	.											.	RAI1	121	.	0			c.G264A						PASS	.	G		283,4099		11,261,1919	12	14	14		264	1.9	0.7	17	dbSNP_129	14	1,8583		0,1,4291	no	coding-synonymous	RAI1	NM_030665.3		11,262,6210	AA,AG,GG		0.0116,6.4582,2.1903		88/1907	17696526	284,12682	2191	4292	6483	SO:0001819	synonymous_variant	10743	exon3			CACACAGCAAGGC	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.264G>A	17.37:g.17696526G>A		69	0	0		89	40	0.449438	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Silent	SNP	ENST00000353383.1	37	CCDS11188.1																																																																																			G|0.980;A|0.020	0.020	strong		0.687	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665		A	17696526	G	A	17696526	2	1	22	1	0	0	0	0	0	0	0	1	13022	962	34	2		2	RAI1	17	17696526	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	666397	17696526	63498684	3430	6331											
TOM1L2	146691	hgsc.bcm.edu	37	chr17	17786042	17786042	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ttctgaattggctgtgatggGgccagtcacactcagagctg	8	11	13	9	0	3	3	2	2	1	1	3	3	3	3	1	3	1	2	1	3	1	2	rs146710625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:17786042G>T	ENST00000379504.3	-	6	720	c.637C>A	c.(637-639)Ccc>Acc	p.P213T	TOM1L2_ENST00000318094.10_Missense_Mutation_p.P168T|TOM1L2_ENST00000395739.4_Missense_Mutation_p.P168T|TOM1L2_ENST00000535933.1_Intron|TOM1L2_ENST00000581396.1_Missense_Mutation_p.P163T|TOM1L2_ENST00000542206.1_Intron|TOM1L2_ENST00000540946.1_Intron	NM_001082968.1	NP_001076437.1	Q6ZVM7	TM1L2_HUMAN	target of myb1-like 2 (chicken)	213					intracellular protein transport (GO:0006886)|negative regulation of mitosis (GO:0045839)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	clathrin binding (GO:0030276)|protein kinase binding (GO:0019901)			endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|prostate(2)	10	all_neural(463;0.228)					GCTGTGATGGGGCCAGTCACA	0.557																																					p.P213T	Melanoma(192;2505 2909 14455 25269)	Atlas-SNP	.											.	TOM1L2	54	.	0			c.C637A						PASS	.	G	THR/PRO,THR/PRO	11,4395	17.9+/-39.9	0,11,2192	96	89	91		487,637	4.7	1	17	dbSNP_134	91	0,8600		0,0,4300	yes	missense,missense	TOM1L2	NM_001033551.2,NM_001082968.1	38,38	0,11,6492	TT,TG,GG		0.0,0.2497,0.0846	benign,benign	163/458,213/508	17786042	11,12995	2203	4300	6503	SO:0001583	missense	146691	exon6			TGATGGGGCCAGT	AJ230803	CCDS32584.1, CCDS42270.1, CCDS74000.1, CCDS74001.1, CCDS74002.1, CCDS74003.1	17p11.2	2008-07-03	2001-11-28		ENSG00000175662	ENSG00000175662			11984	protein-coding gene	gene with protein product		615519	"target of myb1 (chicken) homolog-like 1"			10036180	Standard	NM_001082968		Approved		uc002grz.4	Q6ZVM7	OTTHUMG00000059353	ENST00000379504.3:c.637C>A	17.37:g.17786042G>T	ENSP00000368818:p.Pro213Thr	166	0	0		192	85	0.442708	NM_001082968	B7Z2L7|B7Z7F4|Q86V61|Q8TDE7|Q96M88	Missense_Mutation	SNP	ENST00000379504.3	37	CCDS42270.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.282146	0.80692	0.002497	0.0	ENSG00000175662	ENST00000379504;ENST00000318094;ENST00000395739;ENST00000537091	T;T	0.41065	1.01;1.01	5.7	4.73	0.59995	.	0.096186	0.85682	D	0.000000	T	0.56292	0.1975	M	0.79926	2.475	0.80722	D	1	B;P;B;B	0.50369	0.104;0.934;0.081;0.326	B;P;B;B	0.49361	0.059;0.608;0.067;0.142	T	0.61917	-0.6964	10	0.41790	T	0.15	-7.6658	16.772	0.85541	0.0:0.129:0.871:0.0	.	163;168;213;163	B7Z8F0;Q6ZVM7-3;Q6ZVM7;Q6ZVM7-2	.;.;TM1L2_HUMAN;.	T	213;163;168;163	ENSP00000368818:P213T;ENSP00000379088:P168T	ENSP00000312860:P163T	P	-	1	0	TOM1L2	17726767	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	5.571000	0.67404	1.388000	0.46506	0.655000	0.94253	CCC	G|0.999;T|0.001	0.001	strong		0.557	TOM1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131928.1			T	17786042	G	T	17786042	3	4	22	1	0	0	0	0	1	0	0	0	16368	1232	43	4	926	4	TOM1L2	17	17786042	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	89516	17786042	63409168	3431	6332											
ATPAF2	91647	hgsc.bcm.edu	37	chr17	17924447	17924447	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctcctcacctggtactccTcctccaggcgtgacagcagc	6	9	9	17	1	1	1	1	1	0	0	5	1	5	1	5	2	4	3	5	2	1	1	rs34607655	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:17924447T>C	ENST00000474627.3	-	7	876	c.722A>G	c.(721-723)gAg>gGg	p.E241G	ATPAF2_ENST00000469327.1_5'UTR|ATPAF2_ENST00000585101.1_Intron	NM_145691.3	NP_663729.1	Q8N5M1	ATPF2_HUMAN	ATP synthase mitochondrial F1 complex assembly factor 2	241					proton-transporting ATP synthase complex assembly (GO:0043461)	mitochondrion (GO:0005739)|nuclear speck (GO:0016607)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|urinary_tract(1)	8	all_neural(463;0.228)					CTGGTACTCCTCCTCCAGGCG	0.577													T|||	19	0.00379393	0.0136	0.0014	5008	,	,		20341	0.0		0.0	False		,,,				2504	0.0				p.E241G		Atlas-SNP	.											.	ATPAF2	15	.	0			c.A722G						PASS	.	T	GLY/GLU	39,4367	41.6+/-74.8	0,39,2164	43	35	38		722	5.7	1	17	dbSNP_126	38	0,8600		0,0,4300	yes	missense	ATPAF2	NM_145691.3	98	0,39,6464	CC,CT,TT		0.0,0.8852,0.2999	probably-damaging	241/290	17924447	39,12967	2203	4300	6503	SO:0001583	missense	91647	exon7			TACTCCTCCTCCA	AF052185	CCDS32585.1	17p11.2	2012-10-12			ENSG00000171953	ENSG00000171953		"Mitochondrial respiratory chain complex assembly factors"	18802	protein-coding gene	gene with protein product		608918				11410595, 11997338	Standard	NM_145691		Approved	Atp12p, ATP12, LP3663, MGC29736	uc002gse.1	Q8N5M1	OTTHUMG00000059354	ENST00000474627.3:c.722A>G	17.37:g.17924447T>C	ENSP00000417190:p.Glu241Gly	81	0	0		107	56	0.523364	NM_145691	A6NDE5|A8K2J2|Q6XYC7	Missense_Mutation	SNP	ENST00000474627.3	37	CCDS32585.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	T	28.0	4.877445	0.91664	0.008852	0.0	ENSG00000171953	ENST00000474627	T	0.81330	-1.48	5.7	5.7	0.88788	ATPase assembly, ATP12, domain (1);	0.000000	0.85682	D	0.000000	D	0.84982	0.5593	M	0.88105	2.93	0.80722	D	1	D	0.57257	0.979	P	0.52554	0.702	D	0.88744	0.3245	10	0.66056	D	0.02	-18.6937	15.9482	0.79809	0.0:0.0:0.0:1.0	rs34607655	241	Q8N5M1	ATPF2_HUMAN	G	241	ENSP00000417190:E241G	ENSP00000417190:E241G	E	-	2	0	ATPAF2	17865172	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.945000	0.87732	2.170000	0.68504	0.528000	0.53228	GAG	T|0.996;C|0.004	0.004	strong		0.577	ATPAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131934.3	NM_145691		C	17924447	T	C	17924447	3	2	22	1	0	0	0	0	1	0	0	0	1201	1551	54	3	155	3	ATPAF2	17	17924447	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	138405	17924447	63270763	3432	6333											
MYO15A	51168	hgsc.bcm.edu	37	chr17	18022385	18022385	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caaagctcatgacgcagatgCgcatgggcaagaagaagcgg	14	4	14	9	3	1	4	1	1	0	3	1	4	1	4	0	2	3	4	0	2	4	0			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18022385C>A	ENST00000205890.5	+	2	609	c.271C>A	c.(271-273)Cgc>Agc	p.R91S		NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	91					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)					GACGCAGATGCGCATGGGCAA	0.662																																					p.R91S		Atlas-SNP	.											.	MYO15A	268	.	0			c.C271A						PASS	.						12	15	14					17																	18022385		1990	4132	6122	SO:0001583	missense	51168	exon2			CAGATGCGCATGG	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.271C>A	17.37:g.18022385C>A	ENSP00000205890:p.Arg91Ser	53	0	0		84	48	0.571429	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	C	15.86	2.957666	0.53400	.	.	ENSG00000091536	ENST00000205890	D	0.91407	-2.84	5.05	2.82	0.32997	.	.	.	.	.	D	0.85961	0.5819	L	0.29908	0.895	0.80722	D	1	D	0.54207	0.965	P	0.46479	0.518	D	0.86392	0.1736	9	0.72032	D	0.01	.	10.2951	0.43618	0.2213:0.6572:0.1215:0.0	.	91	Q9UKN7	MYO15_HUMAN	S	91	ENSP00000205890:R91S	ENSP00000205890:R91S	R	+	1	0	MYO15A	17963110	0.968000	0.33430	0.999000	0.59377	0.455000	0.32408	0.304000	0.19228	2.333000	0.79357	0.561000	0.74099	CGC	.	.	none		0.662	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		A	18022385	C	A	18022385	3	1	22	1	0	0	0	0	1	0	0	0	10072	768	27	4	273	4	MYO15A	17	18022385	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	97938	18022385	63172825	3433	6334											
FLII	2314	hgsc.bcm.edu	37	chr17	18148944	18148944	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aagtcggagcatttctcagtCactgcaaagtagcccttctc	10	11	8	12	1	3	0	2	0	2	0	6	1	3	1	1	1	3	3	1	1	3	3	rs113208618	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18148944C>G	ENST00000327031.4	-	28	3759	c.3534G>C	c.(3532-3534)gtG>gtC	p.V1178V	FLII_ENST00000578558.1_Intron|FLII_ENST00000379450.4_Silent_p.V1092V|FLII_ENST00000579294.1_Silent_p.V1167V|FLII_ENST00000545457.2_Silent_p.V1123V	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	1178					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)					ATTTCTCAGTCACTGCAAAGT	0.542													C|||	209	0.0417332	0.1301	0.0259	5008	,	,		22593	0.0079		0.004	False		,,,				2504	0.0072				p.V1178V		Atlas-SNP	.											.	FLII	79	.	0			c.G3534C						PASS	.	C		455,3951	217.1+/-235.6	31,393,1779	221	195	204		3534	3.4	1	17	dbSNP_132	204	46,8554	30.1+/-81.4	0,46,4254	no	coding-synonymous	FLII	NM_002018.2		31,439,6033	GG,GC,CC		0.5349,10.3268,3.8521		1178/1270	18148944	501,12505	2203	4300	6503	SO:0001819	synonymous_variant	2314	exon28			CTCAGTCACTGCA	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.3534G>C	17.37:g.18148944C>G		76	0	0		92	42	0.456522	NM_002018	B4DIL0|F5H407|J3QLG3	Silent	SNP	ENST00000327031.4	37	CCDS11192.1																																																																																			C|0.964;G|0.036	0.036	strong		0.542	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132032.2	NM_002018		G	18148944	C	G	18148944	2	3	22	1	0	0	0	0	0	0	0	1	5933	813	29	4		4	FLII	17	18148944	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	126559	18148944	63046266	3434	6335											
TOP3A	7156	hgsc.bcm.edu	37	chr17	18217958	18217958	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtcggcgatccccttggcCgcgtcgtttttttcggccac	3	12	12	14	6	0	0	0	0	0	0	4	1	1	0	4	4	0	1	4	4	0	4	rs2230153	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18217958C>T	ENST00000321105.5	-	1	349	c.135G>A	c.(133-135)gcG>gcA	p.A45A	TOP3A_ENST00000582230.1_5'UTR|TOP3A_ENST00000542570.1_5'UTR|SMCR8_ENST00000406438.3_5'Flank	NM_004618.3	NP_004609.1	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	45	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						TCCCCTTGGCCGCGTCGTTTT	0.657													C|||	231	0.0461262	0.1596	0.0259	5008	,	,		17522	0.0		0.002	False		,,,				2504	0.0				p.A45A		Atlas-SNP	.											.	TOP3A	85	.	0			c.G135A						PASS	.	C		552,3854	248.1+/-256.1	40,472,1691	55	43	47		135	1	1	17	dbSNP_116	47	48,8552	29.6+/-80.5	0,48,4252	no	coding-synonymous	TOP3A	NM_004618.3		40,520,5943	TT,TC,CC		0.5581,12.5284,4.6133		45/1002	18217958	600,12406	2203	4300	6503	SO:0001819	synonymous_variant	7156	exon1			CTTGGCCGCGTCG	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.135G>A	17.37:g.18217958C>T		107	0	0		175	89	0.508571	NM_004618	A8KA61|B4DK80|D3DXC7|Q13473	Silent	SNP	ENST00000321105.5	37	CCDS11194.1	90	0.04120879120879121	78	0.15853658536585366	11	0.03038674033149171	0	0.0	1	0.0013192612137203166	C	14.01	2.407166	0.42715	0.125284	0.005581	ENSG00000177302	ENST00000412083	.	.	.	5.44	1.01	0.19927	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.09310	P	0.9999999999999994	.	.	.	.	.	.	T	0.11012	-1.0605	3	.	.	.	-26.1119	6.8195	0.23849	0.4676:0.3924:0.0:0.14	rs7212337	.	.	.	S	25	.	.	G	-	1	0	TOP3A	18158683	0.002000	0.14202	1.000000	0.80357	0.984000	0.73092	-1.659000	0.01975	0.367000	0.24454	0.655000	0.94253	GGC	C|0.948;T|0.052	0.052	strong		0.657	TOP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132052.2			T	18217958	C	T	18217958	2	4	22	1	0	0	0	0	0	0	0	1	16382	639	23	1		1	TOP3A	17	18217958	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	69014	18217958	62977252	3435	6336											
EVPLL	645027	hgsc.bcm.edu	37	chr17	18284263	18284263	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atctcccacatgcaagccagCgccgaccaggtggagcggga	10	4	13	14	3	1	0	0	0	1	0	2	3	1	2	4	3	4	1	4	3	1	0	rs116412205|rs386795970	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18284263C>T	ENST00000399134.4	+	2	370	c.12C>T	c.(10-12)agC>agT	p.S4S	RP1-37N7.1_ENST00000579352.1_RNA	NM_001145127.1	NP_001138599.1	A8MZ36	EVPLL_HUMAN	envoplakin-like	4			S -> N (in dbSNP:rs570145). {ECO:0000269|PubMed:14702039}.							NS(1)|endometrium(1)|large_intestine(1)|lung(2)	5						TGCAAGCCAGCGCCGACCAGG	0.657													.|||	71	0.0141773	0.0507	0.0058	5008	,	,		17727	0.0		0.0	False		,,,				2504	0.0				p.S4S		Atlas-SNP	.											.	EVPLL	10	.	0			c.C12T						PASS	.	C		32,1352		3,26,663	99	101	100		12	-0.7	1	17	dbSNP_132	100	0,3182		0,0,1591	no	coding-synonymous	EVPLL	NM_001145127.1		3,26,2254	TT,TC,CC		0.0,2.3121,0.7008		4/302	18284263	32,4534	692	1591	2283	SO:0001819	synonymous_variant	645027	exon2			AGCCAGCGCCGAC		CCDS45626.1	17p11.2	2009-08-25			ENSG00000214860	ENSG00000214860			35236	protein-coding gene	gene with protein product							Standard	NM_001145127		Approved		uc002gte.3	A8MZ36	OTTHUMG00000059095	ENST00000399134.4:c.12C>T	17.37:g.18284263C>T		266	0	0		242	100	0.413223	NM_001145127	B4DPD4	Silent	SNP	ENST00000399134.4	37	CCDS45626.1																																																																																			C|0.993;T|0.007	0.007	strong		0.657	EVPLL-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130836.2	NM_001145127		T	18284263	C	T	18284263	2	4	22	1	0	0	0	0	0	0	0	1	5295	767	27	1		1	EVPLL	17	18284263	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	66305	18284263	62910947	3436	6337											
ZNF286B	729288	hgsc.bcm.edu	37	chr17	18565915	18565915	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaaggttttcttacattcacGgcattcaaagagaattctag	13	13	8	7	1	4	1	2	0	2	1	4	3	4	1	0	2	1	2	0	2	5	7	rs73291461	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18565915G>A	ENST00000545289.1	-	5	1154	c.904C>T	c.(904-906)Cgt>Tgt	p.R302C	ZNF286B_ENST00000285274.5_3'UTR	NM_001145045.1	NP_001138517.1	P0CG31	Z286B_HUMAN	zinc finger protein 286B	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|lung(1)	2						TTACATTCACGGCATTCAAAG	0.398													.|||	424	0.0846645	0.3071	0.0202	5008	,	,		21283	0.0		0.002	False		,,,				2504	0.002				p.R302C		Atlas-SNP	.											.	ZNF286B	75	.	0			c.C904T						PASS	.	T	CYS/ARG	317,1067		31,255,406	74	66	69		904	0.1	0.9	17	dbSNP_130	69	13,3169		0,13,1578	no	missense	ZNF286B	NM_001145045.1	180	31,268,1984	AA,AG,GG		0.4085,22.9046,7.2273	benign	302/523	18565915	330,4236	692	1591	2283	SO:0001583	missense	729288	exon5			ATTCACGGCATTC		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.904C>T	17.37:g.18565915G>A	ENSP00000461413:p.Arg302Cys	330	0	0		299	130	0.434783	NM_001145045		Missense_Mutation	SNP	ENST00000545289.1	37	CCDS58523.1																																																																																			G|0.943;A|0.057	0.057	strong		0.398	ZNF286B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_001723047		A	18565915	G	A	18565915	3	1	22	1	0	0	0	0	1	0	0	0	17839	1116	39	1	668	1	ZNF286B	17	18565915	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	281652	18565915	62629295	3437	6338											
ZNF286B	729288	hgsc.bcm.edu	37	chr17	18566386	18566386	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagtcatagacactattccGtgtcagtctgtctattattg	10	15	8	8	1	4	2	2	0	2	2	5	2	5	2	1	0	0	0	1	0	4	6	rs143643706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18566386G>A	ENST00000545289.1	-	5	683	c.433C>T	c.(433-435)Cgg>Tgg	p.R145W	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						ACACTATTCCGTGTCAGTCTG	0.408													.|||	424	0.0846645	0.3071	0.0202	5008	,	,		22256	0.0		0.002	False		,,,				2504	0.002				p.R145W		Atlas-SNP	.											.	ZNF286B	75	.	0			c.C433T						PASS	.	G	TRP/ARG	315,1069		31,253,408	111	99	102		433	-3.4	0	17	dbSNP_134	102	11,3169		0,11,1579	no	missense	ZNF286B	NM_001145045.1	101	31,264,1987	AA,AG,GG		0.3459,22.7601,7.1429	probably-damaging	145/523	18566386	326,4238	692	1590	2282	SO:0001583	missense	729288	exon5			TATTCCGTGTCAG		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.433C>T	17.37:g.18566386G>A	ENSP00000461413:p.Arg145Trp	390	0	0		353	137	0.388102	NM_001145045		Missense_Mutation	SNP	ENST00000545289.1	37	CCDS58523.1																																																																																			G|0.945;A|0.055	0.055	strong		0.408	ZNF286B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_001723047		A	18566386	G	A	18566386	3	1	22	1	0	0	0	0	1	0	0	0	17839	1144	40	1	1139	1	ZNF286B	17	18566386	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	471	18566386	62628824	3438	6339											
ZNF286B	729288	hgsc.bcm.edu	37	chr17	18566422	18566422	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tattgcaactttgcatgattCtgctttggaaaaatcttgca	11	16	7	7	0	2	1	0	1	2	0	2	2	2	2	0	1	5	4	0	1	4	6	rs146829975	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18566422C>T	ENST00000545289.1	-	5	647	c.397G>A	c.(397-399)Gaa>Aaa	p.E133K	ZNF286B_ENST00000285274.5_3'UTR	NM_001145045.1	NP_001138517.1	P0CG31	Z286B_HUMAN	zinc finger protein 286B	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|lung(1)	2						TTGCATGATTCTGCTTTGGAA	0.408													.|||	165	0.0329473	0.118	0.0115	5008	,	,		22416	0.0		0.001	False		,,,				2504	0.0				p.E133K		Atlas-SNP	.											.	ZNF286B	75	.	0			c.G397A						PASS	.	C	LYS/GLU	110,1274		4,102,586	90	80	83		397	1.6	1	17	dbSNP_134	83	1,3179		0,1,1589	no	missense	ZNF286B	NM_001145045.1	56	4,103,2175	TT,TC,CC		0.0314,7.948,2.4321	benign	133/523	18566422	111,4453	692	1590	2282	SO:0001583	missense	729288	exon5			ATGATTCTGCTTT		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.397G>A	17.37:g.18566422C>T	ENSP00000461413:p.Glu133Lys	416	0	0		381	149	0.391076	NM_001145045		Missense_Mutation	SNP	ENST00000545289.1	37	CCDS58523.1																																																																																			C|0.975;T|0.025	0.025	strong		0.408	ZNF286B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_001723047		T	18566422	C	T	18566422	3	4	22	1	0	0	0	0	1	0	0	0	17839	922	32	2	1175	2	ZNF286B	17	18566422	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	36	18566422	62628788	3439	6340											
FAM83G	644815	hgsc.bcm.edu	37	chr17	18881225	18881225	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgagggttacgtagtcgTcatcatcttcttcttccacc	7	14	7	13	2	5	1	2	1	3	0	7	1	6	1	2	1	1	2	2	1	2	5	rs200348726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18881225T>A	ENST00000388995.6	-	5	1977	c.1754A>T	c.(1753-1755)gAc>gTc	p.D585V	SLC5A10_ENST00000417251.2_Intron|FAM83G_ENST00000345041.4_Missense_Mutation_p.D585V|SLC5A10_ENST00000395647.2_Intron|SLC5A10_ENST00000395643.2_Intron|SLC5A10_ENST00000395642.1_Intron|SLC5A10_ENST00000317977.6_Intron|FAM83G_ENST00000585154.2_Missense_Mutation_p.D585V|SLC5A10_ENST00000395645.3_Intron			A6ND36	FA83G_HUMAN	family with sequence similarity 83, member G	585	Poly-Asp.				BMP signaling pathway (GO:0030509)	cytosol (GO:0005829)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(3)|stomach(1)	22						TACGTAGTCGTCATCATCTTC	0.652													T|||	4	0.000798722	0.003	0.0	5008	,	,		16212	0.0		0.0	False		,,,				2504	0.0				p.D585V		Atlas-SNP	.											.	FAM83G	51	.	0			c.A1754T						PASS	.	T	VAL/ASP,,	12,4022		0,12,2005	45	52	50		1754,,	5.9	0.5	17		50	0,8316		0,0,4158	yes	missense,intron,intron	SLC5A10,FAM83G	NM_001039999.2,NM_001042450.1,NM_152351.3	152,,	0,12,6163	AA,AT,TT		0.0,0.2975,0.0972	probably-damaging,,	585/824,,	18881225	12,12338	2017	4158	6175	SO:0001583	missense	644815	exon5			TAGTCGTCATCAT	AK123558	CCDS42276.1	17p11.2	2014-05-01	2006-03-22		ENSG00000188522	ENSG00000188522			32554	protein-coding gene	gene with protein product	"protein associated with SMAD1"	615886				24554596	Standard	NM_001039999		Approved	FLJ41564, PAWS1	uc002guw.3	A6ND36	OTTHUMG00000059411	ENST00000388995.6:c.1754A>T	17.37:g.18881225T>A	ENSP00000373647:p.Asp585Val	54	0	0		59	35	0.59322	NM_001039999	Q3KQZ4|Q6ZW60	Missense_Mutation	SNP	ENST00000388995.6	37	CCDS42276.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	20.7	4.038233	0.75617	0.002975	0.0	ENSG00000188522	ENST00000388995;ENST00000345041	T;T	0.15139	2.45;2.45	5.91	5.91	0.95273	.	0.446831	0.22573	N	0.058301	T	0.41119	0.1145	M	0.67953	2.075	0.80722	D	1	D	0.71674	0.998	D	0.68353	0.957	T	0.20974	-1.0259	10	0.87932	D	0	-28.3264	16.0171	0.80450	0.0:0.0:0.0:1.0	.	585	A6ND36	FA83G_HUMAN	V	585	ENSP00000373647:D585V;ENSP00000343279:D585V	ENSP00000343279:D585V	D	-	2	0	FAM83G	18821950	0.972000	0.33761	0.512000	0.27736	0.887000	0.51463	2.926000	0.48892	2.269000	0.75478	0.533000	0.62120	GAC	T|1.000;A|0.000	0.000	strong		0.652	FAM83G-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253108.4			A	18881225	T	A	18881225	3	1	22	1	0	0	0	0	1	0	0	0	5647	1667	58	5	725	5	FAM83G	17	18881225	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	314803	18881225	62313985	3440	6341											
B9D1	27077	hgsc.bcm.edu	37	chr17	19246667	19246667	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctggggtgggctgggccccaAcacaccctgtgtatcagaag	8	7	14	12	0	1	1	1	0	0	1	1	1	1	1	3	4	1	2	3	4	3	1	rs7212549	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:19246667A>G	ENST00000261499.4	-	7	723	c.580T>C	c.(580-582)Ttg>Ctg	p.L194L	B9D1_ENST00000461069.2_Intron|B9D1_ENST00000395615.1_3'UTR|MIR1180_ENST00000408613.1_RNA|B9D1_ENST00000477478.2_3'UTR|B9D1_ENST00000575403.1_Intron	NM_015681.3	NP_056496.1	Q9UPM9	B9D1_HUMAN	B9 protein domain 1	194					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)					CTGGGCCCCAACACACCCTGT	0.587													A|||	153	0.0305511	0.0514	0.0029	5008	,	,		18629	0.0079		0.0	False		,,,				2504	0.0767				p.L194L		Atlas-SNP	.											.	B9D1	8	.	0			c.T580C						PASS	.	A		172,4234	113.8+/-151.8	1,170,2032	75	68	70		580	-2.2	0	17	dbSNP_116	70	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	B9D1	NM_015681.3		1,171,6331	GG,GA,AA		0.0116,3.9038,1.3302		194/205	19246667	173,12833	2203	4300	6503	SO:0001819	synonymous_variant	27077	exon7			GCCCCAACACACC	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.580T>C	17.37:g.19246667A>G		59	0	0		82	40	0.487805	NM_015681	Q9BU22	Silent	SNP	ENST00000261499.4	37	CCDS11205.1																																																																																			A|0.980;G|0.020	0.020	strong		0.587	B9D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132494.1	NM_015681		G	19246667	A	G	19246667	2	3	22	1	0	0	0	0	0	0	0	1	1277	40	2	3		3	B9D1	17	19246667	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	365442	19246667	61948543	3441	6342											
MAPK7	5598	hgsc.bcm.edu	37	chr17	19285392	19285392	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgccggcccctgccccagcGccaacgccaaccccaacccc	7	2	8	24	3	0	0	0	0	0	0	0	0	0	0	11	1	6	0	11	1	3	0	rs2233079	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:19285392G>A	ENST00000308406.5	+	5	2162	c.1776G>A	c.(1774-1776)gcG>gcA	p.A592A	MAPK7_ENST00000395602.4_Silent_p.A592A|MAPK7_ENST00000571657.1_Intron|MAPK7_ENST00000395604.3_Silent_p.A592A|MFAP4_ENST00000574313.2_5'Flank|MAPK7_ENST00000299612.7_Silent_p.A453A	NM_139033.2	NP_620602.2	Q13164	MK07_HUMAN	mitogen-activated protein kinase 7	592	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)					ctgccccagcgccaacgccaa	0.657													G|||	165	0.0329473	0.118	0.013	5008	,	,		9722	0.0		0.0	False		,,,				2504	0.0				p.A592A		Atlas-SNP	.											.	MAPK7	72	.	0			c.G1776A						PASS	.	G	,,,	433,3955		29,375,1790	14	13	13		1776,1359,1776,1776	-8.4	0	17	dbSNP_98	13	9,8573		0,9,4282	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MAPK7	NM_002749.3,NM_139032.2,NM_139033.2,NM_139034.2	,,,	29,384,6072	AA,AG,GG		0.1049,9.8678,3.4079	,,,	592/817,453/678,592/817,592/817	19285392	442,12528	2194	4291	6485	SO:0001819	synonymous_variant	5598	exon5			CCCAGCGCCAACG	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.1776G>A	17.37:g.19285392G>A		144	0	0		200	114	0.57	NM_002749	Q16634|Q59F50|Q6QLU7|Q7L4P4|Q969G1|Q96G51	Silent	SNP	ENST00000308406.5	37	CCDS11206.1																																																																																			G|0.959;A|0.041	0.041	strong		0.657	MAPK7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132506.1	NM_139033		A	19285392	G	A	19285392	2	1	22	1	0	0	0	0	0	0	0	1	9291	1074	38	1		1	MAPK7	17	19285392	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	38725	19285392	61909818	3442	6343											
ALDH3A2	224	hgsc.bcm.edu	37	chr17	19559770	19559770	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttctatacgggaaacactgCggttggcaaaattgtcatgg	11	12	11	7	2	2	0	1	0	1	0	2	1	2	1	0	4	3	2	0	4	5	5	rs115977487	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:19559770C>T	ENST00000176643.6	+	4	1009	c.563C>T	c.(562-564)gCg>gTg	p.A188V	ALDH3A2_ENST00000339618.4_Missense_Mutation_p.A188V|ALDH3A2_ENST00000395575.2_Missense_Mutation_p.A188V|ALDH3A2_ENST00000581518.1_Missense_Mutation_p.A188V|ALDH3A2_ENST00000579855.1_Missense_Mutation_p.A188V			P51648	AL3A2_HUMAN	aldehyde dehydrogenase 3 family, member A2	188					cellular aldehyde metabolic process (GO:0006081)|central nervous system development (GO:0007417)|epidermis development (GO:0008544)|oxidation-reduction process (GO:0055114)|peripheral nervous system development (GO:0007422)|phytol metabolic process (GO:0033306)|sesquiterpenoid metabolic process (GO:0006714)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)|peroxisome (GO:0005777)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|long-chain-alcohol oxidase activity (GO:0046577)|long-chain-aldehyde dehydrogenase activity (GO:0050061)|medium-chain-aldehyde dehydrogenase activity (GO:0052814)			endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(2)|ovary(2)|prostate(1)	13	all_cancers(12;1.39e-05)|all_epithelial(12;0.00158)|Breast(13;0.245)					GGAAACACTGCGGTTGGCAAA	0.438													C|||	67	0.0133786	0.0499	0.0014	5008	,	,		21110	0.0		0.0	False		,,,				2504	0.0				p.A188V		Atlas-SNP	.											.	ALDH3A2	41	.	0			c.C563T						PASS	.	C	VAL/ALA,VAL/ALA	141,4265	101.2+/-139.8	3,135,2065	115	108	111		563,563	1.2	0	17	dbSNP_132	111	0,8600		0,0,4300	yes	missense,missense	ALDH3A2	NM_000382.2,NM_001031806.1	64,64	3,135,6365	TT,TC,CC		0.0,3.2002,1.0841	benign,benign	188/486,188/509	19559770	141,12865	2203	4300	6503	SO:0001583	missense	224	exon4			ACACTGCGGTTGG	L47162	CCDS11210.1, CCDS32589.1	17p11.2	2010-05-07			ENSG00000072210	ENSG00000072210	1.2.1.3	"Aldehyde dehydrogenases"	403	protein-coding gene	gene with protein product	"fatty aldehyde dehydrogenase"	609523		SLS, ALDH10		7894487	Standard	NM_000382		Approved	FALDH	uc002gwa.1	P51648	OTTHUMG00000059471	ENST00000176643.6:c.563C>T	17.37:g.19559770C>T	ENSP00000176643:p.Ala188Val	219	1	0.00456621		265	135	0.509434	NM_001031806	Q6I9T3|Q93011|Q96J37	Missense_Mutation	SNP	ENST00000176643.6	37	CCDS11210.1	24	0.01098901098901099	24	0.04878048780487805	0	0.0	0	0.0	0	0.0	C	5.442	0.266672	0.10294	0.032002	0.0	ENSG00000072210	ENST00000176643;ENST00000395575;ENST00000339618	D;D;D	0.85484	-1.99;-1.99;-1.99	5.71	1.24	0.21308	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.860604	0.10663	N	0.648524	T	0.40791	0.1131	M	0.68317	2.08	0.09310	N	1	P;P	0.44044	0.825;0.79	B;B	0.34873	0.191;0.12	T	0.53878	-0.8376	10	0.31617	T	0.26	-0.0192	4.0327	0.09716	0.1051:0.5293:0.2073:0.1584	.	188;188	P51648;P51648-2	AL3A2_HUMAN;.	V	188	ENSP00000176643:A188V;ENSP00000378942:A188V;ENSP00000345774:A188V	ENSP00000176643:A188V	A	+	2	0	ALDH3A2	19500362	0.000000	0.05858	0.000000	0.03702	0.106000	0.19336	0.212000	0.17497	0.336000	0.23639	0.467000	0.42956	GCG	C|0.990;T|0.010	0.010	strong		0.438	ALDH3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132268.1			T	19559770	C	T	19559770	3	4	22	1	0	0	0	0	1	0	0	0	498	768	27	1	577	1	ALDH3A2	17	19559770	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	274378	19559770	61635440	3443	6344											
SLC47A2	146802	hgsc.bcm.edu	37	chr17	19607432	19607432	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcttggcctgcacagtatcCgcagcccccagagccatccc	7	6	9	19	2	0	1	0	0	0	1	2	1	2	1	6	1	3	4	6	1	1	2	rs34169093	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:19607432C>T	ENST00000325411.5	-	11	1127	c.1077G>A	c.(1075-1077)gcG>gcA	p.A359A	SLC47A2_ENST00000350657.5_Silent_p.A337A|SLC47A2_ENST00000463318.1_5'UTR	NM_152908.3	NP_690872.2	Q86VL8	S47A2_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 2	359					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)	GCACAGTATCCGCAGCCCCCA	0.617													C|||	311	0.0621006	0.1831	0.0187	5008	,	,		18054	0.0		0.0268	False		,,,				2504	0.0297				p.A359A		Atlas-SNP	.											.	SLC47A2	61	.	0			c.G1077A						PASS	.	C	,	663,3743	278.7+/-274.4	51,561,1591	50	49	50		969,1077	-0.3	0	17	dbSNP_126	50	237,8363	94.7+/-156.6	2,233,4065	no	coding-synonymous,coding-synonymous	SLC47A2	NM_001099646.1,NM_152908.3	,	53,794,5656	TT,TC,CC		2.7558,15.0477,6.9199	,	323/567,359/603	19607432	900,12106	2203	4300	6503	SO:0001819	synonymous_variant	146802	exon11			AGTATCCGCAGCC	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.1077G>A	17.37:g.19607432C>T		45	0	0		39	20	0.512821	NM_152908	A0JBX9|A0P8Z7|Q63HJ9|Q8IV44|Q96NA1	Silent	SNP	ENST00000325411.5	37	CCDS11211.1																																																																																			C|0.935;T|0.065	0.065	strong		0.617	SLC47A2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132242.2	NM_152908		T	19607432	C	T	19607432	2	4	22	1	0	0	0	0	0	0	0	1	14663	639	23	1		1	SLC47A2	17	19607432	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	47662	19607432	61587778	3444	6345											
AKAP10	11216	hgsc.bcm.edu	37	chr17	19835185	19835185	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccaacagagccaggagcaGtcagcgacacgttcccgccc	10	3	12	16	3	1	1	1	0	0	1	2	3	2	2	4	2	4	2	4	2	1	1	rs141355495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:19835185G>C	ENST00000225737.6	-	10	1731	c.1574C>G	c.(1573-1575)aCt>aGt	p.T525S	RP11-209D14.4_ENST00000583067.1_RNA|AKAP10_ENST00000395536.3_Intron	NM_007202.3	NP_009133.2	O43572	AKA10_HUMAN	A kinase (PRKA) anchor protein 10	525					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)					GCCAGGAGCAGTCAGCGACAC	0.488													G|||	3	0.000599042	0.0023	0.0	5008	,	,		14389	0.0		0.0	False		,,,				2504	0.0				p.T525S		Atlas-SNP	.											.	AKAP10	47	.	0			c.C1574G						PASS	.	G	SER/THR	6,4400	12.9+/-30.5	0,6,2197	85	83	84		1574	2.8	0.2	17	dbSNP_134	84	0,8600		0,0,4300	yes	missense	AKAP10	NM_007202.2	58	0,6,6497	CC,CG,GG		0.0,0.1362,0.0461	benign	525/663	19835185	6,13000	2203	4300	6503	SO:0001583	missense	11216	exon10			GGAGCAGTCAGCG	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.1574C>G	17.37:g.19835185G>C	ENSP00000225737:p.Thr525Ser	55	0	0		64	36	0.5625	NM_007202	B2R650|Q96AJ7	Missense_Mutation	SNP	ENST00000225737.6	37	CCDS11214.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	5.299	0.240537	0.10023	0.001362	0.0	ENSG00000108599	ENST00000225737	T	0.28666	1.6	5.82	2.79	0.32731	.	0.783781	0.12491	N	0.464265	T	0.05914	0.0154	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33752	-0.9856	10	0.09084	T	0.74	0.4362	1.6078	0.02687	0.238:0.1522:0.4703:0.1395	.	525	O43572	AKA10_HUMAN	S	525	ENSP00000225737:T525S	ENSP00000225737:T525S	T	-	2	0	AKAP10	19775777	0.767000	0.28508	0.197000	0.23402	0.325000	0.28411	0.898000	0.28404	0.820000	0.34516	0.650000	0.86243	ACT	G|0.999;C|0.001	0.001	strong		0.488	AKAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132380.2	NM_007202		C	19835185	G	C	19835185	3	2	22	1	0	0	0	0	1	0	0	0	446	1029	36	4	438	4	AKAP10	17	19835185	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	227753	19835185	61360025	3445	6346											
NOS2	4843	hgsc.bcm.edu	37	chr17	26085931	26085931	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agctgaaagaaatagtcctcGacctgctcctcattcaattt	12	12	6	11	1	2	2	2	1	0	1	5	3	4	2	3	0	2	2	3	0	4	3	rs3729662	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:26085931G>A	ENST00000313735.6	-	26	3563	c.3330C>T	c.(3328-3330)gtC>gtT	p.V1110V		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	1110					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)	AATAGTCCTCGACCTGCTCCT	0.607													.|||	73	0.0145767	0.0537	0.0029	5008	,	,		20547	0.0		0.0	False		,,,				2504	0.0				p.V1110V		Atlas-SNP	.											.	NOS2	113	.	0			c.C3330T						PASS	.	G		158,4248	102.5+/-141.1	1,156,2046	30	28	29		3330	-9.7	0.2	17	dbSNP_107	29	1,8591	1.2+/-3.3	0,1,4295	no	coding-synonymous	NOS2	NM_000625.4		1,157,6341	AA,AG,GG		0.0116,3.586,1.2233		1110/1154	26085931	159,12839	2203	4296	6499	SO:0001819	synonymous_variant	4843	exon26			GTCCTCGACCTGC	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.3330C>T	17.37:g.26085931G>A		422	0	0		451	212	0.470067	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Silent	SNP	ENST00000313735.6	37	CCDS11223.1																																																																																			.	.	weak		0.607	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625		A	26085931	G	A	26085931	2	1	22	1	0	0	0	0	0	0	0	1	10552	1045	37	1		1	NOS2	17	26085931	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6250746	26085931	55109279	3446	6347											
NOS2	4843	hgsc.bcm.edu	37	chr17	26107840	26107840	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acaaggtcaggtgggatttcGaagagctcagggtcacggcc	10	7	15	9	2	3	1	3	0	0	1	4	3	3	2	1	5	1	1	1	5	2	1	rs34719207	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:26107840G>A	ENST00000313735.6	-	9	1190	c.957C>T	c.(955-957)ttC>ttT	p.F319F		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	319					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)	GTGGGATTTCGAAGAGCTCAG	0.607													G|||	22	0.00439297	0.0151	0.0014	5008	,	,		19507	0.0		0.001	False		,,,				2504	0.0				p.F319F		Atlas-SNP	.											.	NOS2	113	.	0			c.C957T						PASS	.	G		50,4356	50.9+/-86.3	0,50,2153	80	70	73		957	-11	0.1	17	dbSNP_126	73	0,8600		0,0,4300	no	coding-synonymous	NOS2	NM_000625.4		0,50,6453	AA,AG,GG		0.0,1.1348,0.3844		319/1154	26107840	50,12956	2203	4300	6503	SO:0001819	synonymous_variant	4843	exon9			GATTTCGAAGAGC	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.957C>T	17.37:g.26107840G>A		123	0	0		128	70	0.546875	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Silent	SNP	ENST00000313735.6	37	CCDS11223.1																																																																																			G|0.996;A|0.004	0.004	strong		0.607	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625		A	26107840	G	A	26107840	2	1	22	1	0	0	0	0	0	0	0	1	10552	1049	37	1		1	NOS2	17	26107840	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	21909	26107840	55087370	3447	6348											
SDF2	6388	hgsc.bcm.edu	37	chr17	26982341	26982341	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtgaagtgaagtggtgactAtggaggtttcggccagtgtt	8	12	17	4	1	0	3	0	3	0	0	1	4	0	4	1	5	0	2	1	5	3	3	rs35579310	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:26982341A>G	ENST00000247020.4	-	2	610	c.312T>C	c.(310-312)caT>caC	p.H104H	SDF2_ENST00000592250.1_5'UTR	NM_006923.3	NP_008854.2	Q99470	SDF2_HUMAN	stromal cell-derived factor 2	104	MIR 2. {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)					AGTGGTGACTATGGAGGTTTC	0.537													A|||	47	0.00938498	0.0325	0.0058	5008	,	,		21075	0.0		0.0	False		,,,				2504	0.0				p.H104H		Atlas-SNP	.											.	SDF2	17	.	0			c.T312C						PASS	.	A		123,4283	91.6+/-130.3	1,121,2081	156	134	141		312	-0.8	1	17	dbSNP_126	141	0,8600		0,0,4300	no	coding-synonymous	SDF2	NM_006923.2		1,121,6381	GG,GA,AA		0.0,2.7916,0.9457		104/212	26982341	123,12883	2203	4300	6503	SO:0001819	synonymous_variant	6388	exon2			GTGACTATGGAGG	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.312T>C	17.37:g.26982341A>G		119	0	0		137	58	0.423358	NM_006923	Q9BQ79	Silent	SNP	ENST00000247020.4	37	CCDS11238.1																																																																																			A|0.991;G|0.009	0.009	strong		0.537	SDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255965.2	NM_006923		G	26982341	A	G	26982341	2	3	22	1	0	0	0	0	0	0	0	1	13975	446	16	3		3	SDF2	17	26982341	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	874501	26982341	54212869	3448	6349											
SDF2	6388	hgsc.bcm.edu	37	chr17	26988852	26988852	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caggctggacgctcccacagCgctccacaaaccccccaaca	11	3	7	20	2	0	0	0	0	0	0	2	1	2	1	5	2	3	3	5	2	2	0	rs35404078	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:26988852C>T	ENST00000247020.4	-	1	341	c.43G>A	c.(43-45)Gct>Act	p.A15T	SUPT6H_ENST00000347486.4_5'Flank|SUPT6H_ENST00000314616.6_5'Flank|SDF2_ENST00000592250.1_Intron	NM_006923.3	NP_008854.2	Q99470	SDF2_HUMAN	stromal cell-derived factor 2	15			A -> T (in dbSNP:rs35404078).		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)					GCTCCCACAGCGCTCCACAAA	0.592													C|||	47	0.00938498	0.0325	0.0058	5008	,	,		17083	0.0		0.0	False		,,,				2504	0.0				p.A15T		Atlas-SNP	.											.	SDF2	17	.	0			c.G43A						PASS	.	C	THR/ALA	125,4281	92.5+/-131.2	1,123,2079	152	133	139		43	4.5	1	17	dbSNP_126	139	0,8600		0,0,4300	yes	missense	SDF2	NM_006923.2	58	1,123,6379	TT,TC,CC		0.0,2.837,0.9611	benign	15/212	26988852	125,12881	2203	4300	6503	SO:0001583	missense	6388	exon1			CCACAGCGCTCCA	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.43G>A	17.37:g.26988852C>T	ENSP00000247020:p.Ala15Thr	92	0	0		97	45	0.463918	NM_006923	Q9BQ79	Missense_Mutation	SNP	ENST00000247020.4	37	CCDS11238.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	C	13.72	2.321744	0.41096	0.02837	0.0	ENSG00000132581	ENST00000247020	D	0.84516	-1.86	5.54	4.54	0.55810	.	0.694941	0.13447	N	0.387194	T	0.60064	0.2240	L	0.47716	1.5	0.24340	N	0.994965	B;B	0.26147	0.143;0.143	B;B	0.15484	0.013;0.013	T	0.57522	-0.7797	10	0.13853	T	0.58	-4.1998	15.2037	0.73159	0.0:0.8229:0.177:0.0	rs35404078	15;15	Q6IBU4;Q99470	.;SDF2_HUMAN	T	15	ENSP00000247020:A15T	ENSP00000247020:A15T	A	-	1	0	SDF2	24012979	0.517000	0.26226	0.998000	0.56505	0.367000	0.29736	1.004000	0.29822	2.598000	0.87819	0.561000	0.74099	GCT	C|0.990;T|0.010	0.010	strong		0.592	SDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255965.2	NM_006923		T	26988852	C	T	26988852	3	4	22	1	0	0	0	0	1	0	0	0	13975	768	27	1	604	1	SDF2	17	26988852	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6511	26988852	54206358	3449	6350											
NUFIP2	57532	hgsc.bcm.edu	37	chr17	27620934	27620934	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgaggctgctggtgatgatgGtggtggtggtggttgtggct	3	14	21	3	0	0	3	0	3	0	0	0	3	0	3	0	8	1	4	0	8	0	1	rs1054145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:27620934G>A	ENST00000225388.4	-	1	202	c.144C>T	c.(142-144)caC>caT	p.H48H	NUFIP2_ENST00000579665.1_Silent_p.H48H	NM_020772.2	NP_065823.1	Q7Z417	NUFP2_HUMAN	nuclear fragile X mental retardation protein interacting protein 2	48	His-rich.					cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	24			BRCA - Breast invasive adenocarcinoma(11;0.000457)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551)			ggtgatgatggtggtggtggt	0.592													G|||	77	0.0153754	0.0522	0.0072	5008	,	,		10946	0.0		0.003	False		,,,				2504	0.0				p.H48H		Atlas-SNP	.											NUFIP2,NS,carcinoma,-2,1	NUFIP2	60	1	0			c.C144T						PASS	.	G		227,4179	135.3+/-171.4	7,213,1983	144	141	142		144	3.2	1	17	dbSNP_86	142	2,8598	3.0+/-9.4	0,2,4298	no	coding-synonymous	NUFIP2	NM_020772.2		7,215,6281	AA,AG,GG		0.0233,5.1521,1.7607		48/696	27620934	229,12777	2203	4300	6503	SO:0001819	synonymous_variant	57532	exon1			ATGATGGTGGTGG	AB037742	CCDS32600.1	17q11.1	2006-03-01				ENSG00000108256			17634	protein-coding gene	gene with protein product		609356				12837692, 16407062	Standard	NM_020772		Approved	KIAA1321, MGC117262, PIG1, 182-FIP, FIP-82, 82-FIP	uc002hdy.4	Q7Z417		ENST00000225388.4:c.144C>T	17.37:g.27620934G>A		476	0	0		525	275	0.52381	NM_020772	A1L3A6|Q9P2M5	Silent	SNP	ENST00000225388.4	37	CCDS32600.1																																																																																			G|0.981;A|0.019	0.019	strong		0.592	NUFIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447015.2	NM_020772		A	27620934	G	A	27620934	2	1	22	1	0	0	0	0	0	0	0	1	10758	1252	44	2		2	NUFIP2	17	27620934	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	632082	27620934	53574276	3450	6351											
ANKRD13B	124930	hgsc.bcm.edu	37	chr17	27939427	27939427	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	tcctcatcctcagaaatcccGatcttccacatcctcaacgc	10	10	3	18	2	4	1	3	0	1	1	9	2	9	1	5	0	1	0	5	0	2	1	rs147156385	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:27939427G>C	ENST00000394859.3	+	12	1420	c.1266G>C	c.(1264-1266)ccG>ccC	p.P422P	RP11-68I3.2_ENST00000581474.1_RNA	NM_152345.4	NP_689558.4	Q86YJ7	AN13B_HUMAN	ankyrin repeat domain 13B	422						endosome (GO:0005768)|plasma membrane (GO:0005886)				cervix(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	16						CAGAAATCCCGATCTTCCACA	0.637													G|||	9	0.00179712	0.0068	0.0	5008	,	,		12004	0.0		0.0	False		,,,				2504	0.0				p.P422P		Atlas-SNP	.											ANKRD13B,NS,carcinoma,0,1	ANKRD13B	39	1	0			c.G1266C						PASS	.	G		31,4373		0,31,2171	45	45	45		1266	-0.6	1	17	dbSNP_134	45	2,8596		0,2,4297	no	coding-synonymous	ANKRD13B	NM_152345.4		0,33,6468	CC,CG,GG		0.0233,0.7039,0.2538		422/627	27939427	33,12969	2202	4299	6501	SO:0001819	synonymous_variant	124930	exon12			AATCCCGATCTTC	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.1266G>C	17.37:g.27939427G>C		249	1	0.00401606		213	104	0.488263	NM_152345	Q8N7S9	Silent	SNP	ENST00000394859.3	37	CCDS11251.1																																																																																			G|0.998;C|0.002	0.002	strong		0.637	ANKRD13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256077.1	NM_152345		C	27939427	G	C	27939427	2	2	22	1	0	0	0	0	0	0	0	1	642	1045	37	4		4	ANKRD13B	17	27939427	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	318493	27939427	53255783	3451	6352											
NF1	4763	hgsc.bcm.edu	37	chr17	29652884	29652884	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atttgctgatataccatgtcTtactgactttaaagccatat	12	16	5	8	0	1	2	0	2	1	0	1	2	1	2	2	0	4	1	2	0	6	7	rs10512435	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:29652884T>C	ENST00000358273.4	+	37	5265	c.4882T>C	c.(4882-4884)Tta>Cta	p.L1628L	NF1_ENST00000581113.2_3'UTR|NF1_ENST00000356175.3_Silent_p.L1607L	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1628	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.?(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)		ATACCATGTCTTACTGACTTT	0.338			"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)			T|||	107	0.0213658	0.0802	0.0014	5008	,	,		19715	0.0		0.0	False		,,,				2504	0.0				p.L1628L		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.T4882C						PASS	.	T	,	309,4097	164.7+/-196.3	6,297,1900	116	112	113		4819,4882	4.6	1	17	dbSNP_119	113	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	NF1	NM_000267.3,NM_001042492.2	,	6,298,6199	CC,CT,TT		0.0116,7.0132,2.3835	,	1607/2819,1628/2840	29652884	310,12696	2203	4300	6503	SO:0001819	synonymous_variant	4763	exon37	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	CATGTCTTACTGA		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.4882T>C	17.37:g.29652884T>C		93	0	0		76	42	0.552632	NM_001042492	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	37	CCDS42292.1																																																																																			T|0.979;C|0.021	0.021	strong		0.338	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		C	29652884	T	C	29652884	2	2	22	1	0	0	0	0	0	0	0	1	10365	1606	56	3		3	NF1	17	29652884	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1713457	29652884	51542326	3452	6353											
CDK5R1	8851	hgsc.bcm.edu	37	chr17	30815208	30815208	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tcgctgcttctgcagggctgGcaggaccagggcttcatcac	6	9	13	13	1	3	0	2	0	1	0	4	1	3	1	1	4	2	6	1	4	0	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:30815208G>A	ENST00000313401.3	+	2	1259	c.570G>A	c.(568-570)tgG>tgA	p.W190*		NM_003885.2	NP_003876.1	Q15078	CD5R1_HUMAN	cyclin-dependent kinase 5, regulatory subunit 1 (p35)	190					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)			TGCAGGGCTGGCAGGACCAGG	0.652																																					p.W190X		Atlas-SNP	.											.	CDK5R1	30	.	0			c.G570A						PASS	.						68	71	70					17																	30815208		2203	4300	6503	SO:0001587	stop_gained	8851	exon2			GGGCTGGCAGGAC	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.570G>A	17.37:g.30815208G>A	ENSP00000318486:p.Trp190*	107	0	0		131	20	0.152672	NM_003885	E1P664|Q5U0G3	Nonsense_Mutation	SNP	ENST00000313401.3	37	CCDS11273.1	.	.	.	.	.	.	.	.	.	.	G	43	10.067794	0.99329	.	.	ENSG00000176749	ENST00000313401	.	.	.	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.2883	16.9953	0.86366	0.0:0.0:1.0:0.0	.	.	.	.	X	190	.	ENSP00000318486:W190X	W	+	3	0	CDK5R1	27839321	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.759000	0.98931	2.609000	0.88269	0.557000	0.71058	TGG	.	.	none		0.652	CDK5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256264.1	NM_003885		A	30815208	G	A	30815208	4	1	22	1	0	0	0	0	0	1	0	0	3145	1212	42	2	572	2	CDK5R1	17	30815208	Nonsense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1162324	30815208	50380002	3453	6354											
RFFL	117584	hgsc.bcm.edu	37	chr17	33348541	33348541	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggggacaaggtggaggcaCgagtcctgtcctcctgggag	7	7	17	10	1	0	0	0	0	0	0	3	4	3	3	3	6	0	1	3	6	1	0	rs34747500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:33348541C>T	ENST00000315249.7	-	3	662	c.440G>A	c.(439-441)cGt>cAt	p.R147H	RFFL_ENST00000584655.1_Missense_Mutation_p.R147H|RFFL_ENST00000415395.2_Missense_Mutation_p.R147H|RFFL_ENST00000378516.2_Missense_Mutation_p.R147H|RFFL_ENST00000394597.2_Missense_Mutation_p.R147H|RFFL_ENST00000413582.2_Missense_Mutation_p.R147H|RFFL_ENST00000268850.7_Missense_Mutation_p.R147H|RFFL_ENST00000447669.2_Missense_Mutation_p.R147H|RAD51L3-RFFL_ENST00000593039.1_Intron					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)		GGTGGAGGCACGAGTCCTGTC	0.582													C|||	68	0.0135783	0.0356	0.0029	5008	,	,		19710	0.0188		0.0	False		,,,				2504	0.0				p.R147H		Atlas-SNP	.											.	RFFL	27	.	0			c.G440A						PASS	.	C	HIS/ARG	124,4282	91.6+/-130.3	3,118,2082	81	65	70		440	-4.3	0.4	17	dbSNP_126	70	1,8599	1.2+/-3.3	0,1,4299	yes	missense	RFFL	NM_001017368.1	29	3,119,6381	TT,TC,CC		0.0116,2.8143,0.9611	benign	147/364	33348541	125,12881	2203	4300	6503	SO:0001583	missense	117584	exon3			GAGGCACGAGTCC	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.440G>A	17.37:g.33348541C>T	ENSP00000326170:p.Arg147His	132	0	0		138	65	0.471014	NM_001017368		Missense_Mutation	SNP	ENST00000315249.7	37	CCDS11286.1	31	0.014194139194139194	16	0.032520325203252036	1	0.0027624309392265192	14	0.024475524475524476	0	0.0	C	7.587	0.669935	0.14776	0.028143	1.16E-4	ENSG00000092871	ENST00000315249;ENST00000394597;ENST00000378516;ENST00000268850;ENST00000413582;ENST00000415395	T;T;T;T;T;T	0.46451	0.87;0.87;0.89;0.91;0.89;0.87	5.65	-4.35	0.03656	.	1.494590	0.03679	N	0.245226	T	0.14184	0.0343	L	0.46157	1.445	0.19300	N	0.999975	B;B;B;B	0.10296	0.003;0.003;0.002;0.003	B;B;B;B	0.10450	0.005;0.003;0.001;0.001	T	0.33497	-0.9866	10	0.45353	T	0.12	-0.0021	7.6995	0.28615	0.1025:0.4344:0.0:0.4631	rs34747500	147;147;147;147	C9JN73;Q8WZ73-3;Q8WZ73;Q8WZ73-2	.;.;RFFL_HUMAN;.	H	147	ENSP00000326170:R147H;ENSP00000378096:R147H;ENSP00000367777:R147H;ENSP00000268850:R147H;ENSP00000408513:R147H;ENSP00000412322:R147H	ENSP00000268850:R147H	R	-	2	0	RFFL	30372654	0.000000	0.05858	0.450000	0.26969	0.123000	0.20343	-1.166000	0.03129	-0.526000	0.06383	-0.940000	0.02684	CGT	C|0.986;T|0.014	0.014	strong		0.582	RFFL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256460.2	NM_057178		T	33348541	C	T	33348541	3	4	22	1	0	0	0	0	1	0	0	0	13265	536	19	1	671	1	RFFL	17	33348541	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2533333	33348541	47846669	3454	6355											
UNC45B	146862	hgsc.bcm.edu	37	chr17	33475426	33475426	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctggccacgctttatcggaaCcgggcagcctgtggcctgaa	7	8	13	13	3	0	1	0	1	0	0	1	2	0	2	4	4	2	2	4	4	3	2	rs16970656	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:33475426C>T	ENST00000268876.5	+	2	241	c.144C>T	c.(142-144)aaC>aaT	p.N48N	UNC45B_ENST00000433649.1_Silent_p.N48N|UNC45B_ENST00000394570.2_Silent_p.N48N|UNC45B_ENST00000591048.1_Silent_p.N48N|UNC45B_ENST00000378449.1_Silent_p.N48N	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	48					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)				TTTATCGGAACCGGGCAGCCT	0.637													C|||	90	0.0179712	0.0658	0.0043	5008	,	,		18215	0.0		0.0	False		,,,				2504	0.0				p.N48N		Atlas-SNP	.											.	UNC45B	133	.	0			c.C144T						PASS	.	C	,	259,4147	144.2+/-179.2	2,255,1946	54	51	52		144,144	1.8	1	17	dbSNP_123	52	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	UNC45B	NM_001033576.1,NM_173167.2	,	2,257,6244	TT,TC,CC		0.0233,5.8783,2.0068	,	48/930,48/932	33475426	261,12745	2203	4300	6503	SO:0001819	synonymous_variant	146862	exon2			TCGGAACCGGGCA	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.144C>T	17.37:g.33475426C>T		77	0	0		86	41	0.476744	NM_001267052	Q495Q8|Q495Q9	Silent	SNP	ENST00000268876.5	37	CCDS11292.1																																																																																			C|0.975;T|0.025	0.025	strong		0.637	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2	NM_173167		T	33475426	C	T	33475426	2	4	22	1	0	0	0	0	0	0	0	1	17004	506	18	2		2	UNC45B	17	33475426	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	126885	33475426	47719784	3455	6356											
AMAC1	146861	hgsc.bcm.edu	37	chr17	33520904	33520904	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagagagtgaggacggcggaGcagacggtggaagaaccttt	12	5	17	7	3	0	4	0	1	0	3	0	8	0	7	1	5	2	1	1	5	2	1	rs61753879	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:33520904G>A	ENST00000297307.5	-	1	508	c.423C>T	c.(421-423)tgC>tgT	p.C141C	RP11-799D4.2_ENST00000590144.1_RNA	NM_152462.2	NP_689675.1	Q8N808	S35G3_HUMAN	solute carrier family 35, member G3	141	EamA 1.					integral component of membrane (GO:0016021)											GGACGGCGGAGCAGACGGTGG	0.582													G|||	87	0.0173722	0.0635	0.0043	5008	,	,		19375	0.0		0.0	False		,,,				2504	0.0				p.C141C		Atlas-SNP	.											.	.	.	.	0			c.C423T						PASS	.	G		259,4147	148.4+/-182.8	5,249,1949	163	154	157		423		0.3	17	dbSNP_129	157	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SLC35G3	NM_152462.2		5,250,6248	AA,AG,GG		0.0116,5.8783,1.9991		141/339	33520904	260,12746	2203	4300	6503	SO:0001819	synonymous_variant	146861	exon1			GGCGGAGCAGACG	AK097473	CCDS11293.1	17q21.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000164729	ENSG00000164729		"Solute carriers"	26848	protein-coding gene	gene with protein product			"transmembrane protein 21A", "acyl-malonyl condensing enzyme 1"	TMEM21A, AMAC1			Standard	NM_152462		Approved	FLJ40154	uc002hjd.2	Q8N808	OTTHUMG00000132929	ENST00000297307.5:c.423C>T	17.37:g.33520904G>A		195	0	0		211	104	0.492891	NM_152462	B9EGE9	Silent	SNP	ENST00000297307.5	37	CCDS11293.1																																																																																			G|0.977;A|0.023	0.023	strong		0.582	SLC35G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256445.2	NM_152462		A	33520904	G	A	33520904	2	1	22	1	0	0	0	0	0	0	0	1	559	963	34	2		2	AMAC1	17	33520904	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	45478	33520904	47674306	3456	6357											
SLFN13	146857	hgsc.bcm.edu	37	chr17	33769211	33769211	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attccctgggagaaaggtcgCatttgcttgtgtattaactc	9	14	10	8	1	0	1	0	0	0	1	3	2	1	1	1	2	2	3	1	2	3	5	rs77814846	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:33769211C>T	ENST00000285013.6	-	5	1568	c.1293G>A	c.(1291-1293)atG>atA	p.M431I	SLFN13_ENST00000526861.1_Missense_Mutation_p.M431I|SLFN13_ENST00000360502.2_Missense_Mutation_p.M113I|SLFN13_ENST00000533791.1_Missense_Mutation_p.M431I|SLFN13_ENST00000534689.1_Missense_Mutation_p.M113I|SLFN13_ENST00000542635.1_Missense_Mutation_p.M431I	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	431						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)		AGAAAGGTCGCATTTGCTTGT	0.488													C|||	74	0.0147764	0.053	0.0058	5008	,	,		18201	0.0		0.0	False		,,,				2504	0.0				p.M431I		Atlas-SNP	.											.	SLFN13	79	.	0			c.G1293A						PASS	.	C	ILE/MET	199,4207	124.9+/-162.1	3,193,2007	91	82	85		1293	-6.2	0	17	dbSNP_131	85	2,8598	2.2+/-6.3	0,2,4298	yes	missense	SLFN13	NM_144682.5	10	3,195,6305	TT,TC,CC		0.0233,4.5166,1.5454	benign	431/898	33769211	201,12805	2203	4300	6503	SO:0001583	missense	146857	exon5			AGGTCGCATTTGC	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.1293G>A	17.37:g.33769211C>T	ENSP00000285013:p.Met431Ile	158	0	0		155	76	0.490323	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Missense_Mutation	SNP	ENST00000285013.6	37	CCDS32620.1	31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	c	0.430	-0.903761	0.02453	0.045166	2.33E-4	ENSG00000154760	ENST00000285013;ENST00000360502;ENST00000526861;ENST00000542635;ENST00000534689;ENST00000532210	T;T;T;T;T;T	0.16597	4.64;4.06;4.64;4.64;4.06;2.33	3.09	-6.17	0.02091	.	0.757041	0.12071	N	0.502241	T	0.00552	0.0018	N	0.17474	0.49	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.13407	0.009;0.0	T	0.36866	-0.9730	10	0.05525	T	0.97	.	1.256	0.01991	0.1521:0.2533:0.1508:0.4438	.	113;431	Q68D06-2;Q68D06	.;SLN13_HUMAN	I	431;113;431;431;113;100	ENSP00000285013:M431I;ENSP00000353692:M113I;ENSP00000434439:M431I;ENSP00000444016:M431I;ENSP00000435442:M113I;ENSP00000435328:M100I	ENSP00000285013:M431I	M	-	3	0	SLFN13	30793324	0.000000	0.05858	0.001000	0.08648	0.138000	0.21146	-0.875000	0.04205	-1.010000	0.03396	0.205000	0.17691	ATG	C|0.987;T|0.013	0.013	strong		0.488	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682		T	33769211	C	T	33769211	3	4	22	1	0	0	0	0	1	0	0	0	14751	710	25	2	1408	2	SLFN13	17	33769211	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	248307	33769211	47425999	3457	6358											
C17orf50	146853	hgsc.bcm.edu	37	chr17	34091130	34091130	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggacgaggacgaggacaacCagaggccgctggaggacagc	13	1	17	10	3	0	1	0	0	0	1	0	8	0	6	2	6	2	1	2	6	1	0	rs140052043	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34091130C>A	ENST00000285023.4	+	2	150	c.118C>A	c.(118-120)Cag>Aag	p.Q40K	C17orf50_ENST00000586491.1_Missense_Mutation_p.Q40K|C17orf50_ENST00000588628.1_Missense_Mutation_p.P47Q	NM_145272.3	NP_660315.2	Q8WW18	CQ050_HUMAN	chromosome 17 open reading frame 50	40													Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		cgaggaCAACCAGAGGCCGCT	0.692													C|||	43	0.00858626	0.0318	0.0014	5008	,	,		9618	0.0		0.0	False		,,,				2504	0.0				p.Q40K		Atlas-SNP	.											.	C17orf50	4	.	0			c.C118A						PASS	.	C	LYS/GLN	73,3255		1,71,1592	8	13	11		118	-3.7	0	17	dbSNP_134	11	2,6858		0,2,3428	yes	missense	C17orf50	NM_145272.3	53	1,73,5020	AA,AC,CC		0.0292,2.1935,0.7362	benign	40/175	34091130	75,10113	1664	3430	5094	SO:0001583	missense	146853	exon2			GACAACCAGAGGC	BC021727	CCDS42298.1	17q12	2014-05-06			ENSG00000154768	ENSG00000270806			29581	protein-coding gene	gene with protein product							Standard	NM_145272		Approved		uc002hjx.3	Q8WW18	OTTHUMG00000188389	ENST00000285023.4:c.118C>A	17.37:g.34091130C>A	ENSP00000285023:p.Gln40Lys	71	0	0		76	34	0.447368	NM_145272	Q6Q621	Missense_Mutation	SNP	ENST00000285023.4	37	CCDS42298.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	C	6.499	0.460290	0.12342	0.021935	2.92E-4	ENSG00000154768	ENST00000285023	T	0.42513	0.97	1.86	-3.72	0.04411	.	.	.	.	.	T	0.07052	0.0179	N	0.19112	0.55	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.20571	-1.0271	9	0.54805	T	0.06	-3.6237	0.4196	0.00454	0.216:0.2495:0.3138:0.2207	.	40	Q8WW18	CQ050_HUMAN	K	40	ENSP00000285023:Q40K	ENSP00000285023:Q40K	Q	+	1	0	C17orf50	31115243	0.000000	0.05858	0.016000	0.15963	0.022000	0.10575	-0.033000	0.12246	-0.319000	0.08652	-0.502000	0.04539	CAG	C|0.993;A|0.007	0.007	strong		0.692	C17orf50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449132.1	NM_145272		A	34091130	C	A	34091130	3	1	22	1	0	0	0	0	1	0	0	0	1863	595	21	4	124	4	C17orf50	17	34091130	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	321919	34091130	47104080	3458	6359											
CCL18	6362	hgsc.bcm.edu	37	chr17	34391721	34391721	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatgaagggccttgcagctGccctccttgtcctcgtctgc	4	12	10	15	1	2	1	1	1	1	0	5	1	4	1	4	1	4	2	4	1	1	2	rs73290772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34391721G>A	ENST00000004921.3	+	1	82	c.19G>A	c.(19-21)Gcc>Acc	p.A7T		NM_002988.2	NP_002979.1	P55774	CCL18_HUMAN	chemokine (C-C motif) ligand 18 (pulmonary and activation-regulated)	7					cell chemotaxis (GO:0060326)|cell communication (GO:0007154)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|immune response (GO:0006955)|inflammatory response (GO:0006954)|response to biotic stimulus (GO:0009607)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	chemokine activity (GO:0008009)			endometrium(1)|large_intestine(2)|lung(1)	4		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		CCTTGCAGCTGCCCTCCTTGT	0.587													G|||	32	0.00638978	0.0227	0.0014	5008	,	,		20323	0.0		0.001	False		,,,				2504	0.0				p.A7T		Atlas-SNP	.											.	CCL18	9	.	0			c.G19A						PASS	.	G	THR/ALA	83,4323	70.9+/-108.8	1,81,2121	175	144	154		19	-4.2	0	17	dbSNP_130	154	4,8596	3.7+/-12.6	0,4,4296	yes	missense	CCL18	NM_002988.2	58	1,85,6417	AA,AG,GG		0.0465,1.8838,0.6689	possibly-damaging	7/90	34391721	87,12919	2203	4300	6503	SO:0001583	missense	6362	exon1			GCAGCTGCCCTCC	Y13710	CCDS11306.1	17q11.2	2014-05-06	2002-08-22	2002-08-23	ENSG00000006074	ENSG00000275385		"Chemokine ligands"	10616	protein-coding gene	gene with protein product		603757	"small inducible cytokine subfamily A (Cys-Cys), member 18, pulmonary and activation-regulated"	SCYA18		9233607, 10049593	Standard	NM_002988		Approved	DC-CK1, PARC, AMAC-1, DCCK1, MIP-4, CKb7	uc002hku.3	P55774	OTTHUMG00000188410	ENST00000004921.3:c.19G>A	17.37:g.34391721G>A	ENSP00000004921:p.Ala7Thr	115	0	0		150	74	0.493333	NM_002988	B5BUM2|Q53X71	Missense_Mutation	SNP	ENST00000004921.3	37	CCDS11306.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	15.95	2.982703	0.53827	0.018838	4.65E-4	ENSG00000006074	ENST00000004921	T	0.03468	3.92	4.63	-4.23	0.03789	.	0.749621	0.12687	N	0.447482	T	0.02418	0.0074	.	.	.	0.09310	N	1	D	0.65815	0.995	P	0.53954	0.738	T	0.10382	-1.0632	9	0.37606	T	0.19	.	5.6346	0.17530	0.3533:0.0:0.5254:0.1213	.	7	P55774	CCL18_HUMAN	T	7	ENSP00000004921:A7T	ENSP00000004921:A7T	A	+	1	0	CCL18	31415834	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.697000	0.05098	-0.814000	0.04352	-0.311000	0.09066	GCC	G|0.994;A|0.006	0.006	strong		0.587	CCL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256583.1	NM_002988		A	34391721	G	A	34391721	3	1	22	1	0	0	0	0	1	0	0	0	2891	1319	46	2	21	2	CCL18	17	34391721	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	300591	34391721	46803489	3459	6360											
CCL4L1	388372	hgsc.bcm.edu	37	chr17	34641448	34641448	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtctgctccttgttctacAgattccaaaccaaaagaggc	11	11	7	12	0	2	2	0	0	2	2	4	2	4	2	3	1	3	2	3	1	4	4	rs184899362		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34641448A>G	ENST00000394465.2	+	3	508		c.e3-1		TBC1D3H_ENST00000400684.4_Intron|TBC1D3C_ENST00000308078.7_Intron|TBC1D3H_ENST00000535446.1_Intron|CCL4L2_ENST00000482104.1_3'UTR|CCL4L2_ENST00000339270.6_Splice_Site|TBC1D3C_ENST00000451448.2_Intron			Q8NHW4	CC4L_HUMAN	chemokine (C-C motif) ligand 4-like 2						cell chemotaxis (GO:0060326)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular space (GO:0005615)		p.?(1)		endometrium(1)	1		Breast(25;0.102)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CTTGTTCTACAGATTCCAAAC	0.522																																					.		Atlas-SNP	.											CCL4L2,NS,carcinoma,0,1	.	.	1	1	Unknown(1)	endometrium(1)	c.192-2A>G						scavenged	.						219	152	175					17																	34641448		2159	4154	6313	SO:0001630	splice_region_variant	9560	exon3			TTCTACAGATTCC			17q12	2005-08-09			ENSG00000197262			"Chemokine ligands"	24066	protein-coding gene	gene with protein product		603782				15028295	Standard	NM_001291468		Approved		uc010cuj.3	Q8NHW4	OTTHUMG00000133066	ENST00000394465.2:c.192-1A>G	17.37:g.34641448A>G		871	0	0		334	28	0.0838323	NM_001001435	B2RUZ3|B7ZMA8|Q50EM1|Q50EM2|Q50EM3|Q50EM4|Q50EM5|Q50EM6|Q50EM7|Q50EM8|Q569J2|Q6NSB0	Splice_Site	SNP	ENST00000394465.2	37	CCDS11311.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	N	11.83	1.756201	0.31137	.	.	ENSG00000197262	ENST00000394465;ENST00000339270	.	.	.	3.1	3.1	0.35709	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.8193	0.29278	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CCL4L2	31665561	1.000000	0.71417	0.994000	0.49952	0.682000	0.39822	4.719000	0.61937	1.074000	0.40909	0.344000	0.21773	.	G|1.000;|0.000	1.000	weak		0.522	CCL4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256699.1	NM_207007	Intron	G	34641448	A	G	34641448	5	3	22	1	0	0	0	0	0	0	1	0	2905	202	7	3	491	3	CCL4L1	17	34641448	Splice_Site	SNP	A	TCGA-G8-6324-01A-11D-2210-10	249727	34641448	46553762	3460	6361											
MYO19	80179	hgsc.bcm.edu	37	chr17	34856697	34856697	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgagcatgacggcccgccActgccgctcctgctctcggt	5	8	12	16	4	1	2	0	2	1	0	3	3	2	2	4	2	3	3	4	2	0	0	rs56919948	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34856697A>G	ENST00000431794.3	-	23	2872	c.2350T>C	c.(2350-2352)Tgg>Cgg	p.W784R	MYO19_ENST00000268852.9_Missense_Mutation_p.W584R	NM_001163735.1	NP_001157207.1	Q96H55	MYO19_HUMAN	myosin XIX	784	IQ 2. {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)		ACGGCCCGCCACTGCCGCTCC	0.637													G|||	28	0.00559105	0.0204	0.0014	5008	,	,		18434	0.0		0.0	False		,,,				2504	0.0				p.W784R		Atlas-SNP	.											.	MYO19	130	.	0			c.T2350C						PASS	.	G	ARG/TRP,ARG/TRP	74,4174		1,72,2051	14	18	17		2350,1750	2.8	0.4	17	dbSNP_129	17	0,8448		0,0,4224	yes	missense,missense	MYO19	NM_001163735.1,NM_025109.5	101,101	1,72,6275	GG,GA,AA		0.0,1.742,0.5829	benign,benign	784/971,584/771	34856697	74,12622	2124	4224	6348	SO:0001583	missense	80179	exon24			CCCGCCACTGCCG	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.2350T>C	17.37:g.34856697A>G	ENSP00000409936:p.Trp784Arg	73	0	0		72	26	0.361111	NM_001163735	Q59GS4|Q9H5X2	Missense_Mutation	SNP	ENST00000431794.3	37	CCDS54112.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	G	0.005	-2.234560	0.00277	0.01742	0.0	ENSG00000141140	ENST00000431794;ENST00000268852	T;T	0.53640	0.61;0.61	5.12	2.82	0.32997	.	0.000000	0.42548	N	0.000694	T	0.04770	0.0129	N	0.00197	-1.87	0.24385	N	0.994776	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33727	-0.9857	10	0.05959	T	0.93	.	6.7399	0.23431	0.1403:0.0:0.3167:0.543	rs56919948;rs61753952	784;584	Q96H55;Q96H55-4	MYO19_HUMAN;.	R	784;584	ENSP00000409936:W784R;ENSP00000268852:W584R	ENSP00000268852:W584R	W	-	1	0	MYO19	31930810	0.989000	0.36119	0.423000	0.26634	0.007000	0.05969	1.804000	0.38873	0.033000	0.15463	-1.507000	0.00952	TGG	A|0.996;G|0.004	0.004	strong		0.637	MYO19-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451074.1	NM_025109		G	34856697	A	G	34856697	3	3	22	1	0	0	0	0	1	0	0	0	10076	159	6	3	578	3	MYO19	17	34856697	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	215249	34856697	46338513	3461	6362											
MYO19	80179	hgsc.bcm.edu	37	chr17	34858985	34858985	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcggggccagaggatgtgcAaggatgaagccttcttagta	10	9	15	7	1	1	2	0	1	1	1	2	4	1	4	2	4	2	2	2	4	4	3	rs61743158	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34858985A>G	ENST00000431794.3	-	21	2554	c.2032T>C	c.(2032-2034)Tgc>Cgc	p.C678R	MYO19_ENST00000268852.9_Missense_Mutation_p.C478R	NM_001163735.1	NP_001157207.1	Q96H55	MYO19_HUMAN	myosin XIX	678	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)		GAGGATGTGCAAGGATGAAGC	0.493													G|||	24	0.00479233	0.0174	0.0014	5008	,	,		18666	0.0		0.0	False		,,,				2504	0.0				p.C678R		Atlas-SNP	.											.	MYO19	130	.	0			c.T2032C						PASS	.	G	ARG/CYS,ARG/CYS	77,3859		3,71,1894	191	202	198		2032,1432	4.3	0.6	17	dbSNP_129	198	0,8298		0,0,4149	yes	missense,missense	MYO19	NM_001163735.1,NM_025109.5	180,180	3,71,6043	GG,GA,AA		0.0,1.9563,0.6294	benign,benign	678/971,478/771	34858985	77,12157	1968	4149	6117	SO:0001583	missense	80179	exon22			ATGTGCAAGGATG	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.2032T>C	17.37:g.34858985A>G	ENSP00000409936:p.Cys678Arg	149	0	0		154	65	0.422078	NM_001163735	Q59GS4|Q9H5X2	Missense_Mutation	SNP	ENST00000431794.3	37	CCDS54112.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	G	4.905	0.168151	0.09339	0.019563	0.0	ENSG00000141140	ENST00000431794;ENST00000268852	D;D	0.94966	-3.57;-3.57	5.25	4.27	0.50696	Myosin head, motor domain (1);	.	.	.	.	T	0.70141	0.3190	N	0.00926	-1.1	0.23515	N	0.997514	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.67360	-0.5690	9	0.23302	T	0.38	.	7.8717	0.29569	0.0883:0.1733:0.7385:0.0	.	678;478	Q96H55;Q96H55-4	MYO19_HUMAN;.	R	678;478	ENSP00000409936:C678R;ENSP00000268852:C478R	ENSP00000268852:C478R	C	-	1	0	MYO19	31933098	0.261000	0.24063	0.559000	0.28332	0.034000	0.12701	1.018000	0.30002	0.706000	0.31912	-0.213000	0.12676	TGC	A|0.995;G|0.005	0.005	strong		0.493	MYO19-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451074.1	NM_025109		G	34858985	A	G	34858985	3	3	22	1	0	0	0	0	1	0	0	0	10076	130	5	3	904	3	MYO19	17	34858985	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2288	34858985	46336225	3462	6363											
MYO19	80179	hgsc.bcm.edu	37	chr17	34859831	34859831	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgatatggatggtctccacGaggccacaggcctccagctg	8	8	12	13	1	1	1	0	1	1	0	3	3	2	2	4	4	1	1	4	4	1	1	rs73276768	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34859831G>A	ENST00000431794.3	-	20	2457	c.1935C>T	c.(1933-1935)ctC>ctT	p.L645L	MYO19_ENST00000268852.9_Silent_p.L445L	NM_001163735.1	NP_001157207.1	Q96H55	MYO19_HUMAN	myosin XIX	645	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)		TGGTCTCCACGAGGCCACAGG	0.632													G|||	22	0.00439297	0.0166	0.0	5008	,	,		18572	0.0		0.0	False		,,,				2504	0.0				p.L645L		Atlas-SNP	.											.	MYO19	130	.	0			c.C1935T						PASS	.	G	,	68,4038		3,62,1988	17	21	19		1935,1335	-11.3	0.9	17	dbSNP_130	19	1,8385		0,1,4192	no	coding-synonymous,coding-synonymous	MYO19	NM_001163735.1,NM_025109.5	,	3,63,6180	AA,AG,GG		0.0119,1.6561,0.5524	,	645/971,445/771	34859831	69,12423	2053	4193	6246	SO:0001819	synonymous_variant	80179	exon21			CTCCACGAGGCCA	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.1935C>T	17.37:g.34859831G>A		37	0	0		45	19	0.422222	NM_001163735	Q59GS4|Q9H5X2	Silent	SNP	ENST00000431794.3	37	CCDS54112.1																																																																																			G|0.996;A|0.004	0.004	strong		0.632	MYO19-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451074.1	NM_025109		A	34859831	G	A	34859831	2	1	22	1	0	0	0	0	0	0	0	1	10076	1045	37	1		1	MYO19	17	34859831	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	846	34859831	46335379	3463	6364											
MRM1	79154	hgsc.bcm.edu	37	chr17	34958531	34958531	+	IGR	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tggccgaggcgcgggacattCcagttctgcggcccagacgg	6	6	16	13	5	1	1	0	0	1	1	2	3	2	2	3	5	1	1	3	5	0	2	rs60978234	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34958531C>T	ENST00000251312.5	+	0	1598				MRM1_ENST00000250156.7_Missense_Mutation_p.P98S|MRM1_ENST00000585770.1_5'UTR	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						GCGGGACATTCCAGTTCTGCG	0.701													C|||	23	0.00459265	0.0166	0.0	5008	,	,		15249	0.0		0.001	False		,,,				2504	0.0				p.P98S		Atlas-SNP	.											MRM1,NS,haematopoietic_neoplasm,-2,1	MRM1	19	1	0			c.C292T						PASS	.	C	SER/PRO	68,4320		1,66,2127	22	26	24		292	4.9	1	17	dbSNP_129	24	0,8576		0,0,4288	yes	missense	MRM1	NM_024864.3	74	1,66,6415	TT,TC,CC		0.0,1.5497,0.5245	probably-damaging	98/354	34958531	68,12896	2194	4288	6482	SO:0001628	intergenic_variant	79922	exon1			GACATTCCAGTTC		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		17.37:g.34958531C>T		21	0	0		21	8	0.380952	NM_024864	B2RDZ3|Q9BUC7|Q9H674	Missense_Mutation	SNP	ENST00000251312.5	37	CCDS11315.2	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	14.72	2.620552	0.46736	0.015497	0.0	ENSG00000129282	ENST00000250156	T	0.28666	1.6	4.9	4.9	0.64082	RNA 2-O ribose methyltransferase, substrate binding (2);	0.065831	0.64402	D	0.000006	T	0.21509	0.0518	M	0.69463	2.115	0.80722	D	1	B	0.32968	0.392	B	0.42062	0.374	T	0.07139	-1.0788	10	0.07175	T	0.84	-13.0363	15.1676	0.72840	0.0:1.0:0.0:0.0	rs60978234	98	Q6IN84	MRM1_HUMAN	S	98	ENSP00000250156:P98S	ENSP00000250156:P98S	P	+	1	0	MRM1	32032644	0.845000	0.29573	0.969000	0.41365	0.561000	0.35649	3.772000	0.55325	2.423000	0.82170	0.555000	0.69702	CCA	C|0.993;T|0.007	0.007	strong		0.701	DHRS11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256681.2	NM_024308		T	34958531	C	T	34958531	1	4	22	0	1	0	0	0	0	0	0	0	9780	855	30	2		2	MRM1	17	34958531	IGR	SNP	C	TCGA-G8-6324-01A-11D-2210-10	98700	34958531	46236679	3464	6365											
MRM1	79154	hgsc.bcm.edu	37	chr17	34958760	34958761	+	IGR	INS	-	-	G																															ttcctcggagtggataaggtINScatcaccagccggagaaaca																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34958760_34958761insG	ENST00000251312.5	+	0	1598				MRM1_ENST00000250156.7_Frame_Shift_Ins_p.I175fs|MRM1_ENST00000585770.1_Intron	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						GTGGATAAGGTCATCACCAGCC	0.594																																					p.V174fs		Pindel,Atlas-Indel	.											.	MRM1	19	.	0			c.521_522insG						PASS	.																																			SO:0001628	intergenic_variant	79922	exon1			.		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		17.37:g.34958760_34958761insG		29	0	.		33	12	0.364	NM_024864	B2RDZ3|Q9BUC7|Q9H674	Frame_Shift_Ins	INS	ENST00000251312.5	37	CCDS11315.2																																																																																			.	.	none		0.594	DHRS11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256681.2	NM_024308		G	34958761	-	G	34958760	6	5	22	0	1	1	1	0	0	0	0	0	9780	1667	58	0		0	MRM1	17	34958760	IGR	INS	-	TCGA-G8-6324-01A-11D-2210-10	229	34958760	46236450	3465	6366											
ACACA	31	hgsc.bcm.edu	37	chr17	35470031	35470031	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggcacgctacctgctttcTcggtcagcatacatctccat	9	11	7	14	2	3	0	1	0	2	0	5	0	3	0	2	2	4	4	2	2	3	3	rs55811414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:35470031T>G	ENST00000394406.2	-	51	6523	c.6333A>C	c.(6331-6333)cgA>cgC	p.R2111R	ACACA_ENST00000335166.5_Silent_p.R2033R|ACACA_ENST00000360679.3_Silent_p.R2053R|ACACA_ENST00000361253.5_Silent_p.R237R|ACACA_ENST00000353139.5_Silent_p.R2148R	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	2111	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)	ACCTGCTTTCTCGGTCAGCAT	0.552													T|||	221	0.0441294	0.149	0.0274	5008	,	,		19920	0.0		0.004	False		,,,				2504	0.001				p.R2148R	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-SNP	.											.	ACACA	395	.	0			c.A6444C						PASS	.	T	,,,,	461,3945	218.4+/-236.5	26,409,1768	82	71	75		6444,6333,6159,6099,6333	-1.6	1	17	dbSNP_129	75	32,8568	21.6+/-65.8	0,32,4268	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ACACA	NM_198834.1,NM_198836.1,NM_198837.1,NM_198838.1,NM_198839.1	,,,,	26,441,6036	GG,GT,TT		0.3721,10.463,3.7906	,,,,	2148/2384,2111/2347,2053/2289,2033/2269,2111/2347	35470031	493,12513	2203	4300	6503	SO:0001819	synonymous_variant	31	exon51			GCTTTCTCGGTCA	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.6333A>C	17.37:g.35470031T>G		126	0	0		124	57	0.459677	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Silent	SNP	ENST00000394406.2	37	CCDS11317.1																																																																																			G|0.034;T|0.966	0.034	strong		0.552	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		G	35470031	T	G	35470031	2	3	22	1	0	0	0	0	0	0	0	1	106	1538	54	5		5	ACACA	17	35470031	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	511271	35470031	45725179	3466	6367											
TADA2A	6871	hgsc.bcm.edu	37	chr17	35830554	35830554	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacgggaggaagagcgccttAaacgcactatgctctcagaa	13	6	11	11	3	1	2	1	0	1	2	2	4	1	4	1	2	3	2	1	2	5	2	rs142392695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:35830554A>C	ENST00000394395.2	+	13	1119	c.946A>C	c.(946-948)Aaa>Caa	p.K316Q	TADA2A_ENST00000591992.1_3'UTR|TADA2A_ENST00000225396.6_Missense_Mutation_p.K316Q	NM_001166105.1	NP_001159577.1	O75478	TAD2A_HUMAN	transcriptional adaptor 2A	316					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						AGAGCGCCTTAAACGCACTAT	0.507													A|||	16	0.00319489	0.0121	0.0	5008	,	,		16970	0.0		0.0	False		,,,				2504	0.0				p.K316Q		Atlas-SNP	.											.	TADA2A	91	.	0			c.A946C						PASS	.	A	GLN/LYS,GLN/LYS	52,4354	52.9+/-88.7	0,52,2151	143	135	138		946,946	5.6	1	17	dbSNP_134	138	0,8600		0,0,4300	yes	missense,missense	TADA2A	NM_001166105.1,NM_001488.3	53,53	0,52,6451	CC,CA,AA		0.0,1.1802,0.3998	possibly-damaging,possibly-damaging	316/444,316/444	35830554	52,12954	2203	4300	6503	SO:0001583	missense	6871	exon13			CGCCTTAAACGCA	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.946A>C	17.37:g.35830554A>C	ENSP00000377918:p.Lys316Gln	71	0	0		71	33	0.464789	NM_001488	A8MVD0|B3KMU9|Q9BVJ0|Q9UCW2|Q9UP49	Missense_Mutation	SNP	ENST00000394395.2	37	CCDS11319.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	A	25.5	4.644355	0.87859	0.011802	0.0	ENSG00000108264	ENST00000394395;ENST00000428846;ENST00000225396	T;T	0.43294	0.95;0.95	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.18299	0.0439	N	0.14661	0.345	0.80722	D	1	P	0.47409	0.895	B	0.38056	0.264	T	0.05194	-1.0900	10	0.16420	T	0.52	-20.0499	15.8074	0.78524	1.0:0.0:0.0:0.0	.	316	O75478	TAD2A_HUMAN	Q	316;215;316	ENSP00000377918:K316Q;ENSP00000225396:K316Q	ENSP00000225396:K316Q	K	+	1	0	TADA2A	32904667	1.000000	0.71417	0.998000	0.56505	0.945000	0.59286	8.946000	0.92992	2.127000	0.65507	0.533000	0.62120	AAA	A|0.996;C|0.004	0.004	strong		0.507	TADA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256677.3	NM_001488		C	35830554	A	C	35830554	3	2	22	1	0	0	0	0	1	0	0	0	15525	363	13	5	1087	5	TADA2A	17	35830554	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	360523	35830554	45364656	3467	6368											
GPR179	440435	hgsc.bcm.edu	37	chr17	36482372	36482372	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccaatcccaaggatagacAgtgggaggggtgaattcttc	11	9	12	9	0	1	2	0	1	1	1	4	4	3	4	2	4	0	0	2	4	4	3	rs58740367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:36482372A>C	ENST00000342292.4	-	11	7100	c.7080T>G	c.(7078-7080)acT>acG	p.T2360T	GPR179_ENST00000584976.1_Intron	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	2360					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)				AAGGATAGACAGTGGGAGGGG	0.498													A|||	291	0.058107	0.2148	0.0101	5008	,	,		20612	0.0		0.0	False		,,,				2504	0.0				p.T2360T		Atlas-SNP	.											.	GPR179	170	.	0			c.T7080G						PASS	.	A		644,3154		58,528,1313	73	67	69		7080	1.3	0.1	17	dbSNP_129	69	3,8259		0,3,4128	no	coding-synonymous	GPR179	NM_001004334.2		58,531,5441	CC,CA,AA		0.0363,16.9563,5.3648		2360/2368	36482372	647,11413	1899	4131	6030	SO:0001819	synonymous_variant	440435	exon11			ATAGACAGTGGGA		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.7080T>G	17.37:g.36482372A>C		72	0	0		59	59	1	NM_001004334		Silent	SNP	ENST00000342292.4	37	CCDS42308.1																																																																																			A|0.955;C|0.045	0.045	strong		0.498	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2			C	36482372	A	C	36482372	2	2	22	1	0	0	0	0	0	0	0	1	6682	175	7	5		5	GPR179	17	36482372	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	651818	36482372	44712838	3468	6369											
GPR179	440435	hgsc.bcm.edu	37	chr17	36487060	36487060	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccggctctctgttcgagaggCcttcttggccagcttcctcc	3	12	10	16	2	2	1	0	0	2	1	6	2	4	1	5	3	1	3	5	3	0	4	rs78470373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:36487060C>T	ENST00000342292.4	-	11	2412	c.2392G>A	c.(2392-2394)Gcc>Acc	p.A798T	GPR179_ENST00000584976.1_5'Flank	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	798					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)				GTTCGAGAGGCCTTCTTGGCC	0.652													C|||	53	0.0105831	0.0386	0.0029	5008	,	,		15168	0.0		0.0	False		,,,				2504	0.0				p.A798T		Atlas-SNP	.											.	GPR179	170	.	0			c.G2392A						PASS	.	C	THR/ALA	133,3827		3,127,1850	10	12	11		2392	4.3	0.8	17	dbSNP_131	11	1,8293		0,1,4146	no	missense	GPR179	NM_001004334.2	58	3,128,5996	TT,TC,CC		0.0121,3.3586,1.0935	benign	798/2368	36487060	134,12120	1980	4147	6127	SO:0001583	missense	440435	exon11			GAGAGGCCTTCTT		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.2392G>A	17.37:g.36487060C>T	ENSP00000345060:p.Ala798Thr	47	0	0		46	26	0.565217	NM_001004334		Missense_Mutation	SNP	ENST00000342292.4	37	CCDS42308.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	C	11.74	1.727989	0.30593	0.033586	1.21E-4	ENSG00000188888	ENST00000342292	T	0.54071	0.59	5.3	4.34	0.51931	.	1.005240	0.08006	N	0.989502	T	0.22859	0.0552	L	0.44542	1.39	0.31348	N	0.682852	B	0.26195	0.144	B	0.18263	0.021	T	0.31558	-0.9939	10	0.27785	T	0.31	-0.0366	12.8987	0.58113	0.0:0.9207:0.0:0.0793	.	798	Q6PRD1	GP179_HUMAN	T	798	ENSP00000345060:A798T	ENSP00000345060:A798T	A	-	1	0	GPR179	33740586	0.007000	0.16637	0.813000	0.32504	0.033000	0.12548	1.245000	0.32790	1.469000	0.48083	0.655000	0.94253	GCC	C|0.995;T|0.005	0.005	strong		0.652	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2			T	36487060	C	T	36487060	3	4	22	1	0	0	0	0	1	0	0	0	6682	739	26	2	4715	2	GPR179	17	36487060	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4688	36487060	44708150	3469	6370											
GPR179	440435	hgsc.bcm.edu	37	chr17	36487412	36487412	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatagagcttcttcagctcGtcctgtggggcagcagggag	7	9	15	10	1	2	1	1	0	1	1	4	2	3	2	1	3	3	5	1	3	1	3	rs111770829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:36487412G>A	ENST00000342292.4	-	11	2060	c.2040C>T	c.(2038-2040)gaC>gaT	p.D680D		NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	680					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)				TCTTCAGCTCGTCCTGTGGGG	0.587													G|||	133	0.0265575	0.0998	0.0014	5008	,	,		18185	0.0		0.0	False		,,,				2504	0.0				p.D680D		Atlas-SNP	.											.	GPR179	170	.	0			c.C2040T						PASS	.	G		294,3810		10,274,1768	45	50	48		2040	-9.7	0.5	17	dbSNP_132	48	3,8383		0,3,4190	no	coding-synonymous	GPR179	NM_001004334.2		10,277,5958	AA,AG,GG		0.0358,7.1637,2.3779		680/2368	36487412	297,12193	2052	4193	6245	SO:0001819	synonymous_variant	440435	exon11			CAGCTCGTCCTGT		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.2040C>T	17.37:g.36487412G>A		168	0	0		205	92	0.44878	NM_001004334		Silent	SNP	ENST00000342292.4	37	CCDS42308.1																																																																																			G|0.981;A|0.019	0.019	strong		0.587	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2			A	36487412	G	A	36487412	2	1	22	1	0	0	0	0	0	0	0	1	6682	1136	40	1		1	GPR179	17	36487412	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	352	36487412	44707798	3470	6371											
PIP4K2B	8396	hgsc.bcm.edu	37	chr17	36936846	36936846	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgttgatgggggcgctgcgCgtcactgaattctgataatc	7	12	13	9	3	2	3	1	3	1	0	3	3	2	3	0	2	1	2	0	2	2	3	rs16968328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:36936846C>T	ENST00000269554.3	-	4	846	c.366G>A	c.(364-366)acG>acA	p.T122T	PIP4K2B_ENST00000311500.6_5'UTR	NM_003559.4	NP_003550.1	P78356	PI42B_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, beta	122	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				cell surface receptor signaling pathway (GO:0007166)|intracellular signal transduction (GO:0035556)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)|receptor signaling protein activity (GO:0005057)			endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(8)|ovary(1)	19						GGGCGCTGCGCGTCACTGAAT	0.572													C|||	323	0.0644968	0.2352	0.013	5008	,	,		19211	0.001		0.002	False		,,,				2504	0.0				p.T122T		Atlas-SNP	.											.	PIP4K2B	35	.	0			c.G366A						PASS	.	C		767,3639	313.0+/-292.9	60,647,1496	79	73	75		366	-6.1	0.9	17	dbSNP_123	75	8,8592	5.0+/-18.6	0,8,4292	no	coding-synonymous	PIP4K2B	NM_003559.4		60,655,5788	TT,TC,CC		0.093,17.4081,5.9588		122/417	36936846	775,12231	2203	4300	6503	SO:0001819	synonymous_variant	8396	exon4			GCTGCGCGTCACT	U85245	CCDS11329.1	17q21.2	2007-08-14	2007-08-14	2007-08-14		ENSG00000276293	2.7.1.149		8998	protein-coding gene	gene with protein product		603261	"phosphatidylinositol-4-phosphate 5-kinase, type II, beta"	PIP5K2B		9038203, 14691457, 9367159	Standard	NM_003559		Approved	PIP5KIIB, PIP5KIIbeta	uc002hqs.3	P78356		ENST00000269554.3:c.366G>A	17.37:g.36936846C>T		71	0	0		78	33	0.423077	NM_003559	Q5U0E8|Q8TBP2	Silent	SNP	ENST00000269554.3	37	CCDS11329.1																																																																																			C|0.931;T|0.069	0.069	strong		0.572	PIP4K2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256791.1	NM_003559		T	36936846	C	T	36936846	2	4	22	1	0	0	0	0	0	0	0	1	11946	755	27	1		1	PIP4K2B	17	36936846	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	449434	36936846	44258364	3471	6372											
CWC25	54883	hgsc.bcm.edu	37	chr17	36963226	36963226	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctggttacggtcagagttccGgacctacatcattaaggaaa	12	10	10	9	2	2	1	2	0	0	1	3	3	3	3	2	4	2	2	2	4	4	4	rs3785452	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:36963226G>T	ENST00000225428.5	-	7	991	c.694C>A	c.(694-696)Cgg>Agg	p.R232R	CWC25_ENST00000536127.1_Silent_p.R169R	NM_017748.3	NP_060218.1	Q9NXE8	CWC25_HUMAN	CWC25 spliceosome-associated protein homolog (S. cerevisiae)	232										central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	14						TCAGAGTTCCGGACCTACATC	0.512													T|||	805	0.160743	0.4849	0.049	5008	,	,		18783	0.0556		0.0109	False		,,,				2504	0.0644				p.R232R		Atlas-SNP	.											.	CWC25	24	.	0			c.C694A						PASS	.	T		1555,2235		324,907,664	83	78	80		694	3	0.4	17	dbSNP_107	80	121,8119		0,121,3999	no	coding-synonymous	CWC25	NM_017748.3		324,1028,4663	TT,TG,GG		1.4684,41.029,13.9318		232/426	36963226	1676,10354	1895	4120	6015	SO:0001819	synonymous_variant	54883	exon7			AGTTCCGGACCTA	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.694C>A	17.37:g.36963226G>T		137	0	0		131	131	1	NM_017748	A0JLM3|Q68DK5	Silent	SNP	ENST00000225428.5	37	CCDS45663.1																																																																																			G|0.860;T|0.140	0.140	strong		0.512	CWC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442186.6	NM_017748		T	36963226	G	T	36963226	2	4	22	1	0	0	0	0	0	0	0	1	4071	1115	39	4		4	CWC25	17	36963226	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	26380	36963226	44231984	3472	6373											
CDK12	51755	hgsc.bcm.edu	37	chr17	37619038	37619038	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaacaagatgatagcccctcGggagcttcttatggccaaga	13	8	10	10	1	1	3	0	1	1	2	2	4	1	4	3	2	3	1	3	2	5	3	rs35896550	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:37619038G>A	ENST00000447079.4	+	1	747	c.714G>A	c.(712-714)tcG>tcA	p.S238S	CDK12_ENST00000430627.2_Silent_p.S238S	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	238					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						ATAGCCCCTCGGGAGCTTCTT	0.483			"Mis, N, F"		serous ovarian					TCGA Ovarian(9;0.13)			G|||	291	0.058107	0.2073	0.0159	5008	,	,		18736	0.0		0.003	False		,,,				2504	0.0031				p.S238S		Atlas-SNP	.		Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	CDK12,NS,carcinoma,+1,1	CDK12	161	1	0			c.G714A						PASS	.	G	,	772,3634	306.9+/-289.7	55,662,1486	102	112	109		714,714	-9.9	0.3	17	dbSNP_126	109	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous	CDK12	NM_015083.1,NM_016507.2	,	55,665,5783	AA,AG,GG		0.0349,17.5216,5.9588	,	238/1482,238/1491	37619038	775,12231	2203	4300	6503	SO:0001819	synonymous_variant	51755	exon1			CCCCTCGGGAGCT	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.714G>A	17.37:g.37619038G>A		45	0	0		57	29	0.508772	NM_016507	A7E2B2|B4DYX4|B9EIQ6|O94978	Silent	SNP	ENST00000447079.4	37	CCDS11337.1																																																																																			G|0.933;A|0.067	0.067	strong		0.483	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507		A	37619038	G	A	37619038	2	1	22	1	0	0	0	0	0	0	0	1	3130	1103	39	1		1	CDK12	17	37619038	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	655812	37619038	43576172	3473	6374											
CDK12	51755	hgsc.bcm.edu	37	chr17	37682200	37682200	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagccaaaccgacctgagcAtccctcaaatggcacagctg	13	5	9	14	1	1	2	1	1	0	1	2	3	2	2	4	1	4	3	4	1	2	0	rs61747430	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:37682200A>G	ENST00000447079.4	+	13	3424	c.3391A>G	c.(3391-3393)Atc>Gtc	p.I1131V	CDK12_ENST00000430627.2_Missense_Mutation_p.I1131V	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	1131					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						CGACCTGAGCATCCCTCAAAT	0.507			"Mis, N, F"		serous ovarian					TCGA Ovarian(9;0.13)			A|||	43	0.00858626	0.0325	0.0	5008	,	,		19029	0.0		0.0	False		,,,				2504	0.0				p.I1131V		Atlas-SNP	.		Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	.	CDK12	161	.	0			c.A3391G						PASS	.	A	VAL/ILE,VAL/ILE	148,4258	103.0+/-141.5	3,142,2058	88	75	80		3391,3391	2.6	1	17	dbSNP_129	80	1,8599		0,1,4299	yes	missense,missense	CDK12	NM_016507.2,NM_015083.1	29,29	3,143,6357	GG,GA,AA		0.0116,3.3591,1.1456	benign,benign	1131/1491,1131/1482	37682200	149,12857	2203	4300	6503	SO:0001583	missense	51755	exon13			CTGAGCATCCCTC	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.3391A>G	17.37:g.37682200A>G	ENSP00000398880:p.Ile1131Val	202	0	0		239	106	0.443515	NM_016507	A7E2B2|B4DYX4|B9EIQ6|O94978	Missense_Mutation	SNP	ENST00000447079.4	37	CCDS11337.1	15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	A	4.981	0.182220	0.09495	0.033591	1.16E-4	ENSG00000167258	ENST00000430627;ENST00000447079	T;T	0.67171	-0.23;-0.25	4.82	2.59	0.31030	.	0.151372	0.30374	N	0.009776	T	0.13457	0.0326	N	0.01668	-0.77	0.30087	N	0.808665	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.10917	-1.0609	10	0.30854	T	0.27	-6.9124	7.0706	0.25177	0.6741:0.0:0.3259:0.0	rs61747430	1130;1131;1131	E7EUM9;Q9NYV4;Q9NYV4-2	.;CDK12_HUMAN;.	V	1131	ENSP00000407720:I1131V;ENSP00000398880:I1131V	ENSP00000407720:I1131V	I	+	1	0	CDK12	34935726	0.995000	0.38212	0.998000	0.56505	0.771000	0.43674	1.586000	0.36611	0.811000	0.34303	-0.385000	0.06624	ATC	A|0.989;G|0.011	0.011	strong		0.507	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507		G	37682200	A	G	37682200	3	3	22	1	0	0	0	0	1	0	0	0	3130	217	8	3	3441	3	CDK12	17	37682200	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	63162	37682200	43513010	3474	6375											
PPP1R1B	84152	hgsc.bcm.edu	37	chr17	37791894	37791894	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acctgtggccagggtctggaAgggccctgggagcgcccacc	6	5	16	14	1	1	0	0	0	1	0	1	2	1	2	5	5	1	0	5	5	1	0	rs34257414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:37791894A>G	ENST00000254079.4	+	6	949	c.480A>G	c.(478-480)gaA>gaG	p.E160E	PPP1R1B_ENST00000394265.1_Silent_p.E124E|PPP1R1B_ENST00000394267.2_Silent_p.E124E|PPP1R1B_ENST00000580825.1_Silent_p.E160E|STARD3_ENST00000580611.1_5'Flank|STARD3_ENST00000544210.2_5'Flank|PPP1R1B_ENST00000579000.1_Silent_p.E127E|STARD3_ENST00000394250.4_5'Flank|STARD3_ENST00000336308.5_5'Flank	NM_032192.3	NP_115568.2	Q9UD71	PPR1B_HUMAN	protein phosphatase 1, regulatory (inhibitor) subunit 1B	160					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)			AGGGTCTGGAAGGGCCCTGGG	0.587													G|||	94	0.01877	0.0711	0.0	5008	,	,		19292	0.0		0.0	False		,,,				2504	0.0				p.E160E		Atlas-SNP	.											.	PPP1R1B	9	.	0			c.A480G						PASS	.	G	,,	206,4200	784.3+/-414.7	3,200,2000	74	85	81		372,480,372	2.1	1	17	dbSNP_126	81	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	PPP1R1B	NM_001242464.1,NM_032192.3,NM_181505.3	,,	3,200,6300	GG,GA,AA		0.0,4.6754,1.5839	,,	124/169,160/205,124/169	37791894	206,12800	2203	4300	6503	SO:0001819	synonymous_variant	84152	exon6			TCTGGAAGGGCCC	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.480A>G	17.37:g.37791894A>G		76	0	0		92	43	0.467391	NM_032192	Q547V9|Q547W0|Q9H7G1	Silent	SNP	ENST00000254079.4	37	CCDS11339.1																																																																																			A|0.979;G|0.021	0.021	strong		0.587	PPP1R1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256925.2	NM_032192		G	37791894	A	G	37791894	2	3	22	1	0	0	0	0	0	0	0	1	12380	69	3	3		3	PPP1R1B	17	37791894	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	109694	37791894	43403316	3475	6376											
PNMT	5409	hgsc.bcm.edu	37	chr17	37826249	37826249	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagctgcgagccagggtgaaAcgggtcctgcccatcgacgt	8	6	14	13	4	0	1	0	1	0	0	2	3	1	1	3	2	5	1	3	2	1	0	rs5638	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:37826249A>G	ENST00000269582.2	+	3	774	c.456A>G	c.(454-456)aaA>aaG	p.K152K	PNMT_ENST00000581428.1_3'UTR|PNMT_ENST00000394246.1_Silent_p.K54K	NM_002686.3	NP_002677.1	P11086	PNMT_HUMAN	phenylethanolamine N-methyltransferase	152					catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|epinephrine biosynthetic process (GO:0042418)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phenylethanolamine N-methyltransferase activity (GO:0004603)			NS(1)|breast(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8	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)			CCAGGGTGAAACGGGTCCTGC	0.657													A|||	317	0.0632987	0.1725	0.0317	5008	,	,		16981	0.004		0.0129	False		,,,				2504	0.0511				p.K152K		Atlas-SNP	.											.	PNMT	17	.	0			c.A456G						PASS	.	A		640,3766	252.4+/-258.8	45,550,1608	41	44	43		456	4	1	17	dbSNP_52	43	169,8429	74.5+/-137.1	1,167,4131	no	coding-synonymous	PNMT	NM_002686.3		46,717,5739	GG,GA,AA		1.9656,14.5256,6.2212		152/283	37826249	809,12195	2203	4299	6502	SO:0001819	synonymous_variant	5409	exon3			GGTGAAACGGGTC		CCDS11343.1	17q	2010-04-16			ENSG00000141744	ENSG00000141744	2.1.1.28		9160	protein-coding gene	gene with protein product		171190		PENT		3372503	Standard	NM_002686		Approved		uc002hsi.2	P11086	OTTHUMG00000133209	ENST00000269582.2:c.456A>G	17.37:g.37826249A>G		44	0	0		53	23	0.433962	NM_002686		Silent	SNP	ENST00000269582.2	37	CCDS11343.1																																																																																			A|0.933;G|0.067	0.067	strong		0.657	PNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256923.2	NM_002686		G	37826249	A	G	37826249	2	3	22	1	0	0	0	0	0	0	0	1	12168	40	2	3		3	PNMT	17	37826249	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	34355	37826249	43368961	3476	6377											
ERBB2	2064	hgsc.bcm.edu	37	chr17	37863268	37863268	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accggcacagacatgaagctGcggctccctgccagtcccga	9	5	11	16	3	0	2	0	1	0	1	2	3	2	2	4	2	3	3	4	2	1	0	rs4252610	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:37863268G>A	ENST00000269571.5	+	2	258	c.99G>A	c.(97-99)ctG>ctA	p.L33L	ERBB2_ENST00000406381.2_Silent_p.L3L|ERBB2_ENST00000541774.1_Silent_p.L18L|ERBB2_ENST00000445658.2_Intron|ERBB2_ENST00000540042.1_Silent_p.L3L|ERBB2_ENST00000584450.1_Silent_p.L33L|ERBB2_ENST00000578199.1_Silent_p.L3L|ERBB2_ENST00000584601.1_Silent_p.L3L|ERBB2_ENST00000540147.1_Silent_p.L3L			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	33					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)	ACATGAAGCTGCGGCTCCCTG	0.637		1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)			G|||	90	0.0179712	0.0673	0.0014	5008	,	,		17261	0.0		0.0	False		,,,				2504	0.0				p.L33L		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.G99A						PASS	.	G	,	206,4192		5,196,1998	40	35	37		9,99	2	1	17	dbSNP_111	37	0,8584		0,0,4292	no	coding-synonymous,coding-synonymous	ERBB2	NM_001005862.1,NM_004448.2	,	5,196,6290	AA,AG,GG		0.0,4.6839,1.5868	,	3/1226,33/1256	37863268	206,12776	2199	4292	6491	SO:0001819	synonymous_variant	2064	exon2			GAAGCTGCGGCTC	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.99G>A	17.37:g.37863268G>A		128	0	0		137	63	0.459854	NM_004448	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Silent	SNP	ENST00000269571.5	37	CCDS32642.1																																																																																			G|0.982;A|0.018	0.018	strong		0.637	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			A	37863268	G	A	37863268	2	1	22	1	0	0	0	0	0	0	0	1	5208	1306	46	2		2	ERBB2	17	37863268	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	37019	37863268	43331942	3477	6378											
ERBB2	2064	hgsc.bcm.edu	37	chr17	37872035	37872035	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	caagggctgggcatcagctgGctggggctgcgctcactgag	6	7	17	11	1	2	1	2	1	0	0	2	1	2	1	0	5	2	6	0	5	1	0	rs4252633	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:37872035G>T	ENST00000269571.5	+	12	1515	c.1356G>T	c.(1354-1356)tgG>tgT	p.W452C	ERBB2_ENST00000406381.2_Missense_Mutation_p.W422C|ERBB2_ENST00000541774.1_Missense_Mutation_p.W437C|ERBB2_ENST00000445658.2_Missense_Mutation_p.W176C|ERBB2_ENST00000540042.1_Missense_Mutation_p.W422C|ERBB2_ENST00000584450.1_Missense_Mutation_p.W452C|ERBB2_ENST00000578199.1_Missense_Mutation_p.W422C|ERBB2_ENST00000584601.1_Missense_Mutation_p.W422C|ERBB2_ENST00000540147.1_Missense_Mutation_p.W422C			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	452			W -> C (in dbSNP:rs4252633). {ECO:0000269|Ref.3}.		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)	GCATCAGCTGGCTGGGGCTGC	0.627		1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)			G|||	90	0.0179712	0.0673	0.0014	5008	,	,		19038	0.0		0.0	False		,,,				2504	0.0				p.W452C		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.G1356T						PASS	.	G	CYS/TRP,CYS/TRP	210,4196	129.0+/-165.8	6,198,1999	98	81	86		1266,1356	2.8	1	17	dbSNP_111	86	0,8600		0,0,4300	yes	missense,missense	ERBB2	NM_001005862.1,NM_004448.2	215,215	6,198,6299	TT,TG,GG		0.0,4.7662,1.6146	possibly-damaging,possibly-damaging	422/1226,452/1256	37872035	210,12796	2203	4300	6503	SO:0001583	missense	2064	exon12			CAGCTGGCTGGGG	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.1356G>T	17.37:g.37872035G>T	ENSP00000269571:p.Trp452Cys	42	0	0		66	32	0.484848	NM_004448	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	37	CCDS32642.1	39	0.017857142857142856	38	0.07723577235772358	1	0.0027624309392265192	0	0.0	0	0.0	G	8.363	0.833490	0.16820	0.047662	0.0	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147;ENST00000540042	T;T;T;T;T;T	0.79247	-1.25;-1.25;-1.25;-1.25;-1.25;-1.25	5.93	2.79	0.32731	EGF receptor, L domain (1);	.	.	.	.	T	0.16685	0.0401	L	0.34521	1.04	0.35496	D	0.799411	P;D;D;P	0.57257	0.951;0.979;0.965;0.903	P;P;P;P	0.62885	0.88;0.874;0.762;0.908	T	0.62680	-0.6803	9	0.72032	D	0.01	.	3.232	0.06751	0.1435:0.2503:0.4775:0.1287	rs4252633	176;422;437;452	B4DTR1;F5H1T4;P04626-4;P04626	.;.;.;ERBB2_HUMAN	C	422;437;176;452;422;422	ENSP00000385185:W422C;ENSP00000446466:W437C;ENSP00000404047:W176C;ENSP00000269571:W452C;ENSP00000443562:W422C;ENSP00000446382:W422C	ENSP00000269571:W452C	W	+	3	0	ERBB2	35125561	0.528000	0.26314	0.995000	0.50966	0.899000	0.52679	-0.034000	0.12225	0.381000	0.24851	-0.305000	0.09177	TGG	G|0.979;T|0.021	0.021	strong		0.627	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			T	37872035	G	T	37872035	3	4	22	1	0	0	0	0	1	0	0	0	5208	1212	42	4	1402	4	ERBB2	17	37872035	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	8767	37872035	43323175	3478	6379											
ZPBP2	124626	hgsc.bcm.edu	37	chr17	38027824	38027824	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tttcttataagactgttaaaGcagaaactcaagaagaaaaa	20	10	6	5	0	2	4	1	0	1	4	2	4	2	4	0	0	2	2	0	0	9	4	rs35829084	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38027824G>A	ENST00000348931.4	+	4	543	c.352G>A	c.(352-354)Gca>Aca	p.A118T	ZPBP2_ENST00000377940.3_Missense_Mutation_p.A96T|ZPBP2_ENST00000584588.1_Missense_Mutation_p.A118T	NM_199321.2	NP_955353.1	Q6X784	ZPBP2_HUMAN	zona pellucida binding protein 2	118			A -> T (in dbSNP:rs35829084).		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)				kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	15	Colorectal(19;0.000442)		Lung(15;0.00849)|LUSC - Lung squamous cell carcinoma(15;0.171)			GACTGTTAAAGCAGAAACTCA	0.318													G|||	148	0.0295527	0.1089	0.0058	5008	,	,		16323	0.0		0.0	False		,,,				2504	0.0				p.A118T		Atlas-SNP	.											.	ZPBP2	33	.	0			c.G352A						PASS	.	G	THR/ALA,THR/ALA	382,4024	189.9+/-215.9	25,332,1846	77	80	79		286,352	4.4	1	17	dbSNP_126	79	3,8589	2.2+/-6.3	0,3,4293	yes	missense,missense	ZPBP2	NM_198844.2,NM_199321.2	58,58	25,335,6139	AA,AG,GG		0.0349,8.67,2.962	probably-damaging,probably-damaging	96/317,118/339	38027824	385,12613	2203	4296	6499	SO:0001583	missense	124626	exon4			GTTAAAGCAGAAA	BC043152	CCDS11352.1, CCDS11353.2	17q21.1	2013-01-11			ENSG00000186075	ENSG00000186075		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	20678	protein-coding gene	gene with protein product		608499					Standard	XM_005257031		Approved	ZPBPL, MGC41930	uc002hte.3	Q6X784	OTTHUMG00000133022	ENST00000348931.4:c.352G>A	17.37:g.38027824G>A	ENSP00000335384:p.Ala118Thr	186	0	0		154	85	0.551948	NM_199321	A8K8L8|Q6X783|Q86XL5	Missense_Mutation	SNP	ENST00000348931.4	37	CCDS11352.1	57	0.0260989010989011	55	0.11178861788617886	2	0.0055248618784530384	0	0.0	0	0.0	G	9.022	0.985096	0.18889	0.0867	3.49E-4	ENSG00000186075	ENST00000348931;ENST00000377940	T;T	0.55760	0.5;0.5	5.36	4.39	0.52855	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.455087	0.21308	N	0.076697	T	0.00784	0.0026	L	0.39898	1.24	0.22226	N	0.999272	B;B	0.26635	0.112;0.155	B;B	0.20955	0.029;0.032	T	0.00904	-1.1520	10	0.27785	T	0.31	-4.4881	6.3234	0.21231	0.2041:0.0:0.7959:0.0	rs35829084	96;118	Q6X784-2;Q6X784	.;ZPBP2_HUMAN	T	118;96	ENSP00000335384:A118T;ENSP00000367174:A96T	ENSP00000335384:A118T	A	+	1	0	ZPBP2	35281350	0.997000	0.39634	0.995000	0.50966	0.248000	0.25809	2.785000	0.47782	2.506000	0.84524	0.460000	0.39030	GCA	G|0.968;A|0.032	0.032	strong		0.318	ZPBP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256609.2	NM_198844		A	38027824	G	A	38027824	3	1	22	1	0	0	0	0	1	0	0	0	18235	971	34	2	366	2	ZPBP2	17	38027824	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	155789	38027824	43167386	3479	6380											
ZPBP2	124626	hgsc.bcm.edu	37	chr17	38028635	38028635	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaagaaaatcttggatagTctaatttctgatttgtcatg	12	16	8	5	0	4	3	1	2	3	1	4	4	4	4	0	1	0	0	0	1	5	5	rs61737283	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38028635T>C	ENST00000348931.4	+	5	710	c.519T>C	c.(517-519)agT>agC	p.S173S	ZPBP2_ENST00000377940.3_Silent_p.S151S|ZPBP2_ENST00000584588.1_Intron	NM_199321.2	NP_955353.1	Q6X784	ZPBP2_HUMAN	zona pellucida binding protein 2	173			S -> I (in dbSNP:rs11557467). {ECO:0000269|PubMed:14702039}.		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)				kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	15	Colorectal(19;0.000442)		Lung(15;0.00849)|LUSC - Lung squamous cell carcinoma(15;0.171)			TCTTGGATAGTCTAATTTCTG	0.358													T|||	148	0.0295527	0.1089	0.0058	5008	,	,		14981	0.0		0.0	False		,,,				2504	0.0				p.S173S		Atlas-SNP	.											.	ZPBP2	33	.	0			c.T519C						PASS	.																																			SO:0001819	synonymous_variant	124626	exon5			GGATAGTCTAATT	BC043152	CCDS11352.1, CCDS11353.2	17q21.1	2013-01-11			ENSG00000186075	ENSG00000186075		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	20678	protein-coding gene	gene with protein product		608499					Standard	XM_005257031		Approved	ZPBPL, MGC41930	uc002hte.3	Q6X784	OTTHUMG00000133022	ENST00000348931.4:c.519T>C	17.37:g.38028635T>C		76	0	0		89	48	0.539326	NM_199321	A8K8L8|Q6X783|Q86XL5	Silent	SNP	ENST00000348931.4	37	CCDS11352.1																																																																																			T|0.868;C|0.132	0.132	strong		0.358	ZPBP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256609.2	NM_198844		C	38028635	T	C	38028635	2	2	22	1	0	0	0	0	0	0	0	1	18235	1664	58	3		3	ZPBP2	17	38028635	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	811	38028635	43166575	3480	6381											
GSDMA	284110	hgsc.bcm.edu	37	chr17	38122117	38122117	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tacgtccgcaccgactacacGctgctggatgtgcttgagcc	7	9	11	14	4	0	1	0	1	0	0	1	3	1	2	3	1	5	4	3	1	2	3	rs16965465	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38122117G>A	ENST00000301659.4	+	2	295	c.177G>A	c.(175-177)acG>acA	p.T59T		NM_178171.4	NP_835465.2	Q96QA5	GSDMA_HUMAN	gasdermin A	59					apoptotic process (GO:0006915)	perinuclear region of cytoplasm (GO:0048471)				NS(1)|endometrium(2)|large_intestine(3)|lung(1)	7						CCGACTACACGCTGCTGGATG	0.637													A|||	351	0.0700879	0.2315	0.036	5008	,	,		17304	0.0		0.0149	False		,,,				2504	0.0051				p.T59T		Atlas-SNP	.											GSDMA,NS,carcinoma,+1,1	GSDMA	26	1	0			c.G177A						PASS	.	A		683,3313		60,563,1375	21	24	23		177	1	1	17	dbSNP_123	23	53,8223		1,51,4086	no	coding-synonymous	GSDMA	NM_178171.4		61,614,5461	AA,AG,GG		0.6404,17.0921,5.9974		59/446	38122117	736,11536	1998	4138	6136	SO:0001819	synonymous_variant	284110	exon2			CTACACGCTGCTG	AB093591	CCDS45669.1	17q21.2	2008-07-31	2008-07-31	2008-07-31		ENSG00000167914			13311	protein-coding gene	gene with protein product		611218	"gasdermin", "gasdermin 1"	GSDM, GSDM1		12883658, 15010812, 17350798	Standard	NM_178171		Approved	FLJ39120	uc002htl.1	Q96QA5		ENST00000301659.4:c.177G>A	17.37:g.38122117G>A		56	0	0		42	16	0.380952	NM_178171	Q32MC5|Q86VE7|Q8N1M6	Silent	SNP	ENST00000301659.4	37	CCDS45669.1																																																																																			G|0.930;A|0.070	0.070	strong		0.637	GSDMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446847.1	NM_178171		A	38122117	G	A	38122117	2	1	22	1	0	0	0	0	0	0	0	1	6825	1074	38	1		1	GSDMA	17	38122117	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	93482	38122117	43073093	3481	6382											
MED24	9862	hgsc.bcm.edu	37	chr17	38189659	38189659	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgcgggttgctgagattggCcaggatctctccaagtttca	7	12	12	10	1	2	1	1	1	1	1	4	3	3	2	2	3	2	3	2	3	1	3	rs34585432	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38189659C>T	ENST00000394128.2	-	7	691	c.610G>A	c.(610-612)Gcc>Acc	p.A204T	MED24_ENST00000394127.2_Missense_Mutation_p.A191T|MED24_ENST00000356271.3_Missense_Mutation_p.A191T|MED24_ENST00000501516.3_Missense_Mutation_p.A223T|MED24_ENST00000479829.1_5'Flank|MED24_ENST00000394126.1_Missense_Mutation_p.A229T	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	204			A -> T (in dbSNP:rs34585432). {ECO:0000269|PubMed:8590280}.		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)					CTGAGATTGGCCAGGATCTCT	0.567													C|||	29	0.00579073	0.0204	0.0029	5008	,	,		19434	0.0		0.0	False		,,,				2504	0.0				p.A204T		Atlas-SNP	.											.	MED24	89	.	0			c.G610A						PASS	.	C	THR/ALA,THR/ALA	92,4314	70.9+/-108.8	1,90,2112	43	38	40		571,610	3.7	1	17	dbSNP_126	40	0,8600		0,0,4300	yes	missense,missense	MED24	NM_001079518.1,NM_014815.3	58,58	1,90,6412	TT,TC,CC		0.0,2.0881,0.7074	benign,benign	191/977,204/990	38189659	92,12914	2203	4300	6503	SO:0001583	missense	9862	exon7			GATTGGCCAGGAT	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.610G>A	17.37:g.38189659C>T	ENSP00000377686:p.Ala204Thr	93	0	0		101	47	0.465347	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Missense_Mutation	SNP	ENST00000394128.2	37	CCDS11359.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	C	13.03	2.115269	0.37339	0.020881	0.0	ENSG00000008838	ENST00000394126;ENST00000356271;ENST00000394128;ENST00000535071;ENST00000394127;ENST00000536318;ENST00000543759;ENST00000535508;ENST00000431269;ENST00000428757	T;T;T	0.42131	0.98;0.98;0.98	5.67	3.69	0.42338	Mediator complex, subunit Med24, N-terminal (1);	0.307388	0.34314	N	0.004079	T	0.23054	0.0557	N	0.08118	0	0.25781	N	0.984725	B;B;B;B;B;B;B;B;D	0.71674	0.367;0.166;0.166;0.357;0.034;0.017;0.034;0.042;0.998	B;B;B;B;B;B;B;B;D	0.78314	0.253;0.096;0.096;0.257;0.04;0.005;0.025;0.042;0.991	T	0.07233	-1.0783	10	0.33141	T	0.24	-14.6106	8.965	0.35872	0.0:0.7801:0.0:0.2199	rs34585432	178;191;154;133;154;114;191;204;146	B9TX63;B9TX65;B4DV99;B4DDR8;F5H5K2;F8W9R9;O75448-2;O75448;F5H0K1	.;.;.;.;.;.;.;MED24_HUMAN;.	T	204;204;204;154;191;146;178;178;114;223	ENSP00000377686:A204T;ENSP00000443344:A154T;ENSP00000377685:A191T	ENSP00000348610:A204T	A	-	1	0	MED24	35443185	0.924000	0.31332	1.000000	0.80357	0.613000	0.37349	0.946000	0.29069	1.402000	0.46780	0.655000	0.94253	GCC	C|0.993;T|0.007	0.007	strong		0.567	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815		T	38189659	C	T	38189659	3	4	22	1	0	0	0	0	1	0	0	0	9451	739	26	2	2439	2	MED24	17	38189659	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	67542	38189659	43005551	3482	6383											
NR1D1	9572	hgsc.bcm.edu	37	chr17	38253469	38253469	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagccgtcatcactcaggctGggtggaatgctcccaaagga	10	7	13	11	1	3	0	3	0	0	0	4	3	4	2	2	4	2	2	2	4	2	0	rs9905506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38253469G>A	ENST00000246672.3	-	2	849	c.219C>T	c.(217-219)ccC>ccT	p.P73P		NM_021724.3	NP_068370.1	P20393	NR1D1_HUMAN	nuclear receptor subfamily 1, group D, member 1	73	Crucial for activation of GJA1. {ECO:0000250}.|Modulating.				cell differentiation (GO:0030154)|cellular response to lipopolysaccharide (GO:0071222)|circadian regulation of gene expression (GO:0032922)|circadian temperature homeostasis (GO:0060086)|gene expression (GO:0010467)|glycogen biosynthetic process (GO:0005978)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of receptor biosynthetic process (GO:0010871)|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)|positive regulation of bile acid biosynthetic process (GO:0070859)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasomal protein catabolic process (GO:0010498)|regulation of cholesterol homeostasis (GO:2000188)|regulation of circadian rhythm (GO:0042752)|regulation of fat cell differentiation (GO:0045598)|regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter (GO:0035947)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of lipid metabolic process (GO:0019216)|regulation of type B pancreatic cell proliferation (GO:0061469)|response to leptin (GO:0044321)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|heme binding (GO:0020037)|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 negative regulation of transcription (GO:0001078)|steroid hormone receptor activity (GO:0003707)|transcription corepressor activity (GO:0003714)|transcription corepressor binding (GO:0001222)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(5)|lung(2)|skin(1)|upper_aerodigestive_tract(2)	11	Colorectal(19;0.000442)					CACTCAGGCTGGGTGGAATGC	0.607													G|||	123	0.0245607	0.0908	0.0043	5008	,	,		18042	0.0		0.0	False		,,,				2504	0.0				p.P73P		Atlas-SNP	.											.	NR1D1	45	.	0			c.C219T						PASS	.	G		290,4116	160.3+/-192.7	5,280,1918	75	76	76		219	1.6	1	17	dbSNP_119	76	0,8600		0,0,4300	no	coding-synonymous	NR1D1	NM_021724.3		5,280,6218	AA,AG,GG		0.0,6.5819,2.2297		73/615	38253469	290,12716	2203	4300	6503	SO:0001819	synonymous_variant	9572	exon2			CAGGCTGGGTGGA	X72631	CCDS11361.1	17q11.2	2013-01-16			ENSG00000126368	ENSG00000126368		"Nuclear hormone receptors"	7962	protein-coding gene	gene with protein product		602408		THRAL		1971514	Standard	NM_021724		Approved	ear-1, hRev, Rev-ErbAalpha, THRA1	uc002htz.3	P20393	OTTHUMG00000133327	ENST00000246672.3:c.219C>T	17.37:g.38253469G>A		153	0	0		176	84	0.477273	NM_021724	Q0P5Z4|Q15304	Silent	SNP	ENST00000246672.3	37	CCDS11361.1																																																																																			G|0.979;A|0.021	0.021	strong		0.607	NR1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257135.1			A	38253469	G	A	38253469	2	1	22	1	0	0	0	0	0	0	0	1	10624	1335	47	2		2	NR1D1	17	38253469	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	63810	38253469	42941741	3483	6384											
MSL1	339287	hgsc.bcm.edu	37	chr17	38285681	38285681	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accccagaaaagccccggtcTtcagtggacaccccaccaag	12	4	8	17	1	2	1	1	0	1	1	2	2	2	2	7	2	1	0	7	2	3	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38285681T>C	ENST00000398532.4	+	3	1491	c.1176T>C	c.(1174-1176)tcT>tcC	p.S392S	MSL1_ENST00000578648.1_Silent_p.S392S|MSL1_ENST00000579565.1_Silent_p.S129S|MSL1_ENST00000577454.1_Silent_p.S392S	NM_001012241.1	NP_001012241.1	Q68DK7	MSL1_HUMAN	male-specific lethal 1 homolog (Drosophila)	392					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						AGCCCCGGTCTTCAGTGGACA	0.498																																					p.S129S		Atlas-SNP	.											.	MSL1	21	.	0			c.T387C						PASS	.						52	54	54					17																	38285681		1834	4093	5927	SO:0001819	synonymous_variant	339287	exon4			CCGGTCTTCAGTG		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.1176T>C	17.37:g.38285681T>C		80	0	0		95	5	0.0526316	NM_001012241	Q0VF46|Q69Z03	Silent	SNP	ENST00000398532.4	37																																																																																				.	.	none		0.498	MSL1-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000447409.2	NM_001012241		C	38285681	T	C	38285681	2	2	22	1	0	0	0	0	0	0	0	1	9886	1596	56	3		3	MSL1	17	38285681	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	32212	38285681	42909529	3484	6385											
CDC6	990	hgsc.bcm.edu	37	chr17	38447569	38447569	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaagaaagaatctgcatgTgtgagactattcaagcaaga	16	9	10	6	0	2	5	1	2	1	4	2	6	2	5	0	0	2	2	0	0	6	2	rs1130199	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38447569T>C	ENST00000209728.4	+	3	909	c.438T>C	c.(436-438)tgT>tgC	p.C146C		NM_001254.3	NP_001245.1	Q99741	CDC6_HUMAN	cell division cycle 6	146					DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|positive regulation of chromosome segregation (GO:0051984)|positive regulation of cytokinesis (GO:0032467)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|traversing start control point of mitotic cell cycle (GO:0007089)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|kinase binding (GO:0019900)|nucleotide binding (GO:0000166)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	21						AATCTGCATGTGTGAGACTAT	0.403													T|||	557	0.111222	0.3994	0.0375	5008	,	,		24231	0.0		0.003	False		,,,				2504	0.0				p.C146C		Atlas-SNP	.											.	CDC6	53	.	0			c.T438C						PASS	.	T		1438,2968	453.6+/-350.4	230,978,995	87	90	89		438	0.9	0	17	dbSNP_86	89	10,8590	6.4+/-24.3	0,10,4290	no	coding-synonymous	CDC6	NM_001254.3		230,988,5285	CC,CT,TT		0.1163,32.6373,11.1333		146/561	38447569	1448,11558	2203	4300	6503	SO:0001819	synonymous_variant	990	exon3			TGCATGTGTGAGA	U77949	CCDS11365.1	17q21.3	2013-01-17	2013-01-17		ENSG00000094804	ENSG00000094804			1744	protein-coding gene	gene with protein product		602627	"CDC6 (cell division cycle 6, S. cerevisiae) homolog", "CDC6 cell division cycle 6 homolog (S. cerevisiae)", "cell division cycle 6 homolog (S. cerevisiae)"	CDC18L		8990175, 9566895	Standard	NM_001254		Approved		uc002huj.1	Q99741	OTTHUMG00000133324	ENST00000209728.4:c.438T>C	17.37:g.38447569T>C		154	1	0.00649351		140	139	0.992857	NM_001254	Q8TB30	Silent	SNP	ENST00000209728.4	37	CCDS11365.1																																																																																			T|0.886;C|0.114	0.114	strong		0.403	CDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257129.1			C	38447569	T	C	38447569	2	2	22	1	0	0	0	0	0	0	0	1	3085	1702	59	3		3	CDC6	17	38447569	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	161888	38447569	42747641	3485	6386											
KRT24	192666	hgsc.bcm.edu	37	chr17	38859664	38859664	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgccaaatccagagaccccGccaaagctagaacccccacc	13	3	6	19	1	0	2	0	0	0	2	1	3	1	2	8	0	3	1	8	0	4	1	rs61237409	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38859664G>A	ENST00000264651.2	-	1	338	c.282C>T	c.(280-282)ggC>ggT	p.G94G		NM_019016.2	NP_061889.2	Q2M2I5	K1C24_HUMAN	keratin 24	94	Gly-rich.|Head.					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)				CAGAGACCCCGCCAAAGCTAG	0.572													G|||	192	0.0383387	0.1384	0.0115	5008	,	,		13481	0.0		0.001	False		,,,				2504	0.0				p.G94G	GBM(61;380 1051 14702 23642 31441)	Atlas-SNP	.											.	KRT24	60	.	0			c.C282T						PASS	.	G		416,3990	201.1+/-224.2	22,372,1809	95	118	110		282	-8.3	0	17	dbSNP_129	110	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	KRT24	NM_019016.2		22,375,6106	AA,AG,GG		0.0349,9.4417,3.2216		94/526	38859664	419,12587	2203	4300	6503	SO:0001819	synonymous_variant	192666	exon1			GACCCCGCCAAAG		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.282C>T	17.37:g.38859664G>A		67	0	0		56	28	0.5	NM_019016	Q9NXG7	Silent	SNP	ENST00000264651.2	37	CCDS11372.1																																																																																			G|0.969;A|0.031	0.031	strong		0.572	KRT24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257217.1	NM_019016		A	38859664	G	A	38859664	2	1	22	1	0	0	0	0	0	0	0	1	8470	1074	38	1		1	KRT24	17	38859664	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	412095	38859664	42335546	3486	6387											
KRTAP3-2	83897	hgsc.bcm.edu	37	chr17	39156085	39156085	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagtggggacactgcagctGcgagaggcacagcaatccat	11	5	13	12	1	0	1	0	0	0	1	1	3	1	2	2	3	4	4	2	3	1	0	rs386797022|rs548322379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39156085G>T	ENST00000391587.1	-	1	53	c.21C>A	c.(19-21)cgC>cgA	p.R7R		NM_031959.2	NP_114165.1	Q9BYR7	KRA32_HUMAN	keratin associated protein 3-2	7	3 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.R7R(1)		endometrium(1)|large_intestine(1)|lung(1)	3		Breast(137;0.00043)				CACTGCAGCTGCGAGAGGCAC	0.552													.|||	307	0.0613019	0.2216	0.0173	5008	,	,		18167	0.0		0.002	False		,,,				2504	0.0				p.R7R		Atlas-SNP	.											KRTAP3-2,rectum,carcinoma,0,1	KRTAP3-2	11	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C21A						PASS	.						65	75	72					17																	39156085		2203	4296	6499	SO:0001819	synonymous_variant	83897	exon1			GCAGCTGCGAGAG	AJ406932	CCDS32644.1	17q21.2	2013-06-25			ENSG00000212900	ENSG00000212900		"Keratin associated proteins"	16779	protein-coding gene	gene with protein product						11279113	Standard	NM_031959		Approved	KAP3.2	uc002hvs.3	Q9BYR7	OTTHUMG00000133581	ENST00000391587.1:c.21C>A	17.37:g.39156085G>T		172	0	0		174	58	0.333333	NM_031959		Silent	SNP	ENST00000391587.1	37	CCDS32644.1																																																																																			.	.	none		0.552	KRTAP3-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257685.1			T	39156085	G	T	39156085	2	4	22	1	0	0	0	0	0	0	0	1	8555	1306	46	4		4	KRTAP3-2	17	39156085	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	296421	39156085	42039125	3487	6388											
KRTAP4-7	100132476	hgsc.bcm.edu	37	chr17	39240577	39240577	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgttgcaggaccacctgctAccgccccagctgttgtgtgt	5	11	11	14	1	0	0	0	0	0	0	0	1	0	1	5	1	4	5	5	1	1	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39240577A>G	ENST00000391417.4	+	1	119	c.119A>G	c.(118-120)tAc>tGc	p.Y40C		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	40	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						ACCACCTGCTACCGCCCCAGC	0.657																																					p.Y40C		Atlas-SNP	.											.	KRTAP4-7	49	.	0			c.A119G						PASS	.						13	22	19					17																	39240577		692	1590	2282	SO:0001583	missense	100132476	exon1			CCTGCTACCGCCC	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.119A>G	17.37:g.39240577A>G	ENSP00000375236:p.Tyr40Cys	106	0	0		135	16	0.118519	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	0.001	-2.883871	0.00061	.	.	ENSG00000240871;ENSG00000212722	ENST00000391417;ENST00000377734	T	0.00666	5.91	3.63	1.53	0.23141	.	0.603408	0.12340	N	0.477557	T	0.00412	0.0013	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44390	-0.9331	9	0.02654	T	1	.	5.5941	0.17317	0.2179:0.1587:0.6234:0.0	.	40	Q9BYR0	KRA47_HUMAN	C	40	ENSP00000375236:Y40C	ENSP00000375236:Y40C	Y	+	2	0	KRTAP4-9;KRTAP4-7	36494103	0.873000	0.30073	0.022000	0.16811	0.001000	0.01503	1.032000	0.30178	-0.124000	0.11724	-2.594000	0.00164	TAC	.	.	none		0.657	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1			G	39240577	A	G	39240577	3	3	22	1	0	0	0	0	1	0	0	0	8564	391	14	3	121	3	KRTAP4-7	17	39240577	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	84492	39240577	41954633	3488	6389											
KRTAP4-7	100132476	hgsc.bcm.edu	37	chr17	39240611	39240611	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgtgtgtccagctgctgcagGccccagtgctgccagtctgt	4	11	13	13	0	1	0	0	0	1	0	2	0	2	0	4	1	5	4	4	1	0	0	rs529043715	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39240611G>A	ENST00000391417.4	+	1	153	c.153G>A	c.(151-153)agG>agA	p.R51R		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	51	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						GCTGCTGCAGGCCCCAGTGCT	0.647													g|||	99	0.0197684	0.0726	0.0029	5008	,	,		18224	0.0		0.001	False		,,,				2504	0.0				p.R51R		Atlas-SNP	.											KRTAP4-9_ENST00000377734,NS,carcinoma,+1,2	KRTAP4-7	49	2	0			c.G153A						PASS	.						15	24	21					17																	39240611		691	1591	2282	SO:0001819	synonymous_variant	100132476	exon1			CTGCAGGCCCCAG	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.153G>A	17.37:g.39240611G>A		113	0	0		176	35	0.198864	NM_033061	A0AVM6|A8MQ08|A8MTL4	Silent	SNP	ENST00000391417.4	37	CCDS45673.1																																																																																			.	.	none		0.647	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1			A	39240611	G	A	39240611	2	1	22	1	0	0	0	0	0	0	0	1	8564	1194	42	2		2	KRTAP4-7	17	39240611	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	34	39240611	41954599	3489	6390											
KRTAP4-8	728224	hgsc.bcm.edu	37	chr17	39253797	39253797	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctcagcagcaagaggaggcGcagcacacggggcgggggca	10	1	19	11	3	1	1	1	0	0	1	1	2	1	2	0	6	3	6	0	6	1	0	rs142150852	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39253797G>A	ENST00000333822.4	-	1	596	c.540C>T	c.(538-540)tgC>tgT	p.C180C		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	180					aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						AAGAGGAGGCGCAGCACACGG	0.602													g|||	249	0.0497204	0.1778	0.0159	5008	,	,		17550	0.002		0.001	False		,,,				2504	0.0				p.C180C		Atlas-SNP	.											KRTAP4-8,colon,carcinoma,-2,1	KRTAP4-8	57	1	0			c.C540T						PASS	.						69	80	76					17																	39253797		692	1591	2283	SO:0001819	synonymous_variant	728224	exon1			GGAGGCGCAGCAC	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"Keratin associated proteins"	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.540C>T	17.37:g.39253797G>A		274	0	0		227	81	0.356828	NM_031960	A8MSH3	Silent	SNP	ENST00000333822.4	37	CCDS45674.1																																																																																			G|0.982;A|0.018	0.018	strong		0.602	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960		A	39253797	G	A	39253797	2	1	22	1	0	0	0	0	0	0	0	1	8565	1079	38	1		1	KRTAP4-8	17	39253797	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	13186	39253797	41941413	3490	6391			8	31		9	9	8325	N	T_G_C	3.818482e-05
KRTAP4-8	728224	hgsc.bcm.edu	37	chr17	39253819	39253819	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agcacacggggcgggggcagGtggagatgacacaggctggg	9	3	21	8	2	0	2	0	1	0	1	0	3	0	2	0	8	1	3	0	8	0	0	rs201814486	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39253819G>C	ENST00000333822.4	-	1	574	c.518C>G	c.(517-519)aCc>aGc	p.T173S		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	173					aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						GCGGGGGCAGGTGGAGATGAC	0.632													G|||	264	0.0527157	0.1778	0.0231	5008	,	,		16542	0.0099		0.001	False		,,,				2504	0.002				p.T173S		Atlas-SNP	.											.	KRTAP4-8	57	.	0			c.C518G						PASS	.						53	64	61					17																	39253819		691	1591	2282	SO:0001583	missense	728224	exon1			GGGCAGGTGGAGA	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"Keratin associated proteins"	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.518C>G	17.37:g.39253819G>C	ENSP00000328444:p.Thr173Ser	240	0	0		167	46	0.275449	NM_031960	A8MSH3	Missense_Mutation	SNP	ENST00000333822.4	37	CCDS45674.1	.	.	.	.	.	.	.	.	.	.	.	5.072	0.198925	0.09652	.	.	ENSG00000204880	ENST00000333822;ENST00000332991	T	0.00590	6.36	3.73	2.73	0.32206	.	0.227898	0.21667	U	0.070931	T	0.00815	0.0027	L	0.35854	1.095	0.26449	N	0.975649	D	0.63046	0.992	P	0.57244	0.816	T	0.49597	-0.8923	10	0.07813	T	0.8	.	6.5126	0.22230	0.1366:0.0:0.8634:0.0	.	173	Q9BYQ9	KRA48_HUMAN	S	173;143	ENSP00000328444:T173S	ENSP00000414561:T143S	T	-	2	0	KRTAP4-8	36507345	1.000000	0.71417	1.000000	0.80357	0.560000	0.35617	2.706000	0.47135	1.794000	0.52575	0.449000	0.29647	ACC	.	.	weak		0.632	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960		C	39253819	G	C	39253819	3	2	22	1	0	0	0	0	1	0	0	0	8565	1261	44	4	43	4	KRTAP4-8	17	39253819	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	22	39253819	41941391	3491	6392			8	31		9	9	8325	N	T_G_C	3.818482e-05
KRTAP4-8	728224	hgsc.bcm.edu	37	chr17	39253931	39253931	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggattcacagcaagaggggcGgcagcagctggagatgctgc	10	5	17	9	1	1	2	1	0	0	2	1	4	1	3	0	5	5	5	0	5	1	1	rs150613353	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39253931G>A	ENST00000333822.4	-	1	462	c.406C>T	c.(406-408)Cgc>Tgc	p.R136C		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	136	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						caagaggggcggcagcagctg	0.662													G|||	232	0.0463259	0.1664	0.0159	5008	,	,		14984	0.0		0.001	False		,,,				2504	0.0				p.R136C		Atlas-SNP	.											.	KRTAP4-8	57	.	0			c.C406T						PASS	.						6	8	8					17																	39253931		682	1556	2238	SO:0001583	missense	728224	exon1			AGGGGCGGCAGCA	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"Keratin associated proteins"	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.406C>T	17.37:g.39253931G>A	ENSP00000328444:p.Arg136Cys	84	0	0		123	54	0.439024	NM_031960	A8MSH3	Missense_Mutation	SNP	ENST00000333822.4	37	CCDS45674.1	75	0.034340659340659344	69	0.1402439024390244	6	0.016574585635359115	0	0.0	0	0.0	.	12.52	1.962330	0.34659	.	.	ENSG00000204880	ENST00000333822	T	0.01484	4.84	3.73	3.73	0.42828	.	1.159130	0.06715	U	0.773946	T	0.00039	0.0001	M	0.75447	2.3	0.32957	P	0.47942799999999997	B	0.29936	0.262	B	0.19666	0.026	T	0.33701	-0.9858	9	0.66056	D	0.02	.	7.5536	0.27812	0.1225:0.0:0.8775:0.0	.	136	Q9BYQ9	KRA48_HUMAN	C	136	ENSP00000328444:R136C	ENSP00000328444:R136C	R	-	1	0	KRTAP4-8	36507457	0.000000	0.05858	0.820000	0.32676	0.259000	0.26198	-1.031000	0.03578	1.794000	0.52575	0.449000	0.29647	CGC	G|0.966;A|0.034	0.034	strong		0.662	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960		A	39253931	G	A	39253931	3	1	22	1	0	0	0	0	1	0	0	0	8565	1116	39	1	155	1	KRTAP4-8	17	39253931	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	112	39253931	41941279	3492	6393			8	31		9	9	8325	N	T_G_C	3.818482e-05
KRTAP4-8	728224	hgsc.bcm.edu	37	chr17	39254074	39254074	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agcagctagggtggcagcagGtgggctggcagcacacagac	10	4	17	10	0	0	1	0	0	0	1	0	1	0	1	0	5	4	7	0	5	1	1	rs78662167		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39254074G>T	ENST00000333822.4	-	1	319	c.263C>A	c.(262-264)aCc>aAc	p.T88N		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	88	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						GTGGCAGCAGGTGGGCTGGCA	0.662																																					p.T88N		Atlas-SNP	.											.	KRTAP4-8	57	.	0			c.C263A						PASS	.						7	11	10					17																	39254074		684	1571	2255	SO:0001583	missense	728224	exon1			CAGCAGGTGGGCT	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"Keratin associated proteins"	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.263C>A	17.37:g.39254074G>T	ENSP00000328444:p.Thr88Asn	139	0	0		133	19	0.142857	NM_031960	A8MSH3	Missense_Mutation	SNP	ENST00000333822.4	37	CCDS45674.1	.	.	.	.	.	.	.	.	.	.	.	12.61	1.990330	0.35131	.	.	ENSG00000204880	ENST00000333822;ENST00000332991	T	0.01464	4.86	3.31	-6.61	0.01818	.	.	.	.	.	T	0.02848	0.0085	M	0.87547	2.89	0.09310	N	0.999995	B	0.09022	0.002	B	0.08055	0.003	T	0.35674	-0.9779	9	0.52906	T	0.07	.	2.3202	0.04208	0.2779:0.4366:0.1148:0.1707	.	88	Q9BYQ9	KRA48_HUMAN	N	88;73	ENSP00000328444:T88N	ENSP00000414561:T73N	T	-	2	0	KRTAP4-8	36507600	0.000000	0.05858	0.000000	0.03702	0.921000	0.55340	-5.373000	0.00127	-4.086000	0.00075	0.449000	0.29647	ACC	G|0.500;T|0.500	0.500	weak		0.662	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960		T	39254074	G	T	39254074	3	4	22	1	0	0	0	0	1	0	0	0	8565	1261	44	4	298	4	KRTAP4-8	17	39254074	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	143	39254074	41941136	3493	6394			8	31		9	9	8325	N	T_G_C	3.818482e-05
KRTAP4-8	728224	hgsc.bcm.edu	37	chr17	39254184	39254184	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagactggcagcactggggTctgcagcagcaggacacact	11	5	13	12	0	1	1	0	0	1	1	1	2	1	2	0	4	4	5	0	4	0	0	rs7217470	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39254184T>C	ENST00000333822.4	-	1	209	c.153A>G	c.(151-153)agA>agG	p.R51R		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	51	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						AGCACTGGGGTCTGCAGCAGC	0.652													T|||	241	0.048123	0.1732	0.0159	5008	,	,		15501	0.0		0.001	False		,,,				2504	0.0				p.R51R		Atlas-SNP	.											KRTAP4-8,NS,carcinoma,0,1	KRTAP4-8	57	1	0			c.A153G						scavenged	.	T		192,1192		14,164,514	14	17	16		153	-5.2	0	17	dbSNP_116	16	2,3172		0,2,1585	no	coding-synonymous	KRTAP4-8	NM_031960.2		14,166,2099	CC,CT,TT		0.063,13.8728,4.2563		51/186	39254184	194,4364	692	1587	2279	SO:0001819	synonymous_variant	728224	exon1			CTGGGGTCTGCAG	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"Keratin associated proteins"	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.153A>G	17.37:g.39254184T>C		101	1	0.00990099		146	83	0.568493	NM_031960	A8MSH3	Silent	SNP	ENST00000333822.4	37	CCDS45674.1																																																																																			T|0.820;C|0.180	0.180	strong		0.652	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960		C	39254184	T	C	39254184	2	2	22	1	0	0	0	0	0	0	0	1	8565	1664	58	3		3	KRTAP4-8	17	39254184	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	110	39254184	41941026	3494	6395			8	31		9	9	8325	N	T_G_C	3.818482e-05
KRTAP4-9	100132386	hgsc.bcm.edu	37	chr17	39261717	39261717	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtcaggagacctgctgccGccccagctgctgtgagacca	7	7	12	15	1	1	2	1	1	0	2	1	4	1	2	5	1	4	3	5	1	0	0	rs149483591	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39261717G>A	ENST00000391415.1	+	1	134	c.77G>A	c.(76-78)cGc>cAc	p.R26H		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	26	29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						ACCTGCTGCCGCCCCAGCTGC	0.647													G|||	272	0.0543131	0.1959	0.0173	5008	,	,		18818	0.0		0.001	False		,,,				2504	0.0				p.R26H		Atlas-SNP	.											KRTAP4-9,NS,carcinoma,+1,1	KRTAP4-9	110	1	0			c.G77A						scavenged	.	G	HIS/ARG	218,1166		12,194,486	16	21	19		77	-0.7	1	17	dbSNP_134	19	2,3178		0,2,1588	no	missense	KRTAP4-9	NM_001146041.1	29	12,196,2074	AA,AG,GG		0.0629,15.7514,4.8203	benign	26/211	39261717	220,4344	692	1590	2282	SO:0001583	missense	100132386	exon1			GCTGCCGCCCCAG	AJ406941	CCDS54124.1	17q21.2	2013-06-25			ENSG00000212722	ENSG00000212722		"Keratin associated proteins"	18910	protein-coding gene	gene with protein product							Standard	NM_001146041		Approved	KAP4.9	uc010wfp.2	Q9BYQ8	OTTHUMG00000133584	ENST00000391415.1:c.77G>A	17.37:g.39261717G>A	ENSP00000375234:p.Arg26His	129	2	0.0155039		120	60	0.5	NM_001146041		Missense_Mutation	SNP	ENST00000391415.1	37	CCDS54124.1	95	0.043498168498168496	89	0.18089430894308944	6	0.016574585635359115	0	0.0	0	0.0	.	10.53	1.376288	0.24857	0.157514	6.29E-4	ENSG00000212722	ENST00000391415;ENST00000333994	T	0.32515	1.45	3.31	-0.714	0.11219	.	.	.	.	.	T	0.00073	0.0002	M	0.79614	2.46	0.52099	P	5.999999999994898E-5	B	0.25521	0.128	B	0.20767	0.031	T	0.08310	-1.0728	8	0.37606	T	0.19	.	6.5459	0.22406	0.5339:0.0:0.4661:0.0	.	26	Q9BYQ8	KRA49_HUMAN	H	26	ENSP00000375234:R26H	ENSP00000334461:R26H	R	+	2	0	KRTAP4-9	36515243	0.000000	0.05858	0.986000	0.45419	0.476000	0.33039	-1.656000	0.01980	-0.101000	0.12219	0.194000	0.17425	CGC	G|0.956;A|0.044	0.044	strong		0.647	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041		A	39261717	G	A	39261717	3	1	22	1	0	0	0	0	1	0	0	0	8566	1087	38	1	79	1	KRTAP4-9	17	39261717	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	7533	39261717	41933493	3495	6396			8	31		9	9	8325	N	T_G_C	3.818482e-05
KRTAP4-9	100132386	hgsc.bcm.edu	37	chr17	39261793	39261793	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgtgtatccagctgctgcagGccccagtgctgccagtctgt	5	11	12	13	0	1	0	0	0	1	0	2	0	2	0	4	1	5	5	4	1	1	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39261793G>A	ENST00000391415.1	+	1	210	c.153G>A	c.(151-153)agG>agA	p.R51R		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	51	29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						GCTGCTGCAGGCCCCAGTGCT	0.647																																					p.R51R		Atlas-SNP	.											.	KRTAP4-9	110	.	0			c.G153A						PASS	.						16	23	21					17																	39261793		686	1591	2277	SO:0001819	synonymous_variant	100132386	exon1			CTGCAGGCCCCAG	AJ406941	CCDS54124.1	17q21.2	2013-06-25			ENSG00000212722	ENSG00000212722		"Keratin associated proteins"	18910	protein-coding gene	gene with protein product							Standard	NM_001146041		Approved	KAP4.9	uc010wfp.2	Q9BYQ8	OTTHUMG00000133584	ENST00000391415.1:c.153G>A	17.37:g.39261793G>A		115	0	0		76	14	0.184211	NM_001146041		Silent	SNP	ENST00000391415.1	37	CCDS54124.1																																																																																			.	.	none		0.647	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041		A	39261793	G	A	39261793	2	1	22	1	0	0	0	0	0	0	0	1	8566	1194	42	2		2	KRTAP4-9	17	39261793	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	76	39261793	41933417	3496	6397			8	31		9	9	8325	N	T_G_C	3.818482e-05
KRTAP4-9	100132386	hgsc.bcm.edu	37	chr17	39262091	39262091	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgccagcccaactgctgcCgccccagctgcagcatctcc	6	6	9	20	1	1	0	0	0	1	0	2	0	1	0	6	0	8	5	6	0	1	0	rs571292694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39262091C>T	ENST00000391415.1	+	1	508	c.451C>T	c.(451-453)Cgc>Tgc	p.R151C		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	151	29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						caactgctgccgccccagctg	0.662													C|||	26	0.00519169	0.0197	0.0	5008	,	,		18753	0.0		0.0	False		,,,				2504	0.0				p.R151C		Atlas-SNP	.											.	KRTAP4-9	110	.	0			c.C451T						PASS	.						5	8	7					17																	39262091		667	1548	2215	SO:0001583	missense	100132386	exon1			TGCTGCCGCCCCA	AJ406941	CCDS54124.1	17q21.2	2013-06-25			ENSG00000212722	ENSG00000212722		"Keratin associated proteins"	18910	protein-coding gene	gene with protein product							Standard	NM_001146041		Approved	KAP4.9	uc010wfp.2	Q9BYQ8	OTTHUMG00000133584	ENST00000391415.1:c.451C>T	17.37:g.39262091C>T	ENSP00000375234:p.Arg151Cys	126	0	0		186	64	0.344086	NM_001146041		Missense_Mutation	SNP	ENST00000391415.1	37	CCDS54124.1	.	.	.	.	.	.	.	.	.	.	.	11.75	1.733214	0.30684	.	.	ENSG00000212722	ENST00000377734;ENST00000391415;ENST00000333994	T	0.00609	6.24	3.18	-6.36	0.01969	.	1.407670	0.05656	U	0.586011	T	0.00695	0.0023	M	0.69358	2.11	0.09310	N	0.999995	B	0.13594	0.008	B	0.06405	0.002	T	0.37033	-0.9723	10	0.54805	T	0.06	.	3.1538	0.06497	0.4027:0.2953:0.2179:0.0841	.	151	Q9BYQ8	KRA49_HUMAN	C	139;151;142	ENSP00000375234:R151C	ENSP00000334461:R142C	R	+	1	0	KRTAP4-9	36515617	0.000000	0.05858	0.000000	0.03702	0.674000	0.39518	-0.828000	0.04419	-3.015000	0.00271	-0.443000	0.05667	CGC	.	.	none		0.662	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041		T	39262091	C	T	39262091	3	4	22	1	0	0	0	0	1	0	0	0	8566	652	23	1	453	1	KRTAP4-9	17	39262091	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	298	39262091	41933119	3497	6398			8	31		9	9	8325	N	T_G_C	3.818482e-05
KRTAP4-9	100132386	hgsc.bcm.edu	37	chr17	39262121	39262121	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcatctccagctgctgcCgcccctcttgctgtgaatcc	5	10	9	17	1	2	1	0	1	2	0	4	1	3	1	5	0	5	5	5	0	1	1	rs200757692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39262121C>T	ENST00000391415.1	+	1	538	c.481C>T	c.(481-483)Cgc>Tgc	p.R161C		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	161	29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.R149C(1)|p.R161C(1)		central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						cagctgctgccgcccctcttg	0.657																																					p.R161C		Atlas-SNP	.											KRTAP4-9_ENST00000377734,NS,carcinoma,0,2	KRTAP4-9	110	2	2	Substitution - Missense(2)	endometrium(2)	c.C481T						scavenged	.						7	11	10					17																	39262121		682	1570	2252	SO:0001583	missense	100132386	exon1			TGCTGCCGCCCCT	AJ406941	CCDS54124.1	17q21.2	2013-06-25			ENSG00000212722	ENSG00000212722		"Keratin associated proteins"	18910	protein-coding gene	gene with protein product							Standard	NM_001146041		Approved	KAP4.9	uc010wfp.2	Q9BYQ8	OTTHUMG00000133584	ENST00000391415.1:c.481C>T	17.37:g.39262121C>T	ENSP00000375234:p.Arg161Cys	129	0	0		151	17	0.112583	NM_001146041		Missense_Mutation	SNP	ENST00000391415.1	37	CCDS54124.1	.	.	.	.	.	.	.	.	.	.	.	11.80	1.746361	0.30955	.	.	ENSG00000212722	ENST00000377734;ENST00000391415;ENST00000333994	T	0.00605	6.27	2.98	0.469	0.16741	.	0.000000	0.40640	U	0.001042	T	0.00552	0.0018	M	0.70275	2.135	0.09310	N	1	P	0.34587	0.458	B	0.19391	0.025	T	0.50857	-0.8778	10	0.52906	T	0.07	.	1.9066	0.03278	0.202:0.4678:0.1985:0.1317	.	161	Q9BYQ8	KRA49_HUMAN	C	149;161;152	ENSP00000375234:R161C	ENSP00000334461:R152C	R	+	1	0	KRTAP4-9	36515647	0.000000	0.05858	0.321000	0.25320	0.226000	0.24999	-1.001000	0.03690	0.325000	0.23359	0.197000	0.17608	CGC	.	.	none		0.657	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041		T	39262121	C	T	39262121	3	4	22	1	0	0	0	0	1	0	0	0	8566	652	23	1	483	1	KRTAP4-9	17	39262121	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	30	39262121	41933089	3498	6399			8	31		9	9	8325	N	T_G_C	3.818482e-05
KRTAP4-11	653240	hgsc.bcm.edu	37	chr17	39274212	39274212	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggcagcactggggtctgcagCagctggacacacagcagctg	9	5	15	12	0	1	0	0	0	1	0	1	1	1	1	0	4	6	7	0	4	0	0	rs187464255	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39274212C>T	ENST00000391413.2	-	1	394	c.356G>A	c.(355-357)tGc>tAc	p.C119Y		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	119	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)			gggtctgcagcagctggacac	0.652													c|||	125	0.0249601	0.0923	0.0029	5008	,	,		17401	0.0		0.001	False		,,,				2504	0.0				p.C119Y		Atlas-SNP	.											.	KRTAP4-11	94	.	0			c.G356A						PASS	.						4	8	7					17																	39274212		643	1521	2164	SO:0001583	missense	653240	exon1			CTGCAGCAGCTGG	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.356G>A	17.37:g.39274212C>T	ENSP00000375232:p.Cys119Tyr	120	0	0		118	37	0.313559	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	CCDS45675.1	39	0.017857142857142856	36	0.07317073170731707	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	.	13.97	2.395614	0.42512	.	.	ENSG00000212721	ENST00000391413	T	0.03717	3.83	3.63	3.63	0.41609	.	.	.	.	.	T	0.01489	0.0048	H	0.95365	3.66	0.34837	D	0.740315	P	0.46395	0.877	P	0.54544	0.755	T	0.19063	-1.0317	9	0.72032	D	0.01	.	13.1597	0.59537	0.0:1.0:0.0:0.0	.	119	Q9BYQ6	KR411_HUMAN	Y	119	ENSP00000375232:C119Y	ENSP00000375232:C119Y	C	-	2	0	KRTAP4-11	36527738	0.060000	0.20803	0.929000	0.37066	0.073000	0.16967	0.773000	0.26661	1.757000	0.51966	0.514000	0.50259	TGC	C|0.982;T|0.018	0.018	strong		0.652	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1			T	39274212	C	T	39274212	3	4	22	1	0	0	0	0	1	0	0	0	8558	710	25	2	235	2	KRTAP4-11	17	39274212	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	12091	39274212	41920998	3499	6400											
KRTAP4-11	653240	hgsc.bcm.edu	37	chr17	39274360	39274360	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgacagcagctggagatgcAgcatctggggcggcagcagg	9	4	18	10	2	1	1	0	0	1	1	1	3	1	1	0	5	5	6	0	5	0	0			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39274360A>T	ENST00000391413.2	-	1	246	c.208T>A	c.(208-210)Tgc>Agc	p.C70S		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	70	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].		Missing (in allele KAP4.14). {ECO:0000269|PubMed:15955084}.			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)			CTGGAGATGCAGCATCTGGGG	0.667																																					p.C70S		Atlas-SNP	.											KRTAP4-11,NS,carcinoma,0,1	KRTAP4-11	94	1	0			c.T208A						scavenged	.						7	12	11					17																	39274360		677	1580	2257	SO:0001583	missense	653240	exon1			AGATGCAGCATCT	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.208T>A	17.37:g.39274360A>T	ENSP00000375232:p.Cys70Ser	189	2	0.010582		169	15	0.0887574	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	13.38	2.219303	0.39201	.	.	ENSG00000212721	ENST00000391413	T	0.02280	4.36	3.77	1.34	0.21922	.	0.000000	0.36972	U	0.002304	T	0.04770	0.0129	M	0.90252	3.1	0.23636	N	0.997233	B	0.17268	0.021	B	0.17722	0.019	T	0.23048	-1.0199	10	0.54805	T	0.06	.	4.9719	0.14119	0.7038:0.1861:0.1101:0.0	.	70	Q9BYQ6	KR411_HUMAN	S	70	ENSP00000375232:C70S	ENSP00000375232:C70S	C	-	1	0	KRTAP4-11	36527886	0.844000	0.29557	0.494000	0.27515	0.120000	0.20174	1.052000	0.30429	0.644000	0.30656	0.496000	0.49642	TGC	.	.	none		0.667	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1			T	39274360	A	T	39274360	3	4	22	1	0	0	0	0	1	0	0	0	8558	188	7	5	383	5	KRTAP4-11	17	39274360	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	148	39274360	41920850	3500	6401											
KRTAP4-5	85289	hgsc.bcm.edu	37	chr17	39305760	39305760	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtcctgcagcaggtggtcCtgcagcaggtggtctggcag	5	9	17	10	0	1	0	0	0	1	0	3	0	3	0	2	6	4	5	2	6	0	0	rs427961	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39305760C>T	ENST00000343246.4	-	1	294	c.260G>A	c.(259-261)aGg>aAg	p.R87K		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	87	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)			gcaggtggtcctgcagcaggt	0.657													T|||	184	0.0367412	0.1256	0.0086	5008	,	,		15710	0.001		0.001	False		,,,				2504	0.0102				p.R87K		Atlas-SNP	.											.	KRTAP4-5	34	.	0			c.G260A						PASS	.						17	23	21					17																	39305760		2133	4241	6374	SO:0001583	missense	85289	exon1			GTGGTCCTGCAGC	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.260G>A	17.37:g.39305760C>T	ENSP00000340546:p.Arg87Lys	150	0	0		90	44	0.488889	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	37	CCDS32650.1	.	.	.	.	.	.	.	.	.	.	.	6.445	0.450231	0.12223	.	.	ENSG00000198271	ENST00000343246	T	0.00568	6.53	2.87	-5.75	0.02384	.	.	.	.	.	T	0.00468	0.0015	L	0.56769	1.78	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.43893	-0.9363	9	0.10111	T	0.7	.	5.8578	0.18730	0.1977:0.5979:0.0:0.2045	rs427961	92	Q9BYR2	KRA45_HUMAN	K	87	ENSP00000340546:R87K	ENSP00000340546:R87K	R	-	2	0	KRTAP4-5	36559286	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.772000	0.04694	-2.052000	0.00902	-1.408000	0.01128	AGG	T|1.000;|0.000	1.000	weak		0.657	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1			T	39305760	C	T	39305760	3	4	22	1	0	0	0	0	1	0	0	0	8563	681	24	2	289	2	KRTAP4-5	17	39305760	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	31400	39305760	41889450	3501	6402											
KRTAP4-5	85289	hgsc.bcm.edu	37	chr17	39305774	39305774	+	Missense_Mutation	SNP	C	C	G																															gtggtcctgcagcaggtggtCtggcagcagcaggggcggca																								rs137947981		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39305774C>G	ENST00000343246.4	-	1	280	c.246G>C	c.(244-246)caG>caC	p.Q82H		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	82	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)			agcaggtggtctggcagcagc	0.652																																					p.Q82H		Atlas-SNP	.											KRTAP4-5,NS,carcinoma,0,1	KRTAP4-5	34	1	1	Substitution - Missense(1)	lung(1)	c.G246C						PASS	.						14	21	19					17																	39305774		2102	4215	6317	SO:0001583	missense	85289	exon1			GGTGGTCTGGCAG	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.246G>C	17.37:g.39305774C>G	ENSP00000340546:p.Gln82His	136	0	0		86	50	0.581395	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	37	CCDS32650.1	.	.	.	.	.	.	.	.	.	.	.	6.243	0.412973	0.11812	.	.	ENSG00000198271	ENST00000343246	T	0.00594	6.33	2.03	-0.354	0.12591	.	.	.	.	.	T	0.01320	0.0043	M	0.79693	2.465	0.09310	N	1	B	0.21147	0.052	B	0.35182	0.197	T	0.25950	-1.0117	9	0.45353	T	0.12	.	12.081	0.53671	0.0:0.7361:0.2639:0.0	.	87	Q9BYR2	KRA45_HUMAN	H	82	ENSP00000340546:Q82H	ENSP00000340546:Q82H	Q	-	3	2	KRTAP4-5	36559300	0.000000	0.05858	0.005000	0.12908	0.001000	0.01503	-3.389000	0.00488	-0.371000	0.08004	-1.872000	0.00552	CAG	.	.	weak		0.652	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1			G	39305774	C	G	39305774	3	3	22	1	0	0	0	0	1	0	0	0	8563	912	32	4	303	4	KRTAP4-5	17	39305774	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	14	39305774	41889436	3502	6403	79	2									
KRTAP4-5	85289	hgsc.bcm.edu	37	chr17	39305775	39305775	+	Missense_Mutation	SNP	T	T	C																															tggtcctgcagcaggtggtcTggcagcagcaggggcggcag																								rs535144703|rs141265645|rs58117746	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39305775T>C	ENST00000343246.4	-	1	279	c.245A>G	c.(244-246)cAg>cGg	p.Q82R		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	82	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)			gcaggtggtctggcagcagca	0.657																																					p.Q82R		Atlas-SNP	.											KRTAP4-5,NS,carcinoma,+1,1	KRTAP4-5	34	1	0			c.A245G						PASS	.						14	21	18					17																	39305775		2102	4214	6316	SO:0001583	missense	85289	exon1			GTGGTCTGGCAGC	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.245A>G	17.37:g.39305775T>C	ENSP00000340546:p.Gln82Arg	137	0	0		87	53	0.609195	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	37	CCDS32650.1	.	.	.	.	.	.	.	.	.	.	.	1.564	-0.535892	0.04082	.	.	ENSG00000198271	ENST00000343246	T	0.00581	6.42	2.44	-3.27	0.05048	.	.	.	.	.	T	0.00271	0.0008	N	0.04260	-0.245	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35001	-0.9806	9	0.11794	T	0.64	.	3.3098	0.07013	0.2034:0.3821:0.0:0.4145	.	87	Q9BYR2	KRA45_HUMAN	R	82	ENSP00000340546:Q82R	ENSP00000340546:Q82R	Q	-	2	0	KRTAP4-5	36559301	0.000000	0.05858	0.009000	0.14445	0.001000	0.01503	-1.539000	0.02202	-0.998000	0.03446	-1.710000	0.00715	CAG	.	.	weak		0.657	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1			C	39305775	T	C	39305775	3	2	22	1	0	0	0	0	1	0	0	0	8563	1580	55	3	304	3	KRTAP4-5	17	39305775	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1	39305775	41889435	3503	6404	79	2									
KRTAP4-5	85289	hgsc.bcm.edu	37	chr17	39306004	39306004	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcagagctgacagagccacAacaggagctgaccatggtgt	12	6	12	11	0	1	4	1	2	0	2	1	5	1	5	2	2	4	2	2	2	1	0	rs238829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39306004A>G	ENST00000343246.4	-	1	50	c.16T>C	c.(16-18)Tgt>Cgt	p.C6R		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	6	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].		C -> R (in dbSNP:rs238829).		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)			ACAGAGCCACAACAGGAGCTG	0.592													A|||	189	0.0377396	0.1377	0.0101	5008	,	,		18094	0.0		0.0	False		,,,				2504	0.0				p.C6R		Atlas-SNP	.											.	KRTAP4-5	34	.	0			c.T16C						PASS	.	A	ARG/CYS	502,3898		31,440,1729	34	36	35		16	4.2	1	17	dbSNP_79	35	1,8595		0,1,4297	yes	missense	KRTAP4-5	NM_033188.3	180	31,441,6026	GG,GA,AA		0.0116,11.4091,3.8704	probably-damaging	6/182	39306004	503,12493	2200	4298	6498	SO:0001583	missense	85289	exon1			AGCCACAACAGGA	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.16T>C	17.37:g.39306004A>G	ENSP00000340546:p.Cys6Arg	307	0	0		346	153	0.442197	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	37	CCDS32650.1	76	0.0347985347985348	70	0.14227642276422764	6	0.016574585635359115	0	0.0	0	0.0	.	8.628	0.892905	0.17613	0.114091	1.16E-4	ENSG00000198271	ENST00000343246	T	0.03065	4.06	4.25	4.25	0.50352	.	0.000000	0.40385	U	0.001109	T	0.00178	0.0005	H	0.94698	3.57	0.21325	P	0.999724217	D	0.59767	0.986	P	0.61800	0.894	T	0.04178	-1.0971	9	0.87932	D	0	.	11.6139	0.51078	1.0:0.0:0.0:0.0	rs238829;rs52814152;rs238829	6	Q9BYR2	KRA45_HUMAN	R	6	ENSP00000340546:C6R	ENSP00000340546:C6R	C	-	1	0	KRTAP4-5	36559530	0.995000	0.38212	1.000000	0.80357	0.017000	0.09413	1.548000	0.36201	1.900000	0.55004	0.533000	0.62120	TGT	A|0.962;G|0.038	0.038	strong		0.592	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1			G	39306004	A	G	39306004	3	3	22	1	0	0	0	0	1	0	0	0	8563	130	5	3	533	3	KRTAP4-5	17	39306004	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	229	39306004	41889206	3504	6405											
KRTAP4-4	84616	hgsc.bcm.edu	37	chr17	39316482	39316482	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccacaatggggcctgtagcaCctggacacacagcagctggg	10	5	13	13	0	0	0	0	0	0	0	0	1	0	1	3	4	3	4	3	4	2	1	rs366700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39316482C>G	ENST00000390661.3	-	1	501	c.462G>C	c.(460-462)agG>agC	p.R154S		NM_032524.1	NP_115913.1	Q9BYR3	KRA44_HUMAN	keratin associated protein 4-4	154	26 X 5 AA repeats of C-C-[GRQVCH]-[SPT]- [VSTQR].		R -> S (in dbSNP:rs366700).			keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(5)	7		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			GCCTGTAGCACCTGGACACAC	0.617													c|||	523	0.104433	0.379	0.0288	5008	,	,		20637	0.0		0.002	False		,,,				2504	0.0				p.R154S		Atlas-SNP	.											.	KRTAP4-4	21	.	0			c.G462C						PASS	.	G	SER/ARG	1375,3019		224,927,1046	39	46	44		462	1.5	1	17	dbSNP_80	44	7,8585		0,7,4289	yes	missense	KRTAP4-4	NM_032524.1	110	224,934,5335	GG,GC,CC		0.0815,31.2927,10.6422	benign	154/167	39316482	1382,11604	2197	4296	6493	SO:0001583	missense	84616	exon1			GTAGCACCTGGAC	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.462G>C	17.37:g.39316482C>G	ENSP00000375076:p.Arg154Ser	218	0	0		251	250	0.996016	NM_032524	Q9BYU7	Missense_Mutation	SNP	ENST00000390661.3	37	CCDS11383.1	190	0.08699633699633699	179	0.3638211382113821	11	0.03038674033149171	0	0.0	0	0.0	.	2.548	-0.304815	0.05495	0.312927	8.15E-4	ENSG00000171396	ENST00000390661	T	0.00571	6.5	4.79	1.5	0.22942	.	0.286046	0.18063	U	0.152889	T	0.00012	0.0000	N	0.00159	-1.955	0.54753	P	1.8999999999991246E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.03068	-1.1076	9	0.19147	T	0.46	.	4.8968	0.13755	0.2534:0.289:0.4576:0.0	rs366700;rs52806510;rs366700	154	Q9BYR3	KRA44_HUMAN	S	154	ENSP00000375076:R154S	ENSP00000375076:R154S	R	-	3	2	KRTAP4-4	36570008	0.000000	0.05858	0.990000	0.47175	0.502000	0.33828	-0.971000	0.03806	0.113000	0.18004	-0.335000	0.08231	AGG	C|0.938;G|0.062	0.062	strong		0.617	KRTAP4-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257291.1			G	39316482	C	G	39316482	3	3	22	1	0	0	0	0	1	0	0	0	8562	506	18	4	42	4	KRTAP4-4	17	39316482	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	10478	39316482	41878728	3505	6406											
KRTAP4-4	84616	hgsc.bcm.edu	37	chr17	39316841	39316841	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagcagctggggcggcagcAggtggtcctgcagcaggtgg	7	5	19	10	1	0	0	0	0	0	0	1	0	1	0	1	7	5	6	1	7	0	0	rs444509|rs535200131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39316841A>T	ENST00000390661.3	-	1	142	c.103T>A	c.(103-105)Tgc>Agc	p.C35S		NM_032524.1	NP_115913.1	Q9BYR3	KRA44_HUMAN	keratin associated protein 4-4	35	26 X 5 AA repeats of C-C-[GRQVCH]-[SPT]- [VSTQR].		C -> S (in dbSNP:rs444509).			keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(5)	7		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			GGGCGGCAGCAGGTGGTCCTG	0.647													A|||	522	0.104233	0.3782	0.0288	5008	,	,		19513	0.0		0.002	False		,,,				2504	0.0				p.C35S		Atlas-SNP	.											.	KRTAP4-4	21	.	0			c.T103A						PASS	.	A	SER/CYS	1206,3164		166,874,1145	38	53	48		103	4.5	1	17	dbSNP_80	48	3,8589		0,3,4293	no	missense	KRTAP4-4	NM_032524.1	112	166,877,5438	TT,TA,AA		0.0349,27.5973,9.3273	possibly-damaging	35/167	39316841	1209,11753	2185	4296	6481	SO:0001583	missense	84616	exon1			GGCAGCAGGTGGT	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.103T>A	17.37:g.39316841A>T	ENSP00000375076:p.Cys35Ser	171	0	0		147	147	1	NM_032524	Q9BYU7	Missense_Mutation	SNP	ENST00000390661.3	37	CCDS11383.1	187	0.08562271062271062	176	0.35772357723577236	11	0.03038674033149171	0	0.0	0	0.0	.	14.47	2.545823	0.45280	0.275973	3.49E-4	ENSG00000171396	ENST00000390661	T	0.04406	3.63	4.52	4.52	0.55395	.	0.000000	0.44688	U	0.000438	T	0.00012	0.0000	M	0.93150	3.385	0.34592	P	0.28444	P	0.38551	0.636	P	0.47827	0.558	T	0.34179	-0.9839	9	0.44086	T	0.13	.	11.8038	0.52143	1.0:0.0:0.0:0.0	rs444509;rs61402488	35	Q9BYR3	KRA44_HUMAN	S	35	ENSP00000375076:C35S	ENSP00000375076:C35S	C	-	1	0	KRTAP4-4	36570367	1.000000	0.71417	0.961000	0.40146	0.964000	0.63967	2.062000	0.41413	1.660000	0.50760	0.443000	0.29094	TGC	A|0.912;T|0.088	0.088	strong		0.647	KRTAP4-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257291.1			T	39316841	A	T	39316841	3	4	22	1	0	0	0	0	1	0	0	0	8562	188	7	5	401	5	KRTAP4-4	17	39316841	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	359	39316841	41878369	3506	6407											
KRTAP4-4	84616	hgsc.bcm.edu	37	chr17	39316870	39316870	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgcagcaggtggtctggcagTagctgggacggcagcagttc	7	8	17	9	1	1	0	0	0	1	0	2	1	1	1	0	5	4	8	0	5	1	2	rs385055	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39316870T>C	ENST00000390661.3	-	1	113	c.74A>G	c.(73-75)tAc>tGc	p.Y25C		NM_032524.1	NP_115913.1	Q9BYR3	KRA44_HUMAN	keratin associated protein 4-4	25	26 X 5 AA repeats of C-C-[GRQVCH]-[SPT]- [VSTQR].		Y -> C (in dbSNP:rs385055).			keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(5)	7		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			GGTCTGGCAGTAGCTGGGACG	0.637													C|||	641	0.127995	0.466	0.0331	5008	,	,		19142	0.0		0.002	False		,,,				2504	0.0				p.Y25C		Atlas-SNP	.											KRTAP4-4,NS,carcinoma,-1,1	KRTAP4-4	21	1	0			c.A74G						PASS	.	C	CYS/TYR	1640,2760		330,980,890	50	68	62		74	4.6	0.9	17	dbSNP_80	62	10,8590		0,10,4290	no	missense	KRTAP4-4	NM_032524.1	194	330,990,5180	CC,CT,TT		0.1163,37.2727,12.6923	benign	25/167	39316870	1650,11350	2200	4300	6500	SO:0001583	missense	84616	exon1			TGGCAGTAGCTGG	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.74A>G	17.37:g.39316870T>C	ENSP00000375076:p.Tyr25Cys	188	1	0.00531915		134	134	1	NM_032524	Q9BYU7	Missense_Mutation	SNP	ENST00000390661.3	37	CCDS11383.1	231	0.10576923076923077	218	0.44308943089430897	13	0.03591160220994475	0	0.0	0	0.0	.	0.052	-1.247813	0.01469	0.372727	0.001163	ENSG00000171396	ENST00000390661	T	0.00571	6.5	4.62	4.62	0.57501	.	0.157197	0.29868	N	0.010999	T	0.00012	0.0000	N	0.00005	-3.295	0.42889	P	0.005808000000000035	B	0.02656	0.0	B	0.01281	0.0	T	0.19647	-1.0299	9	0.02654	T	1	.	10.7732	0.46336	0.0:0.9051:0.0:0.0949	rs385055;rs59740078	25	Q9BYR3	KRA44_HUMAN	C	25	ENSP00000375076:Y25C	ENSP00000375076:Y25C	Y	-	2	0	KRTAP4-4	36570396	0.010000	0.17322	0.851000	0.33527	0.345000	0.29048	0.694000	0.25512	0.943000	0.37553	-0.227000	0.12334	TAC	T|0.890;C|0.110	0.110	strong		0.637	KRTAP4-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257291.1			C	39316870	T	C	39316870	3	2	22	1	0	0	0	0	1	0	0	0	8562	1638	57	3	430	3	KRTAP4-4	17	39316870	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	29	39316870	41878340	3507	6408											
KRTAP4-3	85290	hgsc.bcm.edu	37	chr17	39324190	39324190	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagcaggaaggcctgcagcAactggaaatgcagcagctgg	13	4	14	10	0	0	0	0	0	0	0	0	2	0	2	1	4	7	6	1	4	3	0	rs377224840		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39324190A>G	ENST00000391356.2	-	1	234	c.235T>C	c.(235-237)Tgc>Cgc	p.C79R		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	79	29 X 5 AA repeats of C-C-[GIKRQVH]-[SPT]- [STA].				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)			ggcctgcagcaactggaaatg	0.612																																					p.C79R		Atlas-SNP	.											.	KRTAP4-3	40	.	0			c.T235C						PASS	.	A	ARG/CYS	147,2777		0,147,1315	3	5	4		235	4.6	1	17		4	1,6765		0,1,3382	no	missense	KRTAP4-3	NM_033187.1	180	0,148,4697	GG,GA,AA		0.0148,5.0274,1.5273	possibly-damaging	79/196	39324190	148,9542	1462	3383	4845	SO:0001583	missense	85290	exon1			TGCAGCAACTGGA	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.235T>C	17.37:g.39324190A>G	ENSP00000375151:p.Cys79Arg	392	1	0.00255102		166	73	0.439759	NM_033187		Missense_Mutation	SNP	ENST00000391356.2	37	CCDS42331.1	.	.	.	.	.	.	.	.	.	.	.	12.37	1.918720	0.33908	0.050274	1.48E-4	ENSG00000196156	ENST00000391356	T	0.03689	3.84	4.57	4.57	0.56435	.	0.000000	0.34362	U	0.004039	T	0.01523	0.0049	M	0.94142	3.5	0.48571	D	0.999674	P	0.38827	0.649	B	0.39185	0.293	T	0.00288	-1.1845	10	0.66056	D	0.02	.	7.092	0.25289	0.8963:0.0:0.1037:0.0	.	79	Q9BYR4	KRA43_HUMAN	R	79	ENSP00000375151:C79R	ENSP00000375151:C79R	C	-	1	0	KRTAP4-3	36577716	0.718000	0.27976	0.995000	0.50966	0.018000	0.09664	1.969000	0.40510	1.799000	0.52666	0.496000	0.49642	TGC	.	.	weak		0.612	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1			G	39324190	A	G	39324190	3	3	22	1	0	0	0	0	1	0	0	0	8561	130	5	3	356	3	KRTAP4-3	17	39324190	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	7320	39324190	41871020	3508	6409											
KRTAP4-3	85290	hgsc.bcm.edu	37	chr17	39324237	39324237	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcaggtggtcctgcagcagCtgggtttgcagcagctggag	7	8	17	9	0	0	0	0	0	0	0	1	1	1	1	1	4	7	8	1	4	0	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39324237C>G	ENST00000391356.2	-	1	187	c.188G>C	c.(187-189)aGc>aCc	p.S63T		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	63	29 X 5 AA repeats of C-C-[GIKRQVH]-[SPT]- [STA].				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)			cctgcagcagctgggtttgca	0.627																																					p.S63T		Atlas-SNP	.											KRTAP4-3,NS,carcinoma,-1,1	KRTAP4-3	40	1	0			c.G188C						scavenged	.						3	5	4					17																	39324237		1480	3536	5016	SO:0001583	missense	85290	exon1			CAGCAGCTGGGTT	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.188G>C	17.37:g.39324237C>G	ENSP00000375151:p.Ser63Thr	420	0	0		110	18	0.163636	NM_033187		Missense_Mutation	SNP	ENST00000391356.2	37	CCDS42331.1	.	.	.	.	.	.	.	.	.	.	.	0.578	-0.838330	0.02692	.	.	ENSG00000196156	ENST00000391356	T	0.01335	5.0	4.13	-2.75	0.05914	.	.	.	.	.	T	0.01061	0.0035	N	0.20881	0.62	0.09310	N	1	B	0.09022	0.002	B	0.11329	0.006	T	0.47573	-0.9107	9	0.14252	T	0.57	.	8.0489	0.30566	0.3482:0.2735:0.3783:0.0	.	63	Q9BYR4	KRA43_HUMAN	T	63	ENSP00000375151:S63T	ENSP00000375151:S63T	S	-	2	0	KRTAP4-3	36577763	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.870000	0.00346	-0.385000	0.07833	-2.956000	0.00083	AGC	.	.	none		0.627	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1			G	39324237	C	G	39324237	3	3	22	1	0	0	0	0	1	0	0	0	8561	797	28	4	403	4	KRTAP4-3	17	39324237	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	47	39324237	41870973	3509	6410											
KRTAP4-3	85290	hgsc.bcm.edu	37	chr17	39324254	39324254	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagctgggtttgcagcagctGgagatacagcaggaaggcct	10	7	15	9	0	0	1	0	0	0	1	0	3	0	2	1	4	6	6	1	4	2	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39324254G>A	ENST00000391356.2	-	1	170	c.171C>T	c.(169-171)tcC>tcT	p.S57S		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	57	29 X 5 AA repeats of C-C-[GIKRQVH]-[SPT]- [STA].				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)			tgcagcagctggagatacagc	0.642																																					p.S57S		Atlas-SNP	.											.	KRTAP4-3	40	.	0			c.C171T						PASS	.						3	4	4					17																	39324254		1542	3395	4937	SO:0001819	synonymous_variant	85290	exon1			GCAGCTGGAGATA	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.171C>T	17.37:g.39324254G>A		434	0	0		210	33	0.157143	NM_033187		Silent	SNP	ENST00000391356.2	37	CCDS42331.1																																																																																			.	.	none		0.642	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1			A	39324254	G	A	39324254	2	1	22	1	0	0	0	0	0	0	0	1	8561	1335	47	2		2	KRTAP4-3	17	39324254	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	17	39324254	41870956	3510	6411											
KRTAP4-3	85290	hgsc.bcm.edu	37	chr17	39324410	39324410	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcagagcagacagagccacaGcaggagctgaccatggcgtc	12	4	13	12	1	1	4	1	1	0	3	2	5	1	5	2	2	4	3	2	2	0	0	rs73985507	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39324410G>A	ENST00000391356.2	-	1	14	c.15C>T	c.(13-15)tgC>tgT	p.C5C		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	5					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)			CAGAGCCACAGCAGGAGCTGA	0.592													A|||	519	0.103634	0.3759	0.0288	5008	,	,		16931	0.0		0.002	False		,,,				2504	0.0				p.C5C		Atlas-SNP	.											.	KRTAP4-3	40	.	0			c.C15T						PASS	.	A		1379,2993		223,933,1030	29	31	30		15	-1.4	0.9	17	dbSNP_130	30	5,8573		0,5,4284	no	coding-synonymous	KRTAP4-3	NM_033187.1		223,938,5314	AA,AG,GG		0.0583,31.5416,10.6873		5/196	39324410	1384,11566	2186	4289	6475	SO:0001819	synonymous_variant	85290	exon1			GCCACAGCAGGAG	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.15C>T	17.37:g.39324410G>A		148	0	0		211	211	1	NM_033187		Silent	SNP	ENST00000391356.2	37	CCDS42331.1																																																																																			G|0.944;A|0.056	0.056	strong		0.592	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1			A	39324410	G	A	39324410	2	1	22	1	0	0	0	0	0	0	0	1	8561	963	34	2		2	KRTAP4-3	17	39324410	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	156	39324410	41870800	3511	6412											
KRTAP4-2	85291	hgsc.bcm.edu	37	chr17	39334314	39334314	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagcagctggggcggcagcAggtggtcctgcagcaggtgg	7	5	19	10	1	0	0	0	0	0	0	1	0	1	0	1	7	5	6	1	7	0	0	rs200720939		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39334314A>T	ENST00000377726.2	-	1	146	c.103T>A	c.(103-105)Tgc>Agc	p.C35S		NM_033062.3	NP_149051	Q9BYR5	KRA42_HUMAN	keratin associated protein 4-2	35	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)			GGGCGGCAGCAGGTGGTCCTG	0.657																																					p.C35S		Atlas-SNP	.											KRTAP4-2_ENST00000458321,NS,haematopoietic_neoplasm,0,4	KRTAP4-2	93	4	0			c.T103A						scavenged	.						48	52	50					17																	39334314		2199	4289	6488	SO:0001583	missense	85291	exon1			GGCAGCAGGTGGT	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.103T>A	17.37:g.39334314A>T	ENSP00000366955:p.Cys35Ser	179	0	0		246	26	0.105691	NM_033062	A0JP64	Missense_Mutation	SNP	ENST00000377726.2	37	CCDS11384.1	.	.	.	.	.	.	.	.	.	.	.	9.002	0.980423	0.18812	.	.	ENSG00000244537	ENST00000377726;ENST00000458321	T	0.02085	4.46	4.24	4.24	0.50183	.	0.212644	0.23275	U	0.049980	T	0.10035	0.0246	H	0.95402	3.665	0.32423	N	0.54916	B	0.33883	0.43	B	0.40602	0.334	T	0.00912	-1.1517	10	0.49607	T	0.09	.	11.5905	0.50943	1.0:0.0:0.0:0.0	.	35	Q9BYR5	KRA42_HUMAN	S	35;152	ENSP00000366955:C35S	ENSP00000366955:C35S	C	-	1	0	KRTAP4-2	36587840	0.997000	0.39634	0.987000	0.45799	0.045000	0.14185	4.092000	0.57707	1.667000	0.50832	0.421000	0.28195	TGC	.	.	weak		0.657	KRTAP4-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257305.1			T	39334314	A	T	39334314	3	4	22	1	0	0	0	0	1	0	0	0	8560	188	7	5	311	5	KRTAP4-2	17	39334314	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	9904	39334314	41860896	3512	6413											
KRTAP9-2	83899	hgsc.bcm.edu	37	chr17	39383351	39383351	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccctgctgccgcccagccTgctgtgagaccacctgctgc	5	7	11	18	1	0	1	0	1	0	1	0	2	0	1	6	0	7	3	6	0	0	0	rs146532415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39383351T>C	ENST00000377721.3	+	1	452	c.445T>C	c.(445-447)Tgc>Cgc	p.C149R	KRTAP9-2_ENST00000455970.2_Missense_Mutation_p.C133R	NM_031961.2	NP_114167.2	Q9BYQ4	KRA92_HUMAN	keratin associated protein 9-2	149	17 X 5 AA repeats of C-C-[RQVSGE]-[SPTQ]- [TASP].					keratin filament (GO:0045095)				large_intestine(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CCGCCCAGCCTGCTGTGAGAC	0.607													.|||	58	0.0115815	0.0424	0.0029	5008	,	,		19288	0.0		0.0	False		,,,				2504	0.0				p.C149R		Atlas-SNP	.											.	KRTAP9-2	24	.	0			c.T445C						PASS	.	T	ARG/CYS	126,4166		3,120,2023	19	21	20		445	1.8	0	17	dbSNP_134	20	0,8406		0,0,4203	no	missense	KRTAP9-2	NM_031961.2	180	3,120,6226	CC,CT,TT		0.0,2.9357,0.9923	probably-damaging	149/175	39383351	126,12572	2146	4203	6349	SO:0001583	missense	83899	exon1			CCAGCCTGCTGTG	AJ406946	CCDS32651.1	17q21.2	2013-06-25			ENSG00000239886	ENSG00000239886		"Keratin associated proteins"	16926	protein-coding gene	gene with protein product						11279113	Standard	NM_031961		Approved	KAP9.2	uc002hwf.3	Q9BYQ4	OTTHUMG00000133609	ENST00000377721.3:c.445T>C	17.37:g.39383351T>C	ENSP00000366950:p.Cys149Arg	336	1	0.00297619		400	149	0.3725	NM_031961	Q17RK8|Q2TB15|Q6ISF6	Missense_Mutation	SNP	ENST00000377721.3	37	CCDS32651.1	.	.	.	.	.	.	.	.	.	.	.	19.02	3.746233	0.69418	0.029357	0.0	ENSG00000239886	ENST00000377721;ENST00000455970	T;T	0.05139	4.92;3.49	2.89	1.78	0.24846	.	.	.	.	.	T	0.02649	0.0080	M	0.74389	2.26	0.52501	D	0.999959	B	0.25904	0.137	B	0.23852	0.049	T	0.08806	-1.0704	9	0.87932	D	0	.	6.5335	0.22339	0.0:0.1318:0.0:0.8682	.	149	Q9BYQ4	KRA92_HUMAN	R	149;133	ENSP00000366950:C149R;ENSP00000398325:C133R	ENSP00000366950:C149R	C	+	1	0	KRTAP9-2	36636877	0.403000	0.25319	0.010000	0.14722	0.911000	0.54048	0.513000	0.22770	0.325000	0.23359	0.248000	0.18094	TGC	T|0.993;C|0.007	0.007	strong		0.607	KRTAP9-2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257717.1			C	39383351	T	C	39383351	3	2	22	1	0	0	0	0	1	0	0	0	8582	1580	55	3	447	3	KRTAP9-2	17	39383351	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	49037	39383351	41811859	3513	6414											
KRTAP9-9	81870	hgsc.bcm.edu	37	chr17	39411711	39411711	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctggaagcccaccactgtgaCcacctgcagcagcacaccct	10	5	8	18	0	0	1	0	1	0	0	0	2	0	2	5	1	4	3	5	1	1	0	rs150962386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39411711C>G	ENST00000394008.1	+	1	76	c.74C>G	c.(73-75)aCc>aGc	p.T25S		NM_030975.2	NP_112237.2	Q9BYP9	KRA99_HUMAN	keratin associated protein 9-9	30	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)			ACCACTGTGACCACCTGCAGC	0.627													.|||	219	0.04373	0.1566	0.0159	5008	,	,		17225	0.0		0.001	False		,,,				2504	0.0				p.T25S		Atlas-SNP	.											.	KRTAP9-9	24	.	0			c.C74G						PASS	.																																			SO:0001583	missense	81870	exon1			CTGTGACCACCTG	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.74C>G	17.37:g.39411711C>G	ENSP00000377576:p.Thr25Ser	39	0	0		85	43	0.505882	NM_030975	B5MDD6|Q9BYQ1	Missense_Mutation	SNP	ENST00000394008.1	37	CCDS54127.1	82	0.037545787545787544	72	0.14634146341463414	10	0.027624309392265192	0	0.0	0	0.0	.	6.971	0.549071	0.13312	.	.	ENSG00000198083	ENST00000394008	T	0.00724	5.78	2.19	1.14	0.20703	.	.	.	.	.	T	0.00012	0.0000	N	0.13168	0.305	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.40997	-0.9533	9	0.08381	T	0.77	.	7.4223	0.27079	0.0:0.8514:0.0:0.1486	.	30	Q9BYP9	KRA99_HUMAN	S	25	ENSP00000377576:T25S	ENSP00000377576:T25S	T	+	2	0	KRTAP9-9	36665237	0.931000	0.31567	0.005000	0.12908	0.354000	0.29330	2.718000	0.47236	0.474000	0.27392	0.456000	0.33151	ACC	C|0.962;G|0.038	0.038	strong		0.627	KRTAP9-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257710.1	NM_030975		G	39411711	C	G	39411711	3	3	22	1	0	0	0	0	1	0	0	0	8586	507	18	4	76	4	KRTAP9-9	17	39411711	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	28360	39411711	41783499	3514	6415											
KRTAP9-9	81870	hgsc.bcm.edu	37	chr17	39412125	39412125	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcccacctgtgtgtccagctGctgccagccttcttgctgct	3	12	10	16	0	1	0	0	0	1	0	2	0	2	0	5	0	6	4	5	0	0	2	rs144403228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39412125G>C	ENST00000394008.1	+	1	490	c.488G>C	c.(487-489)tGc>tCc	p.C163S		NM_030975.2	NP_112237.2	Q9BYP9	KRA99_HUMAN	keratin associated protein 9-9	148						keratin filament (GO:0045095)				endometrium(3)|skin(2)|upper_aerodigestive_tract(1)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			GTGTCCAGCTGCTGCCAGCCT	0.557													.|||	77	0.0153754	0.056	0.0043	5008	,	,		22420	0.0		0.0	False		,,,				2504	0.0				p.C163S		Atlas-SNP	.											.	KRTAP9-9	24	.	0			c.G488C						PASS	.	G	SER/CYS	216,4190		6,204,1993	163	170	167		488	3.7	1	17	dbSNP_134	167	2,8598		0,2,4298	yes	missense	KRTAP9-9	NM_030975.2	112	6,206,6291	CC,CG,GG		0.0233,4.9024,1.6761	possibly-damaging	163/170	39412125	218,12788	2203	4300	6503	SO:0001583	missense	81870	exon1			CCAGCTGCTGCCA	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.488G>C	17.37:g.39412125G>C	ENSP00000377576:p.Cys163Ser	262	1	0.00381679		263	129	0.490494	NM_030975	B5MDD6|Q9BYQ1	Missense_Mutation	SNP	ENST00000394008.1	37	CCDS54127.1	28	0.01282051282051282	24	0.04878048780487805	4	0.011049723756906077	0	0.0	0	0.0	.	23.2	4.383020	0.82792	0.049024	2.33E-4	ENSG00000198083	ENST00000431129;ENST00000394008	T	0.02323	4.34	3.68	3.68	0.42216	.	.	.	.	.	T	0.01976	0.0062	M	0.81497	2.545	0.30835	N	0.736277	D	0.89917	1.0	D	0.72982	0.979	T	0.00388	-1.1771	9	0.46703	T	0.11	.	11.5975	0.50981	0.0:0.0:1.0:0.0	.	148	Q9BYP9	KRA99_HUMAN	S	169;163	ENSP00000377576:C163S	ENSP00000377576:C163S	C	+	2	0	KRTAP9-9	36665651	0.998000	0.40836	0.998000	0.56505	0.904000	0.53231	1.282000	0.33226	1.971000	0.57363	0.462000	0.41574	TGC	G|0.987;C|0.013	0.013	strong		0.557	KRTAP9-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257710.1	NM_030975		C	39412125	G	C	39412125	3	2	22	1	0	0	0	0	1	0	0	0	8586	1319	46	4	490	4	KRTAP9-9	17	39412125	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	414	39412125	41783085	3515	6416											
KRT33B	3884	hgsc.bcm.edu	37	chr17	39521517	39521517	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtaggactgcagctgctcCgagctggataccacctgctt	7	10	12	12	1	0	0	0	0	0	0	1	3	1	2	3	3	6	6	3	3	2	3	rs553149537	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39521517C>T	ENST00000251646.3	-	5	835	c.786G>A	c.(784-786)tcG>tcA	p.S262S		NM_002279.4	NP_002270.1	Q14525	KT33B_HUMAN	keratin 33B	262	Coil 2.|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)	p.S262S(1)		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)				GCAGCTGCTCCGAGCTGGATA	0.617													C|||	4	0.000798722	0.0008	0.0	5008	,	,		18679	0.0		0.0	False		,,,				2504	0.0031				p.S262S		Atlas-SNP	.											KRT33B,caecum,carcinoma,0,1	KRT33B	46	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G786A						scavenged	.						51	51	51					17																	39521517		2189	4298	6487	SO:0001819	synonymous_variant	3884	exon5			CTGCTCCGAGCTG	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.786G>A	17.37:g.39521517C>T		191	0	0		254	23	0.0905512	NM_002279	O76010	Silent	SNP	ENST00000251646.3	37	CCDS11389.1																																																																																			.	.	none		0.617	KRT33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257292.1	NM_002279		T	39521517	C	T	39521517	2	4	22	1	0	0	0	0	0	0	0	1	8479	639	23	1		1	KRT33B	17	39521517	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	109392	39521517	41673693	3516	6417											
KRT33B	3884	hgsc.bcm.edu	37	chr17	39521726	39521726	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctggtctcgttcaggaccTggttcaggtccacagcggga	6	10	13	12	2	3	0	2	0	1	0	6	2	5	2	3	5	1	2	3	5	0	2	rs61741663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39521726T>C	ENST00000251646.3	-	4	717	c.668A>G	c.(667-669)cAg>cGg	p.Q223R		NM_002279.4	NP_002270.1	Q14525	KT33B_HUMAN	keratin 33B	223	Coil 2.|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)				GTTCAGGACCTGGTTCAGGTC	0.577													T|||	85	0.0169728	0.0635	0.0014	5008	,	,		18746	0.0		0.0	False		,,,				2504	0.0				p.Q223R		Atlas-SNP	.											KRT33B,NS,carcinoma,0,1	KRT33B	46	1	0			c.A668G						PASS	.	T	ARG/GLN	260,4120		25,210,1955	77	73	75		668	1.7	0	17	dbSNP_129	75	0,8600		0,0,4300	no	missense	KRT33B	NM_002279.3	43	25,210,6255	CC,CT,TT		0.0,5.9361,2.0031	benign	223/405	39521726	260,12720	2190	4300	6490	SO:0001583	missense	3884	exon4			AGGACCTGGTTCA	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.668A>G	17.37:g.39521726T>C	ENSP00000251646:p.Gln223Arg	220	0	0		230	111	0.482609	NM_002279	O76010	Missense_Mutation	SNP	ENST00000251646.3	37	CCDS11389.1	39	0.017857142857142856	38	0.07723577235772358	1	0.0027624309392265192	0	0.0	0	0.0	t	0.004	-2.255496	0.00265	0.059361	0.0	ENSG00000131738	ENST00000251646	D	0.88818	-2.43	4.78	1.66	0.24008	Filament (1);	0.334269	0.24422	N	0.038665	T	0.08403	0.0209	N	0.01289	-0.905	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.42531	-0.9446	10	0.02654	T	1	.	7.0528	0.25083	0.0:0.524:0.0:0.476	rs61741663	223	Q14525	KT33B_HUMAN	R	223	ENSP00000251646:Q223R	ENSP00000251646:Q223R	Q	-	2	0	KRT33B	36775252	0.042000	0.20092	0.037000	0.18230	0.025000	0.11179	0.380000	0.20602	0.300000	0.22699	-0.911000	0.02809	CAG	T|0.976;C|0.024	0.024	strong		0.577	KRT33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257292.1	NM_002279		C	39521726	T	C	39521726	3	2	22	1	0	0	0	0	1	0	0	0	8479	1580	55	3	562	3	KRT33B	17	39521726	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	209	39521726	41673484	3517	6418											
KRT33B	3884	hgsc.bcm.edu	37	chr17	39521752	39521752	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtccacagcgggagcagcGtccacctccacgttgaggcg	8	5	14	14	4	0	1	0	1	0	0	3	2	3	2	4	3	3	2	4	3	0	1	rs61741664	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39521752G>A	ENST00000251646.3	-	4	691	c.642C>T	c.(640-642)gaC>gaT	p.D214D		NM_002279.4	NP_002270.1	Q14525	KT33B_HUMAN	keratin 33B	214	Linker 12.|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)				CGGGAGCAGCGTCCACCTCCA	0.542													G|||	72	0.014377	0.0537	0.0014	5008	,	,		19114	0.0		0.0	False		,,,				2504	0.0				p.D214D		Atlas-SNP	.											.	KRT33B	46	.	0			c.C642T						PASS	.	G		204,4178		19,166,2006	66	64	64		642	-4.8	0.7	17	dbSNP_129	64	1,8599		0,1,4299	no	coding-synonymous	KRT33B	NM_002279.3		19,167,6305	AA,AG,GG		0.0116,4.6554,1.5791		214/405	39521752	205,12777	2191	4300	6491	SO:0001819	synonymous_variant	3884	exon4			AGCAGCGTCCACC	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.642C>T	17.37:g.39521752G>A		168	0	0		200	100	0.5	NM_002279	O76010	Silent	SNP	ENST00000251646.3	37	CCDS11389.1																																																																																			G|0.981;A|0.019	0.019	strong		0.542	KRT33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257292.1	NM_002279		A	39521752	G	A	39521752	2	1	22	1	0	0	0	0	0	0	0	1	8479	1136	40	1		1	KRT33B	17	39521752	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	26	39521752	41673458	3518	6419											
KRT31	3881	hgsc.bcm.edu	37	chr17	39551533	39551533	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgcagctcgatctccagggcGttgactgtgcgtctcagctc	5	11	12	13	3	2	1	1	1	2	0	6	2	2	1	1	1	4	4	1	1	0	1	rs6503626	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39551533G>A	ENST00000251645.2	-	5	892	c.840C>T	c.(838-840)aaC>aaT	p.N280N		NM_002277.2	NP_002268.2	Q15323	K1H1_HUMAN	keratin 31	280	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)				TCTCCAGGGCGTTGACTGTGC	0.597													G|||	67	0.0133786	0.0469	0.0	5008	,	,		20660	0.0		0.0	False		,,,				2504	0.0051				p.N280N		Atlas-SNP	.											.	KRT31	158	.	0			c.C840T						PASS	.	G		123,4283	80.9+/-119.3	6,111,2086	98	90	93		840	-4.3	0.9	17	dbSNP_116	93	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	KRT31	NM_002277.2		6,113,6384	AA,AG,GG		0.0233,2.7916,0.9611		280/417	39551533	125,12881	2203	4300	6503	SO:0001819	synonymous_variant	3881	exon5			CAGGGCGTTGACT	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.840C>T	17.37:g.39551533G>A		236	0	0		210	101	0.480952	NM_002277	Q9UE12	Silent	SNP	ENST00000251645.2	37	CCDS11391.1																																																																																			G|0.988;A|0.012	0.012	strong		0.597	KRT31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257286.1	NM_002277		A	39551533	G	A	39551533	2	1	22	1	0	0	0	0	0	0	0	1	8476	1136	40	1		1	KRT31	17	39551533	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	29781	39551533	41643677	3519	6420											
KRT31	3881	hgsc.bcm.edu	37	chr17	39553676	39553676	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agttgcagttgctcacattgGcggggatgttgcaggccccg	6	10	15	10	2	1	0	1	0	0	0	1	1	1	1	2	4	3	6	2	4	0	4	rs6503628	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39553676G>C	ENST00000251645.2	-	1	168	c.116C>G	c.(115-117)gCc>gGc	p.A39G		NM_002277.2	NP_002268.2	Q15323	K1H1_HUMAN	keratin 31	39	Head.		A -> G (in dbSNP:rs6503628).		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)				GCTCACATTGGCGGGGATGTT	0.657													G|||	15	0.00299521	0.0113	0.0	5008	,	,		15172	0.0		0.0	False		,,,				2504	0.0				p.A39G		Atlas-SNP	.											.	KRT31	158	.	0			c.C116G						PASS	.	G	GLY/ALA	45,4361	43.1+/-76.7	0,45,2158	59	61	60		116	4.9	1	17	dbSNP_116	60	0,8600		0,0,4300	no	missense	KRT31	NM_002277.2	60	0,45,6458	CC,CG,GG		0.0,1.0213,0.346	benign	39/417	39553676	45,12961	2203	4300	6503	SO:0001583	missense	3881	exon1			ACATTGGCGGGGA	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.116C>G	17.37:g.39553676G>C	ENSP00000251645:p.Ala39Gly	215	0	0		205	90	0.439024	NM_002277	Q9UE12	Missense_Mutation	SNP	ENST00000251645.2	37	CCDS11391.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	g	6.953	0.545683	0.13312	0.010213	0.0	ENSG00000094796	ENST00000251645	D	0.82167	-1.58	5.87	4.9	0.64082	.	0.000000	0.64402	D	0.000004	T	0.61476	0.2350	L	0.28400	0.85	0.32486	N	0.54088	B	0.12013	0.005	B	0.10450	0.005	T	0.60209	-0.7308	10	0.06365	T	0.9	.	8.4419	0.32820	0.2275:0.0:0.7725:0.0	rs6503628;rs6503628	39	Q15323	K1H1_HUMAN	G	39	ENSP00000251645:A39G	ENSP00000251645:A39G	A	-	2	0	KRT31	36807202	0.992000	0.36948	1.000000	0.80357	0.902000	0.53008	2.205000	0.42770	1.500000	0.48636	0.650000	0.86243	GCC	G|0.997;C|0.003	0.003	strong		0.657	KRT31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257286.1	NM_002277		C	39553676	G	C	39553676	3	2	22	1	0	0	0	0	1	0	0	0	8476	1203	42	4	1162	4	KRT31	17	39553676	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2143	39553676	41641534	3520	6421											
KRT32	3882	hgsc.bcm.edu	37	chr17	39623496	39623496	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcaggccggcagttcacgcCgctggaacagaccgaggcag	9	4	14	14	4	2	1	2	0	0	1	2	3	2	2	3	4	1	4	3	4	1	1	rs115680799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39623496C>T	ENST00000225899.3	-	1	185	c.82G>A	c.(82-84)Ggc>Agc	p.G28S	RNU2-32P_ENST00000411193.1_RNA	NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	28	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)				CAGTTCACGCCGCTGGAACAG	0.637													C|||	89	0.0177716	0.0658	0.0029	5008	,	,		17468	0.0		0.0	False		,,,				2504	0.0				p.G28S		Atlas-SNP	.											.	KRT32	57	.	0			c.G82A						PASS	.	C	SER/GLY	211,4193		4,203,1995	31	34	33		82	-0.2	0	17	dbSNP_132	33	6,8594		0,6,4294	yes	missense	KRT32	NM_002278.3	56	4,209,6289	TT,TC,CC		0.0698,4.7911,1.6687	benign	28/449	39623496	217,12787	2202	4300	6502	SO:0001583	missense	3882	exon1			TCACGCCGCTGGA	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.82G>A	17.37:g.39623496C>T	ENSP00000225899:p.Gly28Ser	80	0	0		95	47	0.494737	NM_002278		Missense_Mutation	SNP	ENST00000225899.3	37	CCDS11393.1	31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	C	0.012	-1.657918	0.00779	0.047911	6.98E-4	ENSG00000108759	ENST00000225899	D	0.86164	-2.08	5.16	-0.18	0.13295	.	0.662243	0.13290	N	0.399058	T	0.14917	0.0360	N	0.01874	-0.695	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.35599	-0.9782	10	0.10377	T	0.69	.	2.9903	0.05981	0.3289:0.3218:0.0:0.3493	.	28	Q14532	K1H2_HUMAN	S	28	ENSP00000225899:G28S	ENSP00000225899:G28S	G	-	1	0	KRT32	36877022	0.000000	0.05858	0.020000	0.16555	0.005000	0.04900	-0.360000	0.07622	0.060000	0.16281	-0.339000	0.08088	GGC	C|0.981;T|0.019	0.019	strong		0.637	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278		T	39623496	C	T	39623496	3	4	22	1	0	0	0	0	1	0	0	0	8477	652	23	1	1292	1	KRT32	17	39623496	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	69820	39623496	41571714	3521	6422											
KRT14	3861	hgsc.bcm.edu	37	chr17	39741280	39741280	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtcaatctgcagaaggacAttggcattgtccactgtggc	9	12	11	9	0	2	1	1	0	1	1	3	2	3	2	1	3	1	2	1	3	2	3	rs35849957	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39741280A>G	ENST00000167586.6	-	2	641	c.555T>C	c.(553-555)aaT>aaC	p.N185N		NM_000526.4	NP_000517	P02533	K1C14_HUMAN	keratin 14	185	Coil 1B.|Rod.				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)				GCAGAAGGACATTGGCATTGT	0.507													.|||	299	0.0597045	0.2118	0.0216	5008	,	,		20159	0.0		0.004	False		,,,				2504	0.0				p.N185N		Atlas-SNP	.											.	KRT14	65	.	0			c.T555C						PASS	.	G		794,3612	751.1+/-412.2	71,652,1480	101	82	89		555	-7	0	17	dbSNP_126	89	6,8594	818.5+/-406.9	0,6,4294	no	coding-synonymous	KRT14	NM_000526.4		71,658,5774	GG,GA,AA		0.0698,18.0209,6.151		185/473	39741280	800,12206	2203	4300	6503	SO:0001819	synonymous_variant	3861	exon2			AAGGACATTGGCA	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.555T>C	17.37:g.39741280A>G		87	0	0		102	55	0.539216	NM_000526	Q14715|Q53XY3|Q9BUE3|Q9UBN2|Q9UBN3|Q9UCY4	Silent	SNP	ENST00000167586.6	37	CCDS11400.1																																																																																			A|0.944;G|0.056	0.056	strong		0.507	KRT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257289.1	NM_000526		G	39741280	A	G	39741280	2	3	22	1	0	0	0	0	0	0	0	1	8460	214	8	3		3	KRT14	17	39741280	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	117784	39741280	41453930	3522	6423											
KRT16	3868	hgsc.bcm.edu	37	chr17	39767947	39767947	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcaatctgcaaaatgggctgCgcattctcaatggtggccgc	9	10	11	11	2	3	0	2	0	2	0	4	0	3	0	1	3	2	3	1	3	4	1	rs144914208	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39767947C>T	ENST00000301653.4	-	2	622	c.558G>A	c.(556-558)gcG>gcA	p.A186A		NM_005557.3	NP_005548.2	P08779	K1C16_HUMAN	keratin 16	186	Coil 1B.|Rod.				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)				AAATGGGCTGCGCATTCTCAA	0.577													c|||	105	0.0209665	0.0749	0.0072	5008	,	,		20382	0.0		0.001	False		,,,				2504	0.0				p.A186A		Atlas-SNP	.											KRT16,colon,carcinoma,-1,1	KRT16	45	1	0			c.G558A						PASS	.	T		282,4124	146.5+/-181.1	7,268,1928	29	27	28		558	-7.1	0.3	17	dbSNP_134	28	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous	KRT16	NM_005557.3		7,269,6224	TT,TC,CC		0.0116,6.4004,2.1769		186/474	39767947	283,12717	2203	4297	6500	SO:0001819	synonymous_variant	3868	exon2			GGGCTGCGCATTC	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.558G>A	17.37:g.39767947C>T		390	0	0		379	169	0.44591	NM_005557	A8K488|P30654|Q16402|Q9UBG8	Silent	SNP	ENST00000301653.4	37	CCDS11401.1																																																																																			C|0.978;T|0.022	0.022	strong		0.577	KRT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257408.1	NM_005557		T	39767947	C	T	39767947	2	4	22	1	0	0	0	0	0	0	0	1	8462	755	27	1		1	KRT16	17	39767947	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	26667	39767947	41427263	3523	6424											
KRT16	3868	hgsc.bcm.edu	37	chr17	39768756	39768756	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catagccgccccccagcccgCaggctcccccagaggagaag	9	2	11	19	2	0	2	0	0	0	2	1	3	1	2	7	2	2	2	7	2	2	1	rs367990963	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39768756C>T	ENST00000301653.4	-	1	249	c.185G>A	c.(184-186)tGc>tAc	p.C62Y		NM_005557.3	NP_005548.2	P08779	K1C16_HUMAN	keratin 16	62	Head.				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)				CCCCAGCCCGCAGGCTCCCCC	0.687													c|||	4	0.000798722	0.003	0.0	5008	,	,		14972	0.0		0.0	False		,,,				2504	0.0				p.C62Y		Atlas-SNP	.											.	KRT16	45	.	0			c.G185A						PASS	.	C	TYR/CYS	4,4352		0,4,2174	28	35	32		185	3.3	1	17		32	0,8536		0,0,4268	no	missense	KRT16	NM_005557.3	194	0,4,6442	TT,TC,CC		0.0,0.0918,0.031	benign	62/474	39768756	4,12888	2178	4268	6446	SO:0001583	missense	3868	exon1			AGCCCGCAGGCTC	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.185G>A	17.37:g.39768756C>T	ENSP00000301653:p.Cys62Tyr	72	0	0		77	37	0.480519	NM_005557	A8K488|P30654|Q16402|Q9UBG8	Missense_Mutation	SNP	ENST00000301653.4	37	CCDS11401.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.484513	0.44147	9.18E-4	0.0	ENSG00000186832	ENST00000301653	T	0.75260	-0.92	4.33	3.33	0.38152	.	0.000000	0.53938	D	0.000045	T	0.55924	0.1951	N	0.19112	0.55	0.30188	N	0.799798	B	0.31256	0.316	B	0.28553	0.091	T	0.55717	-0.8097	10	0.35671	T	0.21	.	9.6049	0.39628	0.1605:0.6847:0.1548:0.0	.	62	P08779	K1C16_HUMAN	Y	62	ENSP00000301653:C62Y	ENSP00000301653:C62Y	C	-	2	0	KRT16	37022282	0.046000	0.20272	0.997000	0.53966	0.971000	0.66376	0.141000	0.16076	1.127000	0.42034	0.462000	0.41574	TGC	.	.	weak		0.687	KRT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257408.1	NM_005557		T	39768756	C	T	39768756	3	4	22	1	0	0	0	0	1	0	0	0	8462	710	25	2	1268	2	KRT16	17	39768756	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	809	39768756	41426454	3524	6425											
PTRF	284119	hgsc.bcm.edu	37	chr17	40556951	40556951	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagaccgcggtcttggagcgCgcgtacaccacgtggtcggg	6	7	16	12	7	1	1	0	0	1	1	2	2	1	2	2	4	2	1	2	4	2	3	rs112332573	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:40556951C>T	ENST00000357037.5	-	2	1346	c.927G>A	c.(925-927)gcG>gcA	p.A309A		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)		TCTTGGAGCGCGCGTACACCA	0.647													C|||	92	0.0183706	0.0696	0.0	5008	,	,		12868	0.0		0.0	False		,,,				2504	0.0				p.A309A		Atlas-SNP	.											.	PTRF	48	.	0			c.G927A						PASS	.	C		259,4147	148.4+/-182.8	10,239,1954	104	89	94		927	0.5	1	17	dbSNP_132	94	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	PTRF	NM_012232.5		10,244,6249	TT,TC,CC		0.0581,5.8783,2.0298		309/391	40556951	264,12742	2203	4300	6503	SO:0001819	synonymous_variant	284119	exon2			GGAGCGCGCGTAC	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.927G>A	17.37:g.40556951C>T		135	0	0		172	92	0.534884	NM_012232		Silent	SNP	ENST00000357037.5	37	CCDS11425.1																																																																																			C|0.981;T|0.019	0.019	strong		0.647	PTRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449938.1	NM_012232		T	40556951	C	T	40556951	2	4	22	1	0	0	0	0	0	0	0	1	12830	755	27	1		1	PTRF	17	40556951	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	788195	40556951	40638259	3525	6426											
CNTNAP1	8506	hgsc.bcm.edu	37	chr17	40841001	40841001	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aactggtcaacctgactctgGtggagggccggcggcttgga	7	8	16	10	2	2	1	1	1	1	0	2	3	2	3	2	7	2	1	2	7	2	1	rs35437096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:40841001G>C	ENST00000264638.4	+	10	1781	c.1564G>C	c.(1564-1566)Gtg>Ctg	p.V522L	CTD-3193K9.3_ENST00000592440.1_RNA	NM_003632.2	NP_003623.1	P78357	CNTP1_HUMAN	contactin associated protein 1	522	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.		V -> L (in dbSNP:rs35437096).		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)		CCTGACTCTGGTGGAGGGCCG	0.562													G|||	202	0.0403355	0.143	0.0173	5008	,	,		17992	0.0		0.001	False		,,,				2504	0.0				p.V522L		Atlas-SNP	.											CNTNAP1,uveal_tract,malignant_melanoma,-1,1	CNTNAP1	116	1	0			c.G1564C						scavenged	.	G	LEU/VAL	536,3870	243.1+/-252.9	38,460,1705	138	126	130		1564	3.7	1	17	dbSNP_126	130	4,8596	3.7+/-12.6	0,4,4296	yes	missense	CNTNAP1	NM_003632.2	32	38,464,6001	CC,CG,GG		0.0465,12.1652,4.1519	benign	522/1385	40841001	540,12466	2203	4300	6503	SO:0001583	missense	8506	exon10			ACTCTGGTGGAGG	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.1564G>C	17.37:g.40841001G>C	ENSP00000264638:p.Val522Leu	118	1	0.00847458		109	53	0.486239	NM_003632		Missense_Mutation	SNP	ENST00000264638.4	37	CCDS11436.1	58	0.026556776556776556	48	0.0975609756097561	9	0.024861878453038673	0	0.0	1	0.0013192612137203166	G	13.62	2.290608	0.40494	0.121652	4.65E-4	ENSG00000108797	ENST00000264638	T	0.76186	-1.0	4.73	3.72	0.42706	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.181748	0.37715	N	0.001970	T	0.01695	0.0054	L	0.45352	1.415	0.33613	D	0.60377	B	0.06786	0.001	B	0.06405	0.002	T	0.37478	-0.9704	10	0.39692	T	0.17	.	9.0628	0.36444	0.083:0.2588:0.6582:0.0	rs35437096	522	P78357	CNTP1_HUMAN	L	522	ENSP00000264638:V522L	ENSP00000264638:V522L	V	+	1	0	CNTNAP1	38094527	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	2.118000	0.41949	2.449000	0.82847	0.561000	0.74099	GTG	G|0.961;C|0.039	0.039	strong		0.562	CNTNAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452342.1	NM_003632		C	40841001	G	C	40841001	3	2	22	1	0	0	0	0	1	0	0	0	3648	1261	44	4	1602	4	CNTNAP1	17	40841001	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	284050	40841001	40354209	3526	6427											
WNK4	65266	hgsc.bcm.edu	37	chr17	40946913	40946913	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctggaacccccatttcccCaggtcccatcttccccatca	7	9	4	21	0	2	0	1	0	1	0	5	1	5	1	8	2	1	0	8	2	1	2	rs56226218	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:40946913C>T	ENST00000246914.5	+	14	2495	c.2474C>T	c.(2473-2475)cCa>cTa	p.P825L		NM_032387.4	NP_115763.2	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	825					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)		CCCATTTCCCCAGGTCCCATC	0.577													C|||	140	0.0279553	0.1021	0.0072	5008	,	,		15756	0.0		0.0	False		,,,				2504	0.0				p.P825L	Esophageal Squamous(6;201 374 4964 23855 42828)	Atlas-SNP	.											.	WNK4	182	.	0			c.C2474T						PASS	.	C	LEU/PRO	391,4015	196.4+/-220.7	17,357,1829	135	123	127		2474	4.6	0.9	17	dbSNP_129	127	1,8599	1.2+/-3.3	0,1,4299	yes	missense	WNK4	NM_032387.4	98	17,358,6128	TT,TC,CC		0.0116,8.8743,3.014	benign	825/1244	40946913	392,12614	2203	4300	6503	SO:0001583	missense	65266	exon14			TTTCCCCAGGTCC	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.2474C>T	17.37:g.40946913C>T	ENSP00000246914:p.Pro825Leu	235	1	0.00425532		279	145	0.519713	NM_032387	B0LPI0|Q8N8X3|Q8N8Z2|Q96DT8|Q9BYS5	Missense_Mutation	SNP	ENST00000246914.5	37	CCDS11439.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	C	12.50	1.956295	0.34565	0.088743	1.16E-4	ENSG00000126562	ENST00000246914;ENST00000316085	T	0.73363	-0.74	5.58	4.59	0.56863	.	0.143817	0.32301	N	0.006288	T	0.04588	0.0125	L	0.29908	0.895	0.47659	D	0.999481	B;B;B	0.32653	0.379;0.261;0.006	B;B;B	0.28553	0.091;0.042;0.012	T	0.14587	-1.0467	10	0.51188	T	0.08	-4.1586	8.3488	0.32290	0.1564:0.7652:0.0:0.0784	rs56226218;rs61755625	825;825;825	Q96J92-3;B0LPI0;Q96J92	.;.;WNK4_HUMAN	L	825;597	ENSP00000246914:P825L	ENSP00000246914:P825L	P	+	2	0	WNK4	38200439	0.989000	0.36119	0.913000	0.36048	0.211000	0.24417	3.653000	0.54446	1.444000	0.47605	0.591000	0.81541	CCA	C|0.974;T|0.026	0.026	strong		0.577	WNK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452389.1			T	40946913	C	T	40946913	3	4	22	1	0	0	0	0	1	0	0	0	17395	594	21	2	2528	2	WNK4	17	40946913	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	105912	40946913	40248297	3527	6428											
BRCA1	672	hgsc.bcm.edu	37	chr17	41245643	41245643	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcaatttgcaattcagtacaAttaggtgggcttagatttct	11	16	8	6	0	3	1	2	0	1	1	3	1	3	1	0	2	2	3	0	2	6	6	rs369373293		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:41245643A>G	ENST00000357654.3	-	10	2023	c.1905T>C	c.(1903-1905)aaT>aaC	p.N635N	BRCA1_ENST00000309486.4_Silent_p.N339N|BRCA1_ENST00000471181.2_Silent_p.N635N|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000493795.1_Silent_p.N588N|BRCA1_ENST00000354071.3_Silent_p.N635N|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000346315.3_Silent_p.N635N|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000591534.1_Intron	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	635					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)		ATTCAGTACAATTAGGTGGGC	0.388			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.N635N		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.T1905C						PASS	.	A	,,,,	2,4404	4.2+/-10.8	0,2,2201	94	92	93		1905,1764,,,1905	1.6	0	17		93	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,intron,intron,coding-synonymous	BRCA1	NM_007294.3,NM_007297.3,NM_007298.3,NM_007299.3,NM_007300.3	,,,,	0,2,6501	GG,GA,AA		0.0,0.0454,0.0154	,,,,	635/1864,588/1817,,,635/1885	41245643	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	672	exon10	Familial Cancer Database		AGTACAATTAGGT	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.1905T>C	17.37:g.41245643A>G		122	0	0		136	61	0.448529	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Silent	SNP	ENST00000357654.3	37	CCDS11453.1																																																																																			.	.	weak		0.388	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		G	41245643	A	G	41245643	2	3	22	1	0	0	0	0	0	0	0	1	1500	98	4	3		3	BRCA1	17	41245643	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	298730	41245643	39949567	3528	6429											
ARL4D	379	hgsc.bcm.edu	37	chr17	41477670	41477670	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tatgagatgatcctcaagagGaagaaggcagctcggggtgg	12	7	16	6	1	1	4	1	2	0	3	3	6	2	5	1	5	1	2	1	5	4	1	rs61749921	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:41477670G>A	ENST00000320033.4	+	2	777	c.570G>A	c.(568-570)agG>agA	p.R190R		NM_001661.3	NP_001652.2	P49703	ARL4D_HUMAN	ADP-ribosylation factor-like 4D	190					GTP catabolic process (GO:0006184)|protein secretion (GO:0009306)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	8		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.155)		TCCTCAAGAGGAAGAAGGCAG	0.622													G|||	83	0.0165735	0.0613	0.0029	5008	,	,		16722	0.0		0.0	False		,,,				2504	0.0				p.R190R		Atlas-SNP	.											.	ARL4D	16	.	0			c.G570A						PASS	.	G		190,4178		2,186,1996	19	19	19		570	-0.6	1	17	dbSNP_129	19	1,8523		0,1,4261	no	coding-synonymous	ARL4D	NM_001661.3		2,187,6257	AA,AG,GG		0.0117,4.3498,1.4815		190/202	41477670	191,12701	2184	4262	6446	SO:0001819	synonymous_variant	379	exon2			CAAGAGGAAGAAG	AB060692	CCDS11463.1	17q21.31	2014-05-09	2005-11-03	2005-11-03	ENSG00000175906	ENSG00000175906		"ADP-ribosylation factors-like", "ADP-ribosylation factors"	656	protein-coding gene	gene with protein product		600732	"ADP-ribosylation factor 4-like"	ARF4L		7590735	Standard	NM_001661		Approved		uc002idt.3	P49703		ENST00000320033.4:c.570G>A	17.37:g.41477670G>A		67	0	0		49	28	0.571429	NM_001661	B2RC59|D3DX43	Silent	SNP	ENST00000320033.4	37	CCDS11463.1																																																																																			G|0.979;A|0.021	0.021	strong		0.622	ARL4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453481.2	NM_001661		A	41477670	G	A	41477670	2	1	22	1	0	0	0	0	0	0	0	1	938	1165	41	2		2	ARL4D	17	41477670	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	232027	41477670	39717540	3529	6430											
DHX8	1659	hgsc.bcm.edu	37	chr17	41570819	41570819	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tggctctccctcaggaagcgGtgggaaggcctggtgcacat	7	8	15	11	1	2	0	1	0	1	0	3	2	2	2	2	6	2	2	2	6	2	0	rs146528228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:41570819G>A	ENST00000262415.3	+	7	942	c.870G>A	c.(868-870)cgG>cgA	p.R290R	DHX8_ENST00000540306.1_Silent_p.R290R	NM_004941.1	NP_004932.1	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	290	S1 motif. {ECO:0000255|PROSITE- ProRule:PRU00180}.				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)		TCAGGAAGCGGTGGGAAGGCC	0.512													G|||	5	0.000998403	0.0038	0.0	5008	,	,		19930	0.0		0.0	False		,,,				2504	0.0				p.R290R	NSCLC(56;1548 1661 49258 49987)	Atlas-SNP	.											.	DHX8	98	.	0			c.G870A						PASS	.	G		31,4375	36.8+/-68.6	0,31,2172	96	92	93		870	0.8	1	17	dbSNP_134	93	0,8600		0,0,4300	no	coding-synonymous	DHX8	NM_004941.1		0,31,6472	AA,AG,GG		0.0,0.7036,0.2384		290/1221	41570819	31,12975	2203	4300	6503	SO:0001819	synonymous_variant	1659	exon7			GAAGCGGTGGGAA	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.870G>A	17.37:g.41570819G>A		109	0	0		127	60	0.472441	NM_004941		Silent	SNP	ENST00000262415.3	37	CCDS11464.1																																																																																			G|0.998;A|0.002	0.002	strong		0.512	DHX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453485.1			A	41570819	G	A	41570819	2	1	22	1	0	0	0	0	0	0	0	1	4517	1248	44	2		2	DHX8	17	41570819	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	93149	41570819	39624391	3530	6431											
C17orf53	78995	hgsc.bcm.edu	37	chr17	42225250	42225250	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcttgtctgctgtggaggatGcagagaaccggtttactggc	7	12	14	8	1	2	1	0	0	2	1	2	4	2	3	1	4	4	3	1	4	2	3	rs35879996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:42225250G>A	ENST00000319977.4	+	3	316	c.79G>A	c.(79-81)Gca>Aca	p.A27T	C17orf53_ENST00000245382.6_Missense_Mutation_p.A27T|C17orf53_ENST00000585683.1_Missense_Mutation_p.A27T	NM_001171251.1|NM_024032.3	NP_001164722.1|NP_076937.2	Q8N3J3	CQ053_HUMAN	chromosome 17 open reading frame 53	27										NS(1)|breast(3)|cervix(1)|kidney(3)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	22		Breast(137;0.0364)|Prostate(33;0.0376)		BRCA - Breast invasive adenocarcinoma(366;0.114)		TGTGGAGGATGCAGAGAACCG	0.532													G|||	94	0.01877	0.0681	0.0058	5008	,	,		20182	0.0		0.0	False		,,,				2504	0.0				p.A27T		Atlas-SNP	.											.	C17orf53	59	.	0			c.G79A						PASS	.	G	THR/ALA,THR/ALA	223,4183	127.4+/-164.3	2,219,1982	57	58	58		79,79	2	1	17	dbSNP_126	58	5,8595	3.7+/-12.6	0,5,4295	yes	missense,missense	C17orf53	NM_001171251.1,NM_024032.3	58,58	2,224,6277	AA,AG,GG		0.0581,5.0613,1.753	probably-damaging,probably-damaging	27/647,27/648	42225250	228,12778	2203	4300	6503	SO:0001583	missense	78995	exon3			GAGGATGCAGAGA	AK021656	CCDS11477.1, CCDS59293.1	17q21.31	2012-10-11			ENSG00000125319	ENSG00000125319			28460	protein-coding gene	gene with protein product							Standard	NM_001171251		Approved	MGC3130	uc002ifi.2	Q8N3J3	OTTHUMG00000181808	ENST00000319977.4:c.79G>A	17.37:g.42225250G>A	ENSP00000313500:p.Ala27Thr	68	0	0		75	37	0.493333	NM_001171251	A8K7A9|Q9BWM9|Q9HAI1	Missense_Mutation	SNP	ENST00000319977.4	37	CCDS11477.1	34	0.015567765567765568	31	0.06300813008130081	3	0.008287292817679558	0	0.0	0	0.0	G	18.70	3.679486	0.68042	0.050613	5.81E-4	ENSG00000125319	ENST00000319977;ENST00000245382;ENST00000253405	T;T	0.52057	0.68;0.68	5.28	2.05	0.26809	.	0.355277	0.25487	N	0.030330	T	0.07098	0.0180	L	0.46157	1.445	0.27350	N	0.956269	P;B;P	0.51537	0.946;0.15;0.946	P;B;P	0.48677	0.586;0.044;0.586	T	0.01834	-1.1264	10	0.40728	T	0.16	-5.352	7.9308	0.29901	0.3513:0.0:0.6487:0.0	rs35879996	27;27;27	A8K7A9;Q8N3J3-3;Q8N3J3	.;.;CQ053_HUMAN	T	27	ENSP00000313500:A27T;ENSP00000245382:A27T	ENSP00000245382:A27T	A	+	1	0	C17orf53	39580776	0.992000	0.36948	1.000000	0.80357	0.960000	0.62799	2.005000	0.40864	0.797000	0.33971	0.561000	0.74099	GCA	G|0.983;A|0.017	0.017	strong		0.532	C17orf53-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457697.1	NM_024032		A	42225250	G	A	42225250	3	1	22	1	0	0	0	0	1	0	0	0	1864	1319	46	2	89	2	C17orf53	17	42225250	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	654431	42225250	38969960	3531	6432											
ASB16	92591	hgsc.bcm.edu	37	chr17	42248205	42248205	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tcctccatgctgcgctctctCcgcctgcagcaggagtggct	4	10	11	16	2	1	0	0	0	1	0	5	1	4	1	4	2	4	5	4	2	0	0	rs56265171	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:42248205C>T	ENST00000293414.1	+	1	132	c.48C>T	c.(46-48)ctC>ctT	p.L16L		NM_080863.4	NP_543139.4	Q96NS5	ASB16_HUMAN	ankyrin repeat and SOCS box containing 16	16					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)		TGCGCTCTCTCCGCCTGCAGC	0.697													C|||	168	0.0335463	0.1203	0.0115	5008	,	,		15859	0.0		0.001	False		,,,				2504	0.0				p.L16L		Atlas-SNP	.											.	ASB16	34	.	0			c.C48T						PASS	.	C		417,3989	196.4+/-220.7	17,383,1803	36	34	35		48	1.8	1	17	dbSNP_129	35	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous	ASB16	NM_080863.4		17,388,6098	TT,TC,CC		0.0581,9.4644,3.2447		16/454	42248205	422,12584	2203	4300	6503	SO:0001819	synonymous_variant	92591	exon1			CTCTCTCCGCCTG	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.48C>T	17.37:g.42248205C>T		180	0	0		190	103	0.542105	NM_080863	B2RBC0|Q8WXK0	Silent	SNP	ENST00000293414.1	37	CCDS11478.1																																																																																			C|0.967;T|0.033	0.033	strong		0.697	ASB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457703.1			T	42248205	C	T	42248205	2	4	22	1	0	0	0	0	0	0	0	1	1020	842	30	2		2	ASB16	17	42248205	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	22955	42248205	38947005	3532	6433											
ASB16	92591	hgsc.bcm.edu	37	chr17	42254165	42254165	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggcagcaggcgagagccAggagacgcccctgcacgtgg	8	3	16	14	3	0	2	0	0	0	2	0	4	0	2	4	4	3	3	4	4	0	0	rs146134954	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:42254165A>G	ENST00000293414.1	+	3	713	c.629A>G	c.(628-630)cAg>cGg	p.Q210R	ASB16-AS1_ENST00000588785.1_RNA|ASB16-AS1_ENST00000592897.1_RNA|ASB16-AS1_ENST00000591166.1_RNA|ASB16-AS1_ENST00000585457.1_RNA	NM_080863.4	NP_543139.4	Q96NS5	ASB16_HUMAN	ankyrin repeat and SOCS box containing 16	210					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)		GGCGAGAGCCAGGAGACGCCC	0.672													A|||	65	0.0129792	0.0477	0.0029	5008	,	,		13770	0.0		0.0	False		,,,				2504	0.0				p.Q210R		Atlas-SNP	.											.	ASB16	34	.	0			c.A629G						PASS	.	A	ARG/GLN,	154,4252	103.4+/-141.9	4,146,2053	52	51	52		629,456	4.7	0.1	17	dbSNP_134	52	2,8598	2.2+/-6.3	0,2,4298	yes	missense,coding-synonymous	ASB16,C17orf65	NM_080863.4,NM_178542.3	43,	4,148,6351	GG,GA,AA		0.0233,3.4952,1.1994	benign,	210/454,152/194	42254165	156,12850	2203	4300	6503	SO:0001583	missense	92591	exon3			AGAGCCAGGAGAC	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.629A>G	17.37:g.42254165A>G	ENSP00000293414:p.Gln210Arg	67	0	0		60	19	0.316667	NM_080863	B2RBC0|Q8WXK0	Missense_Mutation	SNP	ENST00000293414.1	37	CCDS11478.1	29	0.013278388278388278	28	0.056910569105691054	1	0.0027624309392265192	0	0.0	0	0.0	A	2.058	-0.416098	0.04766	0.034952	2.33E-4	ENSG00000161664	ENST00000293414	T	0.63913	-0.07	4.73	4.73	0.59995	Ankyrin repeat-containing domain (3);	0.305652	0.34067	N	0.004299	T	0.05456	0.0144	N	0.16602	0.42	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.04650	-1.0936	10	0.10902	T	0.67	-8.7467	5.8244	0.18546	0.8141:0.0:0.1859:0.0	.	210	Q96NS5	ASB16_HUMAN	R	210	ENSP00000293414:Q210R	ENSP00000293414:Q210R	Q	+	2	0	ASB16	39609691	0.009000	0.17119	0.120000	0.21714	0.087000	0.18053	1.072000	0.30678	1.985000	0.57927	0.374000	0.22700	CAG	A|0.987;G|0.013	0.013	strong		0.672	ASB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457703.1			G	42254165	A	G	42254165	3	3	22	1	0	0	0	0	1	0	0	0	1020	188	7	3	639	3	ASB16	17	42254165	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	5960	42254165	38941045	3533	6434											
UBTF	7343	hgsc.bcm.edu	37	chr17	42284951	42284951	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatcctcatcctcttcatcAtcctcctcggactccttgga	6	14	4	17	1	5	0	4	0	1	0	11	2	10	2	5	2	0	0	5	2	0	2	rs113823176	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:42284951A>G	ENST00000302904.4	-	20	2532	c.2040T>C	c.(2038-2040)gaT>gaC	p.D680D	UBTF_ENST00000526094.1_Silent_p.D643D|UBTF_ENST00000527034.1_Missense_Mutation_p.M642T|UBTF_ENST00000533177.1_Silent_p.D643D|CTB-175E5.7_ENST00000586560.1_RNA|UBTF_ENST00000393606.3_Silent_p.D643D|UBTF_ENST00000529383.1_Silent_p.D680D|UBTF_ENST00000436088.1_Silent_p.D680D|UBTF_ENST00000343638.5_Silent_p.D643D			P17480	UBF1_HUMAN	upstream binding transcription factor, RNA polymerase I	680	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)		cctcttcatcatcctcctcGG	0.587													A|||	59	0.0117812	0.0431	0.0029	5008	,	,		17778	0.0		0.0	False		,,,				2504	0.0				p.D680D		Atlas-SNP	.											.	UBTF	65	.	0			c.T2040C						PASS	.	A	,,	105,4301	82.4+/-120.9	1,103,2099	156	104	122		1929,1929,2040	-5.1	0.5	17	dbSNP_132	122	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	UBTF	NM_001076683.1,NM_001076684.2,NM_014233.3	,,	1,103,6399	GG,GA,AA		0.0,2.3831,0.8073	,,	643/728,643/728,680/765	42284951	105,12901	2203	4300	6503	SO:0001819	synonymous_variant	7343	exon20			TTCATCATCCTCC	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.2040T>C	17.37:g.42284951A>G		177	0	0		223	118	0.529148	NM_014233	A8K6R8	Silent	SNP	ENST00000302904.4	37	CCDS11480.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	A	10.81	1.455714	0.26161	0.023831	0.0	ENSG00000108312	ENST00000527034	D	0.98280	-4.84	5.05	-5.13	0.02884	.	.	.	.	.	D	0.84840	0.5561	.	.	.	0.80722	D	1	.	.	.	.	.	.	D	0.84157	0.0426	6	0.33940	T	0.23	-7.4078	5.2771	0.15655	0.2064:0.218:0.469:0.1066	.	.	.	.	T	642	ENSP00000431539:M642T	ENSP00000431539:M642T	M	-	2	0	UBTF	39640477	0.000000	0.05858	0.464000	0.27143	0.990000	0.78478	-2.032000	0.01426	-1.382000	0.02109	0.402000	0.26972	ATG	A|0.990;G|0.010	0.010	strong		0.587	UBTF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395205.1	NM_014233		G	42284951	A	G	42284951	2	3	22	1	0	0	0	0	0	0	0	1	16924	214	8	3		3	UBTF	17	42284951	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	30786	42284951	38910259	3534	6435											
ITGA2B	3674	hgsc.bcm.edu	37	chr17	42455126	42455126	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accaccctggtctcattctcCttcttctgattacagatgag	8	14	6	13	0	4	3	1	2	4	1	6	3	4	3	3	1	1	0	3	1	1	4	rs114232872	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:42455126C>T	ENST00000262407.5	-	21	2158	c.2127G>A	c.(2125-2127)aaG>aaA	p.K709K	ITGA2B_ENST00000353281.4_Silent_p.K709K	NM_000419.3	NP_000410.2	P08514	ITA2B_HUMAN	integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)	709					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)	TCTCATTCTCCTTCTTCTGAT	0.502													C|||	24	0.00479233	0.0159	0.0043	5008	,	,		14353	0.0		0.0	False		,,,				2504	0.0				p.K709K		Atlas-SNP	.											.	ITGA2B	88	.	0			c.G2127A						PASS	.	C		57,4349	54.9+/-90.9	0,57,2146	86	75	79		2127	0	1	17	dbSNP_132	79	0,8600		0,0,4300	no	coding-synonymous	ITGA2B	NM_000419.3		0,57,6446	TT,TC,CC		0.0,1.2937,0.4383		709/1040	42455126	57,12949	2203	4300	6503	SO:0001819	synonymous_variant	3674	exon21			ATTCTCCTTCTTC		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.2127G>A	17.37:g.42455126C>T		69	0	0		69	36	0.521739	NM_000419	B2RCY8|O95366|Q14443|Q17R67	Silent	SNP	ENST00000262407.5	37	CCDS32665.1																																																																																			C|0.995;T|0.005	0.005	strong		0.502	ITGA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439823.1			T	42455126	C	T	42455126	2	4	22	1	0	0	0	0	0	0	0	1	7885	680	24	2		2	ITGA2B	17	42455126	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	170175	42455126	38740084	3535	6436											
ITGA2B	3674	hgsc.bcm.edu	37	chr17	42457087	42457087	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acatgggtgtctccatgcagCacgacagcaggggccattcc	9	7	12	13	1	1	0	0	0	1	0	3	1	2	0	3	3	3	3	3	3	0	1	rs79289329	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:42457087C>T	ENST00000262407.5	-	18	1879	c.1848G>A	c.(1846-1848)gtG>gtA	p.V616V	ITGA2B_ENST00000353281.4_Silent_p.V616V	NM_000419.3	NP_000410.2	P08514	ITA2B_HUMAN	integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)	616					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)	CTCCATGCAGCACGACAGCAG	0.607													C|||	26	0.00519169	0.0174	0.0043	5008	,	,		19396	0.0		0.0	False		,,,				2504	0.0				p.V616V		Atlas-SNP	.											.	ITGA2B	88	.	0			c.G1848A						PASS	.	C		70,4336	61.7+/-98.7	0,70,2133	109	106	107		1848	1.2	0.9	17	dbSNP_132	107	0,8600		0,0,4300	no	coding-synonymous	ITGA2B	NM_000419.3		0,70,6433	TT,TC,CC		0.0,1.5887,0.5382		616/1040	42457087	70,12936	2203	4300	6503	SO:0001819	synonymous_variant	3674	exon18			ATGCAGCACGACA		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.1848G>A	17.37:g.42457087C>T		107	0	0		116	52	0.448276	NM_000419	B2RCY8|O95366|Q14443|Q17R67	Silent	SNP	ENST00000262407.5	37	CCDS32665.1																																																																																			C|0.994;T|0.006	0.006	strong		0.607	ITGA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439823.1			T	42457087	C	T	42457087	2	4	22	1	0	0	0	0	0	0	0	1	7885	697	25	2		2	ITGA2B	17	42457087	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1961	42457087	38738123	3536	6437											
ITGA2B	3674	hgsc.bcm.edu	37	chr17	42457120	42457120	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccattccagcctccgtgggCggtagggacacattgaggct	7	8	14	12	2	0	1	0	1	0	0	2	2	2	2	4	4	1	2	4	4	1	3	rs5912	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:42457120C>T	ENST00000262407.5	-	18	1846	c.1815G>A	c.(1813-1815)ccG>ccA	p.P605P	ITGA2B_ENST00000353281.4_Silent_p.P605P	NM_000419.3	NP_000410.2	P08514	ITA2B_HUMAN	integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)	605					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)	CCTCCGTGGGCGGTAGGGACA	0.617													C|||	59	0.0117812	0.0318	0.0159	5008	,	,		19144	0.0		0.006	False		,,,				2504	0.0				p.P605P		Atlas-SNP	.											ITGA2B,colon,carcinoma,-1,1	ITGA2B	88	1	0			c.G1815A						PASS	.	C		174,4232	111.6+/-149.8	4,166,2033	94	82	86		1815	-3.7	0	17	dbSNP_52	86	67,8533	39.8+/-96.3	0,67,4233	no	coding-synonymous	ITGA2B	NM_000419.3		4,233,6266	TT,TC,CC		0.7791,3.9492,1.853		605/1040	42457120	241,12765	2203	4300	6503	SO:0001819	synonymous_variant	3674	exon18			CGTGGGCGGTAGG		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.1815G>A	17.37:g.42457120C>T		81	0	0		100	52	0.52	NM_000419	B2RCY8|O95366|Q14443|Q17R67	Silent	SNP	ENST00000262407.5	37	CCDS32665.1																																																																																			C|0.982;T|0.018	0.018	strong		0.617	ITGA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439823.1			T	42457120	C	T	42457120	2	4	22	1	0	0	0	0	0	0	0	1	7885	755	27	1		1	ITGA2B	17	42457120	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	33	42457120	38738090	3537	6438											
GFAP	2670	hgsc.bcm.edu	37	chr17	42985453	42985453	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctccatcccgcatctccacGgtcttcaccacgatgttcct	6	12	5	18	3	4	0	1	0	3	0	8	1	6	0	5	1	0	2	5	1	0	2	rs146298944	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:42985453G>T	ENST00000253408.5	-	8	1301	c.1236C>A	c.(1234-1236)acC>acA	p.T412T	GFAP_ENST00000588735.1_Silent_p.T38T	NM_002055.4	NP_002046.1	P14136	GFAP_HUMAN	glial fibrillary acidic protein	412	Tail.				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)				GCATCTCCACGGTCTTCACCA	0.592													G|||	5	0.000998403	0.0038	0.0	5008	,	,		19484	0.0		0.0	False		,,,				2504	0.0				p.T412T		Atlas-SNP	.											GFAP,colon,carcinoma,0,1	GFAP	88	1	0			c.C1236A						PASS	.	G		20,4386	27.2+/-55.0	0,20,2183	231	198	209		1236	-10.3	0.1	17	dbSNP_134	209	0,8600		0,0,4300	no	coding-synonymous	GFAP	NM_002055.4		0,20,6483	TT,TG,GG		0.0,0.4539,0.1538		412/433	42985453	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	2670	exon8			CTCCACGGTCTTC	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.1236C>A	17.37:g.42985453G>T		155	0	0		149	70	0.469799	NM_002055	B2RD44|D3DX59|E9PAX3|Q53H98|Q5D055|Q6ZQS3|Q7Z5J6|Q7Z5J7|Q96KS4|Q96P18|Q9UFD0	Silent	SNP	ENST00000253408.5	37	CCDS11491.1																																																																																			G|0.999;T|0.001	0.001	strong		0.592	GFAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448701.1	NM_002055		T	42985453	G	T	42985453	2	4	22	1	0	0	0	0	0	0	0	1	6345	1103	39	4		4	GFAP	17	42985453	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	528333	42985453	38209757	3538	6439											
NMT1	4836	hgsc.bcm.edu	37	chr17	43181223	43181223	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttctagacctcatgagcgaCgcccttgtcctcgccaaaat	9	10	7	15	3	2	2	1	1	1	1	4	3	3	2	4	0	1	0	4	0	3	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:43181223C>T	ENST00000592782.1	+	11	1442	c.1311C>T	c.(1309-1311)gaC>gaT	p.D437D	NMT1_ENST00000258960.2_Silent_p.D437D			P30419	NMT1_HUMAN	N-myristoyltransferase 1	437					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)				TCATGAGCGACGCCCTTGTCC	0.567																																					p.D437D		Atlas-SNP	.											.	NMT1	31	.	0			c.C1311T						PASS	.						226	220	222					17																	43181223		2203	4300	6503	SO:0001819	synonymous_variant	4836	exon10			GAGCGACGCCCTT		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.1311C>T	17.37:g.43181223C>T		95	0	0		115	51	0.443478	NM_021079	A8K7C1|Q9UE09	Silent	SNP	ENST00000592782.1	37	CCDS11494.1																																																																																			.	.	none		0.567	NMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449239.1	NM_021079		T	43181223	C	T	43181223	2	4	22	1	0	0	0	0	0	0	0	1	10512	535	19	1		1	NMT1	17	43181223	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	195770	43181223	38013987	3539	6440											
HEXIM2	124790	hgsc.bcm.edu	37	chr17	43246456	43246456	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttccctgcccctgacaccGcggatggagagccactcaga	8	6	12	15	2	1	3	1	1	0	2	2	5	2	4	5	3	2	1	5	3	0	1	rs34207107	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:43246456G>A	ENST00000307275.3	+	4	577	c.141G>A	c.(139-141)ccG>ccA	p.P47P	HEXIM2_ENST00000592695.1_Silent_p.P47P|RP13-890H12.2_ENST00000589451.1_RNA|HEXIM2_ENST00000591576.1_Silent_p.P47P|RP13-890H12.2_ENST00000589796.1_RNA	NM_144608.1	NP_653209.1	Q96MH2	HEXI2_HUMAN	hexamethylene bis-acetamide inducible 2	47					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)			endometrium(1)|large_intestine(3)|lung(1)	5						CCCTGACACCGCGGATGGAGA	0.642													G|||	209	0.0417332	0.143	0.0159	5008	,	,		15993	0.0		0.003	False		,,,				2504	0.0061				p.P47P		Atlas-SNP	.											.	HEXIM2	19	.	0			c.G141A						PASS	.	G		546,3860	240.6+/-251.3	31,484,1688	110	125	120		141	-7.9	0	17	dbSNP_126	120	32,8568	21.6+/-65.8	0,32,4268	no	coding-synonymous	HEXIM2	NM_144608.1		31,516,5956	AA,AG,GG		0.3721,12.3922,4.4441		47/287	43246456	578,12428	2203	4300	6503	SO:0001819	synonymous_variant	124790	exon4			GACACCGCGGATG	AK056946	CCDS11496.1	17q21.31	2011-07-29	2011-07-29			ENSG00000168517			28591	protein-coding gene	gene with protein product		615695				12832472	Standard	NM_144608		Approved	FLJ32384	uc002iih.1	Q96MH2		ENST00000307275.3:c.141G>A	17.37:g.43246456G>A		101	1	0.00990099		100	100	1	NM_144608	D3DX66	Silent	SNP	ENST00000307275.3	37	CCDS11496.1																																																																																			G|0.962;A|0.038	0.038	strong		0.642	HEXIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450181.1	NM_144608		A	43246456	G	A	43246456	2	1	22	1	0	0	0	0	0	0	0	1	7086	1074	38	1		1	HEXIM2	17	43246456	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	65233	43246456	37948754	3540	6441											
PLEKHM1	9842	hgsc.bcm.edu	37	chr17	43552942	43552942	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cggagcagggcggtgggctgGtagtactcatgcaagcgggc	7	6	19	9	3	1	0	1	0	0	0	1	1	1	1	0	6	4	5	0	6	3	2	rs71373588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:43552942G>A	ENST00000430334.3	-	4	580	c.447C>T	c.(445-447)taC>taT	p.Y149Y	PLEKHM1_ENST00000421073.2_Silent_p.Y60Y	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	149	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)					CGGTGGGCTGGTAGTACTCAT	0.637													G|||	20	0.00399361	0.0136	0.0029	5008	,	,		18295	0.0		0.0	False		,,,				2504	0.0				p.Y149Y		Atlas-SNP	.											.	PLEKHM1	69	.	0			c.C447T						PASS	.	G		76,4328	63.5+/-100.7	2,72,2128	41	39	40		447	-2.8	1	17	dbSNP_130	40	0,8600		0,0,4300	no	coding-synonymous	PLEKHM1	NM_014798.2		2,72,6428	AA,AG,GG		0.0,1.7257,0.5844		149/1057	43552942	76,12928	2202	4300	6502	SO:0001819	synonymous_variant	9842	exon4			GGGCTGGTAGTAC	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.447C>T	17.37:g.43552942G>A		247	1	0.00404858		281	131	0.466192	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Silent	SNP	ENST00000430334.3	37	CCDS32671.1																																																																																			G|0.993;A|0.007	0.007	strong		0.637	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798		A	43552942	G	A	43552942	2	1	22	1	0	0	0	0	0	0	0	1	12089	1256	44	2		2	PLEKHM1	17	43552942	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	306486	43552942	37642268	3541	6442											
IMP5	162540	hgsc.bcm.edu	37	chr17	43922535	43922535	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccgctcccccagccagcggcCcctccgccagaccactgcca	6	3	8	24	3	0	1	0	0	0	1	2	1	2	1	10	1	3	1	10	1	0	0	rs116482551	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:43922535C>T	ENST00000329196.5	+	1	280	c.263C>T	c.(262-264)cCc>cTc	p.P88L	MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579244.1_RNA|MAPT-AS1_ENST00000579599.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	88	PA.					endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										AGCCAGCGGCCCCTCCGCCAG	0.682													C|||	19	0.00379393	0.0144	0.0	5008	,	,		15160	0.0		0.0	False		,,,				2504	0.0				p.P88L		Atlas-SNP	.											.	.	.	.	0			c.C263T						PASS	.	C	LEU/PRO	68,4338	56.2+/-92.4	1,66,2136	25	26	26		263	4.8	0.6	17	dbSNP_132	26	0,8598		0,0,4299	yes	missense	IMP5	NM_175882.2	98	1,66,6435	TT,TC,CC		0.0,1.5433,0.5229	probably-damaging	88/685	43922535	68,12936	2203	4299	6502	SO:0001583	missense	162540	exon1			AGCGGCCCCTCCG		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"intramembrane protease 5"	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.263C>T	17.37:g.43922535C>T	ENSP00000332488:p.Pro88Leu	84	0	0		87	47	0.54023	NM_175882	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	ENST00000329196.5	37	CCDS32673.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	15.63	2.890707	0.52014	0.015433	0.0	ENSG00000185294	ENST00000329196	T	0.06068	3.35	4.8	4.8	0.61643	Protease-associated domain, PA (1);	0.000000	0.42172	D	0.000759	T	0.10637	0.0260	M	0.73217	2.22	0.58432	D	0.999998	D	0.69078	0.997	D	0.68943	0.961	T	0.00203	-1.1924	10	0.33940	T	0.23	-5.2725	13.2146	0.59851	0.0:1.0:0.0:0.0	.	88	Q8IUH8	IMP5_HUMAN	L	88	ENSP00000332488:P88L	ENSP00000332488:P88L	P	+	2	0	AC217771.1	41278315	0.895000	0.30542	0.640000	0.29408	0.454000	0.32378	2.391000	0.44424	2.481000	0.83766	0.650000	0.86243	CCC	C|0.995;T|0.005	0.005	strong		0.682	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882		T	43922535	C	T	43922535	3	4	22	1	0	0	0	0	1	0	0	0	7730	623	22	2	265	2	IMP5	17	43922535	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	369593	43922535	37272675	3542	6443											
STH	246744	hgsc.bcm.edu	37	chr17	44076711	44076711	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acaagactgtgcaggtggccGgccctcattgaatgcggggt	8	8	15	10	2	1	2	1	1	0	1	1	2	1	2	2	5	2	1	2	5	2	1	rs73317018	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:44076711G>A	ENST00000537309.1	+	1	96	c.66G>A	c.(64-66)ccG>ccA	p.P22P	MAPT_ENST00000415613.2_Intron|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000347967.5_Intron|MAPT_ENST00000571987.1_Intron|MAPT_ENST00000344290.5_Intron|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000262410.5_Intron|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000431008.3_Intron	NM_001007532.2	NP_001007533.1	Q8IWL8	STH_HUMAN	saitohin	22						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						gcaggtggccggccctcattg	0.537													G|||	178	0.0355431	0.1271	0.0144	5008	,	,		18789	0.0		0.0	False		,,,				2504	0.0				p.P22P		Atlas-SNP	.											.	STH	14	.	0			c.G66A						PASS	.	G	,,,,,,,,	452,3442		19,414,1514	66	65	65		66,,,,,,,,	-2.5	0	17	dbSNP_132	65	1,8263		0,1,4131	no	coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron	MAPT,STH	NM_001007532.2,NM_001123066.3,NM_001123067.3,NM_001203251.1,NM_001203252.1,NM_005910.5,NM_016834.4,NM_016835.4,NM_016841.4	,,,,,,,,	19,415,5645	AA,AG,GG		0.0121,11.6076,3.7259	,,,,,,,,	22/129,,,,,,,,	44076711	453,11705	1947	4132	6079	SO:0001819	synonymous_variant	246744	exon1			GTGGCCGGCCCTC	AA325304	CCDS54136.1	17q21.1	2008-01-22				ENSG00000256762			18839	protein-coding gene	gene with protein product	"microtubule-associated protein tau (MAPT) intronic transcript"	607067				12032355, 16186110	Standard	NM_001007532		Approved	MAPTIT	uc002ijy.2	Q8IWL8		ENST00000537309.1:c.66G>A	17.37:g.44076711G>A		164	0	0		180	90	0.5	NM_001007532	A1L3X7	Silent	SNP	ENST00000537309.1	37	CCDS54136.1																																																																																			A|0.027;C|0.000;G|0.972;T|0.000	0.027	strong		0.537	STH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400444.1			A	44076711	G	A	44076711	2	1	22	1	0	0	0	0	0	0	0	1	15296	1103	39	1		1	STH	17	44076711	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	154176	44076711	37118499	3543	6444											
LRRC37A	9884	hgsc.bcm.edu	37	chr17	44373384	44373386	+	In_Frame_Del	DEL	CAA	CAA	-																															caagcttattatcacttgccCaacattacagttaaacctgc																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:44373384_44373386delCAA	ENST00000320254.5	+	1	888_890	c.885_887delCAA	c.(883-888)cccaac>ccc	p.N296del	ARL17B_ENST00000570618.1_Intron|LRRC37A_ENST00000393465.3_In_Frame_Del_p.N296del|LRRC37A_ENST00000496930.1_Intron	NM_014834.4	NP_055649.4	A6NMS7	L37A1_HUMAN	leucine rich repeat containing 37A	296						integral component of membrane (GO:0016021)				endometrium(1)|lung(2)|pancreas(6)|prostate(1)|skin(1)	11		Melanoma(429;0.211)		BRCA - Breast invasive adenocarcinoma(366;0.232)		ATCACTTGCCCAACATTACAGTT	0.473																																					p.295_296del		Atlas-Indel	.											.	LRRC37A	19	.	0			c.884_886del						PASS	.																																			SO:0001651	inframe_deletion	9884	exon1			.	BC040501	CCDS11504.2	17q21.31	2014-04-01			ENSG00000176681	ENSG00000176681			29069	protein-coding gene	gene with protein product						9628581, 15533724	Standard	NM_014834		Approved	KIAA0563	uc031rbr.1	A6NMS7	OTTHUMG00000149841	ENST00000320254.5:c.885_887delCAA	17.37:g.44373384_44373386delCAA	ENSP00000326324:p.Asn296del	235	0	0		305	21	0.0688525	NM_014834	Q68DY2|Q8IWC7	In_Frame_Del	DEL	ENST00000320254.5	37	CCDS11504.2																																																																																			.	.	none		0.473	LRRC37A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313519.3	NM_014834		-	44373386	CAA	-	44373384	7	5	22	1	0	1	0	1	0	0	0	0	9000	581	21	0	887	0	LRRC37A	17	44373384	In_Frame_Del	DEL	CAA	TCGA-G8-6324-01A-11D-2210-10	296673	44373384	36821826	3544	6445											
LRRC37A2	474170	hgsc.bcm.edu	37	chr17	44590963	44590965	+	In_Frame_Del	DEL	CAA	CAA	-																															caagcttattatcacttgccCaacattacagttaaacctgc																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:44590963_44590965delCAA	ENST00000576629.1	+	2	1380_1382	c.885_887delCAA	c.(883-888)cccaac>ccc	p.N296del	LRRC37A2_ENST00000333412.3_In_Frame_Del_p.N296del			A6NM11	L37A2_HUMAN	leucine rich repeat containing 37, member A2	296						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|pancreas(4)|prostate(2)	15		Melanoma(429;0.211)		BRCA - Breast invasive adenocarcinoma(366;0.232)		ATCACTTGCCCAACATTACAGTT	0.473																																					p.295_296del		Atlas-Indel	.											.	LRRC37A2	37	.	0			c.884_886del						PASS	.																																			SO:0001651	inframe_deletion	474170	exon1			.	AY386262	CCDS42353.1	17q21.31	2013-05-14			ENSG00000238083	ENSG00000238083			32404	protein-coding gene	gene with protein product	"c114 SLIT-like testicular protein"						Standard	NM_001006607		Approved	FLJ45049	uc002ikn.1	A6NM11	OTTHUMG00000178032	ENST00000576629.1:c.885_887delCAA	17.37:g.44590963_44590965delCAA	ENSP00000459551:p.Asn296del	238	0	0		305	20	0.0655738	NM_001006607	B7ZMC3	In_Frame_Del	DEL	ENST00000576629.1	37	CCDS42353.1																																																																																			.	.	none		0.473	LRRC37A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440299.2	NM_001006607		-	44590965	CAA	-	44590963	7	5	22	1	0	1	0	1	0	0	0	0	9001	581	21	0	887	0	LRRC37A2	17	44590963	In_Frame_Del	DEL	CAA	TCGA-G8-6324-01A-11D-2210-10	217579	44590963	36604247	3545	6446											
C17orf57	124989	hgsc.bcm.edu	37	chr17	45471443	45471443	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatactatgatgagcaacacGgaatgcttctctgaaaaatt	15	11	8	7	1	1	3	0	3	1	0	2	5	1	4	0	1	4	2	0	1	6	4	rs7217678	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:45471443G>A	ENST00000331493.2	+	16	2190	c.1779G>A	c.(1777-1779)acG>acA	p.T593T	EFCAB13_ENST00000517484.1_Silent_p.T497T	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	593						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										TGAGCAACACGGAATGCTTCT	0.299													g|||	87	0.0173722	0.0628	0.0029	5008	,	,		14107	0.0		0.002	False		,,,				2504	0.0				p.T593T		Atlas-SNP	.											C17orf57,NS,carcinoma,+1,1	.	.	1	0			c.G1779A						PASS	.	G	,	238,4168	138.0+/-173.8	7,224,1972	106	119	114		1491,1779	-2.9	0.2	17	dbSNP_116	114	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous	C17orf57	NM_001195192.1,NM_152347.4	,	7,228,6268	AA,AG,GG		0.0465,5.4017,1.8607	,	497/785,593/974	45471443	242,12764	2203	4300	6503	SO:0001819	synonymous_variant	124989	exon16			CAACACGGAATGC	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.1779G>A	17.37:g.45471443G>A		162	0	0		159	68	0.427673	NM_152347	G3V128|Q49AG9	Silent	SNP	ENST00000331493.2	37	CCDS11512.1																																																																																			G|0.977;A|0.023	0.023	strong		0.299	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347		A	45471443	G	A	45471443	2	1	22	1	0	0	0	0	0	0	0	1	1867	1103	39	1		1	C17orf57	17	45471443	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	880480	45471443	35723767	3546	6447											
LRRC46	90506	hgsc.bcm.edu	37	chr17	45914125	45914136	+	In_Frame_Del	DEL	AGGAGCTGGAGC	AGGAGCTGGAGC	-																															gcccctcccaggcttcctcaAggagctggagcaggagctga																								rs142960476|rs377191761	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGGAGCTGGAGC	AGGAGCTGGAGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:45914125_45914136delAGGAGCTGGAGC	ENST00000269025.4	+	8	968_979	c.605_616delAGGAGCTGGAGC	c.(604-618)aaggagctggagcag>aag	p.ELEQ203del		NM_033413.3	NP_219481.1	Q96FV0	LRC46_HUMAN	leucine rich repeat containing 46	203										endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)	9						GGCTTCCTCAAGGAGCTGGAGCAGGAGCTGAG	0.684														156	0.0311502	0.1104	0.013	5008	,	,		19410	0.0		0.0	False		,,,				2504	0.001				p.202_205del		Pindel,Atlas-Indel	.											.	LRRC46	25	.	0			c.604_615del						PASS	.			383,3877		24,335,1771						-3.3	0.8		dbSNP_134	24	7,8231		1,5,4113	no	coding	LRRC46	NM_033413.3		25,340,5884	A1A1,A1R,RR		0.085,8.9906,3.1205				390,12108				SO:0001651	inframe_deletion	90506	exon8			.		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.605_616delAGGAGCTGGAGC	17.37:g.45914125_45914136delAGGAGCTGGAGC	ENSP00000269025:p.Glu203_Gln206del	184	0	.		131	35	0.267	NM_033413	A8K9Q0	In_Frame_Del	DEL	ENST00000269025.4	37	CCDS11518.1																																																																																			AGGAGCTGGAGC|0.978;-|0.022	0.022	strong		0.684	LRRC46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441377.1	NM_033413		-	45914136	AGGAGCTGGAGC	-	45914125	7	5	22	1	0	1	0	1	0	0	0	0	9012	72	3	0	635	0	LRRC46	17	45914125	In_Frame_Del	DEL	AGGAGCTGGAGC	TCGA-G8-6324-01A-11D-2210-10	442682	45914125	35281085	3547	6448											
PNPO	55163	hgsc.bcm.edu	37	chr17	46023295	46023295	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctacttccactcccgcccCaagagcagccagattggggc	8	7	10	16	1	0	2	0	0	0	2	2	2	2	2	5	2	4	2	5	2	2	3	rs35974730	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:46023295C>G	ENST00000225573.4	+	5	591	c.486C>G	c.(484-486)ccC>ccG	p.P162P	PNPO_ENST00000534893.1_Silent_p.P67P|RP11-6N17.9_ENST00000582262.1_RNA|PNPO_ENST00000434554.2_Intron|PNPO_ENST00000544840.1_Silent_p.P144P|RP11-6N17.6_ENST00000582142.1_RNA|RP11-6N17.6_ENST00000580372.1_RNA	NM_018129.3	NP_060599.1	Q9NVS9	PNPO_HUMAN	pyridoxamine 5'-phosphate oxidase	162					pyridoxine biosynthetic process (GO:0008615)|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)	FMN binding (GO:0010181)|pyridoxamine-phosphate oxidase activity (GO:0004733)			endometrium(2)|large_intestine(1)|lung(1)|urinary_tract(1)	5						ACTCCCGCCCCAAGAGCAGCC	0.607													C|||	93	0.0185703	0.0681	0.0029	5008	,	,		19973	0.0		0.001	False		,,,				2504	0.0				p.P162P		Atlas-SNP	.											.	PNPO	18	.	0			c.C486G						PASS	.	C		274,4132	155.9+/-189.0	10,254,1939	70	69	69		486	2.1	1	17	dbSNP_126	69	14,8586	9.1+/-34.3	0,14,4286	yes	coding-synonymous	PNPO	NM_018129.3		10,268,6225	GG,GC,CC		0.1628,6.2188,2.2144		162/262	46023295	288,12718	2203	4300	6503	SO:0001819	synonymous_variant	55163	exon5			CCGCCCCAAGAGC	AF468030	CCDS11522.1	17q21.32	2008-11-27	2006-07-12			ENSG00000108439	1.4.3.5		30260	protein-coding gene	gene with protein product		603287	"pyridoxine 5'-phosphate oxidase"			9601034, 15182361	Standard	NM_018129		Approved	PDXPO	uc002imo.3	Q9NVS9		ENST00000225573.4:c.486C>G	17.37:g.46023295C>G		71	0	0		54	30	0.555556	NM_018129	B4E0V0|B4E152|B4E1D7|D3DTT9	Silent	SNP	ENST00000225573.4	37	CCDS11522.1																																																																																			C|0.980;G|0.020	0.020	strong		0.607	PNPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441407.1	NM_018129		G	46023295	C	G	46023295	2	3	22	1	0	0	0	0	0	0	0	1	12181	581	21	4		4	PNPO	17	46023295	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	109170	46023295	35171915	3548	6449											
HOXB8	3218	hgsc.bcm.edu	37	chr17	46690623	46690623	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgcctctggggcccgctccaGcttctgtttctccagctcct	2	12	9	18	2	3	0	0	0	3	0	6	0	5	0	5	2	2	4	5	2	0	2	rs112046402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:46690623G>C	ENST00000239144.4	-	2	907	c.673C>G	c.(673-675)Ctg>Gtg	p.L225V	HOXB7_ENST00000567101.2_Intron|HOXB7_ENST00000239165.7_5'Flank|HOXB8_ENST00000576562.1_Missense_Mutation_p.L224V	NM_024016.3	NP_076921.1	P17481	HXB8_HUMAN	homeobox B8	225					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						GCCCGCTCCAGCTTCTGTTTC	0.612													G|||	155	0.0309505	0.1142	0.0058	5008	,	,		8098	0.0		0.0	False		,,,				2504	0.0				p.L225V		Atlas-SNP	.											.	HOXB8	26	.	0			c.C673G						PASS	.	G	VAL/LEU	341,4065	176.2+/-205.4	7,327,1869	81	83	83		673	1.9	1	17	dbSNP_132	83	1,8599		0,1,4299	yes	missense	HOXB8	NM_024016.3	32	7,328,6168	CC,CG,GG		0.0116,7.7394,2.6296	benign	225/244	46690623	342,12664	2203	4300	6503	SO:0001583	missense	3218	exon2			GCTCCAGCTTCTG		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.673C>G	17.37:g.46690623G>C	ENSP00000239144:p.Leu225Val	143	0	0		141	65	0.460993	NM_024016	Q9H1I2	Missense_Mutation	SNP	ENST00000239144.4	37	CCDS11533.1	46	0.021062271062271064	44	0.08943089430894309	2	0.0055248618784530384	0	0.0	0	0.0	G	7.810	0.715510	0.15306	0.077394	1.16E-4	ENSG00000120068	ENST00000239144	D	0.90324	-2.65	3.04	1.94	0.25998	.	0.473524	0.13687	U	0.369761	T	0.15046	0.0363	N	0.14661	0.345	0.25211	N	0.989973	B	0.12013	0.005	B	0.12156	0.007	T	0.43956	-0.9359	10	0.29301	T	0.29	.	8.2888	0.31946	0.0:0.0:0.4932:0.5068	.	225	P17481	HXB8_HUMAN	V	225	ENSP00000239144:L225V	ENSP00000239144:L225V	L	-	1	2	HOXB8	44045622	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	2.900000	0.48687	1.734000	0.51633	0.479000	0.44913	CTG	G|0.977;C|0.023	0.023	strong		0.612	HOXB8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358092.3			C	46690623	G	C	46690623	3	2	22	1	0	0	0	0	1	0	0	0	7316	962	34	4	62	4	HOXB8	17	46690623	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	667328	46690623	34504587	3549	6450											
ABI3	51225	hgsc.bcm.edu	37	chr17	47295165	47295165	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caccttagccactgtccagcGgctgccccccggccagaagg	7	5	11	18	2	0	1	0	0	0	1	1	1	1	1	7	3	3	1	7	3	2	1	rs137924898	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:47295165G>A	ENST00000225941.1	+	3	848	c.350G>A	c.(349-351)cGg>cAg	p.R117Q	ABI3_ENST00000419580.2_Missense_Mutation_p.R111Q	NM_001135186.1|NM_016428.2	NP_001128658.1|NP_057512	Q9P2A4	ABI3_HUMAN	ABI family, member 3	117					cellular component movement (GO:0006928)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|membrane (GO:0016020)				breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	12			Epithelial(5;6.37e-06)|all cancers(6;6.36e-05)			ACTGTCCAGCGGCTGCCCCCC	0.612										HNSCC(55;0.14)			G|||	11	0.00219649	0.0083	0.0	5008	,	,		13980	0.0		0.0	False		,,,				2504	0.0				p.R117Q		Atlas-SNP	.											.	ABI3	35	.	0			c.G350A						PASS	.	G	GLN/ARG,GLN/ARG	46,4360	47.5+/-82.1	0,46,2157	95	94	94		332,350	2.8	1	17	dbSNP_134	94	1,8599		0,1,4299	yes	missense,missense	ABI3	NM_001135186.1,NM_016428.2	43,43	0,47,6456	AA,AG,GG		0.0116,1.044,0.3614	possibly-damaging,possibly-damaging	111/361,117/367	47295165	47,12959	2203	4300	6503	SO:0001583	missense	51225	exon3			TCCAGCGGCTGCC	AB037886	CCDS11546.1, CCDS45725.1	17q21.3	2011-03-04	2008-09-12		ENSG00000108798	ENSG00000108798			29859	protein-coding gene	gene with protein product		606363				10978530, 11956071	Standard	NM_001135186		Approved	NESH, SSH3BP3	uc002iop.1	Q9P2A4	OTTHUMG00000161306	ENST00000225941.1:c.350G>A	17.37:g.47295165G>A	ENSP00000225941:p.Arg117Gln	64	0	0		59	28	0.474576	NM_016428	C9IZN8|Q9H0P6	Missense_Mutation	SNP	ENST00000225941.1	37	CCDS11546.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	G	12.92	2.082944	0.36758	0.01044	1.16E-4	ENSG00000108798	ENST00000225941;ENST00000419580	T;T	0.09911	2.93;2.97	4.92	2.85	0.33270	Abl-interactor, homeo-domain homologous domain (1);	0.258373	0.28219	N	0.016153	T	0.06325	0.0163	L	0.45581	1.43	0.43390	D	0.995501	B;B	0.11235	0.003;0.004	B;B	0.12837	0.005;0.008	T	0.16276	-1.0408	10	0.39692	T	0.17	-17.6666	5.5446	0.17057	0.1921:0.1608:0.6471:0.0	.	111;117	Q9P2A4-2;Q9P2A4	.;ABI3_HUMAN	Q	117;111	ENSP00000225941:R117Q;ENSP00000406651:R111Q	ENSP00000225941:R117Q	R	+	2	0	ABI3	44650164	1.000000	0.71417	1.000000	0.80357	0.716000	0.41182	1.567000	0.36407	0.604000	0.29930	0.555000	0.69702	CGG	G|0.997;A|0.003	0.003	strong		0.612	ABI3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364475.1	NM_016428		A	47295165	G	A	47295165	3	1	22	1	0	0	0	0	1	0	0	0	90	1116	39	1	360	1	ABI3	17	47295165	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	604542	47295165	33900045	3550	6451											
PDK2	5164	hgsc.bcm.edu	37	chr17	48174794	48174794	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttctcctgccaggatccagCaatgcctgtgagaaaacctc	10	10	8	13	0	1	1	0	1	1	1	4	3	2	2	5	1	4	1	5	1	3	1	rs11546968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48174794C>T	ENST00000503176.1	+	2	287	c.126C>T	c.(124-126)agC>agT	p.S42S	PDK2_ENST00000007708.3_5'UTR|PDK2_ENST00000511026.1_3'UTR	NM_002611.4	NP_002602.2	Q15119	PDK2_HUMAN	pyruvate dehydrogenase kinase, isozyme 2	42					cellular metabolic process (GO:0044237)|cellular response to nutrient (GO:0031670)|cellular response to reactive oxygen species (GO:0034614)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of cellular ketone metabolic process (GO:0010565)|regulation of gluconeogenesis (GO:0006111)|regulation of glucose metabolic process (GO:0010906)|regulation of pH (GO:0006885)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrial pyruvate dehydrogenase complex (GO:0005967)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			central_nervous_system(4)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	20						CAGGATCCAGCAATGCCTGTG	0.552									Autosomal Dominant Polycystic Kidney Disease				C|||	15	0.00299521	0.0113	0.0	5008	,	,		20973	0.0		0.0	False		,,,				2504	0.0				p.S42S		Atlas-SNP	.											.	PDK2	41	.	0			c.C126T						PASS	.	C	,,,	53,4353	52.9+/-88.7	0,53,2150	80	64	69		,,126,126	3.2	1	17	dbSNP_120	69	5,8595	4.3+/-15.6	0,5,4295	no	utr-5,utr-5,coding-synonymous,coding-synonymous	PDK2	NM_001199898.1,NM_001199899.1,NM_001199900.1,NM_002611.4	,,,	0,58,6445	TT,TC,CC		0.0581,1.2029,0.4459	,,,	,,42/200,42/408	48174794	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	5164	exon2	Familial Cancer Database	ADPKD	ATCCAGCAATGCC	L42451	CCDS11559.1, CCDS56039.1	17q21.33	2012-07-18	2005-11-16		ENSG00000005882	ENSG00000005882			8810	protein-coding gene	gene with protein product		602525	"pyruvate dehydrogenase kinase, isoenzyme 2"			7499431	Standard	NM_001199898		Approved	PDHK2	uc002iqc.3	Q15119	OTTHUMG00000161948	ENST00000503176.1:c.126C>T	17.37:g.48174794C>T		47	0	0		56	33	0.589286	NM_002611	A8K3A7|B3KNW0|Q6P515|Q9BS05	Silent	SNP	ENST00000503176.1	37	CCDS11559.1																																																																																			C|0.997;T|0.003	0.003	strong		0.552	PDK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366492.2	NM_002611		T	48174794	C	T	48174794	2	4	22	1	0	0	0	0	0	0	0	1	11685	709	25	2		2	PDK2	17	48174794	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	879629	48174794	33020416	3551	6452											
COL1A1	1277	hgsc.bcm.edu	37	chr17	48263786	48263786	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgggctgagtggggtacacGcaggtctcaccagtctccat	7	9	13	12	1	2	1	1	1	2	0	4	1	2	1	2	4	1	3	2	4	1	1	rs34940368	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48263786G>A	ENST00000225964.5	-	49	4015	c.3897C>T	c.(3895-3897)tgC>tgT	p.C1299C		NM_000088.3	NP_000079	P02452	CO1A1_HUMAN	collagen, type I, alpha 1	1299	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)	TGGGGTACACGCAGGTCTCAC	0.562			T	"PDGFB, USP6"	"dermatofibrosarcoma protuberans, aneurysmal bone cyst "		Osteogenesis imperfecta						G|||	32	0.00638978	0.0227	0.0029	5008	,	,		22768	0.0		0.0	False		,,,				2504	0.0				p.C1299C		Atlas-SNP	.		Dom	yes		17	17q21.31-q22	1277	"collagen, type I, alpha 1"	yes	M	COL1A1,rectum,carcinoma,0,1	COL1A1	158	1	0			c.C3897T	GRCh37	CM012085	COL1A1	M	rs34940368	scavenged	.	G		75,4331	66.4+/-103.9	0,75,2128	160	143	149	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3897	-0.3	1	17	dbSNP_126	149	0,8600		0,0,4300	no	coding-synonymous	COL1A1	NM_000088.3		0,75,6428	AA,AG,GG		0.0,1.7022,0.5767		1299/1465	48263786	75,12931	2203	4300	6503	SO:0001819	synonymous_variant	1277	exon49			GTACACGCAGGTC	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.3897C>T	17.37:g.48263786G>A		134	1	0.00746269		141	63	0.446809	NM_000088	O76045|P78441|Q13896|Q13902|Q13903|Q14037|Q14992|Q15176|Q15201|Q16050|Q59F64|Q7KZ30|Q7KZ34|Q8IVI5|Q8N473|Q9UML6|Q9UMM7	Silent	SNP	ENST00000225964.5	37	CCDS11561.1																																																																																			G|0.994;A|0.006	0.006	strong		0.562	COL1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309036.2			A	48263786	G	A	48263786	2	1	22	1	0	0	0	0	0	0	0	1	3679	1079	38	1		1	COL1A1	17	48263786	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	88992	48263786	32931424	3552	6453											
XYLT2	64132	hgsc.bcm.edu	37	chr17	48434008	48434008	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	caaggcctactgggagaacaCctacgacgcggctgatggcc	10	5	13	13	3	0	2	0	1	0	1	0	4	0	2	3	4	3	1	3	4	4	2	rs151294421	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48434008C>T	ENST00000017003.2	+	8	1668	c.1619C>T	c.(1618-1620)aCc>aTc	p.T540I	XYLT2_ENST00000507602.1_Missense_Mutation_p.T540I	NM_022167.2	NP_071450.2	Q9H1B5	XYLT2_HUMAN	xylosyltransferase II	540					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)					TGGGAGAACACCTACGACGCG	0.627													C|||	21	0.00419329	0.0129	0.0043	5008	,	,		16601	0.0		0.0	False		,,,				2504	0.001				p.T540I		Atlas-SNP	.											.	XYLT2	51	.	0			c.C1619T						PASS	.	C	ILE/THR	52,4354	51.6+/-87.1	0,52,2151	67	71	70		1619	0	0.6	17	dbSNP_134	70	0,8600		0,0,4300	yes	missense	XYLT2	NM_022167.2	89	0,52,6451	TT,TC,CC		0.0,1.1802,0.3998	benign	540/866	48434008	52,12954	2203	4300	6503	SO:0001583	missense	64132	exon8			AGAACACCTACGA	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.1619C>T	17.37:g.48434008C>T	ENSP00000017003:p.Thr540Ile	35	0	0		21	9	0.428571	NM_022167	Q6UY41|Q86V00	Missense_Mutation	SNP	ENST00000017003.2	37	CCDS11563.1	4	0.0018315018315018315	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	C	1.807	-0.475727	0.04414	0.011802	0.0	ENSG00000015532	ENST00000017003;ENST00000507602	T;T	0.38077	1.16;1.16	4.89	-0.0431	0.13861	.	0.659654	0.15078	N	0.281852	T	0.09730	0.0239	N	0.03608	-0.345	0.24112	N	0.995837	B	0.02656	0.0	B	0.04013	0.001	T	0.29792	-1.0000	10	0.15952	T	0.53	-8.2731	9.014	0.36159	0.0:0.3312:0.0:0.6688	.	540	Q9H1B5	XYLT2_HUMAN	I	540	ENSP00000017003:T540I;ENSP00000426501:T540I	ENSP00000017003:T540I	T	+	2	0	XYLT2	45789007	0.101000	0.21875	0.586000	0.28679	0.021000	0.10359	1.227000	0.32576	0.116000	0.18110	-0.253000	0.11424	ACC	C|0.996;T|0.004	0.004	strong		0.627	XYLT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367046.1	NM_022167		T	48434008	C	T	48434008	3	4	22	1	0	0	0	0	1	0	0	0	17479	507	18	2	1649	2	XYLT2	17	48434008	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	170222	48434008	32761202	3553	6454											
EME1	146956	hgsc.bcm.edu	37	chr17	48453219	48453219	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acacggatgccggcagcagaGacaagcaaggcagaaggaaa	17	1	14	9	2	0	2	0	0	0	2	0	5	0	4	1	4	3	4	1	4	4	0	rs114836030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48453219G>A	ENST00000338165.4	+	2	732	c.650G>A	c.(649-651)aGa>aAa	p.R217K	MRPL27_ENST00000225969.4_5'Flank|MRPL27_ENST00000503633.1_5'Flank|MRPL27_ENST00000507088.1_5'Flank|EME1_ENST00000393271.2_Missense_Mutation_p.R217K|MRPL27_ENST00000442592.3_5'Flank|EME1_ENST00000511648.2_Missense_Mutation_p.R217K	NM_152463.2	NP_689676.2	Q96AY2	EME1_HUMAN	essential meiotic structure-specific endonuclease 1	217					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)			CGGCAGCAGAGACAAGCAAGG	0.507								Direct reversal of damage;Homologous recombination					G|||	34	0.00678914	0.0227	0.0058	5008	,	,		22256	0.0		0.0	False		,,,				2504	0.0				p.R217K		Atlas-SNP	.											.	EME1	39	.	0			c.G650A						PASS	.	G	LYS/ARG,LYS/ARG	79,4327	68.7+/-106.4	1,77,2125	82	83	83		650,650	0.3	0	17	dbSNP_132	83	0,8600		0,0,4300	yes	missense,missense	EME1	NM_001166131.1,NM_152463.2	26,26	1,77,6425	AA,AG,GG		0.0,1.793,0.6074	benign,benign	217/584,217/571	48453219	79,12927	2203	4300	6503	SO:0001583	missense	146956	exon2			AGCAGAGACAAGC	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.650G>A	17.37:g.48453219G>A	ENSP00000339897:p.Arg217Lys	64	0	0		78	35	0.448718	NM_152463	Q96N62	Missense_Mutation	SNP	ENST00000338165.4	37	CCDS11565.1	10	0.004578754578754579	8	0.016260162601626018	2	0.0055248618784530384	0	0.0	0	0.0	G	0.100	-1.152905	0.01700	0.01793	0.0	ENSG00000154920	ENST00000338165;ENST00000393271;ENST00000511648	T;T;T	0.10860	2.83;2.87;2.87	5.11	0.34	0.15985	.	1.089720	0.07057	N	0.833034	T	0.03095	0.0091	L	0.34521	1.04	0.09310	N	1	B;B	0.20052	0.041;0.011	B;B	0.14578	0.011;0.003	T	0.42464	-0.9450	10	0.07644	T	0.81	0.1474	5.5521	0.17095	0.4065:0.1533:0.4403:0.0	.	217;217	Q96AY2-2;Q96AY2	.;EME1_HUMAN	K	217	ENSP00000339897:R217K;ENSP00000376952:R217K;ENSP00000421700:R217K	ENSP00000339897:R217K	R	+	2	0	EME1	45808218	0.000000	0.05858	0.000000	0.03702	0.142000	0.21351	0.423000	0.21313	0.189000	0.20188	-0.145000	0.13849	AGA	G|0.994;A|0.006	0.006	strong		0.507	EME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367118.3	NM_152463		A	48453219	G	A	48453219	3	1	22	1	0	0	0	0	1	0	0	0	5090	942	33	2	652	2	EME1	17	48453219	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	19211	48453219	32741991	3554	6455											
CHAD	1101	hgsc.bcm.edu	37	chr17	48542690	48542690	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cagctttcttggacctcttgGtggggaacttgcagctgcgg	5	12	14	10	1	2	0	0	0	2	0	2	2	2	2	1	5	5	3	1	5	1	4	rs2231510	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48542690G>A	ENST00000508540.1	-	3	1201	c.1049C>T	c.(1048-1050)aCc>aTc	p.T350I	ACSF2_ENST00000502667.1_Intron|CHAD_ENST00000258969.4_Missense_Mutation_p.T350I|ACSF2_ENST00000541920.1_Intron|ACSF2_ENST00000300441.4_Intron|ACSF2_ENST00000504392.1_Intron|ACSF2_ENST00000427954.2_Intron	NM_001267.2	NP_001258.2	O15335	CHAD_HUMAN	chondroadherin	350			T -> I (in dbSNP:rs2231510).		bone development (GO:0060348)|cartilage condensation (GO:0001502)|negative regulation of bone trabecula formation (GO:1900155)	proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(2)|ovary(2)	15	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			GGACCTCTTGGTGGGGAACTT	0.597													G|||	100	0.0199681	0.0734	0.0043	5008	,	,		17381	0.0		0.0	False		,,,				2504	0.0				p.T350I		Atlas-SNP	.											.	CHAD	36	.	0			c.C1049T						PASS	.	G	ILE/THR,	338,4068	178.0+/-206.8	13,312,1878	56	52	53		1049,	5.1	1	17	dbSNP_98	53	1,8599	1.2+/-3.3	0,1,4299	yes	missense,intron	CHAD,ACSF2	NM_001267.2,NM_025149.4	89,	13,313,6177	AA,AG,GG		0.0116,7.6714,2.6065	benign,	350/360,	48542690	339,12667	2203	4300	6503	SO:0001583	missense	1101	exon3			CTCTTGGTGGGGA	U96767	CCDS11568.1	17q21.33	2008-02-05			ENSG00000136457	ENSG00000136457		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	1909	protein-coding gene	gene with protein product	"chondroadherin proteoglycan"	602178				9344663	Standard	NM_001267		Approved	SLRR4A	uc010dbr.3	O15335	OTTHUMG00000162129	ENST00000508540.1:c.1049C>T	17.37:g.48542690G>A	ENSP00000423812:p.Thr350Ile	105	0	0		109	50	0.458716	NM_001267	A8K812|Q6GTU0|Q96RJ5	Missense_Mutation	SNP	ENST00000508540.1	37	CCDS11568.1	39|39	0.017857142857142856|0.017857142857142856	38|38	0.07723577235772358|0.07723577235772358	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	G|G	17.86|17.86	3.492361|3.492361	0.64074|0.64074	0.076714|0.076714	1.16E-4|1.16E-4	ENSG00000136457|ENSG00000136457	ENST00000506187|ENST00000508540;ENST00000258969	.|T;T	.|0.56275	.|0.47;0.47	5.12|5.12	5.12|5.12	0.69794|0.69794	.|.	.|0.056342	.|0.64402	.|D	.|0.000001	T|T	0.05960|0.05960	0.0155|0.0155	L|L	0.45352|0.45352	1.415|1.415	0.58432|0.58432	D|D	0.999997|0.999997	.|D	.|0.64830	.|0.994	.|P	.|0.50314	.|0.637	T|T	0.03413|0.03413	-1.1039|-1.1039	5|10	.|0.37606	.|T	.|0.19	.|.	18.5806|18.5806	0.91170|0.91170	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs2231510;rs2231510|rs2231510;rs2231510	.|350	.|O15335	.|CHAD_HUMAN	S|I	33|350	.|ENSP00000423812:T350I;ENSP00000258969:T350I	.|ENSP00000258969:T350I	P|T	-|-	1|2	0|0	CHAD|CHAD	45897689|45897689	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.971000|0.971000	0.66376|0.66376	8.496000|8.496000	0.90485|0.90485	2.380000|2.380000	0.81148|0.81148	0.655000|0.655000	0.94253|0.94253	CCA|ACC	G|0.966;A|0.034	0.034	strong		0.597	CHAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367447.3	NM_001267		A	48542690	G	A	48542690	3	1	22	1	0	0	0	0	1	0	0	0	3312	1261	44	2	34	2	CHAD	17	48542690	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	89471	48542690	32652520	3555	6456											
MYCBPAP	84073	hgsc.bcm.edu	37	chr17	48594973	48594973	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caggtcccggtgacagcttcGatggcagtgaccagatcctg	8	8	13	12	2	0	3	0	2	0	1	3	4	2	3	3	3	1	2	3	3	0	1	rs75706684	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48594973G>A	ENST00000323776.5	+	4	673	c.511G>A	c.(511-513)Gat>Aat	p.D171N	MYCBPAP_ENST00000436259.2_Missense_Mutation_p.D134N	NM_032133.4	NP_115509.4			MYCBP associated protein									p.D134N(1)		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)			TGACAGCTTCGATGGCAGTGA	0.512													G|||	135	0.0269569	0.0961	0.0086	5008	,	,		6764	0.0		0.002	False		,,,				2504	0.0				p.D171N		Atlas-SNP	.											MYCBPAP,NS,NS,0,1	MYCBPAP	135	1	1	Substitution - Missense(1)	pancreas(1)	c.G511A						PASS	.	G	ASN/ASP	371,4035	188.1+/-214.6	26,319,1858	68	68	68		511	-5.3	0	17	dbSNP_131	68	5,8595	3.7+/-12.6	0,5,4295	yes	missense	MYCBPAP	NM_032133.4	23	26,324,6153	AA,AG,GG		0.0581,8.4203,2.891	benign	171/985	48594973	376,12630	2203	4300	6503	SO:0001583	missense	84073	exon4			AGCTTCGATGGCA	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.511G>A	17.37:g.48594973G>A	ENSP00000323184:p.Asp171Asn	169	0	0		196	100	0.510204	NM_032133		Missense_Mutation	SNP	ENST00000323776.5	37	CCDS32680.2	47	0.02152014652014652	41	0.08333333333333333	4	0.011049723756906077	0	0.0	2	0.002638522427440633	G	16.50	3.139471	0.56936	0.084203	5.81E-4	ENSG00000136449	ENST00000323776;ENST00000452039;ENST00000436259	T;T	0.26957	1.72;1.7	5.6	-5.28	0.02755	.	1.777540	0.02671	N	0.108617	T	0.00724	0.0024	L	0.27053	0.805	0.09310	N	1	D;D	0.63880	0.993;0.993	P;P	0.46543	0.52;0.52	T	0.23868	-1.0176	10	0.11794	T	0.64	3.2954	0.1959	0.00139	0.2453:0.2206:0.2006:0.3335	.	134;171	Q8TBZ2;B4DZQ1	MYBPP_HUMAN;.	N	171;186;134	ENSP00000323184:D171N;ENSP00000397209:D134N	ENSP00000323184:D171N	D	+	1	0	MYCBPAP	45949972	0.000000	0.05858	0.000000	0.03702	0.636000	0.38137	0.053000	0.14184	-0.811000	0.04369	-0.219000	0.12488	GAT	G|0.970;A|0.030	0.030	strong		0.512	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133		A	48594973	G	A	48594973	3	1	22	1	0	0	0	0	1	0	0	0	10028	1058	37	1	525	1	MYCBPAP	17	48594973	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	52283	48594973	32600237	3556	6457											
CACNA1G	8913	hgsc.bcm.edu	37	chr17	48653144	48653144	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tctctcgggcagcaggtgtgCgggttgggctgctcagcagc	4	9	17	11	2	2	0	1	0	1	0	4	0	2	0	0	4	5	6	0	4	0	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48653144C>T	ENST00000359106.5	+	8	1381	c.1381C>T	c.(1381-1383)Cgg>Tgg	p.R461W	CACNA1G_ENST00000515411.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000514717.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000515765.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000514079.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000512389.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000513964.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000507609.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000503485.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000513689.2_Missense_Mutation_p.R461W|CACNA1G_ENST00000354983.4_Missense_Mutation_p.R461W|CACNA1G_ENST00000507336.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000505165.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000502264.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000510115.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000360761.4_Missense_Mutation_p.R461W|CACNA1G_ENST00000515165.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000507896.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000416767.4_Missense_Mutation_p.R461W|CACNA1G_ENST00000510366.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000358244.5_Missense_Mutation_p.R461W|CACNA1G_ENST00000352832.5_Missense_Mutation_p.R461W|CACNA1G_ENST00000514181.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000429973.2_Missense_Mutation_p.R461W|CACNA1G_ENST00000442258.2_Missense_Mutation_p.R461W|CACNA1G_ENST00000507510.2_Missense_Mutation_p.R461W	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	461					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)	AGCAGGTGTGCGGGTTGGGCT	0.672																																					p.R461W		Atlas-SNP	.											.	CACNA1G	659	.	0			c.C1381T						PASS	.																																			SO:0001583	missense	8913	exon8			GGTGTGCGGGTTG	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.1381C>T	17.37:g.48653144C>T	ENSP00000352011:p.Arg461Trp	56	0	0		78	44	0.564103	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	37	CCDS45730.1	.	.	.	.	.	.	.	.	.	.	c	11.34	1.610132	0.28712	.	.	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	0.97352	-4.2;-4.21;-4.35;-4.14;-4.2;-4.19;-4.23;-4.28;-4.25;-4.27;-4.28;-4.16;-4.16;-4.22;-4.2;-4.14;-4.23;-4.18;-4.15;-4.23;-4.2;-4.16;-4.22;-4.15;-4.22;-4.22	5.15	5.15	0.70609	.	0.317948	0.29783	N	0.011202	D	0.97241	0.9098	L	0.42632	1.34	0.37962	D	0.932991	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;B;D	0.89917	1.0;0.999;1.0;1.0;1.0;1.0;1.0;0.999;1.0;0.998;1.0;1.0;0.999;0.999;1.0;0.997;1.0;0.999;1.0;1.0;1.0;0.999;1.0;0.999;0.013;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;B;D	0.83275	0.991;0.918;0.984;0.996;0.959;0.984;0.994;0.959;0.994;0.918;0.947;0.975;0.945;0.947;0.994;0.918;0.965;0.926;0.959;0.991;0.988;0.945;0.947;0.918;0.003;0.985	D	0.98292	1.0514	10	0.66056	D	0.02	.	11.91	0.52733	0.2981:0.7019:0.0:0.0	.	461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461	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;.;.	W	461	ENSP00000353990:R461W;ENSP00000339302:R461W;ENSP00000392390:R461W;ENSP00000347078:R461W;ENSP00000409759:R461W;ENSP00000425522:R461W;ENSP00000426261:R461W;ENSP00000425451:R461W;ENSP00000422407:R461W;ENSP00000426814:R461W;ENSP00000427238:R461W;ENSP00000423112:R461W;ENSP00000420918:R461W;ENSP00000426172:R461W;ENSP00000423045:R461W;ENSP00000427173:R461W;ENSP00000426098:R461W;ENSP00000425698:R461W;ENSP00000426232:R461W;ENSP00000423317:R461W;ENSP00000350979:R461W;ENSP00000352011:R461W;ENSP00000414388:R461W;ENSP00000423155:R461W;ENSP00000422268:R461W;ENSP00000421518:R461W	ENSP00000339302:R461W	R	+	1	2	CACNA1G	46008143	0.991000	0.36638	0.995000	0.50966	0.137000	0.21094	2.463000	0.45058	2.388000	0.81334	0.655000	0.94253	CGG	.	.	none		0.672	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896		T	48653144	C	T	48653144	3	4	22	1	0	0	0	0	1	0	0	0	2546	759	27	1	1411	1	CACNA1G	17	48653144	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	58171	48653144	32542066	3557	6458											
ABCC3	8714	hgsc.bcm.edu	37	chr17	48734136	48734136	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccatggcctggtccatggccGggcccctgcccctgttttct	2	11	11	17	1	1	0	0	0	1	0	2	0	2	0	8	4	1	1	8	4	0	2	rs35777968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48734136G>A	ENST00000285238.8	+	3	376	c.296G>A	c.(295-297)cGg>cAg	p.R99Q	ABCC3_ENST00000427699.1_Missense_Mutation_p.R99Q	NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	99					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)	GTCCATGGCCGGGCCCCTGCC	0.617													G|||	61	0.0121805	0.0454	0.0014	5008	,	,		16262	0.0		0.0	False		,,,				2504	0.0				p.R99Q		Atlas-SNP	.											.	ABCC3	138	.	0			c.G296A						PASS	.	G	GLN/ARG,GLN/ARG	157,4249	103.4+/-141.9	2,153,2048	70	71	71		296,296	-2.1	0	17	dbSNP_126	71	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	ABCC3	NM_001144070.1,NM_003786.3	43,43	2,155,6346	AA,AG,GG		0.0233,3.5633,1.2225	benign,benign	99/573,99/1528	48734136	159,12847	2203	4300	6503	SO:0001583	missense	8714	exon3			ATGGCCGGGCCCC	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.296G>A	17.37:g.48734136G>A	ENSP00000285238:p.Arg99Gln	115	0	0		106	51	0.481132	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Missense_Mutation	SNP	ENST00000285238.8	37	CCDS32681.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	G	11.08	1.534357	0.27475	0.035633	2.33E-4	ENSG00000108846	ENST00000427699;ENST00000285238	T;T	0.35236	1.32;1.32	5.53	-2.14	0.07123	.	1.579970	0.03817	N	0.266872	T	0.04137	0.0115	N	0.12182	0.205	0.09310	N	1	B;B	0.17038	0.01;0.02	B;B	0.13407	0.002;0.009	T	0.12372	-1.0550	10	0.12430	T	0.62	0.3777	6.1119	0.20106	0.4088:0.2585:0.3327:0.0	rs35777968;rs45584534;rs59497545	99;99	O15438;O15438-5	MRP3_HUMAN;.	Q	99	ENSP00000395160:R99Q;ENSP00000285238:R99Q	ENSP00000285238:R99Q	R	+	2	0	ABCC3	46089135	0.000000	0.05858	0.018000	0.16275	0.347000	0.29111	0.356000	0.20181	-0.007000	0.14345	0.591000	0.81541	CGG	G|0.987;A|0.013	0.013	strong		0.617	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038		A	48734136	G	A	48734136	3	1	22	1	0	0	0	0	1	0	0	0	54	1116	39	1	306	1	ABCC3	17	48734136	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	80992	48734136	32461074	3558	6459											
ANKRD40	91369	hgsc.bcm.edu	37	chr17	48774319	48774319	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accttccttaacagagtattGggtaactttctgatcttctc	9	16	6	10	0	3	2	0	1	3	1	5	2	4	2	2	1	2	2	2	1	3	7	rs3815378	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48774319G>A	ENST00000285243.6	-	4	1211	c.942C>T	c.(940-942)ccC>ccT	p.P314P	Y_RNA_ENST00000364470.1_RNA|RP11-294J22.6_ENST00000574246.1_RNA	NM_052855.3	NP_443087.1	Q6AI12	ANR40_HUMAN	ankyrin repeat domain 40	314										breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|skin(1)|urinary_tract(1)	11			BRCA - Breast invasive adenocarcinoma(22;2.03e-09)			ACAGAGTATTGGGTAACTTTC	0.438													G|||	215	0.0429313	0.0908	0.0807	5008	,	,		19551	0.0327		0.002	False		,,,				2504	0.0041				p.P314P		Atlas-SNP	.											.	ANKRD40	35	.	0			c.C942T						PASS	.	G		367,4039	187.8+/-214.3	12,343,1848	133	128	130		942	3.4	1	17	dbSNP_107	130	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous	ANKRD40	NM_052855.3		12,356,6135	AA,AG,GG		0.1512,8.3296,2.9217		314/369	48774319	380,12626	2203	4300	6503	SO:0001819	synonymous_variant	91369	exon4			AGTATTGGGTAAC	BC012978	CCDS11572.1	17q21.33	2013-01-10			ENSG00000154945	ENSG00000154945		"Ankyrin repeat domain containing"	28233	protein-coding gene	gene with protein product						12477932	Standard	NM_052855		Approved	MGC15396	uc002iso.3	Q6AI12	OTTHUMG00000162255	ENST00000285243.6:c.942C>T	17.37:g.48774319G>A		123	0	0		115	44	0.382609	NM_052855	Q96E32	Silent	SNP	ENST00000285243.6	37	CCDS11572.1																																																																																			G|0.963;A|0.037	0.037	strong		0.438	ANKRD40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368201.2	NM_052855		A	48774319	G	A	48774319	2	1	22	1	0	0	0	0	0	0	0	1	669	1335	47	2		2	ANKRD40	17	48774319	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	40183	48774319	32420891	3559	6460											
WFIKKN2	124857	hgsc.bcm.edu	37	chr17	48913352	48913352	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgctgggagcaggtggcagcGctgctgctgctgctgctact	4	9	16	12	2	0	0	0	0	0	0	0	1	0	1	0	3	8	9	0	3	1	1	rs117494161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48913352G>A	ENST00000311378.4	+	1	582	c.54G>A	c.(52-54)gcG>gcA	p.A18A	WFIKKN2_ENST00000426127.1_Intron	NM_175575.5	NP_783165.1	Q8TEU8	WFKN2_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	18					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)			AGGTGGCAGCgctgctgctgc	0.682													G|||	94	0.01877	0.0477	0.0101	5008	,	,		18532	0.0218		0.0	False		,,,				2504	0.002				p.A18A		Atlas-SNP	.											.	WFIKKN2	69	.	0			c.G54A						PASS	.	G		190,4206		4,182,2012	14	14	14		54	0.4	1	17	dbSNP_132	14	8,8576		0,8,4284	no	coding-synonymous	WFIKKN2	NM_175575.5		4,190,6296	AA,AG,GG		0.0932,4.3221,1.5254		18/577	48913352	198,12782	2198	4292	6490	SO:0001819	synonymous_variant	124857	exon1			GGCAGCGCTGCTG	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.54G>A	17.37:g.48913352G>A		110	0	0		107	63	0.588785	NM_175575	Q6UXZ9	Silent	SNP	ENST00000311378.4	37	CCDS11575.1																																																																																			G|0.982;A|0.018	0.018	strong		0.682	WFIKKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368358.1	NM_175575		A	48913352	G	A	48913352	2	1	22	1	0	0	0	0	0	0	0	1	17374	1074	38	1		1	WFIKKN2	17	48913352	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	139033	48913352	32281858	3560	6461											
ANKFN1	162282	hgsc.bcm.edu	37	chr17	54450073	54450073	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaagcccaggagagggtgaGtgaactgtctgcccaggtgg	9	6	18	8	0	1	3	0	2	1	1	1	5	1	4	2	5	3	0	2	5	2	0	rs115263675	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:54450073G>A	ENST00000318698.2	+	6	712	c.677G>A	c.(676-678)aGt>aAt	p.S226N	ANKFN1_ENST00000566473.2_Missense_Mutation_p.S226N	NM_153228.2	NP_694960.2	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain containing 1	226										NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(11)|lung(27)|ovary(1)|prostate(1)|skin(1)	53						GAGAGGGTGAGTGAACTGTCT	0.502													G|||	77	0.0153754	0.056	0.0043	5008	,	,		17983	0.0		0.0	False		,,,				2504	0.0				p.S226N		Atlas-SNP	.											.	ANKFN1	115	.	0			c.G677A						PASS	.	G	ASN/SER	210,4196	128.2+/-165.1	3,204,1996	157	148	151		677	2.1	1	17	dbSNP_132	151	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ANKFN1	NM_153228.2	46	3,205,6295	AA,AG,GG		0.0116,4.7662,1.6223	benign	226/764	54450073	211,12795	2203	4300	6503	SO:0001583	missense	162282	exon6			GGGTGAGTGAACT	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.677G>A	17.37:g.54450073G>A	ENSP00000321627:p.Ser226Asn	63	0	0		76	35	0.460526	NM_153228		Missense_Mutation	SNP	ENST00000318698.2	37	CCDS32686.1	29	0.013278388278388278	28	0.056910569105691054	1	0.0027624309392265192	0	0.0	0	0.0	G	6.241	0.412619	0.11812	0.047662	1.16E-4	ENSG00000153930	ENST00000318698	T	0.22539	1.95	5.64	2.14	0.27477	.	0.409722	0.29799	N	0.011164	T	0.00784	0.0026	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33420	-0.9869	10	0.16896	T	0.51	-6.438	4.4468	0.11602	0.1486:0.2008:0.5381:0.1125	.	226	Q8N957	ANKF1_HUMAN	N	226	ENSP00000321627:S226N	ENSP00000321627:S226N	S	+	2	0	ANKFN1	51805072	0.802000	0.28943	0.995000	0.50966	0.985000	0.73830	0.633000	0.24598	1.317000	0.45149	0.462000	0.41574	AGT	G|0.982;A|0.018	0.018	strong		0.502	ANKFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338043.1	NM_153228		A	54450073	G	A	54450073	3	1	22	1	0	0	0	0	1	0	0	0	625	1029	36	2	699	2	ANKFN1	17	54450073	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5536721	54450073	26745137	3561	6462											
AKAP1	8165	hgsc.bcm.edu	37	chr17	55183726	55183726	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aagcccaggatagaggtgtcGagggagaactgggcaatgag	13	5	17	6	1	0	3	0	1	0	2	1	6	0	4	1	4	2	1	1	4	4	1	rs61731968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:55183726G>A	ENST00000337714.3	+	2	1134	c.901G>A	c.(901-903)Gag>Aag	p.E301K	AKAP1_ENST00000539273.1_Missense_Mutation_p.E301K|AKAP1_ENST00000314126.3_Missense_Mutation_p.E301K|AKAP1_ENST00000572557.1_Missense_Mutation_p.E301K|AKAP1_ENST00000571629.1_Missense_Mutation_p.E301K	NM_003488.3	NP_003479.1	Q92667	AKAP1_HUMAN	A kinase (PRKA) anchor protein 1	301					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)					TAGAGGTGTCGAGGGAGAACT	0.547													G|||	345	0.0688898	0.2496	0.0159	5008	,	,		18330	0.002		0.002	False		,,,				2504	0.0				p.E301K		Atlas-SNP	.											.	AKAP1	73	.	0			c.G901A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU	946,3460	357.1+/-313.8	103,740,1360	79	86	84		901,901,901	1.9	0	17	dbSNP_129	84	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense,missense	AKAP1	NM_001242902.1,NM_001242903.1,NM_003488.3	56,56,56	103,745,5655	AA,AG,GG		0.0581,21.4707,7.312	benign,benign,benign	301/904,301/904,301/904	55183726	951,12055	2203	4300	6503	SO:0001583	missense	8165	exon3			GGTGTCGAGGGAG	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.901G>A	17.37:g.55183726G>A	ENSP00000337736:p.Glu301Lys	112	0	0		114	49	0.429825	NM_001242902	A8K8Q1|D3DTZ0|Q13320|Q9BW14	Missense_Mutation	SNP	ENST00000337714.3	37	CCDS11594.1	132	0.06043956043956044	127	0.258130081300813	3	0.008287292817679558	2	0.0034965034965034965	0	0.0	G	10.31	1.315692	0.23908	0.214707	5.81E-4	ENSG00000121057	ENST00000337714;ENST00000314126;ENST00000427138;ENST00000539273	T;T;T	0.17213	2.56;2.29;2.56	5.15	1.85	0.25348	.	1.753900	0.02141	N	0.057175	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.31599	0.33	B	0.18561	0.022	T	0.38329	-0.9666	9	0.21014	T	0.42	2.3366	2.2365	0.04010	0.3265:0.0:0.4319:0.2416	rs61731968	301	Q92667	AKAP1_HUMAN	K	301;301;343;301	ENSP00000337736:E301K;ENSP00000314075:E301K;ENSP00000443139:E301K	ENSP00000314075:E301K	E	+	1	0	AKAP1	52538725	0.000000	0.05858	0.000000	0.03702	0.086000	0.17979	-0.248000	0.08854	0.193000	0.20303	0.561000	0.74099	GAG	G|0.927;A|0.073	0.073	strong		0.547	AKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277069.1			A	55183726	G	A	55183726	3	1	22	1	0	0	0	0	1	0	0	0	445	1059	37	1	903	1	AKAP1	17	55183726	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	733653	55183726	26011484	3562	6463											
OR4D2	124538	hgsc.bcm.edu	37	chr17	56247794	56247794	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caagcatttacctctatgccCggcccttcactccattccct	7	12	4	18	1	2	0	1	0	1	0	4	0	4	0	5	1	3	1	5	1	3	5	rs148697791	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:56247794C>T	ENST00000545221.1	+	1	778	c.778C>T	c.(778-780)Cgg>Tgg	p.R260W		NM_001004707.3	NP_001004707.1	P58180	OR4D2_HUMAN	olfactory receptor, family 4, subfamily D, member 2	260						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						CCTCTATGCCCGGCCCTTCAC	0.542													C|||	23	0.00459265	0.0166	0.0014	5008	,	,		21719	0.0		0.0	False		,,,				2504	0.0				p.R260W		Atlas-SNP	.											.	OR4D2	48	.	0			c.C778T						PASS	.	C	TRP/ARG	59,4347	57.4+/-93.9	0,59,2144	167	129	142		778	5.7	1	17	dbSNP_134	142	0,8600		0,0,4300	yes	missense	OR4D2	NM_001004707.3	101	0,59,6444	TT,TC,CC		0.0,1.3391,0.4536	benign	260/308	56247794	59,12947	2203	4300	6503	SO:0001583	missense	124538	exon1			TATGCCCGGCCCT		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.778C>T	17.37:g.56247794C>T	ENSP00000441354:p.Arg260Trp	361	1	0.00277008		362	191	0.527624	NM_001004707	Q6IFN8|Q96R75	Missense_Mutation	SNP	ENST00000545221.1	37	CCDS32688.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	12.16	1.854682	0.32791	0.013391	0.0	ENSG00000255713	ENST00000545221	T	0.37915	1.17	5.71	5.71	0.89125	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000115	T	0.25082	0.0609	M	0.81341	2.54	0.30651	N	0.755458	B	0.33345	0.409	B	0.34931	0.192	T	0.40887	-0.9539	10	0.30854	T	0.27	-13.8261	11.0572	0.47925	0.0:0.9155:0.0:0.0845	.	260	P58180	OR4D2_HUMAN	W	260	ENSP00000441354:R260W	ENSP00000441354:R260W	R	+	1	2	OR4D2	53602793	0.003000	0.15002	0.994000	0.49952	0.678000	0.39670	1.764000	0.38471	2.860000	0.98153	0.609000	0.83330	CGG	C|0.995;T|0.005	0.005	strong		0.542	OR4D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443366.1			T	56247794	C	T	56247794	3	4	22	1	0	0	0	0	1	0	0	0	11065	643	23	1	780	1	OR4D2	17	56247794	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1064068	56247794	24947416	3563	6464											
BZRAP1	9256	hgsc.bcm.edu	37	chr17	56388356	56388356	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggaggctgaagcaaggggCgctctggcctctgggcttgg	5	7	20	9	1	2	1	0	1	2	0	2	2	2	2	1	8	1	4	1	8	2	1	rs61745692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:56388356C>T	ENST00000343736.4	-	19	3463	c.3300G>A	c.(3298-3300)gcG>gcA	p.A1100A	BZRAP1_ENST00000268893.6_Silent_p.A1040A|BZRAP1_ENST00000355701.3_Silent_p.A1100A			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1100	Pro-rich.					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)					AAGCAAGGGGCGCTCTGGCCT	0.692													C|||	151	0.0301518	0.1097	0.0086	5008	,	,		16644	0.0		0.0	False		,,,				2504	0.0				p.A1100A		Atlas-SNP	.											BZRAP1_ENST00000355701,caecum,carcinoma,0,2	BZRAP1	287	2	0			c.G3300A						PASS	.	C	,	391,4007		15,361,1823	17	22	20		3300,3120	-3.6	0.3	17	dbSNP_129	20	3,8591		0,3,4294	no	coding-synonymous,coding-synonymous	BZRAP1	NM_004758.2,NM_024418.1	,	15,364,6117	TT,TC,CC		0.0349,8.8904,3.0326	,	1100/1858,1040/1798	56388356	394,12598	2199	4297	6496	SO:0001819	synonymous_variant	9256	exon19			AAGGGGCGCTCTG	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.3300G>A	17.37:g.56388356C>T		163	0	0		161	86	0.534162	NM_004758	O75111|Q8N5W3	Silent	SNP	ENST00000343736.4	37	CCDS11605.1																																																																																			C|0.968;T|0.032	0.032	strong		0.692	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758		T	56388356	C	T	56388356	2	4	22	1	0	0	0	0	0	0	0	1	1579	755	27	1		1	BZRAP1	17	56388356	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	140562	56388356	24806854	3564	6465											
C17orf71	55181	hgsc.bcm.edu	37	chr17	57288251	57288251	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agccctcaaggtagaacctcCtcggaaccaagacccagctc	12	5	8	16	1	1	2	1	0	0	2	4	3	2	3	5	2	4	2	5	2	5	1	rs8068240	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:57288251C>T	ENST00000543872.2	+	2	1103	c.839C>T	c.(838-840)cCt>cTt	p.P280L	SMG8_ENST00000300917.5_Missense_Mutation_p.P280L|SMG8_ENST00000578922.1_Missense_Mutation_p.P280L|SMG8_ENST00000580498.1_Intron|CTD-2510F5.6_ENST00000577660.1_Intron			Q8ND04	SMG8_HUMAN	SMG8 nonsense mediated mRNA decay factor	280			P -> L (in dbSNP:rs8068240).		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						GTAGAACCTCCTCGGAACCAA	0.517													C|||	134	0.0267572	0.093	0.0159	5008	,	,		20461	0.0		0.0	False		,,,				2504	0.0				p.P280L		Atlas-SNP	.											.	SMG8	79	.	0			c.C839T						PASS	.	C	LEU/PRO	414,3992	199.4+/-223.0	25,364,1814	69	77	74		839	5.9	1	17	dbSNP_116	74	9,8591	7.1+/-27.0	0,9,4291	yes	missense	SMG8	NM_018149.6	98	25,373,6105	TT,TC,CC		0.1047,9.3963,3.2523	benign	280/992	57288251	423,12583	2203	4300	6503	SO:0001583	missense	55181	exon1			AACCTCCTCGGAA	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.839C>T	17.37:g.57288251C>T	ENSP00000438748:p.Pro280Leu	88	0	0		104	44	0.423077	NM_018149	Q8N5U5|Q8TDN0|Q9H5P5|Q9NVQ1	Missense_Mutation	SNP	ENST00000543872.2	37	CCDS11615.1	45	0.020604395604395604	44	0.08943089430894309	1	0.0027624309392265192	0	0.0	0	0.0	C	11.98	1.801825	0.31869	0.093963	0.001047	ENSG00000167447	ENST00000300917;ENST00000543872	T;T	0.44881	0.91;0.91	5.88	5.88	0.94601	.	0.385695	0.31210	N	0.008044	T	0.01029	0.0034	N	0.14661	0.345	0.41054	D	0.985328	B	0.09022	0.002	B	0.12156	0.007	T	0.01235	-1.1410	10	0.66056	D	0.02	-9.762	12.6648	0.56835	0.0:0.9223:0.0:0.0777	rs8068240;rs52805280;rs56931279;rs8068240	280	Q8ND04	SMG8_HUMAN	L	280	ENSP00000300917:P280L;ENSP00000438748:P280L	ENSP00000300917:P280L	P	+	2	0	SMG8	54643033	0.003000	0.15002	1.000000	0.80357	0.939000	0.58152	0.955000	0.29188	2.769000	0.95229	0.655000	0.94253	CCT	C|0.967;T|0.033	0.033	strong		0.517	SMG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445960.2	NM_018149		T	57288251	C	T	57288251	3	4	22	1	0	0	0	0	1	0	0	0	1880	681	24	2	841	2	C17orf71	17	57288251	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	899895	57288251	23906959	3565	6466											
DHX40	79665	hgsc.bcm.edu	37	chr17	57652789	57652789	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gatgttcaagataccaccctCgatggcttgttaatattgcc	10	13	8	10	1	1	1	1	0	0	1	2	3	1	1	3	1	2	3	3	1	4	6	rs77178464	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:57652789C>T	ENST00000251241.4	+	7	1077	c.930C>T	c.(928-930)ctC>ctT	p.L310L	DHX40_ENST00000451169.2_Silent_p.L211L|DHX40_ENST00000425628.3_Silent_p.L233L	NM_024612.4	NP_078888.4	Q8IX18	DHX40_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 40	310	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)					ATACCACCCTCGATGGCTTGT	0.303													C|||	263	0.052516	0.1914	0.013	5008	,	,		16582	0.001		0.0	False		,,,				2504	0.0				p.L310L		Atlas-SNP	.											.	DHX40	40	.	0			c.C930T						PASS	.	C	,	569,3837	254.3+/-259.9	34,501,1668	112	107	109		699,930	-4.6	1	17	dbSNP_131	109	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	DHX40	NM_001166301.1,NM_024612.4	,	34,501,5967	TT,TC,CC		0.0,12.9142,4.3756	,	233/703,310/780	57652789	569,12435	2203	4299	6502	SO:0001819	synonymous_variant	79665	exon7			CACCCTCGATGGC	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.930C>T	17.37:g.57652789C>T		392	1	0.00255102		386	201	0.520725	NM_024612	B3KTJ5|C9JR60|Q5JPH4|Q8TC86|Q8WY53|Q9BXM1|Q9H6M9	Silent	SNP	ENST00000251241.4	37	CCDS11617.1																																																																																			C|0.957;T|0.043	0.043	strong		0.303	DHX40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446095.1	NM_024612		T	57652789	C	T	57652789	2	4	22	1	0	0	0	0	0	0	0	1	4514	871	31	1		1	DHX40	17	57652789	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	364538	57652789	23542421	3566	6467											
C17orf64	124773	hgsc.bcm.edu	37	chr17	58506748	58506748	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	attctgcgcctcggatgcgcCggagaggtccttgctggccg	4	9	15	13	5	1	1	0	0	1	1	3	3	2	2	4	4	3	1	4	4	0	2	rs57928695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:58506748C>T	ENST00000269127.4	+	5	539	c.455C>T	c.(454-456)cCg>cTg	p.P152L		NM_181707.2	NP_859058.2	Q86WR6	CQ064_HUMAN	chromosome 17 open reading frame 64	152										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)			TCGGATGCGCCGGAGAGGTCC	0.607													C|||	710	0.141773	0.5068	0.0519	5008	,	,		18332	0.0		0.004	False		,,,				2504	0.0				p.P152L		Atlas-SNP	.											.	C17orf64	19	.	0			c.C455T						PASS	.	C	LEU/PRO	1696,2710	493.1+/-362.6	345,1006,852	34	36	35		455	1.6	0	17	dbSNP_129	35	14,8586	9.8+/-36.6	0,14,4286	yes	missense	C17orf64	NM_181707.2	98	345,1020,5138	TT,TC,CC		0.1628,38.493,13.1478	probably-damaging	152/237	58506748	1710,11296	2203	4300	6503	SO:0001583	missense	124773	exon5			ATGCGCCGGAGAG	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.455C>T	17.37:g.58506748C>T	ENSP00000269127:p.Pro152Leu	108	0	0		147	75	0.510204	NM_181707	Q8IY87	Missense_Mutation	SNP	ENST00000269127.4	37	CCDS32698.2	255	0.11675824175824176	237	0.4817073170731707	15	0.04143646408839779	0	0.0	3	0.00395778364116095	C	9.889	1.203580	0.22121	0.38493	0.001628	ENSG00000141371	ENST00000269127	.	.	.	4.82	1.65	0.23941	.	0.420949	0.20436	N	0.092377	T	0.00012	0.0000	M	0.70595	2.14	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.35201	-0.9798	8	0.51188	T	0.08	-4.574	4.2009	0.10466	0.1819:0.6217:0.0:0.1964	rs57928695;rs61745732	152	Q86WR6	CQ064_HUMAN	L	152	.	ENSP00000269127:P152L	P	+	2	0	C17orf64	55861530	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	-0.833000	0.04396	0.094000	0.17404	0.561000	0.74099	CCG	C|0.882;T|0.118	0.118	strong		0.607	C17orf64-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000347743.1	NM_181707		T	58506748	C	T	58506748	3	4	22	1	0	0	0	0	1	0	0	0	1874	652	23	1	473	1	C17orf64	17	58506748	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	853959	58506748	22688462	3567	6468											
C17orf64	124773	hgsc.bcm.edu	37	chr17	58506785	58506785	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgaccgggaagacagtctGcccaagctctgccatgcatg	9	6	12	14	2	2	1	0	0	2	1	2	3	2	2	4	1	4	2	4	1	2	0	rs9913666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:58506785G>T	ENST00000269127.4	+	5	576	c.492G>T	c.(490-492)ctG>ctT	p.L164L		NM_181707.2	NP_859058.2	Q86WR6	CQ064_HUMAN	chromosome 17 open reading frame 64	164										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)			AAGACAGTCTGCCCAAGCTCT	0.622													G|||	541	0.108027	0.3858	0.0418	5008	,	,		17929	0.0		0.002	False		,,,				2504	0.0				p.L164L		Atlas-SNP	.											.	C17orf64	19	.	0			c.G492T						PASS	.	G		1342,3064	443.9+/-347.2	217,908,1078	47	47	47		492	1.7	1	17	dbSNP_119	47	14,8586	9.8+/-36.6	0,14,4286	no	coding-synonymous	C17orf64	NM_181707.2		217,922,5364	TT,TG,GG		0.1628,30.4585,10.426		164/237	58506785	1356,11650	2203	4300	6503	SO:0001819	synonymous_variant	124773	exon5			CAGTCTGCCCAAG	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.492G>T	17.37:g.58506785G>T		104	0	0		127	62	0.488189	NM_181707	Q8IY87	Silent	SNP	ENST00000269127.4	37	CCDS32698.2																																																																																			G|0.912;T|0.088	0.088	strong		0.622	C17orf64-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000347743.1	NM_181707		T	58506785	G	T	58506785	2	4	22	1	0	0	0	0	0	0	0	1	1874	1306	46	4		4	C17orf64	17	58506785	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	37	58506785	22688425	3568	6469											
APPBP2	10513	hgsc.bcm.edu	37	chr17	58603185	58603185	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acatcaaactggatgttctcGggcaaggagcggatgtctcg	10	9	13	9	3	3	0	1	0	2	0	5	3	3	3	0	4	2	2	0	4	2	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:58603185G>C	ENST00000083182.3	-	1	395	c.108C>G	c.(106-108)ccC>ccG	p.P36P	RP11-15E18.1_ENST00000558027.1_RNA|RP11-15E18.1_ENST00000559739.1_RNA	NM_001282476.1|NM_006380.2	NP_001269405.1|NP_006371.2	Q92624	APBP2_HUMAN	amyloid beta precursor protein (cytoplasmic tail) binding protein 2	36					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)			GGATGTTCTCGGGCAAGGAGC	0.602																																					p.P36P		Atlas-SNP	.											.	APPBP2	48	.	0			c.C108G						PASS	.						136	110	119					17																	58603185		2203	4300	6503	SO:0001819	synonymous_variant	10513	exon1			GTTCTCGGGCAAG	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.108C>G	17.37:g.58603185G>C		134	0	0		134	73	0.544776	NM_006380	A8K862|O95095|Q8WVC9	Silent	SNP	ENST00000083182.3	37	CCDS32699.1																																																																																			.	.	none		0.602	APPBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449465.1	NM_006380		C	58603185	G	C	58603185	2	2	22	1	0	0	0	0	0	0	0	1	816	1103	39	4		4	APPBP2	17	58603185	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	96400	58603185	22592025	3569	6470											
NACA2	342538	hgsc.bcm.edu	37	chr17	59668275	59668275	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atagtgactctagtaactccTgtaacctgtagaagacccag	13	10	8	10	0	1	3	0	1	1	2	2	3	2	3	3	0	2	3	3	0	6	5	rs61739271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:59668275T>A	ENST00000521764.1	-	1	288	c.267A>T	c.(265-267)acA>acT	p.T89T		NM_199290.3	NP_954984.1	Q9H009	NACA2_HUMAN	nascent polypeptide-associated complex alpha subunit 2	89	NAC-A/B. {ECO:0000255|PROSITE- ProRule:PRU00507}.				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)					TAGTAACTCCTGTAACCTGTA	0.443													T|||	198	0.0395367	0.1415	0.0144	5008	,	,		21980	0.0		0.001	False		,,,				2504	0.0				p.T89T		Atlas-SNP	.											.	NACA2	33	.	0			c.A267T						PASS	.	T		554,3852	249.6+/-257.0	38,478,1687	231	226	228		267	0.8	1	17	dbSNP_129	228	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	NACA2	NM_199290.3		38,480,5985	AA,AT,TT		0.0233,12.5738,4.275		89/216	59668275	556,12450	2203	4300	6503	SO:0001819	synonymous_variant	342538	exon1			AACTCCTGTAACC	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.267A>T	17.37:g.59668275T>A		310	0	0		257	134	0.521401	NM_199290	Q2VIR9	Silent	SNP	ENST00000521764.1	37	CCDS11630.1																																																																																			T|0.957;A|0.043	0.043	strong		0.443	NACA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255437.2	NM_199290		A	59668275	T	A	59668275	2	1	22	1	0	0	0	0	0	0	0	1	10143	1567	55	5		5	NACA2	17	59668275	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1065090	59668275	21526935	3570	6471											
MED13	9969	hgsc.bcm.edu	37	chr17	60087932	60087932	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtaactgatgttacacttTcctgtccaaaaggtccaact	11	13	6	11	0	0	1	0	1	0	0	3	1	3	1	3	1	3	2	3	1	5	3	rs114223275	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:60087932T>C	ENST00000397786.2	-	9	2022	c.1946A>G	c.(1945-1947)gAa>gGa	p.E649G		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	649					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						TGTTACACTTTCCTGTCCAAA	0.333													T|||	7	0.00139776	0.0053	0.0	5008	,	,		20038	0.0		0.0	False		,,,				2504	0.0				p.E649G		Atlas-SNP	.											.	MED13	181	.	0			c.A1946G						PASS	.	T	GLY/GLU	11,3675		0,11,1832	67	60	62		1946	5.6	1	17	dbSNP_132	62	0,8172		0,0,4086	yes	missense	MED13	NM_005121.2	98	0,11,5918	CC,CT,TT		0.0,0.2984,0.0928	probably-damaging	649/2175	60087932	11,11847	1843	4086	5929	SO:0001583	missense	9969	exon9			ACACTTTCCTGTC	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.1946A>G	17.37:g.60087932T>C	ENSP00000380888:p.Glu649Gly	121	0	0		102	45	0.441176	NM_005121	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	37	CCDS42366.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	T	12.76	2.033391	0.35893	0.002984	0.0	ENSG00000108510	ENST00000397786;ENST00000262436	T	0.75367	-0.93	5.62	5.62	0.85841	.	0.156711	0.44483	D	0.000448	T	0.74604	0.3738	L	0.46157	1.445	0.58432	D	0.999998	P;B	0.44139	0.827;0.181	P;B	0.46758	0.526;0.014	T	0.75639	-0.3248	10	0.46703	T	0.11	-17.8348	15.804	0.78477	0.0:0.0:0.0:1.0	.	162;649	Q9P0Q5;Q9UHV7	.;MED13_HUMAN	G	649;648	ENSP00000380888:E649G	ENSP00000262436:E648G	E	-	2	0	MED13	57442714	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.998000	0.63927	2.131000	0.65755	0.477000	0.44152	GAA	T|0.999;C|0.001	0.001	strong		0.333	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		C	60087932	T	C	60087932	3	2	22	1	0	0	0	0	1	0	0	0	9439	1783	62	3	4666	3	MED13	17	60087932	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	419657	60087932	21107278	3571	6472											
EFCAB3	146779	hgsc.bcm.edu	37	chr17	60451185	60451185	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgttttacaggaaatggaaaGattaatgttaattcaataat	17	15	7	2	0	1	1	1	0	0	1	1	3	1	3	0	2	1	2	0	2	7	6	rs6504103	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:60451185G>C	ENST00000450662.2	+	2	116	c.45G>C	c.(43-45)aaG>aaC	p.K15N		NM_001144933.1	NP_001138405.1	Q8N7B9	EFCB3_HUMAN	EF-hand calcium binding domain 3	0							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)			GAAATGGAAAGATTAATGTTA	0.254													G|||	123	0.0245607	0.0908	0.0029	5008	,	,		14237	0.0		0.001	False		,,,				2504	0.0				p.K15N		Atlas-SNP	.											.	EFCAB3	71	.	0			c.G45C						PASS	.						46	41	43					17																	60451185		692	1584	2276	SO:0001583	missense	146779	exon2			TGGAAAGATTAAT	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	ENST00000450662.2:c.45G>C	17.37:g.60451185G>C	ENSP00000403932:p.Lys15Asn	145	0	0		145	71	0.489655	NM_001144933	J3KQM8	Missense_Mutation	SNP	ENST00000450662.2	37	CCDS45751.1	38	0.0173992673992674	37	0.07520325203252033	0	0.0	0	0.0	1	0.0013192612137203166	.	8.466	0.856348	0.17106	.	.	ENSG00000172421	ENST00000450662	T	0.10668	2.85	4.0	0.787	0.18596	.	.	.	.	.	T	0.00440	0.0014	.	.	.	0.18873	N	0.999986	.	.	.	.	.	.	T	0.42155	-0.9468	6	0.32370	T	0.25	.	5.523	0.16943	0.3862:0.0:0.6138:0.0	rs6504103;rs6504103	.	.	.	N	15	ENSP00000403932:K15N	ENSP00000403932:K15N	K	+	3	2	EFCAB3	57804917	0.869000	0.29996	0.031000	0.17742	0.003000	0.03518	0.480000	0.22244	0.396000	0.25283	0.591000	0.81541	AAG	G|0.983;C|0.017	0.017	strong		0.254	EFCAB3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379315.1	NM_173503		C	60451185	G	C	60451185	3	2	22	1	0	0	0	0	1	0	0	0	4937	933	33	4	51	4	EFCAB3	17	60451185	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	363253	60451185	20744025	3572	6473											
MRC2	9902	hgsc.bcm.edu	37	chr17	60767303	60767303	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aggagccgctgaactacgtgGgctggcaggacggggagccg	8	4	19	10	4	0	1	0	1	0	0	0	4	0	4	2	6	4	3	2	6	2	1	rs77299955	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:60767303G>A	ENST00000303375.5	+	25	4024	c.3622G>A	c.(3622-3624)Ggc>Agc	p.G1208S	MRC2_ENST00000446119.2_Missense_Mutation_p.G74S	NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	1208	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						GAACTACGTGGGCTGGCAGGA	0.677													G|||	39	0.00778754	0.0287	0.0014	5008	,	,		12596	0.0		0.0	False		,,,				2504	0.0				p.G1208S		Atlas-SNP	.											.	MRC2	126	.	0			c.G3622A						PASS	.	G	SER/GLY	95,4295		0,95,2100	13	16	15		3622	1.8	0.2	17	dbSNP_131	15	1,8567		0,1,4283	yes	missense	MRC2	NM_006039.3	56	0,96,6383	AA,AG,GG		0.0117,2.164,0.7409	benign	1208/1480	60767303	96,12862	2195	4284	6479	SO:0001583	missense	9902	exon25			TACGTGGGCTGGC	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.3622G>A	17.37:g.60767303G>A	ENSP00000307513:p.Gly1208Ser	75	0	0		84	38	0.452381	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Missense_Mutation	SNP	ENST00000303375.5	37	CCDS11634.1	17	0.007783882783882784	17	0.034552845528455285	0	0.0	0	0.0	0	0.0	G	11.35	1.614242	0.28712	0.02164	1.17E-4	ENSG00000011028	ENST00000303375;ENST00000446119	T;T	0.53423	0.62;0.62	5.16	1.8	0.24995	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.232107	0.49916	N	0.000124	T	0.08133	0.0203	N	0.08118	0	0.23478	N	0.997599	B;B	0.09022	0.002;0.0	B;B	0.06405	0.002;0.001	T	0.13072	-1.0523	10	0.18276	T	0.48	-17.6713	8.5553	0.33478	0.7771:0.0:0.2229:0.0	.	74;1208	E7EME3;Q9UBG0	.;MRC2_HUMAN	S	1208;74	ENSP00000307513:G1208S;ENSP00000400445:G74S	ENSP00000307513:G1208S	G	+	1	0	MRC2	58121035	0.920000	0.31207	0.177000	0.23020	0.707000	0.40811	1.980000	0.40618	0.124000	0.18369	-0.367000	0.07326	GGC	G|0.991;A|0.009	0.009	strong		0.677	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1			A	60767303	G	A	60767303	3	1	22	1	0	0	0	0	1	0	0	0	9767	1232	43	2	3720	2	MRC2	17	60767303	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	316118	60767303	20427907	3573	6474											
CYB561	1534	hgsc.bcm.edu	37	chr17	61513509	61513509	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgaagacacggtaaaccagCagggctgtgggaggtgagag	12	5	17	7	1	0	3	0	2	0	2	0	5	0	4	1	4	2	3	1	4	3	1	rs35447397	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:61513509C>T	ENST00000392976.1	-	3	506	c.207G>A	c.(205-207)ctG>ctA	p.L69L	CYB561_ENST00000582297.1_Silent_p.L69L|CYB561_ENST00000582034.1_Silent_p.L40L|CYB561_ENST00000581163.1_5'UTR|CYB561_ENST00000581573.1_Silent_p.L69L|CYB561_ENST00000584031.1_Silent_p.L69L|CYB561_ENST00000448884.2_Silent_p.L69L|CYB561_ENST00000542042.1_Silent_p.L136L|CYB561_ENST00000582997.1_Silent_p.L76L|CYB561_ENST00000392975.2_Silent_p.L69L|CYB561_ENST00000360793.3_Silent_p.L69L	NM_001017916.1	NP_001017916.1	P49447	CY561_HUMAN	cytochrome b561	69	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)		GGTAAACCAGCAGGGCTGTGG	0.607													C|||	41	0.0081869	0.031	0.0	5008	,	,		17487	0.0		0.0	False		,,,				2504	0.0				p.L69L		Atlas-SNP	.											.	CYB561	15	.	0			c.G207A						PASS	.	C	,,	114,4290	87.8+/-126.4	1,112,2089	128	94	106		207,207,207	3.9	1	17	dbSNP_126	106	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	CYB561	NM_001017916.1,NM_001017917.1,NM_001915.3	,,	1,112,6389	TT,TC,CC		0.0,2.5886,0.8767	,,	69/252,69/252,69/252	61513509	114,12890	2202	4300	6502	SO:0001819	synonymous_variant	1534	exon3			AACCAGCAGGGCT		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.207G>A	17.37:g.61513509C>T		85	0	0		76	35	0.460526	NM_001915	B2RE96|B7Z775|D3DU11|Q5BJG9|Q9BU05|Q9BWR9	Silent	SNP	ENST00000392976.1	37	CCDS11636.1																																																																																			C|0.989;T|0.011	0.011	strong		0.607	CYB561-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444843.1	NM_001915		T	61513509	C	T	61513509	2	4	22	1	0	0	0	0	0	0	0	1	4121	697	25	2		2	CYB561	17	61513509	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	746206	61513509	19681701	3574	6475											
STRADA	92335	hgsc.bcm.edu	37	chr17	61787892	61787892	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tggatgtagtcgagggccttCagcaccccctgcaggatgta	8	9	13	11	1	1	0	1	0	0	0	2	3	1	2	3	3	2	4	3	3	2	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:61787892C>T	ENST00000336174.6	-	8	652	c.540G>A	c.(538-540)ctG>ctA	p.L180L	STRADA_ENST00000392950.4_Silent_p.L143L|STRADA_ENST00000447001.3_Silent_p.L136L|STRADA_ENST00000375840.4_Silent_p.L122L|RP11-51F16.8_ENST00000580553.1_Intron|STRADA_ENST00000245865.5_Silent_p.L122L|STRADA_ENST00000579340.1_Silent_p.L122L|STRADA_ENST00000580039.1_5'UTR|STRADA_ENST00000582137.1_Silent_p.L151L	NM_001003787.2	NP_001003787.1	Q7RTN6	STRAA_HUMAN	STE20-related kinase adaptor alpha	180	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						CGAGGGCCTTCAGCACCCCCT	0.512																																					p.L180L		Atlas-SNP	.											.	STRADA	27	.	0			c.G540A						PASS	.						109	90	97					17																	61787892		2203	4300	6503	SO:0001819	synonymous_variant	92335	exon8			GGCCTTCAGCACC	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.540G>A	17.37:g.61787892C>T		121	0	0		143	69	0.482517	NM_001003787	B4DDE3|B4DW17|J3KTC9|Q5JPI2|Q7Z4K9|Q8NC31|Q8NCF1|Q9H272	Silent	SNP	ENST00000336174.6	37	CCDS32703.1																																																																																			.	.	none		0.512	STRADA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443894.1			T	61787892	C	T	61787892	2	4	22	1	0	0	0	0	0	0	0	1	15339	813	29	2		2	STRADA	17	61787892	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	274383	61787892	19407318	3575	6476											
FTSJ3	5705	hgsc.bcm.edu	37	chr17	61902011	61902011	+	5'Flank	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccatacctgagctccttgcgCcccaacactctgatgtcctg	7	10	7	17	1	1	2	0	2	1	0	3	2	3	2	6	0	4	1	6	0	2	2	rs9910549	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:61902011C>T	ENST00000310144.6	+	0	0				FTSJ3_ENST00000427159.2_Silent_p.G301G|FTSJ3_ENST00000580295.1_5'Flank|PSMC5_ENST00000580864.1_5'Flank	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						GCTCCTTGCGCCCCAACACTC	0.562													C|||	99	0.0197684	0.0734	0.0029	5008	,	,		19798	0.0		0.0	False		,,,				2504	0.0				p.G301G		Atlas-SNP	.											.	FTSJ3	63	.	0			c.G903A						PASS	.	C		211,4195	130.2+/-166.9	6,199,1998	191	171	178		903	0.5	1	17	dbSNP_119	178	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	FTSJ3	NM_017647.3		6,201,6296	TT,TC,CC		0.0233,4.7889,1.6377		301/848	61902011	213,12793	2203	4300	6503	SO:0001631	upstream_gene_variant	117246	exon10			CTTGCGCCCCAAC	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			17.37:g.61902011C>T	Exception_encountered	209	0	0		207	103	0.497585	NM_017647	A8K3Z3|A8K763|O35051|O43208|P47210|P52915|P52916	Silent	SNP	ENST00000310144.6	37	CCDS11645.1																																																																																			C|0.976;T|0.024	0.024	strong		0.562	PSMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444404.1	NM_002805		T	61902011	C	T	61902011	1	4	22	0	1	0	0	0	0	0	0	0	6097	726	26	2		2	FTSJ3	17	61902011	5'Flank	SNP	C	TCGA-G8-6324-01A-11D-2210-10	114119	61902011	19293199	3576	6477											
CSH2	1443	hgsc.bcm.edu	37	chr17	61950694	61950694	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agccaggagcagggacgtccGggagcctggggagaaaccgg	10	2	19	10	3	0	1	0	0	0	1	1	5	1	4	4	6	4	1	4	6	1	0			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:61950694G>A	ENST00000392886.2	-	2	167	c.16C>T	c.(16-18)Cgg>Tgg	p.R6W	CSH2_ENST00000336844.5_Missense_Mutation_p.R6W|CSH2_ENST00000345366.7_Missense_Mutation_p.R6W|CSH2_ENST00000560142.1_Missense_Mutation_p.R6W	NM_020991.3	NP_066271.1	P0DML3	CSH2_HUMAN	chorionic somatomammotropin hormone 2	6						extracellular region (GO:0005576)	metal ion binding (GO:0046872)			endometrium(2)|large_intestine(1)|lung(3)	6						AGGGACGTCCGGGAGCCTGGG	0.607																																					p.R6W		Atlas-SNP	.											.	CSH2	37	.	0			c.C16T						PASS	.						12	12	12					17																	61950694		2179	4248	6427	SO:0001583	missense	1443	exon2			ACGTCCGGGAGCC	V00573	CCDS11646.1, CCDS42368.1, CCDS42369.1	17q22-q24	2012-10-02							2441	protein-coding gene	gene with protein product	"placental lactogen", "chorionic somatomammotropin B"	118820				593368, 6208192	Standard	NM_020991		Approved	hCS-B, CSB, CS-2	uc002jch.3	P0DML3		ENST00000392886.2:c.16C>T	17.37:g.61950694G>A	ENSP00000376623:p.Arg6Trp	248	0	0		235	55	0.234043	NM_022645	P01243|Q0VDB1|Q14407	Missense_Mutation	SNP	ENST00000392886.2	37	CCDS42369.1	.	.	.	.	.	.	.	.	.	.	g	9.767	1.171702	0.21704	.	.	ENSG00000213218	ENST00000345366;ENST00000336844;ENST00000392886	D;D;D	0.91407	-2.84;-2.17;-2.36	4.1	3.12	0.35913	.	0.628574	0.16367	N	0.217506	D	0.83175	0.5197	L	0.39397	1.21	0.09310	N	1	D;B;D;B	0.54397	0.966;0.035;0.966;0.003	B;B;B;B	0.39660	0.306;0.006;0.306;0.005	T	0.72577	-0.4251	10	0.27082	T	0.32	.	7.9049	0.29757	0.1194:0.0:0.8806:0.0	.	6;6;6;6	P01243;A6NIT4;A8K6C2;B1A4H9	CSH_HUMAN;.;.;.	W	6	ENSP00000308396:R6W;ENSP00000338816:R6W;ENSP00000376623:R6W	ENSP00000338816:R6W	R	-	1	2	CSH2	59304426	0.001000	0.12720	0.003000	0.11579	0.011000	0.07611	0.623000	0.24447	0.839000	0.34971	0.561000	0.74099	CGG	G|0.980;A|0.020	0.020	strong		0.607	CSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417657.1	NM_020991		A	61950694	G	A	61950694	3	1	22	1	0	0	0	0	1	0	0	0	3943	1115	39	1	701	1	CSH2	17	61950694	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	48683	61950694	19244516	3577	6478											
GH2	2689	hgsc.bcm.edu	37	chr17	61957610	61957610	+	3'UTR	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ttattaggacaaggctggtgGgcactggagtagcaccttcc	9	10	13	9	0	0	0	0	0	0	0	1	2	1	2	2	5	1	4	2	5	4	4	rs58696130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:61957610G>T	ENST00000423893.2	-	0	786				GH2_ENST00000456543.2_Missense_Mutation_p.P241T|GH2_ENST00000332800.7_3'UTR|GH2_ENST00000449787.2_3'UTR			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						AAGGCTGGTGGGCACTGGAGT	0.552													G|||	144	0.028754	0.1044	0.0072	5008	,	,		19214	0.0		0.001	False		,,,				2504	0.0				p.P241T		Atlas-SNP	.											.	GH2	73	.	0			c.C721A						PASS	.	G	,,,THR/PRO	304,2350		17,270,1040	36	38	37		,,,721	0.8	0	17	dbSNP_129	37	1,4617		0,1,2308	yes	utr-3,utr-3,utr-3,missense	GH2	NM_002059.3,NM_022556.2,NM_022557.2,NM_022558.2	,,,38	17,271,3348	TT,TG,GG		0.0217,11.4544,4.1942	,,,	,,,241/246	61957610	305,6967	1327	2309	3636	SO:0001624	3_prime_UTR_variant	2689	exon5			CTGGTGGGCACTG	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.*71C>A	17.37:g.61957610G>T		82	0	0		132	71	0.537879	NM_022558	B1A4H5|B1A4H7|O14643|O14644|P09587	Missense_Mutation	SNP	ENST00000423893.2	37	CCDS11647.1	35	0.016025641025641024	34	0.06910569105691057	1	0.0027624309392265192	0	0.0	0	0.0	g	10.77	1.444668	0.25987	0.114544	2.17E-4	ENSG00000136487	ENST00000456543	D	0.89552	-2.53	1.79	0.797	0.18654	.	.	.	.	.	T	0.06735	0.0172	N	0.24115	0.695	0.09310	N	1	B	0.14012	0.009	B	0.09377	0.004	T	0.45279	-0.9272	9	0.87932	D	0	.	4.4826	0.11774	0.2024:0.0:0.7976:0.0	rs58696130;rs61764021	241	O14644	.	T	241	ENSP00000394122:P241T	ENSP00000394122:P241T	P	-	1	0	GH2	59311342	0.006000	0.16342	0.002000	0.10522	0.048000	0.14542	0.969000	0.29370	0.321000	0.23259	-0.699000	0.03677	CCA	G|0.983;T|0.017	0.017	strong		0.552	GH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417665.1	NM_002059		T	61957610	G	T	61957610	1	4	22	0	1	0	0	0	0	0	0	0	6376	1232	43	4		4	GH2	17	61957610	3'UTR	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6916	61957610	19237600	3578	6479											
SCN4A	6329	hgsc.bcm.edu	37	chr17	62018737	62018737	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tctgagaggcggctgtaggcGatgaactgggtggcgtcggg	6	8	20	7	4	1	2	0	2	1	1	2	4	1	2	0	6	1	2	0	6	2	1	rs59081944	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:62018737G>A	ENST00000435607.1	-	24	4981	c.4905C>T	c.(4903-4905)atC>atT	p.I1635I	SCN4A_ENST00000578147.1_Silent_p.I1635I	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1635					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)	GGCTGTAGGCGATGAACTGGG	0.567													G|||	92	0.0183706	0.0681	0.0029	5008	,	,		18690	0.0		0.0	False		,,,				2504	0.0				p.I1635I		Atlas-SNP	.											.	SCN4A	205	.	0			c.C4905T						PASS	.	G		190,4046		4,182,1932	52	59	56		4905	-3.4	0.9	17	dbSNP_129	56	1,8481		0,1,4240	no	coding-synonymous	SCN4A	NM_000334.4		4,183,6172	AA,AG,GG		0.0118,4.4854,1.5018		1635/1837	62018737	191,12527	2118	4241	6359	SO:0001819	synonymous_variant	6329	exon24			GTAGGCGATGAAC	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.4905C>T	17.37:g.62018737G>A		186	0	0		228	101	0.442982	NM_000334	Q15478|Q16447|Q7Z6B1	Silent	SNP	ENST00000435607.1	37	CCDS45761.1																																																																																			G|0.983;A|0.017	0.017	strong		0.567	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		A	62018737	G	A	62018737	2	1	22	1	0	0	0	0	0	0	0	1	13935	1048	37	1		1	SCN4A	17	62018737	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	61127	62018737	19176473	3579	6480											
SCN4A	6329	hgsc.bcm.edu	37	chr17	62029006	62029006	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgggcggctccttcttctcAtcctcgggggcagtctcccc	2	11	11	17	3	3	0	1	0	3	0	9	0	5	0	4	4	0	2	4	4	0	2	rs79893125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:62029006A>G	ENST00000435607.1	-	14	2707	c.2631T>C	c.(2629-2631)gaT>gaC	p.D877D	SCN4A_ENST00000578147.1_Silent_p.D877D	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	877					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)	CCTTCTTCTCATCCTCGGGGG	0.657													G|||	485	0.096845	0.3026	0.0303	5008	,	,		13158	0.0169		0.0199	False		,,,				2504	0.0276				p.D877D		Atlas-SNP	.											.	SCN4A	205	.	0			c.T2631C						PASS	.	G		974,2962		135,704,1129	55	64	61		2631	-7	0.1	17	dbSNP_131	61	153,8095		6,141,3977	no	coding-synonymous	SCN4A	NM_000334.4		141,845,5106	GG,GA,AA		1.855,24.7459,9.2498		877/1837	62029006	1127,11057	1968	4124	6092	SO:0001819	synonymous_variant	6329	exon14			CTTCTCATCCTCG	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.2631T>C	17.37:g.62029006A>G		305	1	0.00327869		332	155	0.466867	NM_000334	Q15478|Q16447|Q7Z6B1	Silent	SNP	ENST00000435607.1	37	CCDS45761.1																																																																																			A|0.936;G|0.064	0.064	strong		0.657	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		G	62029006	A	G	62029006	2	3	22	1	0	0	0	0	0	0	0	1	13935	214	8	3		3	SCN4A	17	62029006	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	10269	62029006	19166204	3580	6481											
ERN1	2081	hgsc.bcm.edu	37	chr17	62137893	62137893	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cccgatgtttgggtagattgTtgggaaatctctccagcatc	8	13	11	9	1	1	1	0	0	1	1	4	3	2	2	2	2	1	4	2	2	2	4	rs79107850	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:62137893T>C	ENST00000433197.3	-	11	1237	c.1142A>G	c.(1141-1143)aAc>aGc	p.N381S		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						GGGTAGATTGTTGGGAAATCT	0.473													T|||	33	0.00658946	0.0234	0.0029	5008	,	,		21401	0.0		0.0	False		,,,				2504	0.0				p.N381S		Atlas-SNP	.											.	ERN1	102	.	0			c.A1142G						PASS	.	T	SER/ASN	60,3790		1,58,1866	164	158	160		1142	5.3	1	17	dbSNP_131	160	0,8276		0,0,4138	yes	missense	ERN1	NM_001433.3	46	1,58,6004	CC,CT,TT		0.0,1.5584,0.4948	benign	381/978	62137893	60,12066	1925	4138	6063	SO:0001583	missense	2081	exon11			AGATTGTTGGGAA	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.1142A>G	17.37:g.62137893T>C	ENSP00000401445:p.Asn381Ser	135	0	0		150	64	0.426667	NM_001433		Missense_Mutation	SNP	ENST00000433197.3	37	CCDS45762.1	17	0.007783882783882784	15	0.03048780487804878	2	0.0055248618784530384	0	0.0	0	0.0	T	8.605	0.887770	0.17540	0.015584	0.0	ENSG00000178607	ENST00000433197	T	0.58060	0.36	5.33	5.33	0.75918	.	0.150729	0.64402	D	0.000013	T	0.11110	0.0271	N	0.14661	0.345	0.30788	N	0.741199	B	0.06786	0.001	B	0.01281	0.0	T	0.16158	-1.0412	10	0.07175	T	0.84	-44.0147	8.0501	0.30572	0.0:0.1225:0.0:0.8775	.	381	O75460	ERN1_HUMAN	S	381	ENSP00000401445:N381S	ENSP00000401445:N381S	N	-	2	0	ERN1	59491625	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.120000	0.57897	2.008000	0.58898	0.379000	0.24179	AAC	T|0.990;C|0.010	0.010	strong		0.473	ERN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443734.2	NM_001433		C	62137893	T	C	62137893	3	2	22	1	0	0	0	0	1	0	0	0	5239	1725	60	3	1839	3	ERN1	17	62137893	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	108887	62137893	19057317	3581	6482											
ERN1	2081	hgsc.bcm.edu	37	chr17	62149423	62149423	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaagtctgctgcttctctccGgtcaggaggtcaataacata	11	11	9	10	1	4	0	2	0	2	0	6	1	5	1	1	3	3	2	1	3	4	3	rs374999844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:62149423G>A	ENST00000433197.3	-	6	491	c.396C>T	c.(394-396)acC>acT	p.T132T	ERN1_ENST00000577567.1_5'UTR	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						GCTTCTCTCCGGTCAGGAGGT	0.448													G|||	2	0.000399361	0.0015	0.0	5008	,	,		20164	0.0		0.0	False		,,,				2504	0.0				p.T132T		Atlas-SNP	.											.	ERN1	102	.	0			c.C396T						PASS	.	G		5,3827		0,5,1911	51	50	51		396	-2.8	1	17		51	1,8269		0,1,4134	no	coding-synonymous	ERN1	NM_001433.3		0,6,6045	AA,AG,GG		0.0121,0.1305,0.0496		132/978	62149423	6,12096	1916	4135	6051	SO:0001819	synonymous_variant	2081	exon6			CTCTCCGGTCAGG	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.396C>T	17.37:g.62149423G>A		72	0	0		64	29	0.453125	NM_001433		Silent	SNP	ENST00000433197.3	37	CCDS45762.1																																																																																			.	.	weak		0.448	ERN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443734.2	NM_001433		A	62149423	G	A	62149423	2	1	22	1	0	0	0	0	0	0	0	1	5239	1103	39	1		1	ERN1	17	62149423	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	11530	62149423	19045787	3582	6483											
DDX5	1655	hgsc.bcm.edu	37	chr17	62499163	62499163	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcaggaaatcttcagcaagCtgtcttacttcttttggcca	9	15	7	10	0	5	0	2	0	3	0	5	1	5	1	1	2	3	2	1	2	3	6	rs56025355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:62499163C>T	ENST00000225792.5	-	8	1265	c.864G>A	c.(862-864)caG>caA	p.Q288Q	DDX5_ENST00000580026.1_5'Flank|MIR3064_ENST00000581130.1_RNA|DDX5_ENST00000450599.2_Silent_p.Q209Q|MIR5047_ENST00000579212.1_RNA|DDX5_ENST00000578804.1_Silent_p.Q288Q	NM_004396.3	NP_004387.1	P17844	DDX5_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 5	288	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				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)			CTTCAGCAAGCTGTCTTACTT	0.398			T	ETV4	prostate								C|||	19	0.00379393	0.0015	0.0029	5008	,	,		20101	0.0		0.0149	False		,,,				2504	0.0				p.Q288Q	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.G864A						PASS	.	C		10,4396	16.8+/-37.8	0,10,2193	180	174	176		864	3.9	1	17	dbSNP_129	176	83,8517	48.9+/-108.6	0,83,4217	no	coding-synonymous	DDX5	NM_004396.3		0,93,6410	TT,TC,CC		0.9651,0.227,0.7151		288/615	62499163	93,12913	2203	4300	6503	SO:0001819	synonymous_variant	1655	exon8			AGCAAGCTGTCTT	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.864G>A	17.37:g.62499163C>T		153	0	0		169	68	0.402367	NM_004396	B4DLW8|B5BU21|D3DU32|E7ETL9|O75681|Q53Y61	Silent	SNP	ENST00000225792.5	37	CCDS11659.1																																																																																			C|0.993;T|0.007	0.007	strong		0.398	DDX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444030.1	NM_004396		T	62499163	C	T	62499163	2	4	22	1	0	0	0	0	0	0	0	1	4369	796	28	2		2	DDX5	17	62499163	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	349740	62499163	18696047	3583	6484											
SMURF2	64750	hgsc.bcm.edu	37	chr17	62567987	62567987	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gttctgttgttatggtcaacGaaataaactctgcctgttgc	9	15	9	8	1	3	0	1	0	2	0	3	1	3	0	1	1	4	4	1	1	5	5	rs34788315	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:62567987G>A	ENST00000262435.9	-	10	1132	c.945C>T	c.(943-945)ttC>ttT	p.F315F	SMURF2_ENST00000578200.1_Intron	NM_022739.3	NP_073576.1	Q9HAU4	SMUF2_HUMAN	SMAD specific E3 ubiquitin protein ligase 2	315	WW 3. {ECO:0000255|PROSITE- ProRule:PRU00224}.				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)			TATGGTCAACGAAATAAACTC	0.383													G|||	160	0.0319489	0.115	0.0115	5008	,	,		17923	0.0		0.0	False		,,,				2504	0.0				p.F315F		Atlas-SNP	.											.	SMURF2	63	.	0			c.C945T						PASS	.	G		414,3992	204.1+/-226.4	13,388,1802	118	106	110		945	0.8	1	17	dbSNP_126	110	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SMURF2	NM_022739.3		13,390,6100	AA,AG,GG		0.0233,9.3963,3.1985		315/749	62567987	416,12590	2203	4300	6503	SO:0001819	synonymous_variant	64750	exon10			GTCAACGAAATAA	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.945C>T	17.37:g.62567987G>A		205	0	0		182	92	0.505495	NM_022739	Q52LL1|Q9H260	Silent	SNP	ENST00000262435.9	37	CCDS32707.1																																																																																			G|0.964;A|0.036	0.036	strong		0.383	SMURF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445227.1	NM_022739		A	62567987	G	A	62567987	2	1	22	1	0	0	0	0	0	0	0	1	14835	1049	37	1		1	SMURF2	17	62567987	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	68824	62567987	18627223	3584	6485											
GNA13	10672	hgsc.bcm.edu	37	chr17	63049709	63049709	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aggaagatattgtaagaaaaCccttgtttccaccattcctt	13	13	6	9	0	0	2	0	0	0	2	2	3	2	3	4	1	1	2	4	1	5	7	rs116700192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:63049709C>T	ENST00000439174.2	-	2	666	c.421G>A	c.(421-423)Gtt>Att	p.V141I	RP11-583F2.5_ENST00000581796.1_RNA|GNA13_ENST00000541118.1_Missense_Mutation_p.V46I	NM_006572.4	NP_006563.2	Q14344	GNA13_HUMAN	guanine nucleotide binding protein (G protein), alpha 13	141					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						TGTAAGAAAACCCTTGTTTCC	0.468													C|||	55	0.0109824	0.0408	0.0014	5008	,	,		16418	0.0		0.0	False		,,,				2504	0.0				p.V141I		Atlas-SNP	.											.	GNA13	69	.	0			c.G421A						PASS	.	C	ILE/VAL	193,4213	121.3+/-158.8	4,185,2014	126	127	127		421	3.4	0	17	dbSNP_132	127	1,8599	1.2+/-3.3	0,1,4299	yes	missense	GNA13	NM_006572.4	29	4,186,6313	TT,TC,CC		0.0116,4.3804,1.4916	benign	141/378	63049709	194,12812	2203	4300	6503	SO:0001583	missense	10672	exon2			AGAAAACCCTTGT	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.421G>A	17.37:g.63049709C>T	ENSP00000400717:p.Val141Ile	104	0	0		105	102	0.971429	NM_006572	B2R977|B7Z7R0|F5H1G8|Q8TD70	Missense_Mutation	SNP	ENST00000439174.2	37	CCDS11661.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	C	13.82	2.351213	0.41700	0.043804	1.16E-4	ENSG00000120063	ENST00000439174;ENST00000541118;ENST00000239138	D;D	0.88818	-2.43;-2.43	5.42	3.44	0.39384	G protein alpha subunit, helical insertion (2);	0.125987	0.30630	N	0.009208	T	0.54431	0.1858	L	0.45470	1.425	0.34370	D	0.691943	B	0.27594	0.182	B	0.31337	0.128	T	0.75269	-0.3377	10	0.37606	T	0.19	.	11.6014	0.51006	0.0:0.8574:0.0:0.1426	.	141	Q14344	GNA13_HUMAN	I	141;46;116	ENSP00000400717:V141I;ENSP00000439647:V46I	ENSP00000239138:V116I	V	-	1	0	GNA13	60480171	0.972000	0.33761	0.014000	0.15608	0.975000	0.68041	2.447000	0.44917	0.664000	0.31047	0.655000	0.94253	GTT	C|0.988;T|0.012	0.012	strong		0.468	GNA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445720.1	NM_006572		T	63049709	C	T	63049709	3	4	22	1	0	0	0	0	1	0	0	0	6509	507	18	2	724	2	GNA13	17	63049709	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	481722	63049709	18145501	3585	6486											
RGS9	8787	hgsc.bcm.edu	37	chr17	63221136	63221136	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagccgggccagcacatggCtcccagcccccatctgaccg	8	4	10	19	2	1	1	0	1	1	0	2	1	2	1	6	2	3	2	6	2	0	0	rs116395890	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:63221136C>T	ENST00000262406.9	+	18	1491	c.1424C>T	c.(1423-1425)gCt>gTt	p.A475V	RGS9_ENST00000449996.3_Missense_Mutation_p.A472V|RGS9_ENST00000443584.3_Missense_Mutation_p.A472V	NM_003835.3	NP_003826.2	O75916	RGS9_HUMAN	regulator of G-protein signaling 9	475					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						CAGCACATGGCTCCCAGCCCC	0.642													C|||	27	0.00539137	0.0197	0.0014	5008	,	,		17870	0.0		0.0	False		,,,				2504	0.0				p.A475V		Atlas-SNP	.											.	RGS9	82	.	0			c.C1424T						PASS	.	C	VAL/ALA,VAL/ALA	66,4064		0,66,1999	96	112	107		1415,1424	3.6	0	17	dbSNP_132	107	0,8416		0,0,4208	yes	missense,missense	RGS9	NM_001081955.2,NM_003835.3	64,64	0,66,6207	TT,TC,CC		0.0,1.5981,0.5261	possibly-damaging,possibly-damaging	472/672,475/675	63221136	66,12480	2065	4208	6273	SO:0001583	missense	8787	exon18			ACATGGCTCCCAG	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.1424C>T	17.37:g.63221136C>T	ENSP00000262406:p.Ala475Val	95	0	0		96	49	0.510417	NM_003835	A8K3C0|O75573|Q696R2|Q8TD64|Q8TD65|Q9HC32|Q9HC33	Missense_Mutation	SNP	ENST00000262406.9	37	CCDS42373.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	C	14.11	2.437293	0.43224	0.015981	0.0	ENSG00000108370	ENST00000262406;ENST00000449996	T;T	0.33216	1.42;1.42	4.56	3.58	0.41010	.	0.420099	0.26742	N	0.022729	T	0.09379	0.0231	N	0.19112	0.55	0.09310	N	1	B;B;B	0.31548	0.099;0.22;0.328	B;B;B	0.24394	0.025;0.024;0.053	T	0.17623	-1.0363	10	0.62326	D	0.03	.	12.4444	0.55643	0.0:0.915:0.0:0.085	.	475;475;472	A8K1G1;O75916;O75916-5	.;RGS9_HUMAN;.	V	475;472	ENSP00000262406:A475V;ENSP00000396329:A472V	ENSP00000262406:A475V	A	+	2	0	RGS9	60651598	0.176000	0.23096	0.018000	0.16275	0.782000	0.44232	2.127000	0.42035	2.450000	0.82876	0.561000	0.74099	GCT	C|0.994;T|0.006	0.006	strong		0.642	RGS9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445885.1	NM_003835		T	63221136	C	T	63221136	3	4	22	1	0	0	0	0	1	0	0	0	13328	797	28	2	1549	2	RGS9	17	63221136	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	171427	63221136	17974074	3586	6487											
APOH	350	hgsc.bcm.edu	37	chr17	64216797	64216797	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gatagagggaattgtttccaGctgatggcttataaacacga	13	11	11	6	1	0	2	0	1	0	1	1	5	1	3	1	2	2	3	1	2	5	5	rs114459902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:64216797G>T	ENST00000205948.6	-	5	516	c.479C>A	c.(478-480)gCt>gAt	p.A160D		NM_000042.2	NP_000033.2	P02749	APOH_HUMAN	apolipoprotein H (beta-2-glycoprotein I)	160	Sushi 3. {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)			ATTGTTTCCAGCTGATGGCTT	0.408													G|||	29	0.00579073	0.0212	0.0014	5008	,	,		19051	0.0		0.0	False		,,,				2504	0.0				p.A160D	Melanoma(155;624 1882 16869 48804 51309)	Atlas-SNP	.											.	APOH	45	.	0			c.C479A						PASS	.	G	ASP/ALA	83,4323	70.3+/-108.2	0,83,2120	127	123	124		479	0.9	0	17	dbSNP_133	124	0,8600		0,0,4300	yes	missense	APOH	NM_000042.2	126	0,83,6420	TT,TG,GG		0.0,1.8838,0.6382	benign	160/346	64216797	83,12923	2203	4300	6503	SO:0001583	missense	350	exon5			TTTCCAGCTGATG		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.479C>A	17.37:g.64216797G>T	ENSP00000205948:p.Ala160Asp	156	0	0		147	57	0.387755	NM_000042	B2R9M3|Q9UCN7	Missense_Mutation	SNP	ENST00000205948.6	37	CCDS11663.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	g	4.559	0.103783	0.08731	0.018838	0.0	ENSG00000091583	ENST00000205948	T	0.30448	1.53	5.2	0.92	0.19397	Complement control module (2);Sushi/SCR/CCP (3);	0.940200	0.09067	N	0.853424	T	0.11665	0.0284	L	0.53729	1.69	0.09310	N	0.999999	B	0.29378	0.243	B	0.22601	0.04	T	0.25398	-1.0133	10	0.15066	T	0.55	.	4.9343	0.13932	0.3059:0.0:0.5587:0.1354	.	160	P02749	APOH_HUMAN	D	160	ENSP00000205948:A160D	ENSP00000205948:A160D	A	-	2	0	APOH	61647259	0.000000	0.05858	0.013000	0.15412	0.335000	0.28730	-0.346000	0.07760	0.036000	0.15547	-0.271000	0.10264	GCT	G|0.993;T|0.007	0.007	strong		0.408	APOH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446926.1	NM_000042		T	64216797	G	T	64216797	3	4	22	1	0	0	0	0	1	0	0	0	804	971	34	4	574	4	APOH	17	64216797	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	995661	64216797	16978413	3587	6488											
NOL11	25926	hgsc.bcm.edu	37	chr17	65735054	65735054	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctttagtcctaagtaatgcAattcttcattcagcatatag	12	15	5	9	0	3	0	2	0	1	0	4	0	4	0	2	0	2	3	2	0	6	9	rs151002760	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:65735054A>G	ENST00000253247.4	+	15	1885	c.1770A>G	c.(1768-1770)gcA>gcG	p.A590A	SNORA38B_ENST00000363524.1_RNA|NOL11_ENST00000535137.1_Silent_p.A408A	NM_015462.3	NP_056277.2	Q9H8H0	NOL11_HUMAN	nucleolar protein 11	590					maturation of SSU-rRNA (GO:0030490)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|t-UTP complex (GO:0034455)	poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	11	all_cancers(12;1.54e-10)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0518)|COAD - Colon adenocarcinoma(4;0.0977)|LUSC - Lung squamous cell carcinoma(166;0.24)			TAAGTAATGCAATTCTTCATT	0.333													A|||	6	0.00119808	0.0045	0.0	5008	,	,		19461	0.0		0.0	False		,,,				2504	0.0				p.A590A		Atlas-SNP	.											.	NOL11	48	.	0			c.A1770G						PASS	.	A		45,4361	48.2+/-83.0	0,45,2158	165	150	155		1770	3.9	1	17	dbSNP_134	155	0,8600		0,0,4300	no	coding-synonymous	NOL11	NM_015462.3		0,45,6458	GG,GA,AA		0.0,1.0213,0.346		590/720	65735054	45,12961	2203	4300	6503	SO:0001819	synonymous_variant	25926	exon15			TAATGCAATTCTT	AK023702	CCDS11671.1	17q24.2	2005-08-08							24557	protein-coding gene	gene with protein product		615366				12477932	Standard	NM_015462		Approved	DKFZP586L0724	uc002jgd.1	Q9H8H0		ENST00000253247.4:c.1770A>G	17.37:g.65735054A>G		103	0	0		117	53	0.452991	NM_015462	B7Z5V9|Q7L5S1|Q9UG18	Silent	SNP	ENST00000253247.4	37	CCDS11671.1																																																																																			A|0.997;G|0.003	0.003	strong		0.333	NOL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448074.1	NM_015462		G	65735054	A	G	65735054	2	3	22	1	0	0	0	0	0	0	0	1	10530	117	5	3		3	NOL11	17	65735054	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1518257	65735054	15460156	3588	6489											
BPTF	2186	hgsc.bcm.edu	37	chr17	65914911	65914911	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcaagtttgagatgggatgaTatggcggccaaggctcctcc	9	9	14	9	1	0	2	0	2	0	1	2	4	2	3	3	4	0	3	3	4	3	2	rs80201495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:65914911T>C	ENST00000321892.4	+	14	5824	c.5763T>C	c.(5761-5763)gaT>gaC	p.D1921D	BPTF_ENST00000424123.3_Silent_p.D1782D|BPTF_ENST00000335221.5_Silent_p.D1921D|BPTF_ENST00000306378.6_Silent_p.D1795D			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	1921					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)			GATGGGATGATATGGCGGCCA	0.458													C|||	95	0.0189696	0.0666	0.0086	5008	,	,		16414	0.0		0.001	False		,,,				2504	0.0				p.D1921D		Atlas-SNP	.											.	BPTF	415	.	0			c.T5763C						PASS	.	C	,	247,4159	804.1+/-415.7	7,233,1963	149	145	147		5763,5385	3.2	1	17	dbSNP_131	147	8,8592	818.9+/-406.8	0,8,4292	no	coding-synonymous,coding-synonymous	BPTF	NM_004459.6,NM_182641.3	,	7,241,6255	CC,CT,TT		0.093,5.606,1.9606	,	1921/2904,1795/2921	65914911	255,12751	2203	4300	6503	SO:0001819	synonymous_variant	2186	exon14			GGATGATATGGCG	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.5763T>C	17.37:g.65914911T>C		153	0	0		148	76	0.513514	NM_004459	Q6NX67|Q7Z7D6|Q9UIG2	Silent	SNP	ENST00000321892.4	37																																																																																				T|0.981;C|0.019	0.019	strong		0.458	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		C	65914911	T	C	65914911	2	2	22	1	0	0	0	0	0	0	0	1	1497	1403	49	3		3	BPTF	17	65914911	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	179857	65914911	15280299	3589	6490											
BPTF	2186	hgsc.bcm.edu	37	chr17	65919092	65919092	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctggaattgtgggagatcagGgcatttgctgagaggtaagg	10	10	17	4	0	1	2	1	1	0	2	1	5	1	3	0	5	1	3	0	5	2	3	rs59088743	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:65919092G>A	ENST00000321892.4	+	16	6133	c.6072G>A	c.(6070-6072)agG>agA	p.R2024R	BPTF_ENST00000424123.3_Silent_p.R1885R|BPTF_ENST00000335221.5_Silent_p.R2024R|BPTF_ENST00000306378.6_Silent_p.R1898R			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2024					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)			GGGAGATCAGGGCATTTGCTG	0.398													G|||	95	0.0189696	0.0666	0.0086	5008	,	,		18950	0.0		0.001	False		,,,				2504	0.0				p.R2024R		Atlas-SNP	.											.	BPTF	415	.	0			c.G6072A						PASS	.	G	,	247,4159	143.1+/-178.2	7,233,1963	144	139	141		6072,5694	3.8	1	17	dbSNP_129	141	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous,coding-synonymous	BPTF	NM_004459.6,NM_182641.3	,	7,241,6255	AA,AG,GG		0.093,5.606,1.9606	,	2024/2904,1898/2921	65919092	255,12751	2203	4300	6503	SO:0001819	synonymous_variant	2186	exon16			GATCAGGGCATTT	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.6072G>A	17.37:g.65919092G>A		107	0	0		138	59	0.427536	NM_004459	Q6NX67|Q7Z7D6|Q9UIG2	Silent	SNP	ENST00000321892.4	37																																																																																				G|0.981;A|0.019	0.019	strong		0.398	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459		A	65919092	G	A	65919092	2	1	22	1	0	0	0	0	0	0	0	1	1497	1223	43	2		2	BPTF	17	65919092	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4181	65919092	15276118	3590	6491											
SLC16A6	9120	hgsc.bcm.edu	37	chr17	66267734	66267734	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagatgacaatgtttaactgTagtaggcccacgaagaggag	15	8	12	6	1	0	3	0	1	0	2	0	5	0	4	1	2	1	3	1	2	6	4	rs61740584	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:66267734T>C	ENST00000327268.4	-	6	731	c.567A>G	c.(565-567)ctA>ctG	p.L189L	SLC16A6_ENST00000580666.1_Silent_p.L189L|ARSG_ENST00000448504.2_Intron	NM_001174166.1	NP_001167637.1	O15403	MOT7_HUMAN	solute carrier family 16, member 6	189					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)	TGTTTAACTGTAGTAGGCCCA	0.473													T|||	118	0.0235623	0.087	0.0043	5008	,	,		18475	0.0		0.0	False		,,,				2504	0.0				p.L189L		Atlas-SNP	.											.	SLC16A6	56	.	0			c.A567G						PASS	.	T	,,	400,4006	199.1+/-222.7	18,364,1821	76	73	74		567,567,	-2.4	0.3	17	dbSNP_129	74	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,intron	SLC16A6,ARSG	NM_001174166.1,NM_004694.4,NM_014960.3	,,	18,365,6120	CC,CT,TT		0.0116,9.0785,3.0832	,,	189/524,189/524,	66267734	401,12605	2203	4300	6503	SO:0001819	synonymous_variant	9120	exon6			TAACTGTAGTAGG	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.567A>G	17.37:g.66267734T>C		134	0	0		119	54	0.453782	NM_001174166	Q6P1X3	Silent	SNP	ENST00000327268.4	37	CCDS11675.1																																																																																			T|0.969;C|0.031	0.031	strong		0.473	SLC16A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448323.1	NM_004694		C	66267734	T	C	66267734	2	2	22	1	0	0	0	0	0	0	0	1	14427	1625	57	3		3	SLC16A6	17	66267734	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	348642	66267734	14927476	3591	6492											
ARSG	22901	hgsc.bcm.edu	37	chr17	66397521	66397521	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgctgttccaccccaacagCggggcagctggagagtttgg	7	8	15	11	1	0	1	0	0	0	1	1	2	1	1	3	4	4	5	3	4	1	2	rs62638719	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:66397521C>T	ENST00000448504.2	+	11	2029	c.1233C>T	c.(1231-1233)agC>agT	p.S411S	ARSG_ENST00000452479.2_Silent_p.S247S|ARSG_ENST00000582154.1_3'UTR	NM_014960.4	NP_055775.2	Q96EG1	ARSG_HUMAN	arylsulfatase G	411					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)			ACCCCAACAGCGGGGCAGCTG	0.557													C|||	11	0.00219649	0.0083	0.0	5008	,	,		19346	0.0		0.0	False		,,,				2504	0.0				p.S411S		Atlas-SNP	.											ARSG,NS,carcinoma,+1,1	ARSG	55	1	0			c.C1233T						PASS	.	C		65,4341	60.5+/-97.4	0,65,2138	90	90	90		1233	-10	0.1	17	dbSNP_129	90	0,8600		0,0,4300	no	coding-synonymous	ARSG	NM_014960.3		0,65,6438	TT,TC,CC		0.0,1.4753,0.4998		411/526	66397521	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	22901	exon11			CAACAGCGGGGCA	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.1233C>T	17.37:g.66397521C>T		124	0	0		173	105	0.606936	NM_001267727	Q6UXF2|Q9Y2K4	Silent	SNP	ENST00000448504.2	37	CCDS11676.1																																																																																			C|0.996;T|0.004	0.004	strong		0.557	ARSG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448369.1	NM_014960		T	66397521	C	T	66397521	2	4	22	1	0	0	0	0	0	0	0	1	992	767	27	1		1	ARSG	17	66397521	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	129787	66397521	14797689	3592	6493											
ARSG	22901	hgsc.bcm.edu	37	chr17	66416511	66416511	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtcctccaagacattgccaaCgacaacatctccagcgcaga	13	6	7	15	2	1	2	0	0	1	2	4	3	3	2	4	0	4	1	4	0	3	1	rs35268505	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:66416511C>T	ENST00000448504.2	+	12	2281	c.1485C>T	c.(1483-1485)aaC>aaT	p.N495N	WIPI1_ENST00000589459.1_5'Flank|ARSG_ENST00000452479.2_Silent_p.N331N|ARSG_ENST00000582154.1_3'UTR|RP11-120M18.2_ENST00000592030.1_RNA	NM_014960.4	NP_055775.2	Q96EG1	ARSG_HUMAN	arylsulfatase G	495					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)			ACATTGCCAACGACAACATCT	0.552													C|||	79	0.0157748	0.0575	0.0043	5008	,	,		20902	0.0		0.0	False		,,,				2504	0.0				p.N495N		Atlas-SNP	.											.	ARSG	55	.	0			c.C1485T						PASS	.	C		231,4175	136.5+/-172.5	2,227,1974	189	180	183		1485	-11.8	0	17	dbSNP_126	183	0,8600		0,0,4300	no	coding-synonymous	ARSG	NM_014960.3		2,227,6274	TT,TC,CC		0.0,5.2429,1.7761		495/526	66416511	231,12775	2203	4300	6503	SO:0001819	synonymous_variant	22901	exon12			TGCCAACGACAAC	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.1485C>T	17.37:g.66416511C>T		238	0	0		240	125	0.520833	NM_001267727	Q6UXF2|Q9Y2K4	Silent	SNP	ENST00000448504.2	37	CCDS11676.1																																																																																			C|0.981;T|0.019	0.019	strong		0.552	ARSG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448369.1	NM_014960		T	66416511	C	T	66416511	2	4	22	1	0	0	0	0	0	0	0	1	992	535	19	1		1	ARSG	17	66416511	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	18990	66416511	14778699	3593	6494											
ABCA8	10351	hgsc.bcm.edu	37	chr17	66928460	66928460	+	Missense_Mutation	SNP	T	T	C																															atcccgaagacccatcattgTcatcaaggccttcatccttt																								rs16973446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:66928460T>C	ENST00000269080.2	-	6	903	c.766A>G	c.(766-768)Aca>Gca	p.T256A	ABCA8_ENST00000586539.1_Missense_Mutation_p.T256A|ABCA8_ENST00000430352.2_Missense_Mutation_p.T256A	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	256			T -> A (in dbSNP:rs16973446).		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)					CCCATCATTGTCATCAAGGCC	0.393													T|||	383	0.0764776	0.2738	0.0231	5008	,	,		20528	0.0		0.005	False		,,,				2504	0.0				p.T256A		Atlas-SNP	.											.	ABCA8	213	.	0			c.A766G						PASS	.	T	ALA/THR	1058,3348	384.9+/-325.5	129,800,1274	86	79	81		766	2.6	0.5	17	dbSNP_123	81	17,8583	12.6+/-44.7	0,17,4283	yes	missense	ABCA8	NM_007168.2	58	129,817,5557	CC,CT,TT		0.1977,24.0127,8.2654	benign	256/1582	66928460	1075,11931	2203	4300	6503	SO:0001583	missense	10351	exon6			TCATTGTCATCAA	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.766A>G	17.37:g.66928460T>C	ENSP00000269080:p.Thr256Ala	76	0	0		91	40	0.43956	NM_007168	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	37	CCDS11680.1	140	0.0641025641025641	128	0.2601626016260163	10	0.027624309392265192	0	0.0	2	0.002638522427440633	T	9.995	1.231776	0.22626	0.240127	0.001977	ENSG00000141338	ENST00000269080;ENST00000430352;ENST00000541225;ENST00000428549	D;D	0.82344	-1.6;-1.6	4.85	2.63	0.31362	.	1.596760	0.03628	N	0.237455	T	0.00039	0.0001	N	0.26130	0.795	0.47407	P	5.819999999999714E-4	B;B;B;B;B	0.22146	0.065;0.02;0.036;0.003;0.02	B;B;B;B;B	0.21360	0.03;0.02;0.021;0.012;0.034	T	0.04041	-1.0982	9	0.42905	T	0.14	.	6.2716	0.20956	0.0:0.1989:0.0:0.8011	rs16973446;rs16973446	195;256;256;256;256	F5H6Z4;A1L3U3;B4DJ11;C9JQE6;O94911	.;.;.;.;ABCA8_HUMAN	A	256;256;195;256	ENSP00000269080:T256A;ENSP00000402814:T256A	ENSP00000269080:T256A	T	-	1	0	ABCA8	64440055	0.856000	0.29760	0.510000	0.27712	0.553000	0.35397	1.060000	0.30530	0.444000	0.26612	-0.385000	0.06624	ACA	T|0.915;C|0.085	0.085	strong		0.393	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		C	66928460	T	C	66928460	3	2	22	1	0	0	0	0	1	0	0	0	38	1667	58	3	4111	3	ABCA8	17	66928460	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	511949	66928460	14266750	3594	6495	80	3									
ABCA8	10351	hgsc.bcm.edu	37	chr17	66928468	66928468	+	Missense_Mutation	SNP	G	G	C																															gacccatcattgtcatcaagGccttcatccttttcctctct																								rs62638729|rs386798698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:66928468G>C	ENST00000269080.2	-	6	895	c.758C>G	c.(757-759)gCc>gGc	p.A253G	ABCA8_ENST00000586539.1_Missense_Mutation_p.A253G|ABCA8_ENST00000430352.2_Missense_Mutation_p.A253G	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	253					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)					TGTCATCAAGGCCTTCATCCT	0.388													C|||	380	0.0758786	0.2716	0.0231	5008	,	,		20420	0.0		0.005	False		,,,				2504	0.0				p.A253G		Atlas-SNP	.											.	ABCA8	213	.	0			c.C758G						PASS	.						89	81	84					17																	66928468		2203	4300	6503	SO:0001583	missense	10351	exon6			ATCAAGGCCTTCA	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.758C>G	17.37:g.66928468G>C	ENSP00000269080:p.Ala253Gly	80	0	0		99	46	0.464646	NM_007168	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	37	CCDS11680.1	132	0.06043956043956044	120	0.24390243902439024	10	0.027624309392265192	0	0.0	2	0.002638522427440633	C	5.598	0.295055	0.10622	.	.	ENSG00000141338	ENST00000269080;ENST00000430352;ENST00000541225;ENST00000428549	D;D	0.87571	-2.27;-2.27	4.85	-0.973	0.10297	.	0.589518	0.15272	N	0.271169	T	0.00039	0.0001	N	0.00483	-1.445	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	0.18398	-1.0338	10	0.52906	T	0.07	.	6.2111	0.20630	0.1354:0.2547:0.5285:0.0813	rs62638729	192;253;253;253;253	F5H6Z4;A1L3U3;B4DJ11;C9JQE6;O94911	.;.;.;.;ABCA8_HUMAN	G	253;253;192;253	ENSP00000269080:A253G;ENSP00000402814:A253G	ENSP00000269080:A253G	A	-	2	0	ABCA8	64440063	0.000000	0.05858	0.000000	0.03702	0.505000	0.33919	-0.762000	0.04745	-0.174000	0.10743	-0.224000	0.12420	GCC	G|0.945;C|0.055	0.055	strong		0.388	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		C	66928468	G	C	66928468	3	2	22	1	0	0	0	0	1	0	0	0	38	1203	42	4	4119	4	ABCA8	17	66928468	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	8	66928468	14266742	3595	6496	80	3									
ABCA8	10351	hgsc.bcm.edu	37	chr17	66928470	66928470	+	Silent	SNP	C	C	T																															cccatcattgtcatcaaggcCttcatccttttcctctctct																								rs28385895|rs386798698|rs202032826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:66928470C>T	ENST00000269080.2	-	6	893	c.756G>A	c.(754-756)aaG>aaA	p.K252K	ABCA8_ENST00000586539.1_Silent_p.K252K|ABCA8_ENST00000430352.2_Silent_p.K252K	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	252					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)					TCATCAAGGCCTTCATCCTTT	0.393													C|||	383	0.0764776	0.2738	0.0231	5008	,	,		20456	0.0		0.005	False		,,,				2504	0.0				p.K252K		Atlas-SNP	.											.	ABCA8	213	.	0			c.G756A						PASS	.																																			SO:0001819	synonymous_variant	10351	exon6			CAAGGCCTTCATC	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.756G>A	17.37:g.66928470C>T		80	0	0		102	48	0.470588	NM_007168	A1L3U3|C9JQE6|Q86WW0	Silent	SNP	ENST00000269080.2	37	CCDS11680.1																																																																																			C|0.959;T|0.041	0.041	strong		0.393	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168		T	66928470	C	T	66928470	2	4	22	1	0	0	0	0	0	0	0	1	38	680	24	2		2	ABCA8	17	66928470	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2	66928470	14266740	3596	6497	80	3									
ABCA9	10350	hgsc.bcm.edu	37	chr17	67031882	67031882	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atttgtgcagattttacaatAagagccattaaagtggccat	14	13	8	6	0	0	2	0	0	0	2	0	2	0	2	2	1	3	1	2	1	5	5	rs16973534	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:67031882A>G	ENST00000340001.4	-	7	1072	c.861T>C	c.(859-861)ctT>ctC	p.L287L	ABCA9_ENST00000453985.2_Silent_p.L287L|ABCA9_ENST00000370732.2_Silent_p.L287L	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	287					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)					ATTTTACAATAAGAGCCATTA	0.423													A|||	141	0.028155	0.1036	0.0058	5008	,	,		16263	0.0		0.0	False		,,,				2504	0.0				p.L287L		Atlas-SNP	.											.	ABCA9	192	.	0			c.T861C						PASS	.	A		442,3964	213.8+/-233.3	27,388,1788	71	67	68		861	-1.6	0	17	dbSNP_123	68	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	ABCA9	NM_080283.3		27,391,6085	GG,GA,AA		0.0349,10.0318,3.4215		287/1625	67031882	445,12561	2203	4300	6503	SO:0001819	synonymous_variant	10350	exon7			TACAATAAGAGCC	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.861T>C	17.37:g.67031882A>G		435	0	0		430	196	0.455814	NM_080283	Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Silent	SNP	ENST00000340001.4	37	CCDS11681.1																																																																																			A|0.970;G|0.030	0.030	strong		0.423	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386		G	67031882	A	G	67031882	2	3	22	1	0	0	0	0	0	0	0	1	39	349	13	3		3	ABCA9	17	67031882	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	103412	67031882	14163328	3597	6498											
ABCA6	23460	hgsc.bcm.edu	37	chr17	67109493	67109493	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccagtagttggttcatctaaAagcaaaatctacagagaatg	16	10	8	7	0	3	1	1	0	2	1	3	2	3	1	1	1	2	4	1	1	7	5	rs2058128	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:67109493A>G	ENST00000284425.2	-	15	2085	c.1911T>C	c.(1909-1911)ctT>ctC	p.L637L		NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	637	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)					GTTCATCTAAAAGCAAAATCT	0.363													G|||	631	0.125998	0.4531	0.0447	5008	,	,		20176	0.0		0.001	False		,,,				2504	0.0				p.L637L		Atlas-SNP	.											.	ABCA6	210	.	0			c.T1911C						PASS	.	G		1650,2756	653.9+/-399.7	293,1064,846	57	56	57		1911	-4	0.7	17	dbSNP_94	57	11,8587	817.7+/-406.9	0,11,4288	no	coding-synonymous	ABCA6	NM_080284.2		293,1075,5134	GG,GA,AA		0.1279,37.4489,12.773		637/1618	67109493	1661,11343	2203	4299	6502	SO:0001819	synonymous_variant	23460	exon15			ATCTAAAAGCAAA	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.1911T>C	17.37:g.67109493A>G		53	0	0		64	30	0.46875	NM_080284	Q6NSH9|Q8N856|Q8WWZ6	Silent	SNP	ENST00000284425.2	37	CCDS11683.1																																																																																			A|0.876;G|0.124	0.124	strong		0.363	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284		G	67109493	A	G	67109493	2	3	22	1	0	0	0	0	0	0	0	1	36	1	1	3		3	ABCA6	17	67109493	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	77611	67109493	14085717	3598	6499											
SLC39A11	201266	hgsc.bcm.edu	37	chr17	70645366	70645366	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	agggaaggctgacagccaggCcctcggggaaattctggatc	10	6	15	10	1	1	1	0	1	1	0	3	4	1	4	2	6	1	1	2	6	2	1	rs115567758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:70645366C>G	ENST00000542342.2	-	8	822	c.734G>C	c.(733-735)gGc>gCc	p.G245A	SLC39A11_ENST00000255559.3_Missense_Mutation_p.G238A|SLC39A11_ENST00000579988.1_5'UTR	NM_001159770.1	NP_001153242.1	Q8N1S5	S39AB_HUMAN	solute carrier family 39, member 11	245					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						GACAGCCAGGCCCTCGGGGAA	0.557													C|||	3	0.000599042	0.0023	0.0	5008	,	,		21013	0.0		0.0	False		,,,				2504	0.0				p.G245A	NSCLC(95;736 1527 12296 39625 41839)	Atlas-SNP	.											.	SLC39A11	32	.	0			c.G734C						PASS	.	C	ALA/GLY,ALA/GLY	25,4381	29.9+/-59.1	0,25,2178	47	51	50		734,713	5.1	1	17	dbSNP_132	50	0,8600		0,0,4300	yes	missense,missense	SLC39A11	NM_001159770.1,NM_139177.3	60,60	0,25,6478	GG,GC,CC		0.0,0.5674,0.1922	probably-damaging,probably-damaging	245/343,238/336	70645366	25,12981	2203	4300	6503	SO:0001583	missense	201266	exon8			GCCAGGCCCTCGG	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.734G>C	17.37:g.70645366C>G	ENSP00000445829:p.Gly245Ala	95	0	0		109	47	0.431193	NM_001159770	B2R8H7|Q8WZ81	Missense_Mutation	SNP	ENST00000542342.2	37	CCDS54160.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	15.55	2.865881	0.51588	0.005674	0.0	ENSG00000133195	ENST00000542342;ENST00000255559	T;T	0.48836	0.8;0.8	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.74642	0.3743	H	0.97051	3.93	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.85832	0.1392	10	0.87932	D	0	.	18.3766	0.90437	0.0:1.0:0.0:0.0	.	245;238	Q8N1S5;Q8N1S5-2	S39AB_HUMAN;.	A	245;238	ENSP00000445829:G245A;ENSP00000255559:G238A	ENSP00000255559:G238A	G	-	2	0	SLC39A11	68156961	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.013000	0.76373	2.504000	0.84457	0.655000	0.94253	GGC	C|0.999;G|0.001	0.001	strong		0.557	SLC39A11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441442.1			G	70645366	C	G	70645366	3	3	22	1	0	0	0	0	1	0	0	0	14629	739	26	4	306	4	SLC39A11	17	70645366	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3535873	70645366	10549844	3599	6500											
TTYH2	94015	hgsc.bcm.edu	37	chr17	72227040	72227040	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttatagtgctgcggtgggcGttggtttctatggaaacagc	7	13	14	7	2	1	0	0	0	1	0	1	1	1	1	0	4	4	3	0	4	4	5	rs150215307	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:72227040G>A	ENST00000269346.4	+	3	390	c.316G>A	c.(316-318)Gtt>Att	p.V106I	TTYH2_ENST00000529107.1_Missense_Mutation_p.V85I	NM_032646.5	NP_116035.5	Q9BSA4	TTYH2_HUMAN	tweety family member 2	106						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						TGCGGTGGGCGTTGGTTTCTA	0.483													g|||	23	0.00459265	0.0159	0.0014	5008	,	,		20070	0.0		0.0	False		,,,				2504	0.001				p.V106I		Atlas-SNP	.											.	TTYH2	63	.	0			c.G316A						PASS	.	A	ILE/VAL	58,4348	56.2+/-92.4	0,58,2145	174	137	150		316	3.4	0.9	17	dbSNP_134	150	2,8598	1.2+/-3.3	0,2,4298	yes	missense	TTYH2	NM_032646.5	29	0,60,6443	AA,AG,GG		0.0233,1.3164,0.4613	benign	106/535	72227040	60,12946	2203	4300	6503	SO:0001583	missense	94015	exon3			GTGGGCGTTGGTT		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.316G>A	17.37:g.72227040G>A	ENSP00000269346:p.Val106Ile	183	0	0		162	59	0.364198	NM_032646	B3KX97|Q3B7H8|Q3B7R9|Q6AWB4|Q8NBB7|Q96PK1	Missense_Mutation	SNP	ENST00000269346.4	37	CCDS32717.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	g	8.083	0.772809	0.16051	0.013164	2.33E-4	ENSG00000141540	ENST00000269346;ENST00000529107	T;T	0.12984	2.63;2.63	5.35	3.38	0.38709	.	0.185685	0.46758	N	0.000263	T	0.06234	0.0161	L	0.41961	1.31	0.80722	D	1	B;B	0.33857	0.429;0.092	B;B	0.28305	0.088;0.037	T	0.24870	-1.0148	10	0.13470	T	0.59	-8.4172	7.2697	0.26250	0.3324:0.0:0.6676:0.0	.	85;106	B4DKD1;Q9BSA4	.;TTYH2_HUMAN	I	106;85	ENSP00000269346:V106I;ENSP00000433089:V85I	ENSP00000269346:V106I	V	+	1	0	TTYH2	69738635	0.567000	0.26626	0.943000	0.38184	0.688000	0.40055	1.396000	0.34531	0.658000	0.30925	-0.119000	0.15052	GTT	G|0.995;A|0.005	0.005	strong		0.483	TTYH2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387459.1			A	72227040	G	A	72227040	3	1	22	1	0	0	0	0	1	0	0	0	16755	1145	40	1	326	1	TTYH2	17	72227040	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1581674	72227040	8968170	3600	6501											
DNAI2	64446	hgsc.bcm.edu	37	chr17	72306239	72306239	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tcccagctggggacaaccacCctgctggaggtctcgcctgg	6	7	13	15	1	1	0	0	0	1	0	3	2	2	2	4	5	3	2	4	5	1	0	rs144035254	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:72306239C>G	ENST00000311014.6	+	11	1498	c.1431C>G	c.(1429-1431)acC>acG	p.T477T	RP11-647F2.2_ENST00000585167.1_RNA|DNAI2_ENST00000582036.1_Silent_p.T465T|AC103809.1_ENST00000516976.1_RNA|DNAI2_ENST00000446837.2_Silent_p.T477T|DNAI2_ENST00000307504.5_Silent_p.T334T|DNAI2_ENST00000579490.1_Silent_p.T534T			Q9GZS0	DNAI2_HUMAN	dynein, axonemal, intermediate chain 2	477					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						GGACAACCACCCTGCTGGAGG	0.627									Kartagener syndrome				C|||	27	0.00539137	0.0204	0.0	5008	,	,		12200	0.0		0.0	False		,,,				2504	0.0				p.T477T		Atlas-SNP	.											.	DNAI2	102	.	0			c.C1431G						PASS	.	C	,	65,4341	61.1+/-98.1	1,63,2139	53	49	50		1395,1431	-4.8	0.9	17	dbSNP_134	50	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	DNAI2	NM_001172810.1,NM_023036.4	,	1,64,6438	GG,GC,CC		0.0116,1.4753,0.5075	,	465/594,477/606	72306239	66,12940	2203	4300	6503	SO:0001819	synonymous_variant	64446	exon11	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AACCACCCTGCTG	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.1431C>G	17.37:g.72306239C>G		69	0	0		72	30	0.416667	NM_023036	C9J0S6|Q8IUW4|Q9H179|Q9NT53	Silent	SNP	ENST00000311014.6	37	CCDS11697.1																																																																																			C|0.996;G|0.004	0.004	strong		0.627	DNAI2-001	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442537.1	NM_023036		G	72306239	C	G	72306239	2	3	22	1	0	0	0	0	0	0	0	1	4612	610	22	4		4	DNAI2	17	72306239	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	79199	72306239	8888971	3601	6502											
KIF19	124602	hgsc.bcm.edu	37	chr17	72340965	72340965	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccacggccgccaaccagacGtcctcccgctcccacgcggt	6	4	9	22	6	0	1	0	0	0	1	3	1	3	1	7	2	1	1	7	2	1	0	rs34914485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:72340965G>A	ENST00000389916.4	+	7	786	c.648G>A	c.(646-648)acG>acA	p.T216T		NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	216	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						CCAACCAGACGTCCTCCCGCT	0.662													G|||	182	0.0363419	0.1278	0.0144	5008	,	,		16134	0.0		0.0	False		,,,				2504	0.0031				p.T216T		Atlas-SNP	.											.	KIF19	102	.	0			c.G648A						PASS	.	G		498,3906	217.4+/-235.8	20,458,1724	38	40	39		648	-4.4	1	17	dbSNP_126	39	10,8588	6.4+/-24.3	0,10,4289	no	coding-synonymous	KIF19	NM_153209.3		20,468,6013	AA,AG,GG		0.1163,11.3079,3.9071		216/999	72340965	508,12494	2202	4299	6501	SO:0001819	synonymous_variant	124602	exon7			CCAGACGTCCTCC	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.648G>A	17.37:g.72340965G>A		127	0	0		156	80	0.512821	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Silent	SNP	ENST00000389916.4	37	CCDS32718.2																																																																																			G|0.965;A|0.035	0.035	strong		0.662	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209		A	72340965	G	A	72340965	2	1	22	1	0	0	0	0	0	0	0	1	8291	1132	40	1		1	KIF19	17	72340965	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	34726	72340965	8854245	3602	6503											
TMEM104	54868	hgsc.bcm.edu	37	chr17	72784931	72784931	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcactcggccccctcagcttCgtgaccaccacctttgtgat	6	10	8	17	2	1	2	1	2	0	0	3	2	1	2	5	1	1	2	5	1	0	2	rs62638676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:72784931C>T	ENST00000335464.5	+	4	333	c.171C>T	c.(169-171)ttC>ttT	p.F57F	TMEM104_ENST00000582330.1_Silent_p.F57F|TMEM104_ENST00000582773.1_Silent_p.F57F|TMEM104_ENST00000417024.2_Silent_p.F70F	NM_017728.3	NP_060198.3	Q8NE00	TM104_HUMAN	transmembrane protein 104	57						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)					CCCTCAGCTTCGTGACCACCA	0.587													c|||	157	0.0313498	0.115	0.0072	5008	,	,		18997	0.0		0.0	False		,,,				2504	0.0				p.F57F		Atlas-SNP	.											.	TMEM104	49	.	0			c.C171T						PASS	.	T		423,3983	206.2+/-227.9	22,379,1802	69	59	62		171	-9.1	0.2	17	dbSNP_129	62	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	TMEM104	NM_017728.3		22,382,6099	TT,TC,CC		0.0349,9.6005,3.2754		57/497	72784931	426,12580	2203	4300	6503	SO:0001819	synonymous_variant	54868	exon4			CAGCTTCGTGACC	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.171C>T	17.37:g.72784931C>T		35	0	0		41	15	0.365854	NM_017728	Q8TEU1|Q9NT56|Q9NXH1	Silent	SNP	ENST00000335464.5	37	CCDS32723.1																																																																																			C|0.968;T|0.032	0.032	strong		0.587	TMEM104-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444442.1	NM_017728		T	72784931	C	T	72784931	2	4	22	1	0	0	0	0	0	0	0	1	16033	883	31	1		1	TMEM104	17	72784931	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	443966	72784931	8410279	3603	6504											
OTOP2	92736	hgsc.bcm.edu	37	chr17	72926879	72926879	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgggtcagtacgccatctcTtactactccatcgtggctgt	6	13	9	13	2	2	0	1	0	1	0	5	0	3	0	2	2	3	2	2	2	3	3	rs16967162	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:72926879T>C	ENST00000580223.1	+	5	1179	c.1149T>C	c.(1147-1149)tcT>tcC	p.S383S	OTOP2_ENST00000331427.4_Silent_p.S383S			Q7RTS6	OTOP2_HUMAN	otopetrin 2	383						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)					ACGCCATCTCTTACTACTCCA	0.637													C|||	334	0.0666933	0.2428	0.0187	5008	,	,		18213	0.0		0.0	False		,,,				2504	0.0				p.S383S		Atlas-SNP	.											.	OTOP2	81	.	0			c.T1149C						PASS	.	C		1004,3402	729.1+/-410.0	132,740,1331	72	63	66		1149	4.3	1	17	dbSNP_123	66	16,8584	818.5+/-406.9	0,16,4284	no	coding-synonymous	OTOP2	NM_178160.2		132,756,5615	CC,CT,TT		0.186,22.7871,7.8425		383/563	72926879	1020,11986	2203	4300	6503	SO:0001819	synonymous_variant	92736	exon6			CATCTCTTACTAC	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.1149T>C	17.37:g.72926879T>C		147	0	0		175	84	0.48	NM_178160		Silent	SNP	ENST00000580223.1	37	CCDS11708.1																																																																																			T|0.925;C|0.075	0.075	strong		0.637	OTOP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445306.1	NM_178160		C	72926879	T	C	72926879	2	2	22	1	0	0	0	0	0	0	0	1	11315	1596	56	3		3	OTOP2	17	72926879	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	141948	72926879	8268331	3604	6505											
SLC16A5	9121	hgsc.bcm.edu	37	chr17	73096199	73096199	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacgcgctggcctcgatgggCgtctccctgggcatcaccct	5	8	12	16	4	2	0	1	0	1	0	4	1	2	0	3	3	1	2	3	3	1	0	rs142993518	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73096199C>T	ENST00000450736.2	+	4	856	c.441C>T	c.(439-441)ggC>ggT	p.G147G	SLC16A5_ENST00000329783.4_Silent_p.G147G|SLC16A5_ENST00000538213.2_Silent_p.G187G|SLC16A5_ENST00000580123.1_Silent_p.G147G			O15375	MOT6_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 5	147					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)	CCTCGATGGGCGTCTCCCTGG	0.642													C|||	6	0.00119808	0.0045	0.0	5008	,	,		16275	0.0		0.0	False		,,,				2504	0.0				p.G147G		Atlas-SNP	.											.	SLC16A5	80	.	0			c.C441T						PASS	.	C		24,4382	30.8+/-60.4	0,24,2179	41	39	40		441	-7.9	0	17	dbSNP_134	40	0,8600		0,0,4300	no	coding-synonymous	SLC16A5	NM_004695.2		0,24,6479	TT,TC,CC		0.0,0.5447,0.1845		147/506	73096199	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	9121	exon5			GATGGGCGTCTCC	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.441C>T	17.37:g.73096199C>T		130	0	0		123	52	0.422764	NM_001271765	B4E288	Silent	SNP	ENST00000450736.2	37	CCDS11713.1																																																																																			C|0.998;T|0.002	0.002	strong		0.642	SLC16A5-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445547.1	NM_004695		T	73096199	C	T	73096199	2	4	22	1	0	0	0	0	0	0	0	1	14426	755	27	1		1	SLC16A5	17	73096199	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	169320	73096199	8099011	3605	6506											
LLGL2	3993	hgsc.bcm.edu	37	chr17	73559453	73559453	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cagcgggacggccgcctgctCgtcagctgtcactctgacgg	5	7	14	15	5	3	1	2	1	1	0	4	2	3	2	2	3	3	2	2	3	0	0	rs139362844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73559453C>T	ENST00000392550.3	+	8	852	c.735C>T	c.(733-735)ctC>ctT	p.L245L	LLGL2_ENST00000167462.5_Silent_p.L245L|LLGL2_ENST00000578363.1_Silent_p.L245L|LLGL2_ENST00000577200.1_Silent_p.L245L|LLGL2_ENST00000375227.4_Silent_p.L245L	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	245					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)			GCCGCCTGCTCGTCAGCTGTC	0.647													C|||	16	0.00319489	0.0121	0.0	5008	,	,		17901	0.0		0.0	False		,,,				2504	0.0				p.L245L		Atlas-SNP	.											.	LLGL2	155	.	0			c.C735T						PASS	.	C	,,	27,4375	30.8+/-60.4	1,25,2175	34	33	33		735,735,735	-7.7	0.6	17	dbSNP_134	33	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	LLGL2	NM_001015002.1,NM_001031803.1,NM_004524.2	,,	1,25,6475	TT,TC,CC		0.0,0.6134,0.2077	,,	245/357,245/1021,245/1016	73559453	27,12975	2201	4300	6501	SO:0001819	synonymous_variant	3993	exon8			CCTGCTCGTCAGC	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.735C>T	17.37:g.73559453C>T		77	0	0		93	49	0.526882	NM_001015002	Q14521|Q9BR62	Silent	SNP	ENST00000392550.3	37	CCDS32733.1																																																																																			C|0.996;T|0.004	0.004	strong		0.647	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524		T	73559453	C	T	73559453	2	4	22	1	0	0	0	0	0	0	0	1	8843	871	31	1		1	LLGL2	17	73559453	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	463254	73559453	7635757	3606	6507											
LLGL2	3993	hgsc.bcm.edu	37	chr17	73566094	73566094	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcggagcaggctgtggagcaGgtggaggccgacctgctgca	7	5	19	10	2	0	0	0	0	0	0	0	4	0	3	2	6	4	5	2	6	0	0	rs115026154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73566094G>C	ENST00000392550.3	+	15	1749	c.1632G>C	c.(1630-1632)caG>caC	p.Q544H	LLGL2_ENST00000167462.5_Missense_Mutation_p.Q544H|LLGL2_ENST00000577200.1_Missense_Mutation_p.Q544H	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	544					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)			CTGTGGAGCAGGTGGAGGCCG	0.672													G|||	70	0.0139776	0.0514	0.0029	5008	,	,		15575	0.0		0.0	False		,,,				2504	0.0				p.Q544H		Atlas-SNP	.											.	LLGL2	155	.	0			c.G1632C						PASS	.	G	HIS/GLN,HIS/GLN	256,4148	140.0+/-175.5	7,242,1953	34	33	34		1632,1632	0.4	1	17	dbSNP_132	34	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	LLGL2	NM_001031803.1,NM_004524.2	24,24	7,243,6252	CC,CG,GG		0.0116,5.8129,1.9763	benign,benign	544/1021,544/1016	73566094	257,12747	2202	4300	6502	SO:0001583	missense	3993	exon15			GGAGCAGGTGGAG	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.1632G>C	17.37:g.73566094G>C	ENSP00000376333:p.Gln544His	87	0	0		100	62	0.62	NM_004524	Q14521|Q9BR62	Missense_Mutation	SNP	ENST00000392550.3	37	CCDS32733.1	33	0.01510989010989011	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	0	0.0	G	10.86	1.471205	0.26423	0.058129	1.16E-4	ENSG00000073350	ENST00000167462;ENST00000392550;ENST00000545227	T;T	0.44083	0.93;0.93	5.2	0.448	0.16614	WD40/YVTN repeat-like-containing domain (1);	0.309685	0.35013	N	0.003504	T	0.01254	0.0041	N	0.16478	0.41	0.27032	N	0.964225	B;B;B;B;B	0.06786	0.001;0.0;0.001;0.0;0.0	B;B;B;B;B	0.10450	0.005;0.002;0.004;0.003;0.001	T	0.05484	-1.0882	10	0.17832	T	0.49	-0.9242	1.9897	0.03444	0.1345:0.225:0.353:0.2875	.	171;533;533;544;544	B4DVR9;B3KX47;G3V1I9;Q6P1M3-2;Q6P1M3	.;.;.;.;L2GL2_HUMAN	H	544;544;533	ENSP00000167462:Q544H;ENSP00000376333:Q544H	ENSP00000167462:Q544H	Q	+	3	2	LLGL2	71077689	0.829000	0.29322	1.000000	0.80357	0.904000	0.53231	0.044000	0.13992	0.541000	0.28827	0.549000	0.68633	CAG	G|0.977;C|0.023	0.023	strong		0.672	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524		C	73566094	G	C	73566094	3	2	22	1	0	0	0	0	1	0	0	0	8843	991	35	4	1721	4	LLGL2	17	73566094	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6641	73566094	7629116	3607	6508											
LLGL2	3993	hgsc.bcm.edu	37	chr17	73566469	73566469	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	accagctggccttggagggcCcactctcccgcgtcaagtcc	6	7	11	17	2	2	0	1	0	1	0	4	1	3	1	5	3	1	1	5	3	1	1	rs150412778	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73566469C>T	ENST00000392550.3	+	16	2032	c.1915C>T	c.(1915-1917)Cca>Tca	p.P639S	LLGL2_ENST00000167462.5_Missense_Mutation_p.P639S|LLGL2_ENST00000577200.1_Missense_Mutation_p.P639S	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	639					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)			CTTGGAGGGCCCACTCTCCCG	0.682													C|||	35	0.00698882	0.0265	0.0	5008	,	,		16144	0.0		0.0	False		,,,				2504	0.0				p.P639S		Atlas-SNP	.											.	LLGL2	155	.	0			c.C1915T						PASS	.	C	SER/PRO,SER/PRO	109,4289	78.3+/-116.7	1,107,2091	34	29	31		1915,1915	4.9	1	17	dbSNP_134	31	1,8591		0,1,4295	yes	missense,missense	LLGL2	NM_001031803.1,NM_004524.2	74,74	1,108,6386	TT,TC,CC		0.0116,2.4784,0.8468	probably-damaging,probably-damaging	639/1021,639/1016	73566469	110,12880	2199	4296	6495	SO:0001583	missense	3993	exon16			GAGGGCCCACTCT	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.1915C>T	17.37:g.73566469C>T	ENSP00000376333:p.Pro639Ser	102	0	0		104	58	0.557692	NM_004524	Q14521|Q9BR62	Missense_Mutation	SNP	ENST00000392550.3	37	CCDS32733.1	17	0.007783882783882784	17	0.034552845528455285	0	0.0	0	0.0	0	0.0	C	15.72	2.916820	0.52546	0.024784	1.16E-4	ENSG00000073350	ENST00000167462;ENST00000392550;ENST00000545227	T;T	0.56611	0.45;0.45	4.95	4.95	0.65309	.	0.000000	0.85682	D	0.000000	T	0.52075	0.1712	M	0.77103	2.36	0.80722	D	1	P;D;D;D;P	0.89917	0.729;1.0;1.0;0.959;0.931	P;D;D;P;P	0.91635	0.544;0.997;0.999;0.835;0.688	T	0.70296	-0.4911	10	0.56958	D	0.05	4.4938	18.2389	0.89960	0.0:1.0:0.0:0.0	.	266;628;628;639;639	B4DVR9;B3KX47;G3V1I9;Q6P1M3-2;Q6P1M3	.;.;.;.;L2GL2_HUMAN	S	639;639;628	ENSP00000167462:P639S;ENSP00000376333:P639S	ENSP00000167462:P639S	P	+	1	0	LLGL2	71078064	1.000000	0.71417	0.996000	0.52242	0.660000	0.38997	7.766000	0.85320	2.314000	0.78098	0.549000	0.68633	CCA	C|0.989;T|0.011	0.011	strong		0.682	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524		T	73566469	C	T	73566469	3	4	22	1	0	0	0	0	1	0	0	0	8843	623	22	2	2008	2	LLGL2	17	73566469	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	375	73566469	7628741	3608	6509											
FBF1	85302	hgsc.bcm.edu	37	chr17	73913827	73913827	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctcacctgctccagcagccGgctctgctcattcagccgtg	5	9	9	18	2	4	0	3	0	1	0	5	0	5	0	5	1	5	4	5	1	0	1	rs150139322	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73913827G>T	ENST00000586717.1	-	22	2722	c.2449C>A	c.(2449-2451)Cgg>Agg	p.R817R	FBF1_ENST00000319129.5_Silent_p.R816R|FBF1_ENST00000389570.4_Silent_p.R817R			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	817					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						TCCAGCAGCCGGCTCTGCTCA	0.697													G|||	17	0.00339457	0.0129	0.0	5008	,	,		17377	0.0		0.0	False		,,,				2504	0.0				p.R816R		Atlas-SNP	.											.	FBF1	48	.	0			c.C2446A						PASS	.	G		36,4118		0,36,2041	25	29	28		2446	3.9	1	17	dbSNP_134	28	1,8413		0,1,4206	no	coding-synonymous	FBF1	NM_001080542.1		0,37,6247	TT,TG,GG		0.0119,0.8666,0.2944		816/1134	73913827	37,12531	2077	4207	6284	SO:0001819	synonymous_variant	85302	exon22			GCAGCCGGCTCTG	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.2449C>A	17.37:g.73913827G>T		161	0	0		185	85	0.459459	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000586717.1	37																																																																																				G|0.997;T|0.003	0.003	strong		0.697	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542		T	73913827	G	T	73913827	2	4	22	1	0	0	0	0	0	0	0	1	5703	1115	39	4		4	FBF1	17	73913827	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	347358	73913827	7281383	3609	6510											
FBF1	85302	hgsc.bcm.edu	37	chr17	73929118	73929118	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaacatctgagatacacctGtggtgtctctggtatgtgaa	10	12	12	7	0	2	2	0	2	2	1	3	4	2	3	1	3	2	1	1	3	4	2	rs149283443	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73929118G>A	ENST00000586717.1	-	4	356	c.83C>T	c.(82-84)aCa>aTa	p.T28I	FBF1_ENST00000319129.5_Missense_Mutation_p.T28I|FBF1_ENST00000389570.4_Missense_Mutation_p.T28I			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	28					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						AGATACACCTGTGGTGTCTCT	0.448													G|||	17	0.00339457	0.0129	0.0	5008	,	,		17472	0.0		0.0	False		,,,				2504	0.0				p.T28I		Atlas-SNP	.											.	FBF1	48	.	0			c.C83T						PASS	.	G	ILE/THR	33,3797		0,33,1882	71	69	70		83	0.6	0	17	dbSNP_134	70	1,8275		0,1,4137	yes	missense	FBF1	NM_001080542.1	89	0,34,6019	AA,AG,GG		0.0121,0.8616,0.2809	benign	28/1134	73929118	34,12072	1915	4138	6053	SO:0001583	missense	85302	exon4			ACACCTGTGGTGT	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.83C>T	17.37:g.73929118G>A	ENSP00000465132:p.Thr28Ile	61	0	0		55	35	0.636364	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000586717.1	37		7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	10.15	1.271825	0.23221	0.008616	1.21E-4	ENSG00000188878	ENST00000337792;ENST00000389570;ENST00000319129;ENST00000427433	T;T	0.20332	2.08;2.08	3.74	0.562	0.17290	.	.	.	.	.	T	0.09512	0.0234	L	0.36672	1.1	0.09310	N	1	B;B;B	0.33583	0.418;0.418;0.418	B;B;B	0.31101	0.124;0.058;0.058	T	0.21655	-1.0239	9	0.59425	D	0.04	6.5178	3.4486	0.07490	0.2201:0.0:0.5802:0.1997	.	42;28;28	Q8TES7-6;Q8TES7;A6NLR5	.;FBF1_HUMAN;.	I	28;28;28;41	ENSP00000374221:T28I;ENSP00000324292:T28I	ENSP00000324292:T28I	T	-	2	0	FBF1	71440713	0.000000	0.05858	0.000000	0.03702	0.167000	0.22549	0.333000	0.19768	0.162000	0.19483	0.557000	0.71058	ACA	G|0.997;A|0.003	0.003	strong		0.448	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542		A	73929118	G	A	73929118	3	1	22	1	0	0	0	0	1	0	0	0	5703	1377	48	2	3422	2	FBF1	17	73929118	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	15291	73929118	7266092	3610	6511											
ACOX1	51	hgsc.bcm.edu	37	chr17	73944496	73944496	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agtgagtaactcctttacacGctggtttacttgtgtaatct	9	16	8	8	1	1	1	0	1	1	0	2	1	2	1	1	1	3	4	1	1	4	7	rs35629489	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73944496G>A	ENST00000301608.4	-	13	1831	c.1771C>T	c.(1771-1773)Cgt>Tgt	p.R591C	ACOX1_ENST00000293217.5_Missense_Mutation_p.R591C|ACOX1_ENST00000537812.1_Missense_Mutation_p.R553C	NM_007292.5	NP_009223.2	Q15067	ACOX1_HUMAN	acyl-CoA oxidase 1, palmitoyl	591					alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid oxidation (GO:0019395)|generation of precursor metabolites and energy (GO:0006091)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|peroxisome fission (GO:0016559)|positive regulation of cholesterol homeostasis (GO:2000189)|prostaglandin metabolic process (GO:0006693)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|FAD binding (GO:0071949)|fatty acid binding (GO:0005504)|flavin adenine dinucleotide binding (GO:0050660)|palmitoyl-CoA oxidase activity (GO:0016401)|PDZ domain binding (GO:0030165)|protein N-terminus binding (GO:0047485)|receptor binding (GO:0005102)			large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(1)	14					Flavin adenine dinucleotide(DB03147)	TCCTTTACACGCTGGTTTACT	0.388													G|||	69	0.013778	0.0461	0.0043	5008	,	,		18689	0.0		0.002	False		,,,				2504	0.0031				p.R591C		Atlas-SNP	.											ACOX1_ENST00000301608,caecum,carcinoma,0,2	ACOX1	85	2	0			c.C1771T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG	111,4295	85.8+/-124.5	1,109,2093	152	132	139		1657,1771,1771	5.2	0.1	17	dbSNP_126	139	12,8588	9.1+/-34.3	0,12,4288	yes	missense,missense,missense	ACOX1	NM_001185039.1,NM_004035.6,NM_007292.5	180,180,180	1,121,6381	AA,AG,GG		0.1395,2.5193,0.9457	probably-damaging,probably-damaging,probably-damaging	553/623,591/661,591/661	73944496	123,12883	2203	4300	6503	SO:0001583	missense	51	exon13			TTACACGCTGGTT	U03254	CCDS11734.1, CCDS11735.1	17q25.1	2012-10-04	2010-04-30		ENSG00000161533	ENSG00000161533	1.3.3.6		119	protein-coding gene	gene with protein product		609751	"acyl-Coenzyme A oxidase 1, palmitoyl"			8159712	Standard	NM_007292		Approved	PALMCOX	uc002jqe.3	Q15067	OTTHUMG00000180027	ENST00000301608.4:c.1771C>T	17.37:g.73944496G>A	ENSP00000301608:p.Arg591Cys	58	0	0		39	12	0.307692	NM_007292	A8K6X8|A8KAA0|B4DK61|F5GYQ8|Q12863|Q15068|Q15101|Q16131|Q7Z3W5|Q9UD31	Missense_Mutation	SNP	ENST00000301608.4	37	CCDS11735.1	25	0.011446886446886446	23	0.046747967479674794	0	0.0	0	0.0	2	0.002638522427440633	G	15.54	2.864717	0.51482	0.025193	0.001395	ENSG00000161533	ENST00000301608;ENST00000293217;ENST00000537812;ENST00000539791;ENST00000538781	T;T;T	0.47177	0.85;0.85;0.85	5.25	5.25	0.73442	Acyl-CoA oxidase, C-terminal (1);Acyl-CoA dehydrogenase/oxidase C-terminal (2);	0.099482	0.64402	D	0.000003	T	0.31575	0.0801	M	0.86178	2.8	0.38755	D	0.954204	D;D;P;B	0.76494	0.999;0.998;0.47;0.268	P;P;B;B	0.60117	0.869;0.869;0.106;0.045	T	0.65796	-0.6081	10	0.72032	D	0.01	-11.4201	19.7385	0.96217	0.0:0.0:1.0:0.0	rs35629489	523;553;591;591	F5H0M0;F5GYQ8;Q15067;Q15067-2	.;.;ACOX1_HUMAN;.	C	591;591;553;591;523	ENSP00000301608:R591C;ENSP00000293217:R591C;ENSP00000441257:R553C	ENSP00000293217:R591C	R	-	1	0	ACOX1	71456091	1.000000	0.71417	0.099000	0.21106	0.405000	0.30901	5.538000	0.67193	2.838000	0.97847	0.655000	0.94253	CGT	G|0.989;A|0.011	0.011	strong		0.388	ACOX1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439503.1			A	73944496	G	A	73944496	3	1	22	1	0	0	0	0	1	0	0	0	158	1087	38	1	219	1	ACOX1	17	73944496	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	15378	73944496	7250714	3611	6512											
EVPL	2125	hgsc.bcm.edu	37	chr17	74006079	74006079	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accacgaccttctccttcacGtccacctccctcttctcaag	7	11	3	20	2	4	0	2	0	3	0	8	1	6	0	6	0	0	0	6	0	1	3	rs79450818	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74006079G>A	ENST00000301607.3	-	22	3460	c.3207C>T	c.(3205-3207)gaC>gaT	p.D1069D	EVPL_ENST00000586740.1_Silent_p.D1091D	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1069	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						TCTCCTTCACGTCCACCTCCC	0.592													G|||	58	0.0115815	0.0431	0.0014	5008	,	,		21848	0.0		0.0	False		,,,				2504	0.0				p.D1069D		Atlas-SNP	.											.	EVPL	155	.	0			c.C3207T						PASS	.	G		141,4265	101.2+/-139.8	2,137,2064	149	140	143		3207	-3.6	0	17	dbSNP_132	143	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	EVPL	NM_001988.2		2,138,6363	AA,AG,GG		0.0116,3.2002,1.0918		1069/2034	74006079	142,12864	2203	4300	6503	SO:0001819	synonymous_variant	2125	exon22			CTTCACGTCCACC	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.3207C>T	17.37:g.74006079G>A		107	0	0		115	70	0.608696	NM_001988	A0AUV5	Silent	SNP	ENST00000301607.3	37	CCDS11737.1																																																																																			G|0.987;A|0.013	0.013	strong		0.592	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988		A	74006079	G	A	74006079	2	1	22	1	0	0	0	0	0	0	0	1	5294	1136	40	1		1	EVPL	17	74006079	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	61583	74006079	7189131	3612	6513											
SRP68	6730	hgsc.bcm.edu	37	chr17	74036544	74036544	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggaggtctctgtttgatgagCgtcgtttgcatctgaaagtt	7	15	13	6	2	2	3	0	3	2	0	4	4	2	4	0	2	2	4	0	2	1	3	rs75353721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74036544C>T	ENST00000307877.2	-	15	1773	c.1612G>A	c.(1612-1614)Gct>Act	p.A538T	SRP68_ENST00000355113.5_Missense_Mutation_p.A437T|SRP68_ENST00000539137.1_Missense_Mutation_p.A500T|SRP68_ENST00000542536.2_5'UTR|SRP68_ENST00000602720.1_Missense_Mutation_p.A199T	NM_014230.3	NP_055045.2	Q9UHB9	SRP68_HUMAN	signal recognition particle 68kDa	538					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						GTTTGATGAGCGTCGTTTGCA	0.438													C|||	43	0.00858626	0.0295	0.0043	5008	,	,		21078	0.001		0.0	False		,,,				2504	0.0				p.A538T		Atlas-SNP	.											SRP68,colon,carcinoma,+2,1	SRP68	61	1	0			c.G1612A						scavenged	.	C	THR/ALA	73,4333	66.4+/-103.9	2,69,2132	150	125	134		1612	-4.7	0	17	dbSNP_131	134	0,8600		0,0,4300	yes	missense	SRP68	NM_014230.2	58	2,69,6432	TT,TC,CC		0.0,1.6568,0.5613	benign	538/628	74036544	73,12933	2203	4300	6503	SO:0001583	missense	6730	exon15			GATGAGCGTCGTT	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.1612G>A	17.37:g.74036544C>T	ENSP00000312066:p.Ala538Thr	225	2	0.00888889		246	127	0.51626	NM_014230	B3KUU5|B3KWY7|G3V1U4|Q8NCJ4|Q8WUK2	Missense_Mutation	SNP	ENST00000307877.2	37	CCDS11738.1	14	0.00641025641025641	12	0.024390243902439025	1	0.0027624309392265192	1	0.0017482517482517483	0	0.0	C	2.222	-0.378212	0.05000	0.016568	0.0	ENSG00000167881	ENST00000411758;ENST00000539137;ENST00000542536;ENST00000307877;ENST00000304220;ENST00000355113	.	.	.	6.07	-4.7	0.03288	.	1.163030	0.05794	N	0.610958	T	0.07143	0.0181	N	0.14661	0.345	0.09310	N	1	B;B	0.12013	0.005;0.003	B;B	0.04013	0.001;0.001	T	0.17440	-1.0369	9	0.14656	T	0.56	-0.5259	0.5188	0.00608	0.2244:0.2613:0.1636:0.3507	.	500;538	G3V1U4;Q9UHB9	.;SRP68_HUMAN	T	278;500;199;538;507;437	.	ENSP00000307756:A507T	A	-	1	0	SRP68	71548139	0.023000	0.18921	0.001000	0.08648	0.069000	0.16628	-0.142000	0.10311	-0.743000	0.04784	-0.266000	0.10368	GCT	C|0.993;T|0.007	0.007	strong		0.438	SRP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449487.1	NM_014230		T	74036544	C	T	74036544	3	4	22	1	0	0	0	0	1	0	0	0	15171	768	27	1	279	1	SRP68	17	74036544	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	30465	74036544	7158666	3613	6514											
SRP68	6730	hgsc.bcm.edu	37	chr17	74060168	74060168	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gataacaagtgaaaccgtttTcggggttcagtgttggcttc	9	13	12	7	2	1	1	1	1	0	0	3	2	1	1	1	3	2	4	1	3	3	6	rs58471646	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74060168T>C	ENST00000307877.2	-	4	611	c.450A>G	c.(448-450)cgA>cgG	p.R150R	SRP68_ENST00000355113.5_Silent_p.R49R|SRP68_ENST00000539137.1_Silent_p.R112R	NM_014230.3	NP_055045.2	Q9UHB9	SRP68_HUMAN	signal recognition particle 68kDa	150					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						GAAACCGTTTTCGGGGTTCAG	0.502													T|||	393	0.0784744	0.2806	0.0317	5008	,	,		19465	0.0		0.0	False		,,,				2504	0.0				p.R150R		Atlas-SNP	.											SRP68,rectum,carcinoma,-1,1	SRP68	61	1	0			c.A450G						scavenged	.	T		1023,3383	380.2+/-323.6	119,785,1299	189	162	171		450	0.2	1	17	dbSNP_129	171	19,8581	11.2+/-40.8	0,19,4281	no	coding-synonymous	SRP68	NM_014230.2		119,804,5580	CC,CT,TT		0.2209,23.2183,8.0117		150/628	74060168	1042,11964	2203	4300	6503	SO:0001819	synonymous_variant	6730	exon4			CCGTTTTCGGGGT	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.450A>G	17.37:g.74060168T>C		222	1	0.0045045		273	115	0.421245	NM_014230	B3KUU5|B3KWY7|G3V1U4|Q8NCJ4|Q8WUK2	Silent	SNP	ENST00000307877.2	37	CCDS11738.1																																																																																			T|0.925;C|0.075	0.075	strong		0.502	SRP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449487.1	NM_014230		C	74060168	T	C	74060168	2	2	22	1	0	0	0	0	0	0	0	1	15171	1770	62	3		3	SRP68	17	74060168	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	23624	74060168	7135042	3614	6515											
ZACN	353174	hgsc.bcm.edu	37	chr17	74076504	74076504	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttctacgctctcagcaacacGggtgctgacagggcaggggc	8	7	14	12	2	2	1	1	1	2	0	3	1	2	1	0	4	4	4	0	4	2	2	rs8066946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74076504G>A	ENST00000334586.5	+	5	626	c.543G>A	c.(541-543)acG>acA	p.T181T	ZACN_ENST00000392503.2_Intron|EXOC7_ENST00000591724.1_5'Flank	NM_180990.3	NP_851321.2	Q401N2	ZACN_HUMAN	zinc activated ligand-gated ion channel	181					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						TCAGCAACACGGGTGCTGACA	0.657													G|||	424	0.0846645	0.3033	0.0331	5008	,	,		16820	0.0		0.0	False		,,,				2504	0.0				p.T181T		Atlas-SNP	.											.	ZACN	29	.	0			c.G543A						PASS	.	G		1144,3262	398.3+/-330.8	151,842,1210	61	56	58		543	-5.2	0.9	17	dbSNP_116	58	20,8580	11.9+/-42.8	0,20,4280	yes	coding-synonymous-near-splice	ZACN	NM_180990.3		151,862,5490	AA,AG,GG		0.2326,25.9646,8.9497		181/413	74076504	1164,11842	2203	4300	6503	SO:0001630	splice_region_variant	353174	exon5			CAACACGGGTGCT	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.544+1G>A	17.37:g.74076504G>A		74	0	0		79	45	0.56962	NM_180990	Q2TB29|Q6ZWK3|Q86YW4	Silent	SNP	ENST00000334586.5	37	CCDS11740.2																																																																																			G|0.913;A|0.087	0.087	strong		0.657	ZACN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347827.2	NM_180990	Silent	A	74076504	G	A	74076504	5	1	22	1	0	0	0	0	0	0	1	0	17525	1130	39	1	561	1	ZACN	17	74076504	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	16336	74076504	7118706	3615	6516											
SEPT9	10801	hgsc.bcm.edu	37	chr17	75471762	75471762	+	Intron	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaggagactgctgggcccacGctgggccggggtggatggag	7	5	20	9	2	0	1	0	0	0	1	0	4	0	3	2	7	1	2	2	7	1	0	rs312821	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:75471762G>A	ENST00000427177.1	+	4	847				SEPT9_ENST00000591198.1_Intron|SEPT9_ENST00000427674.2_Intron|SEPT9_ENST00000590917.1_Intron|SEPT9_ENST00000592420.1_Intron|SEPT9_ENST00000590294.1_Intron|SEPT9_ENST00000591088.1_Intron|SEPT9_ENST00000592481.1_Intron|SEPT9_ENST00000585930.1_Intron|RP11-75C10.9_ENST00000591110.1_RNA|SEPT9_ENST00000541152.2_Intron|SEPT9_ENST00000423034.2_Intron|SEPT9_ENST00000449803.2_Intron|SEPT9_ENST00000592951.1_Intron|SEPT9_ENST00000329047.8_Intron|SEPT9_ENST00000588690.1_Intron|SEPT9_ENST00000431235.2_Intron|SEPT9_ENST00000427180.1_Silent_p.T54T	NM_001113491.1	NP_001106963.1	Q9UHD8	SEPT9_HUMAN	septin 9						cell cycle (GO:0007049)|cell division (GO:0051301)|GTP catabolic process (GO:0006184)|protein heterooligomerization (GO:0051291)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)|stress fiber (GO:0001725)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(2)	16			BRCA - Breast invasive adenocarcinoma(99;0.153)			CTGGGCCCACGCTGGGCCGGG	0.642													G|||	387	0.0772764	0.2799	0.0231	5008	,	,		18847	0.0		0.001	False		,,,				2504	0.0				p.T54T		Atlas-SNP	.											.	SEPT9	105	.	0			c.G162A						PASS	.	G	,,,,,,	718,2418		83,552,933	35	38	37		,,,,162,,	-1.7	0	17	dbSNP_79	37	18,7146		0,18,3564	no	intron,intron,intron,intron,coding-synonymous,intron,intron	SEPT9	NM_001113491.1,NM_001113492.1,NM_001113493.1,NM_001113494.1,NM_001113495.1,NM_001113496.1,NM_006640.4	,,,,,,	83,570,4497	AA,AG,GG		0.2513,22.8954,7.1456	,,,,,,	,,,,54/475,,	75471762	736,9564	1568	3582	5150	SO:0001627	intron_variant	10801	exon1			GCCCACGCTGGGC	AB023208	CCDS45790.1, CCDS45791.1, CCDS45792.1, CCDS45793.1, CCDS45794.1, CCDS45795.1, CCDS74166.1	17q25.3	2014-09-17	2005-01-11	2005-01-12	ENSG00000184640	ENSG00000184640		"Septins"	7323	protein-coding gene	gene with protein product	"Ov/Br septin"	604061	"MLL septin-like fusion"	MSF		10339604, 10485469	Standard	NM_006640		Approved	MSF1, KIAA0991, PNUTL4, AF17q25, SeptD1	uc002jts.4	Q9UHD8		ENST00000427177.1:c.722-6464G>A	17.37:g.75471762G>A		66	0	0		83	44	0.53012	NM_001113495	A8K2V3|B3KPM0|B4DTL9|B4E0N2|B4E274|B7Z654|Q96QF3|Q96QF4|Q96QF5|Q9HA04|Q9UG40|Q9Y5W4	Silent	SNP	ENST00000427177.1	37	CCDS45790.1																																																																																			G|0.937;A|0.063	0.063	strong		0.642	SEPT9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000436304.2	NM_006640		A	75471762	G	A	75471762	1	1	22	0	1	0	0	0	0	0	0	0	14086	1074	38	1		1	SEPT9	17	75471762	Intron	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1395258	75471762	5723448	3616	6517											
DNAH17	8632	hgsc.bcm.edu	37	chr17	76447617	76447617	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagagttggtcctcgagtccAtccctggtgaccaggaagtt	9	10	12	10	1	0	2	0	1	0	1	4	4	3	3	4	3	0	2	4	3	2	2	rs34002770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:76447617A>G	ENST00000585328.1	-	66	10777	c.10653T>C	c.(10651-10653)gaT>gaC	p.D3551D	DNAH17_ENST00000389840.5_Silent_p.D3542D|DNAH17_ENST00000586052.1_5'UTR	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	3542	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)			CCTCGAGTCCATCCCTGGTGA	0.562													A|||	146	0.0291534	0.1044	0.0086	5008	,	,		21631	0.0		0.002	False		,,,				2504	0.0				p.D3556D		Atlas-SNP	.											.	DNAH17	347	.	0			c.T10668C						PASS	.	A		376,4030	191.9+/-217.4	17,342,1844	301	246	265		10668	-3.6	0.8	17	dbSNP_126	265	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	DNAH17	NM_173628.3		17,346,6140	GG,GA,AA		0.0465,8.5338,2.9217		3556/4463	76447617	380,12626	2203	4300	6503	SO:0001819	synonymous_variant	8632	exon66			GAGTCCATCCCTG	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.10653T>C	17.37:g.76447617A>G		237	0	0		267	125	0.468165	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				A|0.969;G|0.031	0.031	strong		0.562	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		G	76447617	A	G	76447617	2	3	22	1	0	0	0	0	0	0	0	1	4603	214	8	3		3	DNAH17	17	76447617	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	975855	76447617	4747593	3617	6518											
DNAH17	8632	hgsc.bcm.edu	37	chr17	76570924	76570924	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aagtaaacccctttggacttGagggactgggggaagcccag	11	7	14	9	0	0	1	0	1	0	0	0	4	0	4	3	4	2	1	3	4	4	3	rs61745225	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:76570924G>A	ENST00000585328.1	-	2	340	c.216C>T	c.(214-216)ctC>ctT	p.L72L	DNAH17_ENST00000389840.5_Silent_p.L72L	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	72	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)			CTTTGGACTTGAGGGACTGGG	0.557													G|||	358	0.0714856	0.2496	0.0375	5008	,	,		17437	0.0		0.002	False		,,,				2504	0.0				p.L72L		Atlas-SNP	.											.	DNAH17	347	.	0			c.C216T						PASS	.	G		781,3257		77,627,1315	118	126	123		216	4.1	1	17	dbSNP_129	123	15,8343		0,15,4164	no	coding-synonymous	DNAH17	NM_173628.3		77,642,5479	AA,AG,GG		0.1795,19.3413,6.4214		72/4463	76570924	796,11600	2019	4179	6198	SO:0001819	synonymous_variant	8632	exon2			GGACTTGAGGGAC	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.216C>T	17.37:g.76570924G>A		206	0	0		205	85	0.414634	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				G|0.948;A|0.052	0.052	strong		0.557	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		A	76570924	G	A	76570924	2	1	22	1	0	0	0	0	0	0	0	1	4603	1277	45	2		2	DNAH17	17	76570924	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	123307	76570924	4624286	3618	6519											
ENGASE	64772	hgsc.bcm.edu	37	chr17	77079854	77079854	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttcttcaggaagaggcggtAgggccctggtaccacctgag	8	9	14	10	1	2	2	1	1	1	1	2	3	2	3	3	5	1	2	3	5	3	4	rs61729127	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:77079854A>G	ENST00000579016.1	+	10	1263	c.1263A>G	c.(1261-1263)gtA>gtG	p.V421V	ENGASE_ENST00000584568.1_3'UTR	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	421						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						AAGAGGCGGTAGGGCCCTGGT	0.652													G|||	405	0.0808706	0.2912	0.0231	5008	,	,		17851	0.0		0.003	False		,,,				2504	0.001				p.V421V		Atlas-SNP	.											.	ENGASE	55	.	0			c.A1263G						PASS	.	G		847,3141		93,661,1240	50	59	56		1263	4.9	0.9	17	dbSNP_129	56	31,8303		0,31,4136	no	coding-synonymous	ENGASE	NM_001042573.1		93,692,5376	GG,GA,AA		0.372,21.2387,7.1255		421/744	77079854	878,11444	1994	4167	6161	SO:0001819	synonymous_variant	64772	exon10			GGCGGTAGGGCCC	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.1263A>G	17.37:g.77079854A>G		63	0	0		85	46	0.541176	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Silent	SNP	ENST00000579016.1	37	CCDS42394.1																																																																																			A|0.956;G|0.044	0.044	strong		0.652	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759		G	77079854	A	G	77079854	2	3	22	1	0	0	0	0	0	0	0	1	5120	407	15	3		3	ENGASE	17	77079854	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	508930	77079854	4115356	3619	6520											
ENGASE	64772	hgsc.bcm.edu	37	chr17	77082390	77082390	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggttccgggtacctcaggccGagtggggcagggcagttctg	5	8	18	10	2	2	0	1	0	1	0	3	1	3	0	3	6	1	5	3	6	1	3	rs11871357	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:77082390G>A	ENST00000579016.1	+	14	2191	c.2191G>A	c.(2191-2193)Gag>Aag	p.E731K		NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	731			E -> K (in dbSNP:rs11871357).			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						ACCTCAGGCCGAGTGGGGCAG	0.652													G|||	226	0.0451278	0.1672	0.0072	5008	,	,		18045	0.0		0.0	False		,,,				2504	0.0				p.E731K		Atlas-SNP	.											ENGASE,NS,carcinoma,-1,1	ENGASE	55	1	0			c.G2191A						PASS	.	G	LYS/GLU	507,3419		28,451,1484	42	50	47		2191	3.7	0.9	17	dbSNP_120	47	12,8276		0,12,4132	yes	missense	ENGASE	NM_001042573.1	56	28,463,5616	AA,AG,GG		0.1448,12.9139,4.2492	possibly-damaging	731/744	77082390	519,11695	1963	4144	6107	SO:0001583	missense	64772	exon14			CAGGCCGAGTGGG	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.2191G>A	17.37:g.77082390G>A	ENSP00000462333:p.Glu731Lys	105	0	0		76	33	0.434211	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Missense_Mutation	SNP	ENST00000579016.1	37	CCDS42394.1	62	0.028388278388278388	61	0.12398373983739837	1	0.0027624309392265192	0	0.0	0	0.0	G	9.605	1.129684	0.21041	0.129139	0.001448	ENSG00000167280	ENST00000545583	.	.	.	4.78	3.74	0.42951	.	0.425847	0.25291	N	0.031721	T	0.00328	0.0010	M	0.65975	2.015	0.42538	D	0.993067	P	0.45011	0.848	B	0.33960	0.173	T	0.06972	-1.0797	9	0.15066	T	0.55	-28.3266	3.1644	0.06530	0.0965:0.1746:0.5481:0.1808	rs11871357;rs11871357	731	Q8NFI3	ENASE_HUMAN	K	731	.	ENSP00000438577:E731K	E	+	1	0	ENGASE	74593985	0.563000	0.26594	0.919000	0.36401	0.056000	0.15407	1.450000	0.35134	2.193000	0.70182	0.591000	0.81541	GAG	G|0.965;A|0.035	0.035	strong		0.652	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759		A	77082390	G	A	77082390	3	1	22	1	0	0	0	0	1	0	0	0	5120	1059	37	1	2245	1	ENGASE	17	77082390	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2536	77082390	4112820	3620	6521											
CBX2	84733	hgsc.bcm.edu	37	chr17	77755894	77755894	+	Intron	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	tgctgcagacaagcactcttCcctcccagggggtccttggg	6	9	12	14	0	1	1	0	0	1	1	4	1	4	1	3	3	3	3	3	3	1	2	rs9912676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:77755894C>G	ENST00000310942.4	+	4	392				CBX2_ENST00000269399.5_Missense_Mutation_p.F194L	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)			AAGCACTCTTCCCTCCCAGGG	0.592													C|||	131	0.0261581	0.0961	0.0058	5008	,	,		17679	0.0		0.0	False		,,,				2504	0.0				p.F194L		Atlas-SNP	.											.	CBX2	50	.	0			c.C582G						PASS	.	C	,LEU/PHE	365,4037		13,339,1849	36	41	39		,582	0.7	0	17	dbSNP_119	39	3,8587		0,3,4292	yes	intron,missense	CBX2	NM_005189.2,NM_032647.3	,22	13,342,6141	GG,GC,CC		0.0349,8.2917,2.8325	,	,194/212	77755894	368,12624	2201	4295	6496	SO:0001627	intron_variant	84733	exon4			ACTCTTCCCTCCC	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+294C>G	17.37:g.77755894C>G		92	0	0		116	42	0.362069	NM_032647	Q0VDA5|Q9BTB1	Missense_Mutation	SNP	ENST00000310942.4	37	CCDS32757.1	44	0.020146520146520148	42	0.08536585365853659	2	0.0055248618784530384	0	0.0	0	0.0	C	0.251	-1.006634	0.02112	0.082917	3.49E-4	ENSG00000173894	ENST00000269399	.	.	.	2.87	0.722	0.18225	.	.	.	.	.	T	0.00815	0.0027	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13388	-1.0511	6	.	.	.	.	5.5063	0.16856	0.2264:0.553:0.2205:0.0	rs9912676	194	Q14781-2	.	L	194	.	.	F	+	3	2	CBX2	75370489	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.028000	0.13644	0.057000	0.16193	0.455000	0.32223	TTC	C|0.976;G|0.024	0.024	strong		0.592	CBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437040.1	NM_032647		G	77755894	C	G	77755894	1	3	22	0	1	0	0	0	0	0	0	0	2720	854	30	4		4	CBX2	17	77755894	Intron	SNP	C	TCGA-G8-6324-01A-11D-2210-10	673504	77755894	3439316	3621	6522											
TBC1D16	125058	hgsc.bcm.edu	37	chr17	77984168	77984168	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcggtgacatcctgcggactGaccgtcgacaagatcccgga	9	7	12	13	5	0	3	0	2	0	1	4	6	2	5	3	3	1	0	3	3	1	0	rs35393459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:77984168G>A	ENST00000310924.2	-	3	685	c.570C>T	c.(568-570)gtC>gtT	p.V190V		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	190							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)			CCTGCGGACTGACCGTCGACA	0.687													G|||	141	0.028155	0.0983	0.0159	5008	,	,		16011	0.0		0.0	False		,,,				2504	0.0				p.V190V	Ovarian(14;397 562 4850 31922 49378)	Atlas-SNP	.											.	TBC1D16	48	.	0			c.C570T						PASS	.	G		397,4003	178.3+/-207.1	23,351,1826	29	33	31		570	3.5	0.1	17	dbSNP_126	31	3,8589	3.0+/-9.4	0,3,4293	no	coding-synonymous	TBC1D16	NM_019020.2		23,354,6119	AA,AG,GG		0.0349,9.0227,3.0788		190/768	77984168	400,12592	2200	4296	6496	SO:0001819	synonymous_variant	125058	exon3			CGGACTGACCGTC	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.570C>T	17.37:g.77984168G>A		141	0	0		112	64	0.571429	NM_019020	B9A6L7|I3L1E0|I3L4U2|Q8N3Z4|Q96DH7	Silent	SNP	ENST00000310924.2	37	CCDS11766.1																																																																																			G|0.967;A|0.033	0.033	strong		0.687	TBC1D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437145.1	NM_019020		A	77984168	G	A	77984168	2	1	22	1	0	0	0	0	0	0	0	1	15620	1277	45	2		2	TBC1D16	17	77984168	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	228274	77984168	3211042	3622	6523											
CCDC40	55036	hgsc.bcm.edu	37	chr17	78014024	78014024	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacggagtcttaggcccgtcGgagcaaatgggccaggtcac	9	6	14	12	3	2	0	1	0	1	0	3	2	2	2	2	5	1	1	2	5	2	1	rs2885349	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78014024G>A	ENST00000397545.4	+	3	534	c.507G>A	c.(505-507)tcG>tcA	p.S169S	CCDC40_ENST00000374876.4_Silent_p.S169S|CCDC40_ENST00000374877.3_Silent_p.S169S|CCDC40_ENST00000269318.5_Silent_p.S169S	NM_017950.3	NP_060420.2	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	169					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)			TAGGCCCGTCGGAGCAAATGG	0.612													G|||	316	0.063099	0.1884	0.0173	5008	,	,		14983	0.001		0.004	False		,,,				2504	0.0511				p.S169S		Atlas-SNP	.											CCDC40_ENST00000374877,rectum,carcinoma,+1,2	CCDC40	198	2	0			c.G507A						PASS	.	G		614,3338		46,522,1408	30	34	33		507	-1.7	0	17	dbSNP_101	33	14,8316		0,14,4151	no	coding-synonymous	CCDC40	NM_017950.3		46,536,5559	AA,AG,GG		0.1681,15.5364,5.1132		169/1143	78014024	628,11654	1976	4165	6141	SO:0001819	synonymous_variant	55036	exon3			CCCGTCGGAGCAA	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.507G>A	17.37:g.78014024G>A		56	0	0		64	32	0.5	NM_017950	A8MTD2|C9JTI9|C9JTJ0|C9JXW1|Q6PE47|Q9HCD2|Q9NWL5	Silent	SNP	ENST00000397545.4	37	CCDS42395.1																																																																																			G|0.968;A|0.032	0.032	strong		0.612	CCDC40-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256005.2	XM_371082		A	78014024	G	A	78014024	2	1	22	1	0	0	0	0	0	0	0	1	2814	1103	39	1		1	CCDC40	17	78014024	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	29856	78014024	3181186	3623	6524											
CCDC40	55036	hgsc.bcm.edu	37	chr17	78032677	78032677	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gacctgtatgtggaccagctCaccactcgagcccagcaact	10	7	9	15	1	1	0	1	0	0	0	2	3	1	1	4	1	4	3	4	1	2	1	rs61734950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78032677C>T	ENST00000397545.4	+	9	1365	c.1338C>T	c.(1336-1338)ctC>ctT	p.L446L	CCDC40_ENST00000374876.4_Intron|CCDC40_ENST00000374877.3_Silent_p.L446L|CCDC40_ENST00000269318.5_Silent_p.L446L	NM_017950.3	NP_060420.2	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	446					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)			TGGACCAGCTCACCACTCGAG	0.562													C|||	292	0.0583067	0.1694	0.0159	5008	,	,		18404	0.0		0.001	False		,,,				2504	0.0573				p.L446L		Atlas-SNP	.											.	CCDC40	198	.	0			c.C1338T						PASS	.	C		578,3600		37,504,1548	87	91	90		1338	-3.2	0.8	17	dbSNP_129	90	3,8431		0,3,4214	no	coding-synonymous	CCDC40	NM_017950.3		37,507,5762	TT,TC,CC		0.0356,13.8344,4.6067		446/1143	78032677	581,12031	2089	4217	6306	SO:0001819	synonymous_variant	55036	exon9			CCAGCTCACCACT	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.1338C>T	17.37:g.78032677C>T		122	0	0		103	60	0.582524	NM_017950	A8MTD2|C9JTI9|C9JTJ0|C9JXW1|Q6PE47|Q9HCD2|Q9NWL5	Silent	SNP	ENST00000397545.4	37	CCDS42395.1																																																																																			C|0.972;T|0.028	0.028	strong		0.562	CCDC40-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256005.2	XM_371082		T	78032677	C	T	78032677	2	4	22	1	0	0	0	0	0	0	0	1	2814	813	29	2		2	CCDC40	17	78032677	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	18653	78032677	3162533	3624	6525											
CCDC40	55036	hgsc.bcm.edu	37	chr17	78069129	78069129	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catggagttggcggttgcccGcagagagaccgtcaccaccc	8	6	13	14	3	1	2	1	0	0	2	1	4	1	3	4	3	1	3	4	3	0	2	rs61686936	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78069129G>T	ENST00000397545.4	+	18	2927	c.2900G>T	c.(2899-2901)cGc>cTc	p.R967L		NM_017950.3	NP_060420.2	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	967					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)			GCGGTTGCCCGCAGAGAGACC	0.667													G|||	137	0.0273562	0.0991	0.0072	5008	,	,		16509	0.0		0.001	False		,,,				2504	0.0				p.R967L		Atlas-SNP	.											CCDC40,colon,carcinoma,0,1	CCDC40	198	1	0			c.G2900T						PASS	.	G	LEU/ARG	367,3957		14,339,1809	54	66	62		2900	-0.6	1	17	dbSNP_129	62	2,8516		0,2,4257	yes	missense	CCDC40	NM_017950.3	102	14,341,6066	TT,TG,GG		0.0235,8.4875,2.8734	possibly-damaging	967/1143	78069129	369,12473	2162	4259	6421	SO:0001583	missense	55036	exon18			TTGCCCGCAGAGA	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.2900G>T	17.37:g.78069129G>T	ENSP00000380679:p.Arg967Leu	215	0	0		250	126	0.504	NM_017950	A8MTD2|C9JTI9|C9JTJ0|C9JXW1|Q6PE47|Q9HCD2|Q9NWL5	Missense_Mutation	SNP	ENST00000397545.4	37	CCDS42395.1	60	0.027472527472527472	58	0.11788617886178862	2	0.0055248618784530384	0	0.0	0	0.0	G	11.65	1.700481	0.30142	0.084875	2.35E-4	ENSG00000141519	ENST00000397545	T	0.57436	0.4	5.38	-0.582	0.11709	.	.	.	.	.	T	0.00666	0.0022	L	0.57536	1.79	0.09310	P	0.9999999999999583	P;B	0.40619	0.724;0.397	B;B	0.36289	0.202;0.221	T	0.06534	-1.0821	8	0.48119	T	0.1	-13.7927	6.9297	0.24434	0.3554:0.0:0.5288:0.1159	rs61686936;rs61749048	967;750	Q4G0X9;Q4G0X9-3	CCD40_HUMAN;.	L	967	ENSP00000380679:R967L	ENSP00000380679:R967L	R	+	2	0	CCDC40	75683724	0.797000	0.28877	0.997000	0.53966	0.125000	0.20455	0.916000	0.28651	0.263000	0.21812	0.563000	0.77884	CGC	A|0.000;G|0.981;T|0.019	0.019	strong		0.667	CCDC40-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256005.2	XM_371082		T	78069129	G	T	78069129	3	4	22	1	0	0	0	0	1	0	0	0	2814	1087	38	4	2970	4	CCDC40	17	78069129	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	36452	78069129	3126081	3625	6526											
GAA	2548	hgsc.bcm.edu	37	chr17	78092081	78092081	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggggaggcccgaggggagctGttctgggacgatggagagag	8	5	22	6	2	1	1	0	0	1	1	1	8	1	5	1	7	1	2	1	7	0	1	rs17853996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78092081G>T	ENST00000302262.3	+	18	2790	c.2571G>T	c.(2569-2571)ctG>ctT	p.L857L	GAA_ENST00000390015.3_Silent_p.L857L	NM_000152.3	NP_000143.2	P10253	LYAG_HUMAN	glucosidase, alpha; acid	857					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)	GAGGGGAGCTGTTCTGGGACG	0.657													G|||	11	0.00219649	0.0083	0.0	5008	,	,		17228	0.0		0.0	False		,,,				2504	0.0				p.L857L		Atlas-SNP	.											.	GAA	66	.	0			c.G2571T						PASS	.	G	,,	48,4358	50.2+/-85.5	0,48,2155	65	74	71		2571,2571,2571	-1.4	1	17	dbSNP_123	71	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	GAA	NM_000152.3,NM_001079803.1,NM_001079804.1	,,	0,48,6455	TT,TG,GG		0.0,1.0894,0.3691	,,	857/953,857/953,857/953	78092081	48,12958	2203	4300	6503	SO:0001819	synonymous_variant	2548	exon19			GGAGCTGTTCTGG		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.2571G>T	17.37:g.78092081G>T		148	0	0		134	67	0.5	NM_001079803	Q09GN4|Q14351|Q16302|Q8IWE7	Silent	SNP	ENST00000302262.3	37	CCDS32760.1																																																																																			G|0.997;T|0.003	0.003	strong		0.657	GAA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437441.1			T	78092081	G	T	78092081	2	4	22	1	0	0	0	0	0	0	0	1	6155	1364	48	4		4	GAA	17	78092081	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	22952	78092081	3103129	3626	6527											
CARD14	79092	hgsc.bcm.edu	37	chr17	78176193	78176193	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	accatgaaggatactgccgcGcacggcaccatccccaacta	12	5	8	16	3	0	1	0	1	0	0	1	2	1	2	5	2	3	2	5	2	4	2	rs35692270	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78176193G>A	ENST00000573882.1	+	17	2729	c.2193G>A	c.(2191-2193)gcG>gcA	p.A731A	RP11-334C17.5_ENST00000576824.1_RNA|CARD14_ENST00000392434.2_3'UTR|RP11-334C17.5_ENST00000573935.1_RNA|RP11-334C17.5_ENST00000572730.1_RNA|RP11-334C17.5_ENST00000573346.1_RNA|RP11-334C17.5_ENST00000570309.1_RNA|CARD14_ENST00000570421.1_Silent_p.A731A|CARD14_ENST00000344227.2_Silent_p.A731A			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	731					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)			ATACTGCCGCGCACGGCACCA	0.632													G|||	32	0.00638978	0.0227	0.0029	5008	,	,		17093	0.0		0.0	False		,,,				2504	0.0				p.A731A		Atlas-SNP	.											.	CARD14	98	.	0			c.G2193A						PASS	.	G		115,4291	88.2+/-126.9	2,111,2090	51	41	44		2193	-4	0	17	dbSNP_126	44	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	CARD14	NM_024110.3		2,114,6387	AA,AG,GG		0.0349,2.6101,0.9073		731/1005	78176193	118,12888	2203	4300	6503	SO:0001819	synonymous_variant	79092	exon15			TGCCGCGCACGGC	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.2193G>A	17.37:g.78176193G>A		70	0	0		78	35	0.448718	NM_024110	B8QQJ3|Q9BVB5	Silent	SNP	ENST00000573882.1	37	CCDS11768.1																																																																																			G|0.992;A|0.008	0.008	strong		0.632	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1			A	78176193	G	A	78176193	2	1	22	1	0	0	0	0	0	0	0	1	2648	1074	38	1		1	CARD14	17	78176193	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	84112	78176193	3019017	3627	6528											
CARD14	79092	hgsc.bcm.edu	37	chr17	78177668	78177668	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccaggacatgactcagcagtGcaccgtgacccgcaaggtga	11	5	12	13	2	1	3	1	3	0	0	1	4	1	4	3	2	2	3	3	2	1	0	rs34822755	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78177668G>A	ENST00000573882.1	+	18	2803	c.2267G>A	c.(2266-2268)tGc>tAc	p.C756Y	RP11-334C17.5_ENST00000576824.1_RNA|CARD14_ENST00000392434.2_3'UTR|RP11-334C17.5_ENST00000573935.1_RNA|RP11-334C17.5_ENST00000572730.1_RNA|RP11-334C17.5_ENST00000573346.1_RNA|RP11-334C17.5_ENST00000570309.1_RNA|CARD14_ENST00000344227.2_Missense_Mutation_p.C756Y			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	756					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)			ACTCAGCAGTGCACCGTGACC	0.672													G|||	38	0.00758786	0.0272	0.0029	5008	,	,		16016	0.0		0.0	False		,,,				2504	0.0				p.C756Y		Atlas-SNP	.											.	CARD14	98	.	0			c.G2267A						PASS	.	G	TYR/CYS	127,4273		2,123,2075	27	24	25		2267	3.1	0.2	17	dbSNP_126	25	4,8592		0,4,4294	yes	missense	CARD14	NM_024110.3	194	2,127,6369	AA,AG,GG		0.0465,2.8864,1.008	benign	756/1005	78177668	131,12865	2200	4298	6498	SO:0001583	missense	79092	exon16			AGCAGTGCACCGT	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.2267G>A	17.37:g.78177668G>A	ENSP00000458715:p.Cys756Tyr	287	0	0		283	139	0.491166	NM_024110	B8QQJ3|Q9BVB5	Missense_Mutation	SNP	ENST00000573882.1	37	CCDS11768.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	7.289	0.610773	0.14066	0.028864	4.65E-4	ENSG00000141527	ENST00000344227	T	0.05258	3.47	4.12	3.12	0.35913	.	0.712962	0.13426	N	0.388808	T	0.01320	0.0043	N	0.14661	0.345	0.33297	D	0.5643	B	0.15141	0.012	B	0.18871	0.023	T	0.17837	-1.0356	10	0.59425	D	0.04	-4.1501	6.7425	0.23443	0.1003:0.1828:0.7169:0.0	rs34822755	756	Q9BXL6	CAR14_HUMAN	Y	756	ENSP00000344549:C756Y	ENSP00000344549:C756Y	C	+	2	0	CARD14	75792263	0.870000	0.30015	0.159000	0.22649	0.311000	0.27955	1.320000	0.33666	0.706000	0.31912	0.485000	0.47835	TGC	G|0.991;A|0.009	0.009	strong		0.672	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1			A	78177668	G	A	78177668	3	1	22	1	0	0	0	0	1	0	0	0	2648	1319	46	2	2490	2	CARD14	17	78177668	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1475	78177668	3017542	3628	6529											
SLC26A11	284129	hgsc.bcm.edu	37	chr17	78199666	78199666	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gactacagaacatccccaggCcgttcttcctgcaggtgtac	9	9	9	14	1	1	1	0	0	1	1	3	2	3	1	4	2	4	3	4	2	3	4	rs115961261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78199666C>G	ENST00000361193.3	+	6	824	c.544C>G	c.(544-546)Ccg>Gcg	p.P182A	SLC26A11_ENST00000411502.3_Missense_Mutation_p.P182A|SLC26A11_ENST00000546047.2_Missense_Mutation_p.P182A|SLC26A11_ENST00000572725.1_Missense_Mutation_p.P182A	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)			CATCCCCAGGCCGTTCTTCCT	0.562													C|||	44	0.00878594	0.0333	0.0	5008	,	,		16297	0.0		0.0	False		,,,				2504	0.0				p.P182A		Atlas-SNP	.											SLC26A11,NS,carcinoma,-1,2	SLC26A11	60	2	0			c.C544G						PASS	.	C	ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO	141,4265	101.6+/-140.2	5,131,2067	200	158	173		544,544,544,544	4.1	1	17	dbSNP_132	173	0,8600		0,0,4300	yes	missense,missense,missense,missense	SLC26A11	NM_001166347.1,NM_001166348.1,NM_001166349.1,NM_173626.3	27,27,27,27	5,131,6367	GG,GC,CC		0.0,3.2002,1.0841	benign,benign,benign,benign	182/607,182/607,182/607,182/607	78199666	141,12865	2203	4300	6503	SO:0001583	missense	284129	exon6			CCCAGGCCGTTCT		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.544C>G	17.37:g.78199666C>G	ENSP00000355384:p.Pro182Ala	116	0	0		131	65	0.496183	NM_173626		Missense_Mutation	SNP	ENST00000361193.3	37	CCDS11771.2	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	C	9.192	1.026307	0.19512	0.032002	0.0	ENSG00000181045	ENST00000411502;ENST00000546047;ENST00000361193	D;D;D	0.92647	-3.08;-3.08;-3.08	4.09	4.09	0.47781	Sulphate transporter (1);	0.424346	0.25997	N	0.026961	T	0.70413	0.3221	N	0.25286	0.73	0.24628	N	0.993634	B	0.22080	0.064	B	0.27170	0.077	T	0.66015	-0.6028	10	0.20519	T	0.43	-11.6618	12.7028	0.57043	0.0:0.8328:0.1672:0.0	.	182	Q86WA9	S2611_HUMAN	A	182	ENSP00000403998:P182A;ENSP00000440724:P182A;ENSP00000355384:P182A	ENSP00000355384:P182A	P	+	1	0	SLC26A11	75814261	0.998000	0.40836	0.970000	0.41538	0.955000	0.61496	3.003000	0.49505	1.811000	0.52892	0.467000	0.42956	CCG	C|0.990;G|0.010	0.010	strong		0.562	SLC26A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257281.1			G	78199666	C	G	78199666	3	3	22	1	0	0	0	0	1	0	0	0	14531	739	26	4	558	4	SLC26A11	17	78199666	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	21998	78199666	2995544	3629	6530											
SLC26A11	284129	hgsc.bcm.edu	37	chr17	78201686	78201686	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaagctgatgcgggaccaCgtgcctcccgtccaccccga	7	6	11	17	4	0	2	0	2	0	0	2	4	2	3	6	1	3	1	6	1	1	0	rs61011315	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78201686C>T	ENST00000361193.3	+	7	943	c.663C>T	c.(661-663)caC>caT	p.H221H	SLC26A11_ENST00000411502.3_Silent_p.H221H|SLC26A11_ENST00000546047.2_Silent_p.H221H|SLC26A11_ENST00000572725.1_Silent_p.H221H	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)			TGCGGGACCACGTGCCTCCCG	0.667													C|||	260	0.0519169	0.1808	0.0115	5008	,	,		13801	0.0		0.0109	False		,,,				2504	0.002				p.H221H		Atlas-SNP	.											.	SLC26A11	60	.	0			c.C663T						PASS	.	C	,,,	718,3688	297.6+/-284.8	61,596,1546	84	67	72		663,663,663,663	-0.2	0.1	17	dbSNP_129	72	113,8487	60.2+/-122.0	2,109,4189	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC26A11	NM_001166347.1,NM_001166348.1,NM_001166349.1,NM_173626.3	,,,	63,705,5735	TT,TC,CC		1.314,16.296,6.3894	,,,	221/607,221/607,221/607,221/607	78201686	831,12175	2203	4300	6503	SO:0001819	synonymous_variant	284129	exon7			GGACCACGTGCCT		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.663C>T	17.37:g.78201686C>T		39	0	0		45	23	0.511111	NM_173626		Silent	SNP	ENST00000361193.3	37	CCDS11771.2																																																																																			C|0.944;T|0.056	0.056	strong		0.667	SLC26A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257281.1			T	78201686	C	T	78201686	2	4	22	1	0	0	0	0	0	0	0	1	14531	535	19	1		1	SLC26A11	17	78201686	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2020	78201686	2993524	3630	6531											
RNF213	57674	hgsc.bcm.edu	37	chr17	78263634	78263634	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgtccaggaagtgaaggcAaggtagggatgcccccgcag	11	5	16	9	1	0	1	0	1	0	0	1	4	1	3	3	4	1	3	3	4	4	1	rs141921176	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78263634A>G	ENST00000582970.1	+	6	1253	c.1110A>G	c.(1108-1110)gcA>gcG	p.A370A	RNF213_ENST00000319921.4_Silent_p.A370A|RNF213_ENST00000508628.2_Silent_p.A419A|RNF213_ENST00000456466.1_Silent_p.A370A	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	370					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)			AAGTGAAGGCAAGGTAGGGAT	0.567													A|||	17	0.00339457	0.0129	0.0	5008	,	,		17512	0.0		0.0	False		,,,				2504	0.0				p.A370A		Atlas-SNP	.											.	RNF213	766	.	0			c.A1110G						PASS	.	A	,	61,4345	54.9+/-90.9	0,61,2142	63	66	65		1257,1110	-6.5	0	17	dbSNP_134	65	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous,coding-synonymous	RNF213	NM_020914.4,NM_020954.2	,	0,63,6440	GG,GA,AA		0.0233,1.3845,0.4844	,	419/5257,370/1064	78263634	63,12943	2203	4300	6503	SO:0001819	synonymous_variant	57674	exon6			GAAGGCAAGGTAG	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.1110A>G	17.37:g.78263634A>G		102	0	0		81	40	0.493827	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	37	CCDS58606.1																																																																																			A|0.995;G|0.005	0.005	strong		0.567	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		G	78263634	A	G	78263634	2	3	22	1	0	0	0	0	0	0	0	1	13492	117	5	3		3	RNF213	17	78263634	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	61948	78263634	2931576	3631	6532											
CHMP6	79643	hgsc.bcm.edu	37	chr17	78972902	78972902	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tctgtttcctccacagaaaaCgtccctgtcaaggccaggcc	9	9	8	15	1	2	1	1	0	1	1	5	1	5	1	5	2	1	1	5	2	3	1	rs35687235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78972902C>T	ENST00000325167.5	+	8	633	c.555C>T	c.(553-555)aaC>aaT	p.N185N	CTD-2561B21.7_ENST00000577061.2_RNA|CTD-2561B21.7_ENST00000576215.1_RNA	NM_024591.4	NP_078867.2	Q96FZ7	CHMP6_HUMAN	charged multivesicular body protein 6	185					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)			CCACAGAAAACGTCCCTGTCA	0.622													C|||	144	0.028754	0.1059	0.0043	5008	,	,		19893	0.0		0.001	False		,,,				2504	0.0				p.N185N		Atlas-SNP	.											.	CHMP6	16	.	0			c.C555T						PASS	.	C		370,4036	187.1+/-213.8	18,334,1851	129	108	115		555	1.3	0.1	17	dbSNP_126	115	0,8600		0,0,4300	no	coding-synonymous	CHMP6	NM_024591.4		18,334,6151	TT,TC,CC		0.0,8.3976,2.8448		185/202	78972902	370,12636	2203	4300	6503	SO:0001819	synonymous_variant	79643	exon8			AGAAAACGTCCCT	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.555C>T	17.37:g.78972902C>T		93	0	0		89	52	0.58427	NM_024591	A8K7U0|Q53FU4|Q9HAE8	Silent	SNP	ENST00000325167.5	37	CCDS11774.1																																																																																			C|0.968;T|0.032	0.032	strong		0.622	CHMP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438215.1	NM_024591		T	78972902	C	T	78972902	2	4	22	1	0	0	0	0	0	0	0	1	3362	535	19	1		1	CHMP6	17	78972902	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	709268	78972902	2222308	3632	6533											
FSCN2	25794	hgsc.bcm.edu	37	chr17	79495890	79495890	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gagccgcacggccgcttcttCggaggcaccgaggaccagct	7	5	14	15	5	1	0	0	0	1	0	2	4	1	2	4	4	2	4	4	4	0	2	rs117946784	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:79495890C>T	ENST00000417245.2	+	1	469	c.333C>T	c.(331-333)ttC>ttT	p.F111F	RP13-766D20.2_ENST00000442532.1_RNA|RP13-766D20.2_ENST00000430912.1_RNA|FSCN2_ENST00000334850.7_Silent_p.F111F	NM_001077182.2|NM_012418.3	NP_001070650.1|NP_036550.1	O14926	FSCN2_HUMAN	fascin actin-bundling protein 2, retinal	111					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)			GCCGCTTCTTCGGAGGCACCG	0.711													C|||	51	0.0101837	0.0023	0.0173	5008	,	,		15165	0.0		0.0209	False		,,,				2504	0.0153				p.F111F		Atlas-SNP	.											.	FSCN2	35	.	0			c.C333T						PASS	.	C	,	16,4090		0,16,2037	5	6	6		333,333	-1.7	0.9	17	dbSNP_132	6	130,8106		0,130,3988	no	coding-synonymous,coding-synonymous	FSCN2	NM_001077182.2,NM_012418.3	,	0,146,6025	TT,TC,CC		1.5784,0.3897,1.183	,	111/517,111/493	79495890	146,12196	2053	4118	6171	SO:0001819	synonymous_variant	25794	exon1			CTTCTTCGGAGGC	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.333C>T	17.37:g.79495890C>T		9	0	0		10	5	0.5	NM_001077182	A0AVC4|A8MRA6	Silent	SNP	ENST00000417245.2	37	CCDS45811.1																																																																																			C|0.990;T|0.010	0.010	strong		0.711	FSCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394746.1	NM_012418		T	79495890	C	T	79495890	2	4	22	1	0	0	0	0	0	0	0	1	6076	883	31	1		1	FSCN2	17	79495890	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	522988	79495890	1699320	3633	6534											
ASPSCR1	79058	hgsc.bcm.edu	37	chr17	79943475	79943475	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcttctcagccattttccAcagatcaggtgagcatcagt	10	11	9	11	0	3	2	3	1	1	1	5	3	4	2	2	1	3	2	2	1	0	3	rs4796860	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:79943475A>G	ENST00000306739.4	+	4	463	c.366A>G	c.(364-366)ccA>ccG	p.P122P	ASPSCR1_ENST00000580534.1_Silent_p.P45P|ASPSCR1_ENST00000306729.7_Silent_p.P122P|ASPSCR1_ENST00000581647.1_Silent_p.P122P	NM_024083.3	NP_076988.1	Q9BZE9	ASPC1_HUMAN	alveolar soft part sarcoma chromosome region, candidate 1	122					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)			GCCATTTTCCACAGATCAGGT	0.582			T	TFE3	alveolar soft part sarcoma								A|||	55	0.0109824	0.0401	0.0029	5008	,	,		19456	0.0		0.0	False		,,,				2504	0.0				p.P122P		Atlas-SNP	.		Dom	yes		17	17q25	79058	"alveolar soft part sarcoma chromosome region, candidate 1"		M	.	ASPSCR1	27	.	0			c.A366G						PASS	.	A		235,4171	136.9+/-172.8	5,225,1973	77	68	71		366	1.8	1	17	dbSNP_111	71	0,8600		0,0,4300	yes	coding-synonymous	ASPSCR1	NM_024083.2		5,225,6273	GG,GA,AA		0.0,5.3336,1.8069		122/554	79943475	235,12771	2203	4300	6503	SO:0001819	synonymous_variant	79058	exon4			TTTTCCACAGATC	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.366A>G	17.37:g.79943475A>G		177	0	0		178	82	0.460674	NM_001251888	A8K3K9|Q7Z6N7|Q8WV59|Q96LS5|Q96M40	Silent	SNP	ENST00000306739.4	37	CCDS11796.1																																																																																			A|0.983;G|0.017	0.017	strong		0.582	ASPSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441972.1	NM_024083		G	79943475	A	G	79943475	2	3	22	1	0	0	0	0	0	0	0	1	1059	146	6	3		3	ASPSCR1	17	79943475	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	447585	79943475	1251735	3634	6535											
TEX19	400629	hgsc.bcm.edu	37	chr17	80320303	80320303	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gcccaggacagcctgtgcagGggggctctgaggcatggggg	6	5	20	10	0	1	1	0	1	1	0	1	2	1	2	2	7	2	3	2	7	0	0	rs147220016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:80320303G>T	ENST00000333437.4	+	2	587	c.277G>T	c.(277-279)Ggg>Tgg	p.G93W		NM_207459.3	NP_997342.1	Q8NA77	TEX19_HUMAN	testis expressed 19	93					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						GCCTGTGCAGGGGGGCTCTGA	0.652													.|||	10	0.00199681	0.0008	0.0086	5008	,	,		18460	0.0		0.002	False		,,,				2504	0.001				p.G93W		Atlas-SNP	.											.	TEX19	17	.	0			c.G277T						PASS	.	G	TRP/GLY	2,4404	4.2+/-10.8	0,2,2201	39	42	41		277	1.9	0	17	dbSNP_134	41	32,8566	21.0+/-64.5	0,32,4267	yes	missense	TEX19	NM_207459.3	184	0,34,6468	TT,TG,GG		0.3722,0.0454,0.2615	probably-damaging	93/165	80320303	34,12970	2203	4299	6502	SO:0001583	missense	400629	exon2			GTGCAGGGGGGCT	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.277G>T	17.37:g.80320303G>T	ENSP00000331500:p.Gly93Trp	51	0	0		74	26	0.351351	NM_207459		Missense_Mutation	SNP	ENST00000333437.4	37	CCDS11809.1	5	0.0022893772893772895	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	G	13.50	2.255828	0.39896	4.54E-4	0.003722	ENSG00000182459	ENST00000333437	.	.	.	3.22	1.94	0.25998	.	.	.	.	.	T	0.39627	0.1085	L	0.29908	0.895	0.09310	N	1	D	0.69078	0.997	D	0.71870	0.975	T	0.20739	-1.0266	8	0.66056	D	0.02	-41.824	8.5403	0.33388	0.0:0.4168:0.5832:0.0	.	93	Q8NA77	TEX19_HUMAN	W	93	.	ENSP00000331500:G93W	G	+	1	0	TEX19	77913592	0.022000	0.18835	0.005000	0.12908	0.002000	0.02628	0.388000	0.20735	0.628000	0.30357	0.462000	0.41574	GGG	G|0.997;T|0.003	0.003	strong		0.652	TEX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256331.1	NM_207459		T	80320303	G	T	80320303	3	4	22	1	0	0	0	0	1	0	0	0	15795	1232	43	4	279	4	TEX19	17	80320303	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	376828	80320303	874907	3635	6536											
C17orf101	79701	hgsc.bcm.edu	37	chr17	80364341	80364341	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acagacagggcccctgagtgCaagtccagaatggatgcctg	11	6	13	11	0	0	3	0	1	0	2	1	4	1	4	4	2	2	1	4	2	2	0	rs34315006	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:80364341C>T	ENST00000313056.5	-	5	592	c.441G>A	c.(439-441)ttG>ttA	p.L147L	OGFOD3_ENST00000329197.5_Silent_p.L147L	NM_024648.2|NM_175902.4	NP_078924.1|NP_787098.3	Q6PK18	OGFD3_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 3	147						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)										CCCCTGAGTGCAAGTCCAGAA	0.532													C|||	8	0.00159744	0.0	0.0072	5008	,	,		18395	0.0		0.002	False		,,,				2504	0.001				p.L147L		Atlas-SNP	.											.	.	.	.	0			c.G441A						PASS	.	C	,	2,4404	4.2+/-10.8	0,2,2201	107	93	98		441,441	3.7	1	17	dbSNP_126	98	34,8566	23.4+/-69.3	0,34,4266	no	coding-synonymous,coding-synonymous	C17orf101	NM_024648.2,NM_175902.4	,	0,36,6467	TT,TC,CC		0.3953,0.0454,0.2768	,	147/320,147/332	80364341	36,12970	2203	4300	6503	SO:0001819	synonymous_variant	79701	exon5			TGAGTGCAAGTCC	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.441G>A	17.37:g.80364341C>T		41	0	0		58	25	0.431034	NM_175902	C9JDC8|Q8IZ37|Q9H6J2	Silent	SNP	ENST00000313056.5	37	CCDS11811.1																																																																																			C|0.997;T|0.003	0.003	strong		0.532	OGFOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442895.1	NM_175902		T	80364341	C	T	80364341	2	4	22	1	0	0	0	0	0	0	0	1	1850	709	25	2		2	C17orf101	17	80364341	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	44038	80364341	830869	3636	6537											
TBCD	6904	hgsc.bcm.edu	37	chr17	80887123	80887123	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cccccacgtgccccaccgagGagaactggaaaagctgtttc	10	6	10	15	2	0	1	0	0	0	1	1	4	0	2	5	2	3	2	5	2	3	1	rs8072406	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:80887123G>T	ENST00000355528.4	+	31	2958	c.2828G>T	c.(2827-2829)gGa>gTa	p.G943V	TBCD_ENST00000539345.2_Missense_Mutation_p.G943V	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	943			G -> V (in dbSNP:rs8072406).		'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)			CCCCACCGAGGAGAACTGGAA	0.637													G|||	119	0.023762	0.084	0.0101	5008	,	,		19308	0.0		0.001	False		,,,				2504	0.0				p.G943V		Atlas-SNP	.											.	TBCD	94	.	0			c.G2828T						PASS	.	G	VAL/GLY	333,3793		15,303,1745	62	66	65		2828	-10.3	0	17	dbSNP_116	65	2,8418		0,2,4208	yes	missense	TBCD	NM_005993.4	109	15,305,5953	TT,TG,GG		0.0238,8.0708,2.6702	possibly-damaging	943/1193	80887123	335,12211	2063	4210	6273	SO:0001583	missense	6904	exon31			ACCGAGGAGAACT	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.2828G>T	17.37:g.80887123G>T	ENSP00000347719:p.Gly943Val	119	0	0		111	53	0.477477	NM_005993	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Missense_Mutation	SNP	ENST00000355528.4	37	CCDS45818.1	45	0.020604395604395604	42	0.08536585365853659	3	0.008287292817679558	0	0.0	0	0.0	G	8.712	0.912371	0.17907	0.080708	2.38E-4	ENSG00000141556	ENST00000355528;ENST00000334614	T	0.29917	1.55	5.13	-10.3	0.00346	Armadillo-type fold (1);Tubulin-specific chaperone D, C-terminal (1);	1.128570	0.06621	N	0.757363	T	0.00666	0.0022	L	0.40543	1.245	0.09310	N	1	B;B;B	0.32010	0.351;0.238;0.351	B;B;B	0.31101	0.076;0.124;0.108	T	0.02933	-1.1092	9	.	.	.	.	11.0645	0.47968	0.6996:0.1867:0.1137:0.0	rs8072406;rs8072406	694;943;943	F8WC00;Q9BTW9;Q9BTW9-4	.;TBCD_HUMAN;.	V	943;694	ENSP00000347719:G943V	.	G	+	2	0	TBCD	78480412	0.019000	0.18553	0.000000	0.03702	0.011000	0.07611	0.131000	0.15870	-2.089000	0.00860	-0.165000	0.13383	GGA	G|0.974;T|0.026	0.026	strong		0.637	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993		T	80887123	G	T	80887123	3	4	22	1	0	0	0	0	1	0	0	0	15648	1174	41	4	2950	4	TBCD	17	80887123	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	522782	80887123	308087	3637	6538											
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2667005	2667005	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtggcatgtatgaatattaTgccagtgaaggacaaaatcc	15	10	10	6	0	0	2	0	2	0	0	1	3	1	3	2	2	1	2	2	2	7	3	rs7239096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:2667005T>C	ENST00000320876.6	+	3	737	c.399T>C	c.(397-399)taT>taC	p.Y133Y	SMCHD1_ENST00000261598.8_Silent_p.Y133Y	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	133					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						ATGAATATTATGCCAGTGAAG	0.378													T|||	159	0.0317492	0.1142	0.0101	5008	,	,		20279	0.0		0.001	False		,,,				2504	0.0				p.Y133Y		Atlas-SNP	.											.	SMCHD1	88	.	0			c.T399C						PASS	.	T		429,3325		30,369,1478	83	72	76		399	5.6	1	18	dbSNP_116	76	7,8219		0,7,4106	no	coding-synonymous	SMCHD1	NM_015295.2		30,376,5584	CC,CT,TT		0.0851,11.4278,3.6394		133/2006	2667005	436,11544	1877	4113	5990	SO:0001819	synonymous_variant	23347	exon3			ATATTATGCCAGT	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.399T>C	18.37:g.2667005T>C		97	0	0		98	54	0.55102	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Silent	SNP	ENST00000320876.6	37	CCDS45822.1																																																																																			T|0.974;C|0.026	0.026	strong		0.378	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			C	2667005	T	C	2667005	2	2	22	1	0	0	0	0	0	0	0	1	14803	1471	51	3		3	SMCHD1	18	2667005	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10		2667005	75410243	3638	6539											
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2728559	2728559	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttagatgaatcagacaacAtaacagcacaaccaaaattg	19	9	5	8	0	1	3	1	1	0	2	1	3	1	3	1	0	4	1	1	0	7	4	rs9961682	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:2728559A>G	ENST00000320876.6	+	23	3216	c.2878A>G	c.(2878-2880)Ata>Gta	p.I960V	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000609587.1_3'UTR|SMCHD1_ENST00000261598.8_Missense_Mutation_p.I960V	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	960			I -> V (in dbSNP:rs9961682).		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						ATCAGACAACATAACAGCACA	0.358													A|||	154	0.0307508	0.1097	0.0101	5008	,	,		17853	0.001		0.001	False		,,,				2504	0.0				p.I960V		Atlas-SNP	.											.	SMCHD1	88	.	0			c.A2878G						PASS	.	A	VAL/ILE	409,3315		26,357,1479	104	100	101		2878	-3.5	0.9	18	dbSNP_119	101	7,8193		0,7,4093	yes	missense	SMCHD1	NM_015295.2	29	26,364,5572	GG,GA,AA		0.0854,10.9828,3.4888	benign	960/2006	2728559	416,11508	1862	4100	5962	SO:0001583	missense	23347	exon23			GACAACATAACAG	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.2878A>G	18.37:g.2728559A>G	ENSP00000326603:p.Ile960Val	65	0	0		58	36	0.62069	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	37	CCDS45822.1	52	0.023809523809523808	46	0.09349593495934959	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	A	10.45	1.352273	0.24512	0.109828	8.54E-4	ENSG00000101596	ENST00000320876;ENST00000261598	T;T	0.24908	1.83;1.84	5.84	-3.46	0.04767	.	0.509376	0.22250	N	0.062565	T	0.00241	0.0007	N	0.14661	0.345	0.26418	N	0.976158	B	0.02656	0.0	B	0.01281	0.0	T	0.16364	-1.0405	10	0.32370	T	0.25	-4.6572	9.6361	0.39809	0.3166:0.2087:0.4747:0.0	rs9961682;rs52802941;rs9961682	960	A6NHR9	SMHD1_HUMAN	V	960	ENSP00000326603:I960V;ENSP00000261598:I960V	ENSP00000261598:I960V	I	+	1	0	SMCHD1	2718559	0.830000	0.29337	0.936000	0.37596	0.999000	0.98932	-0.076000	0.11412	-0.889000	0.03950	0.528000	0.53228	ATA	A|0.969;G|0.031	0.031	strong		0.358	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			G	2728559	A	G	2728559	3	3	22	1	0	0	0	0	1	0	0	0	14803	217	8	3	2968	3	SMCHD1	18	2728559	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	61554	2728559	75348689	3639	6540											
SMCHD1	23347	hgsc.bcm.edu	37	chr18	2740798	2740798	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggttggacttgatagctcAaatttgaaaacaacctttca	13	12	9	7	0	2	2	2	2	0	0	2	3	2	3	1	3	3	2	1	3	5	5	rs115632137	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:2740798A>T	ENST00000320876.6	+	28	3950	c.3612A>T	c.(3610-3612)tcA>tcT	p.S1204S	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Silent_p.S1204S	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1204					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						TTGATAGCTCAAATTTGAAAA	0.313													A|||	154	0.0307508	0.1104	0.0101	5008	,	,		14819	0.0		0.001	False		,,,				2504	0.0				p.S1204S		Atlas-SNP	.											.	SMCHD1	88	.	0			c.A3612T						PASS	.	A		399,3233		26,347,1443	108	110	109		3612	-0.6	1	18	dbSNP_132	109	7,8115		0,7,4054	no	coding-synonymous	SMCHD1	NM_015295.2		26,354,5497	TT,TA,AA		0.0862,10.9857,3.4541		1204/2006	2740798	406,11348	1816	4061	5877	SO:0001819	synonymous_variant	23347	exon28			TAGCTCAAATTTG	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.3612A>T	18.37:g.2740798A>T		129	0	0		129	74	0.573643	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Silent	SNP	ENST00000320876.6	37	CCDS45822.1																																																																																			A|0.973;T|0.027	0.027	strong		0.313	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2			T	2740798	A	T	2740798	2	4	22	1	0	0	0	0	0	0	0	1	14803	117	5	5		5	SMCHD1	18	2740798	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	12239	2740798	75336450	3640	6541											
TGIF1	7050	hgsc.bcm.edu	37	chr18	3452262	3452262	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccacagccgcgtgccctctcCccggagctggggaccaaggc	6	4	13	18	3	1	0	0	0	1	0	2	2	1	2	6	4	3	1	6	4	1	0	rs8098291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:3452262C>T	ENST00000330513.5	+	1	588	c.285C>T	c.(283-285)tcC>tcT	p.S95S	TGIF1_ENST00000343820.5_Intron|TGIF1_ENST00000345133.5_Intron|TGIF1_ENST00000400167.2_5'Flank|TGIF1_ENST00000551541.1_Intron|TGIF1_ENST00000551402.1_Intron|TGIF1_ENST00000405385.3_Intron|TGIF1_ENST00000548489.2_Intron|TGIF1_ENST00000407501.2_Intron|TGIF1_ENST00000577543.1_Intron|TGIF1_ENST00000401449.1_Intron	NM_170695.2	NP_733796.2	Q15583	TGIF1_HUMAN	TGFB-induced factor homeobox 1	95					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)				GTGCCCTCTCCCCGGAGCTGG	0.771													C|||	265	0.0529153	0.1861	0.0245	5008	,	,		9736	0.0		0.002	False		,,,				2504	0.0				p.S95S		Atlas-SNP	.											.	TGIF1	41	.	0			c.C285T						PASS	.	C	,,,,,,	598,3670		33,532,1569	8	9	9		,285,,,,,	3.5	0	18	dbSNP_116	9	17,8359		0,17,4171	no	intron,coding-synonymous,intron,intron,intron,intron,intron	TGIF1	NM_003244.2,NM_170695.2,NM_173207.1,NM_173208.1,NM_173209.1,NM_173210.1,NM_174886.1	,,,,,,	33,549,5740	TT,TC,CC		0.203,14.0112,4.864	,,,,,,	,95/402,,,,,	3452262	615,12029	2134	4188	6322	SO:0001819	synonymous_variant	7050	exon1			CCTCTCCCCGGAG	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	ENST00000330513.5:c.285C>T	18.37:g.3452262C>T		16	0	0		22	14	0.636364	NM_170695	A6NE42|A6NLU7|F8VZB6|Q6ICR0|Q8N5X9|Q9NRS0	Silent	SNP	ENST00000330513.5	37	CCDS11834.1																																																																																			C|0.953;T|0.047	0.047	strong		0.771	TGIF1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254368.4	NM_170695		T	3452262	C	T	3452262	2	4	22	1	0	0	0	0	0	0	0	1	15840	610	22	2		2	TGIF1	18	3452262	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	711464	3452262	74624986	3641	6542											
ARHGAP28	79822	hgsc.bcm.edu	37	chr18	6908976	6908976	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagtcatggttcatcagaatGtattaagattcagaaccaaa	16	11	7	7	0	4	3	4	0	0	3	4	3	4	3	1	1	1	2	1	1	5	4	rs116232392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:6908976G>A	ENST00000383472.4	+	17	2152	c.2048G>A	c.(2047-2049)tGt>tAt	p.C683Y	ARHGAP28_ENST00000419673.2_Missense_Mutation_p.C524Y|ARHGAP28_ENST00000314319.3_Missense_Mutation_p.C524Y|ARHGAP28_ENST00000531294.1_Missense_Mutation_p.C519Y			Q9P2N2	RHG28_HUMAN	Rho GTPase activating protein 28	683					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)				TCATCAGAATGTATTAAGATT	0.284													G|||	125	0.0249601	0.0877	0.0115	5008	,	,		16064	0.0		0.001	False		,,,				2504	0.0				p.C524Y		Atlas-SNP	.											.	ARHGAP28	181	.	0			c.G1571A						PASS	.	G	TYR/CYS	318,4064	152.9+/-186.6	7,304,1880	39	45	43		1571	3	0.9	18	dbSNP_132	43	8,8568	5.7+/-21.5	0,8,4280	yes	missense	ARHGAP28	NM_001010000.2	194	7,312,6160	AA,AG,GG		0.0933,7.257,2.5158	benign	524/571	6908976	326,12632	2191	4288	6479	SO:0001583	missense	79822	exon16			CAGAATGTATTAA	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.2048G>A	18.37:g.6908976G>A	ENSP00000372964:p.Cys683Tyr	149	0	0		141	54	0.382979	NM_001010000	A8MQB7|A8MU88|Q6P160|Q8N4T3|Q9NW53	Missense_Mutation	SNP	ENST00000383472.4	37		53	0.024267399267399268	51	0.10365853658536585	2	0.0055248618784530384	0	0.0	0	0.0	G	7.913	0.736819	0.15574	0.07257	9.33E-4	ENSG00000088756	ENST00000419673;ENST00000531294;ENST00000314319	T;T;T	0.07327	3.2;3.21;3.2	5.8	2.98	0.34508	.	.	.	.	.	T	0.00144	0.0004	N	0.14661	0.345	0.25779	P	0.9847541	B	0.19073	0.033	B	0.16722	0.016	T	0.41270	-0.9518	8	0.05833	T	0.94	.	5.225	0.15389	0.2961:0.1403:0.5637:0.0	.	683	Q9P2N2	RHG28_HUMAN	Y	524;519;524	ENSP00000392660:C524Y;ENSP00000437262:C519Y;ENSP00000313506:C524Y	ENSP00000313506:C524Y	C	+	2	0	ARHGAP28	6898976	0.061000	0.20836	0.902000	0.35471	0.988000	0.76386	1.237000	0.32695	0.343000	0.23821	0.650000	0.86243	TGT	G|0.979;A|0.021	0.021	strong		0.284	ARHGAP28-006	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442123.3	XM_371108		A	6908976	G	A	6908976	3	1	22	1	0	0	0	0	1	0	0	0	877	1377	48	2	1772	2	ARHGAP28	18	6908976	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3456714	6908976	71168272	3642	6543											
LAMA1	284217	hgsc.bcm.edu	37	chr18	6961950	6961950	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acaatgtttcctacctccagTaaacagccttttctcactcc	10	13	3	15	0	1	0	1	0	1	0	5	0	4	0	5	0	3	2	5	0	4	5	rs145257845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:6961950T>C	ENST00000389658.3	-	52	7539	c.7446A>G	c.(7444-7446)ttA>ttG	p.L2482L		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2482					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)				CTACCTCCAGTAAACAGCCTT	0.378													T|||	15	0.00299521	0.0106	0.0014	5008	,	,		20021	0.0		0.0	False		,,,				2504	0.0				p.L2482L		Atlas-SNP	.											.	LAMA1	458	.	0			c.A7446G						PASS	.	T		15,4391	22.3+/-47.3	0,15,2188	130	131	131		7446	-9.1	0	18	dbSNP_134	131	0,8600		0,0,4300	no	coding-synonymous	LAMA1	NM_005559.3		0,15,6488	CC,CT,TT		0.0,0.3404,0.1153		2482/3076	6961950	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	284217	exon52			CTCCAGTAAACAG	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.7446A>G	18.37:g.6961950T>C		310	0	0		300	163	0.543333	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																			T|0.998;C|0.002	0.002	strong		0.378	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		C	6961950	T	C	6961950	2	2	22	1	0	0	0	0	0	0	0	1	8614	1635	57	3		3	LAMA1	18	6961950	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	52974	6961950	71115298	3643	6544											
LAMA1	284217	hgsc.bcm.edu	37	chr18	6966296	6966296	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaagggtcttcattctgggaGctgcaaagcagaagagatga	13	8	14	6	0	3	3	1	1	2	2	3	6	3	4	0	2	3	3	0	2	3	2	rs73390557	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:6966296G>A	ENST00000389658.3	-	49	6993	c.6900C>T	c.(6898-6900)agC>agT	p.S2300S		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2300					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)				CATTCTGGGAGCTGCAAAGCA	0.458													G|||	223	0.0445288	0.1573	0.0187	5008	,	,		17231	0.001		0.001	False		,,,				2504	0.0				p.S2300S		Atlas-SNP	.											.	LAMA1	458	.	0			c.C6900T						PASS	.	G		631,3775	267.7+/-268.0	35,561,1607	40	39	39		6900	0.6	1	18	dbSNP_130	39	6,8594	3.7+/-12.6	0,6,4294	yes	coding-synonymous-near-splice	LAMA1	NM_005559.3		35,567,5901	AA,AG,GG		0.0698,14.3214,4.8977		2300/3076	6966296	637,12369	2203	4300	6503	SO:0001630	splice_region_variant	284217	exon49			CTGGGAGCTGCAA	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.6900-1C>T	18.37:g.6966296G>A		55	0	0		32	13	0.40625	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																			G|0.950;A|0.050	0.050	strong		0.458	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	Silent	A	6966296	G	A	6966296	5	1	22	1	0	0	0	0	0	0	1	0	8614	985	34	2	2387	2	LAMA1	18	6966296	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4346	6966296	71110952	3644	6545											
LAMA1	284217	hgsc.bcm.edu	37	chr18	7040197	7040197	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcgatcacatttttctcctgTataaccttccttacatgggc	8	15	6	12	1	2	0	1	0	1	0	4	1	3	0	3	1	2	1	3	1	3	6	rs62619829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:7040197T>C	ENST00000389658.3	-	10	1393	c.1300A>G	c.(1300-1302)Aca>Gca	p.T434A		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	434	Laminin EGF-like 3. {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)				TTTTCTCCTGTATAACCTTCC	0.507													T|||	77	0.0153754	0.0552	0.0058	5008	,	,		19191	0.0		0.0	False		,,,				2504	0.0				p.T434A		Atlas-SNP	.											.	LAMA1	458	.	0			c.A1300G						PASS	.	T	ALA/THR	190,4216	118.8+/-156.5	2,186,2015	150	136	141		1300	1.4	0.9	18	dbSNP_129	141	5,8595	4.3+/-15.6	0,5,4295	yes	missense	LAMA1	NM_005559.3	58	2,191,6310	CC,CT,TT		0.0581,4.3123,1.4993	benign	434/3076	7040197	195,12811	2203	4300	6503	SO:0001583	missense	284217	exon10			CTCCTGTATAACC	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.1300A>G	18.37:g.7040197T>C	ENSP00000374309:p.Thr434Ala	71	0	0		106	52	0.490566	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	18	0.008241758241758242	16	0.032520325203252036	2	0.0055248618784530384	0	0.0	0	0.0	T	2.627	-0.287315	0.05605	0.043123	5.81E-4	ENSG00000101680	ENST00000389658	T	0.60797	0.16	5.32	1.35	0.21983	EGF-like, laminin (4);	0.395100	0.27622	N	0.018551	T	0.08133	0.0203	N	0.12831	0.26	0.25331	N	0.989032	B	0.02656	0.0	B	0.08055	0.003	T	0.10042	-1.0647	10	0.06891	T	0.86	.	8.4468	0.32847	0.0:0.5006:0.0:0.4994	rs62619829	434	P25391	LAMA1_HUMAN	A	434	ENSP00000374309:T434A	ENSP00000374309:T434A	T	-	1	0	LAMA1	7030197	0.000000	0.05858	0.947000	0.38551	0.982000	0.71751	-0.882000	0.04174	0.407000	0.25591	-0.146000	0.13790	ACA	T|0.986;C|0.014	0.014	strong		0.507	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		C	7040197	T	C	7040197	3	2	22	1	0	0	0	0	1	0	0	0	8614	1638	57	3	8143	3	LAMA1	18	7040197	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	73901	7040197	71037051	3645	6546											
LAMA1	284217	hgsc.bcm.edu	37	chr18	7043335	7043335	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaactgtccagcagtattcAaacttttcttctgctttgca	9	16	6	10	0	3	1	1	1	2	0	4	1	4	1	1	0	5	4	1	0	3	6	rs9950267	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:7043335A>G	ENST00000389658.3	-	8	1139	c.1046T>C	c.(1045-1047)tTg>tCg	p.L349S		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	349	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.		L -> S (in dbSNP:rs9950267).		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)				AGCAGTATTCAAACTTTTCTT	0.358													A|||	305	0.0609026	0.2179	0.0245	5008	,	,		18061	0.0		0.0	False		,,,				2504	0.0				p.L349S		Atlas-SNP	.											.	LAMA1	458	.	0			c.T1046C						PASS	.	A	SER/LEU	821,3585	325.6+/-299.2	69,683,1451	195	169	178		1046	5.8	0.1	18	dbSNP_119	178	11,8589	8.4+/-32.0	0,11,4289	yes	missense	LAMA1	NM_005559.3	145	69,694,5740	GG,GA,AA		0.1279,18.6337,6.397	probably-damaging	349/3076	7043335	832,12174	2203	4300	6503	SO:0001583	missense	284217	exon8			GTATTCAAACTTT	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.1046T>C	18.37:g.7043335A>G	ENSP00000374309:p.Leu349Ser	160	0	0		137	135	0.985401	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	96	0.04395604395604396	87	0.17682926829268292	9	0.024861878453038673	0	0.0	0	0.0	A	13.81	2.349439	0.41599	0.186337	0.001279	ENSG00000101680	ENST00000389658	T	0.20200	2.09	5.76	5.76	0.90799	EGF-like, laminin (3);	0.273866	0.29212	N	0.012820	T	0.00109	0.0003	M	0.84511	2.7	0.25975	P	0.9824494	D	0.76494	0.999	D	0.67900	0.954	T	0.00282	-1.1850	9	0.56958	D	0.05	.	16.3668	0.83335	1.0:0.0:0.0:0.0	rs9950267;rs9950267	349	P25391	LAMA1_HUMAN	S	349	ENSP00000374309:L349S	ENSP00000374309:L349S	L	-	2	0	LAMA1	7033335	0.998000	0.40836	0.125000	0.21846	0.015000	0.08874	6.262000	0.72514	2.322000	0.78497	0.528000	0.53228	TTG	A|0.939;G|0.061	0.061	strong		0.358	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		G	7043335	A	G	7043335	3	3	22	1	0	0	0	0	1	0	0	0	8614	131	5	3	8405	3	LAMA1	18	7043335	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	3138	7043335	71033913	3646	6547											
NDUFV2	4729	hgsc.bcm.edu	37	chr18	9117899	9117899	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagctggaggagctttatttGtggtaagtaattacttagat	11	15	12	3	0	0	1	0	0	0	1	0	4	0	3	0	3	3	4	0	3	5	7	rs75362221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:9117899G>A	ENST00000318388.6	+	2	232	c.118G>A	c.(118-120)Gtg>Atg	p.V40M	RP11-143J12.3_ENST00000579467.1_RNA|NDUFV2_ENST00000400033.1_Missense_Mutation_p.V43M|RP11-21J18.1_ENST00000579126.1_RNA	NM_021074.4	NP_066552.2	P19404	NDUV2_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 2, 24kDa	40					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						AGCTTTATTTGTGGTAAGTAA	0.289													G|||	20	0.00399361	0.0151	0.0	5008	,	,		17599	0.0		0.0	False		,,,				2504	0.0				p.V40M		Atlas-SNP	.											.	NDUFV2	17	.	0			c.G118A						PASS	.	G	MET/VAL	48,4358	45.3+/-79.5	0,48,2155	54	59	57		118	5.5	1	18	dbSNP_131	57	0,8588		0,0,4294	yes	missense	NDUFV2	NM_021074.4	21	0,48,6449	AA,AG,GG		0.0,1.0894,0.3694	benign	40/250	9117899	48,12946	2203	4294	6497	SO:0001583	missense	4729	exon2			TTATTTGTGGTAA	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.118G>A	18.37:g.9117899G>A	ENSP00000327268:p.Val40Met	126	0	0		123	52	0.422764	NM_021074	Q9BV41	Missense_Mutation	SNP	ENST00000318388.6	37	CCDS11842.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	G	17.70	3.453208	0.63290	0.010894	0.0	ENSG00000178127	ENST00000318388;ENST00000400033	T;T	0.52057	0.69;0.68	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.41858	0.1177	M	0.89478	3.035	0.80722	D	1	B	0.30406	0.278	B	0.32677	0.15	T	0.59595	-0.7425	10	0.72032	D	0.01	-16.8798	14.9056	0.70715	0.0709:0.0:0.9291:0.0	.	40	P19404	NDUV2_HUMAN	M	40;43	ENSP00000327268:V40M;ENSP00000382908:V43M	ENSP00000327268:V40M	V	+	1	0	NDUFV2	9107899	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.872000	0.69636	2.738000	0.93877	0.585000	0.79938	GTG	G|0.996;A|0.004	0.004	strong		0.289	NDUFV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254475.2	NM_021074		A	9117899	G	A	9117899	3	1	22	1	0	0	0	0	1	0	0	0	10309	1377	48	2	124	2	NDUFV2	18	9117899	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2074564	9117899	68959349	3647	6548											
RALBP1	10928	hgsc.bcm.edu	37	chr18	9517221	9517221	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	catgatgtatgatggcattcGgctgccagccgttttccgtg	6	13	12	10	3	0	2	0	2	0	0	2	2	1	2	3	2	2	4	3	2	1	4	rs28552921	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:9517221G>A	ENST00000019317.4	+	3	846	c.623G>A	c.(622-624)cGg>cAg	p.R208Q	RNU2-27P_ENST00000516185.1_RNA|RALBP1_ENST00000383432.3_Missense_Mutation_p.R208Q|RP11-61L19.3_ENST00000609094.1_RNA			Q15311	RBP1_HUMAN	ralA binding protein 1	208	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				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)	GATGGCATTCGGCTGCCAGCC	0.458													G|||	21	0.00419329	0.0159	0.0	5008	,	,		18073	0.0		0.0	False		,,,				2504	0.0				p.R208Q		Atlas-SNP	.											.	RALBP1	48	.	0			c.G623A						PASS	.	G	GLN/ARG	41,4365	45.3+/-79.5	0,41,2162	71	66	67		623	4.2	0.9	18	dbSNP_125	67	0,8600		0,0,4300	yes	missense	RALBP1	NM_006788.3	43	0,41,6462	AA,AG,GG		0.0,0.9305,0.3152	benign	208/656	9517221	41,12965	2203	4300	6503	SO:0001583	missense	10928	exon3			GCATTCGGCTGCC	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.623G>A	18.37:g.9517221G>A	ENSP00000019317:p.Arg208Gln	366	1	0.00273224		380	179	0.471053	NM_006788	D3DUI0	Missense_Mutation	SNP	ENST00000019317.4	37	CCDS11845.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	11.16	1.558039	0.27827	0.009305	0.0	ENSG00000017797	ENST00000019317;ENST00000383432;ENST00000458039	T;T	0.22134	1.97;1.97	5.1	4.22	0.49857	Rho GTPase-activating protein domain (3);Rho GTPase activation protein (1);	0.120124	0.56097	D	0.000026	T	0.04724	0.0128	N	0.04768	-0.165	0.43489	D	0.995729	B	0.15473	0.013	B	0.04013	0.001	T	0.14476	-1.0471	10	0.14252	T	0.57	-0.6029	13.6511	0.62312	0.0752:0.0:0.9248:0.0	rs28552921	208	Q15311	RBP1_HUMAN	Q	208	ENSP00000019317:R208Q;ENSP00000372924:R208Q	ENSP00000019317:R208Q	R	+	2	0	RALBP1	9507221	0.992000	0.36948	0.879000	0.34478	0.997000	0.91878	3.800000	0.55537	1.264000	0.44198	0.655000	0.94253	CGG	G|0.996;A|0.004	0.004	strong		0.458	RALBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254479.1	NM_006788		A	9517221	G	A	9517221	3	1	22	1	0	0	0	0	1	0	0	0	13027	1116	39	1	629	1	RALBP1	18	9517221	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	399322	9517221	68560027	3648	6549											
NAPG	8774	hgsc.bcm.edu	37	chr18	10539774	10539774	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	caaaggagatgcagaaactaCcagaggccgttcagctaatt	15	7	10	9	1	1	3	1	0	0	3	1	4	1	3	2	2	4	3	2	2	4	4	rs2228300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:10539774C>T	ENST00000322897.6	+	6	343	c.274C>T	c.(274-276)Cca>Tca	p.P92S	NAPG_ENST00000542979.1_Missense_Mutation_p.P10S	NM_003826.2	NP_003817.1	Q99747	SNAG_HUMAN	N-ethylmaleimide-sensitive factor attachment protein, gamma	92			P -> S (in dbSNP:rs16974765).		intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)				large_intestine(2)|lung(2)	4						GCAGAAACTACCAGAGGCCGT	0.438													C|||	217	0.0433307	0.1573	0.013	5008	,	,		17838	0.0		0.0	False		,,,				2504	0.0				p.P92S		Atlas-SNP	.											.	NAPG	18	.	0			c.C274T						PASS	.	C	SER/PRO	498,3326		28,442,1442	64	64	64		274	4.1	0.1	18	dbSNP_123	64	1,8233		0,1,4116	yes	missense	NAPG	NM_003826.2	74	28,443,5558	TT,TC,CC		0.0121,13.023,4.1383	possibly-damaging	92/313	10539774	499,11559	1912	4117	6029	SO:0001583	missense	8774	exon6			AAACTACCAGAGG	U78107	CCDS45827.1	18p11.21	2013-02-28			ENSG00000134265	ENSG00000134265			7642	protein-coding gene	gene with protein product	"gamma SNAP"	603216				9269766	Standard	NM_003826		Approved		uc002kon.3	Q99747	OTTHUMG00000179119	ENST00000322897.6:c.274C>T	18.37:g.10539774C>T	ENSP00000324628:p.Pro92Ser	132	0	0		115	48	0.417391	NM_003826	B4DFC9|Q9BUV1	Missense_Mutation	SNP	ENST00000322897.6	37	CCDS45827.1	74	0.03388278388278388	69	0.1402439024390244	5	0.013812154696132596	0	0.0	0	0.0	C	10.89	1.479069	0.26511	0.13023	1.21E-4	ENSG00000134265	ENST00000322897;ENST00000542979	T;T	0.75050	-0.9;-0.9	5.82	4.06	0.47325	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.00580	0.0019	L	0.34521	1.04	0.09310	P	0.99999957713	P	0.37101	0.582	B	0.25987	0.065	T	0.28650	-1.0037	9	0.06625	T	0.88	-10.0671	11.8346	0.52316	0.0:0.8645:0.0:0.1355	rs2228300	92	Q99747	SNAG_HUMAN	S	92;10	ENSP00000324628:P92S;ENSP00000442849:P10S	ENSP00000324628:P92S	P	+	1	0	NAPG	10529774	1.000000	0.71417	0.125000	0.21846	0.551000	0.35334	5.446000	0.66600	0.820000	0.34516	0.561000	0.74099	CCA	C|0.965;T|0.035	0.035	strong		0.438	NAPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444873.1	NM_003826		T	10539774	C	T	10539774	3	4	22	1	0	0	0	0	1	0	0	0	10173	507	18	2	296	2	NAPG	18	10539774	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1022553	10539774	67537474	3649	6550											
IMPA2	3613	hgsc.bcm.edu	37	chr18	12009913	12009913	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aagaggccgcggcttctgggGccaagtgtgtgctcacccac	7	7	14	13	2	2	1	1	0	1	1	2	1	2	1	3	4	1	2	3	4	2	1	rs16976948	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:12009913G>A	ENST00000269159.3	+	3	504	c.262G>A	c.(262-264)Gcc>Acc	p.A88T	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	88			A -> T (in dbSNP:rs16976948).		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)	GGCTTCTGGGGCCAAGTGTGT	0.562													G|||	89	0.0177716	0.0605	0.0115	5008	,	,		16273	0.0		0.001	False		,,,				2504	0.0				p.A88T		Atlas-SNP	.											.	IMPA2	27	.	0			c.G262A						PASS	.	G	THR/ALA	260,4146	149.2+/-183.4	4,252,1947	123	122	122		262	3.5	1	18	dbSNP_123	122	1,8599	1.2+/-3.3	0,1,4299	yes	missense	IMPA2	NM_014214.2	58	4,253,6246	AA,AG,GG		0.0116,5.901,2.0068	benign	88/289	12009913	261,12745	2203	4300	6503	SO:0001583	missense	3613	exon3			TCTGGGGCCAAGT	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.262G>A	18.37:g.12009913G>A	ENSP00000269159:p.Ala88Thr	98	0	0		111	55	0.495495	NM_014214	B0YJ29|Q9UJT3	Missense_Mutation	SNP	ENST00000269159.3	37	CCDS11855.1	39	0.017857142857142856	36	0.07317073170731707	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	12.73	2.024554	0.35701	0.05901	1.16E-4	ENSG00000141401	ENST00000269159	T	0.52057	0.68	5.48	3.53	0.40419	.	0.385345	0.27181	N	0.020543	T	0.01940	0.0061	N	0.05259	-0.085	0.80722	D	1	B	0.11235	0.004	B	0.12837	0.008	T	0.02115	-1.1211	10	0.34782	T	0.22	-15.8924	11.554	0.50737	0.0:0.0:0.4818:0.5182	rs16976948;rs16976948	88	O14732	IMPA2_HUMAN	T	88	ENSP00000269159:A88T	ENSP00000269159:A88T	A	+	1	0	IMPA2	11999913	1.000000	0.71417	0.997000	0.53966	0.929000	0.56500	4.218000	0.58554	1.274000	0.44362	0.491000	0.48974	GCC	G|0.979;A|0.021	0.021	strong		0.562	IMPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254601.1			A	12009913	G	A	12009913	3	1	22	1	0	0	0	0	1	0	0	0	7732	1203	42	2	272	2	IMPA2	18	12009913	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1470139	12009913	66067335	3650	6551											
PTPN2	5771	hgsc.bcm.edu	37	chr18	12817348	12817348	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tataatgaaagtgagatattGttctggtttcaccactctaa	13	15	7	6	0	3	2	1	2	2	1	3	3	3	2	1	1	0	2	1	1	5	7	rs78174797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:12817348G>T	ENST00000309660.5	-	6	605	c.512C>A	c.(511-513)aCa>aAa	p.T171K	PTPN2_ENST00000327283.3_Missense_Mutation_p.T171K|PTPN2_ENST00000591115.1_Missense_Mutation_p.T194K|PTPN2_ENST00000353319.4_Missense_Mutation_p.T171K|PTPN2_ENST00000591497.1_Missense_Mutation_p.T142K	NM_002828.3	NP_002819.2	P17706	PTN2_HUMAN	protein tyrosine phosphatase, non-receptor type 2	171	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				B cell differentiation (GO:0030183)|cytokine-mediated signaling pathway (GO:0019221)|erythrocyte differentiation (GO:0030218)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemotaxis (GO:0050922)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of inflammatory response (GO:0050728)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of interleukin-2-mediated signaling pathway (GO:1902206)|negative regulation of interleukin-4-mediated signaling pathway (GO:1902215)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|negative regulation of lipid storage (GO:0010888)|negative regulation of macrophage colony-stimulating factor signaling pathway (GO:1902227)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of positive thymic T cell selection (GO:1902233)|negative regulation of prolactin signaling pathway (GO:1902212)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|negative regulation of tyrosine phosphorylation of Stat1 protein (GO:0042512)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|negative regulation of tyrosine phosphorylation of Stat6 protein (GO:0042527)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of gluconeogenesis (GO:0045722)|regulation of hepatocyte growth factor receptor signaling pathway (GO:1902202)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|T cell differentiation (GO:0030217)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|syntaxin binding (GO:0019905)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|prostate(1)|skin(3)	13		Lung NSC(161;8.94e-06)				GTGAGATATTGTTCTGGTTTC	0.338													G|||	67	0.0133786	0.0477	0.0043	5008	,	,		17923	0.0		0.001	False		,,,				2504	0.0				p.T194K		Atlas-SNP	.											.	PTPN2	37	.	0			c.C581A						PASS	.	G	LYS/THR,LYS/THR,LYS/THR,LYS/THR	222,4184	119.2+/-156.9	3,216,1984	52	54	53		581,512,512,512	3.1	1	18	dbSNP_131	53	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense	PTPN2	NM_001207013.1,NM_002828.3,NM_080422.2,NM_080423.2	78,78,78,78	3,217,6283	TT,TG,GG		0.0116,5.0386,1.7146	benign,benign,benign,benign	194/411,171/416,171/388,171/354	12817348	223,12783	2203	4300	6503	SO:0001583	missense	5771	exon7			GATATTGTTCTGG	M25393	CCDS11863.1, CCDS11864.1, CCDS11865.1, CCDS59306.1	18p11.3-p11.2	2011-06-09			ENSG00000175354	ENSG00000175354		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9650	protein-coding gene	gene with protein product		176887		PTPT		2164224	Standard	NM_002828		Approved	TCELLPTP, TC-PTP, TCPTP	uc002krp.3	P17706	OTTHUMG00000131702	ENST00000309660.5:c.512C>A	18.37:g.12817348G>T	ENSP00000311857:p.Thr171Lys	254	0	0		252	109	0.43254	NM_001207013	A8K955|A8MXU3|K7ENG3|Q96AU5|Q96HR2	Missense_Mutation	SNP	ENST00000309660.5	37	CCDS11865.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	G	10.90	1.481893	0.26598	0.050386	1.16E-4	ENSG00000175354	ENST00000327283;ENST00000353319;ENST00000341361;ENST00000309660	D;D;D	0.83419	-1.72;-1.72;-1.72	5.25	3.09	0.35607	Protein-tyrosine phosphatase, receptor/non-receptor type (4);	0.369486	0.22569	N	0.058367	T	0.14787	0.0357	N	0.21240	0.645	0.31241	N	0.695115	B;B;B;B;B	0.24132	0.025;0.013;0.098;0.055;0.016	B;B;B;B;B	0.18263	0.009;0.008;0.021;0.009;0.014	T	0.50775	-0.8788	10	0.49607	T	0.09	.	4.6107	0.12401	0.1352:0.0:0.4911:0.3736	.	171;171;148;171;171	P17706;P17706-2;Q59F91;Q96AU5;A8K3N4	PTN2_HUMAN;.;.;.;.	K	171;171;148;171	ENSP00000320298:T171K;ENSP00000320546:T171K;ENSP00000311857:T171K	ENSP00000311857:T171K	T	-	2	0	PTPN2	12807348	1.000000	0.71417	0.987000	0.45799	0.981000	0.71138	2.804000	0.47931	1.186000	0.42985	0.591000	0.81541	ACA	G|0.981;T|0.019	0.019	strong		0.338	PTPN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254613.3	NM_002828, NM_080422, NM_080423		T	12817348	G	T	12817348	3	4	22	1	0	0	0	0	1	0	0	0	12798	1377	48	4	777	4	PTPN2	18	12817348	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	807435	12817348	65259900	3651	6552											
CEP192	55125	hgsc.bcm.edu	37	chr18	13040858	13040858	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctattttattagatcaccAgagaagagagaacctattgc	14	11	9	7	0	1	4	1	0	0	4	1	6	1	4	2	1	2	1	2	1	6	6	rs145309087	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:13040858A>G	ENST00000325971.8	+	12	1644	c.51A>G	c.(49-51)ccA>ccG	p.P17P	CEP192_ENST00000430049.2_Silent_p.P138P|CEP192_ENST00000506447.1_Silent_p.P613P			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	17					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						TTAGATCACCAGAGAAGAGAG	0.299													A|||	62	0.0123802	0.0439	0.0058	5008	,	,		17505	0.0		0.0	False		,,,				2504	0.0				p.P613P		Atlas-SNP	.											.	CEP192	340	.	0			c.A1839G						PASS	.	A		158,4248	105.2+/-143.6	1,156,2046	67	70	69		1839	0.3	1	18	dbSNP_134	69	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous	CEP192	NM_032142.3		1,157,6342	GG,GA,AA		0.0116,3.586,1.2231		613/2538	13040858	159,12841	2203	4297	6500	SO:0001819	synonymous_variant	55125	exon14			ATCACCAGAGAAG	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.51A>G	18.37:g.13040858A>G		169	0	0		171	90	0.526316	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Silent	SNP	ENST00000325971.8	37																																																																																				A|0.987;G|0.013	0.013	strong		0.299	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142		G	13040858	A	G	13040858	2	3	22	1	0	0	0	0	0	0	0	1	3253	175	7	3		3	CEP192	18	13040858	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	223510	13040858	65036390	3652	6553											
CEP192	55125	hgsc.bcm.edu	37	chr18	13055915	13055915	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacattatcatctattatccAgaataactctgatacaagaa	18	12	3	8	0	3	3	1	1	2	2	4	3	4	3	1	0	3	0	1	0	9	5	rs11080623	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:13055915A>C	ENST00000325971.8	+	17	3131	c.1538A>C	c.(1537-1539)cAg>cCg	p.Q513P	CEP192_ENST00000430049.2_Missense_Mutation_p.Q634P|CEP192_ENST00000506447.1_Missense_Mutation_p.Q1109P			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	513			Q -> P (in dbSNP:rs11080623).		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						TCTATTATCCAGAATAACTCT	0.393													A|||	39	0.00778754	0.0008	0.0187	5008	,	,		21179	0.0		0.0239	False		,,,				2504	0.001				p.Q1109P		Atlas-SNP	.											.	CEP192	340	.	0			c.A3326C						PASS	.	A	PRO/GLN	22,4384	28.1+/-56.4	0,22,2181	60	59	59		3326	-0.5	0.1	18	dbSNP_120	59	276,8324	103.6+/-164.7	3,270,4027	yes	missense	CEP192	NM_032142.3	76	3,292,6208	CC,CA,AA		3.2093,0.4993,2.2913	benign	1109/2538	13055915	298,12708	2203	4300	6503	SO:0001583	missense	55125	exon19			TTATCCAGAATAA	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.1538A>C	18.37:g.13055915A>C	ENSP00000317156:p.Gln513Pro	125	0	0		107	50	0.46729	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		31	0.014194139194139194	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	22	0.029023746701846966	A	9.745	1.165868	0.21538	0.004993	0.032093	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049	T;T;T	0.24538	1.85;1.85;1.85	4.41	-0.462	0.12168	.	0.484808	0.17160	N	0.184713	T	0.06234	0.0161	L	0.47716	1.5	0.09310	N	1	B;B;B	0.17465	0.011;0.011;0.022	B;B;B	0.15484	0.007;0.007;0.013	T	0.19811	-1.0294	10	0.23891	T	0.37	-1.5367	7.8859	0.29651	0.5467:0.3343:0.0:0.119	rs11080623;rs52829180;rs11080623	634;1109;513	C9JT09;E9PF99;Q8TEP8	.;.;CE192_HUMAN	P	1109;513;513;634	ENSP00000427550:Q1109P;ENSP00000317156:Q513P;ENSP00000389190:Q634P	ENSP00000317156:Q513P	Q	+	2	0	CEP192	13045915	0.013000	0.17824	0.147000	0.22382	0.076000	0.17211	1.283000	0.33237	0.132000	0.18615	0.460000	0.39030	CAG	A|0.980;C|0.020	0.020	strong		0.393	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142		C	13055915	A	C	13055915	3	2	22	1	0	0	0	0	1	0	0	0	3253	188	7	5	3396	5	CEP192	18	13055915	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	15057	13055915	65021333	3653	6554											
CEP192	55125	hgsc.bcm.edu	37	chr18	13056065	13056065	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtaggttggacatcaaaccCtgaggaattggacccgatca	12	8	12	9	1	2	1	2	1	0	0	2	5	2	4	2	5	1	2	2	5	3	3	rs61739695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:13056065C>G	ENST00000325971.8	+	17	3281	c.1688C>G	c.(1687-1689)cCt>cGt	p.P563R	CEP192_ENST00000430049.2_Missense_Mutation_p.P684R|CEP192_ENST00000506447.1_Missense_Mutation_p.P1159R			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	563					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						ACATCAAACCCTGAGGAATTG	0.512													C|||	61	0.0121805	0.0446	0.0029	5008	,	,		19222	0.0		0.0	False		,,,				2504	0.0				p.P1159R		Atlas-SNP	.											.	CEP192	340	.	0			c.C3476G						PASS	.	C	ARG/PRO	163,4243	108.2+/-146.6	2,159,2042	47	48	47		3476	0.8	0	18	dbSNP_129	47	1,8599	1.2+/-3.3	0,1,4299	yes	missense	CEP192	NM_032142.3	103	2,160,6341	GG,GC,CC		0.0116,3.6995,1.261	benign	1159/2538	13056065	164,12842	2203	4300	6503	SO:0001583	missense	55125	exon19			CAAACCCTGAGGA	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.1688C>G	18.37:g.13056065C>G	ENSP00000317156:p.Pro563Arg	91	0	0		68	35	0.514706	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	C	5.196	0.221789	0.09863	0.036995	1.16E-4	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049	T;T;T	0.05382	3.46;3.45;3.46	4.19	0.836	0.18891	.	1.225170	0.05804	N	0.612700	T	0.00580	0.0019	N	0.16478	0.41	0.09310	N	1	B;B;B	0.11235	0.002;0.003;0.004	B;B;B	0.08055	0.002;0.003;0.003	T	0.46775	-0.9167	10	0.19147	T	0.46	0.3765	0.6935	0.00895	0.3617:0.2925:0.1361:0.2097	rs61739695	684;1159;563	C9JT09;E9PF99;Q8TEP8	.;.;CE192_HUMAN	R	1159;563;563;684	ENSP00000427550:P1159R;ENSP00000317156:P563R;ENSP00000389190:P684R	ENSP00000317156:P563R	P	+	2	0	CEP192	13046065	0.000000	0.05858	0.000000	0.03702	0.080000	0.17528	0.012000	0.13287	0.270000	0.21984	0.563000	0.77884	CCT	C|0.986;G|0.014	0.014	strong		0.512	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142		G	13056065	C	G	13056065	3	3	22	1	0	0	0	0	1	0	0	0	3253	681	24	4	3546	4	CEP192	18	13056065	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	150	13056065	65021183	3654	6555											
CEP192	55125	hgsc.bcm.edu	37	chr18	13068191	13068191	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gtggtcactcggctagcaggCccttctgtggtcaaccacat	7	10	11	13	1	3	0	2	0	1	0	4	0	3	0	2	4	2	2	2	4	2	2	rs143595675	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:13068191C>A	ENST00000325971.8	+	21	4518	c.2925C>A	c.(2923-2925)ggC>ggA	p.G975G	CEP192_ENST00000430049.2_Silent_p.G1096G|CEP192_ENST00000506447.1_Silent_p.G1571G			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	975					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						GGCTAGCAGGCCCTTCTGTGG	0.498													C|||	24	0.00479233	0.0174	0.0014	5008	,	,		16806	0.0		0.0	False		,,,				2504	0.0				p.G1571G		Atlas-SNP	.											.	CEP192	340	.	0			c.C4713A						PASS	.	C		51,4355	52.3+/-87.9	0,51,2152	72	74	73		4713	-5.3	0	18	dbSNP_134	73	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CEP192	NM_032142.3		0,52,6451	AA,AC,CC		0.0116,1.1575,0.3998		1571/2538	13068191	52,12954	2203	4300	6503	SO:0001819	synonymous_variant	55125	exon23			AGCAGGCCCTTCT	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.2925C>A	18.37:g.13068191C>A		76	0	0		110	55	0.5	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Silent	SNP	ENST00000325971.8	37																																																																																				C|0.996;A|0.004	0.004	strong		0.498	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142		A	13068191	C	A	13068191	2	1	22	1	0	0	0	0	0	0	0	1	3253	726	26	4		4	CEP192	18	13068191	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	12126	13068191	65009057	3655	6556											
CABYR	26256	hgsc.bcm.edu	37	chr18	21736486	21736486	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaaaatgagcagtcaccaCgagttagtcccaaatctgta	16	8	8	9	1	2	2	1	1	1	1	3	3	3	2	2	0	1	3	2	0	6	2	rs35554127	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:21736486C>T	ENST00000399481.2	+	2	879	c.727C>T	c.(727-729)Cga>Tga	p.R243*	CABYR_ENST00000399499.1_Intron|CABYR_ENST00000581397.1_Intron|RP11-799B12.4_ENST00000583267.1_lincRNA|CABYR_ENST00000327201.6_Intron|CABYR_ENST00000415309.2_Intron|CABYR_ENST00000399496.3_Intron			O75952	CABYR_HUMAN	calcium binding tyrosine-(Y)-phosphorylation regulated	341					epithelial cilium movement (GO:0003351)|sperm capacitation (GO:0048240)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|protein heterodimerization activity (GO:0046982)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)	11	all_cancers(21;9.13e-05)|all_epithelial(16;5.49e-07)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0305)|Ovarian(20;0.17)					GCAGTCACCACGAGTTAGTCC	0.378													C|||	71	0.0141773	0.0537	0.0	5008	,	,		21641	0.0		0.0	False		,,,				2504	0.0				p.R341X		Atlas-SNP	.											.	CABYR	51	.	0			c.C1021T						PASS	.	C	stop/ARG,,,stop/ARG,,	194,4212	118.8+/-156.5	3,188,2012	60	63	62		1021,,,967,,	3.4	1	18	dbSNP_126	62	0,8600		0,0,4300	yes	stop-gained,intron,intron,stop-gained,intron,intron	CABYR	NM_012189.2,NM_138643.1,NM_138644.1,NM_153768.1,NM_153769.1,NM_153770.1	,,,,,	3,188,6312	TT,TC,CC		0.0,4.4031,1.4916	,,,,,	341/494,,,323/476,,	21736486	194,12812	2203	4300	6503	SO:0001587	stop_gained	26256	exon4			TCACCACGAGTTA	AF088868	CCDS11881.1, CCDS11882.1, CCDS11883.1, CCDS42420.1, CCDS45840.1	18q11.2	2009-08-06	2007-11-22		ENSG00000154040	ENSG00000154040			15569	protein-coding gene	gene with protein product	"fibrousheathin 2", "cancer/testis antigen 88"	612135				11820818, 17317841, 16139264	Standard	NM_012189		Approved	FSP-2, CBP86, CT88	uc002kux.3	O75952	OTTHUMG00000037365	ENST00000399481.2:c.727C>T	18.37:g.21736486C>T	ENSP00000382404:p.Arg243*	62	0	0		70	35	0.5	NM_012189	B2R857|Q8WXW5|Q9HAY3|Q9HAY4|Q9HAY5|Q9HCY9	Nonsense_Mutation	SNP	ENST00000399481.2	37		26	0.011904761904761904	26	0.052845528455284556	0	0.0	0	0.0	0	0.0	C	23.4	4.416434	0.83449	0.044031	0.0	ENSG00000154040	ENST00000399481	.	.	.	5.31	3.39	0.38822	.	0.460245	0.20298	N	0.095093	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-4.8475	6.5485	0.22420	0.0:0.784:0.0:0.216	rs35554127	.	.	.	X	243	.	.	R	+	1	2	CABYR	19990484	0.415000	0.25416	0.972000	0.41901	0.862000	0.49288	0.095000	0.15127	1.466000	0.48025	0.655000	0.94253	CGA	C|0.986;T|0.014	0.014	strong		0.378	CABYR-201	KNOWN	basic	protein_coding	protein_coding		NM_153770		T	21736486	C	T	21736486	4	4	22	1	0	0	0	0	0	1	0	0	2538	528	19	1	1031	1	CABYR	18	21736486	Nonsense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	8668295	21736486	56340762	3656	6557											
CABYR	114876	hgsc.bcm.edu	37	chr18	21740032	21740033	+	IGR	DEL	TG	TG	-																															gcaaagcagaaactgaaaacTggtaggtacactttcctacc																								rs149126027	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:21740032_21740033delTG	ENST00000319481.3	-	0	4195				CABYR_ENST00000399499.1_3'UTR|CABYR_ENST00000581397.1_3'UTR|RP11-799B12.4_ENST00000583267.1_lincRNA|CABYR_ENST00000327201.6_3'UTR|CABYR_ENST00000415309.2_3'UTR|CABYR_ENST00000399496.3_3'UTR	NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A						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)					AACTGAAAACTGGTAGGTACAC	0.406														131	0.0261581	0.0976	0.0029	5008	,	,		21848	0.0		0.0	False		,,,				2504	0.0				p.379_380del		Pindel,Atlas-Indel	.											.	CABYR	51	.	0			c.1137_1138del						PASS	.		,,,,,	310,3948		19,272,1838					,,,,,	2.1	1		dbSNP_134	57	0,8248		0,0,4124	no	frameshift-near-splice,frameshift-near-splice,utr-3,frameshift-near-splice,frameshift-near-splice,utr-3	CABYR	NM_153770.1,NM_153769.1,NM_153768.1,NM_138644.1,NM_138643.1,NM_012189.2	,,,,,	19,272,5962	A1A1,A1R,RR		0.0,7.2804,2.4788	,,,,,	,,,,,		310,12196				SO:0001628	intergenic_variant	26256	exon5			.	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		18.37:g.21740032_21740033delTG		57	0	.		77	26	0.338	NM_153769	B7Z7D3|Q9BZF5|Q9NW87	Frame_Shift_Del	DEL	ENST00000319481.3	37	CCDS11884.1																																																																																			TG|0.978;-|0.022	0.022	strong		0.406	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254902.1	NM_080597		-	21740033	TG	-	21740032	6	5	22	0	1	1	0	1	0	0	0	0	2538	1594	55	0		0	CABYR	18	21740032	IGR	DEL	TG	TCGA-G8-6324-01A-11D-2210-10	3546	21740032	56337216	3657	6558											
DSC2	1824	hgsc.bcm.edu	37	chr18	28681903	28681903	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcagccggcagagggctccgTtccaggagccggaggggcgg	6	3	20	12	4	0	1	0	0	0	1	2	3	2	3	4	7	2	4	4	7	0	1	rs868333	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28681903T>C	ENST00000280904.6	-	1	475	c.32A>G	c.(31-33)aAc>aGc	p.N11S	RP11-408H20.2_ENST00000581836.1_RNA|DSC2_ENST00000251081.6_Missense_Mutation_p.N11S	NM_024422.3	NP_077740.1	Q02487	DSC2_HUMAN	desmocollin 2	11			N -> S (in dbSNP:rs868333). {ECO:0000269|PubMed:20031617}.		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)			GAGGGCTCCGTTCCAGGAGCC	0.751													C|||	428	0.0854633	0.3116	0.0216	5008	,	,		8187	0.001		0.0	False		,,,				2504	0.0				p.N11S		Atlas-SNP	.											.	DSC2	168	.	0			c.A32G						PASS	.						1	2	2					18																	28681903		1051	2094	3145	SO:0001583	missense	1824	exon1			GCTCCGTTCCAGG	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.32A>G	18.37:g.28681903T>C	ENSP00000280904:p.Asn11Ser	25	0	0		10	5	0.5	NM_024422		Missense_Mutation	SNP	ENST00000280904.6	37	CCDS11892.1	169	0.07738095238095238	156	0.3170731707317073	7	0.019337016574585635	5	0.008741258741258742	1	0.0013192612137203166	C	7.222	0.597497	0.13875	.	.	ENSG00000134755	ENST00000251081;ENST00000280904;ENST00000399347	T;T	0.57107	0.45;0.42	4.55	3.59	0.41128	.	.	.	.	.	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38001	-0.9681	8	0.02654	T	1	.	4.9282	0.13903	0.2229:0.6676:0.0:0.1095	rs868333	11;11	Q02487;Q02487-2	DSC2_HUMAN;.	S	11	ENSP00000251081:N11S;ENSP00000280904:N11S	ENSP00000251081:N11S	N	-	2	0	DSC2	26935901	0.000000	0.05858	0.506000	0.27664	0.417000	0.31264	0.324000	0.19610	1.139000	0.42245	-0.186000	0.12905	AAC	T|0.923;C|0.077	0.077	strong		0.751	DSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254943.1	NM_004949		C	28681903	T	C	28681903	3	2	22	1	0	0	0	0	1	0	0	0	4768	1725	60	3	2777	3	DSC2	18	28681903	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	6941871	28681903	49395345	3658	6559											
DSC1	1823	hgsc.bcm.edu	37	chr18	28710615	28710615	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctttgccttcatagttataCgaacaaacgtagtcttcaca	12	13	5	11	2	3	0	2	0	1	0	3	1	3	0	2	0	4	2	2	0	6	7	rs1816634	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28710615C>A	ENST00000257198.5	-	16	2808	c.2547G>T	c.(2545-2547)tcG>tcT	p.S849S	RP11-408H20.2_ENST00000581836.1_RNA|RP11-408H20.3_ENST00000582307.1_RNA|DSC1_ENST00000257197.3_3'UTR	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	849					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)			CATAGTTATACGAACAAACGT	0.418													C|||	465	0.0928514	0.2542	0.0533	5008	,	,		18467	0.0		0.0467	False		,,,				2504	0.046				p.S849S		Atlas-SNP	.											.	DSC1	240	.	0			c.G2547T						PASS	.	C	,	886,3520	344.1+/-307.9	88,710,1405	133	134	134		,2547	-12.3	0	18	dbSNP_92	134	344,8256	118.1+/-177.6	6,332,3962	no	utr-3,coding-synonymous	DSC1	NM_004948.3,NM_024421.2	,	94,1042,5367	AA,AC,CC		4.0,20.1089,9.4572	,	,849/895	28710615	1230,11776	2203	4300	6503	SO:0001819	synonymous_variant	1823	exon16			GTTATACGAACAA	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.2547G>T	18.37:g.28710615C>A		244	0	0		256	105	0.410156	NM_024421	Q9HB01	Silent	SNP	ENST00000257198.5	37	CCDS11894.1																																																																																			C|0.914;A|0.086	0.086	strong		0.418	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421		A	28710615	C	A	28710615	2	1	22	1	0	0	0	0	0	0	0	1	4767	523	19	4		4	DSC1	18	28710615	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	28712	28710615	49366633	3659	6560											
DSC1	1823	hgsc.bcm.edu	37	chr18	28712639	28712639	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttagcagtgacacagaaacaTgtaaacagaatacctaaaaa	21	7	6	7	0	0	3	0	1	0	2	0	3	0	3	1	0	4	2	1	0	9	4	rs16961338	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28712639T>C	ENST00000257198.5	-	14	2391	c.2130A>G	c.(2128-2130)acA>acG	p.T710T	RP11-408H20.2_ENST00000581836.1_RNA|RP11-408H20.3_ENST00000582307.1_RNA|DSC1_ENST00000257197.3_Silent_p.T710T	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	710					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)			CACAGAAACATGTAAACAGAA	0.318													T|||	149	0.0297524	0.1097	0.0058	5008	,	,		17598	0.0		0.0	False		,,,				2504	0.0				p.T710T		Atlas-SNP	.											.	DSC1	240	.	0			c.A2130G						PASS	.	T	,	391,4013	195.7+/-220.2	15,361,1826	76	72	73		2130,2130	-3.4	1	18	dbSNP_123	73	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous,coding-synonymous	DSC1	NM_004948.3,NM_024421.2	,	15,363,6124	CC,CT,TT		0.0233,8.8783,3.0221	,	710/841,710/895	28712639	393,12611	2202	4300	6502	SO:0001819	synonymous_variant	1823	exon14			GAAACATGTAAAC	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.2130A>G	18.37:g.28712639T>C		144	0	0		104	50	0.480769	NM_004948	Q9HB01	Silent	SNP	ENST00000257198.5	37	CCDS11894.1																																																																																			T|0.959;C|0.041	0.041	strong		0.318	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421		C	28712639	T	C	28712639	2	2	22	1	0	0	0	0	0	0	0	1	4767	1451	51	3		3	DSC1	18	28712639	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2024	28712639	49364609	3660	6561											
DSG1	1828	hgsc.bcm.edu	37	chr18	28908178	28908178	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcagattgtgctgcaaaccaGcaagttacataccgcatctc	12	10	7	12	1	2	1	1	0	1	1	3	1	2	1	2	0	6	5	2	0	4	3	rs74368609	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28908178G>C	ENST00000257192.4	+	4	455	c.243G>C	c.(241-243)caG>caC	p.Q81H		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	81	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				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)			CTGCAAACCAGCAAGTTACAT	0.368													G|||	26	0.00519169	0.0189	0.0014	5008	,	,		19822	0.0		0.0	False		,,,				2504	0.0				p.Q81H		Atlas-SNP	.											.	DSG1	176	.	0			c.G243C						PASS	.	G	HIS/GLN	97,4309	78.8+/-117.2	0,97,2106	92	89	90		243	2.8	1	18	dbSNP_131	90	0,8598		0,0,4299	yes	missense	DSG1	NM_001942.2	24	0,97,6405	CC,CG,GG		0.0,2.2015,0.7459	probably-damaging	81/1050	28908178	97,12907	2203	4299	6502	SO:0001583	missense	1828	exon4			AAACCAGCAAGTT	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.243G>C	18.37:g.28908178G>C	ENSP00000257192:p.Gln81His	81	0	0		104	56	0.538462	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	17.26	3.343886	0.61073	0.022015	0.0	ENSG00000134760	ENST00000257192	T	0.61158	0.13	5.59	2.78	0.32641	Cadherin (4);Cadherin-like (1);	0.315599	0.27526	N	0.018975	T	0.47021	0.1423	L	0.59436	1.845	0.80722	D	1	D	0.60575	0.988	D	0.66196	0.942	T	0.54275	-0.8318	10	0.26408	T	0.33	.	4.6815	0.12738	0.3769:0.0:0.4739:0.1491	.	81	Q02413	DSG1_HUMAN	H	81	ENSP00000257192:Q81H	ENSP00000257192:Q81H	Q	+	3	2	DSG1	27162176	0.896000	0.30565	1.000000	0.80357	0.992000	0.81027	0.009000	0.13219	0.705000	0.31890	0.563000	0.77884	CAG	G|0.992;C|0.008	0.008	strong		0.368	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942		C	28908178	G	C	28908178	3	2	22	1	0	0	0	0	1	0	0	0	4778	962	34	4	257	4	DSG1	18	28908178	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	195539	28908178	49169070	3661	6562											
DSG1	1828	hgsc.bcm.edu	37	chr18	28923906	28923906	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taggatataaccactgtcatAccacaaataccacctgataa	17	9	4	11	0	1	1	1	1	0	0	1	2	1	2	4	1	3	0	4	1	7	6	rs116081362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28923906A>G	ENST00000257192.4	+	13	2051	c.1839A>G	c.(1837-1839)atA>atG	p.I613M	RP11-534N16.1_ENST00000581856.1_RNA|RP11-534N16.1_ENST00000578119.1_RNA|DSG1_ENST00000462981.2_5'UTR|RNU6-167P_ENST00000384292.1_RNA	NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	613					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)			CCACTGTCATACCACAAATAC	0.318													A|||	142	0.0283546	0.1021	0.0086	5008	,	,		15765	0.0		0.001	False		,,,				2504	0.0				p.I613M		Atlas-SNP	.											.	DSG1	176	.	0			c.A1839G						PASS	.	A	MET/ILE	385,4021	192.6+/-218.0	16,353,1834	124	114	118		1839	0.9	0	18	dbSNP_132	118	3,8593	3.0+/-9.4	0,3,4295	yes	missense	DSG1	NM_001942.2	10	16,356,6129	GG,GA,AA		0.0349,8.7381,2.9842	benign	613/1050	28923906	388,12614	2203	4298	6501	SO:0001583	missense	1828	exon13			TGTCATACCACAA	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.1839A>G	18.37:g.28923906A>G	ENSP00000257192:p.Ile613Met	145	0	0		161	73	0.453416	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	53	0.024267399267399268	49	0.09959349593495935	4	0.011049723756906077	0	0.0	0	0.0	A	7.734	0.699824	0.15106	0.087381	3.49E-4	ENSG00000134760	ENST00000257192	T	0.42513	0.97	4.98	0.91	0.19337	.	0.499779	0.18540	N	0.138233	T	0.00637	0.0021	N	0.14661	0.345	0.09310	N	0.999997	P	0.40266	0.71	P	0.45167	0.472	T	0.02533	-1.1145	10	0.37606	T	0.19	.	3.6502	0.08201	0.3746:0.2209:0.4045:0.0	.	613	Q02413	DSG1_HUMAN	M	613	ENSP00000257192:I613M	ENSP00000257192:I613M	I	+	3	3	DSG1	27177904	0.212000	0.23540	0.009000	0.14445	0.000000	0.00434	0.194000	0.17135	0.046000	0.15833	-0.291000	0.09656	ATA	A|0.967;G|0.033	0.033	strong		0.318	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942		G	28923906	A	G	28923906	3	3	22	1	0	0	0	0	1	0	0	0	4778	381	14	3	1889	3	DSG1	18	28923906	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	15728	28923906	49153342	3662	6563											
ELP2	55250	hgsc.bcm.edu	37	chr18	33744465	33744465	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaagagcatgcagctatcAttctttggaacactacatct	14	11	7	9	0	3	2	1	0	2	2	3	3	3	3	0	1	5	3	0	1	4	4	rs73428967	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:33744465A>G	ENST00000358232.6	+	18	1852	c.1789A>G	c.(1789-1791)Att>Gtt	p.I597V	ELP2_ENST00000442325.2_Missense_Mutation_p.I662V|ELP2_ENST00000423854.2_Missense_Mutation_p.I527V|ELP2_ENST00000350494.6_Missense_Mutation_p.I592V|ELP2_ENST00000542050.1_3'UTR|ELP2_ENST00000542824.1_Missense_Mutation_p.I527V|ELP2_ENST00000351393.6_Missense_Mutation_p.I571V	NM_018255.2	NP_060725.1	Q6IA86	ELP2_HUMAN	elongator acetyltransferase complex subunit 2	597					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						TGCAGCTATCATTCTTTGGAA	0.368													A|||	15	0.00299521	0.0113	0.0	5008	,	,		19841	0.0		0.0	False		,,,				2504	0.0				p.I662V		Atlas-SNP	.											.	ELP2	70	.	0			c.A1984G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	52,4354	52.3+/-87.9	1,50,2152	118	113	115		1984,1774,1711,1579,1579,1789	5.8	1	18	dbSNP_130	115	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense	ELP2	NM_001242875.1,NM_001242876.1,NM_001242877.1,NM_001242878.1,NM_001242879.1,NM_018255.2	29,29,29,29,29,29	1,50,6452	GG,GA,AA		0.0,1.1802,0.3998	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	662/892,592/822,571/801,527/757,527/757,597/827	33744465	52,12954	2203	4300	6503	SO:0001583	missense	55250	exon19			GCTATCATTCTTT	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.1789A>G	18.37:g.33744465A>G	ENSP00000350967:p.Ile597Val	143	0	0		176	80	0.454545	NM_001242875	A8KAI6|B4DTG0|B4DXP0|E7EP23|E9PCX0|Q53GZ0|Q687Y8|Q8N5C2|Q96GV4|Q96PI7|Q9H9N0|Q9NV81	Missense_Mutation	SNP	ENST00000358232.6	37	CCDS11918.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	18.12	3.554080	0.65425	0.011802	0.0	ENSG00000134759	ENST00000358232;ENST00000351393;ENST00000442325;ENST00000423854;ENST00000350494;ENST00000542824	T;T;T;T;T;T	0.65364	-0.15;2.26;1.09;2.26;0.0;-0.15	5.79	5.79	0.91817	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.103034	0.64402	D	0.000005	T	0.62756	0.2454	M	0.67625	2.065	0.54753	D	0.999986	P;P;P;P;P;P	0.49090	0.879;0.879;0.881;0.919;0.619;0.868	P;P;P;P;P;P	0.52031	0.688;0.688;0.527;0.672;0.511;0.472	T	0.66308	-0.5956	10	0.33940	T	0.23	-26.4385	14.0849	0.64949	1.0:0.0:0.0:0.0	.	592;662;527;527;571;597	B4DTG0;E7EP23;E9PCX0;Q6IA86-2;Q6IA86-3;Q6IA86	.;.;.;.;.;ELP2_HUMAN	V	597;571;662;527;592;527	ENSP00000350967:I597V;ENSP00000257191:I571V;ENSP00000414851:I662V;ENSP00000391202:I527V;ENSP00000316051:I592V;ENSP00000443800:I527V	ENSP00000316051:I592V	I	+	1	0	ELP2	31998463	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.037000	0.49775	2.208000	0.71279	0.533000	0.62120	ATT	A|0.997;G|0.003	0.003	strong		0.368	ELP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255800.2	NM_018255		G	33744465	A	G	33744465	3	3	22	1	0	0	0	0	1	0	0	0	5082	217	8	3	1859	3	ELP2	18	33744465	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	4820559	33744465	44332783	3663	6564											
PIK3C3	5289	hgsc.bcm.edu	37	chr18	39576682	39576682	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aagtttagatattatcttacGaatcaagaaaaagtgagtgt	17	13	8	3	1	2	3	1	1	1	2	2	4	2	3	0	0	1	1	0	0	9	5	rs140083392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:39576682G>A	ENST00000262039.4	+	9	1058	c.972G>A	c.(970-972)acG>acA	p.T324T	PIK3C3_ENST00000398870.3_Silent_p.T261T	NM_002647.2	NP_002638.2	Q8NEB9	PK3C3_HUMAN	phosphatidylinositol 3-kinase, catalytic subunit type 3	324	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						ATTATCTTACGAATCAAGAAA	0.279										TSP Lung(28;0.18)			G|||	5	0.000998403	0.0038	0.0	5008	,	,		15613	0.0		0.0	False		,,,				2504	0.0				p.T324T	NSCLC(37;552 1060 2683 16430 37914)	Atlas-SNP	.											PIK3C3,NS,carcinoma,+1,1	PIK3C3	138	1	0			c.G972A						scavenged	.	G		4,4392	8.1+/-20.4	0,4,2194	66	70	68		972	-5.3	1	18	dbSNP_134	68	0,8550		0,0,4275	no	coding-synonymous	PIK3C3	NM_002647.2		0,4,6469	AA,AG,GG		0.0,0.091,0.0309		324/888	39576682	4,12942	2198	4275	6473	SO:0001819	synonymous_variant	5289	exon9			TCTTACGAATCAA	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.972G>A	18.37:g.39576682G>A		186	1	0.00537634		163	65	0.398773	NM_002647	Q15134	Silent	SNP	ENST00000262039.4	37	CCDS11920.1																																																																																			G|0.999;A|0.001	0.001	strong		0.279	PIK3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255804.1	NM_002647		A	39576682	G	A	39576682	2	1	22	1	0	0	0	0	0	0	0	1	11921	1045	37	1		1	PIK3C3	18	39576682	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5832217	39576682	38500566	3664	6565											
TCEB3B	51224	hgsc.bcm.edu	37	chr18	44559578	44559578	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccgccgctgctgctctggctGgagggagtgtggctgcttcc	2	10	16	13	2	1	0	0	0	1	0	2	2	2	2	3	4	3	6	3	4	0	1	rs149717505	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:44559578G>A	ENST00000332567.4	-	1	2410	c.2058C>T	c.(2056-2058)tcC>tcT	p.S686S	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)	686					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						tgctCTGGCTGGAGGGAGTGT	0.627													G|||	9	0.00179712	0.0053	0.0029	5008	,	,		14981	0.0		0.0	False		,,,				2504	0.0				p.S686S		Atlas-SNP	.											.	TCEB3B	141	.	0			c.C2058T						PASS	.	G	,	25,4377		0,25,2176	38	43	41		2058,	1.1	0	18	dbSNP_134	41	0,8598		0,0,4299	no	coding-synonymous,intron	TCEB3B,KATNAL2	NM_016427.2,NM_031303.2	,	0,25,6475	AA,AG,GG		0.0,0.5679,0.1923	,	686/754,	44559578	25,12975	2201	4299	6500	SO:0001819	synonymous_variant	51224	exon1			CTGGCTGGAGGGA	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.2058C>T	18.37:g.44559578G>A		170	0	0		154	77	0.5	NM_016427	Q9P2V9	Silent	SNP	ENST00000332567.4	37	CCDS11932.1																																																																																			G|0.998;A|0.002	0.002	strong		0.627	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427		A	44559578	G	A	44559578	2	1	22	1	0	0	0	0	0	0	0	1	15697	1335	47	2		2	TCEB3B	18	44559578	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4982896	44559578	33517670	3665	6566											
TCEB3B	51224	hgsc.bcm.edu	37	chr18	44561069	44561069	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctcttccgggttgcttcccGggcgcagcgggctcagggcc	2	8	15	16	4	2	0	1	0	1	0	4	0	4	0	4	4	2	4	4	4	0	3	rs139088020	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:44561069G>T	ENST00000332567.4	-	1	919	c.567C>A	c.(565-567)ccC>ccA	p.P189P	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)	189					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						GTTGCTTCCCGGGCGCAGCGG	0.701													G|||	8	0.00159744	0.0053	0.0014	5008	,	,		13286	0.0		0.0	False		,,,				2504	0.0				p.P189P		Atlas-SNP	.											.	TCEB3B	141	.	0			c.C567A						PASS	.	G	,	20,4348		0,20,2164	24	28	27		567,	-0.2	0	18	dbSNP_134	27	0,8562		0,0,4281	no	coding-synonymous,intron	TCEB3B,KATNAL2	NM_016427.2,NM_031303.2	,	0,20,6445	TT,TG,GG		0.0,0.4579,0.1547	,	189/754,	44561069	20,12910	2184	4281	6465	SO:0001819	synonymous_variant	51224	exon1			CTTCCCGGGCGCA	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.567C>A	18.37:g.44561069G>T		50	0	0		70	41	0.585714	NM_016427	Q9P2V9	Silent	SNP	ENST00000332567.4	37	CCDS11932.1																																																																																			G|0.998;T|0.002	0.002	strong		0.701	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427		T	44561069	G	T	44561069	2	4	22	1	0	0	0	0	0	0	0	1	15697	1103	39	4		4	TCEB3B	18	44561069	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1491	44561069	33516179	3666	6567											
HDHD2	84064	hgsc.bcm.edu	37	chr18	44660923	44660923	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatgggtctgacttgtttcCgctctagtaaacttctggct	6	15	10	10	1	3	1	0	1	3	0	4	1	4	1	1	2	1	5	1	2	3	5	rs7230131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:44660923C>T	ENST00000300605.6	-	3	406	c.254G>A	c.(253-255)cGg>cAg	p.R85Q	HDHD2_ENST00000587841.1_Intron	NM_032124.4	NP_115500.1	Q9H0R4	HDHD2_HUMAN	haloacid dehalogenase-like hydrolase domain containing 2	85			R -> Q (in dbSNP:rs7230131).			extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)			kidney(2)|large_intestine(2)|lung(1)|skin(1)	6						GACTTGTTTCCGCTCTAGTAA	0.378													c|||	182	0.0363419	0.1293	0.0101	5008	,	,		18140	0.001		0.001	False		,,,				2504	0.002				p.R85Q		Atlas-SNP	.											.	HDHD2	12	.	0			c.G254A						PASS	.	C	GLN/ARG	435,3971	210.5+/-231.0	13,409,1781	110	108	109		254	3.6	1	18	dbSNP_116	109	4,8596	3.7+/-12.6	0,4,4296	yes	missense	HDHD2	NM_032124.4	43	13,413,6077	TT,TC,CC		0.0465,9.8729,3.3754	benign	85/260	44660923	439,12567	2203	4300	6503	SO:0001583	missense	84064	exon3			TGTTTCCGCTCTA	AL136681	CCDS32829.1	18q21.1	2008-02-05				ENSG00000167220			25364	protein-coding gene	gene with protein product						11230166	Standard	NM_032124		Approved	DKFZP564D1378	uc002lcs.3	Q9H0R4		ENST00000300605.6:c.254G>A	18.37:g.44660923C>T	ENSP00000300605:p.Arg85Gln	128	0	0		93	46	0.494624	NM_032124	A8K7T3|Q96NV4	Missense_Mutation	SNP	ENST00000300605.6	37	CCDS32829.1	55	0.025183150183150184	52	0.10569105691056911	3	0.008287292817679558	0	0.0	0	0.0	c	8.194	0.796607	0.16327	0.098729	4.65E-4	ENSG00000167220	ENST00000300605	T	0.29917	1.55	5.97	3.57	0.40892	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);	0.197776	0.44688	N	0.000433	T	0.00210	0.0006	N	0.02539	-0.55	0.26525	N	0.974354	B	0.02656	0.0	B	0.01281	0.0	T	0.26292	-1.0107	10	0.02654	T	1	2.3857	10.9093	0.47099	0.0:0.1293:0.0:0.8707	rs7230131;rs52803001;rs7230131	85	Q9H0R4	HDHD2_HUMAN	Q	85	ENSP00000300605:R85Q	ENSP00000300605:R85Q	R	-	2	0	HDHD2	42914921	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	4.293000	0.59037	1.077000	0.40990	-0.285000	0.09966	CGG	C|0.966;T|0.034	0.034	strong		0.378	HDHD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450668.2	NM_032124		T	44660923	C	T	44660923	3	4	22	1	0	0	0	0	1	0	0	0	7032	652	23	1	545	1	HDHD2	18	44660923	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	99854	44660923	33416325	3667	6568											
ZBTB7C	201501	hgsc.bcm.edu	37	chr18	45566903	45566903	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccttctctgtgagatggtcTgtcttggaagggctttggtg	4	15	15	7	0	3	1	0	1	3	1	4	3	3	2	1	4	0	1	1	4	1	3	rs114461217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:45566903T>C	ENST00000588982.1	-	3	1077	c.576A>G	c.(574-576)acA>acG	p.T192T	ZBTB7C_ENST00000332053.2_Silent_p.T192T|ZBTB7C_ENST00000535628.2_Silent_p.T192T|ZBTB7C_ENST00000586438.1_Silent_p.T192T|ZBTB7C_ENST00000590800.1_Silent_p.T192T			A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C	192							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						TGAGATGGTCTGTCTTGGAAG	0.567													C|||	43	0.00858626	0.0295	0.0043	5008	,	,		18424	0.0		0.001	False		,,,				2504	0.0				p.T192T		Atlas-SNP	.											.	ZBTB7C	73	.	0			c.A576G						PASS	.	C		134,4272	814.1+/-416.2	2,130,2071	110	107	108		576	-2	1	18	dbSNP_132	108	2,8598	819.2+/-406.8	0,2,4298	no	coding-synonymous	ZBTB7C	NM_001039360.2		2,132,6369	CC,CT,TT		0.0233,3.0413,1.0457		192/620	45566903	136,12870	2203	4300	6503	SO:0001819	synonymous_variant	201501	exon2			ATGGTCTGTCTTG	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.576A>G	18.37:g.45566903T>C		365	1	0.00273973		376	168	0.446809	NM_001039360	O73453	Silent	SNP	ENST00000588982.1	37	CCDS32830.1																																																																																			T|0.990;C|0.010	0.010	strong		0.567	ZBTB7C-025	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450731.1	NM_001039360		C	45566903	T	C	45566903	2	2	22	1	0	0	0	0	0	0	0	1	17570	1567	55	3		3	ZBTB7C	18	45566903	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	905980	45566903	32510345	3668	6569											
C18orf32	497661	hgsc.bcm.edu	37	chr18	47008736	47008736	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tagtctttctttttatcacaGatttctgttggtccttttgt	5	23	6	7	0	4	1	1	0	3	1	5	1	5	1	1	1	0	1	1	1	2	9	rs148432146	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:47008736G>A	ENST00000318240.3	-	3	421	c.210C>T	c.(208-210)atC>atT	p.I70I	C18orf32_ENST00000579820.1_Silent_p.I70I|RPL17-C18orf32_ENST00000332968.6_3'UTR|RPL17-C18orf32_ENST00000584895.1_3'UTR|RP11-110H1.4_ENST00000580150.1_RNA|C18orf32_ENST00000582392.1_Silent_p.I70I	NM_001035005.3	NP_001030177.1	Q8TCD1	CR032_HUMAN	chromosome 18 open reading frame 32	70					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)		signal transducer activity (GO:0004871)			large_intestine(2)|lung(1)	3						TTTTATCACAGATTTCTGTTG	0.348													G|||	5	0.000998403	0.003	0.0014	5008	,	,		17984	0.0		0.0	False		,,,				2504	0.0				p.I70I		Atlas-SNP	.											.	C18orf32	8	.	0			c.C210T						PASS	.	G	,,,	21,4383	28.1+/-56.4	0,21,2181	112	118	116		210,210,,	2.8	0.8	18	dbSNP_134	116	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous,utr-3,utr-3	C18orf32,RPL17-C18ORF32	NM_001035005.3,NM_001199346.1,NM_001199355.1,NM_001199356.1	,,,	0,21,6479	AA,AG,GG		0.0,0.4768,0.1615	,,,	70/77,70/77,,	47008736	21,12979	2202	4298	6500	SO:0001819	synonymous_variant	497661	exon3			ATCACAGATTTCT	AK027111	CCDS32831.1	18q21.1	2012-10-24			ENSG00000177576	ENSG00000177576			31690	protein-coding gene	gene with protein product							Standard	NM_001035005		Approved	FLJ23458	uc002ldl.3	Q8TCD1	OTTHUMG00000179688	ENST00000318240.3:c.210C>T	18.37:g.47008736G>A		104	0	0		96	56	0.583333	NM_001199346		Silent	SNP	ENST00000318240.3	37	CCDS32831.1																																																																																			G|0.999;A|0.001	0.001	strong		0.348	C18orf32-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447656.1	NM_001035005		A	47008736	G	A	47008736	2	1	22	1	0	0	0	0	0	0	0	1	1903	932	33	2		2	C18orf32	18	47008736	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1441833	47008736	31068512	3669	6570											
LIPG	9388	hgsc.bcm.edu	37	chr18	47088741	47088741	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tattgctttgctgcggggagCcccgtaccttttggtccaga	5	13	12	11	2	0	1	0	0	0	1	1	2	1	2	4	3	5	3	4	3	2	6	rs874566	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:47088741C>T	ENST00000261292.4	+	1	341	c.63C>T	c.(61-63)agC>agT	p.S21S	LIPG_ENST00000427224.2_Silent_p.S21S|LIPG_ENST00000577628.1_Intron|LIPG_ENST00000580036.1_Silent_p.S21S	NM_006033.2	NP_006024.1	Q9Y5X9	LIPE_HUMAN	lipase, endothelial	21					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						CTGCGGGGAGCCCCGTACCTT	0.557													C|||	224	0.0447284	0.1551	0.0216	5008	,	,		14167	0.0		0.004	False		,,,				2504	0.0				p.S21S	Pancreas(126;280 1778 12814 26243 34948)	Atlas-SNP	.											.	LIPG	47	.	0			c.C63T						PASS	.	C		677,3729	285.7+/-278.4	57,563,1583	81	81	81		63	2.6	0	18	dbSNP_86	81	37,8563	25.1+/-72.6	0,37,4263	no	coding-synonymous	LIPG	NM_006033.2		57,600,5846	TT,TC,CC		0.4302,15.3654,5.4898		21/501	47088741	714,12292	2203	4300	6503	SO:0001819	synonymous_variant	9388	exon1			GGGGAGCCCCGTA	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.63C>T	18.37:g.47088741C>T		113	0	0		93	46	0.494624	NM_006033	B0LPG6|Q6P9C8|Q6UW82	Silent	SNP	ENST00000261292.4	37	CCDS11938.1																																																																																			C|0.953;T|0.047	0.047	strong		0.557	LIPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447546.1	NM_006033		T	47088741	C	T	47088741	2	4	22	1	0	0	0	0	0	0	0	1	8832	738	26	2		2	LIPG	18	47088741	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	80005	47088741	30988507	3670	6571											
MYO5B	4645	hgsc.bcm.edu	37	chr18	47462657	47462657	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatcgttgggcttgatgcaGcggacatagtgaggtgtcgt	7	12	15	7	3	1	2	1	2	0	0	3	3	1	3	0	3	2	3	0	3	1	3	rs1627232	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:47462657G>A	ENST00000285039.7	-	16	2267	c.1968C>T	c.(1966-1968)cgC>cgT	p.R656R		NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	656	Actin-binding. {ECO:0000255}.|Myosin motor.		R -> C (in DIAR2). {ECO:0000269|PubMed:18724368}.		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)		GCTTGATGCAGCGGACATAGT	0.537													g|||	167	0.0333466	0.0923	0.0043	5008	,	,		19813	0.0268		0.0109	False		,,,				2504	0.0041				p.R656R		Atlas-SNP	.											.	MYO5B	178	.	0			c.C1968T						PASS	.	A		271,3913		12,247,1833	96	99	98		1968	1.7	1	18	dbSNP_89	98	15,8451		0,15,4218	no	coding-synonymous	MYO5B	NM_001080467.2		12,262,6051	AA,AG,GG		0.1772,6.4771,2.2609		656/1849	47462657	286,12364	2092	4233	6325	SO:0001819	synonymous_variant	4645	exon16			GATGCAGCGGACA	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.1968C>T	18.37:g.47462657G>A		145	0	0		143	63	0.440559	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	Silent	SNP	ENST00000285039.7	37	CCDS42436.1																																																																																			G|0.961;A|0.039	0.039	strong		0.537	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2			A	47462657	G	A	47462657	2	1	22	1	0	0	0	0	0	0	0	1	10088	958	34	2		2	MYO5B	18	47462657	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	373916	47462657	30614591	3671	6572											
MYO5B	4645	hgsc.bcm.edu	37	chr18	47506874	47506874	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccacacttccaaggtgcaaGatagaagcaattatcttaaa	16	9	7	9	0	1	2	0	0	1	2	2	2	2	2	2	1	2	2	2	1	8	4	rs16951352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:47506874G>T	ENST00000285039.7	-	9	1295	c.996C>A	c.(994-996)atC>atA	p.I332I		NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	332	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)		CAAGGTGCAAGATAGAAGCAA	0.418													G|||	61	0.0121805	0.0431	0.0043	5008	,	,		18907	0.0		0.001	False		,,,				2504	0.0				p.I332I		Atlas-SNP	.											.	MYO5B	178	.	0			c.C996A						PASS	.	G		125,3877		0,125,1876	117	113	114		996	4.3	1	18	dbSNP_123	114	11,8301		0,11,4145	no	coding-synonymous	MYO5B	NM_001080467.2		0,136,6021	TT,TG,GG		0.1323,3.1234,1.1044		332/1849	47506874	136,12178	2001	4156	6157	SO:0001819	synonymous_variant	4645	exon9			GTGCAAGATAGAA	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.996C>A	18.37:g.47506874G>T		139	0	0		134	60	0.447761	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	Silent	SNP	ENST00000285039.7	37	CCDS42436.1																																																																																			G|0.993;T|0.007	0.007	strong		0.418	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2			T	47506874	G	T	47506874	2	4	22	1	0	0	0	0	0	0	0	1	10088	932	33	4		4	MYO5B	18	47506874	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	44217	47506874	30570374	3672	6573											
CCDC11	220136	hgsc.bcm.edu	37	chr18	47788535	47788535	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attatgcttctgatggctgcGtcggattctttctagatggt	6	17	11	7	2	3	2	0	1	3	1	4	3	3	3	0	3	2	2	0	3	2	5	rs138060809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:47788535G>A	ENST00000398545.4	-	2	241	c.124C>T	c.(124-126)Cgc>Tgc	p.R42C		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)		TGATGGCTGCGTCGGATTCTT	0.433													G|||	5	0.000998403	0.0038	0.0	5008	,	,		18710	0.0		0.0	False		,,,				2504	0.0				p.R42C		Atlas-SNP	.											.	CCDC11	59	.	0			c.C124T						PASS	.	G	CYS/ARG	8,3834		0,8,1913	118	113	115		124	4.2	0	18	dbSNP_134	115	0,8250		0,0,4125	yes	missense	CCDC11	NM_145020.3	180	0,8,6038	AA,AG,GG		0.0,0.2082,0.0662	probably-damaging	42/515	47788535	8,12084	1921	4125	6046	SO:0001583	missense	220136	exon2			GGCTGCGTCGGAT																												ENST00000398545.4:c.124C>T	18.37:g.47788535G>A	ENSP00000381553:p.Arg42Cys	98	0	0		106	57	0.537736	NM_145020		Missense_Mutation	SNP	ENST00000398545.4	37	CCDS11940.2	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	6.779	0.512676	0.12944	0.002082	0.0	ENSG00000172361	ENST00000398545	T	0.35789	1.29	5.12	4.24	0.50183	.	0.138507	0.22268	U	0.062301	T	0.37237	0.0996	L	0.58101	1.795	0.09310	N	0.999996	D	0.64830	0.994	P	0.44477	0.451	T	0.35001	-0.9806	10	0.72032	D	0.01	0.0534	11.0958	0.48143	0.0:0.0:0.8151:0.1849	.	42	Q96M91	CCD11_HUMAN	C	42	ENSP00000381553:R42C	ENSP00000381553:R42C	R	-	1	0	CCDC11	46042533	0.058000	0.20735	0.003000	0.11579	0.110000	0.19582	3.065000	0.49994	1.503000	0.48686	-0.309000	0.09137	CGC	G|0.999;A|0.001	0.001	strong		0.433	CCDC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255922.3			A	47788535	G	A	47788535	3	1	22	1	0	0	0	0	1	0	0	0	2748	1145	40	1	1448	1	CCDC11	18	47788535	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	281661	47788535	30288713	3673	6574											
CXXC1	30827	hgsc.bcm.edu	37	chr18	47809710	47809710	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgctctgaggattatacacAtcacagaagagtcgtgtggc	11	11	11	8	1	2	3	1	1	1	2	3	4	2	4	0	2	2	1	0	2	3	3	rs150530383	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:47809710A>G	ENST00000285106.6	-	13	2310	c.1596T>C	c.(1594-1596)gaT>gaC	p.D532D	MBD1_ENST00000591416.1_5'Flank|CXXC1_ENST00000412036.2_Silent_p.D536D|MBD1_ENST00000585672.1_5'Flank|MBD1_ENST00000585595.1_5'Flank|MBD1_ENST00000424334.2_5'Flank|MBD1_ENST00000347968.3_5'Flank|MBD1_ENST00000457839.2_5'Flank|MBD1_ENST00000436910.1_5'Flank|MBD1_ENST00000587605.1_5'Flank|MBD1_ENST00000382948.5_5'Flank|MBD1_ENST00000269471.5_5'Flank|MBD1_ENST00000353909.3_5'Flank|MBD1_ENST00000349085.2_5'Flank|MBD1_ENST00000269468.5_5'Flank|MBD1_ENST00000398493.1_5'Flank|MBD1_ENST00000590208.1_5'Flank|CXXC1_ENST00000589940.1_Intron|MBD1_ENST00000339998.6_5'Flank|CXXC1_ENST00000587396.1_5'Flank	NM_001101654.1|NM_014593.3	NP_001095124.1|NP_055408.2	Q9P0U4	CXXC1_HUMAN	CXXC finger protein 1	532					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)|histone H3-K4 methylation (GO:0051568)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	24						GATTATACACATCACAGAAGA	0.572													A|||	11	0.00219649	0.0083	0.0	5008	,	,		18925	0.0		0.0	False		,,,				2504	0.0				p.D536D		Atlas-SNP	.											.	CXXC1	50	.	0			c.T1608C						PASS	.	A	,	12,4394	19.1+/-41.9	0,12,2191	133	139	137		1608,1596	1.9	1	18	dbSNP_134	137	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CXXC1	NM_001101654.1,NM_014593.3	,	0,12,6491	GG,GA,AA		0.0,0.2724,0.0923	,	536/661,532/657	47809710	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	30827	exon13			ATACACATCACAG	BC014940	CCDS11945.1, CCDS45866.1	18q12	2014-02-20	2014-02-20		ENSG00000154832	ENSG00000154832		"Zinc fingers, PHD-type"	24343	protein-coding gene	gene with protein product	"CpG binding protein", "DNA-binding protein with PHD finger and CXXC domain", "zinc finger, CpG binding-type containing 1"	609150	"CXXC finger 1 (PHD domain)"			10799292, 10688657	Standard	NM_014593		Approved	HsT2645, PCCX1, hCGBP, PHF18, CGBP, SPP1, CFP1, ZCGPC1	uc002ler.4	Q9P0U4	OTTHUMG00000132670	ENST00000285106.6:c.1596T>C	18.37:g.47809710A>G		108	0	0		147	74	0.503401	NM_001101654	B2RC03|Q8N2W4|Q96BC8|Q9P2V7	Silent	SNP	ENST00000285106.6	37	CCDS11945.1																																																																																			A|0.999;G|0.001	0.001	strong		0.572	CXXC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255927.2	NM_014593		G	47809710	A	G	47809710	2	3	22	1	0	0	0	0	0	0	0	1	4099	214	8	3		3	CXXC1	18	47809710	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	21175	47809710	30267538	3674	6575											
DCC	1630	hgsc.bcm.edu	37	chr18	50705370	50705370	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacacagcctgggtcccttcAgctcactgtgggaaacctga	10	8	10	13	0	2	1	2	1	0	0	3	2	3	2	3	2	4	1	3	2	2	1	rs116498325	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:50705370A>T	ENST00000442544.2	+	9	2073	c.1457A>T	c.(1456-1458)cAg>cTg	p.Q486L	DCC_ENST00000581580.1_Missense_Mutation_p.Q141L|DCC_ENST00000412726.1_Missense_Mutation_p.Q334L	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	486	Fibronectin type-III 1. {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)		GGGTCCCTTCAGCTCACTGTG	0.463													A|||	15	0.00299521	0.0106	0.0014	5008	,	,		16535	0.0		0.0	False		,,,				2504	0.0				p.Q486L		Atlas-SNP	.											.	DCC	360	.	0			c.A1457T						PASS	.	A	LEU/GLN	43,4363	46.0+/-80.4	1,41,2161	100	90	94		1457	5.6	1	18	dbSNP_132	94	0,8600		0,0,4300	yes	missense	DCC	NM_005215.3	113	1,41,6461	TT,TA,AA		0.0,0.9759,0.3306	possibly-damaging	486/1448	50705370	43,12963	2203	4300	6503	SO:0001583	missense	1630	exon9			CCCTTCAGCTCAC	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.1457A>T	18.37:g.50705370A>T	ENSP00000389140:p.Gln486Leu	107	0	0		164	78	0.47561	NM_005215		Missense_Mutation	SNP	ENST00000442544.2	37	CCDS11952.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	A	15.68	2.903669	0.52333	0.009759	0.0	ENSG00000187323	ENST00000442544;ENST00000304775;ENST00000412726	T;T	0.57752	0.38;0.38	5.62	5.62	0.85841	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.076791	0.52532	D	0.000063	T	0.63534	0.2519	M	0.72894	2.215	0.53688	D	0.999971	P;P;D	0.58970	0.769;0.769;0.984	P;P;D	0.65874	0.593;0.593;0.939	T	0.71533	-0.4564	10	0.87932	D	0	.	15.0981	0.72250	1.0:0.0:0.0:0.0	.	334;334;486	E7EQM8;B4DYX2;P43146	.;.;DCC_HUMAN	L	486;419;334	ENSP00000389140:Q486L;ENSP00000397322:Q334L	ENSP00000304146:Q419L	Q	+	2	0	DCC	48959368	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.534000	0.90620	2.266000	0.75297	0.533000	0.62120	CAG	A|0.996;T|0.004	0.004	strong		0.463	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		T	50705370	A	T	50705370	3	4	22	1	0	0	0	0	1	0	0	0	4284	188	7	5	1491	5	DCC	18	50705370	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2895660	50705370	27371878	3675	6576											
DCC	1630	hgsc.bcm.edu	37	chr18	50976898	50976898	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	attggacaaatgcaccccccGcatggcagtgtcactcctca	10	8	8	15	1	2	0	2	0	0	0	3	1	3	1	4	2	1	3	4	2	1	1	rs35891220	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:50976898G>A	ENST00000442544.2	+	23	3874	c.3258G>A	c.(3256-3258)ccG>ccA	p.P1086P	DCC_ENST00000581580.1_Silent_p.P721P	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	1086					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)		TGCACCCCCCGCATGGCAGTG	0.507													g|||	203	0.0405351	0.1172	0.0231	5008	,	,		17120	0.006		0.0119	False		,,,				2504	0.0143				p.P1086P		Atlas-SNP	.											DCC,colon,carcinoma,0,1	DCC	360	1	0			c.G3258A						scavenged	.	A		458,3948	219.1+/-236.9	22,414,1767	104	89	94		3258	-9.3	0.3	18	dbSNP_126	94	30,8570	19.8+/-62.0	0,30,4270	no	coding-synonymous	DCC	NM_005215.3		22,444,6037	AA,AG,GG		0.3488,10.3949,3.7521		1086/1448	50976898	488,12518	2203	4300	6503	SO:0001819	synonymous_variant	1630	exon23			CCCCCCGCATGGC	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.3258G>A	18.37:g.50976898G>A		117	1	0.00854701		127	64	0.503937	NM_005215		Silent	SNP	ENST00000442544.2	37	CCDS11952.1																																																																																			G|0.966;A|0.034	0.034	strong		0.507	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		A	50976898	G	A	50976898	2	1	22	1	0	0	0	0	0	0	0	1	4284	1074	38	1		1	DCC	18	50976898	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	271528	50976898	27100350	3676	6577											
TCF4	6925	hgsc.bcm.edu	37	chr18	52901894	52901894	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcctctcagggccacgccAtcttcacgatgggtccccac	6	8	9	18	2	3	0	2	0	2	0	5	1	4	0	5	2	1	0	5	2	0	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:52901894A>G	ENST00000356073.4	-	16	1982	c.1371T>C	c.(1369-1371)gaT>gaC	p.D457D	TCF4_ENST00000561992.1_Silent_p.D327D|TCF4_ENST00000566279.1_Silent_p.D397D|TCF4_ENST00000566286.1_Silent_p.D454D|TCF4_ENST00000568740.1_Silent_p.D432D|TCF4_ENST00000567880.1_Silent_p.D397D|TCF4_ENST00000570287.2_Silent_p.D297D|TCF4_ENST00000561831.3_Silent_p.D297D|TCF4_ENST00000398339.1_Silent_p.D559D|TCF4_ENST00000537578.1_Silent_p.D433D|TCF4_ENST00000543082.1_Silent_p.D415D|TCF4_ENST00000544241.2_Silent_p.D386D|TCF4_ENST00000540999.1_Silent_p.D433D|TCF4_ENST00000564999.1_Silent_p.D457D|TCF4_ENST00000537856.3_Silent_p.D327D|TCF4_ENST00000564403.2_Silent_p.D463D|TCF4_ENST00000565018.2_Silent_p.D457D|TCF4_ENST00000568673.1_Silent_p.D433D|TCF4_ENST00000570177.2_Silent_p.D327D|TCF4_ENST00000457482.3_Silent_p.D297D|TCF4_ENST00000354452.3_Silent_p.D457D|TCF4_ENST00000564228.1_Silent_p.D386D	NM_003199.2	NP_003190.1	P15884	ITF2_HUMAN	transcription factor 4	457					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)		GGGCCACGCCATCTTCACGAT	0.597											OREG0024990	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D559D		Atlas-SNP	.											.	TCF4	178	.	0			c.T1677C						PASS	.						92	95	94					18																	52901894		2203	4300	6503	SO:0001819	synonymous_variant	6925	exon17			CACGCCATCTTCA	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.1371T>C	18.37:g.52901894A>G		70	0	0	988	85	46	0.541176	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	37	CCDS11960.1																																																																																			.	.	none		0.597	TCF4-002	KNOWN	upstream_uORF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256014.1	NM_003199		G	52901894	A	G	52901894	2	3	22	1	0	0	0	0	0	0	0	1	15710	214	8	3		3	TCF4	18	52901894	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1924996	52901894	25175354	3677	6578											
ONECUT2	9480	hgsc.bcm.edu	37	chr18	55103476	55103477	+	In_Frame_Ins	INS	-	-	CAC																															ctcacccgcaccaccatccgINScaccaccaccaccaccacca																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:55103476_55103477insCAC	ENST00000491143.2	+	1	560_561	c.528_529insCAC	c.(529-531)cac>CACcac	p.177_177H>HH	AC090340.1_ENST00000581316.1_RNA	NM_004852.2	NP_004843.2	O95948	ONEC2_HUMAN	one cut homeobox 2	177	Poly-His.				cell fate commitment (GO:0045165)|cilium assembly (GO:0042384)|endocrine pancreas development (GO:0031018)|epithelial cell development (GO:0002064)|liver development (GO:0001889)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ morphogenesis (GO:0009887)|peripheral nervous system neuron development (GO:0048935)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)	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(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|lung(4)|ovary(2)|skin(1)	15		Colorectal(73;0.234)		READ - Rectum adenocarcinoma(59;0.227)|Colorectal(16;0.245)		accaccatccgcaccaccacca	0.658																																					p.P176delinsPH		Pindel,Atlas-Indel	.											.	ONECUT2	42	.	0			c.528_529insCAC						PASS	.																																			SO:0001652	inframe_insertion	9480	exon1			.	Y18198	CCDS42440.1	18q21.31	2012-03-09	2007-07-16		ENSG00000119547	ENSG00000119547		"Homeoboxes / CUT class"	8139	protein-coding gene	gene with protein product		604894	"one cut domain, family member 2"			9915796	Standard	NM_004852		Approved	OC-2	uc002lgo.3	O95948	OTTHUMG00000159776	ENST00000491143.2:c.550_552dupCAC	18.37:g.55103483_55103485dupCAC	ENSP00000419185:p.His184dup	63	0	.		66	11	0.167	NM_004852		In_Frame_Ins	INS	ENST00000491143.2	37	CCDS42440.1																																																																																			.	.	none		0.658	ONECUT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357264.3			CAC	55103477	-	CAC	55103476	7	5	22	1	0	1	1	0	0	0	0	0	10878	1074	38	0	530	0	ONECUT2	18	55103476	In_Frame_Ins	INS	-	TCGA-G8-6324-01A-11D-2210-10	2201582	55103476	22973772	3678	6579											
ATP8B1	5205	hgsc.bcm.edu	37	chr18	55334339	55334339	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcacttaatatcctccccaTagcagatggtggtgtcttca	9	13	7	12	0	3	1	2	0	1	1	5	1	5	1	3	2	1	1	3	2	3	4			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:55334339T>C	ENST00000283684.4	-	19	2269	c.2270A>G	c.(2269-2271)tAt>tGt	p.Y757C	RP11-35G9.3_ENST00000599199.1_RNA|ATP8B1_ENST00000536015.1_Missense_Mutation_p.Y757C|RP11-35G9.3_ENST00000592201.1_RNA|RP11-35G9.5_ENST00000588925.1_RNA|RP11-35G9.3_ENST00000591854.1_RNA			O43520	AT8B1_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 1	757					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)				ATCCTCCCCATAGCAGATGGT	0.368																																					p.Y757C		Atlas-SNP	.											.	ATP8B1	126	.	0			c.A2270G						PASS	.						114	107	109					18																	55334339		2203	4300	6503	SO:0001583	missense	5205	exon20			TCCCCATAGCAGA	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.2270A>G	18.37:g.55334339T>C	ENSP00000283684:p.Tyr757Cys	91	0	0		95	4	0.0421053	NM_005603	Q9BTP8	Missense_Mutation	SNP	ENST00000283684.4	37	CCDS11965.1	.	.	.	.	.	.	.	.	.	.	T	15.76	2.928583	0.52759	.	.	ENSG00000081923	ENST00000283684;ENST00000536015	T;T	0.67698	-0.28;-0.28	5.15	5.15	0.70609	HAD-like domain (2);	0.000000	0.85682	D	0.000000	T	0.77738	0.4175	L	0.59436	1.845	0.80722	D	1	D	0.65815	0.995	D	0.65773	0.938	T	0.79999	-0.1566	10	0.66056	D	0.02	.	14.945	0.71023	0.0:0.0:0.0:1.0	.	757	O43520	AT8B1_HUMAN	C	757	ENSP00000283684:Y757C;ENSP00000445359:Y757C	ENSP00000283684:Y757C	Y	-	2	0	ATP8B1	53485337	1.000000	0.71417	0.990000	0.47175	0.593000	0.36681	5.781000	0.68964	2.063000	0.61619	0.528000	0.53228	TAT	.	.	none		0.368	ATP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256097.1	NM_005603		C	55334339	T	C	55334339	3	2	22	1	0	0	0	0	1	0	0	0	1194	1406	49	3	1521	3	ATP8B1	18	55334339	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	230863	55334339	22742909	3679	6580											
TNFRSF11A	8792	hgsc.bcm.edu	37	chr18	60036547	60036547	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcgtgggttccccaaaacGtggacccttgccccagtgcg	6	8	11	16	3	0	0	0	0	0	0	2	1	1	1	6	2	3	1	6	2	2	2	rs35993683	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:60036547G>A	ENST00000586569.1	+	9	1435	c.1397G>A	c.(1396-1398)cGt>cAt	p.R466H	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	466					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)				TCCCCAAAACGTGGACCCTTG	0.662													G|||	61	0.0121805	0.0439	0.0043	5008	,	,		18183	0.0		0.0	False		,,,				2504	0.0				p.R466H		Atlas-SNP	.											.	TNFRSF11A	51	.	0			c.G1397A						PASS	.	G	HIS/ARG	142,4260		0,142,2059	37	38	38		1397	-0.8	0.1	18	dbSNP_126	38	1,8587		0,1,4293	yes	missense	TNFRSF11A	NM_003839.2	29	0,143,6352	AA,AG,GG		0.0116,3.2258,1.1008	benign	466/617	60036547	143,12847	2201	4294	6495	SO:0001583	missense	8792	exon9			CAAAACGTGGACC	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.1397G>A	18.37:g.60036547G>A	ENSP00000465500:p.Arg466His	27	0	0		27	12	0.444444	NM_003839	I4EC36|I4EC38|I4EC39|I7JE63|N0GVH0|Q59EP9	Missense_Mutation	SNP	ENST00000586569.1	37	CCDS11980.1	18	0.008241758241758242	16	0.032520325203252036	2	0.0055248618784530384	0	0.0	0	0.0	G	12.75	2.032926	0.35893	0.032258	1.16E-4	ENSG00000141655	ENST00000269485	.	.	.	5.03	-0.8	0.10897	.	3.161140	0.01102	N	0.005394	T	0.06735	0.0172	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.11155	-1.0599	8	.	.	.	0.0539	6.8356	0.23935	0.4461:0.1218:0.4321:0.0	rs35993683;rs61751991	466	Q9Y6Q6	TNR11_HUMAN	H	466	.	.	R	+	2	0	TNFRSF11A	58187527	0.037000	0.19845	0.081000	0.20488	0.362000	0.29581	-0.004000	0.12878	-0.089000	0.12484	-0.244000	0.11960	CGT	G|0.989;A|0.011	0.011	strong		0.662	TNFRSF11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256186.2			A	60036547	G	A	60036547	3	1	22	1	0	0	0	0	1	0	0	0	16299	1145	40	1	1431	1	TNFRSF11A	18	60036547	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4702208	60036547	18040701	3680	6581											
SERPINB12	89777	hgsc.bcm.edu	37	chr18	61234091	61234091	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttgtggaggtggatgaaaaCggtacccaggcagctgcagc	10	8	15	8	1	0	1	0	1	0	0	0	3	0	3	1	5	5	4	1	5	3	2	rs35623491	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61234091C>T	ENST00000269491.1	+	7	1065	c.1065C>T	c.(1063-1065)aaC>aaT	p.N355N	SERPINB12_ENST00000382768.1_Silent_p.N375N	NM_080474.1	NP_536722.1	Q96P63	SPB12_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 12	355					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						TGGATGAAAACGGTACCCAGG	0.453													C|||	184	0.0367412	0.1316	0.0101	5008	,	,		20333	0.0		0.003	False		,,,				2504	0.0				p.N355N		Atlas-SNP	.											.	SERPINB12	55	.	0			c.C1065T						PASS	.	C		482,3924	226.2+/-241.8	30,422,1751	78	82	80		1065	-4.4	0.1	18	dbSNP_126	80	1,8599		0,1,4299	no	coding-synonymous	SERPINB12	NM_080474.1		30,423,6050	TT,TC,CC		0.0116,10.9396,3.7137		355/406	61234091	483,12523	2203	4300	6503	SO:0001819	synonymous_variant	89777	exon7			TGAAAACGGTACC	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.1065C>T	18.37:g.61234091C>T		88	0	0		74	35	0.472973	NM_080474	Q3SYB4	Silent	SNP	ENST00000269491.1	37	CCDS11984.1																																																																																			C|0.962;T|0.038	0.038	strong		0.453	SERPINB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256197.1	NM_080474		T	61234091	C	T	61234091	2	4	22	1	0	0	0	0	0	0	0	1	14114	535	19	1		1	SERPINB12	18	61234091	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1197544	61234091	16843157	3681	6582											
SERPINB12	89777	hgsc.bcm.edu	37	chr18	61234144	61234144	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgtctcggaaaggtcactacGatcttgggtggagtttaatg	9	13	13	6	2	3	0	1	0	2	0	4	3	3	2	0	4	1	1	0	4	3	4	rs56812375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61234144G>A	ENST00000269491.1	+	7	1118	c.1118G>A	c.(1117-1119)cGa>cAa	p.R373Q	SERPINB12_ENST00000382768.1_Missense_Mutation_p.R393Q	NM_080474.1	NP_536722.1	Q96P63	SPB12_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 12	373					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						AGGTCACTACGATCTTGGGTG	0.453													G|||	172	0.034345	0.1256	0.0086	5008	,	,		21067	0.0		0.0	False		,,,				2504	0.0				p.R373Q		Atlas-SNP	.											SERPINB12,colon,carcinoma,0,1	SERPINB12	55	1	0			c.G1118A						PASS	.	G	GLN/ARG	455,3951	218.1+/-236.3	27,401,1775	78	77	77		1118	3.3	0	18	dbSNP_129	77	1,8599		0,1,4299	yes	missense	SERPINB12	NM_080474.1	43	27,402,6074	AA,AG,GG		0.0116,10.3268,3.5061	benign	373/406	61234144	456,12550	2203	4300	6503	SO:0001583	missense	89777	exon7			CACTACGATCTTG	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.1118G>A	18.37:g.61234144G>A	ENSP00000269491:p.Arg373Gln	73	0	0		72	33	0.458333	NM_080474	Q3SYB4	Missense_Mutation	SNP	ENST00000269491.1	37	CCDS11984.1	46	0.021062271062271064	43	0.08739837398373984	3	0.008287292817679558	0	0.0	0	0.0	G	6.154	0.396700	0.11638	0.103268	1.16E-4	ENSG00000166634	ENST00000269491;ENST00000382768	D;D	0.84146	-1.81;-1.81	6.01	3.29	0.37713	Serpin domain (3);	2.339550	0.01636	N	0.023778	T	0.08179	0.0204	N	0.16656	0.425	0.09310	N	1	B;B	0.26363	0.147;0.004	B;B	0.29524	0.103;0.001	T	0.49303	-0.8954	10	0.12766	T	0.61	.	7.6332	0.28251	0.0:0.6835:0.1241:0.1924	rs56812375;rs61741590	393;373	Q3SYB4;Q96P63	.;SPB12_HUMAN	Q	373;393	ENSP00000269491:R373Q;ENSP00000372218:R393Q	ENSP00000269491:R373Q	R	+	2	0	SERPINB12	59385124	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.232000	0.09055	0.892000	0.36259	-0.133000	0.14855	CGA	G|0.972;A|0.028	0.028	strong		0.453	SERPINB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256197.1	NM_080474		A	61234144	G	A	61234144	3	1	22	1	0	0	0	0	1	0	0	0	14114	1058	37	1	1144	1	SERPINB12	18	61234144	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	53	61234144	16843104	3682	6583											
SERPINB4	6318	hgsc.bcm.edu	37	chr18	61310738	61310738	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taggggaatagaagatgttgTtctcttttgattttctgaac	10	17	10	4	0	2	4	0	2	2	2	3	5	2	5	0	2	1	2	0	2	5	8	rs55883719	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61310738T>C	ENST00000341074.5	-	2	189	c.74A>G	c.(73-75)aAc>aGc	p.N25S	SERPINB4_ENST00000356424.6_Missense_Mutation_p.N25S	NM_002974.2	NP_002965.1	P48594	SPB4_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 4	25					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						GAAGATGTTGTTCTCTTTTGA	0.428													T|||	278	0.0555112	0.1989	0.0144	5008	,	,		19831	0.0		0.004	False		,,,				2504	0.001				p.N25S		Atlas-SNP	.											.	SERPINB4	89	.	0			c.A74G						PASS	.	T	SER/ASN	663,3743	282.2+/-276.4	47,569,1587	277	244	255		74	1.3	0	18	dbSNP_129	255	13,8587	9.8+/-36.6	0,13,4287	no	missense	SERPINB4	NM_002974.2	46	47,582,5874	CC,CT,TT		0.1512,15.0477,5.1976		25/391	61310738	676,12330	2203	4300	6503	SO:0001583	missense	6318	exon2			ATGTTGTTCTCTT	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.74A>G	18.37:g.61310738T>C	ENSP00000343445:p.Asn25Ser	550	0	0		547	254	0.464351	NM_002974	A8K847	Missense_Mutation	SNP	ENST00000341074.5	37	CCDS11986.1	97|97	0.044413919413919416|0.044413919413919416	89|89	0.18089430894308944|0.18089430894308944	6|6	0.016574585635359115|0.016574585635359115	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	T|T	4.847|4.847	0.157400|0.157400	0.09236|0.09236	0.150477|0.150477	0.001512|0.001512	ENSG00000206073|ENSG00000206073	ENST00000341074;ENST00000356424;ENST00000436264|ENST00000413673	D;D;D|.	0.83837|.	-1.77;-1.77;-1.77|.	3.83|3.83	1.31|1.31	0.21738|0.21738	Serpin domain (3);|.	1.227650|.	0.06602|.	N|.	0.754050|.	T|T	0.00039|0.00039	0.0001|0.0001	N|N	0.20445|0.20445	0.575|0.575	0.80722|0.80722	P|P	0.0|0.0	B;P|.	0.36183|.	0.102;0.542|.	B;B|.	0.34991|.	0.108;0.193|.	T|T	0.22836|0.22836	-1.0205|-1.0205	9|4	0.66056|.	D|.	0.02|.	.|.	4.2735|4.2735	0.10797|0.10797	0.0:0.277:0.1709:0.5521|0.0:0.277:0.1709:0.5521	rs55883719|rs55883719	25;25|.	P48594;Q9BYF7|.	SPB4_HUMAN;.|.	S|A	25|27	ENSP00000343445:N25S;ENSP00000348795:N25S;ENSP00000399796:N25S|.	ENSP00000343445:N25S|.	N|T	-|-	2|1	0|0	SERPINB4|SERPINB4	59461718|59461718	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.034000|0.034000	0.12701|0.12701	-0.758000|-0.758000	0.04766|0.04766	0.168000|0.168000	0.19655|0.19655	0.416000|0.416000	0.27883|0.27883	AAC|ACA	.	.	weak		0.428	SERPINB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133794.2	NM_175041		C	61310738	T	C	61310738	3	2	22	1	0	0	0	0	1	0	0	0	14118	1725	60	3	1126	3	SERPINB4	18	61310738	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	76594	61310738	16766510	3683	6584											
SERPINB3	6317	hgsc.bcm.edu	37	chr18	61322998	61322998	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctcttcattagttgaagtagGtgatgatccgaatcctacta	11	14	8	8	1	2	3	1	3	1	0	4	4	4	3	2	1	1	2	2	1	6	6	rs73962331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61322998G>A	ENST00000283752.5	-	8	1209	c.1066C>T	c.(1066-1068)Cct>Tct	p.P356S	SERPINB11_ENST00000489748.1_RNA|SERPINB3_ENST00000332821.8_Missense_Mutation_p.P304S	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	356					negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						GTTGAAGTAGGTGATGATCCG	0.463													G|||	286	0.0571086	0.205	0.0144	5008	,	,		20255	0.0		0.004	False		,,,				2504	0.001				p.P356S		Atlas-SNP	.											.	SERPINB3	90	.	0			c.C1066T						PASS	.	G	SER/PRO	674,3732	277.2+/-273.6	53,568,1582	145	147	147		1066	0.5	0	18	dbSNP_130	147	15,8585	9.8+/-36.6	0,15,4285	yes	missense	SERPINB3	NM_006919.2	74	53,583,5867	AA,AG,GG		0.1744,15.2973,5.2976	benign	356/391	61322998	689,12317	2203	4300	6503	SO:0001583	missense	6317	exon8			AAGTAGGTGATGA	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"Serine (or cysteine) peptidase inhibitors"	10569	protein-coding gene	gene with protein product		600517	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.1066C>T	18.37:g.61322998G>A	ENSP00000283752:p.Pro356Ser	215	0	0		203	71	0.349754	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Missense_Mutation	SNP	ENST00000283752.5	37	CCDS11987.1	99	0.04532967032967033	91	0.18495934959349594	6	0.016574585635359115	0	0.0	2	0.002638522427440633	G	1.994	-0.431080	0.04669	0.152973	0.001744	ENSG00000057149	ENST00000283752;ENST00000332821	D;D	0.83673	-1.75;-1.75	2.96	0.496	0.16896	Serpin domain (3);	3.431400	0.01103	N	0.005437	T	0.00178	0.0005	N	0.02181	-0.65	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.45483	-0.9258	9	0.02654	T	1	.	2.8087	0.05435	0.6154:0.1428:0.1014:0.1403	.	304;356	P29508-2;P29508	.;SPB3_HUMAN	S	356;304	ENSP00000283752:P356S;ENSP00000329498:P304S	ENSP00000283752:P356S	P	-	1	0	SERPINB3	59473978	0.018000	0.18449	0.004000	0.12327	0.000000	0.00434	0.503000	0.22610	0.107000	0.17824	-1.316000	0.01300	CCT	G|0.948;A|0.052	0.052	strong		0.463	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919		A	61322998	G	A	61322998	3	1	22	1	0	0	0	0	1	0	0	0	14117	1261	44	2	110	2	SERPINB3	18	61322998	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	12260	61322998	16754250	3684	6585											
SERPINB3	6317	hgsc.bcm.edu	37	chr18	61323011	61323012	+	Frame_Shift_Ins	INS	-	-	GCCA																															aagtaggtgatgatccgaatINScctactacagcggtggcagc																								rs60533853|rs3180227|rs386804125|rs72132327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61323011_61323012insGCCA	ENST00000283752.5	-	8	1195_1196	c.1052_1053insTGGC	c.(1051-1053)ggafs	p.G351fs	SERPINB11_ENST00000489748.1_RNA|SERPINB3_ENST00000332821.8_Frame_Shift_Ins_p.G299fs	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	351			G -> A (increased antiprotease activity and increased MAPK8 inhibition activity; dbSNP:rs3180227). {ECO:0000269|PubMed:12975381, ECO:0000269|PubMed:14970861, ECO:0000269|PubMed:21383048, ECO:0000269|Ref.6}.		negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						ATGATCCGAATCCTACTACAGC	0.49																																					p.G351fs		Atlas-Indel	.											.	SERPINB3	90	.	0			c.1053_1054insTGGC						PASS	.																																			SO:0001589	frameshift_variant	6317	exon8			.	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"Serine (or cysteine) peptidase inhibitors"	10569	protein-coding gene	gene with protein product		600517	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.1052_1053insTGGC	18.37:g.61323011_61323012insGCCA	ENSP00000283752:p.Gly351fs	212	0	0		192	49	0.255208	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Frame_Shift_Ins	INS	ENST00000283752.5	37	CCDS11987.1																																																																																			.	.	alt		0.49	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919		GCCA	61323012	-	GCCA	61323011	7	5	22	1	0	1	1	0	0	0	0	0	14117	1422	50	0	123	0	SERPINB3	18	61323011	Frame_Shift_Ins	INS	-	TCGA-G8-6324-01A-11D-2210-10	13	61323011	16754237	3685	6586	81	3									
SERPINB3	6317	hgsc.bcm.edu	37	chr18	61323012	61323014	+	In_Frame_Del	DEL	CCT	CCT	-																															aagtaggtgatgatccgaatCctactacagcggtggcagct																								rs3180227|rs60286570|rs386804125|rs72132327|rs201374310	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61323012_61323014delCCT	ENST00000283752.5	-	8	1193_1195	c.1050_1052delAGG	c.(1048-1053)gtagga>gta	p.G351del	SERPINB11_ENST00000489748.1_RNA|SERPINB3_ENST00000332821.8_In_Frame_Del_p.G299del	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	351			G -> A (increased antiprotease activity and increased MAPK8 inhibition activity; dbSNP:rs3180227). {ECO:0000269|PubMed:12975381, ECO:0000269|PubMed:14970861, ECO:0000269|PubMed:21383048, ECO:0000269|Ref.6}.		negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						TGATCCGAATCCTACTACAGCGG	0.488																																					p.351_351del		Pindel	.											.	SERPINB3	90	.	0			c.1051_1053del						PASS	.																																			SO:0001651	inframe_deletion	6317	exon8			.	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"Serine (or cysteine) peptidase inhibitors"	10569	protein-coding gene	gene with protein product		600517	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.1050_1052delAGG	18.37:g.61323012_61323014delCCT	ENSP00000283752:p.Gly351del	211	0	.		190	42	0.221	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	In_Frame_Del	DEL	ENST00000283752.5	37	CCDS11987.1																																																																																			.	.	alt		0.488	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919		-	61323014	CCT	-	61323012	7	5	22	1	0	1	0	1	0	0	0	0	14117	855	30	0	124	0	SERPINB3	18	61323012	In_Frame_Del	DEL	CCT	TCGA-G8-6324-01A-11D-2210-10	1	61323012	16754236	3686	6587	81	3									
SERPINB3	6317	hgsc.bcm.edu	37	chr18	61323014	61323014	+	Frame_Shift_Del	DEL	T	T	-																															gtaggtgatgatccgaatccTactacagcggtggcagctgc																								rs201374310|rs386804125|rs60286570	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61323014delT	ENST00000283752.5	-	8	1193	c.1050delA	c.(1048-1050)gtafs	p.V350fs	SERPINB11_ENST00000489748.1_RNA|SERPINB3_ENST00000332821.8_Frame_Shift_Del_p.V298fs	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	350					negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						ATCCGAATCCTACTACAGCGG	0.493																																					p.G351fs		Atlas-Indel	.											.	SERPINB3	90	.	0			c.1051delG						PASS	.			402,3860		46,310,1775	115	125	122			-4	0	18	dbSNP_130	124	9,8245		0,9,4118	no	frameshift	SERPINB3	NM_006919.2		46,319,5893	A1A1,A1R,RR		0.109,9.4322,3.2838			61323014	411,12105	2202	4300	6502	SO:0001589	frameshift_variant	6317	exon8			.	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"Serine (or cysteine) peptidase inhibitors"	10569	protein-coding gene	gene with protein product		600517	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.1050delA	18.37:g.61323014delT	ENSP00000283752:p.Val350fs	209	0	0		182	49	0.269231	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Frame_Shift_Del	DEL	ENST00000283752.5	37	CCDS11987.1																																																																																			T|0.960;-|0.040	0.040	strong		0.493	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919		-	61323014	T	-	61323014	7	5	22	1	0	1	0	1	0	0	0	0	14117	1509	53	0	126	0	SERPINB3	18	61323014	Frame_Shift_Del	DEL	T	TCGA-G8-6324-01A-11D-2210-10	2	61323014	16754234	3687	6588	81	3									
SERPINB3	6317	hgsc.bcm.edu	37	chr18	61323228	61323228	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggtaagtgtaaatcgacaCgtgtctctctcatattctgc	10	13	9	9	2	3	0	1	0	3	0	6	2	3	0	0	1	1	2	0	1	4	4	rs61748838	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61323228C>G	ENST00000283752.5	-	8	979	c.836G>C	c.(835-837)cGt>cCt	p.R279P	SERPINB11_ENST00000489748.1_RNA|SERPINB3_ENST00000332821.8_Missense_Mutation_p.R227P	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	279					negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						TAAATCGACACGTGTCTCTCT	0.413													c|||	286	0.0571086	0.205	0.0144	5008	,	,		20730	0.0		0.004	False		,,,				2504	0.001				p.R279P		Atlas-SNP	.											SERPINB3,caecum,carcinoma,0,1	SERPINB3	90	1	0			c.G836C						PASS	.	G	PRO/ARG	699,3707	292.4+/-282.0	53,593,1557	149	127	135		836	-0.9	0	18	dbSNP_129	135	15,8585	9.8+/-36.6	0,15,4285	no	missense	SERPINB3	NM_006919.2	103	53,608,5842	GG,GC,CC		0.1744,15.8647,5.4898	benign	279/391	61323228	714,12292	2203	4300	6503	SO:0001583	missense	6317	exon8			TCGACACGTGTCT	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"Serine (or cysteine) peptidase inhibitors"	10569	protein-coding gene	gene with protein product		600517	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.836G>C	18.37:g.61323228C>G	ENSP00000283752:p.Arg279Pro	232	0	0		230	121	0.526087	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Missense_Mutation	SNP	ENST00000283752.5	37	CCDS11987.1	100	0.045787545787545784	92	0.18699186991869918	6	0.016574585635359115	0	0.0	2	0.002638522427440633	c	9.127	1.010414	0.19277	0.158647	0.001744	ENSG00000057149	ENST00000283752;ENST00000332821	D;D	0.84944	-1.92;-1.92	3.07	-0.89	0.10577	Serpin domain (3);	4.332970	0.00769	N	0.001198	T	0.00300	0.0009	N	0.16368	0.405	0.80722	P	0.0	B;B	0.20164	0.042;0.0	B;B	0.33454	0.164;0.007	T	0.36529	-0.9744	9	0.66056	D	0.02	.	0.3718	0.00381	0.2731:0.1823:0.1396:0.405	rs61748838	227;279	P29508-2;P29508	.;SPB3_HUMAN	P	279;227	ENSP00000283752:R279P;ENSP00000329498:R227P	ENSP00000283752:R279P	R	-	2	0	SERPINB3	59474208	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.785000	0.04628	-0.480000	0.06803	-2.438000	0.00212	CGT	C|0.940;G|0.060	0.060	strong		0.413	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919		G	61323228	C	G	61323228	3	3	22	1	0	0	0	0	1	0	0	0	14117	536	19	4	340	4	SERPINB3	18	61323228	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	214	61323228	16754020	3688	6589											
SERPINB7	8710	hgsc.bcm.edu	37	chr18	61471593	61471593	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagaattatgaaatgaaacaAtatttgagagccctagggct	17	10	9	5	0	0	4	0	3	0	2	0	5	0	4	1	1	2	1	1	1	8	4	rs11873045	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61471593A>G	ENST00000398019.2	+	8	1192	c.867A>G	c.(865-867)caA>caG	p.Q289Q	SERPINB7_ENST00000540675.1_Silent_p.Q272Q|SERPINB7_ENST00000336429.2_Silent_p.Q289Q|SERPINB7_ENST00000546027.1_Silent_p.Q289Q	NM_003784.3	NP_003775.1	O75635	SPB7_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 7	289					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)				AAATGAAACAATATTTGAGAG	0.398													A|||	252	0.0503195	0.18	0.0173	5008	,	,		18557	0.0		0.002	False		,,,				2504	0.0				p.Q289Q		Atlas-SNP	.											.	SERPINB7	66	.	0			c.A867G						PASS	.	A	,	699,3707	288.4+/-279.8	52,595,1556	49	51	50		867,867	-1.4	0	18	dbSNP_120	50	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous,coding-synonymous	SERPINB7	NM_001040147.1,NM_003784.2	,	52,601,5850	GG,GA,AA		0.0698,15.8647,5.4206	,	289/381,289/381	61471593	705,12301	2203	4300	6503	SO:0001819	synonymous_variant	8710	exon8			GAAACAATATTTG	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.867A>G	18.37:g.61471593A>G		44	0	0		60	35	0.583333	NM_001261830	B4DUW8|F5GZC0|Q1ED45|Q3KPG4	Silent	SNP	ENST00000398019.2	37	CCDS11988.1																																																																																			A|0.943;G|0.057	0.057	strong		0.398	SERPINB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134007.1	NM_003784		G	61471593	A	G	61471593	2	3	22	1	0	0	0	0	0	0	0	1	14121	98	4	3		3	SERPINB7	18	61471593	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	148365	61471593	16605655	3689	6590											
SERPINB2	5055	hgsc.bcm.edu	37	chr18	61565014	61565014	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagaaccccaggcagtagaCttcctagaatgtgcagaaga	14	7	10	10	0	1	5	1	0	0	5	2	5	2	5	3	1	2	3	3	1	5	3	rs6106	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61565014C>T	ENST00000299502.4	+	5	551	c.471C>T	c.(469-471)gaC>gaT	p.D157D	SERPINB2_ENST00000457692.1_Silent_p.D157D|SERPINB2_ENST00000482254.1_3'UTR	NM_002575.2	NP_002566.1	P05120	PAI2_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 2	157					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)	AGGCAGTAGACTTCCTAGAAT	0.343													C|||	313	0.0625	0.2216	0.0259	5008	,	,		19658	0.0		0.002	False		,,,				2504	0.0				p.D157D		Atlas-SNP	.											.	SERPINB2	63	.	0			c.C471T						PASS	.	C	,	781,3625	308.0+/-290.3	67,647,1489	62	67	65		471,471	2.9	0.9	18	dbSNP_52	65	12,8588	9.1+/-34.3	0,12,4288	no	coding-synonymous,coding-synonymous	SERPINB2	NM_001143818.1,NM_002575.2	,	67,659,5777	TT,TC,CC		0.1395,17.7258,6.0972	,	157/416,157/416	61565014	793,12213	2203	4300	6503	SO:0001819	synonymous_variant	5055	exon5			AGTAGACTTCCTA	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.471C>T	18.37:g.61565014C>T		212	0	0		214	106	0.495327	NM_002575	Q96E96	Silent	SNP	ENST00000299502.4	37	CCDS11989.1	130	0.05952380952380952	117	0.23780487804878048	12	0.03314917127071823	0	0.0	1	0.0013192612137203166	C	8.325	0.825088	0.16678	0.177258	0.001395	ENSG00000242550	ENST00000397996;ENST00000418725	.	.	.	5.6	2.87	0.33458	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.09552	-1.0669	3	.	.	.	.	8.4939	0.33117	0.0:0.7035:0.0:0.2965	rs6106;rs6106	.	.	.	F	34	.	.	L	+	1	0	SERPINB10	59715994	1.000000	0.71417	0.946000	0.38457	0.866000	0.49608	0.916000	0.28651	0.418000	0.25898	-0.142000	0.14014	CTT	C|0.933;T|0.067	0.067	strong		0.343	SERPINB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134009.1	NM_002575		T	61565014	C	T	61565014	2	4	22	1	0	0	0	0	0	0	0	1	14116	564	20	2		2	SERPINB2	18	61565014	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	93421	61565014	16512234	3690	6591											
CDH19	28513	hgsc.bcm.edu	37	chr18	64235877	64235877	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttctttcatcaatgataaaaGtacttccagctccagctccc	11	13	4	13	0	3	1	2	1	1	0	6	1	6	1	3	0	3	3	3	0	4	5	rs114375304	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:64235877G>A	ENST00000540086.1	-	3	512	c.266C>T	c.(265-267)aCt>aTt	p.T89I	CDH19_ENST00000262150.2_Missense_Mutation_p.T89I	NM_001271028.1	NP_001257957.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	190	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)			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)				AATGATAAAAGTACTTCCAGC	0.398													G|||	71	0.0141773	0.0499	0.0072	5008	,	,		16014	0.0		0.0	False		,,,				2504	0.0				p.T89I		Atlas-SNP	.											CDH19,NS,carcinoma,-1,1	CDH19	141	1	0			c.C266T						PASS	.	G	ILE/THR	266,4140	150.3+/-184.3	15,236,1952	94	93	94		266	1.9	0.1	18	dbSNP_132	94	2,8594	2.2+/-6.3	0,2,4296	yes	missense	CDH19	NM_021153.2	89	15,238,6248	AA,AG,GG		0.0233,6.0372,2.0612	benign	89/773	64235877	268,12734	2203	4298	6501	SO:0001583	missense	28513	exon3			ATAAAAGTACTTC	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.266C>T	18.37:g.64235877G>A	ENSP00000439593:p.Thr89Ile	107	0	0		107	49	0.457944	NM_021153	O15098	Missense_Mutation	SNP	ENST00000540086.1	37	CCDS59325.1	29	0.013278388278388278	26	0.052845528455284556	3	0.008287292817679558	0	0.0	0	0.0	G	9.972	1.225826	0.22542	0.060372	2.33E-4	ENSG00000071991	ENST00000262150;ENST00000540086;ENST00000454642	T;T	0.51817	0.69;0.69	5.48	1.91	0.25777	Cadherin (5);Cadherin-like (1);	0.572976	0.18606	N	0.136310	T	0.01661	0.0053	N	0.02665	-0.54	0.22127	N	0.999345	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.19943	-1.0290	10	0.02654	T	1	.	7.9396	0.29950	0.7547:0.0:0.2453:0.0	.	89;89	F5H1K0;Q9H159	.;CAD19_HUMAN	I	89;89;34	ENSP00000262150:T89I;ENSP00000439593:T89I	ENSP00000262150:T89I	T	-	2	0	CDH19	62386857	0.762000	0.28451	0.145000	0.22337	0.830000	0.47004	3.161000	0.50747	0.396000	0.25283	-0.469000	0.05056	ACT	G|0.980;A|0.020	0.020	strong		0.398	CDH19-005	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000442285.1	NM_021153		A	64235877	G	A	64235877	3	1	22	1	0	0	0	0	1	0	0	0	3106	1029	36	2	2092	2	CDH19	18	64235877	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2670863	64235877	13841371	3691	6592											
DSEL	92126	hgsc.bcm.edu	37	chr18	65180706	65180706	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgtgaagagtactccacctTtgggcagttgaaggaaccat	11	10	12	8	0	0	3	0	2	0	1	1	4	1	4	3	2	2	3	3	2	4	3	rs9959648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:65180706T>C	ENST00000310045.7	-	2	2643	c.1170A>G	c.(1168-1170)caA>caG	p.Q390Q	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	380					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)				TACTCCACCTTTGGGCAGTTG	0.443													T|||	189	0.0377396	0.1362	0.013	5008	,	,		18891	0.0		0.0	False		,,,				2504	0.0				p.Q390Q		Atlas-SNP	.											.	DSEL	196	.	0			c.A1170G						PASS	.	T		566,3840	252.7+/-259.0	39,488,1676	117	104	108		1170	0.4	1	18	dbSNP_119	108	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	DSEL	NM_032160.2		39,491,5973	CC,CT,TT		0.0349,12.8461,4.3749		390/1223	65180706	569,12437	2203	4300	6503	SO:0001819	synonymous_variant	92126	exon2			CCACCTTTGGGCA	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.1170A>G	18.37:g.65180706T>C		67	0	0		68	68	1	NM_032160	Q17RH1|Q6P5Z3	Silent	SNP	ENST00000310045.7	37	CCDS11995.1																																																																																			T|0.949;C|0.051	0.051	strong		0.443	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160		C	65180706	T	C	65180706	2	2	22	1	0	0	0	0	0	0	0	1	4777	1838	64	3		3	DSEL	18	65180706	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	944829	65180706	12896542	3692	6593											
CCDC102B	79839	hgsc.bcm.edu	37	chr18	66678182	66678182	+	Missense_Mutation	SNP	C	C	A																															ctttgaaaggaattactgaaCcttcaacatgcctactataa																								rs17080065	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:66678182C>A	ENST00000360242.5	+	7	1392	c.1275C>A	c.(1273-1275)aaC>aaA	p.N425K	CCDC102B_ENST00000584156.1_Missense_Mutation_p.N425K|CCDC102B_ENST00000319445.6_Missense_Mutation_p.N425K	NM_024781.2	NP_079057	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B	425			N -> K (in dbSNP:rs17080065).							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)				AATTACTGAACCTTCAACATG	0.323													C|||	129	0.0257588	0.093	0.0086	5008	,	,		17732	0.0		0.0	False		,,,				2504	0.0				p.N425K		Atlas-SNP	.											.	CCDC102B	92	.	0			c.C1275A						PASS	.	C	LYS/ASN,LYS/ASN	354,4052	155.5+/-188.7	19,316,1868	62	60	60		1275,1275	-3.1	0	18	dbSNP_123	60	3,8597	1.2+/-3.3	0,3,4297	yes	missense,missense	CCDC102B	NM_001093729.1,NM_024781.2	94,94	19,319,6165	AA,AC,CC		0.0349,8.0345,2.7449	benign,benign	425/514,425/514	66678182	357,12649	2203	4300	6503	SO:0001583	missense	79839	exon9			ACTGAACCTTCAA	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.1275C>A	18.37:g.66678182C>A	ENSP00000353377:p.Asn425Lys	97	0	0		88	50	0.568182	NM_001093729	Q7Z467|Q8NDK7|Q9H5C1	Missense_Mutation	SNP	ENST00000360242.5	37	CCDS11996.2	47	0.02152014652014652	44	0.08943089430894309	3	0.008287292817679558	0	0.0	0	0.0	C	5.485	0.274466	0.10403	0.080345	3.49E-4	ENSG00000150636	ENST00000319445;ENST00000360242	T;T	0.11169	2.8;2.8	5.4	-3.11	0.05299	.	1.868220	0.02591	N	0.099920	T	0.00241	0.0007	N	0.22421	0.69	0.34315	D	0.685947	B	0.26400	0.148	B	0.24394	0.053	T	0.37572	-0.9700	10	0.10902	T	0.67	1.3033	1.8352	0.03138	0.4717:0.2442:0.0991:0.185	rs17080065;rs58253666;rs17080065	425	Q68D86	C102B_HUMAN	K	425	ENSP00000316237:N425K;ENSP00000353377:N425K	ENSP00000316237:N425K	N	+	3	2	CCDC102B	64829162	0.005000	0.15991	0.007000	0.13788	0.610000	0.37248	-1.893000	0.01609	-0.763000	0.04658	-0.355000	0.07637	AAC	C|0.972;A|0.028	0.028	strong		0.323	CCDC102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256225.2	NM_024781		A	66678182	C	A	66678182	3	1	22	1	0	0	0	0	1	0	0	0	2739	506	18	4	1297	4	CCDC102B	18	66678182	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1497476	66678182	11399066	3693	6594	82	2									
CCDC102B	79839	hgsc.bcm.edu	37	chr18	66678192	66678192	+	Missense_Mutation	SNP	G	G	C																															aattactgaaccttcaacatGcctactataaactaaacaga																								rs9963788	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:66678192G>C	ENST00000360242.5	+	7	1402	c.1285G>C	c.(1285-1287)Gcc>Ccc	p.A429P	CCDC102B_ENST00000584156.1_Missense_Mutation_p.A429P|CCDC102B_ENST00000319445.6_Missense_Mutation_p.A429P	NM_024781.2	NP_079057	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B	429			A -> P (in dbSNP:rs9963788).							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)				CCTTCAACATGCCTACTATAA	0.323													G|||	354	0.0706869	0.2572	0.0202	5008	,	,		17747	0.0		0.0	False		,,,				2504	0.0				p.A429P		Atlas-SNP	.											.	CCDC102B	92	.	0			c.G1285C						PASS	.	G	PRO/ALA,PRO/ALA	913,3493	333.9+/-303.2	116,681,1406	68	66	67		1285,1285	4.5	0.1	18	dbSNP_119	67	9,8591	4.3+/-15.6	0,9,4291	yes	missense,missense	CCDC102B	NM_001093729.1,NM_024781.2	27,27	116,690,5697	CC,CG,GG		0.1047,20.7217,7.089	probably-damaging,probably-damaging	429/514,429/514	66678192	922,12084	2203	4300	6503	SO:0001583	missense	79839	exon9			CAACATGCCTACT	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.1285G>C	18.37:g.66678192G>C	ENSP00000353377:p.Ala429Pro	97	0	0		104	104	1	NM_001093729	Q7Z467|Q8NDK7|Q9H5C1	Missense_Mutation	SNP	ENST00000360242.5	37	CCDS11996.2	127	0.05815018315018315	122	0.24796747967479674	5	0.013812154696132596	0	0.0	0	0.0	G	12.64	1.997195	0.35226	0.207217	0.001047	ENSG00000150636	ENST00000319445;ENST00000360242	T;T	0.12879	2.64;2.64	5.4	4.53	0.55603	.	0.266261	0.26851	N	0.022162	T	0.00012	0.0000	L	0.46157	1.445	0.09310	P	1.0	D	0.89917	1.0	D	0.66979	0.948	T	0.21759	-1.0236	9	0.59425	D	0.04	-2.2619	9.8768	0.41209	0.0944:0.0:0.9056:0.0	rs9963788;rs52813873;rs59666069;rs9963788	429	Q68D86	C102B_HUMAN	P	429	ENSP00000316237:A429P;ENSP00000353377:A429P	ENSP00000316237:A429P	A	+	1	0	CCDC102B	64829172	0.997000	0.39634	0.131000	0.22000	0.981000	0.71138	3.552000	0.53705	1.276000	0.44395	0.650000	0.86243	GCC	G|0.928;C|0.072	0.072	strong		0.323	CCDC102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256225.2	NM_024781		C	66678192	G	C	66678192	3	2	22	1	0	0	0	0	1	0	0	0	2739	1319	46	4	1307	4	CCDC102B	18	66678192	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	10	66678192	11399056	3694	6595	82	2									
NETO1	81832	hgsc.bcm.edu	37	chr18	70417378	70417378	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catctatgtcacaggcatctGcagcatcttgcgagtagctg	9	11	10	11	1	4	0	1	0	3	0	4	1	4	0	0	1	4	5	0	1	2	3	rs17086286	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:70417378G>C	ENST00000327305.6	-	9	2117	c.1460C>G	c.(1459-1461)gCa>gGa	p.A487G	NETO1_ENST00000583169.1_Missense_Mutation_p.A487G|NETO1_ENST00000299430.2_Missense_Mutation_p.A486G|RNA5SP460_ENST00000516789.1_RNA	NM_138966.3	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 1	487			A -> G (in dbSNP:rs17086286).		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)		ACAGGCATCTGCAGCATCTTG	0.488													G|||	94	0.01877	0.0688	0.0043	5008	,	,		18531	0.0		0.0	False		,,,				2504	0.0				p.A487G		Atlas-SNP	.											.	NETO1	178	.	0			c.C1460G						PASS	.	G	GLY/ALA,GLY/ALA	265,4141	149.9+/-184.0	4,257,1942	165	141	149		1460,1460	4.9	0.8	18	dbSNP_123	149	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense	NETO1	NM_001201465.1,NM_138966.3	60,60	4,260,6239	CC,CG,GG		0.0349,6.0145,2.0606	possibly-damaging,possibly-damaging	487/534,487/534	70417378	268,12738	2203	4300	6503	SO:0001583	missense	81832	exon9			GCATCTGCAGCAT	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.1460C>G	18.37:g.70417378G>C	ENSP00000313088:p.Ala487Gly	181	0	0		212	93	0.438679	NM_001201465	Q86W85|Q8ND78|Q8TDF4	Missense_Mutation	SNP	ENST00000327305.6	37	CCDS12000.1	34	0.015567765567765568	34	0.06910569105691057	0	0.0	0	0.0	0	0.0	G	17.20	3.327871	0.60743	0.060145	3.49E-4	ENSG00000166342	ENST00000327305;ENST00000299430	T;T	0.26518	1.74;1.73	5.76	4.86	0.63082	.	0.000000	0.64402	D	0.000014	T	0.02012	0.0063	L	0.42245	1.32	0.80722	D	1	P;P	0.40731	0.728;0.608	B;B	0.41036	0.346;0.188	T	0.00389	-1.1770	10	0.41790	T	0.15	-3.6568	16.2419	0.82418	0.0:0.0:0.8668:0.1332	rs17086286;rs52790393;rs17086286	486;487	Q8TDF5-2;Q8TDF5	.;NETO1_HUMAN	G	487;486	ENSP00000313088:A487G;ENSP00000299430:A486G	ENSP00000299430:A486G	A	-	2	0	NETO1	68568358	1.000000	0.71417	0.836000	0.33094	0.968000	0.65278	7.044000	0.76578	2.725000	0.93324	0.460000	0.39030	GCA	G|0.978;C|0.022	0.022	strong		0.488	NETO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256301.2	NM_138999		C	70417378	G	C	70417378	3	2	22	1	0	0	0	0	1	0	0	0	10348	1319	46	4	149	4	NETO1	18	70417378	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3739186	70417378	7659870	3695	6596											
ZNF407	55628	hgsc.bcm.edu	37	chr18	72344202	72344202	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggcagcacacggtaacagTgtaacctcgaggccaagacc	13	4	11	13	2	0	1	0	0	0	1	1	2	0	1	3	3	3	4	3	3	3	2	rs374837339		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:72344202T>C	ENST00000299687.5	+	1	1227	c.1227T>C	c.(1225-1227)agT>agC	p.S409S	ZNF407_ENST00000309902.6_Silent_p.S409S|ZNF407_ENST00000582337.1_Silent_p.S409S|ZNF407_ENST00000577538.1_Silent_p.S409S	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	409					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)		ACGGTAACAGTGTAACCTCGA	0.453																																					p.S409S		Atlas-SNP	.											.	ZNF407	231	.	0			c.T1227C						PASS	.	T	,,	1,3749		0,1,1874	57	59	58		1227,1227,1227	-3.8	0	18		58	0,8230		0,0,4115	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF407	NM_001146189.1,NM_001146190.1,NM_017757.2	,,	0,1,5989	CC,CT,TT		0.0,0.0267,0.0083	,,	409/1816,409/1661,409/2249	72344202	1,11979	1875	4115	5990	SO:0001819	synonymous_variant	55628	exon1			TAACAGTGTAACC	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.1227T>C	18.37:g.72344202T>C		112	0	0		119	66	0.554622	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Silent	SNP	ENST00000299687.5	37	CCDS45885.1																																																																																			.	.	weak		0.453	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		C	72344202	T	C	72344202	2	2	22	1	0	0	0	0	0	0	0	1	17902	1693	59	3		3	ZNF407	18	72344202	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1926824	72344202	5733046	3696	6597											
TSHZ1	10194	hgsc.bcm.edu	37	chr18	73000131	73000131	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcatgtcggacttgggcccGcaggagagggtgcacatctc	8	8	14	11	2	2	1	1	0	1	1	4	3	2	2	1	4	1	2	1	4	0	1	rs35073557	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:73000131G>A	ENST00000580243.1	+	2	3117	c.2769G>A	c.(2767-2769)ccG>ccA	p.P923P	TSHZ1_ENST00000322038.5_Silent_p.P878P			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	923					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)		ACTTGGGCCCGCAGGAGAGGG	0.592													G|||	69	0.013778	0.0477	0.0086	5008	,	,		19023	0.0		0.0	False		,,,				2504	0.0				p.P878P		Atlas-SNP	.											.	TSHZ1	104	.	0			c.G2634A						PASS	.	G		230,4176	136.5+/-172.5	6,218,1979	56	53	54		2634	-9.1	1	18	dbSNP_126	54	0,8600		0,0,4300	no	coding-synonymous	TSHZ1	NM_005786.4		6,218,6279	AA,AG,GG		0.0,5.2202,1.7684		878/1033	73000131	230,12776	2203	4300	6503	SO:0001819	synonymous_variant	10194	exon2			GGGCCCGCAGGAG	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.2769G>A	18.37:g.73000131G>A		69	0	0		68	37	0.544118	NM_005786	O60534|Q4LE29|Q53EU4	Silent	SNP	ENST00000580243.1	37																																																																																				G|0.981;A|0.019	0.019	strong		0.592	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786		A	73000131	G	A	73000131	2	1	22	1	0	0	0	0	0	0	0	1	16638	1074	38	1		1	TSHZ1	18	73000131	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	655929	73000131	5077117	3697	6598											
ZNF236	7776	hgsc.bcm.edu	37	chr18	74640002	74640002	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccaggtcctggcacaggccGctgggcccactgccacgtct	5	6	13	17	2	1	0	0	0	1	0	2	0	2	0	5	4	1	2	5	4	0	0	rs76679748	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:74640002G>A	ENST00000253159.8	+	25	4726	c.4528G>A	c.(4528-4530)Gct>Act	p.A1510T	ZNF236_ENST00000320610.9_Missense_Mutation_p.A1512T	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	1510					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)		GGCACAGGCCGCTGGGCCCAC	0.542													G|||	28	0.00559105	0.0204	0.0014	5008	,	,		13599	0.0		0.0	False		,,,				2504	0.0				p.A1510T		Atlas-SNP	.											.	ZNF236	325	.	0			c.G4528A						PASS	.	G	THR/ALA	32,3768		0,32,1868	45	49	48		4528	2.3	0	18	dbSNP_131	48	0,8234		0,0,4117	yes	missense	ZNF236	NM_007345.3	58	0,32,5985	AA,AG,GG		0.0,0.8421,0.2659	benign	1510/1846	74640002	32,12002	1900	4117	6017	SO:0001583	missense	7776	exon25			CAGGCCGCTGGGC	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.4528G>A	18.37:g.74640002G>A	ENSP00000253159:p.Ala1510Thr	180	0	0		200	99	0.495	NM_007345	B2RTX9|Q9UL37	Missense_Mutation	SNP	ENST00000253159.8	37	CCDS42447.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	0.098	-1.156936	0.01686	0.008421	0.0	ENSG00000130856	ENST00000253159;ENST00000543926;ENST00000320610	T;T	0.10192	2.9;3.06	5.07	2.3	0.28687	.	0.166139	0.45126	D	0.000391	T	0.02688	0.0081	N	0.04880	-0.145	0.09310	N	1	B	0.13145	0.007	B	0.08055	0.003	T	0.39461	-0.9613	10	0.25751	T	0.34	.	4.3857	0.11316	0.298:0.0:0.4852:0.2168	.	1510	Q9UL36	ZN236_HUMAN	T	1510	ENSP00000253159:A1510T;ENSP00000444524:A1510T	ENSP00000253159:A1510T	A	+	1	0	ZNF236	72768990	0.088000	0.21588	0.015000	0.15790	0.230000	0.25150	0.368000	0.20399	0.660000	0.30964	-1.276000	0.01395	GCT	G|0.996;A|0.004	0.004	strong		0.542	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1			A	74640002	G	A	74640002	3	1	22	1	0	0	0	0	1	0	0	0	17804	1087	38	1	4626	1	ZNF236	18	74640002	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1639871	74640002	3437246	3698	6599											
MBP	4155	hgsc.bcm.edu	37	chr18	74701936	74701936	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcttgaagaagtggactacGgggttttcatcttgggtccg	7	14	13	7	2	3	2	1	1	2	1	4	3	4	3	1	4	1	1	1	4	3	6	rs76912958	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:74701936G>A	ENST00000397869.3	-	2	304	c.258C>T	c.(256-258)ccC>ccT	p.P86P	MBP_ENST00000397865.5_Silent_p.P86P|MBP_ENST00000528160.1_Intron|MBP_ENST00000527041.1_Intron|MBP_ENST00000359645.3_Silent_p.P112P|MBP_ENST00000526111.1_Silent_p.P64P|MBP_ENST00000580402.1_Silent_p.P219P|MBP_ENST00000397875.3_Silent_p.P86P|MBP_ENST00000382582.3_Silent_p.P112P|MBP_ENST00000579129.1_Silent_p.P219P|MBP_ENST00000355994.2_Silent_p.P219P|MBP_ENST00000354542.4_Intron|MBP_ENST00000578193.1_Silent_p.P86P|MBP_ENST00000397866.4_Silent_p.P86P			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)	AGTGGACTACGGGGTTTTCAT	0.572													G|||	129	0.0257588	0.0923	0.0101	5008	,	,		17532	0.0		0.0	False		,,,				2504	0.0				p.P219P	NSCLC(17;72 1131 19392)	Atlas-SNP	.											.	MBP	45	.	0			c.C657T						PASS	.	G	,,,,	327,4079	172.3+/-202.3	8,311,1884	179	160	167		336,258,258,657,336	-6.3	1	18	dbSNP_131	167	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MBP	NM_001025081.1,NM_001025090.1,NM_001025092.1,NM_001025101.1,NM_002385.2	,,,,	8,315,6180	AA,AG,GG		0.0465,7.4217,2.545	,,,,	112/198,86/172,86/161,219/305,112/187	74701936	331,12675	2203	4300	6503	SO:0001819	synonymous_variant	4155	exon5			GACTACGGGGTTT		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.258C>T	18.37:g.74701936G>A		153	0	0		148	72	0.486486	NM_001025101	A6XMW0|B2R5I1|P81448|Q14227|Q6ICT2	Silent	SNP	ENST00000397869.3	37																																																																																				G|0.977;A|0.023	0.023	strong		0.572	MBP-024	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000267964.1	NM_001025081		A	74701936	G	A	74701936	2	1	22	1	0	0	0	0	0	0	0	1	9368	1103	39	1		1	MBP	18	74701936	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	61934	74701936	3375312	3699	6600											
MIER2	54531	hgsc.bcm.edu	37	chr19	307282	307282	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgctgaggtccacatggcTggagatgaggggcagctcct	7	7	15	12	1	0	3	0	2	0	1	2	4	2	3	3	5	1	4	3	5	0	0	rs35042658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:307282T>C	ENST00000264819.4	-	13	1463	c.1453A>G	c.(1453-1455)Agc>Ggc	p.S485G	CTD-3113P16.5_ENST00000591533.1_RNA	NM_017550.1	NP_060020.1	Q8N344	MIER2_HUMAN	mesoderm induction early response 1, family member 2	485			S -> G (in dbSNP:rs35042658).		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)		TCCACATGGCTGGAGATGAGG	0.647													T|||	249	0.0497204	0.1808	0.013	5008	,	,		15517	0.0		0.001	False		,,,				2504	0.0				p.S485G		Atlas-SNP	.											.	MIER2	51	.	0			c.A1453G						PASS	.	T	GLY/SER	552,3848		29,494,1677	28	25	26		1453	3	0.2	19	dbSNP_126	26	9,8589		0,9,4290	yes	missense	MIER2	NM_017550.1	56	29,503,5967	CC,CT,TT		0.1047,12.5455,4.316	benign	485/546	307282	561,12437	2200	4299	6499	SO:0001583	missense	54531	exon13			CATGGCTGGAGAT	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.1453A>G	19.37:g.307282T>C	ENSP00000264819:p.Ser485Gly	133	0	0		161	85	0.52795	NM_017550	Q9ULM7	Missense_Mutation	SNP	ENST00000264819.4	37	CCDS32855.1	112	0.05128205128205128	108	0.21951219512195122	4	0.011049723756906077	0	0.0	0	0.0	T	5.043	0.193576	0.09599	0.125455	0.001047	ENSG00000105556	ENST00000264819	T	0.15834	2.39	4.02	3.0	0.34707	.	0.118436	0.38058	N	0.001834	T	0.00012	0.0000	N	0.25485	0.75	0.42449	P	0.007252000000000036	B	0.06786	0.001	B	0.04013	0.001	T	0.37934	-0.9684	9	0.33940	T	0.23	-8.985	5.2116	0.15320	0.0:0.2476:0.0:0.7524	rs35042658	485	Q8N344	MIER2_HUMAN	G	485	ENSP00000264819:S485G	ENSP00000264819:S485G	S	-	1	0	MIER2	258282	1.000000	0.71417	0.220000	0.23810	0.106000	0.19336	1.279000	0.33191	0.701000	0.31803	0.533000	0.62120	AGC	T|0.946;C|0.054	0.054	strong		0.647	MIER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451784.1	XM_041843		C	307282	T	C	307282	3	2	22	1	0	0	0	0	1	0	0	0	9590	1580	55	3	192	3	MIER2	19	307282	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10		307282	58821701	3700	6601											
THEG	51298	hgsc.bcm.edu	37	chr19	373531	373531	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcggtccagtacacagagggCctggaataagcggacggctc	10	6	14	11	3	0	1	0	0	0	1	3	3	1	3	2	5	2	2	2	5	3	2	rs73489977	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:373531C>T	ENST00000342640.4	-	4	546	c.504G>A	c.(502-504)tgG>tgA	p.W168*	THEG_ENST00000346878.2_Splice_Site_p.R144R	NM_016585.4	NP_057669.1	Q9P2T0	THEG_HUMAN	theg spermatid protein	168					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)		ACACAGAGGGCCTGGAATAAG	0.677													C|||	186	0.0371406	0.1339	0.0115	5008	,	,		15295	0.0		0.001	False		,,,				2504	0.0				p.W168X		Atlas-SNP	.											.	THEG	58	.	0			c.G504A						PASS	.	C	stop/TRP,	514,3892	229.4+/-244.0	23,468,1712	44	39	41		504,432	3	1	19	dbSNP_130	41	3,8597	3.0+/-9.4	0,3,4297	yes	stop-gained-near-splice,coding-synonymous-near-splice	THEG	NM_016585.3,NM_199202.1	,	23,471,6009	TT,TC,CC		0.0349,11.6659,3.9751	,	168/380,144/356	373531	517,12489	2203	4300	6503	SO:0001630	splice_region_variant	51298	exon4			AGAGGGCCTGGAA	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.504-1G>A	19.37:g.373531C>T		134	0	0		166	86	0.518072	NM_016585	A6NMJ8	Nonsense_Mutation	SNP	ENST00000342640.4	37	CCDS12025.1	61	0.027930402930402932	56	0.11382113821138211	5	0.013812154696132596	0	0.0	0	0.0	C	16.59	3.166200	0.57476	0.116659	3.49E-4	ENSG00000105549	ENST00000342640	.	.	.	3.03	3.03	0.35002	.	0.466367	0.16510	N	0.211261	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	.	9.7902	0.40702	0.0:1.0:0.0:0.0	.	.	.	.	X	168	.	ENSP00000340088:W168X	W	-	3	0	THEG	324531	1.000000	0.71417	0.985000	0.45067	0.153000	0.21895	3.225000	0.51246	2.008000	0.58898	0.561000	0.74099	TGG	C|0.960;T|0.040	0.040	strong		0.677	THEG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384431.2		Nonsense_Mutation	T	373531	C	T	373531	5	4	22	1	0	0	0	0	0	0	1	0	15872	753	26	2	655	2	THEG	19	373531	Splice_Site	SNP	C	TCGA-G8-6324-01A-11D-2210-10	66249	373531	58755452	3701	6602											
SHC2	25759	hgsc.bcm.edu	37	chr19	422229	422229	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atactgcccggggttggtgaCgctgtctcgcacaaggaagt	8	9	14	10	3	1	1	0	1	1	0	2	2	1	2	1	4	2	3	1	4	3	2	rs61750917	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:422229C>T	ENST00000264554.6	-	11	1536	c.1537G>A	c.(1537-1539)Gtc>Atc	p.V513I		NM_012435.2	NP_036567.2	P98077	SHC2_HUMAN	SHC (Src homology 2 domain containing) transforming protein 2	513	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				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)		GGGTTGGTGACGCTGTCTCGC	0.672													C|||	93	0.0185703	0.0651	0.0086	5008	,	,		14638	0.0		0.001	False		,,,				2504	0.0				p.V513I		Atlas-SNP	.											SHC2,colon,carcinoma,0,1	SHC2	47	1	0			c.G1537A						PASS	.	C	ILE/VAL	310,4082		12,286,1898	23	29	27		1537	-1.1	1	19	dbSNP_129	27	2,8592		0,2,4295	yes	missense	SHC2	NM_012435.2	29	12,288,6193	TT,TC,CC		0.0233,7.0583,2.4026	benign	513/583	422229	312,12674	2196	4297	6493	SO:0001583	missense	25759	exon11			TGGTGACGCTGTC	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.1537G>A	19.37:g.422229C>T	ENSP00000264554:p.Val513Ile	128	0	0		136	62	0.455882	NM_012435	O60230|Q9NPL5|Q9UCX4	Missense_Mutation	SNP	ENST00000264554.6	37	CCDS45891.1	37	0.01694139194139194	34	0.06910569105691057	3	0.008287292817679558	0	0.0	0	0.0	C	8.377	0.836675	0.16891	0.070583	2.33E-4	ENSG00000129946	ENST00000264554	D	0.88431	-2.38	4.76	-1.12	0.09808	SH2 motif (5);	0.368945	0.29624	N	0.011635	T	0.16642	0.0400	N	0.02985	-0.445	0.24255	N	0.995303	B	0.12630	0.006	B	0.14023	0.01	T	0.49351	-0.8949	10	0.37606	T	0.19	-39.6557	8.286	0.31928	0.0:0.4041:0.0:0.5959	.	513	P98077	SHC2_HUMAN	I	513	ENSP00000264554:V513I	ENSP00000264554:V513I	V	-	1	0	SHC2	373229	0.748000	0.28294	0.991000	0.47740	0.309000	0.27889	-0.010000	0.12743	0.029000	0.15352	-0.812000	0.03155	GTC	C|0.981;T|0.019	0.019	strong		0.672	SHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451840.3			T	422229	C	T	422229	3	4	22	1	0	0	0	0	1	0	0	0	14286	536	19	1	219	1	SHC2	19	422229	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	48698	422229	58706754	3702	6603											
C19orf20	91978	hgsc.bcm.edu	37	chr19	507560	507560	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccaccgccggccggtttcacGgacagcggccgccagtcggt	5	5	14	17	7	1	0	1	0	0	0	2	1	1	1	6	5	1	1	6	5	0	1	rs61746565	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:507560G>A	ENST00000359315.5	+	1	262	c.54G>A	c.(52-54)acG>acA	p.T18T	AC005775.2_ENST00000592413.1_RNA	NM_033513.2	NP_277048.2	Q6ZTW0	TPGS1_HUMAN	tubulin polyglutamylase complex subunit 1	18					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)										CCGGTTTCACGGACAGCGGCC	0.706													G|||	35	0.00698882	0.025	0.0029	5008	,	,		11141	0.0		0.0	False		,,,				2504	0.0				p.T18T		Atlas-SNP	.											.	.	.	.	0			c.G54A						PASS	.						3	5	5					19																	507560		1241	3077	4318	SO:0001819	synonymous_variant	91978	exon1			TTTCACGGACAGC	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.54G>A	19.37:g.507560G>A		18	0	0		24	23	0.958333	NM_033513	Q96GE2	Silent	SNP	ENST00000359315.5	37	CCDS42454.1																																																																																			G|0.991;A|0.009	0.009	strong		0.706	TPGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451887.2	NM_033513		A	507560	G	A	507560	2	1	22	1	0	0	0	0	0	0	0	1	1914	1103	39	1		1	C19orf20	19	507560	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	85331	507560	58621423	3703	6604											
POLRMT	5442	hgsc.bcm.edu	37	chr19	617573	617573	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtcagggagcgccttactcaGagcagaaccgcttgaccagg	10	6	13	12	2	2	3	2	1	0	2	2	4	2	4	3	2	4	2	3	2	2	2	rs142850300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:617573G>A	ENST00000588649.2	-	19	3662	c.3578C>T	c.(3577-3579)tCt>tTt	p.S1193F	AC005559.2_ENST00000591847.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	1193	Mediates interaction with TEFM.				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)		GCCTTACTCAGAGCAGAACCG	0.637													g|||	29	0.00579073	0.0197	0.0043	5008	,	,		11732	0.0		0.0	False		,,,				2504	0.0				p.S1193F		Atlas-SNP	.											.	POLRMT	91	.	0			c.C3578T						PASS	.	G	PHE/SER	73,4333		1,71,2131	42	41	41		3578	2.1	0	19	dbSNP_134	41	0,8600		0,0,4300	yes	missense	POLRMT	NM_005035.3	155	1,71,6431	AA,AG,GG		0.0,1.6568,0.5613	benign	1193/1231	617573	73,12933	2203	4300	6503	SO:0001583	missense	5442	exon19			TACTCAGAGCAGA		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.3578C>T	19.37:g.617573G>A	ENSP00000465759:p.Ser1193Phe	37	0	0		38	25	0.657895	NM_005035	O60370	Missense_Mutation	SNP	ENST00000588649.2	37	CCDS12036.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	.	0.192	-1.052853	0.01965	0.016568	0.0	ENSG00000099821	ENST00000215591	T	0.47528	0.84	3.21	2.12	0.27331	.	1.125910	0.06566	N	0.747594	T	0.31638	0.0803	M	0.68317	2.08	0.09310	N	1	B	0.14805	0.011	B	0.26310	0.068	T	0.36529	-0.9744	10	0.37606	T	0.19	.	7.4584	0.27280	0.0:0.0:0.7418:0.2582	.	1193	O00411	RPOM_HUMAN	F	1193	ENSP00000215591:S1193F	ENSP00000215591:S1193F	S	-	2	0	POLRMT	568573	0.086000	0.21541	0.007000	0.13788	0.002000	0.02628	1.811000	0.38942	0.645000	0.30675	0.431000	0.28591	TCT	G|0.995;A|0.005	0.005	strong		0.637	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035		A	617573	G	A	617573	3	1	22	1	0	0	0	0	1	0	0	0	12247	942	33	2	126	2	POLRMT	19	617573	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	110013	617573	58511410	3704	6605											
POLRMT	5442	hgsc.bcm.edu	37	chr19	617804	617804	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgacggagacatcagctgcGtgagtccagtaacagtcgtg	11	8	13	9	3	1	3	1	2	0	1	3	4	2	3	1	1	3	2	1	1	1	1	rs144281668	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:617804G>A	ENST00000588649.2	-	18	3552	c.3468C>T	c.(3466-3468)caC>caT	p.H1156H	AC005559.2_ENST00000591847.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	1156	Mediates interaction with TEFM.				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)		CATCAGCTGCGTGAGTCCAGT	0.642													g|||	3	0.000599042	0.0023	0.0	5008	,	,		11388	0.0		0.0	False		,,,				2504	0.0				p.H1156H		Atlas-SNP	.											.	POLRMT	91	.	0			c.C3468T						PASS	.	G		13,4391		0,13,2189	83	65	71		3468	-7.8	0	19	dbSNP_134	71	1,8597		0,1,4298	no	coding-synonymous	POLRMT	NM_005035.3		0,14,6487	AA,AG,GG		0.0116,0.2952,0.1077		1156/1231	617804	14,12988	2202	4299	6501	SO:0001819	synonymous_variant	5442	exon18			AGCTGCGTGAGTC		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.3468C>T	19.37:g.617804G>A		128	0	0		139	58	0.417266	NM_005035	O60370	Silent	SNP	ENST00000588649.2	37	CCDS12036.1																																																																																			G|0.999;A|0.001	0.001	strong		0.642	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035		A	617804	G	A	617804	2	1	22	1	0	0	0	0	0	0	0	1	12247	1136	40	1		1	POLRMT	19	617804	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	231	617804	58511179	3705	6606											
POLRMT	5442	hgsc.bcm.edu	37	chr19	622304	622304	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctgcactggcaggggccaggGctgctcccgcagggcctcgg	4	5	17	15	2	0	0	0	0	0	0	2	0	1	0	3	6	2	5	3	6	0	0	rs41545023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:622304G>A	ENST00000588649.2	-	9	1780	c.1696C>T	c.(1696-1698)Ccc>Tcc	p.P566S	LLNLR-299G3.1_ENST00000607288.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	566					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)		AGGGGCCAGGGCTGCTCCCGC	0.706													G|||	32	0.00638978	0.0212	0.0058	5008	,	,		13734	0.0		0.0	False		,,,				2504	0.0				p.P566S		Atlas-SNP	.											.	POLRMT	91	.	0			c.C1696T						PASS	.	G	SER/PRO	59,4143		0,59,2042	5	6	6		1696	3	1	19	dbSNP_127	6	0,8252		0,0,4126	no	missense	POLRMT	NM_005035.3	74	0,59,6168	AA,AG,GG		0.0,1.4041,0.4737	benign	566/1231	622304	59,12395	2101	4126	6227	SO:0001583	missense	5442	exon9			GCCAGGGCTGCTC		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.1696C>T	19.37:g.622304G>A	ENSP00000465759:p.Pro566Ser	34	0	0		42	23	0.547619	NM_005035	O60370	Missense_Mutation	SNP	ENST00000588649.2	37	CCDS12036.1	.	.	.	.	.	.	.	.	.	.	.	7.555	0.663560	0.14710	0.014041	0.0	ENSG00000099821	ENST00000215591	T	0.41065	1.01	4.15	3.02	0.34903	.	0.759629	0.13016	N	0.420516	T	0.26231	0.0640	M	0.64170	1.965	0.26553	N	0.973879	B	0.22683	0.073	B	0.20184	0.028	T	0.12553	-1.0543	10	0.30078	T	0.28	-50.68	2.8775	0.05636	0.1015:0.271:0.4629:0.1646	rs41545023	566	O00411	RPOM_HUMAN	S	566	ENSP00000215591:P566S	ENSP00000215591:P566S	P	-	1	0	POLRMT	573304	0.788000	0.28762	1.000000	0.80357	0.557000	0.35523	1.680000	0.37607	2.309000	0.77851	0.561000	0.74099	CCC	.	.	weak		0.706	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035		A	622304	G	A	622304	3	1	22	1	0	0	0	0	1	0	0	0	12247	1203	42	2	2048	2	POLRMT	19	622304	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4500	622304	58506679	3706	6607											
POLRMT	5442	hgsc.bcm.edu	37	chr19	622834	622834	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gacgcacctgcaggagcatcCgcaccacctcgcgctcgtcc	7	5	10	19	5	0	0	0	0	0	0	4	2	2	1	5	1	2	5	5	1	0	0	rs146178977	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:622834C>G	ENST00000588649.2	-	7	1526	c.1442G>C	c.(1441-1443)cGg>cCg	p.R481P	LLNLR-299G3.1_ENST00000607288.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	481					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)		CAGGAGCATCCGCACCACCTC	0.716													c|||	17	0.00339457	0.0129	0.0	5008	,	,		14871	0.0		0.0	False		,,,				2504	0.0				p.R481P		Atlas-SNP	.											.	POLRMT	91	.	0			c.G1442C						PASS	.	C	PRO/ARG	33,4365		0,33,2166	23	22	22		1442	-8	0	19	dbSNP_134	22	0,8598		0,0,4299	no	missense	POLRMT	NM_005035.3	103	0,33,6465	GG,GC,CC		0.0,0.7503,0.2539	benign	481/1231	622834	33,12963	2199	4299	6498	SO:0001583	missense	5442	exon7			AGCATCCGCACCA		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.1442G>C	19.37:g.622834C>G	ENSP00000465759:p.Arg481Pro	66	0	0		56	36	0.642857	NM_005035	O60370	Missense_Mutation	SNP	ENST00000588649.2	37	CCDS12036.1	.	.	.	.	.	.	.	.	.	.	.	10.38	1.332902	0.24167	0.007503	0.0	ENSG00000099821	ENST00000215591	T	0.41758	0.99	4.01	-8.03	0.01114	.	0.937015	0.08876	N	0.880708	T	0.17577	0.0422	N	0.08118	0	0.09310	N	1	B	0.27594	0.182	B	0.32724	0.151	T	0.32295	-0.9912	10	0.30854	T	0.27	-0.4611	17.4545	0.87603	0.0:0.1116:0.0:0.8884	.	481	O00411	RPOM_HUMAN	P	481	ENSP00000215591:R481P	ENSP00000215591:R481P	R	-	2	0	POLRMT	573834	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.305000	0.08188	-2.543000	0.00484	-2.079000	0.00380	CGG	C|0.997;G|0.003	0.003	strong		0.716	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035		G	622834	C	G	622834	3	3	22	1	0	0	0	0	1	0	0	0	12247	652	23	4	2310	4	POLRMT	19	622834	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	530	622834	58506149	3707	6608											
C19orf21	126353	hgsc.bcm.edu	37	chr19	757354	757354	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacgctgaccccaggaggctGtgtgacctggagcgggagcg	7	5	18	11	3	0	2	0	2	0	0	0	6	0	5	3	4	2	2	3	4	0	0	rs35090443	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:757354G>A	ENST00000215582.6	+	2	511	c.408G>A	c.(406-408)ctG>ctA	p.L136L		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	136					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											CCAGGAGGCTGTGTGACCTGG	0.672													G|||	94	0.01877	0.0681	0.0058	5008	,	,		17272	0.0		0.0	False		,,,				2504	0.0				p.L136L		Atlas-SNP	.											.	C19orf21	56	.	0			c.G408A						PASS	.	G		230,4172	124.5+/-161.8	8,214,1979	41	39	40		408	-8.1	0	19	dbSNP_126	40	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous	C19orf21	NM_173481.2		8,215,6276	AA,AG,GG		0.0116,5.2249,1.7772		136/680	757354	231,12767	2201	4298	6499	SO:0001819	synonymous_variant	126353	exon2			GAGGCTGTGTGAC	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.408G>A	19.37:g.757354G>A		95	0	0		126	61	0.484127	NM_173481		Silent	SNP	ENST00000215582.6	37	CCDS12042.1																																																																																			G|0.982;A|0.018	0.018	strong		0.672	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481		A	757354	G	A	757354	2	1	22	1	0	0	0	0	0	0	0	1	1915	1364	48	2		2	C19orf21	19	757354	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	134520	757354	58371629	3708	6609											
C19orf21	126353	hgsc.bcm.edu	37	chr19	757483	757483	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccggcccacctcggtccacGcccctggaggagaacgtggt	6	5	13	17	4	0	1	0	0	0	1	2	3	1	2	6	5	1	0	6	5	1	0	rs35484463	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:757483G>A	ENST00000215582.6	+	2	640	c.537G>A	c.(535-537)acG>acA	p.T179T		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	179					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											CTCGGTCCACGCCCCTGGAGG	0.652													G|||	94	0.01877	0.0681	0.0058	5008	,	,		16831	0.0		0.0	False		,,,				2504	0.0				p.T179T		Atlas-SNP	.											.	C19orf21	56	.	0			c.G537A						PASS	.	G		220,4166		7,206,1980	19	23	22		537	-5.4	0	19	dbSNP_126	22	1,8587		0,1,4293	no	coding-synonymous	C19orf21	NM_173481.2		7,207,6273	AA,AG,GG		0.0116,5.016,1.7034		179/680	757483	221,12753	2193	4294	6487	SO:0001819	synonymous_variant	126353	exon2			GTCCACGCCCCTG	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.537G>A	19.37:g.757483G>A		95	0	0		95	42	0.442105	NM_173481		Silent	SNP	ENST00000215582.6	37	CCDS12042.1																																																																																			G|0.982;A|0.018	0.018	strong		0.652	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481		A	757483	G	A	757483	2	1	22	1	0	0	0	0	0	0	0	1	1915	1074	38	1		1	C19orf21	19	757483	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	129	757483	58371500	3709	6610											
AZU1	566	hgsc.bcm.edu	37	chr19	831811	831811	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cgaggccctgacttcttcacCcgagtggcgctcttccgaga	6	9	11	15	4	3	2	1	1	2	1	4	5	4	2	3	2	0	1	3	2	0	3	rs588442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:831811C>T	ENST00000233997.2	+	5	711	c.690C>T	c.(688-690)acC>acT	p.T230T		NM_001700.3	NP_001691.1	P20160	CAP7_HUMAN	azurocidin 1	230	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular extravasation (GO:0045123)|defense response to Gram-negative bacterium (GO:0050829)|glial cell migration (GO:0008347)|induction of positive chemotaxis (GO:0050930)|inflammatory response (GO:0006954)|macrophage chemotaxis (GO:0048246)|microglial cell activation (GO:0001774)|monocyte activation (GO:0042117)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell adhesion (GO:0045785)|positive regulation of fractalkine biosynthetic process (GO:0050754)|positive regulation of interleukin-1 beta biosynthetic process (GO:0050725)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of phagocytosis (GO:0050766)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of vascular permeability (GO:0043114)	azurophil granule (GO:0042582)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)|toxic substance binding (GO:0015643)			NS(1)|endometrium(1)|kidney(1)|lung(4)|pancreas(1)|upper_aerodigestive_tract(2)	10		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)		ACTTCTTCACCCGAGTGGCGC	0.711													C|||	405	0.0808706	0.2935	0.0216	5008	,	,		12838	0.0		0.002	False		,,,				2504	0.0				p.T230T		Atlas-SNP	.											.	AZU1	31	.	0			c.C690T						PASS	.	C		1054,3346		120,814,1266	32	36	35		690	0.8	0.1	19	dbSNP_83	35	6,8588		0,6,4291	no	coding-synonymous	AZU1	NM_001700.3		120,820,5557	TT,TC,CC		0.0698,23.9545,8.1576		230/252	831811	1060,11934	2200	4297	6497	SO:0001819	synonymous_variant	566	exon5			CTTCACCCGAGTG	X58794	CCDS12044.1	19p13.3	2012-03-30	2008-08-01		ENSG00000172232	ENSG00000172232			913	protein-coding gene	gene with protein product	"cationic antimicrobial protein 37", "heparin-binding protein", "neutrophil azurocidin"	162815				1919011	Standard	NM_001700		Approved	AZU, CAP37, AZAMP, HBP, NAZC, HUMAZUR	uc002lpz.1	P20160		ENST00000233997.2:c.690C>T	19.37:g.831811C>T		105	0	0		121	54	0.446281	NM_001700	P80014|Q52LG4|Q9UCM1|Q9UCT5	Silent	SNP	ENST00000233997.2	37	CCDS12044.1																																																																																			C|0.897;T|0.103	0.103	strong		0.711	AZU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457472.2	NM_001700		T	831811	C	T	831811	2	4	22	1	0	0	0	0	0	0	0	1	1243	610	22	2		2	AZU1	19	831811	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	74328	831811	58297172	3710	6611											
GRIN3B	116444	hgsc.bcm.edu	37	chr19	1008704	1008704	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctctgctcagctcgctgggcGagcacgccttcttccgcctg	3	10	11	17	4	3	0	1	0	2	0	5	1	4	0	3	1	3	4	3	1	0	2	rs61744375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1008704G>A	ENST00000234389.3	+	7	2573	c.2554G>A	c.(2554-2556)Gag>Aag	p.E852K		NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	852					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)	CTCGCTGGGCGAGCACGCCTT	0.697													g|||	151	0.0301518	0.1059	0.0144	5008	,	,		11084	0.0		0.001	False		,,,				2504	0.0				p.E852K		Atlas-SNP	.											.	GRIN3B	46	.	0			c.G2554A						PASS	.	G	LYS/GLU	422,3978	195.3+/-220.0	23,376,1801	35	30	31		2554	3.8	1	19	dbSNP_129	31	0,8596		0,0,4298	yes	missense	GRIN3B	NM_138690.1	56	23,376,6099	AA,AG,GG		0.0,9.5909,3.2472	probably-damaging	852/1044	1008704	422,12574	2200	4298	6498	SO:0001583	missense	116444	exon7			CTGGGCGAGCACG		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.2554G>A	19.37:g.1008704G>A	ENSP00000234389:p.Glu852Lys	21	0	0		38	26	0.684211	NM_138690	Q5EAK7|Q7RTW9	Missense_Mutation	SNP	ENST00000234389.3	37	CCDS32861.1	58	0.026556776556776556	52	0.10569105691056911	6	0.016574585635359115	0	0.0	0	0.0	G	31	5.090219	0.94149	0.095909	0.0	ENSG00000116032	ENST00000234389	T	0.24350	1.86	3.78	3.78	0.43462	.	0.000000	0.85682	U	0.000000	T	0.01222	0.0040	M	0.68317	2.08	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.00609	-1.1646	10	0.87932	D	0	.	14.2074	0.65744	0.0:0.0:1.0:0.0	rs61744375	852	O60391	NMD3B_HUMAN	K	852	ENSP00000234389:E852K	ENSP00000234389:E852K	E	+	1	0	GRIN3B	959704	1.000000	0.71417	0.982000	0.44146	0.976000	0.68499	9.163000	0.94750	1.661000	0.50771	0.462000	0.41574	GAG	G|0.965;A|0.035	0.035	strong		0.697	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2			A	1008704	G	A	1008704	3	1	22	1	0	0	0	0	1	0	0	0	6793	1059	37	1	2580	1	GRIN3B	19	1008704	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	176893	1008704	58120279	3711	6612											
ABCA7	10347	hgsc.bcm.edu	37	chr19	1052086	1052086	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggctccggctactacctgacGctggtgaaggcccgcctgcc	5	7	13	16	3	0	2	0	2	0	0	1	2	1	2	5	4	3	3	5	4	3	2	rs61576791	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1052086G>A	ENST00000263094.6	+	22	3339	c.3108G>A	c.(3106-3108)acG>acA	p.T1036T	ABCA7_ENST00000433129.1_Silent_p.T1036T|ABCA7_ENST00000435683.2_Silent_p.T898T	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1036	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)		ACTACCTGACGCTGGTGAAGG	0.672													G|||	323	0.0644968	0.2383	0.0101	5008	,	,		10142	0.0		0.001	False		,,,				2504	0.0				p.T1036T		Atlas-SNP	.											.	ABCA7	174	.	0			c.G3108A						PASS	.			761,3593		76,609,1492	29	25	26		3108	-8.9	0	19	dbSNP_129	26	7,8557		0,7,4275	no	coding-synonymous	ABCA7	NM_019112.3		76,616,5767	AA,AG,GG		0.0817,17.4782,5.9452		1036/2147	1052086	768,12150	2177	4282	6459	SO:0001819	synonymous_variant	10347	exon22			CCTGACGCTGGTG	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.3108G>A	19.37:g.1052086G>A		91	0	0		102	44	0.431373	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	37	CCDS12055.1																																																																																			G|0.938;A|0.062	0.062	strong		0.672	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		A	1052086	G	A	1052086	2	1	22	1	0	0	0	0	0	0	0	1	37	1074	38	1		1	ABCA7	19	1052086	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	43382	1052086	58076897	3712	6613											
ABCA7	10347	hgsc.bcm.edu	37	chr19	1058635	1058635	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggagacaggcagttccagtCacccctgcgctgggaggtgg	8	6	16	11	1	1	1	1	0	0	1	2	3	2	2	3	5	1	3	3	5	0	1	rs73505232	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1058635C>T	ENST00000263094.6	+	38	5399	c.5168C>T	c.(5167-5169)tCa>tTa	p.S1723L	ABCA7_ENST00000433129.1_Missense_Mutation_p.S1723L|ABCA7_ENST00000435683.2_Missense_Mutation_p.S1585L	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1723					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)		CAGTTCCAGTCACCCCTGCGC	0.552													C|||	196	0.0391374	0.143	0.0101	5008	,	,		17265	0.0		0.0	False		,,,				2504	0.0				p.S1723L		Atlas-SNP	.											.	ABCA7	174	.	0			c.C5168T						PASS	.	C	LEU/SER	578,3828	256.1+/-261.0	45,488,1670	60	62	61		5168	4.2	1	19	dbSNP_130	61	0,8600		0,0,4300	yes	missense	ABCA7	NM_019112.3	145	45,488,5970	TT,TC,CC		0.0,13.1185,4.4441	probably-damaging	1723/2147	1058635	578,12428	2203	4300	6503	SO:0001583	missense	10347	exon38			TCCAGTCACCCCT	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.5168C>T	19.37:g.1058635C>T	ENSP00000263094:p.Ser1723Leu	92	0	0		96	49	0.510417	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	79	0.036172161172161175	74	0.15040650406504066	5	0.013812154696132596	0	0.0	0	0.0	C	20.3	3.973946	0.74246	0.131185	0.0	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.87650	-2.28;-2.28	4.23	4.23	0.50019	.	.	.	.	.	T	0.09730	0.0239	M	0.88450	2.955	0.28999	N	0.887598	P;D	0.61697	0.899;0.99	P;D	0.67103	0.735;0.949	T	0.35599	-0.9782	9	0.87932	D	0	.	15.318	0.74095	0.0:1.0:0.0:0.0	.	848;1723	D6W5Y0;Q8IZY2	.;ABCA7_HUMAN	L	1723	ENSP00000263094:S1723L;ENSP00000414062:S1723L	ENSP00000263094:S1723L	S	+	2	0	ABCA7	1009635	0.985000	0.35326	0.982000	0.44146	0.997000	0.91878	2.532000	0.45659	2.180000	0.69256	0.561000	0.74099	TCA	C|0.952;T|0.048	0.048	strong		0.552	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		T	1058635	C	T	1058635	3	4	22	1	0	0	0	0	1	0	0	0	37	838	29	2	5314	2	ABCA7	19	1058635	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6549	1058635	58070348	3713	6614											
HMHA1	23526	hgsc.bcm.edu	37	chr19	1079968	1079968	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgatgcatatgcagacggcGccgctgcccgtgcacttcca	8	8	11	14	4	0	2	0	1	0	1	1	2	1	2	3	1	4	4	3	1	1	2	rs34047143	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1079968G>A	ENST00000313093.2	+	13	1785	c.1554G>A	c.(1552-1554)gcG>gcA	p.A518A	HMHA1_ENST00000536472.1_Silent_p.A358A|HMHA1_ENST00000590214.1_Silent_p.A545A|HMHA1_ENST00000586866.1_Silent_p.A522A|HMHA1_ENST00000543365.1_Silent_p.A401A|HMHA1_ENST00000539243.2_Silent_p.A534A|HMHA1_ENST00000590577.1_Silent_p.A153A	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	518					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)		TGCAGACGGCGCCGCTGCCCG	0.672													G|||	176	0.0351438	0.1309	0.0043	5008	,	,		15158	0.0		0.0	False		,,,				2504	0.0				p.A534A		Atlas-SNP	.											.	HMHA1	78	.	0			c.G1602A						PASS	.	G		481,3925	223.3+/-239.8	28,425,1750	74	80	78		1554	-6.9	1	19	dbSNP_126	78	0,8600		0,0,4300	no	coding-synonymous	HMHA1	NM_012292.2		28,425,6050	AA,AG,GG		0.0,10.9169,3.6983		518/1137	1079968	481,12525	2203	4300	6503	SO:0001819	synonymous_variant	23526	exon13			GACGGCGCCGCTG	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.1554G>A	19.37:g.1079968G>A		78	0	0		84	42	0.5	NM_001258328	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Silent	SNP	ENST00000313093.2	37	CCDS32863.1																																																																																			G|0.962;A|0.038	0.038	strong		0.672	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1			A	1079968	G	A	1079968	2	1	22	1	0	0	0	0	0	0	0	1	7249	1074	38	1		1	HMHA1	19	1079968	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	21333	1079968	58049015	3714	6615											
HMHA1	23526	hgsc.bcm.edu	37	chr19	1085690	1085690	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgtccaacgattcggactcGgacctagaggaggcctccga	9	7	13	12	4	0	1	0	0	0	1	4	6	2	4	4	4	1	0	4	4	2	2	rs149960692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1085690G>A	ENST00000313093.2	+	23	3327	c.3096G>A	c.(3094-3096)tcG>tcA	p.S1032S	HMHA1_ENST00000536472.1_Silent_p.S900S|HMHA1_ENST00000590214.1_Silent_p.S1059S|HMHA1_ENST00000586866.1_Silent_p.S1036S|HMHA1_ENST00000543365.1_Silent_p.S915S|POLR2E_ENST00000585838.1_5'Flank|HMHA1_ENST00000539243.2_Silent_p.S1048S|HMHA1_ENST00000590577.1_Silent_p.S667S|HMHA1_ENST00000591169.1_3'UTR	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	1032					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)		ATTCGGACTCGGACCTAGAGG	0.617													g|||	36	0.0071885	0.0272	0.0	5008	,	,		17360	0.0		0.0	False		,,,				2504	0.0				p.S1048S		Atlas-SNP	.											.	HMHA1	78	.	0			c.G3144A						PASS	.	G		87,4271		1,85,2093	10	13	12		3096	-6.4	1	19	dbSNP_134	12	1,8533		0,1,4266	no	coding-synonymous	HMHA1	NM_012292.2		1,86,6359	AA,AG,GG		0.0117,1.9963,0.6826		1032/1137	1085690	88,12804	2179	4267	6446	SO:0001819	synonymous_variant	23526	exon23			GGACTCGGACCTA	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.3096G>A	19.37:g.1085690G>A		129	0	0		119	63	0.529412	NM_001258328	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Silent	SNP	ENST00000313093.2	37	CCDS32863.1																																																																																			G|0.993;A|0.007	0.007	strong		0.617	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1			A	1085690	G	A	1085690	2	1	22	1	0	0	0	0	0	0	0	1	7249	1103	39	1		1	HMHA1	19	1085690	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5722	1085690	58043293	3715	6616											
SBNO2	22904	hgsc.bcm.edu	37	chr19	1109577	1109577	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcaaaggcgtcctcccacttCaggccgcggtccacgctgat	7	7	11	16	4	1	1	1	1	0	0	4	1	4	1	4	3	0	2	4	3	1	1	rs200767766	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1109577C>T	ENST00000361757.3	-	28	3381	c.3144G>A	c.(3142-3144)ctG>ctA	p.L1048L	SBNO2_ENST00000587024.1_Silent_p.L1038L|SBNO2_ENST00000438103.2_Silent_p.L991L	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)	1048					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)		CCTCCCACTTCAGGCCGCGGT	0.697													C|||	31	0.0061901	0.0234	0.0	5008	,	,		7099	0.0		0.0	False		,,,				2504	0.0				p.L1048L		Atlas-SNP	.											.	SBNO2	112	.	0			c.G3144A						PASS	.	C	,	57,3687		0,57,1815	7	9	8		2973,3144	2.3	1	19		8	0,8122		0,0,4061	no	coding-synonymous,coding-synonymous	SBNO2	NM_001100122.1,NM_014963.2	,	0,57,5876	TT,TC,CC		0.0,1.5224,0.4804	,	991/1310,1048/1367	1109577	57,11809	1872	4061	5933	SO:0001819	synonymous_variant	22904	exon28			CCACTTCAGGCCG	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.3144G>A	19.37:g.1109577C>T		88	0	0		104	50	0.480769	NM_014963	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Silent	SNP	ENST00000361757.3	37	CCDS45894.1																																																																																			C|0.986;T|0.014	0.014	strong		0.697	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2	NM_014963		T	1109577	C	T	1109577	2	4	22	1	0	0	0	0	0	0	0	1	13878	813	29	2		2	SBNO2	19	1109577	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	23887	1109577	58019406	3716	6617											
APC2	10297	hgsc.bcm.edu	37	chr19	1469030	1469030	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggagcctccccggtgcccaaAacgccggcgcgcacccttct	6	5	11	19	5	1	0	0	0	1	0	2	1	2	1	6	3	3	1	6	3	2	1	rs265278	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1469030A>G	ENST00000535453.1	+	14	7443	c.5730A>G	c.(5728-5730)aaA>aaG	p.K1910K	APC2_ENST00000233607.2_Silent_p.K1910K|C19orf25_ENST00000588427.1_Intron|APC2_ENST00000238483.4_Silent_p.K1636K			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)		CGGTGCCCAAAACGCCGGCGC	0.756													G|||	998	0.199281	0.6036	0.062	5008	,	,		7467	0.0248		0.0497	False		,,,				2504	0.0838				p.K1910K		Atlas-SNP	.											.	APC2	50	.	0			c.A5730G						PASS	.	G		912,2062		65,782,640	2	3	3		5730	4.1	0	19	dbSNP_79	3	244,6352		4,236,3058	no	coding-synonymous	APC2	NM_005883.2		69,1018,3698	GG,GA,AA		3.6992,30.6658,12.0794		1910/2304	1469030	1156,8414	1487	3298	4785	SO:0001819	synonymous_variant	10297	exon15			GCCCAAAACGCCG		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.5730A>G	19.37:g.1469030A>G		10	0	0		23	17	0.73913	NM_005883	C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	Silent	SNP	ENST00000535453.1	37	CCDS12068.1																																																																																			A|0.833;G|0.167	0.167	strong		0.756	APC2-004	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449539.2	NM_005883		G	1469030	A	G	1469030	2	3	22	1	0	0	0	0	0	0	0	1	764	11	1	3		3	APC2	19	1469030	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	359453	1469030	57659953	3717	6618											
APC2	10297	hgsc.bcm.edu	37	chr19	1469078	1469078	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcacaagacgcagagatcGcccgtgcggatcccgttcat	10	6	11	14	5	1	2	1	0	0	2	3	4	2	3	2	1	2	3	2	1	1	1	rs79021820	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1469078G>A	ENST00000535453.1	+	14	7491	c.5778G>A	c.(5776-5778)tcG>tcA	p.S1926S	APC2_ENST00000233607.2_Silent_p.S1926S|C19orf25_ENST00000588427.1_Intron|APC2_ENST00000238483.4_Silent_p.S1652S			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)		CGCAGAGATCGCCCGTGCGGA	0.771													G|||	198	0.0395367	0.1475	0.0043	5008	,	,		6607	0.0		0.0	False		,,,				2504	0.0				p.S1926S		Atlas-SNP	.											.	APC2	50	.	0			c.G5778A						PASS	.	G		162,2148		1,160,994	1	2	2		5778	-7.8	0.5	19	dbSNP_131	2	3,5457		0,3,2727	no	coding-synonymous	APC2	NM_005883.2		1,163,3721	AA,AG,GG		0.0549,7.013,2.1236		1926/2304	1469078	165,7605	1155	2730	3885	SO:0001819	synonymous_variant	10297	exon15			GAGATCGCCCGTG		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.5778G>A	19.37:g.1469078G>A		11	0	0		29	19	0.655172	NM_005883	C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	Silent	SNP	ENST00000535453.1	37	CCDS12068.1																																																																																			G|0.949;A|0.051	0.051	strong		0.771	APC2-004	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449539.2	NM_005883		A	1469078	G	A	1469078	2	1	22	1	0	0	0	0	0	0	0	1	764	1074	38	1		1	APC2	19	1469078	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	48	1469078	57659905	3718	6619											
REEP6	92840	hgsc.bcm.edu	37	chr19	1495327	1495327	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctaagcctgtatctgctgttCggctacggagcgtctctgct	5	13	11	12	3	2	0	0	0	2	0	4	1	2	1	1	2	5	5	1	2	3	4	rs79574672	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1495327C>T	ENST00000233596.3	+	2	254	c.150C>T	c.(148-150)ttC>ttT	p.F50F		NM_138393.1	NP_612402.1	Q96HR9	REEP6_HUMAN	receptor accessory protein 6	50					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)				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)		ATCTGCTGTTCGGCTACGGAG	0.657													C|||	120	0.0239617	0.09	0.0014	5008	,	,		18573	0.0		0.0	False		,,,				2504	0.0				p.F50F		Atlas-SNP	.											REEP6_ENST00000395484,NS,carcinoma,-2,1	REEP6	21	1	0			c.C150T						PASS	.	C		322,4080	171.2+/-201.5	7,308,1886	114	100	105		150	1.9	1	19	dbSNP_131	105	0,8598		0,0,4299	no	coding-synonymous	REEP6	NM_138393.1		7,308,6185	TT,TC,CC		0.0,7.3149,2.4769		50/185	1495327	322,12678	2201	4299	6500	SO:0001819	synonymous_variant	92840	exon2			GCTGTTCGGCTAC	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.150C>T	19.37:g.1495327C>T		169	0	0		182	85	0.467033	NM_138393	B2RE01|D6W5Z0|Q96LM0	Silent	SNP	ENST00000233596.3	37	CCDS12070.1	51	0.023351648351648352	51	0.10365853658536585	0	0.0	0	0.0	0	0.0	C	12.63	1.996371	0.35226	0.073149	0.0	ENSG00000115255	ENST00000395484	.	.	.	4.61	1.93	0.25924	.	.	.	.	.	T	0.03783	0.0107	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.11299	-1.0593	5	0.87932	D	0	-9.0609	8.2387	0.31645	0.0:0.6717:0.0:0.3283	.	.	.	.	W	118	.	ENSP00000378865:R118W	R	+	1	2	REEP6	1446327	0.890000	0.30428	0.982000	0.44146	0.017000	0.09413	-0.058000	0.11750	0.846000	0.35142	-0.354000	0.07668	CGG	C|0.974;T|0.026	0.026	strong		0.657	REEP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449623.1	NM_138393		T	1495327	C	T	1495327	2	4	22	1	0	0	0	0	0	0	0	1	13224	883	31	1		1	REEP6	19	1495327	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	26249	1495327	57633656	3719	6620											
ADAMTSL5	339366	hgsc.bcm.edu	37	chr19	1506799	1506799	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcggggggctgaggctcCaccccccggggctgaggctg	3	5	19	14	2	0	2	0	2	0	0	1	2	1	2	4	7	1	5	4	7	0	0	rs79538691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1506799C>T	ENST00000413997.2	-	10	1010	c.1011G>A	c.(1009-1011)gtG>gtA	p.V337V	ADAMTSL5_ENST00000330475.4_Silent_p.V327V|ADAMTSL5_ENST00000590562.1_5'UTR|CTB-25B13.9_ENST00000590252.1_RNA|ADAMTSL5_ENST00000395467.2_Silent_p.V96V			Q6ZMM2	ATL5_HUMAN	ADAMTS-like 5	337						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)		GCTGAGGCTCCACCCCCCGGG	0.711													C|||	101	0.0201677	0.0756	0.0014	5008	,	,		10308	0.0		0.0	False		,,,				2504	0.0				p.V327V		Atlas-SNP	.											.	ADAMTSL5	24	.	0			c.G981A						PASS	.	C		192,3668		2,188,1740	7	10	9		981	1.9	0.8	19	dbSNP_131	9	1,7767		0,1,3883	no	coding-synonymous	ADAMTSL5	NM_213604.2		2,189,5623	TT,TC,CC		0.0129,4.9741,1.6598		327/472	1506799	193,11435	1930	3884	5814	SO:0001819	synonymous_variant	339366	exon10			AGGCTCCACCCCC	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.1011G>A	19.37:g.1506799C>T		36	0	0		50	25	0.5	NM_213604	B4DXK7|Q8IW95	Silent	SNP	ENST00000413997.2	37																																																																																				C|0.982;T|0.018	0.018	strong		0.711	ADAMTSL5-202	KNOWN	basic	protein_coding	protein_coding		XM_294919		T	1506799	C	T	1506799	2	4	22	1	0	0	0	0	0	0	0	1	278	581	21	2		2	ADAMTSL5	19	1506799	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	11472	1506799	57622184	3720	6621											
KLF16	83855	hgsc.bcm.edu	37	chr19	1854701	1854701	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggtggtggcgggccagctcGtcggagcgggcgaacttctt	4	8	18	11	6	1	0	0	0	1	0	3	2	1	1	1	6	3	1	1	6	1	2	rs76157530	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1854701G>A	ENST00000250916.4	-	2	586	c.516C>T	c.(514-516)gaC>gaT	p.D172D	KLF16_ENST00000592313.1_5'UTR|CTB-31O20.6_ENST00000592884.1_RNA	NM_031918.3	NP_114124.1	Q9BXK1	KLF16_HUMAN	Kruppel-like factor 16	172					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)		GGGCCAGCTCGTCGGAGCGGG	0.672													G|||	55	0.0109824	0.0401	0.0029	5008	,	,		10702	0.0		0.0	False		,,,				2504	0.0				p.D172D		Atlas-SNP	.											.	KLF16	9	.	0			c.C516T						PASS	.	G		133,4271	90.6+/-129.3	3,127,2072	35	39	37		516	-1.2	1	19	dbSNP_131	37	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KLF16	NM_031918.3		3,128,6371	AA,AG,GG		0.0116,3.02,1.0305		172/253	1854701	134,12870	2202	4300	6502	SO:0001819	synonymous_variant	83855	exon2			CAGCTCGTCGGAG	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.516C>T	19.37:g.1854701G>A		30	0	0		43	25	0.581395	NM_031918		Silent	SNP	ENST00000250916.4	37	CCDS12075.1																																																																																			G|0.989;A|0.011	0.011	strong		0.672	KLF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449214.1			A	1854701	G	A	1854701	2	1	22	1	0	0	0	0	0	0	0	1	8353	1136	40	1		1	KLF16	19	1854701	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	347902	1854701	57274282	3721	6622											
MOBKL2A	126308	hgsc.bcm.edu	37	chr19	2078290	2078290	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tacttggggccccccgacatGacggggcaggactgctccgt	6	7	14	14	3	0	1	0	1	0	0	1	3	1	2	4	5	2	2	4	5	1	2	rs34483500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2078290G>A	ENST00000357066.3	-	3	649	c.270C>T	c.(268-270)gtC>gtT	p.V90V	MOB3A_ENST00000592143.1_Intron|MOB3A_ENST00000592280.1_Silent_p.V90V	NM_130807.2	NP_570719.1	Q96BX8	MOB3A_HUMAN	MOB kinase activator 3A	90						intracellular (GO:0005622)	metal ion binding (GO:0046872)										CCCCCGACATGACGGGGCAGG	0.612													G|||	24	0.00479233	0.0174	0.0014	5008	,	,		16424	0.0		0.0	False		,,,				2504	0.0				p.V90V		Atlas-SNP	.											MOBKL2A,colon,carcinoma,-2,1	.	.	1	0			c.C270T						PASS	.	G		60,4346	57.4+/-93.9	1,58,2144	68	54	59		270	1	1	19	dbSNP_126	59	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MOB3A	NM_130807.2		1,59,6443	AA,AG,GG		0.0116,1.3618,0.469		90/218	2078290	61,12945	2203	4300	6503	SO:0001819	synonymous_variant	126308	exon3			CGACATGACGGGG	AK095471	CCDS12081.1	19p13.3	2011-09-28	2011-09-28	2011-09-28	ENSG00000172081	ENSG00000172081		"MOB kinase activators"	29802	protein-coding gene	gene with protein product	"MOB LAK"		"MOB1, Mps One Binder kinase activator-like 2A (yeast)"	MOBKL2A		12477932	Standard	NM_130807		Approved	MOB1C, MOB-LAK, moblak	uc002luv.3	Q96BX8		ENST00000357066.3:c.270C>T	19.37:g.2078290G>A		152	0	0		165	86	0.521212	NM_130807	B3KTF1|O75249|Q8TF69	Silent	SNP	ENST00000357066.3	37	CCDS12081.1																																																																																			G|0.994;A|0.006	0.006	strong		0.612	MOB3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450893.1	NM_130807		A	2078290	G	A	2078290	2	1	22	1	0	0	0	0	0	0	0	1	9693	1277	45	2		2	MOBKL2A	19	2078290	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	223589	2078290	57050693	3722	6623											
MOBKL2A	126308	hgsc.bcm.edu	37	chr19	2078424	2078424	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggcaactgcacggccagccGcaggtccagcccggcgttca	7	4	14	16	4	1	0	1	0	0	0	2	0	2	0	4	4	4	4	4	4	1	1	rs34059622	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2078424G>T	ENST00000357066.3	-	3	515	c.136C>A	c.(136-138)Cgg>Agg	p.R46R	MOB3A_ENST00000592143.1_Intron|MOB3A_ENST00000592280.1_Silent_p.R46R	NM_130807.2	NP_570719.1	Q96BX8	MOB3A_HUMAN	MOB kinase activator 3A	46						intracellular (GO:0005622)	metal ion binding (GO:0046872)										ACGGCCAGCCGCAGGTCCAGC	0.637													G|||	64	0.0127796	0.0461	0.0043	5008	,	,		15140	0.0		0.0	False		,,,				2504	0.0				p.R46R		Atlas-SNP	.											.	.	.	.	0			c.C136A						PASS	.	G		170,4236	112.5+/-150.6	4,162,2037	51	54	53		136	-2.5	0.3	19	dbSNP_126	53	2,8596	2.2+/-6.3	0,2,4297	no	coding-synonymous	MOB3A	NM_130807.2		4,164,6334	TT,TG,GG		0.0233,3.8584,1.3227		46/218	2078424	172,12832	2203	4299	6502	SO:0001819	synonymous_variant	126308	exon3			CCAGCCGCAGGTC	AK095471	CCDS12081.1	19p13.3	2011-09-28	2011-09-28	2011-09-28	ENSG00000172081	ENSG00000172081		"MOB kinase activators"	29802	protein-coding gene	gene with protein product	"MOB LAK"		"MOB1, Mps One Binder kinase activator-like 2A (yeast)"	MOBKL2A		12477932	Standard	NM_130807		Approved	MOB1C, MOB-LAK, moblak	uc002luv.3	Q96BX8		ENST00000357066.3:c.136C>A	19.37:g.2078424G>T		65	0	0		55	28	0.509091	NM_130807	B3KTF1|O75249|Q8TF69	Silent	SNP	ENST00000357066.3	37	CCDS12081.1																																																																																			G|0.982;T|0.018	0.018	strong		0.637	MOB3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450893.1	NM_130807		T	2078424	G	T	2078424	2	4	22	1	0	0	0	0	0	0	0	1	9693	1086	38	4		4	MOBKL2A	19	2078424	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	134	2078424	57050559	3723	6624											
AP3D1	8943	hgsc.bcm.edu	37	chr19	2116616	2116616	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagctcacccgagccagctcTtcctcgtccgcctccgacgg	5	7	9	20	5	2	0	1	0	1	0	6	2	5	0	6	1	3	2	6	1	0	1	rs73512353	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2116616T>C	ENST00000345016.5	-	17	2220	c.1989A>G	c.(1987-1989)gaA>gaG	p.E663E	AP3D1_ENST00000356926.4_Silent_p.E572E|AP3D1_ENST00000350812.6_Silent_p.E494E|AP3D1_ENST00000355272.6_Silent_p.E663E	NM_003938.6	NP_003929.4	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1 subunit	663					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)		GAGCCAGCTCTTCCTCGTCCG	0.692													T|||	38	0.00758786	0.0265	0.0043	5008	,	,		15549	0.0		0.0	False		,,,				2504	0.0				p.E663E		Atlas-SNP	.											.	AP3D1	81	.	0			c.A1989G						PASS	.	T	,	64,4056		1,62,1997	15	17	16		1716,1989	2.8	1	19	dbSNP_130	16	0,8376		0,0,4188	no	coding-synonymous,coding-synonymous	AP3D1	NM_001077523.1,NM_003938.5	,	1,62,6185	CC,CT,TT		0.0,1.5534,0.5122	,	572/1113,663/1154	2116616	64,12432	2060	4188	6248	SO:0001819	synonymous_variant	8943	exon17			CAGCTCTTCCTCG	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.1989A>G	19.37:g.2116616T>C		67	0	0		59	27	0.457627	NM_001261826	O00202|O75262|Q59HF5|Q96G11|Q9H3C6	Silent	SNP	ENST00000345016.5	37	CCDS42459.1																																																																																			T|0.992;C|0.008	0.008	strong		0.692	AP3D1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450912.1			C	2116616	T	C	2116616	2	2	22	1	0	0	0	0	0	0	0	1	746	1606	56	3		3	AP3D1	19	2116616	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	38192	2116616	57012367	3724	6625											
JSRP1	126306	hgsc.bcm.edu	37	chr19	2253641	2253641	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcacagctggaaagccgaGcccagcagcgccaccagcga	11	1	13	16	4	0	0	0	0	0	0	0	3	0	1	4	2	6	3	4	2	1	0	rs200918439	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2253641G>T	ENST00000300961.6	-	5	478	c.414C>A	c.(412-414)ggC>ggA	p.G138G	JSRP1_ENST00000586471.2_Silent_p.G138G|MIR4321_ENST00000592276.1_RNA	NM_144616.3	NP_653217.1	Q96MG2	JSPR1_HUMAN	junctional sarcoplasmic reticulum protein 1	138	Pro-rich.				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)		GGAAAGCCGAGCCCAGCAGCG	0.716													G|||	54	0.0107827	0.0363	0.0072	5008	,	,		13645	0.0		0.001	False		,,,				2504	0.0				p.G138G		Atlas-SNP	.											.	JSRP1	18	.	0			c.C414A						PASS	.	G		103,3903		0,103,1900	6	10	9		414	1.9	1	19		9	8,7862		0,8,3927	no	coding-synonymous	JSRP1	NM_144616.3		0,111,5827	TT,TG,GG		0.1017,2.5711,0.9347		138/332	2253641	111,11765	2003	3935	5938	SO:0001819	synonymous_variant	126306	exon5			AGCCGAGCCCAGC	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.414C>A	19.37:g.2253641G>T		31	0	0		24	15	0.625	NM_144616		Silent	SNP	ENST00000300961.6	37	CCDS12086.1																																																																																			G|0.996;T|0.004	0.004	strong		0.716	JSRP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451266.2	NM_144616		T	2253641	G	T	2253641	2	4	22	1	0	0	0	0	0	0	0	1	7975	958	34	4		4	JSRP1	19	2253641	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	137025	2253641	56875342	3725	6626											
TMPRSS9	360200	hgsc.bcm.edu	37	chr19	2389793	2389793	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctctgagccatggagcccActgtggctgacgtacacctc	7	9	11	14	1	1	2	0	2	1	0	3	3	1	3	3	2	3	2	3	2	1	1	rs8100709	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2389793A>G	ENST00000332578.3	+	1	10	c.10A>G	c.(10-12)Act>Gct	p.T4A		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	4			T -> A (in dbSNP:rs8100709).		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)		CATGGAGCCCACTGTGGCTGA	0.617													A|||	250	0.0499201	0.1815	0.0101	5008	,	,		19564	0.0		0.003	False		,,,				2504	0.0				p.T4A		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.A10G						PASS	.	A	ALA/THR	754,3652	303.2+/-287.8	55,644,1504	63	45	51		10	-4.2	0	19	dbSNP_116	51	20,8580	13.3+/-46.6	0,20,4280	yes	missense	TMPRSS9	NM_182973.1	58	55,664,5784	GG,GA,AA		0.2326,17.113,5.9511	benign	4/1060	2389793	774,12232	2203	4300	6503	SO:0001583	missense	360200	exon1			GAGCCCACTGTGG	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.10A>G	19.37:g.2389793A>G	ENSP00000330264:p.Thr4Ala	61	0	0		76	41	0.539474	NM_182973	Q6ZND6|Q7Z411	Missense_Mutation	SNP	ENST00000332578.3	37	CCDS12088.1	84	0.038461538461538464	81	0.16463414634146342	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	A	2.015	-0.426184	0.04701	0.17113	0.002326	ENSG00000178297	ENST00000395264;ENST00000332578	D	0.87256	-2.23	4.16	-4.2	0.03823	.	1.292730	0.05536	N	0.564908	T	0.00524	0.0017	N	0.11560	0.145	0.80722	P	0.0	B;B	0.09022	0.0;0.002	B;B	0.04013	0.001;0.001	T	0.07558	-1.0766	9	0.29301	T	0.29	.	12.5441	0.56188	0.2898:0.0:0.7102:0.0	rs8100709;rs52805984;rs8100709	4;4	Q7Z410;E7EMP4	TMPS9_HUMAN;.	A	4	ENSP00000330264:T4A	ENSP00000330264:T4A	T	+	1	0	TMPRSS9	2340793	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.994000	0.03716	-0.882000	0.03987	-0.432000	0.05891	ACT	A|0.948;G|0.052	0.052	strong		0.617	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973		G	2389793	A	G	2389793	3	3	22	1	0	0	0	0	1	0	0	0	16268	159	6	3	12	3	TMPRSS9	19	2389793	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	136152	2389793	56739190	3726	6627											
TMPRSS9	360200	hgsc.bcm.edu	37	chr19	2389813	2389813	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	actgtggctgacgtacacctCgtgcccaggacaaccaagga	11	6	11	13	2	0	1	0	1	0	0	1	3	0	3	3	3	3	2	3	3	3	1	rs8100380	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2389813C>T	ENST00000332578.3	+	1	30	c.30C>T	c.(28-30)ctC>ctT	p.L10L		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	10					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)		ACGTACACCTCGTGCCCAGGA	0.632													C|||	247	0.0493211	0.1793	0.0101	5008	,	,		18167	0.0		0.003	False		,,,				2504	0.0				p.L10L		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.C30T						PASS	.	C		753,3653	306.3+/-289.4	56,641,1506	76	55	62		30	-4.5	0	19	dbSNP_116	62	20,8580	13.3+/-46.6	0,20,4280	no	coding-synonymous	TMPRSS9	NM_182973.1		56,661,5786	TT,TC,CC		0.2326,17.0903,5.9434		10/1060	2389813	773,12233	2203	4300	6503	SO:0001819	synonymous_variant	360200	exon1			ACACCTCGTGCCC	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.30C>T	19.37:g.2389813C>T		81	0	0		86	45	0.523256	NM_182973	Q6ZND6|Q7Z411	Silent	SNP	ENST00000332578.3	37	CCDS12088.1																																																																																			C|0.948;T|0.052	0.052	strong		0.632	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973		T	2389813	C	T	2389813	2	4	22	1	0	0	0	0	0	0	0	1	16268	871	31	1		1	TMPRSS9	19	2389813	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	20	2389813	56739170	3727	6628											
TMPRSS9	360200	hgsc.bcm.edu	37	chr19	2413788	2413788	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggaatcgggtgtgcggaaGcccggcgtccaggggtctat	6	7	19	9	4	1	0	0	0	1	0	3	2	2	2	2	7	2	0	2	7	3	1	rs147023760	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2413788G>A	ENST00000332578.3	+	9	1243	c.1243G>A	c.(1243-1245)Gcc>Acc	p.A415T		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	415	Peptidase S1 1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				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)		GTGTGCGGAAGCCCGGCGTCC	0.652													G|||	78	0.0155751	0.0575	0.0029	5008	,	,		16111	0.0		0.0	False		,,,				2504	0.0				p.A415T		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.G1243A						PASS	.	G	THR/ALA	191,4215	119.2+/-156.9	7,177,2019	56	60	59		1243	2.9	0	19	dbSNP_134	59	0,8600		0,0,4300	yes	missense	TMPRSS9	NM_182973.1	58	7,177,6319	AA,AG,GG		0.0,4.335,1.4686	possibly-damaging	415/1060	2413788	191,12815	2203	4300	6503	SO:0001583	missense	360200	exon9			GCGGAAGCCCGGC	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.1243G>A	19.37:g.2413788G>A	ENSP00000330264:p.Ala415Thr	107	0	0		99	46	0.464646	NM_182973	Q6ZND6|Q7Z411	Missense_Mutation	SNP	ENST00000332578.3	37	CCDS12088.1	31	0.014194139194139194	30	0.06097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	G	9.621	1.133714	0.21123	0.04335	0.0	ENSG00000178297	ENST00000395264;ENST00000332578	D	0.88664	-2.41	3.93	2.87	0.33458	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.157070	0.29806	N	0.011145	T	0.54711	0.1875	N	0.25647	0.755	0.09310	N	1	D;P	0.76494	0.999;0.587	D;P	0.79108	0.992;0.486	T	0.69367	-0.5164	10	0.15066	T	0.55	.	12.189	0.54257	0.0:0.1739:0.8261:0.0	.	415;449	Q7Z410;E7EMP4	TMPS9_HUMAN;.	T	449;415	ENSP00000330264:A415T	ENSP00000330264:A415T	A	+	1	0	TMPRSS9	2364788	0.674000	0.27549	0.004000	0.12327	0.000000	0.00434	2.621000	0.46418	0.637000	0.30526	-0.314000	0.08810	GCC	G|0.983;A|0.017	0.017	strong		0.652	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973		A	2413788	G	A	2413788	3	1	22	1	0	0	0	0	1	0	0	0	16268	971	34	2	1277	2	TMPRSS9	19	2413788	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	23975	2413788	56715195	3728	6629											
LMNB2	84823	hgsc.bcm.edu	37	chr19	2432450	2432450	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgcgcaggatgtacttgggCgtgaacttgtaggcgatctc	7	10	15	9	4	1	1	0	1	1	0	2	3	1	2	0	3	2	3	0	3	3	4	rs11882908	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2432450C>G	ENST00000582871.1	-	9	1580	c.1494G>C	c.(1492-1494)acG>acC	p.T498T	LMNB2_ENST00000475819.1_5'Flank|LMNB2_ENST00000325327.3_Silent_p.T518T	NM_032737.3	NP_116126.3	Q03252	LMNB2_HUMAN	lamin B2	498	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)		TGTACTTGGGCGTGAACTTGT	0.632													C|||	143	0.0285543	0.1059	0.0043	5008	,	,		14898	0.0		0.0	False		,,,				2504	0.0				p.T518T		Atlas-SNP	.											LMNB2,NS,carcinoma,0,2	LMNB2	40	2	0			c.G1554C						scavenged	.	C		491,3915	228.5+/-243.3	26,439,1738	300	225	250		1494	-8.2	0.9	19	dbSNP_120	250	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	LMNB2	NM_032737.2		26,442,6035	GG,GC,CC		0.0349,11.1439,3.7982		498/601	2432450	494,12512	2203	4300	6503	SO:0001819	synonymous_variant	84823	exon9			CTTGGGCGTGAAC	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.1494G>C	19.37:g.2432450C>G		104	1	0.00961538		79	34	0.43038	NM_032737	O75292|Q14734|Q96DF6	Silent	SNP	ENST00000582871.1	37																																																																																				C|0.960;G|0.040	0.040	strong		0.632	LMNB2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032737		G	2432450	C	G	2432450	2	3	22	1	0	0	0	0	0	0	0	1	8859	755	27	4		4	LMNB2	19	2432450	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	18662	2432450	56696533	3729	6630											
THOP1	7064	hgsc.bcm.edu	37	chr19	2790508	2790508	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgcccagcagatagaggagCgcaccagggagctcatcgag	11	4	15	11	2	1	2	1	0	0	2	2	5	1	4	2	2	4	3	2	2	1	1	rs76198851	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2790508C>T	ENST00000307741.6	+	2	309	c.106C>T	c.(106-108)Cgc>Tgc	p.R36C		NM_003249.3	NP_003240.1	P52888	THOP1_HUMAN	thimet oligopeptidase 1	36					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)		GATAGAGGAGCGCACCAGGGA	0.612													C|||	13	0.00259585	0.0098	0.0	5008	,	,		20345	0.0		0.0	False		,,,				2504	0.0				p.R36C		Atlas-SNP	.											.	THOP1	49	.	0			c.C106T						PASS	.	C	CYS/ARG	28,4378	36.0+/-67.5	0,28,2175	115	95	102		106	3.9	0	19	dbSNP_131	102	0,8600		0,0,4300	yes	missense	THOP1	NM_003249.3	180	0,28,6475	TT,TC,CC		0.0,0.6355,0.2153	probably-damaging	36/690	2790508	28,12978	2203	4300	6503	SO:0001583	missense	7064	exon2			GAGGAGCGCACCA		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.106C>T	19.37:g.2790508C>T	ENSP00000304467:p.Arg36Cys	50	0	0		46	27	0.586957	NM_003249	B3KSE2|Q9UCB3	Missense_Mutation	SNP	ENST00000307741.6	37	CCDS12095.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	16.20	3.056103	0.55325	0.006355	0.0	ENSG00000172009	ENST00000307741	T	0.08193	3.12	4.9	3.86	0.44501	Neurolysin/Thimet oligopeptidase, N-terminal (1);	0.130158	0.52532	D	0.000063	T	0.11879	0.0289	M	0.68952	2.095	0.50039	D	0.999846	D	0.67145	0.996	P	0.53450	0.726	T	0.00494	-1.1706	10	0.66056	D	0.02	-22.5297	8.1975	0.31405	0.1546:0.7598:0.0:0.0856	.	36	P52888	THOP1_HUMAN	C	36	ENSP00000304467:R36C	ENSP00000304467:R36C	R	+	1	0	THOP1	2741508	0.704000	0.27836	0.010000	0.14722	0.544000	0.35116	3.482000	0.53186	1.055000	0.40461	0.561000	0.74099	CGC	C|0.998;T|0.002	0.002	strong		0.612	THOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451587.2			T	2790508	C	T	2790508	3	4	22	1	0	0	0	0	1	0	0	0	15886	768	27	1	112	1	THOP1	19	2790508	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	358058	2790508	56338475	3730	6631											
ZNF554	115196	hgsc.bcm.edu	37	chr19	2823100	2823100	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggctgctgggtacctgccccGctggtcccaggtgagatgtc	4	9	15	13	1	0	1	0	1	0	1	2	2	1	1	4	4	3	4	4	4	1	1	rs181024964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2823100G>A	ENST00000317243.5	+	2	314	c.116G>A	c.(115-117)cGc>cAc	p.R39H	ZNF554_ENST00000591265.1_Missense_Mutation_p.R39H	NM_001102651.1	NP_001096121.1	Q86TJ5	ZN554_HUMAN	zinc finger protein 554	39					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)		TACCTGCCCCGCTGGTCCCAG	0.567													G|||	7	0.00139776	0.0045	0.0	5008	,	,		18086	0.001		0.0	False		,,,				2504	0.0				p.R39H		Atlas-SNP	.											.	ZNF554	47	.	0			c.G116A						PASS	.	G	HIS/ARG	7,3795		0,7,1894	51	55	54		116	0.6	0	19		54	0,8248		0,0,4124	yes	missense	ZNF554	NM_001102651.1	29	0,7,6018	AA,AG,GG		0.0,0.1841,0.0581	possibly-damaging	39/539	2823100	7,12043	1901	4124	6025	SO:0001583	missense	115196	exon2			TGCCCCGCTGGTC	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.116G>A	19.37:g.2823100G>A	ENSP00000321132:p.Arg39His	60	0	0		71	34	0.478873	NM_001102651	Q8NAT3|Q9BWN3	Missense_Mutation	SNP	ENST00000317243.5	37	CCDS42462.1	5	0.0022893772893772895	3	0.006097560975609756	0	0.0	2	0.0034965034965034965	0	0.0	G	6.811	0.518786	0.13005	0.001841	0.0	ENSG00000172006	ENST00000317243	T	0.07021	3.23	1.71	0.624	0.17659	Krueppel-associated box (1);	.	.	.	.	T	0.02267	0.0070	N	0.08118	0	0.09310	N	1	P	0.35050	0.482	B	0.24974	0.057	T	0.40813	-0.9543	9	0.56958	D	0.05	.	5.8806	0.18854	0.0:0.6302:0.3698:0.0	.	39	Q86TJ5	ZN554_HUMAN	H	39	ENSP00000321132:R39H	ENSP00000321132:R39H	R	+	2	0	ZNF554	2774100	0.000000	0.05858	0.041000	0.18516	0.029000	0.11900	-0.244000	0.08903	0.276000	0.22118	-0.502000	0.04539	CGC	G|0.998;A|0.002	0.002	strong		0.567	ZNF554-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451598.3	NM_152303		A	2823100	G	A	2823100	3	1	22	1	0	0	0	0	1	0	0	0	18000	1087	38	1	122	1	ZNF554	19	2823100	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	32592	2823100	56305883	3731	6632											
NCLN	56926	hgsc.bcm.edu	37	chr19	3207398	3207398	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttctccacagagtcaagccGgccgtctttgacctgctcct	6	12	8	15	2	3	2	1	1	2	1	5	2	4	2	5	1	2	1	5	1	1	2	rs76473246	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3207398G>A	ENST00000246117.4	+	14	1994	c.1563G>A	c.(1561-1563)ccG>ccA	p.P521P	NCLN_ENST00000590671.1_Silent_p.P447P	NM_020170.3	NP_064555.2	Q969V3	NCLN_HUMAN	nicalin	521					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)		GAGTCAAGCCGGCCGTCTTTG	0.652													A|||	149	0.0297524	0.1059	0.013	5008	,	,		16237	0.0		0.0	False		,,,				2504	0.0				p.P521P		Atlas-SNP	.											.	NCLN	27	.	0			c.G1563A						PASS	.	A		442,3964	778.2+/-414.3	15,412,1776	137	132	134		1563	-8.7	0.7	19	dbSNP_131	134	4,8596	812.7+/-407.1	0,4,4296	no	coding-synonymous	NCLN	NM_020170.3		15,416,6072	AA,AG,GG		0.0465,10.0318,3.4292		521/564	3207398	446,12560	2203	4300	6503	SO:0001819	synonymous_variant	56926	exon14			CAAGCCGGCCGTC	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.1563G>A	19.37:g.3207398G>A		117	0	0		94	46	0.489362	NM_020170	D6W613|O75252|Q6FI60|Q6ZMB7|Q8TAT7|Q96H48|Q96IS7|Q9BQH9|Q9BTX4|Q9NPP2	Silent	SNP	ENST00000246117.4	37	CCDS32869.1																																																																																			G|0.967;A|0.033	0.033	strong		0.652	NCLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452545.1	NM_020170		A	3207398	G	A	3207398	2	1	22	1	0	0	0	0	0	0	0	1	10236	1103	39	1		1	NCLN	19	3207398	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	384298	3207398	55921585	3732	6633											
TJP3	27134	hgsc.bcm.edu	37	chr19	3747890	3747890	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agccgcgttaacagcgactaCgagacggacggcgagggcgg	10	3	17	11	8	0	1	0	0	0	1	0	5	0	2	1	4	4	1	1	4	2	2	rs10409928	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3747890C>T	ENST00000541714.2	+	19	2883	c.2421C>T	c.(2419-2421)taC>taT	p.Y807Y	TJP3_ENST00000589378.1_Silent_p.Y816Y|TJP3_ENST00000262968.9_Silent_p.Y840Y|TJP3_ENST00000539908.2_Silent_p.Y771Y|TJP3_ENST00000587686.1_Silent_p.Y826Y|TJP3_ENST00000382008.3_Silent_p.Y821Y	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	807					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)		ACAGCGACTACGAGACGGACG	0.672													C|||	286	0.0571086	0.177	0.0187	5008	,	,		16934	0.0		0.0	False		,,,				2504	0.0399				p.Y816Y		Atlas-SNP	.											.	TJP3	79	.	0			c.C2448T						PASS	.	C		652,3752	261.0+/-264.0	45,562,1595	35	31	32		2520	-6.7	0.8	19	dbSNP_119	32	4,8592	3.0+/-9.4	0,4,4294	no	coding-synonymous	TJP3	NM_014428.1		45,566,5889	TT,TC,CC		0.0465,14.8047,5.0462		840/953	3747890	656,12344	2202	4298	6500	SO:0001819	synonymous_variant	27134	exon19			CGACTACGAGACG	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.2421C>T	19.37:g.3747890C>T		91	0	0		132	76	0.575758	NM_001267561	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Silent	SNP	ENST00000541714.2	37	CCDS32873.2																																																																																			C|0.946;T|0.054	0.054	strong		0.672	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1			T	3747890	C	T	3747890	2	4	22	1	0	0	0	0	0	0	0	1	15946	547	19	1		1	TJP3	19	3747890	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	540492	3747890	55381093	3733	6634											
TJP3	27134	hgsc.bcm.edu	37	chr19	3747910	3747910	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cgagacggacggcgagggcgGcgcgtacacggatggcgagg	8	2	21	10	9	0	1	0	0	0	1	0	6	0	3	0	7	1	1	0	7	1	1	rs10408494	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3747910G>A	ENST00000541714.2	+	19	2903	c.2441G>A	c.(2440-2442)gGc>gAc	p.G814D	TJP3_ENST00000589378.1_Missense_Mutation_p.G823D|TJP3_ENST00000262968.9_Missense_Mutation_p.G847D|TJP3_ENST00000539908.2_Missense_Mutation_p.G778D|TJP3_ENST00000587686.1_Missense_Mutation_p.G833D|TJP3_ENST00000382008.3_Missense_Mutation_p.G828D	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	814					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)		GGCGAGGGCGGCGCGTACACG	0.692													G|||	244	0.048722	0.1747	0.0187	5008	,	,		15847	0.0		0.0	False		,,,				2504	0.0				p.G823D		Atlas-SNP	.											.	TJP3	79	.	0			c.G2468A						PASS	.	G	ASP/GLY	642,3762	260.7+/-263.8	41,560,1601	36	32	33		2540	2.8	0.9	19	dbSNP_119	33	4,8594	3.0+/-9.4	0,4,4295	yes	missense	TJP3	NM_014428.1	94	41,564,5896	AA,AG,GG		0.0465,14.5777,4.9685	benign	847/953	3747910	646,12356	2202	4299	6501	SO:0001583	missense	27134	exon19			AGGGCGGCGCGTA	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.2441G>A	19.37:g.3747910G>A	ENSP00000439278:p.Gly814Asp	100	0	0		140	80	0.571429	NM_001267561	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Missense_Mutation	SNP	ENST00000541714.2	37	CCDS32873.2	85	0.03891941391941392	81	0.16463414634146342	4	0.011049723756906077	0	0.0	0	0.0	G	9.121	1.008881	0.19199	0.145777	4.65E-4	ENSG00000105289	ENST00000541714;ENST00000539908;ENST00000382008;ENST00000262968	T;T;T;T	0.11821	2.74;2.92;2.78;2.85	2.81	2.81	0.32909	.	0.137458	0.47455	U	0.000231	T	0.00073	0.0002	M	0.62723	1.935	0.31716	P	0.638979	P;P;P;P	0.47762	0.835;0.9;0.745;0.835	B;B;B;B	0.41813	0.367;0.367;0.202;0.367	T	0.18903	-1.0322	9	0.87932	D	0	.	12.4552	0.55700	0.0:0.0:1.0:0.0	rs10408494	833;847;828;814	O95049-3;O95049-2;O95049;F5H2X0	.;.;ZO3_HUMAN;.	D	814;778;828;847	ENSP00000439278:G814D;ENSP00000439991:G778D;ENSP00000371438:G828D;ENSP00000262968:G847D	ENSP00000262968:G847D	G	+	2	0	TJP3	3698910	1.000000	0.71417	0.950000	0.38849	0.016000	0.09150	4.057000	0.57455	1.069000	0.40788	0.511000	0.50034	GGC	G|0.950;A|0.050	0.050	strong		0.692	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1			A	3747910	G	A	3747910	3	1	22	1	0	0	0	0	1	0	0	0	15946	1203	42	2	2610	2	TJP3	19	3747910	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	20	3747910	55381073	3734	6635											
APBA3	9546	hgsc.bcm.edu	37	chr19	3759802	3759802	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcagaggccccctccaccCattctggggagtcagaatcc	9	6	10	16	0	2	2	1	0	1	2	4	3	4	3	5	3	1	1	5	3	1	1	rs35932323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3759802C>A	ENST00000316757.3	-	2	661	c.461G>T	c.(460-462)tGg>tTg	p.W154L	MRPL54_ENST00000330133.4_5'Flank	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	154			W -> L (in dbSNP:rs35932323).		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)		CCCCTCCACCCATTCTGGGGA	0.637													C|||	145	0.0289537	0.1067	0.0058	5008	,	,		15097	0.0		0.0	False		,,,				2504	0.0				p.W154L		Atlas-SNP	.											.	APBA3	28	.	0			c.G461T						PASS	.	C	LEU/TRP	361,4039		17,327,1856	22	26	25		461	2.4	0.2	19	dbSNP_126	25	4,8580		0,4,4288	yes	missense	APBA3	NM_004886.3	61	17,331,6144	AA,AC,CC		0.0466,8.2045,2.8112	possibly-damaging	154/576	3759802	365,12619	2200	4292	6492	SO:0001583	missense	9546	exon2			TCCACCCATTCTG	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.461G>T	19.37:g.3759802C>A	ENSP00000315136:p.Trp154Leu	71	0	0		59	32	0.542373	NM_004886	O60483|Q9UPZ2	Missense_Mutation	SNP	ENST00000316757.3	37	CCDS12110.1	53	0.024267399267399268	50	0.1016260162601626	3	0.008287292817679558	0	0.0	0	0.0	C	8.915	0.959726	0.18507	0.082045	4.66E-4	ENSG00000011132	ENST00000316757	T	0.06849	3.25	4.67	2.42	0.29668	.	0.166985	0.29040	N	0.013333	T	0.00178	0.0005	L	0.27053	0.805	0.22213	N	0.999285	B	0.22003	0.063	B	0.19666	0.026	T	0.45906	-0.9229	10	0.22109	T	0.4	.	6.1778	0.20453	0.1873:0.7142:0.0:0.0985	rs35932323	154	O96018	APBA3_HUMAN	L	154	ENSP00000315136:W154L	ENSP00000315136:W154L	W	-	2	0	APBA3	3710802	0.002000	0.14202	0.211000	0.23655	0.049000	0.14656	0.219000	0.17641	1.041000	0.40125	0.561000	0.74099	TGG	C|0.975;A|0.025	0.025	strong		0.637	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2			A	3759802	C	A	3759802	3	1	22	1	0	0	0	0	1	0	0	0	758	595	21	4	1306	4	APBA3	19	3759802	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	11892	3759802	55369181	3735	6636											
APBA3	9546	hgsc.bcm.edu	37	chr19	3760056	3760056	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggatgggcccaccagatcGcctggcagagcttcaaactg	9	6	14	12	1	1	2	1	0	0	2	2	3	1	3	3	4	2	2	3	4	1	1	rs61729800	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3760056G>A	ENST00000316757.3	-	2	407	c.207C>T	c.(205-207)ggC>ggT	p.G69G	MRPL54_ENST00000330133.4_5'Flank	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	69					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)		CCACCAGATCGCCTGGCAGAG	0.637													G|||	145	0.0289537	0.1067	0.0058	5008	,	,		16441	0.0		0.0	False		,,,				2504	0.0				p.G69G		Atlas-SNP	.											APBA3,colon,carcinoma,0,1	APBA3	28	1	0			c.C207T						PASS	.	G		388,4014	187.4+/-214.1	19,350,1832	46	47	47		207	-8	0	19	dbSNP_129	47	5,8595	2.2+/-6.3	0,5,4295	no	coding-synonymous	APBA3	NM_004886.3		19,355,6127	AA,AG,GG		0.0581,8.8142,3.0226		69/576	3760056	393,12609	2201	4300	6501	SO:0001819	synonymous_variant	9546	exon2			CAGATCGCCTGGC	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.207C>T	19.37:g.3760056G>A		115	0	0		100	42	0.42	NM_004886	O60483|Q9UPZ2	Silent	SNP	ENST00000316757.3	37	CCDS12110.1																																																																																			G|0.973;A|0.027	0.027	strong		0.637	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2			A	3760056	G	A	3760056	2	1	22	1	0	0	0	0	0	0	0	1	758	1074	38	1		1	APBA3	19	3760056	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	254	3760056	55368927	3736	6637											
MATK	4145	hgsc.bcm.edu	37	chr19	3789321	3789321	+	5'Flank	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccgaggtctgccttctcttcGttcagcagggaaatgtccct	6	12	10	13	2	3	0	1	0	2	0	6	2	4	1	3	2	2	2	3	2	1	3	rs74830030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3789321G>A	ENST00000310132.6	-	0	0				MATK_ENST00000395045.2_Nonsense_Mutation_p.R9*|MATK_ENST00000395040.2_5'Flank|MATK_ENST00000590821.1_5'UTR	NM_139355.2	NP_647612.1	P42679	MATK_HUMAN	megakaryocyte-associated tyrosine kinase						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)		ccttctcttcgttcagcaggg	0.493													G|||	104	0.0207668	0.0726	0.0115	5008	,	,		19422	0.0		0.0	False		,,,				2504	0.0				p.R9X		Atlas-SNP	.											.	MATK	108	.	0			c.C25T						PASS	.	G	stop/ARG	253,4153	146.5+/-181.1	8,237,1958	46	44	45		25	-2.8	0	19	dbSNP_131	45	1,8599		0,1,4299	yes	stop-gained	MATK	NM_002378.3		8,238,6257	AA,AG,GG		0.0116,5.7422,1.9529		9/509	3789321	254,12752	2203	4300	6503	SO:0001631	upstream_gene_variant	4145	exon2			CTCTTCGTTCAGC	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			19.37:g.3789321G>A	Exception_encountered	113	0	0		122	68	0.557377	NM_002378	B3KNZ9|Q9NST8	Nonsense_Mutation	SNP	ENST00000310132.6	37	CCDS12114.1	28	0.01282051282051282	25	0.0508130081300813	3	0.008287292817679558	0	0.0	0	0.0	G	19.36	3.813366	0.70912	0.057422	1.16E-4	ENSG00000007264	ENST00000395045	.	.	.	1.4	-2.8	0.05823	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	2.4484	4.5873	0.12289	0.0:0.4596:0.3083:0.2321	.	.	.	.	X	9	.	ENSP00000378485:R9X	R	-	1	2	MATK	3740321	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.190000	0.09615	-0.756000	0.04703	0.455000	0.32223	CGA	G|0.980;A|0.020	0.020	strong		0.493	MATK-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453639.1	NM_139355		A	3789321	G	A	3789321	1	1	22	0	1	0	0	0	0	0	0	0	9341	1153	40	1		1	MATK	19	3789321	5'Flank	SNP	G	TCGA-G8-6324-01A-11D-2210-10	29265	3789321	55339662	3737	6638											
ITGB1BP3	27231	hgsc.bcm.edu	37	chr19	3942110	3942110	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	acggcatgaagtcccgagagGagctcttccgtgaagtcctg	9	8	13	11	3	1	3	0	2	1	1	4	5	4	4	3	2	1	2	3	2	2	1	rs16992131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3942110G>A	ENST00000168977.2	+	8	822	c.532G>A	c.(532-534)Gag>Aag	p.E178K	NMRK2_ENST00000593949.1_Missense_Mutation_p.E183K|NMRK2_ENST00000599576.1_Missense_Mutation_p.G109E	NM_170678.2	NP_733778.1	Q9NPI5	NRK2_HUMAN	nicotinamide riboside kinase 2	178			E -> K (in dbSNP:rs16992131).		NAD biosynthetic process (GO:0009435)|negative regulation of myoblast differentiation (GO:0045662)	intracellular (GO:0005622)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|ribosylnicotinamide kinase activity (GO:0050262)										GTCCCGAGAGGAGCTCTTCCG	0.642													G|||	117	0.0233626	0.084	0.0072	5008	,	,		15546	0.0		0.001	False		,,,				2504	0.0				p.E178K		Atlas-SNP	.											.	.	.	.	0			c.G532A						PASS	.	G	LYS/GLU	299,4107	154.4+/-187.8	9,281,1913	47	47	47		532	2.8	0	19	dbSNP_123	47	7,8593	5.0+/-18.6	0,7,4293	yes	missense	ITGB1BP3	NM_170678.2	56	9,288,6206	AA,AG,GG		0.0814,6.7862,2.3528	benign	178/231	3942110	306,12700	2203	4300	6503	SO:0001583	missense	27231	exon8			CGAGAGGAGCTCT	AF190819	CCDS12115.1, CCDS74259.1	19p13.3	2013-10-28	2012-05-31	2012-05-31	ENSG00000077009	ENSG00000077009			17871	protein-coding gene	gene with protein product	"muscle-specific beta 1 integrin binding protein", "nicotinamide riboside kinase 2"	608705	"integrin beta 1 binding protein 3"	ITGB1BP3		10613898, 15137942	Standard	NM_170678		Approved	MIBP, NRK2	uc002lyz.4	Q9NPI5	OTTHUMG00000181758	ENST00000168977.2:c.532G>A	19.37:g.3942110G>A	ENSP00000168977:p.Glu178Lys	64	0	0		81	38	0.469136	NM_170678	B7ZKR3|Q52M81|Q9NZK3	Missense_Mutation	SNP	ENST00000168977.2	37	CCDS12115.1	41	0.018772893772893772	39	0.07926829268292683	2	0.0055248618784530384	0	0.0	0	0.0	G	11.37	1.619506	0.28801	0.067862	8.14E-4	ENSG00000077009	ENST00000168977;ENST00000395034	T	0.59502	0.26	3.83	2.76	0.32466	.	0.214037	0.37437	U	0.002089	T	0.03959	0.0111	L	0.42245	1.32	0.31116	N	0.709375	B;P	0.37423	0.444;0.594	B;B	0.41412	0.356;0.231	T	0.08994	-1.0695	10	0.18710	T	0.47	-9.412	9.3096	0.37895	0.0:0.2212:0.7788:0.0	rs16992131;rs16992131	183;178	B7ZKR3;Q9NPI5	.;NRK2_HUMAN	K	178;134	ENSP00000168977:E178K	ENSP00000168977:E178K	E	+	1	0	ITGB1BP3	3893110	1.000000	0.71417	0.005000	0.12908	0.070000	0.16714	4.069000	0.57541	0.585000	0.29608	0.485000	0.47835	GAG	G|0.977;A|0.023	0.023	strong		0.642	NMRK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457492.1	NM_014446, NM_170678		A	3942110	G	A	3942110	3	1	22	1	0	0	0	0	1	0	0	0	7902	1175	41	2	558	2	ITGB1BP3	19	3942110	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	152789	3942110	55186873	3738	6639											
EEF2	1938	hgsc.bcm.edu	37	chr19	3980852	3980852	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacgtacccatggcagcctcGtcgtccgggggcccctcgta	5	7	12	17	5	0	0	0	0	0	0	4	0	1	0	5	3	2	3	5	3	2	2	rs140573073	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3980852G>A	ENST00000309311.6	-	8	1225	c.1137C>T	c.(1135-1137)gaC>gaT	p.D379D	SNORD37_ENST00000384048.1_RNA|EEF2_ENST00000600720.1_5'Flank	NM_001961.3	NP_001952.1	P13639	EF2_HUMAN	eukaryotic translation elongation factor 2	379					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)		TGGCAGCCTCGTCGTCCGGGG	0.652													G|||	14	0.00279553	0.0106	0.0	5008	,	,		15721	0.0		0.0	False		,,,				2504	0.0				p.D379D	Colon(165;1804 1908 4071 6587 18799)	Atlas-SNP	.											.	EEF2	57	.	0			c.C1137T						PASS	.	G		39,4347		0,39,2154	13	11	12		1137	-7.7	0.6	19	dbSNP_134	12	0,8556		0,0,4278	no	coding-synonymous	EEF2	NM_001961.3		0,39,6432	AA,AG,GG		0.0,0.8892,0.3013		379/859	3980852	39,12903	2193	4278	6471	SO:0001819	synonymous_variant	1938	exon8			AGCCTCGTCGTCC	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.1137C>T	19.37:g.3980852G>A		32	0	0		53	27	0.509434	NM_001961	B2RMP5|D6W618|Q58J86	Silent	SNP	ENST00000309311.6	37	CCDS12117.1																																																																																			G|0.997;A|0.003	0.003	strong		0.652	EEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457615.2	NM_001961		A	3980852	G	A	3980852	2	1	22	1	0	0	0	0	0	0	0	1	4931	1136	40	1		1	EEF2	19	3980852	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	38742	3980852	55148131	3739	6640											
PIAS4	51588	hgsc.bcm.edu	37	chr19	4012971	4012971	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cttcagatgctcctgggtttCgtgggccggagtaagagtgg	6	11	16	8	2	1	2	1	0	0	2	3	3	2	3	2	4	1	3	2	4	1	3	rs61729790	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4012971C>T	ENST00000262971.2	+	2	193	c.78C>T	c.(76-78)ttC>ttT	p.F26F		NM_015897.2	NP_056981.2	Q8N2W9	PIAS4_HUMAN	protein inhibitor of activated STAT, 4	26	SAP. {ECO:0000255|PROSITE- ProRule:PRU00186, ECO:0000305}.				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)		TCCTGGGTTTCGTGGGCCGGA	0.562													c|||	507	0.101238	0.3699	0.0245	5008	,	,		15489	0.0		0.001	False		,,,				2504	0.0				p.F26F		Atlas-SNP	.											.	PIAS4	40	.	0			c.C78T						PASS	.	T		1226,3180	424.2+/-340.4	166,894,1143	115	110	112		78	-8.9	0.1	19	dbSNP_129	112	11,8589	7.1+/-27.0	0,11,4289	no	coding-synonymous	PIAS4	NM_015897.2		166,905,5432	TT,TC,CC		0.1279,27.8257,9.511		26/511	4012971	1237,11769	2203	4300	6503	SO:0001819	synonymous_variant	51588	exon2			GGGTTTCGTGGGC	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.78C>T	19.37:g.4012971C>T		198	0	0		163	163	1	NM_015897	O75926|Q96G19|Q9UN16	Silent	SNP	ENST00000262971.2	37	CCDS12118.1																																																																																			C|0.910;T|0.090	0.090	strong		0.562	PIAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457496.1	NM_015897		T	4012971	C	T	4012971	2	4	22	1	0	0	0	0	0	0	0	1	11887	883	31	1		1	PIAS4	19	4012971	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	32119	4012971	55116012	3740	6641											
MAP2K2	5605	hgsc.bcm.edu	37	chr19	4110552	4110552	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tccccgtcactgtagaaggcCccgtagaagcccacgatgta	10	7	10	14	3	1	2	1	0	0	2	2	3	2	2	5	1	1	3	5	1	5	3	rs10424722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4110552C>G	ENST00000262948.5	-	3	658	c.405G>C	c.(403-405)ggG>ggC	p.G135G	MAP2K2_ENST00000599345.1_5'UTR|MAP2K2_ENST00000394867.4_Silent_p.G38G	NM_030662.3	NP_109587.1	P36507	MP2K2_HUMAN	mitogen-activated protein kinase kinase 2	135	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)	TGTAGAAGGCCCCGTAGAAGC	0.602													C|||	239	0.0477236	0.1755	0.0101	5008	,	,		16819	0.0		0.0	False		,,,				2504	0.0				p.G135G		Atlas-SNP	.											.	MAP2K2	72	.	0			c.G405C						PASS	.	C		628,3778	272.8+/-271.0	51,526,1626	87	74	79		405	-3.6	1	19	dbSNP_119	79	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	MAP2K2	NM_030662.3		51,531,5921	GG,GC,CC		0.0581,14.2533,4.867		135/401	4110552	633,12373	2203	4300	6503	SO:0001819	synonymous_variant	5605	exon3			GAAGGCCCCGTAG	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.405G>C	19.37:g.4110552C>G		45	0	0		56	38	0.678571	NM_030662		Silent	SNP	ENST00000262948.5	37	CCDS12120.1																																																																																			C|0.956;G|0.044	0.044	strong		0.602	MAP2K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258957.2			G	4110552	C	G	4110552	2	3	22	1	0	0	0	0	0	0	0	1	9246	610	22	4		4	MAP2K2	19	4110552	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	97581	4110552	55018431	3741	6642											
CREB3L3	84699	hgsc.bcm.edu	37	chr19	4171825	4171825	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcgaacctgaccaattcgacGgaggagctggacaacgccac	12	4	12	13	4	0	1	0	1	0	0	1	6	0	4	3	3	3	1	3	3	3	1	rs115268777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4171825G>A	ENST00000078445.2	+	10	1392	c.1245G>A	c.(1243-1245)acG>acA	p.T415T	CREB3L3_ENST00000602147.1_3'UTR|CREB3L3_ENST00000602257.1_Silent_p.T413T|CREB3L3_ENST00000252587.3_3'UTR|CREB3L3_ENST00000595923.1_Silent_p.T414T	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	415					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)		CCAATTCGACGGAGGAGCTGG	0.672													G|||	52	0.0103834	0.0393	0.0	5008	,	,		16107	0.0		0.0	False		,,,				2504	0.0				p.T415T		Atlas-SNP	.											.	CREB3L3	53	.	0			c.G1245A						PASS	.	G		158,4248	104.3+/-142.8	3,152,2048	37	41	40		1245	-4.7	0	19	dbSNP_132	40	1,8589	1.2+/-3.3	0,1,4294	no	coding-synonymous	CREB3L3	NM_032607.1		3,153,6342	AA,AG,GG		0.0116,3.586,1.2235		415/462	4171825	159,12837	2203	4295	6498	SO:0001819	synonymous_variant	84699	exon10			TTCGACGGAGGAG		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.1245G>A	19.37:g.4171825G>A		123	0	0		125	68	0.544	NM_032607	B2R7S6|B7ZL69|M0QYW7|Q6ZMC5|Q96TB9	Silent	SNP	ENST00000078445.2	37	CCDS12121.1																																																																																			G|0.988;A|0.012	0.012	strong		0.672	CREB3L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457922.1	NM_032607		A	4171825	G	A	4171825	2	1	22	1	0	0	0	0	0	0	0	1	3860	1103	39	1		1	CREB3L3	19	4171825	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	61273	4171825	54957158	3742	6643											
ANKRD24	170961	hgsc.bcm.edu	37	chr19	4216829	4216829	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctccagaaaccaaagttaacGgagccgagaccatagatgag	16	5	10	10	2	0	4	0	1	0	3	1	6	1	5	4	1	3	1	4	1	4	2	rs61738959	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4216829G>A	ENST00000600132.1	+	18	1948	c.1672G>A	c.(1672-1674)Gga>Aga	p.G558R	ANKRD24_ENST00000318934.4_Missense_Mutation_p.G558R|ANKRD24_ENST00000262970.5_Missense_Mutation_p.G648R	NM_133475.1	NP_597732.1	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24	558										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)		CAAAGTTAACGGAGCCGAGAC	0.592													G|||	102	0.0203674	0.0749	0.0043	5008	,	,		18749	0.0		0.0	False		,,,				2504	0.0				p.G558R		Atlas-SNP	.											.	ANKRD24	180	.	0			c.G1672A						PASS	.	G	ARG/GLY	191,3851		8,175,1838	19	21	21		1672	3.5	0	19	dbSNP_129	21	4,8382		0,4,4189	yes	missense	ANKRD24	NM_133475.1	125	8,179,6027	AA,AG,GG		0.0477,4.7254,1.569	probably-damaging	558/1147	4216829	195,12233	2021	4193	6214	SO:0001583	missense	170961	exon18			GTTAACGGAGCCG	AB075861	CCDS45925.1	19p13.3	2013-01-10				ENSG00000089847		"Ankyrin repeat domain containing"	29424	protein-coding gene	gene with protein product						11853319	Standard	NM_133475		Approved	KIAA1981	uc010dtt.1	Q8TF21		ENST00000600132.1:c.1672G>A	19.37:g.4216829G>A	ENSP00000471252:p.Gly558Arg	35	0	0		29	14	0.482759	NM_133475	O75268|O95781	Missense_Mutation	SNP	ENST00000600132.1	37	CCDS45925.1	36	0.016483516483516484	35	0.07113821138211382	1	0.0027624309392265192	0	0.0	0	0.0	g	17.79	3.476233	0.63737	0.047254	4.77E-4	ENSG00000089847	ENST00000318934;ENST00000262970	T;T	0.39406	1.08;1.12	3.54	3.54	0.40534	.	0.251067	0.20840	N	0.084734	T	0.04998	0.0134	L	0.29908	0.895	0.26508	N	0.974647	D;D	0.67145	0.993;0.996	P;P	0.62089	0.794;0.898	T	0.01834	-1.1264	10	0.15952	T	0.53	-12.2673	12.9066	0.58156	0.0:0.0:1.0:0.0	rs61738959	558;648	Q8TF21;Q8TF21-2	ANR24_HUMAN;.	R	558;648	ENSP00000321731:G558R;ENSP00000262970:G648R	ENSP00000262970:G648R	G	+	1	0	ANKRD24	4167829	0.332000	0.24722	0.008000	0.14137	0.088000	0.18126	0.933000	0.28897	2.288000	0.76882	0.313000	0.20887	GGA	G|0.982;A|0.018	0.018	strong		0.592	ANKRD24-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458188.1	XM_114000		A	4216829	G	A	4216829	3	1	22	1	0	0	0	0	1	0	0	0	653	1117	39	1	1738	1	ANKRD24	19	4216829	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	45004	4216829	54912154	3743	6644											
ANKRD24	170961	hgsc.bcm.edu	37	chr19	4216931	4216931	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggccacgggagctgaggccAcaggagccaaggtcacagaa	13	2	15	11	1	1	2	1	1	0	1	1	4	1	4	3	5	2	1	3	5	2	0	rs61741405	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4216931A>G	ENST00000600132.1	+	18	2050	c.1774A>G	c.(1774-1776)Aca>Gca	p.T592A	ANKRD24_ENST00000318934.4_Missense_Mutation_p.T592A|ANKRD24_ENST00000262970.5_Missense_Mutation_p.T682A	NM_133475.1	NP_597732.1	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24	592										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)		AGCTGAGGCCACAGGAGCCAA	0.562													A|||	46	0.0091853	0.0325	0.0043	5008	,	,		19640	0.0		0.0	False		,,,				2504	0.0				p.T592A		Atlas-SNP	.											.	ANKRD24	180	.	0			c.A1774G						PASS	.	A	ALA/THR	159,3919		5,149,1885	31	36	35		1774	-6.7	0	19	dbSNP_129	35	1,8381		0,1,4190	yes	missense	ANKRD24	NM_133475.1	58	5,150,6075	GG,GA,AA		0.0119,3.899,1.2841	benign	592/1147	4216931	160,12300	2039	4191	6230	SO:0001583	missense	170961	exon18			GAGGCCACAGGAG	AB075861	CCDS45925.1	19p13.3	2013-01-10				ENSG00000089847		"Ankyrin repeat domain containing"	29424	protein-coding gene	gene with protein product						11853319	Standard	NM_133475		Approved	KIAA1981	uc010dtt.1	Q8TF21		ENST00000600132.1:c.1774A>G	19.37:g.4216931A>G	ENSP00000471252:p.Thr592Ala	46	0	0		28	16	0.571429	NM_133475	O75268|O95781	Missense_Mutation	SNP	ENST00000600132.1	37	CCDS45925.1	27	0.012362637362637362	26	0.052845528455284556	1	0.0027624309392265192	0	0.0	0	0.0	a	2.619	-0.288978	0.05605	0.03899	1.19E-4	ENSG00000089847	ENST00000318934;ENST00000262970	T;T	0.33216	1.47;1.42	3.39	-6.68	0.01778	.	2.468300	0.02265	N	0.067899	T	0.02455	0.0075	N	0.24115	0.695	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.10086	-1.0645	10	0.21540	T	0.41	3.2671	5.3297	0.15926	0.5536:0.0:0.1925:0.2539	rs61741405	592;682	Q8TF21;Q8TF21-2	ANR24_HUMAN;.	A	592;682	ENSP00000321731:T592A;ENSP00000262970:T682A	ENSP00000262970:T682A	T	+	1	0	ANKRD24	4167931	0.000000	0.05858	0.000000	0.03702	0.068000	0.16541	-0.277000	0.08502	-0.988000	0.03489	0.172000	0.16884	ACA	A|0.987;G|0.013	0.013	strong		0.562	ANKRD24-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458188.1	XM_114000		G	4216931	A	G	4216931	3	3	22	1	0	0	0	0	1	0	0	0	653	159	6	3	1840	3	ANKRD24	19	4216931	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	102	4216931	54912052	3744	6645											
UBXN6	80700	hgsc.bcm.edu	37	chr19	4446164	4446164	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccggacgaacccgtacaccGcccccagccgctcccgagcg	7	2	10	22	7	0	0	0	0	0	0	1	3	1	1	7	1	4	2	7	1	2	1	rs34179017	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4446164G>A	ENST00000301281.6	-	10	1206	c.1082C>T	c.(1081-1083)gCg>gTg	p.A361V	CTB-50L17.7_ENST00000588798.1_RNA|UBXN6_ENST00000394765.3_Missense_Mutation_p.A308V|MIR4746_ENST00000579802.1_RNA	NM_025241.2	NP_079517.1	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6	361	UBX. {ECO:0000255|PROSITE- ProRule:PRU00215}.					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						CCCGTACACCGCCCCCAGCCG	0.711													G|||	32	0.00638978	0.0242	0.0	5008	,	,		14161	0.0		0.0	False		,,,				2504	0.0				p.A361V		Atlas-SNP	.											.	UBXN6	27	.	0			c.C1082T						PASS	.	G	VAL/ALA,VAL/ALA	76,4324		1,74,2125	15	19	18		923,1082	-1.2	0	19	dbSNP_126	18	0,8590		0,0,4295	yes	missense,missense	UBXN6	NM_001171091.1,NM_025241.2	64,64	1,74,6420	AA,AG,GG		0.0,1.7273,0.5851	benign,benign	308/389,361/442	4446164	76,12914	2200	4295	6495	SO:0001583	missense	80700	exon10			TACACCGCCCCCA	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.1082C>T	19.37:g.4446164G>A	ENSP00000301281:p.Ala361Val	97	0	0		102	50	0.490196	NM_025241	D6W626|Q96AH1|Q96IK9|Q9BZV0	Missense_Mutation	SNP	ENST00000301281.6	37	CCDS12129.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	5.191	0.220842	0.09863	0.017273	0.0	ENSG00000167671	ENST00000301281;ENST00000394765	T;T	0.44881	0.91;0.91	5.15	-1.23	0.09465	UBX (3);	0.540957	0.20913	N	0.083423	T	0.14399	0.0348	L	0.48260	1.515	0.09310	N	0.999999	B;B	0.23540	0.047;0.087	B;B	0.22880	0.013;0.042	T	0.10019	-1.0648	10	0.25106	T	0.35	-7.5495	4.4434	0.11586	0.2944:0.0:0.4642:0.2414	rs34179017;rs34179017	308;361	Q9BZV1-2;Q9BZV1	.;UBXN6_HUMAN	V	361;308	ENSP00000301281:A361V;ENSP00000378246:A308V	ENSP00000301281:A361V	A	-	2	0	UBXN6	4397164	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	0.189000	0.17037	-0.230000	0.09840	0.561000	0.74099	GCG	G|0.992;A|0.008	0.008	strong		0.711	UBXN6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458447.3	NM_025241		A	4446164	G	A	4446164	3	1	22	1	0	0	0	0	1	0	0	0	16932	1087	38	1	251	1	UBXN6	19	4446164	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	229233	4446164	54682819	3745	6646											
HDGFRP2	84717	hgsc.bcm.edu	37	chr19	4488718	4488718	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cccccgaggccaaccccgccGacggcagtgacgctgacgag	8	2	13	18	6	0	2	0	2	0	0	0	5	0	2	6	2	1	2	6	2	1	0	rs147061912	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4488718G>A	ENST00000301284.4	+	4	398	c.334G>A	c.(334-336)Gac>Aac	p.D112N	HDGFRP2_ENST00000586684.1_Missense_Mutation_p.D112N	NM_001001520.1|NM_032631.2	NP_001001520|NP_116020.1	Q7Z4V5	HDGR2_HUMAN		112					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										CAACCCCGCCGACGGCAGTGA	0.677													G|||	37	0.00738818	0.028	0.0	5008	,	,		14427	0.0		0.0	False		,,,				2504	0.0				p.D112N		Atlas-SNP	.											.	.	.	.	0			c.G334A						PASS	.	G	ASN/ASP,ASN/ASP	96,4038		1,94,1972	11	15	13		334,334	2.5	0	19	dbSNP_134	13	0,8302		0,0,4151	yes	missense,missense	HDGFRP2	NM_032631.2,NM_001001520.1	23,23	1,94,6123	AA,AG,GG		0.0,2.3222,0.772	benign,benign	112/676,112/677	4488718	96,12340	2067	4151	6218	SO:0001583	missense	0	exon4			CCCGCCGACGGCA																												ENST00000301284.4:c.334G>A	19.37:g.4488718G>A	ENSP00000301284:p.Asp112Asn	27	0	0		28	16	0.571429	NM_032631	I3L080|K7EQZ6|Q96GI5|Q9BW08	Missense_Mutation	SNP	ENST00000301284.4	37	CCDS42472.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	G	4.364	0.067010	0.08388	0.023222	0.0	ENSG00000167674	ENST00000301284;ENST00000398364	T	0.46451	0.87	4.86	2.5	0.30297	.	0.387710	0.23889	N	0.043579	T	0.10852	0.0265	L	0.38175	1.15	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.01281	0.0;0.0	T	0.08229	-1.0732	10	0.21014	T	0.42	.	8.9678	0.35887	0.0:0.1609:0.6729:0.1662	.	112;112	C9JEE1;Q7Z4V5	.;HDGR2_HUMAN	N	112;98	ENSP00000301284:D112N	ENSP00000301284:D112N	D	+	1	0	AC011498.1	4439718	0.052000	0.20516	0.003000	0.11579	0.006000	0.05464	2.427000	0.44740	1.143000	0.42306	0.555000	0.69702	GAC	G|0.994;A|0.006	0.006	strong		0.677	HDGFRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458642.1			A	4488718	G	A	4488718	3	1	22	1	0	0	0	0	1	0	0	0	7029	1058	37	1	348	1	HDGFRP2	19	4488718	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	42554	4488718	54640265	3746	6647											
PLIN4	729359	hgsc.bcm.edu	37	chr19	4511913	4511913	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagcacggtcttggccgtgtCtacacctgtctgggcagccc	5	9	12	15	2	3	0	0	0	3	0	3	0	3	0	3	3	3	2	3	3	1	2	rs199927982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4511913C>T	ENST00000301286.3	-	3	2016	c.2017G>A	c.(2017-2019)Gac>Aac	p.D673N		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	673	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						TTGGCCGTGTCTACACCTGTC	0.567													C|||	52	0.0103834	0.0386	0.0014	5008	,	,		29014	0.0		0.0	False		,,,				2504	0.0				p.D673N		Atlas-SNP	.											.	PLIN4	191	.	0			c.G2017A						PASS	.	G	ASN/ASP	151,4073		4,143,1965	139	148	145		2017	3	0.3	19	dbSNP_132	145	0,8444		0,0,4222	yes	missense	PLIN4	NM_001080400.1	23	4,143,6187	TT,TC,CC		0.0,3.5748,1.192	probably-damaging	673/1358	4511913	151,12517	2112	4222	6334	SO:0001583	missense	729359	exon3			CCGTGTCTACACC	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.2017G>A	19.37:g.4511913C>T	ENSP00000301286:p.Asp673Asn	323	0	0		359	137	0.381616	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	27	0.012362637362637362	27	0.054878048780487805	0	0.0	0	0.0	0	0.0	C	13.17	2.155782	0.38021	0.035748	0.0	ENSG00000167676	ENST00000301286	T	0.11063	2.81	5.14	3.0	0.34707	.	0.287773	0.24191	U	0.040720	T	0.02970	0.0088	M	0.85197	2.74	0.20926	N	0.999825	P	0.49961	0.93	P	0.47044	0.535	T	0.04811	-1.0925	10	0.46703	T	0.11	-25.9696	7.1023	0.25344	0.0:0.6943:0.1443:0.1613	.	673	Q96Q06	PLIN4_HUMAN	N	673	ENSP00000301286:D673N	ENSP00000301286:D673N	D	-	1	0	PLIN4	4462913	0.000000	0.05858	0.349000	0.25694	0.008000	0.06430	-0.258000	0.08733	0.567000	0.29293	-0.757000	0.03467	GAC	C|0.988;T|0.012	0.012	strong		0.567	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901		T	4511913	C	T	4511913	3	4	22	1	0	0	0	0	1	0	0	0	12101	913	32	2	2072	2	PLIN4	19	4511913	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	23195	4511913	54617070	3747	6648											
PLIN4	729359	hgsc.bcm.edu	37	chr19	4511944	4511944	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggcagcccctttggccacAttcacagcactggtcacccc	7	8	9	17	0	2	0	2	0	0	0	2	0	2	0	5	3	2	2	5	3	0	2	rs143131726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4511944A>G	ENST00000301286.3	-	3	1985	c.1986T>C	c.(1984-1986)aaT>aaC	p.N662N		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	662	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						CTTTGGCCACATTCACAGCAC	0.577													A|||	40	0.00798722	0.0303	0.0	5008	,	,		25673	0.0		0.0	False		,,,				2504	0.0				p.N662N		Atlas-SNP	.											.	PLIN4	191	.	0			c.T1986C						PASS	.	A		115,4007		6,103,1952	96	106	103		1986	-10.3	0	19	dbSNP_134	103	1,8383		0,1,4191	no	coding-synonymous	PLIN4	NM_001080400.1		6,104,6143	GG,GA,AA		0.0119,2.7899,0.9276		662/1358	4511944	116,12390	2061	4192	6253	SO:0001819	synonymous_variant	729359	exon3			GGCCACATTCACA	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.1986T>C	19.37:g.4511944A>G		321	0	0		306	134	0.437909	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			A|0.994;G|0.006	0.006	strong		0.577	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901		G	4511944	A	G	4511944	2	3	22	1	0	0	0	0	0	0	0	1	12101	214	8	3		3	PLIN4	19	4511944	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	31	4511944	54617039	3748	6649											
PLIN4	729359	hgsc.bcm.edu	37	chr19	4512534	4512534	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gccctggacggcccctttggCcacattcgcagcaccggtga	6	7	12	16	3	0	1	0	1	0	0	1	2	0	2	5	4	1	2	5	4	0	2	rs61730732	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4512534C>T	ENST00000301286.3	-	3	1395	c.1396G>A	c.(1396-1398)Gcc>Acc	p.A466T		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	466	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						GCCCCTTTGGCCACATTCGCA	0.597													C|||	45	0.00898562	0.0333	0.0014	5008	,	,		22756	0.0		0.0	False		,,,				2504	0.0				p.A466T		Atlas-SNP	.											.	PLIN4	191	.	0			c.G1396A						PASS	.	C	THR/ALA	146,3788		3,140,1824	114	122	119		1396	5	1	19	dbSNP_129	119	0,8308		0,0,4154	yes	missense	PLIN4	NM_001080400.1	58	3,140,5978	TT,TC,CC		0.0,3.7112,1.1926	possibly-damaging	466/1358	4512534	146,12096	1967	4154	6121	SO:0001583	missense	729359	exon3			CTTTGGCCACATT	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.1396G>A	19.37:g.4512534C>T	ENSP00000301286:p.Ala466Thr	182	0	0		227	100	0.440529	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	22	0.010073260073260074	22	0.044715447154471545	0	0.0	0	0.0	0	0.0	C	17.51	3.406822	0.62399	0.037112	0.0	ENSG00000167676	ENST00000301286	T	0.09350	2.99	4.99	4.99	0.66335	.	0.000000	0.52532	D	0.000078	T	0.08670	0.0215	M	0.86573	2.825	0.34738	D	0.730428	D	0.61080	0.989	P	0.56474	0.799	T	0.37619	-0.9698	10	0.30854	T	0.27	-55.3504	15.8081	0.78531	0.0:1.0:0.0:0.0	.	466	Q96Q06	PLIN4_HUMAN	T	466	ENSP00000301286:A466T	ENSP00000301286:A466T	A	-	1	0	PLIN4	4463534	0.165000	0.22948	0.996000	0.52242	0.008000	0.06430	1.816000	0.38992	2.342000	0.79632	0.549000	0.68633	GCC	C|0.991;T|0.009	0.009	strong		0.597	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901		T	4512534	C	T	4512534	3	4	22	1	0	0	0	0	1	0	0	0	12101	739	26	2	2693	2	PLIN4	19	4512534	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	590	4512534	54616449	3749	6650											
PLIN5	440503	hgsc.bcm.edu	37	chr19	4529255	4529257	+	In_Frame_Del	DEL	GAG	GAG	-																															tggccaccacgtccttggctGaggtcaccacctggaaggaa																								rs140507757	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4529255_4529257delGAG	ENST00000381848.3	-	5	428_430	c.348_350delCTC	c.(346-351)acctca>aca	p.S117del	CTB-50L17.14_ENST00000586020.1_3'UTR	NM_001013706.2	NP_001013728.2	Q00G26	PLIN5_HUMAN	perilipin 5	117	Essential for lipid droplet targeting. {ECO:0000250}.				lipid particle organization (GO:0034389)|lipid storage (GO:0019915)|mitochondrion localization (GO:0051646)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of lipase activity (GO:0060192)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of triglyceride catabolic process (GO:0010897)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of lipase activity (GO:0060193)|positive regulation of lipid storage (GO:0010884)|positive regulation of sequestering of triglyceride (GO:0010890)|positive regulation of triglyceride biosynthetic process (GO:0010867)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)				endometrium(4)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	10						GTCCTTGGCTGAGGTCACCACCT	0.67														54	0.0107827	0.0401	0.0014	5008	,	,		14860	0.0		0.0	False		,,,				2504	0.0				p.117_117del		Pindel,Atlas-Indel	.											.	PLIN5	27	.	0			c.349_351del						PASS	.			141,3831		9,123,1854						-7.4	1		dbSNP_134	48	0,8030		0,0,4015	no	coding	PLIN5	NM_001013706.2		9,123,5869	A1A1,A1R,RR		0.0,3.5498,1.1748				141,11861				SO:0001651	inframe_deletion	440503	exon5			.	DQ839131	CCDS42473.1	19p13.3	2009-08-12			ENSG00000214456	ENSG00000214456		"Perilipins"	33196	protein-coding gene	gene with protein product	"lipid storage droplet protein 5"	613248				17234449, 19638644	Standard	NM_001013706		Approved	LSDP5, LSDA5, OXPAT, MLDP	uc002mas.3	Q00G26		ENST00000381848.3:c.348_350delCTC	19.37:g.4529255_4529257delGAG	ENSP00000371272:p.Ser117del	143	0	.		118	36	0.305	NM_001013706	A2RRC1|Q6ZS68	In_Frame_Del	DEL	ENST00000381848.3	37	CCDS42473.1																																																																																			GAG|0.986;-|0.014	0.014	strong		0.67	PLIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458647.1	NM_001013706		-	4529257	GAG	-	4529255	7	5	22	1	0	1	0	1	0	0	0	0	12102	1294	45	0	1057	0	PLIN5	19	4529255	In_Frame_Del	DEL	GAG	TCGA-G8-6324-01A-11D-2210-10	16721	4529255	54599728	3750	6651											
SEMA6B	10501	hgsc.bcm.edu	37	chr19	4558422	4558422	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcgccccccagtagcagcagCagaagcagcagggccgggcg	9	1	16	15	3	0	1	0	0	0	1	0	1	0	1	4	2	5	6	4	2	2	1	rs115168835	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4558422C>A	ENST00000586582.1	-	2	358	c.48G>T	c.(46-48)ctG>ctT	p.L16L	SEMA6B_ENST00000586965.1_Silent_p.L16L|SEMA6B_ENST00000301293.3_Silent_p.L16L	NM_032108.3	NP_115484.2	Q9H3T3	SEM6B_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	16					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)		GTAGCAGCAGCAGAAGCAGCA	0.736											OREG0025169	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	94	0.01877	0.0696	0.0029	5008	,	,		9644	0.0		0.0	False		,,,				2504	0.0				p.L16L		Atlas-SNP	.											.	SEMA6B	51	.	0			c.G48T						PASS	.	C		155,3605		0,155,1725	3	5	4		48	2.6	1	19	dbSNP_132	4	1,7703		0,1,3851	no	coding-synonymous	SEMA6B	NM_032108.3		0,156,5576	AA,AC,CC		0.013,4.1223,1.3608		16/889	4558422	156,11308	1880	3852	5732	SO:0001819	synonymous_variant	10501	exon2			CAGCAGCAGAAGC	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.48G>T	19.37:g.4558422C>A		17	0	0	619	31	17	0.548387	NM_032108	A5PKU4|F6IB19|Q9NRK9	Silent	SNP	ENST00000586582.1	37	CCDS12131.1																																																																																			C|0.985;A|0.015	0.015	strong		0.736	SEMA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458656.2	NM_032108		A	4558422	C	A	4558422	2	1	22	1	0	0	0	0	0	0	0	1	14055	697	25	4		4	SEMA6B	19	4558422	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	29167	4558422	54570561	3751	6652											
ALKBH7	84266	hgsc.bcm.edu	37	chr19	6374229	6374229	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcaggccatccacggcttcCgagagacagagaagtcgcgc	10	5	13	13	4	0	2	0	0	0	2	3	5	2	2	3	2	1	2	3	2	1	1	rs116186903	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6374229C>A	ENST00000245812.3	+	2	608	c.220C>A	c.(220-222)Cga>Aga	p.R74R	ALKBH7_ENST00000599849.1_Silent_p.R13R|ALKBH7_ENST00000596657.1_5'UTR	NM_032306.3	NP_115682.1	Q9BT30	ALKB7_HUMAN	alkB, alkylation repair homolog 7 (E. coli)	74					cellular response to DNA damage stimulus (GO:0006974)|fatty acid metabolic process (GO:0006631)|regulation of lipid storage (GO:0010883)|regulation of mitochondrial membrane permeability involved in programmed necrotic cell death (GO:1902445)	mitochondrial matrix (GO:0005759)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6						CCACGGCTTCCGAGAGACAGA	0.657													C|||	33	0.00658946	0.0234	0.0029	5008	,	,		15595	0.0		0.0	False		,,,				2504	0.0				p.R74R		Atlas-SNP	.											.	ALKBH7	18	.	0			c.C220A						PASS	.	C		78,4322		1,76,2123	29	32	31		220	3.6	1	19	dbSNP_132	31	0,8590		0,0,4295	no	coding-synonymous	ALKBH7	NM_032306.3		1,76,6418	AA,AC,CC		0.0,1.7727,0.6005		74/222	6374229	78,12912	2200	4295	6495	SO:0001819	synonymous_variant	84266	exon2			GGCTTCCGAGAGA	AY427650	CCDS12163.1	19p13.3	2008-02-05	2006-02-09	2006-02-09		ENSG00000125652		"Alkylation repair homologs"	21306	protein-coding gene	gene with protein product		613305	"spermatogenesis associated 11"	SPATA11		12477932	Standard	NM_032306		Approved	MGC10974	uc002meo.2	Q9BT30		ENST00000245812.3:c.220C>A	19.37:g.6374229C>A		57	0	0		67	43	0.641791	NM_032306	B2R4U9|Q53FF3	Silent	SNP	ENST00000245812.3	37	CCDS12163.1																																																																																			C|0.994;A|0.006	0.006	strong		0.657	ALKBH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453036.1	NM_032306		A	6374229	C	A	6374229	2	1	22	1	0	0	0	0	0	0	0	1	532	644	23	4		4	ALKBH7	19	6374229	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1815807	6374229	52754754	3752	6653											
DENND1C	79958	hgsc.bcm.edu	37	chr19	6480013	6480013	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcaccctcctgcagggaggCagggcaggccgcttcgaaga	8	5	14	14	2	1	1	1	0	0	1	3	3	2	2	3	4	1	4	3	4	1	1	rs10416003	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6480013C>T	ENST00000381480.2	-	2	179	c.67G>A	c.(67-69)Gcc>Acc	p.A23T	DENND1C_ENST00000591030.1_Intron|DENND1C_ENST00000543576.1_Intron	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	23	UDENN.		A -> T (in dbSNP:rs10416003).		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						TGCAGGGAGGCAGGGCAGGCC	0.607													c|||	50	0.00998403	0.0363	0.0014	5008	,	,		16807	0.0		0.001	False		,,,				2504	0.0				p.A23T		Atlas-SNP	.											.	DENND1C	93	.	0			c.G67A						PASS	.	C	THR/ALA	144,3742		2,140,1801	34	39	37		67	-1.7	0.1	19	dbSNP_119	37	1,8255		0,1,4127	yes	missense	DENND1C	NM_024898.2	58	2,141,5928	TT,TC,CC		0.0121,3.7056,1.1942	benign	23/802	6480013	145,11997	1943	4128	6071	SO:0001583	missense	79958	exon2			GGGAGGCAGGGCA	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.67G>A	19.37:g.6480013C>T	ENSP00000370889:p.Ala23Thr	102	0	0		145	77	0.531034	NM_024898	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Missense_Mutation	SNP	ENST00000381480.2	37	CCDS45938.1	18	0.008241758241758242	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	c	9.626	1.135185	0.21123	0.037056	1.21E-4	ENSG00000205744	ENST00000381480	T	0.08193	3.12	4.95	-1.69	0.08186	uDENN (3);	0.538503	0.18725	N	0.132907	T	0.00695	0.0023	N	0.08118	0	0.09310	N	0.999995	B	0.16396	0.017	B	0.13407	0.009	T	0.44360	-0.9333	10	0.18710	T	0.47	-2.0715	5.3304	0.15930	0.0:0.4706:0.1479:0.3814	rs10416003;rs10416003	23	Q8IV53	DEN1C_HUMAN	T	23	ENSP00000370889:A23T	ENSP00000370889:A23T	A	-	1	0	DENND1C	6431013	0.003000	0.15002	0.132000	0.22025	0.862000	0.49288	-0.763000	0.04740	-0.080000	0.12685	0.558000	0.71614	GCC	C|0.991;T|0.009	0.009	strong		0.607	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898		T	6480013	C	T	6480013	3	4	22	1	0	0	0	0	1	0	0	0	4430	710	25	2	2426	2	DENND1C	19	6480013	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	105784	6480013	52648970	3753	6654											
C3	718	hgsc.bcm.edu	37	chr19	6711070	6711070	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aggaagttgacgttgagggtCtccccgggtctgagctctgt	6	11	15	9	2	3	3	0	3	3	0	4	4	3	4	2	3	1	3	2	3	1	2	rs11569422	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6711070C>G	ENST00000245907.6	-	12	1499	c.1407G>C	c.(1405-1407)gaG>gaC	p.E469D		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	469			E -> D (in dbSNP:rs11569422).		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)	CGTTGAGGGTCTCCCCGGGTC	0.602													C|||	81	0.0161741	0.059	0.0029	5008	,	,		16993	0.0		0.001	False		,,,				2504	0.0				p.E469D		Atlas-SNP	.											.	C3	192	.	0			c.G1407C						PASS	.	C	ASP/GLU	180,4226	116.7+/-154.6	1,178,2024	244	215	225		1407	-10.1	0	19	dbSNP_120	225	3,8597	3.0+/-9.4	0,3,4297	yes	missense	C3	NM_000064.2	45	1,181,6321	GG,GC,CC		0.0349,4.0853,1.407	benign	469/1664	6711070	183,12823	2203	4300	6503	SO:0001583	missense	718	exon12			GAGGGTCTCCCCG	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.1407G>C	19.37:g.6711070C>G	ENSP00000245907:p.Glu469Asp	177	0	0		184	90	0.48913	NM_000064	A7E236	Missense_Mutation	SNP	ENST00000245907.6	37	CCDS32883.1	28	0.01282051282051282	27	0.054878048780487805	1	0.0027624309392265192	0	0.0	0	0.0	C	0.018	-1.468540	0.01053	0.040853	3.49E-4	ENSG00000125730	ENST00000245907	T	0.63417	-0.04	5.03	-10.1	0.00402	Alpha-2-macroglobulin, N-terminal 2 (1);	0.352724	0.35013	N	0.003502	T	0.03739	0.0106	N	0.04655	-0.195	0.09310	N	1	B	0.02656	0.0	B	0.13407	0.009	T	0.41448	-0.9508	10	0.02654	T	1	.	9.8878	0.41272	0.0906:0.1208:0.6374:0.1513	rs11569422	469	P01024	CO3_HUMAN	D	469	ENSP00000245907:E469D	ENSP00000245907:E469D	E	-	3	2	C3	6662070	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-1.288000	0.02783	-0.902000	0.03886	-1.288000	0.01363	GAG	C|0.980;G|0.020	0.020	strong		0.602	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064		G	6711070	C	G	6711070	3	3	22	1	0	0	0	0	1	0	0	0	2206	912	32	4	3704	4	C3	19	6711070	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	231057	6711070	52417913	3754	6655											
TRIP10	9322	hgsc.bcm.edu	37	chr19	6751103	6751103	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agggcactatctctatggccGagggtgaagacctcagtctt	9	10	12	10	1	3	2	1	1	2	1	4	3	3	2	2	3	0	1	2	3	3	3	rs139253875	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6751103G>A	ENST00000313244.9	+	15	1722	c.1687G>A	c.(1687-1689)Gag>Aag	p.E563K	TRIP10_ENST00000596758.1_Silent_p.P516P|TRIP10_ENST00000313285.8_Missense_Mutation_p.E507K|TRIP10_ENST00000600428.1_Missense_Mutation_p.E399K|CTD-3128G10.6_ENST00000594056.1_RNA			Q15642	CIP4_HUMAN	thyroid hormone receptor interactor 10	563	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)	p.E507Q(1)|p.E563Q(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	16						CTCTATGGCCGAGGGTGAAGA	0.532													G|||	7	0.00139776	0.0053	0.0	5008	,	,		15820	0.0		0.0	False		,,,				2504	0.0				p.E507K		Atlas-SNP	.											TRIP10_ENST00000313244,NS,carcinoma,0,2	TRIP10	104	2	2	Substitution - Missense(2)	lung(2)	c.G1519A						PASS	.	G	LYS/GLU	13,4393	20.2+/-43.8	0,13,2190	52	59	57		1519	4.7	1	19	dbSNP_134	57	0,8600		0,0,4300	yes	missense	TRIP10	NM_004240.2	56	0,13,6490	AA,AG,GG		0.0,0.2951,0.1	possibly-damaging	507/546	6751103	13,12993	2203	4300	6503	SO:0001583	missense	9322	exon14			ATGGCCGAGGGTG	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.1687G>A	19.37:g.6751103G>A	ENSP00000320117:p.Glu563Lys	118	0	0		146	65	0.445205	NM_004240	B2R8A6|B7WP22|D6W645|O15184|Q53G22|Q5TZN1|Q6FI24|Q8NFL1|Q8TCY1|Q8TDX3|Q96RJ1	Missense_Mutation	SNP	ENST00000313244.9	37		1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	27.1	4.800102	0.90538	0.002951	0.0	ENSG00000125733	ENST00000313285;ENST00000313244	T;T	0.40756	1.02;1.02	4.66	4.66	0.58398	Src homology-3 domain (4);	0.349695	0.29822	N	0.011119	T	0.60894	0.2304	L	0.59912	1.85	0.80722	D	1	D;D	0.89917	0.996;1.0	D;D	0.85130	0.983;0.997	T	0.63739	-0.6569	10	0.87932	D	0	-32.2852	15.4165	0.74974	0.0:0.0:1.0:0.0	.	563;507	Q15642;Q15642-2	CIP4_HUMAN;.	K	507;563	ENSP00000320493:E507K;ENSP00000320117:E563K	ENSP00000320117:E563K	E	+	1	0	TRIP10	6702103	1.000000	0.71417	0.992000	0.48379	0.699000	0.40488	8.973000	0.93428	2.580000	0.87095	0.305000	0.20034	GAG	G|0.999;A|0.001	0.001	strong		0.532	TRIP10-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000317129.2			A	6751103	G	A	6751103	3	1	22	1	0	0	0	0	1	0	0	0	16569	1059	37	1	1573	1	TRIP10	19	6751103	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	40033	6751103	52377880	3755	6656											
C19orf45	374877	hgsc.bcm.edu	37	chr19	7573225	7573225	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tcctcaggagggcttcgtgcCcctgggcacgcctcaccagc	5	7	12	17	2	2	0	2	0	0	0	4	1	3	1	5	3	2	2	5	3	0	1	rs141790796		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7573225C>T	ENST00000361664.2	+	9	1568	c.1427C>T	c.(1426-1428)cCc>cTc	p.P476L	CTD-2207O23.12_ENST00000599312.1_Intron	NM_198534.2	NP_940936.2	Q8NA69	CS045_HUMAN	chromosome 19 open reading frame 45	476										endometrium(1)|kidney(1)|liver(1)|lung(2)|ovary(2)|stomach(1)	8						GGCTTCGTGCCCCTGGGCACG	0.582																																					p.P476L		Atlas-SNP	.											.	C19orf45	36	.	0			c.C1427T						PASS	.						42	41	41					19																	7573225		2203	4300	6503	SO:0001583	missense	374877	exon9			TCGTGCCCCTGGG	BC029824	CCDS12179.2	19p13.2	2008-02-05			ENSG00000198723	ENSG00000198723			24745	protein-coding gene	gene with protein product						12477932	Standard	NM_198534		Approved	FLJ35784	uc002mgm.2	Q8NA69	OTTHUMG00000157183	ENST00000361664.2:c.1427C>T	19.37:g.7573225C>T	ENSP00000355241:p.Pro476Leu	124	0	0		139	10	0.0719424	NM_198534	Q8N115	Missense_Mutation	SNP	ENST00000361664.2	37	CCDS12179.2	.	.	.	.	.	.	.	.	.	.	C	14.42	2.530201	0.45073	.	.	ENSG00000198723	ENST00000361664	T	0.49139	0.79	4.15	3.09	0.35607	.	0.235290	0.36444	N	0.002596	T	0.43211	0.1237	M	0.63843	1.955	0.46798	D	0.999203	P	0.41597	0.756	B	0.39805	0.31	T	0.45702	-0.9243	10	0.87932	D	0	-24.0027	8.3255	0.32153	0.0:0.8889:0.0:0.1111	.	476	Q8NA69	CS045_HUMAN	L	476	ENSP00000355241:P476L	ENSP00000355241:P476L	P	+	2	0	C19orf45	7479225	0.647000	0.27304	0.555000	0.28281	0.064000	0.16182	1.178000	0.31981	1.090000	0.41315	0.462000	0.41574	CCC	C|1.000;A|0.000	.	alt		0.582	C19orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347808.1	NM_198534		T	7573225	C	T	7573225	3	4	22	1	0	0	0	0	1	0	0	0	1930	623	22	2	1457	2	C19orf45	19	7573225	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	822122	7573225	51555758	3756	6657											
ZNF358	140467	hgsc.bcm.edu	37	chr19	7585762	7585762	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccactcgtggcactgtcaGcccagccctccctaccggcg	5	7	9	20	3	1	0	1	0	0	0	4	0	3	0	5	2	3	1	5	2	1	1	rs116797831	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7585762G>C	ENST00000597229.1	+	2	1804	c.1634G>C	c.(1633-1635)aGc>aCc	p.S545T	ZNF358_ENST00000394341.2_Missense_Mutation_p.S545T|MCOLN1_ENST00000264079.6_5'Flank|CTD-2207O23.11_ENST00000602083.1_RNA	NM_018083.4	NP_060553.4	Q9NW07	ZN358_HUMAN	zinc finger protein 358	545					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						GGCACTGTCAGCCCAGCCCTC	0.662													G|||	130	0.0259585	0.0938	0.0072	5008	,	,		16199	0.0		0.001	False		,,,				2504	0.0				p.S545T		Atlas-SNP	.											.	ZNF358	41	.	0			c.G1634C						PASS	.	G	THR/SER	369,4037	182.9+/-210.6	14,341,1848	88	70	76		1634	4	1	19	dbSNP_132	76	3,8597	3.0+/-9.4	0,3,4297	yes	missense	ZNF358	NM_018083.4	58	14,344,6145	CC,CG,GG		0.0349,8.3749,2.8602	possibly-damaging	545/569	7585762	372,12634	2203	4300	6503	SO:0001583	missense	140467	exon2			CTGTCAGCCCAGC	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.1634G>C	19.37:g.7585762G>C	ENSP00000472305:p.Ser545Thr	183	0	0		207	117	0.565217	NM_018083	Q9BTM7	Missense_Mutation	SNP	ENST00000597229.1	37	CCDS32890.2	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	G	14.68	2.606694	0.46527	0.083749	3.49E-4	ENSG00000198816	ENST00000361576;ENST00000394341	T	0.07021	3.23	4.04	4.04	0.47022	.	.	.	.	.	T	0.00412	0.0013	N	0.24115	0.695	0.24806	N	0.992677	B	0.22851	0.076	B	0.18263	0.021	T	0.20672	-1.0268	9	0.72032	D	0.01	.	14.4919	0.67657	0.0:0.0:1.0:0.0	.	545	Q9NW07	ZN358_HUMAN	T	545	ENSP00000377873:S545T	ENSP00000354703:S545T	S	+	2	0	ZNF358	7491762	0.463000	0.25799	0.996000	0.52242	0.375000	0.29983	2.534000	0.45676	2.547000	0.85894	0.655000	0.94253	AGC	G|0.977;C|0.023	0.023	strong		0.662	ZNF358-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316747.1			C	7585762	G	C	7585762	3	2	22	1	0	0	0	0	1	0	0	0	17882	971	34	4	1636	4	ZNF358	19	7585762	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	12537	7585762	51543221	3757	6658											
KIAA1543	57662	hgsc.bcm.edu	37	chr19	7682862	7682862	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	aagaccatgtccatgagcgtCgatgccttcaccatccaggg	10	8	10	13	2	1	2	1	1	0	1	4	3	3	2	5	1	2	0	5	1	1	1	rs4134883	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7682862C>G	ENST00000160298.4	+	17	3770	c.3669C>G	c.(3667-3669)gtC>gtG	p.V1223V	CAMSAP3_ENST00000446248.2_Silent_p.V1250V	NM_020902.1	NP_065953.1	Q9P1Y5	CAMP3_HUMAN	calmodulin regulated spectrin-associated protein family, member 3	1223	CKK. {ECO:0000255|PROSITE- ProRule:PRU00841}.				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						CCATGAGCGTCGATGCCTTCA	0.642													C|||	194	0.038738	0.1407	0.0115	5008	,	,		15396	0.0		0.0	False		,,,				2504	0.0				p.V1250V		Atlas-SNP	.											.	CAMSAP3	131	.	0			c.C3750G						PASS	.	C	,	540,3516		43,454,1531	52	59	57		3750,3669	0.3	1	19	dbSNP_108	57	2,8342		0,2,4170	no	coding-synonymous,coding-synonymous	CAMSAP3	NM_001080429.2,NM_020902.1	,	43,456,5701	GG,GC,CC		0.024,13.3136,4.371	,	1250/1277,1223/1250	7682862	542,11858	2028	4172	6200	SO:0001819	synonymous_variant	57662	exon19			GAGCGTCGATGCC	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.3669C>G	19.37:g.7682862C>G		126	0	0		96	42	0.4375	NM_001080429	Q8NDF1	Silent	SNP	ENST00000160298.4	37	CCDS42489.1																																																																																			C|0.969;G|0.031	0.031	strong		0.642	CAMSAP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459300.1	XM_048362		G	7682862	C	G	7682862	2	3	22	1	0	0	0	0	0	0	0	1	8252	871	31	4		4	KIAA1543	19	7682862	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	97100	7682862	51446121	3758	6659											
XAB2	56949	hgsc.bcm.edu	37	chr19	7684502	7684502	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcaggctcccaaacactgcGgctggcacgctctgctgctc	6	9	10	16	2	2	0	1	0	1	0	4	0	3	0	1	3	4	6	1	3	1	1	rs4134869	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7684502G>A	ENST00000358368.4	-	19	2575	c.2538C>T	c.(2536-2538)gcC>gcT	p.A846A	XAB2_ENST00000534844.1_Silent_p.A843A	NM_020196.2	NP_064581.2	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	846					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						CAAACACTGCGGCTGGCACGC	0.647								Direct reversal of damage;Nucleotide excision repair (NER)					g|||	196	0.0391374	0.1415	0.0115	5008	,	,		8459	0.001		0.0	False		,,,				2504	0.0				p.A846A		Atlas-SNP	.											.	XAB2	69	.	0			c.C2538T						PASS	.			613,3789		55,503,1643	26	24	25		2538	-7.2	0.1	19	dbSNP_108	25	4,8592		0,4,4294	no	coding-synonymous	XAB2	NM_020196.2		55,507,5937	AA,AG,GG		0.0465,13.9255,4.7469		846/856	7684502	617,12381	2201	4298	6499	SO:0001819	synonymous_variant	56949	exon19			CACTGCGGCTGGC	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.2538C>T	19.37:g.7684502G>A		142	0	0		161	78	0.484472	NM_020196	Q8TET6|Q96HB0|Q96IW0|Q9NRG6|Q9ULP3	Silent	SNP	ENST00000358368.4	37	CCDS32892.1																																																																																			G|0.944;A|0.056	0.056	strong		0.647	XAB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461021.1	NM_020196		A	7684502	G	A	7684502	2	1	22	1	0	0	0	0	0	0	0	1	17433	1103	39	1		1	XAB2	19	7684502	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1640	7684502	51444481	3759	6660											
XAB2	56949	hgsc.bcm.edu	37	chr19	7692132	7692132	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcacctgctaggctcaccttGaggaagcgccgatagcctcg	8	7	12	14	3	1	1	1	1	0	0	2	3	1	2	4	2	3	3	4	2	3	3	rs4134824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7692132G>A	ENST00000358368.4	-	4	556	c.519C>T	c.(517-519)ctC>ctT	p.L173L	XAB2_ENST00000534844.1_Silent_p.L170L|PET100_ENST00000601406.1_5'Flank|PET100_ENST00000594797.1_5'Flank|CTD-3214H19.4_ENST00000595866.1_5'Flank|PET100_ENST00000456958.3_5'Flank	NM_020196.2	NP_064581.2	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	173					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						GGCTCACCTTGAGGAAGCGCC	0.597								Direct reversal of damage;Nucleotide excision repair (NER)					G|||	32	0.00638978	0.0242	0.0	5008	,	,		18719	0.0		0.0	False		,,,				2504	0.0				p.L173L		Atlas-SNP	.											.	XAB2	69	.	0			c.C519T						PASS	.	G		115,4291	87.3+/-125.9	2,111,2090	54	56	56		519	4	1	19	dbSNP_108	56	0,8600		0,0,4300	no	coding-synonymous	XAB2	NM_020196.2		2,111,6390	AA,AG,GG		0.0,2.6101,0.8842		173/856	7692132	115,12891	2203	4300	6503	SO:0001819	synonymous_variant	56949	exon4			CACCTTGAGGAAG	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.519C>T	19.37:g.7692132G>A		29	0	0		39	24	0.615385	NM_020196	Q8TET6|Q96HB0|Q96IW0|Q9NRG6|Q9ULP3	Silent	SNP	ENST00000358368.4	37	CCDS32892.1																																																																																			G|0.990;A|0.010	0.010	strong		0.597	XAB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461021.1	NM_020196		A	7692132	G	A	7692132	2	1	22	1	0	0	0	0	0	0	0	1	17433	1277	45	2		2	XAB2	19	7692132	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	7630	7692132	51436851	3760	6661											
FCER2	2208	hgsc.bcm.edu	37	chr19	7754101	7754101	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aagagtggagaggggcagagGgggtgggcaggcggccgtca	9	3	23	6	2	1	3	1	0	0	3	1	4	1	3	1	8	0	2	1	8	1	0	rs34694289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7754101G>A	ENST00000346664.5	-	11	1156	c.944C>T	c.(943-945)cCc>cTc	p.P315L	FCER2_ENST00000597921.1_Missense_Mutation_p.P315L|FCER2_ENST00000360067.4_Missense_Mutation_p.P314L	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)	315					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						AGGGGCAGAGGGGGTGGGCAG	0.637													G|||	51	0.0101837	0.0386	0.0	5008	,	,		14053	0.0		0.0	False		,,,				2504	0.0				p.P315L		Atlas-SNP	.											.	FCER2	19	.	0			c.C944T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO	130,4276	87.3+/-125.9	4,122,2077	33	32	32		941,944,944	-0.9	0	19	dbSNP_126	32	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	FCER2	NM_001207019.2,NM_001220500.1,NM_002002.4	98,98,98	4,123,6376	AA,AG,GG		0.0116,2.9505,1.0072	probably-damaging,probably-damaging,probably-damaging	314/321,315/322,315/322	7754101	131,12875	2203	4300	6503	SO:0001583	missense	2208	exon11			GCAGAGGGGGTGG	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.944C>T	19.37:g.7754101G>A	ENSP00000264072:p.Pro315Leu	156	0	0		235	138	0.587234	NM_002002		Missense_Mutation	SNP	ENST00000346664.5	37	CCDS12184.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	G	12.45	1.942513	0.34283	0.029505	1.16E-4	ENSG00000104921	ENST00000346664;ENST00000360067	T;T	0.04156	3.69;3.71	2.72	-0.925	0.10458	.	.	.	.	.	T	0.00815	0.0027	N	0.08118	0	0.09310	N	1	B	0.14012	0.009	B	0.12156	0.007	T	0.44544	-0.9321	9	0.87932	D	0	.	4.2641	0.10754	0.1588:0.4449:0.3963:0.0	rs34694289	315	P06734	FCER2_HUMAN	L	315;314	ENSP00000264072:P315L;ENSP00000353178:P314L	ENSP00000264072:P315L	P	-	2	0	FCER2	7660101	0.000000	0.05858	0.000000	0.03702	0.306000	0.27790	-0.171000	0.09883	0.008000	0.14787	0.298000	0.19748	CCC	G|0.990;A|0.010	0.010	strong		0.637	FCER2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461832.1	NM_002002		A	7754101	G	A	7754101	3	1	22	1	0	0	0	0	1	0	0	0	5784	1232	43	2	25	2	FCER2	19	7754101	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	61969	7754101	51374882	3761	6662											
EVI5L	115704	hgsc.bcm.edu	37	chr19	7914022	7914022	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggccaggaggtcctcttcaaCgtcatgaaggtgaggcccag	9	7	14	11	1	3	2	2	2	1	0	4	3	4	3	3	5	1	0	3	5	2	1	rs554853	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7914022C>T	ENST00000270530.4	+	4	739	c.543C>T	c.(541-543)aaC>aaT	p.N181N	EVI5L_ENST00000538904.2_Silent_p.N181N	NM_145245.3	NP_660288.1	Q96CN4	EVI5L_HUMAN	ecotropic viral integration site 5-like	181	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				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						TCCTCTTCAACGTCATGAAGG	0.647													C|||	83	0.0165735	0.0567	0.0101	5008	,	,		19132	0.0		0.001	False		,,,				2504	0.0				p.N181N		Atlas-SNP	.											.	EVI5L	43	.	0			c.C543T						PASS	.	C	,	232,4172	131.4+/-167.9	8,216,1978	34	30	32		543,543	-7.8	0.7	19	dbSNP_83	32	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous,coding-synonymous	EVI5L	NM_001159944.1,NM_145245.3	,	8,221,6273	TT,TC,CC		0.0581,5.2679,1.8225	,	181/806,181/795	7914022	237,12767	2202	4300	6502	SO:0001819	synonymous_variant	115704	exon3			CTTCAACGTCATG	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.543C>T	19.37:g.7914022C>T		65	0	0		73	34	0.465753	NM_001159944	B9A6I9	Silent	SNP	ENST00000270530.4	37	CCDS12188.1																																																																																			C|0.984;T|0.016	0.016	strong		0.647	EVI5L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461347.1	NM_145245		T	7914022	C	T	7914022	2	4	22	1	0	0	0	0	0	0	0	1	5292	535	19	1		1	EVI5L	19	7914022	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	159921	7914022	51214961	3762	6663											
SNAPC2	6618	hgsc.bcm.edu	37	chr19	7987428	7987428	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atatgacggagacgtacctaCgcctgacagccccccagccc	10	5	9	17	3	0	3	0	2	0	1	0	4	0	3	6	1	4	1	6	1	3	3	rs116635738	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7987428C>T	ENST00000221573.6	+	5	835	c.784C>T	c.(784-786)Cgc>Tgc	p.R262C	SNAPC2_ENST00000597584.1_Missense_Mutation_p.R25C	NM_003083.3	NP_003074.1	Q13487	SNPC2_HUMAN	small nuclear RNA activating complex, polypeptide 2, 45kDa	262					gene expression (GO:0010467)|snRNA transcription (GO:0009301)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|urinary_tract(1)	6						GACGTACCTACGCCTGACAGC	0.657													C|||	54	0.0107827	0.0356	0.0072	5008	,	,		16883	0.0		0.0	False		,,,				2504	0.002				p.R262C		Atlas-SNP	.											SNAPC2,colon,carcinoma,0,1	SNAPC2	20	1	0			c.C784T						PASS	.	C	CYS/ARG	140,4266	100.3+/-138.9	1,138,2064	71	70	70		784	2.2	0	19	dbSNP_132	70	4,8596	3.0+/-9.4	0,4,4296	yes	missense	SNAPC2	NM_003083.3	180	1,142,6360	TT,TC,CC		0.0465,3.1775,1.1072	possibly-damaging	262/335	7987428	144,12862	2203	4300	6503	SO:0001583	missense	6618	exon5			TACCTACGCCTGA	U44898	CCDS12190.1	19p13	2008-07-22	2002-08-29			ENSG00000104976			11135	protein-coding gene	gene with protein product		605076	"small nuclear RNA activating complex, polypeptide 2, 45kD"			8633057	Standard	NM_003083		Approved	SNAP45, PTFdelta	uc002miw.2	Q13487		ENST00000221573.6:c.784C>T	19.37:g.7987428C>T	ENSP00000221573:p.Arg262Cys	55	0	0		68	34	0.5	NM_003083	B2RBZ6|D6W663|Q13486	Missense_Mutation	SNP	ENST00000221573.6	37	CCDS12190.1	19	0.0086996336996337	16	0.032520325203252036	3	0.008287292817679558	0	0.0	0	0.0	c	14.33	2.503755	0.44558	0.031775	4.65E-4	ENSG00000104976	ENST00000221573	T	0.48836	0.8	4.44	2.15	0.27550	.	1.239960	0.05573	N	0.571328	T	0.19287	0.0463	N	0.22421	0.69	0.09310	N	1	D	0.67145	0.996	P	0.48227	0.571	T	0.30966	-0.9960	10	0.72032	D	0.01	-0.7906	8.8971	0.35472	0.4346:0.5654:0.0:0.0	.	262	Q13487	SNPC2_HUMAN	C	262	ENSP00000221573:R262C	ENSP00000221573:R262C	R	+	1	0	SNAPC2	7893428	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.478000	0.22212	1.074000	0.40909	-0.509000	0.04479	CGC	C|0.991;T|0.009	0.009	strong		0.657	SNAPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461358.1	NM_003083		T	7987428	C	T	7987428	3	4	22	1	0	0	0	0	1	0	0	0	14850	536	19	1	802	1	SNAPC2	19	7987428	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	73406	7987428	51141555	3763	6664											
FBN3	84467	hgsc.bcm.edu	37	chr19	8137052	8137052	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccggggtgtcctggggtccGgggctgaagcccaggccgga	4	6	19	12	3	0	1	0	1	0	0	3	2	3	2	5	8	1	1	5	8	1	0	rs10420783	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8137052G>A	ENST00000600128.1	-	63	8382	c.7968C>T	c.(7966-7968)ccC>ccT	p.P2656P	FBN3_ENST00000601739.1_Silent_p.P2656P|FBN3_ENST00000270509.2_Silent_p.P2656P			Q75N90	FBN3_HUMAN	fibrillin 3	2656						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						CCTGGGGTCCGGGGCTGAAGC	0.672													G|||	256	0.0511182	0.1846	0.0173	5008	,	,		19707	0.0		0.0	False		,,,				2504	0.0				p.P2656P		Atlas-SNP	.											.	FBN3	300	.	0			c.C7968T						PASS	.	G		653,3753	279.0+/-274.6	45,563,1595	99	107	104		7968	-7.2	0	19	dbSNP_119	104	12,8588	7.7+/-29.5	0,12,4288	no	coding-synonymous	FBN3	NM_032447.3		45,575,5883	AA,AG,GG		0.1395,14.8207,5.113		2656/2810	8137052	665,12341	2203	4300	6503	SO:0001819	synonymous_variant	84467	exon62			GGGTCCGGGGCTG		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.7968C>T	19.37:g.8137052G>A		72	0	0		72	72	1	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			G|0.949;A|0.051	0.051	strong		0.672	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		A	8137052	G	A	8137052	2	1	22	1	0	0	0	0	0	0	0	1	5712	1103	39	1		1	FBN3	19	8137052	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	149624	8137052	50991931	3764	6665											
FBN3	84467	hgsc.bcm.edu	37	chr19	8150353	8150353	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggcccccagccccggccaccCccacagcagcactcggccct	6	2	9	24	2	0	0	0	0	0	0	1	0	0	0	8	3	3	2	8	3	0	0	rs61729617	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8150353C>T	ENST00000600128.1	-	56	7395	c.6981G>A	c.(6979-6981)ggG>ggA	p.G2327G	FBN3_ENST00000601739.1_Silent_p.G2327G|FBN3_ENST00000270509.2_Silent_p.G2327G			Q75N90	FBN3_HUMAN	fibrillin 3	2327	TB 9.					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						CCCGGCCACCCCCACAGCAGC	0.692													C|||	204	0.0407348	0.1445	0.0187	5008	,	,		14856	0.0		0.0	False		,,,				2504	0.0				p.G2327G		Atlas-SNP	.											.	FBN3	300	.	0			c.G6981A						PASS	.	C		418,3948		15,388,1780	9	11	10		6981	3.6	0.8	19	dbSNP_129	10	8,8498		0,8,4245	no	coding-synonymous	FBN3	NM_032447.3		15,396,6025	TT,TC,CC		0.0941,9.574,3.3095		2327/2810	8150353	426,12446	2183	4253	6436	SO:0001819	synonymous_variant	84467	exon55			GCCACCCCCACAG		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.6981G>A	19.37:g.8150353C>T		36	0	0		47	21	0.446809	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			C|0.967;T|0.033	0.033	strong		0.692	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		T	8150353	C	T	8150353	2	4	22	1	0	0	0	0	0	0	0	1	5712	610	22	2		2	FBN3	19	8150353	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	13301	8150353	50978630	3765	6666			9	32		3	3	76	N	G_C	5.78383e-05
FBN3	84467	hgsc.bcm.edu	37	chr19	8150393	8150393	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggtgacagcctcactgctgCtggacagagaccggcacatg	9	7	13	12	1	1	2	1	1	0	1	1	4	1	3	2	3	3	3	2	3	0	0	rs17160151	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8150393C>T	ENST00000600128.1	-	56	7355	c.6941G>A	c.(6940-6942)aGc>aAc	p.S2314N	FBN3_ENST00000601739.1_Missense_Mutation_p.S2314N|FBN3_ENST00000270509.2_Missense_Mutation_p.S2314N			Q75N90	FBN3_HUMAN	fibrillin 3	2314	TB 9.		S -> N (in dbSNP:rs17160151).			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						CTCACTGCTGCTGGACAGAGA	0.672													C|||	349	0.0696885	0.2549	0.0159	5008	,	,		15574	0.0		0.001	False		,,,				2504	0.0				p.S2314N		Atlas-SNP	.											.	FBN3	300	.	0			c.G6941A						PASS	.	C	ASN/SER	998,3396		110,778,1309	12	13	12		6941	2.3	0	19	dbSNP_123	12	19,8551		1,17,4267	yes	missense	FBN3	NM_032447.3	46	111,795,5576	TT,TC,CC		0.2217,22.7128,7.8448	probably-damaging	2314/2810	8150393	1017,11947	2197	4285	6482	SO:0001583	missense	84467	exon55			CTGCTGCTGGACA		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.6941G>A	19.37:g.8150393C>T	ENSP00000470498:p.Ser2314Asn	34	0	0		49	26	0.530612	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	139	0.06364468864468864	134	0.27235772357723576	4	0.011049723756906077	1	0.0017482517482517483	0	0.0	C	16.20	3.056882	0.55325	0.227128	0.002217	ENSG00000142449	ENST00000270509;ENST00000341066	D	0.90844	-2.74	4.72	2.31	0.28768	Matrix fibril-associated (2);TGF-beta binding (1);	0.056067	0.64402	U	0.000001	T	0.00144	0.0004	M	0.73962	2.25	0.37731	P	0.07474400000000003	D;P	0.71674	0.998;0.896	D;P	0.83275	0.996;0.596	T	0.00000	-1.2854	9	0.31617	T	0.26	.	13.4093	0.60933	0.0:0.5983:0.4017:0.0	rs17160151;rs17160151	2314;420	Q75N90;Q6ZNB8	FBN3_HUMAN;.	N	2314;420	ENSP00000270509:S2314N	ENSP00000270509:S2314N	S	-	2	0	FBN3	8056393	1.000000	0.71417	0.041000	0.18516	0.142000	0.21351	1.586000	0.36611	2.170000	0.68504	0.491000	0.48974	AGC	C|0.903;T|0.097	0.097	strong		0.672	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		T	8150393	C	T	8150393	3	4	22	1	0	0	0	0	1	0	0	0	5712	797	28	2	1524	2	FBN3	19	8150393	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	40	8150393	50978590	3766	6667			9	32		3	3	76	N	G_C	5.78383e-05
FBN3	84467	hgsc.bcm.edu	37	chr19	8150428	8150428	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacatggtctgcagcacctcGgcaaagcagggcccctgccg	8	5	12	16	2	1	0	0	0	1	0	2	0	1	0	4	3	4	4	4	3	1	0	rs34514496	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8150428G>A	ENST00000600128.1	-	56	7320	c.6906C>T	c.(6904-6906)gcC>gcT	p.A2302A	FBN3_ENST00000601739.1_Silent_p.A2302A|FBN3_ENST00000270509.2_Silent_p.A2302A			Q75N90	FBN3_HUMAN	fibrillin 3	2302	TB 9.					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						GCAGCACCTCGGCAAAGCAGG	0.647													G|||	228	0.0455272	0.1619	0.0202	5008	,	,		15702	0.0		0.0	False		,,,				2504	0.0				p.A2302A		Atlas-SNP	.											.	FBN3	300	.	0			c.C6906T						PASS	.	G		536,3858		22,492,1683	11	12	12		6906	-6.9	0.9	19	dbSNP_126	12	13,8555		0,13,4271	no	coding-synonymous	FBN3	NM_032447.3		22,505,5954	AA,AG,GG		0.1517,12.1985,4.2355		2302/2810	8150428	549,12413	2197	4284	6481	SO:0001819	synonymous_variant	84467	exon55			CACCTCGGCAAAG		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.6906C>T	19.37:g.8150428G>A		40	0	0		53	26	0.490566	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			G|0.956;A|0.044	0.044	strong		0.647	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		A	8150428	G	A	8150428	2	1	22	1	0	0	0	0	0	0	0	1	5712	1103	39	1		1	FBN3	19	8150428	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	35	8150428	50978555	3767	6668			9	32		3	3	76	N	G_C	5.78383e-05
FBN3	84467	hgsc.bcm.edu	37	chr19	8171068	8171068	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaactgccaaacgtgttgacGcagtcacccccctgacacag	12	6	8	15	2	1	2	1	2	0	0	1	2	1	2	4	0	3	2	4	0	2	1	rs7258713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8171068G>A	ENST00000600128.1	-	38	5151	c.4737C>T	c.(4735-4737)tgC>tgT	p.C1579C	FBN3_ENST00000601739.1_Silent_p.C1579C|FBN3_ENST00000270509.2_Silent_p.C1579C			Q75N90	FBN3_HUMAN	fibrillin 3	1579	EGF-like 24; 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						ACGTGTTGACGCAGTCACCCC	0.572													G|||	366	0.0730831	0.2428	0.0202	5008	,	,		20054	0.0		0.003	False		,,,				2504	0.0286				p.C1579C		Atlas-SNP	.											.	FBN3	300	.	0			c.C4737T						PASS	.	G		836,3570	331.5+/-302.0	86,664,1453	120	85	97		4737	0.9	0.8	19	dbSNP_116	97	25,8575	17.9+/-57.8	0,25,4275	no	coding-synonymous	FBN3	NM_032447.3		86,689,5728	AA,AG,GG		0.2907,18.9741,6.62		1579/2810	8171068	861,12145	2203	4300	6503	SO:0001819	synonymous_variant	84467	exon37			GTTGACGCAGTCA		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.4737C>T	19.37:g.8171068G>A		69	0	0		82	42	0.512195	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			G|0.925;A|0.075	0.075	strong		0.572	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		A	8171068	G	A	8171068	2	1	22	1	0	0	0	0	0	0	0	1	5712	1079	38	1		1	FBN3	19	8171068	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	20640	8171068	50957915	3768	6669											
FBN3	84467	hgsc.bcm.edu	37	chr19	8196645	8196645	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccccccaggcactggcagcGgaaggagccctcggtgttgg	6	5	15	15	2	0	0	0	0	0	0	1	2	0	2	4	6	2	3	4	6	1	1	rs61729592	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8196645G>A	ENST00000600128.1	-	15	2197	c.1783C>T	c.(1783-1785)Cgc>Tgc	p.R595C	FBN3_ENST00000601739.1_Missense_Mutation_p.R595C|FBN3_ENST00000270509.2_Missense_Mutation_p.R595C			Q75N90	FBN3_HUMAN	fibrillin 3	595	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						CACTGGCAGCGGAAGGAGCCC	0.672													G|||	11	0.00219649	0.0083	0.0	5008	,	,		15081	0.0		0.0	False		,,,				2504	0.0				p.R595C		Atlas-SNP	.											.	FBN3	300	.	0			c.C1783T						PASS	.	G	CYS/ARG	23,4383		0,23,2180	22	23	22		1783	3	0.9	19	dbSNP_129	22	1,8595		0,1,4297	yes	missense	FBN3	NM_032447.3	180	0,24,6477	AA,AG,GG		0.0116,0.522,0.1846	probably-damaging	595/2810	8196645	24,12978	2203	4298	6501	SO:0001583	missense	84467	exon14			GGCAGCGGAAGGA		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.1783C>T	19.37:g.8196645G>A	ENSP00000470498:p.Arg595Cys	156	0	0		181	96	0.530387	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	.	.	.	.	.	.	.	.	.	.	g	13.30	2.197312	0.38806	0.00522	1.16E-4	ENSG00000142449	ENST00000270509	D	0.92545	-3.06	3.02	3.02	0.34903	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.063744	0.64402	U	0.000009	D	0.93419	0.7901	M	0.85041	2.73	0.52501	D	0.999955	D	0.65815	0.995	P	0.58077	0.832	D	0.93900	0.7187	10	0.87932	D	0	.	13.9673	0.64216	0.0:0.0:1.0:0.0	.	595	Q75N90	FBN3_HUMAN	C	595	ENSP00000270509:R595C	ENSP00000270509:R595C	R	-	1	0	FBN3	8102645	0.999000	0.42202	0.856000	0.33681	0.121000	0.20230	2.263000	0.43293	1.227000	0.43598	0.185000	0.17295	CGC	G|0.996;A|0.004	0.004	strong		0.672	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		A	8196645	G	A	8196645	3	1	22	1	0	0	0	0	1	0	0	0	5712	1116	39	1	6846	1	FBN3	19	8196645	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	25577	8196645	50932338	3769	6670											
PRAM1	84106	hgsc.bcm.edu	37	chr19	8564288	8564288	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tccttggaaacggagtggccCccagctgtgggaacttcttg	7	10	13	11	1	1	0	0	0	1	0	2	3	2	3	3	4	3	1	3	4	2	3	rs58466313	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8564288C>T	ENST00000423345.4	-	2	924	c.404G>A	c.(403-405)gGg>gAg	p.G135E	PRAM1_ENST00000255612.3_Missense_Mutation_p.G135E			Q96QH2	PRAM_HUMAN	PML-RARA regulated adaptor molecule 1	183	8 X 12 AA repeats of K-P-P-[PQ]-P-[EQ]- [VAF]-T-D-L-P-K.|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						CGGAGTGGCCCCCAGCTGTGG	0.657													T|||	813	0.16234	0.5802	0.0519	5008	,	,		12320	0.0		0.004	False		,,,				2504	0.0061				p.G135E		Atlas-SNP	.											.	PRAM1	53	.	0			c.G404A						PASS	.	T	GLU/GLY	1453,2153		274,905,624	35	39	38		404	3.3	0	19	dbSNP_129	38	54,7706		2,50,3828	yes	missense	PRAM1	NM_032152.4	98	276,955,4452	TT,TC,CC		0.6959,40.294,13.2588	benign	135/671	8564288	1507,9859	1803	3880	5683	SO:0001583	missense	84106	exon2			GTGGCCCCCAGCT	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.404G>A	19.37:g.8564288C>T	ENSP00000408342:p.Gly135Glu	100	0	0		106	105	0.990566	NM_032152	Q8N6W7	Missense_Mutation	SNP	ENST00000423345.4	37	CCDS45954.2	286	0.13095238095238096	266	0.540650406504065	18	0.049723756906077346	0	0.0	2	0.002638522427440633	T	0.056	-1.237003	0.01493	0.40294	0.006959	ENSG00000133246	ENST00000255612;ENST00000423345	T;T	0.11385	2.78;2.78	4.32	3.31	0.37934	.	0.543293	0.15485	N	0.259864	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44159	-0.9346	9	0.02654	T	1	.	2.7649	0.05317	0.1891:0.2063:0.0:0.6046	rs58466313	135;183	Q96QH2-2;Q96QH2	.;PRAM_HUMAN	E	135	ENSP00000255612:G135E;ENSP00000408342:G135E	ENSP00000255612:G135E	G	-	2	0	PRAM1	8470288	0.008000	0.16893	0.008000	0.14137	0.015000	0.08874	1.805000	0.38883	0.811000	0.34303	-0.340000	0.08031	GGG	C|0.891;T|0.109	0.109	strong		0.657	PRAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397040.3	NM_032152		T	8564288	C	T	8564288	3	4	22	1	0	0	0	0	1	0	0	0	12435	623	22	2	1641	2	PRAM1	19	8564288	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	367643	8564288	50564695	3770	6671											
MYO1F	4542	hgsc.bcm.edu	37	chr19	8620636	8620636	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	accatgtcatccacgccgctCtgcttcacgttgtggctctg	5	12	9	15	3	4	0	2	0	2	0	5	0	5	0	3	1	1	4	3	1	0	2	rs73501540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8620636C>T	ENST00000338257.8	-	2	315	c.48G>A	c.(46-48)caG>caA	p.Q16Q		NM_012335.3	NP_036467.2	O00160	MYO1F_HUMAN	myosin IF	16					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						CCACGCCGCTCTGCTTCACGT	0.637													C|||	320	0.0638978	0.2322	0.0187	5008	,	,		13239	0.0		0.0	False		,,,				2504	0.0				p.Q16Q		Atlas-SNP	.											.	MYO1F	128	.	0			c.G48A						PASS	.	C		799,3379		64,671,1354	83	90	87		48	1.9	1	19	dbSNP_130	87	10,8402		0,10,4196	no	coding-synonymous	MYO1F	NM_012335.3		64,681,5550	TT,TC,CC		0.1189,19.124,6.4257		16/1099	8620636	809,11781	2089	4206	6295	SO:0001819	synonymous_variant	4542	exon2			GCCGCTCTGCTTC	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.48G>A	19.37:g.8620636C>T		106	0	0		122	122	1	NM_012335	Q8WWN7	Silent	SNP	ENST00000338257.8	37	CCDS42494.1																																																																																			C|0.966;T|0.034	0.034	strong		0.637	MYO1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342716.2			T	8620636	C	T	8620636	2	4	22	1	0	0	0	0	0	0	0	1	10082	912	32	2		2	MYO1F	19	8620636	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	56348	8620636	50508347	3771	6672											
MUC16	94025	hgsc.bcm.edu	37	chr19	8996460	8996460	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtggtgggtgcagatggcAtccactccagtggctgtccc	5	9	16	11	0	0	1	0	0	0	1	3	1	3	1	3	5	1	3	3	5	0	0	rs115933306	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8996460A>C	ENST00000397910.4	-	61	41315	c.41112T>G	c.(41110-41112)gaT>gaG	p.D13704E	MUC16_ENST00000380951.5_Missense_Mutation_p.D345E	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13706	SEA 11. {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						TGCAGATGGCATCCACTCCAG	0.547													-|||	174	0.0347444	0.1271	0.0086	5008	,	,		19097	0.0		0.0	False		,,,				2504	0.0				p.D13704E		Atlas-SNP	.											.	MUC16	4315	.	0			c.T41112G						PASS	.	A	GLU/ASP	326,3522		18,290,1616	71	66	68		41112	-4.6	0	19	dbSNP_132	68	4,8262		0,4,4129	yes	missense	MUC16	NM_024690.2	45	18,294,5745	CC,CA,AA		0.0484,8.4719,2.7241	probably-damaging	13704/14508	8996460	330,11784	1924	4133	6057	SO:0001583	missense	94025	exon61			GATGGCATCCACT	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.41112T>G	19.37:g.8996460A>C	ENSP00000381008:p.Asp13704Glu	204	0	0		170	170	1	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	43|43	0.019688644688644688|0.019688644688644688	39|39	0.07926829268292683|0.07926829268292683	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	0|0	0.0|0.0	.|.	13.79|13.79	2.342264|2.342264	0.41498|0.41498	0.084719|0.084719	4.84E-4|4.84E-4	ENSG00000181143|ENSG00000181143	ENST00000397910;ENST00000380951|ENST00000542240	T;T|.	0.35048|.	1.33;1.33|.	3.36|3.36	-4.56|-4.56	0.03431|0.03431	SEA (1);|.	0.216241|.	0.23120|.	U|.	0.051715|.	T|T	0.09468|0.09468	0.0233|0.0233	M|M	0.90082|0.90082	3.085|3.085	.|.	.|.	.|.	D;D|.	0.65815|.	0.995;0.959|.	P;D|.	0.67103|.	0.901;0.949|.	T|T	0.61197|0.61197	-0.7111|-0.7111	9|4	0.72032|.	D|.	0.01|.	-11.1203|-11.1203	8.9526|8.9526	0.35799|0.35799	0.6401:0.0:0.3599:0.0|0.6401:0.0:0.3599:0.0	.|.	21349;13704|.	Q8WXI7;B5ME49|.	MUC16_HUMAN;.|.	E|R	13704;345|544	ENSP00000381008:D13704E;ENSP00000370338:D345E|.	ENSP00000370338:D345E|.	D|M	-|-	3|2	2|0	MUC16|MUC16	8857460|8857460	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.010000|0.010000	0.07245|0.07245	-1.743000|-1.743000	0.01834|0.01834	-0.764000|-0.764000	0.04651|0.04651	-0.415000|-0.415000	0.06103|0.06103	GAT|ATG	A|0.974;C|0.026	0.026	strong		0.547	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		C	8996460	A	C	8996460	3	2	22	1	0	0	0	0	1	0	0	0	9982	214	8	5	2507	5	MUC16	19	8996460	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	375824	8996460	50132523	3772	6673											
MUC16	94025	hgsc.bcm.edu	37	chr19	9070186	9070186	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacacttgtatcccccatggCgaaggtgatacccattggag	11	9	10	11	1	0	1	0	1	0	0	1	3	1	2	3	3	2	1	3	3	4	4	rs1559171	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9070186C>T	ENST00000397910.4	-	3	17463	c.17260G>A	c.(17260-17262)Gcc>Acc	p.A5754T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5756	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						TCCCCCATGGCGAAGGTGATA	0.468													t|||	100	0.0199681	0.0734	0.0043	5008	,	,		22084	0.0		0.0	False		,,,				2504	0.0				p.A5754T		Atlas-SNP	.											.	MUC16	4315	.	0			c.G17260A						PASS	.	T	THR/ALA	251,3819		11,229,1795	161	152	155		17260	-3.5	0	19	dbSNP_88	155	5,8383		0,5,4189	yes	missense	MUC16	NM_024690.2	58	11,234,5984	TT,TC,CC		0.0596,6.1671,2.0549	benign	5754/14508	9070186	256,12202	2035	4194	6229	SO:0001583	missense	94025	exon3			CCATGGCGAAGGT	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.17260G>A	19.37:g.9070186C>T	ENSP00000381008:p.Ala5754Thr	273	0	0		282	132	0.468085	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	28	0.01282051282051282	25	0.0508130081300813	3	0.008287292817679558	0	0.0	0	0.0	t	4.044	0.005793	0.07866	0.061671	5.96E-4	ENSG00000181143	ENST00000397910	T	0.20069	2.1	1.73	-3.46	0.04767	.	.	.	.	.	T	0.00724	0.0024	N	0.03608	-0.345	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.26503	-1.0101	8	0.87932	D	0	.	1.5797	0.02632	0.2079:0.4205:0.1629:0.2087	rs1559171;rs1559171	5754	B5ME49	.	T	5754	ENSP00000381008:A5754T	ENSP00000381008:A5754T	A	-	1	0	MUC16	8931186	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.346000	0.07760	-2.492000	0.00516	-0.521000	0.04368	GCC	C|0.987;T|0.013	0.013	strong		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9070186	C	T	9070186	3	4	22	1	0	0	0	0	1	0	0	0	9982	768	27	1	26591	1	MUC16	19	9070186	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	73726	9070186	50058797	3773	6674											
OR7G2	390882	hgsc.bcm.edu	37	chr19	9213396	9213396	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccagttcacagaagaagagcGggatttccaggtctgtgcag	11	8	13	9	1	2	3	1	0	1	3	3	4	3	4	2	2	2	2	2	2	2	2	rs7247751	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9213396G>A	ENST00000305456.2	-	1	586	c.587C>T	c.(586-588)cCg>cTg	p.P196L		NM_001005193.1	NP_001005193.1	Q8NG99	OR7G2_HUMAN	olfactory receptor, family 7, subfamily G, member 2	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)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|skin(3)	16						GAAGAAGAGCGGGATTTCCAG	0.478													-|||	155	0.0309505	0.1127	0.0086	5008	,	,		21697	0.0		0.0	False		,,,				2504	0.0				p.P196L	Esophageal Squamous(67;143 1448 28637 40648)	Atlas-SNP	.											OR7G2,NS,carcinoma,+1,1	OR7G2	48	1	0			c.C587T						PASS	.	G	LEU/PRO	380,4026	190.9+/-216.7	16,348,1839	98	86	90		587	2.2	0	19	dbSNP_116	90	4,8596	3.0+/-9.4	0,4,4296	yes	missense	OR7G2	NM_001005193.1	98	16,352,6135	AA,AG,GG		0.0465,8.6246,2.9525	possibly-damaging	196/346	9213396	384,12622	2203	4300	6503	SO:0001583	missense	390882	exon1			AAGAGCGGGATTT		CCDS32897.1	19p13.2	2013-09-24			ENSG00000170923	ENSG00000170923		"GPCR / Class A : Olfactory receptors"	8466	protein-coding gene	gene with protein product							Standard	NM_001005193		Approved	OST260	uc010xkk.2	Q8NG99	OTTHUMG00000179931	ENST00000305456.2:c.587C>T	19.37:g.9213396G>A	ENSP00000303822:p.Pro196Leu	207	0	0		216	102	0.472222	NM_001005193	Q6IFJ4|Q96RA0	Missense_Mutation	SNP	ENST00000305456.2	37	CCDS32897.1	55	0.025183150183150184	54	0.10975609756097561	1	0.0027624309392265192	0	0.0	0	0.0	g	8.801	0.932843	0.18131	0.086246	4.65E-4	ENSG00000170923	ENST00000305456	T	0.37752	1.18	3.27	2.19	0.27852	GPCR, rhodopsin-like superfamily (1);	0.212960	0.23524	U	0.047241	T	0.00637	0.0021	L	0.58583	1.82	0.09310	N	1	P	0.45672	0.864	B	0.40825	0.341	T	0.01262	-1.1402	10	0.66056	D	0.02	.	9.1271	0.36821	0.0:0.0:0.4786:0.5214	rs7247751;rs52817351;rs7247751	175	Q8NG99	OR7G2_HUMAN	L	196	ENSP00000303822:P196L	ENSP00000303822:P196L	P	-	2	0	OR7G2	9074396	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-0.621000	0.05559	0.954000	0.37851	0.545000	0.68477	CCG	G|0.968;A|0.032	0.032	strong		0.478	OR7G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448994.1			A	9213396	G	A	9213396	3	1	22	1	0	0	0	0	1	0	0	0	11232	1116	39	1	452	1	OR7G2	19	9213396	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	143210	9213396	49915587	3774	6675											
OR7D2	162998	hgsc.bcm.edu	37	chr19	9297196	9297196	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgtgggtctcacctctccGtcgtttctttattttatggg	3	18	9	11	2	3	0	1	0	3	0	6	0	3	0	3	2	0	1	3	2	2	5	rs61739064	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9297196G>A	ENST00000344248.2	+	1	918	c.739G>A	c.(739-741)Gtc>Atc	p.V247I		NM_175883.2	NP_787079.1	Q96RA2	OR7D2_HUMAN	olfactory receptor, family 7, subfamily D, member 2	247					regulation of transcription, DNA-templated (GO:0006355)	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(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(2)	20						TCACCTCTCCGTCGTTTCTTT	0.468													G|||	64	0.0127796	0.0484	0.0	5008	,	,		17847	0.0		0.0	False		,,,				2504	0.0				p.V247I		Atlas-SNP	.											.	OR7D2	55	.	0			c.G739A						PASS	.	G	ILE/VAL	210,4196	127.8+/-164.7	2,206,1995	91	76	81		739	2.2	0	19	dbSNP_129	81	1,8599	1.2+/-3.3	0,1,4299	yes	missense	OR7D2	NM_175883.2	29	2,207,6294	AA,AG,GG		0.0116,4.7662,1.6223	benign	247/313	9297196	211,12795	2203	4300	6503	SO:0001583	missense	162998	exon1			CTCTCCGTCGTTT	AK095468	CCDS32900.1	19p13.2	2012-08-09						"GPCR / Class A : Olfactory receptors"	8378	protein-coding gene	gene with protein product							Standard	NM_175883		Approved	OR19-4, HTPCRH03, FLJ38149	uc002mkz.1	Q96RA2		ENST00000344248.2:c.739G>A	19.37:g.9297196G>A	ENSP00000345563:p.Val247Ile	66	0	0		70	33	0.471429	NM_175883	Q6IFJ7|Q8N133	Missense_Mutation	SNP	ENST00000344248.2	37	CCDS32900.1	23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	G	9.760	1.169781	0.21621	0.047662	1.16E-4	ENSG00000188000	ENST00000344248	T	0.00253	8.43	2.2	2.2	0.27929	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35970	U	0.002872	T	0.00039	0.0001	M	0.78801	2.425	0.09310	N	1	P	0.40197	0.706	B	0.38378	0.272	T	0.38693	-0.9649	10	0.59425	D	0.04	.	11.9676	0.53044	0.0:0.0:1.0:0.0	rs61739064	247	Q96RA2	OR7D2_HUMAN	I	247	ENSP00000345563:V247I	ENSP00000345563:V247I	V	+	1	0	OR7D2	9158196	0.163000	0.22920	0.047000	0.18901	0.020000	0.10135	2.174000	0.42482	1.578000	0.49821	0.505000	0.49811	GTC	G|0.983;A|0.017	0.017	strong		0.468	OR7D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449002.1			A	9297196	G	A	9297196	3	1	22	1	0	0	0	0	1	0	0	0	11228	1145	40	1	741	1	OR7D2	19	9297196	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	83800	9297196	49831787	3775	6676											
ZNF699	374879	hgsc.bcm.edu	37	chr19	9407468	9407468	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttaagggatgaatgatccacGaaggcctttccacactcatg	12	10	9	10	1	1	2	1	2	0	0	3	4	3	3	3	2	0	0	3	2	3	2	rs189167193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9407468G>A	ENST00000591998.1	-	6	840	c.612C>T	c.(610-612)ttC>ttT	p.F204F	ZNF699_ENST00000308650.3_Silent_p.F204F|CTC-325H20.4_ENST00000591336.1_RNA			Q32M78	ZN699_HUMAN	zinc finger protein 699	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)|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						AATGATCCACGAAGGCCTTTC	0.428													G|||	15	0.00299521	0.0113	0.0	5008	,	,		19156	0.0		0.0	False		,,,				2504	0.0				p.F204F		Atlas-SNP	.											.	ZNF699	67	.	0			c.C612T						PASS	.	G		36,3990		0,36,1977	154	140	145		612	-0.2	0	19		145	1,8385		0,1,4192	no	coding-synonymous	ZNF699	NM_198535.1		0,37,6169	AA,AG,GG		0.0119,0.8942,0.2981		204/643	9407468	37,12375	2013	4193	6206	SO:0001819	synonymous_variant	374879	exon5			ATCCACGAAGGCC	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.612C>T	19.37:g.9407468G>A		178	0	0		153	89	0.581699	NM_198535	Q8N9A1	Silent	SNP	ENST00000591998.1	37	CCDS42495.1																																																																																			G|0.998;A|0.002	0.002	strong		0.428	ZNF699-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449010.1	NM_198535		A	9407468	G	A	9407468	2	1	22	1	0	0	0	0	0	0	0	1	18116	1049	37	1		1	ZNF699	19	9407468	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	110272	9407468	49721515	3776	6677											
ZNF559	84527	hgsc.bcm.edu	37	chr19	9453160	9453160	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggtcttataaaacacaggCgaactcacactggagaaaag	17	6	9	9	1	2	1	1	0	1	1	2	3	2	1	0	3	2	0	0	3	6	2	rs150358404	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9453160C>T	ENST00000393883.2	+	6	1681	c.1033C>T	c.(1033-1035)Cga>Tga	p.R345*	ZNF559_ENST00000586255.1_Intron|CTC-325H20.2_ENST00000592371.1_lincRNA|ZNF177_ENST00000602856.1_Intron|ZNF559_ENST00000317221.7_3'UTR|ZNF559_ENST00000603380.1_Nonsense_Mutation_p.R345*|ZNF559_ENST00000587557.1_Nonsense_Mutation_p.R409*|ZNF177_ENST00000605471.1_Intron|ZNF177_ENST00000541595.2_Intron|ZNF177_ENST00000602738.1_Intron|ZNF559_ENST00000538743.1_Nonsense_Mutation_p.R265*|ZNF177_ENST00000446085.4_Intron	NM_001202412.1	NP_001189341.1	Q9BR84	ZN559_HUMAN	zinc finger protein 559	345					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)|large_intestine(7)|lung(15)|ovary(1)|urinary_tract(1)	26						AAAACACAGGCGAACTCACAC	0.408													C|||	5	0.000998403	0.0038	0.0	5008	,	,		20978	0.0		0.0	False		,,,				2504	0.0				p.R409X		Atlas-SNP	.											ZNF559,NS,carcinoma,-1,4	ZNF559	77	4	0			c.C1225T						PASS	.	C	,stop/ARG,stop/ARG,,,,,,,stop/ARG	9,4397	15.5+/-35.6	0,9,2194	62	58	60		,1225,907,,,,,,,1033	-3.7	0	19	dbSNP_134	60	2,8598	2.2+/-6.3	0,2,4298	yes	intron,stop-gained,stop-gained,utr-3,utr-3,utr-3,utr-3,utr-3,intron,stop-gained	ZNF559,ZNF559-ZNF177	NM_001172650.2,NM_001202406.1,NM_001202407.1,NM_001202408.1,NM_001202409.1,NM_001202410.1,NM_001202411.1,NM_001202412.1,NM_001202425.1,NM_032497.2	,,,,,,,,,	0,11,6492	TT,TC,CC		0.0233,0.2043,0.0846	,,,,,,,,,	,409/603,303/497,,,,,,,345/539	9453160	11,12995	2203	4300	6503	SO:0001587	stop_gained	84527	exon6			CACAGGCGAACTC	AL389937	CCDS12211.1, CCDS59349.1, CCDS62531.1, CCDS62532.1	19p13.2	2013-09-20			ENSG00000188321	ENSG00000188321		"Zinc fingers, C2H2-type", "-"	28197	protein-coding gene	gene with protein product						12477932	Standard	NM_001202406		Approved	MGC13105	uc002mle.4	Q9BR84	OTTHUMG00000179942	ENST00000393883.2:c.1033C>T	19.37:g.9453160C>T	ENSP00000377461:p.Arg345*	49	0	0		59	33	0.559322	NM_001202406	K7EMG6	Nonsense_Mutation	SNP	ENST00000393883.2	37	CCDS12211.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	24.8	4.571286	0.86542	0.002043	2.33E-4	ENSG00000188321	ENST00000317221;ENST00000538743;ENST00000393883	.	.	.	1.87	-3.74	0.04385	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.8332	0.18593	0.3663:0.5052:0.1284:0.0	.	.	.	.	X	345;265;345	.	ENSP00000325393:R345X	R	+	1	2	ZNF559	9314160	0.000000	0.05858	0.000000	0.03702	0.493000	0.33554	-2.312000	0.01127	-1.360000	0.02172	0.313000	0.20887	CGA	C|0.999;T|0.001	0.001	strong		0.408	ZNF559-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449021.1	NM_032497		T	9453160	C	T	9453160	4	4	22	1	0	0	0	0	0	1	0	0	18005	760	27	1	1047	1	ZNF559	19	9453160	Nonsense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	45692	9453160	49675823	3777	6678											
ZNF846	162993	hgsc.bcm.edu	37	chr19	9868764	9868764	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gcttttctccagtgtgaattCgcatgtgtaaaataagtcct	10	15	8	8	1	1	1	0	1	1	0	4	1	2	1	2	0	0	3	2	0	4	5	rs60387559	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9868764C>G	ENST00000397902.2	-	6	1402	c.989G>C	c.(988-990)cGa>cCa	p.R330P	ZNF846_ENST00000586293.1_3'UTR|ZNF846_ENST00000592859.1_Missense_Mutation_p.R201P|ZNF846_ENST00000588267.1_Missense_Mutation_p.R201P	NM_001077624.1	NP_001071092.1	Q147U1	ZN846_HUMAN	zinc finger protein 846	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)	p.R330Q(1)		NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22						AGTGTGAATTCGCATGTGTAA	0.388													N|||	64	0.0127796	0.0461	0.0043	5008	,	,		23084	0.0		0.0	False		,,,				2504	0.0				p.R330P		Atlas-SNP	.											ZNF846,NS,carcinoma,0,3	ZNF846	61	3	1	Substitution - Missense(1)	large_intestine(1)	c.G989C						PASS	.	C	PRO/ARG	247,4097		17,213,1942	63	68	66		989	-3.1	0	19	dbSNP_129	66	0,8586		0,0,4293	yes	missense	ZNF846	NM_001077624.1	103	17,213,6235	GG,GC,CC		0.0,5.686,1.9103	probably-damaging	330/534	9868764	247,12683	2172	4293	6465	SO:0001583	missense	162993	exon6			TGAATTCGCATGT	AK097652	CCDS42496.1	19p13.2	2013-01-08			ENSG00000196605	ENSG00000196605		"Zinc fingers, C2H2-type", "-"	27260	protein-coding gene	gene with protein product							Standard	NM_001077624		Approved		uc002mmb.1	Q147U1		ENST00000397902.2:c.989G>C	19.37:g.9868764C>G	ENSP00000380999:p.Arg330Pro	105	0	0		80	39	0.4875	NM_001077624	A8K0H1|B3KUP1	Missense_Mutation	SNP	ENST00000397902.2	37	CCDS42496.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	.	15.85	2.955405	0.53293	0.05686	0.0	ENSG00000196605	ENST00000397902	T	0.25749	1.78	2.01	-3.1	0.05315	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07143	0.0181	M	0.89840	3.065	0.09310	N	1	D	0.71674	0.998	P	0.58013	0.831	T	0.08554	-1.0716	8	.	.	.	.	3.6327	0.08138	0.1949:0.251:0.0:0.5541	rs60387559	330	Q147U1	ZN846_HUMAN	P	330	ENSP00000380999:R330P	.	R	-	2	0	ZNF846	9729764	0.000000	0.05858	0.000000	0.03702	0.688000	0.40055	-1.594000	0.02094	-0.747000	0.04759	0.456000	0.33151	CGA	C|0.992;G|0.007;T|0.000	0.007	strong		0.388	ZNF846-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450253.1	NM_001077624		G	9868764	C	G	9868764	3	3	22	1	0	0	0	0	1	0	0	0	18207	884	31	4	616	4	ZNF846	19	9868764	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	415604	9868764	49260219	3778	6679											
RDH8	50700	hgsc.bcm.edu	37	chr19	10132358	10132358	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcctcttccgctgtccacGcctcctcaaccttggccttc	3	12	5	21	2	2	0	1	0	1	0	7	0	6	0	8	1	1	1	8	1	1	3	rs142753796	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:10132358G>A	ENST00000171214.1	+	6	1118	c.869G>A	c.(868-870)cGc>cAc	p.R290H	RDH8_ENST00000591589.1_Missense_Mutation_p.R310H	NM_015725.2	NP_056540.2	Q9NYR8	RDH8_HUMAN	retinol dehydrogenase 8 (all-trans)	290					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)	CGCTGTCCACGCCTCCTCAAC	0.607													G|||	3	0.000599042	0.0023	0.0	5008	,	,		17925	0.0		0.0	False		,,,				2504	0.0				p.R310H		Atlas-SNP	.											.	RDH8	51	.	0			c.G929A						PASS	.	G	HIS/ARG	7,4399	12.9+/-30.5	0,7,2196	113	108	110		869	0.6	1	19	dbSNP_134	110	0,8600		0,0,4300	yes	missense	RDH8	NM_015725.2	29	0,7,6496	AA,AG,GG		0.0,0.1589,0.0538	benign	290/312	10132358	7,12999	2203	4300	6503	SO:0001583	missense	50700	exon6			GTCCACGCCTCCT	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.869G>A	19.37:g.10132358G>A	ENSP00000171214:p.Arg290His	108	0	0		95	54	0.568421	NM_015725	Q9H838	Missense_Mutation	SNP	ENST00000171214.1	37		1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	12.22	1.874004	0.33069	0.001589	0.0	ENSG00000080511	ENST00000171214	D	0.82803	-1.65	4.23	0.581	0.17407	.	0.728843	0.13435	N	0.388095	T	0.67059	0.2853	N	0.21142	0.635	0.22142	N	0.999337	B	0.11235	0.004	B	0.06405	0.002	T	0.53322	-0.8455	10	0.33940	T	0.23	.	5.0034	0.14275	0.2203:0.3107:0.469:0.0	.	290	Q9NYR8	RDH8_HUMAN	H	290	ENSP00000171214:R290H	ENSP00000171214:R290H	R	+	2	0	RDH8	9993358	0.044000	0.20184	0.991000	0.47740	0.717000	0.41224	1.418000	0.34782	0.730000	0.32425	0.297000	0.19635	CGC	G|0.999;A|0.001	0.001	strong		0.607	RDH8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				A	10132358	G	A	10132358	3	1	22	1	0	0	0	0	1	0	0	0	13211	1087	38	1	891	1	RDH8	19	10132358	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	263594	10132358	48996625	3779	6680											
ICAM5	7087	hgsc.bcm.edu	37	chr19	10404588	10404588	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaccaaccctcggggctcTgcggccaaaaatgtggccgt	8	6	12	15	3	1	0	0	0	1	0	2	0	1	0	5	4	2	1	5	4	3	0	rs116688659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:10404588T>C	ENST00000221980.4	+	7	1743	c.1680T>C	c.(1678-1680)tcT>tcC	p.S560S		NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	560	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)			CTCGGGGCTCTGCGGCCAAAA	0.662													T|||	24	0.00479233	0.0182	0.0	5008	,	,		17413	0.0		0.0	False		,,,				2504	0.0				p.S560S		Atlas-SNP	.											.	ICAM5	53	.	0			c.T1680C						PASS	.	T		55,4349	54.2+/-90.2	0,55,2147	42	49	47		1680	-9.2	0	19	dbSNP_132	47	0,8600		0,0,4300	no	coding-synonymous	ICAM5	NM_003259.3		0,55,6447	CC,CT,TT		0.0,1.2489,0.4229		560/925	10404588	55,12949	2202	4300	6502	SO:0001819	synonymous_variant	7087	exon7			GGGCTCTGCGGCC	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.1680T>C	19.37:g.10404588T>C		45	0	0		36	12	0.333333	NM_003259	Q9Y6F3	Silent	SNP	ENST00000221980.4	37	CCDS12233.1																																																																																			T|0.995;C|0.005	0.005	strong		0.662	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259		C	10404588	T	C	10404588	2	2	22	1	0	0	0	0	0	0	0	1	7492	1567	55	3		3	ICAM5	19	10404588	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	272230	10404588	48724395	3780	6681											
SLC44A2	57153	hgsc.bcm.edu	37	chr19	10713212	10713212	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgccccgccgcggccatggaGgacgagcggaaaaacggagc	10	1	16	14	7	0	0	0	0	0	0	0	5	0	4	4	5	3	0	4	5	2	0	rs115559926	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:10713212G>A	ENST00000407327.4	+	1	27	c.6G>A	c.(4-6)gaG>gaA	p.E2E		NM_001145056.1	NP_001138528.1	Q8IWA5	CTL2_HUMAN	solute carrier family 44 (choline transporter), member 2	2					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)	CGGCCATGGAGGACGAGCGGA	0.771													G|||	86	0.0171725	0.0643	0.0014	5008	,	,		6430	0.0		0.0	False		,,,				2504	0.0				p.E2E		Atlas-SNP	.											.	SLC44A2	56	.	0			c.G6A						PASS	.						7	12	11					19																	10713212		643	1532	2175	SO:0001819	synonymous_variant	57153	exon1			CATGGAGGACGAG	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	ENST00000407327.4:c.6G>A	19.37:g.10713212G>A		21	0	0		21	13	0.619048	NM_001145056	B2RBB1|B3KNH3|B4DFJ0|F2Q9D7|Q658V1|Q658Z2|Q6PJV7|Q8N2F0|Q9NY68	Silent	SNP	ENST00000407327.4	37	CCDS54216.1																																																																																			G|0.986;A|0.014	0.014	strong		0.771	SLC44A2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452044.1			A	10713212	G	A	10713212	2	1	22	1	0	0	0	0	0	0	0	1	14651	991	35	2		2	SLC44A2	19	10713212	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	308624	10713212	48415771	3781	6682											
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11094903	11094903	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccctggcccttcccctggaGccatgctgggccctagcccg	3	7	12	19	1	0	0	0	0	0	0	1	1	1	1	7	3	3	1	7	3	1	2	rs145867502		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11094903G>A	ENST00000429416.3	+	3	357	c.76G>A	c.(76-78)Gcc>Acc	p.A26T	SMARCA4_ENST00000358026.2_Missense_Mutation_p.A26T|SMARCA4_ENST00000590574.1_Missense_Mutation_p.A26T|SMARCA4_ENST00000413806.3_Missense_Mutation_p.A26T|SMARCA4_ENST00000541122.2_Missense_Mutation_p.A26T|SMARCA4_ENST00000450717.3_Missense_Mutation_p.A26T|SMARCA4_ENST00000344626.4_Missense_Mutation_p.A26T|SMARCA4_ENST00000589677.1_Missense_Mutation_p.A26T|SMARCA4_ENST00000444061.3_Missense_Mutation_p.A26T	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	26	Necessary for interaction with SS18L1/CREST. {ECO:0000250}.				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)				TTCCCCTGGAGCCATGCTGGG	0.721			"F, N, Mis"		NSCLC								G|||	1	0.000199681	0.0008	0.0	5008	,	,		15706	0.0		0.0	False		,,,				2504	0.0				p.A26T		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.G76A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	12,4366		0,12,2177	19	24	23		76,76,76,76,76,76,76	4.9	1	19	dbSNP_134	23	0,8566		0,0,4283	no	missense,missense,missense,missense,missense,missense,missense	SMARCA4	NM_003072.3,NM_001128849.1,NM_001128848.1,NM_001128847.1,NM_001128846.1,NM_001128845.1,NM_001128844.1	58,58,58,58,58,58,58	0,12,6460	AA,AG,GG		0.0,0.2741,0.0927	benign,benign,benign,benign,benign,benign,benign	26/1648,26/1680,26/1614,26/1615,26/1617,26/1618,26/1648	11094903	12,12932	2189	4283	6472	SO:0001583	missense	6597	exon2			CCTGGAGCCATGC	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.76G>A	19.37:g.11094903G>A	ENSP00000395654:p.Ala26Thr	58	0	0		76	36	0.473684	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	21.4	4.144345	0.77888	0.002741	0.0	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.86956	-2.18;-2.19;-2.18;-2.17;-2.17;-2.18;-2.17	4.95	4.95	0.65309	.	0.130808	0.49305	D	0.000154	D	0.82879	0.5133	L	0.36672	1.1	0.48087	D	0.999582	B;B;B;B;B;B;B	0.10296	0.003;0.003;0.003;0.0;0.003;0.001;0.003	B;B;B;B;B;B;B	0.08055	0.003;0.003;0.003;0.001;0.003;0.001;0.003	T	0.79579	-0.1745	10	0.66056	D	0.02	-16.4285	17.1334	0.86732	0.0:0.0:1.0:0.0	.	26;26;26;26;26;26;26	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;A7E2E1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	T	26	ENSP00000395654:A26T;ENSP00000350720:A26T;ENSP00000343896:A26T;ENSP00000445036:A26T;ENSP00000392837:A26T;ENSP00000397783:A26T;ENSP00000414727:A26T	ENSP00000343896:A26T	A	+	1	0	SMARCA4	10955903	0.994000	0.37717	1.000000	0.80357	0.996000	0.88848	2.131000	0.42074	2.563000	0.86464	0.655000	0.94253	GCC	G|0.999;A|0.001	0.001	strong		0.721	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		A	11094903	G	A	11094903	3	1	22	1	0	0	0	0	1	0	0	0	14785	971	34	2	78	2	SMARCA4	19	11094903	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	381691	11094903	48034080	3782	6683											
KANK2	25959	hgsc.bcm.edu	37	chr19	11289073	11289073	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccggtgggccgtggggtctgCaacctcctctttccgtttca	3	12	12	14	3	3	0	1	0	2	0	5	0	5	0	5	4	2	2	5	4	1	2	rs115473443	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11289073C>T	ENST00000586659.1	-	6	1782	c.1468G>A	c.(1468-1470)Gca>Aca	p.A490T	KANK2_ENST00000355150.5_Missense_Mutation_p.A490T|KANK2_ENST00000589894.1_Missense_Mutation_p.A490T|KANK2_ENST00000432929.2_Missense_Mutation_p.A498T|KANK2_ENST00000589359.1_Missense_Mutation_p.A498T			Q63ZY3	KANK2_HUMAN	KN motif and ankyrin repeat domains 2	490					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						GTGGGGTCTGCAACCTCCTCT	0.667													c|||	79	0.0157748	0.0575	0.0043	5008	,	,		10474	0.0		0.0	False		,,,				2504	0.0				p.A498T		Atlas-SNP	.											.	KANK2	47	.	0			c.G1492A						PASS	.		THR/ALA,THR/ALA	194,4212	115.9+/-153.8	4,186,2013	24	27	26		1468,1492	-3	0	19	dbSNP_132	26	4,8596	3.0+/-9.4	0,4,4296	yes	missense,missense	KANK2	NM_001136191.2,NM_015493.6	58,58	4,190,6309	TT,TC,CC		0.0465,4.4031,1.5224	benign,benign	490/852,498/860	11289073	198,12808	2203	4300	6503	SO:0001583	missense	25959	exon4			GGTCTGCAACCTC	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.1468G>A	19.37:g.11289073C>T	ENSP00000465650:p.Ala490Thr	81	0	0		102	45	0.441176	NM_015493	B0I1P4|Q3KQZ3|Q6GUF5|Q9H8S4|Q9NUP0|Q9P210	Missense_Mutation	SNP	ENST00000586659.1	37	CCDS12255.1	30	0.013736263736263736	26	0.052845528455284556	4	0.011049723756906077	0	0.0	0	0.0	C	6.571	0.473652	0.12521	0.044031	4.65E-4	ENSG00000197256	ENST00000432929;ENST00000355150	T;T	0.39406	1.08;1.1	5.45	-3.0	0.05480	.	0.449602	0.22279	N	0.062158	T	0.03348	0.0097	L	0.27053	0.805	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.08186	-1.0734	10	0.23891	T	0.37	-18.7177	6.2347	0.20756	0.1484:0.1981:0.0:0.6536	.	490;498	Q63ZY3;Q63ZY3-2	KANK2_HUMAN;.	T	498;490	ENSP00000395650:A498T;ENSP00000347276:A490T	ENSP00000347276:A490T	A	-	1	0	KANK2	11150073	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.342000	0.02645	-0.503000	0.06586	-0.144000	0.13903	GCA	C|0.985;T|0.015	0.015	strong		0.667	KANK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453066.2	NM_015493		T	11289073	C	T	11289073	3	4	22	1	0	0	0	0	1	0	0	0	7986	710	25	2	1119	2	KANK2	19	11289073	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	194170	11289073	47839910	3783	6684											
KANK2	25959	hgsc.bcm.edu	37	chr19	11289129	11289129	+	Intron	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgccgggggcccgcctggaGgggaggacagcggaggtgct	5	4	21	11	3	0	0	0	0	0	0	0	4	0	4	3	8	3	1	3	8	0	0	rs114414326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11289129G>A	ENST00000586659.1	-	6	1732				KANK2_ENST00000355150.5_Intron|KANK2_ENST00000589894.1_Intron|KANK2_ENST00000432929.2_Missense_Mutation_p.P479L|KANK2_ENST00000589359.1_Missense_Mutation_p.P479L			Q63ZY3	KANK2_HUMAN	KN motif and ankyrin repeat domains 2						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						CCCGCCTGGAGGGGAGGACAG	0.677													G|||	79	0.0157748	0.0575	0.0043	5008	,	,		11402	0.0		0.0	False		,,,				2504	0.0				p.P479L		Atlas-SNP	.											.	KANK2	47	.	0			c.C1436T						PASS	.	G	,LEU/PRO	191,4215		4,183,2016	20	25	23		,1436	4.4	0	19	dbSNP_132	23	4,8590		0,4,4293	yes	intron,missense	KANK2	NM_001136191.2,NM_015493.6	,98	4,187,6309	AA,AG,GG		0.0465,4.335,1.5	,	,479/860	11289129	195,12805	2203	4297	6500	SO:0001627	intron_variant	25959	exon4			CCTGGAGGGGAGG	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.1418-6C>T	19.37:g.11289129G>A		64	0	0		80	39	0.4875	NM_015493	B0I1P4|Q3KQZ3|Q6GUF5|Q9H8S4|Q9NUP0|Q9P210	Missense_Mutation	SNP	ENST00000586659.1	37	CCDS12255.1	30	0.013736263736263736	26	0.052845528455284556	4	0.011049723756906077	0	0.0	0	0.0	G	15.34	2.803527	0.50315	0.04335	4.65E-4	ENSG00000197256	ENST00000432929	T	0.34472	1.36	5.45	4.39	0.52855	.	.	.	.	.	T	0.04092	0.0114	.	.	.	0.26307	N	0.977885	P	0.38827	0.649	B	0.32677	0.15	T	0.01776	-1.1276	8	0.31617	T	0.26	.	11.8895	0.52620	0.0841:0.0:0.9159:0.0	.	479	Q63ZY3-2	.	L	479	ENSP00000395650:P479L	ENSP00000395650:P479L	P	-	2	0	KANK2	11150129	0.745000	0.28261	0.002000	0.10522	0.180000	0.23129	1.956000	0.40382	1.283000	0.44513	0.655000	0.94253	CCT	G|0.990;A|0.010	0.010	strong		0.677	KANK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453066.2	NM_015493		A	11289129	G	A	11289129	1	1	22	0	1	0	0	0	0	0	0	0	7986	1000	35	2		2	KANK2	19	11289129	Intron	SNP	G	TCGA-G8-6324-01A-11D-2210-10	56	11289129	47839854	3784	6685											
KANK2	25959	hgsc.bcm.edu	37	chr19	11289307	11289307	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgggctcctgggtgggcaCtcggcctgtgctcttctcag	2	11	16	12	1	2	0	1	0	2	0	5	0	3	0	2	5	1	3	2	5	0	1	rs149142528	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11289307C>T	ENST00000586659.1	-	5	1653	c.1339G>A	c.(1339-1341)Gtg>Atg	p.V447M	KANK2_ENST00000355150.5_Missense_Mutation_p.V447M|KANK2_ENST00000589894.1_Missense_Mutation_p.V447M|KANK2_ENST00000432929.2_Missense_Mutation_p.V447M|KANK2_ENST00000589359.1_Missense_Mutation_p.V447M			Q63ZY3	KANK2_HUMAN	KN motif and ankyrin repeat domains 2	447					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						TGGGTGGGCACTCGGCCTGTG	0.672													C|||	79	0.0157748	0.0575	0.0043	5008	,	,		12124	0.0		0.0	False		,,,				2504	0.0				p.V447M		Atlas-SNP	.											.	KANK2	47	.	0			c.G1339A						PASS	.	C	MET/VAL,MET/VAL	197,4209	123.7+/-161.0	4,189,2010	42	44	43		1339,1339	1.1	0	19	dbSNP_134	43	4,8596	3.0+/-9.4	0,4,4296	yes	missense,missense	KANK2	NM_001136191.2,NM_015493.6	21,21	4,193,6306	TT,TC,CC		0.0465,4.4712,1.5454	benign,benign	447/852,447/860	11289307	201,12805	2203	4300	6503	SO:0001583	missense	25959	exon3			TGGGCACTCGGCC	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.1339G>A	19.37:g.11289307C>T	ENSP00000465650:p.Val447Met	66	0	0		69	29	0.42029	NM_015493	B0I1P4|Q3KQZ3|Q6GUF5|Q9H8S4|Q9NUP0|Q9P210	Missense_Mutation	SNP	ENST00000586659.1	37	CCDS12255.1	30	0.013736263736263736	26	0.052845528455284556	4	0.011049723756906077	0	0.0	0	0.0	C	9.193	1.026620	0.19512	0.044712	4.65E-4	ENSG00000197256	ENST00000432929;ENST00000355150	T;T	0.37411	1.2;1.2	3.5	1.14	0.20703	.	2.220440	0.02225	N	0.064340	T	0.06050	0.0157	L	0.42245	1.32	0.09310	N	1	B;B	0.28512	0.214;0.001	B;B	0.22753	0.041;0.006	T	0.12142	-1.0559	10	0.46703	T	0.11	-28.0739	7.049	0.25063	0.1975:0.6112:0.1913:0.0	.	447;447	Q63ZY3;Q63ZY3-2	KANK2_HUMAN;.	M	447	ENSP00000395650:V447M;ENSP00000347276:V447M	ENSP00000347276:V447M	V	-	1	0	KANK2	11150307	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.164000	0.09983	0.241000	0.21283	0.467000	0.42956	GTG	C|0.987;T|0.013	0.013	strong		0.672	KANK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453066.2	NM_015493		T	11289307	C	T	11289307	3	4	22	1	0	0	0	0	1	0	0	0	7986	565	20	2	1276	2	KANK2	19	11289307	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	178	11289307	47839676	3785	6686											
RAB3D	9545	hgsc.bcm.edu	37	chr19	11436221	11436221	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctcgaagacctgcttcacAttgatgttctccttggcact	7	13	8	13	2	2	2	1	1	1	1	4	3	2	2	2	1	1	4	2	1	1	4	rs12981706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11436221A>G	ENST00000222120.3	-	5	773	c.513T>C	c.(511-513)aaT>aaC	p.N171N	TSPAN16_ENST00000316737.1_Intron|CTC-510F12.6_ENST00000586051.1_RNA|CTC-510F12.4_ENST00000586356.1_RNA|RAB3D_ENST00000589655.1_Silent_p.N171N	NM_004283.3	NP_004274.1	O95716	RAB3D_HUMAN	RAB3D, member RAS oncogene family	171					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						CCTGCTTCACATTGATGTTCT	0.557													A|||	286	0.0571086	0.1762	0.0187	5008	,	,		14659	0.0		0.0318	False		,,,				2504	0.0082				p.N171N		Atlas-SNP	.											.	RAB3D	24	.	0			c.T513C						PASS	.	A	,	617,3789	268.6+/-268.5	43,531,1629	146	132	136		513,	-6.2	1	19	dbSNP_121	136	293,8307	108.0+/-168.7	3,287,4010	no	coding-synonymous,intron	RAB3D,TSPAN16	NM_004283.3,NM_012466.2	,	46,818,5639	GG,GA,AA		3.407,14.0036,6.9968	,	171/220,	11436221	910,12096	2203	4300	6503	SO:0001819	synonymous_variant	9545	exon5			CTTCACATTGATG	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.513T>C	19.37:g.11436221A>G		46	0	0		48	16	0.333333	NM_004283		Silent	SNP	ENST00000222120.3	37	CCDS12257.1																																																																																			A|0.939;G|0.061;T|0.000	0.061	strong		0.557	RAB3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453211.1	NM_004283		G	11436221	A	G	11436221	2	3	22	1	0	0	0	0	0	0	0	1	12949	214	8	3		3	RAB3D	19	11436221	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	146914	11436221	47692762	3786	6687											
EPOR	2057	hgsc.bcm.edu	37	chr19	11489049	11489049	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgggaggtcctcactgggcgGgttccggggcagcaaccatt	6	8	16	11	2	1	0	1	0	0	0	3	1	3	1	3	6	2	3	3	6	1	2	rs35423344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11489049G>C	ENST00000222139.6	-	8	1242	c.1138C>G	c.(1138-1140)Ccg>Gcg	p.P380A	EPOR_ENST00000592375.2_3'UTR	NM_000121.3	NP_000112.1	P19235	EPOR_HUMAN	erythropoietin receptor	380			P -> A (in dbSNP:rs35423344).		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)	TCACTGGGCGGGTTCCGGGGC	0.617											OREG0025254	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	306	0.0611022	0.2231	0.0144	5008	,	,		17759	0.0		0.001	False		,,,				2504	0.0				p.P380A		Atlas-SNP	.											.	EPOR	26	.	0			c.C1138G						PASS	.	G	ALA/PRO	863,3543	335.5+/-303.9	79,705,1419	58	56	57		1138	4.5	0.2	19	dbSNP_126	57	11,8589	6.4+/-24.3	0,11,4289	yes	missense	EPOR	NM_000121.3	27	79,716,5708	CC,CG,GG		0.1279,19.5869,6.72	probably-damaging	380/509	11489049	874,12132	2203	4300	6503	SO:0001583	missense	2057	exon8			TGGGCGGGTTCCG	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.1138C>G	19.37:g.11489049G>C	ENSP00000222139:p.Pro380Ala	32	0	0	672	34	19	0.558824	NM_000121	B2RCG4|Q15443|Q2M205	Missense_Mutation	SNP	ENST00000222139.6	37	CCDS12260.1	109	0.04990842490842491	105	0.21341463414634146	4	0.011049723756906077	0	0.0	0	0.0	G	10.08	1.251233	0.22880	0.195869	0.001279	ENSG00000187266	ENST00000222139	T	0.59364	0.27	4.51	4.51	0.55191	.	0.229422	0.36778	N	0.002409	T	0.00109	0.0003	M	0.67953	2.075	0.42246	P	0.008044000000000051	D	0.76494	0.999	P	0.60609	0.877	T	0.11591	-1.0581	9	0.14656	T	0.56	-28.7314	12.5811	0.56391	0.0:0.0:1.0:0.0	rs35423344;rs57359971	380	P19235	EPOR_HUMAN	A	380	ENSP00000222139:P380A	ENSP00000222139:P380A	P	-	1	0	EPOR	11350049	0.629000	0.27146	0.196000	0.23383	0.027000	0.11550	3.028000	0.49705	2.320000	0.78422	0.650000	0.86243	CCG	G|0.941;C|0.059	0.059	strong		0.617	EPOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458791.1			C	11489049	G	C	11489049	3	2	22	1	0	0	0	0	1	0	0	0	5191	1232	43	4	392	4	EPOR	19	11489049	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	52828	11489049	47639934	3787	6688											
CCDC151	115948	hgsc.bcm.edu	37	chr19	11537006	11537006	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagtttcttctcctcggcGcgcttcttgcactcacttat	4	16	6	15	3	4	0	1	0	3	0	7	0	5	0	2	1	1	3	2	1	1	5	rs61739937	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11537006G>A	ENST00000356392.4	-	7	1008	c.921C>T	c.(919-921)cgC>cgT	p.R307R	CCDC151_ENST00000586836.1_Silent_p.R116R|CCDC151_ENST00000591179.1_Silent_p.R247R|CCDC151_ENST00000545100.1_Silent_p.R253R	NM_145045.4	NP_659482.3	A5D8V7	CC151_HUMAN	coiled-coil domain containing 151	307										endometrium(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	12						TCTCCTCGGCGCGCTTCTTGC	0.627													G|||	129	0.0257588	0.09	0.0072	5008	,	,		14915	0.004		0.001	False		,,,				2504	0.0				p.R307R		Atlas-SNP	.											.	CCDC151	44	.	0			c.C921T						PASS	.	G		295,3731		14,267,1732	41	43	42		921	-8.9	0.1	19	dbSNP_129	42	2,8354		0,2,4176	no	coding-synonymous	CCDC151	NM_145045.4		14,269,5908	AA,AG,GG		0.0239,7.3274,2.3986		307/596	11537006	297,12085	2013	4178	6191	SO:0001819	synonymous_variant	115948	exon7			CTCGGCGCGCTTC		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.921C>T	19.37:g.11537006G>A		52	0	0		43	19	0.44186	NM_145045	B4DXT0|Q96CG5	Silent	SNP	ENST00000356392.4	37	CCDS42501.1																																																																																			G|0.986;A|0.014	0.014	strong		0.627	CCDC151-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458800.1	NM_145045		A	11537006	G	A	11537006	2	1	22	1	0	0	0	0	0	0	0	1	2788	1074	38	1		1	CCDC151	19	11537006	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	47957	11537006	47591977	3788	6689											
ECSIT	51295	hgsc.bcm.edu	37	chr19	11618846	11618846	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatctgctgcacctgttgaGtctttgggcaaaggaacctg	8	11	13	9	0	2	1	0	1	2	0	2	3	2	3	2	3	3	4	2	3	2	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11618846G>C	ENST00000270517.7	-	5	891	c.756C>G	c.(754-756)gaC>gaG	p.D252E	ECSIT_ENST00000591104.1_Missense_Mutation_p.D252E|ECSIT_ENST00000591352.1_5'UTR|ZNF653_ENST00000293771.5_5'Flank|ECSIT_ENST00000588998.1_Missense_Mutation_p.D38E|ZNF653_ENST00000593191.1_5'Flank|CTC-398G3.6_ENST00000585656.1_5'Flank|ECSIT_ENST00000252440.7_Missense_Mutation_p.D252E|ECSIT_ENST00000592312.1_Missense_Mutation_p.D136E|ECSIT_ENST00000417981.2_Missense_Mutation_p.D38E	NM_016581.4	NP_057665.2	Q9BQ95	ECSIT_HUMAN	ECSIT signalling integrator	252					BMP signaling pathway (GO:0030509)|innate immune response (GO:0045087)|mesoderm formation (GO:0001707)|oxidation-reduction process (GO:0055114)|regulation of oxidoreductase activity (GO:0051341)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	oxidoreductase activity, acting on NAD(P)H (GO:0016651)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	11						CACCTGTTGAGTCTTTGGGCA	0.552																																					p.D252E		Atlas-SNP	.											.	ECSIT	32	.	0			c.C756G						PASS	.						104	112	109					19																	11618846		2203	4300	6503	SO:0001583	missense	51295	exon5			TGTTGAGTCTTTG	BC005119	CCDS12262.1, CCDS45979.1, CCDS45980.1, CCDS59353.1	19p13.2	2013-05-24	2013-05-24			ENSG00000130159		"Mitochondrial respiratory chain complex assembly factors"	29548	protein-coding gene	gene with protein product	"signaling intermediate in Toll pathway evolutionarily conserved ortholog (mouse)"	608388	"ECSIT homolog (Drosophila)"			10465784, 22982022	Standard	NM_001142464		Approved	SITPEC	uc002msb.3	Q9BQ95		ENST00000270517.7:c.756C>G	19.37:g.11618846G>C	ENSP00000270517:p.Asp252Glu	129	0	0		143	76	0.531469	NM_001142464	E9PAN9|K7EMM0|Q96HQ7|Q9NYI1	Missense_Mutation	SNP	ENST00000270517.7	37	CCDS12262.1	.	.	.	.	.	.	.	.	.	.	G	10.47	1.360534	0.24598	.	.	ENSG00000130159	ENST00000270517;ENST00000417981;ENST00000252440	T;T;T	0.77098	-1.07;1.56;-1.07	3.81	0.321	0.15883	.	0.520943	0.20641	N	0.088408	T	0.68952	0.3057	M	0.65975	2.015	0.09310	N	1	B;B;B	0.15930	0.015;0.008;0.003	B;B;B	0.19946	0.027;0.009;0.015	T	0.54397	-0.8300	10	0.26408	T	0.33	-23.9198	5.4189	0.16390	0.117:0.4096:0.4734:0.0	.	38;252;252	E9PAN9;Q9BQ95-2;Q9BQ95	.;.;ECSIT_HUMAN	E	252;38;252	ENSP00000270517:D252E;ENSP00000412712:D38E;ENSP00000252440:D252E	ENSP00000252440:D252E	D	-	3	2	ECSIT	11479846	0.109000	0.22037	0.016000	0.15963	0.074000	0.17049	0.357000	0.20199	0.312000	0.23038	0.561000	0.74099	GAC	.	.	none		0.552	ECSIT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442603.2	NM_016581		C	11618846	G	C	11618846	3	2	22	1	0	0	0	0	1	0	0	0	4902	1020	36	4	555	4	ECSIT	19	11618846	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	81840	11618846	47510137	3789	6690											
ACP5	54	hgsc.bcm.edu	37	chr19	11685948	11685948	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagccacccagtgagtcttcAgtcccatagtggaagcgcag	11	7	11	12	1	2	1	1	1	1	0	3	2	3	2	3	1	2	1	3	1	3	2	rs77911902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11685948A>G	ENST00000592828.1	-	7	1257	c.855T>C	c.(853-855)acT>acC	p.T285T	ACP5_ENST00000412435.2_Silent_p.T285T|ACP5_ENST00000433365.2_Silent_p.T285T|ACP5_ENST00000218758.5_Silent_p.T285T|ZNF627_ENST00000588651.1_Intron|ACP5_ENST00000590420.1_Missense_Mutation_p.L43P	NM_001111034.1	NP_001104504.1	P13686	PPA5_HUMAN	acid phosphatase 5, tartrate resistant	285					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						GTGAGTCTTCAGTCCCATAGT	0.572													A|||	148	0.0295527	0.1051	0.013	5008	,	,		21260	0.0		0.0	False		,,,				2504	0.0				p.T285T		Atlas-SNP	.											.	ACP5	30	.	0			c.T855C						PASS	.		,,,	478,3928	225.9+/-241.6	21,436,1746	100	86	91		855,855,855,855	-1.6	0	19	dbSNP_131	91	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ACP5	NM_001111034.1,NM_001111035.1,NM_001111036.1,NM_001611.3	,,,	21,443,6039	GG,GA,AA		0.0814,10.8488,3.729	,,,	285/326,285/326,285/326,285/326	11685948	485,12521	2203	4300	6503	SO:0001819	synonymous_variant	54	exon6			GTCTTCAGTCCCA	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.855T>C	19.37:g.11685948A>G		163	0	0		158	80	0.506329	NM_001111034	A8K3V2|Q2TAB1|Q6IAS6|Q9UCJ5|Q9UCJ6|Q9UCJ7	Silent	SNP	ENST00000592828.1	37	CCDS12265.1																																																																																			A|0.967;G|0.033	0.033	strong		0.572	ACP5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458881.1			G	11685948	A	G	11685948	2	3	22	1	0	0	0	0	0	0	0	1	164	175	7	3		3	ACP5	19	11685948	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	67102	11685948	47443035	3790	6691											
ZNF433	163059	hgsc.bcm.edu	37	chr19	12127370	12127370	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tctccatacacactgctttcGcatgattttactccagtagt	9	15	5	12	1	1	1	0	1	1	0	4	1	2	1	2	0	3	3	2	0	3	5	rs79787738	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12127370G>A	ENST00000344980.6	-	4	482	c.312C>T	c.(310-312)tgC>tgT	p.C104C	ZNF433_ENST00000419886.2_Silent_p.C69C|CTD-2006C1.2_ENST00000476474.1_RNA|CTD-2006C1.2_ENST00000406892.2_RNA|CTD-2006C1.2_ENST00000495324.1_RNA	NM_001080411.1	NP_001073880.1	Q8N7K0	ZN433_HUMAN	zinc finger protein 433	104					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(3)|kidney(1)|large_intestine(4)|lung(1)|prostate(1)|skin(1)	14						CACTGCTTTCGCATGATTTTA	0.408													G|||	15	0.00299521	0.0106	0.0014	5008	,	,		19210	0.0		0.0	False		,,,				2504	0.0				p.C104C		Atlas-SNP	.											.	ZNF433	49	.	0			c.C312T						PASS	.	G		67,4277		0,67,2105	93	93	93		312	-2.4	0	19	dbSNP_132	93	2,8572		0,2,4285	no	coding-synonymous	ZNF433	NM_001080411.1		0,69,6390	AA,AG,GG		0.0233,1.5424,0.5341		104/674	12127370	69,12849	2172	4287	6459	SO:0001819	synonymous_variant	163059	exon4			GCTTTCGCATGAT	AK098300	CCDS45983.1	19p13.13	2013-01-08			ENSG00000197647	ENSG00000197647		"Zinc fingers, C2H2-type", "-"	20811	protein-coding gene	gene with protein product							Standard	NM_001080411		Approved	FLJ40981	uc002msy.1	Q8N7K0	OTTHUMG00000156427	ENST00000344980.6:c.312C>T	19.37:g.12127370G>A		167	0	0		161	72	0.447205	NM_001080411	Q86VX3	Silent	SNP	ENST00000344980.6	37	CCDS45983.1																																																																																			G|0.994;A|0.006	0.006	strong		0.408	ZNF433-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403716.1	NM_152602		A	12127370	G	A	12127370	2	1	22	1	0	0	0	0	0	0	0	1	17922	1079	38	1		1	ZNF433	19	12127370	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	441422	12127370	47001613	3791	6692											
ZNF844	284391	hgsc.bcm.edu	37	chr19	12186372	12186372	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccatataagtgtcaacaacGtaagaaagccttcagatgtc	15	9	8	9	1	2	2	2	0	0	2	3	2	2	2	2	0	3	1	2	0	6	4	rs10422576	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12186372G>A	ENST00000439326.3	+	4	612	c.437G>A	c.(436-438)cGt>cAt	p.R146H	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	146			R -> H (in dbSNP:rs10422576).		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						TGTCAACAACGTAAGAAAGCC	0.423													.|||	104	0.0207668	0.0772	0.0029	5008	,	,		18101	0.0		0.0	False		,,,				2504	0.0				p.R146H		Atlas-SNP	.											.	ZNF844	69	.	0			c.G437A						PASS	.	A	HIS/ARG	76,1308		2,72,618	88	76	79		437	-2.1	0	19	dbSNP_119	79	0,3182		0,0,1591	yes	missense	ZNF844	NM_001136501.1	29	2,72,2209	AA,AG,GG		0.0,5.4913,1.6645	probably-damaging	146/667	12186372	76,4490	692	1591	2283	SO:0001583	missense	284391	exon4			AACAACGTAAGAA	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.437G>A	19.37:g.12186372G>A	ENSP00000392024:p.Arg146His	86	0	0		110	57	0.518182	NM_001136501	Q5JPI8	Missense_Mutation	SNP	ENST00000439326.3	37	CCDS45985.1	38	0.0173992673992674	36	0.07317073170731707	2	0.0055248618784530384	0	0.0	0	0.0	A	6.262	0.416387	0.11870	0.054913	0.0	ENSG00000223547	ENST00000439326;ENST00000541708	T	0.27720	1.65	2.12	-2.12	0.07165	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00815	0.0027	N	0.02916	-0.46	0.18873	N	0.999986	B	0.02656	0.0	B	0.01281	0.0	T	0.21211	-1.0252	9	0.72032	D	0.01	.	6.0456	0.19758	0.4102:0.0:0.5898:0.0	rs56481038	146	Q08AG5	ZN844_HUMAN	H	146	ENSP00000392024:R146H	ENSP00000392024:R146H	R	+	2	0	ZNF844	12047372	0.809000	0.29036	0.000000	0.03702	0.005000	0.04900	1.933000	0.40153	-0.554000	0.06150	-1.906000	0.00525	CGT	.	.	weak		0.423	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2			A	12186372	G	A	12186372	3	1	22	1	0	0	0	0	1	0	0	0	18205	1145	40	1	451	1	ZNF844	19	12186372	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	59002	12186372	46942611	3792	6693											
ZNF20	7568	hgsc.bcm.edu	37	chr19	12244624	12244624	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgacttgtgtccagtgtcaGctctgatatgcgtattaaga	10	14	10	7	1	2	3	1	2	1	1	3	3	3	3	1	0	2	2	1	0	3	4	rs61743205	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12244624G>A	ENST00000334213.5	-	4	601	c.377C>T	c.(376-378)gCt>gTt	p.A126V	ZNF20_ENST00000600335.1_Intron|ZNF20_ENST00000485451.1_5'UTR|ZNF625-ZNF20_ENST00000430024.1_3'UTR	NM_001203250.1|NM_021143.3	NP_001190179.1|NP_066966.2	P17024	ZNF20_HUMAN	zinc finger protein 20	126					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						TCCAGTGTCAGCTCTGATATG	0.408													G|||	103	0.0205671	0.0764	0.0029	5008	,	,		20665	0.0		0.0	False		,,,				2504	0.0				p.A126V		Atlas-SNP	.											.	ZNF20	86	.	0			c.C377T						PASS	.	G	VAL/ALA,VAL/ALA	196,4082		3,190,1946	248	252	251		368,377	-0.3	0	19	dbSNP_129	251	1,8541		0,1,4270	yes	missense,missense	ZNF20	NM_001203250.1,NM_021143.3	64,64	3,191,6216	AA,AG,GG		0.0117,4.5816,1.5367	possibly-damaging,possibly-damaging	123/530,126/533	12244624	197,12623	2139	4271	6410	SO:0001583	missense	7568	exon4			GTGTCAGCTCTGA	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.377C>T	19.37:g.12244624G>A	ENSP00000335437:p.Ala126Val	182	0	0		182	88	0.483516	NM_021143	Q8N457|Q9UG41	Missense_Mutation	SNP	ENST00000334213.5	37	CCDS45986.1	39	0.017857142857142856	38	0.07723577235772358	1	0.0027624309392265192	0	0.0	0	0.0	G	4.410	0.075745	0.08485	0.045816	1.17E-4	ENSG00000132010	ENST00000334213;ENST00000292241;ENST00000418866	T;T	0.13420	3.41;2.59	0.94	-0.349	0.12609	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	.	.	.	.	T	0.00241	0.0007	N	0.04148	-0.265	0.09310	N	1	P	0.44627	0.839	B	0.33454	0.164	T	0.38607	-0.9653	9	0.21540	T	0.41	.	4.7244	0.12935	0.0:0.4015:0.5985:0.0	.	126	P17024	ZNF20_HUMAN	V	126;126;123	ENSP00000335437:A126V;ENSP00000390115:A123V	ENSP00000292241:A126V	A	-	2	0	ZNF20	12105624	0.000000	0.05858	0.029000	0.17559	0.267000	0.26476	-1.626000	0.02035	-0.066000	0.12998	0.313000	0.20887	GCT	G|0.981;A|0.019	0.019	strong		0.408	ZNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344101.1	NM_021143		A	12244624	G	A	12244624	3	1	22	1	0	0	0	0	1	0	0	0	17776	971	34	2	1225	2	ZNF20	19	12244624	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	58252	12244624	46884359	3793	6694											
ZNF442	79973	hgsc.bcm.edu	37	chr19	12462873	12462873	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	atcttcaatgtttgtgtcttCccatttcattcctaaaaggt	9	18	5	9	0	4	0	2	0	2	0	6	0	6	0	2	1	0	1	2	1	3	6	rs73507958	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12462873C>A	ENST00000242804.4	-	5	799	c.217G>T	c.(217-219)Gaa>Taa	p.E73*	ZNF442_ENST00000438182.1_Nonsense_Mutation_p.E4*	NM_030824.2	NP_110451.1	Q9H7R0	ZN442_HUMAN	zinc finger protein 442	73	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(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	31						TTTGTGTCTTCCCATTTCATT	0.353													C|||	39	0.00778754	0.0287	0.0014	5008	,	,		16758	0.0		0.0	False		,,,				2504	0.0				p.E73X		Atlas-SNP	.											.	ZNF442	102	.	0			c.G217T						PASS	.	C	stop/GLU	83,4323	71.4+/-109.4	1,81,2121	123	111	115		217	-1	0.1	19	dbSNP_130	115	1,8599	1.2+/-3.3	0,1,4299	yes	stop-gained	ZNF442	NM_030824.2		1,82,6420	AA,AC,CC		0.0116,1.8838,0.6459		73/628	12462873	84,12922	2203	4300	6503	SO:0001587	stop_gained	79973	exon5			TGTCTTCCCATTT	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.217G>T	19.37:g.12462873C>A	ENSP00000242804:p.Glu73*	133	0	0		118	61	0.516949	NM_030824	B4DJ48	Nonsense_Mutation	SNP	ENST00000242804.4	37	CCDS12271.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	C	13.54	2.268178	0.40095	0.018838	1.16E-4	ENSG00000198342	ENST00000242804;ENST00000438182;ENST00000424168	.	.	.	1.51	-0.994	0.10225	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.21540	T	0.41	.	3.7481	0.08556	0.0:0.4674:0.0:0.5326	.	.	.	.	X	73;4;4	.	ENSP00000242804:E73X	E	-	1	0	ZNF442	12323873	0.001000	0.12720	0.062000	0.19696	0.439000	0.31926	-0.419000	0.07071	-0.071000	0.12886	0.313000	0.20887	GAA	C|0.993;A|0.007	0.007	strong		0.353	ZNF442-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344109.1	NM_030824		A	12462873	C	A	12462873	4	1	22	1	0	0	0	0	0	1	0	0	17930	864	30	4	1674	4	ZNF442	19	12462873	Nonsense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	218249	12462873	46666110	3794	6695											
ZNF799	90576	hgsc.bcm.edu	37	chr19	12502155	12502155	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgagttctttcatgactttTcagtgaactaggacaatcaa	12	14	8	7	0	4	3	3	3	1	0	4	4	4	4	0	1	1	1	0	1	4	5	rs201335235		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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						PASS	.						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	19.37:g.12502155T>G	ENSP00000411084:p.Lys353Gln	91	0	0		111	8	0.0720721	NM_001080821		Missense_Mutation	SNP	ENST00000430385.3	37	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	.	.	weak		0.413	ZNF799-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344099.2	NM_001080821		G	12502155	T	G	12502155	3	3	22	1	0	0	0	0	1	0	0	0	18181	1792	62	5	878	5	ZNF799	19	12502155	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	39282	12502155	46626828	3795	6696											
MAN2B1	4125	hgsc.bcm.edu	37	chr19	12766624	12766624	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataggtgctgaagcccagggCgggcagtgaggctgagaaca	11	5	17	8	1	0	3	0	3	0	1	0	4	0	3	1	4	3	3	1	4	3	1	rs377104016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12766624C>A	ENST00000456935.2	-	14	1754	c.1714G>T	c.(1714-1716)Gcc>Tcc	p.A572S	MAN2B1_ENST00000495617.1_5'Flank|MAN2B1_ENST00000221363.4_Missense_Mutation_p.A571S	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	572					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)	p.A572T(1)		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						AAGCCCAGGGCGGGCAGTGAG	0.612													C|||	2	0.000399361	0.0	0.0	5008	,	,		17585	0.0		0.0	False		,,,				2504	0.002				p.A572S		Atlas-SNP	.											MAN2B1,NS,carcinoma,0,1	MAN2B1	91	1	1	Substitution - Missense(1)	prostate(1)	c.G1714T						PASS	.	C	SER/ALA,SER/ALA	3,4403	8.1+/-20.4	0,3,2200	58	64	62		1714,1711	4	1	19		62	0,8600		0,0,4300	no	missense,missense	MAN2B1	NM_000528.3,NM_001173498.1	99,99	0,3,6500	AA,AC,CC		0.0,0.0681,0.0231	benign,benign	572/1012,571/1011	12766624	3,13003	2203	4300	6503	SO:0001583	missense	4125	exon14			CCAGGGCGGGCAG		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.1714G>T	19.37:g.12766624C>A	ENSP00000395473:p.Ala572Ser	32	0	0		37	21	0.567568	NM_000528	G5E928|O15330|Q16680|Q93094|Q9BW13	Missense_Mutation	SNP	ENST00000456935.2	37	CCDS32919.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.66|19.66	3.869012|3.869012	0.72065|0.72065	6.81E-4|6.81E-4	0.0|0.0	ENSG00000104774|ENSG00000104774	ENST00000456935;ENST00000536796;ENST00000221363|ENST00000433513	T;T|.	0.81163|.	-1.46;-1.46|.	5.16|5.16	4.03|4.03	0.46877|0.46877	Glycosyl hydrolases 38, C-terminal (1);Glycosyl hydrolase, family 13, all-beta (1);Glycoside hydrolase-type carbohydrate-binding (1);|.	0.000000|.	0.33712|.	N|.	0.004633|.	T|T	0.76593|0.76593	0.4009|0.4009	M|M	0.85041|0.85041	2.73|2.73	0.39975|0.39975	D|D	0.974849|0.974849	P;D|.	0.58970|.	0.928;0.984|.	P;P|.	0.59288|.	0.774;0.855|.	T|T	0.80151|0.80151	-0.1502|-0.1502	10|5	0.54805|.	T|.	0.06|.	-16.9432|-16.9432	12.4629|12.4629	0.55741|0.55741	0.0:0.8153:0.1847:0.0|0.0:0.8153:0.1847:0.0	.|.	571;572|.	G5E928;O00754|.	.;MA2B1_HUMAN|.	S|L	572;511;571|107	ENSP00000395473:A572S;ENSP00000221363:A571S|.	ENSP00000221363:A571S|.	A|R	-|-	1|2	0|0	MAN2B1|MAN2B1	12627624|12627624	0.995000|0.995000	0.38212|0.38212	0.986000|0.986000	0.45419|0.45419	0.762000|0.762000	0.43233|0.43233	2.575000|2.575000	0.46025|0.46025	2.389000|2.389000	0.81357|0.81357	0.313000|0.313000	0.20887|0.20887	GCC|CGC	.	.	weak		0.612	MAN2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344062.1			A	12766624	C	A	12766624	3	1	22	1	0	0	0	0	1	0	0	0	9225	768	27	4	1365	4	MAN2B1	19	12766624	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	264469	12766624	46362359	3796	6697											
FBXW9	84261	hgsc.bcm.edu	37	chr19	12800597	12800597	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggataagctggaagcagccgTtgcggttggcgaagacgtgc	9	7	17	8	4	0	1	0	0	0	1	0	4	0	3	1	4	5	4	1	4	3	3	rs73921601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12800597T>C	ENST00000380339.3	-	7	1250	c.1214A>G	c.(1213-1215)aAc>aGc	p.N405S	FBXW9_ENST00000544494.1_Missense_Mutation_p.N113S|CTD-2659N19.2_ENST00000585742.1_RNA|CTD-2192J16.26_ENST00000593554.1_lincRNA|FBXW9_ENST00000393261.3_Missense_Mutation_p.N375S|FBXW9_ENST00000587955.1_Missense_Mutation_p.N395S			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	405					SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						GAAGCAGCCGTTGCGGTTGGC	0.652													T|||	245	0.0489217	0.1679	0.0187	5008	,	,		17279	0.0		0.0099	False		,,,				2504	0.0				p.N375S		Atlas-SNP	.											FBXW9_ENST00000393261,caecum,carcinoma,+1,3	FBXW9	30	3	0			c.A1124G						PASS	.	T	SER/ASN	686,3720	270.4+/-269.6	52,582,1569	60	63	62		1124	-0.8	0	19	dbSNP_130	62	125,8475	61.3+/-123.2	0,125,4175	yes	missense	FBXW9	NM_032301.2	46	52,707,5744	CC,CT,TT		1.4535,15.5697,6.2356	benign	375/459	12800597	811,12195	2203	4300	6503	SO:0001583	missense	84261	exon7			CAGCCGTTGCGGT	BC004290	CCDS12278.2	19p13.2	2013-01-09	2007-02-08		ENSG00000132004	ENSG00000132004		"F-boxes / WD-40 domains", "WD repeat domain containing"	28136	protein-coding gene	gene with protein product		609074	"F-box and WD-40 domain protein 9"			12477932	Standard	NM_032301		Approved	MGC10870, Fbw9	uc002mum.1	Q5XUX1	OTTHUMG00000150152	ENST00000380339.3:c.1214A>G	19.37:g.12800597T>C	ENSP00000369696:p.Asn405Ser	85	0	0		84	29	0.345238	NM_032301	B3KVP7|Q9BT89	Missense_Mutation	SNP	ENST00000380339.3	37		87	0.03983516483516483	73	0.1483739837398374	7	0.019337016574585635	0	0.0	7	0.009234828496042216	T	4.791	0.147100	0.09134	0.155697	0.014535	ENSG00000132004	ENST00000544494;ENST00000393261;ENST00000380339	T;T;T	0.75154	-0.91;-0.91;-0.91	4.32	-0.772	0.10998	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	2.425580	0.01961	N	0.043380	T	0.00384	0.0012	L	0.27053	0.805	0.80722	P	0.0	B;B;B	0.11235	0.001;0.004;0.001	B;B;B	0.12156	0.003;0.007;0.001	T	0.02326	-1.1176	9	0.21540	T	0.41	2.9217	4.636	0.12525	0.0:0.4404:0.1963:0.3633	.	395;405;375	Q5XUX1-2;Q5XUX1;Q5XUX1-3	.;FBXW9_HUMAN;.	S	113;375;405	ENSP00000442714:N113S;ENSP00000376945:N375S;ENSP00000369696:N405S	ENSP00000369696:N405S	N	-	2	0	FBXW9	12661597	0.000000	0.05858	0.001000	0.08648	0.064000	0.16182	-0.137000	0.10389	0.154000	0.19237	0.397000	0.26171	AAC	T|0.944;C|0.056	0.056	strong		0.652	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301		C	12800597	T	C	12800597	3	2	22	1	0	0	0	0	1	0	0	0	5779	1725	60	3	268	3	FBXW9	19	12800597	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	33973	12800597	46328386	3797	6698											
FBXW9	84261	hgsc.bcm.edu	37	chr19	12805431	12805431	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgggtactatttcgcttagTgcctaaggtcttgatcagaa	10	14	10	7	1	2	2	1	1	1	1	3	2	2	2	1	2	2	2	1	2	5	6	rs10424623	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12805431T>C	ENST00000380339.3	-	3	691	c.655A>G	c.(655-657)Act>Gct	p.T219A	FBXW9_ENST00000544494.1_5'UTR|FBXW9_ENST00000393261.3_Missense_Mutation_p.T219A|FBXW9_ENST00000587955.1_Missense_Mutation_p.T209A			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	219			T -> A (in dbSNP:rs10424623).		SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						TTTCGCTTAGTGCCTAAGGTC	0.562													T|||	748	0.149361	0.534	0.0461	5008	,	,		19047	0.0		0.0099	False		,,,				2504	0.0				p.T219A		Atlas-SNP	.											.	FBXW9	30	.	0			c.A655G						PASS	.	T	ALA/THR	1743,2441		372,999,721	65	74	71		655	2.1	0.2	19	dbSNP_119	71	133,8305		1,131,4087	yes	missense	FBXW9	NM_032301.2	58	373,1130,4808	CC,CT,TT		1.5762,41.6587,14.8629	benign	219/459	12805431	1876,10746	2092	4219	6311	SO:0001583	missense	84261	exon3			GCTTAGTGCCTAA	BC004290	CCDS12278.2	19p13.2	2013-01-09	2007-02-08		ENSG00000132004	ENSG00000132004		"F-boxes / WD-40 domains", "WD repeat domain containing"	28136	protein-coding gene	gene with protein product		609074	"F-box and WD-40 domain protein 9"			12477932	Standard	NM_032301		Approved	MGC10870, Fbw9	uc002mum.1	Q5XUX1	OTTHUMG00000150152	ENST00000380339.3:c.655A>G	19.37:g.12805431T>C	ENSP00000369696:p.Thr219Ala	81	0	0		108	48	0.444444	NM_032301	B3KVP7|Q9BT89	Missense_Mutation	SNP	ENST00000380339.3	37		244	0.11172161172161173	220	0.44715447154471544	17	0.04696132596685083	0	0.0	7	0.009234828496042216	T	5.162	0.215402	0.09810	0.416587	0.015762	ENSG00000132004	ENST00000393261;ENST00000380339	T;T	0.51325	1.74;0.71	4.29	2.11	0.27256	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.565790	0.18087	N	0.152109	T	0.00012	0.0000	N	0.24115	0.695	0.21386	P	0.999707688	B;B;B	0.17268	0.013;0.009;0.021	B;B;B	0.16289	0.014;0.015;0.009	T	0.46219	-0.9207	9	0.32370	T	0.25	-17.2872	5.0146	0.14330	0.162:0.0922:0.0:0.7458	rs10424623	209;219;219	Q5XUX1-2;Q5XUX1;Q5XUX1-3	.;FBXW9_HUMAN;.	A	219	ENSP00000376945:T219A;ENSP00000369696:T219A	ENSP00000369696:T219A	T	-	1	0	FBXW9	12666431	0.259000	0.24043	0.235000	0.24058	0.003000	0.03518	0.704000	0.25661	0.190000	0.20209	0.379000	0.24179	ACT	T|0.921;C|0.079	0.079	strong		0.562	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301		C	12805431	T	C	12805431	3	2	22	1	0	0	0	0	1	0	0	0	5779	1696	59	3	753	3	FBXW9	19	12805431	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	4834	12805431	46323552	3798	6699											
FBXW9	84261	hgsc.bcm.edu	37	chr19	12805525	12805525	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tctcgggagcccgacagacaGagtgacccaccctggaaagg	11	4	13	13	2	1	3	0	1	1	2	2	6	1	5	3	3	1	0	3	3	1	0	rs10416965	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12805525G>C	ENST00000380339.3	-	3	597	c.561C>G	c.(559-561)ctC>ctG	p.L187L	FBXW9_ENST00000544494.1_5'UTR|FBXW9_ENST00000393261.3_Silent_p.L187L|FBXW9_ENST00000587955.1_Silent_p.L177L			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	187					SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						CCGACAGACAGAGTGACCCAC	0.632													G|||	749	0.149561	0.5348	0.0461	5008	,	,		18468	0.0		0.0099	False		,,,				2504	0.0				p.L187L		Atlas-SNP	.											.	FBXW9	30	.	0			c.C561G						PASS	.	G		1693,2405		363,967,719	62	68	66		561	-2.5	0.1	19	dbSNP_119	66	131,8263		1,129,4067	no	coding-synonymous	FBXW9	NM_032301.2		364,1096,4786	CC,CG,GG		1.5606,41.3128,14.6013		187/459	12805525	1824,10668	2049	4197	6246	SO:0001819	synonymous_variant	84261	exon3			CAGACAGAGTGAC	BC004290	CCDS12278.2	19p13.2	2013-01-09	2007-02-08		ENSG00000132004	ENSG00000132004		"F-boxes / WD-40 domains", "WD repeat domain containing"	28136	protein-coding gene	gene with protein product		609074	"F-box and WD-40 domain protein 9"			12477932	Standard	NM_032301		Approved	MGC10870, Fbw9	uc002mum.1	Q5XUX1	OTTHUMG00000150152	ENST00000380339.3:c.561C>G	19.37:g.12805525G>C		70	0	0		82	41	0.5	NM_032301	B3KVP7|Q9BT89	Silent	SNP	ENST00000380339.3	37																																																																																				G|0.921;C|0.079	0.079	strong		0.632	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301		C	12805525	G	C	12805525	2	2	22	1	0	0	0	0	0	0	0	1	5779	929	33	4		4	FBXW9	19	12805525	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	94	12805525	46323458	3799	6700											
FBXW9	84261	hgsc.bcm.edu	37	chr19	12807066	12807066	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tggtcagacacgaggtcgcgGagcgcgtggcacacccgcga	8	4	16	13	7	1	1	1	0	0	1	2	4	1	2	1	4	1	1	1	4	0	0	rs6511832	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12807066G>C	ENST00000380339.3	-	1	366	c.330C>G	c.(328-330)ctC>ctG	p.L110L	FBXW9_ENST00000544494.1_5'UTR|FBXW9_ENST00000393261.3_Silent_p.L110L|FBXW9_ENST00000587955.1_Silent_p.L110L			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	110	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						CGAGGTCGCGGAGCGCGTGGC	0.721													C|||	748	0.149361	0.534	0.0461	5008	,	,		12393	0.0		0.0099	False		,,,				2504	0.0				p.L110L		Atlas-SNP	.											.	FBXW9	30	.	0			c.C330G						PASS	.	C		1528,2426		306,916,755	10	14	13		330	2.8	1	19	dbSNP_116	13	117,8057		1,115,3971	no	coding-synonymous	FBXW9	NM_032301.2		307,1031,4726	CC,CG,GG		1.4314,38.6444,13.5637		110/459	12807066	1645,10483	1977	4087	6064	SO:0001819	synonymous_variant	84261	exon1			GTCGCGGAGCGCG	BC004290	CCDS12278.2	19p13.2	2013-01-09	2007-02-08		ENSG00000132004	ENSG00000132004		"F-boxes / WD-40 domains", "WD repeat domain containing"	28136	protein-coding gene	gene with protein product		609074	"F-box and WD-40 domain protein 9"			12477932	Standard	NM_032301		Approved	MGC10870, Fbw9	uc002mum.1	Q5XUX1	OTTHUMG00000150152	ENST00000380339.3:c.330C>G	19.37:g.12807066G>C		38	0	0		50	21	0.42	NM_032301	B3KVP7|Q9BT89	Silent	SNP	ENST00000380339.3	37																																																																																				G|0.902;C|0.098	0.098	strong		0.721	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301		C	12807066	G	C	12807066	2	2	22	1	0	0	0	0	0	0	0	1	5779	1161	41	4		4	FBXW9	19	12807066	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1541	12807066	46321917	3800	6701											
FBXW9	84261	hgsc.bcm.edu	37	chr19	12807187	12807187	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcacttacggccgaaaccCtggacgcggcccgaggctcc	7	5	12	17	5	1	0	1	0	0	0	2	3	2	1	4	4	2	2	4	4	2	1	rs6511833	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12807187C>T	ENST00000380339.3	-	1	245	c.209G>A	c.(208-210)aGg>aAg	p.R70K	FBXW9_ENST00000544494.1_5'UTR|FBXW9_ENST00000393261.3_Missense_Mutation_p.R70K|FBXW9_ENST00000587955.1_Missense_Mutation_p.R70K			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	70			R -> K (in dbSNP:rs6511833).		SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						GGCCGAAACCCTGGACGCGGC	0.692													T|||	748	0.149361	0.5333	0.0461	5008	,	,		12421	0.0		0.0109	False		,,,				2504	0.0				p.R70K		Atlas-SNP	.											.	FBXW9	30	.	0			c.G209A						PASS	.	T	LYS/ARG	1544,2262		327,890,686	14	18	17		209	-0.2	0	19	dbSNP_116	17	128,8068		4,120,3974	yes	missense	FBXW9	NM_032301.2	26	331,1010,4660	TT,TC,CC		1.5617,40.5675,13.931	benign	70/459	12807187	1672,10330	1903	4098	6001	SO:0001583	missense	84261	exon1			GAAACCCTGGACG	BC004290	CCDS12278.2	19p13.2	2013-01-09	2007-02-08		ENSG00000132004	ENSG00000132004		"F-boxes / WD-40 domains", "WD repeat domain containing"	28136	protein-coding gene	gene with protein product		609074	"F-box and WD-40 domain protein 9"			12477932	Standard	NM_032301		Approved	MGC10870, Fbw9	uc002mum.1	Q5XUX1	OTTHUMG00000150152	ENST00000380339.3:c.209G>A	19.37:g.12807187C>T	ENSP00000369696:p.Arg70Lys	44	0	0		69	33	0.478261	NM_032301	B3KVP7|Q9BT89	Missense_Mutation	SNP	ENST00000380339.3	37		244	0.11172161172161173	220	0.44715447154471544	17	0.04696132596685083	0	0.0	7	0.009234828496042216	T	7.621	0.676786	0.14841	0.405675	0.015617	ENSG00000132004	ENST00000393261;ENST00000380339	T;T	0.53857	0.6;0.6	5.0	-0.247	0.13019	.	0.338458	0.20979	N	0.082254	T	0.00012	0.0000	N	0.02916	-0.46	0.46849	P	7.759999999999989E-4	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.41998	-0.9477	9	0.02654	T	1	-7.7148	10.6828	0.45823	0.0:0.4314:0.0:0.5686	rs6511833;rs61227291;rs6511833	70;70	Q5XUX1-2;Q5XUX1-3	.;.	K	70	ENSP00000376945:R70K;ENSP00000369696:R70K	ENSP00000369696:R70K	R	-	2	0	FBXW9	12668187	0.063000	0.20901	0.023000	0.16930	0.194000	0.23727	-0.092000	0.11129	-0.309000	0.08779	-0.521000	0.04368	AGG	C|0.880;T|0.120	0.120	strong		0.692	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301		T	12807187	C	T	12807187	3	4	22	1	0	0	0	0	1	0	0	0	5779	681	24	2	1207	2	FBXW9	19	12807187	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	121	12807187	46321796	3801	6702											
TNPO2	30000	hgsc.bcm.edu	37	chr19	12813683	12813683	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgttgggtcggttaatgatTtccaccaggttgttgaggac	7	14	14	6	1	0	2	0	2	0	0	2	3	1	3	2	4	0	4	2	4	1	5	rs16978630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12813683T>C	ENST00000592287.1	-	20	2367	c.2259A>G	c.(2257-2259)gaA>gaG	p.E753E	TNPO2_ENST00000588216.1_Silent_p.E753E|TNPO2_ENST00000425528.1_Silent_p.E753E|TNPO2_ENST00000441499.1_Silent_p.E753E|TNPO2_ENST00000356861.5_Silent_p.E753E|TNPO2_ENST00000450764.2_Silent_p.E753E	NM_001136196.1	NP_001129668.1	O14787	TNPO2_HUMAN	transportin 2	753					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						GGTTAATGATTTCCACCAGGT	0.632													C|||	747	0.149161	0.5333	0.0461	5008	,	,		16704	0.0		0.0099	False		,,,				2504	0.0				p.E753E		Atlas-SNP	.											.	TNPO2	108	.	0			c.A2259G						PASS	.	C	,,	1692,2404		359,974,715	244	265	258		2259,2259,2259	1	1	19	dbSNP_123	258	127,8261		1,125,4068	no	coding-synonymous,coding-synonymous,coding-synonymous	TNPO2	NM_001136195.1,NM_001136196.1,NM_013433.4	,,	360,1099,4783	CC,CT,TT		1.5141,41.3086,14.5707	,,	753/888,753/898,753/888	12813683	1819,10665	2048	4194	6242	SO:0001819	synonymous_variant	30000	exon20			AATGATTTCCACC	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.2259A>G	19.37:g.12813683T>C		310	0	0		314	141	0.449045	NM_013433	O14655|Q6IN77	Silent	SNP	ENST00000592287.1	37	CCDS45991.1																																																																																			T|0.866;C|0.134	0.134	strong		0.632	TNPO2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450785.1	NM_013433		C	12813683	T	C	12813683	2	2	22	1	0	0	0	0	0	0	0	1	16351	1838	64	3		3	TNPO2	19	12813683	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	6496	12813683	46315300	3802	6703											
TNPO2	30000	hgsc.bcm.edu	37	chr19	12816559	12816559	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ttccacttctggatcagtggGggcatcagcttctggatgta	7	13	12	9	0	4	0	2	0	2	0	5	2	5	2	1	4	1	3	1	4	1	4	rs7248726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12816559G>T	ENST00000592287.1	-	15	1800	c.1692C>A	c.(1690-1692)ccC>ccA	p.P564P	TNPO2_ENST00000588216.1_Silent_p.P564P|TNPO2_ENST00000425528.1_Silent_p.P564P|TNPO2_ENST00000441499.1_Silent_p.P564P|TNPO2_ENST00000356861.5_Silent_p.P564P|SNORD41_ENST00000386967.1_RNA|TNPO2_ENST00000450764.2_Silent_p.P564P	NM_001136196.1	NP_001129668.1	O14787	TNPO2_HUMAN	transportin 2	564					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						GGATCAGTGGGGGCATCAGCT	0.597													G|||	739	0.147564	0.5272	0.0461	5008	,	,		18127	0.0		0.0099	False		,,,				2504	0.0				p.P564P		Atlas-SNP	.											.	TNPO2	108	.	0			c.C1692A						PASS	.	G	,,	1656,2570		326,1004,783	32	32	32		1692,1692,1692	-10.9	0.2	19	dbSNP_116	32	119,8253		2,115,4069	no	coding-synonymous,coding-synonymous,coding-synonymous	TNPO2	NM_001136195.1,NM_001136196.1,NM_013433.4	,,	328,1119,4852	TT,TG,GG		1.4214,39.186,14.0895	,,	564/888,564/898,564/888	12816559	1775,10823	2113	4186	6299	SO:0001819	synonymous_variant	30000	exon15			CAGTGGGGGCATC	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.1692C>A	19.37:g.12816559G>T		127	0	0		149	78	0.52349	NM_013433	O14655|Q6IN77	Silent	SNP	ENST00000592287.1	37	CCDS45991.1																																																																																			G|0.849;T|0.151	0.151	strong		0.597	TNPO2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450785.1	NM_013433		T	12816559	G	T	12816559	2	4	22	1	0	0	0	0	0	0	0	1	16351	1219	43	4		4	TNPO2	19	12816559	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2876	12816559	46312424	3803	6704											
MAST1	22983	hgsc.bcm.edu	37	chr19	12978556	12978556	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatgcagcaagcgattctcCgcgtccgaggccagtttcct	7	9	10	15	4	1	0	0	0	1	0	4	2	3	0	5	1	3	3	5	1	1	2	rs202159363	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12978556C>G	ENST00000251472.4	+	20	2370	c.2331C>G	c.(2329-2331)tcC>tcG	p.S777S		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						AGCGATTCTCCGCGTCCGAGG	0.687													C|||	59	0.0117812	0.0431	0.0029	5008	,	,		13407	0.0		0.0	False		,,,				2504	0.0				p.S777S		Atlas-SNP	.											.	MAST1	214	.	0			c.C2331G						PASS	.	C		118,4146		0,118,2014	7	7	7		2331	-9	0.1	19		7	1,8357		0,1,4178	no	coding-synonymous	MAST1	NM_014975.2		0,119,6192	GG,GC,CC		0.012,2.7674,0.9428		777/1571	12978556	119,12503	2132	4179	6311	SO:0001819	synonymous_variant	22983	exon20			ATTCTCCGCGTCC	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.2331C>G	19.37:g.12978556C>G		61	0	0		62	33	0.532258	NM_014975		Silent	SNP	ENST00000251472.4	37	CCDS32921.1																																																																																			C|0.995;G|0.005	0.005	strong		0.687	MAST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451733.2	NM_014975		G	12978556	C	G	12978556	2	3	22	1	0	0	0	0	0	0	0	1	9333	639	23	4		4	MAST1	19	12978556	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	161997	12978556	46150427	3804	6705											
CACNA1A	773	hgsc.bcm.edu	37	chr19	13323261	13323261	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttccggactccatgtgccCgtcttctggaacatctcctg	5	13	9	14	2	3	0	0	0	3	0	6	2	5	2	4	2	2	1	4	2	1	2	rs7249722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:13323261C>T	ENST00000360228.5	-	42	6125	c.6126G>A	c.(6124-6126)acG>acA	p.T2042T	CACNA1A_ENST00000573710.2_Silent_p.T2043T	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	2043					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)	TCCATGTGCCCGTCTTCTGGA	0.647													C|||	48	0.00958466	0.0356	0.0014	5008	,	,		15991	0.0		0.0	False		,,,				2504	0.0				p.T2043T		Atlas-SNP	.											.	CACNA1A	715	.	0			c.G6129A						PASS	.	C	,,,,	100,3864		1,98,1883	30	34	33		6144,6129,6126,6135,6144	-8.6	0.8	19	dbSNP_116	33	1,8295		0,1,4147	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1A	NM_000068.3,NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2	,,,,	1,99,6030	TT,TC,CC		0.0121,2.5227,0.8238	,,,,	2048/2267,2043/2262,2042/2507,2045/2264,2048/2513	13323261	101,12159	1982	4148	6130	SO:0001819	synonymous_variant	773	exon42			TGTGCCCGTCTTC	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.6126G>A	19.37:g.13323261C>T		106	0	0		109	49	0.449541	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000360228.5	37	CCDS45998.1																																																																																			C|0.996;T|0.004	0.004	strong		0.647	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		T	13323261	C	T	13323261	2	4	22	1	0	0	0	0	0	0	0	1	2540	639	23	1		1	CACNA1A	19	13323261	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	344705	13323261	45805722	3805	6706											
CACNA1A	773	hgsc.bcm.edu	37	chr19	13563767	13563767	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ttgtggaaggcaaacccaagGgcaatgattttaattccagc	13	10	10	8	0	0	1	0	1	0	0	1	2	1	2	2	3	2	2	2	3	5	4	rs1800039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:13563767G>A	ENST00000360228.5	-	3	461	c.462C>T	c.(460-462)gcC>gcT	p.A154A	CACNA1A_ENST00000573710.2_Silent_p.A154A	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	154					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)	CAAACCCAAGGGCAATGATTT	0.493													G|||	48	0.00958466	0.0356	0.0014	5008	,	,		21794	0.0		0.0	False		,,,				2504	0.0				p.A154A		Atlas-SNP	.											.	CACNA1A	715	.	0			c.C462T						PASS	.	G	,,,,	82,3876		1,80,1898	154	150	151		462,462,462,462,462	2.4	1	19	dbSNP_89	151	5,8333		0,5,4164	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1A	NM_000068.3,NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2	,,,,	1,85,6062	AA,AG,GG		0.06,2.0718,0.7075	,,,,	154/2267,154/2262,154/2507,154/2264,154/2513	13563767	87,12209	1979	4169	6148	SO:0001819	synonymous_variant	773	exon3			CCCAAGGGCAATG	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.462C>T	19.37:g.13563767G>A		198	0	0		216	98	0.453704	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000360228.5	37	CCDS45998.1																																																																																			G|0.992;A|0.008	0.008	strong		0.493	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		A	13563767	G	A	13563767	2	1	22	1	0	0	0	0	0	0	0	1	2540	1219	43	2		2	CACNA1A	19	13563767	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	240506	13563767	45565216	3806	6707											
CCDC130	81576	hgsc.bcm.edu	37	chr19	13873793	13873793	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcgccagcaggctcctccCaggaggcagctgacaccccc	7	5	11	18	1	0	1	0	1	0	0	3	2	2	2	5	3	2	4	5	3	0	0	rs138278370	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:13873793C>A	ENST00000586600.1	+	11	1605	c.1102C>A	c.(1102-1104)Cag>Aag	p.Q368K	MRI1_ENST00000040663.6_5'Flank|MRI1_ENST00000319545.8_5'Flank|CCDC130_ENST00000221554.8_Missense_Mutation_p.Q368K			P13994	CC130_HUMAN	coiled-coil domain containing 130	368					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)			AGGCTCCTCCCAGGAGGCAGC	0.667													C|||	22	0.00439297	0.0159	0.0014	5008	,	,		13510	0.0		0.0	False		,,,				2504	0.0				p.Q368K		Atlas-SNP	.											.	CCDC130	25	.	0			c.C1102A						PASS	.	C	LYS/GLN	82,4310		0,82,2114	14	17	16		1102	4.5	0	19	dbSNP_134	16	1,8579		0,1,4289	yes	missense	CCDC130	NM_030818.2	53	0,83,6403	AA,AC,CC		0.0117,1.867,0.6398	benign	368/397	13873793	83,12889	2196	4290	6486	SO:0001583	missense	81576	exon10			TCCTCCCAGGAGG	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.1102C>A	19.37:g.13873793C>A	ENSP00000465776:p.Gln368Lys	52	0	0		40	13	0.325	NM_030818	Q9BQ72	Missense_Mutation	SNP	ENST00000586600.1	37	CCDS12296.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	11.27	1.590016	0.28357	0.01867	1.17E-4	ENSG00000104957	ENST00000221554	T	0.27557	1.66	4.49	4.49	0.54785	.	0.852666	0.09747	N	0.761109	T	0.13970	0.0338	L	0.57536	1.79	0.24401	N	0.994709	B;B	0.27625	0.183;0.183	B;B	0.25506	0.061;0.061	T	0.37407	-0.9707	10	0.06494	T	0.89	-10.5446	8.8286	0.35069	0.0:0.8959:0.0:0.1041	.	368;368	B3KUZ1;P13994	.;CC130_HUMAN	K	368	ENSP00000221554:Q368K	ENSP00000221554:Q368K	Q	+	1	0	CCDC130	13734793	0.003000	0.15002	0.033000	0.17914	0.220000	0.24768	0.327000	0.19663	2.230000	0.72887	0.491000	0.48974	CAG	C|0.994;A|0.006	0.006	strong		0.667	CCDC130-001	KNOWN	alternative_5_UTR|upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453216.2	NM_030818		A	13873793	C	A	13873793	3	1	22	1	0	0	0	0	1	0	0	0	2768	595	21	4	1136	4	CCDC130	19	13873793	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	310026	13873793	45255190	3807	6708											
MRI1	81576	hgsc.bcm.edu	37	chr19	13875453	13875453	+	IGR	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggctccctgcagatcctagaCcagctgctgctgcccaagca	8	7	10	16	0	0	2	0	0	0	2	2	2	2	2	4	1	6	6	4	1	2	1	rs141796284	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:13875453C>T	ENST00000586600.1	+	0	1922				MRI1_ENST00000040663.6_Silent_p.D17D|MRI1_ENST00000319545.8_Silent_p.D17D			P13994	CC130_HUMAN	coiled-coil domain containing 130						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)			AGATCCTAGACCAGCTGCTGC	0.706													C|||	22	0.00439297	0.0159	0.0014	5008	,	,		6970	0.0		0.0	False		,,,				2504	0.0				p.D17D		Atlas-SNP	.											.	MRI1	35	.	0			c.C51T						PASS	.	C	,	91,4295		0,91,2102	24	27	26		51,51	4.1	1	19	dbSNP_134	26	1,8565		0,1,4282	no	coding-synonymous,coding-synonymous	MRI1	NM_001031727.2,NM_032285.2	,	0,92,6384	TT,TC,CC		0.0117,2.0748,0.7103	,	17/370,17/323	13875453	92,12860	2193	4283	6476	SO:0001628	intergenic_variant	84245	exon1			CCTAGACCAGCTG	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			19.37:g.13875453C>T		107	0	0		123	48	0.390244	NM_001031727	Q9BQ72	Silent	SNP	ENST00000586600.1	37	CCDS12296.1																																																																																			C|0.993;T|0.007	0.007	strong		0.706	CCDC130-001	KNOWN	alternative_5_UTR|upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453216.2	NM_030818		T	13875453	C	T	13875453	1	4	22	0	1	0	0	0	0	0	0	0	9779	506	18	2		2	MRI1	19	13875453	IGR	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1660	13875453	45253530	3808	6709											
C19orf57	79173	hgsc.bcm.edu	37	chr19	14006300	14006300	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	caacatggaactctgggggtCcccatagaagtctcctagcc	10	8	10	13	0	2	1	0	0	2	1	4	2	3	2	4	3	3	0	4	3	5	2	rs58722011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14006300C>A	ENST00000586783.1	-	2	90	c.91G>T	c.(91-93)Gac>Tac	p.D31Y	C19orf57_ENST00000346736.2_Missense_Mutation_p.D31Y|C19orf57_ENST00000454313.1_Missense_Mutation_p.D31Y|C19orf57_ENST00000591586.1_Missense_Mutation_p.D31Y			Q0VDD7	CS057_HUMAN	chromosome 19 open reading frame 57	31					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)			CTCTGGGGGTCCCCATAGAAG	0.547													C|||	160	0.0319489	0.118	0.0058	5008	,	,		17727	0.0		0.0	False		,,,				2504	0.0				p.D31Y		Atlas-SNP	.											.	C19orf57	34	.	0			c.G91T						PASS	.	C	TYR/ASP	352,4054	182.9+/-210.6	15,322,1866	171	183	179		91	-1.8	0	19	dbSNP_129	179	1,8599	1.2+/-3.3	0,1,4299	yes	missense	C19orf57	NM_024323.3	160	15,323,6165	AA,AC,CC		0.0116,7.9891,2.7141	probably-damaging	31/638	14006300	353,12653	2203	4300	6503	SO:0001583	missense	79173	exon3			GGGGGTCCCCATA	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.91G>T	19.37:g.14006300C>A	ENSP00000465822:p.Asp31Tyr	146	0	0		174	79	0.454023	NM_024323	Q13411|Q8N825|Q96D63|Q9BU49	Missense_Mutation	SNP	ENST00000586783.1	37		60	0.027472527472527472	59	0.11991869918699187	1	0.0027624309392265192	0	0.0	0	0.0	C	12.10	1.837639	0.32513	0.079891	1.16E-4	ENSG00000132016	ENST00000454313;ENST00000346736	T;T	0.38401	1.14;1.14	4.12	-1.78	0.07957	.	1.528260	0.04542	N	0.388298	T	0.00300	0.0009	N	0.19112	0.55	0.09310	N	1	P	0.42620	0.785	B	0.37346	0.247	T	0.06661	-1.0814	10	0.56958	D	0.05	0.0377	4.2284	0.10590	0.0:0.4118:0.1831:0.4051	rs58722011	31	Q0VDD7-2	.	Y	31	ENSP00000404382:D31Y;ENSP00000254336:D31Y	ENSP00000254336:D31Y	D	-	1	0	C19orf57	13867300	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.800000	0.04555	-0.166000	0.10890	-0.743000	0.03520	GAC	C|0.974;A|0.026	0.026	strong		0.547	C19orf57-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000457947.1	NM_024323		A	14006300	C	A	14006300	3	1	22	1	0	0	0	0	1	0	0	0	1941	855	30	4	1846	4	C19orf57	19	14006300	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	130847	14006300	45122683	3809	6710											
PODNL1	79883	hgsc.bcm.edu	37	chr19	14043843	14043843	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcgcagggcacgcaaccggCggaaggcccggtggtgcaca	8	3	17	13	5	0	0	0	0	0	0	0	1	0	1	2	6	3	4	2	6	2	0	rs80103045	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14043843C>T	ENST00000339560.5	-	8	1487	c.1214G>A	c.(1213-1215)cGc>cAc	p.R405H	PODNL1_ENST00000538517.2_Missense_Mutation_p.R314H|PODNL1_ENST00000254320.3_Missense_Mutation_p.R323H|PODNL1_ENST00000538371.2_Missense_Mutation_p.R403H	NM_024825.3	NP_079101.3	Q6PEZ8	PONL1_HUMAN	podocan-like 1	405	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)			ACGCAACCGGCGGAAGGCCCG	0.711													C|||	153	0.0305511	0.1074	0.0029	5008	,	,		15309	0.0		0.001	False		,,,				2504	0.0082				p.R405H		Atlas-SNP	.											.	PODNL1	27	.	0			c.G1214A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG	318,3856		6,306,1775	6	7	7		1208,941,1214	3.8	0.9	19	dbSNP_131	7	17,8171		0,17,4077	yes	missense,missense,missense	PODNL1	NM_001146254.1,NM_001146255.1,NM_024825.3	29,29,29	6,323,5852	TT,TC,CC		0.2076,7.6186,2.7099	probably-damaging,probably-damaging,probably-damaging	403/511,314/422,405/513	14043843	335,12027	2087	4094	6181	SO:0001583	missense	79883	exon8			AACCGGCGGAAGG	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.1214G>A	19.37:g.14043843C>T	ENSP00000345175:p.Arg405His	4	0	0		4	4	1	NM_024825	B7Z564|Q9H5G9	Missense_Mutation	SNP	ENST00000339560.5	37	CCDS12300.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	C	13.68	2.309090	0.40895	0.076186	0.002076	ENSG00000132000	ENST00000538371;ENST00000538517;ENST00000339560;ENST00000545071;ENST00000254320	T;T;T;T	0.57436	0.4;0.4;0.4;0.4	4.79	3.76	0.43208	.	0.451987	0.18547	N	0.138005	T	0.02267	0.0070	N	0.16066	0.365	0.26971	N	0.965586	B;B;B;B	0.29037	0.046;0.231;0.113;0.224	B;B;B;B	0.33690	0.046;0.115;0.052;0.168	T	0.04400	-1.0954	10	0.51188	T	0.08	.	10.0503	0.42212	0.0:0.9024:0.0:0.0976	.	403;323;314;405	F5H7F9;B7Z3M0;G3V1J6;Q6PEZ8	.;.;.;PONL1_HUMAN	H	403;314;405;255;323	ENSP00000442553:R403H;ENSP00000440080:R314H;ENSP00000345175:R405H;ENSP00000254320:R323H	ENSP00000254320:R323H	R	-	2	0	PODNL1	13904843	0.997000	0.39634	0.903000	0.35520	0.313000	0.28021	2.510000	0.45468	1.015000	0.39444	0.453000	0.30009	CGC	C|0.980;T|0.020	0.020	strong		0.711	PODNL1-003	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457967.1	NM_024825		T	14043843	C	T	14043843	3	4	22	1	0	0	0	0	1	0	0	0	12188	768	27	1	328	1	PODNL1	19	14043843	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	37543	14043843	45085140	3810	6711											
DCAF15	90379	hgsc.bcm.edu	37	chr19	14066772	14066772	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggagatctacagcgacctgTacctgaccgtatgcgagtgg	10	8	13	10	3	1	2	0	1	1	1	1	5	1	2	3	2	4	2	3	2	3	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14066772T>C	ENST00000254337.6	+	4	436	c.415T>C	c.(415-417)Tac>Cac	p.Y139H	PODNL1_ENST00000538517.2_5'Flank|PODNL1_ENST00000588317.1_5'Flank|PODNL1_ENST00000538371.2_5'Flank	NM_138353.2	NP_612362.2	Q66K64	DCA15_HUMAN	DDB1 and CUL4 associated factor 15	139					protein ubiquitination (GO:0016567)					breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)	11						CAGCGACCTGTACCTGACCGT	0.642																																					p.Y139H		Atlas-SNP	.											.	DCAF15	30	.	0			c.T415C						PASS	.						110	101	104					19																	14066772		2203	4300	6503	SO:0001583	missense	90379	exon4			GACCTGTACCTGA	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.415T>C	19.37:g.14066772T>C	ENSP00000254337:p.Tyr139His	87	0	0		113	5	0.0442478	NM_138353	B3KS86|Q96DW0|Q9BU31	Missense_Mutation	SNP	ENST00000254337.6	37	CCDS32926.1	.	.	.	.	.	.	.	.	.	.	t	13.68	2.309631	0.40895	.	.	ENSG00000132017	ENST00000254337	.	.	.	4.02	4.02	0.46733	.	0.000000	0.64402	D	0.000006	T	0.40247	0.1109	L	0.43152	1.355	0.47276	D	0.999373	P	0.42456	0.78	B	0.35353	0.201	T	0.28522	-1.0041	9	0.28530	T	0.3	-18.254	12.2557	0.54623	0.0:0.0:0.0:1.0	.	139	Q66K64	DCA15_HUMAN	H	139	.	ENSP00000254337:Y139H	Y	+	1	0	DCAF15	13927772	1.000000	0.71417	1.000000	0.80357	0.385000	0.30292	7.528000	0.81941	1.610000	0.50200	0.459000	0.35465	TAC	.	.	none		0.642	DCAF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458099.1	NM_138353		C	14066772	T	C	14066772	3	2	22	1	0	0	0	0	1	0	0	0	4269	1638	57	3	429	3	DCAF15	19	14066772	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	22929	14066772	45062211	3811	6712											
PRKACA	5566	hgsc.bcm.edu	37	chr19	14204527	14204527	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccattcttgaggttcccaaaGcgcttggtgagatctacctg	8	12	10	11	1	2	2	0	2	2	1	3	3	3	2	3	2	2	2	3	2	2	5	rs3729858	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14204527G>C	ENST00000308677.4	-	9	1039	c.843C>G	c.(841-843)cgC>cgG	p.R281R	PRKACA_ENST00000590853.1_Intron|PRKACA_ENST00000589994.1_Silent_p.R273R|PRKACA_ENST00000350356.3_5'UTR|SAMD1_ENST00000541938.1_5'Flank	NM_002730.3	NP_002721.1	P17612	KAPCA_HUMAN	protein kinase, cAMP-dependent, catalytic, alpha	281	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						GGTTCCCAAAGCGCTTGGTGA	0.547													G|||	29	0.00579073	0.0219	0.0	5008	,	,		20834	0.0		0.0	False		,,,				2504	0.0				p.R281R		Atlas-SNP	.											.	PRKACA	65	.	0			c.C843G						PASS	.	G	,	80,4326	69.2+/-107.0	1,78,2124	142	126	131		843,819	5.2	1	19	dbSNP_107	131	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PRKACA	NM_002730.3,NM_207518.1	,	1,78,6424	CC,CG,GG		0.0,1.8157,0.6151	,	281/352,273/344	14204527	80,12926	2203	4300	6503	SO:0001819	synonymous_variant	5566	exon9			CCCAAAGCGCTTG		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.843C>G	19.37:g.14204527G>C		179	0	0		165	85	0.515152	NM_002730	Q32P54|Q9H2Y0|Q9NRB4|Q9NRH9	Silent	SNP	ENST00000308677.4	37	CCDS12304.1																																																																																			G|0.995;C|0.005	0.005	strong		0.547	PRKACA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459004.1	NM_002730		C	14204527	G	C	14204527	2	2	22	1	0	0	0	0	0	0	0	1	12509	958	34	4		4	PRKACA	19	14204527	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	137755	14204527	44924456	3812	6713											
EMR3	84658	hgsc.bcm.edu	37	chr19	14740942	14740942	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggccatgacctgggcagctGgacccacctgtagcaagccc	9	5	12	15	0	0	1	0	1	0	0	0	2	0	2	5	3	3	4	5	3	2	1	rs78700925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14740942G>A	ENST00000253673.5	-	14	1821	c.1721C>T	c.(1720-1722)cCa>cTa	p.P574L	EMR3_ENST00000599900.1_Missense_Mutation_p.P359L|EMR3_ENST00000344373.4_Missense_Mutation_p.P522L|EMR3_ENST00000443157.2_Missense_Mutation_p.P448L	NM_032571.3	NP_115960.2	Q9BY15	EMR3_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 3	574					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						CTGGGCAGCTGGACCCACCTG	0.542													G|||	94	0.01877	0.0688	0.0043	5008	,	,		14251	0.0		0.0	False		,,,				2504	0.0				p.P574L		Atlas-SNP	.											.	EMR3	99	.	0			c.C1721T						PASS	.	G	LEU/PRO	203,4203	126.6+/-163.6	4,195,2004	109	92	98		1721	2.7	0	19	dbSNP_131	98	1,8599	1.2+/-3.3	0,1,4299	yes	missense	EMR3	NM_032571.3	98	4,196,6303	AA,AG,GG		0.0116,4.6074,1.5685	possibly-damaging	574/653	14740942	204,12802	2203	4300	6503	SO:0001583	missense	84658	exon14			GCAGCTGGACCCA	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.1721C>T	19.37:g.14740942G>A	ENSP00000253673:p.Pro574Leu	126	0	0		117	56	0.478632	NM_032571		Missense_Mutation	SNP	ENST00000253673.5	37	CCDS12315.1	29	0.013278388278388278	29	0.05894308943089431	0	0.0	0	0.0	0	0.0	G	10.10	1.256668	0.22965	0.046074	1.16E-4	ENSG00000131355	ENST00000443157;ENST00000253673;ENST00000344373	T;T;T	0.41065	1.03;1.01;1.01	3.76	2.72	0.32119	GPCR, family 2-like (1);	.	.	.	.	T	0.19805	0.0476	M	0.88570	2.965	0.20489	N	0.999896	D;D;D	0.89917	1.0;1.0;0.992	D;D;D	0.87578	0.996;0.998;0.968	T	0.17319	-1.0373	9	0.87932	D	0	.	9.204	0.37278	0.1094:0.0:0.8906:0.0	.	448;522;574	E7EW83;Q9BY15-2;Q9BY15	.;.;EMR3_HUMAN	L	448;574;522	ENSP00000396208:P448L;ENSP00000253673:P574L;ENSP00000340758:P522L	ENSP00000253673:P574L	P	-	2	0	EMR3	14601942	0.037000	0.19845	0.031000	0.17742	0.029000	0.11900	2.165000	0.42396	0.923000	0.37045	-0.136000	0.14681	CCA	G|0.984;A|0.016	0.016	strong		0.542	EMR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466488.1	NM_032571		A	14740942	G	A	14740942	3	1	22	1	0	0	0	0	1	0	0	0	5108	1348	47	2	249	2	EMR3	19	14740942	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	536415	14740942	44388041	3813	6714											
OR7C1	26664	hgsc.bcm.edu	37	chr19	14910900	14910900	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatctctgacgttgctgaaaAtcccaggaggagaaattctt	13	11	9	8	1	2	3	0	2	2	1	4	5	3	4	1	2	1	2	1	2	4	3	rs149561973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14910900A>T	ENST00000248073.2	-	1	123	c.49T>A	c.(49-51)Ttt>Att	p.F17I	OR7A5_ENST00000601611.1_Intron	NM_198944.1	NP_945182.1	O76099	OR7C1_HUMAN	olfactory receptor, family 7, subfamily C, member 1	17					spermatogenesis (GO:0007283)	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)|large_intestine(8)|lung(2)|ovary(2)|prostate(1)	18						GTTGCTGAAAATCCCAGGAGG	0.438													.|||	27	0.00539137	0.0204	0.0	5008	,	,		18932	0.0		0.0	False		,,,				2504	0.0				p.F17I		Atlas-SNP	.											.	OR7C1	58	.	0			c.T49A						PASS	.	A	ILE/PHE	29,4371		0,29,2171	94	90	91		49	2.6	0.9	19	dbSNP_134	91	0,8592		0,0,4296	yes	missense	OR7C1	NM_198944.1	21	0,29,6467	TT,TA,AA		0.0,0.6591,0.2232	possibly-damaging	17/321	14910900	29,12963	2200	4296	6496	SO:0001583	missense	26664	exon1			CTGAAAATCCCAG	X89676	CCDS12317.1	19p13.1	2012-08-09						"GPCR / Class A : Olfactory receptors"	8373	protein-coding gene	gene with protein product				OR7C4			Standard	NM_198944		Approved	OR19-5	uc010xnz.2	O76099		ENST00000248073.2:c.49T>A	19.37:g.14910900A>T	ENSP00000248073:p.Phe17Ile	68	0	0		61	31	0.508197	NM_198944	Q15621|Q6IFP2|Q96R94	Missense_Mutation	SNP	ENST00000248073.2	37	CCDS12317.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	a	13.45	2.240147	0.39598	0.006591	0.0	ENSG00000127530	ENST00000248073	T	0.06608	3.28	3.67	2.6	0.31112	.	0.214512	0.23239	U	0.050361	T	0.01870	0.0059	L	0.50919	1.6	0.24836	N	0.992496	P	0.41748	0.761	B	0.37267	0.245	T	0.28170	-1.0052	10	0.54805	T	0.06	.	7.5523	0.27804	0.8084:0.0:0.0:0.1915	.	17	O76099	OR7C1_HUMAN	I	17	ENSP00000248073:F17I	ENSP00000248073:F17I	F	-	1	0	OR7C1	14771900	0.001000	0.12720	0.913000	0.36048	0.090000	0.18270	-0.216000	0.09266	0.552000	0.29026	0.433000	0.28618	TTT	A|0.994;T|0.006	0.006	strong		0.438	OR7C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466519.1			T	14910900	A	T	14910900	3	4	22	1	0	0	0	0	1	0	0	0	11226	101	4	5	915	5	OR7C1	19	14910900	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	169958	14910900	44218083	3814	6715											
OR7A10	390892	hgsc.bcm.edu	37	chr19	14952189	14952189	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atttccatgtgtgtacaaaaGggcagtggcaacaccattaa	14	10	9	8	0	0	0	0	0	0	0	1	0	1	0	2	2	2	3	2	2	5	3	rs114596415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14952189G>T	ENST00000248058.1	-	1	500	c.501C>A	c.(499-501)ccC>ccA	p.P167P		NM_001005190.1	NP_001005190.1	O76100	OR7AA_HUMAN	olfactory receptor, family 7, subfamily A, member 10	167						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)					GTGTACAAAAGGGCAGTGGCA	0.418													.|||	115	0.0229633	0.0832	0.0058	5008	,	,		22672	0.0		0.001	False		,,,				2504	0.0				p.P167P		Atlas-SNP	.											OR7A10,NS,carcinoma,-2,1	OR7A10	33	1	0			c.C501A						PASS	.	G		235,4171	137.7+/-173.5	8,219,1976	81	79	80		501	-4.2	0	19	dbSNP_132	80	1,8599		0,1,4299	no	coding-synonymous	OR7A10	NM_001005190.1		8,220,6275	TT,TG,GG		0.0116,5.3336,1.8145		167/310	14952189	236,12770	2203	4300	6503	SO:0001819	synonymous_variant	390892	exon1			ACAAAAGGGCAGT		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.501C>A	19.37:g.14952189G>T		137	0	0		152	74	0.486842	NM_001005190	Q6IFP0|Q96R97	Silent	SNP	ENST00000248058.1	37	CCDS32936.1																																																																																			G|0.980;T|0.020	0.020	strong		0.418	OR7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466520.1	NM_001005190		T	14952189	G	T	14952189	2	4	22	1	0	0	0	0	0	0	0	1	11223	987	35	4		4	OR7A10	19	14952189	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	41289	14952189	44176794	3815	6716											
CCDC105	126402	hgsc.bcm.edu	37	chr19	15122104	15122104	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgggtgcgacagctgctgcGccagcgcgaggtcaccgacc	6	4	16	15	6	1	0	1	0	0	0	1	3	1	0	3	2	5	2	3	2	0	0	rs199904661	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15122104G>T	ENST00000292574.3	+	1	549	c.467G>T	c.(466-468)cGc>cTc	p.R156L	SLC1A6_ENST00000430939.2_5'Flank	NM_173482.2	NP_775753.2	Q8IYK2	CC105_HUMAN	coiled-coil domain containing 105	156						extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(4)|skin(2)	23						CAGCTGCTGCGCCAGCGCGAG	0.692													G|||	66	0.0131789	0.0469	0.0058	5008	,	,		14563	0.0		0.0	False		,,,				2504	0.0				p.R156L		Atlas-SNP	.											.	CCDC105	53	.	0			c.G467T						PASS	.	G	LEU/ARG	163,3785		3,157,1814	7	8	7		467	2.8	1	19	dbSNP_134	7	3,8257		0,3,4127	yes	missense	CCDC105	NM_173482.2	102	3,160,5941	TT,TG,GG		0.0363,4.1287,1.3598	probably-damaging	156/500	15122104	166,12042	1974	4130	6104	SO:0001583	missense	126402	exon1			TGCTGCGCCAGCG	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.467G>T	19.37:g.15122104G>T	ENSP00000292574:p.Arg156Leu	43	0	0		44	30	0.681818	NM_173482	Q8N7T5|Q8NDL5	Missense_Mutation	SNP	ENST00000292574.3	37	CCDS12322.1	15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	G	17.67	3.446054	0.63178	0.041287	3.63E-4	ENSG00000160994	ENST00000292574	T	0.02579	4.24	3.82	2.78	0.32641	.	0.117336	0.34603	N	0.003821	T	0.01765	0.0056	M	0.67953	2.075	0.25682	N	0.985784	D	0.69078	0.997	D	0.63957	0.92	T	0.05517	-1.0880	10	0.49607	T	0.09	-17.7965	6.322	0.21223	0.1376:0.0:0.8624:0.0	.	156	Q8IYK2	CC105_HUMAN	L	156	ENSP00000292574:R156L	ENSP00000292574:R156L	R	+	2	0	CCDC105	14983104	0.402000	0.25311	0.998000	0.56505	0.645000	0.38454	1.363000	0.34159	1.678000	0.50952	0.462000	0.41574	CGC	G|0.993;T|0.007	0.007	strong		0.692	CCDC105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466293.1	NM_173482		T	15122104	G	T	15122104	3	4	22	1	0	0	0	0	1	0	0	0	2742	1087	38	4	469	4	CCDC105	19	15122104	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	169915	15122104	44006879	3816	6717											
BRD4	23476	hgsc.bcm.edu	37	chr19	15355540	15355540	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ccttcttctgctccctcccgGggtgccccttcttttttgac	1	16	7	17	1	3	1	0	1	3	0	5	1	5	1	5	2	2	1	5	2	0	6	rs149185763	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15355540G>A	ENST00000263377.2	-	12	2413	c.2192C>T	c.(2191-2193)cCc>cTc	p.P731L		NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	731					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)			CTCCCTCCCGGGGTGCCCCTT	0.582			T	C15orf55	lethal midline carcinoma of young people								G|||	13	0.00259585	0.0098	0.0	5008	,	,		13894	0.0		0.0	False		,,,				2504	0.0				p.P731L		Atlas-SNP	.		Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	.	BRD4	172	.	0			c.C2192T						PASS	.	G	LEU/PRO	16,4390	23.3+/-48.9	0,16,2187	144	141	142		2192	3.4	0.8	19	dbSNP_134	142	0,8600		0,0,4300	yes	missense	BRD4	NM_058243.2	98	0,16,6487	AA,AG,GG		0.0,0.3631,0.123	probably-damaging	731/1363	15355540	16,12990	2203	4300	6503	SO:0001583	missense	23476	exon12			CTCCCGGGGTGCC	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.2192C>T	19.37:g.15355540G>A	ENSP00000263377:p.Pro731Leu	107	0	0		142	71	0.5	NM_058243	O60433|Q4G0X8|Q86YS8|Q96PD3	Missense_Mutation	SNP	ENST00000263377.2	37	CCDS12328.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	14.84	2.654846	0.47467	0.003631	0.0	ENSG00000141867	ENST00000263377	T	0.07216	3.21	4.48	3.43	0.39272	.	1.004540	0.08020	N	0.991771	T	0.08980	0.0222	L	0.36672	1.1	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.07751	-1.0756	10	0.42905	T	0.14	-1.3945	10.1453	0.42760	0.1003:0.0:0.8997:0.0	.	731	O60885	BRD4_HUMAN	L	731	ENSP00000263377:P731L	ENSP00000263377:P731L	P	-	2	0	BRD4	15216540	1.000000	0.71417	0.803000	0.32268	0.934000	0.57294	6.710000	0.74670	0.868000	0.35678	0.561000	0.74099	CCC	A|0.001;G|0.999	0.001	strong		0.582	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243		A	15355540	G	A	15355540	3	1	22	1	0	0	0	0	1	0	0	0	1506	1232	43	2	1932	2	BRD4	19	15355540	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	233436	15355540	43773443	3817	6718											
AKAP8L	26993	hgsc.bcm.edu	37	chr19	15512393	15512393	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcaggacggccctcgagtcGcaggactcataagagtcata	11	7	11	12	3	3	1	3	0	0	1	5	4	3	3	1	3	0	1	1	3	2	2	rs61739315	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15512393G>A	ENST00000397410.5	-	5	514	c.384C>T	c.(382-384)tgC>tgT	p.C128C	AKAP8L_ENST00000595879.1_5'Flank|AKAP8L_ENST00000595465.2_Silent_p.C67C	NM_014371.2	NP_055186.2	Q9ULX6	AKP8L_HUMAN	A kinase (PRKA) anchor protein 8-like	128						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						CCCTCGAGTCGCAGGACTCAT	0.597													G|||	43	0.00858626	0.0295	0.0058	5008	,	,		17723	0.0		0.0	False		,,,				2504	0.0				p.C128C		Atlas-SNP	.											.	AKAP8L	64	.	0			c.C384T						PASS	.	G		118,4112		2,114,1999	29	28	29		384	2.4	1	19	dbSNP_129	29	2,8440		0,2,4219	no	coding-synonymous	AKAP8L	NM_014371.2		2,116,6218	AA,AG,GG		0.0237,2.7896,0.947		128/647	15512393	120,12552	2115	4221	6336	SO:0001819	synonymous_variant	26993	exon5			CGAGTCGCAGGAC	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.384C>T	19.37:g.15512393G>A		42	0	0		48	19	0.395833	NM_014371	B4DJ74|B5BU90|O94792|Q96J58|Q9NRQ0|Q9UGM0	Silent	SNP	ENST00000397410.5	37	CCDS46005.1																																																																																			G|0.991;A|0.009	0.009	strong		0.597	AKAP8L-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461301.2	NM_014371		A	15512393	G	A	15512393	2	1	22	1	0	0	0	0	0	0	0	1	458	1079	38	1		1	AKAP8L	19	15512393	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	156853	15512393	43616590	3818	6719											
PGLYRP2	114770	hgsc.bcm.edu	37	chr19	15580694	15580694	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtgtgggcgcccacccagtGccagccgcgtccctcgtaca	5	6	12	18	5	0	0	0	0	0	0	2	0	1	0	5	1	3	1	5	1	1	1	rs61734899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15580694G>A	ENST00000340880.4	-	4	1870	c.1390C>T	c.(1390-1392)Cac>Tac	p.H464Y	PGLYRP2_ENST00000292609.4_Missense_Mutation_p.H464Y	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	464					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						CCCACCCAGTGCCAGCCGCGT	0.716													G|||	124	0.0247604	0.0484	0.0058	5008	,	,		13687	0.006		0.008	False		,,,				2504	0.0429				p.H464Y		Atlas-SNP	.											.	PGLYRP2	116	.	0			c.C1390T						PASS	.	G	TYR/HIS	161,4189		2,157,2016	11	15	14		1390	2.9	1	19	dbSNP_129	14	65,8451		0,65,4193	yes	missense	PGLYRP2	NM_052890.3	83	2,222,6209	AA,AG,GG		0.7633,3.7011,1.7566	benign	464/577	15580694	226,12640	2175	4258	6433	SO:0001583	missense	114770	exon4			CCCAGTGCCAGCC	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.1390C>T	19.37:g.15580694G>A	ENSP00000345968:p.His464Tyr	71	0	0		61	24	0.393443	NM_052890	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Missense_Mutation	SNP	ENST00000340880.4	37	CCDS12330.2	34	0.015567765567765568	21	0.042682926829268296	3	0.008287292817679558	2	0.0034965034965034965	8	0.010554089709762533	G	12.80	2.046263	0.36085	0.037011	0.007633	ENSG00000161031	ENST00000340880;ENST00000292609	T;T	0.17213	2.29;2.29	5.04	2.91	0.33838	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (4);	0.380248	0.27554	N	0.018848	T	0.03564	0.0102	M	0.66378	2.025	0.35512	D	0.80071	B;B	0.09022	0.001;0.002	B;B	0.13407	0.008;0.009	T	0.08249	-1.0731	10	0.35671	T	0.21	-13.9263	4.8686	0.13620	0.1811:0.0:0.6507:0.1682	.	464;464	Q96PD5-2;Q96PD5	.;PGRP2_HUMAN	Y	464	ENSP00000345968:H464Y;ENSP00000292609:H464Y	ENSP00000292609:H464Y	H	-	1	0	PGLYRP2	15441694	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	0.700000	0.25601	0.540000	0.28808	-0.448000	0.05591	CAC	G|0.983;A|0.017	0.017	strong		0.716	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890		A	15580694	G	A	15580694	3	1	22	1	0	0	0	0	1	0	0	0	11803	1319	46	2	348	2	PGLYRP2	19	15580694	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	68301	15580694	43548289	3819	6720											
PGLYRP2	114770	hgsc.bcm.edu	37	chr19	15587067	15587067	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgctgtccaagggcaaattTatgaccctgcgcccttgcag	9	10	10	12	1	0	1	0	1	0	0	1	1	1	1	3	1	3	3	3	1	3	3	rs35927052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15587067T>A	ENST00000340880.4	-	2	894	c.414A>T	c.(412-414)atA>atT	p.I138I	PGLYRP2_ENST00000292609.4_Silent_p.I138I	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	138					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						AGGGCAAATTTATGACCCTGC	0.607													T|||	123	0.0245607	0.0477	0.0058	5008	,	,		18627	0.006		0.008	False		,,,				2504	0.0429				p.I138I		Atlas-SNP	.											.	PGLYRP2	116	.	0			c.A414T						PASS	.	T		193,4213	121.7+/-159.2	3,187,2013	85	77	79		414	-9.2	0	19	dbSNP_126	79	75,8525	44.9+/-103.4	0,75,4225	no	coding-synonymous	PGLYRP2	NM_052890.3		3,262,6238	AA,AT,TT		0.8721,4.3804,2.0606		138/577	15587067	268,12738	2203	4300	6503	SO:0001819	synonymous_variant	114770	exon2			CAAATTTATGACC	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.414A>T	19.37:g.15587067T>A		116	0	0		109	59	0.541284	NM_052890	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Silent	SNP	ENST00000340880.4	37	CCDS12330.2																																																																																			T|0.981;A|0.019	0.019	strong		0.607	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890		A	15587067	T	A	15587067	2	1	22	1	0	0	0	0	0	0	0	1	11803	1744	61	5		5	PGLYRP2	19	15587067	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	6373	15587067	43541916	3820	6721											
PGLYRP2	114770	hgsc.bcm.edu	37	chr19	15587103	15587103	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagccctgcctccagcccCgccagcagaggctccacagc	7	4	10	20	1	0	1	0	0	0	1	2	1	2	1	7	1	6	3	7	1	0	0	rs35973013	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15587103C>T	ENST00000340880.4	-	2	858	c.378G>A	c.(376-378)gcG>gcA	p.A126A	PGLYRP2_ENST00000292609.4_Silent_p.A126A	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	126					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						CCTCCAGCCCCGCCAGCAGAG	0.607													C|||	123	0.0245607	0.0477	0.0058	5008	,	,		19723	0.006		0.008	False		,,,				2504	0.0429				p.A126A		Atlas-SNP	.											.	PGLYRP2	116	.	0			c.G378A						PASS	.	C		193,4213	120.4+/-158.0	3,187,2013	100	86	91		378	-10.3	0.1	19	dbSNP_126	91	75,8525	44.0+/-102.2	0,75,4225	no	coding-synonymous	PGLYRP2	NM_052890.3		3,262,6238	TT,TC,CC		0.8721,4.3804,2.0606		126/577	15587103	268,12738	2203	4300	6503	SO:0001819	synonymous_variant	114770	exon2			CAGCCCCGCCAGC	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.378G>A	19.37:g.15587103C>T		125	0	0		136	76	0.558824	NM_052890	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Silent	SNP	ENST00000340880.4	37	CCDS12330.2																																																																																			C|0.981;T|0.019	0.019	strong		0.607	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890		T	15587103	C	T	15587103	2	4	22	1	0	0	0	0	0	0	0	1	11803	639	23	1		1	PGLYRP2	19	15587103	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	36	15587103	43541880	3821	6722											
CYP4F12	66002	hgsc.bcm.edu	37	chr19	15791066	15791066	+	Missense_Mutation	SNP	C	C	T																															catgtcagctgccattgcacCcaaggataatctcttcatca																								rs61731193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15791066C>T	ENST00000550308.1	+	4	736	c.356C>T	c.(355-357)cCc>cTc	p.P119L	CYP4F12_ENST00000324632.10_Missense_Mutation_p.P119L	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	119					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)	GCCATTGCACCCAAGGATAAT	0.567													.|||	103	0.0205671	0.0734	0.0072	5008	,	,		20736	0.0		0.001	False		,,,				2504	0.0				p.P119L		Atlas-SNP	.											.	CYP4F12	89	.	0			c.C356T						PASS	.	T	LEU/PRO	247,4133		2,243,1945	143	146	145		356	-1.3	0	19	dbSNP_129	145	3,8579		0,3,4288	yes	missense	CYP4F12	NM_023944.3	98	2,246,6233	TT,TC,CC		0.035,5.6393,1.9287	possibly-damaging	119/525	15791066	250,12712	2190	4291	6481	SO:0001583	missense	66002	exon4			TTGCACCCAAGGA	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.356C>T	19.37:g.15791066C>T	ENSP00000448998:p.Pro119Leu	254	0	0		355	89	0.250704	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	40	0.018315018315018316	37	0.07520325203252033	3	0.008287292817679558	0	0.0	0	0.0	.	7.772	0.707735	0.15239	0.056393	3.5E-4	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.69175	-0.38;-0.38	2.36	-1.32	0.09201	.	0.825497	0.10255	N	0.696720	T	0.07863	0.0197	L	0.59912	1.85	0.09310	N	1	B;B;B	0.26512	0.151;0.046;0.014	B;B;B	0.36766	0.232;0.168;0.098	T	0.46857	-0.9161	10	0.52906	T	0.07	.	5.4101	0.16344	0.0:0.5515:0.0:0.4485	rs61731193	119;119;119	B4E2R2;B4E270;Q9HCS2	.;.;CP4FC_HUMAN	L	119	ENSP00000448998:P119L;ENSP00000321821:P119L	ENSP00000321821:P119L	P	+	2	0	CYP4F12	15652066	0.000000	0.05858	0.003000	0.11579	0.000000	0.00434	-0.870000	0.04228	-0.186000	0.10533	-1.139000	0.01908	CCC	C|0.988;T|0.012	0.012	strong		0.567	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9			T	15791066	C	T	15791066	3	4	22	1	0	0	0	0	1	0	0	0	4189	623	22	2	366	2	CYP4F12	19	15791066	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	203963	15791066	43337917	3822	6723	83	3	10	33	7640638	13	9	4874	N	T_G_C_A	8.154492e-07
CYP4F12	66002	hgsc.bcm.edu	37	chr19	15791074	15791074	+	Missense_Mutation	SNP	A	A	G																															ctgccattgcacccaaggatAatctcttcatcaggttcctg																								rs114254919	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15791074A>G	ENST00000550308.1	+	4	744	c.364A>G	c.(364-366)Aat>Gat	p.N122D	CYP4F12_ENST00000324632.10_Missense_Mutation_p.N122D	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	122					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)	ACCCAAGGATAATCTCTTCAT	0.567													.|||	103	0.0205671	0.0734	0.0072	5008	,	,		20731	0.0		0.001	False		,,,				2504	0.0				p.N122D		Atlas-SNP	.											CYP4F12,colon,carcinoma,-1,1	CYP4F12	89	1	0			c.A364G						PASS	.	G	ASP/ASN	190,4188		1,188,2000	139	143	142		364	-5.8	0	19	dbSNP_132	142	3,8585		0,3,4291	yes	missense	CYP4F12	NM_023944.3	23	1,191,6291	GG,GA,AA		0.0349,4.3399,1.4885	benign	122/525	15791074	193,12773	2189	4294	6483	SO:0001583	missense	66002	exon4			AAGGATAATCTCT	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.364A>G	19.37:g.15791074A>G	ENSP00000448998:p.Asn122Asp	266	0	0		372	95	0.255376	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	38	0.0173992673992674	35	0.07113821138211382	3	0.008287292817679558	0	0.0	0	0.0	.	1.398	-0.578943	0.03854	0.043399	3.49E-4	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.78707	-1.2;-1.2	2.92	-5.84	0.02318	.	1.494030	0.04917	N	0.454288	T	0.07458	0.0188	N	0.16567	0.415	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	0.22836	-1.0205	10	0.11794	T	0.64	.	1.4308	0.02333	0.4684:0.1455:0.2397:0.1465	.	122;122;122	B4E2R2;B4E270;Q9HCS2	.;.;CP4FC_HUMAN	D	122	ENSP00000448998:N122D;ENSP00000321821:N122D	ENSP00000321821:N122D	N	+	1	0	CYP4F12	15652074	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.894000	0.00707	-2.136000	0.00810	-1.140000	0.01884	AAT	A|0.989;G|0.011	0.011	strong		0.567	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9			G	15791074	A	G	15791074	3	3	22	1	0	0	0	0	1	0	0	0	4189	362	13	3	374	3	CYP4F12	19	15791074	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	8	15791074	43337909	3823	6724	83	3	10	33	7640638	13	9	4874	N	T_G_C_A	8.154492e-07
CYP4F12	66002	hgsc.bcm.edu	37	chr19	15791081	15791081	+	Missense_Mutation	SNP	T	T	C																															tgcacccaaggataatctctTcatcaggttcctgaagccct																								rs146740964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15791081T>C	ENST00000550308.1	+	4	751	c.371T>C	c.(370-372)tTc>tCc	p.F124S	CYP4F12_ENST00000324632.10_Missense_Mutation_p.F124S	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	124					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)	GATAATCTCTTCATCAGGTTC	0.572													.|||	103	0.0205671	0.0734	0.0072	5008	,	,		20653	0.0		0.001	False		,,,				2504	0.0				p.F124S		Atlas-SNP	.											.	CYP4F12	89	.	0			c.T371C						PASS	.	C	SER/PHE	125,4253		1,123,2065	133	138	136		371	-1	0	19	dbSNP_134	136	2,8586		0,2,4292	yes	missense	CYP4F12	NM_023944.3	155	1,125,6357	CC,CT,TT		0.0233,2.8552,0.9795	benign	124/525	15791081	127,12839	2189	4294	6483	SO:0001583	missense	66002	exon4			ATCTCTTCATCAG	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.371T>C	19.37:g.15791081T>C	ENSP00000448998:p.Phe124Ser	264	0	0		374	93	0.248663	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	37	0.01694139194139194	34	0.06910569105691057	3	0.008287292817679558	0	0.0	0	0.0	.	3.728	-0.056179	0.07362	0.028552	2.33E-4	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.70516	-0.49;-0.49	2.92	-1.0	0.10196	.	0.280349	0.26467	N	0.024209	T	0.08133	0.0203	N	0.17872	0.535	0.09310	N	1	B;P;B	0.34522	0.432;0.455;0.004	B;P;B	0.44811	0.344;0.461;0.091	T	0.20140	-1.0284	10	0.30078	T	0.28	.	4.0942	0.09983	0.1789:0.1265:0.0:0.6945	.	124;124;124	B4E2R2;B4E270;Q9HCS2	.;.;CP4FC_HUMAN	S	124	ENSP00000448998:F124S;ENSP00000321821:F124S	ENSP00000321821:F124S	F	+	2	0	CYP4F12	15652081	0.049000	0.20398	0.004000	0.12327	0.000000	0.00434	0.065000	0.14466	-0.503000	0.06586	-3.688000	0.00024	TTC	T|0.989;C|0.011	0.011	strong		0.572	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9			C	15791081	T	C	15791081	3	2	22	1	0	0	0	0	1	0	0	0	4189	1783	62	3	381	3	CYP4F12	19	15791081	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	7	15791081	43337902	3824	6725	83	3	10	33	7640638	13	9	4874	N	T_G_C_A	8.154492e-07
CYP4F12	66002	hgsc.bcm.edu	37	chr19	15791212	15791212	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gccctactaggagaagggatActgctgagtggcggtgacaa	11	7	15	8	1	0	3	0	2	0	1	0	5	0	4	1	4	3	1	1	4	5	3	rs386807228|rs142773675	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15791212A>C	ENST00000550308.1	+	5	788	c.408A>C	c.(406-408)atA>atC	p.I136I	CYP4F12_ENST00000324632.10_Silent_p.I136I	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	136					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)	GAGAAGGGATACTGCTGAGTG	0.567													.|||	100	0.0199681	0.0711	0.0072	5008	,	,		19609	0.0		0.001	False		,,,				2504	0.0				p.I136I		Atlas-SNP	.											.	CYP4F12	89	.	0			c.A408C						PASS	.						30	35	33					19																	15791212		2202	4298	6500	SO:0001819	synonymous_variant	66002	exon5			AGGGATACTGCTG	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.408A>C	19.37:g.15791212A>C		211	0	0		258	48	0.186047	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	37	CCDS42517.1																																																																																			A|0.969;C|0.031	0.031	strong		0.567	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9			C	15791212	A	C	15791212	2	2	22	1	0	0	0	0	0	0	0	1	4189	381	14	5		5	CYP4F12	19	15791212	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	131	15791212	43337771	3825	6726			10	33	7640638	13	9	4874	N	T_G_C_A	8.154492e-07
CYP4F12	66002	hgsc.bcm.edu	37	chr19	15793238	15793238	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctcagagggcagcagttgtCtggacatgtttgagcacatc	9	10	12	10	0	2	2	1	1	1	1	3	3	2	3	1	2	2	5	1	2	0	2	rs144258147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15793238C>T	ENST00000550308.1	+	6	945	c.565C>T	c.(565-567)Ctg>Ttg	p.L189L	CYP4F12_ENST00000324632.10_Silent_p.L189L	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	189					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)	p.L189V(1)		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)	CAGCAGTTGTCTGGACATGTT	0.557													.|||	31	0.0061901	0.0227	0.0	5008	,	,		20398	0.0		0.001	False		,,,				2504	0.0				p.L189L		Atlas-SNP	.											.	CYP4F12	89	.	1	Substitution - Missense(1)	urinary_tract(1)	c.C565T						PASS	.						81	78	79					19																	15793238		2203	4300	6503	SO:0001819	synonymous_variant	66002	exon6			AGTTGTCTGGACA	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.565C>T	19.37:g.15793238C>T		270	0	0		342	74	0.216374	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	37	CCDS42517.1																																																																																			C|0.990;T|0.010	0.010	strong		0.557	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9			T	15793238	C	T	15793238	2	4	22	1	0	0	0	0	0	0	0	1	4189	912	32	2		2	CYP4F12	19	15793238	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2026	15793238	43335745	3826	6727			10	33	7640638	13	9	4874	N	T_G_C_A	8.154492e-07
CYP4F12	66002	hgsc.bcm.edu	37	chr19	15793282	15793282	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcatgaccttggacagtctAcagaaatgcatcttcagctt	11	12	7	11	0	4	2	2	1	2	1	4	3	4	3	1	1	3	2	1	1	2	4	rs35352350		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15793282A>G	ENST00000550308.1	+	6	989	c.609A>G	c.(607-609)ctA>ctG	p.L203L	CYP4F12_ENST00000324632.10_Silent_p.L203L	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	203					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)	TGGACAGTCTACAGAAATGCA	0.527																																					p.L203L		Atlas-SNP	.											.	CYP4F12	89	.	0			c.A609G						PASS	.	G		62,4344		0,62,2141	115	108	111		609	1.3	1	19	dbSNP_126	111	0,8600		0,0,4300	no	coding-synonymous	CYP4F12	NM_023944.3		0,62,6441	GG,GA,AA		0.0,1.4072,0.4767		203/525	15793282	62,12944	2203	4300	6503	SO:0001819	synonymous_variant	66002	exon6			CAGTCTACAGAAA	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.609A>G	19.37:g.15793282A>G		326	0	0		395	56	0.141772	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	37	CCDS42517.1																																																																																			A|0.991;G|0.009	0.009	strong		0.527	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9			G	15793282	A	G	15793282	2	3	22	1	0	0	0	0	0	0	0	1	4189	378	14	3		3	CYP4F12	19	15793282	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	44	15793282	43335701	3827	6728			10	33	7640638	13	9	4874	N	T_G_C_A	8.154492e-07
CYP4F12	66002	hgsc.bcm.edu	37	chr19	15794411	15794411	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtattacctctcccatgaCgggcggcgcttccacagggc	6	9	11	15	3	1	1	0	1	1	0	3	1	2	1	3	3	1	2	3	3	2	3	rs61731191	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15794411C>T	ENST00000550308.1	+	7	1136	c.756C>T	c.(754-756)gaC>gaT	p.D252D	CYP4F12_ENST00000324632.10_Silent_p.D252D	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	252					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)	TCTCCCATGACGGGCGGCGCT	0.557													.|||	88	0.0175719	0.0635	0.0043	5008	,	,		21374	0.0		0.001	False		,,,				2504	0.0				p.D252D		Atlas-SNP	.											.	CYP4F12	89	.	0			c.C756T						PASS	.	C		286,4104		0,286,1909	76	78	77		756	-4.9	0	19	dbSNP_129	77	4,8584		0,4,4290	yes	coding-synonymous	CYP4F12	NM_023944.3		0,290,6199	TT,TC,CC		0.0466,6.5148,2.2346		252/525	15794411	290,12688	2195	4294	6489	SO:0001819	synonymous_variant	66002	exon7			CCATGACGGGCGG	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.756C>T	19.37:g.15794411C>T		140	0	0		210	58	0.27619	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	37	CCDS42517.1																																																																																			C|0.985;T|0.015	0.015	strong		0.557	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9			T	15794411	C	T	15794411	2	4	22	1	0	0	0	0	0	0	0	1	4189	535	19	1		1	CYP4F12	19	15794411	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1129	15794411	43334572	3828	6729			10	33	7640638	13	9	4874	N	T_G_C_A	8.154492e-07
CYP4F12	66002	hgsc.bcm.edu	37	chr19	15794423	15794423	+	Silent	SNP	C	C	T																															tcccatgacgggcggcgcttCcacagggcctgccgcctggt																								rs114945576|rs386807235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15794423C>T	ENST00000550308.1	+	7	1148	c.768C>T	c.(766-768)ttC>ttT	p.F256F	CYP4F12_ENST00000324632.10_Silent_p.F256F	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	256					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)	GGCGGCGCTTCCACAGGGCCT	0.557													.|||	73	0.0145767	0.0522	0.0043	5008	,	,		20890	0.0		0.001	False		,,,				2504	0.0				p.F256F		Atlas-SNP	.											.	CYP4F12	89	.	0			c.C768T						PASS	.						79	81	80					19																	15794423		2199	4295	6494	SO:0001819	synonymous_variant	66002	exon7			GCGCTTCCACAGG	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.768C>T	19.37:g.15794423C>T		124	0	0		189	52	0.275132	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	37	CCDS42517.1																																																																																			C|0.990;T|0.010	0.010	strong		0.557	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9			T	15794423	C	T	15794423	2	4	22	1	0	0	0	0	0	0	0	1	4189	854	30	2		2	CYP4F12	19	15794423	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	12	15794423	43334560	3829	6730	84	2	10	33	7640638	13	9	4874	N	T_G_C_A	8.154492e-07
CYP4F12	66002	hgsc.bcm.edu	37	chr19	15794425	15794425	+	Missense_Mutation	SNP	A	A	G																															ccatgacgggcggcgcttccAcagggcctgccgcctggtgc																								rs116788636|rs386807235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15794425A>G	ENST00000550308.1	+	7	1150	c.770A>G	c.(769-771)cAc>cGc	p.H257R	CYP4F12_ENST00000324632.10_Missense_Mutation_p.H257R	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	257					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)	CGGCGCTTCCACAGGGCCTGC	0.547													.|||	73	0.0145767	0.0522	0.0043	5008	,	,		20966	0.0		0.001	False		,,,				2504	0.0				p.H257R		Atlas-SNP	.											.	CYP4F12	89	.	0			c.A770G						PASS	.	A	ARG/HIS	173,4223		0,173,2025	79	81	80		770	-4.9	0.1	19	dbSNP_132	80	1,8589		0,1,4294	no	missense	CYP4F12	NM_023944.3	29	0,174,6319	GG,GA,AA		0.0116,3.9354,1.3399	benign	257/525	15794425	174,12812	2198	4295	6493	SO:0001583	missense	66002	exon7			GCTTCCACAGGGC	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.770A>G	19.37:g.15794425A>G	ENSP00000448998:p.His257Arg	124	0	0		184	49	0.266304	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	20	0.009157509157509158	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	.	0.001	-3.865349	0.00003	0.039354	1.16E-4	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.67865	-0.29;-0.29	2.47	-4.94	0.03057	.	1.089430	0.07278	N	0.870346	T	0.05090	0.0136	N	0.00368	-1.59	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.11542	-1.0583	10	0.02654	T	1	.	5.3926	0.16251	0.2262:0.0:0.5255:0.2483	.	257	Q9HCS2	CP4FC_HUMAN	R	257	ENSP00000448998:H257R;ENSP00000321821:H257R	ENSP00000321821:H257R	H	+	2	0	CYP4F12	15655425	0.000000	0.05858	0.056000	0.19401	0.005000	0.04900	-0.089000	0.11180	-1.586000	0.01632	-4.406000	0.00006	CAC	A|0.990;G|0.010	0.010	strong		0.547	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9			G	15794425	A	G	15794425	3	3	22	1	0	0	0	0	1	0	0	0	4189	159	6	3	792	3	CYP4F12	19	15794425	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2	15794425	43334558	3830	6731	84	2	10	33	7640638	13	9	4874	N	T_G_C_A	8.154492e-07
CYP4F12	66002	hgsc.bcm.edu	37	chr19	15794463	15794463	+	Missense_Mutation	SNP	G	G	C																															tgcatgacttcacagacgctGtcatccgggagcggcgtcgc																								rs57578760	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15794463G>C	ENST00000550308.1	+	7	1188	c.808G>C	c.(808-810)Gtc>Ctc	p.V270L	CYP4F12_ENST00000324632.10_Missense_Mutation_p.V270L	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	270					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)	CACAGACGCTGTCATCCGGGA	0.537													.|||	73	0.0145767	0.0522	0.0043	5008	,	,		20833	0.0		0.001	False		,,,				2504	0.0				p.V270L		Atlas-SNP	.											.	CYP4F12	89	.	0			c.G808C						PASS	.	G	LEU/VAL	254,4142		0,254,1944	93	93	93		808	-1	0.1	19	dbSNP_129	93	2,8594		0,2,4296	no	missense	CYP4F12	NM_023944.3	32	0,256,6240	CC,CG,GG		0.0233,5.778,1.9704	possibly-damaging	270/525	15794463	256,12736	2198	4298	6496	SO:0001583	missense	66002	exon7			GACGCTGTCATCC	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.808G>C	19.37:g.15794463G>C	ENSP00000448998:p.Val270Leu	103	0	0		154	44	0.285714	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	25	0.011446886446886446	24	0.04878048780487805	1	0.0027624309392265192	0	0.0	0	0.0	.	11.57	1.677010	0.29783	0.05778	2.33E-4	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.67698	-0.28;-0.28	2.47	-0.985	0.10256	.	0.093718	0.42172	U	0.000741	T	0.25680	0.0625	M	0.76002	2.32	0.31890	N	0.617322	P	0.51147	0.942	P	0.58577	0.841	T	0.62029	-0.6940	10	0.87932	D	0	.	6.6191	0.22792	0.3804:0.0:0.6196:0.0	rs57578760	270	Q9HCS2	CP4FC_HUMAN	L	270	ENSP00000448998:V270L;ENSP00000321821:V270L	ENSP00000321821:V270L	V	+	1	0	CYP4F12	15655463	0.981000	0.34729	0.078000	0.20375	0.184000	0.23303	1.826000	0.39092	-0.124000	0.11724	0.491000	0.48974	GTC	G|0.973;C|0.027	0.027	strong		0.537	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9			C	15794463	G	C	15794463	3	2	22	1	0	0	0	0	1	0	0	0	4189	1377	48	4	830	4	CYP4F12	19	15794463	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	38	15794463	43334520	3831	6732	85	2	10	33	7640638	13	9	4874	N	T_G_C_A	8.154492e-07
CYP4F12	66002	hgsc.bcm.edu	37	chr19	15794470	15794470	+	Missense_Mutation	SNP	G	G	A																															cttcacagacgctgtcatccGggagcggcgtcgcaccctcc																								rs150943202	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15794470G>A	ENST00000550308.1	+	7	1195	c.815G>A	c.(814-816)cGg>cAg	p.R272Q	CYP4F12_ENST00000324632.10_Missense_Mutation_p.R272Q	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	272					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)	GCTGTCATCCGGGAGCGGCGT	0.542													.|||	73	0.0145767	0.0522	0.0043	5008	,	,		20675	0.0		0.001	False		,,,				2504	0.0				p.R272Q		Atlas-SNP	.											CYP4F12,NS,haematopoietic_neoplasm,+1,1	CYP4F12	89	1	0			c.G815A						PASS	.	G	GLN/ARG	240,4156		0,240,1958	93	94	94		815	0.3	1	19	dbSNP_134	94	2,8594		0,2,4296	yes	missense	CYP4F12	NM_023944.3	43	0,242,6254	AA,AG,GG		0.0233,5.4595,1.8627	benign	272/525	15794470	242,12750	2198	4298	6496	SO:0001583	missense	66002	exon7			TCATCCGGGAGCG	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.815G>A	19.37:g.15794470G>A	ENSP00000448998:p.Arg272Gln	101	0	0		155	36	0.232258	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	25	0.011446886446886446	24	0.04878048780487805	1	0.0027624309392265192	0	0.0	0	0.0	.	0.017	-1.504706	0.00992	0.054595	2.33E-4	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.67523	-0.27;-0.27	2.46	0.278	0.15673	.	0.278314	0.28877	N	0.013843	T	0.05456	0.0144	N	0.02751	-0.505	0.24533	N	0.994106	B	0.02656	0.0	B	0.04013	0.001	T	0.14531	-1.0469	10	0.02654	T	1	.	5.8094	0.18457	0.7285:0.0:0.2715:0.0	.	272	Q9HCS2	CP4FC_HUMAN	Q	272	ENSP00000448998:R272Q;ENSP00000321821:R272Q	ENSP00000321821:R272Q	R	+	2	0	CYP4F12	15655470	1.000000	0.71417	0.993000	0.49108	0.356000	0.29392	1.185000	0.32065	-0.008000	0.14320	-0.475000	0.04921	CGG	G|0.989;A|0.011	0.011	strong		0.542	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9			A	15794470	G	A	15794470	3	1	22	1	0	0	0	0	1	0	0	0	4189	1116	39	1	837	1	CYP4F12	19	15794470	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	7	15794470	43334513	3832	6733	85	2	10	33	7640638	13	9	4874	N	T_G_C_A	8.154492e-07
CYP4F12	66002	hgsc.bcm.edu	37	chr19	15795690	15795690	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ggctgacaccttcatgtttgGaggtgagggtcccagtgtgg	6	11	16	8	0	1	2	1	2	0	0	2	3	2	3	2	5	0	2	2	5	0	2	rs61729079	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15795690G>C	ENST00000550308.1	+	8	1363	c.983G>C	c.(982-984)gGa>gCa	p.G328A	CYP4F12_ENST00000324632.10_Missense_Mutation_p.G328A	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	328					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)	TTCATGTTTGGAGGTGAGGGT	0.532													.|||	99	0.0197684	0.0711	0.0058	5008	,	,		18415	0.0		0.001	False		,,,				2504	0.0				p.G328A		Atlas-SNP	.											.	CYP4F12	89	.	0			c.G983C						PASS	.	G	ALA/GLY	380,4022		6,368,1827	89	84	85		983	-5.2	0	19	dbSNP_129	85	3,8597		0,3,4297	yes	missense	CYP4F12	NM_023944.3	60	6,371,6124	CC,CG,GG		0.0349,8.6324,2.9457	benign	328/525	15795690	383,12619	2201	4300	6501	SO:0001583	missense	66002	exon8			TGTTTGGAGGTGA	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.983G>C	19.37:g.15795690G>C	ENSP00000448998:p.Gly328Ala	96	0	0		151	48	0.317881	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	39	0.017857142857142856	37	0.07520325203252033	2	0.0055248618784530384	0	0.0	0	0.0	.	0.001	-3.085659	0.00035	0.086324	3.49E-4	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.64085	-0.08;-0.08	2.58	-5.16	0.02857	.	0.269718	0.28176	N	0.016308	T	0.01029	0.0034	N	0.02368	-0.58	0.09310	N	0.999999	B	0.02656	0.0	B	0.08055	0.003	T	0.17107	-1.0380	10	0.25106	T	0.35	.	8.4642	0.32947	0.2353:0.4491:0.3156:0.0	rs61729079	328	Q9HCS2	CP4FC_HUMAN	A	328	ENSP00000448998:G328A;ENSP00000321821:G328A	ENSP00000321821:G328A	G	+	2	0	CYP4F12	15656690	0.000000	0.05858	0.041000	0.18516	0.005000	0.04900	-1.520000	0.02241	-5.413000	0.00015	-4.134000	0.00010	GGA	G|0.981;C|0.019	0.019	strong		0.532	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9			C	15795690	G	C	15795690	3	2	22	1	0	0	0	0	1	0	0	0	4189	1174	41	4	1009	4	CYP4F12	19	15795690	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1220	15795690	43333293	3833	6734			10	33	7640638	13	9	4874	N	T_G_C_A	8.154492e-07
CYP4F12	66002	hgsc.bcm.edu	37	chr19	15795939	15795939	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaccttgcgaggcacccagaAtaccaggagcgctgccgaca	12	4	11	14	3	0	1	0	0	0	1	0	4	0	2	4	2	5	2	4	2	3	2	rs61729075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15795939A>G	ENST00000550308.1	+	9	1427	c.1047A>G	c.(1045-1047)gaA>gaG	p.E349E	CYP4F12_ENST00000324632.10_Silent_p.E349E	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	349					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)	GGCACCCAGAATACCAGGAGC	0.582													.|||	99	0.0197684	0.0711	0.0058	5008	,	,		18068	0.0		0.001	False		,,,				2504	0.0				p.E349E		Atlas-SNP	.											.	CYP4F12	89	.	0			c.A1047G						PASS	.	G		383,4023		7,369,1827	66	62	63		1047	-0.9	1	19	dbSNP_129	63	3,8597		0,3,4297	no	coding-synonymous	CYP4F12	NM_023944.3		7,372,6124	GG,GA,AA		0.0349,8.6927,2.9679		349/525	15795939	386,12620	2203	4300	6503	SO:0001819	synonymous_variant	66002	exon9			CCCAGAATACCAG	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.1047A>G	19.37:g.15795939A>G		157	0	0		258	71	0.275194	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	37	CCDS42517.1																																																																																			A|0.981;G|0.019	0.019	strong		0.582	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9			G	15795939	A	G	15795939	2	3	22	1	0	0	0	0	0	0	0	1	4189	98	4	3		3	CYP4F12	19	15795939	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	249	15795939	43333044	3834	6735			10	33	7640638	13	9	4874	N	T_G_C_A	8.154492e-07
OR10H5	284433	hgsc.bcm.edu	37	chr19	15904914	15904914	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	catcctcgttggcttctctgCcttcccccacctccagctga	4	12	6	19	1	1	1	0	1	1	0	6	1	4	1	6	1	2	3	6	1	0	3	rs150835909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15904914C>T	ENST00000308940.8	+	1	154	c.56C>T	c.(55-57)gCc>gTc	p.A19V		NM_001004466.1	NP_001004466.1	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H, member 5	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(2)|kidney(2)|large_intestine(3)|liver(1)|lung(9)|ovary(1)	20						GGCTTCTCTGCCTTCCCCCAC	0.582													.|||	34	0.00678914	0.025	0.0014	5008	,	,		19279	0.0		0.0	False		,,,				2504	0.0				p.A19V		Atlas-SNP	.											.	OR10H5	49	.	0			c.C56T						PASS	.	C	VAL/ALA	159,4247		6,147,2050	252	210	225		56	-1.8	0.2	19	dbSNP_134	225	2,8598		0,2,4298	no	missense	OR10H5	NM_001004466.1	64	6,149,6348	TT,TC,CC		0.0233,3.6087,1.2379	benign	19/316	15904914	161,12845	2203	4300	6503	SO:0001583	missense	284433	exon1			TCTCTGCCTTCCC	AC011537	CCDS32940.1	19p13.12	2013-09-24			ENSG00000172519	ENSG00000172519		"GPCR / Class A : Olfactory receptors"	15389	protein-coding gene	gene with protein product							Standard	NM_001004466		Approved		uc010xos.2	Q8NGA6	OTTHUMG00000182284	ENST00000308940.8:c.56C>T	19.37:g.15904914C>T	ENSP00000310704:p.Ala19Val	146	0	0		179	86	0.480447	NM_001004466	Q6IFJ0|Q96R60	Missense_Mutation	SNP	ENST00000308940.8	37	CCDS32940.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	.	4.228	0.041170	0.08196	0.036087	2.33E-4	ENSG00000172519	ENST00000308940	T	0.00330	8.08	3.45	-1.79	0.07932	.	0.432269	0.19564	N	0.111245	T	0.00039	0.0001	N	0.05199	-0.095	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.27673	-1.0067	10	0.41790	T	0.15	.	6.7765	0.23622	0.4443:0.2643:0.2914:0.0	.	19	Q8NGA6	O10H5_HUMAN	V	19	ENSP00000310704:A19V	ENSP00000310704:A19V	A	+	2	0	OR10H5	15765914	0.000000	0.05858	0.153000	0.22517	0.262000	0.26303	-1.472000	0.02341	-0.540000	0.06265	0.573000	0.79308	GCC	C|0.990;T|0.010	0.010	strong		0.582	OR10H5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460363.1			T	15904914	C	T	15904914	3	4	22	1	0	0	0	0	1	0	0	0	10918	739	26	2	58	2	OR10H5	19	15904914	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	108975	15904914	43224069	3835	6736											
CYP4F11	57834	hgsc.bcm.edu	37	chr19	16024605	16024605	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ccaccctctgcgcgcaatatCagctcgggtttcctgcgggg	5	9	12	15	4	2	0	1	0	1	0	4	0	3	0	3	3	3	3	3	3	2	2	rs75284625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16024605C>G	ENST00000402119.4	-	12	1938	c.1512G>C	c.(1510-1512)ctG>ctC	p.L504L	CYP4F11_ENST00000326742.8_3'UTR|CYP4F11_ENST00000248041.8_Silent_p.L504L|CYP4F11_ENST00000591841.1_Silent_p.L179L	NM_021187.3	NP_067010.3			cytochrome P450, family 4, subfamily F, polypeptide 11											NS(1)|breast(3)|endometrium(4)|large_intestine(2)|lung(11)|ovary(1)|skin(3)	25						CGCGCAATATCAGCTCGGGTT	0.632													.|||	36	0.0071885	0.0257	0.0029	5008	,	,		15991	0.0		0.0	False		,,,				2504	0.0				p.L504L		Atlas-SNP	.											.	CYP4F11	83	.	0			c.G1512C						PASS	.	C	,	190,4216	120.8+/-158.4	8,174,2021	62	57	59		1512,1512	1.6	0.2	19	dbSNP_132	59	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	CYP4F11	NM_001128932.1,NM_021187.3	,	8,175,6320	GG,GC,CC		0.0116,4.3123,1.4686	,	504/525,504/525	16024605	191,12815	2203	4300	6503	SO:0001819	synonymous_variant	57834	exon13			CAATATCAGCTCG	AF236085	CCDS12337.1	19p13.1	2011-07-29	2003-01-14		ENSG00000171903	ENSG00000171903		"Cytochrome P450s"	13265	protein-coding gene	gene with protein product		611517	"cytochrome P450, subfamily IVF, polypeptide 11"			10964514, 9068972	Standard	NM_021187		Approved		uc002nbu.2	Q9HBI6		ENST00000402119.4:c.1512G>C	19.37:g.16024605C>G		130	0	0		150	81	0.54	NM_001128932		Silent	SNP	ENST00000402119.4	37	CCDS12337.1																																																																																			C|0.990;G|0.010	0.010	strong		0.632	CYP4F11-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460385.2	NM_021187		G	16024605	C	G	16024605	2	3	22	1	0	0	0	0	0	0	0	1	4188	813	29	4		4	CYP4F11	19	16024605	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	119691	16024605	43104378	3836	6737											
OR10H4	126541	hgsc.bcm.edu	37	chr19	16060453	16060453	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtcacagccctgataggctgTttattcctcatcatcctctc	7	14	6	14	0	4	1	3	1	1	0	7	1	6	1	3	1	1	2	3	1	2	4	rs115548355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16060453T>C	ENST00000322107.1	+	1	636	c.636T>C	c.(634-636)tgT>tgC	p.C212C		NM_001004465.1	NP_001004465.1	Q8NGA5	O10H4_HUMAN	olfactory receptor, family 10, subfamily H, 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)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	17						TGATAGGCTGTTTATTCCTCA	0.488													.|||	43	0.00858626	0.0318	0.0014	5008	,	,		23791	0.0		0.0	False		,,,				2504	0.0				p.C212C		Atlas-SNP	.											.	OR10H4	48	.	0			c.T636C						PASS	.	T		200,4206	125.7+/-162.9	6,188,2009	295	266	276		636	-0.8	0.8	19	dbSNP_132	276	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	OR10H4	NM_001004465.1		6,189,6308	CC,CT,TT		0.0116,4.5393,1.5454		212/317	16060453	201,12805	2203	4300	6503	SO:0001819	synonymous_variant	126541	exon1			AGGCTGTTTATTC	AC011517	CCDS32941.1	19p13.12	2013-09-24			ENSG00000176231	ENSG00000176231		"GPCR / Class A : Olfactory receptors"	15388	protein-coding gene	gene with protein product							Standard	NM_001004465		Approved		uc010xov.2	Q8NGA5	OTTHUMG00000182268	ENST00000322107.1:c.636T>C	19.37:g.16060453T>C		389	1	0.00257069		390	196	0.502564	NM_001004465	Q6IFJ2|Q96R57	Silent	SNP	ENST00000322107.1	37	CCDS32941.1																																																																																			T|0.988;C|0.012	0.012	strong		0.488	OR10H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460311.1			C	16060453	T	C	16060453	2	2	22	1	0	0	0	0	0	0	0	1	10917	1731	60	3		3	OR10H4	19	16060453	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	35848	16060453	43068530	3837	6738											
TPM4	7171	hgsc.bcm.edu	37	chr19	16186865	16186865	+	5'Flank	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtcgtccccaggtggaggaGgagctgacgcacctccagaa	9	6	14	12	2	0	2	0	1	0	1	3	5	2	5	4	4	1	2	4	4	1	0	rs114042568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16186865G>A	ENST00000300933.4	+	0	0				TPM4_ENST00000538887.1_Silent_p.E41E|TPM4_ENST00000344824.6_Silent_p.E41E	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						AGGTGGAGGAGGAGCTGACGC	0.617			T	ALK	ALCL								G|||	90	0.0179712	0.062	0.0115	5008	,	,		14293	0.0		0.0	False		,,,				2504	0.0				p.E41E		Atlas-SNP	.		Dom	yes		19	19p13.1	7171	tropomyosin 4		L	.	TPM4	28	.	0			c.G123A						PASS	.	G		143,2989		7,129,1430	30	31	31		123	1.8	1	19	dbSNP_132	31	1,7153		0,1,3576	no	coding-synonymous	TPM4	NM_001145160.1		7,130,5006	AA,AG,GG		0.014,4.5658,1.4		41/285	16186865	144,10142	1566	3577	5143	SO:0001631	upstream_gene_variant	7171	exon2			GGAGGAGGAGCTG		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		19.37:g.16186865G>A	Exception_encountered	108	0	0		137	67	0.489051	NM_001145160	P07226|Q15659|Q5U0D9|Q9BU85|Q9H8Q3|Q9UCS1|Q9UCS2|Q9UCS3|Q9UCS4	Silent	SNP	ENST00000300933.4	37	CCDS12338.1																																																																																			G|0.989;A|0.011	0.011	strong		0.617	TPM4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459673.2	NM_003290		A	16186865	G	A	16186865	1	1	22	0	1	0	0	0	0	0	0	0	16423	991	35	2		2	TPM4	19	16186865	5'Flank	SNP	G	TCGA-G8-6324-01A-11D-2210-10	126412	16186865	42942118	3838	6739											
HSH2D	84941	hgsc.bcm.edu	37	chr19	16263946	16263946	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggcccacacctcgctggaCgccctggtcaccttccacca	6	7	9	19	2	1	0	1	0	0	0	3	1	2	1	6	3	0	1	6	3	0	1	rs1870354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16263946C>T	ENST00000253680.6	+	6	840	c.309C>T	c.(307-309)gaC>gaT	p.D103D	HSH2D_ENST00000397372.4_Splice_Site|HSH2D_ENST00000593154.2_Silent_p.D103D|HSH2D_ENST00000588246.1_Silent_p.D103D			Q96JZ2	HSH2D_HUMAN	hematopoietic SH2 domain containing	103	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				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						CCTCGCTGGACGCCCTGGTCA	0.617													C|||	96	0.0191693	0.0696	0.0043	5008	,	,		17099	0.0		0.001	False		,,,				2504	0.0				p.D103D		Atlas-SNP	.											.	HSH2D	16	.	0			c.C309T						PASS	.	C		236,3872		5,226,1823	26	30	29		309	-3.9	0.2	19	dbSNP_92	29	3,8351		0,3,4174	no	coding-synonymous	HSH2D	NM_032855.2		5,229,5997	TT,TC,CC		0.0359,5.7449,1.9178		103/353	16263946	239,12223	2054	4177	6231	SO:0001819	synonymous_variant	84941	exon6			GCTGGACGCCCTG	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.309C>T	19.37:g.16263946C>T		73	0	0		55	33	0.6	NM_032855	B5ME72|Q6ZNG7	Silent	SNP	ENST00000253680.6	37		30	0.013736263736263736	27	0.054878048780487805	3	0.008287292817679558	0	0.0	0	0.0	C	0.017	-1.489323	0.01018	0.057449	3.59E-4	ENSG00000196684	ENST00000397372	.	.	.	4.63	-3.9	0.04181	.	.	.	.	.	.	.	.	.	.	.	0.22253	N	0.999254	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.8363	0.13466	0.0:0.3118:0.3055:0.3827	rs1870354;rs1870354	.	.	.	.	-1	.	.	.	+	.	.	HSH2D	16124946	0.000000	0.05858	0.227000	0.23927	0.006000	0.05464	-2.127000	0.01315	-0.294000	0.08973	-0.949000	0.02662	.	C|0.986;T|0.014	0.014	strong		0.617	HSH2D-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032855		T	16263946	C	T	16263946	2	4	22	1	0	0	0	0	0	0	0	1	7409	535	19	1		1	HSH2D	19	16263946	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	77081	16263946	42865037	3839	6740											
MED26	9441	hgsc.bcm.edu	37	chr19	16687870	16687870	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggaggccccggagtctcGtccaccctgtccagctgctg	4	8	14	15	2	1	0	0	0	1	0	4	2	3	2	5	4	2	2	5	4	0	0	rs61734286	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16687870G>A	ENST00000263390.3	-	3	1033	c.771C>T	c.(769-771)gaC>gaT	p.D257D	CTD-3222D19.2_ENST00000409035.1_Silent_p.D265D|CTC-429P9.4_ENST00000593962.1_5'Flank	NM_004831.3	NP_004822.2	O95402	MED26_HUMAN	mediator complex subunit 26	257	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						CCGGAGTCTCGTCCACCCTGT	0.677													G|||	165	0.0329473	0.121	0.0072	5008	,	,		14022	0.0		0.0	False		,,,				2504	0.0				p.D257D		Atlas-SNP	.											.	MED26	25	.	0			c.C771T						PASS	.	G		407,3999	185.0+/-212.2	21,365,1817	30	32	31		771	-9.5	0.1	19	dbSNP_129	31	2,8598		0,2,4298	no	coding-synonymous	MED26	NM_004831.3		21,367,6115	AA,AG,GG		0.0233,9.2374,3.1447		257/601	16687870	409,12597	2203	4300	6503	SO:0001819	synonymous_variant	9441	exon3			AGTCTCGTCCACC	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.771C>T	19.37:g.16687870G>A		106	0	0		89	41	0.460674	NM_004831	A1A4S3|Q0VGB6	Silent	SNP	ENST00000263390.3	37	CCDS12347.1																																																																																			G|0.967;A|0.033	0.033	strong		0.677	MED26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461178.1	NM_004831		A	16687870	G	A	16687870	2	1	22	1	0	0	0	0	0	0	0	1	9453	1136	40	1		1	MED26	19	16687870	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	423924	16687870	42441113	3840	6741											
NWD1	284434	hgsc.bcm.edu	37	chr19	16860001	16860001	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagctcagaggaccgggaacAgggagccaccgtcttcctta	10	6	13	12	2	2	1	1	0	1	1	3	5	3	4	4	3	3	1	4	3	2	2	rs76739123	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16860001A>T	ENST00000552788.1	+	4	548	c.548A>T	c.(547-549)cAg>cTg	p.Q183L	NWD1_ENST00000379808.3_Missense_Mutation_p.Q183L|NWD1_ENST00000523826.1_De_novo_Start_OutOfFrame|NWD1_ENST00000339803.6_Missense_Mutation_p.Q48L|NWD1_ENST00000524140.2_Missense_Mutation_p.Q183L|NWD1_ENST00000549814.1_Missense_Mutation_p.Q183L			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	183							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						GACCGGGAACAGGGAGCCACC	0.572													A|||	120	0.0239617	0.0825	0.0101	5008	,	,		17868	0.0		0.001	False		,,,				2504	0.0031				p.Q183L		Atlas-SNP	.											.	NWD1	303	.	0			c.A548T						PASS	.	A	LEU/GLN	279,4127	157.0+/-190.0	5,269,1929	72	57	62		548	-7.3	0	19	dbSNP_131	62	10,8590	6.4+/-24.3	0,10,4290	yes	missense	NWD1	NM_001007525.3	113	5,279,6219	TT,TA,AA		0.1163,6.3323,2.2221	benign	183/1433	16860001	289,12717	2203	4300	6503	SO:0001583	missense	284434	exon6			GGGAACAGGGAGC	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.548A>T	19.37:g.16860001A>T	ENSP00000447224:p.Gln183Leu	115	0	0		143	79	0.552448	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		49	0.022435897435897436	42	0.08536585365853659	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	a	2.726	-0.265505	0.05754	0.063323	0.001163	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000552788;ENST00000339803	T;T;T;T;T	0.56444	2.07;2.07;2.07;2.07;0.46	4.45	-7.35	0.01422	.	1.747030	0.02870	N	0.131458	T	0.01523	0.0049	L	0.39397	1.21	0.18873	N	0.999986	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.10474	-1.0628	10	0.54805	T	0.06	-3.4934	2.1523	0.03803	0.2044:0.3718:0.2881:0.1356	.	183;48	Q149M9-3;C9J2Y8	.;.	L	48;183;183;183;183;48	ENSP00000428579:Q183L;ENSP00000447548:Q183L;ENSP00000369136:Q183L;ENSP00000447224:Q183L;ENSP00000340159:Q48L	ENSP00000340159:Q48L	Q	+	2	0	NWD1	16721001	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.401000	0.07232	-1.070000	0.03149	-0.499000	0.04595	CAG	A|0.975;T|0.025	0.025	strong		0.572	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525		T	16860001	A	T	16860001	3	4	22	1	0	0	0	0	1	0	0	0	10790	188	7	5	149	5	NWD1	19	16860001	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	172131	16860001	42268982	3841	6742			11	34	1064062	5	5	685	N	T_G_C_A	3.681712e-06
NWD1	284434	hgsc.bcm.edu	37	chr19	16860087	16860087	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaggatggtggaccggctcGcggatggctgcctggacgct	5	9	17	10	4	0	0	0	0	0	0	1	4	0	4	2	7	1	3	2	7	1	1	rs61750949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16860087G>A	ENST00000552788.1	+	4	634	c.634G>A	c.(634-636)Gcg>Acg	p.A212T	NWD1_ENST00000379808.3_Missense_Mutation_p.A212T|NWD1_ENST00000523826.1_Missense_Mutation_p.A6T|NWD1_ENST00000339803.6_Missense_Mutation_p.A77T|NWD1_ENST00000524140.2_Missense_Mutation_p.A212T|NWD1_ENST00000549814.1_Missense_Mutation_p.A212T			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	212							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						GGACCGGCTCGCGGATGGCTG	0.592													G|||	120	0.0239617	0.0825	0.0101	5008	,	,		16617	0.0		0.001	False		,,,				2504	0.0031				p.A212T		Atlas-SNP	.											.	NWD1	303	.	0			c.G634A						PASS	.						74	56	62					19																	16860087		2203	4300	6503	SO:0001583	missense	284434	exon6			CGGCTCGCGGATG	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.634G>A	19.37:g.16860087G>A	ENSP00000447224:p.Ala212Thr	87	0	0		101	51	0.504951	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		49	0.022435897435897436	42	0.08536585365853659	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	g	5.285	0.237974	0.10023	.	.	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.58940	1.72;1.72;1.72;0.3;1.72;0.44	4.52	-3.02	0.05446	.	0.678723	0.14068	N	0.343619	T	0.01287	0.0042	N	0.24115	0.695	0.09310	N	1	P;P;P	0.48230	0.716;0.907;0.85	B;B;B	0.31495	0.041;0.131;0.062	T	0.04946	-1.0916	10	0.17832	T	0.49	-0.4805	16.5319	0.84362	0.0:0.7256:0.2744:0.0	rs61750949	212;212;77	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	T	77;212;212;212;6;212;77	ENSP00000428579:A212T;ENSP00000447548:A212T;ENSP00000369136:A212T;ENSP00000428955:A6T;ENSP00000447224:A212T;ENSP00000340159:A77T	ENSP00000340159:A77T	A	+	1	0	NWD1	16721087	0.000000	0.05858	0.005000	0.12908	0.210000	0.24377	0.594000	0.24014	-0.722000	0.04922	-0.337000	0.08149	GCG	G|0.983;A|0.017	0.017	strong		0.592	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525		A	16860087	G	A	16860087	3	1	22	1	0	0	0	0	1	0	0	0	10790	1087	38	1	235	1	NWD1	19	16860087	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	86	16860087	42268896	3842	6743			11	34	1064062	5	5	685	N	T_G_C_A	3.681712e-06
NWD1	284434	hgsc.bcm.edu	37	chr19	16860558	16860558	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggcacaagacagtgaccGtcctgcggctgctggggacg	7	6	17	11	3	0	2	0	1	0	1	1	3	1	3	2	5	2	3	2	5	1	0	rs61733271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16860558G>A	ENST00000552788.1	+	4	1105	c.1105G>A	c.(1105-1107)Gtc>Atc	p.V369I	NWD1_ENST00000379808.3_Missense_Mutation_p.V369I|NWD1_ENST00000523826.1_Missense_Mutation_p.V163I|NWD1_ENST00000339803.6_Missense_Mutation_p.V234I|NWD1_ENST00000524140.2_Missense_Mutation_p.V369I|NWD1_ENST00000549814.1_Missense_Mutation_p.V369I			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	369	NACHT.						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						GACAGTGACCGTCCTGCGGCT	0.622													g|||	330	0.0658946	0.1785	0.0274	5008	,	,		18889	0.0079		0.0288	False		,,,				2504	0.0389				p.V369I		Atlas-SNP	.											.	NWD1	303	.	0			c.G1105A						PASS	.		ILE/VAL	715,3691		56,603,1544	32	33	32		1105	1	0.2	19	dbSNP_129	32	322,8276		8,306,3985	yes	missense	NWD1	NM_001007525.3	29	64,909,5529	AA,AG,GG		3.7451,16.2279,7.9745	benign	369/1433	16860558	1037,11967	2203	4299	6502	SO:0001583	missense	284434	exon6			GTGACCGTCCTGC	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.1105G>A	19.37:g.16860558G>A	ENSP00000447224:p.Val369Ile	61	0	0		63	63	1	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		121	0.0554029304029304	87	0.17682926829268292	14	0.03867403314917127	1	0.0017482517482517483	19	0.025065963060686015	N	3.273	-0.148788	0.06627	0.162279	0.037451	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05;-1.05;-1.05	4.42	1.02	0.19986	.	0.069867	0.56097	N	0.000032	T	0.00210	0.0006	L	0.28115	0.83	0.33929	P	0.358212	B;B;B	0.27166	0.17;0.066;0.081	B;B;B	0.32624	0.149;0.017;0.029	T	0.04103	-1.0977	9	0.12103	T	0.63	-23.6771	8.4041	0.32603	0.2739:0.0:0.7261:0.0	rs61733271	369;369;234	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	I	234;369;369;369;163;369;234	ENSP00000428579:V369I;ENSP00000447548:V369I;ENSP00000369136:V369I;ENSP00000428955:V163I;ENSP00000447224:V369I;ENSP00000340159:V234I	ENSP00000340159:V234I	V	+	1	0	NWD1	16721558	0.407000	0.25352	0.207000	0.23584	0.656000	0.38851	0.720000	0.25896	0.094000	0.17404	-0.155000	0.13514	GTC	G|0.927;A|0.073	0.073	strong		0.622	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525		A	16860558	G	A	16860558	3	1	22	1	0	0	0	0	1	0	0	0	10790	1145	40	1	706	1	NWD1	19	16860558	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	471	16860558	42268425	3843	6744			11	34	1064062	5	5	685	N	T_G_C_A	3.681712e-06
NWD1	284434	hgsc.bcm.edu	37	chr19	16860602	16860602	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaatgagctcagatgcccgTggcctgctgaagagcatctg	10	8	12	11	1	2	4	1	2	1	2	2	4	2	4	2	1	4	3	2	1	2	0	rs61731252	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16860602T>C	ENST00000552788.1	+	4	1149	c.1149T>C	c.(1147-1149)cgT>cgC	p.R383R	NWD1_ENST00000379808.3_Silent_p.R383R|NWD1_ENST00000523826.1_Silent_p.R177R|NWD1_ENST00000339803.6_Silent_p.R248R|NWD1_ENST00000524140.2_Silent_p.R383R|NWD1_ENST00000549814.1_Silent_p.R383R			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	383	NACHT.						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						CAGATGCCCGTGGCCTGCTGA	0.622													t|||	337	0.0672923	0.1838	0.0274	5008	,	,		17972	0.0079		0.0288	False		,,,				2504	0.0389				p.R383R		Atlas-SNP	.											.	NWD1	303	.	0			c.T1149C						PASS	.			733,3673		58,617,1528	32	34	33		1149	-4.7	0	19	dbSNP_129	33	320,8280		7,306,3987	no	coding-synonymous	NWD1	NM_001007525.3		65,923,5515	CC,CT,TT		3.7209,16.6364,8.0963		383/1433	16860602	1053,11953	2203	4300	6503	SO:0001819	synonymous_variant	284434	exon6			TGCCCGTGGCCTG	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.1149T>C	19.37:g.16860602T>C		52	0	0		56	55	0.982143	NM_001007525	C9J021|Q68CT3	Silent	SNP	ENST00000552788.1	37																																																																																				T|0.927;C|0.073	0.073	strong		0.622	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525		C	16860602	T	C	16860602	2	2	22	1	0	0	0	0	0	0	0	1	10790	1683	59	3		3	NWD1	19	16860602	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	44	16860602	42268381	3844	6745			11	34	1064062	5	5	685	N	T_G_C_A	3.681712e-06
NWD1	284434	hgsc.bcm.edu	37	chr19	16860685	16860685	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccaggttctggacgcccacaCcagggtggtccagtttttcc	6	10	11	14	1	1	0	0	0	1	0	3	1	3	1	5	4	0	2	5	4	0	3	rs61998161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16860685C>T	ENST00000552788.1	+	4	1232	c.1232C>T	c.(1231-1233)aCc>aTc	p.T411I	NWD1_ENST00000379808.3_Missense_Mutation_p.T411I|NWD1_ENST00000523826.1_Missense_Mutation_p.T205I|NWD1_ENST00000339803.6_Missense_Mutation_p.T276I|NWD1_ENST00000524140.2_Missense_Mutation_p.T411I|NWD1_ENST00000549814.1_Missense_Mutation_p.T411I			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	411	NACHT.						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						GACGCCCACACCAGGGTGGTC	0.587													c|||	120	0.0239617	0.0825	0.0101	5008	,	,		18238	0.0		0.001	False		,,,				2504	0.0031				p.T411I		Atlas-SNP	.											.	NWD1	303	.	0			c.C1232T						PASS	.		ILE/THR	266,4134		5,256,1939	55	56	56		1232	-8.4	0	19	dbSNP_129	56	10,8590		0,10,4290	yes	missense	NWD1	NM_001007525.3	89	5,266,6229	TT,TC,CC		0.1163,6.0455,2.1231	benign	411/1433	16860685	276,12724	2200	4300	6500	SO:0001583	missense	284434	exon6			CCCACACCAGGGT	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.1232C>T	19.37:g.16860685C>T	ENSP00000447224:p.Thr411Ile	70	0	0		85	42	0.494118	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		49	0.022435897435897436	42	0.08536585365853659	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	c	5.508	0.278633	0.10458	0.060455	0.001163	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.81078	-1.45;-1.45;-1.45;-1.45;-1.45;-1.45	4.77	-8.37	0.00976	.	1.739930	0.02884	N	0.133179	T	0.07234	0.0183	N	0.19112	0.55	0.09310	N	1	P;B;P	0.39022	0.655;0.435;0.491	B;B;B	0.37198	0.243;0.157;0.243	T	0.48547	-0.9026	10	0.33940	T	0.23	-0.9905	16.403	0.83649	0.0991:0.1543:0.7466:0.0	rs61998161	411;411;276	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	I	276;411;411;411;205;411;276	ENSP00000428579:T411I;ENSP00000447548:T411I;ENSP00000369136:T411I;ENSP00000428955:T205I;ENSP00000447224:T411I;ENSP00000340159:T276I	ENSP00000340159:T276I	T	+	2	0	NWD1	16721685	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.167000	0.09940	-0.626000	0.05596	-0.194000	0.12790	ACC	C|0.979;T|0.021	0.021	strong		0.587	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525		T	16860685	C	T	16860685	3	4	22	1	0	0	0	0	1	0	0	0	10790	507	18	2	833	2	NWD1	19	16860685	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	83	16860685	42268298	3845	6746			11	34	1064062	5	5	685	N	T_G_C_A	3.681712e-06
NWD1	284434	hgsc.bcm.edu	37	chr19	16899852	16899852	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tcgccaactctgcttcaaagGattacacgctgcacttgtgg	9	11	9	12	2	2	0	1	0	1	0	3	1	2	1	1	2	4	3	1	2	3	3	rs140602425		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16899852G>T	ENST00000552788.1	+	11	2791	c.2791G>T	c.(2791-2793)Gat>Tat	p.D931Y	NWD1_ENST00000379808.3_Missense_Mutation_p.D931Y|NWD1_ENST00000523826.1_Missense_Mutation_p.D725Y|NWD1_ENST00000339803.6_Missense_Mutation_p.D796Y|NWD1_ENST00000524140.2_Missense_Mutation_p.D931Y|NWD1_ENST00000549814.1_Missense_Mutation_p.D931Y			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	931							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						TGCTTCAAAGGATTACACGCT	0.498																																					p.D931Y		Atlas-SNP	.											.	NWD1	303	.	0			c.G2791T						PASS	.	G	TYR/ASP	2,4404	4.2+/-10.8	0,2,2201	116	112	113		2791	5.7	0.3	19	dbSNP_134	113	0,8600		0,0,4300	no	missense	NWD1	NM_001007525.3	160	0,2,6501	TT,TG,GG		0.0,0.0454,0.0154	probably-damaging	931/1433	16899852	2,13004	2203	4300	6503	SO:0001583	missense	284434	exon13			TCAAAGGATTACA	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.2791G>T	19.37:g.16899852G>T	ENSP00000447224:p.Asp931Tyr	113	0	0		126	55	0.436508	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		.	.	.	.	.	.	.	.	.	.	G	13.13	2.144107	0.37825	4.54E-4	0.0	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	D;D;D;D;D;D	0.89415	-2.51;-2.51;-2.51;-2.51;-2.51;-2.51	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	0.96914	0.8992	H	0.98701	4.305	0.32370	N	0.55603	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.98435	1.0584	10	0.87932	D	0	-35.093	15.2049	0.73173	0.0:0.0:1.0:0.0	.	931;931;796	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	Y	796;931;931;931;725;931;796	ENSP00000428579:D931Y;ENSP00000447548:D931Y;ENSP00000369136:D931Y;ENSP00000428955:D725Y;ENSP00000447224:D931Y;ENSP00000340159:D796Y	ENSP00000340159:D796Y	D	+	1	0	NWD1	16760852	1.000000	0.71417	0.252000	0.24328	0.003000	0.03518	5.303000	0.65738	2.661000	0.90470	0.591000	0.81541	GAT	G|1.000;T|0.000	0.000	weak		0.498	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525		T	16899852	G	T	16899852	3	4	22	1	0	0	0	0	1	0	0	0	10790	1174	41	4	2420	4	NWD1	19	16899852	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	39167	16899852	42229131	3846	6747											
NWD1	284434	hgsc.bcm.edu	37	chr19	16918459	16918459	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtctggaggttgctgagcagCgcaagctcctatttacgggc	7	10	14	10	2	1	1	0	1	1	0	2	2	2	2	1	3	5	5	1	3	3	4	rs78570914	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16918459C>T	ENST00000552788.1	+	16	3799	c.3799C>T	c.(3799-3801)Cgc>Tgc	p.R1267C	NWD1_ENST00000379808.3_Missense_Mutation_p.R1267C|NWD1_ENST00000523826.1_Missense_Mutation_p.R1061C|NWD1_ENST00000339803.6_Missense_Mutation_p.R1132C|NWD1_ENST00000524140.2_Missense_Mutation_p.R1267C|NWD1_ENST00000549814.1_Missense_Mutation_p.R1225C			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	1267							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						TGCTGAGCAGCGCAAGCTCCT	0.562													C|||	17	0.00339457	0.0121	0.0014	5008	,	,		18437	0.0		0.0	False		,,,				2504	0.0				p.R1267C		Atlas-SNP	.											NWD1_ENST00000524140,NS,carcinoma,-1,3	NWD1	303	3	0			c.C3799T						PASS	.	C	CYS/ARG	34,4372	40.0+/-72.8	1,32,2170	91	95	94		3799	-1.5	0	19	dbSNP_131	94	0,8600		0,0,4300	yes	missense	NWD1	NM_001007525.3	180	1,32,6470	TT,TC,CC		0.0,0.7717,0.2614	benign	1267/1433	16918459	34,12972	2203	4300	6503	SO:0001583	missense	284434	exon18			GAGCAGCGCAAGC	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.3799C>T	19.37:g.16918459C>T	ENSP00000447224:p.Arg1267Cys	125	0	0		123	54	0.439024	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	C	7.773	0.707922	0.15239	0.007717	0.0	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.70749	-0.19;-0.51;-0.19;2.21;1.55;2.21	5.27	-1.54	0.08584	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	1.389700	0.04604	N	0.399111	T	0.39436	0.1078	N	0.14661	0.345	0.09310	N	1	P;P;P	0.38922	0.519;0.651;0.519	B;B;B	0.34722	0.057;0.188;0.057	T	0.42716	-0.9435	10	0.72032	D	0.01	-0.223	1.2256	0.01932	0.3166:0.3553:0.1858:0.1423	.	1267;1267;1132	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	C	1132;1267;1225;1267;1061;1267;1132	ENSP00000428579:R1267C;ENSP00000447548:R1225C;ENSP00000369136:R1267C;ENSP00000428955:R1061C;ENSP00000447224:R1267C;ENSP00000340159:R1132C	ENSP00000340159:R1132C	R	+	1	0	NWD1	16779459	0.911000	0.30947	0.011000	0.14972	0.055000	0.15305	1.787000	0.38704	-0.087000	0.12528	-0.140000	0.14226	CGC	C|0.997;T|0.003	0.003	strong		0.562	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525		T	16918459	C	T	16918459	3	4	22	1	0	0	0	0	1	0	0	0	10790	768	27	1	3448	1	NWD1	19	16918459	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	18607	16918459	42210524	3847	6748											
CPAMD8	27151	hgsc.bcm.edu	37	chr19	17081707	17081707	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gtataagccgttacctggggGggtgcctggaaggagccact	8	8	16	9	1	0	0	0	0	0	0	0	2	0	2	4	5	4	2	4	5	4	3	rs9305083	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17081707G>T	ENST00000443236.1	-	18	2379	c.2348C>A	c.(2347-2349)cCc>cAc	p.P783H	CPAMD8_ENST00000388925.4_3'UTR	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	736						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						TTACCTGGGGGGGTGCCTGGA	0.572													G|||	520	0.103834	0.3608	0.036	5008	,	,		16421	0.0		0.0129	False		,,,				2504	0.0051				p.P783H		Atlas-SNP	.											.	CPAMD8	192	.	0			c.C2348A						PASS	.	G	HIS/PRO	1156,2704		169,818,943	26	29	28		2348	-3.2	0.2	19	dbSNP_119	28	180,8074		3,174,3950	yes	missense	CPAMD8	NM_015692.2	77	172,992,4893	TT,TG,GG		2.1808,29.9482,11.0286	possibly-damaging	783/1933	17081707	1336,10778	1930	4127	6057	SO:0001583	missense	27151	exon18			CTGGGGGGGTGCC	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.2348C>A	19.37:g.17081707G>T	ENSP00000402505:p.Pro783His	34	0	0		38	19	0.5	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	222|222	0.10164835164835165|0.10164835164835165	191|191	0.3882113821138211|0.3882113821138211	19|19	0.052486187845303865|0.052486187845303865	0|0	0.0|0.0	12|12	0.0158311345646438|0.0158311345646438	G|G	11.55|11.55	1.673598|1.673598	0.29693|0.29693	0.299482|0.299482	0.021808|0.021808	ENSG00000160111|ENSG00000160111	ENST00000291440|ENST00000443236	.|.	.|.	.|.	3.19|3.19	-3.22|-3.22	0.05125|0.05125	.|.	1.230310|1.230310	0.06279|0.06279	N|U	0.697038|0.697038	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.36672|0.36672	1.1|1.1	0.09310|0.09310	P|P	1.0|1.0	P|.	0.51653|.	0.947|.	B|.	0.40741|.	0.339|.	T|T	0.44329|0.44329	-0.9335|-0.9335	8|6	0.42905|0.14252	T|T	0.14|0.57	.|.	0.9563|0.9563	0.01386|0.01386	0.342:0.161:0.3358:0.1611|0.342:0.161:0.3358:0.1611	rs9305083;rs52812668;rs9305083|rs9305083;rs52812668;rs9305083	736|.	Q8IZJ3|.	CPMD8_HUMAN|.	H|T	783|794	.|.	ENSP00000291440:P783H|ENSP00000402505:P794T	P|P	-|-	2|1	0|0	CPAMD8|CPAMD8	16942707|16942707	0.013000|0.013000	0.17824|0.17824	0.179000|0.179000	0.23059|0.23059	0.258000|0.258000	0.26162|0.26162	0.758000|0.758000	0.26447|0.26447	-0.437000|-0.437000	0.07243|0.07243	-1.045000|-1.045000	0.02358|0.02358	CCC|CCC	G|0.914;T|0.086	0.086	strong		0.572	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692		T	17081707	G	T	17081707	3	4	22	1	0	0	0	0	1	0	0	0	3797	1232	43	4	3550	4	CPAMD8	19	17081707	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	163248	17081707	42047276	3848	6749											
CPAMD8	27151	hgsc.bcm.edu	37	chr19	17113083	17113083	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccctctttctcacctggcccGcacagtgcctgtctcacagg	5	10	8	18	1	3	0	2	0	3	0	5	0	3	0	4	2	1	1	4	2	0	1	rs10426545	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17113083G>A	ENST00000443236.1	-	9	923	c.892C>T	c.(892-894)Cgg>Tgg	p.R298W	CPAMD8_ENST00000388925.4_Missense_Mutation_p.R251W	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	251						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						CACCTGGCCCGCACAGTGCCT	0.607													N|||	120	0.0239617	0.0885	0.0043	5008	,	,		16334	0.0		0.0	False		,,,				2504	0.0				p.R298W		Atlas-SNP	.											CPAMD8,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,1	CPAMD8	192	1	0			c.C892T						scavenged	.	G	TRP/ARG	332,3516		18,296,1610	21	22	22		892	1.5	0	19	dbSNP_119	22	13,8241		0,13,4114	no	missense	CPAMD8	NM_015692.2	101	18,309,5724	AA,AG,GG		0.1575,8.6279,2.8508	probably-damaging	298/1933	17113083	345,11757	1924	4127	6051	SO:0001583	missense	27151	exon9			TGGCCCGCACAGT	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.892C>T	19.37:g.17113083G>A	ENSP00000402505:p.Arg298Trp	148	1	0.00675676		128	52	0.40625	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	28	0.01282051282051282	25	0.0508130081300813	3	0.008287292817679558	0	0.0	0	0.0	N	15.04	2.714927	0.48622	0.086279	0.001575	ENSG00000160111	ENST00000291440;ENST00000388925	T;T	0.12039	2.72;2.72	2.61	1.51	0.23008	.	1.430970	0.04807	U	0.434632	T	0.00496	0.0016	L	0.46157	1.445	0.31995	N	0.604078	D	0.59357	0.985	B	0.40534	0.332	T	0.29610	-1.0006	10	0.59425	D	0.04	.	8.4214	0.32703	0.0:0.0:0.5788:0.4212	rs10426545;rs10426545	251	Q8IZJ3	CPMD8_HUMAN	W	298;251	ENSP00000291440:R298W;ENSP00000373577:R251W	ENSP00000291440:R298W	R	-	1	2	CPAMD8	16974083	0.962000	0.33011	0.047000	0.18901	0.941000	0.58515	1.586000	0.36611	0.217000	0.20800	0.466000	0.42574	CGG	G|0.982;A|0.018	0.018	strong		0.607	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692		A	17113083	G	A	17113083	3	1	22	1	0	0	0	0	1	0	0	0	3797	1086	38	1	5042	1	CPAMD8	19	17113083	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	31376	17113083	42015900	3849	6750											
GTPBP3	84705	hgsc.bcm.edu	37	chr19	17450038	17450038	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cacgtagtggtcactggaccCcccaatgcgggcaagagcag	10	5	13	13	2	1	1	1	0	0	1	1	2	1	2	3	3	2	3	3	3	3	1	rs11880362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17450038C>T	ENST00000324894.8	+	6	839	c.771C>T	c.(769-771)ccC>ccT	p.P257P	GTPBP3_ENST00000598038.1_3'UTR|GTPBP3_ENST00000358792.7_Silent_p.P289P|GTPBP3_ENST00000361619.5_Silent_p.P279P|GTPBP3_ENST00000600625.1_Silent_p.P257P	NM_032620.3|NM_133644.3	NP_116009.2|NP_598399.2	Q969Y2	GTPB3_HUMAN	GTP binding protein 3 (mitochondrial)	257	TrmE-type G.				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						TCACTGGACCCCCCAATGCGG	0.667													c|||	103	0.0205671	0.0726	0.0101	5008	,	,		12031	0.0		0.0	False		,,,				2504	0.0				p.P289P		Atlas-SNP	.											.	GTPBP3	40	.	0			c.C867T						PASS	.	C	,,,	288,4118		9,270,1924	20	22	21		771,837,771,867	-6.3	0.9	19	dbSNP_120	21	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GTPBP3	NM_001128855.2,NM_001195422.1,NM_032620.3,NM_133644.3	,,,	9,271,6223	TT,TC,CC		0.0116,6.5365,2.2221	,,,	257/472,279/515,257/493,289/525	17450038	289,12717	2203	4300	6503	SO:0001819	synonymous_variant	84705	exon5			TGGACCCCCCAAT	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.771C>T	19.37:g.17450038C>T		43	0	0		47	23	0.489362	NM_133644	A6NFH1|A6NIG5|A6NKR4|A8K7B4|B7Z4V8|Q8TCY6|Q8WUW9|Q969G4|Q9BX61	Silent	SNP	ENST00000324894.8	37	CCDS32951.1																																																																																			C|0.972;T|0.028	0.028	strong		0.667	GTPBP3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463624.1	NM_032620		T	17450038	C	T	17450038	2	4	22	1	0	0	0	0	0	0	0	1	6890	610	22	2		2	GTPBP3	19	17450038	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	336955	17450038	41678945	3850	6751											
FAM129C	199786	hgsc.bcm.edu	37	chr19	17638141	17638141	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaagaggagccccgggagacGacagcagcatgggtgggcgg	10	2	20	9	3	0	2	0	0	0	2	0	6	0	3	2	5	3	2	2	5	1	0	rs73504235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17638141G>A	ENST00000335393.4	+	2	223	c.85G>A	c.(85-87)Gac>Aac	p.D29N	FAM129C_ENST00000300971.2_Missense_Mutation_p.D29N|FAM129C_ENST00000352727.3_Missense_Mutation_p.D29N|FAM129C_ENST00000599164.1_5'UTR|FAM129C_ENST00000449408.2_5'UTR|FAM129C_ENST00000601861.1_5'UTR|FAM129C_ENST00000332386.5_Missense_Mutation_p.D29N|FAM129C_ENST00000597887.1_3'UTR|FAM129C_ENST00000600871.1_5'UTR|FAM129C_ENST00000595684.1_Missense_Mutation_p.D29N|FAM129C_ENST00000599124.1_5'UTR	NM_173544.4	NP_775815	Q86XR2	NIBL2_HUMAN	family with sequence similarity 129, member C	29										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						CCCGGGAGACGACAGCAGCAT	0.687													G|||	46	0.0091853	0.0348	0.0	5008	,	,		11779	0.0		0.0	False		,,,				2504	0.0				p.D29N		Atlas-SNP	.											.	FAM129C	110	.	0			c.G85A						PASS	.	G	ASN/ASP,ASN/ASP	96,3940		1,94,1923	26	21	23		85,85	-6	0	19	dbSNP_130	23	3,7943		0,3,3970	yes	missense,missense	FAM129C	NM_001098524.1,NM_173544.4	23,23	1,97,5893	AA,AG,GG		0.0378,2.3786,0.8262	benign,benign	29/652,29/698	17638141	99,11883	2018	3973	5991	SO:0001583	missense	199786	exon2			GGAGACGACAGCA	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.85G>A	19.37:g.17638141G>A	ENSP00000335040:p.Asp29Asn	238	0	0		221	221	1	NM_001098524	B4DNU3|B4DVN7|Q7Z6H6|Q86XR3|Q86XR4|Q8TEQ3	Missense_Mutation	SNP	ENST00000335393.4	37	CCDS12362.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	7.241	0.601307	0.13939	0.023786	3.78E-4	ENSG00000167483	ENST00000335393;ENST00000332386;ENST00000352727;ENST00000300971	T;T;T;T	0.26518	1.92;2.05;1.73;1.75	3.01	-6.03	0.02185	.	1.713730	0.03912	N	0.282032	T	0.04318	0.0119	N	0.08118	0	0.18873	N	0.999985	B;B	0.10296	0.003;0.003	B;B	0.01281	0.0;0.0	T	0.16100	-1.0414	10	0.14656	T	0.56	.	1.1511	0.01786	0.4056:0.0975:0.15:0.3469	.	29;29	Q86XR2;Q86XR2-3	NIBL2_HUMAN;.	N	29	ENSP00000335040:D29N;ENSP00000333447:D29N;ENSP00000341067:D29N;ENSP00000300971:D29N	ENSP00000300971:D29N	D	+	1	0	FAM129C	17499141	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-4.173000	0.00280	-3.604000	0.00133	-0.339000	0.08088	GAC	G|0.990;A|0.010	0.010	strong		0.687	FAM129C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464206.1	NM_173544		A	17638141	G	A	17638141	3	1	22	1	0	0	0	0	1	0	0	0	5443	1058	37	1	91	1	FAM129C	19	17638141	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	188103	17638141	41490842	3851	6752											
FAM129C	199786	hgsc.bcm.edu	37	chr19	17643125	17643125	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgacccagcttcggggccaCccaccccggtggcagccgat	6	5	12	18	3	0	1	0	1	0	0	1	2	0	1	6	4	2	2	6	4	0	1	rs73504248	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17643125C>T	ENST00000335393.4	+	4	471	c.333C>T	c.(331-333)caC>caT	p.H111H	FAM129C_ENST00000300971.2_Silent_p.H111H|FAM129C_ENST00000352727.3_Silent_p.H111H|FAM129C_ENST00000599164.1_Silent_p.H80H|FAM129C_ENST00000449408.2_5'UTR|FAM129C_ENST00000601861.1_Silent_p.H80H|FAM129C_ENST00000332386.5_Silent_p.H111H|FAM129C_ENST00000597887.1_3'UTR|FAM129C_ENST00000600871.1_Silent_p.H57H|FAM129C_ENST00000595684.1_Silent_p.H111H|FAM129C_ENST00000599124.1_Silent_p.H80H	NM_173544.4	NP_775815	Q86XR2	NIBL2_HUMAN	family with sequence similarity 129, member C	111										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						TTCGGGGCCACCCACCCCGGT	0.647													C|||	105	0.0209665	0.0764	0.0058	5008	,	,		16326	0.0		0.0	False		,,,				2504	0.0				p.H111H		Atlas-SNP	.											.	FAM129C	110	.	0			c.C333T						PASS	.	C	,	316,4090	168.3+/-199.2	13,290,1900	67	66	66		333,333	-2.6	0	19	dbSNP_130	66	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	FAM129C	NM_001098524.1,NM_173544.4	,	13,292,6198	TT,TC,CC		0.0233,7.172,2.445	,	111/652,111/698	17643125	318,12688	2203	4300	6503	SO:0001819	synonymous_variant	199786	exon4			GGGCCACCCACCC	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.333C>T	19.37:g.17643125C>T		168	0	0		219	219	1	NM_001098524	B4DNU3|B4DVN7|Q7Z6H6|Q86XR3|Q86XR4|Q8TEQ3	Silent	SNP	ENST00000335393.4	37	CCDS12362.1																																																																																			C|0.976;T|0.024	0.024	strong		0.647	FAM129C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464206.1	NM_173544		T	17643125	C	T	17643125	2	4	22	1	0	0	0	0	0	0	0	1	5443	506	18	2		2	FAM129C	19	17643125	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4984	17643125	41485858	3852	6753											
SLC5A5	6528	hgsc.bcm.edu	37	chr19	17988794	17988794	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gccctgctcatcaaccaggtCggcctgttcctgatcgtgtc	5	11	10	15	2	2	1	2	1	0	0	6	1	3	1	4	2	2	2	4	2	1	1	rs35209536	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17988794C>T	ENST00000222248.3	+	7	1208	c.861C>T	c.(859-861)gtC>gtT	p.V287V		NM_000453.2	NP_000444.1	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium/iodide cotransporter), member 5	287					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						TCAACCAGGTCGGCCTGTTCC	0.632													C|||	97	0.019369	0.0703	0.0058	5008	,	,		18147	0.0		0.0	False		,,,				2504	0.0				p.V287V	Melanoma(65;1008 1708 7910 46650)	Atlas-SNP	.											.	SLC5A5	67	.	0			c.C861T						PASS	.	C		255,4151	148.4+/-182.8	10,235,1958	104	75	85		861	0.3	1	19	dbSNP_126	85	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SLC5A5	NM_000453.2		10,236,6257	TT,TC,CC		0.0116,5.7876,1.9683		287/644	17988794	256,12750	2203	4300	6503	SO:0001819	synonymous_variant	6528	exon7			CCAGGTCGGCCTG		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.861C>T	19.37:g.17988794C>T		65	0	0		84	41	0.488095	NM_000453	O43702|Q2M335|Q9NYB6	Silent	SNP	ENST00000222248.3	37	CCDS12368.1																																																																																			C|0.982;T|0.018	0.018	strong		0.632	SLC5A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466690.1			T	17988794	C	T	17988794	2	4	22	1	0	0	0	0	0	0	0	1	14683	871	31	1		1	SLC5A5	19	17988794	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	345669	17988794	41140189	3853	6754											
KCNN1	3780	hgsc.bcm.edu	37	chr19	18084724	18084724	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agccacagctacaatggcagCgtggggcggccgctgggcag	8	4	17	12	3	0	0	0	0	0	0	0	0	0	0	2	5	4	4	2	5	2	1	rs77030907	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18084724C>T	ENST00000222249.9	+	3	346	c.27C>T	c.(25-27)agC>agT	p.S9S	RNA5SP468_ENST00000516782.1_RNA	NM_002248.3	NP_002239.2	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	9					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)	ACAATGGCAGCGTGGGGCGGC	0.756													C|||	48	0.00958466	0.0356	0.0014	5008	,	,		12575	0.0		0.0	False		,,,				2504	0.0				p.S9S		Atlas-SNP	.											.	KCNN1	74	.	0			c.C27T						PASS	.						3	3	3					19																	18084724		1475	3351	4826	SO:0001819	synonymous_variant	3780	exon3			TGGCAGCGTGGGG	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.27C>T	19.37:g.18084724C>T		2	0	0		12	7	0.583333	NM_002248	Q5KR10|Q6DJU4	Silent	SNP	ENST00000222249.9	37																																																																																				C|0.990;T|0.010	0.010	strong		0.756	KCNN1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471896.2	NM_002248		T	18084724	C	T	18084724	2	4	22	1	0	0	0	0	0	0	0	1	8087	767	27	1		1	KCNN1	19	18084724	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	95930	18084724	41044259	3854	6755											
KCNN1	3780	hgsc.bcm.edu	37	chr19	18084775	18084775	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccctgggacgagaccctccGgaccctgaggccggccaccc	6	3	13	19	3	0	2	0	1	0	1	1	5	1	4	7	4	0	0	7	4	0	0	rs75754669	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18084775G>A	ENST00000222249.9	+	3	397	c.78G>A	c.(76-78)ccG>ccA	p.P26P	RNA5SP468_ENST00000516782.1_RNA	NM_002248.3	NP_002239.2	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	26					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)	GAGACCCTCCGGACCCTGAGG	0.736													G|||	47	0.00938498	0.0348	0.0014	5008	,	,		10833	0.0		0.0	False		,,,				2504	0.0				p.P26P		Atlas-SNP	.											.	KCNN1	74	.	0			c.G78A						PASS	.	G		61,3441		0,61,1690	6	9	8		78	-0.2	0.2	19	dbSNP_131	8	2,7602		0,2,3800	no	coding-synonymous	KCNN1	NM_002248.3		0,63,5490	AA,AG,GG		0.0263,1.7419,0.5673		26/544	18084775	63,11043	1751	3802	5553	SO:0001819	synonymous_variant	3780	exon3			CCCTCCGGACCCT	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.78G>A	19.37:g.18084775G>A		1	0	0		5	4	0.8	NM_002248	Q5KR10|Q6DJU4	Silent	SNP	ENST00000222249.9	37																																																																																				G|0.990;A|0.010	0.010	strong		0.736	KCNN1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471896.2	NM_002248		A	18084775	G	A	18084775	2	1	22	1	0	0	0	0	0	0	0	1	8087	1103	39	1		1	KCNN1	19	18084775	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	51	18084775	41044208	3855	6756											
PDE4C	5143	hgsc.bcm.edu	37	chr19	18330144	18330144	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccatgtaggccactgatcCgggacatgggctgtggggcc	6	7	16	12	1	0	1	0	1	0	0	1	2	1	2	4	5	0	2	4	5	1	1	rs34503849	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18330144C>T	ENST00000355502.3	-	12	1737	c.866G>A	c.(865-867)cGg>cAg	p.R289Q	PDE4C_ENST00000594465.3_Missense_Mutation_p.R289Q|AC068499.10_ENST00000594805.3_RNA|PDE4C_ENST00000597297.1_Missense_Mutation_p.R59Q|PDE4C_ENST00000539010.1_Missense_Mutation_p.R58Q|PDE4C_ENST00000447275.3_Missense_Mutation_p.R183Q|PDE4C_ENST00000598111.2_Missense_Mutation_p.R59Q|PDE4C_ENST00000594617.3_Missense_Mutation_p.R289Q|PDE4C_ENST00000262805.12_Missense_Mutation_p.R257Q			Q08493	PDE4C_HUMAN	phosphodiesterase 4C, cAMP-specific	289			R -> Q (in dbSNP:rs34503849).		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)	GCCACTGATCCGGGACATGGG	0.642													C|||	87	0.0173722	0.0613	0.0058	5008	,	,		16374	0.001		0.001	False		,,,				2504	0.0				p.R289Q		Atlas-SNP	.											.	PDE4C	80	.	0			c.G866A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	201,4205	125.7+/-162.9	4,193,2006	52	50	51		866,770,548	3.7	1	19	dbSNP_126	51	0,8600		0,0,4300	yes	missense,missense,missense	PDE4C	NM_000923.4,NM_001098818.2,NM_001098819.2	43,43,43	4,193,6306	TT,TC,CC		0.0,4.562,1.5454	benign,benign,benign	289/713,257/681,183/607	18330144	201,12805	2203	4300	6503	SO:0001583	missense	5143	exon9			CTGATCCGGGACA		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.866G>A	19.37:g.18330144C>T	ENSP00000347689:p.Arg289Gln	81	0	0		94	55	0.585106	NM_000923	B3KTC4|Q9UN44|Q9UN45|Q9UN46|Q9UPJ6	Missense_Mutation	SNP	ENST00000355502.3	37	CCDS12373.1	37	0.01694139194139194	33	0.06707317073170732	3	0.008287292817679558	1	0.0017482517482517483	0	0.0	C	0.914	-0.718231	0.03182	0.04562	0.0	ENSG00000105650	ENST00000536045;ENST00000355502;ENST00000536507;ENST00000262805;ENST00000447275;ENST00000545961;ENST00000336173;ENST00000539010;ENST00000543547	T;T;T;T	0.68479	-0.31;-0.33;-0.32;-0.02	4.75	3.65	0.41850	.	1.896290	0.02956	N	0.142375	T	0.01730	0.0055	N	0.00038	-2.52	0.28550	N	0.911646	B;B;B;B	0.11235	0.0;0.004;0.001;0.0	B;B;B;B	0.06405	0.001;0.002;0.002;0.001	T	0.48570	-0.9024	10	0.02654	T	1	.	8.4709	0.32984	0.0:0.0967:0.0:0.9033	rs34503849	289;257;95;59	Q08493;Q08493-3;O43850;O76104	PDE4C_HUMAN;.;.;.	Q	368;289;277;257;183;95;58;58;398	ENSP00000347689:R289Q;ENSP00000262805:R257Q;ENSP00000402091:R183Q;ENSP00000439470:R58Q	ENSP00000262805:R257Q	R	-	2	0	PDE4C	18191144	1.000000	0.71417	0.991000	0.47740	0.118000	0.20060	4.475000	0.60210	0.657000	0.30906	-0.657000	0.03884	CGG	C|0.982;T|0.018	0.018	strong		0.642	PDE4C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466295.1			T	18330144	C	T	18330144	3	4	22	1	0	0	0	0	1	0	0	0	11650	652	23	1	1304	1	PDE4C	19	18330144	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	245369	18330144	40798839	3856	6757											
KIAA1683	80726	hgsc.bcm.edu	37	chr19	18368524	18368524	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggctgcccagctccacccaCgtgacggggtggagcatctg	6	6	14	15	3	1	1	0	1	1	0	2	2	2	2	3	4	3	3	3	4	0	0	rs61740686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18368524C>T	ENST00000600328.3	-	4	3202	c.3009G>A	c.(3007-3009)acG>acA	p.T1003T	KIAA1683_ENST00000600359.3_Silent_p.T957T|PDE4C_ENST00000596647.1_5'Flank|KIAA1683_ENST00000392413.4_Silent_p.T1190T|PDE4C_ENST00000355502.3_5'Flank			Q9H0B3	K1683_HUMAN	KIAA1683	1003						mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						GCTCCACCCACGTGACGGGGT	0.662													C|||	170	0.0339457	0.1248	0.0072	5008	,	,		15480	0.0		0.0	False		,,,				2504	0.0				p.T1190T		Atlas-SNP	.											.	KIAA1683	190	.	0			c.G3570A						PASS	.	C	,,	427,3903		12,403,1750	23	30	28		3570,2871,3009	-2.8	0	19	dbSNP_129	28	0,8468		0,0,4234	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	,,	12,403,5984	TT,TC,CC		0.0,9.8614,3.3365	,,	1190/1368,957/1135,1003/1181	18368524	427,12371	2165	4234	6399	SO:0001819	synonymous_variant	80726	exon4			CACCCACGTGACG	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.3009G>A	19.37:g.18368524C>T		56	0	0		95	93	0.978947	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Silent	SNP	ENST00000600328.3	37	CCDS32958.1																																																																																			C|0.964;T|0.036	0.036	strong		0.662	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3			T	18368524	C	T	18368524	2	4	22	1	0	0	0	0	0	0	0	1	8260	523	19	1		1	KIAA1683	19	18368524	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	38380	18368524	40760459	3857	6758											
KIAA1683	80726	hgsc.bcm.edu	37	chr19	18368748	18368748	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgcctggatagtgatcactgCgaggatgcggatctcctctg	7	10	13	11	3	3	1	1	1	2	0	4	5	3	4	2	3	2	0	2	3	1	1	rs61740685		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18368748C>T	ENST00000600328.3	-	4	2978	c.2785G>A	c.(2785-2787)Gca>Aca	p.A929T	KIAA1683_ENST00000600359.3_Missense_Mutation_p.A883T|PDE4C_ENST00000596647.1_5'Flank|KIAA1683_ENST00000392413.4_Missense_Mutation_p.A1116T|PDE4C_ENST00000355502.3_5'Flank			Q9H0B3	K1683_HUMAN	KIAA1683	929	IQ 2. {ECO:0000255|PROSITE- ProRule:PRU00116}.					mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						GTGATCACTGCGAGGATGCGG	0.677													C|||	1	0.000199681	0.0	0.0	5008	,	,		16152	0.0		0.001	False		,,,				2504	0.0				p.A1116T		Atlas-SNP	.											.	KIAA1683	190	.	0			c.G3346A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	1,4401	2.1+/-5.4	0,1,2200	58	57	57		3346,2647,2785	3.5	0	19	dbSNP_129	57	6,8590	5.0+/-18.6	0,6,4292	yes	missense,missense,missense	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	58,58,58	0,7,6492	TT,TC,CC		0.0698,0.0227,0.0539	probably-damaging,probably-damaging,probably-damaging	1116/1368,883/1135,929/1181	18368748	7,12991	2201	4298	6499	SO:0001583	missense	80726	exon4			TCACTGCGAGGAT	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.2785G>A	19.37:g.18368748C>T	ENSP00000470780:p.Ala929Thr	99	0	0		84	40	0.47619	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	37	CCDS32958.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.27	3.587572	0.66105	2.27E-4	6.98E-4	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634;ENST00000392412;ENST00000411671	T;T;T	0.46819	0.86;0.86;0.86	3.5	3.5	0.40072	.	0.000000	0.32671	N	0.005798	T	0.67373	0.2886	M	0.83603	2.65	0.09310	N	1	D;D	0.89917	1.0;0.999	D;D	0.83275	0.992;0.996	T	0.57877	-0.7735	10	0.51188	T	0.08	-16.8658	10.7032	0.45939	0.0:1.0:0.0:0.0	.	1116;929	E9PDE0;Q9H0B3	.;K1683_HUMAN	T	1116;929;883;193;543	ENSP00000376213:A1116T;ENSP00000352774:A929T;ENSP00000404501:A883T	ENSP00000352774:A929T	A	-	1	0	KIAA1683	18229748	0.809000	0.29036	0.021000	0.16686	0.006000	0.05464	3.249000	0.51437	1.971000	0.57363	0.313000	0.20887	GCA	C|0.999;T|0.001	0.001	strong		0.677	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3			T	18368748	C	T	18368748	3	4	22	1	0	0	0	0	1	0	0	0	8260	768	27	1	761	1	KIAA1683	19	18368748	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	224	18368748	40760235	3858	6759											
KIAA1683	80726	hgsc.bcm.edu	37	chr19	18376509	18376509	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaatgccatgtctgttttcGcctgtttctgggtgccagtc	5	16	10	10	1	2	0	0	0	2	0	4	0	2	0	3	1	2	2	3	1	2	4	rs16982285	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18376509G>A	ENST00000600328.3	-	3	2034	c.1841C>T	c.(1840-1842)gCg>gTg	p.A614V	KIAA1683_ENST00000600359.3_Missense_Mutation_p.A568V|KIAA1683_ENST00000392413.4_Missense_Mutation_p.A614V			Q9H0B3	K1683_HUMAN	KIAA1683	614			A -> V (in dbSNP:rs16982285).			mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						GTCTGTTTTCGCCTGTTTCTG	0.562													A|||	738	0.147364	0.4297	0.1282	5008	,	,		20460	0.0129		0.0288	False		,,,				2504	0.0399				p.A614V		Atlas-SNP	.											KIAA1683_ENST00000392413,colon,carcinoma,0,2	KIAA1683	190	2	0			c.C1841T						PASS	.	A	VAL/ALA,VAL/ALA,VAL/ALA	1675,2731	654.3+/-399.7	321,1033,849	59	64	62		1841,1703,1841	-7.1	0	19	dbSNP_123	62	231,8369	808.4+/-407.2	4,223,4073	yes	missense,missense,missense	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	64,64,64	325,1256,4922	AA,AG,GG		2.686,38.0163,14.6548	benign,benign,benign	614/1368,568/1135,614/1181	18376509	1906,11100	2203	4300	6503	SO:0001583	missense	80726	exon3			GTTTTCGCCTGTT	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.1841C>T	19.37:g.18376509G>A	ENSP00000470780:p.Ala614Val	152	0	0		149	66	0.442953	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	37	CCDS32958.1	278	0.12728937728937728	213	0.4329268292682927	48	0.13259668508287292	1	0.0017482517482517483	16	0.021108179419525065	A	1.743	-0.491261	0.04322	0.380163	0.02686	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634	T;T;T	0.03717	3.9;3.9;3.83	3.81	-7.09	0.01553	.	3.072470	0.01420	N	0.014343	T	0.00012	0.0000	N	0.00583	-1.355	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48502	-0.9030	9	0.20046	T	0.44	-0.0309	4.2064	0.10490	0.1471:0.3414:0.3989:0.1126	rs16982285;rs16982285	614;614	E9PDE0;Q9H0B3	.;K1683_HUMAN	V	614;614;568	ENSP00000376213:A614V;ENSP00000352774:A614V;ENSP00000404501:A568V	ENSP00000352774:A614V	A	-	2	0	KIAA1683	18237509	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.555000	0.05999	-2.263000	0.00689	-2.747000	0.00125	GCG	G|0.854;A|0.146	0.146	strong		0.562	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3			A	18376509	G	A	18376509	3	1	22	1	0	0	0	0	1	0	0	0	8260	1087	38	1	2270	1	KIAA1683	19	18376509	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	7761	18376509	40752474	3859	6760											
KIAA1683	80726	hgsc.bcm.edu	37	chr19	18376780	18376780	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agccttgacatttgccactgTtggagaggccagacacagag	11	8	12	10	0	0	4	0	1	0	3	0	5	0	4	3	2	2	1	3	2	0	3	rs12462974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18376780T>C	ENST00000600328.3	-	3	1763	c.1570A>G	c.(1570-1572)Aca>Gca	p.T524A	KIAA1683_ENST00000600359.3_Missense_Mutation_p.T478A|KIAA1683_ENST00000392413.4_Missense_Mutation_p.T524A			Q9H0B3	K1683_HUMAN	KIAA1683	524			T -> A (in dbSNP:rs12462974).			mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						TTTGCCACTGTTGGAGAGGCC	0.617													T|||	738	0.147364	0.4297	0.1282	5008	,	,		17239	0.0129		0.0288	False		,,,				2504	0.0399				p.T524A		Atlas-SNP	.											.	KIAA1683	190	.	0			c.A1570G						PASS	.	T	ALA/THR,ALA/THR,ALA/THR	1674,2732	510.1+/-367.4	321,1032,850	74	68	70		1570,1432,1570	-7.2	0	19	dbSNP_120	70	231,8369	95.6+/-157.4	4,223,4073	yes	missense,missense,missense	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	58,58,58	325,1255,4923	CC,CT,TT		2.686,37.9936,14.6471	benign,benign,benign	524/1368,478/1135,524/1181	18376780	1905,11101	2203	4300	6503	SO:0001583	missense	80726	exon3			CCACTGTTGGAGA	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.1570A>G	19.37:g.18376780T>C	ENSP00000470780:p.Thr524Ala	127	0	0		153	83	0.542484	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	37	CCDS32958.1	278	0.12728937728937728	213	0.4329268292682927	48	0.13259668508287292	1	0.0017482517482517483	16	0.021108179419525065	T	0.160	-1.082165	0.01888	0.379936	0.02686	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634	T;T;T	0.03242	4.07;4.08;4.0	3.97	-7.21	0.01490	.	1.083510	0.07343	N	0.881096	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47686	-0.9098	9	0.02654	T	1	-2.4415	0.3148	0.00294	0.2788:0.2233:0.1381:0.3598	rs12462974;rs12462974	524;524	E9PDE0;Q9H0B3	.;K1683_HUMAN	A	524;524;478	ENSP00000376213:T524A;ENSP00000352774:T524A;ENSP00000404501:T478A	ENSP00000352774:T524A	T	-	1	0	KIAA1683	18237780	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.232000	0.09055	-1.289000	0.02375	-0.337000	0.08149	ACA	T|0.861;C|0.139	0.139	strong		0.617	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3			C	18376780	T	C	18376780	3	2	22	1	0	0	0	0	1	0	0	0	8260	1725	60	3	2541	3	KIAA1683	19	18376780	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	271	18376780	40752203	3860	6761											
LSM4	25804	hgsc.bcm.edu	37	chr19	18420501	18420501	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacccacctcggccagcgccGcccatgccgcggcctttctg	4	6	11	20	5	1	0	0	0	1	0	2	1	1	0	7	2	2	0	7	2	0	1	rs148380214	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18420501G>A	ENST00000593829.1	-	4	568	c.315C>T	c.(313-315)ggC>ggT	p.G105G	LSM4_ENST00000252816.6_Silent_p.G91G	NM_001252129.1|NM_012321.4	NP_001239058.1|NP_036453.1	Q9Y4Z0	LSM4_HUMAN	LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae)	105					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|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)	cytosol (GO:0005829)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U6 snRNP (GO:0005688)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(2)|lung(3)	6						GGCCAGCGCCGCCCATGCCGC	0.682													g|||	9	0.00179712	0.0068	0.0	5008	,	,		16325	0.0		0.0	False		,,,				2504	0.0				p.G105G		Atlas-SNP	.											.	LSM4	15	.	0			c.C315T						PASS	.			37,4365		0,37,2164	29	28	28		315	-3.1	1	19	dbSNP_134	28	0,8596		0,0,4298	no	coding-synonymous	LSM4	NM_012321.3		0,37,6462	AA,AG,GG		0.0,0.8405,0.2847		105/140	18420501	37,12961	2201	4298	6499	SO:0001819	synonymous_variant	25804	exon4			AGCGCCGCCCATG	AF117235	CCDS12374.1, CCDS62601.1	19p13.1	2008-02-05				ENSG00000130520			17259	protein-coding gene	gene with protein product		607284				10369684, 10523320	Standard	NM_012321		Approved	YER112W	uc002niq.3	Q9Y4Z0		ENST00000593829.1:c.315C>T	19.37:g.18420501G>A		17	0	0		35	26	0.742857	NM_012321		Silent	SNP	ENST00000593829.1	37	CCDS12374.1																																																																																			G|0.997;A|0.003	0.003	strong		0.682	LSM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466321.1			A	18420501	G	A	18420501	2	1	22	1	0	0	0	0	0	0	0	1	9067	1074	38	1		1	LSM4	19	18420501	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	43721	18420501	40708482	3861	6762											
SSBP4	170463	hgsc.bcm.edu	37	chr19	18542201	18542201	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccgtccccccacaaccccaaCgcccccatgatggggcctca	8	4	7	22	2	1	1	1	1	0	0	2	1	2	1	9	2	2	0	9	2	2	0	rs113198578	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18542201C>T	ENST00000270061.7	+	6	702	c.408C>T	c.(406-408)aaC>aaT	p.N136N	SSBP4_ENST00000598159.2_Intron|SSBP4_ENST00000599699.2_5'Flank|SSBP4_ENST00000348495.6_Intron	NM_032627.4	NP_116016.1	Q9BWG4	SSBP4_HUMAN	single stranded DNA binding protein 4	136	Pro-rich.					nucleus (GO:0005634)	single-stranded DNA binding (GO:0003697)			endometrium(2)|kidney(1)|skin(1)	4						ACAACCCCAACGCCCCCATGA	0.697													C|||	148	0.0295527	0.0968	0.0159	5008	,	,		7118	0.0		0.0089	False		,,,				2504	0.0				p.N136N		Atlas-SNP	.											SSBP4,NS,neuroblastoma,0,1	SSBP4	19	1	0			c.C408T						PASS	.	C	,	349,3959		14,321,1819	10	10	10		,408	1	0	19	dbSNP_132	10	52,8436		0,52,4192	no	intron,coding-synonymous	SSBP4	NM_001009998.3,NM_032627.4	,	14,373,6011	TT,TC,CC		0.6126,8.1012,3.1338	,	,136/386	18542201	401,12395	2154	4244	6398	SO:0001819	synonymous_variant	170463	exon6			CCCCAACGCCCCC		CCDS12378.1, CCDS32960.1	19p13.1	2008-02-05				ENSG00000130511			15676	protein-coding gene	gene with protein product		607391				12079286	Standard	NM_032627		Approved		uc002niy.3	Q9BWG4		ENST00000270061.7:c.408C>T	19.37:g.18542201C>T		367	0	0		425	236	0.555294	NM_032627	Q9BWW5	Silent	SNP	ENST00000270061.7	37	CCDS12378.1																																																																																			C|0.976;T|0.024	0.024	strong		0.697	SSBP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466348.3	NM_032627		T	18542201	C	T	18542201	2	4	22	1	0	0	0	0	0	0	0	1	15197	535	19	1		1	SSBP4	19	18542201	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	121700	18542201	40586782	3862	6763											
ISYNA1	51477	hgsc.bcm.edu	37	chr19	18547209	18547209	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acctcacagaagcgctccgtGttcgccgtccacagcactat	9	8	8	16	4	1	1	1	0	0	1	4	1	3	1	4	0	2	3	4	0	2	2	rs61743954	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18547209G>A	ENST00000338128.8	-	6	907	c.690C>T	c.(688-690)aaC>aaT	p.N230N	ISYNA1_ENST00000457269.4_Silent_p.N176N|ISYNA1_ENST00000317018.6_Silent_p.N28N|ISYNA1_ENST00000545187.1_Silent_p.N80N|ISYNA1_ENST00000578963.1_Silent_p.N102N	NM_001170938.1|NM_016368.4	NP_001164409.1|NP_057452.1	Q9NPH2	INO1_HUMAN	inositol-3-phosphate synthase 1	230					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						AGCGCTCCGTGTTCGCCGTCC	0.632																																					p.N230N		Atlas-SNP	.											.	ISYNA1	31	.	0			c.C690T						PASS	.	G	,,	205,4201	129.8+/-166.5	5,195,2003	104	93	97		528,240,690	1.6	0.5	19	dbSNP_129	97	54,8546	34.8+/-89.0	0,54,4246	no	coding-synonymous,coding-synonymous,coding-synonymous	ISYNA1	NM_001170938.1,NM_001170939.1,NM_016368.4	,,	5,249,6249	AA,AG,GG		0.6279,4.6527,1.9914	,,	176/505,80/409,230/559	18547209	259,12747	2203	4300	6503	SO:0001819	synonymous_variant	51477	exon6			CTCCGTGTTCGCC		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.690C>T	19.37:g.18547209G>A		44	0	0		36	12	0.333333	NM_016368	B3KRT1|G5E9U0|Q6NXT5|Q7Z525|Q9BT65|Q9H2Y2|Q9NSU0|Q9NVW7	Silent	SNP	ENST00000338128.8	37	CCDS12379.1																																																																																			G|0.982;A|0.018	0.018	strong		0.632	ISYNA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444469.2	NM_016368		A	18547209	G	A	18547209	2	1	22	1	0	0	0	0	0	0	0	1	7876	1368	48	2		2	ISYNA1	19	18547209	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5008	18547209	40581774	3863	6764											
ELL	8178	hgsc.bcm.edu	37	chr19	18561420	18561420	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcttcttgggcttgctgcgCgaggggctgccgtgtggcct	1	13	16	11	3	2	0	0	0	2	0	2	1	2	0	2	4	3	3	2	4	0	4	rs34078075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18561420C>T	ENST00000262809.4	-	8	1403	c.1332G>A	c.(1330-1332)tcG>tcA	p.S444S	ELL_ENST00000596124.3_Silent_p.S311S	NM_006532.3	NP_006523.1	P55199	ELL_HUMAN	elongation factor RNA polymerase II	444					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)		GCTTGCTGCGCGAGGGGCTGC	0.687			T	MLL	AL								C|||	107	0.0213658	0.0681	0.0144	5008	,	,		14591	0.0		0.007	False		,,,				2504	0.0				p.S444S		Atlas-SNP	.		Dom	yes		19	19p13.1	8178	ELL gene (11-19 lysine-rich leukemia gene)		L	.	ELL	52	.	0			c.G1332A						PASS	.	C		273,4131		5,263,1934	35	21	26		1332	-5.8	0	19	dbSNP_126	26	55,8539		0,55,4242	no	coding-synonymous	ELL	NM_006532.3		5,318,6176	TT,TC,CC		0.64,6.1989,2.5235		444/622	18561420	328,12670	2202	4297	6499	SO:0001819	synonymous_variant	8178	exon8			GCTGCGCGAGGGG	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.1332G>A	19.37:g.18561420C>T		189	0	0		266	134	0.503759	NM_006532		Silent	SNP	ENST00000262809.4	37	CCDS12380.1																																																																																			C|0.976;T|0.024	0.024	strong		0.687	ELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466362.1	NM_006532		T	18561420	C	T	18561420	2	4	22	1	0	0	0	0	0	0	0	1	5064	755	27	1		1	ELL	19	18561420	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	14211	18561420	40567563	3864	6765											
ELL	8178	hgsc.bcm.edu	37	chr19	18561473	18561473	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acagtccgtcagcaggggcaGgccgaggcgcacagtggggg	8	3	19	11	3	1	0	1	0	0	0	2	1	2	0	2	6	1	3	2	6	0	0	rs34868531	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18561473G>A	ENST00000262809.4	-	8	1350	c.1279C>T	c.(1279-1281)Ctg>Ttg	p.L427L	ELL_ENST00000596124.3_Silent_p.L294L	NM_006532.3	NP_006523.1	P55199	ELL_HUMAN	elongation factor RNA polymerase II	427					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)		AGCAGGGGCAGGCCGAGGCGC	0.677			T	MLL	AL								G|||	107	0.0213658	0.0681	0.0144	5008	,	,		12206	0.0		0.007	False		,,,				2504	0.0				p.L427L		Atlas-SNP	.		Dom	yes		19	19p13.1	8178	ELL gene (11-19 lysine-rich leukemia gene)		L	.	ELL	52	.	0			c.C1279T						PASS	.	G		212,4120		2,208,1956	19	11	14		1279	-0.1	0	19	dbSNP_126	14	45,8491		0,45,4223	no	coding-synonymous	ELL	NM_006532.3		2,253,6179	AA,AG,GG		0.5272,4.8938,1.9972		427/622	18561473	257,12611	2166	4268	6434	SO:0001819	synonymous_variant	8178	exon8			GGGGCAGGCCGAG	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.1279C>T	19.37:g.18561473G>A		50	0	0		106	58	0.54717	NM_006532		Silent	SNP	ENST00000262809.4	37	CCDS12380.1																																																																																			G|0.980;A|0.020	0.020	strong		0.677	ELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466362.1	NM_006532		A	18561473	G	A	18561473	2	1	22	1	0	0	0	0	0	0	0	1	5064	991	35	2		2	ELL	19	18561473	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	53	18561473	40567510	3865	6766											
KLHL26	55295	hgsc.bcm.edu	37	chr19	18778879	18778879	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgcagagctgtgccgagatCgacctgttccgcgcggccgt	5	8	14	14	6	0	2	0	0	0	2	2	4	1	2	4	1	3	3	4	1	0	1	rs79044993	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18778879C>T	ENST00000300976.4	+	3	762	c.672C>T	c.(670-672)atC>atT	p.I224I	KLHL26_ENST00000599006.1_Intron	NM_018316.1	NP_060786.1	Q53HC5	KLH26_HUMAN	kelch-like family member 26	224	BACK.									breast(1)|central_nervous_system(1)|kidney(1)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						GTGCCGAGATCGACCTGTTCC	0.677													C|||	49	0.00978435	0.034	0.0043	5008	,	,		14950	0.0		0.001	False		,,,				2504	0.0				p.I224I		Atlas-SNP	.											.	KLHL26	43	.	0			c.C672T						PASS	.	C		121,4285	89.2+/-127.9	1,119,2083	38	38	38		672	-8.3	0.9	19	dbSNP_131	38	4,8592	3.7+/-12.6	0,4,4294	no	coding-synonymous	KLHL26	NM_018316.1		1,123,6377	TT,TC,CC		0.0465,2.7463,0.9614		224/616	18778879	125,12877	2203	4298	6501	SO:0001819	synonymous_variant	55295	exon3			CGAGATCGACCTG		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.672C>T	19.37:g.18778879C>T		41	0	0		71	32	0.450704	NM_018316	Q8TAP0|Q9NUX3	Silent	SNP	ENST00000300976.4	37	CCDS12384.1																																																																																			C|0.988;T|0.012	0.012	strong		0.677	KLHL26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465145.1	NM_018316		T	18778879	C	T	18778879	2	4	22	1	0	0	0	0	0	0	0	1	8390	874	31	1		1	KLHL26	19	18778879	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	217406	18778879	40350104	3866	6767											
KLHL26	55295	hgsc.bcm.edu	37	chr19	18779728	18779728	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacgccatggtgggtgccggCggccgcatctatgccctcgg	4	7	15	15	5	1	0	0	0	1	0	2	0	1	0	4	5	2	1	4	5	1	1	rs73533829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18779728C>T	ENST00000300976.4	+	3	1611	c.1521C>T	c.(1519-1521)ggC>ggT	p.G507G	KLHL26_ENST00000599006.1_Intron	NM_018316.1	NP_060786.1	Q53HC5	KLH26_HUMAN	kelch-like family member 26	507										breast(1)|central_nervous_system(1)|kidney(1)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						TGGGTGCCGGCGGCCGCATCT	0.667													C|||	49	0.00978435	0.034	0.0043	5008	,	,		14368	0.0		0.001	False		,,,				2504	0.0				p.G507G		Atlas-SNP	.											.	KLHL26	43	.	0			c.C1521T						PASS	.	C		121,4283		1,119,2082	37	38	37		1521	-6	0.1	19	dbSNP_130	37	4,8576		0,4,4286	no	coding-synonymous	KLHL26	NM_018316.1		1,123,6368	TT,TC,CC		0.0466,2.7475,0.9627		507/616	18779728	125,12859	2202	4290	6492	SO:0001819	synonymous_variant	55295	exon3			TGCCGGCGGCCGC		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.1521C>T	19.37:g.18779728C>T		24	0	0		36	18	0.5	NM_018316	Q8TAP0|Q9NUX3	Silent	SNP	ENST00000300976.4	37	CCDS12384.1																																																																																			C|0.988;T|0.012	0.012	strong		0.667	KLHL26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465145.1	NM_018316		T	18779728	C	T	18779728	2	4	22	1	0	0	0	0	0	0	0	1	8390	755	27	1		1	KLHL26	19	18779728	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	849	18779728	40349255	3867	6768											
UPF1	5976	hgsc.bcm.edu	37	chr19	18958562	18958562	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgattttttagttactgtggAatacacgatcctgcctgcgt	8	16	9	8	2	0	1	0	1	0	0	1	3	1	2	2	1	4	1	2	1	4	5	rs73526913	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18958562A>T	ENST00000599848.1	+	3	590	c.381A>T	c.(379-381)ggA>ggT	p.G127G	UPF1_ENST00000262803.5_Silent_p.G127G			Q92900	RENT1_HUMAN	UPF1 regulator of nonsense transcripts homolog (yeast)	127	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						GTTACTGTGGAATACACGATC	0.428											OREG0025373	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	43	0.00858626	0.0318	0.0014	5008	,	,		19742	0.0		0.0	False		,,,				2504	0.0				p.G127G		Atlas-SNP	.											.	UPF1	88	.	0			c.A381T						PASS	.	A		130,4276	95.7+/-134.4	3,124,2076	128	120	123		381	-7.9	0.8	19	dbSNP_130	123	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	UPF1	NM_002911.3		3,125,6375	TT,TA,AA		0.0116,2.9505,1.0072		127/1119	18958562	131,12875	2203	4300	6503	SO:0001819	synonymous_variant	5976	exon3			CTGTGGAATACAC	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.381A>T	19.37:g.18958562A>T		146	0	0	729	150	70	0.466667	NM_002911	O00239|O43343|Q86Z25|Q92842	Silent	SNP	ENST00000599848.1	37																																																																																				A|0.991;T|0.009	0.009	strong		0.428	UPF1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464684.1	NM_002911		T	18958562	A	T	18958562	2	4	22	1	0	0	0	0	0	0	0	1	17018	233	9	5		5	UPF1	19	18958562	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	178834	18958562	40170421	3868	6769											
DDX49	54555	hgsc.bcm.edu	37	chr19	19035080	19035080	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catgatgctgcgcaaattcaGcttccccaccgtggctctgc	7	10	9	15	2	2	1	1	1	1	0	3	1	3	1	3	1	4	4	3	1	1	2	rs143159618		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:19035080G>C	ENST00000247003.4	+	7	882	c.815G>C	c.(814-816)aGc>aCc	p.S272T	AC002985.3_ENST00000596918.1_Intron|DDX49_ENST00000599156.1_3'UTR|DDX49_ENST00000438170.2_Missense_Mutation_p.S165T	NM_019070.4	NP_061943.2	Q9Y6V7	DDX49_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 49	272	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						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)			CGCAAATTCAGCTTCCCCACC	0.617													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17489	0.0		0.0	False		,,,				2504	0.0				p.S272T		Atlas-SNP	.											.	DDX49	37	.	0			c.G815C						PASS	.	G	THR/SER	6,4400	11.4+/-27.6	0,6,2197	122	71	88		815	-2.3	0.8	19	dbSNP_134	88	0,8600		0,0,4300	no	missense	DDX49	NM_019070.4	58	0,6,6497	CC,CG,GG		0.0,0.1362,0.0461	benign	272/484	19035080	6,13000	2203	4300	6503	SO:0001583	missense	54555	exon7			AATTCAGCTTCCC		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.815G>C	19.37:g.19035080G>C	ENSP00000247003:p.Ser272Thr	214	0	0		231	99	0.428571	NM_019070	E7ENA0|Q53FJ1|Q9BVQ8	Missense_Mutation	SNP	ENST00000247003.4	37	CCDS12390.1	.	.	.	.	.	.	.	.	.	.	G	13.72	2.320348	0.41096	0.001362	0.0	ENSG00000105671	ENST00000247003;ENST00000438170	T;T	0.04862	3.54;3.54	5.03	-2.29	0.06805	Helicase, C-terminal (3);	0.775582	0.12437	N	0.469041	T	0.05410	0.0143	N	0.19112	0.55	0.24060	N	0.996013	B;B	0.06786	0.001;0.001	B;B	0.19946	0.027;0.027	T	0.29119	-1.0022	10	0.72032	D	0.01	-7.7016	15.0157	0.71581	0.3142:0.0:0.6858:0.0	.	272;272	A8K7A1;Q9Y6V7	.;DDX49_HUMAN	T	272;165	ENSP00000247003:S272T;ENSP00000395377:S165T	ENSP00000247003:S272T	S	+	2	0	DDX49	18896080	0.161000	0.22892	0.824000	0.32777	0.934000	0.57294	0.102000	0.15272	-1.026000	0.03330	-0.339000	0.08088	AGC	G|1.000;C|0.000	0.000	weak		0.617	DDX49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464593.1	NM_019070		C	19035080	G	C	19035080	3	2	22	1	0	0	0	0	1	0	0	0	4368	971	34	4	841	4	DDX49	19	19035080	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	76518	19035080	40093903	3869	6770											
SLC25A42	284439	hgsc.bcm.edu	37	chr19	19217081	19217081	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cctcctgccctgttcagagcCctgcccccttggcctcgcct	2	10	8	21	1	1	1	1	0	0	1	3	1	2	1	8	1	3	1	8	1	0	2	rs61740506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:19217081C>A	ENST00000318596.7	+	6	535	c.384C>A	c.(382-384)gcC>gcA	p.A128A	SLC25A42_ENST00000600275.1_3'UTR	NM_178526.4	NP_848621.2	Q86VD7	S2542_HUMAN	solute carrier family 25, member 42	128					ADP transport (GO:0015866)|AMP transport (GO:0080121)|ATP transport (GO:0015867)|coenzyme A transmembrane transport (GO:0035349)|metabolic process (GO:0008152)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	adenosine-diphosphatase activity (GO:0043262)|ADP transmembrane transporter activity (GO:0015217)|AMP transmembrane transporter activity (GO:0080122)|ATP transmembrane transporter activity (GO:0005347)|coenzyme A transmembrane transporter activity (GO:0015228)			cervix(1)|large_intestine(2)|lung(3)	6			OV - Ovarian serous cystadenocarcinoma(5;5.4e-06)|Epithelial(12;0.000497)			TGTTCAGAGCCCTGCCCCCTT	0.682													C|||	113	0.0225639	0.0749	0.0072	5008	,	,		14862	0.0		0.005	False		,,,				2504	0.0041				p.A128A		Atlas-SNP	.											.	SLC25A42	18	.	0			c.C384A						PASS	.	C		360,4046	184.0+/-211.4	12,336,1855	80	85	83		384	0.3	1	19	dbSNP_129	83	34,8566	23.4+/-69.3	0,34,4266	no	coding-synonymous	SLC25A42	NM_178526.3		12,370,6121	AA,AC,CC		0.3953,8.1707,3.0294		128/319	19217081	394,12612	2203	4300	6503	SO:0001819	synonymous_variant	284439	exon6			CAGAGCCCTGCCC		CCDS32966.1	19p13.11	2013-05-22			ENSG00000181035	ENSG00000181035		"Solute carriers"	28380	protein-coding gene	gene with protein product		610823				16949250, 19429682	Standard	NM_178526		Approved	MGC26694	uc002nlf.3	Q86VD7		ENST00000318596.7:c.384C>A	19.37:g.19217081C>A		113	0	0		91	43	0.472527	NM_178526	D2T2J5|O14553|O43378	Silent	SNP	ENST00000318596.7	37	CCDS32966.1																																																																																			C|0.976;A|0.024	0.024	strong		0.682	SLC25A42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465931.1	NM_178526		A	19217081	C	A	19217081	2	1	22	1	0	0	0	0	0	0	0	1	14522	610	22	4		4	SLC25A42	19	19217081	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	182001	19217081	39911902	3870	6771											
TSSK6	51079	hgsc.bcm.edu	37	chr19	19626087	19626087	+	5'Flank	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaacttgttgacgaagtcCgggggcgctcgccgccggtc	6	7	16	12	6	0	1	0	1	0	0	3	3	1	2	3	4	1	2	3	4	2	2	rs150432013	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:19626087C>T	ENST00000507754.4	+	0	0				NDUFA13_ENST00000252576.5_5'Flank|NDUFA13_ENST00000503283.1_5'Flank|CTC-260F20.3_ENST00000555938.1_5'Flank|NDUFA13_ENST00000512771.3_5'Flank|NDUFA13_ENST00000428459.2_5'Flank|TSSK6_ENST00000585580.3_Silent_p.P50P|TSSK6_ENST00000360913.3_Silent_p.P50P|YJEFN3_ENST00000608404.1_5'Flank			Q9P0J0	NDUAD_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13						apoptotic signaling pathway (GO:0097190)|cellular metabolic process (GO:0044237)|cellular response to interferon-beta (GO:0035458)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell growth (GO:0030308)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of peptidase activity (GO:0010952)|positive regulation of protein catabolic process (GO:0045732)|protein import into mitochondrial inner membrane (GO:0045039)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain (GO:0005746)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|NADH dehydrogenase activity (GO:0003954)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)	12						TGACGAAGTCCGGGGGCGCTC	0.617													C|||	18	0.00359425	0.0136	0.0	5008	,	,		15387	0.0		0.0	False		,,,				2504	0.0				p.P50P		Atlas-SNP	.											.	TSSK6	32	.	0			c.G150A						PASS	.	C		42,4364	44.6+/-78.6	0,42,2161	55	51	52		150	-9.9	0.9	19	dbSNP_134	52	0,8600		0,0,4300	no	coding-synonymous	TSSK6	NM_032037.2		0,42,6461	TT,TC,CC		0.0,0.9532,0.3229		50/274	19626087	42,12964	2203	4300	6503	SO:0001631	upstream_gene_variant	83983	exon1			GAAGTCCGGGGGC	AF261134	CCDS12404.1, CCDS12404.2	19p13.11	2011-07-04			ENSG00000186010	ENSG00000186010		"Mitochondrial respiratory chain complex / Complex I"	17194	protein-coding gene	gene with protein product	"complex I B16.6 subunit"	609435				12837546, 10924506, 15367666	Standard	NM_015965		Approved	CGI-39, CDA016, GRIM-19, GRIM19, B16.6		Q9P0J0	OTTHUMG00000162211		19.37:g.19626087C>T	Exception_encountered	50	0	0		72	38	0.527778	NM_032037	B4DF76|K7EK58|Q6PKI0|Q9H2L3|Q9Y327	Silent	SNP	ENST00000507754.4	37	CCDS12404.2																																																																																			C|0.996;T|0.004	0.004	strong		0.617	NDUFA13-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367916.6	NM_015965		T	19626087	C	T	19626087	1	4	22	0	1	0	0	0	0	0	0	0	16687	639	23	1		1	TSSK6	19	19626087	5'Flank	SNP	C	TCGA-G8-6324-01A-11D-2210-10	409006	19626087	39502896	3871	6772											
ATP13A1	57130	hgsc.bcm.edu	37	chr19	19766365	19766365	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	catacataggcagctgcagcGatggcaaacaccaggaggaa	15	4	12	10	1	0	0	0	0	0	0	0	3	0	2	1	4	5	4	1	4	4	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:19766365G>A	ENST00000357324.6	-	10	1394	c.1368C>T	c.(1366-1368)atC>atT	p.I456I	ATP13A1_ENST00000291503.5_Silent_p.I338I|ATP13A1_ENST00000496082.1_5'UTR	NM_020410.2	NP_065143.2	Q9HD20	AT131_HUMAN	ATPase type 13A1	456	Poly-Ala.					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						CAGCTGCAGCGATGGCAAACA	0.607																																					p.I456I	Esophageal Squamous(142;920 1789 9047 14684 24777)	Atlas-SNP	.											.	ATP13A1	82	.	0			c.C1368T						PASS	.						75	68	70					19																	19766365		2203	4300	6503	SO:0001819	synonymous_variant	57130	exon10			TGCAGCGATGGCA	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.1368C>T	19.37:g.19766365G>A		134	0	0		147	79	0.537415	NM_020410	B3KPJ2|B3KTA7|Q6NT90|Q6ZMG7|Q9H6C6	Silent	SNP	ENST00000357324.6	37	CCDS32970.2																																																																																			.	.	none		0.607	ATP13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329005.1	NM_020410		A	19766365	G	A	19766365	2	1	22	1	0	0	0	0	0	0	0	1	1123	1048	37	1		1	ATP13A1	19	19766365	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	140278	19766365	39362618	3872	6773											
ZNF506	440515	hgsc.bcm.edu	37	chr19	19906131	19906131	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atcaattttcttatatgtagTacgggttgaagactggttaa	12	16	9	4	1	2	2	1	1	1	1	2	2	2	2	0	2	1	4	0	2	7	8	rs16996376	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:19906131T>G	ENST00000540806.2	-	4	653	c.565A>C	c.(565-567)Act>Cct	p.T189P	CTC-559E9.4_ENST00000590274.1_lincRNA|CTC-559E9.6_ENST00000591884.1_RNA|ZNF506_ENST00000443905.2_Missense_Mutation_p.T189P|ZNF506_ENST00000587461.1_Intron|ZNF506_ENST00000450683.2_Missense_Mutation_p.T157P|CTC-559E9.6_ENST00000589657.1_RNA			Q5JVG8	ZN506_HUMAN	zinc finger protein 506	189			T -> P (in dbSNP:rs16996376).		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						TTATATGTAGTACGGGTTGAA	0.303													t|||	327	0.0652955	0.2262	0.0288	5008	,	,		19010	0.0		0.007	False		,,,				2504	0.001				p.T189P		Atlas-SNP	.											.	ZNF506	36	.	0			c.A565C						PASS	.	T	PRO/THR,PRO/THR	787,3387		71,645,1371	51	53	52		565,469	1	0.1	19	dbSNP_123	52	66,8426		1,64,4181	yes	missense,missense	ZNF506	NM_001099269.2,NM_001145404.1	38,38	72,709,5552	GG,GT,TT		0.7772,18.8548,6.7346	possibly-damaging,possibly-damaging	189/445,157/413	19906131	853,11813	2087	4246	6333	SO:0001583	missense	440515	exon4			ATGTAGTACGGGT	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.565A>C	19.37:g.19906131T>G	ENSP00000440625:p.Thr189Pro	66	0	0		50	22	0.44	NM_001099269	B3KTH6	Missense_Mutation	SNP	ENST00000540806.2	37	CCDS42531.1	131	0.059981684981684984	115	0.23373983739837398	13	0.03591160220994475	0	0.0	3	0.00395778364116095	t	13.27	2.185989	0.38609	0.188548	0.007772	ENSG00000081665	ENST00000443905;ENST00000540806;ENST00000450683	T;T;T	0.01172	5.23;5.23;5.23	0.974	0.974	0.19715	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.85373	2.75	0.80722	P	0.0	D;D	0.67145	0.996;0.967	D;P	0.65874	0.939;0.75	T	0.41980	-0.9478	8	0.87932	D	0	.	4.0711	0.09882	0.0:0.0:0.0:1.0	rs16996376;rs60499475;rs16996376	189;157	Q5JVG8;Q5JVG8-2	ZN506_HUMAN;.	P	189;189;157	ENSP00000393835:T189P;ENSP00000440625:T189P;ENSP00000408892:T157P	ENSP00000393835:T189P	T	-	1	0	ZNF506	19767131	0.000000	0.05858	0.061000	0.19648	0.058000	0.15608	-0.102000	0.10956	0.358000	0.24211	0.347000	0.21830	ACT	T|0.935;G|0.065	0.065	strong		0.303	ZNF506-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460794.1	XM_036218		G	19906131	T	G	19906131	3	3	22	1	0	0	0	0	1	0	0	0	17967	1638	57	5	773	5	ZNF506	19	19906131	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	139766	19906131	39222852	3873	6774											
ZNF93	81931	hgsc.bcm.edu	37	chr19	20044810	20044810	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gtgtaataaatgtggcaaagCctttattgcatcctcaaccc	12	12	7	10	0	1	0	1	0	0	0	2	0	2	0	3	1	3	3	3	1	6	5	rs75974774	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:20044810C>T	ENST00000343769.5	+	4	1074	c.1046C>T	c.(1045-1047)gCc>gTc	p.A349V	AC007204.2_ENST00000592245.1_lincRNA	NM_031218.3	NP_112495.2	P35789	ZNF93_HUMAN	zinc finger protein 93	349					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						TGTGGCAAAGCCTTTATTGCA	0.383													c|||	7	0.00139776	0.0053	0.0	5008	,	,		23005	0.0		0.0	False		,,,				2504	0.0				p.A349V		Atlas-SNP	.											.	ZNF93	81	.	0			c.C1046T						PASS	.	C	VAL/ALA	13,4393	20.2+/-43.8	0,13,2190	88	86	87		1046	0.9	0.8	19	dbSNP_131	87	0,8600		0,0,4300	yes	missense	ZNF93	NM_031218.3	64	0,13,6490	TT,TC,CC		0.0,0.2951,0.1	benign	349/621	20044810	13,12993	2203	4300	6503	SO:0001583	missense	81931	exon4			GCAAAGCCTTTAT	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.1046C>T	19.37:g.20044810C>T	ENSP00000342002:p.Ala349Val	70	0	0		92	47	0.51087	NM_031218	A6NMY2|B9EGT2|Q8N8Q4|Q9H9X5|Q9Y2N8	Missense_Mutation	SNP	ENST00000343769.5	37	CCDS32973.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	c	16.93	3.258220	0.59321	0.002951	0.0	ENSG00000184635	ENST00000343769;ENST00000427325	T	0.13778	2.56	0.85	0.85	0.18980	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12305	0.0299	L	0.28458	0.855	0.09310	N	0.999998	D	0.56035	0.974	P	0.60068	0.868	T	0.12760	-1.0535	9	0.52906	T	0.07	.	4.6298	0.12496	0.0:0.5889:0.4111:0.0	.	349	P35789	ZNF93_HUMAN	V	349	ENSP00000342002:A349V	ENSP00000342002:A349V	A	+	2	0	ZNF93	19905810	0.001000	0.12720	0.767000	0.31495	0.766000	0.43426	0.320000	0.19540	0.192000	0.20272	0.195000	0.17529	GCC	C|0.998;T|0.002	0.002	strong		0.383	ZNF93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460808.2	NM_031218		T	20044810	C	T	20044810	3	4	22	1	0	0	0	0	1	0	0	0	18217	739	26	2	1060	2	ZNF93	19	20044810	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	138679	20044810	39084173	3874	6775											
ZNF93	81931	hgsc.bcm.edu	37	chr19	20044886	20044886	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattacaaatgtgaagaatgTggcaaagccttcatttggtc	13	12	9	7	0	1	2	1	1	0	1	2	2	1	2	1	2	2	1	1	2	5	3	rs10401345	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:20044886T>C	ENST00000343769.5	+	4	1150	c.1122T>C	c.(1120-1122)tgT>tgC	p.C374C	AC007204.2_ENST00000592245.1_lincRNA	NM_031218.3	NP_112495.2	P35789	ZNF93_HUMAN	zinc finger protein 93	374					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)	p.C374C(1)		endometrium(6)|kidney(2)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	24						GTGAAGAATGTGGCAAAGCCT	0.388													t|||	601	0.120008	0.2534	0.0447	5008	,	,		22657	0.0506		0.0437	False		,,,				2504	0.1431				p.C374C		Atlas-SNP	.											ZNF93,NS,carcinoma,0,1	ZNF93	81	1	1	Substitution - coding silent(1)	stomach(1)	c.T1122C						PASS	.	T		928,3478	355.1+/-312.9	98,732,1373	89	89	89		1122	0.9	0.5	19	dbSNP_119	89	281,8319	105.4+/-166.3	2,277,4021	no	coding-synonymous	ZNF93	NM_031218.3		100,1009,5394	CC,CT,TT		3.2674,21.0622,9.2957		374/621	20044886	1209,11797	2203	4300	6503	SO:0001819	synonymous_variant	81931	exon4			AGAATGTGGCAAA	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.1122T>C	19.37:g.20044886T>C		65	0	0		81	81	1	NM_031218	A6NMY2|B9EGT2|Q8N8Q4|Q9H9X5|Q9Y2N8	Silent	SNP	ENST00000343769.5	37	CCDS32973.1																																																																																			T|0.908;C|0.092	0.092	strong		0.388	ZNF93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460808.2	NM_031218		C	20044886	T	C	20044886	2	2	22	1	0	0	0	0	0	0	0	1	18217	1702	59	3		3	ZNF93	19	20044886	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	76	20044886	39084097	3875	6776											
ZNF708	7562	hgsc.bcm.edu	37	chr19	21476912	21476912	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggactgtttaaaagctttgcCacattcttcacatttgtagg	10	15	8	8	0	2	0	1	0	1	0	2	1	2	1	1	2	2	3	1	2	3	7	rs112819776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:21476912C>T	ENST00000356929.3	-	4	1053	c.856G>A	c.(856-858)Ggc>Agc	p.G286S		NM_021269.2	NP_067092.2	P17019	ZN708_HUMAN	zinc finger protein 708	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)	p.G286C(1)		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						AAAGCTTTGCCACATTCTTCA	0.383													C|||	27	0.00539137	0.0197	0.0014	5008	,	,		20573	0.0		0.0	False		,,,				2504	0.0				p.G286S		Atlas-SNP	.											ZNF708,NS,carcinoma,0,1	ZNF708	66	1	1	Substitution - Missense(1)	lung(1)	c.G856A						PASS	.	C	SER/GLY	64,4332		0,64,2134	51	55	54		856	1	0.6	19	dbSNP_132	54	1,8595		0,1,4297	no	missense	ZNF708	NM_021269.2	56	0,65,6431	TT,TC,CC		0.0116,1.4559,0.5003	possibly-damaging	286/564	21476912	65,12927	2198	4298	6496	SO:0001583	missense	7562	exon4			CTTTGCCACATTC	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.856G>A	19.37:g.21476912C>T	ENSP00000349401:p.Gly286Ser	31	0	0		23	9	0.391304	NM_021269	Q6ZMR0	Missense_Mutation	SNP	ENST00000356929.3	37	CCDS32980.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	.	13.82	2.351563	0.41700	0.014559	1.16E-4	ENSG00000182141	ENST00000356929	T	0.01455	4.87	1.05	1.05	0.20165	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01558	0.0050	L	0.43701	1.375	0.35437	D	0.794531	D	0.76494	0.999	D	0.81914	0.995	T	0.45614	-0.9249	9	0.62326	D	0.03	.	8.9689	0.35894	0.0:1.0:0.0:0.0	.	286	P17019	ZN708_HUMAN	S	286	ENSP00000349401:G286S	ENSP00000349401:G286S	G	-	1	0	ZNF708	21268752	0.049000	0.20398	0.552000	0.28243	0.491000	0.33493	0.979000	0.29500	0.482000	0.27582	0.485000	0.47835	GGC	C|0.994;T|0.006	0.006	strong		0.383	ZNF708-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463953.1	NM_021269		T	21476912	C	T	21476912	3	4	22	1	0	0	0	0	1	0	0	0	18127	594	21	2	839	2	ZNF708	19	21476912	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1432026	21476912	37652071	3876	6777											
ZNF100	163227	hgsc.bcm.edu	37	chr19	21909548	21909548	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ataaggcttagggactggttAaagtctttaccacattcttc	11	14	8	8	0	2	0	0	0	2	0	3	1	2	1	1	3	1	2	1	3	5	7	rs371600049		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:21909548A>G	ENST00000358296.6	-	5	1764	c.1566T>C	c.(1564-1566)ttT>ttC	p.F522F	ZNF100_ENST00000305570.6_Silent_p.F458F	NM_173531.3	NP_775802.2	Q8IYN0	ZN100_HUMAN	zinc finger protein 100	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)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)	21						GGGACTGGTTAAAGTCTTTAC	0.368													N|||	1	0.000199681	0.0008	0.0	5008	,	,		19310	0.0		0.0	False		,,,				2504	0.0				p.F522F		Atlas-SNP	.											.	ZNF100	62	.	0			c.T1566C						PASS	.	A		3,4315		0,3,2156	71	80	77		1566	-0.4	0.3	19		77	0,8552		0,0,4276	no	coding-synonymous	ZNF100	NM_173531.3		0,3,6432	GG,GA,AA		0.0,0.0695,0.0233		522/543	21909548	3,12867	2159	4276	6435	SO:0001819	synonymous_variant	163227	exon5			CTGGTTAAAGTCT	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.1566T>C	19.37:g.21909548A>G		43	0	0		36	27	0.75	NM_173531	Q7M4M0	Silent	SNP	ENST00000358296.6	37	CCDS42538.1																																																																																			.	.	weak		0.368	ZNF100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464087.1	NM_173531		G	21909548	A	G	21909548	2	3	22	1	0	0	0	0	0	0	0	1	17728	359	13	3		3	ZNF100	19	21909548	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	432636	21909548	37219435	3877	6778											
ZNF43	7594	hgsc.bcm.edu	37	chr19	21991663	21991663	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgtagggtttcttttcagtAtgaattttcttatgtttagt	7	23	8	3	0	3	1	1	1	2	0	3	1	3	1	0	1	0	4	0	1	5	11	rs61733114	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:21991663A>G	ENST00000354959.4	-	4	1345	c.1176T>C	c.(1174-1176)caT>caC	p.H392H	ZNF43_ENST00000595461.1_Silent_p.H386H|ZNF43_ENST00000598381.1_Silent_p.H386H|ZNF43_ENST00000594012.1_Silent_p.H386H	NM_003423.3	NP_003414.2	P17038	ZNF43_HUMAN	zinc finger protein 43	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)			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)		TCTTTTCAGTATGAATTTTCT	0.363													a|||	195	0.0389377	0.1392	0.0159	5008	,	,		20000	0.0		0.0	False		,,,				2504	0.0				p.H401H		Atlas-SNP	.											.	ZNF43	152	.	0			c.T1203C						PASS	.	A		469,3937	213.8+/-233.3	27,415,1761	55	59	58		1176	-2.5	0	19	dbSNP_129	58	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	ZNF43	NM_003423.2		27,423,6053	GG,GA,AA		0.093,10.6446,3.6675		392/810	21991663	477,12529	2203	4300	6503	SO:0001819	synonymous_variant	7594	exon4			TTCAGTATGAATT	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.1176T>C	19.37:g.21991663A>G		52	0	0		49	28	0.571429	NM_001256653	A8K5N8|P28160|Q53XQ2|Q5H9T3|Q96DG1	Silent	SNP	ENST00000354959.4	37	CCDS12413.2																																																																																			A|0.968;G|0.032	0.032	strong		0.363	ZNF43-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250380.2	NM_003423		G	21991663	A	G	21991663	2	3	22	1	0	0	0	0	0	0	0	1	17918	446	16	3		3	ZNF43	19	21991663	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	82115	21991663	37137320	3878	6779											
ZNF208	7757	hgsc.bcm.edu	37	chr19	22155434	22155434	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacatttgtagggtttctcaTcagtatgaattctcttatgt	9	18	7	7	0	3	1	2	1	2	0	5	1	3	1	0	1	0	3	0	1	4	6	rs139351235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22155434T>C	ENST00000397126.4	-	4	2550	c.2402A>G	c.(2401-2403)gAt>gGt	p.D801G	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	801					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)				GGGTTTCTCATCAGTATGAAT	0.363													N|||	152	0.0303514	0.1089	0.0115	5008	,	,		20788	0.0		0.0	False		,,,				2504	0.0				p.D801G		Atlas-SNP	.											.	ZNF208	817	.	0			c.A2402G						PASS	.	C	GLY/ASP	404,3794		23,358,1718	57	66	63		2402	2.6	0.1	19	dbSNP_134	63	3,8493		0,3,4245	no	missense	ZNF208	NM_007153.3	94	23,361,5963	CC,CT,TT		0.0353,9.6236,3.2062	benign	801/1281	22155434	407,12287	2099	4248	6347	SO:0001583	missense	7757	exon4			TTCTCATCAGTAT	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.2402A>G	19.37:g.22155434T>C	ENSP00000380315:p.Asp801Gly	21	0	0		26	16	0.615385	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	61	0.027930402930402932	58	0.11788617886178862	3	0.008287292817679558	0	0.0	0	0.0	t	0.001	-2.962685	0.00049	0.096236	3.53E-4	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.11277	2.79	2.57	2.57	0.30868	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00073	0.0002	.	.	.	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.43327	-0.9398	7	0.02654	T	1	.	5.0553	0.14529	0.0:0.6551:0.213:0.1319	.	701	O43345	ZN208_HUMAN	G	801;701	ENSP00000380315:D801G	ENSP00000380315:D801G	D	-	2	0	ZNF208	21947274	0.000000	0.05858	0.123000	0.21794	0.158000	0.22134	-0.473000	0.06615	0.123000	0.18342	-1.171000	0.01739	GAT	T|0.972;C|0.028	0.028	strong		0.363	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		C	22155434	T	C	22155434	3	2	22	1	0	0	0	0	1	0	0	0	17781	1435	50	3	1444	3	ZNF208	19	22155434	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	163771	22155434	36973549	3879	6780											
ZNF208	7757	hgsc.bcm.edu	37	chr19	22156470	22156470	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aaagcctttgccacattcttCacatttgtagggtgtctctc	8	15	7	11	0	3	0	1	0	2	0	5	0	3	0	2	1	2	1	2	1	2	5	rs7255075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22156470C>G	ENST00000397126.4	-	4	1514	c.1366G>C	c.(1366-1368)Gaa>Caa	p.E456Q	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	456			E -> Q (in dbSNP:rs7255075).		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)				CCACATTCTTCACATTTGTAG	0.378													c|||	152	0.0303514	0.1089	0.0101	5008	,	,		21690	0.0		0.001	False		,,,				2504	0.0				p.E456Q		Atlas-SNP	.											ZNF208_ENST00000428290,NS,carcinoma,+2,3	ZNF208	817	3	0			c.G1366C						PASS	.	C	GLN/GLU	499,3789		22,455,1667	73	79	77		1366	0.6	0	19	dbSNP_116	77	3,8513		0,3,4255	no	missense	ZNF208	NM_007153.3	29	22,458,5922	GG,GC,CC		0.0352,11.6371,3.9206	possibly-damaging	456/1281	22156470	502,12302	2144	4258	6402	SO:0001583	missense	7757	exon4			ATTCTTCACATTT	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.1366G>C	19.37:g.22156470C>G	ENSP00000380315:p.Glu456Gln	64	0	0		80	36	0.45	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	63	0.028846153846153848	59	0.11991869918699187	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	C	12.09	1.832255	0.32421	0.116371	3.52E-4	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.18960	2.18	2.83	0.577	0.17385	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00328	0.0010	.	.	.	0.80722	P	0.0	P	0.44816	0.844	P	0.55667	0.781	T	0.13953	-1.0490	7	0.18710	T	0.47	.	3.6064	0.08043	0.0:0.2616:0.1947:0.5437	rs7255075;rs52824395;rs58613552;rs7255075	456	O43345	ZN208_HUMAN	Q	456	ENSP00000380315:E456Q	ENSP00000380315:E456Q	E	-	1	0	ZNF208	21948310	0.000000	0.05858	0.000000	0.03702	0.358000	0.29455	-4.155000	0.00284	-0.314000	0.08716	0.306000	0.20318	GAA	C|0.961;G|0.039	0.039	strong		0.378	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		G	22156470	C	G	22156470	3	3	22	1	0	0	0	0	1	0	0	0	17781	835	29	4	2480	4	ZNF208	19	22156470	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1036	22156470	36972513	3880	6781											
ZNF257	113835	hgsc.bcm.edu	37	chr19	22256347	22256347	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgtaatatgaagagacatgaGatggtagccaaacccccagg	15	7	11	8	0	0	3	0	2	0	2	0	5	0	3	3	2	2	2	3	2	5	3	rs10423157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22256347G>A	ENST00000594947.1	+	3	351	c.207G>A	c.(205-207)gaG>gaA	p.E69E	ZNF257_ENST00000600162.1_Silent_p.E69E	NM_033468.2	NP_258429.2	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	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)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|lung(4)	6		all_lung(12;0.0961)|Lung NSC(12;0.103)				AGAGACATGAGATGGTAGCCA	0.438													G|||	556	0.111022	0.4054	0.0274	5008	,	,		16022	0.0		0.0	False		,,,				2504	0.001				p.E69E		Atlas-SNP	.											.	ZNF257	156	.	0			c.G207A						PASS	.	G		1613,2793	496.2+/-363.5	291,1031,881	133	145	141		207	-1.7	0	19	dbSNP_119	141	17,8583	11.2+/-40.8	0,17,4283	no	coding-synonymous	ZNF257	NM_033468.2		291,1048,5164	AA,AG,GG		0.1977,36.6092,12.5327		69/564	22256347	1630,11376	2203	4300	6503	SO:0001819	synonymous_variant	113835	exon3			ACATGAGATGGTA	AF070651	CCDS46030.1	19p12	2014-02-14			ENSG00000197134	ENSG00000197134		"Zinc fingers, C2H2-type", "-"	13498	protein-coding gene	gene with protein product		606957				10585455	Standard	NM_033468		Approved	BMZF-4	uc010ecx.3	Q9Y2Q1	OTTHUMG00000182927	ENST00000594947.1:c.207G>A	19.37:g.22256347G>A		55	0	0		61	26	0.42623	NM_033468	B3KPS4|E9PG34|Q8NE34	Silent	SNP	ENST00000594947.1	37	CCDS46030.1																																																																																			G|0.927;A|0.073	0.073	strong		0.438	ZNF257-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464382.1			A	22256347	G	A	22256347	2	1	22	1	0	0	0	0	0	0	0	1	17815	933	33	2		2	ZNF257	19	22256347	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	99877	22256347	36872636	3881	6782											
ZNF257	113835	hgsc.bcm.edu	37	chr19	22256358	22256358	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagacatgagatggtagccaAacccccaggtaggtgagagt	13	6	14	8	0	0	3	0	2	0	3	0	6	0	3	3	3	2	2	3	3	3	2	rs73930397	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22256358A>G	ENST00000594947.1	+	3	362	c.218A>G	c.(217-219)aAa>aGa	p.K73R	ZNF257_ENST00000600162.1_Missense_Mutation_p.K73R	NM_033468.2	NP_258429.2	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	73	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)			haematopoietic_and_lymphoid_tissue(2)|lung(4)	6		all_lung(12;0.0961)|Lung NSC(12;0.103)				ATGGTAGCCAAACCCCCAGGT	0.443													A|||	224	0.0447284	0.1634	0.0115	5008	,	,		15865	0.0		0.0	False		,,,				2504	0.0				p.K73R		Atlas-SNP	.											.	ZNF257	156	.	0			c.A218G						PASS	.	A	ARG/LYS	735,3671	295.3+/-283.6	61,613,1529	125	136	132		218	-1.7	0.2	19	dbSNP_130	132	8,8592	6.4+/-24.3	0,8,4292	yes	missense	ZNF257	NM_033468.2	26	61,621,5821	GG,GA,AA		0.093,16.6818,5.7127	benign	73/564	22256358	743,12263	2203	4300	6503	SO:0001583	missense	113835	exon3			TAGCCAAACCCCC	AF070651	CCDS46030.1	19p12	2014-02-14			ENSG00000197134	ENSG00000197134		"Zinc fingers, C2H2-type", "-"	13498	protein-coding gene	gene with protein product		606957				10585455	Standard	NM_033468		Approved	BMZF-4	uc010ecx.3	Q9Y2Q1	OTTHUMG00000182927	ENST00000594947.1:c.218A>G	19.37:g.22256358A>G	ENSP00000470209:p.Lys73Arg	57	0	0		57	27	0.473684	NM_033468	B3KPS4|E9PG34|Q8NE34	Missense_Mutation	SNP	ENST00000594947.1	37	CCDS46030.1	87	0.03983516483516483	83	0.16869918699186992	4	0.011049723756906077	0	0.0	0	0.0	A	0.702	-0.790515	0.02884	0.166818	9.3E-4	ENSG00000197134	ENST00000435820;ENST00000397123	.	.	.	0.86	-1.72	0.08107	Krueppel-associated box (1);	.	.	.	.	T	0.00039	0.0001	N	0.04508	-0.205	0.80722	P	0.0	B	0.06786	0.001	B	0.10450	0.005	T	0.24297	-1.0164	7	0.30854	T	0.27	.	2.1458	0.03787	0.3751:0.3325:0.2924:0.0	.	73	Q9Y2Q1	ZN257_HUMAN	R	73	.	ENSP00000380312:K73R	K	+	2	0	ZNF257	22048198	0.000000	0.05858	0.249000	0.24280	0.256000	0.26092	-0.441000	0.06879	-1.510000	0.01796	-1.552000	0.00895	AAA	A|0.967;G|0.033	0.033	strong		0.443	ZNF257-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464382.1			G	22256358	A	G	22256358	3	3	22	1	0	0	0	0	1	0	0	0	17815	14	1	3	228	3	ZNF257	19	22256358	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	11	22256358	36872625	3882	6783											
ZNF98	148198	hgsc.bcm.edu	37	chr19	22575504	22575504	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	tacacttgaaagatttctttCcagtatgtcctatcttatgt	10	18	5	8	0	2	2	0	1	2	1	4	2	4	2	2	0	1	1	2	0	5	7	rs116270361	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22575504C>G	ENST00000357774.5	-	4	654	c.533G>C	c.(532-534)gGa>gCa	p.G178A		NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	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)			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)				AGATTTCTTTCCAGTATGTCC	0.303													c|||	102	0.0203674	0.0741	0.0058	5008	,	,		17746	0.0		0.0	False		,,,				2504	0.0				p.G178A		Atlas-SNP	.											.	ZNF98	230	.	0			c.G533C						PASS	.	C	ALA/GLY	286,3752		6,274,1739	26	27	27		533	-1.8	0	19	dbSNP_132	27	2,8428		0,2,4213	no	missense	ZNF98	NM_001098626.1	60	6,276,5952	GG,GC,CC		0.0237,7.0827,2.3099	possibly-damaging	178/573	22575504	288,12180	2019	4215	6234	SO:0001583	missense	148198	exon4			TTCTTTCCAGTAT		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.533G>C	19.37:g.22575504C>G	ENSP00000350418:p.Gly178Ala	280	0	0		287	152	0.529617	NM_001098626		Missense_Mutation	SNP	ENST00000357774.5	37	CCDS46031.1	42	0.019230769230769232	40	0.08130081300813008	2	0.0055248618784530384	0	0.0	0	0.0	.	12.41	1.928642	0.34002	0.070827	2.37E-4	ENSG00000197360	ENST00000357774	T	0.35236	1.32	1.28	-1.83	0.07833	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02767	0.0083	L	0.52905	1.665	0.30794	N	0.740644	P	0.45827	0.867	P	0.55713	0.782	T	0.22103	-1.0226	9	0.66056	D	0.02	.	4.2412	0.10648	0.2247:0.6036:0.0:0.1717	.	178	A6NK75	ZNF98_HUMAN	A	178	ENSP00000350418:G178A	ENSP00000350418:G178A	G	-	2	0	ZNF98	22367344	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	0.168000	0.16622	-0.223000	0.09943	0.305000	0.20034	GGA	C|0.976;G|0.024	0.024	strong		0.303	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626		G	22575504	C	G	22575504	3	3	22	1	0	0	0	0	1	0	0	0	18218	855	30	4	1189	4	ZNF98	19	22575504	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	319146	22575504	36553479	3883	6784											
ZNF492	57615	hgsc.bcm.edu	37	chr19	22846962	22846962	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaacataaaagaattcataGtggagagaaaccctacaaat	20	8	6	7	0	2	2	2	0	0	2	2	4	2	3	1	1	3	0	1	1	8	4	rs138844698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22846962G>C	ENST00000456783.2	+	4	735	c.491G>C	c.(490-492)aGt>aCt	p.S164T	CTC-457E21.9_ENST00000601860.1_RNA	NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492	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)			endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				AGAATTCATAGTGGAGAGAAA	0.338													N|||	246	0.0491214	0.1778	0.0115	5008	,	,		17962	0.0		0.003	False		,,,				2504	0.0				p.S164T		Atlas-SNP	.											.	ZNF492	129	.	0			c.G491C						PASS	.						14	20	18					19																	22846962		1994	4214	6208	SO:0001583	missense	57615	exon4			TTCATAGTGGAGA	AB040906	CCDS46032.1	19p13.11	2013-01-08				ENSG00000229676		"Zinc fingers, C2H2-type"	23707	protein-coding gene	gene with protein product			"zinc finger protein 115 (Y20)"	ZNF115		10819331	Standard	NM_020855		Approved	KIAA1473	uc002nqw.3	Q9P255		ENST00000456783.2:c.491G>C	19.37:g.22846962G>C	ENSP00000413660:p.Ser164Thr	281	2	0.00711744		160	119	0.74375	NM_020855	Q08EI7|Q08EI8	Missense_Mutation	SNP	ENST00000456783.2	37	CCDS46032.1	93	0.042582417582417584	87	0.17682926829268292	4	0.011049723756906077	0	0.0	2	0.002638522427440633	.	0.004	-2.252690	0.00268	.	.	ENSG00000229676	ENST00000456783	T	0.12879	2.64	1.3	1.3	0.21679	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00890	-1.11	0.52501	P	4.999999999999449E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.44452	-0.9327	8	0.02654	T	1	.	6.7224	0.23338	0.0:0.7004:0.2996:0.0	.	164	Q9P255	ZN492_HUMAN	T	164	ENSP00000413660:S164T	ENSP00000413660:S164T	S	+	2	0	ZNF492	22638802	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.346000	0.00503	-0.381000	0.07882	-1.146000	0.01853	AGT	G|0.957;C|0.043	0.043	strong		0.338	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464581.1	NM_020855		C	22846962	G	C	22846962	3	2	22	1	0	0	0	0	1	0	0	0	17958	1029	36	4	501	4	ZNF492	19	22846962	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	271458	22846962	36282021	3884	6785											
ZNF492	57615	hgsc.bcm.edu	37	chr19	22847917	22847917	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctacaagtgtgaagaatgTggcaaagcctttaacaactc	14	9	8	10	0	0	2	0	1	0	1	1	2	0	2	2	1	4	1	2	1	7	3	rs201040917		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22847917T>C	ENST00000456783.2	+	4	1690	c.1446T>C	c.(1444-1446)tgT>tgC	p.C482C	CTC-457E21.9_ENST00000601860.1_RNA	NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492	482					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(6)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				GTGAAGAATGTGGCAAAGCCT	0.373																																					p.C482C		Atlas-SNP	.											ZNF492_ENST00000456783,NS,carcinoma,+1,1	ZNF492	129	1	0			c.T1446C						scavenged	.	T		172,3876		2,168,1854	27	39	36		1446	1.1	0.5	19	dbSNP_134	36	4,8488		0,4,4242	no	coding-synonymous	ZNF492	NM_020855.2		2,172,6096	CC,CT,TT		0.0471,4.249,1.4035		482/532	22847917	176,12364	2024	4246	6270	SO:0001819	synonymous_variant	57615	exon4			AGAATGTGGCAAA	AB040906	CCDS46032.1	19p13.11	2013-01-08				ENSG00000229676		"Zinc fingers, C2H2-type"	23707	protein-coding gene	gene with protein product			"zinc finger protein 115 (Y20)"	ZNF115		10819331	Standard	NM_020855		Approved	KIAA1473	uc002nqw.3	Q9P255		ENST00000456783.2:c.1446T>C	19.37:g.22847917T>C		310	1	0.00322581		26	23	0.884615	NM_020855	Q08EI7|Q08EI8	Silent	SNP	ENST00000456783.2	37	CCDS46032.1																																																																																			T|0.500;C|0.500	0.500	weak		0.373	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464581.1	NM_020855		C	22847917	T	C	22847917	2	2	22	1	0	0	0	0	0	0	0	1	17958	1702	59	3		3	ZNF492	19	22847917	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	955	22847917	36281066	3885	6786											
ZNF91	7644	hgsc.bcm.edu	37	chr19	23556550	23556550	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tcactctcacctacctgtggGttcatccaccatctcatgtt	7	14	5	15	0	4	0	4	0	2	0	7	0	5	0	4	1	1	2	4	1	1	3	rs148956643	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:23556550G>A	ENST00000300619.7	-	3	452	c.247C>T	c.(247-249)Ccc>Tcc	p.P83S	ZNF91_ENST00000397082.2_Intron|ZNF91_ENST00000599743.1_Missense_Mutation_p.P83S	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	83	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)				CTACCTGTGGGTTCATCCACC	0.438													G|||	73	0.0145767	0.0514	0.0072	5008	,	,		12954	0.0		0.0	False		,,,				2504	0.0				p.P83S		Atlas-SNP	.											.	ZNF91	349	.	0			c.C247T						PASS	.	G	SER/PRO	210,4192	127.8+/-164.7	4,202,1995	75	78	77		247	-0.3	0	19	dbSNP_134	77	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ZNF91	NM_003430.2	74	4,203,6294	AA,AG,GG		0.0116,4.7706,1.6228	benign	83/1192	23556550	211,12791	2201	4300	6501	SO:0001583	missense	7644	exon3			CTGTGGGTTCATC	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.247C>T	19.37:g.23556550G>A	ENSP00000300619:p.Pro83Ser	132	0	0		128	58	0.453125	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	37	CCDS42541.1	28	0.01282051282051282	24	0.04878048780487805	4	0.011049723756906077	0	0.0	0	0.0	G	0.005	-2.230572	0.00280	0.047706	1.16E-4	ENSG00000167232	ENST00000300619	T	0.05855	3.38	0.158	-0.317	0.12736	Krueppel-associated box (1);	.	.	.	.	T	0.00815	0.0027	L	0.59436	1.845	0.09310	N	1	B	0.24533	0.105	B	0.17979	0.02	T	0.46582	-0.9181	8	0.17369	T	0.5	.	.	.	.	.	83	Q05481	ZNF91_HUMAN	S	83	ENSP00000300619:P83S	ENSP00000300619:P83S	P	-	1	0	ZNF91	23348390	0.002000	0.14202	0.005000	0.12908	0.006000	0.05464	-0.167000	0.09940	-1.052000	0.03222	-1.038000	0.02383	CCC	G|0.992;A|0.008	0.008	strong		0.438	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		A	23556550	G	A	23556550	3	1	22	1	0	0	0	0	1	0	0	0	18215	1261	44	2	3336	2	ZNF91	19	23556550	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	708633	23556550	35572433	3886	6787											
ZNF254	9534	hgsc.bcm.edu	37	chr19	24310074	24310074	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttcaaatcttactacacaTaagataattcatactggaga	16	13	4	8	0	4	2	2	0	2	2	4	3	4	2	0	1	3	0	0	1	6	7	rs61737179	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:24310074T>C	ENST00000357002.4	+	4	1387	c.1272T>C	c.(1270-1272)caT>caC	p.H424H	ZNF254_ENST00000342944.6_Silent_p.H339H	NM_001278661.1|NM_001278662.1|NM_001278664.1|NM_001278677.1|NM_001278678.1|NM_203282.2	NP_001265590.1|NP_001265591.1|NP_001265593.1|NP_001265606.1|NP_001265607.1|NP_975011.3	O75437	ZN254_HUMAN	zinc finger protein 254	424					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)						all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)				TTACTACACATAAGATAATTC	0.338													T|||	119	0.023762	0.0862	0.0072	5008	,	,		21190	0.0		0.0	False		,,,				2504	0.0				p.H424H		Atlas-SNP	.											.	ZNF254	88	.	0			c.T1272C						PASS	.	T		243,4161	134.9+/-171.1	7,229,1966	37	40	39		1272	1.1	0.1	19	dbSNP_129	39	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ZNF254	NM_203282.2		7,230,6265	CC,CT,TT		0.0116,5.5177,1.8763		424/660	24310074	244,12760	2202	4300	6502	SO:0001819	synonymous_variant	9534	exon4			TACACATAAGATA	AF054180	CCDS32983.1, CCDS62622.1, CCDS62623.1, CCDS74323.1, CCDS74324.1	19p13	2013-01-08				ENSG00000213096		"Zinc fingers, C2H2-type", "-"	13047	protein-coding gene	gene with protein product		604768	"zinc finger protein 539"	ZNF91L, ZNF539		9653160	Standard	NM_001278661		Approved	HD-ZNF1, BMZF-5	uc002nru.3	O75437		ENST00000357002.4:c.1272T>C	19.37:g.24310074T>C		59	0	0		68	28	0.411765	NM_203282	A4QPC0|Q86XL7	Silent	SNP	ENST00000357002.4	37	CCDS32983.1																																																																																			T|0.979;C|0.021	0.021	strong		0.338	ZNF254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466453.1	NM_004876		C	24310074	T	C	24310074	2	2	22	1	0	0	0	0	0	0	0	1	17813	1403	49	3		3	ZNF254	19	24310074	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	753524	24310074	34818909	3887	6788											
C19orf2	8725	hgsc.bcm.edu	37	chr19	30500195	30500195	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	atggtgataacgaccatgagGctttaggggttggagataat	12	11	14	4	1	0	3	0	2	0	1	0	5	0	3	1	5	1	2	1	5	3	5	rs151025990	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:30500195G>C	ENST00000542441.2	+	8	1267	c.970G>C	c.(970-972)Gct>Cct	p.A324P	URI1_ENST00000360605.4_Missense_Mutation_p.A306P|URI1_ENST00000392271.1_Missense_Mutation_p.A248P|URI1_ENST00000312051.6_Missense_Mutation_p.A284P			O94763	RMP_HUMAN	URI1, prefoldin-like chaperone	324					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)										cgaCCATGAGGCTTTAGGGGT	0.378													G|||	2	0.000399361	0.0015	0.0	5008	,	,		21705	0.0		0.0	False		,,,				2504	0.0				p.A324P		Atlas-SNP	.											.	.	.	.	0			c.G970C						PASS	.	G	PRO/ALA,PRO/ALA	13,4393	20.2+/-43.8	0,13,2190	95	82	86		970,850	-3.2	0	19	dbSNP_134	86	0,8600		0,0,4300	yes	missense,missense	C19orf2	NM_003796.2,NM_134447.1	27,27	0,13,6490	CC,CG,GG		0.0,0.2951,0.1	benign,benign	324/536,284/496	30500195	13,12993	2203	4300	6503	SO:0001583	missense	8725	exon8			CATGAGGCTTTAG	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.970G>C	19.37:g.30500195G>C	ENSP00000442436:p.Ala324Pro	88	0	0		95	47	0.494737	NM_003796	A8K805|H7BY42|Q8TC23|Q9UNU3	Missense_Mutation	SNP	ENST00000542441.2	37	CCDS12420.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	15.04	2.714683	0.48622	0.002951	0.0	ENSG00000105176	ENST00000360605;ENST00000392271;ENST00000542441;ENST00000312051	T	0.50001	0.76	5.03	-3.22	0.05125	.	1.234740	0.05290	N	0.520817	T	0.22003	0.0530	N	0.08118	0	0.09310	N	1	P;B;P	0.38642	0.545;0.41;0.641	B;B;B	0.32864	0.147;0.11;0.154	T	0.13019	-1.0525	10	0.37606	T	0.19	-1.217	5.6351	0.17532	0.3821:0.0:0.4983:0.1197	.	284;324;321	F8W9T0;O94763;Q8TC23	.;RMP_HUMAN;.	P	322;248;324;284	ENSP00000442436:A324P	ENSP00000312530:A284P	A	+	1	0	C19orf2	35192035	0.042000	0.20092	0.000000	0.03702	0.248000	0.25809	0.075000	0.14686	-0.488000	0.06726	0.491000	0.48974	GCT	G|0.998;C|0.002	0.002	strong		0.378	URI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439756.1	NM_134447		C	30500195	G	C	30500195	3	2	22	1	0	0	0	0	1	0	0	0	1913	1203	42	4	1000	4	C19orf2	19	30500195	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6190121	30500195	28628788	3888	6789											
ZNF536	9745	hgsc.bcm.edu	37	chr19	31039357	31039357	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggacaaagccctggctgaccCcccttccatgaaagtccacg	10	6	9	16	1	0	2	0	2	0	0	2	3	2	3	6	2	1	1	6	2	2	1	rs61741995	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:31039357C>A	ENST00000355537.3	+	4	2978	c.2831C>A	c.(2830-2832)cCc>cAc	p.P944H		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	944					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)					CTGGCTGACCCCCCTTCCATG	0.522													C|||	77	0.0153754	0.0545	0.0072	5008	,	,		17880	0.0		0.0	False		,,,				2504	0.0				p.P944H		Atlas-SNP	.											.	ZNF536	424	.	0			c.C2831A						PASS	.	C	HIS/PRO	239,4167	141.5+/-176.9	7,225,1971	132	143	139		2831	3.3	0	19	dbSNP_129	139	16,8584	11.2+/-40.8	0,16,4284	yes	missense	ZNF536	NM_014717.1	77	7,241,6255	AA,AC,CC		0.186,5.4244,1.9606	benign	944/1301	31039357	255,12751	2203	4300	6503	SO:0001583	missense	9745	exon4			CTGACCCCCCTTC		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.2831C>A	19.37:g.31039357C>A	ENSP00000347730:p.Pro944His	27	0	0		30	18	0.6	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	37	CCDS32984.1	22	0.010073260073260074	20	0.04065040650406504	2	0.0055248618784530384	0	0.0	0	0.0	C	3.103	-0.184365	0.06340	0.054244	0.00186	ENSG00000198597	ENST00000355537	T	0.08634	3.07	5.69	3.34	0.38264	.	0.451539	0.25613	N	0.029467	T	0.00784	0.0026	N	0.24115	0.695	0.09310	N	1	P;P	0.36495	0.556;0.556	B;B	0.34038	0.174;0.174	T	0.38824	-0.9643	10	0.46703	T	0.11	-2.4559	7.0172	0.24895	0.0:0.6863:0.1357:0.178	rs61741995	944;944	A7E228;O15090	.;ZN536_HUMAN	H	944	ENSP00000347730:P944H	ENSP00000347730:P944H	P	+	2	0	ZNF536	35731197	0.090000	0.21635	0.000000	0.03702	0.954000	0.61252	0.907000	0.28531	0.576000	0.29452	0.491000	0.48974	CCC	C|0.982;A|0.018	0.018	strong		0.522	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		A	31039357	C	A	31039357	3	1	22	1	0	0	0	0	1	0	0	0	17989	623	22	4	2841	4	ZNF536	19	31039357	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	539162	31039357	28089626	3889	6790											
TSHZ3	57616	hgsc.bcm.edu	37	chr19	31767717	31767717	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aagcctaagtgtgactctagGtgactgatgtacgtggaagg	11	10	14	6	1	1	3	0	3	1	0	1	4	1	4	1	3	2	1	1	3	5	3	rs61744745	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:31767717G>A	ENST00000240587.4	-	2	3309	c.2982C>T	c.(2980-2982)caC>caT	p.H994H		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	994					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)					GTGACTCTAGGTGACTGATGT	0.473													G|||	174	0.0347444	0.1301	0.0029	5008	,	,		20088	0.0		0.0	False		,,,				2504	0.0				p.H994H		Atlas-SNP	.											.	TSHZ3	549	.	0			c.C2982T						PASS	.	G		440,3966	211.8+/-231.9	19,402,1782	120	105	110		2982	2.5	1	19	dbSNP_129	110	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	TSHZ3	NM_020856.2		19,406,6078	AA,AG,GG		0.0465,9.9864,3.4138		994/1082	31767717	444,12562	2203	4300	6503	SO:0001819	synonymous_variant	57616	exon2			CTCTAGGTGACTG	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.2982C>T	19.37:g.31767717G>A		155	0	0		167	86	0.51497	NM_020856	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																			G|0.961;A|0.039	0.039	strong		0.473	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		A	31767717	G	A	31767717	2	1	22	1	0	0	0	0	0	0	0	1	16640	1252	44	2		2	TSHZ3	19	31767717	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	728360	31767717	27361266	3890	6791											
TSHZ3	57616	hgsc.bcm.edu	37	chr19	31768491	31768491	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcaggcagggagggcttggcGgccttgcccaggtgaatgtt	6	8	18	9	1	0	1	0	1	0	0	0	2	0	2	2	6	1	4	2	6	1	3	rs139947200	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:31768491G>A	ENST00000240587.4	-	2	2535	c.2208C>T	c.(2206-2208)gcC>gcT	p.A736A		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	736					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)					AGGGCTTGGCGGCCTTGCCCA	0.627													G|||	3	0.000599042	0.0023	0.0	5008	,	,		17340	0.0		0.0	False		,,,				2504	0.0				p.A736A		Atlas-SNP	.											.	TSHZ3	549	.	0			c.C2208T						PASS	.	G		17,4389	22.3+/-47.3	0,17,2186	58	59	59		2208	-10.7	0.3	19	dbSNP_134	59	0,8600		0,0,4300	no	coding-synonymous	TSHZ3	NM_020856.2		0,17,6486	AA,AG,GG		0.0,0.3858,0.1307		736/1082	31768491	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	57616	exon2			CTTGGCGGCCTTG	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.2208C>T	19.37:g.31768491G>A		63	0	0		66	27	0.409091	NM_020856	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																			G|0.999;A|0.001	0.001	strong		0.627	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		A	31768491	G	A	31768491	2	1	22	1	0	0	0	0	0	0	0	1	16640	1103	39	1		1	TSHZ3	19	31768491	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	774	31768491	27360492	3891	6792											
DPY19L3	147991	hgsc.bcm.edu	37	chr19	32930808	32930808	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	actccctggacatgctgccaGcagtgaaggtgagctttgct	8	10	12	11	0	0	2	0	2	0	0	1	3	1	3	2	2	5	4	2	2	1	1	rs139732410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:32930808G>A	ENST00000342179.5	+	8	1062	c.847G>A	c.(847-849)Gca>Aca	p.A283T	DPY19L3_ENST00000586987.1_Missense_Mutation_p.A283T|DPY19L3_ENST00000392250.2_Missense_Mutation_p.A283T	NM_207325.2	NP_997208.2	Q6ZPD9	D19L3_HUMAN	dpy-19-like 3 (C. elegans)	283						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)					CATGCTGCCAGCAGTGAAGGT	0.373													G|||	12	0.00239617	0.0091	0.0	5008	,	,		17998	0.0		0.0	False		,,,				2504	0.0				p.A283T		Atlas-SNP	.											.	DPY19L3	70	.	0			c.G847A						PASS	.	G	THR/ALA,THR/ALA	31,4375	37.6+/-69.7	0,31,2172	153	142	146		847,847	3.5	0.1	19	dbSNP_134	146	0,8600		0,0,4300	yes	missense,missense	DPY19L3	NM_001172774.1,NM_207325.2	58,58	0,31,6472	AA,AG,GG		0.0,0.7036,0.2384	benign,benign	283/717,283/717	32930808	31,12975	2203	4300	6503	SO:0001583	missense	147991	exon8			CTGCCAGCAGTGA		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.847G>A	19.37:g.32930808G>A	ENSP00000344937:p.Ala283Thr	100	0	0		110	51	0.463636	NM_001172774	Q68DC7|Q6ZTB7|Q6ZTS2	Missense_Mutation	SNP	ENST00000342179.5	37	CCDS12422.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	5.569	0.289764	0.10567	0.007036	0.0	ENSG00000178904	ENST00000392250;ENST00000319326;ENST00000342179	T;T	0.54479	0.57;0.57	5.82	3.55	0.40652	.	0.164682	0.52532	D	0.000078	T	0.13927	0.0337	N	0.03084	-0.415	0.28833	N	0.897055	B	0.09022	0.002	B	0.08055	0.003	T	0.24154	-1.0168	10	0.05525	T	0.97	-8.0566	3.27	0.06878	0.1826:0.2943:0.523:0.0	.	283	Q6ZPD9	D19L3_HUMAN	T	283	ENSP00000376081:A283T;ENSP00000344937:A283T	ENSP00000315672:A283T	A	+	1	0	DPY19L3	37622648	0.997000	0.39634	0.084000	0.20598	0.988000	0.76386	3.927000	0.56499	1.448000	0.47680	0.557000	0.71058	GCA	G|0.998;A|0.002	0.002	strong		0.373	DPY19L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450311.1	NM_207325		A	32930808	G	A	32930808	3	1	22	1	0	0	0	0	1	0	0	0	4744	971	34	2	873	2	DPY19L3	19	32930808	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1162317	32930808	26198175	3892	6793											
ANKRD27	84079	hgsc.bcm.edu	37	chr19	33131227	33131227	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttaccaattagggatctcCgttttcacaagcaagtataa	13	13	7	8	1	2	0	1	0	1	0	3	1	2	1	2	1	2	4	2	1	7	6	rs10410241	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33131227C>T	ENST00000306065.4	-	11	1127	c.969G>A	c.(967-969)acG>acA	p.T323T	ANKRD27_ENST00000587352.1_Silent_p.T323T	NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	323	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				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)					TAGGGATCTCCGTTTTCACAA	0.458													C|||	375	0.0748802	0.2738	0.0173	5008	,	,		20964	0.0		0.001	False		,,,				2504	0.0				p.T323T		Atlas-SNP	.											ANKRD27,colon,carcinoma,-1,1	ANKRD27	86	1	0			c.G969A						PASS	.	C		963,3443	364.9+/-317.2	123,717,1363	114	106	109		969	1.7	1	19	dbSNP_119	109	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	ANKRD27	NM_032139.2		123,720,5660	TT,TC,CC		0.0349,21.8566,7.4273		323/1051	33131227	966,12040	2203	4300	6503	SO:0001819	synonymous_variant	84079	exon11			GATCTCCGTTTTC	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.969G>A	19.37:g.33131227C>T		224	0	0		209	91	0.435407	NM_032139	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Silent	SNP	ENST00000306065.4	37	CCDS32986.1																																																																																			C|0.924;T|0.076	0.076	strong		0.458	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450329.1	NM_032139		T	33131227	C	T	33131227	2	4	22	1	0	0	0	0	0	0	0	1	655	639	23	1		1	ANKRD27	19	33131227	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	200419	33131227	25997756	3893	6794											
SLC7A9	11136	hgsc.bcm.edu	37	chr19	33333179	33333179	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagctgaaataattgactaaCgagtttatgtcaccagggat	15	11	9	6	1	1	2	1	2	0	0	1	4	1	3	1	1	2	2	1	1	5	5	rs111630604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33333179C>T	ENST00000023064.4	-	11	1310	c.1119G>A	c.(1117-1119)tcG>tcA	p.S373S	SLC7A9_ENST00000587772.1_Silent_p.S373S|SLC7A9_ENST00000590341.1_Silent_p.S373S	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	373					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)	AATTGACTAACGAGTTTATGT	0.393													C|||	50	0.00998403	0.0325	0.0086	5008	,	,		19257	0.0		0.0	False		,,,				2504	0.001				p.S373S	GBM(181;1335 2108 9644 44178 46689)	Atlas-SNP	.											SLC7A9,NS,carcinoma,-1,3	SLC7A9	78	3	0			c.G1119A						PASS	.	C	,	144,4262	102.1+/-140.7	5,134,2064	114	108	110		1119,1119	-11.4	0	19	dbSNP_132	110	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SLC7A9	NM_001126335.1,NM_014270.4	,	5,134,6364	TT,TC,CC		0.0,3.2683,1.1072	,	373/488,373/488	33333179	144,12862	2203	4300	6503	SO:0001819	synonymous_variant	11136	exon11			GACTAACGAGTTT	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.1119G>A	19.37:g.33333179C>T		72	0	0		76	35	0.460526	NM_001243036	B2R9A6	Silent	SNP	ENST00000023064.4	37	CCDS12425.1																																																																																			C|0.987;T|0.013	0.013	strong		0.393	SLC7A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450585.1			T	33333179	C	T	33333179	2	4	22	1	0	0	0	0	0	0	0	1	14720	523	19	1		1	SLC7A9	19	33333179	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	201952	33333179	25795804	3894	6795											
CCDC123	84902	hgsc.bcm.edu	37	chr19	33406328	33406328	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagttcttggcatttggcacGtaaaatctccagctgttccc	8	13	9	11	1	2	0	0	0	2	0	4	1	3	0	2	2	1	6	2	2	2	5	rs113919201	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33406328G>A	ENST00000305768.5	-	14	1568	c.1480C>T	c.(1480-1482)Cgt>Tgt	p.R494C		NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	494					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						CATTTGGCACGTAAAATCTCC	0.423													G|||	36	0.0071885	0.025	0.0043	5008	,	,		15861	0.0		0.0	False		,,,				2504	0.0				p.R494C		Atlas-SNP	.											CEP89,NS,carcinoma,+1,1	CEP89	82	1	0			c.C1480T						PASS	.	G	CYS/ARG	99,4307	79.9+/-118.3	3,93,2107	123	109	114		1480	3.5	0	19	dbSNP_132	114	0,8600		0,0,4300	yes	missense	CEP89	NM_032816.3	180	3,93,6407	AA,AG,GG		0.0,2.2469,0.7612	benign	494/784	33406328	99,12907	2203	4300	6503	SO:0001583	missense	84902	exon14			TGGCACGTAAAAT	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.1480C>T	19.37:g.33406328G>A	ENSP00000306105:p.Arg494Cys	218	1	0.00458716		244	128	0.52459	NM_032816	B9EGA6|Q8N5J8	Missense_Mutation	SNP	ENST00000305768.5	37	CCDS32987.1	15	0.006868131868131868	12	0.024390243902439025	3	0.008287292817679558	0	0.0	0	0.0	G	6.345	0.431801	0.12045	0.022469	0.0	ENSG00000121289	ENST00000305768	D	0.88201	-2.35	5.6	3.45	0.39498	.	1.178400	0.05586	N	0.573762	T	0.80385	0.4613	L	0.60455	1.87	0.24756	N	0.992952	B;B	0.14438	0.004;0.01	B;B	0.09377	0.004;0.002	T	0.71318	-0.4629	10	0.52906	T	0.07	1.9766	11.2548	0.49048	0.0701:0.1277:0.8023:0.0	.	247;494	Q96ST8-2;Q96ST8	.;CEP89_HUMAN	C	494	ENSP00000306105:R494C	ENSP00000306105:R494C	R	-	1	0	CEP89	38098168	0.414000	0.25408	0.000000	0.03702	0.009000	0.06853	1.725000	0.38074	0.708000	0.31955	0.591000	0.81541	CGT	G|0.991;A|0.009	0.009	strong		0.423	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816		A	33406328	G	A	33406328	3	1	22	1	0	0	0	0	1	0	0	0	2761	1145	40	1	895	1	CCDC123	19	33406328	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	73149	33406328	25722655	3895	6796											
CCDC123	84902	hgsc.bcm.edu	37	chr19	33450806	33450806	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcggcgatctggtacctacCgaggcctcagctgtgaggtg	6	8	16	11	3	2	1	1	1	1	0	2	3	2	1	3	5	3	2	3	5	2	2	rs73926195	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33450806C>T	ENST00000305768.5	-	3	393	c.305G>A	c.(304-306)cGg>cAg	p.R102Q	CEP89_ENST00000590597.2_Splice_Site_p.R102Q	NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	102					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)		p.R102L(1)|p.R102Q(1)		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						TGGTACCTACCGAGGCCTCAG	0.587													C|||	266	0.053115	0.1921	0.0173	5008	,	,		20668	0.0		0.0	False		,,,				2504	0.0				p.R102Q		Atlas-SNP	.											CEP89,colon,carcinoma,-1,4	CEP89	82	4	2	Substitution - Missense(2)	ovary(1)|prostate(1)	c.G305A						PASS	.	C	GLN/ARG	699,3707	291.5+/-281.6	54,591,1558	94	75	81		305	2	0.8	19	dbSNP_130	81	5,8595	3.7+/-12.6	0,5,4295	yes	missense-near-splice	CEP89	NM_032816.3	43	54,596,5853	TT,TC,CC		0.0581,15.8647,5.4129	benign	102/784	33450806	704,12302	2203	4300	6503	SO:0001630	splice_region_variant	84902	exon3			ACCTACCGAGGCC	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.305+1G>A	19.37:g.33450806C>T		131	0	0		144	73	0.506944	NM_032816	B9EGA6|Q8N5J8	Missense_Mutation	SNP	ENST00000305768.5	37	CCDS32987.1	83	0.038003663003663	75	0.1524390243902439	8	0.022099447513812154	0	0.0	0	0.0	C	8.786	0.929433	0.18131	0.158647	5.81E-4	ENSG00000121289	ENST00000305768	T	0.30182	1.54	5.48	2.01	0.26516	.	0.317619	0.28382	N	0.015556	T	0.00039	0.0001	N	0.04203	-0.255	0.31021	P	0.718148	B;B	0.25235	0.017;0.121	B;B	0.14023	0.008;0.01	T	0.33929	-0.9849	8	.	.	.	-1.7133	10.2426	0.43321	0.0:0.7433:0.0:0.2567	.	102;102	Q96ST8-3;Q96ST8	.;CEP89_HUMAN	Q	102	ENSP00000306105:R102Q	.	R	-	2	0	CEP89	38142646	0.975000	0.34042	0.770000	0.31555	0.026000	0.11368	0.915000	0.28638	0.162000	0.19483	0.655000	0.94253	CGG	C|0.944;T|0.056	0.056	strong		0.587	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816	Missense_Mutation	T	33450806	C	T	33450806	5	4	22	1	0	0	0	0	0	0	1	0	2761	666	23	1	2114	1	CCDC123	19	33450806	Splice_Site	SNP	C	TCGA-G8-6324-01A-11D-2210-10	44478	33450806	25678177	3896	6797											
CCDC123	84902	hgsc.bcm.edu	37	chr19	33457328	33457328	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtgcgtggcacagctgccttCggagcaacgctggctgcagg	6	7	16	12	3	0	0	0	0	0	0	1	1	0	1	1	4	6	6	1	4	1	1	rs150504912	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33457328C>T	ENST00000305768.5	-	2	172	c.84G>A	c.(82-84)ccG>ccA	p.P28P	CEP89_ENST00000591863.1_5'Flank|CEP89_ENST00000590597.2_Silent_p.P28P	NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	28					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						CAGCTGCCTTCGGAGCAACGC	0.557													c|||	2	0.000399361	0.0008	0.0	5008	,	,		20181	0.001		0.0	False		,,,				2504	0.0				p.P28P		Atlas-SNP	.											CEP89,caecum,carcinoma,0,1	CEP89	82	1	0			c.G84A						scavenged	.	C		3,4403	6.2+/-15.9	0,3,2200	98	78	85		84	-7.9	1	19	dbSNP_134	85	0,8600		0,0,4300	no	coding-synonymous	CEP89	NM_032816.3		0,3,6500	TT,TC,CC		0.0,0.0681,0.0231		28/784	33457328	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	84902	exon2			TGCCTTCGGAGCA	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.84G>A	19.37:g.33457328C>T		75	1	0.0133333		94	50	0.531915	NM_032816	B9EGA6|Q8N5J8	Silent	SNP	ENST00000305768.5	37	CCDS32987.1																																																																																			C|1.000;T|0.000	0.000	weak		0.557	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816		T	33457328	C	T	33457328	2	4	22	1	0	0	0	0	0	0	0	1	2761	871	31	1		1	CCDC123	19	33457328	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6522	33457328	25671655	3897	6798											
RHPN2	85415	hgsc.bcm.edu	37	chr19	33486992	33486992	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcctcctggtgctgggcgtAcgtgagccgggagcgttcct	3	10	15	13	4	0	1	0	1	0	0	3	2	3	2	4	3	4	3	4	3	1	2	rs75351369	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33486992A>C	ENST00000254260.3	-	11	1395	c.1360T>G	c.(1360-1362)Tac>Gac	p.Y454D	RHPN2_ENST00000400226.4_Missense_Mutation_p.Y303D	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	454	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)					TGCTGGGCGTACGTGAGCCGG	0.627													A|||	129	0.0257588	0.0915	0.0115	5008	,	,		18136	0.0		0.0	False		,,,				2504	0.0				p.Y454D		Atlas-SNP	.											.	RHPN2	107	.	0			c.T1360G						PASS	.	A	ASP/TYR	312,4094	167.6+/-198.6	8,296,1899	82	66	72		1360	3.8	0.8	19	dbSNP_131	72	5,8595	5.0+/-18.6	0,5,4295	no	missense	RHPN2	NM_033103.4	160	8,301,6194	CC,CA,AA		0.0581,7.0813,2.4373	probably-damaging	454/687	33486992	317,12689	2203	4300	6503	SO:0001583	missense	85415	exon11			GGGCGTACGTGAG	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.1360T>G	19.37:g.33486992A>C	ENSP00000254260:p.Tyr454Asp	311	0	0		290	143	0.493103	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	50	0.022893772893772892	47	0.09552845528455285	3	0.008287292817679558	0	0.0	0	0.0	A	15.96	2.987827	0.53934	0.070813	5.81E-4	ENSG00000131941	ENST00000254260;ENST00000544458;ENST00000400226	T;T	0.18502	2.21;2.21	4.86	3.82	0.43975	BRO1 domain (3);	0.230044	0.46758	D	0.000279	T	0.01387	0.0045	M	0.89287	3.02	0.41757	D	0.989692	D	0.56968	0.978	D	0.65233	0.933	T	0.00111	-1.2045	10	0.87932	D	0	0.6788	9.3929	0.38383	0.9165:0.0:0.0835:0.0	.	454	Q8IUC4	RHPN2_HUMAN	D	454;184;303	ENSP00000254260:Y454D;ENSP00000402244:Y303D	ENSP00000254260:Y454D	Y	-	1	0	RHPN2	38178832	0.997000	0.39634	0.822000	0.32727	0.459000	0.32528	2.550000	0.45811	0.669000	0.31146	0.477000	0.44152	TAC	A|0.973;C|0.027	0.027	strong		0.627	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103		C	33486992	A	C	33486992	3	2	22	1	0	0	0	0	1	0	0	0	13366	391	14	5	720	5	RHPN2	19	33486992	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	29664	33486992	25641991	3898	6799											
GPATCH1	55094	hgsc.bcm.edu	37	chr19	33587298	33587298	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtggttctgagagagctggCgatcttggagaaattggact	9	11	16	5	1	2	3	0	1	2	2	2	7	2	4	0	5	1	2	0	5	1	3	rs114017497	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33587298C>T	ENST00000170564.2	+	7	1112	c.798C>T	c.(796-798)ggC>ggT	p.G266G		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	266					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)					AGAGAGCTGGCGATCTTGGAG	0.413													C|||	37	0.00738818	0.0257	0.0043	5008	,	,		16637	0.0		0.0	False		,,,				2504	0.0				p.G266G	Pancreas(67;88 1713 4567 18227)	Atlas-SNP	.											.	GPATCH1	79	.	0			c.C798T						PASS	.	C		114,4292	87.3+/-125.9	4,106,2093	75	78	77		798	2	0	19	dbSNP_132	77	0,8600		0,0,4300	no	coding-synonymous	GPATCH1	NM_018025.2		4,106,6393	TT,TC,CC		0.0,2.5874,0.8765		266/932	33587298	114,12892	2203	4300	6503	SO:0001819	synonymous_variant	55094	exon7			AGCTGGCGATCTT	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.798C>T	19.37:g.33587298C>T		167	0	0		152	73	0.480263	NM_018025	Q8IZV6|Q8N3B7|Q9NW94	Silent	SNP	ENST00000170564.2	37	CCDS12428.1																																																																																			C|0.991;T|0.009	0.009	strong		0.413	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025		T	33587298	C	T	33587298	2	4	22	1	0	0	0	0	0	0	0	1	6598	755	27	1		1	GPATCH1	19	33587298	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	100306	33587298	25541685	3899	6800											
WDR88	126248	hgsc.bcm.edu	37	chr19	33666345	33666345	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctccatcttcaagagtgacaCctcttctgaaatgttcaccc	10	12	5	14	0	5	3	2	2	3	1	6	3	6	3	3	0	0	1	3	0	2	3	rs77589178	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33666345C>A	ENST00000355868.3	+	11	1362	c.1286C>A	c.(1285-1287)aCc>aAc	p.T429N	AC008738.2_ENST00000577275.1_RNA|CTD-2540B15.10_ENST00000590117.1_RNA|WDR88_ENST00000361680.2_3'UTR	NM_173479.3	NP_775750.3	Q6ZMY6	WDR88_HUMAN	WD repeat domain 88	429										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)					AAGAGTGACACCTCTTCTGAA	0.478													C|||	111	0.0221645	0.0832	0.0014	5008	,	,		20731	0.0		0.0	False		,,,				2504	0.0				p.T429N		Atlas-SNP	.											.	WDR88	50	.	0			c.C1286A						PASS	.	C	ASN/THR	263,4143	150.3+/-184.3	11,241,1951	179	171	174		1286	-5.6	0	19	dbSNP_131	174	0,8600		0,0,4300	yes	missense	WDR88	NM_173479.3	65	11,241,6251	AA,AC,CC		0.0,5.9691,2.0221	benign	429/473	33666345	263,12743	2203	4300	6503	SO:0001583	missense	126248	exon11			GTGACACCTCTTC	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.1286C>A	19.37:g.33666345C>A	ENSP00000348129:p.Thr429Asn	257	1	0.00389105		224	103	0.459821	NM_173479	Q8NEF8	Missense_Mutation	SNP	ENST00000355868.3	37	CCDS12429.1	46	0.021062271062271064	45	0.09146341463414634	1	0.0027624309392265192	0	0.0	0	0.0	C	4.208	0.037382	0.08148	0.059691	0.0	ENSG00000166359	ENST00000355868	T	0.56941	0.43	4.92	-5.61	0.02489	.	3.589250	0.00520	N	0.000190	T	0.01189	0.0039	N	0.22421	0.69	0.09310	N	1	B	0.13594	0.008	B	0.09377	0.004	T	0.04140	-1.0974	10	0.40728	T	0.16	.	0.5128	0.00598	0.4107:0.1392:0.196:0.2542	.	429	Q6ZMY6	WDR88_HUMAN	N	429	ENSP00000348129:T429N	ENSP00000348129:T429N	T	+	2	0	WDR88	38358185	0.000000	0.05858	0.000000	0.03702	0.069000	0.16628	-1.093000	0.03362	-0.598000	0.05806	-0.314000	0.08810	ACC	C|0.975;A|0.025	0.025	strong		0.478	WDR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450840.1	NM_173479		A	33666345	C	A	33666345	3	1	22	1	0	0	0	0	1	0	0	0	17350	507	18	4	1328	4	WDR88	19	33666345	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	79047	33666345	25462638	3900	6801											
PEPD	5184	hgsc.bcm.edu	37	chr19	33968991	33968991	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagaatggtattgttgactTcgaacctgtagggcgaaaag	13	10	13	5	2	0	2	0	1	0	1	1	5	0	2	1	2	1	3	1	2	7	5	rs61748998	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33968991T>A	ENST00000244137.7	-	7	542	c.509A>T	c.(508-510)gAa>gTa	p.E170V	PEPD_ENST00000436370.3_Missense_Mutation_p.E106V|PEPD_ENST00000397032.4_Missense_Mutation_p.E170V	NM_000285.3	NP_000276.2	P12955	PEPD_HUMAN	peptidase D	170					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)					ATTGTTGACTTCGAACCTGTA	0.488													T|||	77	0.0153754	0.0567	0.0	5008	,	,		21814	0.0		0.002	False		,,,				2504	0.0				p.E170V		Atlas-SNP	.											.	PEPD	48	.	0			c.A509T						PASS	.	T	VAL/GLU,VAL/GLU,VAL/GLU	155,3897		4,147,1875	87	88	88		509,509,317	3.6	1	19	dbSNP_129	88	1,8361		0,1,4180	yes	missense,missense,missense	PEPD	NM_000285.3,NM_001166056.1,NM_001166057.1	121,121,121	4,148,6055	AA,AT,TT		0.012,3.8253,1.2566	benign,benign,benign	170/494,170/453,106/430	33968991	156,12258	2026	4181	6207	SO:0001583	missense	5184	exon7			TTGACTTCGAACC	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.509A>T	19.37:g.33968991T>A	ENSP00000244137:p.Glu170Val	194	0	0		157	80	0.509554	NM_000285	A8K3Z1|A8K416|A8K696|A8MX47|B4DDB7|B4DGJ1|E9PCE8|Q8TBN9|Q9BT75	Missense_Mutation	SNP	ENST00000244137.7	37	CCDS42544.1	19	0.0086996336996337	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	T	8.903	0.956821	0.18507	0.038253	1.2E-4	ENSG00000124299	ENST00000244137;ENST00000397032;ENST00000436370	T;T;T	0.79749	-1.03;-0.93;-1.3	5.7	3.56	0.40772	.	0.722777	0.15080	N	0.281739	T	0.32194	0.0821	N	0.13168	0.305	0.80722	D	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.31052	-0.9957	10	0.24483	T	0.36	-4.3759	10.1383	0.42719	0.0:0.0:0.3228:0.6772	rs61748998	106;170;170	E9PCE8;A8MX47;P12955	.;.;PEPD_HUMAN	V	170;170;106	ENSP00000244137:E170V;ENSP00000380226:E170V;ENSP00000391890:E106V	ENSP00000244137:E170V	E	-	2	0	PEPD	38660831	1.000000	0.71417	0.994000	0.49952	0.574000	0.36063	0.933000	0.28897	0.387000	0.25024	0.533000	0.62120	GAA	T|0.978;A|0.022	0.022	strong		0.488	PEPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451432.3	NM_000285		A	33968991	T	A	33968991	3	1	22	1	0	0	0	0	1	0	0	0	11737	1783	62	5	1008	5	PEPD	19	33968991	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	302646	33968991	25159992	3901	6802											
DMKN	93099	hgsc.bcm.edu	37	chr19	36002371	36002394	+	In_Frame_Del	DEL	CCACTGCTGCCGCCACTGCTGCCG	CCACTGCTGCCGCCACTGCTGCCG	-																															cactgttgccactgctgccaCcactgctgccgccactgctg																								rs112672248|rs142519211|rs11667007|rs12981076|rs146822312|rs148799704|rs56743379|rs371511253|rs117522133|rs59309505|rs58579970	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCACTGCTGCCGCCACTGCTGCCG	CCACTGCTGCCGCCACTGCTGCCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36002371_36002394delCCACTGCTGCCGCCACTGCTGCCG	ENST00000339686.3	-	5	1013_1036	c.837_860delCGGCAGCAGTGGCGGCAGCAGTGG	c.(835-861)ggcggcagcagtggcggcagcagtggt>ggt	p.279_287GGSSGGSSG>G	DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000447113.2_In_Frame_Del_p.279_287GGSSGGSSG>G|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000451297.2_In_Frame_Del_p.279_287GGSSGGSSG>G|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000440396.1_In_Frame_Del_p.279_287GGSSGGSSG>G|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000424570.2_In_Frame_Del_p.279_287GGSSGGSSG>G|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000418261.1_In_Frame_Del_p.279_287GGSSGGSSG>G	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	279	Gly-rich.		G -> S (in dbSNP:rs11667007). {ECO:0000269|PubMed:17380110}.	G -> GSSSG (in Ref. 4; AAQ88778). {ECO:0000305}.		extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.S274_S290del(1)		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)			actgctgccaccactgctgccgccactgctgccgccactgctgc	0.638																																					p.280_287del		Pindel	.											.	DMKN	116	.	1	Deletion - In frame(1)	ovary(1)	c.838_861del						PASS	.																																			SO:0001651	inframe_deletion	93099	exon5			.	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.837_860delCGGCAGCAGTGGCGGCAGCAGTGG	19.37:g.36002371_36002394delCCACTGCTGCCGCCACTGCTGCCG	ENSP00000342012:p.Gly279_Ser286del	91	0	.		90	25	0.278	NM_033317	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	In_Frame_Del	DEL	ENST00000339686.3	37	CCDS12463.1																																																																																			.	.	none		0.638	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317		-	36002394	CCACTGCTGCCGCCACTGCTGCCG	-	36002371	7	5	22	1	0	1	0	1	0	0	0	0	4584	507	18	0	935	0	DMKN	19	36002371	In_Frame_Del	DEL	CCACTGCTGCCGCCACTGCTGCCG	TCGA-G8-6324-01A-11D-2210-10	2033380	36002371	23126612	3902	6803											
DMKN	93099	hgsc.bcm.edu	37	chr19	36002394	36002394	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctgccgccactgctgccGccactgctgctgccactgct	3	9	10	19	2	0	0	0	0	0	0	0	0	0	0	5	0	8	5	5	0	0	0	rs56743379|rs146822312		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36002394G>A	ENST00000339686.3	-	5	1013	c.837C>T	c.(835-837)ggC>ggT	p.G279G	DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000447113.2_Silent_p.G279G|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000451297.2_Silent_p.G279G|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000440396.1_Silent_p.G279G|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000424570.2_Silent_p.G279G|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000418261.1_Silent_p.G279G	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	279	Gly-rich.			G -> GSSSG (in Ref. 4; AAQ88778). {ECO:0000305}.		extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.S274_S290del(1)		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)			cactgctgccgccactgctgc	0.637																																					p.G279G		Atlas-SNP	.											.	DMKN	116	.	1	Deletion - In frame(1)	ovary(1)	c.C837T						PASS	.						26	20	22					19																	36002394		2165	4212	6377	SO:0001819	synonymous_variant	93099	exon5			GCTGCCGCCACTG	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.837C>T	19.37:g.36002394G>A		92	0	0		89	30	0.337079	NM_001126058	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Silent	SNP	ENST00000339686.3	37	CCDS12463.1																																																																																			G|0.933;A|0.067	0.067	strong		0.637	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317		A	36002394	G	A	36002394	2	1	22	1	0	0	0	0	0	0	0	1	4584	1074	38	1		1	DMKN	19	36002394	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	23	36002394	23126589	3903	6804											
DMKN	93099	hgsc.bcm.edu	37	chr19	36002488	36002488	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctgcccgactgtgagccgCtgcctccctgaggggcagga	5	7	15	14	2	0	2	0	2	0	0	1	4	1	3	4	3	4	3	4	3	0	0	rs57760262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36002488C>A	ENST00000339686.3	-	5	919	c.743G>T	c.(742-744)aGc>aTc	p.S248I	DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000447113.2_Missense_Mutation_p.S248I|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000451297.2_Missense_Mutation_p.S248I|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000440396.1_Missense_Mutation_p.S248I|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000424570.2_Missense_Mutation_p.S248I|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000418261.1_Missense_Mutation_p.S248I	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	248	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)			CTGTGAGCCGCTGCCTCCCTG	0.637													C|||	173	0.0345447	0.1241	0.0101	5008	,	,		18431	0.0		0.002	False		,,,				2504	0.0				p.S248I		Atlas-SNP	.											DMKN,NS,carcinoma,+1,1	DMKN	116	1	0			c.G743T						PASS	.	C	ILE/SER,ILE/SER,ILE/SER,ILE/SER,ILE/SER,,	365,4041	183.6+/-211.2	14,337,1852	34	31	32		743,743,743,743,743,,	2.7	0.7	19	dbSNP_129	32	4,8596	3.0+/-9.4	0,4,4296	yes	missense,missense,missense,missense,missense,intron,intron	DMKN	NM_001126057.2,NM_001126058.2,NM_001190348.1,NM_001190349.1,NM_033317.4,NM_001126056.2,NM_001190347.1	142,142,142,142,142,,	14,341,6148	AA,AC,CC		0.0465,8.2842,2.8372	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,,	248/399,248/387,248/437,248/370,248/477,,	36002488	369,12637	2203	4300	6503	SO:0001583	missense	93099	exon5			GAGCCGCTGCCTC	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.743G>T	19.37:g.36002488C>A	ENSP00000342012:p.Ser248Ile	82	0	0		76	40	0.526316	NM_001126058	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Missense_Mutation	SNP	ENST00000339686.3	37	CCDS12463.1	62	0.028388278388278388	56	0.11382113821138211	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	C	13.09	2.132916	0.37630	0.082842	4.65E-4	ENSG00000161249	ENST00000339686;ENST00000392207;ENST00000447113;ENST00000440396;ENST00000418261;ENST00000424570;ENST00000451297	T;T;T;T;T;T	0.49720	0.77;0.77;0.77;0.77;0.77;0.77	3.78	2.73	0.32206	.	0.880319	0.09618	N	0.777875	T	0.02012	0.0063	L	0.52573	1.65	0.24630	N	0.993629	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.997	D;D;D;D;P	0.69479	0.964;0.964;0.964;0.964;0.899	T	0.01078	-1.1459	10	0.72032	D	0.01	-3.8258	7.2516	0.26152	0.0:0.8755:0.0:0.1245	rs57760262	248;248;248;248;248	E7EUS0;Q6E0U4-7;Q6E0U4-3;Q6E0U4-5;Q6E0U4	.;.;.;.;DMKN_HUMAN	I	248	ENSP00000342012:S248I;ENSP00000394908:S248I;ENSP00000415277:S248I;ENSP00000414743:S248I;ENSP00000388404:S248I;ENSP00000409513:S248I	ENSP00000342012:S248I	S	-	2	0	DMKN	40694328	0.006000	0.16342	0.659000	0.29680	0.091000	0.18340	0.717000	0.25851	0.948000	0.37687	0.561000	0.74099	AGC	C|0.967;A|0.033	0.033	strong		0.637	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317		A	36002488	C	A	36002488	3	1	22	1	0	0	0	0	1	0	0	0	4584	797	28	4	1052	4	DMKN	19	36002488	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	94	36002488	23126495	3904	6805											
SBSN	374897	hgsc.bcm.edu	37	chr19	36018435	36018435	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctcatttccggcctgccccGcagcatggtgggccccctgg	3	8	12	18	2	1	0	1	0	0	0	2	0	2	0	7	4	2	2	7	4	0	1	rs147913080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36018435G>A	ENST00000452271.2	-	1	777	c.749C>T	c.(748-750)gCg>gTg	p.A250V	SBSN_ENST00000518157.1_Intron	NM_001166034.1	NP_001159506.1	Q6UWP8	SBSN_HUMAN	suprabasin	250	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)			GGCCTGCCCCGCAGCATGGTG	0.627													G|||	143	0.0285543	0.1044	0.0072	5008	,	,		20537	0.0		0.0	False		,,,				2504	0.0				p.A250V		Atlas-SNP	.											.	SBSN	58	.	0			c.C749T						PASS	.	G	VAL/ALA,,	148,1236		8,132,552	29	36	34		749,,	-5.1	0	19	dbSNP_134	34	0,3182		0,0,1591	no	missense,intron,intron	SBSN	NM_001166034.1,NM_001166035.1,NM_198538.3	64,,	8,132,2143	AA,AG,GG		0.0,10.6936,3.2413	benign,,	250/591,,	36018435	148,4418	692	1591	2283	SO:0001583	missense	374897	exon1			TGCCCCGCAGCAT	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.749C>T	19.37:g.36018435G>A	ENSP00000430242:p.Ala250Val	6	0	0		5	5	1	NM_001166034	A8K5J0|E9PBV3	Missense_Mutation	SNP	ENST00000452271.2	37	CCDS54253.1	50	0.022893772893772892	40	0.08130081300813008	3	0.008287292817679558	7	0.012237762237762238	0	0.0	G	10.51	1.369069	0.24771	0.106936	0.0	ENSG00000189001	ENST00000452271	T	0.48201	0.82	4.63	-5.14	0.02875	.	.	.	.	.	T	0.00580	0.0019	L	0.40543	1.245	0.09310	N	1	B	0.11235	0.004	B	0.10450	0.005	T	0.16424	-1.0403	9	0.17369	T	0.5	.	7.6648	0.28423	0.3905:0.1283:0.4812:0.0	.	250	E9PBV3	.	V	250	ENSP00000430242:A250V	ENSP00000430242:A250V	A	-	2	0	SBSN	40710275	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.794000	0.01753	-0.578000	0.05959	-1.069000	0.02264	GCG	G|0.977;A|0.023	0.023	strong		0.627	SBSN-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109463.3	NM_198538		A	36018435	G	A	36018435	3	1	22	1	0	0	0	0	1	0	0	0	13879	1087	38	1	1039	1	SBSN	19	36018435	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	15947	36018435	23110548	3905	6806											
RBM42	79171	hgsc.bcm.edu	37	chr19	36124822	36124822	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcccgttggaggtcgtccgCggcctcctgcccccgctgcg	1	8	13	19	6	0	0	0	0	0	0	4	1	3	1	6	3	2	2	6	3	0	1	rs147020112	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36124822C>A	ENST00000262633.4	+	7	1023	c.918C>A	c.(916-918)cgC>cgA	p.R306R	RBM42_ENST00000592202.1_Silent_p.R252R|RBM42_ENST00000360475.4_Silent_p.R277R|RBM42_ENST00000589559.1_Silent_p.R277R|RBM42_ENST00000589871.1_Silent_p.R284R|RBM42_ENST00000588161.1_Silent_p.R276R|RBM42_ENST00000586618.1_Intron	NM_024321.3	NP_077297.2	Q9BTD8	RBM42_HUMAN	RNA binding motif protein 42	306	Necessary for interaction with HNRNPK. {ECO:0000250}.|Pro-rich.					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)			AGGTCGTCCGCGGCCTCCTGC	0.731													C|||	79	0.0157748	0.0598	0.0	5008	,	,		14671	0.0		0.0	False		,,,				2504	0.0				p.R306R		Atlas-SNP	.											.	RBM42	40	.	0			c.C918A						PASS	.	C		157,4183		3,151,2016	7	9	8		918	-10.2	0.1	19	dbSNP_134	8	2,8482		0,2,4240	no	coding-synonymous	RBM42	NM_024321.3		3,153,6256	AA,AC,CC		0.0236,3.6175,1.2399		306/481	36124822	159,12665	2170	4242	6412	SO:0001819	synonymous_variant	79171	exon7			CGTCCGCGGCCTC	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.918C>A	19.37:g.36124822C>A		26	0	0		40	18	0.45	NM_024321	O00320|Q8N5R7|Q9BU66	Silent	SNP	ENST00000262633.4	37	CCDS12468.1																																																																																			C|0.990;A|0.010	0.010	strong		0.731	RBM42-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459057.2	NM_024321		A	36124822	C	A	36124822	2	1	22	1	0	0	0	0	0	0	0	1	13151	755	27	4		4	RBM42	19	36124822	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	106387	36124822	23004161	3906	6807											
PRODH2	58510	hgsc.bcm.edu	37	chr19	36302897	36302897	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atagcttcagccagcctctcGgggctcagctccaaggaggc	8	7	12	14	1	3	0	2	0	1	0	5	1	4	1	3	4	4	3	3	4	2	2	rs145376615	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36302897G>A	ENST00000301175.3	-	5	809	c.792C>T	c.(790-792)ccC>ccT	p.P264P		NM_021232.1	NP_067055.1	Q9UF12	PROD2_HUMAN	proline dehydrogenase (oxidase) 2	264					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)			CCAGCCTCTCGGGGCTCAGCT	0.637													G|||	30	0.00599042	0.0212	0.0029	5008	,	,		18798	0.0		0.0	False		,,,				2504	0.0				p.P264P		Atlas-SNP	.											.	PRODH2	68	.	0			c.C792T						PASS	.	G		87,4319	72.5+/-110.5	0,87,2116	51	47	48		792	-9.5	0.2	19	dbSNP_134	48	0,8600		0,0,4300	no	coding-synonymous	PRODH2	NM_021232.1		0,87,6416	AA,AG,GG		0.0,1.9746,0.6689		264/537	36302897	87,12919	2203	4300	6503	SO:0001819	synonymous_variant	58510	exon5			CCTCTCGGGGCTC	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.792C>T	19.37:g.36302897G>A		97	0	0		97	51	0.525773	NM_021232		Silent	SNP	ENST00000301175.3	37	CCDS12478.1																																																																																			A|0.006;G|0.994;T|0.000	0.006	strong		0.637	PRODH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452552.2	NM_021232		A	36302897	G	A	36302897	2	1	22	1	0	0	0	0	0	0	0	1	12561	1103	39	1		1	PRODH2	19	36302897	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	178075	36302897	22826086	3907	6808											
PRODH2	58510	hgsc.bcm.edu	37	chr19	36304143	36304143	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ttgtaatcccaacactttggGaggccaagaccgaggagttt	11	10	11	9	1	0	1	0	0	0	1	1	4	1	3	3	3	1	2	3	3	3	4	rs138605929	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36304143G>A	ENST00000301175.3	-	1	58	c.41C>T	c.(40-42)tCc>tTc	p.S14F		NM_021232.1	NP_067055.1	Q9UF12	PROD2_HUMAN	proline dehydrogenase (oxidase) 2	14					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)			aacactttgggaggccaagac	0.423													G|||	30	0.00599042	0.0212	0.0029	5008	,	,		21126	0.0		0.0	False		,,,				2504	0.0				p.S14F		Atlas-SNP	.											.	PRODH2	68	.	0			c.C41T						PASS	.	G	PHE/SER	79,4327	54.9+/-90.9	0,79,2124	60	54	56		41	0.4	0	19	dbSNP_134	56	0,8600		0,0,4300	no	missense	PRODH2	NM_021232.1	155	0,79,6424	AA,AG,GG		0.0,1.793,0.6074	possibly-damaging	14/537	36304143	79,12927	2203	4300	6503	SO:0001583	missense	58510	exon1			CTTTGGGAGGCCA	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.41C>T	19.37:g.36304143G>A	ENSP00000301175:p.Ser14Phe	50	0	0		43	28	0.651163	NM_021232		Missense_Mutation	SNP	ENST00000301175.3	37	CCDS12478.1	9	0.004120879120879121	7	0.014227642276422764	2	0.0055248618784530384	0	0.0	0	0.0	G	6.284	0.420467	0.11928	0.01793	0.0	ENSG00000250799	ENST00000301175	T	0.06849	3.25	0.36	0.36	0.16097	.	.	.	.	.	T	0.02571	0.0078	N	0.08118	0	0.09310	N	1	P	0.39520	0.676	P	0.45558	0.485	T	0.41034	-0.9531	8	0.56958	D	0.05	.	.	.	.	.	14	Q9UF12	PROD2_HUMAN	F	14	ENSP00000301175:S14F	ENSP00000301175:S14F	S	-	2	0	PRODH2	40995983	0.037000	0.19845	0.031000	0.17742	0.030000	0.12068	0.477000	0.22196	0.469000	0.27268	0.472000	0.43445	TCC	G|0.992;A|0.008	0.008	strong		0.423	PRODH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452552.2	NM_021232		A	36304143	G	A	36304143	3	1	22	1	0	0	0	0	1	0	0	0	12561	1174	41	2	1613	2	PRODH2	19	36304143	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1246	36304143	22824840	3908	6809											
KIRREL2	84063	hgsc.bcm.edu	37	chr19	36349721	36349721	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccctacccctgaattgctGtggttccgagatggggtcct	5	11	12	13	2	0	2	0	1	0	1	2	3	2	2	5	3	2	2	5	3	2	3	rs57079408	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36349721G>A	ENST00000360202.5	+	4	675	c.477G>A	c.(475-477)ctG>ctA	p.L159L	KIRREL2_ENST00000592409.1_Silent_p.L159L|KIRREL2_ENST00000262625.7_Silent_p.L159L|NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000347900.6_Silent_p.L109L	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	159	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)			CTGAATTGCTGTGGTTCCGAG	0.592													G|||	35	0.00698882	0.0242	0.0043	5008	,	,		18517	0.0		0.0	False		,,,				2504	0.0				p.L159L		Atlas-SNP	.											.	KIRREL2	170	.	0			c.G477A						PASS	.	G	,,	87,4319	72.0+/-110.0	0,87,2116	107	103	104		477,327,477	2.1	1	19	dbSNP_129	104	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	KIRREL2	NM_032123.5,NM_199179.2,NM_199180.2	,,	0,87,6416	AA,AG,GG		0.0,1.9746,0.6689	,,	159/634,109/584,159/709	36349721	87,12919	2203	4300	6503	SO:0001819	synonymous_variant	84063	exon4			ATTGCTGTGGTTC	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.477G>A	19.37:g.36349721G>A		246	1	0.00406504		215	104	0.483721	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Silent	SNP	ENST00000360202.5	37	CCDS12481.1																																																																																			G|0.994;A|0.006	0.006	strong		0.592	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123		A	36349721	G	A	36349721	2	1	22	1	0	0	0	0	0	0	0	1	8334	1364	48	2		2	KIRREL2	19	36349721	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	45578	36349721	22779262	3909	6810											
KIRREL2	84063	hgsc.bcm.edu	37	chr19	36350474	36350474	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggagccacctttgtctgccGggcccggagccaggccctgc	4	7	14	16	2	1	0	0	0	1	0	1	2	1	2	6	4	4	0	6	4	0	1	rs34494265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36350474G>A	ENST00000360202.5	+	5	812	c.614G>A	c.(613-615)cGg>cAg	p.R205Q	KIRREL2_ENST00000592409.1_Missense_Mutation_p.R205Q|KIRREL2_ENST00000262625.7_Missense_Mutation_p.R205Q|NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000347900.6_Missense_Mutation_p.R155Q	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	205	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)		p.R205L(2)		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)			TTTGTCTGCCGGGCCCGGAGC	0.627													G|||	91	0.0181709	0.0673	0.0029	5008	,	,		17806	0.0		0.0	False		,,,				2504	0.0				p.R205Q		Atlas-SNP	.											.	KIRREL2	170	.	2	Substitution - Missense(2)	lung(2)	c.G614A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	235,4171	139.2+/-174.8	4,227,1972	64	63	63		614,464,614	3.7	1	19	dbSNP_126	63	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	KIRREL2	NM_032123.5,NM_199179.2,NM_199180.2	43,43,43	4,228,6271	AA,AG,GG		0.0116,5.3336,1.8145	possibly-damaging,possibly-damaging,possibly-damaging	205/634,155/584,205/709	36350474	236,12770	2203	4300	6503	SO:0001583	missense	84063	exon5			TCTGCCGGGCCCG	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.614G>A	19.37:g.36350474G>A	ENSP00000353331:p.Arg205Gln	53	0	0		68	38	0.558824	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Missense_Mutation	SNP	ENST00000360202.5	37	CCDS12481.1	22	0.010073260073260074	20	0.04065040650406504	2	0.0055248618784530384	0	0.0	0	0.0	G	13.26	2.183768	0.38609	0.053336	1.16E-4	ENSG00000126259	ENST00000262625;ENST00000347900;ENST00000360202	T;T;T	0.74632	-0.86;-0.86;-0.86	4.72	3.68	0.42216	Immunoglobulin subtype (1);CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.203139	0.24398	N	0.038876	T	0.19366	0.0465	L	0.47078	1.49	0.25543	N	0.987161	B;P;P;P	0.38863	0.438;0.65;0.597;0.597	B;B;B;B	0.30716	0.119;0.119;0.072;0.072	T	0.22208	-1.0223	10	0.20519	T	0.43	-18.1018	8.1639	0.31215	0.106:0.0:0.894:0.0	rs34494265;rs34494265	205;205;155;205	F1T0I2;Q6UWL6;Q6UWL6-3;Q6UWL6-2	.;KIRR2_HUMAN;.;.	Q	205;155;205	ENSP00000262625:R205Q;ENSP00000345067:R155Q;ENSP00000353331:R205Q	ENSP00000262625:R205Q	R	+	2	0	KIRREL2	41042314	1.000000	0.71417	0.994000	0.49952	0.292000	0.27327	3.165000	0.50778	2.623000	0.88846	0.549000	0.68633	CGG	G|0.982;A|0.018	0.018	strong		0.627	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123		A	36350474	G	A	36350474	3	1	22	1	0	0	0	0	1	0	0	0	8334	1116	39	1	632	1	KIRREL2	19	36350474	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	753	36350474	22778509	3910	6811											
KIRREL2	84063	hgsc.bcm.edu	37	chr19	36351545	36351545	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acgccgtgggtagcgccaacCgcagtactgcgctggatgtg	7	7	15	12	5	0	0	0	0	0	0	0	1	0	1	3	2	4	4	3	2	3	2	rs73928337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36351545C>A	ENST00000360202.5	+	7	1102	c.904C>A	c.(904-906)Cgc>Agc	p.R302S	KIRREL2_ENST00000592409.1_Missense_Mutation_p.R302S|KIRREL2_ENST00000262625.7_Missense_Mutation_p.R302S|NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000347900.6_Missense_Mutation_p.R252S	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	302	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)			TAGCGCCAACCGCAGTACTGC	0.677													C|||	35	0.00698882	0.0242	0.0043	5008	,	,		16057	0.0		0.0	False		,,,				2504	0.0				p.R302S		Atlas-SNP	.											KIRREL2_ENST00000262625,NS,carcinoma,-1,2	KIRREL2	170	2	0			c.C904A						PASS	.	C	SER/ARG,SER/ARG,SER/ARG	87,4319	72.0+/-110.0	0,87,2116	63	69	67		904,754,904	4	1	19	dbSNP_130	67	0,8600		0,0,4300	yes	missense,missense,missense	KIRREL2	NM_032123.5,NM_199179.2,NM_199180.2	110,110,110	0,87,6416	AA,AC,CC		0.0,1.9746,0.6689	probably-damaging,probably-damaging,probably-damaging	302/634,252/584,302/709	36351545	87,12919	2203	4300	6503	SO:0001583	missense	84063	exon7			GCCAACCGCAGTA	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.904C>A	19.37:g.36351545C>A	ENSP00000353331:p.Arg302Ser	107	0	0		109	50	0.458716	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Missense_Mutation	SNP	ENST00000360202.5	37	CCDS12481.1	12	0.005494505494505495	8	0.016260162601626018	4	0.011049723756906077	0	0.0	0	0.0	c	21.8	4.203992	0.79127	0.019746	0.0	ENSG00000126259	ENST00000262625;ENST00000347900;ENST00000360202;ENST00000341658	T;T;T	0.14766	2.48;2.48;2.48	3.99	3.99	0.46301	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.42053	D	0.000769	T	0.10766	0.0263	N	0.22421	0.69	0.37484	D	0.916104	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.998;0.998	D;D;D;D;D	0.85130	0.993;0.988;0.997;0.994;0.994	T	0.04191	-1.0970	10	0.35671	T	0.21	-18.2581	11.8642	0.52484	0.0:1.0:0.0:0.0	.	302;282;302;252;302	F1T0I2;Q6UWL6-4;Q6UWL6;Q6UWL6-3;Q6UWL6-2	.;.;KIRR2_HUMAN;.;.	S	302;252;302;282	ENSP00000262625:R302S;ENSP00000345067:R252S;ENSP00000353331:R302S	ENSP00000262625:R302S	R	+	1	0	KIRREL2	41043385	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	2.485000	0.45250	2.257000	0.74773	0.444000	0.29173	CGC	C|0.994;A|0.006	0.006	strong		0.677	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123		A	36351545	C	A	36351545	3	1	22	1	0	0	0	0	1	0	0	0	8334	652	23	4	930	4	KIRREL2	19	36351545	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1071	36351545	22777438	3911	6812											
KIRREL2	84063	hgsc.bcm.edu	37	chr19	36351906	36351906	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgcgggaacccgcttccaCgggtaacctggacccgccgc	6	4	14	17	6	0	0	0	0	0	0	1	2	1	2	5	4	2	2	5	4	2	2	rs73928338	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36351906C>A	ENST00000360202.5	+	8	1222	c.1024C>A	c.(1024-1026)Cgg>Agg	p.R342R	KIRREL2_ENST00000592409.1_Silent_p.R342R|KIRREL2_ENST00000262625.7_Silent_p.R342R|NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000347900.6_Silent_p.R292R	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	342	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)			CCCGCTTCCACGGGTAACCTG	0.662													C|||	35	0.00698882	0.0242	0.0043	5008	,	,		13850	0.0		0.0	False		,,,				2504	0.0				p.R342R		Atlas-SNP	.											.	KIRREL2	170	.	0			c.C1024A						PASS	.	C	,,	76,4284		0,76,2104	11	13	12		1024,874,1024	4.5	1	19	dbSNP_130	12	1,8531		0,1,4265	no	coding-synonymous,coding-synonymous,coding-synonymous	KIRREL2	NM_032123.5,NM_199179.2,NM_199180.2	,,	0,77,6369	AA,AC,CC		0.0117,1.7431,0.5973	,,	342/634,292/584,342/709	36351906	77,12815	2180	4266	6446	SO:0001819	synonymous_variant	84063	exon8			CTTCCACGGGTAA	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.1024C>A	19.37:g.36351906C>A		50	0	0		69	30	0.434783	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Silent	SNP	ENST00000360202.5	37	CCDS12481.1																																																																																			C|0.994;A|0.006	0.006	strong		0.662	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123		A	36351906	C	A	36351906	2	1	22	1	0	0	0	0	0	0	0	1	8334	527	19	4		4	KIRREL2	19	36351906	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	361	36351906	22777077	3912	6813											
KIRREL2	84063	hgsc.bcm.edu	37	chr19	36353880	36353880	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgcgaatccctggcagcaGcgacggctccagttcacgag	9	6	13	13	4	1	0	1	0	0	0	3	4	3	0	2	2	3	4	2	2	1	1	rs35775934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36353880G>A	ENST00000360202.5	+	13	1865	c.1667G>A	c.(1666-1668)aGc>aAc	p.S556N	KIRREL2_ENST00000592409.1_Missense_Mutation_p.S521N|KIRREL2_ENST00000262625.7_Missense_Mutation_p.S556N|NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000347900.6_Missense_Mutation_p.S506N	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	556			S -> N (in dbSNP:rs35775934).		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)			CCTGGCAGCAGCGACGGCTCC	0.607													G|||	165	0.0329473	0.121	0.0072	5008	,	,		16611	0.0		0.0	False		,,,				2504	0.0				p.S556N		Atlas-SNP	.											KIRREL2_ENST00000262625,NS,carcinoma,-1,2	KIRREL2	170	2	0			c.G1667A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER	503,3901		19,465,1718	38	36	37		1667,1517,1667	3.9	0.9	19	dbSNP_126	37	4,8592		0,4,4294	yes	missense,missense,missense	KIRREL2	NM_032123.5,NM_199179.2,NM_199180.2	46,46,46	19,469,6012	AA,AG,GG		0.0465,11.4214,3.9	benign,benign,benign	556/634,506/584,556/709	36353880	507,12493	2202	4298	6500	SO:0001583	missense	84063	exon13			GCAGCAGCGACGG	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.1667G>A	19.37:g.36353880G>A	ENSP00000353331:p.Ser556Asn	65	0	0		65	65	1	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Missense_Mutation	SNP	ENST00000360202.5	37	CCDS12481.1	45	0.020604395604395604	39	0.07926829268292683	6	0.016574585635359115	0	0.0	0	0.0	G	13.69	2.311961	0.40895	0.114214	4.65E-4	ENSG00000126259	ENST00000262625;ENST00000347900;ENST00000360202;ENST00000341658;ENST00000270294	T;T;T	0.65178	-0.13;0.1;-0.14	4.98	3.94	0.45596	.	0.000000	0.45126	D	0.000386	T	0.03651	0.0104	L	0.56769	1.78	0.25267	N	0.989546	D;D;D;D;D	0.71674	0.993;0.998;0.993;0.996;0.996	D;D;D;D;D	0.80764	0.968;0.994;0.968;0.986;0.986	T	0.05451	-1.0884	10	0.21540	T	0.41	-13.9497	8.3131	0.32084	0.1065:0.0:0.8935:0.0	rs35775934	556;536;556;506;556	F1T0I2;Q6UWL6-4;Q6UWL6;Q6UWL6-3;Q6UWL6-2	.;.;KIRR2_HUMAN;.;.	N	556;506;556;536;67	ENSP00000262625:S556N;ENSP00000345067:S506N;ENSP00000353331:S556N	ENSP00000262625:S556N	S	+	2	0	KIRREL2	41045720	0.958000	0.32768	0.945000	0.38365	0.102000	0.19082	1.580000	0.36547	2.321000	0.78463	0.561000	0.74099	AGC	G|0.959;A|0.041	0.041	strong		0.607	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123		A	36353880	G	A	36353880	3	1	22	1	0	0	0	0	1	0	0	0	8334	971	34	2	1717	2	KIRREL2	19	36353880	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1974	36353880	22775103	3913	6814											
C19orf46	163183	hgsc.bcm.edu	37	chr19	36497747	36497747	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgcaggatctgctccagggCtgcccaggccctgggctcac	5	6	13	17	1	2	0	1	0	1	0	3	1	3	1	4	4	2	4	4	4	0	0	rs77925409	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36497747C>G	ENST00000324444.3	-	4	634	c.523G>C	c.(523-525)Gcc>Ccc	p.A175P	AC002116.8_ENST00000473572.2_RNA|ALKBH6_ENST00000495116.2_5'Flank|SYNE4_ENST00000340477.5_Intron	NM_001039876.1	NP_001034965.1	Q8N205	SYNE4_HUMAN	spectrin repeat containing, nuclear envelope family member 4	175					establishment of epithelial cell apical/basal polarity (GO:0045198)	integral component of nuclear outer membrane (GO:0031309)											TGCTCCAGGGCTGCCCAGGCC	0.687													C|||	140	0.0279553	0.1006	0.0101	5008	,	,		14555	0.0		0.0	False		,,,				2504	0.0				p.A175P		Atlas-SNP	.											.	.	.	.	0			c.G523C						PASS	.	C	PRO/ALA	304,3792		11,282,1755	14	21	19		523	-1.4	0	19	dbSNP_131	19	6,8318		0,6,4156	yes	missense	C19orf46	NM_001039876.1	27	11,288,5911	GG,GC,CC		0.0721,7.4219,2.496	possibly-damaging	175/405	36497747	310,12110	2048	4162	6210	SO:0001583	missense	163183	exon4			CCAGGGCTGCCCA	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.523G>C	19.37:g.36497747C>G	ENSP00000316130:p.Ala175Pro	81	0	0		85	36	0.423529	NM_001039876	A8MRS0|A8MYE3|Q7Z7L3	Missense_Mutation	SNP	ENST00000324444.3	37	CCDS42553.1	40	0.018315018315018316	34	0.06910569105691057	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	C	13.03	2.114112	0.37339	0.074219	7.21E-4	ENSG00000181392	ENST00000324444;ENST00000490730	T;T	0.53206	0.63;0.63	5.95	-1.44	0.08856	.	0.656922	0.16361	N	0.217750	T	0.02380	0.0073	L	0.40543	1.245	0.09310	N	1	B;B	0.21381	0.055;0.001	B;B	0.20577	0.03;0.002	T	0.07046	-1.0793	10	0.48119	T	0.1	-12.2768	2.0383	0.03545	0.2949:0.4044:0.1655:0.1353	.	175;175	D6RAE3;Q8N205	.;SYNE4_HUMAN	P	175	ENSP00000316130:A175P;ENSP00000422716:A175P	ENSP00000316130:A175P	A	-	1	0	C19orf46	41189587	0.002000	0.14202	0.030000	0.17652	0.956000	0.61745	-0.333000	0.07894	-0.067000	0.12976	-0.262000	0.10625	GCC	C|0.979;G|0.021	0.021	strong		0.687	SYNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109525.3	NM_001039876		G	36497747	C	G	36497747	3	3	22	1	0	0	0	0	1	0	0	0	1931	797	28	4	711	4	C19orf46	19	36497747	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	143867	36497747	22631236	3914	6815											
WDR62	284403	hgsc.bcm.edu	37	chr19	36583692	36583692	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcagcagcacacaaatgacaAgaagcggagtggccacccca	15	2	11	13	1	0	2	0	1	0	1	0	3	0	3	3	2	3	3	3	2	3	0	rs61747277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36583692A>G	ENST00000270301.7	+	19	2312	c.2312A>G	c.(2311-2313)aAg>aGg	p.K771R	WDR62_ENST00000401500.2_Missense_Mutation_p.K771R			O43379	WDR62_HUMAN	WD repeat domain 62	771					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)			ACAAATGACAAGAAGCGGAGT	0.622													A|||	92	0.0183706	0.0673	0.0029	5008	,	,		16554	0.0		0.001	False		,,,				2504	0.0				p.K771R		Atlas-SNP	.											.	WDR62	102	.	0			c.A2312G						PASS	.	A	ARG/LYS,ARG/LYS	268,4138	149.9+/-184.0	11,246,1946	72	75	74		2312,2312	-4.4	0	19	dbSNP_129	74	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	WDR62	NM_001083961.1,NM_173636.4	26,26	11,252,6240	GG,GA,AA		0.0698,6.0826,2.1067	benign,benign	771/1524,771/1519	36583692	274,12732	2203	4300	6503	SO:0001583	missense	284403	exon19			ATGACAAGAAGCG	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.2312A>G	19.37:g.36583692A>G	ENSP00000270301:p.Lys771Arg	151	0	0		170	76	0.447059	NM_173636	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Missense_Mutation	SNP	ENST00000270301.7	37	CCDS33001.1	34	0.015567765567765568	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	A	5.908	0.351581	0.11182	0.060826	6.98E-4	ENSG00000075702	ENST00000401500;ENST00000270301	T;T	0.43294	0.95;0.95	5.01	-4.44	0.03557	.	0.201397	0.41938	D	0.000797	T	0.00906	0.0030	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	0.18935	-1.0321	10	0.15952	T	0.53	0.0189	7.3192	0.26517	0.5771:0.1282:0.2946:0.0	rs61747277	771;771	O43379-4;O43379	.;WDR62_HUMAN	R	771	ENSP00000384792:K771R;ENSP00000270301:K771R	ENSP00000270301:K771R	K	+	2	0	WDR62	41275532	.	.	0.000000	0.03702	0.001000	0.01503	.	.	-0.452000	0.07087	-0.132000	0.14878	AAG	A|0.982;G|0.018	0.018	strong		0.622	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671		G	36583692	A	G	36583692	3	3	22	1	0	0	0	0	1	0	0	0	17328	72	3	3	2386	3	WDR62	19	36583692	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	85945	36583692	22545291	3915	6816											
WDR62	284403	hgsc.bcm.edu	37	chr19	36594404	36594404	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggccactgccagctcccGtgccaggatatcacgcagca	9	5	12	15	2	1	0	1	0	0	0	2	2	2	2	4	3	4	3	4	3	1	1	rs61743589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36594404G>A	ENST00000270301.7	+	30	3659	c.3659G>A	c.(3658-3660)cGt>cAt	p.R1220H	WDR62_ENST00000401500.2_Missense_Mutation_p.R1225H			O43379	WDR62_HUMAN	WD repeat domain 62	1220					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)			GCCAGCTCCCGTGCCAGGATA	0.652													G|||	112	0.0223642	0.0794	0.0101	5008	,	,		19415	0.0		0.0	False		,,,				2504	0.0				p.R1225H		Atlas-SNP	.											.	WDR62	102	.	0			c.G3674A						PASS	.	G	HIS/ARG,HIS/ARG	315,4091	168.7+/-199.5	11,293,1899	88	82	84		3674,3659	-9.4	0	19	dbSNP_129	84	5,8595	3.0+/-9.4	0,5,4295	yes	missense,missense	WDR62	NM_001083961.1,NM_173636.4	29,29	11,298,6194	AA,AG,GG		0.0581,7.1493,2.4604	benign,benign	1225/1524,1220/1519	36594404	320,12686	2203	4300	6503	SO:0001583	missense	284403	exon30			GCTCCCGTGCCAG	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.3659G>A	19.37:g.36594404G>A	ENSP00000270301:p.Arg1220His	133	0	0		119	56	0.470588	NM_001083961	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Missense_Mutation	SNP	ENST00000270301.7	37	CCDS33001.1	33	0.01510989010989011	31	0.06300813008130081	2	0.0055248618784530384	0	0.0	0	0.0	G	1.107	-0.659223	0.03454	0.071493	5.81E-4	ENSG00000075702	ENST00000401500;ENST00000270301	T;T	0.48201	0.91;0.82	4.93	-9.42	0.00610	.	1.133150	0.06589	N	0.751672	T	0.01558	0.0050	N	0.12182	0.205	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.002	T	0.13845	-1.0494	10	0.13853	T	0.58	1.1471	9.9297	0.41514	0.2448:0.0:0.6539:0.1013	rs61743589	1225;1220	O43379-4;O43379	.;WDR62_HUMAN	H	1225;1220	ENSP00000384792:R1225H;ENSP00000270301:R1220H	ENSP00000270301:R1220H	R	+	2	0	WDR62	41286244	0.000000	0.05858	0.026000	0.17262	0.275000	0.26752	-0.741000	0.04855	-2.003000	0.00962	-1.360000	0.01215	CGT	G|0.981;A|0.019	0.019	strong		0.652	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671		A	36594404	G	A	36594404	3	1	22	1	0	0	0	0	1	0	0	0	17328	1145	40	1	3792	1	WDR62	19	36594404	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	10712	36594404	22534579	3916	6817											
ZFP14	57677	hgsc.bcm.edu	37	chr19	36832427	36832427	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttccattatatcccactgaaAtgaatatatttcataaatgt	15	16	3	7	0	1	2	1	2	0	0	3	2	3	2	2	0	0	0	2	0	8	7	rs115297808	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36832427A>T	ENST00000270001.7	-	5	416	c.301T>A	c.(301-303)Ttt>Att	p.F101I		NM_020917.2	NP_065968.1	Q9HCL3	ZFP14_HUMAN	ZFP14 zinc finger protein	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)			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)					TCCCACTGAAATGAATATATT	0.343													A|||	69	0.013778	0.0507	0.0029	5008	,	,		17204	0.0		0.0	False		,,,				2504	0.0				p.F101I		Atlas-SNP	.											.	ZFP14	68	.	0			c.T301A						PASS	.	A	ILE/PHE	147,4259	94.8+/-133.5	4,139,2060	52	54	53		301	2	0.5	19	dbSNP_132	53	2,8586	1.2+/-3.3	0,2,4292	yes	missense	ZFP14	NM_020917.2	21	4,141,6352	TT,TA,AA		0.0233,3.3364,1.1467	benign	101/534	36832427	149,12845	2203	4294	6497	SO:0001583	missense	57677	exon5			ACTGAAATGAATA	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.301T>A	19.37:g.36832427A>T	ENSP00000270001:p.Phe101Ile	136	0	0		118	61	0.516949	NM_020917	A7MD23	Missense_Mutation	SNP	ENST00000270001.7	37	CCDS33002.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	a	3.299	-0.143207	0.06669	0.033364	2.33E-4	ENSG00000142065	ENST00000270001;ENST00000392172	T	0.06528	3.29	4.2	2.05	0.26809	.	0.326738	0.22483	N	0.059470	T	0.00666	0.0022	L	0.38175	1.15	0.19775	N	0.999956	B;B	0.16603	0.018;0.005	B;B	0.12837	0.008;0.008	T	0.44907	-0.9297	10	0.21014	T	0.42	.	4.3827	0.11302	0.691:0.2011:0.1079:0.0	.	101;101	A8KAN8;Q9HCL3	.;ZFP14_HUMAN	I	101	ENSP00000270001:F101I	ENSP00000270001:F101I	F	-	1	0	ZFP14	41524267	0.005000	0.15991	0.453000	0.27007	0.613000	0.37349	1.042000	0.30303	0.240000	0.21263	0.523000	0.50628	TTT	A|0.990;T|0.010	0.010	strong		0.343	ZFP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452528.1	NM_020917		T	36832427	A	T	36832427	3	4	22	1	0	0	0	0	1	0	0	0	17654	101	4	5	1304	5	ZFP14	19	36832427	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	238023	36832427	22296556	3917	6818											
ZFP82	284406	hgsc.bcm.edu	37	chr19	36884651	36884651	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccacattccttacattcataCggtttttcaccagtatgaat	11	15	4	11	1	2	1	2	1	0	0	3	1	3	1	3	1	2	2	3	1	4	7	rs114627398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36884651C>A	ENST00000392161.3	-	5	833	c.591G>T	c.(589-591)ccG>ccT	p.P197P	ZFP82_ENST00000392171.1_Silent_p.P197P	NM_133466.2	NP_597723.1	Q8N141	ZFP82_HUMAN	ZFP82 zinc finger protein	197					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						TACATTCATACGGTTTTTCAC	0.408													G|||	68	0.0135783	0.0499	0.0029	5008	,	,		22380	0.0		0.0	False		,,,				2504	0.0				p.P197P		Atlas-SNP	.											.	ZFP82	71	.	0			c.G591T						PASS	.	G		150,4256		4,142,2057	88	78	81		591	-4.1	1	19	dbSNP_132	81	2,8598		0,2,4298	no	coding-synonymous	ZFP82	NM_133466.2		4,144,6355	AA,AC,CC		0.0233,3.4044,1.1687		197/533	36884651	152,12854	2203	4300	6503	SO:0001819	synonymous_variant	284406	exon5			TTCATACGGTTTT	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.591G>T	19.37:g.36884651C>A		168	0	0		176	90	0.511364	NM_133466	Q8NC63|Q8TF53	Silent	SNP	ENST00000392161.3	37	CCDS12493.1																																																																																			C|0.989;A|0.011	0.011	strong		0.408	ZFP82-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109552.2	NM_133466		A	36884651	C	A	36884651	2	1	22	1	0	0	0	0	0	0	0	1	17668	523	19	4		4	ZFP82	19	36884651	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	52224	36884651	22244332	3918	6819											
ZNF566	84924	hgsc.bcm.edu	37	chr19	36940675	36940675	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaatgtgaaggatggatggTgactcaaagtgggcagatct	12	10	15	4	0	2	3	1	2	1	1	2	5	2	5	0	4	0	2	0	4	3	1	rs35217571	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36940675T>C	ENST00000434377.2	-	5	542	c.461A>G	c.(460-462)cAc>cGc	p.H154R	ZNF566_ENST00000454319.1_Missense_Mutation_p.H155R|ZNF566_ENST00000424129.2_Missense_Mutation_p.H154R|ZNF566_ENST00000493391.1_Missense_Mutation_p.H50R|ZNF566_ENST00000392170.2_Missense_Mutation_p.H155R	NM_032838.4	NP_116227.1	Q969W8	ZN566_HUMAN	zinc finger protein 566	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)			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)					GGATGGATGGTGACTCAAAGT	0.393													T|||	78	0.0155751	0.0575	0.0029	5008	,	,		19069	0.0		0.0	False		,,,				2504	0.0				p.H155R		Atlas-SNP	.											.	ZNF566	40	.	0			c.A464G						PASS	.	T	ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS	208,4198	129.0+/-165.8	6,196,2001	146	145	145		464,461,461,461	2.8	0.6	19	dbSNP_126	145	7,8593	5.7+/-21.5	0,7,4293	yes	missense,missense,missense,missense	ZNF566	NM_001145343.1,NM_001145344.1,NM_001145345.1,NM_032838.4	29,29,29,29	6,203,6294	CC,CT,TT		0.0814,4.7208,1.6531	benign,benign,benign,benign	155/420,154/419,154/419,154/419	36940675	215,12791	2203	4300	6503	SO:0001583	missense	84924	exon5			GGATGGTGACTCA	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.461A>G	19.37:g.36940675T>C	ENSP00000415520:p.His154Arg	183	0	0		159	89	0.559748	NM_001145343	B7ZL95|Q2M3J1	Missense_Mutation	SNP	ENST00000434377.2	37	CCDS12494.1	23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	T	0.347	-0.946931	0.02304	0.047208	8.14E-4	ENSG00000186017	ENST00000454319;ENST00000434377;ENST00000392170;ENST00000424129;ENST00000452939;ENST00000427002	T;T;T;T;T;T	0.04862	3.66;3.65;3.66;3.65;3.54;6.16	3.77	2.76	0.32466	.	0.718904	0.12064	N	0.502915	T	0.00637	0.0021	L	0.28054	0.825	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.46582	-0.9181	10	0.20046	T	0.44	.	3.8345	0.08888	0.0:0.1142:0.2214:0.6644	rs35217571	155;154	B7ZL95;Q969W8	.;ZN566_HUMAN	R	155;154;155;154;154;155	ENSP00000394207:H155R;ENSP00000415520:H154R;ENSP00000376010:H155R;ENSP00000401259:H154R;ENSP00000411526:H154R;ENSP00000400651:H155R	ENSP00000376010:H155R	H	-	2	0	ZNF566	41632515	0.045000	0.20229	0.589000	0.28718	0.313000	0.28021	0.622000	0.24433	0.836000	0.34901	0.454000	0.30748	CAC	T|0.986;C|0.014	0.014	strong		0.393	ZNF566-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000341054.1	NM_032838		C	36940675	T	C	36940675	3	2	22	1	0	0	0	0	1	0	0	0	18012	1696	59	3	799	3	ZNF566	19	36940675	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	56024	36940675	22188308	3919	6820											
ZNF790	388536	hgsc.bcm.edu	37	chr19	37309790	37309790	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctgaaccacgaaaaaaggTctttccacattccttacatt	13	13	4	11	1	2	1	0	1	2	0	4	2	4	1	3	1	2	0	3	1	5	5	rs4369791	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:37309790T>A	ENST00000356725.4	-	5	1576	c.1456A>T	c.(1456-1458)Acc>Tcc	p.T486S	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	486			T -> S (in dbSNP:rs4369791).		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)			CGAAAAAAGGTCTTTCCACAT	0.388													T|||	20	0.00399361	0.0151	0.0	5008	,	,		20361	0.0		0.0	False		,,,				2504	0.0				p.T486S		Atlas-SNP	.											.	ZNF790	89	.	0			c.A1456T						PASS	.	T	SER/THR,SER/THR,SER/THR,SER/THR	72,4334	65.3+/-102.7	1,70,2132	83	80	81		1456,1456,1456,1456	-1	0	19	dbSNP_111	81	0,8600		0,0,4300	yes	missense,missense,missense,missense	ZNF790	NM_001242800.1,NM_001242801.1,NM_001242802.1,NM_206894.3	58,58,58,58	1,70,6432	AA,AT,TT		0.0,1.6341,0.5536	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	486/637,486/637,486/637,486/637	37309790	72,12934	2203	4300	6503	SO:0001583	missense	388536	exon5			AAAAGGTCTTTCC	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.1456A>T	19.37:g.37309790T>A	ENSP00000349161:p.Thr486Ser	48	0	0		41	19	0.463415	NM_206894		Missense_Mutation	SNP	ENST00000356725.4	37	CCDS12496.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	T	8.684	0.905767	0.17760	0.016341	0.0	ENSG00000197863	ENST00000356725	T	0.19105	2.17	3.14	-0.997	0.10215	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03477	0.0100	N	0.03903	-0.33	0.09310	N	1	B	0.22604	0.072	B	0.23018	0.043	T	0.32079	-0.9920	9	0.41790	T	0.15	.	4.173	0.10339	0.2887:0.4551:0.0:0.2562	rs4369791;rs52825956;rs4369791	486	Q6PG37	ZN790_HUMAN	S	486	ENSP00000349161:T486S	ENSP00000349161:T486S	T	-	1	0	ZNF790	42001630	0.000000	0.05858	0.034000	0.17996	0.389000	0.30415	0.069000	0.14552	-0.105000	0.12132	0.402000	0.26972	ACC	T|0.995;A|0.005	0.005	strong		0.388	ZNF790-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385341.2	NM_206894		A	37309790	T	A	37309790	3	1	22	1	0	0	0	0	1	0	0	0	18177	1667	58	5	458	5	ZNF790	19	37309790	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	369115	37309790	21819193	3920	6821											
ZNF420	147923	hgsc.bcm.edu	37	chr19	37618157	37618157	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaagagtccaattccagggaTtatttggaagccaaaggcaa	15	8	11	7	0	0	1	0	0	0	1	2	4	2	3	3	3	1	1	3	3	6	3	rs78427535	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:37618157T>C	ENST00000337995.3	+	5	479	c.264T>C	c.(262-264)gaT>gaC	p.D88D	ZNF585A_ENST00000588723.1_Intron|CTC-454I21.4_ENST00000587645.1_RNA|ZNF420_ENST00000304239.7_Silent_p.D88D	NM_144689.3	NP_653290.2	Q8TAQ5	ZN420_HUMAN	zinc finger protein 420	88					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)			ATTCCAGGGATTATTTGGAAG	0.373													T|||	88	0.0175719	0.0628	0.0072	5008	,	,		18952	0.0		0.0	False		,,,				2504	0.0				p.D88D		Atlas-SNP	.											.	ZNF420	71	.	0			c.T264C						PASS	.	T		250,4156	145.0+/-179.8	7,236,1960	83	83	83		264	-4.2	0	19	dbSNP_131	83	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	ZNF420	NM_144689.3		7,243,6253	CC,CT,TT		0.0814,5.6741,1.976		88/689	37618157	257,12749	2203	4300	6503	SO:0001819	synonymous_variant	147923	exon5			CAGGGATTATTTG	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.264T>C	19.37:g.37618157T>C		141	0	0		148	72	0.486486	NM_144689	B2RDY6|Q96ML5	Silent	SNP	ENST00000337995.3	37	CCDS12498.1																																																																																			T|0.984;C|0.016	0.016	strong		0.373	ZNF420-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109587.3	NM_144689		C	37618157	T	C	37618157	2	2	22	1	0	0	0	0	0	0	0	1	17912	1490	52	3		3	ZNF420	19	37618157	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	308367	37618157	21510826	3921	6822											
ZNF585B	92285	hgsc.bcm.edu	37	chr19	37697988	37697988	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagccagggctgaggatttcTggggtgaggtccaactagct	8	9	16	8	0	1	2	0	2	1	0	2	4	2	3	2	5	3	2	2	5	2	2	rs145040657		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:37697988T>C	ENST00000532828.2	-	2	277	c.26A>G	c.(25-27)cAg>cGg	p.Q9R	ZNF585B_ENST00000527838.1_Missense_Mutation_p.Q9R|ZNF585B_ENST00000534363.1_5'Flank|CTC-454I21.3_ENST00000585860.2_Missense_Mutation_p.Q9R	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	9					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)			TGAGGATTTCTGGGGTGAGGT	0.532													T|||	1	0.000199681	0.0008	0.0	5008	,	,		19866	0.0		0.0	False		,,,				2504	0.0				p.Q9R	Melanoma(93;882 1454 18863 28917 48427)	Atlas-SNP	.											.	ZNF585B	91	.	0			c.A26G						PASS	.	T	ARG/GLN	5,4401	9.9+/-24.2	0,5,2198	120	104	109		26	0.6	0	19	dbSNP_134	109	0,8600		0,0,4300	yes	missense	ZNF585B	NM_152279.3	43	0,5,6498	CC,CT,TT		0.0,0.1135,0.0384	benign	9/770	37697988	5,13001	2203	4300	6503	SO:0001583	missense	92285	exon2			GATTTCTGGGGTG	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.26A>G	19.37:g.37697988T>C	ENSP00000433773:p.Gln9Arg	76	0	0		77	39	0.506494	NM_152279	Q8IZD3|Q96JW6	Missense_Mutation	SNP	ENST00000532828.2	37	CCDS12500.1	.	.	.	.	.	.	.	.	.	.	T	8.991	0.977714	0.18812	0.001135	0.0	ENSG00000245680	ENST00000532828;ENST00000527838	T;T	0.06933	3.24;6.86	1.79	0.647	0.17796	.	.	.	.	.	T	0.06690	0.0171	L	0.52573	1.65	0.09310	N	1	B	0.31655	0.334	B	0.15870	0.014	T	0.32534	-0.9903	9	0.87932	D	0	.	3.6073	0.08048	0.374:0.0:0.0:0.626	.	9	Q52M93	Z585B_HUMAN	R	9	ENSP00000433773:Q9R;ENSP00000435268:Q9R	ENSP00000432760:Q9R	Q	-	2	0	ZNF585B	42389828	0.048000	0.20356	0.004000	0.12327	0.700000	0.40528	0.118000	0.15605	0.117000	0.18138	0.260000	0.18958	CAG	T|1.000;C|0.000	0.000	strong		0.532	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388272.2	NM_152279		C	37697988	T	C	37697988	3	2	22	1	0	0	0	0	1	0	0	0	18033	1580	55	3	2299	3	ZNF585B	19	37697988	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	79831	37697988	21430995	3922	6823											
ZNF570	148268	hgsc.bcm.edu	37	chr19	37975400	37975400	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgcacacctagttcaacaTctgcgagttcatactggaga	13	10	8	10	1	3	1	2	0	1	1	3	3	3	1	1	1	4	3	1	1	4	4	rs78317808	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:37975400T>C	ENST00000330173.1	+	5	1405	c.876T>C	c.(874-876)caT>caC	p.H292H	ZNF570_ENST00000586475.1_Silent_p.H348H|ZNF570_ENST00000388801.3_Silent_p.H89H	NM_144694.1	NP_653295.1	Q96NI8	ZN570_HUMAN	zinc finger protein 570	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)			endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(1)	27			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TAGTTCAACATCTGCGAGTTC	0.423													T|||	91	0.0181709	0.0651	0.0072	5008	,	,		21985	0.0		0.0	False		,,,				2504	0.0				p.H292H		Atlas-SNP	.											.	ZNF570	58	.	0			c.T876C						PASS	.	T		263,4143	148.0+/-182.4	8,247,1948	77	73	74		876	2.2	1	19	dbSNP_131	74	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	ZNF570	NM_144694.1		8,253,6242	CC,CT,TT		0.0698,5.9691,2.0683		292/537	37975400	269,12737	2203	4300	6503	SO:0001819	synonymous_variant	148268	exon5			TCAACATCTGCGA	AK055353	CCDS12504.1, CCDS74355.1	19q13.12	2013-09-20			ENSG00000171827	ENSG00000171827		"Zinc fingers, C2H2-type", "-"	26416	protein-coding gene	gene with protein product							Standard	XM_005258567		Approved	FLJ30791	uc002ogk.1	Q96NI8	OTTHUMG00000048176	ENST00000330173.1:c.876T>C	19.37:g.37975400T>C		68	0	0		61	36	0.590164	NM_144694	A1L472|B4DMP1	Silent	SNP	ENST00000330173.1	37	CCDS12504.1																																																																																			T|0.983;C|0.017	0.017	strong		0.423	ZNF570-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109600.1	NM_144694		C	37975400	T	C	37975400	2	2	22	1	0	0	0	0	0	0	0	1	18017	1432	50	3		3	ZNF570	19	37975400	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	277412	37975400	21153583	3923	6824											
ZNF540	163255	hgsc.bcm.edu	37	chr19	38102955	38102955	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttactctttacccacaactTaatcgacatcagaaaattca	15	13	2	11	1	3	1	2	0	1	1	4	2	3	1	1	0	3	0	1	0	6	6	rs115588579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38102955T>C	ENST00000592533.1	+	5	1106	c.774T>C	c.(772-774)ctT>ctC	p.L258L	ZNF540_ENST00000589117.1_Silent_p.L226L|ZNF540_ENST00000316433.4_Silent_p.L258L|ZNF540_ENST00000343599.5_Silent_p.L258L	NM_152606.4	NP_689819.1	Q8NDQ6	ZN540_HUMAN	zinc finger protein 540	258					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)			ACCCACAACTTAATCGACATC	0.343													T|||	33	0.00658946	0.0227	0.0043	5008	,	,		18475	0.0		0.0	False		,,,				2504	0.0				p.L258L		Atlas-SNP	.											.	ZNF540	75	.	0			c.T774C						PASS	.	T	,,	77,4329	64.7+/-102.0	1,75,2127	33	35	35		774,678,774	1.3	0	19	dbSNP_132	35	1,8595		0,1,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF540	NM_001172225.1,NM_001172226.1,NM_152606.3	,,	1,76,6424	CC,CT,TT		0.0116,1.7476,0.5999	,,	258/661,226/629,258/661	38102955	78,12924	2203	4298	6501	SO:0001819	synonymous_variant	163255	exon5			ACAACTTAATCGA	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.774T>C	19.37:g.38102955T>C		68	0	0		51	26	0.509804	NM_152606	A0AVS5|A8K371|Q05D58|Q3LIC5|Q6ZN36|Q7Z3C8|Q86T31	Silent	SNP	ENST00000592533.1	37	CCDS12506.1																																																																																			T|0.992;C|0.008	0.008	strong		0.343	ZNF540-009	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459481.1	NM_152606		C	38102955	T	C	38102955	2	2	22	1	0	0	0	0	0	0	0	1	17990	1741	61	3		3	ZNF540	19	38102955	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	127555	38102955	21026028	3924	6825											
ZNF781	163115	hgsc.bcm.edu	37	chr19	38160255	38160255	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagagctgaacaattgttaaAagctctaccacattctttac	15	12	5	9	0	2	2	0	1	2	1	2	2	2	2	1	0	5	3	1	0	7	6	rs73932934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38160255A>C	ENST00000590008.1	-	5	1647	c.795T>G	c.(793-795)ctT>ctG	p.L265L	ZNF781_ENST00000593040.1_5'Flank|ZNF781_ENST00000358582.4_Silent_p.L265L|ZFP30_ENST00000586732.1_Intron			Q8N8C0	ZN781_HUMAN	zinc finger protein 781	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)			NS(1)|breast(2)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24						CAATTGTTAAAAGCTCTACCA	0.383													A|||	189	0.0377396	0.1354	0.0144	5008	,	,		20442	0.0		0.0	False		,,,				2504	0.0				p.L265L		Atlas-SNP	.											.	ZNF781	66	.	0			c.T795G						PASS	.	A		401,4005	196.7+/-221.0	20,361,1822	87	91	90		795	1.4	0	19	dbSNP_130	90	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	ZNF781	NM_152605.3		20,364,6119	CC,CA,AA		0.0349,9.1012,3.1063		265/328	38160255	404,12602	2203	4300	6503	SO:0001819	synonymous_variant	163115	exon4			TGTTAAAAGCTCT	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.795T>G	19.37:g.38160255A>C		93	0	0		77	37	0.480519	NM_152605	Q2VPJ8	Silent	SNP	ENST00000590008.1	37	CCDS12507.1																																																																																			A|0.967;C|0.033	0.033	strong		0.383	ZNF781-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000459495.2	NM_152605		C	38160255	A	C	38160255	2	2	22	1	0	0	0	0	0	0	0	1	18169	1	1	5		5	ZNF781	19	38160255	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	57300	38160255	20968728	3925	6826											
SIPA1L3	23094	hgsc.bcm.edu	37	chr19	38610394	38610394	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggtgttcaactgctactgcGgggatgtcattggctggact	6	13	14	8	1	2	0	2	0	0	0	2	2	2	2	0	5	4	3	0	5	2	3	rs140119542	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38610394G>A	ENST00000222345.6	+	9	3249	c.2740G>A	c.(2740-2742)Ggg>Agg	p.G914R		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	914					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)			CTGCTACTGCGGGGATGTCAT	0.532													G|||	3	0.000599042	0.0008	0.0	5008	,	,		20769	0.0		0.0	False		,,,				2504	0.002				p.G914R		Atlas-SNP	.											SIPA1L3,caecum,carcinoma,0,1	SIPA1L3	150	1	0			c.G2740A						PASS	.	G	ARG/GLY	1,4403	2.1+/-5.4	0,1,2201	98	108	105		2740	5.8	1	19	dbSNP_134	105	1,8599	1.2+/-3.3	0,1,4299	no	missense	SIPA1L3	NM_015073.1	125	0,2,6500	AA,AG,GG		0.0116,0.0227,0.0154	benign	914/1782	38610394	2,13002	2202	4300	6502	SO:0001583	missense	23094	exon9			TACTGCGGGGATG	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.2740G>A	19.37:g.38610394G>A	ENSP00000222345:p.Gly914Arg	61	0	0		66	33	0.5	NM_015073	Q2TV87	Missense_Mutation	SNP	ENST00000222345.6	37	CCDS33007.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	8.917	0.960050	0.18507	2.27E-4	1.16E-4	ENSG00000105738	ENST00000222345	T	0.73152	-0.72	5.75	5.75	0.90469	.	0.183723	0.47852	D	0.000205	T	0.44871	0.1314	N	0.02345	-0.59	0.38997	D	0.959275	B	0.17852	0.024	B	0.14578	0.011	T	0.51725	-0.8669	10	0.02654	T	1	-42.3387	18.7237	0.91705	0.0:0.0:1.0:0.0	.	914	O60292	SI1L3_HUMAN	R	914	ENSP00000222345:G914R	ENSP00000222345:G914R	G	+	1	0	SIPA1L3	43302234	0.002000	0.14202	0.997000	0.53966	0.994000	0.84299	0.479000	0.22228	2.725000	0.93324	0.655000	0.94253	GGG	G|1.000;A|0.000	0.000	strong		0.532	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278		A	38610394	G	A	38610394	3	1	22	1	0	0	0	0	1	0	0	0	14346	1116	39	1	2766	1	SIPA1L3	19	38610394	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	450139	38610394	20518589	3926	6827											
CATSPERG	57828	hgsc.bcm.edu	37	chr19	38834974	38834974	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggcttcctgaagagagaccGggacaataacatccaattca	14	7	9	11	2	1	3	1	1	0	2	3	5	3	4	3	2	1	1	3	2	4	3	rs61732182	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38834974G>A	ENST00000409235.3	+	6	750	c.635G>A	c.(634-636)cGg>cAg	p.R212Q	CATSPERG_ENST00000410018.1_Missense_Mutation_p.R212Q|CATSPERG_ENST00000215069.4_Missense_Mutation_p.R197Q	NM_021185.4	NP_067008.3	Q6ZRH7	CTSRG_HUMAN	catsper channel auxiliary subunit gamma	212					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						AAGAGAGACCGGGACAATAAC	0.537													G|||	14	0.00279553	0.0106	0.0	5008	,	,		19650	0.0		0.0	False		,,,				2504	0.0				p.R212Q		Atlas-SNP	.											.	CATSPERG	121	.	0			c.G635A						PASS	.	G	GLN/ARG	24,1360		0,24,668	133	116	121		635	-6.7	0	19	dbSNP_129	121	0,3182		0,0,1591	no	missense	CATSPERG	NM_021185.4	43	0,24,2259	AA,AG,GG		0.0,1.7341,0.5256	benign	212/1160	38834974	24,4542	692	1591	2283	SO:0001583	missense	57828	exon6			GAGACCGGGACAA	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.635G>A	19.37:g.38834974G>A	ENSP00000386962:p.Arg212Gln	117	0	0		127	69	0.543307	NM_021185	A6NEG6|Q659E1	Missense_Mutation	SNP	ENST00000409235.3	37	CCDS12514.2	4	0.0018315018315018315	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	G	2.197	-0.383886	0.04966	0.017341	0.0	ENSG00000099338	ENST00000410018;ENST00000409235;ENST00000409410;ENST00000215069	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	4.61	-6.69	0.01772	.	2.425480	0.01465	N	0.016055	T	0.06096	0.0158	N	0.03177	-0.4	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.15350	-1.0440	10	0.27785	T	0.31	5.2025	7.9175	0.29827	0.255:0.2965:0.4485:0.0	rs61732182	212;212	Q6ZRH7;B8ZZI7	CTSRG_HUMAN;.	Q	212;212;212;197	ENSP00000387057:R212Q;ENSP00000386962:R212Q;ENSP00000386950:R212Q;ENSP00000215069:R197Q	ENSP00000215069:R197Q	R	+	2	0	CATSPERG	43526814	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.727000	0.00807	-1.348000	0.02205	-1.068000	0.02270	CGG	G|0.997;A|0.003	0.003	strong		0.537	CATSPERG-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330204.1	NM_021185		A	38834974	G	A	38834974	3	1	22	1	0	0	0	0	1	0	0	0	2694	1116	39	1	653	1	CATSPERG	19	38834974	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	224580	38834974	20294009	3927	6828											
GGN	199720	hgsc.bcm.edu	37	chr19	38876944	38876944	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gggaggaccagagcacccttCgccgtctccatcacctccct	7	7	9	18	2	2	1	1	0	1	1	5	3	3	3	6	2	1	1	6	2	0	1	rs151268424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38876944C>T	ENST00000334928.6	-	3	1090	c.958G>A	c.(958-960)Gaa>Aaa	p.E320K	GGN_ENST00000591809.1_Intron|AC005789.9_ENST00000585411.1_RNA|SPRED3_ENST00000587013.1_5'Flank	NM_152657.3	NP_689870.3	Q86UU5	GGN_HUMAN	gametogenetin	320	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)			GAGCACCCTTCGCCGTCTCCA	0.682													C|||	14	0.00279553	0.0106	0.0	5008	,	,		13386	0.0		0.0	False		,,,				2504	0.0				p.E320K		Atlas-SNP	.											.	GGN	50	.	0			c.G958A						PASS	.	C	LYS/GLU	53,4345		0,53,2146	24	28	27		958	3.3	1	19	dbSNP_134	27	0,8600		0,0,4300	yes	missense	GGN	NM_152657.3	56	0,53,6446	TT,TC,CC		0.0,1.2051,0.4078	possibly-damaging	320/653	38876944	53,12945	2199	4300	6499	SO:0001583	missense	199720	exon3			ACCCTTCGCCGTC	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.958G>A	19.37:g.38876944C>T	ENSP00000334940:p.Glu320Lys	33	0	0		32	10	0.3125	NM_152657	Q7RTU6|Q86UU4|Q8NAA1	Missense_Mutation	SNP	ENST00000334928.6	37	CCDS12516.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	15.63	2.891749	0.52014	0.012051	0.0	ENSG00000179168	ENST00000334928	.	.	.	3.33	3.33	0.38152	.	0.000000	0.38005	N	0.001858	T	0.37183	0.0994	L	0.29908	0.895	0.30484	N	0.77204	D;D	0.76494	0.999;0.999	D;D	0.76071	0.987;0.987	T	0.28235	-1.0050	9	0.17369	T	0.5	-7.3092	10.004	0.41946	0.0:1.0:0.0:0.0	.	237;320	Q86UU5-2;Q86UU5	.;GGN_HUMAN	K	320	.	ENSP00000334940:E320K	E	-	1	0	GGN	43568784	0.987000	0.35691	1.000000	0.80357	0.788000	0.44548	1.158000	0.31737	1.679000	0.50963	0.462000	0.41574	GAA	C|0.996;T|0.004	0.004	strong		0.682	GGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459205.1	NM_152657		T	38876944	C	T	38876944	3	4	22	1	0	0	0	0	1	0	0	0	6366	893	31	1	1008	1	GGN	19	38876944	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	41970	38876944	20252039	3928	6829											
RYR1	6261	hgsc.bcm.edu	37	chr19	38964275	38964275	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgctcagctgggggctggAgcgaggcagagaacggcaaa	10	3	18	10	3	1	1	1	0	0	1	1	4	1	2	1	5	3	5	1	5	2	0	rs34694816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38964275A>G	ENST00000359596.3	+	28	4024	c.4024A>G	c.(4024-4026)Agc>Ggc	p.S1342G	RYR1_ENST00000355481.4_Missense_Mutation_p.S1342G|RYR1_ENST00000360985.3_Missense_Mutation_p.S1342G			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1342	6 X approximate repeats.		S -> G (in dbSNP:rs34694816). {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)	TGGGGGCTGGAGCGAGGCAGA	0.741													G|||	271	0.0541134	0.1936	0.0187	5008	,	,		12448	0.0		0.002	False		,,,				2504	0.0				p.S1342G		Atlas-SNP	.											.	RYR1	708	.	0			c.A4024G						PASS	.	G	GLY/SER,GLY/SER	450,3742		20,410,1666	6	8	7		4024,4024	4	1	19	dbSNP_126	7	5,8089		0,5,4042	yes	missense,missense	RYR1	NM_000540.2,NM_001042723.1	56,56	20,415,5708	GG,GA,AA		0.0618,10.7347,3.7034	benign,benign	1342/5039,1342/5034	38964275	455,11831	2096	4047	6143	SO:0001583	missense	6261	exon28			GGCTGGAGCGAGG	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.4024A>G	19.37:g.38964275A>G	ENSP00000352608:p.Ser1342Gly	11	0	0		24	10	0.416667	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	114	0.0521978021978022	104	0.21138211382113822	9	0.024861878453038673	0	0.0	1	0.0013192612137203166	G	9.860	1.196031	0.22037	0.107347	6.18E-4	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.96745	-4.11;-4.11;-4.11	5.07	4.03	0.46877	.	0.085426	0.46758	N	0.000270	T	0.00440	0.0014	N	0.08118	0	0.51012	P	9.199999999998099E-5	B;B	0.09022	0.0;0.002	B;B	0.04013	0.0;0.001	T	0.47355	-0.9124	9	0.20519	T	0.43	.	8.5434	0.33406	0.1826:0.0:0.8174:0.0	rs34694816	1342;1342	P21817-2;P21817	.;RYR1_HUMAN	G	1342	ENSP00000352608:S1342G;ENSP00000347667:S1342G;ENSP00000354254:S1342G	ENSP00000347667:S1342G	S	+	1	0	RYR1	43656115	1.000000	0.71417	0.983000	0.44433	0.196000	0.23810	4.468000	0.60162	1.142000	0.42291	-0.355000	0.07637	AGC	A|0.949;G|0.051	0.051	strong		0.741	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			G	38964275	A	G	38964275	3	3	22	1	0	0	0	0	1	0	0	0	13783	304	11	3	4134	3	RYR1	19	38964275	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	87331	38964275	20164708	3929	6830											
EIF3K	27335	hgsc.bcm.edu	37	chr19	39125677	39125677	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcaaatacggctggagtgccGacgagtcggggcagatcttc	9	7	15	10	4	1	1	0	0	1	1	3	4	1	2	1	4	2	3	1	4	2	2	rs138580388	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39125677G>A	ENST00000538434.1	+	6	518	c.283G>A	c.(283-285)Gac>Aac	p.D95N	EIF3K_ENST00000545173.2_Missense_Mutation_p.D182N|EIF3K_ENST00000588934.1_Intron|EIF3K_ENST00000248342.4_Missense_Mutation_p.D182N|EIF3K_ENST00000593149.1_Missense_Mutation_p.D95N|EIF3K_ENST00000592558.1_Missense_Mutation_p.D156N					eukaryotic translation initiation factor 3, subunit K										EIF3K/CYP39A1(2)	central_nervous_system(1)|endometrium(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	8	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)			CTGGAGTGCCGACGAGTCGGG	0.542											OREG0025450	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	12	0.00239617	0.0091	0.0	5008	,	,		18892	0.0		0.0	False		,,,				2504	0.0				p.D182N		Atlas-SNP	.											.	EIF3K	22	.	0			c.G544A						PASS	.	G	ASN/ASP	25,4381	31.7+/-61.6	0,25,2178	89	80	83		544	3.2	0.1	19	dbSNP_134	83	0,8600		0,0,4300	yes	missense	EIF3K	NM_013234.2	23	0,25,6478	AA,AG,GG		0.0,0.5674,0.1922	benign	182/219	39125677	25,12981	2203	4300	6503	SO:0001583	missense	27335	exon7			AGTGCCGACGAGT	AB019392	CCDS12517.1, CCDS74360.1	19q13.2	2012-05-28	2007-07-27	2007-07-27	ENSG00000178982	ENSG00000178982			24656	protein-coding gene	gene with protein product		609596	"eukaryotic translation initiation factor 3, subunit 12"	EIF3S12		11042152, 14519125	Standard	XM_006723147		Approved	eIF3k, PRO1474, HSPC029, PTD001, PLAC-24, M9, ARG134	uc002oiz.1	Q9UBQ5		ENST00000538434.1:c.283G>A	19.37:g.39125677G>A	ENSP00000440999:p.Asp95Asn	70	0	0	883	106	46	0.433962	NM_013234		Missense_Mutation	SNP	ENST00000538434.1	37		3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	5.726	0.318348	0.10845	0.005674	0.0	ENSG00000178982	ENST00000248342;ENST00000538434;ENST00000545173	.	.	.	5.36	3.2	0.36748	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.062209	0.64402	D	0.000005	T	0.18676	0.0448	N	0.25201	0.72	0.09310	N	0.999998	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.14504	-1.0470	9	0.87932	D	0	-16.4366	5.4949	0.16797	0.1755:0.0:0.661:0.1635	.	95;182;182	B4DQ48;B7ZAM9;Q9UBQ5	.;.;EIF3K_HUMAN	N	182;95;182	.	ENSP00000248342:D182N	D	+	1	0	EIF3K	43817517	0.010000	0.17322	0.080000	0.20451	0.512000	0.34134	0.612000	0.24283	1.397000	0.46682	0.549000	0.68633	GAC	G|0.998;A|0.002	0.002	strong		0.542	EIF3K-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000453409.1	NM_013234		A	39125677	G	A	39125677	3	1	22	1	0	0	0	0	1	0	0	0	5023	1058	37	1	570	1	EIF3K	19	39125677	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	161402	39125677	20003306	3930	6831											
ACTN4	81	hgsc.bcm.edu	37	chr19	39212226	39212226	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctacgagacggccacactatCggacatcaaagccctcattc	12	7	7	15	3	2	1	2	0	0	1	4	3	2	2	2	2	2	0	2	2	3	3	rs140271107		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39212226C>T	ENST00000252699.2	+	12	1416	c.1340C>T	c.(1339-1341)tCg>tTg	p.S447L	ACTN4_ENST00000424234.2_Intron|ACTN4_ENST00000390009.3_Missense_Mutation_p.S228L	NM_004924.4	NP_004915.2	O43707	ACTN4_HUMAN	actinin, alpha 4	447					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)			GCCACACTATCGGACATCAAA	0.632													C|||	1	0.000199681	0.0	0.0	5008	,	,		20965	0.0		0.001	False		,,,				2504	0.0				p.S447L	Colon(168;199 1940 10254 46213 46384)	Atlas-SNP	.											.	ACTN4	69	.	0			c.C1340T						PASS	.						125	101	109					19																	39212226		2203	4300	6503	SO:0001583	missense	81	exon12			CACTATCGGACAT	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.1340C>T	19.37:g.39212226C>T	ENSP00000252699:p.Ser447Leu	68	0	0		90	43	0.477778	NM_004924	A4K467|D6PXK4|O76048	Missense_Mutation	SNP	ENST00000252699.2	37	CCDS12518.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.50	3.636731	0.67130	.	.	ENSG00000130402	ENST00000252699;ENST00000445727;ENST00000390009	T;T	0.51325	0.71;0.71	4.21	4.21	0.49690	.	0.194257	0.34959	N	0.003557	T	0.54271	0.1848	M	0.65498	2.005	0.80722	D	1	B;B	0.32382	0.091;0.368	B;B	0.40636	0.335;0.154	T	0.61133	-0.7124	10	0.59425	D	0.04	.	15.8417	0.78852	0.0:1.0:0.0:0.0	.	447;447	E7EV83;O43707	.;ACTN4_HUMAN	L	447;447;228	ENSP00000252699:S447L;ENSP00000439497:S228L	ENSP00000252699:S447L	S	+	2	0	ACTN4	43904066	1.000000	0.71417	0.962000	0.40283	0.599000	0.36880	7.651000	0.83577	2.340000	0.79590	0.462000	0.41574	TCG	C|1.000;T|0.000	0.000	strong		0.632	ACTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268091.1			T	39212226	C	T	39212226	3	4	22	1	0	0	0	0	1	0	0	0	207	893	31	1	1386	1	ACTN4	19	39212226	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	86549	39212226	19916757	3931	6832											
CAPN12	147968	hgsc.bcm.edu	37	chr19	39226163	39226163	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggagagactgcaggtctgcGctgatcacgtcgtcgatctc	7	10	13	11	4	3	2	1	1	2	1	6	5	3	3	0	2	2	2	0	2	0	0	rs141009431	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39226163G>A	ENST00000328867.4	-	13	1913	c.1605C>T	c.(1603-1605)agC>agT	p.S535S	CAPN12_ENST00000601953.1_Silent_p.S386S|CTD-2540F13.2_ENST00000602255.1_RNA	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	535	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)			GCAGGTCTGCGCTGATCACGT	0.647													G|||	11	0.00219649	0.0083	0.0	5008	,	,		8622	0.0		0.0	False		,,,				2504	0.0				p.S535S		Atlas-SNP	.											.	CAPN12	43	.	0			c.C1605T						PASS	.	G		27,4355	30.8+/-60.4	0,27,2164	38	37	37		1605	3	1	19	dbSNP_134	37	0,8590		0,0,4295	no	coding-synonymous	CAPN12	NM_144691.3		0,27,6459	AA,AG,GG		0.0,0.6162,0.2081		535/720	39226163	27,12945	2191	4295	6486	SO:0001819	synonymous_variant	147968	exon13			GTCTGCGCTGATC	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.1605C>T	19.37:g.39226163G>A		100	0	0		107	43	0.401869	NM_144691		Silent	SNP	ENST00000328867.4	37	CCDS12519.1																																																																																			G|0.998;A|0.002	0.002	strong		0.647	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1			A	39226163	G	A	39226163	2	1	22	1	0	0	0	0	0	0	0	1	2627	1078	38	1		1	CAPN12	19	39226163	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	13937	39226163	19902820	3932	6833											
CAPN12	147968	hgsc.bcm.edu	37	chr19	39227889	39227889	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggacagaaggaccgtgcaCttgggcgtgcggcccccccg	7	4	16	14	4	0	1	0	0	0	1	0	3	0	3	4	4	2	1	4	4	1	1	rs202082771	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39227889C>T	ENST00000328867.4	-	10	1577	c.1269G>A	c.(1267-1269)aaG>aaA	p.K423K	CAPN12_ENST00000601953.1_Silent_p.K274K|CTD-2540F13.2_ENST00000602255.1_RNA	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	423	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)			GGACCGTGCACTTGGGCGTGC	0.692													C|||	11	0.00219649	0.0083	0.0	5008	,	,		5252	0.0		0.0	False		,,,				2504	0.0				p.K423K		Atlas-SNP	.											.	CAPN12	43	.	0			c.G1269A						PASS	.	C		14,4130		0,14,2058	15	13	14		1269	0.4	1	19		14	0,8264		0,0,4132	yes	coding-synonymous	CAPN12	NM_144691.3		0,14,6190	TT,TC,CC		0.0,0.3378,0.1128		423/720	39227889	14,12394	2072	4132	6204	SO:0001819	synonymous_variant	147968	exon10			CGTGCACTTGGGC	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.1269G>A	19.37:g.39227889C>T		28	0	0		35	20	0.571429	NM_144691		Silent	SNP	ENST00000328867.4	37	CCDS12519.1																																																																																			.	.	weak		0.692	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1			T	39227889	C	T	39227889	2	4	22	1	0	0	0	0	0	0	0	1	2627	564	20	2		2	CAPN12	19	39227889	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1726	39227889	19901094	3933	6834											
CAPN12	147968	hgsc.bcm.edu	37	chr19	39234674	39234674	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aagtaagggtcgcggaacagGatccccgaatccaggcaggc	12	4	14	11	3	0	0	0	0	0	0	3	3	2	2	3	5	1	2	3	5	4	1	rs111831826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39234674G>A	ENST00000328867.4	-	1	440	c.132C>T	c.(130-132)atC>atT	p.I44I	CAPN12_ENST00000601953.1_Intron	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	44					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)			CGCGGAACAGGATCCCCGAAT	0.637													g|||	11	0.00219649	0.0083	0.0	5008	,	,		16631	0.0		0.0	False		,,,				2504	0.0				p.I44I		Atlas-SNP	.											.	CAPN12	43	.	0			c.C132T						PASS	.	G		27,4379	32.6+/-62.9	0,27,2176	82	67	72		132	2.6	1	19	dbSNP_132	72	0,8600		0,0,4300	no	coding-synonymous	CAPN12	NM_144691.3		0,27,6476	AA,AG,GG		0.0,0.6128,0.2076		44/720	39234674	27,12979	2203	4300	6503	SO:0001819	synonymous_variant	147968	exon1			GAACAGGATCCCC	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.132C>T	19.37:g.39234674G>A		69	0	0		79	37	0.468354	NM_144691		Silent	SNP	ENST00000328867.4	37	CCDS12519.1																																																																																			G|0.998;A|0.002	0.002	strong		0.637	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1			A	39234674	G	A	39234674	2	1	22	1	0	0	0	0	0	0	0	1	2627	1164	41	2		2	CAPN12	19	39234674	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6785	39234674	19894309	3934	6835											
CAPN12	147968	hgsc.bcm.edu	37	chr19	39234723	39234723	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgcctcatagctctggcccCgaaaaagctgcaggcgcccg	8	7	11	15	3	2	0	1	0	1	0	2	1	2	0	4	2	4	3	4	2	3	2	rs112433506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39234723C>T	ENST00000328867.4	-	1	391	c.83G>A	c.(82-84)cGg>cAg	p.R28Q	CAPN12_ENST00000601953.1_Intron	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	28					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)			GCTCTGGCCCCGAAAAAGCTG	0.632													c|||	11	0.00219649	0.0083	0.0	5008	,	,		14500	0.0		0.0	False		,,,				2504	0.0				p.R28Q		Atlas-SNP	.											.	CAPN12	43	.	0			c.G83A						PASS	.	C	GLN/ARG	26,4380	29.9+/-59.1	0,26,2177	61	57	58		83	3.7	0.3	19	dbSNP_132	58	0,8600		0,0,4300	yes	missense	CAPN12	NM_144691.3	43	0,26,6477	TT,TC,CC		0.0,0.5901,0.1999	benign	28/720	39234723	26,12980	2203	4300	6503	SO:0001583	missense	147968	exon1			TGGCCCCGAAAAA	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.83G>A	19.37:g.39234723C>T	ENSP00000331636:p.Arg28Gln	65	0	0		63	30	0.47619	NM_144691		Missense_Mutation	SNP	ENST00000328867.4	37	CCDS12519.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	c	12.17	1.858222	0.32791	0.005901	0.0	ENSG00000182472	ENST00000328867	T	0.41065	1.01	4.74	3.7	0.42460	Peptidase C2, calpain, catalytic domain (1);	0.749962	0.11830	N	0.525296	T	0.18087	0.0434	L	0.39898	1.24	0.09310	N	1	P	0.37997	0.614	B	0.27887	0.084	T	0.07616	-1.0763	10	0.13853	T	0.58	.	5.2383	0.15458	0.2025:0.6908:0.0:0.1066	.	28	Q6ZSI9	CAN12_HUMAN	Q	28	ENSP00000331636:R28Q	ENSP00000331636:R28Q	R	-	2	0	CAPN12	43926563	0.001000	0.12720	0.349000	0.25694	0.717000	0.41224	-0.261000	0.08694	1.204000	0.43247	0.457000	0.33378	CGG	C|0.998;T|0.002	0.002	strong		0.632	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1			T	39234723	C	T	39234723	3	4	22	1	0	0	0	0	1	0	0	0	2627	652	23	1	2160	1	CAPN12	19	39234723	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	49	39234723	19894260	3935	6836											
SARS2	54938	hgsc.bcm.edu	37	chr19	39410465	39410465	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcaggagggctccagccccGcgcaggtaataggaccggtg	8	5	16	12	3	0	0	0	0	0	0	1	2	1	2	4	5	2	4	4	5	2	2	rs35389151	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39410465G>A	ENST00000221431.6	-	7	855	c.696C>T	c.(694-696)cgC>cgT	p.R232R	SARS2_ENST00000600042.1_Silent_p.R234R|SARS2_ENST00000448145.2_Silent_p.R232R|SARS2_ENST00000430193.3_Silent_p.R232R|SARS2_ENST00000594171.1_Silent_p.R42R|SARS2_ENST00000598831.1_5'Flank|CTC-360G5.8_ENST00000599996.1_Missense_Mutation_p.R302W	NM_017827.3	NP_060297.1	Q9NP81	SYSM_HUMAN	seryl-tRNA synthetase 2, mitochondrial	232					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)			CTCCAGCCCCGCGCAGGTAAT	0.652													g|||	4	0.000798722	0.0015	0.0	5008	,	,		15718	0.001		0.0	False		,,,				2504	0.001				p.R234R		Atlas-SNP	.											.	SARS2	33	.	0			c.C702T						PASS	.	G	,	23,4383	28.1+/-56.4	0,23,2180	36	37	37		702,696	-9.3	0.2	19	dbSNP_126	37	5,8595	5.0+/-18.6	0,5,4295	no	coding-synonymous,coding-synonymous	SARS2	NM_001145901.1,NM_017827.3	,	0,28,6475	AA,AG,GG		0.0581,0.522,0.2153	,	234/521,232/519	39410465	28,12978	2203	4300	6503	SO:0001819	synonymous_variant	54938	exon8			AGCCCCGCGCAGG	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.696C>T	19.37:g.39410465G>A		124	0	0		153	80	0.522876	NM_001145901	A6NHW7|B4DE10|Q9BVP3	Silent	SNP	ENST00000221431.6	37	CCDS33017.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	g	4.214	0.038427	0.08148	0.00522	5.81E-4	ENSG00000104835	ENST00000455102	T	0.30182	1.54	4.63	-9.26	0.00662	.	.	.	.	.	T	0.11410	0.0278	.	.	.	.	.	.	.	.	.	.	.	.	T	0.17319	-1.0373	5	0.18710	T	0.47	.	9.0126	0.36150	0.6017:0.0:0.1514:0.2469	rs35389151	.	.	.	V	211	ENSP00000414954:A211V	ENSP00000414954:A211V	A	-	2	0	FBXO17	44102305	0.000000	0.05858	0.195000	0.23364	0.321000	0.28281	-4.751000	0.00190	-2.795000	0.00354	-4.032000	0.00013	GCG	G|0.997;A|0.003	0.003	strong		0.652	SARS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463139.1	NM_017827		A	39410465	G	A	39410465	2	1	22	1	0	0	0	0	0	0	0	1	13860	1074	38	1		1	SARS2	19	39410465	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	175742	39410465	19718518	3936	6837											
SARS2	54938	hgsc.bcm.edu	37	chr19	39416935	39416935	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgcctcagctcctgccatgtCgagatctggggtggatataa	8	11	12	10	1	2	1	1	0	1	1	4	3	3	2	3	3	3	1	3	3	2	2	rs144229840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39416935C>T	ENST00000221431.6	-	2	432	c.273G>A	c.(271-273)tcG>tcA	p.S91S	SARS2_ENST00000600042.1_Silent_p.S91S|SARS2_ENST00000448145.2_Silent_p.S91S|SARS2_ENST00000430193.3_Silent_p.S91S|SARS2_ENST00000594171.1_5'UTR|CTC-360G5.8_ENST00000599996.1_Missense_Mutation_p.D161N	NM_017827.3	NP_060297.1	Q9NP81	SYSM_HUMAN	seryl-tRNA synthetase 2, mitochondrial	91					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)	p.S91S(1)		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)			CCTGCCATGTCGAGATCTGGG	0.612													C|||	38	0.00758786	0.0265	0.0029	5008	,	,		19704	0.0		0.001	False		,,,				2504	0.0				p.S91S		Atlas-SNP	.											SARS2,rectum,carcinoma,0,1	SARS2	33	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G273A						PASS	.	C	,	75,4331	65.3+/-102.7	1,73,2129	50	42	45		273,273	-8.9	0	19	dbSNP_134	45	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	SARS2	NM_001145901.1,NM_017827.3	,	1,76,6426	TT,TC,CC		0.0349,1.7022,0.5997	,	91/521,91/519	39416935	78,12928	2203	4300	6503	SO:0001819	synonymous_variant	54938	exon2			CCATGTCGAGATC	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.273G>A	19.37:g.39416935C>T		39	0	0		26	12	0.461538	NM_001145901	A6NHW7|B4DE10|Q9BVP3	Silent	SNP	ENST00000221431.6	37	CCDS33017.1																																																																																			C|0.995;T|0.005	0.005	strong		0.612	SARS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463139.1	NM_017827		T	39416935	C	T	39416935	2	4	22	1	0	0	0	0	0	0	0	1	13860	871	31	1		1	SARS2	19	39416935	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6470	39416935	19712048	3937	6838											
PAPL	390928	hgsc.bcm.edu	37	chr19	39575987	39575987	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggagtccaggggtccctgggGgctcccagcgctgccccaga	5	5	16	15	1	0	1	0	0	0	1	3	2	3	2	5	5	2	2	5	5	0	0	rs544041	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39575987G>A	ENST00000331256.5	+	2	352	c.78G>A	c.(76-78)ggG>ggA	p.G26G	PAPL_ENST00000594229.1_Silent_p.G26G	NM_001004318.2	NP_001004318.2	Q6ZNF0	PAPL_HUMAN		26						extracellular region (GO:0005576)	acid phosphatase activity (GO:0003993)|metal ion binding (GO:0046872)										GGTCCCTGGGGGCTCCCAGCG	0.592													g|||	691	0.137979	0.4962	0.0447	5008	,	,		19220	0.0		0.004	False		,,,				2504	0.0				p.G26G		Atlas-SNP	.											.	.	.	.	0			c.G78A						PASS	.	G		1854,2552	538.2+/-374.9	377,1100,726	124	113	117		78	-0.7	0	19	dbSNP_83	117	29,8571	19.8+/-62.0	0,29,4271	no	coding-synonymous	PAPL	NM_001004318.2		377,1129,4997	AA,AG,GG		0.3372,42.079,14.4779		26/439	39575987	1883,11123	2203	4300	6503	SO:0001819	synonymous_variant	0	exon2			CCTGGGGGCTCCC																												ENST00000331256.5:c.78G>A	19.37:g.39575987G>A		126	0	0		122	121	0.991803	NM_001004318	B2RN68	Silent	SNP	ENST00000331256.5	37	CCDS33018.1																																																																																			G|0.870;A|0.130	0.130	strong		0.592	PAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463810.1			A	39575987	G	A	39575987	2	1	22	1	0	0	0	0	0	0	0	1	11436	1219	43	2		2	PAPL	19	39575987	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	159052	39575987	19552996	3938	6839											
IL28B	282617	hgsc.bcm.edu	37	chr19	39735535	39735535	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagagccccgcggagcctggCgacaggaactgctccagtca	9	4	14	14	3	1	1	1	0	0	1	2	5	2	3	4	3	4	1	4	3	1	0	rs141536970	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39735535C>A	ENST00000413851.2	-	1	111	c.73G>T	c.(73-75)Gcc>Tcc	p.A25S	IFNL4_ENST00000606380.1_RNA	NM_172139.2	NP_742151.2	Q8IZI9	IFNL3_HUMAN	interferon, lambda 3	25					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)											CGGAGCCTGGCGACAGGAACT	0.617													C|||	14	0.00279553	0.0098	0.0014	5008	,	,		20221	0.0		0.0	False		,,,				2504	0.0				p.A25S		Atlas-SNP	.											.	.	.	.	0			c.G73T						PASS	.	C	SER/ALA	29,4377	34.3+/-65.2	0,29,2174	61	58	59		73	-4.4	0	19	dbSNP_134	59	0,8600		0,0,4300	no	missense	IL28B	NM_172139.2	99	0,29,6474	AA,AC,CC		0.0,0.6582,0.223	benign	25/197	39735535	29,12977	2203	4300	6503	SO:0001583	missense	282617	exon1			GCCTGGCGACAGG	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.73G>T	19.37:g.39735535C>A	ENSP00000409000:p.Ala25Ser	321	1	0.00311526		322	171	0.531056	NM_172139	A2BDE1|Q6VN56|Q7Z4J3|Q8IWL6	Missense_Mutation	SNP	ENST00000413851.2	37	CCDS12530.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	8.463	0.855868	0.17106	0.006582	0.0	ENSG00000197110	ENST00000413851	T	0.13657	2.57	3.14	-4.41	0.03590	.	0.976044	0.08385	N	0.953834	T	0.01156	0.0038	N	0.00347	-1.61	0.09310	N	1	B	0.14438	0.01	B	0.17433	0.018	T	0.40757	-0.9546	10	0.30854	T	0.27	-2.8121	1.9017	0.03269	0.1148:0.1693:0.2396:0.4763	.	25	Q8IZI9	IL28B_HUMAN	S	25	ENSP00000409000:A25S	ENSP00000409000:A25S	A	-	1	0	IL28B	44427375	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.104000	0.10923	-0.417000	0.07461	-1.495000	0.00966	GCC	A|0.003;C|0.997	0.003	strong		0.617	IFNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463832.1	NM_172139		A	39735535	C	A	39735535	3	1	22	1	0	0	0	0	1	0	0	0	7692	768	27	4	536	4	IL28B	19	39735535	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	159548	39735535	19393448	3939	6840											
LRFN1	57622	hgsc.bcm.edu	37	chr19	39805188	39805188	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcgcgggtcagccgccgCagccagagcagctcgcagtt	6	6	13	16	5	1	1	1	0	0	1	4	1	2	1	4	1	4	5	4	1	0	1	rs115860908	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39805188C>T	ENST00000248668.4	-	1	788	c.789G>A	c.(787-789)ctG>ctA	p.L263L	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	263	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)			TCAGCCGCCGCAGCCAGAGCA	0.682													C|||	131	0.0261581	0.0908	0.0144	5008	,	,		14203	0.0		0.001	False		,,,				2504	0.0				p.L263L		Atlas-SNP	.											.	LRFN1	59	.	0			c.G789A						PASS	.	C		280,4082		10,260,1911	14	19	17		789	0.8	1	19	dbSNP_132	17	7,8559		0,7,4276	no	coding-synonymous	LRFN1	NM_020862.1		10,267,6187	TT,TC,CC		0.0817,6.4191,2.22		263/772	39805188	287,12641	2181	4283	6464	SO:0001819	synonymous_variant	57622	exon1			CCGCCGCAGCCAG	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.789G>A	19.37:g.39805188C>T		44	0	0		51	34	0.666667	NM_020862	Q8TBS9	Silent	SNP	ENST00000248668.4	37	CCDS46071.1																																																																																			C|0.971;T|0.029	0.029	strong		0.682	LRFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463835.1	NM_020862		T	39805188	C	T	39805188	2	4	22	1	0	0	0	0	0	0	0	1	8946	697	25	2		2	LRFN1	19	39805188	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	69653	39805188	19323795	3940	6841											
GMFG	9535	hgsc.bcm.edu	37	chr19	39826131	39826131	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggaatttcctcagcttttctGttagctctgggtctacctcg	5	16	9	11	1	4	0	1	0	3	0	6	1	5	1	2	2	3	3	2	2	3	5	rs1801733	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39826131G>T	ENST00000597595.1	-	2	252	c.44C>A	c.(43-45)aCa>aAa	p.T15K	GMFG_ENST00000595636.1_Missense_Mutation_p.T15K|GMFG_ENST00000600322.1_5'UTR|GMFG_ENST00000253054.8_5'UTR|GMFG_ENST00000594700.1_Missense_Mutation_p.T15K|GMFG_ENST00000598034.1_Missense_Mutation_p.T15K|GMFG_ENST00000601387.1_Intron|GMFG_ENST00000602185.1_Intron	NM_004877.2	NP_004868.1	O60234	GMFG_HUMAN	glia maturation factor, gamma	15	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)			CAGCTTTTCTGTTAGCTCTGG	0.572													G|||	79	0.0157748	0.056	0.0072	5008	,	,		17456	0.0		0.0	False		,,,				2504	0.0				p.T15K		Atlas-SNP	.											.	GMFG	16	.	0			c.C44A						PASS	.	G	LYS/THR	212,4194	127.0+/-164.0	8,196,1999	149	116	127		44	2.1	1	19	dbSNP_89	127	13,8587	9.8+/-36.6	0,13,4287	yes	missense	GMFG	NM_004877.2	78	8,209,6286	TT,TG,GG		0.1512,4.8116,1.73	benign	15/143	39826131	225,12781	2203	4300	6503	SO:0001583	missense	9535	exon2			TTTTCTGTTAGCT	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.44C>A	19.37:g.39826131G>T	ENSP00000472249:p.Thr15Lys	165	0	0		179	74	0.413408	NM_004877	Q6IB37	Missense_Mutation	SNP	ENST00000597595.1	37	CCDS12532.1	41	0.018772893772893772	37	0.07520325203252033	4	0.011049723756906077	0	0.0	0	0.0	G	0.825	-0.747109	0.03065	0.048116	0.001512	ENSG00000130755	ENST00000253054	.	.	.	4.18	2.07	0.26955	Actin-binding, cofilin/tropomyosin type (3);	0.077251	0.46442	N	0.000283	T	0.00241	0.0007	N	0.00265	-1.74	0.28216	N	0.926737	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29640	-1.0005	9	0.02654	T	1	-19.027	1.2964	0.02070	0.1769:0.1034:0.1922:0.5276	rs1801733;rs52801314	15;15	O60234;Q6IB37	GMFG_HUMAN;.	K	15	.	ENSP00000253054:T15K	T	-	2	0	GMFG	44517971	0.864000	0.29904	0.990000	0.47175	0.765000	0.43378	0.310000	0.19356	0.188000	0.20168	-1.238000	0.01547	ACA	G|0.980;T|0.020	0.020	strong		0.572	GMFG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463839.1			T	39826131	G	T	39826131	3	4	22	1	0	0	0	0	1	0	0	0	6498	1377	48	4	408	4	GMFG	19	39826131	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	20943	39826131	19302852	3941	6842											
SAMD4B	55095	hgsc.bcm.edu	37	chr19	39873877	39873877	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcctgggcctgacctggagAtcaatcccactctggagtct	7	11	10	13	0	3	2	1	1	2	1	5	4	5	3	4	3	0	0	4	3	1	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39873877A>G	ENST00000314471.6	+	15	3037	c.2002A>G	c.(2002-2004)Atc>Gtc	p.I668V	SAMD4B_ENST00000596368.1_Intron|SAMD4B_ENST00000598913.1_Missense_Mutation_p.I668V	NM_018028.2	NP_060498.2	Q5PRF9	SMAG2_HUMAN	sterile alpha motif domain containing 4B	668					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)			TGACCTGGAGATCAATCCCAC	0.577																																					p.I668V		Atlas-SNP	.											SAMD4B,NS,carcinoma,0,2	SAMD4B	48	2	0			c.A2002G						PASS	.						169	131	144					19																	39873877		2203	4300	6503	SO:0001583	missense	55095	exon15			CTGGAGATCAATC		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.2002A>G	19.37:g.39873877A>G	ENSP00000317224:p.Ile668Val	169	0	0		160	76	0.475	NM_018028	A5Z0M6|Q6P194	Missense_Mutation	SNP	ENST00000314471.6	37	CCDS33020.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.187852	0.78789	.	.	ENSG00000179134	ENST00000314471	.	.	.	4.2	4.2	0.49525	.	0.000000	0.64402	D	0.000001	T	0.63379	0.2506	L	0.43152	1.355	0.43846	D	0.996437	P;P	0.43314	0.803;0.803	P;P	0.55824	0.785;0.785	T	0.66559	-0.5893	9	0.87932	D	0	.	11.256	0.49054	1.0:0.0:0.0:0.0	.	668;668	Q5PRF9;A5Z0M6	SMAG2_HUMAN;.	V	668	.	ENSP00000317224:I668V	I	+	1	0	SAMD4B	44565717	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	8.422000	0.90262	1.774000	0.52232	0.240000	0.17902	ATC	.	.	none		0.577	SAMD4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464467.1	NM_018028		G	39873877	A	G	39873877	3	3	22	1	0	0	0	0	1	0	0	0	13837	333	12	3	2044	3	SAMD4B	19	39873877	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	47746	39873877	19255106	3942	6843											
ZFP36	7538	hgsc.bcm.edu	37	chr19	39898521	39898521	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctggggtcacctcccgcctgCctggccgctccaccagccta	4	7	10	20	2	1	0	1	0	0	0	3	0	3	0	8	3	2	1	8	3	1	1	rs2229272		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39898521C>T	ENST00000248673.3	+	2	221	c.163C>T	c.(163-165)Cct>Tct	p.P55S	ZFP36_ENST00000594045.1_3'UTR|ZFP36_ENST00000597629.1_Missense_Mutation_p.P61S|MIR4530_ENST00000581459.1_RNA	NM_003407.3	NP_003398.2	P26651	TTP_HUMAN	ZFP36 ring finger protein	55			P -> S (in dbSNP:rs2229272).		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)			CTCCCGCCTGCCTGGCCGCTC	0.736													C|||	1	0.000199681	0.0008	0.0	5008	,	,		11689	0.0		0.0	False		,,,				2504	0.0				p.P61S	NSCLC(67;1164 1324 12056 21056 30097)	Atlas-SNP	.											.	ZFP36	19	.	0			c.C181T						PASS	.	C	SER/PRO	3,4271		0,3,2134	15	19	18		163	2.8	1	19	dbSNP_98	18	0,8330		0,0,4165	no	missense	ZFP36	NM_003407.2	74	0,3,6299	TT,TC,CC		0.0,0.0702,0.0238	benign	55/327	39898521	3,12601	2137	4165	6302	SO:0001583	missense	7538	exon2			CGCCTGCCTGGCC	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.163C>T	19.37:g.39898521C>T	ENSP00000248673:p.Pro55Ser	25	0	0		32	18	0.5625	NM_003407	B2RA54	Missense_Mutation	SNP	ENST00000248673.3	37		2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	11.91	1.779652	0.31502	7.02E-4	0.0	ENSG00000128016	ENST00000248673	T	0.18174	2.23	3.91	2.84	0.33178	.	0.070080	0.56097	D	0.000022	T	0.10809	0.0264	N	0.24115	0.695	0.26691	N	0.971344	B	0.20052	0.041	B	0.18871	0.023	T	0.22347	-1.0219	10	0.29301	T	0.29	-3.1484	10.0703	0.42328	0.2111:0.7889:0.0:0.0	rs2229272	55	P26651	TTP_HUMAN	S	55	ENSP00000248673:P55S	ENSP00000248673:P55S	P	+	1	0	ZFP36	44590361	0.842000	0.29525	1.000000	0.80357	0.750000	0.42670	1.235000	0.32671	0.799000	0.34018	0.549000	0.68633	CCT	C|0.998;T|0.002	0.002	strong		0.736	ZFP36-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding				T	39898521	C	T	39898521	3	4	22	1	0	0	0	0	1	0	0	0	17660	739	26	2	169	2	ZFP36	19	39898521	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	24644	39898521	19230462	3943	6844											
PLEKHG2	64857	hgsc.bcm.edu	37	chr19	39908215	39908215	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaactagggaagcactgggcGgagggcccaggcactggggg	9	3	20	9	1	0	0	0	0	0	0	0	3	0	2	1	7	2	2	1	7	3	1	rs142309421		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39908215G>A	ENST00000409794.3	+	8	1615	c.765G>A	c.(763-765)gcG>gcA	p.A255A	PLEKHG2_ENST00000458508.2_Silent_p.A196A|PLEKHG2_ENST00000409797.2_Silent_p.A255A|PLEKHG2_ENST00000425673.1_Silent_p.A255A|PLEKHG2_ENST00000378550.1_Silent_p.A255A	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	255	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)|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)			AGCACTGGGCGGAGGGCCCAG	0.572																																					p.A255A		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.G765A						PASS	.	G		4,4402	8.1+/-20.4	0,4,2199	56	50	52		765	-9.4	0	19	dbSNP_134	52	0,8600		0,0,4300	no	coding-synonymous	PLEKHG2	NM_022835.2		0,4,6499	AA,AG,GG		0.0,0.0908,0.0308		255/1387	39908215	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	64857	exon8			CTGGGCGGAGGGC	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.765G>A	19.37:g.39908215G>A		93	0	0		98	55	0.561224	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Silent	SNP	ENST00000409794.3	37	CCDS33022.2	.	.	.	.	.	.	.	.	.	.	G	0.870	-0.732282	0.03135	9.08E-4	0.0	ENSG00000090924	ENST00000205135	.	.	.	4.68	-9.36	0.00629	.	.	.	.	.	T	0.33760	0.0874	.	.	.	0.46901	D	0.999249	.	.	.	.	.	.	T	0.52064	-0.8625	4	.	.	.	.	1.5973	0.02666	0.2022:0.2901:0.2917:0.216	.	.	.	.	Q	152	.	.	R	+	2	0	PLEKHG2	44600055	0.000000	0.05858	0.019000	0.16419	0.184000	0.23303	-5.033000	0.00158	-4.337000	0.00055	-2.075000	0.00382	CGG	G|1.000;A|0.000	0.000	weak		0.572	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835		A	39908215	G	A	39908215	2	1	22	1	0	0	0	0	0	0	0	1	12078	1103	39	1		1	PLEKHG2	19	39908215	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	9694	39908215	19220768	3944	6845											
PLEKHG2	64857	hgsc.bcm.edu	37	chr19	39915677	39915677	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcctgggggaggggcccccGcagcctcccggggctcctgg	2	4	19	16	2	0	0	0	0	0	0	2	1	2	1	6	8	1	2	6	8	0	0	rs34603507		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39915677G>A	ENST00000409794.3	+	19	4754	c.3904G>A	c.(3904-3906)Gca>Aca	p.A1302T	PLEKHG2_ENST00000458508.2_Intron|PLEKHG2_ENST00000409797.2_Intron|PLEKHG2_ENST00000425673.1_Missense_Mutation_p.A1273T|CTB-60E11.4_ENST00000601124.1_lincRNA|PLEKHG2_ENST00000378550.1_Intron	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	1302			A -> T (in dbSNP:rs34603507).		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)			AGGGGCCCCCGCAGCCTCCCG	0.721													G|||	1	0.000199681	0.0008	0.0	5008	,	,		11603	0.0		0.0	False		,,,				2504	0.0				p.A1302T		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.G3904A						PASS	.	G	THR/ALA	5,4237		0,5,2116	13	16	15		3904	-7.2	0	19	dbSNP_126	15	0,8448		0,0,4224	no	missense	PLEKHG2	NM_022835.2	58	0,5,6340	AA,AG,GG		0.0,0.1179,0.0394	benign	1302/1387	39915677	5,12685	2121	4224	6345	SO:0001583	missense	64857	exon19			GCCCCCGCAGCCT	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.3904G>A	19.37:g.39915677G>A	ENSP00000386733:p.Ala1302Thr	27	0	0		26	17	0.653846	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	37	CCDS33022.2	.	.	.	.	.	.	.	.	.	.	G	10.97	1.500290	0.26861	0.001179	0.0	ENSG00000090924	ENST00000409794;ENST00000425673	T;T	0.67171	-0.24;-0.25	4.35	-7.16	0.01516	.	1.186420	0.06463	N	0.729685	T	0.34513	0.0900	N	0.05383	-0.06	0.09310	N	1	B;B	0.12013	0.005;0.003	B;B	0.06405	0.002;0.001	T	0.13602	-1.0503	9	.	.	.	.	2.4588	0.04536	0.1357:0.2896:0.4002:0.1745	rs34603507	1273;1302	Q9H7P9-3;Q9H7P9	.;PKHG2_HUMAN	T	1302;1273	ENSP00000386733:A1302T;ENSP00000392906:A1273T	.	A	+	1	0	PLEKHG2	44607517	0.000000	0.05858	0.000000	0.03702	0.833000	0.47200	-0.923000	0.04000	-1.368000	0.02149	-1.305000	0.01319	GCA	G|0.970;A|0.030	0.030	strong		0.721	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835		A	39915677	G	A	39915677	3	1	22	1	0	0	0	0	1	0	0	0	12078	1087	38	1	3974	1	PLEKHG2	19	39915677	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	7462	39915677	19213306	3945	6846											
FBL	2091	hgsc.bcm.edu	37	chr19	40329747	40329747	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtagagaaccttagccccCggtttgatgtggatctggtc	8	11	13	9	1	1	2	0	1	1	1	2	4	1	3	3	4	2	2	3	4	3	3	rs150137200	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40329747C>T	ENST00000221801.3	-	5	590	c.477G>A	c.(475-477)ccG>ccA	p.P159P	FBL_ENST00000593503.1_5'Flank	NM_001436.3	NP_001427.2	P22087	FBRL_HUMAN	fibrillarin	159					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)		CCTTAGCCCCCGGTTTGATGT	0.577													C|||	12	0.00239617	0.0076	0.0	5008	,	,		20414	0.0		0.0	False		,,,				2504	0.002				p.P159P		Atlas-SNP	.											.	FBL	37	.	0			c.G477A						PASS	.	C		35,4371	40.0+/-72.8	0,35,2168	143	128	133		477	-9.6	0.9	19	dbSNP_134	133	0,8600		0,0,4300	no	coding-synonymous	FBL	NM_001436.3		0,35,6468	TT,TC,CC		0.0,0.7944,0.2691		159/322	40329747	35,12971	2203	4300	6503	SO:0001819	synonymous_variant	2091	exon5			AGCCCCCGGTTTG	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.477G>A	19.37:g.40329747C>T		180	0	0		183	81	0.442623	NM_001436	B5BUE8|O75259|Q6IAT5|Q9UPI6	Silent	SNP	ENST00000221801.3	37	CCDS12545.1																																																																																			C|0.996;T|0.004	0.004	strong		0.577	FBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462509.4	NM_001436		T	40329747	C	T	40329747	2	4	22	1	0	0	0	0	0	0	0	1	5704	639	23	1		1	FBL	19	40329747	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	414070	40329747	18799236	3946	6847											
FCGBP	8857	hgsc.bcm.edu	37	chr19	40364011	40364011	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgggccaagacataggagcaGgagccatgcaggtcgtagac	12	5	15	9	1	0	2	0	0	0	2	1	4	0	4	2	4	3	3	2	4	3	2	rs78835791	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40364011G>A	ENST00000221347.6	-	31	14638	c.14631C>T	c.(14629-14631)tcC>tcT	p.S4877S		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4877	VWFD 12. {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)			CATAGGAGCAGGAGCCATGCA	0.602													G|||	61	0.0121805	0.0439	0.0029	5008	,	,		20928	0.0		0.001	False		,,,				2504	0.0				p.S4877S		Atlas-SNP	.											.	FCGBP	416	.	0			c.C14631T						PASS	.	G		151,4255	103.8+/-142.4	1,149,2053	94	82	86		14631	4	1	19	dbSNP_131	86	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FCGBP	NM_003890.2		1,150,6352	AA,AG,GG		0.0116,3.4271,1.1687		4877/5406	40364011	152,12854	2203	4300	6503	SO:0001819	synonymous_variant	8857	exon31			GGAGCAGGAGCCA	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.14631C>T	19.37:g.40364011G>A		146	0	0		146	65	0.445205	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			G|0.988;A|0.012	0.012	strong		0.602	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		A	40364011	G	A	40364011	2	1	22	1	0	0	0	0	0	0	0	1	5786	987	35	2		2	FCGBP	19	40364011	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	34264	40364011	18764972	3947	6848											
FCGBP	8857	hgsc.bcm.edu	37	chr19	40364397	40364397	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcacagggcaggagtcacCgcagagctcatagtggctgt	9	7	14	11	1	3	1	3	0	0	1	3	2	3	2	1	3	1	5	1	3	1	1	rs148917660		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40364397C>T	ENST00000221347.6	-	31	14252	c.14245G>A	c.(14245-14247)Ggt>Agt	p.G4749S		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4749	TIL 11.					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)			CAGGAGTCACCGCAGAGCTCA	0.647													C|||	1	0.000199681	0.0008	0.0	5008	,	,		14509	0.0		0.0	False		,,,				2504	0.0				p.G4749S		Atlas-SNP	.											.	FCGBP	416	.	0			c.G14245A						PASS	.	C	SER/GLY	28,4376		0,28,2174	36	35	35		14245	4.1	0	19	dbSNP_134	35	0,8600		0,0,4300	no	missense	FCGBP	NM_003890.2	56	0,28,6474	TT,TC,CC		0.0,0.6358,0.2153	probably-damaging	4749/5406	40364397	28,12976	2202	4300	6502	SO:0001583	missense	8857	exon31			AGTCACCGCAGAG	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.14245G>A	19.37:g.40364397C>T	ENSP00000221347:p.Gly4749Ser	60	0	0		77	41	0.532468	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	11.23	1.577576	0.28180	0.006358	0.0	ENSG00000090920	ENST00000221347	T	0.77750	-1.12	5.14	4.1	0.47936	Protease inhibitor I8, cysteine-rich trypsin inhibitor-like (2);	0.072904	0.53938	U	0.000047	T	0.59932	0.2230	M	0.66439	2.03	0.09310	N	1	P	0.40731	0.728	B	0.30495	0.116	T	0.58645	-0.7600	10	0.06891	T	0.86	.	12.6598	0.56808	0.0:0.9183:0.0:0.0817	.	4749	Q9Y6R7	FCGBP_HUMAN	S	4749	ENSP00000221347:G4749S	ENSP00000221347:G4749S	G	-	1	0	FCGBP	45056237	0.096000	0.21769	0.026000	0.17262	0.357000	0.29423	2.708000	0.47152	1.312000	0.45043	0.313000	0.20887	GGT	C|0.997;T|0.003	0.003	strong		0.647	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		T	40364397	C	T	40364397	3	4	22	1	0	0	0	0	1	0	0	0	5786	652	23	1	1996	1	FCGBP	19	40364397	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	386	40364397	18764586	3948	6849											
FCGBP	8857	hgsc.bcm.edu	37	chr19	40384035	40384035	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcacttaacacgaaacccGcgtcgcactggcagccctcc	10	5	8	18	4	0	0	0	0	0	0	2	1	1	0	3	1	4	3	3	1	2	1	rs367618328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40384035G>A	ENST00000221347.6	-	21	9582	c.9575C>T	c.(9574-9576)gCg>gTg	p.A3192V		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	3192	TIL 7.					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)			CACGAAACCCGCGTCGCACTG	0.662													G|||	65	0.0129792	0.0446	0.0058	5008	,	,		24198	0.001		0.001	False		,,,				2504	0.0				p.A3192V		Atlas-SNP	.											FCGBP,NS,haematopoietic_neoplasm,-1,1	FCGBP	416	1	0			c.C9575T						scavenged	.	G	VAL/ALA	47,2527		0,47,1240	4	4	4		9575	-4.6	0	19		4	1,5829		0,1,2914	no	missense	FCGBP	NM_003890.2	64	0,48,4154	AA,AG,GG		0.0172,1.826,0.5712	possibly-damaging	3192/5406	40384035	48,8356	1287	2915	4202	SO:0001583	missense	8857	exon21			AAACCCGCGTCGC	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.9575C>T	19.37:g.40384035G>A	ENSP00000221347:p.Ala3192Val	585	1	0.0017094		639	130	0.203443	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	G	7.646	0.681900	0.14907	0.01826	1.72E-4	ENSG00000090920	ENST00000221347	T	0.30981	1.51	3.48	-4.63	0.03359	Protease inhibitor I8, cysteine-rich trypsin inhibitor-like (2);	.	.	.	.	T	0.18676	0.0448	L	0.49350	1.555	0.09310	N	1	D	0.56287	0.975	P	0.54372	0.75	T	0.25082	-1.0142	9	0.33141	T	0.24	.	7.6572	0.28381	0.0999:0.0:0.2726:0.6275	.	3192	Q9Y6R7	FCGBP_HUMAN	V	3192	ENSP00000221347:A3192V	ENSP00000221347:A3192V	A	-	2	0	FCGBP	45075875	0.000000	0.05858	0.001000	0.08648	0.033000	0.12548	-0.286000	0.08399	-0.448000	0.07128	-0.513000	0.04457	GCG	.	.	weak		0.662	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		A	40384035	G	A	40384035	3	1	22	1	0	0	0	0	1	0	0	0	5786	1087	38	1	6706	1	FCGBP	19	40384035	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	19638	40384035	18744948	3949	6850											
FCGBP	8857	hgsc.bcm.edu	37	chr19	40399508	40399508	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgctgacgggctggcagcCgtgctggccggatggcagga	5	7	19	10	3	0	1	0	1	0	0	0	3	0	3	2	6	3	5	2	6	0	0			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40399508C>T	ENST00000221347.6	-	13	6194	c.6187G>A	c.(6187-6189)Ggc>Agc	p.G2063S		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2063						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)			GGCTGGCAGCCGTGCTGGCCG	0.657																																					p.G2063S		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	1	0			c.G6187A						scavenged	.						1	1	1					19																	40399508		183	426	609	SO:0001583	missense	8857	exon13			GGCAGCCGTGCTG	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.6187G>A	19.37:g.40399508C>T	ENSP00000221347:p.Gly2063Ser	141	0	0		138	28	0.202899	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.485186	0.44147	.	.	ENSG00000090920	ENST00000221347	T	0.05025	3.51	3.01	3.01	0.34805	von Willebrand factor, type D domain (1);	.	.	.	.	T	0.20170	0.0485	M	0.77103	2.36	0.31064	N	0.713759	D	0.76494	0.999	D	0.66196	0.942	T	0.07868	-1.0750	9	0.14656	T	0.56	.	12.9123	0.58187	0.0:1.0:0.0:0.0	.	2063	Q9Y6R7	FCGBP_HUMAN	S	2063	ENSP00000221347:G2063S	ENSP00000221347:G2063S	G	-	1	0	FCGBP	45091348	0.935000	0.31712	0.871000	0.34182	0.831000	0.47069	-0.229000	0.09098	1.536000	0.49237	0.298000	0.19748	GGC	.	.	weak		0.657	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		T	40399508	C	T	40399508	3	4	22	1	0	0	0	0	1	0	0	0	5786	652	23	1	10126	1	FCGBP	19	40399508	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	15473	40399508	18729475	3950	6851											
ZNF780A	284323	hgsc.bcm.edu	37	chr19	40580426	40580426	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttccacattccttacattcaAgatgccttctcacctgtgtg	8	15	5	13	0	2	1	2	0	1	1	5	1	4	1	4	0	2	0	4	0	2	5	rs399405	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40580426A>G	ENST00000595687.2	-	6	2132	c.1923T>C	c.(1921-1923)tcT>tcC	p.S641S	ZNF780A_ENST00000340963.5_Silent_p.S641S|ZNF780A_ENST00000455521.1_Silent_p.S642S|AC005614.5_ENST00000595508.1_RNA|ZNF780A_ENST00000594395.1_Silent_p.S642S|ZNF780A_ENST00000414720.2_Intron|ZNF780A_ENST00000450241.2_Silent_p.S607S	NM_001010880.2	NP_001010880.2	O75290	Z780A_HUMAN	zinc finger protein 780A	641					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)					CTTACATTCAAGATGCCTTCT	0.418													a|||	547	0.109225	0.3449	0.0403	5008	,	,		22537	0.0069		0.0109	False		,,,				2504	0.046				p.S642S		Atlas-SNP	.											.	ZNF780A	156	.	0			c.T1926C						PASS	.	A	,,,	1370,3036	454.7+/-350.8	220,930,1053	153	148	150		1923,1926,1923,	-2.3	0	19	dbSNP_80	150	68,8532	41.7+/-99.0	1,66,4233	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	ZNF780A	NM_001010880.2,NM_001142577.1,NM_001142578.1,NM_001142579.1	,,,	221,996,5286	GG,GA,AA		0.7907,31.094,11.0564	,,,	641/642,642/643,641/642,	40580426	1438,11568	2203	4300	6503	SO:0001819	synonymous_variant	284323	exon6			CATTCAAGATGCC	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.1923T>C	19.37:g.40580426A>G		247	0	0		268	268	1	NM_001142577	E9PB48|Q6ZN87	Silent	SNP	ENST00000595687.2	37	CCDS33026.2																																																																																			A|0.899;G|0.101	0.101	strong		0.418	ZNF780A-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000470066.1	NM_001010880		G	40580426	A	G	40580426	2	3	22	1	0	0	0	0	0	0	0	1	18167	59	3	3		3	ZNF780A	19	40580426	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	180918	40580426	18548557	3951	6852											
ZNF780A	284323	hgsc.bcm.edu	37	chr19	40581677	40581677	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctaaaggcctttccacattcGttacattcaaaaggtttctc	11	14	5	11	1	2	0	1	0	1	0	5	0	3	0	2	2	1	2	2	2	5	6	rs337795	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40581677G>A	ENST00000595687.2	-	6	881	c.672C>T	c.(670-672)aaC>aaT	p.N224N	ZNF780A_ENST00000340963.5_Silent_p.N224N|ZNF780A_ENST00000455521.1_Silent_p.N225N|AC005614.5_ENST00000595508.1_RNA|ZNF780A_ENST00000594395.1_Silent_p.N225N|ZNF780A_ENST00000414720.2_Intron|ZNF780A_ENST00000450241.2_Silent_p.N190N	NM_001010880.2	NP_001010880.2	O75290	Z780A_HUMAN	zinc finger protein 780A	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)			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)					TTCCACATTCGTTACATTCAA	0.398													G|||	385	0.076877	0.2761	0.0274	5008	,	,		22376	0.0		0.001	False		,,,				2504	0.0				p.N225N		Atlas-SNP	.											.	ZNF780A	156	.	0			c.C675T						PASS	.	G	,,,	1084,3322	393.5+/-328.9	143,798,1262	92	92	92		672,675,672,	-3.5	0.8	19	dbSNP_79	92	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	ZNF780A	NM_001010880.2,NM_001142577.1,NM_001142578.1,NM_001142579.1	,,,	143,809,5551	AA,AG,GG		0.1279,24.6028,8.4192	,,,	224/642,225/643,224/642,	40581677	1095,11911	2203	4300	6503	SO:0001819	synonymous_variant	284323	exon6			ACATTCGTTACAT	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.672C>T	19.37:g.40581677G>A		89	0	0		139	139	1	NM_001142577	E9PB48|Q6ZN87	Silent	SNP	ENST00000595687.2	37	CCDS33026.2																																																																																			G|0.928;A|0.072	0.072	strong		0.398	ZNF780A-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000470066.1	NM_001010880		A	40581677	G	A	40581677	2	1	22	1	0	0	0	0	0	0	0	1	18167	1136	40	1		1	ZNF780A	19	40581677	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1251	40581677	18547306	3952	6853											
PLD3	23646	hgsc.bcm.edu	37	chr19	40882588	40882588	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtcaaggtgcgcctgctcatCagctgctggggacactcgga	7	8	14	12	2	3	0	3	0	0	0	4	2	3	2	1	4	4	3	1	4	1	0	rs57187324	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40882588C>T	ENST00000409587.1	+	11	1489	c.1092C>T	c.(1090-1092)atC>atT	p.I364I	PLD3_ENST00000409735.4_Silent_p.I364I|PLD3_ENST00000356508.5_Silent_p.I364I|PLD3_ENST00000409281.1_Silent_p.I364I|PLD3_ENST00000409419.1_Silent_p.I364I			Q8IV08	PLD3_HUMAN	phospholipase D family, member 3	364					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)			GCCTGCTCATCAGCTGCTGGG	0.632													c|||	39	0.00778754	0.0295	0.0	5008	,	,		16027	0.0		0.0	False		,,,				2504	0.0				p.I364I		Atlas-SNP	.											.	PLD3	71	.	0			c.C1092T						PASS	.		,	124,4282	92.0+/-130.7	2,120,2081	79	72	74		1092,1092	3.2	1	19	dbSNP_129	74	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PLD3	NM_001031696.2,NM_012268.2	,	2,120,6381	TT,TC,CC		0.0,2.8143,0.9534	,	364/491,364/491	40882588	124,12882	2203	4300	6503	SO:0001819	synonymous_variant	23646	exon11			GCTCATCAGCTGC	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.1092C>T	19.37:g.40882588C>T		62	0	0		49	23	0.469388	NM_012268	Q92853|Q9BW87	Silent	SNP	ENST00000409587.1	37	CCDS33027.1																																																																																			C|0.990;T|0.010	0.010	strong		0.632	PLD3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327721.1	NM_012268		T	40882588	C	T	40882588	2	4	22	1	0	0	0	0	0	0	0	1	12056	816	29	2		2	PLD3	19	40882588	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	300911	40882588	18246395	3953	6854											
HIPK4	147746	hgsc.bcm.edu	37	chr19	40895493	40895493	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtggcgggcggggaggggcGcgaagttgttctccttctgg	3	10	20	8	4	2	0	0	0	2	0	3	2	2	1	1	7	0	2	1	7	1	3	rs79236726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40895493G>A	ENST00000291823.2	-	1	601	c.317C>T	c.(316-318)gCg>gTg	p.A106V		NM_144685.3	NP_653286.2	Q8NE63	HIPK4_HUMAN	homeodomain interacting protein kinase 4	106	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		A -> T (in dbSNP:rs34434715). {ECO:0000269|PubMed:17344846}.		histone phosphorylation (GO:0016572)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of signal transduction by p53 class mediator (GO:1901796)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	20			Lung(22;4.95e-05)|LUSC - Lung squamous cell carcinoma(20;0.000292)			GGGGAGGGGCGCGAAGTTGTT	0.577													G|||	32	0.00638978	0.0242	0.0	5008	,	,		9839	0.0		0.0	False		,,,				2504	0.0				p.A106V		Atlas-SNP	.											HIPK4_ENST00000291823,colon,carcinoma,+1,2	HIPK4	100	2	0			c.C317T						scavenged	.	G	VAL/ALA	104,4302	82.4+/-120.9	2,100,2101	58	62	61		317	2.9	0.7	19	dbSNP_131	61	0,8600		0,0,4300	yes	missense	HIPK4	NM_144685.3	64	2,100,6401	AA,AG,GG		0.0,2.3604,0.7996	possibly-damaging	106/617	40895493	104,12902	2203	4300	6503	SO:0001583	missense	147746	exon1			AGGGGCGCGAAGT	BC034501	CCDS12555.1	19q13.2	2008-02-05				ENSG00000160396			19007	protein-coding gene	gene with protein product		611712					Standard	NM_144685		Approved	FLJ32818	uc002onp.3	Q8NE63		ENST00000291823.2:c.317C>T	19.37:g.40895493G>A	ENSP00000291823:p.Ala106Val	96	1	0.0104167		104	53	0.509615	NM_144685	A8K863|Q96M54	Missense_Mutation	SNP	ENST00000291823.2	37	CCDS12555.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	G	14.62	2.590686	0.46214	0.023604	0.0	ENSG00000160396	ENST00000291823;ENST00000452139	T	0.63255	-0.03	5.08	2.91	0.33838	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	0.000083	T	0.27241	0.0668	N	0.04787	-0.16	0.34206	D	0.67376	P	0.50528	0.936	P	0.46419	0.516	T	0.54357	-0.8306	10	0.52906	T	0.07	.	9.804	0.40781	0.0:0.2864:0.5655:0.1481	.	106	Q8NE63	HIPK4_HUMAN	V	106;71	ENSP00000291823:A106V	ENSP00000291823:A106V	A	-	2	0	HIPK4	45587333	0.003000	0.15002	0.726000	0.30738	0.995000	0.86356	1.122000	0.31295	0.708000	0.31955	0.462000	0.41574	GCG	G|0.992;A|0.008	0.008	strong		0.577	HIPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462593.1	NM_144685		A	40895493	G	A	40895493	3	1	22	1	0	0	0	0	1	0	0	0	7128	1087	38	1	1549	1	HIPK4	19	40895493	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	12905	40895493	18233490	3954	6855											
NUMBL	9253	hgsc.bcm.edu	37	chr19	41190455	41190455	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaacttgttcatggtgcccGccccgtctggtgacacagga	7	10	12	12	2	2	1	1	1	1	0	2	2	2	2	3	3	2	2	3	3	1	3	rs143941883	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41190455G>T	ENST00000252891.4	-	3	283	c.116C>A	c.(115-117)gCg>gAg	p.A39E	NUMBL_ENST00000540131.1_5'UTR|NUMBL_ENST00000598779.1_5'UTR|NUMBL_ENST00000599594.1_5'UTR	NM_004756.3	NP_004747.1	Q9Y6R0	NUMBL_HUMAN	numb homolog (Drosophila)-like	39					adherens junction organization (GO:0034332)|axonogenesis (GO:0007409)|cytokine-mediated signaling pathway (GO:0019221)|lateral ventricle development (GO:0021670)|nervous system development (GO:0007399)|neuroblast division in subventricular zone (GO:0021849)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of neurogenesis (GO:0050769)|protein metabolic process (GO:0019538)	cytoplasm (GO:0005737)				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)	16			Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105)			CATGGTGCCCGCCCCGTCTGG	0.662													G|||	74	0.0147764	0.053	0.0058	5008	,	,		12097	0.0		0.0	False		,,,				2504	0.0				p.A39E		Atlas-SNP	.											.	NUMBL	49	.	0			c.C116A						PASS	.	G	GLU/ALA	198,4208	112.9+/-151.0	5,188,2010	20	20	20		116	4.1	1	19	dbSNP_134	20	0,8600		0,0,4300	yes	missense	NUMBL	NM_004756.3	107	5,188,6310	TT,TG,GG		0.0,4.4939,1.5224	benign	39/610	41190455	198,12808	2203	4300	6503	SO:0001583	missense	9253	exon3			GTGCCCGCCCCGT	AF015401	CCDS12561.1	19q13.13-q13.2	2008-07-17	2001-11-28			ENSG00000105245			8061	protein-coding gene	gene with protein product		604018	"numb (Drosophila) homolog-like"			9225980, 9303539	Standard	XM_006723471		Approved	NUMB-R, CTG3a, CAG3A, TNRC23, NUMBR, NUMBLIKE	uc002oon.3	Q9Y6R0		ENST00000252891.4:c.116C>A	19.37:g.41190455G>T	ENSP00000252891:p.Ala39Glu	145	0	0		147	58	0.394558	NM_004756	Q7Z4J9	Missense_Mutation	SNP	ENST00000252891.4	37	CCDS12561.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	G	20.8	4.045316	0.75846	0.044939	0.0	ENSG00000105245	ENST00000252891	T	0.56776	0.44	5.17	4.14	0.48551	.	0.189579	0.32287	N	0.006318	T	0.08935	0.0221	N	0.08118	0	0.80722	D	1	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.002	T	0.04440	-1.0951	10	0.66056	D	0.02	-15.7799	11.0624	0.47955	0.0867:0.0:0.9133:0.0	.	39;39	A8K033;Q9Y6R0	.;NUMBL_HUMAN	E	39	ENSP00000252891:A39E	ENSP00000252891:A39E	A	-	2	0	NUMBL	45882295	0.627000	0.27129	0.999000	0.59377	0.995000	0.86356	1.270000	0.33086	1.423000	0.47198	0.591000	0.81541	GCG	G|0.987;T|0.013	0.013	strong		0.662	NUMBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462749.2	NM_004756		T	41190455	G	T	41190455	3	4	22	1	0	0	0	0	1	0	0	0	10761	1087	38	4	1745	4	NUMBL	19	41190455	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	294962	41190455	17938528	3955	6856											
ADCK4	79934	hgsc.bcm.edu	37	chr19	41198210	41198210	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttcccccgacccaaagtcAtaagggccctgggtggcgaa	9	7	12	13	2	1	0	1	0	0	0	2	2	2	0	4	3	0	1	4	3	3	2	rs17851001	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41198210A>G	ENST00000324464.3	-	15	1666	c.1365T>C	c.(1363-1365)taT>taC	p.Y455Y	ADCK4_ENST00000243583.6_Silent_p.Y414Y|NUMBL_ENST00000252891.4_5'Flank|NUMBL_ENST00000540131.1_5'Flank|NUMBL_ENST00000598779.1_5'Flank|NUMBL_ENST00000599594.1_5'Flank|ADCK4_ENST00000450541.1_Silent_p.Y414Y	NM_024876.3	NP_079152.3	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4	455						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)			ACCCAAAGTCATAAGGGCCCT	0.672													A|||	68	0.0135783	0.0484	0.0058	5008	,	,		15061	0.0		0.0	False		,,,				2504	0.0				p.Y455Y		Atlas-SNP	.											.	ADCK4	92	.	0			c.T1365C						PASS	.	A	,	195,4211	116.3+/-154.2	5,185,2013	27	27	27		1242,1365	-10.1	0.4	19	dbSNP_123	27	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	ADCK4	NM_001142555.2,NM_024876.3	,	5,185,6312	GG,GA,AA		0.0,4.4258,1.4995	,	414/504,455/545	41198210	195,12809	2203	4299	6502	SO:0001819	synonymous_variant	79934	exon15			AAAGTCATAAGGG	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.1365T>C	19.37:g.41198210A>G		86	0	0		94	38	0.404255	NM_024876	Q8TAJ1|Q9HA52	Silent	SNP	ENST00000324464.3	37	CCDS12562.1																																																																																			A|0.986;G|0.014	0.014	strong		0.672	ADCK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462731.1	NM_024876		G	41198210	A	G	41198210	2	3	22	1	0	0	0	0	0	0	0	1	290	224	8	3		3	ADCK4	19	41198210	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	7755	41198210	17930773	3956	6857											
ITPKC	80271	hgsc.bcm.edu	37	chr19	41223387	41223387	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagcaaaagacggagccagAcaggtccagcctccggacgc	13	2	12	14	3	0	2	0	0	0	2	2	4	2	4	4	3	3	1	4	3	3	0	rs145275994	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41223387A>T	ENST00000263370.2	+	1	380	c.347A>T	c.(346-348)gAc>gTc	p.D116V	ADCK4_ENST00000243583.6_5'Flank|ADCK4_ENST00000324464.3_5'Flank|ADCK4_ENST00000450541.1_5'Flank	NM_025194.2	NP_079470.1	Q96DU7	IP3KC_HUMAN	inositol-trisphosphate 3-kinase C	116					inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	14			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			ACGGAGCCAGACAGGTCCAGC	0.602													A|||	17	0.00339457	0.0121	0.0014	5008	,	,		13975	0.0		0.0	False		,,,				2504	0.0				p.D116V		Atlas-SNP	.											.	ITPKC	36	.	0			c.A347T						PASS	.	A	VAL/ASP	41,4363	43.1+/-76.7	0,41,2161	52	59	57		347	1.9	0	19	dbSNP_134	57	0,8600		0,0,4300	yes	missense	ITPKC	NM_025194.2	152	0,41,6461	TT,TA,AA		0.0,0.931,0.3153	benign	116/684	41223387	41,12963	2202	4300	6502	SO:0001583	missense	80271	exon1			AGCCAGACAGGTC	Y11999	CCDS12563.1	19q13.1	2011-04-28	2011-04-28		ENSG00000086544	ENSG00000086544	2.7.1.127		14897	protein-coding gene	gene with protein product		606476	"inositol 1,4,5-trisphosphate 3-kinase C"			11085927	Standard	NM_025194		Approved	IP3KC, IP3-3KC	uc002oot.3	Q96DU7		ENST00000263370.2:c.347A>T	19.37:g.41223387A>T	ENSP00000263370:p.Asp116Val	53	0	0		95	44	0.463158	NM_025194	Q9UE25|Q9Y475	Missense_Mutation	SNP	ENST00000263370.2	37	CCDS12563.1	2	9.157509157509158E-4	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	A	2.482	-0.319454	0.05386	0.00931	0.0	ENSG00000086544	ENST00000263370	.	.	.	4.07	1.93	0.25924	.	0.659632	0.13336	N	0.395559	T	0.17789	0.0427	N	0.19112	0.55	0.19775	N	0.999958	B	0.17667	0.023	B	0.15870	0.014	T	0.17107	-1.0380	9	0.27785	T	0.31	-3.0482	6.4104	0.21688	0.7762:0.0:0.2238:0.0	.	116	Q96DU7	IP3KC_HUMAN	V	116	.	ENSP00000263370:D116V	D	+	2	0	ITPKC	45915227	0.122000	0.22280	0.001000	0.08648	0.323000	0.28346	0.708000	0.25719	0.248000	0.21435	0.397000	0.26171	GAC	A|0.997;T|0.003	0.003	strong		0.602	ITPKC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463104.1	NM_025194		T	41223387	A	T	41223387	3	4	22	1	0	0	0	0	1	0	0	0	7928	275	10	5	349	5	ITPKC	19	41223387	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	25177	41223387	17905596	3957	6858											
C19orf54	284325	hgsc.bcm.edu	37	chr19	41248532	41248532	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	actcttgccctgcttggacaGcaggtagacagctcccgggg	7	8	13	13	1	1	1	0	0	1	1	2	2	2	2	2	4	4	4	2	4	1	3	rs36071297	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41248532G>A	ENST00000378313.2	-	6	981	c.862C>T	c.(862-864)Ctg>Ttg	p.L288L	C19orf54_ENST00000598485.2_Intron|C19orf54_ENST00000470681.1_3'UTR|C19orf54_ENST00000594163.1_5'Flank|C19orf54_ENST00000339153.3_Silent_p.L116L|C19orf54_ENST00000598729.1_Silent_p.L116L	NM_198476.3	NP_940878.3	Q5BKX5	CS054_HUMAN	chromosome 19 open reading frame 54	288										breast(1)|lung(1)|urinary_tract(2)	4			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			TGCTTGGACAGCAGGTAGACA	0.657													G|||	137	0.0273562	0.0998	0.0072	5008	,	,		19677	0.0		0.0	False		,,,				2504	0.0				p.L288L		Atlas-SNP	.											.	C19orf54	13	.	0			c.C862T						PASS	.	G		321,4085	170.1+/-200.6	11,299,1893	43	38	39		862	5.5	1	19	dbSNP_126	39	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	C19orf54	NM_198476.3		11,302,6190	AA,AG,GG		0.0349,7.2855,2.4912		288/352	41248532	324,12682	2203	4300	6503	SO:0001819	synonymous_variant	284325	exon6			TGGACAGCAGGTA	AK123126	CCDS12564.2	19q13.2	2012-10-26			ENSG00000188493	ENSG00000188493			24758	protein-coding gene	gene with protein product							Standard	NM_198476		Approved	FLJ41131	uc002oou.1	Q5BKX5	OTTHUMG00000150174	ENST00000378313.2:c.862C>T	19.37:g.41248532G>A		127	0	0		145	78	0.537931	NM_198476	A8MSZ5|B4DNU7	Silent	SNP	ENST00000378313.2	37	CCDS12564.2																																																																																			G|0.905;A|0.095	0.095	strong		0.657	C19orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316701.1	NM_198476		A	41248532	G	A	41248532	2	1	22	1	0	0	0	0	0	0	0	1	1938	962	34	2		2	C19orf54	19	41248532	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	25145	41248532	17880451	3958	6859											
EGLN2	112398	hgsc.bcm.edu	37	chr19	41306771	41306771	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagagtgaaggcgctgcagcGctggtcaccaaggggtgcca	9	5	16	11	2	1	2	1	1	0	1	1	2	1	2	2	4	3	3	2	4	2	0	rs143206553	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41306771G>A	ENST00000593726.1	+	1	1322	c.294G>A	c.(292-294)gcG>gcA	p.A98A	EGLN2_ENST00000303961.4_Silent_p.A98A|RAB4B-EGLN2_ENST00000594136.1_3'UTR|CTC-490E21.12_ENST00000601627.1_5'Flank|EGLN2_ENST00000594140.1_5'Flank|EGLN2_ENST00000406058.2_Silent_p.A98A			Q96KS0	EGLN2_HUMAN	egl-9 family hypoxia-inducible factor 2	98	Bipartite nuclear localization signal.				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)	GCGCTGCAGCGCTGGTCACCA	0.677													G|||	18	0.00359425	0.0129	0.0014	5008	,	,		16000	0.0		0.0	False		,,,				2504	0.0				p.A98A		Atlas-SNP	.											.	EGLN2	31	.	0			c.G294A						PASS	.	G	,	77,4321		0,77,2122	14	16	15		294,294	-3.8	0.7	19	dbSNP_134	15	0,8582		0,0,4291	no	coding-synonymous,coding-synonymous	EGLN2	NM_053046.3,NM_080732.3	,	0,77,6413	AA,AG,GG		0.0,1.7508,0.5932	,	98/408,98/408	41306771	77,12903	2199	4291	6490	SO:0001819	synonymous_variant	112398	exon2			TGCAGCGCTGGTC	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.294G>A	19.37:g.41306771G>A		45	0	0		63	31	0.492063	NM_053046	A8K5S0|Q8WWY4|Q9BV14	Silent	SNP	ENST00000593726.1	37	CCDS12567.1																																																																																			G|0.993;A|0.007	0.007	strong		0.677	EGLN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463218.1			A	41306771	G	A	41306771	2	1	22	1	0	0	0	0	0	0	0	1	4971	1074	38	1		1	EGLN2	19	41306771	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	58239	41306771	17822212	3959	6860											
CEACAM21	90273	hgsc.bcm.edu	37	chr19	42092225	42092225	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctgacagctccatctcctagGtaagactgtccgttcccaat	9	11	7	14	1	1	2	0	1	1	1	5	2	4	2	4	1	1	3	4	1	3	3	rs62119455	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42092225G>A	ENST00000401445.2	+	6	908		c.e6+1		CEACAM21_ENST00000407170.2_Splice_Site|CEACAM21_ENST00000482870.2_Intron|CEACAM21_ENST00000187608.9_Splice_Site			Q3KPI0	CEA21_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 21							integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|urinary_tract(1)	13						CATCTCCTAGGTAAGACTGTC	0.592													g|||	124	0.0247604	0.0825	0.0072	5008	,	,		17365	0.0		0.0099	False		,,,				2504	0.0				.		Atlas-SNP	.											.	CEACAM21	52	.	0			c.882+1G>A						PASS	.	G	,	261,3973		8,245,1864	63	66	65		,	1.2	0	19	dbSNP_129	65	58,8460		1,56,4202	yes	splice-5,splice-5	CEACAM21	NM_001098506.1,NM_033543.3	,	9,301,6066	AA,AG,GG		0.6809,6.1644,2.5016	,	,	42092225	319,12433	2117	4259	6376	SO:0001630	splice_region_variant	90273	exon6			TCCTAGGTAAGAC	AK023602	CCDS46086.1, CCDS46087.1, CCDS74373.1	19q13.2	2013-01-29			ENSG00000007129	ENSG00000007129		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	28834	protein-coding gene	gene with protein product						12477932	Standard	XM_005278397		Approved	R29124_1, FLJ13540	uc002ore.4	Q3KPI0	OTTHUMG00000151062	ENST00000401445.2:c.879+1G>A	19.37:g.42092225G>A		140	1	0.00714286		158	158	1	NM_001098506	B7WNQ6|O75296|Q6UY47|Q96ER7	Splice_Site	SNP	ENST00000401445.2	37	CCDS46086.1																																																																																			G|0.981;A|0.019	0.019	strong		0.592	CEACAM21-005	KNOWN	non_canonical_polymorphism|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321140.1	NM_033543	Intron	A	42092225	G	A	42092225	5	1	22	1	0	0	0	0	0	0	1	0	3194	1275	44	2	905	2	CEACAM21	19	42092225	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	785454	42092225	17036758	3960	6861											
CEACAM4	1089	hgsc.bcm.edu	37	chr19	42125709	42125709	+	Silent	SNP	G	G	A																															gctcccagaggaacctaagaGaccacatctgctttgtggtc																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42125709G>A	ENST00000221954.2	-	7	839	c.729C>T	c.(727-729)gtC>gtT	p.V243V		NM_001817.2	NP_001808.2	O75871	CEAM4_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 4	243						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						GAACCTAAGAGACCACATCTG	0.532																																					p.V243V		Atlas-SNP	.											CEACAM4,NS,neuroblastoma,0,1	CEACAM4	42	1	0			c.C729T						PASS	.						113	108	110					19																	42125709		2203	4300	6503	SO:0001819	synonymous_variant	1089	exon7			CTAAGAGACCACA	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.729C>T	19.37:g.42125709G>A		100	0	0		114	54	0.473684	NM_001817	Q03715|Q7LDZ7	Silent	SNP	ENST00000221954.2	37	CCDS33033.1																																																																																			.	.	none		0.532	CEACAM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321148.1	NM_001817		A	42125709	G	A	42125709	2	1	22	1	0	0	0	0	0	0	0	1	3196	929	33	2		2	CEACAM4	19	42125709	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	33484	42125709	17003274	3961	6862	86	2									
CEACAM4	1089	hgsc.bcm.edu	37	chr19	42125710	42125710	+	Missense_Mutation	SNP	A	A	G																															ctcccagaggaacctaagagAccacatctgctttgtggtcg																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42125710A>G	ENST00000221954.2	-	7	838	c.728T>C	c.(727-729)gTc>gCc	p.V243A		NM_001817.2	NP_001808.2	O75871	CEAM4_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 4	243						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						AACCTAAGAGACCACATCTGC	0.532																																					p.V243A		Atlas-SNP	.											CEACAM4,NS,neuroblastoma,+1,1	CEACAM4	42	1	0			c.T728C						PASS	.						114	109	111					19																	42125710		2203	4300	6503	SO:0001583	missense	1089	exon7			TAAGAGACCACAT	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.728T>C	19.37:g.42125710A>G	ENSP00000221954:p.Val243Ala	103	0	0		116	55	0.474138	NM_001817	Q03715|Q7LDZ7	Missense_Mutation	SNP	ENST00000221954.2	37	CCDS33033.1	.	.	.	.	.	.	.	.	.	.	A	0.008	-1.908731	0.00508	.	.	ENSG00000105352	ENST00000221954	T	0.01139	5.28	2.4	-3.74	0.04385	.	.	.	.	.	T	0.00440	0.0014	N	0.02142	-0.665	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.43956	-0.9359	9	0.06365	T	0.9	.	3.7364	0.08512	0.3171:0.4027:0.2802:0.0	.	243	O75871	CEAM4_HUMAN	A	243	ENSP00000221954:V243A	ENSP00000221954:V243A	V	-	2	0	CEACAM4	46817550	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.439000	0.02414	-0.683000	0.05190	-0.427000	0.05922	GTC	.	.	none		0.532	CEACAM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321148.1	NM_001817		G	42125710	A	G	42125710	3	3	22	1	0	0	0	0	1	0	0	0	3196	275	10	3	10	3	CEACAM4	19	42125710	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1	42125710	17003273	3962	6863	86	2									
CEACAM5	1048	hgsc.bcm.edu	37	chr19	42221418	42221418	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagcaacaactccaaccccGtggaggatgaggatgctgta	12	6	11	12	1	0	1	0	1	0	0	1	4	1	4	4	3	5	3	4	3	4	1	rs75927810	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42221418G>A	ENST00000221992.6	+	5	1117	c.1003G>A	c.(1003-1005)Gtg>Atg	p.V335M	CEACAM5_ENST00000398599.4_Missense_Mutation_p.V334M|CEACAM5_ENST00000405816.1_Missense_Mutation_p.V335M|CEA_ENST00000598976.1_Intron	NM_004363.2	NP_004354.2	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 5	335	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)		CTCCAACCCCGTGGAGGATGA	0.532													g|||	97	0.019369	0.0688	0.0072	5008	,	,		21742	0.0		0.001	False		,,,				2504	0.0				p.V335M		Atlas-SNP	.											CEACAM5,NS,carcinoma,-2,1	CEACAM5	84	1	0			c.G1003A						PASS	.	G	MET/VAL	231,4175	135.7+/-171.8	6,219,1978	143	144	144		1003	-5.6	0	19	dbSNP_131	144	7,8593	5.7+/-21.5	0,7,4293	yes	missense	CEACAM5	NM_004363.2	21	6,226,6271	AA,AG,GG		0.0814,5.2429,1.8299	benign	335/703	42221418	238,12768	2203	4300	6503	SO:0001583	missense	1048	exon5			AACCCCGTGGAGG	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.1003G>A	19.37:g.42221418G>A	ENSP00000221992:p.Val335Met	142	0	0		172	91	0.52907	NM_004363	H9KVA7	Missense_Mutation	SNP	ENST00000221992.6	37	CCDS12584.1	25|25	0.011446886446886446|0.011446886446886446	19|19	0.03861788617886179|0.03861788617886179	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	G|G	7.757|7.757	0.704676|0.704676	0.15172|0.15172	0.052429|0.052429	8.14E-4|8.14E-4	ENSG00000105388|ENSG00000105388	ENST00000398599|ENST00000221992;ENST00000405816	.|T;T	.|0.72167	.|-0.63;-0.63	2.77|2.77	-5.55|-5.55	0.02536|0.02536	.|Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|.	.|.	.|.	.|.	T|T	0.38852|0.38852	0.1056|0.1056	M|M	0.83603|0.83603	2.65|2.65	0.09310|0.09310	N|N	1|1	.|P;D	.|0.63880	.|0.881;0.993	.|P;D	.|0.64042	.|0.572;0.921	T|T	0.60697|0.60697	-0.7212|-0.7212	5|9	.|0.56958	.|D	.|0.05	.|.	0.9149|0.9149	0.01302|0.01302	0.3457:0.1551:0.3423:0.1569|0.3457:0.1551:0.3423:0.1569	.|.	.|335;335	.|P06731;Q53G30	.|CEAM5_HUMAN;.	H|M	330|335	.|ENSP00000221992:V335M;ENSP00000385072:V335M	.|ENSP00000221992:V335M	R|V	+|+	2|1	0|0	CEACAM5|CEACAM5	46913258|46913258	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.009000|0.009000	0.06853|0.06853	-1.341000|-1.341000	0.02647|0.02647	-1.658000|-1.658000	0.01490|0.01490	-0.706000|-0.706000	0.03657|0.03657	CGT|GTG	G|0.985;A|0.015	0.015	strong		0.532	CEACAM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321132.2	NM_004363		A	42221418	G	A	42221418	3	1	22	1	0	0	0	0	1	0	0	0	3197	1145	40	1	1021	1	CEACAM5	19	42221418	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	95708	42221418	16907565	3963	6864											
CEACAM6	4680	hgsc.bcm.edu	37	chr19	42260697	42260697	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aattgtaggatatgtaatagGaactcaacaagctaccccag	16	9	8	8	0	1	0	1	0	0	0	1	2	1	2	2	2	4	3	2	2	9	6	rs61736638	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42260697G>A	ENST00000199764.6	+	2	472	c.254G>A	c.(253-255)gGa>gAa	p.G85E	AC011513.4_ENST00000601409.1_RNA|CEA_ENST00000598976.1_Intron	NM_002483.4	NP_002474.3	P40199	CEAM6_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 6 (non-specific cross reacting antigen)	85	Ig-like V-type.				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)		TATGTAATAGGAACTCAACAA	0.498													g|||	146	0.0291534	0.1074	0.0043	5008	,	,		18669	0.0		0.001	False		,,,				2504	0.0				p.G85E		Atlas-SNP	.											.	CEACAM6	52	.	0			c.G254A						PASS	.	G	GLU/GLY	359,4047	184.3+/-211.7	13,333,1857	246	230	235		254	-3.8	0	19	dbSNP_129	235	7,8589	5.0+/-18.6	0,7,4291	no	missense	CEACAM6	NM_002483.4	98	13,340,6148	AA,AG,GG		0.0814,8.148,2.815	benign	85/345	42260697	366,12636	2203	4298	6501	SO:0001583	missense	4680	exon2			TAATAGGAACTCA	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.254G>A	19.37:g.42260697G>A	ENSP00000199764:p.Gly85Glu	446	1	0.00224215		429	205	0.477855	NM_002483	Q13774|Q14920|Q53XP7	Missense_Mutation	SNP	ENST00000199764.6	37	CCDS12585.1	51	0.023351648351648352	47	0.09552845528455285	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	G	0.011	-1.703438	0.00719	0.08148	8.14E-4	ENSG00000086548	ENST00000199764	T	0.64085	-0.08	1.92	-3.84	0.04256	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.01189	0.0039	N	0.16903	0.455	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.02333	-1.1175	9	0.54805	T	0.06	.	5.4199	0.16394	0.2722:0.4787:0.2491:0.0	rs61736638	85	P40199	CEAM6_HUMAN	E	85	ENSP00000199764:G85E	ENSP00000199764:G85E	G	+	2	0	CEACAM6	46952537	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.930000	0.00689	-3.925000	0.00091	-3.948000	0.00015	GGA	G|0.974;A|0.026	0.026	strong		0.498	CEACAM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321147.1			A	42260697	G	A	42260697	3	1	22	1	0	0	0	0	1	0	0	0	3198	1174	41	2	260	2	CEACAM6	19	42260697	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	39279	42260697	16868286	3964	6865											
LYPD4	147719	hgsc.bcm.edu	37	chr19	42343355	42343355	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	caagtctcaaatgctggggtCccatggccctgtgtctgggt	6	11	13	11	0	2	0	1	0	2	0	4	0	3	0	2	4	1	1	2	4	2	0			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42343355C>G	ENST00000330743.3	-	2	1216	c.5G>C	c.(4-6)gGa>gCa	p.G2A	LYPD4_ENST00000601246.1_Missense_Mutation_p.G2A|LYPD4_ENST00000343055.4_Missense_Mutation_p.G2A	NM_173506.4	NP_775777.3	Q6UWN0	LYPD4_HUMAN	LY6/PLAUR domain containing 4	2						anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)	12						ATGCTGGGGTCCCATGGCCCT	0.542																																					p.G2A		Atlas-SNP	.											.	LYPD4	30	.	0			c.G5C						PASS	.						123	117	119					19																	42343355		2203	4300	6503	SO:0001583	missense	147719	exon2			TGGGGTCCCATGG	AY358726	CCDS12587.1	19q13.2	2008-02-05				ENSG00000273111			28659	protein-coding gene	gene with protein product						12975309	Standard	XM_005278383		Approved	MGC42718	uc002orp.1	Q6UWN0		ENST00000330743.3:c.5G>C	19.37:g.42343355C>G	ENSP00000328737:p.Gly2Ala	112	0	0		102	49	0.480392	NM_173506	Q8IYW0	Missense_Mutation	SNP	ENST00000330743.3	37	CCDS12587.1	.	.	.	.	.	.	.	.	.	.	C	13.50	2.255112	0.39896	.	.	ENSG00000183103	ENST00000330743;ENST00000343055	T;T	0.13657	3.41;2.57	3.9	2.83	0.33086	.	0.430475	0.17224	N	0.182217	T	0.13030	0.0316	L	0.46157	1.445	0.23827	N	0.996738	P;P	0.49961	0.93;0.793	P;B	0.44477	0.451;0.264	T	0.12708	-1.0537	10	0.23302	T	0.38	-2.1155	8.5663	0.33543	0.241:0.759:0.0:0.0	.	2;2	Q6UWN0-2;Q6UWN0	.;LYPD4_HUMAN	A	2	ENSP00000328737:G2A;ENSP00000339568:G2A	ENSP00000328737:G2A	G	-	2	0	LYPD4	47035195	0.988000	0.35896	0.975000	0.42487	0.942000	0.58702	0.660000	0.25009	1.156000	0.42514	0.551000	0.68910	GGA	.	.	none		0.542	LYPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463039.1	NM_173506		G	42343355	C	G	42343355	3	3	22	1	0	0	0	0	1	0	0	0	9121	855	30	4	751	4	LYPD4	19	42343355	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	82658	42343355	16785628	3965	6866											
GRIK5	2901	hgsc.bcm.edu	37	chr19	42560893	42560893	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggacaaactcagggtagaagGggtgggacgtgttgaacatg	12	7	17	5	1	1	2	1	1	0	1	1	4	1	4	0	5	2	2	0	5	4	2	rs139340543	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42560893G>A	ENST00000262895.3	-	7	823	c.824C>T	c.(823-825)cCc>cTc	p.P275L	GRIK5_ENST00000593562.1_Missense_Mutation_p.P275L|GRIK5_ENST00000301218.4_Missense_Mutation_p.P275L	NM_002088.4	NP_002079.3	Q16478	GRIK5_HUMAN	glutamate receptor, ionotropic, kainate 5	275					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)				AGGGTAGAAGGGGTGGGACGT	0.577													G|||	7	0.00139776	0.0053	0.0	5008	,	,		20492	0.0		0.0	False		,,,				2504	0.0				p.P275L		Atlas-SNP	.											.	GRIK5	220	.	0			c.C824T						PASS	.	G	LEU/PRO	7,4399	12.9+/-30.5	0,7,2196	135	120	125		824	4.9	1	19	dbSNP_134	125	0,8600		0,0,4300	yes	missense	GRIK5	NM_002088.3	98	0,7,6496	AA,AG,GG		0.0,0.1589,0.0538	possibly-damaging	275/981	42560893	7,12999	2203	4300	6503	SO:0001583	missense	2901	exon7			TAGAAGGGGTGGG		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.824C>T	19.37:g.42560893G>A	ENSP00000262895:p.Pro275Leu	126	0	0		122	54	0.442623	NM_002088	Q8WWG8	Missense_Mutation	SNP	ENST00000262895.3	37	CCDS12595.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	21.6	4.178464	0.78564	0.001589	0.0	ENSG00000105737	ENST00000262895;ENST00000301218	D;D	0.84873	-1.91;-1.91	4.93	4.93	0.64822	Extracellular ligand-binding receptor (1);	0.073753	0.53938	D	0.000048	D	0.88209	0.6375	M	0.64170	1.965	0.80722	D	1	B	0.33637	0.42	P	0.45138	0.471	D	0.88944	0.3382	10	0.72032	D	0.01	.	17.2807	0.87127	0.0:0.0:1.0:0.0	.	275	Q16478	GRIK5_HUMAN	L	275	ENSP00000262895:P275L;ENSP00000301218:P275L	ENSP00000262895:P275L	P	-	2	0	GRIK5	47252733	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.555000	0.82223	2.442000	0.82660	0.467000	0.42956	CCC	G|0.999;A|0.001	0.001	strong		0.577	GRIK5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463453.1			A	42560893	G	A	42560893	3	1	22	1	0	0	0	0	1	0	0	0	6786	1232	43	2	2170	2	GRIK5	19	42560893	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	217538	42560893	16568090	3966	6867											
CIC	23152	hgsc.bcm.edu	37	chr19	42794829	42794831	+	In_Frame_Del	DEL	AAG	AAG	-																															cactggtgctgcccccaaacAaggaggagcaagagggcggc																								rs587778196		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42794829_42794831delAAG	ENST00000575354.2	+	10	1949_1951	c.1909_1911delAAG	c.(1909-1911)aagdel	p.K637del	CIC_ENST00000572681.2_In_Frame_Del_p.K1546del|CIC_ENST00000160740.3_In_Frame_Del_p.K637del	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	637	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)				GCCCCCAAACAAGGAGGAGCAAG	0.695			"Mis, F, S"		oligodendroglioma																																p.636_637del		Pindel,Atlas-Indel	.		Rec	yes		19	19q13.2	23152	capicua homolog		O	.	CIC	249	.	0			c.1908_1910del						PASS	.																																			SO:0001651	inframe_deletion	23152	exon10			.	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.1909_1911delAAG	19.37:g.42794829_42794831delAAG	ENSP00000458663:p.Lys637del	87	0	.		107	33	0.308	NM_015125	Q7LGI1|Q9UEG5|Q9Y6T1	In_Frame_Del	DEL	ENST00000575354.2	37	CCDS12601.1																																																																																			.	.	none		0.695	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2			-	42794831	AAG	-	42794829	7	5	22	1	0	1	0	1	0	0	0	0	3426	131	5	0	1947	0	CIC	19	42794829	In_Frame_Del	DEL	AAG	TCGA-G8-6324-01A-11D-2210-10	233936	42794829	16334154	3967	6868											
MEGF8	1954	hgsc.bcm.edu	37	chr19	42873089	42873089	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caccacgactgcaacgagacGcagaattgccacgaccagcc	13	3	9	16	4	0	2	0	0	0	2	0	5	0	2	4	0	4	2	4	0	2	1	rs10425783	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42873089G>A	ENST00000251268.6	+	37	6576	c.6576G>A	c.(6574-6576)acG>acA	p.T2192T	MEGF8_ENST00000334370.4_Silent_p.T2125T|MEGF8_ENST00000378073.4_5'Flank	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	2192	EGF-like 5. {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)				GCAACGAGACGCAGAATTGCC	0.662													G|||	133	0.0265575	0.093	0.0115	5008	,	,		17876	0.0		0.002	False		,,,				2504	0.0				p.T2192T		Atlas-SNP	.											.	MEGF8	358	.	0			c.G6576A						PASS	.	G		335,4071	176.9+/-206.0	17,301,1885	82	84	83		6375	-9.5	0	19	dbSNP_119	83	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous	MEGF8	NM_001410.2		17,311,6175	AA,AG,GG		0.1163,7.6033,2.6526		2125/2779	42873089	345,12661	2203	4300	6503	SO:0001819	synonymous_variant	1954	exon37			CGAGACGCAGAAT	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.6576G>A	19.37:g.42873089G>A		78	0	0		89	48	0.539326	NM_001271938	A8KAY0|O75097	Silent	SNP	ENST00000251268.6	37																																																																																				G|0.969;A|0.031	0.031	strong		0.662	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		A	42873089	G	A	42873089	2	1	22	1	0	0	0	0	0	0	0	1	9472	1074	38	1		1	MEGF8	19	42873089	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	78260	42873089	16255894	3968	6869											
MEGF8	1954	hgsc.bcm.edu	37	chr19	42874900	42874900	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtgaagacgaggccgtgtgCgtgaactgccagaataacag	13	6	14	8	3	0	4	0	2	0	2	0	5	0	4	2	1	4	0	2	1	4	1	rs28483598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42874900C>T	ENST00000251268.6	+	40	7053	c.7053C>T	c.(7051-7053)tgC>tgT	p.C2351C	MEGF8_ENST00000334370.4_Silent_p.C2284C|MEGF8_ENST00000378073.4_5'UTR	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	2351					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)				AGGCCGTGTGCGTGAACTGCC	0.562													C|||	92	0.0183706	0.0635	0.0072	5008	,	,		10552	0.001		0.002	False		,,,				2504	0.0				p.C2351C		Atlas-SNP	.											.	MEGF8	358	.	0			c.C7053T						PASS	.	C		213,4191		7,199,1996	65	56	59		6852	-2.4	1	19	dbSNP_125	59	10,8586		0,10,4288	no	coding-synonymous	MEGF8	NM_001410.2		7,209,6284	TT,TC,CC		0.1163,4.8365,1.7154		2284/2779	42874900	223,12777	2202	4298	6500	SO:0001819	synonymous_variant	1954	exon40			CGTGTGCGTGAAC	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.7053C>T	19.37:g.42874900C>T		108	0	0		144	82	0.569444	NM_001271938	A8KAY0|O75097	Silent	SNP	ENST00000251268.6	37																																																																																				C|0.981;T|0.019	0.019	strong		0.562	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		T	42874900	C	T	42874900	2	4	22	1	0	0	0	0	0	0	0	1	9472	776	27	1		1	MEGF8	19	42874900	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1811	42874900	16254083	3969	6870											
LIPE	3991	hgsc.bcm.edu	37	chr19	42906914	42906914	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accctcggggaaggcggcacGgacgcccaggcctctgtcca	7	4	14	16	4	1	0	0	0	1	0	3	2	2	2	4	6	0	1	4	6	1	0	rs7246232	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42906914G>T	ENST00000244289.4	-	9	3088	c.2812C>A	c.(2812-2814)Cgt>Agt	p.R938S	LIPE-AS1_ENST00000594624.2_RNA|LIPE-AS1_ENST00000597203.1_RNA|LIPE-AS1_ENST00000599276.1_RNA|LIPE-AS1_ENST00000593491.2_RNA	NM_005357.2	NP_005348.2	Q05469	LIPS_HUMAN	lipase, hormone-sensitive	938			R -> S (in dbSNP:rs7246232). {ECO:0000269|Ref.3}.		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)				AAGGCGGCACGGACGCCCAGG	0.602													G|||	101	0.0201677	0.0711	0.0072	5008	,	,		16054	0.0		0.002	False		,,,				2504	0.0				p.R938S		Atlas-SNP	.											.	LIPE	83	.	0			c.C2812A						PASS	.	G	SER/ARG	227,4179	135.7+/-171.8	6,215,1982	72	61	64		2812	-10.8	0	19	dbSNP_116	64	11,8589	8.4+/-32.0	0,11,4289	yes	missense	LIPE	NM_005357.2	110	6,226,6271	TT,TG,GG		0.1279,5.1521,1.8299	benign	938/1077	42906914	238,12768	2203	4300	6503	SO:0001583	missense	3991	exon9			CGGCACGGACGCC	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.2812C>A	19.37:g.42906914G>T	ENSP00000244289:p.Arg938Ser	115	0	0		122	57	0.467213	NM_005357	Q3LRT2|Q6NSL7	Missense_Mutation	SNP	ENST00000244289.4	37	CCDS12607.1	49	0.022435897435897436	44	0.08943089430894309	3	0.008287292817679558	0	0.0	2	0.002638522427440633	G	6.053	0.378025	0.11466	0.051521	0.001279	ENSG00000079435	ENST00000244289	T	0.03272	3.99	5.38	-10.8	0.00216	.	1.425700	0.04445	N	0.371619	T	0.00109	0.0003	N	0.19112	0.55	0.09310	N	1	B	0.09022	0.002	B	0.15870	0.014	T	0.33727	-0.9857	10	0.26408	T	0.33	5.9579	9.2186	0.37362	0.0796:0.1474:0.6138:0.1592	rs7246232;rs56962270;rs7246232	938	Q05469	LIPS_HUMAN	S	938	ENSP00000244289:R938S	ENSP00000244289:R938S	R	-	1	0	LIPE	47598754	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.465000	0.00995	-3.013000	0.00272	-1.669000	0.00746	CGT	G|0.970;T|0.030	0.030	strong		0.602	LIPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463861.1	NM_005357		T	42906914	G	T	42906914	3	4	22	1	0	0	0	0	1	0	0	0	8830	1116	39	4	426	4	LIPE	19	42906914	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	32014	42906914	16222069	3970	6871											
LIPE	3991	hgsc.bcm.edu	37	chr19	42910416	42910416	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaggctgcagcattgtggcCgggtaggctgccatgatgcc	6	8	16	11	1	0	1	0	1	0	0	0	1	0	1	3	4	4	6	3	4	1	2	rs28657829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42910416C>T	ENST00000244289.4	-	7	2538	c.2262G>A	c.(2260-2262)ccG>ccA	p.P754P	LIPE_ENST00000602000.1_5'Flank|LIPE-AS1_ENST00000594624.2_RNA|LIPE-AS1_ENST00000597203.1_RNA|LIPE-AS1_ENST00000599276.1_RNA|LIPE-AS1_ENST00000593491.2_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)				GCATTGTGGCCGGGTAGGCTG	0.662													C|||	103	0.0205671	0.0726	0.0072	5008	,	,		14500	0.0		0.002	False		,,,				2504	0.0				p.P754P		Atlas-SNP	.											LIPE,rectum,carcinoma,-1,1	LIPE	83	1	0			c.G2262A						PASS	.	C		229,4177	131.4+/-167.9	6,217,1980	47	45	45		2262	-10.2	0.1	19	dbSNP_125	45	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous	LIPE	NM_005357.2		6,227,6270	TT,TC,CC		0.1163,5.1975,1.8376		754/1077	42910416	239,12767	2203	4300	6503	SO:0001819	synonymous_variant	3991	exon7			TGTGGCCGGGTAG	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.2262G>A	19.37:g.42910416C>T		92	0	0		124	56	0.451613	NM_005357	Q3LRT2|Q6NSL7	Silent	SNP	ENST00000244289.4	37	CCDS12607.1																																																																																			C|0.978;T|0.022	0.022	strong		0.662	LIPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463861.1	NM_005357		T	42910416	C	T	42910416	2	4	22	1	0	0	0	0	0	0	0	1	8830	639	23	1		1	LIPE	19	42910416	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3502	42910416	16218567	3971	6872											
LIPE	3991	hgsc.bcm.edu	37	chr19	42931004	42931004	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagcagcaccctttggatgtAaggtgattgctgtggtgcgg	7	11	16	7	1	0	1	0	1	0	0	0	3	0	2	1	4	4	4	1	4	1	3	rs16975750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42931004A>G	ENST00000244289.4	-	1	574	c.298T>C	c.(298-300)Tac>Cac	p.Y100H	LIPE-AS1_ENST00000457234.2_RNA|LIPE-AS1_ENST00000593740.2_RNA|LIPE-AS1_ENST00000594624.2_RNA|LIPE-AS1_ENST00000597203.1_RNA|CTB-50E14.4_ENST00000596781.1_RNA|LIPE-AS1_ENST00000594688.1_RNA	NM_005357.2	NP_005348.2	Q05469	LIPS_HUMAN	lipase, hormone-sensitive	100			Y -> H (in dbSNP:rs16975750). {ECO:0000269|Ref.3}.		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)				CTTTGGATGTAAGGTGATTGC	0.502													G|||	393	0.0784744	0.2799	0.0288	5008	,	,		19320	0.0		0.003	False		,,,				2504	0.0				p.Y100H		Atlas-SNP	.											.	LIPE	83	.	0			c.T298C						PASS	.	G	HIS/TYR	997,3409	730.3+/-410.1	128,741,1334	167	172	171		298	-1.8	0	19	dbSNP_123	171	18,8582	818.6+/-406.8	0,18,4282	yes	missense	LIPE	NM_005357.2	83	128,759,5616	GG,GA,AA		0.2093,22.6282,7.8041	benign	100/1077	42931004	1015,11991	2203	4300	6503	SO:0001583	missense	3991	exon1			GGATGTAAGGTGA	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.298T>C	19.37:g.42931004A>G	ENSP00000244289:p.Tyr100His	434	1	0.00230415		434	193	0.4447	NM_005357	Q3LRT2|Q6NSL7	Missense_Mutation	SNP	ENST00000244289.4	37	CCDS12607.1	152	0.0695970695970696	136	0.2764227642276423	13	0.03591160220994475	0	0.0	3	0.00395778364116095	G	0.044	-1.272008	0.01421	0.226282	0.002093	ENSG00000079435	ENST00000244289	T	0.21361	2.01	4.4	-1.76	0.08006	.	0.581795	0.14398	N	0.322096	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42327	-0.9458	9	0.12430	T	0.62	-3.0127	1.9171	0.03299	0.4826:0.1392:0.2367:0.1415	rs16975750;rs52836316;rs58365984;rs16975750	100	Q05469	LIPS_HUMAN	H	100	ENSP00000244289:Y100H	ENSP00000244289:Y100H	Y	-	1	0	LIPE	47622844	0.018000	0.18449	0.025000	0.17156	0.087000	0.18053	-0.426000	0.07008	-0.446000	0.07149	-0.213000	0.12676	TAC	A|0.915;G|0.085	0.085	strong		0.502	LIPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463861.1	NM_005357		G	42931004	A	G	42931004	3	3	22	1	0	0	0	0	1	0	0	0	8830	362	13	3	2972	3	LIPE	19	42931004	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	20588	42931004	16197979	3972	6873											
CEACAM1	634	hgsc.bcm.edu	37	chr19	43031369	43031369	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tagcttgttgagttcctattGcatatcctacaatttgacgg	9	16	8	8	1	0	2	0	2	0	0	2	2	2	2	2	1	3	4	2	1	5	9	rs8110904	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43031369G>A	ENST00000161559.6	-	2	382	c.248C>T	c.(247-249)gCa>gTa	p.A83V	CEACAM1_ENST00000358394.3_Missense_Mutation_p.A83V|LIPE-AS1_ENST00000457234.2_RNA|CEACAM1_ENST00000403461.1_Missense_Mutation_p.A83V|LIPE-AS1_ENST00000594624.2_RNA|CEACAM1_ENST00000308072.4_Missense_Mutation_p.A43V|CEACAM1_ENST00000599389.1_Missense_Mutation_p.A83V|CEACAM1_ENST00000352591.5_Missense_Mutation_p.A83V|CEACAM1_ENST00000403444.3_Missense_Mutation_p.A83V|LIPE-AS1_ENST00000594688.1_RNA|CEACAM1_ENST00000351134.3_Missense_Mutation_p.A83V	NM_001712.4	NP_001703.2	P13688	CEAM1_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein)	83	Ig-like V-type.		A -> V (in dbSNP:rs8110904). {ECO:0000269|Ref.9}.		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)	AGTTCCTATTGCATATCCTAC	0.507													a|||	526	0.105032	0.3707	0.0447	5008	,	,		20268	0.0		0.005	False		,,,				2504	0.0				p.A83V		Atlas-SNP	.											.	CEACAM1	43	.	0			c.C248T						PASS	.	A	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	1359,3047		96,1167,940	318	255	276		248,248,248,248,248,248	-6.2	0	19	dbSNP_116	276	22,8578		0,22,4278	yes	missense,missense,missense,missense,missense,missense	CEACAM1	NM_001024912.2,NM_001184813.1,NM_001184815.1,NM_001184816.1,NM_001205344.1,NM_001712.4	64,64,64,64,64,64	96,1189,5218	AA,AG,GG		0.2558,30.8443,10.6182	benign,benign,benign,benign,benign,benign	83/465,83/431,83/462,83/369,83/469,83/527	43031369	1381,11625	2203	4300	6503	SO:0001583	missense	634	exon2			CCTATTGCATATC	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.248C>T	19.37:g.43031369G>A	ENSP00000161559:p.Ala83Val	449	1	0.00222717		456	238	0.52193	NM_001184816	A6NE38|A8MY49|O60430|Q069I7|Q13854|Q13857|Q13858|Q13859|Q13860|Q15600|Q15601|Q16170|Q5UB49|Q7KYP5|Q96CA7|Q9UQV9	Missense_Mutation	SNP	ENST00000161559.6	37	CCDS12609.1	199	0.09111721611721611	176	0.35772357723577236	18	0.049723756906077346	0	0.0	5	0.006596306068601583	a	0.459	-0.889785	0.02511	0.308443	0.002558	ENSG00000079385	ENST00000161559;ENST00000358394;ENST00000351134;ENST00000446434;ENST00000378065;ENST00000352591;ENST00000403444;ENST00000403461;ENST00000308072;ENST00000377806;ENST00000344391;ENST00000403136	T;T;T;T;T;T;T	0.62639	0.01;0.01;0.01;0.01;0.01;0.01;0.01	3.76	-6.23	0.02052	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.00053	-2.39	0.80722	P	0.0	B;B;B;B;B;B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.0;0.001;0.001;0.0;0.0;0.0	B;B;B;B;B;B;B;B;B;B	0.08055	0.002;0.001;0.0;0.001;0.001;0.003;0.002;0.001;0.001;0.001	T	0.04140	-1.0974	8	0.02654	T	1	.	2.5662	0.04784	0.2081:0.1227:0.4308:0.2384	rs8110904;rs10408262;rs12979523;rs60053543;rs8110904	83;83;83;83;83;83;83;83;83;83	P13688-7;P13688-10;P13688-3;P13688-4;P13688-2;P13688-11;P13688-6;P13688-5;P13688-8;P13688	.;.;.;.;.;.;.;.;.;CEAM1_HUMAN	V	83;83;83;110;43;83;83;83;43;83;83;83	ENSP00000161559:A83V;ENSP00000351165:A83V;ENSP00000325946:A83V;ENSP00000244291:A83V;ENSP00000384709:A83V;ENSP00000384083:A83V;ENSP00000312184:A43V	ENSP00000161559:A83V	A	-	2	0	CEACAM1	47723209	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.328000	0.00510	-2.234000	0.00715	-0.361000	0.07541	GCA	G|0.900;A|0.100	0.100	strong		0.507	CEACAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321190.2	NM_001712		A	43031369	G	A	43031369	3	1	22	1	0	0	0	0	1	0	0	0	3189	1319	46	2	1461	2	CEACAM1	19	43031369	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	100365	43031369	16097614	3973	6874											
CEACAM1	634	hgsc.bcm.edu	37	chr19	43031514	43031514	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	catggattcagtagtgagctGggcagtggtgggcgggttcc	6	10	18	7	1	1	1	1	1	0	0	2	2	2	2	1	5	1	4	1	5	1	3	rs8111171	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43031514G>T	ENST00000161559.6	-	2	237	c.103C>A	c.(103-105)Cag>Aag	p.Q35K	CEACAM1_ENST00000358394.3_Missense_Mutation_p.Q35K|LIPE-AS1_ENST00000457234.2_RNA|CEACAM1_ENST00000403461.1_Missense_Mutation_p.Q35K|LIPE-AS1_ENST00000594624.2_RNA|CEACAM1_ENST00000308072.4_5'UTR|CEACAM1_ENST00000599389.1_Missense_Mutation_p.Q35K|CEACAM1_ENST00000352591.5_Missense_Mutation_p.Q35K|CEACAM1_ENST00000403444.3_Missense_Mutation_p.Q35K|LIPE-AS1_ENST00000594688.1_RNA|CEACAM1_ENST00000351134.3_Missense_Mutation_p.Q35K	NM_001712.4	NP_001703.2	P13688	CEAM1_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein)	35	Ig-like V-type.		Q -> K (in dbSNP:rs8111171). {ECO:0000269|Ref.9}.		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)	GTAGTGAGCTGGGCAGTGGTG	0.502													g|||	596	0.11901	0.4228	0.0461	5008	,	,		19075	0.0		0.005	False		,,,				2504	0.0				p.Q35K		Atlas-SNP	.											.	CEACAM1	43	.	0			c.C103A						PASS	.	G	LYS/GLN,LYS/GLN,LYS/GLN,LYS/GLN,LYS/GLN,LYS/GLN	1556,2850	488.5+/-361.2	290,976,937	140	134	136		103,103,103,103,103,103	-0.2	0	19	dbSNP_116	136	22,8578	12.6+/-44.7	0,22,4278	yes	missense,missense,missense,missense,missense,missense	CEACAM1	NM_001024912.2,NM_001184813.1,NM_001184815.1,NM_001184816.1,NM_001205344.1,NM_001712.4	53,53,53,53,53,53	290,998,5215	TT,TG,GG		0.2558,35.3155,12.1329	benign,benign,benign,benign,benign,benign	35/465,35/431,35/462,35/369,35/469,35/527	43031514	1578,11428	2203	4300	6503	SO:0001583	missense	634	exon2			TGAGCTGGGCAGT	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.103C>A	19.37:g.43031514G>T	ENSP00000161559:p.Gln35Lys	214	0	0		219	124	0.56621	NM_001184816	A6NE38|A8MY49|O60430|Q069I7|Q13854|Q13857|Q13858|Q13859|Q13860|Q15600|Q15601|Q16170|Q5UB49|Q7KYP5|Q96CA7|Q9UQV9	Missense_Mutation	SNP	ENST00000161559.6	37	CCDS12609.1	220	0.10073260073260074	196	0.3983739837398374	19	0.052486187845303865	0	0.0	5	0.006596306068601583	g	11.90	1.776621	0.31411	0.353155	0.002558	ENSG00000079385	ENST00000161559;ENST00000358394;ENST00000351134;ENST00000446434;ENST00000352591;ENST00000403444;ENST00000403461;ENST00000377806;ENST00000344391;ENST00000403136	T;T;T;T;T;T	0.01647	4.71;4.71;4.71;4.71;4.71;4.71	3.6	-0.184	0.13280	Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.49778	1.585	0.58432	P	2.9999999999752447E-6	B;B;B;B;B;B;B;B;B;B	0.22983	0.004;0.009;0.001;0.001;0.002;0.001;0.039;0.009;0.078;0.047	B;B;B;B;B;B;B;B;B;B	0.20184	0.006;0.003;0.005;0.003;0.002;0.004;0.028;0.008;0.015;0.027	T	0.36065	-0.9763	8	0.38643	T	0.18	.	6.2066	0.20606	0.0:0.3764:0.4131:0.2105	rs8111171;rs59246809	35;35;35;35;35;35;35;35;35;35	P13688-7;P13688-10;P13688-3;P13688-4;P13688-2;P13688-11;P13688-6;P13688-5;P13688-8;P13688	.;.;.;.;.;.;.;.;.;CEAM1_HUMAN	K	35;35;35;62;35;35;35;35;35;35	ENSP00000161559:Q35K;ENSP00000351165:Q35K;ENSP00000325946:Q35K;ENSP00000244291:Q35K;ENSP00000384709:Q35K;ENSP00000384083:Q35K	ENSP00000161559:Q35K	Q	-	1	0	CEACAM1	47723354	0.691000	0.27709	0.001000	0.08648	0.306000	0.27790	0.186000	0.16978	0.061000	0.16311	0.491000	0.48974	CAG	G|0.888;T|0.112	0.112	strong		0.502	CEACAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321190.2	NM_001712		T	43031514	G	T	43031514	3	4	22	1	0	0	0	0	1	0	0	0	3189	1357	47	4	1606	4	CEACAM1	19	43031514	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	145	43031514	16097469	3974	6875											
CEACAM8	1088	hgsc.bcm.edu	37	chr19	43087428	43087428	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaccctggccagtactccAatcatgatgctgacagtggc	9	8	10	14	0	1	2	1	2	0	0	2	2	2	2	4	2	2	2	4	2	2	1	rs8103051	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43087428A>C	ENST00000244336.5	-	5	1121	c.1020T>G	c.(1018-1020)atT>atG	p.I340M	LIPE-AS1_ENST00000594624.2_RNA|CEACAM8_ENST00000599005.1_Missense_Mutation_p.I42M|LIPE-AS1_ENST00000594688.1_RNA	NM_001816.3	NP_001807.2	P31997	CEAM8_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 8	340			I -> M (in dbSNP:rs8103051).		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)				CCAGTACTCCAATCATGATGC	0.458													A|||	359	0.0716853	0.2572	0.0231	5008	,	,		21532	0.0		0.003	False		,,,				2504	0.0				p.I340M		Atlas-SNP	.											.	CEACAM8	44	.	0			c.T1020G						PASS	.	A	MET/ILE	878,3528	342.0+/-307.0	92,694,1417	99	89	93		1020	0.6	0.1	19	dbSNP_116	93	18,8582	10.5+/-38.8	0,18,4282	no	missense	CEACAM8	NM_001816.3	10	92,712,5699	CC,CA,AA		0.2093,19.9274,6.8891	probably-damaging	340/350	43087428	896,12110	2203	4300	6503	SO:0001583	missense	1088	exon5			TACTCCAATCATG	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.1020T>G	19.37:g.43087428A>C	ENSP00000244336:p.Ile340Met	323	0	0		318	157	0.493711	NM_001816	O60399|Q16574	Missense_Mutation	SNP	ENST00000244336.5	37	CCDS12610.1	124	0.056776556776556776	110	0.22357723577235772	11	0.03038674033149171	0	0.0	3	0.00395778364116095	a	11.22	1.574497	0.28092	0.199274	0.002093	ENSG00000124469	ENST00000244336	T	0.21734	1.99	1.7	0.575	0.17374	.	.	.	.	.	T	0.00039	0.0001	M	0.78049	2.395	0.80722	P	0.0	D	0.76494	0.999	D	0.63488	0.915	T	0.05750	-1.0866	8	0.87932	D	0	.	3.7257	0.08474	0.6637:0.0:0.0:0.3363	rs8103051;rs8103051	340	P31997	CEAM8_HUMAN	M	340	ENSP00000244336:I340M	ENSP00000244336:I340M	I	-	3	3	CEACAM8	47779268	0.002000	0.14202	0.069000	0.20011	0.113000	0.19764	-0.125000	0.10579	0.101000	0.17610	0.254000	0.18369	ATT	A|0.937;C|0.063	0.063	strong		0.458	CEACAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321430.1			C	43087428	A	C	43087428	3	2	22	1	0	0	0	0	1	0	0	0	3200	126	5	5	33	5	CEACAM8	19	43087428	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	55914	43087428	16041555	3975	6876											
CEACAM8	1088	hgsc.bcm.edu	37	chr19	43093718	43093718	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	acactgagtagagtgagggtCctgttgccattggacagctg	9	10	14	8	0	0	3	0	2	0	1	1	4	1	4	2	2	2	3	2	2	1	3	rs10413332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43093718C>T	ENST00000244336.5	-	3	695	c.594G>A	c.(592-594)agG>agA	p.R198R	LIPE-AS1_ENST00000594624.2_RNA|CEACAM8_ENST00000599005.1_Intron|LIPE-AS1_ENST00000594688.1_RNA	NM_001816.3	NP_001807.2	P31997	CEAM8_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 8	198	Ig-like C2-type 1.				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)				GAGTGAGGGTCCTGTTGCCAT	0.522													C|||	355	0.0708866	0.2542	0.0231	5008	,	,		18633	0.0		0.003	False		,,,				2504	0.0				p.R198R		Atlas-SNP	.											.	CEACAM8	44	.	0			c.G594A						PASS	.	C		874,3532	341.2+/-306.6	92,690,1421	271	241	251		594	1.3	0.6	19	dbSNP_119	251	18,8582	10.5+/-38.8	0,18,4282	no	coding-synonymous	CEACAM8	NM_001816.3		92,708,5703	TT,TC,CC		0.2093,19.8366,6.8584		198/350	43093718	892,12114	2203	4300	6503	SO:0001819	synonymous_variant	1088	exon3			GAGGGTCCTGTTG	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.594G>A	19.37:g.43093718C>T		243	0	0		291	123	0.42268	NM_001816	O60399|Q16574	Silent	SNP	ENST00000244336.5	37	CCDS12610.1																																																																																			C|0.938;T|0.062	0.062	strong		0.522	CEACAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321430.1			T	43093718	C	T	43093718	2	4	22	1	0	0	0	0	0	0	0	1	3200	854	30	2		2	CEACAM8	19	43093718	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6290	43093718	16035265	3976	6877											
CEACAM8	1088	hgsc.bcm.edu	37	chr19	43093793	43093793	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acccaccacaggtaggttgtGttctgagtctcaggttcaca	9	11	10	11	0	3	1	2	1	2	0	4	1	3	1	2	3	0	4	2	3	1	4	rs10418988	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43093793G>A	ENST00000244336.5	-	3	620	c.519C>T	c.(517-519)aaC>aaT	p.N173N	LIPE-AS1_ENST00000594624.2_RNA|CEACAM8_ENST00000599005.1_Intron|LIPE-AS1_ENST00000594688.1_RNA	NM_001816.3	NP_001807.2	P31997	CEAM8_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 8	173	Ig-like C2-type 1.				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)				GGTAGGTTGTGTTCTGAGTCT	0.567													G|||	102	0.0203674	0.0719	0.0072	5008	,	,		17179	0.0		0.002	False		,,,				2504	0.0				p.N173N		Atlas-SNP	.											.	CEACAM8	44	.	0			c.C519T						PASS	.	G		240,4166	141.5+/-176.9	6,228,1969	220	192	201		519	1.4	0.5	19	dbSNP_119	201	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous	CEACAM8	NM_001816.3		6,239,6258	AA,AG,GG		0.1279,5.4471,1.9299		173/350	43093793	251,12755	2203	4300	6503	SO:0001819	synonymous_variant	1088	exon3			GGTTGTGTTCTGA	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.519C>T	19.37:g.43093793G>A		206	0	0		231	104	0.450216	NM_001816	O60399|Q16574	Silent	SNP	ENST00000244336.5	37	CCDS12610.1																																																																																			G|0.977;A|0.023	0.023	strong		0.567	CEACAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321430.1			A	43093793	G	A	43093793	2	1	22	1	0	0	0	0	0	0	0	1	3200	1368	48	2		2	CEACAM8	19	43093793	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	75	43093793	16035190	3977	6878											
CEACAM8	1088	hgsc.bcm.edu	37	chr19	43098931	43098931	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cctcacctgtgagcaggagcCcctgccaggggatgcgccat	7	6	13	15	1	1	1	1	1	0	0	1	3	1	3	6	3	4	1	6	3	0	0	rs28367882	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43098931C>A	ENST00000244336.5	-	1	151	c.50G>T	c.(49-51)gGg>gTg	p.G17V	LIPE-AS1_ENST00000594624.2_RNA|CEACAM8_ENST00000599005.1_Missense_Mutation_p.G17V|LIPE-AS1_ENST00000594688.1_RNA	NM_001816.3	NP_001807.2	P31997	CEAM8_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 8	17			G -> V (in dbSNP:rs28367882).		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)				GAGCAGGAGCCCCTGCCAGGG	0.632													.|||	355	0.0708866	0.2542	0.0231	5008	,	,		18261	0.0		0.003	False		,,,				2504	0.0				p.G17V		Atlas-SNP	.											.	CEACAM8	44	.	0			c.G50T						PASS	.	C	VAL/GLY	873,3533	340.5+/-306.2	92,689,1422	102	95	97		50	-0.8	0	19	dbSNP_125	97	18,8582	10.5+/-38.8	0,18,4282	no	missense	CEACAM8	NM_001816.3	109	92,707,5704	AA,AC,CC		0.2093,19.8139,6.8507	possibly-damaging	17/350	43098931	891,12115	2203	4300	6503	SO:0001583	missense	1088	exon1			AGGAGCCCCTGCC	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.50G>T	19.37:g.43098931C>A	ENSP00000244336:p.Gly17Val	85	0	0		64	33	0.515625	NM_001816	O60399|Q16574	Missense_Mutation	SNP	ENST00000244336.5	37	CCDS12610.1	124	0.056776556776556776	110	0.22357723577235772	11	0.03038674033149171	0	0.0	3	0.00395778364116095	c	6.456	0.452336	0.12283	0.198139	0.002093	ENSG00000124469	ENST00000244336	T	0.21031	2.03	1.48	-0.838	0.10762	.	.	.	.	.	T	0.00012	0.0000	M	0.88704	2.975	0.80722	P	0.0	P	0.40000	0.698	P	0.46758	0.526	T	0.05716	-1.0868	8	0.72032	D	0.01	.	4.0532	0.09804	0.0:0.5677:0.0:0.4323	rs28367882;rs59229803	17	P31997	CEAM8_HUMAN	V	17	ENSP00000244336:G17V	ENSP00000244336:G17V	G	-	2	0	CEACAM8	47790771	0.000000	0.05858	0.010000	0.14722	0.009000	0.06853	0.062000	0.14389	-0.173000	0.10761	-0.671000	0.03813	GGG	C|0.939;A|0.061	0.061	strong		0.632	CEACAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321430.1			A	43098931	C	A	43098931	3	1	22	1	0	0	0	0	1	0	0	0	3200	623	22	4	1019	4	CEACAM8	19	43098931	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	5138	43098931	16030052	3978	6879											
PSG3	5671	hgsc.bcm.edu	37	chr19	43237080	43237080	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caactgcaagctgtgagtcaTagggaggctctgaccattca	11	9	11	10	0	3	2	2	2	1	0	3	3	3	3	1	2	3	3	1	2	3	2	rs76931703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43237080T>C	ENST00000327495.5	-	3	749	c.565A>G	c.(565-567)Atg>Gtg	p.M189V	PSG3_ENST00000490592.1_5'Flank|PSG3_ENST00000595140.1_Missense_Mutation_p.M189V	NM_021016.3	NP_066296.2	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	189	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)				CTGTGAGTCATAGGGAGGCTC	0.498													.|||	53	0.0105831	0.0378	0.0043	5008	,	,		20000	0.0		0.0	False		,,,				2504	0.0				p.M189V		Atlas-SNP	.											.	PSG3	82	.	0			c.A565G						PASS	.	T	VAL/MET	167,4239		4,159,2040	240	239	239		565	-1.4	0	19	dbSNP_131	239	1,8599		0,1,4299	yes	missense	PSG3	NM_021016.3	21	4,160,6339	CC,CT,TT		0.0116,3.7903,1.2917	benign	189/429	43237080	168,12838	2203	4300	6503	SO:0001583	missense	5671	exon3			GAGTCATAGGGAG		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.565A>G	19.37:g.43237080T>C	ENSP00000332215:p.Met189Val	237	0	0		235	116	0.493617	NM_021016	Q08265|Q9BRW2|Q9UPL4|Q9UQ77	Missense_Mutation	SNP	ENST00000327495.5	37	CCDS12611.1	20	0.009157509157509158	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	0	0.0	-	0.003	-2.475018	0.00167	0.037903	1.16E-4	ENSG00000221826	ENST00000327495	T	0.08458	3.09	1.59	-1.36	0.09085	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00524	0.0017	N	0.02275	-0.615	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.41752	-0.9491	9	0.02654	T	1	.	4.1694	0.10322	0.0:0.5437:0.0:0.4563	.	167;189	Q08266;Q16557	.;PSG3_HUMAN	V	189	ENSP00000332215:M189V	ENSP00000332215:M189V	M	-	1	0	PSG3	47928920	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.084000	0.03393	-0.464000	0.06963	-0.562000	0.04174	ATG	T|0.988;C|0.012	0.012	strong		0.498	PSG3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321423.2	NM_021016		C	43237080	T	C	43237080	3	2	22	1	0	0	0	0	1	0	0	0	12668	1406	49	3	737	3	PSG3	19	43237080	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	138149	43237080	15891903	3979	6880											
PSG8	440533	hgsc.bcm.edu	37	chr19	43268242	43268242	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccatatataattatttgacCgtctactacatatgatgtaa	14	15	4	8	1	1	2	0	2	1	0	1	2	1	2	2	0	2	1	2	0	8	9	rs76352186	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43268242C>T	ENST00000306511.4	-	2	353	c.256G>A	c.(256-258)Ggt>Agt	p.G86S	PSG8_ENST00000406636.3_Intron|PSG8_ENST00000404209.4_Missense_Mutation_p.G86S|PSG8_ENST00000401467.2_Missense_Mutation_p.G86S	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	86	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)				ATTATTTGACCGTCTACTACA	0.433													.|||	285	0.0569089	0.1952	0.0202	5008	,	,		22232	0.0		0.006	False		,,,				2504	0.0072				p.G86S		Atlas-SNP	.											.	PSG8	101	.	0			c.G256A						PASS	.	T	SER/GLY,,SER/GLY	772,3634	311.9+/-292.3	84,604,1515	248	265	259		256,,256	-2.7	0	19	dbSNP_131	259	131,8467	67.3+/-129.8	1,129,4169	no	missense,intron,missense	PSG8	NM_001130167.1,NM_001130168.1,NM_182707.2	56,,56	85,733,5684	TT,TC,CC		1.5236,17.5216,6.944	benign,,benign	86/420,,86/427	43268242	903,12101	2203	4299	6502	SO:0001583	missense	440533	exon2			TTTGACCGTCTAC	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.256G>A	19.37:g.43268242C>T	ENSP00000305005:p.Gly86Ser	247	1	0.00404858		233	98	0.420601	NM_001130167	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Missense_Mutation	SNP	ENST00000306511.4	37	CCDS33037.1	126	0.057692307692307696	112	0.22764227642276422	8	0.022099447513812154	0	0.0	6	0.0079155672823219	c	0.005	-2.167646	0.00315	0.175216	0.015236	ENSG00000124467	ENST00000404209;ENST00000401467;ENST00000407488;ENST00000306511	T;T;T	0.63913	-0.07;-0.07;-0.07	1.35	-2.7	0.06004	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.15975	0.35	0.80722	P	0.0	B;B;B;B;B	0.20780	0.002;0.003;0.048;0.001;0.001	B;B;B;B;B	0.23018	0.004;0.011;0.043;0.005;0.009	T	0.06303	-1.0834	8	0.08599	T	0.76	.	5.2757	0.15649	0.0:0.4599:0.1655:0.3746	.	86;86;86;86;86	B5MCQ0;Q9UQ74;E7ENH0;Q9UQ74-3;A5PKV3	.;PSG8_HUMAN;.;.;.	S	86	ENSP00000385869:G86S;ENSP00000386090:G86S;ENSP00000305005:G86S	ENSP00000305005:G86S	G	-	1	0	PSG8	47960082	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.991000	0.01478	-3.700000	0.00119	-2.741000	0.00127	GGT	C|0.936;T|0.064	0.064	strong		0.433	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1			T	43268242	C	T	43268242	3	4	22	1	0	0	0	0	1	0	0	0	12673	652	23	1	1061	1	PSG8	19	43268242	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	31162	43268242	15860741	3980	6881											
PSG8	440533	hgsc.bcm.edu	37	chr19	43269686	43269686	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacctgtgagcaggagcccCttccaggtgatgcgctgtgt	6	10	13	12	1	1	2	1	2	0	0	2	3	2	3	4	2	3	2	4	2	0	1	rs61393109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43269686C>T	ENST00000306511.4	-	1	145	c.48G>A	c.(46-48)aaG>aaA	p.K16K	PSG8_ENST00000406636.3_Silent_p.K16K|PSG8_ENST00000404209.4_Silent_p.K16K|PSG8_ENST00000401467.2_Intron	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	16						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)				GCAGGAGCCCCTTCCAGGTGA	0.577													.|||	54	0.0107827	0.0386	0.0043	5008	,	,		18083	0.0		0.0	False		,,,				2504	0.0				p.K16K		Atlas-SNP	.											.	PSG8	101	.	0			c.G48A						PASS	.	C	,,	106,2916		3,100,1408	111	113	112		48,48,48	-2	0	19	dbSNP_129	112	1,5417		0,1,2708	no	coding-synonymous,coding-synonymous,coding-synonymous	PSG8	NM_001130167.1,NM_001130168.1,NM_182707.2	,,	3,101,4116	TT,TC,CC		0.0185,3.5076,1.2678	,,	16/420,16/298,16/427	43269686	107,8333	1511	2709	4220	SO:0001819	synonymous_variant	440533	exon1			GAGCCCCTTCCAG	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.48G>A	19.37:g.43269686C>T		31	0	0		43	20	0.465116	NM_001130168	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Silent	SNP	ENST00000306511.4	37	CCDS33037.1																																																																																			C|0.988;T|0.012	0.012	strong		0.577	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1			T	43269686	C	T	43269686	2	4	22	1	0	0	0	0	0	0	0	1	12673	680	24	2		2	PSG8	19	43269686	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1444	43269686	15859297	3981	6882											
PSG6	5675	hgsc.bcm.edu	37	chr19	43411150	43411150	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acagagcaagcatagagcccGctatgatttgtagtaatttg	13	11	10	7	1	0	3	0	1	0	2	0	3	0	3	1	0	3	5	1	0	5	6	rs78024453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43411150G>A	ENST00000292125.2	-	5	1208	c.1164C>T	c.(1162-1164)agC>agT	p.S388S	PSG6_ENST00000187910.2_Silent_p.S388S|PSG6_ENST00000402603.4_Silent_p.S295S	NM_002782.4	NP_002773.1	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6	388	Ig-like C2-type 3.				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)				CATAGAGCCCGCTATGATTTG	0.458													.|||	116	0.0231629	0.0825	0.0101	5008	,	,		19776	0.0		0.0	False		,,,				2504	0.0				p.S388S		Atlas-SNP	.											.	PSG6	89	.	0			c.C1164T						PASS	.	T	,	343,4059		23,297,1881	192	203	199		1164,1164	-3.1	0	19	dbSNP_131	199	2,8596		0,2,4297	no	coding-synonymous,coding-synonymous	PSG6	NM_001031850.2,NM_002782.3	,	23,299,6178	AA,AG,GG		0.0233,7.7919,2.6538	,	388/425,388/436	43411150	345,12655	2201	4299	6500	SO:0001819	synonymous_variant	5675	exon5			GAGCCCGCTATGA		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.1164C>T	19.37:g.43411150G>A		199	0	0		171	70	0.409357	NM_001031850	O75244|Q15224|Q15235|Q549K1	Silent	SNP	ENST00000292125.2	37	CCDS12613.1																																																																																			G|0.976;A|0.024	0.024	strong		0.458	PSG6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321436.1	NM_002782		A	43411150	G	A	43411150	2	1	22	1	0	0	0	0	0	0	0	1	12671	1078	38	1		1	PSG6	19	43411150	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	141464	43411150	15717833	3982	6883											
PSG6	5675	hgsc.bcm.edu	37	chr19	43414875	43414875	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagctgcaacctgtgagtcAtagggaggttctgaccattc	10	10	11	10	0	2	2	1	2	1	0	3	3	2	3	2	2	3	3	2	2	2	3	rs59587483	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43414875A>C	ENST00000292125.2	-	3	607	c.563T>G	c.(562-564)aTg>aGg	p.M188R	PSG6_ENST00000187910.2_Missense_Mutation_p.M188R|PSG6_ENST00000402603.4_Missense_Mutation_p.M188R	NM_002782.4	NP_002773.1	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6	188	Ig-like C2-type 1.		M -> R (in dbSNP:rs59587483).		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)				CCTGTGAGTCATAGGGAGGTT	0.488																																					p.M188R		Atlas-SNP	.											.	PSG6	89	.	0			c.T563G						PASS	.	G	ARG/MET,ARG/MET	490,3912		33,424,1744	229	231	230		563,563	-3.3	0	19	dbSNP_129	230	4,8596		0,4,4296	yes	missense,missense	PSG6	NM_001031850.2,NM_002782.3	91,91	33,428,6040	CC,CA,AA		0.0465,11.1313,3.7994	,	188/425,188/436	43414875	494,12508	2201	4300	6501	SO:0001583	missense	5675	exon3			TGAGTCATAGGGA		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.563T>G	19.37:g.43414875A>C	ENSP00000292125:p.Met188Arg	278	0	0		294	133	0.452381	NM_001031850	O75244|Q15224|Q15235|Q549K1	Missense_Mutation	SNP	ENST00000292125.2	37	CCDS12613.1	74	0.03388278388278388	67	0.13617886178861788	5	0.013812154696132596	2	0.0034965034965034965	0	0.0	N	0.033	-1.323644	0.01309	0.111313	4.65E-4	ENSG00000170848	ENST00000187910;ENST00000402603;ENST00000292125;ENST00000402456	T;T;T	0.00705	5.81;5.81;5.81	1.64	-3.28	0.05033	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;B;B	0.30973	0.018;0.074;0.302	B;B;B	0.28709	0.048;0.056;0.093	T	0.42361	-0.9456	8	0.51188	T	0.08	.	2.1928	0.03904	0.4901:0.193:0.0:0.3168	rs59587483	188;188;188	Q00889;Q00889-2;B5MCE1	PSG6_HUMAN;.;.	R	188	ENSP00000187910:M188R;ENSP00000385736:M188R;ENSP00000292125:M188R	ENSP00000187910:M188R	M	-	2	0	PSG6	48106715	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.991000	0.00318	-0.913000	0.03832	-1.229000	0.01577	ATG	A|0.960;C|0.040	0.040	strong		0.488	PSG6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321436.1	NM_002782		C	43414875	A	C	43414875	3	2	22	1	0	0	0	0	1	0	0	0	12671	217	8	5	799	5	PSG6	19	43414875	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	3725	43414875	15714108	3983	6884											
PSG6	5675	hgsc.bcm.edu	37	chr19	43420290	43420290	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactcacagtataaggtgacAgtgaaatatccagttactcc	14	10	7	10	0	1	2	1	2	0	0	3	2	3	2	2	1	1	2	2	1	5	4	rs76022539	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43420290A>G	ENST00000292125.2	-	2	458	c.414T>C	c.(412-414)acT>acC	p.T138T	PSG6_ENST00000601833.1_Silent_p.T67T|PSG6_ENST00000187910.2_Silent_p.T138T|PSG6_ENST00000402603.4_Silent_p.T138T	NM_002782.4	NP_002773.1	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6	138	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)				ATAAGGTGACAGTGAAATATC	0.512													.|||	179	0.0357428	0.1225	0.0101	5008	,	,		19988	0.0089		0.0	False		,,,				2504	0.001				p.T138T		Atlas-SNP	.											.	PSG6	89	.	0			c.T414C						PASS	.	G	,	501,3901		35,431,1735	253	220	231		414,414	0.1	0	19	dbSNP_131	231	4,8594		0,4,4295	no	coding-synonymous,coding-synonymous	PSG6	NM_001031850.2,NM_002782.3	,	35,435,6030	GG,GA,AA		0.0465,11.3812,3.8846	,	138/425,138/436	43420290	505,12495	2201	4299	6500	SO:0001819	synonymous_variant	5675	exon2			GGTGACAGTGAAA		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.414T>C	19.37:g.43420290A>G		207	0	0		176	89	0.505682	NM_001031850	O75244|Q15224|Q15235|Q549K1	Silent	SNP	ENST00000292125.2	37	CCDS12613.1																																																																																			A|0.961;G|0.039	0.039	strong		0.512	PSG6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321436.1	NM_002782		G	43420290	A	G	43420290	2	3	22	1	0	0	0	0	0	0	0	1	12671	175	7	3		3	PSG6	19	43420290	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	5415	43420290	15708693	3984	6885											
PSG2	5670	hgsc.bcm.edu	37	chr19	43576029	43576029	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccggtgggttagagttcgCgaagcaagacaagtagaggt	11	8	16	6	3	0	3	0	0	0	3	1	4	0	3	1	3	2	4	1	3	5	3	rs112235686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43576029C>T	ENST00000406487.1	-	4	885	c.787G>A	c.(787-789)Gcg>Acg	p.A263T		NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	263	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)				TTAGAGTTCGCGAAGCAAGAC	0.438													C|||	8	0.00159744	0.0061	0.0	5008	,	,		20011	0.0		0.0	False		,,,				2504	0.0				p.A263T		Atlas-SNP	.											PSG2,colon,carcinoma,+1,2	PSG2	84	2	0			c.G787A						PASS	.	C	THR/ALA	27,4377	33.5+/-64.1	2,23,2177	180	191	187		787	0	0	19	dbSNP_132	187	10,8588	7.7+/-29.5	0,10,4289	yes	missense	PSG2	NM_031246.3	58	2,33,6466	TT,TC,CC		0.1163,0.6131,0.2846		263/336	43576029	37,12965	2202	4299	6501	SO:0001583	missense	5670	exon4			AGTTCGCGAAGCA		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.787G>A	19.37:g.43576029C>T	ENSP00000385706:p.Ala263Thr	194	0	0		195	89	0.45641	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Missense_Mutation	SNP	ENST00000406487.1	37	CCDS12616.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	c	1.983	-0.433771	0.04669	0.006131	0.001163	ENSG00000242221	ENST00000406487;ENST00000329509;ENST00000401942;ENST00000406917	T	0.15603	2.41	1.26	-0.0241	0.13940	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.10981	0.0268	M	0.73372	2.23	0.09310	N	1	B;B	0.22414	0.069;0.003	B;B	0.20767	0.031;0.022	T	0.35400	-0.9790	9	0.20519	T	0.43	.	3.758	0.08593	0.0:0.7179:0.0:0.2821	.	263;263	B5MCM8;P11465	.;PSG2_HUMAN	T	263	ENSP00000385706:A263T	ENSP00000332984:A263T	A	-	1	0	PSG2	48267869	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.248000	0.08854	-0.149000	0.11215	0.398000	0.26397	GCG	C|0.998;T|0.002	0.002	strong		0.438	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246		T	43576029	C	T	43576029	3	4	22	1	0	0	0	0	1	0	0	0	12667	768	27	1	228	1	PSG2	19	43576029	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	155739	43576029	15552954	3985	6886											
PSG2	5670	hgsc.bcm.edu	37	chr19	43585286	43585286	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atgtagccagtaagattctgGggcaaattgtggacaagtag	13	10	13	5	0	1	1	0	0	1	1	1	2	1	2	1	3	1	4	1	3	5	5			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43585286G>A	ENST00000406487.1	-	2	275	c.177C>T	c.(175-177)ccC>ccT	p.P59P	PSG2_ENST00000491995.1_5'Flank	NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	59	Ig-like V-type.				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)				TAAGATTCTGGGGCAAATTGT	0.458																																					p.P59P		Atlas-SNP	.											PSG2,colon,carcinoma,-2,4	PSG2	84	4	0			c.C177T						scavenged	.						113	116	115					19																	43585286		2203	4296	6499	SO:0001819	synonymous_variant	5670	exon2			ATTCTGGGGCAAA		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.177C>T	19.37:g.43585286G>A		314	0	0		357	15	0.0420168	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Silent	SNP	ENST00000406487.1	37	CCDS12616.1																																																																																			.	.	none		0.458	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246		A	43585286	G	A	43585286	2	1	22	1	0	0	0	0	0	0	0	1	12667	1219	43	2		2	PSG2	19	43585286	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	9257	43585286	15543697	3986	6887											
LYPD3	27076	hgsc.bcm.edu	37	chr19	43967423	43967423	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cactccacgccgttgggcggGtatgcactctcattacctgc	6	10	10	15	3	1	0	1	0	1	0	3	0	2	0	3	2	3	3	3	2	2	3	rs79420167	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43967423G>A	ENST00000244333.3	-	4	487	c.399C>T	c.(397-399)taC>taT	p.Y133Y		NM_014400.2	NP_055215.2	O95274	LYPD3_HUMAN	LY6/PLAUR domain containing 3	133					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)				CGTTGGGCGGGTATGCACTCT	0.647													G|||	52	0.0103834	0.0378	0.0029	5008	,	,		15418	0.0		0.0	False		,,,				2504	0.0				p.Y133Y		Atlas-SNP	.											.	LYPD3	24	.	0			c.C399T						PASS	.	G		130,4276	94.8+/-133.5	4,122,2077	49	46	47		399	-2.9	0	19	dbSNP_132	47	0,8600		0,0,4300	no	coding-synonymous	LYPD3	NM_014400.2		4,122,6377	AA,AG,GG		0.0,2.9505,0.9995		133/347	43967423	130,12876	2203	4300	6503	SO:0001819	synonymous_variant	27076	exon4			GGGCGGGTATGCA	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.399C>T	19.37:g.43967423G>A		18	0	0		34	15	0.441176	NM_014400	Q9UJ74	Silent	SNP	ENST00000244333.3	37	CCDS12620.1																																																																																			G|0.987;A|0.013	0.013	strong		0.647	LYPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463177.1	NM_014400		A	43967423	G	A	43967423	2	1	22	1	0	0	0	0	0	0	0	1	9120	1256	44	2		2	LYPD3	19	43967423	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	382137	43967423	15161560	3987	6888											
IRGQ	126298	hgsc.bcm.edu	37	chr19	44096772	44096772	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggaacactggcggcggcgcCtcctccagcacctcccacgt	6	5	12	18	4	0	0	0	0	0	0	3	1	3	1	5	4	2	1	5	4	1	0	rs114508854	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44096772C>T	ENST00000602269.1	-	2	1463	c.1278G>A	c.(1276-1278)gaG>gaA	p.E426E	IRGQ_ENST00000422989.1_Silent_p.E426E|L34079.2_ENST00000594374.1_Intron|IRGQ_ENST00000601520.1_Intron			Q8WZA9	IRGQ_HUMAN	immunity-related GTPase family, Q	426	IRG-type G.									endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(3)	18		Prostate(69;0.0199)				GCGGCGGCGCCTCCTCCAGCA	0.687													C|||	128	0.0255591	0.0613	0.0029	5008	,	,		13730	0.0308		0.0	False		,,,				2504	0.0143				p.E426E		Atlas-SNP	.											.	IRGQ	40	.	0			c.G1278A						PASS	.	C		173,4233	106.5+/-144.9	4,165,2034	39	44	42		1278	2	0.9	19	dbSNP_132	42	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	IRGQ	NM_001007561.2		4,169,6330	TT,TC,CC		0.0465,3.9265,1.3609		426/624	44096772	177,12829	2203	4300	6503	SO:0001819	synonymous_variant	126298	exon3			CGGCGCCTCCTCC	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.1278G>A	19.37:g.44096772C>T		21	0	0		26	13	0.5	NM_001007561	B2RNP3	Silent	SNP	ENST00000602269.1	37	CCDS33040.1																																																																																			C|0.981;T|0.019	0.019	strong		0.687	IRGQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463205.1	NM_001007561		T	44096772	C	T	44096772	2	4	22	1	0	0	0	0	0	0	0	1	7848	680	24	2		2	IRGQ	19	44096772	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	129349	44096772	15032211	3988	6889											
ZNF230	7773	hgsc.bcm.edu	37	chr19	44514859	44514859	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agtccacactggagagaaacCattcaaatgtgagcaatgtg	15	8	10	8	0	1	2	1	1	0	1	2	4	2	3	2	1	2	1	2	1	3	1	rs147553354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44514859C>T	ENST00000429154.2	+	5	896	c.668C>T	c.(667-669)cCa>cTa	p.P223L		NM_006300.3	NP_006291.2	Q9UIE0	ZN230_HUMAN	zinc finger protein 230	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)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(10)|skin(1)|stomach(3)|urinary_tract(2)	22		Prostate(69;0.0352)				GGAGAGAAACCATTCAAATGT	0.428													C|||	11	0.00219649	0.0083	0.0	5008	,	,		22817	0.0		0.0	False		,,,				2504	0.0				p.P223L	GBM(175;914 2069 22996 47111 52600)	Atlas-SNP	.											.	ZNF230	44	.	0			c.C668T						PASS	.	C	LEU/PRO	37,4369	40.0+/-72.8	0,37,2166	101	103	103		668	2.7	0.1	19	dbSNP_134	103	0,8600		0,0,4300	yes	missense	ZNF230	NM_006300.3	98	0,37,6466	TT,TC,CC		0.0,0.8398,0.2845	benign	223/475	44514859	37,12969	2203	4300	6503	SO:0001583	missense	7773	exon5			AGAAACCATTCAA	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.668C>T	19.37:g.44514859C>T	ENSP00000409318:p.Pro223Leu	110	0	0		120	50	0.416667	NM_006300	O15322|Q504X7|Q86W84|Q9P1U6	Missense_Mutation	SNP	ENST00000429154.2	37	CCDS33044.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	13.17	2.158672	0.38119	0.008398	0.0	ENSG00000159882	ENST00000429154	T	0.27557	1.66	2.67	2.67	0.31697	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.29256	0.0728	M	0.80422	2.495	0.80722	D	1	B	0.25105	0.118	B	0.26310	0.068	T	0.44697	-0.9311	9	0.66056	D	0.02	.	12.4612	0.55733	0.0:1.0:0.0:0.0	.	223	Q9UIE0	ZN230_HUMAN	L	223	ENSP00000409318:P223L	ENSP00000409318:P223L	P	+	2	0	ZNF230	49206699	0.016000	0.18221	0.064000	0.19789	0.067000	0.16453	1.315000	0.33608	1.468000	0.48064	0.407000	0.27541	CCA	C|0.998;T|0.002	0.002	strong		0.428	ZNF230-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460456.1			T	44514859	C	T	44514859	3	4	22	1	0	0	0	0	1	0	0	0	17799	594	21	2	682	2	ZNF230	19	44514859	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	418087	44514859	14614124	3989	6890											
ZNF284	342909	hgsc.bcm.edu	37	chr19	44590753	44590753	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacaaaccatataattgtaaTgtatgtgggaagggcttcag	14	11	11	5	0	1	0	1	0	0	0	1	2	1	1	1	2	1	3	1	2	6	6	rs114253786	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44590753T>C	ENST00000421176.3	+	5	1338	c.1122T>C	c.(1120-1122)aaT>aaC	p.N374N	ZNF223_ENST00000591793.1_3'UTR|RNU6-902P_ENST00000517212.1_RNA	NM_001037813.2	NP_001032902.1	Q2VY69	ZN284_HUMAN	zinc finger protein 284	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)			NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	15		Prostate(69;0.0435)				ATAATTGTAATGTATGTGGGA	0.433													T|||	24	0.00479233	0.0166	0.0029	5008	,	,		21791	0.0		0.0	False		,,,				2504	0.0				p.N374N		Atlas-SNP	.											.	ZNF284	38	.	0			c.T1122C						PASS	.	T		65,4171		0,65,2053	93	100	98		1122	-4.8	0	19	dbSNP_132	98	0,8480		0,0,4240	no	coding-synonymous	ZNF284	NM_001037813.2		0,65,6293	CC,CT,TT		0.0,1.5345,0.5112		374/594	44590753	65,12651	2118	4240	6358	SO:0001819	synonymous_variant	342909	exon5			TTGTAATGTATGT	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.1122T>C	19.37:g.44590753T>C		196	0	0		149	74	0.496644	NM_001037813	Q86WM1	Silent	SNP	ENST00000421176.3	37	CCDS46099.1																																																																																			T|0.995;C|0.005	0.005	strong		0.433	ZNF284-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460473.1	NM_001037813		C	44590753	T	C	44590753	2	2	22	1	0	0	0	0	0	0	0	1	17836	1461	51	3		3	ZNF284	19	44590753	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	75894	44590753	14538230	3990	6891											
ZNF285	26974	hgsc.bcm.edu	37	chr19	44891748	44891748	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgggccgcattacgttttTcaaccgttgatttcataccc	8	14	7	12	3	2	1	2	1	0	0	2	1	2	1	3	1	3	3	3	1	3	6	rs60800862	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44891748T>C	ENST00000330997.4	-	4	723	c.659A>G	c.(658-660)gAa>gGa	p.E220G	CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000591679.1_Missense_Mutation_p.E227G|ZNF285_ENST00000544719.2_Missense_Mutation_p.E220G	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	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(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						ATTACGTTTTTCAACCGTTGA	0.463													T|||	110	0.0219649	0.0809	0.0043	5008	,	,		19447	0.0		0.0	False		,,,				2504	0.0				p.E220G		Atlas-SNP	.											.	ZNF285	86	.	0			c.A659G						PASS	.	T	GLY/GLU	255,4151	145.4+/-180.2	6,243,1954	103	100	101		659	-0.2	0	19	dbSNP_129	101	1,8599		0,1,4299	yes	missense	ZNF285	NM_152354.3	98	6,244,6253	CC,CT,TT		0.0116,5.7876,1.9683		220/591	44891748	256,12750	2203	4300	6503	SO:0001583	missense	26974	exon4			CGTTTTTCAACCG	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.659A>G	19.37:g.44891748T>C	ENSP00000333595:p.Glu220Gly	134	0	0		133	60	0.451128	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Missense_Mutation	SNP	ENST00000330997.4	37	CCDS12638.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	T	6.112	0.388881	0.11581	0.057876	1.16E-4	ENSG00000062370	ENST00000544719;ENST00000330997	T	0.28454	1.61	3.27	-0.157	0.13387	.	.	.	.	.	T	0.01905	0.0060	L	0.38175	1.15	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.21075	-1.0256	9	0.24483	T	0.36	.	3.8075	0.08783	0.1682:0.3505:0.0:0.4813	rs60800862	244;220	B7ZLR9;Q96NJ3	.;ZN285_HUMAN	G	243;220	ENSP00000333595:E220G	ENSP00000333595:E220G	E	-	2	0	ZNF285	49583588	0.000000	0.05858	0.002000	0.10522	0.168000	0.22595	-0.057000	0.11768	0.046000	0.15833	0.373000	0.22412	GAA	T|0.983;C|0.017	0.017	strong		0.463	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354		C	44891748	T	C	44891748	3	2	22	1	0	0	0	0	1	0	0	0	17837	1783	62	3	1117	3	ZNF285	19	44891748	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	300995	44891748	14237235	3991	6892											
ZNF180	7733	hgsc.bcm.edu	37	chr19	45001398	45001398	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcttccatgctctcctccaGgcacagcagggtgctgaggt	6	10	11	14	0	2	1	0	1	2	0	5	1	4	1	3	3	3	4	3	3	0	1	rs10423647	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45001398G>A	ENST00000221327.4	-	2	351	c.70C>T	c.(70-72)Ctg>Ttg	p.L24L	ZNF180_ENST00000586637.1_5'UTR|ZNF180_ENST00000587047.1_Silent_p.A25A|ZNF180_ENST00000592529.1_5'UTR|ZNF180_ENST00000391956.4_Silent_p.L24L|ZNF180_ENST00000585514.1_5'UTR	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	24					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)				CTCTCCTCCAGGCACAGCAGG	0.622													G|||	453	0.0904553	0.3275	0.0173	5008	,	,		16153	0.0		0.004	False		,,,				2504	0.0041				p.L24L	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											.	ZNF180	103	.	0			c.C70T						PASS	.	G		1089,3317	389.3+/-327.3	128,833,1242	42	39	40		70	2.5	0.2	19	dbSNP_119	40	10,8590	5.7+/-21.5	0,10,4290	no	coding-synonymous	ZNF180	NM_013256.3		128,843,5532	AA,AG,GG		0.1163,24.7163,8.4499		24/693	45001398	1099,11907	2203	4300	6503	SO:0001819	synonymous_variant	7733	exon2			CCTCCAGGCACAG	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.70C>T	19.37:g.45001398G>A		32	0	0		44	20	0.454545	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Silent	SNP	ENST00000221327.4	37	CCDS12639.1																																																																																			G|0.906;A|0.094	0.094	strong		0.622	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256		A	45001398	G	A	45001398	2	1	22	1	0	0	0	0	0	0	0	1	17763	991	35	2		2	ZNF180	19	45001398	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	109650	45001398	14127585	3992	6893											
CEACAM20	125931	hgsc.bcm.edu	37	chr19	45017301	45017301	+	RNA	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgacagccaggatcccgaTgacaataccagcgatggccc	13	5	10	13	2	0	2	0	2	0	0	1	5	1	3	4	2	3	0	4	2	3	1	rs34921521	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45017301T>C	ENST00000454753.1	-	0	1635							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)				AGGATCCCGATGACAATACCA	0.567											OREG0025538	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	78	0.0155751	0.0575	0.0029	5008	,	,		15361	0.0		0.0	False		,,,				2504	0.0				p.I453V		Atlas-SNP	.											CEACAM20,NS,carcinoma,0,1	CEACAM20	31	1	0			c.A1357G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	166,3902		5,156,1873	76	76	76		1357,1078,1078,1357	-5.6	0	19	dbSNP_126	76	1,8347		0,1,4173	yes	missense,missense,missense,missense	CEACAM20	NM_001102597.1,NM_001102598.1,NM_001102599.1,NM_001102600.1	29,29,29,29	5,157,6046	CC,CT,TT		0.012,4.0806,1.345	benign,benign,benign,benign	453/597,360/492,360/504,453/585	45017301	167,12249	2034	4174	6208			125931	exon7			TCCCGATGACAAT	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		19.37:g.45017301T>C		67	0	0	928	81	37	0.45679	NM_001102600		Missense_Mutation	SNP	ENST00000454753.1	37																																																																																				T|0.986;C|0.014	0.014	strong		0.567	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444		C	45017301	T	C	45017301	1	2	22	0	1	0	0	0	0	0	0	0	3193	1464	51	3		3	CEACAM20	19	45017301	RNA	SNP	T	TCGA-G8-6324-01A-11D-2210-10	15903	45017301	14111682	3993	6894											
PVR	5817	hgsc.bcm.edu	37	chr19	45150763	45150763	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgttcgggttgcgcgtagaGgatgaaggcaactacacctg	10	9	14	8	3	0	2	0	1	0	1	1	3	0	3	1	3	3	4	1	3	4	4	rs10421291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45150763G>A	ENST00000425690.3	+	2	647	c.348G>A	c.(346-348)gaG>gaA	p.E116E	PVR_ENST00000403059.4_Silent_p.E116E|PVR_ENST00000406449.4_Silent_p.E116E|PVR_ENST00000344956.4_Silent_p.E116E|CTB-171A8.1_ENST00000590796.1_RNA	NM_006505.3	NP_006496.3	P15151	PVR_HUMAN	poliovirus receptor	116	Ig-like V-type.				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)		TGCGCGTAGAGGATGAAGGCA	0.617													G|||	250	0.0499201	0.1755	0.0259	5008	,	,		10654	0.0		0.0	False		,,,				2504	0.0				p.E116E		Atlas-SNP	.											.	PVR	23	.	0			c.G348A						PASS	.	G	,,,	658,3748	275.2+/-272.4	60,538,1605	59	53	55		348,348,348,348	-5.9	0	19	dbSNP_119	55	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PVR	NM_001135768.1,NM_001135769.1,NM_001135770.1,NM_006505.3	,,,	60,544,5899	AA,AG,GG		0.0698,14.9342,5.1053	,,,	116/373,116/365,116/393,116/418	45150763	664,12342	2203	4300	6503	SO:0001819	synonymous_variant	5817	exon2			CGTAGAGGATGAA	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.348G>A	19.37:g.45150763G>A		86	0	0		94	41	0.43617	NM_001135769	B4DTS9|P15152|Q15267|Q15268|Q96BJ1	Silent	SNP	ENST00000425690.3	37	CCDS12640.1																																																																																			G|0.937;A|0.063	0.063	strong		0.617	PVR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323017.2	NM_006505		A	45150763	G	A	45150763	2	1	22	1	0	0	0	0	0	0	0	1	12852	991	35	2		2	PVR	19	45150763	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	133462	45150763	13978220	3994	6895											
PVR	5817	hgsc.bcm.edu	37	chr19	45161070	45161070	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctttgctgtggcccagggcGcccagctcctgatccgtcct	3	10	11	17	2	0	1	0	1	0	0	3	1	3	1	6	2	2	2	6	2	0	1	rs35365841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45161070G>A	ENST00000425690.3	+	5	1182	c.883G>A	c.(883-885)Gcc>Acc	p.A295T	PVR_ENST00000403059.4_Missense_Mutation_p.A295T|PVR_ENST00000406449.4_Missense_Mutation_p.A295T|PVR_ENST00000344956.4_Missense_Mutation_p.A295T|CTB-171A8.1_ENST00000590796.1_RNA	NM_006505.3	NP_006496.3	P15151	PVR_HUMAN	poliovirus receptor	295	Ig-like C2-type 2.		A -> T (in dbSNP:rs35365841).		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)		GGCCCAGGGCGCCCAGCTCCT	0.587											OREG0025540	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	257	0.0513179	0.1755	0.0259	5008	,	,		18444	0.0		0.001	False		,,,				2504	0.0061				p.A295T		Atlas-SNP	.											.	PVR	23	.	0			c.G883A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA	656,3750	279.9+/-275.1	61,534,1608	61	53	55		883,883,883,883	-10.2	0	19	dbSNP_126	55	8,8592	5.7+/-21.5	0,8,4292	yes	missense,missense,missense,missense	PVR	NM_001135768.1,NM_001135769.1,NM_001135770.1,NM_006505.3	58,58,58,58	61,542,5900	AA,AG,GG		0.093,14.8888,5.1053	benign,benign,benign,benign	295/373,295/365,295/393,295/418	45161070	664,12342	2203	4300	6503	SO:0001583	missense	5817	exon5			CAGGGCGCCCAGC	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.883G>A	19.37:g.45161070G>A	ENSP00000402060:p.Ala295Thr	84	0	0	929	93	42	0.451613	NM_001135769	B4DTS9|P15152|Q15267|Q15268|Q96BJ1	Missense_Mutation	SNP	ENST00000425690.3	37	CCDS12640.1	116	0.05311355311355311	101	0.20528455284552846	14	0.03867403314917127	0	0.0	1	0.0013192612137203166	G	10.75	1.438622	0.25900	0.148888	9.3E-4	ENSG00000073008	ENST00000344956;ENST00000425690;ENST00000406449;ENST00000403059	T;T;T;T	0.16743	2.32;2.32;2.32;2.32	5.08	-10.2	0.00374	Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	2.148170	0.02353	N	0.076098	T	0.00012	0.0000	N	0.12746	0.255	0.80722	P	0.0	B;B;B;B	0.30361	0.038;0.154;0.097;0.277	B;B;B;B	0.28305	0.027;0.049;0.031;0.088	T	0.22765	-1.0207	9	0.14252	T	0.57	.	1.6961	0.02862	0.118:0.3407:0.2586:0.2827	rs35365841	295;295;295;295	P15151-2;P15151-3;P15151-4;P15151	.;.;.;PVR_HUMAN	T	295	ENSP00000340870:A295T;ENSP00000402060:A295T;ENSP00000383907:A295T;ENSP00000385344:A295T	ENSP00000340870:A295T	A	+	1	0	PVR	49852910	0.000000	0.05858	0.000000	0.03702	0.123000	0.20343	-2.189000	0.01248	-2.865000	0.00325	-0.165000	0.13383	GCC	G|0.951;A|0.049	0.049	strong		0.587	PVR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323017.2	NM_006505		A	45161070	G	A	45161070	3	1	22	1	0	0	0	0	1	0	0	0	12852	1087	38	1	901	1	PVR	19	45161070	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	10307	45161070	13967913	3995	6896											
CBLC	23624	hgsc.bcm.edu	37	chr19	45281375	45281375	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagaggtggcccattctcggCgggcggccggcggaggcggc	4	4	21	12	6	1	1	0	0	1	1	2	3	1	2	2	9	0	0	2	9	0	1	rs115775900	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45281375C>T	ENST00000270279.3	+	1	250	c.187C>T	c.(187-189)Cgg>Tgg	p.R63W	CBLC_ENST00000341505.4_Missense_Mutation_p.R63W	NM_012116.3	NP_036248.3	Q9ULV8	CBLC_HUMAN	Cbl proto-oncogene C, E3 ubiquitin protein ligase	63	4H.|Cbl-PTB. {ECO:0000255|PROSITE- ProRule:PRU00839}.				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)				CCATTCTcggcgggcggccgg	0.711			M		AML								c|||	64	0.0127796	0.0454	0.0043	5008	,	,		8428	0.0		0.0	False		,,,				2504	0.001				p.R63W		Atlas-SNP	.		Rec	yes		19	19q13.2	23624	Cas-Br-M (murine) ecotropic retroviral transforming sequence c		L	.	CBLC	41	.	0			c.C187T						PASS	.		TRP/ARG,TRP/ARG	85,3747		1,83,1832	8	11	10		187,187	-2.5	0	19	dbSNP_132	10	1,7799		0,1,3899	yes	missense,missense	CBLC	NM_001130852.1,NM_012116.3	101,101	1,84,5731	TT,TC,CC		0.0128,2.2182,0.7393	probably-damaging,probably-damaging	63/429,63/475	45281375	86,11546	1916	3900	5816	SO:0001583	missense	23624	exon1			TCTCGGCGGGCGG	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.187C>T	19.37:g.45281375C>T	ENSP00000270279:p.Arg63Trp	6	0	0		10	8	0.8	NM_001130852	Q8N1E5|Q9Y5Z2|Q9Y5Z3	Missense_Mutation	SNP	ENST00000270279.3	37	CCDS12643.1	32	0.014652014652014652	29	0.05894308943089431	3	0.008287292817679558	0	0.0	0	0.0	.	16.25	3.071238	0.55646	0.022182	1.28E-4	ENSG00000142273	ENST00000270279;ENST00000341505	T;T	0.76968	-1.06;-1.06	3.35	-2.49	0.06403	Adaptor protein Cbl, N-terminal helical (3);Adaptor protein Cbl, PTB domain (1);	0.588184	0.13455	N	0.386611	T	0.40272	0.1110	M	0.65975	2.015	0.09310	N	1	D;D	0.71674	0.998;0.998	P;P	0.62491	0.903;0.756	T	0.63506	-0.6622	10	0.87932	D	0	-6.6255	10.0273	0.42079	0.6988:0.3012:0.0:0.0	.	63;63	Q9ULV8-2;Q9ULV8	.;CBLC_HUMAN	W	63	ENSP00000270279:R63W;ENSP00000340250:R63W	ENSP00000270279:R63W	R	+	1	2	CBLC	49973215	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.696000	0.05104	-0.081000	0.12662	0.556000	0.70494	CGG	C|0.983;T|0.017	0.017	strong		0.711	CBLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319732.2	NM_012116		T	45281375	C	T	45281375	3	4	22	1	0	0	0	0	1	0	0	0	2704	759	27	1	189	1	CBLC	19	45281375	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	120305	45281375	13847608	3996	6897											
CBLC	23624	hgsc.bcm.edu	37	chr19	45284495	45284495	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgggctgagtttgagtccCtcctgggcacctgccaccct	4	10	11	16	0	0	2	0	2	0	0	2	2	2	2	6	2	1	3	6	2	0	1	rs114569424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45284495C>T	ENST00000270279.3	+	3	595	c.532C>T	c.(532-534)Ctc>Ttc	p.L178F	CBLC_ENST00000341505.4_Missense_Mutation_p.L178F	NM_012116.3	NP_036248.3	Q9ULV8	CBLC_HUMAN	Cbl proto-oncogene C, E3 ubiquitin protein ligase	178	Cbl-PTB. {ECO:0000255|PROSITE- ProRule:PRU00839}.|EF-hand-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)				GTTTGAGTCCCTCCTGGGCAC	0.652			M		AML								c|||	39	0.00778754	0.0242	0.0058	5008	,	,		16049	0.0		0.0	False		,,,				2504	0.0031				p.L178F		Atlas-SNP	.		Rec	yes		19	19q13.2	23624	Cas-Br-M (murine) ecotropic retroviral transforming sequence c		L	.	CBLC	41	.	0			c.C532T						PASS	.		PHE/LEU,PHE/LEU	59,4347		0,59,2144	68	57	61		532,532	1.7	0	19	dbSNP_132	61	0,8600		0,0,4300	yes	missense,missense	CBLC	NM_001130852.1,NM_012116.3	22,22	0,59,6444	TT,TC,CC		0.0,1.3391,0.4536	probably-damaging,probably-damaging	178/429,178/475	45284495	59,12947	2203	4300	6503	SO:0001583	missense	23624	exon3			GAGTCCCTCCTGG	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.532C>T	19.37:g.45284495C>T	ENSP00000270279:p.Leu178Phe	91	0	0		97	48	0.494845	NM_001130852	Q8N1E5|Q9Y5Z2|Q9Y5Z3	Missense_Mutation	SNP	ENST00000270279.3	37	CCDS12643.1	21	0.009615384615384616	17	0.034552845528455285	4	0.011049723756906077	0	0.0	0	0.0	.	12.98	2.099594	0.37048	0.013391	0.0	ENSG00000142273	ENST00000270279;ENST00000341505	D;D	0.87256	-2.23;-2.23	3.95	1.72	0.24424	Adaptor protein Cbl, PTB domain (1);EF-hand-like domain (1);Adaptor protein Cbl, EF hand-like (1);	0.976806	0.08347	N	0.959896	T	0.74238	0.3690	L	0.57536	1.79	0.09310	N	1	D;D	0.61697	0.958;0.99	P;P	0.53549	0.682;0.729	T	0.68142	-0.5487	10	0.23891	T	0.37	-15.6691	7.2319	0.26046	0.1838:0.4585:0.3578:0.0	.	178;178	Q9ULV8-2;Q9ULV8	.;CBLC_HUMAN	F	178	ENSP00000270279:L178F;ENSP00000340250:L178F	ENSP00000270279:L178F	L	+	1	0	CBLC	49976335	0.003000	0.15002	0.005000	0.12908	0.756000	0.42949	1.111000	0.31159	0.318000	0.23185	0.306000	0.20318	CTC	C|0.994;T|0.006	0.006	strong		0.652	CBLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319732.2	NM_012116		T	45284495	C	T	45284495	3	4	22	1	0	0	0	0	1	0	0	0	2704	681	24	2	542	2	CBLC	19	45284495	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3120	45284495	13844488	3997	6898											
CBLC	23624	hgsc.bcm.edu	37	chr19	45285734	45285734	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gagcgtctgcaggcctgcagGgacaagccaggcaggtaaag	11	4	16	10	1	1	0	0	0	1	0	1	2	1	1	2	4	4	4	2	4	3	1	rs10416628	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45285734G>A	ENST00000270279.3	+	4	828	c.765G>A	c.(763-765)agG>agA	p.R255R	CBLC_ENST00000341505.4_Silent_p.R255R	NM_012116.3	NP_036248.3	Q9ULV8	CBLC_HUMAN	Cbl proto-oncogene C, E3 ubiquitin protein ligase	255	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)				AGGCCTGCAGGGACAAGCCAG	0.612			M		AML								G|||	144	0.028754	0.1021	0.013	5008	,	,		17150	0.0		0.0	False		,,,				2504	0.0				p.R255R		Atlas-SNP	.		Rec	yes		19	19q13.2	23624	Cas-Br-M (murine) ecotropic retroviral transforming sequence c		L	.	CBLC	41	.	0			c.G765A						PASS	.	G	,	407,3999		15,377,1811	62	57	59		765,765	-2.1	1	19	dbSNP_119	59	4,8596		0,4,4296	no	coding-synonymous,coding-synonymous	CBLC	NM_001130852.1,NM_012116.3	,	15,381,6107	AA,AG,GG		0.0465,9.2374,3.1601	,	255/429,255/475	45285734	411,12595	2203	4300	6503	SO:0001819	synonymous_variant	23624	exon4			CTGCAGGGACAAG	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.765G>A	19.37:g.45285734G>A		118	0	0		119	62	0.521008	NM_001130852	Q8N1E5|Q9Y5Z2|Q9Y5Z3	Silent	SNP	ENST00000270279.3	37	CCDS12643.1																																																																																			G|0.958;A|0.042	0.042	strong		0.612	CBLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319732.2	NM_012116		A	45285734	G	A	45285734	2	1	22	1	0	0	0	0	0	0	0	1	2704	1223	43	2		2	CBLC	19	45285734	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1239	45285734	13843249	3998	6899											
PVRL2	5819	hgsc.bcm.edu	37	chr19	45368805	45368805	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagaggcagagctccaggaCgccacgctggccctccacgg	9	3	13	16	3	0	2	0	0	0	2	2	3	2	3	4	4	1	3	4	4	0	0	rs34929997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45368805C>T	ENST00000252483.5	+	2	366	c.366C>T	c.(364-366)gaC>gaT	p.D122D	PVRL2_ENST00000252485.4_Silent_p.D122D	NM_001042724.1	NP_001036189.1	Q92692	PVRL2_HUMAN	poliovirus receptor-related 2 (herpesvirus entry mediator B)	122	Ig-like V-type.				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)		AGCTCCAGGACGCCACGCTGG	0.662													T|||	87	0.0173722	0.0651	0.0	5008	,	,		19055	0.0		0.001	False		,,,				2504	0.0				p.D122D		Atlas-SNP	.											.	PVRL2	58	.	0			c.C366T						PASS	.	T	,	215,4179		4,207,1986	22	20	20		366,366	-6.6	0.3	19	dbSNP_126	20	4,8566		0,4,4281	no	coding-synonymous,coding-synonymous	PVRL2	NM_001042724.1,NM_002856.2	,	4,211,6267	TT,TC,CC		0.0467,4.893,1.6893	,	122/539,122/480	45368805	219,12745	2197	4285	6482	SO:0001819	synonymous_variant	5819	exon2			CCAGGACGCCACG	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.366C>T	19.37:g.45368805C>T		47	0	0		33	11	0.333333	NM_002856	A8K5L5|O75455|Q6IBI6|Q96J29	Silent	SNP	ENST00000252483.5	37	CCDS42576.1																																																																																			C|0.980;T|0.020	0.020	strong		0.662	PVRL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453231.1	NM_002856		T	45368805	C	T	45368805	2	4	22	1	0	0	0	0	0	0	0	1	12855	535	19	1		1	PVRL2	19	45368805	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	83071	45368805	13760178	3999	6900											
APOC2	344	hgsc.bcm.edu	37	chr19	45452429	45452429	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccccagggacttgtacagcAaaagcacagcagccatgagc	13	5	10	13	0	0	1	0	1	0	0	1	2	1	2	3	1	6	4	3	1	3	2	rs5126	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45452429A>C	ENST00000590360.1	+	4	351	c.229A>C	c.(229-231)Aaa>Caa	p.K77Q	APOC2_ENST00000585786.1_3'UTR|APOC4-APOC2_ENST00000589057.1_Missense_Mutation_p.K154Q|APOC2_ENST00000592257.1_3'UTR|APOC2_ENST00000252490.4_Missense_Mutation_p.K77Q|APOC4_ENST00000419266.2_3'UTR|APOC2_ENST00000591597.1_Missense_Mutation_p.K63Q			P02655	APOC2_HUMAN	apolipoprotein C-II	77	Lipoprotein lipase cofactor.		K -> Q (in Africa; dbSNP:rs5126). {ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:3944271}.		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)			kidney(1)|large_intestine(1)|liver(1)|lung(3)	6	Lung NSC(12;0.00858)|all_lung(12;0.0197)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|Epithelial(262;0.174)		CTTGTACAGCAAAAGCACAGC	0.567													A|||	39	0.00778754	0.0287	0.0014	5008	,	,		15843	0.0		0.0	False		,,,				2504	0.0				p.K77Q		Atlas-SNP	.											.	APOC2	9	.	0			c.A229C						PASS	.	A	GLN/LYS	85,4321	47.5+/-82.1	1,83,2119	79	66	71	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	229	2	0.4	19	dbSNP_52	71	0,8600		0,0,4300	yes	missense	APOC2	NM_000483.4	53	1,83,6419	CC,CA,AA		0.0,1.9292,0.6535	probably-damaging	77/102	45452429	85,12921	2203	4300	6503	SO:0001583	missense	344	exon4			TACAGCAAAAGCA	X00568	CCDS12650.1	19q13.2	2013-01-24			ENSG00000234906	ENSG00000234906		"Apolipoproteins"	609	protein-coding gene	gene with protein product		608083					Standard	NM_000483		Approved			P02655	OTTHUMG00000180847	ENST00000590360.1:c.229A>C	19.37:g.45452429A>C	ENSP00000466775:p.Lys77Gln	122	0	0		123	59	0.479675	NM_000483	C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	Missense_Mutation	SNP	ENST00000590360.1	37	CCDS12650.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	A	15.05	2.717211	0.48622	0.019292	0.0	ENSG00000234906	ENST00000252490	D	0.86164	-2.08	4.25	1.97	0.26223	ApoC-II domain (1);	0.331465	0.21058	U	0.080867	T	0.66616	0.2807	M	0.77820	2.39	0.19300	N	0.999973	P	0.39216	0.664	B	0.36504	0.226	T	0.68573	-0.5373	10	0.48119	T	0.1	-0.0013	4.4429	0.11582	0.621:0.2662:0.1128:0.0	rs5126;rs52806093;rs5126	77	P02655	APOC2_HUMAN	Q	77	ENSP00000252490:K77Q	ENSP00000252490:K77Q	K	+	1	0	APOC2	50144269	0.077000	0.21312	0.448000	0.26945	0.770000	0.43624	0.076000	0.14712	0.113000	0.18004	0.323000	0.21402	AAA	A|0.991;C|0.009	0.009	strong		0.567	APOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453261.1	NM_000483		C	45452429	A	C	45452429	3	2	22	1	0	0	0	0	1	0	0	0	798	131	5	5	239	5	APOC2	19	45452429	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	83624	45452429	13676554	4000	6901											
SFRS16	11129	hgsc.bcm.edu	37	chr19	45561014	45561014	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcccctttctcaggctggcAgagaagaaggcttccatcgg	8	9	11	13	1	1	2	1	0	1	2	5	3	3	2	3	4	0	3	3	4	2	2	rs76953457	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45561014A>G	ENST00000221455.3	+	7	569	c.471A>G	c.(469-471)gcA>gcG	p.A157A	CLASRP_ENST00000544944.2_Silent_p.A157A|CLASRP_ENST00000391953.4_Silent_p.A95A	NM_007056.2	NP_008987	Q8N2M8	CLASR_HUMAN	CLK4-associating serine/arginine rich protein	157					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						TCAGGCTGGCAGAGAAGAAGG	0.637													A|||	50	0.00998403	0.034	0.0072	5008	,	,		19589	0.0		0.0	False		,,,				2504	0.0				p.A157A		Atlas-SNP	.											.	CLASRP	44	.	0			c.A471G						PASS	.	A		108,4298	85.3+/-124.0	1,106,2096	111	99	103		471	-5.3	0.9	19	dbSNP_131	103	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CLASRP	NM_007056.2		1,107,6395	GG,GA,AA		0.0116,2.4512,0.8381		157/675	45561014	109,12897	2203	4300	6503	SO:0001819	synonymous_variant	11129	exon7			GCTGGCAGAGAAG	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.471A>G	19.37:g.45561014A>G		75	0	0		70	29	0.414286	NM_007056	B4DDT8|F8WAG9|O96026|Q6UW71|Q96DX2	Silent	SNP	ENST00000221455.3	37	CCDS12652.2																																																																																			A|0.990;G|0.010	0.010	strong		0.637	CLASRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316749.1	NM_007056		G	45561014	A	G	45561014	2	3	22	1	0	0	0	0	0	0	0	1	14187	175	7	3		3	SFRS16	19	45561014	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	108585	45561014	13567969	4001	6902											
KLC3	147700	hgsc.bcm.edu	37	chr19	45848946	45848946	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcctggctgggcacctggcGgaggccctggcgggacaggg	4	4	21	12	2	0	0	0	0	0	0	0	2	0	2	3	9	0	2	3	9	0	0	rs114640964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45848946G>A	ENST00000391946.2	+	2	249	c.147G>A	c.(145-147)gcG>gcA	p.A49A	KLC3_ENST00000470402.1_Silent_p.A63A|KLC3_ENST00000585434.1_Silent_p.A49A	NM_177417.2	NP_803136.2	Q6P597	KLC3_HUMAN	kinesin light chain 3	49					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)		GGCACCTGGCGGAGGCCCTGG	0.716													g|||	75	0.014976	0.0552	0.0029	5008	,	,		13066	0.0		0.0	False		,,,				2504	0.0				p.A49A		Atlas-SNP	.											.	KLC3	37	.	0			c.G147A						PASS	.	A		150,3632		0,150,1741	5	8	7		147	-4.1	0.9	19	dbSNP_132	7	2,7914		0,2,3956	no	coding-synonymous	KLC3	NM_177417.2		0,152,5697	AA,AG,GG		0.0253,3.9662,1.2994		49/505	45848946	152,11546	1891	3958	5849	SO:0001819	synonymous_variant	147700	exon2			CCTGGCGGAGGCC	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.147G>A	19.37:g.45848946G>A		42	0	0		42	22	0.52381	NM_177417	A0AVM3|A2RUT6|Q6GMU2|Q8NAL1|Q8WWJ9	Silent	SNP	ENST00000391946.2	37	CCDS12660.2																																																																																			G|0.990;A|0.010	0.010	strong		0.716	KLC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289776.1	NM_145275		A	45848946	G	A	45848946	2	1	22	1	0	0	0	0	0	0	0	1	8344	1103	39	1		1	KLC3	19	45848946	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	287932	45848946	13280037	4002	6903											
EML2	24139	hgsc.bcm.edu	37	chr19	46142624	46142624	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagggtctcacccagctccaAagctactcatggcggcgggt	9	7	12	13	2	2	0	2	0	1	0	4	0	3	0	2	4	3	2	2	4	3	1	rs201822741	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:46142624A>C	ENST00000245925.3	-	1	61	c.11T>G	c.(10-12)tTt>tGt	p.F4C	EML2_ENST00000587152.1_Intron|EML2_ENST00000536630.1_Intron|EML2_ENST00000589876.1_Missense_Mutation_p.F4C|MIR330_ENST00000362196.1_RNA|AC006132.1_ENST00000593161.1_5'Flank	NM_012155.2	NP_036287.1	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like 2	4					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)		CCCAGCTCCAAAGCTACTCAT	0.726													A|||	48	0.00958466	0.0325	0.0072	5008	,	,		12182	0.0		0.0	False		,,,				2504	0.0				p.F4C		Atlas-SNP	.											.	EML2	64	.	0			c.T11G						PASS	.		,,CYS/PHE	90,4006		0,90,1958	15	17	16		,,11	4.6	1	19	dbSNP_134	16	1,8033		0,1,4016	yes	intron,intron,missense	EML2	NM_001193268.1,NM_001193269.1,NM_012155.2	,,205	0,91,5974	CC,CA,AA		0.0124,2.1973,0.7502	,,	,,4/650	46142624	91,12039	2048	4017	6065	SO:0001583	missense	24139	exon1			GCTCCAAAGCTAC	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.11T>G	19.37:g.46142624A>C	ENSP00000245925:p.Phe4Cys	45	0	0		56	29	0.517857	NM_012155	B7Z3I2|B7Z3Q9|K7ERL7|Q59EN8|Q8N5A2|Q9UG50	Missense_Mutation	SNP	ENST00000245925.3	37	CCDS12670.1	13	0.005952380952380952	8	0.016260162601626018	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	A	14.61	2.585437	0.46110	0.021973	1.24E-4	ENSG00000125746	ENST00000245925	T	0.26067	1.76	4.58	4.58	0.56647	.	1.865290	0.03249	U	0.181627	T	0.26666	0.0652	L	0.29908	0.895	0.80722	D	1	D;B	0.76494	0.999;0.118	D;B	0.74674	0.984;0.053	T	0.03034	-1.1080	10	0.59425	D	0.04	44.314	10.2951	0.43618	1.0:0.0:0.0:0.0	.	4;4	B7Z918;O95834	.;EMAL2_HUMAN	C	4	ENSP00000245925:F4C	ENSP00000245925:F4C	F	-	2	0	EML2	50834464	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.633000	0.54295	1.932000	0.55993	0.454000	0.30748	TTT	A|0.994;C|0.006	0.006	strong		0.726	EML2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459608.1	NM_012155		C	46142624	A	C	46142624	3	2	22	1	0	0	0	0	1	0	0	0	5099	14	1	5	2014	5	EML2	19	46142624	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	293678	46142624	12986359	4003	6904											
CCDC8	83987	hgsc.bcm.edu	37	chr19	46915182	46915182	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	actatctgcagcctctccccCctgatcagcctcgatgtctg	6	11	7	17	1	4	1	1	1	3	0	6	2	4	1	5	0	3	1	5	0	1	1	rs11880658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:46915182C>T	ENST00000307522.3	-	1	1659	c.886G>A	c.(886-888)Ggg>Agg	p.G296R		NM_032040.4	NP_114429.2	Q9H0W5	CCDC8_HUMAN	coiled-coil domain containing 8	296			G -> R (in dbSNP:rs11880658).		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)		GCCTCTCCCCCCTGATCAGCC	0.642													C|||	215	0.0429313	0.1558	0.0101	5008	,	,		16994	0.0		0.002	False		,,,				2504	0.0				p.G296R		Atlas-SNP	.											.	CCDC8	56	.	0			c.G886A						PASS	.	C	ARG/GLY	511,3895	229.4+/-244.0	26,459,1718	85	85	85		886	-0.9	0.2	19	dbSNP_120	85	4,8596	2.2+/-6.3	0,4,4296	yes	missense	CCDC8	NM_032040.3	125	26,463,6014	TT,TC,CC		0.0465,11.5978,3.9597	benign	296/539	46915182	515,12491	2203	4300	6503	SO:0001583	missense	83987	exon1			CTCCCCCCTGATC	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.886G>A	19.37:g.46915182C>T	ENSP00000303158:p.Gly296Arg	111	0	0		106	53	0.5	NM_032040	Q8TB26	Missense_Mutation	SNP	ENST00000307522.3	37	CCDS12685.1	80	0.03663003663003663	76	0.15447154471544716	4	0.011049723756906077	0	0.0	0	0.0	C	4.694	0.129001	0.08981	0.115978	4.65E-4	ENSG00000169515	ENST00000307522	T	0.10668	2.85	3.87	-0.89	0.10577	.	0.845492	0.09922	N	0.738356	T	0.00039	0.0001	N	0.02011	-0.69	0.29953	N	0.820099	B	0.06786	0.001	B	0.08055	0.003	T	0.48007	-0.9072	10	0.11485	T	0.65	-2.0588	8.1056	0.30883	0.0:0.5064:0.0:0.4936	rs11880658	296	Q9H0W5	CCDC8_HUMAN	R	296	ENSP00000303158:G296R	ENSP00000303158:G296R	G	-	1	0	CCDC8	51607022	0.000000	0.05858	0.194000	0.23346	0.165000	0.22458	-0.753000	0.04792	-0.122000	0.11766	0.655000	0.94253	GGG	C|0.962;T|0.038	0.038	strong		0.642	CCDC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368598.1	NM_032040		T	46915182	C	T	46915182	3	4	22	1	0	0	0	0	1	0	0	0	2855	623	22	2	734	2	CCDC8	19	46915182	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	772558	46915182	12213801	4004	6905											
PNMAL1	55228	hgsc.bcm.edu	37	chr19	46973315	46973315	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggcgcctcctgggctctcGgcttctgcccgggcatcctg	2	9	14	16	3	2	0	0	0	2	0	5	1	4	0	4	4	1	3	4	4	0	1	rs61628326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:46973315G>A	ENST00000313683.10	-	2	1283	c.978C>T	c.(976-978)gcC>gcT	p.A326A	PNMAL1_ENST00000602246.1_Intron|PNMAL1_ENST00000438932.2_Silent_p.A326A	NM_001103149.1|NM_018215.3	NP_001096619.1|NP_060685.2	Q86V59	PNML1_HUMAN	paraneoplastic Ma antigen family-like 1	326										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)		CTGGGCTCTCGGCTTCTGCCC	0.602													G|||	75	0.014976	0.0545	0.0043	5008	,	,		17043	0.0		0.0	False		,,,				2504	0.0				p.A326A		Atlas-SNP	.											.	PNMAL1	87	.	0			c.C978T						PASS	.	G	,	195,4211	118.0+/-155.7	8,179,2016	110	122	118		978,978	-7.3	0	19	dbSNP_129	118	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous	PNMAL1	NM_001103149.1,NM_018215.3	,	8,183,6312	AA,AG,GG		0.0465,4.4258,1.5301	,	326/379,326/440	46973315	199,12807	2203	4300	6503	SO:0001819	synonymous_variant	55228	exon2			GCTCTCGGCTTCT	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.978C>T	19.37:g.46973315G>A		94	0	0		97	54	0.556701	NM_018215	A8K2F3|Q5U638|Q8N3H4|Q9NVE8	Silent	SNP	ENST00000313683.10	37	CCDS33059.1																																																																																			G|0.982;A|0.018	0.018	strong		0.602	PNMAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403929.1	NM_018215		A	46973315	G	A	46973315	2	1	22	1	0	0	0	0	0	0	0	1	12166	1103	39	1		1	PNMAL1	19	46973315	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	58133	46973315	12155668	4005	6906											
PNMAL1	55228	hgsc.bcm.edu	37	chr19	46973693	46973693	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccacctctgctgcaagcccCggttctttcttcaccttcct	4	13	5	19	1	4	0	1	0	3	0	5	0	5	0	6	1	3	3	6	1	1	4	rs73552938	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:46973693C>T	ENST00000313683.10	-	2	905	c.600G>A	c.(598-600)ccG>ccA	p.P200P	PNMAL1_ENST00000602246.1_Intron|PNMAL1_ENST00000438932.2_Silent_p.P200P	NM_001103149.1|NM_018215.3	NP_001096619.1|NP_060685.2	Q86V59	PNML1_HUMAN	paraneoplastic Ma antigen family-like 1	200										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)		CTGCAAGCCCCGGTTCTTTCT	0.592													C|||	99	0.0197684	0.0696	0.0101	5008	,	,		18070	0.0		0.0	False		,,,				2504	0.0				p.P200P		Atlas-SNP	.											PNMAL1_ENST00000438932,lower_third,carcinoma,-1,2	PNMAL1	87	2	0			c.G600A						scavenged	.	C	,	250,4156	143.5+/-178.5	4,242,1957	58	60	59		600,600	-7.7	0	19	dbSNP_130	59	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	PNMAL1	NM_001103149.1,NM_018215.3	,	4,244,6255	TT,TC,CC		0.0233,5.6741,1.9376	,	200/379,200/440	46973693	252,12754	2203	4300	6503	SO:0001819	synonymous_variant	55228	exon2			AAGCCCCGGTTCT	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.600G>A	19.37:g.46973693C>T		61	1	0.0163934		65	64	0.984615	NM_018215	A8K2F3|Q5U638|Q8N3H4|Q9NVE8	Silent	SNP	ENST00000313683.10	37	CCDS33059.1	41	0.018772893772893772	38	0.07723577235772358	3	0.008287292817679558	0	0.0	0	0.0	C	4.609	0.113215	0.08831	0.056741	2.33E-4	ENSG00000182013	ENST00000417103	.	.	.	3.84	-7.67	0.01272	.	.	.	.	.	T	0.01558	0.0050	.	.	.	0.21386	N	0.99971	.	.	.	.	.	.	T	0.13845	-1.0494	5	0.46703	T	0.11	-21.5671	4.3527	0.11163	0.0894:0.1015:0.3706:0.4386	.	.	.	.	R	180	.	ENSP00000389114:G180R	G	-	1	0	PNMAL1	51665533	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-5.361000	0.00128	-3.560000	0.00141	-0.345000	0.07892	GGG	C|0.977;T|0.023	0.023	strong		0.592	PNMAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403929.1	NM_018215		T	46973693	C	T	46973693	2	4	22	1	0	0	0	0	0	0	0	1	12166	639	23	1		1	PNMAL1	19	46973693	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	378	46973693	12155290	4006	6907											
CALM3	808	hgsc.bcm.edu	37	chr19	47112207	47112207	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagatgatcagggaggctgaCatcgatggagatggccaggt	11	7	17	6	1	1	4	1	2	0	2	2	8	1	5	1	5	0	1	1	5	0	0	rs35617141	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47112207C>T	ENST00000291295.9	+	5	589	c.390C>T	c.(388-390)gaC>gaT	p.D130D	CALM3_ENST00000477244.1_3'UTR|CALM3_ENST00000594523.1_Silent_p.D94D|CTB-12A17.3_ENST00000597609.1_RNA|CALM3_ENST00000599839.1_Silent_p.D94D|CALM3_ENST00000596362.1_Silent_p.D130D|CALM3_ENST00000391918.2_Silent_p.D94D|CALM3_ENST00000597743.1_Silent_p.D64D|CALM3_ENST00000598871.1_Silent_p.D94D	NM_005184.2	NP_005175.2	P62158	CALM_HUMAN	calmodulin 3 (phosphorylase kinase, delta)	130	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|detection of calcium ion (GO:0005513)|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)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nitric oxide metabolic process (GO:0046209)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cyclic nucleotide metabolic process (GO:0030801)|positive regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051343)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|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 cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of cytokinesis (GO:0032465)|regulation of heart rate (GO:0002027)|regulation of high voltage-gated calcium channel activity (GO:1901841)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|response to corticosterone (GO:0051412)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcomere (GO:0030017)|spindle microtubule (GO:0005876)|spindle pole (GO:0000922)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|N-terminal myristoylation domain binding (GO:0031997)|nitric-oxide synthase regulator activity (GO:0030235)|phospholipase binding (GO:0043274)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|protein phosphatase activator activity (GO:0072542)|protein serine/threonine kinase activator activity (GO:0043539)|thioesterase binding (GO:0031996)|titin binding (GO:0031432)			breast(1)|cervix(2)|endometrium(1)|lung(1)|ovary(1)	6		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000338)|all cancers(93;0.000683)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0341)	Aprindine(DB01429)|Bepridil(DB01244)|Chlorpromazine(DB00477)|Cinchocaine(DB00527)|Felodipine(DB01023)|Flunarizine(DB04841)|Fluphenazine(DB00623)|Isoflurane(DB00753)|Loperamide(DB00836)|Melatonin(DB01065)|Nicardipine(DB00622)|Nifedipine(DB01115)|Perphenazine(DB00850)|Phenoxybenzamine(DB00925)|Pimozide(DB01100)|Promethazine(DB01069)|Trifluoperazine(DB00831)	GGGAGGCTGACATCGATGGAG	0.542													C|||	37	0.00738818	0.0265	0.0029	5008	,	,		21757	0.0		0.0	False		,,,				2504	0.0				p.D130D		Atlas-SNP	.											.	CALM3	9	.	0			c.C390T						PASS	.	C		98,4308	79.9+/-118.3	0,98,2105	93	71	79		390	4.8	1	19	dbSNP_126	79	0,8600		0,0,4300	no	coding-synonymous	CALM3	NM_005184.2		0,98,6405	TT,TC,CC		0.0,2.2242,0.7535		130/150	47112207	98,12908	2203	4300	6503	SO:0001819	synonymous_variant	808	exon5			GGCTGACATCGAT		CCDS33061.1	19q13.2-q13.3	2013-02-25			ENSG00000160014	ENSG00000160014		"EF-hand domain containing", "Endogenous ligands"	1449	protein-coding gene	gene with protein product	"prepro-calmodulin 3"	114183					Standard	NM_005184		Approved	PHKD	uc002pew.3	P62158	OTTHUMG00000133517	ENST00000291295.9:c.390C>T	19.37:g.47112207C>T		86	0	0		83	47	0.566265	NM_005184	P02593|P70667|P99014|Q13942|Q53S29|Q61379|Q61380|Q96HK3	Silent	SNP	ENST00000291295.9	37	CCDS33061.1																																																																																			C|0.990;T|0.010	0.010	strong		0.542	CALM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257483.2			T	47112207	C	T	47112207	2	4	22	1	0	0	0	0	0	0	0	1	2588	477	17	2		2	CALM3	19	47112207	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	138514	47112207	12016776	4007	6908											
PTGIR	5739	hgsc.bcm.edu	37	chr19	47124579	47124579	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggcttctgctttggacgaCgttcccacggcgctgccgct	3	11	12	15	5	1	0	0	0	1	0	2	2	2	1	2	3	2	5	2	3	0	3	rs2229130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47124579C>T	ENST00000291294.2	-	3	1252	c.1119G>A	c.(1117-1119)acG>acA	p.T373T	PTGIR_ENST00000594275.1_Silent_p.T130T|PTGIR_ENST00000597185.1_Silent_p.T102T|PTGIR_ENST00000598865.1_Silent_p.T161T	NM_000960.3	NP_000951.1	P43119	PI2R_HUMAN	prostaglandin I2 (prostacyclin) receptor (IP)	373					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of GTPase activity (GO:0043547)|response to lipopolysaccharide (GO:0032496)	cytosol (GO:0005829)|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)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	13		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000327)|all cancers(93;0.000641)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0331)	Dinoprost Tromethamine(DB01160)|Epoprostenol(DB01240)|Iloprost(DB01088)|Treprostinil(DB00374)	CTTTGGACGACGTTCCCACGG	0.632													C|||	64	0.0127796	0.0446	0.0072	5008	,	,		16398	0.0		0.0	False		,,,				2504	0.0				p.T373T		Atlas-SNP	.											.	PTGIR	31	.	0			c.G1119A						PASS	.	C		207,4199	121.7+/-159.2	7,193,2003	44	47	46		1119	-9.5	0	19	dbSNP_98	46	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	PTGIR	NM_000960.3		7,196,6300	TT,TC,CC		0.0349,4.6981,1.6146		373/387	47124579	210,12796	2203	4300	6503	SO:0001819	synonymous_variant	5739	exon3			GGACGACGTTCCC		CCDS12686.1	19q13.3	2012-08-08				ENSG00000160013		"GPCR / Class A : Prostanoid receptors"	9602	protein-coding gene	gene with protein product		600022				7759114	Standard	NM_000960		Approved	IP	uc002pex.3	P43119		ENST00000291294.2:c.1119G>A	19.37:g.47124579C>T		136	0	0		124	62	0.5	NM_000960		Silent	SNP	ENST00000291294.2	37	CCDS12686.1																																																																																			C|0.984;T|0.016	0.016	strong		0.632	PTGIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466581.1			T	47124579	C	T	47124579	2	4	22	1	0	0	0	0	0	0	0	1	12764	523	19	1		1	PTGIR	19	47124579	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	12372	47124579	12004404	4008	6909											
PTGIR	5739	hgsc.bcm.edu	37	chr19	47124742	47124742	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gctgggaaaggggtgtctgcGagtctccgtgggcaggcccg	5	7	19	10	3	2	0	0	0	2	0	3	2	2	1	2	5	1	2	2	5	1	0	rs28590598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47124742G>C	ENST00000291294.2	-	3	1089	c.956C>G	c.(955-957)tCg>tGg	p.S319W	PTGIR_ENST00000594275.1_Missense_Mutation_p.S76W|PTGIR_ENST00000597185.1_Missense_Mutation_p.S48W|PTGIR_ENST00000598865.1_Missense_Mutation_p.S107W	NM_000960.3	NP_000951.1	P43119	PI2R_HUMAN	prostaglandin I2 (prostacyclin) receptor (IP)	319			S -> W (in dbSNP:rs28590598).		adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of GTPase activity (GO:0043547)|response to lipopolysaccharide (GO:0032496)	cytosol (GO:0005829)|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)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	13		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000327)|all cancers(93;0.000641)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0331)	Dinoprost Tromethamine(DB01160)|Epoprostenol(DB01240)|Iloprost(DB01088)|Treprostinil(DB00374)	GGGTGTCTGCGAGTCTCCGTG	0.647													G|||	136	0.0271565	0.0968	0.0101	5008	,	,		18475	0.0		0.001	False		,,,				2504	0.0				p.S319W		Atlas-SNP	.											.	PTGIR	31	.	0			c.C956G						PASS	.	G	TRP/SER	405,4001	184.3+/-211.7	22,361,1820	42	48	46		956	0.2	0	19	dbSNP_125	46	2,8598	2.2+/-6.3	0,2,4298	yes	missense	PTGIR	NM_000960.3	177	22,363,6118	CC,CG,GG		0.0233,9.192,3.1293	probably-damaging	319/387	47124742	407,12599	2203	4300	6503	SO:0001583	missense	5739	exon3			GTCTGCGAGTCTC		CCDS12686.1	19q13.3	2012-08-08				ENSG00000160013		"GPCR / Class A : Prostanoid receptors"	9602	protein-coding gene	gene with protein product		600022				7759114	Standard	NM_000960		Approved	IP	uc002pex.3	P43119		ENST00000291294.2:c.956C>G	19.37:g.47124742G>C	ENSP00000291294:p.Ser319Trp	114	0	0		115	59	0.513043	NM_000960		Missense_Mutation	SNP	ENST00000291294.2	37	CCDS12686.1	52	0.023809523809523808	49	0.09959349593495935	3	0.008287292817679558	0	0.0	0	0.0	G	13.66	2.304672	0.40795	0.09192	2.33E-4	ENSG00000160013	ENST00000291294	T	0.41065	1.01	4.39	0.217	0.15264	.	0.792252	0.10334	N	0.687165	T	0.00998	0.0033	N	0.24115	0.695	0.09310	N	1	D	0.63046	0.992	P	0.51866	0.682	T	0.03202	-1.1061	10	0.66056	D	0.02	-8.4268	6.0489	0.19775	0.5271:0.0:0.4729:0.0	rs28590598	319	P43119	PI2R_HUMAN	W	319	ENSP00000291294:S319W	ENSP00000291294:S319W	S	-	2	0	PTGIR	51816582	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	0.177000	0.16801	-0.057000	0.13199	-0.258000	0.10820	TCG	G|0.973;C|0.027	0.027	strong		0.647	PTGIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466581.1			C	47124742	G	C	47124742	3	2	22	1	0	0	0	0	1	0	0	0	12764	1059	37	4	208	4	PTGIR	19	47124742	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	163	47124742	12004241	4009	6910											
ZC3H4	23211	hgsc.bcm.edu	37	chr19	47575170	47575170	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tccagggccgtagggcatcaTtggagggccgccagggccca	7	5	16	13	2	1	0	1	0	0	0	2	1	2	1	5	5	0	2	5	5	1	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47575170T>C	ENST00000253048.5	-	13	2048	c.2011A>G	c.(2011-2013)Atg>Gtg	p.M671V	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	671	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)		TAGGGCATCATTGGAGGGCCG	0.617																																					p.M671V		Atlas-SNP	.											.	ZC3H4	96	.	0			c.A2011G						PASS	.						33	39	37					19																	47575170		2040	4187	6227	SO:0001583	missense	23211	exon13			GCATCATTGGAGG	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.2011A>G	19.37:g.47575170T>C	ENSP00000253048:p.Met671Val	92	0	0		117	63	0.538462	NM_015168	Q9Y420	Missense_Mutation	SNP	ENST00000253048.5	37	CCDS42582.1	.	.	.	.	.	.	.	.	.	.	T	11.74	1.728939	0.30684	.	.	ENSG00000130749	ENST00000253048	T	0.18174	2.23	5.35	5.35	0.76521	.	0.784041	0.11696	N	0.538401	T	0.13415	0.0325	L	0.34521	1.04	0.46499	D	0.999079	B	0.31485	0.325	B	0.21917	0.037	T	0.12167	-1.0558	10	0.15499	T	0.54	.	14.3108	0.66415	0.0:0.0:0.0:1.0	.	671	Q9UPT8	ZC3H4_HUMAN	V	671	ENSP00000253048:M671V	ENSP00000253048:M671V	M	-	1	0	ZC3H4	52267010	1.000000	0.71417	0.982000	0.44146	0.507000	0.33981	6.886000	0.75611	2.028000	0.59812	0.523000	0.50628	ATG	.	.	none		0.617	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1			C	47575170	T	C	47575170	3	2	22	1	0	0	0	0	1	0	0	0	17585	1493	52	3	1912	3	ZC3H4	19	47575170	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	450428	47575170	11553813	4010	6911											
ZC3H4	23211	hgsc.bcm.edu	37	chr19	47575291	47575291	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcatgtcggggtgcatgtcAggatgcattggaccgcccat	7	10	14	10	2	1	0	1	0	0	0	2	2	1	2	2	4	3	3	2	4	0	1	rs144210335|rs79459609	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47575291A>G	ENST00000253048.5	-	13	1927	c.1890T>C	c.(1888-1890)ccT>ccC	p.P630P	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	630	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)		ggtgcatgtcaggatgcatTG	0.647													A|||	130	0.0259585	0.0908	0.0115	5008	,	,		17612	0.0		0.002	False		,,,				2504	0.0				p.P630P		Atlas-SNP	.											.	ZC3H4	96	.	0			c.T1890C						PASS	.	A		211,3961		8,195,1883	29	34	32		1890	-9	0.7	19	dbSNP_131	32	18,8402		0,18,4192	no	coding-synonymous	ZC3H4	NM_015168.1		8,213,6075	GG,GA,AA		0.2138,5.0575,1.8186		630/1304	47575291	229,12363	2086	4210	6296	SO:0001819	synonymous_variant	23211	exon13			CATGTCAGGATGC	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.1890T>C	19.37:g.47575291A>G		117	0	0		97	50	0.515464	NM_015168	Q9Y420	Silent	SNP	ENST00000253048.5	37	CCDS42582.1																																																																																			A|0.983;G|0.017	0.017	strong		0.647	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1			G	47575291	A	G	47575291	2	3	22	1	0	0	0	0	0	0	0	1	17585	175	7	3		3	ZC3H4	19	47575291	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	121	47575291	11553692	4011	6912											
ZC3H4	23211	hgsc.bcm.edu	37	chr19	47584869	47584869	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggtgtggtacagcttacaCgggaaatcacgttcatggca	10	10	13	8	2	2	0	2	0	0	0	2	1	2	1	0	4	3	4	0	4	3	3	rs73943616	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47584869C>T	ENST00000253048.5	-	11	1378	c.1341G>A	c.(1339-1341)ccG>ccA	p.P447P	ZC3H4_ENST00000594019.1_Intron|RN7SL533P_ENST00000584468.1_RNA	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	447							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)		ACAGCTTACACGGGAAATCAC	0.522													C|||	133	0.0265575	0.093	0.0115	5008	,	,		20932	0.0		0.002	False		,,,				2504	0.0				p.P447P		Atlas-SNP	.											.	ZC3H4	96	.	0			c.G1341A						PASS	.	C		287,3833		14,259,1787	120	121	121		1341	-11.4	0.2	19	dbSNP_130	121	30,8360		0,30,4165	no	coding-synonymous	ZC3H4	NM_015168.1		14,289,5952	TT,TC,CC		0.3576,6.966,2.534		447/1304	47584869	317,12193	2060	4195	6255	SO:0001819	synonymous_variant	23211	exon11			CTTACACGGGAAA	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.1341G>A	19.37:g.47584869C>T		139	0	0		144	84	0.583333	NM_015168	Q9Y420	Silent	SNP	ENST00000253048.5	37	CCDS42582.1																																																																																			C|0.986;T|0.014	0.014	strong		0.522	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1			T	47584869	C	T	47584869	2	4	22	1	0	0	0	0	0	0	0	1	17585	523	19	1		1	ZC3H4	19	47584869	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	9578	47584869	11544114	4012	6913											
GPR77	27202	hgsc.bcm.edu	37	chr19	47844899	47844899	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctcatcgtgggccttgccctCgctcacagctgcctcaatcc	5	10	8	18	2	3	0	3	0	0	0	6	0	4	0	4	1	3	2	4	1	1	1	rs34085015	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47844899C>T	ENST00000595464.1	+	2	1061	c.843C>T	c.(841-843)ctC>ctT	p.L281L	C5AR2_ENST00000600626.1_Silent_p.L281L|C5AR2_ENST00000257267.2_Silent_p.L281L	NM_001271749.1	NP_001258678.1	Q9P296	C5AR2_HUMAN	complement component 5a receptor 2	281					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)										GCCTTGCCCTCGCTCACAGCT	0.667													C|||	27	0.00539137	0.0174	0.0043	5008	,	,		16697	0.0		0.001	False		,,,				2504	0.0				p.L281L		Atlas-SNP	.											.	.	.	.	0			c.C843T						PASS	.	C		92,4314	75.2+/-113.4	1,90,2112	59	59	59		843	-7.9	0	19	dbSNP_126	59	0,8600		0,0,4300	no	coding-synonymous	GPR77	NM_018485.1		1,90,6412	TT,TC,CC		0.0,2.0881,0.7074		281/338	47844899	92,12914	2203	4300	6503	SO:0001819	synonymous_variant	27202	exon2			TGCCCTCGCTCAC	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.843C>T	19.37:g.47844899C>T		107	0	0		86	48	0.55814	NM_001271750	B2RA09	Silent	SNP	ENST00000595464.1	37	CCDS12699.1																																																																																			C|0.992;T|0.008	0.008	strong		0.667	C5AR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466926.1	NM_018485		T	47844899	C	T	47844899	2	4	22	1	0	0	0	0	0	0	0	1	6717	871	31	1		1	GPR77	19	47844899	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	260030	47844899	11284084	4013	6914											
GLTSCR1	29998	hgsc.bcm.edu	37	chr19	48182859	48182859	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatggcggggcaggcccgacGggcgctggaggggcagcggc	5	2	23	11	5	0	0	0	0	0	0	0	3	0	1	1	9	1	3	1	9	0	0	rs60219834	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48182859G>A	ENST00000396720.3	+	6	626	c.432G>A	c.(430-432)acG>acA	p.T144T	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	144										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)		CAGGCCCGACGGGCGCTGGAG	0.741													G|||	283	0.0565096	0.1997	0.0245	5008	,	,		10296	0.0		0.002	False		,,,				2504	0.0				p.T144T		Atlas-SNP	.											.	GLTSCR1	79	.	0			c.G432A						PASS	.						8	10	9					19																	48182859		677	1571	2248	SO:0001819	synonymous_variant	29998	exon6			CCCGACGGGCGCT	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.432G>A	19.37:g.48182859G>A		4	0	0		12	8	0.666667	NM_015711	A8MW01	Silent	SNP	ENST00000396720.3	37	CCDS46134.1																																																																																			G|0.943;A|0.057	0.057	strong		0.741	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711		A	48182859	G	A	48182859	2	1	22	1	0	0	0	0	0	0	0	1	6482	1103	39	1		1	GLTSCR1	19	48182859	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	337960	48182859	10946124	4014	6915											
TPRX1	284355	hgsc.bcm.edu	37	chr19	48305731	48305731	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gggcctgggtttgggcctggGatcgggcctgggtttgggcc	1	10	21	9	1	0	0	0	0	0	0	1	1	0	1	4	7	0	2	4	7	0	2	rs79291962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48305731G>T	ENST00000322175.3	-	2	692	c.537C>A	c.(535-537)atC>atA	p.I179I	TPRX1_ENST00000535759.1_Silent_p.I276I|TPRX1_ENST00000543508.1_Silent_p.I169I	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	179	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)		ttgggcctgggatcgggcctg	0.662													G|||	40	0.00798722	0.0295	0.0014	5008	,	,		13670	0.0		0.0	False		,,,				2504	0.0				p.I179I	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											.	TPRX1	46	.	0			c.C537A						PASS	.	G		80,3372		0,80,1646	15	13	14		537	0.3	0.1	19	dbSNP_131	14	1,6371		0,1,3185	no	coding-synonymous	TPRX1	NM_198479.2		0,81,4831	TT,TG,GG		0.0157,2.3175,0.8245		179/412	48305731	81,9743	1726	3186	4912	SO:0001819	synonymous_variant	284355	exon2			GCCTGGGATCGGG		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.537C>A	19.37:g.48305731G>T		111	0	0		129	60	0.465116	NM_198479	A5D8Y3|B2RPL5	Silent	SNP	ENST00000322175.3	37	CCDS33066.1																																																																																			G|0.993;T|0.007	0.007	strong		0.662	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479		T	48305731	G	T	48305731	2	4	22	1	0	0	0	0	0	0	0	1	16437	1164	41	4		4	TPRX1	19	48305731	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	122872	48305731	10823252	4015	6916											
PLA2G4C	8605	hgsc.bcm.edu	37	chr19	48558159	48558159	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acaggcatctatgttgaacaGgggaaaatgcatcaccactg	14	8	10	9	0	2	1	1	1	1	0	2	2	2	2	1	3	2	3	1	3	4	2	rs2307280	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48558159G>A	ENST00000599921.1	-	15	1762	c.1405C>T	c.(1405-1407)Ctg>Ttg	p.L469L	PLA2G4C_ENST00000596510.1_5'UTR|PLA2G4C_ENST00000599111.1_Silent_p.L479L|PLA2G4C_ENST00000413144.2_Silent_p.L469L|PLA2G4C_ENST00000354276.3_Silent_p.L469L			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	469	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)		ATGTTGAACAGGGGAAAATGC	0.517													g|||	408	0.0814696	0.2965	0.0231	5008	,	,		18425	0.0		0.0	False		,,,				2504	0.0				p.L479L		Atlas-SNP	.											.	PLA2G4C	76	.	0			c.C1435T						PASS	.	G	,,	996,3410	372.2+/-320.3	116,764,1323	110	102	105		1435,1405,1405	1.9	0.9	19	dbSNP_100	105	12,8588	7.7+/-29.5	0,12,4288	no	coding-synonymous,coding-synonymous,coding-synonymous	PLA2G4C	NM_001159322.1,NM_001159323.1,NM_003706.2	,,	116,776,5611	AA,AG,GG		0.1395,22.6055,7.7503	,,	479/552,469/528,469/542	48558159	1008,11998	2203	4300	6503	SO:0001819	synonymous_variant	8605	exon15			TGAACAGGGGAAA	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.1405C>T	19.37:g.48558159G>A		121	0	0		130	66	0.507692	NM_001159322	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Silent	SNP	ENST00000599921.1	37	CCDS12710.1																																																																																			G|0.926;A|0.074	0.074	strong		0.517	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1			A	48558159	G	A	48558159	2	1	22	1	0	0	0	0	0	0	0	1	12012	991	35	2		2	PLA2G4C	19	48558159	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	252428	48558159	10570824	4016	6917											
PLA2G4C	8605	hgsc.bcm.edu	37	chr19	48602933	48602933	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggaatgacttacttctcTggtttgcttagagataacca	10	14	9	8	0	1	2	0	1	1	1	2	4	1	3	1	2	3	2	1	2	4	5	rs2307282	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48602933T>C	ENST00000599921.1	-	5	799	c.442A>G	c.(442-444)Aga>Gga	p.R148G	PLA2G4C_ENST00000599111.1_Missense_Mutation_p.R158G|PLA2G4C_ENST00000413144.2_Missense_Mutation_p.R148G|PLA2G4C_ENST00000354276.3_Missense_Mutation_p.R148G			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	148	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.		R -> G (in dbSNP:rs2307282). {ECO:0000269|Ref.3}.		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)		CTTACTTCTCTGGTTTGCTTA	0.527													T|||	221	0.0441294	0.1566	0.013	5008	,	,		17533	0.0		0.0	False		,,,				2504	0.0051				p.R158G		Atlas-SNP	.											PLA2G4C,middle_lobe,carcinoma,+1,1	PLA2G4C	76	1	0			c.A472G						PASS	.	T	GLY/ARG,GLY/ARG,GLY/ARG	504,3902	234.6+/-247.4	33,438,1732	102	98	99		472,442,442	0.8	0.4	19	dbSNP_100	99	13,8587	8.4+/-32.0	0,13,4287	yes	missense,missense,missense	PLA2G4C	NM_001159322.1,NM_001159323.1,NM_003706.2	125,125,125	33,451,6019	CC,CT,TT		0.1512,11.4389,3.9751	probably-damaging,probably-damaging,probably-damaging	158/552,148/528,148/542	48602933	517,12489	2203	4300	6503	SO:0001583	missense	8605	exon5			CTTCTCTGGTTTG	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.442A>G	19.37:g.48602933T>C	ENSP00000469473:p.Arg148Gly	113	0	0		84	38	0.452381	NM_001159322	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Missense_Mutation	SNP	ENST00000599921.1	37	CCDS12710.1	73	0.033424908424908424	67	0.13617886178861788	6	0.016574585635359115	0	0.0	0	0.0	T	16.81	3.226912	0.58668	0.114389	0.001512	ENSG00000105499	ENST00000354276;ENST00000413144	T;T	0.03920	3.76;3.76	3.17	0.779	0.18550	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.158082	0.39985	U	0.001218	T	0.00039	0.0001	N	0.05487	-0.04	0.26973	N	0.965549	D;D;D	0.63046	0.992;0.992;0.992	D;D;D	0.63192	0.912;0.912;0.912	T	0.44143	-0.9347	10	0.15499	T	0.54	-15.3518	7.5148	0.27593	0.0:0.0:0.4963:0.5037	rs2307282;rs52815563;rs56435935;rs2307282	158;148;148	B4DI40;Q8WWC5;Q9UP65	.;.;PA24C_HUMAN	G	148	ENSP00000346228:R148G;ENSP00000400036:R148G	ENSP00000346228:R148G	R	-	1	2	PLA2G4C	53294745	0.937000	0.31787	0.417000	0.26559	0.668000	0.39293	0.459000	0.21908	-0.144000	0.11314	0.338000	0.21704	AGA	T|0.956;C|0.044	0.044	strong		0.527	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1			C	48602933	T	C	48602933	3	2	22	1	0	0	0	0	1	0	0	0	12012	1588	55	3	1239	3	PLA2G4C	19	48602933	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	44774	48602933	10526050	4017	6918											
CYTH2	9266	hgsc.bcm.edu	37	chr19	48977189	48977189	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctatggagctttcgcctaccCggagaggcccagaaaattga	11	8	11	11	2	0	3	0	1	0	2	1	5	0	4	3	3	2	1	3	3	4	4	rs28582663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48977189C>T	ENST00000452733.2	+	6	938	c.462C>T	c.(460-462)ccC>ccT	p.P154P	CYTH2_ENST00000427476.1_Silent_p.P154P			Q99418	CYH2_HUMAN	cytohesin 2	154	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				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						TTCGCCTACCCGGAGAGGCCC	0.607													C|||	61	0.0121805	0.0431	0.0043	5008	,	,		16544	0.0		0.0	False		,,,				2504	0.001				p.P154P		Atlas-SNP	.											.	CYTH2	33	.	0			c.C462T						PASS	.	C	,	193,4213	123.3+/-160.7	1,191,2011	48	47	47		462,462	-7.4	0.9	19	dbSNP_125	47	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	CYTH2	NM_004228.6,NM_017457.5	,	1,192,6310	TT,TC,CC		0.0116,4.3804,1.4916	,	154/400,154/401	48977189	194,12812	2203	4300	6503	SO:0001819	synonymous_variant	9266	exon6			CCTACCCGGAGAG	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.462C>T	19.37:g.48977189C>T		89	0	0		74	74	1	NM_017457	A8K8P0|Q8IXY9|Q92958	Silent	SNP	ENST00000452733.2	37	CCDS12722.1																																																																																			C|0.982;T|0.018	0.018	strong		0.607	CYTH2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317060.1	NM_004228		T	48977189	C	T	48977189	2	4	22	1	0	0	0	0	0	0	0	1	4206	639	23	1		1	CYTH2	19	48977189	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	374256	48977189	10151794	4018	6919											
SPHK2	56848	hgsc.bcm.edu	37	chr19	49131317	49131317	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acggtctcgggagacgggctGctccatgaggtagagcagga	9	6	17	9	3	1	3	0	1	1	2	3	5	2	4	1	5	2	4	1	5	1	1	rs116785119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49131317G>T	ENST00000245222.4	+	5	1113	c.747G>T	c.(745-747)ctG>ctT	p.L249L	SPHK2_ENST00000443164.1_Silent_p.L311L|SPHK2_ENST00000600537.1_Silent_p.L190L|SPHK2_ENST00000601712.1_Silent_p.L213L|SPHK2_ENST00000598088.1_Silent_p.L249L|SPHK2_ENST00000599029.1_Silent_p.L213L|SPHK2_ENST00000340932.3_Silent_p.L213L|SPHK2_ENST00000599748.1_Silent_p.L213L	NM_001204158.2|NM_001243876.1|NM_020126.4	NP_001191087.1|NP_001230805.1|NP_064511.2	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2	249	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				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)		GAGACGGGCTGCTCCATGAGG	0.647													G|||	17	0.00339457	0.0121	0.0014	5008	,	,		16367	0.0		0.0	False		,,,				2504	0.0				p.L249L		Atlas-SNP	.											.	SPHK2	62	.	0			c.G747T						PASS	.	G	,,,	56,4350	55.5+/-91.7	1,54,2148	55	60	58		570,747,639,747	4.6	1	19	dbSNP_132	58	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPHK2	NM_001204158.2,NM_001204159.2,NM_001204160.2,NM_020126.4	,,,	1,54,6448	TT,TG,GG		0.0,1.271,0.4306	,,,	190/596,249/655,213/619,249/655	49131317	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	56848	exon5			CGGGCTGCTCCAT	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.747G>T	19.37:g.49131317G>T		61	0	0		65	37	0.569231	NM_020126	A0T4C8|B4DU87|Q9BRN1|Q9H0Q2|Q9NWU7	Silent	SNP	ENST00000245222.4	37	CCDS12727.1																																																																																			G|0.996;T|0.004	0.004	strong		0.647	SPHK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466153.1			T	49131317	G	T	49131317	2	4	22	1	0	0	0	0	0	0	0	1	15062	1306	46	4		4	SPHK2	19	49131317	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	154128	49131317	9997666	4019	6920											
SPHK2	56848	hgsc.bcm.edu	37	chr19	49132646	49132646	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctccgctgggcaccccgctGcccccagactgggtgacgct	4	6	12	19	3	0	2	0	1	0	1	1	2	1	2	6	2	1	4	6	2	0	0	rs75629654	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49132646G>A	ENST00000245222.4	+	7	1947	c.1581G>A	c.(1579-1581)ctG>ctA	p.L527L	SPHK2_ENST00000443164.1_Silent_p.L589L|SPHK2_ENST00000600537.1_Silent_p.L468L|SPHK2_ENST00000598088.1_Silent_p.L527L|SPHK2_ENST00000599029.1_Silent_p.L491L|SPHK2_ENST00000340932.3_Silent_p.L489L|SPHK2_ENST00000599748.1_Silent_p.L491L	NM_001204158.2|NM_001243876.1|NM_020126.4	NP_001191087.1|NP_001230805.1|NP_064511.2	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2	527					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)		GCACCCCGCTGCCCCCAGACT	0.711													G|||	273	0.0545128	0.1944	0.0216	5008	,	,		12771	0.001		0.0	False		,,,				2504	0.0				p.L527L		Atlas-SNP	.											.	SPHK2	62	.	0			c.G1581A						PASS	.	G	,,,	717,3679		52,613,1533	19	21	20		1404,1581,1473,1581	0.3	0.9	19	dbSNP_131	20	4,8590		0,4,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPHK2	NM_001204158.2,NM_001204159.2,NM_001204160.2,NM_020126.4	,,,	52,617,5826	AA,AG,GG		0.0465,16.3103,5.5504	,,,	468/596,527/655,491/619,527/655	49132646	721,12269	2198	4297	6495	SO:0001819	synonymous_variant	56848	exon7			CCCGCTGCCCCCA	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.1581G>A	19.37:g.49132646G>A		29	0	0		56	56	1	NM_020126	A0T4C8|B4DU87|Q9BRN1|Q9H0Q2|Q9NWU7	Silent	SNP	ENST00000245222.4	37	CCDS12727.1																																																																																			G|0.940;A|0.060	0.060	strong		0.711	SPHK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466153.1			A	49132646	G	A	49132646	2	1	22	1	0	0	0	0	0	0	0	1	15062	1306	46	2		2	SPHK2	19	49132646	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1329	49132646	9996337	4020	6921											
SPHK2	56848	hgsc.bcm.edu	37	chr19	49133020	49133020	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcctcctggctgcccggggcGggagccctgaaactaaacaa	9	5	13	14	2	0	1	0	1	0	0	1	2	1	2	4	4	4	1	4	4	4	1	rs11881285	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49133020G>A	ENST00000245222.4	+	7	2321	c.1955G>A	c.(1954-1956)cGg>cAg	p.R652Q	SPHK2_ENST00000443164.1_Intron|SPHK2_ENST00000600537.1_Missense_Mutation_p.R593Q|SPHK2_ENST00000598088.1_Missense_Mutation_p.R652Q|SPHK2_ENST00000599029.1_Intron|SPHK2_ENST00000340932.3_Missense_Mutation_p.R614Q|SPHK2_ENST00000599748.1_Missense_Mutation_p.R616Q	NM_001204158.2|NM_001243876.1|NM_020126.4	NP_001191087.1|NP_001230805.1|NP_064511.2	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2	652			R -> Q (in dbSNP:rs11881285).		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)		TGCCCGGGGCGGGAGCCCTGA	0.657													G|||	274	0.0547125	0.1959	0.0216	5008	,	,		14281	0.0		0.0	False		,,,				2504	0.0				p.R652Q		Atlas-SNP	.											.	SPHK2	62	.	0			c.G1955A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	687,3701		44,599,1551	13	14	13		1955,1847,1955,1778	0.8	0	19	dbSNP_120	13	3,8561		0,3,4279	yes	missense,missense,missense,missense	SPHK2	NM_020126.4,NM_001204160.2,NM_001204159.2,NM_001204158.2	43,43,43,43	44,602,5830	AA,AG,GG		0.035,15.6563,5.3274	benign,benign,benign,benign	652/655,616/619,652/655,593/596	49133020	690,12262	2194	4282	6476	SO:0001583	missense	56848	exon7			CGGGGCGGGAGCC	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.1955G>A	19.37:g.49133020G>A	ENSP00000245222:p.Arg652Gln	150	1	0.00666667		165	165	1	NM_020126	A0T4C8|B4DU87|Q9BRN1|Q9H0Q2|Q9NWU7	Missense_Mutation	SNP	ENST00000245222.4	37	CCDS12727.1	94	0.04304029304029304	84	0.17073170731707318	10	0.027624309392265192	0	0.0	0	0.0	G	13.95	2.389587	0.42410	0.156563	3.5E-4	ENSG00000063176	ENST00000245222;ENST00000406269;ENST00000340932	T;T	0.26067	2.04;1.76	4.57	0.757	0.18427	.	1.133370	0.06720	N	0.774700	T	0.00039	0.0001	N	0.00926	-1.1	0.09310	N	1	B;B	0.10296	0.001;0.003	B;B	0.01281	0.0;0.0	T	0.29882	-0.9997	10	0.87932	D	0	.	4.2933	0.10888	0.1758:0.4248:0.3994:0.0	rs11881285;rs11881285	593;652	B4DU87;Q9NRA0	.;SPHK2_HUMAN	Q	652;625;614	ENSP00000245222:R652Q;ENSP00000341091:R614Q	ENSP00000245222:R652Q	R	+	2	0	SPHK2	53824832	0.005000	0.15991	0.003000	0.11579	0.039000	0.13416	0.222000	0.17699	0.076000	0.16826	0.555000	0.69702	CGG	G|0.942;A|0.058	0.058	strong		0.657	SPHK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466153.1			A	49133020	G	A	49133020	3	1	22	1	0	0	0	0	1	0	0	0	15062	1116	39	1	1977	1	SPHK2	19	49133020	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	374	49133020	9995963	4021	6922											
FUT1	2523	hgsc.bcm.edu	37	chr19	49253717	49253717	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aacgtcacatcgccctgggaGgtgtcgatgttttctttaca	8	13	10	10	3	2	0	1	0	1	0	4	2	2	1	1	2	2	1	1	2	2	4	rs838138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49253717G>T	ENST00000310160.3	-	4	1796	c.822C>A	c.(820-822)acC>acA	p.T274T	FUT1_ENST00000601931.1_5'Flank	NM_000148.3	NP_000139.1	P19526	FUT1_HUMAN	fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, H blood group)	274					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)		CGCCCTGGGAGGTGTCGATGT	0.577													G|||	267	0.0533147	0.1884	0.0259	5008	,	,		20123	0.0		0.0	False		,,,				2504	0.0				p.T274T		Atlas-SNP	.											.	FUT1	44	.	0			c.C822A						PASS	.	G		653,3753	279.0+/-274.6	52,549,1602	166	127	140		822	1.1	0.3	19	dbSNP_86	140	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	FUT1	NM_000148.3		52,551,5900	TT,TG,GG		0.0233,14.8207,5.0361		274/366	49253717	655,12351	2203	4300	6503	SO:0001819	synonymous_variant	2523	exon4			CTGGGAGGTGTCG		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.822C>A	19.37:g.49253717G>T		77	0	0		55	55	1	NM_000148	O14505|O14506|O14507	Silent	SNP	ENST00000310160.3	37	CCDS12733.1																																																																																			G|0.955;T|0.045	0.045	strong		0.577	FUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466194.1	NM_000148		T	49253717	G	T	49253717	2	4	22	1	0	0	0	0	0	0	0	1	6109	987	35	4		4	FUT1	19	49253717	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	120697	49253717	9875266	4022	6923											
PPP1R15A	23645	hgsc.bcm.edu	37	chr19	49377120	49377120	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacagaacctctacttctgcCttgtctccaggatccaagcc	9	10	6	16	0	3	1	0	0	3	1	5	2	4	2	5	1	4	0	5	1	3	3	rs34899467	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49377120C>T	ENST00000200453.5	+	2	899	c.630C>T	c.(628-630)gcC>gcT	p.A210A		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	210	Glu-rich.				apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		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;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		CTACTTCTGCCTTGTCTCCAG	0.512													C|||	82	0.0163738	0.0545	0.0014	5008	,	,		18999	0.002		0.0	False		,,,				2504	0.0072				p.A210A		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.C630T						PASS	.	C		201,4205	124.9+/-162.1	2,197,2004	128	141	137		630	-0.7	0	19	dbSNP_126	137	0,8600		0,0,4300	no	coding-synonymous	PPP1R15A	NM_014330.3		2,197,6304	TT,TC,CC		0.0,4.562,1.5454		210/675	49377120	201,12805	2203	4300	6503	SO:0001819	synonymous_variant	23645	exon2			TTCTGCCTTGTCT	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14375	protein-coding gene	gene with protein product	"growth arrest and DNA-damage-inducible 34"	611048	"protein phosphatase 1, regulatory (inhibitor) subunit 15A"			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.630C>T	19.37:g.49377120C>T		93	0	0		76	35	0.460526	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Silent	SNP	ENST00000200453.5	37	CCDS12738.1																																																																																			C|0.984;T|0.016	0.016	strong		0.512	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330		T	49377120	C	T	49377120	2	4	22	1	0	0	0	0	0	0	0	1	12375	668	24	2		2	PPP1R15A	19	49377120	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	123403	49377120	9751863	4023	6924											
LHB	3972	hgsc.bcm.edu	37	chr19	49519518	49519518	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cgaagcgcacatcacggtagGtgcacaccacctgaggcagg	11	4	13	13	3	1	1	1	1	0	0	1	2	1	1	2	4	2	4	2	4	2	1	rs116437960	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49519518G>T	ENST00000221421.2	-	3	232	c.233C>A	c.(232-234)aCc>aAc	p.T78N	CTB-60B18.10_ENST00000600007.1_lincRNA	NM_000894.2	NP_000885.1	P01229	LSHB_HUMAN	luteinizing hormone beta polypeptide	78					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)		ATCACGGTAGGTGCACACCAC	0.677													G|||	71	0.0141773	0.0507	0.0058	5008	,	,		17306	0.0		0.0	False		,,,				2504	0.0				p.T78N		Atlas-SNP	.											.	LHB	20	.	0			c.C233A						PASS	.	G	ASN/THR	181,4223	113.3+/-151.4	8,165,2029	89	80	83		233	1.4	1	19	dbSNP_132	83	3,8595	3.0+/-9.4	0,3,4296	no	missense	LHB	NM_000894.2	65	8,168,6325	TT,TG,GG		0.0349,4.1099,1.4152	benign	78/142	49519518	184,12818	2202	4299	6501	SO:0001583	missense	3972	exon3			CGGTAGGTGCACA		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.233C>A	19.37:g.49519518G>T	ENSP00000221421:p.Thr78Asn	112	0	0		119	48	0.403361	NM_000894	Q9UDI0	Missense_Mutation	SNP	ENST00000221421.2	37	CCDS12748.1	23	0.010531135531135532	20	0.04065040650406504	3	0.008287292817679558	0	0.0	0	0.0	G	3.147	-0.175109	0.06421	0.041099	3.49E-4	ENSG00000104826	ENST00000221421;ENST00000391870	D	0.91792	-2.91	4.71	1.35	0.21983	Cystine knot (1);	0.000000	0.85682	D	0.000000	T	0.61185	0.2327	N	0.21448	0.665	0.45390	D	0.998374	B	0.10296	0.003	B	0.12156	0.007	T	0.66011	-0.6029	10	0.32370	T	0.25	-7.5582	11.6053	0.51029	0.0:0.0:0.6162:0.3838	.	78	P01229	LSHB_HUMAN	N	78;94	ENSP00000221421:T78N	ENSP00000221421:T78N	T	-	2	0	LHB	54211330	1.000000	0.71417	0.999000	0.59377	0.009000	0.06853	2.435000	0.44811	0.173000	0.19788	-3.593000	0.00028	ACC	G|0.988;T|0.012	0.012	strong		0.677	LHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466246.1	NM_000894		T	49519518	G	T	49519518	3	4	22	1	0	0	0	0	1	0	0	0	8770	1261	44	4	196	4	LHB	19	49519518	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	142398	49519518	9609465	4024	6925											
HRC	3270	hgsc.bcm.edu	37	chr19	49657526	49657526	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tcaacctcttcctttctgtgGtcttggtgcctgtgggcctg	2	16	11	12	0	4	0	1	0	3	0	5	0	5	0	4	3	2	0	4	3	1	3	rs150557795	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49657526G>A	ENST00000252825.4	-	1	1155	c.969C>T	c.(967-969)gaC>gaT	p.D323D	HRC_ENST00000595625.1_Silent_p.D323D	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	323	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)		CCTTTCTGTGGTCTTGGTGCC	0.542													G|||	63	0.0125799	0.0401	0.0029	5008	,	,		27949	0.0		0.005	False		,,,				2504	0.0031				p.D323D	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											HRC,NS,carcinoma,0,1	HRC	85	1	0			c.C969T						scavenged	.						212	161	178					19																	49657526		2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			TCTGTGGTCTTGG		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.969C>T	19.37:g.49657526G>A		253	1	0.00395257		283	36	0.127208	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	37	CCDS12759.1																																																																																			G|0.999;A|0.001	0.001	weak		0.542	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		A	49657526	G	A	49657526	2	1	22	1	0	0	0	0	0	0	0	1	7361	1252	44	2		2	HRC	19	49657526	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	138008	49657526	9471457	4025	6926											
SLC6A16	28968	hgsc.bcm.edu	37	chr19	49793620	49793620	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcatcaagagcagtgcccaCggtgggtatggtcgaagcac	11	7	13	10	2	2	1	2	0	0	1	3	2	2	1	1	3	3	3	1	3	3	1	rs34817563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49793620C>T	ENST00000335875.4	-	12	2212	c.1971G>A	c.(1969-1971)ccG>ccA	p.P657P	SLC6A16_ENST00000454748.3_3'UTR	NM_014037.2	NP_054756.2	Q9GZN6	S6A16_HUMAN	solute carrier family 6, member 16	657					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)		GCAGTGCCCACGGTGGGTATG	0.488													T|||	106	0.0211661	0.0711	0.0144	5008	,	,		20056	0.0		0.001	False		,,,				2504	0.001				p.P657P		Atlas-SNP	.											.	SLC6A16	62	.	0			c.G1971A						PASS	.	T		221,3697		6,209,1744	68	66	67		1971	-4.6	0	19	dbSNP_126	67	2,8306		0,2,4152	no	coding-synonymous	SLC6A16	NM_014037.2		6,211,5896	TT,TC,CC		0.0241,5.6406,1.824		657/737	49793620	223,12003	1959	4154	6113	SO:0001819	synonymous_variant	28968	exon12			TGCCCACGGTGGG	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.1971G>A	19.37:g.49793620C>T		134	0	0		133	68	0.511278	NM_014037	Q8IYV4|Q9Y5I9	Silent	SNP	ENST00000335875.4	37	CCDS42590.1																																																																																			C|0.989;T|0.011	0.011	strong		0.488	SLC6A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465503.2	NM_014037		T	49793620	C	T	49793620	2	4	22	1	0	0	0	0	0	0	0	1	14694	523	19	1		1	SLC6A16	19	49793620	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	136094	49793620	9335363	4026	6927											
TEAD2	8463	hgsc.bcm.edu	37	chr19	49852070	49852070	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gggcgatggggtaggtggggGcaggggtgagagggcttggg	5	6	27	3	1	0	1	0	1	0	1	0	3	0	1	0	10	0	3	0	10	1	2	rs201393859	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49852070G>A	ENST00000311227.2	-	8	715	c.625C>T	c.(625-627)Ccc>Tcc	p.P209S	TEAD2_ENST00000598810.1_Missense_Mutation_p.P213S|TEAD2_ENST00000598397.1_5'UTR|TEAD2_ENST00000593945.1_Missense_Mutation_p.P213S|TEAD2_ENST00000601519.1_Missense_Mutation_p.P212S|TEAD2_ENST00000377214.4_Missense_Mutation_p.P212S|TEAD2_ENST00000539846.1_Missense_Mutation_p.P81S	NM_001256659.1|NM_003598.1	NP_001243588.1|NP_003589.1	Q15562	TEAD2_HUMAN	TEA domain family member 2	209	Pro-rich.|Transcriptional activation. {ECO:0000255}.				gene expression (GO:0010467)|hippo signaling (GO:0035329)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	29		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)		GTAGGTGGGGGCAGGGGTGAG	0.577													G|||	35	0.00698882	0.0265	0.0	5008	,	,		9950	0.0		0.0	False		,,,				2504	0.0				p.P213S		Atlas-SNP	.											.	TEAD2	70	.	0			c.C637T						PASS	.	G	SER/PRO	94,4128		2,90,2019	11	14	13		625	3.6	1	19		13	2,8324		0,2,4161	yes	missense	TEAD2	NM_003598.1	74	2,92,6180	AA,AG,GG		0.024,2.2264,0.7651	benign	209/448	49852070	96,12452	2111	4163	6274	SO:0001583	missense	8463	exon9			GTGGGGGCAGGGG	X94440	CCDS12761.1, CCDS58670.1, CCDS58671.1, CCDS59406.1	19q13.3	2008-07-22							11715	protein-coding gene	gene with protein product		601729				9889009, 8702974	Standard	NM_003598		Approved	TEF-4, ETF, TEF4	uc031rls.1	Q15562		ENST00000311227.2:c.625C>T	19.37:g.49852070G>A	ENSP00000310701:p.Pro209Ser	114	0	0		127	57	0.448819	NM_001256660	B4DTJ6|M0R1T9|Q8NA25|Q96IG3	Missense_Mutation	SNP	ENST00000311227.2	37	CCDS12761.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	5.217	0.225622	0.09916	0.022264	2.4E-4	ENSG00000074219	ENST00000311227;ENST00000377214;ENST00000539846	T;T;T	0.34275	1.37;1.37;1.37	5.73	3.58	0.41010	.	0.229512	0.31031	N	0.008399	T	0.08980	0.0222	N	0.04148	-0.265	0.48975	D	0.999734	B;B;B	0.16166	0.01;0.016;0.006	B;B;B	0.22753	0.018;0.041;0.018	T	0.04930	-1.0917	10	0.30854	T	0.27	-21.1627	11.4865	0.50356	0.1569:0.0:0.8431:0.0	.	81;209;212	B4DTJ6;Q15562;Q8NA25	.;TEAD2_HUMAN;.	S	209;212;81	ENSP00000310701:P209S;ENSP00000366419:P212S;ENSP00000437928:P81S	ENSP00000310701:P209S	P	-	1	0	TEAD2	54543882	1.000000	0.71417	1.000000	0.80357	0.072000	0.16883	5.441000	0.66569	1.577000	0.49804	-0.150000	0.13652	CCC	G|0.995;A|0.005	0.005	strong		0.577	TEAD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465465.1	NM_003598		A	49852070	G	A	49852070	3	1	22	1	0	0	0	0	1	0	0	0	15754	1203	42	2	738	2	TEAD2	19	49852070	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	58450	49852070	9276913	4027	6928											
CCDC155	147872	hgsc.bcm.edu	37	chr19	49920719	49920719	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttggcccgtccccacctccCacctggccccacctccagct	4	7	6	24	1	0	0	0	0	0	0	3	0	3	0	10	2	1	1	10	2	0	1	rs79452032	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49920719C>T	ENST00000447857.3	+	20	1846	c.1641C>T	c.(1639-1641)ccC>ccT	p.P547P		NM_144688.4	NP_653289.3	Q8N6L0	KASH5_HUMAN	coiled-coil domain containing 155	547						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						CCCCACCTCCCACCTGGCCCC	0.632													c|||	104	0.0207668	0.0673	0.013	5008	,	,		14619	0.0		0.006	False		,,,				2504	0.0				p.P547P		Atlas-SNP	.											.	CCDC155	46	.	0			c.C1641T						PASS	.			159,4033		5,149,1942	47	49	48		1641	-1.5	0.9	19	dbSNP_132	48	33,8283		1,31,4126	no	coding-synonymous	CCDC155	NM_144688.4		6,180,6068	TT,TC,CC		0.3968,3.7929,1.535		547/563	49920719	192,12316	2096	4158	6254	SO:0001819	synonymous_variant	147872	exon20			ACCTCCCACCTGG		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.1641C>T	19.37:g.49920719C>T		62	0	0		83	41	0.493976	NM_144688	Q96MC3	Silent	SNP	ENST00000447857.3	37	CCDS46140.1																																																																																			C|0.987;T|0.013	0.013	strong		0.632	CCDC155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465436.2	NM_144688		T	49920719	C	T	49920719	2	4	22	1	0	0	0	0	0	0	0	1	2790	581	21	2		2	CCDC155	19	49920719	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	68649	49920719	9208264	4028	6929											
ALDH16A1	126133	hgsc.bcm.edu	37	chr19	49965956	49965956	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatgggggcccggggggctGccgcatgtgacctggtccag	5	6	18	12	2	0	1	0	1	0	0	1	1	1	1	4	6	1	2	4	6	0	0	rs10406757	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49965956G>A	ENST00000293350.4	+	8	1205	c.1042G>A	c.(1042-1044)Gcc>Acc	p.A348T	ALDH16A1_ENST00000540132.1_Missense_Mutation_p.A185T|ALDH16A1_ENST00000455361.2_Missense_Mutation_p.A297T|CTD-3148I10.9_ENST00000599536.1_5'Flank|ALDH16A1_ENST00000433981.2_Missense_Mutation_p.A183T	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	348						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)		CCGGGGGGCTGCCGCATGTGA	0.687													G|||	187	0.0373403	0.1324	0.0159	5008	,	,		12025	0.0		0.001	False		,,,				2504	0.0				p.A348T		Atlas-SNP	.											.	ALDH16A1	54	.	0			c.G1042A						PASS	.	G	THR/ALA,THR/ALA	423,3981		21,381,1800	23	26	25		889,1042	2.8	0.5	19	dbSNP_119	25	4,8592		0,4,4294	yes	missense,missense	ALDH16A1	NM_001145396.1,NM_153329.3	58,58	21,385,6094	AA,AG,GG		0.0465,9.6049,3.2846	probably-damaging,probably-damaging	297/752,348/803	49965956	427,12573	2202	4298	6500	SO:0001583	missense	126133	exon8			GGGGCTGCCGCAT	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.1042G>A	19.37:g.49965956G>A	ENSP00000293350:p.Ala348Thr	275	0	0		323	171	0.529412	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Missense_Mutation	SNP	ENST00000293350.4	37	CCDS12766.1	52	0.023809523809523808	45	0.09146341463414634	7	0.019337016574585635	0	0.0	0	0.0	G	13.56	2.274535	0.40194	0.096049	4.65E-4	ENSG00000161618	ENST00000293350;ENST00000455361;ENST00000540132;ENST00000433981	T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1	5.03	2.77	0.32553	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.412335	0.24688	N	0.036418	T	0.11410	0.0278	L	0.55834	1.745	0.09310	N	1	D;D;D	0.76494	0.999;0.998;0.997	D;D;D	0.69307	0.943;0.963;0.932	T	0.22906	-1.0203	10	0.32370	T	0.25	-22.8219	6.9006	0.24281	0.0956:0.0:0.7322:0.1723	rs10406757	185;297;348	F5H4B6;B4DLQ1;Q8IZ83	.;.;A16A1_HUMAN	T	348;297;185;183	ENSP00000293350:A348T;ENSP00000410142:A297T;ENSP00000445088:A185T;ENSP00000398675:A183T	ENSP00000293350:A348T	A	+	1	0	ALDH16A1	54657768	0.494000	0.26043	0.530000	0.27963	0.649000	0.38597	3.254000	0.51477	1.286000	0.44565	0.485000	0.47835	GCC	A|0.034;C|0.000;G|0.965	0.034	strong		0.687	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329		A	49965956	G	A	49965956	3	1	22	1	0	0	0	0	1	0	0	0	488	1319	46	2	1072	2	ALDH16A1	19	49965956	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	45237	49965956	9163027	4029	6930											
ALDH16A1	126133	hgsc.bcm.edu	37	chr19	49967996	49967996	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgttccctcaaccctgccGgctgggcctgaaatagggcc	6	8	12	15	1	1	1	1	1	0	0	2	1	2	1	5	3	2	3	5	3	3	2	rs10421522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49967996G>A	ENST00000293350.4	+	12	1708	c.1545G>A	c.(1543-1545)ccG>ccA	p.P515P	ALDH16A1_ENST00000540132.1_Silent_p.P352P|ALDH16A1_ENST00000455361.2_Silent_p.P464P|CTD-3148I10.9_ENST00000599536.1_3'UTR|ALDH16A1_ENST00000433981.2_Silent_p.P350P	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	515						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)		CAACCCTGCCGGCTGGGCCTG	0.617													g|||	197	0.0393371	0.1399	0.0159	5008	,	,		14923	0.0		0.001	False		,,,				2504	0.0				p.P515P		Atlas-SNP	.											.	ALDH16A1	54	.	0			c.G1545A						PASS	.	A	,	461,3945	218.4+/-236.5	24,413,1766	105	113	111		1392,1545	-8.9	0	19	dbSNP_119	111	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	ALDH16A1	NM_001145396.1,NM_153329.3	,	24,418,6061	AA,AG,GG		0.0581,10.463,3.583	,	464/752,515/803	49967996	466,12540	2203	4300	6503	SO:0001819	synonymous_variant	126133	exon12			CCTGCCGGCTGGG	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.1545G>A	19.37:g.49967996G>A		67	0	0		79	40	0.506329	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Silent	SNP	ENST00000293350.4	37	CCDS12766.1																																																																																			G|0.964;A|0.036	0.036	strong		0.617	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329		A	49967996	G	A	49967996	2	1	22	1	0	0	0	0	0	0	0	1	488	1103	39	1		1	ALDH16A1	19	49967996	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2040	49967996	9160987	4030	6931											
ALDH16A1	126133	hgsc.bcm.edu	37	chr19	49969501	49969501	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcgcaagacgacttcgggcGtggggggcccgggtgcaggc	6	4	20	11	5	0	1	0	0	0	1	1	2	0	1	1	6	2	2	1	6	1	1	rs61732839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49969501G>A	ENST00000293350.4	+	14	2062	c.1899G>A	c.(1897-1899)gcG>gcA	p.A633A	ALDH16A1_ENST00000540132.1_Silent_p.A470A|ALDH16A1_ENST00000455361.2_Silent_p.A582A|CTD-3148I10.9_ENST00000599536.1_Intron|ALDH16A1_ENST00000433981.2_Silent_p.A468A	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	633						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)		GACTTCGGGCGTGGGGGGCCC	0.716													G|||	188	0.0375399	0.1324	0.0159	5008	,	,		14127	0.001		0.001	False		,,,				2504	0.0				p.A633A		Atlas-SNP	.											.	ALDH16A1	54	.	0			c.G1899A						PASS	.	G	,	360,3874		8,344,1765	9	11	11		1746,1899	-8.7	0	19	dbSNP_129	11	9,8349		0,9,4170	no	coding-synonymous,coding-synonymous	ALDH16A1	NM_001145396.1,NM_153329.3	,	8,353,5935	AA,AG,GG		0.1077,8.5026,2.9304	,	582/752,633/803	49969501	369,12223	2117	4179	6296	SO:0001819	synonymous_variant	126133	exon14			TCGGGCGTGGGGG	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.1899G>A	19.37:g.49969501G>A		40	0	0		50	20	0.4	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Silent	SNP	ENST00000293350.4	37	CCDS12766.1																																																																																			G|0.975;A|0.025	0.025	strong		0.716	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329		A	49969501	G	A	49969501	2	1	22	1	0	0	0	0	0	0	0	1	488	1132	40	1		1	ALDH16A1	19	49969501	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1505	49969501	9159482	4031	6932											
ALDH16A1	126133	hgsc.bcm.edu	37	chr19	49969522	49969522	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tggggggcccgggtgcaggcCcaaggccacaccctgcaggt	6	4	17	14	1	0	0	0	0	0	0	0	0	0	0	4	7	2	2	4	7	1	0	rs116631301	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49969522C>T	ENST00000293350.4	+	14	2083	c.1920C>T	c.(1918-1920)gcC>gcT	p.A640A	ALDH16A1_ENST00000540132.1_Silent_p.A477A|ALDH16A1_ENST00000455361.2_Silent_p.A589A|CTD-3148I10.9_ENST00000599536.1_Intron|ALDH16A1_ENST00000433981.2_Silent_p.A475A	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	640						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)		GGGTGCAGGCCCAAGGCCACA	0.701													C|||	44	0.00878594	0.031	0.0043	5008	,	,		14666	0.0		0.0	False		,,,				2504	0.0				p.A640A		Atlas-SNP	.											.	ALDH16A1	54	.	0			c.C1920T						PASS	.	C	,	145,4033		0,145,1944	7	9	8		1767,1920	3.3	1	19	dbSNP_132	8	3,8237		0,3,4117	no	coding-synonymous,coding-synonymous	ALDH16A1	NM_001145396.1,NM_153329.3	,	0,148,6061	TT,TC,CC		0.0364,3.4706,1.1918	,	589/752,640/803	49969522	148,12270	2089	4120	6209	SO:0001819	synonymous_variant	126133	exon14			GCAGGCCCAAGGC	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.1920C>T	19.37:g.49969522C>T		34	0	0		34	16	0.470588	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Silent	SNP	ENST00000293350.4	37	CCDS12766.1																																																																																			C|0.992;T|0.008	0.008	strong		0.701	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329		T	49969522	C	T	49969522	2	4	22	1	0	0	0	0	0	0	0	1	488	610	22	2		2	ALDH16A1	19	49969522	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	21	49969522	9159461	4032	6933											
FLT3LG	2323	hgsc.bcm.edu	37	chr19	49977929	49977929	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgccagcctggagcccaacAgtgcgtaaaccccagggaca	11	3	12	15	2	0	0	0	0	0	0	0	2	0	2	5	2	5	1	5	2	3	1	rs75750998	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49977929A>G	ENST00000594009.1	+	1	112	c.33A>G	c.(31-33)acA>acG	p.T11T	FLT3LG_ENST00000597551.1_Splice_Site_p.T11T|FLT3LG_ENST00000204637.2_5'UTR|CTD-3148I10.15_ENST00000595815.1_RNA|FLT3LG_ENST00000600429.1_Splice_Site_p.T11T|CTD-3148I10.9_ENST00000599536.1_3'UTR|FLT3LG_ENST00000344019.3_Splice_Site_p.T11T|FLT3LG_ENST00000595510.1_5'UTR|FLT3LG_ENST00000596435.1_Splice_Site_p.T11T	NM_001204503.1	NP_001191432.1	P49771	FLT3L_HUMAN	fms-related tyrosine kinase 3 ligand	11					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)		GGAGCCCAACAGTGCGTAAAC	0.612													a|||	162	0.0323482	0.1036	0.0259	5008	,	,		12436	0.0		0.007	False		,,,				2504	0.0				p.T11T		Atlas-SNP	.											.	FLT3LG	22	.	0			c.A33G						PASS	.	A	,,	347,4059	173.0+/-202.9	13,321,1869	40	38	38		33,33,33	-4.8	0.9	19	dbSNP_131	38	13,8585	9.8+/-36.6	0,13,4286	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	FLT3LG	NM_001204502.1,NM_001204503.1,NM_001459.3	,,	13,334,6155	GG,GA,AA		0.1512,7.8756,2.7684	,,	11/236,11/236,11/236	49977929	360,12644	2203	4299	6502	SO:0001630	splice_region_variant	2323	exon1			CCCAACAGTGCGT	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.33+1A>G	19.37:g.49977929A>G		285	0	0		357	183	0.512605	NM_001204503	A0AVC2|B9EGH2|Q05C96	Silent	SNP	ENST00000594009.1	37	CCDS12767.1																																																																																			A|0.974;G|0.026	0.026	strong		0.612	FLT3LG-007	KNOWN	alternative_3_UTR|alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465305.1		Silent	G	49977929	A	G	49977929	5	3	22	1	0	0	0	0	0	0	1	0	5951	202	7	3	35	3	FLT3LG	19	49977929	Splice_Site	SNP	A	TCGA-G8-6324-01A-11D-2210-10	8407	49977929	9151054	4033	6934											
FCGRT	2217	hgsc.bcm.edu	37	chr19	50017191	50017191	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcggtgtcctcgcctgccccGgggactcctgccttctgggt	1	10	14	16	3	1	0	0	0	1	0	4	1	3	1	6	4	2	0	6	4	0	1	rs11551281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50017191G>T	ENST00000221466.5	+	3	612	c.126G>T	c.(124-126)ccG>ccT	p.P42P	FCGRT_ENST00000596975.1_Silent_p.P42P|FCGRT_ENST00000426395.3_Silent_p.P42P|FCGRT_ENST00000594823.1_3'UTR|FCGRT_ENST00000599988.1_Intron	NM_001136019.2	NP_001129491.1	P55899	FCGRN_HUMAN	Fc fragment of IgG, receptor, transporter, alpha	42	Alpha-1.				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)		CGCCTGCCCCGGGGACTCCTG	0.652													G|||	98	0.0195687	0.0363	0.0029	5008	,	,		13393	0.0456		0.0	False		,,,				2504	0.002				p.P42P		Atlas-SNP	.											.	FCGRT	23	.	0			c.G126T						PASS	.	G	,	151,4255	103.0+/-141.5	3,145,2055	108	109	109		126,126	-5.5	0	19	dbSNP_120	109	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous	FCGRT	NM_001136019.2,NM_004107.4	,	3,148,6352	TT,TG,GG		0.0349,3.4271,1.1841	,	42/366,42/366	50017191	154,12852	2203	4300	6503	SO:0001819	synonymous_variant	2217	exon3			TGCCCCGGGGACT	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.126G>T	19.37:g.50017191G>T		170	0	0		162	88	0.54321	NM_001136019	Q5HYM5|Q9HBV7|Q9NZ19	Silent	SNP	ENST00000221466.5	37	CCDS12770.1																																																																																			G|0.984;T|0.016	0.016	strong		0.652	FCGRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465267.1			T	50017191	G	T	50017191	2	4	22	1	0	0	0	0	0	0	0	1	5794	1103	39	4		4	FCGRT	19	50017191	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	39262	50017191	9111792	4034	6935											
SCAF1	58506	hgsc.bcm.edu	37	chr19	50156762	50156762	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaagaggaagaggaggaggAgcagcagcctgctaccacca	14	2	16	9	0	0	2	0	0	0	2	0	7	0	7	3	5	5	3	3	5	3	1	rs201628577		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50156762A>T	ENST00000360565.3	+	7	3240	c.3116A>T	c.(3115-3117)gAg>gTg	p.E1039V		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	1039	Glu-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)		gaggaggaggagCAGCAGCCT	0.692																																					p.E1039V		Atlas-SNP	.											.	SCAF1	78	.	0			c.A3116T						PASS	.	A	VAL/GLU	4,4388		0,4,2192	9	12	11		3116	4.7	1	19		11	0,8566		0,0,4283	no	missense	SCAF1	NM_021228.2	121	0,4,6475	TT,TA,AA		0.0,0.0911,0.0309	possibly-damaging	1039/1313	50156762	4,12954	2196	4283	6479	SO:0001583	missense	58506	exon7			AGGAGGAGCAGCA	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.3116A>T	19.37:g.50156762A>T	ENSP00000353769:p.Glu1039Val	33	0	0		27	12	0.444444	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Missense_Mutation	SNP	ENST00000360565.3	37	CCDS33074.1	.	.	.	.	.	.	.	.	.	.	A	10.60	1.395512	0.25205	9.11E-4	0.0	ENSG00000126461	ENST00000360565	T	0.33865	1.39	5.74	4.67	0.58626	.	.	.	.	.	T	0.25344	0.0616	N	0.19112	0.55	0.24915	N	0.992013	P	0.41131	0.739	B	0.41332	0.354	T	0.05784	-1.0864	8	.	.	.	-21.1177	9.6199	0.39714	0.8441:0.0:0.0:0.1559	.	1039	Q9H7N4	SFR19_HUMAN	V	1039	ENSP00000353769:E1039V	.	E	+	2	0	SCAF1	54848574	1.000000	0.71417	1.000000	0.80357	0.216000	0.24613	1.552000	0.36244	2.189000	0.69895	0.533000	0.62120	GAG	.	.	weak		0.692	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228		T	50156762	A	T	50156762	3	4	22	1	0	0	0	0	1	0	0	0	13883	304	11	5	3138	5	SCAF1	19	50156762	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	139571	50156762	8972221	4035	6936											
SCAF1	58506	hgsc.bcm.edu	37	chr19	50157980	50157980	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcccacctctttgggtctGccccctggcccctccagcta	3	10	9	19	0	2	0	0	0	2	0	3	0	3	0	7	2	3	1	7	2	1	2	rs61741228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50157980G>A	ENST00000360565.3	+	9	3595	c.3471G>A	c.(3469-3471)ctG>ctA	p.L1157L		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	1157					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)		CTTTGGGTCTGCCCCCTGGCC	0.672													g|||	32	0.00638978	0.0234	0.0014	5008	,	,		15138	0.0		0.0	False		,,,				2504	0.0				p.L1157L		Atlas-SNP	.											.	SCAF1	78	.	0			c.G3471A						PASS	.			84,4322	71.4+/-109.4	2,80,2121	85	77	80		3471	-1	1	19	dbSNP_129	80	0,8600		0,0,4300	no	coding-synonymous	SCAF1	NM_021228.2		2,80,6421	AA,AG,GG		0.0,1.9065,0.6459		1157/1313	50157980	84,12922	2203	4300	6503	SO:0001819	synonymous_variant	58506	exon9			GGGTCTGCCCCCT	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.3471G>A	19.37:g.50157980G>A		53	0	0		66	29	0.439394	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Silent	SNP	ENST00000360565.3	37	CCDS33074.1																																																																																			G|0.993;A|0.007	0.007	strong		0.672	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228		A	50157980	G	A	50157980	2	1	22	1	0	0	0	0	0	0	0	1	13883	1306	46	2		2	SCAF1	19	50157980	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1218	50157980	8971003	4036	6937											
TSKS	60385	hgsc.bcm.edu	37	chr19	50248556	50248556	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcccactggcctaggaagcCgtcgaccctgccgcccaggc	6	5	11	19	3	0	0	0	0	0	0	2	2	1	1	6	3	2	0	6	3	2	1	rs34082111	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50248556C>T	ENST00000246801.3	-	7	1172	c.1090G>A	c.(1090-1092)Ggc>Agc	p.G364S	TSKS_ENST00000358830.3_Missense_Mutation_p.G164S	NM_021733.1	NP_068379.1	Q9UJT2	TSKS_HUMAN	testis-specific serine kinase substrate	364					negative regulation of phosphatase activity (GO:0010923)	centriole (GO:0005814)	protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|prostate(3)|skin(3)	38		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;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)		CCTAGGAAGCCGTCGACCCTG	0.706													C|||	54	0.0107827	0.0401	0.0014	5008	,	,		13851	0.0		0.0	False		,,,				2504	0.0				p.G364S		Atlas-SNP	.											.	TSKS	97	.	0			c.G1090A						PASS	.	C	SER/GLY	120,4282		3,114,2084	23	23	23		1090	3.8	1	19	dbSNP_126	23	1,8595		0,1,4297	yes	missense	TSKS	NM_021733.1	56	3,115,6381	TT,TC,CC		0.0116,2.726,0.9309	probably-damaging	364/593	50248556	121,12877	2201	4298	6499	SO:0001583	missense	60385	exon7			GGAAGCCGTCGAC	BC058862	CCDS12780.1	19q13.3	2014-06-13							30719	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 161"	608253				11444856, 18495105	Standard	NM_021733		Approved	TSSKS, PPP1R161	uc002ppm.3	Q9UJT2		ENST00000246801.3:c.1090G>A	19.37:g.50248556C>T	ENSP00000246801:p.Gly364Ser	26	0	0		61	38	0.622951	NM_021733	Q8WXJ0	Missense_Mutation	SNP	ENST00000246801.3	37	CCDS12780.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	C	25.2	4.614167	0.87359	0.02726	1.16E-4	ENSG00000126467	ENST00000246801;ENST00000358830	T;T	0.55588	0.51;0.51	4.89	3.84	0.44239	.	0.000000	0.53938	D	0.000058	T	0.14227	0.0344	L	0.29908	0.895	0.34627	D	0.719177	P	0.39964	0.697	B	0.32393	0.145	T	0.40403	-0.9565	10	0.35671	T	0.21	-19.1441	10.8376	0.46696	0.0:0.91:0.0:0.09	rs34082111	364	Q9UJT2	TSKS_HUMAN	S	364;164	ENSP00000246801:G364S;ENSP00000351691:G164S	ENSP00000246801:G364S	G	-	1	0	TSKS	54940368	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.050000	0.41297	1.273000	0.44346	0.561000	0.74099	GGC	C|0.991;T|0.009	0.009	strong		0.706	TSKS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465795.1	NM_021733		T	50248556	C	T	50248556	3	4	22	1	0	0	0	0	1	0	0	0	16641	652	23	1	708	1	TSKS	19	50248556	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	90576	50248556	8880427	4037	6938											
TSKS	60385	hgsc.bcm.edu	37	chr19	50251701	50251701	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtgatggagtctttggcgCggaccaatccactgttgacc	7	11	13	10	2	1	2	0	2	1	0	2	4	2	4	3	4	0	1	3	4	1	2	rs199829146		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50251701C>T	ENST00000246801.3	-	3	507	c.425G>A	c.(424-426)cGc>cAc	p.R142H	TSKS_ENST00000358830.3_5'Flank	NM_021733.1	NP_068379.1	Q9UJT2	TSKS_HUMAN	testis-specific serine kinase substrate	142					negative regulation of phosphatase activity (GO:0010923)	centriole (GO:0005814)	protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|prostate(3)|skin(3)	38		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;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)		GTCTTTGGCGCGGACCAATCC	0.557																																					p.R142H		Atlas-SNP	.											TSKS,NS,carcinoma,+1,2	TSKS	97	2	0			c.G425A						PASS	.	C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	115	94	101		425	3.8	0.8	19		101	0,8600		0,0,4300	yes	missense	TSKS	NM_021733.1	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	142/593	50251701	1,13005	2203	4300	6503	SO:0001583	missense	60385	exon3			TTGGCGCGGACCA	BC058862	CCDS12780.1	19q13.3	2014-06-13							30719	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 161"	608253				11444856, 18495105	Standard	NM_021733		Approved	TSSKS, PPP1R161	uc002ppm.3	Q9UJT2		ENST00000246801.3:c.425G>A	19.37:g.50251701C>T	ENSP00000246801:p.Arg142His	167	0	0		165	71	0.430303	NM_021733	Q8WXJ0	Missense_Mutation	SNP	ENST00000246801.3	37	CCDS12780.1	.	.	.	.	.	.	.	.	.	.	C	14.73	2.621834	0.46840	2.27E-4	0.0	ENSG00000126467	ENST00000246801	T	0.48522	0.81	4.85	3.82	0.43975	.	0.122950	0.34628	N	0.003810	T	0.35098	0.0920	L	0.29908	0.895	0.80722	D	1	B	0.20459	0.045	B	0.16722	0.016	T	0.23440	-1.0188	10	0.72032	D	0.01	-9.0121	10.2244	0.43216	0.0:0.9063:0.0:0.0937	.	142	Q9UJT2	TSKS_HUMAN	H	142	ENSP00000246801:R142H	ENSP00000246801:R142H	R	-	2	0	TSKS	54943513	0.829000	0.29322	0.834000	0.33040	0.990000	0.78478	1.653000	0.37323	1.274000	0.44362	0.462000	0.41574	CGC	.	.	weak		0.557	TSKS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465795.1	NM_021733		T	50251701	C	T	50251701	3	4	22	1	0	0	0	0	1	0	0	0	16641	768	27	1	1389	1	TSKS	19	50251701	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3145	50251701	8877282	4038	6939											
PTOV1	53635	hgsc.bcm.edu	37	chr19	50361874	50361874	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcaccaaggacctggagacActgaagagcctgtgccggat	11	7	12	11	1	1	3	1	1	0	2	1	6	1	5	4	3	2	0	4	3	2	1	rs35389621	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50361874A>G	ENST00000601675.1	+	10	1109	c.1005A>G	c.(1003-1005)acA>acG	p.T335T	PTOV1_ENST00000600603.1_Silent_p.T303T|AC018766.5_ENST00000601893.1_RNA|PTOV1_ENST00000599732.1_Silent_p.T335T|PTOV1_ENST00000598325.1_3'UTR|AC018766.5_ENST00000599259.1_RNA|AC018766.5_ENST00000593654.1_RNA|AC018766.4_ENST00000596624.1_RNA|PTOV1_ENST00000601638.1_Silent_p.T303T|PTOV1_ENST00000391842.1_Silent_p.T335T|PTOV1_ENST00000221557.9_Silent_p.T303T			Q86YD1	PTOV1_HUMAN	prostate tumor overexpressed 1	335	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)		ACCTGGAGACACTGAAGAGCC	0.667													A|||	48	0.00958466	0.034	0.0043	5008	,	,		16455	0.0		0.0	False		,,,				2504	0.0				p.T335T		Atlas-SNP	.											.	PTOV1	41	.	0			c.A1005G						PASS	.	A		125,4277	87.3+/-125.9	2,121,2078	43	30	35		1005	-5.7	0.3	19	dbSNP_126	35	0,8598		0,0,4299	no	coding-synonymous	PTOV1	NM_017432.3		2,121,6377	GG,GA,AA		0.0,2.8396,0.9615		335/417	50361874	125,12875	2201	4299	6500	SO:0001819	synonymous_variant	53635	exon10			GGAGACACTGAAG	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.1005A>G	19.37:g.50361874A>G		99	0	0		85	43	0.505882	NM_017432	Q6UXX7|Q96BU3|Q9HBN4|Q9NYL1	Silent	SNP	ENST00000601675.1	37	CCDS12782.1																																																																																			A|0.990;G|0.010	0.010	strong		0.667	PTOV1-007	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465347.1	NM_017432		G	50361874	A	G	50361874	2	3	22	1	0	0	0	0	0	0	0	1	12782	146	6	3		3	PTOV1	19	50361874	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	110173	50361874	8767109	4039	6940											
TBC1D17	79735	hgsc.bcm.edu	37	chr19	50386253	50386253	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgagccccagcctgcggcgCgaggcctggaagttcctcct	5	7	13	16	3	0	1	0	1	0	0	2	3	2	2	6	3	3	1	6	3	1	1	rs61741174	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50386253C>T	ENST00000221543.5	+	9	1250	c.951C>T	c.(949-951)cgC>cgT	p.R317R	TBC1D17_ENST00000535102.2_Silent_p.R284R	NM_024682.2	NP_078958	Q9HA65	TBC17_HUMAN	TBC1 domain family, member 17	317	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				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)		GCCTGCGGCGCGAGGCCTGGA	0.637													C|||	49	0.00978435	0.0348	0.0043	5008	,	,		19944	0.0		0.0	False		,,,				2504	0.0				p.R317R		Atlas-SNP	.											.	TBC1D17	39	.	0			c.C951T						PASS	.	C	,	146,4258		5,136,2061	31	32	32		852,951	-10.1	0	19	dbSNP_129	32	0,8592		0,0,4296	no	coding-synonymous,coding-synonymous	TBC1D17	NM_001168222.1,NM_024682.2	,	5,136,6357	TT,TC,CC		0.0,3.3152,1.1234	,	284/616,317/649	50386253	146,12850	2202	4296	6498	SO:0001819	synonymous_variant	79735	exon9			GCGGCGCGAGGCC	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.951C>T	19.37:g.50386253C>T		99	0	0		113	62	0.548673	NM_024682	B4DT12|B9A6L8|F5H1W7	Silent	SNP	ENST00000221543.5	37	CCDS12785.1																																																																																			C|0.989;T|0.011	0.011	strong		0.637	TBC1D17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466404.1	NM_024682		T	50386253	C	T	50386253	2	4	22	1	0	0	0	0	0	0	0	1	15621	755	27	1		1	TBC1D17	19	50386253	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	24379	50386253	8742730	4040	6941											
IL4I1	259307	hgsc.bcm.edu	37	chr19	50393743	50393743	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctcgatctgcacgtgcacAtcgtgcggtccctgggtcat	5	11	12	13	4	3	0	1	0	2	0	6	1	4	0	1	2	3	2	1	2	0	0	rs61740372	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50393743A>G	ENST00000391826.2	-	8	1030	c.888T>C	c.(886-888)gaT>gaC	p.D296D	IL4I1_ENST00000595948.1_Silent_p.D318D|IL4I1_ENST00000341114.3_Silent_p.D318D|MIR4750_ENST00000584564.1_RNA	NM_152899.1	NP_690863.1	Q96RQ9	OXLA_HUMAN	interleukin 4 induced 1	296						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)	GCACGTGCACATCGTGCGGTC	0.692											OREG0025629	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	83	0.0165735	0.059	0.0072	5008	,	,		12580	0.0		0.0	False		,,,				2504	0.0				p.D318D		Atlas-SNP	.											.	IL4I1	50	.	0			c.T954C						PASS	.	A	,	242,4162	131.8+/-168.3	9,224,1969	28	27	27		888,954	-7.9	0	19	dbSNP_129	27	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	IL4I1	NM_152899.1,NM_172374.1	,	9,225,6268	GG,GA,AA		0.0116,5.495,1.8687	,	296/568,318/590	50393743	243,12761	2202	4300	6502	SO:0001819	synonymous_variant	259307	exon10			GTGCACATCGTGC	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.888T>C	19.37:g.50393743A>G		63	0	0	969	76	40	0.526316	NM_172374	Q1WMJ3|Q4GZN1|Q4GZN2|Q6P2Q3|Q8TEM5|Q96RQ8	Silent	SNP	ENST00000391826.2	37	CCDS12787.1																																																																																			A|0.982;G|0.018	0.018	strong		0.692	IL4I1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466413.1			G	50393743	A	G	50393743	2	3	22	1	0	0	0	0	0	0	0	1	7706	214	8	3		3	IL4I1	19	50393743	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	7490	50393743	8735240	4041	6942											
MYH14	79784	hgsc.bcm.edu	37	chr19	50810405	50810405	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cggagggtggctgaccagctCcgggaccaggtaagcagctg	8	5	17	11	2	0	1	0	1	0	0	1	3	1	3	3	5	3	5	3	5	1	1	rs201839634	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50810405C>T	ENST00000596571.1	+	38	5655	c.5655C>T	c.(5653-5655)ctC>ctT	p.L1885L	MYH14_ENST00000376970.2_Silent_p.L1918L|CTB-191K22.5_ENST00000595563.1_RNA|MYH14_ENST00000601313.1_Silent_p.L1926L|MYH14_ENST00000598205.1_Silent_p.L1893L|MYH14_ENST00000440075.2_Silent_p.L1926L|MYH14_ENST00000262269.8_Silent_p.L1926L|MYH14_ENST00000425460.1_Silent_p.L1893L			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1885					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)		CTGACCAGCTCCGGGACCAGG	0.592													C|||	2	0.000399361	0.0015	0.0	5008	,	,		20297	0.0		0.0	False		,,,				2504	0.0				p.L1926L		Atlas-SNP	.											.	MYH14	261	.	0			c.C5778T						PASS	.	C	,,	2,3712		0,2,1855	39	49	46		5679,5778,5655	2	1	19		46	0,7216		0,0,3608	no	coding-synonymous,coding-synonymous,coding-synonymous	MYH14	NM_001077186.1,NM_001145809.1,NM_024729.3	,,	0,2,5463	TT,TC,CC		0.0,0.0539,0.0183	,,	1893/2004,1926/2037,1885/1996	50810405	2,10928	1857	3608	5465	SO:0001819	synonymous_variant	79784	exon41			CCAGCTCCGGGAC	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.5655C>T	19.37:g.50810405C>T		66	0	0		40	17	0.425	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent	SNP	ENST00000596571.1	37	CCDS59411.1																																																																																			C|0.999;T|0.001	0.001	strong		0.592	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		T	50810405	C	T	50810405	2	4	22	1	0	0	0	0	0	0	0	1	10042	842	30	2		2	MYH14	19	50810405	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	416662	50810405	8318578	4042	6943											
KLK14	43847	hgsc.bcm.edu	37	chr19	51582090	51582090	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctgacaagagtccttcccGccctggggaactcctgcaca	9	7	9	16	1	0	2	0	1	0	1	3	3	3	3	5	2	2	1	5	2	2	1	rs79507858	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51582090G>A	ENST00000156499.2	-	6	851	c.633C>T	c.(631-633)ggC>ggT	p.G211G	KLK14_ENST00000391802.1_Silent_p.G211G			Q9P0G3	KLK14_HUMAN	kallikrein-related peptidase 14	211	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				epidermis morphogenesis (GO:0048730)|fertilization (GO:0009566)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|proteolysis (GO:0006508)|seminal clot liquefaction (GO:0070684)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)			kidney(4)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(1)	11		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00422)		AGTCCTTCCCGCCCTGGGGAA	0.542													g|||	153	0.0305511	0.1089	0.0115	5008	,	,		18957	0.0		0.001	False		,,,				2504	0.0				p.G211G	GBM(117;2161 2172 2448 22911)	Atlas-SNP	.											.	KLK14	49	.	0			c.C633T						PASS	.			376,3538		15,346,1596	234	237	236		633	-9	0.2	19	dbSNP_131	236	7,8311		0,7,4152	no	coding-synonymous	KLK14	NM_022046.4		15,353,5748	AA,AG,GG		0.0842,9.6065,3.1311		211/268	51582090	383,11849	1957	4159	6116	SO:0001819	synonymous_variant	43847	exon6			CTTCCCGCCCTGG	AF283670	CCDS12823.2	19q13.3-q13.4	2008-02-05	2006-10-27		ENSG00000129437	ENSG00000129437		"Kallikreins"	6362	protein-coding gene	gene with protein product		606135	"kallikrein 14"			16800724, 16800723	Standard	XM_006723224		Approved	KLK-L6	uc002pvs.1	Q9P0G3	OTTHUMG00000143721	ENST00000156499.2:c.633C>T	19.37:g.51582090G>A		61	0	0		93	93	1	NM_022046	A7UNK5|Q1RMZ2|Q6B089	Silent	SNP	ENST00000156499.2	37	CCDS12823.2																																																																																			G|0.981;A|0.019	0.019	strong		0.542	KLK14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289774.2	NM_022046		A	51582090	G	A	51582090	2	1	22	1	0	0	0	0	0	0	0	1	8411	1074	38	1		1	KLK14	19	51582090	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	771685	51582090	7546893	4043	6944											
SIGLEC9	27180	hgsc.bcm.edu	37	chr19	51628395	51628395	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggctggatttaccctggccCagtagttcatggctactggt	6	13	12	10	0	1	0	1	0	0	0	1	1	1	1	2	5	2	4	2	5	3	5	rs144549146		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51628395C>T	ENST00000250360.3	+	1	231	c.164C>T	c.(163-165)cCa>cTa	p.P55L	SIGLEC9_ENST00000440804.3_Missense_Mutation_p.P55L	NM_014441.2	NP_055256.1	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9	55	Ig-like V-type.				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)		TACCCTGGCCCAGTAGTTCAT	0.602													.|||	1	0.000199681	0.0008	0.0	5008	,	,		16792	0.0		0.0	False		,,,				2504	0.0				p.P55L		Atlas-SNP	.											.	SIGLEC9	85	.	0			c.C164T						PASS	.	C	LEU/PRO,LEU/PRO	3,4403		0,3,2200	120	87	98		164,164	0.7	0	19	dbSNP_134	98	0,8600		0,0,4300	no	missense,missense	SIGLEC9	NM_001198558.1,NM_014441.2	98,98	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	possibly-damaging,possibly-damaging	55/480,55/464	51628395	3,13003	2203	4300	6503	SO:0001583	missense	27180	exon1			CTGGCCCAGTAGT	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.164C>T	19.37:g.51628395C>T	ENSP00000250360:p.Pro55Leu	210	0	0		227	108	0.475771	NM_001198558	Q6GTU4|Q9BYI9	Missense_Mutation	SNP	ENST00000250360.3	37	CCDS12825.1	.	.	.	.	.	.	.	.	.	.	.	11.96	1.794120	0.31777	6.81E-4	0.0	ENSG00000129450	ENST00000440804;ENST00000250360	T;T	0.54071	0.59;0.59	2.88	0.675	0.17952	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	5.876730	0.00810	N	0.001498	T	0.62344	0.2420	M	0.80183	2.485	0.09310	N	1	P	0.41947	0.766	P	0.46208	0.507	T	0.41466	-0.9507	10	0.62326	D	0.03	.	4.9958	0.14237	0.0:0.6975:0.0:0.3025	.	55	Q9Y336	SIGL9_HUMAN	L	55	ENSP00000413861:P55L;ENSP00000250360:P55L	ENSP00000250360:P55L	P	+	2	0	SIGLEC9	56320207	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.035000	0.12205	0.010000	0.14839	0.397000	0.26171	CCA	C|1.000;T|0.000	0.000	strong		0.602	SIGLEC9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464224.1	NM_014441		T	51628395	C	T	51628395	3	4	22	1	0	0	0	0	1	0	0	0	14330	594	21	2	166	2	SIGLEC9	19	51628395	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	46305	51628395	7500588	4044	6945											
SIGLEC9	27180	hgsc.bcm.edu	37	chr19	51628622	51628622	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaagtataaaatggaattatAaacatcaccggctctctgtg	15	11	8	7	1	2	0	1	0	1	0	3	2	2	1	1	2	1	2	1	2	8	4	rs16988910	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51628622A>C	ENST00000250360.3	+	1	458	c.391A>C	c.(391-393)Aaa>Caa	p.K131Q	SIGLEC9_ENST00000440804.3_Missense_Mutation_p.K131Q	NM_014441.2	NP_055256.1	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9	131	Ig-like V-type.		K -> Q (in dbSNP:rs16988910).		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)		ATGGAATTATAAACATCACCG	0.498													.|||	482	0.096246	0.3495	0.0288	5008	,	,		19570	0.0		0.0	False		,,,				2504	0.0				p.K131Q		Atlas-SNP	.											.	SIGLEC9	85	.	0			c.A391C						PASS	.	A	GLN/LYS,GLN/LYS	1306,3100		197,912,1094	54	54	54		391,391	-6.1	0	19	dbSNP_123	54	9,8591		0,9,4291	yes	missense,missense	SIGLEC9	NM_001198558.1,NM_014441.2	53,53	197,921,5385	CC,CA,AA		0.1047,29.6414,10.1107	benign,benign	131/480,131/464	51628622	1315,11691	2203	4300	6503	SO:0001583	missense	27180	exon1			AATTATAAACATC	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.391A>C	19.37:g.51628622A>C	ENSP00000250360:p.Lys131Gln	60	0	0		54	28	0.518519	NM_001198558	Q6GTU4|Q9BYI9	Missense_Mutation	SNP	ENST00000250360.3	37	CCDS12825.1	177	0.08104395604395605	167	0.3394308943089431	10	0.027624309392265192	0	0.0	0	0.0	.	2.109	-0.404270	0.04832	0.296414	0.001047	ENSG00000129450	ENST00000440804;ENST00000250360	T;T	0.45668	0.89;0.89	3.03	-6.06	0.02165	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	3.634600	0.01116	N	0.005689	T	0.00012	0.0000	L	0.35542	1.07	0.80722	P	0.0	B	0.13145	0.007	B	0.11329	0.006	T	0.28138	-1.0053	9	0.19147	T	0.46	.	0.854	0.01178	0.2909:0.3232:0.227:0.1589	rs16988910;rs57111846;rs16988910	131	Q9Y336	SIGL9_HUMAN	Q	131	ENSP00000413861:K131Q;ENSP00000250360:K131Q	ENSP00000250360:K131Q	K	+	1	0	SIGLEC9	56320434	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.430000	0.02434	-1.179000	0.02737	-0.476000	0.04901	AAA	A|0.895;C|0.105	0.105	strong		0.498	SIGLEC9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464224.1	NM_014441		C	51628622	A	C	51628622	3	2	22	1	0	0	0	0	1	0	0	0	14330	363	13	5	393	5	SIGLEC9	19	51628622	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	227	51628622	7500361	4045	6946											
SIGLEC9	27180	hgsc.bcm.edu	37	chr19	51630485	51630485	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggtgcacctgagggatgcagCtgaattcacctgcagagctc	9	8	13	11	0	1	3	1	2	0	1	2	4	1	4	2	2	5	5	2	2	1	1	rs273688	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51630485C>A	ENST00000250360.3	+	4	1014	c.947C>A	c.(946-948)gCt>gAt	p.A316D	SIGLEC9_ENST00000440804.3_Missense_Mutation_p.A316D	NM_014441.2	NP_055256.1	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9	316	Ig-like C2-type 2.		A -> D (in dbSNP:rs273688).		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)		AGGGATGCAGCTGAATTCACC	0.637													.|||	529	0.105631	0.3805	0.0331	5008	,	,		20814	0.0		0.0	False		,,,				2504	0.0031				p.A316D		Atlas-SNP	.											SIGLEC9,NS,carcinoma,+1,1	SIGLEC9	85	1	0			c.C947A						PASS	.	A	ASP/ALA,ASP/ALA	1473,2933		252,969,982	41	40	40		947,947	0	0	19	dbSNP_79	40	11,8589		0,11,4289	no	missense,missense	SIGLEC9	NM_001198558.1,NM_014441.2	126,126	252,980,5271	AA,AC,CC		0.1279,33.4317,11.4101	benign,benign	316/480,316/464	51630485	1484,11522	2203	4300	6503	SO:0001583	missense	27180	exon4			ATGCAGCTGAATT	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.947C>A	19.37:g.51630485C>A	ENSP00000250360:p.Ala316Asp	121	0	0		105	58	0.552381	NM_001198558	Q6GTU4|Q9BYI9	Missense_Mutation	SNP	ENST00000250360.3	37	CCDS12825.1	196	0.08974358974358974	183	0.3719512195121951	13	0.03591160220994475	0	0.0	0	0.0	.	6.207	0.406368	0.11754	0.334317	0.001279	ENSG00000129450	ENST00000440804;ENST00000250360	T;T	0.12255	2.7;2.7	2.3	-0.0215	0.13951	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.635768	0.12920	N	0.428257	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.16166	0.016	B	0.12156	0.007	T	0.46665	-0.9175	9	0.72032	D	0.01	.	5.4292	0.16444	0.1485:0.2067:0.6448:0.0	rs273688;rs60086561;rs273688	316	Q9Y336	SIGL9_HUMAN	D	316	ENSP00000413861:A316D;ENSP00000250360:A316D	ENSP00000250360:A316D	A	+	2	0	SIGLEC9	56322297	0.018000	0.18449	0.000000	0.03702	0.001000	0.01503	0.516000	0.22817	-0.622000	0.05626	-3.343000	0.00043	GCT	C|0.895;A|0.105	0.105	strong		0.637	SIGLEC9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464224.1	NM_014441		A	51630485	C	A	51630485	3	1	22	1	0	0	0	0	1	0	0	0	14330	797	28	4	961	4	SIGLEC9	19	51630485	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1863	51630485	7498498	4046	6947											
CD33	945	hgsc.bcm.edu	37	chr19	51729594	51729594	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaacccaacaactggtatcTttccaggagatggctcaggt	12	9	10	10	0	2	2	1	0	1	2	3	3	3	2	2	4	3	2	2	4	4	2	rs11882250|rs201473304	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51729594T>C	ENST00000262262.4	+	4	748	c.727T>C	c.(727-729)Ttt>Ctt	p.F243L	CD33_ENST00000421133.2_Missense_Mutation_p.F116L|CD33_ENST00000436584.2_Missense_Mutation_p.F116L|CD33_ENST00000391796.3_Missense_Mutation_p.F243L	NM_001772.3	NP_001763.3	P20138	CD33_HUMAN	CD33 molecule	243			F -> L (in dbSNP:rs11882250).		cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|negative regulation of cell proliferation (GO:0008285)|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)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(15)|skin(1)|stomach(1)	24		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	Gemtuzumab ozogamicin(DB00056)	AACTGGTATCTTTCCAGGAGA	0.502													t|||	186	0.0371406	0.1271	0.0245	5008	,	,		18721	0.0		0.001	False		,,,				2504	0.0				p.F243L		Atlas-SNP	.											.	CD33	55	.	0			c.T727C						PASS	.	T	LEU/PHE,LEU/PHE,LEU/PHE	478,3928		26,426,1751	92	86	88		346,727,727	2.9	0	19	dbSNP_120	88	4,8596		0,4,4296	yes	missense,missense,missense	CD33	NM_001082618.1,NM_001177608.1,NM_001772.3	22,22,22	26,430,6047	CC,CT,TT		0.0465,10.8488,3.706	benign,benign,benign	116/238,243/311,243/365	51729594	482,12524	2203	4300	6503	SO:0001583	missense	945	exon4			GGTATCTTTCCAG	M23197	CCDS33084.1, CCDS46157.1, CCDS54299.1	19q13.3	2013-01-29	2006-03-28		ENSG00000105383	ENSG00000105383		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1659	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 3"	159590	"CD33 antigen (gp67)"			3139766, 9465907	Standard	NM_001772		Approved	SIGLEC3, SIGLEC-3, p67, FLJ00391	uc002pwa.2	P20138		ENST00000262262.4:c.727T>C	19.37:g.51729594T>C	ENSP00000262262:p.Phe243Leu	94	0	0		108	56	0.518519	NM_001772	B4E3P8|C9JEN7|F8WAL2|Q8TD24	Missense_Mutation	SNP	ENST00000262262.4	37	CCDS33084.1	64	0.029304029304029304	51	0.10365853658536585	12	0.03314917127071823	0	0.0	1	0.0013192612137203166	.	9.409	1.079972	0.20309	0.108488	4.65E-4	ENSG00000105383	ENST00000436584;ENST00000262262;ENST00000421133;ENST00000391796	T;T;T;T	0.34667	1.35;2.53;1.55;2.36	2.88	2.88	0.33553	.	.	.	.	.	T	0.00496	0.0016	L	0.40543	1.245	0.80722	P	0.0	B;B;B	0.26975	0.066;0.165;0.048	B;B;B	0.23852	0.028;0.049;0.023	T	0.06935	-1.0799	8	0.33141	T	0.24	.	7.4754	0.27374	0.0:0.0:0.0:1.0	rs11882250;rs52835930;rs56510285;rs57266763;rs11882250	116;243;243	C9JEN7;F8WAL2;P20138	.;.;CD33_HUMAN	L	116;243;116;243	ENSP00000403331:F116L;ENSP00000262262:F243L;ENSP00000410126:F116L;ENSP00000375673:F243L	ENSP00000262262:F243L	F	+	1	0	CD33	56421406	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	0.212000	0.17497	1.322000	0.45245	0.379000	0.24179	TTT	T|0.958;C|0.042	0.042	strong		0.502	CD33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464199.2	NM_001772		C	51729594	T	C	51729594	3	2	22	1	0	0	0	0	1	0	0	0	3007	1609	56	3	741	3	CD33	19	51729594	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	99109	51729594	7399389	4047	6948											
CD33	945	hgsc.bcm.edu	37	chr19	51738465	51738465	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggccattggaggagctggtGttacagccctgctcgctctt	5	11	14	11	1	1	0	0	0	1	0	2	2	1	2	2	4	4	4	2	4	1	3	rs58981829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51738465G>A	ENST00000262262.4	+	5	820	c.799G>A	c.(799-801)Gtt>Att	p.V267I	CD33_ENST00000421133.2_Missense_Mutation_p.V140I|CD33_ENST00000436584.2_Missense_Mutation_p.V140I|CD33_ENST00000391796.3_Missense_Mutation_p.V267I	NM_001772.3	NP_001763.3	P20138	CD33_HUMAN	CD33 molecule	267			V -> I (in dbSNP:rs58981829).		cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|negative regulation of cell proliferation (GO:0008285)|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)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(15)|skin(1)|stomach(1)	24		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	Gemtuzumab ozogamicin(DB00056)	AGGAGCTGGTGTTACAGCCCT	0.502													g|||	203	0.0405351	0.1399	0.0245	5008	,	,		19411	0.0		0.001	False		,,,				2504	0.0				p.V267I		Atlas-SNP	.											CD33,NS,carcinoma,0,1	CD33	55	1	0			c.G799A						PASS	.	A	ILE/VAL,ILE/VAL,ILE/VAL	521,3885		29,463,1711	151	123	133		418,799,799	1.9	0	19	dbSNP_129	133	5,8595		0,5,4295	yes	missense,missense,missense	CD33	NM_001082618.1,NM_001177608.1,NM_001772.3	29,29,29	29,468,6006	AA,AG,GG		0.0581,11.8248,4.0443	benign,benign,benign	140/238,267/311,267/365	51738465	526,12480	2203	4300	6503	SO:0001583	missense	945	exon5			GCTGGTGTTACAG	M23197	CCDS33084.1, CCDS46157.1, CCDS54299.1	19q13.3	2013-01-29	2006-03-28		ENSG00000105383	ENSG00000105383		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1659	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 3"	159590	"CD33 antigen (gp67)"			3139766, 9465907	Standard	NM_001772		Approved	SIGLEC3, SIGLEC-3, p67, FLJ00391	uc002pwa.2	P20138		ENST00000262262.4:c.799G>A	19.37:g.51738465G>A	ENSP00000262262:p.Val267Ile	212	0	0		224	121	0.540179	NM_001772	B4E3P8|C9JEN7|F8WAL2|Q8TD24	Missense_Mutation	SNP	ENST00000262262.4	37	CCDS33084.1	67	0.030677655677655676	54	0.10975609756097561	12	0.03314917127071823	0	0.0	1	0.0013192612137203166	.	6.151	0.396010	0.11638	0.118248	5.81E-4	ENSG00000105383	ENST00000436584;ENST00000262262;ENST00000421133;ENST00000391796	T;T;T;T	0.39997	1.05;2.69;2.69;2.16	4.13	1.93	0.25924	.	1.922710	0.03611	N	0.234840	T	0.00524	0.0017	L	0.35644	1.08	0.80722	P	0.0	B;B;B	0.10296	0.0;0.003;0.001	B;B;B	0.12156	0.002;0.007;0.002	T	0.10405	-1.0631	9	0.26408	T	0.33	.	9.5522	0.39317	0.195:0.0:0.805:0.0	rs58981829;rs61736474	140;267;267	C9JEN7;F8WAL2;P20138	.;.;CD33_HUMAN	I	140;267;140;267	ENSP00000403331:V140I;ENSP00000262262:V267I;ENSP00000410126:V140I;ENSP00000375673:V267I	ENSP00000262262:V267I	V	+	1	0	CD33	56430277	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.249000	0.18216	0.169000	0.19679	-0.939000	0.02691	GTT	G|0.955;A|0.045	0.045	strong		0.502	CD33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464199.2	NM_001772		A	51738465	G	A	51738465	3	1	22	1	0	0	0	0	1	0	0	0	3007	1377	48	2	817	2	CD33	19	51738465	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	8871	51738465	7390518	4048	6949											
CD33	945	hgsc.bcm.edu	37	chr19	51742839	51742839	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctgttcaggtgccgcccctActgtggagatggatgaggag	7	9	16	9	1	1	2	1	1	0	1	1	5	1	4	3	4	2	2	3	4	1	2	rs35632246	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51742839A>G	ENST00000262262.4	+	7	1012	c.991A>G	c.(991-993)Act>Gct	p.T331A	CD33_ENST00000421133.2_Missense_Mutation_p.T204A|CD33_ENST00000600557.1_3'UTR	NM_001772.3	NP_001763.3	P20138	CD33_HUMAN	CD33 molecule	331			T -> A (in dbSNP:rs35632246).		cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|negative regulation of cell proliferation (GO:0008285)|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)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(15)|skin(1)|stomach(1)	24		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	Gemtuzumab ozogamicin(DB00056)	TGCCGCCCCTACTGTGGAGAT	0.517													a|||	62	0.0123802	0.0454	0.0029	5008	,	,		18838	0.0		0.0	False		,,,				2504	0.0				p.T331A		Atlas-SNP	.											.	CD33	55	.	0			c.A991G						PASS	.	A	ALA/THR,ALA/THR	194,4212	121.3+/-158.8	6,182,2015	115	99	105		610,991	-5	0	19	dbSNP_126	105	2,8598	1.2+/-3.3	0,2,4298	yes	missense,missense	CD33	NM_001082618.1,NM_001772.3	58,58	6,184,6313	GG,GA,AA		0.0233,4.4031,1.507	benign,benign	204/238,331/365	51742839	196,12810	2203	4300	6503	SO:0001583	missense	945	exon7			GCCCCTACTGTGG	M23197	CCDS33084.1, CCDS46157.1, CCDS54299.1	19q13.3	2013-01-29	2006-03-28		ENSG00000105383	ENSG00000105383		"CD molecules", "Sialic acid binding Ig-like lectins", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	1659	protein-coding gene	gene with protein product	"sialic acid binding Ig-like lectin 3"	159590	"CD33 antigen (gp67)"			3139766, 9465907	Standard	NM_001772		Approved	SIGLEC3, SIGLEC-3, p67, FLJ00391	uc002pwa.2	P20138		ENST00000262262.4:c.991A>G	19.37:g.51742839A>G	ENSP00000262262:p.Thr331Ala	133	0	0		116	57	0.491379	NM_001772	B4E3P8|C9JEN7|F8WAL2|Q8TD24	Missense_Mutation	SNP	ENST00000262262.4	37	CCDS33084.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	A	3.525	-0.096917	0.07010	0.044031	2.33E-4	ENSG00000105383	ENST00000262262;ENST00000421133	T;T	0.04758	3.56;3.56	2.51	-5.02	0.02982	.	.	.	.	.	T	0.00552	0.0018	L	0.39147	1.195	0.09310	N	1	B;B	0.15141	0.012;0.012	B;B	0.11329	0.006;0.006	T	0.44528	-0.9322	9	0.22706	T	0.39	.	3.2402	0.06778	0.2436:0.0:0.2473:0.5091	rs35632246	204;331	C9JEN7;P20138	.;CD33_HUMAN	A	331;204	ENSP00000262262:T331A;ENSP00000410126:T204A	ENSP00000262262:T331A	T	+	1	0	CD33	56434651	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-1.760000	0.01806	-1.514000	0.01786	0.260000	0.18958	ACT	A|0.986;G|0.014	0.014	strong		0.517	CD33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464199.2	NM_001772		G	51742839	A	G	51742839	3	3	22	1	0	0	0	0	1	0	0	0	3007	391	14	3	1030	3	CD33	19	51742839	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	4374	51742839	7386144	4049	6950											
CLDND2	125875	hgsc.bcm.edu	37	chr19	51870771	51870771	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataggaccaagagaagaagaCgttgttcttccacgcattct	13	10	9	9	2	2	3	0	0	2	3	3	5	3	4	2	1	0	3	2	1	4	5	rs61737052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51870771C>A	ENST00000291715.1	-	3	795	c.370G>T	c.(370-372)Gtc>Ttc	p.V124F	CTD-2616J11.10_ENST00000595500.1_RNA|ETFB_ENST00000309244.4_5'Flank|CTD-2616J11.11_ENST00000600067.1_Intron|CLDND2_ENST00000601435.1_Missense_Mutation_p.V124F	NM_152353.2	NP_689566.1	Q8NHS1	CLDN2_HUMAN	claudin domain containing 2	124						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(2)	4		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000211)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		GAGAAGAAGACGTTGTTCTTC	0.582													C|||	269	0.0537141	0.1906	0.0245	5008	,	,		14710	0.0		0.0	False		,,,				2504	0.0				p.V124F		Atlas-SNP	.											.	CLDND2	11	.	0			c.G370T						PASS	.	C	PHE/VAL	698,3708	280.2+/-275.2	57,584,1562	72	73	73		370	1.1	0.3	19	dbSNP_129	73	11,8589	7.1+/-27.0	0,11,4289	yes	missense	CLDND2	NM_152353.2	50	57,595,5851	AA,AC,CC		0.1279,15.842,5.4513	possibly-damaging	124/168	51870771	709,12297	2203	4300	6503	SO:0001583	missense	125875	exon3			AGAAGACGTTGTT	BC029518	CCDS12829.1	19q13.41	2008-02-05				ENSG00000160318			28511	protein-coding gene	gene with protein product						12477932	Standard	NM_152353		Approved	MGC33839	uc002pwi.1	Q8NHS1		ENST00000291715.1:c.370G>T	19.37:g.51870771C>A	ENSP00000291715:p.Val124Phe	179	0	0		192	101	0.526042	NM_152353		Missense_Mutation	SNP	ENST00000291715.1	37	CCDS12829.1	86	0.039377289377289376	74	0.15040650406504066	12	0.03314917127071823	0	0.0	0	0.0	C	17.60	3.430878	0.62844	0.15842	0.001279	ENSG00000160318	ENST00000291715	D	0.88586	-2.4	4.63	1.11	0.20524	.	0.377447	0.18697	N	0.133682	T	0.01835	0.0058	M	0.67953	2.075	0.80722	P	0.0	P	0.50272	0.933	P	0.48982	0.597	T	0.58081	-0.7699	9	0.10636	T	0.68	-10.6815	5.0991	0.14749	0.0:0.6298:0.17:0.2002	.	124	Q8NHS1	CLDN2_HUMAN	F	124	ENSP00000291715:V124F	ENSP00000291715:V124F	V	-	1	0	CLDND2	56562583	0.348000	0.24861	0.346000	0.25655	0.864000	0.49448	0.320000	0.19540	0.362000	0.24319	0.491000	0.48974	GTC	C|0.949;A|0.051	0.051	strong		0.582	CLDND2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464268.1	NM_152353		A	51870771	C	A	51870771	3	1	22	1	0	0	0	0	1	0	0	0	3496	536	19	4	141	4	CLDND2	19	51870771	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	127932	51870771	7258212	4050	6951											
CLDND2	125875	hgsc.bcm.edu	37	chr19	51871157	51871157	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	caccgccgaggaagaggaagGcgctcgtggtctggccccgc	7	4	16	14	5	1	1	0	0	1	1	2	4	1	3	4	5	0	1	4	5	2	0	rs74538792	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51871157G>A	ENST00000291715.1	-	2	718	c.293C>T	c.(292-294)gCc>gTc	p.A98V	CTD-2616J11.10_ENST00000595500.1_RNA|ETFB_ENST00000309244.4_5'Flank|CTD-2616J11.11_ENST00000600067.1_Missense_Mutation_p.A33V|CLDND2_ENST00000601435.1_Missense_Mutation_p.A98V	NM_152353.2	NP_689566.1	Q8NHS1	CLDN2_HUMAN	claudin domain containing 2	98						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(2)	4		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000211)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		GAAGAGGAAGGCGCTCGTGGT	0.721													G|||	174	0.0347444	0.1195	0.0202	5008	,	,		12598	0.001		0.001	False		,,,				2504	0.0				p.A98V		Atlas-SNP	.											.	CLDND2	11	.	0			c.C293T						PASS	.	G	VAL/ALA	394,3980		20,354,1813	18	21	20		293	-2.1	0	19	dbSNP_131	20	6,8554		0,6,4274	yes	missense	CLDND2	NM_152353.2	64	20,360,6087	AA,AG,GG		0.0701,9.0078,3.0926	benign	98/168	51871157	400,12534	2187	4280	6467	SO:0001583	missense	125875	exon2			AGGAAGGCGCTCG	BC029518	CCDS12829.1	19q13.41	2008-02-05				ENSG00000160318			28511	protein-coding gene	gene with protein product						12477932	Standard	NM_152353		Approved	MGC33839	uc002pwi.1	Q8NHS1		ENST00000291715.1:c.293C>T	19.37:g.51871157G>A	ENSP00000291715:p.Ala98Val	61	0	0		80	41	0.5125	NM_152353		Missense_Mutation	SNP	ENST00000291715.1	37	CCDS12829.1	59	0.027014652014652016	49	0.09959349593495935	10	0.027624309392265192	0	0.0	0	0.0	G	13.11	2.139648	0.37728	0.090078	7.01E-4	ENSG00000160318	ENST00000291715	D	0.88046	-2.33	4.69	-2.13	0.07144	.	2.567250	0.01253	N	0.008934	T	0.08758	0.0217	L	0.31664	0.95	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.49844	-0.8896	10	0.09590	T	0.72	-3.6824	5.168	0.15096	0.4412:0.164:0.3948:0.0	.	98	Q8NHS1	CLDN2_HUMAN	V	98	ENSP00000291715:A98V	ENSP00000291715:A98V	A	-	2	0	CLDND2	56562969	0.000000	0.05858	0.000000	0.03702	0.107000	0.19398	-0.512000	0.06313	-0.169000	0.10834	0.561000	0.74099	GCC	G|0.968;A|0.032	0.032	strong		0.721	CLDND2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464268.1	NM_152353		A	51871157	G	A	51871157	3	1	22	1	0	0	0	0	1	0	0	0	3496	1203	42	2	222	2	CLDND2	19	51871157	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	386	51871157	7257826	4051	6952											
SIGLEC12	89858	hgsc.bcm.edu	37	chr19	51994926	51994926	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgttgatctcggagtactcaTagccgatggcctcctgttcc	6	13	10	12	2	2	1	1	1	1	0	5	3	4	2	4	2	2	3	4	2	2	4	rs7245807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51994926T>C	ENST00000291707.3	-	8	1812	c.1757A>G	c.(1756-1758)tAt>tGt	p.Y586C	SIGLEC12_ENST00000598614.1_Missense_Mutation_p.Y468C	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	586			Y -> C (in dbSNP:rs7245807).		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)		GGAGTACTCATAGCCGATGGC	0.572													t|||	234	0.0467252	0.1437	0.0144	5008	,	,		14528	0.0327		0.001	False		,,,				2504	0.0				p.Y586C		Atlas-SNP	.											.	SIGLEC12	243	.	0			c.A1757G						PASS	.	T	CYS/TYR,CYS/TYR	523,3883		36,451,1716	122	106	111		1403,1757	-4.5	0	19	dbSNP_116	111	5,8595		0,5,4295	yes	missense,missense	SIGLEC12	NM_033329.1,NM_053003.2	194,194	36,456,6011	CC,CT,TT		0.0581,11.8702,4.0597	benign,benign	468/478,586/596	51994926	528,12478	2203	4300	6503	SO:0001583	missense	89858	exon8			TACTCATAGCCGA	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.1757A>G	19.37:g.51994926T>C	ENSP00000291707:p.Tyr586Cys	113	0	0		124	71	0.572581	NM_053003	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	37	CCDS12833.1	91	0.041666666666666664	66	0.13414634146341464	6	0.016574585635359115	19	0.033216783216783216	0	0.0	.	0.031	-1.337170	0.01287	0.118702	5.81E-4	ENSG00000254521	ENST00000291707	T	0.04654	3.58	2.23	-4.47	0.03525	.	.	.	.	.	T	0.00039	0.0001	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	0.39502	-0.9611	9	0.44086	T	0.13	.	0.9451	0.01364	0.1876:0.1548:0.2634:0.3942	rs7245807;rs59181054;rs7245807	586;468	Q96PQ1;Q96PQ1-2	SIG12_HUMAN;.	C	586	ENSP00000291707:Y586C	ENSP00000291707:Y586C	Y	-	2	0	SIGLEC12	56686738	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.806000	0.00361	-5.302000	0.00017	-1.158000	0.01797	TAT	T|0.956;C|0.044	0.044	strong		0.572	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003		C	51994926	T	C	51994926	3	2	22	1	0	0	0	0	1	0	0	0	14323	1406	49	3	34	3	SIGLEC12	19	51994926	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	123769	51994926	7134057	4052	6953											
SIGLEC12	89858	hgsc.bcm.edu	37	chr19	52000616	52000616	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctcacacaacgaagatgaTgcagaagtacaggaagacca	17	5	10	9	1	1	4	1	1	0	3	1	6	1	5	1	1	4	3	1	1	5	1	rs28572419	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52000616T>C	ENST00000291707.3	-	6	1544	c.1489A>G	c.(1489-1491)Atc>Gtc	p.I497V	SIGLEC12_ENST00000598614.1_Missense_Mutation_p.I379V	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	497					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)		ACGAAGATGATGCAGAAGTAC	0.567													N|||	165	0.0329473	0.1203	0.0086	5008	,	,		17500	0.0		0.0	False		,,,				2504	0.0				p.I497V		Atlas-SNP	.											.	SIGLEC12	243	.	0			c.A1489G						PASS	.	C	VAL/ILE,VAL/ILE	455,3951		24,407,1772	157	138	144		1135,1489	-3.4	0	19	dbSNP_125	144	5,8595		0,5,4295	yes	missense,missense	SIGLEC12	NM_033329.1,NM_053003.2	29,29	24,412,6067	CC,CT,TT		0.0581,10.3268,3.5368	benign,benign	379/478,497/596	52000616	460,12546	2203	4300	6503	SO:0001583	missense	89858	exon6			AGATGATGCAGAA	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.1489A>G	19.37:g.52000616T>C	ENSP00000291707:p.Ile497Val	184	1	0.00543478		212	120	0.566038	NM_053003	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	37	CCDS12833.1	61	0.027930402930402932	57	0.11585365853658537	4	0.011049723756906077	0	0.0	0	0.0	.	0.004	-2.281268	0.00251	0.103268	5.81E-4	ENSG00000254521	ENST00000291707	T	0.35236	1.32	1.69	-3.38	0.04883	.	.	.	.	.	T	0.00178	0.0005	N	0.05124	-0.11	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.0;0.003	T	0.16041	-1.0416	9	0.29301	T	0.29	.	0.7952	0.01065	0.1706:0.202:0.3393:0.2881	rs28572419	497;379	Q96PQ1;Q96PQ1-2	SIG12_HUMAN;.	V	497	ENSP00000291707:I497V	ENSP00000291707:I497V	I	-	1	0	SIGLEC12	56692428	0.000000	0.05858	0.000000	0.03702	0.060000	0.15804	-2.840000	0.00738	-1.881000	0.01123	-0.751000	0.03497	ATC	T|0.968;C|0.032	0.032	strong		0.567	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003		C	52000616	T	C	52000616	3	2	22	1	0	0	0	0	1	0	0	0	14323	1464	51	3	310	3	SIGLEC12	19	52000616	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	5690	52000616	7128367	4053	6954											
ZNF175	7728	hgsc.bcm.edu	37	chr19	52090671	52090671	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cacacactagaaagaagcccTataaatgccatgactgtgga	16	7	8	10	0	0	3	0	1	0	2	0	4	0	4	2	1	2	0	2	1	6	3	rs60097262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52090671T>A	ENST00000262259.2	+	5	1445	c.1087T>A	c.(1087-1089)Tat>Aat	p.Y363N	ZNF175_ENST00000436511.2_Intron	NM_007147.2	NP_009078.1	Q9Y473	ZN175_HUMAN	zinc finger protein 175	363			Y -> N (in dbSNP:rs60097262).		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)			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)		AAAGAAGCCCTATAAATGCCA	0.398													T|||	100	0.0199681	0.0711	0.0086	5008	,	,		22349	0.0		0.0	False		,,,				2504	0.0				p.Y363N		Atlas-SNP	.											.	ZNF175	65	.	0			c.T1087A						PASS	.	T	ASN/TYR	232,4174	138.4+/-174.2	5,222,1976	105	109	108		1087	0.1	1	19	dbSNP_129	108	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ZNF175	NM_007147.2	143	5,223,6275	AA,AT,TT		0.0116,5.2655,1.7915	benign	363/712	52090671	233,12773	2203	4300	6503	SO:0001583	missense	7728	exon5			AAGCCCTATAAAT	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.1087T>A	19.37:g.52090671T>A	ENSP00000262259:p.Tyr363Asn	99	0	0		130	56	0.430769	NM_007147	A8K9H2	Missense_Mutation	SNP	ENST00000262259.2	37	CCDS12837.1	30	0.013736263736263736	29	0.05894308943089431	1	0.0027624309392265192	0	0.0	0	0.0	T	10.98	1.503898	0.26949	0.052655	1.16E-4	ENSG00000105497	ENST00000262259	T	0.25749	1.78	2.3	0.113	0.14631	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03520	0.0101	M	0.89030	3	0.80722	D	1	P	0.41041	0.736	B	0.37304	0.246	T	0.02437	-1.1159	9	0.87932	D	0	.	4.9985	0.14253	0.0:0.4369:0.0:0.5631	rs60097262;rs61736481	363	Q9Y473	ZN175_HUMAN	N	363	ENSP00000262259:Y363N	ENSP00000262259:Y363N	Y	+	1	0	ZNF175	56782483	0.001000	0.12720	0.972000	0.41901	0.872000	0.50106	1.063000	0.30567	0.020000	0.15106	0.460000	0.39030	TAT	T|0.983;A|0.017	0.017	strong		0.398	ZNF175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396205.1	NM_007147		A	52090671	T	A	52090671	3	1	22	1	0	0	0	0	1	0	0	0	17760	1522	53	5	1101	5	ZNF175	19	52090671	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	90055	52090671	7038312	4054	6955											
HAS1	3036	hgsc.bcm.edu	37	chr19	52223026	52223026	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccgtagcgatcggaggccagCggcaccccggcggcgtaggc	6	3	17	15	7	0	0	0	0	0	0	1	2	0	1	4	6	2	3	4	6	2	2	rs61736497	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52223026C>A	ENST00000222115.1	-	2	169	c.135G>T	c.(133-135)ccG>ccT	p.P45P	HAS1_ENST00000540069.2_Silent_p.P44P|HAS1_ENST00000601714.1_Silent_p.P52P|HAS1_ENST00000594621.1_5'Flank	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	45					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)		CGGAGGCCAGCGGCACCCCGG	0.711													c|||	271	0.0541134	0.1891	0.0202	5008	,	,		12432	0.0		0.003	False		,,,				2504	0.0041				p.P45P	NSCLC(132;636 2450 45807 47979)	Atlas-SNP	.											.	HAS1	61	.	0			c.G135T						PASS	.	C		634,3594		36,562,1516	5	7	6		135	-6.3	1	19	dbSNP_129	6	8,8282		0,8,4137	no	coding-synonymous	HAS1	NM_001523.2		36,570,5653	AA,AC,CC		0.0965,14.9953,5.1286		45/579	52223026	642,11876	2114	4145	6259	SO:0001819	synonymous_variant	3036	exon2			GGCCAGCGGCACC	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.135G>T	19.37:g.52223026C>A		20	0	0		27	16	0.592593	NM_001523	Q14470|Q9NS49	Silent	SNP	ENST00000222115.1	37	CCDS12838.1																																																																																			C|0.947;A|0.053	0.053	strong		0.711	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523		A	52223026	C	A	52223026	2	1	22	1	0	0	0	0	0	0	0	1	6970	755	27	4		4	HAS1	19	52223026	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	132355	52223026	6905957	4055	6956											
ZNF577	84765	hgsc.bcm.edu	37	chr19	52375809	52375809	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgatacaatatctgtaagAtacaagatataatttattac	17	15	4	5	0	2	3	0	1	2	2	2	3	2	3	0	0	3	1	0	0	10	9	rs142094475	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52375809A>G	ENST00000301399.5	-	7	1799	c.1434T>C	c.(1432-1434)taT>taC	p.Y478Y	ZNF577_ENST00000451628.2_Silent_p.Y419Y|ZNF577_ENST00000412216.1_Intron|ZNF577_ENST00000420592.1_Silent_p.Y419Y|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)		TATCTGTAAGATACAAGATAT	0.353													A|||	8	0.00159744	0.0023	0.0072	5008	,	,		19580	0.0		0.0	False		,,,				2504	0.0				p.Y478Y		Atlas-SNP	.											.	ZNF577	63	.	0			c.T1434C						PASS	.	A	,	19,4385		0,19,2183	40	40	40		1257,1434	1.9	0	19	dbSNP_134	40	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ZNF577	NM_001135590.1,NM_032679.2	,	0,19,6483	GG,GA,AA		0.0,0.4314,0.1461	,	419/427,478/486	52375809	19,12985	2202	4300	6502	SO:0001819	synonymous_variant	84765	exon7			TGTAAGATACAAG	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.1434T>C	19.37:g.52375809A>G		67	0	0		56	26	0.464286	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Silent	SNP	ENST00000301399.5	37	CCDS12842.2																																																																																			A|0.998;G|0.002	0.002	strong		0.353	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679		G	52375809	A	G	52375809	2	3	22	1	0	0	0	0	0	0	0	1	18024	340	12	3		3	ZNF577	19	52375809	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	152783	52375809	6753174	4056	6957											
ZNF841	284371	hgsc.bcm.edu	37	chr19	52569479	52569479	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgaaccgaaaggtatccaccGtaattaaagaccttgccaca	15	8	7	11	2	0	2	0	1	0	1	1	3	1	2	5	1	2	2	5	1	6	4	rs61738706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52569479G>A	ENST00000426391.2	-	5	1859	c.1308C>T	c.(1306-1308)taC>taT	p.Y436Y	ZNF841_ENST00000594295.1_Silent_p.Y552Y|ZNF432_ENST00000598446.1_Intron|ZNF841_ENST00000359973.2_Intron|CTC-471J1.2_ENST00000569091.1_RNA|ZNF841_ENST00000389534.4_Silent_p.Y552Y			Q6ZN19	ZN841_HUMAN	zinc finger protein 841	436					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						GGTATCCACCGTAATTAAAGA	0.403													g|||	110	0.0219649	0.0772	0.0101	5008	,	,		22430	0.0		0.001	False		,,,				2504	0.0				p.Y552Y		Atlas-SNP	.											.	ZNF841	183	.	0			c.C1656T						PASS	.	A		87,1297		3,81,608	93	81	85		1656	-4.5	0	19	dbSNP_129	85	0,3182		0,0,1591	no	coding-synonymous	ZNF841	NM_001136499.1		3,81,2199	AA,AG,GG		0.0,6.2861,1.9054		552/925	52569479	87,4479	692	1591	2283	SO:0001819	synonymous_variant	284371	exon7			TCCACCGTAATTA	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.1308C>T	19.37:g.52569479G>A		48	0	0		53	21	0.396226	NM_001136499	B9EG58|Q6ZN82|Q6ZP71|Q8N9U7	Silent	SNP	ENST00000426391.2	37																																																																																				G|0.979;A|0.021	0.021	strong		0.403	ZNF841-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000462435.1	XM_209155		A	52569479	G	A	52569479	2	1	22	1	0	0	0	0	0	0	0	1	18204	1140	40	1		1	ZNF841	19	52569479	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	193670	52569479	6559504	4057	6958											
ZNF578	147660	hgsc.bcm.edu	37	chr19	53014492	53014492	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtcacactagtgagaaaccTtacaagtgtaatgaatgtgg	14	11	10	6	0	1	2	1	2	0	1	1	3	1	2	1	1	2	1	1	1	6	3	rs145508251	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53014492T>A	ENST00000421239.2	+	6	1102	c.858T>A	c.(856-858)ccT>ccA	p.P286P	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	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)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		GTGAGAAACCTTACAAGTGTA	0.378													T|||	51	0.0101837	0.0363	0.0029	5008	,	,		24259	0.0		0.001	False		,,,				2504	0.0				p.P286P		Atlas-SNP	.											.	.	.	.	0			c.T858A						PASS	.	T		92,4314		0,92,2111	111	115	114		858	-0.1	0.3	19	dbSNP_134	114	8,8590		0,8,4291	no	coding-synonymous	ZNF578	NM_001099694.1		0,100,6402	AA,AT,TT		0.093,2.0881,0.769		286/591	53014492	100,12904	2203	4299	6502	SO:0001819	synonymous_variant	147660	exon6			GAAACCTTACAAG	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.858T>A	19.37:g.53014492T>A		106	0	0		153	68	0.444444	NM_001099694	B4DR51|I3L1Y6	Silent	SNP	ENST00000421239.2	37	CCDS54310.1																																																																																			T|0.993;A|0.007	0.007	strong		0.378	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472		A	53014492	T	A	53014492	2	1	22	1	0	0	0	0	0	0	0	1	18025	1596	56	5		5	ZNF578	19	53014492	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	445013	53014492	6114491	4058	6959											
ZNF808	388558	hgsc.bcm.edu	37	chr19	53057031	53057031	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acactggagagaaaccttacAagtgtaaagagtgtggaaag	17	7	12	5	0	0	2	0	0	0	2	0	5	0	4	1	2	2	1	1	2	6	2	rs116132766	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53057031A>G	ENST00000359798.4	+	5	1042	c.862A>G	c.(862-864)Aag>Gag	p.K288E		NM_001039886.3	NP_001034975.2	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	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)|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)		GAAACCTTACAAGTGTAAAGA	0.398													A|||	13	0.00259585	0.0083	0.0029	5008	,	,		22244	0.0		0.0	False		,,,				2504	0.0				p.K288E		Atlas-SNP	.											.	ZNF808	81	.	0			c.A862G						PASS	.	A	GLU/LYS	56,4350		0,56,2147	147	148	148		862	-1.1	0	19	dbSNP_132	148	1,8599		0,1,4299	no	missense	ZNF808	NM_001039886.3	56	0,57,6446	GG,GA,AA		0.0116,1.271,0.4383	possibly-damaging	288/904	53057031	57,12949	2203	4300	6503	SO:0001583	missense	388558	exon5			CCTTACAAGTGTA	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.862A>G	19.37:g.53057031A>G	ENSP00000352846:p.Lys288Glu	162	0	0		151	53	0.350993	NM_001039886	Q68CN7	Missense_Mutation	SNP	ENST00000359798.4	37	CCDS46167.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	.	0.202	-1.043775	0.01997	0.01271	1.16E-4	ENSG00000198482	ENST00000359798	T	0.16196	2.36	1.38	-1.15	0.09709	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09730	0.0239	L	0.49350	1.555	0.09310	N	1	P	0.42941	0.794	B	0.43754	0.43	T	0.20974	-1.0259	9	0.13470	T	0.59	.	3.8277	0.08861	0.6228:0.2188:0.1583:0.0	.	288	Q8N4W9	ZN808_HUMAN	E	288	ENSP00000352846:K288E	ENSP00000352846:K288E	K	+	1	0	ZNF808	57748843	0.000000	0.05858	0.009000	0.14445	0.029000	0.11900	-1.383000	0.02544	-0.207000	0.10187	-1.020000	0.02445	AAG	A|0.996;G|0.004	0.004	strong		0.398	ZNF808-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350447.3	NM_001039886		G	53057031	A	G	53057031	3	3	22	1	0	0	0	0	1	0	0	0	18188	131	5	3	872	3	ZNF808	19	53057031	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	42539	53057031	6071952	4059	6960											
ZNF611	81856	hgsc.bcm.edu	37	chr19	53219140	53219140	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttctgagctgcttcctcaCgtaacatgagtctttaggaa	9	14	8	10	1	4	2	1	2	3	0	5	3	5	3	1	1	3	3	1	1	3	5	rs146379839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53219140C>T	ENST00000319783.1	-	5	324	c.8G>A	c.(7-9)cGt>cAt	p.R3H	ZNF611_ENST00000595798.1_De_novo_Start_OutOfFrame|ZNF611_ENST00000602162.1_Intron|ZNF611_ENST00000543227.1_Missense_Mutation_p.R3H|ZNF611_ENST00000596702.1_Missense_Mutation_p.R3H|ZNF611_ENST00000453741.2_De_novo_Start_OutOfFrame|ZNF611_ENST00000540744.1_Missense_Mutation_p.R3H|ZNF611_ENST00000600943.1_Missense_Mutation_p.R3H	NM_030972.3	NP_112234.3	Q8N823	ZN611_HUMAN	zinc finger protein 611	3					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)		TGCTTCCTCACGTAACATGAG	0.428													-|||	5	0.000998403	0.003	0.0	5008	,	,		22412	0.001		0.0	False		,,,				2504	0.0				p.R3H		Atlas-SNP	.											.	ZNF611	72	.	0			c.G8A						PASS	.	C	HIS/ARG,HIS/ARG,,HIS/ARG	4,3018		0,4,1507	186	202	196		8,8,,8	-2.1	0	19	dbSNP_134	196	1,5417		0,1,2708	no	missense,missense,utr-5,missense	ZNF611	NM_001161499.1,NM_001161500.1,NM_001161501.1,NM_030972.3	29,29,,29	0,5,4215	TT,TC,CC		0.0185,0.1324,0.0592	benign,benign,,benign	3/706,3/706,,3/706	53219140	5,8435	1511	2709	4220	SO:0001583	missense	81856	exon5			TCCTCACGTAACA	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.8G>A	19.37:g.53219140C>T	ENSP00000322427:p.Arg3His	54	0	0		37	13	0.351351	NM_030972	B3KRD5|Q69YG9	Missense_Mutation	SNP	ENST00000319783.1	37	CCDS12855.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	.	7.679	0.688533	0.14973	0.001324	1.85E-4	ENSG00000213020	ENST00000543227;ENST00000540744;ENST00000319783	T;T;T	0.08282	3.11;3.11;3.11	1.87	-2.06	0.07298	.	.	.	.	.	T	0.05044	0.0135	L	0.29908	0.895	0.18873	N	0.999986	B	0.02656	0.0	B	0.01281	0.0	T	0.41520	-0.9504	9	0.33141	T	0.24	.	2.9174	0.05757	0.361:0.2646:0.3743:0.0	.	3	Q8N823	ZN611_HUMAN	H	3	ENSP00000437616:R3H;ENSP00000439211:R3H;ENSP00000322427:R3H	ENSP00000322427:R3H	R	-	2	0	ZNF611	57910952	0.000000	0.05858	0.000000	0.03702	0.491000	0.33493	-0.868000	0.04236	-0.407000	0.07576	0.298000	0.19748	CGT	C|0.999;T|0.001	0.001	strong		0.428	ZNF611-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337612.1	NM_030972		T	53219140	C	T	53219140	3	4	22	1	0	0	0	0	1	0	0	0	18052	536	19	1	2121	1	ZNF611	19	53219140	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	162109	53219140	5909843	4060	6961											
ZNF28	7576	hgsc.bcm.edu	37	chr19	53304448	53304448	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggatttgccactctcaataCattggaaagatttttctctc	11	15	6	9	0	2	1	1	0	2	1	5	3	2	3	1	2	2	0	1	2	3	5	rs143289804	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53304448C>T	ENST00000457749.2	-	4	769	c.650G>A	c.(649-651)tGt>tAt	p.C217Y	ZNF28_ENST00000438150.2_Missense_Mutation_p.C164Y|ZNF28_ENST00000360272.4_Missense_Mutation_p.C164Y|ZNF28_ENST00000414252.2_Missense_Mutation_p.C164Y	NM_006969.3	NP_008900.3	P17035	ZNF28_HUMAN	zinc finger protein 28	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)			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)		ACTCTCAATACATTGGAAAGA	0.328													-|||	6	0.00119808	0.0045	0.0	5008	,	,		21480	0.0		0.0	False		,,,				2504	0.0				p.C217Y		Atlas-SNP	.											.	ZNF28	191	.	0			c.G650A						PASS	.	C	TYR/CYS	22,4384		0,22,2181	118	121	120		650	-3.5	0	19	dbSNP_134	120	0,8600		0,0,4300	yes	missense	ZNF28	NM_006969.3	194	0,22,6481	TT,TC,CC		0.0,0.4993,0.1692	benign	217/719	53304448	22,12984	2203	4300	6503	SO:0001583	missense	7576	exon4			TCAATACATTGGA	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.650G>A	19.37:g.53304448C>T	ENSP00000397693:p.Cys217Tyr	109	0	0		98	46	0.469388	NM_006969	A8KAK9|B4E3G0|B9EIK7|Q5H9V1|Q5HYM9|Q6ZML9|Q6ZN56	Missense_Mutation	SNP	ENST00000457749.2	37	CCDS33093.2	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	-	3.805	-0.040964	0.07452	0.004993	0.0	ENSG00000198538	ENST00000438150;ENST00000457749;ENST00000360272;ENST00000414252;ENST00000391783	T;T;T;T;T	0.58358	0.34;0.34;0.34;0.34;0.34	1.74	-3.48	0.04739	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.49236	0.1545	H	0.94183	3.505	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.55885	-0.8070	9	0.66056	D	0.02	.	5.4015	0.16299	0.0:0.5647:0.168:0.2673	.	217	P17035	ZNF28_HUMAN	Y	164;217;164;164;164	ENSP00000412143:C164Y;ENSP00000397693:C217Y;ENSP00000353410:C164Y;ENSP00000444965:C164Y;ENSP00000375661:C164Y	ENSP00000353410:C164Y	C	-	2	0	ZNF28	57996260	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	1.019000	0.30014	-1.136000	0.02892	-1.497000	0.00963	TGT	C|0.998;T|0.002	0.002	strong		0.328	ZNF28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336038.2	NM_006969		T	53304448	C	T	53304448	3	4	22	1	0	0	0	0	1	0	0	0	17828	478	17	2	1510	2	ZNF28	19	53304448	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	85308	53304448	5824535	4061	6962											
VN1R4	317703	hgsc.bcm.edu	37	chr19	53770846	53770846	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggagagataatggagaagaaCagagaagctccccaggactc	16	4	13	8	0	0	4	0	0	0	4	2	9	1	6	2	3	2	1	2	3	4	1	rs112743505	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53770846C>G	ENST00000311170.4	-	1	126	c.73G>C	c.(73-75)Gtt>Ctt	p.V25L	CTD-2245F17.9_ENST00000599803.1_lincRNA	NM_173857.2	NP_776256.2	Q7Z5H5	VN1R4_HUMAN	vomeronasal 1 receptor 4	25					response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			central_nervous_system(1)|large_intestine(4)|lung(10)|ovary(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	22				GBM - Glioblastoma multiforme(134;0.00294)		TGGAGAAGAACAGAGAAGCTC	0.493										HNSCC(26;0.072)			G|||	256	0.0511182	0.1831	0.0159	5008	,	,		19164	0.002		0.001	False		,,,				2504	0.0				p.V25L		Atlas-SNP	.											.	VN1R4	65	.	0			c.G73C						PASS	.	G	LEU/VAL	706,3700	745.0+/-411.6	70,566,1567	57	63	61		73	1.2	0	19	dbSNP_134	61	8,8592	817.1+/-406.9	0,8,4292	yes	missense	VN1R4	NM_173857.2	32	70,574,5859	GG,GC,CC		0.093,16.0236,5.4898	benign	25/302	53770846	714,12292	2203	4300	6503	SO:0001583	missense	317703	exon1			GAAGAACAGAGAA	AY114733	CCDS33099.1	19q13.42	2012-08-22			ENSG00000228567	ENSG00000228567		"Vomeronasal receptors / Type 1", "GPCR / Unclassified : Vomeronasal receptors, type 1"	19871	protein-coding gene	gene with protein product						12123587	Standard	NM_173857		Approved	V1RL4	uc010ydu.2	Q7Z5H5		ENST00000311170.4:c.73G>C	19.37:g.53770846C>G	ENSP00000310856:p.Val25Leu	332	0	0		394	192	0.48731	NM_173857	Q2M3E2|Q7Z5H6|Q7Z5H7|Q8TDU2	Missense_Mutation	SNP	ENST00000311170.4	37	CCDS33099.1	93	0.042582417582417584	75	0.1524390243902439	8	0.022099447513812154	4	0.006993006993006993	6	0.0079155672823219	G	0.008	-1.870615	0.00542	0.160236	9.3E-4	ENSG00000228567	ENST00000311170	T	0.44482	0.92	2.26	1.19	0.21007	GPCR, rhodopsin-like superfamily (1);	0.610624	0.12496	N	0.463795	T	0.00073	0.0002	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.24905	-1.0147	9	0.02654	T	1	.	3.7996	0.08753	0.1549:0.2523:0.5928:0.0	.	25	Q7Z5H5	VN1R4_HUMAN	L	25	ENSP00000310856:V25L	ENSP00000310856:V25L	V	-	1	0	VN1R4	58462658	0.016000	0.18221	0.008000	0.14137	0.008000	0.06430	0.420000	0.21263	0.090000	0.17273	-0.275000	0.10095	GTT	C|0.953;G|0.047	0.047	strong		0.493	VN1R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464287.1	NM_173857		G	53770846	C	G	53770846	3	3	22	1	0	0	0	0	1	0	0	0	17195	478	17	4	835	4	VN1R4	19	53770846	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	466398	53770846	5358137	4062	6963											
BIRC8	112401	hgsc.bcm.edu	37	chr19	53793162	53793162	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttctgtagtgtctttctgagCgctcactagatctgcaacaa	9	14	8	10	1	5	2	1	1	4	1	5	2	5	2	0	0	3	3	0	0	4	4	rs35880972	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53793162C>T	ENST00000426466.1	-	1	1713	c.466G>A	c.(466-468)Gct>Act	p.A156T		NM_033341.4	NP_203127.3	Q96P09	BIRC8_HUMAN	baculoviral IAP repeat containing 8	156			A -> T (in dbSNP:rs35880972).		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)		TCTTTCTGAGCGCTCACTAGA	0.413													c|||	346	0.0690895	0.2466	0.0274	5008	,	,		18539	0.0		0.001	False		,,,				2504	0.0				p.A156T		Atlas-SNP	.											.	BIRC8	54	.	0			c.G466A						PASS	.	C	THR/ALA	885,3521	343.3+/-307.6	86,713,1404	102	102	102		466	-0.8	0	19	dbSNP_126	102	8,8592	5.0+/-18.6	0,8,4292	yes	missense	BIRC8	NM_033341.4	58	86,721,5696	TT,TC,CC		0.093,20.0862,6.8661	probably-damaging	156/237	53793162	893,12113	2203	4300	6503	SO:0001583	missense	112401	exon1			TCTGAGCGCTCAC	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.466G>A	19.37:g.53793162C>T	ENSP00000412957:p.Ala156Thr	199	0	0		221	101	0.457014	NM_033341	Q6IPY1|Q96RW5	Missense_Mutation	SNP	ENST00000426466.1	37	CCDS12863.1	120	0.054945054945054944	111	0.22560975609756098	9	0.024861878453038673	0	0.0	0	0.0	C	8.392	0.840001	0.16891	0.200862	9.3E-4	ENSG00000163098	ENST00000426466	T	0.37915	1.17	0.628	-0.793	0.10922	.	.	.	.	.	T	0.00012	0.0000	M	0.79475	2.455	0.80722	P	0.0	P	0.37500	0.597	B	0.23852	0.049	T	0.06862	-1.0803	8	0.42905	T	0.14	-4.5555	5.2502	0.15517	0.0:0.7589:0.0:0.2411	rs35880972	156	Q96P09	BIRC8_HUMAN	T	156	ENSP00000412957:A156T	ENSP00000412957:A156T	A	-	1	0	BIRC8	58484974	0.119000	0.22226	0.005000	0.12908	0.004000	0.04260	0.493000	0.22451	-0.150000	0.11195	-0.356000	0.07607	GCT	C|0.937;T|0.063	0.063	strong		0.413	BIRC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464357.1	NM_033341		T	53793162	C	T	53793162	3	4	22	1	0	0	0	0	1	0	0	0	1440	768	27	1	248	1	BIRC8	19	53793162	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	22316	53793162	5335821	4063	6964											
ZNF765	91661	hgsc.bcm.edu	37	chr19	53901281	53901281	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agtcagggatggctcttcctCaggtgagatgatattcttgg	8	13	13	7	0	4	2	2	2	2	1	5	4	5	3	1	4	0	1	1	4	1	4	rs141876832	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53901281C>G	ENST00000396408.3	+	2	130	c.13C>G	c.(13-15)Cag>Gag	p.Q5E	ZNF765_ENST00000594030.1_Missense_Mutation_p.Q5E	NM_001040185.1	NP_001035275.1	Q7L2R6	ZN765_HUMAN	zinc finger protein 765	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(1)|lung(3)	4				GBM - Glioblastoma multiforme(134;0.00379)		GGCTCTTCCTCAGGTGAGATG	0.433													.|||	88	0.0175719	0.0651	0.0029	5008	,	,		21689	0.0		0.0	False		,,,				2504	0.0				p.Q5E		Atlas-SNP	.											ZNF765_ENST00000396408,NS,carcinoma,-2,1	ZNF765	61	1	0			c.C13G						PASS	.	C	GLU/GLN	237,4169	139.2+/-174.8	4,229,1970	183	155	164		13	0.9	0	19	dbSNP_134	164	2,8598	2.2+/-6.3	0,2,4298	no	missense	ZNF765	NM_001040185.1	29	4,231,6268	GG,GC,CC		0.0233,5.379,1.8376	benign	5/524	53901281	239,12767	2203	4300	6503	SO:0001583	missense	91661	exon2			CTTCCTCAGGTGA	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.13C>G	19.37:g.53901281C>G	ENSP00000379689:p.Gln5Glu	68	0	0		79	37	0.468354	NM_001040185	A8MYG0|B4DF18|B7ZAI5|B9EIL1|Q9BV49	Missense_Mutation	SNP	ENST00000396408.3	37	CCDS46171.1	83	0.038003663003663	44	0.08943089430894309	11	0.03038674033149171	14	0.024475524475524476	14	0.018469656992084433	C	2.310	-0.358135	0.05138	0.05379	2.33E-4	ENSG00000196417	ENST00000396408	T	0.00940	5.52	0.924	0.924	0.19418	Krueppel-associated box (1);	.	.	.	.	T	0.00073	0.0002	M	0.72894	2.215	0.09310	N	1	D	0.54772	0.968	P	0.44732	0.459	T	0.53078	-0.8489	9	0.66056	D	0.02	.	5.23	0.15416	0.0:1.0:0.0:0.0	.	5	Q7L2R6	ZN765_HUMAN	E	5	ENSP00000379689:Q5E	ENSP00000379689:Q5E	Q	+	1	0	ZNF765	58593093	0.446000	0.25665	0.033000	0.17914	0.161000	0.22273	0.533000	0.23082	0.829000	0.34733	0.194000	0.17425	CAG	C|0.962;G|0.038	0.038	strong		0.433	ZNF765-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371603.1	NM_138372		G	53901281	C	G	53901281	3	3	22	1	0	0	0	0	1	0	0	0	18154	827	29	4	15	4	ZNF765	19	53901281	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	108119	53901281	5227702	4064	6965											
ZNF765	91661	hgsc.bcm.edu	37	chr19	53911041	53911041	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggacatctcaaagacatgAaagtcatcacaatggagatt	17	8	9	7	0	3	3	3	1	1	2	4	5	3	4	0	2	0	0	0	2	3	1	rs116731689	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53911041A>G	ENST00000396408.3	+	4	350	c.233A>G	c.(232-234)gAa>gGa	p.E78G	ZNF765_ENST00000594030.1_Intron	NM_001040185.1	NP_001035275.1	Q7L2R6	ZN765_HUMAN	zinc finger protein 765	78	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(3)	4				GBM - Glioblastoma multiforme(134;0.00379)		CAAAGACATGAAAGTCATCAC	0.378													.|||	152	0.0303514	0.1112	0.0029	5008	,	,		19693	0.0		0.003	False		,,,				2504	0.0				p.E78G		Atlas-SNP	.											.	ZNF765	61	.	0			c.A233G						PASS	.	A	GLY/GLU	374,4018	175.9+/-205.1	16,342,1838	73	74	74		233	1.2	0	19	dbSNP_132	74	6,8586	3.0+/-9.4	0,6,4290	yes	missense	ZNF765	NM_001040185.1	98	16,348,6128	GG,GA,AA		0.0698,8.5155,2.9267	benign	78/524	53911041	380,12604	2196	4296	6492	SO:0001583	missense	91661	exon4			GACATGAAAGTCA	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.233A>G	19.37:g.53911041A>G	ENSP00000379689:p.Glu78Gly	209	0	0		264	129	0.488636	NM_001040185	A8MYG0|B4DF18|B7ZAI5|B9EIL1|Q9BV49	Missense_Mutation	SNP	ENST00000396408.3	37	CCDS46171.1	47	0.02152014652014652	44	0.08943089430894309	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	A	13.11	2.139154	0.37728	0.085155	6.98E-4	ENSG00000196417	ENST00000396408;ENST00000505866	T;T	0.08896	3.04;4.0	1.21	1.21	0.21127	Krueppel-associated box (1);	.	.	.	.	T	0.00241	0.0007	N	0.17082	0.46	0.09310	N	1	B	0.34241	0.444	B	0.38880	0.284	T	0.47471	-0.9115	8	.	.	.	.	4.4592	0.11657	1.0:0.0:0.0:0.0	.	78	Q7L2R6	ZN765_HUMAN	G	78;25	ENSP00000379689:E78G;ENSP00000421579:E25G	.	E	+	2	0	ZNF765	58602853	0.000000	0.05858	0.013000	0.15412	0.045000	0.14185	0.406000	0.21032	0.523000	0.28482	0.147000	0.16070	GAA	A|0.975;G|0.025	0.025	strong		0.378	ZNF765-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371603.1	NM_138372		G	53911041	A	G	53911041	3	3	22	1	0	0	0	0	1	0	0	0	18154	246	9	3	243	3	ZNF765	19	53911041	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	9760	53911041	5217942	4065	6966											
ZNF813	126017	hgsc.bcm.edu	37	chr19	53994083	53994083	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggaataatttccggaattcTtcgttactcacacaaaaaca	15	11	6	9	2	2	0	1	0	1	0	4	2	3	2	1	2	2	1	1	2	6	5	rs150664026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53994083T>C	ENST00000396403.4	+	4	725	c.597T>C	c.(595-597)tcT>tcC	p.S199S	ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	199					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)		TCCGGAATTCTTCGTTACTCA	0.368													.|||	12	0.00239617	0.0083	0.0014	5008	,	,		20858	0.0		0.0	False		,,,				2504	0.0				p.S199S		Atlas-SNP	.											ZNF813_ENST00000396403,NS,carcinoma,+1,1	ZNF813	81	1	0			c.T597C						PASS	.	T		31,4353		0,31,2161	79	87	84		597	0.5	0	19	dbSNP_134	84	2,8584		0,2,4291	no	coding-synonymous	ZNF813	NM_001004301.3		0,33,6452	CC,CT,TT		0.0233,0.7071,0.2544		199/618	53994083	33,12937	2192	4293	6485	SO:0001819	synonymous_variant	126017	exon4			GAATTCTTCGTTA	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.597T>C	19.37:g.53994083T>C		249	0	0		248	119	0.479839	NM_001004301		Silent	SNP	ENST00000396403.4	37	CCDS46172.1																																																																																			T|0.999;C|0.001	0.001	strong		0.368	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301		C	53994083	T	C	53994083	2	2	22	1	0	0	0	0	0	0	0	1	18190	1596	56	3		3	ZNF813	19	53994083	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	83042	53994083	5134900	4066	6967											
PRKCG	5582	hgsc.bcm.edu	37	chr19	54410114	54410114	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgtgcacccggatgcccgcAgccccaccagcccagtgcct	6	5	10	20	3	0	0	0	0	0	0	1	1	0	1	7	1	5	2	7	1	0	0	rs73937614	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54410114A>G	ENST00000263431.3	+	18	2341	c.2059A>G	c.(2059-2061)Agc>Ggc	p.S687G	PRKCG_ENST00000540413.1_Missense_Mutation_p.S687G|PRKCG_ENST00000542049.1_Missense_Mutation_p.S538G|CACNG7_ENST00000391767.1_5'Flank	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	687					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)	GGATGCCCGCAGCCCCACCAG	0.677											OREG0025667	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	58	0.0115815	0.0408	0.0058	5008	,	,		12287	0.0		0.0	False		,,,				2504	0.0				p.S687G		Atlas-SNP	.											.	PRKCG	246	.	0			c.A2059G						PASS	.	A	GLY/SER	118,4288	81.9+/-120.4	1,116,2086	38	48	45		2059	2.1	1	19	dbSNP_130	45	1,8597		0,1,4298	yes	missense	PRKCG	NM_002739.3	56	1,117,6384	GG,GA,AA		0.0116,2.6782,0.9151	possibly-damaging	687/698	54410114	119,12885	2203	4299	6502	SO:0001583	missense	5582	exon18			GCCCGCAGCCCCA	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.2059A>G	19.37:g.54410114A>G	ENSP00000263431:p.Ser687Gly	180	0	0	1000	208	89	0.427885	NM_002739	B7Z8Q0	Missense_Mutation	SNP	ENST00000263431.3	37	CCDS12867.1	13	0.005952380952380952	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	0	0.0	A	16.20	3.056968	0.55325	0.026782	1.16E-4	ENSG00000126583	ENST00000540413;ENST00000263431;ENST00000542049	T;T;T	0.70631	-0.5;-0.5;-0.5	4.23	2.1	0.27182	.	.	.	.	.	T	0.33527	0.0866	L	0.43152	1.355	0.24531	N	0.994117	B;B;B	0.26876	0.118;0.041;0.162	B;B;B	0.24394	0.017;0.004;0.053	T	0.45041	-0.9288	9	0.59425	D	0.04	.	4.5914	0.12307	0.7265:0.0:0.0996:0.1739	.	538;687;687	B7Z8Q0;F5H5C4;P05129	.;.;KPCG_HUMAN	G	687;687;538	ENSP00000443493:S687G;ENSP00000263431:S687G;ENSP00000438090:S538G	ENSP00000263431:S687G	S	+	1	0	PRKCG	59101926	0.991000	0.36638	1.000000	0.80357	0.980000	0.70556	1.765000	0.38481	0.752000	0.32923	-0.496000	0.04628	AGC	A|0.993;G|0.007	0.007	strong		0.677	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739		G	54410114	A	G	54410114	3	3	22	1	0	0	0	0	1	0	0	0	12524	188	7	3	2129	3	PRKCG	19	54410114	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	416031	54410114	4718869	4067	6968											
CACNG6	59285	hgsc.bcm.edu	37	chr19	54501540	54501540	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaccacgggggagaatgcaCgcatctttcagagaaccaca	13	6	10	12	2	3	2	2	0	1	2	3	4	3	2	2	2	2	2	2	2	2	1	rs78495589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54501540C>T	ENST00000252729.2	+	2	969	c.379C>T	c.(379-381)Cgc>Tgc	p.R127C	CACNG6_ENST00000352529.1_Intron|CACNG6_ENST00000346968.2_Missense_Mutation_p.R127C	NM_145814.1	NP_665813.1	Q9BXT2	CCG6_HUMAN	calcium channel, voltage-dependent, gamma subunit 6	127					calcium ion transport (GO:0006816)	voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15	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;0.168)		GGAGAATGCACGCATCTTTCA	0.502													C|||	79	0.0157748	0.0567	0.0058	5008	,	,		18465	0.0		0.0	False		,,,				2504	0.0				p.R127C		Atlas-SNP	.											.	CACNG6	42	.	0			c.C379T						PASS	.	C	,CYS/ARG,CYS/ARG	179,4227		5,169,2029	104	93	97		,379,379	5.4	0.2	19	dbSNP_131	97	1,8599		0,1,4299	yes	intron,missense,missense	CACNG6	NM_031897.2,NM_145814.1,NM_145815.1	,180,180	5,170,6328	TT,TC,CC		0.0116,4.0626,1.384	,possibly-damaging,possibly-damaging	,127/261,127/215	54501540	180,12826	2203	4300	6503	SO:0001583	missense	59285	exon2			AATGCACGCATCT	AF288386	CCDS12870.1, CCDS12871.1	19q13.4	2008-05-02			ENSG00000130433	ENSG00000130433		"Calcium channel subunits"	13625	protein-coding gene	gene with protein product		606898				11170751	Standard	NM_145814		Approved		uc002qct.3	Q9BXT2	OTTHUMG00000064907	ENST00000252729.2:c.379C>T	19.37:g.54501540C>T	ENSP00000252729:p.Arg127Cys	63	0	0		56	38	0.678571	NM_145815		Missense_Mutation	SNP	ENST00000252729.2	37	CCDS12870.1	30	0.013736263736263736	29	0.05894308943089431	1	0.0027624309392265192	0	0.0	0	0.0	.	16.01	3.000193	0.54147	0.040626	1.16E-4	ENSG00000130433	ENST00000252729;ENST00000346968	T;T	0.31769	1.48;1.48	5.36	5.36	0.76844	.	0.633990	0.14809	N	0.297160	T	0.03608	0.0103	N	0.22421	0.69	0.40471	D	0.980344	D;D	0.61697	0.987;0.99	P;P	0.48114	0.555;0.567	T	0.01039	-1.1472	10	0.62326	D	0.03	-13.2984	14.9705	0.71229	0.0:1.0:0.0:0.0	.	127;127	A6NFR2;Q9BXT2	.;CCG6_HUMAN	C	127	ENSP00000252729:R127C;ENSP00000319097:R127C	ENSP00000252729:R127C	R	+	1	0	CACNG6	59193352	0.024000	0.19004	0.244000	0.24202	0.499000	0.33736	2.549000	0.45803	2.685000	0.91497	0.655000	0.94253	CGC	C|0.986;T|0.014	0.014	strong		0.502	CACNG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139359.1			T	54501540	C	T	54501540	3	4	22	1	0	0	0	0	1	0	0	0	2563	536	19	1	385	1	CACNG6	19	54501540	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	91426	54501540	4627443	4068	6969											
OSCAR	126014	hgsc.bcm.edu	37	chr19	54599119	54599119	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggggcggaggaggcgggccGggcctcagggccctcacctt	4	5	19	13	3	2	0	2	0	0	0	2	2	2	2	4	8	0	0	4	8	0	1	rs1110643	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54599119G>A	ENST00000284648.6	-	5	870	c.673C>T	c.(673-675)Cgg>Tgg	p.R225W	OSCAR_ENST00000391761.1_Missense_Mutation_p.R214W|OSCAR_ENST00000391760.1_3'UTR|OSCAR_ENST00000356532.3_Intron|OSCAR_ENST00000359649.4_Missense_Mutation_p.R229W|OSCAR_ENST00000358375.4_Intron|OSCAR_ENST00000351806.4_Intron			Q8IYS5	OSCAR_HUMAN	osteoclast associated, immunoglobulin-like receptor	225						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)					gaggcgggccgggCCTCAGGG	0.697													G|||	37	0.00738818	0.0272	0.0014	5008	,	,		11125	0.0		0.0	False		,,,				2504	0.0				p.R229W		Atlas-SNP	.											.	OSCAR	22	.	0			c.C685T						PASS	.	G	,,,TRP/ARG	77,4115		0,77,2019	7	8	8		,,,685	-4.1	0	19	dbSNP_86	8	0,8172		0,0,4086	yes	intron,intron,intron,missense	OSCAR	NM_130771.3,NM_133168.3,NM_133169.3,NM_206818.1	,,,101	0,77,6105	AA,AG,GG		0.0,1.8368,0.6228	,,,benign	,,,229/287	54599119	77,12287	2096	4086	6182	SO:0001583	missense	126014	exon5			CGGGCCGGGCCTC	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.673C>T	19.37:g.54599119G>A	ENSP00000365808:p.Arg225Trp	61	0	0		96	53	0.552083	NM_206818	B7WNS2|Q5GRG5|Q8N763|Q8NHL4|Q8WXQ0|Q8WXQ1|Q8WXQ2	Missense_Mutation	SNP	ENST00000284648.6	37		12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	G	14.75	2.627173	0.46944	0.018368	0.0	ENSG00000170909	ENST00000391761;ENST00000359649;ENST00000284648	T;T;T	0.00524	6.82;6.85;6.83	2.03	-4.06	0.03986	.	.	.	.	.	T	0.00144	0.0004	N	0.08118	0	0.09310	N	0.999999	D;D;D	0.71674	0.997;0.998;0.996	B;P;P	0.50136	0.428;0.632;0.48	T	0.40664	-0.9551	9	0.02654	T	1	.	0.9438	0.01361	0.1669:0.2216:0.3875:0.2239	rs1110643	225;214;229	Q8IYS5;Q8IYS5-4;Q8IYS5-7	OSCAR_HUMAN;.;.	W	214;229;225	ENSP00000375641:R214W;ENSP00000352671:R229W;ENSP00000365808:R225W	ENSP00000365808:R225W	R	-	1	2	OSCAR	59290931	0.010000	0.17322	0.005000	0.12908	0.115000	0.19883	-0.599000	0.05700	-0.941000	0.03700	0.289000	0.19496	CGG	G|0.993;A|0.007	0.007	strong		0.697	OSCAR-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000139493.4	NM_133169		A	54599119	G	A	54599119	3	1	22	1	0	0	0	0	1	0	0	0	11294	1115	39	1	320	1	OSCAR	19	54599119	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	97579	54599119	4529864	4069	6970											
MBOAT7	79143	hgsc.bcm.edu	37	chr19	54682538	54682538	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atatactgcgccagccaccaCtgcaccgtcatgttccagta	10	9	7	15	2	1	0	1	0	0	0	2	0	2	0	5	0	4	3	5	0	3	4	rs116423748	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54682538C>T	ENST00000245615.1	-	7	1455	c.975G>A	c.(973-975)caG>caA	p.Q325Q	MBOAT7_ENST00000431666.2_Silent_p.Q252Q|MBOAT7_ENST00000391754.1_Silent_p.Q325Q|MBOAT7_ENST00000338624.6_Silent_p.Q252Q	NM_024298.3	NP_077274.3	Q96N66	MBOA7_HUMAN	membrane bound O-acyltransferase domain containing 7	325					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)					CCAGCCACCACTGCACCGTCA	0.567													C|||	37	0.00738818	0.0272	0.0014	5008	,	,		19150	0.0		0.0	False		,,,				2504	0.0				p.Q325Q	NSCLC(97;826 2151 10470 22540)	Atlas-SNP	.											.	MBOAT7	37	.	0			c.G975A						PASS	.	C	,,,	116,4290	86.3+/-125.0	2,112,2089	85	63	70		756,975,756,975	2.5	1	19	dbSNP_132	70	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MBOAT7	NM_001146056.1,NM_001146082.1,NM_001146083.1,NM_024298.3	,,,	2,113,6388	TT,TC,CC		0.0116,2.6328,0.8996	,,,	252/400,325/345,252/400,325/473	54682538	117,12889	2203	4300	6503	SO:0001819	synonymous_variant	79143	exon7			CCACCACTGCACC	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.975G>A	19.37:g.54682538C>T		100	0	0		121	61	0.504132	NM_001146082	A9C4B6|B0V3I5|B4DQ87|Q05DF0|Q7L5N2|Q99908|Q9BPV2|Q9BRE9	Silent	SNP	ENST00000245615.1	37	CCDS12883.1																																																																																			C|0.991;T|0.009	0.009	strong		0.567	MBOAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142203.1	NM_024298		T	54682538	C	T	54682538	2	4	22	1	0	0	0	0	0	0	0	1	9367	564	20	2		2	MBOAT7	19	54682538	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	83419	54682538	4446445	4070	6971											
LILRB3	11025	hgsc.bcm.edu	37	chr19	54720967	54720967	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgcgtaccccccgggctagtGgatggccagagtggcgtaga	7	7	16	11	3	0	2	0	0	0	2	0	3	0	3	4	4	2	3	4	4	3	3	rs114510580	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54720967G>A	ENST00000391750.1	-	14	2027	c.1891C>T	c.(1891-1893)Cac>Tac	p.H631Y	LILRA6_ENST00000440558.2_Missense_Mutation_p.H631Y|LILRB3_ENST00000346401.6_Missense_Mutation_p.H643Y|LILRB3_ENST00000245620.9_Missense_Mutation_p.H632Y|LILRA6_ENST00000391735.3_3'UTR|LILRA6_ENST00000419410.2_Missense_Mutation_p.H632Y|LILRB3_ENST00000469273.1_5'Flank|LILRB3_ENST00000407860.2_Missense_Mutation_p.H648Y|LILRA6_ENST00000270464.5_Missense_Mutation_p.H632Y|LILRB3_ENST00000424807.1_Missense_Mutation_p.H631Y			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	631					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)		CCGGGCTAGTGGATGGCCAGA	0.627													.|||	171	0.0341454	0.1271	0.0043	5008	,	,		17170	0.0		0.0	False		,,,				2504	0.0				p.H632Y		Atlas-SNP	.											.	LILRB3	67	.	0			c.C1894T						PASS	.	G	TYR/HIS,TYR/HIS	442,3964	213.5+/-233.1	18,406,1779	90	84	86		1894,1891	0.7	0	19	dbSNP_132	86	3,8597	3.0+/-9.4	0,3,4297	no	missense,missense	LILRB3	NM_001081450.1,NM_006864.2	83,83	18,409,6076	AA,AG,GG		0.0349,10.0318,3.4215	probably-damaging,probably-damaging	632/633,631/632	54720967	445,12561	2203	4300	6503	SO:0001583	missense	11025	exon13			GCTAGTGGATGGC	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.1891C>T	19.37:g.54720967G>A	ENSP00000375630:p.His631Tyr	280	0	0		333	140	0.42042	NM_001081450	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	60	0.027472527472527472	57	0.11585365853658537	1	0.0027624309392265192	2	0.0034965034965034965	0	0.0	G	13.16	2.154570	0.38021	0.100318	3.49E-4	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410	T;T;T;T;T;T;T;T	0.00630	6.11;6.11;6.17;6.13;6.16;6.1;6.11;6.14	2.92	0.672	0.17935	.	.	.	.	.	T	0.00039	0.0001	M	0.73598	2.24	0.09310	N	1	D;P;B;P;P;P;P	0.71674	0.998;0.644;0.226;0.956;0.791;0.721;0.849	D;B;B;P;B;B;P	0.79784	0.993;0.425;0.064;0.61;0.324;0.056;0.555	T	0.52845	-0.8521	9	0.87932	D	0	.	2.9682	0.05915	0.1554:0.0:0.5739:0.2707	.	648;631;632;643;648;631;632	B5MCX0;F8WCY4;D3YTC4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;.;LIRB3_HUMAN;.	Y	631;631;643;632;648;631;632;632	ENSP00000375630:H631Y;ENSP00000412771:H631Y;ENSP00000345184:H643Y;ENSP00000245620:H632Y;ENSP00000384274:H648Y;ENSP00000390120:H631Y;ENSP00000270464:H632Y;ENSP00000411227:H632Y	ENSP00000270464:H632Y	H	-	1	0	LILRB3;LILRA6	59412779	0.015000	0.18098	0.004000	0.12327	0.059000	0.15707	2.746000	0.47467	0.274000	0.22072	0.472000	0.43445	CAC	G|0.962;A|0.038	0.038	strong		0.627	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864		A	54720967	G	A	54720967	3	1	22	1	0	0	0	0	1	0	0	0	8801	1348	47	2	8	2	LILRB3	19	54720967	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	38429	54720967	4408016	4071	6972											
LILRB3	11025	hgsc.bcm.edu	37	chr19	54721272	54721272	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgaggagggaggagaggcCatttctctcctaggactgga	10	8	16	7	0	1	2	0	1	1	1	3	7	2	6	2	6	0	0	2	6	1	2	rs114189491	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54721272C>T	ENST00000391750.1	-	13	1801	c.1665G>A	c.(1663-1665)atG>atA	p.M555I	LILRA6_ENST00000440558.2_Missense_Mutation_p.M555I|LILRB3_ENST00000346401.6_Missense_Mutation_p.M567I|LILRB3_ENST00000245620.9_Missense_Mutation_p.M556I|LILRA6_ENST00000391735.3_3'UTR|LILRA6_ENST00000419410.2_Missense_Mutation_p.M556I|LILRB3_ENST00000469273.1_5'UTR|LILRB3_ENST00000407860.2_Missense_Mutation_p.M572I|LILRA6_ENST00000270464.5_Missense_Mutation_p.M556I|LILRB3_ENST00000424807.1_Missense_Mutation_p.M555I			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	555					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)		GAGGAGAGGCCATTTCTCTCC	0.577													.|||	174	0.0347444	0.1293	0.0043	5008	,	,		17886	0.0		0.0	False		,,,				2504	0.0				p.M556I		Atlas-SNP	.											.	LILRB3	67	.	0			c.G1668A						PASS	.	C	ILE/MET,ILE/MET	451,3953	216.4+/-235.1	26,399,1777	130	130	130		1668,1665	-0.9	0	19	dbSNP_132	130	3,8597	3.0+/-9.4	0,3,4297	no	missense,missense	LILRB3	NM_001081450.1,NM_006864.2	10,10	26,402,6074	TT,TC,CC		0.0349,10.2407,3.4912	benign,benign	556/633,555/632	54721272	454,12550	2202	4300	6502	SO:0001583	missense	11025	exon12			AGAGGCCATTTCT	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.1665G>A	19.37:g.54721272C>T	ENSP00000375630:p.Met555Ile	602	0	0		418	208	0.497608	NM_001081450	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	63	0.028846153846153848	62	0.12601626016260162	1	0.0027624309392265192	0	0.0	0	0.0	C	12.21	1.870077	0.33069	0.102407	3.49E-4	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410	T;T;T;T;T;T;T;T	0.00477	7.16;7.16;7.14;7.17;7.14;7.16;7.16;7.18	2.45	-0.895	0.10560	.	.	.	.	.	T	0.00012	0.0000	L	0.50919	1.6	0.09310	N	1	D;B;B;B;B;B;P	0.56287	0.975;0.39;0.197;0.121;0.014;0.006;0.78	D;B;B;B;B;B;P	0.65684	0.937;0.026;0.109;0.015;0.002;0.001;0.458	T	0.55179	-0.8181	9	0.54805	T	0.06	.	2.7524	0.05284	0.0:0.4373:0.2613:0.3014	.	572;555;556;567;572;555;556	B5MCX0;F8WCY4;D3YTC4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;.;LIRB3_HUMAN;.	I	555;555;567;556;572;555;556;556	ENSP00000375630:M555I;ENSP00000412771:M555I;ENSP00000345184:M567I;ENSP00000245620:M556I;ENSP00000384274:M572I;ENSP00000390120:M555I;ENSP00000270464:M556I;ENSP00000411227:M556I	ENSP00000270464:M556I	M	-	3	0	LILRB3;LILRA6	59413084	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-0.049000	0.11924	-0.089000	0.12484	0.121000	0.15741	ATG	C|0.961;T|0.039	0.039	strong		0.577	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864		T	54721272	C	T	54721272	3	4	22	1	0	0	0	0	1	0	0	0	8801	594	21	2	238	2	LILRB3	19	54721272	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	305	54721272	4407711	4072	6973											
LILRB3	11025	hgsc.bcm.edu	37	chr19	54721337	54721337	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcctgggggtcttcatcgtGtgggctctgctggagagaga	5	11	17	8	1	3	2	1	0	2	2	4	4	3	2	1	4	2	2	1	4	0	1	rs75437884	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54721337G>A	ENST00000391750.1	-	13	1736	c.1600C>T	c.(1600-1602)Cac>Tac	p.H534Y	LILRA6_ENST00000440558.2_Missense_Mutation_p.H534Y|LILRB3_ENST00000346401.6_Missense_Mutation_p.H546Y|LILRB3_ENST00000245620.9_Missense_Mutation_p.H535Y|LILRA6_ENST00000391735.3_3'UTR|LILRA6_ENST00000419410.2_Missense_Mutation_p.H535Y|LILRB3_ENST00000469273.1_5'UTR|LILRB3_ENST00000407860.2_Missense_Mutation_p.H551Y|LILRA6_ENST00000270464.5_Missense_Mutation_p.H535Y|LILRB3_ENST00000424807.1_Missense_Mutation_p.H534Y			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	534					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)		TCTTCATCGTGTGGGCTCTGC	0.577																																					p.H535Y		Atlas-SNP	.											LILRB3,NS,lymphoid_neoplasm,+2,1	LILRB3	67	1	0			c.C1603T						PASS	.	G	TYR/HIS,TYR/HIS	47,4355	43.1+/-76.7	0,47,2154	76	81	80		1603,1600	-1.2	0	19	dbSNP_131	80	1,8597		0,1,4298	no	missense,missense	LILRB3	NM_001081450.1,NM_006864.2	83,83	0,48,6452	AA,AG,GG		0.0116,1.0677,0.3692	possibly-damaging,possibly-damaging	535/633,534/632	54721337	48,12952	2201	4299	6500	SO:0001583	missense	11025	exon12			CATCGTGTGGGCT	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.1600C>T	19.37:g.54721337G>A	ENSP00000375630:p.His534Tyr	534	0	0		384	90	0.234375	NM_001081450	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	8	0.003663003663003663	6	0.012195121951219513	2	0.0055248618784530384	0	0.0	0	0.0	G	10.80	1.452361	0.26074	0.010677	1.16E-4	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410	T;T;T;T;T;T;T;T	0.00487	7.1;7.1;7.07;7.07;7.05;7.1;7.07;7.09	2.47	-1.25	0.09405	.	.	.	.	.	T	0.00384	0.0012	L	0.54323	1.7	0.09310	N	1	D;B;D;P;B;P;P	0.56968	0.969;0.009;0.978;0.832;0.411;0.536;0.593	P;B;P;B;B;B;B	0.51615	0.65;0.004;0.675;0.249;0.059;0.031;0.32	T	0.51164	-0.8740	9	0.33141	T	0.24	.	5.0801	0.14651	0.1499:0.4983:0.3518:0.0	.	551;534;535;546;551;534;535	B5MCX0;F8WCY4;D3YTC4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;.;LIRB3_HUMAN;.	Y	534;534;546;535;551;534;535;535	ENSP00000375630:H534Y;ENSP00000412771:H534Y;ENSP00000345184:H546Y;ENSP00000245620:H535Y;ENSP00000384274:H551Y;ENSP00000390120:H534Y;ENSP00000270464:H535Y;ENSP00000411227:H535Y	ENSP00000270464:H535Y	H	-	1	0	LILRB3;LILRA6	59413149	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.974000	0.03794	-0.122000	0.11766	-0.506000	0.04501	CAC	G|0.996;A|0.004	0.004	strong		0.577	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864		A	54721337	G	A	54721337	3	1	22	1	0	0	0	0	1	0	0	0	8801	1377	48	2	303	2	LILRB3	19	54721337	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	65	54721337	4407646	4073	6974											
LILRA6	79168	hgsc.bcm.edu	37	chr19	54744771	54744771	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggagaggttgtgtgcaccAtagcacctgtactggccccc	8	8	13	12	0	0	1	0	0	0	1	0	3	0	1	4	3	3	4	4	3	2	3	rs142457810	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54744771A>G	ENST00000396365.2	-	5	930	c.891T>C	c.(889-891)taT>taC	p.Y297Y	LILRA6_ENST00000440558.2_Silent_p.Y297Y|LILRA6_ENST00000391735.3_3'UTR|LILRA6_ENST00000419410.2_Silent_p.Y297Y|LILRA6_ENST00000245621.5_Silent_p.Y297Y|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000270464.5_Intron	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	297	Ig-like C2-type 1.				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)		TGTGTGCACCATAGCACCTGT	0.687																																					p.Y297Y		Atlas-SNP	.											.	LILRA6	75	.	0			c.T891C						PASS	.						57	71	67					19																	54744771		2203	4300	6503	SO:0001819	synonymous_variant	79168	exon5			TGCACCATAGCAC	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.891T>C	19.37:g.54744771A>G		380	1	0.00263158		471	124	0.26327	NM_024318		Silent	SNP	ENST00000396365.2	37	CCDS42610.1																																																																																			A|0.570;G|0.430	0.430	strong		0.687	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318		G	54744771	A	G	54744771	2	3	22	1	0	0	0	0	0	0	0	1	8798	224	8	3		3	LILRA6	19	54744771	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	23434	54744771	4384212	4074	6975											
LILRA6	79168	hgsc.bcm.edu	37	chr19	54745659	54745659	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cttcatcagaacaaaatggtGatatcccttctgtgagccac	12	11	7	11	0	3	3	2	2	1	1	4	3	4	3	2	1	2	0	2	1	4	3	rs200657736		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54745659G>C	ENST00000396365.2	-	4	490	c.451C>G	c.(451-453)Cac>Gac	p.H151D	LILRA6_ENST00000440558.2_Missense_Mutation_p.H151D|LILRA6_ENST00000391735.3_Missense_Mutation_p.H151D|LILRA6_ENST00000419410.2_Missense_Mutation_p.H151D|LILRA6_ENST00000245621.5_Missense_Mutation_p.H151D|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000270464.5_Missense_Mutation_p.H151D	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	151					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)		ACAAAATGGTGATATCCCTTC	0.592																																					p.H151D		Atlas-SNP	.											LILRA6,NS,carcinoma,0,2	LILRA6	75	2	0			c.C451G						scavenged	.						23	37	32					19																	54745659		2100	4266	6366	SO:0001583	missense	79168	exon4			AATGGTGATATCC	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.451C>G	19.37:g.54745659G>C	ENSP00000379651:p.His151Asp	500	1	0.002		875	120	0.137143	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	g	0	-2.647560	0.00111	.	.	ENSG00000244482	ENST00000440558;ENST00000270464;ENST00000419410;ENST00000391735;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T;T;T	0.10960	2.82;2.82;2.82;4.04;2.82;2.82	2.64	-5.28	0.02755	Immunoglobulin-like fold (1);	2.010510	0.02119	N	0.055507	T	0.01870	0.0059	N	0.00237	-1.79	0.09310	N	1	B;B;B;B;B;B	0.09022	0.002;0.0;0.002;0.0;0.0;0.0	B;B;B;B;B;B	0.08055	0.003;0.0;0.003;0.001;0.002;0.001	T	0.25537	-1.0129	10	0.02654	T	1	.	3.0381	0.06129	0.2388:0.2899:0.373:0.0983	.	151;151;151;151;151;151	C9JFH3;Q6PI73-2;Q6PI73;F8WCY4;D3YTC4;F8W6G6	.;.;LIRA6_HUMAN;.;.;.	D	151	ENSP00000390120:H151D;ENSP00000270464:H151D;ENSP00000411227:H151D;ENSP00000375615:H151D;ENSP00000379651:H151D;ENSP00000245621:H151D	ENSP00000245621:H151D	H	-	1	0	LILRA6	59437471	.	.	0.000000	0.03702	0.020000	0.10135	.	.	-3.099000	0.00245	-1.962000	0.00476	CAC	G|0.999;C|0.001	0.001	weak		0.592	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318		C	54745659	G	C	54745659	3	2	22	1	0	0	0	0	1	0	0	0	8798	1290	45	4	1014	4	LILRA6	19	54745659	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	888	54745659	4383324	4075	6976											
LILRB2	10288	hgsc.bcm.edu	37	chr19	54782165	54782165	+	Missense_Mutation	SNP	C	C	T																															gtgagacagcaggtaggggtCggagttgagtgagccgtagc																								rs4993133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54782165C>T	ENST00000391749.4	-	7	1478	c.1207G>A	c.(1207-1209)Gac>Aac	p.D403N	LILRB2_ENST00000471216.1_5'Flank|LILRB2_ENST00000391746.1_Missense_Mutation_p.D403N|LILRB2_ENST00000314446.5_Missense_Mutation_p.D403N|LILRB2_ENST00000434421.1_Missense_Mutation_p.D287N|LILRB2_ENST00000391748.1_Missense_Mutation_p.D403N	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	403	Ig-like C2-type 4.		D -> N (in dbSNP:rs4993133).		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)		AGGTAGGGGTCGGAGTTGAGT	0.592													.|||	31	0.0061901	0.0204	0.0014	5008	,	,		17568	0.0		0.002	False		,,,				2504	0.001				p.D403N		Atlas-SNP	.											.	LILRB2	94	.	0			c.G1207A						PASS	.	T	ASN/ASP,ASN/ASP	51,4355	821.0+/-416.4	1,49,2153	101	94	96		1207,1207	-2.2	0	19	dbSNP_113	96	5,8595	818.7+/-406.8	0,5,4295	no	missense,missense	LILRB2	NM_001080978.2,NM_005874.3	23,23	1,54,6448	TT,TC,CC		0.0581,1.1575,0.4306	benign,benign	403/598,403/599	54782165	56,12950	2203	4300	6503	SO:0001583	missense	10288	exon7			AGGGGTCGGAGTT	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.1207G>A	19.37:g.54782165C>T	ENSP00000375629:p.Asp403Asn	190	0	0		142	61	0.429577	NM_005874	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Missense_Mutation	SNP	ENST00000391749.4	37	CCDS12886.1	9	0.004120879120879121	7	0.014227642276422764	0	0.0	0	0.0	2	0.002638522427440633	T	1.465	-0.561273	0.03939	0.011575	5.81E-4	ENSG00000131042	ENST00000391748;ENST00000314446;ENST00000391749;ENST00000391746;ENST00000434421	T;T;T;T;T	0.00717	5.79;5.79;5.79;5.79;5.79	1.88	-2.23	0.06930	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	3.810930	0.01046	N	0.004391	T	0.00300	0.0009	N	0.03294	-0.36	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.06405	0.002;0.002;0.002	T	0.43653	-0.9378	10	0.06494	T	0.89	.	0.3448	0.00339	0.2691:0.185:0.1425:0.4034	rs4993133	403;420;403	A8MU67;E7EVY1;Q8N423	.;.;LIRB2_HUMAN	N	403;403;403;403;287	ENSP00000375628:D403N;ENSP00000319960:D403N;ENSP00000375629:D403N;ENSP00000375626:D403N;ENSP00000410117:D287N	ENSP00000319960:D403N	D	-	1	0	LILRB2	59473977	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-3.319000	0.00514	-1.728000	0.01366	-2.542000	0.00179	GAC	C|0.995;T|0.005	0.005	strong		0.592	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1			T	54782165	C	T	54782165	3	4	22	1	0	0	0	0	1	0	0	0	8800	884	31	1	621	1	LILRB2	19	54782165	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	36506	54782165	4346818	4076	6977	87	2									
LILRB2	10288	hgsc.bcm.edu	37	chr19	54782173	54782173	+	Missense_Mutation	SNP	A	A	C																															gcaggtaggggtcggagttgAgtgagccgtagcacctgtag																								rs4993130		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54782173A>C	ENST00000391749.4	-	7	1470	c.1199T>G	c.(1198-1200)cTc>cGc	p.L400R	LILRB2_ENST00000471216.1_5'Flank|LILRB2_ENST00000391746.1_Missense_Mutation_p.L400R|LILRB2_ENST00000314446.5_Missense_Mutation_p.L400R|LILRB2_ENST00000434421.1_Missense_Mutation_p.L284R|LILRB2_ENST00000391748.1_Missense_Mutation_p.L400R	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	400	Ig-like C2-type 4.				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)		GTCGGAGTTGAGTGAGCCGTA	0.582																																					p.L400R		Atlas-SNP	.											.	LILRB2	94	.	0			c.T1199G						PASS	.	C	ARG/LEU,ARG/LEU	1,4405	825.9+/-416.6	0,1,2202	113	105	107		1199,1199	-3.8	0	19	dbSNP_113	107	1,8599		0,1,4299	no	missense,missense	LILRB2	NM_005874.3,NM_001080978.2	102,102	0,2,6501	CC,CA,AA		0.0116,0.0227,0.0154	benign,benign	400/599,400/598	54782173	2,13004	2203	4300	6503	SO:0001583	missense	10288	exon7			GAGTTGAGTGAGC	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.1199T>G	19.37:g.54782173A>C	ENSP00000375629:p.Leu400Arg	199	0	0		172	77	0.447674	NM_005874	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Missense_Mutation	SNP	ENST00000391749.4	37	CCDS12886.1	.	.	.	.	.	.	.	.	.	.	C	0.006	-2.109135	0.00353	2.27E-4	1.16E-4	ENSG00000131042	ENST00000391748;ENST00000314446;ENST00000391749;ENST00000391746;ENST00000434421	T;T;T;T;T	0.00745	5.75;5.75;5.75;5.75;5.75	1.88	-3.77	0.04346	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	6.345920	0.00496	N	0.000144	T	0.00580	0.0019	N	0.05592	-0.015	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.17979	0.013;0.013;0.02	T	0.47471	-0.9115	10	0.19590	T	0.45	.	5.0707	0.14606	0.1536:0.252:0.0:0.5944	.	400;417;400	A8MU67;E7EVY1;Q8N423	.;.;LIRB2_HUMAN	R	400;400;400;400;284	ENSP00000375628:L400R;ENSP00000319960:L400R;ENSP00000375629:L400R;ENSP00000375626:L400R;ENSP00000410117:L284R	ENSP00000319960:L400R	L	-	2	0	LILRB2	59473985	0.000000	0.05858	0.000000	0.03702	0.061000	0.15899	-4.942000	0.00167	-5.508000	0.00013	-3.110000	0.00062	CTC	A|1.000;C|0.000	0.000	weak		0.582	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1			C	54782173	A	C	54782173	3	2	22	1	0	0	0	0	1	0	0	0	8800	304	11	5	629	5	LILRB2	19	54782173	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	8	54782173	4346810	4077	6978	87	2									
LILRA3	11026	hgsc.bcm.edu	37	chr19	54803141	54803141	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcccacggagaagatggccCgggatgacccacgggcatgg	9	3	17	12	3	0	3	0	1	0	2	0	5	0	4	3	6	0	1	3	6	1	0	rs147561158	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54803141C>T	ENST00000251390.3	-	4	627	c.536G>A	c.(535-537)cGg>cAg	p.R179Q	LILRA3_ENST00000391744.3_Intron|LILRA3_ENST00000391745.1_Missense_Mutation_p.R196Q	NM_006865.3	NP_006856.3	Q8N6C8	LIRA3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 3	179	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)		GAAGATGGCCCGGGATGACCC	0.567													.|||	5	0.000998403	0.0038	0.0	5008	,	,		15432	0.0		0.0	False		,,,				2504	0.0				p.R179Q		Atlas-SNP	.											LILRA3,right_upper_lobe,carcinoma,0,2	LILRA3	65	2	0			c.G536A						scavenged	.	C	,GLN/ARG	25,4365		1,23,2171	139	115	123		,536	-0.2	0	19	dbSNP_134	123	0,8332		0,0,4166	yes	intron,missense	LILRA3	NM_001172654.1,NM_006865.3	,43	1,23,6337	TT,TC,CC		0.0,0.5695,0.1965	,	,179/440	54803141	25,12697	2195	4166	6361	SO:0001583	missense	11026	exon4			ATGGCCCGGGATG	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.536G>A	19.37:g.54803141C>T	ENSP00000251390:p.Arg179Gln	315	2	0.00634921		346	167	0.482659	NM_006865	J3KPM2|O15469|O15470|O75016|Q8N151|Q8N154|Q8NHJ1|Q8NHJ2|Q8NHJ3|Q8NHJ4	Missense_Mutation	SNP	ENST00000251390.3	37	CCDS12887.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	0.015	-1.559568	0.00910	0.005695	0.0	ENSG00000170866	ENST00000251390;ENST00000391745	T;T	0.02890	4.12;4.12	2.07	-0.183	0.13284	Immunoglobulin-like fold (1);	0.611757	0.12604	N	0.454468	T	0.00695	0.0023	N	0.02391	-0.57	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.46693	-0.9173	10	0.02654	T	1	.	4.3936	0.11351	0.0:0.4019:0.0:0.5981	.	179	Q8N6C8	LIRA3_HUMAN	Q	179;196	ENSP00000251390:R179Q;ENSP00000375625:R196Q	ENSP00000251390:R179Q	R	-	2	0	LILRA3	59494953	0.000000	0.05858	0.003000	0.11579	0.000000	0.00434	-0.534000	0.06150	-0.089000	0.12484	-0.350000	0.07774	CGG	C|0.998;T|0.002	0.002	strong		0.567	LILRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140236.1			T	54803141	C	T	54803141	3	4	22	1	0	0	0	0	1	0	0	0	8795	652	23	1	799	1	LILRA3	19	54803141	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	20968	54803141	4325842	4078	6979											
LAIR2	3904	hgsc.bcm.edu	37	chr19	55019379	55019379	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atggtctgagcacagtgactTcctggagctgctggtgaaag	9	10	14	8	0	1	3	0	3	1	0	2	4	2	4	1	3	3	3	1	3	1	1	rs34429135	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55019379T>A	ENST00000301202.2	+	3	466	c.344T>A	c.(343-345)tTc>tAc	p.F115Y	LAIR2_ENST00000351841.2_Missense_Mutation_p.F115Y	NM_002288.4	NP_002279.2	Q6ISS4	LAIR2_HUMAN	leukocyte-associated immunoglobulin-like receptor 2	115	Ig-like C2-type.		F -> Y (in dbSNP:rs34429135).			extracellular region (GO:0005576)				central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)	18	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0967)		CACAGTGACTTCCTGGAGCTG	0.577													T|||	284	0.0567093	0.2005	0.0245	5008	,	,		17434	0.0		0.002	False		,,,				2504	0.0				p.F115Y		Atlas-SNP	.											.	LAIR2	30	.	0			c.T344A						PASS	.	T	TYR/PHE,TYR/PHE	773,3633	307.7+/-290.2	60,653,1490	89	92	91		344,344	-7.6	0	19	dbSNP_126	91	14,8586	8.4+/-32.0	0,14,4286	yes	missense,missense	LAIR2	NM_002288.4,NM_021270.3	22,22	60,667,5776	AA,AT,TT		0.1628,17.5443,6.0511	benign,benign	115/153,115/136	55019379	787,12219	2203	4300	6503	SO:0001583	missense	3904	exon3			GTGACTTCCTGGA	AF013250	CCDS12897.1, CCDS12898.1	19q13.4	2013-01-29	2006-03-23		ENSG00000167618	ENSG00000167618		"Leukocyte-associated Ig like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6478	protein-coding gene	gene with protein product		602993	"leukocyte-associated Ig-like receptor 2"			9285412	Standard	XM_005277264		Approved	CD306	uc002qgc.3	Q6ISS4	OTTHUMG00000065697	ENST00000301202.2:c.344T>A	19.37:g.55019379T>A	ENSP00000301202:p.Phe115Tyr	107	0	0		127	55	0.433071	NM_002288	Q6PEZ4	Missense_Mutation	SNP	ENST00000301202.2	37	CCDS12897.1	99	0.04532967032967033	87	0.17682926829268292	10	0.027624309392265192	0	0.0	2	0.002638522427440633	T	0.013	-1.619502	0.00828	0.175443	0.001628	ENSG00000167618	ENST00000301202;ENST00000351841	T;T	0.11277	2.79;2.79	3.77	-7.55	0.01327	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	8.928910	0.00166	N	0.000000	T	0.00012	0.0000	N	0.02315	-0.6	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.09377	0.001;0.004	T	0.35822	-0.9773	8	.	.	.	.	0.0766	0.00027	0.2872:0.2456:0.1969:0.2703	rs34429135	115;115	Q6ISS4-2;Q6ISS4	.;LAIR2_HUMAN	Y	115	ENSP00000301202:F115Y;ENSP00000301203:F115Y	.	F	+	2	0	LAIR2	59711191	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.540000	0.00218	-3.651000	0.00126	-0.907000	0.02831	TTC	T|0.943;A|0.057	0.057	strong		0.577	LAIR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140801.1			A	55019379	T	A	55019379	3	1	22	1	0	0	0	0	1	0	0	0	8612	1783	62	5	354	5	LAIR2	19	55019379	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	216238	55019379	4109604	4079	6980											
LILRA2	11027	hgsc.bcm.edu	37	chr19	55098736	55098736	+	Missense_Mutation	SNP	G	G	C																															gcatgggtgtggctggcttgGtcctggtggtcctcgggatt																								rs73939007	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55098736G>C	ENST00000251377.3	+	9	1508	c.1375G>C	c.(1375-1377)Gtc>Ctc	p.V459L	LILRA2_ENST00000391737.1_Missense_Mutation_p.V430L|LILRA2_ENST00000251376.3_Missense_Mutation_p.V442L|CTB-83J4.2_ENST00000596330.1_lincRNA|LILRA2_ENST00000391738.3_Missense_Mutation_p.V459L|LILRB1_ENST00000448689.1_Intron|LILRB1_ENST00000418536.2_Intron|LILRB1_ENST00000396321.2_Intron			Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2	459					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)		GGCTGGCTTGGTCCTGGTGGT	0.567													g|||	51	0.0101837	0.0378	0.0014	5008	,	,		17382	0.0		0.0	False		,,,				2504	0.0				p.V459L		Atlas-SNP	.											.	LILRA2	99	.	0			c.G1375C						PASS	.	G	LEU/VAL,LEU/VAL	100,4306	79.3+/-117.8	0,100,2103	111	96	101		1375,1324	-5.5	0	19	dbSNP_130	101	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	LILRA2	NM_001130917.1,NM_006866.2	32,32	0,102,6401	CC,CG,GG		0.0233,2.2696,0.7843	,	459/484,442/467	55098736	102,12904	2203	4300	6503	SO:0001583	missense	11027	exon8			GGCTTGGTCCTGG	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.1375G>C	19.37:g.55098736G>C	ENSP00000251377:p.Val459Leu	228	1	0.00438596		257	115	0.447471	NM_001130917	O75020	Missense_Mutation	SNP	ENST00000251377.3	37	CCDS46179.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	G	9.895	1.205412	0.22205	0.022696	2.33E-4	ENSG00000239998	ENST00000251377;ENST00000391738;ENST00000251376;ENST00000391737	T;T;T;T	0.00617	6.41;6.41;6.35;6.19	2.74	-5.49	0.02584	.	30.411000	0.00832	N	0.001664	T	0.00241	0.0007	L	0.43923	1.385	0.09310	N	0.999998	B;B;B	0.24258	0.098;0.1;0.024	B;B;B	0.25614	0.051;0.062;0.028	T	0.42965	-0.9420	10	0.49607	T	0.09	.	7.5721	0.27913	0.1909:0.1704:0.6387:0.0	.	430;459;442	A8MZH0;Q8N149;Q8N149-2	.;LIRA2_HUMAN;.	L	459;459;442;430	ENSP00000251377:V459L;ENSP00000375618:V459L;ENSP00000251376:V442L;ENSP00000375617:V430L	ENSP00000251376:V442L	V	+	1	0	LILRA2	59790548	0.005000	0.15991	0.002000	0.10522	0.162000	0.22319	-0.202000	0.09451	-1.128000	0.02922	-0.320000	0.08662	GTC	G|0.991;C|0.009	0.009	strong		0.567	LILRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140813.2			C	55098736	G	C	55098736	3	2	22	1	0	0	0	0	1	0	0	0	8794	1261	44	4	1405	4	LILRA2	19	55098736	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	79357	55098736	4030247	4080	6981	88	2									
LILRA2	11027	hgsc.bcm.edu	37	chr19	55098742	55098742	+	Missense_Mutation	SNP	G	G	T																															gtgtggctggcttggtcctgGtggtcctcgggattctgcta																								rs73939008	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55098742G>T	ENST00000251377.3	+	9	1514	c.1381G>T	c.(1381-1383)Gtg>Ttg	p.V461L	LILRA2_ENST00000391737.1_Missense_Mutation_p.V432L|LILRA2_ENST00000251376.3_Missense_Mutation_p.V444L|CTB-83J4.2_ENST00000596330.1_lincRNA|LILRA2_ENST00000391738.3_Missense_Mutation_p.V461L|LILRB1_ENST00000448689.1_Intron|LILRB1_ENST00000418536.2_Intron|LILRB1_ENST00000396321.2_Intron			Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2	461					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)		CTTGGTCCTGGTGGTCCTCGG	0.562													g|||	51	0.0101837	0.0378	0.0014	5008	,	,		17380	0.0		0.0	False		,,,				2504	0.0				p.V461L		Atlas-SNP	.											LILRA2,right_upper_lobe,carcinoma,0,1	LILRA2	99	1	0			c.G1381T						PASS	.	G	LEU/VAL,LEU/VAL	100,4306	78.3+/-116.7	0,100,2103	111	96	101		1381,1330	-4.3	0	19	dbSNP_130	101	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	LILRA2	NM_001130917.1,NM_006866.2	32,32	0,102,6401	TT,TG,GG		0.0233,2.2696,0.7843	,	461/484,444/467	55098742	102,12904	2203	4300	6503	SO:0001583	missense	11027	exon8			GTCCTGGTGGTCC	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.1381G>T	19.37:g.55098742G>T	ENSP00000251377:p.Val461Leu	227	0	0		253	109	0.43083	NM_001130917	O75020	Missense_Mutation	SNP	ENST00000251377.3	37	CCDS46179.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	G	10.21	1.287724	0.23478	0.022696	2.33E-4	ENSG00000239998	ENST00000251377;ENST00000391738;ENST00000251376;ENST00000391737	T;T;T;T	0.00529	6.98;6.98;6.86;6.78	2.74	-4.29	0.03721	.	22.652400	0.00166	N	0.000016	T	0.00109	0.0003	N	0.25094	0.71	0.09310	N	0.999998	B;B;P	0.45126	0.341;0.09;0.851	B;B;P	0.47402	0.066;0.026;0.546	T	0.55755	-0.8091	10	0.02654	T	1	.	5.1841	0.15174	0.0:0.3589:0.2798:0.3612	.	432;461;444	A8MZH0;Q8N149;Q8N149-2	.;LIRA2_HUMAN;.	L	461;461;444;432	ENSP00000251377:V461L;ENSP00000375618:V461L;ENSP00000251376:V444L;ENSP00000375617:V432L	ENSP00000251376:V444L	V	+	1	0	LILRA2	59790554	0.003000	0.15002	0.035000	0.18076	0.160000	0.22226	-1.113000	0.03296	-0.357000	0.08175	0.609000	0.83330	GTG	G|0.991;T|0.009	0.009	strong		0.562	LILRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140813.2			T	55098742	G	T	55098742	3	4	22	1	0	0	0	0	1	0	0	0	8794	1261	44	4	1411	4	LILRA2	19	55098742	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6	55098742	4030241	4081	6982	88	2									
LILRA1	11024	hgsc.bcm.edu	37	chr19	55107869	55107869	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcctgtgacctcagcccacTcggggacctacaggtgctac	7	8	11	15	1	1	1	1	1	0	0	3	2	2	2	4	3	4	1	4	3	2	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55107869T>G	ENST00000251372.3	+	7	1356	c.1174T>G	c.(1174-1176)Tcg>Gcg	p.S392A	LILRA1_ENST00000453777.1_Intron|LILRA1_ENST00000473156.1_3'UTR|LILRB1_ENST00000448689.1_Intron|LILRB1_ENST00000418536.2_Intron|LILRB1_ENST00000396321.2_Intron	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	392	Ig-like C2-type 4.				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)	p.S392T(1)		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)		CTCAGCCCACTCGGGGACCTA	0.587																																					p.S392A		Atlas-SNP	.											LILRA1,NS,carcinoma,0,2	LILRA1	105	2	1	Substitution - Missense(1)	lung(1)	c.T1174G						scavenged	.						144	135	138					19																	55107869		2203	4300	6503	SO:0001583	missense	11024	exon7			GCCCACTCGGGGA	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.1174T>G	19.37:g.55107869T>G	ENSP00000251372:p.Ser392Ala	200	0	0		254	14	0.0551181	NM_006863	O75018|Q3MJA6	Missense_Mutation	SNP	ENST00000251372.3	37	CCDS12901.1	.	.	.	.	.	.	.	.	.	.	G	0.006	-2.088474	0.00367	.	.	ENSG00000104974	ENST00000251372	T	0.03553	3.89	1.8	-3.59	0.04583	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.846833	0.09755	N	0.760012	T	0.00608	0.0020	N	0.00123	-2.06	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.33292	-0.9874	10	0.02654	T	1	.	0.6627	0.00845	0.4001:0.1718:0.2547:0.1734	.	392	O75019	LIRA1_HUMAN	A	392	ENSP00000251372:S392A	ENSP00000251372:S392A	S	+	1	0	LILRA1	59799681	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.554000	0.02172	-1.875000	0.01132	-0.982000	0.02568	TCG	.	.	none		0.587	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863		G	55107869	T	G	55107869	3	3	22	1	0	0	0	0	1	0	0	0	8793	1551	54	5	1196	5	LILRA1	19	55107869	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	9127	55107869	4021114	4082	6983											
NLRP7	199713	hgsc.bcm.edu	37	chr19	55441971	55441971	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccaggtttgtgaggctgcaGgcttcttggagcgcctctga	5	12	14	10	1	2	2	0	2	2	0	3	3	3	3	2	4	2	4	2	4	0	3	rs61746780	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55441971G>A	ENST00000590030.1	-	8	2746	c.2706C>T	c.(2704-2706)gcC>gcT	p.A902A	NLRP7_ENST00000340844.2_Silent_p.A902A|NLRP7_ENST00000328092.5_Silent_p.A874A|NLRP7_ENST00000448121.2_Silent_p.A874A|NLRP7_ENST00000588756.1_Silent_p.A902A|NLRP7_ENST00000446217.1_Silent_p.A930A|NLRP7_ENST00000592784.1_Silent_p.A902A			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	902							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)		TGAGGCTGCAGGCTTCTTGGA	0.463													.|||	128	0.0255591	0.09	0.0086	5008	,	,		17972	0.0		0.002	False		,,,				2504	0.001				p.A902A		Atlas-SNP	.											.	NLRP7	411	.	0			c.C2706T						PASS	.	G	,,	368,4038	187.4+/-214.1	15,338,1850	132	126	128		2706,2622,2706	-1.7	0	19	dbSNP_129	128	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	NLRP7	NM_001127255.1,NM_139176.3,NM_206828.3	,,	15,342,6146	AA,AG,GG		0.0465,8.3522,2.8602	,,	902/1038,874/1010,902/981	55441971	372,12634	2203	4300	6503	SO:0001819	synonymous_variant	199713	exon9			GCTGCAGGCTTCT	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.2706C>T	19.37:g.55441971G>A		105	0	0		111	63	0.567568	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Silent	SNP	ENST00000590030.1	37	CCDS33109.1																																																																																			G|0.976;A|0.024	0.024	strong		0.463	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		A	55441971	G	A	55441971	2	1	22	1	0	0	0	0	0	0	0	1	10491	987	35	2		2	NLRP7	19	55441971	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	334102	55441971	3687012	4083	6984											
NLRP7	199713	hgsc.bcm.edu	37	chr19	55451083	55451083	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcttcagagtcgtgcacacAatccagcacaccgcgggggc	10	5	12	14	3	1	1	1	0	0	1	3	1	2	1	2	2	3	3	2	2	1	1	rs1654636	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55451083A>G	ENST00000590030.1	-	3	1144	c.1104T>C	c.(1102-1104)atT>atC	p.I368I	NLRP7_ENST00000340844.2_Silent_p.I368I|NLRP7_ENST00000328092.5_Silent_p.I368I|NLRP7_ENST00000448121.2_Silent_p.I368I|NLRP7_ENST00000588756.1_Silent_p.I368I|NLRP7_ENST00000446217.1_Silent_p.I396I|NLRP7_ENST00000592784.1_Silent_p.I368I			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	368	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)		TCGTGCACACAATCCAGCACA	0.642													.|||	123	0.0245607	0.0666	0.0202	5008	,	,		16521	0.002		0.0189	False		,,,				2504	0.0				p.I368I		Atlas-SNP	.											NLRP7_ENST00000328092,NS,carcinoma,-2,2	NLRP7	411	2	0			c.T1104C						scavenged	.						37	40	39					19																	55451083		2201	4299	6500	SO:0001819	synonymous_variant	199713	exon4			GCACACAATCCAG	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.1104T>C	19.37:g.55451083A>G		199	0	0		94	18	0.191489	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Silent	SNP	ENST00000590030.1	37	CCDS33109.1																																																																																			A|0.949;G|0.051	0.051	strong		0.642	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		G	55451083	A	G	55451083	2	3	22	1	0	0	0	0	0	0	0	1	10491	126	5	3		3	NLRP7	19	55451083	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	9112	55451083	3677900	4084	6985											
PPP1R12C	54776	hgsc.bcm.edu	37	chr19	55606944	55606944	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcttcaggaggccaaagcGcctggagaagggggcctctt	8	8	15	10	1	3	1	1	0	2	1	3	3	3	2	3	5	1	0	3	5	2	2	rs35849605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55606944G>A	ENST00000263433.3	-	10	1270	c.1255C>T	c.(1255-1257)Cgc>Tgc	p.R419C	PPP1R12C_ENST00000435544.2_Missense_Mutation_p.R345C|PPP1R12C_ENST00000376393.2_Missense_Mutation_p.R419C	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)		AGGCCAAAGCGCCTGGAGAAG	0.627													G|||	126	0.0251597	0.0923	0.0058	5008	,	,		14816	0.0		0.0	False		,,,				2504	0.0				p.R419C		Atlas-SNP	.											.	PPP1R12C	46	.	0			c.C1255T						PASS	.	G	CYS/ARG	353,4039		9,335,1852	10	12	11		1255	2.9	1	19	dbSNP_126	11	3,8557		0,3,4277	yes	missense	PPP1R12C	NM_017607.2	180	9,338,6129	AA,AG,GG		0.035,8.0373,2.7486	probably-damaging	419/783	55606944	356,12596	2196	4280	6476	SO:0001583	missense	54776	exon10			CAAAGCGCCTGGA	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.1255C>T	19.37:g.55606944G>A	ENSP00000263433:p.Arg419Cys	56	0	0		76	39	0.513158	NM_017607		Missense_Mutation	SNP	ENST00000263433.3	37	CCDS12916.1	51	0.023351648351648352	49	0.09959349593495935	2	0.0055248618784530384	0	0.0	0	0.0	G	18.24	3.580072	0.65992	0.080373	3.5E-4	ENSG00000125503	ENST00000263433;ENST00000376393;ENST00000435544	T;T;T	0.70045	-0.3;-0.32;-0.45	3.95	2.91	0.33838	.	0.302492	0.23868	N	0.043762	T	0.05044	0.0135	M	0.72353	2.195	0.43703	D	0.99616	D;D;D	0.61697	0.99;0.987;0.978	P;P;P	0.50896	0.556;0.653;0.451	T	0.36672	-0.9738	10	0.87932	D	0	.	6.5557	0.22460	0.1281:0.0:0.8719:0.0	rs35849605	345;418;419	B4DME2;Q9BZL4-3;Q9BZL4	.;.;PP12C_HUMAN	C	419;419;345	ENSP00000263433:R419C;ENSP00000365573:R419C;ENSP00000387833:R345C	ENSP00000263433:R419C	R	-	1	0	PPP1R12C	60298756	0.719000	0.27986	0.986000	0.45419	0.973000	0.67179	0.866000	0.27954	2.147000	0.66899	0.549000	0.68633	CGC	G|0.958;A|0.042	0.042	strong		0.627	PPP1R12C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451814.2	NM_017607		A	55606944	G	A	55606944	3	1	22	1	0	0	0	0	1	0	0	0	12368	1087	38	1	1145	1	PPP1R12C	19	55606944	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	155861	55606944	3522039	4085	6986											
PPP1R12C	54776	hgsc.bcm.edu	37	chr19	55607447	55607447	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttcttccccctcatcctcGtcctggatggggggcccccc	2	10	9	20	1	2	0	1	0	1	0	6	1	5	1	8	4	0	0	8	4	0	2	rs35641913	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55607447G>A	ENST00000263433.3	-	8	1140	c.1125C>T	c.(1123-1125)gaC>gaT	p.D375D	PPP1R12C_ENST00000435544.2_Silent_p.D301D|PPP1R12C_ENST00000376393.2_Silent_p.D375D	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)		CCTCATCCTCGTCCTGGATGG	0.642													G|||	111	0.0221645	0.0825	0.0029	5008	,	,		14673	0.0		0.0	False		,,,				2504	0.0				p.D375D		Atlas-SNP	.											PPP1R12C,NS,carcinoma,0,1	PPP1R12C	46	1	0			c.C1125T						PASS	.	G		328,4078	163.6+/-195.4	9,310,1884	53	66	62		1125	-7.5	0.4	19	dbSNP_126	62	1,8595		0,1,4297	no	coding-synonymous	PPP1R12C	NM_017607.2		9,311,6181	AA,AG,GG		0.0116,7.4444,2.5304		375/783	55607447	329,12673	2203	4298	6501	SO:0001819	synonymous_variant	54776	exon8			ATCCTCGTCCTGG	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.1125C>T	19.37:g.55607447G>A		29	0	0		40	20	0.5	NM_017607		Silent	SNP	ENST00000263433.3	37	CCDS12916.1																																																																																			G|0.976;A|0.024	0.024	strong		0.642	PPP1R12C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451814.2	NM_017607		A	55607447	G	A	55607447	2	1	22	1	0	0	0	0	0	0	0	1	12368	1136	40	1		1	PPP1R12C	19	55607447	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	503	55607447	3521536	4086	6987											
PPP1R12C	54776	hgsc.bcm.edu	37	chr19	55623871	55623871	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccttcagcagcccctccaTggcgtccgactcggccaggt	5	7	11	18	4	1	0	1	0	0	0	4	1	3	0	6	3	2	1	6	3	0	1	rs116840455	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55623871T>G	ENST00000263433.3	-	3	550	c.535A>C	c.(535-537)Atg>Ctg	p.M179L	PPP1R12C_ENST00000435544.2_Missense_Mutation_p.M105L|PPP1R12C_ENST00000376393.2_Missense_Mutation_p.M179L	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)		AGCCCCTCCATGGCGTCCGAC	0.701													T|||	47	0.00938498	0.0356	0.0	5008	,	,		12736	0.0		0.0	False		,,,				2504	0.0				p.M179L		Atlas-SNP	.											.	PPP1R12C	46	.	0			c.A535C						PASS	.	T	LEU/MET	136,4270		0,136,2067	22	28	26		535	2	1	19	dbSNP_132	26	0,8596		0,0,4298	yes	missense	PPP1R12C	NM_017607.2	15	0,136,6365	GG,GT,TT		0.0,3.0867,1.046	possibly-damaging	179/783	55623871	136,12866	2203	4298	6501	SO:0001583	missense	54776	exon3			CCTCCATGGCGTC	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.535A>C	19.37:g.55623871T>G	ENSP00000263433:p.Met179Leu	122	0	0		93	38	0.408602	NM_017607		Missense_Mutation	SNP	ENST00000263433.3	37	CCDS12916.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	T	17.05	3.291102	0.59976	0.030867	0.0	ENSG00000125503	ENST00000263433;ENST00000376393;ENST00000435544	T;T;T	0.51574	0.7;0.7;0.7	5.24	2.02	0.26589	Ankyrin repeat-containing domain (3);	0.106312	0.64402	D	0.000009	T	0.12263	0.0298	L	0.31578	0.945	0.41995	D	0.990866	B;B;B	0.25441	0.126;0.122;0.075	B;B;B	0.23150	0.02;0.044;0.02	T	0.03875	-1.0996	10	0.44086	T	0.13	.	7.5728	0.27918	0.0:0.2535:0.0:0.7465	.	105;179;179	B4DME2;Q9BZL4-3;Q9BZL4	.;.;PP12C_HUMAN	L	179;179;105	ENSP00000263433:M179L;ENSP00000365573:M179L;ENSP00000387833:M105L	ENSP00000263433:M179L	M	-	1	0	PPP1R12C	60315683	1.000000	0.71417	0.994000	0.49952	0.926000	0.56050	2.280000	0.43443	0.421000	0.25980	0.459000	0.35465	ATG	T|0.990;G|0.010	0.010	strong		0.701	PPP1R12C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451814.2	NM_017607		G	55623871	T	G	55623871	3	3	22	1	0	0	0	0	1	0	0	0	12368	1464	51	5	1893	5	PPP1R12C	19	55623871	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	16424	55623871	3505112	4087	6988											
BRSK1	84446	hgsc.bcm.edu	37	chr19	55815072	55815072	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gtggattctcccatgctgagCcgtcacgggaagcggcgacc	7	7	14	13	4	2	1	1	1	1	0	3	4	2	3	3	3	3	1	3	3	1	1	rs17851414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55815072C>T	ENST00000309383.1	+	12	1441	c.1164C>T	c.(1162-1164)agC>agT	p.S388S	BRSK1_ENST00000326848.7_Silent_p.S83S|BRSK1_ENST00000590333.1_Silent_p.S404S	NM_032430.1	NP_115806.1	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1	388					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)		CCATGCTGAGCCGTCACGGGA	0.617													C|||	156	0.0311502	0.115	0.0058	5008	,	,		15985	0.0		0.0	False		,,,				2504	0.0				p.S388S		Atlas-SNP	.											.	BRSK1	192	.	0			c.C1164T						PASS	.	C		400,4006		19,362,1822	63	72	69		1164	4	1	19	dbSNP_123	69	3,8597		0,3,4297	no	coding-synonymous	BRSK1	NM_032430.1		19,365,6119	TT,TC,CC		0.0349,9.0785,3.0986		388/779	55815072	403,12603	2203	4300	6503	SO:0001819	synonymous_variant	84446	exon12			GCTGAGCCGTCAC	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.1164C>T	19.37:g.55815072C>T		158	0	0		122	60	0.491803	NM_032430	F1DG44|Q5J5B5|Q8NDD0|Q8NDR4|Q8TDC2|Q96AV4|Q96JL4	Silent	SNP	ENST00000309383.1	37	CCDS12921.1																																																																																			C|0.969;T|0.031	0.031	strong		0.617	BRSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452787.1	NM_032430		T	55815072	C	T	55815072	2	4	22	1	0	0	0	0	0	0	0	1	1525	738	26	2		2	BRSK1	19	55815072	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	191201	55815072	3313911	4088	6989											
BRSK1	84446	hgsc.bcm.edu	37	chr19	55823421	55823421	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	aagctcctggccaccaacggGacccctctgccctgacccca	8	5	8	20	1	1	1	0	1	1	0	2	2	2	2	8	2	3	1	8	2	2	0	rs113284733	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55823421G>C	ENST00000309383.1	+	19	2599	c.2322G>C	c.(2320-2322)ggG>ggC	p.G774G	CTD-2105E13.14_ENST00000596786.1_RNA|BRSK1_ENST00000326848.7_Silent_p.G469G|BRSK1_ENST00000590333.1_Silent_p.G790G	NM_032430.1	NP_115806.1	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1	774					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)		CCACCAACGGGACCCCTCTGC	0.706													G|||	16	0.00319489	0.0113	0.0014	5008	,	,		6575	0.0		0.0	False		,,,				2504	0.0				p.G774G		Atlas-SNP	.											.	BRSK1	192	.	0			c.G2322C						PASS	.	G		13,3847		0,13,1917	6	7	7		2322	2.6	1	19	dbSNP_132	7	0,7676		0,0,3838	no	coding-synonymous	BRSK1	NM_032430.1		0,13,5755	CC,CG,GG		0.0,0.3368,0.1127		774/779	55823421	13,11523	1930	3838	5768	SO:0001819	synonymous_variant	84446	exon19			CAACGGGACCCCT	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.2322G>C	19.37:g.55823421G>C		71	0	0		60	27	0.45	NM_032430	F1DG44|Q5J5B5|Q8NDD0|Q8NDR4|Q8TDC2|Q96AV4|Q96JL4	Silent	SNP	ENST00000309383.1	37	CCDS12921.1																																																																																			G|0.998;C|0.002	0.002	strong		0.706	BRSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452787.1	NM_032430		C	55823421	G	C	55823421	2	2	22	1	0	0	0	0	0	0	0	1	1525	1161	41	4		4	BRSK1	19	55823421	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	8349	55823421	3305562	4089	6990											
ZNF628	89887	hgsc.bcm.edu	37	chr19	55994975	55994975	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcatcgttctgcagaatgtGgggggtggggaggcagggcc	6	8	19	8	1	2	1	1	0	1	1	3	2	2	2	1	7	1	3	1	7	1	1	rs114065657	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55994975G>T	ENST00000598519.1	+	3	2968	c.2415G>T	c.(2413-2415)gtG>gtT	p.V805V	NAT14_ENST00000587400.1_5'Flank|ZNF628_ENST00000391718.2_Silent_p.V801V|NAT14_ENST00000205194.4_5'Flank|NAT14_ENST00000591590.1_5'Flank			Q5EBL2	ZN628_HUMAN	zinc finger protein 628	805	Gly-rich.				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)		TGCAGAATGTGGGGGGTGGGG	0.692													g|||	82	0.0163738	0.0598	0.0029	5008	,	,		13204	0.0		0.001	False		,,,				2504	0.0				p.V805V		Atlas-SNP	.											.	ZNF628	75	.	0			c.G2415T						PASS	.	G		212,4192		2,208,1992	32	41	38		2403	-1.7	0.8	19	dbSNP_132	38	2,8592		0,2,4295	no	coding-synonymous	ZNF628	NM_033113.2		2,210,6287	TT,TG,GG		0.0233,4.8138,1.6464		801/1056	55994975	214,12784	2202	4297	6499	SO:0001819	synonymous_variant	89887	exon3			GAATGTGGGGGGT	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.2415G>T	19.37:g.55994975G>T		72	0	0		93	50	0.537634	NM_033113	Q86X34	Silent	SNP	ENST00000598519.1	37	CCDS33116.3																																																																																			G|0.980;T|0.020	0.020	strong		0.692	ZNF628-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317934.2	XM_058964		T	55994975	G	T	55994975	2	4	22	1	0	0	0	0	0	0	0	1	18067	1335	47	4		4	ZNF628	19	55994975	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	171554	55994975	3134008	4090	6991											
NLRP11	204801	hgsc.bcm.edu	37	chr19	56303806	56303806	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactcttccaagggcgctgcAgcaattttcagtgagacagc	10	9	10	12	1	2	1	1	1	1	1	3	2	3	1	1	1	3	3	1	1	2	3	rs80143194	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56303806A>C	ENST00000589093.1	-	7	2467	c.2374T>G	c.(2374-2376)Tgc>Ggc	p.C792G	NLRP11_ENST00000592953.1_Missense_Mutation_p.C693G|NLRP11_ENST00000589824.2_Missense_Mutation_p.C738G|NLRP11_ENST00000443188.1_Missense_Mutation_p.C792G|NLRP11_ENST00000360133.3_Missense_Mutation_p.C738G			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	792							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)		AGGGCGCTGCAGCAATTTTCA	0.498													A|||	151	0.0301518	0.1097	0.0086	5008	,	,		19216	0.0		0.0	False		,,,				2504	0.0				p.C792G		Atlas-SNP	.											.	NLRP11	139	.	0			c.T2374G						PASS	.	A	GLY/CYS	357,4049	184.0+/-211.4	11,335,1857	110	102	105		2374	-0.1	0	19	dbSNP_131	105	7,8593	4.3+/-15.6	0,7,4293	yes	missense	NLRP11	NM_145007.3	159	11,342,6150	CC,CA,AA		0.0814,8.1026,2.7987	probably-damaging	792/1034	56303806	364,12642	2203	4300	6503	SO:0001583	missense	204801	exon9			CGCTGCAGCAATT	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.2374T>G	19.37:g.56303806A>C	ENSP00000466285:p.Cys792Gly	122	0	0		124	62	0.5	NM_145007	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Missense_Mutation	SNP	ENST00000589093.1	37	CCDS12935.1	41	0.018772893772893772	40	0.08130081300813008	1	0.0027624309392265192	0	0.0	0	0.0	A	10.23	1.292437	0.23564	0.081026	8.14E-4	ENSG00000179873	ENST00000443188;ENST00000360133	T;T	0.53423	0.62;0.62	2.18	-0.114	0.13564	.	.	.	.	.	T	0.10637	0.0260	M	0.93062	3.375	0.09310	N	1	D;D	0.76494	0.999;0.999	D;D	0.71656	0.942;0.974	T	0.24368	-1.0162	9	0.87932	D	0	.	2.8277	0.05490	0.5109:0.3169:0.1722:0.0	.	792;738	P59045;P59045-2	NAL11_HUMAN;.	G	792;738	ENSP00000409898:C792G;ENSP00000353251:C738G	ENSP00000353251:C738G	C	-	1	0	NLRP11	60995618	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.262000	0.18460	-0.089000	0.12484	-0.340000	0.08031	TGC	A|0.976;C|0.024	0.024	strong		0.498	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007		C	56303806	A	C	56303806	3	2	22	1	0	0	0	0	1	0	0	0	10482	188	7	5	743	5	NLRP11	19	56303806	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	308831	56303806	2825177	4091	6992											
NLRP4	147945	hgsc.bcm.edu	37	chr19	56369095	56369095	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaattcagccgcttatggtcCagcaagtctgtcactgagat	11	11	9	10	1	3	1	2	1	1	1	4	2	4	1	2	1	2	2	2	1	3	2	rs147356242	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56369095C>T	ENST00000301295.6	+	3	758	c.336C>T	c.(334-336)tcC>tcT	p.S112S	NLRP4_ENST00000587891.1_Silent_p.S37S|NLRP4_ENST00000346986.5_Silent_p.S112S	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	112					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)		GCTTATGGTCCAGCAAGTCTG	0.473													C|||	26	0.00519169	0.0189	0.0014	5008	,	,		19927	0.0		0.0	False		,,,				2504	0.0				p.S112S		Atlas-SNP	.											.	NLRP4	331	.	0			c.C336T						PASS	.	C		58,4348	57.4+/-93.9	0,58,2145	114	106	109		336	2.4	0	19	dbSNP_134	109	0,8600		0,0,4300	no	coding-synonymous	NLRP4	NM_134444.4		0,58,6445	TT,TC,CC		0.0,1.3164,0.4459		112/995	56369095	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	147945	exon3			ATGGTCCAGCAAG	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.336C>T	19.37:g.56369095C>T		41	0	0		55	29	0.527273	NM_134444	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																			C|0.994;T|0.006	0.006	strong		0.473	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444		T	56369095	C	T	56369095	2	4	22	1	0	0	0	0	0	0	0	1	10488	581	21	2		2	NLRP4	19	56369095	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	65289	56369095	2759888	4092	6993											
NLRP4	147945	hgsc.bcm.edu	37	chr19	56369668	56369668	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	taccagccccggggattcaaCgagagtgataggttagtgta	11	9	13	8	2	1	2	1	1	0	1	1	4	1	3	3	3	3	2	3	3	5	5	rs112565033	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56369668C>T	ENST00000301295.6	+	3	1331	c.909C>T	c.(907-909)aaC>aaT	p.N303N	NLRP4_ENST00000587891.1_Silent_p.N228N|NLRP4_ENST00000346986.5_Silent_p.N303N	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	303	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)		GGGGATTCAACGAGAGTGATA	0.507													C|||	26	0.00519169	0.0189	0.0014	5008	,	,		18203	0.0		0.0	False		,,,				2504	0.0				p.N303N		Atlas-SNP	.											.	NLRP4	331	.	0			c.C909T						PASS	.	C		56,4350	56.2+/-92.4	0,56,2147	73	78	76		909	-8.2	0	19	dbSNP_132	76	0,8600		0,0,4300	yes	coding-synonymous	NLRP4	NM_134444.4		0,56,6447	TT,TC,CC		0.0,1.271,0.4306		303/995	56369668	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	147945	exon3			ATTCAACGAGAGT	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.909C>T	19.37:g.56369668C>T		174	0	0		143	78	0.545455	NM_134444	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																			C|0.994;T|0.006	0.006	strong		0.507	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444		T	56369668	C	T	56369668	2	4	22	1	0	0	0	0	0	0	0	1	10488	535	19	1		1	NLRP4	19	56369668	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	573	56369668	2759315	4093	6994											
ZNF444	55311	hgsc.bcm.edu	37	chr19	56669889	56669889	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcctcccccgatgggtcGtcagcaacgagggtgcctca	7	6	13	15	3	2	0	2	0	0	0	4	2	3	0	4	2	4	2	4	2	1	0	rs61736530	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56669889G>A	ENST00000337080.3	+	4	691	c.324G>A	c.(322-324)tcG>tcA	p.S108S	ZNF444_ENST00000592171.1_3'UTR|ZNF444_ENST00000592949.1_Silent_p.S108S	NM_001253792.1|NM_018337.3	NP_001240721.1|NP_060807.2	Q8N0Y2	ZN444_HUMAN	zinc finger protein 444	108					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(1)|lung(5)	7		Colorectal(82;3.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0531)		CCGATGGGTCGTCAGCAACGA	0.597													g|||	64	0.0127796	0.0461	0.0014	5008	,	,		17153	0.001		0.001	False		,,,				2504	0.0				p.S108S		Atlas-SNP	.											.	ZNF444	15	.	0			c.G324A						PASS	.	A		220,4186	131.8+/-168.3	3,214,1986	74	64	68		324	-5.4	0	19	dbSNP_129	68	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	ZNF444	NM_018337.2		3,216,6284	AA,AG,GG		0.0233,4.9932,1.7069		108/328	56669889	222,12784	2203	4300	6503	SO:0001819	synonymous_variant	55311	exon4			TGGGTCGTCAGCA	AB052954	CCDS12939.1, CCDS59426.1	19q13.43	2013-01-09			ENSG00000167685	ENSG00000167685		"-", "Zinc fingers, C2H2-type"	16052	protein-coding gene	gene with protein product		607874				11978792, 19760602	Standard	NM_001253792		Approved	ZSCAN17, FLJ11137, EZF2	uc002qmm.3	Q8N0Y2		ENST00000337080.3:c.324G>A	19.37:g.56669889G>A		214	0	0		214	214	1	NM_001253792	Q8TEQ9|Q8WU35|Q9NUU1	Silent	SNP	ENST00000337080.3	37	CCDS12939.1																																																																																			G|0.981;A|0.019	0.019	strong		0.597	ZNF444-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457503.1	NM_018337		A	56669889	G	A	56669889	2	1	22	1	0	0	0	0	0	0	0	1	17932	1132	40	1		1	ZNF444	19	56669889	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	300221	56669889	2459094	4094	6995											
ZNF444	55311	hgsc.bcm.edu	37	chr19	56671359	56671359	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gtgctgcgagtgtggcaagaCcttctactggcgcgagcacc	7	8	14	12	3	1	1	0	0	1	1	1	3	1	1	2	2	4	3	2	2	2	2	rs145075834	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56671359C>G	ENST00000337080.3	+	5	1140	c.773C>G	c.(772-774)aCc>aGc	p.T258S	ZNF444_ENST00000592949.1_Missense_Mutation_p.T257S	NM_001253792.1|NM_018337.3	NP_001240721.1|NP_060807.2	Q8N0Y2	ZN444_HUMAN	zinc finger protein 444	258					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(1)|lung(5)	7		Colorectal(82;3.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0531)		TGTGGCAAGACCTTCTACTGG	0.746													C|||	62	0.0123802	0.0461	0.0014	5008	,	,		9131	0.0		0.0	False		,,,				2504	0.0				p.T258S		Atlas-SNP	.											.	ZNF444	15	.	0			c.C773G						PASS	.	C	SER/THR	95,3577		0,95,1741	3	2	3		773	3.4	1	19	dbSNP_134	3	0,7290		0,0,3645	yes	missense	ZNF444	NM_018337.2	58	0,95,5386	GG,GC,CC		0.0,2.5871,0.8666	probably-damaging	258/328	56671359	95,10867	1836	3645	5481	SO:0001583	missense	55311	exon5			GCAAGACCTTCTA	AB052954	CCDS12939.1, CCDS59426.1	19q13.43	2013-01-09			ENSG00000167685	ENSG00000167685		"-", "Zinc fingers, C2H2-type"	16052	protein-coding gene	gene with protein product		607874				11978792, 19760602	Standard	NM_001253792		Approved	ZSCAN17, FLJ11137, EZF2	uc002qmm.3	Q8N0Y2		ENST00000337080.3:c.773C>G	19.37:g.56671359C>G	ENSP00000338860:p.Thr258Ser	21	0	0		6	6	1	NM_018337	Q8TEQ9|Q8WU35|Q9NUU1	Missense_Mutation	SNP	ENST00000337080.3	37	CCDS12939.1	29	0.013278388278388278	28	0.056910569105691054	1	0.0027624309392265192	0	0.0	0	0.0	C	13.37	2.215791	0.39102	0.025871	0.0	ENSG00000167685	ENST00000337080	T	0.27402	1.67	3.43	3.43	0.39272	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.203463	0.24681	N	0.036467	T	0.01454	0.0047	N	0.01473	-0.845	0.24823	N	0.992574	B;P	0.48089	0.106;0.905	B;P	0.47118	0.047;0.538	T	0.07986	-1.0744	10	0.21540	T	0.41	.	12.7548	0.57328	0.0:1.0:0.0:0.0	.	257;258	Q8N0Y2-2;Q8N0Y2	.;ZN444_HUMAN	S	258	ENSP00000338860:T258S	ENSP00000338860:T258S	T	+	2	0	ZNF444	61363171	0.072000	0.21174	1.000000	0.80357	0.965000	0.64279	0.403000	0.20982	1.938000	0.56188	0.455000	0.32223	ACC	C|0.987;G|0.013	0.013	strong		0.746	ZNF444-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457503.1	NM_018337		G	56671359	C	G	56671359	3	3	22	1	0	0	0	0	1	0	0	0	17932	507	18	4	783	4	ZNF444	19	56671359	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1470	56671359	2457624	4095	6996											
ZNF582	147948	hgsc.bcm.edu	37	chr19	56901457	56901457	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gatcacatcaggtttggaaaCggcaagacctggagatgaga	14	7	13	7	1	2	3	2	1	0	3	2	7	2	4	1	4	1	2	1	4	2	1	rs61743722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56901457C>T	ENST00000301310.4	-	4	303	c.145G>A	c.(145-147)Gtt>Att	p.V49I	ZNF582_ENST00000586929.1_Missense_Mutation_p.V49I|AC006116.12_ENST00000589671.1_RNA	NM_144690.1	NP_653291.1	Q96NG8	ZN582_HUMAN	zinc finger protein 582	49	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)|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)		GGTTTGGAAACGGCAAGACCT	0.542													C|||	133	0.0265575	0.093	0.0144	5008	,	,		17157	0.0		0.0	False		,,,				2504	0.0				p.V49I	Ovarian(183;1887 2032 4349 30507 51343)	Atlas-SNP	.											.	ZNF582	56	.	0			c.G145A						PASS	.	C	ILE/VAL	389,4017	196.7+/-221.0	18,353,1832	91	86	88		145	-9.4	0	19	dbSNP_129	88	2,8598		0,2,4298	yes	missense	ZNF582	NM_144690.1	29	18,355,6130	TT,TC,CC		0.0233,8.8289,3.0063	benign	49/518	56901457	391,12615	2203	4300	6503	SO:0001583	missense	147948	exon4			TGGAAACGGCAAG	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.145G>A	19.37:g.56901457C>T	ENSP00000301310:p.Val49Ile	83	0	0		93	44	0.473118	NM_144690	B4DQZ9|B7Z9R3|Q6PJT6	Missense_Mutation	SNP	ENST00000301310.4	37	CCDS33121.1	52	0.023809523809523808	46	0.09349593495934959	6	0.016574585635359115	0	0.0	0	0.0	C	6.754	0.507989	0.12883	0.088289	2.33E-4	ENSG00000018869	ENST00000301310	T	0.00808	5.67	4.82	-9.39	0.00619	Krueppel-associated box (3);	.	.	.	.	T	0.00039	0.0001	N	0.05012	-0.13	0.28889	N	0.893944	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47459	-0.9116	9	0.06757	T	0.87	.	15.7899	0.78345	0.1051:0.7097:0.0:0.1853	.	49;80	Q96NG8;B4DQZ9	ZN582_HUMAN;.	I	49	ENSP00000301310:V49I	ENSP00000301310:V49I	V	-	1	0	ZNF582	61593269	0.000000	0.05858	0.000000	0.03702	0.945000	0.59286	-3.092000	0.00608	-2.299000	0.00659	-0.238000	0.12139	GTT	C|0.972;T|0.028	0.028	strong		0.542	ZNF582-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458387.2	NM_144690		T	56901457	C	T	56901457	3	4	22	1	0	0	0	0	1	0	0	0	18029	536	19	1	1416	1	ZNF582	19	56901457	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	230098	56901457	2227526	4096	6997											
ZNF667	63934	hgsc.bcm.edu	37	chr19	56952615	56952615	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcccacatttactacattcAtagggtttctctgaagaatg	11	15	6	9	0	2	2	1	1	1	1	4	2	3	2	1	1	2	1	1	1	5	7	rs61740673	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56952615A>G	ENST00000504904.3	-	7	2468	c.1749T>C	c.(1747-1749)taT>taC	p.Y583Y	ZNF667_ENST00000292069.6_Silent_p.Y583Y|ZNF667_ENST00000591790.1_3'UTR|ZNF667_ENST00000342634.3_Silent_p.Y711Y			Q5HYK9	ZN667_HUMAN	zinc finger protein 667	583					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)		TACTACATTCATAGGGTTTCT	0.398													A|||	158	0.0315495	0.0961	0.0159	5008	,	,		20645	0.0		0.0159	False		,,,				2504	0.0041				p.Y583Y		Atlas-SNP	.											ZNF667,NS,NS,-2,1	ZNF667	95	1	0			c.T1749C						PASS	.	A		393,4013	197.7+/-221.8	16,361,1826	120	115	117		1749	-0.7	0.4	19	dbSNP_129	117	96,8504	53.1+/-113.8	0,96,4204	no	coding-synonymous	ZNF667	NM_022103.3		16,457,6030	GG,GA,AA		1.1163,8.9197,3.7598		583/611	56952615	489,12517	2203	4300	6503	SO:0001819	synonymous_variant	63934	exon5			ACATTCATAGGGT		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.1749T>C	19.37:g.56952615A>G		98	0	0		94	40	0.425532	NM_022103	B2RMS6|B9EK36|Q6B093|Q9H807	Silent	SNP	ENST00000504904.3	37	CCDS12944.1																																																																																			A|0.965;G|0.035	0.035	strong		0.398	ZNF667-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458394.1	NM_022103		G	56952615	A	G	56952615	2	3	22	1	0	0	0	0	0	0	0	1	18089	224	8	3		3	ZNF667	19	56952615	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	51158	56952615	2176368	4097	6998											
ZFP28	140612	hgsc.bcm.edu	37	chr19	57050521	57050521	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cttggccctccctgcccgggGaaggccgcgctcaaggaatg	6	6	14	15	3	1	0	1	0	0	0	2	2	2	2	4	5	1	1	4	5	3	1	rs199655023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57050521G>A	ENST00000301318.3	+	1	205	c.134G>A	c.(133-135)gGa>gAa	p.G45E	AC005498.3_ENST00000593218.1_lincRNA|ZFP28_ENST00000594386.1_3'UTR|ZFP28_ENST00000591844.1_Missense_Mutation_p.G45E	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	45					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)		CCTGCCCGGGGAAGGCCGCGC	0.726													G|||	19	0.00379393	0.0144	0.0	5008	,	,		8689	0.0		0.0	False		,,,				2504	0.0				p.G45E	Ovarian(124;554 1662 19430 21141 52494)	Atlas-SNP	.											.	ZFP28	99	.	0			c.G134A						PASS	.	G	GLU/GLY	32,4078		0,32,2023	6	8	7		134	2.7	1	19		7	2,8204		0,2,4101	yes	missense	ZFP28	NM_020828.1	98	0,34,6124	AA,AG,GG		0.0244,0.7786,0.2761	probably-damaging	45/869	57050521	34,12282	2055	4103	6158	SO:0001583	missense	140612	exon1			CCCGGGGAAGGCC		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.134G>A	19.37:g.57050521G>A	ENSP00000301318:p.Gly45Glu	37	0	0		57	26	0.45614	NM_020828	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Missense_Mutation	SNP	ENST00000301318.3	37	CCDS12946.1	.	.	.	.	.	.	.	.	.	.	G	14.82	2.650497	0.47362	0.007786	2.44E-4	ENSG00000196867	ENST00000301318	T	0.05717	3.4	2.74	2.74	0.32292	.	0.000000	0.31301	U	0.007892	T	0.06280	0.0162	N	0.24115	0.695	0.34331	D	0.687738	D;D	0.89917	0.999;1.0	D;D	0.87578	0.998;0.998	T	0.11227	-1.0596	10	0.06757	T	0.87	.	9.1377	0.36883	0.0:0.0:1.0:0.0	.	45;45	Q8NHY6;A8K0L8	ZFP28_HUMAN;.	E	45	ENSP00000301318:G45E	ENSP00000301318:G45E	G	+	2	0	ZFP28	61742333	0.909000	0.30893	0.986000	0.45419	0.823000	0.46562	0.683000	0.25349	1.817000	0.53016	0.462000	0.41574	GGA	.	.	weak		0.726	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828		A	57050521	G	A	57050521	3	1	22	1	0	0	0	0	1	0	0	0	17657	1174	41	2	136	2	ZFP28	19	57050521	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	97906	57050521	2078462	4098	6999											
ZNF71	58491	hgsc.bcm.edu	37	chr19	57132879	57132879	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggggctcagtacccgcatGtcatgaactgaaggcatttg	10	9	13	9	1	2	2	2	2	0	0	2	2	2	2	1	3	2	4	1	3	3	2	rs79950845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57132879G>A	ENST00000328070.6	+	3	458	c.224G>A	c.(223-225)tGt>tAt	p.C75Y		NM_021216.4	NP_067039.1	Q9NQZ8	ZNF71_HUMAN	zinc finger protein 71	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)|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)		GTACCCGCATGTCATGAACTG	0.622													G|||	99	0.0197684	0.0741	0.0014	5008	,	,		17597	0.0		0.0	False		,,,				2504	0.0				p.C75Y		Atlas-SNP	.											.	ZNF71	69	.	0			c.G224A						PASS	.	G	TYR/CYS	263,4143	149.5+/-183.7	5,253,1945	57	54	55		224	2.9	0	19	dbSNP_131	55	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ZNF71	NM_021216.4	194	5,254,6244	AA,AG,GG		0.0116,5.9691,2.0298	possibly-damaging	75/490	57132879	264,12742	2203	4300	6503	SO:0001583	missense	58491	exon3			CCGCATGTCATGA	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.224G>A	19.37:g.57132879G>A	ENSP00000328245:p.Cys75Tyr	72	0	0		77	43	0.558442	NM_021216	Q15919|Q9UC09|Q9UQD3	Missense_Mutation	SNP	ENST00000328070.6	37	CCDS12947.1	39	0.017857142857142856	38	0.07723577235772358	1	0.0027624309392265192	0	0.0	0	0.0	G	13.10	2.134948	0.37728	0.059691	1.16E-4	ENSG00000197951	ENST00000328070	T	0.07114	3.22	2.91	2.91	0.33838	.	.	.	.	.	T	0.00815	0.0027	M	0.91249	3.19	0.09310	N	1	B	0.26318	0.146	B	0.22753	0.041	T	0.04203	-1.0969	9	0.62326	D	0.03	.	9.5203	0.39131	0.0:0.0:1.0:0.0	.	75	Q9NQZ8	ZNF71_HUMAN	Y	75	ENSP00000328245:C75Y	ENSP00000328245:C75Y	C	+	2	0	ZNF71	61824691	0.006000	0.16342	0.002000	0.10522	0.001000	0.01503	0.648000	0.24828	1.942000	0.56320	0.561000	0.74099	TGT	G|0.976;A|0.024	0.024	strong		0.622	ZNF71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459798.2	NM_021216		A	57132879	G	A	57132879	3	1	22	1	0	0	0	0	1	0	0	0	18129	1377	48	2	226	2	ZNF71	19	57132879	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	82358	57132879	1996104	4099	7000											
USP29	57663	hgsc.bcm.edu	37	chr19	57641887	57641887	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agactgtggagatgcaagccAagagcagcatcagagagacc	15	4	13	9	0	1	5	1	0	0	5	1	7	1	5	2	1	4	3	2	1	2	0	rs74511605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57641887A>G	ENST00000254181.4	+	4	2298	c.1844A>G	c.(1843-1845)cAa>cGa	p.Q615R	USP29_ENST00000598197.1_Missense_Mutation_p.Q615R	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	615	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)		GATGCAAGCCAAGAGCAGCAT	0.493													A|||	12	0.00239617	0.0091	0.0	5008	,	,		20449	0.0		0.0	False		,,,				2504	0.0				p.Q615R		Atlas-SNP	.											.	USP29	186	.	0			c.A1844G						PASS	.	A	ARG/GLN	50,4356	51.6+/-87.1	0,50,2153	73	72	72		1844	1.4	0	19	dbSNP_131	72	0,8600		0,0,4300	yes	missense	USP29	NM_020903.2	43	0,50,6453	GG,GA,AA		0.0,1.1348,0.3844	benign	615/923	57641887	50,12956	2203	4300	6503	SO:0001583	missense	57663	exon4			CAAGCCAAGAGCA		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.1844A>G	19.37:g.57641887A>G	ENSP00000254181:p.Gln615Arg	132	0	0		120	74	0.616667	NM_020903		Missense_Mutation	SNP	ENST00000254181.4	37	CCDS33124.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	A	0.013	-1.643501	0.00792	0.011348	0.0	ENSG00000131864	ENST00000254181	T	0.74002	-0.8	2.43	1.4	0.22301	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	.	.	.	.	T	0.37571	0.1008	N	0.11313	0.125	0.09310	N	1	B	0.14805	0.011	B	0.14578	0.011	T	0.32402	-0.9908	9	0.02654	T	1	0.0203	4.2465	0.10674	0.8306:0.0:0.1694:0.0	.	615	Q9HBJ7	UBP29_HUMAN	R	615	ENSP00000254181:Q615R	ENSP00000254181:Q615R	Q	+	2	0	USP29	62333699	0.021000	0.18746	0.003000	0.11579	0.085000	0.17905	2.747000	0.47475	0.347000	0.23924	0.383000	0.25322	CAA	A|0.995;G|0.005	0.005	strong		0.493	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1			G	57641887	A	G	57641887	3	3	22	1	0	0	0	0	1	0	0	0	17074	130	5	3	1846	3	USP29	19	57641887	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	509008	57641887	1487096	4100	7001											
ZNF264	9422	hgsc.bcm.edu	37	chr19	57723182	57723182	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcacagaatgtgggaaaacCtttattaagagcacacatct	15	10	8	8	0	1	2	0	0	1	2	1	3	1	3	1	1	3	2	1	1	5	3	rs61730346	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57723182C>T	ENST00000263095.6	+	4	1131	c.717C>T	c.(715-717)acC>acT	p.T239T	ZNF264_ENST00000536056.1_Silent_p.T239T	NM_003417.4	NP_003408.1	O43296	ZN264_HUMAN	zinc finger protein 264	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)			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)		GTGGGAAAACCTTTATTAAGA	0.448													.|||	48	0.00958466	0.0356	0.0	5008	,	,		21386	0.0		0.001	False		,,,				2504	0.0				p.T239T		Atlas-SNP	.											.	ZNF264	65	.	0			c.C717T						PASS	.	C		120,4286	89.2+/-127.9	2,116,2085	97	96	96		717	-2.4	0	19	dbSNP_129	96	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ZNF264	NM_003417.4		2,118,6383	TT,TC,CC		0.0233,2.7236,0.938		239/628	57723182	122,12884	2203	4300	6503	SO:0001819	synonymous_variant	9422	exon4			GAAAACCTTTATT	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.717C>T	19.37:g.57723182C>T		65	0	0		81	47	0.580247	NM_003417	A8K8Y9|Q9P1V0	Silent	SNP	ENST00000263095.6	37	CCDS33127.1																																																																																			C|0.990;T|0.010	0.010	strong		0.448	ZNF264-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465080.1			T	57723182	C	T	57723182	2	4	22	1	0	0	0	0	0	0	0	1	17819	668	24	2		2	ZNF264	19	57723182	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	81295	57723182	1405801	4101	7002											
AURKC	6795	hgsc.bcm.edu	37	chr19	57743518	57743518	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	attgtggccctgaaggttctCttcaagtcgcagatagagaa	11	11	11	8	1	2	3	1	1	1	2	4	4	2	3	1	2	0	2	1	2	4	4	rs142351971	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57743518C>T	ENST00000302804.7	+	3	408	c.222C>T	c.(220-222)ctC>ctT	p.L74L	AURKC_ENST00000599062.1_Silent_p.L71L|AURKC_ENST00000598785.1_Silent_p.L40L|AURKC_ENST00000415300.2_Silent_p.L55L|AURKC_ENST00000448930.1_Silent_p.L40L	NM_001015878.1	NP_001015878.1	Q9UQB9	AURKC_HUMAN	aurora kinase C	74	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				attachment of spindle microtubules to kinetochore (GO:0008608)|cytokinesis (GO:0000910)|histone modification (GO:0016570)|meiotic nuclear division (GO:0007126)|positive regulation of cytokinesis (GO:0032467)|protein phosphorylation (GO:0006468)|spindle midzone assembly involved in mitosis (GO:0051256)	chromosome passenger complex (GO:0032133)|chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			breast(1)|endometrium(1)|large_intestine(9)|lung(9)|ovary(3)|prostate(1)|stomach(1)	25		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;0.0122)		TGAAGGTTCTCTTCAAGTCGC	0.517													c|||	7	0.00139776	0.0053	0.0	5008	,	,		18570	0.0		0.0	False		,,,				2504	0.0				p.L74L		Atlas-SNP	.											AURKC_ENST00000302804,colon,carcinoma,+2,2	AURKC	97	2	0			c.C222T						PASS	.	C	,,	20,4386	28.1+/-56.4	1,18,2184	61	52	55		222,165,120	-4.8	1	19	dbSNP_134	55	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	AURKC	NM_001015878.1,NM_001015879.1,NM_003160.2	,,	1,18,6484	TT,TC,CC		0.0,0.4539,0.1538	,,	74/310,55/291,40/276	57743518	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	6795	exon3			GGTTCTCTTCAAG		CCDS33128.1, CCDS46205.1, CCDS46206.1	19q13.43	2013-09-19	2003-07-21	2003-07-23	ENSG00000105146	ENSG00000105146			11391	protein-coding gene	gene with protein product		603495	"serine/threonine kinase 13 (aurora/IPL1-like)"	STK13		9799611	Standard	XR_430209		Approved	AurC, ARK3	uc002qoe.3	Q9UQB9	OTTHUMG00000183106	ENST00000302804.7:c.222C>T	19.37:g.57743518C>T		68	0	0		66	19	0.287879	NM_001015878	O60681|O75442|Q6AZY8|Q6DLZ0|Q9UPK5	Silent	SNP	ENST00000302804.7	37	CCDS33128.1																																																																																			C|0.999;T|0.001	0.001	strong		0.517	AURKC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465089.1	NM_003160		T	57743518	C	T	57743518	2	4	22	1	0	0	0	0	0	0	0	1	1224	900	32	2		2	AURKC	19	57743518	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	20336	57743518	1385465	4102	7003											
ZNF460	10794	hgsc.bcm.edu	37	chr19	57802782	57802782	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgtggaaaggcctttacctaCcgctccaattttgtcttgca	8	14	8	11	1	1	0	0	0	1	0	2	1	2	1	4	2	3	2	4	2	4	6	rs80302225	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57802782C>T	ENST00000360338.3	+	3	1195	c.873C>T	c.(871-873)taC>taT	p.Y291Y	ZNF460_ENST00000537645.1_Silent_p.Y250Y	NM_006635.3	NP_006626.3	Q14592	ZN460_HUMAN	zinc finger protein 460	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)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CCTTTACCTACCGCTCCAATT	0.493													c|||	23	0.00459265	0.0166	0.0014	5008	,	,		22183	0.0		0.0	False		,,,				2504	0.0				p.Y291Y		Atlas-SNP	.											.	ZNF460	59	.	0			c.C873T						PASS	.	C		66,4340	62.9+/-100.1	2,62,2139	88	81	83		873	0.3	0	19	dbSNP_132	83	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ZNF460	NM_006635.3		2,63,6438	TT,TC,CC		0.0116,1.498,0.5151		291/563	57802782	67,12939	2203	4300	6503	SO:0001819	synonymous_variant	10794	exon3			TACCTACCGCTCC	X78931	CCDS12949.1	19q13.4	2013-01-08				ENSG00000197714		"Zinc fingers, C2H2-type", "-"	21628	protein-coding gene	gene with protein product		604755	"zinc finger protein 272"	ZNF272		15004467	Standard	NM_006635		Approved	HZF8	uc002qog.2	Q14592		ENST00000360338.3:c.873C>T	19.37:g.57802782C>T		76	0	0		63	27	0.428571	NM_006635	A4FU64|B4DNX9|Q2VPC7|Q6VSF8	Silent	SNP	ENST00000360338.3	37	CCDS12949.1																																																																																			C|0.994;T|0.006	0.006	strong		0.493	ZNF460-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465727.1	NM_006635		T	57802782	C	T	57802782	2	4	22	1	0	0	0	0	0	0	0	1	17939	518	18	2		2	ZNF460	19	57802782	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	59264	57802782	1326201	4103	7004											
ZNF211	10520	hgsc.bcm.edu	37	chr19	58152182	58152182	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gttcatcttcccagaatgccGactcctgtgaaatatgttgc	9	13	8	11	1	2	2	1	1	1	1	4	3	4	2	3	0	2	2	3	0	3	4	rs34897843	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58152182G>A	ENST00000347302.3	+	3	507	c.328G>A	c.(328-330)Gac>Aac	p.D110N	ZNF211_ENST00000544273.1_Missense_Mutation_p.D122N|ZNF211_ENST00000420680.1_Missense_Mutation_p.D114N|ZNF211_ENST00000391703.3_Missense_Mutation_p.D49N|ZNF211_ENST00000254182.7_Missense_Mutation_p.D101N|ZNF211_ENST00000541801.1_Missense_Mutation_p.D101N|ZNF211_ENST00000299871.5_Missense_Mutation_p.D175N|ZNF211_ENST00000240731.4_Missense_Mutation_p.D123N	NM_198855.2	NP_942152.1	Q13398	ZN211_HUMAN	zinc finger protein 211	110			D -> N (in dbSNP:rs34897843).		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)		CCAGAATGCCGACTCCTGTGA	0.453													g|||	32	0.00638978	0.0204	0.0043	5008	,	,		21518	0.0		0.001	False		,,,				2504	0.001				p.D175N		Atlas-SNP	.											.	ZNF211	78	.	0			c.G523A						PASS	.	A	ASN/ASP,ASN/ASP	123,4283	91.1+/-129.8	1,121,2081	98	98	98		367,328	-0.9	0	19	dbSNP_126	98	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	ZNF211	NM_006385.3,NM_198855.2	23,23	1,122,6380	AA,AG,GG		0.0116,2.7916,0.9534	benign,benign	123/578,110/565	58152182	124,12882	2203	4300	6503	SO:0001583	missense	10520	exon5			AATGCCGACTCCT	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.328G>A	19.37:g.58152182G>A	ENSP00000339562:p.Asp110Asn	251	0	0		242	115	0.475207	NM_001265597	B4DH10|B4DLC9|B4E3C9|B9ZVS7|B9ZVW1|F8WDV2|Q05BQ7|Q2TAL7|Q59EG4|Q59G36|Q5EBL6	Missense_Mutation	SNP	ENST00000347302.3	37	CCDS12957.1	13|13	0.005952380952380952|0.005952380952380952	11|11	0.022357723577235773|0.022357723577235773	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	G|G	10.25|10.25	1.298596|1.298596	0.23650|0.23650	0.027916|0.027916	1.16E-4|1.16E-4	ENSG00000121417|ENSG00000121417	ENST00000420680;ENST00000347302;ENST00000254182;ENST00000391703;ENST00000541801;ENST00000299871;ENST00000544273;ENST00000240731|ENST00000407202	T;T;T;T;T;T;T;T|.	0.06768|.	3.31;3.33;3.26;3.27;3.26;3.37;3.33;3.33|.	3.7|3.7	-0.942|-0.942	0.10398|0.10398	.|.	.|.	.|.	.|.	.|.	T|T	0.02304|0.02304	0.0071|0.0071	N|N	0.01493|0.01493	-0.835|-0.835	0.09310|0.09310	N|N	1|1	B;B;B;P;B;B|.	0.39060|.	0.091;0.038;0.001;0.657;0.011;0.011|.	B;B;B;B;B;B|.	0.31812|.	0.013;0.008;0.0;0.136;0.004;0.006|.	T|T	0.30297|0.30297	-0.9983|-0.9983	9|5	0.20519|.	T|.	0.43|.	.|.	0.6887|0.6887	0.00887|0.00887	0.1784:0.3318:0.1832:0.3066|0.1784:0.3318:0.1832:0.3066	rs34897843|rs34897843	114;122;175;101;110;123|.	Q13398-4;Q13398-3;F8WDV2;Q13398-2;Q13398;B9ZVW1|.	.;.;.;.;ZN211_HUMAN;.|.	N|Q	114;110;101;49;101;175;122;123|113	ENSP00000399193:D114N;ENSP00000339562:D110N;ENSP00000254182:D101N;ENSP00000375584:D49N;ENSP00000442601:D101N;ENSP00000299871:D175N;ENSP00000441386:D122N;ENSP00000240731:D123N|.	ENSP00000240731:D123N|.	D|R	+|+	1|2	0|0	ZNF211|ZNF211	62843994|62843994	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.248000|0.248000	0.25809|0.25809	-0.035000|-0.035000	0.12205|0.12205	-0.041000|-0.041000	0.13558|0.13558	-1.230000|-1.230000	0.01575|0.01575	GAC|CGA	G|0.991;A|0.009	0.009	strong		0.453	ZNF211-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397502.1			A	58152182	G	A	58152182	3	1	22	1	0	0	0	0	1	0	0	0	17782	1058	37	1	381	1	ZNF211	19	58152182	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	349400	58152182	976801	4104	7005											
ZNF587	84914	hgsc.bcm.edu	37	chr19	58370744	58370744	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcttgttcacactggagaaGggccttatgagtgtagagaa	12	10	13	6	0	1	3	1	1	0	2	1	5	1	3	1	2	1	3	1	2	4	4	rs201869821	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58370744G>A	ENST00000339656.5	+	3	1146	c.964G>A	c.(964-966)Ggg>Agg	p.G322R	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597652.1_5'Flank|ZNF814_ENST00000597832.1_Intron|ZNF587_ENST00000423137.1_Missense_Mutation_p.G321R|ZNF587_ENST00000419854.1_Missense_Mutation_p.G279R	NM_001204817.1|NM_032828.3	NP_001191746.1|NP_116217.1	Q96SQ5	ZN587_HUMAN	zinc finger protein 587	322					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)		CACTGGAGAAGGGCCTTATGA	0.473													.|||	671	0.133986	0.4274	0.0504	5008	,	,		18971	0.0526		0.0149	False		,,,				2504	0.0031				p.G322R	Pancreas(59;641 1233 1885 20055 50741)	Atlas-SNP	.											.	ZNF587	53	.	0			c.G964A						PASS	.	G	ARG/GLY,ARG/GLY	780,3588		221,338,1625	105	146	133		961,964	0.6	0.2	19	dbSNP_132	133	4,8596		0,4,4296	no	missense,missense	ZNF587	NM_001204817.1,NM_032828.3	125,125	221,342,5921	AA,AG,GG		0.0465,17.8571,6.0457	benign,benign	321/575,322/576	58370744	784,12184	2184	4300	6484	SO:0001583	missense	84914	exon3			GGAGAAGGGCCTT	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.964G>A	19.37:g.58370744G>A	ENSP00000345479:p.Gly322Arg	232	0	0		201	63	0.313433	NM_032828	A0AV72|G3V0H5|Q6ZMK8	Missense_Mutation	SNP	ENST00000339656.5	37	CCDS12964.1	.	.	.	.	.	.	.	.	.	.	.	0.013	-1.627794	0.00813	0.178571	4.65E-4	ENSG00000198466	ENST00000376209;ENST00000423137;ENST00000339656;ENST00000540851;ENST00000419854	T;T;T	0.15603	2.41;2.41;2.41	1.76	0.637	0.17735	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00069	-2.28	0.27094	N	0.962789	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.42103	-0.9471	8	0.10902	T	0.67	.	5.5186	0.16919	0.8297:0.0:0.1703:0.0	.	321;322	G3V0H5;Q96SQ5	.;ZN587_HUMAN	R	279;321;322;322;279	ENSP00000393865:G321R;ENSP00000345479:G322R;ENSP00000406999:G279R	ENSP00000345479:G322R	G	+	1	0	ZNF587	63062556	0.000000	0.05858	0.162000	0.22713	0.192000	0.23643	1.091000	0.30915	-0.047000	0.13423	0.195000	0.17529	GGG	G|0.999;A|0.001	0.001	weak		0.473	ZNF587-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337594.2	NM_032828		A	58370744	G	A	58370744	3	1	22	1	0	0	0	0	1	0	0	0	18035	1000	35	2	974	2	ZNF587	19	58370744	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	218562	58370744	758239	4105	7006											
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385987	58385987	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgaactctctgatgattactCaagctagcatatttgctaaa	13	14	6	8	0	2	3	1	3	1	0	3	3	2	3	0	0	5	3	0	0	7	5	rs111291730	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58385987C>G	ENST00000435989.2	-	3	1005	c.771G>C	c.(769-771)ttG>ttC	p.L257F	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597832.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	257					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						GATGATTACTCAAGCTAGCAT	0.398													.|||	16	0.00319489	0.0121	0.0	5008	,	,		23651	0.0		0.0	False		,,,				2504	0.0				p.L257F		Atlas-SNP	.											.	ZNF814	93	.	0			c.G771C						PASS	.						120	91	100					19																	58385987		692	1591	2283	SO:0001583	missense	730051	exon3			ATTACTCAAGCTA		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.771G>C	19.37:g.58385987C>G	ENSP00000410545:p.Leu257Phe	234	1	0.0042735		257	126	0.490272	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	.	6.736	0.504632	0.12822	.	.	ENSG00000204514	ENST00000435989	T	0.52057	0.68	2.23	-1.06	0.10002	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.32010	0.0815	M	0.62723	1.935	0.09310	N	1	B	0.14805	0.011	B	0.12156	0.007	T	0.30208	-0.9986	9	0.49607	T	0.09	.	5.757	0.18178	0.2141:0.4859:0.3:0.0	.	257	B7Z6K7	ZN814_HUMAN	F	257	ENSP00000410545:L257F	ENSP00000410545:L257F	L	-	3	2	ZNF814	63077799	0.005000	0.15991	0.000000	0.03702	0.011000	0.07611	0.213000	0.17521	-0.743000	0.04784	-2.575000	0.00170	TTG	C|0.998;G|0.002	0.002	strong		0.398	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		G	58385987	C	G	58385987	3	3	22	1	0	0	0	0	1	0	0	0	18191	825	29	4	1800	4	ZNF814	19	58385987	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	15243	58385987	742996	4106	7007											
ZNF814	730051	hgsc.bcm.edu	37	chr19	58386314	58386314	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcctcctcaacactccctctGtagggtttctctccaatgtg	6	13	7	15	0	3	0	1	0	2	0	7	0	6	0	4	1	1	2	4	1	3	2	rs111313171	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58386314G>A	ENST00000435989.2	-	3	678	c.444C>T	c.(442-444)taC>taT	p.Y148Y	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597832.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	148					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						CACTCCCTCTGTAGGGTTTCT	0.483													.|||	397	0.0792732	0.2821	0.0331	5008	,	,		22387	0.0		0.001	False		,,,				2504	0.0				p.Y148Y		Atlas-SNP	.											.	ZNF814	93	.	0			c.C444T						PASS	.	G		365,1019		52,261,379	59	50	53		444	-5.5	0	19	dbSNP_132	53	7,3173		0,7,1583	no	coding-synonymous	ZNF814	NM_001144989.1		52,268,1962	AA,AG,GG		0.2201,26.3728,8.1507		148/856	58386314	372,4192	692	1590	2282	SO:0001819	synonymous_variant	730051	exon3			CCCTCTGTAGGGT		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.444C>T	19.37:g.58386314G>A		744	1	0.00134409		779	332	0.426187	NM_001144989	A6NF35	Silent	SNP	ENST00000435989.2	37	CCDS46212.1																																																																																			G|0.941;A|0.059	0.059	strong		0.483	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		A	58386314	G	A	58386314	2	1	22	1	0	0	0	0	0	0	0	1	18191	1372	48	2		2	ZNF814	19	58386314	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	327	58386314	742669	4107	7008											
ZNF135	7694	hgsc.bcm.edu	37	chr19	58579464	58579464	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagccagcttgctcccctcAttcagcatcagaggatccac	9	9	7	16	0	4	1	4	0	0	1	6	2	6	2	4	1	4	3	4	1	0	2	rs73938600	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58579464A>G	ENST00000313434.5	+	5	1713	c.1612A>G	c.(1612-1614)Att>Gtt	p.I538V	ZNF135_ENST00000359978.6_Intron|ZNF135_ENST00000511556.1_Missense_Mutation_p.I550V|ZNF135_ENST00000401053.4_Missense_Mutation_p.I562V|RN7SL526P_ENST00000469492.2_RNA|ZNF135_ENST00000506786.1_Missense_Mutation_p.I496V|ZNF135_ENST00000439855.2_Missense_Mutation_p.I538V	NM_003436.3	NP_003427.3	P52742	ZN135_HUMAN	zinc finger protein 135	538					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)		TGCTCCCCTCATTCAGCATCA	0.542													A|||	23	0.00459265	0.0159	0.0014	5008	,	,		19819	0.0		0.001	False		,,,				2504	0.0				p.I562V		Atlas-SNP	.											.	ZNF135	159	.	0			c.A1684G						PASS	.	A	,,VAL/ILE,VAL/ILE	74,4332	66.4+/-103.9	2,70,2131	80	76	77		,,1648,1684	3.4	1	19	dbSNP_130	77	2,8592	2.2+/-6.3	0,2,4295	no	utr-3,intron,missense,missense	ZNF135	NM_001164529.1,NM_001164530.1,NM_003436.3,NM_007134.1	,,29,29	2,72,6426	GG,GA,AA		0.0233,1.6795,0.5846	,,benign,benign	,,550/671,562/683	58579464	76,12924	2203	4297	6500	SO:0001583	missense	7694	exon4			CCCCTCATTCAGC	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.1612A>G	19.37:g.58579464A>G	ENSP00000321406:p.Ile538Val	66	0	0		67	31	0.462687	NM_007134	B4DHH9|E9PEV2|F5GYY9|I3L0B3|Q5U5L3|Q8N1I7	Missense_Mutation	SNP	ENST00000313434.5	37		8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	A	3.025	-0.200904	0.06219	0.016795	2.33E-4	ENSG00000176293	ENST00000401053;ENST00000439855;ENST00000313434;ENST00000511556;ENST00000506786	T;T;T;T;T	0.35605	4.1;4.1;4.1;4.1;1.3	3.37	3.37	0.38596	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13030	0.0316	N	0.11364	0.135	0.09310	N	1	P;P	0.43287	0.591;0.802	B;P	0.48873	0.437;0.593	T	0.04650	-1.0936	9	0.23891	T	0.37	.	6.8432	0.23975	0.8839:0.0:0.1161:0.0	.	550;538	E9PEV2;P52742	.;ZN135_HUMAN	V	562;538;538;550;496	ENSP00000441410:I562V;ENSP00000444828:I538V;ENSP00000321406:I538V;ENSP00000422074:I550V;ENSP00000427691:I496V	ENSP00000321406:I538V	I	+	1	0	ZNF135	63271276	0.000000	0.05858	1.000000	0.80357	0.831000	0.47069	-1.095000	0.03356	1.545000	0.49373	0.455000	0.32223	ATT	.	.	weak		0.542	ZNF135-003	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000361899.2	NM_003436		G	58579464	A	G	58579464	3	3	22	1	0	0	0	0	1	0	0	0	17740	217	8	3	1815	3	ZNF135	19	58579464	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	193150	58579464	549519	4108	7009											
ZSCAN18	65982	hgsc.bcm.edu	37	chr19	58597611	58597611	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtccagcctggaggcagcGtcaggctgggaaagctgata	9	7	16	9	1	1	1	1	1	0	0	2	3	2	3	2	4	3	3	2	4	2	1	rs147947490	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58597611G>C	ENST00000240727.6	-	6	1167	c.768C>G	c.(766-768)gaC>gaG	p.D256E	ZSCAN18_ENST00000600404.1_Missense_Mutation_p.D312E|ZSCAN18_ENST00000601144.1_Missense_Mutation_p.D256E|ZSCAN18_ENST00000421612.2_Missense_Mutation_p.D121E	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													G|||	25	0.00499201	0.0174	0.0014	5008	,	,		17998	0.0		0.001	False		,,,				2504	0.0				p.D312E		Atlas-SNP	.											.	ZSCAN18	104	.	0			c.C936G						PASS	.	G	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	74,4332	65.3+/-102.7	1,72,2130	74	64	67		936,768,363,768	-1.3	0	19	dbSNP_134	67	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense,missense	ZSCAN18	NM_001145542.1,NM_001145543.1,NM_001145544.1,NM_023926.4	45,45,45,45	1,74,6428	CC,CG,GG		0.0233,1.6795,0.5843	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	312/567,256/511,121/375,256/511	58597611	76,12930	2203	4300	6503	SO:0001583	missense	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>G	19.37:g.58597611G>C	ENSP00000240727:p.Asp256Glu	90	0	0		106	48	0.45283	NM_001145542	B4DG23|E9PBI0|Q9BRK7|Q9H9A0	Missense_Mutation	SNP	ENST00000240727.6	37	CCDS12971.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	12.06	1.825940	0.32237	0.016795	2.33E-4	ENSG00000121413	ENST00000433686;ENST00000240727;ENST00000421612	T;T	0.02197	4.64;4.4	3.3	-1.28	0.09318	.	0.195954	0.25233	N	0.032148	T	0.00845	0.0028	N	0.14661	0.345	0.09310	N	1	D;D;D;P	0.56521	0.976;0.976;0.972;0.953	P;P;P;B	0.48270	0.506;0.506;0.572;0.369	T	0.52990	-0.8501	10	0.28530	T	0.3	-5.2194	7.362	0.26752	0.4923:0.0:0.5077:0.0	.	312;121;256;256	B4DG23;E9PBI0;Q8TBC5-2;Q8TBC5	.;.;.;ZSC18_HUMAN	E	312;256;121	ENSP00000240727:D256E;ENSP00000392653:D121E	ENSP00000240727:D256E	D	-	3	2	ZSCAN18	63289423	0.065000	0.20965	0.014000	0.15608	0.577000	0.36160	0.093000	0.15086	-0.370000	0.08016	-0.291000	0.09656	GAC	G|0.993;C|0.007	0.007	strong		0.542	ZSCAN18-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466706.1	NM_023926		C	58597611	G	C	58597611	3	2	22	1	0	0	0	0	1	0	0	0	18245	1136	40	4	772	4	ZSCAN18	19	58597611	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	18147	58597611	531372	4109	7010											
ZNF446	55663	hgsc.bcm.edu	37	chr19	58991075	58991075	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gatgcgatgctggagaagtaCggcacagtggtctccctggg	8	8	16	9	2	1	1	0	0	1	1	2	4	1	1	1	4	3	3	1	4	2	1	rs140158663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58991075C>T	ENST00000594369.1	+	5	1074	c.693C>T	c.(691-693)taC>taT	p.Y231Y	ZNF446_ENST00000596341.1_Silent_p.Y231Y|ZNF446_ENST00000335841.4_Intron	NM_017908.2	NP_060378.1	Q9NWS9	ZN446_HUMAN	zinc finger protein 446	231	KRAB.				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)		TGGAGAAGTACGGCACAGTGG	0.667													C|||	8	0.00159744	0.0061	0.0	5008	,	,		13917	0.0		0.0	False		,,,				2504	0.0				p.Y231Y		Atlas-SNP	.											.	ZNF446	22	.	0			c.C693T						PASS	.	C		19,4387	25.3+/-52.1	0,19,2184	106	93	97		693	-0.8	0.5	19	dbSNP_134	97	0,8600		0,0,4300	no	coding-synonymous	ZNF446	NM_017908.2		0,19,6484	TT,TC,CC		0.0,0.4312,0.1461		231/451	58991075	19,12987	2203	4300	6503	SO:0001819	synonymous_variant	55663	exon5			GAAGTACGGCACA		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.693C>T	19.37:g.58991075C>T		87	0	0		99	43	0.434343	NM_017908		Silent	SNP	ENST00000594369.1	37	CCDS12982.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	18.25	3.582969	0.65992	0.004312	0.0	ENSG00000083838	ENST00000391694	.	.	.	4.99	-0.83	0.10792	.	.	.	.	.	T	0.24122	0.0584	.	.	.	0.21675	N	0.999593	.	.	.	.	.	.	T	0.37126	-0.9719	5	0.87932	D	0	-20.9173	7.3852	0.26878	0.0:0.4473:0.0:0.5527	.	.	.	.	M	61	.	ENSP00000375576:T61M	T	+	2	0	ZNF446	63682887	0.000000	0.05858	0.518000	0.27811	0.871000	0.50021	-0.566000	0.05922	0.062000	0.16340	0.655000	0.94253	ACG	C|0.998;T|0.002	0.002	strong		0.667	ZNF446-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467052.1	NM_017908		T	58991075	C	T	58991075	2	4	22	1	0	0	0	0	0	0	0	1	17934	547	19	1		1	ZNF446	19	58991075	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	393464	58991075	137908	4110	7011											
SLC27A5	10998	hgsc.bcm.edu	37	chr19	59023213	59023213	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcaacatgtgggatcccccAggagccagcgcagggtcaag	10	4	14	13	2	1	0	1	0	0	0	2	2	2	2	3	3	3	2	3	3	2	0	rs146147877	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:59023213A>C	ENST00000263093.2	-	1	219	c.110T>G	c.(109-111)cTg>cGg	p.L37R	SLC27A5_ENST00000601355.1_Missense_Mutation_p.L37R	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	37					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)		GGGATCCCCCAGGAGCCAGCG	0.687													A|||	24	0.00479233	0.0182	0.0	5008	,	,		17742	0.0		0.0	False		,,,				2504	0.0				p.L37R		Atlas-SNP	.											.	SLC27A5	58	.	0			c.T110G						PASS	.	A	ARG/LEU	53,4285		0,53,2116	8	9	9		110	4.3	1	19	dbSNP_134	9	0,8524		0,0,4262	yes	missense	SLC27A5	NM_012254.2	102	0,53,6378	CC,CA,AA		0.0,1.2218,0.4121	probably-damaging	37/691	59023213	53,12809	2169	4262	6431	SO:0001583	missense	10998	exon1			TCCCCCAGGAGCC	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.110T>G	19.37:g.59023213A>C	ENSP00000263093:p.Leu37Arg	58	0	0		74	37	0.5	NM_012254	B3KVP6|B4DPQ1	Missense_Mutation	SNP	ENST00000263093.2	37	CCDS12983.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	a	14.75	2.628307	0.46944	0.012218	0.0	ENSG00000083807	ENST00000263093	T	0.59638	0.25	4.31	4.31	0.51392	.	0.334193	0.17602	N	0.168398	T	0.48241	0.1489	M	0.62723	1.935	0.37946	D	0.932495	D	0.58620	0.983	P	0.53401	0.725	T	0.66368	-0.5941	10	0.87932	D	0	-16.4075	10.4112	0.44294	1.0:0.0:0.0:0.0	.	37	Q9Y2P5	S27A5_HUMAN	R	37	ENSP00000263093:L37R	ENSP00000263093:L37R	L	-	2	0	SLC27A5	63715025	1.000000	0.71417	0.975000	0.42487	0.133000	0.20885	3.179000	0.50887	1.889000	0.54706	0.374000	0.22700	CTG	A|0.995;C|0.005	0.005	strong		0.687	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254		C	59023213	A	C	59023213	3	2	22	1	0	0	0	0	1	0	0	0	14544	188	7	5	2002	5	SLC27A5	19	59023213	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	32138	59023213	105770	4111	7012											
RBCK1	10616	hgsc.bcm.edu	37	chr20	398175	398175	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgctgttctctgcaggctgtGggtgagcgtggaggatgctc	4	12	17	8	1	1	1	0	1	1	0	3	3	1	3	0	4	4	5	0	4	0	1	rs143804674	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:398175G>C	ENST00000356286.5	+	3	878	c.173G>C	c.(172-174)tGg>tCg	p.W58S	RBCK1_ENST00000353660.3_Missense_Mutation_p.W16S|RBCK1_ENST00000382181.2_5'UTR	NM_031229.2	NP_112506.2	Q9BYM8	HOIL1_HUMAN	RanBP-type and C3HC4-type zinc finger containing 1	58	Interaction with IRF3.|Interaction with TAB2.|Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				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)				TGCAGGCTGTGGGTGAGCGTG	0.587																																					p.W58S		Atlas-SNP	.											.	RBCK1	38	.	0			c.G173C						PASS	.	G	SER/TRP,SER/TRP	5,4401	9.9+/-24.2	0,5,2198	66	55	58		47,173	4.2	1	20	dbSNP_134	58	0,8600		0,0,4300	yes	missense,missense	RBCK1	NM_006462.4,NM_031229.2	177,177	0,5,6498	CC,CG,GG		0.0,0.1135,0.0384	benign,benign	16/469,58/511	398175	5,13001	2203	4300	6503	SO:0001583	missense	10616	exon3			GGCTGTGGGTGAG	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.173G>C	20.37:g.398175G>C	ENSP00000348632:p.Trp58Ser	85	0	0		94	54	0.574468	NM_031229	O95623|Q86SL2|Q96BS3|Q9BYM9	Missense_Mutation	SNP	ENST00000356286.5	37	CCDS13000.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.67|14.67	2.605738|2.605738	0.46527|0.46527	0.001135|0.001135	0.0|0.0	ENSG00000125826|ENSG00000125826	ENST00000414880|ENST00000411647;ENST00000356286;ENST00000441733;ENST00000353660;ENST00000400244;ENST00000400243	.|T;T;T;T	.|0.10477	.|2.87;2.87;2.87;2.87	5.12|5.12	4.17|4.17	0.49024|0.49024	.|Ubiquitin supergroup (1);	.|0.578121	.|0.16613	.|N	.|0.206802	T|T	0.09905|0.09905	0.0243|0.0243	L|L	0.47716|0.47716	1.5|1.5	0.80722|0.80722	D|D	1|1	.|B;B;B	.|0.19817	.|0.002;0.034;0.039	.|B;B;B	.|0.21708	.|0.002;0.036;0.01	T|T	0.08391|0.08391	-1.0724|-1.0724	5|10	.|0.12430	.|T	.|0.62	-21.4854|-21.4854	9.3395|9.3395	0.38071|0.38071	0.0967:0.0:0.9033:0.0|0.0967:0.0:0.9033:0.0	.|.	.|48;16;58	.|B4E0F5;Q9BYM8-3;Q9BYM8	.|.;.;HOIL1_HUMAN	R|S	91|58;58;57;16;58;99	.|ENSP00000415080:W58S;ENSP00000348632:W58S;ENSP00000387799:W57S;ENSP00000254960:W16S	.|ENSP00000254960:W16S	G|W	+|+	1|2	0|0	RBCK1|RBCK1	346175|346175	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.780000|0.780000	0.44128|0.44128	1.134000|1.134000	0.31442|0.31442	1.374000|1.374000	0.46228|0.46228	0.557000|0.557000	0.71058|0.71058	GGG|TGG	G|1.000;C|0.000	0.000	strong		0.587	RBCK1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077461.3	NM_031229		C	398175	G	C	398175	3	2	22	1	0	0	0	0	1	0	0	0	13122	1357	47	4	202	4	RBCK1	20	398175	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10		398175	62627345	4112	7013											
C20orf54	113278	hgsc.bcm.edu	37	chr20	744510	744510	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tggaggacaaagaacgccacGaggcagcaggccatcatgat	14	4	13	10	2	1	2	1	1	0	1	1	5	1	4	2	4	2	2	2	4	2	0	rs3746806	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:744510G>A	ENST00000217254.7	-	3	946	c.705C>T	c.(703-705)ctC>ctT	p.L235L	SLC52A3_ENST00000473664.1_Intron|SLC52A3_ENST00000381944.3_Silent_p.L235L	NM_033409.3	NP_212134.3	Q9NQ40	S52A3_HUMAN	solute carrier family 52 (riboflavin transporter), member 3	235					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)										AGAACGCCACGAGGCAGCAGG	0.622																																					p.L235L		Atlas-SNP	.											C20orf54,colon,carcinoma,-2,1	.	.	1	0			c.C705T						PASS	.	G		140,4266	98.9+/-137.6	3,134,2066	80	72	75		705	0.5	0	20	dbSNP_107	75	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	C20orf54	NM_033409.3		3,137,6363	AA,AG,GG		0.0349,3.1775,1.0995		235/470	744510	143,12863	2203	4300	6503	SO:0001819	synonymous_variant	113278	exon3			CGCCACGAGGCAG	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.705C>T	20.37:g.744510G>A		71	0	0		87	37	0.425287	NM_033409	A8K6P1|Q5W1A0|Q5W1A1|Q8NCL7|Q96GD5	Silent	SNP	ENST00000217254.7	37	CCDS13007.1																																																																																			A|0.009;C|0.000;G|0.991	0.009	strong		0.622	SLC52A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077482.2	NM_033409		A	744510	G	A	744510	2	1	22	1	0	0	0	0	0	0	0	1	2116	1045	37	1		1	C20orf54	20	744510	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	346335	744510	62281010	4113	7014											
FAM110A	83541	hgsc.bcm.edu	37	chr20	825579	825579	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggaaaccgagcgctgtggaGcgcctggaggccgacaaggc	9	3	17	12	5	0	0	0	0	0	0	0	5	0	3	3	5	3	1	3	5	2	0	rs8124809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:825579G>A	ENST00000304189.2	+	3	513	c.132G>A	c.(130-132)gaG>gaA	p.E44E	FAM110A_ENST00000541082.1_Silent_p.E44E|FAM110A_ENST00000381941.3_Silent_p.E44E|FAM110A_ENST00000381939.1_Silent_p.E44E|FAM110A_ENST00000246100.3_Silent_p.E44E			Q9BQ89	F110A_HUMAN	family with sequence similarity 110, member A	44						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|lung(2)	3						GCGCTGTGGAGCGCCTGGAGG	0.687													G|||	73	0.0145767	0.053	0.0043	5008	,	,		11046	0.0		0.0	False		,,,				2504	0.0				p.E44E		Atlas-SNP	.											.	FAM110A	18	.	0			c.G132A						PASS	.	G	,,	204,4158		1,202,1978	12	12	12		132,132,132	4	1	20	dbSNP_116	12	3,8543		0,3,4270	no	coding-synonymous,coding-synonymous,coding-synonymous	FAM110A	NM_001042353.1,NM_031424.4,NM_207121.3	,,	1,205,6248	AA,AG,GG		0.0351,4.6768,1.6037	,,	44/296,44/296,44/296	825579	207,12701	2181	4273	6454	SO:0001819	synonymous_variant	83541	exon2			TGTGGAGCGCCTG	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.132G>A	20.37:g.825579G>A		87	0	0		157	86	0.547771	NM_207121	D3DVW2|Q5R1M7	Silent	SNP	ENST00000304189.2	37	CCDS13008.1																																																																																			A|0.020;C|0.000;G|0.979	0.020	strong		0.687	FAM110A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077489.1	NM_031424		A	825579	G	A	825579	2	1	22	1	0	0	0	0	0	0	0	1	5401	962	34	2		2	FAM110A	20	825579	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	81069	825579	62199941	4114	7015											
ANGPT4	51378	hgsc.bcm.edu	37	chr20	854973	854973	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagacagtggtcgttgtcTgagtcaagggtgctaaagct	10	10	14	7	1	2	2	1	1	1	1	3	3	2	2	0	2	2	3	0	2	3	2	rs62641668	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:854973T>G	ENST00000381922.3	-	8	1407	c.1305A>C	c.(1303-1305)tcA>tcC	p.S435S	ANGPT4_ENST00000546022.1_Intron	NM_015985.2	NP_057069.1	Q9Y264	ANGP4_HUMAN	angiopoietin 4	435	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				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						GGTCGTTGTCTGAGTCAAGGG	0.612													T|||	75	0.014976	0.0416	0.0144	5008	,	,		20786	0.004		0.006	False		,,,				2504	0.0				p.S435S	Pancreas(181;481 2077 3259 31286 49856)	Atlas-SNP	.											ANGPT4,bladder,carcinoma,-1,1	ANGPT4	77	1	0			c.A1305C						PASS	.	T		163,4243	109.9+/-148.2	5,153,2045	123	93	103		1305	-10.3	0	20	dbSNP_129	103	52,8548	32.8+/-85.7	0,52,4248	no	coding-synonymous	ANGPT4	NM_015985.2		5,205,6293	GG,GT,TT		0.6047,3.6995,1.6531		435/504	854973	215,12791	2203	4300	6503	SO:0001819	synonymous_variant	51378	exon8			GTTGTCTGAGTCA	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.1305A>C	20.37:g.854973T>G		176	0	0		216	103	0.476852	NM_015985	B4E3J9|Q5TFF4|Q9H4Z4	Silent	SNP	ENST00000381922.3	37	CCDS13009.1																																																																																			T|0.983;G|0.017	0.017	strong		0.612	ANGPT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077493.1	NM_015985		G	854973	T	G	854973	2	3	22	1	0	0	0	0	0	0	0	1	612	1567	55	5		5	ANGPT4	20	854973	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	29394	854973	62170547	4115	7016											
ANGPT4	51378	hgsc.bcm.edu	37	chr20	861853	861853	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttggacacctggatggtgtaGacaccactggcactggcccc	8	8	12	13	0	0	1	0	0	0	1	0	3	0	3	4	5	0	2	4	5	1	2	rs6086328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:861853G>A	ENST00000381922.3	-	5	1014	c.912C>T	c.(910-912)gtC>gtT	p.V304V	ANGPT4_ENST00000546022.1_Silent_p.V304V	NM_015985.2	NP_057069.1	Q9Y264	ANGP4_HUMAN	angiopoietin 4	304	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				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						GGATGGTGTAGACACCACTGG	0.572													G|||	335	0.066893	0.2405	0.0216	5008	,	,		18573	0.0		0.002	False		,,,				2504	0.0				p.V304V	Pancreas(181;481 2077 3259 31286 49856)	Atlas-SNP	.											.	ANGPT4	77	.	0			c.C912T						PASS	.	G		986,3420	370.0+/-319.4	106,774,1323	74	62	66		912	4.9	1	20	dbSNP_114	66	14,8586	9.1+/-34.3	0,14,4286	no	coding-synonymous	ANGPT4	NM_015985.2		106,788,5609	AA,AG,GG		0.1628,22.3786,7.6888		304/504	861853	1000,12006	2203	4300	6503	SO:0001819	synonymous_variant	51378	exon5			GGTGTAGACACCA	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.912C>T	20.37:g.861853G>A		121	0	0		111	48	0.432432	NM_015985	B4E3J9|Q5TFF4|Q9H4Z4	Silent	SNP	ENST00000381922.3	37	CCDS13009.1																																																																																			A|0.066;G|0.934	0.066	strong		0.572	ANGPT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077493.1	NM_015985		A	861853	G	A	861853	2	1	22	1	0	0	0	0	0	0	0	1	612	929	33	2		2	ANGPT4	20	861853	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6880	861853	62163667	4116	7017											
PSMF1	9491	hgsc.bcm.edu	37	chr20	1106143	1106143	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caactgtggtcttcccagccGggtcccaatgataagaagtc	10	9	10	12	1	1	2	0	1	1	1	4	2	3	2	3	2	2	0	3	2	4	2	rs35517343	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1106143G>A	ENST00000335877.6	+	2	308	c.132G>A	c.(130-132)ccG>ccA	p.P44P	PSMF1_ENST00000333082.3_Silent_p.P44P|PSMF1_ENST00000381898.4_5'UTR|PSMF1_ENST00000438768.2_Silent_p.P44P|PSMF1_ENST00000246015.4_Silent_p.P44P	NM_006814.3	NP_006805.2	Q92530	PSMF1_HUMAN	proteasome (prosome, macropain) inhibitor subunit 1 (PI31)	44	Important for homodimerization and interaction with FBXO7.				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						CTTCCCAGCCGGGTCCCAATG	0.458													G|||	15	0.00299521	0.0113	0.0	5008	,	,		21820	0.0		0.0	False		,,,				2504	0.0				p.P44P		Atlas-SNP	.											.	PSMF1	27	.	0			c.G132A						PASS	.	G	,	61,4345	58.7+/-95.3	0,61,2142	77	70	72		132,132	-3.1	0.1	20	dbSNP_126	72	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous	PSMF1	NM_006814.3,NM_178578.2	,	0,62,6441	AA,AG,GG		0.0116,1.3845,0.4767	,	44/272,44/272	1106143	62,12944	2203	4300	6503	SO:0001819	synonymous_variant	9491	exon2			CCAGCCGGGTCCC	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.132G>A	20.37:g.1106143G>A		90	0	0		106	52	0.490566	NM_006814	A0AVQ9|D3DVW3|Q9H4I1	Silent	SNP	ENST00000335877.6	37	CCDS13010.1																																																																																			G|0.995;A|0.005	0.005	strong		0.458	PSMF1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077504.2	NM_178578		A	1106143	G	A	1106143	2	1	22	1	0	0	0	0	0	0	0	1	12722	1103	39	1		1	PSMF1	20	1106143	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	244290	1106143	61919377	4117	7018											
NSFL1C	55968	hgsc.bcm.edu	37	chr20	1433171	1433171	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaccctcgccagtgaaggctTtgaaggctcctttgggcttc	6	11	12	12	1	0	2	0	2	0	0	3	3	1	2	3	3	0	3	3	3	2	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1433171T>C	ENST00000216879.4	-	7	1619	c.752A>G	c.(751-753)aAa>aGa	p.K251R	NSFL1C_ENST00000461211.1_5'UTR|NSFL1C_ENST00000381658.4_Missense_Mutation_p.K140R|NSFL1C_ENST00000476071.1_Missense_Mutation_p.K253R|NSFL1C_ENST00000353088.2_Missense_Mutation_p.K220R|NSFL1C_ENST00000350991.4_Missense_Mutation_p.K253R	NM_016143.4	NP_057227.2	Q9UNZ2	NSF1C_HUMAN	NSFL1 (p97) cofactor (p47)	251						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						AGTGAAGGCTTTGAAGGCTCC	0.577																																					p.K251R		Atlas-SNP	.											.	NSFL1C	38	.	0			c.A752G						PASS	.						158	139	146					20																	1433171		2203	4300	6503	SO:0001583	missense	55968	exon7			AAGGCTTTGAAGG	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.752A>G	20.37:g.1433171T>C	ENSP00000216879:p.Lys251Arg	99	0	0		96	34	0.354167	NM_016143	A2A2L1|B2RD74|Q5JXA4|Q5JXA5|Q7Z533|Q9H102|Q9NVL9|Q9UI06	Missense_Mutation	SNP	ENST00000216879.4	37	CCDS13015.1	.	.	.	.	.	.	.	.	.	.	T	16.27	3.076548	0.55753	.	.	ENSG00000088833	ENST00000353088;ENST00000476071;ENST00000216879;ENST00000381658;ENST00000350991	T;T;T;T;T	0.49432	0.79;0.78;0.78;0.82;0.78	5.13	2.85	0.33270	SEP domain (3);	0.000000	0.85682	D	0.000000	T	0.42337	0.1198	M	0.62016	1.91	0.58432	D	0.999995	B;B;B	0.11235	0.004;0.001;0.001	B;B;B	0.12156	0.007;0.005;0.005	T	0.30937	-0.9961	10	0.51188	T	0.08	-10.0824	8.1784	0.31296	0.0:0.294:0.0:0.706	.	220;140;251	Q9UNZ2-4;Q9UNZ2-6;Q9UNZ2	.;.;NSF1C_HUMAN	R	220;253;251;140;253	ENSP00000338643:K220R;ENSP00000418529:K253R;ENSP00000216879:K251R;ENSP00000371074:K140R;ENSP00000202584:K253R	ENSP00000216879:K251R	K	-	2	0	NSFL1C	1381171	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.908000	0.28545	0.503000	0.28060	0.533000	0.62120	AAA	.	.	none		0.577	NSFL1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077525.2	NM_016143		C	1433171	T	C	1433171	3	2	22	1	0	0	0	0	1	0	0	0	10681	1841	64	3	372	3	NSFL1C	20	1433171	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	327028	1433171	61592349	4118	7019											
SIRPB1	10326	hgsc.bcm.edu	37	chr20	1546906	1546906	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtggagcagtaggagccagCgctgcttctggaaatcaggg	10	7	16	8	1	2	0	1	0	1	0	2	3	2	3	1	4	4	4	1	4	2	2	rs11907593	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1546906C>T	ENST00000381605.4	-	5	1156	c.1092G>A	c.(1090-1092)gcG>gcA	p.A364A	SIRPB1_ENST00000381603.3_Silent_p.A147A|RP4-576H24.4_ENST00000564763.1_Intron|SIRPB1_ENST00000262929.5_Silent_p.A146A	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1	364					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						TAGGAGCCAGCGCTGCTTCTG	0.607													.|||	92	0.0183706	0.0666	0.0058	5008	,	,		16446	0.0		0.0	False		,,,				2504	0.0				p.A364A		Atlas-SNP	.											.	SIRPB1	83	.	0			c.G1092A						PASS	.	C	,	172,4234		4,164,2035	42	35	38		441,1092	-6	0	20	dbSNP_120	38	4,8592		0,4,4294	no	coding-synonymous,coding-synonymous	SIRPB1	NM_001083910.2,NM_006065.3	,	4,168,6329	TT,TC,CC		0.0465,3.9038,1.3536	,	147/182,364/399	1546906	176,12826	2203	4298	6501	SO:0001819	synonymous_variant	10326	exon5			AGCCAGCGCTGCT	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.1092G>A	20.37:g.1546906C>T		71	0	0		73	51	0.69863	NM_006065	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Silent	SNP	ENST00000381605.4	37	CCDS13019.1																																																																																			C|0.984;T|0.016	0.016	strong		0.607	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065		T	1546906	C	T	1546906	2	4	22	1	0	0	0	0	0	0	0	1	14348	755	27	1		1	SIRPB1	20	1546906	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	113735	1546906	61478614	4119	7020											
TGM3	7053	hgsc.bcm.edu	37	chr20	2291722	2291722	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcaggaagatgccggcatcAtctttgtgggaagcacaaac	12	9	11	9	1	3	1	2	0	1	1	3	3	3	3	1	3	3	2	1	3	3	2	rs6048066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:2291722A>C	ENST00000381458.5	+	4	550	c.487A>C	c.(487-489)Atc>Ctc	p.I163L		NM_003245.3	NP_003236.3	Q08188	TGM3_HUMAN	transglutaminase 3	163			I -> L (in dbSNP:rs6048066). {ECO:0000269|Ref.3}.		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)	TGCCGGCATCATCTTTGTGGG	0.458													A|||	605	0.120807	0.4304	0.0519	5008	,	,		21488	0.0		0.0	False		,,,				2504	0.0				p.I163L		Atlas-SNP	.											.	TGM3	105	.	0			c.A487C						PASS	.	A	LEU/ILE	1503,2903	479.4+/-358.5	255,993,955	158	148	151		487	5.7	0.5	20	dbSNP_114	151	11,8589	7.1+/-27.0	0,11,4289	yes	missense	TGM3	NM_003245.3	5	255,1004,5244	CC,CA,AA		0.1279,34.1126,11.6408	possibly-damaging	163/694	2291722	1514,11492	2203	4300	6503	SO:0001583	missense	7053	exon4			GGCATCATCTTTG	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.487A>C	20.37:g.2291722A>C	ENSP00000370867:p.Ile163Leu	169	0	0		169	93	0.550296	NM_003245	A8K5N6|B2RCR6|D3DVX1|O95933|Q32ML9|Q32MM0	Missense_Mutation	SNP	ENST00000381458.5	37	CCDS33435.1	224	0.10256410256410256	203	0.41260162601626016	19	0.052486187845303865	0	0.0	2	0.002638522427440633	A	18.58	3.653803	0.67472	0.341126	0.001279	ENSG00000125780	ENST00000381458;ENST00000420960	D	0.85171	-1.95	5.71	5.71	0.89125	.	0.243134	0.42821	D	0.000652	T	0.00012	0.0000	M	0.81179	2.53	0.20403	P	0.9999028236	P	0.48407	0.91	D	0.80764	0.994	T	0.00000	-1.2810	9	0.72032	D	0.01	.	13.9352	0.64021	1.0:0.0:0.0:0.0	rs6048066;rs7272340;rs52800893;rs6048066	163	Q08188	TGM3_HUMAN	L	163	ENSP00000370867:I163L	ENSP00000370867:I163L	I	+	1	0	TGM3	2239722	0.997000	0.39634	0.532000	0.27989	0.430000	0.31655	3.089000	0.50183	2.184000	0.69523	0.454000	0.30748	ATC	A|0.871;C|0.129	0.129	strong		0.458	TGM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077579.2	NM_003245		C	2291722	A	C	2291722	3	2	22	1	0	0	0	0	1	0	0	0	15846	217	8	5	501	5	TGM3	20	2291722	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	744816	2291722	60733798	4120	7021											
TGM6	343641	hgsc.bcm.edu	37	chr20	2377204	2377204	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agacaggagtacgtgctcagCgacagcggcatcatcttccg	10	7	12	12	4	3	1	2	0	1	1	4	3	4	2	1	2	4	3	1	2	1	2	rs16984872	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:2377204C>T	ENST00000202625.2	+	4	538	c.477C>T	c.(475-477)agC>agT	p.S159S	TGM6_ENST00000381423.1_Silent_p.S159S|TGM6_ENST00000477505.1_Intron	NM_198994.2	NP_945345.2	O95932	TGM3L_HUMAN	transglutaminase 6	159					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)	ACGTGCTCAGCGACAGCGGCA	0.612													C|||	193	0.0385383	0.1225	0.0259	5008	,	,		19129	0.0		0.0099	False		,,,				2504	0.0031				p.S159S		Atlas-SNP	.											TGM6,NS,carcinoma,0,1	TGM6	126	1	0			c.C477T						PASS	.	C		447,3959	215.8+/-234.7	28,391,1784	96	85	89		477	-5.3	0.9	20	dbSNP_123	89	87,8513	49.4+/-109.1	0,87,4213	no	coding-synonymous	TGM6	NM_198994.2		28,478,5997	TT,TC,CC		1.0116,10.1453,4.1058		159/707	2377204	534,12472	2203	4300	6503	SO:0001819	synonymous_variant	343641	exon4			GCTCAGCGACAGC	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.477C>T	20.37:g.2377204C>T		252	0	0		266	124	0.466165	NM_198994	Q5JXU4|Q5JXU5|Q719M2|Q719M3|Q9Y4U8	Silent	SNP	ENST00000202625.2	37	CCDS13025.1																																																																																			C|0.960;T|0.040	0.040	strong		0.612	TGM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077581.2	NM_198994		T	2377204	C	T	2377204	2	4	22	1	0	0	0	0	0	0	0	1	15849	767	27	1		1	TGM6	20	2377204	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	85482	2377204	60648316	4121	7022											
TGM6	343641	hgsc.bcm.edu	37	chr20	2411118	2411118	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaatcccaattacaatatctTactctaagtataaagaagac	18	11	4	8	0	2	2	0	0	2	2	3	3	3	2	1	0	2	1	1	0	11	6	rs142406714	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:2411118T>A	ENST00000202625.2	+	11	1766	c.1705T>A	c.(1705-1707)Tac>Aac	p.Y569N	TGM6_ENST00000381423.1_Missense_Mutation_p.Y569N	NM_198994.2	NP_945345.2	O95932	TGM3L_HUMAN	transglutaminase 6	569					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)	TACAATATCTTACTCTAAGTA	0.458													T|||	3	0.000599042	0.0023	0.0	5008	,	,		19164	0.0		0.0	False		,,,				2504	0.0				p.Y569N		Atlas-SNP	.											.	TGM6	126	.	0			c.T1705A						PASS	.	T	ASN/TYR	5,4401	9.9+/-24.2	0,5,2198	92	87	88		1705	5.9	1	20	dbSNP_134	88	0,8600		0,0,4300	yes	missense	TGM6	NM_198994.2	143	0,5,6498	AA,AT,TT		0.0,0.1135,0.0384	probably-damaging	569/707	2411118	5,13001	2203	4300	6503	SO:0001583	missense	343641	exon11			ATATCTTACTCTA	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.1705T>A	20.37:g.2411118T>A	ENSP00000202625:p.Tyr569Asn	57	0	0		70	41	0.585714	NM_198994	Q5JXU4|Q5JXU5|Q719M2|Q719M3|Q9Y4U8	Missense_Mutation	SNP	ENST00000202625.2	37	CCDS13025.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.069978	0.76301	0.001135	0.0	ENSG00000166948	ENST00000202625;ENST00000381423	T;T	0.71341	-0.56;-0.56	5.88	5.88	0.94601	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.203565	0.43919	D	0.000512	D	0.84428	0.5470	M	0.83384	2.64	0.43846	D	0.996433	D;D	0.89917	1.0;1.0	D;D	0.83275	0.994;0.996	D	0.86612	0.1873	10	0.87932	D	0	-31.5353	12.6797	0.56914	0.0:0.0:0.0:1.0	.	569;569	O95932-2;O95932	.;TGM3L_HUMAN	N	569	ENSP00000202625:Y569N;ENSP00000370831:Y569N	ENSP00000202625:Y569N	Y	+	1	0	TGM6	2359118	1.000000	0.71417	0.998000	0.56505	0.961000	0.63080	4.493000	0.60341	2.242000	0.73789	0.533000	0.62120	TAC	T|1.000;A|0.000	0.000	weak		0.458	TGM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077581.2	NM_198994		A	2411118	T	A	2411118	3	1	22	1	0	0	0	0	1	0	0	0	15849	1754	61	5	1747	5	TGM6	20	2411118	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	33914	2411118	60614402	4122	7023											
TMC2	117532	hgsc.bcm.edu	37	chr20	2582839	2582839	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcgtgtcctggccaacttTctcatcatctgctgtttgtg	4	17	8	12	1	3	0	2	0	2	0	6	0	4	0	2	1	2	2	2	1	1	3	rs140733869	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:2582839T>A	ENST00000358864.1	+	11	1320	c.1305T>A	c.(1303-1305)ttT>ttA	p.F435L	TMC2_ENST00000496948.1_3'UTR	NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	435					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						TGGCCAACTTTCTCATCATCT	0.388													T|||	15	0.00299521	0.0106	0.0014	5008	,	,		20141	0.0		0.0	False		,,,				2504	0.0				p.F435L		Atlas-SNP	.											.	TMC2	121	.	0			c.T1305A						PASS	.	T	LEU/PHE	26,4380	32.6+/-62.9	0,26,2177	199	174	182		1305	-4.7	1	20	dbSNP_134	182	0,8600		0,0,4300	yes	missense	TMC2	NM_080751.2	22	0,26,6477	AA,AT,TT		0.0,0.5901,0.1999	possibly-damaging	435/907	2582839	26,12980	2203	4300	6503	SO:0001583	missense	117532	exon11			CAACTTTCTCATC	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.1305T>A	20.37:g.2582839T>A	ENSP00000351732:p.Phe435Leu	226	0	0		245	137	0.559184	NM_080751	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Missense_Mutation	SNP	ENST00000358864.1	37	CCDS13029.2	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	T	17.98	3.520320	0.64747	0.005901	0.0	ENSG00000149488	ENST00000358864	T	0.80994	-1.44	5.58	-4.7	0.03288	.	0.171732	0.56097	D	0.000039	T	0.64811	0.2632	L	0.60845	1.875	0.39342	D	0.965601	B;B;P;P	0.45986	0.382;0.209;0.866;0.87	B;B;P;P	0.50570	0.064;0.031;0.644;0.542	T	0.76044	-0.3103	10	0.09084	T	0.74	-13.3661	15.7824	0.78272	0.0:0.7271:0.0:0.2729	.	266;267;435;435	B4DFB3;B7ZAE6;Q8TDI7-3;Q8TDI7	.;.;.;TMC2_HUMAN	L	435	ENSP00000351732:F435L	ENSP00000351732:F435L	F	+	3	2	TMC2	2530839	0.062000	0.20869	0.972000	0.41901	0.959000	0.62525	-0.545000	0.06069	-0.718000	0.04949	-1.151000	0.01829	TTT	T|0.997;A|0.003	0.003	strong		0.388	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2			A	2582839	T	A	2582839	3	1	22	1	0	0	0	0	1	0	0	0	16000	1780	62	5	1347	5	TMC2	20	2582839	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	171721	2582839	60442681	4123	7024											
PTPRA	5786	hgsc.bcm.edu	37	chr20	2969015	2969015	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gtgccacttctggccagatcCccaagcaccaacaggaaata	13	6	8	14	0	1	1	0	0	1	1	2	2	2	2	5	2	3	1	5	2	4	2	rs61742610	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:2969015C>G	ENST00000216877.6	+	8	1006	c.606C>G	c.(604-606)tcC>tcG	p.S202S	PTPRA_ENST00000425918.2_Silent_p.S222S|PTPRA_ENST00000356147.3_Silent_p.S202S|PTPRA_ENST00000318266.5_Silent_p.S202S|PTPRA_ENST00000380393.3_Silent_p.S211S|PTPRA_ENST00000358719.4_Silent_p.S67S|PTPRA_ENST00000399903.2_Silent_p.S211S	NM_080840.2	NP_543030.1	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	211					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						TGGCCAGATCCCCAAGCACCA	0.547													C|||	147	0.029353	0.0802	0.0231	5008	,	,		17950	0.001		0.003	False		,,,				2504	0.0215				p.S211S		Atlas-SNP	.											.	PTPRA	75	.	0			c.C633G						PASS	.	C	,,	279,4127	155.5+/-188.7	9,261,1933	96	95	96		633,606,606	0.8	1	20	dbSNP_129	96	16,8584	11.9+/-42.8	0,16,4284	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPRA	NM_002836.3,NM_080840.2,NM_080841.2	,,	9,277,6217	GG,GC,CC		0.186,6.3323,2.2682	,,	211/803,202/794,202/794	2969015	295,12711	2203	4300	6503	SO:0001819	synonymous_variant	5786	exon13			CAGATCCCCAAGC		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.606C>G	20.37:g.2969015C>G		133	0	0		145	80	0.551724	NM_002836	A8K2G8|D3DVX5|Q14513|Q7Z2I2|Q96TD9	Silent	SNP	ENST00000216877.6	37	CCDS13039.1																																																																																			C|0.977;G|0.023	0.023	strong		0.547	PTPRA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077682.3			G	2969015	C	G	2969015	2	3	22	1	0	0	0	0	0	0	0	1	12810	610	22	4		4	PTPRA	20	2969015	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	386176	2969015	60056505	4124	7025											
SLC4A11	83959	hgsc.bcm.edu	37	chr20	3209254	3209254	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggccatagagcacgggcttGgggatccactgaagcgggac	10	5	16	10	2	0	2	0	1	0	1	1	4	1	4	2	5	2	2	2	5	2	2	rs139086376	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:3209254G>A	ENST00000380056.3	-	17	2387	c.2340C>T	c.(2338-2340)ccC>ccT	p.P780P	SLC4A11_ENST00000488544.1_5'Flank|SLC4A11_ENST00000380059.3_Silent_p.P807P|SLC4A11_ENST00000539553.2_Silent_p.P764P	NM_032034.3	NP_114423.1	Q8NBS3	S4A11_HUMAN	solute carrier family 4, sodium borate transporter, member 11	780	Membrane (bicarbonate transporter).				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						GCACGGGCTTGGGGATCCACT	0.652													G|||	31	0.0061901	0.0219	0.0029	5008	,	,		17235	0.0		0.0	False		,,,				2504	0.0				p.P807P	NSCLC(190;922 2139 10266 10292 38692)	Atlas-SNP	.											.	SLC4A11	188	.	0			c.C2421T						PASS	.	G	,,	78,4328	65.8+/-103.3	0,78,2125	75	69	71		2292,2421,2340	4	1	20	dbSNP_134	71	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC4A11	NM_001174089.1,NM_001174090.1,NM_032034.3	,,	0,79,6424	AA,AG,GG		0.0116,1.7703,0.6074	,,	764/876,807/919,780/892	3209254	79,12927	2203	4300	6503	SO:0001819	synonymous_variant	83959	exon18			GGGCTTGGGGATC	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.2340C>T	20.37:g.3209254G>A		184	0	0		153	72	0.470588	NM_001174090	B4DKC8|B4DKX9|G3V1M3|Q2TB62|Q2TB63|Q9BXF4|Q9NTW9	Silent	SNP	ENST00000380056.3	37	CCDS13052.1																																																																																			G|0.994;A|0.006	0.006	strong		0.652	SLC4A11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077728.1			A	3209254	G	A	3209254	2	1	22	1	0	0	0	0	0	0	0	1	14667	1335	47	2		2	SLC4A11	20	3209254	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	240239	3209254	59816266	4125	7026											
GFRA4	64096	hgsc.bcm.edu	37	chr20	3640568	3640568	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcctaatcagagcagggcCgggagagccaggacaggaag	12	4	16	9	1	1	2	1	0	0	2	2	5	2	4	3	4	2	1	3	4	2	1	rs74740423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:3640568C>T	ENST00000319242.3	-	5	887	c.888G>A	c.(886-888)ccG>ccA	p.P296P	GFRA4_ENST00000290417.2_Silent_p.P266P			Q9GZZ7	GFRA4_HUMAN	GDNF family receptor alpha 4	296					negative regulation of ossification (GO:0030279)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)			large_intestine(1)|lung(2)	3						AGAGCAGGGCCGGGAGAGCCA	0.647													C|||	147	0.029353	0.1051	0.0115	5008	,	,		18655	0.0		0.0	False		,,,				2504	0.0				p.P296P		Atlas-SNP	.											.	GFRA4	10	.	0			c.G888A						PASS	.	C	,	405,3999		13,379,1810	29	30	29		798,888	2.8	0.3	20	dbSNP_131	29	3,8589		0,3,4293	no	coding-synonymous,coding-synonymous	GFRA4	NM_022139.3,NM_145762.2	,	13,382,6103	TT,TC,CC		0.0349,9.1962,3.1394	,	266/270,296/300	3640568	408,12588	2202	4296	6498	SO:0001819	synonymous_variant	64096	exon5			CAGGGCCGGGAGA	AF253318	CCDS13055.1, CCDS13056.1	20p13-p12	2008-07-16			ENSG00000125861	ENSG00000125861			13821	protein-coding gene	gene with protein product	"persephin receptor"					10958791, 15225646	Standard	XM_005260793		Approved		uc002win.3	Q9GZZ7	OTTHUMG00000031748	ENST00000319242.3:c.888G>A	20.37:g.3640568C>T		37	0	0		41	23	0.560976	NM_145762	Q5JT74|Q9H191|Q9H192	Silent	SNP	ENST00000319242.3	37	CCDS13056.1																																																																																			C|0.968;T|0.032	0.032	strong		0.647	GFRA4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077744.1	NM_145762		T	3640568	C	T	3640568	2	4	22	1	0	0	0	0	0	0	0	1	6358	639	23	1		1	GFRA4	20	3640568	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	431314	3640568	59384952	4126	7027											
SIGLEC1	6614	hgsc.bcm.edu	37	chr20	3670646	3670646	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggaggtagaggcagagccCaggacatttgaggcagaaca	13	5	16	7	0	0	4	0	1	0	3	0	6	0	6	1	5	2	3	1	5	2	2	rs8115679	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:3670646C>T	ENST00000344754.4	-	18	4856	c.4857G>A	c.(4855-4857)ctG>ctA	p.L1619L	SIGLEC1_ENST00000202578.4_Silent_p.L1619L	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	1619	Ig-like C2-type 16.				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						AGGCAGAGCCCAGGACATTTG	0.597													C|||	117	0.0233626	0.0862	0.0043	5008	,	,		19707	0.0		0.0	False		,,,				2504	0.0				p.L1619L		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.G4857A						PASS	.	C		310,4094	164.4+/-196.0	11,288,1903	44	38	40		4857	4.6	1	20	dbSNP_116	40	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SIGLEC1	NM_023068.3		11,290,6201	TT,TC,CC		0.0233,7.0391,2.3993		1619/1710	3670646	312,12692	2202	4300	6502	SO:0001819	synonymous_variant	6614	exon18			AGAGCCCAGGACA	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.4857G>A	20.37:g.3670646C>T		178	0	0		178	75	0.421348	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Silent	SNP	ENST00000344754.4	37	CCDS13060.1	33	0.01510989010989011	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	0	0.0	C	8.307	0.821130	0.16678	0.070391	2.33E-4	ENSG00000088827	ENST00000419548	.	.	.	5.55	4.6	0.57074	.	.	.	.	.	T	0.12305	0.0299	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21211	-1.0252	4	.	.	.	.	12.3752	0.55275	0.0:0.8305:0.1695:0.0	rs8115679;rs8115679	.	.	.	R	433	.	.	G	-	1	0	SIGLEC1	3618646	1.000000	0.71417	0.996000	0.52242	0.785000	0.44390	1.377000	0.34317	1.320000	0.45209	0.561000	0.74099	GGG	C|0.974;T|0.026	0.026	strong		0.597	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068		T	3670646	C	T	3670646	2	4	22	1	0	0	0	0	0	0	0	1	14320	581	21	2		2	SIGLEC1	20	3670646	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	30078	3670646	59354874	4127	7028											
SIGLEC1	6614	hgsc.bcm.edu	37	chr20	3672746	3672746	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	accttgccatcatgagatagGgccagctcagcaggtggctc	9	8	12	12	0	2	1	2	1	0	1	3	2	2	1	3	3	3	3	3	3	1	2	rs34921899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:3672746G>A	ENST00000344754.4	-	16	4133	c.4134C>T	c.(4132-4134)gcC>gcT	p.A1378A	SIGLEC1_ENST00000202578.4_Silent_p.A1378A	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	1378	Ig-like C2-type 14.				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						CATGAGATAGGGCCAGCTCAG	0.637													G|||	103	0.0205671	0.0772	0.0014	5008	,	,		19801	0.0		0.0	False		,,,				2504	0.0				p.A1378A		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.C4134T						PASS	.	G		234,4170	138.0+/-173.8	7,220,1975	45	37	40		4134	1.1	0.3	20	dbSNP_126	40	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	SIGLEC1	NM_023068.3		7,224,6271	AA,AG,GG		0.0465,5.3134,1.8302		1378/1710	3672746	238,12766	2202	4300	6502	SO:0001819	synonymous_variant	6614	exon16			AGATAGGGCCAGC	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.4134C>T	20.37:g.3672746G>A		39	0	0		41	22	0.536585	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Silent	SNP	ENST00000344754.4	37	CCDS13060.1	32	0.014652014652014652	31	0.06300813008130081	0	0.0	0	0.0	1	0.0013192612137203166	G	6.234	0.411258	0.11812	0.053134	4.65E-4	ENSG00000088827	ENST00000419548	.	.	.	5.5	1.12	0.20585	.	.	.	.	.	T	0.07098	0.0180	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	T	0.03193	-1.1062	4	.	.	.	.	3.0219	0.06078	0.1405:0.1464:0.5625:0.1506	rs34921899	.	.	.	S	192	.	.	P	-	1	0	SIGLEC1	3620746	0.613000	0.27009	0.313000	0.25210	0.552000	0.35366	0.539000	0.23175	-0.009000	0.14296	0.655000	0.94253	CCT	G|0.979;A|0.021	0.021	strong		0.637	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068		A	3672746	G	A	3672746	2	1	22	1	0	0	0	0	0	0	0	1	14320	1219	43	2		2	SIGLEC1	20	3672746	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2100	3672746	59352774	4128	7029											
SIGLEC1	6614	hgsc.bcm.edu	37	chr20	3674170	3674170	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acaccgcagcggtaggaggtGgcatccctgactgtgacgtt	8	8	14	11	3	0	2	0	2	0	0	1	3	1	3	2	4	1	4	2	4	1	2	rs61734520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:3674170G>A	ENST00000344754.4	-	13	3431	c.3432C>T	c.(3430-3432)gcC>gcT	p.A1144A	SIGLEC1_ENST00000202578.4_Silent_p.A1144A	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	1144	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						GGTAGGAGGTGGCATCCCTGA	0.662													G|||	103	0.0205671	0.0772	0.0014	5008	,	,		15685	0.0		0.0	False		,,,				2504	0.0				p.A1144A		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.C3432T						PASS	.	G		233,4173	136.9+/-172.8	7,219,1977	53	47	49		3432	-3	0.7	20	dbSNP_129	49	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	SIGLEC1	NM_023068.3		7,223,6273	AA,AG,GG		0.0465,5.2882,1.8222		1144/1710	3674170	237,12769	2203	4300	6503	SO:0001819	synonymous_variant	6614	exon13			GGAGGTGGCATCC	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.3432C>T	20.37:g.3674170G>A		130	0	0		119	69	0.579832	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Silent	SNP	ENST00000344754.4	37	CCDS13060.1																																																																																			G|0.980;A|0.020	0.020	strong		0.662	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068		A	3674170	G	A	3674170	2	1	22	1	0	0	0	0	0	0	0	1	14320	1335	47	2		2	SIGLEC1	20	3674170	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1424	3674170	59351350	4129	7030											
C20orf27	54976	hgsc.bcm.edu	37	chr20	3736160	3736160	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggagcttgaggtgcaggctgGggacaggtgcctcgcggaca	7	6	19	9	2	0	1	0	1	0	0	1	4	0	4	1	7	3	3	1	7	0	1	rs140915844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:3736160G>A	ENST00000379772.3	-	4	1067	c.257C>T	c.(256-258)cCc>cTc	p.P86L	C20orf27_ENST00000217195.8_Missense_Mutation_p.P111L	NM_001258429.1	NP_001245358.1	Q9GZN8	CT027_HUMAN	chromosome 20 open reading frame 27	86										central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)|urinary_tract(1)	7						GTGCAGGCTGGGGACAGGTGC	0.617													G|||	7	0.00139776	0.0053	0.0	5008	,	,		20807	0.0		0.0	False		,,,				2504	0.0				p.P111L		Atlas-SNP	.											.	C20orf27	17	.	0			c.C332T						PASS	.	G	LEU/PRO	20,4386	27.2+/-55.0	0,20,2183	80	64	69		332	3.2	1	20	dbSNP_134	69	0,8600		0,0,4300	yes	missense	C20orf27	NM_001039140.1	98	0,20,6483	AA,AG,GG		0.0,0.4539,0.1538	benign	111/200	3736160	20,12986	2203	4300	6503	SO:0001583	missense	54976	exon4			AGGCTGGGGACAG	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.257C>T	20.37:g.3736160G>A	ENSP00000369097:p.Pro86Leu	48	0	0		65	27	0.415385	NM_001039140	A8K4J0|D3DVX8|Q5JX81|Q9NWX3	Missense_Mutation	SNP	ENST00000379772.3	37	CCDS58763.1	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	16.38|16.38	3.108437|3.108437	0.56291|0.56291	0.004539|0.004539	0.0|0.0	ENSG00000101220|ENSG00000101220	ENST00000379772;ENST00000217195;ENST00000399672;ENST00000379765|ENST00000399683	.|.	.|.	.|.	4.15|4.15	3.17|3.17	0.36434|0.36434	.|.	0.139643|0.139643	0.48286|0.48286	U|N	0.000198|0.000198	T|T	0.67915|0.67915	0.2944|0.2944	M|M	0.74881|0.74881	2.28|2.28	0.80722|0.80722	D|D	1|1	B;B;D|.	0.57257|.	0.001;0.435;0.979|.	B;B;P|.	0.59487|.	0.003;0.215;0.858|.	T|T	0.64179|0.64179	-0.6468|-0.6468	9|7	0.72032|0.19147	D|T	0.01|0.46	-3.9217|-3.9217	11.1696|11.1696	0.48563|0.48563	0.0:0.0:0.8075:0.1925|0.0:0.0:0.8075:0.1925	.|.	86;111;86|.	Q9GZN8;Q9GZN8-2;E9PAL2|.	CT027_HUMAN;.;.|.	L|S	86;111;86;86|80	.|.	ENSP00000217195:P111L|ENSP00000382591:P80S	P|P	-|-	2|1	0|0	C20orf27|C20orf27	3684160|3684160	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.901000|0.901000	0.52897|0.52897	4.963000|4.963000	0.63694|0.63694	1.297000|1.297000	0.44761|0.44761	0.561000|0.561000	0.74099|0.74099	CCC|CCA	G|0.999;A|0.001	0.001	strong		0.617	C20orf27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077750.2	NM_001039140		A	3736160	G	A	3736160	3	1	22	1	0	0	0	0	1	0	0	0	2109	1232	43	2	279	2	C20orf27	20	3736160	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	61990	3736160	59289360	4130	7031											
PROKR2	128674	hgsc.bcm.edu	37	chr20	5283051	5283051	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcggcagcgcagccgcttgcGaatctgctccgtctggaacc	6	7	13	15	5	2	0	0	0	2	0	3	2	3	1	3	2	5	4	3	2	2	1	rs148868355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:5283051G>A	ENST00000217270.3	-	2	789	c.790C>T	c.(790-792)Cgc>Tgc	p.R264C	PROKR2_ENST00000546004.1_Missense_Mutation_p.R264C	NM_144773.2	NP_658986.1	Q8NFJ6	PKR2_HUMAN	prokineticin receptor 2	264					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						AGCCGCTTGCGAATCTGCTCC	0.612										HNSCC(71;0.22)			G|||	4	0.000798722	0.003	0.0	5008	,	,		20081	0.0		0.0	False		,,,				2504	0.0				p.R264C		Atlas-SNP	.											.	PROKR2	90	.	0			c.C790T						PASS	.	G	CYS/ARG	8,4398	14.3+/-33.2	0,8,2195	53	49	50		790	5.1	1	20	dbSNP_134	50	0,8600		0,0,4300	yes	missense	PROKR2	NM_144773.2	180	0,8,6495	AA,AG,GG		0.0,0.1816,0.0615	probably-damaging	264/385	5283051	8,12998	2203	4300	6503	SO:0001583	missense	128674	exon2			GCTTGCGAATCTG	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.790C>T	20.37:g.5283051G>A	ENSP00000217270:p.Arg264Cys	74	0	0		78	37	0.474359	NM_144773	A5JUU1|Q2M3C0|Q5TDY1|Q9NTT0	Missense_Mutation	SNP	ENST00000217270.3	37	CCDS13089.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	17.99	3.522846	0.64747	0.001816	0.0	ENSG00000101292	ENST00000546004;ENST00000217270	T;T	0.38401	1.14;1.14	5.05	5.05	0.67936	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.64713	0.2623	M	0.84585	2.705	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.71069	-0.4699	10	0.72032	D	0.01	.	15.9064	0.79433	0.0:0.0:1.0:0.0	.	264	Q8NFJ6	PKR2_HUMAN	C	264	ENSP00000440790:R264C;ENSP00000217270:R264C	ENSP00000217270:R264C	R	-	1	0	PROKR2	5231051	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	2.754000	0.47532	2.370000	0.80446	0.655000	0.94253	CGC	G|0.999;A|0.001	0.001	strong		0.612	PROKR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077854.1	NM_144773		A	5283051	G	A	5283051	3	1	22	1	0	0	0	0	1	0	0	0	12565	1058	37	1	367	1	PROKR2	20	5283051	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1546891	5283051	57742469	4131	7032											
MCM8	84515	hgsc.bcm.edu	37	chr20	5935303	5935303	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagattcaagcatttgaaaaAtttttcacaaggcatattga	17	13	6	5	0	2	3	2	2	0	1	2	3	2	3	0	1	1	2	0	1	6	6	rs6117014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:5935303A>C	ENST00000378896.3	+	4	680	c.303A>C	c.(301-303)aaA>aaC	p.K101N	MCM8_ENST00000378886.2_Missense_Mutation_p.K101N|MCM8_ENST00000265187.4_Missense_Mutation_p.K101N|MCM8_ENST00000378883.1_Missense_Mutation_p.K101N	NM_001281520.1|NM_032485.4|NM_182802.1	NP_001268449.1|NP_115874.3|NP_877954.1	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	101			K -> N (in dbSNP:rs6117014).		cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)|G1/S transition of mitotic cell cycle (GO:0000082)|male gamete generation (GO:0048232)|mitotic cell cycle (GO:0000278)	MCM8-MCM9 complex (GO:0097362)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	23						CATTTGAAAAATTTTTCACAA	0.373													A|||	351	0.0700879	0.1626	0.1009	5008	,	,		19997	0.001		0.0199	False		,,,				2504	0.046				p.K101N		Atlas-SNP	.											.	MCM8	125	.	0			c.A303C						PASS	.	A	ASN/LYS,ASN/LYS	652,3750	276.0+/-272.9	51,550,1600	101	97	98		303,303	-10.4	0.5	20	dbSNP_114	98	183,8417	83.1+/-145.7	2,179,4119	yes	missense,missense	MCM8	NM_032485.4,NM_182802.1	94,94	53,729,5719	CC,CA,AA		2.1279,14.8114,6.4221	benign,benign	101/841,101/825	5935303	835,12167	2201	4300	6501	SO:0001583	missense	84515	exon4			TGAAAAATTTTTC	AJ439063	CCDS13094.1, CCDS13095.1, CCDS63226.1, CCDS63227.1	20p12.3	2007-04-04	2007-04-04	2003-07-09	ENSG00000125885	ENSG00000125885			16147	protein-coding gene	gene with protein product	"REC homolog (Drosophila)"	608187	"chromosome 20 open reading frame 154"	C20orf154		12527764	Standard	NM_032485		Approved	MGC4816, MGC12866, MGC119522, MGC119523, dJ967N21.5, REC	uc002wmi.3	Q9UJA3	OTTHUMG00000031822	ENST00000378896.3:c.303A>C	20.37:g.5935303A>C	ENSP00000368174:p.Lys101Asn	94	0	0		103	50	0.485437	NM_032485	B2RBG7|D3DW08|E7EQU7|Q495R4|Q495R6|Q495R7|Q86US4|Q969I5	Missense_Mutation	SNP	ENST00000378896.3	37	CCDS13094.1	145	0.06639194139194139	92	0.18699186991869918	29	0.08011049723756906	2	0.0034965034965034965	22	0.029023746701846966	A	11.02	1.515159	0.27123	0.148114	0.021279	ENSG00000125885	ENST00000378896;ENST00000378883;ENST00000399350;ENST00000378886;ENST00000265187	T;T;T;T	0.04119	3.7;3.7;3.7;3.7	5.37	-10.4	0.00318	Nucleic acid-binding, OB-fold-like (1);	0.302307	0.39475	N	0.001357	T	0.00012	0.0000	L	0.29908	0.895	0.27511	P	0.9516967	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.001;0.002;0.001	T	0.38265	-0.9669	9	0.11485	T	0.65	-1.2423	2.7834	0.05367	0.2356:0.137:0.3949:0.2325	rs6117014;rs52802444;rs6117014	101;101;101;101	Q9UJA3-2;E7EQU7;Q9UJA3-3;Q9UJA3	.;.;.;MCM8_HUMAN	N	101	ENSP00000368174:K101N;ENSP00000368161:K101N;ENSP00000368164:K101N;ENSP00000265187:K101N	ENSP00000265187:K101N	K	+	3	2	MCM8	5883303	0.041000	0.20044	0.522000	0.27862	0.993000	0.82548	-1.262000	0.02852	-1.754000	0.01321	-0.250000	0.11733	AAA	A|0.936;C|0.064	0.064	strong		0.373	MCM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077900.1	NM_032485		C	5935303	A	C	5935303	3	2	22	1	0	0	0	0	1	0	0	0	9402	98	4	5	313	5	MCM8	20	5935303	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	652252	5935303	57090217	4132	7033											
MCM8	84515	hgsc.bcm.edu	37	chr20	5943985	5943985	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agctctcctctcacagttacGatggactggcagtcaatcaa	11	10	8	12	1	4	0	3	0	2	0	6	2	4	1	1	2	2	3	1	2	3	1	rs35102646	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:5943985G>A	ENST00000378896.3	+	8	1232	c.855G>A	c.(853-855)acG>acA	p.T285T	Y_RNA_ENST00000384650.1_RNA|MCM8_ENST00000378886.2_Silent_p.T285T|MCM8_ENST00000265187.4_Silent_p.T285T|MCM8_ENST00000378883.1_Silent_p.T285T	NM_001281520.1|NM_032485.4|NM_182802.1	NP_001268449.1|NP_115874.3|NP_877954.1	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	285					cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)|G1/S transition of mitotic cell cycle (GO:0000082)|male gamete generation (GO:0048232)|mitotic cell cycle (GO:0000278)	MCM8-MCM9 complex (GO:0097362)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	23						TCACAGTTACGATGGACTGGC	0.408													A|||	49	0.00978435	0.0363	0.0014	5008	,	,		16509	0.0		0.0	False		,,,				2504	0.0				p.T285T		Atlas-SNP	.											.	MCM8	125	.	0			c.G855A						PASS	.	A	,	87,4319	818.4+/-416.3	0,87,2116	123	107	112		855,855	-8.8	0	20	dbSNP_126	112	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	MCM8	NM_032485.4,NM_182802.1	,	0,87,6416	AA,AG,GG		0.0,1.9746,0.6689	,	285/841,285/825	5943985	87,12919	2203	4300	6503	SO:0001819	synonymous_variant	84515	exon8			AGTTACGATGGAC	AJ439063	CCDS13094.1, CCDS13095.1, CCDS63226.1, CCDS63227.1	20p12.3	2007-04-04	2007-04-04	2003-07-09	ENSG00000125885	ENSG00000125885			16147	protein-coding gene	gene with protein product	"REC homolog (Drosophila)"	608187	"chromosome 20 open reading frame 154"	C20orf154		12527764	Standard	NM_032485		Approved	MGC4816, MGC12866, MGC119522, MGC119523, dJ967N21.5, REC	uc002wmi.3	Q9UJA3	OTTHUMG00000031822	ENST00000378896.3:c.855G>A	20.37:g.5943985G>A		58	0	0		54	23	0.425926	NM_032485	B2RBG7|D3DW08|E7EQU7|Q495R4|Q495R6|Q495R7|Q86US4|Q969I5	Silent	SNP	ENST00000378896.3	37	CCDS13094.1																																																																																			G|0.992;A|0.008	0.008	strong		0.408	MCM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077900.1	NM_032485		A	5943985	G	A	5943985	2	1	22	1	0	0	0	0	0	0	0	1	9402	1045	37	1		1	MCM8	20	5943985	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	8682	5943985	57081535	4133	7034											
MCM8	84515	hgsc.bcm.edu	37	chr20	5974265	5974265	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atttatttctgctctcaacaAcgttgctgaaagaacttata	13	15	5	8	1	2	2	1	1	2	1	3	2	2	2	0	0	5	3	0	0	7	6	rs16991638	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:5974265A>G	ENST00000378896.3	+	18	2731	c.2354A>G	c.(2353-2355)aAc>aGc	p.N785S	MCM8_ENST00000378886.2_Missense_Mutation_p.N825S|MCM8_ENST00000265187.4_Missense_Mutation_p.N769S|MCM8_ENST00000378883.1_Missense_Mutation_p.N738S	NM_001281520.1|NM_032485.4|NM_182802.1	NP_001268449.1|NP_115874.3|NP_877954.1	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	785			N -> S (in dbSNP:rs16991638).		cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)|G1/S transition of mitotic cell cycle (GO:0000082)|male gamete generation (GO:0048232)|mitotic cell cycle (GO:0000278)	MCM8-MCM9 complex (GO:0097362)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	23						GCTCTCAACAACGTTGCTGAA	0.358													A|||	378	0.0754792	0.1853	0.1009	5008	,	,		18096	0.001		0.0199	False		,,,				2504	0.0429				p.N785S		Atlas-SNP	.											.	MCM8	125	.	0			c.A2354G						PASS	.	A	SER/ASN,SER/ASN	703,3703	283.4+/-277.1	58,587,1558	57	62	61		2354,2306	0.4	1	20	dbSNP_123	61	181,8419	82.3+/-144.9	2,177,4121	yes	missense,missense	MCM8	NM_032485.4,NM_182802.1	46,46	60,764,5679	GG,GA,AA		2.1047,15.9555,6.7969	benign,benign	785/841,769/825	5974265	884,12122	2203	4300	6503	SO:0001583	missense	84515	exon18			TCAACAACGTTGC	AJ439063	CCDS13094.1, CCDS13095.1, CCDS63226.1, CCDS63227.1	20p12.3	2007-04-04	2007-04-04	2003-07-09	ENSG00000125885	ENSG00000125885			16147	protein-coding gene	gene with protein product	"REC homolog (Drosophila)"	608187	"chromosome 20 open reading frame 154"	C20orf154		12527764	Standard	NM_032485		Approved	MGC4816, MGC12866, MGC119522, MGC119523, dJ967N21.5, REC	uc002wmi.3	Q9UJA3	OTTHUMG00000031822	ENST00000378896.3:c.2354A>G	20.37:g.5974265A>G	ENSP00000368174:p.Asn785Ser	46	0	0		48	17	0.354167	NM_032485	B2RBG7|D3DW08|E7EQU7|Q495R4|Q495R6|Q495R7|Q86US4|Q969I5	Missense_Mutation	SNP	ENST00000378896.3	37	CCDS13094.1	128	0.05860805860805861	86	0.17479674796747968	26	0.0718232044198895	1	0.0017482517482517483	15	0.01978891820580475	A	9.100	1.003892	0.19199	0.159555	0.021047	ENSG00000125885	ENST00000378896;ENST00000378883;ENST00000378886;ENST00000265187	T;T;T;T	0.02812	4.25;4.15;4.23;4.25	5.82	0.411	0.16392	.	0.769958	0.13000	N	0.421768	T	0.00012	0.0000	N	0.01576	-0.805	0.54753	P	1.3000000000040757E-5	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	0.45056	-0.9287	9	0.17832	T	0.49	-3.3433	6.6121	0.22757	0.2319:0.3374:0.4307:0.0	rs16991638;rs56419414;rs16991638	738;825;769;785	Q9UJA3-2;E7EQU7;Q9UJA3-3;Q9UJA3	.;.;.;MCM8_HUMAN	S	785;738;825;769	ENSP00000368174:N785S;ENSP00000368161:N738S;ENSP00000368164:N825S;ENSP00000265187:N769S	ENSP00000265187:N769S	N	+	2	0	MCM8	5922265	0.001000	0.12720	0.997000	0.53966	0.995000	0.86356	-0.073000	0.11468	0.055000	0.16094	0.533000	0.62120	AAC	A|0.934;G|0.066	0.066	strong		0.358	MCM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077900.1	NM_032485		G	5974265	A	G	5974265	3	3	22	1	0	0	0	0	1	0	0	0	9402	43	2	3	2420	3	MCM8	20	5974265	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	30280	5974265	57051255	4134	7035											
LRRN4	164312	hgsc.bcm.edu	37	chr20	6021703	6021703	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gagccccagcgggtaatcatCaaaggccgggtttttgtagg	9	9	14	9	2	2	0	2	0	0	0	2	1	2	0	3	4	2	3	3	4	3	4	rs116777692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:6021703C>T	ENST00000378858.4	-	5	2412	c.2188G>A	c.(2188-2190)Gat>Aat	p.D730N		NM_152611.4	NP_689824.2	Q8WUT4	LRRN4_HUMAN	leucine rich repeat neuronal 4	730					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						GGGTAATCATCAAAGGCCGGG	0.612													C|||	25	0.00499201	0.0189	0.0	5008	,	,		17219	0.0		0.0	False		,,,				2504	0.0				p.D730N		Atlas-SNP	.											.	LRRN4	54	.	0			c.G2188A						PASS	.	C	ASN/ASP	144,4262	91.6+/-130.3	3,138,2062	37	36	36		2188	2	0	20	dbSNP_132	36	1,8599		0,1,4299	yes	missense	LRRN4	NM_152611.3	23	3,139,6361	TT,TC,CC		0.0116,3.2683,1.1149	benign	730/741	6021703	145,12861	2203	4300	6503	SO:0001583	missense	164312	exon5			AATCATCAAAGGC	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.2188G>A	20.37:g.6021703C>T	ENSP00000368135:p.Asp730Asn	177	0	0		198	78	0.393939	NM_152611	A8K258|Q5JWV6|Q9H419	Missense_Mutation	SNP	ENST00000378858.4	37	CCDS13097.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	13.49	2.252207	0.39797	0.032683	1.16E-4	ENSG00000125872	ENST00000378858	T	0.61392	0.11	3.97	2.01	0.26516	.	0.648332	0.14770	N	0.299431	T	0.16514	0.0397	N	0.19112	0.55	0.09310	N	1	P	0.44877	0.845	B	0.43478	0.421	T	0.07366	-1.0776	10	0.09590	T	0.72	.	8.1533	0.31154	0.0:0.7545:0.1586:0.0869	.	730	Q8WUT4	LRRN4_HUMAN	N	730	ENSP00000368135:D730N	ENSP00000368135:D730N	D	-	1	0	LRRN4	5969703	0.075000	0.21258	0.001000	0.08648	0.305000	0.27757	1.403000	0.34612	0.618000	0.30179	0.655000	0.94253	GAT	C|0.990;T|0.010	0.010	strong		0.612	LRRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077907.2	NM_152611		T	6021703	C	T	6021703	3	4	22	1	0	0	0	0	1	0	0	0	9046	826	29	2	38	2	LRRN4	20	6021703	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	47438	6021703	57003817	4135	7036											
HAO1	54363	hgsc.bcm.edu	37	chr20	7920986	7920986	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcttcatcatttgccccagaCctgtaatagtcatatataga	12	14	5	10	0	4	2	3	0	1	2	4	2	4	2	3	0	1	1	3	0	5	7	rs33931524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:7920986C>T	ENST00000378789.3	-	1	135	c.84G>A	c.(82-84)agG>agA	p.R28R		NM_017545.2	NP_060015.1	Q9UJM8	HAOX1_HUMAN	hydroxyacid oxidase (glycolate oxidase) 1	28	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)			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						TTGCCCCAGACCTGTAATAGT	0.318													C|||	161	0.0321486	0.1082	0.0187	5008	,	,		17203	0.0		0.003	False		,,,				2504	0.002				p.R28R		Atlas-SNP	.											.	HAO1	71	.	0			c.G84A						PASS	.	C		456,3950	215.1+/-234.2	17,422,1764	70	70	70		84	-3.4	0.8	20	dbSNP_126	70	41,8559	25.7+/-73.6	0,41,4259	no	coding-synonymous	HAO1	NM_017545.2		17,463,6023	TT,TC,CC		0.4767,10.3495,3.8213		28/371	7920986	497,12509	2203	4300	6503	SO:0001819	synonymous_variant	54363	exon1			CCCAGACCTGTAA	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.84G>A	20.37:g.7920986C>T		100	0	0		98	53	0.540816	NM_017545	Q14CQ0|Q9UPZ0|Q9Y3I7	Silent	SNP	ENST00000378789.3	37	CCDS13100.1																																																																																			C|0.966;T|0.034	0.034	strong		0.318	HAO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077926.2			T	7920986	C	T	7920986	2	4	22	1	0	0	0	0	0	0	0	1	6960	506	18	2		2	HAO1	20	7920986	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1899283	7920986	55104534	4136	7037											
JAG1	182	hgsc.bcm.edu	37	chr20	10624502	10624502	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tctccatccacacaggtgccGctgttgtaactaagaaagca	12	9	8	12	1	1	1	0	0	1	1	3	1	2	1	3	1	3	4	3	1	3	3	rs56225585	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:10624502G>A	ENST00000254958.5	-	20	2897	c.2382C>T	c.(2380-2382)agC>agT	p.S794S	JAG1_ENST00000488480.1_RNA|JAG1_ENST00000423891.2_Silent_p.S635S	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	794	EGF-like 15; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				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						CACAGGTGCCGCTGTTGTAAC	0.522									Alagille Syndrome				G|||	475	0.0948482	0.3396	0.0375	5008	,	,		16433	0.0		0.0	False		,,,				2504	0.0				p.S794S		Atlas-SNP	.											.	JAG1	213	.	0			c.C2382T						PASS	.	G		1227,3179	422.3+/-339.7	166,895,1142	72	60	64		2382	-5.8	0.8	20	dbSNP_129	64	22,8578	15.3+/-51.7	0,22,4278	no	coding-synonymous	JAG1	NM_000214.2		166,917,5420	AA,AG,GG		0.2558,27.8484,9.6033		794/1219	10624502	1249,11757	2203	4300	6503	SO:0001819	synonymous_variant	182	exon20	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	GGTGCCGCTGTTG	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.2382C>T	20.37:g.10624502G>A		58	0	0		58	58	1	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Silent	SNP	ENST00000254958.5	37	CCDS13112.1																																																																																			G|0.914;A|0.086	0.086	strong		0.522	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214		A	10624502	G	A	10624502	2	1	22	1	0	0	0	0	0	0	0	1	7943	1078	38	1		1	JAG1	20	10624502	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2703516	10624502	52401018	4137	7038											
C20orf7	79133	hgsc.bcm.edu	37	chr20	13797179	13797179	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gacacaatgctggcagctgcGgcagtgtacagaggtaaggg	11	6	16	8	1	0	1	0	0	0	1	0	2	0	1	0	4	4	6	0	4	3	2	rs34901599	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:13797179G>A	ENST00000378106.5	+	9	968	c.849G>A	c.(847-849)gcG>gcA	p.A283A	NDUFAF5_ENST00000463598.1_Silent_p.A255A|NDUFAF5_ENST00000475968.1_3'UTR	NM_024120.4	NP_077025.2	Q5TEU4	NDUF5_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 5	283					mitochondrial respiratory chain complex I assembly (GO:0032981)	extrinsic component of mitochondrial inner membrane (GO:0031314)	methyltransferase activity (GO:0008168)										TGGCAGCTGCGGCAGTGTACA	0.493													G|||	228	0.0455272	0.1619	0.0101	5008	,	,		17420	0.0		0.007	False		,,,				2504	0.0				p.A283A		Atlas-SNP	.											.	.	.	.	0			c.G849A						PASS	.	G	,	560,3846	249.0+/-256.6	25,510,1668	114	98	104		765,849	-11.2	0	20	dbSNP_126	104	10,8590	6.4+/-24.3	0,10,4290	no	coding-synonymous,coding-synonymous	C20orf7	NM_001039375.2,NM_024120.4	,	25,520,5958	AA,AG,GG		0.1163,12.7099,4.3826	,	255/318,283/346	13797179	570,12436	2203	4300	6503	SO:0001819	synonymous_variant	79133	exon9			AGCTGCGGCAGTG		CCDS13118.1, CCDS33441.1	20p12.1	2012-10-12	2012-05-08	2012-05-08	ENSG00000101247	ENSG00000101247		"Mitochondrial respiratory chain complex assembly factors"	15899	protein-coding gene	gene with protein product		612360	"chromosome 20 open reading frame 7"	C20orf7		18940309, 21607760	Standard	NM_024120		Approved	dJ842G6.1	uc002wom.3	Q5TEU4	OTTHUMG00000031909	ENST00000378106.5:c.849G>A	20.37:g.13797179G>A		108	0	0		94	45	0.478723	NM_024120	A8K166|Q6GPH3|Q9H6F4	Silent	SNP	ENST00000378106.5	37	CCDS13118.1																																																																																			G|0.960;A|0.040	0.040	strong		0.493	NDUFAF5-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078057.2	NM_001039375		A	13797179	G	A	13797179	2	1	22	1	0	0	0	0	0	0	0	1	2117	1103	39	1		1	C20orf7	20	13797179	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3172677	13797179	49228341	4138	7039											
KIF16B	55614	hgsc.bcm.edu	37	chr20	16492163	16492163	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcacacgttcgttataaatTtctaagtagctaaaaattta	15	15	4	7	2	2	0	1	0	1	0	3	0	2	0	0	0	1	4	0	0	9	9	rs16997775	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:16492163T>C	ENST00000354981.2	-	6	613	c.456A>G	c.(454-456)gaA>gaG	p.E152E	KIF16B_ENST00000378003.2_5'UTR|KIF16B_ENST00000355755.3_Silent_p.E152E|KIF16B_ENST00000408042.1_Silent_p.E152E	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	152	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				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						CGTTATAAATTTCTAAGTAGC	0.353													T|||	114	0.0227636	0.084	0.0029	5008	,	,		17037	0.0		0.001	False		,,,				2504	0.0				p.E152E		Atlas-SNP	.											.	KIF16B	305	.	0			c.A456G						PASS	.	T	,,	254,4152	141.9+/-177.2	7,240,1956	43	43	43		456,456,456	3.2	1	20	dbSNP_123	43	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	KIF16B	NM_001199865.1,NM_001199866.1,NM_024704.4	,,	7,241,6255	CC,CT,TT		0.0116,5.7649,1.9606	,,	152/1267,152/1393,152/1318	16492163	255,12751	2203	4300	6503	SO:0001819	synonymous_variant	55614	exon6			ATAAATTTCTAAG	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.456A>G	20.37:g.16492163T>C		40	0	0		50	21	0.42	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	37	CCDS13122.1																																																																																			T|0.978;C|0.022	0.022	strong		0.353	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683		C	16492163	T	C	16492163	2	2	22	1	0	0	0	0	0	0	0	1	8287	1838	64	3		3	KIF16B	20	16492163	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	2694984	16492163	46533357	4139	7040											
SNX5	27131	hgsc.bcm.edu	37	chr20	17923043	17923043	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atacagctctgcaaaagggaGacattgttctgtggggaaaa	14	9	12	6	0	2	1	0	0	2	1	2	3	2	2	0	3	3	3	0	3	5	3	rs17349809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:17923043G>A	ENST00000377768.3	-	14	1485	c.1173C>T	c.(1171-1173)gtC>gtT	p.V391V	SNX5_ENST00000377759.4_Silent_p.V391V|SNX5_ENST00000483485.1_5'UTR	NM_152227.1	NP_689413.1	Q9Y5X3	SNX5_HUMAN	sorting nexin 5	391	BAR.				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						GCAAAAGGGAGACATTGTTCT	0.408													G|||	148	0.0295527	0.1097	0.0014	5008	,	,		18450	0.0		0.001	False		,,,				2504	0.001				p.V391V		Atlas-SNP	.											.	SNX5	38	.	0			c.C1173T						PASS	.	G	,	452,3954	217.8+/-236.0	19,414,1770	111	101	105		1173,1173	1	1	20	dbSNP_123	105	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous	SNX5	NM_014426.2,NM_152227.1	,	19,418,6066	AA,AG,GG		0.0465,10.2587,3.5061	,	391/405,391/405	17923043	456,12550	2203	4300	6503	SO:0001819	synonymous_variant	27131	exon13			AAGGGAGACATTG	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	ENST00000377768.3:c.1173C>T	20.37:g.17923043G>A		123	0	0		125	66	0.528	NM_014426	B7ZKN3|D3DW26|Q52LC4|Q7KZN0|Q9BWP0	Silent	SNP	ENST00000377768.3	37	CCDS13130.1																																																																																			G|1.000;|0.000	.	weak		0.408	SNX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078137.4			A	17923043	G	A	17923043	2	1	22	1	0	0	0	0	0	0	0	1	14920	929	33	2		2	SNX5	20	17923043	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1430880	17923043	45102477	4140	7041											
CRNKL1	51340	hgsc.bcm.edu	37	chr20	20033194	20033194	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggctgcgcgtcctccttGcggcagcgcgtggagtgcgg	3	7	17	14	6	0	0	0	0	0	0	2	1	2	1	3	4	4	2	3	4	0	1	rs145198573	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:20033194G>T	ENST00000377340.2	-	2	307	c.276C>A	c.(274-276)cgC>cgA	p.R92R	CRNKL1_ENST00000377327.4_Silent_p.R80R|CRNKL1_ENST00000536226.1_5'Flank|C20orf26_ENST00000377309.2_5'UTR|C20orf26_ENST00000377306.1_5'Flank|C20orf26_ENST00000245957.5_5'Flank|C20orf26_ENST00000389656.3_5'UTR	NM_001278628.1|NM_016652.4	NP_001265557.1|NP_057736.4	Q9BZJ0	CRNL1_HUMAN	crooked neck pre-mRNA splicing factor 1	92					mRNA splicing, via spliceosome (GO:0000398)|spliceosomal complex assembly (GO:0000245)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|cervix(2)|endometrium(7)|large_intestine(11)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(6)	45						CGTCCTCCTTGCGGCAGCGCG	0.662													G|||	20	0.00399361	0.0151	0.0	5008	,	,		18175	0.0		0.0	False		,,,				2504	0.0				p.R92R		Atlas-SNP	.											.	CRNKL1	101	.	0			c.C276A						PASS	.	G	,	67,4339	60.5+/-97.4	0,67,2136	51	47	48		,276	-2.9	0	20	dbSNP_134	48	2,8598	1.2+/-3.3	0,2,4298	no	utr-5,coding-synonymous	C20orf26,CRNKL1	NM_015585.3,NM_016652.4	,	0,69,6434	TT,TG,GG		0.0233,1.5207,0.5305	,	,92/849	20033194	69,12937	2203	4300	6503	SO:0001819	synonymous_variant	51340	exon2			CTCCTTGCGGCAG	AF255443	CCDS33446.1, CCDS63238.1, CCDS63239.1	20p11.2	2013-10-03	2013-10-03		ENSG00000101343	ENSG00000101343			15762	protein-coding gene	gene with protein product	"SYF3 pre-mRNA-splicing factor"	610952	"crooked neck (Drosophila Crn homolog)-like 1", "Crn, crooked neck-like 1 (Drosophila)", "crooked neck pre-mRNA splicing factor-like 1 (Drosophila)"				Standard	NM_016652		Approved	CRN, CLF, SYF3, Clf1	uc002wrs.3	Q9BZJ0	OTTHUMG00000032000	ENST00000377340.2:c.276C>A	20.37:g.20033194G>T		68	0	0		76	37	0.486842	NM_016652	A8K9T4|Q5JY64|Q8WYI5|Q9BZI9|Q9BZJ1|Q9BZJ2|Q9GZW7|Q9H8F8|Q9NQH5|Q9NYD8	Silent	SNP	ENST00000377340.2	37	CCDS33446.1																																																																																			G|0.996;T|0.004	0.004	strong		0.662	CRNKL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000127787.1			T	20033194	G	T	20033194	2	4	22	1	0	0	0	0	0	0	0	1	3893	1306	46	4		4	CRNKL1	20	20033194	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2110151	20033194	42992326	4141	7042											
C20orf26	26074	hgsc.bcm.edu	37	chr20	20340872	20340872	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaggaagatcttccttccAtagagcagttagcccatcaa	13	9	9	10	0	2	2	1	0	1	2	4	4	4	4	3	2	2	2	3	2	4	4	rs75487354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:20340872A>G	ENST00000245957.5	+	27	3608	c.3532A>G	c.(3532-3534)Ata>Gta	p.I1178V	C20orf26_ENST00000377309.2_3'UTR	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		1178										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)		TCTTCCTTCCATAGAGCAGTT	0.418											OREG0025807	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	a|||	68	0.0135783	0.0507	0.0014	5008	,	,		18359	0.0		0.0	False		,,,				2504	0.0				p.I1178V		Atlas-SNP	.											.	C20orf26	188	.	0			c.A3532G						PASS	.		VAL/ILE	217,4189	131.4+/-167.9	6,205,1992	144	155	151		3532	0.1	0.7	20	dbSNP_131	151	5,8595	3.7+/-12.6	0,5,4295	yes	missense	C20orf26	NM_015585.3	29	6,210,6287	GG,GA,AA		0.0581,4.9251,1.7069	benign	1178/1238	20340872	222,12784	2203	4300	6503	SO:0001583	missense	26074	exon27			CCTTCCATAGAGC																												ENST00000245957.5:c.3532A>G	20.37:g.20340872A>G	ENSP00000245957:p.Ile1178Val	63	0	0	740	62	29	0.467742	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Missense_Mutation	SNP	ENST00000245957.5	37	CCDS33447.1	17	0.007783882783882784	17	0.034552845528455285	0	0.0	0	0.0	0	0.0	a	7.203	0.593934	0.13875	0.049251	5.81E-4	ENSG00000089101	ENST00000343997;ENST00000389655;ENST00000245957	T	0.09255	3.0	5.09	0.0811	0.14423	.	0.335985	0.22190	N	0.063396	T	0.00695	0.0023	N	0.19112	0.55	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.48043	-0.9069	10	0.17369	T	0.5	.	2.2354	0.04007	0.5253:0.1361:0.0764:0.2623	.	1178	Q8NHU2	CT026_HUMAN	V	1118;1144;1178	ENSP00000245957:I1178V	ENSP00000245957:I1178V	I	+	1	0	C20orf26	20288872	0.027000	0.19231	0.727000	0.30756	0.085000	0.17905	-0.093000	0.11111	0.028000	0.15324	0.441000	0.28932	ATA	A|0.984;G|0.016	0.016	strong		0.418	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3			G	20340872	A	G	20340872	3	3	22	1	0	0	0	0	1	0	0	0	2108	217	8	3	3666	3	C20orf26	20	20340872	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	307678	20340872	42684648	4142	7043											
FOXA2	3170	hgsc.bcm.edu	37	chr20	22563134	22563134	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaggtagcagccgttctcgAacatgttgcccgagtcaggg	8	8	14	11	3	2	0	1	0	1	0	3	2	2	0	2	2	4	5	2	2	2	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:22563134A>G	ENST00000377115.4	-	3	909	c.728T>C	c.(727-729)tTc>tCc	p.F243S	FOXA2_ENST00000419308.2_Missense_Mutation_p.F249S	NM_153675.2	NP_710141.1	Q9Y261	FOXA2_HUMAN	forkhead box A2	243					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)					GCCGTTCTCGAACATGTTGCC	0.662																																					p.F249S		Atlas-SNP	.											.	FOXA2	48	.	0			c.T746C						PASS	.						19	22	21					20																	22563134		2203	4300	6503	SO:0001583	missense	3170	exon2			TTCTCGAACATGT	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.728T>C	20.37:g.22563134A>G	ENSP00000366319:p.Phe243Ser	107	0	0		110	38	0.345455	NM_021784	Q8WUW4|Q96DF7	Missense_Mutation	SNP	ENST00000377115.4	37	CCDS13147.1	.	.	.	.	.	.	.	.	.	.	A	19.21	3.784481	0.70222	.	.	ENSG00000125798	ENST00000377115;ENST00000419308;ENST00000319993;ENST00000444877	D;D;D	0.96073	-3.9;-3.9;-3.9	4.98	3.87	0.44632	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.64402	U	0.000006	D	0.97629	0.9223	M	0.88512	2.96	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.994;0.996	D	0.97315	0.9940	10	0.87932	D	0	.	10.4372	0.44443	0.9206:0.0:0.0794:0.0	.	243;249	Q9Y261;B0ZTD4	FOXA2_HUMAN;.	S	243;243;249;129	ENSP00000366319:F243S;ENSP00000400341:F243S;ENSP00000315955:F249S	ENSP00000315955:F249S	F	-	2	0	FOXA2	22511134	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.437000	0.80417	0.723000	0.32274	0.468000	0.43344	TTC	.	.	none		0.662	FOXA2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078289.1			G	22563134	A	G	22563134	3	3	22	1	0	0	0	0	1	0	0	0	5998	246	9	3	649	3	FOXA2	20	22563134	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2222262	22563134	40462386	4143	7044											
THBD	7056	hgsc.bcm.edu	37	chr20	23029971	23029971	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gagcgcactgtcattaggtgGccccgcagtccgtcgcagat	7	8	13	13	4	1	1	1	0	0	1	3	2	2	1	3	2	1	3	3	2	1	1	rs201268201	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:23029971G>T	ENST00000377103.2	-	1	407	c.171C>A	c.(169-171)ggC>ggA	p.G57G		NM_000361.2	NP_000352.1	P07204	TRBM_HUMAN	thrombomodulin	57	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)	TCATTAGGTGGCCCCGCAGTC	0.677													G|||	2	0.000399361	0.0015	0.0	5008	,	,		11359	0.0		0.0	False		,,,				2504	0.0				p.G57G		Atlas-SNP	.											.	THBD	26	.	0			c.C171A						PASS	.	G		3,4261		0,3,2129	8	9	9		171	1.3	1	20		9	0,8380		0,0,4190	no	coding-synonymous	THBD	NM_000361.2		0,3,6319	TT,TG,GG		0.0,0.0704,0.0237		57/576	23029971	3,12641	2132	4190	6322	SO:0001819	synonymous_variant	7056	exon1			TAGGTGGCCCCGC		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.171C>A	20.37:g.23029971G>T		32	0	0		40	30	0.75	NM_000361	Q8IV29|Q9UC32	Silent	SNP	ENST00000377103.2	37	CCDS13148.1																																																																																			G|0.999;T|0.001	0.001	strong		0.677	THBD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078307.2			T	23029971	G	T	23029971	2	4	22	1	0	0	0	0	0	0	0	1	15867	1190	42	4		4	THBD	20	23029971	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	466837	23029971	39995549	4144	7045											
CST4	1472	hgsc.bcm.edu	37	chr20	23669488	23669488	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cacgctgtacccactcatcaTtgaggtctgcatcatagatg	10	11	8	12	1	4	2	3	1	1	1	4	2	4	2	1	1	2	3	1	1	2	3	rs73902130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:23669488T>C	ENST00000217423.3	-	1	189	c.119A>G	c.(118-120)aAt>aGt	p.N40S		NM_001899.2	NP_001890.1	P01036	CYTS_HUMAN	cystatin S	40					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	16	Lung NSC(19;0.0789)|Colorectal(13;0.0993)|all_lung(19;0.169)					CCACTCATCATTGAGGTCTGC	0.577													.|||	170	0.0339457	0.1225	0.0115	5008	,	,		18118	0.0		0.0	False		,,,				2504	0.0				p.N40S		Atlas-SNP	.											CST4,colon,carcinoma,-1,1	CST4	37	1	0			c.A119G						PASS	.	T	SER/ASN	409,3997	201.1+/-224.2	18,373,1812	145	124	131		119	1	0	20	dbSNP_130	131	3,8597	2.2+/-6.3	0,3,4297	yes	missense	CST4	NM_001899.2	46	18,376,6109	CC,CT,TT		0.0349,9.2828,3.1678	benign	40/142	23669488	412,12594	2203	4300	6503	SO:0001583	missense	1472	exon1			TCATCATTGAGGT		CCDS13159.1	20p11.2	2008-04-15			ENSG00000101441	ENSG00000101441			2476	protein-coding gene	gene with protein product		123857				1801729	Standard	NM_001899		Approved		uc002wto.1	P01036	OTTHUMG00000032083	ENST00000217423.3:c.119A>G	20.37:g.23669488T>C	ENSP00000217423:p.Asn40Ser	217	0	0		274	144	0.525547	NM_001899	Q9UBI5|Q9UCS9	Missense_Mutation	SNP	ENST00000217423.3	37	CCDS13159.1	58	0.026556776556776556	51	0.10365853658536585	7	0.019337016574585635	0	0.0	0	0.0	T	5.380	0.255435	0.10185	0.092828	3.49E-4	ENSG00000101441	ENST00000217423	T	0.15256	2.44	2.19	1.01	0.19927	Proteinase inhibitor I25, cystatin (2);	0.362807	0.27236	N	0.020294	T	0.00241	0.0007	N	0.26042	0.785	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.36286	-0.9754	10	0.20519	T	0.43	.	4.081	0.09925	0.0:0.1933:0.0:0.8067	.	40	P01036	CYTS_HUMAN	S	40	ENSP00000217423:N40S	ENSP00000217423:N40S	N	-	2	0	CST4	23617488	0.000000	0.05858	0.001000	0.08648	0.015000	0.08874	0.251000	0.18257	0.094000	0.17404	0.358000	0.22013	AAT	T|0.964;C|0.036	0.036	strong		0.577	CST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078349.2	NM_001899		C	23669488	T	C	23669488	3	2	22	1	0	0	0	0	1	0	0	0	3976	1493	52	3	318	3	CST4	20	23669488	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	639517	23669488	39356032	4145	7046											
CST4	1472	hgsc.bcm.edu	37	chr20	23669584	23669584	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtagccatcaggagtagcAgggtacacagaggccgggcc	10	4	17	10	1	1	1	1	0	0	1	1	2	1	2	3	5	3	4	3	5	3	3	rs73902131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:23669584A>T	ENST00000217423.3	-	1	93	c.23T>A	c.(22-24)cTg>cAg	p.L8Q		NM_001899.2	NP_001890.1	P01036	CYTS_HUMAN	cystatin S	8					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	16	Lung NSC(19;0.0789)|Colorectal(13;0.0993)|all_lung(19;0.169)					CAGGAGTAGCAGGGTACACAG	0.602													.|||	170	0.0339457	0.1225	0.0115	5008	,	,		15657	0.0		0.0	False		,,,				2504	0.0				p.L8Q		Atlas-SNP	.											.	CST4	37	.	0			c.T23A						PASS	.	A	GLN/LEU	411,3995	201.5+/-224.5	18,375,1810	53	52	52		23	0.4	0	20	dbSNP_130	52	3,8597	2.2+/-6.3	0,3,4297	yes	missense	CST4	NM_001899.2	113	18,378,6107	TT,TA,AA		0.0349,9.3282,3.1831	possibly-damaging	8/142	23669584	414,12592	2203	4300	6503	SO:0001583	missense	1472	exon1			AGTAGCAGGGTAC		CCDS13159.1	20p11.2	2008-04-15			ENSG00000101441	ENSG00000101441			2476	protein-coding gene	gene with protein product		123857				1801729	Standard	NM_001899		Approved		uc002wto.1	P01036	OTTHUMG00000032083	ENST00000217423.3:c.23T>A	20.37:g.23669584A>T	ENSP00000217423:p.Leu8Gln	102	0	0		122	48	0.393443	NM_001899	Q9UBI5|Q9UCS9	Missense_Mutation	SNP	ENST00000217423.3	37	CCDS13159.1	58	0.026556776556776556	51	0.10365853658536585	7	0.019337016574585635	0	0.0	0	0.0	A	2.719	-0.266983	0.05754	0.093282	3.49E-4	ENSG00000101441	ENST00000217423	T	0.08458	3.09	1.45	0.431	0.16523	.	1.397050	0.04408	N	0.365592	T	0.00109	0.0003	N	0.08118	0	0.09310	N	1	P	0.50156	0.932	B	0.34991	0.193	T	0.28522	-1.0041	10	0.54805	T	0.06	.	3.6086	0.08052	0.2712:0.0:0.7288:0.0	.	8	P01036	CYTS_HUMAN	Q	8	ENSP00000217423:L8Q	ENSP00000217423:L8Q	L	-	2	0	CST4	23617584	0.005000	0.15991	0.001000	0.08648	0.003000	0.03518	1.018000	0.30002	0.157000	0.19338	-0.483000	0.04790	CTG	A|0.964;T|0.036	0.036	strong		0.602	CST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078349.2	NM_001899		T	23669584	A	T	23669584	3	4	22	1	0	0	0	0	1	0	0	0	3976	188	7	5	414	5	CST4	20	23669584	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	96	23669584	39355936	4146	7047											
CST4	1472	hgsc.bcm.edu	37	chr20	23669598	23669598	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	agtagcagggtacacagaggCcgggccatggtctcctcaga	10	6	14	11	1	2	2	1	0	1	2	3	2	2	2	3	4	2	3	3	4	2	2	rs73902132	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:23669598C>T	ENST00000217423.3	-	1	79	c.9G>A	c.(7-9)cgG>cgA	p.R3R		NM_001899.2	NP_001890.1	P01036	CYTS_HUMAN	cystatin S	3					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	16	Lung NSC(19;0.0789)|Colorectal(13;0.0993)|all_lung(19;0.169)					TACACAGAGGCCGGGCCATGG	0.617													.|||	170	0.0339457	0.1225	0.0115	5008	,	,		15350	0.0		0.0	False		,,,				2504	0.0				p.R3R		Atlas-SNP	.											.	CST4	37	.	0			c.G9A						PASS	.	C		418,3988	202.5+/-225.2	18,382,1803	44	44	44		9	-0.2	0	20	dbSNP_130	44	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	CST4	NM_001899.2		18,385,6100	TT,TC,CC		0.0349,9.4871,3.237		3/142	23669598	421,12585	2203	4300	6503	SO:0001819	synonymous_variant	1472	exon1			CAGAGGCCGGGCC		CCDS13159.1	20p11.2	2008-04-15			ENSG00000101441	ENSG00000101441			2476	protein-coding gene	gene with protein product		123857				1801729	Standard	NM_001899		Approved		uc002wto.1	P01036	OTTHUMG00000032083	ENST00000217423.3:c.9G>A	20.37:g.23669598C>T		93	0	0		109	40	0.366972	NM_001899	Q9UBI5|Q9UCS9	Silent	SNP	ENST00000217423.3	37	CCDS13159.1																																																																																			C|0.964;T|0.036	0.036	strong		0.617	CST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078349.2	NM_001899		T	23669598	C	T	23669598	2	4	22	1	0	0	0	0	0	0	0	1	3976	726	26	2		2	CST4	20	23669598	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	14	23669598	39355922	4147	7048											
GGTLC1	92086	hgsc.bcm.edu	37	chr20	23966316	23966316	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcccacctggtcaatgttTctctccactgtcgtgacgtt	6	13	8	14	2	2	1	1	1	1	0	5	1	3	1	3	1	1	2	3	1	1	2	rs111546926	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:23966316T>C	ENST00000335694.4	-	5	723	c.519A>G	c.(517-519)agA>agG	p.R173R	GGTLC1_ENST00000278765.4_Silent_p.R173R|GGTLC1_ENST00000286890.4_Silent_p.R173R	NM_178311.2	NP_842563.1	Q9BX51	GGTL1_HUMAN	gamma-glutamyltransferase light chain 1	173					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						GGTCAATGTTTCTCTCCACTG	0.597													.|||	337	0.0672923	0.2239	0.0274	5008	,	,		16839	0.002		0.0089	False		,,,				2504	0.0112				p.R173R		Atlas-SNP	.											.	GGTLC1	37	.	0			c.A519G						PASS	.	T	,	856,3550	316.3+/-294.6	75,706,1422	52	54	53		519,519	0.8	0.4	20	dbSNP_132	53	103,8489	51.9+/-112.3	1,101,4194	no	coding-synonymous,coding-synonymous	GGTLC1	NM_178311.2,NM_178312.2	,	76,807,5616	CC,CT,TT		1.1988,19.4281,7.3781	,	173/226,173/226	23966316	959,12039	2203	4296	6499	SO:0001819	synonymous_variant	92086	exon5			AATGTTTCTCTCC	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.519A>G	20.37:g.23966316T>C		73	0	0		87	45	0.517241	NM_178311	D3DW43|Q08246	Silent	SNP	ENST00000335694.4	37	CCDS13163.1																																																																																			T|0.937;C|0.063	0.063	strong		0.597	GGTLC1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078366.2	NM_178311.2		C	23966316	T	C	23966316	2	2	22	1	0	0	0	0	0	0	0	1	6373	1780	62	3		3	GGTLC1	20	23966316	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	296718	23966316	39059204	4148	7049											
ACSS1	84532	hgsc.bcm.edu	37	chr20	25038484	25038484	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tcccagacggtgtggtagggGgtgtcccacacgagagtgtc	7	8	16	10	2	0	2	0	0	0	2	3	3	2	2	2	4	0	1	2	4	1	1	rs66817095	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:25038484G>A	ENST00000323482.4	-	1	334	c.255C>T	c.(253-255)acC>acT	p.T85T	ACSS1_ENST00000376726.3_Silent_p.T85T|ACSS1_ENST00000432802.2_Silent_p.T85T	NM_001252675.1|NM_032501.3	NP_001239604.1|NP_115890.2	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	85					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)	TGTGGTAGGGGGTGTCCCACA	0.662																																					p.T85T		Atlas-SNP	.											.	ACSS1	46	.	0			c.C255T						PASS	.						42	47	45					20																	25038484		2203	4300	6503	SO:0001819	synonymous_variant	84532	exon1			GTAGGGGGTGTCC		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.255C>T	20.37:g.25038484G>A		141	0	0		135	66	0.488889	NM_001252677	B3KXL2|B4DJZ3|D3DW48|F5H6F4|F8W7Y1|Q5TF42|Q8IV99|Q8N234|Q96JI1|Q96JX6|Q9NU28	Silent	SNP	ENST00000323482.4	37	CCDS13167.1																																																																																			G|0.845;T|0.155	.	alt		0.662	ACSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078386.2	NM_032501		A	25038484	G	A	25038484	2	1	22	1	0	0	0	0	0	0	0	1	188	1219	43	2		2	ACSS1	20	25038484	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1072168	25038484	37987036	4149	7050											
ABHD12	26090	hgsc.bcm.edu	37	chr20	25319977	25319977	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcctcaggcgcaaccacaCgccctttcgcctgcaagaga	9	7	8	17	3	1	1	1	0	0	1	3	2	2	1	4	1	2	2	4	1	2	2	rs11904930	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:25319977C>T	ENST00000339157.5	-	2	474	c.202G>A	c.(202-204)Gtg>Atg	p.V68M	ABHD12_ENST00000376542.3_Missense_Mutation_p.V68M	NM_001042472.2	NP_001035937.1	Q8N2K0	ABD12_HUMAN	abhydrolase domain containing 12	68					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						CGCAACCACACGCCCTTTCGC	0.423													C|||	23	0.00459265	0.0166	0.0014	5008	,	,		17996	0.0		0.0	False		,,,				2504	0.0				p.V68M		Atlas-SNP	.											.	ABHD12	46	.	0			c.G202A						PASS	.	C	MET/VAL,MET/VAL	88,4318	74.1+/-112.3	1,86,2116	102	92	95		202,202	2.1	1	20	dbSNP_120	95	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	ABHD12	NM_001042472.2,NM_015600.4	21,21	1,88,6414	TT,TC,CC		0.0233,1.9973,0.692	benign,benign	68/399,68/405	25319977	90,12916	2203	4300	6503	SO:0001583	missense	26090	exon2			ACCACACGCCCTT	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.202G>A	20.37:g.25319977C>T	ENSP00000341408:p.Val68Met	126	0	0		108	48	0.444444	NM_001042472	A6NED4|A6NJ90|A8K450|B4DE71|Q5T710|Q5T711|Q96CR1|Q9BX05|Q9NPX7|Q9UFV6	Missense_Mutation	SNP	ENST00000339157.5	37	CCDS42857.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	10.04	1.241327	0.22711	0.019973	2.33E-4	ENSG00000100997	ENST00000376542;ENST00000339157;ENST00000526543;ENST00000450393	T;T;T	0.25749	1.78;1.78;1.78	5.51	2.13	0.27403	.	0.327344	0.28409	N	0.015448	T	0.04452	0.0122	N	0.08118	0	0.19300	N	0.999971	B;B;B	0.12013	0.001;0.001;0.005	B;B;B	0.06405	0.002;0.001;0.002	T	0.15464	-1.0436	10	0.44086	T	0.13	0.0354	1.0324	0.01541	0.1484:0.1871:0.2866:0.378	rs11904930	23;68;68	Q5T712;Q8N2K0;Q8N2K0-2	.;ABD12_HUMAN;.	M	68;68;30;23	ENSP00000365725:V68M;ENSP00000341408:V68M;ENSP00000413311:V23M	ENSP00000341408:V68M	V	-	1	0	ABHD12	25267977	0.214000	0.23563	0.996000	0.52242	0.608000	0.37181	0.149000	0.16243	0.676000	0.31285	-0.226000	0.12346	GTG	C|0.993;T|0.007	0.007	strong		0.423	ABHD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078423.2	NM_015600		T	25319977	C	T	25319977	3	4	22	1	0	0	0	0	1	0	0	0	76	536	19	1	1104	1	ABHD12	20	25319977	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	281493	25319977	37705543	4150	7051											
DEFB119	245932	hgsc.bcm.edu	37	chr20	29965208	29965211	+	Frame_Shift_Del	DEL	ACTG	ACTG	-																															caagaggccctacaaattccActgttacccatgcatcgaag																								rs374993061	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	ACTG	ACTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:29965208_29965211delACTG	ENST00000376321.3	-	2	212_215	c.93_96delCAGT	c.(91-96)aacagtfs	p.NS31fs	SNORA40_ENST00000390832.1_RNA|DEFB119_ENST00000339144.3_3'UTR|DEFB119_ENST00000492344.1_5'UTR	NM_153289.3	NP_695021.2	Q8N690	DB119_HUMAN	defensin, beta 119	31					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				large_intestine(2)|lung(1)|prostate(1)	4	all_hematologic(12;0.158)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			TACAAATTCCACTGTTACCCATGC	0.431														26	0.00519169	0.0182	0.0029	5008	,	,		21220	0.0		0.0	False		,,,				2504	0.0				p.32_33del		Pindel,Atlas-Indel	.											DEFB119_ENST00000376321,NS,malignant_melanoma,+1,2	DEFB119	37	2	0			c.94_97del						PASS	.		,	106,4154		3,100,2027					,	3.3	0.3			168	2,8248		0,2,4123	no	utr-3,frameshift	DEFB119	NM_173460.1,NM_153289.2	,	3,102,6150	A1A1,A1R,RR		0.0242,2.4883,0.8633	,	,		108,12402				SO:0001589	frameshift_variant	245932	exon2			.	AA939044	CCDS13178.1, CCDS33455.1	20q11.21	2007-02-19	2003-10-06		ENSG00000180483	ENSG00000180483		"Defensins, beta"	18099	protein-coding gene	gene with protein product			"defensin, beta 120"	DEFB120		11854508	Standard	NM_153289		Approved	DEFB-19, DEFB-20	uc002wvu.2	Q8N690	OTTHUMG00000032172	ENST00000376321.3:c.93_96delCAGT	20.37:g.29965208_29965211delACTG	ENSP00000365499:p.Asn31fs	110	0	.		88	36	0.409	NM_153289	Q5GRG1|Q5JWP1|Q5TH42|Q8N689	Frame_Shift_Del	DEL	ENST00000376321.3	37	CCDS13178.1																																																																																			.	.	weak		0.431	DEFB119-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078514.1	NM_153289		-	29965211	ACTG	-	29965208	7	5	22	1	0	1	0	1	0	0	0	0	4409	156	6	0	162	0	DEFB119	20	29965208	Frame_Shift_Del	DEL	ACTG	TCGA-G8-6324-01A-11D-2210-10	4645231	29965208	33060312	4151	7052											
POFUT1	23509	hgsc.bcm.edu	37	chr20	30822455	30822455	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggccccctaagctgcgggaCgagttctgattctggccgga	7	8	14	12	3	2	1	0	1	2	0	2	4	2	3	3	4	2	2	3	4	1	3	rs7263390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:30822455C>T	ENST00000375749.3	+	7	1220	c.1158C>T	c.(1156-1158)gaC>gaT	p.D386D	POFUT1_ENST00000539210.1_Silent_p.D175D	NM_015352.1	NP_056167.1	Q9H488	OFUT1_HUMAN	protein O-fucosyltransferase 1	386					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)			AGCTGCGGGACGAGTTCTGAT	0.632													C|||	92	0.0183706	0.0651	0.0086	5008	,	,		18001	0.0		0.0	False		,,,				2504	0.0				p.D386D		Atlas-SNP	.											.	POFUT1	52	.	0			c.C1158T						PASS	.	C		233,4173	136.1+/-172.1	8,217,1978	54	54	54		1158	-3.8	1	20	dbSNP_116	54	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	POFUT1	NM_015352.1		8,224,6271	TT,TC,CC		0.0814,5.2882,1.8453		386/389	30822455	240,12766	2203	4300	6503	SO:0001819	synonymous_variant	23509	exon7			GCGGGACGAGTTC	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.1158C>T	20.37:g.30822455C>T		95	0	0		91	44	0.483516	NM_015352	A8K4R8|E1P5M4|Q14685|Q5W185|Q9BW76	Silent	SNP	ENST00000375749.3	37	CCDS13198.1																																																																																			C|0.973;T|0.027	0.027	strong		0.632	POFUT1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078613.1	NM_015352		T	30822455	C	T	30822455	2	4	22	1	0	0	0	0	0	0	0	1	12192	535	19	1		1	POFUT1	20	30822455	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	857247	30822455	32203065	4152	7053											
ASXL1	171023	hgsc.bcm.edu	37	chr20	31022480	31022480	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggtggcggcggggccacCgatgagggaggtggcagagg	7	3	24	7	3	0	2	0	1	0	1	0	5	0	4	2	10	0	1	2	10	0	0	rs79865730	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31022480C>T	ENST00000375687.4	+	13	2389	c.1965C>T	c.(1963-1965)acC>acT	p.T655T	ASXL1_ENST00000306058.5_Silent_p.T650T	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	655	Gly-rich.|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)	p.T639_G659>PPWD(1)|p.A640_S664>PCSGG(1)|p.T655fs*8(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						GCGGGGCCACCGATGAGGGAG	0.701			"F, N, Mis"		"MDS, CMML"								C|||	39	0.00778754	0.025	0.0043	5008	,	,		12008	0.0		0.003	False		,,,				2504	0.0				p.T655T		Atlas-SNP	.		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	.	ASXL1	1114	.	3	Complex - deletion inframe(2)|Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(3)	c.C1965T						PASS	.	C		53,4213		1,51,2081	8	9	9		1965	1.2	1	20	dbSNP_131	9	2,8376		0,2,4187	no	coding-synonymous	ASXL1	NM_015338.5		1,53,6268	TT,TC,CC		0.0239,1.2424,0.435		655/1542	31022480	55,12589	2133	4189	6322	SO:0001819	synonymous_variant	171023	exon12			GGCCACCGATGAG	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.1965C>T	20.37:g.31022480C>T		29	0	0		54	33	0.611111	NM_015338	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Silent	SNP	ENST00000375687.4	37	CCDS13201.1																																																																																			C|0.993;T|0.007	0.007	strong		0.701	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338		T	31022480	C	T	31022480	2	4	22	1	0	0	0	0	0	0	0	1	1066	639	23	1		1	ASXL1	20	31022480	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	200025	31022480	32003040	4153	7054											
ASXL1	171023	hgsc.bcm.edu	37	chr20	31024488	31024488	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggcctgcggacccgatgcctCttcctgctgagatccctcca	5	9	10	17	2	1	1	0	1	1	1	4	4	4	2	6	2	3	1	6	2	0	1	rs6057581	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31024488C>T	ENST00000375687.4	+	13	4397	c.3973C>T	c.(3973-3975)Ctt>Ttt	p.L1325F	ASXL1_ENST00000306058.5_Missense_Mutation_p.L1320F	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	1325			L -> F (in dbSNP:rs6057581).		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						CCCGATGCCTCTTCCTGCTGA	0.572			"F, N, Mis"		"MDS, CMML"								C|||	145	0.0289537	0.1044	0.0058	5008	,	,		17355	0.0		0.003	False		,,,				2504	0.0				p.L1325F		Atlas-SNP	.		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	.	ASXL1	1114	.	0			c.C3973T						PASS	.	C	PHE/LEU	386,4020	187.4+/-214.1	13,360,1830	41	44	43		3973	1.3	0	20	dbSNP_114	43	4,8596	3.7+/-12.6	0,4,4296	yes	missense	ASXL1	NM_015338.5	22	13,364,6126	TT,TC,CC		0.0465,8.7608,2.9986	probably-damaging	1325/1542	31024488	390,12616	2203	4300	6503	SO:0001583	missense	171023	exon12			ATGCCTCTTCCTG	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.3973C>T	20.37:g.31024488C>T	ENSP00000364839:p.Leu1325Phe	79	0	0		69	31	0.449275	NM_015338	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Missense_Mutation	SNP	ENST00000375687.4	37	CCDS13201.1	47	0.02152014652014652	42	0.08536585365853659	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	C	9.497	1.102092	0.20632	0.087608	4.65E-4	ENSG00000171456	ENST00000358956;ENST00000375687;ENST00000421155;ENST00000412498;ENST00000306058	T;T	0.16597	2.33;2.33	4.56	1.29	0.21616	.	0.227351	0.28011	N	0.016945	T	0.00580	0.0019	L	0.36672	1.1	0.09310	N	1	D;D	0.64830	0.994;0.994	P;P	0.59221	0.854;0.854	T	0.09164	-1.0687	10	0.16896	T	0.51	-9.4128	1.2537	0.01987	0.1414:0.4193:0.1563:0.2829	rs6057581;rs6057581	1320;1325	A6NIZ6;Q8IXJ9	.;ASXL1_HUMAN	F	1325;1325;1325;1246;1320	ENSP00000364839:L1325F;ENSP00000305119:L1320F	ENSP00000305119:L1320F	L	+	1	0	ASXL1	30488149	0.000000	0.05858	0.010000	0.14722	0.276000	0.26787	-0.141000	0.10327	0.336000	0.23639	0.561000	0.74099	CTT	C|0.971;T|0.029	0.029	strong		0.572	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338		T	31024488	C	T	31024488	3	4	22	1	0	0	0	0	1	0	0	0	1066	913	32	2	4029	2	ASXL1	20	31024488	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2008	31024488	32001032	4154	7055											
DNMT3B	1789	hgsc.bcm.edu	37	chr20	31388080	31388080	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatatcaaatacgtgaacgaCgtgaggaacatcacaaagaa	20	6	8	7	3	2	3	2	2	0	1	2	5	2	4	0	1	3	0	0	1	8	2	rs17123657	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31388080C>T	ENST00000328111.2	+	17	2202	c.1881C>T	c.(1879-1881)gaC>gaT	p.D627D	DNMT3B_ENST00000201963.3_Silent_p.D619D|DNMT3B_ENST00000375623.4_3'UTR|DNMT3B_ENST00000344505.4_Silent_p.D607D|DNMT3B_ENST00000353855.2_Silent_p.D607D|DNMT3B_ENST00000348286.2_Silent_p.D607D|DNMT3B_ENST00000443239.3_Silent_p.D565D|DNMT3B_ENST00000456297.2_Silent_p.D531D	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta	627	S-adenosyl-L-methionine binding. {ECO:0000250}.|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 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						ACGTGAACGACGTGAGGAACA	0.498													C|||	277	0.0553115	0.1944	0.0144	5008	,	,		21823	0.0		0.007	False		,,,				2504	0.0031				p.D627D		Atlas-SNP	.											DNMT3B_ENST00000201963,NS,carcinoma,+2,4	DNMT3B	196	4	0			c.C1881T						PASS	.	C	,,,,,	762,3644	312.7+/-292.7	71,620,1512	198	170	180		1695,1593,1881,1821,1821,1857	-1.8	0.9	20	dbSNP_123	180	30,8570	21.0+/-64.5	0,30,4270	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DNMT3B	NM_001207055.1,NM_001207056.1,NM_006892.3,NM_175848.1,NM_175849.1,NM_175850.2	,,,,,	71,650,5782	TT,TC,CC		0.3488,17.2946,6.0895	,,,,,	565/729,531/695,627/854,607/834,607/771,619/846	31388080	792,12214	2203	4300	6503	SO:0001819	synonymous_variant	1789	exon17			GAACGACGTGAGG		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.1881C>T	20.37:g.31388080C>T		94	0	0		106	56	0.528302	NM_006892	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Silent	SNP	ENST00000328111.2	37	CCDS13205.1																																																																																			C|0.944;T|0.056	0.056	strong		0.498	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892		T	31388080	C	T	31388080	2	4	22	1	0	0	0	0	0	0	0	1	4679	535	19	1		1	DNMT3B	20	31388080	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	363592	31388080	31637440	4155	7056											
BPIL1	80341	hgsc.bcm.edu	37	chr20	31598909	31598909	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctggactggagtggagaggcGcttcagcccaccaggtgagt	8	7	16	10	1	1	2	1	1	0	1	1	5	1	4	2	5	1	1	2	5	0	1	rs61734339	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31598909G>A	ENST00000170150.3	+	3	384	c.189G>A	c.(187-189)gcG>gcA	p.A63A		NM_025227.1	NP_079503.1	Q8N4F0	BPIB2_HUMAN	BPI fold containing family B, member 2	63			A -> V (in dbSNP:rs34128772).			extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										GTGGAGAGGCGCTTCAGCCCA	0.622													G|||	26	0.00519169	0.0159	0.0014	5008	,	,		18832	0.0		0.004	False		,,,				2504	0.0				p.A63A		Atlas-SNP	.											.	.	.	.	0			c.G189A						PASS	.	G		72,4334	65.3+/-102.7	1,70,2132	89	74	79		189	2.5	0	20	dbSNP_129	79	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	BPIFB2	NM_025227.1		1,75,6427	AA,AG,GG		0.0581,1.6341,0.592		63/459	31598909	77,12929	2203	4300	6503	SO:0001819	synonymous_variant	80341	exon3			AGAGGCGCTTCAG	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.189G>A	20.37:g.31598909G>A		116	0	0		93	42	0.451613	NM_025227	Q6UWN3|Q6ZME0|Q8NFQ7	Silent	SNP	ENST00000170150.3	37	CCDS13210.1																																																																																			G|0.992;A|0.008	0.008	strong		0.622	BPIFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078652.2	NM_025227		A	31598909	G	A	31598909	2	1	22	1	0	0	0	0	0	0	0	1	1493	1074	38	1		1	BPIL1	20	31598909	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	210829	31598909	31426611	4156	7057											
C20orf185	359710	hgsc.bcm.edu	37	chr20	31644436	31644436	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggggcctcttgggctcaggAgggctgcttggaggaggcgg	4	7	21	9	2	2	0	1	0	1	0	2	3	2	3	1	9	1	3	1	9	0	2	rs35539872	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31644436A>C	ENST00000375494.3	+	2	213	c.213A>C	c.(211-213)ggA>ggC	p.G71G	AL121756.1_ENST00000579962.1_RNA	NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	71	Leu-rich.				innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										TGGGCTCAGGAGGGCTGCTTG	0.617													A|||	232	0.0463259	0.1679	0.0144	5008	,	,		17539	0.0		0.0	False		,,,				2504	0.0				p.G71G		Atlas-SNP	.											.	.	.	.	0			c.A213C						PASS	.	A		604,3802	265.9+/-266.9	52,500,1651	89	90	90		213	0.8	0.6	20	dbSNP_126	90	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous	BPIFB3	NM_182658.1		52,505,5946	CC,CA,AA		0.0581,13.7086,4.6825		71/477	31644436	609,12397	2203	4300	6503	SO:0001819	synonymous_variant	359710	exon2			CTCAGGAGGGCTG	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.213A>C	20.37:g.31644436A>C		97	0	0		129	64	0.496124	NM_182658	Q5TDX7	Silent	SNP	ENST00000375494.3	37	CCDS13212.1																																																																																			A|0.957;C|0.043	0.043	strong		0.617	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658		C	31644436	A	C	31644436	2	2	22	1	0	0	0	0	0	0	0	1	2099	291	11	5		5	C20orf185	20	31644436	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	45527	31644436	31381084	4157	7058											
C20orf185	359710	hgsc.bcm.edu	37	chr20	31661399	31661399	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaatgctgttgtgctgacCgtggcatcctgaggctgaga	8	10	14	9	1	0	4	0	3	0	2	1	5	1	4	2	2	2	5	2	2	1	1	rs114341725	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31661399C>T	ENST00000375494.3	+	15	1419	c.1419C>T	c.(1417-1419)acC>acT	p.T473T		NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	473					innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)	p.T473T(1)									TTGTGCTGACCGTGGCATCCT	0.552													C|||	27	0.00539137	0.0204	0.0	5008	,	,		19225	0.0		0.0	False		,,,				2504	0.0				p.T473T		Atlas-SNP	.											C20orf185,caecum,carcinoma,+2,1	.	.	1	1	Substitution - coding silent(1)	lung(1)	c.C1419T						scavenged	.	C		71,4335	65.3+/-102.7	0,71,2132	237	182	201		1419	-2.5	1	20	dbSNP_132	201	0,8600		0,0,4300	yes	coding-synonymous	BPIFB3	NM_182658.1		0,71,6432	TT,TC,CC		0.0,1.6114,0.5459		473/477	31661399	71,12935	2203	4300	6503	SO:0001819	synonymous_variant	359710	exon15			GCTGACCGTGGCA	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.1419C>T	20.37:g.31661399C>T		184	1	0.00543478		218	109	0.5	NM_182658	Q5TDX7	Silent	SNP	ENST00000375494.3	37	CCDS13212.1																																																																																			C|0.993;T|0.007	0.007	strong		0.552	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658		T	31661399	C	T	31661399	2	4	22	1	0	0	0	0	0	0	0	1	2099	639	23	1		1	C20orf185	20	31661399	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	16963	31661399	31364121	4158	7059											
C20orf70	140683	hgsc.bcm.edu	37	chr20	31757078	31757078	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tggaacctgttcttcacgagGgacttgagacagttgacaat	11	11	11	8	1	2	2	1	2	1	1	2	6	2	4	1	2	1	2	1	2	2	4	rs6059139	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31757078G>A	ENST00000253362.2	+	2	273	c.127G>A	c.(127-129)Gga>Aga	p.G43R	BPIFA2_ENST00000354932.5_Missense_Mutation_p.G43R			Q96DR5	BPIA2_HUMAN	BPI fold containing family A, member 2	43			G -> R (in dbSNP:rs6059139).			extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)										TCTTCACGAGGGACTTGAGAC	0.463													G|||	141	0.028155	0.0998	0.0058	5008	,	,		20844	0.0		0.005	False		,,,				2504	0.0				p.G43R		Atlas-SNP	.											.	.	.	.	0			c.G127A						PASS	.	G	ARG/GLY	408,3998	201.8+/-224.7	16,376,1811	145	120	128		127	2.2	0	20	dbSNP_114	128	17,8583	12.6+/-44.7	0,17,4283	yes	missense	BPIFA2	NM_080574.2	125	16,393,6094	AA,AG,GG		0.1977,9.2601,3.2677	possibly-damaging	43/250	31757078	425,12581	2203	4300	6503	SO:0001583	missense	140683	exon2			CACGAGGGACTTG	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.127G>A	20.37:g.31757078G>A	ENSP00000253362:p.Gly43Arg	91	0	0		95	31	0.326316	NM_080574	Q9BQQ0	Missense_Mutation	SNP	ENST00000253362.2	37	CCDS13214.1	59	0.027014652014652016	52	0.10569105691056911	3	0.008287292817679558	0	0.0	4	0.005277044854881266	G	2.971	-0.212453	0.06140	0.092601	0.001977	ENSG00000131050	ENST00000253362;ENST00000354932	T;T	0.13089	2.62;2.62	4.16	2.22	0.28083	.	0.708924	0.12096	N	0.499960	T	0.00241	0.0007	L	0.41824	1.3	0.80722	P	0.0	P	0.36010	0.532	B	0.36922	0.236	T	0.20075	-1.0286	9	0.51188	T	0.08	-10.3634	6.3866	0.21563	0.2201:0.0:0.7799:0.0	rs6059139;rs52815538;rs6059139	43	Q96DR5	BPIA2_HUMAN	R	43	ENSP00000253362:G43R;ENSP00000347012:G43R	ENSP00000253362:G43R	G	+	1	0	BPIFA2	31220739	0.001000	0.12720	0.002000	0.10522	0.009000	0.06853	0.736000	0.26130	0.707000	0.31934	0.655000	0.94253	GGA	G|0.962;A|0.038	0.038	strong		0.463	BPIFA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257117.1	NM_080574		A	31757078	G	A	31757078	3	1	22	1	0	0	0	0	1	0	0	0	2118	1233	43	2	129	2	C20orf70	20	31757078	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	95679	31757078	31268442	4159	7060											
C20orf70	140683	hgsc.bcm.edu	37	chr20	31761885	31761885	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gaattgtgggtttcacacagGttgaaaatcagcaactccct	12	11	9	9	0	2	1	2	1	0	0	3	2	3	1	1	2	2	3	1	2	4	3	rs61734343	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31761885G>T	ENST00000253362.2	+	4	449	c.303G>T	c.(301-303)ggG>ggT	p.G101G	BPIFA2_ENST00000354932.5_Splice_Site_p.G101G			Q96DR5	BPIA2_HUMAN	BPI fold containing family A, member 2	101						extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)										TTTCACACAGGTTGAAAATCA	0.537													G|||	23	0.00459265	0.0174	0.0	5008	,	,		19612	0.0		0.0	False		,,,				2504	0.0				p.G101G		Atlas-SNP	.											.	.	.	.	0			c.G303T						PASS	.	G		72,4334	64.1+/-101.4	0,72,2131	164	110	128		303	0.6	0.6	20	dbSNP_129	128	3,8597	3.0+/-9.4	0,3,4297	yes	coding-synonymous-near-splice	BPIFA2	NM_080574.2		0,75,6428	TT,TG,GG		0.0349,1.6341,0.5767		101/250	31761885	75,12931	2203	4300	6503	SO:0001630	splice_region_variant	140683	exon4			ACACAGGTTGAAA	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.303-1G>T	20.37:g.31761885G>T		121	0	0		138	58	0.42029	NM_080574	Q9BQQ0	Silent	SNP	ENST00000253362.2	37	CCDS13214.1																																																																																			A|0.003;G|0.992;T|0.005	0.005	strong		0.537	BPIFA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257117.1	NM_080574	Silent	T	31761885	G	T	31761885	5	4	22	1	0	0	0	0	0	0	1	0	2118	1275	44	4	313	4	C20orf70	20	31761885	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4807	31761885	31263635	4160	7061											
C20orf71	128861	hgsc.bcm.edu	37	chr20	31812206	31812206	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gactgtggtgggatccagatAtcattccataaggagtggtt	10	12	13	6	0	1	1	1	0	0	1	3	4	3	3	2	4	0	1	2	4	2	4	rs112731808	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31812206A>G	ENST00000375454.3	+	3	534	c.324A>G	c.(322-324)atA>atG	p.I108M	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	108						extracellular region (GO:0005576)	lipid binding (GO:0008289)										GGATCCAGATATCATTCCATA	0.483													G|||	99	0.0197684	0.0446	0.0072	5008	,	,		20967	0.0308		0.004	False		,,,				2504	0.0				p.I108M		Atlas-SNP	.											.	.	.	.	0			c.A324G						PASS	.	G	,MET/ILE	187,4219	809.5+/-416.0	5,177,2021	173	153	160		,324	3.4	0.6	20	dbSNP_132	160	13,8587	818.7+/-406.8	0,13,4287	yes	intron,missense	BPIFA3	NM_001042439.1,NM_178466.3	,10	5,190,6308	GG,GA,AA		0.1512,4.2442,1.5378	,benign	,108/255	31812206	200,12806	2203	4300	6503	SO:0001583	missense	128861	exon3			CCAGATATCATTC		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.324A>G	20.37:g.31812206A>G	ENSP00000364603:p.Ile108Met	168	0	0		190	94	0.494737	NM_178466	Q5JWG8|Q6NZ38	Missense_Mutation	SNP	ENST00000375454.3	37	CCDS13216.2	55	0.025183150183150184	28	0.056910569105691054	3	0.008287292817679558	20	0.03496503496503497	4	0.005277044854881266	G	0.006	-2.099179	0.00360	0.042442	0.001512	ENSG00000131059	ENST00000375454	T	0.04970	3.52	4.35	3.41	0.39046	.	0.313773	0.27986	N	0.017055	T	0.00300	0.0009	N	0.01168	-0.975	0.43841	D	0.996421	B	0.02656	0.0	B	0.04013	0.001	T	0.55016	-0.8206	10	0.30854	T	0.27	-4.1596	7.0156	0.24887	0.2026:0.0:0.7974:0.0	.	108	Q9BQP9	BPIA3_HUMAN	M	108	ENSP00000364603:I108M	ENSP00000364603:I108M	I	+	3	3	BPIFA3	31275867	0.997000	0.39634	0.603000	0.28903	0.084000	0.17831	1.446000	0.35090	0.804000	0.34136	-0.213000	0.12676	ATA	A|0.983;G|0.017	0.017	strong		0.483	BPIFA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078672.1	NM_178466		G	31812206	A	G	31812206	3	3	22	1	0	0	0	0	1	0	0	0	2119	439	16	3	334	3	C20orf71	20	31812206	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	50321	31812206	31213314	4161	7062											
C20orf71	128861	hgsc.bcm.edu	37	chr20	31812949	31812949	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atgtgtgcacatatgagcatCgttgtggagttctggctgga	8	13	14	6	1	1	1	0	1	1	0	2	3	1	3	0	3	2	5	0	3	1	3	rs147632261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31812949C>T	ENST00000375454.3	+	4	642	c.432C>T	c.(430-432)atC>atT	p.I144I	BPIFA3_ENST00000490499.1_3'UTR|BPIFA3_ENST00000375452.3_Silent_p.I108I	NM_178466.3	NP_848561.2	Q9BQP9	BPIA3_HUMAN	BPI fold containing family A, member 3	144						extracellular region (GO:0005576)	lipid binding (GO:0008289)										ATATGAGCATCGTTGTGGAGT	0.522													C|||	24	0.00479233	0.0136	0.0029	5008	,	,		22489	0.0		0.004	False		,,,				2504	0.0				p.I144I		Atlas-SNP	.											.	.	.	.	0			c.C432T						PASS	.	C	,	54,4352	52.9+/-88.7	0,54,2149	205	196	199		324,432	2.5	0.1	20	dbSNP_134	199	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous,coding-synonymous	BPIFA3	NM_001042439.1,NM_178466.3	,	0,64,6439	TT,TC,CC		0.1163,1.2256,0.4921	,	108/219,144/255	31812949	64,12942	2203	4300	6503	SO:0001819	synonymous_variant	128861	exon4			GAGCATCGTTGTG		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.432C>T	20.37:g.31812949C>T		136	0	0		162	84	0.518519	NM_178466	Q5JWG8|Q6NZ38	Silent	SNP	ENST00000375454.3	37	CCDS13216.2																																																																																			C|0.995;T|0.005	0.005	strong		0.522	BPIFA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078672.1	NM_178466		T	31812949	C	T	31812949	2	4	22	1	0	0	0	0	0	0	0	1	2119	874	31	1		1	C20orf71	20	31812949	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	743	31812949	31212571	4162	7063											
C20orf114	92747	hgsc.bcm.edu	37	chr20	31877770	31877770	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aggagctgctagtcaagatcCccctggacatggtggctgga	9	8	14	10	0	1	1	1	0	0	1	2	4	2	4	2	5	2	3	2	5	2	1	rs114635109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31877770C>T	ENST00000253354.1	+	4	498	c.337C>T	c.(337-339)Ccc>Tcc	p.P113S		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													C|||	45	0.00898562	0.0318	0.0029	5008	,	,		19004	0.0		0.001	False		,,,				2504	0.0				p.P113S		Atlas-SNP	.											.	.	.	.	0			c.C337T						PASS	.	C	SER/PRO	170,4236	111.6+/-149.8	4,162,2037	124	95	105		337	5.4	1	20	dbSNP_132	105	1,8599	1.2+/-3.3	0,1,4299	yes	missense	BPIFB1	NM_033197.2	74	4,163,6336	TT,TC,CC		0.0116,3.8584,1.3148	probably-damaging	113/485	31877770	171,12835	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>T	20.37:g.31877770C>T	ENSP00000253354:p.Pro113Ser	115	0	0		112	63	0.5625	NM_033197	A8K2H8|Q5QP43|Q6UWY1|Q6ZRU7|Q96HK6|Q9BQP8|Q9BWZ6|Q9H4V6	Missense_Mutation	SNP	ENST00000253354.1	37	CCDS13218.1	14	0.00641025641025641	12	0.024390243902439025	2	0.0055248618784530384	0	0.0	0	0.0	C	19.64	3.865475	0.71949	0.038584	1.16E-4	ENSG00000125999	ENST00000423645;ENST00000253354	T;T	0.06142	3.34;3.7	5.4	5.4	0.78164	.	0.000000	0.64402	D	0.000008	T	0.06645	0.0170	M	0.80847	2.515	0.39655	D	0.970525	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.00099	-1.2067	10	0.38643	T	0.18	-35.2487	15.0609	0.71951	0.0:1.0:0.0:0.0	.	113;113	B2R7Z6;Q8TDL5	.;BPIB1_HUMAN	S	113	ENSP00000390471:P113S;ENSP00000253354:P113S	ENSP00000253354:P113S	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	0.012	strong		0.582	BPIFB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106499.2	NM_033197		T	31877770	C	T	31877770	3	4	22	1	0	0	0	0	1	0	0	0	2084	623	22	2	347	2	C20orf114	20	31877770	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	64821	31877770	31147750	4163	7064											
NECAB3	63941	hgsc.bcm.edu	37	chr20	32248088	32248088	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagccatgggcctgggcctcCagggtatctgacgccccctc	5	7	12	17	1	1	1	0	1	1	0	3	1	2	1	6	3	1	1	6	3	1	1	rs146604647	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:32248088C>T	ENST00000246190.6	-	6	556	c.501G>A	c.(499-501)ctG>ctA	p.L167L	RP1-63M2.6_ENST00000607224.1_RNA|C20orf144_ENST00000375222.3_5'Flank|NECAB3_ENST00000375238.4_Silent_p.L167L|NECAB3_ENST00000606525.1_5'UTR	NM_031232.3	NP_112509.3	Q96P71	NECA3_HUMAN	N-terminal EF-hand calcium binding protein 3	167					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						CCTGGGCCTCCAGGGTATCTG	0.622													C|||	10	0.00199681	0.0076	0.0	5008	,	,		18803	0.0		0.0	False		,,,				2504	0.0				p.L167L		Atlas-SNP	.											.	NECAB3	27	.	0			c.G501A						PASS	.	C	,	24,4058		0,24,2017	48	54	52		501,501	3.9	1	20	dbSNP_134	52	0,8376		0,0,4188	no	coding-synonymous,coding-synonymous	NECAB3	NM_031231.3,NM_031232.3	,	0,24,6205	TT,TC,CC		0.0,0.5879,0.1926	,	167/363,167/397	32248088	24,12434	2041	4188	6229	SO:0001819	synonymous_variant	63941	exon6			GGCCTCCAGGGTA	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.501G>A	20.37:g.32248088C>T		69	0	0		54	23	0.425926	NM_031232	A8K780|E1P5N2|Q5JWF5|Q5JWF6|Q5JWF7|Q86VV1|Q9H433|Q9H8G8|Q9HBW7|Q9HCQ9	Silent	SNP	ENST00000246190.6	37	CCDS42866.1																																																																																			C|0.996;T|0.004	0.004	strong		0.622	NECAB3-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078724.2			T	32248088	C	T	32248088	2	4	22	1	0	0	0	0	0	0	0	1	10315	581	21	2		2	NECAB3	20	32248088	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	370318	32248088	30777432	4164	7065											
NCOA6	23054	hgsc.bcm.edu	37	chr20	33338099	33338099	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccttgttgctggaccatctgGccctgggagggcacgatttg	5	11	14	11	1	1	0	0	0	1	0	1	3	1	2	3	4	1	3	3	4	0	3	rs61736335	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33338099G>A	ENST00000374796.2	-	10	4469	c.1899C>T	c.(1897-1899)ggC>ggT	p.G633G	NCOA6_ENST00000359003.2_Silent_p.G633G			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	633	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						GGACCATCTGGCCCTGGGAGG	0.587													G|||	11	0.00219649	0.0083	0.0	5008	,	,		17579	0.0		0.0	False		,,,				2504	0.0				p.G633G		Atlas-SNP	.											.	NCOA6	219	.	0			c.C1899T						PASS	.	G	,	60,4346	58.1+/-94.6	0,60,2143	112	100	104		1899,1899	-0.8	1	20	dbSNP_129	104	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	NCOA6	NM_001242539.1,NM_014071.3	,	0,61,6442	AA,AG,GG		0.0116,1.3618,0.469	,	633/1071,633/2064	33338099	61,12945	2203	4300	6503	SO:0001819	synonymous_variant	23054	exon9			CATCTGGCCCTGG	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.1899C>T	20.37:g.33338099G>A		155	0	0		198	101	0.510101	NM_014071	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Silent	SNP	ENST00000374796.2	37	CCDS13241.1																																																																																			G|0.996;A|0.004	0.004	strong		0.587	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		A	33338099	G	A	33338099	2	1	22	1	0	0	0	0	0	0	0	1	10242	1190	42	2		2	NCOA6	20	33338099	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1090011	33338099	29687421	4165	7066											
GGT7	2686	hgsc.bcm.edu	37	chr20	33447314	33447314	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgggccggaggtgccaagtaCatccagcacctcagccaggt	9	5	13	14	2	1	0	1	0	0	0	2	1	2	1	5	4	4	2	5	4	2	1	rs61319953	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33447314C>T	ENST00000336431.5	-	7	990	c.946G>A	c.(946-948)Gta>Ata	p.V316I		NM_178026.2	NP_821158.2	Q9UJ14	GGT7_HUMAN	gamma-glutamyltransferase 7	316					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						GTGCCAAGTACATCCAGCACC	0.657													C|||	177	0.0353435	0.1256	0.0159	5008	,	,		13069	0.0		0.0	False		,,,				2504	0.0				p.V316I		Atlas-SNP	.											.	GGT7	41	.	0			c.G946A						PASS	.	C	ILE/VAL	418,3988	196.0+/-220.5	16,386,1801	36	31	33		946	-3.3	0	20	dbSNP_129	33	4,8594	2.2+/-6.3	0,4,4295	yes	missense	GGT7	NM_178026.2	29	16,390,6096	TT,TC,CC		0.0465,9.4871,3.2452	benign	316/663	33447314	422,12582	2203	4299	6502	SO:0001583	missense	2686	exon7			CAAGTACATCCAG	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.946G>A	20.37:g.33447314C>T	ENSP00000338964:p.Val316Ile	76	0	0		70	34	0.485714	NM_178026	Q8N899|Q8NF66|Q9BYP5|Q9BYP6	Missense_Mutation	SNP	ENST00000336431.5	37	CCDS13242.2	57	0.0260989010989011	50	0.1016260162601626	7	0.019337016574585635	0	0.0	0	0.0	C	10.57	1.386090	0.25031	0.094871	4.65E-4	ENSG00000131067	ENST00000336431	T	0.06218	3.33	5.84	-3.3	0.05003	.	1.463100	0.03616	N	0.235604	T	0.00073	0.0002	N	0.02011	-0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.42949	-0.9421	10	0.17369	T	0.5	-16.9643	1.2329	0.01947	0.249:0.302:0.0955:0.3535	rs61319953	316;316	A4FU32;Q9UJ14	.;GGT7_HUMAN	I	316	ENSP00000338964:V316I	ENSP00000338964:V316I	V	-	1	0	GGT7	32910975	0.000000	0.05858	0.004000	0.12327	0.858000	0.48976	-0.023000	0.12456	-0.350000	0.08262	-0.254000	0.11334	GTA	C|0.971;T|0.029	0.029	strong		0.657	GGT7-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078816.2	NM_178026		T	33447314	C	T	33447314	3	4	22	1	0	0	0	0	1	0	0	0	6372	478	17	2	1078	2	GGT7	20	33447314	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	109215	33447314	29578206	4166	7067											
ACSS2	55902	hgsc.bcm.edu	37	chr20	33513983	33513983	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgcagaggcagctgtggtggGccaccctcatcctgtgaagg	7	8	15	11	0	1	2	1	1	0	1	2	2	2	2	3	4	2	3	3	4	1	0	rs45486997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33513983G>C	ENST00000360596.2	+	16	2013	c.1802G>C	c.(1801-1803)gGc>gCc	p.G601A	ACSS2_ENST00000336325.4_Missense_Mutation_p.G551A|ACSS2_ENST00000253382.5_Missense_Mutation_p.G614A|ACSS2_ENST00000476922.1_Intron	NM_018677.3	NP_061147.1	Q9NR19	ACSA_HUMAN	acyl-CoA synthetase short-chain family member 2	601					acetate biosynthetic process (GO:0019413)|acetyl-CoA biosynthetic process from acetate (GO:0019427)|ethanol oxidation (GO:0006069)|lipid biosynthetic process (GO:0008610)|propionate biosynthetic process (GO:0019542)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	acetate-CoA ligase activity (GO:0003987)|AMP binding (GO:0016208)|ATP binding (GO:0005524)			cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(9)	21					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	GCTGTGGTGGGCCACCCTCAT	0.557													G|||	190	0.0379393	0.1316	0.0231	5008	,	,		19053	0.0		0.0	False		,,,				2504	0.0				p.G614A		Atlas-SNP	.											.	ACSS2	75	.	0			c.G1841C						PASS	.	G	ALA/GLY,ALA/GLY,ALA/GLY	487,3919	224.3+/-240.5	27,433,1743	138	105	116		1841,1517,1802	4.3	0.9	20	dbSNP_127	116	17,8583	11.9+/-42.8	0,17,4283	yes	missense,missense,missense	ACSS2	NM_001076552.2,NM_001242393.1,NM_018677.3	60,60,60	27,450,6026	CC,CG,GG		0.1977,11.0531,3.8751	benign,benign,benign	614/715,506/607,601/702	33513983	504,12502	2203	4300	6503	SO:0001583	missense	55902	exon17			TGGTGGGCCACCC	AF263614	CCDS13243.1, CCDS42868.1, CCDS42868.2	20q11.22	2012-07-13	2005-09-08	2005-09-08	ENSG00000131069	ENSG00000131069	6.2.1.1	"Acyl-CoA synthetase family"	15814	protein-coding gene	gene with protein product		605832	"acetyl-Coenzyme A synthetase 2 (ADP forming)"	ACAS2		10843999	Standard	NM_018677		Approved	ACS, ACSA, AceCS, dJ1161H23.1	uc010gey.2	Q9NR19	OTTHUMG00000032317	ENST00000360596.2:c.1802G>C	20.37:g.33513983G>C	ENSP00000353804:p.Gly601Ala	185	0	0		182	95	0.521978	NM_001076552	A6NE90|Q5QPH2|Q5QPH3|Q8N238|Q96EL0|Q9NQP7|Q9UJ15	Missense_Mutation	SNP	ENST00000360596.2	37	CCDS13243.1	57	0.0260989010989011	50	0.1016260162601626	7	0.019337016574585635	0	0.0	0	0.0	G	15.09	2.729599	0.48833	0.110531	0.001977	ENSG00000131069	ENST00000336325;ENST00000360596;ENST00000374693;ENST00000542204;ENST00000253382	T;T;T	0.62941	-0.01;-0.01;-0.01	5.25	4.29	0.51040	.	0.241356	0.49305	N	0.000155	T	0.02083	0.0065	L	0.53780	1.695	0.51012	D	0.9999	B;B	0.10296	0.001;0.003	B;B	0.12156	0.007;0.007	T	0.15983	-1.0418	10	0.87932	D	0	-12.1309	15.8996	0.79362	0.0:0.1355:0.8645:0.0	rs45486997;rs60500786	614;601	Q5QPH3;Q9NR19	.;ACSA_HUMAN	A	551;601;599;309;614	ENSP00000337190:G551A;ENSP00000353804:G601A;ENSP00000253382:G614A	ENSP00000253382:G614A	G	+	2	0	ACSS2	32977644	1.000000	0.71417	0.898000	0.35279	0.962000	0.63368	7.711000	0.84669	1.417000	0.47077	0.563000	0.77884	GGC	G|0.968;C|0.032	0.032	strong		0.557	ACSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078823.3	NM_018677		C	33513983	G	C	33513983	3	2	22	1	0	0	0	0	1	0	0	0	189	1203	42	4	1907	4	ACSS2	20	33513983	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	66669	33513983	29511537	4167	7068											
MYH7B	57644	hgsc.bcm.edu	37	chr20	33568455	33568455	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatacggcctccgtagtggcTgcttacaagggaaagcgccg	9	8	13	11	4	0	0	0	0	0	0	1	1	1	1	3	3	4	3	3	3	6	4	rs61746163	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33568455T>C	ENST00000262873.7	+	6	635	c.543T>C	c.(541-543)gcT>gcC	p.A181A	MYH7B_ENST00000481922.1_3'UTR	NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	139	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)			CCGTAGTGGCTGCTTACAAGG	0.557													C|||	16	0.00319489	0.0121	0.0	5008	,	,		17350	0.0		0.0	False		,,,				2504	0.0				p.A181A		Atlas-SNP	.											.	MYH7B	145	.	0			c.T543C						PASS	.	C		58,4302	745.2+/-411.6	0,58,2122	100	111	107		543	-8.9	0.1	20	dbSNP_129	107	1,8587	799.2+/-407.4	0,1,4293	no	coding-synonymous	MYH7B	NM_020884.3		0,59,6415	CC,CT,TT		0.0116,1.3303,0.4557		181/1984	33568455	59,12889	2180	4294	6474	SO:0001819	synonymous_variant	57644	exon8			AGTGGCTGCTTAC	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.543T>C	20.37:g.33568455T>C		201	0	0		171	89	0.520468	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Silent	SNP	ENST00000262873.7	37	CCDS42869.1																																																																																			T|0.994;C|0.006	0.006	strong		0.557	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884		C	33568455	T	C	33568455	2	2	22	1	0	0	0	0	0	0	0	1	10049	1567	55	3		3	MYH7B	20	33568455	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	54472	33568455	29457065	4168	7069											
MYH7B	57644	hgsc.bcm.edu	37	chr20	33574784	33574784	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgatggggaggagctcatcGccaccgacgtatgagctctg	9	8	14	10	3	2	2	1	2	1	0	3	5	2	4	2	3	2	3	2	3	1	1	rs115275866	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33574784G>A	ENST00000262873.7	+	13	1218	c.1126G>A	c.(1126-1128)Gcc>Acc	p.A376T		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	334	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)			GGAGCTCATCGCCACCGACGT	0.607													G|||	16	0.00319489	0.0121	0.0	5008	,	,		18635	0.0		0.0	False		,,,				2504	0.0				p.A376T		Atlas-SNP	.											MYH7B,colon,carcinoma,0,1	MYH7B	145	1	0			c.G1126A						PASS	.	G	THR/ALA	57,4197		0,57,2070	77	76	76		1126	3.7	1	20	dbSNP_132	76	1,8471		0,1,4235	yes	missense	MYH7B	NM_020884.3	58	0,58,6305	AA,AG,GG		0.0118,1.3399,0.4558	possibly-damaging	376/1984	33574784	58,12668	2127	4236	6363	SO:0001583	missense	57644	exon15			CTCATCGCCACCG	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.1126G>A	20.37:g.33574784G>A	ENSP00000262873:p.Ala376Thr	66	0	0		93	50	0.537634	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Missense_Mutation	SNP	ENST00000262873.7	37	CCDS42869.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	19.22	3.786240	0.70337	0.013399	1.18E-4	ENSG00000078814	ENST00000262873	D	0.87491	-2.26	3.66	3.66	0.41972	Myosin head, motor domain (2);	0.000000	0.35708	N	0.003040	T	0.81612	0.4859	M	0.80847	2.515	0.39394	D	0.966466	P	0.51240	0.943	P	0.47299	0.543	D	0.87287	0.2296	10	0.72032	D	0.01	.	12.3325	0.55048	0.0878:0.0:0.9122:0.0	.	334	A7E2Y1	MYH7B_HUMAN	T	376	ENSP00000262873:A376T	ENSP00000262873:A376T	A	+	1	0	MYH7B	33038445	0.861000	0.29849	1.000000	0.80357	0.538000	0.34931	2.633000	0.46519	2.356000	0.79943	0.655000	0.94253	GCC	G|0.993;A|0.007	0.007	strong		0.607	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884		A	33574784	G	A	33574784	3	1	22	1	0	0	0	0	1	0	0	0	10049	1087	38	1	1176	1	MYH7B	20	33574784	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6329	33574784	29450736	4169	7070											
MYH7B	26133	hgsc.bcm.edu	37	chr20	33588874	33588874	+	IGR	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagaagacgctggagcagacGgtgcgcgagctccaggcccg	10	3	16	12	5	0	3	0	0	0	3	1	5	1	4	2	3	3	3	2	3	2	0	rs76931580	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33588874G>A	ENST00000252015.2	-	0	3226				MYH7B_ENST00000262873.7_Silent_p.T1838T			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)			TGGAGCAGACGGTGCGCGAGC	0.647													G|||	66	0.0131789	0.0469	0.0058	5008	,	,		17893	0.0		0.0	False		,,,				2504	0.0				p.T1838T		Atlas-SNP	.											.	MYH7B	145	.	0			c.G5514A						PASS	.	G		149,4255	97.1+/-135.8	0,149,2053	40	50	47		5514	-9.1	0.1	20	dbSNP_131	47	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	MYH7B	NM_020884.3		0,151,6351	AA,AG,GG		0.0233,3.3833,1.1612		1838/1984	33588874	151,12853	2202	4300	6502	SO:0001628	intergenic_variant	57644	exon41			GCAGACGGTGCGC	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		20.37:g.33588874G>A		198	0	0		192	85	0.442708	NM_020884	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Silent	SNP	ENST00000252015.2	37	CCDS13246.1																																																																																			G|0.996;A|0.004	0.004	strong		0.647	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638		A	33588874	G	A	33588874	1	1	22	0	1	0	0	0	0	0	0	0	10049	1103	39	1		1	MYH7B	20	33588874	IGR	SNP	G	TCGA-G8-6324-01A-11D-2210-10	14090	33588874	29436646	4170	7071											
UQCC	55245	hgsc.bcm.edu	37	chr20	33971876	33971876	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atacttcctattcagctgtaTgtctattccaggaatctgtt	9	17	6	9	0	3	0	1	0	2	0	5	1	5	1	2	1	2	3	2	1	5	8	rs114745625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33971876T>C	ENST00000374385.5	-	3	367	c.190A>G	c.(190-192)Ata>Gta	p.I64V	UQCC1_ENST00000349714.5_Missense_Mutation_p.I64V|UQCC1_ENST00000374384.2_Missense_Mutation_p.I64V|UQCC1_ENST00000407996.2_Missense_Mutation_p.I64V|UQCC1_ENST00000491125.1_5'UTR|UQCC1_ENST00000397556.3_Intron|UQCC1_ENST00000540457.1_Intron|UQCC1_ENST00000374377.5_Intron|UQCC1_ENST00000542501.1_Missense_Mutation_p.I64V|UQCC1_ENST00000359226.2_Missense_Mutation_p.I64V|UQCC1_ENST00000397554.1_Missense_Mutation_p.I64V|UQCC1_ENST00000374380.2_Intron	NM_018244.4	NP_060714.3	Q9NVA1	UQCC1_HUMAN	ubiquinol-cytochrome c reductase complex assembly factor 1	64						cytoplasmic membrane-bounded vesicle (GO:0016023)|mitochondrion (GO:0005739)											TTCAGCTGTATGTCTATTCCA	0.438													T|||	13	0.00259585	0.0098	0.0	5008	,	,		21480	0.0		0.0	False		,,,				2504	0.0				p.I64V		Atlas-SNP	.											.	UQCC	41	.	0			c.A190G						PASS	.	T	,VAL/ILE,VAL/ILE	57,4349	56.2+/-92.4	1,55,2147	184	149	161		,190,190	-1.4	0	20	dbSNP_132	161	0,8600		0,0,4300	yes	intron,missense,missense	UQCC	NM_001184977.1,NM_018244.4,NM_199487.2	,29,29	1,55,6447	CC,CT,TT		0.0,1.2937,0.4383	,benign,benign	,64/300,64/274	33971876	57,12949	2203	4300	6503	SO:0001583	missense	55245	exon3			GCTGTATGTCTAT	AK001712	CCDS13252.1, CCDS13253.1, CCDS13253.2, CCDS54458.1	20q11.22	2013-09-20	2013-09-20	2013-09-20	ENSG00000101019	ENSG00000101019		"Mitochondrial respiratory chain complex assembly factors"	15891	protein-coding gene	gene with protein product	"Basic FGF-repressed Zic-binding protein", "cytochrome B protein synthesis 3 homolog (S. cerevisiae)"	611797	"chromosome 20 open reading frame 44", "ubiquinol-cytochrome c reductase complex chaperone"	C20orf44, UQCC			Standard	NM_018244		Approved	FLJ10850, CBP3, BFZB	uc002xcd.3	Q9NVA1	OTTHUMG00000032335	ENST00000374385.5:c.190A>G	20.37:g.33971876T>C	ENSP00000363506:p.Ile64Val	217	0	0		218	104	0.477064	NM_018244	B1AKV5|Q0VF37|Q5T348|Q5T351|Q5T353|Q86YU3|Q86YU4|Q96H66|Q9H438|Q9H452|Q9H9K8|Q9H9R5	Missense_Mutation	SNP	ENST00000374385.5	37	CCDS13252.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	T	0.042	-1.280171	0.01398	0.012937	0.0	ENSG00000101019	ENST00000349714;ENST00000359226;ENST00000374384;ENST00000374385;ENST00000407996;ENST00000542501;ENST00000438533;ENST00000397554	T;T;T;T;T;T;T;T	0.42900	1.55;1.57;1.66;1.66;0.96;1.54;1.62;1.62	5.02	-1.38	0.09027	.	0.874131	0.10138	N	0.711165	T	0.13500	0.0327	N	0.12961	0.28	0.09310	N	1	B;B;B;B;B	0.14012	0.009;0.0;0.002;0.0;0.0	B;B;B;B;B	0.13407	0.009;0.0;0.001;0.0;0.0	T	0.18777	-1.0326	10	0.27785	T	0.31	-3.4421	0.9374	0.01347	0.1611:0.3029:0.1662:0.3698	.	64;64;64;64;64	B7Z7J8;B7ZBG3;B1AKV2;B7ZBG4;Q9NVA1	.;.;.;.;UQCC_HUMAN	V	64;64;64;64;64;64;78;64	ENSP00000335364:I64V;ENSP00000352161:I64V;ENSP00000363505:I64V;ENSP00000363506:I64V;ENSP00000386064:I64V;ENSP00000445059:I64V;ENSP00000398531:I78V;ENSP00000380686:I64V	ENSP00000335364:I64V	I	-	1	0	UQCC	33435290	0.000000	0.05858	0.004000	0.12327	0.135000	0.20990	-0.025000	0.12413	0.080000	0.16959	0.533000	0.62120	ATA	T|0.997;C|0.003	0.003	strong		0.438	UQCC1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078866.1	NM_018244		C	33971876	T	C	33971876	3	2	22	1	0	0	0	0	1	0	0	0	17030	1464	51	3	741	3	UQCC	20	33971876	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	383002	33971876	29053644	4171	7072											
UQCC	55245	hgsc.bcm.edu	37	chr20	33981906	33981906	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	aaatcttacctgggaagtgcGagacagagccctgtccccct	10	8	10	13	1	1	2	0	0	1	2	2	4	2	3	4	1	3	0	4	1	3	1	rs75909303	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33981906G>C	ENST00000374385.5	-	2	295	c.118C>G	c.(118-120)Cgc>Ggc	p.R40G	UQCC1_ENST00000349714.5_Missense_Mutation_p.R40G|UQCC1_ENST00000374384.2_Missense_Mutation_p.R40G|UQCC1_ENST00000407996.2_Missense_Mutation_p.R40G|UQCC1_ENST00000491125.1_5'UTR|UQCC1_ENST00000397556.3_5'UTR|UQCC1_ENST00000540457.1_Intron|UQCC1_ENST00000374377.5_Missense_Mutation_p.S20W|UQCC1_ENST00000542501.1_Missense_Mutation_p.R40G|UQCC1_ENST00000359226.2_Missense_Mutation_p.R40G|UQCC1_ENST00000397554.1_Missense_Mutation_p.R40G|UQCC1_ENST00000374380.2_Missense_Mutation_p.R40G	NM_018244.4	NP_060714.3	Q9NVA1	UQCC1_HUMAN	ubiquinol-cytochrome c reductase complex assembly factor 1	40						cytoplasmic membrane-bounded vesicle (GO:0016023)|mitochondrion (GO:0005739)											TGGGAAGTGCGAGACAGAGCC	0.433													C|||	31	0.0061901	0.0227	0.0014	5008	,	,		19195	0.0		0.0	False		,,,				2504	0.0				p.R40G		Atlas-SNP	.											UQCC,NS,carcinoma,0,1	UQCC	41	1	0			c.C118G						PASS	.	C	GLY/ARG,GLY/ARG,GLY/ARG	95,4311	817.7+/-416.3	2,91,2110	124	117	120		118,118,118	4.8	1	20	dbSNP_131	120	0,8600		0,0,4300	yes	missense,missense,missense	UQCC	NM_001184977.1,NM_018244.4,NM_199487.2	125,125,125	2,91,6410	CC,CG,GG		0.0,2.1562,0.7304	benign,benign,benign	40/232,40/300,40/274	33981906	95,12911	2203	4300	6503	SO:0001583	missense	55245	exon2			AAGTGCGAGACAG	AK001712	CCDS13252.1, CCDS13253.1, CCDS13253.2, CCDS54458.1	20q11.22	2013-09-20	2013-09-20	2013-09-20	ENSG00000101019	ENSG00000101019		"Mitochondrial respiratory chain complex assembly factors"	15891	protein-coding gene	gene with protein product	"Basic FGF-repressed Zic-binding protein", "cytochrome B protein synthesis 3 homolog (S. cerevisiae)"	611797	"chromosome 20 open reading frame 44", "ubiquinol-cytochrome c reductase complex chaperone"	C20orf44, UQCC			Standard	NM_018244		Approved	FLJ10850, CBP3, BFZB	uc002xcd.3	Q9NVA1	OTTHUMG00000032335	ENST00000374385.5:c.118C>G	20.37:g.33981906G>C	ENSP00000363506:p.Arg40Gly	77	0	0		75	35	0.466667	NM_018244	B1AKV5|Q0VF37|Q5T348|Q5T351|Q5T353|Q86YU3|Q86YU4|Q96H66|Q9H438|Q9H452|Q9H9K8|Q9H9R5	Missense_Mutation	SNP	ENST00000374385.5	37	CCDS13252.1	8|8	0.003663003663003663|0.003663003663003663	8|8	0.016260162601626018|0.016260162601626018	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	2.061|2.061	-0.415323|-0.415323	0.04766|0.04766	0.021562|0.021562	0.0|0.0	ENSG00000101019|ENSG00000101019	ENST00000349714;ENST00000359226;ENST00000374384;ENST00000374380;ENST00000374385;ENST00000407996;ENST00000424405;ENST00000542501;ENST00000438533;ENST00000397554|ENST00000374377	T;T;T;T;T;T;T;T;T;T|.	0.05382|.	3.45;3.45;3.45;3.45;3.45;3.45;3.45;3.45;3.45;3.45|.	4.76|4.76	4.76|4.76	0.60689|0.60689	.|.	0.246918|.	0.36034|.	N|.	0.002824|.	T|T	0.03959|0.03959	0.0111|0.0111	N|N	0.00182|0.00182	-1.905|-1.905	0.09310|0.09310	N|N	0.999994|0.999994	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|T	0.12863|0.12863	-1.0531|-1.0531	10|6	0.02654|0.87932	T|D	1|0	0.7758|0.7758	11.0424|11.0424	0.47838|0.47838	0.0:0.8127:0.1873:0.0|0.0:0.8127:0.1873:0.0	.|.	40;40;40;40;40|.	B1AKV5;B7Z7J8;B7ZBG3;B7ZBG4;Q9NVA1|.	.;.;.;.;UQCC_HUMAN|.	G|W	40|20	ENSP00000335364:R40G;ENSP00000352161:R40G;ENSP00000363505:R40G;ENSP00000363501:R40G;ENSP00000363506:R40G;ENSP00000386064:R40G;ENSP00000399713:R40G;ENSP00000445059:R40G;ENSP00000398531:R40G;ENSP00000380686:R40G|.	ENSP00000335364:R40G|ENSP00000363497:S20W	R|S	-|-	1|2	0|0	UQCC|UQCC	33445320|33445320	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.857000|0.857000	0.48899|0.48899	1.417000|1.417000	0.34770|0.34770	1.248000|1.248000	0.43934|0.43934	-0.127000|-0.127000	0.14921|0.14921	CGC|TCG	G|0.994;C|0.006	0.006	strong		0.433	UQCC1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078866.1	NM_018244		C	33981906	G	C	33981906	3	2	22	1	0	0	0	0	1	0	0	0	17030	1058	37	4	817	4	UQCC	20	33981906	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	10030	33981906	29043614	4172	7073											
GDF5	8200	hgsc.bcm.edu	37	chr20	34022344	34022344	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agatgtcgaacacctcccagCcagatccgtccaggcctggc	9	6	10	16	2	0	2	0	0	0	2	4	3	3	2	6	2	2	0	6	2	1	0			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34022344C>T	ENST00000374372.1	-	4	1372	c.869G>A	c.(868-870)gGc>gAc	p.G290D	GDF5OS_ENST00000374375.1_Missense_Mutation_p.P130S|GDF5_ENST00000374369.3_Missense_Mutation_p.G290D			P43026	GDF5_HUMAN	growth differentiation factor 5	290					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)			CACCTCCCAGCCAGATCCGTC	0.682																																					p.G290D		Atlas-SNP	.											.	GDF5	66	.	0			c.G869A						PASS	.						17	19	18					20																	34022344		2197	4298	6495	SO:0001583	missense	8200	exon2			TCCCAGCCAGATC	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.869G>A	20.37:g.34022344C>T	ENSP00000363492:p.Gly290Asp	97	0	0		88	4	0.0454545	NM_000557	E1P5Q2|Q96SB1	Missense_Mutation	SNP	ENST00000374372.1	37	CCDS13254.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.00|14.00	2.403881|2.403881	0.42613|0.42613	.|.	.|.	ENSG00000125965|ENSG00000204183	ENST00000374369;ENST00000374372|ENST00000374375	T;T|.	0.69806|.	-0.43;-0.43|.	4.56|4.56	4.56|4.56	0.56223|0.56223	Transforming growth factor-beta, N-terminal (1);|.	0.494665|.	0.18574|.	N|.	0.137222|.	T|T	0.41834|0.41834	0.1176|0.1176	L|L	0.47190|0.47190	1.495|1.495	0.29135|0.29135	N|N	0.87936|0.87936	B;P|.	0.34615|.	0.316;0.459|.	B;B|.	0.39465|.	0.3;0.245|.	T|T	0.46693|0.46693	-0.9173|-0.9173	10|6	0.17832|0.87932	T|D	0.49|0	.|.	5.4132|5.4132	0.16360|0.16360	0.0:0.7525:0.0:0.2475|0.0:0.7525:0.0:0.2475	.|.	290;290|.	F1T0J1;P43026|.	.;GDF5_HUMAN|.	D|S	290|130	ENSP00000363489:G290D;ENSP00000363492:G290D|.	ENSP00000363489:G290D|ENSP00000363495:P130S	G|P	-|+	2|1	0|0	GDF5|GDF5OS	33485758|33485758	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	2.633000|2.633000	0.46519|0.46519	2.353000|2.353000	0.79882|0.79882	0.491000|0.491000	0.48974|0.48974	GGC|CCA	.	.	none		0.682	GDF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078875.2			T	34022344	C	T	34022344	3	4	22	1	0	0	0	0	1	0	0	0	6324	739	26	2	640	2	GDF5	20	34022344	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	40438	34022344	29003176	4173	7074											
CEP250	11190	hgsc.bcm.edu	37	chr20	34084415	34084415	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctctttttagcctgactctGtcactgatggaaaaggaaca	11	13	8	9	0	3	2	1	2	2	0	4	4	3	4	1	2	2	0	1	2	4	3	rs224376	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34084415G>C	ENST00000397527.1	+	25	3897	c.3177G>C	c.(3175-3177)ctG>ctC	p.L1059L	CEP250_ENST00000342580.4_Silent_p.L1003L	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	1059	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)			GCCTGACTCTGTCACTGATGG	0.453													G|||	31	0.0061901	0.0234	0.0	5008	,	,		19409	0.0		0.0	False		,,,				2504	0.0				p.L1059L		Atlas-SNP	.											.	CEP250	141	.	0			c.G3177C						PASS	.	G		131,4275	95.7+/-134.4	2,127,2074	72	68	69		3177	3.8	1	20	dbSNP_79	69	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	CEP250	NM_007186.3		2,130,6371	CC,CG,GG		0.0349,2.9732,1.0303		1059/2443	34084415	134,12872	2203	4300	6503	SO:0001819	synonymous_variant	11190	exon25			GACTCTGTCACTG	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.3177G>C	20.37:g.34084415G>C		60	0	0		64	32	0.5	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Silent	SNP	ENST00000397527.1	37	CCDS13255.1																																																																																			G|0.991;C|0.009	0.009	strong		0.453	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		C	34084415	G	C	34084415	2	2	22	1	0	0	0	0	0	0	0	1	3254	1364	48	4		4	CEP250	20	34084415	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	62071	34084415	28941105	4174	7075											
CEP250	11190	hgsc.bcm.edu	37	chr20	34089679	34089679	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcttctcaaagagaaatcCaagtgggaaggaaagcagaa	17	6	10	8	0	2	2	1	0	2	2	4	5	3	4	2	2	1	1	2	2	6	1	rs224379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34089679C>T	ENST00000397527.1	+	29	4626	c.3906C>T	c.(3904-3906)tcC>tcT	p.S1302S	CEP250_ENST00000342580.4_Silent_p.S1246S	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	1302	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)			AAGAGAAATCCAAGTGGGAAG	0.493													C|||	14	0.00279553	0.0106	0.0	5008	,	,		22493	0.0		0.0	False		,,,				2504	0.0				p.S1302S		Atlas-SNP	.											.	CEP250	141	.	0			c.C3906T						PASS	.	C		58,4346	56.2+/-92.4	0,58,2144	50	50	50		3906	1.9	1	20	dbSNP_79	50	0,8600		0,0,4300	no	coding-synonymous	CEP250	NM_007186.3		0,58,6444	TT,TC,CC		0.0,1.317,0.446		1302/2443	34089679	58,12946	2202	4300	6502	SO:0001819	synonymous_variant	11190	exon29			GAAATCCAAGTGG	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.3906C>T	20.37:g.34089679C>T		31	0	0		35	21	0.6	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Silent	SNP	ENST00000397527.1	37	CCDS13255.1																																																																																			C|0.996;T|0.004	0.004	strong		0.493	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		T	34089679	C	T	34089679	2	4	22	1	0	0	0	0	0	0	0	1	3254	581	21	2		2	CEP250	20	34089679	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	5264	34089679	28935841	4175	7076											
CEP250	11190	hgsc.bcm.edu	37	chr20	34091624	34091624	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agtcaactggatgaggcccaGagagccctagcccagaggga	12	4	14	11	0	1	3	1	1	0	2	1	6	1	5	3	3	3	0	3	3	2	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34091624G>A	ENST00000397527.1	+	30	6147	c.5427G>A	c.(5425-5427)caG>caA	p.Q1809Q	CEP250_ENST00000342580.4_Silent_p.Q1753Q	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	1809	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)			ATGAGGCCCAGAGAGCCCTAG	0.597																																					p.Q1809Q		Atlas-SNP	.											.	CEP250	141	.	0			c.G5427A						PASS	.						55	59	58					20																	34091624		2203	4300	6503	SO:0001819	synonymous_variant	11190	exon30			GGCCCAGAGAGCC	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.5427G>A	20.37:g.34091624G>A		57	0	0		85	41	0.482353	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Silent	SNP	ENST00000397527.1	37	CCDS13255.1																																																																																			.	.	none		0.597	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		A	34091624	G	A	34091624	2	1	22	1	0	0	0	0	0	0	0	1	3254	933	33	2		2	CEP250	20	34091624	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1945	34091624	28933896	4176	7077											
SPAG4	6676	hgsc.bcm.edu	37	chr20	34204168	34204168	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctctcagcagaagccagcGcctcggagccacaactggca	11	4	11	15	2	1	1	1	0	1	1	3	2	1	2	3	2	6	3	3	2	2	0	rs115161777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34204168G>A	ENST00000374273.3	+	1	355	c.243G>A	c.(241-243)gcG>gcA	p.A81A		NM_003116.1	NP_003107.1	Q9NPE6	SPAG4_HUMAN	sperm associated antigen 4	81					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)			AGAAGCCAGCGCCTCGGAGCC	0.731													G|||	107	0.0213658	0.0779	0.0058	5008	,	,		8847	0.0		0.0	False		,,,				2504	0.0				p.A81A		Atlas-SNP	.											.	SPAG4	36	.	0			c.G243A						PASS	.	G		185,3729		2,181,1774	5	8	7		243	4.6	1	20	dbSNP_132	7	4,7996		0,4,3996	no	coding-synonymous	SPAG4	NM_003116.1		2,185,5770	AA,AG,GG		0.05,4.7266,1.5864		81/438	34204168	189,11725	1957	4000	5957	SO:0001819	synonymous_variant	6676	exon1			GCCAGCGCCTCGG	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.243G>A	20.37:g.34204168G>A		32	0	0		40	15	0.375	NM_003116	O43648	Silent	SNP	ENST00000374273.3	37	CCDS13259.1																																																																																			G|0.980;A|0.020	0.020	strong		0.731	SPAG4-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078896.1	NM_003116		A	34204168	G	A	34204168	2	1	22	1	0	0	0	0	0	0	0	1	14995	1074	38	1		1	SPAG4	20	34204168	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	112544	34204168	28821352	4177	7078											
SPAG4	6676	hgsc.bcm.edu	37	chr20	34205080	34205080	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccgactgggtctccagtagtCtctgaggagccgctcgacct	6	9	12	14	3	2	1	0	1	2	0	5	4	2	2	4	2	1	2	4	2	1	1	rs116016997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34205080C>T	ENST00000374273.3	+	2	439	c.327C>T	c.(325-327)gtC>gtT	p.V109V	SPAG4_ENST00000462896.1_3'UTR	NM_003116.1	NP_003107.1	Q9NPE6	SPAG4_HUMAN	sperm associated antigen 4	109					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)			CTCCAGTAGTCTCTGAGGAGC	0.637													C|||	107	0.0213658	0.0779	0.0058	5008	,	,		11937	0.0		0.0	False		,,,				2504	0.0				p.V109V		Atlas-SNP	.											.	SPAG4	36	.	0			c.C327T						PASS	.	C		232,4174		2,228,1973	24	26	25		327	2.1	0.8	20	dbSNP_132	25	3,8595		0,3,4296	no	coding-synonymous	SPAG4	NM_003116.1		2,231,6269	TT,TC,CC		0.0349,5.2655,1.8071		109/438	34205080	235,12769	2203	4299	6502	SO:0001819	synonymous_variant	6676	exon2			AGTAGTCTCTGAG	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.327C>T	20.37:g.34205080C>T		65	0	0		83	35	0.421687	NM_003116	O43648	Silent	SNP	ENST00000374273.3	37	CCDS13259.1																																																																																			C|0.982;T|0.018	0.018	strong		0.637	SPAG4-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078896.1	NM_003116		T	34205080	C	T	34205080	2	4	22	1	0	0	0	0	0	0	0	1	14995	900	32	2		2	SPAG4	20	34205080	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	912	34205080	28820440	4178	7079											
SPAG4	6676	hgsc.bcm.edu	37	chr20	34208869	34208869	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggccacccccgtttcacGtgcttgtatcgagtccgtgc	4	11	12	14	4	1	0	1	0	0	0	3	1	2	0	4	2	2	3	4	2	1	3	rs34962502	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34208869G>A	ENST00000374273.3	+	12	1351	c.1239G>A	c.(1237-1239)acG>acA	p.T413T		NM_003116.1	NP_003107.1	Q9NPE6	SPAG4_HUMAN	sperm associated antigen 4	413	SUN. {ECO:0000255|PROSITE- ProRule:PRU00802}.				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)			CCCGTTTCACGTGCTTGTATC	0.557													G|||	51	0.0101837	0.0378	0.0014	5008	,	,		15888	0.0		0.0	False		,,,				2504	0.0				p.T413T		Atlas-SNP	.											SPAG4,colon,carcinoma,+1,1	SPAG4	36	1	0			c.G1239A						PASS	.	G		183,4223	118.4+/-156.1	4,175,2024	82	83	83		1239	-11.1	0.2	20	dbSNP_126	83	2,8598	2.2+/-6.3	0,2,4298	yes	coding-synonymous	SPAG4	NM_003116.1		4,177,6322	AA,AG,GG		0.0233,4.1534,1.4224		413/438	34208869	185,12821	2203	4300	6503	SO:0001819	synonymous_variant	6676	exon12			TTTCACGTGCTTG	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.1239G>A	20.37:g.34208869G>A		92	0	0		116	66	0.568965	NM_003116	O43648	Silent	SNP	ENST00000374273.3	37	CCDS13259.1																																																																																			G|0.986;A|0.014	0.014	strong		0.557	SPAG4-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078896.1	NM_003116		A	34208869	G	A	34208869	2	1	22	1	0	0	0	0	0	0	0	1	14995	1132	40	1		1	SPAG4	20	34208869	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3789	34208869	28816651	4179	7080											
RBM12	10137	hgsc.bcm.edu	37	chr20	34241530	34241530	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caacaagaacatgtacagcaTtttcatccactgggattcct	13	11	6	11	0	1	1	1	0	0	1	3	2	3	2	2	1	4	2	2	1	4	4	rs17092928	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34241530T>C	ENST00000374114.3	-	3	1978	c.1715A>G	c.(1714-1716)aAt>aGt	p.N572S	CPNE1_ENST00000397443.1_Intron|RP1-309K20.6_ENST00000541176.2_Intron|RBM12_ENST00000359646.1_Missense_Mutation_p.N572S|RBM12_ENST00000374104.3_Missense_Mutation_p.N572S|CPNE1_ENST00000397442.1_Intron|CPNE1_ENST00000317677.5_5'UTR|CPNE1_ENST00000397445.1_Intron|CPNE1_ENST00000352393.4_Intron|CPNE1_ENST00000317619.3_Intron|CPNE1_ENST00000397446.1_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	572			N -> S (in dbSNP:rs17092928).			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)			ATGTACAGCATTTTCATCCAC	0.408													T|||	124	0.0247604	0.09	0.0072	5008	,	,		22183	0.0		0.0	False		,,,				2504	0.0				p.N572S		Atlas-SNP	.											.	RBM12	93	.	0			c.A1715G						PASS	.	T	SER/ASN,SER/ASN,,,SER/ASN,SER/ASN,,,,	267,4139	150.7+/-184.7	3,261,1939	194	187	189		1715,1715,,,1715,1715,,,,	3.7	1	20	dbSNP_123	189	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense,intron,utr-5,missense,missense,intron,intron,intron,intron	CPNE1,RBM12	NM_001198838.1,NM_001198840.1,NM_001198863.1,NM_003915.5,NM_006047.5,NM_152838.3,NM_152925.2,NM_152926.2,NM_152927.2,NM_152928.2	46,46,,,46,46,,,,	3,265,6235	CC,CT,TT		0.0465,6.0599,2.0837	benign,benign,,,benign,benign,,,,	572/933,572/933,,,572/933,572/933,,,,	34241530	271,12735	2203	4300	6503	SO:0001583	missense	10137	exon2			ACAGCATTTTCAT	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.1715A>G	20.37:g.34241530T>C	ENSP00000363228:p.Asn572Ser	149	0	0		148	78	0.527027	NM_001198840	B3KRU2|E1P5R6|O94865|Q8N3B1|Q9H196	Missense_Mutation	SNP	ENST00000374114.3	37	CCDS13261.1	48	0.02197802197802198	43	0.08739837398373984	5	0.013812154696132596	0	0.0	0	0.0	T	8.105	0.777613	0.16120	0.060599	4.65E-4	ENSG00000244462	ENST00000374114;ENST00000359646;ENST00000374104;ENST00000349942	T;T;T	0.15487	2.42;2.42;2.42	4.83	3.69	0.42338	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.200400	0.42682	N	0.000670	T	0.00496	0.0016	L	0.38175	1.15	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.17289	-1.0374	10	0.37606	T	0.19	-5.5476	10.7607	0.46264	0.0:0.0756:0.0:0.9244	rs17092928;rs52836153;rs17092928	572	Q9NTZ6	RBM12_HUMAN	S	572;572;572;371	ENSP00000363228:N572S;ENSP00000352668:N572S;ENSP00000363217:N572S	ENSP00000339879:N371S	N	-	2	0	RBM12	33704944	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.686000	0.61700	0.827000	0.34685	0.460000	0.39030	AAT	T|0.978;C|0.022	0.022	strong		0.408	RBM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078894.1	NM_006047		C	34241530	T	C	34241530	3	2	22	1	0	0	0	0	1	0	0	0	13128	1493	52	3	1087	3	RBM12	20	34241530	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	32661	34241530	28783990	4180	7081											
EPB41L1	2036	hgsc.bcm.edu	37	chr20	34782156	34782156	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagttctcccgcccagcctcGgtcagcgagaaccatgatgc	8	7	11	15	3	2	2	1	1	1	1	4	4	2	2	4	1	4	1	4	1	1	1	rs111865221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34782156G>A	ENST00000338074.2	+	12	1484	c.1323G>A	c.(1321-1323)tcG>tcA	p.S441S	EPB41L1_ENST00000441639.1_Silent_p.S379S|EPB41L1_ENST00000373950.2_Silent_p.S344S|EPB41L1_ENST00000202028.5_Silent_p.S379S|EPB41L1_ENST00000373946.3_Silent_p.S410S|EPB41L1_ENST00000373941.1_Silent_p.S441S	NM_001258329.1|NM_012156.2	NP_001245258.1|NP_036288.2	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	441					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)			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)					GCCCAGCCTCGGTCAGCGAGA	0.627													G|||	32	0.00638978	0.0234	0.0014	5008	,	,		20291	0.0		0.0	False		,,,				2504	0.0				p.S441S		Atlas-SNP	.											.	EPB41L1	111	.	0			c.G1323A						PASS	.	G	,	93,4313	77.8+/-116.1	2,89,2112	60	52	55		1323,1137	-10.4	0	20	dbSNP_132	55	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	EPB41L1	NM_012156.2,NM_177996.1	,	2,89,6412	AA,AG,GG		0.0,2.1108,0.7151	,	441/882,379/780	34782156	93,12913	2203	4300	6503	SO:0001819	synonymous_variant	2036	exon13			AGCCTCGGTCAGC	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.1323G>A	20.37:g.34782156G>A		137	0	0		170	77	0.452941	NM_001258329	O15046|Q4VXM6|Q4VXM7|Q4VXM8|Q4VXN4|Q6ZT61|Q8IUU7|Q96CV5|Q96L65	Silent	SNP	ENST00000338074.2	37	CCDS13271.1	16	0.007326007326007326	15	0.03048780487804878	1	0.0027624309392265192	0	0.0	0	0.0	G	1.735	-0.493136	0.04322	0.021108	0.0	ENSG00000088367	ENST00000451082	.	.	.	5.18	-10.4	0.00318	.	.	.	.	.	T	0.16514	0.0397	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72204	-0.4361	4	.	.	.	.	1.9428	0.03350	0.0936:0.1922:0.346:0.3681	.	.	.	.	Q	19	.	.	R	+	2	0	EPB41L1	34245570	0.000000	0.05858	0.002000	0.10522	0.521000	0.34408	-9.217000	0.00013	-7.995000	0.00000	-3.875000	0.00017	CGG	G|0.991;A|0.009	0.009	strong		0.627	EPB41L1-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078978.3	NM_012156		A	34782156	G	A	34782156	2	1	22	1	0	0	0	0	0	0	0	1	5154	1103	39	1		1	EPB41L1	20	34782156	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	540626	34782156	28243364	4181	7082											
MYL9	10398	hgsc.bcm.edu	37	chr20	35176541	35176541	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggggagaagctgaacggcacGgaccccgaggatgtgattcg	10	5	17	9	4	0	3	0	2	0	1	1	7	0	5	2	5	2	2	2	5	2	1	rs11553089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:35176541G>A	ENST00000279022.2	+	3	395	c.291G>A	c.(289-291)acG>acA	p.T97T	MYL9_ENST00000346786.2_Intron|RP5-977B1.7_ENST00000439595.1_RNA|RP5-977B1.7_ENST00000425233.1_RNA|RP5-977B1.11_ENST00000561134.1_RNA	NM_006097.4	NP_006088.2	P24844	MYL9_HUMAN	myosin, light chain 9, regulatory	97					axon guidance (GO:0007411)|muscle contraction (GO:0006936)|platelet aggregation (GO:0070527)|regulation of muscle contraction (GO:0006937)	cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|stress fiber (GO:0001725)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|structural constituent of muscle (GO:0008307)			endometrium(2)|kidney(1)|large_intestine(3)|lung(2)	8	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				TGAACGGCACGGACCCCGAGG	0.607													G|||	112	0.0223642	0.0787	0.0101	5008	,	,		17578	0.0		0.0	False		,,,				2504	0.001				p.T97T		Atlas-SNP	.											.	MYL9	13	.	0			c.G291A						PASS	.	G	,	262,4144	151.0+/-185.0	10,242,1951	114	78	91		291,	-9.7	0.1	20	dbSNP_120	91	1,8599		0,1,4299	no	coding-synonymous,intron	MYL9	NM_006097.3,NM_181526.1	,	10,243,6250	AA,AG,GG		0.0116,5.9464,2.0221	,	97/173,	35176541	263,12743	2203	4300	6503	SO:0001819	synonymous_variant	10398	exon3			CGGCACGGACCCC	J02854	CCDS13276.1, CCDS13277.1	20q11.23	2013-01-10	2006-09-29		ENSG00000101335	ENSG00000101335		"Myosins / Light chain", "EF-hand domain containing"	15754	protein-coding gene	gene with protein product	"myosin regulatory light chain 2, smooth muscle isoform", "myosin regulatory light chain 1"	609905	"myosin, light polypeptide 9, regulatory"			2526655	Standard	NM_006097		Approved	MYRL2, MLC2, LC20, MRLC1	uc002xfl.2	P24844	OTTHUMG00000032387	ENST00000279022.2:c.291G>A	20.37:g.35176541G>A		117	0	0		101	60	0.594059	NM_006097	E1P5T6|Q9BQL9|Q9BUF9|Q9H136	Silent	SNP	ENST00000279022.2	37	CCDS13276.1																																																																																			G|0.975;A|0.025	0.025	strong		0.607	MYL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079015.2	NM_006097		A	35176541	G	A	35176541	2	1	22	1	0	0	0	0	0	0	0	1	10063	1103	39	1		1	MYL9	20	35176541	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	394385	35176541	27848979	4182	7083											
SLA2	84174	hgsc.bcm.edu	37	chr20	35242745	35242745	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgagtggtgtcctctgcaCagtcacaggtaggggtatat	8	12	14	7	0	2	1	1	1	1	0	3	1	3	1	1	4	1	4	1	4	3	4	rs34834764	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:35242745C>T	ENST00000262866.4	-	7	1050	c.628G>A	c.(628-630)Gtg>Atg	p.V210M	SLA2_ENST00000360672.2_Missense_Mutation_p.C193Y	NM_032214.3|NM_175077.2	NP_115590.1|NP_778252.1	Q9H6Q3	SLAP2_HUMAN	Src-like-adaptor 2	210	SLA C-terminal.		V -> M (in dbSNP:rs34834764).		antigen receptor-mediated signaling pathway (GO:0050851)|B cell mediated immunity (GO:0019724)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of B cell activation (GO:0050869)|negative regulation of calcium-mediated signaling (GO:0050849)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of signal transduction (GO:0009967)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome membrane (GO:0010008)|late endosome (GO:0005770)|plasma membrane (GO:0005886)	protein N-terminus binding (GO:0047485)|SH3/SH2 adaptor activity (GO:0005070)			endometrium(1)|lung(2)|skin(2)	5	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)				GTCCTCTGCACAGTCACAGGT	0.572													C|||	149	0.0297524	0.1067	0.0115	5008	,	,		21213	0.0		0.0	False		,,,				2504	0.0				p.V210M	Ovarian(59;720 1165 26994 46188 51693)	Atlas-SNP	.											.	SLA2	12	.	0			c.G628A						PASS	.	C	MET/VAL,TYR/CYS	374,4032	191.2+/-216.9	17,340,1846	152	144	147		628,578	5.4	1	20	dbSNP_126	147	1,8599		0,1,4299	yes	missense,missense	SLA2	NM_032214.2,NM_175077.1	21,194	17,341,6145	TT,TC,CC		0.0116,8.4884,2.8833	probably-damaging,probably-damaging	210/262,193/211	35242745	375,12631	2203	4300	6503	SO:0001583	missense	84174	exon7			TCTGCACAGTCAC	AF326353	CCDS13282.1, CCDS13283.1	20q11.23	2013-02-14			ENSG00000101082	ENSG00000101082		"SH2 domain containing"	17329	protein-coding gene	gene with protein product		606577		C20orf156		11696592	Standard	NM_032214		Approved	FLJ21992, SLAP-2	uc002xfv.3	Q9H6Q3	OTTHUMG00000032393	ENST00000262866.4:c.628G>A	20.37:g.35242745C>T	ENSP00000262866:p.Val210Met	176	0	0		205	105	0.512195	NM_032214	A8K648|E1P5U1|E1P5U2|Q5TH27|Q5TH28|Q8WY18|Q96QI4|Q9H135	Missense_Mutation	SNP	ENST00000262866.4	37	CCDS13282.1	45|45	0.020604395604395604|0.020604395604395604	42|42	0.08536585365853659|0.08536585365853659	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	C|C	15.68|15.68	2.904261|2.904261	0.52333|0.52333	0.084884|0.084884	1.16E-4|1.16E-4	ENSG00000101082|ENSG00000101082	ENST00000360672|ENST00000262866	T|T	0.74632|0.79033	-0.86|-1.23	5.43|5.43	5.43|5.43	0.79202|0.79202	.|.	.|0.131339	.|0.49916	.|D	.|0.000132	T|T	0.09862|0.09862	0.0242|0.0242	.|.	.|.	.|.	0.26547|0.26547	N|N	0.973972|0.973972	B|B	0.14012|0.29988	0.009|0.264	B|B	0.04013|0.33846	0.001|0.171	T|T	0.36187|0.36187	-0.9758|-0.9758	8|9	0.45353|0.39692	T|T	0.12|0.17	-19.6165|-19.6165	16.7763|16.7763	0.85551|0.85551	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs34834764|rs34834764	193|210	Q9H6Q3-2|Q9H6Q3	.|SLAP2_HUMAN	Y|M	193|210	ENSP00000353890:C193Y|ENSP00000262866:V210M	ENSP00000353890:C193Y|ENSP00000262866:V210M	C|V	-|-	2|1	0|0	SLA2|SLA2	34676159|34676159	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.904000|0.904000	0.53231|0.53231	2.488000|2.488000	0.45276|0.45276	2.824000|2.824000	0.97209|0.97209	0.655000|0.655000	0.94253|0.94253	TGT|GTG	C|0.968;T|0.032	0.032	strong		0.572	SLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079037.2	NM_175077		T	35242745	C	T	35242745	3	4	22	1	0	0	0	0	1	0	0	0	14379	478	17	2	165	2	SLA2	20	35242745	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	66204	35242745	27782775	4183	7084											
CTNNBL1	56259	hgsc.bcm.edu	37	chr20	36396429	36396429	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagggtcttctacagtggCtgttgaagaggctgaaggtg	9	10	16	6	0	2	3	0	2	2	1	2	3	2	3	0	4	2	4	0	4	3	3	rs186475150	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:36396429C>G	ENST00000361383.6	+	7	850	c.733C>G	c.(733-735)Ctg>Gtg	p.L245V	CTNNBL1_ENST00000405275.2_Missense_Mutation_p.L218V|CTNNBL1_ENST00000373473.1_Missense_Mutation_p.L58V|CTNNBL1_ENST00000473857.1_3'UTR	NM_030877.3	NP_110517.2	Q8WYA6	CTBL1_HUMAN	catenin, beta like 1	245					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)				TCTACAGTGGCTGTTGAAGAG	0.517													C|||	15	0.00299521	0.0113	0.0	5008	,	,		18099	0.0		0.0	False		,,,				2504	0.0				p.L245V	Ovarian(184;582 2038 3273 4106 42608)	Atlas-SNP	.											.	CTNNBL1	78	.	0			c.C733G						PASS	.						108	108	108					20																	36396429		2203	4300	6503	SO:0001583	missense	56259	exon7			CAGTGGCTGTTGA	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.733C>G	20.37:g.36396429C>G	ENSP00000355050:p.Leu245Val	180	0	0		199	107	0.537688	NM_030877	B4DE16|Q0VAL9|Q0VAM0|Q53HI8|Q5JWZ2|Q5JWZ3|Q5JWZ7|Q5JWZ8|Q8N454|Q8NCL2|Q8TBD6|Q96KD2|Q9H7A5|Q9NQF9|Q9NTX0|Q9Y3M7	Missense_Mutation	SNP	ENST00000361383.6	37	CCDS13298.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	C	18.66	3.670848	0.67814	.	.	ENSG00000132792	ENST00000361383;ENST00000405275;ENST00000373473	T;T;T	0.69806	-0.28;-0.28;-0.43	5.8	2.36	0.29203	Armadillo-like helical (1);Armadillo-type fold (1);	0.071705	0.64402	N	0.000019	T	0.58991	0.2161	M	0.76727	2.345	0.80722	D	1	D;D	0.57571	0.98;0.964	P;P	0.53401	0.725;0.629	T	0.70389	-0.4885	10	0.52906	T	0.07	-14.1169	11.9885	0.53161	0.0:0.7773:0.0:0.2227	.	245;58	Q8WYA6;Q8WYA6-2	CTBL1_HUMAN;.	V	245;218;58	ENSP00000355050:L245V;ENSP00000384355:L218V;ENSP00000362572:L58V	ENSP00000355050:L245V	L	+	1	2	CTNNBL1	35829843	1.000000	0.71417	0.988000	0.46212	0.998000	0.95712	0.916000	0.28651	0.797000	0.33971	0.655000	0.94253	CTG	C|0.995;G|0.005	0.005	strong		0.517	CTNNBL1-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079125.1	NM_030877		G	36396429	C	G	36396429	3	3	22	1	0	0	0	0	1	0	0	0	4020	796	28	4	759	4	CTNNBL1	20	36396429	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1153684	36396429	26629091	4184	7085											
KIAA1755	85449	hgsc.bcm.edu	37	chr20	36841536	36841536	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaagctgcccccagtgaggcGagggacctggctctgcctgg	6	6	16	13	1	1	1	0	1	1	0	1	4	1	2	4	4	3	2	4	4	1	0	rs142596886	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:36841536G>A	ENST00000279024.4	-	14	3782	c.3511C>T	c.(3511-3513)Cgc>Tgc	p.R1171C		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	1171										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)				CCAGTGAGGCGAGGGACCTGG	0.637													G|||	6	0.00119808	0.0045	0.0	5008	,	,		17653	0.0		0.0	False		,,,				2504	0.0				p.R1171C		Atlas-SNP	.											.	KIAA1755	145	.	0			c.C3511T						PASS	.	G	CYS/ARG	23,4383	30.8+/-60.4	0,23,2180	38	40	40		3511	2.9	0.1	20	dbSNP_134	40	0,8600		0,0,4300	yes	missense	KIAA1755	NM_001029864.1	180	0,23,6480	AA,AG,GG		0.0,0.522,0.1768	possibly-damaging	1171/1201	36841536	23,12983	2203	4300	6503	SO:0001583	missense	85449	exon14			TGAGGCGAGGGAC	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.3511C>T	20.37:g.36841536G>A	ENSP00000279024:p.Arg1171Cys	72	0	0		56	23	0.410714	NM_001029864	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	37	CCDS33467.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	10.17	1.275548	0.23307	0.00522	0.0	ENSG00000149633	ENST00000279024	T	0.05855	3.38	4.88	2.94	0.34122	.	1.496300	0.03995	N	0.295521	T	0.04227	0.0117	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36089	-0.9762	10	0.72032	D	0.01	.	6.9683	0.24635	0.2031:0.0:0.7969:0.0	.	1171	Q5JYT7	K1755_HUMAN	C	1171	ENSP00000279024:R1171C	ENSP00000279024:R1171C	R	-	1	0	KIAA1755	36274950	0.139000	0.22563	0.060000	0.19600	0.030000	0.12068	1.048000	0.30379	0.660000	0.30964	0.561000	0.74099	CGC	G|0.999;A|0.001	0.001	strong		0.637	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864		A	36841536	G	A	36841536	3	1	22	1	0	0	0	0	1	0	0	0	8266	1058	37	1	95	1	KIAA1755	20	36841536	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	445107	36841536	26183984	4185	7086											
KIAA1755	85449	hgsc.bcm.edu	37	chr20	36856579	36856579	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgcagggcgctgaccagaccGggctgtgggggctgtctcct	4	8	17	12	2	1	2	0	1	1	1	2	2	1	2	3	4	1	4	3	4	0	0	rs74723843	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:36856579G>A	ENST00000279024.4	-	6	2206	c.1935C>T	c.(1933-1935)ccC>ccT	p.P645P		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	645										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)				TGACCAGACCGGGCTGTGGGG	0.602													g|||	114	0.0227636	0.0794	0.0101	5008	,	,		17204	0.0		0.0	False		,,,				2504	0.002				p.P645P		Atlas-SNP	.											.	KIAA1755	145	.	0			c.C1935T						PASS	.	G		301,4103	160.0+/-192.4	14,273,1915	36	37	37		1935	-9.6	0	20	dbSNP_131	37	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KIAA1755	NM_001029864.1		14,274,6214	AA,AG,GG		0.0116,6.8347,2.3224		645/1201	36856579	302,12702	2202	4300	6502	SO:0001819	synonymous_variant	85449	exon6			CAGACCGGGCTGT	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.1935C>T	20.37:g.36856579G>A		37	0	0		27	12	0.444444	NM_001029864	Q9C0A8	Silent	SNP	ENST00000279024.4	37	CCDS33467.1																																																																																			G|0.974;A|0.026	0.026	strong		0.602	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864		A	36856579	G	A	36856579	2	1	22	1	0	0	0	0	0	0	0	1	8266	1103	39	1		1	KIAA1755	20	36856579	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	15043	36856579	26168941	4186	7087											
BPI	671	hgsc.bcm.edu	37	chr20	36954790	36954790	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggatgtccaggcctttgccGtcctccccaactcctccctg	4	11	8	18	1	0	0	0	0	0	0	5	1	5	1	8	2	2	0	8	2	1	1	rs5743524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:36954790G>A	ENST00000262865.4	+	10	1218	c.1129G>A	c.(1129-1131)Gtc>Atc	p.V377I	BPI_ENST00000489102.1_3'UTR|CTD-2308N23.2_ENST00000437016.1_RNA	NM_001725.2	NP_001716.2	P17213	BPI_HUMAN	bactericidal/permeability-increasing protein	377			V -> I (in dbSNP:rs5743524).		defense response to bacterium (GO:0042742)|immune response (GO:0006955)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of macrophage activation (GO:0043031)|negative regulation of tumor necrosis factor production (GO:0032720)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	lipopolysaccharide binding (GO:0001530)			kidney(1)|large_intestine(6)|lung(15)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	30		Myeloproliferative disorder(115;0.00878)				GGCCTTTGCCGTCCTCCCCAA	0.597													g|||	209	0.0417332	0.1475	0.0187	5008	,	,		19366	0.0		0.001	False		,,,				2504	0.0				p.V377I		Atlas-SNP	.											.	BPI	67	.	0			c.G1129A						PASS	.	A	ILE/VAL	508,3898	235.5+/-248.0	28,452,1723	90	70	77		1129	-3.8	0	20	dbSNP_114	77	8,8592	6.4+/-24.3	0,8,4292	yes	missense	BPI	NM_001725.2	29	28,460,6015	AA,AG,GG		0.093,11.5297,3.9674	benign	377/488	36954790	516,12490	2203	4300	6503	SO:0001583	missense	671	exon10			TTTGCCGTCCTCC	J04739	CCDS13303.1	20q11.23	2011-08-16			ENSG00000101425	ENSG00000101425		"BPI fold containing"	1095	protein-coding gene	gene with protein product	"BPI fold containing family D, member 1"	109195				8432532	Standard	NM_001725		Approved	BPIFD1	uc002xia.2	P17213	OTTHUMG00000032441	ENST00000262865.4:c.1129G>A	20.37:g.36954790G>A	ENSP00000262865:p.Val377Ile	143	0	0		123	52	0.422764	NM_001725	B2RCY2|Q1ZZU8|Q5JRW0|Q8IW58|Q9BYZ9|Q9H1L2|Q9H1M8|Q9H203|Q9UCT4|Q9UD65	Missense_Mutation	SNP	ENST00000262865.4	37	CCDS13303.1	85	0.03891941391941392	80	0.16260162601626016	5	0.013812154696132596	0	0.0	0	0.0	g	3.739	-0.053900	0.07362	0.115297	9.3E-4	ENSG00000101425	ENST00000262865	T	0.09163	3.01	4.39	-3.78	0.04333	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	1.053620	0.07393	N	0.889378	T	0.00039	0.0001	N	0.11927	0.2	0.53688	P	2.8000000000028002E-5	B	0.20988	0.05	B	0.11329	0.006	T	0.48175	-0.9058	9	0.06757	T	0.87	-18.082	13.0633	0.59020	0.743:0.0:0.257:0.0	rs5743524;rs5743524	377	P17213	BPI_HUMAN	I	377	ENSP00000262865:V377I	ENSP00000262865:V377I	V	+	1	0	BPI	36388204	0.008000	0.16893	0.003000	0.11579	0.011000	0.07611	-0.063000	0.11655	-0.933000	0.03737	-2.146000	0.00336	GTC	G|0.949;A|0.051	0.051	strong		0.597	BPI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079157.2	NM_001725		A	36954790	G	A	36954790	3	1	22	1	0	0	0	0	1	0	0	0	1492	1145	40	1	1167	1	BPI	20	36954790	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	98211	36954790	26070730	4187	7088											
LBP	3929	hgsc.bcm.edu	37	chr20	36982785	36982785	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	gaggcccacagttactgcctCcagctgcagcagtgacatcg	9	7	11	14	1	0	1	0	1	0	0	2	2	1	1	3	1	5	4	3	1	1	1	rs2232586	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:36982785C>G	ENST00000217407.2	+	4	631	c.470C>G	c.(469-471)tCc>tGc	p.S157C		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	157			S -> C (in dbSNP:rs2232586).	VTAS -> GYCL (in Ref. 1; AAA59493). {ECO:0000305}.	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)				GTTACTGCCTCCAGCTGCAGC	0.592													C|||	28	0.00559105	0.0204	0.0014	5008	,	,		17413	0.0		0.0	False		,,,				2504	0.0				p.S157C		Atlas-SNP	.											.	LBP	60	.	0			c.C470G						PASS	.	C	CYS/SER	45,4361	46.7+/-81.2	1,43,2159	66	56	59		470	3.8	0.2	20	dbSNP_98	59	0,8600		0,0,4300	yes	missense	LBP	NM_004139.2	112	1,43,6459	GG,GC,CC		0.0,1.0213,0.346	probably-damaging	157/482	36982785	45,12961	2203	4300	6503	SO:0001583	missense	3929	exon4			CTGCCTCCAGCTG		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.470C>G	20.37:g.36982785C>G	ENSP00000217407:p.Ser157Cys	66	0	0		56	32	0.571429	NM_004139	B2R938|O43438|Q92672|Q9H403|Q9UD66	Missense_Mutation	SNP	ENST00000217407.2	37	CCDS13304.1	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	C	11.79	1.743153	0.30865	0.010213	0.0	ENSG00000129988	ENST00000217407;ENST00000538599	T	0.07688	3.17	4.77	3.75	0.43078	Lipid-binding serum glycoprotein, N-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.281808	0.30437	N	0.009628	T	0.10766	0.0263	M	0.85041	2.73	0.09310	N	1	D	0.89917	1.0	D	0.80764	0.994	T	0.00759	-1.1578	10	0.62326	D	0.03	-21.3368	9.7646	0.40552	0.2055:0.7945:0.0:0.0	rs2232586	157	P18428	LBP_HUMAN	C	157	ENSP00000217407:S157C	ENSP00000217407:S157C	S	+	2	0	LBP	36416199	0.012000	0.17670	0.193000	0.23327	0.108000	0.19459	2.151000	0.42263	2.648000	0.89879	0.561000	0.74099	TCC	C|0.994;G|0.006	0.006	strong		0.592	LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139		G	36982785	C	G	36982785	3	3	22	1	0	0	0	0	1	0	0	0	8660	855	30	4	484	4	LBP	20	36982785	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	27995	36982785	26042735	4188	7089											
LPIN3	64900	hgsc.bcm.edu	37	chr20	39977300	39977300	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgcacctcacccatcccttgGgggggtctgtctggcttccc	3	11	11	16	0	3	0	1	0	2	0	5	0	5	0	4	4	1	2	4	4	0	2	rs150562240	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:39977300G>C	ENST00000373257.3	+	4	421	c.330G>C	c.(328-330)tgG>tgC	p.W110C		NM_022896.1	NP_075047.1	Q9BQK8	LPIN3_HUMAN	lipin 3	110					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)				CCATCCCTTGGGGGGGTCTGT	0.662																																					p.W110C		Atlas-SNP	.											.	LPIN3	69	.	0			c.G330C						PASS	.	G	CYS/TRP	0,4406		0,0,2203	33	37	36		330	2.2	1	20	dbSNP_134	36	3,8597	1.2+/-3.3	0,3,4297	yes	missense	LPIN3	NM_022896.1	215	0,3,6500	CC,CG,GG		0.0349,0.0,0.0231	benign	110/852	39977300	3,13003	2203	4300	6503	SO:0001583	missense	64900	exon4			CCCTTGGGGGGGT	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.330G>C	20.37:g.39977300G>C	ENSP00000362354:p.Trp110Cys	44	0	0		44	17	0.386364	NM_022896	B2RTT5|Q5TDB9|Q9NPY8|Q9UJE5	Missense_Mutation	SNP	ENST00000373257.3	37	CCDS33469.1	.	.	.	.	.	.	.	.	.	.	G	11.33	1.606536	0.28623	0.0	3.49E-4	ENSG00000132793	ENST00000373257	T	0.76316	-1.01	4.22	2.19	0.27852	Lipin, N-terminal (1);	0.299857	0.26016	N	0.026860	T	0.53753	0.1816	N	0.08118	0	0.46874	D	0.999231	B;B	0.18968	0.002;0.032	B;B	0.19391	0.005;0.025	T	0.30592	-0.9973	9	.	.	.	-2.1502	8.2485	0.31704	0.0:0.1724:0.6488:0.1788	.	110;110	Q9BQK8-2;Q9BQK8	.;LPIN3_HUMAN	C	110	ENSP00000362354:W110C	.	W	+	3	0	LPIN3	39410714	1.000000	0.71417	0.971000	0.41717	0.955000	0.61496	2.688000	0.46984	0.488000	0.27723	0.557000	0.71058	TGG	G|0.999;C|0.001	0.001	strong		0.662	LPIN3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080393.1	NM_022896		C	39977300	G	C	39977300	3	2	22	1	0	0	0	0	1	0	0	0	8929	1241	43	4	340	4	LPIN3	20	39977300	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2994515	39977300	23048220	4189	7090											
PTPRT	11122	hgsc.bcm.edu	37	chr20	41408886	41408886	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaaggacccggacctcGtccacggcgatgtagccagg	9	5	14	13	4	0	1	0	1	0	0	2	4	1	3	4	4	2	2	4	4	2	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:41408886G>A	ENST00000373187.1	-	4	539	c.540C>T	c.(538-540)gaC>gaT	p.D180D	PTPRT_ENST00000373193.3_Silent_p.D180D|PTPRT_ENST00000373190.1_Silent_p.D180D|PTPRT_ENST00000373184.1_Silent_p.D180D|PTPRT_ENST00000356100.2_Silent_p.D180D|PTPRT_ENST00000373201.1_Silent_p.D180D|PTPRT_ENST00000373198.4_Silent_p.D180D			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	180	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)				CCCGGACCTCGTCCACGGCGA	0.532																																					p.D180D		Atlas-SNP	.											PTPRT,NS,carcinoma,0,2	PTPRT	372	2	0			c.C540T						scavenged	.						131	131	131					20																	41408886		2076	4217	6293	SO:0001819	synonymous_variant	11122	exon4			GACCTCGTCCACG	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.540C>T	20.37:g.41408886G>A		52	1	0.0192308		65	20	0.307692	NM_007050	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Silent	SNP	ENST00000373187.1	37	CCDS42874.1																																																																																			.	.	none		0.532	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			A	41408886	G	A	41408886	2	1	22	1	0	0	0	0	0	0	0	1	12827	1136	40	1		1	PTPRT	20	41408886	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1431586	41408886	21616634	4190	7091											
MYBL2	4605	hgsc.bcm.edu	37	chr20	42310449	42310449	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcagctgagggccctggtgaGgcagtttggacagcaggact	8	7	17	9	0	0	2	0	2	0	0	0	4	0	4	1	5	2	5	1	5	0	1	rs150704861	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:42310449G>A	ENST00000217026.4	+	3	267	c.140G>A	c.(139-141)aGg>aAg	p.R47K	MYBL2_ENST00000396863.4_Intron	NM_002466.2	NP_002457.1	P10244	MYBB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 2	47	HTH myb-type 1. {ECO:0000255|PROSITE- ProRule:PRU00625}.				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)			GCCCTGGTGAGGCAGTTTGGA	0.617													G|||	5	0.000998403	0.003	0.0014	5008	,	,		17008	0.0		0.0	False		,,,				2504	0.0				p.R47K		Atlas-SNP	.											.	MYBL2	82	.	0			c.G140A						PASS	.	G	LYS/ARG	11,4395	17.9+/-39.9	0,11,2192	80	67	71		140	3.7	1	20	dbSNP_134	71	0,8600		0,0,4300	yes	missense	MYBL2	NM_002466.2	26	0,11,6492	AA,AG,GG		0.0,0.2497,0.0846	benign	47/701	42310449	11,12995	2203	4300	6503	SO:0001583	missense	4605	exon3			TGGTGAGGCAGTT		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.140G>A	20.37:g.42310449G>A	ENSP00000217026:p.Arg47Lys	135	0	0		122	49	0.401639	NM_002466	B2RBS5|B7Z8D9|F8W6N6|Q53F07	Missense_Mutation	SNP	ENST00000217026.4	37	CCDS13322.1	.	.	.	.	.	.	.	.	.	.	G	13.64	2.297518	0.40694	0.002497	0.0	ENSG00000101057	ENST00000217026	T	0.12774	2.65	5.61	3.68	0.42216	Transcription regulator HTH, Myb-type, DNA-binding (1);Myb, DNA-binding (1);SANT domain, DNA binding (1);Homeodomain-related (1);Homeodomain-like (1);	0.198434	0.53938	N	0.000054	T	0.05640	0.0148	N	0.03224	-0.385	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.31503	-0.9941	10	0.35671	T	0.21	-32.0158	7.5543	0.27814	0.3171:0.0:0.6829:0.0	.	47	P10244	MYBB_HUMAN	K	47	ENSP00000217026:R47K	ENSP00000217026:R47K	R	+	2	0	MYBL2	41743863	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.841000	0.48223	0.872000	0.35775	0.655000	0.94253	AGG	G|0.998;A|0.002	0.002	strong		0.617	MYBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080408.1	NM_002466		A	42310449	G	A	42310449	3	1	22	1	0	0	0	0	1	0	0	0	10019	1000	35	2	150	2	MYBL2	20	42310449	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	901563	42310449	20715071	4191	7092											
TTPAL	79183	hgsc.bcm.edu	37	chr20	43117986	43117986	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaggagtatgggggcacggCtggggagctggacactgcca	9	5	18	9	1	0	0	0	0	0	0	0	3	0	3	1	7	2	4	1	7	2	1	rs59069332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43117986C>G	ENST00000372904.3	+	6	976	c.833C>G	c.(832-834)gCt>gGt	p.A278G	TTPAL_ENST00000372906.2_3'UTR|TTPAL_ENST00000262605.4_Missense_Mutation_p.A278G	NM_024331.4	NP_077307.2	Q9BTX7	TTPAL_HUMAN	tocopherol (alpha) transfer protein-like	278	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.		A -> G (in dbSNP:rs59069332).			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						GGGGGCACGGCTGGGGAGCTG	0.527													C|||	125	0.0249601	0.0923	0.0043	5008	,	,		20272	0.0		0.0	False		,,,				2504	0.0				p.A278G		Atlas-SNP	.											.	TTPAL	31	.	0			c.C833G						PASS	.	C	GLY/ALA,GLY/ALA	308,4098	166.2+/-197.5	16,276,1911	67	64	65		833,833	6.2	0.3	20	dbSNP_129	65	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	TTPAL	NM_001039199.1,NM_024331.3	60,60	16,278,6209	GG,GC,CC		0.0233,6.9905,2.3835	benign,benign	278/343,278/343	43117986	310,12696	2203	4300	6503	SO:0001583	missense	79183	exon5			GCACGGCTGGGGA	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.833C>G	20.37:g.43117986C>G	ENSP00000361995:p.Ala278Gly	125	0	0		144	83	0.576389	NM_001039199	E1P5X3|Q5QPC1|Q9H1G2|Q9NQG8	Missense_Mutation	SNP	ENST00000372904.3	37	CCDS13332.2	43	0.019688644688644688	41	0.08333333333333333	2	0.0055248618784530384	0	0.0	0	0.0	C	13.21	2.168458	0.38315	0.069905	2.33E-4	ENSG00000124120	ENST00000262605;ENST00000372904;ENST00000456317	D;D;D	0.84516	-1.86;-1.86;-1.86	6.17	6.17	0.99709	Cellular retinaldehyde-binding/triple function, C-terminal (4);	0.045191	0.85682	D	0.000000	T	0.24236	0.0587	N	0.03016	-0.435	0.80722	D	1	D;D	0.71674	0.998;0.982	P;P	0.62089	0.898;0.505	T	0.70174	-0.4944	10	0.21540	T	0.41	-16.9013	20.8794	0.99867	0.0:1.0:0.0:0.0	rs59069332	215;278	B2RA57;Q9BTX7	.;TTPAL_HUMAN	G	278;278;244	ENSP00000262605:A278G;ENSP00000361995:A278G;ENSP00000412720:A244G	ENSP00000262605:A278G	A	+	2	0	TTPAL	42551400	1.000000	0.71417	0.336000	0.25522	0.456000	0.32438	5.874000	0.69652	2.941000	0.99782	0.655000	0.94253	GCT	C|0.976;G|0.024	0.024	strong		0.527	TTPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106886.2	NM_024331		G	43117986	C	G	43117986	3	3	22	1	0	0	0	0	1	0	0	0	16752	797	28	4	847	4	TTPAL	20	43117986	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	807537	43117986	19907534	4192	7093											
KCNK15	60598	hgsc.bcm.edu	37	chr20	43374694	43374694	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtccagaagcggggcgctcTccggaggaagttcggcttct	6	8	16	11	4	2	1	0	0	2	1	5	3	3	3	2	6	1	3	2	6	2	2	rs144556326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43374694T>C	ENST00000372861.3	+	1	274	c.143T>C	c.(142-144)cTc>cCc	p.L48P	RP11-445H22.4_ENST00000445420.1_RNA|RP11-445H22.4_ENST00000427303.1_RNA	NM_022358.3	NP_071753.2	Q9H427	KCNKF_HUMAN	potassium channel, subfamily K, member 15	48					regulation of ion transmembrane transport (GO:0034765)	integral component of membrane (GO:0016021)	potassium channel activity (GO:0005267)			NS(1)|endometrium(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(2)	10		Myeloproliferative disorder(115;0.0122)				CGGGGCGCTCTCCGGAGGAAG	0.706													T|||	106	0.0211661	0.0726	0.0144	5008	,	,		11543	0.0		0.0	False		,,,				2504	0.0				p.L48P		Atlas-SNP	.											.	KCNK15	19	.	0			c.T143C						PASS	.	T	PRO/LEU	166,4206		2,162,2022	10	15	13		143	2.9	0.9	20	dbSNP_134	13	6,8538		0,6,4266	yes	missense	KCNK15	NM_022358.3	98	2,168,6288	CC,CT,TT		0.0702,3.7969,1.3317	probably-damaging	48/331	43374694	172,12744	2186	4272	6458	SO:0001583	missense	60598	exon1			GCGCTCTCCGGAG	AF257081	CCDS13337.1	20q13.12	2012-03-07			ENSG00000124249	ENSG00000124249		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	13814	protein-coding gene	gene with protein product		607368		KCNK11, KCNK14		11409881, 11431495, 16382106	Standard	NM_022358		Approved	K2p15.1, dJ781B1.1, KT3.3, KIAA0237, TASK5, TASK-5	uc002xmr.3	Q9H427	OTTHUMG00000032544	ENST00000372861.3:c.143T>C	20.37:g.43374694T>C	ENSP00000361952:p.Leu48Pro	41	0	0		37	15	0.405405	NM_022358	Q52LL3|Q9HBC8	Missense_Mutation	SNP	ENST00000372861.3	37	CCDS13337.1	43	0.019688644688644688	36	0.07317073170731707	7	0.019337016574585635	0	0.0	0	0.0	T	14.77	2.635968	0.47049	0.037969	7.02E-4	ENSG00000124249	ENST00000372861	T	0.17854	2.25	4.04	2.91	0.33838	.	0.349704	0.29892	N	0.010923	T	0.03827	0.0108	M	0.87180	2.865	0.80722	D	1	D	0.63880	0.993	P	0.61070	0.883	T	0.00295	-1.1839	10	0.87932	D	0	.	8.6904	0.34262	0.1705:0.0:0.0:0.8295	.	48	Q9H427	KCNKF_HUMAN	P	48	ENSP00000361952:L48P	ENSP00000361952:L48P	L	+	2	0	KCNK15	42808108	0.968000	0.33430	0.914000	0.36105	0.012000	0.07955	4.497000	0.60367	0.577000	0.29470	0.455000	0.32223	CTC	T|0.981;C|0.019	0.019	strong		0.706	KCNK15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079378.2	NM_022358		C	43374694	T	C	43374694	3	2	22	1	0	0	0	0	1	0	0	0	8071	1551	54	3	145	3	KCNK15	20	43374694	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	256708	43374694	19650826	4193	7094											
SEMG1	6406	hgsc.bcm.edu	37	chr20	43836237	43836237	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gacaaaatcacaacgacatcTaggtggaagtcaacaactgc	17	6	8	10	1	3	0	2	0	1	0	3	3	3	1	0	2	4	0	0	2	7	1	rs61729393	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43836237T>A	ENST00000372781.3	+	2	356	c.299T>A	c.(298-300)cTa>cAa	p.L100Q	SEMG1_ENST00000244069.6_Missense_Mutation_p.L100Q	NM_003007.3	NP_002998.1	P04279	SEMG1_HUMAN	semenogelin I	100	Repeat-rich region. {ECO:0000250}.			L -> Q (in Ref. 3; AAP82463). {ECO:0000305}.	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)				CAACGACATCTAGGTGGAAGT	0.393													T|||	63	0.0125799	0.0371	0.0086	5008	,	,		22065	0.0		0.004	False		,,,				2504	0.0041				p.L100Q		Atlas-SNP	.											.	SEMG1	71	.	0			c.T299A						PASS	.	T	GLN/LEU	144,4262	100.7+/-139.4	1,142,2060	143	123	130		299	-2.1	0	20	dbSNP_129	130	18,8582	12.6+/-44.7	0,18,4282	yes	missense	SEMG1	NM_003007.3	113	1,160,6342	AA,AT,TT		0.2093,3.2683,1.2456		100/463	43836237	162,12844	2203	4300	6503	SO:0001583	missense	6406	exon2			GACATCTAGGTGG		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.299T>A	20.37:g.43836237T>A	ENSP00000361867:p.Leu100Gln	157	0	0		193	92	0.476684	NM_003007	Q53ZV0|Q53ZV1|Q53ZV2|Q6X4I9|Q6Y809|Q6Y822|Q6Y823|Q86U64|Q96QM3	Missense_Mutation	SNP	ENST00000372781.3	37	CCDS13345.1	23	0.010531135531135532	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	T	10.92	1.485748	0.26686	0.032683	0.002093	ENSG00000124233	ENST00000244069;ENST00000372781	T;T	0.09445	2.98;2.98	1.07	-2.13	0.07144	.	.	.	.	.	T	0.07007	0.0178	L	0.54323	1.7	0.09310	N	1	D;D;D	0.63880	0.985;0.993;0.988	P;D;P	0.71414	0.693;0.973;0.796	T	0.08513	-1.0718	9	0.62326	D	0.03	.	4.0698	0.09877	0.0:0.4746:0.0:0.5254	rs61729393	100;100;100	P04279-2;P04279;E7EPD3	.;SEMG1_HUMAN;.	Q	100	ENSP00000244069:L100Q;ENSP00000361867:L100Q	ENSP00000244069:L100Q	L	+	2	0	SEMG1	43269651	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.238000	0.01199	-0.505000	0.06568	-0.321000	0.08615	CTA	T|0.988;A|0.012	0.012	strong		0.393	SEMG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079416.3	NM_003007		A	43836237	T	A	43836237	3	1	22	1	0	0	0	0	1	0	0	0	14059	1522	53	5	305	5	SEMG1	20	43836237	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	461543	43836237	19189283	4194	7095											
SEMG1	6406	hgsc.bcm.edu	37	chr20	43837053	43837053	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcagaaagatgtatcccaacGcagtatttatagccaaactg	15	9	8	9	1	0	2	0	0	0	2	1	2	1	2	2	0	3	4	2	0	7	5	rs2233887	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43837053G>T	ENST00000372781.3	+	2	1172	c.1115G>T	c.(1114-1116)cGc>cTc	p.R372L	SEMG1_ENST00000244069.6_Missense_Mutation_p.R312L	NM_003007.3	NP_002998.1	P04279	SEMG1_HUMAN	semenogelin I	372	2 X 60 AA tandem repeats, type 1.|Repeat-rich region. {ECO:0000250}.		R -> L (in dbSNP:rs2233887). {ECO:0000269|PubMed:14629036}.		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)				GTATCCCAACGCAGTATTTAT	0.413													G|||	63	0.0125799	0.0371	0.0086	5008	,	,		22334	0.0		0.004	False		,,,				2504	0.0041				p.R372L		Atlas-SNP	.											SEMG1,bladder,carcinoma,+1,3	SEMG1	71	3	0			c.G1115T						PASS	.	G	LEU/ARG	143,4263	100.3+/-138.9	1,141,2061	75	70	72		1115	-0.4	0	20	dbSNP_98	72	18,8582	12.6+/-44.7	0,18,4282	yes	missense	SEMG1	NM_003007.3	102	1,159,6343	TT,TG,GG		0.2093,3.2456,1.2379		372/463	43837053	161,12845	2203	4300	6503	SO:0001583	missense	6406	exon2			CCCAACGCAGTAT		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.1115G>T	20.37:g.43837053G>T	ENSP00000361867:p.Arg372Leu	151	0	0		166	85	0.512048	NM_003007	Q53ZV0|Q53ZV1|Q53ZV2|Q6X4I9|Q6Y809|Q6Y822|Q6Y823|Q86U64|Q96QM3	Missense_Mutation	SNP	ENST00000372781.3	37	CCDS13345.1	23	0.010531135531135532	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	6.094	0.385541	0.11524	0.032456	0.002093	ENSG00000124233	ENST00000244069;ENST00000372781	T;T	0.06218	3.33;3.33	0.951	-0.436	0.12275	.	.	.	.	.	T	0.00967	0.0032	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.42849	-0.9427	9	0.72032	D	0.01	.	3.6742	0.08286	0.0:0.0:0.5676:0.4324	rs2233887;rs52805273;rs2233887	312;372	P04279-2;P04279	.;SEMG1_HUMAN	L	312;372	ENSP00000244069:R312L;ENSP00000361867:R372L	ENSP00000244069:R312L	R	+	2	0	SEMG1	43270467	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.312000	0.08113	-0.121000	0.11787	0.404000	0.27445	CGC	G|0.984;T|0.016	0.016	strong		0.413	SEMG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079416.3	NM_003007		T	43837053	G	T	43837053	3	4	22	1	0	0	0	0	1	0	0	0	14059	1087	38	4	1121	4	SEMG1	20	43837053	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	816	43837053	19188467	4195	7096											
SEMG2	6407	hgsc.bcm.edu	37	chr20	43851101	43851101	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaaaaaatctcagtcaagaTcaagagcatggccggaaggc	17	5	10	9	1	3	2	3	0	1	2	4	3	3	3	1	3	1	1	1	3	6	0	rs2233902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43851101T>C	ENST00000372769.3	+	2	918	c.828T>C	c.(826-828)gaT>gaC	p.D276D		NM_003008.2	NP_002999.1	Q02383	SEMG2_HUMAN	semenogelin II	276	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)				TCAGTCAAGATCAAGAGCATG	0.398													T|||	79	0.0157748	0.0484	0.0101	5008	,	,		22551	0.0		0.004	False		,,,				2504	0.0041				p.D276D		Atlas-SNP	.											.	SEMG2	92	.	0			c.T828C						PASS	.	T		177,4229	114.6+/-152.6	3,171,2029	93	90	91		828	-1.5	0	20	dbSNP_98	91	18,8582	12.6+/-44.7	0,18,4282	no	coding-synonymous	SEMG2	NM_003008.2		3,189,6311	CC,CT,TT		0.2093,4.0172,1.4993		276/583	43851101	195,12811	2203	4300	6503	SO:0001819	synonymous_variant	6407	exon2			TCAAGATCAAGAG		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.828T>C	20.37:g.43851101T>C		158	0	0		151	78	0.516556	NM_003008	Q53ZU2|Q6X2M5|Q6X2M6	Silent	SNP	ENST00000372769.3	37	CCDS13346.1																																																																																			T|0.985;C|0.015	0.015	strong		0.398	SEMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079417.1	NM_003008		C	43851101	T	C	43851101	2	2	22	1	0	0	0	0	0	0	0	1	14060	1432	50	3		3	SEMG2	20	43851101	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	14048	43851101	19174419	4196	7097											
RBPJL	11317	hgsc.bcm.edu	37	chr20	43938284	43938284	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acagtgtgaacagactgtgcGgatcctgcatgccaaggtgg	10	8	14	9	1	0	2	0	1	0	1	1	3	1	3	2	3	4	1	2	3	2	0	rs35032855	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43938284G>A	ENST00000343694.3	+	3	281	c.209G>A	c.(208-210)cGg>cAg	p.R70Q	MATN4_ENST00000372751.4_5'Flank|RBPJL_ENST00000372741.3_Missense_Mutation_p.R70Q|RBPJL_ENST00000372743.1_Missense_Mutation_p.R70Q|MATN4_ENST00000537548.1_5'Flank|MATN4_ENST00000360607.6_5'Flank|MATN4_ENST00000353917.5_5'Flank|MATN4_ENST00000342716.4_5'Flank	NM_001281448.1|NM_001281449.1|NM_014276.2	NP_001268377.1|NP_001268378.1|NP_055091.2	Q9UBG7	RBPJL_HUMAN	recombination signal binding protein for immunoglobulin kappa J region-like	70					positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Myeloproliferative disorder(115;0.0122)				CAGACTGTGCGGATCCTGCAT	0.607													G|||	57	0.0113818	0.034	0.0058	5008	,	,		19804	0.0		0.004	False		,,,				2504	0.0041				p.R70Q		Atlas-SNP	.											.	RBPJL	67	.	0			c.G209A						PASS	.	G	GLN/ARG	165,4241	109.5+/-147.8	3,159,2041	114	93	100		209	5.5	1	20	dbSNP_126	100	17,8583	12.6+/-44.7	0,17,4283	yes	missense	RBPJL	NM_014276.2	43	3,176,6324	AA,AG,GG		0.1977,3.7449,1.3994	benign	70/518	43938284	182,12824	2203	4300	6503	SO:0001583	missense	11317	exon3			CTGTGCGGATCCT	AB024964	CCDS13349.1, CCDS63283.1, CCDS63284.1	20q13.12	2013-10-18	2007-02-26	2007-02-26	ENSG00000124232	ENSG00000124232			13761	protein-coding gene	gene with protein product			"recombining binding protein suppressor of hairless (Drosophila)-like"	RBPSUHL		9929984	Standard	NM_014276		Approved	RBP-L, SUH, SUHL	uc002xns.3	Q9UBG7	OTTHUMG00000033055	ENST00000343694.3:c.209G>A	20.37:g.43938284G>A	ENSP00000341243:p.Arg70Gln	119	0	0		93	39	0.419355	NM_014276	O95723|Q5QPU9|Q5QPV0|Q9ULV9	Missense_Mutation	SNP	ENST00000343694.3	37	CCDS13349.1	23	0.010531135531135532	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	20.6	4.012876	0.75161	0.037449	0.001977	ENSG00000124232	ENST00000372743;ENST00000372741;ENST00000343694	D;D;D	0.82711	-1.64;-1.64;-1.64	5.53	5.53	0.82687	LAG1, DNA binding (2);p53-like transcription factor, DNA-binding (1);	0.860937	0.10327	N	0.688044	T	0.41213	0.1149	N	0.22421	0.69	0.20307	N	0.999911	P;P	0.46621	0.881;0.708	B;B	0.35073	0.195;0.189	T	0.57573	-0.7788	10	0.66056	D	0.02	-7.9496	12.2068	0.54356	0.0:0.0:0.7307:0.2693	rs35032855	70;70	Q5QPV1;Q9UBG7	.;RBPJL_HUMAN	Q	70	ENSP00000361828:R70Q;ENSP00000361826:R70Q;ENSP00000341243:R70Q	ENSP00000341243:R70Q	R	+	2	0	RBPJL	43371698	0.992000	0.36948	0.998000	0.56505	0.917000	0.54804	1.776000	0.38594	2.622000	0.88805	0.456000	0.33151	CGG	G|0.988;A|0.012	0.012	strong		0.607	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276		A	43938284	G	A	43938284	3	1	22	1	0	0	0	0	1	0	0	0	13177	1116	39	1	219	1	RBPJL	20	43938284	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	87183	43938284	19087236	4197	7098											
RBPJL	11317	hgsc.bcm.edu	37	chr20	43940531	43940542	+	In_Frame_Del	DEL	CAGCGCGTCCGG	CAGCGCGTCCGG	-																															tgcggttacatgggactggaCagcgcgtccggcagcgccac																								rs142744285|rs367731607	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CAGCGCGTCCGG	CAGCGCGTCCGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43940531_43940542delCAGCGCGTCCGG	ENST00000343694.3	+	5	453_464	c.381_392delCAGCGCGTCCGG	c.(379-393)gacagcgcgtccggc>gac	p.SASG128del	RBPJL_ENST00000372741.3_In_Frame_Del_p.SASG128del|RBPJL_ENST00000372743.1_In_Frame_Del_p.SASG128del	NM_001281448.1|NM_001281449.1|NM_014276.2	NP_001268377.1|NP_001268378.1|NP_055091.2	Q9UBG7	RBPJL_HUMAN	recombination signal binding protein for immunoglobulin kappa J region-like	128					positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Myeloproliferative disorder(115;0.0122)				TGGGACTGGACAGCGCGTCCGGCAGCGCCACT	0.66											OREG0025979	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		73	0.0145767	0.0454	0.0072	5008	,	,		19337	0.0		0.004	False		,,,				2504	0.0041				p.127_131del		Pindel,Atlas-Indel	.											.	RBPJL	67	.	0			c.380_391del						PASS	.			129,3693		18,93,1800						4.2	1		dbSNP_134	9	24,7388		7,10,3689	no	coding	RBPJL	NM_014276.2		25,103,5489	A1A1,A1R,RR		0.3238,3.3752,1.3619				153,11081				SO:0001651	inframe_deletion	11317	exon5			.	AB024964	CCDS13349.1, CCDS63283.1, CCDS63284.1	20q13.12	2013-10-18	2007-02-26	2007-02-26	ENSG00000124232	ENSG00000124232			13761	protein-coding gene	gene with protein product			"recombining binding protein suppressor of hairless (Drosophila)-like"	RBPSUHL		9929984	Standard	NM_014276		Approved	RBP-L, SUH, SUHL	uc002xns.3	Q9UBG7	OTTHUMG00000033055	ENST00000343694.3:c.381_392delCAGCGCGTCCGG	20.37:g.43940531_43940542delCAGCGCGTCCGG	ENSP00000341243:p.Ser128_Gly131del	127	0	.	920	118	45	0.381	NM_014276	O95723|Q5QPU9|Q5QPV0|Q9ULV9	In_Frame_Del	DEL	ENST00000343694.3	37	CCDS13349.1																																																																																			CAGCGCGTCCGG|0.987;-|0.013	0.013	strong		0.66	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276		-	43940542	CAGCGCGTCCGG	-	43940531	7	5	22	1	0	1	0	1	0	0	0	0	13177	477	17	0	399	0	RBPJL	20	43940531	In_Frame_Del	DEL	CAGCGCGTCCGG	TCGA-G8-6324-01A-11D-2210-10	2247	43940531	19084989	4198	7099											
RBPJL	11317	hgsc.bcm.edu	37	chr20	43945377	43945377	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gacgtggcggccttctgcagCgactggcgctggctgcgcgc	3	7	17	14	6	1	0	0	0	1	0	1	2	1	0	1	4	3	3	1	4	0	1	rs35220957	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43945377C>A	ENST00000343694.3	+	12	1404	c.1332C>A	c.(1330-1332)agC>agA	p.S444R	RBPJL_ENST00000464504.1_3'UTR|RBPJL_ENST00000372741.3_Silent_p.R448R|RBPJL_ENST00000372743.1_Missense_Mutation_p.S443R	NM_001281448.1|NM_001281449.1|NM_014276.2	NP_001268377.1|NP_001268378.1|NP_055091.2	Q9UBG7	RBPJL_HUMAN	recombination signal binding protein for immunoglobulin kappa J region-like	444	IPT/TIG.				positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Myeloproliferative disorder(115;0.0122)				CCTTCTGCAGCGACTGGCGCT	0.701													C|||	73	0.0145767	0.0454	0.0072	5008	,	,		12791	0.0		0.004	False		,,,				2504	0.0041				p.S444R		Atlas-SNP	.											.	RBPJL	67	.	0			c.C1332A						PASS	.	C	ARG/SER	179,4221		1,177,2022	17	23	21		1332	-2	0.7	20	dbSNP_126	21	17,8571		0,17,4277	yes	missense	RBPJL	NM_014276.2	110	1,194,6299	AA,AC,CC		0.198,4.0682,1.5091	possibly-damaging	444/518	43945377	196,12792	2200	4294	6494	SO:0001583	missense	11317	exon12			CTGCAGCGACTGG	AB024964	CCDS13349.1, CCDS63283.1, CCDS63284.1	20q13.12	2013-10-18	2007-02-26	2007-02-26	ENSG00000124232	ENSG00000124232			13761	protein-coding gene	gene with protein product			"recombining binding protein suppressor of hairless (Drosophila)-like"	RBPSUHL		9929984	Standard	NM_014276		Approved	RBP-L, SUH, SUHL	uc002xns.3	Q9UBG7	OTTHUMG00000033055	ENST00000343694.3:c.1332C>A	20.37:g.43945377C>A	ENSP00000341243:p.Ser444Arg	45	0	0		39	25	0.641026	NM_014276	O95723|Q5QPU9|Q5QPV0|Q9ULV9	Missense_Mutation	SNP	ENST00000343694.3	37	CCDS13349.1	29	0.013278388278388278	22	0.044715447154471545	3	0.008287292817679558	0	0.0	4	0.005277044854881266	C	16.39	3.108689	0.56291	0.040682	0.00198	ENSG00000124232	ENST00000372743;ENST00000343694	T;T	0.17054	2.3;2.3	5.48	-2.02	0.07388	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.121014	0.56097	D	0.000034	T	0.02727	0.0082	L	0.42245	1.32	0.37489	D	0.916303	D	0.57257	0.979	P	0.48189	0.57	T	0.35101	-0.9802	10	0.19147	T	0.46	-19.8204	5.1298	0.14903	0.2229:0.4288:0.0:0.3483	rs35220957;rs59797878	444	Q9UBG7	RBPJL_HUMAN	R	443;444	ENSP00000361828:S443R;ENSP00000341243:S444R	ENSP00000341243:S444R	S	+	3	2	RBPJL	43378791	0.191000	0.23288	0.652000	0.29579	0.983000	0.72400	-0.568000	0.05909	-0.198000	0.10333	0.549000	0.68633	AGC	C|0.988;A|0.012	0.012	strong		0.701	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276		A	43945377	C	A	43945377	3	1	22	1	0	0	0	0	1	0	0	0	13177	767	27	4	1378	4	RBPJL	20	43945377	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4846	43945377	19080143	4199	7100											
RBPJL	11317	hgsc.bcm.edu	37	chr20	43945487	43945487	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctacaccccggaatacagcgTgcggccgggtcaccccggcg	7	4	13	17	6	1	0	1	0	0	0	1	1	1	1	5	4	4	0	5	4	3	2	rs34078698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43945487T>C	ENST00000343694.3	+	12	1514	c.1442T>C	c.(1441-1443)gTg>gCg	p.V481A	RBPJL_ENST00000464504.1_3'UTR|RBPJL_ENST00000372741.3_3'UTR|RBPJL_ENST00000372743.1_Missense_Mutation_p.V480A	NM_001281448.1|NM_001281449.1|NM_014276.2	NP_001268377.1|NP_001268378.1|NP_055091.2	Q9UBG7	RBPJL_HUMAN	recombination signal binding protein for immunoglobulin kappa J region-like	481	IPT/TIG.				positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Myeloproliferative disorder(115;0.0122)				GAATACAGCGTGCGGCCGGGT	0.667													C|||	84	0.0167732	0.0484	0.0086	5008	,	,		13248	0.0		0.004	False		,,,				2504	0.0102				p.V481A		Atlas-SNP	.											RBPJL,colon,carcinoma,+1,1	RBPJL	67	1	0			c.T1442C						PASS	.	C	ALA/VAL	200,4206	790.0+/-415.0	4,192,2007	41	50	47		1442	-1.1	0.3	20	dbSNP_126	47	17,8583	809.0+/-407.2	0,17,4283	yes	missense	RBPJL	NM_014276.2	64	4,209,6290	CC,CT,TT		0.1977,4.5393,1.6685	benign	481/518	43945487	217,12789	2203	4300	6503	SO:0001583	missense	11317	exon12			ACAGCGTGCGGCC	AB024964	CCDS13349.1, CCDS63283.1, CCDS63284.1	20q13.12	2013-10-18	2007-02-26	2007-02-26	ENSG00000124232	ENSG00000124232			13761	protein-coding gene	gene with protein product			"recombining binding protein suppressor of hairless (Drosophila)-like"	RBPSUHL		9929984	Standard	NM_014276		Approved	RBP-L, SUH, SUHL	uc002xns.3	Q9UBG7	OTTHUMG00000033055	ENST00000343694.3:c.1442T>C	20.37:g.43945487T>C	ENSP00000341243:p.Val481Ala	66	0	0		57	24	0.421053	NM_014276	O95723|Q5QPU9|Q5QPV0|Q9ULV9	Missense_Mutation	SNP	ENST00000343694.3	37	CCDS13349.1	33	0.01510989010989011	25	0.0508130081300813	4	0.011049723756906077	0	0.0	4	0.005277044854881266	C	1.885	-0.456982	0.04540	0.045393	0.001977	ENSG00000124232	ENST00000372743;ENST00000343694	T;T	0.35789	1.29;1.29	5.06	-1.14	0.09741	.	1.055390	0.07430	N	0.895594	T	0.01156	0.0038	N	0.00436	-1.5	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20405	-1.0276	10	0.18710	T	0.47	-0.9329	2.3328	0.04239	0.1025:0.2059:0.3513:0.3403	rs34078698;rs60037526	481	Q9UBG7	RBPJL_HUMAN	A	480;481	ENSP00000361828:V480A;ENSP00000341243:V481A	ENSP00000341243:V481A	V	+	2	0	RBPJL	43378901	0.000000	0.05858	0.271000	0.24616	0.392000	0.30506	-0.499000	0.06413	-0.341000	0.08376	-0.386000	0.06593	GTG	T|0.986;C|0.014	0.014	strong		0.667	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276		C	43945487	T	C	43945487	3	2	22	1	0	0	0	0	1	0	0	0	13177	1696	59	3	1488	3	RBPJL	20	43945487	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	110	43945487	19080033	4200	7101											
SPINLW1	57119	hgsc.bcm.edu	37	chr20	44174306	44174306	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agatctaaacatttttttccGcagctgaagacacaacactt	14	12	5	10	1	1	3	0	1	1	2	2	3	2	3	1	0	3	2	1	0	4	5	rs374858005		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:44174306G>A	ENST00000354280.4	-	2	261	c.195C>T	c.(193-195)tgC>tgT	p.C65C	EPPIN_ENST00000555685.1_Silent_p.C65C|EPPIN_ENST00000409554.1_Silent_p.C65C|EPPIN-WFDC6_ENST00000504988.1_Silent_p.C65C|EPPIN_ENST00000336443.3_Silent_p.C49C	NM_020398.3	NP_065131.1	O95925	EPPI_HUMAN	epididymal peptidase inhibitor	65	WAP. {ECO:0000255|PROSITE- ProRule:PRU00722}.				defense response to bacterium (GO:0042742)|negative regulation of peptidase activity (GO:0010466)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										ATTTTTTTCCGCAGCTGAAGA	0.453													G|||	1	0.000199681	0.0	0.0	5008	,	,		20884	0.0		0.0	False		,,,				2504	0.001				p.C65C		Atlas-SNP	.											.	.	.	.	0			c.C195T						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	320	284	296		195,195	-3.6	0.9	20		296	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	SPINLW1,SPINLW1-WFDC6	NM_001198986.1,NM_020398.3	,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	,	65/180,65/134	44174306	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	100526773	exon2			TTTTCCGCAGCTG	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	ENST00000354280.4:c.195C>T	20.37:g.44174306G>A		256	1	0.00390625		278	132	0.47482	NM_001198986	A6PVD6|Q86TP9|Q96SD7|Q9HD30	Silent	SNP	ENST00000354280.4	37	CCDS13359.1																																																																																			.	.	weak		0.453	EPPIN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079467.4			A	44174306	G	A	44174306	2	1	22	1	0	0	0	0	0	0	0	1	15082	1079	38	1		1	SPINLW1	20	44174306	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	228819	44174306	18851214	4201	7102											
SPINT4	391253	hgsc.bcm.edu	37	chr20	44351095	44351095	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggtggtgttaataaaattgCggagaagatatgtggagacc	13	10	15	3	1	0	3	0	0	0	3	0	5	0	3	1	4	1	1	1	4	5	4	rs16990631	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:44351095C>A	ENST00000279058.3	+	1	106	c.89C>A	c.(88-90)gCg>gAg	p.A30E		NM_178455.1	NP_848550.1	Q6UDR6	SPIT4_HUMAN	serine peptidase inhibitor, Kunitz type 4	30			A -> E (in dbSNP:rs16990631).			extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			lung(6)|ovary(1)|skin(1)	8		Myeloproliferative disorder(115;0.028)				AATAAAATTGCGGAGAAGATA	0.403													C|||	130	0.0259585	0.0212	0.0389	5008	,	,		22012	0.0		0.0398	False		,,,				2504	0.0358				p.A30E		Atlas-SNP	.											.	SPINT4	17	.	0			c.C89A						PASS	.	C	GLU/ALA	102,4304	80.4+/-118.8	1,100,2102	146	137	140		89	-3.5	0	20	dbSNP_123	140	406,8194	128.8+/-187.0	13,380,3907	yes	missense	SPINT4	NM_178455.1	107	14,480,6009	AA,AC,CC		4.7209,2.315,3.9059	benign	30/100	44351095	508,12498	2203	4300	6503	SO:0001583	missense	391253	exon1			AAATTGCGGAGAA	AY372174	CCDS33477.1	20q13.12	2012-08-20	2005-10-18	2005-10-25	ENSG00000149651	ENSG00000149651			16130	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 137", "serine peptidase inhibitor, Kunitz type 4"	C20orf137		21988899	Standard	NM_178455		Approved	dJ601O1.1	uc002xpe.1	Q6UDR6	OTTHUMG00000130153	ENST00000279058.3:c.89C>A	20.37:g.44351095C>A	ENSP00000279058:p.Ala30Glu	197	0	0		192	99	0.515625	NM_178455	Q9BQN3	Missense_Mutation	SNP	ENST00000279058.3	37	CCDS33477.1	49	0.022435897435897436	12	0.024390243902439025	12	0.03314917127071823	0	0.0	25	0.032981530343007916	C	9.484	1.098836	0.20552	0.02315	0.047209	ENSG00000149651	ENST00000279058	T	0.54675	0.56	3.97	-3.46	0.04767	.	1.136080	0.06683	N	0.768367	T	0.05777	0.0151	.	.	.	0.09310	N	1	B	0.31077	0.307	B	0.23419	0.046	T	0.11690	-1.0577	9	0.66056	D	0.02	0.4807	0.4623	0.00518	0.2335:0.3326:0.1375:0.2964	rs16990631;rs16990631	30	Q6UDR6	SPIT4_HUMAN	E	30	ENSP00000279058:A30E	ENSP00000279058:A30E	A	+	2	0	SPINT4	43784509	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.705000	0.05052	-0.636000	0.05524	-0.143000	0.13931	GCG	C|0.963;A|0.037	0.037	strong		0.403	SPINT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252463.2	XM_372869		A	44351095	C	A	44351095	3	1	22	1	0	0	0	0	1	0	0	0	15085	768	27	4	91	4	SPINT4	20	44351095	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	176789	44351095	18674425	4202	7103											
ZSWIM1	90204	hgsc.bcm.edu	37	chr20	44512013	44512013	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cttccagagcctcgaggtcaCcacccacatcctcagccagt	9	7	7	18	1	2	1	2	0	0	1	5	2	4	1	6	1	2	0	6	1	0	1	rs115926000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:44512013C>G	ENST00000372523.1	+	2	877	c.782C>G	c.(781-783)aCc>aGc	p.T261S	ZSWIM1_ENST00000372520.1_Missense_Mutation_p.T261S	NM_080603.4	NP_542170.3	Q9BR11	ZSWM1_HUMAN	zinc finger, SWIM-type containing 1	261						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)				CTCGAGGTCACCACCCACATC	0.562													C|||	11	0.00219649	0.0068	0.0	5008	,	,		20333	0.0		0.002	False		,,,				2504	0.0				p.T261S		Atlas-SNP	.											.	ZSWIM1	35	.	0			c.C782G						PASS	.	C	SER/THR	31,4375	37.6+/-69.7	0,31,2172	110	94	99		782	3.1	1	20	dbSNP_132	99	4,8596	3.7+/-12.6	0,4,4296	yes	missense	ZSWIM1	NM_080603.4	58	0,35,6468	GG,GC,CC		0.0465,0.7036,0.2691	benign	261/486	44512013	35,12971	2203	4300	6503	SO:0001583	missense	90204	exon2			AGGTCACCACCCA	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.782C>G	20.37:g.44512013C>G	ENSP00000361601:p.Thr261Ser	172	0	0		203	106	0.522168	NM_080603	Q5JZH2|Q9BR12|Q9BV30	Missense_Mutation	SNP	ENST00000372523.1	37	CCDS13382.2	4	0.0018315018315018315	3	0.006097560975609756	0	0.0	0	0.0	1	0.0013192612137203166	C	12.19	1.864270	0.32977	0.007036	4.65E-4	ENSG00000168612	ENST00000372523;ENST00000372520	T;T	0.24151	1.87;1.87	5.13	3.11	0.35812	.	0.437391	0.18795	U	0.130955	T	0.09905	0.0243	N	0.24115	0.695	0.19300	N	0.999977	B	0.30482	0.281	B	0.30029	0.11	T	0.26744	-1.0094	10	0.10902	T	0.67	-20.7697	8.035	0.30486	0.0:0.6753:0.0:0.3247	.	261	Q9BR11	ZSWM1_HUMAN	S	261	ENSP00000361601:T261S;ENSP00000361598:T261S	ENSP00000361598:T261S	T	+	2	0	ZSWIM1	43945420	0.268000	0.24133	0.996000	0.52242	0.990000	0.78478	0.495000	0.22483	0.669000	0.31146	0.555000	0.69702	ACC	C|0.998;G|0.002	0.002	strong		0.562	ZSWIM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157064.2	NM_080603		G	44512013	C	G	44512013	3	3	22	1	0	0	0	0	1	0	0	0	18255	507	18	4	784	4	ZSWIM1	20	44512013	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	160918	44512013	18513507	4203	7104											
ELMO2	63916	hgsc.bcm.edu	37	chr20	45014804	45014804	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtcccacggtgatttcctcGgctatcttctggtacagact	6	14	9	12	2	2	2	0	1	2	1	5	2	4	2	2	3	1	2	2	3	2	4	rs201990540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:45014804G>A	ENST00000290246.6	-	9	830	c.636C>T	c.(634-636)gcC>gcT	p.A212A	ELMO2_ENST00000439931.2_Silent_p.A212A|ELMO2_ENST00000445496.2_Silent_p.A29A|ELMO2_ENST00000352077.2_Silent_p.A210A|ELMO2_ENST00000372176.1_Silent_p.A124A|ELMO2_ENST00000396391.1_Silent_p.A212A|ELMO2_ENST00000488853.1_5'UTR	NM_133171.3	NP_573403.1	Q96JJ3	ELMO2_HUMAN	engulfment and cell motility 2	212					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)				TGATTTCCTCGGCTATCTTCT	0.527													g|||	3	0.000599042	0.0015	0.0014	5008	,	,		19968	0.0		0.0	False		,,,				2504	0.0				p.A212A		Atlas-SNP	.											ELMO2,NS,carcinoma,-1,1	ELMO2	51	1	0			c.C636T						scavenged	.						135	124	128					20																	45014804		2203	4300	6503	SO:0001819	synonymous_variant	63916	exon8			TTCCTCGGCTATC	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.636C>T	20.37:g.45014804G>A		95	1	0.0105263		111	5	0.045045	NM_182764	E1P5T3|Q5JVZ6|Q7Z5G9|Q96CJ2|Q96ME5|Q96PA9|Q9H938|Q9H9L5|Q9HAH0|Q9NQQ6	Silent	SNP	ENST00000290246.6	37	CCDS13398.1																																																																																			G|0.998;A|0.002	0.002	strong		0.527	ELMO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080466.1	NM_022086		A	45014804	G	A	45014804	2	1	22	1	0	0	0	0	0	0	0	1	5068	1103	39	1		1	ELMO2	20	45014804	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	502791	45014804	18010716	4204	7105											
NCOA3	8202	hgsc.bcm.edu	37	chr20	46264805	46264805	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ccaatatgaatattacccaaCcaagtaaagtaagcaatcag	19	8	5	9	0	1	1	1	1	0	0	1	1	1	1	3	0	3	3	3	0	11	5	rs2230781	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:46264805C>T	ENST00000371998.3	+	12	1866	c.1675C>T	c.(1675-1677)Cca>Tca	p.P559S	NCOA3_ENST00000372004.3_Missense_Mutation_p.P559S|NCOA3_ENST00000371997.3_Missense_Mutation_p.P569S|NCOA3_ENST00000341724.6_Missense_Mutation_p.P569S			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	559	Ser-rich.		P -> S (in dbSNP:rs2230781). {ECO:0000269|Ref.5}.		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						TATTACCCAACCAAGTAAAGT	0.443													C|||	96	0.0191693	0.0651	0.0101	5008	,	,		17392	0.0		0.003	False		,,,				2504	0.0				p.P569S		Atlas-SNP	.											.	NCOA3	156	.	0			c.C1705T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO,SER/PRO	246,4160	143.1+/-178.2	7,232,1964	90	89	89		1675,1705,1675,1675	3.7	0.8	20	dbSNP_98	89	4,8596	3.0+/-9.4	0,4,4296	yes	missense,missense,missense,missense	NCOA3	NM_001174087.1,NM_001174088.1,NM_006534.3,NM_181659.2	74,74,74,74	7,236,6260	TT,TC,CC		0.0465,5.5833,1.9222	benign,benign,benign,benign	559/1424,569/1416,559/1421,559/1425	46264805	250,12756	2203	4300	6503	SO:0001583	missense	8202	exon12			ACCCAACCAAGTA	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.1675C>T	20.37:g.46264805C>T	ENSP00000361066:p.Pro559Ser	134	0	0		155	87	0.56129	NM_001174088	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Missense_Mutation	SNP	ENST00000371998.3	37	CCDS13407.1	38	0.0173992673992674	33	0.06707317073170732	3	0.008287292817679558	0	0.0	2	0.002638522427440633	C	8.392	0.839981	0.16891	0.055833	4.65E-4	ENSG00000124151	ENST00000340189;ENST00000341724;ENST00000372004;ENST00000371998;ENST00000371997	T;T;T;T	0.16743	2.32;2.32;2.32;2.32	5.72	3.7	0.42460	.	0.351919	0.27627	N	0.018540	T	0.01061	0.0035	L	0.44542	1.39	0.26797	N	0.969286	B;B;B;B;B;B	0.25312	0.088;0.123;0.088;0.088;0.029;0.038	B;B;B;B;B;B	0.30572	0.103;0.117;0.103;0.103;0.098;0.071	T	0.24870	-1.0148	10	0.05833	T	0.94	-3.6234	16.0462	0.80722	0.0:0.7459:0.2541:0.0	rs2230781;rs52817019;rs2230781	559;569;563;559;559;559	A8K0W8;Q9Y6Q9-3;Q59EE8;Q0IIN7;Q9Y6Q9-5;Q9Y6Q9	.;.;.;.;.;NCOA3_HUMAN	S	559;569;559;559;569	ENSP00000342123:P569S;ENSP00000361073:P559S;ENSP00000361066:P559S;ENSP00000361065:P569S	ENSP00000345671:P559S	P	+	1	0	NCOA3	45698212	0.993000	0.37304	0.828000	0.32881	0.927000	0.56198	1.799000	0.38824	0.693000	0.31634	0.655000	0.94253	CCA	C|0.981;T|0.019	0.019	strong		0.443	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534		T	46264805	C	T	46264805	3	4	22	1	0	0	0	0	1	0	0	0	10239	507	18	2	1743	2	NCOA3	20	46264805	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1250001	46264805	16760715	4205	7106											
SULF2	55959	hgsc.bcm.edu	37	chr20	46292910	46292910	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggagcctctgtgcttgaggCggcctttgtgctgggtgtgg	2	13	18	8	1	1	1	0	1	1	0	1	2	1	2	2	5	3	2	2	5	0	2	rs10048853	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:46292910C>T	ENST00000359930.4	-	15	2872	c.2021G>A	c.(2020-2022)cGc>cAc	p.R674H	SULF2_ENST00000467815.1_Missense_Mutation_p.R674H|SULF2_ENST00000484875.1_Missense_Mutation_p.R674H|SULF2_ENST00000361612.4_Missense_Mutation_p.R674H	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	674			R -> H (in dbSNP:rs10048853).		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						GTGCTTGAGGCGGCCTTTGTG	0.607											OREG0026005	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	90	0.0179712	0.0582	0.0159	5008	,	,		17857	0.0		0.002	False		,,,				2504	0.0				p.R674H		Atlas-SNP	.											.	SULF2	131	.	0			c.G2021A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG	189,4217	116.7+/-154.6	4,181,2018	55	47	50		2021,2021,2021	3.1	1	20	dbSNP_119	50	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense,missense	SULF2	NM_001161841.1,NM_018837.3,NM_198596.2	29,29,29	4,184,6315	TT,TC,CC		0.0349,4.2896,1.4762	benign,benign,benign	674/871,674/871,674/868	46292910	192,12814	2203	4300	6503	SO:0001583	missense	55959	exon15			TTGAGGCGGCCTT	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.2021G>A	20.37:g.46292910C>T	ENSP00000353007:p.Arg674His	92	0	0	938	106	57	0.537736	NM_001161841	E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	Missense_Mutation	SNP	ENST00000359930.4	37	CCDS13408.1	25|25	0.011446886446886446|0.011446886446886446	16|16	0.032520325203252036|0.032520325203252036	7|7	0.019337016574585635|0.019337016574585635	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	C|C	13.33|13.33	2.203972|2.203972	0.38905|0.38905	0.042896|0.042896	3.49E-4|3.49E-4	ENSG00000196562|ENSG00000196562	ENST00000495544|ENST00000359930;ENST00000484875;ENST00000361612;ENST00000371978;ENST00000467815	.|T;T;T;T	.|0.22134	.|1.97;1.97;1.97;1.97	5.08|5.08	3.1|3.1	0.35709|0.35709	.|Alkaline-phosphatase-like, core domain (1);	.|0.302855	.|0.32769	.|N	.|0.005668	T|T	0.01523|0.01523	0.0049|0.0049	N|N	0.04959|0.04959	-0.14|-0.14	0.29204|0.29204	N|N	0.875005|0.875005	.|B;B	.|0.09022	.|0.002;0.001	.|B;B	.|0.06405	.|0.002;0.001	T|T	0.29518|0.29518	-1.0009|-1.0009	5|10	.|0.13108	.|T	.|0.6	-22.8637|-22.8637	4.1427|4.1427	0.10201|0.10201	0.0:0.5786:0.1901:0.2313|0.0:0.5786:0.1901:0.2313	rs10048853;rs10048853|rs10048853;rs10048853	.|674;674	.|Q8IWU5-2;Q8IWU5	.|.;SULF2_HUMAN	T|H	29|674;674;674;93;674	.|ENSP00000353007:R674H;ENSP00000418290:R674H;ENSP00000354662:R674H;ENSP00000418442:R674H	.|ENSP00000353007:R674H	A|R	-|-	1|2	0|0	SULF2|SULF2	45726317|45726317	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.796000|0.796000	0.44982|0.44982	1.968000|1.968000	0.40500|0.40500	0.689000|0.689000	0.31550|0.31550	-0.254000|-0.254000	0.11334|0.11334	GCC|CGC	C|0.983;T|0.017	0.017	strong		0.607	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1	NM_018837		T	46292910	C	T	46292910	3	4	22	1	0	0	0	0	1	0	0	0	15386	768	27	1	619	1	SULF2	20	46292910	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	28105	46292910	16732610	4206	7107											
PREX1	57580	hgsc.bcm.edu	37	chr20	47274733	47274733	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccttgttcttctcctcgaTgtcaaagccatagtcctcct	7	14	6	14	1	3	0	1	0	2	0	7	1	5	0	5	0	2	1	5	0	2	4	rs62621889	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:47274733T>C	ENST00000371941.3	-	17	1937	c.1915A>G	c.(1915-1917)Atc>Gtc	p.I639V	PREX1_ENST00000396220.1_Missense_Mutation_p.I639V	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	639	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)			TTCTCCTCGATGTCAAAGCCA	0.672											OREG0026010	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	51	0.0101837	0.0378	0.0014	5008	,	,		19323	0.0		0.0	False		,,,				2504	0.0				p.I639V		Atlas-SNP	.											.	PREX1	441	.	0			c.A1915G						PASS	.	T	VAL/ILE	146,4260	102.5+/-141.1	1,144,2058	285	256	266		1915	3.9	1	20	dbSNP_129	266	1,8599	1.2+/-3.3	0,1,4299	yes	missense	PREX1	NM_020820.3	29	1,145,6357	CC,CT,TT		0.0116,3.3137,1.1302	benign	639/1660	47274733	147,12859	2203	4300	6503	SO:0001583	missense	57580	exon17			CCTCGATGTCAAA	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.1915A>G	20.37:g.47274733T>C	ENSP00000361009:p.Ile639Val	155	0	0	945	161	68	0.42236	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	37	CCDS13410.1	15	0.006868131868131868	14	0.028455284552845527	1	0.0027624309392265192	0	0.0	0	0.0	T	12.08	1.832013	0.32421	0.033137	1.16E-4	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.18016	2.24;2.24	4.98	3.86	0.44501	Winged helix-turn-helix transcription repressor DNA-binding (1);PDZ/DHR/GLGF (3);	0.406056	0.19926	U	0.102980	T	0.02494	0.0076	N	0.08118	0	0.34912	D	0.747534	B	0.02656	0.0	B	0.04013	0.001	T	0.12656	-1.0539	10	0.56958	D	0.05	.	6.8339	0.23925	0.0:0.0776:0.2974:0.625	rs62621889	639	Q8TCU6	PREX1_HUMAN	V	639	ENSP00000361009:I639V;ENSP00000379522:I639V	ENSP00000361009:I639V	I	-	1	0	PREX1	46708140	1.000000	0.71417	0.981000	0.43875	0.935000	0.57460	3.185000	0.50934	0.714000	0.32081	0.533000	0.62120	ATC	T|0.989;C|0.011	0.011	strong		0.672	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		C	47274733	T	C	47274733	3	2	22	1	0	0	0	0	1	0	0	0	12488	1464	51	3	3160	3	PREX1	20	47274733	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	981823	47274733	15750787	4207	7108											
PREX1	57580	hgsc.bcm.edu	37	chr20	47295906	47295906	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agagtaacttacttgatcacCggggtgtagaggctgtgaag	11	10	14	6	1	1	4	1	2	0	2	1	4	1	4	1	3	2	3	1	3	4	4			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:47295906C>T	ENST00000371941.3	-	13	1603	c.1581G>A	c.(1579-1581)ccG>ccA	p.P527P	PREX1_ENST00000396220.1_Silent_p.P527P	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	527	DEP 2. {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)			ACTTGATCACCGGGGTGTAGA	0.512																																					p.P527P		Atlas-SNP	.											.	PREX1	441	.	0			c.G1581A						PASS	.						117	112	114					20																	47295906		2203	4300	6503	SO:0001819	synonymous_variant	57580	exon13			GATCACCGGGGTG	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.1581G>A	20.37:g.47295906C>T		36	0	0		34	16	0.470588	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Silent	SNP	ENST00000371941.3	37	CCDS13410.1																																																																																			.	.	none		0.512	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		T	47295906	C	T	47295906	2	4	22	1	0	0	0	0	0	0	0	1	12488	639	23	1		1	PREX1	20	47295906	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	21173	47295906	15729614	4208	7109											
ARFGEF2	10564	hgsc.bcm.edu	37	chr20	47588949	47588949	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atggtcattcagactctgacGaggatctgtgcaggtatttc	9	13	11	8	1	4	2	2	1	2	1	5	4	4	3	0	3	1	2	0	3	1	3	rs116550473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:47588949G>A	ENST00000371917.4	+	11	1512	c.1512G>A	c.(1510-1512)acG>acA	p.T504T		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	504					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)			AGACTCTGACGAGGATCTGTG	0.408													G|||	17	0.00339457	0.0121	0.0014	5008	,	,		20979	0.0		0.0	False		,,,				2504	0.0				p.T504T	Esophageal Squamous(176;1738 1974 26285 33069 35354)	Atlas-SNP	.											.	ARFGEF2	160	.	0			c.G1512A						PASS	.	G		56,4350	56.2+/-92.4	0,56,2147	84	81	82		1512	-6.9	0.9	20	dbSNP_132	82	0,8600		0,0,4300	no	coding-synonymous	ARFGEF2	NM_006420.2		0,56,6447	AA,AG,GG		0.0,1.271,0.4306		504/1786	47588949	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	10564	exon11			TCTGACGAGGATC	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.1512G>A	20.37:g.47588949G>A		64	0	0		67	32	0.477612	NM_006420	Q5TFT9|Q9NTS1	Silent	SNP	ENST00000371917.4	37	CCDS13411.1																																																																																			G|0.996;A|0.004	0.004	strong		0.408	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420		A	47588949	G	A	47588949	2	1	22	1	0	0	0	0	0	0	0	1	853	1045	37	1		1	ARFGEF2	20	47588949	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	293043	47588949	15436571	4209	7110											
DDX27	55661	hgsc.bcm.edu	37	chr20	47838020	47838020	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctgggcagacgacaaaaagCtttggggaagaaccgcagtg	13	5	15	8	2	0	2	0	0	0	2	0	4	0	3	1	3	2	4	1	3	4	1	rs114928867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:47838020C>T	ENST00000371764.4	+	2	227	c.218C>T	c.(217-219)gCt>gTt	p.A73V	DDX27_ENST00000484427.1_3'UTR	NM_017895.7	NP_060365.7	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	73	Asp/Glu/Lys-rich.					nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			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)			CGACAAAAAGCTTTGGGGAAG	0.522													C|||	14	0.00279553	0.0106	0.0	5008	,	,		18783	0.0		0.0	False		,,,				2504	0.0				p.A73V		Atlas-SNP	.											.	DDX27	74	.	0			c.C218T						PASS	.	C	VAL/ALA	47,4359	50.2+/-85.5	0,47,2156	83	72	76		218	5.2	1	20	dbSNP_132	76	0,8600		0,0,4300	yes	missense	DDX27	NM_017895.7	64	0,47,6456	TT,TC,CC		0.0,1.0667,0.3614	benign	73/797	47838020	47,12959	2203	4300	6503	SO:0001583	missense	55661	exon2			AAAAAGCTTTGGG	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.218C>T	20.37:g.47838020C>T	ENSP00000360828:p.Ala73Val	115	0	0		126	59	0.468254	NM_017895	A0AVB6|B7ZLY1|Q5VXM7|Q8WYG4|Q969N7|Q96F57|Q96L97|Q9BWY9|Q9BXF0|Q9H990|Q9NWU3|Q9P0C2|Q9UGD6	Missense_Mutation	SNP	ENST00000371764.4	37	CCDS13416.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	13.11	2.138594	0.37728	0.010667	0.0	ENSG00000124228	ENST00000535160;ENST00000371764	T	0.01474	4.85	5.16	5.16	0.70880	.	0.553075	0.18353	N	0.143813	T	0.01156	0.0038	N	0.22421	0.69	0.37063	D	0.89816	B	0.24823	0.112	B	0.19148	0.024	T	0.60459	-0.7259	10	0.30078	T	0.28	-17.0082	11.1111	0.48232	0.1841:0.8159:0.0:0.0	.	73	Q96GQ7	DDX27_HUMAN	V	73	ENSP00000360828:A73V	ENSP00000360828:A73V	A	+	2	0	DDX27	47271427	0.984000	0.35163	1.000000	0.80357	0.550000	0.35303	1.360000	0.34125	2.698000	0.92095	0.561000	0.74099	GCT	C|0.997;T|0.003	0.003	strong		0.522	DDX27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080485.1			T	47838020	C	T	47838020	3	4	22	1	0	0	0	0	1	0	0	0	4356	797	28	2	224	2	DDX27	20	47838020	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	249071	47838020	15187500	4210	7111											
DDX27	55661	hgsc.bcm.edu	37	chr20	47849904	47849904	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccgaatgtgttcccaccacCgccagaccatgctcttctcg	7	10	7	17	3	2	1	0	0	2	1	5	2	4	1	6	0	1	2	6	0	1	2	rs145681733		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:47849904C>T	ENST00000371764.4	+	10	1195	c.1186C>T	c.(1186-1188)Cgc>Tgc	p.R396C	DDX27_ENST00000484427.1_3'UTR	NM_017895.7	NP_060365.7	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	396	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			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)			TTCCCACCACCGCCAGACCAT	0.582																																					p.R396C		Atlas-SNP	.											.	DDX27	74	.	0			c.C1186T						PASS	.	C	CYS/ARG	0,4406		0,0,2203	87	69	75		1186	6	1	20	dbSNP_134	75	1,8599	1.2+/-3.3	0,1,4299	no	missense	DDX27	NM_017895.7	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	396/797	47849904	1,13005	2203	4300	6503	SO:0001583	missense	55661	exon10			CACCACCGCCAGA	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.1186C>T	20.37:g.47849904C>T	ENSP00000360828:p.Arg396Cys	85	0	0		83	34	0.409639	NM_017895	A0AVB6|B7ZLY1|Q5VXM7|Q8WYG4|Q969N7|Q96F57|Q96L97|Q9BWY9|Q9BXF0|Q9H990|Q9NWU3|Q9P0C2|Q9UGD6	Missense_Mutation	SNP	ENST00000371764.4	37	CCDS13416.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.700821	0.88924	0.0	1.16E-4	ENSG00000124228	ENST00000371764	T	0.49432	0.78	5.97	5.97	0.96955	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.71929	0.3398	M	0.81614	2.55	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74234	-0.3731	10	0.87932	D	0	-14.1308	17.9218	0.88969	0.0:1.0:0.0:0.0	.	396	Q96GQ7	DDX27_HUMAN	C	396	ENSP00000360828:R396C	ENSP00000360828:R396C	R	+	1	0	DDX27	47283311	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.548000	0.53670	2.837000	0.97791	0.655000	0.94253	CGC	C|1.000;T|0.000	0.000	weak		0.582	DDX27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080485.1			T	47849904	C	T	47849904	3	4	22	1	0	0	0	0	1	0	0	0	4356	652	23	1	1224	1	DDX27	20	47849904	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	11884	47849904	15175616	4211	7112											
DDX27	55661	hgsc.bcm.edu	37	chr20	47858695	47858695	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagcgaagaggaatcgcagaGccaagcgggcccgagcaatg	13	3	15	10	4	0	2	0	0	0	2	1	5	0	3	2	2	4	2	2	2	5	1	rs143843778	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:47858695G>A	ENST00000371764.4	+	18	2170	c.2161G>A	c.(2161-2163)Gcc>Acc	p.A721T	ZNFX1_ENST00000371754.4_Intron|DDX27_ENST00000484427.1_3'UTR|ZNFX1_ENST00000469991.1_Intron	NM_017895.7	NP_060365.7	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	721						nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			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)			GAATCGCAGAGCCAAGCGGGC	0.567													G|||	17	0.00339457	0.0121	0.0014	5008	,	,		17319	0.0		0.0	False		,,,				2504	0.0				p.A721T		Atlas-SNP	.											.	DDX27	74	.	0			c.G2161A						PASS	.	G	THR/ALA	54,4352	54.9+/-90.9	0,54,2149	48	45	46		2161	1.7	1	20	dbSNP_134	46	0,8600		0,0,4300	yes	missense	DDX27	NM_017895.7	58	0,54,6449	AA,AG,GG		0.0,1.2256,0.4152	benign	721/797	47858695	54,12952	2203	4300	6503	SO:0001583	missense	55661	exon18			CGCAGAGCCAAGC	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.2161G>A	20.37:g.47858695G>A	ENSP00000360828:p.Ala721Thr	139	0	0		133	56	0.421053	NM_017895	A0AVB6|B7ZLY1|Q5VXM7|Q8WYG4|Q969N7|Q96F57|Q96L97|Q9BWY9|Q9BXF0|Q9H990|Q9NWU3|Q9P0C2|Q9UGD6	Missense_Mutation	SNP	ENST00000371764.4	37	CCDS13416.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	G	12.62	1.992729	0.35131	0.012256	0.0	ENSG00000124228	ENST00000371764	T	0.01438	4.89	5.83	1.74	0.24563	.	0.354569	0.32473	N	0.006059	T	0.00695	0.0023	N	0.22421	0.69	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.58222	-0.7674	10	0.17369	T	0.5	-2.8822	4.7211	0.12918	0.3373:0.1498:0.513:0.0	.	721	Q96GQ7	DDX27_HUMAN	T	721	ENSP00000360828:A721T	ENSP00000360828:A721T	A	+	1	0	DDX27	47292102	0.998000	0.40836	0.996000	0.52242	0.995000	0.86356	0.954000	0.29175	0.098000	0.17522	0.561000	0.74099	GCC	G|0.996;A|0.004	0.004	strong		0.567	DDX27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080485.1			A	47858695	G	A	47858695	3	1	22	1	0	0	0	0	1	0	0	0	4356	971	34	2	2231	2	DDX27	20	47858695	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	8791	47858695	15166825	4212	7113											
SLC9A8	23315	hgsc.bcm.edu	37	chr20	48472098	48472098	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaagtattctcaacgatgcAgtctccattgttctgaccaa	12	12	7	10	1	3	1	1	1	3	0	5	3	3	1	2	0	2	3	2	0	4	4	rs35137210	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:48472098A>G	ENST00000361573.2	+	8	735	c.693A>G	c.(691-693)gcA>gcG	p.A231A	SLC9A8_ENST00000541138.1_5'UTR|SLC9A8_ENST00000417961.1_Silent_p.A247A|SLC9A8_ENST00000539601.1_Silent_p.A12A			Q9Y2E8	SL9A8_HUMAN	solute carrier family 9, subfamily A (NHE8, cation proton antiporter 8), member 8	231					ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	potassium:proton antiporter activity (GO:0015386)|sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	30			BRCA - Breast invasive adenocarcinoma(9;3.91e-07)			TCAACGATGCAGTCTCCATTG	0.463													A|||	18	0.00359425	0.0136	0.0	5008	,	,		22384	0.0		0.0	False		,,,				2504	0.0				p.A247A		Atlas-SNP	.											.	SLC9A8	63	.	0			c.A741G						PASS	.	A		60,4346	56.2+/-92.4	0,60,2143	107	92	97		693	-10.5	0	20	dbSNP_126	97	0,8600		0,0,4300	no	coding-synonymous	SLC9A8	NM_015266.1		0,60,6443	GG,GA,AA		0.0,1.3618,0.4613		231/582	48472098	60,12946	2203	4300	6503	SO:0001819	synonymous_variant	23315	exon8			CGATGCAGTCTCC	AB023156	CCDS13421.1, CCDS58774.1	20q13.13	2013-05-22	2012-03-22		ENSG00000197818	ENSG00000197818		"Solute carriers"	20728	protein-coding gene	gene with protein product		612730	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 8", "solute carrier family 9 (sodium/hydrogen exchanger), member 8"			12409279	Standard	NM_001260491		Approved	KIAA0939, NHE8	uc002xuv.2	Q9Y2E8	OTTHUMG00000032710	ENST00000361573.2:c.693A>G	20.37:g.48472098A>G		164	0	0		161	85	0.52795	NM_001260491	B4DTQ8|Q2M1U9|Q68CZ8|Q9BX15|Q9Y507	Silent	SNP	ENST00000361573.2	37	CCDS13421.1																																																																																			A|0.994;G|0.006	0.006	strong		0.463	SLC9A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106483.3	XM_030524		G	48472098	A	G	48472098	2	3	22	1	0	0	0	0	0	0	0	1	14735	175	7	3		3	SLC9A8	20	48472098	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	613403	48472098	14553422	4213	7114											
SPATA2	9825	hgsc.bcm.edu	37	chr20	48522263	48522263	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcaggggtcataatggtaagCgctgaggcaggcgtcacatg	10	7	16	8	2	2	1	2	1	0	0	2	1	2	1	0	5	1	4	0	5	2	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:48522263C>T	ENST00000422556.1	-	3	1805	c.1456G>A	c.(1456-1458)Gct>Act	p.A486T	SPATA2_ENST00000289431.5_Missense_Mutation_p.A486T|SPATA2_ENST00000543716.1_Missense_Mutation_p.A349T	NM_001135773.1	NP_001129245.1	Q9UM82	SPAT2_HUMAN	spermatogenesis associated 2	486					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)			TAATGGTAAGCGCTGAGGCAG	0.562																																					p.A486T		Atlas-SNP	.											.	SPATA2	36	.	0			c.G1456A						PASS	.						167	154	159					20																	48522263		2203	4300	6503	SO:0001583	missense	9825	exon3			GGTAAGCGCTGAG	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.1456G>A	20.37:g.48522263C>T	ENSP00000416799:p.Ala486Thr	342	0	0		371	188	0.506739	NM_006038	E1P626|O94857	Missense_Mutation	SNP	ENST00000422556.1	37	CCDS13422.1	.	.	.	.	.	.	.	.	.	.	C	15.06	2.721788	0.48728	.	.	ENSG00000158480	ENST00000289431;ENST00000422556;ENST00000543716	T;T;T	0.48201	0.83;0.83;0.82	5.08	0.988	0.19796	.	0.293281	0.28198	N	0.016236	T	0.40570	0.1122	L	0.59436	1.845	0.36765	D	0.883515	B	0.18968	0.032	B	0.14023	0.01	T	0.36601	-0.9741	10	0.42905	T	0.14	-10.862	10.0211	0.42044	0.0:0.7242:0.0:0.2758	.	486	Q9UM82	SPAT2_HUMAN	T	486;486;349	ENSP00000289431:A486T;ENSP00000416799:A486T;ENSP00000438855:A349T	ENSP00000289431:A486T	A	-	1	0	SPATA2	47955670	1.000000	0.71417	0.974000	0.42286	0.448000	0.32197	2.904000	0.48719	0.057000	0.16193	0.455000	0.32223	GCT	.	.	none		0.562	SPATA2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079658.1	NM_006038		T	48522263	C	T	48522263	3	4	22	1	0	0	0	0	1	0	0	0	15020	768	27	1	110	1	SPATA2	20	48522263	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	50165	48522263	14503257	4214	7115											
SNAI1	6615	hgsc.bcm.edu	37	chr20	48600475	48600475	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catctgggactctgtcctggCgccccaagcccagccaattg	7	8	10	16	1	2	0	0	0	2	0	3	1	3	1	5	2	2	0	5	2	2	1	rs34261470	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:48600475C>T	ENST00000244050.2	+	2	258	c.197C>T	c.(196-198)gCg>gTg	p.A66V		NM_005985.3	NP_005976.2	O95863	SNAI1_HUMAN	snail family zinc finger 1	66			A -> V (in dbSNP:rs34261470).		cartilage morphogenesis (GO:0060536)|cell migration (GO:0016477)|epithelial to mesenchymal transition (GO:0001837)|hair follicle morphogenesis (GO:0031069)|left/right pattern formation (GO:0060972)|mesoderm formation (GO:0001707)|negative regulation of cell differentiation involved in embryonic placenta development (GO:0060806)|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 (GO:1902230)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|Notch signaling involved in heart development (GO:0061314)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of tight junction assembly (GO:2000810)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	kinase binding (GO:0019900)|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 regulatory region sequence-specific DNA binding (GO:0000977)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)	17			BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			TCTGTCCTGGCGCCCCAAGCC	0.657													C|||	140	0.0279553	0.093	0.0101	5008	,	,		14457	0.0		0.0	False		,,,				2504	0.0102				p.A66V		Atlas-SNP	.											.	SNAI1	28	.	0			c.C197T						PASS	.	C	VAL/ALA	321,4085	168.3+/-199.2	18,285,1900	45	50	48		197	1.8	0.9	20	dbSNP_126	48	7,8593	5.7+/-21.5	0,7,4293	no	missense	SNAI1	NM_005985.3	64	18,292,6193	TT,TC,CC		0.0814,7.2855,2.5219	benign	66/265	48600475	328,12678	2203	4300	6503	SO:0001583	missense	6615	exon2			TCCTGGCGCCCCA	AF125377	CCDS13423.1	20q13.2	2013-05-23	2013-05-23		ENSG00000124216	ENSG00000124216		"Snail homologs", "Zinc fingers, C2H2-type"	11128	protein-coding gene	gene with protein product		604238	"snail 1 (drosophila homolog), zinc finger protein", "snail homolog 1 (Drosophila)"			10585766	Standard	NM_005985		Approved	SNA, SLUGH2, SNAH, SNAIL1, SNAIL	uc002xuz.3	O95863	OTTHUMG00000033048	ENST00000244050.2:c.197C>T	20.37:g.48600475C>T	ENSP00000244050:p.Ala66Val	43	0	0		50	19	0.38	NM_005985	B2R842|Q9P113|Q9UBP7|Q9UHH7	Missense_Mutation	SNP	ENST00000244050.2	37	CCDS13423.1	38	0.0173992673992674	32	0.06504065040650407	6	0.016574585635359115	0	0.0	0	0.0	C	12.23	1.875633	0.33162	0.072855	8.14E-4	ENSG00000124216	ENST00000244050	T	0.20332	2.08	4.94	1.81	0.25067	.	1.159810	0.06133	N	0.670998	T	0.01061	0.0035	L	0.33485	1.01	0.23704	N	0.997068	B	0.11235	0.004	B	0.04013	0.001	T	0.32134	-0.9918	10	0.13853	T	0.58	-4.3384	7.28	0.26306	0.0:0.6314:0.0:0.3686	rs34261470	66	O95863	SNAI1_HUMAN	V	66	ENSP00000244050:A66V	ENSP00000244050:A66V	A	+	2	0	SNAI1	48033882	0.003000	0.15002	0.936000	0.37596	0.943000	0.58893	1.315000	0.33608	0.429000	0.26202	0.557000	0.71058	GCG	C|0.979;T|0.021	0.021	strong		0.657	SNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080350.1			T	48600475	C	T	48600475	3	4	22	1	0	0	0	0	1	0	0	0	14841	768	27	1	203	1	SNAI1	20	48600475	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	78212	48600475	14425045	4215	7116											
PTPN1	5770	hgsc.bcm.edu	37	chr20	49191191	49191191	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctagaattggaaaaccttacAgtgagtatagcacacacttc	15	10	7	9	0	0	2	0	1	0	1	1	3	0	3	1	1	3	2	1	1	7	6	rs35414863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:49191191A>G	ENST00000371621.3	+	5	666	c.492A>G	c.(490-492)acA>acG	p.T164T	RP4-530I15.9_ENST00000431019.1_RNA|PTPN1_ENST00000541713.1_Splice_Site_p.T91T	NM_001278618.1|NM_002827.2	NP_001265547.1|NP_002818.1	P18031	PTN1_HUMAN	protein tyrosine phosphatase, non-receptor type 1	164	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|endoplasmic reticulum unfolded protein response (GO:0030968)|insulin receptor signaling pathway (GO:0008286)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|peptidyl-tyrosine dephosphorylation (GO:0035335)|peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity (GO:1990264)|platelet activation (GO:0030168)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|regulation of endocytosis (GO:0030100)|regulation of hepatocyte growth factor receptor signaling pathway (GO:1902202)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of signal transduction (GO:0009966)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|sorting endosome (GO:0097443)	enzyme binding (GO:0019899)|ephrin receptor binding (GO:0046875)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|skin(2)	16		Lung NSC(126;0.163)			Tiludronate(DB01133)	aAAACCTTACAGTGAGTATAG	0.398													A|||	113	0.0225639	0.0772	0.0144	5008	,	,		21947	0.0		0.001	False		,,,				2504	0.0				p.T164T		Atlas-SNP	.											.	PTPN1	36	.	0			c.A492G						PASS	.	A		344,4062	179.7+/-208.2	11,322,1870	117	116	117		492	-10.3	0	20	dbSNP_126	117	19,8581	13.3+/-46.6	0,19,4281	yes	coding-synonymous-near-splice	PTPN1	NM_002827.2		11,341,6151	GG,GA,AA		0.2209,7.8075,2.791		164/436	49191191	363,12643	2203	4300	6503	SO:0001630	splice_region_variant	5770	exon5			CCTTACAGTGAGT		CCDS13430.1, CCDS63309.1	20q13.1-q13.2	2011-06-09			ENSG00000196396	ENSG00000196396		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9642	protein-coding gene	gene with protein product		176885		PTP1B		2164224	Standard	NM_002827		Approved		uc002xvl.3	P18031	OTTHUMG00000032729	ENST00000371621.3:c.492+1A>G	20.37:g.49191191A>G		89	0	0		99	51	0.515152	NM_002827	Q5TGD8|Q9BQV9|Q9NQQ4	Silent	SNP	ENST00000371621.3	37	CCDS13430.1																																																																																			A|0.976;G|0.024	0.024	strong		0.398	PTPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079694.2		Silent	G	49191191	A	G	49191191	5	3	22	1	0	0	0	0	0	0	1	0	12792	202	7	3	510	3	PTPN1	20	49191191	Splice_Site	SNP	A	TCGA-G8-6324-01A-11D-2210-10	590716	49191191	13834329	4216	7117											
PTPN1	5770	hgsc.bcm.edu	37	chr20	49197955	49197955	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cccttcctggtcaacatgtgCgtggctacggtcctcacggc	5	10	11	15	3	2	0	2	0	0	0	4	0	4	0	3	4	3	1	3	4	2	2	rs74607837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:49197955C>T	ENST00000371621.3	+	9	1416	c.1242C>T	c.(1240-1242)tgC>tgT	p.C414C	PTPN1_ENST00000541713.1_Silent_p.C341C	NM_001278618.1|NM_002827.2	NP_001265547.1|NP_002818.1	P18031	PTN1_HUMAN	protein tyrosine phosphatase, non-receptor type 1	414					actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|endoplasmic reticulum unfolded protein response (GO:0030968)|insulin receptor signaling pathway (GO:0008286)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|peptidyl-tyrosine dephosphorylation (GO:0035335)|peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity (GO:1990264)|platelet activation (GO:0030168)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|regulation of endocytosis (GO:0030100)|regulation of hepatocyte growth factor receptor signaling pathway (GO:1902202)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of signal transduction (GO:0009966)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|sorting endosome (GO:0097443)	enzyme binding (GO:0019899)|ephrin receptor binding (GO:0046875)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|skin(2)	16		Lung NSC(126;0.163)			Tiludronate(DB01133)	TCAACATGTGCGTGGCTACGG	0.627													C|||	81	0.0161741	0.059	0.0043	5008	,	,		18745	0.0		0.0	False		,,,				2504	0.0				p.C414C		Atlas-SNP	.											.	PTPN1	36	.	0			c.C1242T						PASS	.	C		223,4183	133.7+/-170.0	6,211,1986	110	74	86		1242	0.4	0.8	20	dbSNP_132	86	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	PTPN1	NM_002827.2		6,215,6282	TT,TC,CC		0.0465,5.0613,1.7453		414/436	49197955	227,12779	2203	4300	6503	SO:0001819	synonymous_variant	5770	exon9			CATGTGCGTGGCT		CCDS13430.1, CCDS63309.1	20q13.1-q13.2	2011-06-09			ENSG00000196396	ENSG00000196396		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9642	protein-coding gene	gene with protein product		176885		PTP1B		2164224	Standard	NM_002827		Approved		uc002xvl.3	P18031	OTTHUMG00000032729	ENST00000371621.3:c.1242C>T	20.37:g.49197955C>T		138	0	0		162	81	0.5	NM_002827	Q5TGD8|Q9BQV9|Q9NQQ4	Silent	SNP	ENST00000371621.3	37	CCDS13430.1																																																																																			C|0.980;T|0.020	0.020	strong		0.627	PTPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079694.2			T	49197955	C	T	49197955	2	4	22	1	0	0	0	0	0	0	0	1	12792	776	27	1		1	PTPN1	20	49197955	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6764	49197955	13827565	4217	7118											
ATP9A	10079	hgsc.bcm.edu	37	chr20	50310559	50310559	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ctactcacggcggccgtgggGagcctctgcgtgcaggccac	5	6	15	15	4	2	0	1	0	1	0	2	1	2	1	3	5	4	1	3	5	1	1	rs2031344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:50310559G>A	ENST00000338821.5	-	7	894	c.630C>T	c.(628-630)ctC>ctT	p.L210L	ATP9A_ENST00000311637.5_Intron|ATP9A_ENST00000402822.1_Intron	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	210					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						CGGCCGTGGGGAGCCTCTGCG	0.627													G|||	70	0.0139776	0.0499	0.0043	5008	,	,		14542	0.0		0.001	False		,,,				2504	0.0				p.L210L		Atlas-SNP	.											.	ATP9A	135	.	0			c.C630T						PASS	.	G		171,4235	96.7+/-135.4	3,165,2035	42	45	44		630	-3	1	20	dbSNP_94	44	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ATP9A	NM_006045.1		3,166,6334	AA,AG,GG		0.0116,3.8811,1.3225		210/1048	50310559	172,12834	2203	4300	6503	SO:0001819	synonymous_variant	10079	exon7			CGTGGGGAGCCTC	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.630C>T	20.37:g.50310559G>A		218	0	0		188	82	0.43617	NM_006045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Silent	SNP	ENST00000338821.5	37	CCDS33489.1																																																																																			G|0.985;A|0.015	0.015	strong		0.627	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045		A	50310559	G	A	50310559	2	1	22	1	0	0	0	0	0	0	0	1	1198	1161	41	2		2	ATP9A	20	50310559	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1112604	50310559	12714961	4218	7119											
SALL4	57167	hgsc.bcm.edu	37	chr20	50406646	50406646	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgatgctttcggcttgactAttggccggggagagtgcctg	5	13	15	8	2	0	3	0	2	0	1	1	4	0	3	2	4	2	2	2	4	1	5	rs143601538	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:50406646A>G	ENST00000217086.4	-	2	2487	c.2376T>C	c.(2374-2376)aaT>aaC	p.N792N	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	792					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						CGGCTTGACTATTGGCCGGGG	0.547													A|||	4	0.000798722	0.003	0.0	5008	,	,		17547	0.0		0.0	False		,,,				2504	0.0				p.N792N		Atlas-SNP	.											.	SALL4	168	.	0			c.T2376C						PASS	.	A		11,4395	17.9+/-39.9	0,11,2192	79	73	75		2376	2.2	1	20	dbSNP_134	75	0,8600		0,0,4300	no	coding-synonymous	SALL4	NM_020436.3		0,11,6492	GG,GA,AA		0.0,0.2497,0.0846		792/1054	50406646	11,12995	2203	4300	6503	SO:0001819	synonymous_variant	57167	exon2			TTGACTATTGGCC	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.2376T>C	20.37:g.50406646A>G		323	0	0		302	158	0.523179	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																			A|0.999;G|0.001	0.001	strong		0.547	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3			G	50406646	A	G	50406646	2	3	22	1	0	0	0	0	0	0	0	1	13828	446	16	3		3	SALL4	20	50406646	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	96087	50406646	12618874	4219	7120											
SALL4	57167	hgsc.bcm.edu	37	chr20	50406892	50406892	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtggatgctgggaagaggCgtggggaccttggaggagct	8	7	21	5	1	0	1	0	0	0	1	0	7	0	6	1	7	2	2	1	7	1	1	rs61737143	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:50406892C>T	ENST00000217086.4	-	2	2241	c.2130G>A	c.(2128-2130)acG>acA	p.T710T	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	710					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						TGGGAAGAGGCGTGGGGACCT	0.587													C|||	91	0.0181709	0.0643	0.0072	5008	,	,		18206	0.0		0.001	False		,,,				2504	0.0				p.T710T		Atlas-SNP	.											.	SALL4	168	.	0			c.G2130A						PASS	.	C		253,4153	143.5+/-178.5	11,231,1961	41	38	39		2130	-6	0	20	dbSNP_129	39	0,8600		0,0,4300	no	coding-synonymous	SALL4	NM_020436.3		11,231,6261	TT,TC,CC		0.0,5.7422,1.9453		710/1054	50406892	253,12753	2203	4300	6503	SO:0001819	synonymous_variant	57167	exon2			AAGAGGCGTGGGG	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.2130G>A	20.37:g.50406892C>T		171	0	0		158	55	0.348101	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																			C|0.982;T|0.018	0.018	strong		0.587	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3			T	50406892	C	T	50406892	2	4	22	1	0	0	0	0	0	0	0	1	13828	755	27	1		1	SALL4	20	50406892	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	246	50406892	12618628	4220	7121											
SALL4	57167	hgsc.bcm.edu	37	chr20	50408614	50408614	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtcctctgagctgccgccAttctccctgtgacagtcctt	5	13	8	15	1	2	2	0	2	2	0	5	2	4	2	5	0	2	1	5	0	0	2	rs76870996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:50408614A>G	ENST00000217086.4	-	2	519	c.408T>C	c.(406-408)aaT>aaC	p.N136N	SALL4_ENST00000483130.1_5'UTR|SALL4_ENST00000371539.3_Intron|SALL4_ENST00000395997.3_Silent_p.N136N	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	136					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						AGCTGCCGCCATTCTCCCTGT	0.592													A|||	67	0.0133786	0.0469	0.0058	5008	,	,		16786	0.0		0.001	False		,,,				2504	0.0				p.N136N		Atlas-SNP	.											.	SALL4	168	.	0			c.T408C						PASS	.	A		172,4234	113.3+/-151.4	6,160,2037	128	134	132		408	-7.7	0	20	dbSNP_131	132	0,8600		0,0,4300	no	coding-synonymous	SALL4	NM_020436.3		6,160,6337	GG,GA,AA		0.0,3.9038,1.3225		136/1054	50408614	172,12834	2203	4300	6503	SO:0001819	synonymous_variant	57167	exon2			GCCGCCATTCTCC	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.408T>C	20.37:g.50408614A>G		125	0	0		117	49	0.418803	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																			A|0.988;G|0.012	0.012	strong		0.592	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3			G	50408614	A	G	50408614	2	3	22	1	0	0	0	0	0	0	0	1	13828	214	8	3		3	SALL4	20	50408614	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1722	50408614	12616906	4221	7122											
TSHZ2	128553	hgsc.bcm.edu	37	chr20	51872038	51872038	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctctgagcaatgggtgcGccctcgccaaccacgccccg	6	6	11	18	4	1	1	0	1	1	0	2	1	1	1	5	1	4	2	5	1	2	0	rs6097319	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:51872038G>A	ENST00000371497.5	+	2	2928	c.2041G>A	c.(2041-2043)Gcc>Acc	p.A681T	RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000603338.2_Missense_Mutation_p.A678T|TSHZ2_ENST00000329613.6_Missense_Mutation_p.A678T	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	681			A -> T (in dbSNP:rs6097319).		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)			CAATGGGTGCGCCCTCGCCAA	0.637													G|||	308	0.0615016	0.2231	0.013	5008	,	,		16470	0.0		0.004	False		,,,				2504	0.0				p.A681T		Atlas-SNP	.											.	TSHZ2	209	.	0			c.G2041A						PASS	.	G	THR/ALA,THR/ALA	827,3579	325.6+/-299.2	98,631,1474	50	46	48		2032,2041	-1.2	0	20	dbSNP_114	48	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	TSHZ2	NM_001193421.1,NM_173485.5	58,58	98,637,5768	AA,AG,GG		0.0698,18.7699,6.4047	benign,benign	678/1032,681/1035	51872038	833,12173	2203	4300	6503	SO:0001583	missense	128553	exon2			GGGTGCGCCCTCG	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.2041G>A	20.37:g.51872038G>A	ENSP00000360552:p.Ala681Thr	45	0	0		48	28	0.583333	NM_173485	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	37	CCDS33490.1	122	0.055860805860805864	118	0.23983739837398374	4	0.011049723756906077	0	0.0	0	0.0	G	2.194	-0.384541	0.04966	0.187699	6.98E-4	ENSG00000182463	ENST00000371497;ENST00000329613;ENST00000450262	T;T	0.37752	1.18;1.18	5.53	-1.21	0.09524	.	0.276183	0.39020	N	0.001485	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.29579	-1.0007	9	0.10111	T	0.7	1.382	2.2477	0.04035	0.3252:0.1119:0.4479:0.115	rs6097319;rs6097319	681	Q9NRE2	TSH2_HUMAN	T	681;678;207	ENSP00000360552:A681T;ENSP00000333114:A678T	ENSP00000333114:A678T	A	+	1	0	TSHZ2	51305445	0.046000	0.20272	0.000000	0.03702	0.029000	0.11900	0.728000	0.26013	-0.174000	0.10743	0.643000	0.83706	GCC	G|0.935;A|0.065	0.065	strong		0.637	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485		A	51872038	G	A	51872038	3	1	22	1	0	0	0	0	1	0	0	0	16639	1087	38	1	2047	1	TSHZ2	20	51872038	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1463424	51872038	11153482	4222	7123											
ZNF217	7764	hgsc.bcm.edu	37	chr20	52192308	52192308	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggactaccagcaggcacacAagtgtaaagtggcccggagc	12	5	13	11	1	0	0	0	0	0	0	0	2	0	2	2	4	3	3	2	4	4	2	rs61758384	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:52192308A>C	ENST00000371471.2	-	4	3420	c.2995T>G	c.(2995-2997)Tgt>Ggt	p.C999G	RP4-724E16.2_ENST00000424252.1_RNA|ZNF217_ENST00000302342.3_Missense_Mutation_p.C999G			O75362	ZN217_HUMAN	zinc finger protein 217	999					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)			GCAGGCACACAAGTGTAAAGT	0.527													A|||	51	0.0101837	0.0356	0.0058	5008	,	,		21128	0.0		0.0	False		,,,				2504	0.0				p.C999G		Atlas-SNP	.											ZNF217,NS,carcinoma,+1,1	ZNF217	227	1	0			c.T2995G						PASS	.	A	GLY/CYS	187,4219	116.3+/-154.2	1,185,2017	61	58	59		2995	4.8	0	20	dbSNP_129	59	2,8598	2.2+/-6.3	0,2,4298	yes	missense	ZNF217	NM_006526.2	159	1,187,6315	CC,CA,AA		0.0233,4.2442,1.4532	possibly-damaging	999/1049	52192308	189,12817	2203	4300	6503	SO:0001583	missense	7764	exon3			GCACACAAGTGTA	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.2995T>G	20.37:g.52192308A>C	ENSP00000360526:p.Cys999Gly	32	0	0		40	17	0.425	NM_006526	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	37	CCDS13443.1	18	0.008241758241758242	16	0.032520325203252036	2	0.0055248618784530384	0	0.0	0	0.0	A	16.16	3.044296	0.55110	0.042442	2.33E-4	ENSG00000171940	ENST00000371471;ENST00000302342;ENST00000437222;ENST00000395971	T;T	0.11821	2.74;2.74	4.79	4.79	0.61399	.	0.463445	0.23003	N	0.053056	T	0.07773	0.0195	L	0.59436	1.845	0.19945	N	0.999949	D	0.71674	0.998	P	0.60682	0.878	T	0.01081	-1.1458	10	0.72032	D	0.01	-8.6365	12.5619	0.56286	1.0:0.0:0.0:0.0	rs61758384	999	O75362	ZN217_HUMAN	G	999;999;87;159	ENSP00000360526:C999G;ENSP00000304308:C999G	ENSP00000304308:C999G	C	-	1	0	ZNF217	51625715	0.948000	0.32251	0.008000	0.14137	0.003000	0.03518	5.216000	0.65246	1.791000	0.52520	0.528000	0.53228	TGT	A|0.985;C|0.015	0.015	strong		0.527	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		C	52192308	A	C	52192308	3	2	22	1	0	0	0	0	1	0	0	0	17787	130	5	5	159	5	ZNF217	20	52192308	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	320270	52192308	10833212	4223	7124											
ZNF217	7764	hgsc.bcm.edu	37	chr20	52198619	52198619	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccttgtggagagtctgtctgCgcgctgctggtaccgaaagc	6	10	14	11	3	2	1	0	0	2	1	2	3	2	1	2	2	4	3	2	2	2	2	rs78786003	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:52198619C>A	ENST00000371471.2	-	2	1172	c.747G>T	c.(745-747)gcG>gcT	p.A249A	ZNF217_ENST00000540425.1_5'Flank|ZNF217_ENST00000302342.3_Silent_p.A249A			O75362	ZN217_HUMAN	zinc finger protein 217	249					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)			AGTCTGTCTGCGCGCTGCTGG	0.488													C|||	50	0.00998403	0.0348	0.0058	5008	,	,		21092	0.0		0.0	False		,,,				2504	0.0				p.A249A		Atlas-SNP	.											.	ZNF217	227	.	0			c.G747T						PASS	.	C		187,4219	118.4+/-156.1	1,185,2017	101	98	99		747	-8	0	20	dbSNP_131	99	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ZNF217	NM_006526.2		1,187,6315	AA,AC,CC		0.0233,4.2442,1.4532		249/1049	52198619	189,12817	2203	4300	6503	SO:0001819	synonymous_variant	7764	exon1			TGTCTGCGCGCTG	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.747G>T	20.37:g.52198619C>A		118	0	0		111	52	0.468468	NM_006526	E1P5Y6|Q14DB8	Silent	SNP	ENST00000371471.2	37	CCDS13443.1																																																																																			C|0.985;A|0.015	0.015	strong		0.488	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		A	52198619	C	A	52198619	2	1	22	1	0	0	0	0	0	0	0	1	17787	755	27	4		4	ZNF217	20	52198619	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6311	52198619	10826901	4224	7125											
BCAS1	8537	hgsc.bcm.edu	37	chr20	52611552	52611552	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacacttccaactacctaccGtgtcttctgggtcctttttt	6	16	5	14	1	2	0	0	0	2	0	4	0	4	0	4	1	3	0	4	1	3	7	rs60878965	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:52611552G>A	ENST00000395961.3	-	6	1092	c.926C>T	c.(925-927)aCg>aTg	p.T309M	BCAS1_ENST00000434986.2_Splice_Site_p.T22M|BCAS1_ENST00000371440.3_Splice_Site_p.T309M|BCAS1_ENST00000371435.2_Splice_Site_p.T309M	NM_003657.2	NP_003648.2	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1	309						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)			ACTACCTACCGTGTCTTCTGG	0.343													G|||	449	0.0896565	0.3245	0.0274	5008	,	,		16173	0.0		0.001	False		,,,				2504	0.0				p.T309M		Atlas-SNP	.											.	BCAS1	77	.	0			c.C926T						PASS	.	G	MET/THR	1210,3196	421.1+/-339.2	174,862,1167	185	200	195		926	2.5	1	20	dbSNP_129	195	11,8589	8.4+/-32.0	0,11,4289	yes	missense-near-splice	BCAS1	NM_003657.2	81	174,873,5456	AA,AG,GG		0.1279,27.4626,9.388	possibly-damaging	309/585	52611552	1221,11785	2203	4300	6503	SO:0001630	splice_region_variant	8537	exon6			CCTACCGTGTCTT	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.927+1C>T	20.37:g.52611552G>A		55	0	0		63	24	0.380952	NM_003657	A0AVG5|Q68CZ3	Missense_Mutation	SNP	ENST00000395961.3	37	CCDS13444.1	163|163	0.07463369963369963|0.07463369963369963	155|155	0.3150406504065041|0.3150406504065041	8|8	0.022099447513812154|0.022099447513812154	0|0	0.0|0.0	0|0	0.0|0.0	G|G	16.69|16.69	3.194122|3.194122	0.58017|0.58017	0.274626|0.274626	0.001279|0.001279	ENSG00000064787|ENSG00000064787	ENST00000422805|ENST00000448484;ENST00000371440;ENST00000448710;ENST00000395961;ENST00000371435;ENST00000434986	.|T;T;T;T;T	.|0.08458	.|3.09;3.09;3.09;3.09;3.09	5.84|5.84	2.46|2.46	0.29980|0.29980	.|.	.|0.270974	.|0.35525	.|N	.|0.003141	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.61703|0.61703	1.905|1.905	0.09310|0.09310	P|P	0.9999999999996939|0.9999999999996939	.|D;P;D;P;D;D	.|0.89917	.|1.0;0.777;1.0;0.944;0.993;0.993	.|D;B;D;B;P;P	.|0.65773	.|0.938;0.1;0.938;0.332;0.596;0.596	T|T	0.40365|0.40365	-0.9567|-0.9567	4|9	.|0.54805	.|T	.|0.06	-4.1201|-4.1201	11.7384|11.7384	0.51778|0.51778	0.0:0.0:0.3884:0.6116|0.0:0.0:0.3884:0.6116	rs60878965;rs61731748|rs60878965;rs61731748	.|309;22;309;309;309;309	.|B2RCQ5;B4DFL4;O75363-2;G3XAF7;A0AVG7;O75363	.|.;.;.;.;.;BCAS1_HUMAN	W|M	28|171;309;187;309;309;22	.|ENSP00000396361:T171M;ENSP00000360495:T309M;ENSP00000379290:T309M;ENSP00000360490:T309M;ENSP00000409956:T22M	.|ENSP00000360490:T309M	R|T	-|-	1|2	2|0	BCAS1|BCAS1	52044959|52044959	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.929000|0.929000	0.56500|0.56500	1.044000|1.044000	0.30329|0.30329	0.727000|0.727000	0.32360|0.32360	0.655000|0.655000	0.94253|0.94253	CGG|ACG	G|0.916;A|0.084	0.084	strong		0.343	BCAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079766.2	NM_003657	Missense_Mutation	A	52611552	G	A	52611552	5	1	22	1	0	0	0	0	0	0	1	0	1350	1159	40	1	856	1	BCAS1	20	52611552	Splice_Site	SNP	G	TCGA-G8-6324-01A-11D-2210-10	412933	52611552	10413968	4225	7126											
CASS4	57091	hgsc.bcm.edu	37	chr20	55027509	55027509	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cgactcctccagctcttcctCggaggagtcagcaaaggagc	9	7	11	14	2	2	0	1	0	1	0	6	4	5	3	3	3	3	2	3	3	1	1	rs34899200	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:55027509C>T	ENST00000360314.3	+	6	1502	c.1277C>T	c.(1276-1278)tCg>tTg	p.S426L	CASS4_ENST00000371336.3_Missense_Mutation_p.S426L|CASS4_ENST00000434344.1_Intron	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	426	Ser-rich.				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						AGCTCTTCCTCGGAGGAGTCA	0.572													C|||	94	0.01877	0.0681	0.0043	5008	,	,		20870	0.0		0.001	False		,,,				2504	0.0				p.S426L		Atlas-SNP	.											CASS4,rectum,adenoma,-1,1	CASS4	121	1	0			c.C1277T						PASS	.	C	LEU/SER,,LEU/SER,LEU/SER	242,4164	137.7+/-173.5	9,224,1970	44	40	41		1115,,1277,1277	2.7	0	20	dbSNP_126	41	5,8593	4.3+/-15.6	0,5,4294	yes	missense,intron,missense,missense	CASS4	NM_001164114.1,NM_001164115.1,NM_001164116.1,NM_020356.3	145,,145,145	9,229,6264	TT,TC,CC		0.0582,5.4925,1.8994	possibly-damaging,,possibly-damaging,possibly-damaging	372/733,,426/787,426/787	55027509	247,12757	2203	4299	6502	SO:0001583	missense	57091	exon5			CTTCCTCGGAGGA	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.1277C>T	20.37:g.55027509C>T	ENSP00000353462:p.Ser426Leu	82	0	0		87	45	0.517241	NM_020356	E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Missense_Mutation	SNP	ENST00000360314.3	37	CCDS33492.1	31	0.014194139194139194	30	0.06097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	C	15.20	2.762107	0.49468	0.054925	5.82E-4	ENSG00000087589	ENST00000360314;ENST00000371336	T;T	0.16597	2.33;2.33	5.6	2.65	0.31530	.	0.315398	0.35708	N	0.003026	T	0.01940	0.0061	M	0.76002	2.32	0.09310	N	1	B;B;B	0.31640	0.225;0.333;0.225	B;B;B	0.25506	0.028;0.061;0.028	T	0.04537	-1.0944	10	0.42905	T	0.14	-1.5677	11.146	0.48430	0.0:0.8005:0.0:0.1995	rs34899200	372;426;426	B4DII4;Q9NQ75-2;Q9NQ75	.;.;CASS4_HUMAN	L	426	ENSP00000353462:S426L;ENSP00000360387:S426L	ENSP00000353462:S426L	S	+	2	0	CASS4	54460916	0.617000	0.27043	0.002000	0.10522	0.864000	0.49448	2.043000	0.41231	0.416000	0.25844	-0.157000	0.13467	TCG	C|0.984;T|0.016	0.016	strong		0.572	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079789.2	NM_020356		T	55027509	C	T	55027509	3	4	22	1	0	0	0	0	1	0	0	0	2685	893	31	1	1295	1	CASS4	20	55027509	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2415957	55027509	7998011	4226	7127											
ZNF831	128611	hgsc.bcm.edu	37	chr20	57766397	57766397	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccacccaggtggggaagcCggcggcccctacgctgacgg	6	3	15	17	4	0	1	0	1	0	0	0	2	0	2	6	6	2	1	6	6	2	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:57766397C>T	ENST00000371030.2	+	1	323	c.323C>T	c.(322-324)cCg>cTg	p.P108L		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	108	Pro-rich.						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)					GTGGGGAAGCCGGCGGCCCCT	0.701																																					p.P108L		Atlas-SNP	.											.	ZNF831	287	.	0			c.C323T						PASS	.						9	12	11					20																	57766397		2020	4160	6180	SO:0001583	missense	128611	exon1			GGAAGCCGGCGGC	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.323C>T	20.37:g.57766397C>T	ENSP00000360069:p.Pro108Leu	35	0	0		47	25	0.531915	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	37	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	C	12.91	2.079440	0.36662	.	.	ENSG00000124203	ENST00000371030	T	0.05649	3.41	5.2	3.14	0.36123	.	.	.	.	.	T	0.03739	0.0106	N	0.19112	0.55	0.09310	N	1	P	0.42908	0.793	B	0.31547	0.132	T	0.39722	-0.9600	9	0.66056	D	0.02	-0.6362	7.8433	0.29410	0.2296:0.6849:0.0:0.0855	.	108	Q5JPB2	ZN831_HUMAN	L	108	ENSP00000360069:P108L	ENSP00000360069:P108L	P	+	2	0	ZNF831	57199792	0.703000	0.27826	0.694000	0.30210	0.923000	0.55619	1.411000	0.34702	1.194000	0.43101	0.561000	0.74099	CCG	.	.	none		0.701	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		T	57766397	C	T	57766397	3	4	22	1	0	0	0	0	1	0	0	0	18200	652	23	1	325	1	ZNF831	20	57766397	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2738888	57766397	5259123	4227	7128											
SYCP2	10388	hgsc.bcm.edu	37	chr20	58441612	58441612	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgagctgttttccaagactgCgtagtaaaataactcaacat	14	12	7	8	1	1	2	1	1	0	1	2	2	2	2	1	0	4	4	1	0	6	5	rs58905758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:58441612C>T	ENST00000357552.3	-	40	4383	c.4158G>A	c.(4156-4158)acG>acA	p.T1386T	SYCP2_ENST00000371001.2_Silent_p.T1386T			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	1386					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)			TCCAAGACTGCGTAGTAAAAT	0.318													C|||	87	0.0173722	0.0635	0.0029	5008	,	,		15377	0.0		0.001	False		,,,				2504	0.0				p.T1386T		Atlas-SNP	.											.	SYCP2	204	.	0			c.G4158A						PASS	.	C		199,4207	122.5+/-159.9	4,191,2008	85	87	86		4158	-2.6	0.1	20	dbSNP_129	86	2,8594	2.2+/-6.3	0,2,4296	no	coding-synonymous	SYCP2	NM_014258.2		4,193,6304	TT,TC,CC		0.0233,4.5166,1.5459		1386/1531	58441612	201,12801	2203	4298	6501	SO:0001819	synonymous_variant	10388	exon39			AGACTGCGTAGTA	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.4158G>A	20.37:g.58441612C>T		63	0	0		47	29	0.617021	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Silent	SNP	ENST00000357552.3	37	CCDS13482.1																																																																																			C|0.983;T|0.017	0.017	strong		0.318	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258		T	58441612	C	T	58441612	2	4	22	1	0	0	0	0	0	0	0	1	15447	755	27	1		1	SYCP2	20	58441612	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	675215	58441612	4583908	4228	7129											
SYCP2	10388	hgsc.bcm.edu	37	chr20	58496438	58496438	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcacatcttcacaaatatcaAtttgcaaaagtgttttcaaa	16	14	3	8	0	5	0	4	0	1	0	5	0	5	0	0	0	1	2	0	0	6	5	rs61730337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:58496438A>G	ENST00000357552.3	-	4	320	c.95T>C	c.(94-96)aTt>aCt	p.I32T	SYCP2_ENST00000476314.1_5'UTR|SYCP2_ENST00000371001.2_Missense_Mutation_p.I32T			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	32					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)			ACAAATATCAATTTGCAAAAG	0.308													A|||	98	0.0195687	0.0711	0.0043	5008	,	,		15338	0.0		0.001	False		,,,				2504	0.0				p.I32T		Atlas-SNP	.											.	SYCP2	204	.	0			c.T95C						PASS	.	A	THR/ILE	248,4154	140.0+/-175.5	7,234,1960	55	52	53		95	1.3	1	20	dbSNP_129	53	2,8578	2.2+/-6.3	0,2,4288	yes	missense	SYCP2	NM_014258.2	89	7,236,6248	GG,GA,AA		0.0233,5.6338,1.9257	possibly-damaging	32/1531	58496438	250,12732	2201	4290	6491	SO:0001583	missense	10388	exon3			ATATCAATTTGCA	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.95T>C	20.37:g.58496438A>G	ENSP00000350162:p.Ile32Thr	165	0	0		193	101	0.523316	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Missense_Mutation	SNP	ENST00000357552.3	37	CCDS13482.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	A	0.025	-1.384165	0.01194	0.056338	2.33E-4	ENSG00000196074	ENST00000371001;ENST00000357552;ENST00000446834;ENST00000425931	T;T;T;T	0.39997	2.62;2.62;2.37;1.05	5.04	1.3	0.21679	.	0.654897	0.15121	N	0.279380	T	0.01421	0.0046	N	0.22421	0.69	0.21553	N	0.999649	B	0.20052	0.041	B	0.14578	0.011	T	0.10706	-1.0618	10	0.12766	T	0.61	-9.6108	1.5416	0.02557	0.3441:0.1539:0.3533:0.1487	.	32	Q9BX26	SYCP2_HUMAN	T	32;32;32;31	ENSP00000360040:I32T;ENSP00000350162:I32T;ENSP00000402456:I32T;ENSP00000399300:I31T	ENSP00000350162:I32T	I	-	2	0	SYCP2	57929833	0.892000	0.30473	0.999000	0.59377	0.442000	0.32017	0.388000	0.20735	0.357000	0.24183	-0.538000	0.04264	ATT	A|0.979;G|0.021	0.021	strong		0.308	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258		G	58496438	A	G	58496438	3	3	22	1	0	0	0	0	1	0	0	0	15447	101	4	3	4665	3	SYCP2	20	58496438	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	54826	58496438	4529082	4229	7130											
ADRM1	11047	hgsc.bcm.edu	37	chr20	60883770	60883778	+	In_Frame_Del	DEL	GACACGAAG	GACACGAAG	-																															agcccgagcagaaagagggcGacacgaaggacaagaaggac																								rs374034164		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GACACGAAG	GACACGAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:60883770_60883778delGACACGAAG	ENST00000253003.2	+	10	1223_1231	c.1177_1185delGACACGAAG	c.(1177-1185)gacacgaagdel	p.DTK393del	LAMA5_ENST00000492698.1_Intron|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	393	Interaction with UCHL5.				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)			GAAAGAGGGCGACACGAAGGACAAGAAGG	0.574																																					p.392_395del		Pindel,Atlas-Indel	.											.	ADRM1	28	.	0			c.1176_1184del						PASS	.		,	23,2,4215		0,0,23,0,2,2095					,	-0.2	0.8			134	185,0,8059		3,0,179,0,0,3940	no	codingComplex,codingComplex	ADRM1	NM_175573.1,NM_007002.2	,	3,0,202,0,2,6035	A1A1,A1A2,A1R,A2A2,A2R,RR		2.2441,0.5896,1.6822	,	,		208,2,12274				SO:0001651	inframe_deletion	11047	exon10			.	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.1177_1185delGACACGAAG	20.37:g.60883770_60883778delGACACGAAG	ENSP00000253003:p.Asp393_Lys395del	250	0	.		243	56	0.23	NM_007002	A0PKB1|Q96FJ7|Q9H1P2	In_Frame_Del	DEL	ENST00000253003.2	37	CCDS13496.1																																																																																			GACACGAAG|0.012;-|0.988	0.988	strong		0.574	ADRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080007.1			-	60883778	GACACGAAG	-	60883770	7	5	22	1	0	1	0	1	0	0	0	0	345	1058	37	0	1211	0	ADRM1	20	60883770	In_Frame_Del	DEL	GACACGAAG	TCGA-G8-6324-01A-11D-2210-10	2387332	60883770	2141750	4230	7131											
LAMA5	3911	hgsc.bcm.edu	37	chr20	60884473	60884473	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgacgggggaccggttcacCgccagcctcctcatgcagcc	6	5	13	17	4	2	0	2	0	0	0	3	2	3	1	6	3	3	2	6	3	0	1	rs115306720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:60884473C>T	ENST00000252999.3	-	80	11073	c.11007G>A	c.(11005-11007)gcG>gcA	p.A3669A	LAMA5_ENST00000492698.1_5'Flank	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	3669	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)			ACCGGTTCACCGCCAGCCTCC	0.706													C|||	143	0.0285543	0.1044	0.0058	5008	,	,		7633	0.0		0.001	False		,,,				2504	0.0				p.A3669A		Atlas-SNP	.											.	LAMA5	268	.	0			c.G11007A						PASS	.			311,3885		5,301,1792	7	9	9		11007	1.9	0	20	dbSNP_132	9	2,8320		0,2,4159	no	coding-synonymous	LAMA5	NM_005560.3		5,303,5951	TT,TC,CC		0.024,7.4118,2.5004		3669/3696	60884473	313,12205	2098	4161	6259	SO:0001819	synonymous_variant	3911	exon80			GTTCACCGCCAGC	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.11007G>A	20.37:g.60884473C>T		28	0	0		32	21	0.65625	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			C|0.976;T|0.024	0.024	strong		0.706	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		T	60884473	C	T	60884473	2	4	22	1	0	0	0	0	0	0	0	1	8618	639	23	1		1	LAMA5	20	60884473	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	703	60884473	2141047	4231	7132											
C20orf151	140893	hgsc.bcm.edu	37	chr20	60989243	60989243	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcagagtctgagccgactggTagggagggcagcatctcccc	8	7	14	12	1	3	2	1	1	2	1	4	4	3	3	3	3	2	3	3	3	1	1	rs34446012	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:60989243T>C	ENST00000252998.1	-	10	1320	c.1164A>G	c.(1162-1164)ctA>ctG	p.L388L		NM_080833.2	NP_543023.2	Q8NC74	RB8NL_HUMAN	RBBP8 N-terminal like	388						extracellular space (GO:0005615)											AGCCGACTGGTAGGGAGGGCA	0.701													T|||	25	0.00499201	0.0174	0.0029	5008	,	,		12717	0.0		0.0	False		,,,				2504	0.0				p.L388L		Atlas-SNP	.											.	.	.	.	0			c.A1164G						PASS	.	T		45,4287		0,45,2121	13	14	13		1164	-10.1	0	20	dbSNP_126	13	0,8462		0,0,4231	no	coding-synonymous	C20orf151	NM_080833.2		0,45,6352	CC,CT,TT		0.0,1.0388,0.3517		388/665	60989243	45,12749	2166	4231	6397	SO:0001819	synonymous_variant	140893	exon10			GACTGGTAGGGAG	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.1164A>G	20.37:g.60989243T>C		61	0	0		65	33	0.507692	NM_080833	B2RP98|Q8N4Z9|Q9BR75|Q9H0Y9	Silent	SNP	ENST00000252998.1	37	CCDS13498.1																																																																																			T|0.996;C|0.004	0.004	strong		0.701	RBBP8NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080029.1	NM_080833		C	60989243	T	C	60989243	2	2	22	1	0	0	0	0	0	0	0	1	2093	1625	57	3		3	C20orf151	20	60989243	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	104770	60989243	2036277	4232	7133											
SLCO4A1	28231	hgsc.bcm.edu	37	chr20	61292475	61292475	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accagttgaaggacagcagcCgtggggaggcgagcaacccg	11	3	16	11	3	0	1	0	1	0	0	0	4	0	3	3	4	4	3	3	4	2	1	rs201057493		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61292475C>T	ENST00000370507.1	+	4	1165	c.1069C>T	c.(1069-1071)Cgt>Tgt	p.R357C	RP11-93B14.5_ENST00000433126.1_RNA|SLCO4A1_ENST00000217159.1_Missense_Mutation_p.R357C|RP11-93B14.5_ENST00000411824.1_RNA|RP11-93B14.5_ENST00000451648.1_RNA			Q96BD0	SO4A1_HUMAN	solute carrier organic anion transporter family, member 4A1	357					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)	GGACAGCAGCCGTGGGGAGGC	0.622													c|||	1	0.000199681	0.0	0.0	5008	,	,		11244	0.0		0.001	False		,,,				2504	0.0				p.R357C	Pancreas(168;741 2006 10379 40139 45334)	Atlas-SNP	.											SLCO4A1,uveal_tract,malignant_melanoma,0,1	SLCO4A1	65	1	0			c.C1069T						PASS	.		CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	89	80	83		1069	3.2	0	20		83	0,8600		0,0,4300	no	missense	SLCO4A1	NM_016354.3	180	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	357/723	61292475	1,13005	2203	4300	6503	SO:0001583	missense	28231	exon5			AGCAGCCGTGGGG	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.1069C>T	20.37:g.61292475C>T	ENSP00000359538:p.Arg357Cys	40	0	0		62	25	0.403226	NM_016354	Q9H4T7|Q9H4T8|Q9H8P2|Q9NWX8|Q9UI35|Q9UIG7	Missense_Mutation	SNP	ENST00000370507.1	37	CCDS13501.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	c	6.688	0.495496	0.12762	2.27E-4	0.0	ENSG00000101187	ENST00000217159;ENST00000370512;ENST00000370507	T;T	0.41400	1.0;1.0	4.25	3.22	0.36961	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	6.950440	0.00447	N	0.000090	T	0.42810	0.1219	L	0.54323	1.7	0.19300	N	0.999972	B	0.15473	0.013	B	0.15484	0.013	T	0.30707	-0.9969	10	0.56958	D	0.05	.	7.3638	0.26762	0.0:0.7375:0.1713:0.0912	.	357	Q96BD0	SO4A1_HUMAN	C	357	ENSP00000217159:R357C;ENSP00000359538:R357C	ENSP00000217159:R357C	R	+	1	0	SLCO4A1	60762920	0.092000	0.21681	0.008000	0.14137	0.002000	0.02628	2.568000	0.45965	1.940000	0.56252	0.450000	0.29827	CGT	C|1.000;T|0.000	0.000	strong		0.622	SLCO4A1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080048.2	NM_016354		T	61292475	C	T	61292475	3	4	22	1	0	0	0	0	1	0	0	0	14744	652	23	1	1083	1	SLCO4A1	20	61292475	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	303232	61292475	1733045	4233	7134											
OGFR	11054	hgsc.bcm.edu	37	chr20	61443871	61443871	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaagcccagctctctgcccCatccgctcgagggctccagg	6	7	10	18	2	2	0	1	0	1	0	6	1	4	0	5	2	3	3	5	2	1	0	rs77478162	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61443871C>T	ENST00000290291.6	+	7	929	c.904C>T	c.(904-906)Cat>Tat	p.H302Y	OGFR_ENST00000370461.1_Missense_Mutation_p.H250Y	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	302					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)					CTCTCTGCCCCATCCGCTCGA	0.682													C|||	91	0.0181709	0.0666	0.0043	5008	,	,		13687	0.0		0.0	False		,,,				2504	0.0				p.H302Y		Atlas-SNP	.											.	OGFR	63	.	0			c.C904T						PASS	.	C	TYR/HIS	186,4136		0,186,1975	8	8	8		904	-1.5	0	20	dbSNP_131	8	2,8478		0,2,4238	yes	missense	OGFR	NM_007346.2	83	0,188,6213	TT,TC,CC		0.0236,4.3036,1.4685	benign	302/678	61443871	188,12614	2161	4240	6401	SO:0001583	missense	11054	exon7			CTGCCCCATCCGC	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.904C>T	20.37:g.61443871C>T	ENSP00000290291:p.His302Tyr	60	0	0		65	32	0.492308	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Missense_Mutation	SNP	ENST00000290291.6	37	CCDS13504.1	31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	C	8.778	0.927439	0.18056	0.043036	2.36E-4	ENSG00000060491	ENST00000290291;ENST00000370468;ENST00000357163;ENST00000370469;ENST00000370461	T;T;T	0.43688	1.94;0.94;1.52	3.86	-1.55	0.08558	.	4.120900	0.01321	N	0.010938	T	0.02848	0.0085	N	0.22421	0.69	0.09310	N	1	B;B;B	0.24651	0.035;0.006;0.108	B;B;B	0.23018	0.031;0.001;0.043	T	0.06752	-1.0809	10	0.37606	T	0.19	0.1436	0.781	0.01041	0.2558:0.3046:0.1089:0.3306	.	302;285;302	B3KMQ6;Q05BV5;Q9NZT2	.;.;OGFR_HUMAN	Y	302;302;302;157;250	ENSP00000290291:H302Y;ENSP00000359499:H302Y;ENSP00000359491:H250Y	ENSP00000290291:H302Y	H	+	1	0	OGFR	60914316	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.754000	0.04787	-0.100000	0.12241	-0.254000	0.11334	CAT	C|0.984;T|0.016	0.016	strong		0.682	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1			T	61443871	C	T	61443871	3	4	22	1	0	0	0	0	1	0	0	0	10852	594	21	2	930	2	OGFR	20	61443871	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	151396	61443871	1581649	4234	7135											
OGFR	11054	hgsc.bcm.edu	37	chr20	61444900	61444900	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcggagaccccaggccccAgcccggcaggacctacaagg	10	2	12	17	2	0	1	0	0	0	1	1	3	0	2	6	5	2	1	6	5	2	1	rs61735508	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61444900A>C	ENST00000290291.6	+	7	1958	c.1933A>C	c.(1933-1935)Agc>Cgc	p.S645R	OGFR_ENST00000370461.1_Missense_Mutation_p.S593R	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	645	7 X 20 AA approximate tandem repeats of [ST]-P-S-E-T-P-G-P-[SR]-P-A-G-P-[AT]- [GR]-D-E-P-A-[EK].				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)					CCCAGGCCCCAGCCCGGCAGG	0.692													a|||	178	0.0355431	0.1233	0.0086	5008	,	,		13505	0.0		0.004	False		,,,				2504	0.0051				p.S645R		Atlas-SNP	.											.	OGFR	63	.	0			c.A1933C						PASS	.	A	ARG/SER	255,4123		7,241,1941	24	29	28		1933	-0.6	0	20	dbSNP_129	28	10,8570		0,10,4280	no	missense	OGFR	NM_007346.2	110	7,251,6221	CC,CA,AA		0.1166,5.8246,2.0451	possibly-damaging	645/678	61444900	265,12693	2189	4290	6479	SO:0001583	missense	11054	exon7			GGCCCCAGCCCGG	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.1933A>C	20.37:g.61444900A>C	ENSP00000290291:p.Ser645Arg	64	0	0		64	37	0.578125	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Missense_Mutation	SNP	ENST00000290291.6	37	CCDS13504.1	60	0.027472527472527472	53	0.10772357723577236	4	0.011049723756906077	1	0.0017482517482517483	2	0.002638522427440633	A	6.697	0.497303	0.12762	0.058246	0.001166	ENSG00000060491	ENST00000290291;ENST00000357163;ENST00000370469;ENST00000370461	T;T	0.13089	2.62;2.62	0.584	-0.628	0.11537	.	.	.	.	.	T	0.00109	0.0003	N	0.03608	-0.345	0.09310	N	1	P;P;P	0.52842	0.956;0.956;0.956	P;P;P	0.45829	0.494;0.494;0.494	T	0.18493	-1.0335	9	0.22109	T	0.4	.	1.7819	0.03033	0.4838:0.0:0.2359:0.2802	rs61735508	645;628;645	B3KMQ6;Q05BV5;Q9NZT2	.;.;OGFR_HUMAN	R	645;625;480;593	ENSP00000290291:S645R;ENSP00000359491:S593R	ENSP00000290291:S645R	S	+	1	0	OGFR	60915345	0.004000	0.15560	0.002000	0.10522	0.050000	0.14768	-0.440000	0.06888	-0.224000	0.09928	0.076000	0.15429	AGC	A|0.975;C|0.025	0.025	strong		0.692	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1			C	61444900	A	C	61444900	3	2	22	1	0	0	0	0	1	0	0	0	10852	188	7	5	1959	5	OGFR	20	61444900	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1029	61444900	1580620	4235	7136											
DIDO1	11083	hgsc.bcm.edu	37	chr20	61525488	61525488	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttaagtcttctttcttaacAgaagctgacaatttttgttt	10	20	5	6	0	3	2	0	1	3	1	3	2	3	2	0	0	2	2	0	0	4	8	rs112062101	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61525488A>G	ENST00000266070.4	-	12	2956	c.2631T>C	c.(2629-2631)tcT>tcC	p.S877S	DIDO1_ENST00000395340.1_Silent_p.S877S|DIDO1_ENST00000395335.2_Silent_p.S877S|DIDO1_ENST00000395343.1_Silent_p.S877S	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	877					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)					CTTTCTTAACAGAAGCTGACA	0.517													A|||	38	0.00758786	0.0265	0.0043	5008	,	,		19309	0.0		0.0	False		,,,				2504	0.0				p.S877S	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											DIDO1,NS,carcinoma,-1,1	DIDO1	321	1	0			c.T2631C						PASS	.	A	,,,	111,4295	80.9+/-119.3	0,111,2092	102	117	112		2631,2631,2631,2631	-5	0	20	dbSNP_132	112	1,8593		0,1,4296	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DIDO1	NM_001193369.1,NM_001193370.1,NM_033081.2,NM_080797.3	,,,	0,112,6388	GG,GA,AA		0.0116,2.5193,0.8615	,,,	877/2241,877/1190,877/2241,877/1190	61525488	112,12888	2203	4297	6500	SO:0001819	synonymous_variant	11083	exon12			CTTAACAGAAGCT	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.2631T>C	20.37:g.61525488A>G		82	0	0		79	39	0.493671	NM_080797	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Silent	SNP	ENST00000266070.4	37	CCDS33506.1																																																																																			A|0.994;G|0.006	0.006	strong		0.517	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		G	61525488	A	G	61525488	2	3	22	1	0	0	0	0	0	0	0	1	4524	175	7	3		3	DIDO1	20	61525488	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	80588	61525488	1500032	4236	7137											
YTHDF1	54915	hgsc.bcm.edu	37	chr20	61834169	61834169	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctctttcgggttgtagctgtGagcagccttcagtttttcaa	6	16	10	9	1	3	1	2	1	1	0	4	1	3	1	1	1	3	5	1	1	2	6	rs34379989	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61834169G>A	ENST00000370339.3	-	4	1464	c.1123C>T	c.(1123-1125)Cac>Tac	p.H375Y	YTHDF1_ENST00000370334.4_Intron|YTHDF1_ENST00000370333.4_Missense_Mutation_p.H325Y	NM_017798.3	NP_060268.2	Q9BYJ9	YTHD1_HUMAN	YTH domain family, member 1	375							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						TTGTAGCTGTGAGCAGCCTTC	0.537													G|||	66	0.0131789	0.0477	0.0043	5008	,	,		18939	0.0		0.0	False		,,,				2504	0.0				p.H375Y		Atlas-SNP	.											.	YTHDF1	66	.	0			c.C1123T						PASS	.	G	TYR/HIS	145,4261	98.9+/-137.6	2,141,2060	87	89	88		1123	4.7	1	20	dbSNP_126	88	0,8600		0,0,4300	yes	missense	YTHDF1	NM_017798.3	83	2,141,6360	AA,AG,GG		0.0,3.291,1.1149	possibly-damaging	375/560	61834169	145,12861	2203	4300	6503	SO:0001583	missense	54915	exon4			AGCTGTGAGCAGC	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.1123C>T	20.37:g.61834169G>A	ENSP00000359364:p.His375Tyr	140	0	0		148	66	0.445946	NM_017798	Q8N3G5|Q8TBT1|Q96AN4|Q96S57|Q9BTI7|Q9NX79	Missense_Mutation	SNP	ENST00000370339.3	37	CCDS13511.1	21	0.009615384615384616	20	0.04065040650406504	1	0.0027624309392265192	0	0.0	0	0.0	G	14.56	2.572951	0.45798	0.03291	0.0	ENSG00000149658	ENST00000370339;ENST00000370333;ENST00000342761	T;T	0.23147	1.92;1.92	4.72	4.72	0.59763	.	0.000000	0.85682	D	0.000000	T	0.09512	0.0234	M	0.63428	1.95	0.58432	D	0.999999	P	0.39696	0.683	B	0.40565	0.333	T	0.06499	-1.0823	10	0.87932	D	0	-43.1736	18.0486	0.89341	0.0:0.0:1.0:0.0	rs34379989	375	Q9BYJ9	YTHD1_HUMAN	Y	375;325;191	ENSP00000359364:H375Y;ENSP00000359358:H325Y	ENSP00000339489:H191Y	H	-	1	0	YTHDF1	61304614	1.000000	0.71417	1.000000	0.80357	0.712000	0.41017	7.661000	0.83786	2.339000	0.79563	0.591000	0.81541	CAC	G|0.991;A|0.009	0.009	strong		0.537	YTHDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080110.2	NM_017798		A	61834169	G	A	61834169	3	1	22	1	0	0	0	0	1	0	0	0	17513	1290	45	2	564	2	YTHDF1	20	61834169	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	308681	61834169	1191351	4237	7138											
COL20A1	57642	hgsc.bcm.edu	37	chr20	61959758	61959758	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttggagcagaagctggagcCgggcactgagcccctggggt	7	6	17	11	1	0	2	0	1	0	1	0	4	0	4	3	5	4	3	3	5	1	1	rs115749294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61959758C>T	ENST00000358894.6	+	34	3789	c.3689C>T	c.(3688-3690)cCg>cTg	p.P1230L	COL20A1_ENST00000422202.1_Missense_Mutation_p.P1243L|COL20A1_ENST00000435874.1_Missense_Mutation_p.P1243L|COL20A1_ENST00000326996.6_Missense_Mutation_p.P1262L	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	1230				P -> Q (in Ref. 2; AAH43183). {ECO:0000305}.	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)					AAGCTGGAGCCGGGCACTGAG	0.662													C|||	37	0.00738818	0.028	0.0	5008	,	,		15679	0.0		0.0	False		,,,				2504	0.0				p.P1230L		Atlas-SNP	.											.	COL20A1	137	.	0			c.C3689T						PASS	.	C	LEU/PRO	92,3808		1,90,1859	26	31	29		3689	1.2	0	20	dbSNP_132	29	4,8234		0,4,4115	yes	missense	COL20A1	NM_020882.2	98	1,94,5974	TT,TC,CC		0.0486,2.359,0.7909	benign	1230/1285	61959758	96,12042	1950	4119	6069	SO:0001583	missense	57642	exon34			TGGAGCCGGGCAC	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.3689C>T	20.37:g.61959758C>T	ENSP00000351767:p.Pro1230Leu	88	0	0		131	75	0.572519	NM_020882	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Missense_Mutation	SNP	ENST00000358894.6	37	CCDS46628.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	C	4.851	0.158169	0.09236	0.02359	4.86E-4	ENSG00000101203	ENST00000358894;ENST00000326996;ENST00000435874;ENST00000422202;ENST00000415763;ENST00000455906	D;D;D;D;D;D	0.90900	-2.22;-2.18;-2.14;-2.14;-2.75;-2.59	3.37	1.25	0.21368	.	0.343274	0.25598	N	0.029561	T	0.56848	0.2013	N	0.12746	0.255	0.09310	N	1	B;B	0.12013	0.003;0.005	B;B	0.08055	0.001;0.003	T	0.58983	-0.7539	10	0.35671	T	0.21	.	5.6298	0.17504	0.0:0.6946:0.0:0.3054	.	1243;1230	Q9P218-2;Q9P218	.;COKA1_HUMAN	L	1230;1262;1243;1243;371;226	ENSP00000351767:P1230L;ENSP00000323077:P1262L;ENSP00000408690:P1243L;ENSP00000414753:P1243L;ENSP00000410799:P371L;ENSP00000406345:P226L	ENSP00000323077:P1262L	P	+	2	0	COL20A1	61430202	0.006000	0.16342	0.001000	0.08648	0.097000	0.18754	0.478000	0.22212	0.356000	0.24157	0.313000	0.20887	CCG	C|0.995;T|0.005	0.005	strong		0.662	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882		T	61959758	C	T	61959758	3	4	22	1	0	0	0	0	1	0	0	0	3681	652	23	1	3761	1	COL20A1	20	61959758	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	125589	61959758	1065762	4238	7139											
COL20A1	57642	hgsc.bcm.edu	37	chr20	61960961	61960961	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctggagctgttggtcagaTgggcagccctgggcagcagg	6	7	18	10	0	1	1	1	0	0	1	1	2	1	2	2	5	3	5	2	5	0	1	rs6011740	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61960961T>C	ENST00000358894.6	+	35	3906	c.3806T>C	c.(3805-3807)aTg>aCg	p.M1269T	COL20A1_ENST00000422202.1_Missense_Mutation_p.M1282T|COL20A1_ENST00000496810.1_3'UTR|COL20A1_ENST00000435874.1_Missense_Mutation_p.M1282T|COL20A1_ENST00000326996.6_Missense_Mutation_p.M1301T	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	1269					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)					GTTGGTCAGATGGGCAGCCCT	0.652													C|||	244	0.048722	0.1611	0.0072	5008	,	,		18080	0.0		0.0	False		,,,				2504	0.0266				p.M1269T		Atlas-SNP	.											.	COL20A1	137	.	0			c.T3806C						PASS	.	C	THR/MET	497,3519		37,423,1548	28	33	32		3806	-4.9	0	20	dbSNP_114	32	5,8331		0,5,4163	yes	missense	COL20A1	NM_020882.2	81	37,428,5711	CC,CT,TT		0.06,12.3755,4.0641	benign	1269/1285	61960961	502,11850	2008	4168	6176	SO:0001583	missense	57642	exon35			GTCAGATGGGCAG	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.3806T>C	20.37:g.61960961T>C	ENSP00000351767:p.Met1269Thr	39	0	0		31	14	0.451613	NM_020882	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Missense_Mutation	SNP	ENST00000358894.6	37	CCDS46628.1	72	0.03296703296703297	70	0.14227642276422764	2	0.0055248618784530384	0	0.0	0	0.0	C	0.007	-1.963878	0.00461	0.123755	6.0E-4	ENSG00000101203	ENST00000358894;ENST00000326996;ENST00000435874;ENST00000422202	D;D;D;D	0.85955	-2.02;-2.05;-2.02;-2.02	3.15	-4.86	0.03132	.	3.567220	0.01372	N	0.012620	T	0.00695	0.0023	N	0.01874	-0.695	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27502	-1.0072	9	0.19147	T	0.46	.	1.7705	0.03010	0.1455:0.2136:0.1439:0.497	rs6011740;rs6011740	1282;1269	Q9P218-2;Q9P218	.;COKA1_HUMAN	T	1269;1301;1282;1282	ENSP00000351767:M1269T;ENSP00000323077:M1301T;ENSP00000408690:M1282T;ENSP00000414753:M1282T	ENSP00000323077:M1301T	M	+	2	0	COL20A1	61431405	0.000000	0.05858	0.000000	0.03702	0.124000	0.20399	-3.643000	0.00405	-1.192000	0.02691	-0.642000	0.03964	ATG	T|0.949;C|0.051	0.051	strong		0.652	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882		C	61960961	T	C	61960961	3	2	22	1	0	0	0	0	1	0	0	0	3681	1464	51	3	3882	3	COL20A1	20	61960961	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1203	61960961	1064559	4239	7140											
KCNQ2	3785	hgsc.bcm.edu	37	chr20	62078184	62078184	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	acgaggcaggagaaaaccagGaggaacctgggggcagggaa	15	1	18	7	1	0	1	0	0	0	1	0	6	0	4	2	7	2	2	2	7	4	0	rs145415996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:62078184G>C	ENST00000359125.2	-	2	477	c.303C>G	c.(301-303)ctC>ctG	p.L101L	KCNQ2_ENST00000344425.5_Silent_p.L101L|KCNQ2_ENST00000354587.3_Silent_p.L101L|KCNQ2_ENST00000344462.4_Silent_p.L101L|KCNQ2_ENST00000370224.1_Silent_p.L101L|KCNQ2_ENST00000359689.1_Silent_p.L101L|KCNQ2_ENST00000360480.3_Silent_p.L101L|KCNQ2_ENST00000357249.2_Silent_p.L101L|RP11-358D14.2_ENST00000436263.1_RNA	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	101					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)	AGAAAACCAGGAGGAACCTGG	0.632													G|||	7	0.00139776	0.0053	0.0	5008	,	,		11541	0.0		0.0	False		,,,				2504	0.0				p.L101L		Atlas-SNP	.											.	KCNQ2	201	.	0			c.C303G						PASS	.	G	,,,,	22,4384	29.0+/-57.7	0,22,2181	80	75	77		303,303,303,303,303	0.6	1	20	dbSNP_134	77	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KCNQ2	NM_004518.4,NM_172106.1,NM_172107.2,NM_172108.3,NM_172109.1	,,,,	0,24,6479	CC,CG,GG		0.0233,0.4993,0.1845	,,,,	101/845,101/855,101/873,101/842,101/394	62078184	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	3785	exon2			AACCAGGAGGAAC	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.303C>G	20.37:g.62078184G>C		114	0	0		91	39	0.428571	NM_172106	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Silent	SNP	ENST00000359125.2	37	CCDS13520.1																																																																																			G|0.998;C|0.002	0.002	strong		0.632	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109		C	62078184	G	C	62078184	2	2	22	1	0	0	0	0	0	0	0	1	8092	1161	41	4		4	KCNQ2	20	62078184	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	117223	62078184	947336	4240	7141											
OPRL1	4987	hgsc.bcm.edu	37	chr20	62729843	62729843	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actcggctggtgctggtggtAgtggctgtgttcgtgggctg	2	13	19	7	2	0	0	0	0	0	0	2	0	0	0	0	6	1	6	0	6	1	2	rs34874539	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:62729843A>G	ENST00000349451.3	+	6	1216	c.804A>G	c.(802-804)gtA>gtG	p.V268V	OPRL1_ENST00000336866.2_Silent_p.V268V|OPRL1_ENST00000355631.4_Silent_p.V268V	NM_001200019.1	NP_001186948.1	P41146	OPRX_HUMAN	opiate receptor-like 1	268					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)					TGCTGGTGGTAGTGGCTGTGT	0.672													G|||	99	0.0197684	0.0719	0.0058	5008	,	,		16073	0.0		0.0	False		,,,				2504	0.0				p.V268V		Atlas-SNP	.											.	OPRL1	47	.	0			c.A804G						PASS	.		,,	263,4139	793.7+/-415.2	9,245,1947	70	63	65		804,804,804	1	1	20	dbSNP_126	65	1,8593		0,1,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	OPRL1	NM_000913.4,NM_001200019.1,NM_182647.2	,,	9,246,6243	GG,GA,AA		0.0116,5.9746,2.0314	,,	268/371,268/371,268/371	62729843	264,12732	2201	4297	6498	SO:0001819	synonymous_variant	4987	exon4			GGTGGTAGTGGCT		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.804A>G	20.37:g.62729843A>G		190	0	0		224	114	0.508929	NM_000913	Q8TD34|Q8WYH9|Q9H4K4	Silent	SNP	ENST00000349451.3	37	CCDS13556.1																																																																																			A|0.979;G|0.021	0.021	strong		0.672	OPRL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080295.1	NM_182647		G	62729843	A	G	62729843	2	3	22	1	0	0	0	0	0	0	0	1	10895	407	15	3		3	OPRL1	20	62729843	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	651659	62729843	295677	4241	7142											
RBM11	54033	hgsc.bcm.edu	37	chr21	15591968	15591968	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttgtctgctttaaacacccaGaatcggtgtcttatgccata	10	14	7	10	1	2	1	0	0	2	1	3	1	2	1	2	1	3	1	2	1	5	5	rs141942958	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:15591968G>A	ENST00000400577.3	+	2	190	c.181G>A	c.(181-183)Gaa>Aaa	p.E61K	RBM11_ENST00000468643.1_3'UTR	NM_144770.3	NP_658983.3	P57052	RBM11_HUMAN	RNA binding motif protein 11	61	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				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)		TAAACACCCAGAATCGGTGTC	0.398													.|||	17	0.00339457	0.0106	0.0043	5008	,	,		16689	0.0		0.0	False		,,,				2504	0.0				p.E61K		Atlas-SNP	.											RBM11,NS,neuroblastoma,-1,1	RBM11	41	1	0			c.G181A						PASS	.	G	LYS/GLU	44,3092		0,44,1524	86	80	82		181	5.3	1	21	dbSNP_134	82	0,7162		0,0,3581	yes	missense	RBM11	NM_144770.3	56	0,44,5105	AA,AG,GG		0.0,1.4031,0.4273	possibly-damaging	61/282	15591968	44,10254	1568	3581	5149	SO:0001583	missense	54033	exon2			CACCCAGAATCGG	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.181G>A	21.37:g.15591968G>A	ENSP00000383421:p.Glu61Lys	143	0	0		146	88	0.60274	NM_144770	Q6YNC2|Q8NBA1|Q8NFF6	Missense_Mutation	SNP	ENST00000400577.3	37	CCDS46635.1	10	0.004578754578754579	8	0.016260162601626018	2	0.0055248618784530384	0	0.0	0	0.0	G	29.4	5.004735	0.93287	0.014031	0.0	ENSG00000185272	ENST00000400577	T	0.78364	-1.17	5.29	5.29	0.74685	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.64402	D	0.000009	T	0.72220	0.3433	M	0.66378	2.025	0.58432	D	0.999994	P	0.41420	0.749	P	0.48189	0.57	T	0.78703	-0.2101	10	0.48119	T	0.1	-20.9416	18.9174	0.92512	0.0:0.0:1.0:0.0	.	61	P57052	RBM11_HUMAN	K	61	ENSP00000383421:E61K	ENSP00000383421:E61K	E	+	1	0	RBM11	14513839	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.772000	0.85439	2.661000	0.90470	0.655000	0.94253	GAA	G|0.995;A|0.005	0.005	strong		0.398	RBM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157818.1	NM_144770		A	15591968	G	A	15591968	3	1	22	1	0	0	0	0	1	0	0	0	13127	943	33	2	187	2	RBM11	21	15591968	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10		15591968	32537927	4242	7143											
RBM11	54033	hgsc.bcm.edu	37	chr21	15599354	15599354	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggactcaccaacaaccaagtGactctgacctttatcagatg	13	9	7	12	0	3	3	2	2	1	1	3	4	3	4	3	1	2	0	3	1	4	2	rs139439630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:15599354G>A	ENST00000400577.3	+	5	595	c.586G>A	c.(586-588)Gac>Aac	p.D196N	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													.|||	17	0.00339457	0.0008	0.0072	5008	,	,		21404	0.0		0.0099	False		,,,				2504	0.001				p.D196N		Atlas-SNP	.											.	RBM11	41	.	0			c.G586A						PASS	.	G	ASN/ASP	9,3953		0,9,1972	326	307	313		586	1.9	0.1	21	dbSNP_134	313	140,8188		2,136,4026	yes	missense	RBM11	NM_144770.3	23	2,145,5998	AA,AG,GG		1.6811,0.2272,1.2124	probably-damaging	196/282	15599354	149,12141	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>A	21.37:g.15599354G>A	ENSP00000383421:p.Asp196Asn	342	0	0		361	160	0.443213	NM_144770	Q6YNC2|Q8NBA1|Q8NFF6	Missense_Mutation	SNP	ENST00000400577.3	37	CCDS46635.1	13	0.005952380952380952	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	9	0.011873350923482849	G	9.181	1.023488	0.19433	0.002272	0.016811	ENSG00000185272	ENST00000400577	T	0.08720	3.06	1.87	1.87	0.25490	.	0.067005	0.64402	D	0.000010	T	0.03827	0.0108	N	0.08118	0	0.22926	N	0.998552	D	0.57571	0.98	P	0.61658	0.892	T	0.38308	-0.9667	10	0.17832	T	0.49	.	11.1988	0.48728	0.0:0.0:1.0:0.0	.	196	P57052	RBM11_HUMAN	N	196	ENSP00000383421:D196N	ENSP00000383421:D196N	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	0.012	strong		0.468	RBM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157818.1	NM_144770		A	15599354	G	A	15599354	3	1	22	1	0	0	0	0	1	0	0	0	13127	1290	45	2	604	2	RBM11	21	15599354	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	7386	15599354	32530541	4243	7144											
NRIP1	8204	hgsc.bcm.edu	37	chr21	16337448	16337448	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	agcccagattctggtctagaCcctgcacagcccaagtgctc	9	8	9	15	0	2	2	0	0	2	2	3	2	2	2	3	1	4	2	3	1	2	2	rs28707654	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:16337448C>A	ENST00000400202.1	-	3	3778	c.3066G>T	c.(3064-3066)ggG>ggT	p.G1022G	AF127577.10_ENST00000446301.1_RNA|NRIP1_ENST00000318948.4_Silent_p.G1022G|NRIP1_ENST00000400199.1_Silent_p.G1022G			P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	1022	Interaction with ZNF366.				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)		CTGGTCTAGACCCTGCACAGC	0.478													C|||	112	0.0223642	0.0787	0.0115	5008	,	,		19106	0.0		0.0	False		,,,				2504	0.0				p.G1022G		Atlas-SNP	.											.	NRIP1	103	.	0			c.G3066T						PASS	.	C		332,4072	171.6+/-201.8	15,302,1885	51	49	50		3066	-4.7	0	21	dbSNP_125	50	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	NRIP1	NM_003489.3		15,303,6183	AA,AC,CC		0.0116,7.5386,2.5611		1022/1159	16337448	333,12669	2202	4299	6501	SO:0001819	synonymous_variant	8204	exon4			TCTAGACCCTGCA	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.3066G>T	21.37:g.16337448C>A		48	0	0		78	43	0.551282	NM_003489	Q8IWE8	Silent	SNP	ENST00000400202.1	37	CCDS13568.1																																																																																			C|0.978;A|0.022	0.022	strong		0.478	NRIP1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157926.1	NM_003489		A	16337448	C	A	16337448	2	1	22	1	0	0	0	0	0	0	0	1	10661	494	18	4		4	NRIP1	21	16337448	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	738094	16337448	31792447	4244	7145											
NRIP1	8204	hgsc.bcm.edu	37	chr21	16337538	16337538	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcctgttatccatgcaactGctgggctgagtggaactgta	8	12	12	9	0	0	1	0	1	0	0	2	2	2	2	2	2	4	5	2	2	4	2	rs28587162	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:16337538G>A	ENST00000400202.1	-	3	3688	c.2976C>T	c.(2974-2976)agC>agT	p.S992S	AF127577.10_ENST00000446301.1_RNA|NRIP1_ENST00000318948.4_Silent_p.S992S|NRIP1_ENST00000400199.1_Silent_p.S992S			P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	992	Interaction with ZNF366.				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)		CCATGCAACTGCTGGGCTGAG	0.428													G|||	112	0.0223642	0.0787	0.0115	5008	,	,		21468	0.0		0.0	False		,,,				2504	0.0				p.S992S		Atlas-SNP	.											.	NRIP1	103	.	0			c.C2976T						PASS	.	G		334,4072	175.9+/-205.1	15,304,1884	70	62	65		2976	4	0	21	dbSNP_125	65	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	NRIP1	NM_003489.3		15,305,6182	AA,AG,GG		0.0116,7.5806,2.5761		992/1159	16337538	335,12669	2203	4299	6502	SO:0001819	synonymous_variant	8204	exon4			GCAACTGCTGGGC	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.2976C>T	21.37:g.16337538G>A		127	0	0		143	69	0.482517	NM_003489	Q8IWE8	Silent	SNP	ENST00000400202.1	37	CCDS13568.1																																																																																			G|0.979;A|0.021	0.021	strong		0.428	NRIP1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157926.1	NM_003489		A	16337538	G	A	16337538	2	1	22	1	0	0	0	0	0	0	0	1	10661	1310	46	2		2	NRIP1	21	16337538	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	90	16337538	31792357	4245	7146											
NRIP1	8204	hgsc.bcm.edu	37	chr21	16338814	16338814	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccagagagtgttgagagagaTtgatgggagaccctgctttg	10	10	15	6	0	0	5	0	2	0	4	0	9	0	5	2	1	1	2	2	1	0	3	rs9975169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:16338814T>C	ENST00000400202.1	-	3	2412	c.1700A>G	c.(1699-1701)aAt>aGt	p.N567S	AF127577.10_ENST00000446301.1_RNA|NRIP1_ENST00000318948.4_Missense_Mutation_p.N567S|NRIP1_ENST00000400199.1_Missense_Mutation_p.N567S			P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	567	Repression domain 2.		N -> S (in dbSNP:rs9975169).		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)		TTGAGAGAGATTGATGGGAGA	0.443													T|||	116	0.0231629	0.0809	0.013	5008	,	,		20094	0.0		0.0	False		,,,				2504	0.0				p.N567S		Atlas-SNP	.											.	NRIP1	103	.	0			c.A1700G						PASS	.	T	SER/ASN	356,4050	183.6+/-211.2	17,322,1864	240	238	238		1700	6	1	21	dbSNP_119	238	1,8599	1.2+/-3.3	0,1,4299	yes	missense	NRIP1	NM_003489.3	46	17,323,6163	CC,CT,TT		0.0116,8.0799,2.7449	probably-damaging	567/1159	16338814	357,12649	2203	4300	6503	SO:0001583	missense	8204	exon4			GAGAGATTGATGG	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.1700A>G	21.37:g.16338814T>C	ENSP00000383063:p.Asn567Ser	223	1	0.00448431		232	118	0.508621	NM_003489	Q8IWE8	Missense_Mutation	SNP	ENST00000400202.1	37	CCDS13568.1	39	0.017857142857142856	35	0.07113821138211382	4	0.011049723756906077	0	0.0	0	0.0	T	17.23	3.337615	0.60963	0.080799	1.16E-4	ENSG00000180530	ENST00000400199;ENST00000400202;ENST00000318948	T;T;T	0.20200	2.09;2.09;2.09	6.02	6.02	0.97574	.	0.204155	0.42172	D	0.000750	T	0.02455	0.0075	L	0.53249	1.67	0.45490	D	0.998455	D	0.59767	0.986	P	0.58520	0.84	T	0.00019	-1.2359	10	0.62326	D	0.03	-19.3161	16.5446	0.84426	0.0:0.0:0.0:1.0	rs9975169;rs52814028;rs9975169	567	P48552	NRIP1_HUMAN	S	567	ENSP00000383060:N567S;ENSP00000383063:N567S;ENSP00000327213:N567S	ENSP00000327213:N567S	N	-	2	0	NRIP1	15260685	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.714000	0.61902	2.311000	0.77944	0.533000	0.62120	AAT	T|0.973;C|0.027	0.027	strong		0.443	NRIP1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157926.1	NM_003489		C	16338814	T	C	16338814	3	2	22	1	0	0	0	0	1	0	0	0	10661	1493	52	3	1780	3	NRIP1	21	16338814	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1276	16338814	31791081	4246	7147											
TMPRSS15	5651	hgsc.bcm.edu	37	chr21	19704422	19704422	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaagccagattagggtagcTgtttggaaagttcgtagaac	13	10	13	5	1	0	2	0	0	0	2	1	4	0	3	1	2	3	5	1	2	6	5	rs8134187	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:19704422T>A	ENST00000284885.3	-	14	1666	c.1633A>T	c.(1633-1635)Agc>Tgc	p.S545C		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	545	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.		S -> C (in dbSNP:rs8134187).			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						TTAGGGTAGCTGTTTGGAAAG	0.428													T|||	277	0.0553115	0.202	0.0115	5008	,	,		17236	0.0		0.002	False		,,,				2504	0.0				p.S545C		Atlas-SNP	.											.	TMPRSS15	189	.	0			c.A1633T						PASS	.	T	CYS/SER	707,3699	295.9+/-283.9	60,587,1556	148	149	149		1633	1.7	0.7	21	dbSNP_116	149	2,8598	2.2+/-6.3	0,2,4298	yes	missense	TMPRSS15	NM_002772.2	112	60,589,5854	AA,AT,TT		0.0233,16.0463,5.4513	probably-damaging	545/1020	19704422	709,12297	2203	4300	6503	SO:0001583	missense	5651	exon14			GGTAGCTGTTTGG		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.1633A>T	21.37:g.19704422T>A	ENSP00000284885:p.Ser545Cys	65	0	0		79	37	0.468354	NM_002772	Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	37	CCDS13571.1	80	0.03663003663003663	73	0.1483739837398374	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	T	17.24	3.338863	0.60963	0.160463	2.33E-4	ENSG00000154646	ENST00000284885	T	0.19669	2.13	5.43	1.7	0.24286	CUB (5);	0.918548	0.09459	N	0.799265	T	0.00210	0.0006	M	0.86502	2.82	0.47094	P	6.829999999999892E-4	D	0.63046	0.992	P	0.57101	0.813	T	0.04373	-1.0956	8	.	.	.	.	8.8856	0.35400	0.0:0.2218:0.0:0.7782	rs8134187;rs52812192;rs8134187	545	P98073	ENTK_HUMAN	C	545	ENSP00000284885:S545C	.	S	-	1	0	TMPRSS15	18626293	0.208000	0.23494	0.691000	0.30163	0.977000	0.68977	0.449000	0.21744	0.107000	0.17824	-0.263000	0.10527	AGC	T|0.954;A|0.046	0.046	strong		0.428	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772		A	19704422	T	A	19704422	3	1	22	1	0	0	0	0	1	0	0	0	16261	1580	55	5	1474	5	TMPRSS15	21	19704422	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	3365608	19704422	28425473	4247	7148											
NCAM2	4685	hgsc.bcm.edu	37	chr21	22790831	22790831	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatgactttggacgctataaTtgcacagccactaatcatat	14	12	6	9	1	1	1	1	1	0	0	1	2	1	2	1	1	2	2	1	1	5	6	rs986371	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:22790831T>C	ENST00000400546.1	+	11	1671	c.1422T>C	c.(1420-1422)aaT>aaC	p.N474N	NCAM2_ENST00000284894.7_Silent_p.N332N	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	474	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)		GACGCTATAATTGCACAGCCA	0.299													T|||	30	0.00599042	0.0204	0.0043	5008	,	,		16315	0.0		0.0	False		,,,				2504	0.0				p.N474N		Atlas-SNP	.											.	NCAM2	220	.	0			c.T1422C						PASS	.	T		102,3546		0,102,1722	110	109	109		1422	-3.3	1	21	dbSNP_86	109	0,8166		0,0,4083	no	coding-synonymous	NCAM2	NM_004540.3		0,102,5805	CC,CT,TT		0.0,2.7961,0.8634		474/838	22790831	102,11712	1824	4083	5907	SO:0001819	synonymous_variant	4685	exon11			CTATAATTGCACA		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.1422T>C	21.37:g.22790831T>C		237	0	0		290	139	0.47931	NM_004540	A8MQ06|B7Z841|Q7Z7F2	Silent	SNP	ENST00000400546.1	37	CCDS42910.1																																																																																			T|0.992;C|0.008	0.008	strong		0.299	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		C	22790831	T	C	22790831	2	2	22	1	0	0	0	0	0	0	0	1	10212	1490	52	3		3	NCAM2	21	22790831	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	3086409	22790831	25339064	4248	7149											
ATP5J	2551	hgsc.bcm.edu	37	chr21	27107251	27107251	+	5'UTR	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccgcccccacacgcctaccCgccatcgcaatgcattatgg	8	7	7	19	4	0	0	0	0	0	0	2	0	1	0	6	1	2	2	6	1	3	2	rs71649640	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:27107251C>G	ENST00000354828.3	+	0	371				ATP5J_ENST00000400093.3_Intron|ATP5J_ENST00000400090.3_Intron|ATP5J_ENST00000400094.1_5'Flank|ATP5J_ENST00000457143.2_Splice_Site_p.G6R|ATP5J_ENST00000284971.3_5'UTR|GABPA_ENST00000400075.3_5'Flank|ATP5J_ENST00000400099.1_Intron|ATP5J_ENST00000400087.3_Intron	NM_001197297.1	NP_001184226.1	Q06546	GABPA_HUMAN	GA binding protein transcription factor, alpha subunit 60kDa						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						CACGCCTACCCGCCATCGCAA	0.662													C|||	60	0.0119808	0.0446	0.0014	5008	,	,		16320	0.0		0.0	False		,,,				2504	0.0				p.G6R		Atlas-SNP	.											.	ATP5J	13	.	0			c.G16C						PASS	.	C	,,ARG/GLY,,	126,3852		2,122,1865	15	22	20		,,16,,	3.9	1	21	dbSNP_130	20	1,8301		0,1,4150	yes	intron,intron,missense-near-splice,utr-5,intron	ATP5J	NM_001003696.1,NM_001003697.1,NM_001003701.1,NM_001003703.1,NM_001685.4	,,125,,	2,123,6015	GG,GC,CC		0.012,3.1674,1.0342	,,,,	,,6/117,,	27107251	127,12153	1989	4151	6140	SO:0001623	5_prime_UTR_variant	522	exon1			CCTACCCGCCATC		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.-157C>G	21.37:g.27107251C>G		100	0	0		99	52	0.525253	NM_001003701	Q12939	Missense_Mutation	SNP	ENST00000354828.3	37	CCDS13575.1	20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	C	21.0	4.088791	0.76756	0.031674	1.2E-4	ENSG00000154723	ENST00000457143	.	.	.	4.83	3.92	0.45320	.	.	.	.	.	T	0.29817	0.0745	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46062	-0.9218	5	0.37606	T	0.19	.	11.0432	0.47844	0.0:0.8121:0.1879:0.0	.	.	.	.	R	6	.	ENSP00000389649:G6R	G	-	1	0	ATP5J	26029122	0.918000	0.31147	0.990000	0.47175	0.998000	0.95712	1.903000	0.39858	1.359000	0.45940	0.655000	0.94253	GGA	C|0.990;G|0.010	0.010	strong		0.662	GABPA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171365.1	NM_002040		G	27107251	C	G	27107251	1	3	22	0	1	0	0	0	0	0	0	0	1158	666	23	4		4	ATP5J	21	27107251	5'UTR	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4316420	27107251	21022644	4249	7150											
APP	351	hgsc.bcm.edu	37	chr21	27326977	27326977	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagactgattcatgcgctcAtaaatcacacggaggtgtgt	12	10	11	8	2	3	2	3	1	0	1	3	4	3	3	0	2	1	1	0	2	2	2	rs45537238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:27326977A>G	ENST00000346798.3	-	13	1647	c.1614T>C	c.(1612-1614)taT>taC	p.Y538Y	APP_ENST00000358918.3_Silent_p.Y538Y|APP_ENST00000448388.2_Silent_p.Y428Y|APP_ENST00000354192.3_Silent_p.Y407Y|APP_ENST00000359726.3_Silent_p.Y482Y|APP_ENST00000357903.3_Silent_p.Y519Y|APP_ENST00000440126.3_Silent_p.Y514Y|APP_ENST00000439274.2_Silent_p.Y482Y|APP_ENST00000348990.5_Silent_p.Y463Y	NM_000484.3	NP_000475.1	P05067	A4_HUMAN	amyloid beta (A4) precursor protein	538	Collagen-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)				TCATGCGCTCATAAATCACAC	0.458													G|||	124	0.0247604	0.0893	0.0072	5008	,	,		20225	0.0		0.001	False		,,,				2504	0.0				p.Y538Y		Atlas-SNP	.											.	APP	90	.	0			c.T1614C						PASS	.	G	,,,,,,,,,	332,4074	796.0+/-415.3	16,300,1887	104	81	89		1614,1542,1221,1446,1284,1614,1557,1389,1557,1389	-9.4	0.7	21	dbSNP_127	89	5,8595	818.8+/-406.8	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	APP	NM_000484.3,NM_001136016.3,NM_001136129.2,NM_001136130.2,NM_001136131.2,NM_001204301.1,NM_001204302.1,NM_001204303.1,NM_201413.2,NM_201414.2	,,,,,,,,,	16,305,6182	GG,GA,AA		0.0581,7.5352,2.5911	,,,,,,,,,	538/771,514/747,407/640,482/715,428/661,538/753,519/734,463/678,519/752,463/696	27326977	337,12669	2203	4300	6503	SO:0001819	synonymous_variant	351	exon13			GCGCTCATAAATC	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.1614T>C	21.37:g.27326977A>G		140	0	0		153	81	0.529412	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	Silent	SNP	ENST00000346798.3	37	CCDS13576.1	40	0.018315018315018316	36	0.07317073170731707	4	0.011049723756906077	0	0.0	0	0.0	G	8.620	0.891207	0.17613	0.075352	5.81E-4	ENSG00000142192	ENST00000448850	.	.	.	5.52	-9.36	0.00629	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-19.8727	19.7142	0.96108	0.2996:0.0:0.7004:0.0	rs45537238;rs60681122	.	.	.	R	441	.	.	X	-	1	0	APP	26248848	0.000000	0.05858	0.669000	0.29828	0.984000	0.73092	-1.770000	0.01791	-2.333000	0.00631	-1.115000	0.02055	TGA	A|0.977;G|0.023	0.023	strong		0.458	APP-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171340.1	NM_000484		G	27326977	A	G	27326977	2	3	22	1	0	0	0	0	0	0	0	1	815	224	8	3		3	APP	21	27326977	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	219726	27326977	20802918	4250	7151											
ADAMTS1	9510	hgsc.bcm.edu	37	chr21	28214238	28214238	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttctatgacggagcagctTctgctcggatcacacacagt	9	11	9	12	2	4	1	1	1	3	0	5	3	4	3	0	2	3	3	0	2	1	3	rs77718820	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:28214238T>C	ENST00000284984.3	-	3	1603	c.1149A>G	c.(1147-1149)agA>agG	p.R383R		NM_006988.3	NP_008919.3	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 1	383	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				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)		CGGAGCAGCTTCTGCTCGGAT	0.433													T|||	59	0.0117812	0.0439	0.0014	5008	,	,		17992	0.0		0.0	False		,,,				2504	0.0				p.R383R		Atlas-SNP	.											.	ADAMTS1	131	.	0			c.A1149G						PASS	.	T		150,4256	103.4+/-141.9	3,144,2056	119	102	108		1149	0.5	1	21	dbSNP_131	108	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ADAMTS1	NM_006988.3		3,145,6355	CC,CT,TT		0.0116,3.4044,1.161		383/968	28214238	151,12855	2203	4300	6503	SO:0001819	synonymous_variant	9510	exon3			GCAGCTTCTGCTC	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.1149A>G	21.37:g.28214238T>C		146	0	0		131	67	0.51145	NM_006988	D3DSD5|Q9NSJ8|Q9P2K0|Q9UH83|Q9UP80	Silent	SNP	ENST00000284984.3	37	CCDS33524.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	T	11.14	1.552302	0.27739	0.034044	1.16E-4	ENSG00000154734	ENST00000451462	.	.	.	5.55	0.507	0.16967	.	.	.	.	.	T	0.14743	0.0356	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.06862	-1.0803	4	.	.	.	.	6.0716	0.19893	0.0:0.3189:0.3426:0.3385	.	.	.	.	G	165	.	.	E	-	2	0	ADAMTS1	27136109	0.985000	0.35326	0.995000	0.50966	0.974000	0.67602	0.136000	0.15974	-0.047000	0.13423	0.533000	0.62120	GAA	T|0.990;C|0.010	0.010	strong		0.433	ADAMTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171650.2			C	28214238	T	C	28214238	2	2	22	1	0	0	0	0	0	0	0	1	255	1780	62	3		3	ADAMTS1	21	28214238	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	887261	28214238	19915657	4251	7152											
CCT8	10694	hgsc.bcm.edu	37	chr21	30433876	30433876	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgttgctccacctccgggtaCaagacgtttatcctgtatgt	7	14	9	11	2	0	1	0	0	0	1	3	1	3	1	4	1	2	5	4	1	4	5	rs8129954	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:30433876C>T	ENST00000286788.4	-	12	1431	c.1225G>A	c.(1225-1227)Gta>Ata	p.V409I	AF129075.5_ENST00000457162.2_RNA|CCT8_ENST00000540844.1_Missense_Mutation_p.V336I|CCT8_ENST00000542732.1_Missense_Mutation_p.V390I|CCT8_ENST00000470450.1_5'UTR	NM_006585.2	NP_006576.2	P50990	TCPQ_HUMAN	chaperonin containing TCP1, subunit 8 (theta)	409			V -> I (in dbSNP:rs8129954).		'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						CCTCCGGGTACAAGACGTTTA	0.363													C|||	115	0.0229633	0.0809	0.0043	5008	,	,		17710	0.003		0.002	False		,,,				2504	0.0				p.V409I		Atlas-SNP	.											.	CCT8	38	.	0			c.G1225A						PASS	.	C	ILE/VAL	346,4060	179.0+/-207.6	14,318,1871	87	83	84		1225	4.3	1	21	dbSNP_116	84	3,8597	2.2+/-6.3	0,3,4297	yes	missense	CCT8	NM_006585.2	29	14,321,6168	TT,TC,CC		0.0349,7.8529,2.6834	benign	409/549	30433876	349,12657	2203	4300	6503	SO:0001583	missense	10694	exon12			CGGGTACAAGACG	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.1225G>A	21.37:g.30433876C>T	ENSP00000286788:p.Val409Ile	67	0	0		76	35	0.460526	NM_006585	A6NN54|B4DEM7|B4DQH4|Q4VBP8	Missense_Mutation	SNP	ENST00000286788.4	37	CCDS33528.1	30	0.013736263736263736	28	0.056910569105691054	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	15.31	2.797070	0.50208	0.078529	3.49E-4	ENSG00000156261	ENST00000389159;ENST00000286788;ENST00000542732;ENST00000540844	D;D;D	0.82526	-1.62;-1.62;-1.62	5.19	4.3	0.51218	.	0.194901	0.43110	D	0.000602	T	0.28067	0.0692	M	0.64260	1.97	0.44454	D	0.997383	B;B;B;B;B	0.22746	0.074;0.057;0.071;0.058;0.01	B;B;B;B;B	0.35770	0.151;0.151;0.21;0.133;0.019	T	0.66638	-0.5873	10	0.51188	T	0.08	-15.0082	15.657	0.77144	0.1381:0.8619:0.0:0.0	rs8129954;rs8129954	336;390;409;408;409	B4DQH4;B4DEM7;Q53HU0;G5E9B2;P50990	.;.;.;.;TCPQ_HUMAN	I	408;409;390;336	ENSP00000286788:V409I;ENSP00000444984:V390I;ENSP00000442730:V336I	ENSP00000286788:V409I	V	-	1	0	CCT8	29355747	1.000000	0.71417	0.994000	0.49952	0.915000	0.54546	2.928000	0.48908	1.542000	0.49330	0.650000	0.86243	GTA	C|0.973;T|0.027	0.027	strong		0.363	CCT8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171822.1			T	30433876	C	T	30433876	3	4	22	1	0	0	0	0	1	0	0	0	2962	478	17	2	437	2	CCT8	21	30433876	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2219638	30433876	17696019	4252	7153											
KRTAP26-1	388818	hgsc.bcm.edu	37	chr21	31691993	31691993	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcctcagtggacgacagcCgctggacacatacctctgtg	8	7	12	14	3	2	0	1	0	1	0	2	3	2	2	3	3	2	1	3	3	1	1	rs77018583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31691993C>T	ENST00000360542.3	-	1	614	c.361G>A	c.(361-363)Ggc>Agc	p.G121S		NM_203405.1	NP_981950.1	Q6PEX3	KR261_HUMAN	keratin associated protein 26-1	121						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						GGACGACAGCCGCTGGACACA	0.547													C|||	50	0.00998403	0.0325	0.0029	5008	,	,		20333	0.004		0.0	False		,,,				2504	0.001				p.G121S		Atlas-SNP	.											KRTAP26-1,colon,carcinoma,+1,1	KRTAP26-1	58	1	0			c.G361A						PASS	.	C	SER/GLY	138,4268	98.9+/-137.6	0,138,2065	116	119	118		361	-5.4	0	21	dbSNP_131	118	0,8600		0,0,4300	yes	missense	KRTAP26-1	NM_203405.1	56	0,138,6365	TT,TC,CC		0.0,3.1321,1.061	benign	121/211	31691993	138,12868	2203	4300	6503	SO:0001583	missense	388818	exon1			GACAGCCGCTGGA	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.361G>A	21.37:g.31691993C>T	ENSP00000353742:p.Gly121Ser	106	0	0		150	77	0.513333	NM_203405	B0RZD3	Missense_Mutation	SNP	ENST00000360542.3	37	CCDS13588.1	20	0.009157509157509158	16	0.032520325203252036	2	0.0055248618784530384	2	0.0034965034965034965	0	0.0	C	0.014	-1.585008	0.00872	0.031321	0.0	ENSG00000197683	ENST00000360542	T	0.01902	4.57	5.21	-5.39	0.02664	.	1.102650	0.07134	N	0.846044	T	0.00356	0.0011	N	0.04132	-0.27	0.09310	N	1	B	0.14438	0.01	B	0.09377	0.004	T	0.48747	-0.9008	10	0.16896	T	0.51	0.1935	1.5488	0.02571	0.1297:0.3086:0.2657:0.2961	.	121	Q6PEX3	KR261_HUMAN	S	121	ENSP00000353742:G121S	ENSP00000353742:G121S	G	-	1	0	KRTAP26-1	30613864	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-1.339000	0.02652	-0.734000	0.04843	-0.290000	0.09829	GGC	C|0.989;T|0.011	0.011	strong		0.547	KRTAP26-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128218.1	NM_203405		T	31691993	C	T	31691993	3	4	22	1	0	0	0	0	1	0	0	0	8552	652	23	1	275	1	KRTAP26-1	21	31691993	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1258117	31691993	16437902	4253	7154											
KRTAP26-1	388818	hgsc.bcm.edu	37	chr21	31692173	31692173	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggcagctggttggttcacCgcaggtctcttggcagttgt	4	13	14	10	1	2	0	1	0	1	0	3	0	2	0	1	5	1	7	1	5	0	4	rs78165499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31692173C>T	ENST00000360542.3	-	1	434	c.181G>A	c.(181-183)Ggt>Agt	p.G61S		NM_203405.1	NP_981950.1	Q6PEX3	KR261_HUMAN	keratin associated protein 26-1	61						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						GTTGGTTCACCGCAGGTCTCT	0.572													C|||	49	0.00978435	0.0325	0.0029	5008	,	,		19017	0.003		0.0	False		,,,				2504	0.001				p.G61S		Atlas-SNP	.											.	KRTAP26-1	58	.	0			c.G181A						PASS	.	C	SER/GLY	143,4263	101.2+/-139.8	1,141,2061	115	113	113		181	-0.3	0	21	dbSNP_131	113	0,8600		0,0,4300	yes	missense	KRTAP26-1	NM_203405.1	56	1,141,6361	TT,TC,CC		0.0,3.2456,1.0995	benign	61/211	31692173	143,12863	2203	4300	6503	SO:0001583	missense	388818	exon1			GTTCACCGCAGGT	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.181G>A	21.37:g.31692173C>T	ENSP00000353742:p.Gly61Ser	231	0	0		196	114	0.581633	NM_203405	B0RZD3	Missense_Mutation	SNP	ENST00000360542.3	37	CCDS13588.1	21	0.009615384615384616	16	0.032520325203252036	2	0.0055248618784530384	3	0.005244755244755245	0	0.0	C	5.629	0.300713	0.10678	0.032456	0.0	ENSG00000197683	ENST00000360542	T	0.03242	4.0	5.01	-0.306	0.12780	.	1.404840	0.04481	N	0.377750	T	0.00936	0.0031	N	0.19112	0.55	0.09310	N	1	B	0.21753	0.06	B	0.22753	0.041	T	0.45469	-0.9259	10	0.42905	T	0.14	2.1832	3.3195	0.07045	0.1879:0.4114:0.0:0.4007	.	61	Q6PEX3	KR261_HUMAN	S	61	ENSP00000353742:G61S	ENSP00000353742:G61S	G	-	1	0	KRTAP26-1	30614044	0.000000	0.05858	0.000000	0.03702	0.960000	0.62799	-0.293000	0.08320	0.113000	0.18004	0.655000	0.94253	GGT	C|0.988;T|0.012	0.012	strong		0.572	KRTAP26-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128218.1	NM_203405		T	31692173	C	T	31692173	3	4	22	1	0	0	0	0	1	0	0	0	8552	652	23	1	455	1	KRTAP26-1	21	31692173	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	180	31692173	16437722	4254	7155											
KRTAP26-1	388818	hgsc.bcm.edu	37	chr21	31692346	31692346	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcccgagcagtagttggggCaagacatagtgaggttgtga	10	10	15	6	1	0	3	0	2	0	1	1	4	1	3	1	3	1	5	1	3	3	5	rs115381362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31692346C>T	ENST00000360542.3	-	1	261	c.8G>A	c.(7-9)tGc>tAc	p.C3Y		NM_203405.1	NP_981950.1	Q6PEX3	KR261_HUMAN	keratin associated protein 26-1	3						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						GTAGTTGGGGCAAGACATAGT	0.512													C|||	25	0.00499201	0.0182	0.0014	5008	,	,		17989	0.0		0.0	False		,,,				2504	0.0				p.C3Y		Atlas-SNP	.											.	KRTAP26-1	58	.	0			c.G8A						PASS	.	C	TYR/CYS	90,4308		0,90,2109	31	34	33		8	2.9	0.9	21	dbSNP_132	33	1,8591		0,1,4295	yes	missense	KRTAP26-1	NM_203405.1	194	0,91,6404	TT,TC,CC		0.0116,2.0464,0.7005	probably-damaging	3/211	31692346	91,12899	2199	4296	6495	SO:0001583	missense	388818	exon1			TTGGGGCAAGACA	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.8G>A	21.37:g.31692346C>T	ENSP00000353742:p.Cys3Tyr	111	0	0		141	65	0.460993	NM_203405	B0RZD3	Missense_Mutation	SNP	ENST00000360542.3	37	CCDS13588.1	15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	C	15.21	2.765058	0.49574	0.020464	1.16E-4	ENSG00000197683	ENST00000360542	T	0.16073	2.37	4.95	2.91	0.33838	.	1.072940	0.07352	U	0.882550	T	0.07863	0.0197	N	0.08118	0	0.22975	N	0.998487	D	0.65815	0.995	D	0.66497	0.944	T	0.44081	-0.9351	10	0.72032	D	0.01	-3.9981	10.796	0.46461	0.0:0.6254:0.3746:0.0	.	3	Q6PEX3	KR261_HUMAN	Y	3	ENSP00000353742:C3Y	ENSP00000353742:C3Y	C	-	2	0	KRTAP26-1	30614217	0.953000	0.32496	0.911000	0.35937	0.718000	0.41266	0.656000	0.24948	1.347000	0.45714	0.655000	0.94253	TGC	C|0.993;T|0.007	0.007	strong		0.512	KRTAP26-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128218.1	NM_203405		T	31692346	C	T	31692346	3	4	22	1	0	0	0	0	1	0	0	0	8552	710	25	2	628	2	KRTAP26-1	21	31692346	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	173	31692346	16437549	4255	7156											
KRTAP27-1	643812	hgsc.bcm.edu	37	chr21	31709935	31709935	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccatgtgtgatggcagagaGtggtggggcattgtggaagc	8	9	19	5	0	0	2	0	1	0	1	0	4	0	3	1	5	1	2	1	5	1	1	rs149814034	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31709935G>A	ENST00000382835.2	-	1	77	c.52C>T	c.(52-54)Ctc>Ttc	p.L18F		NM_001077711.1	NP_001071179.1	Q3LI81	KR271_HUMAN	keratin associated protein 27-1	18						intermediate filament (GO:0005882)				endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(1)	18						ATGGCAGAGAGTGGTGGGGCA	0.453													G|||	9	0.00179712	0.0061	0.0014	5008	,	,		19096	0.0		0.0	False		,,,				2504	0.0				p.L18F		Atlas-SNP	.											.	KRTAP27-1	53	.	0			c.C52T						PASS	.	G	PHE/LEU	23,4383	30.8+/-60.4	0,23,2180	103	98	100		52	4.3	1	21	dbSNP_134	100	0,8600		0,0,4300	yes	missense	KRTAP27-1	NM_001077711.1	22	0,23,6480	AA,AG,GG		0.0,0.522,0.1768	probably-damaging	18/208	31709935	23,12983	2203	4300	6503	SO:0001583	missense	643812	exon1			CAGAGAGTGGTGG	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.52C>T	21.37:g.31709935G>A	ENSP00000372286:p.Leu18Phe	192	0	0		211	94	0.445498	NM_001077711		Missense_Mutation	SNP	ENST00000382835.2	37	CCDS33532.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	G	14.33	2.502796	0.44558	0.00522	0.0	ENSG00000206107	ENST00000382835	T	0.03330	3.97	4.29	4.29	0.51040	.	0.619122	0.14168	U	0.336909	T	0.10594	0.0259	M	0.63428	1.95	0.36763	D	0.88338	D	0.89917	1.0	D	0.91635	0.999	T	0.00862	-1.1536	10	0.59425	D	0.04	-6.9941	12.5116	0.56009	0.0:0.0:1.0:0.0	.	18	Q3LI81	KR271_HUMAN	F	18	ENSP00000372286:L18F	ENSP00000372286:L18F	L	-	1	0	KRTAP27-1	30631806	0.995000	0.38212	0.952000	0.39060	0.168000	0.22595	3.701000	0.54793	2.665000	0.90641	0.579000	0.79373	CTC	G|0.997;A|0.003	0.003	strong		0.453	KRTAP27-1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132470.3	NM_001077711		A	31709935	G	A	31709935	3	1	22	1	0	0	0	0	1	0	0	0	8553	1029	36	2	575	2	KRTAP27-1	21	31709935	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	17589	31709935	16419960	4256	7157											
KRTAP13-2	337959	hgsc.bcm.edu	37	chr21	31744287	31744287	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagcaaggaggttctggggCggtagcaggaggtctggcag	9	6	20	6	1	2	1	0	0	2	1	2	3	2	3	0	8	2	5	0	8	2	2	rs113360916	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31744287C>T	ENST00000399889.2	-	1	270	c.245G>A	c.(244-246)cGc>cAc	p.R82H		NM_181621.3	NP_853652.1	Q52LG2	KR132_HUMAN	keratin associated protein 13-2	82	5 X 10 AA approximate repeats.					intermediate filament (GO:0005882)				endometrium(1)|kidney(1)|lung(14)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	21						GGTTCTGGGGCGGTAGCAGGA	0.607													C|||	41	0.0081869	0.0295	0.0029	5008	,	,		19842	0.0		0.0	False		,,,				2504	0.0				p.R82H		Atlas-SNP	.											.	KRTAP13-2	29	.	0			c.G245A						PASS	.	C	HIS/ARG	124,4282	92.0+/-130.7	0,124,2079	59	59	59		245	1.4	0.1	21	dbSNP_132	59	2,8598	2.2+/-6.3	0,2,4298	yes	missense	KRTAP13-2	NM_181621.3	29	0,126,6377	TT,TC,CC		0.0233,2.8143,0.9688	benign	82/176	31744287	126,12880	2203	4300	6503	SO:0001583	missense	337959	exon1			CTGGGGCGGTAGC	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.245G>A	21.37:g.31744287C>T	ENSP00000382777:p.Arg82His	178	0	0		182	86	0.472527	NM_181621		Missense_Mutation	SNP	ENST00000399889.2	37	CCDS13589.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	C	7.773	0.707941	0.15239	0.028143	2.33E-4	ENSG00000182816	ENST00000399889	T	0.03496	3.91	4.26	1.36	0.22044	.	0.161204	0.28871	N	0.013862	T	0.00906	0.0030	L	0.39326	1.205	0.09310	N	1	B	0.24258	0.1	B	0.22601	0.04	T	0.46978	-0.9152	10	0.18710	T	0.47	.	4.1563	0.10263	0.1829:0.6128:0.0:0.2043	.	82	Q52LG2	KR132_HUMAN	H	82	ENSP00000382777:R82H	ENSP00000382777:R82H	R	-	2	0	KRTAP13-2	30666158	0.000000	0.05858	0.054000	0.19295	0.994000	0.84299	-1.818000	0.01717	0.138000	0.18790	0.655000	0.94253	CGC	C|0.990;T|0.010	0.010	strong		0.607	KRTAP13-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128245.1			T	31744287	C	T	31744287	3	4	22	1	0	0	0	0	1	0	0	0	8532	768	27	1	286	1	KRTAP13-2	21	31744287	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	34352	31744287	16385608	4257	7158											
KRTAP13-2	337959	hgsc.bcm.edu	37	chr21	31744456	31744456	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctggggtaggaaaagccacGtgaggatgctgggtagcgca	10	6	18	7	2	0	1	0	1	0	0	0	3	0	3	1	5	3	5	1	5	4	2	rs16986753	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31744456G>A	ENST00000399889.2	-	1	101	c.76C>T	c.(76-78)Cgt>Tgt	p.R26C		NM_181621.3	NP_853652.1	Q52LG2	KR132_HUMAN	keratin associated protein 13-2	26			R -> C (in dbSNP:rs16986753).			intermediate filament (GO:0005882)				endometrium(1)|kidney(1)|lung(14)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	21						GAAAAGCCACGTGAGGATGCT	0.562													A|||	26	0.00519169	0.0189	0.0014	5008	,	,		19332	0.0		0.0	False		,,,				2504	0.0				p.R26C		Atlas-SNP	.											.	KRTAP13-2	29	.	0			c.C76T						PASS	.	A	CYS/ARG	99,4307	816.6+/-416.3	1,97,2105	134	119	124		76	2	0.1	21	dbSNP_123	124	1,8599	819.2+/-406.8	0,1,4299	no	missense	KRTAP13-2	NM_181621.3	180	1,98,6404	AA,AG,GG		0.0116,2.2469,0.7689	benign	26/176	31744456	100,12906	2203	4300	6503	SO:0001583	missense	337959	exon1			AGCCACGTGAGGA	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.76C>T	21.37:g.31744456G>A	ENSP00000382777:p.Arg26Cys	273	0	0		247	116	0.469636	NM_181621		Missense_Mutation	SNP	ENST00000399889.2	37	CCDS13589.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	A	0.003	-2.531073	0.00145	0.022469	1.16E-4	ENSG00000182816	ENST00000399889	T	0.02974	4.09	4.64	2.01	0.26516	.	0.321942	0.22259	N	0.062423	T	0.00241	0.0007	N	0.00337	-1.62	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.43877	-0.9364	10	0.02654	T	1	.	1.3696	0.02208	0.5367:0.1853:0.0995:0.1786	rs16986753;rs52808457;rs16986753	26	Q52LG2	KR132_HUMAN	C	26	ENSP00000382777:R26C	ENSP00000382777:R26C	R	-	1	0	KRTAP13-2	30666327	0.992000	0.36948	0.144000	0.22314	0.017000	0.09413	1.031000	0.30165	0.330000	0.23485	-1.228000	0.01579	CGT	G|0.989;A|0.011	0.011	strong		0.562	KRTAP13-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128245.1			A	31744456	G	A	31744456	3	1	22	1	0	0	0	0	1	0	0	0	8532	1145	40	1	455	1	KRTAP13-2	21	31744456	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	169	31744456	16385439	4258	7159											
KRTAP13-3	337960	hgsc.bcm.edu	37	chr21	31797919	31797919	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcagggagcagcagctattGgatccaaaaccccgagaccc	12	5	10	14	1	1	1	1	0	0	1	2	4	2	3	4	2	4	3	4	2	3	2	rs73356706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31797919G>A	ENST00000390690.2	-	1	367	c.312C>T	c.(310-312)tcC>tcT	p.S104S		NM_181622.1	NP_853653.1	Q3SY46	KR133_HUMAN	keratin associated protein 13-3	104						intermediate filament (GO:0005882)				endometrium(1)|large_intestine(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	14						AGCAGCTATTGGATCCAAAAC	0.532													-|||	210	0.0419329	0.1505	0.0144	5008	,	,		18568	0.0		0.001	False		,,,				2504	0.0				p.S104S		Atlas-SNP	.											.	KRTAP13-3	47	.	0			c.C312T						PASS	.	G		432,3908		23,386,1761	51	57	55		312	3.4	0.3	21	dbSNP_130	55	9,8569		0,9,4280	no	coding-synonymous	KRTAP13-3	NM_181622.1		23,395,6041	AA,AG,GG		0.1049,9.9539,3.4138		104/173	31797919	441,12477	2170	4289	6459	SO:0001819	synonymous_variant	337960	exon1			GCTATTGGATCCA	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.312C>T	21.37:g.31797919G>A		132	0	0		107	47	0.439252	NM_181622	Q3LI78	Silent	SNP	ENST00000390690.2	37	CCDS13591.1																																																																																			G|0.975;A|0.025	0.025	strong		0.532	KRTAP13-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128228.2			A	31797919	G	A	31797919	2	1	22	1	0	0	0	0	0	0	0	1	8533	1335	47	2		2	KRTAP13-3	21	31797919	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	53463	31797919	16331976	4259	7160											
KRTAP13-4	284827	hgsc.bcm.edu	37	chr21	31802621	31802621	+	Missense_Mutation	SNP	T	T	A																															acaactgctgctctagaaacTtctcctcccgctcctttggg																								rs73899382	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31802621T>A	ENST00000334068.2	+	1	50	c.28T>A	c.(28-30)Ttc>Atc	p.F10I		NM_181600.1	NP_853631.1	Q3LI77	KR134_HUMAN	keratin associated protein 13-4	10						intermediate filament (GO:0005882)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	15						CTCTAGAAACTTCTCCTCCCG	0.542													-|||	32	0.00638978	0.0234	0.0014	5008	,	,		18495	0.0		0.0	False		,,,				2504	0.0				p.F10I	NSCLC(196;2401 3038 18004 35753)	Atlas-SNP	.											.	KRTAP13-4	46	.	0			c.T28A						PASS	.	T	ILE/PHE	90,4316	74.7+/-112.8	1,88,2114	112	113	113		28	2.5	1	21	dbSNP_130	113	0,8600		0,0,4300	yes	missense	KRTAP13-4	NM_181600.1	21	1,88,6414	AA,AT,TT		0.0,2.0427,0.692	probably-damaging	10/161	31802621	90,12916	2203	4300	6503	SO:0001583	missense	284827	exon1			AGAAACTTCTCCT	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.28T>A	21.37:g.31802621T>A	ENSP00000334834:p.Phe10Ile	206	0	0		238	102	0.428571	NM_181600	A2RRL3	Missense_Mutation	SNP	ENST00000334068.2	37	CCDS13592.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	t	14.16	2.452391	0.43531	0.020427	0.0	ENSG00000186971	ENST00000334068	T	0.03496	3.91	4.95	2.47	0.30058	.	0.000000	0.46442	D	0.000291	T	0.06096	0.0158	M	0.87971	2.92	0.26406	N	0.976344	D	0.89917	1.0	D	0.91635	0.999	T	0.01345	-1.1379	10	0.66056	D	0.02	.	9.5117	0.39080	0.0:0.0:0.3442:0.6558	.	10	Q3LI77	KR134_HUMAN	I	10	ENSP00000334834:F10I	ENSP00000334834:F10I	F	+	1	0	KRTAP13-4	30724492	0.999000	0.42202	0.996000	0.52242	0.025000	0.11179	1.211000	0.32382	0.388000	0.25054	-0.321000	0.08615	TTC	T|0.992;A|0.008	0.008	strong		0.542	KRTAP13-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128222.1			A	31802621	T	A	31802621	3	1	22	1	0	0	0	0	1	0	0	0	8534	1609	56	5	30	5	KRTAP13-4	21	31802621	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	4702	31802621	16327274	4260	7161	89	2									
KRTAP13-4	284827	hgsc.bcm.edu	37	chr21	31802629	31802629	+	Silent	SNP	C	C	T																															tgctctagaaacttctcctcCcgctcctttgggggctacct																								rs73356729	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31802629C>T	ENST00000334068.2	+	1	58	c.36C>T	c.(34-36)tcC>tcT	p.S12S		NM_181600.1	NP_853631.1	Q3LI77	KR134_HUMAN	keratin associated protein 13-4	12						intermediate filament (GO:0005882)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	15						ACTTCTCCTCCCGCTCCTTTG	0.547													-|||	220	0.0439297	0.1581	0.0144	5008	,	,		18637	0.0		0.001	False		,,,				2504	0.0				p.S12S	NSCLC(196;2401 3038 18004 35753)	Atlas-SNP	.											.	KRTAP13-4	46	.	0			c.C36T						PASS	.	C		473,3933		25,423,1755	109	111	110		36	0.1	0.1	21	dbSNP_130	110	10,8590		0,10,4290	no	coding-synonymous	KRTAP13-4	NM_181600.1		25,433,6045	TT,TC,CC		0.1163,10.7354,3.7137		12/161	31802629	483,12523	2203	4300	6503	SO:0001819	synonymous_variant	284827	exon1			CTCCTCCCGCTCC	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.36C>T	21.37:g.31802629C>T		208	0	0		242	104	0.429752	NM_181600	A2RRL3	Silent	SNP	ENST00000334068.2	37	CCDS13592.1																																																																																			C|0.963;T|0.037	0.037	strong		0.547	KRTAP13-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128222.1			T	31802629	C	T	31802629	2	4	22	1	0	0	0	0	0	0	0	1	8534	610	22	2		2	KRTAP13-4	21	31802629	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	8	31802629	16327266	4261	7162	89	2									
KRTAP19-6	337973	hgsc.bcm.edu	37	chr21	31914013	31914013	+	Missense_Mutation	SNP	G	G	A																															atccatatccttcacggcatGatgggcggcagcagccatat																								rs115563631	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31914013G>A	ENST00000334046.5	-	1	170	c.140C>T	c.(139-141)tCa>tTa	p.S47L		NM_181612.2	NP_853643.1	Q3LI70	KR196_HUMAN	keratin associated protein 19-6	47						intermediate filament (GO:0005882)				breast(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	9						TTCACGGCATGATGGGCGGCA	0.507													g|||	55	0.0109824	0.0401	0.0029	5008	,	,		15048	0.0		0.0	False		,,,				2504	0.0				p.S47L		Atlas-SNP	.											.	KRTAP19-6	16	.	0			c.C140T						PASS	.	G	LEU/SER	161,4245	109.1+/-147.4	2,157,2044	110	120	117		140	2.1	0	21	dbSNP_132	117	3,8597	3.7+/-12.6	0,3,4297	yes	missense	KRTAP19-6	NM_181612.2	145	2,160,6341	AA,AG,GG		0.0349,3.6541,1.261	possibly-damaging	47/59	31914013	164,12842	2203	4300	6503	SO:0001583	missense	337973	exon1			CGGCATGATGGGC	AP001708	CCDS13598.1	21q22.1	2010-09-30			ENSG00000186925	ENSG00000186925		"Keratin associated proteins"	18941	protein-coding gene	gene with protein product						12359730	Standard	NM_181612		Approved	KAP19.6	uc002yok.1	Q3LI70	OTTHUMG00000057779	ENST00000334046.5:c.140C>T	21.37:g.31914013G>A	ENSP00000375107:p.Ser47Leu	94	0	0		94	42	0.446809	NM_181612	Q3LI71	Missense_Mutation	SNP	ENST00000334046.5	37	CCDS13598.1	17	0.007783882783882784	15	0.03048780487804878	2	0.0055248618784530384	0	0.0	0	0.0	g	7.582	0.668877	0.14776	0.036541	3.49E-4	ENSG00000186925	ENST00000334046;ENST00000437381	T	0.10005	2.92	3.96	2.1	0.27182	.	2.101130	0.03499	N	0.217738	T	0.02380	0.0073	.	.	.	0.09310	N	1	P	0.36616	0.561	B	0.36504	0.226	T	0.30179	-0.9987	9	0.87932	D	0	.	6.6627	0.23022	0.2276:0.0:0.7724:0.0	.	47	Q3LI70	KR196_HUMAN	L	47	ENSP00000375107:S47L	ENSP00000375107:S47L	S	-	2	0	KRTAP19-6	30835884	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.310000	0.08135	0.272000	0.22027	0.597000	0.82753	TCA	G|0.985;A|0.015	0.015	strong		0.507	KRTAP19-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128231.4			A	31914013	G	A	31914013	3	1	22	1	0	0	0	0	1	0	0	0	8542	1294	45	2	40	2	KRTAP19-6	21	31914013	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	111384	31914013	16215882	4262	7163	90	2									
KRTAP19-6	337973	hgsc.bcm.edu	37	chr21	31914019	31914019	+	Missense_Mutation	SNP	C	C	T																															atccttcacggcatgatgggCggcagcagccatatctatag																								rs77807247	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31914019C>T	ENST00000334046.5	-	1	164	c.134G>A	c.(133-135)cGc>cAc	p.R45H		NM_181612.2	NP_853643.1	Q3LI70	KR196_HUMAN	keratin associated protein 19-6	45						intermediate filament (GO:0005882)				breast(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	9						GCATGATGGGCGGCAGCAGCC	0.498													c|||	161	0.0321486	0.1135	0.0115	5008	,	,		14661	0.0		0.001	False		,,,				2504	0.002				p.R45H		Atlas-SNP	.											.	KRTAP19-6	16	.	0			c.G134A						PASS	.	C	HIS/ARG	371,4035	188.5+/-214.9	13,345,1845	110	120	116		134	-6.1	0	21	dbSNP_131	116	12,8588	9.8+/-36.6	0,12,4288	yes	missense	KRTAP19-6	NM_181612.2	29	13,357,6133	TT,TC,CC		0.1395,8.4203,2.9448	benign	45/59	31914019	383,12623	2203	4300	6503	SO:0001583	missense	337973	exon1			GATGGGCGGCAGC	AP001708	CCDS13598.1	21q22.1	2010-09-30			ENSG00000186925	ENSG00000186925		"Keratin associated proteins"	18941	protein-coding gene	gene with protein product						12359730	Standard	NM_181612		Approved	KAP19.6	uc002yok.1	Q3LI70	OTTHUMG00000057779	ENST00000334046.5:c.134G>A	21.37:g.31914019C>T	ENSP00000375107:p.Arg45His	94	0	0		97	43	0.443299	NM_181612	Q3LI71	Missense_Mutation	SNP	ENST00000334046.5	37	CCDS13598.1	64	0.029304029304029304	58	0.11788617886178862	6	0.016574585635359115	0	0.0	0	0.0	c	6.926	0.540492	0.13250	0.084203	0.001395	ENSG00000186925	ENST00000334046;ENST00000437381	T	0.11169	2.8	4.39	-6.09	0.02145	.	0.598882	0.13443	N	0.387478	T	0.00109	0.0003	.	.	.	0.09310	N	1	B	0.12013	0.005	B	0.04013	0.001	T	0.32587	-0.9901	9	0.87932	D	0	-1.818	7.3473	0.26670	0.1168:0.3112:0.0:0.5719	.	45	Q3LI70	KR196_HUMAN	H	45	ENSP00000375107:R45H	ENSP00000375107:R45H	R	-	2	0	KRTAP19-6	30835890	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.929000	0.03976	-1.347000	0.02208	-1.903000	0.00527	CGC	C|0.969;T|0.031	0.031	strong		0.498	KRTAP19-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128231.4			T	31914019	C	T	31914019	3	4	22	1	0	0	0	0	1	0	0	0	8542	768	27	1	46	1	KRTAP19-6	21	31914019	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6	31914019	16215876	4263	7164	90	2									
KRTAP6-2	337967	hgsc.bcm.edu	37	chr21	31971075	31971076	+	Frame_Shift_Ins	INS	-	-	A																															ggagccgtagccatgaccatINSagccacagcaggagctatag																								rs74773890|rs113467703|rs113674499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31971075_31971076insA	ENST00000334897.3	-	1	143_144	c.118_119insT	c.(118-120)tatfs	p.Y40fs	KRTAP22-1_ENST00000334680.2_5'Flank	NM_181604.1	NP_853635.1	Q3LI66	KRA62_HUMAN	keratin associated protein 6-2	40						intermediate filament (GO:0005882)				endometrium(2)|kidney(1)|large_intestine(4)|lung(4)	11						GCCATGACCATAGCCACAGCAG	0.564													A|A|AA|insertion	66	0.0131789	0.0484	0.0029	5008	,	,		15138	0.0		0.0	False		,,,				2504	0.0				p.Y40fs		Pindel,Atlas-Indel	.											.	KRTAP6-2	24	.	0			c.119_120insT						PASS	.			171,4093		4,163,1965						-6.6	0		dbSNP_132	106	1,8253		0,1,4126	no	frameshift	KRTAP6-2	NM_181604.1		4,164,6091	A1A1,A1R,RR		0.0121,4.0103,1.374				172,12346				SO:0001589	frameshift_variant	337967	exon1			.	AP001708	CCDS13600.1	21q22.1	2011-02-10			ENSG00000186930	ENSG00000186930		"Keratin associated proteins"	18932	protein-coding gene	gene with protein product						12359730	Standard	NM_181604		Approved	KAP6.2	uc011adc.2	Q3LI66	OTTHUMG00000057794	ENST00000334897.3:c.119dupT	21.37:g.31971076_31971076dupA	ENSP00000334560:p.Tyr40fs	206	0	.		200	60	0.3	NM_181604		Frame_Shift_Ins	INS	ENST00000334897.3	37	CCDS13600.1																																																																																			-|0.990;A|0.010	0.010	strong		0.564	KRTAP6-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128246.3			A	31971076	-	A	31971075	7	5	22	1	0	1	1	0	0	0	0	0	8579	1406	49	0	72	0	KRTAP6-2	21	31971075	Frame_Shift_Ins	INS	-	TCGA-G8-6324-01A-11D-2210-10	57056	31971075	16158820	4264	7165											
HUNK	30811	hgsc.bcm.edu	37	chr21	33371442	33371442	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctgcccccactgcagccccTagcccctgtgaaccttgcct	5	8	7	21	0	0	1	0	1	0	0	0	1	0	1	9	0	6	1	9	0	2	2	rs150499320	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:33371442T>C	ENST00000270112.2	+	11	2450	c.2090T>C	c.(2089-2091)cTa>cCa	p.L697P		NM_014586.1	NP_055401.1	P57058	HUNK_HUMAN	hormonally up-regulated Neu-associated kinase	697					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						CTGCAGCCCCTAGCCCCTGTG	0.582													T|||	5	0.000998403	0.0038	0.0	5008	,	,		17188	0.0		0.0	False		,,,				2504	0.0				p.L697P		Atlas-SNP	.											.	HUNK	74	.	0			c.T2090C						PASS	.	T	PRO/LEU	9,4397	14.3+/-33.2	0,9,2194	63	71	69		2090	-2.9	0	21	dbSNP_134	69	0,8600		0,0,4300	yes	missense	HUNK	NM_014586.1	98	0,9,6494	CC,CT,TT		0.0,0.2043,0.0692	benign	697/715	33371442	9,12997	2203	4300	6503	SO:0001583	missense	30811	exon11			AGCCCCTAGCCCC	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.2090T>C	21.37:g.33371442T>C	ENSP00000270112:p.Leu697Pro	123	0	0		128	55	0.429688	NM_014586		Missense_Mutation	SNP	ENST00000270112.2	37	CCDS13610.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	T	3.433	-0.115606	0.06881	0.002043	0.0	ENSG00000142149	ENST00000270112	T	0.70164	-0.46	4.42	-2.92	0.05615	.	1.836150	0.03075	N	0.157723	T	0.39306	0.1073	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.40553	-0.9557	10	0.51188	T	0.08	-1.0E-4	10.8545	0.46792	0.0:0.2362:0.0:0.7638	.	697	P57058	HUNK_HUMAN	P	697	ENSP00000270112:L697P	ENSP00000270112:L697P	L	+	2	0	HUNK	32293313	0.002000	0.14202	0.011000	0.14972	0.070000	0.16714	-0.019000	0.12546	-0.588000	0.05882	-0.462000	0.05337	CTA	T|0.999;C|0.001	0.001	strong		0.582	HUNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192782.1	NM_014586		C	33371442	T	C	33371442	3	2	22	1	0	0	0	0	1	0	0	0	7467	1522	53	3	2132	3	HUNK	21	33371442	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1400367	33371442	14758453	4265	7166											
C21orf63	59271	hgsc.bcm.edu	37	chr21	33867447	33867447	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagcccctgtttgccaggcGtgaaaaaatacctcactgtg	11	9	10	11	1	1	1	1	1	0	0	1	2	1	1	4	1	3	1	4	1	5	2	rs61744983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:33867447G>A	ENST00000300255.2	+	5	1218	c.745G>A	c.(745-747)Gtg>Atg	p.V249M	EVA1C_ENST00000401402.3_Intron|EVA1C_ENST00000485488.1_3'UTR|EVA1C_ENST00000382699.3_Missense_Mutation_p.V249M	NM_058187.3	NP_478067.2	P58658	EVA1C_HUMAN	eva-1 homolog C (C. elegans)	249	SUEL-type lectin 2. {ECO:0000255|PROSITE- ProRule:PRU00260}.					integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)										TTTGCCAGGCGTGAAAAAATA	0.507													G|||	16	0.00319489	0.0121	0.0	5008	,	,		18504	0.0		0.0	False		,,,				2504	0.0				p.V249M		Atlas-SNP	.											.	.	.	.	0			c.G745A						PASS	.	G	MET/VAL	36,4370	40.0+/-72.8	0,36,2167	133	106	115		745	5.6	1	21	dbSNP_129	115	0,8600		0,0,4300	yes	missense	C21orf63	NM_058187.3	21	0,36,6467	AA,AG,GG		0.0,0.8171,0.2768	possibly-damaging	249/442	33867447	36,12970	2203	4300	6503	SO:0001583	missense	59271	exon5			CCAGGCGTGAAAA	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.745G>A	21.37:g.33867447G>A	ENSP00000300255:p.Val249Met	145	0	0		159	88	0.553459	NM_058187	A6ND58|Q8IXZ0	Missense_Mutation	SNP	ENST00000300255.2	37	CCDS13614.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	24.5	4.540898	0.85917	0.008171	0.0	ENSG00000166979	ENST00000300255;ENST00000382699	T;T	0.19250	2.16;2.16	5.62	5.62	0.85841	D-galactoside/L-rhamnose binding SUEL lectin domain (2);	0.245509	0.41605	D	0.000854	T	0.41766	0.1173	M	0.75884	2.315	0.46564	D	0.999108	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.987	T	0.40664	-0.9551	10	0.56958	D	0.05	0.1652	19.264	0.93979	0.0:0.0:1.0:0.0	rs61744983	249;249	A6ND58;P58658	.;CU063_HUMAN	M	249	ENSP00000300255:V249M;ENSP00000372146:V249M	ENSP00000300255:V249M	V	+	1	0	C21orf63	32789318	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	6.445000	0.73456	2.631000	0.89168	0.655000	0.94253	GTG	G|0.997;A|0.003	0.003	strong		0.507	EVA1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139403.1	NM_058187		A	33867447	G	A	33867447	3	1	22	1	0	0	0	0	1	0	0	0	2133	1145	40	1	763	1	C21orf63	21	33867447	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	496005	33867447	14262448	4266	7167											
IFNAR1	3454	hgsc.bcm.edu	37	chr21	34713317	34713317	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctttaaagaactgggatggaTaattggataaaattgtctgg	14	13	11	3	0	1	1	0	0	1	1	1	4	1	4	0	4	1	0	0	4	6	6	rs9981753	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:34713317T>C	ENST00000270139.3	+	3	365	c.213T>C	c.(211-213)gaT>gaC	p.D71D	IFNAR1_ENST00000416947.2_Silent_p.D2D|IFNAR1_ENST00000442357.2_Silent_p.D71D	NM_000629.2	NP_000620.2	P17181	INAR1_HUMAN	interferon (alpha, beta and omega) receptor 1	71	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)"	CTGGGATGGATAATTGGATAA	0.284													T|||	95	0.0189696	0.0658	0.0072	5008	,	,		17150	0.0		0.003	False		,,,				2504	0.0				p.D71D	Esophageal Squamous(73;817 1211 32990 35667 42746)	Atlas-SNP	.											.	IFNAR1	44	.	0			c.T213C						PASS	.	T		244,4162	132.1+/-168.6	6,232,1965	55	59	58		213	3.1	0	21	dbSNP_119	58	14,8582	9.8+/-36.6	0,14,4284	no	coding-synonymous	IFNAR1	NM_000629.2		6,246,6249	CC,CT,TT		0.1629,5.5379,1.9843		71/558	34713317	258,12744	2203	4298	6501	SO:0001819	synonymous_variant	3454	exon3			GATGGATAATTGG		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.213T>C	21.37:g.34713317T>C		140	0	0		100	42	0.42	NM_000629	B2R6L9|B4DNT3|D3DSF0|Q53GW9|Q53H11|Q6PKD7|Q7M4L2|Q8WTZ2	Silent	SNP	ENST00000270139.3	37	CCDS13624.1																																																																																			T|0.986;C|0.014	0.014	strong		0.284	IFNAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139823.4			C	34713317	T	C	34713317	2	2	22	1	0	0	0	0	0	0	0	1	7553	1403	49	3		3	IFNAR1	21	34713317	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	845870	34713317	13416578	4267	7168											
IFNAR1	3454	hgsc.bcm.edu	37	chr21	34721782	34721782	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaaaacagtctggaaacaCgcctgtgatccaggattatc	13	9	8	11	1	1	1	0	1	1	0	4	3	3	3	3	2	2	0	3	2	4	1	rs17875834	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:34721782C>T	ENST00000270139.3	+	8	1228	c.1076C>T	c.(1075-1077)aCg>aTg	p.T359M	IFNAR1_ENST00000416947.2_Missense_Mutation_p.T290M|IFNAR1_ENST00000442357.2_Missense_Mutation_p.T359M	NM_000629.2	NP_000620.2	P17181	INAR1_HUMAN	interferon (alpha, beta and omega) receptor 1	359	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.		T -> M (in dbSNP:rs17875834). {ECO:0000269|Ref.5}.		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)"	TCTGGAAACACGCCTGTGATC	0.338													C|||	315	0.0628994	0.2307	0.0101	5008	,	,		17009	0.002		0.001	False		,,,				2504	0.0				p.T359M	Esophageal Squamous(73;817 1211 32990 35667 42746)	Atlas-SNP	.											IFNAR1,caecum,carcinoma,0,1	IFNAR1	44	1	0			c.C1076T						PASS	.	C	MET/THR	677,3729	286.0+/-278.5	47,583,1573	56	55	55		1076	-1	0	21	dbSNP_124	55	4,8594	3.0+/-9.4	0,4,4295	yes	missense	IFNAR1	NM_000629.2	81	47,587,5868	TT,TC,CC		0.0465,15.3654,5.2369	benign	359/558	34721782	681,12323	2203	4299	6502	SO:0001583	missense	3454	exon8			GAAACACGCCTGT		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.1076C>T	21.37:g.34721782C>T	ENSP00000270139:p.Thr359Met	117	0	0		106	49	0.462264	NM_000629	B2R6L9|B4DNT3|D3DSF0|Q53GW9|Q53H11|Q6PKD7|Q7M4L2|Q8WTZ2	Missense_Mutation	SNP	ENST00000270139.3	37	CCDS13624.1	130	0.05952380952380952	126	0.25609756097560976	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	C	8.320	0.823991	0.16678	0.153654	4.65E-4	ENSG00000142166	ENST00000416947;ENST00000270139;ENST00000442357	T;T;T	0.40756	1.02;1.02;1.55	4.43	-1.01	0.10169	Fibronectin, type III (2);Interferon alpha/beta receptor, beta chain (1);Immunoglobulin-like fold (1);	1.665550	0.02913	N	0.136918	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B	0.22146	0.065	B	0.11329	0.006	T	0.20538	-1.0272	9	0.45353	T	0.12	.	0.7942	0.01063	0.4848:0.1669:0.1883:0.16	rs17875834;rs17875834	359	P17181	INAR1_HUMAN	M	290;359;359	ENSP00000395606:T290M;ENSP00000270139:T359M;ENSP00000407406:T359M	ENSP00000270139:T359M	T	+	2	0	IFNAR1	33643652	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.564000	0.05936	-0.375000	0.07955	-0.272000	0.10252	ACG	C|0.930;T|0.070	0.070	strong		0.338	IFNAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139823.4			T	34721782	C	T	34721782	3	4	22	1	0	0	0	0	1	0	0	0	7553	536	19	1	1106	1	IFNAR1	21	34721782	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	8465	34721782	13408113	4268	7169											
CHAF1B	8208	hgsc.bcm.edu	37	chr21	37787615	37787615	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaataaacttaacacccttaAagacggacactccaccaagt	17	7	5	12	1	0	1	0	0	0	1	1	3	1	2	3	1	2	0	3	1	7	3	rs74900401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:37787615A>C	ENST00000314103.5	+	13	1667	c.1516A>C	c.(1516-1518)Aag>Cag	p.K506Q		NM_005441.2	NP_005432.1	Q13112	CAF1B_HUMAN	chromatin assembly factor 1, subunit B (p60)	506			K -> Q (in dbSNP:rs2230638).		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						AACACCCTTAAAGACGGACAC	0.358													A|||	94	0.01877	0.0666	0.0086	5008	,	,		18323	0.0		0.0	False		,,,				2504	0.0				p.K506Q		Atlas-SNP	.											.	CHAF1B	47	.	0			c.A1516C						PASS	.	A	GLN/LYS	231,4175	137.7+/-173.5	11,209,1983	94	93	94		1516	5.3	1	21	dbSNP_131	94	3,8597	2.2+/-6.3	0,3,4297	no	missense	CHAF1B	NM_005441.2	53	11,212,6280	CC,CA,AA		0.0349,5.2429,1.7992	benign	506/560	37787615	234,12772	2203	4300	6503	SO:0001583	missense	8208	exon13			CCCTTAAAGACGG	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.1516A>C	21.37:g.37787615A>C	ENSP00000315700:p.Lys506Gln	38	0	0		50	20	0.4	NM_005441	Q99548	Missense_Mutation	SNP	ENST00000314103.5	37	CCDS13644.1	31	0.014194139194139194	27	0.054878048780487805	4	0.011049723756906077	0	0.0	0	0.0	A	15.24	2.773669	0.49786	0.052429	3.49E-4	ENSG00000159259	ENST00000314103	T	0.56444	0.46	5.27	5.27	0.74061	.	0.467856	0.25244	N	0.032064	T	0.09949	0.0244	L	0.34521	1.04	0.41488	D	0.988205	P	0.46706	0.883	B	0.41571	0.36	T	0.02868	-1.1100	10	0.28530	T	0.3	-21.6711	13.7766	0.63057	1.0:0.0:0.0:0.0	rs2230638;rs16994063;rs52813568;rs16994063	506	Q13112	CAF1B_HUMAN	Q	506	ENSP00000315700:K506Q	ENSP00000315700:K506Q	K	+	1	0	CHAF1B	36709485	1.000000	0.71417	0.995000	0.50966	0.553000	0.35397	5.445000	0.66594	1.991000	0.58162	0.533000	0.62120	AAG	A|0.984;C|0.016;T|0.000	0.016	strong		0.358	CHAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194616.2	NM_005441		C	37787615	A	C	37787615	3	2	22	1	0	0	0	0	1	0	0	0	3314	15	1	5	1562	5	CHAF1B	21	37787615	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	3065833	37787615	10342280	4269	7170											
CLDN14	23562	hgsc.bcm.edu	37	chr21	37833361	37833361	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ttgtaggcagctggtggctgGtaggcaggtgcggtgtttgc	4	12	19	6	1	0	0	0	0	0	0	0	0	0	0	0	7	3	7	0	7	2	4	rs61745291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:37833361G>A	ENST00000399137.1	-	3	1499	c.633C>T	c.(631-633)taC>taT	p.Y211Y	AP000695.6_ENST00000429588.1_RNA|AP000695.4_ENST00000428667.1_RNA|CLDN14_ENST00000399135.1_Silent_p.Y211Y|CLDN14_ENST00000342108.2_Silent_p.Y211Y|CLDN14_ENST00000399136.1_Silent_p.Y211Y|AP000695.4_ENST00000454980.1_RNA|CLDN14_ENST00000399139.1_Silent_p.Y211Y	NM_144492.2	NP_652763.1	O95500	CLD14_HUMAN	claudin 14	211					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						CTGGTGGCTGGTAGGCAGGTG	0.657													G|||	118	0.0235623	0.0862	0.0043	5008	,	,		17127	0.0		0.001	False		,,,				2504	0.0				p.Y211Y		Atlas-SNP	.											.	CLDN14	25	.	0			c.C633T						PASS	.	G	,,,,	278,4128	154.4+/-187.8	11,256,1936	96	86	90		633,633,633,633,633	4.8	0.8	21	dbSNP_129	90	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CLDN14	NM_001146077.1,NM_001146078.1,NM_001146079.1,NM_012130.2,NM_144492.2	,,,,	11,258,6234	AA,AG,GG		0.0233,6.3096,2.1529	,,,,	211/240,211/240,211/240,211/240,211/240	37833361	280,12726	2203	4300	6503	SO:0001819	synonymous_variant	23562	exon3			TGGCTGGTAGGCA	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.633C>T	21.37:g.37833361G>A		332	0	0		419	228	0.544153	NM_144492		Silent	SNP	ENST00000399137.1	37	CCDS13645.1																																																																																			G|0.976;A|0.024	0.024	strong		0.657	CLDN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194697.1	NM_144492		A	37833361	G	A	37833361	2	1	22	1	0	0	0	0	0	0	0	1	3477	1256	44	2		2	CLDN14	21	37833361	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	45746	37833361	10296534	4270	7171											
DSCR6	53820	hgsc.bcm.edu	37	chr21	38390419	38390419	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gggcatcaaccaagggcagcGatcctcaggagggggtgacc	10	4	16	11	1	2	1	2	1	0	0	3	3	3	2	3	5	2	2	3	5	2	0	rs61735126	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:38390419G>A	ENST00000329553.2	+	4	695	c.485G>A	c.(484-486)cGa>cAa	p.R162Q	RIPPLY3_ENST00000485272.1_3'UTR	NM_018962.2	NP_061835.1	P57055	DSCR6_HUMAN	ripply transcriptional repressor 3	162					heart development (GO:0007507)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pharyngeal system development (GO:0060037)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)											CAAGGGCAGCGATCCTCAGGA	0.627													G|||	67	0.0133786	0.0469	0.0058	5008	,	,		16442	0.0		0.001	False		,,,				2504	0.0				p.R162Q		Atlas-SNP	.											.	DSCR6	16	.	0			c.G485A						PASS	.	G	GLN/ARG	146,4260	99.4+/-138.0	4,138,2061	47	46	46		485	0.1	0	21	dbSNP_129	46	1,8599	1.2+/-3.3	0,1,4299	yes	missense	DSCR6	NM_018962.2	43	4,139,6360	AA,AG,GG		0.0116,3.3137,1.1302	probably-damaging	162/191	38390419	147,12859	2203	4300	6503	SO:0001583	missense	53820	exon4			GGCAGCGATCCTC	AB037158	CCDS13648.1	21q22.2	2013-07-23	2013-07-23	2013-06-04	ENSG00000183145	ENSG00000183145			3047	protein-coding gene	gene with protein product		609892	"Down syndrome critical region gene 6", "ripply3 homolog (zebrafish)"	DSCR6		10814524, 22354841	Standard	NM_018962		Approved			P57055	OTTHUMG00000086639	ENST00000329553.2:c.485G>A	21.37:g.38390419G>A	ENSP00000331734:p.Arg162Gln	35	0	0		55	26	0.472727	NM_018962		Missense_Mutation	SNP	ENST00000329553.2	37	CCDS13648.1	25	0.011446886446886446	22	0.044715447154471545	3	0.008287292817679558	0	0.0	0	0.0	G	10.33	1.319066	0.23994	0.033137	1.16E-4	ENSG00000183145	ENST00000329553	.	.	.	3.52	0.127	0.14727	.	1.934300	0.03067	N	0.156638	T	0.06188	0.0160	N	0.19112	0.55	0.09310	N	1	D	0.63880	0.993	P	0.46543	0.52	T	0.12967	-1.0527	9	0.45353	T	0.12	2.0523	6.2061	0.20604	0.0:0.4264:0.3815:0.1922	rs61735126	162	P57055	DSCR6_HUMAN	Q	162	.	ENSP00000331734:R162Q	R	+	2	0	DSCR6	37312289	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.614000	0.05604	0.232000	0.21100	-0.311000	0.09066	CGA	G|0.989;A|0.011	0.011	strong		0.627	RIPPLY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194703.1			A	38390419	G	A	38390419	3	1	22	1	0	0	0	0	1	0	0	0	4775	1058	37	1	499	1	DSCR6	21	38390419	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	557058	38390419	9739476	4271	7172											
TTC3	7267	hgsc.bcm.edu	37	chr21	38524226	38524226	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agactgaaagaagacaaaaaAttgaagagaaagatccaaaa	25	4	8	4	0	0	7	0	2	0	5	1	8	1	7	1	0	0	0	1	0	9	1	rs2835632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:38524226A>G	ENST00000399017.2	+	26	5057	c.2310A>G	c.(2308-2310)aaA>aaG	p.K770K	TTC3_ENST00000355666.1_Silent_p.K770K|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000540756.1_Silent_p.K460K|TTC3_ENST00000354749.2_Silent_p.K770K	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	770					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)				AAGACAAAAAATTGAAGAGAA	0.338													A|||	528	0.105431	0.2466	0.1715	5008	,	,		18165	0.0407		0.003	False		,,,				2504	0.0399				p.K770K	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.A2310G						PASS	.	A	,	912,3494	336.3+/-304.3	94,724,1385	67	66	66		2310,2310	0.3	0.2	21	dbSNP_100	66	16,8582	11.2+/-40.8	0,16,4283	no	coding-synonymous,coding-synonymous	TTC3	NM_001001894.1,NM_003316.3	,	94,740,5668	GG,GA,AA		0.1861,20.699,7.1363	,	770/2026,770/2026	38524226	928,12076	2203	4299	6502	SO:0001819	synonymous_variant	7267	exon26			CAAAAAATTGAAG	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.2310A>G	21.37:g.38524226A>G		193	0	0		192	105	0.546875	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Silent	SNP	ENST00000399017.2	37	CCDS13651.1	197	0.0902014652014652	113	0.22967479674796748	51	0.1408839779005525	31	0.05419580419580419	2	0.002638522427440633	A	6.749	0.507112	0.12883	0.20699	0.001861	ENSG00000182670	ENST00000414818	.	.	.	5.42	0.33	0.15929	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.25717	P	0.9854106	.	.	.	.	.	.	T	0.17561	-1.0365	3	.	.	.	-5.4385	8.4056	0.32612	0.6847:0.0:0.3153:0.0	rs2835632;rs3737425	.	.	.	S	134	.	.	N	+	2	0	TTC3	37446096	0.645000	0.27286	0.218000	0.23776	0.987000	0.75469	1.103000	0.31062	-0.103000	0.12175	-0.274000	0.10170	AAT	A|0.931;G|0.069	0.069	strong		0.338	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			G	38524226	A	G	38524226	2	3	22	1	0	0	0	0	0	0	0	1	16712	98	4	3		3	TTC3	21	38524226	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	133807	38524226	9605669	4272	7173											
TTC3	7267	hgsc.bcm.edu	37	chr21	38538319	38538319	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctagacaagtttctgaggAtgggcaacccaaaggggtct	11	10	12	8	0	3	2	0	1	3	1	3	3	3	3	1	4	1	2	1	4	4	3	rs61998236	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:38538319A>G	ENST00000399017.2	+	33	6550	c.3803A>G	c.(3802-3804)gAt>gGt	p.D1268G	TTC3_ENST00000355666.1_Missense_Mutation_p.D1268G|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000354749.2_Missense_Mutation_p.D1268G	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1268					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)				GTTTCTGAGGATGGGCAACCC	0.473													A|||	125	0.0249601	0.0908	0.0058	5008	,	,		18238	0.0		0.001	False		,,,				2504	0.0				p.D1268G	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.A3803G						PASS	.	A	GLY/ASP,GLY/ASP	324,4080	159.2+/-191.8	10,304,1888	60	67	65		3803,3803	1.4	0	21	dbSNP_129	65	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	TTC3	NM_001001894.1,NM_003316.3	94,94	10,306,6186	GG,GA,AA		0.0233,7.3569,2.5069	possibly-damaging,possibly-damaging	1268/2026,1268/2026	38538319	326,12678	2202	4300	6502	SO:0001583	missense	7267	exon33			CTGAGGATGGGCA	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.3803A>G	21.37:g.38538319A>G	ENSP00000381981:p.Asp1268Gly	194	0	0		184	88	0.478261	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	58	0.026556776556776556	53	0.10772357723577236	5	0.013812154696132596	0	0.0	0	0.0	A	11.72	1.723822	0.30593	0.073569	2.33E-4	ENSG00000182670	ENST00000355666;ENST00000399017;ENST00000354749	T;T;T	0.13196	2.61;2.61;2.61	3.85	1.38	0.22167	.	0.913911	0.09206	N	0.834038	T	0.00241	0.0007	L	0.51422	1.61	0.09310	N	1	B;B	0.17268	0.021;0.001	B;B	0.15484	0.013;0.002	T	0.38308	-0.9667	9	.	.	.	-2.4084	3.1193	0.06386	0.6771:0.0:0.1149:0.208	rs61998236	326;1268	Q5GIT6;P53804	.;TTC3_HUMAN	G	1268	ENSP00000347889:D1268G;ENSP00000381981:D1268G;ENSP00000346791:D1268G	.	D	+	2	0	TTC3	37460189	0.001000	0.12720	0.000000	0.03702	0.406000	0.30931	0.854000	0.27791	0.292000	0.22492	0.533000	0.62120	GAT	A|0.974;G|0.026	0.026	strong		0.473	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			G	38538319	A	G	38538319	3	3	22	1	0	0	0	0	1	0	0	0	16712	333	12	3	3929	3	TTC3	21	38538319	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	14093	38538319	9591576	4273	7174											
DSCR3	10311	hgsc.bcm.edu	37	chr21	38605694	38605694	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgataaattcacaggtctttGtcaagtccttggccaacaga	12	11	8	10	1	3	1	2	0	1	1	4	2	4	1	2	2	1	0	2	2	4	4	rs145630556	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:38605694G>A	ENST00000309117.6	-	4	638	c.401C>T	c.(400-402)aCa>aTa	p.T134I	DSCR3_ENST00000539844.1_Intron|DSCR3_ENST00000398998.1_Missense_Mutation_p.T86I|DSCR3_ENST00000399000.3_5'UTR|AP001432.14_ENST00000440629.1_lincRNA|DSCR3_ENST00000399001.1_Intron|DSCR3_ENST00000476950.1_Intron|DSCR3_ENST00000288304.5_Missense_Mutation_p.T92I	NM_006052.1	NP_006043.1	O14972	DSCR3_HUMAN	Down syndrome critical region gene 3	134						nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(3)|lung(3)	9						ACAGGTCTTTGTCAAGTCCTT	0.463													G|||	11	0.00219649	0.0083	0.0	5008	,	,		17905	0.0		0.0	False		,,,				2504	0.0				p.T134I		Atlas-SNP	.											.	DSCR3	21	.	0			c.C401T						PASS	.	G	ILE/THR	26,4380	31.7+/-61.6	0,26,2177	112	98	103		401	5	0.9	21	dbSNP_134	103	0,8600		0,0,4300	yes	missense	DSCR3	NM_006052.1	89	0,26,6477	AA,AG,GG		0.0,0.5901,0.1999	benign	134/298	38605694	26,12980	2203	4300	6503	SO:0001583	missense	10311	exon4			GTCTTTGTCAAGT	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.401C>T	21.37:g.38605694G>A	ENSP00000311399:p.Thr134Ile	73	0	0		74	33	0.445946	NM_006052	B2R6T8|B7Z6B1|D3DSH4|Q2TAY6	Missense_Mutation	SNP	ENST00000309117.6	37	CCDS33553.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	G	17.52	3.411061	0.62399	0.005901	0.0	ENSG00000157538	ENST00000309117;ENST00000288304;ENST00000398998	T	0.06933	3.24	5.0	5.0	0.66597	.	0.051278	0.85682	D	0.000000	T	0.11707	0.0285	M	0.72894	2.215	0.48288	D	0.99962	P	0.40834	0.73	B	0.42361	0.385	T	0.01504	-1.1338	10	0.38643	T	0.18	-0.2541	18.6523	0.91435	0.0:0.0:1.0:0.0	.	134	O14972	DSCR3_HUMAN	I	134;92;86	ENSP00000311399:T134I	ENSP00000288304:T92I	T	-	2	0	DSCR3	37527564	1.000000	0.71417	0.939000	0.37840	0.996000	0.88848	5.652000	0.67959	2.462000	0.83206	0.455000	0.32223	ACA	G|0.998;A|0.002	0.002	strong		0.463	DSCR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194807.1			A	38605694	G	A	38605694	3	1	22	1	0	0	0	0	1	0	0	0	4773	1377	48	2	512	2	DSCR3	21	38605694	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	67375	38605694	9524201	4274	7175											
BRWD1	54014	hgsc.bcm.edu	37	chr21	40570830	40570830	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgggttcatttccattttatGacatttcccatcttctctat	7	20	4	10	0	3	1	1	1	2	0	6	1	5	1	2	1	0	1	2	1	2	7	rs2234547	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:40570830G>C	ENST00000333229.2	-	40	5839	c.5512C>G	c.(5512-5514)Cat>Gat	p.H1838D	BRWD1_ENST00000380800.3_Missense_Mutation_p.H1838D|BRWD1_ENST00000342449.3_Missense_Mutation_p.H1838D	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	1838					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)				TCCATTTTATGACATTTCCCA	0.373													G|||	17	0.00339457	0.0121	0.0014	5008	,	,		19409	0.0		0.0	False		,,,				2504	0.0				p.H1838D	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.C5512G						PASS	.	G	ASP/HIS,ASP/HIS	15,4389	22.3+/-47.3	0,15,2187	134	133	133		5512,5512	3.2	0.2	21	dbSNP_98	133	0,8600		0,0,4300	yes	missense,missense	BRWD1	NM_018963.4,NM_033656.3	81,81	0,15,6487	CC,CG,GG		0.0,0.3406,0.1153	benign,benign	1838/2321,1838/2270	40570830	15,12989	2202	4300	6502	SO:0001583	missense	54014	exon40			TTTTATGACATTT	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.5512C>G	21.37:g.40570830G>C	ENSP00000330753:p.His1838Asp	155	0	0		172	84	0.488372	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	37	CCDS13662.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	G	11.80	1.746199	0.30955	0.003406	0.0	ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800	T;T;T	0.44083	0.93;0.93;0.93	5.48	3.18	0.36537	.	0.908791	0.09391	N	0.808490	T	0.14098	0.0341	L	0.54323	1.7	0.09310	N	1	B;B	0.26775	0.095;0.159	B;B	0.24155	0.051;0.021	T	0.08534	-1.0717	10	0.35671	T	0.21	-2.3847	4.7666	0.13135	0.1553:0.4107:0.434:0.0	rs2234547;rs2234547	1838;1838	Q9NSI6-2;Q9NSI6	.;BRWD1_HUMAN	D	1838	ENSP00000330753:H1838D;ENSP00000344333:H1838D;ENSP00000370178:H1838D	ENSP00000330753:H1838D	H	-	1	0	BRWD1	39492700	0.000000	0.05858	0.203000	0.23512	0.374000	0.29953	0.674000	0.25218	2.576000	0.86940	0.655000	0.94253	CAT	G|0.997;C|0.003	0.003	strong		0.373	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		C	40570830	G	C	40570830	3	2	22	1	0	0	0	0	1	0	0	0	1527	1290	45	4	1701	4	BRWD1	21	40570830	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1965136	40570830	7559065	4275	7176											
BRWD1	54014	hgsc.bcm.edu	37	chr21	40590176	40590176	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tatgtacacaaatcaacaggGcctgcaaaagctgctgctat	14	9	8	10	0	1	0	1	0	0	0	1	0	1	0	1	1	6	5	1	1	7	3	rs76171323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:40590176G>T	ENST00000333229.2	-	31	3888	c.3561C>A	c.(3559-3561)ggC>ggA	p.G1187G	BRWD1-IT1_ENST00000435608.1_RNA|BRWD1_ENST00000380800.3_Silent_p.G1187G|BRWD1_ENST00000342449.3_Silent_p.G1187G	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	1187	Bromo 1. {ECO:0000255|PROSITE- ProRule:PRU00035}.				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)				AATCAACAGGGCCTGCAAAAG	0.378													G|||	75	0.014976	0.0545	0.0014	5008	,	,		15406	0.0		0.002	False		,,,				2504	0.0				p.G1187G	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											BRWD1_ENST00000333229,NS,lymphoid_neoplasm,0,2	BRWD1	325	2	0			c.C3561A						PASS	.	G	,	182,4224	118.8+/-156.5	1,180,2022	108	107	107		3561,3561	-0.7	1	21	dbSNP_131	107	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	BRWD1	NM_018963.4,NM_033656.3	,	1,181,6321	TT,TG,GG		0.0116,4.1307,1.407	,	1187/2321,1187/2270	40590176	183,12823	2203	4300	6503	SO:0001819	synonymous_variant	54014	exon31			AACAGGGCCTGCA	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.3561C>A	21.37:g.40590176G>T		114	0	0		112	66	0.589286	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Silent	SNP	ENST00000333229.2	37	CCDS13662.1	40	0.018315018315018316	40	0.08130081300813008	0	0.0	0	0.0	0	0.0	G	9.823	1.186196	0.21870	0.041307	1.16E-4	ENSG00000185658	ENST00000424441	.	.	.	5.56	-0.669	0.11388	.	.	.	.	.	T	0.04861	0.0131	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.04115	-1.0976	4	.	.	.	-8.3462	7.2761	0.26286	0.5235:0.1169:0.3596:0.0	.	.	.	.	T	173	.	.	P	-	1	0	BRWD1	39512046	0.888000	0.30383	0.993000	0.49108	0.904000	0.53231	0.108000	0.15396	-0.032000	0.13758	0.462000	0.41574	CCC	G|0.984;T|0.016	0.016	strong		0.378	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		T	40590176	G	T	40590176	2	4	22	1	0	0	0	0	0	0	0	1	1527	1190	42	4		4	BRWD1	21	40590176	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	19346	40590176	7539719	4276	7177											
IGSF5	150084	hgsc.bcm.edu	37	chr21	41142958	41142958	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccggatatttcctgggagctCggtctcctggtcagccattc	5	12	11	13	2	2	0	1	0	1	0	6	2	3	2	4	4	2	1	4	4	1	3	rs61737685	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:41142958C>T	ENST00000380588.4	+	4	637	c.534C>T	c.(532-534)ctC>ctT	p.L178L	IGSF5_ENST00000479378.1_3'UTR	NM_001080444.1	NP_001073913.1	Q9NSI5	IGSF5_HUMAN	immunoglobulin superfamily, member 5	178	Ig-like V-type 2.				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)				CCTGGGAGCTCGGTCTCCTGG	0.517													C|||	230	0.0459265	0.1664	0.0144	5008	,	,		15063	0.0		0.0	False		,,,				2504	0.0				p.L178L		Atlas-SNP	.											.	IGSF5	62	.	0			c.C534T						PASS	.	C		580,3826	258.3+/-262.4	35,510,1658	68	66	66		534	-2.5	0	21	dbSNP_129	66	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	IGSF5	NM_001080444.1		35,516,5952	TT,TC,CC		0.0698,13.1639,4.5056		178/408	41142958	586,12420	2203	4300	6503	SO:0001819	synonymous_variant	150084	exon4			GGAGCTCGGTCTC		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.534C>T	21.37:g.41142958C>T		47	0	0		53	30	0.566038	NM_001080444		Silent	SNP	ENST00000380588.4	37	CCDS33562.1																																																																																			C|0.957;T|0.043	0.043	strong		0.517	IGSF5-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195005.1			T	41142958	C	T	41142958	2	4	22	1	0	0	0	0	0	0	0	1	7611	871	31	1		1	IGSF5	21	41142958	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	552782	41142958	6986937	4277	7178											
IGSF5	150084	hgsc.bcm.edu	37	chr21	41143018	41143018	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcccagcgaccttcaaagTgcagtgagcatcctggctct	9	8	11	13	1	2	1	1	1	1	0	3	3	3	1	3	1	4	3	3	1	1	1	rs74817033	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:41143018T>A	ENST00000380588.4	+	4	697	c.594T>A	c.(592-594)agT>agA	p.S198R	IGSF5_ENST00000479378.1_3'UTR	NM_001080444.1	NP_001073913.1	Q9NSI5	IGSF5_HUMAN	immunoglobulin superfamily, member 5	198	Ig-like V-type 2.				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)				ACCTTCAAAGTGCAGTGAGCA	0.557													T|||	215	0.0429313	0.1551	0.0144	5008	,	,		15696	0.0		0.0	False		,,,				2504	0.0				p.S198R		Atlas-SNP	.											.	IGSF5	62	.	0			c.T594A						PASS	.	T	ARG/SER	560,3846	251.8+/-258.4	34,492,1677	76	72	73		594	-3.7	0	21	dbSNP_131	73	5,8595	3.7+/-12.6	0,5,4295	yes	missense	IGSF5	NM_001080444.1	110	34,497,5972	AA,AT,TT		0.0581,12.7099,4.3441	benign	198/408	41143018	565,12441	2203	4300	6503	SO:0001583	missense	150084	exon4			TCAAAGTGCAGTG		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.594T>A	21.37:g.41143018T>A	ENSP00000369962:p.Ser198Arg	64	0	0		70	35	0.5	NM_001080444		Missense_Mutation	SNP	ENST00000380588.4	37	CCDS33562.1	87	0.03983516483516483	78	0.15853658536585366	9	0.024861878453038673	0	0.0	0	0.0	T	17.24	3.339873	0.60963	0.127099	5.81E-4	ENSG00000183067	ENST00000380588	T	0.12147	2.71	5.11	-3.69	0.04450	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.194230	0.52532	N	0.000061	T	0.00039	0.0001	L	0.40543	1.245	0.80722	P	0.0	P	0.37708	0.606	B	0.37198	0.243	T	0.40175	-0.9577	9	0.14252	T	0.57	-6.954	5.6797	0.17769	0.0:0.2935:0.239:0.4676	.	198	Q9NSI5	IGSF5_HUMAN	R	198	ENSP00000369962:S198R	ENSP00000369962:S198R	S	+	3	2	IGSF5	40064888	0.001000	0.12720	0.000000	0.03702	0.931000	0.56810	-0.287000	0.08388	-0.719000	0.04942	0.528000	0.53228	AGT	T|0.959;A|0.041	0.041	strong		0.557	IGSF5-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195005.1			A	41143018	T	A	41143018	3	1	22	1	0	0	0	0	1	0	0	0	7611	1693	59	5	608	5	IGSF5	21	41143018	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	60	41143018	6986877	4278	7179											
PLAC4	25825	hgsc.bcm.edu	37	chr21	42551183	42551183	+	Intron	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgtccagggtgaggagtgagGgagtccagggtgaggagtga	9	7	21	4	0	0	4	0	4	0	0	2	7	2	7	2	5	0	0	2	5	0	0	rs202000983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:42551183G>A	ENST00000330333.6	+	1	775				PLAC4_ENST00000430327.2_RNA|PLAC4_ENST00000440221.2_RNA|PLAC4_ENST00000414699.1_RNA|BACE2-IT1_ENST00000433378.1_RNA|BACE2_ENST00000328735.6_Intron|PLAC4_ENST00000536486.1_RNA|BACE2_ENST00000347667.5_Intron	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)				gaggagtgagggagtccaggg	0.607													G|||	14	0.00279553	0.0098	0.0014	5008	,	,		20303	0.0		0.0	False		,,,				2504	0.0				p.P125S		Atlas-SNP	.											.	.	.	.	0			c.C373T						PASS	.	G	,,,SER/PRO	16,4350		0,16,2167	126	106	113		,,,373	0.2	0	21		113	0,8470		0,0,4235	yes	intron,intron,intron,missense	BACE2,PLAC4	NM_012105.3,NM_138991.1,NM_138992.1,NM_182832.2	,,,74	0,16,6402	AA,AG,GG		0.0,0.3665,0.1246	,,,possibly-damaging	,,,125/151	42551183	16,12820	2183	4235	6418	SO:0001627	intron_variant	191585	exon1			AGTGAGGGAGTCC	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+10681G>A	21.37:g.42551183G>A		263	1	0.00380228		297	158	0.531987	NM_182832	A8K7P1|Q5DIH8|Q8N2D4|Q9H2V8|Q9NZL1|Q9NZL2|Q9UJT6	Missense_Mutation	SNP	ENST00000330333.6	37	CCDS13668.1																																																																																			.	.	weak		0.607	BACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195056.1			A	42551183	G	A	42551183	1	1	22	0	1	0	0	0	0	0	0	0	12023	1232	43	2		2	PLAC4	21	42551183	Intron	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1408165	42551183	5578712	4279	7180											
UMODL1	89766	hgsc.bcm.edu	37	chr21	43524188	43524188	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agattgaccggcaggggacaCgcgtgcaaggtatggcccag	10	5	16	10	3	0	2	0	1	0	1	0	3	0	3	2	5	1	3	2	5	2	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:43524188C>T	ENST00000408910.2	+	9	1510	c.1510C>T	c.(1510-1512)Cgc>Tgc	p.R504C	C21orf128_ENST00000329015.2_Intron|UMODL1_ENST00000400427.1_Missense_Mutation_p.R432C|UMODL1_ENST00000400424.2_Missense_Mutation_p.R432C|UMODL1_ENST00000408989.2_Missense_Mutation_p.R504C	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	504	SEA 1. {ECO:0000255|PROSITE- ProRule:PRU00188}.				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						GCAGGGGACACGCGTGCAAGG	0.587																																					p.R504C	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.C1510T						PASS	.						48	50	49					21																	43524188		2203	4300	6503	SO:0001583	missense	89766	exon9			GGGACACGCGTGC		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.1510C>T	21.37:g.43524188C>T	ENSP00000386147:p.Arg504Cys	49	0	0		47	7	0.148936	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	.	.	.	.	.	.	.	.	.	.	C	8.034	0.762462	0.15914	.	.	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910	D;T;D;T	0.82167	-1.58;-0.65;-1.58;-0.67	3.67	0.744	0.18353	.	4.413020	0.00541	N	0.000220	D	0.85331	0.5672	L	0.47716	1.5	0.09310	N	0.999994	D;D;P	0.67145	0.98;0.996;0.939	P;P;P	0.59703	0.711;0.862;0.513	T	0.67321	-0.5700	10	0.37606	T	0.19	0.2373	4.6354	0.12521	0.0:0.4456:0.3484:0.206	.	432;504;504	Q5DID0-3;Q5DID0-2;Q5DID0	.;.;UROL1_HUMAN	C	432;432;504;504	ENSP00000383279:R432C;ENSP00000383276:R432C;ENSP00000386126:R504C;ENSP00000386147:R504C	ENSP00000383276:R432C	R	+	1	0	UMODL1	42397257	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-0.543000	0.06084	0.140000	0.18849	0.655000	0.94253	CGC	.	.	none		0.587	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2			T	43524188	C	T	43524188	3	4	22	1	0	0	0	0	1	0	0	0	16995	536	19	1	1544	1	UMODL1	21	43524188	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	973005	43524188	4605707	4280	7181											
UMODL1	89766	hgsc.bcm.edu	37	chr21	43536047	43536047	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tactcagaatcctttcgcaaCgcaagcagccaggagtatcg	12	8	9	12	3	1	1	1	0	0	1	4	2	2	2	2	1	4	4	2	1	5	3	rs141581454	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:43536047C>T	ENST00000408910.2	+	14	2427	c.2427C>T	c.(2425-2427)aaC>aaT	p.N809N	UMODL1_ENST00000400427.1_Silent_p.N865N|UMODL1_ENST00000400424.2_Silent_p.N737N|UMODL1_ENST00000408989.2_Silent_p.N937N	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	809	SEA 2. {ECO:0000255|PROSITE- ProRule:PRU00188}.				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						CCTTTCGCAACGCAAGCAGCC	0.468													C|||	6	0.00119808	0.0038	0.0014	5008	,	,		17984	0.0		0.0	False		,,,				2504	0.0				p.N937N	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.C2811T						PASS	.	C	,,,	20,3852		0,20,1916	96	98	97		2427,2595,2211,2811	-6.4	0	21	dbSNP_134	97	0,8284		0,0,4142	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	,,,	0,20,6058	TT,TC,CC		0.0,0.5165,0.1645	,,,	809/1319,865/1375,737/1247,937/1447	43536047	20,12136	1936	4142	6078	SO:0001819	synonymous_variant	89766	exon13			TCGCAACGCAAGC		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.2427C>T	21.37:g.43536047C>T		212	0	0		233	116	0.497854	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Silent	SNP	ENST00000408910.2	37	CCDS42936.1																																																																																			C|0.998;T|0.002	0.002	strong		0.468	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2			T	43536047	C	T	43536047	2	4	22	1	0	0	0	0	0	0	0	1	16995	535	19	1		1	UMODL1	21	43536047	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	11859	43536047	4593848	4281	7182											
SLC37A1	54020	hgsc.bcm.edu	37	chr21	43954850	43954850	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcttgggatgaagctgacGtcaggttcagcagccagaac	10	8	13	10	1	2	3	2	2	0	1	2	4	2	4	1	2	5	4	1	2	2	2	rs115669950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:43954850G>A	ENST00000352133.2	+	4	1163	c.181G>A	c.(181-183)Gtc>Atc	p.V61I	SLC37A1_ENST00000398341.3_Missense_Mutation_p.V61I			P57057	GLPT_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 1	61					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						TGAAGCTGACGTCAGGTTCAG	0.602													G|||	91	0.0181709	0.0673	0.0029	5008	,	,		19958	0.0		0.0	False		,,,				2504	0.0				p.V61I		Atlas-SNP	.											.	SLC37A1	48	.	0			c.G181A						PASS	.	G	ILE/VAL	215,4191	130.6+/-167.2	6,203,1994	98	90	93		181	1.4	0	21	dbSNP_132	93	0,8600		0,0,4300	yes	missense	SLC37A1	NM_018964.3	29	6,203,6294	AA,AG,GG		0.0,4.8797,1.6531	benign	61/534	43954850	215,12791	2203	4300	6503	SO:0001583	missense	54020	exon5			GCTGACGTCAGGT	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.181G>A	21.37:g.43954850G>A	ENSP00000344648:p.Val61Ile	101	0	0		118	68	0.576271	NM_018964	D3DSJ7|Q9HAQ1	Missense_Mutation	SNP	ENST00000352133.2	37	CCDS13689.1	22	0.010073260073260074	20	0.04065040650406504	2	0.0055248618784530384	0	0.0	0	0.0	G	3.524	-0.097237	0.07010	0.048797	0.0	ENSG00000160190	ENST00000398341;ENST00000352133	T;T	0.22743	1.94;1.94	4.36	1.44	0.22558	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.175660	0.06063	N	0.658658	T	0.01353	0.0044	N	0.08118	0	0.09310	N	1	B	0.14012	0.009	B	0.10450	0.005	T	0.34428	-0.9829	10	0.22706	T	0.39	-15.6473	2.5906	0.04841	0.1086:0.2627:0.4637:0.165	.	61	P57057	GLPT_HUMAN	I	61	ENSP00000381383:V61I;ENSP00000344648:V61I	ENSP00000344648:V61I	V	+	1	0	SLC37A1	42827919	0.009000	0.17119	0.000000	0.03702	0.010000	0.07245	1.076000	0.30729	0.170000	0.19704	0.655000	0.94253	GTC	G|0.984;A|0.016	0.016	strong		0.602	SLC37A1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195377.1			A	43954850	G	A	43954850	3	1	22	1	0	0	0	0	1	0	0	0	14612	1145	40	1	191	1	SLC37A1	21	43954850	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	418803	43954850	4175045	4282	7183											
PDE9A	5152	hgsc.bcm.edu	37	chr21	44179112	44179112	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttctcctgtgcccacagatgCtgagctgcctggagcacatg	7	10	11	13	0	1	2	0	1	1	1	2	3	1	3	3	1	5	3	3	1	0	1	rs146382324	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:44179112C>G	ENST00000291539.6	+	11	874	c.814C>G	c.(814-816)Ctg>Gtg	p.L272V	PDE9A_ENST00000335440.6_Missense_Mutation_p.L170V|PDE9A_ENST00000470987.1_3'UTR|PDE9A_ENST00000349112.3_Missense_Mutation_p.L144V|PDE9A_ENST00000398224.3_Missense_Mutation_p.L145V|PDE9A_ENST00000398236.3_Missense_Mutation_p.L186V|PDE9A_ENST00000398225.3_Missense_Mutation_p.L231V|PDE9A_ENST00000398227.3_Missense_Mutation_p.L112V|PDE9A_ENST00000328862.6_Missense_Mutation_p.L246V|PDE9A_ENST00000539837.1_Missense_Mutation_p.L144V|PDE9A_ENST00000398234.3_Missense_Mutation_p.L171V|PDE9A_ENST00000398232.3_Missense_Mutation_p.L205V|PDE9A_ENST00000335512.4_Missense_Mutation_p.L212V|PDE9A_ENST00000398229.3_Missense_Mutation_p.L138V|PDE9A_ENST00000380328.2_Missense_Mutation_p.L219V	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	272					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)	CCCACAGATGCTGAGCTGCCT	0.637													C|||	2	0.000399361	0.0015	0.0	5008	,	,		19507	0.0		0.0	False		,,,				2504	0.0				p.L272V		Atlas-SNP	.											.	PDE9A	69	.	0			c.C814G						PASS	.	C	VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU	11,4395	17.9+/-39.9	0,11,2192	81	65	71		634,433,430,655,511,193,193,556,334,163,412,508,193,163,613,691,736,193,193,814	5.1	1	21	dbSNP_134	71	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	PDE9A	NM_001001567.1,NM_001001568.1,NM_001001569.1,NM_001001570.1,NM_001001571.1,NM_001001572.1,NM_001001573.1,NM_001001574.1,NM_001001575.1,NM_001001576.1,NM_001001577.1,NM_001001578.1,NM_001001579.1,NM_001001580.1,NM_001001581.1,NM_001001582.1,NM_001001583.1,NM_001001584.2,NM_001001585.1,NM_002606.2	32,32,32,32,32,32,32,32,32,32,32,32,32,32,32,32,32,32,32,32	0,11,6492	GG,GC,CC		0.0,0.2497,0.0846	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	212/534,145/467,144/466,219/541,171/493,65/387,65/387,186/508,112/434,55/377,138/460,170/492,65/387,55/377,205/527,231/553,246/568,65/387,65/387,272/594	44179112	11,12995	2203	4300	6503	SO:0001583	missense	5152	exon11			CAGATGCTGAGCT	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.814C>G	21.37:g.44179112C>G	ENSP00000291539:p.Leu272Val	99	0	0		133	71	0.533835	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	37	CCDS13690.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	18.52	3.641532	0.67244	0.002497	0.0	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	0.75938	-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98	5.1	5.1	0.69264	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.000000	0.85682	D	0.000000	T	0.79387	0.4437	L	0.53780	1.695	0.52099	D	0.999942	B;B;B;B;B;B;P;B;B;B;B;B;P;B;B;B	0.38597	0.079;0.101;0.101;0.237;0.101;0.161;0.639;0.237;0.101;0.101;0.237;0.11;0.579;0.441;0.101;0.027	B;B;B;B;B;B;P;B;B;B;B;B;B;B;B;B	0.48030	0.092;0.064;0.102;0.092;0.162;0.319;0.564;0.216;0.064;0.064;0.092;0.158;0.442;0.216;0.102;0.048	T	0.81147	-0.1065	10	0.66056	D	0.02	.	18.5908	0.91212	0.0:1.0:0.0:0.0	.	144;205;186;171;246;231;164;212;55;112;138;144;170;219;145;272	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	V	212;144;272;219;205;171;186;246;170;231;138;112;144;145	ENSP00000335242:L212V;ENSP00000441899:L144V;ENSP00000291539:L272V;ENSP00000369685:L219V;ENSP00000381287:L205V;ENSP00000381289:L171V;ENSP00000381291:L186V;ENSP00000328699:L246V;ENSP00000335365:L170V;ENSP00000381281:L231V;ENSP00000381285:L138V;ENSP00000381283:L112V;ENSP00000344730:L144V;ENSP00000381280:L145V	ENSP00000291539:L272V	L	+	1	2	PDE9A	43052181	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.526000	0.60566	2.388000	0.81334	0.650000	0.86243	CTG	C|0.999;G|0.001	0.001	strong		0.637	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1			G	44179112	C	G	44179112	3	3	22	1	0	0	0	0	1	0	0	0	11664	796	28	4	936	4	PDE9A	21	44179112	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	224262	44179112	3950783	4283	7184											
PDE9A	5152	hgsc.bcm.edu	37	chr21	44192574	44192574	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagaagactgacagcttgaCgtctggggccaccgagaagt	12	6	14	9	2	1	5	0	2	1	3	1	7	1	5	2	2	1	1	2	2	3	1	rs147305658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:44192574C>T	ENST00000291539.6	+	19	1772	c.1712C>T	c.(1711-1713)aCg>aTg	p.T571M	PDE9A_ENST00000335440.6_Missense_Mutation_p.T469M|PDE9A_ENST00000470987.1_3'UTR|PDE9A_ENST00000349112.3_Missense_Mutation_p.T443M|PDE9A_ENST00000398224.3_Missense_Mutation_p.T444M|PDE9A_ENST00000398236.3_Missense_Mutation_p.T485M|PDE9A_ENST00000398225.3_Missense_Mutation_p.T530M|PDE9A_ENST00000398227.3_Missense_Mutation_p.T411M|PDE9A_ENST00000328862.6_Missense_Mutation_p.T545M|PDE9A_ENST00000539837.1_Missense_Mutation_p.T443M|PDE9A_ENST00000398234.3_Missense_Mutation_p.T470M|PDE9A_ENST00000398232.3_Missense_Mutation_p.T504M|PDE9A_ENST00000335512.4_Missense_Mutation_p.T511M|PDE9A_ENST00000398229.3_Missense_Mutation_p.T437M|PDE9A_ENST00000380328.2_Missense_Mutation_p.T518M	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	571					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)	GACAGCTTGACGTCTGGGGCC	0.527													C|||	3	0.000599042	0.0023	0.0	5008	,	,		18440	0.0		0.0	False		,,,				2504	0.0				p.T571M		Atlas-SNP	.											.	PDE9A	69	.	0			c.C1712T						PASS	.	C	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	23,4381	29.9+/-59.1	0,23,2179	68	55	59		1532,1331,1328,1553,1409,1091,1091,1454,1232,1061,1310,1406,1091,1061,1511,1589,1634,1091,1091,1712	1.4	0	21	dbSNP_134	59	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	PDE9A	NM_001001567.1,NM_001001568.1,NM_001001569.1,NM_001001570.1,NM_001001571.1,NM_001001572.1,NM_001001573.1,NM_001001574.1,NM_001001575.1,NM_001001576.1,NM_001001577.1,NM_001001578.1,NM_001001579.1,NM_001001580.1,NM_001001581.1,NM_001001582.1,NM_001001583.1,NM_001001584.2,NM_001001585.1,NM_002606.2	81,81,81,81,81,81,81,81,81,81,81,81,81,81,81,81,81,81,81,81	0,23,6479	TT,TC,CC		0.0,0.5223,0.1769	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	511/534,444/467,443/466,518/541,470/493,364/387,364/387,485/508,411/434,354/377,437/460,469/492,364/387,354/377,504/527,530/553,545/568,364/387,364/387,571/594	44192574	23,12981	2202	4300	6502	SO:0001583	missense	5152	exon19			GCTTGACGTCTGG	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.1712C>T	21.37:g.44192574C>T	ENSP00000291539:p.Thr571Met	100	0	0		62	38	0.612903	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	37	CCDS13690.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	8.057	0.767372	0.15983	0.005223	0.0	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	0.69926	-0.4;-0.39;-0.42;-0.41;-0.44;-0.4;-0.4;-0.43;-0.41;-0.42;-0.4;-0.4;-0.39;-0.4	3.3	1.42	0.22433	.	2.420000	0.01711	N	0.027724	T	0.45756	0.1358	L	0.32530	0.975	0.09310	N	1	P;B;B;P;P;P;B;B;B;B;B;P;B;B;B	0.45044	0.588;0.069;0.145;0.759;0.849;0.759;0.145;0.069;0.145;0.145;0.301;0.849;0.301;0.145;0.308	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.36244	0.216;0.028;0.04;0.176;0.176;0.115;0.093;0.013;0.079;0.049;0.124;0.176;0.22;0.102;0.048	T	0.48055	-0.9068	10	0.48119	T	0.1	.	6.1538	0.20326	0.0:0.7003:0.1902:0.1095	.	504;485;470;545;530;463;511;354;411;437;443;469;518;444;571	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	M	511;443;571;518;504;470;485;545;469;530;437;411;443;444	ENSP00000335242:T511M;ENSP00000441899:T443M;ENSP00000291539:T571M;ENSP00000369685:T518M;ENSP00000381287:T504M;ENSP00000381289:T470M;ENSP00000381291:T485M;ENSP00000328699:T545M;ENSP00000335365:T469M;ENSP00000381281:T530M;ENSP00000381285:T437M;ENSP00000381283:T411M;ENSP00000344730:T443M;ENSP00000381280:T444M	ENSP00000291539:T571M	T	+	2	0	PDE9A	43065643	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.028000	0.13644	0.392000	0.25172	-0.234000	0.12200	ACG	C|0.999;T|0.001	0.001	strong		0.527	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1			T	44192574	C	T	44192574	3	4	22	1	0	0	0	0	1	0	0	0	11664	536	19	1	1866	1	PDE9A	21	44192574	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	13462	44192574	3937321	4284	7185											
WDR4	10785	hgsc.bcm.edu	37	chr21	44273691	44273691	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtctcacctgccactggtcGcccacaggcctgtagagcac	8	7	10	16	1	1	1	1	0	1	1	3	1	1	1	4	2	2	2	4	2	1	1	rs146863277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:44273691G>A	ENST00000398208.2	-	9	1022	c.963C>T	c.(961-963)ggC>ggT	p.G321G	WDR4_ENST00000330317.2_Silent_p.G321G|WDR4_ENST00000492742.1_5'UTR	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)		GCCACTGGTCGCCCACAGGCC	0.622													G|||	23	0.00459265	0.0151	0.0029	5008	,	,		15951	0.0		0.001	False		,,,				2504	0.0				p.G321G		Atlas-SNP	.											.	WDR4	35	.	0			c.C963T						PASS	.	G	,	65,4339	56.2+/-92.4	1,63,2138	26	26	26		963,963	-6	0	21	dbSNP_134	26	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	WDR4	NM_018669.4,NM_033661.3	,	1,66,6435	AA,AG,GG		0.0349,1.4759,0.5229	,	321/413,321/413	44273691	68,12936	2202	4300	6502	SO:0001819	synonymous_variant	10785	exon9			CTGGTCGCCCACA	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.963C>T	21.37:g.44273691G>A		61	0	0		69	43	0.623188	NM_018669		Silent	SNP	ENST00000398208.2	37	CCDS13691.1																																																																																			G|0.995;A|0.005	0.005	strong		0.622	WDR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195479.1			A	44273691	G	A	44273691	2	1	22	1	0	0	0	0	0	0	0	1	17308	1074	38	1		1	WDR4	21	44273691	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	81117	44273691	3856204	4285	7186											
CSTB	1476	hgsc.bcm.edu	37	chr21	45196136	45196136	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccggctgcgtggcggagggCgccccgcacatcatcttggc	4	6	16	15	5	2	0	1	0	1	0	2	1	2	1	3	5	1	2	3	5	0	1	rs4533	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45196136C>A	ENST00000291568.5	-	1	190	c.15G>T	c.(13-15)gcG>gcT	p.A5A		NM_000100.3	NP_000091.1	P04080	CYTB_HUMAN	cystatin B (stefin B)	5					adult locomotory behavior (GO:0008344)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|endopeptidase inhibitor activity (GO:0004866)|poly(A) RNA binding (GO:0044822)|protease binding (GO:0002020)			lung(1)|prostate(1)	2				STAD - Stomach adenocarcinoma(101;0.168)		TGGCGGAGGGCGCCCCGCACA	0.746													C|||	86	0.0171725	0.062	0.0058	5008	,	,		9141	0.0		0.0	False		,,,				2504	0.0				p.A5A	Esophageal Squamous(58;831 1093 17019 29789 35147)	Atlas-SNP	.											.	CSTB	3	.	0			c.G15T						PASS	.	C		142,3048		0,142,1453	4	7	6		15	1.4	0	21	dbSNP_52	6	2,5900		0,2,2949	no	coding-synonymous	CSTB	NM_000100.2		0,144,4402	AA,AC,CC		0.0339,4.4514,1.5838		5/99	45196136	144,8948	1595	2951	4546	SO:0001819	synonymous_variant	1476	exon1			GGAGGGCGCCCCG	L03558	CCDS13701.1	21q22.3	2014-09-17			ENSG00000160213	ENSG00000160213			2482	protein-coding gene	gene with protein product		601145		EPM1, STFB		8596935	Standard	NM_000100		Approved	CST6, PME	uc002zdr.4	P04080	OTTHUMG00000086886	ENST00000291568.5:c.15G>T	21.37:g.45196136C>A		13	0	0		28	16	0.571429	NM_000100		Silent	SNP	ENST00000291568.5	37	CCDS13701.1																																																																																			C|0.988;A|0.012	0.012	strong		0.746	CSTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195689.1	NM_000100		A	45196136	C	A	45196136	2	1	22	1	0	0	0	0	0	0	0	1	3984	755	27	4		4	CSTB	21	45196136	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	922445	45196136	2933759	4286	7187											
TRAPPC10	7109	hgsc.bcm.edu	37	chr21	45518396	45518396	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaatctgatgagcatttttcGacaaagcttatgtatgaagg	13	13	10	5	1	1	3	0	3	1	0	2	5	1	3	0	1	2	3	0	1	5	4	rs115989144	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45518396G>A	ENST00000291574.4	+	21	3502	c.3327G>A	c.(3325-3327)tcG>tcA	p.S1109S		NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	1109					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						AGCATTTTTCGACAAAGCTTA	0.527													G|||	12	0.00239617	0.0091	0.0	5008	,	,		20869	0.0		0.0	False		,,,				2504	0.0				p.S1109S		Atlas-SNP	.											TRAPPC10,colon,carcinoma,+1,1	TRAPPC10	109	1	0			c.G3327A						PASS	.	G		35,4371	40.8+/-73.8	0,35,2168	103	103	103		3327	-11.1	0	21	dbSNP_132	103	0,8600		0,0,4300	no	coding-synonymous	TRAPPC10	NM_003274.4		0,35,6468	AA,AG,GG		0.0,0.7944,0.2691		1109/1260	45518396	35,12971	2203	4300	6503	SO:0001819	synonymous_variant	7109	exon21			TTTTTCGACAAAG	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.3327G>A	21.37:g.45518396G>A		62	0	0		68	39	0.573529	NM_003274	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Silent	SNP	ENST00000291574.4	37	CCDS13704.1																																																																																			G|0.996;A|0.004	0.004	strong		0.527	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274		A	45518396	G	A	45518396	2	1	22	1	0	0	0	0	0	0	0	1	16472	1045	37	1		1	TRAPPC10	21	45518396	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	322260	45518396	2611499	4287	7188											
PWP2	5822	hgsc.bcm.edu	37	chr21	45538685	45538685	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctcagtggccatcaatagctCgggggactggattgcttttg	7	12	13	9	1	2	0	2	0	0	0	3	2	2	2	1	4	2	2	1	4	2	4	rs150440839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45538685C>T	ENST00000291576.7	+	9	1149	c.1022C>T	c.(1021-1023)tCg>tTg	p.S341L		NM_005049.2	NP_005040.2	Q15269	PWP2_HUMAN	PWP2 periodic tryptophan protein homolog (yeast)	341					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)		ATCAATAGCTCGGGGGACTGG	0.607													C|||	13	0.00259585	0.0098	0.0	5008	,	,		16887	0.0		0.0	False		,,,				2504	0.0				p.S341L		Atlas-SNP	.											.	PWP2	64	.	0			c.C1022T						PASS	.	C	LEU/SER	38,4368	43.1+/-76.7	0,38,2165	127	99	108		1022	5.1	0.9	21	dbSNP_134	108	0,8600		0,0,4300	yes	missense	PWP2	NM_005049.2	145	0,38,6465	TT,TC,CC		0.0,0.8625,0.2922	benign	341/920	45538685	38,12968	2203	4300	6503	SO:0001583	missense	5822	exon9			ATAGCTCGGGGGA		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.1022C>T	21.37:g.45538685C>T	ENSP00000291576:p.Ser341Leu	176	0	0		188	95	0.505319	NM_005049	B2RAG8|Q96A77	Missense_Mutation	SNP	ENST00000291576.7	37	CCDS33579.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	19.96	3.924314	0.73213	0.008625	0.0	ENSG00000241945	ENST00000291576	T	0.44881	0.91	5.05	5.05	0.67936	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (2);WD40-repeat-containing domain (1);	0.462069	0.24755	N	0.035863	T	0.22205	0.0535	L	0.59436	1.845	0.41576	D	0.988714	P	0.39352	0.669	B	0.27887	0.084	T	0.32214	-0.9915	10	0.49607	T	0.09	-12.9707	16.9482	0.86236	0.0:1.0:0.0:0.0	.	341	Q15269	PWP2_HUMAN	L	341	ENSP00000291576:S341L	ENSP00000291576:S341L	S	+	2	0	PWP2	44363113	1.000000	0.71417	0.933000	0.37362	0.909000	0.53808	5.017000	0.64047	2.501000	0.84356	0.555000	0.69702	TCG	C|0.996;T|0.004	0.004	strong		0.607	PWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195736.3	NM_005049		T	45538685	C	T	45538685	3	4	22	1	0	0	0	0	1	0	0	0	12859	893	31	1	1056	1	PWP2	21	45538685	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	20289	45538685	2591210	4288	7189											
AIRE	326	hgsc.bcm.edu	37	chr21	45712983	45712983	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagcacctgccggctccgccTtctgcagccccgctgccagg	5	6	11	19	3	1	0	0	0	1	0	2	0	2	0	7	2	5	4	7	2	1	1	rs61737072	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45712983T>C	ENST00000291582.5	+	10	1330	c.1203T>C	c.(1201-1203)ccT>ccC	p.P401P	AIRE_ENST00000355347.4_Silent_p.P194P|AIRE_ENST00000329347.4_Intron	NM_000383.3	NP_000374.1	O43918	AIRE_HUMAN	autoimmune regulator	401					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)		CGGCTCCGCCTTCTGCAGCCC	0.677									Autoimmune PolyEndocrinopathy Candidiasis Ectodermal Dystrophy				T|||	232	0.0463259	0.1649	0.0202	5008	,	,		10975	0.0		0.0	False		,,,				2504	0.0				p.P401P		Atlas-SNP	.											.	AIRE	61	.	0			c.T1203C						PASS	.	T	,	665,3717		60,545,1586	22	26	24		1203,612	-2.4	0	21	dbSNP_129	24	2,8586		0,2,4292	no	coding-synonymous,coding-synonymous	AIRE	NM_000383.2,NM_000658.2	,	60,547,5878	CC,CT,TT		0.0233,15.1757,5.1426	,	401/546,204/349	45712983	667,12303	2191	4294	6485	SO:0001819	synonymous_variant	326	exon10	Familial Cancer Database	APECED	TCCGCCTTCTGCA	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.1203T>C	21.37:g.45712983T>C		32	0	0		46	20	0.434783	NM_000383	B2RP50|O43922|O43932|O75745	Silent	SNP	ENST00000291582.5	37	CCDS13706.1																																																																																			T|0.951;C|0.049	0.049	strong		0.677	AIRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195842.2			C	45712983	T	C	45712983	2	2	22	1	0	0	0	0	0	0	0	1	437	1596	56	3		3	AIRE	21	45712983	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	174298	45712983	2416912	4289	7190											
C21orf2	755	hgsc.bcm.edu	37	chr21	45750713	45750713	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccgccactcaccctgcccCtgtggctgctcgaggcatcc	4	7	10	20	2	1	0	1	0	0	0	3	1	2	0	6	2	2	3	6	2	0	0	rs62000360	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45750713C>T	ENST00000339818.4	-	6	842	c.635G>A	c.(634-636)aGg>aAg	p.R212K	C21orf2_ENST00000325223.7_Missense_Mutation_p.R211K|AP001062.8_ENST00000422357.1_RNA|C21orf2_ENST00000397956.3_Missense_Mutation_p.R211K|AP001062.7_ENST00000448927.1_RNA|C21orf2_ENST00000496321.1_5'UTR	NM_001271440.1|NM_004928.2	NP_001258369.1|NP_004919.1	O43822	CU002_HUMAN	chromosome 21 open reading frame 2	212					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)		CACCCTGCCCCTGTGGCTGCT	0.697													C|||	126	0.0251597	0.0855	0.0159	5008	,	,		13869	0.0		0.002	False		,,,				2504	0.0				p.R212K		Atlas-SNP	.											.	C21orf2	10	.	0			c.G635A						PASS	.	C	LYS/ARG	228,4128		4,220,1954	11	13	12		635	-5.5	0	21	dbSNP_129	12	0,8504		0,0,4252	yes	missense	C21orf2	NM_004928.2	26	4,220,6206	TT,TC,CC		0.0,5.2342,1.7729	benign	212/257	45750713	228,12632	2178	4252	6430	SO:0001583	missense	755	exon6			CTGCCCCTGTGGC	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.635G>A	21.37:g.45750713C>T	ENSP00000344566:p.Arg212Lys	157	0	0		155	80	0.516129	NM_004928	A8MPS9|O14993|Q8N5X6|Q99837|Q99838	Missense_Mutation	SNP	ENST00000339818.4	37	CCDS13709.1	39	0.017857142857142856	34	0.06910569105691057	5	0.013812154696132596	0	0.0	0	0.0	C	1.956	-0.440014	0.04636	0.052342	0.0	ENSG00000160226	ENST00000339818;ENST00000397956;ENST00000325223	T;T;T	0.30448	1.65;1.53;1.61	4.25	-5.48	0.02592	.	0.521247	0.22438	N	0.060048	T	0.00608	0.0020	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	0.01281	0.0;0.0;0.0;0.0	T	0.17410	-1.0370	10	0.02654	T	1	-26.1772	5.5943	0.17319	0.0:0.3756:0.2867:0.3377	.	211;211;212;171	G5E952;Q8N5X6;O43822;O43822-2	.;.;CU002_HUMAN;.	K	212;211;211	ENSP00000344566:R212K;ENSP00000381047:R211K;ENSP00000317302:R211K	ENSP00000317302:R211K	R	-	2	0	C21orf2	44575141	0.000000	0.05858	0.029000	0.17559	0.002000	0.02628	-1.437000	0.02419	-1.158000	0.02811	-0.768000	0.03414	AGG	C|0.976;T|0.024	0.024	strong		0.697	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195799.1	NM_004928		T	45750713	C	T	45750713	3	4	22	1	0	0	0	0	1	0	0	0	2125	681	24	2	143	2	C21orf2	21	45750713	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	37730	45750713	2379182	4290	7191											
C21orf2	755	hgsc.bcm.edu	37	chr21	45750725	45750725	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccctgcccctgtggctgctcGaggcatccctggctgagagg	4	8	14	15	1	0	1	0	1	0	1	2	3	1	1	4	4	2	4	4	4	0	0	rs148023924	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45750725G>A	ENST00000339818.4	-	6	830	c.623C>T	c.(622-624)tCg>tTg	p.S208L	C21orf2_ENST00000325223.7_Missense_Mutation_p.S207L|AP001062.8_ENST00000422357.1_RNA|C21orf2_ENST00000397956.3_Missense_Mutation_p.S207L|AP001062.7_ENST00000448927.1_RNA|C21orf2_ENST00000496321.1_5'UTR	NM_001271440.1|NM_004928.2	NP_001258369.1|NP_004919.1	O43822	CU002_HUMAN	chromosome 21 open reading frame 2	208					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)		GTGGCTGCTCGAGGCATCCCT	0.682													G|||	12	0.00239617	0.0068	0.0	5008	,	,		13283	0.0		0.001	False		,,,				2504	0.002				p.S208L		Atlas-SNP	.											.	C21orf2	10	.	0			c.C623T						PASS	.	G	LEU/SER	23,4355		0,23,2166	14	15	15		623	-5.4	0	21	dbSNP_134	15	0,8590		0,0,4295	yes	missense	C21orf2	NM_004928.2	145	0,23,6461	AA,AG,GG		0.0,0.5254,0.1774	benign	208/257	45750725	23,12945	2189	4295	6484	SO:0001583	missense	755	exon6			CTGCTCGAGGCAT	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.623C>T	21.37:g.45750725G>A	ENSP00000344566:p.Ser208Leu	166	0	0		160	79	0.49375	NM_004928	A8MPS9|O14993|Q8N5X6|Q99837|Q99838	Missense_Mutation	SNP	ENST00000339818.4	37	CCDS13709.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	9.377	1.072041	0.20147	0.005254	0.0	ENSG00000160226	ENST00000339818;ENST00000397956;ENST00000325223	T;T;T	0.35973	1.61;1.28;1.61	4.25	-5.4	0.02656	.	2.084300	0.02418	N	0.082253	T	0.08223	0.0205	N	0.02011	-0.69	0.09310	N	1	B;B;B;B	0.06786	0.001;0.001;0.0;0.001	B;B;B;B	0.04013	0.001;0.0;0.0;0.001	T	0.09292	-1.0681	10	0.28530	T	0.3	-0.0966	1.5726	0.02618	0.5044:0.1437:0.2077:0.1442	.	207;207;208;167	G5E952;Q8N5X6;O43822;O43822-2	.;.;CU002_HUMAN;.	L	208;207;207	ENSP00000344566:S208L;ENSP00000381047:S207L;ENSP00000317302:S207L	ENSP00000317302:S207L	S	-	2	0	C21orf2	44575153	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.798000	0.04565	-0.617000	0.05664	-0.137000	0.14449	TCG	G|0.997;A|0.003	0.003	strong		0.682	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195799.1	NM_004928		A	45750725	G	A	45750725	3	1	22	1	0	0	0	0	1	0	0	0	2125	1059	37	1	155	1	C21orf2	21	45750725	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	12	45750725	2379170	4291	7192											
C21orf2	755	hgsc.bcm.edu	37	chr21	45755646	45755646	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcaggagcgaggtacctgagCgtgatcacctccaggctggg	8	6	16	11	2	1	2	1	2	0	0	2	4	2	3	3	4	3	3	3	4	1	1	rs146104157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45755646C>T	ENST00000339818.4	-	3	345	c.138G>A	c.(136-138)acG>acA	p.T46T	C21orf2_ENST00000325223.7_Silent_p.T46T|C21orf2_ENST00000397956.3_Silent_p.T46T|AP001062.7_ENST00000448927.1_RNA|C21orf2_ENST00000496321.1_5'UTR	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													C|||	13	0.00259585	0.0091	0.0	5008	,	,		20080	0.0		0.0	False		,,,				2504	0.001				p.T46T		Atlas-SNP	.											.	C21orf2	10	.	0			c.G138A						PASS	.	C		35,4369		0,35,2167	65	42	50		138	-3.1	1	21	dbSNP_134	50	1,8587		0,1,4293	no	coding-synonymous	C21orf2	NM_004928.2		0,36,6460	TT,TC,CC		0.0116,0.7947,0.2771		46/257	45755646	36,12956	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>A	21.37:g.45755646C>T		140	0	0		178	79	0.44382	NM_004928	A8MPS9|O14993|Q8N5X6|Q99837|Q99838	Silent	SNP	ENST00000339818.4	37	CCDS13709.1																																																																																			C|0.997;T|0.003	0.003	strong		0.607	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195799.1	NM_004928		T	45755646	C	T	45755646	2	4	22	1	0	0	0	0	0	0	0	1	2125	755	27	1		1	C21orf2	21	45755646	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4921	45755646	2374249	4292	7193											
TRPM2	7226	hgsc.bcm.edu	37	chr21	45786709	45786709	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccagcactgggggctggacGtccccaatctcttgatctcg	6	9	11	15	2	2	1	0	1	2	0	5	2	3	2	3	3	1	2	3	3	1	1	rs45544142	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45786709G>A	ENST00000397928.1	+	4	941	c.496G>A	c.(496-498)Gtc>Atc	p.V166I	TRPM2_ENST00000300482.5_Missense_Mutation_p.V166I|TRPM2_ENST00000397932.2_Missense_Mutation_p.V166I|TRPM2_ENST00000300481.9_Missense_Mutation_p.V166I	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	166			V -> I (in dbSNP:rs45544142). {ECO:0000269|Ref.6}.		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						GGGGCTGGACGTCCCCAATCT	0.612													G|||	148	0.0295527	0.1044	0.0101	5008	,	,		16186	0.003		0.0	False		,,,				2504	0.0				p.V166I		Atlas-SNP	.											.	TRPM2	196	.	0			c.G496A						PASS	.	G	ILE/VAL	454,3952	216.4+/-235.1	24,406,1773	61	57	58		496	2.3	0.1	21	dbSNP_127	58	6,8594	4.3+/-15.6	0,6,4294	yes	missense	TRPM2	NM_003307.3	29	24,412,6067	AA,AG,GG		0.0698,10.3041,3.5368	benign	166/1504	45786709	460,12546	2203	4300	6503	SO:0001583	missense	7226	exon4			CTGGACGTCCCCA	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.496G>A	21.37:g.45786709G>A	ENSP00000381023:p.Val166Ile	51	0	0		65	33	0.507692	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	37	CCDS13710.1	60	0.027472527472527472	55	0.11178861788617886	3	0.008287292817679558	2	0.0034965034965034965	0	0.0	G	5.471	0.271913	0.10349	0.103041	6.98E-4	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932	T;T;T;T	0.55930	0.49;0.49;0.49;0.49	4.12	2.28	0.28536	.	0.459727	0.21621	U	0.071660	T	0.00754	0.0025	L	0.39397	1.21	0.09310	N	1	B;B	0.23377	0.084;0.039	B;B	0.17433	0.018;0.007	T	0.02821	-1.1106	10	0.22109	T	0.4	-28.3824	5.9165	0.19057	0.2468:0.1389:0.6143:0.0	rs45544142;rs61747092	166;166	E9PGK7;O94759	.;TRPM2_HUMAN	I	166	ENSP00000300482:V166I;ENSP00000381023:V166I;ENSP00000300481:V166I;ENSP00000381026:V166I	ENSP00000300481:V166I	V	+	1	0	TRPM2	44611137	0.000000	0.05858	0.110000	0.21437	0.394000	0.30568	0.164000	0.16542	0.314000	0.23086	0.297000	0.19635	GTC	G|0.962;A|0.038	0.038	strong		0.612	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307		A	45786709	G	A	45786709	3	1	22	1	0	0	0	0	1	0	0	0	16601	1145	40	1	510	1	TRPM2	21	45786709	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	31063	45786709	2343186	4293	7194											
TRPM2	7226	hgsc.bcm.edu	37	chr21	45799018	45799018	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatccagcagaaactgagcGtgttcttccaggagatgttt	10	12	11	8	1	1	4	0	2	1	2	3	5	3	4	2	1	3	3	2	1	1	3	rs45485992	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45799018G>A	ENST00000397928.1	+	8	1598	c.1153G>A	c.(1153-1155)Gtg>Atg	p.V385M	TRPM2_ENST00000300482.5_Missense_Mutation_p.V385M|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000397932.2_Missense_Mutation_p.V385M|TRPM2_ENST00000300481.9_Missense_Mutation_p.V385M	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	385			V -> M (in dbSNP:rs45485992). {ECO:0000269|Ref.6}.		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						GAAACTGAGCGTGTTCTTCCA	0.587													G|||	14	0.00279553	0.0106	0.0	5008	,	,		22548	0.0		0.0	False		,,,				2504	0.0				p.V385M		Atlas-SNP	.											.	TRPM2	196	.	0			c.G1153A						PASS	.	G	MET/VAL	53,4353	54.2+/-90.2	2,49,2152	127	92	104		1153	-7.7	0	21	dbSNP_127	104	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TRPM2	NM_003307.3	21	2,50,6451	AA,AG,GG		0.0116,1.2029,0.4152	benign	385/1504	45799018	54,12952	2203	4300	6503	SO:0001583	missense	7226	exon8			CTGAGCGTGTTCT	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.1153G>A	21.37:g.45799018G>A	ENSP00000381023:p.Val385Met	75	0	0		78	38	0.487179	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	37	CCDS13710.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	3.161	-0.172171	0.06421	0.012029	1.16E-4	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932	T;T;T;T	0.36699	1.24;1.24;1.24;1.24	3.84	-7.69	0.01263	.	1.065880	0.07211	N	0.859284	T	0.10380	0.0254	L	0.36672	1.1	0.09310	N	1	B;B	0.25743	0.133;0.133	B;B	0.13407	0.009;0.003	T	0.09037	-1.0693	10	0.45353	T	0.12	-4.1705	3.8491	0.08948	0.4825:0.2381:0.193:0.0864	rs45485992;rs61737083	385;385	E9PGK7;O94759	.;TRPM2_HUMAN	M	385	ENSP00000300482:V385M;ENSP00000381023:V385M;ENSP00000300481:V385M;ENSP00000381026:V385M	ENSP00000300481:V385M	V	+	1	0	TRPM2	44623446	0.000000	0.05858	0.002000	0.10522	0.332000	0.28634	-0.968000	0.03817	-2.737000	0.00381	-1.087000	0.02190	GTG	G|0.994;A|0.006	0.006	strong		0.587	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307		A	45799018	G	A	45799018	3	1	22	1	0	0	0	0	1	0	0	0	16601	1145	40	1	1183	1	TRPM2	21	45799018	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	12309	45799018	2330877	4294	7195											
TRPM2	7226	hgsc.bcm.edu	37	chr21	45825818	45825818	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgacgctgtaccccgggcgCgtcatcctctctctggactt	4	10	11	16	5	3	0	1	0	2	0	5	2	4	1	3	2	1	2	3	2	1	2	rs17004645	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45825818C>T	ENST00000397928.1	+	18	3133	c.2688C>T	c.(2686-2688)cgC>cgT	p.R896R	TRPM2_ENST00000300482.5_Silent_p.R896R|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000397932.2_Silent_p.R896R|TRPM2_ENST00000300481.9_Silent_p.R876R	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	896					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						ACCCCGGGCGCGTCATCCTCT	0.612													t|||	18	0.00359425	0.0136	0.0	5008	,	,		17476	0.0		0.0	False		,,,				2504	0.0				p.R896R		Atlas-SNP	.											TRPM2,NS,carcinoma,+1,1	TRPM2	196	1	0			c.C2688T						PASS	.	T		64,4342	814.1+/-416.2	3,58,2142	87	90	89		2688	1.1	0.8	21	dbSNP_123	89	0,8598		0,0,4299	no	coding-synonymous	TRPM2	NM_003307.3		3,58,6441	TT,TC,CC		0.0,1.4526,0.4922		896/1504	45825818	64,12940	2203	4299	6502	SO:0001819	synonymous_variant	7226	exon18			CGGGCGCGTCATC	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.2688C>T	21.37:g.45825818C>T		55	0	0		46	21	0.456522	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Silent	SNP	ENST00000397928.1	37	CCDS13710.1																																																																																			C|0.993;T|0.007	0.007	strong		0.612	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307		T	45825818	C	T	45825818	2	4	22	1	0	0	0	0	0	0	0	1	16601	755	27	1		1	TRPM2	21	45825818	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	26800	45825818	2304077	4295	7196											
TRPM2	7226	hgsc.bcm.edu	37	chr21	45856963	45856963	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtggaggcggaacgaggaTggagccatctgcaggaagag	12	4	19	6	2	1	1	0	0	1	1	1	7	1	6	1	7	3	1	1	7	2	0	rs11910471	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45856963T>C	ENST00000397928.1	+	29	4525	c.4080T>C	c.(4078-4080)gaT>gaC	p.D1360D	snoZ6_ENST00000583496.1_RNA|TRPM2_ENST00000300482.5_Silent_p.D1360D|snoZ6_ENST00000581669.1_RNA|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000397932.2_Silent_p.D1410D|TRPM2_ENST00000300481.9_Silent_p.D1306D	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	1360	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				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						GGAACGAGGATGGAGCCATCT	0.687													C|||	432	0.086262	0.3109	0.0288	5008	,	,		14340	0.0		0.001	False		,,,				2504	0.0				p.D1360D		Atlas-SNP	.											.	TRPM2	196	.	0			c.T4080C						PASS	.	C		892,2978		106,680,1149	92	66	75		4080	-6.6	0.2	21	dbSNP_120	75	8,7486		0,8,3739	no	coding-synonymous	TRPM2	NM_003307.3		106,688,4888	CC,CT,TT		0.1068,23.0491,7.9197		1360/1504	45856963	900,10464	1935	3747	5682	SO:0001819	synonymous_variant	7226	exon29			CGAGGATGGAGCC	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.4080T>C	21.37:g.45856963T>C		45	0	0		54	31	0.574074	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Silent	SNP	ENST00000397928.1	37	CCDS13710.1																																																																																			T|0.901;C|0.099	0.099	strong		0.687	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307		C	45856963	T	C	45856963	2	2	22	1	0	0	0	0	0	0	0	1	16601	1461	51	3		3	TRPM2	21	45856963	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	31145	45856963	2272932	4296	7197											
C21orf29	54084	hgsc.bcm.edu	37	chr21	45929192	45929192	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggacttgcatctccacatcGtagctgtgactgtttgccac	7	13	9	12	1	1	1	0	1	1	0	3	2	1	2	2	1	3	4	2	1	1	3	rs115847549	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45929192G>A	ENST00000323084.4	-	10	1709	c.1644C>T	c.(1642-1644)taC>taT	p.Y548Y	TSPEAR_ENST00000397916.1_Silent_p.Y480Y|TSPEAR-AS1_ENST00000451035.1_RNA|TSPEAR-AS1_ENST00000430181.1_RNA	NM_001272037.1|NM_144991.2	NP_001258966.1|NP_659428.2	Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	548					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						TCTCCACATCGTAGCTGTGAC	0.537													G|||	41	0.0081869	0.0287	0.0043	5008	,	,		13812	0.0		0.0	False		,,,				2504	0.0				p.Y548Y		Atlas-SNP	.											.	TSPEAR	110	.	0			c.C1644T						PASS	.	G		138,4268	100.7+/-139.4	6,126,2071	202	127	152		1644	-1	0.9	21	dbSNP_132	152	19,8581	13.3+/-46.6	0,19,4281	no	coding-synonymous	TSPEAR	NM_144991.2		6,145,6352	AA,AG,GG		0.2209,3.1321,1.2071		548/670	45929192	157,12849	2203	4300	6503	SO:0001819	synonymous_variant	54084	exon10			CACATCGTAGCTG	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.1644C>T	21.37:g.45929192G>A		133	0	0		184	97	0.527174	NM_144991		Silent	SNP	ENST00000323084.4	37	CCDS13712.1																																																																																			G|0.988;A|0.012	0.012	strong		0.537	TSPEAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098761.1	NM_144991		A	45929192	G	A	45929192	2	1	22	1	0	0	0	0	0	0	0	1	2126	1140	40	1		1	C21orf29	21	45929192	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	72229	45929192	2200703	4297	7198											
C21orf29	54084	hgsc.bcm.edu	37	chr21	45953576	45953576	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgggtacctacatgtccacCgggaggccgcagtccgtggt	6	8	15	12	3	0	0	0	0	0	0	2	1	2	1	5	4	2	2	5	4	2	2	rs148713881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45953576C>T	ENST00000323084.4	-	3	599	c.534G>A	c.(532-534)ccG>ccA	p.P178P	TSPEAR_ENST00000397916.1_Silent_p.P110P	NM_001272037.1|NM_144991.2	NP_001258966.1|NP_659428.2	Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	178	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						ACATGTCCACCGGGAGGCCGC	0.677													C|||	31	0.0061901	0.0227	0.0014	5008	,	,		13631	0.0		0.0	False		,,,				2504	0.0				p.P178P		Atlas-SNP	.											TSPEAR,caecum,carcinoma,0,1	TSPEAR	110	1	0			c.G534A						PASS	.	C		104,4254		5,94,2080	19	19	19		534	-0.2	0.7	21	dbSNP_134	19	0,8526		0,0,4263	no	coding-synonymous	TSPEAR	NM_144991.2		5,94,6343	TT,TC,CC		0.0,2.3864,0.8072		178/670	45953576	104,12780	2179	4263	6442	SO:0001819	synonymous_variant	54084	exon3			GTCCACCGGGAGG	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.534G>A	21.37:g.45953576C>T		85	0	0		101	44	0.435644	NM_144991		Silent	SNP	ENST00000323084.4	37	CCDS13712.1																																																																																			C|0.990;T|0.010	0.010	strong		0.677	TSPEAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098761.1	NM_144991		T	45953576	C	T	45953576	2	4	22	1	0	0	0	0	0	0	0	1	2126	639	23	1		1	C21orf29	21	45953576	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	24384	45953576	2176319	4298	7199											
KRTAP10-1	386677	hgsc.bcm.edu	37	chr21	45959279	45959279	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcaggaggaggcaggggcaCagcaggaggagacaggcata	13	1	20	7	0	0	1	0	0	0	1	0	5	0	4	0	9	1	5	0	9	1	1	rs28644341	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45959279C>T	ENST00000400375.1	-	1	799	c.755G>A	c.(754-756)tGt>tAt	p.C252Y	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198691.2	NP_941964.2	P60331	KR101_HUMAN	keratin associated protein 10-1	252	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						GGCAGGGGCACAGCAGGAGGA	0.726													C|||	48	0.00958466	0.0356	0.0014	5008	,	,		14804	0.0		0.0	False		,,,				2504	0.0				p.C252Y		Atlas-SNP	.											.	KRTAP10-1	34	.	0			c.G755A						PASS	.	C	TYR/CYS,	119,4287	82.4+/-120.9	6,107,2090	43	50	48		755,	2	0	21	dbSNP_125	48	0,8600		0,0,4300	no	missense,intron	TSPEAR,KRTAP10-1	NM_198691.2,NM_144991.2	194,	6,107,6390	TT,TC,CC		0.0,2.7009,0.915	probably-damaging,	252/283,	45959279	119,12887	2203	4300	6503	SO:0001583	missense	386677	exon1			GGGGCACAGCAGG	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.755G>A	21.37:g.45959279C>T	ENSP00000383226:p.Cys252Tyr	89	0	0		81	42	0.518519	NM_198691	Q0VAR0|Q0VAR1	Missense_Mutation	SNP	ENST00000400375.1	37	CCDS42954.1	18	0.008241758241758242	17	0.034552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	c	0.012	-1.682141	0.00745	0.027009	0.0	ENSG00000215455	ENST00000400375	T	0.02345	4.33	2.93	2.0	0.26442	.	.	.	.	.	T	0.05090	0.0136	M	0.90922	3.16	0.09310	N	1	D	0.59357	0.985	D	0.63488	0.915	T	0.02313	-1.1178	9	0.46703	T	0.11	.	8.9015	0.35497	0.0:0.5471:0.4529:0.0	rs28644341	252	P60331	KR101_HUMAN	Y	252	ENSP00000383226:C252Y	ENSP00000383226:C252Y	C	-	2	0	KRTAP10-1	44783707	0.050000	0.20438	0.003000	0.11579	0.018000	0.09664	0.887000	0.28254	0.532000	0.28657	-0.499000	0.04595	TGT	C|0.991;T|0.009	0.009	strong		0.726	KRTAP10-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128030.1			T	45959279	C	T	45959279	3	4	22	1	0	0	0	0	1	0	0	0	8514	478	17	2	97	2	KRTAP10-1	21	45959279	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	5703	45959279	2170616	4299	7200											
KRTAP10-3	386682	hgsc.bcm.edu	37	chr21	45978128	45978128	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggcggcagaggagggacacGgaggaggagggtctgcagca	10	2	22	7	2	1	1	0	0	1	1	1	6	1	6	0	8	2	3	0	8	0	0	rs186210430	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45978128G>A	ENST00000391620.1	-	1	515	c.471C>T	c.(469-471)tcC>tcT	p.S157S	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198696.2	NP_941969.2	P60369	KR103_HUMAN	keratin associated protein 10-3	157	18 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				kidney(1)|lung(4)|prostate(1)|skin(1)	7						GGAGGGACACGGAGGAGGAGG	0.692													G|||	70	0.0139776	0.0484	0.0086	5008	,	,		16657	0.0		0.0	False		,,,				2504	0.0				p.S157S		Atlas-SNP	.											.	KRTAP10-3	17	.	0			c.C471T						PASS	.	G	,	263,4143	147.3+/-181.8	4,255,1944	90	98	95		,471	-5.3	0	21		95	0,8600		0,0,4300	no	intron,coding-synonymous	TSPEAR,KRTAP10-3	NM_144991.2,NM_198696.2	,	4,255,6244	AA,AG,GG		0.0,5.9691,2.0221	,	,157/222	45978128	263,12743	2203	4300	6503	SO:0001819	synonymous_variant	386682	exon1			GGACACGGAGGAG	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.471C>T	21.37:g.45978128G>A		149	0	0		189	99	0.52381	NM_198696	A3KN67|Q70LJ4	Silent	SNP	ENST00000391620.1	37	CCDS42956.1																																																																																			G|0.992;A|0.008	0.008	strong		0.692	KRTAP10-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128031.1			A	45978128	G	A	45978128	2	1	22	1	0	0	0	0	0	0	0	1	8519	1103	39	1		1	KRTAP10-3	21	45978128	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	18849	45978128	2151767	4300	7201											
KRTAP10-4	386672	hgsc.bcm.edu	37	chr21	45993990	45993990	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtctgctgcaagactgtcTgctgcaagcctgtgtgctgt	5	12	12	12	1	2	1	0	0	2	1	2	1	2	1	2	0	6	5	2	0	2	0	rs79601471		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45993990T>C	ENST00000400374.3	+	1	385	c.355T>C	c.(355-357)Tgc>Cgc	p.C119R	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_5'Flank	NM_198687.1	NP_941960.1	P60372	KR104_HUMAN	keratin associated protein 10-4	119	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						CAAGACTGTCTGCTGCAAGCC	0.647																																					p.C119R		Atlas-SNP	.											.	KRTAP10-4	44	.	0			c.T355C						PASS	.	T	ARG/CYS,	498,3906		0,498,1704	117	107	111		355,	3.2	0.5	21	dbSNP_131	111	2,8590		0,2,4294	no	missense,intron	TSPEAR,KRTAP10-4	NM_198687.1,NM_144991.2	180,	0,500,5998	CC,CT,TT		0.0233,11.3079,3.8473	probably-damaging,	119/402,	45993990	500,12496	2202	4296	6498	SO:0001583	missense	386672	exon1			ACTGTCTGCTGCA	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.355T>C	21.37:g.45993990T>C	ENSP00000383225:p.Cys119Arg	575	0	0		530	140	0.264151	NM_198687	Q08AS0	Missense_Mutation	SNP	ENST00000400374.3	37	CCDS42957.1	97	0.044413919413919416	86	0.17479674796747968	11	0.03038674033149171	0	0.0	0	0.0	N	6.327	0.428441	0.11987	0.113079	2.33E-4	ENSG00000215454	ENST00000400374	T	0.01043	5.41	4.37	3.18	0.36537	.	.	.	.	.	T	0.00012	0.0000	M	0.90870	3.155	0.23780	P	0.99686138	D	0.54772	0.968	P	0.50970	0.655	T	0.16928	-1.0386	8	0.87932	D	0	.	7.1933	0.25839	0.3572:0.0:0.0:0.6428	.	119	P60372	KR104_HUMAN	R	119	ENSP00000383225:C119R	ENSP00000383225:C119R	C	+	1	0	KRTAP10-4	44818418	0.622000	0.27085	0.456000	0.27044	0.149000	0.21700	0.699000	0.25586	0.514000	0.28300	0.386000	0.25728	TGC	T|0.955;C|0.045	0.045	strong		0.647	KRTAP10-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128045.1	NM_198687		C	45993990	T	C	45993990	3	2	22	1	0	0	0	0	1	0	0	0	8520	1580	55	3	357	3	KRTAP10-4	21	45993990	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	15862	45993990	2135905	4301	7202											
KRTAP10-4	386672	hgsc.bcm.edu	37	chr21	45994763	45994763	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcccgcctgctgcgtgccCgtcccttcctgctgtgctcc	1	10	11	19	3	0	0	0	0	0	0	3	0	3	0	6	1	5	3	6	1	0	1	rs115169164	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45994763C>T	ENST00000400374.3	+	1	1158	c.1128C>T	c.(1126-1128)ccC>ccT	p.P376P	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_5'Flank	NM_198687.1	NP_941960.1	P60372	KR104_HUMAN	keratin associated protein 10-4	376	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						GCTGCGTGCCCGTCCCTTCCT	0.711													.|||	103	0.0205671	0.0696	0.0144	5008	,	,		17408	0.0		0.0	False		,,,				2504	0.001				p.P376P		Atlas-SNP	.											.	KRTAP10-4	44	.	0			c.C1128T						PASS	.	C	,	273,4133	143.8+/-178.8	3,267,1933	59	72	68		,1128	2.3	0.1	21	dbSNP_132	68	1,8589		0,1,4294	no	intron,coding-synonymous	TSPEAR,KRTAP10-4	NM_144991.2,NM_198687.1	,	3,268,6227	TT,TC,CC		0.0116,6.1961,2.1083	,	,376/402	45994763	274,12722	2203	4295	6498	SO:0001819	synonymous_variant	386672	exon1			CGTGCCCGTCCCT	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.1128C>T	21.37:g.45994763C>T		127	0	0		104	52	0.5	NM_198687	Q08AS0	Silent	SNP	ENST00000400374.3	37	CCDS42957.1																																																																																			C|0.980;T|0.020	0.020	strong		0.711	KRTAP10-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128045.1	NM_198687		T	45994763	C	T	45994763	2	4	22	1	0	0	0	0	0	0	0	1	8520	639	23	1		1	KRTAP10-4	21	45994763	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	773	45994763	2135132	4302	7203											
KRTAP10-6	386674	hgsc.bcm.edu	37	chr21	46011406	46011406	+	Silent	SNP	G	G	T																															gcagaggcaccacaggagggGacgggcacgcagcaggtgga																								rs374116165	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46011406G>T	ENST00000400368.1	-	1	980	c.960C>A	c.(958-960)gtC>gtA	p.V320V	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	320	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						CACAGGAGGGGACGGGCACGC	0.701													.|||	155	0.0309505	0.1127	0.0086	5008	,	,		19947	0.0		0.0	False		,,,				2504	0.0				p.V320V		Atlas-SNP	.											.	KRTAP10-6	57	.	0			c.C960A						PASS	.						68	83	78					21																	46011406		2201	4300	6501	SO:0001819	synonymous_variant	386674	exon1			GGAGGGGACGGGC	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.960C>A	21.37:g.46011406G>T		362	0	0		258	46	0.178295	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			.	.	weak		0.701	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688		T	46011406	G	T	46011406	2	4	22	1	0	0	0	0	0	0	0	1	8522	1161	41	4		4	KRTAP10-6	21	46011406	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	16643	46011406	2118489	4303	7204	91	3									
KRTAP10-6	386674	hgsc.bcm.edu	37	chr21	46011409	46011409	+	Silent	SNP	G	G	A																															gaggcaccacaggaggggacGggcacgcagcaggtggactt																								rs144363824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46011409G>A	ENST00000400368.1	-	1	977	c.957C>T	c.(955-957)ccC>ccT	p.P319P	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	319	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						AGGAGGGGACGGGCACGCAGC	0.697													.|||	155	0.0309505	0.1127	0.0086	5008	,	,		18795	0.0		0.0	False		,,,				2504	0.0				p.P319P		Atlas-SNP	.											.	KRTAP10-6	57	.	0			c.C957T						PASS	.						70	85	80					21																	46011409		2201	4300	6501	SO:0001819	synonymous_variant	386674	exon1			GGGGACGGGCACG	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.957C>T	21.37:g.46011409G>A		364	0	0		265	54	0.203774	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			G|0.975;A|0.025	0.025	strong		0.697	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688		A	46011409	G	A	46011409	2	1	22	1	0	0	0	0	0	0	0	1	8522	1103	39	1		1	KRTAP10-6	21	46011409	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3	46011409	2118486	4304	7205	91	3									
KRTAP10-6	386674	hgsc.bcm.edu	37	chr21	46011415	46011415	+	Silent	SNP	G	G	A																															ccacaggaggggacgggcacGcagcaggtggacttgcacac																								rs145570198		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46011415G>A	ENST00000400368.1	-	1	971	c.951C>T	c.(949-951)tgC>tgT	p.C317C	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	317	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						GGACGGGCACGCAGCAGGTGG	0.687																																					p.C317C		Atlas-SNP	.											.	KRTAP10-6	57	.	0			c.C951T						PASS	.						70	84	79					21																	46011415		2202	4300	6502	SO:0001819	synonymous_variant	386674	exon1			GGGCACGCAGCAG	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.951C>T	21.37:g.46011415G>A		358	0	0		261	58	0.222222	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			G|0.976;A|0.024	0.024	strong		0.687	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688		A	46011415	G	A	46011415	2	1	22	1	0	0	0	0	0	0	0	1	8522	1079	38	1		1	KRTAP10-6	21	46011415	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6	46011415	2118480	4305	7206	91	3									
KRTAP10-6	386674	hgsc.bcm.edu	37	chr21	46011526	46011526	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctagactgctggcagcatgaTgtggaagccccagagcagac	11	6	13	11	0	0	4	0	1	0	3	0	5	0	5	2	2	4	4	2	2	2	1	rs371768583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46011526T>A	ENST00000400368.1	-	1	860	c.840A>T	c.(838-840)acA>acT	p.T280T	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	280	29 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)		p.T280T(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(6)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23						GGCAGCATGATGTGGAAGCCC	0.652													.|||	5	0.000998403	0.0008	0.0	5008	,	,		22429	0.001		0.0	False		,,,				2504	0.0031				p.T280T		Atlas-SNP	.											KRTAP10-6,NS,carcinoma,0,2	KRTAP10-6	57	2	1	Substitution - coding silent(1)	kidney(1)	c.A840T						scavenged	.						106	110	109					21																	46011526		2203	4300	6503	SO:0001819	synonymous_variant	386674	exon1			GCATGATGTGGAA	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.840A>T	21.37:g.46011526T>A		245	2	0.00816326		300	34	0.113333	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			.	.	weak		0.652	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688		A	46011526	T	A	46011526	2	1	22	1	0	0	0	0	0	0	0	1	8522	1451	51	5		5	KRTAP10-6	21	46011526	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	111	46011526	2118369	4306	7207											
KRTAP10-6	386674	hgsc.bcm.edu	37	chr21	46011544	46011544	+	Silent	SNP	G	G	C																															gatgtggaagccccagagcaGacgggcacacagcaggcgtg																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46011544G>C	ENST00000400368.1	-	1	842	c.822C>G	c.(820-822)gtC>gtG	p.V274V	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	274	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						CCCCAGAGCAGACGGGCACAC	0.647																																					p.V274V		Atlas-SNP	.											.	KRTAP10-6	57	.	0			c.C822G						PASS	.						112	115	114					21																	46011544		2203	4300	6503	SO:0001819	synonymous_variant	386674	exon1			AGAGCAGACGGGC	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.822C>G	21.37:g.46011544G>C		257	0	0		327	33	0.100917	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			.	.	none		0.647	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688		C	46011544	G	C	46011544	2	2	22	1	0	0	0	0	0	0	0	1	8522	929	33	4		4	KRTAP10-6	21	46011544	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	18	46011544	2118351	4307	7208	92	2									
KRTAP10-6	386674	hgsc.bcm.edu	37	chr21	46011547	46011547	+	Silent	SNP	G	G	A																															gtggaagccccagagcagacGggcacacagcaggcgtgctg																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46011547G>A	ENST00000400368.1	-	1	839	c.819C>T	c.(817-819)ccC>ccT	p.P273P	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	273	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						CAGAGCAGACGGGCACACAGC	0.652																																					p.P273P		Atlas-SNP	.											.	KRTAP10-6	57	.	0			c.C819T						PASS	.						114	115	115					21																	46011547		2203	4300	6503	SO:0001819	synonymous_variant	386674	exon1			GCAGACGGGCACA	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.819C>T	21.37:g.46011547G>A		254	0	0		330	34	0.10303	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			.	.	none		0.652	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688		A	46011547	G	A	46011547	2	1	22	1	0	0	0	0	0	0	0	1	8522	1103	39	1		1	KRTAP10-6	21	46011547	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3	46011547	2118348	4308	7209	92	2									
KRTAP10-6	386674	hgsc.bcm.edu	37	chr21	46011571	46011571	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acacagcaggcgtgctggcaGggggaggaggtgcagcaagc	10	3	19	9	1	0	0	0	0	0	0	0	2	0	2	0	6	5	5	0	6	1	0			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46011571G>T	ENST00000400368.1	-	1	815	c.795C>A	c.(793-795)ccC>ccA	p.P265P	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	265	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						CGTGCTGGCAGGGGGAGGAGG	0.642																																					p.P265P		Atlas-SNP	.											.	KRTAP10-6	57	.	0			c.C795A						PASS	.						118	120	119					21																	46011571		2203	4300	6503	SO:0001819	synonymous_variant	386674	exon1			CTGGCAGGGGGAG	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.795C>A	21.37:g.46011571G>T		280	0	0		341	21	0.0615836	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			.	.	none		0.642	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688		T	46011571	G	T	46011571	2	4	22	1	0	0	0	0	0	0	0	1	8522	987	35	4		4	KRTAP10-6	21	46011571	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	24	46011571	2118324	4309	7210											
KRTAP10-6	386674	hgsc.bcm.edu	37	chr21	46012225	46012226	+	In_Frame_Ins	INS	-	-	CAGCAGCTGGGGGCA																															tcaggcagggggccggggcgINScagcaggggggctcacagca																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46012225_46012226insCAGCAGCTGGGGGCA	ENST00000400368.1	-	1	160_161	c.140_141insTGCCCCCAGCTGCTG	c.(139-141)tgc>tgTGCCCCCAGCTGCTGc	p.47_47C>CAPSCC	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	47	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						GGGCCGGGGCGCAGCAGGGGGG	0.683																																					p.C47delinsCAPSCC		Pindel	.											.	KRTAP10-6	57	.	0			c.141_142insTGCCCCCAGCTGCTG						PASS	.																																			SO:0001652	inframe_insertion	386674	exon1			.	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.140_141insTGCCCCCAGCTGCTG	21.37:g.46012225_46012226insCAGCAGCTGGGGGCA	Exception_encountered	93	0	.		58	14	0.241	NM_198688		In_Frame_Ins	INS	ENST00000400368.1	37	CCDS42959.1																																																																																			.	.	none		0.683	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688		CAGCAGCTGGGGGCA	46012226	-	CAGCAGCTGGGGGCA	46012225	7	5	22	1	0	1	1	0	0	0	0	0	8522	1079	38	0	960	0	KRTAP10-6	21	46012225	In_Frame_Ins	INS	-	TCGA-G8-6324-01A-11D-2210-10	654	46012225	2117670	4310	7211											
KRTAP10-7	386675	hgsc.bcm.edu	37	chr21	46021546	46021546	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccccacctcctcctgccaggCcagctgctgccgcccagcct	4	6	8	23	1	0	0	0	0	0	0	2	0	2	0	10	1	5	2	10	1	0	0	rs116074123	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46021546C>G	ENST00000380102.2	+	1	1050	c.1025C>G	c.(1024-1026)gCc>gGc	p.A342G	TSPEAR_ENST00000323084.4_Intron	NM_198689.2	NP_941962.1	P60409	KR107_HUMAN	keratin associated protein 10-7	342	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						TCCTGCCAGGCCAGCTGCTGC	0.711													-|||	183	0.0365415	0.1331	0.0101	5008	,	,		15282	0.0		0.0	False		,,,				2504	0.0				p.A337G		Atlas-SNP	.											.	KRTAP10-7	41	.	0			c.C1010G						PASS	.	C	,GLY/ALA	439,3945		20,399,1773	32	38	36		,1025	3.7	1	21	dbSNP_132	36	4,8554		0,4,4275	no	intron,missense	TSPEAR,KRTAP10-7	NM_144991.2,NM_198689.2	,60	20,403,6048	GG,GC,CC		0.0467,10.0137,3.423	,benign	,342/376	46021546	443,12499	2192	4279	6471	SO:0001583	missense	386675	exon2			GCCAGGCCAGCTG	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.1025C>G	21.37:g.46021546C>G	ENSP00000369445:p.Ala342Gly	59	0	0		114	83	0.72807	NM_198689	Q0VDJ8|Q70LJ2	Missense_Mutation	SNP	ENST00000380102.2	37		50	0.022893772893772892	45	0.09146341463414634	5	0.013812154696132596	0	0.0	0	0.0	c	11.47	1.647906	0.29336	0.100137	4.67E-4	ENSG00000205441	ENST00000380102	T	0.00675	5.88	3.73	3.73	0.42828	.	.	.	.	.	T	0.00039	0.0001	N	0.24115	0.695	0.19575	N	0.999963	B	0.17038	0.02	B	0.14023	0.01	T	0.52586	-0.8556	9	0.72032	D	0.01	.	7.4909	0.27460	0.0:0.8767:0.0:0.1233	.	337	P60409-2	.	G	342	ENSP00000369445:A342G	ENSP00000369445:A342G	A	+	2	0	KRTAP10-7	44845974	0.490000	0.26012	1.000000	0.80357	0.413000	0.31143	1.890000	0.39728	1.805000	0.52779	0.467000	0.42956	GCC	C|0.974;G|0.026	0.026	strong		0.711	KRTAP10-7-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128038.1	NM_198689		G	46021546	C	G	46021546	3	3	22	1	0	0	0	0	1	0	0	0	8523	739	26	4	1016	4	KRTAP10-7	21	46021546	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	9321	46021546	2108349	4311	7212											
KRTAP10-10	353333	hgsc.bcm.edu	37	chr21	46057343	46057343	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccactccagcatggccgcCtccaccatgtccatctgctc	6	8	6	21	1	1	0	0	0	1	0	5	0	4	0	8	1	2	2	8	1	0	0	rs76468958	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46057343C>A	ENST00000380095.1	+	1	71	c.9C>A	c.(7-9)gcC>gcA	p.A3A	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	3						keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						GCATGGCCGCCTCCACCATGT	0.647													A|||	197	0.0393371	0.1362	0.0043	5008	,	,		18834	0.002		0.001	False		,,,				2504	0.0112				p.A3A		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.C9A						PASS	.	A	,	601,3805	770.0+/-413.7	46,509,1648	107	115	112		,9	-4.6	0	21	dbSNP_131	112	5,8595	818.7+/-406.8	0,5,4295	no	intron,coding-synonymous	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,	46,514,5943	AA,AC,CC		0.0581,13.6405,4.6594	,	,3/252	46057343	606,12400	2203	4300	6503	SO:0001819	synonymous_variant	353333	exon1			GGCCGCCTCCACC	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.9C>A	21.37:g.46057343C>A		192	0	0		219	103	0.47032	NM_181688		Silent	SNP	ENST00000380095.1	37	CCDS33585.1																																																																																			C|0.960;A|0.040	0.040	strong		0.647	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688		A	46057343	C	A	46057343	2	1	22	1	0	0	0	0	0	0	0	1	8515	668	24	4		4	KRTAP10-10	21	46057343	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	35797	46057343	2072552	4312	7213			12	35		9	5	701	N	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA_T_G_C	4.03183e-06
KRTAP10-10	353333	hgsc.bcm.edu	37	chr21	46057635	46057635	+	Missense_Mutation	SNP	G	G	A																															gctgtgtgcctgtctgctgtGtgcccgtctgctgcgtgccc																								rs114397261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46057635G>A	ENST00000380095.1	+	1	363	c.301G>A	c.(301-303)Gtg>Atg	p.V101M	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	101	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						tgtctgctgtgtgcccgtctg	0.632													A|||	306	0.0611022	0.2118	0.0173	5008	,	,		18765	0.002		0.001	False		,,,				2504	0.0112				p.V101M		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.G301A						PASS	.	A	,MET/VAL	438,3968		76,286,1841	130	123	125		,301	-1.7	0	21	dbSNP_132	125	2,8594		0,2,4296	no	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,21	76,288,6137	AA,AG,GG		0.0233,9.941,3.3841	,possibly-damaging	,101/252	46057635	440,12562	2203	4298	6501	SO:0001583	missense	353333	exon1			TGCTGTGTGCCCG	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.301G>A	21.37:g.46057635G>A	ENSP00000369438:p.Val101Met	204	0	0		273	120	0.43956	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	.	.	.	.	.	.	.	.	.	.	a	1.285	-0.609223	0.03690	0.09941	2.33E-4	ENSG00000221859	ENST00000380095	T	0.01430	4.9	2.86	-1.68	0.08212	.	.	.	.	.	T	0.00073	0.0002	L	0.36672	1.1	0.09310	N	1	B	0.26195	0.144	B	0.34452	0.183	T	0.44128	-0.9348	9	0.44086	T	0.13	.	9.7593	0.40522	0.4446:0.0:0.5554:0.0	.	101	P60014	KR10A_HUMAN	M	101	ENSP00000369438:V101M	ENSP00000369438:V101M	V	+	1	0	KRTAP10-10	44882063	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-0.140000	0.10342	-1.728000	0.01366	-2.786000	0.00116	GTG	G|0.928;A|0.072	0.072	strong		0.632	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688		A	46057635	G	A	46057635	3	1	22	1	0	0	0	0	1	0	0	0	8515	1377	48	2	303	2	KRTAP10-10	21	46057635	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	292	46057635	2072260	4313	7214	93	2	12	35		9	5	701	N	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA_T_G_C	4.03183e-06
KRTAP10-10	353333	hgsc.bcm.edu	37	chr21	46057636	46057636	+	Missense_Mutation	SNP	T	T	A																															ctgtgtgcctgtctgctgtgTgcccgtctgctgcgtgcccg																								rs115298124	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46057636T>A	ENST00000380095.1	+	1	364	c.302T>A	c.(301-303)gTg>gAg	p.V101E	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	101	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						gtctgctgtgtgcccgtctgc	0.627													A|||	306	0.0611022	0.2118	0.0173	5008	,	,		19037	0.002		0.001	False		,,,				2504	0.0112				p.V101E		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.T302A						PASS	.	A	,GLU/VAL	550,3856		77,396,1730	131	124	126		,302	-5.7	0	21	dbSNP_132	126	2,8594		0,2,4296	no	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,121	77,398,6026	AA,AT,TT		0.0233,12.483,4.2455	,benign	,101/252	46057636	552,12450	2203	4298	6501	SO:0001583	missense	353333	exon1			GCTGTGTGCCCGT	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.302T>A	21.37:g.46057636T>A	ENSP00000369438:p.Val101Glu	205	0	0		273	120	0.43956	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	.	.	.	.	.	.	.	.	.	.	a	0.032	-1.330391	0.01298	0.12483	2.33E-4	ENSG00000221859	ENST00000380095	T	0.01323	5.01	2.86	-5.72	0.02406	.	.	.	.	.	T	0.00012	0.0000	N	0.10874	0.06	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.39165	-0.9627	9	0.22706	T	0.39	.	1.3737	0.02215	0.2016:0.1241:0.184:0.4903	.	101	P60014	KR10A_HUMAN	E	101	ENSP00000369438:V101E	ENSP00000369438:V101E	V	+	2	0	KRTAP10-10	44882064	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.107000	0.03316	-4.925000	0.00027	-3.683000	0.00024	GTG	T|0.928;A|0.072	0.072	strong		0.627	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688		A	46057636	T	A	46057636	3	1	22	1	0	0	0	0	1	0	0	0	8515	1696	59	5	304	5	KRTAP10-10	21	46057636	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1	46057636	2072259	4314	7215	93	2	12	35		9	5	701	N	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA_T_G_C	4.03183e-06
KRTAP10-10	353333	hgsc.bcm.edu	37	chr21	46057766	46057766	+	Missense_Mutation	SNP	G	G	C																															acctcctccccatgccagcaGgcctgctgtgtgcctgtctg																								rs142146787	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46057766G>C	ENST00000380095.1	+	1	494	c.432G>C	c.(430-432)caG>caC	p.Q144H	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	144	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						CATGCCAGCAGGCCTGCTGTG	0.602													G|||	3	0.000599042	0.0015	0.0	5008	,	,		23205	0.0		0.0	False		,,,				2504	0.001				p.Q144H		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.G432C						PASS	.	G	,HIS/GLN	7,4399	12.9+/-30.5	0,7,2196	293	265	274		,432	-0.5	0.1	21	dbSNP_134	274	0,8600		0,0,4300	yes	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,24	0,7,6496	CC,CG,GG		0.0,0.1589,0.0538	,probably-damaging	,144/252	46057766	7,12999	2203	4300	6503	SO:0001583	missense	353333	exon1			CCAGCAGGCCTGC	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.432G>C	21.37:g.46057766G>C	ENSP00000369438:p.Gln144His	155	0	0		172	53	0.30814	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	.	.	.	.	.	.	.	.	.	.	g	8.829	0.939468	0.18281	0.001589	0.0	ENSG00000221859	ENST00000380095	T	0.01178	5.22	3.27	-0.456	0.12190	.	.	.	.	.	T	0.05273	0.0140	M	0.91300	3.195	0.09310	N	1	D	0.56746	0.977	P	0.56343	0.796	T	0.12760	-1.0535	9	0.87932	D	0	.	5.8436	0.18647	0.632:0.0:0.368:0.0	.	144	P60014	KR10A_HUMAN	H	144	ENSP00000369438:Q144H	ENSP00000369438:Q144H	Q	+	3	2	KRTAP10-10	44882194	0.000000	0.05858	0.109000	0.21407	0.190000	0.23558	-1.200000	0.03029	0.065000	0.16485	0.461000	0.40582	CAG	G|1.000;C|0.000	0.000	weak		0.602	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688		C	46057766	G	C	46057766	3	2	22	1	0	0	0	0	1	0	0	0	8515	991	35	4	434	4	KRTAP10-10	21	46057766	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	130	46057766	2072129	4315	7216	94	2	12	35		9	5	701	N	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA_T_G_C	4.03183e-06
KRTAP10-10	353333	hgsc.bcm.edu	37	chr21	46057775	46057804	+	In_Frame_Del	DEL	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	-																															ccatgccagcaggcctgctgTgtgcctgtctgctctaagtc																								rs138406502|rs587625812|rs587722247|rs146378555|rs587701287	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46057775_46057804delTGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	ENST00000380095.1	+	1	503_532	c.441_470delTGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	c.(439-471)tgtgtgcctgtctgctctaagtccgtctgctat>tgt	p.VPVCSKSVCY148del	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	148	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						AGGCCTGCTGTGTGCCTGTCTGCTCTAAGTCCGTCTGCTATGTGCCTGTG	0.622																																					p.147_157del		Atlas-Indel	.											.	KRTAP10-10	37	.	0			c.440_469del						PASS	.		,	9,4255		1,7,2124					,	2.3	0			280	5,8249		2,1,4124	no	coding,intron	TSPEAR,KRTAP10-10	NM_181688.1,NM_144991.2	,	3,8,6248	A1A1,A1R,RR		0.0606,0.2111,0.1118	,	,		14,12504				SO:0001651	inframe_deletion	353333	exon1			.	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.441_470delTGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	21.37:g.46057775_46057804delTGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	ENSP00000369438:p.Val148_Tyr157del	151	0	0		167	45	0.269461	NM_181688		In_Frame_Del	DEL	ENST00000380095.1	37	CCDS33585.1																																																																																			.	.	none		0.622	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688		-	46057804	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	-	46057775	7	5	22	1	0	1	0	1	0	0	0	0	8515	1702	59	0	443	0	KRTAP10-10	21	46057775	In_Frame_Del	DEL	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	TCGA-G8-6324-01A-11D-2210-10	9	46057775	2072120	4316	7217	94	2	12	35		9	5	701	N	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA_T_G_C	4.03183e-06
KRTAP10-10	353333	hgsc.bcm.edu	37	chr21	46057943	46057943	+	Silent	SNP	C	C	T																															gtgtgcaagtccacctgctgCgtgcccgtcccctcctgcgg																								rs77446663		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46057943C>T	ENST00000380095.1	+	1	671	c.609C>T	c.(607-609)tgC>tgT	p.C203C	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	203	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						CCACCTGCTGCGTGCCCGTCC	0.692																																					p.C203C		Atlas-SNP	.											KRTAP10-10,NS,carcinoma,+2,1	KRTAP10-10	37	1	0			c.C609T						PASS	.						97	100	99					21																	46057943		2203	4300	6503	SO:0001819	synonymous_variant	353333	exon1			CTGCTGCGTGCCC	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.609C>T	21.37:g.46057943C>T		293	0	0		456	117	0.256579	NM_181688		Silent	SNP	ENST00000380095.1	37	CCDS33585.1																																																																																			C|0.982;T|0.018	0.018	strong		0.692	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688		T	46057943	C	T	46057943	2	4	22	1	0	0	0	0	0	0	0	1	8515	776	27	1		1	KRTAP10-10	21	46057943	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	168	46057943	2071952	4317	7218	95	3	12	35		9	5	701	N	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA_T_G_C	4.03183e-06
KRTAP10-10	353333	hgsc.bcm.edu	37	chr21	46057949	46057949	+	Silent	SNP	C	C	T																															aagtccacctgctgcgtgccCgtcccctcctgcggtgcctc																								rs78352751	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46057949C>T	ENST00000380095.1	+	1	677	c.615C>T	c.(613-615)ccC>ccT	p.P205P	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	205	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						GCTGCGTGCCCGTCCCCTCCT	0.701													C|||	103	0.0205671	0.0756	0.0043	5008	,	,		20099	0.0		0.0	False		,,,				2504	0.0				p.P205P		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.C615T						PASS	.						95	98	97					21																	46057949		2203	4300	6503	SO:0001819	synonymous_variant	353333	exon1			CGTGCCCGTCCCC	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.615C>T	21.37:g.46057949C>T		297	0	0		471	121	0.2569	NM_181688		Silent	SNP	ENST00000380095.1	37	CCDS33585.1																																																																																			C|0.982;T|0.018	0.018	strong		0.701	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688		T	46057949	C	T	46057949	2	4	22	1	0	0	0	0	0	0	0	1	8515	639	23	1		1	KRTAP10-10	21	46057949	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6	46057949	2071946	4318	7219	95	3	12	35		9	5	701	N	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA_T_G_C	4.03183e-06
KRTAP10-10	353333	hgsc.bcm.edu	37	chr21	46057952	46057952	+	Silent	SNP	C	C	A																															tccacctgctgcgtgcccgtCccctcctgcggtgcctctgc																								rs74701761	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46057952C>A	ENST00000380095.1	+	1	680	c.618C>A	c.(616-618)gtC>gtA	p.V206V	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	206	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						GCGTGCCCGTCCCCTCCTGCG	0.706													C|||	103	0.0205671	0.0756	0.0043	5008	,	,		19027	0.0		0.0	False		,,,				2504	0.0				p.V206V		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.C618A						PASS	.						91	95	94					21																	46057952		2203	4300	6503	SO:0001819	synonymous_variant	353333	exon1			GCCCGTCCCCTCC	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.618C>A	21.37:g.46057952C>A		294	0	0		473	113	0.238901	NM_181688		Silent	SNP	ENST00000380095.1	37	CCDS33585.1																																																																																			C|0.982;A|0.018	0.018	strong		0.706	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688		A	46057952	C	A	46057952	2	1	22	1	0	0	0	0	0	0	0	1	8515	842	30	4		4	KRTAP10-10	21	46057952	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3	46057952	2071943	4319	7220	95	3	12	35		9	5	701	N	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA_T_G_C	4.03183e-06
KRTAP10-10	353333	hgsc.bcm.edu	37	chr21	46058043	46058043	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgccgccccgtgtgctccCgccctgcctgctacagcctc	2	9	9	21	3	1	0	0	0	1	0	3	0	2	0	7	0	6	2	7	0	1	1	rs77109703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46058043C>T	ENST00000380095.1	+	1	771	c.709C>T	c.(709-711)Cgc>Tgc	p.R237C	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	237						keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						CGTGTGCTCCCGCCCTGCCTG	0.692																																					p.R237C		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.C709T						PASS	.	C	,CYS/ARG	389,4017	164.7+/-196.3	0,389,1814	49	53	52		,709	-1.5	0	21	dbSNP_131	52	4,8590	1.2+/-3.3	0,4,4293	no	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,180	0,393,6107	TT,TC,CC		0.0465,8.8289,3.0231	,benign	,237/252	46058043	393,12607	2203	4297	6500	SO:0001583	missense	353333	exon1			TGCTCCCGCCCTG	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.709C>T	21.37:g.46058043C>T	ENSP00000369438:p.Arg237Cys	218	0	0		380	84	0.221053	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	48	0.02197802197802198	47	0.09552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	c	4.111	0.018755	0.07959	0.088289	4.65E-4	ENSG00000221859	ENST00000380095	T	0.01422	4.91	3.52	-1.53	0.08611	.	.	.	.	.	T	0.00073	0.0002	M	0.78285	2.405	0.36787	D	0.884654	B	0.28636	0.218	B	0.18871	0.023	T	0.50466	-0.8825	9	0.66056	D	0.02	.	4.2298	0.10597	0.3112:0.4801:0.0:0.2088	.	237	P60014	KR10A_HUMAN	C	237	ENSP00000369438:R237C	ENSP00000369438:R237C	R	+	1	0	KRTAP10-10	44882471	0.000000	0.05858	0.038000	0.18304	0.008000	0.06430	-1.152000	0.03172	-0.202000	0.10268	-0.444000	0.05651	CGC	C|0.966;T|0.034	0.034	strong		0.692	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688		T	46058043	C	T	46058043	3	4	22	1	0	0	0	0	1	0	0	0	8515	652	23	1	711	1	KRTAP10-10	21	46058043	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	91	46058043	2071852	4320	7221			12	35		9	5	701	N	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA_T_G_C	4.03183e-06
KRTAP10-12	386685	hgsc.bcm.edu	37	chr21	46117553	46117553	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcttgctgcatctcctcccCgtgtcaacagtcctgctgtg	5	12	9	15	1	2	0	1	0	1	0	5	0	4	0	4	0	5	4	4	0	1	1	rs35076450	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46117553C>A	ENST00000400365.3	+	1	467	c.437C>A	c.(436-438)cCg>cAg	p.P146Q	TSPEAR_ENST00000323084.4_Intron	NM_198699.1	NP_941972.1	P60413	KR10C_HUMAN	keratin associated protein 10-12	146	19 X 5 AA repeats of C-C-X(3).		P -> Q (in dbSNP:rs35076450).			keratin filament (GO:0045095)				large_intestine(1)|lung(8)	9						ATCTCCTCCCCGTGTCAACAG	0.612													C|||	19	0.00379393	0.0136	0.0014	5008	,	,		19291	0.0		0.0	False		,,,				2504	0.0				p.P146Q		Atlas-SNP	.											.	KRTAP10-12	21	.	0			c.C437A						PASS	.	C	GLN/PRO,	66,4340	61.7+/-98.7	1,64,2138	161	165	164		437,	0.9	0.1	21	dbSNP_126	164	0,8600		0,0,4300	no	missense,intron	TSPEAR,KRTAP10-12	NM_198699.1,NM_144991.2	76,	1,64,6438	AA,AC,CC		0.0,1.498,0.5075	possibly-damaging,	146/246,	46117553	66,12940	2203	4300	6503	SO:0001583	missense	386685	exon1			CCTCCCCGTGTCA	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.437C>A	21.37:g.46117553C>A	ENSP00000383216:p.Pro146Gln	221	1	0.00452489		265	136	0.513208	NM_198699	B2RPA3	Missense_Mutation	SNP	ENST00000400365.3	37	CCDS42967.1	7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	c	0.797	-0.756781	0.03019	0.01498	0.0	ENSG00000189169	ENST00000400365;ENST00000452870	T	0.00644	6.01	2.19	0.906	0.19314	.	.	.	.	.	T	0.00552	0.0018	L	0.56280	1.765	0.09310	N	1	P	0.36660	0.564	B	0.32149	0.141	T	0.48536	-0.9027	9	0.54805	T	0.06	.	5.9287	0.19126	0.0:0.5224:0.4776:0.0	rs35076450	146	P60413	KR10C_HUMAN	Q	146;54	ENSP00000383216:P146Q	ENSP00000383216:P146Q	P	+	2	0	KRTAP10-12	44941981	0.001000	0.12720	0.088000	0.20740	0.003000	0.03518	0.160000	0.16462	0.881000	0.35993	0.305000	0.20034	CCG	C|0.995;A|0.005	0.005	strong		0.612	KRTAP10-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128032.1	NM_198699		A	46117553	C	A	46117553	3	1	22	1	0	0	0	0	1	0	0	0	8517	652	23	4	439	4	KRTAP10-12	21	46117553	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	59510	46117553	2012342	4321	7222											
KRTAP10-12	386685	hgsc.bcm.edu	37	chr21	46117746	46117746	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agacccgcccgccgcgtgccCgtcccctcctgctgtgtccc	2	7	10	22	5	0	1	0	0	0	1	3	1	3	1	8	0	2	1	8	0	0	0	rs112431728	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46117746C>T	ENST00000400365.3	+	1	660	c.630C>T	c.(628-630)ccC>ccT	p.P210P	TSPEAR_ENST00000323084.4_Intron	NM_198699.1	NP_941972.1	P60413	KR10C_HUMAN	keratin associated protein 10-12	210	19 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(8)	9						GCCGCGTGCCCGTCCCCTCCT	0.721													a|||	33	0.00658946	0.0242	0.0014	5008	,	,		14658	0.0		0.0	False		,,,				2504	0.0				p.P210P		Atlas-SNP	.											.	KRTAP10-12	21	.	0			c.C630T						PASS	.	A	,	115,4287		1,113,2087	53	68	63		,630	0.8	0.4	21	dbSNP_132	63	1,8581		0,1,4290	no	intron,coding-synonymous	TSPEAR,KRTAP10-12	NM_144991.2,NM_198699.1	,	1,114,6377	TT,TC,CC		0.0117,2.6124,0.8934	,	,210/246	46117746	116,12868	2201	4291	6492	SO:0001819	synonymous_variant	386685	exon1			CGTGCCCGTCCCC	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.630C>T	21.37:g.46117746C>T		83	0	0		81	44	0.54321	NM_198699	B2RPA3	Silent	SNP	ENST00000400365.3	37	CCDS42967.1																																																																																			C|0.994;T|0.006	0.006	strong		0.721	KRTAP10-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128032.1	NM_198699		T	46117746	C	T	46117746	2	4	22	1	0	0	0	0	0	0	0	1	8517	639	23	1		1	KRTAP10-12	21	46117746	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	193	46117746	2012149	4322	7223											
C21orf70	85395	hgsc.bcm.edu	37	chr21	46380068	46380068	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agaaaatgaagctgaggcgtGagcaatggttgcagagtaag	15	7	15	4	1	0	5	0	3	0	2	0	5	0	5	0	2	3	5	0	2	5	2	rs141593051	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46380068G>A	ENST00000291634.6	+	3	385	c.337G>A	c.(337-339)Gag>Aag	p.E113K	FAM207A_ENST00000479127.1_3'UTR|FAM207A_ENST00000397826.3_Missense_Mutation_p.E98K	NM_058190.2	NP_478070.1	Q9NSI2	F207A_HUMAN	family with sequence similarity 207, member A	113																	GCTGAGGCGTGAGCAATGGTT	0.572													G|||	2	0.000399361	0.0015	0.0	5008	,	,		21685	0.0		0.0	False		,,,				2504	0.0				p.E113K		Atlas-SNP	.											.	.	.	.	0			c.G337A						PASS	.	G	LYS/GLU	5,4401	11.4+/-27.6	0,5,2198	128	101	110		337	3.2	0.4	21	dbSNP_134	110	0,8600		0,0,4300	yes	missense	FAM207A	NM_058190.2	56	0,5,6498	AA,AG,GG		0.0,0.1135,0.0384	benign	113/231	46380068	5,13001	2203	4300	6503	SO:0001583	missense	85395	exon3			AGGCGTGAGCAAT		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.337G>A	21.37:g.46380068G>A	ENSP00000291634:p.Glu113Lys	114	0	0		95	47	0.494737	NM_058190		Missense_Mutation	SNP	ENST00000291634.6	37	CCDS13718.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	10.04	1.240186	0.22711	0.001135	0.0	ENSG00000160256	ENST00000291634;ENST00000397826;ENST00000458015	T;T;T	0.47177	0.85;0.85;0.85	3.24	3.24	0.37175	.	0.168860	0.50627	D	0.000105	T	0.36276	0.0961	L	0.55743	1.74	0.40834	D	0.983615	P;B	0.46142	0.873;0.021	B;B	0.44044	0.439;0.037	T	0.48281	-0.9049	10	0.62326	D	0.03	-19.5017	10.2398	0.43305	0.0:0.0:1.0:0.0	.	98;113	Q9NSI2-2;Q9NSI2	.;F207A_HUMAN	K	113;98;98	ENSP00000291634:E113K;ENSP00000380926:E98K;ENSP00000404964:E98K	ENSP00000291634:E113K	E	+	1	0	C21orf70	45204496	0.782000	0.28689	0.427000	0.26684	0.158000	0.22134	2.095000	0.41729	2.110000	0.64415	0.650000	0.86243	GAG	G|0.999;A|0.001	0.001	strong		0.572	FAM207A-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206639.1	NM_058190		A	46380068	G	A	46380068	3	1	22	1	0	0	0	0	1	0	0	0	2135	1291	45	2	347	2	C21orf70	21	46380068	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	262322	46380068	1749827	4323	7224											
POFUT2	23275	hgsc.bcm.edu	37	chr21	46685550	46685550	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	actgaggtgccaataaaaaaCctgcaaaggatcacagaggt	17	6	10	8	0	1	2	1	1	0	1	1	3	1	3	2	3	3	1	2	3	5	1	rs112907087	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46685550C>T	ENST00000349485.5	-	9	1163	c.1137G>A	c.(1135-1137)agG>agA	p.R379R	POFUT2_ENST00000331343.7_3'UTR|POFUT2_ENST00000471540.1_5'UTR	NM_133635.4	NP_598368.2	Q9Y2G5	OFUT2_HUMAN	protein O-fucosyltransferase 2	379					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)		CAATAAAAAACCTGCAAAGGA	0.493													C|||	27	0.00539137	0.0204	0.0	5008	,	,		16487	0.0		0.0	False		,,,				2504	0.0				p.R379R		Atlas-SNP	.											.	POFUT2	77	.	0			c.G1137A						PASS	.	C	,	86,4320	74.1+/-112.3	1,84,2118	52	57	56		,1137	3.9	1	21	dbSNP_132	56	0,8600		0,0,4300	yes	utr-3,coding-synonymous-near-splice	POFUT2	NM_015227.4,NM_133635.4	,	1,84,6418	TT,TC,CC		0.0,1.9519,0.6612	,	,379/430	46685550	86,12920	2203	4300	6503	SO:0001630	splice_region_variant	23275	exon9			AAAAAACCTGCAA	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.1137-1G>A	21.37:g.46685550C>T		62	0	0		48	23	0.479167	NM_133635	Q6PJV1|Q7Z4N0|Q8WWU6|Q9BQS4|Q9BQS5|Q9UFY3	Silent	SNP	ENST00000349485.5	37	CCDS13719.1																																																																																			C|0.992;T|0.008	0.008	strong		0.493	POFUT2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192573.2	NM_015227	Silent	T	46685550	C	T	46685550	5	4	22	1	0	0	0	0	0	0	1	0	12193	521	18	2	156	2	POFUT2	21	46685550	Splice_Site	SNP	C	TCGA-G8-6324-01A-11D-2210-10	305482	46685550	1444345	4324	7225											
COL18A1	80781	hgsc.bcm.edu	37	chr21	46900062	46900062	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caggaccctccttcagacacGacaagctggtaagtcccgcc	10	6	9	16	2	1	1	1	0	0	1	3	3	3	2	4	2	1	2	4	2	2	2	rs61738822	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46900062G>A	ENST00000359759.4	+	10	2656	c.2635G>A	c.(2635-2637)Gac>Aac	p.D879N	COL18A1_ENST00000400337.2_Missense_Mutation_p.D464N|COL18A1_ENST00000355480.5_Missense_Mutation_p.D644N			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	879	Nonhelical region 3 (NC3).				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)		CTTCAGACACGACAAGCTGGT	0.642													G|||	17	0.00339457	0.0121	0.0014	5008	,	,		14900	0.0		0.0	False		,,,				2504	0.0				p.D644N		Atlas-SNP	.											.	COL18A1	129	.	0			c.G1930A						PASS	.	G	ASN/ASP,ASN/ASP	53,3705		0,53,1826	17	22	21		1930,1390	3.2	0.9	21	dbSNP_129	21	0,8226		0,0,4113	yes	missense,missense	COL18A1	NM_030582.3,NM_130445.2	23,23	0,53,5939	AA,AG,GG		0.0,1.4103,0.4423	possibly-damaging,possibly-damaging	644/1520,464/1340	46900062	53,11931	1879	4113	5992	SO:0001583	missense	80781	exon10			AGACACGACAAGC		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.2635G>A	21.37:g.46900062G>A	ENSP00000352798:p.Asp879Asn	44	0	0		76	41	0.539474	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	37		8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	17.19	3.325962	0.60743	0.014103	0.0	ENSG00000182871	ENST00000400337;ENST00000400347;ENST00000355480;ENST00000359759;ENST00000539645	D;D;D	0.90788	-2.72;-2.73;-2.64	3.19	3.19	0.36642	.	0.545209	0.16627	N	0.206240	D	0.88385	0.6422	L	0.56769	1.78	0.40960	D	0.984616	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.992;0.997;0.997	D	0.89130	0.3509	10	0.59425	D	0.04	.	10.0536	0.42230	0.0:0.0:1.0:0.0	rs61738822	879;644;464	P39060;P39060-1;P39060-2	COIA1_HUMAN;.;.	N	464;464;644;879;879	ENSP00000383191:D464N;ENSP00000347665:D644N;ENSP00000352798:D879N	ENSP00000347665:D644N	D	+	1	0	COL18A1	45724490	1.000000	0.71417	0.858000	0.33744	0.334000	0.28698	5.592000	0.67543	1.812000	0.52913	0.561000	0.74099	GAC	G|0.996;A|0.004	0.004	strong		0.642	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			A	46900062	G	A	46900062	3	1	22	1	0	0	0	0	1	0	0	0	3677	1058	37	1	2787	1	COL18A1	21	46900062	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	214512	46900062	1229833	4325	7226											
COL18A1	80781	hgsc.bcm.edu	37	chr21	46900670	46900670	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgtcccaggcctgcccggCgagccaggccgctttggggt	3	7	17	14	3	0	0	0	0	0	0	1	1	1	0	5	6	2	1	5	6	0	1	rs112723616	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46900670C>T	ENST00000359759.4	+	12	2775	c.2754C>T	c.(2752-2754)ggC>ggT	p.G918G	COL18A1_ENST00000400337.2_Silent_p.G503G|COL18A1_ENST00000355480.5_Silent_p.G683G			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	918	Triple-helical region 3 (COL3).				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)		GCCTGCCCGGCGAGCCAGGCC	0.716													C|||	68	0.0135783	0.0454	0.0115	5008	,	,		11100	0.0		0.0	False		,,,				2504	0.0				p.G683G		Atlas-SNP	.											.	COL18A1	129	.	0			c.C2049T						PASS	.	C	,	141,3665		4,133,1766	21	26	24		2049,1509	-8.1	0.9	21	dbSNP_132	24	1,8213		0,1,4106	no	coding-synonymous,coding-synonymous	COL18A1	NM_030582.3,NM_130445.2	,	4,134,5872	TT,TC,CC		0.0122,3.7047,1.1814	,	683/1520,503/1340	46900670	142,11878	1903	4107	6010	SO:0001819	synonymous_variant	80781	exon12			GCCCGGCGAGCCA		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.2754C>T	21.37:g.46900670C>T		31	0	0		57	36	0.631579	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																				C|0.990;T|0.010	0.010	strong		0.716	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			T	46900670	C	T	46900670	2	4	22	1	0	0	0	0	0	0	0	1	3677	755	27	1		1	COL18A1	21	46900670	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	608	46900670	1229225	4326	7227											
COL6A2	1292	hgsc.bcm.edu	37	chr21	47535816	47535816	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcaacatgggtgagccgggaGagcctggccagaagggaaga	12	3	18	8	1	0	4	0	1	0	3	0	6	0	5	3	4	3	1	3	4	3	0	rs61735835	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:47535816G>A	ENST00000300527.4	+	6	936	c.832G>A	c.(832-834)Gag>Aag	p.E278K	COL6A2_ENST00000409416.1_Missense_Mutation_p.E278K|COL6A2_ENST00000357838.4_Missense_Mutation_p.E278K|COL6A2_ENST00000310645.5_Missense_Mutation_p.E278K|COL6A2_ENST00000397763.1_Missense_Mutation_p.E278K	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	278	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)		TGAGCCGGGAGAGCCTGGCCA	0.657													G|||	41	0.0081869	0.028	0.0014	5008	,	,		15727	0.003		0.0	False		,,,				2504	0.0				p.E278K		Atlas-SNP	.											.	COL6A2	351	.	0			c.G832A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU	105,4295	83.4+/-121.9	2,101,2097	63	57	59		832,832,832	4	1	21	dbSNP_129	59	2,8596	1.2+/-3.3	0,2,4297	yes	missense,missense,missense	COL6A2	NM_001849.3,NM_058174.2,NM_058175.2	56,56,56	2,103,6394	AA,AG,GG		0.0233,2.3864,0.8232	possibly-damaging,possibly-damaging,possibly-damaging	278/1020,278/919,278/829	47535816	107,12891	2200	4299	6499	SO:0001583	missense	1292	exon6			CCGGGAGAGCCTG	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.832G>A	21.37:g.47535816G>A	ENSP00000300527:p.Glu278Lys	42	0	0		58	32	0.551724	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Missense_Mutation	SNP	ENST00000300527.4	37	CCDS13728.1	20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	G	12.81	2.050127	0.36181	0.023864	2.33E-4	ENSG00000142173	ENST00000300527;ENST00000357838;ENST00000310645;ENST00000409416;ENST00000397763	D;D;D;D;D	0.94184	-3.37;-3.37;-3.37;-3.37;-3.37	3.98	3.98	0.46160	.	1.534500	0.03661	N	0.242608	T	0.77418	0.4127	N	0.22421	0.69	0.25510	N	0.987462	P;P;P	0.49090	0.897;0.919;0.55	P;P;B	0.51615	0.675;0.514;0.198	T	0.78476	-0.2189	10	0.11485	T	0.65	-9.2802	11.7636	0.51918	0.0:0.0:0.7742:0.2258	rs61735835	278;278;278	P12110;P12110-2;P12110-3	CO6A2_HUMAN;.;.	K	278	ENSP00000300527:E278K;ENSP00000350497:E278K;ENSP00000312529:E278K;ENSP00000387115:E278K;ENSP00000380870:E278K	ENSP00000300527:E278K	E	+	1	0	COL6A2	46360244	0.075000	0.21258	1.000000	0.80357	0.787000	0.44495	0.977000	0.29475	1.956000	0.56807	0.555000	0.69702	GAG	G|0.991;A|0.009	0.009	strong		0.657	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1			A	47535816	G	A	47535816	3	1	22	1	0	0	0	0	1	0	0	0	3702	943	33	2	850	2	COL6A2	21	47535816	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	635146	47535816	594079	4327	7228											
COL6A2	1292	hgsc.bcm.edu	37	chr21	47545889	47545889	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctcatcaaggagagccggcgCcagaagacacgtgtgtttgc	10	7	13	11	3	2	3	2	0	0	3	2	4	2	3	2	2	2	1	2	2	2	1	rs61735829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:47545889C>G	ENST00000300527.4	+	26	2264	c.2160C>G	c.(2158-2160)cgC>cgG	p.R720R	COL6A2_ENST00000409416.1_Silent_p.R720R|COL6A2_ENST00000357838.4_Silent_p.R720R|COL6A2_ENST00000310645.5_Silent_p.R720R|COL6A2_ENST00000397763.1_Silent_p.R720R	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	720	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)|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)		AGAGCCGGCGCCAGAAGACAC	0.637													C|||	82	0.0163738	0.059	0.0058	5008	,	,		14676	0.0		0.0	False		,,,				2504	0.0				p.R720R		Atlas-SNP	.											COL6A2_ENST00000357838,NS,carcinoma,+2,3	COL6A2	351	3	0			c.C2160G						PASS	.	C	,,	227,4179	135.3+/-171.4	6,215,1982	68	67	67		2160,2160,2160	0.1	1	21	dbSNP_129	67	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A2	NM_001849.3,NM_058174.2,NM_058175.2	,,	6,218,6279	GG,GC,CC		0.0349,5.1521,1.7684	,,	720/1020,720/919,720/829	47545889	230,12776	2203	4300	6503	SO:0001819	synonymous_variant	1292	exon26			CCGGCGCCAGAAG	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.2160C>G	21.37:g.47545889C>G		148	0	0		166	86	0.518072	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Silent	SNP	ENST00000300527.4	37	CCDS13728.1																																																																																			C|0.982;G|0.018	0.018	strong		0.637	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1			G	47545889	C	G	47545889	2	3	22	1	0	0	0	0	0	0	0	1	3702	726	26	4		4	COL6A2	21	47545889	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	10073	47545889	584006	4328	7229											
C21orf56	84221	hgsc.bcm.edu	37	chr21	47581508	47581508	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcgctgaacgccgggtgcaCgtcgcggctgtagcccagct	5	7	14	15	6	0	1	0	1	0	0	2	1	0	1	2	2	4	5	2	2	2	1	rs74518516	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:47581508C>A	ENST00000291672.5	-	5	1869	c.808G>T	c.(808-810)Gtg>Ttg	p.V270L	SPATC1L_ENST00000330205.6_Missense_Mutation_p.V116L	NM_001142854.1	NP_001136326.1	Q9H0A9	SPC1L_HUMAN	spermatogenesis and centriole associated 1-like	270																	GCCGGGTGCACGTCGCGGCTG	0.692													C|||	122	0.024361	0.0877	0.0086	5008	,	,		12794	0.0		0.0	False		,,,				2504	0.0				p.V270L		Atlas-SNP	.											.	.	.	.	0			c.G808T						PASS	.	C	LEU/VAL,LEU/VAL	406,3986		22,362,1812	23	25	24		808,346	4.3	1	21	dbSNP_131	24	4,8584		0,4,4290	yes	missense,missense	C21orf56	NM_001142854.1,NM_032261.4	32,32	22,366,6102	AA,AC,CC		0.0466,9.2441,3.1587	benign,benign	270/341,116/187	47581508	410,12570	2196	4294	6490	SO:0001583	missense	84221	exon5			GGTGCACGTCGCG	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.808G>T	21.37:g.47581508C>A	ENSP00000291672:p.Val270Leu	67	0	0		99	57	0.575758	NM_001142854	B4E323|Q52LS9|Q6FIH5|Q6P0L3|Q9NSE5	Missense_Mutation	SNP	ENST00000291672.5	37	CCDS46653.1	57	0.0260989010989011	52	0.10569105691056911	5	0.013812154696132596	0	0.0	0	0.0	C	13.27	2.188243	0.38609	0.092441	4.66E-4	ENSG00000160284	ENST00000330205;ENST00000291672	T;T	0.50001	0.76;0.76	4.27	4.27	0.50696	.	0.098443	0.41938	D	0.000800	T	0.00637	0.0021	L	0.38838	1.175	0.27740	N	0.944518	B	0.32968	0.392	B	0.27380	0.079	T	0.02411	-1.1163	10	0.51188	T	0.08	-27.6288	8.1902	0.31363	0.0:0.8871:0.0:0.1129	.	270	Q9H0A9	CU056_HUMAN	L	116;270	ENSP00000333869:V116L;ENSP00000291672:V270L	ENSP00000291672:V270L	V	-	1	0	C21orf56	46405936	0.803000	0.28956	0.979000	0.43373	0.918000	0.54935	1.358000	0.34102	1.929000	0.55896	0.591000	0.81541	GTG	C|0.971;A|0.029	0.029	strong		0.692	SPATC1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376654.1	NM_032261		A	47581508	C	A	47581508	3	1	22	1	0	0	0	0	1	0	0	0	2129	536	19	4	218	4	C21orf56	21	47581508	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	35619	47581508	548387	4329	7230											
C21orf56	84221	hgsc.bcm.edu	37	chr21	47588365	47588365	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gcaaggggctcaggagcgggGacagcttcctgtcggtgcct	6	7	17	11	2	1	0	1	0	0	0	3	2	2	2	2	6	3	3	2	6	1	1	rs73908565	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:47588365G>A	ENST00000291672.5	-	3	1462	c.401C>T	c.(400-402)tCc>tTc	p.S134F	SPATC1L_ENST00000330205.6_5'UTR	NM_001142854.1	NP_001136326.1	Q9H0A9	SPC1L_HUMAN	spermatogenesis and centriole associated 1-like	134																	CAGGAGCGGGGACAGCTTCCT	0.647													G|||	123	0.0245607	0.09	0.0058	5008	,	,		16558	0.0		0.0	False		,,,				2504	0.0				p.S134F		Atlas-SNP	.											.	.	.	.	0			c.C401T						PASS	.	G	PHE/SER,	106,1278		7,92,593	49	52	51		401,	3.2	0.7	21	dbSNP_130	51	1,3181		0,1,1590	yes	missense,utr-5	C21orf56	NM_001142854.1,NM_032261.4	155,	7,93,2183	AA,AG,GG		0.0314,7.659,2.3434	probably-damaging,	134/341,	47588365	107,4459	692	1591	2283	SO:0001583	missense	84221	exon3			AGCGGGGACAGCT	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.401C>T	21.37:g.47588365G>A	ENSP00000291672:p.Ser134Phe	116	0	0		127	57	0.448819	NM_001142854	B4E323|Q52LS9|Q6FIH5|Q6P0L3|Q9NSE5	Missense_Mutation	SNP	ENST00000291672.5	37	CCDS46653.1	46	0.021062271062271064	44	0.08943089430894309	2	0.0055248618784530384	0	0.0	0	0.0	G	10.80	1.453781	0.26161	0.07659	3.14E-4	ENSG00000160284	ENST00000291672	T	0.55588	0.51	5.21	3.23	0.37069	.	0.477138	0.17215	N	0.182544	T	0.02193	0.0068	L	0.29908	0.895	0.09310	N	0.999992	P	0.44195	0.828	P	0.45138	0.471	T	0.00449	-1.1732	10	0.31617	T	0.26	-26.6257	12.7958	0.57558	0.0:0.3352:0.6648:0.0	.	134	Q9H0A9	CU056_HUMAN	F	134	ENSP00000291672:S134F	ENSP00000291672:S134F	S	-	2	0	C21orf56	46412793	0.073000	0.21202	0.739000	0.30968	0.521000	0.34408	0.543000	0.23237	1.164000	0.42652	0.467000	0.42956	TCC	G|0.978;A|0.022	0.022	strong		0.647	SPATC1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376654.1	NM_032261		A	47588365	G	A	47588365	3	1	22	1	0	0	0	0	1	0	0	0	2129	1174	41	2	633	2	C21orf56	21	47588365	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	6857	47588365	541530	4330	7231											
PCNT	5116	hgsc.bcm.edu	37	chr21	47754576	47754576	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcacaatcagtgaccaccAaccggaacagcgtgggatgt	12	7	11	11	2	2	1	2	1	0	0	2	3	2	3	3	2	3	1	3	2	3	1	rs200285580		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:47754576A>C	ENST00000359568.5	+	3	640	c.533A>C	c.(532-534)cAa>cCa	p.Q178P	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	178					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)					AGTGACCACCAACCGGAACAG	0.537																																					p.Q178P		Atlas-SNP	.											.	PCNT	283	.	0			c.A533C						PASS	.						205	139	161					21																	47754576		2203	4300	6503	SO:0001583	missense	5116	exon3			ACCACCAACCGGA	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.533A>C	21.37:g.47754576A>C	ENSP00000352572:p.Gln178Pro	293	0	0		333	48	0.144144	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	C	3.018	-0.202461	0.06219	.	.	ENSG00000160299	ENST00000359568;ENST00000337772	T	0.01258	5.09	0.235	0.235	0.15431	.	.	.	.	.	T	0.00754	0.0025	N	0.03608	-0.345	0.09310	N	1	B;B	0.20368	0.044;0.026	B;B	0.13407	0.009;0.004	T	0.47849	-0.9085	8	0.30854	T	0.27	.	.	.	.	.	60;178	O95613-2;O95613	.;PCNT_HUMAN	P	178;165	ENSP00000352572:Q178P	ENSP00000338675:Q165P	Q	+	2	0	PCNT	46579004	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-2.630000	0.00871	0.263000	0.21812	0.260000	0.18958	CAA	A|0.999;G|0.001	.	alt		0.537	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		C	47754576	A	C	47754576	3	2	22	1	0	0	0	0	1	0	0	0	11599	130	5	5	543	5	PCNT	21	47754576	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	166211	47754576	375319	4331	7232											
PCNT	5116	hgsc.bcm.edu	37	chr21	47766113	47766113	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagatgaggctggcctgcaTcagagtcaggtgacccggcg	9	6	16	10	2	2	4	2	2	0	2	2	5	2	4	2	4	1	2	2	4	1	0	rs34500739	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:47766113T>G	ENST00000359568.5	+	4	818	c.711T>G	c.(709-711)caT>caG	p.H237Q	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	237	Glu-rich.				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)					CTGGCCTGCATCAGAGTCAGG	0.602													G|||	128	0.0255591	0.028	0.0303	5008	,	,		16755	0.001		0.0646	False		,,,				2504	0.0041				p.H237Q		Atlas-SNP	.											.	PCNT	283	.	0			c.T711G						PASS	.	G	GLN/HIS	192,4214	807.9+/-415.9	5,182,2016	83	74	77		711	3.3	1	21	dbSNP_126	77	528,8072	795.4+/-407.5	11,506,3783	yes	missense	PCNT	NM_006031.5	24	16,688,5799	GG,GT,TT		6.1395,4.3577,5.5359	benign	237/3337	47766113	720,12286	2203	4300	6503	SO:0001583	missense	5116	exon4			CCTGCATCAGAGT	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.711T>G	21.37:g.47766113T>G	ENSP00000352572:p.His237Gln	100	0	0		129	71	0.550388	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	92	0.04212454212454213	21	0.042682926829268296	16	0.04419889502762431	1	0.0017482517482517483	54	0.0712401055408971	G	2.436	-0.329782	0.05314	0.043577	0.061395	ENSG00000160299	ENST00000359568;ENST00000337772	T	0.01279	5.06	3.27	3.27	0.37495	.	.	.	.	.	T	0.00073	0.0002	N	0.00926	-1.1	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45145	-0.9281	9	0.09084	T	0.74	.	8.0049	0.30319	0.0:0.0:0.7564:0.2436	rs34500739	119;237	O95613-2;O95613	.;PCNT_HUMAN	Q	237;224	ENSP00000352572:H237Q	ENSP00000338675:H224Q	H	+	3	2	PCNT	46590541	0.057000	0.20700	0.965000	0.40720	0.171000	0.22731	0.660000	0.25009	0.988000	0.38734	-0.648000	0.03929	CAT	T|0.949;G|0.051	0.051	strong		0.602	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		G	47766113	T	G	47766113	3	3	22	1	0	0	0	0	1	0	0	0	11599	1432	50	5	725	5	PCNT	21	47766113	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	11537	47766113	363782	4332	7233											
CCT8L2	150160	hgsc.bcm.edu	37	chr22	17071899	17071899	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acgatttcatctacagtcacGagctgtagcaccacctcagc	11	9	7	14	2	4	0	3	0	1	0	4	2	4	0	2	0	4	3	2	0	2	3	rs547801677	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:17071899G>A	ENST00000359963.3	-	1	1801	c.1542C>T	c.(1540-1542)ctC>ctT	p.L514L		NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2	514					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)				CTACAGTCACGAGCTGTAGCA	0.498													g|||	3	0.000599042	0.0	0.0	5008	,	,		18283	0.003		0.0	False		,,,				2504	0.0				p.L514L		Atlas-SNP	.											CCT8L2,NS,carcinoma,-2,2	CCT8L2	150	2	0			c.C1542T						PASS	.						103	96	98					22																	17071899		2203	4298	6501	SO:0001819	synonymous_variant	150160	exon1			AGTCACGAGCTGT	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	ENST00000359963.3:c.1542C>T	22.37:g.17071899G>A		148	0	0		173	94	0.543353	NM_014406	A4QPH3|Q9UJS3	Silent	SNP	ENST00000359963.3	37	CCDS13738.1																																																																																			.	.	none		0.498	CCT8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280580.1			A	17071899	G	A	17071899	2	1	22	1	0	0	0	0	0	0	0	1	2963	1045	37	1		1	CCT8L2	22	17071899	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10		17071899	34232667	4333	7234											
CCT8L2	150160	hgsc.bcm.edu	37	chr22	17072347	17072347	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caggtgtgcctgtacattccCattcaaataccacagccaaa	13	9	6	13	0	1	0	1	0	0	0	2	0	2	0	4	1	4	1	4	1	4	4	rs139948519	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:17072347C>T	ENST00000359963.3	-	1	1353	c.1094G>A	c.(1093-1095)tGg>tAg	p.W365*		NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2	365					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)				TGTACATTCCCATTCAAATAC	0.612													c|||	113	0.0225639	0.0598	0.0029	5008	,	,		18689	0.0		0.002	False		,,,				2504	0.0307				p.W365X		Atlas-SNP	.											.	CCT8L2	150	.	0			c.G1094A						PASS	.	C	stop/TRP	301,4105	164.7+/-196.3	7,287,1909	88	83	85		1094	2	0.2	22	dbSNP_134	85	28,8572	19.2+/-60.6	0,28,4272	no	stop-gained	CCT8L2	NM_014406.4		7,315,6181	TT,TC,CC		0.3256,6.8316,2.5296		365/558	17072347	329,12677	2203	4300	6503	SO:0001587	stop_gained	150160	exon1			CATTCCCATTCAA	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	ENST00000359963.3:c.1094G>A	22.37:g.17072347C>T	ENSP00000353048:p.Trp365*	69	0	0		53	29	0.54717	NM_014406	A4QPH3|Q9UJS3	Nonsense_Mutation	SNP	ENST00000359963.3	37	CCDS13738.1	29	0.013278388278388278	26	0.052845528455284556	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	c	18.96	3.734449	0.69189	0.068316	0.003256	ENSG00000198445	ENST00000359963	.	.	.	1.98	1.98	0.26296	.	0.261754	0.21132	U	0.079635	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	-8.0904	7.4423	0.27190	0.0:1.0:0.0:0.0	.	.	.	.	X	365	.	ENSP00000353048:W365X	W	-	2	0	CCT8L2	15452347	0.722000	0.28017	0.224000	0.23877	0.129000	0.20672	1.546000	0.36179	1.115000	0.41800	0.379000	0.24179	TGG	C|0.982;T|0.018	0.018	strong		0.612	CCT8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280580.1			T	17072347	C	T	17072347	4	4	22	1	0	0	0	0	0	1	0	0	2963	595	21	2	583	2	CCT8L2	22	17072347	Nonsense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	448	17072347	34232219	4334	7235											
XKR3	150165	hgsc.bcm.edu	37	chr22	17288849	17288849	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acagtagagaacagttgagaAgataatgctaaaaggaaagc	20	6	11	4	0	0	3	0	1	0	3	0	6	0	4	0	1	3	3	0	1	7	4	rs150400922	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:17288849A>G	ENST00000331428.5	-	2	217	c.115T>C	c.(115-117)Ttc>Ctc	p.F39L		NM_175878.3	NP_787074.2	Q5GH77	XKR3_HUMAN	XK, Kell blood group complex subunit-related family, member 3	39						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(6)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	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)				ACAGTTGAGAAGATAATGCTA	0.388													.|||	22	0.00439297	0.0159	0.0014	5008	,	,		19510	0.0		0.0	False		,,,				2504	0.0				p.F39L		Atlas-SNP	.											.	XKR3	51	.	0			c.T115C						PASS	.	A	LEU/PHE	71,3691		0,71,1810	115	110	112		115	0.5	0	22	dbSNP_134	112	0,8218		0,0,4109	yes	missense	XKR3	NM_175878.3	22	0,71,5919	GG,GA,AA		0.0,1.8873,0.5927	benign	39/460	17288849	71,11909	1881	4109	5990	SO:0001583	missense	150165	exon2			TTGAGAAGATAAT	AY989815	CCDS42975.1	22q11.1	2007-01-16	2006-01-12		ENSG00000172967	ENSG00000172967			28778	protein-coding gene	gene with protein product		611674	"X Kell blood group precursor-related family, member 3"			16431037	Standard	NM_175878		Approved	MGC57211, XTES	uc002zlv.3	Q5GH77	OTTHUMG00000143726	ENST00000331428.5:c.115T>C	22.37:g.17288849A>G	ENSP00000331704:p.Phe39Leu	185	0	0		209	94	0.449761	NM_175878	B2RPN1|Q52PG8|Q8N7E1	Missense_Mutation	SNP	ENST00000331428.5	37	CCDS42975.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	.	4.134	0.023117	0.08006	0.018873	0.0	ENSG00000172967	ENST00000331428	T	0.61859	0.07	0.539	0.539	0.17156	.	0.396682	0.23023	U	0.052823	T	0.17577	0.0422	N	0.22421	0.69	0.19775	N	0.999951	B	0.02656	0.0	B	0.01281	0.0	T	0.04090	-1.0978	10	0.13853	T	0.58	.	2.6787	0.05087	0.5696:1.0E-4:0.0:0.4304	.	39	Q5GH77	XKR3_HUMAN	L	39	ENSP00000331704:F39L	ENSP00000331704:F39L	F	-	1	0	XKR3	15668849	0.930000	0.31532	0.021000	0.16686	0.010000	0.07245	0.129000	0.15830	0.485000	0.27652	0.246000	0.17985	TTC	A|0.996;G|0.004	0.004	strong		0.388	XKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289789.1	NM_175878		G	17288849	A	G	17288849	3	3	22	1	0	0	0	0	1	0	0	0	17447	72	3	3	1276	3	XKR3	22	17288849	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	216502	17288849	34015717	4335	7236											
GAB4	128954	hgsc.bcm.edu	37	chr22	17445710	17445710	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tctgtgttggtgatgctctgCgtggagatggggtgttggga	4	14	19	4	1	2	2	0	1	2	1	2	4	2	3	0	5	2	3	0	5	0	2	rs5992599	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:17445710C>T	ENST00000400588.1	-	8	1529	c.1422G>A	c.(1420-1422)acG>acA	p.T474T	GAB4_ENST00000523144.1_5'Flank	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	474										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)				TGATGCTCTGCGTGGAGATGG	0.572													C|||	202	0.0403355	0.1498	0.0058	5008	,	,		19710	0.0		0.0	False		,,,				2504	0.0				p.T474T		Atlas-SNP	.											.	GAB4	95	.	0			c.G1422A						PASS	.	C		504,3876	213.5+/-233.1	31,442,1717	151	162	158		1422	-3.9	0.3	22	dbSNP_114	158	2,8580	2.2+/-6.3	0,2,4289	no	coding-synonymous	GAB4	NM_001037814.1		31,444,6006	TT,TC,CC		0.0233,11.5068,3.9037		474/575	17445710	506,12456	2190	4291	6481	SO:0001819	synonymous_variant	128954	exon8			GCTCTGCGTGGAG	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.1422G>A	22.37:g.17445710C>T		208	1	0.00480769		259	127	0.490348	NM_001037814		Silent	SNP	ENST00000400588.1	37	CCDS42976.1																																																																																			C|0.954;T|0.046	0.046	strong		0.572	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882		T	17445710	C	T	17445710	2	4	22	1	0	0	0	0	0	0	0	1	6159	755	27	1		1	GAB4	22	17445710	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	156861	17445710	33858856	4336	7237											
GAB4	128954	hgsc.bcm.edu	37	chr22	17447237	17447237	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaatgctgtctgacaggccCacaagcgttcttcctggcta	8	10	10	13	1	2	1	0	1	2	0	3	1	3	1	2	2	2	4	2	2	3	3	rs115898475	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:17447237C>G	ENST00000400588.1	-	6	1148	c.1041G>C	c.(1039-1041)gtG>gtC	p.V347V	GAB4_ENST00000523144.1_5'Flank	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	347										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)				CTGACAGGCCCACAAGCGTTC	0.527													C|||	31	0.0061901	0.0227	0.0014	5008	,	,		21894	0.0		0.0	False		,,,				2504	0.0				p.V347V		Atlas-SNP	.											.	GAB4	95	.	0			c.G1041C						PASS	.	C		72,3902		0,72,1915	26	28	28		1041	1.7	0.2	22	dbSNP_132	28	0,8384		0,0,4192	no	coding-synonymous	GAB4	NM_001037814.1		0,72,6107	GG,GC,CC		0.0,1.8118,0.5826		347/575	17447237	72,12286	1987	4192	6179	SO:0001819	synonymous_variant	128954	exon6			CAGGCCCACAAGC	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.1041G>C	22.37:g.17447237C>G		64	0	0		55	33	0.6	NM_001037814		Silent	SNP	ENST00000400588.1	37	CCDS42976.1																																																																																			C|0.994;G|0.006	0.006	strong		0.527	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882		G	17447237	C	G	17447237	2	3	22	1	0	0	0	0	0	0	0	1	6159	581	21	4		4	GAB4	22	17447237	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1527	17447237	33857329	4337	7238											
GAB4	128954	hgsc.bcm.edu	37	chr22	17472785	17472785	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgctttcctcctgcctgaaGccacagatctgacagatgct	8	11	9	13	0	1	4	0	2	1	2	3	4	3	4	4	0	4	2	4	0	1	1	rs116325774	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:17472785G>A	ENST00000400588.1	-	2	563	c.456C>T	c.(454-456)ggC>ggT	p.G152G	GAB4_ENST00000523144.1_5'UTR	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	152	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)				CCTGCCTGAAGCCACAGATCT	0.547													G|||	30	0.00599042	0.0227	0.0	5008	,	,		21341	0.0		0.0	False		,,,				2504	0.0				p.G152G		Atlas-SNP	.											GAB4,NS,carcinoma,-1,1	GAB4	95	1	0			c.C456T						scavenged	.	G		60,4346	55.5+/-91.7	1,58,2144	241	243	242		456	1.8	1	22	dbSNP_132	242	0,8600		0,0,4300	no	coding-synonymous	GAB4	NM_001037814.1		1,58,6444	AA,AG,GG		0.0,1.3618,0.4613		152/575	17472785	60,12946	2203	4300	6503	SO:0001819	synonymous_variant	128954	exon2			CCTGAAGCCACAG	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.456C>T	22.37:g.17472785G>A		272	2	0.00735294		284	136	0.478873	NM_001037814		Silent	SNP	ENST00000400588.1	37	CCDS42976.1																																																																																			G|0.994;A|0.006	0.006	strong		0.547	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882		A	17472785	G	A	17472785	2	1	22	1	0	0	0	0	0	0	0	1	6159	958	34	2		2	GAB4	22	17472785	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	25548	17472785	33831781	4338	7239											
IL17RA	23765	hgsc.bcm.edu	37	chr22	17589983	17589983	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagcgggcgcccctggtgcGcgagcctggctcccaggcct	4	5	16	16	4	0	0	0	0	0	0	1	2	1	0	5	4	3	1	5	4	1	0	rs189025188		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:17589983G>A	ENST00000319363.6	+	13	2007	c.1874G>A	c.(1873-1875)cGc>cAc	p.R625H		NM_014339.5	NP_055154.3	Q96F46	I17RA_HUMAN	interleukin 17 receptor A	625					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)		CCCCTGGTGCGCGAGCCTGGC	0.677													G|||	1	0.000199681	0.0008	0.0	5008	,	,		13392	0.0		0.0	False		,,,				2504	0.0				p.R625H		Atlas-SNP	.											.	IL17RA	62	.	0			c.G1874A						PASS	.	G	HIS/ARG	1,4309		0,1,2154	7	6	6		1874	-4.2	0	22		6	0,8498		0,0,4249	no	missense	IL17RA	NM_014339.5	29	0,1,6403	AA,AG,GG		0.0,0.0232,0.0078	benign	625/867	17589983	1,12807	2155	4249	6404	SO:0001583	missense	23765	exon13			TGGTGCGCGAGCC	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.1874G>A	22.37:g.17589983G>A	ENSP00000320936:p.Arg625His	10	0	0		16	12	0.75	NM_014339	O43844|Q20WK1	Missense_Mutation	SNP	ENST00000319363.6	37	CCDS13739.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	7.477	0.647869	0.14516	2.32E-4	0.0	ENSG00000177663	ENST00000425985;ENST00000319363	T	0.07800	3.16	5.1	-4.19	0.03835	.	0.588863	0.17907	N	0.157988	T	0.04363	0.0120	N	0.21583	0.68	0.09310	N	1	B;B	0.17038	0.01;0.02	B;B	0.10450	0.002;0.005	T	0.31475	-0.9942	10	0.37606	T	0.19	-15.8275	7.1335	0.25515	0.4871:0.0:0.4036:0.1092	.	573;625	D3YTB4;Q96F46	.;I17RA_HUMAN	H	573;625	ENSP00000320936:R625H	ENSP00000320936:R625H	R	+	2	0	IL17RA	15969983	0.000000	0.05858	0.016000	0.15963	0.002000	0.02628	-0.188000	0.09642	-0.559000	0.06110	-0.254000	0.11334	CGC	G|0.999;A|0.001	0.001	strong		0.677	IL17RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315820.1	NM_014339		A	17589983	G	A	17589983	3	1	22	1	0	0	0	0	1	0	0	0	7648	1087	38	1	1924	1	IL17RA	22	17589983	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	117198	17589983	33714583	4339	7240											
USP18	11274	hgsc.bcm.edu	37	chr22	18644597	18644597	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgacgagcagaggagaagcGtccctttccagatgcttctg	9	9	12	11	2	1	4	0	1	1	3	3	6	3	4	2	1	3	2	2	1	1	2	rs143481018		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:18644597G>A	ENST00000215794.7	+	4	725	c.295G>A	c.(295-297)Gtc>Atc	p.V99I		NM_017414.3	NP_059110.2	Q9UMW8	UBP18_HUMAN	ubiquitin specific peptidase 18	99	USP.				cytokine-mediated signaling pathway (GO:0019221)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|stomach(1)	10						GAGGAGAAGCGTCCCTTTCCA	0.577																																					p.V99I		Atlas-SNP	.											.	USP18	22	.	0			c.G295A						PASS	.						23	20	21					22																	18644597		2202	4295	6497	SO:0001583	missense	11274	exon4			AGAAGCGTCCCTT	AJ243526	CCDS13752.1	22q11.2	2008-04-11	2005-08-08		ENSG00000184979	ENSG00000184979		"Ubiquitin-specific peptidases"	12616	protein-coding gene	gene with protein product		607057	"ubiquitin specific protease 18"			12838346	Standard	NM_017414		Approved		uc002zny.3	Q9UMW8	OTTHUMG00000150104	ENST00000215794.7:c.295G>A	22.37:g.18644597G>A	ENSP00000215794:p.Val99Ile	324	0	0		439	127	0.289294	NM_017414	Q53Y90|Q6IAD9|Q9NY71	Missense_Mutation	SNP	ENST00000215794.7	37	CCDS13752.1	.	.	.	.	.	.	.	.	.	.	.	16.12	3.034318	0.54896	.	.	ENSG00000184979	ENST00000215794	T	0.32023	1.47	5.57	2.19	0.27852	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.490245	0.22485	N	0.059456	T	0.24967	0.0606	N	0.26042	0.785	0.24638	N	0.993584	D	0.69078	0.997	P	0.57548	0.823	T	0.12863	-1.0531	10	0.08837	T	0.75	.	3.4873	0.07625	0.0914:0.1718:0.559:0.1778	.	99	Q9UMW8	UBP18_HUMAN	I	99	ENSP00000215794:V99I	ENSP00000215794:V99I	V	+	1	0	USP18	17024597	0.992000	0.36948	0.971000	0.41717	0.704000	0.40688	1.496000	0.35638	0.640000	0.30582	0.650000	0.86243	GTC	.	.	weak		0.577	USP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316368.1			A	18644597	G	A	18644597	3	1	22	1	0	0	0	0	1	0	0	0	17064	1145	40	1	305	1	USP18	22	18644597	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1054614	18644597	32659969	4340	7241											
TSSK2	23617	hgsc.bcm.edu	37	chr22	19118992	19118992	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggttcctacgcaaaagtcaAatctgcctactctgagcgcc	10	9	9	13	2	3	1	1	1	2	0	4	1	4	1	3	1	4	2	3	1	5	3	rs3747052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:19118992A>G	ENST00000399635.2	+	1	672	c.80A>G	c.(79-81)aAa>aGa	p.K27R	DGCR14_ENST00000252137.6_3'UTR	NM_053006.4	NP_443732.3	Q96PF2	TSSK2_HUMAN	testis-specific serine kinase 2	27	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		K -> R (may be associated with infertility; dbSNP:rs3747052). {ECO:0000269|PubMed:17344846}.		multicellular organismal development (GO:0007275)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(2)|lung(2)|prostate(4)|stomach(1)	11	Colorectal(54;0.0993)					GCAAAAGTCAAATCTGCCTAC	0.517													.|||	196	0.0391374	0.1165	0.0144	5008	,	,		22180	0.0198		0.008	False		,,,				2504	0.0041				p.K27R		Atlas-SNP	.											.	TSSK2	29	.	0			c.A80G						PASS	.	A	,ARG/LYS	482,3924	225.9+/-241.6	25,432,1746	82	70	74		,80	4.6	1	22	dbSNP_107	74	5,8595	3.7+/-12.6	0,5,4295	yes	utr-3,missense	DGCR14,TSSK2	NM_022719.2,NM_053006.4	,26	25,437,6041	GG,GA,AA		0.0581,10.9396,3.7444	,benign	,27/359	19118992	487,12519	2203	4300	6503	SO:0001583	missense	23617	exon1			AAGTCAAATCTGC	AF362953	CCDS13755.1	22q11.21	2007-01-30	2005-03-10	2005-03-12	ENSG00000206203	ENSG00000206203			11401	protein-coding gene	gene with protein product		610710	"serine/threonine kinase 22B (spermiogenesis associated)"	STK22B		10591208	Standard	NM_053006		Approved	SPOGA2, FLJ38613	uc002zow.2	Q96PF2	OTTHUMG00000150118	ENST00000399635.2:c.80A>G	22.37:g.19118992A>G	ENSP00000382544:p.Lys27Arg	107	0	0		95	60	0.631579	NM_053006	Q8IY55	Missense_Mutation	SNP	ENST00000399635.2	37	CCDS13755.1	89	0.04075091575091575	63	0.12804878048780488	6	0.016574585635359115	13	0.022727272727272728	7	0.009234828496042216	A	16.33	3.091896	0.55968	0.109396	5.81E-4	ENSG00000206203	ENST00000399635	D	0.82619	-1.63	5.62	4.56	0.56223	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	0.53938	D	0.000060	T	0.02727	0.0082	N	0.13327	0.33	0.32898	D	0.51277	B	0.23185	0.081	B	0.42882	0.401	T	0.58446	-0.7635	10	0.72032	D	0.01	.	9.692	0.40134	0.845:0.0:0.0:0.155	rs3747052;rs3747052	27	Q96PF2	TSSK2_HUMAN	R	27	ENSP00000382544:K27R	ENSP00000382544:K27R	K	+	2	0	TSSK2	17498992	1.000000	0.71417	0.984000	0.44739	0.986000	0.74619	5.829000	0.69316	0.912000	0.36772	0.460000	0.39030	AAA	A|0.959;G|0.041	0.041	strong		0.517	TSSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316431.1			G	19118992	A	G	19118992	3	3	22	1	0	0	0	0	1	0	0	0	16684	14	1	3	82	3	TSSK2	22	19118992	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	474395	19118992	32185574	4341	7242											
CLTCL1	8218	hgsc.bcm.edu	37	chr22	19178854	19178854	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtccaggtgtggtccagccGgggtgaaagcaccagcagca	9	6	15	11	1	0	1	0	1	0	0	2	1	2	1	4	4	4	3	4	4	1	0	rs190366603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:19178854G>A	ENST00000263200.10	-	27	4357	c.4285C>T	c.(4285-4287)Cgg>Tgg	p.R1429W	CLTCL1_ENST00000427926.1_Missense_Mutation_p.R1429W|CLTCL1_ENST00000442042.2_5'UTR|CLTCL1_ENST00000353891.5_Missense_Mutation_p.R1429W	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	1429	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)					TGGTCCAGCCGGGGTGAAAGC	0.493			T	?	ALCL								G|||	3	0.000599042	0.0023	0.0	5008	,	,		16783	0.0		0.0	False		,,,				2504	0.0				p.R1429W		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"clathrin, heavy polypeptide-like 1"		L	CLTCL1,NS,carcinoma,0,1	CLTCL1	115	1	0			c.C4285T						PASS	.	G	TRP/ARG,TRP/ARG	5,3907		0,5,1951	80	84	83		4285,4285	3.6	1	22		83	0,8286		0,0,4143	yes	missense,missense	CLTCL1	NM_007098.3,NM_001835.3	101,101	0,5,6094	AA,AG,GG		0.0,0.1278,0.041	benign,benign	1429/1641,1429/1584	19178854	5,12193	1956	4143	6099	SO:0001583	missense	8218	exon27			CCAGCCGGGGTGA		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.4285C>T	22.37:g.19178854G>A	ENSP00000445677:p.Arg1429Trp	91	0	0		88	51	0.579545	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	37	CCDS46662.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	18.39	3.613700	0.66672	0.001278	0.0	ENSG00000070371	ENST00000353891;ENST00000263200;ENST00000427926	T;T;T	0.20332	2.08;2.08;2.08	3.61	3.61	0.41365	Tetratricopeptide-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000002	T	0.40956	0.1138	M	0.92649	3.33	0.80722	D	1	B;B;B	0.33171	0.4;0.318;0.266	B;B;B	0.39217	0.283;0.256;0.294	T	0.57888	-0.7733	10	0.87932	D	0	-17.9135	15.4348	0.75137	0.0:0.0:1.0:0.0	.	1429;252;1429	P53675-2;B7Z1Z7;P53675	.;.;CLH2_HUMAN	W	1429	ENSP00000439662:R1429W;ENSP00000445677:R1429W;ENSP00000441158:R1429W	ENSP00000445677:R1429W	R	-	1	2	CLTCL1	17558854	1.000000	0.71417	0.998000	0.56505	0.787000	0.44495	2.973000	0.49264	1.868000	0.54150	0.585000	0.79938	CGG	G|0.999;A|0.001	0.001	strong		0.493	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098		A	19178854	G	A	19178854	3	1	22	1	0	0	0	0	1	0	0	0	3569	1115	39	1	661	1	CLTCL1	22	19178854	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	59862	19178854	32125712	4342	7243											
CLTCL1	8218	hgsc.bcm.edu	37	chr22	19196449	19196449	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tactgctcctgctggctgacTgaacaacttccaggtaagag	10	10	10	11	0	0	3	0	2	0	1	2	3	2	3	2	2	5	4	2	2	4	3	rs182543131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:19196449T>C	ENST00000263200.10	-	21	3497	c.3425A>G	c.(3424-3426)cAg>cGg	p.Q1142R	CLTCL1_ENST00000427926.1_Missense_Mutation_p.Q1142R|CLTCL1_ENST00000442042.2_5'Flank|CLTCL1_ENST00000353891.5_Missense_Mutation_p.Q1142R	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	1142	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)					GCTGGCTGACTGAACAACTTC	0.517			T	?	ALCL								T|||	3	0.000599042	0.0023	0.0	5008	,	,		19417	0.0		0.0	False		,,,				2504	0.0				p.Q1142R		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"clathrin, heavy polypeptide-like 1"		L	.	CLTCL1	115	.	0			c.A3425G						PASS	.	T	ARG/GLN,ARG/GLN	5,3951		0,5,1973	58	59	59		3425,3425	2.8	1	22		59	0,8310		0,0,4155	yes	missense,missense	CLTCL1	NM_001835.3,NM_007098.3	43,43	0,5,6128	CC,CT,TT		0.0,0.1264,0.0408	benign,benign	1142/1584,1142/1641	19196449	5,12261	1978	4155	6133	SO:0001583	missense	8218	exon21			GCTGACTGAACAA		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.3425A>G	22.37:g.19196449T>C	ENSP00000445677:p.Gln1142Arg	103	0	0		96	53	0.552083	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	37	CCDS46662.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	T	12.81	2.050304	0.36181	0.001264	0.0	ENSG00000070371	ENST00000353891;ENST00000263200;ENST00000427926	T;T;T	0.19532	2.14;2.14;2.14	3.85	2.82	0.32997	Tetratricopeptide-like helical (1);Armadillo-type fold (1);	0.229394	0.37577	N	0.002026	T	0.15565	0.0375	N	0.26042	0.785	0.35290	D	0.782104	B;B	0.22541	0.003;0.071	B;B	0.31390	0.02;0.129	T	0.13899	-1.0492	10	0.39692	T	0.17	-8.2343	8.8849	0.35398	0.0:0.0903:0.0:0.9097	.	1142;1142	P53675-2;P53675	.;CLH2_HUMAN	R	1142	ENSP00000439662:Q1142R;ENSP00000445677:Q1142R;ENSP00000441158:Q1142R	ENSP00000445677:Q1142R	Q	-	2	0	CLTCL1	17576449	1.000000	0.71417	0.975000	0.42487	0.916000	0.54674	5.366000	0.66122	0.537000	0.28751	0.533000	0.62120	CAG	T|0.999;C|0.001	0.001	strong		0.517	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098		C	19196449	T	C	19196449	3	2	22	1	0	0	0	0	1	0	0	0	3569	1580	55	3	1545	3	CLTCL1	22	19196449	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	17595	19196449	32108117	4343	7244											
HIRA	7290	hgsc.bcm.edu	37	chr22	19340928	19340928	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagccaatggcggtactcGtggctggactgcagggtgag	8	7	18	8	2	0	1	0	1	0	0	1	3	0	3	1	6	3	3	1	6	2	1	rs34000365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:19340928G>A	ENST00000263208.5	-	23	3055	c.2799C>T	c.(2797-2799)caC>caT	p.H933H	HIRA_ENST00000340170.4_Silent_p.H726H|HIRA_ENST00000541063.1_Silent_p.H889H|HIRA_ENST00000546308.1_3'UTR	NM_003325.3	NP_003316.3	P54198	HIRA_HUMAN	histone cell cycle regulator	933	Interaction with histone H4.				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)					GGCGGTACTCGTGGCTGGACT	0.622													G|||	35	0.00698882	0.0257	0.0014	5008	,	,		20446	0.0		0.0	False		,,,				2504	0.0				p.H933H		Atlas-SNP	.											.	HIRA	100	.	0			c.C2799T						PASS	.	G		124,4282	91.1+/-129.8	3,118,2082	73	48	57		2799	-2.7	1	22	dbSNP_126	57	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	HIRA	NM_003325.3		3,126,6374	AA,AG,GG		0.093,2.8143,1.0149		933/1018	19340928	132,12874	2203	4300	6503	SO:0001819	synonymous_variant	7290	exon23			GTACTCGTGGCTG	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.2799C>T	22.37:g.19340928G>A		96	0	0		107	50	0.46729	NM_003325	Q05BU9|Q8IXN2	Silent	SNP	ENST00000263208.5	37	CCDS13759.1																																																																																			G|0.990;A|0.010	0.010	strong		0.622	HIRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316488.2	NM_003325		A	19340928	G	A	19340928	2	1	22	1	0	0	0	0	0	0	0	1	7129	1136	40	1		1	HIRA	22	19340928	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	144479	19340928	31963638	4344	7245											
COMT	1312	hgsc.bcm.edu	37	chr22	19950268	19950268	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcggagcccgggaacgcacaGagcgtgctggaggccattga	9	4	17	11	4	0	2	0	1	0	1	0	5	0	5	2	4	4	2	2	4	1	1	rs740602	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:19950268G>A	ENST00000361682.6	+	3	601	c.219G>A	c.(217-219)caG>caA	p.Q73Q	MIR4761_ENST00000585066.1_RNA|COMT_ENST00000407537.1_Silent_p.Q23Q|COMT_ENST00000403710.1_Silent_p.Q73Q|COMT_ENST00000403184.1_Silent_p.Q73Q|COMT_ENST00000449653.1_Silent_p.Q23Q|COMT_ENST00000406520.3_Silent_p.Q73Q	NM_000754.3	NP_000745.1	P21964	COMT_HUMAN	catechol-O-methyltransferase	73					cellular response to phosphate starvation (GO:0016036)|dopamine catabolic process (GO:0042420)|estrogen metabolic process (GO:0008210)|female pregnancy (GO:0007565)|learning (GO:0007612)|methylation (GO:0032259)|multicellular organismal reproductive process (GO:0048609)|negative regulation of dopamine metabolic process (GO:0045963)|negative regulation of smooth muscle cell proliferation (GO:0048662)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter catabolic process (GO:0042135)|positive regulation of homocysteine metabolic process (GO:0050668)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to organic cyclic compound (GO:0014070)|response to pain (GO:0048265)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	catechol O-methyltransferase activity (GO:0016206)|magnesium ion binding (GO:0000287)|O-methyltransferase activity (GO:0008171)			kidney(1)|lung(1)|ovary(1)|prostate(1)|stomach(1)	5	Colorectal(54;0.0993)				Conjugated Estrogens(DB00286)|Diethylstilbestrol(DB00255)|Dobutamine(DB00841)|Dopamine(DB00988)|Entacapone(DB00494)|Methyldopa(DB00968)|Micafungin(DB01141)|S-Adenosylmethionine(DB00118)|Testosterone Propionate(DB01420)|Tolcapone(DB00323)	GGAACGCACAGAGCGTGCTGG	0.622													G|||	300	0.0599042	0.2005	0.0202	5008	,	,		18048	0.0		0.0089	False		,,,				2504	0.0123				p.Q73Q		Atlas-SNP	.											.	COMT	10	.	0			c.G219A						PASS	.	G	,,,	790,3616	314.4+/-293.6	72,646,1485	80	75	77		219,219,219,69	2.2	1	22	dbSNP_86	77	39,8561	25.7+/-73.6	0,39,4261	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	COMT	NM_000754.3,NM_001135161.1,NM_001135162.1,NM_007310.2	,,,	72,685,5746	AA,AG,GG		0.4535,17.9301,6.374	,,,	73/272,73/272,73/272,23/222	19950268	829,12177	2203	4300	6503	SO:0001819	synonymous_variant	1312	exon3			CGCACAGAGCGTG		CCDS13770.1, CCDS46663.1	22q11.21	2012-10-02			ENSG00000093010	ENSG00000093010	2.1.1.6		2228	protein-coding gene	gene with protein product		116790				1572656	Standard	NM_000754		Approved		uc002zqu.3	P21964	OTTHUMG00000150529	ENST00000361682.6:c.219G>A	22.37:g.19950268G>A		116	0	0		109	47	0.431193	NM_000754	A8MPV9|Q6IB07|Q6ICE6|Q9BWC7	Silent	SNP	ENST00000361682.6	37	CCDS13770.1																																																																																			A|0.059;C|0.007	0.059	strong		0.622	COMT-011	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318936.2	NM_000754		A	19950268	G	A	19950268	2	1	22	1	0	0	0	0	0	0	0	1	3727	933	33	2		2	COMT	22	19950268	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	609340	19950268	31354298	4345	7246											
ARVCF	421	hgsc.bcm.edu	37	chr22	19960666	19960666	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggccacgagagccaccaacGctggcaccccgcgtgcctgc	8	3	12	18	4	0	1	0	0	0	1	0	2	0	1	6	2	4	2	6	2	1	0	rs115736959	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:19960666G>A	ENST00000263207.3	-	14	2705	c.2414C>T	c.(2413-2415)gCg>gTg	p.A805V	ARVCF_ENST00000406259.1_Missense_Mutation_p.A799V|ARVCF_ENST00000401994.1_Missense_Mutation_p.A742V|ARVCF_ENST00000406522.1_Missense_Mutation_p.A736V|ARVCF_ENST00000344269.3_Missense_Mutation_p.A742V	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	805					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)					AGCCACCAACGCTGGCACCCC	0.711													G|||	64	0.0127796	0.0446	0.0072	5008	,	,		10944	0.0		0.0	False		,,,				2504	0.0				p.A805V		Atlas-SNP	.											.	ARVCF	54	.	0			c.C2414T						PASS	.	G	VAL/ALA	188,4196		0,188,2004	19	18	18		2414	3.2	0.1	22	dbSNP_132	18	2,8574		0,2,4286	yes	missense	ARVCF	NM_001670.2	64	0,190,6290	AA,AG,GG		0.0233,4.2883,1.466	benign	805/963	19960666	190,12770	2192	4288	6480	SO:0001583	missense	421	exon14			ACCAACGCTGGCA		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.2414C>T	22.37:g.19960666G>A	ENSP00000263207:p.Ala805Val	24	0	0		38	19	0.5	NM_001670	B7WNV2	Missense_Mutation	SNP	ENST00000263207.3	37	CCDS13771.1	25	0.011446886446886446	22	0.044715447154471545	3	0.008287292817679558	0	0.0	0	0.0	G	15.10	2.734386	0.48939	0.042883	2.33E-4	ENSG00000099889	ENST00000263207;ENST00000344269;ENST00000401994;ENST00000406522;ENST00000406259	T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83	4.34	3.24	0.37175	Armadillo-like helical (1);Armadillo-type fold (1);	0.113654	0.56097	D	0.000025	T	0.06325	0.0163	N	0.22421	0.69	0.36590	D	0.874035	P;D	0.54601	0.782;0.967	B;B	0.34779	0.189;0.163	T	0.07986	-1.0744	9	.	.	.	-12.0845	9.633	0.39791	0.0:0.0:0.6411:0.3589	.	805;321	O00192;E7EV58	ARVC_HUMAN;.	V	805;742;742;736;799	ENSP00000263207:A805V;ENSP00000342042:A742V;ENSP00000384341:A742V;ENSP00000384732:A736V;ENSP00000385444:A799V	.	A	-	2	0	ARVCF	18340666	0.895000	0.30542	0.102000	0.21198	0.078000	0.17371	3.057000	0.49931	2.416000	0.81992	0.561000	0.74099	GCG	G|0.985;A|0.015	0.015	strong		0.711	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670		A	19960666	G	A	19960666	3	1	22	1	0	0	0	0	1	0	0	0	1003	1087	38	1	498	1	ARVCF	22	19960666	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	10398	19960666	31343900	4346	7247											
RANBP1	5902	hgsc.bcm.edu	37	chr22	20112868	20112868	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgaagcccaacgcaggtagCgaccgtgcctgggtctggaa	9	6	14	12	3	1	1	0	1	1	0	1	3	1	2	3	3	4	2	3	3	4	1	rs111311060	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:20112868C>T	ENST00000331821.3	+	4	450	c.348C>T	c.(346-348)agC>agT	p.S116S	SNORA77_ENST00000578179.1_RNA|RANBP1_ENST00000430524.1_Silent_p.S26S|RANBP1_ENST00000402752.1_Silent_p.S116S	NM_002882.2	NP_002873.1	P43487	RANG_HUMAN	RAN binding protein 1	116	RanBD1. {ECO:0000255|PROSITE- ProRule:PRU00164}.				intracellular transport (GO:0046907)|positive regulation of mitotic centrosome separation (GO:0046604)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)|spindle organization (GO:0007051)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|GTPase activator activity (GO:0005096)|Ran GTPase binding (GO:0008536)			breast(1)|large_intestine(1)|lung(1)|ovary(1)	4	Colorectal(54;0.0993)					ACGCAGGTAGCGACCGTGCCT	0.607													C|||	15	0.00299521	0.0113	0.0	5008	,	,		18036	0.0		0.0	False		,,,				2504	0.0				p.S116S		Atlas-SNP	.											.	RANBP1	19	.	0			c.C348T						PASS	.	C		33,4373	38.4+/-70.7	0,33,2170	62	57	59		348	-10	0.4	22	dbSNP_132	59	0,8600		0,0,4300	no	coding-synonymous	RANBP1	NM_002882.2		0,33,6470	TT,TC,CC		0.0,0.749,0.2537		116/202	20112868	33,12973	2203	4300	6503	SO:0001819	synonymous_variant	5902	exon4			AGGTAGCGACCGT	D38076	CCDS13775.1, CCDS63408.1, CCDS74823.1	22q11.21	2008-06-16			ENSG00000099901	ENSG00000099901			9847	protein-coding gene	gene with protein product		601180				7616957, 10330396	Standard	NM_001278639		Approved	HTF9A	uc002zro.1	P43487	OTTHUMG00000150490	ENST00000331821.3:c.348C>T	22.37:g.20112868C>T		166	0	0		180	91	0.505556	NM_002882	Q53EY3	Silent	SNP	ENST00000331821.3	37	CCDS13775.1																																																																																			C|0.997;T|0.003	0.003	strong		0.607	RANBP1-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343733.1	NM_002882		T	20112868	C	T	20112868	2	4	22	1	0	0	0	0	0	0	0	1	13040	767	27	1		1	RANBP1	22	20112868	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	152202	20112868	31191698	4347	7248											
ZNF74	7625	hgsc.bcm.edu	37	chr22	20760106	20760106	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggcgttccgccagagctcCtccctcacgctgcaccggcg	6	6	11	18	5	1	1	1	0	0	1	4	1	4	1	5	2	2	4	5	2	1	1	rs2229316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:20760106C>T	ENST00000400451.2	+	5	1297	c.783C>T	c.(781-783)tcC>tcT	p.S261S	ZNF74_ENST00000356671.5_Silent_p.S261S|ZNF74_ENST00000405993.1_Silent_p.S229S|ZNF74_ENST00000403682.3_3'UTR|ZNF74_ENST00000357502.5_3'UTR	NM_003426.3	NP_003417.2	Q16587	ZNF74_HUMAN	zinc finger protein 74	261					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)			GCCAGAGCTCCTCCCTCACGC	0.687													C|||	95	0.0189696	0.0696	0.0043	5008	,	,		15500	0.0		0.0	False		,,,				2504	0.0				p.S261S		Atlas-SNP	.											.	ZNF74	54	.	0			c.C783T						PASS	.	C		188,4216		6,176,2020	21	25	23		783	-7	0	22	dbSNP_98	23	3,8593		0,3,4295	no	coding-synonymous	ZNF74	NM_003426.2		6,179,6315	TT,TC,CC		0.0349,4.2688,1.4692		261/645	20760106	191,12809	2202	4298	6500	SO:0001819	synonymous_variant	7625	exon5			GAGCTCCTCCCTC	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.783C>T	22.37:g.20760106C>T		39	0	0		42	42	1	NM_003426	B5MCE3|B7Z5Y2|Q6IBV2|Q6PJP1|Q9UC04|Q9UF05|Q9UF06|Q9UF07	Silent	SNP	ENST00000400451.2	37	CCDS42982.1																																																																																			C|0.982;T|0.018	0.018	strong		0.687	ZNF74-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319648.2	NM_003426		T	20760106	C	T	20760106	2	4	22	1	0	0	0	0	0	0	0	1	18142	668	24	2		2	ZNF74	22	20760106	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	647238	20760106	30544460	4348	7249											
MED15	51586	hgsc.bcm.edu	37	chr22	20909389	20909389	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ccgcctcctgggacctcgggGatggcccctcacagcatggc	5	6	13	17	2	1	0	1	0	0	0	3	2	2	2	6	5	1	1	6	5	0	0	rs147554746	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:20909389G>A	ENST00000263205.7	+	5	474	c.405G>A	c.(403-405)ggG>ggA	p.G135G	MED15_ENST00000406969.1_Silent_p.G109G|MED15_ENST00000292733.7_Silent_p.G135G|MED15_ENST00000425759.2_Intron|MED15_ENST00000382974.2_Intron|MED15_ENST00000541476.1_Silent_p.G109G|MED15_ENST00000542773.1_Intron	NM_001003891.1	NP_001003891.1	Q96RN5	MED15_HUMAN	mediator complex subunit 15	135					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)			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)			GGACCTCGGGGATGGCCCCTC	0.612													G|||	2	0.000399361	0.0015	0.0	5008	,	,		17772	0.0		0.0	False		,,,				2504	0.0				p.G135G		Atlas-SNP	.											.	MED15	68	.	0			c.G405A						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	29	29	29		405,405	-2	1	22	dbSNP_134	29	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	MED15	NM_001003891.1,NM_015889.3	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	135/789,135/749	20909389	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	51586	exon5			CTCGGGGATGGCC	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.405G>A	22.37:g.20909389G>A		47	0	0		53	24	0.45283	NM_015889	D3DX31|D3DX32|O15413|Q6IC31|Q8NF16|Q96CT0|Q96IH7|Q9P1T3	Silent	SNP	ENST00000263205.7	37	CCDS33602.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	11.36	1.615678	0.28801	2.27E-4	0.0	ENSG00000099917	ENST00000423862	.	.	.	5.46	-2.03	0.07365	.	.	.	.	.	T	0.39279	0.1072	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31724	-0.9933	4	.	.	.	.	1.4274	0.02326	0.2499:0.2738:0.3381:0.1381	.	.	.	.	N	76	.	.	D	+	1	0	MED15	19239389	0.446000	0.25665	0.981000	0.43875	0.986000	0.74619	-0.516000	0.06282	-0.109000	0.12044	-0.225000	0.12378	GAT	G|1.000;A|0.000	0.000	strong		0.612	MED15-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320177.2	NM_015889		A	20909389	G	A	20909389	2	1	22	1	0	0	0	0	0	0	0	1	9442	1161	41	2		2	MED15	22	20909389	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	149283	20909389	30395177	4349	7250											
AIFM3	150209	hgsc.bcm.edu	37	chr22	21333605	21333605	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcgcaggaggcggagatgaGcactgtgccctacctctgga	8	6	16	11	2	1	2	0	1	1	1	1	5	1	4	2	5	3	2	2	5	1	1	rs61356271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:21333605G>C	ENST00000399167.2	+	17	1763	c.1523G>C	c.(1522-1524)aGc>aCc	p.S508T	AIFM3_ENST00000440238.2_Missense_Mutation_p.S508T|AIFM3_ENST00000465606.1_3'UTR|LZTR1_ENST00000215739.8_5'Flank|XXbac-B135H6.18_ENST00000610278.1_lincRNA|AIFM3_ENST00000399163.2_Missense_Mutation_p.S508T|AIFM3_ENST00000335375.5_Missense_Mutation_p.S496T|AIFM3_ENST00000333607.6_Missense_Mutation_p.S508T|AIFM3_ENST00000405089.1_Missense_Mutation_p.S514T	NM_144704.2	NP_653305.1	Q96NN9	AIFM3_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 3	508			S -> T (in dbSNP:rs61356271).		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)			GCGGAGATGAGCACTGTGCCC	0.672													g|||	270	0.0539137	0.1936	0.0202	5008	,	,		12709	0.0		0.0	False		,,,				2504	0.0				p.S514T		Atlas-SNP	.											.	AIFM3	49	.	0			c.G1541C						PASS	.	C	THR/SER,THR/SER,THR/SER	570,3784		38,494,1645	32	25	27		1523,1541,1523	0.2	0.8	22	dbSNP_129	27	8,8502		0,8,4247	yes	missense,missense,missense	AIFM3	NM_001018060.2,NM_001146288.1,NM_144704.2	58,58,58	38,502,5892	CC,CG,GG		0.094,13.0914,4.4932	,,	508/599,514/605,508/606	21333605	578,12286	2177	4255	6432	SO:0001583	missense	150209	exon17			AGATGAGCACTGT	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.1523G>C	22.37:g.21333605G>C	ENSP00000382120:p.Ser508Thr	133	0	0		183	98	0.535519	NM_001146288	B7WP37|D3DX37|D3DX38|Q6ZT44|Q8N1V3|Q8N5E0	Missense_Mutation	SNP	ENST00000399167.2	37	CCDS13786.1	83	0.038003663003663	75	0.1524390243902439	8	0.022099447513812154	0	0.0	0	0.0	g	5.235	0.228779	0.09916	0.130914	9.4E-4	ENSG00000183773	ENST00000399167;ENST00000399163;ENST00000405089;ENST00000335375;ENST00000440238;ENST00000333607	T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97	4.65	0.178	0.15058	FAD/NAD-linked reductase, dimerisation (1);	0.334108	0.35772	N	0.003000	T	0.00109	0.0003	N	0.16266	0.395	0.54753	P	1.2000000000012001E-5	B;B;B;B	0.22983	0.078;0.05;0.05;0.029	B;B;B;B	0.18561	0.022;0.022;0.022;0.01	T	0.24333	-1.0163	9	0.10636	T	0.68	-15.7117	5.9493	0.19237	0.3378:0.1331:0.5291:0.0	rs61356271	496;514;508;508	B7Z9S7;Q96NN9-2;Q96NN9-3;Q96NN9	.;.;.;AIFM3_HUMAN	T	508;508;514;496;508;508	ENSP00000382120:S508T;ENSP00000382116:S508T;ENSP00000385800:S514T;ENSP00000335369:S496T;ENSP00000390798:S508T;ENSP00000327671:S508T	ENSP00000327671:S508T	S	+	2	0	AIFM3	19663605	0.785000	0.28726	0.846000	0.33378	0.236000	0.25371	0.863000	0.27913	-0.250000	0.09555	-2.308000	0.00257	AGC	G|0.946;C|0.054	0.054	strong		0.672	AIFM3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320150.1	NM_144704		C	21333605	G	C	21333605	3	2	22	1	0	0	0	0	1	0	0	0	428	971	34	4	1603	4	AIFM3	22	21333605	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	424216	21333605	29970961	4350	7251											
SLC7A4	6545	hgsc.bcm.edu	37	chr22	21385427	21385427	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagggtgcaaagccgccttcGtcagcgctccagttgtgagg	8	8	14	11	3	1	1	1	1	0	0	3	1	2	1	3	2	3	3	3	2	2	2	rs80061703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:21385427G>C	ENST00000382932.2	-	2	742	c.675C>G	c.(673-675)gaC>gaG	p.D225E	AC002472.11_ENST00000450652.1_RNA|SLC7A4_ENST00000403586.1_Missense_Mutation_p.D225E	NM_004173.2	NP_004164.2	O43246	CTR4_HUMAN	solute carrier family 7, member 4	225					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)	AGCCGCCTTCGTCAGCGCTCC	0.597													G|||	150	0.0299521	0.1104	0.0058	5008	,	,		20919	0.0		0.0	False		,,,				2504	0.0				p.D225E		Atlas-SNP	.											.	SLC7A4	50	.	0			c.C675G						PASS	.	G	GLU/ASP	446,3960	209.5+/-230.2	21,404,1778	55	56	56		675	0.6	0.2	22	dbSNP_131	56	5,8595	4.3+/-15.6	0,5,4295	yes	missense	SLC7A4	NM_004173.2	45	21,409,6073	CC,CG,GG		0.0581,10.1226,3.4676	benign	225/636	21385427	451,12555	2203	4300	6503	SO:0001583	missense	6545	exon2			GCCTTCGTCAGCG	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.675C>G	22.37:g.21385427G>C	ENSP00000372390:p.Asp225Glu	39	0	0		54	34	0.62963	NM_004173	Q0P5U2|Q3KNQ6|Q4VC45|Q6IBY8|Q96H88	Missense_Mutation	SNP	ENST00000382932.2	37	CCDS33608.1	51	0.023351648351648352	47	0.09552845528455285	4	0.011049723756906077	0	0.0	0	0.0	G	0.007	-1.958563	0.00465	0.101226	5.81E-4	ENSG00000099960	ENST00000403586;ENST00000382932	D;D	0.89123	-2.47;-2.47	5.28	0.649	0.17806	Amino acid permease domain (1);	0.917457	0.09445	N	0.801263	T	0.03263	0.0095	N	0.00811	-1.165	0.20563	N	0.999887	B	0.02656	0.0	B	0.08055	0.003	T	0.40251	-0.9573	10	0.02654	T	1	.	2.2473	0.04034	0.1467:0.403:0.2873:0.1629	.	225	O43246	CTR4_HUMAN	E	225	ENSP00000384278:D225E;ENSP00000372390:D225E	ENSP00000372390:D225E	D	-	3	2	SLC7A4	19715427	0.085000	0.21516	0.212000	0.23672	0.016000	0.09150	0.308000	0.19314	0.022000	0.15160	-1.219000	0.01604	GAC	G|0.969;C|0.031	0.031	strong		0.597	SLC7A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320467.1	NM_004173		C	21385427	G	C	21385427	3	2	22	1	0	0	0	0	1	0	0	0	14714	1136	40	4	1248	4	SLC7A4	22	21385427	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	51822	21385427	29919139	4351	7252											
UBE2L3	7332	hgsc.bcm.edu	37	chr22	21965298	21965298	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtctgccagtaattagtgcCgaaaactggaagccagcaac	13	8	10	10	1	1	0	0	0	1	0	1	2	1	1	3	1	6	2	3	1	6	2	rs61133050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:21965298C>G	ENST00000342192.4	+	3	474	c.276C>G	c.(274-276)gcC>gcG	p.A92A	UBE2L3_ENST00000545681.1_Silent_p.A60A|UBE2L3_ENST00000458578.2_Silent_p.A150A	NM_003347.3	NP_003338.1	P68036	UB2L3_HUMAN	ubiquitin-conjugating enzyme E2L 3	92					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)					TAATTAGTGCCGAAAACTGGA	0.512													T|||	162	0.0323482	0.1172	0.0101	5008	,	,		17052	0.0		0.0	False		,,,				2504	0.0				p.A150A		Atlas-SNP	.											.	UBE2L3	11	.	0			c.C450G						PASS	.	T		393,4013		18,357,1828	38	38	38		276	4.6	1	22	dbSNP_129	38	4,8596		0,4,4296	no	coding-synonymous	UBE2L3	NM_003347.2		18,361,6124	GG,GC,CC		0.0465,8.9197,3.0524		92/155	21965298	397,12609	2203	4300	6503	SO:0001819	synonymous_variant	7332	exon3			TAGTGCCGAAAAC	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.276C>G	22.37:g.21965298C>G		446	0	0		459	203	0.442266	NM_001256355	B2R4A7|B4DDG1|B4DSZ4|E7EWS7|P51966|P70653|Q9HAV1	Silent	SNP	ENST00000342192.4	37	CCDS13790.1																																																																																			C|0.964;G|0.036	0.036	strong		0.512	UBE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320219.1	NM_198157		G	21965298	C	G	21965298	2	3	22	1	0	0	0	0	0	0	0	1	16878	639	23	4		4	UBE2L3	22	21965298	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	579871	21965298	29339268	4352	7253											
CCDC116	164592	hgsc.bcm.edu	37	chr22	21989230	21989230	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgacctgcctggctactgtcCgctccgtgagccccatcgca	5	8	10	18	4	0	1	0	1	0	0	3	2	2	1	6	1	3	3	6	1	1	1	rs41279987	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:21989230C>T	ENST00000292779.3	+	4	1039	c.878C>T	c.(877-879)cCg>cTg	p.P293L	CCDC116_ENST00000607942.1_Missense_Mutation_p.P293L	NM_152612.2	NP_689825.2	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	293			P -> L (in dbSNP:rs41279987).							endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(5)	22	Colorectal(54;0.105)					GGCTACTGTCCGCTCCGTGAG	0.597													C|||	124	0.0247604	0.0893	0.0086	5008	,	,		19728	0.0		0.0	False		,,,				2504	0.0				p.P293L		Atlas-SNP	.											CCDC116,NS,carcinoma,-1,1	CCDC116	56	1	0			c.C878T						PASS	.	C	LEU/PRO	278,4128	155.5+/-188.7	7,264,1932	78	80	79		878	2.1	0	22	dbSNP_127	79	3,8597	3.0+/-9.4	0,3,4297	yes	missense	CCDC116	NM_152612.2	98	7,267,6229	TT,TC,CC		0.0349,6.3096,2.1605	benign	293/614	21989230	281,12725	2203	4300	6503	SO:0001583	missense	164592	exon4			ACTGTCCGCTCCG	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.878C>T	22.37:g.21989230C>T	ENSP00000292779:p.Pro293Leu	56	0	0		62	27	0.435484	NM_152612	Q8N9Y9	Missense_Mutation	SNP	ENST00000292779.3	37	CCDS13791.1	49	0.022435897435897436	45	0.09146341463414634	4	0.011049723756906077	0	0.0	0	0.0	C	11.67	1.706989	0.30232	0.063096	3.49E-4	ENSG00000161180	ENST00000292779	T	0.12465	2.68	4.39	2.13	0.27403	.	0.960630	0.08582	N	0.924354	T	0.00328	0.0010	L	0.34521	1.04	0.09310	N	1	P;P	0.38863	0.65;0.65	B;B	0.29524	0.103;0.064	T	0.33624	-0.9861	10	0.72032	D	0.01	-14.4612	4.7066	0.12853	0.2143:0.6741:0.0:0.1116	rs41279987	293;293	B7Z7H5;Q8IYX3-2	.;.	L	293	ENSP00000292779:P293L	ENSP00000292779:P293L	P	+	2	0	CCDC116	20319230	0.000000	0.05858	0.003000	0.11579	0.260000	0.26232	0.439000	0.21575	1.216000	0.43427	0.561000	0.74099	CCG	C|0.974;T|0.026	0.026	strong		0.597	CCDC116-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320199.1	NM_152612		T	21989230	C	T	21989230	3	4	22	1	0	0	0	0	1	0	0	0	2755	652	23	1	888	1	CCDC116	22	21989230	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	23932	21989230	29315336	4353	7254											
CCDC116	164592	hgsc.bcm.edu	37	chr22	21991224	21991224	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctacatgtctgcctgcacCggcatgggttccagtccccc	5	10	9	17	1	2	0	0	0	2	0	4	0	4	0	5	2	3	3	5	2	1	2	rs45533832	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:21991224C>T	ENST00000292779.3	+	5	1868	c.1707C>T	c.(1705-1707)acC>acT	p.T569T		NM_152612.2	NP_689825.2	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	0										endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(5)	22	Colorectal(54;0.105)					CTGCCTGCACCGGCATGGGTT	0.577													C|||	124	0.0247604	0.0893	0.0086	5008	,	,		20745	0.0		0.0	False		,,,				2504	0.0				p.T569T		Atlas-SNP	.											.	CCDC116	56	.	0			c.C1707T						PASS	.	C		279,4127	155.5+/-188.7	7,265,1931	77	78	78		1707	-7.8	0	22	dbSNP_127	78	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	CCDC116	NM_152612.2		7,269,6227	TT,TC,CC		0.0465,6.3323,2.1759		569/614	21991224	283,12723	2203	4300	6503	SO:0001819	synonymous_variant	164592	exon5			CTGCACCGGCATG	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.1707C>T	22.37:g.21991224C>T		87	0	0		90	44	0.488889	NM_152612	Q8N9Y9	Silent	SNP	ENST00000292779.3	37	CCDS13791.1																																																																																			C|0.974;T|0.026	0.026	strong		0.577	CCDC116-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320199.1	NM_152612		T	21991224	C	T	21991224	2	4	22	1	0	0	0	0	0	0	0	1	2755	639	23	1		1	CCDC116	22	21991224	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1994	21991224	29313342	4354	7255											
ZNF280B	140883	hgsc.bcm.edu	37	chr22	22842484	22842484	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgtttctacatcagcaaagaCcgacgatctataatggcaaa	15	10	7	9	2	3	1	1	0	2	1	3	3	3	1	1	1	2	3	1	1	5	4	rs57235089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:22842484C>T	ENST00000406426.1	-	4	1982	c.1240G>A	c.(1240-1242)Gtc>Atc	p.V414I	ZNF280B_ENST00000360412.2_Missense_Mutation_p.V414I			Q86YH2	Z280B_HUMAN	zinc finger protein 280B	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)			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)		TCAGCAAAGACCGACGATCTA	0.403													C|||	151	0.0301518	0.0877	0.0072	5008	,	,		19574	0.0		0.0099	False		,,,				2504	0.0204				p.V414I		Atlas-SNP	.											.	ZNF280B	67	.	0			c.G1240A						PASS	.	C	ILE/VAL	339,4067	176.9+/-206.0	15,309,1879	131	122	125		1240	-1.6	0	22	dbSNP_129	125	106,8494	56.0+/-117.1	2,102,4196	no	missense	ZNF280B	NM_080764.2	29	17,411,6075	TT,TC,CC		1.2326,7.6941,3.4215	benign	414/544	22842484	445,12561	2203	4300	6503	SO:0001583	missense	140883	exon4			CAAAGACCGACGA	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.1240G>A	22.37:g.22842484C>T	ENSP00000385998:p.Val414Ile	286	0	0		266	110	0.413534	NM_080764		Missense_Mutation	SNP	ENST00000406426.1	37	CCDS13799.1	38	0.0173992673992674	26	0.052845528455284556	3	0.008287292817679558	0	0.0	9	0.011873350923482849	C	0.005	-2.182245	0.00308	0.076941	0.012326	ENSG00000198477	ENST00000406426;ENST00000360412	T;T	0.28069	1.63;1.63	4.32	-1.63	0.08345	Zinc finger, C2H2-like (1);	.	.	.	.	T	0.00695	0.0023	N	0.25890	0.77	0.09310	N	1	B	0.21905	0.062	B	0.18871	0.023	T	0.24764	-1.0151	9	0.06625	T	0.88	5.8306	4.7941	0.13263	0.4233:0.4085:0.0:0.1682	rs57235089;rs61910698	414	Q86YH2	Z280B_HUMAN	I	414	ENSP00000385998:V414I;ENSP00000353586:V414I	ENSP00000353586:V414I	V	-	1	0	ZNF280B	21172484	0.945000	0.32115	0.000000	0.03702	0.099000	0.18886	2.087000	0.41653	-0.168000	0.10853	-0.152000	0.13540	GTC	C|0.973;T|0.027	0.027	strong		0.403	ZNF280B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321170.2	NM_080764		T	22842484	C	T	22842484	3	4	22	1	0	0	0	0	1	0	0	0	17830	507	18	2	395	2	ZNF280B	22	22842484	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	851260	22842484	28462082	4355	7256											
BCR	613	hgsc.bcm.edu	37	chr22	23651650	23651650	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggacagagactggcagcgcAccgtcatcgccatgaatggg	11	5	14	11	3	1	2	1	1	0	1	2	4	1	3	2	3	1	2	2	3	1	0			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:23651650A>G	ENST00000305877.8	+	17	3803	c.3052A>G	c.(3052-3054)Acc>Gcc	p.T1018A	BCR_ENST00000359540.3_Missense_Mutation_p.T974A	NM_004327.3	NP_004318.3	P11274	BCR_HUMAN	breakpoint cluster region	1018					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)	CTGGCAGCGCACCGTCATCGC	0.607			T	"ABL1,  FGFR1, JAK2 "	"CML, ALL, AML"																																p.T1018A		Atlas-SNP	.		Dom	yes		22	22q11.21	613	breakpoint cluster region		L	BCR,NS,carcinoma,0,1	BCR	74	1	0			c.A3052G						scavenged	.						33	25	28					22																	23651650		2201	4300	6501	SO:0001583	missense	613	exon17			CAGCGCACCGTCA		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.3052A>G	22.37:g.23651650A>G	ENSP00000303507:p.Thr1018Ala	330	0	0		294	108	0.367347	NM_004327	P78501|Q12842|Q4LE80|Q6NZI3	Missense_Mutation	SNP	ENST00000305877.8	37	CCDS13806.1	.	.	.	.	.	.	.	.	.	.	A	7.060	0.566244	0.13560	.	.	ENSG00000186716	ENST00000305877;ENST00000359540;ENST00000334149	T;T	0.39787	1.06;1.8	4.7	2.52	0.30459	C2 calcium/lipid-binding domain, CaLB (1);	0.051625	0.85682	D	0.000000	T	0.28067	0.0692	L	0.44542	1.39	0.80722	D	1	B;B;B	0.22909	0.077;0.059;0.077	B;B;B	0.26614	0.071;0.039;0.044	T	0.04203	-1.0969	10	0.12430	T	0.62	.	4.6914	0.12783	0.6936:0.0:0.1642:0.1422	.	607;974;1018	B4E065;P11274-2;P11274	.;.;BCR_HUMAN	A	1018;974;683	ENSP00000303507:T1018A;ENSP00000352535:T974A	ENSP00000303507:T1018A	T	+	1	0	BCR	21981650	1.000000	0.71417	0.512000	0.27736	0.011000	0.07611	4.359000	0.59449	0.765000	0.33221	-0.991000	0.02546	ACC	A|0.500;G|0.500	0.500	weak		0.607	BCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075819.1	NM_004327		G	23651650	A	G	23651650	3	3	22	1	0	0	0	0	1	0	0	0	1388	159	6	3	3118	3	BCR	22	23651650	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	809166	23651650	27652916	4356	7257											
IGLL1	3543	hgsc.bcm.edu	37	chr22	23917176	23917176	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaaacggtgagctgggtcccGctgccaaacacatgcgtcac	11	6	11	13	3	1	1	1	1	0	0	2	1	2	1	2	2	5	2	2	2	3	0	rs115303391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:23917176G>A	ENST00000330377.2	-	2	417	c.300C>T	c.(298-300)agC>agT	p.S100S	AP000345.2_ENST00000454863.1_RNA|IGLL1_ENST00000249053.3_Intron|AP000345.2_ENST00000458318.1_RNA	NM_020070.3	NP_064455.1	P15814	IGLL1_HUMAN	immunoglobulin lambda-like polypeptide 1	100	J region (By similarity to lambda light- chain).				immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				kidney(1)|large_intestine(1)|lung(5)|skin(4)|stomach(1)	12						GCTGGGTCCCGCTGCCAAACA	0.577													g|||	176	0.0351438	0.1263	0.0115	5008	,	,		17917	0.0		0.001	False		,,,				2504	0.0				p.S100S		Atlas-SNP	.											.	IGLL1	27	.	0			c.C300T						PASS	.	G	,	537,3869		35,467,1701	70	59	63		300,	-3.2	0	22	dbSNP_132	63	11,8589		0,11,4289	no	coding-synonymous,intron	IGLL1	NM_020070.2,NM_152855.1	,	35,478,5990	AA,AG,GG		0.1279,12.1879,4.2134	,	100/214,	23917176	548,12458	2203	4300	6503	SO:0001819	synonymous_variant	3543	exon2			GGTCCCGCTGCCA	X52204	CCDS13809.1, CCDS13810.1	22q11.23	2014-09-17			ENSG00000128322	ENSG00000128322		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	5870	protein-coding gene	gene with protein product		146770		IGLL		3139558, 2511029	Standard	NM_020070		Approved	IGVPB, IGL5, 14.1, CD179B	uc002zxd.3	P15814	OTTHUMG00000150673	ENST00000330377.2:c.300C>T	22.37:g.23917176G>A		110	0	0		154	72	0.467532	NM_020070	Q0P681	Silent	SNP	ENST00000330377.2	37	CCDS13809.1																																																																																			G|0.965;A|0.035	0.035	strong		0.577	IGLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319569.1	NM_020070		A	23917176	G	A	23917176	2	1	22	1	0	0	0	0	0	0	0	1	7602	1078	38	1		1	IGLL1	22	23917176	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	265526	23917176	27387390	4357	7258											
MMP11	4320	hgsc.bcm.edu	37	chr22	24124471	24124471	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggccccgcacccctcacCgagctgggcctggtgaggtt	4	7	14	16	2	1	1	1	1	0	0	1	2	1	1	6	4	1	3	6	4	0	1	rs28382569	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:24124471C>A	ENST00000215743.3	+	7	1186	c.1134C>A	c.(1132-1134)acC>acA	p.T378T	AP000349.1_ENST00000598975.1_Missense_Mutation_p.R248L	NM_005940.3	NP_005931.2	P24347	MMP11_HUMAN	matrix metallopeptidase 11 (stromelysin 3)	378					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)	cacccctcaccgagctGGGCC	0.632													C|||	54	0.0107827	0.0371	0.0029	5008	,	,		18519	0.0		0.003	False		,,,				2504	0.0				p.T378T		Atlas-SNP	.											.	MMP11	53	.	0			c.C1134A						PASS	.	C		168,4238	112.1+/-150.2	5,158,2040	59	57	58		1134	-2.9	0.6	22	dbSNP_125	58	0,8600		0,0,4300	no	coding-synonymous	MMP11	NM_005940.3		5,158,6340	AA,AC,CC		0.0,3.813,1.2917		378/489	24124471	168,12838	2203	4300	6503	SO:0001819	synonymous_variant	4320	exon7			CCTCACCGAGCTG		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.1134C>A	22.37:g.24124471C>A		87	0	0		84	46	0.547619	NM_005940	Q5FX24|Q6PEZ6|Q9UC26	Silent	SNP	ENST00000215743.3	37	CCDS13816.1																																																																																			A|0.014;C|0.986	0.014	strong		0.632	MMP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319891.2	NM_005940		A	24124471	C	A	24124471	2	1	22	1	0	0	0	0	0	0	0	1	9659	639	23	4		4	MMP11	22	24124471	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	207295	24124471	27180095	4358	7259											
GGT5	2687	hgsc.bcm.edu	37	chr22	24622124	24622124	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgggacgtgcctgtcccgtgGccccaggcctcggccaagct	4	7	14	16	3	0	0	0	0	0	0	2	1	1	1	6	4	2	1	6	4	1	0	rs73879043	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:24622124G>A	ENST00000327365.4	-	8	1565	c.1149C>T	c.(1147-1149)ggC>ggT	p.G383G	GGT5_ENST00000263112.7_Silent_p.G351G|GGT5_ENST00000418439.2_Silent_p.G306G|GGT5_ENST00000398292.3_Silent_p.G383G	NM_001099781.1|NM_004121.2	NP_001093251.1|NP_004112.2	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5	383					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						CTGTCCCGTGGCCCCAGGCCT	0.687													G|||	101	0.0201677	0.0711	0.0101	5008	,	,		14159	0.0		0.0	False		,,,				2504	0.0				p.G383G		Atlas-SNP	.											.	GGT5	61	.	0			c.C1149T						PASS	.	G	,,	236,4170	131.8+/-168.3	6,224,1973	30	32	31		1149,1053,1149	1.6	0.1	22	dbSNP_130	31	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	GGT5	NM_001099781.1,NM_001099782.1,NM_004121.2	,,	6,224,6271	AA,AG,GG		0.0,5.3563,1.8151	,,	383/588,351/555,383/587	24622124	236,12766	2203	4298	6501	SO:0001819	synonymous_variant	2687	exon8			CCCGTGGCCCCAG	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.1149C>T	22.37:g.24622124G>A		122	0	0		101	54	0.534653	NM_001099781	Q53XM9|Q6GMP0|Q96FC1|Q9UFM5	Silent	SNP	ENST00000327365.4	37	CCDS13825.1																																																																																			G|0.981;A|0.019	0.019	strong		0.687	GGT5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320119.1	NM_004121		A	24622124	G	A	24622124	2	1	22	1	0	0	0	0	0	0	0	1	6370	1190	42	2		2	GGT5	22	24622124	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	497653	24622124	26682442	4359	7260											
CYTSA	23384	hgsc.bcm.edu	37	chr22	24761502	24761502	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgcacaggagggagcgtcGccagcctctctgatggctat	7	9	13	12	2	2	1	0	1	2	0	4	3	2	3	2	3	3	2	2	3	1	1	rs139166286	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:24761502G>A	ENST00000314328.9	+	13	3171	c.2886G>A	c.(2884-2886)tcG>tcA	p.S962S	SPECC1L-ADORA2A_ENST00000358654.2_3'UTR|SPECC1L_ENST00000437398.1_Silent_p.S962S|SPECC1L_ENST00000541492.1_Silent_p.S962S	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	962					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						AGGGAGCGTCGCCAGCCTCTC	0.502																																					p.S962S		Atlas-SNP	.											.	SPECC1L	85	.	0			c.G2886A						PASS	.	G	,	18,4388	25.3+/-52.1	0,18,2185	109	84	92		2886,2886	-11.1	0	22	dbSNP_134	92	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SPECC1L	NM_001145468.1,NM_015330.2	,	0,18,6485	AA,AG,GG		0.0,0.4085,0.1384	,	962/1118,962/1118	24761502	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	23384	exon12			AGCGTCGCCAGCC	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.2886G>A	22.37:g.24761502G>A		67	0	0		72	36	0.5	NM_001145468	B7Z758|F5H1H6|O15081	Silent	SNP	ENST00000314328.9	37	CCDS33619.1																																																																																			A|0.002;G|0.998	0.002	strong		0.502	SPECC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319986.2	NM_015330		A	24761502	G	A	24761502	2	1	22	1	0	0	0	0	0	0	0	1	4211	1074	38	1		1	CYTSA	22	24761502	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	139378	24761502	26543064	4360	7261											
C22orf36	2678	hgsc.bcm.edu	37	chr22	24984261	24984261	+	Intron	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggtggtagatgagctgtcGgcagatcttgtccgaggact	8	10	16	7	2	1	3	0	1	1	2	3	6	2	4	1	4	1	3	1	4	1	2	rs201281973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:24984261G>A	ENST00000248923.4	+	1	59				FAM211B_ENST00000318753.8_Nonsense_Mutation_p.R115*|FAM211B_ENST00000495297.1_5'Flank	NM_013430.2	NP_038347.2	P19440	GGT1_HUMAN	gamma-glutamyltransferase 1						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)	ATGAGCTGTCGGCAGATCTTG	0.617													G|||	2	0.000399361	0.0015	0.0	5008	,	,		19843	0.0		0.0	False		,,,				2504	0.0				p.R115X		Atlas-SNP	.											C22orf36,colon,carcinoma,0,1	.	.	1	0			c.C343T						PASS	.	G	,stop/ARG	4,4270		0,4,2133	116	128	124		,343	-0.4	0	22		124	0,8470		0,0,4235	yes	intron,stop-gained	GGT1,C22orf36	NM_013430.2,NM_207644.2	,	0,4,6368	AA,AG,GG		0.0,0.0936,0.0314	,	,115/316	24984261	4,12740	2137	4235	6372	SO:0001627	intron_variant	388886	exon3			GCTGTCGGCAGAT	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	ENST00000248923.4:c.-429+4485G>A	22.37:g.24984261G>A		195	0	0		201	106	0.527363	NM_207644	Q08247|Q14404|Q8TBS1|Q9UMK1	Nonsense_Mutation	SNP	ENST00000248923.4	37	CCDS42992.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	15.90	2.969710	0.53614	9.36E-4	0.0	ENSG00000178026	ENST00000318753	.	.	.	3.5	-0.358	0.12575	.	0.000000	0.64402	U	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.9843	0.09509	0.3955:0.0:0.4411:0.1634	.	.	.	.	X	115	.	ENSP00000320520:R115X	R	-	1	2	C22orf36	23314261	0.993000	0.37304	0.045000	0.18777	0.635000	0.38103	0.761000	0.26489	-0.007000	0.14345	0.462000	0.41574	CGA	G|1.000;A|0.000	0.000	strong		0.617	GGT1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319110.1	NM_013430		A	24984261	G	A	24984261	1	1	22	0	1	0	0	0	0	0	0	0	2148	1124	39	1		1	C22orf36	22	24984261	Intron	SNP	G	TCGA-G8-6324-01A-11D-2210-10	222759	24984261	26320305	4361	7262											
GGT1	2678	hgsc.bcm.edu	37	chr22	25010746	25010746	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatgtgccacatggcagggaTgcactgcgggacggtggctc	7	8	16	10	2	0	0	0	0	0	0	1	2	0	2	1	5	3	3	1	5	1	1	rs4049881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:25010746T>C	ENST00000400382.1	+	6	923	c.168T>C	c.(166-168)gaT>gaC	p.D56D	GGT1_ENST00000248923.4_Silent_p.D56D|GGT1_ENST00000406383.2_Silent_p.D56D|GGT1_ENST00000400383.1_Silent_p.D56D|GGT1_ENST00000400380.1_Silent_p.D56D			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	56					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)	ATGGCAGGGATGCACTGCGGG	0.622													t|||	343	0.0684904	0.2209	0.0231	5008	,	,		14046	0.003		0.002	False		,,,				2504	0.0307				p.D56D		Atlas-SNP	.											.	GGT1	68	.	0			c.T168C						PASS	.	C	,,,	589,3461		50,489,1486	41	46	45		168,168,168,168	-7.5	0	22	dbSNP_108	45	5,8363		0,5,4179	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GGT1	NM_001032364.2,NM_001032365.2,NM_005265.2,NM_013430.2	,,,	50,494,5665	CC,CT,TT		0.0598,14.5432,4.7834	,,,	56/570,56/570,56/570,56/570	25010746	594,11824	2025	4184	6209	SO:0001819	synonymous_variant	2678	exon6			CAGGGATGCACTG	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.168T>C	22.37:g.25010746T>C		230	0	0		269	127	0.472119	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Silent	SNP	ENST00000400382.1	37	CCDS42992.1																																																																																			T|0.970;C|0.030	0.030	strong		0.622	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430		C	25010746	T	C	25010746	2	2	22	1	0	0	0	0	0	0	0	1	6369	1461	51	3		3	GGT1	22	25010746	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	26485	25010746	26293820	4362	7263											
SGSM1	129049	hgsc.bcm.edu	37	chr22	25294155	25294155	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgcccagcggaacacccccAcggtgctgcgacctagggat	9	4	12	16	4	0	0	0	0	0	0	0	3	0	2	4	3	4	1	4	3	2	1	rs6004350	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:25294155A>C	ENST00000400359.4	+	20	2411	c.2404A>C	c.(2404-2406)Acg>Ccg	p.T802P	SGSM1_ENST00000400358.4_Missense_Mutation_p.T747P|SNORD56_ENST00000362913.1_RNA	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	802	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.		T -> P (in dbSNP:rs6004350).			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						GAACACCCCCACGGTGCTGCG	0.627													C|||	496	0.0990415	0.3578	0.0317	5008	,	,		20487	0.0		0.001	False		,,,				2504	0.0				p.T802P		Atlas-SNP	.											SGSM1_ENST00000400359,NS,carcinoma,-1,2	SGSM1	150	2	0			c.A2404C						PASS	.	C	PRO/THR,PRO/THR,PRO/THR,PRO/THR	1165,3097		173,819,1139	52	64	60		2404,2239,2056,2221	0.4	0	22	dbSNP_114	60	10,8508		0,10,4249	yes	missense,missense,missense,missense	SGSM1	NM_001039948.2,NM_001098497.1,NM_001098498.1,NM_133454.2	38,38,38,38	173,829,5388	CC,CA,AA		0.1174,27.3346,9.1941	benign,benign,benign,benign	802/1149,747/1094,686/1033,741/1088	25294155	1175,11605	2131	4259	6390	SO:0001583	missense	129049	exon20			ACCCCCACGGTGC	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.2404A>C	22.37:g.25294155A>C	ENSP00000383212:p.Thr802Pro	104	0	0		118	66	0.559322	NM_001039948	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Missense_Mutation	SNP	ENST00000400359.4	37	CCDS46674.1	169	0.07738095238095238	159	0.3231707317073171	10	0.027624309392265192	0	0.0	0	0.0	C	2.963	-0.214065	0.06101	0.273346	0.001174	ENSG00000167037	ENST00000403206;ENST00000400358;ENST00000400359	T;T	0.07021	3.23;3.24	5.24	0.383	0.16239	Rab-GAP/TBC domain (2);	0.597033	0.15795	N	0.244222	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	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	0.48875	-0.8996	9	0.28530	T	0.3	-11.8193	5.2429	0.15481	0.2279:0.4713:0.2332:0.0676	rs6004350;rs52792982;rs6004350	747;802;819;802	Q2NKQ1-4;C9J7S8;Q2NKQ1-3;Q2NKQ1	.;.;.;SGSM1_HUMAN	P	802;747;802	ENSP00000383211:T747P;ENSP00000383212:T802P	ENSP00000383211:T747P	T	+	1	0	SGSM1	23624155	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.080000	0.14802	0.007000	0.14760	-0.187000	0.12897	ACG	A|0.872;C|0.128	0.128	strong		0.627	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	XM_059318		C	25294155	A	C	25294155	3	2	22	1	0	0	0	0	1	0	0	0	14237	159	6	5	2482	5	SGSM1	22	25294155	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	283409	25294155	26010411	4363	7264											
MYO18B	84700	hgsc.bcm.edu	37	chr22	26168333	26168333	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gagctggaccaggtcgaggaCctggcctctctcatcagtgt	7	9	13	12	1	3	0	2	0	1	0	5	4	3	2	3	4	1	1	3	4	0	0	rs185388626	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:26168333C>T	ENST00000407587.2	+	7	1894	c.1725C>T	c.(1723-1725)gaC>gaT	p.D575D	MYO18B_ENST00000536101.1_Silent_p.D575D|MYO18B_ENST00000335473.7_Silent_p.D575D			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	575	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						AGGTCGAGGACCTGGCCTCTC	0.607													C|||	18	0.00359425	0.0136	0.0	5008	,	,		11926	0.0		0.0	False		,,,				2504	0.0				p.D575D		Atlas-SNP	.											.	MYO18B	322	.	0			c.C1725T						PASS	.	C		70,3950		0,70,1940	108	107	107		1725	2	1	22		107	0,8346		0,0,4173	no	coding-synonymous	MYO18B	NM_032608.5		0,70,6113	TT,TC,CC		0.0,1.7413,0.5661		575/2568	26168333	70,12296	2010	4173	6183	SO:0001819	synonymous_variant	84700	exon7			CGAGGACCTGGCC	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.1725C>T	22.37:g.26168333C>T		82	0	0		94	53	0.56383	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37																																																																																				C|0.998;T|0.002	0.002	strong		0.607	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		T	26168333	C	T	26168333	2	4	22	1	0	0	0	0	0	0	0	1	10075	506	18	2		2	MYO18B	22	26168333	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	874178	26168333	25136233	4364	7265											
MYO18B	84700	hgsc.bcm.edu	37	chr22	26272270	26272270	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcctctacttagtgccaccAttggaactgagcagctccga	10	9	9	13	1	1	1	0	1	1	0	2	3	2	2	4	1	6	2	4	1	3	3	rs695633	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:26272270A>G	ENST00000407587.2	+	24	4367	c.4198A>G	c.(4198-4200)Att>Gtt	p.I1400V	MYO18B_ENST00000536101.1_Missense_Mutation_p.I1399V|MYO18B_ENST00000335473.7_Missense_Mutation_p.I1399V			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1399						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						TAGTGCCACCATTGGAACTGA	0.582													A|||	180	0.0359425	0.1316	0.0086	5008	,	,		16872	0.0		0.0	False		,,,				2504	0.0				p.I1399V		Atlas-SNP	.											.	MYO18B	322	.	0			c.A4195G						PASS	.	A	VAL/ILE	447,3717		25,397,1660	37	42	40		4195	-8.4	0	22	dbSNP_83	40	11,8423		0,11,4206	yes	missense	MYO18B	NM_032608.5	29	25,408,5866	GG,GA,AA		0.1304,10.7349,3.6355	benign	1399/2568	26272270	458,12140	2082	4217	6299	SO:0001583	missense	84700	exon24			GCCACCATTGGAA	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.4198A>G	22.37:g.26272270A>G	ENSP00000386096:p.Ile1400Val	99	0	0		103	102	0.990291	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		55	0.025183150183150184	51	0.10365853658536585	4	0.011049723756906077	0	0.0	0	0.0	A	5.587	0.293142	0.10567	0.107349	0.001304	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.86297	-2.08;-2.08;-2.1	4.83	-8.43	0.00953	.	0.552403	0.17941	N	0.156858	T	0.05364	0.0142	M	0.63428	1.95	0.80722	P	0.0	B;B;B;B	0.17268	0.007;0.007;0.021;0.013	B;B;B;B	0.14023	0.01;0.004;0.009;0.01	T	0.45906	-0.9229	9	0.37606	T	0.19	.	0.9513	0.01376	0.2422:0.331:0.22:0.2068	rs695633;rs695633	912;1399;1400;1399	Q8IUG5-2;Q8IUG5;F5GXR6;F5GYU7	.;MY18B_HUMAN;.;.	V	1399;1399;1400	ENSP00000441229:I1399V;ENSP00000334563:I1399V;ENSP00000386096:I1400V	ENSP00000334563:I1399V	I	+	1	0	MYO18B	24602270	0.000000	0.05858	0.000000	0.03702	0.935000	0.57460	-1.506000	0.02271	-1.625000	0.01554	0.528000	0.53228	ATT	A|0.967;G|0.033	0.033	strong		0.582	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		G	26272270	A	G	26272270	3	3	22	1	0	0	0	0	1	0	0	0	10075	217	8	3	4285	3	MYO18B	22	26272270	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	103937	26272270	25032296	4365	7266											
MYO18B	84700	hgsc.bcm.edu	37	chr22	26422993	26422993	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaaacccaattcagttcctgCgagtccctcttagaatccag	12	10	6	13	1	2	1	1	0	1	1	5	2	5	1	4	0	2	1	4	0	5	3	rs7290069	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:26422993C>T	ENST00000407587.2	+	43	7225	c.7056C>T	c.(7054-7056)tgC>tgT	p.C2352C	MYO18B_ENST00000536101.1_Silent_p.C2351C|MYO18B_ENST00000335473.7_Silent_p.C2351C			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2351						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						TCAGTTCCTGCGAGTCCCTCT	0.567													C|||	172	0.034345	0.1256	0.0072	5008	,	,		19058	0.001		0.0	False		,,,				2504	0.0				p.C2351C		Atlas-SNP	.											MYO18B,NS,carcinoma,+2,1	MYO18B	322	1	0			c.C7053T						PASS	.	C		437,3431		26,385,1523	79	88	85		7053	-0.2	1	22	dbSNP_116	85	3,8269		0,3,4133	no	coding-synonymous	MYO18B	NM_032608.5		26,388,5656	TT,TC,CC		0.0363,11.2978,3.6244		2351/2568	26422993	440,11700	1934	4136	6070	SO:0001819	synonymous_variant	84700	exon43			TTCCTGCGAGTCC	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.7056C>T	22.37:g.26422993C>T		45	0	0		41	19	0.463415	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37		65	0.02976190476190476	63	0.12804878048780488	1	0.0027624309392265192	1	0.0017482517482517483	0	0.0	C	8.758	0.922959	0.18056	0.112978	3.63E-4	ENSG00000133454	ENST00000543971	.	.	.	4.89	-0.211	0.13172	.	.	.	.	.	T	0.00496	0.0016	.	.	.	0.09310	P	0.9999999999999841	.	.	.	.	.	.	T	0.17961	-1.0352	3	.	.	.	.	9.1903	0.37195	0.0:0.5439:0.0:0.4561	rs7290069	.	.	.	V	301	.	.	A	+	2	0	MYO18B	24752993	0.125000	0.22332	0.988000	0.46212	0.824000	0.46624	-1.147000	0.03188	0.125000	0.18397	0.462000	0.41574	GCG	C|0.968;T|0.032	0.032	strong		0.567	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		T	26422993	C	T	26422993	2	4	22	1	0	0	0	0	0	0	0	1	10075	776	27	1		1	MYO18B	22	26422993	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	150723	26422993	24881573	4366	7267											
MYO18B	84700	hgsc.bcm.edu	37	chr22	26423124	26423124	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gtcctctgtggacgatgcggGctgtccagaccttggaaagg	7	9	15	10	2	1	1	0	0	1	1	3	4	3	3	3	4	1	1	3	4	1	1	rs6004901	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:26423124G>C	ENST00000407587.2	+	43	7356	c.7187G>C	c.(7186-7188)gGc>gCc	p.G2396A	MYO18B_ENST00000536101.1_Missense_Mutation_p.G2395A|MYO18B_ENST00000335473.7_Missense_Mutation_p.G2395A			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2395						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						GACGATGCGGGCTGTCCAGAC	0.592													G|||	488	0.0974441	0.2663	0.0476	5008	,	,		15885	0.004		0.0348	False		,,,				2504	0.0654				p.G2395A		Atlas-SNP	.											.	MYO18B	322	.	0			c.G7184C						PASS	.	G	ALA/GLY	855,3101		95,665,1218	66	72	70		7184	-1.6	0	22	dbSNP_114	70	253,8029		6,241,3894	yes	missense	MYO18B	NM_032608.5	60	101,906,5112	CC,CG,GG		3.0548,21.6127,9.0538	benign	2395/2568	26423124	1108,11130	1978	4141	6119	SO:0001583	missense	84700	exon43			ATGCGGGCTGTCC	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.7187G>C	22.37:g.26423124G>C	ENSP00000386096:p.Gly2396Ala	86	0	0		88	39	0.443182	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		166|166	0.076007326007326|0.076007326007326	119|119	0.241869918699187|0.241869918699187	22|22	0.06077348066298342|0.06077348066298342	4|4	0.006993006993006993|0.006993006993006993	21|21	0.027704485488126648|0.027704485488126648	G|G	0.007|0.007	-1.985354|-1.985354	0.00443|0.00443	0.216127|0.216127	0.030548|0.030548	ENSG00000133454|ENSG00000133454	ENST00000543971|ENST00000536101;ENST00000335473;ENST00000407587	.|D;D;D	.|0.86956	.|-2.17;-2.17;-2.19	5.12|5.12	-1.6|-1.6	0.08426|0.08426	.|.	.|0.491877	.|0.18417	.|N	.|0.141867	T|T	0.00073|0.00073	0.0002|0.0002	L|L	0.45581|0.45581	1.43|1.43	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B;B;B	.|0.06786	.|0.001;0.001;0.001;0.001;0.001	.|B;B;B;B;B	.|0.08055	.|0.003;0.001;0.001;0.003;0.003	T|T	0.02877|0.02877	-1.1099|-1.1099	4|9	.|0.19147	.|T	.|0.46	.|.	1.509|1.509	0.02492|0.02492	0.1649:0.2383:0.3545:0.2424|0.1649:0.2383:0.3545:0.2424	rs6004901;rs52824215;rs6004901|rs6004901;rs52824215;rs6004901	.|1908;2397;2395;2396;2395	.|Q8IUG5-2;B0QYF5;Q8IUG5;F5GXR6;F5GYU7	.|.;.;MY18B_HUMAN;.;.	P|A	345|2395;2395;2396	.|ENSP00000441229:G2395A;ENSP00000334563:G2395A;ENSP00000386096:G2396A	.|ENSP00000334563:G2395A	A|G	+|+	1|2	0|0	MYO18B|MYO18B	24753124|24753124	0.003000|0.003000	0.15002|0.15002	0.011000|0.011000	0.14972|0.14972	0.130000|0.130000	0.20726|0.20726	0.135000|0.135000	0.15952|0.15952	0.154000|0.154000	0.19237|0.19237	-0.264000|-0.264000	0.10439|0.10439	GCT|GGC	G|0.912;C|0.088	0.088	strong		0.592	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		C	26423124	G	C	26423124	3	2	22	1	0	0	0	0	1	0	0	0	10075	1203	42	4	7350	4	MYO18B	22	26423124	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	131	26423124	24881442	4367	7268											
MYO18B	84700	hgsc.bcm.edu	37	chr22	26423477	26423477	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgactcgtcctcatcctccGgctccatcgtgtccttcaaa	6	12	6	17	3	2	1	2	1	0	0	9	1	7	1	5	1	0	1	5	1	1	1	rs7284177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:26423477G>A	ENST00000407587.2	+	43	7709	c.7540G>A	c.(7540-7542)Ggc>Agc	p.G2514S	MYO18B_ENST00000536101.1_Missense_Mutation_p.G2513S|MYO18B_ENST00000335473.7_Missense_Mutation_p.G2513S			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2513	Poly-Ser.					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						CTCATCCTCCGGCTCCATCGT	0.587													A|||	352	0.0702875	0.2005	0.0259	5008	,	,		18932	0.004		0.0179	False		,,,				2504	0.0481				p.G2513S		Atlas-SNP	.											.	MYO18B	322	.	0			c.G7537A						PASS	.	A	SER/GLY	695,3407		58,579,1414	53	55	55		7537	1.8	1	22	dbSNP_116	55	146,8242		1,144,4049	yes	missense	MYO18B	NM_032608.5	56	59,723,5463	AA,AG,GG		1.7406,16.943,6.7334	benign	2513/2568	26423477	841,11649	2051	4194	6245	SO:0001583	missense	84700	exon43			TCCTCCGGCTCCA	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.7540G>A	22.37:g.26423477G>A	ENSP00000386096:p.Gly2514Ser	61	0	0		56	21	0.375	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		123	0.05631868131868132	92	0.18699186991869918	13	0.03591160220994475	4	0.006993006993006993	14	0.018469656992084433	A	4.656	0.121893	0.08931	0.16943	0.017406	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.85088	-1.92;-1.92;-1.94	5.17	1.8	0.24995	.	0.170297	0.37437	N	0.002083	T	0.00109	0.0003	N	0.00729	-1.24	0.54753	P	1.0999999999983245E-5	B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.001	B;B;B;B;B	0.06405	0.002;0.001;0.001;0.002;0.002	T	0.12426	-1.0548	9	0.02654	T	1	.	4.0444	0.09766	0.4128:0.0:0.4136:0.1736	rs7284177;rs52837742;rs59696890;rs7284177	2026;2515;2513;2514;2513	Q8IUG5-2;B0QYF5;Q8IUG5;F5GXR6;F5GYU7	.;.;MY18B_HUMAN;.;.	S	2513;2513;2514	ENSP00000441229:G2513S;ENSP00000334563:G2513S;ENSP00000386096:G2514S	ENSP00000334563:G2513S	G	+	1	0	MYO18B	24753477	0.459000	0.25768	0.958000	0.39756	0.893000	0.52053	0.694000	0.25512	-0.007000	0.14345	-0.361000	0.07541	GGC	G|0.931;A|0.069	0.069	strong		0.587	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		A	26423477	G	A	26423477	3	1	22	1	0	0	0	0	1	0	0	0	10075	1116	39	1	7703	1	MYO18B	22	26423477	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	353	26423477	24881089	4368	7269											
SEZ6L	23544	hgsc.bcm.edu	37	chr22	26688401	26688401	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccgagggagatgctagccctTtgggtccttacctcctgccc	5	10	11	15	1	0	1	0	0	0	1	2	3	2	1	6	2	4	1	6	2	2	3	rs16981666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:26688401T>C	ENST00000248933.6	+	2	219	c.124T>C	c.(124-126)Ttg>Ctg	p.L42L	SEZ6L_ENST00000529632.2_Silent_p.L42L|SEZ6L_ENST00000402979.1_5'UTR|SEZ6L_ENST00000343706.4_Silent_p.L42L|SEZ6L_ENST00000404234.3_Silent_p.L42L|SEZ6L_ENST00000360929.3_Silent_p.L42L|SEZ6L_ENST00000403121.1_5'UTR			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	42					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						TGCTAGCCCTTTGGGTCCTTA	0.562													T|||	452	0.0902556	0.2322	0.0216	5008	,	,		18973	0.1012		0.0	False		,,,				2504	0.0286				p.L42L		Atlas-SNP	.											.	SEZ6L	174	.	0			c.T124C						PASS	.	T	,,,,,	955,3451	354.1+/-312.5	100,755,1348	47	39	42		124,124,124,124,124,124	-1.8	0	22	dbSNP_123	42	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEZ6L	NM_001184773.1,NM_001184774.1,NM_001184775.1,NM_001184776.1,NM_001184777.1,NM_021115.4	,,,,,	100,762,5641	CC,CT,TT		0.0814,21.675,7.3966	,,,,,	42/1024,42/1014,42/1012,42/950,42/949,42/1025	26688401	962,12044	2203	4300	6503	SO:0001819	synonymous_variant	23544	exon2			AGCCCTTTGGGTC	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.124T>C	22.37:g.26688401T>C		62	0	0		60	32	0.533333	NM_001184777	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Silent	SNP	ENST00000248933.6	37	CCDS13833.1																																																																																			T|0.927;C|0.073	0.073	strong		0.562	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3			C	26688401	T	C	26688401	2	2	22	1	0	0	0	0	0	0	0	1	14158	1838	64	3		3	SEZ6L	22	26688401	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	264924	26688401	24616165	4369	7270											
MN1	4330	hgsc.bcm.edu	37	chr22	28193097	28193097	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtggatctcgtcgggtggCggggcgccgctgctgctcgt	1	9	20	11	6	1	0	0	0	1	0	4	1	1	1	1	6	2	3	1	6	0	0	rs45471598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:28193097C>T	ENST00000302326.4	-	1	4389	c.3435G>A	c.(3433-3435)ccG>ccA	p.P1145P		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	1145					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						CGTCGGGTGGCGGGGCGCCGC	0.711			T	ETV6	"AML, meningioma"								C|||	265	0.0529153	0.1936	0.013	5008	,	,		13060	0.0		0.0	False		,,,				2504	0.0				p.P1145P		Atlas-SNP	.		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"L, O"	MN1,colon,carcinoma,0,1	MN1	122	1	0			c.G3435A						PASS	.	C		505,3385		19,467,1459	6	7	7		3435	-3.9	0	22	dbSNP_127	7	8,8188		0,8,4090	no	coding-synonymous	MN1	NM_002430.2		19,475,5549	TT,TC,CC		0.0976,12.982,4.2446		1145/1321	28193097	513,11573	1945	4098	6043	SO:0001819	synonymous_variant	4330	exon1			GGGTGGCGGGGCG	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.3435G>A	22.37:g.28193097C>T		22	0	0		38	18	0.473684	NM_002430	A9Z1V9	Silent	SNP	ENST00000302326.4	37	CCDS42998.1																																																																																			C|0.962;T|0.038	0.038	strong		0.711	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430		T	28193097	C	T	28193097	2	4	22	1	0	0	0	0	0	0	0	1	9682	755	27	1		1	MN1	22	28193097	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1504696	28193097	23111469	4370	7271											
MN1	4330	hgsc.bcm.edu	37	chr22	28194912	28194913	+	In_Frame_Ins	INS	-	-	TGC																															gctgctgttgctgttgctgtINStgctgctgctgctgctgctg																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:28194912_28194913insTGC	ENST00000302326.4	-	1	2573_2574	c.1619_1620insGCA	c.(1618-1620)caa>caGCAa	p.540_540Q>QQ		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	540	Poly-Gln.				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						gctgttgctgttgctgctgctg	0.658			T	ETV6	"AML, meningioma"																																p.Q540delinsQQ		Atlas-Indel	.		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"L, O"	MN1,NS,carcinoma,0,1	MN1	122	1	0			c.1620_1621insGCA						PASS	.																																			SO:0001652	inframe_insertion	4330	exon1			.	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.1617_1619dupGCA	22.37:g.28194919_28194921dupTGC	ENSP00000304956:p.Gln550dup	42	0	0		56	27	0.482143	NM_002430	A9Z1V9	In_Frame_Ins	INS	ENST00000302326.4	37	CCDS42998.1																																																																																			.	.	weak		0.658	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430		TGC	28194913	-	TGC	28194912	7	5	22	1	0	1	1	0	0	0	0	0	9682	1722	60	0	2350	0	MN1	22	28194912	In_Frame_Ins	INS	-	TCGA-G8-6324-01A-11D-2210-10	1815	28194912	23109654	4371	7272											
NEFH	4744	hgsc.bcm.edu	37	chr22	29886341	29886341	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagataagaaaaaagtcccCaccccagagaaggaggctcc	17	3	10	11	0	0	3	0	0	0	3	2	6	2	4	5	2	0	1	5	2	6	1	rs61744118	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:29886341C>T	ENST00000310624.6	+	4	2745	c.2712C>T	c.(2710-2712)ccC>ccT	p.P904P		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	910	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						AAAAAGTCCCCACCCCAGAGA	0.502													C|||	49	0.00978435	0.0363	0.0014	5008	,	,		18928	0.0		0.0	False		,,,				2504	0.0				p.P904P		Atlas-SNP	.											.	NEFH	178	.	0			c.C2712T						PASS	.	C		129,4277	88.7+/-127.4	2,125,2076	55	60	59		2712	-6.6	0	22	dbSNP_129	59	0,8600		0,0,4300	no	coding-synonymous	NEFH	NM_021076.3		2,125,6376	TT,TC,CC		0.0,2.9278,0.9918		904/1021	29886341	129,12877	2203	4300	6503	SO:0001819	synonymous_variant	4744	exon4			AGTCCCCACCCCA		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.2712C>T	22.37:g.29886341C>T		140	1	0.00714286		136	135	0.992647	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Silent	SNP	ENST00000310624.6	37	CCDS13858.1																																																																																			C|0.990;T|0.010	0.010	strong		0.502	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		T	29886341	C	T	29886341	2	4	22	1	0	0	0	0	0	0	0	1	10323	581	21	2		2	NEFH	22	29886341	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1691429	29886341	21418225	4372	7273											
MTMR3	8897	hgsc.bcm.edu	37	chr22	30403307	30403307	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gacctttctgacgtggagttCggtaaggtgctccctggacc	6	11	13	11	2	1	1	0	1	1	0	3	4	2	3	3	4	1	3	3	4	1	3	rs146523702	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30403307C>T	ENST00000401950.2	+	10	1218	c.876C>T	c.(874-876)ttC>ttT	p.F292F	MTMR3_ENST00000406629.1_Splice_Site_p.F292F|MTMR3_ENST00000351488.3_Splice_Site_p.F292F|MTMR3_ENST00000333027.3_Splice_Site_p.F292F|CTA-85E5.10_ENST00000429350.1_RNA|MTMR3_ENST00000323630.5_Splice_Site_p.F156F	NM_021090.3	NP_066576.1	Q13615	MTMR3_HUMAN	myotubularin related protein 3	292	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				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)			ACGTGGAGTTCGGTAAGGTGC	0.458													C|||	12	0.00239617	0.0091	0.0	5008	,	,		21375	0.0		0.0	False		,,,				2504	0.0				p.F292F		Atlas-SNP	.											MTMR3_ENST00000401950,NS,lymphoid_neoplasm,+2,1	MTMR3	106	1	0			c.C876T						PASS	.	C	,,	47,4359	46.0+/-80.4	0,47,2156	46	40	42		876,876,876	-3	1	22	dbSNP_134	42	2,8598	2.2+/-6.3	0,2,4298	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	MTMR3	NM_021090.3,NM_153050.2,NM_153051.2	,,	0,49,6454	TT,TC,CC		0.0233,1.0667,0.3767	,,	292/1199,292/1171,292/1162	30403307	49,12957	2203	4300	6503	SO:0001630	splice_region_variant	8897	exon10			GGAGTTCGGTAAG	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.877+1C>T	22.37:g.30403307C>T		63	0	0		64	64	1	NM_021090	A5PL26|A7MD32|Q9NYN5|Q9NYN6|Q9UDX6|Q9UEG3	Silent	SNP	ENST00000401950.2	37	CCDS13870.1																																																																																			C|0.997;T|0.003	0.003	strong		0.458	MTMR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322066.1	NM_021090	Silent	T	30403307	C	T	30403307	5	4	22	1	0	0	0	0	0	0	1	0	9954	898	31	1	906	1	MTMR3	22	30403307	Splice_Site	SNP	C	TCGA-G8-6324-01A-11D-2210-10	516966	30403307	20901259	4373	7274											
CCDC157	550631	hgsc.bcm.edu	37	chr22	30761995	30761995	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccaggatctgtgaggatggcGcacctgctgggcagccaggc	7	6	16	12	1	1	1	0	1	1	0	1	3	1	3	3	5	2	3	3	5	0	0	rs61732271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30761995G>A	ENST00000405659.1	+	3	715	c.6G>A	c.(4-6)gcG>gcA	p.A2A	CCDC157_ENST00000338306.3_Silent_p.A2A|CCDC157_ENST00000399824.2_Silent_p.A2A			Q569K6	CC157_HUMAN	coiled-coil domain containing 157	2										central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(1)	15						TGAGGATGGCGCACCTGCTGG	0.657													G|||	89	0.0177716	0.0651	0.0029	5008	,	,		18741	0.0		0.001	False		,,,				2504	0.0				p.A2A		Atlas-SNP	.											.	CCDC157	86	.	0			c.G6A						PASS	.	G		69,1315		1,67,624	21	27	25		6	-10.5	0.8	22	dbSNP_129	25	0,3182		0,0,1591	no	coding-synonymous	CCDC157	NM_001017437.2		1,67,2215	AA,AG,GG		0.0,4.9855,1.5112		2/753	30761995	69,4497	692	1591	2283	SO:0001819	synonymous_variant	550631	exon3			GATGGCGCACCTG	BC018040	CCDS33632.2	22q12.2	2009-03-05			ENSG00000187860	ENSG00000187860			33854	protein-coding gene	gene with protein product							Standard	NM_001017437		Approved		uc011aku.2	Q569K6	OTTHUMG00000151007	ENST00000405659.1:c.6G>A	22.37:g.30761995G>A		21	0	0		20	5	0.25	NM_001017437	Q0VD76|Q9BYA4	Silent	SNP	ENST00000405659.1	37	CCDS33632.2																																																																																			G|0.990;A|0.010	0.010	strong		0.657	CCDC157-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320936.1	NM_001017437		A	30761995	G	A	30761995	2	1	22	1	0	0	0	0	0	0	0	1	2791	1074	38	1		1	CCDC157	22	30761995	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	358688	30761995	20542571	4374	7275											
CCDC157	550631	hgsc.bcm.edu	37	chr22	30765502	30765502	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgccccctgcacaggctgcGgggccctgcatgtccgtggg	4	7	15	15	2	0	0	0	0	0	0	1	0	1	0	4	4	4	3	4	4	0	0	rs5749080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30765502G>C	ENST00000405659.1	+	4	1039	c.330G>C	c.(328-330)gcG>gcC	p.A110A	CCDC157_ENST00000338306.3_Silent_p.A110A			Q569K6	CC157_HUMAN	coiled-coil domain containing 157	110										central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(1)	15						CACAGGCTGCGGGGCCCTGCA	0.652													G|||	51	0.0101837	0.0378	0.0014	5008	,	,		17743	0.0		0.0	False		,,,				2504	0.0				p.A110A		Atlas-SNP	.											.	CCDC157	86	.	0			c.G330C						PASS	.						41	40	41					22																	30765502		2203	4300	6503	SO:0001819	synonymous_variant	550631	exon4			GGCTGCGGGGCCC	BC018040	CCDS33632.2	22q12.2	2009-03-05			ENSG00000187860	ENSG00000187860			33854	protein-coding gene	gene with protein product							Standard	NM_001017437		Approved		uc011aku.2	Q569K6	OTTHUMG00000151007	ENST00000405659.1:c.330G>C	22.37:g.30765502G>C		96	0	0		107	69	0.64486	NM_001017437	Q0VD76|Q9BYA4	Silent	SNP	ENST00000405659.1	37	CCDS33632.2																																																																																			A|0.198;C|0.000;G|0.802	0.000	strong		0.652	CCDC157-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320936.1	NM_001017437		C	30765502	G	C	30765502	2	2	22	1	0	0	0	0	0	0	0	1	2791	1103	39	4		4	CCDC157	22	30765502	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3507	30765502	20539064	4375	7276											
CCDC157	550631	hgsc.bcm.edu	37	chr22	30772567	30772567	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagccctgcacatccccaTctcggcagccctgcagccag	7	5	10	19	1	1	0	0	0	1	0	3	0	2	0	5	2	5	4	5	2	0	0	rs202178544	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30772567T>C	ENST00000405659.1	+	12	2801	c.2092T>C	c.(2092-2094)Tct>Cct	p.S698P	RP1-130H16.16_ENST00000332468.4_RNA|CCDC157_ENST00000338306.3_Missense_Mutation_p.S698P			Q569K6	CC157_HUMAN	coiled-coil domain containing 157	698										central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(1)	15						CACATCCCCATCTCGGCAGCC	0.667													T|||	6	0.00119808	0.0038	0.0014	5008	,	,		15299	0.0		0.0	False		,,,				2504	0.0				p.S698P		Atlas-SNP	.											CCDC157_ENST00000405659,bladder,carcinoma,0,4	CCDC157	86	4	0			c.T2092C						PASS	.						71	79	76					22																	30772567		2203	4300	6503	SO:0001583	missense	550631	exon12			TCCCCATCTCGGC	BC018040	CCDS33632.2	22q12.2	2009-03-05			ENSG00000187860	ENSG00000187860			33854	protein-coding gene	gene with protein product							Standard	NM_001017437		Approved		uc011aku.2	Q569K6	OTTHUMG00000151007	ENST00000405659.1:c.2092T>C	22.37:g.30772567T>C	ENSP00000385357:p.Ser698Pro	109	0	0		125	15	0.12	NM_001017437	Q0VD76|Q9BYA4	Missense_Mutation	SNP	ENST00000405659.1	37	CCDS33632.2	.	.	.	.	.	.	.	.	.	.	T	7.336	0.619980	0.14193	.	.	ENSG00000187860	ENST00000405659;ENST00000338306	T;T	0.39229	1.09;1.09	3.04	-2.83	0.05769	.	1.188910	0.06203	N	0.683596	T	0.20373	0.0490	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19549	-1.0302	10	0.25106	T	0.35	-1.9381	7.0241	0.24930	0.0:0.3799:0.0:0.6201	.	698	Q569K6	CC157_HUMAN	P	698	ENSP00000385357:S698P;ENSP00000343087:S698P	ENSP00000343087:S698P	S	+	1	0	CCDC157	29102567	0.000000	0.05858	0.008000	0.14137	0.026000	0.11368	-0.341000	0.07811	-0.707000	0.05022	-0.415000	0.06103	TCT	.	.	weak		0.667	CCDC157-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320936.1	NM_001017437		C	30772567	T	C	30772567	3	2	22	1	0	0	0	0	1	0	0	0	2791	1435	50	3	2130	3	CCDC157	22	30772567	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	7065	30772567	20531999	4376	7277											
MTP18	51537	hgsc.bcm.edu	37	chr22	30824659	30824660	+	3'UTR	INS	-	-	A																															tttgagctggacagaagcttINSagagacaaaggcttcaagaa																								rs527818803|rs149958301	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30824659_30824660insA	ENST00000266263.5	+	0	989_990				MTFP1_ENST00000355143.4_Stop_Codon_Ins|MTFP1_ENST00000407550.3_3'UTR|RP4-539M6.19_ENST00000439838.1_3'UTR	NM_016498.4	NP_057582.2	Q9UDX5	MTFP1_HUMAN	mitochondrial fission process 1						apoptotic process (GO:0006915)|mitochondrial fission (GO:0000266)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(1)|large_intestine(1)|lung(2)	4						GACAGAAGCTTAGAGACAAAGG	0.559													A|A|AA|insertion	54	0.0107827	0.0393	0.0029	5008	,	,		20262	0.0		0.0	False		,,,				2504	0.0				p.X136delinsX		Pindel,Atlas-Indel	.											.	MTFP1	7	.	0			c.406_407insA						PASS	.		,	105,4159		0,105,2027					,	-0.6	0		dbSNP_134	38	1,8253		0,1,4126	yes	utr-3,frameshift	MTFP1	NM_016498.4,NM_001003704.2	,	0,106,6153	A1A1,A1R,RR		0.0121,2.4625,0.8468	,	,		106,12412				SO:0001624	3_prime_UTR_variant	51537	exon3			.	AF151076	CCDS33634.1, CCDS33635.1	22q	2010-09-02			ENSG00000242114	ENSG00000242114			26945	protein-coding gene	gene with protein product		610235				15155745, 15985469	Standard	NM_016498		Approved	MTP18, HSPC242		Q9UDX5	OTTHUMG00000151057	ENST00000266263.5:c.*139->A	22.37:g.30824660_30824660dupA		72	0	.		75	27	0.36	NM_001003704	A6NFQ5|Q9H3K1|Q9P0N6	Frame_Shift_Ins	INS	ENST00000266263.5	37	CCDS33635.1																																																																																			-|0.993;A|0.007	0.007	strong		0.559	MTFP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321126.3	NM_016498		A	30824660	-	A	30824659	6	5	22	0	1	1	1	0	0	0	0	0	9964	1767	61	0		0	MTP18	22	30824659	3'UTR	INS	-	TCGA-G8-6324-01A-11D-2210-10	52092	30824659	20479907	4377	7278											
SEC14L3	266629	hgsc.bcm.edu	37	chr22	30860831	30860831	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caacacaataattttcctgcGagtgtcctcactcaggaatg	12	11	7	11	1	2	0	2	0	0	0	4	2	4	1	2	1	2	0	2	1	4	3	rs115090125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30860831G>A	ENST00000215812.4	-	8	730	c.640C>T	c.(640-642)Cgc>Tgc	p.R214C	SEC14L3_ENST00000401751.1_Missense_Mutation_p.R155C|SEC14L3_ENST00000539629.1_Missense_Mutation_p.R155C|SEC14L3_ENST00000415957.2_Missense_Mutation_p.R155C|SEC14L3_ENST00000402286.1_Missense_Mutation_p.R137C|SEC14L3_ENST00000403066.1_Missense_Mutation_p.R155C|SEC14L3_ENST00000540910.1_Missense_Mutation_p.R137C	NM_174975.4	NP_777635.1	Q9UDX4	S14L3_HUMAN	SEC14-like 3 (S. cerevisiae)	214	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.		R -> H (in dbSNP:rs2269961).			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)	ATTTTCCTGCGAGTGTCCTCA	0.443													G|||	18	0.00359425	0.0129	0.0014	5008	,	,		23216	0.0		0.0	False		,,,				2504	0.0				p.R214C	Esophageal Squamous(108;290 1516 3584 23771 37333)	Atlas-SNP	.											.	SEC14L3	46	.	0			c.C640T						PASS	.	G	CYS/ARG	34,4372	40.0+/-72.8	0,34,2169	179	154	162		640	4.4	1	22	dbSNP_132	162	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SEC14L3	NM_174975.4	180	0,35,6468	AA,AG,GG		0.0116,0.7717,0.2691	probably-damaging	214/401	30860831	35,12971	2203	4300	6503	SO:0001583	missense	266629	exon8			TCCTGCGAGTGTC	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.640C>T	22.37:g.30860831G>A	ENSP00000215812:p.Arg214Cys	135	0	0		148	75	0.506757	NM_174975	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Missense_Mutation	SNP	ENST00000215812.4	37	CCDS13877.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	20.1	3.931583	0.73442	0.007717	1.16E-4	ENSG00000100012	ENST00000403066;ENST00000415957;ENST00000215812;ENST00000402286;ENST00000401751;ENST00000539629;ENST00000540910	T;T;T;T;T;T;T	0.79454	-1.27;-1.27;-1.27;-1.27;-1.27;-1.27;-1.27	5.5	4.43	0.53597	Cellular retinaldehyde-binding/triple function, C-terminal (5);	0.000000	0.85682	D	0.000000	D	0.86615	0.5975	M	0.91510	3.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.71414	0.973;0.973	D	0.90030	0.4134	10	0.87932	D	0	-11.635	14.7515	0.69530	0.0:0.0:0.8547:0.1453	.	137;214	E9PE57;Q9UDX4	.;S14L3_HUMAN	C	155;155;214;137;155;155;137	ENSP00000385941:R155C;ENSP00000401864:R155C;ENSP00000215812:R214C;ENSP00000385004:R137C;ENSP00000383896:R155C;ENSP00000444691:R155C;ENSP00000439752:R137C	ENSP00000215812:R214C	R	-	1	0	SEC14L3	29190831	1.000000	0.71417	0.996000	0.52242	0.707000	0.40811	4.312000	0.59154	2.593000	0.87608	0.655000	0.94253	CGC	G|0.997;A|0.003	0.003	strong		0.443	SEC14L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321950.4	NM_174975		A	30860831	G	A	30860831	3	1	22	1	0	0	0	0	1	0	0	0	13998	1058	37	1	582	1	SEC14L3	22	30860831	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	36172	30860831	20443735	4378	7279											
SEC14L3	266629	hgsc.bcm.edu	37	chr22	30864545	30864545	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgcgctcacagtccctcaTcttggtcttgagcaggtcct	6	12	10	13	1	4	1	2	1	2	0	6	2	6	1	2	2	2	2	2	2	0	2	rs115380280	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30864545T>A	ENST00000215812.4	-	5	463	c.373A>T	c.(373-375)Atg>Ttg	p.M125L	SEC14L3_ENST00000401751.1_Missense_Mutation_p.M66L|SEC14L3_ENST00000539629.1_Missense_Mutation_p.M66L|SEC14L3_ENST00000415957.2_Missense_Mutation_p.M66L|SEC14L3_ENST00000402286.1_Missense_Mutation_p.M48L|SEC14L3_ENST00000403066.1_Missense_Mutation_p.M66L|SEC14L3_ENST00000540910.1_Missense_Mutation_p.M48L	NM_174975.4	NP_777635.1	Q9UDX4	S14L3_HUMAN	SEC14-like 3 (S. cerevisiae)	125	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.					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)	CAGTCCCTCATCTTGGTCTTG	0.602													T|||	18	0.00359425	0.0129	0.0014	5008	,	,		18253	0.0		0.0	False		,,,				2504	0.0				p.M125L	Esophageal Squamous(108;290 1516 3584 23771 37333)	Atlas-SNP	.											.	SEC14L3	46	.	0			c.A373T						PASS	.	T	LEU/MET	33,4373	39.2+/-71.8	0,33,2170	176	130	145		373	4.6	1	22	dbSNP_132	145	0,8600		0,0,4300	yes	missense	SEC14L3	NM_174975.4	15	0,33,6470	AA,AT,TT		0.0,0.749,0.2537	benign	125/401	30864545	33,12973	2203	4300	6503	SO:0001583	missense	266629	exon5			CCCTCATCTTGGT	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.373A>T	22.37:g.30864545T>A	ENSP00000215812:p.Met125Leu	112	0	0		113	57	0.504425	NM_174975	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Missense_Mutation	SNP	ENST00000215812.4	37	CCDS13877.1	2|2	9.157509157509158E-4|9.157509157509158E-4	2|2	0.0040650406504065045|0.0040650406504065045	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	T|T	10.11|10.11	1.260683|1.260683	0.23051|0.23051	0.00749|0.00749	0.0|0.0	ENSG00000100012|ENSG00000100012	ENST00000403066;ENST00000415957;ENST00000215812;ENST00000402286;ENST00000401751;ENST00000539629;ENST00000540910|ENST00000435069	T;T;T;T;T;T;T|.	0.72835|.	-0.69;-0.69;-0.69;-0.69;-0.69;-0.69;-0.69|.	4.55|4.55	4.55|4.55	0.56014|0.56014	Cellular retinaldehyde-binding/triple function, C-terminal (5);|.	0.222920|.	0.48286|.	D|.	0.000195|.	T|T	0.25754|0.25754	0.0627|0.0627	N|N	0.05592|0.05592	-0.015|-0.015	0.80722|0.80722	D|D	1|1	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.08055|.	0.003;0.003|.	T|T	0.11251|0.11251	-1.0595|-1.0595	10|5	0.15952|.	T|.	0.53|.	-18.6063|-18.6063	9.2656|9.2656	0.37639|0.37639	0.205:0.0:0.0:0.795|0.205:0.0:0.0:0.795	.|.	48;125|.	E9PE57;Q9UDX4|.	.;S14L3_HUMAN|.	L|S	66;66;125;48;66;66;48|90	ENSP00000385941:M66L;ENSP00000401864:M66L;ENSP00000215812:M125L;ENSP00000385004:M48L;ENSP00000383896:M66L;ENSP00000444691:M66L;ENSP00000439752:M48L|.	ENSP00000215812:M125L|.	M|R	-|-	1|3	0|2	SEC14L3|SEC14L3	29194545|29194545	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	3.513000|3.513000	0.53414|0.53414	1.810000|1.810000	0.52873|0.52873	0.519000|0.519000	0.50382|0.50382	ATG|AGA	T|0.998;A|0.002	0.002	strong		0.602	SEC14L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321950.4	NM_174975		A	30864545	T	A	30864545	3	1	22	1	0	0	0	0	1	0	0	0	13998	1435	50	5	861	5	SEC14L3	22	30864545	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	3714	30864545	20440021	4379	7280											
TCN2	6948	hgsc.bcm.edu	37	chr22	31011350	31011350	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctcaaacttcaaccctggtCggagacaacggatcaccatg	12	7	9	13	2	3	1	3	0	0	1	4	3	3	2	2	3	3	1	2	3	3	1	rs35838082	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:31011350C>T	ENST00000215838.3	+	5	1137	c.643C>T	c.(643-645)Cgg>Tgg	p.R215W	TCN2_ENST00000407817.3_Missense_Mutation_p.R188W|TCN2_ENST00000405742.3_Missense_Mutation_p.R211W			P20062	TCO2_HUMAN	transcobalamin II	215			R -> W (in dbSNP:rs35838082).		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)	endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	cobalamin binding (GO:0031419)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|prostate(2)|urinary_tract(1)	22					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CAACCCTGGTCGGAGACAACG	0.557													C|||	365	0.0728834	0.2443	0.0159	5008	,	,		21382	0.001		0.006	False		,,,				2504	0.0245				p.R215W		Atlas-SNP	.											.	TCN2	44	.	0			c.C643T						PASS	.	C	TRP/ARG,TRP/ARG	1044,3362	382.1+/-324.3	124,796,1283	87	77	81		643,562	5.8	0	22	dbSNP_126	81	58,8542	35.9+/-90.5	0,58,4242	yes	missense,missense	TCN2	NM_000355.3,NM_001184726.1	101,101	124,854,5525	TT,TC,CC		0.6744,23.695,8.473	probably-damaging,probably-damaging	215/428,188/401	31011350	1102,11904	2203	4300	6503	SO:0001583	missense	6948	exon5			CCTGGTCGGAGAC		CCDS13881.1, CCDS54519.1	22q12.2	2014-09-17	2010-05-11		ENSG00000185339	ENSG00000185339			11653	protein-coding gene	gene with protein product	"macrocytic anemia"	613441	"transcobalamin II; macrocytic anemia"			1708393, 7742531	Standard	NM_000355		Approved	D22S676, D22S750, TC2	uc003aip.2	P20062	OTTHUMG00000151095	ENST00000215838.3:c.643C>T	22.37:g.31011350C>T	ENSP00000215838:p.Arg215Trp	183	0	0		208	208	1	NM_000355	Q96FD4|Q9BVI8|Q9UCI5|Q9UCI6|Q9UDM0	Missense_Mutation	SNP	ENST00000215838.3	37	CCDS13881.1	126	0.057692307692307696	115	0.23373983739837398	5	0.013812154696132596	0	0.0	6	0.0079155672823219	C	20.4	3.985921	0.74589	0.23695	0.006744	ENSG00000185339	ENST00000215838;ENST00000405742;ENST00000407817	T;T;T	0.15952	2.38;2.38;2.38	5.82	5.82	0.92795	.	0.978539	0.08426	N	0.947638	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.9999999999999691	D;D;D	0.60575	0.975;0.988;0.988	P;P;P	0.51229	0.663;0.559;0.559	T	0.48525	-0.9028	9	0.62326	D	0.03	-1.0E-4	17.0097	0.86403	0.0:1.0:0.0:0.0	rs35838082;rs61224137	188;211;215	Q96FD4;B5MBX2;P20062	.;.;TCO2_HUMAN	W	215;211;188	ENSP00000215838:R215W;ENSP00000385914:R211W;ENSP00000384914:R188W	ENSP00000215838:R215W	R	+	1	2	TCN2	29341350	0.001000	0.12720	0.009000	0.14445	0.013000	0.08279	1.271000	0.33098	2.756000	0.94617	0.561000	0.74099	CGG	C|0.925;T|0.075	0.075	strong		0.557	TCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321282.2	NM_000355		T	31011350	C	T	31011350	3	4	22	1	0	0	0	0	1	0	0	0	15722	875	31	1	661	1	TCN2	22	31011350	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	146805	31011350	20293216	4380	7281											
SLC35E4	339665	hgsc.bcm.edu	37	chr22	31032881	31032881	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accacacctctgttcaccctGgccctgtcggcgctgctgct	4	10	9	18	2	2	0	1	0	1	0	3	0	2	0	4	2	2	4	4	2	0	1	rs8136373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:31032881G>A	ENST00000343605.4	+	1	1243	c.444G>A	c.(442-444)ctG>ctA	p.L148L	SLC35E4_ENST00000300385.8_Silent_p.L148L|SLC35E4_ENST00000406566.1_Silent_p.L148L	NM_001001479.2	NP_001001479.1	Q6ICL7	S35E4_HUMAN	solute carrier family 35, member E4	148	EamA.|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						TGTTCACCCTGGCCCTGTCGG	0.677													G|||	440	0.0878594	0.2988	0.0303	5008	,	,		14087	0.0		0.0149	False		,,,				2504	0.0092				p.L148L		Atlas-SNP	.											.	SLC35E4	22	.	0			c.G444A						PASS	.	G		1219,3185	391.9+/-328.3	165,889,1148	65	36	46		444	5.2	1	22	dbSNP_116	46	171,8429	72.9+/-135.5	1,169,4130	no	coding-synonymous	SLC35E4	NM_001001479.2		166,1058,5278	AA,AG,GG		1.9884,27.6794,10.689		148/351	31032881	1390,11614	2202	4300	6502	SO:0001819	synonymous_variant	339665	exon1			CACCCTGGCCCTG		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.444G>A	22.37:g.31032881G>A		46	0	0		39	38	0.974359	NM_001001479	Q567P0	Silent	SNP	ENST00000343605.4	37	CCDS13882.1																																																																																			G|0.900;A|0.100	0.100	strong		0.677	SLC35E4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321382.1	XM_290973		A	31032881	G	A	31032881	2	1	22	1	0	0	0	0	0	0	0	1	14602	1335	47	2		2	SLC35E4	22	31032881	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	21531	31032881	20271685	4381	7282											
C22orf30	253143	hgsc.bcm.edu	37	chr22	32109305	32109305	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttcttcgcaaaggcaccaTgtatttgatcacacccagca	11	11	6	13	1	2	1	1	1	1	0	3	1	2	1	2	1	1	4	2	1	2	4	rs112331962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:32109305T>C	ENST00000327423.6	-	4	4709	c.4520A>G	c.(4519-4521)cAt>cGt	p.H1507R	PRR14L_ENST00000397493.2_Missense_Mutation_p.H1507R|PRR14L_ENST00000434485.1_Missense_Mutation_p.H1507R	NM_173566.2	NP_775837.2	Q5THK1	PR14L_HUMAN	proline rich 14-like	1507										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(5)|skin(1)|urinary_tract(2)	14						AAAGGCACCATGTATTTGATC	0.473													T|||	191	0.038139	0.1377	0.013	5008	,	,		19854	0.0		0.0	False		,,,				2504	0.0				p.H1507R		Atlas-SNP	.											.	PRR14L	198	.	0			c.A4520G						PASS	.	T	ARG/HIS	138,1246		3,132,557	169	140	149		4520	-0.7	0	22	dbSNP_132	149	3,3179		0,3,1588	yes	missense	PRR14L	NM_173566.2	29	3,135,2145	CC,CT,TT		0.0943,9.9711,3.088	benign	1507/2152	32109305	141,4425	692	1591	2283	SO:0001583	missense	253143	exon4			GCACCATGTATTT	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.4520A>G	22.37:g.32109305T>C	ENSP00000331845:p.His1507Arg	101	0	0		100	50	0.5	NM_173566	Q5THK4|Q6ZNN1|Q6ZWH0|Q8IW74|Q9H5T4	Missense_Mutation	SNP	ENST00000327423.6	37	CCDS13900.2	66	0.03021978021978022	63	0.12804878048780488	3	0.008287292817679558	0	0.0	0	0.0	T	3.362	-0.130293	0.06753	0.099711	9.43E-4	ENSG00000183530	ENST00000397493;ENST00000327423;ENST00000434485	T;T;T	0.05786	3.39;3.41;3.4	5.59	-0.745	0.11098	.	0.617385	0.14488	N	0.316502	T	0.00039	0.0001	L	0.44542	1.39	0.09310	N	1	B;B;B	0.12013	0.003;0.003;0.005	B;B;B	0.09377	0.004;0.003;0.004	T	0.44892	-0.9298	9	.	.	.	0.0323	1.9244	0.03314	0.1203:0.3338:0.2122:0.3338	.	1507;1507;1507	Q5THK1-2;Q5THK1;Q5THK1-4	.;PR14L_HUMAN;.	R	1507	ENSP00000380630:H1507R;ENSP00000331845:H1507R;ENSP00000388314:H1507R	.	H	-	2	0	PRR14L	30439305	0.000000	0.05858	0.024000	0.17045	0.610000	0.37248	-1.136000	0.03222	0.073000	0.16731	-1.151000	0.01829	CAT	T|0.975;C|0.025	0.025	strong		0.473	PRR14L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074993.2	NM_173566		C	32109305	T	C	32109305	3	2	22	1	0	0	0	0	1	0	0	0	2144	1464	51	3	1959	3	C22orf30	22	32109305	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1076424	32109305	19195261	4382	7283											
RFPL3	10738	hgsc.bcm.edu	37	chr22	32756807	32756807	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gatgctccagtccgtcctggGgaggccaaataagccgccac	9	6	12	14	2	0	0	0	0	0	0	3	2	3	1	6	3	2	1	6	3	2	1	rs78565810	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:32756807G>C	ENST00000249007.4	+	2	1147	c.942G>C	c.(940-942)ggG>ggC	p.G314G	RFPL3S_ENST00000461833.1_5'UTR|RFPL3S_ENST00000400234.1_Silent_p.S77S|RFPL3_ENST00000397468.1_Silent_p.G285G|RFPL3S_ENST00000382084.4_Silent_p.S48S|RFPL3_ENST00000382088.3_Silent_p.G285G	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	314							zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						TCCGTCCTGGGGAGGCCAAAT	0.443													g|||	99	0.0197684	0.0734	0.0029	5008	,	,		15426	0.0		0.0	False		,,,				2504	0.0				p.G314G		Atlas-SNP	.											.	RFPL3	91	.	0			c.G942C						PASS	.	G	,	237,4113		2,233,1940	44	48	47		942,855	-0.6	0	22	dbSNP_131	47	0,8528		0,0,4264	no	coding-synonymous,coding-synonymous	RFPL3	NM_001098535.1,NM_006604.2	,	2,233,6204	CC,CG,GG		0.0,5.4483,1.8403	,	314/318,285/289	32756807	237,12641	2175	4264	6439	SO:0001819	synonymous_variant	10738	exon2			TCCTGGGGAGGCC	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.942G>C	22.37:g.32756807G>C		198	0	0		216	86	0.398148	NM_001098535	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Silent	SNP	ENST00000249007.4	37	CCDS43011.1																																																																																			G|0.978;C|0.022	0.022	strong		0.443	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604		C	32756807	G	C	32756807	2	2	22	1	0	0	0	0	0	0	0	1	13270	1219	43	4		4	RFPL3	22	32756807	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	647502	32756807	18547759	4383	7284											
BPIL2	254240	hgsc.bcm.edu	37	chr22	32843312	32843312	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggtatttggaaatgaaaaGgcactgatttttatactgta	14	14	10	3	0	0	2	0	2	0	0	0	4	0	3	0	3	1	3	0	3	7	7	rs28733723	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:32843312G>A	ENST00000397452.1	-	4	371	c.261C>T	c.(259-261)gcC>gcT	p.A87A	BPIFC_ENST00000432451.2_5'UTR|BPIFC_ENST00000300399.3_Silent_p.A87A|BPIFC_ENST00000534972.1_5'UTR			Q8NFQ6	BPIFC_HUMAN	BPI fold containing family C	87						extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)|phospholipid binding (GO:0005543)										GAAATGAAAAGGCACTGATTT	0.463													G|||	147	0.029353	0.1074	0.0072	5008	,	,		18029	0.0		0.0	False		,,,				2504	0.0				p.A87A		Atlas-SNP	.											.	.	.	.	0			c.C261T						PASS	.	G		387,4019	189.2+/-215.4	14,359,1830	98	90	93		261	1.2	1	22	dbSNP_125	93	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	BPIFC	NM_174932.2		14,362,6127	AA,AG,GG		0.0349,8.7835,2.9986		87/508	32843312	390,12616	2203	4300	6503	SO:0001819	synonymous_variant	254240	exon3			TGAAAAGGCACTG	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.261C>T	22.37:g.32843312G>A		102	0	0		78	43	0.551282	NM_174932	A2RRF1	Silent	SNP	ENST00000397452.1	37	CCDS13906.1																																																																																			G|0.968;A|0.032	0.032	strong		0.463	BPIFC-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129029.2	NM_174932		A	32843312	G	A	32843312	2	1	22	1	0	0	0	0	0	0	0	1	1494	987	35	2		2	BPIL2	22	32843312	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	86505	32843312	18461254	4384	7285											
TOM1	10043	hgsc.bcm.edu	37	chr22	35713931	35713931	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcaacatggagatctgcgaCatcatcaacgagacggagga	14	6	11	10	3	4	2	3	0	1	2	4	7	4	4	0	3	3	0	0	3	2	0	rs57755951	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:35713931C>T	ENST00000449058.2	+	2	239	c.114C>T	c.(112-114)gaC>gaT	p.D38D	TOM1_ENST00000436462.2_Missense_Mutation_p.T17I|TOM1_ENST00000382034.5_5'UTR|TOM1_ENST00000411850.1_Silent_p.D38D|TOM1_ENST00000447733.1_Silent_p.D5D|TOM1_ENST00000425375.1_Silent_p.D38D	NM_005488.2	NP_005479.1	O60784	TOM1_HUMAN	target of myb1 (chicken)	38	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						AGATCTGCGACATCATCAACG	0.597													C|||	80	0.0159744	0.0582	0.0043	5008	,	,		20039	0.0		0.0	False		,,,				2504	0.0				p.D38D		Atlas-SNP	.											.	TOM1	43	.	0			c.C114T						PASS	.	C	,,,	211,4195	130.2+/-166.9	8,195,2000	107	106	106		15,114,114,114	5.4	1	22	dbSNP_129	106	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TOM1	NM_001135729.1,NM_001135730.1,NM_001135732.1,NM_005488.2	,,,	8,197,6298	TT,TC,CC		0.0233,4.7889,1.6377	,,,	5/461,38/448,38/494,38/493	35713931	213,12793	2203	4300	6503	SO:0001819	synonymous_variant	10043	exon2			CTGCGACATCATC	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.114C>T	22.37:g.35713931C>T		181	0	0		197	94	0.477157	NM_001135732	B4DEL9|B4DNA1|Q5TIJ6|Q86X74	Silent	SNP	ENST00000449058.2	37	CCDS13913.1	23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	C	13.28	2.189681	0.38707	0.047889	2.33E-4	ENSG00000100284	ENST00000436462	T	0.21361	2.01	5.36	5.36	0.76844	.	.	.	.	.	T	0.01695	0.0054	.	.	.	0.80722	D	1	D	0.53312	0.959	B	0.43623	0.425	T	0.08351	-1.0726	8	0.02654	T	1	-30.6633	12.4314	0.55575	0.0:0.9231:0.0:0.0769	rs57755951	17	E7EPD0	.	I	17	ENSP00000402556:T17I	ENSP00000402556:T17I	T	+	2	0	TOM1	34043931	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	4.017000	0.57167	2.502000	0.84385	0.561000	0.74099	ACA	C|0.982;T|0.018	0.018	strong		0.597	TOM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320641.1	NM_005488		T	35713931	C	T	35713931	2	4	22	1	0	0	0	0	0	0	0	1	16366	477	17	2		2	TOM1	22	35713931	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2870619	35713931	15590635	4385	7286											
MYH9	4627	hgsc.bcm.edu	37	chr22	36678816	36678816	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	attcggcggggcacgacaaaCggcaggtccccgcgcctggg	7	4	16	14	6	0	0	0	0	0	0	2	1	1	0	3	6	1	2	3	6	1	1	rs80050551	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:36678816C>A	ENST00000216181.5	-	41	6011	c.5781G>T	c.(5779-5781)ccG>ccT	p.P1927P	MYH9_ENST00000475726.1_5'Flank	NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1927					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)	p.P1927P(1)		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						GCACGACAAACGGCAGGTCCC	0.672			T	ALK	ALCL		"Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"		Hereditary Macrothrombocytopenia, MYH9-associated				.|||	138	0.0275559	0.0991	0.0101	5008	,	,		14735	0.0		0.0	False		,,,				2504	0.0				p.P1927P		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"myosin, heavy polypeptide 9, non-muscle"	yes	L	MYH9,NS,NS,0,1	MYH9	225	1	1	Substitution - coding silent(1)	pancreas(1)	c.G5781T						PASS	.			364,4042	178.0+/-206.8	14,336,1853	34	30	32		5781	-7.5	0.7	22	dbSNP_131	32	5,8593	3.0+/-9.4	0,5,4294	no	coding-synonymous	MYH9	NM_002473.4		14,341,6147	AA,AC,CC		0.0582,8.2615,2.8376		1927/1961	36678816	369,12635	2203	4299	6502	SO:0001819	synonymous_variant	4627	exon41	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	GACAAACGGCAGG		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.5781G>T	22.37:g.36678816C>A		28	0	0		42	26	0.619048	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Silent	SNP	ENST00000216181.5	37	CCDS13927.1																																																																																			C|0.969;A|0.031	0.031	strong		0.672	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473		A	36678816	C	A	36678816	2	1	22	1	0	0	0	0	0	0	0	1	10051	523	19	4		4	MYH9	22	36678816	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	964885	36678816	14625750	4386	7287											
FOXRED2	80020	hgsc.bcm.edu	37	chr22	36886178	36886178	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcgcctgcctgtgggggcAtagtcccgcaggagcctgct	5	7	16	13	2	0	0	0	0	0	0	1	1	1	1	4	4	3	3	4	4	1	1	rs73409777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:36886178A>G	ENST00000397224.4	-	9	2025	c.1932T>C	c.(1930-1932)taT>taC	p.Y644Y	FOXRED2_ENST00000397223.4_Silent_p.Y644Y|FOXRED2_ENST00000366463.3_Silent_p.Y196Y|FOXRED2_ENST00000216187.6_Silent_p.Y644Y	NM_001102371.1	NP_001095841.1	Q8IWF2	FXRD2_HUMAN	FAD-dependent oxidoreductase domain containing 2	644					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						CTGTGGGGGCATAGTCCCGCA	0.652													A|||	142	0.0283546	0.1044	0.0043	5008	,	,		16850	0.0		0.001	False		,,,				2504	0.0				p.Y644Y		Atlas-SNP	.											.	FOXRED2	48	.	0			c.T1932C						PASS	.	A	,	385,4021	187.8+/-214.3	21,343,1839	47	51	50		1932,1932	-3.8	0	22	dbSNP_130	50	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	FOXRED2	NM_001102371.1,NM_024955.5	,	21,346,6136	GG,GA,AA		0.0349,8.7381,2.9832	,	644/685,644/685	36886178	388,12618	2203	4300	6503	SO:0001819	synonymous_variant	80020	exon9			GGGGGCATAGTCC	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.1932T>C	22.37:g.36886178A>G		68	0	0		81	39	0.481481	NM_001102371	B2RDI4|Q8N378|Q96BD1|Q9H5L5|Q9H6M8	Silent	SNP	ENST00000397224.4	37	CCDS13929.1																																																																																			A|0.975;G|0.025	0.025	strong		0.652	FOXRED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104098.2	NM_024955		G	36886178	A	G	36886178	2	3	22	1	0	0	0	0	0	0	0	1	6042	224	8	3		3	FOXRED2	22	36886178	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	207362	36886178	14418388	4387	7288											
FOXRED2	80020	hgsc.bcm.edu	37	chr22	36902259	36902259	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgcggtgccgcgggtagcGtgtgaagaagctgccgggcc	5	7	18	11	5	0	2	0	1	0	1	0	2	0	2	3	3	5	2	3	3	3	2	rs56767103	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:36902259G>A	ENST00000397224.4	-	2	304	c.211C>T	c.(211-213)Cgc>Tgc	p.R71C	FOXRED2_ENST00000397223.4_Missense_Mutation_p.R71C|FOXRED2_ENST00000216187.6_Missense_Mutation_p.R71C	NM_001102371.1	NP_001095841.1	Q8IWF2	FXRD2_HUMAN	FAD-dependent oxidoreductase domain containing 2	71			R -> C (in dbSNP:rs56767103).		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						CGCGGGTAGCGTGTGAAGAAG	0.667													G|||	144	0.028754	0.1059	0.0043	5008	,	,		16027	0.0		0.001	False		,,,				2504	0.0				p.R71C		Atlas-SNP	.											.	FOXRED2	48	.	0			c.C211T						PASS	.	G	CYS/ARG,CYS/ARG	385,4021	193.3+/-218.5	22,341,1840	70	52	59		211,211	5	1	22	dbSNP_129	59	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	FOXRED2	NM_001102371.1,NM_024955.5	180,180	22,344,6137	AA,AG,GG		0.0349,8.7381,2.9832	possibly-damaging,possibly-damaging	71/685,71/685	36902259	388,12618	2203	4300	6503	SO:0001583	missense	80020	exon2			GGTAGCGTGTGAA	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.211C>T	22.37:g.36902259G>A	ENSP00000380401:p.Arg71Cys	93	0	0		93	49	0.526882	NM_001102371	B2RDI4|Q8N378|Q96BD1|Q9H5L5|Q9H6M8	Missense_Mutation	SNP	ENST00000397224.4	37	CCDS13929.1	46	0.021062271062271064	44	0.08943089430894309	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	22.6	4.317138	0.81469	0.087381	3.49E-4	ENSG00000100350	ENST00000397224;ENST00000216187;ENST00000397223;ENST00000423980	T;T;T;T	0.23950	1.88;1.88;1.88;1.88	5.04	5.04	0.67666	Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (1);	0.201070	0.44097	D	0.000489	T	0.02083	0.0065	M	0.79123	2.44	0.40354	D	0.979162	D	0.65815	0.995	P	0.59703	0.862	T	0.00936	-1.1508	10	0.48119	T	0.1	-31.9668	7.8809	0.29621	0.0837:0.0:0.7553:0.161	rs56767103	71	Q8IWF2	FXRD2_HUMAN	C	71	ENSP00000380401:R71C;ENSP00000216187:R71C;ENSP00000380400:R71C;ENSP00000409692:R71C	ENSP00000216187:R71C	R	-	1	0	FOXRED2	35232205	1.000000	0.71417	0.977000	0.42913	0.953000	0.61014	4.550000	0.60733	2.337000	0.79520	0.561000	0.74099	CGC	G|0.974;A|0.026	0.026	strong		0.667	FOXRED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104098.2	NM_024955		A	36902259	G	A	36902259	3	1	22	1	0	0	0	0	1	0	0	0	6042	1145	40	1	1875	1	FOXRED2	22	36902259	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	16081	36902259	14402307	4388	7289											
C22orf33	339669	hgsc.bcm.edu	37	chr22	37397876	37397876	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcctggcccctgctatgacAcctgctcctcggagaccagc	6	8	9	18	1	0	2	0	1	0	1	3	3	2	2	6	2	3	2	6	2	1	1	rs148258673	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:37397876A>G	ENST00000405091.2	-	4	741		c.e4+1		TEX33_ENST00000402860.3_Splice_Site|TEX33_ENST00000381821.1_Splice_Site			O43247	TEX33_HUMAN	testis expressed 33																		CTGCTATGACACCTGCTCCTC	0.493													A|||	11	0.00219649	0.0076	0.0014	5008	,	,		21381	0.0		0.0	False		,,,				2504	0.0				.		Atlas-SNP	.											.	TEX33	25	.	0			c.489+2T>C						PASS	.	A	,	62,4344		0,62,2141	86	58	68		,	4.6	1	22	dbSNP_134	68	0,8600		0,0,4300	yes	splice-5,splice-5	C22orf33	NM_001163857.1,NM_178552.3	,	0,62,6441	GG,GA,AA		0.0,1.4072,0.4767	,	,	37397876	62,12944	2203	4300	6503	SO:0001630	splice_region_variant	339669	exon4			TATGACACCTGCT	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.489+1T>C	22.37:g.37397876A>G		107	0	0		101	44	0.435644	NM_001163857	B1AH46|Q6ICF2|Q8IVQ2|Q9Y4V8	Splice_Site	SNP	ENST00000405091.2	37	CCDS54524.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	A	15.90	2.968886	0.53614	0.014072	0.0	ENSG00000185264	ENST00000402860;ENST00000405091;ENST00000381821	.	.	.	5.68	4.64	0.57946	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.1587	0.37009	0.9146:0.0:0.0854:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C22orf33	35727822	0.995000	0.38212	0.992000	0.48379	0.817000	0.46193	3.503000	0.53340	2.159000	0.67721	0.533000	0.62120	.	A|0.997;G|0.003	0.003	strong		0.493	TEX33-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318778.2	NM_178552	Intron	G	37397876	A	G	37397876	5	3	22	1	0	0	0	0	0	0	1	0	2147	173	6	3	367	3	C22orf33	22	37397876	Splice_Site	SNP	A	TCGA-G8-6324-01A-11D-2210-10	495617	37397876	13906690	4389	7290											
SSTR3	6753	hgsc.bcm.edu	37	chr22	37602611	37602611	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggtagctgatgcgcatcgtgCtggacttctccccagtggaa	7	10	13	11	2	1	1	0	1	1	0	3	3	1	3	2	3	3	4	2	3	2	2	rs229568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:37602611C>G	ENST00000328544.3	-	2	1765	c.1232G>C	c.(1231-1233)aGc>aCc	p.S411T	SSTR3_ENST00000402501.1_Missense_Mutation_p.S411T	NM_001051.3	NP_001042.1	P32745	SSR3_HUMAN	somatostatin receptor 3	411			S -> T (in dbSNP:rs229568).		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)	GCGCATCGTGCTGGACTTCTC	0.657													C|||	319	0.0636981	0.2284	0.0202	5008	,	,		16100	0.0		0.003	False		,,,				2504	0.0				p.S411T		Atlas-SNP	.											.	SSTR3	42	.	0			c.G1232C						PASS	.	C	THR/SER	912,3494	340.7+/-306.4	97,718,1388	55	59	58		1232	3.4	0	22	dbSNP_79	58	7,8593	5.7+/-21.5	0,7,4293	yes	missense	SSTR3	NM_001051.2	58	97,725,5681	GG,GC,CC		0.0814,20.699,7.066	benign	411/419	37602611	919,12087	2203	4300	6503	SO:0001583	missense	6753	exon2			ATCGTGCTGGACT		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.1232G>C	22.37:g.37602611C>G	ENSP00000330138:p.Ser411Thr	64	0	0		72	34	0.472222	NM_001051	A8K550|Q53ZR7	Missense_Mutation	SNP	ENST00000328544.3	37	CCDS13944.1	117	0.05357142857142857	107	0.21747967479674796	8	0.022099447513812154	0	0.0	2	0.002638522427440633	C	8.330	0.826175	0.16749	0.20699	8.14E-4	ENSG00000183473	ENST00000328544;ENST00000402501	T;T	0.73047	-0.71;-0.71	5.51	3.4	0.38934	.	1.198980	0.05892	N	0.628461	T	0.00073	0.0002	L	0.43152	1.355	0.42474	P	0.00717000000000001	B	0.27559	0.181	B	0.19148	0.024	T	0.04255	-1.0965	9	0.56958	D	0.05	.	12.2253	0.54457	0.0:0.8595:0.0:0.1405	rs229568;rs16997931;rs229568	411	P32745	SSR3_HUMAN	T	411	ENSP00000330138:S411T;ENSP00000384904:S411T	ENSP00000330138:S411T	S	-	2	0	SSTR3	35932557	0.000000	0.05858	0.027000	0.17364	0.063000	0.16089	0.291000	0.18994	1.328000	0.45358	0.491000	0.48974	AGC	C|0.934;G|0.066	0.066	strong		0.657	SSTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318802.1			G	37602611	C	G	37602611	3	3	22	1	0	0	0	0	1	0	0	0	15214	797	28	4	28	4	SSTR3	22	37602611	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	204735	37602611	13701955	4390	7291											
CYTH4	27128	hgsc.bcm.edu	37	chr22	37693632	37693632	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtatttcattgagcacaagCtgctgacccctgacgtccag	10	10	9	12	1	1	3	1	3	0	0	2	3	2	3	3	0	3	4	3	0	2	3	rs73887105	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:37693632C>T	ENST00000248901.6	+	5	449	c.262C>T	c.(262-264)Ctg>Ttg	p.L88L	CYTH4_ENST00000439667.1_3'UTR|CYTH4_ENST00000405206.3_Silent_p.L88L|CYTH4_ENST00000402997.1_Silent_p.L88L	NM_013385.3	NP_037517.1	Q9UIA0	CYH4_HUMAN	cytohesin 4	88	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				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						TGAGCACAAGCTGCTGACCCC	0.572													C|||	31	0.0061901	0.0227	0.0014	5008	,	,		20239	0.0		0.0	False		,,,				2504	0.0				p.L88L		Atlas-SNP	.											.	CYTH4	51	.	0			c.C262T						PASS	.	C		102,4304	81.4+/-119.9	1,100,2102	74	68	70		262	4	1	22	dbSNP_130	70	0,8600		0,0,4300	no	coding-synonymous	CYTH4	NM_013385.3		1,100,6402	TT,TC,CC		0.0,2.315,0.7843		88/395	37693632	102,12904	2203	4300	6503	SO:0001819	synonymous_variant	27128	exon5			CACAAGCTGCTGA	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.262C>T	22.37:g.37693632C>T		123	0	0		93	48	0.516129	NM_013385	Q5R3F9|Q9UGT6	Silent	SNP	ENST00000248901.6	37	CCDS13946.1																																																																																			C|0.992;T|0.008	0.008	strong		0.572	CYTH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318917.1			T	37693632	C	T	37693632	2	4	22	1	0	0	0	0	0	0	0	1	4208	796	28	2		2	CYTH4	22	37693632	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	91021	37693632	13610934	4391	7292											
TRIOBP	11078	hgsc.bcm.edu	37	chr22	38129311	38129311	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatttgctcataggaagtcCgaggcagcgggggccttcca	8	8	14	11	2	1	0	1	0	0	0	3	2	3	1	3	4	2	3	3	4	2	3	rs200990219	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:38129311C>T	ENST00000406386.3	+	8	4209	c.3954C>T	c.(3952-3954)tcC>tcT	p.S1318S		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	1318					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)					ATAGGAAGTCCGAGGCAGCGG	0.652													C|||	10	0.00199681	0.0076	0.0	5008	,	,		15854	0.0		0.0	False		,,,				2504	0.0				p.S1318S		Atlas-SNP	.											.	TRIOBP	262	.	0			c.C3954T						PASS	.	C		12,3732		0,12,1860	8	14	12		3954	-1.1	1	22		12	0,7806		0,0,3903	no	coding-synonymous	TRIOBP	NM_001039141.2		0,12,5763	TT,TC,CC		0.0,0.3205,0.1039		1318/2366	38129311	12,11538	1872	3903	5775	SO:0001819	synonymous_variant	11078	exon8			GAAGTCCGAGGCA	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.3954C>T	22.37:g.38129311C>T		171	0	0		170	80	0.470588	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Silent	SNP	ENST00000406386.3	37	CCDS43015.1																																																																																			C|0.998;T|0.002	0.002	strong		0.652	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			T	38129311	C	T	38129311	2	4	22	1	0	0	0	0	0	0	0	1	16568	639	23	1		1	TRIOBP	22	38129311	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	435679	38129311	13175255	4392	7293											
GCAT	23464	hgsc.bcm.edu	37	chr22	38211728	38211728	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcggcagcgcgcccggccAtacctcttctccaacagtct	6	8	9	18	4	3	0	0	0	3	0	4	0	3	0	4	2	4	1	4	2	2	2	rs34340481	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:38211728A>G	ENST00000248924.6	+	7	929	c.873A>G	c.(871-873)ccA>ccG	p.P291P	GCAT_ENST00000323205.6_Silent_p.P317P	NM_014291.3	NP_055106.1	O75600	KBL_HUMAN	glycine C-acetyltransferase	291					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)	GCGCCCGGCCATACCTCTTCT	0.642													A|||	228	0.0455272	0.1649	0.0115	5008	,	,		17865	0.0		0.002	False		,,,				2504	0.0				p.P317P		Atlas-SNP	.											.	GCAT	27	.	0			c.A951G						PASS	.	A	,	584,3822	255.5+/-260.7	37,510,1656	88	97	94		951,873	-0.2	1	22	dbSNP_126	94	24,8576	15.3+/-51.7	0,24,4276	no	coding-synonymous,coding-synonymous	GCAT	NM_001171690.1,NM_014291.3	,	37,534,5932	GG,GA,AA		0.2791,13.2547,4.6748	,	317/446,291/420	38211728	608,12398	2203	4300	6503	SO:0001819	synonymous_variant	23464	exon7			CCGGCCATACCTC	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.873A>G	22.37:g.38211728A>G		214	0	0		263	119	0.452471	NM_001171690	E2QC23|Q6ZWF1|Q96CA9	Silent	SNP	ENST00000248924.6	37	CCDS13957.1																																																																																			A|0.958;G|0.042	0.042	strong		0.642	GCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319506.1	NM_014291.2		G	38211728	A	G	38211728	2	3	22	1	0	0	0	0	0	0	0	1	6292	204	8	3		3	GCAT	22	38211728	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	82417	38211728	13092838	4393	7294											
MICALL1	85377	hgsc.bcm.edu	37	chr22	38302469	38302469	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctgctggcctggtgccgcCgccagtgcgagggctaccgc	3	6	16	16	5	0	0	0	0	0	0	0	1	0	0	5	3	4	3	5	3	1	1	rs146549351	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:38302469C>T	ENST00000215957.6	+	1	166	c.40C>T	c.(40-42)Cgc>Tgc	p.R14C		NM_033386.3	NP_203744.1	Q8N3F8	MILK1_HUMAN	MICAL-like 1	14	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)					CTGGTGCCGCCGCCAGTGCGA	0.786													c|||	50	0.00998403	0.0371	0.0014	5008	,	,		3679	0.0		0.0	False		,,,				2504	0.0				p.R14C		Atlas-SNP	.											.	MICALL1	53	.	0			c.C40T						PASS	.		CYS/ARG	44,3156		1,42,1557	4	4	4		40	1	1	22	dbSNP_134	4	0,6182		0,0,3091	no	missense	MICALL1	NM_033386.3	180	1,42,4648	TT,TC,CC		0.0,1.375,0.469	probably-damaging	14/864	38302469	44,9338	1600	3091	4691	SO:0001583	missense	85377	exon1			TGCCGCCGCCAGT	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.40C>T	22.37:g.38302469C>T	ENSP00000215957:p.Arg14Cys	5	0	0		4	4	1	NM_033386	Q5TI16|Q7RTP5|Q8N3N8|Q9BVL9|Q9BY92|Q9UH43|Q9UH44|Q9UH45	Missense_Mutation	SNP	ENST00000215957.6	37	CCDS13961.1	128	0.05860805860805861	70	0.14227642276422764	22	0.06077348066298342	12	0.02097902097902098	24	0.0316622691292876	c	14.95	2.687334	0.48097	0.01375	0.0	ENSG00000100139	ENST00000215957	D	0.95342	-3.68	2.15	1.04	0.20106	Calponin homology domain (5);	.	.	.	.	T	0.15046	0.0363	M	0.92317	3.295	0.80722	D	1	B	0.14438	0.01	B	0.14023	0.01	T	0.69442	-0.5144	9	0.87932	D	0	.	8.698	0.34307	0.0:0.8737:0.0:0.1263	.	14	Q8N3F8	MILK1_HUMAN	C	14	ENSP00000215957:R14C	ENSP00000215957:R14C	R	+	1	0	MICALL1	36632415	1.000000	0.71417	0.985000	0.45067	0.590000	0.36582	4.587000	0.60991	0.179000	0.19938	0.165000	0.16767	CGC	C|0.942;T|0.058	0.058	strong		0.786	MICALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319545.4	NM_033386		T	38302469	C	T	38302469	3	4	22	1	0	0	0	0	1	0	0	0	9582	652	23	1	42	1	MICALL1	22	38302469	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	90741	38302469	13002097	4394	7295											
C22orf23	84645	hgsc.bcm.edu	37	chr22	38341124	38341124	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttcttttccgttcctccaTgtccttccctgtggcaaaga	5	16	6	14	1	1	1	0	0	1	1	6	1	6	1	5	1	0	2	5	1	1	5	rs35562630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:38341124T>G	ENST00000249079.2	-	5	662	c.406A>C	c.(406-408)Atg>Ctg	p.M136L	C22orf23_ENST00000403026.1_Missense_Mutation_p.M136L|C22orf23_ENST00000403305.1_Missense_Mutation_p.M136L			Q9BZE7	EVG1_HUMAN	chromosome 22 open reading frame 23	136			M -> L (in dbSNP:rs35562630).							endometrium(3)|kidney(2)|large_intestine(7)	12	Melanoma(58;0.045)					CGTTCCTCCATGTCCTTCCCT	0.512													G|||	204	0.0407348	0.1513	0.0043	5008	,	,		16932	0.0		0.001	False		,,,				2504	0.0				p.M136L		Atlas-SNP	.											.	C22orf23	21	.	0			c.A406C						PASS	.	G	LEU/MET,LEU/MET	504,3902	779.8+/-414.4	23,458,1722	162	158	159		343,406	-8.1	0	22	dbSNP_126	159	7,8593	819.0+/-406.8	0,7,4293	yes	missense,missense	C22orf23	NM_001207062.1,NM_032561.4	15,15	23,465,6015	GG,GT,TT		0.0814,11.4389,3.929	benign,benign	115/197,136/218	38341124	511,12495	2203	4300	6503	SO:0001583	missense	84645	exon5			CCTCCATGTCCTT	AF324466	CCDS13962.1, CCDS74860.1	22q13.1	2013-10-11			ENSG00000128346	ENSG00000128346			18589	protein-coding gene	gene with protein product						11237012	Standard	NM_032561		Approved	FLJ32787, EVG1, LOC84645	uc003auj.2	Q9BZE7	OTTHUMG00000150672	ENST00000249079.2:c.406A>C	22.37:g.38341124T>G	ENSP00000249079:p.Met136Leu	348	0	0		368	163	0.442935	NM_032561	Q5JYU9|Q96M68	Missense_Mutation	SNP	ENST00000249079.2	37	CCDS13962.1	74	0.03388278388278388	72	0.14634146341463414	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	13.88	2.367954	0.42003	0.114389	8.14E-4	ENSG00000128346	ENST00000403305;ENST00000249079;ENST00000403026;ENST00000418863	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	5.27	-8.07	0.01098	.	2.120180	0.02082	N	0.052461	T	0.00073	0.0002	N	0.02202	-0.64	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.05599	-1.0875	9	0.25751	T	0.34	8.7692	3.5531	0.07854	0.1443:0.121:0.2065:0.5283	rs35562630	136	Q9BZE7	EVG1_HUMAN	L	136	ENSP00000384667:M136L;ENSP00000249079:M136L;ENSP00000384618:M136L;ENSP00000395077:M136L	ENSP00000249079:M136L	M	-	1	0	C22orf23	36671070	0.000000	0.05858	0.000000	0.03702	0.465000	0.32709	-0.628000	0.05515	-1.268000	0.02439	-0.121000	0.15023	ATG	T|0.946;G|0.054	0.054	strong		0.512	C22orf23-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319564.1	NM_032561		G	38341124	T	G	38341124	3	3	22	1	0	0	0	0	1	0	0	0	2139	1464	51	5	259	5	C22orf23	22	38341124	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	38655	38341124	12963442	4395	7296											
SOX10	6663	hgsc.bcm.edu	37	chr22	38379543	38379543	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgggcaccagcgtccagtcGtagccgctgagcacctggct	7	7	13	14	3	0	1	0	1	0	0	2	1	1	1	4	2	3	5	4	2	1	1	rs73415876	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:38379543G>A	ENST00000396884.2	-	2	531	c.249C>T	c.(247-249)taC>taT	p.Y83Y	POLR2F_ENST00000407936.1_Intron|POLR2F_ENST00000405557.1_Intron|SOX10_ENST00000360880.2_Silent_p.Y83Y|SOX10_ENST00000470555.1_Intron	NM_006941.3	NP_008872.1	P56693	SOX10_HUMAN	SRY (sex determining region Y)-box 10	83					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)					GCGTCCAGTCGTAGCCGCTGA	0.657													G|||	205	0.0409345	0.152	0.0043	5008	,	,		11391	0.0		0.001	False		,,,				2504	0.0				p.Y83Y	Melanoma(39;342 1098 6220 32775 40068)|GBM(21;140 497 5227 16059 19275)	Atlas-SNP	.											.	SOX10	48	.	0			c.C249T	GRCh37	CM981855	SOX10	M	rs73415876	PASS	.	G		496,3910	215.5+/-234.4	22,452,1729	64	40	48	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	249	1.1	1	22	dbSNP_130	48	7,8591	4.3+/-15.6	0,7,4292	no	coding-synonymous	SOX10	NM_006941.3		22,459,6021	AA,AG,GG		0.0814,11.2574,3.868		83/467	38379543	503,12501	2203	4299	6502	SO:0001819	synonymous_variant	6663	exon2			CCAGTCGTAGCCG		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.249C>T	22.37:g.38379543G>A		84	0	0		120	65	0.541667	NM_006941	B4DV62|Q6FHW7	Silent	SNP	ENST00000396884.2	37	CCDS13964.1																																																																																			A|0.044;G|0.956	0.044	strong		0.657	SOX10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313875.1	NM_006941		A	38379543	G	A	38379543	2	1	22	1	0	0	0	0	0	0	0	1	14956	1140	40	1		1	SOX10	22	38379543	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	38419	38379543	12925023	4396	7297											
APOBEC3A	200315	hgsc.bcm.edu	37	chr22	39357634	39357634	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccccctatataaggaggcActgcaaatgctgcgggatgc	11	7	12	11	1	0	0	0	0	0	0	0	3	0	2	2	3	4	3	2	3	4	3	rs2294363		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:39357634A>G	ENST00000402255.1	+	4	621	c.417A>G	c.(415-417)gcA>gcG	p.A139A	APOBEC3A_ENST00000249116.2_Silent_p.A139A			P31941	ABC3A_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A	139					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)					ATAAGGAGGCACTGCAAATGC	0.577																																					p.A139A		Atlas-SNP	.											.	APOBEC3A	20	.	0			c.A417G						PASS	.						38	49	46					22																	39357634		1812	3940	5752	SO:0001819	synonymous_variant	200315	exon3			GGAGGCACTGCAA	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.417A>G	22.37:g.39357634A>G		51	0	0		45	45	1	NM_145699	A0AVM1|Q12807|Q5JZ93|Q9UH18	Silent	SNP	ENST00000402255.1	37	CCDS13981.1																																																																																			A|0.167;G|0.833	0.833	weak		0.577	APOBEC3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320915.2	NM_145699		G	39357634	A	G	39357634	2	3	22	1	0	0	0	0	0	0	0	1	789	146	6	3		3	APOBEC3A	22	39357634	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	978091	39357634	11946932	4397	7298											
APOBEC3B	9582	hgsc.bcm.edu	37	chr22	39380131	39380131	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttctacgacaactttgaaaaCgaacccatcctctatggtcg	12	11	6	12	3	2	1	0	1	2	0	4	3	3	1	2	1	4	0	2	1	6	4	rs113972364	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:39380131C>T	ENST00000333467.3	+	2	114	c.69C>T	c.(67-69)aaC>aaT	p.N23N	APOBEC3B_ENST00000407298.3_Silent_p.N23N|APOBEC3B_ENST00000402182.3_Silent_p.N23N	NM_001270411.1|NM_004900.4	NP_001257340.1|NP_004891	Q9UH17	ABC3B_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B	23					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)					ACTTTGAAAACGAACCCATCC	0.522													C|||	118	0.0235623	0.087	0.0043	5008	,	,		17697	0.0		0.0	False		,,,				2504	0.0				p.N23N		Atlas-SNP	.											.	APOBEC3B	32	.	0			c.C69T						PASS	.	C		276,4118		27,222,1948	73	76	75		69	0.2	0	22	dbSNP_132	75	3,8517		0,3,4257	no	coding-synonymous	APOBEC3B	NM_004900.3		27,225,6205	TT,TC,CC		0.0352,6.2813,2.1604		23/383	39380131	279,12635	2197	4260	6457	SO:0001819	synonymous_variant	9582	exon2			TGAAAACGAACCC	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.69C>T	22.37:g.39380131C>T		243	0	0		244	96	0.393443	NM_004900	B0QYD2|O95618|Q20WL1|Q5IFJ4|Q7Z2N3|Q7Z6D6|Q9UE74	Silent	SNP	ENST00000333467.3	37	CCDS13982.1																																																																																			C|0.974;T|0.026	0.026	strong		0.522	APOBEC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321233.1	NM_004900		T	39380131	C	T	39380131	2	4	22	1	0	0	0	0	0	0	0	1	790	535	19	1		1	APOBEC3B	22	39380131	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	22497	39380131	11924435	4398	7299											
APOBEC3B	9582	hgsc.bcm.edu	37	chr22	39381957	39381957	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gactgtgtggcgaagctggcCgaattcctgtctgagcaccc	7	9	13	12	2	1	1	0	1	1	0	2	4	2	1	3	2	2	2	3	2	2	1	rs150187552	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:39381957C>T	ENST00000333467.3	+	3	360	c.315C>T	c.(313-315)gcC>gcT	p.A105A	APOBEC3B_ENST00000407298.3_Silent_p.A105A|APOBEC3B_ENST00000402182.3_Silent_p.A105A	NM_001270411.1|NM_004900.4	NP_001257340.1|NP_004891	Q9UH17	ABC3B_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B	105					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)					CGAAGCTGGCCGAATTCCTGT	0.572													C|||	20	0.00399361	0.0151	0.0	5008	,	,		14653	0.0		0.0	False		,,,				2504	0.0				p.A105A		Atlas-SNP	.											.	APOBEC3B	32	.	0			c.C315T						PASS	.	C		28,4376		3,22,2177	156	149	151		315	-4.2	0	22	dbSNP_134	151	0,8596		0,0,4298	no	coding-synonymous	APOBEC3B	NM_004900.3		3,22,6475	TT,TC,CC		0.0,0.6358,0.2154		105/383	39381957	28,12972	2202	4298	6500	SO:0001819	synonymous_variant	9582	exon3			GCTGGCCGAATTC	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.315C>T	22.37:g.39381957C>T		306	0	0		323	112	0.346749	NM_004900	B0QYD2|O95618|Q20WL1|Q5IFJ4|Q7Z2N3|Q7Z6D6|Q9UE74	Silent	SNP	ENST00000333467.3	37	CCDS13982.1																																																																																			C|0.998;T|0.002	0.002	strong		0.572	APOBEC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321233.1	NM_004900		T	39381957	C	T	39381957	2	4	22	1	0	0	0	0	0	0	0	1	790	639	23	1		1	APOBEC3B	22	39381957	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1826	39381957	11922609	4399	7300											
APOBEC3C	27350	hgsc.bcm.edu	37	chr22	39413957	39413957	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaatctcaccatcttcaccGcccgcctctactacttccag	8	11	4	18	2	4	1	2	1	3	0	6	1	5	1	5	0	2	0	5	0	3	4	rs141108460		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:39413957G>A	ENST00000361441.4	+	3	641	c.361G>A	c.(361-363)Gcc>Acc	p.A121T	APOBEC3D_ENST00000381568.4_Intron	NM_014508.2	NP_055323.2	Q9NRW3	ABC3C_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3C	121					cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA demethylation (GO:0080111)|innate immune response (GO:0045087)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines (GO:0016814)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(1)|skin(1)	6	Melanoma(58;0.04)					CATCTTCACCGCCCGCCTCTA	0.587																																					p.A121T		Atlas-SNP	.											.	APOBEC3C	21	.	0			c.G361A						PASS	.	G	THR/ALA	1,4405		0,1,2202	113	118	117		361	-2.5	0	22	dbSNP_134	117	0,8600		0,0,4300	no	missense	APOBEC3C	NM_014508.2	58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	121/191	39413957	1,13005	2203	4300	6503	SO:0001583	missense	27350	exon3			TTCACCGCCCGCC	AF165520	CCDS13983.1	22q13.1-q13.2	2014-01-28			ENSG00000244509	ENSG00000244509		"Apolipoprotein B mRNA editing enzymes"	17353	protein-coding gene	gene with protein product		607750				11863358	Standard	NM_014508		Approved	APOBEC1L, PBI, bK150C2.3, ARDC2, ARDC4, ARP5	uc003awr.3	Q9NRW3	OTTHUMG00000151087	ENST00000361441.4:c.361G>A	22.37:g.39413957G>A	ENSP00000355340:p.Ala121Thr	281	0	0		276	114	0.413043	NM_014508	B2R884|Q5JZ92|Q7Z2N7|Q96F12	Missense_Mutation	SNP	ENST00000361441.4	37	CCDS13983.1	.	.	.	.	.	.	.	.	.	.	.	15.12	2.740041	0.49045	2.27E-4	0.0	ENSG00000244509	ENST00000361441	T	0.67523	-0.27	2.01	-2.48	0.06423	APOBEC-like, N-terminal (1);Cytidine deaminase-like (1);	.	.	.	.	T	0.79936	0.4532	M	0.89095	3.005	0.38181	D	0.939611	D	0.89917	1.0	D	0.72982	0.979	T	0.79897	-0.1609	9	0.87932	D	0	.	8.5433	0.33406	0.0:0.0:0.4067:0.5932	.	121	Q9NRW3	ABC3C_HUMAN	T	121	ENSP00000355340:A121T	ENSP00000355340:A121T	A	+	1	0	APOBEC3C	37743903	0.644000	0.27277	0.035000	0.18076	0.027000	0.11550	0.674000	0.25218	-0.470000	0.06901	0.479000	0.44913	GCC	G|1.000;A|0.000	0.000	weak		0.587	APOBEC3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321241.2	NM_014508		A	39413957	G	A	39413957	3	1	22	1	0	0	0	0	1	0	0	0	791	1087	38	1	371	1	APOBEC3C	22	39413957	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	32000	39413957	11890609	4400	7301											
ATF4	468	hgsc.bcm.edu	37	chr22	39918323	39918323	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	ttctctgtgggtctgcccgtCccaaaccttacgatcctcct	5	13	7	16	2	2	0	0	0	2	0	6	1	5	0	5	1	3	0	5	1	2	2	rs1803323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:39918323C>G	ENST00000337304.2	+	2	1654	c.772C>G	c.(772-774)Ccc>Gcc	p.P258A	ATF4_ENST00000396680.1_Missense_Mutation_p.P258A|ATF4_ENST00000404241.2_Missense_Mutation_p.P258A	NM_001675.2	NP_001666.2	P18848	ATF4_HUMAN	activating transcription factor 4	258			P -> A (in dbSNP:rs1803323).		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)	GTCTGCCCGTCCCAAACCTTA	0.522													C|||	86	0.0171725	0.0628	0.0043	5008	,	,		19286	0.0		0.0	False		,,,				2504	0.0				p.P258A		Atlas-SNP	.											.	ATF4	27	.	0			c.C772G						PASS	.	C	ALA/PRO,ALA/PRO	169,4237	99.8+/-138.5	5,159,2039	24	25	24		772,772	2	0.2	22	dbSNP_89	24	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	ATF4	NM_001675.2,NM_182810.1	27,27	5,161,6337	GG,GC,CC		0.0233,3.8357,1.3148	possibly-damaging,possibly-damaging	258/352,258/352	39918323	171,12835	2203	4300	6503	SO:0001583	missense	468	exon2			GCCCGTCCCAAAC	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.772C>G	22.37:g.39918323C>G	ENSP00000336790:p.Pro258Ala	303	0	0		329	178	0.541033	NM_001675	Q9UH31	Missense_Mutation	SNP	ENST00000337304.2	37	CCDS13996.1	23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	C	10.09	1.255962	0.22965	0.038357	2.33E-4	ENSG00000128272	ENST00000404241;ENST00000337304;ENST00000396680	T;T;T	0.24350	1.86;1.86;1.86	5.24	2.04	0.26737	.	0.251601	0.40640	N	0.001054	T	0.04998	0.0134	M	0.68952	2.095	0.28571	N	0.910626	P	0.48294	0.908	B	0.44224	0.444	T	0.03784	-1.1004	10	0.87932	D	0	-11.5679	9.0061	0.36113	0.0:0.6756:0.0:0.3244	rs1803323;rs52835171;rs1803323	258	P18848	ATF4_HUMAN	A	258	ENSP00000384587:P258A;ENSP00000336790:P258A;ENSP00000379912:P258A	ENSP00000336790:P258A	P	+	1	0	ATF4	38248269	0.003000	0.15002	0.178000	0.23040	0.066000	0.16364	0.129000	0.15830	0.219000	0.20840	0.462000	0.41574	CCC	C|0.987;G|0.013	0.013	strong		0.522	ATF4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321305.1	NM_001675		G	39918323	C	G	39918323	3	3	22	1	0	0	0	0	1	0	0	0	1082	855	30	4	778	4	ATF4	22	39918323	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	504366	39918323	11386243	4401	7302											
CCDC134	79879	hgsc.bcm.edu	37	chr22	42209767	42209767	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atctgcagatggcccaggagCtggggatcagtgagaaagac	12	6	15	8	0	2	3	1	1	1	3	2	6	2	5	1	4	2	2	1	4	1	0			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:42209767C>T	ENST00000255784.5	+	6	609	c.505C>T	c.(505-507)Ctg>Ttg	p.L169L	CCDC134_ENST00000402061.3_Intron	NM_024821.2	NP_079097.1	Q9H6E4	CC134_HUMAN	coiled-coil domain containing 134	169						extracellular region (GO:0005576)|membrane (GO:0016020)				large_intestine(1)|lung(2)|ovary(2)|skin(1)	6						GGCCCAGGAGCTGGGGATCAG	0.532																																					p.L169L		Atlas-SNP	.											.	CCDC134	19	.	0			c.C505T						PASS	.						100	96	97					22																	42209767		2203	4300	6503	SO:0001819	synonymous_variant	79879	exon6			CAGGAGCTGGGGA	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.505C>T	22.37:g.42209767C>T		99	0	0		96	45	0.46875	NM_024821		Silent	SNP	ENST00000255784.5	37	CCDS33654.1																																																																																			.	.	none		0.532	CCDC134-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000321964.1	NM_024821		T	42209767	C	T	42209767	2	4	22	1	0	0	0	0	0	0	0	1	2770	796	28	2		2	CCDC134	22	42209767	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2291444	42209767	9094799	4402	7303											
FAM109B	150368	hgsc.bcm.edu	37	chr22	42473586	42473586	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctttgatgcccctggagtgCgcccacacctgctggccgca	5	8	12	16	2	0	1	0	1	0	0	0	2	0	2	5	2	3	3	5	2	0	1	rs61736039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:42473586C>T	ENST00000321753.3	+	3	476	c.289C>T	c.(289-291)Cgc>Tgc	p.R97C	snoU13_ENST00000458891.1_RNA|SMDT1_ENST00000331479.3_5'Flank	NM_001002034.2	NP_001002034.2	Q6ICB4	SESQ2_HUMAN	family with sequence similarity 109, member B	97	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				endosome organization (GO:0007032)|receptor recycling (GO:0001881)|retrograde transport, endosome to Golgi (GO:0042147)	clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(2)|liver(2)|lung(1)|prostate(1)	8						CCCTGGAGTGCGCCCACACCT	0.662													C|||	111	0.0221645	0.0794	0.0058	5008	,	,		16709	0.0		0.002	False		,,,				2504	0.0				p.R97C		Atlas-SNP	.											.	FAM109B	22	.	0			c.C289T						PASS	.	C	CYS/ARG	356,4050	184.0+/-211.4	14,328,1861	69	73	72		289	4	0.8	22	dbSNP_129	72	2,8598	2.2+/-6.3	0,2,4298	yes	missense	FAM109B	NM_001002034.2	180	14,330,6159	TT,TC,CC		0.0233,8.0799,2.7526	probably-damaging	97/260	42473586	358,12648	2203	4300	6503	SO:0001583	missense	150368	exon3			GGAGTGCGCCCAC	BX648402	CCDS33655.1	22q13.2	2013-01-10			ENSG00000177096	ENSG00000177096		"Pleckstrin homology (PH) domain containing"	27161	protein-coding gene	gene with protein product		614240				12477932	Standard	NM_001002034		Approved	DKFZp686J07229	uc003bbz.3	Q6ICB4	OTTHUMG00000151285	ENST00000321753.3:c.289C>T	22.37:g.42473586C>T	ENSP00000312753:p.Arg97Cys	100	0	0		129	60	0.465116	NM_001002034	Q3SXQ3|Q8N6L9	Missense_Mutation	SNP	ENST00000321753.3	37	CCDS33655.1	33	0.01510989010989011	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	0	0.0	C	14.36	2.512399	0.44660	0.080799	2.33E-4	ENSG00000177096	ENST00000321753;ENST00000419475	T;T	0.76839	-1.05;-1.05	5.01	3.95	0.45737	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.211920	0.38492	N	0.001667	T	0.33206	0.0855	M	0.83012	2.62	0.51012	D	0.999905	D	0.76494	0.999	P	0.61201	0.885	T	0.69738	-0.5064	10	0.66056	D	0.02	-12.5019	13.5179	0.61551	0.2769:0.7231:0.0:0.0	rs61736039	97	Q6ICB4	SESQ2_HUMAN	C	97	ENSP00000312753:R97C;ENSP00000396170:R97C	ENSP00000312753:R97C	R	+	1	0	FAM109B	40803532	1.000000	0.71417	0.758000	0.31321	0.031000	0.12232	3.245000	0.51407	2.299000	0.77371	0.655000	0.94253	CGC	C|0.975;T|0.025	0.025	strong		0.662	FAM109B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322084.1	NM_001002034		T	42473586	C	T	42473586	3	4	22	1	0	0	0	0	1	0	0	0	5400	768	27	1	291	1	FAM109B	22	42473586	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	263819	42473586	8830980	4403	7304											
NFAM1	150372	hgsc.bcm.edu	37	chr22	42805444	42805444	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagcactgatcccgtaccttGttccagagcagcagggccgt	8	8	12	13	2	0	2	0	1	0	1	2	3	2	2	4	1	4	5	4	1	1	3	rs17003048	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:42805444G>C	ENST00000329021.5	-	3	598	c.561C>G	c.(559-561)aaC>aaG	p.N187K		NM_145912.5	NP_666017.1	Q8NET5	NFAM1_HUMAN	NFAT activating protein with ITAM motif 1	187			N -> K (in dbSNP:rs17003048).		B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of cytokine production (GO:0001819)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of B cell differentiation (GO:0045577)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			large_intestine(1)|lung(3)	4						CCCGTACCTTGTTCCAGAGCA	0.662													C|||	158	0.0315495	0.1157	0.0058	5008	,	,		16803	0.0		0.001	False		,,,				2504	0.0				p.N187K		Atlas-SNP	.											.	NFAM1	12	.	0			c.C561G						PASS	.	C	LYS/ASN	450,3956	785.4+/-414.7	22,406,1775	102	96	98		561	4.8	1	22	dbSNP_123	98	3,8597	818.9+/-406.8	0,3,4297	yes	missense	NFAM1	NM_145912.5	94	22,409,6072	CC,CG,GG		0.0349,10.2133,3.483	benign	187/271	42805444	453,12553	2203	4300	6503	SO:0001583	missense	150372	exon3			TACCTTGTTCCAG	BC038241	CCDS14034.1	22q13.2	2005-02-01			ENSG00000235568	ENSG00000235568			29872	protein-coding gene	gene with protein product		608740				12615919	Standard	NM_145912		Approved	CNAIP	uc003bcn.4	Q8NET5	OTTHUMG00000150923	ENST00000329021.5:c.561C>G	22.37:g.42805444G>C	ENSP00000333680:p.Asn187Lys	72	0	0		80	42	0.525	NM_145912	B0QYD0|Q20WL2|Q5JZ96|Q8IUY8|Q8TEM8	Missense_Mutation	SNP	ENST00000329021.5	37	CCDS14034.1	55	0.025183150183150184	53	0.10772357723577236	2	0.0055248618784530384	0	0.0	0	0.0	C	0.145	-1.097589	0.01843	0.102133	3.49E-4	ENSG00000235568	ENST00000329021	T	0.18174	2.23	4.8	4.8	0.61643	.	0.000000	0.46145	N	0.000311	T	0.00073	0.0002	N	0.00159	-1.955	0.19300	N	0.99998	B	0.02656	0.0	B	0.01281	0.0	T	0.39354	-0.9618	10	0.02654	T	1	-15.1863	11.2161	0.48827	0.0:0.8139:0.1861:0.0	rs17003048;rs17003048	187	Q8NET5	NFAM1_HUMAN	K	187	ENSP00000333680:N187K	ENSP00000333680:N187K	N	-	3	2	NFAM1	41135388	1.000000	0.71417	1.000000	0.80357	0.058000	0.15608	1.335000	0.33839	1.036000	0.39998	-0.322000	0.08575	AAC	G|0.962;C|0.038	0.038	strong		0.662	NFAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320541.1	NM_145912		C	42805444	G	C	42805444	3	2	22	1	0	0	0	0	1	0	0	0	10367	1368	48	4	267	4	NFAM1	22	42805444	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	331858	42805444	8499122	4404	7305											
RRP7A	27341	hgsc.bcm.edu	37	chr22	42910142	42910142	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctctctcgatgctgccaggCgtagaagttgagcagctctt	7	11	12	11	2	2	2	0	1	2	1	4	3	2	2	1	1	4	6	1	1	2	3	rs61731241	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:42910142C>T	ENST00000323013.6	-	6	742	c.727G>A	c.(727-729)Gcc>Acc	p.A243T	SERHL_ENST00000359906.2_RNA	NM_015703.4	NP_056518.2	Q9Y3A4	RRP7A_HUMAN	ribosomal RNA processing 7 homolog A (S. cerevisiae)	243							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|liver(2)|lung(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	10						TGCTGCCAGGCGTAGAAGTTG	0.667													C|||	247	0.0493211	0.1793	0.013	5008	,	,		21135	0.0		0.001	False		,,,				2504	0.0				p.A243T		Atlas-SNP	.											.	RRP7A	25	.	0			c.G727A						PASS	.	C	THR/ALA	589,3817		31,527,1645	53	36	42		727	3.7	0.9	22	dbSNP_129	42	18,8582		0,18,4282	yes	missense	RRP7A	NM_015703.4	58	31,545,5927	TT,TC,CC		0.2093,13.3681,4.6671	benign	243/281	42910142	607,12399	2203	4300	6503	SO:0001583	missense	27341	exon6			GCCAGGCGTAGAA	BC035992	CCDS14036.1	22q13.2	2008-08-08			ENSG00000189306	ENSG00000189306			24286	protein-coding gene	gene with protein product						10810093, 12087473	Standard	NM_015703		Approved	CGI-96	uc003bcq.3	Q9Y3A4	OTTHUMG00000150891	ENST00000323013.6:c.727G>A	22.37:g.42910142C>T	ENSP00000321449:p.Ala243Thr	49	0	0		75	35	0.466667	NM_015703	A4FTX2|B2RBG4|Q0VAD0|Q5JZ94|Q6P4B5|Q8IVR9|Q8IVY0|Q8N5Q3|Q8NEY6|Q9Y3H5	Missense_Mutation	SNP	ENST00000323013.6	37	CCDS14036.1	84	0.038461538461538464	78	0.15853658536585366	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	.	6.304	0.424130	0.11928	0.133681	0.002093	ENSG00000189306	ENST00000323013	T	0.22539	1.95	3.66	3.66	0.41972	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.164932	0.53938	D	0.000046	T	0.00039	0.0001	N	0.03999	-0.3	0.21967	P	0.999444231	P;B	0.45396	0.857;0.364	B;B	0.35510	0.204;0.121	T	0.42292	-0.9460	9	0.16420	T	0.52	-28.9794	15.7164	0.77672	0.0:1.0:0.0:0.0	.	243;66	Q9Y3A4;Q9NSQ0	RRP7A_HUMAN;RRP7B_HUMAN	T	243	ENSP00000321449:A243T	ENSP00000321449:A243T	A	-	1	0	RRP7A	41240086	0.995000	0.38212	0.922000	0.36590	0.018000	0.09664	3.198000	0.51035	1.747000	0.51819	0.205000	0.17691	GCC	C|0.958;T|0.042	0.042	strong		0.667	RRP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320451.1	NM_015703		T	42910142	C	T	42910142	3	4	22	1	0	0	0	0	1	0	0	0	13704	768	27	1	123	1	RRP7A	22	42910142	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	104698	42910142	8394424	4405	7306											
ARFGAP3	26286	hgsc.bcm.edu	37	chr22	43195134	43195134	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaactgcgccatgtcgggggCgttgggcagcacactggaca	8	6	16	11	3	0	0	0	0	0	0	1	2	0	1	1	4	3	3	1	4	1	1	rs36003980	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:43195134C>T	ENST00000263245.5	-	15	1663	c.1444G>A	c.(1444-1446)Gcc>Acc	p.A482T	ARFGAP3_ENST00000429508.2_Missense_Mutation_p.A410T|ARFGAP3_ENST00000437119.2_Missense_Mutation_p.A438T	NM_001142293.1|NM_014570.4	NP_001135765.1|NP_055385.3	Q9NP61	ARFG3_HUMAN	ADP-ribosylation factor GTPase activating protein 3	482			A -> T (in dbSNP:rs36003980).		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						ATGTCGGGGGCGTTGGGCAGC	0.562													C|||	80	0.0159744	0.0575	0.0043	5008	,	,		17224	0.0		0.001	False		,,,				2504	0.0				p.A482T	GBM(58;544 1030 21460 27159 48838)	Atlas-SNP	.											.	ARFGAP3	48	.	0			c.G1444A						PASS	.	C	THR/ALA,THR/ALA	192,4214	120.8+/-158.4	4,184,2015	144	126	132		1312,1444	3.6	0.4	22	dbSNP_126	132	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	ARFGAP3	NM_001142293.1,NM_014570.4	58,58	4,187,6312	TT,TC,CC		0.0349,4.3577,1.4993	benign,benign	438/473,482/517	43195134	195,12811	2203	4300	6503	SO:0001583	missense	26286	exon15			CGGGGGCGTTGGG	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.1444G>A	22.37:g.43195134C>T	ENSP00000263245:p.Ala482Thr	65	0	0		76	43	0.565789	NM_014570	E9PB03|Q9BSC6|Q9H9J0|Q9NT10|Q9NUP5|Q9Y4V3|Q9Y4V4	Missense_Mutation	SNP	ENST00000263245.5	37	CCDS14042.1	27	0.012362637362637362	27	0.054878048780487805	0	0.0	0	0.0	0	0.0	C	11.57	1.678342	0.29783	0.043577	3.49E-4	ENSG00000242247	ENST00000263245;ENST00000429508;ENST00000437119	T;T;T	0.07021	3.4;3.23;3.35	4.65	3.63	0.41609	.	0.000000	0.85682	D	0.000000	T	0.01092	0.0036	L	0.48260	1.515	0.53005	D	0.999964	B;B	0.33212	0.066;0.402	B;B	0.20184	0.028;0.027	T	0.31943	-0.9925	10	0.51188	T	0.08	0.0519	11.8638	0.52482	0.0:0.9119:0.0:0.0881	rs36003980	438;482	E9PB03;Q9NP61	.;ARFG3_HUMAN	T	482;410;438	ENSP00000263245:A482T;ENSP00000393959:A410T;ENSP00000388791:A438T	ENSP00000263245:A482T	A	-	1	0	ARFGAP3	41525078	1.000000	0.71417	0.437000	0.26809	0.135000	0.20990	4.958000	0.63660	0.951000	0.37770	-0.137000	0.14449	GCC	C|0.983;T|0.017	0.017	strong		0.562	ARFGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319747.2	NM_014570		T	43195134	C	T	43195134	3	4	22	1	0	0	0	0	1	0	0	0	851	768	27	1	114	1	ARFGAP3	22	43195134	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	284992	43195134	8109432	4406	7307											
PARVB	29780	hgsc.bcm.edu	37	chr22	44495953	44495953	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagaacgaggagcgcacgAtgattgaccccacttccaag	13	5	12	11	3	0	3	0	2	0	1	1	7	1	4	3	2	2	1	3	2	2	2	rs56194750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:44495953A>G	ENST00000338758.7	+	3	286	c.223A>G	c.(223-225)Atg>Gtg	p.M75V	PARVB_ENST00000477795.1_3'UTR|PARVB_ENST00000404989.1_Missense_Mutation_p.M38V|PARVB_ENST00000406477.3_Missense_Mutation_p.M108V	NM_013327.4	NP_037459.2	Q9HBI1	PARVB_HUMAN	parvin, beta	75					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)				GGAGCGCACGATGATTGACCC	0.572													A|||	3	0.000599042	0.0	0.0014	5008	,	,		18925	0.0		0.002	False		,,,				2504	0.0				p.M108V		Atlas-SNP	.											.	PARVB	44	.	0			c.A322G						PASS	.	A	VAL/MET,VAL/MET	4,4402	8.1+/-20.4	0,4,2199	123	100	108		322,223	3.5	0.9	22	dbSNP_129	108	35,8565	23.4+/-69.3	0,35,4265	yes	missense,missense	PARVB	NM_001003828.2,NM_013327.4	21,21	0,39,6464	GG,GA,AA		0.407,0.0908,0.2999	benign,benign	108/398,75/365	44495953	39,12967	2203	4300	6503	SO:0001583	missense	29780	exon4			CGCACGATGATTG	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.223A>G	22.37:g.44495953A>G	ENSP00000342492:p.Met75Val	78	0	0		97	48	0.494845	NM_001003828	B0QYM8|B0QYN1|B2R9X6|Q5TGJ5|Q86X93|Q96PN1|Q9NSP7|Q9UGT3|Q9Y368|Q9Y3L6|Q9Y3L7	Missense_Mutation	SNP	ENST00000338758.7	37	CCDS14056.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	A	12.33	1.905546	0.33628	9.08E-4	0.00407	ENSG00000188677	ENST00000406477;ENST00000338758;ENST00000402876;ENST00000444029;ENST00000404989	T;T;T;T;T	0.34275	1.37;1.37;1.37;1.37;1.37	4.5	3.45	0.39498	Calponin homology domain (1);	0.131379	0.64402	N	0.000001	T	0.31513	0.0799	L	0.52905	1.665	0.47511	D	0.999442	B;B;B;B	0.16166	0.005;0.001;0.003;0.016	B;B;B;B	0.23018	0.006;0.005;0.008;0.043	T	0.07908	-1.0748	10	0.40728	T	0.16	-2.8779	7.5657	0.27876	0.8909:0.0:0.1091:0.0	rs56194750	75;38;75;108	A6NG58;B0QYM8;Q9HBI1;Q9HBI1-2	.;.;PARVB_HUMAN;.	V	108;75;75;73;38	ENSP00000384515:M108V;ENSP00000342492:M75V;ENSP00000385331:M75V;ENSP00000393758:M73V;ENSP00000384353:M38V	ENSP00000342492:M75V	M	+	1	0	PARVB	42827286	1.000000	0.71417	0.919000	0.36401	0.989000	0.77384	4.938000	0.63519	0.585000	0.29608	0.460000	0.39030	ATG	A|0.997;G|0.003	0.003	strong		0.572	PARVB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319518.2	NM_001003828		G	44495953	A	G	44495953	3	3	22	1	0	0	0	0	1	0	0	0	11478	333	12	3	452	3	PARVB	22	44495953	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1300819	44495953	6808613	4407	7308											
PARVG	64098	hgsc.bcm.edu	37	chr22	44586519	44586519	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gacctctccctcccaaccaaCgtccaggtggaggtcatcac	9	7	8	17	1	3	0	2	0	1	0	6	2	5	1	5	3	2	0	5	3	2	0	rs3842780	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:44586519C>A	ENST00000444313.3	+	7	961	c.477C>A	c.(475-477)aaC>aaA	p.N159K	PARVG_ENST00000415224.1_Missense_Mutation_p.N159K|PARVG_ENST00000422871.1_Missense_Mutation_p.N159K	NM_022141.5	NP_071424.1	Q9HBI0	PARVG_HUMAN	parvin, gamma	159					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)				TCCCAACCAACGTCCAGGTGG	0.602													C|||	70	0.0139776	0.053	0.0	5008	,	,		19412	0.0		0.0	False		,,,				2504	0.0				p.N159K		Atlas-SNP	.											PARVG,NS,carcinoma,0,1	PARVG	41	1	0			c.C477A						PASS	.	C	LYS/ASN,LYS/ASN,LYS/ASN	218,4188	133.7+/-170.0	2,214,1987	89	71	77		477,477,477	-2.7	0	22	dbSNP_107	77	0,8600		0,0,4300	yes	missense,missense,missense	PARVG	NM_001137605.1,NM_001137606.1,NM_022141.5	94,94,94	2,214,6287	AA,AC,CC		0.0,4.9478,1.6761	probably-damaging,probably-damaging,probably-damaging	159/332,159/332,159/332	44586519	218,12788	2203	4300	6503	SO:0001583	missense	64098	exon7			AACCAACGTCCAG	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.477C>A	22.37:g.44586519C>A	ENSP00000391583:p.Asn159Lys	71	0	0		83	32	0.385542	NM_001137606	B4DDW5|E7EVM6|Q9BQX5|Q9NSG1	Missense_Mutation	SNP	ENST00000444313.3	37	CCDS14057.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	C	11.29	1.594965	0.28445	0.049478	0.0	ENSG00000138964	ENST00000422871;ENST00000444313;ENST00000415224	T;T;T	0.58506	0.33;0.33;0.33	3.46	-2.74	0.05932	Calponin homology domain (1);	0.347388	0.28130	N	0.016483	T	0.17450	0.0419	M	0.77313	2.365	0.30861	N	0.733509	P	0.50819	0.939	P	0.46253	0.509	T	0.53795	-0.8388	10	0.56958	D	0.05	-1.8351	8.7897	0.34843	0.0:0.5205:0.0:0.4795	rs3842780	159	Q9HBI0	PARVG_HUMAN	K	159	ENSP00000391453:N159K;ENSP00000391583:N159K;ENSP00000416761:N159K	ENSP00000349378:N159K	N	+	3	2	PARVG	42917852	0.015000	0.18098	0.018000	0.16275	0.401000	0.30781	-0.744000	0.04839	-0.298000	0.08921	0.561000	0.74099	AAC	C|0.985;A|0.015	0.015	strong		0.602	PARVG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318238.4	NM_022141		A	44586519	C	A	44586519	3	1	22	1	0	0	0	0	1	0	0	0	11479	535	19	4	495	4	PARVG	22	44586519	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	90566	44586519	6718047	4408	7309											
ARHGAP8	23779	hgsc.bcm.edu	37	chr22	45221404	45221404	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcacgagggccggacgcCgcctcccaccaagacaccac	9	2	10	20	4	0	1	0	0	0	1	1	3	1	2	7	2	1	1	7	2	1	0	rs74393756	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:45221404C>T	ENST00000389774.2	+	8	761	c.620C>T	c.(619-621)cCg>cTg	p.P207L	PRR5-ARHGAP8_ENST00000352766.7_Missense_Mutation_p.P386L|ARHGAP8_ENST00000336963.4_Missense_Mutation_p.P176L|ARHGAP8_ENST00000517296.3_Missense_Mutation_p.P386L|ARHGAP8_ENST00000389773.5_Missense_Mutation_p.P298L|PRR5-ARHGAP8_ENST00000361473.5_Missense_Mutation_p.P307L|ARHGAP8_ENST00000356099.6_Missense_Mutation_p.P176L	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	207					positive regulation of ERK1 and ERK2 cascade (GO:0070374)|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)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(9)|prostate(1)|skin(7)	29		all_neural(38;0.00409)|Ovarian(80;0.00976)|Glioma(61;0.0649)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0204)		GGCCGGACGCCGCCTCCCACC	0.647													c|||	92	0.0183706	0.0666	0.0043	5008	,	,		12937	0.0		0.0	False		,,,				2504	0.001				p.P298L		Atlas-SNP	.											.	PRR5-ARHGAP8	53	.	0			c.C893T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	258,4146	146.1+/-180.8	6,246,1950	35	37	36		620,527,893,527	1.2	0	22	dbSNP_131	36	4,8594	3.7+/-12.6	0,4,4295	yes	missense,missense,missense,missense	ARHGAP8,PRR5-ARHGAP8	NM_001017526.1,NM_001198726.1,NM_181334.4,NM_181335.2	98,98,98,98	6,250,6245	TT,TC,CC		0.0465,5.8583,2.0151	benign,benign,benign,benign	207/465,176/306,298/556,176/434	45221404	262,12740	2202	4299	6501	SO:0001583	missense	553158	exon10			GGACGCCGCCTCC	AF177331	CCDS14060.2, CCDS33664.1, CCDS56233.1	22q13.3	2010-05-11			ENSG00000241484	ENSG00000241484		"Rho GTPase activating proteins"	677	protein-coding gene	gene with protein product		609405				10591208	Standard	NM_001198726		Approved	FLJ20185, BPGAP1		P85298	OTTHUMG00000030234	ENST00000389774.2:c.620C>T	22.37:g.45221404C>T	ENSP00000374424:p.Pro207Leu	150	0	0		185	83	0.448649	NM_181334	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Missense_Mutation	SNP	ENST00000389774.2	37	CCDS33664.1	32|32	0.014652014652014652|0.014652014652014652	30|30	0.06097560975609756|0.06097560975609756	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	c|c	11.26|11.26	1.586905|1.586905	0.28268|0.28268	0.058583|0.058583	4.65E-4|4.65E-4	ENSG00000248405;ENSG00000248405;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484|ENSG00000248405	ENST00000361473;ENST00000352766;ENST00000517296;ENST00000389773;ENST00000389774;ENST00000336963;ENST00000356099|ENST00000515632	T;T;T;T;T;T;T|.	0.60548|.	2.27;2.25;2.25;2.27;2.2;0.18;2.21|.	4.6|4.6	1.18|1.18	0.20946|0.20946	.|.	1.887620|.	0.03242|.	N|.	0.180497|.	T|T	0.07863|0.07863	0.0197|0.0197	M|M	0.67953|0.67953	2.075|2.075	0.09310|0.09310	N|N	0.999994|0.999994	B;B;P;B;B;B;B|.	0.48640|.	0.214;0.007;0.913;0.318;0.049;0.002;0.328|.	B;B;B;B;B;B;B|.	0.28553|.	0.018;0.002;0.091;0.018;0.004;0.001;0.011|.	T|T	0.07597|0.07597	-1.0764|-1.0764	10|5	0.52906|.	T|.	0.07|.	.|.	7.5251|7.5251	0.27650|0.27650	0.0:0.7049:0.0:0.2951|0.0:0.7049:0.0:0.2951	.|.	212;176;212;207;217;386;307|.	B7ZMA4;A6ZJ79;A2RU51;P85298;Q6PCC7;B1AHC4;B1AHC3|.	.;.;.;RHG08_HUMAN;.;.;.|.	L|C	307;386;386;298;207;176;176|230	ENSP00000354732:P307L;ENSP00000262731:P386L;ENSP00000429240:P386L;ENSP00000374423:P298L;ENSP00000374424:P207L;ENSP00000337287:P176L;ENSP00000348407:P176L|.	ENSP00000337287:P176L|.	P|R	+|+	2|1	0|0	PRR5-ARHGAP8;ARHGAP8|PRR5-ARHGAP8	43600068|43600068	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.734000|0.734000	0.26101|0.26101	0.120000|0.120000	0.18254|0.18254	-0.130000|-0.130000	0.14895|0.14895	CCG|CGC	C|0.978;T|0.022	0.022	strong		0.647	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701		T	45221404	C	T	45221404	3	4	22	1	0	0	0	0	1	0	0	0	888	652	23	1	646	1	ARHGAP8	22	45221404	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	634885	45221404	6083162	4409	7310											
UPK3A	7380	hgsc.bcm.edu	37	chr22	45683309	45683309	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cagggcctctgtaacgcaccCctgtcggcagccacggagta	8	6	12	15	3	1	0	0	0	1	0	2	1	1	1	4	3	2	4	4	3	2	2	rs62001037	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:45683309C>T	ENST00000216211.4	+	3	497	c.465C>T	c.(463-465)ccC>ccT	p.P155P	UPK3A_ENST00000396082.2_Intron	NM_006953.3	NP_008884.1	O75631	UPK3A_HUMAN	uroplakin 3A	155					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)		GTAACGCACCCCTGTCGGCAG	0.607													C|||	116	0.0231629	0.084	0.0058	5008	,	,		16168	0.0		0.001	False		,,,				2504	0.0				p.P155P		Atlas-SNP	.											.	UPK3A	14	.	0			c.C465T						PASS	.	C	,	338,4066		14,310,1878	28	27	28		,465	0.4	1	22	dbSNP_129	28	1,8599		0,1,4299	no	intron,coding-synonymous	UPK3A	NM_001167574.1,NM_006953.3	,	14,311,6177	TT,TC,CC		0.0116,7.6748,2.6069	,	,155/288	45683309	339,12665	2202	4300	6502	SO:0001819	synonymous_variant	7380	exon3			CGCACCCCTGTCG	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.465C>T	22.37:g.45683309C>T		67	0	0		67	30	0.447761	NM_006953	B0QY25|O60261|Q32N05|Q5TII6	Silent	SNP	ENST00000216211.4	37	CCDS14064.1																																																																																			C|0.973;T|0.027	0.027	strong		0.607	UPK3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000322276.1	NM_006953		T	45683309	C	T	45683309	2	4	22	1	0	0	0	0	0	0	0	1	17025	610	22	2		2	UPK3A	22	45683309	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	461905	45683309	5621257	4410	7311											
SMC1B	27127	hgsc.bcm.edu	37	chr22	45741416	45741416	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatgactatcatctgaaacTggtcttgagtttgctctttg	9	16	9	7	0	4	4	1	3	3	1	4	4	4	4	0	1	2	2	0	1	2	4	rs61737925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:45741416T>A	ENST00000357450.4	-	24	3529	c.3530A>T	c.(3529-3531)cAg>cTg	p.Q1177L	SMC1B_ENST00000404354.3_Missense_Mutation_p.Q1103L	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	1177					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)		CATCTGAAACTGGTCTTGAGT	0.448													T|||	55	0.0109824	0.0408	0.0014	5008	,	,		18744	0.0		0.0	False		,,,				2504	0.0				p.Q1177L		Atlas-SNP	.											.	SMC1B	215	.	0			c.A3530T						PASS	.	T	LEU/GLN	155,3629		4,147,1741	133	127	129		3530	5.6	1	22	dbSNP_129	129	0,8236		0,0,4118	yes	missense	SMC1B	NM_148674.3	113	4,147,5859	AA,AT,TT		0.0,4.0962,1.2895	probably-damaging	1177/1236	45741416	155,11865	1892	4118	6010	SO:0001583	missense	27127	exon24			TGAAACTGGTCTT	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.3530A>T	22.37:g.45741416T>A	ENSP00000350036:p.Gln1177Leu	125	0	0		148	78	0.527027	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Missense_Mutation	SNP	ENST00000357450.4	37	CCDS43027.1	18	0.008241758241758242	18	0.036585365853658534	0	0.0	0	0.0	0	0.0	T	18.42	3.620931	0.66787	0.040962	0.0	ENSG00000077935	ENST00000357450;ENST00000404354	T;T	0.77358	2.94;-1.09	5.61	5.61	0.85477	.	0.105145	0.42682	D	0.000676	T	0.46580	0.1400	L	0.43152	1.355	0.28411	N	0.91821	P;P	0.41848	0.763;0.573	P;B	0.44897	0.463;0.236	T	0.62779	-0.6782	10	0.40728	T	0.16	.	15.8023	0.78463	0.0:0.0:0.0:1.0	rs61737925	1103;1177	Q8NDV3-2;Q8NDV3-3	.;.	L	1177;1103	ENSP00000350036:Q1177L;ENSP00000385902:Q1103L	ENSP00000350036:Q1177L	Q	-	2	0	SMC1B	44120080	1.000000	0.71417	0.991000	0.47740	0.981000	0.71138	3.975000	0.56859	2.142000	0.66516	0.397000	0.26171	CAG	T|0.960;A|0.040	0.040	strong		0.448	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674		A	45741416	T	A	45741416	3	1	22	1	0	0	0	0	1	0	0	0	14797	1580	55	5	185	5	SMC1B	22	45741416	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	58107	45741416	5563150	4411	7312											
PKDREJ	10343	hgsc.bcm.edu	37	chr22	46656562	46656562	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctcacattgagtgttggAtaaaaacaatttctgcagtg	12	13	9	7	0	2	1	1	1	1	0	2	2	2	2	0	1	3	3	0	1	4	4	rs7287371	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46656562A>G	ENST00000253255.5	-	1	2657	c.2658T>C	c.(2656-2658)taT>taC	p.Y886Y		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	886	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				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)			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)		TGAGTGTTGGATAAAAACAAT	0.388													A|||	265	0.0529153	0.1899	0.0144	5008	,	,		21079	0.0		0.0	False		,,,				2504	0.0041				p.Y886Y		Atlas-SNP	.											.	PKDREJ	195	.	0			c.T2658C						PASS	.	A		777,3629	311.9+/-292.3	72,633,1498	83	84	83		2658	-10.1	0	22	dbSNP_116	83	14,8586	9.8+/-36.6	0,14,4286	no	coding-synonymous	PKDREJ	NM_006071.1		72,647,5784	GG,GA,AA		0.1628,17.635,6.0818		886/2254	46656562	791,12215	2203	4300	6503	SO:0001819	synonymous_variant	10343	exon1			TGTTGGATAAAAA	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.2658T>C	22.37:g.46656562A>G		142	0	0		139	74	0.532374	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																			A|0.942;G|0.058	0.058	strong		0.388	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		G	46656562	A	G	46656562	2	3	22	1	0	0	0	0	0	0	0	1	11979	340	12	3		3	PKDREJ	22	46656562	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	915146	46656562	4648004	4412	7313											
CELSR1	9620	hgsc.bcm.edu	37	chr22	46760037	46760037	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agcccagggaagacgtgcgcGaggatgtggggctctgctca	8	6	17	10	3	2	1	1	0	1	1	2	4	2	3	1	4	3	2	1	4	1	0	rs375307146|rs6008777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46760037G>A	ENST00000262738.3	-	34	8890	c.8891C>T	c.(8890-8892)tCg>tTg	p.S2964L		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2964			S -> L (in NTD; shows reduced protein localization to the cell membrane; dbSNP:rs6008777). {ECO:0000269|PubMed:22095531}.		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)		AGACGTGCGCGAGGATGTGGG	0.682													G|||	116	0.0231629	0.0832	0.0086	5008	,	,		14793	0.0		0.0	False		,,,				2504	0.0				p.S2964L		Atlas-SNP	.											CELSR1,colon,carcinoma,+1,1	CELSR1	242	1	0			c.C8891T						PASS	.	G	LEU/SER	399,4005	190.2+/-216.2	29,341,1832	40	46	44		8891	4.8	0.1	22	dbSNP_114	44	4,8594	3.0+/-9.4	0,4,4295	yes	missense	CELSR1	NM_014246.1	145	29,345,6127	AA,AG,GG		0.0465,9.0599,3.0995	probably-damaging	2964/3015	46760037	403,12599	2202	4299	6501	SO:0001583	missense	9620	exon34			GTGCGCGAGGATG	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.8891C>T	22.37:g.46760037G>A	ENSP00000262738:p.Ser2964Leu	122	0	0		159	85	0.534591	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	37	0.01694139194139194	35	0.07113821138211382	2	0.0055248618784530384	0	0.0	0	0.0	G	14.11	2.438063	0.43326	0.090599	4.65E-4	ENSG00000075275	ENST00000262738	T	0.71579	-0.58	4.85	4.85	0.62838	.	0.000000	0.36374	U	0.002632	T	0.11367	0.0277	M	0.74258	2.255	0.37738	D	0.925504	D	0.67145	0.996	P	0.47786	0.557	T	0.57046	-0.7878	10	0.33141	T	0.24	.	17.569	0.87930	0.0:0.0:1.0:0.0	rs6008777	2964	Q9NYQ6	CELR1_HUMAN	L	2964	ENSP00000262738:S2964L	ENSP00000262738:S2964L	S	-	2	0	CELSR1	45138701	0.994000	0.37717	0.060000	0.19600	0.011000	0.07611	3.602000	0.54066	2.211000	0.71520	0.563000	0.77884	TCG	G|0.971;A|0.029	0.029	strong		0.682	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		A	46760037	G	A	46760037	3	1	22	1	0	0	0	0	1	0	0	0	3223	1059	37	1	161	1	CELSR1	22	46760037	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	103475	46760037	4544529	4413	7314											
CELSR1	9620	hgsc.bcm.edu	37	chr22	46760102	46760102	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcccttcagcgtctgctcCgtcagcgtcagcggcggcgg	3	7	15	16	7	4	0	3	0	1	0	5	0	5	0	2	4	4	1	2	4	0	1	rs6008778	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46760102C>T	ENST00000262738.3	-	34	8825	c.8826G>A	c.(8824-8826)acG>acA	p.T2942T		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2942					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)		GCGTCTGCTCCGTCAGCGTCA	0.662													C|||	272	0.0543131	0.1974	0.013	5008	,	,		15944	0.0		0.001	False		,,,				2504	0.001				p.T2942T		Atlas-SNP	.											.	CELSR1	242	.	0			c.G8826A						PASS	.	C		761,3639		66,629,1505	38	47	44		8826	-1.3	0.3	22	dbSNP_114	44	18,8570		0,18,4276	no	coding-synonymous	CELSR1	NM_014246.1		66,647,5781	TT,TC,CC		0.2096,17.2955,5.9978		2942/3015	46760102	779,12209	2200	4294	6494	SO:0001819	synonymous_variant	9620	exon34			CTGCTCCGTCAGC	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.8826G>A	22.37:g.46760102C>T		41	0	0		65	34	0.523077	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	37	CCDS14076.1																																																																																			C|0.948;T|0.052	0.052	strong		0.662	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		T	46760102	C	T	46760102	2	4	22	1	0	0	0	0	0	0	0	1	3223	639	23	1		1	CELSR1	22	46760102	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	65	46760102	4544464	4414	7315											
CELSR1	9620	hgsc.bcm.edu	37	chr22	46761135	46761135	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cccacacactcacctttgggGgtgctgtggacggcgcccct	5	8	12	16	2	1	0	1	0	0	0	1	1	1	1	4	4	1	1	4	4	0	1	rs9627424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46761135G>T	ENST00000262738.3	-	32	8546	c.8547C>A	c.(8545-8547)acC>acA	p.T2849T		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2849					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)		CACCTTTGGGGGTGCTGTGGA	0.652													G|||	441	0.0880591	0.3177	0.0259	5008	,	,		17157	0.001		0.001	False		,,,				2504	0.001				p.T2849T		Atlas-SNP	.											.	CELSR1	242	.	0			c.C8547A						PASS	.	G		1269,3107	414.6+/-336.9	175,919,1094	28	27	27		8547	4.9	1	22	dbSNP_119	27	26,8564	16.6+/-54.9	0,26,4269	no	coding-synonymous	CELSR1	NM_014246.1		175,945,5363	TT,TG,GG		0.3027,28.9991,9.9877		2849/3015	46761135	1295,11671	2188	4295	6483	SO:0001819	synonymous_variant	9620	exon32			TTTGGGGGTGCTG	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.8547C>A	22.37:g.46761135G>T		75	0	0		55	28	0.509091	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	37	CCDS14076.1																																																																																			G|0.911;T|0.089	0.089	strong		0.652	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		T	46761135	G	T	46761135	2	4	22	1	0	0	0	0	0	0	0	1	3223	1219	43	4		4	CELSR1	22	46761135	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1033	46761135	4543431	4415	7316											
CELSR1	9620	hgsc.bcm.edu	37	chr22	46777896	46777896	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcggtgccaggccccgggCgcgtggtctgcggggtggtc	1	8	19	13	5	2	0	0	0	2	0	4	0	2	0	3	7	2	0	3	7	0	0	rs7287089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46777896C>G	ENST00000262738.3	-	21	6934	c.6935G>C	c.(6934-6936)cGc>cCc	p.R2312P		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2312			R -> P (does not affect protein localization to the cell membrane; dbSNP:rs7287089). {ECO:0000269|PubMed:22095531}.		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)		AGGCCCCGGGCGCGTGGTCTG	0.682													.|||	85	0.0169728	0.0605	0.0072	5008	,	,		12386	0.0		0.0	False		,,,				2504	0.0				p.R2312P		Atlas-SNP	.											.	CELSR1	242	.	0			c.G6935C						PASS	.	C	PRO/ARG	163,4111		1,161,1975	8	9	9		6935	-3.2	0	22	dbSNP_116	9	2,8374		0,2,4186	no	missense	CELSR1	NM_014246.1	103	1,163,6161	GG,GC,CC		0.0239,3.8138,1.3043	benign	2312/3015	46777896	165,12485	2137	4188	6325	SO:0001583	missense	9620	exon21			CCCGGGCGCGTGG	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.6935G>C	22.37:g.46777896C>G	ENSP00000262738:p.Arg2312Pro	15	0	0		29	12	0.413793	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	32	0.014652014652014652	31	0.06300813008130081	1	0.0027624309392265192	0	0.0	0	0.0	C	9.166	1.020045	0.19433	0.038138	2.39E-4	ENSG00000075275	ENST00000262738	T	0.67698	-0.28	4.89	-3.18	0.05186	Domain of unknown function DUF3497 (1);	1.362770	0.05247	N	0.513271	T	0.05777	0.0151	N	0.08118	0	0.09310	N	1	B;B	0.10296	0.003;0.001	B;B	0.11329	0.006;0.002	T	0.04413	-1.0953	10	0.20519	T	0.43	.	3.427	0.07414	0.1112:0.33:0.384:0.1748	rs7287089	633;2312	B7Z7U7;Q9NYQ6	.;CELR1_HUMAN	P	2312	ENSP00000262738:R2312P	ENSP00000262738:R2312P	R	-	2	0	CELSR1	45156560	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.121000	0.03270	-0.119000	0.11830	0.555000	0.69702	CGC	C|0.985;G|0.015	0.015	strong		0.682	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		G	46777896	C	G	46777896	3	3	22	1	0	0	0	0	1	0	0	0	3223	768	27	4	2169	4	CELSR1	22	46777896	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	16761	46777896	4526670	4416	7317											
CELSR1	9620	hgsc.bcm.edu	37	chr22	46859701	46859701	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtagcagaggtcgatctcCgtctcgcagtagtcgccggt	7	9	14	11	5	2	1	0	0	2	1	6	3	2	1	2	2	1	4	2	2	2	2	rs140328042	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46859701C>T	ENST00000262738.3	-	2	4085	c.4086G>A	c.(4084-4086)acG>acA	p.T1362T	CELSR1_ENST00000395964.1_Silent_p.T1362T	NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1362					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)		GGTCGATCTCCGTCTCGCAGT	0.692													C|||	11	0.00219649	0.0083	0.0	5008	,	,		13548	0.0		0.0	False		,,,				2504	0.0				p.T1362T		Atlas-SNP	.											.	CELSR1	242	.	0			c.G4086A						PASS	.	C		37,4357		0,37,2160	33	33	33		4086	-9.5	0.7	22	dbSNP_134	33	0,8594		0,0,4297	no	coding-synonymous	CELSR1	NM_014246.1		0,37,6457	TT,TC,CC		0.0,0.8421,0.2849		1362/3015	46859701	37,12951	2197	4297	6494	SO:0001819	synonymous_variant	9620	exon2			GATCTCCGTCTCG	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.4086G>A	22.37:g.46859701C>T		61	0	0		58	27	0.465517	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	37	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	C	8.918	0.960317	0.18507	0.008421	0.0	ENSG00000075275	ENST00000454637	.	.	.	4.75	-9.49	0.00587	.	.	.	.	.	T	0.25232	0.0613	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37911	-0.9685	4	.	.	.	.	1.2491	0.01978	0.1999:0.3436:0.1613:0.2952	.	.	.	.	Q	737	.	.	R	-	2	0	CELSR1	45238365	0.000000	0.05858	0.651000	0.29564	0.922000	0.55478	-3.266000	0.00534	-2.191000	0.00756	-0.892000	0.02923	CGG	C|0.997;T|0.003	0.003	strong		0.692	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		T	46859701	C	T	46859701	2	4	22	1	0	0	0	0	0	0	0	1	3223	639	23	1		1	CELSR1	22	46859701	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	81805	46859701	4444865	4417	7318											
CELSR1	9620	hgsc.bcm.edu	37	chr22	46932079	46932079	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggtggccgagcgcggcggcGtactgtagtccacggctttc	4	9	16	12	6	0	0	0	0	0	0	2	1	1	0	2	5	2	3	2	5	2	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46932079G>A	ENST00000262738.3	-	1	988	c.989C>T	c.(988-990)aCg>aTg	p.T330M	CELSR1_ENST00000497509.1_5'Flank|CELSR1_ENST00000395964.1_Missense_Mutation_p.T330M	NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	330	Cadherin 1. {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)		GCGCGGCGGCGTACTGTAGTC	0.647																																					p.T330M		Atlas-SNP	.											.	CELSR1	242	.	0			c.C989T						PASS	.						116	95	102					22																	46932079		2201	4300	6501	SO:0001583	missense	9620	exon1			GGCGGCGTACTGT	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.989C>T	22.37:g.46932079G>A	ENSP00000262738:p.Thr330Met	95	0	0		89	45	0.505618	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	G	3.466	-0.109044	0.06924	.	.	ENSG00000075275	ENST00000262738;ENST00000395964	T;T	0.01838	4.61;4.61	4.32	-0.683	0.11335	Cadherin (4);Cadherin-like (1);	0.310145	0.26203	U	0.025732	T	0.01800	0.0057	L	0.35854	1.095	0.09310	N	0.999999	P	0.34522	0.455	B	0.32805	0.153	T	0.48305	-0.9047	10	0.32370	T	0.25	.	6.6282	0.22841	0.1613:0.2739:0.5649:0.0	.	330	Q9NYQ6	CELR1_HUMAN	M	330	ENSP00000262738:T330M;ENSP00000379293:T330M	ENSP00000262738:T330M	T	-	2	0	CELSR1	45310743	0.376000	0.25098	0.741000	0.31004	0.009000	0.06853	3.037000	0.49775	-0.001000	0.14495	-0.391000	0.06502	ACG	.	.	none		0.647	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		A	46932079	G	A	46932079	3	1	22	1	0	0	0	0	1	0	0	0	3223	1145	40	1	8195	1	CELSR1	22	46932079	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	72378	46932079	4372487	4418	7319											
BRD1	23774	hgsc.bcm.edu	37	chr22	50217387	50217387	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcgcagtgcgactccttctcGaagcggtccatcaggaactc	8	9	10	14	4	2	0	1	0	1	0	7	3	4	1	2	2	3	1	2	2	2	1	rs11912787	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50217387G>A	ENST00000216267.8	-	1	1065	c.579C>T	c.(577-579)ttC>ttT	p.F193F	BRD1_ENST00000342989.5_5'Flank|BRD1_ENST00000457780.2_Silent_p.F193F|BRD1_ENST00000404760.1_Silent_p.F193F|BRD1_ENST00000459821.1_5'Flank|BRD1_ENST00000404034.1_Silent_p.F193F|BRD1_ENST00000542442.1_5'Flank	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	193					histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			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)		ACTCCTTCTCGAAGCGGTCCA	0.602													G|||	508	0.101438	0.1664	0.0432	5008	,	,		21111	0.003		0.0746	False		,,,				2504	0.184				p.F193F		Atlas-SNP	.											.	BRD1	144	.	0			c.C579T						PASS	.	G		801,3605	322.9+/-297.8	69,663,1471	72	61	65		579	-5.2	1	22	dbSNP_120	65	702,7898	172.6+/-223.3	31,640,3629	no	coding-synonymous	BRD1	NM_014577.1		100,1303,5100	AA,AG,GG		8.1628,18.1798,11.5562		193/1059	50217387	1503,11503	2203	4300	6503	SO:0001819	synonymous_variant	23774	exon1			CTTCTCGAAGCGG	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.579C>T	22.37:g.50217387G>A		105	0	0		104	50	0.480769	NM_014577	A6ZJA4	Silent	SNP	ENST00000216267.8	37	CCDS14080.1																																																																																			G|0.899;A|0.101	0.101	strong		0.602	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577		A	50217387	G	A	50217387	2	1	22	1	0	0	0	0	0	0	0	1	1503	1049	37	1		1	BRD1	22	50217387	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3285308	50217387	1087179	4419	7320											
ZBED4	9889	hgsc.bcm.edu	37	chr22	50278588	50278588	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ataggggaggcctcggcgtcCtctcctgagaagcagcaggc	8	6	15	12	2	1	1	0	1	1	1	4	3	2	2	3	5	2	2	3	5	2	1	rs61731526	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50278588C>T	ENST00000216268.5	+	2	1755	c.1278C>T	c.(1276-1278)tcC>tcT	p.S426S		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	426						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)		CCTCGGCGTCCTCTCCTGAGA	0.532													C|||	23	0.00459265	0.0159	0.0029	5008	,	,		19928	0.0		0.0	False		,,,				2504	0.0				p.S426S		Atlas-SNP	.											.	ZBED4	102	.	0			c.C1278T						PASS	.	C		44,4362	40.8+/-73.8	0,44,2159	59	63	62		1278	-0.5	0.3	22	dbSNP_129	62	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ZBED4	NM_014838.2		0,46,6457	TT,TC,CC		0.0233,0.9986,0.3537		426/1172	50278588	46,12960	2203	4300	6503	SO:0001819	synonymous_variant	9889	exon2			GGCGTCCTCTCCT	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.1278C>T	22.37:g.50278588C>T		42	0	0		55	19	0.345455	NM_014838	B2RZH1|Q1ECU0|Q9UGG8	Silent	SNP	ENST00000216268.5	37	CCDS33677.1																																																																																			C|0.996;T|0.004	0.004	strong		0.532	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838		T	50278588	C	T	50278588	2	4	22	1	0	0	0	0	0	0	0	1	17535	668	24	2		2	ZBED4	22	50278588	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	61201	50278588	1025978	4420	7321											
ZBED4	9889	hgsc.bcm.edu	37	chr22	50279749	50279749	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtcaccgacaacgccagcatCgggaagacgctgaacgaggg	12	3	14	12	5	1	2	1	1	0	1	2	5	1	3	2	2	3	2	2	2	3	0	rs61731524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50279749C>T	ENST00000216268.5	+	2	2916	c.2439C>T	c.(2437-2439)atC>atT	p.I813I		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	813						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)		ACGCCAGCATCGGGAAGACGC	0.617													C|||	18	0.00359425	0.0083	0.0029	5008	,	,		19867	0.0		0.0	False		,,,				2504	0.0051				p.I813I		Atlas-SNP	.											.	ZBED4	102	.	0			c.C2439T						PASS	.	C		14,4392	20.2+/-43.8	0,14,2189	38	38	38		2439	-9.5	0.2	22	dbSNP_129	38	0,8598		0,0,4299	no	coding-synonymous	ZBED4	NM_014838.2		0,14,6488	TT,TC,CC		0.0,0.3177,0.1077		813/1172	50279749	14,12990	2203	4299	6502	SO:0001819	synonymous_variant	9889	exon2			CAGCATCGGGAAG	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.2439C>T	22.37:g.50279749C>T		61	0	0		72	28	0.388889	NM_014838	B2RZH1|Q1ECU0|Q9UGG8	Silent	SNP	ENST00000216268.5	37	CCDS33677.1																																																																																			C|0.998;T|0.002	0.002	strong		0.617	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838		T	50279749	C	T	50279749	2	4	22	1	0	0	0	0	0	0	0	1	17535	874	31	1		1	ZBED4	22	50279749	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1161	50279749	1024817	4421	7322											
TUBGCP6	85378	hgsc.bcm.edu	37	chr22	50667859	50667859	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacgaggcccttgctgtacaAagagtccaggacgggctgca	10	6	13	12	2	0	1	0	0	0	1	1	3	1	2	2	3	3	4	2	3	2	2	rs6010211	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50667859A>G	ENST00000248846.5	-	4	1368	c.1264T>C	c.(1264-1266)Ttg>Ctg	p.L422L	TUBGCP6_ENST00000439308.2_Silent_p.L422L			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	422					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)		TTGCTGTACAAAGAGTCCAGG	0.567													A|||	297	0.0593051	0.2171	0.0144	5008	,	,		20076	0.0		0.0	False		,,,				2504	0.0				p.L422L		Atlas-SNP	.											.	TUBGCP6	132	.	0			c.T1264C						PASS	.	A		817,3585	317.4+/-295.1	79,659,1463	78	57	64		1264	-2.6	0	22	dbSNP_114	64	0,8600		0,0,4300	no	coding-synonymous	TUBGCP6	NM_020461.3		79,659,5763	GG,GA,AA		0.0,18.5597,6.2836		422/1820	50667859	817,12185	2201	4300	6501	SO:0001819	synonymous_variant	85378	exon4			TGTACAAAGAGTC	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.1264T>C	22.37:g.50667859A>G		158	0	0		208	86	0.413462	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Silent	SNP	ENST00000248846.5	37	CCDS14087.1																																																																																			A|0.936;G|0.064	0.064	strong		0.567	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461		G	50667859	A	G	50667859	2	3	22	1	0	0	0	0	0	0	0	1	16785	11	1	3		3	TUBGCP6	22	50667859	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	388110	50667859	636707	4422	7323											
PLXNB2	23654	hgsc.bcm.edu	37	chr22	50716068	50716068	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caggcatccatgaaggtctgCgcgatgactgacagcgaggc	10	6	14	11	3	1	3	0	3	1	0	2	5	2	3	1	3	2	1	1	3	1	0	rs11547732	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50716068C>T	ENST00000449103.1	-	33	5288	c.5148G>A	c.(5146-5148)gcG>gcA	p.A1716A	PLXNB2_ENST00000359337.4_Silent_p.A1716A			O15031	PLXB2_HUMAN	plexin B2	1716					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)		TGAAGGTCTGCGCGATGACTG	0.632													C|||	471	0.0940495	0.3374	0.0303	5008	,	,		16203	0.0		0.004	False		,,,				2504	0.0				p.A1716A		Atlas-SNP	.											.	PLXNB2	172	.	0			c.G5148A						PASS	.	C		1148,3132		141,866,1133	60	66	64		5148	-7.9	0	22	dbSNP_120	64	10,8510		0,10,4250	no	coding-synonymous	PLXNB2	NM_012401.3		141,876,5383	TT,TC,CC		0.1174,26.8224,9.0469		1716/1839	50716068	1158,11642	2140	4260	6400	SO:0001819	synonymous_variant	23654	exon33			GGTCTGCGCGATG		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.5148G>A	22.37:g.50716068C>T		153	0	0		188	95	0.505319	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Silent	SNP	ENST00000449103.1	37	CCDS43035.1	161	0.07371794871794872	147	0.29878048780487804	13	0.03591160220994475	0	0.0	1	0.0013192612137203166	C	0.034	-1.315528	0.01331	0.268224	0.001174	ENSG00000196576	ENST00000399964	.	.	.	3.94	-7.87	0.01183	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999955255	.	.	.	.	.	.	T	0.48937	-0.8990	4	0.87932	D	0	.	3.99	0.09533	0.1301:0.3253:0.341:0.2036	rs11547732	.	.	.	H	346	.	ENSP00000382845:R346H	R	-	2	0	PLXNB2	49058195	0.000000	0.05858	0.009000	0.14445	0.067000	0.16453	-3.257000	0.00537	-6.532000	0.00003	-2.734000	0.00129	CGC	T|0.048;G|0.000;C|0.952;A|0.000	0.048	strong		0.632	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401		T	50716068	C	T	50716068	2	4	22	1	0	0	0	0	0	0	0	1	12133	755	27	1		1	PLXNB2	22	50716068	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	48209	50716068	588498	4423	7324											
PLXNB2	23654	hgsc.bcm.edu	37	chr22	50718941	50718941	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgcagcatcagcttggggttCttggccaccacgtactgctc	6	10	11	14	2	2	0	1	0	1	0	3	0	2	0	2	3	4	6	2	3	1	4	rs73891209	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50718941C>T	ENST00000449103.1	-	25	4292	c.4152G>A	c.(4150-4152)aaG>aaA	p.K1384K	PLXNB2_ENST00000359337.4_Silent_p.K1384K|PLXNB2_ENST00000496720.1_5'Flank			O15031	PLXB2_HUMAN	plexin B2	1384					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)		GCTTGGGGTTCTTGGCCACCA	0.692													C|||	222	0.0443291	0.1619	0.0115	5008	,	,		9618	0.0		0.0	False		,,,				2504	0.0				p.K1384K		Atlas-SNP	.											.	PLXNB2	172	.	0			c.G4152A						PASS	.	C		556,3828		45,466,1681	75	80	78		4152	4.3	1	22	dbSNP_130	78	1,8583		0,1,4291	no	coding-synonymous	PLXNB2	NM_012401.3		45,467,5972	TT,TC,CC		0.0116,12.6825,4.2952		1384/1839	50718941	557,12411	2192	4292	6484	SO:0001819	synonymous_variant	23654	exon25			GGGGTTCTTGGCC		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.4152G>A	22.37:g.50718941C>T		22	0	0		29	11	0.37931	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Silent	SNP	ENST00000449103.1	37	CCDS43035.1																																																																																			C|0.976;G|0.000;T|0.024	0.024	strong		0.692	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401		T	50718941	C	T	50718941	2	4	22	1	0	0	0	0	0	0	0	1	12133	912	32	2		2	PLXNB2	22	50718941	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2873	50718941	585625	4424	7325											
PLXNB2	23654	hgsc.bcm.edu	37	chr22	50720430	50720430	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atcagcaccgtgaggttgtaGgcctctggctcctcaggcac	7	9	12	13	1	3	1	2	1	1	0	4	1	4	1	3	4	1	5	3	4	1	2	rs56110807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50720430G>C	ENST00000449103.1	-	20	3338	c.3198C>G	c.(3196-3198)gcC>gcG	p.A1066A	PLXNB2_ENST00000359337.4_Silent_p.A1066A|PLXNB2_ENST00000496720.1_5'Flank			O15031	PLXB2_HUMAN	plexin B2	1066	IPT/TIG 3.				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)		TGAGGTTGTAGGCCTCTGGCT	0.612													G|||	436	0.0870607	0.3169	0.0245	5008	,	,		17944	0.0		0.0	False		,,,				2504	0.0				p.A1066A		Atlas-SNP	.											.	PLXNB2	172	.	0			c.C3198G						PASS	.	G		954,3276		106,742,1267	54	61	59		3198	2.5	1	22	dbSNP_129	59	2,8428		0,2,4213	no	coding-synonymous	PLXNB2	NM_012401.3		106,744,5480	CC,CG,GG		0.0237,22.5532,7.5513		1066/1839	50720430	956,11704	2115	4215	6330	SO:0001819	synonymous_variant	23654	exon20			GTTGTAGGCCTCT		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.3198C>G	22.37:g.50720430G>C		48	0	0		41	23	0.560976	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Silent	SNP	ENST00000449103.1	37	CCDS43035.1	154	0.07051282051282051	144	0.2926829268292683	10	0.027624309392265192	0	0.0	0	0.0	G	6.393	0.440700	0.12104	0.225532	2.37E-4	ENSG00000196576	ENST00000427829	.	.	.	4.63	2.46	0.29980	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.20538	-1.0272	3	.	.	.	.	10.4218	0.44354	0.1674:0.0:0.8326:0.0	rs56110807	.	.	.	R	84	.	.	P	-	2	0	PLXNB2	49062557	1.000000	0.71417	1.000000	0.80357	0.432000	0.31715	2.715000	0.47210	1.146000	0.42352	0.313000	0.20887	CCT	G|0.953;C|0.047	0.047	strong		0.612	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401		C	50720430	G	C	50720430	2	2	22	1	0	0	0	0	0	0	0	1	12133	987	35	4		4	PLXNB2	22	50720430	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1489	50720430	584136	4425	7326											
FAM116B	414918	hgsc.bcm.edu	37	chr22	50752258	50752258	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tataccttgagcagccgtttGagcagcgccttgtcgcggtg	6	11	13	11	4	0	2	0	2	0	0	1	2	0	2	3	1	5	3	3	1	2	5	rs115446109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50752258G>A	ENST00000413817.3	-	14	1259	c.1188C>T	c.(1186-1188)ctC>ctT	p.L396L	XX-C283C717.1_ENST00000453835.1_RNA	NM_001001794.3	NP_001001794.3	Q8NEG7	DEN6B_HUMAN	DENN/MADD domain containing 6B	396					positive regulation of Rab GTPase activity (GO:0032851)	endosome (GO:0005768)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)										GCAGCCGTTTGAGCAGCGCCT	0.677													G|||	61	0.0121805	0.0446	0.0029	5008	,	,		10156	0.0		0.0	False		,,,				2504	0.0				p.L396L		Atlas-SNP	.											.	.	.	.	0			c.C1188T						PASS	.	G		202,3980		3,196,1892	34	40	38		1188	1	1	22	dbSNP_132	38	2,8408		0,2,4203	no	coding-synonymous	FAM116B	NM_001001794.3		3,198,6095	AA,AG,GG		0.0238,4.8302,1.6201		396/586	50752258	204,12388	2091	4205	6296	SO:0001819	synonymous_variant	414918	exon14			CCGTTTGAGCAGC	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.1188C>T	22.37:g.50752258G>A		97	0	0		126	59	0.468254	NM_001001794	A6X8I5	Silent	SNP	ENST00000413817.3	37	CCDS46732.1																																																																																			G|0.984;A|0.016	0.016	strong		0.677	DENND6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316845.3	NM_001001794		A	50752258	G	A	50752258	2	1	22	1	0	0	0	0	0	0	0	1	5413	1277	45	2		2	FAM116B	22	50752258	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	31828	50752258	552308	4426	7327											
SAPS2	9701	hgsc.bcm.edu	37	chr22	50874851	50874851	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcgtggaggagacgctgacGgagacgaaccgcaggaacac	12	4	15	10	5	0	3	0	1	0	2	1	8	0	5	1	4	2	2	1	4	2	1	rs78837601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50874851G>A	ENST00000216061.5	+	15	1942	c.1572G>A	c.(1570-1572)acG>acA	p.T524T	PPP6R2_ENST00000395744.3_Silent_p.T524T|PPP6R2_ENST00000395741.3_Silent_p.T525T|PPP6R2_ENST00000359139.3_Silent_p.T524T			O75170	PP6R2_HUMAN	protein phosphatase 6, regulatory subunit 2	524						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						AGACGCTGACGGAGACGAACC	0.687													G|||	105	0.0209665	0.0719	0.0086	5008	,	,		17157	0.004		0.0	False		,,,				2504	0.0				p.T525T		Atlas-SNP	.											.	PPP6R2	71	.	0			c.G1575A						PASS	.	G	,,,	322,4064		9,304,1880	53	34	41		1572,1575,1572,1572	-9.1	0	22	dbSNP_131	41	2,8584		0,2,4291	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PPP6R2	NM_001242898.1,NM_001242899.1,NM_001242900.1,NM_014678.4	,,,	9,306,6171	AA,AG,GG		0.0233,7.3415,2.4977	,,,	524/960,525/934,524/928,524/933	50874851	324,12648	2193	4293	6486	SO:0001819	synonymous_variant	9701	exon14			GCTGACGGAGACG	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.1572G>A	22.37:g.50874851G>A		314	0	0		342	166	0.48538	NM_001242899	A6PVG3|B7Z7T3|Q5U5P3|Q7Z2L2|Q7Z5G5|Q7Z731|Q9UGB9	Silent	SNP	ENST00000216061.5	37																																																																																				G|0.976;A|0.024	0.024	strong		0.687	PPP6R2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316809.1	NM_014678		A	50874851	G	A	50874851	2	1	22	1	0	0	0	0	0	0	0	1	13852	1103	39	1		1	SAPS2	22	50874851	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	122593	50874851	429715	4427	7328											
SBF1	6305	hgsc.bcm.edu	37	chr22	50899103	50899103	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttacggaagagctcggcgctGtcagaccccacctcctcgtc	7	8	10	16	4	1	2	1	0	0	2	5	3	2	3	4	2	2	2	4	2	2	1	rs77064034	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50899103G>A	ENST00000390679.3	-	24	3190	c.3006C>T	c.(3004-3006)gaC>gaT	p.D1002D	SBF1_ENST00000348911.6_Silent_p.D1003D|SBF1_ENST00000380817.3_Silent_p.D1002D			O95248	MTMR5_HUMAN	SET binding factor 1	1002					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)		GCTCGGCGCTGTCAGACCCCA	0.627													G|||	99	0.0197684	0.0711	0.0072	5008	,	,		16560	0.0		0.0	False		,,,				2504	0.0				p.D1002D		Atlas-SNP	.											.	SBF1	211	.	0			c.C3006T						PASS	.	G		270,3750		8,254,1748	87	92	90		3006	-3.9	1	22	dbSNP_131	90	1,8301		0,1,4150	no	coding-synonymous	SBF1	NM_002972.2		8,255,5898	AA,AG,GG		0.012,6.7164,2.1993		1002/1894	50899103	271,12051	2010	4151	6161	SO:0001819	synonymous_variant	6305	exon24			GGCGCTGTCAGAC	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.3006C>T	22.37:g.50899103G>A		96	0	0		96	43	0.447917	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Silent	SNP	ENST00000390679.3	37																																																																																				G|0.990;A|0.010	0.010	strong		0.627	SBF1-201	KNOWN	basic	protein_coding	protein_coding				A	50899103	G	A	50899103	2	1	22	1	0	0	0	0	0	0	0	1	13873	1368	48	2		2	SBF1	22	50899103	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	24252	50899103	405463	4428	7329											
ASMTL	8623	hgsc.bcm.edu	37	chrX	1522325	1522325	+	Missense_Mutation	SNP	C	C	T																															tcagtgactgcatcagggcgCgctgcgccaccctcttctcc																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:1522325C>T	ENST00000381317.3	-	13	1735	c.1703G>A	c.(1702-1704)cGc>cAc	p.R568H	ASMTL_ENST00000534940.1_Missense_Mutation_p.R510H|ASMTL_ENST00000381333.4_Missense_Mutation_p.R552H|ASMTL-AS1_ENST00000420411.2_RNA|ASMTL-AS1_ENST00000602357.1_RNA|ASMTL_ENST00000416733.2_Missense_Mutation_p.R492H|ASMTL-AS1_ENST00000419737.2_RNA|ASMTL-AS1_ENST00000443929.1_RNA|ASMTL-AS1_ENST00000425740.2_RNA	NM_004192.3	NP_004183.2	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	568	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)				CATCAGGGCGCGCTGCGCCAC	0.652													c|||	99	0.0197684	0.0726	0.0043	5008	,	,		19958	0.0		0.0	False		,,,				2504	0.0				p.R568H		Atlas-SNP	.											.	ASMTL	56	.	0			c.G1703A						PASS	.		HIS/ARG,HIS/ARG,HIS/ARG	309,3951		11,287,1832	78	86	84		1529,1655,1703	1.3	0	X	dbSNP_134	84	4,8470		0,4,4233	no	missense,missense,missense	ASMTL	NM_001173473.1,NM_001173474.1,NM_004192.3	29,29,29	11,291,6065	TT,TC,CC		0.0472,7.2535,2.458	possibly-damaging,possibly-damaging,possibly-damaging	510/564,552/606,568/622	1522325	313,12421	2130	4237	6367	SO:0001583	missense	8623	exon13			AGGGCGCGCTGCG	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.1703G>A	X.37:g.1522325C>T	ENSP00000370718:p.Arg568His	151	0	0		192	100	0.520833	NM_004192	B4DX75|F5GXH4|J3JS33|Q5JQ53|Q8NBH5|Q96G02|Q9BUL6	Missense_Mutation	SNP	ENST00000381317.3	37	CCDS43917.1	50	0.022893772893772892	50	0.1016260162601626	0	0.0	0	0.0	0	0.0	c	4.831	0.154519	0.09236	0.072535	4.72E-4	ENSG00000169093	ENST00000416733;ENST00000534940;ENST00000381333;ENST00000381317	T;T;T;T	0.22743	1.94;1.94;1.94;1.94	1.31	1.31	0.21738	O-methyltransferase, family 2 (1);	0.432093	0.20024	U	0.100843	T	0.00724	0.0024	L	0.50333	1.59	0.25285	N	0.989409	D;D;D	0.76494	0.998;0.999;0.999	D;D;P	0.64506	0.926;0.909;0.908	T	0.04481	-1.0948	10	0.13108	T	0.6	.	5.3914	0.16245	0.0:0.6424:0.3576:0.0	.	492;552;568	E7ER97;O95671-2;O95671	.;.;ASML_HUMAN	H	492;510;552;568	ENSP00000410578:R492H;ENSP00000446410:R510H;ENSP00000370734:R552H;ENSP00000370718:R568H	ENSP00000370718:R568H	R	-	2	0	ASMTL	1482325	0.000000	0.05858	0.001000	0.08648	0.046000	0.14306	-2.266000	0.01171	0.693000	0.31634	0.115000	0.15696	CGC	C|0.977;T|0.023	0.023	strong		0.652	ASMTL-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055595.1	NM_004192		T	1522325	C	T	1522325	3	4	22	1	0	0	0	0	1	0	0	0	1046	768	27	1	166	1	ASMTL	23	1522325	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10		1522325	153748235	4429	7330	96	2									
ASMTL	8623	hgsc.bcm.edu	37	chrX	1522330	1522330	+	Silent	SNP	C	C	T																															gactgcatcagggcgcgctgCgccaccctcttctcctcatc																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:1522330C>T	ENST00000381317.3	-	13	1730	c.1698G>A	c.(1696-1698)gcG>gcA	p.A566A	ASMTL_ENST00000534940.1_Silent_p.A508A|ASMTL_ENST00000381333.4_Silent_p.A550A|ASMTL-AS1_ENST00000420411.2_RNA|ASMTL-AS1_ENST00000602357.1_RNA|ASMTL_ENST00000416733.2_Silent_p.A490A|ASMTL-AS1_ENST00000419737.2_RNA|ASMTL-AS1_ENST00000443929.1_RNA|ASMTL-AS1_ENST00000425740.2_RNA	NM_004192.3	NP_004183.2	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	566	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)				GGGCGCGCTGCGCCACCCTCT	0.652													c|||	79	0.0157748	0.059	0.0014	5008	,	,		19966	0.0		0.0	False		,,,				2504	0.0				p.A566A		Atlas-SNP	.											.	ASMTL	56	.	0			c.G1698A						PASS	.		,,	259,3999		9,241,1879	76	84	81		1524,1650,1698	0.3	0	X	dbSNP_134	81	2,8470		0,2,4234	no	coding-synonymous,coding-synonymous,coding-synonymous	ASMTL	NM_001173473.1,NM_001173474.1,NM_004192.3	,,	9,243,6113	TT,TC,CC		0.0236,6.0827,2.0503	,,	508/564,550/606,566/622	1522330	261,12469	2129	4236	6365	SO:0001819	synonymous_variant	8623	exon13			GCGCTGCGCCACC	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.1698G>A	X.37:g.1522330C>T		154	0	0		189	98	0.518519	NM_004192	B4DX75|F5GXH4|J3JS33|Q5JQ53|Q8NBH5|Q96G02|Q9BUL6	Silent	SNP	ENST00000381317.3	37	CCDS43917.1																																																																																			C|0.982;T|0.018	0.018	strong		0.652	ASMTL-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055595.1	NM_004192		T	1522330	C	T	1522330	2	4	22	1	0	0	0	0	0	0	0	1	1046	755	27	1		1	ASMTL	23	1522330	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	5	1522330	153748230	4430	7331	96	2									
ASMTL	8623	hgsc.bcm.edu	37	chrX	1531701	1531701	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtcatgcaggatccggcaCaggacgtacagctcagcgct	10	6	12	13	3	2	0	2	0	0	0	3	2	3	2	1	3	4	5	1	3	1	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:1531701C>T	ENST00000381317.3	-	12	1601	c.1569G>A	c.(1567-1569)ctG>ctA	p.L523L	ASMTL_ENST00000534940.1_Silent_p.L465L|ASMTL_ENST00000381333.4_Silent_p.L507L|ASMTL-AS1_ENST00000420411.2_RNA|ASMTL-AS1_ENST00000602357.1_RNA|ASMTL_ENST00000416733.2_Silent_p.L447L|ASMTL-AS1_ENST00000419737.2_RNA|ASMTL-AS1_ENST00000425740.2_RNA	NM_004192.3	NP_004183.2	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	523	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)				GGATCCGGCACAGGACGTACA	0.562													c|||	95	0.0189696	0.0703	0.0014	5008	,	,		16507	0.0		0.001	False		,,,				2504	0.0				p.L523L		Atlas-SNP	.											.	ASMTL	56	.	0			c.G1569A						PASS	.		,,	280,3766		9,262,1752	160	174	169		1395,1521,1569	-1.9	0	X	dbSNP_134	169	2,8348		0,2,4173	no	coding-synonymous,coding-synonymous,coding-synonymous	ASMTL	NM_001173473.1,NM_001173474.1,NM_004192.3	,,	9,264,5925	TT,TC,CC		0.024,6.9204,2.2749	,,	465/564,507/606,523/622	1531701	282,12114	2023	4175	6198	SO:0001819	synonymous_variant	8623	exon12			CCGGCACAGGACG	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.1569G>A	X.37:g.1531701C>T		404	1	0.00247525		448	211	0.470982	NM_004192	B4DX75|F5GXH4|J3JS33|Q5JQ53|Q8NBH5|Q96G02|Q9BUL6	Silent	SNP	ENST00000381317.3	37	CCDS43917.1																																																																																			C|0.981;T|0.019	0.019	strong		0.562	ASMTL-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055595.1	NM_004192		T	1531701	C	T	1531701	2	4	22	1	0	0	0	0	0	0	0	1	1046	465	17	2		2	ASMTL	23	1531701	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	9371	1531701	153738859	4431	7332											
NLGN4X	57502	hgsc.bcm.edu	37	chrX	5821468	5821468	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tacatgaacttgatagtctcCcgcaaagtgtctttcccttc	9	14	6	12	1	2	2	0	2	2	0	5	2	3	2	2	0	2	1	2	0	4	5	rs61741754	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:5821468C>G	ENST00000381095.3	-	5	1878	c.1251G>C	c.(1249-1251)cgG>cgC	p.R417R	NLGN4X_ENST00000275857.6_Silent_p.R417R|NLGN4X_ENST00000381093.2_Silent_p.R437R|NLGN4X_ENST00000381092.1_Silent_p.R417R|NLGN4X_ENST00000538097.1_Silent_p.R417R	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	417					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						TGATAGTCTCCCGCAAAGTGT	0.542													c|||	232	0.061457	0.1604	0.0259	3775	,	,		12595	0.0		0.002	False		,,,				2504	0.0				p.R417R		Atlas-SNP	.											.	NLGN4X	191	.	0			c.G1251C						PASS	.	G	,	580,2948		38,395,109,1058,437	6	7	7		1251,1251	-1.2	0	X	dbSNP_134	7	4,6426		0,4,0,2331,1760	no	coding-synonymous,coding-synonymous	NLGN4X	NM_020742.2,NM_181332.1	,	38,399,109,3389,2197	GG,GC,G,CC,C		0.0622,16.4399,5.8646	,	417/817,417/817	5821468	584,9374	2037	4095	6132	SO:0001819	synonymous_variant	57502	exon5			AGTCTCCCGCAAA	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.1251G>C	X.37:g.5821468C>G		173	0	0		229	125	0.545852	NM_181332	Q6UX10|Q9ULG0	Silent	SNP	ENST00000381095.3	37	CCDS14126.1																																																																																			C|0.870;G|0.130	0.130	strong		0.542	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742		G	5821468	C	G	5821468	2	3	22	1	0	0	0	0	0	0	0	1	10473	610	22	4		4	NLGN4X	23	5821468	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4289767	5821468	149449092	4432	7333											
FAM9A	171482	hgsc.bcm.edu	37	chrX	8764370	8764370	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttggttttcctgtaagctgCtttatctatttttatcattt	6	23	5	7	0	2	0	1	0	1	0	3	0	3	0	1	1	2	4	1	1	4	11	rs148031370	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:8764370C>T	ENST00000543214.1	-	6	562	c.427G>A	c.(427-429)Gca>Aca	p.A143T	FAM9A_ENST00000381003.3_Missense_Mutation_p.A143T	NM_001171186.1	NP_001164657.1	Q8IZU1	FAM9A_HUMAN	family with sequence similarity 9, member A	143						nucleus (GO:0005634)				endometrium(11)|kidney(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	18		Hepatocellular(5;0.219)				CTGTAAGCTGCTTTATCTATT	0.294													c|||	11	0.00291391	0.0	0.0	3775	,	,		13462	0.0		0.0099	False		,,,				2504	0.001				p.A143T		Atlas-SNP	.											.	FAM9A	57	.	0			c.G427A						PASS	.	T	THR/ALA,THR/ALA	2,3833		0,2,0,1630,571	163	125	138		427,427	-0.3	0	X	dbSNP_134	138	35,6691		0,24,11,2404,1859	yes	missense,missense	FAM9A	NM_001171186.1,NM_174951.3	58,58	0,26,11,4034,2430	TT,TC,T,CC,C		0.5204,0.0522,0.3503	possibly-damaging,possibly-damaging	143/333,143/333	8764370	37,10524	2203	4298	6501	SO:0001583	missense	171482	exon6			AAGCTGCTTTATC		CCDS14131.1	Xp22.32	2012-11-29			ENSG00000183304	ENSG00000183304			18403	protein-coding gene	gene with protein product	"testis expressed 39A"	300477					Standard	NM_174951		Approved	TEX39A	uc004csg.3	Q8IZU1	OTTHUMG00000021110	ENST00000543214.1:c.427G>A	X.37:g.8764370C>T	ENSP00000440163:p.Ala143Thr	148	0	0		140	65	0.464286	NM_174951	B7ZLH5|Q2M2D1	Missense_Mutation	SNP	ENST00000543214.1	37	CCDS14131.1	8	0.004822182037371911	0	0.0	0	0.0	0	0.0	6	0.007957559681697613	c	5.235	0.228805	0.09916	5.22E-4	0.005204	ENSG00000183304	ENST00000381003;ENST00000543214	.	.	.	0.678	-0.327	0.12694	.	.	.	.	.	T	0.21307	0.0513	N	0.22421	0.69	0.09310	N	1	D	0.58620	0.983	P	0.53861	0.736	T	0.17379	-1.0371	7	0.14656	T	0.56	.	.	.	.	.	143	Q8IZU1	FAM9A_HUMAN	T	143	.	ENSP00000370391:A143T	A	-	1	0	FAM9A	8724370	0.971000	0.33674	0.000000	0.03702	0.005000	0.04900	0.178000	0.16820	-0.205000	0.10219	0.458000	0.33432	GCA	C|0.996;T|0.004	0.004	strong		0.294	FAM9A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055697.1	NM_174951		T	8764370	C	T	8764370	3	4	22	1	0	0	0	0	1	0	0	0	5667	797	28	2	587	2	FAM9A	23	8764370	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2942902	8764370	146506190	4433	7334											
SHROOM2	357	hgsc.bcm.edu	37	chrX	9863929	9863929	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggaggcggaggatggcaccGgccgctggagggccgggttg	5	4	23	9	4	0	0	0	0	0	0	0	4	0	4	3	9	0	3	3	9	0	1	rs146519576	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:9863929G>A	ENST00000380913.3	+	4	2071	c.1981G>A	c.(1981-1983)Ggc>Agc	p.G661S		NM_001649.2	NP_001640.1	Q13796	SHRM2_HUMAN	shroom family member 2	661					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)				GGATGGCACCGGCCGCTGGAG	0.652													G|||	6	0.0015894	0.0038	0.0014	3775	,	,		11713	0.0		0.0	False		,,,				2504	0.0				p.G661S		Atlas-SNP	.											.	SHROOM2	139	.	0			c.G1981A						PASS	.	G	SER/GLY	8,3745		0,6,2,1598,543	10	10	10		1981	1.2	0	X	dbSNP_134	10	4,6600		0,4,0,2400,1796	yes	missense	SHROOM2	NM_001649.2	56	0,10,2,3998,2339	AA,AG,A,GG,G		0.0606,0.2132,0.1159	benign	661/1617	9863929	12,10345	2149	4200	6349	SO:0001583	missense	357	exon4			GGCACCGGCCGCT	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.1981G>A	X.37:g.9863929G>A	ENSP00000370299:p.Gly661Ser	106	0	0		138	63	0.456522	NM_001649	B9EIQ7	Missense_Mutation	SNP	ENST00000380913.3	37	CCDS14135.1	.	.	.	.	.	.	.	.	.	.	G	4.289	0.052893	0.08291	0.002132	6.06E-4	ENSG00000146950	ENST00000380913	T	0.39406	1.08	4.92	1.21	0.21127	Apx/shroom, ASD1 (1);	1.413420	0.04081	N	0.309622	T	0.28830	0.0715	L	0.44542	1.39	0.20196	N	0.999928	P	0.40398	0.716	B	0.25405	0.06	T	0.18335	-1.0340	10	0.11485	T	0.65	-1.4736	9.2772	0.37707	0.3048:0.0:0.6952:0.0	.	661	Q13796	SHRM2_HUMAN	S	661	ENSP00000370299:G661S	ENSP00000370299:G661S	G	+	1	0	SHROOM2	9823929	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.067000	0.14510	-0.181000	0.10619	-1.129000	0.01985	GGC	G|0.998;A|0.002	0.002	strong		0.652	SHROOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055721.1	NM_001649		A	9863929	G	A	9863929	3	1	22	1	0	0	0	0	1	0	0	0	14309	1116	39	1	1995	1	SHROOM2	23	9863929	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1099559	9863929	145406631	4434	7335											
WWC3	55841	hgsc.bcm.edu	37	chrX	10085227	10085227	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtccctagcctccagccgTgggtctctggcctccagccg	3	8	13	17	2	1	0	0	0	1	0	5	0	4	0	7	3	3	0	7	3	1	1	rs7058143	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:10085227T>C	ENST00000380861.4	+	11	1519	c.1128T>C	c.(1126-1128)cgT>cgC	p.R376R	WWC3_ENST00000454666.1_Silent_p.R376R	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	376	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						CCTCCAGCCGTGGGTCTCTGG	0.672													C|||	774	0.205033	0.5401	0.0648	3775	,	,		12301	0.0		0.0149	False		,,,				2504	0.0				p.R376R		Atlas-SNP	.											.	WWC3	142	.	0			c.T1128C						PASS	.	C		2272,1558		575,780,342,277,224	36	44	41		1128	-3.3	0.3	X	dbSNP_116	41	142,6583		0,105,37,2323,1832	no	coding-synonymous	WWC3	NM_015691.3		575,885,379,2600,2056	CC,CT,C,TT,T		2.1115,40.6789,22.8707		376/1093	10085227	2414,8141	2198	4297	6495	SO:0001819	synonymous_variant	55841	exon11			CAGCCGTGGGTCT	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.1128T>C	X.37:g.10085227T>C		106	0	0		123	51	0.414634	NM_015691	A8KA96|Q659C1|Q9BTQ1	Silent	SNP	ENST00000380861.4	37	CCDS14136.1																																																																																			0|0.004;C|0.221	0.221	strong		0.672	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691		C	10085227	T	C	10085227	2	2	22	1	0	0	0	0	0	0	0	1	17428	1683	59	3		3	WWC3	23	10085227	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	221298	10085227	145185333	4435	7336											
WWC3	55841	hgsc.bcm.edu	37	chrX	10106971	10106971	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcctgctgcgggaggccgagCggcaggtgggggtcccctgt	3	6	20	12	3	0	0	0	0	0	0	1	2	1	1	4	6	3	2	4	6	0	0	rs377116582		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:10106971C>T	ENST00000380861.4	+	21	3470	c.3079C>T	c.(3079-3081)Cgg>Tgg	p.R1027W	WWC3_ENST00000454666.1_Missense_Mutation_p.R1027W	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	1027					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						GGAGGCCGAGCGGCAGGTGGG	0.711																																					p.R1027W		Atlas-SNP	.											.	WWC3	142	.	0			c.C3079T						PASS	.	C	TRP/ARG	2,3724		0,1,1,1592,539	8	9	9		3079	-6.4	0.5	X		9	1,6500		0,1,0,2373,1753	no	missense	WWC3	NM_015691.3	101	0,2,1,3965,2292	TT,TC,T,CC,C		0.0154,0.0537,0.0293	probably-damaging	1027/1093	10106971	3,10224	2133	4127	6260	SO:0001583	missense	55841	exon21			GCCGAGCGGCAGG	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.3079C>T	X.37:g.10106971C>T	ENSP00000370242:p.Arg1027Trp	10	0	0		19	16	0.842105	NM_015691	A8KA96|Q659C1|Q9BTQ1	Missense_Mutation	SNP	ENST00000380861.4	37	CCDS14136.1	.	.	.	.	.	.	.	.	.	.	C	18.48	3.632188	0.67015	5.37E-4	1.54E-4	ENSG00000047644	ENST00000380861;ENST00000454666;ENST00000543412	T;T	0.44482	0.92;0.92	4.8	-6.37	0.01963	.	0.044151	0.85682	D	0.000000	T	0.56396	0.1982	M	0.67953	2.075	0.43032	D	0.994601	D	0.76494	0.999	D	0.74348	0.983	T	0.64748	-0.6334	9	.	.	.	-20.9116	18.8956	0.92421	0.2618:0.7382:0.0:0.0	.	1027	Q9ULE0	WWC3_HUMAN	W	1027;1027;522	ENSP00000370242:R1027W;ENSP00000399584:R1027W	.	R	+	1	2	WWC3	10066971	1.000000	0.71417	0.517000	0.27799	0.613000	0.37349	2.008000	0.40893	-1.390000	0.02087	-0.436000	0.05848	CGG	.	.	weak		0.711	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691		T	10106971	C	T	10106971	3	4	22	1	0	0	0	0	1	0	0	0	17428	759	27	1	3157	1	WWC3	23	10106971	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	21744	10106971	145163589	4436	7337											
BMX	660	hgsc.bcm.edu	37	chrX	15555339	15555339	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagtggtccagctgggcaaGtggaaggggcagtatgatgt	9	8	19	5	0	0	1	0	1	0	0	1	3	1	3	1	6	1	4	1	6	3	1	rs376617024		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:15555339G>A	ENST00000357607.2	+	14	1493	c.1305G>A	c.(1303-1305)aaG>aaA	p.K435K	BMX_ENST00000348343.6_Silent_p.K435K|BMX_ENST00000342014.6_Silent_p.K435K			P51813	BMX_HUMAN	BMX non-receptor tyrosine kinase	435	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)					AGCTGGGCAAGTGGAAGGGGC	0.473													g|||	2	0.000529801	0.0	0.0	3775	,	,		13134	0.002		0.0	False		,,,				2504	0.0				p.K435K		Atlas-SNP	.											.	BMX	73	.	0			c.G1305A						PASS	.	G	,	1,3834		0,1,1631,571	187	167	174		1305,1305	3.5	1	X		174	0,6728		0,0,2428,1872	no	coding-synonymous,coding-synonymous	BMX	NM_001721.6,NM_203281.2	,	0,1,4059,2443	AA,AG,GG,G		0.0,0.0261,0.0095	,	435/676,435/676	15555339	1,10562	2203	4300	6503	SO:0001819	synonymous_variant	660	exon14			GGGCAAGTGGAAG	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.1305G>A	X.37:g.15555339G>A		177	0	0		217	100	0.460829	NM_001721	A6NIH9|O60564|Q12871	Silent	SNP	ENST00000357607.2	37	CCDS14168.1																																																																																			.	.	weak		0.473	BMX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055877.1	NM_001721		A	15555339	G	A	15555339	2	1	22	1	0	0	0	0	0	0	0	1	1473	1020	36	2		2	BMX	23	15555339	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5448368	15555339	139715221	4437	7338											
EIF2S3	1968	hgsc.bcm.edu	37	chrX	24073785	24073785	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttatcagcagacaagccacAattaacataggtaagagtaa	18	8	8	7	0	1	2	1	0	0	2	1	2	1	2	1	1	3	4	1	1	7	5	rs56229020	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:24073785A>G	ENST00000253039.4	+	2	376	c.123A>G	c.(121-123)acA>acG	p.T41T		NM_001415.3	NP_001406.1	P41091	IF2G_HUMAN	eukaryotic translation initiation factor 2, subunit 3 gamma, 52kDa	41	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				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						GACAAGCCACAATTAACATAG	0.348													A|||	10	0.00264901	0.0061	0.0014	3775	,	,		16856	0.0		0.001	False		,,,				2504	0.0				p.T41T		Atlas-SNP	.											.	EIF2S3	31	.	0			c.A123G						PASS	.	A		20,3815		0,19,1,1613,570	86	71	76		123	0.8	1	X	dbSNP_129	76	3,6725		0,2,1,2426,1871	no	coding-synonymous	EIF2S3	NM_001415.3		0,21,2,4039,2441	GG,GA,G,AA,A		0.0446,0.5215,0.2177		41/473	24073785	23,10540	2203	4300	6503	SO:0001819	synonymous_variant	1968	exon2			AGCCACAATTAAC	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.123A>G	X.37:g.24073785A>G		364	0	0		370	169	0.456757	NM_001415	B5BTZ4	Silent	SNP	ENST00000253039.4	37	CCDS14210.1	4	0.0024110910186859553	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	A	9.881	1.201486	0.22121	0.005215	4.46E-4	ENSG00000130741	ENST00000423068	.	.	.	4.68	0.75	0.18387	.	.	.	.	.	T	0.42877	0.1222	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29458	-1.0011	4	.	.	.	.	4.9157	0.13844	0.6333:0.0:0.2319:0.1348	rs56229020	.	.	.	D	41	.	.	N	+	1	0	EIF2S3	23983706	0.992000	0.36948	1.000000	0.80357	0.903000	0.53119	0.389000	0.20751	0.110000	0.17919	0.339000	0.21740	AAT	A|0.998;G|0.002	0.002	strong		0.348	EIF2S3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056079.1	NM_001415		G	24073785	A	G	24073785	2	3	22	1	0	0	0	0	0	0	0	1	5013	117	5	3		3	EIF2S3	23	24073785	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	8518446	24073785	131196775	4438	7339											
FAM48B2	170067	hgsc.bcm.edu	37	chrX	24329793	24329793	+	IGR	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgcccggcagctggacggCgcctgctagctttaataaga	8	7	14	12	4	0	1	0	0	0	1	0	2	0	2	2	4	3	4	2	4	3	4	rs139232512		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:24329793C>T								AC096509.1 (24999 upstream) : AC004552.1 (37132 downstream)																							AGCTGGACGGCGCCTGCTAGC	0.637													C|||	170	0.0450331	0.1218	0.013	3775	,	,		10526	0.0		0.0	False		,,,				2504	0.0				p.R547H		Atlas-SNP	.											.	.	.	.	0			c.G1640A						PASS	.	C	HIS/ARG	385,2240		27,253,78,778,431	11	11	11		1640	-1	0	X	dbSNP_134	11	4,5486		0,4,0,1912,1658	yes	missense	FAM48B2	NM_001136233.1	29	27,257,78,2690,2089	TT,TC,T,CC,C		0.0729,14.6667,4.7936	possibly-damaging	547/818	24329793	389,7726	1567	3574	5141	SO:0001628	intergenic_variant	170067	exon1			GGACGGCGCCTGC																													X.37:g.24329793C>T		194	0	0		223	129	0.578475	NM_001136233		Missense_Mutation	SNP		37																																																																																				C|0.963;T|0.037	0.037	strong	0	0.637									T	24329793	C	T	24329793	1	4	22	0	1	0	0	0	0	0	0	0	5582	768	27	1		1	FAM48B2	23	24329793	IGR	SNP	C	TCGA-G8-6324-01A-11D-2210-10	256008	24329793	130940767	4439	7340											
DCAF8L2	347442	hgsc.bcm.edu	37	chrX	27765405	27765405	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggggaggaggaggaagaggaGgaggaggaggaggaggagga	14	0	27	0	0	0	1	0	0	0	1	0	13	0	13	0	13	0	0	0	13	1	0			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:27765405G>A	ENST00000451261.2	+	5	792	c.393G>A	c.(391-393)gaG>gaA	p.E131E		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	131	Glu-rich.									central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						aggaagaggaggaggaggagg	0.562																																					p.E131E		Atlas-SNP	.											.	DCAF8L2	79	.	0			c.G393A						PASS	.						20	18	18					X																	27765405		692	1587	2279	SO:0001819	synonymous_variant	347442	exon1			AGAGGAGGAGGAG		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.393G>A	X.37:g.27765405G>A		45	0	0		56	7	0.125	NM_001136533	B2RXH9|J3KT06	Silent	SNP	ENST00000451261.2	37	CCDS59162.1																																																																																			.	.	none		0.562	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354		A	27765405	G	A	27765405	2	1	22	1	0	0	0	0	0	0	0	1	4280	991	35	2		2	DCAF8L2	23	27765405	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3435612	27765405	127505155	4440	7341											
DCAF8L2	347442	hgsc.bcm.edu	37	chrX	27766474	27766474	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggagtgagtttgtagtgagcGgtagtgattgcgggcacatc	8	11	17	5	2	0	3	0	3	0	0	1	4	0	4	0	3	2	4	0	3	2	4	rs375048390		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:27766474G>A	ENST00000451261.2	+	5	1861	c.1462G>A	c.(1462-1464)Ggt>Agt	p.G488S		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	488										central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						TGTAGTGAGCGGTAGTGATTG	0.438													G|||	1	0.000264901	0.0008	0.0	3775	,	,		15465	0.0		0.0	False		,,,				2504	0.0				p.G488S		Atlas-SNP	.											.	DCAF8L2	79	.	0			c.G1462A						PASS	.	G	SER/GLY	2,1207		0,1,1,516,174	86	63	70		1462	3.8	0.8	X		70	0,2391		0,0,0,800,791	no	missense	DCAF8L2	NM_001136533.1	56	0,1,1,1316,965	AA,AG,A,GG,G		0.0,0.1654,0.0556	probably-damaging	488/632	27766474	2,3598	692	1591	2283	SO:0001583	missense	347442	exon1			GTGAGCGGTAGTG		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.1462G>A	X.37:g.27766474G>A	ENSP00000462745:p.Gly488Ser	295	1	0.00338983		250	138	0.552	NM_001136533	B2RXH9|J3KT06	Missense_Mutation	SNP	ENST00000451261.2	37	CCDS59162.1																																																																																			.	.	weak		0.438	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354		A	27766474	G	A	27766474	3	1	22	1	0	0	0	0	1	0	0	0	4280	1116	39	1	1464	1	DCAF8L2	23	27766474	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1069	27766474	127504086	4441	7342											
FTHL17	53940	hgsc.bcm.edu	37	chrX	31089873	31089873	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcctcatcagcttctgggcAtgctccattttgtcgtccga	6	13	9	13	2	3	0	2	0	1	0	6	1	5	0	3	1	3	3	3	1	0	3	rs73617043	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:31089873A>T	ENST00000359202.3	-	1	297	c.198T>A	c.(196-198)caT>caA	p.H66Q		NM_031894.2	NP_114100.1	Q9BXU8	FHL17_HUMAN	ferritin, heavy polypeptide-like 17	66	Ferritin-like diiron. {ECO:0000255|PROSITE-ProRule:PRU00085}.				cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)		ferric iron binding (GO:0008199)			endometrium(2)|large_intestine(2)|liver(1)|lung(13)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	23						GCTTCTGGGCATGCTCCATTT	0.592													A|||	11	0.00291391	0.0083	0.0	3775	,	,		13041	0.0		0.0	False		,,,				2504	0.0				p.H66Q		Atlas-SNP	.											.	FTHL17	99	.	0			c.T198A						PASS	.	A	GLN/HIS	31,3802		0,27,4,1604,567	73	66	69		198	-3.3	0	X	dbSNP_130	69	0,6728		0,0,0,2428,1872	yes	missense	FTHL17	NM_031894.2	24	0,27,4,4032,2439	TT,TA,T,AA,A		0.0,0.8088,0.2935	benign	66/184	31089873	31,10530	2202	4300	6502	SO:0001583	missense	53940	exon1			CTGGGCATGCTCC	AF285592	CCDS14227.1	Xp21.2	2010-07-06			ENSG00000132446	ENSG00000132446			3987	protein-coding gene	gene with protein product	"cancer/testis antigen 38"	300308				11279525	Standard	NM_031894		Approved	CT38	uc004dcl.1	Q9BXU8	OTTHUMG00000021332	ENST00000359202.3:c.198T>A	X.37:g.31089873A>T	ENSP00000368207:p.His66Gln	180	0	0		186	87	0.467742	NM_031894	Q6NT24|Q6NTE2	Missense_Mutation	SNP	ENST00000359202.3	37	CCDS14227.1	8	0.004822182037371911	5	0.0102880658436214	0	0.0	0	0.0	0	0.0	A	10.22	1.290499	0.23478	0.008088	0.0	ENSG00000132446	ENST00000359202	T	0.72051	-0.62	3.44	-3.29	0.05017	Ferritin/ribonucleotide reductase-like (1);Ferritin-related (1);Ferritin/DPS protein domain (1);Ferritin-like (1);	0.401704	0.26156	N	0.026011	T	0.48804	0.1520	M	0.70595	2.14	0.21220	N	0.999756	B	0.32800	0.385	B	0.29353	0.101	T	0.48822	-0.9001	10	0.59425	D	0.04	.	1.8231	0.03115	0.4037:0.1354:0.331:0.1299	.	66	Q9BXU8	FHL17_HUMAN	Q	66	ENSP00000368207:H66Q	ENSP00000368207:H66Q	H	-	3	2	FTHL17	30999794	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	-1.291000	0.02775	-1.082000	0.03101	-1.413000	0.01118	CAT	A|0.996;T|0.004	0.004	strong		0.592	FTHL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056178.1	NM_031894		T	31089873	A	T	31089873	3	4	22	1	0	0	0	0	1	0	0	0	6091	214	8	5	357	5	FTHL17	23	31089873	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	3323399	31089873	124180687	4442	7343											
DMD	1756	hgsc.bcm.edu	37	chrX	32466654	32466654	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtttcaagttccttttttaaGgcctcttgtgctacaggtgg	6	17	10	8	0	2	0	1	0	1	0	3	0	3	0	2	3	2	3	2	3	3	7	rs143628111	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:32466654G>A	ENST00000357033.4	-	27	3911	c.3705C>T	c.(3703-3705)gcC>gcT	p.A1235A	DMD_ENST00000378677.2_Silent_p.A1231A	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	1235					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)				CCTTTTTTAAGGCCTCTTGTG	0.438													G|||	71	0.0188079	0.0537	0.0	3775	,	,		13391	0.0		0.0	False		,,,				2504	0.0				p.A1235A		Atlas-SNP	.											.	DMD	2127	.	0			c.C3705T						PASS	.	G	,,,,	183,3650		3,143,34,1485,537	199	158	172		3681,3705,3336,3693,3336	4	1	X	dbSNP_134	172	2,6725		0,2,0,2426,1871	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DMD	NM_000109.3,NM_004006.2,NM_004007.2,NM_004009.3,NM_004010.3	,,,,	3,145,34,3911,2408	AA,AG,A,GG,G		0.0297,4.7743,1.7519	,,,,	1227/3678,1235/3686,1112/3563,1231/3682,1112/3563	32466654	185,10375	2202	4299	6501	SO:0001819	synonymous_variant	1756	exon27			TTTTAAGGCCTCT	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.3705C>T	X.37:g.32466654G>A		269	0	0		258	127	0.492248	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Silent	SNP	ENST00000357033.4	37	CCDS14233.1																																																																																			G|0.983;A|0.017	0.017	strong		0.438	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		A	32466654	G	A	32466654	2	1	22	1	0	0	0	0	0	0	0	1	4582	987	35	2		2	DMD	23	32466654	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1376781	32466654	122803906	4443	7344											
DMD	1756	hgsc.bcm.edu	37	chrX	32716110	32716110	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tatccctgtgctagactgacCgtgatctgcagagaagggtt	9	11	12	9	1	1	4	0	2	1	2	2	5	2	4	2	1	2	3	2	1	3	3	rs1800265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:32716110C>T	ENST00000357033.4	-	9	1043	c.837G>A	c.(835-837)acG>acA	p.T279T	DMD_ENST00000288447.4_Silent_p.T271T|DMD_ENST00000378677.2_Silent_p.T275T	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	279			T -> A (in CMD3B). {ECO:0000269|PubMed:9170407}.		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)				CTAGACTGACCGTGATCTGCA	0.488													T|||	570	0.150993	0.3805	0.0865	3775	,	,		11752	0.002		0.002	False		,,,				2504	0.0031				p.T279T		Atlas-SNP	.											.	DMD	2127	.	0			c.G837A						PASS	.	T	,,,,	1838,1995		386,779,287,466,284	105	73	84		813,837,468,825,468	-1.6	1	X	dbSNP_89	84	21,6701		0,17,4,2410,1864	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DMD	NM_000109.3,NM_004006.2,NM_004007.2,NM_004009.3,NM_004010.3	,,,,	386,796,291,2876,2148	TT,TC,T,CC,C		0.3124,47.952,17.6125	,,,,	271/3678,279/3686,156/3563,275/3682,156/3563	32716110	1859,8696	2202	4295	6497	SO:0001819	synonymous_variant	1756	exon9			ACTGACCGTGATC	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.837G>A	X.37:g.32716110C>T		121	0	0		150	77	0.513333	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Silent	SNP	ENST00000357033.4	37	CCDS14233.1																																																																																			C|0.852;T|0.148	0.148	strong		0.488	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		T	32716110	C	T	32716110	2	4	22	1	0	0	0	0	0	0	0	1	4582	639	23	1		1	DMD	23	32716110	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	249456	32716110	122554450	4444	7345											
FAM47C	442444	hgsc.bcm.edu	37	chrX	37028762	37028762	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gcctcttgagactcgcgtatCtcatctccgcccggagcctc	5	10	9	17	4	3	1	1	1	3	1	7	3	3	2	4	1	1	1	4	1	1	2	rs61730910	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:37028762C>G	ENST00000358047.3	+	1	2331	c.2279C>G	c.(2278-2280)tCt>tGt	p.S760C		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	760										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						ACTCGCGTATCTCATCTCCGC	0.632													c|||	23	0.00609272	0.0166	0.0014	3775	,	,		11549	0.0		0.0	False		,,,				2504	0.0				p.S760C		Atlas-SNP	.											.	FAM47C	267	.	0			c.C2279G						PASS	.	C	CYS/SER	66,3767		3,52,8,1576,563	46	44	45		2279	0.9	0	X	dbSNP_129	45	0,6728		0,0,0,2428,1872	yes	missense	FAM47C	NM_001013736.2	112	3,52,8,4004,2435	GG,GC,G,CC,C		0.0,1.7219,0.6249	probably-damaging	760/1036	37028762	66,10495	2202	4300	6502	SO:0001583	missense	442444	exon1			GCGTATCTCATCT	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.2279C>G	X.37:g.37028762C>G	ENSP00000367913:p.Ser760Cys	123	0	0		150	80	0.533333	NM_001013736	Q6ZU46	Missense_Mutation	SNP	ENST00000358047.3	37	CCDS35227.1	8	0.004822182037371911	6	0.012244897959183673	1	0.0027624309392265192	0	0.0	0	0.0	-	5.654	0.305291	0.10678	0.017219	0.0	ENSG00000198173	ENST00000358047	T	0.20332	2.08	0.895	0.895	0.19247	.	.	.	.	.	T	0.21631	0.0521	M	0.81341	2.54	0.09310	N	1	D	0.58268	0.982	P	0.58873	0.847	T	0.08932	-1.0698	9	0.62326	D	0.03	.	3.8459	0.08934	0.0:0.67:0.0:0.33	rs61730910	760	Q5HY64	FA47C_HUMAN	C	760	ENSP00000367913:S760C	ENSP00000367913:S760C	S	+	2	0	FAM47C	36938683	0.005000	0.15991	0.002000	0.10522	0.002000	0.02628	0.436000	0.21526	0.163000	0.19507	0.165000	0.16767	TCT	C|0.993;G|0.007	0.007	strong		0.632	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736		G	37028762	C	G	37028762	3	3	22	1	0	0	0	0	1	0	0	0	5579	913	32	4	2281	4	FAM47C	23	37028762	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	4312652	37028762	118241798	4445	7346											
CYBB	1536	hgsc.bcm.edu	37	chrX	37663234	37663234	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aagtgcccaaaggtgtccaaGctggagtggcacccttttac	10	9	11	11	0	0	0	0	0	0	0	1	1	1	1	3	3	3	2	3	3	4	2	rs2228117	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:37663234G>A	ENST00000378588.4	+	9	1069	c.1002G>A	c.(1000-1002)aaG>aaA	p.K334K	CYBB_ENST00000492288.1_3'UTR|CYBB_ENST00000545017.1_Silent_p.K302K|CYBB_ENST00000536160.1_Silent_p.K67K|TM4SF2_ENST00000465127.1_Intron	NM_000397.3	NP_000388.2	P04839	CY24B_HUMAN	cytochrome b-245, beta polypeptide	334	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				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)	AGGTGTCCAAGCTGGAGTGGC	0.483													G|||	110	0.0291391	0.0719	0.0216	3775	,	,		14198	0.0		0.0	False		,,,				2504	0.0				p.K334K		Atlas-SNP	.											.	CYBB	62	.	0			c.G1002A						PASS	.	G		707,3126		70,466,101,1095,470	110	99	103		1002	-2.1	0.2	X	dbSNP_98	103	2,6726		0,2,0,2426,1872	no	coding-synonymous	CYBB	NM_000397.3		70,468,101,3521,2342	AA,AG,A,GG,G		0.0297,18.4451,6.7134		334/571	37663234	709,9852	2202	4300	6502	SO:0001819	synonymous_variant	1536	exon9			GTCCAAGCTGGAG	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.1002G>A	X.37:g.37663234G>A		324	1	0.00308642		367	190	0.517711	NM_000397	A8K138|Q2PP16	Silent	SNP	ENST00000378588.4	37	CCDS14242.1																																																																																			0|0.006;A|0.061	0.061	strong		0.483	CYBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080881.1			A	37663234	G	A	37663234	2	1	22	1	0	0	0	0	0	0	0	1	4135	962	34	2		2	CYBB	23	37663234	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	634472	37663234	117607326	4446	7347											
CXorf27	25763	hgsc.bcm.edu	37	chrX	37850385	37850385	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaccgtgagccccacagcgCtgagagtgatgtgactcgct	9	7	12	13	3	0	4	0	4	0	1	1	5	0	4	3	0	3	2	3	0	1	0	rs61737321		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:37850385C>T	ENST00000341016.3	+	1	316	c.293C>T	c.(292-294)gCt>gTt	p.A98V	TM4SF2_ENST00000465127.1_Intron	NM_012274.1	NP_036406.1	O75409	HYPM_HUMAN		98										central_nervous_system(2)|endometrium(3)|large_intestine(1)|lung(2)	8						CCCCACAGCGCTGAGAGTGAT	0.527													C|||	50	0.013245	0.0356	0.0043	3775	,	,		15106	0.0		0.0	False		,,,				2504	0.0				p.A98V		Atlas-SNP	.											.	CXorf27	14	.	0			c.C293T						PASS	.	C	VAL/ALA	116,3567		3,85,25,1468,546	99	104	102		293	-6.5	0	X	dbSNP_129	102	0,6600		0,0,0,2392,1816	yes	missense	CXorf27	NM_012274.1	64	3,85,25,3860,2362	TT,TC,T,CC,C		0.0,3.1496,1.1281	benign	98/118	37850385	116,10167	2127	4208	6335	SO:0001583	missense	25763	exon1			ACAGCGCTGAGAG																												ENST00000341016.3:c.293C>T	X.37:g.37850385C>T	ENSP00000339511:p.Ala98Val	152	0	0		209	105	0.502392	NM_012274	A1A4D3	Missense_Mutation	SNP	ENST00000341016.3	37	CCDS43929.1	10	0.006027727546714889	5	0.010245901639344262	2	0.005555555555555556	0	0.0	0	0.0	C	4.372	0.068603	0.08436	0.031496	0.0	ENSG00000187516	ENST00000341016	T	0.39787	1.06	3.24	-6.47	0.01902	Histone-fold (1);	.	.	.	.	T	0.04952	0.0133	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.13202	-1.0518	9	0.25751	T	0.34	.	1.5554	0.02583	0.1509:0.3307:0.3038:0.2146	rs61737321	98	O75409	HYPM_HUMAN	V	98	ENSP00000339511:A98V	ENSP00000339511:A98V	A	+	2	0	CXorf27	37735329	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.422000	0.02453	-1.678000	0.01454	-0.505000	0.04504	GCT	C|0.994;T|0.006	0.006	strong		0.527	CXorf27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080888.1			T	37850385	C	T	37850385	3	4	22	1	0	0	0	0	1	0	0	0	4107	797	28	2	295	2	CXorf27	23	37850385	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	187151	37850385	117420175	4447	7348											
SRPX	8406	hgsc.bcm.edu	37	chrX	38033415	38033415	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagagctggcctactcacgtTtgcagatgaccttgtcagac	9	10	10	12	1	2	4	2	1	0	3	2	4	2	4	2	1	3	3	2	1	1	3	rs35474361	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38033415T>C	ENST00000378533.3	-	3	453	c.347A>G	c.(346-348)aAa>aGa	p.K116R	SRPX_ENST00000538295.1_Missense_Mutation_p.K116R|TM4SF2_ENST00000465127.1_Intron|SRPX_ENST00000432886.2_Missense_Mutation_p.K116R|SRPX_ENST00000544439.1_Missense_Mutation_p.K96R|SRPX_ENST00000343800.6_Missense_Mutation_p.K103R	NM_006307.4	NP_006298.1	P78539	SRPX_HUMAN	sushi-repeat containing protein, X-linked	116	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				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						CTACTCACGTTTGCAGATGAC	0.493													T|||	274	0.0725828	0.1952	0.0231	3775	,	,		15221	0.0		0.0	False		,,,				2504	0.0				p.K116R		Atlas-SNP	.											.	SRPX	53	.	0			c.A347G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	901,2932		90,578,143,963,428	127	98	108		287,347,347,347	5.7	1	X	dbSNP_126	108	6,6722		0,5,1,2423,1871	yes	missense,missense,missense,missense	SRPX	NM_001170750.1,NM_001170751.1,NM_001170752.1,NM_006307.4	26,26,26,26	90,583,144,3386,2299	CC,CT,C,TT,T		0.0892,23.5064,8.5882	benign,benign,benign,benign	96/445,116/406,116/380,116/465	38033415	907,9654	2202	4300	6502	SO:0001583	missense	8406	exon3			TCACGTTTGCAGA	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.347A>G	X.37:g.38033415T>C	ENSP00000367794:p.Lys116Arg	120	0	0		112	56	0.5	NM_001170751	A8K065|B3KWP8|B4DDB8|B4DQH5|F5H4D7|G3V1L0|Q4VX66|Q99652|Q99913	Missense_Mutation	SNP	ENST00000378533.3	37	CCDS14245.1	83	0.050030138637733576	51	0.11486486486486487	7	0.019444444444444445	0	0.0	0	0.0	T	1.424	-0.572093	0.03882	0.235064	8.92E-4	ENSG00000101955	ENST00000544439;ENST00000432886;ENST00000538295;ENST00000378533;ENST00000343800	T;T;T;T;T	0.73897	1.88;-0.79;1.88;1.88;1.87	5.7	5.7	0.88788	Complement control module (1);Sushi/SCR/CCP (1);	0.137867	0.64402	D	0.000003	T	0.00039	0.0001	N	0.13043	0.29	0.24140	P	0.99573811	B;B;B;B	0.24618	0.007;0.107;0.058;0.071	B;B;B;B	0.27262	0.043;0.078;0.022;0.038	T	0.04281	-1.0963	9	0.07644	T	0.81	-13.8523	14.935	0.70948	0.0:0.0:0.0:1.0	rs35474361	116;116;96;116	F5H4D7;B4DQH5;G3V1L0;P78539	.;.;.;SRPX_HUMAN	R	96;116;116;116;103	ENSP00000440758:K96R;ENSP00000411165:K116R;ENSP00000445034:K116R;ENSP00000367794:K116R;ENSP00000339211:K103R	ENSP00000339211:K103R	K	-	2	0	SRPX	37918359	1.000000	0.71417	1.000000	0.80357	0.385000	0.30292	3.342000	0.52159	1.909000	0.55274	0.486000	0.48141	AAA	T|0.921;C|0.079	0.079	strong		0.493	SRPX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056243.1	NM_006307		C	38033415	T	C	38033415	3	2	22	1	0	0	0	0	1	0	0	0	15179	1841	64	3	1079	3	SRPX	23	38033415	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	183030	38033415	117237145	4448	7349											
RPGR	6103	hgsc.bcm.edu	37	chrX	38145199	38145201	+	Intron	DEL	TCC	TCC	-																															cctccccttccacttcccctTcctcttcttcctccccttct																								rs200955614		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38145199_38145201delTCC	ENST00000339363.3	-	14	2688				RPGR_ENST00000378505.2_In_Frame_Del_p.1017_1018EE>E|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000318842.7_Intron|RPGR_ENST00000342811.3_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						cacttccccttcctcttcttcct	0.581														38	0.0100662	0.0265	0.0043	3775	,	,		8305	0.0		0.0	False		,,,				2504	0.0				p.1018_1018del		Pindel	.											.	RPGR	175	.	0			c.3052_3054del	GRCh37	CD004123	orf15	D		PASS	.		,	173,3490		4,136,29,1439,476					,	-0.5	0			35	175,6221		2,108,63,2240,1633	no	coding,intron	RPGR	NM_001034853.1,NM_000328.2	,	6,244,92,3679,2109	A1A1,A1R,A1,RR,R		2.7361,4.7229,3.4596	,	,		348,9711				SO:0001627	intron_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.2520+1145GGA>-	X.37:g.38145199_38145201delTCC		29	0	.		55	10	0.182	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	In_Frame_Del	DEL	ENST00000339363.3	37																																																																																				TCC|0.992;-|0.008	0.008	strong		0.581	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328		-	38145201	TCC	-	38145199	6	5	22	0	1	1	0	1	0	0	0	0	13563	1783	62	0		0	RPGR	23	38145199	Intron	DEL	TCC	TCGA-G8-6324-01A-11D-2210-10	111784	38145199	117125361	4449	7350			13	36		5	5	720	N	TCCTCCTCTTCCCCCTCCCCTTCC_TCC_T_C	4.478898e-06
RPGR	6103	hgsc.bcm.edu	37	chrX	38145694	38145717	+	Intron	DEL	TCCTCCTCTTCCCCCTCCCCTTCC	TCCTCCTCTTCCCCCTCCCCTTCC	-																															cctcccctttcccttctcctTcctcctcttccccctcccct																										TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCCTCCTCTTCCCCCTCCCCTTCC	TCCTCCTCTTCCCCCTCCCCTTCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38145694_38145717delTCCTCCTCTTCCCCCTCCCCTTCC	ENST00000339363.3	-	14	2688				RPGR_ENST00000378505.2_In_Frame_Del_p.845_853EEGEGEEEE>E|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000318842.7_Intron|RPGR_ENST00000342811.3_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						cccttctccttcctcctcttccccctccccttcctcctcttccc	0.607																																					p.846_853del		Pindel	.											.	RPGR	175	.	0			c.2536_2559del	GRCh37	CD022920|CD077431|CI033306|CM004110|CM066945	orf15	D|I|M		PASS	.																																			SO:0001627	intron_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.2520+629GGAAGGGGAGGGGGAAGAGGAGGA>-	X.37:g.38145694_38145717delTCCTCCTCTTCCCCCTCCCCTTCC		100	0	.		120	24	0.2	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	In_Frame_Del	DEL	ENST00000339363.3	37																																																																																				.	.	none		0.607	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328		-	38145717	TCCTCCTCTTCCCCCTCCCCTTCC	-	38145694	6	5	22	0	1	1	0	1	0	0	0	0	13563	1783	62	0		0	RPGR	23	38145694	Intron	DEL	TCCTCCTCTTCCCCCTCCCCTTCC	TCGA-G8-6324-01A-11D-2210-10	495	38145694	117124866	4450	7351			13	36		5	5	720	N	TCCTCCTCTTCCCCCTCCCCTTCC_TCC_T_C	4.478898e-06
RPGR	6103	hgsc.bcm.edu	37	chrX	38145715	38145715	+	Intron	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcctcttccccctcccctTcctcctcttccccctcccct	0	13	0	28	0	2	0	0	0	2	0	9	0	9	0	12	0	0	0	12	0	0	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38145715T>C	ENST00000339363.3	-	14	2688				RPGR_ENST00000378505.2_Missense_Mutation_p.E846G|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000318842.7_Intron|RPGR_ENST00000342811.3_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						cccctccccttcctcctcttc	0.602																																					p.E846G		Atlas-SNP	.											.	RPGR	175	.	0			c.A2537G						PASS	.						39	26	31					X																	38145715		1741	3341	5082	SO:0001627	intron_variant	6103	exon15			TCCCCTTCCTCCT	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+631A>G	X.37:g.38145715T>C		113	0	0		115	8	0.0695652	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Missense_Mutation	SNP	ENST00000339363.3	37		.	.	.	.	.	.	.	.	.	.	t	5.065	0.197625	0.09652	.	.	ENSG00000156313	ENST00000378505	T	0.02525	4.26	1.54	1.54	0.23209	.	1.854680	0.04946	U	0.459387	T	0.04137	0.0115	L	0.50333	1.59	0.45676	D	0.998598	B	0.13594	0.008	B	0.06405	0.002	T	0.32745	-0.9895	10	0.66056	D	0.02	.	4.6898	0.12776	0.0:0.1904:0.0:0.8096	.	846	E9PE28	.	G	846	ENSP00000367766:E846G	ENSP00000367766:E846G	E	-	2	0	RPGR	38030659	0.004000	0.15560	0.004000	0.12327	0.000000	0.00434	0.336000	0.19823	0.671000	0.31185	0.000000	0.15137	GAA	.	.	none		0.602	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328		C	38145715	T	C	38145715	1	2	22	0	1	0	0	0	0	0	0	0	13563	1783	62	3		3	RPGR	23	38145715	Intron	SNP	T	TCGA-G8-6324-01A-11D-2210-10	21	38145715	117124845	4451	7352			13	36		5	5	720	N	TCCTCCTCTTCCCCCTCCCCTTCC_TCC_T_C	4.478898e-06
RPGR	6103	hgsc.bcm.edu	37	chrX	38145841	38145841	+	Intron	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctcctctttttcctcccctCtcccctctgtttcctcctct	0	18	1	22	0	4	0	0	0	4	0	10	0	9	0	9	0	0	1	9	0	0	3	rs147388235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38145841C>T	ENST00000339363.3	-	14	2688				RPGR_ENST00000378505.2_Missense_Mutation_p.R804K|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000318842.7_Intron|RPGR_ENST00000342811.3_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						ttcctcccctctcccctctgt	0.572													C|||	38	0.0100662	0.0265	0.0043	3775	,	,		7854	0.0		0.0	False		,,,				2504	0.0				p.R804K		Atlas-SNP	.											.	RPGR	175	.	0			c.G2411A						PASS	.		,LYS/ARG	114,3133		2,98,12,1355,325	209	149	170		,2411	-0.9	0	X	dbSNP_134	170	3,5559		0,0,3,2116,1327	yes	intron,missense	RPGR	NM_000328.2,NM_001034853.1	,26	2,98,15,3471,1652	TT,TC,T,CC,C		0.0539,3.5109,1.3282	,benign	,804/1153	38145841	117,8692	1792	3446	5238	SO:0001627	intron_variant	6103	exon15			TCCCCTCTCCCCT	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+505G>A	X.37:g.38145841C>T		469	1	0.0021322		522	236	0.452107	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Missense_Mutation	SNP	ENST00000339363.3	37		13	0.007836045810729355	9	0.018367346938775512	3	0.008287292817679558	0	0.0	0	0.0	c	5.090	0.202211	0.09652	0.035109	5.39E-4	ENSG00000156313	ENST00000378505	T	0.02301	4.35	2.0	-0.924	0.10462	.	0.274603	0.23272	U	0.050002	T	0.00300	0.0009	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46400	-0.9194	10	0.31617	T	0.26	.	4.6346	0.12518	0.0:0.4094:0.1765:0.4141	.	804	E9PE28	.	K	804	ENSP00000367766:R804K	ENSP00000367766:R804K	R	-	2	0	RPGR	38030785	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	0.188000	0.17018	-0.612000	0.05701	-0.921000	0.02739	AGA	C|0.985;T|0.015	0.015	strong		0.572	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328		T	38145841	C	T	38145841	1	4	22	0	1	0	0	0	0	0	0	0	13563	913	32	2		2	RPGR	23	38145841	Intron	SNP	C	TCGA-G8-6324-01A-11D-2210-10	126	38145841	117124719	4452	7353			13	36		5	5	720	N	TCCTCCTCTTCCCCCTCCCCTTCC_TCC_T_C	4.478898e-06
RPGR	6103	hgsc.bcm.edu	37	chrX	38145918	38145918	+	Intron	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctccttccccgctctttcCtcctttttcctctctccttc	0	19	1	21	1	2	0	0	0	2	0	11	0	9	0	8	0	0	1	8	0	0	5	rs201730068		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38145918C>T	ENST00000339363.3	-	14	2688				RPGR_ENST00000378505.2_Silent_p.E778E|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000318842.7_Intron|RPGR_ENST00000342811.3_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						ccgctctttcctcctttttcc	0.537																																					p.E778E		Atlas-SNP	.											.	RPGR	175	.	0			c.G2334A						PASS	.						315	191	233					X																	38145918		1858	3627	5485	SO:0001627	intron_variant	6103	exon15			TCTTTCCTCCTTT	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+428G>A	X.37:g.38145918C>T		459	0	0		294	15	0.0510204	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Silent	SNP	ENST00000339363.3	37																																																																																				.	.	none		0.537	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328		T	38145918	C	T	38145918	1	4	22	0	1	0	0	0	0	0	0	0	13563	680	24	2		2	RPGR	23	38145918	Intron	SNP	C	TCGA-G8-6324-01A-11D-2210-10	77	38145918	117124642	4453	7354			13	36		5	5	720	N	TCCTCCTCTTCCCCCTCCCCTTCC_TCC_T_C	4.478898e-06
OTC	5009	hgsc.bcm.edu	37	chrX	38260570	38260570	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcagtattggctcgagtgtaTaaacaatcagatttggacac	13	11	10	7	1	1	1	1	0	0	1	2	3	1	2	0	2	1	4	0	2	5	5	rs145777402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38260570T>C	ENST00000039007.4	+	5	581	c.429T>C	c.(427-429)taT>taC	p.Y143Y	OTC_ENST00000488812.1_3'UTR|TM4SF2_ENST00000465127.1_Intron	NM_000531.5	NP_000522.3	P00480	OTC_HUMAN	ornithine carbamoyltransferase	143					ammonia homeostasis (GO:0097272)|arginine biosynthetic process (GO:0006526)|cellular nitrogen compound metabolic process (GO:0034641)|citrulline biosynthetic process (GO:0019240)|liver development (GO:0001889)|midgut development (GO:0007494)|ornithine catabolic process (GO:0006593)|protein homotrimerization (GO:0070207)|response to biotin (GO:0070781)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|ornithine carbamoyltransferase activity (GO:0004585)|phosphate ion binding (GO:0042301)|phospholipid binding (GO:0005543)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22					L-Citrulline(DB00155)|L-Ornithine(DB00129)	CTCGAGTGTATAAACAATCAG	0.393													T|||	12	0.00317881	0.0091	0.0	3775	,	,		10235	0.0		0.0	False		,,,				2504	0.0				p.Y143Y		Atlas-SNP	.											.	OTC	60	.	0			c.T429C						PASS	.	T		45,3788		0,40,5,1591,566	103	78	86		429	-0.4	1	X	dbSNP_134	86	0,6728		0,0,0,2428,1872	no	coding-synonymous	OTC	NM_000531.5		0,40,5,4019,2438	CC,CT,C,TT,T		0.0,1.174,0.4261		143/355	38260570	45,10516	2202	4300	6502	SO:0001819	synonymous_variant	5009	exon5			AGTGTATAAACAA	K02100	CCDS14247.1	Xp21.1	2014-06-28			ENSG00000036473	ENSG00000036473	2.1.3.3		8512	protein-coding gene	gene with protein product		300461					Standard	NM_000531		Approved		uc004def.4	P00480	OTTHUMG00000022727	ENST00000039007.4:c.429T>C	X.37:g.38260570T>C		229	0	0		179	74	0.413408	NM_000531	A8K9P2|D3DWB0|Q3KNR1|Q6B0I1|Q9NYJ5	Silent	SNP	ENST00000039007.4	37	CCDS14247.1																																																																																			T|0.994;C|0.006	0.006	strong		0.393	OTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059006.2			C	38260570	T	C	38260570	2	2	22	1	0	0	0	0	0	0	0	1	11310	1413	49	3		3	OTC	23	38260570	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	114652	38260570	117009990	4454	7355											
ATP6AP2	10159	hgsc.bcm.edu	37	chrX	40464822	40464822	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctatattgtagaagaacccaGcaagtccctataaccttgca	14	10	6	11	0	0	2	0	0	0	2	1	2	1	2	3	0	4	3	3	0	8	7	rs35798522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:40464822G>C	ENST00000378438.4	+	9	1026	c.868G>C	c.(868-870)Gca>Cca	p.A290P	ATP6AP2_ENST00000535539.1_Missense_Mutation_p.A258P|ATP6AP2_ENST00000535777.1_Missense_Mutation_p.A212P|ATP6AP2_ENST00000544975.1_Missense_Mutation_p.A214P	NM_005765.2	NP_005756.2	O75787	RENR_HUMAN	ATPase, H+ transporting, lysosomal accessory protein 2	290			A -> P (in dbSNP:rs35798522).		angiotensin maturation (GO:0002003)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|eye pigmentation (GO:0048069)|head morphogenesis (GO:0060323)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of Wnt signaling pathway (GO:0030177)|proteolysis (GO:0006508)|regulation of MAPK cascade (GO:0043408)|rostrocaudal neural tube patterning (GO:0021903)	cell body (GO:0044297)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|receptor activity (GO:0004872)			endometrium(1)|large_intestine(1)|lung(2)	4						GAAGAACCCAGCAAGTCCCTA	0.343													G|||	83	0.0219868	0.0613	0.0029	3775	,	,		13663	0.0		0.0	False		,,,				2504	0.0				p.A290P		Atlas-SNP	.											.	ATP6AP2	45	.	0			c.G868C						PASS	.	G	PRO/ALA	239,3596		5,190,39,1437,532	61	57	58		868	-8.4	0	X	dbSNP_126	58	0,6726		0,0,0,2427,1872	yes	missense	ATP6AP2	NM_005765.2	27	5,190,39,3864,2404	CC,CG,C,GG,G		0.0,6.2321,2.263	benign	290/351	40464822	239,10322	2203	4299	6502	SO:0001583	missense	10159	exon9			AACCCAGCAAGTC	AF248966	CCDS14252.1	Xp11.4	2014-06-17	2003-08-28	2003-08-29	ENSG00000182220	ENSG00000182220			18305	protein-coding gene	gene with protein product	"prorenin receptor", "renin receptor"	300556	"ATPase, H+ transporting, lysosomal interacting protein 2"	ATP6IP2		9556572, 11590366	Standard	NM_005765		Approved	M8-9, APT6M8-9, ATP6M8-9, PRR, RENR	uc004det.3	O75787	OTTHUMG00000024103	ENST00000378438.4:c.868G>C	X.37:g.40464822G>C	ENSP00000367697:p.Ala290Pro	25	0	0		34	19	0.558824	NM_005765	B7Z9I3|Q5QTQ7|Q6T7F5|Q8NBP3|Q8NG15|Q96FV6|Q96LB5|Q9H2P8|Q9UG89	Missense_Mutation	SNP	ENST00000378438.4	37	CCDS14252.1	29|29	0.017480409885473176|0.017480409885473176	19|19	0.04025423728813559|0.04025423728813559	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	14.15|14.15	2.450072|2.450072	0.43531|0.43531	0.062321|0.062321	0.0|0.0	ENSG00000182220|ENSG00000182220	ENST00000535539;ENST00000378438;ENST00000544975;ENST00000535777|ENST00000423649	T;T;T;T|.	0.45276|.	0.9;0.9;0.9;0.9|.	5.65|5.65	-8.41|-8.41	0.00961|0.00961	.|.	1.054090|.	0.07412|.	N|.	0.892481|.	T|T	0.00845|0.00845	0.0028|0.0028	N|N	0.03608|0.03608	-0.345|-0.345	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B|.	0.29531|.	0.0;0.0;0.0;0.247|.	B;B;B;B|.	0.32289|.	0.0;0.002;0.0;0.143|.	T|T	0.15263|0.15263	-1.0443|-1.0443	9|4	0.28530|.	T|.	0.3|.	-34.4303|-34.4303	1.913|1.913	0.03291|0.03291	0.1093:0.2223:0.4974:0.171|0.1093:0.2223:0.4974:0.171	rs35798522|rs35798522	212;258;214;290|.	B7Z1I9;B7Z9I3;B7Z413;O75787|.	.;.;.;RENR_HUMAN|.	P|T	258;290;214;212|230	ENSP00000438415:A258P;ENSP00000367697:A290P;ENSP00000440459:A214P;ENSP00000441536:A212P|.	ENSP00000367697:A290P|.	A|S	+|+	1|2	0|0	ATP6AP2|ATP6AP2	40349766|40349766	0.019000|0.019000	0.18553|0.18553	0.000000|0.000000	0.03702|0.03702	0.689000|0.689000	0.40095|0.40095	1.088000|1.088000	0.30877|0.30877	-3.069000|-3.069000	0.00254|0.00254	0.600000|0.600000	0.82982|0.82982	GCA|AGC	G|0.977;C|0.023	0.023	strong		0.343	ATP6AP2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060679.1	NM_005765		C	40464822	G	C	40464822	3	2	22	1	0	0	0	0	1	0	0	0	1167	971	34	4	902	4	ATP6AP2	23	40464822	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2204252	40464822	114805738	4455	7356											
CXorf38	159013	hgsc.bcm.edu	37	chrX	40496354	40496354	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgaaaatctcgaagccacgTagaagatactttcatctctg	13	11	7	10	2	3	3	1	1	2	2	5	4	3	3	1	0	2	1	1	0	6	3	rs17145855	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:40496354T>C	ENST00000327877.5	-	4	552	c.526A>G	c.(526-528)Acg>Gcg	p.T176A	CXorf38_ENST00000378421.1_Missense_Mutation_p.T57A|CXorf38_ENST00000440784.2_Missense_Mutation_p.T91A|CXorf38_ENST00000378426.1_Missense_Mutation_p.T57A	NM_144970.2	NP_659407.1	Q8TB03	CX038_HUMAN	chromosome X open reading frame 38	176			T -> A (in dbSNP:rs17145855).							NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	12						CGAAGCCACGTAGAAGATACT	0.358													T|||	57	0.0150993	0.0424	0.0014	3775	,	,		14154	0.0		0.0	False		,,,				2504	0.0				p.T176A		Atlas-SNP	.											.	CXorf38	29	.	0			c.A526G						PASS	.	T	ALA/THR	179,3656		2,151,24,1479,547	56	51	53		526	-7.7	0	X	dbSNP_123	53	0,6728		0,0,0,2428,1872	yes	missense	CXorf38	NM_144970.2	58	2,151,24,3907,2419	CC,CT,C,TT,T		0.0,4.6675,1.6946	benign	176/320	40496354	179,10384	2203	4300	6503	SO:0001583	missense	159013	exon4			GCCACGTAGAAGA	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.526A>G	X.37:g.40496354T>C	ENSP00000330488:p.Thr176Ala	319	0	0		323	155	0.479876	NM_144970	B3KW28|D3DWB5|Q5JPF5|Q8N941	Missense_Mutation	SNP	ENST00000327877.5	37	CCDS14253.1	16	0.009644364074743821	9	0.01882845188284519	0	0.0	0	0.0	0	0.0	T	0.117	-1.130194	0.01756	0.046675	0.0	ENSG00000185753	ENST00000378426;ENST00000327877;ENST00000378421;ENST00000440784	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	4.95	-7.7	0.01259	.	1.658950	0.02974	N	0.144773	T	0.02610	0.0079	N	0.14661	0.345	0.34371	P	0.30793899999999996	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.10776	-1.0615	9	0.08837	T	0.75	0.4805	2.9505	0.05860	0.1431:0.3119:0.0909:0.4542	rs17145855;rs52818878;rs17145855	91;176	E7EN46;Q8TB03	.;CX038_HUMAN	A	57;176;57;91	ENSP00000367683:T57A;ENSP00000330488:T176A;ENSP00000367677:T57A;ENSP00000400019:T91A	ENSP00000330488:T176A	T	-	1	0	CXorf38	40381298	0.000000	0.05858	0.003000	0.11579	0.414000	0.31173	-1.312000	0.02720	-1.183000	0.02723	-0.537000	0.04273	ACG	0|0.003;C|0.018	0.018	strong		0.358	CXorf38-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060685.3	NM_144970		C	40496354	T	C	40496354	3	2	22	1	0	0	0	0	1	0	0	0	4109	1638	57	3	445	3	CXorf38	23	40496354	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	31532	40496354	114774206	4456	7357											
MED14	9282	hgsc.bcm.edu	37	chrX	40551993	40551993	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttggttctggtctgtttcccGgtttttgtacgaaaaaccaa	8	16	9	8	2	2	0	0	0	2	0	3	1	3	0	2	3	2	4	2	3	4	6	rs10127014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:40551993G>A	ENST00000324817.1	-	14	1930	c.1812C>T	c.(1810-1812)acC>acT	p.T604T		NM_004229.3	NP_004220.2	O60244	MED14_HUMAN	mediator complex subunit 14	604	Interaction with SREBF1.				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						TCTGTTTCCCGGTTTTTGTAC	0.433													G|||	105	0.0278146	0.0719	0.0029	3775	,	,		13717	0.0		0.0	False		,,,				2504	0.0082				p.T604T		Atlas-SNP	.											.	MED14	108	.	0			c.C1812T						PASS	.	G		275,3560		4,230,37,1398,534	137	113	121		1812	-9.3	0	X	dbSNP_119	121	0,6728		0,0,0,2428,1872	no	coding-synonymous	MED14	NM_004229.3		4,230,37,3826,2406	AA,AG,A,GG,G		0.0,7.1708,2.6034		604/1455	40551993	275,10288	2203	4300	6503	SO:0001819	synonymous_variant	9282	exon14			TTTCCCGGTTTTT	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.1812C>T	X.37:g.40551993G>A		178	0	0		236	128	0.542373	NM_004229	Q4KMR7|Q9UNB3	Silent	SNP	ENST00000324817.1	37	CCDS14254.1																																																																																			G|0.966;A|0.034	0.034	strong		0.433	MED14-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060692.1	NM_004229		A	40551993	G	A	40551993	2	1	22	1	0	0	0	0	0	0	0	1	9441	1103	39	1		1	MED14	23	40551993	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	55639	40551993	114718567	4457	7358											
DDX3X	1654	hgsc.bcm.edu	37	chrX	41204446	41204446	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atgacagatacttggtgttaGatgaagctgatcggatgttg	11	13	13	4	1	0	5	0	3	0	2	1	6	0	6	0	2	2	3	0	2	3	4			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:41204446G>C	ENST00000399959.2	+	11	1894	c.1039G>C	c.(1039-1041)Gat>Cat	p.D347H	RN7SL15P_ENST00000582825.1_RNA|DDX3X_ENST00000542215.1_3'UTR|DDX3X_ENST00000478993.1_3'UTR|DDX3X_ENST00000457138.2_Missense_Mutation_p.D331H|DDX3X_ENST00000441189.2_Intron	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	347	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.|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						CTTGGTGTTAGATGAAGCTGA	0.393										HNSCC(61;0.18)																											p.D347H		Atlas-SNP	.											.	DDX3X	138	.	0			c.G1039C						PASS	.						145	134	137					X																	41204446		2102	4246	6348	SO:0001583	missense	1654	exon11			GTGTTAGATGAAG	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.1039G>C	X.37:g.41204446G>C	ENSP00000382840:p.Asp347His	129	0	0		131	25	0.19084	NM_001193416	A8K538|B4E3E8|O15536	Missense_Mutation	SNP	ENST00000399959.2	37	CCDS43931.1	.	.	.	.	.	.	.	.	.	.	g	25.1	4.598675	0.87055	.	.	ENSG00000215301	ENST00000399959;ENST00000457138	T;T	0.55588	0.51;0.51	5.5	5.5	0.81552	RNA helicase, ATP-dependent, DEAD-box, conserved site (1);DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.099615	0.64402	D	0.000001	D	0.85106	0.5621	H	0.99299	4.505	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;0.997;0.997	D	0.91820	0.5466	10	0.87932	D	0	-16.0361	18.5127	0.90923	0.0:0.0:1.0:0.0	.	347;331;359;347	B4DLU5;B4E3E8;Q59GX6;O00571	.;.;.;DDX3X_HUMAN	H	347;331	ENSP00000382840:D347H;ENSP00000392494:D331H	ENSP00000382840:D347H	D	+	1	0	DDX3X	41089390	1.000000	0.71417	0.998000	0.56505	0.869000	0.49853	9.807000	0.99171	2.313000	0.78055	0.597000	0.82753	GAT	.	.	none		0.393	DDX3X-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056253.1	NM_024005		C	41204446	G	C	41204446	3	2	22	1	0	0	0	0	1	0	0	0	4360	942	33	4	1081	4	DDX3X	23	41204446	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	652453	41204446	114066114	4458	7359											
CXorf36	79742	hgsc.bcm.edu	37	chrX	45011018	45011018	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaggacttctgggtctgggCggatgctgtccccacactga	7	9	13	12	1	2	1	0	1	2	0	3	3	3	3	2	4	1	1	2	4	1	1	rs143817529		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:45011018C>A	ENST00000398000.2	-	5	1255	c.1181G>T	c.(1180-1182)cGc>cTc	p.R394L	CXorf36_ENST00000477281.1_5'UTR	NM_176819.3	NP_789789.2	Q9H7Y0	DIA1R_HUMAN	chromosome X open reading frame 36	394						extracellular region (GO:0005576)				endometrium(1)|large_intestine(2)|lung(4)	7						TGGGTCTGGGCGGATGCTGTC	0.572													C||||C|||	161|161	0.042649|0.042649	0.1188|0.1188	0.0043|0.0043	3775|3775	,|,	,|,		12325|12325	0.0|0.0		0.001|0.001	False|False		,,,|,,,				2504|2504	0.0|0.0				p.R394L		Atlas-SNP	.											.	CXorf36	53	.	0			c.G1181T						PASS	.	C	LEU/ARG	336,2291		19,221,77,819,432	63	57	59		1181	0.3	0	X	dbSNP_134	59	0,5498		0,0,0,1916,1666	yes	missense	CXorf36	NM_176819.3	102	19,221,77,2735,2098	AA,AC,A,CC,C		0.0,12.7903,4.1354	benign	394/434	45011018	336,7789	1568	3582	5150	SO:0001583	missense	79742	exon5			TCTGGGCGGATGC	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.1181G>T	X.37:g.45011018C>A	ENSP00000381086:p.Arg394Leu	121	0	0		109	108	0.990826	NM_176819	A8MUU5|B2RPN7|Q6UWJ5	Missense_Mutation	SNP	ENST00000398000.2	37	CCDS48096.1	50	0.030138637733574444	36	0.07692307692307693	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	1.583	-0.531173	0.04112	0.127903	0.0	ENSG00000147113	ENST00000398000	T	0.28895	1.59	5.17	0.326	0.15908	.	1.193830	0.06015	N	0.650241	T	0.00178	0.0005	N	0.16307	0.4	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.24476	-1.0159	9	0.27082	T	0.32	.	3.0329	0.06112	0.3241:0.4237:0.0931:0.1592	.	394	Q9H7Y0	CX036_HUMAN	L	394	ENSP00000381086:R394L	ENSP00000381086:R394L	R	-	2	0	CXorf36	44895962	0.000000	0.05858	0.001000	0.08648	0.055000	0.15305	-0.848000	0.04326	-0.006000	0.14370	-0.215000	0.12644	CGC	C|0.970;A|0.030	0.030	strong		0.572	CXorf36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056333.2	NM_024689		A	45011018	C	A	45011018	3	1	22	1	0	0	0	0	1	0	0	0	4108	768	27	4	124	4	CXorf36	23	45011018	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	3806572	45011018	110259542	4459	7360											
CXorf36	79742	hgsc.bcm.edu	37	chrX	45059838	45059838	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ttatttgattgatattctgaCcttatttcttctttaaagaa	11	21	4	5	0	3	4	0	3	3	1	3	4	3	4	1	0	0	0	1	0	6	10			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:45059838C>A	ENST00000398000.2	-	1	308		c.e1+1		RP11-342D14.1_ENST00000438181.1_RNA|CXorf36_ENST00000377934.4_Splice_Site|RP11-342D14.1_ENST00000450527.1_RNA	NM_176819.3	NP_789789.2	Q9H7Y0	DIA1R_HUMAN	chromosome X open reading frame 36							extracellular region (GO:0005576)				endometrium(1)|large_intestine(2)|lung(4)	7						GATATTCTGACCTTATTTCTT	0.368																																					.		Atlas-SNP	.											.	CXorf36	53	.	0			c.233+1G>T						PASS	.						45	43	43					X																	45059838		2203	4299	6502	SO:0001630	splice_region_variant	79742	exon2			TTCTGACCTTATT	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.233+1G>T	X.37:g.45059838C>A		155	0	0		127	67	0.527559	NM_176819	A8MUU5|B2RPN7|Q6UWJ5	Splice_Site	SNP	ENST00000398000.2	37	CCDS48096.1	.	.	.	.	.	.	.	.	.	.	C	17.24	3.340498	0.60963	.	.	ENSG00000147113	ENST00000398000;ENST00000377934	.	.	.	5.0	5.0	0.66597	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7275	0.77774	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CXorf36	44944782	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	5.738000	0.68613	2.074000	0.62210	0.415000	0.27848	.	.	.	none		0.368	CXorf36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056333.2	NM_024689	Intron	A	45059838	C	A	45059838	5	1	22	1	0	0	0	0	0	0	1	0	4108	521	18	4	1142	4	CXorf36	23	45059838	Splice_Site	SNP	C	TCGA-G8-6324-01A-11D-2210-10	48820	45059838	110210722	4460	7361											
RBM10	8241	hgsc.bcm.edu	37	chrX	47041414	47041414	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tactactatgacccccagacCggcctctactatgaccccaa	11	8	5	17	1	1	3	0	2	1	1	1	3	1	3	6	1	3	0	6	1	6	5	rs112102343	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47041414C>T	ENST00000377604.3	+	16	2500	c.1758C>T	c.(1756-1758)acC>acT	p.T586T	RBM10_ENST00000345781.6_Silent_p.T509T|RBM10_ENST00000329236.7_Silent_p.T508T	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	586	Tyr-rich.				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						ACCCCCAGACCGGCCTCTACT	0.602													C|||	41	0.0108609	0.028	0.0043	3775	,	,		13729	0.001		0.0	False		,,,				2504	0.0				p.T651T	Melanoma(171;120 2705 19495 39241)	Atlas-SNP	.											.	RBM10	117	.	0			c.C1953T						PASS	.		,,,,	149,3686		3,118,25,1511,546	84	75	78		1527,1755,1953,1758,1524	-8.1	0.9	X	dbSNP_132	78	2,6726		0,2,0,2426,1872	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RBM10	NM_001204466.1,NM_001204467.1,NM_001204468.1,NM_005676.4,NM_152856.2	,,,,	3,120,25,3937,2418	TT,TC,T,CC,C		0.0297,3.8853,1.4295	,,,,	509/854,585/930,651/996,586/931,508/853	47041414	151,10412	2203	4300	6503	SO:0001819	synonymous_variant	8241	exon16			CCAGACCGGCCTC	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.1758C>T	X.37:g.47041414C>T		111	0	0		144	73	0.506944	NM_001204468	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Silent	SNP	ENST00000377604.3	37	CCDS14274.1																																																																																			C|0.986;T|0.014	0.014	strong		0.602	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676		T	47041414	C	T	47041414	2	4	22	1	0	0	0	0	0	0	0	1	13126	639	23	1		1	RBM10	23	47041414	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1981576	47041414	108229146	4461	7362											
UBA1	7317	hgsc.bcm.edu	37	chrX	47070261	47070261	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcacaagctcaggagcgccGttctggtctgggcccaaacg	8	7	12	14	3	4	0	2	0	2	0	4	1	4	1	2	3	3	2	2	3	2	1	rs2230147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47070261G>A	ENST00000335972.6	+	19	2403	c.2220G>A	c.(2218-2220)ccG>ccA	p.P740P	UBA1_ENST00000377351.4_Silent_p.P740P|UBA1_ENST00000377269.3_Silent_p.P188P	NM_003334.3	NP_003325.2	P22314	UBA1_HUMAN	ubiquitin-like modifier activating enzyme 1	740					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						CAGGAGCGCCGTTCTGGTCTG	0.537													G|||	364	0.0964238	0.2648	0.0202	3775	,	,		14687	0.0		0.0	False		,,,				2504	0.0				p.P740P		Atlas-SNP	.											.	UBA1	89	.	0			c.G2220A						PASS	.	G	,	1067,2768		149,620,149,863,422	105	81	89		2220,2220	-9.5	0	X	dbSNP_98	89	14,6714		0,10,4,2418,1868	no	coding-synonymous,coding-synonymous	UBA1	NM_003334.3,NM_153280.2	,	149,630,153,3281,2290	AA,AG,A,GG,G		0.2081,27.8227,10.2338	,	740/1059,740/1059	47070261	1081,9482	2203	4300	6503	SO:0001819	synonymous_variant	7317	exon19			AGCGCCGTTCTGG	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.2220G>A	X.37:g.47070261G>A		177	0	0		180	94	0.522222	NM_153280	Q5JRR8|Q96E13	Silent	SNP	ENST00000335972.6	37	CCDS14275.1																																																																																			0|0.004;A|0.126	0.126	strong		0.537	UBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056389.1	NM_003334		A	47070261	G	A	47070261	2	1	22	1	0	0	0	0	0	0	0	1	16842	1132	40	1		1	UBA1	23	47070261	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	28847	47070261	108200299	4462	7363											
UBA1	7317	hgsc.bcm.edu	37	chrX	47070468	47070468	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actatgtgatggctgctgccAacctgtttgcccagacctac	8	11	9	13	0	0	2	0	1	0	1	0	2	0	2	4	1	5	3	4	1	3	3	rs143044923	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47070468A>C	ENST00000335972.6	+	20	2491	c.2308A>C	c.(2308-2310)Aac>Cac	p.N770H	UBA1_ENST00000377351.4_Missense_Mutation_p.N770H|UBA1_ENST00000377269.3_Missense_Mutation_p.N218H	NM_003334.3	NP_003325.2	P22314	UBA1_HUMAN	ubiquitin-like modifier activating enzyme 1	770					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						GGCTGCTGCCAACCTGTTTGC	0.622													A|||	15	0.00397351	0.0106	0.0014	3775	,	,		14662	0.0		0.0	False		,,,				2504	0.0				p.N770H		Atlas-SNP	.											.	UBA1	89	.	0			c.A2308C						PASS	.	A	HIS/ASN,HIS/ASN	80,3755		1,63,15,1568,556	94	71	79		2308,2308	4.7	1	X	dbSNP_134	79	1,6727		0,1,0,2427,1872	yes	missense,missense	UBA1	NM_003334.3,NM_153280.2	68,68	1,64,15,3995,2428	CC,CA,C,AA,A		0.0149,2.086,0.7668	probably-damaging,probably-damaging	770/1059,770/1059	47070468	81,10482	2203	4300	6503	SO:0001583	missense	7317	exon20			GCTGCCAACCTGT	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.2308A>C	X.37:g.47070468A>C	ENSP00000338413:p.Asn770His	128	0	0		143	69	0.482517	NM_153280	Q5JRR8|Q96E13	Missense_Mutation	SNP	ENST00000335972.6	37	CCDS14275.1	5	0.0030138637733574444	2	0.004098360655737705	0	0.0	0	0.0	0	0.0	A	21.3	4.124412	0.77436	0.02086	1.49E-4	ENSG00000130985	ENST00000377351;ENST00000335972;ENST00000377269	T;T;T	0.74632	-0.86;-0.86;-0.86	4.66	4.66	0.58398	Molybdenum cofactor biosynthesis, MoeB (1);Ubiquitin-like 1 activating enzyme, catalytic cysteine domain (1);	0.043287	0.85682	D	0.000000	T	0.82125	0.4969	H	0.95114	3.625	0.58432	D	0.999996	D;D	0.89917	0.999;1.0	D;D	0.91635	0.985;0.999	D	0.87031	0.2135	10	0.40728	T	0.16	-28.4035	12.3807	0.55305	1.0:0.0:0.0:0.0	.	218;770	Q5JRR6;P22314	.;UBA1_HUMAN	H	770;770;218	ENSP00000366568:N770H;ENSP00000338413:N770H;ENSP00000366481:N218H	ENSP00000338413:N770H	N	+	1	0	UBA1	46955412	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.197000	0.51028	1.837000	0.53436	0.430000	0.28490	AAC	A|0.994;C|0.006	0.006	strong		0.622	UBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056389.1	NM_003334		C	47070468	A	C	47070468	3	2	22	1	0	0	0	0	1	0	0	0	16842	130	5	5	2382	5	UBA1	23	47070468	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	207	47070468	108200092	4463	7364											
USP11	8237	hgsc.bcm.edu	37	chrX	47107038	47107038	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttgcctgcaacaaggacagCggccagtggcactactttga	10	9	11	11	1	0	1	0	1	0	0	0	2	0	2	2	3	5	2	2	3	3	3			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47107038C>T	ENST00000218348.3	+	20	2694	c.2694C>T	c.(2692-2694)agC>agT	p.S898S	USP11_ENST00000377107.2_Silent_p.S855S	NM_004651.3	NP_004642.2	P51784	UBP11_HUMAN	ubiquitin specific peptidase 11	898	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|ovary(3)|pancreas(1)|stomach(1)	40						ACAAGGACAGCGGCCAGTGGC	0.512																																					p.S898S		Atlas-SNP	.											.	USP11	93	.	0			c.C2694T						PASS	.						156	114	129					X																	47107038		2203	4300	6503	SO:0001819	synonymous_variant	8237	exon20			GGACAGCGGCCAG	U44839	CCDS14277.1	Xp11.23	2008-02-05	2005-08-08		ENSG00000102226	ENSG00000102226		"Ubiquitin-specific peptidases"	12609	protein-coding gene	gene with protein product		300050	"ubiquitin specific protease 11"			12838346	Standard	XM_005272674		Approved	UHX1	uc004dhp.3	P51784	OTTHUMG00000021437	ENST00000218348.3:c.2694C>T	X.37:g.47107038C>T		256	0	0		240	111	0.4625	NM_004651	B2RTX1|Q8IUG6|Q9BWE1	Silent	SNP	ENST00000218348.3	37	CCDS14277.1																																																																																			.	.	none		0.512	USP11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_004651		T	47107038	C	T	47107038	2	4	22	1	0	0	0	0	0	0	0	1	17057	767	27	1		1	USP11	23	47107038	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	36570	47107038	108163522	4464	7365											
ZNF157	7712	hgsc.bcm.edu	37	chrX	47272480	47272480	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tatgagtgtggtgaatgtggGaaattcttccgaatgaagat	12	13	13	3	1	1	4	0	3	1	1	2	6	2	5	1	2	0	0	1	2	5	3	rs61736399	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47272480G>A	ENST00000377073.3	+	4	1094	c.1008G>A	c.(1006-1008)ggG>ggA	p.G336G		NM_003446.3	NP_003437.2	P51786	ZN157_HUMAN	zinc finger protein 157	336					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						GTGAATGTGGGAAATTCTTCC	0.418													G|||	23	0.00609272	0.0144	0.0043	3775	,	,		15735	0.0		0.001	False		,,,				2504	0.0				p.G336G		Atlas-SNP	.											.	ZNF157	46	.	0			c.G1008A						PASS	.	G		119,3716		3,94,19,1535,552	39	37	38		1008	0.3	0.6	X	dbSNP_129	38	1,6726		0,1,0,2427,1871	no	coding-synonymous	ZNF157	NM_003446.3		3,95,19,3962,2423	AA,AG,A,GG,G		0.0149,3.103,1.1361		336/507	47272480	120,10442	2203	4299	6502	SO:0001819	synonymous_variant	7712	exon4			ATGTGGGAAATTC	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.1008G>A	X.37:g.47272480G>A		93	0	0		81	27	0.333333	NM_003446	Q96LE9	Silent	SNP	ENST00000377073.3	37	CCDS14278.1																																																																																			G|0.990;A|0.010	0.010	strong		0.418	ZNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056415.1	NM_003446		A	47272480	G	A	47272480	2	1	22	1	0	0	0	0	0	0	0	1	17752	1161	41	2		2	ZNF157	23	47272480	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	165442	47272480	107998080	4465	7366											
ZNF157	7712	hgsc.bcm.edu	37	chrX	47272970	47272970	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taggctggtcctggcgttgtAcaatgaagaaagcctctcac	10	10	11	10	1	1	2	1	1	1	1	3	2	2	2	2	3	2	3	2	3	5	3	rs61736398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47272970A>G	ENST00000377073.3	+	4	1584	c.1498A>G	c.(1498-1500)Aca>Gca	p.T500A		NM_003446.3	NP_003437.2	P51786	ZN157_HUMAN	zinc finger protein 157	500					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						CTGGCGTTGTACAATGAAGAA	0.493													A|||	37	0.00980132	0.025	0.0043	3775	,	,		14772	0.0		0.001	False		,,,				2504	0.0				p.T500A		Atlas-SNP	.											.	ZNF157	46	.	0			c.A1498G						PASS	.	A	ALA/THR	191,3644		3,153,32,1476,539	71	60	64		1498	-2	0	X	dbSNP_129	64	5,6723		0,4,1,2424,1871	yes	missense	ZNF157	NM_003446.3	58	3,157,33,3900,2410	GG,GA,G,AA,A		0.0743,4.9804,1.8555	benign	500/507	47272970	196,10367	2203	4300	6503	SO:0001583	missense	7712	exon4			CGTTGTACAATGA	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.1498A>G	X.37:g.47272970A>G	ENSP00000366273:p.Thr500Ala	150	0	0		139	53	0.381295	NM_003446	Q96LE9	Missense_Mutation	SNP	ENST00000377073.3	37	CCDS14278.1	12	0.007233273056057866	4	0.008264462809917356	2	0.005555555555555556	0	0.0	1	0.0013192612137203166	A	2.829	-0.243005	0.05906	0.049804	7.43E-4	ENSG00000147117	ENST00000377073	T	0.06068	3.35	2.85	-1.99	0.07457	.	.	.	.	.	T	0.00637	0.0021	N	0.16790	0.44	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28808	-1.0032	8	0.59425	D	0.04	.	9.8782	0.41216	0.2684:0.0:0.7316:0.0	rs61736398	500	P51786	ZN157_HUMAN	A	500	ENSP00000366273:T500A	ENSP00000366273:T500A	T	+	1	0	ZNF157	47157914	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.258000	0.08733	-0.564000	0.06070	-0.466000	0.05196	ACA	A|0.984;G|0.016	0.016	strong		0.493	ZNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056415.1	NM_003446		G	47272970	A	G	47272970	3	3	22	1	0	0	0	0	1	0	0	0	17752	391	14	3	1512	3	ZNF157	23	47272970	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	490	47272970	107997590	4466	7367											
ZNF41	7592	hgsc.bcm.edu	37	chrX	47308509	47308509	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctatgggggaaattgttaccAtttccaaaaatcttgccaag	13	12	8	8	0	1	0	0	0	1	0	2	1	2	1	3	2	2	1	3	2	6	5	rs34301930	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47308509A>C	ENST00000377065.4	-	5	1299	c.660T>G	c.(658-660)aaT>aaG	p.N220K	ZNF41_ENST00000397050.2_Missense_Mutation_p.N230K|ZNF41_ENST00000465311.1_5'Flank|ZNF41_ENST00000313116.7_Missense_Mutation_p.N220K	NM_153380.2	NP_700359.1	P51814	ZNF41_HUMAN	zinc finger protein 41	262					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)				AATTGTTACCATTTCCAAAAA	0.368													A|||	113	0.0299338	0.0832	0.0043	3775	,	,		14437	0.0		0.0	False		,,,				2504	0.0				p.N220K		Atlas-SNP	.											.	ZNF41	71	.	0			c.T660G						PASS	.	A	LYS/ASN,LYS/ASN	343,3492		8,285,42,1339,529	150	140	144		660,660	3.2	0.3	X	dbSNP_126	144	3,6725		0,3,0,2425,1872	yes	missense,missense	ZNF41	NM_007130.2,NM_153380.2	94,94	8,288,42,3764,2401	CC,CA,C,AA,A		0.0446,8.9439,3.2756	possibly-damaging,possibly-damaging	220/780,220/780	47308509	346,10217	2203	4300	6503	SO:0001583	missense	7592	exon5			GTTACCATTTCCA	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.660T>G	X.37:g.47308509A>C	ENSP00000366265:p.Asn220Lys	197	0	0		230	123	0.534783	NM_007130	A8K1V6|B4DH01|Q96LE8|Q9UMC4|Q9UMV5|Q9UMV6|Q9UMV7|Q9UMV8|Q9UMV9|Q9UMW0|Q9UMW1	Missense_Mutation	SNP	ENST00000377065.4	37	CCDS14279.1	36	0.0216998191681736	25	0.05296610169491525	0	0.0	0	0.0	0	0.0	A	4.551	0.102356	0.08731	0.089439	4.46E-4	ENSG00000147124	ENST00000313116;ENST00000377065;ENST00000397050	T;T;T	0.06068	3.35;3.35;3.35	3.2	3.2	0.36748	.	0.000000	0.37715	N	0.001972	T	0.00210	0.0006	N	0.08118	0	0.44254	P	0.0028960000000000097	P;P;B;P;P	0.50156	0.932;0.932;0.257;0.932;0.888	B;B;B;P;B	0.47981	0.424;0.424;0.074;0.563;0.36	T	0.37957	-0.9683	9	0.62326	D	0.03	.	9.1657	0.37050	1.0:0.0:0.0:0.0	rs34301930	220;222;230;254;262	P51814-6;P51814-2;P51814-3;P51814-5;P51814	.;.;.;.;ZNF41_HUMAN	K	220;220;230	ENSP00000315173:N220K;ENSP00000366265:N220K;ENSP00000380243:N230K	ENSP00000315173:N220K	N	-	3	2	ZNF41	47193453	0.000000	0.05858	0.255000	0.24374	0.075000	0.17131	0.061000	0.14366	1.514000	0.48869	0.412000	0.27726	AAT	A|0.966;C|0.034	0.034	strong		0.368	ZNF41-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056429.1	NM_153380		C	47308509	A	C	47308509	3	2	22	1	0	0	0	0	1	0	0	0	17904	214	8	5	1683	5	ZNF41	23	47308509	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	35539	47308509	107962051	4467	7368											
ELK1	2002	hgsc.bcm.edu	37	chrX	47498400	47498400	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcccctgcaggagctgcaCtggggagcaccacagcaggc	8	4	14	15	0	0	0	0	0	0	0	0	2	0	2	3	4	6	5	3	4	0	0	rs1059579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47498400C>T	ENST00000247161.3	-	3	647	c.548G>A	c.(547-549)aGt>aAt	p.S183N	ELK1_ENST00000592066.1_Missense_Mutation_p.S129N|ELK1_ENST00000376983.3_Missense_Mutation_p.S183N|ELK1_ENST00000343894.4_Intron	NM_005229.4	NP_005220.2	P19419	ELK1_HUMAN	ELK1, member of ETS oncogene family	183			S -> N (in dbSNP:rs1059579). {ECO:0000269|PubMed:2539641}.		cell differentiation (GO:0030154)|innate immune response (GO:0045087)|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 transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|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)	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)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|skin(2)	10						AGGAGCTGCACTGGGGAGCAC	0.672													T|||	537	0.142252	0.3366	0.0317	3775	,	,		12344	0.0625		0.005	False		,,,				2504	0.002				p.S183N		Atlas-SNP	.											.	ELK1	54	.	0			c.G548A						PASS	.	T	ASN/SER,ASN/SER	1349,2481		198,751,202,682,366	17	13	14		548,548	-0.9	0.3	X	dbSNP_86	14	28,6691		1,19,7,2407,1858	no	missense,missense	ELK1	NM_001114123.1,NM_005229.3	46,46	199,770,209,3089,2224	TT,TC,T,CC,C		0.4167,35.2219,13.0534	benign,benign	183/429,183/429	47498400	1377,9172	2199	4292	6491	SO:0001583	missense	2002	exon4			GCTGCACTGGGGA	M25269	CCDS14283.1, CCDS59165.1	Xp11.23	2010-07-20			ENSG00000126767	ENSG00000126767			3321	protein-coding gene	gene with protein product		311040				2539641	Standard	NM_001114123		Approved		uc010nhv.4	P19419	OTTHUMG00000021452	ENST00000247161.3:c.548G>A	X.37:g.47498400C>T	ENSP00000247161:p.Ser183Asn	186	0	0		180	59	0.327778	NM_001114123	B2R7H4|O75606|O95058|Q969X8|Q9UJM4	Missense_Mutation	SNP	ENST00000247161.3	37	CCDS14283.1	230	0.13863773357444242	123	0.33064516129032256	10	0.027932960893854747	26	0.046762589928057555	1	0.0013192612137203166	T	7.193	0.592017	0.13812	0.352219	0.004167	ENSG00000126767	ENST00000247161;ENST00000376983	T;T	0.21734	1.99;1.99	4.02	-0.858	0.10689	.	1.043230	0.07432	N	0.895821	T	0.00012	0.0000	N	0.02539	-0.55	0.09310	P	0.9999999769773	B	0.02656	0.0	B	0.01281	0.0	T	0.49679	-0.8914	9	0.16420	T	0.52	.	10.7665	0.46297	0.0:0.6834:0.0:0.3166	rs1059579	183	P19419	ELK1_HUMAN	N	183	ENSP00000247161:S183N;ENSP00000366182:S183N	ENSP00000247161:S183N	S	-	2	0	ELK1	47383344	0.256000	0.24012	0.318000	0.25279	0.616000	0.37450	-0.277000	0.08502	-0.454000	0.07066	-0.407000	0.06327	AGT	C|0.847;T|0.153	0.153	strong		0.672	ELK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056436.1	NM_005229		T	47498400	C	T	47498400	3	4	22	1	0	0	0	0	1	0	0	0	5061	565	20	2	754	2	ELK1	23	47498400	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	189891	47498400	107772160	4468	7369											
SLC38A5	92745	hgsc.bcm.edu	37	chrX	48326270	48326270	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgactcaccccacagcatcCgaagggagggctccattcat	10	7	9	15	1	2	1	2	1	0	0	4	3	4	2	4	2	1	2	4	2	1	1	rs34099520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:48326270C>T	ENST00000376876.3	-	2	885	c.42G>A	c.(40-42)tcG>tcA	p.S14S	SLC38A5_ENST00000376875.1_5'Flank|SLC38A5_ENST00000317669.5_Silent_p.S14S			Q8WUX1	S38A5_HUMAN	solute carrier family 38, member 5	14					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine transmembrane transporter activity (GO:0015187)			breast(1)|cervix(1)|endometrium(6)|large_intestine(2)|lung(5)|ovary(3)|skin(1)	19						CCACAGCATCCGAAGGGAGGG	0.557													C|||	15	0.00397351	0.0113	0.0	3775	,	,		13307	0.0		0.0	False		,,,				2504	0.0				p.S14S		Atlas-SNP	.											.	SLC38A5	98	.	0			c.G42A						PASS	.	C		45,3790		1,34,9,1597,562	58	47	51		42	-2.4	0	X	dbSNP_126	51	1,6725		0,0,1,2428,1869	no	coding-synonymous	SLC38A5	NM_033518.2		1,34,10,4025,2431	TT,TC,T,CC,C		0.0149,1.1734,0.4356		14/473	48326270	46,10515	2203	4298	6501	SO:0001819	synonymous_variant	92745	exon3			AGCATCCGAAGGG	AF276889	CCDS14293.1	Xp11.23	2013-05-22			ENSG00000017483	ENSG00000017483		"Solute carriers"	18070	protein-coding gene	gene with protein product		300649				11243884	Standard	NM_033518		Approved	SN2, JM24	uc010nid.3	Q8WUX1	OTTHUMG00000024117	ENST00000376876.3:c.42G>A	X.37:g.48326270C>T		121	0	0		145	64	0.441379	NM_033518	B3KT20|B5MDE6|B7WPJ9|Q6PIW9|Q8WYU2|Q96PQ4	Silent	SNP	ENST00000376876.3	37	CCDS14293.1																																																																																			C|0.997;T|0.003	0.003	strong		0.557	SLC38A5-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060724.1	NM_033518		T	48326270	C	T	48326270	2	4	22	1	0	0	0	0	0	0	0	1	14622	639	23	1		1	SLC38A5	23	48326270	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	827870	48326270	106944290	4469	7370											
WAS	7454	hgsc.bcm.edu	37	chrX	48546837	48546837	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgcggcaggagatgaggcGccagggtgagaccctgcttc	7	7	17	10	2	0	3	0	2	0	2	1	5	0	3	2	4	2	2	2	4	0	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:48546837G>A	ENST00000376701.4	+	9	1001	c.926G>A	c.(925-927)cGc>cAc	p.R309H		NM_000377.2	NP_000368.1	P42768	WASP_HUMAN	Wiskott-Aldrich syndrome	309					actin filament polymerization (GO:0030041)|actin filament-based movement (GO:0030048)|actin polymerization or depolymerization (GO:0008154)|blood coagulation (GO:0007596)|defense response (GO:0006952)|endosomal transport (GO:0016197)|epidermis development (GO:0008544)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|protein complex assembly (GO:0006461)|regulation of catalytic activity (GO:0050790)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|vesicle membrane (GO:0012506)	identical protein binding (GO:0042802)|phospholipase binding (GO:0043274)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|small GTPase regulator activity (GO:0005083)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	28		all_lung(315;1.27e-10)				GAGATGAGGCGCCAGGGTGAG	0.562			"Mis, N, F, S"			lymphoma																															p.R309H		Atlas-SNP	.		X-linked recessive		Wiskott-Aldrich syndrome	X	Xp11.23-p11.22	7454	Wiskott-Aldrich syndrome		L	.	WAS	51	.	0			c.G926A						PASS	.						41	35	37					X																	48546837		2203	4300	6503	SO:0001583	missense	7454	exon9			TGAGGCGCCAGGG	AF115548	CCDS14303.1	Xp11.4-p11.21	2014-09-17	2012-07-12		ENSG00000015285	ENSG00000015285			12731	protein-coding gene	gene with protein product	"eczema-thrombocytopenia"	300392	"thrombocytopenia 1 (X-linked)", "Wiskott-Aldrich syndrome (eczema-thrombocytopenia)"	IMD2, THC		7795648	Standard	NM_000377		Approved	WASP	uc004dkm.4	P42768	OTTHUMG00000034483	ENST00000376701.4:c.926G>A	X.37:g.48546837G>A	ENSP00000365891:p.Arg309His	238	0	0		255	68	0.266667	NM_000377	Q9BU11|Q9UNJ9	Missense_Mutation	SNP	ENST00000376701.4	37	CCDS14303.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.110307	0.77210	.	.	ENSG00000015285	ENST00000376701	D	0.95918	-3.85	4.71	4.71	0.59529	Wiscott-Aldrich syndrome, C-terminal (1);	0.055809	0.64402	D	0.000002	D	0.96679	0.8916	L	0.57536	1.79	0.43947	D	0.99661	D	0.89917	1.0	D	0.69142	0.962	D	0.97151	0.9831	10	0.72032	D	0.01	-11.737	14.3592	0.66757	0.0:0.0:1.0:0.0	.	309	P42768	WASP_HUMAN	H	309	ENSP00000365891:R309H	ENSP00000365891:R309H	R	+	2	0	WAS	48431781	1.000000	0.71417	0.997000	0.53966	0.961000	0.63080	4.816000	0.62642	2.055000	0.61198	0.431000	0.28591	CGC	.	.	none		0.562	WAS-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083379.1	NM_000377		A	48546837	G	A	48546837	3	1	22	1	0	0	0	0	1	0	0	0	17266	1087	38	1	960	1	WAS	23	48546837	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	220567	48546837	106723723	4470	7371											
GPKOW	27238	hgsc.bcm.edu	37	chrX	48970655	48970655	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cttggcagttgcaccaaagcCcggctccgtgctctgtcccg	5	9	11	16	3	1	0	0	0	1	0	3	0	3	0	4	2	3	5	4	2	1	2	rs34057359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:48970655C>T	ENST00000156109.5	-	11	1413	c.1335G>A	c.(1333-1335)cgG>cgA	p.R445R		NM_015698.4	NP_056513.2	Q92917	GPKOW_HUMAN	G patch domain and KOW motifs	445						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(2)	21						GCACCAAAGCCCGGCTCCGTG	0.562													C|||	409	0.108344	0.289	0.0375	3775	,	,		16222	0.0		0.001	False		,,,				2504	0.0				p.R445R		Atlas-SNP	.											.	GPKOW	38	.	0			c.G1335A						PASS	.	C		1294,2541		185,734,190,713,381	148	110	123		1335	0.5	0.4	X	dbSNP_126	123	8,6720		0,8,0,2420,1872	no	coding-synonymous	GPKOW	NM_015698.4		185,742,190,3133,2253	TT,TC,T,CC,C		0.1189,33.7419,12.326		445/477	48970655	1302,9261	2203	4300	6503	SO:0001819	synonymous_variant	27238	exon11			CAAAGCCCGGCTC	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.1335G>A	X.37:g.48970655C>T		231	0	0		207	102	0.492754	NM_015698	Q59EK5|Q9BQA8	Silent	SNP	ENST00000156109.5	37	CCDS35251.1																																																																																			C|0.873;T|0.127	0.127	strong		0.562	GPKOW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056535.2	NM_015698		T	48970655	C	T	48970655	2	4	22	1	0	0	0	0	0	0	0	1	6621	610	22	2		2	GPKOW	23	48970655	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	423818	48970655	106299905	4471	7372											
CACNA1F	778	hgsc.bcm.edu	37	chrX	49070329	49070329	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctgcccaccacaataagagCgtcaaacgtgttccaggcat	12	7	9	13	2	1	1	1	0	0	1	2	1	2	1	3	1	3	3	3	1	3	2	rs34308720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:49070329C>T	ENST00000376265.2	-	31	3836	c.3775G>A	c.(3775-3777)Gct>Act	p.A1259T	CACNA1F_ENST00000376251.1_Missense_Mutation_p.A1194T|CACNA1F_ENST00000323022.5_Missense_Mutation_p.A1248T	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	1259			A -> T (in dbSNP:rs34308720).		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)	ACAATAAGAGCGTCAAACGTG	0.512													c|||	16	0.00423841	0.0121	0.0	3775	,	,		15638	0.0		0.0	False		,,,				2504	0.0				p.A1259T		Atlas-SNP	.											.	CACNA1F	218	.	0			c.G3775A						PASS	.	C	THR/ALA	73,3762		0,64,9,1568,562	135	88	104		3775	5	1	X	dbSNP_126	104	0,6728		0,0,0,2428,1872	yes	missense	CACNA1F	NM_005183.2	58	0,64,9,3996,2434	TT,TC,T,CC,C		0.0,1.9035,0.6911	possibly-damaging	1259/1978	49070329	73,10490	2203	4300	6503	SO:0001583	missense	778	exon31			TAAGAGCGTCAAA	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.3775G>A	X.37:g.49070329C>T	ENSP00000365441:p.Ala1259Thr	116	0	0		117	55	0.470085	NM_005183	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Missense_Mutation	SNP	ENST00000376265.2	37	CCDS35253.1	4	0.0024110910186859553	3	0.006122448979591836	0	0.0	0	0.0	0	0.0	C	22.4	4.288051	0.80803	0.019035	0.0	ENSG00000102001	ENST00000376251;ENST00000323022;ENST00000376265	D;D;D	0.98400	-4.91;-4.91;-4.91	4.97	4.97	0.65823	Ion transport (1);	0.053644	0.64402	D	0.000001	D	0.96002	0.8698	L	0.28014	0.82	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.87578	0.998;0.973	D	0.94804	0.7973	10	0.72032	D	0.01	.	16.1084	0.81241	0.0:1.0:0.0:0.0	rs34308720	1248;1259	F5CIQ9;O60840	.;CAC1F_HUMAN	T	1194;1248;1259	ENSP00000365427:A1194T;ENSP00000321618:A1248T;ENSP00000365441:A1259T	ENSP00000321618:A1248T	A	-	1	0	CACNA1F	48957273	0.995000	0.38212	1.000000	0.80357	0.634000	0.38068	1.260000	0.32968	2.053000	0.61076	0.529000	0.55759	GCT	C|0.993;T|0.007	0.007	strong		0.512	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183		T	49070329	C	T	49070329	3	4	22	1	0	0	0	0	1	0	0	0	2545	768	27	1	2230	1	CACNA1F	23	49070329	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	99674	49070329	106200231	4472	7373											
PPP1R3F	89801	hgsc.bcm.edu	37	chrX	49142987	49142987	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcccgttctgtggtagccaCgatgggagatgtgtggctcc	5	10	16	10	2	1	1	0	0	1	1	2	3	2	1	3	4	1	3	3	4	1	2	rs372361395		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:49142987C>T	ENST00000055335.6	+	4	1851	c.1835C>T	c.(1834-1836)aCg>aTg	p.T612M	PPP1R3F_ENST00000495799.1_Missense_Mutation_p.T266M|PPP1R3F_ENST00000466508.1_Missense_Mutation_p.T266M|PPP1R3F_ENST00000376188.1_Missense_Mutation_p.T266M|PPP1R3F_ENST00000438316.1_Missense_Mutation_p.T283M	NM_033215.4	NP_149992.3	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory subunit 3F	612					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)					GTGGTAGCCACGATGGGAGAT	0.612													C|||	1	0.000264901	0.0	0.0	3775	,	,		12213	0.001		0.0	False		,,,				2504	0.0				p.T612M		Atlas-SNP	.											.	PPP1R3F	56	.	0			c.C1835T						PASS	.		MET/THR,MET/THR	1,3833		0,1,1631,570	36	26	29		797,1835	3.8	0.9	X		29	0,6728		0,0,2428,1872	no	missense,missense	PPP1R3F	NM_001184745.1,NM_033215.4	81,81	0,1,4059,2442	TT,TC,CC,C		0.0,0.0261,0.0095	probably-damaging,probably-damaging	266/454,612/800	49142987	1,10561	2202	4300	6502	SO:0001583	missense	89801	exon4			TAGCCACGATGGG		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.1835C>T	X.37:g.49142987C>T	ENSP00000055335:p.Thr612Met	89	0	0		110	54	0.490909	NM_033215	A2VDJ8|B3KPW2|E9PCM3	Missense_Mutation	SNP	ENST00000055335.6	37	CCDS35254.1	.	.	.	.	.	.	.	.	.	.	C	13.75	2.331209	0.41297	2.61E-4	0.0	ENSG00000049769	ENST00000466508;ENST00000438316;ENST00000055335;ENST00000495799;ENST00000376188	T;T;T;T;T	0.59224	0.7;0.71;0.28;0.7;0.7	4.71	3.82	0.43975	.	0.521490	0.17939	N	0.156901	T	0.60625	0.2283	L	0.27053	0.805	0.26861	N	0.967952	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.65987	0.917;0.917;0.94	T	0.53408	-0.8443	10	0.87932	D	0	-0.2653	10.192	0.43032	0.0:0.8014:0.1986:0.0	.	283;297;612	F5H262;A2VDJ8;Q6ZSY5	.;.;PPR3F_HUMAN	M	266;283;612;266;266	ENSP00000420687:T266M;ENSP00000415548:T283M;ENSP00000055335:T612M;ENSP00000417535:T266M;ENSP00000365359:T266M	ENSP00000055335:T612M	T	+	2	0	PPP1R3F	49029931	0.942000	0.31987	0.876000	0.34364	0.775000	0.43874	0.261000	0.18442	1.027000	0.39758	0.509000	0.49947	ACG	.	.	weak		0.612	PPP1R3F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060819.2	NM_033215		T	49142987	C	T	49142987	3	4	22	1	0	0	0	0	1	0	0	0	12387	536	19	1	1849	1	PPP1R3F	23	49142987	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	72658	49142987	106127573	4473	7374											
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50350751	50350751	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcctcctcctcctcctcctGttgcttctgctgctgctgtt	0	17	6	18	0	1	0	0	0	1	0	7	0	7	0	6	0	4	6	6	0	0	3	rs201290098		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:50350751G>C	ENST00000289292.7	-	6	3674	c.3391C>G	c.(3391-3393)Cag>Gag	p.Q1131E	SHROOM4_ENST00000376020.2_Missense_Mutation_p.Q1131E|SHROOM4_ENST00000460112.3_Missense_Mutation_p.Q1015E			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1131	Gln-rich.			KQQ -> QQQQKQQE (in Ref. 1; BAA86516 and 3; AAI51241). {ECO:0000305}.	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)					tcctcctcctgttgcttctgc	0.582																																					p.Q1131E		Atlas-SNP	.											.	SHROOM4	171	.	0			c.C3391G						PASS	.						15	14	15					X																	50350751		2199	4294	6493	SO:0001583	missense	57477	exon6			CCTCCTGTTGCTT	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.3391C>G	X.37:g.50350751G>C	ENSP00000289292:p.Gln1131Glu	111	0	0		70	6	0.0857143	NM_020717	A7E2X9|D6RFW0|Q96LA0	Missense_Mutation	SNP	ENST00000289292.7	37	CCDS35277.1	.	.	.	.	.	.	.	.	.	.	G	0.015	-1.554911	0.00918	.	.	ENSG00000158352	ENST00000289292;ENST00000376020;ENST00000460112	T;T;T	0.06449	3.3;3.3;3.3	4.89	-0.0454	0.13851	.	1.383290	0.04423	N	0.367895	T	0.03827	0.0108	N	0.24115	0.695	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.36456	-0.9747	10	0.02654	T	1	.	4.0399	0.09746	0.093:0.4322:0.3193:0.1556	.	1131	Q9ULL8	SHRM4_HUMAN	E	1131;1131;1015	ENSP00000289292:Q1131E;ENSP00000365188:Q1131E;ENSP00000421450:Q1015E	ENSP00000289292:Q1131E	Q	-	1	0	SHROOM4	50367491	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	0.374000	0.20501	-0.047000	0.13423	-0.434000	0.05882	CAG	.	.	weak		0.582	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		C	50350751	G	C	50350751	3	2	22	1	0	0	0	0	1	0	0	0	14311	1386	48	4	1106	4	SHROOM4	23	50350751	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1207764	50350751	104919809	4474	7375											
IQSEC2	23096	hgsc.bcm.edu	37	chrX	53263764	53263764	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggcaggactgtacaggggCagtggggatgtgggctggtg	6	7	23	5	0	0	0	0	0	0	0	0	2	0	2	0	9	1	4	0	9	1	1	rs184087864		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:53263764C>T	ENST00000375368.5	-	14	4274	c.4074G>A	c.(4072-4074)ctG>ctA	p.L1358L	IQSEC2_ENST00000396435.3_Silent_p.L1368L|IQSEC2_ENST00000375365.2_3'UTR			Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2	1358	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						TGTACAGGGGCAGTGGGGATG	0.672													c|||	294	0.0778808	0.2133	0.0173	3775	,	,		4478	0.0		0.0	False		,,,				2504	0.0				p.L1368L		Atlas-SNP	.											.	IQSEC2	195	.	0			c.G4104A						PASS	.						10	11	10					X																	53263764		689	1580	2269	SO:0001819	synonymous_variant	23096	exon15			CAGGGGCAGTGGG	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.4074G>A	X.37:g.53263764C>T		225	0	0		222	97	0.436937	NM_001111125	B3KT97|C7SDG1|O60275|Q5JUX1	Silent	SNP	ENST00000375368.5	37																																																																																				C|0.937;T|0.063	0.063	strong		0.672	IQSEC2-201	KNOWN	basic	protein_coding	protein_coding		XM_291345		T	53263764	C	T	53263764	2	4	22	1	0	0	0	0	0	0	0	1	7827	697	25	2		2	IQSEC2	23	53263764	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	2913013	53263764	102006796	4475	7376											
GNL3L	54552	hgsc.bcm.edu	37	chrX	54578725	54578725	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcccctatctcccaatgcagCgggaagatcagcttctatat	10	11	7	13	1	3	1	1	0	2	1	5	2	4	2	3	1	3	2	3	1	5	4	rs147602603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:54578725C>T	ENST00000336470.4	+	13	1321	c.1182C>T	c.(1180-1182)agC>agT	p.S394S	GNL3L_ENST00000360845.2_Splice_Site_p.S394S	NM_019067.5	NP_061940.1	Q9NVN8	GNL3L_HUMAN	guanine nucleotide binding protein-like 3 (nucleolar)-like	394					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						CCCAATGCAGCGGGAAGATCA	0.507													C|||	7	0.0018543	0.0053	0.0	3775	,	,		13898	0.0		0.0	False		,,,				2504	0.0				p.S394S		Atlas-SNP	.											.	GNL3L	73	.	0			c.C1182T						PASS	.	C	,	19,3816		0,17,2,1615,569	169	132	144		1182,1182	-7.2	0.4	X	dbSNP_134	144	0,6728		0,0,0,2428,1872	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	GNL3L	NM_001184819.1,NM_019067.5	,	0,17,2,4043,2441	TT,TC,T,CC,C		0.0,0.4954,0.1799	,	394/583,394/583	54578725	19,10544	2203	4300	6503	SO:0001630	splice_region_variant	54552	exon13			ATGCAGCGGGAAG	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.1182-1C>T	X.37:g.54578725C>T		207	0	0		204	93	0.455882	NM_001184819		Silent	SNP	ENST00000336470.4	37	CCDS14360.1																																																																																			C|0.998;T|0.002	0.002	strong		0.507	GNL3L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056805.1	NM_019067	Silent	T	54578725	C	T	54578725	5	4	22	1	0	0	0	0	0	0	1	0	6546	782	27	1	1228	1	GNL3L	23	54578725	Splice_Site	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1314961	54578725	100691835	4476	7377											
ITIH5L	347365	hgsc.bcm.edu	37	chrX	54783952	54783952	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcggtttaagagataataagAttttaggggtcttggacaag	13	13	12	3	1	1	2	0	0	1	2	2	4	1	3	0	4	0	1	0	4	5	7	rs150850201	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:54783952A>G	ENST00000218436.6	-	8	2584	c.2555T>C	c.(2554-2556)aTc>aCc	p.I852T		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	852	Pro-rich.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										AGATAATAAGATTTTAGGGGT	0.507													A|||	43	0.0113907	0.0303	0.0043	3775	,	,		13466	0.0		0.0	False		,,,				2504	0.0				p.I852T		Atlas-SNP	.											.	.	.	.	0			c.T2555C						PASS	.	-	THR/ILE	166,3669		3,134,26,1495,545	74	71	72		2555	1.4	0	X	dbSNP_134	72	2,6726		0,1,1,2427,1871	yes	missense	ITIH5L	NM_198510.2	89	3,135,27,3922,2416	GG,GA,G,AA,A		0.0297,4.3286,1.5905	possibly-damaging	852/1314	54783952	168,10395	2203	4300	6503	SO:0001583	missense	347365	exon8			AATAAGATTTTAG	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.2555T>C	X.37:g.54783952A>G	ENSP00000218436:p.Ile852Thr	153	0	0		227	115	0.506608	NM_198510	A6NN03	Missense_Mutation	SNP	ENST00000218436.6	37	CCDS14361.1	20	0.012055455093429777	8	0.01694915254237288	0	0.0	0	0.0	0	0.0	A	9.484	1.098979	0.20552	0.043286	2.97E-4	ENSG00000102313	ENST00000218436	T	0.02863	4.13	3.91	1.43	0.22495	.	14.783200	0.01116	U	0.005696	T	0.00608	0.0020	N	0.14661	0.345	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.42032	-0.9475	9	0.72032	D	0.01	.	5.1877	0.15193	0.4176:0.0:0.5824:0.0	.	852	Q6UXX5	ITH5L_HUMAN	T	852	ENSP00000218436:I852T	ENSP00000218436:I852T	I	-	2	0	ITIH5L	54800677	0.003000	0.15002	0.007000	0.13788	0.008000	0.06430	0.571000	0.23669	0.275000	0.22094	0.380000	0.24917	ATC	A|0.982;G|0.018	0.018	strong		0.507	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510		G	54783952	A	G	54783952	3	3	22	1	0	0	0	0	1	0	0	0	7917	333	12	3	1410	3	ITIH5L	23	54783952	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	205227	54783952	100486608	4477	7378											
ITIH5L	347365	hgsc.bcm.edu	37	chrX	54815065	54815065	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cctctcgatcctggtggatgGgggtgaatccacctcacctg	6	10	12	13	1	2	1	1	1	1	0	5	3	4	2	5	4	0	0	5	4	1	0	rs140757238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:54815065G>C	ENST00000218436.6	-	5	663	c.634C>G	c.(634-636)Cca>Gca	p.P212A	ITIH6_ENST00000498398.1_5'Flank	NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	212					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										CTGGTGGATGGGGGTGAATCC	0.587													G|||	52	0.0137748	0.0371	0.0043	3775	,	,		11601	0.0		0.0	False		,,,				2504	0.0				p.P212A		Atlas-SNP	.											.	.	.	.	0			c.C634G						PASS	.	G	ALA/PRO	212,3623		3,177,29,1452,542	65	44	51		634	1.7	0	X	dbSNP_134	51	3,6725		0,1,2,2427,1870	yes	missense	ITIH5L	NM_198510.2	27	3,178,31,3879,2412	CC,CG,C,GG,G		0.0446,5.528,2.0354	possibly-damaging	212/1314	54815065	215,10348	2203	4300	6503	SO:0001583	missense	347365	exon5			TGGATGGGGGTGA	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.634C>G	X.37:g.54815065G>C	ENSP00000218436:p.Pro212Ala	81	0	0		105	50	0.47619	NM_198510	A6NN03	Missense_Mutation	SNP	ENST00000218436.6	37	CCDS14361.1	24	0.014466546112115732	11	0.023404255319148935	0	0.0	0	0.0	0	0.0	G	1.845	-0.466354	0.04476	0.05528	4.46E-4	ENSG00000102313	ENST00000218436	T	0.02177	4.41	3.88	1.7	0.24286	.	0.424226	0.19726	U	0.107470	T	0.00271	0.0008	L	0.39898	1.24	0.42463	P	0.007206000000000046	B	0.14805	0.011	B	0.19148	0.024	T	0.37888	-0.9686	9	0.14656	T	0.56	.	6.3923	0.21593	0.1233:0.0:0.6815:0.1952	.	212	Q6UXX5	ITH5L_HUMAN	A	212	ENSP00000218436:P212A	ENSP00000218436:P212A	P	-	1	0	ITIH5L	54831790	1.000000	0.71417	0.042000	0.18584	0.218000	0.24690	1.253000	0.32886	0.488000	0.27723	0.171000	0.16805	CCA	G|0.976;C|0.024	0.024	strong		0.587	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510		C	54815065	G	C	54815065	3	2	22	1	0	0	0	0	1	0	0	0	7917	1232	43	4	3343	4	ITIH5L	23	54815065	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	31113	54815065	100455495	4478	7379											
MAGED2	10916	hgsc.bcm.edu	37	chrX	54837277	54837277	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagcatctggatggggaagaGgatggcagcagtgatcagag	13	6	17	5	0	2	3	1	1	1	2	2	6	2	6	0	5	2	3	0	5	2	0	rs12014977	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:54837277G>C	ENST00000375068.1	+	4	794	c.561G>C	c.(559-561)gaG>gaC	p.E187D	MAGED2_ENST00000347546.4_Missense_Mutation_p.E169D|MAGED2_ENST00000375060.1_Missense_Mutation_p.E149D|MAGED2_ENST00000375053.2_Missense_Mutation_p.E187D|MAGED2_ENST00000218439.4_Missense_Mutation_p.E187D|MAGED2_ENST00000396224.1_Missense_Mutation_p.E187D|MAGED2_ENST00000375058.1_Missense_Mutation_p.E187D|MAGED2_ENST00000375062.4_Missense_Mutation_p.E149D|MAGED2_ENST00000497484.1_3'UTR			Q9UNF1	MAGD2_HUMAN	melanoma antigen family D, 2	187			E -> D (in dbSNP:rs12014977).			membrane (GO:0016020)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	26						ATGGGGAAGAGGATGGCAGCA	0.552													G|||	91	0.024106	0.0666	0.0043	3775	,	,		4773	0.0		0.0	False		,,,				2504	0.0				p.E187D		Atlas-SNP	.											.	MAGED2	74	.	0			c.G561C						PASS	.	G	ASP/GLU,ASP/GLU,ASP/GLU	275,3560		8,225,34,1399,537	59	57	58		561,561,561	2.1	1	X	dbSNP_120	58	4,6724		0,4,0,2424,1872	yes	missense,missense,missense	MAGED2	NM_014599.4,NM_177433.1,NM_201222.1	45,45,45	8,229,34,3823,2409	CC,CG,C,GG,G		0.0595,7.1708,2.6413	probably-damaging,probably-damaging,probably-damaging	187/607,187/607,187/607	54837277	279,10284	2203	4300	6503	SO:0001583	missense	10916	exon4			GGAAGAGGATGGC	AF128527	CCDS14362.1	Xp11.2	2008-08-01			ENSG00000102316	ENSG00000102316			16353	protein-coding gene	gene with protein product	"hepatocellular carcinoma associated protein", "breast cancer associated gene 1", "melanoma-associated antigen D2", "hepatocellular carcinoma-associated protein HCA10"	300470					Standard	NM_014599		Approved	JCL-1, BCG1, 11B6, MAGE-D2, HCA10, MAGED, MGC8386	uc004dtk.1	Q9UNF1	OTTHUMG00000021638	ENST00000375068.1:c.561G>C	X.37:g.54837277G>C	ENSP00000364209:p.Glu187Asp	150	0	0		196	105	0.535714	NM_201222	A6NMX0|O76058|Q5BJF3|Q8NAL6|Q9H218|Q9P0U9|Q9UM52	Missense_Mutation	SNP	ENST00000375068.1	37	CCDS14362.1	35	0.02109704641350211	20	0.0425531914893617	1	0.0028089887640449437	0	0.0	0	0.0	G	16.72	3.200742	0.58126	0.071708	5.95E-4	ENSG00000102316	ENST00000375068;ENST00000375053;ENST00000347546;ENST00000343474;ENST00000375062;ENST00000218439;ENST00000375058;ENST00000375060;ENST00000396224	T;T;T;T;T;T;T;T;T	0.71698	1.26;1.26;3.95;-0.59;0.91;1.26;1.26;0.91;1.26	3.85	2.06	0.26882	.	0.000000	0.44097	D	0.000493	T	0.15998	0.0385	L	0.27053	0.805	0.38540	P	0.05080499999999999	D;P;D	0.61697	0.99;0.956;0.982	D;D;D	0.72982	0.979;0.931;0.952	T	0.56866	-0.7908	9	0.29301	T	0.29	.	7.4321	0.27134	0.2294:0.0:0.7706:0.0	rs12014977;rs52798808;rs12014977	169;149;187	Q9UNF1-2;Q5H907;Q9UNF1	.;.;MAGD2_HUMAN	D	187;187;131;169;149;187;187;149;187	ENSP00000364209:E187D;ENSP00000364193:E187D;ENSP00000336962:E131D;ENSP00000340290:E169D;ENSP00000364202:E149D;ENSP00000218439:E187D;ENSP00000364198:E187D;ENSP00000364200:E149D;ENSP00000379526:E187D	ENSP00000218439:E187D	E	+	3	2	MAGED2	54854002	0.885000	0.30320	1.000000	0.80357	0.993000	0.82548	-0.682000	0.05185	0.430000	0.26230	-0.192000	0.12808	GAG	G|0.973;C|0.027	0.027	strong		0.552	MAGED2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056821.2	NM_014599		C	54837277	G	C	54837277	3	2	22	1	0	0	0	0	1	0	0	0	9193	991	35	4	571	4	MAGED2	23	54837277	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	22212	54837277	100433283	4479	7380											
FAM123B	139285	hgsc.bcm.edu	37	chrX	63410110	63410110	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggtgtgagggacgagctagTtgaggcccagattccccagg	9	7	16	9	1	0	3	0	2	0	1	1	5	1	4	3	4	1	2	3	4	1	3	rs61730681	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:63410110T>C	ENST00000330258.3	-	2	3329	c.3057A>G	c.(3055-3057)caA>caG	p.Q1019Q	AMER1_ENST00000403336.1_Intron|AMER1_ENST00000374869.3_Intron	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	1019	Pro-rich.				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)									GACGAGCTAGTTGAGGCCCAG	0.567													C|||	1022	0.270728	0.7012	0.0937	3775	,	,		13676	0.003		0.0119	False		,,,				2504	0.0153				p.Q1019Q		Atlas-SNP	.											.	.	.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.A3057G						PASS	.	C		2803,865		883,571,466,95,104	54	61	58		3057	1.9	0.7	X	dbSNP_129	58	101,6502		0,78,23,2314,1796	no	coding-synonymous	FAM123B	NM_152424.3		883,649,489,2409,1900	CC,CT,C,TT,T		1.5296,23.5823,28.2738		1019/1136	63410110	2904,7367	2119	4211	6330	SO:0001819	synonymous_variant	139285	exon2			AGCTAGTTGAGGC	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.3057A>G	X.37:g.63410110T>C		149	0	0		157	157	1	NM_152424	A2IB86|Q8N885	Silent	SNP	ENST00000330258.3	37	CCDS14377.2																																																																																			T|0.758;C|0.242	0.242	strong		0.567	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		C	63410110	T	C	63410110	2	2	22	1	0	0	0	0	0	0	0	1	5428	1722	60	3		3	FAM123B	23	63410110	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	8572833	63410110	91860450	4480	7381											
FAM123B	139285	hgsc.bcm.edu	37	chrX	63412690	63412690	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttggcttgggcatagagggAaacttctcagccacagcttt	9	12	11	9	0	1	1	1	0	1	1	2	2	1	2	1	3	3	3	1	3	2	5	rs34677493	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:63412690A>C	ENST00000330258.3	-	2	749	c.477T>G	c.(475-477)ttT>ttG	p.F159L	AMER1_ENST00000403336.1_Missense_Mutation_p.F159L|AMER1_ENST00000374869.3_Missense_Mutation_p.F159L	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	159			F -> L (in dbSNP:rs34677493).		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)									GCATAGAGGGAAACTTCTCAG	0.532													A|||	528	0.139868	0.3722	0.0288	3775	,	,		12073	0.0		0.004	False		,,,				2504	0.0123				p.F159L		Atlas-SNP	.											.	.	.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.T477G						PASS	.	A	LEU/PHE	1683,2152		332,780,239,520,332	42	43	43		477	0.9	0	X	dbSNP_126	43	42,6686		0,35,7,2393,1865	yes	missense	FAM123B	NM_152424.3	22	332,815,246,2913,2197	CC,CA,C,AA,A		0.6243,43.8853,16.3306	benign	159/1136	63412690	1725,8838	2203	4300	6503	SO:0001583	missense	139285	exon2			AGAGGGAAACTTC	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.477T>G	X.37:g.63412690A>C	ENSP00000329117:p.Phe159Leu	63	0	0		70	35	0.5	NM_152424	A2IB86|Q8N885	Missense_Mutation	SNP	ENST00000330258.3	37	CCDS14377.2	193	0.11633514165159735	121	0.32180851063829785	7	0.019886363636363636	0	0.0	1	0.0013227513227513227	A	0.031	-1.334923	0.01287	0.438853	0.006243	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	T;T;T	0.16457	2.34;2.34;2.34	4.93	0.952	0.19584	.	0.964567	0.08637	N	0.916136	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.48410	-0.9038	9	0.27082	T	0.32	0.9455	0.4629	0.00519	0.2626:0.1486:0.1604:0.4284	rs34677493	159	Q5JTC6	F123B_HUMAN	L	159	ENSP00000364003:F159L;ENSP00000329117:F159L;ENSP00000384722:F159L	ENSP00000329117:F159L	F	-	3	2	FAM123B	63329415	0.000000	0.05858	0.000000	0.03702	0.092000	0.18411	-0.359000	0.07632	0.182000	0.20032	0.486000	0.48141	TTT	0|0.013;C|0.188	0.188	strong		0.532	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		C	63412690	A	C	63412690	3	2	22	1	0	0	0	0	1	0	0	0	5428	243	9	5	2934	5	FAM123B	23	63412690	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2580	63412690	91857870	4481	7382											
ZC4H2	55906	hgsc.bcm.edu	37	chrX	64139051	64139051	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atggggggctcctgaggttcTgtctgccattctgctttctg	3	15	13	10	0	4	1	0	1	4	0	5	1	5	1	2	4	2	3	2	4	0	3	rs6524946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:64139051T>C	ENST00000374839.3	-	4	538	c.432A>G	c.(430-432)acA>acG	p.T144T	ZC4H2_ENST00000337990.2_Silent_p.T121T|ZC4H2_ENST00000488608.1_5'UTR|ZC4H2_ENST00000447788.2_Intron|ZC4H2_ENST00000545618.1_Silent_p.T139T	NM_018684.3	NP_061154.1	Q9NQZ6	ZC4H2_HUMAN	zinc finger, C4H2 domain containing	144					nervous system development (GO:0007399)|neuromuscular junction development (GO:0007528)|spinal cord motor neuron differentiation (GO:0021522)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	metal ion binding (GO:0046872)			endometrium(2)|large_intestine(4)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						CCTGAGGTTCTGTCTGCCATT	0.547													C|||	354	0.0937748	0.2549	0.0245	3775	,	,		13414	0.0		0.0	False		,,,				2504	0.0				p.T144T		Atlas-SNP	.											.	ZC4H2	64	.	0			c.A432G						PASS	.	C	,,	1115,2720		134,678,169,820,402	60	51	54		363,,432	-4.2	0.3	X	dbSNP_116	54	4,6724		0,2,2,2426,1870	no	coding-synonymous,intron,coding-synonymous	ZC4H2	NM_001178032.2,NM_001178033.2,NM_018684.3	,,	134,680,171,3246,2272	CC,CT,C,TT,T		0.0595,29.0743,10.5936	,,	121/202,,144/225	64139051	1119,9444	2203	4300	6503	SO:0001819	synonymous_variant	55906	exon4			AGGTTCTGTCTGC	AF270491	CCDS14380.1, CCDS55431.1, CCDS55432.1	Xq11.1	2013-07-23	2008-10-01	2008-10-01	ENSG00000126970	ENSG00000126970		"Zinc fingers"	24931	protein-coding gene	gene with protein product		300897	"KIAA1166", "Wieacker-Wolff syndrome"	KIAA1166, WWS		10574461, 12097419, 23623388	Standard	NM_018684		Approved	HCA127	uc004dvu.3	Q9NQZ6	OTTHUMG00000021712	ENST00000374839.3:c.432A>G	X.37:g.64139051T>C		154	0	0		129	62	0.48062	NM_018684	B2RDC2|B3KVZ5|B4DED0|E7EM74|G3V1L3|Q53H73|Q5JTF9|Q9H9C3|Q9H9H7|Q9ULQ4	Silent	SNP	ENST00000374839.3	37	CCDS14380.1																																																																																			T|0.894;C|0.106	0.106	strong		0.547	ZC4H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056958.1	NM_018684		C	64139051	T	C	64139051	2	2	22	1	0	0	0	0	0	0	0	1	17593	1567	55	3		3	ZC4H2	23	64139051	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	726361	64139051	91131509	4482	7383											
AR	367	hgsc.bcm.edu	37	chrX	66765164	66765164	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtttgctgctgctgcagcAgcagcagcagcagcagcagc	9	6	13	13	0	0	0	0	0	0	0	0	0	0	0	0	0	12	12	0	0	0	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:66765164A>T	ENST00000374690.3	+	1	700	c.176A>T	c.(175-177)cAg>cTg	p.Q59L	AR_ENST00000504326.1_Missense_Mutation_p.Q59L|AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.Q59L	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	59	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)	CTGCTgcagcagcagcagcag	0.677									Androgen Insensitivity Syndrome																												p.Q59L		Atlas-SNP	.											.	AR	249	.	0			c.A176T						PASS	.						7	10	9					X																	66765164		2055	4063	6118	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	TGCAGCAGCAGCA	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.176A>T	X.37:g.66765164A>T	ENSP00000363822:p.Gln59Leu	64	0	0		68	4	0.0588235	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	37	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	12.32	1.901651	0.33535	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.69175	-0.38;-0.38;-0.38	.	.	.	.	1.117170	0.06949	N	0.814177	T	0.47060	0.1425	N	0.19112	0.55	0.09310	N	0.999999	B;B	0.34313	0.448;0.448	B;B	0.36534	0.227;0.227	T	0.31724	-0.9933	8	0.13108	T	0.6	.	.	.	.	.	59;59	E7EVX6;D3YPQ2	.;.	L	59	ENSP00000363822:Q59L;ENSP00000421155:Q59L;ENSP00000379359:Q59L	ENSP00000363822:Q59L	Q	+	2	0	AR	66681889	0.995000	0.38212	0.864000	0.33941	0.503000	0.33858	0.245000	0.18142	0.000000	0.14550	0.000000	0.15137	CAG	.	.	none		0.677	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		T	66765164	A	T	66765164	3	4	22	1	0	0	0	0	1	0	0	0	836	188	7	5	178	5	AR	23	66765164	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	2626113	66765164	88505396	4483	7384											
STARD8	9754	hgsc.bcm.edu	37	chrX	67938392	67938392	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	atgaggctgaggctgcggggCccctggctggactccaggca	6	6	17	12	1	0	2	0	2	0	0	1	3	1	3	3	7	1	4	3	7	0	0	rs58255923	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:67938392C>T	ENST00000252336.6	+	5	1768	c.1396C>T	c.(1396-1398)Ccc>Tcc	p.P466S	STARD8_ENST00000374597.3_Missense_Mutation_p.P466S|STARD8_ENST00000374599.3_Missense_Mutation_p.P546S	NM_014725.4	NP_055540.2	Q92502	STAR8_HUMAN	StAR-related lipid transfer (START) domain containing 8	466				P -> S (in Ref. 1; BAA11506). {ECO:0000305}.	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						GGCTGCGGGGCCCCTGGCTGG	0.587													C|||	148	0.0392053	0.0991	0.0173	3775	,	,		10820	0.0		0.005	False		,,,				2504	0.0				p.P546S		Atlas-SNP	.											.	STARD8	282	.	0			c.C1636T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO	468,3367		23,336,86,1273,485	46	39	41		1636,1396,1396	1.8	0	X	dbSNP_129	41	22,6706		0,15,7,2413,1865	yes	missense,missense,missense	STARD8	NM_001142503.2,NM_001142504.2,NM_014725.4	74,74,74	23,351,93,3686,2350	TT,TC,T,CC,C		0.327,12.2034,4.6388	benign,benign,benign	546/1104,466/1024,466/1024	67938392	490,10073	2203	4300	6503	SO:0001583	missense	9754	exon6			GCGGGGCCCCTGG	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.1396C>T	X.37:g.67938392C>T	ENSP00000252336:p.Pro466Ser	156	0	0		147	75	0.510204	NM_001142503	A8K6T2|D3DVT9|Q5JST0|Q68DG7	Missense_Mutation	SNP	ENST00000252336.6	37	CCDS14390.1	48	0.028933092224231464	28	0.059322033898305086	5	0.014124293785310734	0	0.0	1	0.0013192612137203166	C	1.597	-0.527487	0.04141	0.122034	0.00327	ENSG00000130052	ENST00000252336;ENST00000374599;ENST00000374597	T;T;T	0.06218	3.33;3.33;3.33	4.26	1.76	0.24704	.	0.487629	0.17593	N	0.168718	T	0.00039	0.0001	N	0.00347	-1.61	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.39722	-0.9600	9	0.06494	T	0.89	.	3.9538	0.09380	0.0:0.1325:0.2824:0.5851	rs58255923;rs61736965	546;466	Q92502-2;Q92502	.;STAR8_HUMAN	S	466;546;466	ENSP00000252336:P466S;ENSP00000363727:P546S;ENSP00000363725:P466S	ENSP00000252336:P466S	P	+	1	0	STARD8	67855117	0.000000	0.05858	0.002000	0.10522	0.932000	0.56968	0.017000	0.13399	0.106000	0.17784	-0.340000	0.08031	CCC	C|0.955;T|0.045	0.045	strong		0.587	STARD8-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057026.2	NM_014725		T	67938392	C	T	67938392	3	4	22	1	0	0	0	0	1	0	0	0	15278	739	26	2	1658	2	STARD8	23	67938392	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1173228	67938392	87332168	4484	7385											
AWAT1	158833	hgsc.bcm.edu	37	chrX	69455671	69455671	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggactggaagaccccagagcGaggtaagactcacagaccta	14	4	12	11	1	1	4	1	0	0	4	1	7	1	6	3	3	1	1	3	3	3	2	rs61995694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:69455671G>A	ENST00000374521.3	+	2	223	c.182G>A	c.(181-183)cGa>cAa	p.R61Q	AWAT1_ENST00000480702.1_3'UTR	NM_001013579.2	NP_001013597.1	Q58HT5	AWAT1_HUMAN	acyl-CoA wax alcohol acyltransferase 1	61					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						ACCCCAGAGCGAGGTAAGACT	0.512													g|||	113	0.0299338	0.0825	0.0058	3775	,	,		15173	0.0		0.0	False		,,,				2504	0.0				p.R61Q		Atlas-SNP	.											.	AWAT1	74	.	0			c.G182A						PASS	.		GLN/ARG	342,3493		13,270,46,1349,525	184	144	158		182	1.1	0.6	X	dbSNP_129	158	2,6726		0,2,0,2426,1872	yes	missense	AWAT1	NM_001013579.2	43	13,272,46,3775,2397	AA,AG,A,GG,G		0.0297,8.9179,3.2567	benign	61/329	69455671	344,10219	2203	4300	6503	SO:0001583	missense	158833	exon2			CAGAGCGAGGTAA	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.182G>A	X.37:g.69455671G>A	ENSP00000363645:p.Arg61Gln	127	0	0		119	49	0.411765	NM_001013579	Q5JT21|Q6IEE4	Missense_Mutation	SNP	ENST00000374521.3	37	CCDS35321.1	46	0.027727546714888487	32	0.06808510638297872	3	0.008287292817679558	0	0.0	0	0.0	g	2.423	-0.332574	0.05314	0.089179	2.97E-4	ENSG00000204195	ENST00000374521	T	0.17528	2.27	5.03	1.06	0.20224	.	0.715401	0.13082	N	0.415230	T	0.00241	0.0007	N	0.04162	-0.26	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.09377	0.004	T	0.42749	-0.9433	9	0.02654	T	1	-0.016	7.6926	0.28577	0.6396:0.0:0.3604:0.0	rs61995694	61	Q58HT5	AWAT1_HUMAN	Q	61	ENSP00000363645:R61Q	ENSP00000363645:R61Q	R	+	2	0	AWAT1	69372396	0.002000	0.14202	0.579000	0.28588	0.849000	0.48306	0.034000	0.13776	-0.029000	0.13827	-0.372000	0.07161	CGA	G|0.967;A|0.033	0.033	strong		0.512	AWAT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057066.3	NM_001013579		A	69455671	G	A	69455671	3	1	22	1	0	0	0	0	1	0	0	0	1234	1058	37	1	188	1	AWAT1	23	69455671	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1517279	69455671	85814889	4485	7386											
CXorf65	158830	hgsc.bcm.edu	37	chrX	70325881	70325881	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgttccaccttacaaacgtaGtaggtgcttcgagctgtaag	10	11	10	10	3	0	0	0	0	0	0	2	1	1	0	2	1	4	6	2	1	5	6	rs138762266	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:70325881G>A	ENST00000374251.5	-	3	267	c.219C>T	c.(217-219)taC>taT	p.Y73Y		NM_001025265.2	NP_001020436.1	A6NEN9	CX065_HUMAN	chromosome X open reading frame 65	73										breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(3)	10						TACAAACGTAGTAGGTGCTTC	0.443													G|||	10	0.00264901	0.0068	0.0014	3775	,	,		16348	0.0		0.0	False		,,,				2504	0.0				p.Y73Y		Atlas-SNP	.											.	CXorf65	23	.	0			c.C219T						PASS	.	G		41,3794		0,37,4,1595,567	169	128	142		219	3.1	0.9	X	dbSNP_134	142	0,6728		0,0,0,2428,1872	no	coding-synonymous	CXorf65	NM_001025265.2		0,37,4,4023,2439	AA,AG,A,GG,G		0.0,1.0691,0.3881		73/184	70325881	41,10522	2203	4300	6503	SO:0001819	synonymous_variant	158830	exon3			AACGTAGTAGGTG	BC144434	CCDS35324.1	Xq13.1	2009-03-06			ENSG00000204165	ENSG00000204165			33713	protein-coding gene	gene with protein product							Standard	NM_001025265		Approved		uc011mpo.2	A6NEN9	OTTHUMG00000021785	ENST00000374251.5:c.219C>T	X.37:g.70325881G>A		200	0	0		174	77	0.442529	NM_001025265		Silent	SNP	ENST00000374251.5	37	CCDS35324.1																																																																																			G|0.996;A|0.004	0.004	strong		0.443	CXorf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057089.2	NM_001025265		A	70325881	G	A	70325881	2	1	22	1	0	0	0	0	0	0	0	1	4119	1024	36	2		2	CXorf65	23	70325881	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	870210	70325881	84944679	4486	7387											
MED12	9968	hgsc.bcm.edu	37	chrX	70339715	70339715	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcaccaagccactcacgcaActagccaaaaaggtaaggta	16	4	9	12	1	1	0	1	0	0	0	1	0	1	0	3	3	3	4	3	3	7	3	rs201566660		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:70339715A>G	ENST00000374080.3	+	3	416	c.384A>G	c.(382-384)caA>caG	p.Q128Q	MED12_ENST00000333646.6_Silent_p.Q128Q|MED12_ENST00000374102.1_Silent_p.Q128Q			Q93074	MED12_HUMAN	mediator complex subunit 12	128					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)					CACTCACGCAACTAGCCAAAA	0.502			"M, S"		uterine leiomyoma		Opitz-Kaveggia Syndrome						.|||	9	0.00238411	0.0061	0.0014	3775	,	,		15678	0.0		0.0	False		,,,				2504	0.0				p.Q128Q		Atlas-SNP	.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12	984	.	0			c.A384G						PASS	.	A		31,3377		0,27,4,1392,566	33	32	33		384	-3.8	1	X		33	0,6498		0,0,0,2353,1792	no	coding-synonymous	MED12	NM_005120.2		0,27,4,3745,2358	GG,GA,G,AA,A		0.0,0.9096,0.3129		128/2178	70339715	31,9875	1989	4145	6134	SO:0001819	synonymous_variant	9968	exon3			CACGCAACTAGCC	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.384A>G	X.37:g.70339715A>G		121	0	0		152	68	0.447368	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Silent	SNP	ENST00000374080.3	37	CCDS43970.1	2	0.0012055455093429777	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	.	6.865	0.528992	0.13127	0.009096	0.0	ENSG00000184634	ENST00000429213	.	.	.	5.73	-3.76	0.04359	.	.	.	.	.	T	0.33585	0.0868	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35226	-0.9797	4	.	.	.	-1.517	4.2759	0.10809	0.1879:0.4151:0.308:0.089	.	.	.	.	S	113	.	.	N	+	2	0	MED12	70256440	1.000000	0.71417	0.980000	0.43619	0.912000	0.54170	0.874000	0.28065	-0.477000	0.06832	-1.276000	0.01395	AAC	A|0.999;G|0.001	0.001	strong		0.502	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120		G	70339715	A	G	70339715	2	3	22	1	0	0	0	0	0	0	0	1	9437	40	2	3		3	MED12	23	70339715	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	13834	70339715	84930845	4487	7388											
TAF1	6872	hgsc.bcm.edu	37	chrX	70586196	70586196	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcgatttgctgctgcggaCagcagctaccatcactgctg	7	10	11	13	2	1	0	1	0	0	0	1	2	1	1	1	1	8	5	1	1	1	2	rs139510844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:70586196C>T	ENST00000373790.4	+	1	83	c.32C>T	c.(31-33)aCa>aTa	p.T11I	TAF1_ENST00000276072.3_Missense_Mutation_p.T11I|TAF1_ENST00000449580.1_Missense_Mutation_p.T11I|TAF1_ENST00000423759.1_Missense_Mutation_p.T11I	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	11	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)				CTGCTGCGGACAGCAGCTACC	0.562													c|||	27	0.00715232	0.0189	0.0029	3775	,	,		5194	0.0		0.0	False		,,,				2504	0.0				p.T11I		Atlas-SNP	.											.	TAF1	439	.	0			c.C32T						PASS	.	C	ILE/THR,ILE/THR	98,3737		0,86,12,1546,559	66	56	59		32,32	-5.4	0	X	dbSNP_134	59	0,6728		0,0,0,2428,1872	yes	missense,missense	TAF1	NM_004606.3,NM_138923.2	89,89	0,86,12,3974,2431	TT,TC,T,CC,C		0.0,2.5554,0.9278	possibly-damaging,possibly-damaging	11/1894,11/1873	70586196	98,10465	2203	4300	6503	SO:0001583	missense	6872	exon1			TGCGGACAGCAGC		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.32C>T	X.37:g.70586196C>T	ENSP00000362895:p.Thr11Ile	303	1	0.00330033		351	183	0.521368	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	37	CCDS35325.1	12	0.007233273056057866	6	0.012345679012345678	1	0.002777777777777778	1	0.0017482517482517483	0	0.0	.	10.35	1.325295	0.24080	0.025554	0.0	ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000276072	T;T;T;T	0.08720	3.06;3.12;3.13;3.08	4.36	-5.37	0.02681	.	4.117550	0.00760	N	0.001123	T	0.01254	0.0041	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	0.34304	-0.9834	10	0.39692	T	0.17	.	4.0791	0.09917	0.4281:0.2007:0.0:0.3712	.	11;11	P21675;P21675-2	TAF1_HUMAN;.	I	11	ENSP00000362895:T11I;ENSP00000389000:T11I;ENSP00000406549:T11I;ENSP00000276072:T11I	ENSP00000276072:T11I	T	+	2	0	TAF1	70502921	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.175000	0.03102	-1.604000	0.01595	0.399000	0.26434	ACA	C|0.989;T|0.011	0.011	strong		0.562	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		T	70586196	C	T	70586196	3	4	22	1	0	0	0	0	1	0	0	0	15528	478	17	2	34	2	TAF1	23	70586196	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	246481	70586196	84684364	4488	7389											
TAF1	6872	hgsc.bcm.edu	37	chrX	70595132	70595132	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggaccaggattctattacTggtggtaagtagagattgtc	12	12	12	5	0	1	1	0	0	1	1	2	4	1	3	1	4	1	2	1	4	5	6	rs5981106	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:70595132T>C	ENST00000373790.4	+	4	579	c.528T>C	c.(526-528)acT>acC	p.T176T	TAF1_ENST00000276072.3_Silent_p.T176T|TAF1_ENST00000449580.1_Silent_p.T176T|TAF1_ENST00000423759.1_Silent_p.T176T	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	176	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)				ATTCTATTACTGGTGGTAAGT	0.438													C|||	293	0.0776159	0.2012	0.0274	3775	,	,		12232	0.0		0.005	False		,,,				2504	0.0031				p.T176T		Atlas-SNP	.											.	TAF1	439	.	0			c.T528C						PASS	.	C	,	921,2914		89,609,134,934,437	96	82	87		528,528	-6.1	0	X	dbSNP_114	87	38,6690		0,28,10,2400,1862	no	coding-synonymous,coding-synonymous	TAF1	NM_004606.3,NM_138923.2	,	89,637,144,3334,2299	CC,CT,C,TT,T		0.5648,24.0156,9.0789	,	176/1894,176/1873	70595132	959,9604	2203	4300	6503	SO:0001819	synonymous_variant	6872	exon4			TATTACTGGTGGT		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.528T>C	X.37:g.70595132T>C		141	0	0		158	67	0.424051	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Silent	SNP	ENST00000373790.4	37	CCDS35325.1																																																																																			T|0.891;C|0.109	0.109	strong		0.438	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		C	70595132	T	C	70595132	2	2	22	1	0	0	0	0	0	0	0	1	15528	1567	55	3		3	TAF1	23	70595132	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	8936	70595132	84675428	4489	7390											
TAF1	6872	hgsc.bcm.edu	37	chrX	70627477	70627477	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccctatggtgacgctgtcGtccatcttggagtctatcat	7	13	10	11	2	3	1	1	1	2	0	5	3	4	2	2	2	0	1	2	2	2	3	rs7050748	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:70627477G>A	ENST00000373790.4	+	27	4209	c.4158G>A	c.(4156-4158)tcG>tcA	p.S1386S	TAF1_ENST00000276072.3_Silent_p.S1407S|TAF1_ENST00000449580.1_Silent_p.S1386S|TAF1_ENST00000423759.1_Silent_p.S1407S	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	1386	Interaction with ASF1A and ASF1B.				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)				TGACGCTGTCGTCCATCTTGG	0.438													A|||	293	0.0776159	0.2012	0.0274	3775	,	,		15657	0.0		0.005	False		,,,				2504	0.0031				p.S1407S		Atlas-SNP	.											.	TAF1	439	.	0			c.G4221A						PASS	.	A	,	921,2914		89,609,134,934,437	129	111	117		4221,4158	0.9	1	X	dbSNP_116	117	39,6689		0,29,10,2399,1862	no	coding-synonymous,coding-synonymous	TAF1	NM_004606.3,NM_138923.2	,	89,638,144,3333,2299	AA,AG,A,GG,G		0.5797,24.0156,9.0883	,	1407/1894,1386/1873	70627477	960,9603	2203	4300	6503	SO:0001819	synonymous_variant	6872	exon27			GCTGTCGTCCATC		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.4158G>A	X.37:g.70627477G>A		316	0	0		316	136	0.43038	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Silent	SNP	ENST00000373790.4	37	CCDS35325.1	117	0.0705244122965642	71	0.1658878504672897	6	0.01694915254237288	0	0.0	3	0.003968253968253968	.	8.199	0.797814	0.16327	0.240156	0.005797	ENSG00000147133	ENST00000463163;ENST00000437147	.	.	.	4.95	0.941	0.19519	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999938	.	.	.	.	.	.	T	0.28396	-1.0045	3	.	.	.	.	1.3732	0.02215	0.2938:0.111:0.1437:0.4515	rs7050748	.	.	.	H	52;41	.	.	R	+	2	0	TAF1	70544202	0.020000	0.18652	0.992000	0.48379	0.891000	0.51852	-0.742000	0.04850	-0.381000	0.07882	-0.574000	0.04147	CGT	0|0.003;A|0.098	0.098	strong		0.438	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		A	70627477	G	A	70627477	2	1	22	1	0	0	0	0	0	0	0	1	15528	1132	40	1		1	TAF1	23	70627477	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	32345	70627477	84643083	4490	7391											
OGT	8473	hgsc.bcm.edu	37	chrX	70777435	70777435	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aagaataggttgccttctgtGcatcctcatcatagtatgct	10	14	8	9	0	3	1	2	0	1	1	4	1	4	1	2	1	3	4	2	1	5	5	rs34739713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:70777435G>A	ENST00000373719.3	+	12	1732	c.1515G>A	c.(1513-1515)gtG>gtA	p.V505V	OGT_ENST00000373701.3_Silent_p.V495V	NM_181672.2|NM_181673.2	NP_858058.1|NP_858059.1	O15294	OGT1_HUMAN	O-linked N-acetylglucosamine (GlcNAc) transferase	505					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)					TGCCTTCTGTGCATCCTCATC	0.433													G|||	160	0.0423841	0.1127	0.0144	3775	,	,		14352	0.0		0.001	False		,,,				2504	0.0				p.V505V		Atlas-SNP	.											.	OGT	207	.	0			c.G1515A						PASS	.	G	,	533,3302		27,404,75,1201,496	158	104	122		1515,1485	1.5	1	X	dbSNP_126	122	2,6726		0,2,0,2426,1872	no	coding-synonymous,coding-synonymous	OGT	NM_181672.2,NM_181673.2	,	27,406,75,3627,2368	AA,AG,A,GG,G		0.0297,13.8983,5.0648	,	505/1047,495/1037	70777435	535,10028	2203	4300	6503	SO:0001819	synonymous_variant	8473	exon12			TTCTGTGCATCCT	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.1515G>A	X.37:g.70777435G>A		156	0	0		185	90	0.486486	NM_181672	Q7Z3K0|Q8WWM8|Q96CC1|Q9UG57	Silent	SNP	ENST00000373719.3	37	CCDS14414.1																																																																																			G|0.947;A|0.053	0.053	strong		0.433	OGT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000081829.3	NM_003605, NM_181672		A	70777435	G	A	70777435	2	1	22	1	0	0	0	0	0	0	0	1	10856	1306	46	2		2	OGT	23	70777435	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	149958	70777435	84493125	4491	7392											
RGAG4	340526	hgsc.bcm.edu	37	chrX	71350294	71350294	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcttgctgaaaagccctcAtgcgcttcctctggtccttg	5	14	8	14	1	3	1	1	1	2	0	6	1	5	1	3	1	3	2	3	1	2	3	rs146618350		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:71350294A>G	ENST00000545866.1	-	1	1464	c.1097T>C	c.(1096-1098)aTg>aCg	p.M366T	RGAG4_ENST00000609883.1_Missense_Mutation_p.M366T|NHSL2_ENST00000540800.1_Intron	NM_001024455.3	NP_001019626.1	Q5HYW3	RGAG4_HUMAN	retrotransposon gag domain containing 4	366										cervix(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|skin(1)	24	Renal(35;0.156)					AAAAGCCCTCATGCGCTTCCT	0.498													A|||	19	0.00503311	0.0144	0.0	3775	,	,		14735	0.0		0.0	False		,,,				2504	0.0				p.M366T		Atlas-SNP	.											.	RGAG4	63	.	0			c.T1097C						PASS	.	A	,THR/MET	57,3395		0,49,8,1392,562	43	36	39		,1097	2.9	0	X	dbSNP_134	39	0,6522		0,0,0,2358,1806	yes	intron,missense	RGAG4,NHSL2	NM_001013627.2,NM_001024455.3	,81	0,49,8,3750,2368	GG,GA,G,AA,A		0.0,1.6512,0.5715	,benign	,366/570	71350294	57,9917	2011	4164	6175	SO:0001583	missense	340526	exon1			GCCCTCATGCGCT	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.1097T>C	X.37:g.71350294A>G	ENSP00000441366:p.Met366Thr	205	0	0		238	237	0.995798	NM_001024455	A7E2W7|Q8NCM4|Q9NPX1	Missense_Mutation	SNP	ENST00000545866.1	37	CCDS55446.1	10	0.006027727546714889	7	0.01440329218106996	0	0.0	0	0.0	0	0.0	A	9.812	1.183556	0.21870	0.016512	0.0	ENSG00000242732	ENST00000545866;ENST00000479991	T;T	0.12984	2.63;2.63	4.13	2.94	0.34122	.	.	.	.	.	T	0.03305	0.0096	N	0.14661	0.345	0.09310	N	1	B	0.22276	0.067	B	0.15052	0.012	T	0.39742	-0.9599	8	.	.	.	-2.2205	8.3218	0.32134	0.8026:0.1974:0.0:0.0	.	366	Q5HYW3	RGAG4_HUMAN	T	366	ENSP00000441366:M366T;ENSP00000418667:M366T	.	M	-	2	0	RGAG4	71267019	0.000000	0.05858	0.001000	0.08648	0.122000	0.20287	0.748000	0.26305	0.701000	0.31803	0.486000	0.48141	ATG	A|0.994;G|0.006	0.006	strong		0.498	RGAG4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057171.1	NM_001024455		G	71350294	A	G	71350294	3	3	22	1	0	0	0	0	1	0	0	0	13290	217	8	3	616	3	RGAG4	23	71350294	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	572859	71350294	83920266	4492	7393											
COX7B	1349	hgsc.bcm.edu	37	chrX	77158147	77158147	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gttttcctgtaagttcgaagCattcagcaaacaatggcaag	13	11	9	8	1	1	0	1	0	0	0	3	1	2	0	1	1	3	6	1	1	5	5	rs61752458	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:77158147C>A	ENST00000481445.1	+	2	164	c.48C>A	c.(46-48)agC>agA	p.S16R	COX7B_ENST00000475465.1_3'UTR	NM_001866.2	NP_001857.1	P24311	COX7B_HUMAN	cytochrome c oxidase subunit VIIb	16					cellular metabolic process (GO:0044237)|central nervous system development (GO:0007417)|hydrogen ion transmembrane transport (GO:1902600)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)	cytochrome-c oxidase activity (GO:0004129)			endometrium(2)	2						AAGTTCGAAGCATTCAGCAAA	0.388													C|||	49	0.0129801	0.0356	0.0029	3775	,	,		15718	0.0		0.0	False		,,,				2504	0.0				p.S16R		Atlas-SNP	.											.	COX7B	8	.	0			c.C48A						PASS	.	C	ARG/SER	101,3734		1,83,16,1548,555	138	107	118		48	3.1	1	X	dbSNP_129	118	0,6728		0,0,0,2428,1872	yes	missense	COX7B	NM_001866.2	110	1,83,16,3976,2427	AA,AC,A,CC,C		0.0,2.6336,0.9562	benign	16/81	77158147	101,10462	2203	4300	6503	SO:0001583	missense	1349	exon2			TCGAAGCATTCAG	Z14244	CCDS14437.1	Xq21.1	2011-07-04			ENSG00000131174	ENSG00000131174		"Mitochondrial respiratory chain complex / Complex IV"	2291	protein-coding gene	gene with protein product		300885				8382530	Standard	NM_001866		Approved		uc004ecu.1	P24311	OTTHUMG00000022718	ENST00000481445.1:c.48C>A	X.37:g.77158147C>A	ENSP00000417656:p.Ser16Arg	78	0	0		87	42	0.482759	NM_001866	B2R4M3|Q6ICR1	Missense_Mutation	SNP	ENST00000481445.1	37	CCDS14437.1	11	0.006630500301386378	4	0.008298755186721992	1	0.002777777777777778	0	0.0	0	0.0	C	17.45	3.392912	0.62066	0.026336	0.0	ENSG00000131174	ENST00000481445	T	0.48836	0.8	4.92	3.13	0.36017	.	0.349121	0.32401	N	0.006153	T	0.29288	0.0729	.	.	.	0.40351	P	0.02086100000000002	P	0.43542	0.81	P	0.53062	0.717	T	0.56619	-0.7949	8	0.52906	T	0.07	-0.0019	6.4067	0.21668	0.1816:0.7202:0.0:0.0982	rs61752458	16	P24311	COX7B_HUMAN	R	16	ENSP00000417656:S16R	ENSP00000417656:S16R	S	+	3	2	COX7B	77044803	1.000000	0.71417	0.997000	0.53966	0.814000	0.46013	0.699000	0.25586	0.330000	0.23485	0.523000	0.50628	AGC	C|0.991;A|0.009	0.009	strong		0.388	COX7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058970.1	NM_001866		A	77158147	C	A	77158147	3	1	22	1	0	0	0	0	1	0	0	0	3784	709	25	4	54	4	COX7B	23	77158147	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	5807853	77158147	78112413	4493	7394											
PGAM4	441531	hgsc.bcm.edu	37	chrX	77225099	77225099	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctccaggttccatgtgctctCgccgtgccggatcagcacca	6	9	10	16	3	2	0	1	0	1	0	5	1	4	1	5	2	3	3	5	2	0	1	rs6622613	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:77225099C>T	ENST00000458128.1	-	1	36	c.37G>A	c.(37-39)Gag>Aag	p.E13K	ATP7A_ENST00000343533.5_Intron|ATP7A_ENST00000350425.4_Intron|ATP7A_ENST00000341514.6_Intron	NM_001029891.2	NP_001025062.1	Q8N0Y7	PGAM4_HUMAN	phosphoglycerate mutase family member 4	13					glycolytic process (GO:0006096)|positive regulation of sperm motility (GO:1902093)	extracellular vesicular exosome (GO:0070062)|sperm principal piece (GO:0097228)	bisphosphoglycerate 2-phosphatase activity (GO:0004083)|bisphosphoglycerate mutase activity (GO:0004082)|phosphoglycerate mutase activity (GO:0004619)			endometrium(2)|lung(4)	6						CATGTGCTCTCGCCGTGCCGG	0.587													C|||	52	0.0137748	0.0363	0.0058	3775	,	,		12671	0.0		0.0	False		,,,				2504	0.0				p.E13K		Atlas-SNP	.											.	PGAM4	28	.	0			c.G37A						PASS	.	C	,LYS/GLU	101,3734		1,82,17,1549,554	55	54	54		,37	0.1	0.6	X	dbSNP_116	54	9,6713		0,7,2,2420,1866	no	intron,missense	ATP7A,PGAM4	NM_000052.4,NM_001029891.2	,56	1,89,19,3969,2420	TT,TC,T,CC,C		0.1339,2.6336,1.042	,possibly-damaging	,13/255	77225099	110,10447	2203	4295	6498	SO:0001583	missense	441531	exon1			TGCTCTCGCCGTG	AF465731	CCDS35338.1	Xq21.1	2011-02-09	2006-02-09		ENSG00000226784	ENSG00000226784			21731	protein-coding gene	gene with protein product		300567	"phosphoglycerate mutase family 4"			11961099, 9370262	Standard	NM_001029891		Approved	dJ1000K24.1, PGAM3, PGAM-B, PGAM1	uc004ecy.1	Q8N0Y7	OTTHUMG00000057865	ENST00000458128.1:c.37G>A	X.37:g.77225099C>T	ENSP00000412189:p.Glu13Lys	470	1	0.00212766		488	248	0.508197	NM_001029891	Q5JPN2|Q8NI24|Q8NI25|Q8NI26	Missense_Mutation	SNP	ENST00000458128.1	37	CCDS35338.1	13	0.007836045810729355	4	0.008298755186721992	4	0.011111111111111112	0	0.0	0	0.0	C	17.78	3.473730	0.63737	0.026336	0.001339	ENSG00000226784	ENST00000458128	D	0.83163	-1.69	0.119	0.119	0.14685	Histidine phosphatase superfamily, clade-1 (2);	0.000000	0.85682	U	0.000000	T	0.53916	0.1826	L	0.55743	1.74	0.22675	P	0.99886112	B	0.31077	0.307	B	0.35655	0.207	T	0.64266	-0.6448	8	.	.	.	-7.1432	6.135	0.20227	0.0:0.9996:0.0:4.0E-4	rs6622613	13	Q8N0Y7	PGAM4_HUMAN	K	13	ENSP00000412189:E13K	.	E	-	1	0	PGAM4	77111755	1.000000	0.71417	0.623000	0.29173	0.641000	0.38312	3.649000	0.54417	0.260000	0.21731	0.264000	0.19307	GAG	C|0.990;T|0.010	0.010	strong		0.587	PGAM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128371.2	NM_001029891		T	77225099	C	T	77225099	3	4	22	1	0	0	0	0	1	0	0	0	11784	893	31	1	731	1	PGAM4	23	77225099	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	66952	77225099	78045461	4494	7395											
CYLC1	1538	hgsc.bcm.edu	37	chrX	83128911	83128911	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	agaatgatgacaagaaaaagGatgcaaagaaaattacattc	22	7	8	4	0	0	5	0	2	0	3	1	6	0	6	0	1	2	1	0	1	8	2	rs12008888	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:83128911G>C	ENST00000329312.4	+	4	1232	c.1195G>C	c.(1195-1197)Gat>Cat	p.D399H		NM_021118.1	NP_066941.1	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head cytoskeleton 1	399			D -> H (in dbSNP:rs12008888).		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						CAAGAAAAAGGATGCAAAGAA	0.343													G|||	200	0.0529801	0.1384	0.0231	3775	,	,		14297	0.0		0.001	False		,,,				2504	0.0				p.D399H		Atlas-SNP	.											.	CYLC1	272	.	0			c.G1195C						PASS	.	G	HIS/ASP	581,3240		41,402,97,1184,470	30	24	26		1195	3.2	0	X	dbSNP_120	26	5,6711		0,5,0,2421,1864	yes	missense	CYLC1	NM_021118.1	81	41,407,97,3605,2334	CC,CG,C,GG,G		0.0744,15.2054,5.5614	probably-damaging	399/652	83128911	586,9951	2194	4290	6484	SO:0001583	missense	1538	exon4			AAAAAGGATGCAA	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.1195G>C	X.37:g.83128911G>C	ENSP00000331556:p.Asp399His	106	0	0		91	44	0.483516	NM_021118	A0AVQ8|Q5JQQ9	Missense_Mutation	SNP	ENST00000329312.4	37	CCDS35341.1	75	0.045207956600361664	41	0.09234234234234234	5	0.014204545454545454	0	0.0	0	0.0	g	2.122	-0.401166	0.04865	0.152054	7.44E-4	ENSG00000183035	ENST00000329312;ENST00000544771	T	0.28895	1.59	4.12	3.24	0.37175	.	.	.	.	.	T	0.00271	0.0008	L	0.49126	1.545	0.80722	P	0.0	D;D	0.89917	1.0;1.0	D;D	0.73380	0.98;0.98	T	0.06588	-1.0818	8	0.66056	D	0.02	-7.8087	6.0759	0.19915	0.1403:0.0:0.8597:0.0	rs12008888;rs52819056;rs12008888	399;399	P35663;F5H4V5	CYLC1_HUMAN;.	H	399	ENSP00000331556:D399H	ENSP00000331556:D399H	D	+	1	0	CYLC1	83015567	0.979000	0.34478	0.008000	0.14137	0.011000	0.07611	3.108000	0.50337	2.026000	0.59711	0.600000	0.82982	GAT	0|0.017;C|0.055	0.055	strong		0.343	CYLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057371.1	NM_021118		C	83128911	G	C	83128911	3	2	22	1	0	0	0	0	1	0	0	0	4143	1174	41	4	1209	4	CYLC1	23	83128911	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5903812	83128911	72141649	4495	7396											
HDX	139324	hgsc.bcm.edu	37	chrX	83591879	83591879	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catcattcggaacaacttcaTtgggctcttctacagaaaaa	14	11	6	10	1	4	1	2	0	2	1	5	2	4	2	0	2	3	1	0	2	5	5	rs77791258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:83591879T>C	ENST00000297977.5	-	7	1781	c.1670A>G	c.(1669-1671)aAt>aGt	p.N557S	HDX_ENST00000506585.2_Missense_Mutation_p.N499S|HDX_ENST00000373177.2_Missense_Mutation_p.N557S	NM_001177479.1|NM_144657.4	NP_001170950.1|NP_653258.2	Q7Z353	HDX_HUMAN	highly divergent homeobox	557						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						AACAACTTCATTGGGCTCTTC	0.333													t|||	172	0.0455629	0.1188	0.0216	3775	,	,		12736	0.0		0.0	False		,,,				2504	0.0				p.N557S	Pancreas(53;231 1169 36156 43751 51139)	Atlas-SNP	.											.	HDX	124	.	0			c.A1670G						PASS	.	C	SER/ASN,SER/ASN,SER/ASN	503,3330		35,338,95,1258,476	86	72	76		1496,1670,1670	-7.3	0.4	X	dbSNP_131	76	4,6720		0,4,0,2423,1870	yes	missense,missense,missense	HDX	NM_001177478.1,NM_001177479.1,NM_144657.4	46,46,46	35,342,95,3681,2346	CC,CT,C,TT,T		0.0595,13.1229,4.8025	benign,benign,benign	499/633,557/691,557/691	83591879	507,10050	2202	4297	6499	SO:0001583	missense	139324	exon7			ACTTCATTGGGCT	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.1670A>G	X.37:g.83591879T>C	ENSP00000297977:p.Asn557Ser	66	0	0		67	26	0.38806	NM_144657	A8K1Y5|B7ZL18|Q5JZB4|Q96NK7	Missense_Mutation	SNP	ENST00000297977.5	37	CCDS35342.1	60	0.03616636528028933	39	0.08369098712446352	4	0.011363636363636364	0	0.0	0	0.0	T	0.666	-0.803647	0.02841	0.131229	5.95E-4	ENSG00000165259	ENST00000297977;ENST00000373177;ENST00000506585	T;T;T	0.27557	1.66;1.66;1.66	5.33	-7.27	0.01461	.	0.753578	0.13237	N	0.403154	T	0.00144	0.0004	N	0.11560	0.145	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.31888	-0.9927	9	0.06757	T	0.87	-14.8311	16.4567	0.84019	0.0:0.6124:0.0:0.3876	.	557	Q7Z353	HDX_HUMAN	S	557;499;557	ENSP00000297977:N557S;ENSP00000362272:N499S;ENSP00000423670:N557S	ENSP00000297977:N557S	N	-	2	0	HDX	83478535	0.008000	0.16893	0.432000	0.26747	0.605000	0.37080	-2.080000	0.01368	-1.696000	0.01421	0.409000	0.27619	AAT	T|0.950;C|0.050	0.050	strong		0.333	HDX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057379.2	NM_144657		C	83591879	T	C	83591879	3	2	22	1	0	0	0	0	1	0	0	0	7035	1493	52	3	418	3	HDX	23	83591879	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	462968	83591879	71678681	4496	7397											
POF1B	79983	hgsc.bcm.edu	37	chrX	84600948	84600948	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gattatttcctgtgatggctTggatttgctggctagaatca	8	16	11	6	0	1	2	1	1	0	1	2	4	2	3	1	3	1	3	1	3	3	5	rs60768249	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:84600948T>C	ENST00000262753.4	-	6	786	c.641A>G	c.(640-642)cAa>cGa	p.Q214R	POF1B_ENST00000373145.3_Missense_Mutation_p.Q214R	NM_024921.3	NP_079197.3	Q8WVV4	POF1B_HUMAN	premature ovarian failure, 1B	214						tight junction (GO:0005923)				central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|liver(2)|lung(17)|ovary(1)|prostate(1)	35						TGTGATGGCTTGGATTTGCTG	0.463													T|||	135	0.0357616	0.0946	0.0144	3775	,	,		12542	0.0		0.0	False		,,,				2504	0.0				p.Q214R		Atlas-SNP	.											.	POF1B	77	.	0			c.A641G						PASS	.	T	ARG/GLN	462,3373		16,338,92,1278,479	234	189	204		641	4.6	0	X	dbSNP_129	204	2,6726		0,1,1,2427,1871	yes	missense	POF1B	NM_024921.3	43	16,339,93,3705,2350	CC,CT,C,TT,T		0.0297,12.0469,4.3927	possibly-damaging	214/590	84600948	464,10099	2203	4300	6503	SO:0001583	missense	79983	exon6			ATGGCTTGGATTT	BC017500	CCDS14452.1	Xq21.2	2008-02-05			ENSG00000124429	ENSG00000124429			13711	protein-coding gene	gene with protein product		300603				11299520	Standard	NM_024921		Approved	POF, FLJ22792	uc004eer.2	Q8WVV4	OTTHUMG00000021934	ENST00000262753.4:c.641A>G	X.37:g.84600948T>C	ENSP00000262753:p.Gln214Arg	228	0	0		202	106	0.524752	NM_024921	A8K2U5|Q5H9E9|Q5H9F0|Q8NG12|Q9H5Y2|Q9H738|Q9H744	Missense_Mutation	SNP	ENST00000262753.4	37	CCDS14452.1	53	0.031946955997588906	32	0.06926406926406926	3	0.008426966292134831	0	0.0	0	0.0	T	6.220	0.408732	0.11812	0.120469	2.97E-4	ENSG00000124429	ENST00000262753;ENST00000373145;ENST00000276124	T;T	0.10763	2.84;2.84	4.56	4.56	0.56223	.	0.364164	0.23070	N	0.052276	T	0.00178	0.0005	L	0.53249	1.67	0.80722	P	0.0	B;B	0.25272	0.058;0.122	B;B	0.25291	0.059;0.04	T	0.05801	-1.0863	9	0.66056	D	0.02	.	9.2182	0.37360	0.0:0.0:0.0:1.0	rs60768249	214;214	Q8WVV4-1;Q8WVV4	.;POF1B_HUMAN	R	214	ENSP00000262753:Q214R;ENSP00000362238:Q214R	ENSP00000262753:Q214R	Q	-	2	0	POF1B	84487604	0.828000	0.29307	0.049000	0.19019	0.045000	0.14185	3.232000	0.51302	1.775000	0.52247	0.481000	0.45027	CAA	T|0.958;C|0.042	0.042	strong		0.463	POF1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057391.2	NM_024921		C	84600948	T	C	84600948	3	2	22	1	0	0	0	0	1	0	0	0	12191	1812	63	3	1176	3	POF1B	23	84600948	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1009069	84600948	70669612	4497	7398											
PCDH11X	27328	hgsc.bcm.edu	37	chrX	91090533	91090533	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttgtccgggacgtacattttCgcggtcctgctagcatgcgt	5	13	12	11	5	0	0	0	0	0	0	3	1	2	1	2	2	4	3	2	2	2	5	rs56704613	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:91090533C>T	ENST00000373094.1	+	1	875	c.30C>T	c.(28-30)ttC>ttT	p.F10F	PCDH11X_ENST00000395337.2_Silent_p.F10F|PCDH11X_ENST00000504220.2_Silent_p.F10F|PCDH11X_ENST00000298274.8_Silent_p.F10F|PCDH11X_ENST00000361724.1_Silent_p.F10F|PCDH11X_ENST00000373088.1_Silent_p.F10F|PCDH11X_ENST00000361655.2_Silent_p.F10F|PCDH11X_ENST00000373097.1_Silent_p.F10F|PCDH11X_ENST00000406881.1_Silent_p.F10F	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	10					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						CGTACATTTTCGCGGTCCTGC	0.488													C|||	266	0.0704636	0.1868	0.0245	3775	,	,		12350	0.0		0.002	False		,,,				2504	0.0				p.F10F	NSCLC(38;925 1092 2571 38200 45895)	Atlas-SNP	.											.	PCDH11X	714	.	0			c.C30T						PASS	.	C	,,,,,,,	788,3047		66,529,127,1037,444	131	105	114		30,30,30,30,30,30,30,30	1	1	X	dbSNP_129	114	5,6723		0,4,1,2424,1871	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PCDH11X	NM_001168360.1,NM_001168361.1,NM_001168362.1,NM_001168363.1,NM_014522.1,NM_032967.2,NM_032968.3,NM_032969.3	,,,,,,,	66,533,128,3461,2315	TT,TC,T,CC,C		0.0743,20.5476,7.5073	,,,,,,,	10/1340,10/1066,10/1311,10/1330,10/1022,10/1026,10/1348,10/1338	91090533	793,9770	2203	4300	6503	SO:0001819	synonymous_variant	27328	exon1			CATTTTCGCGGTC	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.30C>T	X.37:g.91090533C>T		517	0	0		479	477	0.995825	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	37	CCDS14461.1																																																																																			C|0.922;T|0.078	0.078	strong		0.488	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969		T	91090533	C	T	91090533	2	4	22	1	0	0	0	0	0	0	0	1	11517	883	31	1		1	PCDH11X	23	91090533	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	6489585	91090533	64180027	4498	7399											
DIAPH2	1730	hgsc.bcm.edu	37	chrX	96354707	96354707	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttagaaccttgtgaaacaTcttcctgagcagaagatact	13	13	7	8	0	1	5	0	2	1	3	2	5	2	5	2	0	4	1	2	0	5	5	rs20387	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:96354707T>C	ENST00000324765.8	+	20	2609	c.2262T>C	c.(2260-2262)caT>caC	p.H754H	DIAPH2_ENST00000373061.3_Silent_p.H754H|DIAPH2_ENST00000373054.4_Silent_p.H750H|DIAPH2_ENST00000373049.4_Silent_p.H754H|DIAPH2_ENST00000355827.4_Silent_p.H754H			O60879	DIAP2_HUMAN	diaphanous-related formin 2	754	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						TTGTGAAACATCTTCCTGAGC	0.308													T|||	17	0.00450331	0.0121	0.0014	3775	,	,		10804	0.0		0.0	False		,,,				2504	0.0				p.H754H		Atlas-SNP	.											.	DIAPH2	148	.	0			c.T2262C						PASS	.	T	,	74,3761		0,62,12,1570,559	84	69	74		2262,2262	0.1	0.9	X	dbSNP_67	74	1,6727		0,0,1,2428,1871	no	coding-synonymous,coding-synonymous	DIAPH2	NM_006729.4,NM_007309.3	,	0,62,13,3998,2430	CC,CT,C,TT,T		0.0149,1.9296,0.71	,	754/1102,754/1097	96354707	75,10488	2203	4300	6503	SO:0001819	synonymous_variant	1730	exon20			GAAACATCTTCCT	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.2262T>C	X.37:g.96354707T>C		124	0	0		142	75	0.528169	NM_007309	A6NG19|O60878|Q8WX06|Q8WX48|Q9UJL2	Silent	SNP	ENST00000324765.8	37	CCDS14467.1																																																																																			T|0.993;C|0.007	0.007	strong		0.308	DIAPH2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058871.2	NM_006729, NM_007309		C	96354707	T	C	96354707	2	2	22	1	0	0	0	0	0	0	0	1	4521	1432	50	3		3	DIAPH2	23	96354707	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	5264174	96354707	58915853	4499	7400											
SYTL4	94121	hgsc.bcm.edu	37	chrX	99955925	99955925	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccgctcctgaatgatcttTcttcctggccagatgtcacc	6	13	8	14	1	3	3	1	2	2	1	5	3	5	3	5	1	1	1	5	1	1	2	rs16983588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:99955925T>C	ENST00000372989.1	-	7	838	c.507A>G	c.(505-507)agA>agG	p.R169R	SYTL4_ENST00000276141.6_Silent_p.R169R|SYTL4_ENST00000454200.2_Silent_p.R169R|SYTL4_ENST00000455616.1_Silent_p.R169R|SYTL4_ENST00000263033.5_Silent_p.R169R|SYTL4_ENST00000372981.1_Silent_p.R169R	NM_080737.2	NP_542775.2	Q96C24	SYTL4_HUMAN	synaptotagmin-like 4	169					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|multivesicular body sorting pathway (GO:0071985)|negative regulation of insulin secretion (GO:0046676)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)	neurexin family protein binding (GO:0042043)|phospholipid binding (GO:0005543)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(2)	27					"""Insulin(DB00071)|Insulin Regular(DB00030)"	GAATGATCTTTCTTCCTGGCC	0.408													t|||	572	0.151523	0.4077	0.0432	3775	,	,		13506	0.0		0.002	False		,,,				2504	0.001				p.R169R		Atlas-SNP	.											.	SYTL4	72	.	0			c.A507G						PASS	.		,,	1688,2147		321,777,269,534,302	142	127	133		507,507,507	3.4	1	X	dbSNP_123	133	24,6704		0,19,5,2409,1867	no	coding-synonymous,coding-synonymous,coding-synonymous	SYTL4	NM_001129896.2,NM_001174068.1,NM_080737.2	,,	321,796,274,2943,2169	CC,CT,C,TT,T		0.3567,44.0156,16.2075	,,	169/672,169/672,169/672	99955925	1712,8851	2203	4300	6503	SO:0001819	synonymous_variant	94121	exon6			GATCTTTCTTCCT		CCDS14472.1	Xq21.33	2008-07-31	2008-07-31		ENSG00000102362	ENSG00000102362			15588	protein-coding gene	gene with protein product	"granuphilin-a", "exophilin-2"	300723					Standard	NM_080737		Approved		uc010nnc.3	Q96C24	OTTHUMG00000022004	ENST00000372989.1:c.507A>G	X.37:g.99955925T>C		318	0	0		269	269	1	NM_001129896	Q5H9J3|Q5JPG8|Q8N9P4|Q9H4R0|Q9H4R1	Silent	SNP	ENST00000372989.1	37	CCDS14472.1																																																																																			0|0.004;C|0.166	0.166	strong		0.408	SYTL4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057488.1	NM_080737		C	99955925	T	C	99955925	2	2	22	1	0	0	0	0	0	0	0	1	15500	1780	62	3		3	SYTL4	23	99955925	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	3601218	99955925	55314635	4500	7401											
TRMT2B	79979	hgsc.bcm.edu	37	chrX	100278558	100278558	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagtatccaccttcatgaaaTacaaggcagggctccaatgg	13	8	9	11	0	1	1	1	1	0	0	3	1	3	1	3	3	1	3	3	3	5	3	rs61745518	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:100278558T>C	ENST00000372936.3	-	8	1429	c.657A>G	c.(655-657)gtA>gtG	p.V219V	TRMT2B_ENST00000478422.1_5'Flank|TRMT2B_ENST00000372939.1_Silent_p.V174V|TRMT2B_ENST00000338687.7_Silent_p.V174V|TRMT2B_ENST00000545398.1_Silent_p.V219V|TRMT2B_ENST00000372931.5_Silent_p.V219V|TRMT2B_ENST00000372935.1_Silent_p.V219V	NM_024917.5	NP_079193.2	Q96GJ1	TRM2_HUMAN	tRNA methyltransferase 2 homolog B (S. cerevisiae)	219						mitochondrion (GO:0005739)	S-adenosylmethionine-dependent tRNA (m5U54) methyltransferase activity (GO:0030697)			breast(3)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	24						CTTCATGAAATACAAGGCAGG	0.458													T|||	74	0.0196026	0.0545	0.0029	3775	,	,		14763	0.0		0.0	False		,,,				2504	0.0				p.V219V		Atlas-SNP	.											.	TRMT2B	33	.	0			c.A657G						PASS	.	T	,,,	236,3599		8,187,33,1437,538	142	110	121		657,522,657,657	0.3	0.6	X	dbSNP_129	121	1,6727		0,1,0,2427,1872	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRMT2B	NM_001167970.1,NM_001167971.1,NM_001167972.1,NM_024917.5	,,,	8,188,33,3864,2410	CC,CT,C,TT,T		0.0149,6.1538,2.2437	,,,	219/505,174/460,219/505,219/505	100278558	237,10326	2203	4300	6503	SO:0001819	synonymous_variant	79979	exon7			ATGAAATACAAGG	BC020116	CCDS14477.1, CCDS55464.1	Xq22.1	2012-06-12	2012-06-12	2008-09-17	ENSG00000188917	ENSG00000188917			25748	protein-coding gene	gene with protein product			"chromosome X open reading frame 34"	CXorf34		14702039	Standard	NM_024917		Approved	FLJ12687	uc004egq.3	Q96GJ1	OTTHUMG00000022017	ENST00000372936.3:c.657A>G	X.37:g.100278558T>C		165	0	0		180	175	0.972222	NM_001167972	A6NDG5|A6NEI9|A6NMG6|Q5JPF0|Q5JVY6|Q96HU7|Q96IH9|Q9H9K2	Silent	SNP	ENST00000372936.3	37	CCDS14477.1																																																																																			T|0.979;C|0.021	0.021	strong		0.458	TRMT2B-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057512.1	NM_024917		C	100278558	T	C	100278558	2	2	22	1	0	0	0	0	0	0	0	1	16581	1393	49	3		3	TRMT2B	23	100278558	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	322633	100278558	54992002	4501	7402											
BTK	695	hgsc.bcm.edu	37	chrX	100617218	100617218	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcttccggtgagaactcccAggttttaagcctgcaaaaca	11	10	9	11	1	1	1	0	1	1	1	3	2	3	1	3	2	4	2	3	2	4	3	rs148358153	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:100617218A>G	ENST00000308731.7	-	7	694	c.531T>C	c.(529-531)ccT>ccC	p.P177P	BTK_ENST00000372880.1_Silent_p.P177P	NM_000061.2	NP_000052.1	Q06187	BTK_HUMAN	Bruton agammaglobulinemia tyrosine kinase	177					adaptive immune response (GO:0002250)|apoptotic signaling pathway (GO:0097190)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|calcium-mediated signaling (GO:0019722)|cell maturation (GO:0048469)|Fc-epsilon receptor signaling pathway (GO:0038095)|histamine secretion by mast cell (GO:0002553)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of B cell apoptotic process (GO:0002902)|regulation of B cell cytokine production (GO:0002721)|response to organic substance (GO:0010033)|response to reactive oxygen species (GO:0000302)|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)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein tyrosine kinase activity (GO:0004713)			breast(4)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(25)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						GAGAACTCCCAGGTTTTAAGC	0.498									Agammaglobulinemia, X-linked				A|||	26	0.00688742	0.0182	0.0029	3775	,	,		13779	0.0		0.0	False		,,,				2504	0.0				p.P177P		Atlas-SNP	.											.	BTK	87	.	0			c.T531C						PASS	.	A		73,3762		0,67,6,1565,565	111	95	100		531	2.7	1	X	dbSNP_134	100	0,6728		0,0,0,2428,1872	no	coding-synonymous	BTK	NM_000061.2		0,67,6,3993,2437	GG,GA,G,AA,A		0.0,1.9035,0.6911		177/660	100617218	73,10490	2203	4300	6503	SO:0001819	synonymous_variant	695	exon7	Familial Cancer Database	Bruton Type Agammaglobulinemia	ACTCCCAGGTTTT	AK057105	CCDS14482.1, CCDS76002.1, CCDS76003.1	Xq21.33-q22	2014-09-17			ENSG00000010671	ENSG00000010671	2.7.10.1	"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	1133	protein-coding gene	gene with protein product		300300		AGMX1, IMD1		8380905	Standard	NM_000061		Approved	ATK, XLA, PSCTK1	uc004ehg.2	Q06187	OTTHUMG00000022022	ENST00000308731.7:c.531T>C	X.37:g.100617218A>G		126	0	0		101	46	0.455446	NM_000061	B2RAW1|Q32ML5	Silent	SNP	ENST00000308731.7	37	CCDS14482.1																																																																																			A|0.993;G|0.007	0.007	strong		0.498	BTK-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057532.2	NM_000061		G	100617218	A	G	100617218	2	3	22	1	0	0	0	0	0	0	0	1	1559	175	7	3		3	BTK	23	100617218	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	338660	100617218	54653342	4502	7403											
ARMCX2	9823	hgsc.bcm.edu	37	chrX	100912065	100912065	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accgctgccctggaagtctcCgcttctctgggagcttctgc	4	11	11	15	2	3	0	0	0	3	0	5	2	3	2	3	2	3	3	3	2	1	2	rs78189978	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:100912065C>T	ENST00000328766.5	-	5	963	c.510G>A	c.(508-510)gcG>gcA	p.A170A	ARMCX2_ENST00000356824.4_Silent_p.A170A|ARMCX2_ENST00000467416.1_5'Flank|ARMCX2_ENST00000330154.2_Silent_p.A170A	NM_014782.5	NP_055597.1	Q7L311	ARMX2_HUMAN	armadillo repeat containing, X-linked 2	170	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						TGGAAGTCTCCGCTTCTCTGG	0.652													C|||	57	0.0150993	0.0416	0.0029	3775	,	,		11432	0.0		0.0	False		,,,				2504	0.0				p.A170A		Atlas-SNP	.											.	ARMCX2	75	.	0			c.G510A						PASS	.	C	,	213,3621		7,168,31,1457,539	28	29	28		510,510	-0.1	0	X	dbSNP_131	28	1,6713		0,1,0,2427,1858	no	coding-synonymous,coding-synonymous	ARMCX2	NM_014782.5,NM_177949.2	,	7,169,31,3884,2397	TT,TC,T,CC,C		0.0149,5.5556,2.0288	,	170/633,170/633	100912065	214,10334	2202	4286	6488	SO:0001819	synonymous_variant	9823	exon5			AGTCTCCGCTTCT	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.510G>A	X.37:g.100912065C>T		116	0	0		74	46	0.621622	NM_014782	O60267|Q5H9D9	Silent	SNP	ENST00000328766.5	37	CCDS14490.1																																																																																			C|0.981;T|0.019	0.019	strong		0.652	ARMCX2-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057586.1	NM_014782		T	100912065	C	T	100912065	2	4	22	1	0	0	0	0	0	0	0	1	960	639	23	1		1	ARMCX2	23	100912065	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	294847	100912065	54358495	4503	7404											
GPRASP1	9737	hgsc.bcm.edu	37	chrX	101912465	101912465	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaaccttgcttaattatccGtcctcccgagttagaacaag	12	11	7	11	2	0	1	0	0	0	1	3	3	3	1	4	0	3	2	4	0	6	4	rs1124050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:101912465G>T	ENST00000361600.5	+	5	4425	c.3624G>T	c.(3622-3624)ccG>ccT	p.P1208P	RP4-769N13.7_ENST00000602441.1_RNA|GPRASP1_ENST00000537097.1_Silent_p.P1208P|GPRASP1_ENST00000444152.1_Silent_p.P1208P|GPRASP1_ENST00000415986.1_Silent_p.P1208P	NM_014710.4	NP_055525.3	Q5JY77	GASP1_HUMAN	G protein-coupled receptor associated sorting protein 1	1208	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						TTAATTATCCGTCCTCCCGAG	0.383													G|||	50	0.013245	0.0371	0.0014	3775	,	,		15018	0.0		0.0	False		,,,				2504	0.0				p.P1208P		Atlas-SNP	.											.	GPRASP1	140	.	0			c.G3624T						PASS	.	G	,,,,	148,3687		2,116,28,1514,543	103	93	97		3624,3624,3624,,3624	-5.8	0.1	X	dbSNP_86	97	0,6728		0,0,0,2428,1872	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous	GPRASP1,ARMCX5-GPRASP2	NM_001099410.1,NM_001099411.1,NM_001184727.1,NM_001199818.1,NM_014710.4	,,,,	2,116,28,3942,2415	TT,TG,T,GG,G		0.0,3.8592,1.4011	,,,,	1208/1396,1208/1396,1208/1396,,1208/1396	101912465	148,10415	2203	4300	6503	SO:0001819	synonymous_variant	9737	exon3			TTATCCGTCCTCC	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.3624G>T	X.37:g.101912465G>T		280	1	0.00357143		293	107	0.365188	NM_001099411	O43168|Q96LA1	Silent	SNP	ENST00000361600.5	37	CCDS35352.1																																																																																			0|0.003;A|0.000;G|0.981;T|0.016	0.016	strong		0.383	GPRASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057634.2	NM_014710		T	101912465	G	T	101912465	2	4	22	1	0	0	0	0	0	0	0	1	6731	1132	40	4		4	GPRASP1	23	101912465	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1000400	101912465	53358095	4504	7405											
GPRASP2	114928	hgsc.bcm.edu	37	chrX	101970662	101970662	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggatctgaggatgaggccAgcaacccattctccttctgg	8	10	11	12	0	3	2	0	2	3	0	4	4	3	4	3	4	2	1	3	4	1	2	rs113336462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:101970662A>G	ENST00000535209.1	+	4	1696	c.865A>G	c.(865-867)Agc>Ggc	p.S289G	GPRASP2_ENST00000332262.5_Missense_Mutation_p.S289G|GPRASP2_ENST00000543253.1_Missense_Mutation_p.S289G			Q96D09	GASP2_HUMAN	G protein-coupled receptor associated sorting protein 2	289						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						GGATGAGGCCAGCAACCCATT	0.507													.|||	50	0.013245	0.0371	0.0014	3775	,	,		14521	0.0		0.0	False		,,,				2504	0.0				p.S289G		Atlas-SNP	.											.	GPRASP2	89	.	0			c.A865G						PASS	.	G	GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER	148,3687		2,116,28,1514,543	112	111	112		865,865,865,865,865,865	1.3	0	X	dbSNP_132	112	0,6728		0,0,0,2428,1872	yes	missense,missense,missense,missense,missense,missense	GPRASP2,ARMCX5-GPRASP2	NM_001004051.3,NM_001184874.2,NM_001184875.2,NM_001184876.2,NM_001199818.1,NM_138437.5	56,56,56,56,56,56	2,116,28,3942,2415	GG,GA,G,AA,A		0.0,3.8592,1.4011	benign,benign,benign,benign,benign,benign	289/839,289/839,289/839,289/839,289/839,289/839	101970662	148,10415	2203	4300	6503	SO:0001583	missense	114928	exon4			GAGGCCAGCAACC	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.865A>G	X.37:g.101970662A>G	ENSP00000437394:p.Ser289Gly	130	0	0		157	64	0.407643	NM_138437	D3DXA0|Q8NAB4	Missense_Mutation	SNP	ENST00000535209.1	37	CCDS14501.1	15	0.009041591320072333	11	0.022727272727272728	0	0.0	0	0.0	0	0.0	G	0.001	-3.165628	0.00028	0.038592	0.0	ENSG00000158301	ENST00000543253;ENST00000535209;ENST00000332262	T;T;T	0.06218	3.33;3.33;3.33	4.2	1.33	0.21861	.	0.304465	0.24078	N	0.041755	T	0.00524	0.0017	N	0.02539	-0.55	0.18873	N	0.999988	B	0.02656	0.0	B	0.01281	0.0	T	0.46373	-0.9196	10	0.22706	T	0.39	-0.1711	4.5595	0.12152	0.2852:0.0:0.5594:0.1554	.	289	Q96D09	GASP2_HUMAN	G	289	ENSP00000437872:S289G;ENSP00000437394:S289G;ENSP00000339057:S289G	ENSP00000339057:S289G	S	+	1	0	GPRASP2	101857318	0.826000	0.29277	0.037000	0.18230	0.001000	0.01503	0.260000	0.18424	-0.074000	0.12820	-0.834000	0.03071	AGC	A|0.986;G|0.014	0.014	strong		0.507	GPRASP2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057626.2	NM_138437		G	101970662	A	G	101970662	3	3	22	1	0	0	0	0	1	0	0	0	6732	188	7	3	867	3	GPRASP2	23	101970662	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	58197	101970662	53299898	4505	7406											
GPRASP2	114928	hgsc.bcm.edu	37	chrX	101970877	101970877	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacaaagaagatcctaatacTgccttgaaactcagggccca	15	7	8	11	0	1	3	1	1	0	2	2	4	2	3	3	1	3	0	3	1	5	3	rs113906002	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:101970877T>C	ENST00000535209.1	+	4	1911	c.1080T>C	c.(1078-1080)acT>acC	p.T360T	GPRASP2_ENST00000332262.5_Silent_p.T360T|GPRASP2_ENST00000543253.1_Silent_p.T360T			Q96D09	GASP2_HUMAN	G protein-coupled receptor associated sorting protein 2	360						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						ATCCTAATACTGCCTTGAAAC	0.463													.|||	50	0.013245	0.0371	0.0014	3775	,	,		14732	0.0		0.0	False		,,,				2504	0.0				p.T360T		Atlas-SNP	.											.	GPRASP2	89	.	0			c.T1080C						PASS	.	C	,,,,,	148,3687		2,116,28,1514,543	90	84	86		1080,1080,1080,1080,1080,1080	0.1	0	X	dbSNP_132	86	0,6728		0,0,0,2428,1872	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GPRASP2,ARMCX5-GPRASP2	NM_001004051.3,NM_001184874.2,NM_001184875.2,NM_001184876.2,NM_001199818.1,NM_138437.5	,,,,,	2,116,28,3942,2415	CC,CT,C,TT,T		0.0,3.8592,1.4011	,,,,,	360/839,360/839,360/839,360/839,360/839,360/839	101970877	148,10415	2203	4300	6503	SO:0001819	synonymous_variant	114928	exon4			TAATACTGCCTTG	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.1080T>C	X.37:g.101970877T>C		104	0	0		113	38	0.336283	NM_138437	D3DXA0|Q8NAB4	Silent	SNP	ENST00000535209.1	37	CCDS14501.1																																																																																			T|0.986;C|0.014	0.014	strong		0.463	GPRASP2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057626.2	NM_138437		C	101970877	T	C	101970877	2	2	22	1	0	0	0	0	0	0	0	1	6732	1567	55	3		3	GPRASP2	23	101970877	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	215	101970877	53299683	4506	7407											
BHLHB9	80823	hgsc.bcm.edu	37	chrX	102004046	102004046	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aggcctgtagccaagaccagGgccaaagcaaaagccaagac	16	2	11	12	0	0	2	0	0	0	2	0	2	0	2	5	2	3	2	5	2	6	1	rs17003869	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102004046G>A	ENST00000372735.1	+	4	708	c.123G>A	c.(121-123)agG>agA	p.R41R	BHLHB9_ENST00000447531.1_Silent_p.R41R|BHLHB9_ENST00000361229.4_Silent_p.R41R|BHLHB9_ENST00000457056.1_Silent_p.R41R|BHLHB9_ENST00000448867.1_Silent_p.R41R			Q6PI77	BHLH9_HUMAN	basic helix-loop-helix domain containing, class B, 9	41					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						CCAAGACCAGGGCCAAAGCAA	0.502													G|||	50	0.013245	0.0371	0.0014	3775	,	,		15788	0.0		0.0	False		,,,				2504	0.0				p.R41R		Atlas-SNP	.											.	BHLHB9	60	.	0			c.G123A						PASS	.	G	,,,,,,,	149,3686		2,117,28,1513,543	120	102	108		123,123,123,123,123,123,123,123	-3.2	0	X	dbSNP_123	108	0,6728		0,0,0,2428,1872	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BHLHB9	NM_001142524.1,NM_001142525.1,NM_001142526.1,NM_001142527.1,NM_001142528.1,NM_001142529.1,NM_001142530.1,NM_030639.2	,,,,,,,	2,117,28,3941,2415	AA,AG,A,GG,G		0.0,3.8853,1.4106	,,,,,,,	41/548,41/548,41/548,41/548,41/548,41/548,41/548,41/548	102004046	149,10414	2203	4300	6503	SO:0001819	synonymous_variant	80823	exon2			GACCAGGGCCAAA	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.123G>A	X.37:g.102004046G>A		322	0	0		412	145	0.351942	NM_001142530	Q9C0G2	Silent	SNP	ENST00000372735.1	37	CCDS14502.1																																																																																			0|0.003;A|0.015	0.015	strong		0.502	BHLHB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057630.1	NM_030639		A	102004046	G	A	102004046	2	1	22	1	0	0	0	0	0	0	0	1	1420	1223	43	2		2	BHLHB9	23	102004046	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	33169	102004046	53266514	4507	7408											
BHLHB9	80823	hgsc.bcm.edu	37	chrX	102005371	102005371	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgcagccagagacatgatcaAtatgaaggcattggcagcat	14	8	11	8	0	1	3	1	2	0	1	1	4	1	3	1	2	3	4	1	2	3	2			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102005371A>T	ENST00000372735.1	+	4	2033	c.1448A>T	c.(1447-1449)aAt>aTt	p.N483I	BHLHB9_ENST00000447531.1_Missense_Mutation_p.N483I|BHLHB9_ENST00000361229.4_Missense_Mutation_p.N483I|BHLHB9_ENST00000457056.1_Missense_Mutation_p.N483I|BHLHB9_ENST00000448867.1_Missense_Mutation_p.N483I			Q6PI77	BHLH9_HUMAN	basic helix-loop-helix domain containing, class B, 9	483					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						GACATGATCAATATGAAGGCA	0.363																																					p.N483I		Atlas-SNP	.											.	BHLHB9	60	.	0			c.A1448T						PASS	.						120	119	119					X																	102005371		2203	4300	6503	SO:0001583	missense	80823	exon2			TGATCAATATGAA	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.1448A>T	X.37:g.102005371A>T	ENSP00000361820:p.Asn483Ile	438	0	0		429	59	0.137529	NM_001142530	Q9C0G2	Missense_Mutation	SNP	ENST00000372735.1	37	CCDS14502.1	.	.	.	.	.	.	.	.	.	.	A	13.45	2.240331	0.39598	.	.	ENSG00000198908	ENST00000457056;ENST00000361229;ENST00000447531;ENST00000448867;ENST00000372735	T;T;T;T;T	0.32272	1.46;1.46;1.46;1.46;1.46	4.24	1.84	0.25277	Armadillo-like helical (1);Armadillo-type fold (1);	0.647734	0.13738	N	0.366174	T	0.23210	0.0561	N	0.08118	0	0.09310	N	1	D	0.53462	0.96	P	0.57101	0.813	T	0.08411	-1.0723	9	.	.	.	-29.9634	5.1019	0.14764	0.7516:0.0:0.2484:0.0	.	483	Q6PI77	BHLH9_HUMAN	I	483	ENSP00000403226:N483I;ENSP00000354675:N483I;ENSP00000405893:N483I;ENSP00000391722:N483I;ENSP00000361820:N483I	.	N	+	2	0	BHLHB9	101892027	0.006000	0.16342	0.005000	0.12908	0.995000	0.86356	0.712000	0.25779	0.262000	0.21774	0.339000	0.21740	AAT	.	.	none		0.363	BHLHB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057630.1	NM_030639		T	102005371	A	T	102005371	3	4	22	1	0	0	0	0	1	0	0	0	1420	101	4	5	1450	5	BHLHB9	23	102005371	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1325	102005371	53265189	4508	7409											
RAB40AL	282808	hgsc.bcm.edu	37	chrX	102192372	102192372	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gacggcacggccgagtccccGtacagtcacctggggggaat	8	5	15	13	4	1	0	1	0	0	0	2	3	2	1	4	5	1	2	4	5	2	1	rs61745023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102192372G>A	ENST00000218249.5	+	1	173	c.126G>A	c.(124-126)ccG>ccA	p.P42P	LL0XNC01-237H1.3_ENST00000413528.1_RNA	NM_001031834.1	NP_001027004.1	P0C0E4	RB40L_HUMAN	RAB40A, member RAS oncogene family-like	42					protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(4)|large_intestine(2)|lung(3)|ovary(3)	12						CCGAGTCCCCGTACAGTCACC	0.622													.|||	67	0.0177483	0.0477	0.0058	3775	,	,		11299	0.0		0.0	False		,,,				2504	0.0				p.P42P		Atlas-SNP	.											.	RAB40AL	33	.	0			c.G126A						PASS	.	G		213,3622		4,171,34,1457,537	115	109	111		126	-1.7	0	X	dbSNP_129	111	0,6728		0,0,0,2428,1872	no	coding-synonymous	RAB40AL	NM_001031834.1		4,171,34,3885,2409	AA,AG,A,GG,G		0.0,5.5541,2.0165		42/279	102192372	213,10350	2203	4300	6503	SO:0001819	synonymous_variant	282808	exon1			GTCCCCGTACAGT	BC101169	CCDS35353.1	Xq22.2	2008-02-05			ENSG00000102128	ENSG00000102128			25410	protein-coding gene	gene with protein product	"Ras like GTPase"	300405					Standard	NM_001031834		Approved	RAR2, RLGP	uc004ejs.3	P0C0E4	OTTHUMG00000022084	ENST00000218249.5:c.126G>A	X.37:g.102192372G>A		507	0	0		455	145	0.318681	NM_001031834	Q495H3	Silent	SNP	ENST00000218249.5	37	CCDS35353.1																																																																																			G|0.981;A|0.019	0.019	strong		0.622	RAB40AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057679.1	NM_001031834		A	102192372	G	A	102192372	2	1	22	1	0	0	0	0	0	0	0	1	12955	1132	40	1		1	RAB40AL	23	102192372	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	187001	102192372	53078188	4509	7410											
RAB40AL	282808	hgsc.bcm.edu	37	chrX	102192885	102192885	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catctggtggacaagctcccGctccccattgccttaagaag	9	9	9	14	1	1	1	0	0	1	1	3	2	3	2	4	2	2	2	4	2	3	2	rs7876193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102192885G>A	ENST00000218249.5	+	1	686	c.639G>A	c.(637-639)ccG>ccA	p.P213P	LL0XNC01-237H1.3_ENST00000413528.1_RNA	NM_001031834.1	NP_001027004.1	P0C0E4	RB40L_HUMAN	RAB40A, member RAS oncogene family-like	213	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(4)|large_intestine(2)|lung(3)|ovary(3)	12						ACAAGCTCCCGCTCCCCATTG	0.592													.|||	68	0.0180132	0.0477	0.0058	3775	,	,		13822	0.0		0.0	False		,,,				2504	0.001				p.P213P		Atlas-SNP	.											.	RAB40AL	33	.	0			c.G639A						PASS	.	G		213,3622		4,171,34,1457,537	145	117	127		639	-0.3	0.4	X	dbSNP_116	127	0,6728		0,0,0,2428,1872	no	coding-synonymous	RAB40AL	NM_001031834.1		4,171,34,3885,2409	AA,AG,A,GG,G		0.0,5.5541,2.0165		213/279	102192885	213,10350	2203	4300	6503	SO:0001819	synonymous_variant	282808	exon1			GCTCCCGCTCCCC	BC101169	CCDS35353.1	Xq22.2	2008-02-05			ENSG00000102128	ENSG00000102128			25410	protein-coding gene	gene with protein product	"Ras like GTPase"	300405					Standard	NM_001031834		Approved	RAR2, RLGP	uc004ejs.3	P0C0E4	OTTHUMG00000022084	ENST00000218249.5:c.639G>A	X.37:g.102192885G>A		266	0	0		310	111	0.358065	NM_001031834	Q495H3	Silent	SNP	ENST00000218249.5	37	CCDS35353.1																																																																																			G|0.981;A|0.019	0.019	strong		0.592	RAB40AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057679.1	NM_001031834		A	102192885	G	A	102192885	2	1	22	1	0	0	0	0	0	0	0	1	12955	1074	38	1		1	RAB40AL	23	102192885	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	513	102192885	53077675	4510	7411											
TCEAL3	85012	hgsc.bcm.edu	37	chrX	102864251	102864251	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgagggcaagccagcctccCaggcaaagccagagagccag	12	1	14	14	1	0	1	0	0	0	1	1	3	1	1	5	2	4	2	5	2	2	0	rs12009847	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102864251C>G	ENST00000372628.1	+	3	617	c.259C>G	c.(259-261)Cag>Gag	p.Q87E	TCEAL3_ENST00000372627.5_Missense_Mutation_p.Q87E|TCEAL3_ENST00000477014.1_Intron|TCEAL3_ENST00000243286.3_Missense_Mutation_p.Q87E			Q969E4	TCAL3_HUMAN	transcription elongation factor A (SII)-like 3	87			Q -> E (in dbSNP:rs12009847).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)	16						GCCAGCCTCCCAGGCAAAGCC	0.617													C|||	235	0.0622517	0.1679	0.0173	3775	,	,		11795	0.0		0.001	False		,,,				2504	0.0				p.Q87E		Atlas-SNP	.											.	TCEAL3	24	.	0			c.C259G						PASS	.	C	GLU/GLN,GLU/GLN	702,3133		56,485,105,1091,466	97	92	94		259,259	2.3	0.2	X	dbSNP_120	94	6,6722		0,5,1,2423,1871	no	missense,missense	TCEAL3	NM_001006933.1,NM_032926.2	29,29	56,490,106,3514,2337	GG,GC,G,CC,C		0.0892,18.3051,6.7026	benign,benign	87/201,87/201	102864251	708,9855	2203	4300	6503	SO:0001583	missense	85012	exon3			GCCTCCCAGGCAA	BC008703	CCDS14511.1	Xq22.2	2014-03-21			ENSG00000196507	ENSG00000196507			28247	protein-coding gene	gene with protein product						16221301	Standard	NM_032926		Approved	MGC15737, WEX8	uc004ekr.3	Q969E4	OTTHUMG00000022106	ENST00000372628.1:c.259C>G	X.37:g.102864251C>G	ENSP00000361711:p.Gln87Glu	379	1	0.00263852		389	379	0.974293	NM_001006933	D3DXA4	Missense_Mutation	SNP	ENST00000372628.1	37	CCDS14511.1	84	0.05063291139240506	50	0.11682242990654206	2	0.0055248618784530384	0	0.0	0	0.0	C	0.004	-2.241804	0.00274	0.183051	8.92E-4	ENSG00000196507	ENST00000372628;ENST00000372627;ENST00000243286	T;T;T	0.21361	2.01;2.01;2.01	4.18	2.34	0.29019	.	0.536654	0.14096	N	0.341716	T	0.00039	0.0001	N	0.16602	0.42	0.80722	P	0.0	B	0.15141	0.012	B	0.12156	0.007	T	0.33085	-0.9882	9	0.02654	T	1	.	10.3974	0.44209	0.0:0.7424:0.2576:0.0	rs12009847;rs12009847	87	Q969E4	TCAL3_HUMAN	E	87	ENSP00000361711:Q87E;ENSP00000361710:Q87E;ENSP00000243286:Q87E	ENSP00000243286:Q87E	Q	+	1	0	TCEAL3	102750907	0.890000	0.30428	0.249000	0.24280	0.183000	0.23260	1.387000	0.34430	0.496000	0.27904	0.538000	0.68166	CAG	C|0.936;G|0.064	0.064	strong		0.617	TCEAL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057737.1	NM_032926		G	102864251	C	G	102864251	3	3	22	1	0	0	0	0	1	0	0	0	15687	595	21	4	261	4	TCEAL3	23	102864251	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	671366	102864251	52406309	4511	7412											
GLRA4	441509	hgsc.bcm.edu	37	chrX	102962343	102962343	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggaggttggggactataaaTgccagaaccttccattggac	11	10	12	8	0	0	1	0	0	0	1	1	4	1	4	3	5	2	1	3	5	4	5	rs61744012		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102962343T>C	ENST00000372617.4	-	9	1603	c.1183A>G	c.(1183-1185)Att>Gtt	p.I395V		NM_001024452.2	NP_001019623.2	Q5JXX5	GLRA4_HUMAN	glycine receptor, alpha 4	395						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						GGACTATAAATGCCAGAACCT	0.527													T|||	48	0.0127152	0.0348	0.0029	3775	,	,		14232	0.0		0.0	False		,,,				2504	0.0				p.I395V		Atlas-SNP	.											.	GLRA4	86	.	0			c.A1183G						PASS	.	T	VAL/ILE	94,3180		0,77,17,1275,553	105	100	102		1183	5	1	X	dbSNP_129	102	1,6426		0,1,0,2321,1783	yes	missense	GLRA4	NM_001024452.2	29	0,78,17,3596,2336	CC,CT,C,TT,T		0.0156,2.8711,0.9793	benign	395/418	102962343	95,9606	1922	4105	6027	SO:0001583	missense	441509	exon9			TATAAATGCCAGA	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.1183A>G	X.37:g.102962343T>C	ENSP00000361700:p.Ile395Val	116	0	0		136	84	0.617647	NM_001024452		Missense_Mutation	SNP	ENST00000372617.4	37	CCDS43980.2	16	0.009644364074743821	12	0.024691358024691357	1	0.0027624309392265192	0	0.0	0	0.0	t	2.377	-0.343098	0.05243	0.028711	1.56E-4	ENSG00000188828	ENST00000372617	T	0.77877	-1.13	4.99	4.99	0.66335	.	1.027970	0.07653	N	0.932363	T	0.31263	0.0791	N	0.02539	-0.55	0.27370	N	0.955726	B	0.02656	0.0	B	0.01281	0.0	T	0.31223	-0.9951	10	0.25106	T	0.35	.	9.8284	0.40925	0.0:0.0:0.0:1.0	.	395	Q5JXX5	GLRA4_HUMAN	V	395	ENSP00000361700:I395V	ENSP00000361700:I395V	I	-	1	0	GLRA4	102848999	0.380000	0.25131	0.999000	0.59377	0.987000	0.75469	0.625000	0.24477	1.844000	0.53588	0.441000	0.28932	ATT	T|0.990;C|0.010	0.010	strong		0.527	GLRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057742.2	NM_001024452		C	102962343	T	C	102962343	3	2	22	1	0	0	0	0	1	0	0	0	6465	1464	51	3	73	3	GLRA4	23	102962343	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	98092	102962343	52308217	4512	7413											
GLRA4	441509	hgsc.bcm.edu	37	chrX	102979184	102979184	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atattctcggtaggacaggcGtgggtcattccactgttgcc	7	12	12	10	2	2	0	1	0	1	0	4	1	3	1	2	4	1	2	2	4	2	5	rs16984014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102979184G>A	ENST00000372617.4	-	4	736	c.316C>T	c.(316-318)Cgc>Tgc	p.R106C	GLRA4_ENST00000469567.1_5'Flank	NM_001024452.2	NP_001019623.2	Q5JXX5	GLRA4_HUMAN	glycine receptor, alpha 4	106						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						TAGGACAGGCGTGGGTCATTC	0.542													G|||	280	0.0741722	0.2065	0.0101	3775	,	,		14747	0.0		0.0	False		,,,				2504	0.0				p.R106C		Atlas-SNP	.											.	GLRA4	86	.	0			c.C316T						PASS	.	G	CYS/ARG,CYS/ARG	690,2992		49,480,112,1027,458	109	107	108		316,316	5.4	1	X	dbSNP_123	108	4,6663		0,4,0,2404,1851	yes	missense,missense	GLRA4	NM_001024452.2,NM_001172285.1	180,180	49,484,112,3431,2309	AA,AG,A,GG,G		0.06,18.7398,6.706	probably-damaging,probably-damaging	106/418,106/343	102979184	694,9655	2126	4259	6385	SO:0001583	missense	441509	exon4			ACAGGCGTGGGTC	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.316C>T	X.37:g.102979184G>A	ENSP00000361700:p.Arg106Cys	144	0	0		150	98	0.653333	NM_001024452		Missense_Mutation	SNP	ENST00000372617.4	37	CCDS43980.2	105	0.06329113924050633	66	0.15865384615384615	1	0.0027624309392265192	0	0.0	0	0.0	G	24.1	4.494287	0.85069	0.187398	6.0E-4	ENSG00000188828	ENST00000372617	D	0.82344	-1.6	5.37	5.37	0.77165	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	T	0.01905	0.0060	H	0.95917	3.74	0.09310	P	0.99999999821083	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.17349	-1.0372	9	0.87932	D	0	.	15.3872	0.74711	0.0:0.0:1.0:0.0	rs16984014;rs56514211;rs16984014	106;65	Q5JXX5;B9WSA6	GLRA4_HUMAN;.	C	106	ENSP00000361700:R106C	ENSP00000361700:R106C	R	-	1	0	GLRA4	102865840	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.903000	0.87398	2.224000	0.72417	0.513000	0.50165	CGC	0|0.009;A|0.067	0.067	strong		0.542	GLRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057742.2	NM_001024452		A	102979184	G	A	102979184	3	1	22	1	0	0	0	0	1	0	0	0	6465	1145	40	1	1056	1	GLRA4	23	102979184	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	16841	102979184	52291376	4513	7414											
ZCCHC18	644353	hgsc.bcm.edu	37	chrX	103359334	103359334	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accagactcgcttgcaacagCttcttttaggcgctgagctg	8	11	10	12	2	1	2	0	1	1	1	2	2	1	2	1	1	4	5	1	1	2	4	rs61745269	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:103359334C>T	ENST00000537356.3	+	2	1946	c.532C>T	c.(532-534)Ctt>Ttt	p.L178F	SLC25A53_ENST00000357421.4_Intron|ZCCHC18_ENST00000422784.1_Intron			P0CG32	ZCC18_HUMAN	zinc finger, CCHC domain containing 18	178							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)										CTTGCAACAGCTTCTTTTAGG	0.498													C|||	164	0.0434437	0.118	0.0101	3775	,	,		14288	0.0		0.001	False		,,,				2504	0.0				p.L178F		Atlas-SNP	.											.	.	.	.	0			c.C532T						PASS	.	C	,PHE/LEU	164,1045		12,119,21,386,154	40	32	35		,532	2.7	0.3	X	dbSNP_129	35	1,2390		0,1,0,799,791	yes	intron,missense	MCART6,ZCCHC18	NM_001012755.3,NM_001143978.1	,22	12,120,21,1185,945	TT,TC,T,CC,C		0.0418,13.5649,4.5833	,benign	,178/404	103359334	165,3435	692	1591	2283	SO:0001583	missense	644353	exon3			CAACAGCTTCTTT	AF086548	CCDS65304.1	Xq22.2	2013-01-31	2009-02-03		ENSG00000166707	ENSG00000166707		"Zinc fingers, CCHC domain containing", "Paraneoplastic Ma antigens"	32459	protein-coding gene	gene with protein product	"paraneoplastic Ma antigen family member 7B"		"zinc finger, CCHC domain containing 12 pseudogene 1"				Standard	NM_001143978		Approved	SIZN2, PNMA7B	uc011msh.2	P0CG32	OTTHUMG00000022123	ENST00000537356.3:c.532C>T	X.37:g.103359334C>T	ENSP00000473824:p.Leu178Phe	314	0	0		259	148	0.571429	NM_001143978		Missense_Mutation	SNP	ENST00000537356.3	37																																																																																				C|0.962;T|0.038	0.038	strong		0.498	ZCCHC18-006	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471686.1	NM_001143978		T	103359334	C	T	103359334	3	4	22	1	0	0	0	0	1	0	0	0	17601	797	28	2	534	2	ZCCHC18	23	103359334	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	380150	103359334	51911226	4514	7415											
ESX1	80712	hgsc.bcm.edu	37	chrX	103495007	103495007	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cacatgtgacctgggtggcaGaggcgccatgggcggcccgg	6	5	18	12	3	0	2	0	1	0	1	0	2	0	2	3	6	0	1	3	6	0	0	rs78191648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:103495007G>C	ENST00000372588.4	-	4	1206	c.1123C>G	c.(1123-1125)Ctg>Gtg	p.L375V		NM_153448.3	NP_703149.1	Q8N693	ESX1_HUMAN	ESX homeobox 1	375	15 X 9 AA tandem repeats of P-P-x-x-P-x- P-P-x.				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						CTGGGTGGCAGAGGCGCCATG	0.667													T|||	187	0.0495364	0.1346	0.0101	3775	,	,		7462	0.0		0.001	False		,,,				2504	0.001				p.L375V	Pancreas(200;1705 2227 25194 28471 45274)	Atlas-SNP	.											.	ESX1	57	.	0			c.C1123G						PASS	.	T	VAL/LEU	553,3282		42,388,81,1202,490	36	34	35		1123	-8.3	0	X	dbSNP_131	35	7,6721		0,7,0,2421,1872	yes	missense	ESX1	NM_153448.3	32	42,395,81,3623,2362	CC,CG,C,GG,G		0.104,14.4198,5.3015	benign	375/407	103495007	560,10003	2203	4300	6503	SO:0001583	missense	80712	exon4			GTGGCAGAGGCGC	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.1123C>G	X.37:g.103495007G>C	ENSP00000361669:p.Leu375Val	53	0	0		53	29	0.54717	NM_153448	B0QYU3|Q7Z6K7	Missense_Mutation	SNP	ENST00000372588.4	37	CCDS14516.1	75	0.045207956600361664	55	0.1206140350877193	1	0.002777777777777778	0	0.0	0	0.0	T	0.004	-2.247286	0.00271	0.144198	0.00104	ENSG00000123576	ENST00000372588	T	0.73152	-0.72	4.14	-8.28	0.01013	.	.	.	.	.	T	0.00356	0.0011	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10706	-1.0618	8	0.42905	T	0.14	0.5915	7.4597	0.27287	0.1697:0.6473:0.0849:0.0981	.	375	Q8N693	ESX1_HUMAN	V	375	ENSP00000361669:L375V	ENSP00000361669:L375V	L	-	1	2	ESX1	103381663	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-4.954000	0.00166	-3.304000	0.00192	-2.542000	0.00179	CTG	G|0.948;C|0.052	0.052	strong		0.667	ESX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057763.2	NM_153448		C	103495007	G	C	103495007	3	2	22	1	0	0	0	0	1	0	0	0	5265	933	33	4	101	4	ESX1	23	103495007	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	135673	103495007	51775553	4515	7416											
TEX13A	56157	hgsc.bcm.edu	37	chrX	104464674	104464674	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctctctttctgcacctccacGaggctggtctgggccattct	4	13	9	15	1	4	0	0	0	4	0	6	1	5	0	3	3	1	2	3	3	0	2	rs183606927		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:104464674G>A	ENST00000413579.1	-	2	519	c.408C>T	c.(406-408)ctC>ctT	p.L136L	IL1RAPL2_ENST00000344799.4_Intron|TEX13A_ENST00000372575.1_Silent_p.L136L|IL1RAPL2_ENST00000372582.1_Intron|TEX13A_ENST00000372578.3_Silent_p.L136L			Q9BXU3	TX13A_HUMAN	testis expressed 13A	136							zinc ion binding (GO:0008270)			large_intestine(5)|ovary(2)|upper_aerodigestive_tract(1)	8						GCACCTCCACGAGGCTGGTCT	0.607													G|||	61	0.0161589	0.0363	0.0072	3775	,	,		11953	0.0		0.003	False		,,,				2504	0.0051				p.L136L		Atlas-SNP	.											.	TEX13A	55	.	0			c.C408T						PASS	.	G	,	245,3427		5,188,47,1358,523	36	36	36		,408	-0.1	0	X		36	4,6586		0,1,3,2385,1815	no	intron,coding-synonymous	IL1RAPL2,TEX13A	NM_017416.1,NM_031274.3	,	5,189,50,3743,2338	AA,AG,A,GG,G		0.0607,6.6721,2.4264	,	,136/410	104464674	249,10013	2121	4204	6325	SO:0001819	synonymous_variant	56157	exon2			CTCCACGAGGCTG	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.408C>T	X.37:g.104464674G>A		71	0	0		80	25	0.3125	NM_031274	B1B1G8|Q32NB6	Silent	SNP	ENST00000413579.1	37																																																																																				G|0.992;A|0.008	0.008	strong		0.607	TEX13A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_031274		A	104464674	G	A	104464674	2	1	22	1	0	0	0	0	0	0	0	1	15791	1045	37	1		1	TEX13A	23	104464674	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	969667	104464674	50805886	4516	7417											
NRK	203447	hgsc.bcm.edu	37	chrX	105168689	105168689	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attggagcttgttgtcagggCaagctatggcagagatggaa	11	10	15	5	0	1	1	1	0	0	1	1	4	1	3	0	4	2	5	0	4	3	4	rs16984889	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:105168689C>A	ENST00000243300.9	+	19	3281	c.2978C>A	c.(2977-2979)gCa>gAa	p.A993E	NRK_ENST00000428173.2_Missense_Mutation_p.A994E	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	993			A -> E (in dbSNP:rs16984889).		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						GTTGTCAGGGCAAGCTATGGC	0.408										HNSCC(51;0.14)			C|||	462	0.122384	0.3306	0.0331	3775	,	,		16586	0.0		0.002	False		,,,				2504	0.0				p.A993E		Atlas-SNP	.											.	NRK	321	.	0			c.C2978A						PASS	.	C	GLU/ALA	1205,2084		184,619,218,559,347	26	24	25		2978	1.8	0.1	X	dbSNP_123	25	9,6498		0,8,1,2351,1788	yes	missense	NRK	NM_198465.2	107	184,627,219,2910,2135	AA,AC,A,CC,C		0.1383,36.6373,12.3928	benign	993/1583	105168689	1214,8582	1927	4148	6075	SO:0001583	missense	203447	exon19			TCAGGGCAAGCTA	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.2978C>A	X.37:g.105168689C>A	ENSP00000434830:p.Ala993Glu	254	0	0		267	163	0.610487	NM_198465	Q32ND6|Q5H9K2|Q6ZMP2	Missense_Mutation	SNP	ENST00000243300.9	37		168	0.10126582278481013	109	0.2794871794871795	4	0.011299435028248588	0	0.0	0	0.0	C	12.01	1.808484	0.31961	0.366373	0.001383	ENSG00000123572	ENST00000243300;ENST00000428173	T;T	0.79554	-1.27;-1.28	4.85	1.79	0.24919	.	0.766382	0.11121	N	0.597389	T	0.00012	0.0000	N	0.19112	0.55	0.58432	P	9.99999999995449E-6	B;B	0.30281	0.275;0.037	B;B	0.27796	0.083;0.011	T	0.14671	-1.0464	9	0.62326	D	0.03	.	1.9029	0.03271	0.212:0.4677:0.2021:0.1183	rs16984889;rs52799695;rs16984889	661;993	Q7Z2Y5-2;Q7Z2Y5	.;NRK_HUMAN	E	993;994	ENSP00000434830:A993E;ENSP00000438378:A994E	ENSP00000434830:A993E	A	+	2	0	NRK	105055345	0.038000	0.19896	0.138000	0.22173	0.767000	0.43475	-0.107000	0.10873	0.901000	0.36495	0.513000	0.50165	GCA	0|0.008;A|0.143	0.143	strong		0.408	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465		A	105168689	C	A	105168689	3	1	22	1	0	0	0	0	1	0	0	0	10664	710	25	4	3052	4	NRK	23	105168689	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	704015	105168689	50101871	4517	7418											
CXorf57	55086	hgsc.bcm.edu	37	chrX	105883826	105883826	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagcagctagagtagaaatTcaagaaagaaatggtaaacg	20	6	10	5	1	1	4	1	0	0	4	1	4	1	4	0	1	3	4	0	1	9	4	rs5962707	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:105883826T>G	ENST00000372548.4	+	10	1888	c.1779T>G	c.(1777-1779)atT>atG	p.I593M	CXorf57_ENST00000372544.2_Missense_Mutation_p.I496M|CXorf57_ENST00000497124.1_3'UTR|MIR548AN_ENST00000408286.2_RNA	NM_018015.5	NP_060485.4	Q6NSI4	CX057_HUMAN	chromosome X open reading frame 57	593			I -> M (in dbSNP:rs5962707). {ECO:0000269|PubMed:15489334}.				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						GAGTAGAAATTCAAGAAAGAA	0.333													T|||	445	0.117881	0.3185	0.0346	3775	,	,		11888	0.0		0.0	False		,,,				2504	0.0				p.I593M		Atlas-SNP	.											.	CXorf57	107	.	0			c.T1779G						PASS	.	T	MET/ILE,MET/ILE	1450,2385		216,789,229,627,342	118	111	113		1488,1779	1	0	X	dbSNP_114	113	8,6720		0,7,1,2421,1871	yes	missense,missense	CXorf57	NM_001184782.1,NM_018015.5	10,10	216,796,230,3048,2213	GG,GT,G,TT,T		0.1189,37.8096,13.8029	benign,benign	496/759,593/856	105883826	1458,9105	2203	4300	6503	SO:0001583	missense	55086	exon10			AGAAATTCAAGAA	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.1779T>G	X.37:g.105883826T>G	ENSP00000361628:p.Ile593Met	406	0	0		419	145	0.346062	NM_018015	H7BY89|Q4G0L7|Q5JQS1|Q5JRF9|Q6PHY5|Q6PII9|Q6PJU8|Q9H7W5|Q9NWA6	Missense_Mutation	SNP	ENST00000372548.4	37	CCDS14519.1	168	0.10126582278481013	105	0.2734375	6	0.01694915254237288	0	0.0	0	0.0	T	6.656	0.489589	0.12641	0.378096	0.001189	ENSG00000147231	ENST00000372544;ENST00000372548;ENST00000421550	T;T;T	0.64618	0.88;-0.11;0.88	3.51	0.993	0.19825	.	1.046520	0.07422	N	0.894082	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.12630	0.006;0.006	B;B	0.06405	0.002;0.002	T	0.28808	-1.0032	9	0.56958	D	0.05	0.7933	3.0646	0.06210	0.0:0.141:0.2513:0.6078	rs5962707;rs52800882;rs5962707	593;593	A8K6R5;Q6NSI4	.;CX057_HUMAN	M	496;593;304	ENSP00000361623:I496M;ENSP00000361628:I593M;ENSP00000405866:I304M	ENSP00000361623:I496M	I	+	3	3	CXorf57	105770482	0.005000	0.15991	0.001000	0.08648	0.152000	0.21847	0.853000	0.27777	0.098000	0.17522	0.339000	0.21740	ATT	0|0.014;G|0.148	0.148	strong		0.333	CXorf57-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057800.2	NM_018015		G	105883826	T	G	105883826	3	3	22	1	0	0	0	0	1	0	0	0	4115	1771	62	5	1817	5	CXorf57	23	105883826	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	715137	105883826	49386734	4518	7419											
TBC1D8B	54885	hgsc.bcm.edu	37	chrX	106083304	106083304	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaaaaatgaaggaacagtcAtggaaaatactgtttgcaga	19	8	10	4	0	1	2	1	1	0	1	1	5	1	4	0	2	3	2	0	2	8	2	rs56825776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:106083304A>G	ENST00000357242.5	+	9	1554	c.1380A>G	c.(1378-1380)tcA>tcG	p.S460S	TBC1D8B_ENST00000276175.3_Silent_p.S454S|TBC1D8B_ENST00000310452.2_Silent_p.S460S	NM_017752.2	NP_060222.2	Q0IIM8	TBC8B_HUMAN	TBC1 domain family, member 8B (with GRAM domain)	460							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						AGGAACAGTCATGGAAAATAC	0.343													A|||	263	0.0696689	0.1876	0.0202	3775	,	,		13833	0.0		0.001	False		,,,				2504	0.0				p.S460S		Atlas-SNP	.											.	TBC1D8B	181	.	0			c.A1380G						PASS	.	A	,	857,2978		87,555,128,990,443	116	108	111		1380,1380	-3.8	1	X	dbSNP_129	111	2,6726		0,1,1,2427,1871	no	coding-synonymous,coding-synonymous	TBC1D8B	NM_017752.2,NM_198881.1	,	87,556,129,3417,2314	GG,GA,G,AA,A		0.0297,22.3468,8.1322	,	460/1121,460/633	106083304	859,9704	2203	4300	6503	SO:0001819	synonymous_variant	54885	exon9			ACAGTCATGGAAA	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.1380A>G	X.37:g.106083304A>G		338	1	0.00295858		318	318	1	NM_198881	B9A6K5|B9A6K6|Q5JRB7|Q6ZVX5|Q9NXE3	Silent	SNP	ENST00000357242.5	37	CCDS14522.1																																																																																			A|0.923;G|0.077	0.077	strong		0.343	TBC1D8B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057807.2	NM_017752		G	106083304	A	G	106083304	2	3	22	1	0	0	0	0	0	0	0	1	15641	204	8	3		3	TBC1D8B	23	106083304	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	199478	106083304	49187256	4519	7420											
CAPN6	827	hgsc.bcm.edu	37	chrX	110491865	110491865	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgcgaccatgctggaacatGgttgggacaagcacatagtt	11	9	13	8	1	0	0	0	0	0	0	0	3	0	2	1	3	4	4	1	3	3	3	rs17879776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:110491865G>A	ENST00000324068.1	-	10	1583	c.1416C>T	c.(1414-1416)acC>acT	p.T472T	CAPN6_ENST00000541758.1_Silent_p.T217T	NM_014289.3	NP_055104.2	Q9Y6Q1	CAN6_HUMAN	calpain 6	472	Domain III.				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						GCTGGAACATGGTTGGGACAA	0.522													G|||	24	0.00635762	0.0174	0.0014	3775	,	,		13145	0.0		0.0	False		,,,				2504	0.0				p.T472T		Atlas-SNP	.											.	CAPN6	120	.	0			c.C1416T						PASS	.	G		91,3744		1,78,11,1553,560	105	87	93		1416	4.2	1	X	dbSNP_124	93	0,6728		0,0,0,2428,1872	no	coding-synonymous	CAPN6	NM_014289.3		1,78,11,3981,2432	AA,AG,A,GG,G		0.0,2.3729,0.8615		472/642	110491865	91,10472	2203	4300	6503	SO:0001819	synonymous_variant	827	exon10			GAACATGGTTGGG	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.1416C>T	X.37:g.110491865G>A		150	0	0		141	50	0.35461	NM_014289	D3DUY7|Q9UEQ1|Q9UJA8	Silent	SNP	ENST00000324068.1	37	CCDS14555.1																																																																																			G|0.991;A|0.009	0.009	strong		0.522	CAPN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057922.1			A	110491865	G	A	110491865	2	1	22	1	0	0	0	0	0	0	0	1	2632	1335	47	2		2	CAPN6	23	110491865	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	4408561	110491865	44778695	4520	7421											
TRPC5	7224	hgsc.bcm.edu	37	chrX	111020096	111020096	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctcttggatttggcccgagcCccaccactgccatcattatt	7	12	7	15	1	2	0	1	0	1	0	2	2	2	1	5	2	2	0	5	2	1	4	rs141761268	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:111020096C>A	ENST00000262839.2	-	11	3285	c.2367G>T	c.(2365-2367)ggG>ggT	p.G789G		NM_012471.2	NP_036603.1	Q9UL62	TRPC5_HUMAN	transient receptor potential cation channel, subfamily C, member 5	789					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						TGGCCCGAGCCCCACCACTGC	0.478													C|||	5	0.0013245	0.0038	0.0	3775	,	,		12501	0.0		0.0	False		,,,				2504	0.0				p.G789G		Atlas-SNP	.											.	TRPC5	142	.	0			c.G2367T						PASS	.	C		13,3822		0,9,4,1623,567	137	143	141		2367	2.8	1	X	dbSNP_134	141	0,6728		0,0,0,2428,1872	no	coding-synonymous	TRPC5	NM_012471.2		0,9,4,4051,2439	AA,AC,A,CC,C		0.0,0.339,0.1231		789/974	111020096	13,10550	2203	4300	6503	SO:0001819	synonymous_variant	7224	exon11			CCGAGCCCCACCA	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.2367G>T	X.37:g.111020096C>A		177	0	0		160	101	0.63125	NM_012471	B2RP53|O75233|Q5JXY8|Q9Y514	Silent	SNP	ENST00000262839.2	37	CCDS14561.1																																																																																			C|0.998;A|0.002	0.002	strong		0.478	TRPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057945.1	NM_012471		A	111020096	C	A	111020096	2	1	22	1	0	0	0	0	0	0	0	1	16597	610	22	4		4	TRPC5	23	111020096	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	528231	111020096	44250464	4521	7422											
AMOT	154796	hgsc.bcm.edu	37	chrX	112022687	112022687	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtggtgatggtggcagcagTggcagtgatggcggcagcag	7	7	21	6	1	0	2	0	2	0	0	0	2	0	2	0	7	2	5	0	7	0	0	rs147791527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:112022687T>C	ENST00000524145.1	-	11	2769	c.2695A>G	c.(2695-2697)Act>Gct	p.T899A	MIR4329_ENST00000582643.1_RNA|AMOT_ENST00000371959.3_Missense_Mutation_p.T899A|AMOT_ENST00000371962.1_Missense_Mutation_p.T667A|AMOT_ENST00000304758.1_Missense_Mutation_p.T490A			Q4VCS5	AMOT_HUMAN	angiomotin	899					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						gtggcagcagtggcagtgatg	0.607													T|||	32	0.00847682	0.0242	0.0	3775	,	,		10806	0.0		0.0	False		,,,				2504	0.0				p.T899A		Atlas-SNP	.											.	AMOT	204	.	0			c.A2695G						PASS	.	T	ALA/THR,ALA/THR	65,3719		0,54,11,1560,545	47	27	34		1468,2695	-1.9	0	X	dbSNP_134	34	0,6636		0,0,0,2405,1826	yes	missense,missense	AMOT	NM_133265.2,NM_001113490.1	58,58	0,54,11,3965,2371	CC,CT,C,TT,T		0.0,1.7178,0.6238	benign,benign	490/676,899/1085	112022687	65,10355	2170	4231	6401	SO:0001583	missense	154796	exon10			CAGCAGTGGCAGT	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.2695A>G	X.37:g.112022687T>C	ENSP00000429013:p.Thr899Ala	94	0	0		116	82	0.706897	NM_001113490	Q504X5|Q9HD27|Q9UPT1	Missense_Mutation	SNP	ENST00000524145.1	37	CCDS48154.1	14	0.008438818565400843	10	0.02066115702479339	0	0.0	0	0.0	0	0.0	T	7.595	0.671638	0.14776	0.017178	0.0	ENSG00000126016	ENST00000304758;ENST00000371959;ENST00000371962;ENST00000524145;ENST00000432214	T;T;T;T	0.39592	1.07;2.17;2.41;2.17	5.08	-1.92	0.07618	.	0.574197	0.15760	N	0.245998	T	0.10637	0.0260	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16897	-1.0387	10	0.08599	T	0.76	0.0865	1.9616	0.03387	0.1442:0.3726:0.1459:0.3373	.	899	Q4VCS5	AMOT_HUMAN	A	490;899;667;899;139	ENSP00000305557:T490A;ENSP00000361027:T899A;ENSP00000361030:T667A;ENSP00000429013:T899A	ENSP00000305557:T490A	T	-	1	0	AMOT	111909343	0.990000	0.36364	0.019000	0.16419	0.904000	0.53231	1.464000	0.35288	-0.085000	0.12573	0.430000	0.28490	ACT	T|0.990;C|0.010	0.010	strong		0.607	AMOT-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378570.1	NM_133265		C	112022687	T	C	112022687	3	2	22	1	0	0	0	0	1	0	0	0	582	1696	59	3	567	3	AMOT	23	112022687	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1002591	112022687	43247873	4522	7423											
DOCK11	139818	hgsc.bcm.edu	37	chrX	117680019	117680019	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgttctcagaagggtggtgtGataaaacaaggctggttgca	11	11	14	5	0	1	2	1	1	1	1	2	2	1	2	0	4	2	4	0	4	4	3	rs61740837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:117680019G>C	ENST00000276202.7	+	6	561	c.498G>C	c.(496-498)gtG>gtC	p.V166V	DOCK11_ENST00000276204.6_Silent_p.V166V	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	166	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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						AGGGTGGTGTGATAAAACAAG	0.338													G|||	33	0.00874172	0.0234	0.0014	3775	,	,		12505	0.0		0.001	False		,,,				2504	0.0				p.V166V		Atlas-SNP	.											.	DOCK11	185	.	0			c.G498C						PASS	.	G		75,3760		0,67,8,1565,563	143	120	128		498	2.2	1	X	dbSNP_129	128	0,6728		0,0,0,2428,1872	no	coding-synonymous	DOCK11	NM_144658.3		0,67,8,3993,2435	CC,CG,C,GG,G		0.0,1.9557,0.71		166/2074	117680019	75,10488	2203	4300	6503	SO:0001819	synonymous_variant	139818	exon6			TGGTGTGATAAAA	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.498G>C	X.37:g.117680019G>C		192	0	0		201	77	0.383085	NM_144658	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Silent	SNP	ENST00000276202.7	37	CCDS35373.1																																																																																			G|0.993;C|0.007	0.007	strong		0.338	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658		C	117680019	G	C	117680019	2	2	22	1	0	0	0	0	0	0	0	1	4688	1277	45	4		4	DOCK11	23	117680019	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	5657332	117680019	37590541	4523	7424											
ANKRD58	347454	hgsc.bcm.edu	37	chrX	118893390	118893390	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggagagcggcagcgggtgcAccaacctgaacaacaacagc	13	3	13	12	2	0	2	0	1	0	1	0	3	0	2	2	3	8	2	2	3	4	0	rs12841259		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:118893390A>G	ENST00000343905.3	+	1	815	c.760A>G	c.(760-762)Acc>Gcc	p.T254A		NM_001105576.2	NP_001099046.1	A6NJG2	SWAHD_HUMAN	sosondowah ankyrin repeat domain family member D	254			T -> A (in dbSNP:rs12841259).														CAGCGGGTGCACCAACCTGAA	0.697													A|||	174	0.0460927	0.0764	0.0072	3775	,	,		10862	0.0377		0.002	False		,,,				2504	0.0286				p.T254A		Atlas-SNP	.											.	.	.	.	0			c.A760G						PASS	.	A	ALA/THR	249,3366		5,194,45,1337,498	7	10	9		760	-7	0	X	dbSNP_121	9	19,6433		0,15,4,2340,1738	yes	missense	ANKRD58	NM_001105576.2	58	5,209,49,3677,2236	GG,GA,G,AA,A		0.2945,6.888,2.6622	benign	254/316	118893390	268,9799	2079	4097	6176	SO:0001583	missense	347454	exon1			GGGTGCACCAACC		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.760A>G	X.37:g.118893390A>G	ENSP00000340975:p.Thr254Ala	100	0	0		97	59	0.608247	NM_001105576		Missense_Mutation	SNP	ENST00000343905.3	37	CCDS43984.1	67	0.04038577456298975	23	0.04893617021276596	4	0.011111111111111112	20	0.03597122302158273	0	0.0	A	5.179	0.218585	0.09810	0.06888	0.002945	ENSG00000187808	ENST00000343905	T	0.13420	2.59	4.24	-7.04	0.01578	.	.	.	.	.	T	0.00412	0.0013	N	0.08118	0	0.80722	P	0.0	B	0.10296	0.003	B	0.08055	0.003	T	0.47005	-0.9150	8	0.09084	T	0.74	1.5969	11.8996	0.52675	0.1977:0.1212:0.681:0.0	rs12841259	254	A6NJG2	ANR58_HUMAN	A	254	ENSP00000340975:T254A	ENSP00000340975:T254A	T	+	1	0	ANKRD58	118777418	0.000000	0.05858	0.000000	0.03702	0.077000	0.17291	-1.267000	0.02839	-1.676000	0.01457	0.314000	0.21332	ACC	A|0.958;G|0.042	0.042	strong		0.697	SOWAHD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356469.1	NM_001105576		G	118893390	A	G	118893390	3	3	22	1	0	0	0	0	1	0	0	0	684	159	6	3	762	3	ANKRD58	23	118893390	Missense_Mutation	SNP	A	TCGA-G8-6324-01A-11D-2210-10	1213371	118893390	36377170	4524	7425											
CT47B1	643311	hgsc.bcm.edu	37	chrX	120008932	120008932	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctctgggaccgacgcggccTcctggaccgacgcagcctcc	5	5	13	18	5	1	0	0	0	1	0	3	4	3	2	6	3	1	2	6	3	0	0	rs193289998		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:120008932T>C	ENST00000371311.3	-	1	847	c.593A>G	c.(592-594)gAg>gGg	p.E198G		NM_001145718.1	NP_001139190.1	P0C2W7	CT47B_HUMAN	cancer/testis antigen family 47, member B1	198										breast(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|lung(9)|ovary(1)|skin(1)	22						CGACGCGGCCTCCTGGACCGA	0.711													N|||	78	0.0206623	0.053	0.0115	3775	,	,		9887	0.0		0.0	False		,,,				2504	0.0				p.E198G		Atlas-SNP	.											.	CT47B1	67	.	0			c.A593G						PASS	.	T	GLY/GLU	86,1123		1,78,6,438,169	28	28	28		593	0.7	0	X		28	0,2389		0,0,0,800,789	no	missense	CT47B1	NM_001145718.1	98	1,78,6,1238,958	CC,CT,C,TT,T		0.0,7.1133,2.3902	benign	198/300	120008932	86,3512	692	1589	2281	SO:0001583	missense	643311	exon1			GCGGCCTCCTGGA		CCDS48161.1	Xq24	2014-05-06	2011-03-24		ENSG00000236446	ENSG00000236446			33293	protein-coding gene	gene with protein product	"cancer/testis CT47 family, member 13"	300790				16382448	Standard	NM_001145718		Approved	CT47.13	uc011muc.2	P0C2W7	OTTHUMG00000187483	ENST00000371311.3:c.593A>G	X.37:g.120008932T>C	ENSP00000360360:p.Glu198Gly	94	0	0		77	22	0.285714	NM_001145718	A6NM97	Missense_Mutation	SNP	ENST00000371311.3	37	CCDS48161.1	25	0.015069318866787222	15	0.03125	2	0.00558659217877095	0	0.0	0	0.0	T	10.45	1.352922	0.24512	0.071133	0.0	ENSG00000236446	ENST00000371311	.	.	.	1.89	0.714	0.18180	.	.	.	.	.	T	0.01029	0.0034	N	0.08118	0	0.80722	P	0.0	B	0.19817	0.039	B	0.08055	0.003	T	0.15492	-1.0435	7	0.35671	T	0.21	.	3.0134	0.06052	0.0:0.4121:0.0:0.5879	.	198	P0C2W7	CT47B_HUMAN	G	198	.	ENSP00000360360:E198G	E	-	2	0	CT47B1	119892960	0.000000	0.05858	0.000000	0.03702	0.093000	0.18481	-1.020000	0.03618	0.129000	0.18514	0.143000	0.16000	GAG	T|0.985;C|0.015	0.015	strong		0.711	CT47B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058121.1	NM_001145718		C	120008932	T	C	120008932	3	2	22	1	0	0	0	0	1	0	0	0	3991	1551	54	3	314	3	CT47B1	23	120008932	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1115542	120008932	35261628	4525	7426											
ODZ1	10178	hgsc.bcm.edu	37	chrX	123775824	123775824	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatgccatggttggaacacaTtgggtctaggcagtcctctg	8	11	13	9	0	2	0	0	0	2	0	3	2	3	1	2	4	2	2	2	4	2	3	rs16999334	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:123775824T>C	ENST00000371130.3	-	11	1957	c.1894A>G	c.(1894-1896)Atg>Gtg	p.M632V	TENM1_ENST00000422452.2_Missense_Mutation_p.M632V	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	632	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.		M -> V (in dbSNP:rs16999334).		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)										TTGGAACACATTGGGTCTAGG	0.468													T|||	168	0.0445033	0.121	0.0086	3775	,	,		14477	0.0		0.001	False		,,,				2504	0.001				p.M632V		Atlas-SNP	.											.	.	.	.	0			c.A1894G						PASS	.	T	VAL/MET,VAL/MET,VAL/MET	562,3273		49,384,80,1199,491	196	175	182		1894,1891,1894	4.2	1	X	dbSNP_123	182	3,6725		0,3,0,2425,1872	yes	missense,missense,missense	ODZ1	NM_001163278.1,NM_001163279.1,NM_014253.3	21,21,21	49,387,80,3624,2363	CC,CT,C,TT,T		0.0446,14.6545,5.3489	benign,benign,benign	632/2733,631/2732,632/2726	123775824	565,9998	2203	4300	6503	SO:0001583	missense	10178	exon11			AACACATTGGGTC	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.1894A>G	X.37:g.123775824T>C	ENSP00000360171:p.Met632Val	155	0	0		159	56	0.352201	NM_001163278	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	59	0.03556359252561784	41	0.08836206896551724	3	0.008379888268156424	0	0.0	0	0.0	T	13.41	2.228398	0.39399	0.146545	4.46E-4	ENSG00000009694	ENST00000371130;ENST00000422452	T;T	0.03212	4.01;4.01	5.32	4.15	0.48705	Epidermal growth factor-like (1);	0.119478	0.56097	D	0.000024	T	0.00039	0.0001	N	0.21373	0.66	0.27607	P	0.9487963	B;B;B	0.27351	0.176;0.111;0.006	B;B;B	0.17098	0.016;0.017;0.005	T	0.48864	-0.8997	9	0.38643	T	0.18	.	10.3355	0.43847	0.0:0.0784:0.0:0.9216	rs16999334;rs52832334;rs58243564;rs16999334	631;632;632	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	V	632	ENSP00000360171:M632V;ENSP00000403954:M632V	ENSP00000360171:M632V	M	-	1	0	ODZ1	123603505	0.989000	0.36119	1.000000	0.80357	0.978000	0.69477	2.162000	0.42367	0.675000	0.31264	0.481000	0.45027	ATG	0|0.018;C|0.053	0.053	strong		0.468	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		C	123775824	T	C	123775824	3	2	22	1	0	0	0	0	1	0	0	0	10843	1493	52	3	6392	3	ODZ1	23	123775824	Missense_Mutation	SNP	T	TCGA-G8-6324-01A-11D-2210-10	3766892	123775824	31494736	4526	7427											
ODZ1	10178	hgsc.bcm.edu	37	chrX	123838882	123838882	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccaatcacataggctagtaaCaaggccaaagtcactgtgat	15	8	8	10	0	2	1	2	1	0	0	2	1	2	1	2	2	1	2	2	2	6	3	rs138596900	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:123838882C>T	ENST00000371130.3	-	5	1059	c.996G>A	c.(994-996)ttG>ttA	p.L332L	TENM1_ENST00000422452.2_Silent_p.L332L	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	332					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)										AGGCTAGTAACAAGGCCAAAG	0.453													C|||	71	0.0188079	0.0514	0.0043	3775	,	,		14198	0.0		0.0	False		,,,				2504	0.0				p.L332L		Atlas-SNP	.											.	.	.	.	0			c.G996A						PASS	.	C	,,	212,3623		5,173,29,1454,542	163	146	152		996,996,996	5.7	1	X	dbSNP_134	152	0,6728		0,0,0,2428,1872	no	coding-synonymous,coding-synonymous,coding-synonymous	ODZ1	NM_001163278.1,NM_001163279.1,NM_014253.3	,,	5,173,29,3882,2414	TT,TC,T,CC,C		0.0,5.528,2.007	,,	332/2733,332/2732,332/2726	123838882	212,10351	2203	4300	6503	SO:0001819	synonymous_variant	10178	exon5			TAGTAACAAGGCC	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.996G>A	X.37:g.123838882C>T		131	0	0		128	40	0.3125	NM_001163278	B2RTR5|Q5JZ17	Silent	SNP	ENST00000371130.3	37	CCDS14609.1																																																																																			C|0.979;T|0.021	0.021	strong		0.453	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		T	123838882	C	T	123838882	2	4	22	1	0	0	0	0	0	0	0	1	10843	477	17	2		2	ODZ1	23	123838882	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	63058	123838882	31431678	4527	7428											
FRMD7	90167	hgsc.bcm.edu	37	chrX	131212487	131212487	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgggctctacatagctatGtggacttgtcctttcctctg	6	15	10	10	0	2	0	0	0	2	0	4	1	4	1	2	2	2	2	2	2	3	5	rs61742429	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:131212487G>C	ENST00000298542.4	-	12	1733	c.1558C>G	c.(1558-1560)Cat>Gat	p.H520D	FRMD7_ENST00000464296.1_Missense_Mutation_p.H505D|FRMD7_ENST00000370879.1_Missense_Mutation_p.H400D	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	520					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)					ACATAGCTATGTGGACTTGTC	0.493													C|||	35	0.00927152	0.0257	0.0014	3775	,	,		13862	0.0		0.0	False		,,,				2504	0.0				p.H520D		Atlas-SNP	.											.	FRMD7	69	.	0			c.C1558G						PASS	.	C	ASP/HIS	75,3760		0,62,13,1570,558	164	160	162		1558	3.6	0.4	X	dbSNP_129	162	0,6728		0,0,0,2428,1872	yes	missense	FRMD7	NM_194277.2	81	0,62,13,3998,2430	CC,CG,C,GG,G		0.0,1.9557,0.71	benign	520/715	131212487	75,10488	2203	4300	6503	SO:0001583	missense	90167	exon12			AGCTATGTGGACT	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.1558C>G	X.37:g.131212487G>C	ENSP00000298542:p.His520Asp	204	0	0		215	84	0.390698	NM_194277	C0LLJ3|Q5JX99	Missense_Mutation	SNP	ENST00000298542.4	37	CCDS35397.1	3	0.0018083182640144665	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	0.001	-3.523968	0.00010	0.019557	0.0	ENSG00000165694	ENST00000370879;ENST00000298542;ENST00000464296	D;D;D	0.84800	-1.9;-1.55;-1.67	4.55	3.59	0.41128	.	0.259811	0.32041	N	0.006663	T	0.37461	0.1004	N	0.01168	-0.975	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.49244	-0.8960	10	0.02654	T	1	.	4.1382	0.10181	0.1501:0.4756:0.2878:0.0865	rs61742429	505;520	Q6ZUT3-2;Q6ZUT3	.;FRMD7_HUMAN	D	400;520;505	ENSP00000359916:H400D;ENSP00000298542:H520D;ENSP00000417996:H505D	ENSP00000298542:H520D	H	-	1	0	FRMD7	131040168	0.727000	0.28069	0.447000	0.26932	0.007000	0.05969	0.526000	0.22971	1.017000	0.39495	-0.170000	0.13304	CAT	G|0.982;C|0.018	0.018	strong		0.493	FRMD7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355031.1	NM_194277		C	131212487	G	C	131212487	3	2	22	1	0	0	0	0	1	0	0	0	6063	1377	48	4	590	4	FRMD7	23	131212487	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	7373605	131212487	24058073	4528	7429											
TFDP3	51270	hgsc.bcm.edu	37	chrX	132352230	132352230	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	ggggcggctggtctggttctCgtccattaagaccttgagtt	5	13	14	9	2	2	2	0	1	2	1	4	2	3	2	2	5	0	3	2	5	1	4	rs28455963	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:132352230C>G	ENST00000310125.4	-	1	146	c.58G>C	c.(58-60)Gag>Cag	p.E20Q		NM_016521.2	NP_057605.3	Q5H9I0	TFDP3_HUMAN	transcription factor Dp family, member 3	20					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)					GTCTGGTTCTCGTCCATTAAG	0.483													G|||	383	0.101457	0.2247	0.0389	3775	,	,		13274	0.002		0.0288	False		,,,				2504	0.0286				p.E20Q		Atlas-SNP	.											.	TFDP3	92	.	0			c.G58C						PASS	.	G	GLN/GLU	304,905		40,182,42,295,133	63	47	52		58	0.2	0	X	dbSNP_125	52	85,2306		3,62,17,735,774	yes	missense	TFDP3	NM_016521.2	29	43,244,59,1030,907	GG,GC,G,CC,C		3.555,25.1447,10.8056	benign	20/406	132352230	389,3211	692	1591	2283	SO:0001583	missense	51270	exon1			GGTTCTCGTCCAT	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.58G>C	X.37:g.132352230C>G	ENSP00000385461:p.Glu20Gln	186	0	0		170	116	0.682353	NM_016521	Q6DK49|Q9NZ54	Missense_Mutation	SNP	ENST00000310125.4	37	CCDS14636.2	154	0.09282700421940929	74	0.17703349282296652	13	0.03651685393258427	2	0.0034965034965034965	14	0.01907356948228883	G	0.008	-1.897626	0.00517	0.251447	0.03555	ENSG00000183434	ENST00000310125	T	0.19806	2.12	0.235	0.235	0.15431	.	.	.	.	.	T	0.00012	0.0000	N	0.00260	-1.75	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34378	-0.9831	7	0.02654	T	1	.	.	.	.	rs28455963	20	Q5H9I0	TFDP3_HUMAN	Q	20	ENSP00000385461:E20Q	ENSP00000385461:E20Q	E	-	1	0	TFDP3	132179896	0.988000	0.35896	0.016000	0.15963	0.016000	0.09150	0.556000	0.23438	-0.705000	0.05035	-0.699000	0.03677	GAG	C|0.877;G|0.123	0.123	strong		0.483	TFDP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058337.1	NM_016521		G	132352230	C	G	132352230	3	3	22	1	0	0	0	0	1	0	0	0	15814	893	31	4	1163	4	TFDP3	23	132352230	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	1139743	132352230	22918330	4529	7430											
GPC3	2719	hgsc.bcm.edu	37	chrX	132670269	132670269	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctcgttgtccttcggagtTgcctgctgactgtttccagg	4	15	11	11	2	1	1	0	1	1	0	5	2	3	2	3	2	2	4	3	2	0	4	rs61754631	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:132670269T>C	ENST00000370818.3	-	8	2071	c.1626A>G	c.(1624-1626)gcA>gcG	p.A542A	GPC3_ENST00000394299.2_Silent_p.A565A|GPC3_ENST00000543339.1_Silent_p.A488A	NM_001164618.1|NM_004484.3	NP_001158090.1|NP_004475.1	P51654	GPC3_HUMAN	glypican 3	542					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)					CCTTCGGAGTTGCCTGCTGAC	0.502			"T, D, Mis, N, F, S"			Wilms tumour			Simpson-Golabi-Behmel syndrome				C|||	203	0.0537748	0.1505	0.0058	3775	,	,		12135	0.0		0.0	False		,,,				2504	0.0				p.A565A		Atlas-SNP	.	yes	Rec/X		Simpson-Golabi-Behmel syndrome	X	Xq26.1	2719	glypican 3		O	.	GPC3	88	.	0			c.A1695G						PASS	.	C	,,,	741,3094		68,494,111,1070,460	274	217	236		1695,1578,1464,1626	2.1	0	X	dbSNP_129	236	5,6723		0,2,3,2426,1869	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GPC3	NM_001164617.1,NM_001164618.1,NM_001164619.1,NM_004484.3	,,,	68,496,114,3496,2329	CC,CT,C,TT,T		0.0743,19.322,7.0624	,,,	565/604,526/565,488/527,542/581	132670269	746,9817	2203	4300	6503	SO:0001819	synonymous_variant	2719	exon9	Familial Cancer Database	SGBS	CGGAGTTGCCTGC	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.1626A>G	X.37:g.132670269T>C		172	0	0		193	119	0.61658	NM_001164617	C9JLE3|G3V1R0|Q2L880|Q2L882	Silent	SNP	ENST00000370818.3	37	CCDS14638.1																																																																																			T|0.927;C|0.073	0.073	strong		0.502	GPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058356.1	NM_004484		C	132670269	T	C	132670269	2	2	22	1	0	0	0	0	0	0	0	1	6607	1799	63	3		3	GPC3	23	132670269	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	318039	132670269	22600291	4530	7431											
GPC3	2719	hgsc.bcm.edu	37	chrX	132730541	132730541	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaatgcactcatcttcatcAtcaccgcagtctccactttc	9	12	3	17	1	6	0	4	0	2	0	8	0	6	0	3	0	1	2	3	0	1	2	rs2314298	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:132730541A>G	ENST00000370818.3	-	7	1945	c.1500T>C	c.(1498-1500)gaT>gaC	p.D500D	GPC3_ENST00000394299.2_Silent_p.D523D|GPC3_ENST00000543339.1_Silent_p.D446D	NM_001164618.1|NM_004484.3	NP_001158090.1|NP_004475.1	P51654	GPC3_HUMAN	glypican 3	500					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)					CATCTTCATCATCACCGCAGT	0.448			"T, D, Mis, N, F, S"			Wilms tumour			Simpson-Golabi-Behmel syndrome				a|||	247	0.0654305	0.1823	0.0086	3775	,	,		13843	0.0		0.0	False		,,,				2504	0.0				p.D523D		Atlas-SNP	.	yes	Rec/X		Simpson-Golabi-Behmel syndrome	X	Xq26.1	2719	glypican 3		O	.	GPC3	88	.	0			c.T1569C						PASS	.	A	,,,	844,2991		83,548,130,1001,441	240	203	216		1569,1452,1338,1500	-8.8	0	X	dbSNP_100	216	9,6719		0,6,3,2422,1869	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GPC3	NM_001164617.1,NM_001164618.1,NM_001164619.1,NM_004484.3	,,,	83,554,133,3423,2310	GG,GA,G,AA,A		0.1338,22.0078,8.0754	,,,	523/604,484/565,446/527,500/581	132730541	853,9710	2203	4300	6503	SO:0001819	synonymous_variant	2719	exon8	Familial Cancer Database	SGBS	TTCATCATCACCG	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.1500T>C	X.37:g.132730541A>G		421	0	0		461	297	0.644252	NM_001164617	C9JLE3|G3V1R0|Q2L880|Q2L882	Silent	SNP	ENST00000370818.3	37	CCDS14638.1	88	0.05304400241109102	57	0.1313364055299539	1	0.002777777777777778	0	0.0	0	0.0	a	2.240	-0.373954	0.05034	0.220078	0.001338	ENSG00000147257	ENST00000406757	.	.	.	4.73	-8.77	0.00827	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.21290	P	0.99973057	.	.	.	.	.	.	T	0.40997	-0.9533	3	.	.	.	.	17.6231	0.88087	0.3063:0.0:0.6937:0.0	rs2314298;rs60128560;rs2314298	.	.	.	T	230	.	.	M	-	2	0	GPC3	132558207	0.013000	0.17824	0.034000	0.17996	0.609000	0.37215	-1.591000	0.02100	-2.800000	0.00352	-3.172000	0.00057	ATG	A|0.905;G|0.095	0.095	strong		0.448	GPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058356.1	NM_004484		G	132730541	A	G	132730541	2	3	22	1	0	0	0	0	0	0	0	1	6607	214	8	3		3	GPC3	23	132730541	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	60272	132730541	22540019	4531	7432											
CCDC160	347475	hgsc.bcm.edu	37	chrX	133378851	133378851	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atggatgctagaagaaaacaCtggaaggagaatatgtttac	17	9	11	4	0	0	3	0	0	0	3	0	6	0	5	0	3	3	2	0	3	8	4			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:133378851C>T	ENST00000517294.1	+	3	404	c.21C>T	c.(19-21)caC>caT	p.H7H	CCDC160_ENST00000370809.4_Silent_p.H7H			A6NGH7	CC160_HUMAN	coiled-coil domain containing 160	7										endometrium(1)|kidney(2)|large_intestine(10)|lung(2)|prostate(1)|skin(1)	17						GAAGAAAACACTGGAAGGAGA	0.373																																					p.H7H		Atlas-SNP	.											.	CCDC160	38	.	0			c.C21T						PASS	.						20	18	19					X																	133378851		1825	4074	5899	SO:0001819	synonymous_variant	347475	exon2			AAAACACTGGAAG	BC017958	CCDS48171.1	Xq26.2	2010-02-17			ENSG00000203952	ENSG00000203952			37286	protein-coding gene	gene with protein product							Standard	NM_001101357		Approved		uc011mvj.2	A6NGH7	OTTHUMG00000164183	ENST00000517294.1:c.21C>T	X.37:g.133378851C>T		149	0	0		146	91	0.623288	NM_001101357		Silent	SNP	ENST00000517294.1	37	CCDS48171.1																																																																																			.	.	none		0.373	CCDC160-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377679.1	NM_001101357		T	133378851	C	T	133378851	2	4	22	1	0	0	0	0	0	0	0	1	2794	564	20	2		2	CCDC160	23	133378851	Silent	SNP	C	TCGA-G8-6324-01A-11D-2210-10	648310	133378851	21891709	4532	7433											
HTATSF1	27336	hgsc.bcm.edu	37	chrX	135593167	135593167	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaaactgcaactggaatggcGtttgaagaacctatagatga	15	9	11	6	1	0	4	0	2	0	2	0	6	0	5	1	2	4	2	1	2	7	3	rs1058376	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:135593167G>A	ENST00000218364.4	+	9	1437	c.1263G>A	c.(1261-1263)gcG>gcA	p.A421A	HTATSF1_ENST00000535601.1_Silent_p.A421A	NM_014500.4	NP_055315.2	O43719	HTSF1_HUMAN	HIV-1 Tat specific factor 1	421	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)					CTGGAATGGCGTTTGAAGAAC	0.448													g|||	513	0.135894	0.329	0.0447	3775	,	,		14100	0.0337		0.0089	False		,,,				2504	0.0041				p.A421A		Atlas-SNP	.											.	HTATSF1	66	.	0			c.G1263A						PASS	.	A	,	1427,2408		222,748,235,662,336	115	126	123		1263,1263	-3.1	0	X	dbSNP_86	123	73,6655		0,49,24,2379,1848	no	coding-synonymous,coding-synonymous	HTATSF1	NM_001163280.1,NM_014500.4	,	222,797,259,3041,2184	AA,AG,A,GG,G		1.085,37.2099,14.2005	,	421/756,421/756	135593167	1500,9063	2203	4300	6503	SO:0001819	synonymous_variant	27336	exon10			AATGGCGTTTGAA	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.1263G>A	X.37:g.135593167G>A		260	0	0		252	251	0.996032	NM_001163280	D3DWG9|Q59G06|Q99730	Silent	SNP	ENST00000218364.4	37	CCDS14657.1																																																																																			0|0.004;A|0.148	0.148	strong		0.448	HTATSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058497.1	NM_014500		A	135593167	G	A	135593167	2	1	22	1	0	0	0	0	0	0	0	1	7442	1132	40	1		1	HTATSF1	23	135593167	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	2214316	135593167	19677393	4533	7434											
F9	2158	hgsc.bcm.edu	37	chrX	138643939	138643939	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcttccacaaagggagatcAgctttagttcttcagtacct	10	13	8	10	0	4	1	2	0	2	1	5	2	5	1	2	1	2	3	2	1	3	6	rs112057482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:138643939A>G	ENST00000218099.2	+	8	1102	c.1095A>G	c.(1093-1095)tcA>tcG	p.S365S	F9_ENST00000394090.2_Silent_p.S327S	NM_000133.3	NP_000124.1	P00740	FA9_HUMAN	coagulation factor IX	365	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)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|skin(1)	35	Acute lymphoblastic leukemia(192;0.000127)				Antihemophilic Factor(DB00025)|Menadione(DB00170)	AAGGGAGATCAGCTTTAGTTC	0.438													A|||	42	0.0111258	0.0287	0.0058	3775	,	,		14652	0.0		0.0	False		,,,				2504	0.0				p.S365S		Atlas-SNP	.											.	F9	107	.	0			c.A1095G	GRCh37	CD010617	F9	D	rs112057482	PASS	.	A		127,3708		1,104,21,1527,550	141	117	125		1095	-9.5	0	X	dbSNP_132	125	1,6727		0,1,0,2427,1872	no	coding-synonymous	F9	NM_000133.3		1,105,21,3954,2422	GG,GA,G,AA,A		0.0149,3.3116,1.2118		365/462	138643939	128,10435	2203	4300	6503	SO:0001819	synonymous_variant	2158	exon8			GAGATCAGCTTTA	M11309	CCDS14666.1	Xq26.3-q27.1	2014-09-17	2008-08-01		ENSG00000101981	ENSG00000101981	3.4.21.22		3551	protein-coding gene	gene with protein product	"Factor IX", "plasma thromboplastic component", "Christmas disease", "hemophilia B"	300746					Standard	NM_000133		Approved	FIX	uc004fas.1	P00740	OTTHUMG00000022536	ENST00000218099.2:c.1095A>G	X.37:g.138643939A>G		140	0	0		136	85	0.625	NM_000133	A8K9N4|F2RM36|Q5FBE1|Q5JYJ8	Silent	SNP	ENST00000218099.2	37	CCDS14666.1																																																																																			A|0.989;G|0.011	0.011	strong		0.438	F9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058557.1			G	138643939	A	G	138643939	2	3	22	1	0	0	0	0	0	0	0	1	5356	175	7	3		3	F9	23	138643939	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	3050772	138643939	16626621	4534	7435											
SLITRK4	139065	hgsc.bcm.edu	37	chrX	142717383	142717383	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcaactgatcaaggaccccActgacaggcaggtacatgaa	14	6	10	11	0	1	3	1	3	0	0	1	4	1	4	2	3	3	3	2	3	4	1	rs73577386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:142717383A>G	ENST00000381779.4	-	2	1767	c.1542T>C	c.(1540-1542)agT>agC	p.S514S	SLITRK4_ENST00000338017.4_Silent_p.S514S|SLITRK4_ENST00000356928.1_Silent_p.S514S	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	514						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)					CAAGGACCCCACTGACAGGCA	0.473													A|||	528	0.139868	0.3812	0.0317	3775	,	,		13652	0.0		0.002	False		,,,				2504	0.0				p.S514S		Atlas-SNP	.											.	SLITRK4	162	.	0			c.T1542C						PASS	.	A	,,	1667,2168		315,787,250,530,321	133	136	135		1542,1542,1542	-3	1	X	dbSNP_130	135	17,6711		0,11,6,2417,1866	no	coding-synonymous,coding-synonymous,coding-synonymous	SLITRK4	NM_001184749.1,NM_001184750.1,NM_173078.3	,,	315,798,256,2947,2187	GG,GA,G,AA,A		0.2527,43.4681,15.9424	,,	514/838,514/838,514/838	142717383	1684,8879	2203	4300	6503	SO:0001819	synonymous_variant	139065	exon2			GACCCCACTGACA	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.1542T>C	X.37:g.142717383A>G		199	1	0.00502513		168	168	1	NM_001184750	Q5JXG3|Q8TCM8|Q96DL3	Silent	SNP	ENST00000381779.4	37	CCDS14679.1																																																																																			A|0.836;G|0.164	0.164	strong		0.473	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078		G	142717383	A	G	142717383	2	3	22	1	0	0	0	0	0	0	0	1	14760	156	6	3		3	SLITRK4	23	142717383	Silent	SNP	A	TCGA-G8-6324-01A-11D-2210-10	4073444	142717383	12553177	4535	7436											
SPANXN1	494118	hgsc.bcm.edu	37	chrX	144337286	144337286	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gtattagcgttttgctacagGaaagctaagaaaatacattc	15	12	8	6	1	0	1	0	0	0	1	1	2	0	2	0	1	5	4	0	1	8	8	rs75090998	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:144337286G>A	ENST00000370493.3	+	2	930	c.171G>A	c.(169-171)agG>agA	p.R57R		NM_001009614.2	NP_001009614.1	Q5VSR9	SPXN1_HUMAN	SPANX family, member N1	57										endometrium(2)|kidney(2)|lung(8)|prostate(1)|urinary_tract(1)	14	Acute lymphoblastic leukemia(192;6.56e-05)					TTTGCTACAGGAAAGCTAAGA	0.443													G|||	280	0.0741722	0.208	0.0072	3775	,	,		15977	0.0		0.0	False		,,,				2504	0.0				p.R57R		Atlas-SNP	.											.	SPANXN1	23	.	0			c.G171A						PASS	.	G		826,3009		83,540,120,1009,451	186	161	170		171	1.5	0	X	dbSNP_131	170	9,6716		1,5,2,2422,1867	no	coding-synonymous	SPANXN1	NM_001009614.2		84,545,122,3431,2318	AA,AG,A,GG,G		0.1338,21.5385,7.9072		57/73	144337286	835,9725	2203	4297	6500	SO:0001819	synonymous_variant	494118	exon2			CTACAGGAAAGCT		CCDS35421.1	Xq27.3	2009-03-25				ENSG00000203923			33174	protein-coding gene	gene with protein product	"cancer/testis antigen family 11, member 6"	300664				14973187, 17012309	Standard	NM_001009614		Approved	SPANX-N1, CT11.6	uc004fcb.2	Q5VSR9		ENST00000370493.3:c.171G>A	X.37:g.144337286G>A		374	0	0		365	363	0.994521	NM_001009614		Silent	SNP	ENST00000370493.3	37	CCDS35421.1																																																																																			G|0.919;A|0.081	0.081	strong		0.443	SPANXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058631.2	NM_001009614		A	144337286	G	A	144337286	2	1	22	1	0	0	0	0	0	0	0	1	15005	1165	41	2		2	SPANXN1	23	144337286	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1619903	144337286	10933274	4536	7437											
AFF2	2334	hgsc.bcm.edu	37	chrX	148035200	148035200	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcggagagcagctctgagtcGgattcagacactgaaagtag	12	8	13	8	2	2	4	1	2	1	2	4	6	2	5	0	2	2	3	0	2	2	2	rs12011040	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:148035200G>A	ENST00000370460.2	+	10	1967	c.1488G>A	c.(1486-1488)tcG>tcA	p.S496S	AFF2_ENST00000342251.3_Silent_p.S463S|AFF2_ENST00000286437.5_Silent_p.S137S|AFF2_ENST00000370457.5_Silent_p.S463S	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	496					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)					GCTCTGAGTCGGATTCAGACA	0.587													A|||	536	0.141987	0.3381	0.0476	3775	,	,		11768	0.003		0.0388	False		,,,				2504	0.0143				p.S496S		Atlas-SNP	.											.	AFF2	679	.	0			c.G1488A						PASS	.	A	,,,,,	1531,2304		268,774,221,590,350	126	118	121		1389,1458,1383,1371,411,1488	-10	0	X	dbSNP_120	121	287,6441		3,196,85,2229,1787	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AFF2	NM_001169122.1,NM_001169123.1,NM_001169124.1,NM_001169125.1,NM_001170628.1,NM_002025.3	,,,,,	271,970,306,2819,2137	AA,AG,A,GG,G		4.2658,39.9218,17.211	,,,,,	463/1277,486/1302,461/1277,457/1273,137/953,496/1312	148035200	1818,8745	2203	4300	6503	SO:0001819	synonymous_variant	2334	exon10			TGAGTCGGATTCA	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.1488G>A	X.37:g.148035200G>A		352	0	0		415	140	0.337349	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Silent	SNP	ENST00000370460.2	37	CCDS14684.1																																																																																			0|0.003;A|0.180	0.180	strong		0.587	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025		A	148035200	G	A	148035200	2	1	22	1	0	0	0	0	0	0	0	1	357	1103	39	1		1	AFF2	23	148035200	Silent	SNP	G	TCGA-G8-6324-01A-11D-2210-10	3697914	148035200	7235360	4537	7438											
IDS	3423	hgsc.bcm.edu	37	chrX	148579705	148579705	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggaagaaaggactggctgacGttttcatcttttccaacaac	12	11	9	9	1	2	2	1	1	1	1	3	4	3	4	1	3	2	2	1	3	4	4	rs61736892	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:148579705G>A	ENST00000340855.6	-	5	850	c.641C>T	c.(640-642)aCg>aTg	p.T214M	IDS_ENST00000541269.1_Missense_Mutation_p.T3M|IDS_ENST00000490775.1_5'UTR|IDS_ENST00000422081.2_Missense_Mutation_p.T3M|IDS_ENST00000370441.4_Missense_Mutation_p.T214M|IDS_ENST00000370443.4_Missense_Mutation_p.T214M	NM_000202.5|NM_001166550.1	NP_000193.1|NP_001160022.1	P22304	IDS_HUMAN	iduronate 2-sulfatase	214					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)					ACTGGCTGACGTTTTCATCTT	0.527													G|||	60	0.015894	0.0439	0.0029	3775	,	,		14709	0.0		0.0	False		,,,				2504	0.0				p.T214M		Atlas-SNP	.											.	IDS	46	.	0			c.C641T	GRCh37	CS961600	IDS	S	rs61736892	PASS	.	G	MET/THR,MET/THR,MET/THR	184,3651		7,143,27,1482,544	160	136	144		641,371,641	1.7	0.2	X	dbSNP_129	144	0,6728		0,0,0,2428,1872	yes	missense,missense,missense	IDS	NM_000202.5,NM_001166550.1,NM_006123.4	81,81,81	7,143,27,3910,2416	AA,AG,A,GG,G		0.0,4.7979,1.7419	benign,benign,benign	214/551,124/461,214/344	148579705	184,10379	2203	4300	6503	SO:0001583	missense	3423	exon5			GCTGACGTTTTCA	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.641C>T	X.37:g.148579705G>A	ENSP00000339801:p.Thr214Met	240	0	0		234	110	0.470085	NM_006123	D3DWT4|Q14604|Q9BRM3	Missense_Mutation	SNP	ENST00000340855.6	37	CCDS14685.1	24	0.014466546112115732	17	0.035416666666666666	1	0.0027624309392265192	0	0.0	0	0.0	G	13.84	2.358547	0.41801	0.047979	0.0	ENSG00000010404	ENST00000340855;ENST00000541269;ENST00000370441;ENST00000370443	D;D;D;D	0.99900	-7.62;-5.85;-7.62;-7.62	5.12	1.68	0.24146	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.624103	0.18240	N	0.147268	D	0.97676	0.9238	L	0.56340	1.77	0.80722	P	0.0	D;D;D	0.61697	0.987;0.973;0.99	P;P;P	0.59595	0.781;0.806;0.86	D	0.90347	0.4363	9	0.46703	T	0.11	.	3.6256	0.08112	0.0979:0.1075:0.4765:0.318	.	214;124;214	P22304-2;B4DGD7;P22304	.;.;IDS_HUMAN	M	214;3;214;214	ENSP00000339801:T214M;ENSP00000441261:T3M;ENSP00000359470:T214M;ENSP00000359472:T214M	ENSP00000339801:T214M	T	-	2	0	IDS	148387610	0.031000	0.19500	0.151000	0.22473	0.933000	0.57130	0.398000	0.20899	0.865000	0.35603	-0.395000	0.06472	ACG	G|0.982;A|0.018	0.018	strong		0.527	IDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058677.3			A	148579705	G	A	148579705	3	1	22	1	0	0	0	0	1	0	0	0	7512	1145	40	1	1061	1	IDS	23	148579705	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	544505	148579705	6690855	4538	7439											
MAGEA8	4107	hgsc.bcm.edu	37	chrX	149013963	149013963	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	agttcgcatttcctacccatCcctgcatgaagaggctttgg	8	12	9	12	1	0	2	0	1	0	1	3	2	2	2	3	2	2	4	3	2	2	4	rs12010332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:149013963C>T	ENST00000542674.1	+	3	1438	c.917C>T	c.(916-918)tCc>tTc	p.S306F	MAGEA8_ENST00000286482.1_Missense_Mutation_p.S306F|MAGEA8_ENST00000535454.1_Missense_Mutation_p.S306F	NM_001166401.1	NP_001159873.1	P43361	MAGA8_HUMAN	melanoma antigen family A, 8	306	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.		S -> F (in dbSNP:rs12010332).							NS(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(12)|upper_aerodigestive_tract(1)	20	Acute lymphoblastic leukemia(192;6.56e-05)					TCCTACCCATCCCTGCATGAA	0.572													c|||	182	0.0482119	0.1248	0.0144	3775	,	,		15794	0.004		0.002	False		,,,				2504	0.001				p.S306F		Atlas-SNP	.											.	MAGEA8	40	.	0			c.C917T						PASS	.	C	PHE/SER,PHE/SER,PHE/SER	568,3267		39,405,85,1188,486	92	88	89		917,917,917	0.7	0	X	dbSNP_120	89	8,6718		0,6,2,2422,1868	yes	missense,missense,missense	MAGEA8	NM_001166400.1,NM_001166401.1,NM_005364.4	155,155,155	39,411,87,3610,2354	TT,TC,T,CC,C		0.1189,14.811,5.454	probably-damaging,probably-damaging,probably-damaging	306/319,306/319,306/319	149013963	576,9985	2203	4298	6501	SO:0001583	missense	4107	exon3			ACCCATCCCTGCA		CCDS14692.1	Xq28	2009-03-13			ENSG00000156009	ENSG00000156009			6806	protein-coding gene	gene with protein product	"MAGE-8 antigen", "cancer/testis antigen family 1, member 8"	300341		MAGE8		8575766	Standard	NM_005364		Approved	MGC2182, CT1.8	uc004fdw.2	P43361	OTTHUMG00000022635	ENST00000542674.1:c.917C>T	X.37:g.149013963C>T	ENSP00000443776:p.Ser306Phe	284	0	0		293	293	1	NM_005364	Q9BUN9	Missense_Mutation	SNP	ENST00000542674.1	37	CCDS14692.1	72	0.0433996383363472	47	0.10262008733624454	3	0.008426966292134831	1	0.0017482517482517483	1	0.0013192612137203166	.	3.559	-0.090020	0.07053	0.14811	0.001189	ENSG00000156009	ENST00000535454;ENST00000542674;ENST00000286482	T;T;T	0.01871	4.59;4.59;4.59	0.68	0.68	0.17980	.	5.208330	0.00397	N	0.000056	T	0.00039	0.0001	L	0.59967	1.855	0.80722	P	0.0	D	0.71674	0.998	P	0.57679	0.825	T	0.48210	-0.9055	8	0.08837	T	0.75	.	.	.	.	rs12010332;rs52806623;rs12010332	306	P43361	MAGA8_HUMAN	F	306	ENSP00000438293:S306F;ENSP00000443776:S306F;ENSP00000286482:S306F	ENSP00000286482:S306F	S	+	2	0	MAGEA8	148774621	0.000000	0.05858	0.001000	0.08648	0.501000	0.33797	-0.990000	0.03732	0.588000	0.29660	0.190000	0.17370	TCC	C|0.947;T|0.053	0.053	strong		0.572	MAGEA8-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058728.1	NM_005364		T	149013963	C	T	149013963	3	4	22	1	0	0	0	0	1	0	0	0	9180	855	30	2	919	2	MAGEA8	23	149013963	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	434258	149013963	6256597	4539	7440											
PASD1	139135	hgsc.bcm.edu	37	chrX	150840690	150840690	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caagaacaacacctgaaggaGcagcagcggcagctgcggga	14	2	14	11	2	0	2	0	1	0	1	0	4	0	4	1	3	7	4	1	3	4	0	rs370395923		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:150840690G>T	ENST00000370357.4	+	14	1718	c.1473G>T	c.(1471-1473)gaG>gaT	p.E491D		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	491						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)					acctgaaggagcagcagcggc	0.527													G|||	16	0.00423841	0.0121	0.0	3775	,	,		14023	0.0		0.0	False		,,,				2504	0.0				p.E491D		Atlas-SNP	.											.	PASD1	286	.	0			c.G1473T						PASS	.	G	ASP/GLU	35,3366		0,33,2,1472,389	10	10	10		1473	1	0	X		10	1,5850		0,0,1,2208,1434	yes	missense	PASD1	NM_173493.2	45	0,33,3,3680,1823	TT,TG,T,GG,G		0.0171,1.0291,0.3891	possibly-damaging	491/774	150840690	36,9216	1896	3643	5539	SO:0001583	missense	139135	exon14			GAAGGAGCAGCAG	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.1473G>T	X.37:g.150840690G>T	ENSP00000359382:p.Glu491Asp	84	0	0		115	48	0.417391	NM_173493	Q3MNE0|Q69HD7|Q8N7X9	Missense_Mutation	SNP	ENST00000370357.4	37	CCDS35431.1	.	.	.	.	.	.	.	.	.	.	G	9.223	1.033777	0.19590	0.010291	1.71E-4	ENSG00000166049	ENST00000370357	T	0.17691	2.26	2.03	1.04	0.20106	.	.	.	.	.	T	0.03871	0.0109	N	0.08118	0	0.09310	N	1	P	0.50710	0.938	B	0.37387	0.248	T	0.23904	-1.0175	9	0.15066	T	0.55	.	4.9456	0.13987	0.0:0.0:0.6449:0.355	.	491	Q8IV76	PASD1_HUMAN	D	491	ENSP00000359382:E491D	ENSP00000359382:E491D	E	+	3	2	PASD1	150591346	0.001000	0.12720	0.004000	0.12327	0.251000	0.25915	-0.444000	0.06854	0.252000	0.21531	0.462000	0.41574	GAG	.	.	weak		0.527	PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2	NM_173493		T	150840690	G	T	150840690	3	4	22	1	0	0	0	0	1	0	0	0	11480	962	34	4	1523	4	PASD1	23	150840690	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	1826727	150840690	4429870	4540	7441											
CNGA2	1260	hgsc.bcm.edu	37	chrX	150912171	150912171	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaaacactacatgcagttccGaaaggtcagcaaggggatgg	14	6	13	8	1	1	0	1	0	0	0	2	3	2	1	1	4	4	3	1	4	4	2	rs150539917	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:150912171G>A	ENST00000329903.4	+	6	1229	c.1196G>A	c.(1195-1197)cGa>cAa	p.R399Q		NM_005140.1	NP_005131.1	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	399			R -> Q (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		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)	p.R399Q(1)		breast(4)|endometrium(4)|large_intestine(5)|lung(34)|prostate(2)	49	Acute lymphoblastic leukemia(192;6.56e-05)					ATGCAGTTCCGAAAGGTCAGC	0.493													G|||	104	0.0275497	0.0726	0.0072	3775	,	,		18285	0.0		0.003	False		,,,				2504	0.0				p.R399Q		Atlas-SNP	.											.	CNGA2	136	.	1	Substitution - Missense(1)	breast(1)	c.G1196A						PASS	.	G	GLN/ARG	355,3480		19,261,56,1352,515	93	82	86		1196	3.2	1	X	dbSNP_134	86	2,6726		0,1,1,2427,1871	yes	missense	CNGA2	NM_005140.1	43	19,262,57,3779,2386	AA,AG,A,GG,G		0.0297,9.2568,3.3797	probably-damaging	399/665	150912171	357,10206	2203	4300	6503	SO:0001583	missense	1260	exon7			AGTTCCGAAAGGT	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.1196G>A	X.37:g.150912171G>A	ENSP00000328478:p.Arg399Gln	91	0	0		80	34	0.425	NM_005140	A0AVD0	Missense_Mutation	SNP	ENST00000329903.4	37	CCDS14701.1	48	0.028933092224231464	33	0.07051282051282051	2	0.005555555555555556	0	0.0	1	0.0013192612137203166	G	15.92	2.975018	0.53720	0.092568	2.97E-4	ENSG00000183862	ENST00000329903	D	0.97066	-4.23	4.96	3.18	0.36537	Cyclic nucleotide-binding-like (1);	0.057024	0.64402	D	0.000001	T	0.77745	0.4176	M	0.88450	2.955	0.20764	P	0.999856176	D	0.89917	1.0	D	0.79108	0.992	T	0.79874	-0.1619	9	0.46703	T	0.11	.	9.1566	0.36996	0.1872:0.0:0.8128:0.0	.	399	Q16280	CNGA2_HUMAN	Q	399	ENSP00000328478:R399Q	ENSP00000328478:R399Q	R	+	2	0	CNGA2	150662827	1.000000	0.71417	0.996000	0.52242	0.974000	0.67602	5.415000	0.66411	0.437000	0.26423	-0.344000	0.07964	CGA	G|0.964;A|0.036	0.036	strong		0.493	CNGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060888.1	NM_005140		A	150912171	G	A	150912171	3	1	22	1	0	0	0	0	1	0	0	0	3599	1058	37	1	1218	1	CNGA2	23	150912171	Missense_Mutation	SNP	G	TCGA-G8-6324-01A-11D-2210-10	71481	150912171	4358389	4541	7442											
ATP2B3	492	hgsc.bcm.edu	37	chrX	152830495	152830495	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgaggaagagatcgaccaTgccgagcgggagctccgcag	10	3	17	11	5	0	1	0	0	0	1	2	7	1	3	3	3	3	2	3	3	1	0	rs5986910	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:152830495T>C	ENST00000349466.2	+	20	3602	c.3276T>C	c.(3274-3276)caT>caC	p.H1092H	ATP2B3_ENST00000393842.1_Silent_p.H1078H|ATP2B3_ENST00000263519.4_Silent_p.H1092H|ATP2B3_ENST00000370181.2_Silent_p.H1078H|ATP2B3_ENST00000370186.1_Silent_p.H1078H|ATP2B3_ENST00000359149.3_Silent_p.H1092H			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	1092					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)					AGATCGACCATGCCGAGCGGG	0.672													C|||	206	0.0545695	0.1467	0.0144	3775	,	,		12860	0.0		0.002	False		,,,				2504	0.0				p.H1092H		Atlas-SNP	.											.	ATP2B3	552	.	0			c.T3276C						PASS	.		,	667,3161		51,473,92,1107,474	24	23	23		3276,3276	0.6	1	X	dbSNP_114	23	13,6711		0,8,5,2420,1863	no	coding-synonymous,coding-synonymous	ATP2B3	NM_001001344.2,NM_021949.3	,	51,481,97,3527,2337	CC,CT,C,TT,T		0.1933,17.4242,6.4443	,	1092/1221,1092/1174	152830495	680,9872	2197	4296	6493	SO:0001819	synonymous_variant	492	exon19			CGACCATGCCGAG	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.3276T>C	X.37:g.152830495T>C		185	0	0		194	64	0.329897	NM_001001344	B7WNR8|B7WNY5|Q12995|Q16858	Silent	SNP	ENST00000349466.2	37	CCDS35440.1																																																																																			T|0.920;C|0.080	0.080	strong		0.672	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060957.1	NM_021949		C	152830495	T	C	152830495	2	2	22	1	0	0	0	0	0	0	0	1	1141	1461	51	3		3	ATP2B3	23	152830495	Silent	SNP	T	TCGA-G8-6324-01A-11D-2210-10	1918324	152830495	2440065	4542	7443											
FLNA	2316	hgsc.bcm.edu	37	chrX	153581214	153581214	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggggcagtaggtgaccctgCacgtcccgtcctccaggtcc	5	8	13	15	2	0	1	0	1	0	0	4	1	4	1	5	4	1	3	5	4	1	1			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:153581214C>A	ENST00000369850.3	-	39	6541	c.6305G>T	c.(6304-6306)tGc>tTc	p.C2102F	FLNA_ENST00000422373.1_Missense_Mutation_p.C2094F|FLNA_ENST00000369856.3_Missense_Mutation_p.C235F|FLNA_ENST00000344736.4_Missense_Mutation_p.C2062F|FLNA_ENST00000360319.4_Missense_Mutation_p.C2094F|FLNA_ENST00000498491.1_5'Flank	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	2102					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)					GGTGACCCTGCACGTCCCGTC	0.607																																					p.C2102F		Atlas-SNP	.											.	FLNA	373	.	0			c.G6305T						PASS	.						108	109	109					X																	153581214		2157	4239	6396	SO:0001583	missense	2316	exon39			ACCCTGCACGTCC	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.6305G>T	X.37:g.153581214C>A	ENSP00000358866:p.Cys2102Phe	167	0	0		182	41	0.225275	NM_001110556	E9KL45|Q5HY53|Q5HY55|Q8NF52	Missense_Mutation	SNP	ENST00000369850.3	37	CCDS48194.1	.	.	.	.	.	.	.	.	.	.	C	16.87	3.241318	0.58995	.	.	ENSG00000196924	ENST00000360319;ENST00000422373;ENST00000369850;ENST00000369856;ENST00000344736;ENST00000444578	D;D;D;D;D;D	0.83673	-1.75;-1.75;-1.75;-1.75;-1.75;-1.75	5.64	5.64	0.86602	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.90477	0.7017	M	0.73217	2.22	0.80722	D	1	D;D;B;B	0.71674	0.994;0.998;0.407;0.407	P;D;B;B	0.67900	0.89;0.954;0.356;0.356	D	0.91224	0.5009	10	0.72032	D	0.01	.	18.7428	0.91780	0.0:1.0:0.0:0.0	.	235;2094;2102;2102	E9PHF0;P21333-2;P21333;E9KL45	.;.;FLNA_HUMAN;.	F	2094;2094;2102;235;2062;83	ENSP00000353467:C2094F;ENSP00000416926:C2094F;ENSP00000358866:C2102F;ENSP00000358872:C235F;ENSP00000358863:C2062F;ENSP00000397824:C83F	ENSP00000358863:C2062F	C	-	2	0	FLNA	153234408	1.000000	0.71417	0.989000	0.46669	0.513000	0.34164	7.779000	0.85648	2.372000	0.80975	0.513000	0.50165	TGC	.	.	none		0.607	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3			A	153581214	C	A	153581214	3	1	22	1	0	0	0	0	1	0	0	0	5941	710	25	4	1678	4	FLNA	23	153581214	Missense_Mutation	SNP	C	TCGA-G8-6324-01A-11D-2210-10	750719	153581214	1689346	4543	7444											
HES4	57801	hgsc.bcm.edu	37	chr1	934951	934951	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgcaggtgtctcacggtcaTctccaggatgtccgccttct	5	11	10	15	3	4	0	2	0	3	0	7	1	5	1	4	3	0	1	4	3	0	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:934951T>C	ENST00000304952.6	-	3	384	c.247A>G	c.(247-249)Atg>Gtg	p.M83V	RP11-54O7.17_ENST00000606034.1_lincRNA|HES4_ENST00000484667.2_Missense_Mutation_p.M51V|HES4_ENST00000428771.2_Missense_Mutation_p.M109V			Q9HCC6	HES4_HUMAN	hes family bHLH transcription factor 4	83	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				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)|transcription factor binding (GO:0008134)			lung(2)	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)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;9.36e-38)|OV - Ovarian serous cystadenocarcinoma(86;4.41e-23)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00237)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		CTCACGGTCATCTCCAGGATG	0.736																																					p.M109V		Atlas-SNP	.											.	HES4	9	.	0			c.A325G						PASS	.						13	17	15					1																	934951		2167	4263	6430	SO:0001583	missense	57801	exon2			CGGTCATCTCCAG	BC012351	CCDS5.1, CCDS44034.1	1p36	2013-10-17	2013-10-17		ENSG00000188290	ENSG00000188290		"Basic helix-loop-helix proteins"	24149	protein-coding gene	gene with protein product		608060	"hairy and enhancer of split 4 (Drosophila)"			11260262, 15254753	Standard	NM_021170		Approved	bHLHb42	uc001aci.2	Q9HCC6	OTTHUMG00000040758	ENST00000304952.6:c.247A>G	1.37:g.934951T>C	ENSP00000304595:p.Met83Val	29	0	0		50	32	0.64	NM_001142467	Q5SVA5	Missense_Mutation	SNP	ENST00000304952.6	37	CCDS5.1	.	.	.	.	.	.	.	.	.	.	T	11.83	1.756340	0.31137	.	.	ENSG00000188290	ENST00000428771;ENST00000304952;ENST00000484667	D;D;T	0.98090	-4.71;-4.71;1.1	3.29	2.15	0.27550	Helix-loop-helix DNA-binding (5);	0.176901	0.26820	U	0.022332	D	0.97932	0.9320	M	0.86178	2.8	0.43868	D	0.996478	P;P	0.46859	0.883;0.885	P;P	0.55222	0.771;0.688	D	0.96838	0.9616	10	0.56958	D	0.05	.	9.0774	0.36531	0.0:0.0:0.1982:0.8018	.	109;83	E9PB28;Q9HCC6	.;HES4_HUMAN	V	109;83;51	ENSP00000393198:M109V;ENSP00000304595:M83V;ENSP00000425085:M51V	ENSP00000304595:M83V	M	-	1	0	HES4	924814	1.000000	0.71417	0.980000	0.43619	0.960000	0.62799	2.653000	0.46691	0.366000	0.24427	0.334000	0.21626	ATG	.	.	none		0.736	HES4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097944.1	NM_021170		C	934951	T	C	934951	3	2	23	1	0	0	0	0	1	0	0	0	7077	1435	50	3	426	3	HES4	1	934951	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10		934951	248315670	1	7445											
TNFRSF18	8784	hgsc.bcm.edu	37	chr1	1140871	1140871	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactcggaacagcactcctcGcctgggcaggagacaggcca	10	4	12	15	2	0	1	0	0	0	1	3	3	1	2	3	4	2	2	3	4	1	0	rs142770542	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:1140871G>A	ENST00000379268.2	-	2	308	c.189C>T	c.(187-189)ggC>ggT	p.G63G	TNFRSF18_ENST00000328596.6_Splice_Site_p.G63G|TNFRSF18_ENST00000486728.1_5'UTR|TNFRSF18_ENST00000379265.5_Splice_Site_p.G63G	NM_004195.2|NM_148902.1	NP_004186.1|NP_683700.1	Q9Y5U5	TNR18_HUMAN	tumor necrosis factor receptor superfamily, member 18	63					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	tumor necrosis factor-activated receptor activity (GO:0005031)			lung(1)	1	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;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|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)		AGCACTCCTCGCCTGGGCAGG	0.682													g|||	4	0.000798722	0.0015	0.0014	5008	,	,		16517	0.0		0.001	False		,,,				2504	0.0				p.G63G	GBM(157;472 1934 13810 14591 35952)	Atlas-SNP	.											.	TNFRSF18	13	.	0			c.C189T						PASS	.	G	,,	0,4394		0,0,2197	42	37	39		189,189,189	-4.2	0	1	dbSNP_134	39	21,8573	16.0+/-53.3	0,21,4276	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	TNFRSF18	NM_004195.2,NM_148901.1,NM_148902.1	,,	0,21,6473	AA,AG,GG		0.2444,0.0,0.1617	,,	63/242,63/256,63/235	1140871	21,12967	2197	4297	6494	SO:0001630	splice_region_variant	8784	exon2			CTCCTCGCCTGGG	AF125304	CCDS9.1, CCDS10.1, CCDS30552.1	1p36.3	2011-08-11			ENSG00000186891	ENSG00000186891		"Tumor necrosis factor receptor superfamily", "CD molecules"	11914	protein-coding gene	gene with protein product		603905				9177197, 10037686	Standard	NM_004195		Approved	AITR, GITR, CD357	uc001add.3	Q9Y5U5	OTTHUMG00000001414	ENST00000379268.2:c.188-1C>T	1.37:g.1140871G>A		139	0	0		132	71	0.537879	NM_148902	B1AME1|O95851|Q5U0I4|Q9NYJ9	Silent	SNP	ENST00000379268.2	37	CCDS10.1																																																																																			G|0.998;A|0.002	0.002	strong		0.682	TNFRSF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004083.2	NM_004195	Silent	A	1140871	G	A	1140871	5	1	23	1	0	0	0	0	0	0	1	0	16306	1101	38	1	805	1	TNFRSF18	1	1140871	Splice_Site	SNP	G	TCGA-G8-6325-01A-11D-2210-10	205920	1140871	248109750	2	7446											
MMEL1	79258	hgsc.bcm.edu	37	chr1	2535672	2535672	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggcaggtttgcatcctcccGcagcaacgtggccactgaca	8	7	12	14	2	0	1	0	1	0	0	2	1	2	1	3	3	3	5	3	3	1	1	rs143132254	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:2535672G>A	ENST00000378412.3	-	10	1026	c.865C>T	c.(865-867)Cgg>Tgg	p.R289W	MMEL1_ENST00000288709.6_Missense_Mutation_p.R280W|MMEL1_ENST00000502556.1_Intron			Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	289						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)		GCATCCTCCCGCAGCAACGTG	0.667																																					p.R289W		Atlas-SNP	.											.	MMEL1	64	.	0			c.C865T						PASS	.	G	TRP/ARG	0,4406		0,0,2203	60	61	61		865	1.2	0.1	1	dbSNP_134	61	2,8598	2.2+/-6.3	0,2,4298	no	missense	MMEL1	NM_033467.3	101	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	289/780	2535672	2,13004	2203	4300	6503	SO:0001583	missense	79258	exon10			CCTCCCGCAGCAA	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.865C>T	1.37:g.2535672G>A	ENSP00000367668:p.Arg289Trp	223	0	0		193	99	0.512953	NM_033467	B9DI79|Q495T7|Q495T8|Q5SZS6|Q96PH9	Missense_Mutation	SNP	ENST00000378412.3	37	CCDS30569.2	.	.	.	.	.	.	.	.	.	.	G	14.08	2.429289	0.43122	0.0	2.33E-4	ENSG00000142606	ENST00000288709;ENST00000378412	T;T	0.73897	-0.79;-0.79	4.43	1.16	0.20824	Peptidase M13 (1);	0.058612	0.64402	D	0.000002	D	0.84511	0.5488	M	0.80847	2.515	0.41175	D	0.986192	D	0.89917	1.0	D	0.97110	1.0	D	0.84034	0.0361	10	0.59425	D	0.04	-37.0008	12.2645	0.54670	0.0:0.0:0.5439:0.4561	.	289	Q495T6	MMEL1_HUMAN	W	280;289	ENSP00000288709:R280W;ENSP00000367668:R289W	ENSP00000288709:R280W	R	-	1	2	MMEL1	2525532	0.933000	0.31639	0.080000	0.20451	0.522000	0.34438	1.210000	0.32370	0.006000	0.14734	0.485000	0.47835	CGG	G|1.000;A|0.000	0.000	strong		0.667	MMEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002395.2	NM_033467		A	2535672	G	A	2535672	3	1	23	1	0	0	0	0	1	0	0	0	9655	1086	38	1	1534	1	MMEL1	1	2535672	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1394801	2535672	246714949	3	7447											
MEGF6	1953	hgsc.bcm.edu	37	chr1	3411235	3411235	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcagctgccgttgctggcGtggcacaggcccccatttct	5	9	13	14	2	1	0	0	0	1	0	1	1	1	0	3	3	4	5	3	3	0	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:3411235G>A	ENST00000356575.4	-	31	4168	c.3942C>T	c.(3940-3942)caC>caT	p.H1314H	MEGF6_ENST00000294599.4_Silent_p.H1079H	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	1314	EGF-like 24. {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)		CGTTGCTGGCGTGGCACAGGC	0.701																																					p.H1314H	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.C3942T						PASS	.						9	13	12					1																	3411235		2003	4143	6146	SO:0001819	synonymous_variant	1953	exon31			GCTGGCGTGGCAC	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.3942C>T	1.37:g.3411235G>A		51	0	0		28	17	0.607143	NM_001409	Q4AC86|Q5VV39	Silent	SNP	ENST00000356575.4	37	CCDS41237.1	.	.	.	.	.	.	.	.	.	.	g	0.020	-1.445500	0.01089	.	.	ENSG00000162591	ENST00000491842	.	.	.	3.72	-0.402	0.12404	.	.	.	.	.	T	0.57519	0.2059	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51841	-0.8654	4	.	.	.	-25.4103	10.398	0.44211	0.3477:0.0:0.6523:0.0	.	.	.	.	M	88	.	.	T	-	2	0	MEGF6	3401095	0.001000	0.12720	0.046000	0.18839	0.039000	0.13416	0.019000	0.13444	-0.178000	0.10672	-1.295000	0.01343	ACG	.	.	none		0.701	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409		A	3411235	G	A	3411235	2	1	23	1	0	0	0	0	0	0	0	1	9471	1136	40	1		1	MEGF6	1	3411235	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	875563	3411235	245839386	4	7448											
CASZ1	54897	hgsc.bcm.edu	37	chr1	10725469	10725469	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctcttggtcccggggctgcGatgggctgccctccgtgtgg	1	10	17	13	3	1	0	0	0	1	0	3	1	3	0	3	5	2	3	3	5	0	1	rs149479567	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:10725469G>A	ENST00000377022.3	-	5	493	c.176C>T	c.(175-177)tCg>tTg	p.S59L	CASZ1_ENST00000344008.5_Missense_Mutation_p.S59L|CASZ1_ENST00000478728.2_5'UTR	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	59					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)		CCGGGGCTGCGATGGGCTGCC	0.687													G|||	24	0.00479233	0.0008	0.0086	5008	,	,		15263	0.001		0.0149	False		,,,				2504	0.001				p.S59L		Atlas-SNP	.											.	CASZ1	150	.	0			c.C176T						PASS	.	G	LEU/SER,LEU/SER	7,4247		0,7,2120	28	34	32		176,176	2.1	0	1	dbSNP_134	32	95,8333		1,93,4120	yes	missense,missense	CASZ1	NM_001079843.1,NM_017766.3	145,145	1,100,6240	AA,AG,GG		1.1272,0.1646,0.8043	benign,benign	59/1760,59/1167	10725469	102,12580	2127	4214	6341	SO:0001583	missense	54897	exon5			GGCTGCGATGGGC	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.176C>T	1.37:g.10725469G>A	ENSP00000366221:p.Ser59Leu	65	0	0		32	24	0.75	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	37	CCDS41246.1	17	0.007783882783882784	0	0.0	5	0.013812154696132596	1	0.0017482517482517483	11	0.014511873350923483	G	3.148	-0.174917	0.06421	0.001646	0.011272	ENSG00000130940	ENST00000377022;ENST00000344008	.	.	.	4.42	2.11	0.27256	.	0.674203	0.13380	N	0.392225	T	0.08670	0.0215	N	0.03608	-0.345	0.09310	N	1	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.31641	-0.9936	9	0.06891	T	0.86	-2.4618	4.9221	0.13874	0.6052:0.0:0.3948:0.0	.	83;59;59	B7Z1S3;Q86V15-2;Q86V15	.;.;CASZ1_HUMAN	L	59	.	ENSP00000339445:S59L	S	-	2	0	CASZ1	10648056	0.004000	0.15560	0.008000	0.14137	0.008000	0.06430	1.763000	0.38461	0.692000	0.31613	-0.424000	0.05967	TCG	G|0.993;A|0.007	0.007	strong		0.687	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766		A	10725469	G	A	10725469	3	1	23	1	0	0	0	0	1	0	0	0	2687	1059	37	1	5175	1	CASZ1	1	10725469	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	7314234	10725469	238525152	5	7449											
FBXO44	93611	hgsc.bcm.edu	37	chr1	11718859	11718859	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctcctgtcgtccgcgcaCgcgcctctggggaccttcca	4	8	11	18	5	1	0	0	0	1	0	5	1	4	1	5	2	1	2	5	2	0	1	rs150816569	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:11718859C>T	ENST00000251547.5	+	5	637	c.555C>T	c.(553-555)caC>caT	p.H185H	FBXO44_ENST00000251546.4_Missense_Mutation_p.R144C|FBXO44_ENST00000376768.1_Missense_Mutation_p.R176C|FBXO44_ENST00000376760.1_Missense_Mutation_p.R144C|FBXO44_ENST00000376762.4_Missense_Mutation_p.R144C|FBXO44_ENST00000376770.1_Silent_p.H185H	NM_033182.5	NP_149438.2	Q9H4M3	FBX44_HUMAN	F-box protein 44	185	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)		CGTCCGCGCACGCGCCTCTGG	0.692													C|||	24	0.00479233	0.0008	0.0159	5008	,	,		14300	0.0		0.0119	False		,,,				2504	0.0				p.R144C		Atlas-SNP	.											.	FBXO44	20	.	0			c.C430T						PASS	.	C	,,CYS/ARG,CYS/ARG	16,4390	23.3+/-48.9	0,16,2187	61	61	61		555,555,430,430	-3.8	0.1	1	dbSNP_134	61	83,8517	48.9+/-108.6	2,79,4219	yes	coding-synonymous,coding-synonymous,missense,missense	FBXO44	NM_001014765.1,NM_033182.5,NM_183412.2,NM_183413.2	,,180,180	2,95,6406	TT,TC,CC		0.9651,0.3631,0.7612	,,,	185/256,185/256,144/225,144/225	11718859	99,12907	2203	4300	6503	SO:0001819	synonymous_variant	93611	exon4			CGCGCACGCGCCT	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.555C>T	1.37:g.11718859C>T		67	0	0		77	54	0.701299	NM_183412	B3KNZ2|B7Z743|Q5TGX2|Q5TGX4|Q5TGX5|Q68DJ9|Q8WWY2	Missense_Mutation	SNP	ENST00000251547.5	37	CCDS132.1	17	0.007783882783882784	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	8	0.010554089709762533	C	5.363	0.252260	0.10185	0.003631	0.009651	ENSG00000132879	ENST00000251546;ENST00000425796;ENST00000376768;ENST00000376762;ENST00000376760	T;T;T;T;T	0.40225	1.3;1.12;1.04;1.3;1.3	5.01	-3.78	0.04333	.	0.423822	0.29737	N	0.011321	T	0.14700	0.0355	.	.	.	0.09310	N	0.999995	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.10965	-1.0607	9	0.41790	T	0.15	-28.3452	13.2172	0.59867	0.0:0.7229:0.0:0.2771	.	176;144	B7Z1P2;Q9H4M3-2	.;.	C	144;144;176;144;144	ENSP00000251546:R144C;ENSP00000389820:R144C;ENSP00000365959:R176C;ENSP00000365953:R144C;ENSP00000365951:R144C	ENSP00000251546:R144C	R	+	1	0	FBXO44	11641446	0.000000	0.05858	0.059000	0.19551	0.034000	0.12701	-1.363000	0.02592	-0.722000	0.04922	-0.409000	0.06214	CGC	C|0.992;T|0.008	0.008	strong		0.692	FBXO44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005761.1	NM_183412		T	11718859	C	T	11718859	2	4	23	1	0	0	0	0	0	0	0	1	5761	536	19	1		1	FBXO44	1	11718859	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	993390	11718859	237531762	6	7450											
FBXO6	26270	hgsc.bcm.edu	37	chr1	11733846	11733846	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctccgaggctcagcctgggCagaagcatggacaggaggag	10	4	16	11	1	1	1	1	0	0	1	2	5	2	4	3	5	2	3	3	5	1	0	rs148957324	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:11733846C>A	ENST00000376753.4	+	6	955	c.820C>A	c.(820-822)Cag>Aag	p.Q274K		NM_018438.5	NP_060908.1	Q9NRD1	FBX6_HUMAN	F-box protein 6	274					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|proteolysis (GO:0006508)|response to unfolded protein (GO:0006986)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	carbohydrate binding (GO:0030246)|glycoprotein binding (GO:0001948)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|large_intestine(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(2)	6	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;5.25e-06)|COAD - Colon adenocarcinoma(227;0.000251)|BRCA - Breast invasive adenocarcinoma(304;0.000297)|Kidney(185;0.000747)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		TCAGCCTGGGCAGAAGCATGG	0.607													C|||	10	0.00199681	0.0	0.0	5008	,	,		18989	0.0		0.0089	False		,,,				2504	0.001				p.Q274K	NSCLC(54;506 1562 46490 51389)	Atlas-SNP	.											.	FBXO6	17	.	0			c.C820A						PASS	.	C	LYS/GLN	11,4395	17.9+/-39.9	0,11,2192	79	77	78		820	-9.2	0	1	dbSNP_134	78	85,8515	48.9+/-108.6	1,83,4216	yes	missense	FBXO6	NM_018438.5	53	1,94,6408	AA,AC,CC		0.9884,0.2497,0.7381	benign	274/294	11733846	96,12910	2203	4300	6503	SO:0001583	missense	26270	exon6			CCTGGGCAGAAGC	AF129536	CCDS133.1	1p36.22	2008-05-14	2004-06-15		ENSG00000116663	ENSG00000116663		"F-boxes /  "other""	13585	protein-coding gene	gene with protein product		605647	"F-box only protein 6"			10531035, 10945468	Standard	NM_018438		Approved	FBX6, FBG2, FBS2, Fbx6b	uc001aso.3	Q9NRD1	OTTHUMG00000002229	ENST00000376753.4:c.820C>A	1.37:g.11733846C>A	ENSP00000365944:p.Gln274Lys	264	0	0		243	95	0.390947	NM_018438	B1AK42|B2RC88|Q9UKT3	Missense_Mutation	SNP	ENST00000376753.4	37	CCDS133.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	C	0.015	-1.552659	0.00918	0.002497	0.009884	ENSG00000116663	ENST00000376753	T	0.21734	1.99	4.63	-9.25	0.00666	.	6.681920	0.00166	N	0.000000	T	0.05868	0.0153	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.15206	-1.0445	10	0.22109	T	0.4	.	11.0102	0.47659	0.1177:0.5049:0.3774:0.0	.	274	Q9NRD1	FBX6_HUMAN	K	274	ENSP00000365944:Q274K	ENSP00000365944:Q274K	Q	+	1	0	FBXO6	11656433	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.870000	0.04228	-2.568000	0.00469	-3.108000	0.00062	CAG	C|0.994;A|0.006	0.006	strong		0.607	FBXO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006332.1	NM_018438		A	11733846	C	A	11733846	3	1	23	1	0	0	0	0	1	0	0	0	5767	711	25	4	838	4	FBXO6	1	11733846	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	14987	11733846	237516775	7	7451											
MFN2	9927	hgsc.bcm.edu	37	chr1	12061598	12061598	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggattcagaaagcccagggCatgcctgaaggaggtaatga	14	6	14	7	0	1	3	1	2	0	1	1	5	1	5	2	4	2	2	2	4	3	2	rs41278632	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:12061598C>T	ENST00000235329.5	+	9	1279	c.957C>T	c.(955-957)ggC>ggT	p.G319G	MFN2_ENST00000444836.1_Silent_p.G319G	NM_014874.3	NP_055689.1	O95140	MFN2_HUMAN	mitofusin 2	319	Dynamin-type G.				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)		AAGCCCAGGGCATGCCTGAAG	0.517											OREG0013107	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	22	0.00439297	0.0015	0.0072	5008	,	,		19027	0.0		0.0099	False		,,,				2504	0.0051				p.G319G		Atlas-SNP	.											.	MFN2	83	.	0			c.C957T						PASS	.	C	,	11,4395	19.1+/-41.9	0,11,2192	80	75	77		957,957	3.3	1	1	dbSNP_127	77	95,8505	53.6+/-114.3	0,95,4205	no	coding-synonymous,coding-synonymous	MFN2	NM_001127660.1,NM_014874.3	,	0,106,6397	TT,TC,CC		1.1047,0.2497,0.815	,	319/758,319/758	12061598	106,12900	2203	4300	6503	SO:0001819	synonymous_variant	9927	exon9			CCAGGGCATGCCT	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.957C>T	1.37:g.12061598C>T		107	0	0	677	135	79	0.585185	NM_014874	A8K1B3|O95572|Q5JXC3|Q5JXC4|Q9H131|Q9NSX8	Silent	SNP	ENST00000235329.5	37	CCDS30587.1																																																																																			C|0.991;T|0.009	0.009	strong		0.517	MFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006859.2	NM_014874		T	12061598	C	T	12061598	2	4	23	1	0	0	0	0	0	0	0	1	9533	697	25	2		2	MFN2	1	12061598	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	327752	12061598	237189023	8	7452											
VPS13D	55187	hgsc.bcm.edu	37	chr1	12429611	12429611	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcattggattatgcctgggaCgaacccaccttgccaccttt	8	12	8	13	1	1	0	1	0	0	0	1	3	1	2	5	2	3	0	5	2	2	4	rs2295338	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:12429611C>T	ENST00000358136.3	+	54	10792	c.10662C>T	c.(10660-10662)gaC>gaT	p.D3554D	VPS13D_ENST00000496628.1_3'UTR|VPS13D_ENST00000356315.4_Silent_p.D3529D	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)		ATGCCTGGGACGAACCCACCT	0.502													C|||	324	0.0646965	0.1142	0.0634	5008	,	,		17469	0.0179		0.0427	False		,,,				2504	0.0695				p.D3554D		Atlas-SNP	.											.	VPS13D	316	.	0			c.C10662T						PASS	.	C	,	457,3949	216.1+/-234.9	24,409,1770	143	144	144		10662,10587	-6.5	0.7	1	dbSNP_100	144	313,8287	111.8+/-172.0	8,297,3995	no	coding-synonymous,coding-synonymous	VPS13D	NM_015378.2,NM_018156.2	,	32,706,5765	TT,TC,CC		3.6395,10.3722,5.9203	,	3554/4389,3529/4364	12429611	770,12236	2203	4300	6503	SO:0001819	synonymous_variant	55187	exon54			CTGGGACGAACCC	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.10662C>T	1.37:g.12429611C>T		138	0	0		157	69	0.43949	NM_015378		Silent	SNP	ENST00000358136.3	37	CCDS30588.1	139	0.06364468864468864	56	0.11382113821138211	33	0.09116022099447514	14	0.024475524475524476	36	0.047493403693931395	C	9.101	1.004065	0.19199	0.103722	0.036395	ENSG00000048707	ENST00000011700	.	.	.	5.93	-6.53	0.01866	.	.	.	.	.	T	0.02083	0.0065	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.51371	-0.8714	3	.	.	.	.	18.7169	0.91679	0.0:0.1617:0.0:0.8383	rs2295338;rs56588517;rs2295338	.	.	.	M	2376	.	.	T	+	2	0	VPS13D	12352198	0.771000	0.28555	0.748000	0.31131	0.959000	0.62525	-0.140000	0.10342	-1.561000	0.01684	-0.806000	0.03193	ACG	C|0.940;T|0.060	0.060	strong		0.502	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		T	12429611	C	T	12429611	2	4	23	1	0	0	0	0	0	0	0	1	17207	535	19	1		1	VPS13D	1	12429611	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	368013	12429611	236821010	9	7453											
CLCNKB	1188	hgsc.bcm.edu	37	chr1	16382243	16382243	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gaagctgtccccagagacttCcctgcatgaggtaacgggga	10	7	13	11	1	0	2	0	1	0	1	2	5	2	3	3	3	3	3	3	3	2	2	rs375375144		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:16382243C>A	ENST00000375679.4	+	18	2030	c.1919C>A	c.(1918-1920)tCc>tAc	p.S640Y	CLCNKB_ENST00000375667.3_Missense_Mutation_p.S470Y|FAM131C_ENST00000494078.1_5'Flank	NM_000085.4	NP_000076.2	P51801	CLCKB_HUMAN	chloride channel, voltage-sensitive Kb	640	CBS 2. {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)|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)		CCAGAGACTTCCCTGCATGAG	0.617											OREG0013133	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S640Y		Atlas-SNP	.											.	CLCNKB	50	.	0			c.C1919A						PASS	.	C	TYR/SER,TYR/SER	0,4406		0,0,2203	70	68	68		1919,1412	4.7	1	1		68	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	CLCNKB	NM_000085.3,NM_001165945.1	144,144	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	benign,benign	640/688,471/519	16382243	1,13005	2203	4300	6503	SO:0001583	missense	1188	exon18			AGACTTCCCTGCA	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.1919C>A	1.37:g.16382243C>A	ENSP00000364831:p.Ser640Tyr	170	0	0	709	135	54	0.4	NM_000085	B3KUY3|Q5T5Q7|Q5T5Q8	Missense_Mutation	SNP	ENST00000375679.4	37	CCDS168.1	.	.	.	.	.	.	.	.	.	.	c	19.03	3.747160	0.69418	0.0	1.16E-4	ENSG00000184908	ENST00000375668;ENST00000375679;ENST00000375667;ENST00000431772	D;D;D	0.95035	-3.59;-3.59;-2.62	4.7	4.7	0.59300	Cystathionine beta-synthase, core (3);	0.067228	0.64402	D	0.000011	D	0.96191	0.8758	M	0.90198	3.095	0.80722	D	1	B;B	0.27380	0.177;0.078	B;B	0.39503	0.301;0.135	D	0.96375	0.9277	10	0.72032	D	0.01	.	15.1589	0.72764	0.0:1.0:0.0:0.0	.	470;640	Q5T5Q7;P51801	.;CLCKB_HUMAN	Y	137;640;470;128	ENSP00000364831:S640Y;ENSP00000364819:S470Y;ENSP00000389344:S128Y	ENSP00000364819:S470Y	S	+	2	0	CLCNKB	16254830	0.957000	0.32711	0.995000	0.50966	0.702000	0.40608	4.220000	0.58567	2.322000	0.78497	0.555000	0.69702	TCC	.	.	none		0.617	CLCNKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026331.1	NM_000085		A	16382243	C	A	16382243	3	1	23	1	0	0	0	0	1	0	0	0	3472	855	30	4	2133	4	CLCNKB	1	16382243	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	3952632	16382243	232868378	10	7454											
PINK1	65018	hgsc.bcm.edu	37	chr1	20971158	20971158	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gccggacgctgttcctcgttAtgaagaagtaagtgacagca	11	9	12	9	3	0	3	0	2	0	1	2	4	1	4	2	1	1	5	2	1	4	3	rs139226733		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:20971158A>T	ENST00000321556.4	+	4	1046	c.952A>T	c.(952-954)Atg>Ttg	p.M318L	PINK1-AS_ENST00000451424.1_RNA|PINK1_ENST00000492302.1_3'UTR	NM_032409.2	NP_115785.1	Q9BXM7	PINK1_HUMAN	PTEN induced putative kinase 1	318	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.		M -> L. {ECO:0000269|PubMed:15596610}.		activation of protein kinase B activity (GO:0032148)|cell death (GO:0008219)|cellular response to hypoxia (GO:0071456)|cellular response to toxic substance (GO:0097237)|intracellular signal transduction (GO:0035556)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of gene expression (GO:0010629)|negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway (GO:1903384)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|peptidyl-serine autophosphorylation (GO:0036289)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial electron transport, NADH to ubiquinone (GO:1902958)|positive regulation of peptidase activity (GO:0010952)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of mitochondrion degradation (GO:1903146)|regulation of protein complex assembly (GO:0043254)|regulation of protein ubiquitination (GO:0031396)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|TORC2 signaling (GO:0038203)|ubiquitin-dependent protein catabolic process (GO:0006511)	astrocyte projection (GO:0097449)|axon (GO:0030424)|cell body (GO:0044297)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of mitochondrial outer membrane (GO:0031307)|Lewy body (GO:0097413)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|C3HC4-type RING finger domain binding (GO:0055131)|calcium-dependent protein kinase activity (GO:0010857)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)|protein kinase B binding (GO:0043422)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)	14		all_lung(284;2.72e-05)|Lung NSC(340;2.94e-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;0.0182)|COAD - Colon adenocarcinoma(152;1.21e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000146)|Kidney(64;0.000182)|GBM - Glioblastoma multiforme(114;0.000497)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GTTCCTCGTTATGAAGAAGTA	0.632													A|||	1	0.000199681	0.0	0.0	5008	,	,		18148	0.0		0.001	False		,,,				2504	0.0				p.M318L	Esophageal Squamous(145;853 1803 8146 34412 35011)	Atlas-SNP	.											.	PINK1	37	.	0			c.A952T	GRCh37	CM053378	PINK1	M	rs139226733	PASS	.	A	LEU/MET	2,4404	4.2+/-10.8	0,2,2201	47	44	45		952	6.1	0.9	1	dbSNP_134	45	7,8593	4.3+/-15.6	0,7,4293	yes	missense	PINK1	NM_032409.2	15	0,9,6494	TT,TA,AA		0.0814,0.0454,0.0692	probably-damaging	318/582	20971158	9,12997	2203	4300	6503	SO:0001583	missense	65018	exon4			CTCGTTATGAAGA	AB053323	CCDS211.1	1p36.12	2011-07-21			ENSG00000158828	ENSG00000158828		"Parkinson disease"	14581	protein-coding gene	gene with protein product		608309	"Parkinson disease (autosomal recessive) 6"	PARK6		11494141, 15349860	Standard	NM_032409		Approved		uc001bdm.3	Q9BXM7	OTTHUMG00000002841	ENST00000321556.4:c.952A>T	1.37:g.20971158A>T	ENSP00000364204:p.Met318Leu	56	0	0		51	24	0.470588	NM_032409	Q8N6T9|Q8NBU3|Q96DE4	Missense_Mutation	SNP	ENST00000321556.4	37	CCDS211.1	.	.	.	.	.	.	.	.	.	.	A	19.96	3.923054	0.73213	4.54E-4	8.14E-4	ENSG00000158828	ENST00000321556	T	0.75589	-0.95	6.07	6.07	0.98685	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	0.72120	0.3421	L	0.60845	1.875	0.80722	D	1	B	0.23650	0.089	B	0.26517	0.07	T	0.70749	-0.4787	10	0.72032	D	0.01	-15.4264	13.0206	0.58784	1.0:0.0:0.0:0.0	.	318	Q9BXM7	PINK1_HUMAN	L	318	ENSP00000364204:M318L	ENSP00000364204:M318L	M	+	1	0	PINK1	20843745	1.000000	0.71417	0.946000	0.38457	0.934000	0.57294	7.964000	0.87933	2.326000	0.78906	0.533000	0.62120	ATG	A|0.999;T|0.001	0.001	strong		0.632	PINK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007954.1	NM_032409		T	20971158	A	T	20971158	3	4	23	1	0	0	0	0	1	0	0	0	11941	449	16	5	966	5	PINK1	1	20971158	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	4588915	20971158	228279463	11	7455											
C1QB	713	hgsc.bcm.edu	37	chr1	22987744	22987744	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aacaccttccaggtcaccacCggtggcatggtcctcaagct	9	8	9	15	1	2	0	2	0	0	0	4	0	4	0	5	4	2	2	5	4	2	1	rs149718049	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:22987744C>T	ENST00000314933.6	+	3	759	c.627C>T	c.(625-627)acC>acT	p.T209T	C1QB_ENST00000509305.1_Silent_p.T207T	NM_000491.3	NP_000482.3	P02746	C1QB_HUMAN	complement component 1, q subcomponent, B chain	209	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|inner ear development (GO:0048839)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|complement component C1 complex (GO:0005602)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(2)|large_intestine(1)|lung(9)|prostate(1)	14		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;7.06e-27)|Colorectal(126;1.58e-07)|GBM - Glioblastoma multiforme(114;6.72e-06)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000551)|KIRC - Kidney renal clear cell carcinoma(1967;0.0027)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)	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)	AGGTCACCACCGGTGGCATGG	0.587																																					p.T209T		Atlas-SNP	.											.	C1QB	40	.	0			c.C627T						PASS	.	C		0,4406		0,0,2203	60	55	57		627	-6.8	0	1	dbSNP_134	57	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	C1QB	NM_000491.3		0,8,6495	TT,TC,CC		0.093,0.0,0.0615		209/254	22987744	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	713	exon3			CACCACCGGTGGC	X03084	CCDS228.1	1p36.3-p34.1	2014-09-17	2006-02-09		ENSG00000173369	ENSG00000173369		"Complement system"	1242	protein-coding gene	gene with protein product		120570	"complement component 1, q subcomponent, beta polypeptide"			1537612	Standard	XM_005245982		Approved		uc001bgd.3	P02746	OTTHUMG00000002896	ENST00000314933.6:c.627C>T	1.37:g.22987744C>T		122	0	0		91	54	0.593407	NM_000491	Q5T959|Q96H17	Silent	SNP	ENST00000314933.6	37	CCDS228.1																																																																																			C|0.999;T|0.001	0.001	strong		0.587	C1QB-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_000491		T	22987744	C	T	22987744	2	4	23	1	0	0	0	0	0	0	0	1	1957	639	23	1		1	C1QB	1	22987744	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	2016586	22987744	226262877	12	7456											
RHD	6007	hgsc.bcm.edu	37	chr1	25629896	25629896	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccttctccgtggcttgccatGgtgctgggtcttgtggctgg	1	14	15	11	1	2	0	0	0	2	0	3	0	2	0	3	5	2	3	3	5	0	3	rs371803235		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:25629896G>T	ENST00000328664.4	+	6	1040	c.885G>T	c.(883-885)atG>atT	p.M295I	RHD_ENST00000423253.1_3'UTR|RHD_ENST00000568195.1_Missense_Mutation_p.M295I|RHD_ENST00000423810.2_Missense_Mutation_p.M295I|RHD_ENST00000454452.2_Missense_Mutation_p.M295I|RHD_ENST00000342055.5_Missense_Mutation_p.M295I|RHD_ENST00000417538.2_Missense_Mutation_p.M295I|RHD_ENST00000357542.4_Missense_Mutation_p.M295I	NM_001282867.1|NM_016124.3	NP_001269796.1|NP_057208	Q02161	RHD_HUMAN	Rh blood group, D antigen	295						integral component of plasma membrane (GO:0005887)	ammonium transmembrane transporter activity (GO:0008519)			breast(2)|large_intestine(4)|lung(7)|prostate(1)	14		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;7.39e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000332)|BRCA - Breast invasive adenocarcinoma(304;0.000438)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000908)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GGCTTGCCATGGTGCTGGGTC	0.572																																					p.M295I		Atlas-SNP	.											.	RHD	38	.	0			c.G885T	GRCh37	CM994723	RHD	M		PASS	.	G	ILE/MET,ILE/MET	0,4226		0,0,2113	85	59	68		885,885	3.2	1	1		68	1,7421		0,1,3710	no	missense,missense	RHD	NM_001127691.1,NM_016124.3	10,10	0,1,5823	TT,TG,GG		0.0135,0.0,0.0086	probably-damaging,probably-damaging	295/322,295/418	25629896	1,11647	2113	3711	5824	SO:0001583	missense	6007	exon6			TGCCATGGTGCTG	AB012623	CCDS262.1, CCDS53285.1, CCDS60027.1, CCDS60028.1, CCDS60029.1, CCDS60030.1, CCDS60031.1	1p36.11	2014-07-19	2013-10-02		ENSG00000187010	ENSG00000187010		"CD molecules", "Blood group antigens"	10009	protein-coding gene	gene with protein product		111680	"Rhesus blood group, D antigen", "Rh blood group, D antigen"	RH		8220426	Standard	NM_016124		Approved	Rh30a, Rh4, RhPI, RhII, DIIIc, CD240D	uc001bjz.3	Q02161	OTTHUMG00000003476	ENST00000328664.4:c.885G>T	1.37:g.25629896G>T	ENSP00000331871:p.Met295Ile	154	0	0		247	101	0.408907	NM_001127691	Q02162|Q07618|Q16147|Q16235|Q16355|Q5VSK0|Q5XLS9|Q5XLT1|Q5XLT2|Q9NPK0|Q9UQ20|Q9UQ21|Q9UQ22|Q9UQ23	Missense_Mutation	SNP	ENST00000328664.4	37	CCDS262.1	.	.	.	.	.	.	.	.	.	.	.	7.093	0.572463	0.13623	0.0	1.35E-4	ENSG00000187010	ENST00000328664;ENST00000419831;ENST00000454452;ENST00000342055;ENST00000357542;ENST00000417538;ENST00000423810	T;T;T;T;T;T	0.20738	2.05;2.05;2.05;2.05;2.05;2.05	3.19	3.19	0.36642	Ammonium transporter AmtB-like (3);	0.000000	0.85682	D	0.000000	T	0.38852	0.1056	M	0.61703	1.905	0.58432	D	0.999998	D;D;P;D;D;P;D;D	0.89917	1.0;1.0;0.86;1.0;1.0;0.947;1.0;1.0	D;D;P;D;D;D;D;D	0.97110	1.0;0.999;0.844;1.0;1.0;0.932;0.999;1.0	T	0.11131	-1.0600	10	0.42905	T	0.14	-40.782	9.7501	0.40470	0.0:0.0:1.0:0.0	.	295;295;295;295;295;295;295;295	B4DLT8;Q5XLT1;Q5XLS9;Q5XLT2;Q5XLT3;E7EVW1;Q5XLT0;Q02161	.;.;.;.;.;.;.;RHD_HUMAN	I	295	ENSP00000331871:M295I;ENSP00000413849:M295I;ENSP00000339577:M295I;ENSP00000350150:M295I;ENSP00000396420:M295I;ENSP00000399640:M295I	ENSP00000331871:M295I	M	+	3	0	RHD	25502483	1.000000	0.71417	0.994000	0.49952	0.027000	0.11550	5.868000	0.69605	1.623000	0.50342	0.393000	0.25936	ATG	.	.	none		0.572	RHD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009660.5	NM_016124		T	25629896	G	T	25629896	3	4	23	1	0	0	0	0	1	0	0	0	13342	1348	47	4	907	4	RHD	1	25629896	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	2642152	25629896	223620725	13	7457											
PUM1	9698	hgsc.bcm.edu	37	chr1	31441316	31441316	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggtttggggtcaaaggacgTtggctggctcctccacggag	6	10	16	9	2	1	0	1	0	0	0	3	2	3	2	2	7	0	4	2	7	1	2	rs202191174	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:31441316T>C	ENST00000257075.5	-	11	1623	c.1530A>G	c.(1528-1530)caA>caG	p.Q510Q	PUM1_ENST00000424085.2_Silent_p.Q268Q|PUM1_ENST00000423018.2_Silent_p.Q414Q|PUM1_ENST00000373742.2_Silent_p.Q451Q|PUM1_ENST00000373741.4_Silent_p.Q546Q|PUM1_ENST00000490546.1_5'UTR|SNORD85_ENST00000363311.1_RNA|PUM1_ENST00000426105.2_Silent_p.Q510Q|PUM1_ENST00000373747.3_Silent_p.Q511Q|PUM1_ENST00000440538.2_Silent_p.Q511Q	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	510	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)		TCAAAGGACGTTGGCTGGCTC	0.522													T|||	2	0.000399361	0.0	0.0014	5008	,	,		18651	0.0		0.0	False		,,,				2504	0.001				p.Q510Q		Atlas-SNP	.											.	PUM1	107	.	0			c.A1530G						PASS	.	T	,	0,4406		0,0,2203	105	96	99		1530,1530	0.6	1	1		99	7,8593	5.7+/-21.5	0,7,4293	yes	coding-synonymous,coding-synonymous	PUM1	NM_001020658.1,NM_014676.2	,	0,7,6496	CC,CT,TT		0.0814,0.0,0.0538	,	510/1189,510/1187	31441316	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	9698	exon11			AGGACGTTGGCTG	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.1530A>G	1.37:g.31441316T>C		139	0	0		100	29	0.29	NM_014676	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Silent	SNP	ENST00000257075.5	37	CCDS338.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	T	9.593	1.126645	0.20959	0.0	8.14E-4	ENSG00000134644	ENST00000525843;ENST00000498419;ENST00000532678	.	.	.	5.77	0.558	0.17266	.	.	.	.	.	T	0.58836	0.2150	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53940	-0.8367	4	.	.	.	-4.9988	11.0358	0.47799	0.0:0.6746:0.0:0.3254	.	.	.	.	A	528;222;198	.	.	T	-	1	0	PUM1	31213903	1.000000	0.71417	0.999000	0.59377	0.955000	0.61496	0.888000	0.28268	0.136000	0.18733	-0.912000	0.02778	ACG	T|1.000;C|0.000	0.000	strong		0.522	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1			C	31441316	T	C	31441316	2	2	23	1	0	0	0	0	0	0	0	1	12840	1722	60	3		3	PUM1	1	31441316	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	5811420	31441316	217809305	14	7458											
AK2	204	hgsc.bcm.edu	37	chr1	33502357	33502357	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggtccctttaccggcccCgggaggccccagcagcacgg	5	5	14	17	3	0	0	0	0	0	0	1	1	1	1	6	5	3	2	6	5	1	2	rs199641857		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:33502357C>T	ENST00000487289.1	-	1	88	c.73G>A	c.(73-75)Ggg>Agg	p.G25R	AK2_ENST00000480134.1_Missense_Mutation_p.G25R|AK2_ENST00000548033.1_Missense_Mutation_p.G25R|AK2_ENST00000467905.1_Missense_Mutation_p.G25R|AK2_ENST00000373449.2_Missense_Mutation_p.G25R|AK2_ENST00000354858.6_Missense_Mutation_p.G25R					adenylate kinase 2											kidney(1)|large_intestine(2)|lung(4)|skin(1)	8		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				TTACCGGCCCCGGGAGGCCCC	0.672																																					p.G25R		Atlas-SNP	.											.	AK2	27	.	0			c.G73A						PASS	.						10	11	11					1																	33502357		2201	4289	6490	SO:0001583	missense	204	exon1			CGGCCCCGGGAGG	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	ENST00000487289.1:c.73G>A	1.37:g.33502357C>T	ENSP00000446849:p.Gly25Arg	339	0	0		229	14	0.0611354	NM_001199199		Missense_Mutation	SNP	ENST00000487289.1	37		.	.	.	.	.	.	.	.	.	.	C	27.9	4.874354	0.91664	.	.	ENSG00000004455	ENST00000373449;ENST00000548033;ENST00000467905;ENST00000480134;ENST00000354858;ENST00000398192;ENST00000487289	D;D;D;D;D;D	0.91686	-2.89;-2.89;-2.89;-2.89;-2.89;-2.89	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	D	0.97470	0.9172	H	0.99958	5.055	0.80722	D	1	P;P;D;P	0.54207	0.895;0.826;0.965;0.895	P;B;P;P	0.52710	0.459;0.142;0.707;0.459	D	0.98100	1.0414	10	0.72032	D	0.01	-23.3449	13.8506	0.63494	0.0:1.0:0.0:0.0	.	25;25;25;25	P54819-5;F8VY04;P54819;P54819-2	.;.;KAD2_HUMAN;.	R	25	ENSP00000362548:G25R;ENSP00000449003:G25R;ENSP00000447082:G25R;ENSP00000450109:G25R;ENSP00000346921:G25R;ENSP00000446849:G25R	ENSP00000346921:G25R	G	-	1	0	AK2	33274944	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.868000	0.56055	2.724000	0.93272	0.563000	0.77884	GGG	.	.	weak		0.672	AK2-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000011889.4	NM_001625		T	33502357	C	T	33502357	3	4	23	1	0	0	0	0	1	0	0	0	440	652	23	1	679	1	AK2	1	33502357	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	2061041	33502357	215748264	15	7459											
CSMD2	114784	hgsc.bcm.edu	37	chr1	34052137	34052137	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggtggtccttcaaactgcaGgtaggttccaagtttgcagg	8	11	14	8	0	1	0	1	0	0	0	3	0	3	0	2	5	3	5	2	5	3	4	rs371199413		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:34052137G>A	ENST00000373381.4	-	46	7194	c.7018C>T	c.(7018-7020)Ctg>Ttg	p.L2340L		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2342	Sushi 13. {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)				TCAAACTGCAGGTAGGTTCCA	0.483																																					p.L2342L		Atlas-SNP	.											.	CSMD2	946	.	0			c.C7024T						PASS	.	G		0,4406		0,0,2203	109	99	102		7024	4	1	1		102	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CSMD2	NM_052896.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		2342/3488	34052137	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	114784	exon47			ACTGCAGGTAGGT	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.7018C>T	1.37:g.34052137G>A		146	0	0		92	36	0.391304	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Silent	SNP	ENST00000373381.4	37																																																																																				.	.	none		0.483	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896		A	34052137	G	A	34052137	2	1	23	1	0	0	0	0	0	0	0	1	3947	991	35	2		2	CSMD2	1	34052137	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	549780	34052137	215198484	16	7460											
ZMYM4	9202	hgsc.bcm.edu	37	chr1	35853073	35853073	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggcaaaatgtttcagttcTgtggcaagaattgttctgat	11	14	11	5	0	3	2	1	1	2	1	3	2	3	2	0	2	0	5	0	2	4	4			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:35853073T>A	ENST00000314607.6	+	13	2211	c.2131T>A	c.(2131-2133)Tgt>Agt	p.C711S	ZMYM4_ENST00000373297.2_Missense_Mutation_p.C622S	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	711					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)				GTTTCAGTTCTGTGGCAAGAA	0.299																																					p.C711S		Atlas-SNP	.											.	ZMYM4	143	.	0			c.T2131A						PASS	.						55	61	59					1																	35853073		2203	4300	6503	SO:0001583	missense	9202	exon13			CAGTTCTGTGGCA	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.2131T>A	1.37:g.35853073T>A	ENSP00000322915:p.Cys711Ser	110	0	0		82	4	0.0487805	NM_005095	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Missense_Mutation	SNP	ENST00000314607.6	37	CCDS389.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.9|20.9	4.064116|4.064116	0.76187|0.76187	.|.	.|.	ENSG00000146463|ENSG00000146463	ENST00000314607;ENST00000373297|ENST00000457946	T;T|.	0.39787|.	1.16;1.06|.	5.36|5.36	5.36|5.36	0.76844|0.76844	TRASH (1);Zinc finger, MYM-type (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.75324|0.75324	0.3834|0.3834	M|M	0.79258|0.79258	2.445|2.445	0.54753|0.54753	D|D	0.999988|0.999988	D|.	0.71674|.	0.998|.	D|.	0.79784|.	0.993|.	T|T	0.76955|0.76955	-0.2767|-0.2767	10|5	0.66056|.	D|.	0.02|.	-8.763|-8.763	14.5294|14.5294	0.67915|0.67915	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	711|.	Q5VZL5|.	ZMYM4_HUMAN|.	S|Q	711;622|370	ENSP00000322915:C711S;ENSP00000362394:C622S|.	ENSP00000322915:C711S|.	C|L	+|+	1|2	0|0	ZMYM4|ZMYM4	35625660|35625660	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	5.706000|5.706000	0.68362|0.68362	2.021000|2.021000	0.59480|0.59480	0.533000|0.533000	0.62120|0.62120	TGT|CTG	.	.	none		0.299	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095		A	35853073	T	A	35853073	3	1	23	1	0	0	0	0	1	0	0	0	17717	1580	55	5	2181	5	ZMYM4	1	35853073	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	1800936	35853073	213397548	17	7461											
EIF2C1	26523	hgsc.bcm.edu	37	chr1	36367665	36367665	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgcccatcttgcagtacggCggccgggtgagcagggtcag	6	6	17	12	4	2	1	1	1	1	0	2	1	2	1	2	4	3	3	2	4	1	2	rs61751003	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:36367665C>T	ENST00000373204.4	+	10	1470	c.1257C>T	c.(1255-1257)ggC>ggT	p.G419G	AGO1_ENST00000373206.1_Silent_p.G344G	NM_012199.2	NP_036331.1	Q9UL18	AGO1_HUMAN	argonaute RISC catalytic component 1	419					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)										TGCAGTACGGCGGCCGGGTGA	0.582													C|||	3	0.000599042	0.0	0.0	5008	,	,		17254	0.0		0.002	False		,,,				2504	0.001				p.G419G		Atlas-SNP	.											.	.	.	.	0			c.C1257T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	50	56	54		1257	2.7	1	1	dbSNP_129	54	30,8570	21.6+/-65.8	0,30,4270	no	coding-synonymous	EIF2C1	NM_012199.2		0,32,6471	TT,TC,CC		0.3488,0.0454,0.246		419/858	36367665	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	26523	exon10			GTACGGCGGCCGG	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.1257C>T	1.37:g.36367665C>T		110	0	0		118	75	0.635593	NM_012199	Q5TA57|Q6P4S0	Silent	SNP	ENST00000373204.4	37	CCDS398.1																																																																																			C|0.998;T|0.002	0.002	strong		0.582	AGO1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019337.3			T	36367665	C	T	36367665	2	4	23	1	0	0	0	0	0	0	0	1	5007	755	27	1		1	EIF2C1	1	36367665	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	514592	36367665	212882956	18	7462											
MAP7D1	55700	hgsc.bcm.edu	37	chr1	36636774	36636774	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctaggccagcccccccgcaGgaagagtccccttcctctga	7	6	9	19	1	1	2	0	1	1	1	3	3	3	3	8	2	1	1	8	2	2	2	rs139650826	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:36636774G>A	ENST00000373151.2	+	2	465	c.249G>A	c.(247-249)caG>caA	p.Q83Q	MAP7D1_ENST00000316156.4_Silent_p.Q83Q|MAP7D1_ENST00000373150.4_Silent_p.Q83Q	NM_018067.3	NP_060537.3	Q3KQU3	MA7D1_HUMAN	MAP7 domain containing 1	83	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)				CCCCCCCGCAGGAAGAGTCCC	0.642													G|||	23	0.00459265	0.0008	0.0043	5008	,	,		13296	0.0		0.0179	False		,,,				2504	0.001				p.Q83Q		Atlas-SNP	.											.	MAP7D1	62	.	0			c.G249A						PASS	.	G		12,4394	19.1+/-41.9	0,12,2191	39	43	41		249	2.2	1	1	dbSNP_134	41	125,8475	62.4+/-124.4	1,123,4176	no	coding-synonymous	MAP7D1	NM_018067.3		1,135,6367	AA,AG,GG		1.4535,0.2724,1.0534		83/842	36636774	137,12869	2203	4300	6503	SO:0001819	synonymous_variant	55700	exon2			CCCGCAGGAAGAG	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.249G>A	1.37:g.36636774G>A		112	0	0		100	74	0.74	NM_018067	D3DPS4|Q7L8J5|Q8N905|Q8TAK0|Q9HBQ2|Q9NW29|Q9ULN3	Silent	SNP	ENST00000373151.2	37	CCDS30673.1																																																																																			G|0.992;A|0.008	0.008	strong		0.642	MAP7D1-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382095.1	NM_018067		A	36636774	G	A	36636774	2	1	23	1	0	0	0	0	0	0	0	1	9276	991	35	2		2	MAP7D1	1	36636774	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	269109	36636774	212613847	19	7463											
KIAA0754	643314	hgsc.bcm.edu	37	chr1	39876573	39876573	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtgcaagattttaaaaacttAagtggagactgccaggactt	14	11	10	6	0	0	2	0	0	0	2	0	4	0	3	1	2	3	1	1	2	5	4	rs74607331	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:39876573A>C	ENST00000530275.1	+	1	423	c.228A>C	c.(226-228)ttA>ttC	p.L76F	MACF1_ENST00000289893.4_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000564288.1_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000545844.1_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	76	13 X 13 AA approximate tandem repeat of P-T-S-P-A-A-A-V-P-T-P-E-E.									central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	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)			TTAAAAACTTAAGTGGAGACT	0.448											OREG0013393	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	22	0.00439297	0.0	0.0086	5008	,	,		21714	0.0		0.0159	False		,,,				2504	0.0				p.L212F		Atlas-SNP	.											KIAA0754_ENST00000530275,NS,carcinoma,+2,2	KIAA0754	93	2	0			c.A636C						PASS	.	A	,,PHE/LEU	11,3737		0,11,1863	72	73	72		,,636	-0.7	0.6	1	dbSNP_132	72	110,8098		2,106,3996	yes	intron,intron,missense	MACF1,KIAA0754	NM_012090.4,NM_033044.3,NM_015038.1	,,22	2,117,5859	CC,CA,AA		1.3402,0.2935,1.012	,,benign	,,212/1428	39876573	121,11835	1874	4104	5978	SO:0001583	missense	643314	exon1			AAACTTAAGTGGA			1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.228A>C	1.37:g.39876573A>C	ENSP00000431179:p.Leu76Phe	206	0	0	889	176	51	0.289773	NM_015038	E9PMC2|Q6ZSB2	Missense_Mutation	SNP	ENST00000530275.1	37		16	0.007326007326007326	0	0.0	4	0.011049723756906077	0	0.0	12	0.0158311345646438	A	11.25	1.583420	0.28268	0.002935	0.013402	ENSG00000255103	ENST00000530275	T	0.31247	1.5	4.78	-0.745	0.11098	.	.	.	.	.	T	0.08714	0.0216	L	0.27053	0.805	0.09310	N	1	B	0.27932	0.194	B	0.26094	0.066	T	0.24977	-1.0145	9	0.87932	D	0	.	2.8467	0.05546	0.1825:0.4305:0.2676:0.1194	.	76	O94854	K0754_HUMAN	F	76	ENSP00000431179:L76F	ENSP00000431179:L76F	L	+	3	2	RP4-562N20.1	39649160	0.000000	0.05858	0.643000	0.29450	0.853000	0.48598	0.209000	0.17435	0.196000	0.20367	0.454000	0.30748	TTA	A|0.988;C|0.012	0.012	strong		0.448	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038		C	39876573	A	C	39876573	3	2	23	1	0	0	0	0	1	0	0	0	8201	359	13	5	638	5	KIAA0754	1	39876573	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	3239799	39876573	209374048	20	7464											
BMP8A	353500	hgsc.bcm.edu	37	chr1	39988708	39988708	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcgccccccaaggctactcAgcctattactgtgaggggga	9	8	11	13	1	1	1	1	1	0	0	2	2	1	2	4	3	3	1	4	3	4	3	rs2889739	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:39988708A>G	ENST00000331593.5	+	6	1324	c.978A>G	c.(976-978)tcA>tcG	p.S326S	RP11-69E11.4_ENST00000458207.1_RNA|RP11-69E11.4_ENST00000440190.1_RNA|RP11-69E11.4_ENST00000441741.1_RNA|RP11-69E11.4_ENST00000331856.2_RNA|RP11-69E11.4_ENST00000431553.1_RNA|RP11-69E11.4_ENST00000417869.1_RNA|RP11-69E11.4_ENST00000450157.1_RNA	NM_181809.3	NP_861525.2	Q7Z5Y6	BMP8A_HUMAN	bone morphogenetic protein 8a	326					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)			AAGGCTACTCAGCCTATTACT	0.627													A|||	130	0.0259585	0.0045	0.0303	5008	,	,		17612	0.0		0.0905	False		,,,				2504	0.0123				p.S326S		Atlas-SNP	.											.	BMP8A	24	.	0			c.A978G						PASS	.	A		70,4336	64.1+/-101.4	1,68,2134	184	161	169		978	-8.4	0.3	1	dbSNP_101	169	664,7936	167.8+/-219.5	21,622,3657	no	coding-synonymous	BMP8A	NM_181809.3		22,690,5791	GG,GA,AA		7.7209,1.5887,5.6435		326/403	39988708	734,12272	2203	4300	6503	SO:0001819	synonymous_variant	353500	exon6			CTACTCAGCCTAT	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.978A>G	1.37:g.39988708A>G		153	0	0		150	59	0.393333	NM_181809	Q5T3A5	Silent	SNP	ENST00000331593.5	37	CCDS437.1																																																																																			A|0.945;G|0.055	0.055	strong		0.627	BMP8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023079.1	NM_181809		G	39988708	A	G	39988708	2	3	23	1	0	0	0	0	0	0	0	1	1466	175	7	3		3	BMP8A	1	39988708	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	112135	39988708	209261913	21	7465											
ZSWIM5	57643	hgsc.bcm.edu	37	chr1	45500064	45500064	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcgtgaaccagcgaggataaCggctgggcaccacagacacc	12	3	13	13	3	0	2	0	1	0	1	0	4	0	3	3	3	3	2	3	3	2	1	rs182892990	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:45500064C>T	ENST00000359600.5	-	11	2574	c.2369G>A	c.(2368-2370)cGt>cAt	p.R790H	AL359473.1_ENST00000583502.1_RNA	NM_020883.1	NP_065934.1	Q9P217	ZSWM5_HUMAN	zinc finger, SWIM-type containing 5	790						extracellular space (GO:0005615)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|liver(1)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Acute lymphoblastic leukemia(166;0.155)					GCGAGGATAACGGCTGGGCAC	0.517													C|||	9	0.00179712	0.0	0.0101	5008	,	,		19192	0.0		0.002	False		,,,				2504	0.0				p.R790H		Atlas-SNP	.											.	ZSWIM5	72	.	0			c.G2369A						PASS	.	C	HIS/ARG	0,4164		0,0,2082	123	124	124		2369	4.6	1	1		124	6,8430		0,6,4212	yes	missense	ZSWIM5	NM_020883.1	29	0,6,6294	TT,TC,CC		0.0711,0.0,0.0476	possibly-damaging	790/1186	45500064	6,12594	2082	4218	6300	SO:0001583	missense	57643	exon11			GGATAACGGCTGG	AB040944	CCDS41319.1	1p34.1	2010-06-16			ENSG00000162415	ENSG00000162415		"Zinc fingers, SWIM-type"	29299	protein-coding gene	gene with protein product						10819331	Standard	NM_020883		Approved	KIAA1511	uc001cnd.2	Q9P217	OTTHUMG00000008950	ENST00000359600.5:c.2369G>A	1.37:g.45500064C>T	ENSP00000352614:p.Arg790His	100	0	0		82	23	0.280488	NM_020883	Q5SXQ9	Missense_Mutation	SNP	ENST00000359600.5	37	CCDS41319.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	c	35	5.453739	0.96223	0.0	7.11E-4	ENSG00000162415	ENST00000359600	T	0.49432	0.78	4.56	4.56	0.56223	.	0.000000	0.85682	D	0.000000	T	0.60766	0.2294	M	0.77103	2.36	0.80722	D	1	D	0.60160	0.987	P	0.50049	0.629	T	0.69281	-0.5186	10	0.66056	D	0.02	-8.8461	18.2179	0.89893	0.0:1.0:0.0:0.0	.	790	Q9P217	ZSWM5_HUMAN	H	790	ENSP00000352614:R790H	ENSP00000352614:R790H	R	-	2	0	ZSWIM5	45272651	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.561000	0.82288	2.479000	0.83701	0.563000	0.77884	CGT	C|0.999;T|0.001	0.001	strong		0.517	ZSWIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024823.2	XM_046581		T	45500064	C	T	45500064	3	4	23	1	0	0	0	0	1	0	0	0	18259	536	19	1	1204	1	ZSWIM5	1	45500064	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	5511356	45500064	203750557	22	7466											
FAAH	2166	hgsc.bcm.edu	37	chr1	46871746	46871746	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggctgtgtctatggacaggaGgcaggtgaggtccgtggtgc	6	9	19	7	1	1	1	0	1	1	0	2	3	2	3	1	7	1	2	1	7	1	1	rs41305628	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:46871746G>A	ENST00000243167.8	+	6	906	c.822G>A	c.(820-822)gaG>gaA	p.E274E	FAAH_ENST00000493735.1_3'UTR	NM_001441.2	NP_001432.2	O00519	FAAH1_HUMAN	fatty acid amide hydrolase	274					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)	ATGGACAGGAGGCAGGTGAGG	0.632											OREG0013458	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	71	0.0141773	0.0008	0.0231	5008	,	,		16684	0.0		0.0427	False		,,,				2504	0.0112				p.E274E		Atlas-SNP	.											.	FAAH	36	.	0			c.G822A						PASS	.	G		44,4362	47.5+/-82.1	0,44,2159	77	77	77		822	-1.5	0.2	1	dbSNP_127	77	390,8210	125.0+/-183.6	10,370,3920	no	coding-synonymous	FAAH	NM_001441.2		10,414,6079	AA,AG,GG		4.5349,0.9986,3.3369		274/580	46871746	434,12572	2203	4300	6503	SO:0001819	synonymous_variant	2166	exon6			ACAGGAGGCAGGT	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.822G>A	1.37:g.46871746G>A		87	0	0	942	104	66	0.634615	NM_001441	D3DQ19|Q52M86|Q5TDF8	Silent	SNP	ENST00000243167.8	37	CCDS535.1																																																																																			G|0.970;A|0.030	0.030	strong		0.632	FAAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021443.1	NM_001441		A	46871746	G	A	46871746	2	1	23	1	0	0	0	0	0	0	0	1	5358	991	35	2		2	FAAH	1	46871746	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1371682	46871746	202378875	23	7467											
LDLRAD1	388633	hgsc.bcm.edu	37	chr1	54480033	54480033	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcagcagaggtggccgccGcctgctgtgtgggggggaaa	7	5	20	9	2	0	1	0	0	0	1	0	3	0	2	3	5	3	3	3	5	1	0			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:54480033G>A	ENST00000371360.1	-	3	95	c.78C>T	c.(76-78)ggC>ggT	p.G26G	LDLRAD1_ENST00000420619.1_Intron|LDLRAD1_ENST00000545928.1_Intron|LDLRAD1_ENST00000371362.3_Intron	NM_001010978.2	NP_001010978.2	Q5T700	LRAD1_HUMAN	low density lipoprotein receptor class A domain containing 1	26						integral component of membrane (GO:0016021)				large_intestine(3)|prostate(1)|skin(3)	7						GGTGGCCGCCGCCTGCTGTGT	0.692																																					p.G26G		Atlas-SNP	.											.	LDLRAD1	22	.	0			c.C78T						PASS	.						12	13	12					1																	54480033		1980	3842	5822	SO:0001819	synonymous_variant	388633	exon3			GCCGCCGCCTGCT		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.78C>T	1.37:g.54480033G>A		90	0	0		61	34	0.557377	NM_001010978	A0PJY0|B7ZME3|Q5T6Z9	Silent	SNP	ENST00000371360.1	37	CCDS30725.1																																																																																			.	.	none		0.692	LDLRAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023243.1	NM_001010978		A	54480033	G	A	54480033	2	1	23	1	0	0	0	0	0	0	0	1	8714	1074	38	1		1	LDLRAD1	1	54480033	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	7608287	54480033	194770588	24	7468											
TMEM61	199964	hgsc.bcm.edu	37	chr1	55451850	55451850	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtggttctggtggccgggacGctctgcttcgcttggtggag	2	12	18	9	3	2	0	0	0	2	0	3	2	2	2	1	6	1	4	1	6	0	3	rs148773188		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:55451850G>A	ENST00000371268.3	+	2	370	c.96G>A	c.(94-96)acG>acA	p.T32T	RP11-12C17.2_ENST00000436960.1_RNA	NM_182532.1	NP_872338.1	Q8N0U2	TMM61_HUMAN	transmembrane protein 61	32						integral component of membrane (GO:0016021)				endometrium(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	4						TGGCCGGGACGCTCTGCTTCG	0.667																																					p.T32T		Atlas-SNP	.											.	TMEM61	22	.	0			c.G96A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	51	52	51		96	-7.4	0.2	1	dbSNP_134	51	0,8600		0,0,4300	no	coding-synonymous	TMEM61	NM_182532.1		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		32/211	55451850	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	199964	exon2			CGGGACGCTCTGC	BC029775	CCDS601.1	1p32.3	2008-02-05			ENSG00000143001	ENSG00000143001			27296	protein-coding gene	gene with protein product						12477932	Standard	NM_182532		Approved		uc001cyd.3	Q8N0U2	OTTHUMG00000009991	ENST00000371268.3:c.96G>A	1.37:g.55451850G>A		111	0	0		61	25	0.409836	NM_182532		Silent	SNP	ENST00000371268.3	37	CCDS601.1																																																																																			G|1.000;A|0.000	0.000	weak		0.667	TMEM61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027683.1	NM_182532		A	55451850	G	A	55451850	2	1	23	1	0	0	0	0	0	0	0	1	16203	1074	38	1		1	TMEM61	1	55451850	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	971817	55451850	193798771	25	7469											
USP24	23358	hgsc.bcm.edu	37	chr1	55589175	55589175	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agaagagacaaagcctctccCgcaatcagcgagtctttggt	12	8	10	11	2	3	2	1	0	2	2	4	4	3	2	2	1	2	1	2	1	3	1	rs145599916		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:55589175C>T	ENST00000294383.6	-	36	4220	c.4221G>A	c.(4219-4221)gcG>gcA	p.A1407A	USP24_ENST00000407756.1_Silent_p.A1247A	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	1407					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						AAGCCTCTCCCGCAATCAGCG	0.507													C|||	1	0.000199681	0.0	0.0	5008	,	,		17947	0.0		0.001	False		,,,				2504	0.0				p.A1407A		Atlas-SNP	.											.	USP24	323	.	0			c.G4221A						PASS	.	C		1,3863		0,1,1931	64	63	63		4221	-10.2	0.3	1	dbSNP_134	63	11,8251		0,11,4120	no	coding-synonymous	USP24	NM_015306.2		0,12,6051	TT,TC,CC		0.1331,0.0259,0.099		1407/2621	55589175	12,12114	1932	4131	6063	SO:0001819	synonymous_variant	23358	exon36			CTCTCCCGCAATC	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.4221G>A	1.37:g.55589175C>T		124	0	0		124	50	0.403226	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Silent	SNP	ENST00000294383.6	37	CCDS44154.2																																																																																			C|1.000;T|0.000	0.000	strong		0.507	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			T	55589175	C	T	55589175	2	4	23	1	0	0	0	0	0	0	0	1	17070	639	23	1		1	USP24	1	55589175	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	137325	55589175	193661446	26	7470											
UBE2U	148581	hgsc.bcm.edu	37	chr1	64672478	64672478	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caactgacaatacattttacAtcggagtacaactatgctcc	14	11	5	11	1	0	1	0	1	0	0	2	2	1	2	1	1	6	2	1	1	7	5	rs35112334	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:64672478A>G	ENST00000371076.3	+	3	424	c.180A>G	c.(178-180)acA>acG	p.T60T		NM_152489.1	NP_689702.1	Q5VVX9	UBE2U_HUMAN	ubiquitin-conjugating enzyme E2U (putative)	60					protein ubiquitination (GO:0016567)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)			large_intestine(3)|lung(2)|skin(1)	6						TACATTTTACATCGGAGTACA	0.299													A|||	51	0.0101837	0.0	0.0159	5008	,	,		16516	0.004		0.0288	False		,,,				2504	0.0072				p.T60T		Atlas-SNP	.											.	UBE2U	16	.	0			c.A180G						PASS	.	A		22,4380	29.9+/-59.1	0,22,2179	56	58	57		180	-2.9	0	1	dbSNP_126	57	265,8319	99.5+/-161.0	7,251,4034	no	coding-synonymous	UBE2U	NM_152489.1		7,273,6213	GG,GA,AA		3.0871,0.4998,2.2101		60/227	64672478	287,12699	2201	4292	6493	SO:0001819	synonymous_variant	148581	exon3			TTTTACATCGGAG	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.180A>G	1.37:g.64672478A>G		265	0	0		225	87	0.386667	NM_152489	Q8N1D4	Silent	SNP	ENST00000371076.3	37	CCDS627.1																																																																																			A|0.982;G|0.018	0.018	strong		0.299	UBE2U-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025005.1	NM_152489		G	64672478	A	G	64672478	2	3	23	1	0	0	0	0	0	0	0	1	16889	204	8	3		3	UBE2U	1	64672478	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	9083303	64672478	184578143	27	7471											
TYW3	127253	hgsc.bcm.edu	37	chr1	75199023	75199023	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttgacgaggatgtggtagAgcttgtgcagtttctgaaca	9	13	14	5	1	1	3	0	2	1	1	1	5	1	4	0	2	3	5	0	2	2	4	rs143670067	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:75199023A>C	ENST00000370867.3	+	1	184	c.95A>C	c.(94-96)gAg>gCg	p.E32A	CRYZ_ENST00000370872.3_5'Flank|TYW3_ENST00000479111.1_5'UTR|TYW3_ENST00000457880.2_Missense_Mutation_p.E32A|TYW3_ENST00000421739.2_Missense_Mutation_p.E32A|CRYZ_ENST00000417775.1_5'UTR|CRYZ_ENST00000370871.3_5'Flank|CRYZ_ENST00000340866.5_5'Flank	NM_138467.2	NP_612476.1	Q6IPR3	TYW3_HUMAN	tRNA-yW synthesizing protein 3 homolog (S. cerevisiae)	32					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						GATGTGGTAGAGCTTGTGCAG	0.572													A|||	10	0.00199681	0.0	0.0029	5008	,	,		19178	0.0		0.008	False		,,,				2504	0.0				p.E32A		Atlas-SNP	.											.	TYW3	36	.	0			c.A95C						PASS	.	A	,,,ALA/GLU,,ALA/GLU	6,4400	11.4+/-27.6	0,6,2197	142	114	123		,,,95,,95	3.5	0.4	1	dbSNP_134	123	35,8565	24.6+/-71.5	0,35,4265	yes	utr-5,utr-5,utr-5,missense,utr-5,missense	CRYZ,TYW3	NM_001130042.1,NM_001130043.1,NM_001134759.1,NM_001162916.1,NM_001889.3,NM_138467.2	,,,107,,107	0,41,6462	CC,CA,AA		0.407,0.1362,0.3152	,,,possibly-damaging,,possibly-damaging	,,,32/227,,32/260	75199023	41,12965	2203	4300	6503	SO:0001583	missense	127253	exon1			TGGTAGAGCTTGT	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.95A>C	1.37:g.75199023A>C	ENSP00000359904:p.Glu32Ala	99	0	0		84	32	0.380952	NM_001162916	B4DSP9|E9PGR7|Q5HYJ0|Q8N7L1	Missense_Mutation	SNP	ENST00000370867.3	37	CCDS666.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	A	12.16	1.854352	0.32791	0.001362	0.00407	ENSG00000162623	ENST00000457880;ENST00000370867;ENST00000421739	T;T;T	0.31247	1.5;1.5;1.5	4.61	3.49	0.39957	tRNA wybutosine-synthesizing protein (2);	0.257365	0.39615	N	0.001304	T	0.10981	0.0268	M	0.66378	2.025	0.09310	N	1	B;P;B	0.40970	0.153;0.734;0.056	B;B;B	0.34452	0.076;0.183;0.053	T	0.12116	-1.0560	10	0.24483	T	0.36	-7.0777	7.3561	0.26719	0.8192:0.0:0.1808:0.0	.	32;32;32	B4DFU6;E9PGR7;Q6IPR3	.;.;TYW3_HUMAN	A	32	ENSP00000407025:E32A;ENSP00000359904:E32A;ENSP00000409336:E32A	ENSP00000359904:E32A	E	+	2	0	TYW3	74971611	0.089000	0.21612	0.445000	0.26908	0.987000	0.75469	1.673000	0.37534	0.797000	0.33971	0.459000	0.35465	GAG	A|0.997;C|0.003	0.003	strong		0.572	TYW3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026573.1	NM_138467		C	75199023	A	C	75199023	3	2	23	1	0	0	0	0	1	0	0	0	16835	304	11	5	97	5	TYW3	1	75199023	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	10526545	75199023	174051598	28	7472											
LPAR3	23566	hgsc.bcm.edu	37	chr1	85331462	85331462	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaagttggtgagggaagcAgtcaagctactgtccagaag	13	7	14	7	0	1	2	1	1	0	1	2	3	2	3	1	2	4	4	1	2	5	2	rs41289037	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:85331462A>C	ENST00000440886.1	-	1	380	c.342T>G	c.(340-342)acT>acG	p.T114T	LPAR3_ENST00000491034.1_5'UTR|LPAR3_ENST00000370611.3_Silent_p.T114T			Q9UBY5	LPAR3_HUMAN	lysophosphatidic acid receptor 3	114					activation of MAPK activity (GO:0000187)|bleb assembly (GO:0032060)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of collateral sprouting (GO:0048672)|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)|synaptic transmission (GO:0007268)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|lysophosphatidic acid receptor activity (GO:0070915)|phospholipid binding (GO:0005543)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|urinary_tract(1)	24						TGAGGGAAGCAGTCAAGCTAC	0.502													A|||	24	0.00479233	0.0015	0.0086	5008	,	,		18401	0.0		0.0159	False		,,,				2504	0.0				p.T114T		Atlas-SNP	.											.	LPAR3	53	.	0			c.T342G						PASS	.	A		11,4395	19.1+/-41.9	0,11,2192	189	195	193		342	-11.3	0.2	1	dbSNP_127	193	118,8482	62.1+/-124.0	2,114,4184	no	coding-synonymous	LPAR3	NM_012152.2		2,125,6376	CC,CA,AA		1.3721,0.2497,0.9918		114/354	85331462	129,12877	2203	4300	6503	SO:0001819	synonymous_variant	23566	exon2			GGAAGCAGTCAAG	AF127138	CCDS700.1	1p22.3	2012-08-08	2008-04-11	2008-04-11	ENSG00000171517	ENSG00000171517		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	14298	protein-coding gene	gene with protein product		605106	"endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 7"	EDG7		10488122	Standard	NM_012152		Approved	LP-A3, Edg-7, RP4-678I3, HOFNH30, LPA3	uc009wcj.1	Q9UBY5	OTTHUMG00000009925	ENST00000440886.1:c.342T>G	1.37:g.85331462A>C		206	0	0		170	104	0.611765	NM_012152	A0AVA3	Silent	SNP	ENST00000440886.1	37	CCDS700.1																																																																																			A|0.991;C|0.009	0.009	strong		0.502	LPAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027467.1	NM_012152		C	85331462	A	C	85331462	2	2	23	1	0	0	0	0	0	0	0	1	8915	175	7	5		5	LPAR3	1	85331462	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	10132439	85331462	163919159	29	7473											
ALG14	199857	hgsc.bcm.edu	37	chr1	95538424	95538424	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaaaaccgccacagctcctgCggccgcagctagaacgagaa	13	3	11	14	4	0	2	0	0	0	2	1	4	1	2	4	1	5	3	4	1	5	1	rs34364382	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:95538424C>T	ENST00000370205.5	-	1	77	c.31G>A	c.(31-33)Gca>Aca	p.A11T	ALG14_ENST00000495856.1_5'UTR	NM_144988.3	NP_659425.1	Q96F25	ALG14_HUMAN	ALG14, UDP-N-acetylglucosaminyltransferase subunit	11					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)		ACAGCTCCTGCGGCCGCAGCT	0.582													C|||	9	0.00179712	0.0008	0.0029	5008	,	,		18389	0.0		0.005	False		,,,				2504	0.001				p.A11T		Atlas-SNP	.											.	ALG14	13	.	0			c.G31A						PASS	.	C	THR/ALA	6,4400	11.4+/-27.6	0,6,2197	79	77	78		31	3.3	0	1	dbSNP_126	78	101,8499	56.0+/-117.1	0,101,4199	yes	missense	ALG14	NM_144988.3	58	0,107,6396	TT,TC,CC		1.1744,0.1362,0.8227	possibly-damaging	11/217	95538424	107,12899	2203	4300	6503	SO:0001583	missense	199857	exon1			CTCCTGCGGCCGC		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.31G>A	1.37:g.95538424C>T	ENSP00000359224:p.Ala11Thr	53	0	0		38	16	0.421053	NM_144988	A8K030	Missense_Mutation	SNP	ENST00000370205.5	37	CCDS752.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	14.66	2.600442	0.46423	0.001362	0.011744	ENSG00000172339	ENST00000370205	T	0.44083	0.93	5.21	3.34	0.38264	.	1.316220	0.04936	N	0.457681	T	0.09247	0.0228	N	0.08118	0	0.09310	N	1	B	0.16166	0.016	B	0.06405	0.002	T	0.25502	-1.0130	10	0.22109	T	0.4	0.4063	9.4756	0.38869	0.0:0.8285:0.0:0.1715	rs34364382	11	Q96F25	ALG14_HUMAN	T	11	ENSP00000359224:A11T	ENSP00000359224:A11T	A	-	1	0	ALG14	95311012	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	0.652000	0.24888	0.772000	0.33382	0.591000	0.81541	GCA	C|0.994;T|0.006	0.006	strong		0.582	ALG14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029699.2	NM_144988		T	95538424	C	T	95538424	3	4	23	1	0	0	0	0	1	0	0	0	516	768	27	1	635	1	ALG14	1	95538424	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	10206962	95538424	153712197	30	7474											
SPAG17	200162	hgsc.bcm.edu	37	chr1	118535211	118535211	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggggcactcactagctgttTggactcaatgcaaaggcctt	9	10	11	11	1	2	0	2	0	0	0	2	1	2	1	1	4	2	4	1	4	3	3	rs35290515	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:118535211T>C	ENST00000336338.5	-	36	5304	c.5239A>G	c.(5239-5241)Aaa>Gaa	p.K1747E		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1747						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)		ACTAGCTGTTTGGACTCAATG	0.448													T|||	65	0.0129792	0.0008	0.0288	5008	,	,		15614	0.0		0.0318	False		,,,				2504	0.0123				p.K1747E		Atlas-SNP	.											.	SPAG17	263	.	0			c.A5239G						PASS	.	T	GLU/LYS	26,4380	32.6+/-62.9	0,26,2177	92	90	91		5239	-1.9	0	1	dbSNP_126	91	285,8315	105.4+/-166.3	4,277,4019	yes	missense	SPAG17	NM_206996.2	56	4,303,6196	CC,CT,TT		3.314,0.5901,2.3912	probably-damaging	1747/2224	118535211	311,12695	2203	4300	6503	SO:0001583	missense	200162	exon36			GCTGTTTGGACTC		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.5239A>G	1.37:g.118535211T>C	ENSP00000337804:p.Lys1747Glu	185	0	0		181	75	0.414365	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	35	0.016025641025641024	0	0.0	13	0.03591160220994475	0	0.0	22	0.029023746701846966	T	12.87	2.068360	0.36470	0.005901	0.03314	ENSG00000155761	ENST00000336338;ENST00000437255	T	0.21734	1.99	5.6	-1.87	0.07737	.	0.536654	0.20400	N	0.093080	T	0.10465	0.0256	M	0.61703	1.905	0.09310	N	1	P	0.38078	0.617	B	0.37144	0.242	T	0.25328	-1.0135	10	0.49607	T	0.09	.	15.5645	0.76281	0.0:0.0:0.5819:0.4181	rs35290515	1747	Q6Q759	SPG17_HUMAN	E	1747;227	ENSP00000337804:K1747E	ENSP00000337804:K1747E	K	-	1	0	SPAG17	118336734	0.176000	0.23096	0.004000	0.12327	0.059000	0.15707	0.839000	0.27586	0.049000	0.15920	-0.313000	0.08912	AAA	T|0.979;C|0.021	0.021	strong		0.448	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996		C	118535211	T	C	118535211	3	2	23	1	0	0	0	0	1	0	0	0	14994	1821	63	3	1484	3	SPAG17	1	118535211	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	22996787	118535211	130715410	31	7475											
HMGCS2	3158	hgsc.bcm.edu	37	chr1	120293454	120293454	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acgccgggcatactttcggcGatgctgctcgtccactcgct	5	10	11	15	6	0	0	0	0	0	0	4	1	1	0	2	2	3	4	2	2	1	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:120293454G>A	ENST00000369406.3	-	9	1547	c.1498C>T	c.(1498-1500)Cgc>Tgc	p.R500C	HMGCS2_ENST00000544913.2_Missense_Mutation_p.R458C	NM_005518.3	NP_005509.1	P54868	HMCS2_HUMAN	3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)	500			R -> H (in HMGCS deficiency). {ECO:0000269|PubMed:11479731}.		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)		TACTTTCGGCGATGCTGCTCG	0.517																																					p.R500C		Atlas-SNP	.											.	HMGCS2	58	.	0			c.C1498T						PASS	.						78	68	72					1																	120293454		2203	4300	6503	SO:0001583	missense	3158	exon9			TTCGGCGATGCTG	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.1498C>T	1.37:g.120293454G>A	ENSP00000358414:p.Arg500Cys	113	0	0		114	60	0.526316	NM_005518	B7Z8R3|D3Y5K6|Q5SZU2|Q6IBF4	Missense_Mutation	SNP	ENST00000369406.3	37	CCDS905.1	.	.	.	.	.	.	.	.	.	.	G	17.89	3.499155	0.64298	.	.	ENSG00000134240	ENST00000369406;ENST00000544913	D;D	0.90324	-2.65;-2.65	5.3	5.3	0.74995	Hydroxymethylglutaryl-coenzyme A synthase C-terminal (1);Thiolase-like (1);	0.000000	0.64402	D	0.000002	D	0.95928	0.8674	M	0.93638	3.44	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.96419	0.9310	10	0.87932	D	0	-2.0E-4	12.9248	0.58254	0.0:0.0:0.8377:0.1623	.	458;500	B7Z8R3;P54868	.;HMCS2_HUMAN	C	500;458	ENSP00000358414:R500C;ENSP00000439495:R458C	ENSP00000358414:R500C	R	-	1	0	HMGCS2	120094977	1.000000	0.71417	0.511000	0.27724	0.425000	0.31504	5.604000	0.67626	2.633000	0.89246	0.561000	0.74099	CGC	.	.	none		0.517	HMGCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033469.2	NM_005518		A	120293454	G	A	120293454	3	1	23	1	0	0	0	0	1	0	0	0	7242	1058	37	1	32	1	HMGCS2	1	120293454	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1758243	120293454	128957167	32	7476											
NOTCH2	4853	hgsc.bcm.edu	37	chr1	120458122	120458122	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtagggatgctcaccctggAggtgaccactgtgactgggt	7	9	16	9	0	1	2	1	2	0	0	1	4	1	4	2	5	1	2	2	5	1	1	rs35586704	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:120458122A>T	ENST00000256646.2	-	34	7442	c.7223T>A	c.(7222-7224)cTc>cAc	p.L2408H		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	2408					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)		CTCACCCTGGAGGTGACCACT	0.567			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome				A|||	4	0.000798722	0.0	0.0	5008	,	,		21639	0.0		0.004	False		,,,				2504	0.0				p.L2408H		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.T7223A						PASS	.	A	HIS/LEU	5,4401	9.9+/-24.2	0,5,2198	123	108	113		7223	5.3	1	1	dbSNP_126	113	22,8578	16.6+/-54.9	0,22,4278	yes	missense	NOTCH2	NM_024408.3	99	0,27,6476	TT,TA,AA		0.2558,0.1135,0.2076	probably-damaging	2408/2472	120458122	27,12979	2203	4300	6503	SO:0001583	missense	4853	exon34	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	CCCTGGAGGTGAC	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.7223T>A	1.37:g.120458122A>T	ENSP00000256646:p.Leu2408His	129	0	0		124	73	0.58871	NM_024408	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	37	CCDS908.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	15.05	2.717318	0.48622	0.001135	0.002558	ENSG00000134250	ENST00000256646	T	0.77489	-1.1	5.35	5.35	0.76521	Domain of unknown function DUF3454, notch (1);	0.000000	0.32769	U	0.005675	T	0.79375	0.4435	L	0.43923	1.385	0.34826	D	0.739179	D	0.76494	0.999	D	0.70487	0.969	D	0.83604	0.0130	10	0.87932	D	0	.	14.5066	0.67758	1.0:0.0:0.0:0.0	rs35586704	2408	Q04721	NOTC2_HUMAN	H	2408	ENSP00000256646:L2408H	ENSP00000256646:L2408H	L	-	2	0	NOTCH2	120259645	0.946000	0.32159	1.000000	0.80357	0.958000	0.62258	2.431000	0.44775	2.027000	0.59764	0.482000	0.46254	CTC	A|0.998;T|0.002	0.002	strong		0.567	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		T	120458122	A	T	120458122	3	4	23	1	0	0	0	0	1	0	0	0	10557	304	11	5	196	5	NOTCH2	1	120458122	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	164668	120458122	128792499	33	7477											
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144859816	144859816	+	Missense_Mutation	SNP	T	T	C																															ggctgggaagttctggttaaTggaggaggggctgaggctgg																								rs587702923	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:144859816T>C	ENST00000369354.3	-	38	6457	c.6268A>G	c.(6268-6270)Att>Gtt	p.I2090V	PDE4DIP_ENST00000530740.1_Missense_Mutation_p.I2175V|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.I2226V|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.I1984V|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.I2090V			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2090					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)		TTCTGGTTAATGGAGGAGGGG	0.577			T	PDGFRB	MPD																																p.I2090V		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A6268G						PASS	.						65	63	63					1																	144859816		2203	4300	6503	SO:0001583	missense	9659	exon38			GGTTAATGGAGGA	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.6268A>G	1.37:g.144859816T>C	ENSP00000358360:p.Ile2090Val	309	0	0		409	26	0.0635697	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	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	T	0.010	-1.760839	0.00657	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01685	4.69;4.78;4.78;4.8;4.79	4.63	-9.26	0.00662	.	.	.	.	.	T	0.00178	0.0005	N	0.03608	-0.345	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.47058	-0.9146	9	0.02654	T	1	.	5.9795	0.19399	0.0819:0.4615:0.1653:0.2913	.	1984;2090	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	V	1984;2090;2090;2175;2226	ENSP00000327209:I1984V;ENSP00000358360:I2090V;ENSP00000358363:I2090V;ENSP00000435654:I2175V;ENSP00000358366:I2226V	ENSP00000327209:I1984V	I	-	1	0	PDE4DIP	143571173	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.249000	0.00266	-3.114000	0.00240	-1.162000	0.01777	ATT	.	.	none		0.577	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		C	144859816	T	C	144859816	3	2	23	1	0	0	0	0	1	0	0	0	11652	1464	51	3	800	3	PDE4DIP	1	144859816	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	24401694	144859816	104390805	34	7478	97	2	1	37		4	3	91	N	T_G	2.429474e-06
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144859817	144859817	+	Silent	SNP	G	G	A																															gctgggaagttctggttaatGgaggaggggctgaggctggc																								rs587702923	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:144859817G>A	ENST00000369354.3	-	38	6456	c.6267C>T	c.(6265-6267)tcC>tcT	p.S2089S	PDE4DIP_ENST00000530740.1_Silent_p.S2174S|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000369359.4_Silent_p.S2225S|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000313382.9_Silent_p.S1983S|PDE4DIP_ENST00000369356.4_Silent_p.S2089S			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2089					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)		TCTGGTTAATGGAGGAGGGGC	0.582			T	PDGFRB	MPD																																p.S2089S		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C6267T						PASS	.						65	62	63					1																	144859817		2203	4300	6503	SO:0001819	synonymous_variant	9659	exon38			GTTAATGGAGGAG	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.6267C>T	1.37:g.144859817G>A		307	0	0		402	26	0.0646766	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	37	CCDS30824.1																																																																																			.	.	none		0.582	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		A	144859817	G	A	144859817	2	1	23	1	0	0	0	0	0	0	0	1	11652	1335	47	2		2	PDE4DIP	1	144859817	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1	144859817	104390804	35	7479	97	2	1	37		4	3	91	N	T_G	2.429474e-06
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144859879	144859879	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgctgttgcagctgcagtcGcagacaattgttcccctgaa	8	11	10	12	1	0	2	0	1	0	1	2	2	1	2	2	0	4	7	2	0	2	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:144859879G>A	ENST00000369354.3	-	38	6394	c.6205C>T	c.(6205-6207)Cga>Tga	p.R2069*	PDE4DIP_ENST00000530740.1_Nonsense_Mutation_p.R2154*|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000369359.4_Nonsense_Mutation_p.R2205*|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000313382.9_Nonsense_Mutation_p.R1963*|PDE4DIP_ENST00000369356.4_Nonsense_Mutation_p.R2069*			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2069					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)		AGCTGCAGTCGCAGACAATTG	0.582			T	PDGFRB	MPD																																p.R2069X		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C6205T						PASS	.						70	67	68					1																	144859879		2203	4298	6501	SO:0001587	stop_gained	9659	exon38			GCAGTCGCAGACA	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.6205C>T	1.37:g.144859879G>A	ENSP00000358360:p.Arg2069*	242	0	0		307	27	0.0879479	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	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	G	44	11.091583	0.99515	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	.	.	.	4.95	1.8	0.24995	.	.	.	.	.	.	.	.	.	.	.	0.39652	D	0.97048	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.6096	0.28122	0.0839:0.0:0.6302:0.2859	.	.	.	.	X	1963;2069;2069;2154;2205	.	ENSP00000327209:R1963X	R	-	1	2	PDE4DIP	143571236	0.995000	0.38212	0.113000	0.21522	0.000000	0.00434	0.225000	0.17757	0.604000	0.29930	-0.911000	0.02809	CGA	.	.	none		0.582	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		A	144859879	G	A	144859879	4	1	23	1	0	0	0	0	0	1	0	0	11652	1095	38	1	863	1	PDE4DIP	1	144859879	Nonsense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	62	144859879	104390742	36	7480			1	37		4	3	91	N	T_G	2.429474e-06
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144859906	144859906	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	attgttcccctgaatgctctGctccagctgccctctcagag	6	12	8	15	0	2	2	1	1	2	1	5	2	4	2	4	0	4	4	4	0	1	2	rs182136884		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:144859906G>T	ENST00000369354.3	-	38	6367	c.6178C>A	c.(6178-6180)Cag>Aag	p.Q2060K	PDE4DIP_ENST00000530740.1_Missense_Mutation_p.Q2145K|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.Q2196K|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.Q1954K|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.Q2060K			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2060					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)		TGAATGCTCTGCTCCAGCTGC	0.577			T	PDGFRB	MPD																																p.Q2060K		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C6178A						PASS	.						82	77	79					1																	144859906		2203	4298	6501	SO:0001583	missense	9659	exon38			TGCTCTGCTCCAG	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.6178C>A	1.37:g.144859906G>T	ENSP00000358360:p.Gln2060Lys	251	0	0		306	17	0.0555556	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	37	CCDS30824.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	1.396	-0.579398	0.03854	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01505	4.82;4.91;4.91;4.92;4.91	5.1	0.961	0.19638	.	.	.	.	.	T	0.00608	0.0020	L	0.43152	1.355	0.80722	D	1	B;B	0.10296	0.003;0.0	B;B	0.09377	0.004;0.0	T	0.45731	-0.9241	9	0.34782	T	0.22	.	2.6421	0.04974	0.1614:0.2665:0.4356:0.1366	.	1954;2060	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	K	1954;2060;2060;2145;2196	ENSP00000327209:Q1954K;ENSP00000358360:Q2060K;ENSP00000358363:Q2060K;ENSP00000435654:Q2145K;ENSP00000358366:Q2196K	ENSP00000327209:Q1954K	Q	-	1	0	PDE4DIP	143571263	0.990000	0.36364	0.996000	0.52242	0.001000	0.01503	0.798000	0.27014	0.255000	0.21593	-0.894000	0.02916	CAG	G|1.000;T|0.000	0.000	strong		0.577	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		T	144859906	G	T	144859906	3	4	23	1	0	0	0	0	1	0	0	0	11652	1328	46	4	890	4	PDE4DIP	1	144859906	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	27	144859906	104390715	37	7481			1	37		4	3	91	N	T_G	2.429474e-06
ZNF687	5298	hgsc.bcm.edu	37	chr1	151263677	151263678	+	IGR	INS	-	-	ACA																															tcggcagggggctgttggggINSacaactagtctccaaggcct																								rs145032688	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:151263677_151263678insACA	ENST00000368873.1	-	0	3340				ZNF687_ENST00000368879.2_3'UTR			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)			GGCTGTTGGGGACAACTAGTCT	0.584														82	0.0163738	0.0023	0.0144	5008	,	,		16222	0.0		0.0547	False		,,,				2504	0.0143				p.D1236delinsDN	Colon(154;765 1838 9854 28443 37492)	Pindel,Atlas-Indel	.											.	ZNF687	94	.	0			c.3706_3707insACA						PASS	.			59,4025		4,51,1987						4.7	1		dbSNP_134	30	528,7434		53,422,3506	no	coding	ZNF687	NM_020832.1		57,473,5493	A1A1,A1R,RR		6.6315,1.4447,4.873				587,11459				SO:0001628	intergenic_variant	57592	exon9			.	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.151263678_151263680dupACA		25	0	.		32	14	0.438	NM_020832	B4DGI2|O15096|P78405|Q5VWB9|Q5VWC0|Q5VWC1|Q9BWR6	In_Frame_Ins	INS	ENST00000368873.1	37																																																																																				-|0.977;ACA|0.023	0.023	strong		0.584	PI4KB-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000034400.3	NM_002651		ACA	151263678	-	ACA	151263677	6	5	23	0	1	1	1	0	0	0	0	0	18107	1174	41	0		0	ZNF687	1	151263677	IGR	INS	-	TCGA-G8-6325-01A-11D-2210-10	6403771	151263677	97986944	38	7482											
MRPL9	65005	hgsc.bcm.edu	37	chr1	151735913	151735913	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagccgtccagcgcccgcccGcagcagagctctgcccgggg	5	3	14	19	5	1	1	0	0	1	1	2	1	2	1	5	2	5	3	5	2	0	0	rs199630729		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:151735913G>A	ENST00000368830.3	-	1	127	c.43C>T	c.(43-45)Cgg>Tgg	p.R15W	RP11-98D18.2_ENST00000420382.1_RNA|MRPL9_ENST00000467306.1_5'UTR|OAZ3_ENST00000321531.5_Intron|OAZ3_ENST00000315067.8_Intron|MRPL9_ENST00000368829.3_Missense_Mutation_p.R15W|OAZ3_ENST00000453029.2_5'Flank|RP11-98D18.3_ENST00000512280.1_RNA|OAZ3_ENST00000479764.1_5'Flank	NM_031420.2	NP_113608.1	Q9BYD2	RM09_HUMAN	mitochondrial ribosomal protein L9	15					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	12	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			GCGCCCGCCCGCAGCAGAGCT	0.692													G|||	1	0.000199681	0.0	0.0	5008	,	,		10868	0.0		0.001	False		,,,				2504	0.0				p.R15W		Atlas-SNP	.											.	MRPL9	21	.	0			c.C43T						PASS	.	G	,TRP/ARG	0,4330		0,0,2165	8	10	9		,43	0.8	0	1		9	13,8467		0,13,4227	yes	intron,missense	OAZ3,MRPL9	NM_001134939.1,NM_031420.2	,101	0,13,6392	AA,AG,GG		0.1533,0.0,0.1015	,probably-damaging	,15/268	151735913	13,12797	2165	4240	6405	SO:0001583	missense	65005	exon1			CCGCCCGCAGCAG	AK026363	CCDS1003.1, CCDS72916.1	1q21	2012-09-13			ENSG00000143436	ENSG00000143436		"Mitochondrial ribosomal proteins / large subunits"	14277	protein-coding gene	gene with protein product		611824					Standard	XM_005245455		Approved		uc001eyv.3	Q9BYD2	OTTHUMG00000013063	ENST00000368830.3:c.43C>T	1.37:g.151735913G>A	ENSP00000357823:p.Arg15Trp	52	0	0		46	31	0.673913	NM_031420	B2RD99|Q5SZR2|Q9BSW8	Missense_Mutation	SNP	ENST00000368830.3	37	CCDS1003.1	.	.	.	.	.	.	.	.	.	.	G	17.03	3.285275	0.59867	0.0	0.001533	ENSG00000143436	ENST00000368830;ENST00000368829	T;T	0.31510	1.5;1.49	4.93	0.779	0.18550	.	0.716541	0.14023	N	0.346675	T	0.04588	0.0125	N	0.12746	0.255	0.09310	N	1	B;B;B	0.19331	0.013;0.035;0.001	B;B;B	0.10450	0.002;0.005;0.001	T	0.37033	-0.9723	10	0.42905	T	0.14	-0.4378	3.2367	0.06767	0.3201:0.0:0.4969:0.183	.	15;15;15	B4DDZ7;B4DUJ1;Q9BYD2	.;.;RM09_HUMAN	W	15	ENSP00000357823:R15W;ENSP00000357822:R15W	ENSP00000357822:R15W	R	-	1	2	MRPL9	150002537	0.005000	0.15991	0.002000	0.10522	0.008000	0.06430	0.245000	0.18142	-0.015000	0.14150	-0.140000	0.14226	CGG	.	.	weak		0.692	MRPL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036653.2	NM_031420		A	151735913	G	A	151735913	3	1	23	1	0	0	0	0	1	0	0	0	9829	1086	38	1	788	1	MRPL9	1	151735913	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	472236	151735913	97514708	39	7483											
THEM4	117145	hgsc.bcm.edu	37	chr1	151867528	151867528	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaatccattcagtaggtgtaCgtttatatgaaggcaaacgt	13	12	10	6	2	1	1	1	1	0	0	2	2	2	1	1	2	2	4	1	2	7	6	rs114800758	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:151867528C>T	ENST00000368814.3	-	2	591	c.242G>A	c.(241-243)cGt>cAt	p.R81H	THEM4_ENST00000489410.1_Missense_Mutation_p.R81H	NM_053055.4	NP_444283.2	Q5T1C6	THEM4_HUMAN	thioesterase superfamily member 4	81					epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|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)|protein kinase B signaling (GO:0043491)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)	cell projection (GO:0042995)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	palmitoyl-CoA hydrolase activity (GO:0016290)			endometrium(1)|large_intestine(4)|lung(3)|urinary_tract(1)	9	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			AGTAGGTGTACGTTTATATGA	0.408													C|||	10	0.00199681	0.0	0.0	5008	,	,		18187	0.0		0.0099	False		,,,				2504	0.0				p.R81H		Atlas-SNP	.											.	THEM4	19	.	0			c.G242A						PASS	.	C	HIS/ARG	14,4392	21.2+/-45.6	0,14,2189	121	120	121		242	-6.8	0	1	dbSNP_132	121	82,8518	47.6+/-106.9	0,82,4218	yes	missense	THEM4	NM_053055.4	29	0,96,6407	TT,TC,CC		0.9535,0.3177,0.7381	benign	81/241	151867528	96,12910	2203	4300	6503	SO:0001583	missense	117145	exon2			GGTGTACGTTTAT	AJ313515	CCDS1006.1	1q21.3	2008-02-05			ENSG00000159445	ENSG00000159445			17947	protein-coding gene	gene with protein product	"C-terminal modulator protein"	606388				11598301	Standard	NM_053055		Approved	CTMP	uc001ezj.2	Q5T1C6	OTTHUMG00000013049	ENST00000368814.3:c.242G>A	1.37:g.151867528C>T	ENSP00000357804:p.Arg81His	141	0	0		149	100	0.671141	NM_053055	B2RBX2|Q96KR2	Missense_Mutation	SNP	ENST00000368814.3	37	CCDS1006.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	7.135	0.580580	0.13686	0.003177	0.009535	ENSG00000159445	ENST00000368814;ENST00000489410	T;T	0.24538	1.86;1.85	3.39	-6.77	0.01727	.	1.373530	0.04534	N	0.386920	T	0.04588	0.0125	L	0.50333	1.59	0.09310	N	1	B	0.31968	0.349	B	0.28916	0.096	T	0.20042	-1.0287	10	0.15952	T	0.53	6.1133	1.5837	0.02639	0.2296:0.1696:0.1141:0.4867	.	81	Q5T1C6	THEM4_HUMAN	H	81	ENSP00000357804:R81H;ENSP00000433304:R81H	ENSP00000357804:R81H	R	-	2	0	THEM4	150134152	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-3.893000	0.00340	-2.045000	0.00910	-0.157000	0.13467	CGT	C|0.994;T|0.006	0.006	strong		0.408	THEM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036615.1	NM_053055		T	151867528	C	T	151867528	3	4	23	1	0	0	0	0	1	0	0	0	15873	536	19	1	500	1	THEM4	1	151867528	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	131615	151867528	97383093	40	7484											
ADAR	103	hgsc.bcm.edu	37	chr1	154560614	154560614	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cactcaccgttctccaccttGgtgcggagctttccttgttt	4	15	8	14	2	2	0	1	0	1	0	4	1	3	1	4	2	2	3	4	2	0	5			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:154560614G>A	ENST00000368474.4	-	11	3205	c.3006C>T	c.(3004-3006)acC>acT	p.T1002T	ADAR_ENST00000292205.5_Silent_p.T1045T|ADAR_ENST00000368471.3_Silent_p.T707T	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	1002	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)		TCTCCACCTTGGTGCGGAGCT	0.552																																					p.T1002T		Atlas-SNP	.											.	ADAR	113	.	0			c.C3006T						PASS	.						256	231	239					1																	154560614		2203	4300	6503	SO:0001819	synonymous_variant	103	exon11			CACCTTGGTGCGG	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.3006C>T	1.37:g.154560614G>A		72	0	0		90	39	0.433333	NM_001111	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Silent	SNP	ENST00000368474.4	37	CCDS1071.1																																																																																			.	.	none		0.552	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111		A	154560614	G	A	154560614	2	1	23	1	0	0	0	0	0	0	0	1	281	1335	47	2		2	ADAR	1	154560614	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	2693086	154560614	94690007	41	7485											
SHC1	6464	hgsc.bcm.edu	37	chr1	154938076	154938076	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgcccactctgcaagccagtGagcacatactggccaggtgt	9	8	11	13	0	1	1	0	1	1	0	1	1	1	1	3	2	5	2	3	2	2	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:154938076G>A	ENST00000368445.5	-	11	1780	c.1566C>T	c.(1564-1566)ctC>ctT	p.L522L	SHC1_ENST00000368450.1_Silent_p.L412L|SHC1_ENST00000606391.1_Silent_p.L323L|SHC1_ENST00000368453.4_Silent_p.L413L|SHC1_ENST00000448116.2_Silent_p.L523L|PYGO2_ENST00000483463.1_5'Flank|SHC1_ENST00000490667.1_Intron|SHC1_ENST00000368449.4_Silent_p.L293L|RP11-307C12.12_ENST00000605085.1_RNA	NM_183001.4	NP_892113.4	P29353	SHC1_HUMAN	SHC (Src homology 2 domain containing) transforming protein 1	522	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				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)			GCAAGCCAGTGAGCACATACT	0.607																																					p.L523L	NSCLC(4;32 234 1864 2492 3259 13747 17376)	Atlas-SNP	.											.	SHC1	91	.	0			c.C1569T						PASS	.						110	92	98					1																	154938076		2203	4300	6503	SO:0001819	synonymous_variant	6464	exon11			GCCAGTGAGCACA	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.1566C>T	1.37:g.154938076G>A		239	0	0		288	37	0.128472	NM_001130040	B5BU19|D3DV78|O15290|Q5T180|Q5T183|Q5T184|Q5T185|Q5T186|Q8N4K5|Q96CL1	Silent	SNP	ENST00000368445.5	37	CCDS30881.1	.	.	.	.	.	.	.	.	.	.	G	8.211	0.800408	0.16397	.	.	ENSG00000160691	ENST00000444664	.	.	.	4.76	2.74	0.32292	.	.	.	.	.	T	0.38506	0.1043	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.32455	-0.9906	4	.	.	.	.	5.1264	0.14886	0.2088:0.3259:0.4652:0.0	.	.	.	.	Y	186	.	.	H	-	1	0	SHC1	153204700	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	0.970000	0.29383	1.235000	0.43724	0.557000	0.71058	CAC	.	.	none		0.607	SHC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090781.2	NM_183001		A	154938076	G	A	154938076	2	1	23	1	0	0	0	0	0	0	0	1	14285	1277	45	2		2	SHC1	1	154938076	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	377462	154938076	94312545	42	7486											
ADAM15	8751	hgsc.bcm.edu	37	chr1	155023917	155023917	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgggcgcgggcagccctctgCcttcctggccgctcccaaat	4	8	12	17	3	1	0	0	0	1	0	3	0	3	0	5	3	2	2	5	3	1	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:155023917C>T	ENST00000356955.2	+	1	156	c.55C>T	c.(55-57)Cct>Tct	p.P19S	ADAM15_ENST00000368413.1_Missense_Mutation_p.P19S|ADAM15_ENST00000447332.3_Missense_Mutation_p.P19S|ADAM15_ENST00000472434.1_3'UTR|ADAM15_ENST00000355956.2_Missense_Mutation_p.P19S|ADAM15_ENST00000271836.6_Missense_Mutation_p.P19S|ADAM15_ENST00000368410.2_Missense_Mutation_p.P19S|ADAM15_ENST00000359280.4_Missense_Mutation_p.P19S|ADAM15_ENST00000368412.3_Missense_Mutation_p.P19S|ADAM15_ENST00000360674.4_Missense_Mutation_p.P19S|ADAM15_ENST00000531455.1_Missense_Mutation_p.P19S|ADAM15_ENST00000449910.2_Missense_Mutation_p.P19S	NM_207197.2	NP_997080.1	Q13444	ADA15_HUMAN	ADAM metallopeptidase domain 15	19					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)			CAGCCCTCTGCCTTCCTGGCC	0.701																																					p.P19S		Atlas-SNP	.											.	ADAM15	92	.	0			c.C55T						PASS	.																																			SO:0001583	missense	8751	exon1			CCTCTGCCTTCCT	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.55C>T	1.37:g.155023917C>T	ENSP00000349436:p.Pro19Ser	25	0	0		21	11	0.52381	NM_003815	B3KQU5|B4DLB5|B4DMH8|E9PN65|Q13493|Q53XQ0|Q5SR68|Q5SR69|Q6R267|Q71S61|Q71S62|Q71S63|Q71S64|Q71S65|Q71S66|Q71S67|Q71S68|Q71S69|Q96C78|U3KQL5	Missense_Mutation	SNP	ENST00000356955.2	37	CCDS1087.1	.	.	.	.	.	.	.	.	.	.	C	15.15	2.747467	0.49257	.	.	ENSG00000143537	ENST00000356955;ENST00000449910;ENST00000359280;ENST00000360674;ENST00000368412;ENST00000355956;ENST00000368410;ENST00000271836;ENST00000368413;ENST00000531455	T;T;T;T;T;T;T;T;T;T	0.03889	5.77;5.76;5.77;5.67;5.56;5.77;3.77;5.75;3.78;5.73	4.56	1.58	0.23477	.	0.195638	0.25189	N	0.032473	T	0.00998	0.0033	L	0.27053	0.805	0.21020	N	0.999802	B;B;B;B;B;B;B;B;B;B	0.27765	0.118;0.118;0.118;0.188;0.188;0.188;0.188;0.188;0.188;0.118	B;B;B;B;B;B;B;B;B;B	0.25759	0.029;0.029;0.029;0.063;0.063;0.063;0.063;0.063;0.063;0.029	T	0.47661	-0.9100	10	0.41790	T	0.15	.	3.3412	0.07119	0.2058:0.5753:0.0:0.2189	.	19;19;19;19;19;19;19;19;19;19	E9PN65;B7Z390;B4DMH8;Q13444-10;Q13444-2;Q13444-4;Q13444-5;Q13444-3;Q13444-9;Q13444	.;.;.;.;.;.;.;.;.;ADA15_HUMAN	S	19	ENSP00000349436:P19S;ENSP00000403843:P19S;ENSP00000352226:P19S;ENSP00000353892:P19S;ENSP00000357397:P19S;ENSP00000348227:P19S;ENSP00000357395:P19S;ENSP00000271836:P19S;ENSP00000357398:P19S;ENSP00000432927:P19S	ENSP00000271836:P19S	P	+	1	0	ADAM15	153290541	0.990000	0.36364	0.995000	0.50966	0.543000	0.35085	0.603000	0.24149	0.354000	0.24105	0.313000	0.20887	CCT	.	.	none		0.701	ADAM15-019	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387168.1	NM_003815		T	155023917	C	T	155023917	3	4	23	1	0	0	0	0	1	0	0	0	237	739	26	2	57	2	ADAM15	1	155023917	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	85841	155023917	94226704	43	7487											
IQGAP3	128239	hgsc.bcm.edu	37	chr1	156508792	156508792	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcaccactgttgggttgccTgtcaccacgtcctggggctg	4	11	12	14	1	2	0	2	0	0	0	3	0	3	0	4	3	1	3	4	3	0	2	rs79402045	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:156508792T>C	ENST00000361170.2	-	26	3100	c.3090A>G	c.(3088-3090)acA>acG	p.T1030T	IQGAP3_ENST00000498755.1_5'UTR	NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	1030	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				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)					TTGGGTTGCCTGTCACCACGT	0.542													T|||	21	0.00419329	0.0015	0.0	5008	,	,		21851	0.001		0.0139	False		,,,				2504	0.0041				p.T1030T		Atlas-SNP	.											.	IQGAP3	146	.	0			c.A3090G						PASS	.	T		13,4393	17.9+/-39.9	0,13,2190	72	64	67		3090	-2.6	1	1	dbSNP_132	67	117,8483	61.7+/-123.6	0,117,4183	no	coding-synonymous	IQGAP3	NM_178229.4		0,130,6373	CC,CT,TT		1.3605,0.2951,0.9995		1030/1632	156508792	130,12876	2203	4300	6503	SO:0001819	synonymous_variant	128239	exon26			GTTGCCTGTCACC	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.3090A>G	1.37:g.156508792T>C		167	0	0		209	114	0.545455	NM_178229	Q5T3H8	Silent	SNP	ENST00000361170.2	37	CCDS1144.1																																																																																			T|0.992;C|0.008	0.008	strong		0.542	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229		C	156508792	T	C	156508792	2	2	23	1	0	0	0	0	0	0	0	1	7825	1567	55	3		3	IQGAP3	1	156508792	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	1484875	156508792	92741829	44	7488											
ARHGEF11	9826	hgsc.bcm.edu	37	chr1	156910020	156910020	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atcttccagagcggagtcagCgagcccttccatgaacagag	11	7	11	12	2	2	3	1	1	1	2	4	5	4	4	3	1	4	0	3	1	1	2	rs144803270		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:156910020C>T	ENST00000361409.2	-	35	4334	c.3592G>A	c.(3592-3594)Gct>Act	p.A1198T	ARHGEF11_ENST00000487682.1_5'UTR|ARHGEF11_ENST00000368194.3_Missense_Mutation_p.A1238T|ARHGEF11_ENST00000315174.8_Missense_Mutation_p.A614T	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	1198					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)					GCGGAGTCAGCGAGCCCTTCC	0.627																																					p.A1238T		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.G3712A						PASS	.	C	THR/ALA,THR/ALA	0,4406		0,0,2203	77	69	72		3592,3712	4.2	0.8	1	dbSNP_134	72	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ARHGEF11	NM_014784.2,NM_198236.1	58,58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	1198/1523,1238/1563	156910020	1,13005	2203	4300	6503	SO:0001583	missense	9826	exon36			AGTCAGCGAGCCC	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.3592G>A	1.37:g.156910020C>T	ENSP00000354644:p.Ala1198Thr	135	0	0		168	85	0.505952	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Missense_Mutation	SNP	ENST00000361409.2	37	CCDS1162.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.569825	0.86439	0.0	1.16E-4	ENSG00000132694	ENST00000368194;ENST00000361409;ENST00000315174	T;T;T	0.76709	-1.0;-0.99;-1.04	4.16	4.16	0.48862	.	0.000000	0.48286	D	0.000200	T	0.77738	0.4175	L	0.34521	1.04	0.40759	D	0.982985	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.993;0.997	T	0.79708	-0.1690	10	0.48119	T	0.1	-10.0453	15.3955	0.74790	0.0:1.0:0.0:0.0	.	614;1198;1238	F8W8P9;O15085;O15085-2	.;ARHGB_HUMAN;.	T	1238;1198;614	ENSP00000357177:A1238T;ENSP00000354644:A1198T;ENSP00000313470:A614T	ENSP00000313470:A614T	A	-	1	0	ARHGEF11	155176644	0.999000	0.42202	0.770000	0.31555	0.925000	0.55904	5.158000	0.64917	2.135000	0.66039	0.561000	0.74099	GCT	C|1.000;T|0.000	0.000	weak		0.627	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236		T	156910020	C	T	156910020	3	4	23	1	0	0	0	0	1	0	0	0	896	768	27	1	1000	1	ARHGEF11	1	156910020	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	401228	156910020	92340601	45	7489											
CD1D	912	hgsc.bcm.edu	37	chr1	158151892	158151892	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctcaaataacttcttccaTgtagcatttcaaggaaaaga	15	11	6	9	0	3	1	2	0	1	1	4	2	4	2	2	1	2	2	2	1	6	5	rs140563679	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:158151892T>C	ENST00000368171.3	+	4	898	c.399T>C	c.(397-399)caT>caC	p.H133H		NM_001766.3	NP_001757.1	P15813	CD1D_HUMAN	CD1d molecule	133					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)					ACTTCTTCCATGTAGCATTTC	0.498													T|||	3	0.000599042	0.0	0.0	5008	,	,		19718	0.0		0.003	False		,,,				2504	0.0				p.H133H		Atlas-SNP	.											.	CD1D	60	.	0			c.T399C						PASS	.	T		0,4406		0,0,2203	130	143	138		399	-9.5	0	1	dbSNP_134	138	17,8583	12.6+/-44.7	0,17,4283	no	coding-synonymous	CD1D	NM_001766.3		0,17,6486	CC,CT,TT		0.1977,0.0,0.1307		133/336	158151892	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	912	exon4			CTTCCATGTAGCA	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.399T>C	1.37:g.158151892T>C		206	0	0		291	160	0.549828	NM_001766	D3DVD5|Q5W0J3|Q9UMM3|Q9Y5M4	Silent	SNP	ENST00000368171.3	37	CCDS1173.1																																																																																			T|0.999;C|0.001	0.001	strong		0.498	CD1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058340.1	NM_001766		C	158151892	T	C	158151892	2	2	23	1	0	0	0	0	0	0	0	1	2979	1461	51	3		3	CD1D	1	158151892	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	1241872	158151892	91098729	46	7490											
OR6N1	128372	hgsc.bcm.edu	37	chr1	158736217	158736217	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aatggtctttttctcactgaGcaagtttgccagcatcttag	9	15	8	9	0	3	1	1	1	3	0	4	1	3	1	1	1	3	3	1	1	3	4	rs857828	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:158736217G>A	ENST00000335094.2	-	1	275	c.256C>T	c.(256-258)Ctc>Ttc	p.L86F		NM_001005185.1	NP_001005185.1	Q8NGY5	OR6N1_HUMAN	olfactory receptor, family 6, subfamily N, member 1	86				L -> F (in Ref. 3; AAK95093). {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)|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)					TTCTCACTGAGCAAGTTTGCC	0.498													G|||	18	0.00359425	0.0	0.0	5008	,	,		20366	0.0		0.0099	False		,,,				2504	0.0082				p.L86F		Atlas-SNP	.											.	OR6N1	96	.	0			c.C256T						PASS	.	G	PHE/LEU	10,4396	17.9+/-39.9	0,10,2193	82	76	78		256	5.1	1	1	dbSNP_86	78	79,8521	46.7+/-105.8	1,77,4222	yes	missense	OR6N1	NM_001005185.1	22	1,87,6415	AA,AG,GG		0.9186,0.227,0.6843	probably-damaging	86/313	158736217	89,12917	2203	4300	6503	SO:0001583	missense	128372	exon1			CACTGAGCAAGTT	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.256C>T	1.37:g.158736217G>A	ENSP00000335535:p.Leu86Phe	84	0	0		118	76	0.644068	NM_001005185	Q5VUU8|Q96R35	Missense_Mutation	SNP	ENST00000335094.2	37	CCDS30905.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	G	15.99	2.995570	0.54147	0.00227	0.009186	ENSG00000197403	ENST00000335094	T	0.10668	2.85	5.1	5.1	0.69264	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41605	D	0.000856	T	0.11707	0.0285	L	0.46157	1.445	0.30949	N	0.725006	D	0.61080	0.989	P	0.60949	0.881	T	0.06162	-1.0842	10	0.23302	T	0.38	-21.3514	13.7262	0.62759	0.0:0.1556:0.8444:0.0	rs857828;rs1633200	86	Q8NGY5	OR6N1_HUMAN	F	86	ENSP00000335535:L86F	ENSP00000335535:L86F	L	-	1	0	OR6N1	157002841	0.011000	0.17503	1.000000	0.80357	0.995000	0.86356	0.349000	0.20055	2.623000	0.88846	0.655000	0.94253	CTC	G|0.994;A|0.006	0.006	strong		0.498	OR6N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059067.1	NM_001005185		A	158736217	G	A	158736217	3	1	23	1	0	0	0	0	1	0	0	0	11215	971	34	2	685	2	OR6N1	1	158736217	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	584325	158736217	90514404	47	7491											
CASQ1	844	hgsc.bcm.edu	37	chr1	160162591	160162591	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aatcataatccttccctccaGttagcagcccaagtcctaga	12	10	5	14	0	1	1	1	0	0	1	5	1	5	1	5	0	2	2	5	0	5	4	rs145486953	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:160162591G>C	ENST00000368078.3	+	2	475		c.e2-1		CASQ1_ENST00000368079.3_Splice_Site			P31415	CASQ1_HUMAN	calsequestrin 1 (fast-twitch, skeletal muscle)						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)			CTTCCCTCCAGTTAGCAGCCC	0.488											OREG0013927	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	3	0.000599042	0.0	0.0	5008	,	,		16886	0.0		0.003	False		,,,				2504	0.0				.		Atlas-SNP	.											.	CASQ1	55	.	0			c.280-1G>C						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	115	123	121			4.5	1	1	dbSNP_134	121	19,8581	14.0+/-48.4	0,19,4281	yes	splice-3	CASQ1	NM_001231.4		0,20,6483	CC,CG,GG		0.2209,0.0227,0.1538			160162591	20,12986	2203	4300	6503	SO:0001630	splice_region_variant	844	exon2			CCTCCAGTTAGCA	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.280-1G>C	1.37:g.160162591G>C		117	0	0	1806	144	51	0.354167	NM_001231	B1AKZ2|B2R863|Q8TBW7	Splice_Site	SNP	ENST00000368078.3	37	CCDS1198.2	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	18.18	3.566858	0.65651	2.27E-4	0.002209	ENSG00000143318	ENST00000368079;ENST00000368078	.	.	.	4.54	4.54	0.55810	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2739	0.82634	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CASQ1	158429215	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	8.990000	0.93510	2.358000	0.79984	0.449000	0.29647	.	G|0.998;C|0.002	0.002	strong		0.488	CASQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077412.1	NM_001231	Intron	C	160162591	G	C	160162591	5	2	23	1	0	0	0	0	0	0	1	0	2682	1043	36	4	285	4	CASQ1	1	160162591	Splice_Site	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1426374	160162591	89088030	48	7492											
C1orf192	257177	hgsc.bcm.edu	37	chr1	161335414	161335414	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcagcaccagcagttgtacGggaggtcagggtcacccgag	9	5	16	11	2	2	0	2	0	0	0	2	2	2	1	2	4	3	5	2	4	1	2	rs141881555	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:161335414G>A	ENST00000367974.1	-	4	255	c.250C>T	c.(250-252)Cgt>Tgt	p.R84C	RP11-122G18.5_ENST00000437833.2_lincRNA	NM_001013625.2	NP_001013647.2	Q5VTH2	CA192_HUMAN	chromosome 1 open reading frame 192	84										endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	10	all_cancers(52;4.64e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			GCAGTTGTACGGGAGGTCAGG	0.507													g|||	3	0.000599042	0.0	0.0	5008	,	,		16556	0.0		0.002	False		,,,				2504	0.001				p.R84C		Atlas-SNP	.											.	C1orf192	20	.	0			c.C250T						PASS	.	G	CYS/ARG	0,4406		0,0,2203	142	150	148		250	3.5	0.9	1	dbSNP_134	148	15,8585	11.2+/-40.8	0,15,4285	yes	missense	C1orf192	NM_001013625.2	180	0,15,6488	AA,AG,GG		0.1744,0.0,0.1153	probably-damaging	84/178	161335414	15,12991	2203	4300	6503	SO:0001583	missense	257177	exon4			TTGTACGGGAGGT		CCDS30921.1	1q23.3	2014-02-21			ENSG00000188931	ENSG00000188931			32325	protein-coding gene	gene with protein product							Standard	NM_001013625		Approved	Flattop, Fltp	uc001gal.4	Q5VTH2	OTTHUMG00000034462	ENST00000367974.1:c.250C>T	1.37:g.161335414G>A	ENSP00000356951:p.Arg84Cys	186	0	0		276	175	0.634058	NM_001013625		Missense_Mutation	SNP	ENST00000367974.1	37	CCDS30921.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	19.41	3.821832	0.71028	0.0	0.001744	ENSG00000188931	ENST00000367974	.	.	.	5.49	3.5	0.40072	.	0.074082	0.53938	N	0.000057	T	0.56877	0.2015	M	0.66939	2.045	0.36982	D	0.894331	D	0.89917	1.0	D	0.97110	1.0	T	0.62955	-0.6744	8	0.72032	D	0.01	-12.236	8.235	0.31620	0.0838:0.0:0.7599:0.1564	.	84	Q5VTH2	CA192_HUMAN	C	84	.	ENSP00000356951:R84C	R	-	1	0	C1orf192	159602038	1.000000	0.71417	0.902000	0.35471	0.983000	0.72400	3.636000	0.54317	1.456000	0.47831	0.655000	0.94253	CGT	G|0.999;A|0.001	0.001	strong		0.507	C1orf192-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083309.1	NM_001013625		A	161335414	G	A	161335414	3	1	23	1	0	0	0	0	1	0	0	0	2026	1116	39	1	291	1	C1orf192	1	161335414	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1172823	161335414	87915207	49	7493											
FMO1	2326	hgsc.bcm.edu	37	chr1	171249933	171249933	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gattgcttccaggtgttcctCagcaccaccggagggggatg	7	9	14	11	1	1	0	1	0	0	0	3	3	3	2	4	4	2	3	4	4	0	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:171249933C>T	ENST00000354841.4	+	5	767	c.636C>T	c.(634-636)ctC>ctT	p.L212L	FMO1_ENST00000402921.2_Silent_p.L149L|FMO1_ENST00000367750.3_Silent_p.L212L|FMO1_ENST00000469112.1_3'UTR	NM_001282692.1	NP_001269621.1	Q01740	FMO1_HUMAN	flavin containing monooxygenase 1	212					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)	AGGTGTTCCTCAGCACCACCG	0.498																																					p.L212L		Atlas-SNP	.											.	FMO1	79	.	0			c.C636T						PASS	.						82	70	74					1																	171249933		2203	4300	6503	SO:0001819	synonymous_variant	2326	exon6			GTTCCTCAGCACC	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.636C>T	1.37:g.171249933C>T		136	0	0		160	24	0.15	NM_002021	A8K248|B7Z3P4|Q5QPT2|Q9UJC2	Silent	SNP	ENST00000354841.4	37	CCDS1294.1																																																																																			.	.	none		0.498	FMO1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086212.1	NM_002021		T	171249933	C	T	171249933	2	4	23	1	0	0	0	0	0	0	0	1	5962	813	29	2		2	FMO1	1	171249933	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	9914519	171249933	78000688	50	7494											
FAM5B	57795	hgsc.bcm.edu	37	chr1	177245369	177245369	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgcctgagtatctgcgtgagCgctttgtagctgcagcactc	6	12	12	11	2	1	2	0	2	1	0	2	2	1	2	1	0	6	6	1	0	2	3	rs145109858	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:177245369C>T	ENST00000361539.4	+	6	1123	c.811C>T	c.(811-813)Cgc>Tgc	p.R271C	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	271	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)	extracellular region (GO:0005576)											TCTGCGTGAGCGCTTTGTAGC	0.562																																					p.R271C		Atlas-SNP	.											FAM5B,NS,carcinoma,0,3	FAM5B	191	3	0			c.C811T						PASS	.	C	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	68	61	64		811	6.1	1	1	dbSNP_134	64	7,8593	5.7+/-21.5	0,7,4293	yes	missense	FAM5B	NM_021165.2	180	0,8,6495	TT,TC,CC		0.0814,0.0227,0.0615	probably-damaging	271/784	177245369	8,12998	2203	4300	6503	SO:0001583	missense	57795	exon6			CGTGAGCGCTTTG		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.811C>T	1.37:g.177245369C>T	ENSP00000354481:p.Arg271Cys	193	0	0		224	126	0.5625	NM_021165	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	37	CCDS1320.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.939863	0.73557	2.27E-4	8.14E-4	ENSG00000198797	ENST00000536589;ENST00000361539	T	0.15834	2.39	6.07	6.07	0.98685	Membrane attack complex component/perforin (MACPF) domain (1);	0.000000	0.85682	D	0.000000	T	0.38719	0.1051	M	0.63843	1.955	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.993	D;P;P	0.67725	0.953;0.899;0.548	T	0.03453	-1.1035	10	0.87932	D	0	-25.4339	15.0142	0.71570	0.1424:0.8576:0.0:0.0	.	21;166;271	F5H8E0;Q9C0B6-2;Q9C0B6	.;.;FAM5B_HUMAN	C	21;271	ENSP00000354481:R271C	ENSP00000354481:R271C	R	+	1	0	FAM5B	175511992	0.998000	0.40836	1.000000	0.80357	0.989000	0.77384	0.813000	0.27225	2.884000	0.98904	0.655000	0.94253	CGC	C|1.000;T|0.000	0.000	strong		0.562	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165		T	177245369	C	T	177245369	3	4	23	1	0	0	0	0	1	0	0	0	5601	768	27	1	829	1	FAM5B	1	177245369	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	5995436	177245369	72005252	51	7495											
CACNA1E	777	hgsc.bcm.edu	37	chr1	181724381	181724381	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctctgtccacaggccgtcttCgactgcgtagtgacctcctt	5	12	9	15	3	2	1	0	1	2	0	5	2	4	1	4	1	1	1	4	1	1	3	rs41315709	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:181724381C>T	ENST00000367573.2	+	28	3837	c.3837C>T	c.(3835-3837)ttC>ttT	p.F1279F	CACNA1E_ENST00000360108.3_Silent_p.F1260F|CACNA1E_ENST00000526775.1_Silent_p.F1260F|CACNA1E_ENST00000367567.4_Silent_p.F886F|CACNA1E_ENST00000357570.5_Silent_p.F1230F|CACNA1E_ENST00000358338.5_Silent_p.F1211F|CACNA1E_ENST00000367570.1_Silent_p.F1279F	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1279					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						AGGCCGTCTTCGACTGCGTAG	0.512													C|||	4	0.000798722	0.0008	0.0	5008	,	,		21515	0.001		0.002	False		,,,				2504	0.0				p.F1279F		Atlas-SNP	.											CACNA1E_ENST00000367573,caecum,carcinoma,0,2	CACNA1E	778	2	0			c.C3837T						PASS	.	C	,,	0,4012		0,0,2006	120	116	118		3837,3837,3780	-5.9	0.9	1	dbSNP_127	118	7,8373		0,7,4183	no	coding-synonymous,coding-synonymous,coding-synonymous	CACNA1E	NM_000721.3,NM_001205293.1,NM_001205294.1	,,	0,7,6189	TT,TC,CC		0.0835,0.0,0.0565	,,	1279/2271,1279/2314,1260/2252	181724381	7,12385	2006	4190	6196	SO:0001819	synonymous_variant	777	exon28			CGTCTTCGACTGC	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.3837C>T	1.37:g.181724381C>T		54	0	0		86	41	0.476744	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Silent	SNP	ENST00000367573.2	37	CCDS55664.1																																																																																			C|0.999;T|0.001	0.001	strong		0.512	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		T	181724381	C	T	181724381	2	4	23	1	0	0	0	0	0	0	0	1	2544	883	31	1		1	CACNA1E	1	181724381	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	4479012	181724381	67526240	52	7496											
CFHR5	81494	hgsc.bcm.edu	37	chr1	196953220	196953220	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aaacaatgagaaaaacatttCgtgtgtagaacggggctggt	15	9	12	5	2	0	2	0	1	0	2	1	3	0	2	0	3	3	2	0	3	6	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:196953220C>T	ENST00000256785.4	+	3	492	c.383C>T	c.(382-384)tCg>tTg	p.S128L	CFHR5_ENST00000367414.5_Missense_Mutation_p.S152L			Q9BXR6	FHR5_HUMAN	complement factor H-related 5	128	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						AAAAACATTTCGTGTGTAGAA	0.378																																					p.S128L		Atlas-SNP	.											CFHR5_ENST00000367414,NS,malignant_melanoma,0,6	CFHR5	150	6	0			c.C383T						PASS	.						96	86	89					1																	196953220		2203	4300	6503	SO:0001583	missense	81494	exon3			ACATTTCGTGTGT	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.383C>T	1.37:g.196953220C>T	ENSP00000256785:p.Ser128Leu	87	0	0		95	11	0.115789	NM_030787	Q2NKK2	Missense_Mutation	SNP	ENST00000256785.4	37	CCDS1387.1	.	.	.	.	.	.	.	.	.	.	C	12.35	1.912751	0.33721	.	.	ENSG00000134389	ENST00000367414;ENST00000256785	T;T	0.63580	-0.05;-0.05	3.89	0.396	0.16309	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.44767	0.1309	L	0.36672	1.1	0.09310	N	1	B	0.26363	0.147	B	0.26202	0.067	T	0.26155	-1.0111	9	0.19590	T	0.45	.	4.7535	0.13071	0.3661:0.5179:0.0:0.116	.	128	Q9BXR6	FHR5_HUMAN	L	152;128	ENSP00000356384:S152L;ENSP00000256785:S128L	ENSP00000256785:S128L	S	+	2	0	CFHR5	195219843	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.282000	0.08445	0.212000	0.20703	0.467000	0.42956	TCG	.	.	none		0.378	CFHR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088814.2	NM_030787		T	196953220	C	T	196953220	3	4	23	1	0	0	0	0	1	0	0	0	3290	893	31	1	393	1	CFHR5	1	196953220	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	15228839	196953220	52297401	53	7497											
F13B	2165	hgsc.bcm.edu	37	chr1	197029592	197029592	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcatgacagaaaaactgaaCgacatctccttcttcatagg	14	11	6	10	1	4	3	2	2	2	1	5	4	4	3	1	1	2	0	1	1	4	4	rs145637157		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:197029592C>T	ENST00000367412.1	-	5	752	c.709G>A	c.(709-711)Gtt>Att	p.V237I		NM_001994.2	NP_001985.2	P05160	F13B_HUMAN	coagulation factor XIII, B polypeptide	237	Sushi 4. {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						AAAAACTGAACGACATCTCCT	0.313																																					p.V237I		Atlas-SNP	.											.	F13B	137	.	0			c.G709A						PASS	.	C	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	66	73	71		709	3.9	0.8	1	dbSNP_134	71	6,8588	5.0+/-18.6	0,6,4291	yes	missense	F13B	NM_001994.2	29	0,7,6493	TT,TC,CC		0.0698,0.0227,0.0538	probably-damaging	237/662	197029592	7,12993	2203	4297	6500	SO:0001583	missense	2165	exon5			ACTGAACGACATC	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.709G>A	1.37:g.197029592C>T	ENSP00000356382:p.Val237Ile	184	0	0		203	105	0.517241	NM_001994	A8K3E5|Q5VYL5	Missense_Mutation	SNP	ENST00000367412.1	37	CCDS1388.1	.	.	.	.	.	.	.	.	.	.	C	15.69	2.908059	0.52333	2.27E-4	6.98E-4	ENSG00000143278	ENST00000367412	T	0.68331	-0.32	5.76	3.86	0.44501	Complement control module (2);Sushi/SCR/CCP (3);	0.296520	0.18406	N	0.142199	T	0.68220	0.2977	L	0.50847	1.595	0.34229	D	0.676347	D	0.54772	0.968	P	0.49085	0.6	T	0.73707	-0.3898	10	0.35671	T	0.21	.	15.9628	0.79945	0.0:0.8763:0.0:0.1237	.	237	P05160	F13B_HUMAN	I	237	ENSP00000356382:V237I	ENSP00000356382:V237I	V	-	1	0	F13B	195296215	0.828000	0.29307	0.781000	0.31783	0.963000	0.63663	1.393000	0.34497	0.448000	0.26722	-0.813000	0.03139	GTT	C|1.000;T|0.000	0.000	weak		0.313	F13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088821.2	NM_001994		T	197029592	C	T	197029592	3	4	23	1	0	0	0	0	1	0	0	0	5343	536	19	1	1308	1	F13B	1	197029592	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	76372	197029592	52221029	54	7498											
PTPN7	5778	hgsc.bcm.edu	37	chr1	202124690	202124690	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gttggcattgatgtaatctcCgtcctcctggctctgtgccc	4	14	10	13	1	2	1	0	1	2	0	5	1	4	1	4	2	1	4	4	2	1	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:202124690C>T	ENST00000308986.5	-	5	569	c.439G>A	c.(439-441)Gga>Aga	p.G147R	PTPN7_ENST00000492977.1_5'UTR|PTPN7_ENST00000543735.1_5'UTR|PTPN7_ENST00000309017.3_Missense_Mutation_p.G252R|PTPN7_ENST00000544762.1_Intron|PTPN7_ENST00000367279.4_Missense_Mutation_p.G186R			P35236	PTN7_HUMAN	protein tyrosine phosphatase, non-receptor type 7	147	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	protein tyrosine phosphatase activity (GO:0004725)	p.G186*(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)|soft_tissue(1)|urinary_tract(1)	13						ATGTAATCTCCGTCCTCCTGG	0.542																																					p.G252R		Atlas-SNP	.											PTPN7,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	PTPN7	31	1	1	Substitution - Nonsense(1)	central_nervous_system(1)	c.G754A						PASS	.						93	77	83					1																	202124690		2203	4300	6503	SO:0001583	missense	5778	exon5			AATCTCCGTCCTC	BC001746	CCDS1422.1, CCDS1423.1, CCDS1423.2	1q32.1	2011-06-09			ENSG00000143851	ENSG00000143851		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9659	protein-coding gene	gene with protein product		176889				1510684	Standard	NM_002832		Approved	HEPTP, LC-PTP	uc010ppx.2	P35236	OTTHUMG00000035931	ENST00000308986.5:c.439G>A	1.37:g.202124690C>T	ENSP00000311133:p.Gly147Arg	109	0	0		111	50	0.45045	NM_002832	B3KXE1|Q53XK4|Q5SXQ0|Q5SXQ1|Q9BV05	Missense_Mutation	SNP	ENST00000308986.5	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.66|12.66	2.005836|2.005836	0.35415|0.35415	.|.	.|.	ENSG00000143851|ENSG00000143851	ENST00000367279;ENST00000309017;ENST00000308986;ENST00000477554;ENST00000476061;ENST00000467283;ENST00000464870|ENST00000477625;ENST00000435759	T;T;T;T;T;T;T|.	0.14022|.	2.54;2.54;2.54;2.54;2.75;2.75;2.75|.	5.26|5.26	4.33|4.33	0.51752|0.51752	Protein-tyrosine phosphatase, receptor/non-receptor type (3);|.	0.239923|.	0.29459|.	N|.	0.012088|.	T|T	0.49270|0.49270	0.1547|0.1547	M|M	0.62088|0.62088	1.915|1.915	0.19775|0.19775	N|N	0.999951|0.999951	P;B;B;B;P|.	0.43578|.	0.811;0.076;0.229;0.123;0.508|.	P;B;B;B;B|.	0.49561|.	0.615;0.223;0.256;0.223;0.314|.	T|T	0.44862|0.44862	-0.9300|-0.9300	10|6	0.87932|0.87932	D|D	0|0	-12.8237|-12.8237	9.366|9.366	0.38226|0.38226	0.0:0.8348:0.0:0.1652|0.0:0.8348:0.0:0.1652	.|.	221;95;99;147;186|.	B4DZD9;B4DVF0;Q8NFX3;P35236;P35236-2|.	.;.;.;PTN7_HUMAN;.|.	R|Q	186;252;147;228;146;146;147|78;153	ENSP00000356248:G186R;ENSP00000309116:G252R;ENSP00000311133:G147R;ENSP00000418416:G228R;ENSP00000419993:G146R;ENSP00000418837:G146R;ENSP00000420434:G147R|.	ENSP00000311133:G147R|ENSP00000406042:R153Q	G|R	-|-	1|2	0|0	PTPN7|PTPN7	200391313|200391313	0.005000|0.005000	0.15991|0.15991	0.011000|0.011000	0.14972|0.14972	0.665000|0.665000	0.39181|0.39181	1.125000|1.125000	0.31332|0.31332	1.180000|1.180000	0.42898|0.42898	0.655000|0.655000	0.94253|0.94253	GGA|CGG	.	.	none		0.542	PTPN7-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_002832		T	202124690	C	T	202124690	3	4	23	1	0	0	0	0	1	0	0	0	12808	661	23	1	667	1	PTPN7	1	202124690	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	5095098	202124690	47125931	55	7499											
BTG2	7832	hgsc.bcm.edu	37	chr1	203274867	203274867	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tcagcggggcgctccaggagGcactcacaggtgagcgcatg	8	5	16	12	3	2	1	2	1	0	0	3	2	3	2	1	5	2	3	1	5	0	0			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:203274867G>T	ENST00000290551.4	+	1	204	c.133G>T	c.(133-135)Gca>Tca	p.A45S	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	45					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.A45T(1)		haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			GCTCCAGGAGGCACTCACAGG	0.706																																					p.A45S		Atlas-SNP	.											BTG2,lymph_node,lymphoid_neoplasm,-1,2	BTG2	16	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G133T						PASS	.						11	13	13					1																	203274867		2020	3950	5970	SO:0001583	missense	7832	exon1			CAGGAGGCACTCA		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.133G>T	1.37:g.203274867G>T	ENSP00000290551:p.Ala45Ser	95	0	0		87	11	0.126437	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.877798	0.51801	.	.	ENSG00000159388	ENST00000290551	T	0.23754	1.89	4.4	4.4	0.53042	Anti-proliferative protein (3);	0.078518	0.49916	D	0.000121	T	0.28928	0.0718	L	0.43152	1.355	0.43417	D	0.995564	B	0.15930	0.015	B	0.33521	0.165	T	0.09907	-1.0653	10	0.40728	T	0.16	-33.413	15.7078	0.77598	0.0:0.0:1.0:0.0	.	45	P78543	BTG2_HUMAN	S	45	ENSP00000290551:A45S	ENSP00000290551:A45S	A	+	1	0	BTG2	201541490	1.000000	0.71417	0.991000	0.47740	0.943000	0.58893	4.326000	0.59241	2.282000	0.76494	0.471000	0.43371	GCA	.	.	none		0.706	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		T	203274867	G	T	203274867	3	4	23	1	0	0	0	0	1	0	0	0	1556	1203	42	4	135	4	BTG2	1	203274867	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1150177	203274867	45975754	56	7500											
PIK3C2B	5287	hgsc.bcm.edu	37	chr1	204433627	204433627	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agcctgtcacacaacacagtCaccttcaggttgacctcatc	11	9	6	15	0	4	1	4	1	0	0	5	1	4	1	3	1	2	1	3	1	1	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:204433627C>T	ENST00000367187.3	-	5	1696	c.1140G>A	c.(1138-1140)gtG>gtA	p.V380V	PIK3C2B_ENST00000424712.2_Silent_p.V380V	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	380	PI3K-RBD. {ECO:0000255|PROSITE- ProRule:PRU00879}.				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)			ACAACACAGTCACCTTCAGGT	0.547																																					p.V380V		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.G1140A						PASS	.						149	127	134					1																	204433627		2203	4300	6503	SO:0001819	synonymous_variant	5287	exon5			CACAGTCACCTTC	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.1140G>A	1.37:g.204433627C>T		148	0	0		197	21	0.106599	NM_002646	O95666|Q5SW99	Silent	SNP	ENST00000367187.3	37	CCDS1446.1																																																																																			.	.	none		0.547	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646		T	204433627	C	T	204433627	2	4	23	1	0	0	0	0	0	0	0	1	11919	813	29	2		2	PIK3C2B	1	204433627	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1158760	204433627	44816994	57	7501											
NUAK2	81788	hgsc.bcm.edu	37	chr1	205273040	205273040	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccccactcacaaacacgtcGcctgcgtccaagagctcccc	9	6	6	20	3	1	1	1	0	0	1	5	1	4	1	6	0	3	1	6	0	2	0	rs56069742	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:205273040G>A	ENST00000367157.3	-	7	1551	c.1425C>T	c.(1423-1425)ggC>ggT	p.G475G		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)			CAAACACGTCGCCTGCGTCCA	0.582													G|||	11	0.00219649	0.0	0.0072	5008	,	,		16957	0.001		0.005	False		,,,				2504	0.0				p.G475G		Atlas-SNP	.											.	NUAK2	107	.	0			c.C1425T						PASS	.	G		12,4394	16.8+/-37.8	0,12,2191	35	34	34		1425	-9.7	0	1	dbSNP_129	34	132,8468	66.7+/-129.0	0,132,4168	no	coding-synonymous	NUAK2	NM_030952.1		0,144,6359	AA,AG,GG		1.5349,0.2724,1.1072		475/629	205273040	144,12862	2203	4300	6503	SO:0001819	synonymous_variant	81788	exon7			CACGTCGCCTGCG	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.1425C>T	1.37:g.205273040G>A		134	0	0		116	59	0.508621	NM_030952		Silent	SNP	ENST00000367157.3	37	CCDS1453.1																																																																																			G|0.992;A|0.008	0.008	strong		0.582	NUAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090390.1	NM_030952		A	205273040	G	A	205273040	2	1	23	1	0	0	0	0	0	0	0	1	10722	1074	38	1		1	NUAK2	1	205273040	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	839413	205273040	43977581	58	7502											
MAPKAPK2	9261	hgsc.bcm.edu	37	chr1	206905040	206905040	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cccacccagagaatgaccatCaccgagtttatgaaccaccc	13	6	6	16	1	1	3	1	2	0	1	1	5	1	3	6	0	1	1	6	0	3	2	rs34526867	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:206905040C>T	ENST00000367103.3	+	8	1141	c.948C>T	c.(946-948)atC>atT	p.I316I	MAPKAPK2_ENST00000479009.1_3'UTR|MAPKAPK2_ENST00000294981.4_Silent_p.I316I	NM_004759.4|NM_032960.3	NP_004750.1|NP_116584.2	P49137	MAPK2_HUMAN	mitogen-activated protein kinase-activated protein kinase 2	316	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|activation of MAPK activity (GO:0000187)|arachidonic acid metabolic process (GO:0019369)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|G2 DNA damage checkpoint (GO:0031572)|gene expression (GO:0010467)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|leukotriene metabolic process (GO:0006691)|macropinocytosis (GO:0044351)|MAPK cascade (GO:0000165)|mRNA metabolic process (GO:0016071)|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)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of interleukin-6 production (GO:0032675)|regulation of tumor necrosis factor production (GO:0032680)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)|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)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	19	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.211)			GAATGACCATCACCGAGTTTA	0.562													C|||	204	0.0407348	0.1248	0.0288	5008	,	,		18568	0.0		0.0149	False		,,,				2504	0.0041				p.I316I		Atlas-SNP	.											.	MAPKAPK2	45	.	0			c.C948T						PASS	.	C	,	516,3890	237.7+/-249.4	28,460,1715	135	133	134		948,948	5.1	1	1	dbSNP_126	134	111,8489	59.1+/-120.7	0,111,4189	no	coding-synonymous,coding-synonymous	MAPKAPK2	NM_004759.4,NM_032960.3	,	28,571,5904	TT,TC,CC		1.2907,11.7113,4.8209	,	316/371,316/401	206905040	627,12379	2203	4300	6503	SO:0001819	synonymous_variant	9261	exon8			GACCATCACCGAG	U12779	CCDS1466.1, CCDS31001.1	1q32	2008-02-05			ENSG00000162889	ENSG00000162889			6887	protein-coding gene	gene with protein product		602006				8179591, 8280084	Standard	NM_004759		Approved		uc001hem.2	P49137	OTTHUMG00000036342	ENST00000367103.3:c.948C>T	1.37:g.206905040C>T		182	0	0		212	107	0.504717	NM_004759	Q5SY30|Q5SY41|Q8IYD6	Silent	SNP	ENST00000367103.3	37	CCDS31001.1																																																																																			C|0.956;T|0.044	0.044	strong		0.562	MAPKAPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088465.1	NM_004759		T	206905040	C	T	206905040	2	4	23	1	0	0	0	0	0	0	0	1	9298	816	29	2		2	MAPKAPK2	1	206905040	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1632000	206905040	42345581	59	7503											
FCAMR	83953	hgsc.bcm.edu	37	chr1	207140447	207140447	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcattttccatcccgccctcCtgctggtgacctgcaaaaaa	9	10	7	15	1	0	1	0	1	0	0	3	1	3	1	5	1	2	3	5	1	3	2	rs199884709	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:207140447C>T	ENST00000324852.4	-	3	593	c.119G>A	c.(118-120)aGg>aAg	p.R40K	FCAMR_ENST00000400962.3_Missense_Mutation_p.R40K|FCAMR_ENST00000450945.2_Missense_Mutation_p.R40K	NM_001170631.1	NP_001164102.1	Q8WWV6	FCAMR_HUMAN	Fc receptor, IgA, IgM, high affinity	339					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						TCCCGCCCTCCTGCTGGTGAC	0.527													C|||	3	0.000599042	0.0	0.0014	5008	,	,		20112	0.0		0.001	False		,,,				2504	0.001				p.R40K	Ovarian(199;1883 2142 16966 44409 45154)	Atlas-SNP	.											.	FCAMR	125	.	0			c.G119A						PASS	.	C	LYS/ARG,LYS/ARG,LYS/ARG	2,3134		0,2,1566	61	55	57		119,119,119	-5.3	0	1		57	22,7142		0,22,3560	yes	missense,missense,missense	FCAMR	NM_001122979.2,NM_001170631.1,NM_032029.4	26,26,26	0,24,5126	TT,TC,CC		0.3071,0.0638,0.233	,,	40/266,40/578,40/266	207140447	24,10276	1568	3582	5150	SO:0001583	missense	83953	exon3			GCCCTCCTGCTGG	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.119G>A	1.37:g.207140447C>T	ENSP00000316491:p.Arg40Lys	91	0	0		119	42	0.352941	NM_001170631	Q32M82|Q8WWV5|Q96SA2	Missense_Mutation	SNP	ENST00000324852.4	37	CCDS53468.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	9.612	1.131495	0.21041	6.38E-4	0.003071	ENSG00000162897	ENST00000400962;ENST00000324852;ENST00000450945	T;T;T	0.06768	3.26;3.55;3.26	5.35	-5.32	0.02722	.	.	.	.	.	T	0.03011	0.0089	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.47861	-0.9084	6	0.11182	T	0.66	2.788	5.9013	0.18967	0.2988:0.471:0.0:0.2302	.	.	.	.	K	40	ENSP00000383746:R40K;ENSP00000316491:R40K;ENSP00000392707:R40K	ENSP00000316491:R40K	R	-	2	0	FCAMR	205207070	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.129000	0.03244	-0.509000	0.06532	-0.302000	0.09304	AGG	C|0.999;T|0.001	0.001	strong		0.527	FCAMR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088969.2	NM_032029		T	207140447	C	T	207140447	3	4	23	1	0	0	0	0	1	0	0	0	5780	681	24	2	1638	2	FCAMR	1	207140447	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	235407	207140447	42110174	60	7504											
PLXNA2	5362	hgsc.bcm.edu	37	chr1	208227814	208227814	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcatgaactctggcttacaCtcgccaatacacaggcgtac	11	9	8	13	2	2	1	1	1	1	0	3	1	2	1	1	2	4	2	1	2	5	3	rs2274447	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:208227814C>T	ENST00000367033.3	-	14	3565	c.2808G>A	c.(2806-2808)gaG>gaA	p.E936E		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	936	IPT/TIG 1.				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)		CTGGCTTACACTCGCCAATAC	0.582													C|||	52	0.0103834	0.0	0.0029	5008	,	,		21260	0.0129		0.004	False		,,,				2504	0.0337				p.E936E		Atlas-SNP	.											PLXNA2,caecum,carcinoma,-2,1	PLXNA2	178	1	0			c.G2808A						scavenged	.	C		6,4400	11.4+/-27.6	0,6,2197	105	83	90		2808	3.5	1	1	dbSNP_100	90	35,8565	24.0+/-70.4	0,35,4265	no	coding-synonymous	PLXNA2	NM_025179.3		0,41,6462	TT,TC,CC		0.407,0.1362,0.3152		936/1895	208227814	41,12965	2203	4300	6503	SO:0001819	synonymous_variant	5362	exon14			CTTACACTCGCCA	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.2808G>A	1.37:g.208227814C>T		87	1	0.0114943		127	52	0.409449	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Silent	SNP	ENST00000367033.3	37	CCDS31013.1																																																																																			C|0.995;T|0.005	0.005	strong		0.582	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		T	208227814	C	T	208227814	2	4	23	1	0	0	0	0	0	0	0	1	12129	564	20	2		2	PLXNA2	1	208227814	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1087367	208227814	41022807	61	7505											
GPATCH2	55105	hgsc.bcm.edu	37	chr1	217793484	217793484	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tcatgccatagaggtcttttCcctcgaacattattatttaa	11	16	5	9	1	2	1	1	0	1	1	4	2	3	1	2	1	2	0	2	1	5	7	rs140815718	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:217793484C>T	ENST00000366935.3	-	2	524	c.414G>A	c.(412-414)ggG>ggA	p.G138G	GPATCH2_ENST00000366934.3_Silent_p.G138G	NM_018040.2	NP_060510.1	Q9NW75	GPTC2_HUMAN	G patch domain containing 2	138					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)		GAGGTCTTTTCCCTCGAACAT	0.408													C|||	18	0.00359425	0.0008	0.0043	5008	,	,		20562	0.0		0.0139	False		,,,				2504	0.0				p.G138G		Atlas-SNP	.											.	GPATCH2	53	.	0			c.G414A						PASS	.	C		5,4401	9.9+/-24.2	0,5,2198	131	120	124		414	-5.8	0.7	1	dbSNP_134	124	93,8507	51.1+/-111.2	0,93,4207	no	coding-synonymous	GPATCH2	NM_018040.2		0,98,6405	TT,TC,CC		1.0814,0.1135,0.7535		138/529	217793484	98,12908	2203	4300	6503	SO:0001819	synonymous_variant	55105	exon2			TCTTTTCCCTCGA	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.414G>A	1.37:g.217793484C>T		94	0	0		76	37	0.486842	NM_018040	Q5VYK7|Q5VYK8|Q86YE7	Silent	SNP	ENST00000366935.3	37	CCDS1518.1																																																																																			C|0.994;T|0.006	0.006	strong		0.408	GPATCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001272.1	NM_018040		T	217793484	C	T	217793484	2	4	23	1	0	0	0	0	0	0	0	1	6599	842	30	2		2	GPATCH2	1	217793484	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	9565670	217793484	31457137	62	7506											
COG2	22796	hgsc.bcm.edu	37	chr1	230810858	230810858	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttaatcctgggaatcccgaTgcatttcatgaggtatctcc	9	14	8	10	1	2	1	1	1	1	0	5	3	4	2	3	2	1	2	3	2	3	4	rs113173809	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:230810858T>C	ENST00000366669.4	+	9	1129	c.1014T>C	c.(1012-1014)gaT>gaC	p.D338D	COG2_ENST00000535166.1_Silent_p.D222D|COG2_ENST00000366668.3_Silent_p.D338D|COG2_ENST00000534989.1_Silent_p.D279D	NM_001145036.1|NM_007357.2	NP_001138508.1|NP_031383.1	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2	338					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)				GGAATCCCGATGCATTTCATG	0.418													T|||	6	0.00119808	0.0	0.0014	5008	,	,		14495	0.0		0.002	False		,,,				2504	0.0031				p.D338D		Atlas-SNP	.											.	COG2	61	.	0			c.T1014C						PASS	.	T	,	4,4402	8.1+/-20.4	0,4,2199	103	104	103		1014,1014	-0.5	0.2	1	dbSNP_132	103	48,8552	31.2+/-83.2	0,48,4252	no	coding-synonymous,coding-synonymous	COG2	NM_001145036.1,NM_007357.2	,	0,52,6451	CC,CT,TT		0.5581,0.0908,0.3998	,	338/738,338/739	230810858	52,12954	2203	4300	6503	SO:0001819	synonymous_variant	22796	exon9			TCCCGATGCATTT	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.1014T>C	1.37:g.230810858T>C		183	0	0		184	95	0.516304	NM_007357	Q86U99	Silent	SNP	ENST00000366669.4	37	CCDS1584.1																																																																																			T|0.997;C|0.003	0.003	strong		0.418	COG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092087.1	NM_007357		C	230810858	T	C	230810858	2	2	23	1	0	0	0	0	0	0	0	1	3660	1461	51	3		3	COG2	1	230810858	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	13017374	230810858	18439763	63	7507											
SIPA1L2	57568	hgsc.bcm.edu	37	chr1	232650163	232650163	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctctcctccagctcagacGtgaacttgaaagtttcgtgc	8	11	10	12	2	2	3	1	2	1	1	5	3	3	3	2	1	3	3	2	1	2	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:232650163G>A	ENST00000366630.1	-	2	1281	c.923C>T	c.(922-924)aCg>aTg	p.T308M	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.T308M			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	308					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)				CAGCTCAGACGTGAACTTGAA	0.458																																					p.T308M		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.C923T						PASS	.						57	59	58					1																	232650163		1921	4141	6062	SO:0001583	missense	57568	exon1			TCAGACGTGAACT	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.923C>T	1.37:g.232650163G>A	ENSP00000355589:p.Thr308Met	60	0	0		66	26	0.393939	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	37	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	G	12.56	1.974684	0.34848	.	.	ENSG00000116991	ENST00000366630;ENST00000262861	T;T	0.78924	-1.22;-1.22	5.39	4.48	0.54585	.	0.295098	0.33144	N	0.005238	T	0.58452	0.2123	N	0.08118	0	0.34703	D	0.726925	P	0.35493	0.505	B	0.32465	0.146	T	0.68123	-0.5492	10	0.33141	T	0.24	-5.5177	14.1111	0.65121	0.0719:0.0:0.9281:0.0	.	308	Q9P2F8	SI1L2_HUMAN	M	308	ENSP00000355589:T308M;ENSP00000262861:T308M	ENSP00000262861:T308M	T	-	2	0	SIPA1L2	230716786	1.000000	0.71417	0.818000	0.32626	0.930000	0.56654	4.769000	0.62300	1.503000	0.48686	0.650000	0.86243	ACG	.	.	none		0.458	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		A	232650163	G	A	232650163	3	1	23	1	0	0	0	0	1	0	0	0	14345	1145	40	1	4329	1	SIPA1L2	1	232650163	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1839305	232650163	16600458	64	7508											
KIF26B	55083	hgsc.bcm.edu	37	chr1	245772651	245772651	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccatctcttggctcttcaagCtcataaacgaacgcaaggaa	13	9	7	12	2	4	0	2	0	2	0	5	2	4	1	1	2	3	3	1	2	6	3	rs61754955	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:245772651C>G	ENST00000407071.2	+	8	2175	c.1735C>G	c.(1735-1737)Ctc>Gtc	p.L579V	KIF26B_ENST00000366518.4_Missense_Mutation_p.L198V	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	579	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)			GCTCTTCAAGCTCATAAACGA	0.552													C|||	107	0.0213658	0.0053	0.0648	5008	,	,		17935	0.0278		0.0149	False		,,,				2504	0.0123				p.L579V		Atlas-SNP	.											.	KIF26B	343	.	0			c.C1735G						PASS	.	C	VAL/LEU	28,3818		0,28,1895	38	38	38		1735	5.2	1	1	dbSNP_129	38	154,8102		2,150,3976	yes	missense	KIF26B	NM_018012.3	32	2,178,5871	GG,GC,CC		1.8653,0.728,1.5039	probably-damaging	579/2109	245772651	182,11920	1923	4128	6051	SO:0001583	missense	55083	exon8			TTCAAGCTCATAA	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.1735C>G	1.37:g.245772651C>G	ENSP00000385545:p.Leu579Val	203	0	0		225	105	0.466667	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	37	CCDS44342.1	54	0.024725274725274724	5	0.01016260162601626	20	0.055248618784530384	14	0.024475524475524476	15	0.01978891820580475	C	16.22	3.060277	0.55432	0.00728	0.018653	ENSG00000162849	ENST00000407071;ENST00000366518;ENST00000413001	T;T	0.74947	-0.89;-0.89	5.22	5.22	0.72569	Kinesin, motor domain (4);	.	.	.	.	T	0.37073	0.0990	L	0.52759	1.655	0.58432	D	0.999999	P;P	0.47191	0.891;0.877	P;P	0.59948	0.866;0.809	T	0.65751	-0.6092	9	0.56958	D	0.05	.	12.9655	0.58481	0.0:0.915:0.0:0.085	rs61754955	198;579	B7WPD9;Q2KJY2	.;KI26B_HUMAN	V	579;198;195	ENSP00000385545:L579V;ENSP00000355475:L198V	ENSP00000355475:L198V	L	+	1	0	KIF26B	243839274	1.000000	0.71417	0.991000	0.47740	0.947000	0.59692	2.028000	0.41088	2.590000	0.87494	0.650000	0.86243	CTC	C|0.976;G|0.024	0.024	strong		0.552	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		G	245772651	C	G	245772651	3	3	23	1	0	0	0	0	1	0	0	0	8304	797	28	4	1765	4	KIF26B	1	245772651	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	13122488	245772651	3477970	65	7509											
KIF26B	55083	hgsc.bcm.edu	37	chr1	245772692	245772692	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaccggcgcccgtttctcAgtccgggtttccgccgtgga	5	9	13	14	6	1	1	1	0	1	1	4	2	3	2	5	3	0	2	5	3	1	2	rs61755865	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:245772692A>C	ENST00000407071.2	+	8	2216	c.1776A>C	c.(1774-1776)tcA>tcC	p.S592S	KIF26B_ENST00000366518.4_Silent_p.S211S	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	592	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)			CCCGTTTCTCAGTCCGGGTTT	0.612													A|||	142	0.0283546	0.0318	0.0648	5008	,	,		16776	0.0278		0.0149	False		,,,				2504	0.0123				p.S592S		Atlas-SNP	.											.	KIF26B	343	.	0			c.A1776C						PASS	.	A		107,3701		1,105,1798	26	29	28		1776	-10.4	0.9	1	dbSNP_129	28	150,8090		2,146,3972	no	coding-synonymous	KIF26B	NM_018012.3		3,251,5770	CC,CA,AA		1.8204,2.8099,2.1331		592/2109	245772692	257,11791	1904	4120	6024	SO:0001819	synonymous_variant	55083	exon8			TTTCTCAGTCCGG	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.1776A>C	1.37:g.245772692A>C		223	0	0		228	102	0.447368	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Silent	SNP	ENST00000407071.2	37	CCDS44342.1																																																																																			A|0.970;C|0.030	0.030	strong		0.612	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354		C	245772692	A	C	245772692	2	2	23	1	0	0	0	0	0	0	0	1	8304	175	7	5		5	KIF26B	1	245772692	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	41	245772692	3477929	66	7510											
ZNF496	84838	hgsc.bcm.edu	37	chr1	247473018	247473018	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cacccaagtaggagacctggGgcacttctttgccctggaga	9	8	12	12	0	1	2	0	0	1	2	1	4	1	2	3	4	1	2	3	4	2	3	rs149858668	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:247473018G>A	ENST00000294753.4	-	7	1339	c.875C>T	c.(874-876)cCc>cTc	p.P292L	ZNF496_ENST00000462139.1_5'UTR|ZNF496_ENST00000366498.2_Missense_Mutation_p.P328L	NM_032752.1	NP_116141.1	Q96IT1	ZN496_HUMAN	zinc finger protein 496	292					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)			GGAGACCTGGGGCACTTCTTT	0.572													G|||	2	0.000399361	0.0008	0.0014	5008	,	,		17285	0.0		0.0	False		,,,				2504	0.0				p.P292L		Atlas-SNP	.											.	ZNF496	80	.	0			c.C875T						PASS	.	G	LEU/PRO	0,4406		0,0,2203	86	76	80		875	4.7	0.9	1	dbSNP_134	80	6,8594	5.0+/-18.6	0,6,4294	yes	missense	ZNF496	NM_032752.1	98	0,6,6497	AA,AG,GG		0.0698,0.0,0.0461	benign	292/588	247473018	6,13000	2203	4300	6503	SO:0001583	missense	84838	exon7			ACCTGGGGCACTT	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.875C>T	1.37:g.247473018G>A	ENSP00000294753:p.Pro292Leu	94	0	0		95	48	0.505263	NM_032752	Q8TBS2	Missense_Mutation	SNP	ENST00000294753.4	37	CCDS1631.1	.	.	.	.	.	.	.	.	.	.	G	13.26	2.184918	0.38609	0.0	6.98E-4	ENSG00000162714	ENST00000294753;ENST00000366498	T;T	0.07800	3.18;3.16	4.7	4.7	0.59300	.	0.508746	0.16561	N	0.209034	T	0.07098	0.0180	N	0.24115	0.695	0.46260	D	0.998956	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.001	T	0.30707	-0.9969	10	0.33940	T	0.23	-9.6614	13.5458	0.61702	0.0:0.0:1.0:0.0	.	328;292	Q96IT1-2;Q96IT1	.;ZN496_HUMAN	L	292;328	ENSP00000294753:P292L;ENSP00000355454:P328L	ENSP00000294753:P292L	P	-	2	0	ZNF496	245539641	0.976000	0.34144	0.911000	0.35937	0.925000	0.55904	1.892000	0.39748	2.341000	0.79615	0.561000	0.74099	CCC	G|0.999;A|0.001	0.001	strong		0.572	ZNF496-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098655.2	NM_032752		A	247473018	G	A	247473018	3	1	23	1	0	0	0	0	1	0	0	0	17960	1232	43	2	900	2	ZNF496	1	247473018	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1700326	247473018	1777603	67	7511											
OR2AK2	391191	hgsc.bcm.edu	37	chr1	248129304	248129304	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggacttattatcttgctacTaccattcctagccattctgg	8	16	6	11	0	2	0	0	0	2	0	3	1	3	1	3	2	4	1	3	2	5	8	rs143777155	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248129304T>C	ENST00000366480.3	+	1	770	c.671T>C	c.(670-672)cTa>cCa	p.L224P	OR2L13_ENST00000366478.2_Intron	NM_001004491.1	NP_001004491.1	Q8NG84	O2AK2_HUMAN	olfactory receptor, family 2, subfamily AK, member 2	224						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)			ATCTTGCTACTACCATTCCTA	0.453													.|||	8	0.00159744	0.0	0.0029	5008	,	,		20749	0.0		0.003	False		,,,				2504	0.0031				p.L224P	Melanoma(45;390 1181 23848 28461 41504)	Atlas-SNP	.											.	OR2AK2	90	.	0			c.T671C						PASS	.	T	PRO/LEU,	2,4404		0,2,2201	92	80	84		671,	1.3	0	1	dbSNP_134	84	11,8589		0,11,4289	yes	missense,intron	OR2L13,OR2AK2	NM_001004491.1,NM_175911.2	98,	0,13,6490	CC,CT,TT		0.1279,0.0454,0.1	probably-damaging,	224/336,	248129304	13,12993	2203	4300	6503	SO:0001583	missense	391191	exon1			TGCTACTACCATT	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.671T>C	1.37:g.248129304T>C	ENSP00000355436:p.Leu224Pro	179	0	0		150	77	0.513333	NM_001004491	B2RND1|Q6IF05	Missense_Mutation	SNP	ENST00000366480.3	37	CCDS31102.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	.	10.89	1.477945	0.26511	4.54E-4	0.001279	ENSG00000187080	ENST00000366480	T	0.45668	0.89	2.48	1.33	0.21861	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.52041	0.1710	L	0.50847	1.595	0.09310	N	0.999995	D	0.89917	1.0	D	0.79108	0.992	T	0.31724	-0.9933	9	0.56958	D	0.05	.	5.7206	0.17985	0.0:0.1483:0.0:0.8517	.	224	Q8NG84	O2AK2_HUMAN	P	224	ENSP00000355436:L224P	ENSP00000355436:L224P	L	+	2	0	OR2AK2	246195927	0.000000	0.05858	0.005000	0.12908	0.130000	0.20726	-0.642000	0.05427	0.372000	0.24591	0.379000	0.24179	CTA	T|0.998;C|0.002	0.002	strong		0.453	OR2AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096858.2	NM_001004491		C	248129304	T	C	248129304	3	2	23	1	0	0	0	0	1	0	0	0	10995	1522	53	3	673	3	OR2AK2	1	248129304	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	656286	248129304	1121317	68	7512											
OR2T5	401993	hgsc.bcm.edu	37	chr1	248652049	248652049	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgtcctgatccttctgataCactgtgacgcccacctccac	7	11	6	17	1	1	3	0	3	1	0	4	3	4	3	5	0	1	0	5	0	1	2	rs554643879		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248652049C>T	ENST00000366473.2	+	1	165	c.160C>T	c.(160-162)Cac>Tac	p.H54Y		NM_001004697.1	NP_001004697.1	Q6IEZ7	OR2T5_HUMAN	olfactory receptor, family 2, subfamily T, member 5	54						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)|lung(2)|ovary(2)|pancreas(1)|skin(2)	9	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)			CCTTCTGATACACTGTGACGC	0.478													.|||	1	0.000199681	0.0	0.0	5008	,	,		22734	0.0		0.001	False		,,,				2504	0.0				p.H54Y		Atlas-SNP	.											.	OR2T5	17	.	0			c.C160T						PASS	.						26	58	47					1																	248652049		2151	4276	6427	SO:0001583	missense	401993	exon1			CTGATACACTGTG	BK004465	CCDS31118.1	1q44	2012-08-09			ENSG00000203661	ENSG00000203661		"GPCR / Class A : Olfactory receptors"	15017	protein-coding gene	gene with protein product							Standard	NM_001004697		Approved		uc001iem.1	Q6IEZ7	OTTHUMG00000040481	ENST00000366473.2:c.160C>T	1.37:g.248652049C>T	ENSP00000355429:p.His54Tyr	702	0	0		1045	302	0.288995	NM_001004697		Missense_Mutation	SNP	ENST00000366473.2	37	CCDS31118.1	.	.	.	.	.	.	.	.	.	.	c	0.003	-2.443662	0.00178	.	.	ENSG00000203661	ENST00000366473	T	0.02863	4.13	2.64	-5.28	0.02755	GPCR, rhodopsin-like superfamily (1);	0.834465	0.10259	N	0.696179	T	0.01353	0.0044	N	0.26092	0.79	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.49579	-0.8925	10	0.02654	T	1	.	0.9068	0.01286	0.1456:0.2245:0.233:0.3969	.	54	Q6IEZ7	OR2T5_HUMAN	Y	54	ENSP00000355429:H54Y	ENSP00000355429:H54Y	H	+	1	0	OR2T5	246718672	0.000000	0.05858	0.093000	0.20910	0.019000	0.09904	-3.180000	0.00569	-0.589000	0.05874	-0.506000	0.04501	CAC	.	.	none		0.478	OR2T5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097422.1	NM_001004697		T	248652049	C	T	248652049	3	4	23	1	0	0	0	0	1	0	0	0	11037	478	17	2	162	2	OR2T5	1	248652049	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	522745	248652049	598572	69	7513											
TPO	7173	hgsc.bcm.edu	37	chr2	1418210	1418210	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcgctgtgctgtctgtcacGctggttatggcctgcacaga	5	12	12	12	2	2	1	1	0	1	1	3	1	2	1	1	2	2	5	1	2	1	1	rs28909989	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:1418210G>A	ENST00000345913.4	+	2	121	c.30G>A	c.(28-30)acG>acA	p.T10T	TPO_ENST00000337415.3_Silent_p.T10T|TPO_ENST00000382198.1_Silent_p.T10T|TPO_ENST00000346956.3_Silent_p.T10T|TPO_ENST00000329066.4_Silent_p.T10T|TPO_ENST00000539820.1_Silent_p.T10T|TPO_ENST00000382269.3_Silent_p.T10T|TPO_ENST00000497517.2_Intron|TPO_ENST00000349624.3_Silent_p.T10T|TPO_ENST00000382201.3_Silent_p.T10T	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	10					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)	TGTCTGTCACGCTGGTTATGG	0.498													G|||	9	0.00179712	0.0008	0.0	5008	,	,		17467	0.0		0.007	False		,,,				2504	0.001				p.T10T		Atlas-SNP	.											TPO,NS,carcinoma,+1,1	TPO	224	1	0			c.G30A						scavenged	.	G	,,,,,	6,4400	11.4+/-27.6	0,6,2197	87	81	83		30,30,30,30,30,30	-9.9	0	2	dbSNP_125	83	50,8550	32.3+/-84.9	0,50,4250	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TPO	NM_000547.5,NM_001206744.1,NM_001206745.1,NM_175719.3,NM_175721.3,NM_175722.3	,,,,,	0,56,6447	AA,AG,GG		0.5814,0.1362,0.4306	,,,,,	10/934,10/934,10/877,10/877,10/890,10/761	1418210	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	7173	exon2			TGTCACGCTGGTT		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.30G>A	2.37:g.1418210G>A		184	1	0.00543478		141	53	0.375887	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Silent	SNP	ENST00000345913.4	37	CCDS1643.1																																																																																			G|0.996;A|0.004	0.004	strong		0.498	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		A	1418210	G	A	1418210	2	1	23	1	0	0	0	0	0	0	0	1	16425	1074	38	1		1	TPO	2	1418210	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10		1418210	241781163	70	7514											
NBAS	51594	hgsc.bcm.edu	37	chr2	15679410	15679410	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcacagttcctgtgctttcGgcataggccagtagggtaca	8	11	11	11	1	1	0	1	0	0	0	3	0	2	0	2	3	2	5	2	3	3	5	rs147692911	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:15679410G>A	ENST00000281513.5	-	7	475	c.450C>T	c.(448-450)gcC>gcT	p.A150A	NBAS_ENST00000441750.1_Silent_p.A150A	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	150					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						CTGTGCTTTCGGCATAGGCCA	0.443													G|||	2	0.000399361	0.0	0.0	5008	,	,		18414	0.0		0.002	False		,,,				2504	0.0				p.A150A		Atlas-SNP	.											.	NBAS	246	.	0			c.C450T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	116	104	108		450	-11.6	0	2	dbSNP_134	108	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	NBAS	NM_015909.2		0,5,6498	AA,AG,GG		0.0465,0.0227,0.0384		150/2372	15679410	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	51594	exon7			GCTTTCGGCATAG	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.450C>T	2.37:g.15679410G>A		185	0	0		186	77	0.413978	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Silent	SNP	ENST00000281513.5	37	CCDS1685.1																																																																																			G|0.999;A|0.001	0.001	strong		0.443	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		A	15679410	G	A	15679410	2	1	23	1	0	0	0	0	0	0	0	1	10195	1103	39	1		1	NBAS	2	15679410	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	14261200	15679410	227519963	71	7515											
PUM2	23369	hgsc.bcm.edu	37	chr2	20494189	20494189	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttgctgactggctgtgttaTttgccgcagctgcagcttgc	4	14	12	11	1	0	1	0	1	0	0	0	1	0	1	1	1	6	7	1	1	1	4	rs34032508	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:20494189T>C	ENST00000361078.2	-	8	1122	c.1100A>G	c.(1099-1101)aAt>aGt	p.N367S	PUM2_ENST00000403432.1_Missense_Mutation_p.N367S|PUM2_ENST00000338086.5_Missense_Mutation_p.N367S|PUM2_ENST00000319801.5_Missense_Mutation_p.N367S|PUM2_ENST00000536417.1_Missense_Mutation_p.N311S			Q8TB72	PUM2_HUMAN	pumilio RNA-binding family member 2	367	Ala-rich.|Gln-rich.		N -> S (in dbSNP:rs34032508).		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)					GGCTGTGTTATTTGCCGCAGC	0.488													T|||	11	0.00219649	0.0	0.0014	5008	,	,		16235	0.0		0.0099	False		,,,				2504	0.0				p.N367S		Atlas-SNP	.											.	PUM2	91	.	0			c.A1100G						PASS	.	T	SER/ASN	3,4403	6.2+/-15.9	0,3,2200	117	111	113		1100	3.3	1	2	dbSNP_126	113	28,8572	19.8+/-62.0	0,28,4272	yes	missense	PUM2	NM_015317.1	46	0,31,6472	CC,CT,TT		0.3256,0.0681,0.2384	benign	367/1065	20494189	31,12975	2203	4300	6503	SO:0001583	missense	23369	exon8			GTGTTATTTGCCG	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.1100A>G	2.37:g.20494189T>C	ENSP00000354370:p.Asn367Ser	98	0	0		114	56	0.491228	NM_015317	B3KSL0|B4E2B6|D6W527|O00234|Q53TV7|Q8WY43|Q9HAN2	Missense_Mutation	SNP	ENST00000361078.2	37		7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	T	2.595	-0.294380	0.05568	6.81E-4	0.003256	ENSG00000055917	ENST00000338086;ENST00000361078;ENST00000319801;ENST00000440577;ENST00000403432;ENST00000536417	T;T;T;T;T;T	0.17528	2.3;2.54;2.55;2.27;2.3;2.3	5.81	3.32	0.38043	.	0.390535	0.33180	N	0.005192	T	0.03390	0.0098	N	0.01576	-0.805	0.24245	N	0.995342	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.04013	0.001;0.0;0.001	T	0.38265	-0.9669	10	0.19147	T	0.46	-4.0477	6.8251	0.23878	0.0:0.1485:0.1398:0.7117	rs34032508	311;367;367	B4E2B6;B7ZL34;Q8TB72-3	.;.;.	S	367;367;367;258;367;311	ENSP00000338173:N367S;ENSP00000354370:N367S;ENSP00000326746:N367S;ENSP00000409905:N258S;ENSP00000385992:N367S;ENSP00000440093:N311S	ENSP00000326746:N367S	N	-	2	0	PUM2	20357670	1.000000	0.71417	1.000000	0.80357	0.183000	0.23260	1.260000	0.32968	1.044000	0.40200	0.455000	0.32223	AAT	T|0.996;C|0.004	0.004	strong		0.488	PUM2-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015317		C	20494189	T	C	20494189	3	2	23	1	0	0	0	0	1	0	0	0	12841	1493	52	3	2146	3	PUM2	2	20494189	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	4814779	20494189	222705184	72	7516											
OTOF	9381	hgsc.bcm.edu	37	chr2	26696374	26696374	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcacactcgatgtccaccCgtggccggtccacctgggcc	5	7	11	18	3	0	0	0	0	0	0	3	1	2	0	6	3	1	1	6	3	0	0	rs56054534	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:26696374C>T	ENST00000272371.2	-	28	3596	c.3470G>A	c.(3469-3471)cGg>cAg	p.R1157Q	OTOF_ENST00000402415.3_Missense_Mutation_p.R467Q|OTOF_ENST00000403946.3_Missense_Mutation_p.R1157Q|OTOF_ENST00000338581.6_Missense_Mutation_p.R410Q|OTOF_ENST00000339598.3_Missense_Mutation_p.R410Q	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	1157			R -> Q (in dbSNP:rs56054534). {ECO:0000269|PubMed:16371502}.		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)					GATGTCCACCCGTGGCCGGTC	0.592													C|||	23	0.00459265	0.0	0.013	5008	,	,		16468	0.0		0.0139	False		,,,				2504	0.0				p.R1157Q	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.G3470A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	14,4392	20.2+/-43.8	0,14,2189	63	63	63	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1229,3470,1400,1229	5.2	1	2	dbSNP_129	63	129,8471	66.0+/-128.3	1,127,4172	yes	missense,missense,missense,missense	OTOF	NM_004802.3,NM_194248.2,NM_194322.2,NM_194323.2	43,43,43,43	1,141,6361	TT,TC,CC		1.5,0.3177,1.0995	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	410/1231,1157/1998,467/1308,410/1231	26696374	143,12863	2203	4300	6503	SO:0001583	missense	9381	exon28			TCCACCCGTGGCC	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.3470G>A	2.37:g.26696374C>T	ENSP00000272371:p.Arg1157Gln	79	0	0		91	42	0.461538	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	37	CCDS1725.1	12	0.005494505494505495	0	0.0	4	0.011049723756906077	0	0.0	8	0.010554089709762533	C	15.19	2.761009	0.49468	0.003177	0.015	ENSG00000115155	ENST00000338581;ENST00000339598;ENST00000402415;ENST00000272371;ENST00000403946	D;D;D;T;T	0.84516	-1.86;-1.86;-1.86;-0.22;-0.22	5.21	5.21	0.72293	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.76807	0.4039	N	0.03281	-0.365	0.80722	D	1	D;P;D;B	0.89917	1.0;0.477;0.99;0.304	D;B;P;B	0.87578	0.998;0.08;0.596;0.08	T	0.76650	-0.2881	10	0.07813	T	0.8	-22.4695	18.3421	0.90309	0.0:1.0:0.0:0.0	rs56054534	1157;410;467;410	Q9HC10;Q9HC10-2;Q9HC10-3;Q9HC10-4	OTOF_HUMAN;.;.;.	Q	410;410;467;1157;1157	ENSP00000345137:R410Q;ENSP00000344521:R410Q;ENSP00000383906:R467Q;ENSP00000272371:R1157Q;ENSP00000385255:R1157Q	ENSP00000272371:R1157Q	R	-	2	0	OTOF	26549878	0.995000	0.38212	0.997000	0.53966	0.870000	0.49936	3.321000	0.51999	2.436000	0.82500	0.484000	0.47621	CGG	C|0.991;T|0.009	0.009	strong		0.592	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3			T	26696374	C	T	26696374	3	4	23	1	0	0	0	0	1	0	0	0	11312	652	23	1	2784	1	OTOF	2	26696374	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	6202185	26696374	216502999	73	7517											
TRIM54	57159	hgsc.bcm.edu	37	chr2	27521506	27521506	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccgtttccgctgcccatcGtgcaggcatgaggttgtcct	4	11	13	13	3	0	1	0	1	0	0	3	1	2	1	4	3	2	5	4	3	0	2	rs540676343		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:27521506G>A	ENST00000380075.2	+	2	580	c.240G>A	c.(238-240)tcG>tcA	p.S80S	TRIM54_ENST00000296098.4_Silent_p.S80S	NM_187841.2	NP_912730.2	Q9BYV2	TRI54_HUMAN	tripartite motif containing 54	80					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)					GCTGCCCATCGTGCAGGCATG	0.567													G|||	1	0.000199681	0.0	0.0	5008	,	,		19839	0.0		0.0	False		,,,				2504	0.001				p.S80S		Atlas-SNP	.											.	TRIM54	35	.	0			c.G240A						PASS	.						85	70	75					2																	27521506		2203	4300	6503	SO:0001819	synonymous_variant	57159	exon2			CCCATCGTGCAGG	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.240G>A	2.37:g.27521506G>A		137	0	0		190	25	0.131579	NM_187841	A5D8T7|Q53SY4|Q9BYV3	Silent	SNP	ENST00000380075.2	37	CCDS1746.2																																																																																			.	.	none		0.567	TRIM54-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214199.2	NM_187841		A	27521506	G	A	27521506	2	1	23	1	0	0	0	0	0	0	0	1	16543	1132	40	1		1	TRIM54	2	27521506	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	825132	27521506	215677867	74	7518											
WDR43	23160	hgsc.bcm.edu	37	chr2	29164387	29164387	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taatggaaagcagagtcaaaActtttcagaaactttcacac	17	10	6	8	0	3	2	3	0	0	2	3	3	3	3	0	1	3	1	0	1	5	4	rs200896154		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:29164387A>G	ENST00000407426.3	+	15	1737	c.1681A>G	c.(1681-1683)Act>Gct	p.T561A		NM_015131.1	NP_055946.1	Q15061	WDR43_HUMAN	WD repeat domain 43	561						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)					CAGAGTCAAAACTTTTCAGAA	0.383																																					p.T561A		Atlas-SNP	.											.	WDR43	38	.	0			c.A1681G						PASS	.	A	ALA/THR	1,3707		0,1,1853	96	89	91		1681	5.5	1	2		91	6,8144		0,6,4069	yes	missense	WDR43	NM_015131.1	58	0,7,5922	GG,GA,AA		0.0736,0.027,0.059	possibly-damaging	561/678	29164387	7,11851	1854	4075	5929	SO:0001583	missense	23160	exon15			GTCAAAACTTTTC	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.1681A>G	2.37:g.29164387A>G	ENSP00000384302:p.Thr561Ala	95	0	0		102	55	0.539216	NM_015131	Q15395|Q92577	Missense_Mutation	SNP	ENST00000407426.3	37	CCDS46251.1	.	.	.	.	.	.	.	.	.	.	A	16.06	3.016175	0.54468	2.7E-4	7.36E-4	ENSG00000163811	ENST00000407426	T	0.66460	-0.21	5.51	5.51	0.81932	.	0.171968	0.56097	D	0.000034	T	0.73094	0.3543	L	0.50333	1.59	0.34623	D	0.71884	D	0.63880	0.993	P	0.58928	0.848	T	0.76049	-0.3101	10	0.21014	T	0.42	-17.4972	15.9198	0.79552	1.0:0.0:0.0:0.0	.	561	Q15061	WDR43_HUMAN	A	561	ENSP00000384302:T561A	ENSP00000384302:T561A	T	+	1	0	WDR43	29017891	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	4.032000	0.57274	2.222000	0.72286	0.454000	0.30748	ACT	.	.	weak		0.383	WDR43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324865.1	XM_087089		G	29164387	A	G	29164387	3	3	23	1	0	0	0	0	1	0	0	0	17310	43	2	3	1739	3	WDR43	2	29164387	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	1642881	29164387	214034986	75	7519											
ALK	238	hgsc.bcm.edu	37	chr2	29543663	29543663	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttagggtcctgacctgccaTtgaggagtgtggggtgacag	7	11	16	7	0	0	3	0	3	0	0	1	4	1	4	3	4	1	0	3	4	1	3	rs2293564	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:29543663T>C	ENST00000389048.3	-	7	2406	c.1500A>G	c.(1498-1500)caA>caG	p.Q500Q	ALK_ENST00000498037.1_5'Flank|ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	500	MAM 2. {ECO:0000255|PROSITE- ProRule:PRU00128}.				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)	TGACCTGCCATTGAGGAGTGT	0.547			"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				t|||	3889	0.776558	0.4334	0.8847	5008	,	,		17652	0.9206		0.9235	False		,,,				2504	0.864				p.Q500Q		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	.	ALK	533	.	0			c.A1500G						PASS	.	T		2356,2050	609.3+/-391.3	618,1120,465	184	157	166		1500	1	0.1	2	dbSNP_100	166	7931,669	789.2+/-407.6	3657,617,26	no	coding-synonymous	ALK	NM_004304.4		4275,1737,491	CC,CT,TT		7.7791,46.5275,20.9057		500/1621	29543663	10287,2719	2203	4300	6503	SO:0001819	synonymous_variant	238	exon7	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	CTGCCATTGAGGA	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.1500A>G	2.37:g.29543663T>C		210	1	0.0047619		187	187	1	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			T|0.203;C|0.797	0.797	strong		0.547	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		C	29543663	T	C	29543663	2	2	23	1	0	0	0	0	0	0	0	1	525	1490	52	3		3	ALK	2	29543663	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	379276	29543663	213655710	76	7520											
ALK	238	hgsc.bcm.edu	37	chr2	29940529	29940529	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaataatcaggagaaggagaAggcatgtttgttggtgattc	14	11	13	3	0	1	3	1	1	0	2	2	5	1	3	0	4	0	3	0	4	4	4	rs2246745	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:29940529A>T	ENST00000389048.3	-	2	1608	c.702T>A	c.(700-702)ccT>ccA	p.P234P	ALK_ENST00000431873.1_Silent_p.P234P	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	234					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)	GAGAAGGAGAAGGCATGTTTG	0.408			"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				A|||	2951	0.589257	0.1513	0.6902	5008	,	,		20442	0.7827		0.7913	False		,,,				2504	0.7025				p.P234P		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	ALK,NS,carcinoma,-1,1	ALK	533	1	0			c.T702A						PASS	.	A		1172,3234	409.7+/-335.1	157,858,1188	165	142	150		702	1.8	0.9	2	dbSNP_100	150	6983,1617	742.8+/-407.2	2840,1303,157	no	coding-synonymous	ALK	NM_004304.4		2997,2161,1345	TT,TA,AA		18.8023,26.6001,37.2982		234/1621	29940529	8155,4851	2203	4300	6503	SO:0001819	synonymous_variant	238	exon2	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	AGGAGAAGGCATG	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.702T>A	2.37:g.29940529A>T		264	0	0		247	247	1	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			A|0.355;T|0.645	0.645	strong		0.408	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		T	29940529	A	T	29940529	2	4	23	1	0	0	0	0	0	0	0	1	525	59	3	5		5	ALK	2	29940529	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	396866	29940529	213258844	77	7521											
LTBP1	4052	hgsc.bcm.edu	37	chr2	33540307	33540307	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgtctgccagcagggtttctCaatctctgcagatggccgta	7	12	11	11	1	3	1	1	0	3	1	5	1	3	1	2	2	3	4	2	2	2	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:33540307C>T	ENST00000404816.2	+	24	4054	c.3701C>T	c.(3700-3702)tCa>tTa	p.S1234L	LTBP1_ENST00000390003.4_Missense_Mutation_p.S909L|LTBP1_ENST00000404525.1_Missense_Mutation_p.S855L|LTBP1_ENST00000418533.2_Missense_Mutation_p.S908L|LTBP1_ENST00000402934.1_Missense_Mutation_p.S855L|LTBP1_ENST00000407925.1_Missense_Mutation_p.S908L|LTBP1_ENST00000272273.5_Missense_Mutation_p.S174L|LTBP1_ENST00000354476.3_Missense_Mutation_p.S1235L			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1234	EGF-like 12; 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)				CAGGGTTTCTCAATCTCTGCA	0.433																																					p.S1234L		Atlas-SNP	.											.	LTBP1	317	.	0			c.C3701T						PASS	.						115	102	107					2																	33540307		2203	4300	6503	SO:0001583	missense	4052	exon24			GTTTCTCAATCTC		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.3701C>T	2.37:g.33540307C>T	ENSP00000386043:p.Ser1234Leu	118	0	0		129	21	0.162791	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	37	CCDS33177.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.2|20.2	3.943601|3.943601	0.73672|0.73672	.|.	.|.	ENSG00000049323|ENSG00000049323	ENST00000415140|ENST00000404816;ENST00000354476;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925;ENST00000272273;ENST00000422669	.|D;D;D;D;D;D;D;D;D	.|0.86865	.|-2.18;-2.18;-2.18;-2.18;-2.18;-2.18;-2.18;-2.18;-2.18	4.98|4.98	4.98|4.98	0.66077|0.66077	.|EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.|.	.|.	.|.	.|.	.|D	.|0.85885	.|0.5801	L|L	0.38531|0.38531	1.155|1.155	0.40185|0.40185	D|D	0.977332|0.977332	.|B;B;P;B;P;P;P	.|0.41624	.|0.005;0.343;0.757;0.078;0.746;0.58;0.47	.|B;B;B;B;P;B;B	.|0.45610	.|0.027;0.392;0.293;0.087;0.487;0.407;0.341	.|D	.|0.86865	.|0.2032	.|9	.|0.46703	.|T	.|0.11	.|.	18.2782|18.2782	0.90089|0.90089	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|174;1234;908;855;908;909;1235	.|E7EUU6;Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4	.|.;LTBP1_HUMAN;.;.;.;.;.	X|L	196|1234;1235;909;908;855;855;908;174;112	.|ENSP00000386043:S1234L;ENSP00000346467:S1235L;ENSP00000374653:S909L;ENSP00000393057:S908L;ENSP00000384373:S855L;ENSP00000385359:S855L;ENSP00000384091:S908L;ENSP00000272273:S174L;ENSP00000395211:S112L	.|ENSP00000272273:S174L	Q|S	+|+	1|2	0|0	LTBP1|LTBP1	33393811|33393811	1.000000|1.000000	0.71417|0.71417	0.984000|0.984000	0.44739|0.44739	0.886000|0.886000	0.51366|0.51366	5.677000|5.677000	0.68142|0.68142	2.295000|2.295000	0.77249|0.77249	0.655000|0.655000	0.94253|0.94253	CAA|TCA	.	.	none		0.433	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		T	33540307	C	T	33540307	3	4	23	1	0	0	0	0	1	0	0	0	9082	838	29	2	3850	2	LTBP1	2	33540307	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	3599778	33540307	209659066	78	7522											
LTBP1	4052	hgsc.bcm.edu	37	chr2	33567990	33567990	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccttccgctgcctctgttaTcagggctttcaagccccaca	6	12	7	16	1	3	0	2	0	1	0	5	0	5	0	5	1	2	3	5	1	2	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:33567990T>C	ENST00000404816.2	+	25	4169	c.3816T>C	c.(3814-3816)taT>taC	p.Y1272Y	LTBP1_ENST00000390003.4_Silent_p.Y947Y|LTBP1_ENST00000404525.1_Silent_p.Y893Y|LTBP1_ENST00000418533.2_Intron|LTBP1_ENST00000402934.1_Silent_p.Y893Y|LTBP1_ENST00000407925.1_Silent_p.Y946Y|LTBP1_ENST00000272273.5_Intron|LTBP1_ENST00000354476.3_Silent_p.Y1273Y			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1272	EGF-like 13; 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)				GCCTCTGTTATCAGGGCTTTC	0.448																																					p.Y1272Y		Atlas-SNP	.											.	LTBP1	317	.	0			c.T3816C						PASS	.						101	85	90					2																	33567990		2203	4300	6503	SO:0001819	synonymous_variant	4052	exon25			CTGTTATCAGGGC		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.3816T>C	2.37:g.33567990T>C		137	0	0		138	83	0.601449	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Silent	SNP	ENST00000404816.2	37	CCDS33177.2	.	.	.	.	.	.	.	.	.	.	T	9.629	1.135806	0.21123	.	.	ENSG00000049323	ENST00000415140	.	.	.	5.91	3.39	0.38822	.	.	.	.	.	T	0.55924	0.1951	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50792	-0.8786	4	.	.	.	.	7.2434	0.26109	0.0:0.3609:0.0:0.6391	.	.	.	.	T	234	.	.	I	+	2	0	LTBP1	33421494	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.377000	0.44300	0.932000	0.37266	0.455000	0.32223	ATC	.	.	none		0.448	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		C	33567990	T	C	33567990	2	2	23	1	0	0	0	0	0	0	0	1	9082	1442	50	3		3	LTBP1	2	33567990	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	27683	33567990	209631383	79	7523											
CEBPZ	10153	hgsc.bcm.edu	37	chr2	37455232	37455232	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttacaaagcagctcatgagcCacggtaagggctcgagtttt	11	10	11	9	2	1	1	1	1	0	0	2	2	1	1	1	2	4	5	1	2	3	4	rs35414551	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:37455232C>A	ENST00000234170.5	-	2	1249	c.1104G>T	c.(1102-1104)gtG>gtT	p.V368V		NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	368					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)				GCTCATGAGCCACGGTAAGGG	0.423													C|||	19	0.00379393	0.0023	0.0029	5008	,	,		20686	0.0		0.0139	False		,,,				2504	0.0				p.V368V		Atlas-SNP	.											.	CEBPZ	68	.	0			c.G1104T						PASS	.	C		23,4383	29.9+/-59.1	0,23,2180	91	98	95		1104	-1.6	0.1	2	dbSNP_126	95	164,8436	77.5+/-140.1	1,162,4137	no	coding-synonymous	CEBPZ	NM_005760.2		1,185,6317	AA,AC,CC		1.907,0.522,1.4378		368/1055	37455232	187,12819	2203	4300	6503	SO:0001819	synonymous_variant	10153	exon2			ATGAGCCACGGTA	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.1104G>T	2.37:g.37455232C>A		135	0	0		158	78	0.493671	NM_005760	Q8NE75	Silent	SNP	ENST00000234170.5	37	CCDS1787.1																																																																																			C|0.989;A|0.011	0.011	strong		0.423	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760		A	37455232	C	A	37455232	2	1	23	1	0	0	0	0	0	0	0	1	3206	581	21	4		4	CEBPZ	2	37455232	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	3887242	37455232	205744141	80	7524											
CCDC88A	55704	hgsc.bcm.edu	37	chr2	55615950	55615950	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atctgtctcaccaaaatggaTagattgtgcattctaagtga	13	13	8	7	0	3	2	1	1	3	1	4	3	3	3	1	1	1	1	1	1	4	4	rs147639776	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:55615950T>C	ENST00000436346.1	-	3	1078	c.237A>G	c.(235-237)ctA>ctG	p.L79L	CCDC88A_ENST00000413716.2_Silent_p.L79L|CCDC88A_ENST00000336838.6_Silent_p.L79L|CCDC88A_ENST00000263630.8_Silent_p.L79L	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	79					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						CCAAAATGGATAGATTGTGCA	0.269													T|||	3	0.000599042	0.0	0.0029	5008	,	,		12742	0.0		0.001	False		,,,				2504	0.0				p.L79L		Atlas-SNP	.											.	CCDC88A	336	.	0			c.A237G						PASS	.	T	,	2,4400	4.2+/-10.8	0,2,2199	69	74	72		237,237	-11.9	0.1	2	dbSNP_134	72	23,8531	17.3+/-56.4	0,23,4254	no	coding-synonymous,coding-synonymous	CCDC88A	NM_001135597.1,NM_018084.4	,	0,25,6453	CC,CT,TT		0.2689,0.0454,0.193	,	79/1871,79/1844	55615950	25,12931	2201	4277	6478	SO:0001819	synonymous_variant	55704	exon3			AATGGATAGATTG	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.237A>G	2.37:g.55615950T>C		262	0	0		304	141	0.463816	NM_018084	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	Silent	SNP	ENST00000436346.1	37																																																																																				T|0.998;C|0.002	0.002	strong		0.269	CCDC88A-203	KNOWN	basic	protein_coding	protein_coding		NM_017571		C	55615950	T	C	55615950	2	2	23	1	0	0	0	0	0	0	0	1	2865	1393	49	3		3	CCDC88A	2	55615950	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	18160718	55615950	187583423	81	7525											
FAM161A	84140	hgsc.bcm.edu	37	chr2	62066986	62066986	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgctcctgggctctcagctGtgtcctaaggtttcgataga	7	13	11	10	1	1	1	1	0	1	1	5	2	3	1	2	2	2	4	2	2	2	3	rs139266382	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:62066986G>C	ENST00000405894.3	-	3	1254	c.1153C>G	c.(1153-1155)Cag>Gag	p.Q385E	FAM161A_ENST00000404929.1_Missense_Mutation_p.Q385E	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	385					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						GCTCTCAGCTGTGTCCTAAGG	0.453													G|||	4	0.000798722	0.0015	0.0	5008	,	,		19117	0.0		0.002	False		,,,				2504	0.0				p.Q385E		Atlas-SNP	.											.	FAM161A	200	.	0			c.C1153G						PASS	.	G	GLU/GLN,GLU/GLN	4,3922		0,4,1959	100	101	101		1153,1153	3.8	0	2	dbSNP_134	101	39,8259		0,39,4110	yes	missense,missense	FAM161A	NM_001201543.1,NM_032180.2	29,29	0,43,6069	CC,CG,GG		0.47,0.1019,0.3518	possibly-damaging,possibly-damaging	385/717,385/661	62066986	43,12181	1963	4149	6112	SO:0001583	missense	84140	exon3			TCAGCTGTGTCCT		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.1153C>G	2.37:g.62066986G>C	ENSP00000385893:p.Gln385Glu	276	0	0		257	114	0.44358	NM_032180	B4DJV7|Q9H8R2	Missense_Mutation	SNP	ENST00000405894.3	37	CCDS42687.2	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	15.89	2.967701	0.53507	0.001019	0.0047	ENSG00000170264	ENST00000404929;ENST00000405894	T;T	0.21191	2.02;2.02	5.67	3.83	0.44106	.	0.603842	0.18460	N	0.140544	T	0.34716	0.0907	M	0.72894	2.215	0.09310	N	1	D;D	0.58620	0.982;0.983	P;P	0.56434	0.764;0.798	T	0.12630	-1.0540	10	0.27785	T	0.31	-12.0385	9.065	0.36458	0.0702:0.0:0.6683:0.2615	.	385;385	Q3B820;Q3B820-3	F161A_HUMAN;.	E	385	ENSP00000385158:Q385E;ENSP00000385893:Q385E	ENSP00000385158:Q385E	Q	-	1	0	FAM161A	61920490	0.918000	0.31147	0.000000	0.03702	0.014000	0.08584	3.936000	0.56568	0.700000	0.31782	-0.140000	0.14226	CAG	G|0.998;C|0.002	0.002	strong		0.453	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180		C	62066986	G	C	62066986	3	2	23	1	0	0	0	0	1	0	0	0	5477	1386	48	4	845	4	FAM161A	2	62066986	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	6451036	62066986	181132387	82	7526											
PLEK	5341	hgsc.bcm.edu	37	chr2	68607984	68607984	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgaaggaggccagaaatttGccaggaaatctaccaggagg	14	7	13	7	0	1	2	0	1	1	1	1	5	1	5	3	5	2	0	3	5	4	3	rs147263237		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:68607984G>T	ENST00000234313.7	+	3	507	c.328G>T	c.(328-330)Gcc>Tcc	p.A110S		NM_002664.2	NP_002655.2	P08567	PLEK_HUMAN	pleckstrin	110					actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cell projection organization (GO:0030030)|cortical actin cytoskeleton organization (GO:0030866)|hematopoietic progenitor cell differentiation (GO:0002244)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of calcium-mediated signaling (GO:0050849)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of inositol phosphate biosynthetic process (GO:0010920)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-inhibiting G-protein coupled receptor signaling pathway (GO:0030845)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of inositol-polyphosphate 5-phosphatase activity (GO:0010925)|positive regulation of integrin activation (GO:0033625)|positive regulation of platelet activation (GO:0010572)|protein kinase C signaling (GO:0070528)|protein secretion by platelet (GO:0070560)|regulation of cell diameter (GO:0060305)|ruffle organization (GO:0031529)|thrombin receptor signaling pathway (GO:0070493)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|membrane (GO:0016020)|ruffle membrane (GO:0032587)	phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)	p.A110T(1)		autonomic_ganglia(1)|endometrium(3)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	24		Ovarian(717;0.0129)		STAD - Stomach adenocarcinoma(1183;0.00159)|READ - Rectum adenocarcinoma(193;0.0419)		CCAGAAATTTGCCAGGAAATC	0.478																																					p.A110S		Atlas-SNP	.											PLEK,NS,carcinoma,0,2	PLEK	64	2	1	Substitution - Missense(1)	endometrium(1)	c.G328T						PASS	.	G	SER/ALA	0,4406		0,0,2203	143	137	139		328	2.9	0.9	2	dbSNP_134	139	2,8598	2.2+/-6.3	0,2,4298	yes	missense	PLEK	NM_002664.2	99	0,2,6501	TT,TG,GG		0.0233,0.0,0.0154	benign	110/351	68607984	2,13004	2203	4300	6503	SO:0001583	missense	5341	exon3			AAATTTGCCAGGA	X07743	CCDS1887.1	2p13.3	2013-01-10			ENSG00000115956	ENSG00000115956		"Pleckstrin homology (PH) domain containing"	9070	protein-coding gene	gene with protein product		173570				2897630, 12054651	Standard	NM_002664		Approved	P47	uc002sen.4	P08567	OTTHUMG00000129562	ENST00000234313.7:c.328G>T	2.37:g.68607984G>T	ENSP00000234313:p.Ala110Ser	94	0	0		77	24	0.311688	NM_002664	B2R9E8|Q53SU8|Q6FGM8|Q6FGQ1|Q8WV81	Missense_Mutation	SNP	ENST00000234313.7	37	CCDS1887.1	.	.	.	.	.	.	.	.	.	.	G	13.27	2.187751	0.38609	0.0	2.33E-4	ENSG00000115956	ENST00000234313	T	0.19806	2.12	5.8	2.87	0.33458	.	0.192484	0.56097	N	0.000035	T	0.16599	0.0399	L	0.31065	0.9	0.53005	D	0.999968	B;B	0.13145	0.007;0.003	B;B	0.12156	0.007;0.004	T	0.03212	-1.1060	10	0.28530	T	0.3	.	15.4457	0.75228	0.0:0.0:0.3642:0.6358	.	128;110	Q59GZ2;P08567	.;PLEK_HUMAN	S	110	ENSP00000234313:A110S	ENSP00000234313:A110S	A	+	1	0	PLEK	68461488	1.000000	0.71417	0.941000	0.38009	0.953000	0.61014	3.637000	0.54324	0.295000	0.22570	-0.274000	0.10170	GCC	G|1.000;T|0.000	0.000	weak		0.478	PLEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251755.1	NM_002664		T	68607984	G	T	68607984	3	4	23	1	0	0	0	0	1	0	0	0	12062	1319	46	4	338	4	PLEK	2	68607984	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	6540998	68607984	174591389	83	7527											
MPHOSPH10	10199	hgsc.bcm.edu	37	chr2	71360055	71360055	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gagggattggcatcaaagttCacttctttaacaaaagtgct	13	12	9	7	0	3	0	2	0	1	0	3	2	3	1	0	2	2	3	0	2	4	5			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:71360055C>T	ENST00000244230.2	+	2	469	c.117C>T	c.(115-117)ttC>ttT	p.F39F	MPHOSPH10_ENST00000498451.2_Silent_p.F39F|MPHOSPH10_ENST00000468427.1_3'UTR|MCEE_ENST00000244217.5_5'Flank	NM_005791.2	NP_005782.1	O00566	MPP10_HUMAN	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	39					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						CATCAAAGTTCACTTCTTTAA	0.308																																					p.F39F		Atlas-SNP	.											.	MPHOSPH10	81	.	0			c.C117T						PASS	.						34	40	38					2																	71360055		2151	4271	6422	SO:0001819	synonymous_variant	10199	exon2			AAAGTTCACTTCT	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.117C>T	2.37:g.71360055C>T		161	0	0		155	76	0.490323	NM_005791	A0AVJ8	Silent	SNP	ENST00000244230.2	37	CCDS1916.1																																																																																			.	.	none		0.308	MPHOSPH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251924.2	NM_005791		T	71360055	C	T	71360055	2	4	23	1	0	0	0	0	0	0	0	1	9734	825	29	2		2	MPHOSPH10	2	71360055	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	2752071	71360055	171839318	84	7528											
C2orf78	388960	hgsc.bcm.edu	37	chr2	74043857	74043857	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cactgctgtgaccagtctccGgtcactgcccaagcctcaaa	9	8	8	16	1	3	1	2	1	1	0	4	1	3	1	4	1	3	1	4	1	2	0	rs539780072		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:74043857G>A	ENST00000409561.1	+	3	2628	c.2507G>A	c.(2506-2508)cGg>cAg	p.R836Q		NM_001080474.1	NP_001073943.1	A6NCI8	CB078_HUMAN	chromosome 2 open reading frame 78	836								p.R806Q(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|soft_tissue(1)|urinary_tract(1)	34						ACCAGTCTCCGGTCACTGCCC	0.512													G|||	1	0.000199681	0.0	0.0014	5008	,	,		19547	0.0		0.0	False		,,,				2504	0.0				p.R836Q		Atlas-SNP	.											C2orf78,striated_muscle,rhabdoid_tumour,0,1	C2orf78	150	1	1	Substitution - Missense(1)	soft_tissue(1)	c.G2507A						scavenged	.						95	91	93					2																	74043857		1940	4145	6085	SO:0001583	missense	388960	exon3			GTCTCCGGTCACT	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.2507G>A	2.37:g.74043857G>A	ENSP00000387124:p.Arg836Gln	124	1	0.00806452		127	16	0.125984	NM_001080474		Missense_Mutation	SNP	ENST00000409561.1	37	CCDS46338.1	.	.	.	.	.	.	.	.	.	.	G	1.645	-0.515425	0.04200	.	.	ENSG00000187833	ENST00000409561;ENST00000342345	T	0.40225	1.04	5.35	-3.06	0.05379	.	1.732830	0.04010	N	0.297965	T	0.08670	0.0215	N	0.00119	-2.075	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.15867	-1.0422	10	0.14252	T	0.57	-2.5945	3.6028	0.08031	0.3735:0.0:0.3371:0.2893	.	836	A6NCI8	CB078_HUMAN	Q	836;806	ENSP00000387124:R836Q	ENSP00000340692:R806Q	R	+	2	0	C2orf78	73897365	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.105000	0.15333	-0.429000	0.07329	-1.440000	0.01072	CGG	.	.	none		0.512	C2orf78-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000328083.1	NM_001080474		A	74043857	G	A	74043857	3	1	23	1	0	0	0	0	1	0	0	0	2197	1116	39	1	2517	1	C2orf78	2	74043857	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	2683802	74043857	169155516	85	7529											
STAMBP	10617	hgsc.bcm.edu	37	chr2	74077556	74077556	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	atccccaagcaaagtgctggGtctgattactgcaacacaga	13	8	9	11	0	1	2	0	1	1	1	2	2	2	2	2	1	5	3	2	1	4	1	rs77000353	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:74077556G>T	ENST00000394070.2	+	7	1424	c.921G>T	c.(919-921)ggG>ggT	p.G307G	STAMBP_ENST00000409707.1_Silent_p.G307G|STAMBP_ENST00000339566.3_Silent_p.G307G|STAMBP_ENST00000394073.1_Silent_p.G307G|STAMBP_ENST00000486458.1_3'UTR	NM_213622.2	NP_998787.1	O95630	STABP_HUMAN	STAM binding protein	307	MPN.				JAK-STAT cascade (GO:0007259)|mitotic cytokinesis (GO:0000281)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of cell proliferation (GO:0008284)|protein deubiquitination (GO:0016579)	cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|ubiquitin-specific protease activity (GO:0004843)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	18						AAAGTGCTGGGTCTGATTACT	0.468													G|||	56	0.0111821	0.0015	0.0086	5008	,	,		19685	0.006		0.0169	False		,,,				2504	0.0256				p.G307G		Atlas-SNP	.											.	STAMBP	37	.	0			c.G921T						PASS	.	G	,,	18,4388	23.3+/-48.9	0,18,2185	149	131	137		921,921,921	-4	0.9	2	dbSNP_133	137	132,8468	66.3+/-128.7	0,132,4168	yes	coding-synonymous,coding-synonymous,coding-synonymous	STAMBP	NM_006463.4,NM_201647.2,NM_213622.2	,,	0,150,6353	TT,TG,GG		1.5349,0.4085,1.1533	,,	307/425,307/425,307/425	74077556	150,12856	2203	4300	6503	SO:0001819	synonymous_variant	10617	exon8			TGCTGGGTCTGAT	BC007682	CCDS1929.1	2p24.3-p24.1	2008-02-05			ENSG00000124356	ENSG00000124356			16950	protein-coding gene	gene with protein product		606247				10383417	Standard	NM_006463		Approved	AMSH	uc002sjs.3	O95630	OTTHUMG00000129817	ENST00000394070.2:c.921G>T	2.37:g.74077556G>T		204	0	0		187	185	0.989305	NM_006463	B5M0B6|D6W5H7|Q3MJE7	Silent	SNP	ENST00000394070.2	37	CCDS1929.1																																																																																			G|0.988;T|0.012	0.012	strong		0.468	STAMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252048.2	NM_006463		T	74077556	G	T	74077556	2	4	23	1	0	0	0	0	0	0	0	1	15265	1248	44	4		4	STAMBP	2	74077556	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	33699	74077556	169121817	86	7530											
DCTN1	1639	hgsc.bcm.edu	37	chr2	74589828	74589828	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaagctgagccacttgctcCataagttgggccgacgggct	8	10	12	11	2	0	1	0	1	0	0	1	2	1	1	3	2	3	4	3	2	2	4	rs200834352		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:74589828C>T	ENST00000361874.3	-	30	3875	c.3558G>A	c.(3556-3558)atG>atA	p.M1186I	DCTN1_ENST00000409868.1_Missense_Mutation_p.M1164I|DCTN1_ENST00000394003.3_Missense_Mutation_p.M1179I|DCTN1_ENST00000409567.3_Missense_Mutation_p.M1161I|DCTN1_ENST00000409438.1_Missense_Mutation_p.M1047I|DCTN1_ENST00000407639.2_Missense_Mutation_p.M1052I|DCTN1_ENST00000409240.1_Missense_Mutation_p.M1144I|RP11-287D1.3_ENST00000451608.2_Missense_Mutation_p.M99I	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	1186					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						CCACTTGCTCCATAAGTTGGG	0.572																																					p.M1186I		Atlas-SNP	.											.	DCTN1	110	.	0			c.G3558A						PASS	.	C	ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET	0,4406		0,0,2203	62	49	53		3483,3141,3432,3537,3558,3156	4.7	1	2		53	3,8597	2.2+/-6.3	0,3,4297	no	missense,missense,missense,missense,missense,missense	DCTN1	NM_001135040.2,NM_001135041.2,NM_001190836.1,NM_001190837.1,NM_004082.4,NM_023019.3	10,10,10,10,10,10	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	benign,benign,benign,benign,benign,benign	1161/1254,1047/1140,1144/1237,1179/1272,1186/1279,1052/1145	74589828	3,13003	2203	4300	6503	SO:0001583	missense	1639	exon30			TTGCTCCATAAGT		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.3558G>A	2.37:g.74589828C>T	ENSP00000354791:p.Met1186Ile	84	0	0		86	50	0.581395	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Missense_Mutation	SNP	ENST00000361874.3	37	CCDS1939.1	.	.	.	.	.	.	.	.	.	.	C	10.15	1.269980	0.23221	0.0	3.49E-4	ENSG00000204843	ENST00000361874;ENST00000394003;ENST00000393999;ENST00000407639;ENST00000409438;ENST00000409240;ENST00000409868;ENST00000409567	T;T;T;T;T;T;T	0.76186	-1.0;-1.0;-1.0;-1.0;-1.0;-1.0;-1.0	5.53	4.65	0.58169	.	0.185557	0.25978	N	0.027082	T	0.59702	0.2213	N	0.19112	0.55	0.34587	D	0.715042	B;B;B;B;B;B;B	0.09022	0.0;0.0;0.001;0.0;0.002;0.0;0.0	B;B;B;B;B;B;B	0.10450	0.0;0.0;0.0;0.0;0.005;0.001;0.001	T	0.61964	-0.6954	10	0.25751	T	0.34	-3.2341	13.1932	0.59723	0.0:0.9221:0.0:0.0779	.	1161;1144;1186;1179;1052;1047;1169	E9PGE1;E9PFS5;Q14203;A8MY36;Q14203-2;G5E9H4;A8MWX9	.;.;DCTN1_HUMAN;.;.;.;.	I	1186;1179;1169;1052;1047;1144;1164;1161	ENSP00000354791:M1186I;ENSP00000377571:M1179I;ENSP00000384844:M1052I;ENSP00000387270:M1047I;ENSP00000386406:M1144I;ENSP00000387327:M1164I;ENSP00000386843:M1161I	ENSP00000354791:M1186I	M	-	3	0	DCTN1	74443336	1.000000	0.71417	1.000000	0.80357	0.213000	0.24496	1.852000	0.39348	1.332000	0.45431	-0.218000	0.12543	ATG	C|0.999;T|0.001	0.001	weak		0.572	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082		T	74589828	C	T	74589828	3	4	23	1	0	0	0	0	1	0	0	0	4308	594	21	2	290	2	DCTN1	2	74589828	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	512272	74589828	168609545	87	7531											
DOK1	1796	hgsc.bcm.edu	37	chr2	74783100	74783100	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggctcctacgtgctgagggtGgaggctgaaaggctgactct	7	9	16	9	1	1	3	0	3	1	0	2	4	2	4	1	5	2	4	1	5	2	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:74783100G>A	ENST00000233668.5	+	4	1203	c.534G>A	c.(532-534)gtG>gtA	p.V178V	DOK1_ENST00000409429.1_Silent_p.V39V|M1AP_ENST00000464686.1_5'Flank|LOXL3_ENST00000409549.1_5'Flank|LOXL3_ENST00000264094.3_5'Flank|DOK1_ENST00000480318.1_3'UTR|DOK1_ENST00000340004.6_Intron|LOXL3_ENST00000393937.2_5'Flank|LOXL3_ENST00000409986.1_5'Flank	NM_001381.3	NP_001372.1	Q99704	DOK1_HUMAN	docking protein 1, 62kDa (downstream of tyrosine kinase 1)	178	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						TGCTGAGGGTGGAGGCTGAAA	0.617																																					p.V178V	Esophageal Squamous(36;520 860 12502 33616 51270)	Atlas-SNP	.											.	DOK1	39	.	0			c.G534A						PASS	.						55	57	56					2																	74783100		2203	4300	6503	SO:0001819	synonymous_variant	1796	exon4			GAGGGTGGAGGCT	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.534G>A	2.37:g.74783100G>A		127	0	0		127	22	0.173228	NM_001381	O43204|Q53TY2|Q9UHG6	Silent	SNP	ENST00000233668.5	37	CCDS1954.1																																																																																			.	.	none		0.617	DOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252218.3	NM_001381		A	74783100	G	A	74783100	2	1	23	1	0	0	0	0	0	0	0	1	4698	1335	47	2		2	DOK1	2	74783100	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	193272	74783100	168416273	88	7532											
SEMA4F	10505	hgsc.bcm.edu	37	chr2	74883750	74883750	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgcctcccacacactttatGttggcgcccgggacaccatc	7	9	8	17	2	0	0	0	0	0	0	2	1	1	1	4	2	1	1	4	2	1	3	rs139676653	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:74883750G>A	ENST00000357877.2	+	2	384	c.235G>A	c.(235-237)Gtt>Att	p.V79I	SEMA4F_ENST00000339773.5_Missense_Mutation_p.V79I	NM_004263.3	NP_004254.2	O95754	SEM4F_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F	79	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						CACACTTTATGTTGGCGCCCG	0.577													G|||	14	0.00279553	0.0	0.0043	5008	,	,		18054	0.0		0.0109	False		,,,				2504	0.0				p.V79I		Atlas-SNP	.											.	SEMA4F	89	.	0			c.G235A						PASS	.	G	ILE/VAL	4,4402	11.4+/-27.6	0,4,2199	121	108	112		235	3.1	1	2	dbSNP_134	112	66,8534	39.8+/-96.3	0,66,4234	yes	missense	SEMA4F	NM_004263.3	29	0,70,6433	AA,AG,GG		0.7674,0.0908,0.5382	probably-damaging	79/771	74883750	70,12936	2203	4300	6503	SO:0001583	missense	10505	exon2			CTTTATGTTGGCG	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.235G>A	2.37:g.74883750G>A	ENSP00000350547:p.Val79Ile	176	0	0		153	72	0.470588	NM_001271662	Q542Y7|Q9NS35	Missense_Mutation	SNP	ENST00000357877.2	37	CCDS1955.1	20	0.009157509157509158	1	0.0020325203252032522	3	0.008287292817679558	1	0.0017482517482517483	15	0.01978891820580475	G	12.16	1.855717	0.32791	9.08E-4	0.007674	ENSG00000135622	ENST00000357877;ENST00000339773;ENST00000434486;ENST00000453930	T;T;T;T	0.23147	1.92;1.92;1.92;1.92	4.9	3.12	0.35913	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.176655	0.38164	N	0.001800	T	0.18509	0.0444	L	0.37697	1.125	0.21579	N	0.999638	B;B;B;D	0.55605	0.005;0.003;0.002;0.972	B;B;B;D	0.66716	0.015;0.01;0.007;0.946	T	0.03403	-1.1040	10	0.29301	T	0.29	.	7.4621	0.27302	0.1937:0.0:0.8063:0.0	.	79;79;79;79	B7Z931;C9K0A1;O95754-2;O95754	.;.;.;SEM4F_HUMAN	I	79	ENSP00000350547:V79I;ENSP00000342675:V79I;ENSP00000407698:V79I;ENSP00000409141:V79I	ENSP00000342675:V79I	V	+	1	0	SEMA4F	74737258	1.000000	0.71417	0.996000	0.52242	0.966000	0.64601	2.773000	0.47686	0.688000	0.31529	-0.143000	0.13931	GTT	G|0.993;A|0.007	0.007	strong		0.577	SEMA4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252214.2	NM_004263		A	74883750	G	A	74883750	3	1	23	1	0	0	0	0	1	0	0	0	14050	1377	48	2	241	2	SEMA4F	2	74883750	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	100650	74883750	168315623	89	7533											
HK2	3099	hgsc.bcm.edu	37	chr2	75107651	75107651	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agactcatgccagtgcccccGtcaagatgctgcccacctac	9	7	8	17	1	2	2	2	0	0	2	2	2	2	2	5	0	5	1	5	0	2	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:75107651G>A	ENST00000290573.2	+	10	2125	c.1525G>A	c.(1525-1527)Gtc>Atc	p.V509I	HK2_ENST00000409174.1_Missense_Mutation_p.V481I	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	509	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)	p.V509I(2)		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						CAGTGCCCCCGTCAAGATGCT	0.597																																					p.V509I		Atlas-SNP	.											HK2,NS,carcinoma,0,1	HK2	85	1	2	Substitution - Missense(2)	lung(2)	c.G1525A						PASS	.						74	73	73					2																	75107651		2203	4300	6503	SO:0001583	missense	3099	exon10			GCCCCCGTCAAGA		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.1525G>A	2.37:g.75107651G>A	ENSP00000290573:p.Val509Ile	135	0	0		203	22	0.108374	NM_000189	D6W5J2|Q8WU87|Q9UN82	Missense_Mutation	SNP	ENST00000290573.2	37	CCDS1956.1	.	.	.	.	.	.	.	.	.	.	G	17.31	3.358474	0.61403	.	.	ENSG00000159399	ENST00000290573;ENST00000535740;ENST00000409174	D;D	0.98345	-4.88;-4.88	4.99	4.99	0.66335	Hexokinase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98270	0.9427	L	0.51853	1.615	0.80722	D	1	D	0.61697	0.99	D	0.73380	0.98	D	0.97702	1.0185	10	0.35671	T	0.21	-40.4869	16.1435	0.81544	0.0:0.0:1.0:0.0	.	509	P52789	HXK2_HUMAN	I	509;509;481	ENSP00000290573:V509I;ENSP00000387140:V481I	ENSP00000290573:V509I	V	+	1	0	HK2	74961159	1.000000	0.71417	0.963000	0.40424	0.607000	0.37147	7.613000	0.82986	2.756000	0.94617	0.655000	0.94253	GTC	.	.	none		0.597	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2	NM_000189		A	75107651	G	A	75107651	3	1	23	1	0	0	0	0	1	0	0	0	7200	1145	40	1	1563	1	HK2	2	75107651	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	223901	75107651	168091722	90	7534											
CTNNA2	1496	hgsc.bcm.edu	37	chr2	80646660	80646660	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctcattgaggctgcaaagagCggaaatgaaaaggaagtgaa	17	6	13	5	1	1	4	1	3	0	1	1	6	1	6	0	3	2	2	0	3	6	1	rs148134866	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:80646660C>T	ENST00000402739.4	+	8	1229	c.1224C>T	c.(1222-1224)agC>agT	p.S408S	CTNNA2_ENST00000343114.3_Silent_p.S87S|CTNNA2_ENST00000540488.1_Silent_p.S408S|CTNNA2_ENST00000496558.1_Silent_p.S408S|CTNNA2_ENST00000361291.4_Silent_p.S442S|CTNNA2_ENST00000541047.1_Silent_p.S408S|CTNNA2_ENST00000466387.1_Silent_p.S408S	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	408					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						CTGCAAAGAGCGGAAATGAAA	0.443													C|||	5	0.000998403	0.0023	0.0014	5008	,	,		15925	0.0		0.001	False		,,,				2504	0.0				p.S408S		Atlas-SNP	.											.	CTNNA2	462	.	0			c.C1224T						PASS	.	C	,	27,4035		0,27,2004	117	116	116		1224,1224	-3.1	0.9	2	dbSNP_134	116	4,8432		0,4,4214	no	coding-synonymous,coding-synonymous	CTNNA2	NM_001164883.1,NM_004389.3	,	0,31,6218	TT,TC,CC		0.0474,0.6647,0.248	,	408/861,408/906	80646660	31,12467	2031	4218	6249	SO:0001819	synonymous_variant	1496	exon9			AAAGAGCGGAAAT		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.1224C>T	2.37:g.80646660C>T		67	0	0		60	29	0.483333	NM_001164883	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Silent	SNP	ENST00000402739.4	37																																																																																				C|0.998;T|0.002	0.002	strong		0.443	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389		T	80646660	C	T	80646660	2	4	23	1	0	0	0	0	0	0	0	1	4015	767	27	1		1	CTNNA2	2	80646660	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	5539009	80646660	162552713	91	7535											
C2orf89	129293	hgsc.bcm.edu	37	chr2	85059204	85059204	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgggtcgtccagcaggggCgtgttctacctcatagcctt	6	11	13	11	2	2	0	1	0	1	0	4	1	3	0	3	3	3	2	3	3	2	4	rs201984217		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:85059204C>T	ENST00000409520.2	-	5	1099	c.1057G>A	c.(1057-1059)Gcc>Acc	p.A353T	TRABD2A_ENST00000479944.1_5'UTR|TRABD2A_ENST00000335459.5_Missense_Mutation_p.A304T	NM_001277053.1	NP_001263982.1	Q86V40	TIKI1_HUMAN	TraB domain containing 2A	353					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)										CCAGCAGGGGCGTGTTCTACC	0.562													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19756	0.0		0.0	False		,,,				2504	0.0				p.V304I		Atlas-SNP	.											.	.	.	.	0			c.G910A						PASS	.						135	134	134					2																	85059204		2027	4201	6228	SO:0001583	missense	129293	exon4			CAGGGGCGTGTTC	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.1057G>A	2.37:g.85059204C>T	ENSP00000387075:p.Ala353Thr	113	0	0		145	66	0.455172	NM_001080824	B4DKK8|I6UMB9	Missense_Mutation	SNP	ENST00000409520.2	37		.	.	.	.	.	.	.	.	.	.	C	0.676	-0.799962	0.02841	.	.	ENSG00000186854	ENST00000335459;ENST00000409520	T;T	0.19532	2.25;2.14	2.76	0.829	0.18847	.	0.419056	0.20863	N	0.084306	T	0.07503	0.0189	.	.	.	0.23492	N	0.997562	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.30534	-0.9975	9	0.10636	T	0.68	.	2.0163	0.03499	0.277:0.4522:0.0:0.2708	.	353;304	Q86V40;Q86V40-2	CB089_HUMAN;.	T	304;353	ENSP00000335004:A304T;ENSP00000387075:A353T	ENSP00000335004:A304T	A	-	1	0	C2orf89	84912715	1.000000	0.71417	0.990000	0.47175	0.749000	0.42624	0.750000	0.26334	0.465000	0.27167	0.462000	0.41574	GCC	C|0.998;T|0.002	0.002	weak		0.562	TRABD2A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001080824		T	85059204	C	T	85059204	3	4	23	1	0	0	0	0	1	0	0	0	2205	768	27	1	472	1	C2orf89	2	85059204	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	4412544	85059204	158140169	92	7536											
SFTPB	6439	hgsc.bcm.edu	37	chr2	85893842	85893842	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggaggacgttgcactcctgCtccaggaacttcctcatcgt	7	10	11	13	2	1	0	1	0	0	0	5	3	4	3	3	3	3	3	3	3	1	2	rs34682912	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:85893842C>T	ENST00000519937.2	-	4	310	c.291G>A	c.(289-291)gaG>gaA	p.E97E	SFTPB_ENST00000342375.3_Silent_p.E97E|SFTPB_ENST00000409383.1_Silent_p.E109E|SFTPB_ENST00000393822.3_Silent_p.E109E			P07988	PSPB_HUMAN	surfactant protein B	97	Saposin B-type 1. {ECO:0000255|PROSITE- ProRule:PRU00415}.				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						TGCACTCCTGCTCCAGGAACT	0.612													C|||	14	0.00279553	0.0	0.0014	5008	,	,		18379	0.0		0.001	False		,,,				2504	0.0123				p.E109E		Atlas-SNP	.											.	SFTPB	49	.	0			c.G327A						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	163	144	151		327,327	-2.2	0.2	2	dbSNP_126	151	26,8574	19.2+/-60.6	0,26,4274	no	coding-synonymous,coding-synonymous	SFTPB	NM_000542.3,NM_198843.2	,	0,27,6476	TT,TC,CC		0.3023,0.0227,0.2076	,	109/394,109/394	85893842	27,12979	2203	4300	6503	SO:0001819	synonymous_variant	6439	exon5			CTCCTGCTCCAGG	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.291G>A	2.37:g.85893842C>T		77	0	0		83	38	0.457831	NM_198843	Q96R04	Silent	SNP	ENST00000519937.2	37		.	.	.	.	.	.	.	.	.	.	C	0.073	-1.197902	0.01594	2.27E-4	0.003023	ENSG00000168878	ENST00000428225	.	.	.	4.47	-2.19	0.07015	.	.	.	.	.	T	0.47930	0.1472	.	.	.	0.35445	D	0.795177	.	.	.	.	.	.	T	0.52003	-0.8633	4	.	.	.	-12.307	9.1563	0.36994	0.0:0.3994:0.0:0.6006	rs34682912	.	.	.	T	94	.	.	A	-	1	0	SFTPB	85747353	0.023000	0.18921	0.170000	0.22879	0.066000	0.16364	-0.258000	0.08733	-0.589000	0.05874	-0.291000	0.09656	GCA	C|0.997;T|0.003	0.003	strong		0.612	SFTPB-001	KNOWN	alternative_3_UTR|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000252499.3	NM_198843		T	85893842	C	T	85893842	2	4	23	1	0	0	0	0	0	0	0	1	14206	796	28	2		2	SFTPB	2	85893842	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	834638	85893842	157305531	93	7537											
TEKT4	150483	hgsc.bcm.edu	37	chr2	95537568	95537568	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agacccaggcgctggcgcagCgcacgcagcaagactccacg	10	2	13	16	5	0	2	0	0	0	2	1	2	1	2	2	2	2	5	2	2	1	0	rs80243548	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:95537568C>T	ENST00000295201.4	+	1	381	c.244C>T	c.(244-246)Cgc>Tgc	p.R82C	TEKT4_ENST00000427593.2_Missense_Mutation_p.R82C|AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	82					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						GCTGGCGCAGCGCACGCAGCA	0.692													.|||	53	0.0105831	0.0	0.0072	5008	,	,		16615	0.001		0.0169	False		,,,				2504	0.0307				p.R82C		Atlas-SNP	.											TEKT4,bladder,carcinoma,-2,2	TEKT4	72	2	0			c.C244T						PASS	.	C	CYS/ARG	12,4370		0,12,2179	16	17	17		244	2	0.7	2	dbSNP_131	17	182,8356		2,178,4089	no	missense	TEKT4	NM_144705.2	180	2,190,6268	TT,TC,CC		2.1316,0.2738,1.5015	benign	82/436	95537568	194,12726	2191	4269	6460	SO:0001583	missense	150483	exon1			GCGCAGCGCACGC	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.244C>T	2.37:g.95537568C>T	ENSP00000295201:p.Arg82Cys	36	0	0		16	10	0.625	NM_144705		Missense_Mutation	SNP	ENST00000295201.4	37	CCDS2005.1	14	0.00641025641025641	0	0.0	1	0.0027624309392265192	1	0.0017482517482517483	12	0.0158311345646438	.	13.71	2.317321	0.40996	0.002738	0.021316	ENSG00000163060	ENST00000295201;ENST00000427593	T;T	0.02863	4.13;4.13	1.97	1.97	0.26223	.	0.121716	0.56097	N	0.000027	T	0.01592	0.0051	L	0.55990	1.75	0.80722	D	1	B	0.27997	0.197	B	0.25405	0.06	T	0.49808	-0.8900	10	0.37606	T	0.19	-10.6904	9.5816	0.39490	0.0:1.0:0.0:0.0	.	82	Q8WW24	TEKT4_HUMAN	C	82	ENSP00000295201:R82C;ENSP00000407596:R82C	ENSP00000295201:R82C	R	+	1	0	TEKT4	94901295	0.174000	0.23070	0.741000	0.31004	0.479000	0.33129	-0.002000	0.12924	1.094000	0.41399	0.558000	0.71614	CGC	C|0.978;G|0.007;T|0.015	0.015	strong		0.692	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705		T	95537568	C	T	95537568	3	4	23	1	0	0	0	0	1	0	0	0	15770	768	27	1	246	1	TEKT4	2	95537568	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	9643726	95537568	147661805	94	7538											
ADRA2B	151	hgsc.bcm.edu	37	chr2	96780863	96780863	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atagcacccacgcccctgccCaggagcacctggccacgtag	9	4	10	18	2	0	0	0	0	0	0	0	1	0	1	6	2	3	3	6	2	2	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:96780863C>G	ENST00000409345.3	-	1	1121	c.1026G>C	c.(1024-1026)ctG>ctC	p.L342L		NM_000682.5	NP_000673	P18089	ADA2B_HUMAN	adrenoceptor alpha 2B	342					activation of MAPK activity by adrenergic receptor signaling pathway (GO:0071883)|activation of protein kinase B activity (GO:0032148)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|MAPK cascade (GO:0000165)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of norepinephrine secretion (GO:0010700)|platelet activation (GO:0030168)|positive regulation of blood pressure (GO:0045777)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of uterine smooth muscle contraction (GO:0070474)|regulation of vascular smooth muscle contraction (GO:0003056)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha2-adrenergic receptor activity (GO:0004938)|epinephrine binding (GO:0051379)			endometrium(2)|large_intestine(2)|lung(9)|ovary(3)	16					Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Apraclonidine(DB00964)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bethanidine(DB00217)|Brimonidine(DB00484)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Desipramine(DB01151)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Etomidate(DB00292)|Fenoldopam(DB00800)|Guanabenz(DB00629)|Guanfacine(DB01018)|Lisuride(DB00589)|Loxapine(DB00408)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Prazosin(DB00457)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Tizanidine(DB00697)|Tolazoline(DB00797)|Trimipramine(DB00726)|Xylometazoline(DB06694)|Yohimbine(DB01392)|Ziprasidone(DB00246)	CGCCCCTGCCCAGGAGCACCT	0.701																																					p.L342L		Atlas-SNP	.											.	ADRA2B	115	.	0			c.G1026C						PASS	.																																			SO:0001819	synonymous_variant	151	exon1			CCTGCCCAGGAGC	M34041	CCDS56129.1	2q11.1	2014-05-06	2012-05-09		ENSG00000222040	ENSG00000274286		"GPCR / Class A : Adrenoceptors : alpha"	282	protein-coding gene	gene with protein product		104260	"adrenergic, alpha-2B-, receptor"	ADRA2L1, ADRA2RL1		2164221	Standard	NM_000682		Approved	ADRARL1	uc021vlh.1	P18089	OTTHUMG00000188276	ENST00000409345.3:c.1026G>C	2.37:g.96780863C>G		106	0	0		71	34	0.478873	NM_000682	Q4TUH9|Q53RF2|Q9BZK0	Silent	SNP	ENST00000409345.3	37	CCDS56129.1																																																																																			.	.	none		0.701	ADRA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334990.1			G	96780863	C	G	96780863	2	3	23	1	0	0	0	0	0	0	0	1	338	581	21	4		4	ADRA2B	2	96780863	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1243295	96780863	146418510	95	7539											
FER1L5	81562	hgsc.bcm.edu	37	chr2	97368800	97368800	+	IGR	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggacaatgacatcttctcccCcgacgacttcctaggtgagg	9	9	10	13	2	2	2	0	2	2	0	4	5	3	3	3	3	0	0	3	3	2	3	rs373937760		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:97368800C>A	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						ATCTTCTCCCCCGACGACTTC	0.557																																					p.P1864H		Atlas-SNP	.											.	FER1L5	113	.	0			c.C5591A						PASS	.	C	HIS/PRO	0,4002		0,0,2001	70	66	68		5591	-2.4	0	2		68	1,8327		0,1,4163	no	missense	FER1L5	NM_001113382.1	77	0,1,6164	AA,AC,CC		0.012,0.0,0.0081	benign	1864/2094	97368800	1,12329	2001	4164	6165	SO:0001628	intergenic_variant	90342	exon48			TCTCCCCCGACGA	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		2.37:g.97368800C>A		184	0	0		205	96	0.468293	NM_001113382	B4DSH3|D3DXH6|Q53GV3|Q53S67|Q63HN6|Q8NBQ6|Q9BQ14	Missense_Mutation	SNP	ENST00000264963.4	37	CCDS2023.1	.	.	.	.	.	.	.	.	.	.	C	10.53	1.376462	0.24857	0.0	1.2E-4	ENSG00000214272	ENST00000414152;ENST00000436930;ENST00000397978	.	.	.	5.67	-2.36	0.06663	C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.693696	0.11893	U	0.519455	T	0.61627	0.2362	L	0.52126	1.63	.	.	.	P;D;P	0.57571	0.954;0.98;0.944	P;P;B	0.54590	0.482;0.756;0.35	T	0.64960	-0.6284	8	0.15499	T	0.54	2.0843	18.405	0.90532	0.0:0.1727:0.7607:0.0667	.	572;1864;573	B7ZLI3;A0AVI2;A0AVI2-2	.;FR1L5_HUMAN;.	H	1864;1868;573	.	ENSP00000442027:P573H	P	+	2	0	FER1L5	96732527	0.000000	0.05858	0.000000	0.03702	0.987000	0.75469	-0.594000	0.05733	-0.882000	0.03987	0.655000	0.94253	CCC	.	.	weak		0.557	LMAN2L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252844.1	NM_030805		A	97368800	C	A	97368800	1	1	23	0	1	0	0	0	0	0	0	0	5822	623	22	4		4	FER1L5	2	97368800	IGR	SNP	C	TCGA-G8-6325-01A-11D-2210-10	587937	97368800	145830573	96	7540											
MFSD9	84804	hgsc.bcm.edu	37	chr2	103343356	103343356	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acattggtggctgctccgagAaggagatagcccagagcact	11	7	13	10	1	0	3	0	0	0	3	1	5	1	3	2	3	3	3	2	3	2	2	rs34997861	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:103343356A>C	ENST00000258436.5	-	4	418	c.375T>G	c.(373-375)ctT>ctG	p.L125L		NM_032718.3	NP_116107.3	Q8NBP5	MFSD9_HUMAN	major facilitator superfamily domain containing 9	125					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						CTGCTCCGAGAAGGAGATAGC	0.493																																					p.L125L		Atlas-SNP	.											.	MFSD9	56	.	0			c.T375G						PASS	.	A		0,4406		0,0,2203	79	77	78		375	-4.7	0.1	2	dbSNP_126	78	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	MFSD9	NM_032718.3		0,8,6495	CC,CA,AA		0.093,0.0,0.0615		125/475	103343356	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	84804	exon4			TCCGAGAAGGAGA		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.375T>G	2.37:g.103343356A>C		207	0	0		181	91	0.502762	NM_032718	Q4ZG89|Q53TU0|Q96GQ4|Q9BRI8	Silent	SNP	ENST00000258436.5	37	CCDS2063.1																																																																																			A|0.999;C|0.001	0.001	strong		0.493	MFSD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253295.2	NM_032718		C	103343356	A	C	103343356	2	2	23	1	0	0	0	0	0	0	0	1	9548	233	9	5		5	MFSD9	2	103343356	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	5974556	103343356	139856017	97	7541											
TGFBRAP1	9392	hgsc.bcm.edu	37	chr2	105924731	105924731	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcccgctccacagcagagaCaagcgtaaaggctttgatgc	11	7	10	13	2	0	2	0	1	0	1	2	3	2	2	2	1	3	4	2	1	3	2	rs201941079		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:105924731C>G	ENST00000393359.2	-	2	454	c.28G>C	c.(28-30)Gtc>Ctc	p.V10L	TGFBRAP1_ENST00000258449.1_Missense_Mutation_p.V10L			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	10					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						ACAGCAGAGACAAGCGTAAAG	0.522																																					p.V10L	Esophageal Squamous(183;794 2019 9730 21801 48859)	Atlas-SNP	.											.	TGFBRAP1	70	.	0			c.G28C						PASS	.	C	LEU/VAL,LEU/VAL	0,4406		0,0,2203	36	36	36		28,28	4.8	1	2		36	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	TGFBRAP1	NM_001142621.1,NM_004257.4	32,32	0,3,6500	GG,GC,CC		0.0349,0.0,0.0231	probably-damaging,probably-damaging	10/861,10/861	105924731	3,13003	2203	4300	6503	SO:0001583	missense	9392	exon2			CAGAGACAAGCGT	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.28G>C	2.37:g.105924731C>G	ENSP00000377027:p.Val10Leu	58	0	0		56	23	0.410714	NM_004257	A8K5R7|D3DVJ8|O60466	Missense_Mutation	SNP	ENST00000393359.2	37	CCDS2067.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	20.4	3.979858	0.74360	0.0	3.49E-4	ENSG00000135966	ENST00000393359;ENST00000258449	T;T	0.49139	0.79;0.79	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	T	0.44265	0.1285	M	0.67953	2.075	0.80722	D	1	B	0.31968	0.349	B	0.24848	0.056	T	0.42949	-0.9421	10	0.10377	T	0.69	-44.8777	18.4493	0.90697	0.0:1.0:0.0:0.0	.	10	Q8WUH2	TGFA1_HUMAN	L	10	ENSP00000377027:V10L;ENSP00000258449:V10L	ENSP00000258449:V10L	V	-	1	0	TGFBRAP1	105291163	1.000000	0.71417	0.981000	0.43875	0.983000	0.72400	5.892000	0.69790	2.654000	0.90174	0.655000	0.94253	GTC	C|0.999;G|0.001	0.001	strong		0.522	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257		G	105924731	C	G	105924731	3	3	23	1	0	0	0	0	1	0	0	0	15839	478	17	4	2598	4	TGFBRAP1	2	105924731	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	2581375	105924731	137274642	98	7542											
SH3RF3	344558	hgsc.bcm.edu	37	chr2	110065649	110065649	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cccactctgcagcccaggctCaggaccggccaactgccacc	8	4	9	20	1	2	0	1	0	1	0	2	1	2	1	6	3	4	2	6	3	1	0	rs201796718	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:110065649C>G	ENST00000309415.6	+	8	1852	c.1852C>G	c.(1852-1854)Cag>Gag	p.Q618E		NM_001099289.1	NP_001092759.1	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3	618							zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(5)|ovary(2)	18						AGCCCAGGCTCAGGACCGGCC	0.647													C|||	4	0.000798722	0.0	0.0029	5008	,	,		16125	0.0		0.002	False		,,,				2504	0.0				p.Q618E		Atlas-SNP	.											.	SH3RF3	62	.	0			c.C1852G						PASS	.	C	GLU/GLN	7,4313		0,7,2153	18	24	22		1852	5.2	0.4	2		22	31,8479		0,31,4224	yes	missense	SH3RF3	NM_001099289.1	29	0,38,6377	GG,GC,CC		0.3643,0.162,0.2962	benign	618/883	110065649	38,12792	2160	4255	6415	SO:0001583	missense	344558	exon8			CAGGCTCAGGACC	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.1852C>G	2.37:g.110065649C>G	ENSP00000309186:p.Gln618Glu	237	0	0		216	120	0.555556	NM_001099289	A0SDZ7|A8MPR1|Q8NDU1	Missense_Mutation	SNP	ENST00000309415.6	37		.	.	.	.	.	.	.	.	.	.	C	10.24	1.295937	0.23564	0.00162	0.003643	ENSG00000172985	ENST00000418513;ENST00000309415	T;T	0.58210	0.35;2.12	5.15	5.15	0.70609	.	0.409870	0.27294	N	0.020036	T	0.48732	0.1516	.	.	.	0.28576	N	0.910391	P	0.45428	0.858	P	0.46389	0.515	T	0.40384	-0.9566	9	0.13108	T	0.6	-22.3701	18.8174	0.92081	0.0:1.0:0.0:0.0	.	618	Q8TEJ3	SH3R3_HUMAN	E	618	ENSP00000414997:Q618E;ENSP00000309186:Q618E	ENSP00000309186:Q618E	Q	+	1	0	SH3RF3	109432081	0.996000	0.38824	0.421000	0.26609	0.136000	0.21042	3.743000	0.55104	2.680000	0.91292	0.655000	0.94253	CAG	C|0.999;G|0.001	0.001	weak		0.647	SH3RF3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001099289		G	110065649	C	G	110065649	3	3	23	1	0	0	0	0	1	0	0	0	14275	827	29	4	1882	4	SH3RF3	2	110065649	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	4140918	110065649	133133724	99	7543											
BUB1	699	hgsc.bcm.edu	37	chr2	111413444	111413444	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gggttttgttgcagcgaataCcccatacagttgagtcatcc	9	12	10	10	1	1	1	1	1	0	0	2	2	2	1	3	1	4	4	3	1	3	6			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:111413444C>G	ENST00000302759.6	-	16	1866	c.1748G>C	c.(1747-1749)gGt>gCt	p.G583A	BUB1_ENST00000535254.1_Missense_Mutation_p.G563A|BUB1_ENST00000409311.1_Missense_Mutation_p.G583A	NM_004336.3	NP_004327.1	O43683	BUB1_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase	583					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)		GCAGCGAATACCCCATACAGT	0.468																																					p.G583A		Atlas-SNP	.											.	BUB1	91	.	0			c.G1748C						PASS	.						263	252	256					2																	111413444		2203	4300	6503	SO:0001583	missense	699	exon16			CGAATACCCCATA	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.1748G>C	2.37:g.111413444C>G	ENSP00000302530:p.Gly583Ala	219	1	0.00456621		247	119	0.481781	NM_004336	E9PC26|F5GXI5|O43430|O43643|O60626|Q53QE4	Missense_Mutation	SNP	ENST00000302759.6	37	CCDS33273.1	.	.	.	.	.	.	.	.	.	.	C	18.21	3.573710	0.65765	.	.	ENSG00000169679	ENST00000535254;ENST00000409311;ENST00000302759;ENST00000541432	T;T;T	0.52057	1.41;0.68;1.71	5.73	5.73	0.89815	.	0.211524	0.48286	D	0.000188	T	0.58293	0.2112	L	0.49640	1.575	0.36843	D	0.887494	D;D;D	0.76494	0.999;0.997;0.993	D;P;P	0.71870	0.975;0.788;0.725	T	0.55848	-0.8076	10	0.14252	T	0.57	-20.8313	13.0477	0.58937	0.0:0.8385:0.1615:0.0	.	563;583;583	F5GXI5;E9PC26;O43683	.;.;BUB1_HUMAN	A	563;583;583;583	ENSP00000441013:G563A;ENSP00000386701:G583A;ENSP00000302530:G583A	ENSP00000302530:G583A	G	-	2	0	BUB1	111129917	0.928000	0.31464	0.986000	0.45419	0.975000	0.68041	1.580000	0.36547	2.687000	0.91594	0.655000	0.94253	GGT	.	.	none		0.468	BUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331925.1	NM_004336		G	111413444	C	G	111413444	3	3	23	1	0	0	0	0	1	0	0	0	1572	507	18	4	1549	4	BUB1	2	111413444	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1347795	111413444	131785929	100	7544											
IL1A	3552	hgsc.bcm.edu	37	chr2	113539246	113539246	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggattggcttaaactcaacCgtctcttcttcagaaccttc	9	14	6	12	1	4	1	2	0	2	1	6	2	4	2	2	2	3	1	2	2	4	5	rs3783531	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:113539246C>T	ENST00000263339.3	-	4	409	c.254G>A	c.(253-255)cGg>cAg	p.R85Q		NM_000575.3	NP_000566.3	P01583	IL1A_HUMAN	interleukin 1, alpha	85			R -> Q (in dbSNP:rs3783531). {ECO:0000269|Ref.10}.		apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|cytokine-mediated signaling pathway (GO:0019221)|ectopic germ cell programmed cell death (GO:0035234)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fever generation (GO:0001660)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell division (GO:0051781)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of mitosis (GO:0045840)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation vascular endothelial growth factor production (GO:0010575)|response to copper ion (GO:0046688)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	copper ion binding (GO:0005507)|cytokine activity (GO:0005125)			breast(2)|large_intestine(1)|lung(9)	12					Rilonacept(DB06372)	TAAACTCAACCGTCTCTTCTT	0.453													C|||	3	0.000599042	0.0	0.0014	5008	,	,		23078	0.0		0.002	False		,,,				2504	0.0				p.R85Q		Atlas-SNP	.											.	IL1A	19	.	0			c.G254A						PASS	.	C	GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	230	211	217		254	4.9	0.1	2	dbSNP_107	217	23,8577	16.6+/-54.9	0,23,4277	yes	missense	IL1A	NM_000575.3	43	0,25,6478	TT,TC,CC		0.2674,0.0454,0.1922	probably-damaging	85/272	113539246	25,12981	2203	4300	6503	SO:0001583	missense	3552	exon4			CTCAACCGTCTCT	M28983	CCDS2101.1	2q14	2014-01-30			ENSG00000115008	ENSG00000115008		"Interleukins and interleukin receptors", "Endogenous ligands"	5991	protein-coding gene	gene with protein product	"preinterleukin 1 alpha", "hematopoietin-1", "pro-interleukin-1-alpha"	147760		IL1		8188271, 2989698	Standard	NM_000575		Approved	IL1F1, IL-1A, IL1-ALPHA	uc002tig.3	P01583	OTTHUMG00000131315	ENST00000263339.3:c.254G>A	2.37:g.113539246C>T	ENSP00000263339:p.Arg85Gln	268	0	0		306	124	0.405229	NM_000575	Q53QF9|Q7RU02	Missense_Mutation	SNP	ENST00000263339.3	37	CCDS2101.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	19.02	3.745767	0.69418	4.54E-4	0.002674	ENSG00000115008	ENST00000263339	T	0.47177	0.85	5.78	4.88	0.63580	Interleukin-1 propeptide (1);	0.000000	0.52532	D	0.000061	T	0.66742	0.2820	M	0.80847	2.515	0.09310	N	1	D	0.89917	1.0	D	0.74348	0.983	T	0.60672	-0.7217	10	0.27082	T	0.32	-17.4428	12.36	0.55197	0.1687:0.8313:0.0:0.0	rs3783531;rs3783531	85	P01583	IL1A_HUMAN	Q	85	ENSP00000263339:R85Q	ENSP00000263339:R85Q	R	-	2	0	IL1A	113255717	0.053000	0.20554	0.081000	0.20488	0.602000	0.36980	3.439000	0.52878	1.543000	0.49345	0.655000	0.94253	CGG	C|0.998;T|0.002	0.002	strong		0.453	IL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254084.1	NM_000575		T	113539246	C	T	113539246	3	4	23	1	0	0	0	0	1	0	0	0	7659	652	23	1	577	1	IL1A	2	113539246	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	2125802	113539246	129660127	101	7545											
CLASP1	23332	hgsc.bcm.edu	37	chr2	122104692	122104692	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	attgccactaagcaaaacacGctggccttacgcacactact	13	8	6	14	2	0	0	0	0	0	0	0	0	0	0	2	1	5	3	2	1	5	4	rs374603441		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:122104692G>A	ENST00000263710.4	-	39	4841	c.4452C>T	c.(4450-4452)agC>agT	p.S1484S	CLASP1_ENST00000455322.2_Silent_p.S1440S|CLASP1_ENST00000541859.1_Silent_p.S1201S|CLASP1_ENST00000545861.1_Silent_p.S1191S|CLASP1_ENST00000397587.3_Silent_p.S1424S|CLASP1_ENST00000409078.3_Silent_p.S1417S|CLASP1_ENST00000541377.1_Silent_p.S1423S	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	1484	Interaction with CLIP2. {ECO:0000250}.|Interaction with PHLDB2 and RSN.|Localization to kinetochores.				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)					AGCAAAACACGCTGGCCTTAC	0.468																																					p.S1484S		Atlas-SNP	.											.	CLASP1	135	.	0			c.C4452T						PASS	.	G	,,,	0,4100		0,0,2050	93	89	90		4275,4251,4269,4452	-5.2	0.9	2		90	1,8377		0,1,4188	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CLASP1	NM_001142273.1,NM_001142274.1,NM_001207051.1,NM_015282.2	,,,	0,1,6238	AA,AG,GG		0.0119,0.0,0.0080	,,,	1425/1480,1417/1472,1423/1478,1484/1539	122104692	1,12477	2050	4189	6239	SO:0001819	synonymous_variant	23332	exon38			AAACACGCTGGCC	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.4452C>T	2.37:g.122104692G>A		148	0	0		137	59	0.430657	NM_015282	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Silent	SNP	ENST00000263710.4	37																																																																																				.	.	weak		0.468	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282		A	122104692	G	A	122104692	2	1	23	1	0	0	0	0	0	0	0	1	3456	1078	38	1		1	CLASP1	2	122104692	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	8565446	122104692	121094681	102	7546											
HS6ST1	9394	hgsc.bcm.edu	37	chr2	129026358	129026358	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cacacatatgcaacgacgtcTtccacgtggcacccctctgc	9	8	7	17	3	2	0	0	0	2	0	3	1	3	0	3	1	3	2	3	1	2	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:129026358T>C	ENST00000259241.6	-	2	627	c.614A>G	c.(613-615)aAg>aGg	p.K205R		NM_004807.2	NP_004798.3	O60243	H6ST1_HUMAN	heparan sulfate 6-O-sulfotransferase 1	205					angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|labyrinthine layer blood vessel development (GO:0060716)|lung alveolus development (GO:0048286)|neuron development (GO:0048666)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)|sulfotransferase activity (GO:0008146)			endometrium(3)|liver(1)|lung(7)|pancreas(1)|prostate(2)|skin(1)	15	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.117)		CAACGACGTCTTCCACGTGGC	0.637																																					p.K205R		Atlas-SNP	.											.	HS6ST1	31	.	0			c.A614G						PASS	.						37	41	40					2																	129026358		2136	4244	6380	SO:0001583	missense	9394	exon2			GACGTCTTCCACG	AB006179	CCDS42748.1	2q21	2010-03-19		2002-08-23	ENSG00000136720	ENSG00000136720		"Sulfotransferases, membrane-bound"	5201	protein-coding gene	gene with protein product		604846		HS6ST		9535912	Standard	NM_004807		Approved		uc002tpt.4	O60243	OTTHUMG00000153542	ENST00000259241.6:c.614A>G	2.37:g.129026358T>C	ENSP00000259241:p.Lys205Arg	239	0	0		265	30	0.113208	NM_004807	B4DEP2|B4DJ29|Q53SL2|Q9BVI1	Missense_Mutation	SNP	ENST00000259241.6	37	CCDS42748.1	.	.	.	.	.	.	.	.	.	.	T	19.05	3.752695	0.69533	.	.	ENSG00000136720	ENST00000259241	T	0.75050	-0.9	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	D	0.84410	0.5466	M	0.72576	2.205	0.80722	D	1	D	0.69078	0.997	D	0.79108	0.992	D	0.85075	0.0942	9	.	.	.	.	14.4384	0.67298	0.0:0.0:0.0:1.0	.	205	O60243	H6ST1_HUMAN	R	205	ENSP00000259241:K205R	.	K	-	2	0	HS6ST1	128742828	1.000000	0.71417	1.000000	0.80357	0.511000	0.34104	5.971000	0.70440	1.813000	0.52934	0.379000	0.24179	AAG	.	.	none		0.637	HS6ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331572.1	NM_004807		C	129026358	T	C	129026358	3	2	23	1	0	0	0	0	1	0	0	0	7379	1609	56	3	625	3	HS6ST1	2	129026358	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	6921666	129026358	114173015	103	7547											
POTEF	728378	hgsc.bcm.edu	37	chr2	130832364	130832364	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgaacctatagccatgctcgGtgaggatcttcatgaggtag	10	11	12	8	1	2	3	1	3	1	0	3	4	2	4	2	3	3	2	2	3	4	4	rs185469611	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:130832364G>A	ENST00000409914.2	-	17	3080	c.2681C>T	c.(2680-2682)aCc>aTc	p.T894I	POTEF_ENST00000357462.5_Missense_Mutation_p.T894I	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	894	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						GCCATGCTCGGTGAGGATCTT	0.582													.|||	89	0.0177716	0.0424	0.013	5008	,	,		11371	0.0		0.0229	False		,,,				2504	0.001				p.T894I		Atlas-SNP	.											.	POTEF	140	.	0			c.C2681T						PASS	.	G	ILE/THR	58,3640		3,52,1794	20	28	25		2681		0.1	2		25	120,7650		23,74,3788	no	missense	POTEF	NM_001099771.2	89	26,126,5582	AA,AG,GG		1.5444,1.5684,1.5521	probably-damaging	894/1076	130832364	178,11290	1849	3885	5734	SO:0001583	missense	728378	exon17			TGCTCGGTGAGGA	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.2681C>T	2.37:g.130832364G>A	ENSP00000386786:p.Thr894Ile	250	0	0		409	362	0.885086	NM_001099771	A6NC34	Missense_Mutation	SNP	ENST00000409914.2	37	CCDS46409.1	25	0.011446886446886446	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	13	0.017150395778364115	.	14.01	2.406630	0.42715	0.015684	0.015444	ENSG00000196604	ENST00000357462;ENST00000409914	D;D	0.94613	-3.47;-3.47	.	.	.	.	.	.	.	.	D	0.89371	0.6696	M	0.90650	3.135	0.80722	D	1	B	0.18863	0.031	B	0.22152	0.038	D	0.86999	0.2115	8	0.87932	D	0	.	5.9051	0.18992	8.0E-4:0.0:0.9992:0.0	.	894	A5A3E0	POTEF_HUMAN	I	894	ENSP00000350052:T894I;ENSP00000386786:T894I	ENSP00000350052:T894I	T	-	2	0	POTEF	130548834	1.000000	0.71417	0.105000	0.21289	0.105000	0.19272	4.869000	0.63028	0.119000	0.18210	0.121000	0.15741	ACC	G|0.988;A|0.012	0.012	strong		0.582	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771		A	130832364	G	A	130832364	3	1	23	1	0	0	0	0	1	0	0	0	12274	1261	44	2	550	2	POTEF	2	130832364	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1806006	130832364	112367009	104	7548											
TANC1	85461	hgsc.bcm.edu	37	chr2	160074132	160074132	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ttttgtgcagcacgccagggGcattggcaggtacccagggg	7	8	16	10	1	0	0	0	0	0	0	0	0	0	0	2	6	3	5	2	6	1	4	rs373000954	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:160074132G>T	ENST00000263635.6	+	20	3606	c.3369G>T	c.(3367-3369)ggG>ggT	p.G1123G	TANC1_ENST00000454300.1_Silent_p.G1017G	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	1123					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						CACGCCAGGGGCATTGGCAGG	0.592													G|||	3	0.000599042	0.0	0.0	5008	,	,		20076	0.0		0.003	False		,,,				2504	0.0				p.G1123G		Atlas-SNP	.											TANC1,NS,NS,+2,1	TANC1	157	1	0			c.G3369T						PASS	.	G	,	0,3934		0,0,1967	61	68	66		3345,3369	-5.3	1	2		66	7,8347		0,7,4170	no	coding-synonymous,coding-synonymous	TANC1	NM_001145909.1,NM_033394.2	,	0,7,6137	TT,TG,GG		0.0838,0.0,0.057	,	1115/1391,1123/1862	160074132	7,12281	1967	4177	6144	SO:0001819	synonymous_variant	85461	exon20			CCAGGGGCATTGG	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.3369G>T	2.37:g.160074132G>T		106	0	0		150	82	0.546667	NM_033394	C9JD88|Q49AI8	Silent	SNP	ENST00000263635.6	37	CCDS42766.1																																																																																			.	.	weak		0.592	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1			T	160074132	G	T	160074132	2	4	23	1	0	0	0	0	0	0	0	1	15559	1190	42	4		4	TANC1	2	160074132	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	29241768	160074132	83125241	105	7549											
MARCH7	64844	hgsc.bcm.edu	37	chr2	160604781	160604781	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttgacagcttcacagtcccGtagtaatgtaccatcagctt	10	12	7	12	1	2	1	2	1	0	0	3	1	3	1	2	0	3	5	2	0	3	6	rs142330597		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:160604781G>A	ENST00000259050.4	+	5	1102	c.980G>A	c.(979-981)cGt>cAt	p.R327H	MARCH7_ENST00000409591.1_Missense_Mutation_p.R289H|MARCH7_ENST00000539065.1_Missense_Mutation_p.R271H|MARCH7_ENST00000409175.1_Missense_Mutation_p.R327H	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	327	Ser-rich.				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						TCACAGTCCCGTAGTAATGTA	0.398													G|||	1	0.000199681	0.0	0.0	5008	,	,		19489	0.0		0.001	False		,,,				2504	0.0				p.R327H		Atlas-SNP	.											MARCH7,NS,carcinoma,+1,1	MARCH7	48	1	0			c.G980A						PASS	.	G	HIS/ARG	0,4404		0,0,2202	52	56	54		980	5.7	1	2	dbSNP_134	54	11,8589	8.4+/-32.0	0,11,4289	yes	missense	MARCH7	NM_022826.2	29	0,11,6491	AA,AG,GG		0.1279,0.0,0.0846	possibly-damaging	327/705	160604781	11,12993	2202	4300	6502	SO:0001583	missense	64844	exon5			AGTCCCGTAGTAA	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.980G>A	2.37:g.160604781G>A	ENSP00000259050:p.Arg327His	77	0	0		97	41	0.42268	NM_022826	A8K9X1|B7Z7P5|D3DPB0|Q53GQ1|Q9BTR9	Missense_Mutation	SNP	ENST00000259050.4	37	CCDS2210.1	.	.	.	.	.	.	.	.	.	.	G	19.19	3.780091	0.70222	0.0	0.001279	ENSG00000136536	ENST00000409175;ENST00000539065;ENST00000259050;ENST00000409591	T;T;T;T	0.36520	1.25;1.25;1.25;1.25	5.72	5.72	0.89469	.	0.363453	0.33382	N	0.004966	T	0.45637	0.1352	L	0.29908	0.895	0.30173	N	0.801097	D;D;D	0.69078	0.997;0.99;0.99	P;P;B	0.57548	0.823;0.469;0.374	T	0.36432	-0.9748	10	0.41790	T	0.15	-7.7841	19.8788	0.96888	0.0:0.0:1.0:0.0	.	271;289;327	F5H6W4;B7Z7P5;Q9H992	.;.;MARH7_HUMAN	H	327;271;327;289	ENSP00000386830:R327H;ENSP00000442992:R271H;ENSP00000259050:R327H;ENSP00000387238:R289H	ENSP00000259050:R327H	R	+	2	0	MARCH7	160313027	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	6.983000	0.76180	2.683000	0.91414	0.655000	0.94253	CGT	G|0.999;A|0.001	0.001	strong		0.398	MARCH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255040.3	NM_022826		A	160604781	G	A	160604781	3	1	23	1	0	0	0	0	1	0	0	0	9315	1145	40	1	994	1	MARCH7	2	160604781	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	530649	160604781	82594592	106	7550											
COBLL1	22837	hgsc.bcm.edu	37	chr2	165578602	165578602	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccttatctgtctcatccaCgctcatggatttcactatac	9	14	4	14	1	4	0	3	0	2	0	6	1	5	1	2	1	1	1	2	1	3	4	rs74459242	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:165578602C>T	ENST00000392717.2	-	7	1097	c.1093G>A	c.(1093-1095)Gtg>Atg	p.V365M	COBLL1_ENST00000342193.4_Missense_Mutation_p.V327M|COBLL1_ENST00000375458.2_Missense_Mutation_p.V327M|COBLL1_ENST00000409184.3_Missense_Mutation_p.V365M|COBLL1_ENST00000194871.6_Missense_Mutation_p.V393M|COBLL1_ENST00000491126.2_Intron			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	365						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						GTCTCATCCACGCTCATGGAT	0.458													C|||	63	0.0125799	0.0023	0.0202	5008	,	,		16844	0.0		0.0368	False		,,,				2504	0.0092				p.V327M		Atlas-SNP	.											.	COBLL1	122	.	0			c.G979A						PASS	.	C	MET/VAL	34,4372	40.0+/-72.8	0,34,2169	77	83	81		979	1.4	0.5	2	dbSNP_132	81	421,8179	130.5+/-188.4	13,395,3892	yes	missense	COBLL1	NM_014900.3	21	13,429,6061	TT,TC,CC		4.8953,0.7717,3.4984	probably-damaging	327/1167	165578602	455,12551	2203	4300	6503	SO:0001583	missense	22837	exon6			CATCCACGCTCAT	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.1093G>A	2.37:g.165578602C>T	ENSP00000376478:p.Val365Met	130	0	0		130	71	0.546154	NM_014900	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Missense_Mutation	SNP	ENST00000392717.2	37		41	0.018772893772893772	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	29	0.03825857519788918	C	12.89	2.073757	0.36566	0.007717	0.048953	ENSG00000082438	ENST00000375458;ENST00000342193;ENST00000409184;ENST00000392717;ENST00000194871	D	0.93076	-3.16	6.17	1.37	0.22104	Cordon-bleu domain (1);	0.602245	0.17823	N	0.160815	T	0.75428	0.3848	L	0.47716	1.5	0.21553	N	0.999649	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74023	0.982;0.982;0.968	T	0.76080	-0.3090	10	0.52906	T	0.07	-0.5122	2.5206	0.04679	0.1029:0.3543:0.2961:0.2466	.	365;393;365	Q53SF7;B7Z2P5;Q53SF7-2	COBL1_HUMAN;.;.	M	327;327;365;365;393	ENSP00000194871:V393M	ENSP00000194871:V393M	V	-	1	0	COBLL1	165286848	0.099000	0.21834	0.503000	0.27626	0.406000	0.30931	0.134000	0.15932	0.180000	0.19960	0.655000	0.94253	GTG	C|0.971;T|0.029	0.029	strong		0.458	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900		T	165578602	C	T	165578602	3	4	23	1	0	0	0	0	1	0	0	0	3656	536	19	1	2557	1	COBLL1	2	165578602	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	4973821	165578602	77620771	107	7551											
SCN1A	6323	hgsc.bcm.edu	37	chr2	166850872	166850872	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acagatgagaatcatgatgcTtatgtcaaaaacttgtctgg	14	12	9	6	0	3	3	2	2	1	2	3	4	3	3	0	1	2	1	0	1	4	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:166850872T>G	ENST00000303395.4	-	25	4635	c.4636A>C	c.(4636-4638)Agc>Cgc	p.S1546R	SCN1A_ENST00000375405.3_Missense_Mutation_p.S1535R|SCN1A_ENST00000409050.1_Missense_Mutation_p.S1518R|AC010127.3_ENST00000597623.1_RNA|SCN1A_ENST00000423058.2_Missense_Mutation_p.S1546R|AC010127.3_ENST00000595647.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1546					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)	ATCATGATGCTTATGTCAAAA	0.363																																					p.S1546R		Atlas-SNP	.											.	SCN1A	641	.	0			c.A4636C						PASS	.						129	113	118					2																	166850872		2203	4300	6503	SO:0001583	missense	6323	exon25			TGATGCTTATGTC	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.4636A>C	2.37:g.166850872T>G	ENSP00000303540:p.Ser1546Arg	182	0	0		160	21	0.13125	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	37	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	T	18.59	3.657766	0.67586	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.97404	-4.37;-4.37;-4.37;-4.37	5.9	5.9	0.94986	.	0.118890	0.64402	D	0.000011	D	0.97278	0.9110	M	0.61703	1.905	0.32543	N	0.533434	D	0.59357	0.985	P	0.59012	0.85	D	0.99104	1.0844	10	0.62326	D	0.03	.	10.6319	0.45541	0.0:0.0709:0.0:0.9291	.	1535	P35498-2	.	R	1546;1546;1535;1518	ENSP00000407030:S1546R;ENSP00000303540:S1546R;ENSP00000364554:S1535R;ENSP00000386312:S1518R	ENSP00000303540:S1546R	S	-	1	0	SCN1A	166559118	0.452000	0.25713	0.998000	0.56505	0.995000	0.86356	0.724000	0.25954	2.251000	0.74343	0.528000	0.53228	AGC	.	.	none		0.363	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		G	166850872	T	G	166850872	3	3	23	1	0	0	0	0	1	0	0	0	13929	1609	56	5	1401	5	SCN1A	2	166850872	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	1272270	166850872	76348501	108	7552											
XIRP2	129446	hgsc.bcm.edu	37	chr2	168106803	168106803	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgaaacagtttgaagcagaGccaaataaaagtggccttaa	17	8	10	6	0	0	3	0	2	0	1	0	3	0	3	2	1	3	2	2	1	6	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:168106803G>C	ENST00000409195.1	+	9	8990	c.8901G>C	c.(8899-8901)gaG>gaC	p.E2967D	XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.E2967D|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.E2745D	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2792				S -> A (in Ref. 8; CAD91141). {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)				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						TTGAAGCAGAGCCAAATAAAA	0.383																																					p.E2967D		Atlas-SNP	.											.	XIRP2	914	.	0			c.G8901C						PASS	.						90	88	88					2																	168106803		1822	4088	5910	SO:0001583	missense	129446	exon9			AGCAGAGCCAAAT	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.8901G>C	2.37:g.168106803G>C	ENSP00000386840:p.Glu2967Asp	182	0	0		194	29	0.149485	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	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	G	9.715	1.158030	0.21454	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.03212	4.01;4.01;4.01	6.02	-1.98	0.07480	.	0.623038	0.17625	N	0.167595	T	0.02848	0.0085	L	0.40543	1.245	0.09310	N	0.999996	B;B;B	0.17667	0.013;0.023;0.023	B;B;B	0.18871	0.01;0.023;0.023	T	0.38134	-0.9675	10	0.40728	T	0.16	-11.4362	3.8151	0.08812	0.394:0.0974:0.4094:0.0991	.	2792;2792;2745	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	D	2967;2967;2745;381	ENSP00000386840:E2967D;ENSP00000295237:E2967D;ENSP00000387255:E2745D	ENSP00000295237:E2967D	E	+	3	2	XIRP2	167815049	0.595000	0.26857	0.958000	0.39756	0.978000	0.69477	-0.106000	0.10890	-0.277000	0.09193	-0.150000	0.13652	GAG	.	.	none		0.383	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		C	168106803	G	C	168106803	3	2	23	1	0	0	0	0	1	0	0	0	17445	962	34	4	8931	4	XIRP2	2	168106803	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1255931	168106803	75092570	109	7553											
ITGA6	3655	hgsc.bcm.edu	37	chr2	173362720	173362720	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taggttcgagtgactgtgttTccctcaaagactgtagctca	9	13	10	9	1	2	2	2	1	0	1	4	3	3	2	1	1	1	4	1	1	3	4	rs139596061	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:173362720T>C	ENST00000264106.6	+	25	3326	c.3123T>C	c.(3121-3123)ttT>ttC	p.F1041F	ITGA6_ENST00000409532.1_Silent_p.F883F|ITGA6_ENST00000343713.4_Silent_p.F997F|ITGA6_ENST00000375221.2_Silent_p.F1041F|ITGA6_ENST00000409080.1_Silent_p.F1002F|AC093818.1_ENST00000442417.1_RNA|ITGA6_ENST00000264107.7_Silent_p.F1002F			P23229	ITA6_HUMAN	integrin, alpha 6	1041					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)			TGACTGTGTTTCCCTCAAAGA	0.438													T|||	4	0.000798722	0.0008	0.0	5008	,	,		18824	0.0		0.003	False		,,,				2504	0.0				p.F1002F		Atlas-SNP	.											.	ITGA6	171	.	0			c.T3006C						PASS	.	T	,	2,4404	4.2+/-10.8	0,2,2201	248	214	225		3006,3006	3.8	1	2	dbSNP_134	225	12,8588	8.4+/-32.0	0,12,4288	no	coding-synonymous,coding-synonymous	ITGA6	NM_000210.2,NM_001079818.1	,	0,14,6489	CC,CT,TT		0.1395,0.0454,0.1076	,	1002/1074,1002/1092	173362720	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	3655	exon24			TGTGTTTCCCTCA		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.3123T>C	2.37:g.173362720T>C		243	0	0		252	107	0.424603	NM_001079818	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Silent	SNP	ENST00000264106.6	37																																																																																				T|0.999;C|0.001	0.001	strong		0.438	ITGA6-201	KNOWN	basic	protein_coding	protein_coding				C	173362720	T	C	173362720	2	2	23	1	0	0	0	0	0	0	0	1	7889	1780	62	3		3	ITGA6	2	173362720	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	5255917	173362720	69836653	110	7554											
TTN	7273	hgsc.bcm.edu	37	chr2	179582738	179582738	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ctgccttgcatgaatactctCccacatcactgtgatccact	9	12	5	15	0	2	2	1	2	1	0	4	2	3	2	3	0	3	1	3	0	2	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:179582738C>T	ENST00000591111.1	-	84	24268	c.24044G>A	c.(24043-24045)gGa>gAa	p.G8015E	TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.G8332E|TTN_ENST00000342175.6_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.G7088E			Q8WZ42	TITIN_HUMAN	titin	12207	Ig-like 62.				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)			TGAATACTCTCCCACATCACT	0.418																																					p.G8332E		Atlas-SNP	.											.	TTN	18412	.	0			c.G24995A						PASS	.						209	199	202					2																	179582738		2017	4178	6195	SO:0001583	missense	7273	exon86			TACTCTCCCACAT	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.24044G>A	2.37:g.179582738C>T	ENSP00000465570:p.Gly8015Glu	120	0	0		152	80	0.526316	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	37		.	.	.	.	.	.	.	.	.	.	C	12.42	1.934003	0.34096	.	.	ENSG00000155657	ENST00000342992	D	0.86956	-2.19	6.03	6.03	0.97812	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.97012	0.9024	H	0.99545	4.62	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.98008	1.0364	9	0.87932	D	0	.	20.5753	0.99366	0.0:1.0:0.0:0.0	.	8015	Q8WZ42	TITIN_HUMAN	E	7088	ENSP00000343764:G7088E	ENSP00000343764:G7088E	G	-	2	0	TTN	179290983	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	6.027000	0.70881	2.868000	0.98415	0.557000	0.71058	GGA	.	.	none		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179582738	C	T	179582738	3	4	23	1	0	0	0	0	1	0	0	0	16750	855	30	2	79642	2	TTN	2	179582738	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	6220018	179582738	63616635	111	7555											
TTN	7273	hgsc.bcm.edu	37	chr2	179613651	179613651	+	Intron	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctttaatgaaaaggctttGtcatcaatcttcttttgagg	10	17	8	6	0	4	2	2	2	2	0	4	2	4	2	0	2	1	2	0	2	4	6	rs72648904	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:179613651G>A	ENST00000591111.1	-	45	10585				TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Intron|TTN_ENST00000360870.5_Silent_p.D4492D|TTN_ENST00000342175.6_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_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)			AAAAGGCTTTGTCATCAATCT	0.313													G|||	55	0.0109824	0.0015	0.0231	5008	,	,		19218	0.0		0.0239	False		,,,				2504	0.0133				p.D4492D		Atlas-SNP	.											.	TTN	18412	.	0			c.C13476T						PASS	.	G	,,,,	32,4374	37.6+/-69.7	0,32,2171	96	95	96		,,13476,,	0.9	0	2	dbSNP_130	96	306,8290	110.2+/-170.6	13,280,4005	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	13,312,6176	AA,AG,GG		3.5598,0.7263,2.5996	,,,,	,,4492/5605,,	179613651	338,12664	2203	4298	6501	SO:0001627	intron_variant	7273	exon46			GGCTTTGTCATCA	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+4199C>T	2.37:g.179613651G>A		83	0	0		100	47	0.47	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	Silent	SNP	ENST00000591111.1	37																																																																																				G|0.977;A|0.023	0.023	strong		0.313	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179613651	G	A	179613651	1	1	23	0	1	0	0	0	0	0	0	0	16750	1368	48	2		2	TTN	2	179613651	Intron	SNP	G	TCGA-G8-6325-01A-11D-2210-10	30913	179613651	63585722	112	7556											
CCDC150	284992	hgsc.bcm.edu	37	chr2	197521469	197521470	+	Frame_Shift_Del	DEL	TG	TG	-																															cagatattttatggaagaacTgtgagtttctggtaaatcga																								rs143904259		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:197521469_197521470delTG	ENST00000389175.4	+	3	424_425	c.289_290delTG	c.(289-291)tgtfs	p.C97fs	CCDC150_ENST00000272831.7_Intron|CCDC150_ENST00000472405.2_5'UTR|CCDC150_ENST00000423093.2_Intron	NM_001080539.1	NP_001074008.1	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150	97										breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(14)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	33						ATGGAAGAACTGTGAGTTTCTG	0.411																																					p.96_97del		Pindel,Atlas-Indel	.											.	CCDC150	96	.	0			c.288_289del						PASS	.			9,3541		2,5,1768						5	1		dbSNP_134	110	123,7711		1,121,3795	no	frameshift	CCDC150	NM_001080539.1		3,126,5563	A1A1,A1R,RR		1.5701,0.2535,1.1595				132,11252				SO:0001589	frameshift_variant	284992	exon3			.		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.289_290delTG	2.37:g.197521471_197521472delTG	ENSP00000373827:p.Cys97fs	142	0	.		151	50	0.331	NM_001080539	Q6P5U6|Q6P663|Q8N8V5	Frame_Shift_Del	DEL	ENST00000389175.4	37	CCDS46478.1																																																																																			TG|0.989;-|0.011	0.011	strong		0.411	CCDC150-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335377.2	NM_001080539		-	197521470	TG	-	197521469	7	5	23	1	0	1	0	1	0	0	0	0	2787	1580	55	0	299	0	CCDC150	2	197521469	Frame_Shift_Del	DEL	TG	TCGA-G8-6325-01A-11D-2210-10	17907818	197521469	45677904	113	7557											
SF3B1	23451	hgsc.bcm.edu	37	chr2	198270017	198270017	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accaatagtttatcaaagtaTtgaatatcatcaggttttaa	16	15	5	5	0	3	1	3	1	0	0	3	1	3	1	1	1	0	3	1	1	8	8	rs35493573	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:198270017T>C	ENST00000335508.6	-	10	1510	c.1419A>G	c.(1417-1419)caA>caG	p.Q473Q	SNORA4_ENST00000365564.1_RNA|SF3B1_ENST00000462613.1_5'Flank	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	473	Interaction with PPP1R8.				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)			TATCAAAGTATTGAATATCAT	0.303			Mis		myelodysplastic syndrome								T|||	68	0.0135783	0.0091	0.0014	5008	,	,		16834	0.0		0.002	False		,,,				2504	0.0542				p.Q473Q		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	SF3B1,NS,carcinoma,-2,1	SF3B1	1038	1	0			c.A1419G						PASS	.	T		9,4397	15.5+/-35.6	0,9,2194	43	46	45		1419	0.5	1	2	dbSNP_126	45	23,8573	16.6+/-54.9	0,23,4275	no	coding-synonymous	SF3B1	NM_012433.2		0,32,6469	CC,CT,TT		0.2676,0.2043,0.2461		473/1305	198270017	32,12970	2203	4298	6501	SO:0001819	synonymous_variant	23451	exon10			AAAGTATTGAATA	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.1419A>G	2.37:g.198270017T>C		134	0	0		133	77	0.578947	NM_012433	E9PCH3	Silent	SNP	ENST00000335508.6	37	CCDS33356.1																																																																																			T|0.994;C|0.006	0.006	strong		0.303	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			C	198270017	T	C	198270017	2	2	23	1	0	0	0	0	0	0	0	1	14164	1490	52	3		3	SF3B1	2	198270017	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	748548	198270017	44929356	114	7558											
COQ10B	80219	hgsc.bcm.edu	37	chr2	198334871	198334871	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggtcttcctggctacccAagaacttgtaccttggattt	8	13	8	12	0	1	1	0	0	1	1	2	2	2	2	4	3	3	2	4	3	4	6	rs140640160		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:198334871A>C	ENST00000263960.2	+	4	663	c.525A>C	c.(523-525)ccA>ccC	p.P175P	COQ10B_ENST00000409010.1_Silent_p.P147P|COQ10B_ENST00000409398.1_Silent_p.P125P|COQ10B_ENST00000545340.1_Silent_p.P132P	NM_025147.3	NP_079423.1	Q9H8M1	CQ10B_HUMAN	coenzyme Q10 homolog B (S. cerevisiae)	175						mitochondrial inner membrane (GO:0005743)				endometrium(1)|large_intestine(2)|lung(3)	6			Epithelial(96;0.231)|OV - Ovarian serous cystadenocarcinoma(117;0.246)			CTGGCTACCCAAGAACTTGTA	0.353													A|||	1	0.000199681	0.0008	0.0	5008	,	,		16923	0.0		0.0	False		,,,				2504	0.0				p.P175P		Atlas-SNP	.											.	COQ10B	18	.	0			c.A525C						PASS	.	A		3,4403	4.2+/-10.8	0,3,2200	126	111	116		525	-0.2	1	2	dbSNP_134	116	14,8586	8.4+/-32.0	0,14,4286	no	coding-synonymous	COQ10B	NM_025147.3		0,17,6486	CC,CA,AA		0.1628,0.0681,0.1307		175/239	198334871	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	80219	exon4			CTACCCAAGAACT	AK023510	CCDS2319.1	2q33.1	2008-02-05	2006-04-04		ENSG00000115520	ENSG00000115520			25819	protein-coding gene	gene with protein product			"coenzyme Q10 homolog B (yeast)"				Standard	NM_025147		Approved	FLJ13448	uc002uuh.1	Q9H8M1	OTTHUMG00000132745	ENST00000263960.2:c.525A>C	2.37:g.198334871A>C		308	0	0		329	165	0.50152	NM_025147	B7Z1Y4	Silent	SNP	ENST00000263960.2	37	CCDS2319.1																																																																																			A|0.998;C|0.002	0.002	strong		0.353	COQ10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256105.2	NM_025147		C	198334871	A	C	198334871	2	2	23	1	0	0	0	0	0	0	0	1	3746	117	5	5		5	COQ10B	2	198334871	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	64854	198334871	44864502	115	7559											
INO80D	54891	hgsc.bcm.edu	37	chr2	206872126	206872126	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atctcattggcaatgtcatcCggcaactcatcagcactcag	11	10	7	13	1	5	0	5	0	1	0	7	0	6	0	1	2	2	3	1	2	2	1	rs116331438	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:206872126C>T	ENST00000403263.1	-	10	2204	c.1800G>A	c.(1798-1800)ccG>ccA	p.P600P	Vault_ENST00000516676.1_RNA	NM_017759.4	NP_060229.3	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	600					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.P600P(1)|p.P495P(1)		NS(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	26						CAATGTCATCCGGCAACTCAT	0.498													C|||	2	0.000399361	0.0	0.0	5008	,	,		19913	0.0		0.001	False		,,,				2504	0.001				p.P600P		Atlas-SNP	.											INO80D_ENST00000403263,NS,carcinoma,0,2	INO80D	134	2	2	Substitution - coding silent(2)	kidney(2)	c.G1800A						PASS	.	C		3,4115		0,3,2056	130	130	130		1800	2.8	1	2	dbSNP_132	130	22,8406		0,22,4192	no	coding-synonymous	INO80D	NM_017759.4		0,25,6248	TT,TC,CC		0.261,0.0729,0.1993		600/1028	206872126	25,12521	2059	4214	6273	SO:0001819	synonymous_variant	54891	exon10			GTCATCCGGCAAC		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.1800G>A	2.37:g.206872126C>T		266	0	0		309	145	0.469256	NM_017759	B3KU68|B9EG77|Q6PJC6|Q6PJU1|Q6PKA1|Q9NXD5	Silent	SNP	ENST00000403263.1	37	CCDS46500.1																																																																																			C|0.999;T|0.001	0.001	strong		0.498	INO80D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336459.1	NM_017759		T	206872126	C	T	206872126	2	4	23	1	0	0	0	0	0	0	0	1	7758	639	23	1		1	INO80D	2	206872126	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	8537255	206872126	36327247	116	7560											
ERBB4	2066	hgsc.bcm.edu	37	chr2	212251864	212251864	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcaaaacctccatctcggtaTacaaactggttctgttaata	13	12	6	10	1	2	0	0	0	2	0	4	0	3	0	2	2	3	4	2	2	7	5	rs3748962	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:212251864T>C	ENST00000342788.4	-	27	3505	c.3195A>G	c.(3193-3195)gtA>gtG	p.V1065V	ERBB4_ENST00000402597.1_Silent_p.V1055V|ERBB4_ENST00000436443.1_Silent_p.V1049V	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	1065					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)	CATCTCGGTATACAAACTGGT	0.433										TSP Lung(8;0.080)			T|||	1117	0.223043	0.0756	0.2983	5008	,	,		18765	0.2887		0.2992	False		,,,				2504	0.2229				p.V1065V		Atlas-SNP	.											.	ERBB4	480	.	0			c.A3195G						PASS	.	T	,	444,3962	214.5+/-233.7	29,386,1788	110	113	112		3147,3195	-8.9	0.3	2	dbSNP_107	112	2843,5757	447.9+/-361.7	499,1845,1956	no	coding-synonymous,coding-synonymous	ERBB4	NM_001042599.1,NM_005235.2	,	528,2231,3744	CC,CT,TT		33.0581,10.0772,25.273	,	1049/1293,1065/1309	212251864	3287,9719	2203	4300	6503	SO:0001819	synonymous_variant	2066	exon27			TCGGTATACAAAC	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.3195A>G	2.37:g.212251864T>C		245	0	0		266	137	0.515038	NM_005235	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Silent	SNP	ENST00000342788.4	37	CCDS2394.1																																																																																			T|0.756;C|0.244	0.244	strong		0.433	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		C	212251864	T	C	212251864	2	2	23	1	0	0	0	0	0	0	0	1	5211	1393	49	3		3	ERBB4	2	212251864	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	5379738	212251864	30947509	117	7561											
SPAG16	79582	hgsc.bcm.edu	37	chr2	214160817	214160817	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	taactgaagcatctgaagatGactatgaatatgaagaggta	17	10	10	4	0	1	7	0	5	1	2	1	7	1	7	0	1	2	2	0	1	8	4	rs61752198	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:214160817G>A	ENST00000331683.5	+	2	261	c.166G>A	c.(166-168)Gac>Aac	p.D56N	SPAG16_ENST00000272898.7_Missense_Mutation_p.D56N|SPAG16_ENST00000447990.1_Missense_Mutation_p.D56N|SPAG16_ENST00000374309.3_Start_Codon_SNP_p.M1I|SPAG16_ENST00000414961.2_3'UTR|SPAG16_ENST00000413312.1_Intron|SPAG16_ENST00000432529.2_Missense_Mutation_p.D56N	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	56					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)		ATCTGAAGATGACTATGAATA	0.279													G|||	61	0.0121805	0.0053	0.0043	5008	,	,		15997	0.004		0.0159	False		,,,				2504	0.0317				p.D56N		Atlas-SNP	.											.	SPAG16	134	.	0			c.G166A						PASS	.	G	ASN/ASP,ASN/ASP	32,4372	37.6+/-69.7	0,32,2170	91	100	97		166,166	5.3	1	2	dbSNP_129	97	153,8431	72.9+/-135.5	2,149,4141	yes	missense,missense	SPAG16	NM_001025436.1,NM_024532.3	23,23	2,181,6311	AA,AG,GG		1.7824,0.7266,1.4244	benign,benign	56/184,56/632	214160817	185,12803	2202	4292	6494	SO:0001583	missense	79582	exon2			GAAGATGACTATG	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.166G>A	2.37:g.214160817G>A	ENSP00000332592:p.Asp56Asn	158	0	0		161	87	0.540373	NM_024532	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Missense_Mutation	SNP	ENST00000331683.5	37	CCDS2396.1	23|23	0.010531135531135532|0.010531135531135532	6|6	0.012195121951219513|0.012195121951219513	2|2	0.0055248618784530384|0.0055248618784530384	2|2	0.0034965034965034965|0.0034965034965034965	13|13	0.017150395778364115|0.017150395778364115	G|G	11.78|11.78	1.742080|1.742080	0.30865|0.30865	0.007266|0.007266	0.017824|0.017824	ENSG00000144451|ENSG00000144451	ENST00000331683;ENST00000432529;ENST00000272898;ENST00000447990|ENST00000374309	T|T	0.60299|0.55588	0.2|0.51	5.27|5.27	5.27|5.27	0.74061|0.74061	.|.	0.175804|.	0.33419|.	N|.	0.004932|.	T|T	0.31670|0.31670	0.0804|0.0804	L|L	0.43152|0.43152	1.355|1.355	0.09310|0.09310	N|N	0.999998|0.999998	D;D;D|B	0.76494|0.25667	0.964;0.999;0.979|0.131	P;D;P|B	0.66979|0.22386	0.637;0.948;0.801|0.039	T|T	0.39396|0.39396	-0.9616|-0.9616	10|9	0.46703|0.87932	T|D	0.11|0	.|.	14.7325|14.7325	0.69393|0.69393	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs61752198|rs61752198	56;56;56|1	Q8N0X2;E7EWV3;Q8N0X2-4|B4DYB5	SPG16_HUMAN;.;.|.	N|I	56|1	ENSP00000332592:D56N|ENSP00000363428:M1I	ENSP00000272898:D56N|ENSP00000363428:M1I	D|M	+|+	1|3	0|0	SPAG16|SPAG16	213869062|213869062	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.795000|0.795000	0.44927|0.44927	5.541000|5.541000	0.67212|0.67212	2.597000|2.597000	0.87782|0.87782	0.585000|0.585000	0.79938|0.79938	GAC|ATG	G|0.985;A|0.015	0.015	strong		0.279	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532		A	214160817	G	A	214160817	3	1	23	1	0	0	0	0	1	0	0	0	14993	1290	45	2	172	2	SPAG16	2	214160817	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1908953	214160817	29038556	118	7562											
SPAG16	79582	hgsc.bcm.edu	37	chr2	214354811	214354811	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	actccatgaacttccagtgaGctggtaggatttttgatgtt	9	15	10	7	0	0	3	0	3	0	0	2	4	2	4	2	2	2	3	2	2	2	5	rs61752199	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:214354811G>A	ENST00000331683.5	+	10	1162	c.1067G>A	c.(1066-1068)aGc>aAc	p.S356N	SPAG16_ENST00000374309.3_Missense_Mutation_p.S262N	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	356					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)		CTTCCAGTGAGCTGGTAGGAT	0.318													G|||	62	0.0123802	0.0053	0.0058	5008	,	,		16436	0.004		0.0159	False		,,,				2504	0.0317				p.S356N		Atlas-SNP	.											.	SPAG16	134	.	0			c.G1067A						PASS	.	G	ASN/SER	33,4369	38.4+/-70.7	0,33,2168	51	55	54		1067	5	1	2	dbSNP_129	54	154,8440	72.9+/-135.5	2,150,4145	yes	missense	SPAG16	NM_024532.3	46	2,183,6313	AA,AG,GG		1.7919,0.7497,1.4389	probably-damaging	356/632	214354811	187,12809	2201	4297	6498	SO:0001583	missense	79582	exon10			CAGTGAGCTGGTA	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.1067G>A	2.37:g.214354811G>A	ENSP00000332592:p.Ser356Asn	279	0	0		251	119	0.474104	NM_024532	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Missense_Mutation	SNP	ENST00000331683.5	37	CCDS2396.1	24	0.01098901098901099	6	0.012195121951219513	3	0.008287292817679558	2	0.0034965034965034965	13	0.017150395778364115	G	17.80	3.477248	0.63849	0.007497	0.017919	ENSG00000144451	ENST00000331683;ENST00000374309;ENST00000451561	T;T;T	0.59364	0.27;0.27;0.27	5.93	5.03	0.67393	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.106321	0.64402	D	0.000016	T	0.57695	0.2071	M	0.72894	2.215	0.34970	D	0.753049	P;D;P;P	0.89917	0.951;1.0;0.599;0.872	P;D;P;P	0.87578	0.636;0.998;0.574;0.636	T	0.73145	-0.4075	10	0.22109	T	0.4	.	12.9132	0.58190	0.0:0.1628:0.8372:0.0	rs61752199	262;207;296;356	B4DYB5;Q8N0X2-2;Q4G1A2;Q8N0X2	.;.;.;SPG16_HUMAN	N	356;262;42	ENSP00000332592:S356N;ENSP00000363428:S262N;ENSP00000416600:S42N	ENSP00000332592:S356N	S	+	2	0	SPAG16	214063056	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	2.442000	0.44873	1.454000	0.47793	0.555000	0.69702	AGC	G|0.984;A|0.016	0.016	strong		0.318	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532		A	214354811	G	A	214354811	3	1	23	1	0	0	0	0	1	0	0	0	14993	971	34	2	1121	2	SPAG16	2	214354811	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	193994	214354811	28844562	119	7563											
WNT10A	80326	hgsc.bcm.edu	37	chr2	219754822	219754822	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgtgatgcgtcccggcgaGgggacgaggaggccttccgt	5	7	18	11	5	0	1	0	1	0	0	2	5	2	3	3	5	1	1	3	5	0	1	rs77583146	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:219754822G>A	ENST00000258411.3	+	3	1126	c.493G>A	c.(493-495)Ggg>Agg	p.G165R		NM_025216.2	NP_079492.2	Q9GZT5	WN10A_HUMAN	wingless-type MMTV integration site family, member 10A	165					cell fate commitment (GO:0045165)|cellular response to transforming growth factor beta stimulus (GO:0071560)|epidermis morphogenesis (GO:0048730)|hair follicle development (GO:0001942)|hair follicle morphogenesis (GO:0031069)|neural crest cell differentiation (GO:0014033)|neuron differentiation (GO:0030182)|odontogenesis (GO:0042476)|positive regulation of gene expression (GO:0010628)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|sebaceous gland development (GO:0048733)|skin development (GO:0043588)|tongue development (GO:0043586)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|cervix(1)|endometrium(2)|lung(6)|skin(2)	12		Renal(207;0.0474)		Epithelial(149;4.26e-07)|all cancers(144;8.8e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GTCCCGGCGAGGGGACGAGGA	0.642													G|||	11	0.00219649	0.0015	0.0014	5008	,	,		18771	0.0		0.007	False		,,,				2504	0.001				p.G165R		Atlas-SNP	.											.	WNT10A	35	.	0			c.G493A						PASS	.	G	ARG/GLY	10,4396	16.8+/-37.8	0,10,2193	68	56	60		493	4.5	1	2	dbSNP_131	60	92,8508	51.1+/-111.2	0,92,4208	yes	missense	WNT10A	NM_025216.2	125	0,102,6401	AA,AG,GG		1.0698,0.227,0.7843	probably-damaging	165/418	219754822	102,12904	2203	4300	6503	SO:0001583	missense	80326	exon3			CGGCGAGGGGACG	AB059569	CCDS2426.1	2q35	2008-05-23			ENSG00000135925	ENSG00000135925		"Wingless-type MMTV integration sites"	13829	protein-coding gene	gene with protein product		606268				11350055, 17847007	Standard	NM_025216		Approved		uc002vjd.1	Q9GZT5	OTTHUMG00000133085	ENST00000258411.3:c.493G>A	2.37:g.219754822G>A	ENSP00000258411:p.Gly165Arg	64	0	0		83	44	0.53012	NM_025216	Q53S44|Q96TA7|Q9H7S8	Missense_Mutation	SNP	ENST00000258411.3	37	CCDS2426.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	16.51	3.143104	0.57044	0.00227	0.010698	ENSG00000135925	ENST00000258411	T	0.76060	-0.99	4.46	4.46	0.54185	.	0.457875	0.21825	N	0.068570	T	0.69296	0.3095	M	0.66297	2.02	0.80722	D	1	B	0.24576	0.106	B	0.31751	0.135	T	0.74444	-0.3663	10	0.59425	D	0.04	.	16.2054	0.82126	0.0:0.0:1.0:0.0	.	165	Q9GZT5	WN10A_HUMAN	R	165	ENSP00000258411:G165R	ENSP00000258411:G165R	G	+	1	0	WNT10A	219463066	1.000000	0.71417	0.989000	0.46669	0.487000	0.33371	7.398000	0.79919	2.478000	0.83669	0.655000	0.94253	GGG	G|0.993;A|0.007	0.007	strong		0.642	WNT10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256730.2	NM_025216		A	219754822	G	A	219754822	3	1	23	1	0	0	0	0	1	0	0	0	17397	1000	35	2	503	2	WNT10A	2	219754822	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	5400011	219754822	23444551	120	7564											
SLC23A3	151295	hgsc.bcm.edu	37	chr2	220034377	220034377	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcaggtgggagacacagagCagagaagccatgaccaagac	16	2	14	9	0	0	5	0	1	0	4	0	7	0	5	2	2	3	2	2	2	2	0			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:220034377C>A	ENST00000409878.3	-	2	218	c.186G>T	c.(184-186)ctG>ctT	p.L62L	SLC23A3_ENST00000295738.7_Silent_p.L62L|SLC23A3_ENST00000455516.2_Silent_p.L62L|SLC23A3_ENST00000396775.3_Silent_p.L4L	NM_001144889.1	NP_001138361.1	Q6PIS1	S23A3_HUMAN	solute carrier family 23, member 3	62					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)		AGACACAGAGCAGAGAAGCCA	0.532																																					p.L62L		Atlas-SNP	.											.	SLC23A3	60	.	0			c.G186T						PASS	.						57	76	69					2																	220034377		2091	4226	6317	SO:0001819	synonymous_variant	151295	exon2			ACAGAGCAGAGAA	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.186G>T	2.37:g.220034377C>A		107	0	0		105	5	0.047619	NM_001144890	B7Z512|Q2PYN6|Q96NA6	Silent	SNP	ENST00000409878.3	37	CCDS46518.1																																																																																			.	.	none		0.532	SLC23A3-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336331.2	NM_144712		A	220034377	C	A	220034377	2	1	23	1	0	0	0	0	0	0	0	1	14479	697	25	4		4	SLC23A3	2	220034377	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	279555	220034377	23164996	121	7565											
OBSL1	23363	hgsc.bcm.edu	37	chr2	220422126	220422126	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgcacaggtactccccagcGtccccgctccgtgccccctg	4	7	9	21	4	0	0	0	0	0	0	4	0	3	0	7	1	3	3	7	1	1	1	rs375716830	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:220422126G>A	ENST00000404537.1	-	12	4061	c.4005C>T	c.(4003-4005)gaC>gaT	p.D1335D	OBSL1_ENST00000265317.5_Intron|OBSL1_ENST00000373876.1_Intron|OBSL1_ENST00000265318.4_Silent_p.D1243D|OBSL1_ENST00000603926.1_Silent_p.D1335D|RP11-256I23.2_ENST00000597192.1_RNA	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	1335	Ig-like 11.				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)		ACTCCCCAGCGTCCCCGCTCC	0.692													G|||	6	0.00119808	0.0	0.0014	5008	,	,		14604	0.0		0.005	False		,,,				2504	0.0				p.D1335D		Atlas-SNP	.											.	OBSL1	120	.	0			c.C4005T						PASS	.	G	,	4,4268		0,4,2132	16	20	19		4005,4005	-1.8	1	2	dbSNP_134	19	33,8311		0,33,4139	no	coding-synonymous,coding-synonymous	OBSL1	NM_001173431.1,NM_015311.2	,	0,37,6271	AA,AG,GG		0.3955,0.0936,0.2933	,	1335/1544,1335/1897	220422126	37,12579	2136	4172	6308	SO:0001819	synonymous_variant	23363	exon12			CCCAGCGTCCCCG	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.4005C>T	2.37:g.220422126G>A		22	0	0		25	19	0.76	NM_001173431	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Silent	SNP	ENST00000404537.1	37	CCDS46520.1																																																																																			.	.	weak		0.692	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1			A	220422126	G	A	220422126	2	1	23	1	0	0	0	0	0	0	0	1	10822	1136	40	1		1	OBSL1	2	220422126	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	387749	220422126	22777247	122	7566											
COL4A4	1286	hgsc.bcm.edu	37	chr2	228004877	228004877	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ttggtctttacatcacttacCcgagaccccttttcaggaac	9	13	6	13	1	3	1	2	0	1	1	3	3	3	2	3	2	3	0	3	2	3	6			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:228004877C>T	ENST00000396625.3	-	4	399	c.192G>A	c.(190-192)cgG>cgA	p.R64R	COL4A4_ENST00000329662.7_Splice_Site_p.R64R	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	64	7S domain.				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)		CATCACTTACCCGAGACCCCT	0.393																																					p.R64R		Atlas-SNP	.											COL4A4,NS,lymphoid_neoplasm,-1,2	COL4A4	215	2	0			c.G192A						PASS	.						117	112	114					2																	228004877		1885	4096	5981	SO:0001630	splice_region_variant	1286	exon4			ACTTACCCGAGAC		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.192+1G>A	2.37:g.228004877C>T		172	0	0		142	81	0.570423	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Silent	SNP	ENST00000396625.3	37	CCDS42828.1																																																																																			.	.	none		0.393	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092	Silent	T	228004877	C	T	228004877	5	4	23	1	0	0	0	0	0	0	1	0	3695	637	22	2	5060	2	COL4A4	2	228004877	Splice_Site	SNP	C	TCGA-G8-6325-01A-11D-2210-10	7582751	228004877	15194496	123	7567											
ITM2C	81618	hgsc.bcm.edu	37	chr2	231742138	231742138	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggacctacctgccgcagacGtacatcatccaggaggagat	11	6	12	12	2	1	2	1	0	0	2	2	5	2	4	4	3	3	2	4	3	2	2	rs34910213	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:231742138G>A	ENST00000326427.6	+	5	711	c.585G>A	c.(583-585)acG>acA	p.T195T	ITM2C_ENST00000326407.6_Silent_p.T158T|ITM2C_ENST00000409704.2_Silent_p.T133T|ITM2C_ENST00000335005.6_Silent_p.T148T	NM_030926.4	NP_112188.1	Q9NQX7	ITM2C_HUMAN	integral membrane protein 2C	195	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)		TGCCGCAGACGTACATCATCC	0.607													G|||	23	0.00459265	0.0	0.0072	5008	,	,		18458	0.0		0.0179	False		,,,				2504	0.0				p.T195T		Atlas-SNP	.											.	ITM2C	17	.	0			c.G585A						PASS	.	G	,,	24,4382	29.9+/-59.1	0,24,2179	86	79	81		444,474,585	0.3	1	2	dbSNP_126	81	140,8460	69.7+/-132.2	1,138,4161	no	coding-synonymous,coding-synonymous,coding-synonymous	ITM2C	NM_001012514.1,NM_001012516.1,NM_030926.4	,,	1,162,6340	AA,AG,GG		1.6279,0.5447,1.261	,,	148/221,158/231,195/268	231742138	164,12842	2203	4300	6503	SO:0001819	synonymous_variant	81618	exon5			GCAGACGTACATC	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.585G>A	2.37:g.231742138G>A		164	0	0		181	84	0.464088	NM_030926	B3KPG4|Q4G0A8|Q53H84|Q6IAE7|Q86VK5|Q8N288|Q8TAW0|Q9BUP8	Silent	SNP	ENST00000326427.6	37	CCDS2479.1																																																																																			G|0.988;A|0.012	0.012	strong		0.607	ITM2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256954.2	NM_030926		A	231742138	G	A	231742138	2	1	23	1	0	0	0	0	0	0	0	1	7923	1132	40	1		1	ITM2C	2	231742138	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	3737261	231742138	11457235	124	7568											
HJURP	55355	hgsc.bcm.edu	37	chr2	234752863	234752863	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acactcaccgggggcaggcaCggcaggtgaggccagtgaag	10	3	17	11	2	1	2	1	2	0	0	1	2	1	2	2	6	0	3	2	6	1	0	rs140874442	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:234752863C>T	ENST00000411486.2	-	7	627	c.562G>A	c.(562-564)Gtg>Atg	p.V188M	HJURP_ENST00000434039.1_Intron|HJURP_ENST00000432087.1_Missense_Mutation_p.V134M|HJURP_ENST00000441687.1_Missense_Mutation_p.V103M	NM_018410.3	NP_060880.3	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	188					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)		GGGGCAGGCACGGCAGGTGAG	0.532													C|||	4	0.000798722	0.0008	0.0014	5008	,	,		21900	0.0		0.002	False		,,,				2504	0.0				p.V188M		Atlas-SNP	.											.	HJURP	72	.	0			c.G562A						PASS	.	C	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	101	98	99		562	-4.4	0	2	dbSNP_134	99	36,8564	24.0+/-70.4	0,36,4264	yes	missense	HJURP	NM_018410.3	21	0,37,6466	TT,TC,CC		0.4186,0.0227,0.2845	benign	188/749	234752863	37,12969	2203	4300	6503	SO:0001583	missense	55355	exon7			CAGGCACGGCAGG		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.562G>A	2.37:g.234752863C>T	ENSP00000414109:p.Val188Met	84	0	0		110	54	0.490909	NM_018410	A8IRH5|B4DWR0|B4DZV4|Q9BUT2|Q9NSL8	Missense_Mutation	SNP	ENST00000411486.2	37	CCDS33406.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	7.453	0.642993	0.14451	2.27E-4	0.004186	ENSG00000123485	ENST00000411486;ENST00000432087;ENST00000441687;ENST00000414924;ENST00000454020	T;T;T;T;T	0.32023	3.25;3.24;3.22;2.91;1.47	4.09	-4.38	0.03622	.	2.541040	0.01846	N	0.035607	T	0.09291	0.0229	N	0.00538	-1.39	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.002;0.002;0.001	T	0.27020	-1.0086	10	0.44086	T	0.13	0.4745	6.3534	0.21389	0.0:0.4492:0.1535:0.3973	.	103;134;188	Q8NCD3-3;Q8NCD3-2;Q8NCD3	.;.;HJURP_HUMAN	M	188;134;103;103;147	ENSP00000414109:V188M;ENSP00000407208:V134M;ENSP00000401944:V103M;ENSP00000393253:V103M;ENSP00000414051:V147M	ENSP00000414109:V188M	V	-	1	0	HJURP	234417602	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.680000	0.05197	-0.832000	0.04251	-1.085000	0.02201	GTG	C|0.998;T|0.002	0.002	strong		0.532	HJURP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130996.6	NM_018410		T	234752863	C	T	234752863	3	4	23	1	0	0	0	0	1	0	0	0	7198	536	19	1	1696	1	HJURP	2	234752863	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	3010725	234752863	8446510	125	7569											
SPP2	6694	hgsc.bcm.edu	37	chr2	234959642	234959642	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	agtgtacgactacgatccatCctccttaagggatgccctca	10	10	8	13	2	1	0	1	0	0	0	4	3	4	1	4	1	3	1	4	1	3	3	rs34347825	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:234959642C>T	ENST00000168148.3	+	2	201	c.113C>T	c.(112-114)tCc>tTc	p.S38F	SPP2_ENST00000373368.1_Missense_Mutation_p.S38F|SPP2_ENST00000492481.1_3'UTR	NM_006944.2	NP_008875.1	Q13103	SPP24_HUMAN	secreted phosphoprotein 2, 24kDa	38			S -> F (in dbSNP:rs34347825). {ECO:0000269|PubMed:15062857}.		bone remodeling (GO:0046849)|negative regulation of endopeptidase activity (GO:0010951)|protein complex assembly (GO:0006461)|skeletal system development (GO:0001501)	extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	endopeptidase inhibitor activity (GO:0004866)			breast(1)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)	12		Breast(86;0.0109)|Renal(207;0.019)|all_lung(227;0.13)|all_hematologic(139;0.182)		Epithelial(121;5.73e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000166)|Lung(119;0.00539)|LUSC - Lung squamous cell carcinoma(224;0.00846)		TACGATCCATCCTCCTTAAGG	0.512													C|||	17	0.00339457	0.0	0.0144	5008	,	,		19633	0.0		0.007	False		,,,				2504	0.0				p.S38F		Atlas-SNP	.											.	SPP2	35	.	0			c.C113T						PASS	.	C	PHE/SER	7,4399	12.9+/-30.5	0,7,2196	141	118	126		113	4.4	0.1	2	dbSNP_126	126	64,8536	38.8+/-94.9	0,64,4236	yes	missense	SPP2	NM_006944.2	155	0,71,6432	TT,TC,CC		0.7442,0.1589,0.5459	possibly-damaging	38/212	234959642	71,12935	2203	4300	6503	SO:0001583	missense	6694	exon2			ATCCATCCTCCTT		CCDS2511.1	2q37.1	2012-08-14	2002-08-29		ENSG00000072080	ENSG00000072080			11256	protein-coding gene	gene with protein product		602637	"secreted phosphoprotein 2, 24kD"			9533032	Standard	XM_005246102		Approved	SPP24	uc002vvk.1	Q13103	OTTHUMG00000059208	ENST00000168148.3:c.113C>T	2.37:g.234959642C>T	ENSP00000168148:p.Ser38Phe	176	0	0		184	91	0.494565	NM_006944	A4QMV3|Q3B892|Q546M5	Missense_Mutation	SNP	ENST00000168148.3	37	CCDS2511.1	9	0.004120879120879121	0	0.0	5	0.013812154696132596	0	0.0	4	0.005277044854881266	C	12.60	1.987057	0.35036	0.001589	0.007442	ENSG00000072080	ENST00000373368;ENST00000168148	T;T	0.50001	0.76;0.76	5.38	4.45	0.53987	.	1.384140	0.04525	N	0.385354	T	0.51568	0.1682	L	0.51422	1.61	0.09310	N	1	D	0.62365	0.991	P	0.55161	0.77	T	0.48163	-0.9059	10	0.66056	D	0.02	-4.2781	11.2458	0.48996	0.0:0.8155:0.1844:0.0	rs34347825;rs34347825	38	Q13103	SPP24_HUMAN	F	38	ENSP00000362466:S38F;ENSP00000168148:S38F	ENSP00000168148:S38F	S	+	2	0	SPP2	234624381	0.002000	0.14202	0.140000	0.22221	0.020000	0.10135	1.445000	0.35079	2.528000	0.85240	0.650000	0.86243	TCC	C|0.995;T|0.005	0.005	strong		0.512	SPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131313.3	NM_006944		T	234959642	C	T	234959642	3	4	23	1	0	0	0	0	1	0	0	0	15102	855	30	2	119	2	SPP2	2	234959642	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	206779	234959642	8239731	126	7570											
EDEM1	9695	hgsc.bcm.edu	37	chr3	5229643	5229643	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cgtctgaggagccccgacggCcccgcgtcgcccacctcggg	4	4	14	19	7	1	1	0	1	1	0	3	3	1	2	6	3	1	0	6	3	0	0	rs144177905	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:5229643C>T	ENST00000256497.4	+	1	286	c.153C>T	c.(151-153)ggC>ggT	p.G51G	AC026202.1_ENST00000600805.1_Missense_Mutation_p.A114T|AC026202.3_ENST00000439325.1_RNA|EDEM1_ENST00000445686.1_5'Flank	NM_014674.2	NP_055489.1	Q92611	EDEM1_HUMAN	ER degradation enhancer, mannosidase alpha-like 1	51					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)		GCCCCGACGGCCCCGCGTCGC	0.736													c|||	84	0.0167732	0.0008	0.013	5008	,	,		8316	0.001		0.0408	False		,,,				2504	0.0327				p.G51G		Atlas-SNP	.											.	EDEM1	45	.	0			c.C153T						PASS	.			18,3802		0,18,1892	4	5	5		153	3.5	0.3	3	dbSNP_134	5	227,7631		2,223,3704	no	coding-synonymous	EDEM1	NM_014674.2		2,241,5596	TT,TC,CC		2.8888,0.4712,2.098		51/658	5229643	245,11433	1910	3929	5839	SO:0001819	synonymous_variant	9695	exon1			CGACGGCCCCGCG	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.153C>T	3.37:g.5229643C>T		39	0	0		21	15	0.714286	NM_014674	A8K9C8|B4DXP3	Silent	SNP	ENST00000256497.4	37	CCDS33686.1																																																																																			C|0.985;T|0.015	0.015	strong		0.736	EDEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337566.2	NM_014674		T	5229643	C	T	5229643	2	4	23	1	0	0	0	0	0	0	0	1	4913	726	26	2		2	EDEM1	3	5229643	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10		5229643	192792787	127	7571											
IL17RC	84818	hgsc.bcm.edu	37	chr3	9970062	9970062	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcagagctggctgctggaCgcaccgtgctcgctgcccgc	4	7	14	16	4	0	1	0	0	0	1	1	2	0	2	2	2	5	7	2	2	0	0	rs151110374	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:9970062C>T	ENST00000295981.3	+	11	1382	c.1164C>T	c.(1162-1164)gaC>gaT	p.D388D	IL17RC_ENST00000498214.1_3'UTR|IL17RC_ENST00000455057.1_Silent_p.D302D|IL17RC_ENST00000413608.1_Silent_p.D317D|IL17RC_ENST00000403601.3_Silent_p.D317D|IL17RC_ENST00000416074.2_Silent_p.D173D|IL17RC_ENST00000383812.4_Silent_p.D302D	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	388					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						GGCTGCTGGACGCACCGTGCT	0.682													C|||	30	0.00599042	0.0	0.0	5008	,	,		15079	0.0		0.0	False		,,,				2504	0.0307				p.D388D		Atlas-SNP	.											.	IL17RC	55	.	0			c.C1164T						PASS	.	C	,,,,,	3,4403	6.2+/-15.9	0,3,2200	30	36	34		951,951,906,906,951,1164	-7.9	0	3	dbSNP_134	34	6,8592	5.0+/-18.6	0,6,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IL17RC	NM_001203263.1,NM_001203264.1,NM_001203265.1,NM_032732.5,NM_153460.3,NM_153461.3	,,,,,	0,9,6493	TT,TC,CC		0.0698,0.0681,0.0692	,,,,,	317/708,317/691,302/689,302/706,317/721,388/792	9970062	9,12995	2203	4299	6502	SO:0001819	synonymous_variant	84818	exon11			GCTGGACGCACCG	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.1164C>T	3.37:g.9970062C>T		42	0	0		30	10	0.333333	NM_153461	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	Silent	SNP	ENST00000295981.3	37	CCDS2590.1																																																																																			C|0.999;T|0.001	0.001	strong		0.682	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732		T	9970062	C	T	9970062	2	4	23	1	0	0	0	0	0	0	0	1	7650	535	19	1		1	IL17RC	3	9970062	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	4740419	9970062	188052368	128	7572											
C3orf19	51244	hgsc.bcm.edu	37	chr3	14712433	14712433	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggatactggtcgaagaggcAgtcagatctccgggctgaga	10	8	15	8	2	2	3	1	1	1	3	4	6	2	4	1	4	1	2	1	4	2	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:14712433A>G	ENST00000383794.3	+	11	1209	c.1136A>G	c.(1135-1137)cAg>cGg	p.Q379R	CCDC174_ENST00000303688.7_Missense_Mutation_p.Q303R|CCDC174_ENST00000476763.1_3'UTR	NM_016474.4	NP_057558.3	Q6PII3	CC174_HUMAN	coiled-coil domain containing 174	379						cytoplasm (GO:0005737)|nucleus (GO:0005634)											TCGAAGAGGCAGTCAGATCTC	0.423																																					p.Q379R		Atlas-SNP	.											.	.	.	.	0			c.A1136G						PASS	.						44	42	42					3																	14712433		2203	4300	6503	SO:0001583	missense	51244	exon11			AGAGGCAGTCAGA	AF151046	CCDS2620.2	3p25.1	2012-09-20	2012-09-20	2012-09-20	ENSG00000154781	ENSG00000154781			28033	protein-coding gene	gene with protein product			"chromosome 3 open reading frame 19"	C3orf19		11042152	Standard	NM_016474		Approved	FLJ33839	uc003byw.3	Q6PII3	OTTHUMG00000129837	ENST00000383794.3:c.1136A>G	3.37:g.14712433A>G	ENSP00000373304:p.Gln379Arg	165	0	0		206	91	0.441748	NM_016474	Q96CS5	Missense_Mutation	SNP	ENST00000383794.3	37	CCDS2620.2	.	.	.	.	.	.	.	.	.	.	A	10.78	1.447406	0.25987	.	.	ENSG00000154781	ENST00000383794;ENST00000303688;ENST00000285042	T;T	0.41065	1.01;1.07	5.38	5.38	0.77491	.	0.056905	0.64402	D	0.000002	T	0.28499	0.0705	L	0.43923	1.385	0.24589	N	0.993836	B	0.06786	0.001	B	0.06405	0.002	T	0.22173	-1.0224	10	0.11794	T	0.64	-35.5946	4.9429	0.13975	0.751:0.0:0.0857:0.1633	.	379	Q6PII3	CC019_HUMAN	R	379;303;206	ENSP00000373304:Q379R;ENSP00000302344:Q303R	ENSP00000285042:Q206R	Q	+	2	0	C3orf19	14687437	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.611000	0.54132	2.042000	0.60477	0.482000	0.46254	CAG	.	.	none		0.423	CCDC174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252077.2	NM_016474		G	14712433	A	G	14712433	3	3	23	1	0	0	0	0	1	0	0	0	2214	188	7	3	1178	3	C3orf19	3	14712433	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	4742371	14712433	183309997	129	7573											
FGD5	152273	hgsc.bcm.edu	37	chr3	14860968	14860968	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctgctccgggtgcaggagcGctgagcagggagggtgagga	7	5	21	8	2	0	2	0	2	0	0	1	5	1	5	1	5	4	5	1	5	0	0			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:14860968G>A	ENST00000285046.5	+	1	500	c.390G>A	c.(388-390)gcG>gcA	p.A130A	FGD5_ENST00000543601.1_De_novo_Start_InFrame	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	130	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						GTGCAGGAGCGCTGAGCAGGG	0.627																																					p.A130A		Atlas-SNP	.											FGD5_ENST00000285046,NS,carcinoma,+1,1	FGD5	248	1	0			c.G390A						PASS	.						19	22	22					3																	14860968		692	1591	2283	SO:0001819	synonymous_variant	152273	exon1			AGGAGCGCTGAGC	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.390G>A	3.37:g.14860968G>A		212	0	0		293	126	0.430034	NM_152536	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Silent	SNP	ENST00000285046.5	37	CCDS46767.1																																																																																			.	.	none		0.627	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536		A	14860968	G	A	14860968	2	1	23	1	0	0	0	0	0	0	0	1	5844	1074	38	1		1	FGD5	3	14860968	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	148535	14860968	183161462	130	7574											
FGD5	152273	hgsc.bcm.edu	37	chr3	14861665	14861665	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttttgcagcgagagctgtTctcctctttctgaatcagcg	6	15	9	11	2	4	2	1	1	3	1	5	3	4	2	1	0	4	3	1	0	1	4			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:14861665T>C	ENST00000285046.5	+	1	1197	c.1087T>C	c.(1087-1089)Tct>Cct	p.S363P	FGD5_ENST00000543601.1_Missense_Mutation_p.S122P	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	363					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						CGAGAGCTGTTCTCCTCTTTC	0.532																																					p.S363P		Atlas-SNP	.											.	FGD5	248	.	0			c.T1087C						PASS	.						59	60	59					3																	14861665		1909	4138	6047	SO:0001583	missense	152273	exon1			AGCTGTTCTCCTC	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.1087T>C	3.37:g.14861665T>C	ENSP00000285046:p.Ser363Pro	115	0	0		149	6	0.0402685	NM_152536	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Missense_Mutation	SNP	ENST00000285046.5	37	CCDS46767.1	.	.	.	.	.	.	.	.	.	.	T	10.62	1.401385	0.25291	.	.	ENSG00000154783	ENST00000285046;ENST00000543601	T;T	0.76316	-1.01;-0.85	5.34	-3.2	0.05156	.	0.543869	0.16888	N	0.195436	T	0.53883	0.1824	N	0.20986	0.625	0.09310	N	1	B;B	0.10296	0.003;0.001	B;B	0.08055	0.003;0.002	T	0.30475	-0.9977	10	0.38643	T	0.18	-0.7487	1.4964	0.02467	0.1367:0.2613:0.302:0.3	.	122;363	B7ZM68;Q6ZNL6	.;FGD5_HUMAN	P	363;122	ENSP00000285046:S363P;ENSP00000445949:S122P	ENSP00000285046:S363P	S	+	1	0	FGD5	14836669	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.262000	0.08682	-0.905000	0.03871	-0.250000	0.11733	TCT	.	.	none		0.532	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536		C	14861665	T	C	14861665	3	2	23	1	0	0	0	0	1	0	0	0	5844	1783	62	3	1089	3	FGD5	3	14861665	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	697	14861665	183160765	131	7575											
SH3BP5	9467	hgsc.bcm.edu	37	chr3	15298590	15298590	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttcagacacaaagttgctaCagctgtcatcttcaaaggcc	12	10	7	12	0	4	1	3	0	1	1	4	1	4	1	1	1	3	3	1	1	3	4	rs149397155	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:15298590C>T	ENST00000383791.3	-	8	1140	c.920G>A	c.(919-921)tGt>tAt	p.C307Y	SH3BP5-AS1_ENST00000420195.1_RNA|SH3BP5-AS1_ENST00000413977.1_RNA|SH3BP5_ENST00000426925.1_Missense_Mutation_p.C150Y|SH3BP5_ENST00000408919.3_Missense_Mutation_p.C150Y|SH3BP5_ENST00000253688.5_Missense_Mutation_p.C150Y|SH3BP5-AS1_ENST00000436602.1_RNA	NM_004844.4	NP_004835.2	O60239	3BP5_HUMAN	SH3-domain binding protein 5 (BTK-associated)	307	Ser-rich.				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						AAAGTTGCTACAGCTGTCATC	0.527													C|||	2	0.000399361	0.0	0.0	5008	,	,		21362	0.0		0.002	False		,,,				2504	0.0				p.C307Y		Atlas-SNP	.											.	SH3BP5	32	.	0			c.G920A						PASS	.	C	TYR/CYS,TYR/CYS	1,4405	2.1+/-5.4	0,1,2202	92	83	86		449,920	5.7	1	3	dbSNP_134	86	13,8587	9.8+/-36.6	0,13,4287	yes	missense,missense	SH3BP5	NM_001018009.2,NM_004844.3	194,194	0,14,6489	TT,TC,CC		0.1512,0.0227,0.1076	possibly-damaging,possibly-damaging	150/299,307/456	15298590	14,12992	2203	4300	6503	SO:0001583	missense	9467	exon8			TTGCTACAGCTGT	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.920G>A	3.37:g.15298590C>T	ENSP00000373301:p.Cys307Tyr	91	0	0		107	54	0.504673	NM_004844	B3KQW6|Q5JWV9	Missense_Mutation	SNP	ENST00000383791.3	37	CCDS2625.2	.	.	.	.	.	.	.	.	.	.	C	20.7	4.041622	0.75732	2.27E-4	0.001512	ENSG00000131370	ENST00000383791;ENST00000426925;ENST00000253688;ENST00000408919	.	.	.	5.65	5.65	0.86999	.	0.307183	0.40554	N	0.001077	T	0.47544	0.1451	L	0.58101	1.795	0.53005	D	0.999962	P	0.48640	0.913	B	0.37601	0.254	T	0.53215	-0.8470	9	0.48119	T	0.1	-27.3345	14.2486	0.66004	0.1492:0.8508:0.0:0.0	.	307	O60239	3BP5_HUMAN	Y	307;150;150;150	.	ENSP00000253688:C150Y	C	-	2	0	SH3BP5	15273594	1.000000	0.71417	0.998000	0.56505	0.966000	0.64601	5.359000	0.66074	2.683000	0.91414	0.456000	0.33151	TGT	C|0.999;T|0.001	0.001	strong		0.527	SH3BP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340740.2	NM_004844		T	15298590	C	T	15298590	3	4	23	1	0	0	0	0	1	0	0	0	14262	478	17	2	455	2	SH3BP5	3	15298590	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	436925	15298590	182723840	132	7576											
MLH1	4292	hgsc.bcm.edu	37	chr3	37053568	37053568	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtggacaatattcgctccAtctttggaaatgctgttagt	9	14	9	9	2	1	0	0	0	1	0	3	2	2	2	2	2	1	3	2	2	4	4	rs1799977	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:37053568A>G	ENST00000231790.2	+	8	871	c.655A>G	c.(655-657)Atc>Gtc	p.I219V	MLH1_ENST00000539477.1_5'UTR|MLH1_ENST00000536378.1_5'UTR|MLH1_ENST00000435176.1_Missense_Mutation_p.I121V|MLH1_ENST00000455445.2_5'UTR|MLH1_ENST00000458205.2_5'UTR	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	219			I -> V (common polymorphism; found in 37% of alleles; dbSNP:rs1799977). {ECO:0000269|PubMed:10375096, ECO:0000269|PubMed:10777691, ECO:0000269|PubMed:11754112, ECO:0000269|PubMed:12115348, ECO:0000269|PubMed:12200596, ECO:0000269|PubMed:12362047, ECO:0000269|PubMed:9032648, ECO:0000269|PubMed:9067757, ECO:0000269|PubMed:9087566, ECO:0000269|PubMed:9218993, ECO:0000269|PubMed:9833759, ECO:0000269|Ref.5}.		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.I219V(1)|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						TATTCGCTCCATCTTTGGAAA	0.368		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				A|||	649	0.129593	0.0386	0.1686	5008	,	,		18149	0.0258		0.325	False		,,,				2504	0.1309				p.I219V		Atlas-SNP	.	yes	Rec	yes	"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	3	3p21.3	4292	E.coli MutL homolog gene		"E, O"	MLH1,NS,carcinoma,0,1	MLH1	226	1	2	Substitution - Missense(1)|Whole gene deletion(1)	ovary(1)|prostate(1)	c.A655G	GRCh37	CM970958	MLH1	M	rs1799977	PASS	.	A	VAL/ILE,VAL/ILE,,	406,4000	199.4+/-223.0	27,352,1824	145	129	135	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	655,361,,	4.6	1	3	dbSNP_89	135	2754,5846	438.0+/-358.8	442,1870,1988	yes	missense,missense,utr-5,utr-5	MLH1	NM_000249.3,NM_001167617.1,NM_001167618.1,NM_001167619.1	29,29,,	469,2222,3812	GG,GA,AA		32.0233,9.2147,24.2965	benign,benign,,	219/757,121/659,,	37053568	3160,9846	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	CGCTCCATCTTTG	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.655A>G	3.37:g.37053568A>G	ENSP00000231790:p.Ile219Val	99	0	0		93	55	0.591398	NM_000249	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	37	CCDS2663.1	374	0.17124542124542125	28	0.056910569105691054	72	0.19889502762430938	16	0.027972027972027972	258	0.3403693931398417	A	14.01	2.408011	0.42715	0.092147	0.320233	ENSG00000076242	ENST00000231790;ENST00000436867;ENST00000537937;ENST00000383761;ENST00000435176	D;D	0.83591	-1.74;-1.74	5.76	4.61	0.57282	Ribosomal protein S5 domain 2-type fold (1);DNA mismatch repair protein, N-terminal (1);ATPase-like, ATP-binding domain (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);DNA mismatch repair protein, C-terminal (1);	0.113678	0.64402	D	0.000010	T	0.00012	0.0000	N	0.25992	0.78	0.09310	P	1.0	B;B;B	0.16603	0.018;0.018;0.018	B;B;B	0.26864	0.028;0.074;0.06	T	0.07424	-1.0773	9	0.12430	T	0.62	-17.9526	7.4844	0.27423	0.7886:0.0:0.2114:0.0	rs1799977;rs2229023;rs11541861;rs17809298;rs52803721;rs56722302;rs1799977	121;219;219	E9PCU2;Q53GX1;P40692	.;.;MLH1_HUMAN	V	219;185;185;83;121	ENSP00000231790:I219V;ENSP00000402564:I121V	ENSP00000231790:I219V	I	+	1	0	MLH1	37028572	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.446000	0.44908	2.209000	0.71365	0.533000	0.62120	ATC	A|0.799;G|0.201	0.201	strong		0.368	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249		G	37053568	A	G	37053568	3	3	23	1	0	0	0	0	1	0	0	0	9626	217	8	3	685	3	MLH1	3	37053568	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	21754978	37053568	160968862	133	7577											
MLH1	4292	hgsc.bcm.edu	37	chr3	37089130	37089130	+	Missense_Mutation	SNP	A	A	G																															ttgttgagtttctgaagaagAaggctgagatgcttgcagac																								rs587778949|rs35502531|rs35001569	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:37089130A>G	ENST00000231790.2	+	16	2068	c.1852A>G	c.(1852-1854)Aag>Gag	p.K618E	MLH1_ENST00000539477.1_Missense_Mutation_p.K377E|MLH1_ENST00000536378.1_Missense_Mutation_p.K377E|MLH1_ENST00000435176.1_Missense_Mutation_p.K520E|MLH1_ENST00000455445.2_Missense_Mutation_p.K377E|MLH1_ENST00000458205.2_Missense_Mutation_p.K377E	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	618	Interaction with EXO1.		K -> A (common polymorphism; requires 2 nucleotide substitutions; dbSNP:rs35502531). {ECO:0000269|PubMed:10598809, ECO:0000269|PubMed:10713887, ECO:0000269|PubMed:11726306, ECO:0000269|PubMed:11870161, ECO:0000269|PubMed:12200596, ECO:0000269|PubMed:12373605, ECO:0000269|PubMed:16083711, ECO:0000269|PubMed:18033691, ECO:0000269|PubMed:9311737}.|K -> R (in colorectal cancer; dbSNP:rs63750449). {ECO:0000269|PubMed:14504054}.|K -> T (in HNPCC2; type II). {ECO:0000269|PubMed:10573010, ECO:0000269|PubMed:11839723, ECO:0000269|PubMed:12095971, ECO:0000269|PubMed:7757073, ECO:0000269|PubMed:8872463}.|Missing (in HNPCC2). {ECO:0000269|PubMed:16451135}.		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.K618del(1)|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						TCTGAAGAAGAAGGCTGAGAT	0.428		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				A|||	16	0.00319489	0.0008	0.0072	5008	,	,		20450	0.0		0.0099	False		,,,				2504	0.0				p.K618E		Atlas-SNP	.	yes	Rec	yes	"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	3	3p21.3	4292	E.coli MutL homolog gene		"E, O"	MLH1,colon,carcinoma,-1,5	MLH1	226	5	2	Whole gene deletion(1)|Deletion - In frame(1)	ovary(1)|large_intestine(1)	c.A1852G	GRCh37	CD951778|CM973729|CM981294|CP035449|CX973308	MLH1	D|M|X	rs35001569	scavenged	.	A	GLU/LYS,GLU/LYS,GLU/LYS,GLU/LYS	9,4397	15.5+/-35.6	0,9,2194	158	161	160	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1852,1558,1129,1129	5.3	1	3	dbSNP_126	160	39,8561	16.6+/-54.9	0,39,4261	yes	missense,missense,missense,missense	MLH1	NM_000249.3,NM_001167617.1,NM_001167618.1,NM_001167619.1	56,56,56,56	0,48,6455	GG,GA,AA		0.4535,0.2043,0.3691	probably-damaging,probably-damaging,probably-damaging,probably-damaging	618/757,520/659,377/516,377/516	37089130	48,12958	2203	4300	6503	SO:0001583	missense	4292	exon16	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	AAGAAGAAGGCTG	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.1852A>G	3.37:g.37089130A>G	ENSP00000231790:p.Lys618Glu	131	1	0.00763359		134	80	0.597015	NM_000249	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	37	CCDS2663.1	9	0.004120879120879121	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	4	0.005277044854881266	A	24.4	4.530975	0.85706	0.002043	0.004535	ENSG00000076242	ENST00000231790;ENST00000383761;ENST00000458205;ENST00000539477;ENST00000455445;ENST00000435176;ENST00000536378	D;D;D;D;D;D	0.94613	-3.47;-3.47;-3.47;-3.47;-3.47;-3.47	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	D	0.96583	0.8885	M	0.91406	3.205	0.58432	D	0.999999	D;D;D;D	0.76494	0.999;0.993;0.999;0.993	D;P;D;P	0.64042	0.921;0.779;0.921;0.868	D	0.95740	0.8782	10	0.66056	D	0.02	-23.9591	15.372	0.74573	1.0:0.0:0.0:0.0	rs35001569	520;618;618;618	E9PCU2;B2R6K0;Q53GX1;P40692	.;.;.;MLH1_HUMAN	E	618;482;377;377;377;520;377	ENSP00000231790:K618E;ENSP00000402667:K377E;ENSP00000443665:K377E;ENSP00000398272:K377E;ENSP00000402564:K520E;ENSP00000444286:K377E	ENSP00000231790:K618E	K	+	1	0	MLH1	37064134	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.070000	0.76763	2.044000	0.60594	0.477000	0.44152	AAG	.	.	alt		0.428	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249		G	37089130	A	G	37089130	3	3	23	1	0	0	0	0	1	0	0	0	9626	247	9	3	1914	3	MLH1	3	37089130	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	35562	37089130	160933300	134	7578	98	2									
MLH1	4292	hgsc.bcm.edu	37	chr3	37089131	37089131	+	Missense_Mutation	SNP	A	A	C																															tgttgagtttctgaagaagaAggctgagatgcttgcagact																								rs587778949|rs63749986|rs35502531|rs63750449	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:37089131A>C	ENST00000231790.2	+	16	2069	c.1853A>C	c.(1852-1854)aAg>aCg	p.K618T	MLH1_ENST00000539477.1_Missense_Mutation_p.K377T|MLH1_ENST00000536378.1_Missense_Mutation_p.K377T|MLH1_ENST00000435176.1_Missense_Mutation_p.K520T|MLH1_ENST00000455445.2_Missense_Mutation_p.K377T|MLH1_ENST00000458205.2_Missense_Mutation_p.K377T	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	618	Interaction with EXO1.		K -> A (common polymorphism; requires 2 nucleotide substitutions; dbSNP:rs35502531). {ECO:0000269|PubMed:10598809, ECO:0000269|PubMed:10713887, ECO:0000269|PubMed:11726306, ECO:0000269|PubMed:11870161, ECO:0000269|PubMed:12200596, ECO:0000269|PubMed:12373605, ECO:0000269|PubMed:16083711, ECO:0000269|PubMed:18033691, ECO:0000269|PubMed:9311737}.|K -> R (in colorectal cancer; dbSNP:rs63750449). {ECO:0000269|PubMed:14504054}.|K -> T (in HNPCC2; type II). {ECO:0000269|PubMed:10573010, ECO:0000269|PubMed:11839723, ECO:0000269|PubMed:12095971, ECO:0000269|PubMed:7757073, ECO:0000269|PubMed:8872463}.|Missing (in HNPCC2). {ECO:0000269|PubMed:16451135}.		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.K618del(1)|p.0?(1)|p.K618T(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						CTGAAGAAGAAGGCTGAGATG	0.428		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				A|||	16	0.00319489	0.0008	0.0072	5008	,	,		20491	0.0		0.0099	False		,,,				2504	0.0				p.K618T		Atlas-SNP	.	yes	Rec	yes	"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	3	3p21.3	4292	E.coli MutL homolog gene		"E, O"	MLH1,colon,carcinoma,0,5	MLH1	226	5	3	Substitution - Missense(1)|Whole gene deletion(1)|Deletion - In frame(1)	large_intestine(2)|ovary(1)	c.A1853C	GRCh37	CM950808	MLH1	M	rs63750449	PASS	.	A	THR/LYS,THR/LYS,THR/LYS,THR/LYS	9,4397	15.5+/-35.6	0,9,2194	158	161	160	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1853,1559,1130,1130	5.3	1	3	dbSNP_130	160	40,8560	22.2+/-67.0	0,40,4260	yes	missense,missense,missense,missense	MLH1	NM_000249.3,NM_001167617.1,NM_001167618.1,NM_001167619.1	78,78,78,78	0,49,6454	CC,CA,AA		0.4651,0.2043,0.3767	probably-damaging,probably-damaging,probably-damaging,probably-damaging	618/757,520/659,377/516,377/516	37089131	49,12957	2203	4300	6503	SO:0001583	missense	4292	exon16	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	AGAAGAAGGCTGA	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.1853A>C	3.37:g.37089131A>C	ENSP00000231790:p.Lys618Thr	130	0	0		134	80	0.597015	NM_000249	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	37	CCDS2663.1	9	0.004120879120879121	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	4	0.005277044854881266	A	23.0	4.366099	0.82463	0.002043	0.004651	ENSG00000076242	ENST00000231790;ENST00000383761;ENST00000458205;ENST00000539477;ENST00000455445;ENST00000435176;ENST00000536378	D;D;D;D;D;D	0.94650	-3.48;-3.48;-3.48;-3.48;-3.48;-3.48	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	D	0.96430	0.8835	M	0.87097	2.86	0.80722	D	1	D;D;D;D	0.76494	0.999;0.997;0.999;0.997	D;D;D;D	0.73708	0.981;0.968;0.981;0.975	D	0.95622	0.8682	10	0.66056	D	0.02	-23.9591	15.372	0.74573	1.0:0.0:0.0:0.0	rs63750449	520;618;618;618	E9PCU2;B2R6K0;Q53GX1;P40692	.;.;.;MLH1_HUMAN	T	618;482;377;377;377;520;377	ENSP00000231790:K618T;ENSP00000402667:K377T;ENSP00000443665:K377T;ENSP00000398272:K377T;ENSP00000402564:K520T;ENSP00000444286:K377T	ENSP00000231790:K618T	K	+	2	0	MLH1	37064135	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.339000	0.79282	2.044000	0.60594	0.477000	0.44152	AAG	A|0.995;C|0.005	0.005	strong		0.428	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249		C	37089131	A	C	37089131	3	2	23	1	0	0	0	0	1	0	0	0	9626	72	3	5	1915	5	MLH1	3	37089131	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	1	37089131	160933299	135	7579	98	2									
ITGA9	3680	hgsc.bcm.edu	37	chr3	37860417	37860417	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cgaaggtacaaagaaattatCgaagctgagaagaaccggaa	19	5	11	6	3	0	3	0	1	0	3	1	7	0	4	1	2	3	2	1	2	9	2	rs142961075		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:37860417C>T	ENST00000264741.5	+	28	3301	c.3045C>T	c.(3043-3045)atC>atT	p.I1015I	AC093415.2_ENST00000420870.1_RNA|AC093415.2_ENST00000594579.1_RNA|AC093415.2_ENST00000430620.1_RNA|AC093415.2_ENST00000429532.1_RNA|AC093415.2_ENST00000366441.2_RNA|AC093415.2_ENST00000457661.1_RNA|AC093415.2_ENST00000608505.1_RNA|AC093415.2_ENST00000445429.1_RNA|AC093415.2_ENST00000438136.1_RNA|AC093415.2_ENST00000450990.1_RNA	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	1015					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)		AAGAAATTATCGAAGCTGAGA	0.473													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18335	0.0		0.0	False		,,,				2504	0.0				p.I1015I		Atlas-SNP	.											.	ITGA9	98	.	0			c.C3045T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	67	68	68		3045	-8.5	0.7	3	dbSNP_134	68	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	ITGA9	NM_002207.2		0,16,6487	TT,TC,CC		0.1628,0.0454,0.123		1015/1036	37860417	16,12990	2203	4300	6503	SO:0001819	synonymous_variant	3680	exon28			AATTATCGAAGCT	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.3045C>T	3.37:g.37860417C>T		148	0	0		144	82	0.569444	NM_002207	Q14638	Silent	SNP	ENST00000264741.5	37	CCDS2669.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	8.284	0.816181	0.16607	4.54E-4	0.001628	ENSG00000144668	ENST00000411817	.	.	.	6.17	-8.54	0.00912	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	21.0516	0.99944	0.0:0.7126:0.0:0.2874	.	.	.	.	X	49	.	.	R	+	1	2	ITGA9	37835421	0.027000	0.19231	0.654000	0.29608	0.922000	0.55478	-0.950000	0.03889	-1.656000	0.01495	-0.794000	0.03295	CGA	C|0.999;T|0.001	0.001	strong		0.473	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207		T	37860417	C	T	37860417	2	4	23	1	0	0	0	0	0	0	0	1	7892	874	31	1		1	ITGA9	3	37860417	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	771286	37860417	160162013	136	7580											
XIRP1	165904	hgsc.bcm.edu	37	chr3	39228774	39228774	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aacttgtggacagaacccgcGgggatggacccagcgattac	11	6	13	11	3	0	1	0	0	0	1	0	5	0	4	2	4	4	0	2	4	3	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:39228774G>A	ENST00000340369.3	-	2	2391	c.2163C>T	c.(2161-2163)ccC>ccT	p.P721P	XIRP1_ENST00000396251.1_Silent_p.P721P|XIRP1_ENST00000421646.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	721					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)		CAGAACCCGCGGGGATGGACC	0.582																																					p.P721P		Atlas-SNP	.											.	XIRP1	173	.	0			c.C2163T						PASS	.						52	55	54					3																	39228774		2203	4300	6503	SO:0001819	synonymous_variant	165904	exon2			ACCCGCGGGGATG	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.2163C>T	3.37:g.39228774G>A		115	0	0		105	39	0.371429	NM_001198621	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Silent	SNP	ENST00000340369.3	37	CCDS2683.1																																																																																			.	.	none		0.582	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522		A	39228774	G	A	39228774	2	1	23	1	0	0	0	0	0	0	0	1	17444	1103	39	1		1	XIRP1	3	39228774	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1368357	39228774	158793656	137	7581											
ENTPD3	956	hgsc.bcm.edu	37	chr3	40453432	40453432	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccattcacctgggagccaCggctgggatgcgcttgctga	6	8	13	14	2	1	1	1	1	0	0	1	3	1	3	4	3	3	3	4	3	0	2	rs377644776		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:40453432C>T	ENST00000301825.3	+	5	534	c.416C>T	c.(415-417)aCg>aTg	p.T139M	ENTPD3-AS1_ENST00000425156.1_RNA|ENTPD3-AS1_ENST00000452768.1_RNA|ENTPD3-AS1_ENST00000439293.1_RNA|ENTPD3_ENST00000445129.1_Missense_Mutation_p.T139M|ENTPD3_ENST00000456402.1_Missense_Mutation_p.T139M	NM_001248.2	NP_001239.2	O75355	ENTP3_HUMAN	ectonucleoside triphosphate diphosphohydrolase 3	139					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)		CTGGGAGCCACGGCTGGGATG	0.517													C|||	1	0.000199681	0.0	0.0	5008	,	,		15474	0.0		0.0	False		,,,				2504	0.001				p.T139M		Atlas-SNP	.											.	ENTPD3	48	.	0			c.C416T						PASS	.	C	MET/THR	1,4405	2.1+/-5.4	0,1,2202	60	49	52		416	5.6	1	3		52	1,8599	1.2+/-3.3	0,1,4299	no	missense	ENTPD3	NM_001248.2	81	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging	139/530	40453432	2,13004	2203	4300	6503	SO:0001583	missense	956	exon5			GAGCCACGGCTGG	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.416C>T	3.37:g.40453432C>T	ENSP00000301825:p.Thr139Met	40	0	0		38	27	0.710526	NM_001248	B2R8D0|G5E9N0|O60495|Q8N6K2	Missense_Mutation	SNP	ENST00000301825.3	37	CCDS2691.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.653329	0.88056	2.27E-4	1.16E-4	ENSG00000168032	ENST00000301825;ENST00000456402;ENST00000445129	T;T;T	0.35421	1.31;1.31;1.31	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.72407	0.3456	H	0.95437	3.67	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80542	-0.1336	10	0.87932	D	0	-14.6669	17.579	0.87960	0.0:1.0:0.0:0.0	.	139	O75355	ENTP3_HUMAN	M	139	ENSP00000301825:T139M;ENSP00000401565:T139M;ENSP00000404671:T139M	ENSP00000301825:T139M	T	+	2	0	ENTPD3	40428436	1.000000	0.71417	0.984000	0.44739	0.875000	0.50365	6.934000	0.75880	2.832000	0.97577	0.655000	0.94253	ACG	.	.	weak		0.517	ENTPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254179.2	NM_001248		T	40453432	C	T	40453432	3	4	23	1	0	0	0	0	1	0	0	0	5142	536	19	1	430	1	ENTPD3	3	40453432	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1224658	40453432	157568998	138	7582											
ZNF621	285268	hgsc.bcm.edu	37	chr3	40574395	40574395	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatcctgttctgcttcagcCgtagctgtgccttcactgac	5	13	10	13	1	3	1	2	1	1	0	4	2	4	2	3	1	4	4	3	1	1	4	rs151057224		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:40574395C>T	ENST00000339296.5	+	5	1586	c.1134C>T	c.(1132-1134)gcC>gcT	p.A378A	ZNF621_ENST00000403205.2_Silent_p.A378A|ZNF621_ENST00000310898.1_Intron|ZNF621_ENST00000490457.1_Intron|ZNF621_ENST00000431278.1_Silent_p.A267A	NM_198484.3	NP_940886.1	Q6ZSS3	ZN621_HUMAN	zinc finger protein 621	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0515)|Kidney(284;0.0648)		ctgcttcagccgtagctgtgc	0.527													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19238	0.0		0.0	False		,,,				2504	0.0				p.A378A		Atlas-SNP	.											.	ZNF621	42	.	0			c.C1134T						PASS	.	C	,	3,4397		0,3,2197	102	72	82		1134,1134	-6.8	0	3	dbSNP_134	82	1,8595		0,1,4297	no	coding-synonymous,coding-synonymous	ZNF621	NM_001098414.1,NM_198484.3	,	0,4,6494	TT,TC,CC		0.0116,0.0682,0.0308	,	378/440,378/440	40574395	4,12992	2200	4298	6498	SO:0001819	synonymous_variant	285268	exon5			TTCAGCCGTAGCT	AK127181	CCDS2693.1, CCDS74920.1	3p21.33	2013-01-08			ENSG00000172888	ENSG00000172888		"Zinc fingers, C2H2-type", "-"	24787	protein-coding gene	gene with protein product							Standard	XM_005265079		Approved	FLJ45246	uc003ckm.2	Q6ZSS3	OTTHUMG00000131389	ENST00000339296.5:c.1134C>T	3.37:g.40574395C>T		216	0	0		162	55	0.339506	NM_001098414	Q14DC7|Q8TE91	Silent	SNP	ENST00000339296.5	37	CCDS2693.1																																																																																			C|1.000;T|0.000	0.000	strong		0.527	ZNF621-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254178.2	NM_198484		T	40574395	C	T	40574395	2	4	23	1	0	0	0	0	0	0	0	1	18060	639	23	1		1	ZNF621	3	40574395	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	120963	40574395	157448035	139	7583											
VIPR1	7433	hgsc.bcm.edu	37	chr3	42568935	42568935	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accggctacaccattggctaCggcctgtccctcgccaccct	6	8	8	19	3	0	0	0	0	0	0	2	0	1	0	6	3	2	2	6	3	2	3	rs201579976		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:42568935C>T	ENST00000325123.4	+	5	563	c.450C>T	c.(448-450)taC>taT	p.Y150Y	VIPR1_ENST00000433647.1_Silent_p.Y109Y|VIPR1_ENST00000543411.1_Silent_p.Y102Y|VIPR1-AS1_ENST00000593621.1_RNA|VIPR1-AS1_ENST00000602176.1_RNA|VIPR1_ENST00000473575.1_3'UTR|VIPR1-AS1_ENST00000593611.1_RNA|VIPR1_ENST00000438259.2_Intron|VIPR1-AS1_ENST00000601312.1_RNA|VIPR1-AS1_ENST00000600342.1_RNA|VIPR1-AS1_ENST00000596630.1_RNA|VIPR1-AS1_ENST00000598837.1_RNA|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	150					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)		CCATTGGCTACGGCCTGTCCC	0.602																																					p.Y150Y		Atlas-SNP	.											VIPR1,NS,carcinoma,0,1	VIPR1	45	1	0			c.C450T						PASS	.	T		2,4404	4.2+/-10.8	0,2,2201	118	105	110		450	4.1	1	3		110	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	VIPR1	NM_004624.3		0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231		150/458	42568935	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	7433	exon5			TGGCTACGGCCTG	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.450C>T	3.37:g.42568935C>T		74	0	0		53	35	0.660377	NM_004624	A5JUT9|B3KPV1|B4DEB5|B4DGI4|F5H1F5|G3V0I1|Q15871|Q6P2M6	Silent	SNP	ENST00000325123.4	37	CCDS2698.1																																																																																			C|0.999;T|0.001	0.001	strong		0.602	VIPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254728.4	NM_004624		T	42568935	C	T	42568935	2	4	23	1	0	0	0	0	0	0	0	1	17184	547	19	1		1	VIPR1	3	42568935	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1994540	42568935	155453495	140	7584											
WDR6	11180	hgsc.bcm.edu	37	chr3	49044932	49044932	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tatactcctcccagtgacggGtctggagtgcgtgggggacc	6	9	15	11	2	1	1	0	1	1	0	3	3	3	3	3	4	2	0	3	4	2	2	rs62262472	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:49044932G>T	ENST00000608424.1	+	1	107	c.68G>T	c.(67-69)gGt>gTt	p.G23V	WDR6_ENST00000395474.3_Missense_Mutation_p.G53V|WDR6_ENST00000489684.1_3'UTR|WDR6_ENST00000448293.1_5'Flank|WDR6_ENST00000415265.2_Missense_Mutation_p.G23V			Q9NNW5	WDR6_HUMAN	WD repeat domain 6	23					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)		CCAGTGACGGGTCTGGAGTGC	0.657													g|||	3	0.000599042	0.0	0.0	5008	,	,		15634	0.0		0.003	False		,,,				2504	0.0				p.G53V		Atlas-SNP	.											.	WDR6	79	.	0			c.G158T						PASS	.		VAL/GLY	9,4397	15.5+/-35.6	0,9,2194	48	43	45		158	4.1	1	3	dbSNP_129	45	42,8558	26.8+/-75.7	0,42,4258	yes	missense	WDR6	NM_018031.3	109	0,51,6452	TT,TG,GG		0.4884,0.2043,0.3921	probably-damaging	53/1152	49044932	51,12955	2203	4300	6503	SO:0001583	missense	11180	exon1			TGACGGGTCTGGA	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.68G>T	3.37:g.49044932G>T	ENSP00000477389:p.Gly23Val	169	0	0		162	80	0.493827	NM_018031	B4DHK2|Q3MIT1|Q9UF63	Missense_Mutation	SNP	ENST00000608424.1	37		1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	g	14.52	2.560336	0.45590	0.002043	0.004884	ENSG00000178252	ENST00000395474;ENST00000438660;ENST00000354294;ENST00000415265	T;T	0.69685	-0.34;-0.42	5.02	4.08	0.47627	.	0.245193	0.30930	N	0.008587	T	0.62889	0.2465	N	0.19112	0.55	0.80722	D	1	B;D	0.64830	0.002;0.994	B;P	0.56865	0.003;0.808	T	0.65619	-0.6124	10	0.59425	D	0.04	-10.7481	10.8606	0.46825	0.0:0.2887:0.7113:0.0	rs62262472	23;23	E9PBK6;B4DK45	.;.	V	53;23;23;23	ENSP00000378857:G53V;ENSP00000387692:G23V	ENSP00000346247:G23V	G	+	2	0	WDR6	49019936	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	1.989000	0.40707	2.505000	0.84491	0.645000	0.84053	GGT	G|0.997;T|0.003	0.003	strong		0.657	WDR6-024	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471652.1			T	49044932	G	T	49044932	3	4	23	1	0	0	0	0	1	0	0	0	17325	1261	44	4	160	4	WDR6	3	49044932	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	6475997	49044932	148977498	141	7585											
GNAT1	2779	hgsc.bcm.edu	37	chr3	50232262	50232262	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ttcctcgagctcaacatgcgGcgcgacgtgaaggagatcta	10	8	12	11	5	2	2	1	1	1	1	4	5	3	2	1	2	3	1	1	2	3	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:50232262G>T	ENST00000433068.1	+	8	983	c.927G>T	c.(925-927)cgG>cgT	p.R309R	GNAT1_ENST00000232461.3_Silent_p.R309R	NM_000172.3	NP_000163.2	P11488	GNAT1_HUMAN	guanine nucleotide binding protein (G protein), alpha transducing activity polypeptide 1	309					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)		TCAACATGCGGCGCGACGTGA	0.577											OREG0015580	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R309R		Atlas-SNP	.											.	GNAT1	39	.	0			c.G927T						PASS	.						91	73	79					3																	50232262		2203	4300	6503	SO:0001819	synonymous_variant	2779	exon8			CATGCGGCGCGAC		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.927G>T	3.37:g.50232262G>T		95	0	0	968	87	31	0.356322	NM_144499	Q4VBN2	Silent	SNP	ENST00000433068.1	37	CCDS2812.1																																																																																			.	.	none		0.577	GNAT1-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345957.1	NM_000172		T	50232262	G	T	50232262	2	4	23	1	0	0	0	0	0	0	0	1	6519	1190	42	4		4	GNAT1	3	50232262	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1187330	50232262	147790168	142	7586											
VPRBP	9730	hgsc.bcm.edu	37	chr3	51475454	51475454	+	Intron	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagaatgagtcgctgctcgaTagcaggagtcataggataaa	14	8	13	6	2	1	2	1	1	0	1	3	6	1	4	0	2	2	3	0	2	5	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:51475454T>C	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)		CGCTGCTCGATAGCAGGAGTC	0.433																																					p.I325V		Atlas-SNP	.											.	VPRBP	107	.	0			c.A973G						PASS	.						68	60	63					3																	51475454		1873	4112	5985	SO:0001627	intron_variant	9730	exon8			GCTCGATAGCAGG	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+300A>G	3.37:g.51475454T>C		123	0	0		145	68	0.468966	NM_014703	Q2YD74|Q8TBD9|Q9HCA1|Q9UG37	Missense_Mutation	SNP	ENST00000335891.5	37		.	.	.	.	.	.	.	.	.	.	T	9.759	1.169677	0.21621	.	.	ENSG00000145041	ENST00000504652	D	0.98684	-5.07	5.5	4.27	0.50696	Armadillo-type fold (1);	0.050174	0.85682	D	0.000000	D	0.97185	0.9080	N	0.19112	0.55	0.80722	D	1	P	0.38863	0.65	P	0.54140	0.743	D	0.95430	0.8515	10	0.19147	T	0.46	-17.7053	12.3368	0.55071	0.1262:0.0:0.0:0.8738	.	325	Q9Y4B6	VPRBP_HUMAN	V	325	ENSP00000421724:I325V	ENSP00000421724:I325V	I	-	1	0	VPRBP	51450494	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.890000	0.69774	2.209000	0.71365	0.533000	0.62120	ATC	.	.	none		0.433	VPRBP-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014703		C	51475454	T	C	51475454	1	2	23	0	1	0	0	0	0	0	0	0	17200	1406	49	3		3	VPRBP	3	51475454	Intron	SNP	T	TCGA-G8-6325-01A-11D-2210-10	1243192	51475454	146546976	143	7587											
CHDH	55349	hgsc.bcm.edu	37	chr3	53855738	53855738	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcagcattcccgatgccagaGagcatgagcagctgtggaga	11	7	13	10	1	1	3	1	1	0	2	2	6	2	3	2	1	5	4	2	1	0	1	rs35064726	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:53855738G>C	ENST00000315251.6	-	5	1358	c.921C>G	c.(919-921)ctC>ctG	p.L307L		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	307					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)	CGATGCCAGAGAGCATGAGCA	0.562													G|||	123	0.0245607	0.0023	0.0216	5008	,	,		19271	0.0		0.0527	False		,,,				2504	0.0532				p.L307L		Atlas-SNP	.											.	CHDH	34	.	0			c.C921G						PASS	.	G		50,4356	50.9+/-86.3	0,50,2153	142	126	131		921	-2.7	0.6	3	dbSNP_126	131	472,8128	138.7+/-195.5	17,438,3845	no	coding-synonymous	CHDH	NM_018397.4		17,488,5998	CC,CG,GG		5.4884,1.1348,4.0135		307/595	53855738	522,12484	2203	4300	6503	SO:0001819	synonymous_variant	55349	exon5			GCCAGAGAGCATG	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.921C>G	3.37:g.53855738G>C		77	0	0		98	42	0.428571	NM_018397	Q9NY17	Silent	SNP	ENST00000315251.6	37	CCDS2873.1																																																																																			G|0.958;C|0.042	0.042	strong		0.562	CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397		C	53855738	G	C	53855738	2	2	23	1	0	0	0	0	0	0	0	1	3335	929	33	4		4	CHDH	3	53855738	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	2380284	53855738	144166692	144	7588											
C3orf63	23272	hgsc.bcm.edu	37	chr3	56680943	56680943	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	taactgatacacttcaggccGaaaaatataggcatgcaaac	17	8	7	9	1	1	1	1	1	0	0	1	2	1	1	1	2	4	2	1	2	7	5			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:56680943G>A	ENST00000493960.2	-	14	1832	c.1822C>T	c.(1822-1824)Cgg>Tgg	p.R608W	FAM208A_ENST00000431842.2_Missense_Mutation_p.R212W|FAM208A_ENST00000355628.5_Missense_Mutation_p.R608W	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	608							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						ACTTCAGGCCGAAAAATATAG	0.308																																					p.R608W		Atlas-SNP	.											.	FAM208A	113	.	0			c.C1822T						PASS	.						33	34	34					3																	56680943		2199	4297	6496	SO:0001583	missense	23272	exon14			CAGGCCGAAAAAT	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.1822C>T	3.37:g.56680943G>A	ENSP00000417509:p.Arg608Trp	109	0	0		119	27	0.226891	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Missense_Mutation	SNP	ENST00000493960.2	37	CCDS46853.1	.	.	.	.	.	.	.	.	.	.	G	15.81	2.944599	0.53079	.	.	ENSG00000163946	ENST00000431842;ENST00000493960;ENST00000355628	T;T;T	0.12255	2.7;2.88;2.88	5.38	4.51	0.55191	.	1.076610	0.07180	N	0.853813	T	0.12433	0.0302	N	0.08118	0	0.26200	N	0.979465	D;D;D	0.71674	0.998;0.997;0.997	P;P;P	0.52856	0.711;0.533;0.648	T	0.21177	-1.0253	10	0.66056	D	0.02	1.8924	4.9438	0.13978	0.0785:0.2888:0.5061:0.1265	.	608;608;212	Q9UK61-3;Q9UK61-4;Q9UK61-2	.;.;.	W	212;608;608	ENSP00000399410:R212W;ENSP00000417509:R608W;ENSP00000347845:R608W	ENSP00000347845:R608W	R	-	1	2	C3orf63	56655983	0.528000	0.26314	0.955000	0.39395	0.975000	0.68041	1.045000	0.30341	1.505000	0.48720	-0.140000	0.14226	CGG	.	.	none		0.308	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224		A	56680943	G	A	56680943	3	1	23	1	0	0	0	0	1	0	0	0	2241	1057	37	1	3294	1	C3orf63	3	56680943	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	2825205	56680943	141341487	145	7589											
APPL1	26060	hgsc.bcm.edu	37	chr3	57293908	57293908	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agttatttattgtccgattcCttggttcaatggaggtgaaa	10	16	10	5	1	1	1	1	1	0	0	3	3	3	2	2	3	0	2	2	3	4	7			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:57293908C>A	ENST00000288266.3	+	17	1666	c.1519C>A	c.(1519-1521)Ctt>Att	p.L507I		NM_012096.2	NP_036228.1	Q9UKG1	DP13A_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1	507	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				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)		TGTCCGATTCCTTGGTTCAAT	0.318																																					p.L507I		Atlas-SNP	.											.	APPL1	59	.	0			c.C1519A						PASS	.						76	75	76					3																	57293908		2203	4300	6503	SO:0001583	missense	26060	exon17			CGATTCCTTGGTT	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.1519C>A	3.37:g.57293908C>A	ENSP00000288266:p.Leu507Ile	184	0	0		137	23	0.167883	NM_012096	Q9P2B9	Missense_Mutation	SNP	ENST00000288266.3	37	CCDS2882.1	.	.	.	.	.	.	.	.	.	.	C	32	5.114466	0.94339	.	.	ENSG00000157500	ENST00000288266	T	0.33216	1.42	5.43	5.43	0.79202	Phosphotyrosine interaction domain (2);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	T	0.60077	0.2241	M	0.77313	2.365	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.63287	-0.6671	10	0.87932	D	0	.	19.6173	0.95639	0.0:1.0:0.0:0.0	.	490;507	B4DQX8;Q9UKG1	.;DP13A_HUMAN	I	507	ENSP00000288266:L507I	ENSP00000288266:L507I	L	+	1	0	APPL1	57268948	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.729000	0.84864	2.712000	0.92718	0.557000	0.71058	CTT	.	.	none		0.318	APPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258196.2	NM_012096		A	57293908	C	A	57293908	3	1	23	1	0	0	0	0	1	0	0	0	817	681	24	4	1585	4	APPL1	3	57293908	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	612965	57293908	140728522	146	7590											
ACOX2	8309	hgsc.bcm.edu	37	chr3	58517520	58517520	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgggcctggaccagggcAtgggtggctgaccgtcccac	6	6	16	13	1	0	1	0	1	0	0	1	2	1	2	4	5	1	3	4	5	0	0	rs57216393	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:58517520A>G	ENST00000302819.5	-	6	894	c.603T>C	c.(601-603)caT>caC	p.H201H	ACOX2_ENST00000459701.2_Silent_p.H201H	NM_003500.3	NP_003491.1	Q99424	ACOX2_HUMAN	acyl-CoA oxidase 2, branched chain	201					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)		GGACCAGGGCATGGGTGGCTG	0.627													G|||	355	0.0708866	0.2262	0.0375	5008	,	,		18088	0.0		0.0189	False		,,,				2504	0.0112				p.H201H		Atlas-SNP	.											.	ACOX2	53	.	0			c.T603C						PASS	.	G		884,3522	741.6+/-411.3	92,700,1411	59	53	55		603	-9.4	0.1	3	dbSNP_129	55	184,8416	810.9+/-407.1	3,178,4119	no	coding-synonymous	ACOX2	NM_003500.3		95,878,5530	GG,GA,AA		2.1395,20.0635,8.2116		201/682	58517520	1068,11938	2203	4300	6503	SO:0001819	synonymous_variant	8309	exon6			CAGGGCATGGGTG	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.603T>C	3.37:g.58517520A>G		70	0	0		64	29	0.453125	NM_003500	A6NF16|B2R8U5	Silent	SNP	ENST00000302819.5	37	CCDS33775.1																																																																																			A|0.923;G|0.077	0.077	strong		0.627	ACOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353541.1			G	58517520	A	G	58517520	2	3	23	1	0	0	0	0	0	0	0	1	159	214	8	3		3	ACOX2	3	58517520	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	1223612	58517520	139504910	147	7591											
EPHA3	2042	hgsc.bcm.edu	37	chr3	89448610	89448610	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacgaacagccgcaagtttgAgtttgaaactagtccagact	13	9	10	9	2	0	3	0	2	0	1	1	5	1	3	2	0	3	3	2	0	4	3	rs150469112		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:89448610A>T	ENST00000336596.2	+	7	1799	c.1574A>T	c.(1573-1575)gAg>gTg	p.E525V	EPHA3_ENST00000452448.2_Missense_Mutation_p.E525V|EPHA3_ENST00000494014.1_Missense_Mutation_p.E525V	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	525	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		CGCAAGTTTGAGTTTGAAACT	0.448										TSP Lung(6;0.00050)																											p.E525V		Atlas-SNP	.											.	EPHA3	501	.	0			c.A1574T						PASS	.	A	VAL/GLU,VAL/GLU	0,4406		0,0,2203	106	98	101		1574,1574	5.5	1	3	dbSNP_134	101	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	EPHA3	NM_005233.5,NM_182644.2	121,121	0,1,6502	TT,TA,AA		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	525/984,525/540	89448610	1,13005	2203	4300	6503	SO:0001583	missense	2042	exon7			AGTTTGAGTTTGA	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.1574A>T	3.37:g.89448610A>T	ENSP00000337451:p.Glu525Val	93	0	0		58	33	0.568965	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.578556	0.86645	0.0	1.16E-4	ENSG00000044524	ENST00000336596;ENST00000452448;ENST00000494014	T;T;T	0.53423	0.62;0.62;0.62	5.53	5.53	0.82687	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.051723	0.85682	D	0.000000	T	0.61502	0.2352	M	0.67700	2.07	0.80722	D	1	B;D	0.53312	0.181;0.959	B;P	0.56088	0.134;0.791	T	0.62191	-0.6906	9	.	.	.	.	15.6643	0.77213	1.0:0.0:0.0:0.0	.	525;525	P29320;P29320-2	EPHA3_HUMAN;.	V	525	ENSP00000337451:E525V;ENSP00000399926:E525V;ENSP00000419190:E525V	.	E	+	2	0	EPHA3	89531300	1.000000	0.71417	1.000000	0.80357	0.617000	0.37484	9.339000	0.96797	2.107000	0.64212	0.460000	0.39030	GAG	A|1.000;T|0.000	0.000	weak		0.448	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		T	89448610	A	T	89448610	3	4	23	1	0	0	0	0	1	0	0	0	5170	304	11	5	1600	5	EPHA3	3	89448610	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	30931090	89448610	108573820	148	7592											
OR5H1	26341	hgsc.bcm.edu	37	chr3	97852291	97852291	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catctcttctctgtctctttAtactatggaccccttctctt	5	19	3	14	0	4	0	0	0	4	0	8	1	4	1	2	1	1	0	2	1	3	7	rs112819024	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:97852291A>G	ENST00000354565.2	+	1	750	c.750A>G	c.(748-750)ttA>ttG	p.L250L	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005338.1	NP_001005338.1	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H, 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)			breast(1)|endometrium(7)|kidney(8)|large_intestine(3)|lung(13)|ovary(1)|skin(1)	34						CTGTCTCTTTATACTATGGAC	0.418													A|||	18	0.00359425	0.0008	0.0029	5008	,	,		17560	0.0		0.0099	False		,,,				2504	0.0051				p.L250L		Atlas-SNP	.											OR5H1,NS,carcinoma,+2,1	OR5H1	71	1	0			c.A750G						PASS	.	A		15,4391	22.3+/-47.3	0,15,2188	123	133	130		750	-0.3	0.8	3	dbSNP_132	130	115,8483	60.2+/-122.0	3,109,4187	no	coding-synonymous	OR5H1	NM_001005338.1		3,124,6375	GG,GA,AA		1.3375,0.3404,0.9997		250/314	97852291	130,12874	2203	4299	6502	SO:0001819	synonymous_variant	26341	exon1			CTCTTTATACTAT	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.750A>G	3.37:g.97852291A>G		302	0	0		346	165	0.476879	NM_001005338		Silent	SNP	ENST00000354565.2	37	CCDS33797.1																																																																																			A|0.993;G|0.007	0.007	strong		0.418	OR5H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359100.2	NM_001005338		G	97852291	A	G	97852291	2	3	23	1	0	0	0	0	0	0	0	1	11168	446	16	3		3	OR5H1	3	97852291	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	8403681	97852291	100170139	149	7593											
MYH15	22989	hgsc.bcm.edu	37	chr3	108147510	108147510	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagatgcagaagttgtctcAaagtgcagagtggcctcttc	12	10	11	8	0	2	3	1	0	2	3	4	3	2	3	1	1	2	3	1	1	3	2	rs201473403	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:108147510A>G	ENST00000273353.3	-	28	3647	c.3591T>C	c.(3589-3591)ttT>ttC	p.F1197F		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1197						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						AAGTTGTCTCAAAGTGCAGAG	0.483													A|||	5	0.000998403	0.0	0.0014	5008	,	,		19235	0.0		0.004	False		,,,				2504	0.0				p.F1197F		Atlas-SNP	.											.	MYH15	223	.	0			c.T3591C						PASS	.	A		2,3922		0,2,1960	130	125	126		3591	-3.7	0.3	3		126	19,8307		0,19,4144	no	coding-synonymous	MYH15	NM_014981.1		0,21,6104	GG,GA,AA		0.2282,0.051,0.1714		1197/1947	108147510	21,12229	1962	4163	6125	SO:0001819	synonymous_variant	22989	exon28			TGTCTCAAAGTGC	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.3591T>C	3.37:g.108147510A>G		234	0	0		261	139	0.532567	NM_014981		Silent	SNP	ENST00000273353.3	37	CCDS43127.1																																																																																			A|0.999;G|0.001	0.001	strong		0.483	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		G	108147510	A	G	108147510	2	3	23	1	0	0	0	0	0	0	0	1	10043	127	5	3		3	MYH15	3	108147510	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	10295219	108147510	89874920	150	7594											
MYH15	22989	hgsc.bcm.edu	37	chr3	108163559	108163559	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tttgctttcagttcctccctCtgaaactctgatttctccaa	7	17	4	13	0	4	2	1	2	3	0	7	2	6	2	3	0	2	2	3	0	2	4	rs148022324	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:108163559C>T	ENST00000273353.3	-	23	2699	c.2643G>A	c.(2641-2643)caG>caA	p.Q881Q		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	881						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						GTTCCTCCCTCTGAAACTCTG	0.428													C|||	8	0.00159744	0.0	0.0014	5008	,	,		17597	0.0		0.003	False		,,,				2504	0.0041				p.Q881Q		Atlas-SNP	.											.	MYH15	223	.	0			c.G2643A						PASS	.	C		1,3779		0,1,1889	122	114	117		2643	2.1	0.2	3	dbSNP_134	117	16,8238		0,16,4111	no	coding-synonymous	MYH15	NM_014981.1		0,17,6000	TT,TC,CC		0.1938,0.0265,0.1413		881/1947	108163559	17,12017	1890	4127	6017	SO:0001819	synonymous_variant	22989	exon23			CTCCCTCTGAAAC	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.2643G>A	3.37:g.108163559C>T		277	1	0.00361011		247	106	0.42915	NM_014981		Silent	SNP	ENST00000273353.3	37	CCDS43127.1																																																																																			C|0.998;T|0.002	0.002	strong		0.428	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988		T	108163559	C	T	108163559	2	4	23	1	0	0	0	0	0	0	0	1	10043	912	32	2		2	MYH15	3	108163559	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	16049	108163559	89858871	151	7595											
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121413239	121413239	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctagagctttaacagttctcTccagagcactaattttctct	10	15	5	11	0	2	2	0	0	2	2	5	2	3	2	1	0	3	3	1	0	3	7	rs75383249	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:121413239T>G	ENST00000340645.5	-	13	6241	c.6116A>C	c.(6115-6117)gAg>gCg	p.E2039A	GOLGB1_ENST00000393667.3_Missense_Mutation_p.E2044A	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	2039					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)		AACAGTTCTCTCCAGAGCACT	0.368													T|||	9	0.00179712	0.0	0.0	5008	,	,		19970	0.0		0.0089	False		,,,				2504	0.0				p.E2044A		Atlas-SNP	.											.	GOLGB1	319	.	0			c.A6131C						PASS	.	T	ALA/GLU	6,4400	9.9+/-24.2	0,6,2197	109	110	110		6116	5.5	1	3	dbSNP_132	110	38,8560	25.1+/-72.6	0,38,4261	yes	missense	GOLGB1	NM_004487.3	107	0,44,6458	GG,GT,TT		0.442,0.1362,0.3384	probably-damaging	2039/3260	121413239	44,12960	2203	4299	6502	SO:0001583	missense	2804	exon13			GTTCTCTCCAGAG	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.6116A>C	3.37:g.121413239T>G	ENSP00000341848:p.Glu2039Ala	130	0	0		105	54	0.514286	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	9	0.004120879120879121	0	0.0	0	0.0	0	0.0	9	0.011873350923482849	T	9.851	1.193741	0.22037	0.001362	0.00442	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.20069	2.1;2.1	5.46	5.46	0.80206	.	0.000000	0.53938	D	0.000051	T	0.30885	0.0779	L	0.49640	1.575	0.34058	D	0.656894	D;D;P;D	0.71674	0.998;0.998;0.607;0.977	D;D;B;P	0.81914	0.995;0.995;0.255;0.69	T	0.45381	-0.9265	10	0.37606	T	0.19	.	13.5212	0.61569	0.0:0.0:0.0:1.0	.	1964;2044;2044;2039	F1T0J2;E7EP74;B2ZZ91;Q14789	.;.;.;GOGB1_HUMAN	A	2039;2044	ENSP00000341848:E2039A;ENSP00000377275:E2044A	ENSP00000341848:E2039A	E	-	2	0	GOLGB1	122895929	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	2.911000	0.48774	2.289000	0.77006	0.482000	0.46254	GAG	T|0.997;G|0.003	0.003	strong		0.368	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		G	121413239	T	G	121413239	3	3	23	1	0	0	0	0	1	0	0	0	6573	1551	54	5	3703	5	GOLGB1	3	121413239	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	13249680	121413239	76609191	152	7596											
PARP14	54625	hgsc.bcm.edu	37	chr3	122419210	122419210	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aattataagcgcattgaagtTgagaacaaagaagttcttca	17	11	8	5	1	2	3	1	2	1	2	2	4	2	3	0	0	2	3	0	0	7	6			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:122419210T>C	ENST00000474629.2	+	6	2075	c.1809T>C	c.(1807-1809)gtT>gtC	p.V603V		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	603					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)		GCATTGAAGTTGAGAACAAAG	0.393																																					p.V603V		Atlas-SNP	.											.	PARP14	242	.	0			c.T1809C						PASS	.						37	35	36					3																	122419210		1870	4093	5963	SO:0001819	synonymous_variant	54625	exon6			TGAAGTTGAGAAC	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.1809T>C	3.37:g.122419210T>C		74	0	0		72	16	0.222222	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Silent	SNP	ENST00000474629.2	37	CCDS46894.1																																																																																			.	.	none		0.393	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		C	122419210	T	C	122419210	2	2	23	1	0	0	0	0	0	0	0	1	11467	1799	63	3		3	PARP14	3	122419210	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	1005971	122419210	75603220	153	7597											
MYLK	4638	hgsc.bcm.edu	37	chr3	123332995	123332995	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccccttcaccttcctccatcGtttccacaatgagctctgct	6	13	4	18	1	2	1	1	1	1	0	6	1	5	1	6	0	2	3	6	0	1	3	rs200490629		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:123332995G>A	ENST00000475616.1	-	31	5701	c.5702C>T	c.(5701-5703)aCg>aTg	p.T1901M	MYLK_ENST00000354792.5_Missense_Mutation_p.T701M|MYLK-AS1_ENST00000470449.1_RNA|MYLK_ENST00000578202.1_Missense_Mutation_p.T140M|MYLK_ENST00000583087.1_Missense_Mutation_p.T141M|MYLK_ENST00000418370.2_Missense_Mutation_p.T141M|MYLK_ENST00000360772.3_Missense_Mutation_p.T1850M|MYLK_ENST00000346322.5_Missense_Mutation_p.T1832M|MYLK_ENST00000360304.3_Missense_Mutation_p.T1901M|MYLK-AS1_ENST00000485162.1_RNA|MYLK-AS1_ENST00000463408.1_RNA|MYLK_ENST00000359169.1_Missense_Mutation_p.T1850M			Q15746	MYLK_HUMAN	myosin light chain kinase	1901					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)		TTCCTCCATCGTTTCCACAAT	0.448													G|||	1	0.000199681	0.0	0.0	5008	,	,		19431	0.0		0.001	False		,,,				2504	0.0				p.T1901M		Atlas-SNP	.											.	MYLK	224	.	0			c.C5702T						PASS	.	G	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	0,4406		0,0,2203	171	177	175		5702,5495,5549,5342,419,422	5.3	1	3		175	1,8599		0,1,4299	yes	missense,missense,missense,missense,missense,missense	MYLK	NM_053025.3,NM_053026.3,NM_053027.3,NM_053028.3,NM_053031.2,NM_053032.2	81,81,81,81,81,81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	1901/1915,1832/1846,1850/1864,1781/1795,140/154,141/155	123332995	1,13005	2203	4300	6503	SO:0001583	missense	4638	exon34			TCCATCGTTTCCA	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.5702C>T	3.37:g.123332995G>A	ENSP00000418335:p.Thr1901Met	112	0	0		142	78	0.549296	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	37	CCDS46896.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	17.77	3.471882	0.63737	0.0	1.16E-4	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000418370;ENST00000346322;ENST00000354792;ENST00000475616	T;T;T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99;0.99;0.99	5.27	5.27	0.74061	.	.	.	.	.	T	0.42698	0.1214	N	0.08118	0	0.36368	D	0.86111	D;D;D;D;D;P	0.89917	1.0;0.999;1.0;1.0;1.0;0.889	D;D;D;D;D;B	0.74674	0.984;0.928;0.96;0.97;0.964;0.03	T	0.54227	-0.8325	9	0.52906	T	0.07	.	12.4119	0.55471	0.0761:0.0:0.9239:0.0	.	1900;1781;1850;1832;1901;213	Q15746-6;Q15746-4;Q15746-3;Q15746-2;Q15746;Q05D81	.;.;.;.;MYLK_HUMAN;.	M	1850;1901;1850;141;1832;701;1901	ENSP00000354004:T1850M;ENSP00000353452:T1901M;ENSP00000352088:T1850M;ENSP00000428967:T141M;ENSP00000320622:T1832M;ENSP00000346846:T701M;ENSP00000418335:T1901M	ENSP00000320622:T1832M	T	-	2	0	MYLK	124815685	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.648000	0.67930	2.732000	0.93576	0.650000	0.86243	ACG	G|1.000;A|0.000	0.000	strong		0.448	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025		A	123332995	G	A	123332995	3	1	23	1	0	0	0	0	1	0	0	0	10065	1145	40	1	46	1	MYLK	3	123332995	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	913785	123332995	74689435	154	7598											
KALRN	8997	hgsc.bcm.edu	37	chr3	123953756	123953756	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaataagacaggaagacctgCggaaactcgtgacgtatttg	14	8	12	7	3	0	3	0	1	0	2	1	6	0	5	1	2	2	1	1	2	5	3	rs144465315	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:123953756C>A	ENST00000240874.3	+	3	380	c.223C>A	c.(223-225)Cgg>Agg	p.R75R	KALRN_ENST00000360013.3_Silent_p.R75R|KALRN_ENST00000460856.1_Silent_p.R75R	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	75	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				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						GGAAGACCTGCGGAAACTCGT	0.582													C|||	4	0.000798722	0.0	0.0	5008	,	,		20662	0.0		0.002	False		,,,				2504	0.002				p.R75R		Atlas-SNP	.											.	KALRN	556	.	0			c.C223A						PASS	.		,	1,4405	2.1+/-5.4	0,1,2202	49	41	44		223,223	2.5	1	3	dbSNP_134	44	11,8587	7.1+/-27.0	0,11,4288	no	coding-synonymous,coding-synonymous	KALRN	NM_001024660.3,NM_003947.4	,	0,12,6490	AA,AC,CC		0.1279,0.0227,0.0923	,	75/2987,75/1664	123953756	12,12992	2203	4299	6502	SO:0001819	synonymous_variant	8997	exon3			GACCTGCGGAAAC	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.223C>A	3.37:g.123953756C>A		75	0	0		81	30	0.37037	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	37	CCDS3027.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	c	10.77	1.444443	0.25987	2.27E-4	0.001279	ENSG00000160145	ENST00000448253;ENST00000354186	.	.	.	5.49	2.54	0.30619	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.0069	0.64470	0.52:0.48:0.0:0.0	.	.	.	.	X	102;52	.	.	C	+	3	2	KALRN	125436446	1.000000	0.71417	0.999000	0.59377	0.941000	0.58515	1.511000	0.35801	0.672000	0.31204	0.651000	0.88453	TGC	C|0.999;A|0.001	0.001	strong		0.582	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		A	123953756	C	A	123953756	2	1	23	1	0	0	0	0	0	0	0	1	7984	759	27	4		4	KALRN	3	123953756	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	620761	123953756	74068674	155	7599											
UROC1	131669	hgsc.bcm.edu	37	chr3	126207049	126207049	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaccttcttaccagcccacGccccctccgttgtgaagggc	8	8	8	17	2	1	1	0	1	1	0	2	1	2	1	6	1	3	1	6	1	3	3	rs139120643	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:126207049G>A	ENST00000290868.2	-	18	1835	c.1782C>T	c.(1780-1782)ggC>ggT	p.G594G	UROC1_ENST00000383579.3_Silent_p.G654G	NM_144639.2	NP_653240.1	Q96N76	HUTU_HUMAN	urocanate hydratase 1	594					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)	p.G594G(1)		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)		ACCAGCCCACGCCCCCTCCGT	0.602													G|||	3	0.000599042	0.0	0.0014	5008	,	,		19645	0.0		0.001	False		,,,				2504	0.001				p.G654G		Atlas-SNP	.											UROC1,NS,carcinoma,0,1	UROC1	150	1	1	Substitution - coding silent(1)	lung(1)	c.C1962T						PASS	.	G	,	5,4401	9.9+/-24.2	0,5,2198	166	159	161		1962,1782	-3.2	1	3	dbSNP_134	161	19,8581	14.0+/-48.4	0,19,4281	no	coding-synonymous,coding-synonymous	UROC1	NM_001165974.1,NM_144639.2	,	0,24,6479	AA,AG,GG		0.2209,0.1135,0.1845	,	654/737,594/677	126207049	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	131669	exon19			GCCCACGCCCCCT	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.1782C>T	3.37:g.126207049G>A		114	0	0		136	71	0.522059	NM_001165974	E9PE13|Q14C64|Q68CJ7	Silent	SNP	ENST00000290868.2	37	CCDS3038.1																																																																																			G|0.999;A|0.001	0.001	strong		0.602	UROC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370325.2	NM_144639		A	126207049	G	A	126207049	2	1	23	1	0	0	0	0	0	0	0	1	17043	1074	38	1		1	UROC1	3	126207049	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	2253293	126207049	71815381	156	7600											
PLXND1	23129	hgsc.bcm.edu	37	chr3	129297255	129297255	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccaggggtgagagcagggTccgggggcagtcctgagggc	6	5	21	9	1	0	2	0	2	0	1	2	3	2	2	3	6	2	2	3	6	0	0	rs112755880	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:129297255T>C	ENST00000324093.4	-	9	2441	c.2263A>G	c.(2263-2265)Acc>Gcc	p.T755A	PLXND1_ENST00000393239.1_Missense_Mutation_p.T755A	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	755					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						GAGAGCAGGGTCCGGGGGCAG	0.617																																					p.T755A	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.A2263G						PASS	.	T	ALA/THR	5,4399		0,5,2197	32	36	35		2263	4.6	1	3	dbSNP_132	35	30,8566		0,30,4268	yes	missense	PLXND1	NM_015103.2	58	0,35,6465	CC,CT,TT		0.349,0.1135,0.2692	benign	755/1926	129297255	35,12965	2202	4298	6500	SO:0001583	missense	23129	exon9			GCAGGGTCCGGGG	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.2263A>G	3.37:g.129297255T>C	ENSP00000317128:p.Thr755Ala	125	0	0		133	64	0.481203	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	37	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	T	10.99	1.505945	0.26949	0.001135	0.00349	ENSG00000004399	ENST00000324093;ENST00000393239	T;T	0.33654	1.45;1.4	4.62	4.62	0.57501	.	0.643158	0.13899	N	0.355056	T	0.23572	0.0570	N	0.14661	0.345	0.23581	N	0.997361	B	0.12630	0.006	B	0.06405	0.002	T	0.16600	-1.0397	10	0.87932	D	0	.	10.4209	0.44350	0.0:0.0:0.0:1.0	.	755	Q9Y4D7	PLXD1_HUMAN	A	755	ENSP00000317128:T755A;ENSP00000376931:T755A	ENSP00000317128:T755A	T	-	1	0	PLXND1	130779945	1.000000	0.71417	1.000000	0.80357	0.483000	0.33249	2.729000	0.47327	1.708000	0.51301	0.459000	0.35465	ACC	T|0.997;C|0.003	0.003	strong		0.617	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103		C	129297255	T	C	129297255	3	2	23	1	0	0	0	0	1	0	0	0	12136	1667	58	3	3626	3	PLXND1	3	129297255	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	3090206	129297255	68725175	157	7601											
DNAJC13	23317	hgsc.bcm.edu	37	chr3	132221139	132221139	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ttttattctctcagagtattCcccgcgtagctgctcttggg	5	16	9	11	2	3	1	1	0	2	1	5	1	4	1	2	1	2	4	2	1	3	7	rs55825559	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:132221139C>T	ENST00000260818.6	+	40	4791	c.4543C>T	c.(4543-4545)Ccc>Tcc	p.P1515S		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	1515			P -> S (in dbSNP:rs55825559).		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						TCAGAGTATTCCCCGCGTAGC	0.413													C|||	60	0.0119808	0.0	0.0245	5008	,	,		15388	0.0		0.0368	False		,,,				2504	0.0061				p.P1515S		Atlas-SNP	.											.	DNAJC13	253	.	0			c.C4543T						PASS	.	C	SER/PRO	26,4380	32.6+/-62.9	0,26,2177	117	113	115		4543	5.8	1	3	dbSNP_129	115	239,8361	94.5+/-156.4	5,229,4066	yes	missense	DNAJC13	NM_015268.3	74	5,255,6243	TT,TC,CC		2.7791,0.5901,2.0375	benign	1515/2244	132221139	265,12741	2203	4300	6503	SO:0001583	missense	23317	exon40			AGTATTCCCCGCG	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.4543C>T	3.37:g.132221139C>T	ENSP00000260818:p.Pro1515Ser	135	0	0		144	50	0.347222	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	37	CCDS33857.1	34	0.015567765567765568	0	0.0	9	0.024861878453038673	0	0.0	25	0.032981530343007916	C	14.92	2.678748	0.47886	0.005901	0.027791	ENSG00000138246	ENST00000260818;ENST00000538066	T	0.52057	0.68	5.81	5.81	0.92471	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.24812	0.0602	M	0.69185	2.1	0.54753	D	0.999985	B	0.20368	0.044	B	0.15870	0.014	T	0.17653	-1.0362	10	0.40728	T	0.16	.	16.3288	0.82997	0.0:0.868:0.132:0.0	rs55825559;rs61748104	1515	O75165	DJC13_HUMAN	S	1515;162	ENSP00000260818:P1515S	ENSP00000260818:P1515S	P	+	1	0	DNAJC13	133703829	1.000000	0.71417	0.998000	0.56505	0.614000	0.37383	4.644000	0.61397	2.734000	0.93682	0.650000	0.86243	CCC	C|0.981;T|0.019	0.019	strong		0.413	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268		T	132221139	C	T	132221139	3	4	23	1	0	0	0	0	1	0	0	0	4634	855	30	2	4697	2	DNAJC13	3	132221139	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	2923884	132221139	65801291	158	7602											
RASA2	5922	hgsc.bcm.edu	37	chr3	141295907	141295907	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttcgtttctttgctgtagccGtagtatcacctcatactttt	6	19	6	10	2	3	0	2	0	1	0	4	0	3	0	2	0	3	5	2	0	4	9	rs201190266		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:141295907G>A	ENST00000452898.1	+	15	1584	c.1549G>A	c.(1549-1551)Gta>Ata	p.V517I	RASA2_ENST00000286364.3_Missense_Mutation_p.V517I	NM_006506.2	NP_006497.2	Q15283	RASA2_HUMAN	RAS p21 protein activator 2	517	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				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)	p.V517I(2)		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						TGCTGTAGCCGTAGTATCACC	0.353																																					p.V517I		Atlas-SNP	.											RASA2_ENST00000286364,NS,carcinoma,0,2	RASA2	169	2	2	Substitution - Missense(2)	kidney(2)	c.G1549A						PASS	.						228	215	219					3																	141295907		2203	4300	6503	SO:0001583	missense	5922	exon15			GTAGCCGTAGTAT	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.1549G>A	3.37:g.141295907G>A	ENSP00000391677:p.Val517Ile	156	0	0		170	98	0.576471	NM_006506	A8K7K1|G3V0F9|O00695|Q15284|Q92594|Q99577|Q9UEQ2	Missense_Mutation	SNP	ENST00000452898.1	37		.	.	.	.	.	.	.	.	.	.	G	7.080	0.570046	0.13560	.	.	ENSG00000155903	ENST00000286364;ENST00000452898;ENST00000423660	T;T	0.71934	-0.61;-0.61	6.03	4.24	0.50183	Ras GTPase-activating protein, conserved site (1);Rho GTPase activation protein (1);Ras GTPase-activating protein (4);	0.059991	0.64402	N	0.000004	T	0.35653	0.0939	N	0.00808	-1.17	0.49213	D	0.999769	B;B;B;B	0.21147	0.052;0.005;0.004;0.005	B;B;B;B	0.21917	0.037;0.012;0.007;0.012	T	0.43376	-0.9395	10	0.02654	T	1	.	12.1791	0.54202	0.1391:0.0:0.8609:0.0	.	109;517;517;517	E7EU60;A8K7K1;G3V0F9;Q15283	.;.;.;RASA2_HUMAN	I	517;517;109	ENSP00000286364:V517I;ENSP00000391677:V517I	ENSP00000286364:V517I	V	+	1	0	RASA2	142778597	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.269000	0.72558	0.870000	0.35726	0.557000	0.71058	GTA	G|0.999;T|0.001	.	alt		0.353	RASA2-201	KNOWN	basic	protein_coding	protein_coding		NM_006506		A	141295907	G	A	141295907	3	1	23	1	0	0	0	0	1	0	0	0	13076	1145	40	1	1607	1	RASA2	3	141295907	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	9074768	141295907	56726523	159	7603											
WWTR1	25937	hgsc.bcm.edu	37	chr3	149290781	149290781	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgccatgtggtgattttttcTatgtgactaaaagaaggaaa	13	14	10	4	0	1	3	0	2	1	1	1	4	1	4	1	2	1	0	1	2	5	5			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:149290781T>G	ENST00000465804.1	-	4	694	c.438A>C	c.(436-438)atA>atC	p.I146I	WWTR1_ENST00000360632.3_Silent_p.I146I|WWTR1_ENST00000467467.1_Silent_p.I146I	NM_001168278.1	NP_001161750.1	Q9GZV5	WWTR1_HUMAN	WW domain containing transcription regulator 1	146	WW. {ECO:0000255|PROSITE- ProRule:PRU00224}.				cilium morphogenesis (GO:0060271)|gene expression (GO:0010467)|glomerulus development (GO:0032835)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of SMAD protein import into nucleus (GO:0060390)|regulation of transcription, DNA-templated (GO:0006355)|stem cell division (GO:0017145)|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)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(5)|cervix(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	23			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			TGATTTTTTCTATGTGACTAA	0.388			T	CAMTA1	epitheliod hemangioendothelioma																																p.I146I		Atlas-SNP	.		Dom	yes		3	3q23-q24	607392	WW domain containing transcription regulator 1		M	.	WWTR1	42	.	0			c.A438C						PASS	.						125	118	120					3																	149290781		2203	4300	6503	SO:0001819	synonymous_variant	25937	exon4			TTTTTCTATGTGA	AK022036	CCDS3144.1	3q23-q24	2004-12-03			ENSG00000018408	ENSG00000018408			24042	protein-coding gene	gene with protein product		607392				11118213, 15096513	Standard	NM_015472		Approved	TAZ, DKFZp586I1419	uc021xfm.1	Q9GZV5	OTTHUMG00000159614	ENST00000465804.1:c.438A>C	3.37:g.149290781T>G		92	0	0		95	15	0.157895	NM_001168278	D3DNH7|Q8N3P2|Q9Y3W6	Silent	SNP	ENST00000465804.1	37	CCDS3144.1																																																																																			.	.	none		0.388	WWTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356498.1	NM_015472		G	149290781	T	G	149290781	2	3	23	1	0	0	0	0	0	0	0	1	17432	1512	53	5		5	WWTR1	3	149290781	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	7994874	149290781	48731649	160	7604											
SGEF	26084	hgsc.bcm.edu	37	chr3	153943770	153943770	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtctacttctttctctttaaCgatgtgctcattatcaccaa	9	17	4	11	1	5	0	2	0	3	0	6	1	5	0	1	0	3	1	1	0	4	6	rs74965475	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:153943770C>G	ENST00000356448.4	+	11	2345	c.2061C>G	c.(2059-2061)aaC>aaG	p.N687K	ARHGEF26_ENST00000483068.1_3'UTR|ARHGEF26_ENST00000465817.1_Intron|ARHGEF26_ENST00000465093.1_Missense_Mutation_p.N687K	NM_001251962.1	NP_001238891.1	Q96DR7	ARHGQ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 26	687	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.			N -> K (in Ref. 6; AAH16628). {ECO:0000305}.	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						TTCTCTTTAACGATGTGCTCA	0.398													C|||	37	0.00738818	0.003	0.0101	5008	,	,		18598	0.0		0.0189	False		,,,				2504	0.0072				p.N687K	GBM(163;191 2003 24758 29593 48540)|Ovarian(152;631 1885 20165 22910 51013)	Atlas-SNP	.											.	ARHGEF26	158	.	0			c.C2061G						PASS	.	C	LYS/ASN	15,3767		0,15,1876	104	91	95		2061	-6	0.7	3	dbSNP_131	95	158,8064		1,156,3954	yes	missense	ARHGEF26	NM_015595.3	94	1,171,5830	GG,GC,CC		1.9217,0.3966,1.4412	probably-damaging	687/872	153943770	173,11831	1891	4111	6002	SO:0001583	missense	26084	exon11			CTTTAACGATGTG	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.2061C>G	3.37:g.153943770C>G	ENSP00000348828:p.Asn687Lys	187	0	0		221	105	0.475113	NM_001251962	B3KVP8|E9PBD0|Q68CL1|Q6AZ96|Q6Q8Q8|Q96AW8|Q96DR6|Q9H9D7|Q9H9R2|Q9UFW5	Missense_Mutation	SNP	ENST00000356448.4	37	CCDS46938.1	17	0.007783882783882784	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	13	0.017150395778364115	C	17.13	3.310099	0.60414	0.003966	0.019217	ENSG00000114790	ENST00000356448;ENST00000465093	T;T	0.68331	-0.32;-0.32	5.65	-5.96	0.02234	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.66616	0.2807	M	0.84219	2.685	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.81914	0.991;0.995	T	0.80441	-0.1381	10	0.87932	D	0	-33.6174	16.1896	0.81977	0.0:0.3521:0.0:0.6479	.	687;687	E9PBD0;Q96DR7	.;ARHGQ_HUMAN	K	687	ENSP00000348828:N687K;ENSP00000423418:N687K	ENSP00000348828:N687K	N	+	3	2	ARHGEF26	155426460	0.000000	0.05858	0.726000	0.30738	0.884000	0.51177	-3.244000	0.00542	-0.995000	0.03459	-1.193000	0.01689	AAC	C|0.990;G|0.010	0.010	strong		0.398	ARHGEF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353287.3	NM_015595		G	153943770	C	G	153943770	3	3	23	1	0	0	0	0	1	0	0	0	14220	535	19	4	2099	4	SGEF	3	153943770	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	4652989	153943770	44078660	161	7605											
OTOL1	131149	hgsc.bcm.edu	37	chr3	161220819	161220819	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aattttccatttcaggtgaaCctggccctaagggagataaa	13	11	9	8	0	1	2	1	1	0	1	2	3	2	2	3	3	1	0	3	3	5	5	rs149127996	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:161220819C>A	ENST00000327928.4	+	4	523	c.523C>A	c.(523-525)Cct>Act	p.P175T		NM_001080440.1	NP_001073909.1	A6NHN0	OTOL1_HUMAN	otolin 1	175	Collagen-like 1.					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						TTCAGGTGAACCTGGCCCTAA	0.398													C|||	14	0.00279553	0.0015	0.0043	5008	,	,		14597	0.0		0.0089	False		,,,				2504	0.0				p.P175T		Atlas-SNP	.											.	OTOL1	63	.	0			c.C523A						PASS	.	C	THR/PRO	4,3334		0,4,1665	7	6	6		523	1.9	1	3	dbSNP_134	6	28,7420		0,28,3696	yes	missense	OTOL1	NM_001080440.1	38	0,32,5361	AA,AC,CC		0.3759,0.1198,0.2967	benign	175/478	161220819	32,10754	1669	3724	5393	SO:0001583	missense	131149	exon4			GGTGAACCTGGCC		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.523C>A	3.37:g.161220819C>A	ENSP00000330808:p.Pro175Thr	170	0	0		184	77	0.418478	NM_001080440		Missense_Mutation	SNP	ENST00000327928.4	37	CCDS46948.1	11	0.005036630036630037	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	7	0.009234828496042216	C	5.563	0.288736	0.10513	0.001198	0.003759	ENSG00000182447	ENST00000327928	D	0.96651	-4.08	4.94	1.94	0.25998	.	1.313780	0.05051	N	0.478274	D	0.90741	0.7094	L	0.41906	1.305	0.09310	N	1	B	0.20887	0.049	B	0.26693	0.072	T	0.81556	-0.0879	10	0.37606	T	0.19	.	2.6803	0.05091	0.2842:0.3954:0.2304:0.09	.	175	A6NHN0	OTOL1_HUMAN	T	175	ENSP00000330808:P175T	ENSP00000330808:P175T	P	+	1	0	OTOL1	162703513	0.004000	0.15560	0.987000	0.45799	0.976000	0.68499	0.410000	0.21098	0.462000	0.27095	0.557000	0.71058	CCT	C|0.995;A|0.005	0.005	strong		0.398	OTOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353184.1	NM_001080440		A	161220819	C	A	161220819	3	1	23	1	0	0	0	0	1	0	0	0	11313	507	18	4	537	4	OTOL1	3	161220819	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	7277049	161220819	36801611	162	7606											
ZBBX	79740	hgsc.bcm.edu	37	chr3	167035332	167035332	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcatcaccagtggtttcaTgtggatgtgggaacgtatct	8	13	13	7	1	3	0	2	0	1	0	3	2	3	2	1	3	2	3	1	3	2	2	rs34465133	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:167035332T>C	ENST00000392766.2	-	13	1377	c.1037A>G	c.(1036-1038)cAt>cGt	p.H346R	ZBBX_ENST00000307529.5_Missense_Mutation_p.H346R|ZBBX_ENST00000469220.1_Intron|ZBBX_ENST00000392764.1_Missense_Mutation_p.H317R|ZBBX_ENST00000392767.2_Missense_Mutation_p.H346R|ZBBX_ENST00000455345.2_Missense_Mutation_p.H346R	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	346			H -> R (in dbSNP:rs34465133).			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						AGTGGTTTCATGTGGATGTGG	0.333													C|||	28	0.00559105	0.0008	0.0058	5008	,	,		17626	0.0		0.0229	False		,,,				2504	0.0				p.H346R		Atlas-SNP	.											.	ZBBX	299	.	0			c.A1037G						PASS	.	C	ARG/HIS,ARG/HIS,ARG/HIS	8,3698		0,8,1845	191	174	179		1037,950,1037	0.3	0	3	dbSNP_126	179	179,8009		1,177,3916	yes	missense,missense,missense	ZBBX	NM_001199201.1,NM_001199202.1,NM_024687.3	29,29,29	1,185,5761	CC,CT,TT		2.1861,0.2159,1.5722	benign,benign,benign	346/840,317/772,346/801	167035332	187,11707	1853	4094	5947	SO:0001583	missense	79740	exon13			GTTTCATGTGGAT	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.1037A>G	3.37:g.167035332T>C	ENSP00000376519:p.His346Arg	189	0	0		219	78	0.356164	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	37	CCDS3199.2	26	0.011904761904761904	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	22	0.029023746701846966	C	7.094	0.572764	0.13623	0.002159	0.021861	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764	T;T;T;T;T	0.08896	3.21;3.21;3.21;3.21;3.04	5.34	0.327	0.15913	.	0.965568	0.08617	N	0.919032	T	0.01287	0.0042	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	0.47636	-0.9102	10	0.11182	T	0.66	3.6647	5.0072	0.14293	0.0:0.4377:0.1458:0.4165	rs34465133	346;346	A8MT70-2;A8MT70	.;ZBBX_HUMAN	R	346;346;346;346;317	ENSP00000376519:H346R;ENSP00000376520:H346R;ENSP00000390232:H346R;ENSP00000305065:H346R;ENSP00000376517:H317R	ENSP00000305065:H346R	H	-	2	0	ZBBX	168518026	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-1.546000	0.02188	-0.059000	0.13154	-0.128000	0.14901	CAT	T|0.987;C|0.013	0.013	strong		0.333	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687		C	167035332	T	C	167035332	3	2	23	1	0	0	0	0	1	0	0	0	17531	1464	51	3	1401	3	ZBBX	3	167035332	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	5814513	167035332	30987098	163	7607											
GOLIM4	27333	hgsc.bcm.edu	37	chr3	167747707	167747707	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cctctgctggtgcaaagcttCctggtgttcccgcagctgct	4	12	11	14	1	1	0	0	0	1	0	3	0	3	0	3	2	5	7	3	2	1	2	rs140974195	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:167747707C>T	ENST00000470487.1	-	10	1983	c.1294G>A	c.(1294-1296)Gaa>Aaa	p.E432K	GOLIM4_ENST00000309027.4_Missense_Mutation_p.E404K	NM_014498.3	NP_055313.1	O00461	GOLI4_HUMAN	golgi integral membrane protein 4	432	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						tgcaaagcttcctggtgttcc	0.587													C|||	6	0.00119808	0.0	0.0043	5008	,	,		15802	0.0		0.003	False		,,,				2504	0.0				p.E432K		Atlas-SNP	.											.	GOLIM4	71	.	0			c.G1294A						PASS	.	C	LYS/GLU	0,4406		0,0,2203	71	65	67		1294	4.7	0.9	3	dbSNP_134	67	19,8581	14.0+/-48.4	0,19,4281	yes	missense	GOLIM4	NM_014498.3	56	0,19,6484	TT,TC,CC		0.2209,0.0,0.1461	possibly-damaging	432/697	167747707	19,12987	2203	4300	6503	SO:0001583	missense	27333	exon10			AAGCTTCCTGGTG	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.1294G>A	3.37:g.167747707C>T	ENSP00000417354:p.Glu432Lys	116	0	0		118	40	0.338983	NM_014498		Missense_Mutation	SNP	ENST00000470487.1	37	CCDS3204.1	6	0.0027472527472527475	0	0.0	3	0.008287292817679558	0	0.0	3	0.00395778364116095	C	28.6	4.935733	0.92458	0.0	0.002209	ENSG00000173905	ENST00000470487;ENST00000309027	.	.	.	5.65	4.74	0.60224	.	0.188818	0.56097	D	0.000034	T	0.62768	0.2455	M	0.71581	2.175	0.33996	D	0.64974	D;P	0.54397	0.966;0.941	P;P	0.56216	0.794;0.731	T	0.76069	-0.3094	9	0.45353	T	0.12	-10.4908	16.3164	0.82930	0.0:0.868:0.132:0.0	.	404;432	F8W785;O00461	.;GOLI4_HUMAN	K	432;404	.	ENSP00000309893:E404K	E	-	1	0	GOLIM4	169230401	1.000000	0.71417	0.950000	0.38849	0.833000	0.47200	4.851000	0.62896	2.694000	0.91930	0.555000	0.69702	GAA	C|0.998;T|0.002	0.002	strong		0.587	GOLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351278.2			T	167747707	C	T	167747707	3	4	23	1	0	0	0	0	1	0	0	0	6574	864	30	2	824	2	GOLIM4	3	167747707	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	712375	167747707	30274723	164	7608											
PHC3	80012	hgsc.bcm.edu	37	chr3	169846937	169846937	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaatttggccctggctggagAgctgatgacacaagagggtg	11	8	15	7	0	0	4	0	2	0	2	0	5	0	4	1	4	1	2	1	4	2	1	rs373112767		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:169846937A>G	ENST00000494943.1	-	8	1355	c.1287T>C	c.(1285-1287)gcT>gcC	p.A429A	PHC3_ENST00000495893.2_Silent_p.A441A|PHC3_ENST00000467570.1_Silent_p.A388A			Q8NDX5	PHC3_HUMAN	polyhomeotic homolog 3 (Drosophila)	429	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)			CTGGCTGGAGAGCTGATGACA	0.493													A|||	1	0.000199681	0.0	0.0	5008	,	,		22525	0.0		0.001	False		,,,				2504	0.0				p.A441A		Atlas-SNP	.											.	PHC3	113	.	0			c.T1323C						PASS	.	A		0,4170		0,0,2085	61	64	63		1323	2.4	1	3		63	1,8431		0,1,4215	no	coding-synonymous	PHC3	NM_024947.3		0,1,6300	GG,GA,AA		0.0119,0.0,0.0079		441/996	169846937	1,12601	2085	4216	6301	SO:0001819	synonymous_variant	80012	exon8			CTGGAGAGCTGAT		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.1287T>C	3.37:g.169846937A>G		128	0	0		131	58	0.442748	NM_024947	A2RRP9|Q5HYF0|Q6NSG2|Q8NFT7|Q8NFZ1|Q8TBM2|Q9H971|Q9H9I4	Silent	SNP	ENST00000494943.1	37																																																																																				.	.	weak		0.493	PHC3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000352182.3	NM_024947		G	169846937	A	G	169846937	2	3	23	1	0	0	0	0	0	0	0	1	11827	291	11	3		3	PHC3	3	169846937	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	2099230	169846937	28175493	165	7609											
EIF4G1	1981	hgsc.bcm.edu	37	chr3	184037523	184037523	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcagcagtttcccactggCgtggcccccaccccagtttt	5	10	10	16	1	0	0	0	0	0	0	1	0	1	0	5	2	2	4	5	2	0	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:184037523C>T	ENST00000346169.2	+	7	742	c.471C>T	c.(469-471)ggC>ggT	p.G157G	EIF4G1_ENST00000435046.2_5'Flank|EIF4G1_ENST00000342981.4_Silent_p.G157G|EIF4G1_ENST00000352767.3_Silent_p.G164G|EIF4G1_ENST00000319274.6_Silent_p.G157G|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000441154.1_5'Flank|EIF4G1_ENST00000434061.2_5'Flank|EIF4G1_ENST00000392537.2_Silent_p.G70G|EIF4G1_ENST00000382330.3_Silent_p.G164G|EIF4G1_ENST00000411531.1_Silent_p.G117G|EIF4G1_ENST00000427845.1_Silent_p.G70G|EIF4G1_ENST00000350481.5_5'UTR|EIF4G1_ENST00000414031.1_Silent_p.G117G|EIF4G1_ENST00000424196.1_Silent_p.G164G	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	157					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)			TTCCCACTGGCGTGGCCCCCA	0.622																																					p.G164G		Atlas-SNP	.											.	EIF4G1	151	.	0			c.C492T						PASS	.						28	24	26					3																	184037523		2203	4299	6502	SO:0001819	synonymous_variant	1981	exon8			CACTGGCGTGGCC	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.471C>T	3.37:g.184037523C>T		315	0	0		392	230	0.586735	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Silent	SNP	ENST00000346169.2	37	CCDS3259.1																																																																																			.	.	none		0.622	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917		T	184037523	C	T	184037523	2	4	23	1	0	0	0	0	0	0	0	1	5038	755	27	1		1	EIF4G1	3	184037523	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	14190586	184037523	13984907	166	7610											
ST6GAL1	6480	hgsc.bcm.edu	37	chr3	186760520	186760520	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccaacctgaagaaaaagtTcagctgctgcgtcctggtct	11	9	9	12	1	2	2	1	1	1	1	3	2	3	2	3	1	4	3	3	1	4	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:186760520T>G	ENST00000169298.3	+	4	703	c.29T>G	c.(28-30)tTc>tGc	p.F10C	ST6GAL1_ENST00000457772.2_Intron|ST6GAL1_ENST00000448044.1_Missense_Mutation_p.F10C	NM_173216.2	NP_775323.1	P15907	SIAT1_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 1	10					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)		AAGAAAAAGTTCAGCTGCTGC	0.403																																					p.F10C		Atlas-SNP	.											ST6GAL1,NS,carcinoma,+1,1	ST6GAL1	36	1	0			c.T29G						PASS	.						165	161	163					3																	186760520		2203	4300	6503	SO:0001583	missense	6480	exon3			AAAAGTTCAGCTG	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.29T>G	3.37:g.186760520T>G	ENSP00000169298:p.Phe10Cys	184	0	0		196	23	0.117347	NM_003032	A8KA14|B2R513|D3DNV3	Missense_Mutation	SNP	ENST00000169298.3	37	CCDS3285.1	.	.	.	.	.	.	.	.	.	.	T	18.32	3.599029	0.66332	.	.	ENSG00000073849	ENST00000169298;ENST00000458216;ENST00000430309;ENST00000417392;ENST00000438590;ENST00000448408;ENST00000440338;ENST00000448044;ENST00000416235;ENST00000423451;ENST00000446170	T;T	0.23950	1.88;1.88	5.44	5.44	0.79542	.	0.415059	0.26804	N	0.022416	T	0.24586	0.0596	L	0.52364	1.645	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.03103	-1.1072	10	0.33940	T	0.23	-27.897	12.2097	0.54373	0.0:0.0:0.0:1.0	.	10	P15907	SIAT1_HUMAN	C	10	ENSP00000169298:F10C;ENSP00000389337:F10C	ENSP00000169298:F10C	F	+	2	0	ST6GAL1	188243214	0.614000	0.27017	0.996000	0.52242	0.933000	0.57130	1.719000	0.38011	2.200000	0.70718	0.459000	0.35465	TTC	.	.	none		0.403	ST6GAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344399.1	NM_173216		G	186760520	T	G	186760520	3	3	23	1	0	0	0	0	1	0	0	0	15236	1783	62	5	31	5	ST6GAL1	3	186760520	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	2722997	186760520	11261910	167	7611			2	38		3	3	72	N	T_C	1.507897e-06
ST6GAL1	6480	hgsc.bcm.edu	37	chr3	186760533	186760533	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	aaaaagttcagctgctgcgtCctggtctttcttctgtttgc	6	16	9	10	1	4	0	1	0	3	0	5	0	5	0	1	1	4	4	1	1	2	4			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:186760533C>T	ENST00000169298.3	+	4	716	c.42C>T	c.(40-42)gtC>gtT	p.V14V	ST6GAL1_ENST00000457772.2_Intron|ST6GAL1_ENST00000448044.1_Silent_p.V14V	NM_173216.2	NP_775323.1	P15907	SIAT1_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 1	14					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)		GCTGCTGCGTCCTGGTCTTTC	0.403																																					p.V14V		Atlas-SNP	.											.	ST6GAL1	36	.	0			c.C42T						PASS	.						165	161	162					3																	186760533		2203	4300	6503	SO:0001819	synonymous_variant	6480	exon3			CTGCGTCCTGGTC	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.42C>T	3.37:g.186760533C>T		193	0	0		207	22	0.10628	NM_003032	A8KA14|B2R513|D3DNV3	Silent	SNP	ENST00000169298.3	37	CCDS3285.1																																																																																			.	.	none		0.403	ST6GAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344399.1	NM_173216		T	186760533	C	T	186760533	2	4	23	1	0	0	0	0	0	0	0	1	15236	842	30	2		2	ST6GAL1	3	186760533	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	13	186760533	11261897	168	7612			2	38		3	3	72	N	T_C	1.507897e-06
ST6GAL1	6480	hgsc.bcm.edu	37	chr3	186760591	186760591	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggaaaagaagaaagggagtTactatgattcctttaaattg	17	11	10	3	0	0	3	0	1	0	2	1	5	1	5	1	2	1	1	1	2	8	6			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:186760591T>A	ENST00000169298.3	+	4	774	c.100T>A	c.(100-102)Tac>Aac	p.Y34N	ST6GAL1_ENST00000457772.2_Intron|ST6GAL1_ENST00000448044.1_Missense_Mutation_p.Y34N	NM_173216.2	NP_775323.1	P15907	SIAT1_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 1	34					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)		GAAAGGGAGTTACTATGATTC	0.438																																					p.Y34N		Atlas-SNP	.											.	ST6GAL1	36	.	0			c.T100A						PASS	.						132	134	134					3																	186760591		2203	4300	6503	SO:0001583	missense	6480	exon3			GGGAGTTACTATG	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.100T>A	3.37:g.186760591T>A	ENSP00000169298:p.Tyr34Asn	174	0	0		189	20	0.10582	NM_003032	A8KA14|B2R513|D3DNV3	Missense_Mutation	SNP	ENST00000169298.3	37	CCDS3285.1	.	.	.	.	.	.	.	.	.	.	T	10.93	1.489702	0.26686	.	.	ENSG00000073849	ENST00000169298;ENST00000430309;ENST00000417392;ENST00000438590;ENST00000448408;ENST00000440338;ENST00000448044;ENST00000416235;ENST00000423451;ENST00000446170	T;T	0.24350	1.86;1.86	5.44	2.95	0.34219	.	0.288497	0.39020	N	0.001500	T	0.21347	0.0514	M	0.61703	1.905	0.80722	D	1	P	0.38582	0.638	B	0.34242	0.178	T	0.04440	-1.0951	10	0.15066	T	0.55	-39.6557	9.6725	0.40021	0.0:0.0:0.3568:0.6432	.	34	P15907	SIAT1_HUMAN	N	34	ENSP00000169298:Y34N;ENSP00000389337:Y34N	ENSP00000169298:Y34N	Y	+	1	0	ST6GAL1	188243285	1.000000	0.71417	0.826000	0.32828	0.613000	0.37349	1.659000	0.37387	0.410000	0.25675	0.459000	0.35465	TAC	.	.	none		0.438	ST6GAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344399.1	NM_173216		A	186760591	T	A	186760591	3	1	23	1	0	0	0	0	1	0	0	0	15236	1754	61	5	102	5	ST6GAL1	3	186760591	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	58	186760591	11261839	169	7613			2	38		3	3	72	N	T_C	1.507897e-06
OSTN	344901	hgsc.bcm.edu	37	chr3	190936577	190936577	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgtgcagtcaacacccacAgtcagggaagagaaatcagc	15	5	11	10	0	3	1	3	0	0	1	3	4	3	2	1	1	3	1	1	1	3	0	rs34687554	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:190936577A>G	ENST00000339051.1	+	2	144	c.144A>G	c.(142-144)acA>acG	p.T48T	OSTN-AS1_ENST00000430375.1_RNA|OSTN_ENST00000445281.1_Silent_p.T48T	NM_198184.1	NP_937827.1	P61366	OSTN_HUMAN	osteocrin	48					cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|endochondral bone growth (GO:0003416)|negative regulation of glucose import (GO:0046325)|negative regulation of osteoblast differentiation (GO:0045668)|ossification (GO:0001503)|positive regulation of cGMP biosynthetic process (GO:0030828)	extracellular space (GO:0005615)				kidney(1)|large_intestine(3)|lung(6)|pancreas(1)|skin(2)	13	all_cancers(143;6.79e-09)|Ovarian(172;0.103)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000254)		CAACACCCACAGTCAGGGAAG	0.418													A|||	32	0.00638978	0.0	0.0072	5008	,	,		18556	0.0		0.0149	False		,,,				2504	0.0123				p.T48T		Atlas-SNP	.											.	OSTN	25	.	0			c.A144G						PASS	.	A		10,4396	16.8+/-37.8	0,10,2193	140	127	132		144	5.5	0.9	3	dbSNP_126	132	96,8504	54.0+/-114.7	2,92,4206	no	coding-synonymous	OSTN	NM_198184.1		2,102,6399	GG,GA,AA		1.1163,0.227,0.815		48/134	190936577	106,12900	2203	4300	6503	SO:0001819	synonymous_variant	344901	exon2			ACCCACAGTCAGG	AY398681	CCDS3299.1	3q29	2004-01-22			ENSG00000188729	ENSG00000188729			29961	protein-coding gene	gene with protein product		610280				14523025	Standard	NM_198184		Approved		uc011bsn.2	P61366	OTTHUMG00000156190	ENST00000339051.1:c.144A>G	3.37:g.190936577A>G		78	0	0		68	29	0.426471	NM_198184	A1A4U3	Silent	SNP	ENST00000339051.1	37	CCDS3299.1																																																																																			A|0.992;G|0.008	0.008	strong		0.418	OSTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343350.1	NM_198184		G	190936577	A	G	190936577	2	3	23	1	0	0	0	0	0	0	0	1	11308	175	7	3		3	OSTN	3	190936577	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	4175986	190936577	7085853	170	7614											
KIAA0226	9711	hgsc.bcm.edu	37	chr3	197427515	197427515	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggaggcaatgctggtatcCgaatgggagcgaatgtggct	9	9	16	7	2	0	0	0	0	0	0	1	4	1	2	1	5	2	4	1	5	4	1	rs116791711	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:197427515C>T	ENST00000296343.5	-	7	1229	c.1230G>A	c.(1228-1230)tcG>tcA	p.S410S	KIAA0226_ENST00000273582.5_Silent_p.S350S|KIAA0226_ENST00000467303.1_5'Flank|KIAA0226_ENST00000389665.5_Silent_p.S410S|KIAA0226_ENST00000449205.1_Silent_p.S410S	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	410	Ser-rich.				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)		TGCTGGTATCCGAATGGGAGC	0.547													C|||	33	0.00658946	0.0	0.0058	5008	,	,		18378	0.0		0.0278	False		,,,				2504	0.001				p.S410S	Esophageal Squamous(3;167 355 3763 15924)	Atlas-SNP	.											Q96CK5_HUMAN,NS,carcinoma,-1,6	KIAA0226	136	6	0			c.G1230A						PASS	.	C	,	18,4026		0,18,2004	83	84	84		1050,1230	-10.9	0.1	3	dbSNP_132	84	155,8197		1,153,4022	no	coding-synonymous,coding-synonymous	KIAA0226	NM_001145642.2,NM_014687.1	,	1,171,6026	TT,TC,CC		1.8558,0.4451,1.3956	,	350/928,410/973	197427515	173,12223	2022	4176	6198	SO:0001819	synonymous_variant	9711	exon7			GGTATCCGAATGG	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.1230G>A	3.37:g.197427515C>T		204	0	0		209	77	0.368421	NM_014687	Q96CK5	Silent	SNP	ENST00000296343.5	37	CCDS43195.1	23|23	0.010531135531135532|0.010531135531135532	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	22|22	0.029023746701846966|0.029023746701846966	C|C	5.052|5.052	0.195309|0.195309	0.09599|0.09599	0.004451|0.004451	0.018558|0.018558	ENSG00000145016|ENSG00000145016	ENST00000413360|ENST00000415452	.|.	.|.	.|.	5.46|5.46	-10.9|-10.9	0.00192|0.00192	.|.	.|.	.|.	.|.	.|.	T|T	0.21962|0.21962	0.0529|0.0529	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.59616|0.59616	-0.7421|-0.7421	4|4	.|.	.|.	.|.	.|.	8.7159|8.7159	0.34411|0.34411	0.1713:0.5525:0.0677:0.2085|0.1713:0.5525:0.0677:0.2085	.|.	.|.	.|.	.|.	R|Q	389|169	.|.	.|.	G|R	-|-	1|2	0|0	KIAA0226|KIAA0226	198911912|198911912	0.000000|0.000000	0.05858|0.05858	0.145000|0.145000	0.22337|0.22337	0.727000|0.727000	0.41649|0.41649	-3.954000|-3.954000	0.00326|0.00326	-3.421000|-3.421000	0.00166|0.00166	-1.099000|-1.099000	0.02127|0.02127	GGA|CGG	C|0.987;T|0.013	0.013	strong		0.547	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901		T	197427515	C	T	197427515	2	4	23	1	0	0	0	0	0	0	0	1	8171	639	23	1		1	KIAA0226	3	197427515	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	6490938	197427515	594915	171	7615											
GAK	2580	hgsc.bcm.edu	37	chr4	877187	877187	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggtgcttggagtccaggaaCaaccgcacatcttcgatgtt	9	10	12	10	2	1	0	0	0	1	0	3	3	2	2	2	3	3	3	2	3	2	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:877187C>A	ENST00000314167.4	-	13	1430	c.1320G>T	c.(1318-1320)ttG>ttT	p.L440F	GAK_ENST00000511163.1_Missense_Mutation_p.L361F	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	440	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)		AGTCCAGGAACAACCGCACAT	0.577																																					p.L440F		Atlas-SNP	.											.	GAK	104	.	0			c.G1320T						PASS	.						208	174	185					4																	877187		2203	4300	6503	SO:0001583	missense	2580	exon13			CAGGAACAACCGC	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.1320G>T	4.37:g.877187C>A	ENSP00000314499:p.Leu440Phe	72	0	0		118	18	0.152542	NM_005255	Q5U4P5|Q9BVY6	Missense_Mutation	SNP	ENST00000314167.4	37	CCDS3340.1	.	.	.	.	.	.	.	.	.	.	C	12.34	1.910103	0.33721	.	.	ENSG00000178950	ENST00000314167;ENST00000511163	D;D	0.98602	-5.02;-5.02	5.34	1.53	0.23141	Phosphatase tensin type (1);	0.171640	0.38663	N	0.001620	D	0.95965	0.8686	L	0.48642	1.525	0.58432	D	0.999996	P;P;P;P	0.48640	0.913;0.848;0.849;0.849	P;P;B;B	0.47891	0.56;0.56;0.379;0.288	D	0.91526	0.5238	10	0.30854	T	0.27	-4.0961	5.1519	0.15015	0.139:0.515:0.2693:0.0766	.	361;361;440;336	Q5U4P5;E9PGR2;O14976;Q59HA5	.;.;GAK_HUMAN;.	F	440;361	ENSP00000314499:L440F;ENSP00000421361:L361F	ENSP00000314499:L440F	L	-	3	2	GAK	867187	0.927000	0.31430	0.089000	0.20774	0.004000	0.04260	0.128000	0.15810	-0.028000	0.13850	-1.047000	0.02352	TTG	.	.	none		0.577	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255		A	877187	C	A	877187	3	1	23	1	0	0	0	0	1	0	0	0	6203	477	17	4	2679	4	GAK	4	877187	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10		877187	190277089	172	7616											
SH3BP2	6452	hgsc.bcm.edu	37	chr4	2828969	2828969	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cattgcagcgactccagctcGgacacagacagcttctacgg	10	7	10	14	3	1	1	0	0	1	1	3	3	2	2	1	2	5	3	1	2	1	3	rs145235325	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:2828969G>A	ENST00000356331.5	+	6	702	c.441G>A	c.(439-441)tcG>tcA	p.S147S	SH3BP2_ENST00000515183.1_3'UTR|SH3BP2_ENST00000435136.2_Silent_p.S147S|SH3BP2_ENST00000442312.2_Silent_p.S175S|SH3BP2_ENST00000511747.1_Silent_p.S147S|SH3BP2_ENST00000452765.2_Silent_p.S147S|SH3BP2_ENST00000503393.2_Silent_p.S204S	NM_003023.4	NP_003014.3	P78314	3BP2_HUMAN	SH3-domain binding protein 2	147					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)		ACTCCAGCTCGGACACAGACA	0.602									Cherubism				g|||	3	0.000599042	0.0008	0.0	5008	,	,		22783	0.0		0.002	False		,,,				2504	0.0				p.S204S		Atlas-SNP	.											.	SH3BP2	43	.	0			c.G612A						PASS	.		,,,	1,4405	2.1+/-5.4	0,1,2202	133	107	116		441,525,612,441	-9.9	0.9	4	dbSNP_134	116	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SH3BP2	NM_001122681.1,NM_001145855.1,NM_001145856.1,NM_003023.4	,,,	0,12,6491	AA,AG,GG		0.1279,0.0227,0.0923	,,,	147/562,175/590,204/619,147/562	2828969	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	6452	exon6	Familial Cancer Database	Familial Benign Giant-cell Tumor of the Jaw, Familial Multilocular Cystic Disease	CAGCTCGGACACA	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.441G>A	4.37:g.2828969G>A		55	0	0		58	30	0.517241	NM_001145856	A6NNC2|B2R5R6|B4DT04|D3DVR0|D6R919|O00500|O15373|P78315	Silent	SNP	ENST00000356331.5	37	CCDS33944.1																																																																																			G|0.999;A|0.001	0.001	strong		0.602	SH3BP2-007	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362406.2	NM_003023		A	2828969	G	A	2828969	2	1	23	1	0	0	0	0	0	0	0	1	14260	1103	39	1		1	SH3BP2	4	2828969	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1951782	2828969	188325307	173	7617											
EVC	2121	hgsc.bcm.edu	37	chr4	5806512	5806512	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagaactcagcaacccttcGtcgggcagcaggacggcagg	11	4	13	13	3	1	1	1	0	0	1	3	2	1	2	1	4	4	4	1	4	3	1	rs115976359	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:5806512G>A	ENST00000264956.6	+	17	2689	c.2505G>A	c.(2503-2505)tcG>tcA	p.S835S	EVC_ENST00000382674.2_Silent_p.S835S	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	835					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)				GCAACCCTTCGTCGGGCAGCA	0.552													G|||	66	0.0131789	0.0008	0.0043	5008	,	,		20795	0.0		0.0109	False		,,,				2504	0.0521				p.S835S		Atlas-SNP	.											EVC,colon,carcinoma,0,3	EVC	90	3	0			c.G2505A						PASS	.	G		10,4396	16.8+/-37.8	0,10,2193	113	110	111		2505	-5	0	4	dbSNP_132	111	123,8477	64.2+/-126.4	1,121,4178	no	coding-synonymous	EVC	NM_153717.2		1,131,6371	AA,AG,GG		1.4302,0.227,1.0226		835/993	5806512	133,12873	2203	4300	6503	SO:0001819	synonymous_variant	2121	exon17			CCCTTCGTCGGGC	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.2505G>A	4.37:g.5806512G>A		54	0	0		96	40	0.416667	NM_153717		Silent	SNP	ENST00000264956.6	37	CCDS3383.1																																																																																			G|0.991;A|0.009	0.009	strong		0.552	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1			A	5806512	G	A	5806512	2	1	23	1	0	0	0	0	0	0	0	1	5287	1132	40	1		1	EVC	4	5806512	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	2977543	5806512	185347764	174	7618											
SLIT2	9353	hgsc.bcm.edu	37	chr4	20533613	20533613	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcttttttcttcaggcgtctCaataataatgaatttaccgt	10	18	5	8	2	4	1	2	1	3	0	5	1	4	1	1	1	1	0	1	1	5	8	rs150677598	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:20533613C>G	ENST00000504154.1	+	17	1872	c.1620C>G	c.(1618-1620)ctC>ctG	p.L540L	SLIT2_ENST00000503837.1_Silent_p.L536L|SLIT2_ENST00000273739.5_Silent_p.L544L|SLIT2_ENST00000503823.1_Silent_p.L532L	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	540					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						TCAGGCGTCTCAATAATAATG	0.279													C|||	8	0.00159744	0.0015	0.0029	5008	,	,		15813	0.0		0.002	False		,,,				2504	0.002				p.L540L		Atlas-SNP	.											SLIT2,NS,carcinoma,+2,1	SLIT2	290	1	0			c.C1620G						PASS	.	C		3,4403	4.2+/-10.8	0,3,2200	45	44	45		1620	3	1	4	dbSNP_134	45	30,8560	21.0+/-64.5	0,30,4265	no	coding-synonymous	SLIT2	NM_004787.1		0,33,6465	GG,GC,CC		0.3492,0.0681,0.2539		540/1530	20533613	33,12963	2203	4295	6498	SO:0001819	synonymous_variant	9353	exon17			GCGTCTCAATAAT	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.1620C>G	4.37:g.20533613C>G		286	0	0		265	128	0.483019	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Silent	SNP	ENST00000504154.1	37	CCDS3426.1																																																																																			C|0.998;G|0.002	0.002	strong		0.279	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			G	20533613	C	G	20533613	2	3	23	1	0	0	0	0	0	0	0	1	14755	813	29	4		4	SLIT2	4	20533613	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	14727101	20533613	170620663	175	7619											
KLF3	51274	hgsc.bcm.edu	37	chr4	38690515	38690515	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttcggcgtgccgctgtccAtgccaccagtgatggcagct	5	9	12	15	3	0	1	0	1	0	0	2	1	1	1	5	2	3	3	5	2	0	1	rs199559194		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:38690515A>G	ENST00000261438.5	+	3	672	c.367A>G	c.(367-369)Atg>Gtg	p.M123V	KLF3_ENST00000514033.1_Missense_Mutation_p.M123V	NM_016531.5	NP_057615.3	P57682	KLF3_HUMAN	Kruppel-like factor 3 (basic)	123	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						GCCGCTGTCCATGCCACCAGT	0.632																																					p.M123V		Atlas-SNP	.											.	KLF3	40	.	0			c.A367G						PASS	.	A	VAL/MET	0,4406		0,0,2203	51	54	53		367	5.5	1	4		53	1,8599	1.2+/-3.3	0,1,4299	no	missense	KLF3	NM_016531.5	21	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign	123/346	38690515	1,13005	2203	4300	6503	SO:0001583	missense	51274	exon3			CTGTCCATGCCAC	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.367A>G	4.37:g.38690515A>G	ENSP00000261438:p.Met123Val	141	0	0		161	73	0.453416	NM_016531	Q6PIR1|Q86TN0|Q9P2X6	Missense_Mutation	SNP	ENST00000261438.5	37	CCDS3444.1	.	.	.	.	.	.	.	.	.	.	A	14.68	2.607253	0.46527	0.0	1.16E-4	ENSG00000109787	ENST00000261438;ENST00000514033	T;T	0.42900	0.96;0.96	5.53	5.53	0.82687	.	0.059640	0.64402	D	0.000002	T	0.24160	0.0585	N	0.08118	0	0.28589	N	0.909727	B	0.02656	0.0	B	0.01281	0.0	T	0.06917	-1.0800	10	0.14656	T	0.56	.	15.827	0.78718	1.0:0.0:0.0:0.0	.	123	P57682	KLF3_HUMAN	V	123	ENSP00000261438:M123V;ENSP00000421252:M123V	ENSP00000261438:M123V	M	+	1	0	KLF3	38366910	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	4.350000	0.59392	2.324000	0.78689	0.533000	0.62120	ATG	A|0.999;G|0.001	0.001	weak		0.632	KLF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215093.2			G	38690515	A	G	38690515	3	3	23	1	0	0	0	0	1	0	0	0	8356	217	8	3	373	3	KLF3	4	38690515	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	18156902	38690515	152463761	176	7620											
KLF3	51274	hgsc.bcm.edu	37	chr4	38696385	38696385	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aggaatcacccttcggtcatCgtgcagcctgggaagagacc	10	7	12	12	2	2	1	2	0	0	1	4	4	2	3	3	3	2	1	3	3	2	1	rs142916199	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:38696385C>T	ENST00000261438.5	+	5	1019	c.714C>T	c.(712-714)atC>atT	p.I238I		NM_016531.5	NP_057615.3	P57682	KLF3_HUMAN	Kruppel-like factor 3 (basic)	238	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						CTTCGGTCATCGTGCAGCCTG	0.458													C|||	2	0.000399361	0.0	0.0014	5008	,	,		19533	0.0		0.001	False		,,,				2504	0.0				p.I238I		Atlas-SNP	.											.	KLF3	40	.	0			c.C714T						PASS	.	C		0,4406		0,0,2203	137	135	136		714	-12.3	0.3	4	dbSNP_134	136	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	KLF3	NM_016531.5		0,6,6497	TT,TC,CC		0.0698,0.0,0.0461		238/346	38696385	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	51274	exon5			GGTCATCGTGCAG	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.714C>T	4.37:g.38696385C>T		109	0	0		126	67	0.531746	NM_016531	Q6PIR1|Q86TN0|Q9P2X6	Silent	SNP	ENST00000261438.5	37	CCDS3444.1																																																																																			C|0.999;T|0.001	0.001	strong		0.458	KLF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215093.2			T	38696385	C	T	38696385	2	4	23	1	0	0	0	0	0	0	0	1	8356	874	31	1		1	KLF3	4	38696385	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	5870	38696385	152457891	177	7621											
TLR1	7096	hgsc.bcm.edu	37	chr4	38799493	38799493	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcatattcgaaaagatttcAtagatataactttgcggaaa	16	14	6	5	2	2	2	2	0	0	2	3	4	2	3	0	1	2	0	0	1	7	8	rs200631178		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:38799493A>G	ENST00000502213.2	-	3	1189	c.960T>C	c.(958-960)taT>taC	p.Y320Y	TLR1_ENST00000308979.2_Silent_p.Y320Y			Q15399	TLR1_HUMAN	toll-like receptor 1	320					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						AAAAGATTTCATAGATATAAC	0.413																																					p.Y320Y	GBM(5;216 373 40795 46382)	Atlas-SNP	.											.	TLR1	70	.	0			c.T960C						PASS	.	A		1,4405	2.1+/-5.4	0,1,2202	58	61	60		960	-4.8	0	4		60	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TLR1	NM_003263.3		0,2,6501	GG,GA,AA		0.0116,0.0227,0.0154		320/787	38799493	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	7096	exon4			GATTTCATAGATA	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.960T>C	4.37:g.38799493A>G		55	0	0		46	26	0.565217	NM_003263	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Silent	SNP	ENST00000502213.2	37	CCDS33973.1																																																																																			A|0.999;G|0.001	0.001	weak		0.413	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3			G	38799493	A	G	38799493	2	3	23	1	0	0	0	0	0	0	0	1	15964	224	8	3		3	TLR1	4	38799493	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	103108	38799493	152354783	178	7622											
GUF1	60558	hgsc.bcm.edu	37	chr4	44680660	44680660	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atgtggaccctcgtgggtcgGggctgggggtgcgcacgcgc	3	7	20	11	5	0	0	0	0	0	0	2	1	0	1	1	6	1	2	1	6	0	0			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:44680660G>A	ENST00000281543.5	+	1	215	c.21G>A	c.(19-21)cgG>cgA	p.R7R	GUF1_ENST00000506793.1_Intron	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						TCGTGGGTCGGGGCTGGGGGT	0.721																																					p.R7R		Atlas-SNP	.											.	GUF1	72	.	0			c.G21A						PASS	.						5	6	5					4																	44680660		1813	3768	5581	SO:0001819	synonymous_variant	60558	exon1			GGGTCGGGGCTGG		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.21G>A	4.37:g.44680660G>A		44	0	0		34	16	0.470588	NM_021927		Silent	SNP	ENST00000281543.5	37	CCDS3468.1																																																																																			.	.	none		0.721	GUF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250469.3	NM_021927		A	44680660	G	A	44680660	2	1	23	1	0	0	0	0	0	0	0	1	6908	1219	43	2		2	GUF1	4	44680660	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	5881167	44680660	146473616	179	7623											
LPHN3	23284	hgsc.bcm.edu	37	chr4	62845326	62845326	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ttctggatgtgatcacgtggGttggaattttgctgtccctt	5	17	12	7	1	2	1	1	1	1	0	3	3	3	3	1	3	1	2	1	3	1	5			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:62845326G>A	ENST00000514591.1	+	17	2976	c.2647G>A	c.(2647-2649)Gtt>Att	p.V883I	LPHN3_ENST00000514157.1_Missense_Mutation_p.V883I|LPHN3_ENST00000506746.1_Missense_Mutation_p.V951I|LPHN3_ENST00000512091.2_Missense_Mutation_p.V883I|LPHN3_ENST00000509896.1_Missense_Mutation_p.V951I|LPHN3_ENST00000507164.1_Missense_Mutation_p.V951I|LPHN3_ENST00000506700.1_Missense_Mutation_p.V883I|LPHN3_ENST00000508693.1_Missense_Mutation_p.V951I|LPHN3_ENST00000506720.1_Missense_Mutation_p.V951I|LPHN3_ENST00000545650.1_Missense_Mutation_p.V883I|LPHN3_ENST00000514996.1_Missense_Mutation_p.V883I|LPHN3_ENST00000504896.1_Missense_Mutation_p.V883I|LPHN3_ENST00000507625.1_Missense_Mutation_p.V951I|LPHN3_ENST00000508946.1_Missense_Mutation_p.V883I|LPHN3_ENST00000511324.1_Missense_Mutation_p.V951I			Q9HAR2	LPHN3_HUMAN	latrophilin 3	870					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						GATCACGTGGGTTGGAATTTT	0.458																																					p.V883I		Atlas-SNP	.											.	LPHN3	800	.	0			c.G2647A						PASS	.						321	314	316					4																	62845326		1998	4191	6189	SO:0001583	missense	23284	exon15			ACGTGGGTTGGAA	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.2647G>A	4.37:g.62845326G>A	ENSP00000422533:p.Val883Ile	417	0	0		435	66	0.151724	NM_015236	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	37	CCDS54768.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.8|25.8	4.679692|4.679692	0.88542|0.88542	.|.	.|.	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	.|0.54279	.|0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58	5.5|5.5	5.5|5.5	0.81552|0.81552	.|GPCR, family 2-like (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.64789|0.64789	0.2630|0.2630	L|L	0.37800|0.37800	1.135|1.135	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.69078	.|0.997;0.997;0.996	.|D;D;D	.|0.79108	.|0.992;0.992;0.987	T|T	0.61207|0.61207	-0.7109|-0.7109	5|10	.|0.35671	.|T	.|0.21	.|.	19.0068|19.0068	0.92854|0.92854	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|883;870;883	.|E9PE04;Q9HAR2;Q9HAR2-2	.|.;LPHN3_HUMAN;.	D|I	340|883;883;951;951;883;883;870;883;951;951;951;883;883;883;951;951;883	.|ENSP00000423388:V883I;ENSP00000422533:V883I;ENSP00000423787:V951I;ENSP00000425033:V951I;ENSP00000424120:V883I;ENSP00000439831:V883I;ENSP00000421476:V951I;ENSP00000424030:V951I;ENSP00000421372:V951I;ENSP00000425201:V883I;ENSP00000423434:V883I;ENSP00000421627:V883I;ENSP00000420931:V951I;ENSP00000425884:V951I;ENSP00000424258:V883I	.|ENSP00000280009:V883I	G|V	+|+	2|1	0|0	LPHN3|LPHN3	62527921|62527921	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	9.808000|9.808000	0.99193|0.99193	2.580000|2.580000	0.87095|0.87095	0.467000|0.467000	0.42956|0.42956	GGT|GTT	.	.	none		0.458	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1			A	62845326	G	A	62845326	3	1	23	1	0	0	0	0	1	0	0	0	8926	1261	44	2	2705	2	LPHN3	4	62845326	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	18164666	62845326	128308950	180	7624											
UGT2B4	7363	hgsc.bcm.edu	37	chr4	70361163	70361163	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcaaatcttgactcctgtagTttcttcataagtttcttatt	9	20	4	8	0	5	1	2	1	3	0	6	1	6	1	1	0	0	3	1	0	4	8			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:70361163T>C	ENST00000305107.6	-	1	463	c.417A>G	c.(415-417)aaA>aaG	p.K139K	UGT2B4_ENST00000512583.1_Silent_p.K139K|UGT2B4_ENST00000381096.3_Intron|UGT2B4_ENST00000506580.1_5'UTR	NM_021139.2	NP_066962.2	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B4	139					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)	ACTCCTGTAGTTTCTTCATAA	0.368																																					p.K139K		Atlas-SNP	.											.	UGT2B4	105	.	0			c.A417G						PASS	.						37	38	38					4																	70361163		2144	4283	6427	SO:0001819	synonymous_variant	7363	exon1			CTGTAGTTTCTTC	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.417A>G	4.37:g.70361163T>C		135	0	0		157	28	0.178344	NM_021139	A6NCP7|B4DT75|G5E9X8|O60731|O60867|O75614|P36538|Q1HBF9|Q6QQX7	Silent	SNP	ENST00000305107.6	37	CCDS43234.1																																																																																			.	.	none		0.368	UGT2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365526.1	NM_021139		C	70361163	T	C	70361163	2	2	23	1	0	0	0	0	0	0	0	1	16976	1722	60	3		3	UGT2B4	4	70361163	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	7515837	70361163	120793113	181	7625											
UGT2B4	7363	hgsc.bcm.edu	37	chr4	70361334	70361334	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atatcctcaaactcagttttAgttaaagatacaggataaac	17	12	5	7	0	2	1	2	0	0	1	3	2	3	2	1	1	3	2	1	1	8	6			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:70361334A>C	ENST00000305107.6	-	1	292	c.246T>G	c.(244-246)acT>acG	p.T82T	UGT2B4_ENST00000512583.1_Silent_p.T82T|UGT2B4_ENST00000381096.3_Intron|UGT2B4_ENST00000506580.1_5'UTR	NM_021139.2	NP_066962.2	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B4	82					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)	ACTCAGTTTTAGTTAAAGATA	0.373																																					p.T82T		Atlas-SNP	.											.	UGT2B4	105	.	0			c.T246G						PASS	.						53	54	54					4																	70361334		2133	4279	6412	SO:0001819	synonymous_variant	7363	exon1			AGTTTTAGTTAAA	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.246T>G	4.37:g.70361334A>C		136	0	0		143	24	0.167832	NM_021139	A6NCP7|B4DT75|G5E9X8|O60731|O60867|O75614|P36538|Q1HBF9|Q6QQX7	Silent	SNP	ENST00000305107.6	37	CCDS43234.1																																																																																			.	.	none		0.373	UGT2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365526.1	NM_021139		C	70361334	A	C	70361334	2	2	23	1	0	0	0	0	0	0	0	1	16976	407	15	5		5	UGT2B4	4	70361334	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	171	70361334	120792942	182	7626											
DSPP	1834	hgsc.bcm.edu	37	chr4	88536321	88536321	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tagtgacagcagcgatagcaGcaacagcagtgatagcagcg	14	5	13	9	2	0	2	0	2	0	0	0	3	0	2	0	0	8	5	0	0	4	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:88536321G>A	ENST00000282478.7	+	4	2540	c.2507G>A	c.(2506-2508)aGc>aAc	p.S836N	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.S836N			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	836	Asp/Ser-rich.			S -> C (in Ref. 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)		agcgatagcagcaacagcagt	0.498																																					p.S836N		Atlas-SNP	.											.	DSPP	174	.	0			c.G2507A						PASS	.						87	109	101					4																	88536321		1645	2951	4596	SO:0001583	missense	1834	exon5			ATAGCAGCAACAG	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.2507G>A	4.37:g.88536321G>A	ENSP00000282478:p.Ser836Asn	415	0	0		389	18	0.0462725	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	g	2.602	-0.292775	0.05568	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.87412	-2.25;-2.25	0.918	0.918	0.19386	.	.	.	.	.	T	0.80623	0.4658	L	0.46157	1.445	0.09310	N	1	B	0.19817	0.039	B	0.20384	0.029	T	0.70281	-0.4915	9	0.54805	T	0.06	.	5.1892	0.15201	0.0:0.0:1.0:0.0	.	836	Q9NZW4	DSPP_HUMAN	N	836	ENSP00000382213:S836N;ENSP00000282478:S836N	ENSP00000282478:S836N	S	+	2	0	DSPP	88755345	0.550000	0.26489	0.027000	0.17364	0.003000	0.03518	0.902000	0.28459	0.792000	0.33850	0.165000	0.16767	AGC	.	.	none		0.498	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		A	88536321	G	A	88536321	3	1	23	1	0	0	0	0	1	0	0	0	4784	971	34	2	2521	2	DSPP	4	88536321	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	18174987	88536321	102617955	183	7627											
FAM13A	10144	hgsc.bcm.edu	37	chr4	89950630	89950630	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatgctgcgtcaaatattcCactatattccacactactgc	11	12	4	14	1	1	0	1	0	0	0	3	0	3	0	3	0	4	1	3	0	5	6			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:89950630C>G	ENST00000264344.5	-	2	405	c.198G>C	c.(196-198)gtG>gtC	p.V66V	FAM13A_ENST00000515600.1_Silent_p.V66V|FAM13A_ENST00000502459.1_5'UTR|FAM13A_ENST00000509094.1_Silent_p.V66V|FAM13A_ENST00000511976.1_5'UTR	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	66	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)			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						TCAAATATTCCACTATATTCC	0.393																																					p.V66V		Atlas-SNP	.											.	FAM13A	181	.	0			c.G198C						PASS	.						158	152	154					4																	89950630		2203	4300	6503	SO:0001819	synonymous_variant	10144	exon2			ATATTCCACTATA	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.198G>C	4.37:g.89950630C>G		124	0	0		137	17	0.124088	NM_014883	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Silent	SNP	ENST00000264344.5	37	CCDS34029.1																																																																																			.	.	none		0.393	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1			G	89950630	C	G	89950630	2	3	23	1	0	0	0	0	0	0	0	1	5457	581	21	4		4	FAM13A	4	89950630	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1414309	89950630	101203646	184	7628											
TET2	54790	hgsc.bcm.edu	37	chr4	106183003	106183003	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacctgatgcatataataatCaggtaagtttaaataatcat	17	13	5	6	0	2	1	2	1	0	0	2	1	2	1	1	1	1	3	1	1	7	7			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:106183003C>A	ENST00000540549.1	+	8	4902	c.4042C>A	c.(4042-4044)Cag>Aag	p.Q1348K	TET2_ENST00000513237.1_Missense_Mutation_p.Q1369K|TET2_ENST00000380013.4_Missense_Mutation_p.Q1348K|TET2_ENST00000545826.1_3'UTR			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1348					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)		ATATAATAATCAGGTAAGTTT	0.308			"Mis N, F"		MDS																																p.Q1348K		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	0			c.C4042A						PASS	.						66	58	60					4																	106183003		692	1587	2279	SO:0001583	missense	54790	exon8			AATAATCAGGTAA	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.4042C>A	4.37:g.106183003C>A	ENSP00000442788:p.Gln1348Lys	269	0	0		253	28	0.110672	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Missense_Mutation	SNP	ENST00000540549.1	37	CCDS47120.1	.	.	.	.	.	.	.	.	.	.	C	32	5.148220	0.94603	.	.	ENSG00000168769	ENST00000540549;ENST00000513237;ENST00000380013	T;T;T	0.14266	2.52;2.52;2.52	5.36	5.36	0.76844	TET cysteine-rich domain (1);	.	.	.	.	T	0.45034	0.1322	M	0.86268	2.805	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.91635	0.999;0.999	T	0.50566	-0.8813	9	0.87932	D	0	-11.679	19.0905	0.93225	0.0:1.0:0.0:0.0	.	1369;1348	E7EQS8;Q6N021	.;TET2_HUMAN	K	1348;1369;1348	ENSP00000442788:Q1348K;ENSP00000425443:Q1369K;ENSP00000369351:Q1348K	ENSP00000369351:Q1348K	Q	+	1	0	TET2	106402452	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.585000	0.82584	2.526000	0.85167	0.555000	0.69702	CAG	.	.	none		0.308	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		A	106183003	C	A	106183003	3	1	23	1	0	0	0	0	1	0	0	0	15785	827	29	4	4153	4	TET2	4	106183003	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	16232373	106183003	84971273	185	7629											
TET2	54790	hgsc.bcm.edu	37	chr4	106197061	106197061	+	Frame_Shift_Del	DEL	A	A	-																															cacacagctaatgggttatcAaagatgcttccagctcttaa																										TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:106197061delA	ENST00000540549.1	+	11	6254	c.5394delA	c.(5392-5394)tcafs	p.S1798fs	TET2_ENST00000513237.1_Frame_Shift_Del_p.S1819fs|TET2_ENST00000380013.4_Frame_Shift_Del_p.S1798fs|TET2_ENST00000545826.1_3'UTR			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1798					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)		ATGGGTTATCAAAGATGCTTC	0.463			"Mis N, F"		MDS																																p.S1798X		Atlas-Indel	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	0			c.5393delC						PASS	.						23	21	21					4																	106197061		692	1591	2283	SO:0001589	frameshift_variant	54790	exon11			.	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.5394delA	4.37:g.106197061delA	ENSP00000442788:p.Ser1798fs	140	0	0		130	22	0.169231	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Frame_Shift_Del	DEL	ENST00000540549.1	37	CCDS47120.1																																																																																			.	.	none		0.463	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		-	106197061	A	-	106197061	7	5	23	1	0	1	0	1	0	0	0	0	15785	117	5	0	5517	0	TET2	4	106197061	Frame_Shift_Del	DEL	A	TCGA-G8-6325-01A-11D-2210-10	14058	106197061	84957215	186	7630											
CFI	3426	hgsc.bcm.edu	37	chr4	110682723	110682723	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgaaatcctggtaacccataGttcttctcttagtaaaagta	13	13	6	9	1	2	0	0	0	2	0	4	1	3	0	2	1	1	4	2	1	7	7	rs138346388	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:110682723G>A	ENST00000394634.2	-	4	815	c.608C>T	c.(607-609)aCt>aTt	p.T203I	CFI_ENST00000512148.1_Missense_Mutation_p.T203I|CFI_ENST00000394635.3_Missense_Mutation_p.T203I	NM_000204.3	NP_000195	P05156	CFAI_HUMAN	complement factor I	203	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				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)		GTAACCCATAGTTCTTCTCTT	0.393													G|||	2	0.000399361	0.0	0.0029	5008	,	,		20003	0.0		0.0	False		,,,				2504	0.0				p.T203I		Atlas-SNP	.											.	CFI	59	.	0			c.C608T						PASS	.	G	ILE/THR	0,4406		0,0,2203	166	155	159		608	0.1	0	4	dbSNP_134	159	7,8593	5.7+/-21.5	0,7,4293	yes	missense	CFI	NM_000204.3	89	0,7,6496	AA,AG,GG		0.0814,0.0,0.0538	benign	203/584	110682723	7,12999	2203	4300	6503	SO:0001583	missense	3426	exon4			CCCATAGTTCTTC	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.608C>T	4.37:g.110682723G>A	ENSP00000378130:p.Thr203Ile	134	0	0		132	59	0.44697	NM_000204	O60442	Missense_Mutation	SNP	ENST00000394634.2	37	CCDS34049.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	8.946	0.967013	0.18659	0.0	8.14E-4	ENSG00000205403	ENST00000394635;ENST00000394634;ENST00000540104;ENST00000512148;ENST00000536228	T;T;T	0.36878	1.23;1.23;1.23	5.36	0.101	0.14517	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	1.803530	0.01919	N	0.040391	T	0.27489	0.0675	L	0.41236	1.265	0.09310	N	1	B;B;B	0.24721	0.03;0.11;0.063	B;B;B	0.19946	0.01;0.025;0.027	T	0.10405	-1.0631	10	0.37606	T	0.19	-0.3525	1.2864	0.02052	0.1647:0.3065:0.2732:0.2555	.	203;203;203	E7ETH0;G3XAM2;P05156	.;.;CFAI_HUMAN	I	203;203;203;203;185	ENSP00000378131:T203I;ENSP00000378130:T203I;ENSP00000427438:T203I	ENSP00000378130:T203I	T	-	2	0	CFI	110902172	0.000000	0.05858	0.000000	0.03702	0.086000	0.17979	0.324000	0.19610	-0.031000	0.13781	-0.274000	0.10170	ACT	G|0.999;A|0.001	0.001	strong		0.393	CFI-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_000204		A	110682723	G	A	110682723	3	1	23	1	0	0	0	0	1	0	0	0	3291	1029	36	2	1183	2	CFI	4	110682723	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	4485662	110682723	80471553	187	7631											
EGF	1950	hgsc.bcm.edu	37	chr4	110884396	110884396	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttagcccagtatcctgggaAtgtgattgctttcctgggta	7	14	11	9	0	0	1	0	1	0	0	2	2	2	2	3	2	2	3	3	2	4	5	rs11568953	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:110884396A>G	ENST00000265171.5	+	9	1825	c.1380A>G	c.(1378-1380)gaA>gaG	p.E460E	EGF_ENST00000503392.1_Silent_p.E460E|EGF_ENST00000509793.1_Silent_p.E418E	NM_001178130.1|NM_001963.4	NP_001171601.1|NP_001954.2	P01133	EGF_HUMAN	epidermal growth factor	460	EGF-like 4. {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)	TATCCTGGGAATGTGATTGCT	0.453													A|||	22	0.00439297	0.0015	0.0043	5008	,	,		15769	0.0		0.0169	False		,,,				2504	0.0				p.E460E		Atlas-SNP	.											.	EGF	113	.	0			c.A1380G						PASS	.	A	,,	9,4397	15.5+/-35.6	0,9,2194	223	208	213		1380,1254,1380	0.7	1	4	dbSNP_120	213	123,8477	64.2+/-126.4	2,119,4179	no	coding-synonymous,coding-synonymous,coding-synonymous	EGF	NM_001178130.1,NM_001178131.1,NM_001963.4	,,	2,128,6373	GG,GA,AA		1.4302,0.2043,1.0149	,,	460/1167,418/1166,460/1208	110884396	132,12874	2203	4300	6503	SO:0001819	synonymous_variant	1950	exon9			CTGGGAATGTGAT	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.1380A>G	4.37:g.110884396A>G		148	0	0		132	66	0.5	NM_001963	B4DRK7|E7EVD2|E9PBF0|Q52LZ6	Silent	SNP	ENST00000265171.5	37	CCDS3689.1																																																																																			A|0.990;G|0.010	0.010	strong		0.453	EGF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255065.1			G	110884396	A	G	110884396	2	3	23	1	0	0	0	0	0	0	0	1	4964	98	4	3		3	EGF	4	110884396	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	201673	110884396	80269880	188	7632											
ANK2	287	hgsc.bcm.edu	37	chr4	114274519	114274519	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagcagtgtgcagagctctcGgtctgagagaggattagttg	10	10	15	6	1	2	3	0	1	2	2	3	5	2	4	0	2	3	4	0	2	2	2	rs138842207	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:114274519G>A	ENST00000357077.4	+	38	4798	c.4745G>A	c.(4744-4746)cGg>cAg	p.R1582Q	ANK2_ENST00000510275.2_Intron|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000264366.6_Missense_Mutation_p.R1549Q|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000506722.1_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	1582					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)		CAGAGCTCTCGGTCTGAGAGA	0.408													G|||	2	0.000399361	0.0	0.0	5008	,	,		21338	0.0		0.002	False		,,,				2504	0.0				p.R1582Q		Atlas-SNP	.											ANK2,rectum,carcinoma,+1,1	ANK2	576	1	0			c.G4745A						PASS	.	G	,GLN/ARG,	0,4406		0,0,2203	82	88	86		,4745,	0.9	0	4	dbSNP_134	86	11,8589	9.1+/-34.3	0,11,4289	yes	intron,missense,intron	ANK2	NM_001127493.1,NM_001148.4,NM_020977.3	,43,	0,11,6492	AA,AG,GG		0.1279,0.0,0.0846	,benign,	,1582/3958,	114274519	11,12995	2203	4300	6503	SO:0001583	missense	287	exon38			GCTCTCGGTCTGA	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.4745G>A	4.37:g.114274519G>A	ENSP00000349588:p.Arg1582Gln	195	0	0		211	101	0.478673	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	0	-2.736183	0.00088	0.0	0.001279	ENSG00000145362	ENST00000503423;ENST00000504454;ENST00000357077;ENST00000264366	T;T;T;T	0.65364	0.08;-0.02;-0.11;-0.15	4.9	0.954	0.19595	.	1.073890	0.07232	N	0.862650	T	0.28732	0.0712	N	0.02539	-0.55	0.19575	N	0.999967	B;B	0.10296	0.001;0.003	B;B	0.06405	0.001;0.002	T	0.22661	-1.0210	10	0.11182	T	0.66	.	1.566	0.02605	0.549:0.1302:0.1777:0.143	.	1549;1582	Q01484;Q01484-4	ANK2_HUMAN;.	Q	1495;1597;1582;1549	ENSP00000421011:R1495Q;ENSP00000424722:R1597Q;ENSP00000349588:R1582Q;ENSP00000264366:R1549Q	ENSP00000264366:R1549Q	R	+	2	0	ANK2	114493968	0.622000	0.27085	0.017000	0.16124	0.013000	0.08279	0.864000	0.27926	0.340000	0.23745	0.557000	0.71058	CGG	G|0.999;A|0.001	0.001	strong		0.408	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148		A	114274519	G	A	114274519	3	1	23	1	0	0	0	0	1	0	0	0	621	1116	39	1	4960	1	ANK2	4	114274519	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	3390123	114274519	76879757	189	7633											
MAD2L1	4085	hgsc.bcm.edu	37	chr4	120981323	120981323	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catgctatttactttgtggaTtgtagtagtaaatgaacgaa	13	15	9	4	1	0	1	0	1	0	0	0	3	0	2	0	1	3	4	0	1	8	8	rs61752608	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:120981323T>C	ENST00000296509.6	-	5	907	c.568A>G	c.(568-570)Atc>Gtc	p.I190V		NM_002358.3	NP_002349.1	Q13257	MD2L1_HUMAN	MAD2 mitotic arrest deficient-like 1 (yeast)	190	HORMA. {ECO:0000255|PROSITE- ProRule:PRU00109}.			I -> V (in Ref. 11; AAH70283). {ECO:0000305}.	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						ACTTTGTGGATTGTAGTAGTA	0.378													T|||	15	0.00299521	0.0015	0.0058	5008	,	,		17896	0.0		0.006	False		,,,				2504	0.0031				p.I190V		Atlas-SNP	.											.	MAD2L1	17	.	0			c.A568G						PASS	.	T	VAL/ILE	8,4398	14.3+/-33.2	0,8,2195	119	116	117		568	3.9	1	4	dbSNP_129	117	49,8551	31.2+/-83.2	1,47,4252	no	missense	MAD2L1	NM_002358.3	29	1,55,6447	CC,CT,TT		0.5698,0.1816,0.4383	benign	190/206	120981323	57,12949	2203	4300	6503	SO:0001583	missense	4085	exon5			TGTGGATTGTAGT	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.568A>G	4.37:g.120981323T>C	ENSP00000296509:p.Ile190Val	107	0	0		111	58	0.522523	NM_002358	Q53F56|Q548X9|Q6IRW7|Q8IZX3	Missense_Mutation	SNP	ENST00000296509.6	37	CCDS3715.1	6	0.0027472527472527475	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	T	12.85	2.062016	0.36373	0.001816	0.005698	ENSG00000164109	ENST00000296509	.	.	.	5.13	3.94	0.45596	DNA-binding HORMA (4);	0.000000	0.85682	D	0.000000	T	0.37210	0.0995	L	0.33753	1.03	0.80722	D	1	B	0.31274	0.317	B	0.34824	0.19	T	0.16453	-1.0402	9	0.21540	T	0.41	-14.1793	11.0557	0.47915	0.0:0.0739:0.0:0.9261	rs61752608	190	Q13257	MD2L1_HUMAN	V	190	.	ENSP00000296509:I190V	I	-	1	0	MAD2L1	121200771	1.000000	0.71417	0.974000	0.42286	0.993000	0.82548	5.799000	0.69101	0.888000	0.36160	0.482000	0.46254	ATC	T|0.997;C|0.003	0.003	strong		0.378	MAD2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256525.2			C	120981323	T	C	120981323	3	2	23	1	0	0	0	0	1	0	0	0	9157	1493	52	3	53	3	MAD2L1	4	120981323	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	6706804	120981323	70172953	190	7634											
QRFPR	84109	hgsc.bcm.edu	37	chr4	122301595	122301595	+	Missense_Mutation	SNP	C	C	A																															catggccttgctgcgggtcaCcacgtagaacaccagagcat																								rs55693553	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:122301595C>A	ENST00000394427.2	-	1	619	c.208G>T	c.(208-210)Gtg>Ttg	p.V70L	QRFPR_ENST00000334383.5_Missense_Mutation_p.V70L	NM_198179.2	NP_937822.2	Q96P65	QRFPR_HUMAN	pyroglutamylated RFamide peptide receptor	70					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						CTGCGGGTCACCACGTAGAAC	0.612													C|||	38	0.00758786	0.0008	0.0187	5008	,	,		15467	0.0		0.0239	False		,,,				2504	0.0				p.V70L		Atlas-SNP	.											.	QRFPR	65	.	0			c.G208T						PASS	.						93	74	81					4																	122301595		2203	4300	6503	SO:0001583	missense	84109	exon1			GGGTCACCACGTA	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.208G>T	4.37:g.122301595C>A	ENSP00000377948:p.Val70Leu	159	0	0		180	94	0.522222	NM_198179		Missense_Mutation	SNP	ENST00000394427.2	37	CCDS3719.1	22	0.010073260073260074	0	0.0	6	0.016574585635359115	0	0.0	16	0.021108179419525065	C	26.5	4.740826	0.89573	.	.	ENSG00000186867	ENST00000394427;ENST00000334383	T;T	0.35048	1.33;1.33	5.18	5.18	0.71444	GPCR, rhodopsin-like superfamily (1);	0.054824	0.64402	D	0.000001	T	0.24236	0.0587	L	0.46947	1.48	0.58432	D	0.999997	P;P;P	0.47841	0.626;0.901;0.88	B;P;P	0.45610	0.233;0.487;0.47	T	0.04078	-1.0979	10	0.34782	T	0.22	.	18.2778	0.90088	0.0:1.0:0.0:0.0	rs55693553;rs61741355	70;70;70	F2Z3L3;Q96P65;G4XH69	.;QRFPR_HUMAN;.	L	70	ENSP00000377948:V70L;ENSP00000335610:V70L	ENSP00000335610:V70L	V	-	1	0	QRFPR	122521045	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.614000	0.46359	2.383000	0.81215	0.467000	0.42956	GTG	C|0.987;A|0.013	0.013	strong		0.612	QRFPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256641.2	NM_198179		A	122301595	C	A	122301595	3	1	23	1	0	0	0	0	1	0	0	0	12893	507	18	4	1111	4	QRFPR	4	122301595	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1320272	122301595	68852681	191	7635	99	2									
QRFPR	84109	hgsc.bcm.edu	37	chr4	122301597	122301597	+	Missense_Mutation	SNP	A	A	C																															tggccttgctgcgggtcaccAcgtagaacaccagagcattg																								rs34270076	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:122301597A>C	ENST00000394427.2	-	1	617	c.206T>G	c.(205-207)gTg>gGg	p.V69G	QRFPR_ENST00000334383.5_Missense_Mutation_p.V69G	NM_198179.2	NP_937822.2	Q96P65	QRFPR_HUMAN	pyroglutamylated RFamide peptide receptor	69					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						GCGGGTCACCACGTAGAACAC	0.612													A|||	38	0.00758786	0.0008	0.0187	5008	,	,		15547	0.0		0.0239	False		,,,				2504	0.0				p.V69G		Atlas-SNP	.											.	QRFPR	65	.	0			c.T206G						PASS	.						92	74	80					4																	122301597		2203	4300	6503	SO:0001583	missense	84109	exon1			GTCACCACGTAGA	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.206T>G	4.37:g.122301597A>C	ENSP00000377948:p.Val69Gly	156	0	0		180	93	0.516667	NM_198179		Missense_Mutation	SNP	ENST00000394427.2	37	CCDS3719.1	22	0.010073260073260074	0	0.0	6	0.016574585635359115	0	0.0	16	0.021108179419525065	A	24.8	4.575947	0.86645	.	.	ENSG00000186867	ENST00000394427;ENST00000334383	T;T	0.46451	0.87;0.87	5.18	5.18	0.71444	GPCR, rhodopsin-like superfamily (1);	0.053895	0.64402	D	0.000001	T	0.60143	0.2246	H	0.95679	3.705	0.80722	D	1	D;D;D	0.76494	0.986;0.999;0.999	P;D;D	0.74674	0.907;0.984;0.963	T	0.79184	-0.1908	10	0.87932	D	0	.	14.6829	0.69031	1.0:0.0:0.0:0.0	rs34270076	69;69;69	F2Z3L3;Q96P65;G4XH69	.;QRFPR_HUMAN;.	G	69	ENSP00000377948:V69G;ENSP00000335610:V69G	ENSP00000335610:V69G	V	-	2	0	QRFPR	122521047	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.979000	0.93455	1.930000	0.55929	0.383000	0.25322	GTG	A|0.987;C|0.013	0.013	strong		0.612	QRFPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256641.2	NM_198179		C	122301597	A	C	122301597	3	2	23	1	0	0	0	0	1	0	0	0	12893	159	6	5	1113	5	QRFPR	4	122301597	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	2	122301597	68852679	192	7636	99	2									
POU4F2	5458	hgsc.bcm.edu	37	chr4	147561147	147561147	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacagccccttcaaaccggaCgccacctaccacactatgaa	13	5	5	18	2	1	1	1	1	0	0	1	2	1	2	6	1	3	0	6	1	4	3	rs147517729	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:147561147C>A	ENST00000281321.3	+	2	665	c.417C>A	c.(415-417)gaC>gaA	p.D139E	AC093887.1_ENST00000584185.1_RNA	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN	POU class 4 homeobox 2	139					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)					TCAAACCGGACGCCACCTACC	0.657													C|||	10	0.00199681	0.0008	0.0014	5008	,	,		13029	0.0		0.007	False		,,,				2504	0.001				p.D139E		Atlas-SNP	.											.	POU4F2	83	.	0			c.C417A						PASS	.	C	GLU/ASP	16,4390	23.3+/-48.9	0,16,2187	118	143	135		417	5.8	1	4	dbSNP_134	135	111,8489	59.8+/-121.6	2,107,4191	yes	missense	POU4F2	NM_004575.2	45	2,123,6378	AA,AC,CC		1.2907,0.3631,0.9765	probably-damaging	139/410	147561147	127,12879	2203	4300	6503	SO:0001583	missense	5458	exon2			ACCGGACGCCACC	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.417C>A	4.37:g.147561147C>A	ENSP00000281321:p.Asp139Glu	82	0	0		78	36	0.461538	NM_004575	B1PJR6|B2RC84|Q13883|Q14987	Missense_Mutation	SNP	ENST00000281321.3	37	CCDS34074.1	7	0.003205128205128205	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	C	19.43	3.826606	0.71143	0.003631	0.012907	ENSG00000151615	ENST00000281321	T	0.25912	1.77	5.77	5.77	0.91146	.	0.000000	0.43110	D	0.000613	T	0.39064	0.1064	L	0.58510	1.815	0.80722	D	1	D	0.89917	1.0	D	0.70227	0.968	T	0.04976	-1.0914	10	0.23891	T	0.37	.	18.7641	0.91865	0.0:1.0:0.0:0.0	.	139	Q12837	PO4F2_HUMAN	E	139	ENSP00000281321:D139E	ENSP00000281321:D139E	D	+	3	2	POU4F2	147780597	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.140000	0.50585	2.729000	0.93468	0.467000	0.42956	GAC	C|0.992;A|0.008	0.008	strong		0.657	POU4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367020.1	NM_004575		A	147561147	C	A	147561147	3	1	23	1	0	0	0	0	1	0	0	0	12288	535	19	4	423	4	POU4F2	4	147561147	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	25259550	147561147	43593129	193	7637											
EDNRA	1909	hgsc.bcm.edu	37	chr4	148461071	148461071	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgaagaaaactgtgtataacGagatggacaagaaccgatgt	17	8	11	5	2	0	4	0	1	0	3	0	7	0	5	1	1	3	1	1	1	7	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:148461071G>A	ENST00000324300.5	+	6	1518	c.1003G>A	c.(1003-1005)Gag>Aag	p.E335K	EDNRA_ENST00000339690.5_3'UTR|EDNRA_ENST00000358556.4_Missense_Mutation_p.E226K|EDNRA_ENST00000503721.1_3'UTR|EDNRA_ENST00000506066.1_Missense_Mutation_p.E226K|EDNRA_ENST00000511804.1_Missense_Mutation_p.E110K	NM_001957.3	NP_001948.1	P25101	EDNRA_HUMAN	endothelin receptor type A	335					activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|artery smooth muscle contraction (GO:0014824)|cell proliferation (GO:0008283)|cellular response to mechanical stimulus (GO:0071260)|endothelin receptor signaling pathway (GO:0086100)|enteric nervous system development (GO:0048484)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|glomerular filtration (GO:0003094)|glucose transport (GO:0015758)|head development (GO:0060322)|heart development (GO:0007507)|histamine secretion (GO:0001821)|in utero embryonic development (GO:0001701)|maternal process involved in parturition (GO:0060137)|metabolic process (GO:0008152)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cAMP biosynthetic process (GO:0030818)|neural crest cell development (GO:0014032)|patterning of blood vessels (GO:0001569)|penile erection (GO:0043084)|positive regulation of cell proliferation (GO:0008284)|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 ERK1 and ERK2 cascade (GO:0070374)|positive regulation of inflammatory response (GO:0050729)|positive regulation of kidney development (GO:0090184)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of odontogenesis (GO:0042482)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of blood pressure (GO:0008217)|regulation of epithelial cell proliferation (GO:0050678)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|Rho protein signal transduction (GO:0007266)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|smooth muscle cell proliferation (GO:0048659)|smooth muscle contraction (GO:0006939)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	endothelin receptor activity (GO:0004962)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(3)|ovary(1)	17	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.154)	Acetylsalicylic acid(DB00945)|Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	TGTGTATAACGAGATGGACAA	0.348																																					p.E335K		Atlas-SNP	.											EDNRA,NS,carcinoma,-1,2	EDNRA	48	2	0			c.G1003A						PASS	.						183	182	182					4																	148461071		2203	4300	6503	SO:0001583	missense	1909	exon6			TATAACGAGATGG	D90348	CCDS3769.1, CCDS54810.1, CCDS58927.1	4q31.22	2013-09-20			ENSG00000151617	ENSG00000151617		"GPCR / Class A : Endothelin receptors"	3179	protein-coding gene	gene with protein product		131243				1659806	Standard	NM_001957		Approved		uc003iky.3	P25101	OTTHUMG00000161354	ENST00000324300.5:c.1003G>A	4.37:g.148461071G>A	ENSP00000315011:p.Glu335Lys	155	0	0		174	30	0.172414	NM_001957	B2R723|B4E2V6|B7Z9G6|D3DP03|E7ER36|O43441|Q16432|Q16433|Q8TBH2	Missense_Mutation	SNP	ENST00000324300.5	37	CCDS3769.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.333880	0.81801	.	.	ENSG00000151617	ENST00000358556;ENST00000324300;ENST00000511804;ENST00000506066	T;T;T;T	0.71817	-0.6;-0.6;-0.6;-0.6	5.44	4.59	0.56863	GPCR, rhodopsin-like superfamily (1);	0.197416	0.53938	D	0.000053	T	0.78246	0.4253	M	0.74258	2.255	0.80722	D	1	P;D	0.57899	0.951;0.981	B;P	0.51055	0.24;0.657	T	0.81680	-0.0823	10	0.59425	D	0.04	-18.8044	16.5127	0.84290	0.0:0.131:0.869:0.0	.	226;335	P25101-4;P25101	.;EDNRA_HUMAN	K	226;335;110;226	ENSP00000351359:E226K;ENSP00000315011:E335K;ENSP00000425354:E110K;ENSP00000425281:E226K	ENSP00000315011:E335K	E	+	1	0	EDNRA	148680521	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	3.186000	0.50942	1.409000	0.46915	0.650000	0.86243	GAG	.	.	none		0.348	EDNRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364635.1			A	148461071	G	A	148461071	3	1	23	1	0	0	0	0	1	0	0	0	4921	1059	37	1	1021	1	EDNRA	4	148461071	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	899924	148461071	42693205	194	7638											
PRMT10	90826	hgsc.bcm.edu	37	chr4	148589711	148589711	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tatgatgtcttcttatctctGcacattctactgccatccca	8	16	4	13	0	4	1	0	1	4	0	6	1	5	1	2	0	3	1	2	0	3	5	rs146854725	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:148589711G>A	ENST00000322396.6	-	6	1174	c.932C>T	c.(931-933)gCa>gTa	p.A311V	TMEM184C_ENST00000508208.1_Intron|PRMT10_ENST00000541232.1_Missense_Mutation_p.A198V	NM_138364.2	NP_612373.2	Q6P2P2	ANM9_HUMAN		311	SAM-dependent MTase PRMT-type 1. {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						TCTTATCTCTGCACATTCTAC	0.348													G|||	4	0.000798722	0.0	0.0	5008	,	,		19299	0.0		0.004	False		,,,				2504	0.0				p.A311V		Atlas-SNP	.											.	PRMT10	68	.	0			c.C932T						PASS	.	G	VAL/ALA	5,4399	9.9+/-24.2	0,5,2197	133	123	126		932	4.2	1	4	dbSNP_134	126	50,8550	31.2+/-83.2	0,50,4250	yes	missense	PRMT10	NM_138364.2	64	0,55,6447	AA,AG,GG		0.5814,0.1135,0.4229	benign	311/846	148589711	55,12949	2202	4300	6502	SO:0001583	missense	90826	exon6			ATCTCTGCACATT																												ENST00000322396.6:c.932C>T	4.37:g.148589711G>A	ENSP00000314396:p.Ala311Val	113	0	0		110	51	0.463636	NM_138364	A8KA39|B3KU92|Q6ZR58|Q8N383|Q9BT55|Q9NT98	Missense_Mutation	SNP	ENST00000322396.6	37	CCDS3771.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	13.63	2.295916	0.40594	0.001135	0.005814	ENSG00000164169	ENST00000322396;ENST00000541232	T;T	0.43294	0.95;0.95	5.9	4.17	0.49024	.	0.605454	0.18477	N	0.140055	T	0.21022	0.0506	N	0.25647	0.755	0.29735	N	0.837584	B	0.02656	0.0	B	0.04013	0.001	T	0.13469	-1.0508	10	0.28530	T	0.3	-30.4136	9.1674	0.37060	0.0703:0.0:0.617:0.3127	.	311	Q6P2P2	ANM10_HUMAN	V	311;198	ENSP00000314396:A311V;ENSP00000439508:A198V	ENSP00000314396:A311V	A	-	2	0	PRMT10	148809161	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.665000	0.37449	0.836000	0.34901	0.453000	0.30009	GCA	G|0.996;A|0.004	0.004	strong		0.348	PRMT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364650.1			A	148589711	G	A	148589711	3	1	23	1	0	0	0	0	1	0	0	0	12548	1319	46	2	1633	2	PRMT10	4	148589711	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	128640	148589711	42564565	195	7639											
FHDC1	85462	hgsc.bcm.edu	37	chr4	153886104	153886104	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctaaacttttcagaaaaattGcatcatgttcagaagactgc	15	12	6	8	0	3	3	3	0	0	3	3	3	3	3	0	0	3	2	0	0	5	5	rs2018007	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:153886104G>A	ENST00000511601.1	+	9	1265	c.1077G>A	c.(1075-1077)ttG>ttA	p.L359L	FHDC1_ENST00000260008.3_Silent_p.L359L			Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	359	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)					CAGAAAAATTGCATCATGTTC	0.303													G|||	113	0.0225639	0.0749	0.0086	5008	,	,		18165	0.0		0.005	False		,,,				2504	0.0031				p.L359L		Atlas-SNP	.											.	FHDC1	102	.	0			c.G1077A						PASS	.	G		277,4129	152.2+/-185.9	13,251,1939	75	81	79		1077	0.9	0	4	dbSNP_92	79	37,8557	24.6+/-71.5	1,35,4261	no	coding-synonymous	FHDC1	NM_033393.2		14,286,6200	AA,AG,GG		0.4305,6.2869,2.4154		359/1144	153886104	314,12686	2203	4297	6500	SO:0001819	synonymous_variant	85462	exon8			AAAATTGCATCAT	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.1077G>A	4.37:g.153886104G>A		359	0	0		401	183	0.456359	NM_033393		Silent	SNP	ENST00000511601.1	37	CCDS34081.1																																																																																			G|0.973;A|0.027	0.027	strong		0.303	FHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364981.2	NM_033393		A	153886104	G	A	153886104	2	1	23	1	0	0	0	0	0	0	0	1	5884	1310	46	2		2	FHDC1	4	153886104	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	5296393	153886104	37268172	196	7640											
DCHS2	54798	hgsc.bcm.edu	37	chr4	155158284	155158284	+	Nonsense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgatattgtatccagaagtAatacgggactgatagtaaat	15	13	9	4	1	0	3	0	2	0	1	1	4	1	4	1	1	1	3	1	1	8	8	rs146298768	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:155158284A>C	ENST00000357232.4	-	25	6154	c.6155T>G	c.(6154-6156)tTa>tGa	p.L2052*		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2052	Cadherin 18. {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)		ATCCAGAAGTAATACGGGACT	0.378																																					p.L2052X		Atlas-SNP	.											.	DCHS2	594	.	0			c.T6155G						PASS	.	A	stop/LEU	2,4402	4.2+/-10.8	0,2,2200	69	71	70		6155	2	0	4	dbSNP_134	70	34,8566	22.2+/-67.0	0,34,4266	yes	stop-gained	DCHS2	NM_017639.3		0,36,6466	CC,CA,AA		0.3953,0.0454,0.2768		2052/2917	155158284	36,12968	2202	4300	6502	SO:0001587	stop_gained	54798	exon25			AGAAGTAATACGG	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.6155T>G	4.37:g.155158284A>C	ENSP00000349768:p.Leu2052*	102	0	0		102	52	0.509804	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Nonsense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	42	9.636087	0.99226	4.54E-4	0.003953	ENSG00000197410	ENST00000357232	.	.	.	5.67	2.04	0.26737	.	1.456590	0.04346	N	0.354832	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.17369	T	0.5	.	5.7442	0.18110	0.5901:0.1313:0.2786:0.0	.	.	.	.	X	2052	.	ENSP00000349768:L2052X	L	-	2	0	DCHS2	155377734	0.000000	0.05858	0.007000	0.13788	0.558000	0.35554	0.244000	0.18124	0.130000	0.18549	0.455000	0.32223	TTA	A|0.998;C|0.002	0.002	strong		0.378	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		C	155158284	A	C	155158284	4	2	23	1	0	0	0	0	0	1	0	0	4290	372	13	5	2599	5	DCHS2	4	155158284	Nonsense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	1272180	155158284	35995992	197	7641											
DCHS2	54798	hgsc.bcm.edu	37	chr4	155219540	155219540	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aatggtgaatgcaccagaagCctcatcagtcagaaaatact	16	8	8	9	0	3	3	3	1	0	2	3	3	3	3	2	1	3	1	2	1	6	1	rs141467714	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:155219540C>A	ENST00000357232.4	-	18	4560	c.4561G>T	c.(4561-4563)Gct>Tct	p.A1521S		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1521	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)		GCACCAGAAGCCTCATCAGTC	0.483																																					p.A1521S		Atlas-SNP	.											.	DCHS2	594	.	0			c.G4561T						PASS	.	C	SER/ALA	2,4404	4.2+/-10.8	0,2,2201	133	126	128		4561	0.8	0	4	dbSNP_134	128	33,8567	22.8+/-68.1	0,33,4267	yes	missense	DCHS2	NM_017639.3	99	0,35,6468	AA,AC,CC		0.3837,0.0454,0.2691	benign	1521/2917	155219540	35,12971	2203	4300	6503	SO:0001583	missense	54798	exon18			CAGAAGCCTCATC	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.4561G>T	4.37:g.155219540C>A	ENSP00000349768:p.Ala1521Ser	160	0	0		159	79	0.496855	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	0.010	-1.763380	0.00651	4.54E-4	0.003837	ENSG00000197410	ENST00000357232	T	0.49432	0.78	5.76	0.801	0.18679	Cadherin (4);Cadherin-like (1);	0.619653	0.16206	N	0.224698	T	0.19685	0.0473	N	0.11724	0.165	0.09310	N	1	B	0.14438	0.01	B	0.17433	0.018	T	0.15925	-1.0420	10	0.09084	T	0.74	.	0.908	0.01288	0.3676:0.2927:0.1326:0.2071	.	1521	Q6V1P9	PCD23_HUMAN	S	1521	ENSP00000349768:A1521S	ENSP00000349768:A1521S	A	-	1	0	DCHS2	155438990	0.000000	0.05858	0.000000	0.03702	0.135000	0.20990	0.074000	0.14662	-0.106000	0.12110	0.650000	0.86243	GCT	C|0.998;A|0.002	0.002	strong		0.483	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		A	155219540	C	A	155219540	3	1	23	1	0	0	0	0	1	0	0	0	4290	739	26	4	4221	4	DCHS2	4	155219540	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	61256	155219540	35934736	198	7642											
TDO2	6999	hgsc.bcm.edu	37	chr4	156830085	156830085	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggttgtttctcggatgcaccGagtgtcagtgatcctgaaac	8	12	12	9	2	2	2	1	2	1	0	4	4	3	3	2	2	2	3	2	2	1	2	rs375801975		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:156830085G>A	ENST00000536354.2	+	5	414	c.350G>A	c.(349-351)cGa>cAa	p.R117Q		NM_005651.3	NP_005642.1			tryptophan 2,3-dioxygenase											breast(3)|endometrium(1)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	18	all_hematologic(180;0.24)	Renal(120;0.0854)		KIRC - Kidney renal clear cell carcinoma(143;0.0455)|Kidney(143;0.0568)|COAD - Colon adenocarcinoma(41;0.141)		CGGATGCACCGAGTGTCAGTG	0.443																																					p.R117Q	Colon(57;928 1036 2595 6946 26094)	Atlas-SNP	.											.	TDO2	51	.	0			c.G350A						PASS	.	G	GLN/ARG	0,4406		0,0,2203	112	100	104		350	5.3	0.9	4		104	1,8599	1.2+/-3.3	0,1,4299	no	missense	TDO2	NM_005651.2	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	117/407	156830085	1,13005	2203	4300	6503	SO:0001583	missense	6999	exon5			TGCACCGAGTGTC		CCDS34086.1	4q31-q32	2008-02-05				ENSG00000151790	1.13.11.11		11708	protein-coding gene	gene with protein product		191070					Standard	NM_005651		Approved	TDO, TPH2	uc003ipf.2	P48775		ENST00000536354.2:c.350G>A	4.37:g.156830085G>A	ENSP00000444788:p.Arg117Gln	96	0	0		75	38	0.506667	NM_005651		Missense_Mutation	SNP	ENST00000536354.2	37	CCDS34086.1	.	.	.	.	.	.	.	.	.	.	G	35	5.453794	0.96223	0.0	1.16E-4	ENSG00000151790	ENST00000506072;ENST00000507590;ENST00000536354	.	.	.	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	D	0.89791	0.6817	H	0.95917	3.74	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92677	0.6155	9	0.87932	D	0	-12.6575	19.4005	0.94627	0.0:0.0:1.0:0.0	.	117	P48775	T23O_HUMAN	Q	10;10;117	.	ENSP00000281525:R117Q	R	+	2	0	TDO2	157049535	1.000000	0.71417	0.852000	0.33557	0.908000	0.53690	9.388000	0.97237	2.663000	0.90544	0.650000	0.86243	CGA	.	.	weak		0.443	TDO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366209.3	NM_005651		A	156830085	G	A	156830085	3	1	23	1	0	0	0	0	1	0	0	0	15742	1058	37	1	368	1	TDO2	4	156830085	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1610545	156830085	34324191	199	7643											
KLHL2	11275	hgsc.bcm.edu	37	chr4	166239083	166239083	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aacaaccgataaatggacagTtgtgtcatcgtgtatgagca	14	10	10	7	2	1	1	1	1	0	0	2	3	1	2	1	1	3	3	1	1	5	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:166239083T>G	ENST00000226725.6	+	14	1974	c.1715T>G	c.(1714-1716)gTt>gGt	p.V572G	KLHL2_ENST00000509028.1_3'UTR|KLHL2_ENST00000421009.2_Missense_Mutation_p.V475G|KLHL2_ENST00000514860.1_Missense_Mutation_p.V576G|KLHL2_ENST00000506761.1_Missense_Mutation_p.V406G|KLHL2_ENST00000538127.1_Missense_Mutation_p.V484G	NM_007246.3	NP_009177.3	O95198	KLHL2_HUMAN	kelch-like family member 2	572					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)		AAATGGACAGTTGTGTCATCG	0.388																																					p.V576G		Atlas-SNP	.											.	KLHL2	42	.	0			c.T1727G						PASS	.						159	154	156					4																	166239083		2203	4300	6503	SO:0001583	missense	11275	exon14			GGACAGTTGTGTC	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.1715T>G	4.37:g.166239083T>G	ENSP00000226725:p.Val572Gly	155	0	0		154	19	0.123377	NM_001161521	A6NCM7|B2RD18|B4DFH7|F5H6M3|Q8N484|Q8TBH5	Missense_Mutation	SNP	ENST00000226725.6	37	CCDS34094.1	.	.	.	.	.	.	.	.	.	.	T	19.82	3.897708	0.72639	.	.	ENSG00000109466	ENST00000226725;ENST00000514860;ENST00000538127;ENST00000421009;ENST00000506761	T;T;T;T;T	0.78126	-1.15;-1.15;-1.15;-1.15;-1.15	6.17	6.17	0.99709	Galactose oxidase, beta-propeller (1);	0.125811	0.56097	D	0.000040	T	0.73651	0.3614	L	0.28192	0.835	0.80722	D	1	P;B;P	0.37015	0.578;0.361;0.578	B;B;B	0.42625	0.393;0.298;0.393	T	0.76503	-0.2935	10	0.87932	D	0	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	576;572;572	B4DFH7;B2RD18;O95198	.;.;KLHL2_HUMAN	G	572;576;484;475;406	ENSP00000226725:V572G;ENSP00000424198:V576G;ENSP00000437526:V484G;ENSP00000408974:V475G;ENSP00000424108:V406G	ENSP00000226725:V572G	V	+	2	0	KLHL2	166458533	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	7.655000	0.83696	2.371000	0.80710	0.533000	0.62120	GTT	.	.	none		0.388	KLHL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364439.1			G	166239083	T	G	166239083	3	3	23	1	0	0	0	0	1	0	0	0	8383	1725	60	5	1811	5	KLHL2	4	166239083	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	9408998	166239083	24915193	200	7644											
KLKB1	3818	hgsc.bcm.edu	37	chr4	187178437	187178437	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttggtaacaaatgaagaatGccagaaaagatatcaagatt	19	10	8	4	0	1	5	1	1	0	4	1	5	1	5	1	1	2	1	1	1	8	4	rs121964951	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:187178437G>A	ENST00000264690.6	+	14	1830	c.1643G>A	c.(1642-1644)tGc>tAc	p.C548Y	KLKB1_ENST00000513864.1_Intron	NM_000892.3	NP_000883.2	P03952	KLKB1_HUMAN	kallikrein B, plasma (Fletcher factor) 1	548	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		C -> Y (in PKK deficiency). {ECO:0000269|PubMed:14652634}.		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)	p.C548Y(2)		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)		AATGAAGAATGCCAGAAAAGA	0.338																																					p.C548Y		Atlas-SNP	.											KLKB1_ENST00000264690,colon,carcinoma,0,2	KLKB1	155	2	2	Substitution - Missense(2)	large_intestine(2)	c.G1643A	GRCh37	CM033394	KLKB1	M	rs121964951	scavenged	.	G	TYR/CYS	0,4402		0,0,2201	72	84	80	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1643	5.8	1	4	dbSNP_133	80	4,8590	3.7+/-12.6	0,4,4293	yes	missense	KLKB1	NM_000892.3	194	0,4,6494	AA,AG,GG		0.0465,0.0,0.0308	probably-damaging	548/639	187178437	4,12992	2201	4297	6498	SO:0001583	missense	3818	exon14			AAGAATGCCAGAA	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.1643G>A	4.37:g.187178437G>A	ENSP00000264690:p.Cys548Tyr	125	1	0.008		130	55	0.423077	NM_000892	A6NH96|B2R8H9|Q17RE8|Q17RE9|Q4W5C3	Missense_Mutation	SNP	ENST00000264690.6	37	CCDS34120.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.5|21.5	4.165611|4.165611	0.78339|0.78339	0.0|0.0	4.65E-4|4.65E-4	ENSG00000164344|ENSG00000164344	ENST00000511608|ENST00000264690	.|D	.|0.96992	.|-4.2	5.75|5.75	5.75|5.75	0.90469|0.90469	.|Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.99102|0.99102	0.9691|0.9691	H|H	0.99042|0.99042	4.41|4.41	0.80722|0.80722	A|A	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;0.997	D|D	0.98891|0.98891	1.0773|1.0773	4|9	.|0.87932	.|D	.|0	.|.	19.9525|19.9525	0.97208|0.97208	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|548;548	.|A8K9A9;P03952	.|.;KLKB1_HUMAN	T|Y	596|548	.|ENSP00000264690:C548Y	.|ENSP00000264690:C548Y	A|C	+|+	1|2	0|0	KLKB1|KLKB1	187415431|187415431	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.898000|0.898000	0.52572|0.52572	6.062000|6.062000	0.71155|0.71155	2.719000|2.719000	0.93026|0.93026	0.655000|0.655000	0.94253|0.94253	GCC|TGC	G|1.000;A|0.000	0.000	strong		0.338	KLKB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317732.1	NM_000892		A	187178437	G	A	187178437	3	1	23	1	0	0	0	0	1	0	0	0	8421	1319	46	2	1693	2	KLKB1	4	187178437	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	20939354	187178437	3975839	201	7645											
FAT1	2195	hgsc.bcm.edu	37	chr4	187549443	187549443	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaagcggtgaaccacggggCgtggtcattcgtgtcgctga	7	8	17	9	5	1	2	1	2	0	0	3	3	1	3	1	5	2	1	1	5	2	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:187549443C>T	ENST00000441802.2	-	9	4884	c.4675G>A	c.(4675-4677)Gcc>Acc	p.A1559T		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1559	Cadherin 13. {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						AACCACGGGGCGTGGTCATTC	0.498										HNSCC(5;0.00058)																											p.A1559T	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.G4675A						PASS	.						56	58	57					4																	187549443		2103	4226	6329	SO:0001583	missense	2195	exon9			ACGGGGCGTGGTC	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.4675G>A	4.37:g.187549443C>T	ENSP00000406229:p.Ala1559Thr	167	0	0		192	85	0.442708	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	16.42	3.117363	0.56505	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.03181	4.02	5.36	4.52	0.55395	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.100704	0.64402	D	0.000002	T	0.06600	0.0169	M	0.72894	2.215	0.80722	D	1	B	0.24920	0.114	B	0.17722	0.019	T	0.20605	-1.0270	10	0.19590	T	0.45	.	15.7693	0.78152	0.1368:0.8631:0.0:0.0	.	1559	Q14517	FAT1_HUMAN	T	1559;1558	ENSP00000406229:A1559T	ENSP00000260147:A1558T	A	-	1	0	FAT1	187786437	0.945000	0.32115	0.915000	0.36163	0.916000	0.54674	2.092000	0.41700	1.477000	0.48234	0.563000	0.77884	GCC	.	.	none		0.498	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		T	187549443	C	T	187549443	3	4	23	1	0	0	0	0	1	0	0	0	5697	768	27	1	9167	1	FAT1	4	187549443	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	371006	187549443	3604833	202	7646											
IRX2	153572	hgsc.bcm.edu	37	chr5	2749539	2749539	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgccctcctgcgccttgtcGggactctcgtccttgcttct	1	14	10	16	3	2	0	0	0	2	0	6	1	4	1	4	1	3	1	4	1	0	3	rs61748183	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:2749539G>C	ENST00000382611.6	-	2	860	c.612C>G	c.(610-612)ccC>ccG	p.P204P	C5orf38_ENST00000457752.2_5'Flank|C5orf38_ENST00000334000.3_5'Flank|C5orf38_ENST00000397835.4_5'Flank|C5orf38_ENST00000515640.1_5'Flank|IRX2_ENST00000302057.5_Silent_p.P204P|IRX2_ENST00000502957.1_5'UTR|C5orf38_ENST00000505778.1_5'Flank	NM_001134222.1	NP_001127694.1	Q9BZI1	IRX2_HUMAN	iroquois homeobox 2	204					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)			breast(1)|central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2)	26				GBM - Glioblastoma multiforme(108;0.204)		GCGCCTTGTCGGGACTCTCGT	0.652													G|||	5	0.000998403	0.0	0.0	5008	,	,		14303	0.0		0.004	False		,,,				2504	0.001				p.P204P		Atlas-SNP	.											.	IRX2	60	.	0			c.C612G						PASS	.	G	,	3,4403	6.2+/-15.9	0,3,2200	94	86	89		612,612	-6.5	0	5	dbSNP_129	89	47,8553	30.1+/-81.4	0,47,4253	no	coding-synonymous,coding-synonymous	IRX2	NM_001134222.1,NM_033267.4	,	0,50,6453	CC,CG,GG		0.5465,0.0681,0.3844	,	204/472,204/472	2749539	50,12956	2203	4300	6503	SO:0001819	synonymous_variant	153572	exon2			CTTGTCGGGACTC	AF319967	CCDS3868.1	5p15.33	2011-06-20	2007-07-13		ENSG00000170561	ENSG00000170561		"Homeoboxes / TALE class"	14359	protein-coding gene	gene with protein product		606198				11435706	Standard	NM_033267		Approved		uc003jdb.3	Q9BZI1	OTTHUMG00000090377	ENST00000382611.6:c.612C>G	5.37:g.2749539G>C		232	0	0		266	155	0.582707	NM_001134222	Q68A19|Q7Z2I7	Silent	SNP	ENST00000382611.6	37	CCDS3868.1																																																																																			G|0.997;C|0.003	0.003	strong		0.652	IRX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206749.2			C	2749539	G	C	2749539	2	2	23	1	0	0	0	0	0	0	0	1	7853	1103	39	4		4	IRX2	5	2749539	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10		2749539	178165721	203	7647											
KIAA0947	23379	hgsc.bcm.edu	37	chr5	5461976	5461976	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcttagagaaaataacaaTcctgtagaattcaagaccac	17	10	5	9	0	2	3	1	0	1	3	3	4	3	3	2	0	1	1	2	0	8	5	rs72646682	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:5461976T>C	ENST00000296564.7	+	13	2751	c.2529T>C	c.(2527-2529)aaT>aaC	p.N843N		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		843					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						AAAATAACAATCCTGTAGAAT	0.403													t|||	4	0.000798722	0.0	0.0029	5008	,	,		19727	0.0		0.002	False		,,,				2504	0.0				p.N843N		Atlas-SNP	.											.	KIAA0947	301	.	0			c.T2529C						PASS	.			2,3766		0,2,1882	86	80	82		2529	-5.2	0	5	dbSNP_130	82	21,8215		0,21,4097	no	coding-synonymous	KIAA0947	NM_015325.1		0,23,5979	CC,CT,TT		0.255,0.0531,0.1916		843/2267	5461976	23,11981	1884	4118	6002	SO:0001819	synonymous_variant	23379	exon13			TAACAATCCTGTA																												ENST00000296564.7:c.2529T>C	5.37:g.5461976T>C		132	0	0		147	58	0.394558	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Silent	SNP	ENST00000296564.7	37	CCDS47187.1																																																																																			T|0.998;C|0.002	0.002	strong		0.403	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			C	5461976	T	C	5461976	2	2	23	1	0	0	0	0	0	0	0	1	8211	1432	50	3		3	KIAA0947	5	5461976	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	2712437	5461976	175453284	204	7648											
CDH6	1004	hgsc.bcm.edu	37	chr5	31294254	31294254	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aacagaaggacagggagaccCgtggagcccgagtctgaatt	13	5	14	9	2	1	3	0	1	1	2	1	7	1	5	2	3	2	0	2	3	3	1	rs147617483	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:31294254C>T	ENST00000265071.2	+	3	679	c.414C>T	c.(412-414)ccC>ccT	p.P138P	CDH6_ENST00000514738.1_Silent_p.P83P	NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	138	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)	p.P138P(1)		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						CAGGGAGACCCGTGGAGCCCG	0.473													C|||	6	0.00119808	0.0	0.0043	5008	,	,		18421	0.0		0.003	False		,,,				2504	0.0				p.P138P		Atlas-SNP	.											.	CDH6	175	.	1	Substitution - coding silent(1)	lung(1)	c.C414T						PASS	.	C		8,4398	12.9+/-30.5	0,8,2195	134	135	134		414	-11.5	0.2	5	dbSNP_134	134	55,8545	35.3+/-89.8	0,55,4245	no	coding-synonymous	CDH6	NM_004932.3		0,63,6440	TT,TC,CC		0.6395,0.1816,0.4844		138/791	31294254	63,12943	2203	4300	6503	SO:0001819	synonymous_variant	1004	exon3			GAGACCCGTGGAG	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.414C>T	5.37:g.31294254C>T		88	0	0		107	55	0.514019	NM_004932	A8K5H5|Q9BWS0	Silent	SNP	ENST00000265071.2	37	CCDS3894.1																																																																																			C|0.995;T|0.005	0.005	strong		0.473	CDH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207355.2	NM_004932		T	31294254	C	T	31294254	2	4	23	1	0	0	0	0	0	0	0	1	3116	639	23	1		1	CDH6	5	31294254	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	25832278	31294254	149621006	205	7649											
SPEF2	79925	hgsc.bcm.edu	37	chr5	35759812	35759812	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagtaaagacaattctgaaaGccagcttaggtaaggcaggc	15	8	11	7	0	1	2	0	1	1	1	1	2	1	2	1	3	2	4	1	3	7	5	rs201517270	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:35759812G>T	ENST00000356031.3	+	25	3765	c.3611G>T	c.(3610-3612)aGc>aTc	p.S1204I	CTD-2113L7.1_ENST00000510433.1_RNA|SPEF2_ENST00000440995.2_Missense_Mutation_p.S1199I	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	1204					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)			AATTCTGAAAGCCAGCTTAGG	0.348													G|||	3	0.000599042	0.0	0.0	5008	,	,		16893	0.0		0.003	False		,,,				2504	0.0				p.S1204I		Atlas-SNP	.											.	SPEF2	324	.	0			c.G3611T						PASS	.	G	ILE/SER	2,3688		0,2,1843	90	87	88		3611	-10.7	0	5		88	10,8146		0,10,4068	yes	missense	SPEF2	NM_024867.3	142	0,12,5911	TT,TG,GG		0.1226,0.0542,0.1013	benign	1204/1823	35759812	12,11834	1845	4078	5923	SO:0001583	missense	79925	exon25			CTGAAAGCCAGCT	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.3611G>T	5.37:g.35759812G>T	ENSP00000348314:p.Ser1204Ile	129	0	0		149	76	0.510067	NM_024867	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Missense_Mutation	SNP	ENST00000356031.3	37	CCDS43309.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	3.572	-0.087472	0.07097	5.42E-4	0.001226	ENSG00000152582	ENST00000356031;ENST00000440995	T;T	0.36520	1.25;1.25	5.33	-10.7	0.00240	.	1.448510	0.03545	N	0.224510	T	0.27278	0.0669	L	0.50333	1.59	0.24410	N	0.994669	B;B	0.20261	0.043;0.014	B;B	0.20955	0.032;0.005	T	0.04870	-1.0921	10	0.19147	T	0.46	.	10.1477	0.42774	0.5976:0.0:0.229:0.1733	.	1199;1204	Q9C093-2;Q9C093	.;SPEF2_HUMAN	I	1204;1199	ENSP00000348314:S1204I;ENSP00000412125:S1199I	ENSP00000348314:S1204I	S	+	2	0	SPEF2	35795569	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-1.033000	0.03571	-2.982000	0.00282	-0.793000	0.03317	AGC	G|0.999;T|0.001	0.001	strong		0.348	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722		T	35759812	G	T	35759812	3	4	23	1	0	0	0	0	1	0	0	0	15050	971	34	4	3730	4	SPEF2	5	35759812	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	4465558	35759812	145155448	206	7650											
LIFR	3977	hgsc.bcm.edu	37	chr5	38510603	38510603	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gttccaaatatgttatcttcGgttgtaaaaactacatttgt	12	17	6	6	1	1	0	0	0	1	0	3	0	2	0	1	1	2	4	1	1	7	8	rs61748202	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:38510603G>A	ENST00000263409.4	-	7	1116	c.954C>T	c.(952-954)acC>acT	p.T318T	LIFR_ENST00000453190.2_Silent_p.T318T|LIFR_ENST00000503088.1_5'UTR	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	318					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)					TGTTATCTTCGGTTGTAAAAA	0.348			T	PLAG1	salivary adenoma								G|||	10	0.00199681	0.0	0.0058	5008	,	,		18085	0.0		0.004	False		,,,				2504	0.002				p.T318T	Melanoma(13;4 730 6426 9861 34751)	Atlas-SNP	.		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	.	LIFR	348	.	0			c.C954T						PASS	.	G	,	6,4400	12.9+/-30.5	0,6,2197	77	75	75		954,954	1.6	0	5	dbSNP_129	75	41,8559	27.4+/-76.7	0,41,4259	no	coding-synonymous,coding-synonymous	LIFR	NM_001127671.1,NM_002310.5	,	0,47,6456	AA,AG,GG		0.4767,0.1362,0.3614	,	318/1098,318/1098	38510603	47,12959	2203	4300	6503	SO:0001819	synonymous_variant	3977	exon7			ATCTTCGGTTGTA	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.954C>T	5.37:g.38510603G>A		112	0	0		135	52	0.385185	NM_002310	Q6LCD9	Silent	SNP	ENST00000263409.4	37	CCDS3927.1																																																																																			G|0.997;A|0.003	0.003	strong		0.348	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310		A	38510603	G	A	38510603	2	1	23	1	0	0	0	0	0	0	0	1	8789	1103	39	1		1	LIFR	5	38510603	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	2750791	38510603	142404657	207	7651											
C6	729	hgsc.bcm.edu	37	chr5	41160293	41160293	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagttctcaccataggtgccActctgacacacacacagaca	13	7	6	15	0	2	2	1	1	2	1	3	2	2	2	2	1	1	1	2	1	1	2	rs62361567	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:41160293A>G	ENST00000263413.3	-	11	1899	c.1635T>C	c.(1633-1635)agT>agC	p.S545S	C6_ENST00000337836.5_Silent_p.S545S|C6_ENST00000475349.1_5'Flank	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	545	EGF-like.				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)				CATAGGTGCCACTCTGACACA	0.468													A|||	56	0.0111821	0.0038	0.0187	5008	,	,		20151	0.0		0.0358	False		,,,				2504	0.002				p.S545S		Atlas-SNP	.											.	C6	197	.	0			c.T1635C						PASS	.	A	,	23,4383	31.7+/-61.6	0,23,2180	160	152	154		1635,1635	-12.1	0	5	dbSNP_129	154	299,8301	109.2+/-169.8	5,289,4006	no	coding-synonymous,coding-synonymous	C6	NM_000065.2,NM_001115131.1	,	5,312,6186	GG,GA,AA		3.4767,0.522,2.4758	,	545/935,545/935	41160293	322,12684	2203	4300	6503	SO:0001819	synonymous_variant	729	exon11			GGTGCCACTCTGA	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.1635T>C	5.37:g.41160293A>G		162	0	0		204	78	0.382353	NM_001115131		Silent	SNP	ENST00000263413.3	37	CCDS3936.1																																																																																			A|0.978;G|0.022	0.022	strong		0.468	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1			G	41160293	A	G	41160293	2	3	23	1	0	0	0	0	0	0	0	1	2317	156	6	3		3	C6	5	41160293	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	2649690	41160293	139754967	208	7652											
OXCT1	5019	hgsc.bcm.edu	37	chr5	41862819	41862819	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgtataaaacttggtatggcGatgagcactggtggaaaagg	13	10	14	4	1	0	1	0	1	0	0	0	3	0	2	0	5	2	3	0	5	6	4	rs76956231	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:41862819G>A	ENST00000196371.5	-	2	272	c.112C>T	c.(112-114)Cgc>Tgc	p.R38C		NM_000436.3	NP_000427.1	P55809	SCOT1_HUMAN	3-oxoacid CoA transferase 1	38					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)	TTGGTATGGCGATGAGCACTG	0.378													G|||	15	0.00299521	0.0008	0.0029	5008	,	,		14176	0.0		0.0099	False		,,,				2504	0.002				p.R38C		Atlas-SNP	.											OXCT1,NS,carcinoma,+1,1	OXCT1	54	1	0			c.C112T						PASS	.	G	CYS/ARG	4,4402	8.1+/-20.4	0,4,2199	120	107	112		112	3.8	0	5	dbSNP_132	112	83,8517	47.6+/-106.9	0,83,4217	yes	missense	OXCT1	NM_000436.3	180	0,87,6416	AA,AG,GG		0.9651,0.0908,0.6689	possibly-damaging	38/521	41862819	87,12919	2203	4300	6503	SO:0001583	missense	5019	exon2			TATGGCGATGAGC	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.112C>T	5.37:g.41862819G>A	ENSP00000196371:p.Arg38Cys	160	0	0		125	61	0.488	NM_000436	B2R5V2|B7Z528	Missense_Mutation	SNP	ENST00000196371.5	37	CCDS3937.1	10	0.004578754578754579	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	G	11.72	1.723995	0.30593	9.08E-4	0.009651	ENSG00000083720	ENST00000196371	D	0.86164	-2.08	5.56	3.8	0.43715	.	0.298519	0.35495	N	0.003180	T	0.67411	0.2890	N	0.08118	0	0.21473	N	0.999674	B	0.09022	0.002	B	0.08055	0.003	T	0.60949	-0.7161	10	0.44086	T	0.13	0.7598	11.4381	0.50081	0.1494:0.0:0.8506:0.0	.	38	P55809	SCOT1_HUMAN	C	38	ENSP00000196371:R38C	ENSP00000196371:R38C	R	-	1	0	OXCT1	41898576	0.439000	0.25610	0.027000	0.17364	0.805000	0.45488	3.805000	0.55575	0.725000	0.32318	-0.216000	0.12614	CGC	G|0.994;A|0.006	0.006	strong		0.378	OXCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211594.2	NM_000436		A	41862819	G	A	41862819	3	1	23	1	0	0	0	0	1	0	0	0	11338	1058	37	1	1514	1	OXCT1	5	41862819	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	702526	41862819	139052441	209	7653											
FST	10468	hgsc.bcm.edu	37	chr5	52781029	52781029	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgctcctcaggtgtgctactGgaagtaaagcactccggatc	9	10	11	11	1	1	0	1	0	0	0	4	2	3	2	2	3	4	4	2	3	4	2	rs11746136	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:52781029G>A	ENST00000256759.3	+	5	1307	c.924G>A	c.(922-924)ctG>ctA	p.L308L	FST_ENST00000396947.3_Silent_p.L308L	NM_013409.2	NP_037541.1	P19883	FST_HUMAN	follistatin	308	Kazal-like 3. {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)				GTGTGCTACTGGAAGTAAAGC	0.502													G|||	45	0.00898562	0.0144	0.013	5008	,	,		17704	0.0		0.0169	False		,,,				2504	0.0				p.L308L		Atlas-SNP	.											.	FST	42	.	0			c.G924A						PASS	.	G	,	81,4325	70.9+/-108.8	1,79,2123	120	105	110		924,924	3.5	1	5	dbSNP_120	110	140,8460	69.4+/-131.9	2,136,4162	no	coding-synonymous,coding-synonymous	FST	NM_006350.3,NM_013409.2	,	3,215,6285	AA,AG,GG		1.6279,1.8384,1.6992	,	308/318,308/345	52781029	221,12785	2203	4300	6503	SO:0001819	synonymous_variant	10468	exon5			GCTACTGGAAGTA	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.924G>A	5.37:g.52781029G>A		52	0	0		57	27	0.473684	NM_013409	B5BU94|Q9BTH0	Silent	SNP	ENST00000256759.3	37	CCDS3959.1	31	0.014194139194139194	11	0.022357723577235773	4	0.011049723756906077	0	0.0	16	0.021108179419525065	G	3.057	-0.193992	0.06259	0.018384	0.016279	ENSG00000134363	ENST00000497789	.	.	.	5.35	3.52	0.40303	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-12.3382	7.2089	0.25923	0.1577:0.0:0.6997:0.1425	rs11746136	.	.	.	X	93	.	.	W	+	2	0	FST	52816786	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.792000	0.47837	0.705000	0.31890	0.655000	0.94253	TGG	G|0.983;A|0.017	0.017	strong		0.502	FST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253906.1	NM_013409		A	52781029	G	A	52781029	2	1	23	1	0	0	0	0	0	0	0	1	6084	1335	47	2		2	FST	5	52781029	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	10918210	52781029	128134231	210	7654											
MAP3K1	4214	hgsc.bcm.edu	37	chr5	56155672	56155672	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acgcagtccttctcctggcaActccccatcaggtcgcacag	8	8	8	17	2	2	0	1	0	1	0	6	0	4	0	4	2	1	3	4	2	1	1	rs56069227	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:56155672A>G	ENST00000399503.3	+	3	764	c.764A>G	c.(763-765)aAc>aGc	p.N255S	snoU13_ENST00000459264.1_RNA|AC008937.2_ENST00000415589.1_RNA	NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	255					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)		TCTCCTGGCAACTCCCCATCA	0.488													A|||	83	0.0165735	0.025	0.0216	5008	,	,		15055	0.0		0.0338	False		,,,				2504	0.001				p.N255S		Atlas-SNP	.											.	MAP3K1	355	.	0			c.A764G						PASS	.	A	SER/ASN	79,3755		1,77,1839	42	42	42		764	3.9	0.9	5	dbSNP_129	42	229,8029		5,219,3905	yes	missense	MAP3K1	NM_005921.1	46	6,296,5744	GG,GA,AA		2.7731,2.0605,2.5471	benign	255/1513	56155672	308,11784	1917	4129	6046	SO:0001583	missense	4214	exon3			CTGGCAACTCCCC	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.764A>G	5.37:g.56155672A>G	ENSP00000382423:p.Asn255Ser	217	0	0		229	116	0.50655	NM_005921		Missense_Mutation	SNP	ENST00000399503.3	37	CCDS43318.1	40	0.018315018315018316	6	0.012195121951219513	9	0.024861878453038673	0	0.0	25	0.032981530343007916	A	13.57	2.277282	0.40294	0.020605	0.027731	ENSG00000095015	ENST00000399503	T	0.63255	-0.03	5.72	3.93	0.45458	.	0.316826	0.39544	N	0.001335	T	0.10465	0.0256	N	0.01352	-0.895	0.26121	N	0.98055	B	0.02656	0.0	B	0.01281	0.0	T	0.14448	-1.0472	10	0.02654	T	1	.	11.7667	0.51935	0.1441:0.0:0.8559:0.0	rs56069227;rs61736548	255	Q13233	M3K1_HUMAN	S	255	ENSP00000382423:N255S	ENSP00000382423:N255S	N	+	2	0	MAP3K1	56191429	1.000000	0.71417	0.938000	0.37757	0.734000	0.41952	3.001000	0.49488	0.871000	0.35750	-0.242000	0.12053	AAC	A|0.976;G|0.024	0.024	strong		0.488	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066		G	56155672	A	G	56155672	3	3	23	1	0	0	0	0	1	0	0	0	9252	43	2	3	774	3	MAP3K1	5	56155672	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	3374643	56155672	124759588	211	7655											
AP3B1	8546	hgsc.bcm.edu	37	chr5	77423965	77423965	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagtatgagataaggtgccAagctggaaatgatctctatc	14	10	11	6	0	1	3	0	2	1	2	3	5	1	4	1	2	2	2	1	2	5	3	rs115892142	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:77423965A>C	ENST00000255194.6	-	17	2032	c.1857T>G	c.(1855-1857)ctT>ctG	p.L619L	AP3B1_ENST00000519295.1_Silent_p.L570L	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	619					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)		ATAAGGTGCCAAGCTGGAAAT	0.373									Hermansky-Pudlak syndrome				A|||	5	0.000998403	0.0	0.0	5008	,	,		16956	0.0		0.005	False		,,,				2504	0.0				p.L619L		Atlas-SNP	.											.	AP3B1	94	.	0			c.T1857G						PASS	.	A		4,4402	4.2+/-10.8	0,4,2199	48	48	48		1857	3.5	1	5	dbSNP_132	48	22,8578	8.4+/-32.0	1,20,4279	no	coding-synonymous	AP3B1	NM_003664.3		1,24,6478	CC,CA,AA		0.2558,0.0908,0.1999		619/1095	77423965	26,12980	2203	4300	6503	SO:0001819	synonymous_variant	8546	exon17	Familial Cancer Database	HPS, HPS1-8	GGTGCCAAGCTGG	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.1857T>G	5.37:g.77423965A>C		35	0	0		45	21	0.466667	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Silent	SNP	ENST00000255194.6	37	CCDS4041.1																																																																																			A|0.998;C|0.002	0.002	strong		0.373	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2			C	77423965	A	C	77423965	2	2	23	1	0	0	0	0	0	0	0	1	744	117	5	5		5	AP3B1	5	77423965	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	21268293	77423965	103491295	212	7656											
CMYA5	202333	hgsc.bcm.edu	37	chr5	79025592	79025592	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgattctcccctaaatgccaCatctgcattggagcacacag	11	10	7	13	0	2	1	0	1	2	0	3	2	2	2	3	1	3	2	3	1	2	3	rs114648445	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:79025592C>T	ENST00000446378.2	+	2	1035	c.1004C>T	c.(1003-1005)aCa>aTa	p.T335I		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	335					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)		CTAAATGCCACATCTGCATTG	0.463													C|||	13	0.00259585	0.0008	0.0029	5008	,	,		21455	0.0		0.0099	False		,,,				2504	0.0				p.T335I		Atlas-SNP	.											.	CMYA5	643	.	0			c.C1004T						PASS	.	C	ILE/THR	3,3987		0,3,1992	68	65	66		1004	3.4	0	5	dbSNP_132	66	56,8284		0,56,4114	yes	missense	CMYA5	NM_153610.3	89	0,59,6106	TT,TC,CC		0.6715,0.0752,0.4785	possibly-damaging	335/4070	79025592	59,12271	1995	4170	6165	SO:0001583	missense	202333	exon2			ATGCCACATCTGC	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.1004C>T	5.37:g.79025592C>T	ENSP00000394770:p.Thr335Ile	131	0	0		171	76	0.444444	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	10.74	1.435181	0.25813	7.52E-4	0.006715	ENSG00000164309	ENST00000446378	T	0.43688	0.94	5.15	3.36	0.38483	.	1.320480	0.05114	N	0.489480	T	0.19406	0.0466	N	0.14661	0.345	0.09310	N	1	B	0.30763	0.294	B	0.27887	0.084	T	0.25813	-1.0121	10	0.87932	D	0	.	3.333	0.07091	0.2023:0.565:0.0:0.2327	.	335	Q8N3K9	CMYA5_HUMAN	I	335	ENSP00000394770:T335I	ENSP00000394770:T335I	T	+	2	0	CMYA5	79061348	0.000000	0.05858	0.012000	0.15200	0.079000	0.17450	0.580000	0.23803	0.729000	0.32403	-0.181000	0.13052	ACA	C|0.997;T|0.003	0.003	strong		0.463	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		T	79025592	C	T	79025592	3	4	23	1	0	0	0	0	1	0	0	0	3592	478	17	2	1010	2	CMYA5	5	79025592	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1601627	79025592	101889668	213	7657											
FAM172A	83989	hgsc.bcm.edu	37	chr5	93410379	93410379	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggtagtcttttctttttcAtctggacctccctgctggat	4	17	9	11	1	4	0	1	0	3	0	5	2	5	2	2	3	1	2	2	3	1	5			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:93410379A>T	ENST00000395965.3	-	2	220	c.78T>A	c.(76-78)gaT>gaA	p.D26E	FAM172A_ENST00000505869.1_Intron|FAM172A_ENST00000509163.1_Intron|FAM172A_ENST00000504768.2_5'UTR|FAM172A_ENST00000509739.1_5'UTR	NM_032042.5	NP_114431.2	Q8WUF8	F172A_HUMAN	family with sequence similarity 172, member A	26						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)				endometrium(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	9						TTTCTTTTTCATCTGGACCTC	0.368																																					p.D26E		Atlas-SNP	.											.	FAM172A	38	.	0			c.T78A						PASS	.						145	131	136					5																	93410379		2203	4300	6503	SO:0001583	missense	83989	exon2			TTTTTCATCTGGA		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.78T>A	5.37:g.93410379A>T	ENSP00000379294:p.Asp26Glu	154	0	0		143	16	0.111888	NM_032042	B2R7C6|B4DJ14|B4DLG5|Q9H0U8	Missense_Mutation	SNP	ENST00000395965.3	37	CCDS4069.1	.	.	.	.	.	.	.	.	.	.	A	14.71	2.617897	0.46736	.	.	ENSG00000113391	ENST00000395965	T	0.41400	1.0	5.88	5.88	0.94601	.	0.370321	0.31495	N	0.007554	T	0.22666	0.0547	N	0.20685	0.6	0.80722	D	1	B;P	0.43094	0.01;0.799	B;B	0.35278	0.013;0.199	T	0.17107	-1.0380	10	0.02654	T	1	-0.91	13.8025	0.63208	1.0:0.0:0.0:0.0	.	26;26	Q8WUF8;Q8WUF8-2	F172A_HUMAN;.	E	26	ENSP00000379294:D26E	ENSP00000379294:D26E	D	-	3	2	FAM172A	93436135	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.859000	0.55987	2.243000	0.73865	0.533000	0.62120	GAT	.	.	none		0.368	FAM172A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254100.3	NM_032042		T	93410379	A	T	93410379	3	4	23	1	0	0	0	0	1	0	0	0	5497	214	8	5	1212	5	FAM172A	5	93410379	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	14384787	93410379	87504881	214	7658											
TTC37	9652	hgsc.bcm.edu	37	chr5	94834122	94834122	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacagccacactgcggcctTggagtgcataaatcgctgat	10	8	11	12	2	0	1	0	1	0	0	1	2	0	2	2	2	3	3	2	2	2	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:94834122T>C	ENST00000358746.2	-	33	3813	c.3515A>G	c.(3514-3516)cAa>cGa	p.Q1172R		NM_014639.3	NP_055454.1	Q6PGP7	TTC37_HUMAN	tetratricopeptide repeat domain 37	1172						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						ACTGCGGCCTTGGAGTGCATA	0.393																																					p.Q1172R		Atlas-SNP	.											.	TTC37	128	.	0			c.A3515G						PASS	.						208	199	202					5																	94834122		2203	4300	6503	SO:0001583	missense	9652	exon33			CGGCCTTGGAGTG	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.3515A>G	5.37:g.94834122T>C	ENSP00000351596:p.Gln1172Arg	250	0	0		258	146	0.565891	NM_014639	O15077|Q6PJI3	Missense_Mutation	SNP	ENST00000358746.2	37	CCDS4072.1	.	.	.	.	.	.	.	.	.	.	T	17.09	3.299214	0.60195	.	.	ENSG00000198677	ENST00000358746	T	0.38401	1.14	5.72	5.72	0.89469	Tetratricopeptide-like helical (1);	0.054387	0.85682	D	0.000000	T	0.57140	0.2033	M	0.66939	2.045	0.50467	D	0.99987	D	0.89917	1.0	D	0.74023	0.982	T	0.53019	-0.8497	10	0.26408	T	0.33	.	16.0084	0.80380	0.0:0.0:0.0:1.0	.	1172	Q6PGP7	TTC37_HUMAN	R	1172	ENSP00000351596:Q1172R	ENSP00000351596:Q1172R	Q	-	2	0	TTC37	94859878	1.000000	0.71417	0.946000	0.38457	0.425000	0.31504	5.509000	0.67012	2.180000	0.69256	0.460000	0.39030	CAA	.	.	none		0.393	TTC37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241651.1	NM_014639		C	94834122	T	C	94834122	3	2	23	1	0	0	0	0	1	0	0	0	16720	1812	63	3	1223	3	TTC37	5	94834122	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	1423743	94834122	86081138	215	7659											
TTC37	9652	hgsc.bcm.edu	37	chr5	94882781	94882781	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttaccttacagtgtttcaaaGcttctttgtattctttgttt	7	22	5	7	0	3	0	1	0	2	0	3	0	3	0	1	0	3	4	1	0	4	9			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:94882781G>A	ENST00000358746.2	-	4	372	c.74C>T	c.(73-75)gCt>gTt	p.A25V		NM_014639.3	NP_055454.1	Q6PGP7	TTC37_HUMAN	tetratricopeptide repeat domain 37	25						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						GTGTTTCAAAGCTTCTTTGTA	0.338																																					p.A25V		Atlas-SNP	.											.	TTC37	128	.	0			c.C74T						PASS	.						178	180	179					5																	94882781		2203	4300	6503	SO:0001583	missense	9652	exon4			TTCAAAGCTTCTT	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.74C>T	5.37:g.94882781G>A	ENSP00000351596:p.Ala25Val	103	0	0		84	35	0.416667	NM_014639	O15077|Q6PJI3	Missense_Mutation	SNP	ENST00000358746.2	37	CCDS4072.1	.	.	.	.	.	.	.	.	.	.	G	16.59	3.165839	0.57476	.	.	ENSG00000198677	ENST00000358746;ENST00000514952;ENST00000513823	D;T;D	0.83591	-1.74;-0.69;-1.74	5.38	4.5	0.54988	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.064313	0.64402	N	0.000008	T	0.81983	0.4938	M	0.67953	2.075	0.51767	D	0.999938	B;B	0.20887	0.032;0.049	B;B	0.31390	0.016;0.129	T	0.78758	-0.2079	10	0.49607	T	0.09	.	10.6469	0.45626	0.1497:0.0:0.8503:0.0	.	25;25	D6RCE2;Q6PGP7	.;TTC37_HUMAN	V	25	ENSP00000351596:A25V;ENSP00000423742:A25V;ENSP00000425403:A25V	ENSP00000351596:A25V	A	-	2	0	TTC37	94908537	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.086000	0.64474	1.235000	0.43724	0.591000	0.81541	GCT	.	.	none		0.338	TTC37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241651.1	NM_014639		A	94882781	G	A	94882781	3	1	23	1	0	0	0	0	1	0	0	0	16720	971	34	2	4780	2	TTC37	5	94882781	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	48659	94882781	86032479	216	7660											
ELL2	22936	hgsc.bcm.edu	37	chr5	95234091	95234091	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agacttctttttggacttttTgtgagacattgaatggtttt	8	20	9	4	0	1	3	0	2	1	2	1	5	1	4	0	2	0	1	0	2	1	8			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:95234091T>C	ENST00000237853.4	-	8	1727	c.1378A>G	c.(1378-1380)Aaa>Gaa	p.K460E	ELL2_ENST00000431061.2_Missense_Mutation_p.K210E	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	460					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)		TTGGACTTTTTGTGAGACATT	0.378																																					p.K460E		Atlas-SNP	.											.	ELL2	63	.	0			c.A1378G						PASS	.						130	134	132					5																	95234091		2203	4300	6503	SO:0001583	missense	22936	exon8			ACTTTTTGTGAGA	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.1378A>G	5.37:g.95234091T>C	ENSP00000237853:p.Lys460Glu	311	0	0		330	165	0.5	NM_012081	B4DNK7	Missense_Mutation	SNP	ENST00000237853.4	37	CCDS4080.1	.	.	.	.	.	.	.	.	.	.	T	17.41	3.381477	0.61845	.	.	ENSG00000118985	ENST00000237853;ENST00000431061	T;T	0.30981	1.83;1.51	5.5	5.5	0.81552	.	0.235233	0.50627	N	0.000120	T	0.43299	0.1241	M	0.64997	1.995	0.58432	D	0.999996	D	0.60575	0.988	P	0.52343	0.696	T	0.26052	-1.0114	10	0.32370	T	0.25	2.215	15.2489	0.73529	0.0:0.0:0.0:1.0	.	460	O00472	ELL2_HUMAN	E	460;210	ENSP00000237853:K460E;ENSP00000399704:K210E	ENSP00000237853:K460E	K	-	1	0	ELL2	95259847	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	3.564000	0.53791	2.073000	0.62155	0.482000	0.46254	AAA	.	.	none		0.378	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081		C	95234091	T	C	95234091	3	2	23	1	0	0	0	0	1	0	0	0	5065	1821	63	3	564	3	ELL2	5	95234091	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	351310	95234091	85681169	217	7661											
SNCAIP	9627	hgsc.bcm.edu	37	chr5	121780312	121780312	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agaaccacgctggggaaaagCcctcccagagcgccgagcgg	11	2	14	14	4	0	2	0	0	0	2	1	4	1	3	4	3	4	1	4	3	3	0			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:121780312C>A	ENST00000261368.8	+	8	1739	c.1477C>A	c.(1477-1479)Ccc>Acc	p.P493T	SNCAIP_ENST00000542191.1_Missense_Mutation_p.P51T|SNCAIP_ENST00000379538.3_Missense_Mutation_p.P127T|SNCAIP_ENST00000379533.2_Missense_Mutation_p.P540T|CTC-210G5.1_ENST00000510972.1_RNA|SNCAIP_ENST00000504884.2_3'UTR|SNCAIP_ENST00000414317.2_Missense_Mutation_p.P95T|SNCAIP_ENST00000261367.7_Missense_Mutation_p.P540T|CTC-210G5.1_ENST00000503529.1_RNA|SNCAIP_ENST00000503116.2_3'UTR|CTC-210G5.1_ENST00000509993.1_RNA|SNCAIP_ENST00000379536.2_Missense_Mutation_p.P433T|CTC-210G5.1_ENST00000506053.1_RNA|CTC-210G5.1_ENST00000505546.1_RNA	NM_005460.2	NP_005451.2	Q9Y6H5	SNCAP_HUMAN	synuclein, alpha interacting protein	493					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)		TGGGGAAAAGCCCTCCCAGAG	0.547																																					p.P493T		Atlas-SNP	.											.	SNCAIP	308	.	0			c.C1477A						PASS	.						105	100	102					5																	121780312		2203	4300	6503	SO:0001583	missense	9627	exon8			GAAAAGCCCTCCC	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.1477C>A	5.37:g.121780312C>A	ENSP00000261368:p.Pro493Thr	125	0	0		115	55	0.478261	NM_005460	D3DSZ1|Q05BS1|Q1PSC2|Q49AC6|Q504U9|Q6L984|Q6L985|Q6L986|Q9HC59	Missense_Mutation	SNP	ENST00000261368.8	37	CCDS4131.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.501545	0.85176	.	.	ENSG00000064692	ENST00000542191;ENST00000509154;ENST00000261368;ENST00000379533;ENST00000379536;ENST00000379538;ENST00000261367;ENST00000414317;ENST00000447854	T;T;T;T;T;T;T;T	0.70869	0.99;0.14;0.14;0.14;0.14;0.99;0.14;-0.52	5.66	5.66	0.87406	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.91126	0.7206	H	0.98276	4.19	0.53688	D	0.999971	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	0.998;0.999;0.997;0.988;0.999;0.988;0.996;0.993	D	0.94040	0.7308	10	0.72032	D	0.01	-20.578	19.7543	0.96284	0.0:1.0:0.0:0.0	.	433;121;95;433;127;127;540;493	D6R9G8;Q9NVG1;B7Z995;Q9Y6H5-4;Q9Y6H5-5;Q9Y6H5-2;Q9Y6H5-3;Q9Y6H5	.;.;.;.;.;.;.;SNCAP_HUMAN	T	51;433;493;540;433;127;540;95;133	ENSP00000441681:P51T;ENSP00000422106:P433T;ENSP00000261368:P493T;ENSP00000368848:P540T;ENSP00000368851:P433T;ENSP00000368854:P127T;ENSP00000261367:P540T;ENSP00000394392:P95T	ENSP00000261367:P540T	P	+	1	0	SNCAIP	121808211	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	5.903000	0.69877	2.680000	0.91292	0.561000	0.74099	CCC	.	.	none		0.547	SNCAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250888.1			A	121780312	C	A	121780312	3	1	23	1	0	0	0	0	1	0	0	0	14856	739	26	4	1503	4	SNCAIP	5	121780312	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	26546221	121780312	59134948	218	7662											
CEP120	153241	hgsc.bcm.edu	37	chr5	122720648	122720648	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgtgaaatgcattaccctTgtgctgctataacaggcaca	11	12	8	10	0	1	1	0	1	1	0	1	1	1	1	1	1	5	4	1	1	4	4	rs147430819		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:122720648T>A	ENST00000306467.5	-	11	2064	c.1760A>T	c.(1759-1761)cAa>cTa	p.Q587L	CEP120_ENST00000306481.6_Missense_Mutation_p.Q561L|CEP120_ENST00000328236.5_Missense_Mutation_p.Q587L			Q8N960	CE120_HUMAN	centrosomal protein 120kDa	587					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						GCATTACCCTTGTGCTGCTAT	0.373																																					p.Q587L		Atlas-SNP	.											.	CEP120	72	.	0			c.A1760T						PASS	.	T	LEU/GLN,LEU/GLN	1,4405	2.1+/-5.4	0,1,2202	103	95	97		1682,1760	5.5	1	5	dbSNP_134	97	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	CEP120	NM_001166226.1,NM_153223.3	113,113	0,2,6501	AA,AT,TT		0.0116,0.0227,0.0154	possibly-damaging,possibly-damaging	561/961,587/987	122720648	2,13004	2203	4300	6503	SO:0001583	missense	153241	exon12			TACCCTTGTGCTG	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.1760A>T	5.37:g.122720648T>A	ENSP00000303058:p.Gln587Leu	95	0	0		117	62	0.529915	NM_153223	Q6AI52|Q6AW89|Q8IWB5|Q8N9Y0|Q8NDE8	Missense_Mutation	SNP	ENST00000306467.5	37	CCDS4134.2	.	.	.	.	.	.	.	.	.	.	T	23.5	4.419777	0.83559	2.27E-4	1.16E-4	ENSG00000168944	ENST00000306467;ENST00000328236;ENST00000306481;ENST00000508442	T;T;T;T	0.51071	0.72;0.72;0.72;0.72	5.52	5.52	0.82312	.	0.126760	0.53938	D	0.000049	T	0.47838	0.1467	L	0.50333	1.59	0.80722	D	1	P	0.48640	0.913	P	0.44394	0.448	T	0.47100	-0.9143	10	0.41790	T	0.15	.	15.6517	0.77099	0.0:0.0:0.0:1.0	.	587	Q8N960	CE120_HUMAN	L	587;587;561;561	ENSP00000303058:Q587L;ENSP00000327504:Q587L;ENSP00000307419:Q561L;ENSP00000421620:Q561L	ENSP00000303058:Q587L	Q	-	2	0	CEP120	122748547	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.532000	0.81985	2.108000	0.64289	0.477000	0.44152	CAA	T|1.000;A|0.000	0.000	weak		0.373	CEP120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250899.2	NM_153223		A	122720648	T	A	122720648	3	1	23	1	0	0	0	0	1	0	0	0	3248	1812	63	5	1240	5	CEP120	5	122720648	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	940336	122720648	58194612	219	7663											
CDKN2AIPNL	91368	hgsc.bcm.edu	37	chr5	133747354	133747354	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagaccatggagagggagagCagctggtccaggcggccact	10	4	16	11	1	0	3	0	0	0	3	1	5	1	3	3	5	2	2	3	5	0	0	rs141449831	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:133747354C>G	ENST00000458198.2	-	1	235	c.192G>C	c.(190-192)ctG>ctC	p.L64L	CDKN2AIPNL_ENST00000395009.3_Silent_p.L64L	NM_080656.2	NP_542387.1	Q96HQ2	C2AIL_HUMAN	CDKN2A interacting protein N-terminal like	64										central_nervous_system(1)|kidney(2)|prostate(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGAGGGAGAGCAGCTGGTCCA	0.657											OREG0016789	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	76	0.0151757	0.0008	0.0144	5008	,	,		14144	0.0		0.0398	False		,,,				2504	0.0256				p.L64L		Atlas-SNP	.											.	CDKN2AIPNL	5	.	0			c.G192C						PASS	.	C		22,4380		0,22,2179	18	22	20		192	3.6	1	5	dbSNP_134	20	241,8349		3,235,4057	no	coding-synonymous	CDKN2AIPNL	NM_080656.2		3,257,6236	GG,GC,CC		2.8056,0.4998,2.0243		64/117	133747354	263,12729	2201	4295	6496	SO:0001819	synonymous_variant	91368	exon1			GGAGAGCAGCTGG	BC008293	CCDS4175.1	5q31.1	2008-02-05			ENSG00000237190	ENSG00000237190			30545	protein-coding gene	gene with protein product						12477932	Standard	NM_080656		Approved	MGC13017	uc011cxs.2	Q96HQ2	OTTHUMG00000129123	ENST00000458198.2:c.192G>C	5.37:g.133747354C>G		421	0	0	1605	476	161	0.338235	NM_080656	Q8WVE3	Silent	SNP	ENST00000458198.2	37	CCDS4175.1																																																																																			C|0.982;G|0.018	0.018	strong		0.657	CDKN2AIPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251171.2	NM_080656		G	133747354	C	G	133747354	2	3	23	1	0	0	0	0	0	0	0	1	3165	697	25	4		4	CDKN2AIPNL	5	133747354	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	11026706	133747354	47167906	220	7664											
CATSPER3	347732	hgsc.bcm.edu	37	chr5	134345062	134345062	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatcgtctgactctctaggActccatcagaaagtttgagc	10	11	8	12	1	3	3	1	2	2	1	6	4	4	4	2	1	1	1	2	1	2	2	rs72800379	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:134345062A>G	ENST00000282611.6	+	6	904	c.818A>G	c.(817-819)gAc>gGc	p.D273G		NM_178019.2	NP_821138.1	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	273					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)			ACTCTCTAGGACTCCATCAGA	0.562													A|||	2	0.000399361	0.0	0.0	5008	,	,		21912	0.0		0.002	False		,,,				2504	0.0				p.D273G		Atlas-SNP	.											.	CATSPER3	38	.	0			c.A818G						PASS	.	A	GLY/ASP	3,4403	8.1+/-20.4	0,3,2200	131	121	125		818	2.6	1	5	dbSNP_130	125	26,8574	19.2+/-60.6	0,26,4274	yes	missense-near-splice	CATSPER3	NM_178019.2	94	0,29,6474	GG,GA,AA		0.3023,0.0681,0.223	probably-damaging	273/399	134345062	29,12977	2203	4300	6503	SO:0001630	splice_region_variant	347732	exon6			TCTAGGACTCCAT	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.817-1A>G	5.37:g.134345062A>G		74	0	0		96	61	0.635417	NM_178019	Q86XS6	Missense_Mutation	SNP	ENST00000282611.6	37	CCDS4181.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	8.757	0.922728	0.18056	6.81E-4	0.003023	ENSG00000152705	ENST00000282611	D	0.97256	-4.31	5.18	2.63	0.31362	.	0.441063	0.21510	N	0.073389	D	0.94440	0.8211	L	0.59436	1.845	0.32616	N	0.523999	P	0.46987	0.888	B	0.42062	0.374	D	0.92979	0.6404	10	0.59425	D	0.04	-12.8622	5.9345	0.19158	0.6619:0.1727:0.0:0.1654	.	273	Q86XQ3	CTSR3_HUMAN	G	273	ENSP00000282611:D273G	ENSP00000282611:D273G	D	+	2	0	CATSPER3	134372961	0.982000	0.34865	0.995000	0.50966	0.200000	0.23975	1.330000	0.33781	0.430000	0.26230	0.533000	0.62120	GAC	A|0.998;G|0.002	0.002	strong		0.562	CATSPER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251191.2	NM_178019	Missense_Mutation	G	134345062	A	G	134345062	5	3	23	1	0	0	0	0	0	0	1	0	2691	289	10	3	840	3	CATSPER3	5	134345062	Splice_Site	SNP	A	TCGA-G8-6325-01A-11D-2210-10	597708	134345062	46570198	221	7665											
PCDHAC1	56135	hgsc.bcm.edu	37	chr5	140307485	140307485	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgactgacgtgaacgatcaTgcccccgaactggacttcct	9	9	10	13	3	1	3	1	3	0	0	2	6	2	4	3	1	3	0	3	1	2	1	rs147219331	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140307485T>C	ENST00000253807.2	+	1	1008	c.1008T>C	c.(1006-1008)caT>caC	p.H336H	PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHAC1_ENST00000409700.3_Silent_p.H336H|PCDHA13_ENST00000409494.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1	336	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(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)			TGAACGATCATGCCCCCGAAC	0.532													t|||	2	0.000399361	0.0	0.0	5008	,	,		21222	0.0		0.002	False		,,,				2504	0.0				p.H336H		Atlas-SNP	.											.	PCDHAC1	141	.	0			c.T1008C						PASS	.	T	,,,,,,,,,,,,,,,,,	5,4401	9.9+/-24.2	0,5,2198	174	160	164		1008,,,,,,,,,,,,,,,,,1008	-0.5	0.3	5	dbSNP_134	164	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHAC1,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018898.3,NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018904.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031882.2	,,,,,,,,,,,,,,,,,	0,16,6487	CC,CT,TT		0.1279,0.1135,0.123	,,,,,,,,,,,,,,,,,	336/964,,,,,,,,,,,,,,,,,336/819	140307485	16,12990	2203	4300	6503	SO:0001819	synonymous_variant	56135	exon1			CGATCATGCCCCC	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.1008T>C	5.37:g.140307485T>C		185	0	0		194	61	0.314433	NM_031882	Q9Y5F5|Q9Y5I5	Silent	SNP	ENST00000253807.2	37	CCDS4241.1																																																																																			T|0.999;C|0.001	0.001	strong		0.532	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	NM_018898		C	140307485	T	C	140307485	2	2	23	1	0	0	0	0	0	0	0	1	11541	1461	51	3		3	PCDHAC1	5	140307485	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	5962423	140307485	40607775	222	7666											
PCDHGA8	9708	hgsc.bcm.edu	37	chr5	140774505	140774505	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgtcttcctcgcctttgtcGctgtgcttctggggctcagg	1	15	13	12	2	3	0	1	0	2	0	6	0	4	0	2	3	1	3	2	3	0	3	rs367656720		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140774505G>T	ENST00000398604.2	+	1	2125	c.2125G>T	c.(2125-2127)Gct>Tct	p.A709S	PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	709					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)			CGCCTTTGTCGCTGTGCTTCT	0.602																																					p.A709S		Atlas-SNP	.											.	PCDHGA8	146	.	0			c.G2125T						PASS	.	G	,SER/ALA,,,,,,,,,,,SER/ALA	0,4378		0,0,2189	35	40	38		,2125,,,,,,,,,,,2125	0.6	0	5		38	1,8587		0,1,4293	no	intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHGB4,PCDHGA8,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_014004.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_032088.1	,99,,,,,,,,,,,99	0,1,6482	TT,TG,GG		0.0116,0.0,0.0077	,,,,,,,,,,,,	,709/821,,,,,,,,,,,709/933	140774505	1,12965	2189	4294	6483	SO:0001583	missense	9708	exon1			TTTGTCGCTGTGC	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.2125G>T	5.37:g.140774505G>T	ENSP00000381605:p.Ala709Ser	141	0	0		130	89	0.684615	NM_014004	A7MCZ4|O15039	Missense_Mutation	SNP	ENST00000398604.2	37	CCDS47291.1	.	.	.	.	.	.	.	.	.	.	.	6.375	0.437282	0.12104	0.0	1.16E-4	ENSG00000253767	ENST00000398604	T	0.14266	2.52	4.5	0.627	0.17675	.	0.671943	0.11133	U	0.596072	T	0.07908	0.0198	N	0.14661	0.345	0.09310	N	1	B;B	0.22851	0.024;0.076	B;B	0.26310	0.032;0.068	T	0.36383	-0.9750	10	0.87932	D	0	.	4.7807	0.13201	0.4634:0.3303:0.2063:0.0	.	709;709	Q9Y5G5;Q9Y5G5-2	PCDG8_HUMAN;.	S	709	ENSP00000381605:A709S	ENSP00000381605:A709S	A	+	1	0	PCDHGA8	140754689	0.000000	0.05858	0.008000	0.14137	0.021000	0.10359	-0.022000	0.12480	-0.041000	0.13558	-0.910000	0.02820	GCT	.	.	weak		0.602	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088		T	140774505	G	T	140774505	3	4	23	1	0	0	0	0	1	0	0	0	11569	1087	38	4	2127	4	PCDHGA8	5	140774505	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	467020	140774505	40140755	223	7667											
PCDHGB6	56100	hgsc.bcm.edu	37	chr5	140788107	140788107	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaagctgtggtggaaaatcCtttaaatatttttcatgtca	12	15	9	5	0	2	0	2	0	0	0	3	2	3	2	1	3	1	1	1	3	6	5	rs201370009		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140788107C>T	ENST00000520790.1	+	1	338	c.338C>T	c.(337-339)cCt>cTt	p.P113L	PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB2_ENST00000522605.1_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	113	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)			GTGGAAAATCCTTTAAATATT	0.383													.|||	1	0.000199681	0.0	0.0	5008	,	,		17773	0.0		0.001	False		,,,				2504	0.0				p.P113L		Atlas-SNP	.											PCDHGB6,right_lower_lobe,carcinoma,0,1	PCDHGB6	120	1	0			c.C338T						PASS	.	C	,,,,,,,,,,,,,LEU/PRO,,LEU/PRO	1,3661		0,1,1830	156	162	160		,,,,,,,,,,,,,338,,338	5.4	1	5		160	14,8126		0,14,4056	no	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,intron,missense	PCDHGB4,PCDHGA8,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_032088.1,NM_032100.1	,,,,,,,,,,,,,98,,98	0,15,5886	TT,TC,CC		0.172,0.0273,0.1271	,,,,,,,,,,,,,,,	,,,,,,,,,,,,,113/931,,113/821	140788107	15,11787	1831	4070	5901	SO:0001583	missense	56100	exon1			AAAATCCTTTAAA	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.338C>T	5.37:g.140788107C>T	ENSP00000428603:p.Pro113Leu	186	1	0.00537634		206	115	0.558252	NM_032100	Q9Y5C5	Missense_Mutation	SNP	ENST00000520790.1	37	CCDS54929.1	.	.	.	.	.	.	.	.	.	.	c	18.01	3.528330	0.64860	2.73E-4	0.00172	ENSG00000253305	ENST00000520790	T	0.37235	1.21	5.38	5.38	0.77491	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.72391	0.3454	H	0.95574	3.69	0.58432	D	0.999998	D;D	0.71674	0.998;0.998	D;D	0.71414	0.973;0.969	T	0.81824	-0.0755	9	0.87932	D	0	.	19.1331	0.93415	0.0:1.0:0.0:0.0	.	113;113	Q9Y5F9;Q9Y5F9-2	PCDGI_HUMAN;.	L	113	ENSP00000428603:P113L	ENSP00000428603:P113L	P	+	2	0	PCDHGB6	140768291	1.000000	0.71417	0.995000	0.50966	0.378000	0.30076	7.779000	0.85648	2.517000	0.84864	0.467000	0.42956	CCT	C|0.994;T|0.006	0.006	strong		0.383	PCDHGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374746.1	NM_018926		T	140788107	C	T	140788107	3	4	23	1	0	0	0	0	1	0	0	0	11576	681	24	2	340	2	PCDHGB6	5	140788107	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	13602	140788107	40127153	224	7668											
KIAA0141	9812	hgsc.bcm.edu	37	chr5	141309152	141309152	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctggctctttccagcactgCgacaacacatcctccccagc	8	8	7	18	1	1	0	0	0	1	0	4	1	4	0	4	1	4	3	4	1	1	1	rs114623503	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:141309152C>T	ENST00000432126.2	+	5	552	c.418C>T	c.(418-420)Cga>Tga	p.R140*	KIAA0141_ENST00000194118.4_Nonsense_Mutation_p.R140*	NM_001142603.1|NM_014773.3	NP_001136075.1|NP_055588.3	Q14154	DELE_HUMAN	KIAA0141	140					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)			TCCAGCACTGCGACAACACAT	0.632													C|||	2	0.000399361	0.0	0.0	5008	,	,		17987	0.0		0.002	False		,,,				2504	0.0				p.R140X		Atlas-SNP	.											.	KIAA0141	44	.	0			c.C418T						PASS	.	C	stop/ARG,stop/ARG	2,4404	4.2+/-10.8	0,2,2201	68	71	70		418,418	1.9	0.7	5	dbSNP_132	70	16,8584	11.2+/-40.8	0,16,4284	yes	stop-gained,stop-gained	KIAA0141	NM_001142603.1,NM_014773.3	,	0,18,6485	TT,TC,CC		0.186,0.0454,0.1384	,	140/516,140/516	141309152	18,12988	2203	4300	6503	SO:0001587	stop_gained	9812	exon5			GCACTGCGACAAC	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.418C>T	5.37:g.141309152C>T	ENSP00000396225:p.Arg140*	109	0	0		109	40	0.366972	NM_001142603	Q969R4|Q96EU9	Nonsense_Mutation	SNP	ENST00000432126.2	37	CCDS4268.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	14.47	2.543632	0.45280	4.54E-4	0.00186	ENSG00000081791	ENST00000432126;ENST00000194118;ENST00000508751	.	.	.	3.95	1.87	0.25490	.	0.181406	0.33040	N	0.005360	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.4383	8.0362	0.30493	0.4754:0.5246:0.0:0.0	.	.	.	.	X	140	.	ENSP00000194118:R140X	R	+	1	2	KIAA0141	141289336	0.059000	0.20769	0.661000	0.29709	0.048000	0.14542	0.121000	0.15667	0.827000	0.34685	0.305000	0.20034	CGA	C|0.999;T|0.001	0.001	strong		0.632	KIAA0141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251863.2	NM_014773		T	141309152	C	T	141309152	4	4	23	1	0	0	0	0	0	1	0	0	8165	760	27	1	436	1	KIAA0141	5	141309152	Nonsense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	521045	141309152	39606108	225	7669											
PCDH12	51294	hgsc.bcm.edu	37	chr5	141337177	141337177	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgagcaagccttcctcagaGtccacctgaatggggagcgc	9	7	12	13	1	1	3	1	2	0	1	3	4	3	4	4	2	3	1	4	2	2	1	rs138689340	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:141337177G>C	ENST00000231484.3	-	1	1450	c.240C>G	c.(238-240)gaC>gaG	p.D80E	PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	80	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)			CTTCCTCAGAGTCCACCTGAA	0.637													G|||	28	0.00559105	0.0008	0.013	5008	,	,		17451	0.0		0.0149	False		,,,				2504	0.0031				p.D80E		Atlas-SNP	.											.	PCDH12	133	.	0			c.C240G						PASS	.	G	GLU/ASP	15,4391	22.3+/-47.3	0,15,2188	52	53	53		240	-1.3	0	5	dbSNP_134	53	145,8455	70.0+/-132.6	1,143,4156	yes	missense	PCDH12	NM_016580.2	45	1,158,6344	CC,CG,GG		1.686,0.3404,1.2302	benign	80/1185	141337177	160,12846	2203	4300	6503	SO:0001583	missense	51294	exon1			CTCAGAGTCCACC	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.240C>G	5.37:g.141337177G>C	ENSP00000231484:p.Asp80Glu	195	0	0		198	125	0.631313	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	37	CCDS4269.1	21	0.009615384615384616	3	0.006097560975609756	6	0.016574585635359115	0	0.0	12	0.0158311345646438	G	5.339	0.247807	0.10130	0.003404	0.01686	ENSG00000113555	ENST00000231484	T	0.27890	1.64	4.81	-1.34	0.09143	Cadherin, N-terminal (1);Cadherin (4);	0.577641	0.19689	N	0.108338	T	0.13841	0.0335	L	0.57130	1.785	0.09310	N	1	B	0.12013	0.005	B	0.13407	0.009	T	0.20874	-1.0262	10	0.49607	T	0.09	.	9.9206	0.41462	0.5973:0.0:0.4027:0.0	.	80	Q9NPG4	PCD12_HUMAN	E	80	ENSP00000231484:D80E	ENSP00000231484:D80E	D	-	3	2	PCDH12	141317361	0.000000	0.05858	0.007000	0.13788	0.138000	0.21146	-1.159000	0.03150	-0.212000	0.10109	0.563000	0.77884	GAC	G|0.986;C|0.014	0.014	strong		0.637	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580		C	141337177	G	C	141337177	3	2	23	1	0	0	0	0	1	0	0	0	11519	1020	36	4	3330	4	PCDH12	5	141337177	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	28025	141337177	39578083	226	7670											
C5orf62	85027	hgsc.bcm.edu	37	chr5	150175109	150175109	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caccattgtcatcatgacctCgttgttgctgtgcccagcca	7	12	8	14	1	2	1	2	1	0	0	3	1	2	1	4	0	3	3	4	0	0	3	rs61736140	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:150175109C>T	ENST00000526627.1	+	2	1145	c.107C>T	c.(106-108)tCg>tTg	p.S36L	AC010441.1_ENST00000600109.1_3'UTR	NM_032947.4	NP_116565.3	Q9BZL3	SMIM3_HUMAN	small integral membrane protein 3	36						integral component of membrane (GO:0016021)											ATCATGACCTCGTTGTTGCTG	0.547													C|||	10	0.00199681	0.0	0.0029	5008	,	,		22069	0.0		0.008	False		,,,				2504	0.0				p.S36L		Atlas-SNP	.											.	.	.	.	0			c.C107T						PASS	.																																			SO:0001583	missense	85027	exon2			TGACCTCGTTGTT	AF313413	CCDS47312.1, CCDS47312.2	5q33.1	2012-10-01	2012-10-01	2012-10-01	ENSG00000256235	ENSG00000256235			30248	protein-coding gene	gene with protein product		608324	"chromosome 5 open reading frame 62"	C5orf62		11288140	Standard	NM_032947		Approved	MSTP150, NID67	uc003lsw.3	Q9BZL3	OTTHUMG00000163646	ENST00000526627.1:c.107C>T	5.37:g.150175109C>T	ENSP00000436897:p.Ser36Leu	59	0	0		58	40	0.689655	NM_032947	Q3MIG3|Q6ZUV4	Missense_Mutation	SNP	ENST00000526627.1	37	CCDS47312.2	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	18.98	3.737622	0.69304	.	.	ENSG00000256235	ENST00000526627	.	.	.	5.11	5.11	0.69529	.	.	.	.	.	T	0.65554	0.2702	.	.	.	0.38915	D	0.957602	.	.	.	.	.	.	T	0.69514	-0.5125	4	.	.	.	.	16.8482	0.85986	0.0:1.0:0.0:0.0	rs61736140	.	.	.	L	36	.	.	S	+	2	0	C5orf62	150155302	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.723000	0.54955	2.768000	0.95171	0.491000	0.48974	TCG	C|0.996;T|0.004	0.004	strong		0.547	SMIM3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374647.2	NM_032947		T	150175109	C	T	150175109	3	4	23	1	0	0	0	0	1	0	0	0	2316	893	31	1	109	1	C5orf62	5	150175109	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	8837932	150175109	30740151	227	7671											
LARP1	23367	hgsc.bcm.edu	37	chr5	154092616	154092616	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cagcgtggccttggcagctgCcccgaggaaggagcccacag	8	4	15	14	2	0	0	0	0	0	0	0	3	0	2	4	4	4	2	4	4	1	1	rs148235669	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:154092616C>T	ENST00000336314.4	+	1	155	c.131C>T	c.(130-132)gCc>gTc	p.A44V		NM_015315.3	NP_056130.2	Q6PKG0	LARP1_HUMAN	La ribonucleoprotein domain family, member 1	62					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)			TTGGCAGCTGCCCCGAGGAAG	0.602													C|||	3	0.000599042	0.0008	0.0014	5008	,	,		17738	0.0		0.0	False		,,,				2504	0.001				p.A44V		Atlas-SNP	.											.	LARP1	187	.	0			c.C131T						PASS	.	C	VAL/ALA	2,4404	4.2+/-10.8	0,2,2201	53	53	53		131	2.9	0.8	5	dbSNP_134	53	22,8578	16.0+/-53.3	0,22,4278	yes	missense	LARP1	NM_015315.3	64	0,24,6479	TT,TC,CC		0.2558,0.0454,0.1845		44/1020	154092616	24,12982	2203	4300	6503	SO:0001583	missense	23367	exon1			CAGCTGCCCCGAG	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.131C>T	5.37:g.154092616C>T	ENSP00000336721:p.Ala44Val	285	0	0		269	90	0.334572	NM_015315	O94836|Q8N4M2|Q8NB73|Q9UFD7	Missense_Mutation	SNP	ENST00000336314.4	37	CCDS4328.1	.	.	.	.	.	.	.	.	.	.	C	6.440	0.449233	0.12223	4.54E-4	0.002558	ENSG00000155506	ENST00000336314	T	0.25085	1.82	3.81	2.94	0.34122	.	.	.	.	.	T	0.17577	0.0422	.	.	.	0.19300	N	0.999973	B	0.27997	0.197	B	0.29176	0.099	T	0.19484	-1.0304	8	0.30078	T	0.28	.	8.8895	0.35425	0.2222:0.7778:0.0:0.0	.	44	Q6PKG0-3	.	V	44	ENSP00000336721:A44V	ENSP00000336721:A44V	A	+	2	0	LARP1	154072809	0.960000	0.32886	0.823000	0.32752	0.013000	0.08279	2.833000	0.48159	1.182000	0.42928	-0.310000	0.09108	GCC	C|0.998;T|0.002	0.002	strong		0.602	LARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252509.1	NM_033551		T	154092616	C	T	154092616	3	4	23	1	0	0	0	0	1	0	0	0	8637	739	26	2	133	2	LARP1	5	154092616	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	3917507	154092616	26822644	228	7672											
SOX30	11063	hgsc.bcm.edu	37	chr5	157078632	157078632	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggtttcgacggcccctcgaGgccccactgactgatccagg	6	7	12	16	4	0	2	0	2	0	0	3	4	1	2	5	4	0	1	5	4	0	1	rs13181859	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:157078632G>A	ENST00000265007.6	-	1	796	c.455C>T	c.(454-456)cCt>cTt	p.P152L	SOX30_ENST00000519442.1_Intron|SOX30_ENST00000311371.5_Missense_Mutation_p.P152L	NM_178424.1	NP_848511.1	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30	152					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)			GGCCCCTCGAGGCCCCACTGA	0.682													.|||	16	0.00319489	0.0	0.0072	5008	,	,		14330	0.0		0.002	False		,,,				2504	0.0092				p.P152L	Esophageal Squamous(31;525 799 19355 21125 41744)	Atlas-SNP	.											.	SOX30	67	.	0			c.C455T						PASS	.	G	LEU/PRO,LEU/PRO	1,4355		0,1,2177	15	18	17		455,455	2.2	0	5	dbSNP_121	17	28,8462		0,28,4217	yes	missense,missense	SOX30	NM_007017.2,NM_178424.1	98,98	0,29,6394	AA,AG,GG		0.3298,0.023,0.2258	benign,benign	152/502,152/754	157078632	29,12817	2178	4245	6423	SO:0001583	missense	11063	exon1			CCTCGAGGCCCCA	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.455C>T	5.37:g.157078632G>A	ENSP00000265007:p.Pro152Leu	100	0	0		128	89	0.695312	NM_178424	O94995|Q8IYX6	Missense_Mutation	SNP	ENST00000265007.6	37	CCDS4339.1	3	0.0013736263736263737	0	0.0	3	0.008287292817679558	0	0.0	0	0.0	G	3.133	-0.178037	0.06380	2.3E-4	0.003298	ENSG00000039600	ENST00000311371;ENST00000265007	D;D	0.97665	-4.48;-4.13	4.09	2.25	0.28309	.	1.098170	0.07137	N	0.846598	D	0.89220	0.6653	N	0.19112	0.55	0.09310	N	0.999999	B;B	0.32829	0.386;0.0	B;B	0.28232	0.087;0.0	D	0.84664	0.0708	10	0.72032	D	0.01	.	2.6853	0.05106	0.094:0.1461:0.3488:0.4112	rs13181859	152;152	O94993-2;O94993	.;SOX30_HUMAN	L	152	ENSP00000309343:P152L;ENSP00000265007:P152L	ENSP00000265007:P152L	P	-	2	0	SOX30	157011210	0.001000	0.12720	0.000000	0.03702	0.006000	0.05464	0.788000	0.26872	0.351000	0.24027	0.305000	0.20034	CCT	G|0.998;A|0.002	0.002	strong		0.682	SOX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252571.2	NM_007017		A	157078632	G	A	157078632	3	1	23	1	0	0	0	0	1	0	0	0	14967	1000	35	2	1826	2	SOX30	5	157078632	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	2986016	157078632	23836628	229	7673											
CCNJL	79616	hgsc.bcm.edu	37	chr5	159682580	159682580	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcaggatttcaatacacgtgCtgaggtgctccagggaatag	11	9	13	8	1	1	1	1	1	0	0	2	3	2	3	1	3	3	3	1	3	4	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:159682580C>T	ENST00000393977.3	-	6	1148	c.863G>A	c.(862-864)aGc>aAc	p.S288N	CCNJL_ENST00000541762.1_Missense_Mutation_p.S239N|CCNJL_ENST00000257536.7_Missense_Mutation_p.S240N|CCNJL_ENST00000519673.1_Missense_Mutation_p.S240N|CCNJL_ENST00000377503.2_5'UTR	NM_024565.5	NP_078841.3	Q8IV13	CCNJL_HUMAN	cyclin J-like	288						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)			AATACACGTGCTGAGGTGCTC	0.552																																					p.S288N		Atlas-SNP	.											.	CCNJL	36	.	0			c.G863A						PASS	.						174	175	174					5																	159682580		1905	4140	6045	SO:0001583	missense	79616	exon6			CACGTGCTGAGGT	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.863G>A	5.37:g.159682580C>T	ENSP00000377547:p.Ser288Asn	159	0	0		199	67	0.336683	NM_024565	Q6ZN43|Q9H7W8	Missense_Mutation	SNP	ENST00000393977.3	37	CCDS4350.2	.	.	.	.	.	.	.	.	.	.	C	8.336	0.827560	0.16749	.	.	ENSG00000135083	ENST00000393977;ENST00000257536;ENST00000519673;ENST00000541762	T;T;T;T	0.21543	2.0;2.0;2.0;2.0	5.61	3.79	0.43588	Cyclin, C-terminal (1);Cyclin-like (3);	0.173358	0.51477	D	0.000099	T	0.09818	0.0241	N	0.20685	0.6	0.31077	N	0.712353	B;B;P	0.34724	0.014;0.099;0.465	B;B;B	0.30401	0.036;0.036;0.115	T	0.10965	-1.0607	10	0.19590	T	0.45	-12.2999	4.6847	0.12752	0.1373:0.4338:0.3483:0.0806	.	240;240;288	E7EN43;B4DZA8;Q8IV13	.;.;CCNJL_HUMAN	N	288;240;240;239	ENSP00000377547:S288N;ENSP00000257536:S240N;ENSP00000427960:S240N;ENSP00000446367:S239N	ENSP00000257536:S240N	S	-	2	0	CCNJL	159615158	1.000000	0.71417	0.976000	0.42696	0.446000	0.32137	2.239000	0.43079	1.334000	0.45468	0.655000	0.94253	AGC	.	.	none		0.552	CCNJL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252674.1	NM_024565		T	159682580	C	T	159682580	3	4	23	1	0	0	0	0	1	0	0	0	2931	797	28	2	452	2	CCNJL	5	159682580	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	2603948	159682580	21232680	230	7674											
FAF2	23197	hgsc.bcm.edu	37	chr5	175919324	175919324	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctgtcttctaccagggaacGtacagccaggtcagtgccat	9	9	10	13	1	3	0	1	0	2	0	3	1	3	1	4	2	5	1	4	2	3	3	rs78597771	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:175919324G>A	ENST00000261942.6	+	5	527	c.474G>A	c.(472-474)acG>acA	p.T158T		NM_014613.2	NP_055428.1	Q96CS3	FAF2_HUMAN	Fas associated factor family member 2	158					lipid particle organization (GO:0034389)|negative regulation of catalytic activity (GO:0043086)|response to unfolded protein (GO:0006986)	Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)	lipase binding (GO:0035473)|lipase inhibitor activity (GO:0055102)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	10						ACCAGGGAACGTACAGCCAGG	0.493													G|||	42	0.00838658	0.0015	0.0144	5008	,	,		20504	0.0		0.0288	False		,,,				2504	0.001				p.T158T		Atlas-SNP	.											.	FAF2	38	.	0			c.G474A						PASS	.	G		27,4379	32.6+/-62.9	0,27,2176	62	57	59		474	0.4	1	5	dbSNP_132	59	286,8314	107.0+/-167.8	4,278,4018	no	coding-synonymous	FAF2	NM_014613.2		4,305,6194	AA,AG,GG		3.3256,0.6128,2.4066		158/446	175919324	313,12693	2203	4300	6503	SO:0001819	synonymous_variant	23197	exon5			GGGAACGTACAGC	BC015791	CCDS34296.1	5q35.2	2011-06-28	2008-07-25	2008-07-25	ENSG00000113194	ENSG00000113194		"UBX domain containing"	24666	protein-coding gene	gene with protein product	"expressed in T cells and eosinophils in atopic dermatitis", "UBX domain protein 3B"		"UBX domain containing 8"	UBXD8		10048485, 12372427	Standard	NM_014613		Approved	ETEA, KIAA0887, UBXN3B	uc003mej.4	Q96CS3	OTTHUMG00000163228	ENST00000261942.6:c.474G>A	5.37:g.175919324G>A		80	0	0		76	27	0.355263	NM_014613	O94963|Q8IUF2|Q9BRP2|Q9BVM7	Silent	SNP	ENST00000261942.6	37	CCDS34296.1																																																																																			G|0.978;A|0.022	0.022	strong		0.493	FAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372194.1	NM_014613		A	175919324	G	A	175919324	2	1	23	1	0	0	0	0	0	0	0	1	5375	1132	40	1		1	FAF2	5	175919324	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	16236744	175919324	4995936	231	7675											
HK3	3101	hgsc.bcm.edu	37	chr5	176309082	176309082	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgagtccccaggcacgccCgccacattccggagctcctc	6	6	9	20	3	0	1	0	1	0	0	4	2	3	2	7	2	1	2	7	2	0	1	rs34127573	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:176309082C>T	ENST00000292432.5	-	16	2191	c.2100G>A	c.(2098-2100)gcG>gcA	p.A700A		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	700	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)			CAGGCACGCCCGCCACATTCC	0.597													C|||	20	0.00399361	0.003	0.0014	5008	,	,		18484	0.0		0.0139	False		,,,				2504	0.001				p.A700A		Atlas-SNP	.											.	HK3	210	.	0			c.G2100A						PASS	.	C		10,4396	12.9+/-30.5	0,10,2193	52	50	51		2100	-10.1	0	5	dbSNP_126	51	119,8479	55.6+/-116.7	1,117,4181	no	coding-synonymous	HK3	NM_002115.2		1,127,6374	TT,TC,CC		1.384,0.227,0.992		700/924	176309082	129,12875	2203	4299	6502	SO:0001819	synonymous_variant	3101	exon16			CACGCCCGCCACA		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.2100G>A	5.37:g.176309082C>T		121	0	0		130	82	0.630769	NM_002115	Q8N1E7	Silent	SNP	ENST00000292432.5	37	CCDS4407.1																																																																																			C|0.992;T|0.008	0.008	strong		0.597	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1			T	176309082	C	T	176309082	2	4	23	1	0	0	0	0	0	0	0	1	7201	639	23	1		1	HK3	5	176309082	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	389758	176309082	4606178	232	7676											
ZNF354A	6940	hgsc.bcm.edu	37	chr5	178139379	178139379	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	gagttacacctgaatgttttCccacactcgttacatttata	11	15	5	10	1	0	1	0	1	0	0	2	2	1	1	2	0	2	3	2	0	5	7	rs201342253	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:178139379C>G	ENST00000335815.2	-	5	1697	c.1500G>C	c.(1498-1500)ggG>ggC	p.G500G		NM_005649.2	NP_005640.2	O60765	Z354A_HUMAN	zinc finger protein 354A	500					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)		TGAATGTTTTCCCACACTCGT	0.393													C|||	14	0.00279553	0.0008	0.0029	5008	,	,		20195	0.0		0.0089	False		,,,				2504	0.002				p.G500G		Atlas-SNP	.											.	ZNF354A	74	.	0			c.G1500C						PASS	.						122	119	120					5																	178139379		2203	4300	6503	SO:0001819	synonymous_variant	6940	exon5			TGTTTTCCCACAC	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.1500G>C	5.37:g.178139379C>G		188	0	0		126	7	0.0555556	NM_005649	Q9UNJ8	Silent	SNP	ENST00000335815.2	37	CCDS4438.1																																																																																			C|0.999;G|0.001	0.001	weak		0.393	ZNF354A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253481.1	NM_005649		G	178139379	C	G	178139379	2	3	23	1	0	0	0	0	0	0	0	1	17879	842	30	4		4	ZNF354A	5	178139379	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1830297	178139379	2775881	233	7677											
ZNF354B	117608	hgsc.bcm.edu	37	chr5	178309735	178309735	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagagcacacctaaaatgacAaagtcaactcaaactcagga	20	5	6	10	0	3	2	3	1	0	1	3	3	3	3	1	1	3	1	1	1	6	1	rs148284462	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:178309735A>C	ENST00000322434.3	+	5	508	c.282A>C	c.(280-282)acA>acC	p.T94T	RNU1-39P_ENST00000383897.1_RNA	NM_058230.2	NP_478137.1	Q96LW1	Z354B_HUMAN	zinc finger protein 354B	94					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)			CTAAAATGACAAAGTCAACTC	0.373																																					p.T94T		Atlas-SNP	.											.	ZNF354B	67	.	0			c.A282C						PASS	.	A		0,4388		0,0,2194	60	61	61		282	2.3	1	5	dbSNP_134	61	3,8587		0,3,4292	no	coding-synonymous	ZNF354B	NM_058230.2		0,3,6486	CC,CA,AA		0.0349,0.0,0.0231		94/613	178309735	3,12975	2194	4295	6489	SO:0001819	synonymous_variant	117608	exon5			AATGACAAAGTCA	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.282A>C	5.37:g.178309735A>C		149	0	0		160	70	0.4375	NM_058230	A8K0V2|Q5U5Z4	Silent	SNP	ENST00000322434.3	37	CCDS4439.1																																																																																			A|0.999;C|0.001	0.001	strong		0.373	ZNF354B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253482.1	NM_058230		C	178309735	A	C	178309735	2	2	23	1	0	0	0	0	0	0	0	1	17880	117	5	5		5	ZNF354B	5	178309735	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	170356	178309735	2605525	234	7678											
ZNF354C	30832	hgsc.bcm.edu	37	chr5	178503472	178503472	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgacattcagggatgtggcCgtgttcttcagccaggacga	8	10	14	9	2	3	1	2	1	1	0	3	4	3	3	2	3	1	1	2	3	0	3	rs116407910	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:178503472C>T	ENST00000315475.6	+	3	360	c.54C>T	c.(52-54)gcC>gcT	p.A18A		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	18	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(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)		GGGATGTGGCCGTGTTCTTCA	0.552													C|||	11	0.00219649	0.0	0.0072	5008	,	,		17713	0.0		0.006	False		,,,				2504	0.0				p.A18A		Atlas-SNP	.											ZNF354C,NS,carcinoma,+2,1	ZNF354C	77	1	0			c.C54T						PASS	.	C		4,4402	8.1+/-20.4	0,4,2199	173	153	160		54	-5.6	0.3	5	dbSNP_132	160	40,8560	26.8+/-75.7	0,40,4260	no	coding-synonymous	ZNF354C	NM_014594.1		0,44,6459	TT,TC,CC		0.4651,0.0908,0.3383		18/555	178503472	44,12962	2203	4300	6503	SO:0001819	synonymous_variant	30832	exon3			TGTGGCCGTGTTC		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.54C>T	5.37:g.178503472C>T		290	0	0		287	164	0.571429	NM_014594	Q6P4P9|Q8NFX1	Silent	SNP	ENST00000315475.6	37	CCDS4443.1																																																																																			C|0.996;T|0.004	0.004	strong		0.552	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2			T	178503472	C	T	178503472	2	4	23	1	0	0	0	0	0	0	0	1	17881	639	23	1		1	ZNF354C	5	178503472	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	193737	178503472	2411788	235	7679											
ADAMTS2	9509	hgsc.bcm.edu	37	chr5	178564906	178564906	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cggctgcagagctggaagtcGtaggcaaggcccgagcaggt	9	5	17	10	3	0	1	0	0	0	1	1	3	0	2	1	5	3	6	1	5	3	1	rs369654932		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:178564906G>A	ENST00000251582.7	-	12	1916	c.1815C>T	c.(1813-1815)taC>taT	p.Y605Y		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	605	TSP type-1 1. {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)		GCTGGAAGTCGTAGGCAAGGC	0.682																																					p.Y605Y		Atlas-SNP	.											ADAMTS2,colon,carcinoma,0,1	ADAMTS2	190	1	0			c.C1815T						PASS	.	G		0,4264		0,0,2132	14	14	14		1815	-0.5	1	5		14	2,8428		0,2,4213	no	coding-synonymous	ADAMTS2	NM_014244.4		0,2,6345	AA,AG,GG		0.0237,0.0,0.0158		605/1212	178564906	2,12692	2132	4215	6347	SO:0001819	synonymous_variant	9509	exon12			GAAGTCGTAGGCA	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.1815C>T	5.37:g.178564906G>A		132	0	0		77	24	0.311688	NM_014244		Silent	SNP	ENST00000251582.7	37	CCDS4444.1																																																																																			.	.	weak		0.682	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244		A	178564906	G	A	178564906	2	1	23	1	0	0	0	0	0	0	0	1	265	1140	40	1		1	ADAMTS2	5	178564906	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	61434	178564906	2350354	236	7680											
TRIM41	90933	hgsc.bcm.edu	37	chr5	180661468	180661468	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggggatgccagctcctcgcGccatcaccatcgccgccgcc	5	5	11	20	6	1	0	1	0	0	0	4	1	2	1	7	2	2	1	7	2	0	0			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:180661468G>A	ENST00000315073.5	+	6	2296	c.1586G>A	c.(1585-1587)cGc>cAc	p.R529H	TRIM41_ENST00000351937.5_Intron|TRIM41_ENST00000510072.1_3'UTR	NM_033549.4	NP_291027.3	Q8WV44	TRI41_HUMAN	tripartite motif containing 41	529	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)			AGCTCCTCGCGCCATCACCAT	0.692																																					p.R529H		Atlas-SNP	.											.	TRIM41	96	.	0			c.G1586A						PASS	.						21	23	22					5																	180661468		2200	4296	6496	SO:0001583	missense	90933	exon6			CCTCGCGCCATCA	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.1586G>A	5.37:g.180661468G>A	ENSP00000320869:p.Arg529His	122	0	0		80	34	0.425	NM_033549	B3KNJ6|D3DWR9|Q5BKT0|Q7L484|Q96Q10|Q9BSL8	Missense_Mutation	SNP	ENST00000315073.5	37	CCDS4466.1	.	.	.	.	.	.	.	.	.	.	G	12.61	1.989186	0.35131	.	.	ENSG00000146063	ENST00000315073;ENST00000438174	T	0.55413	0.52	5.32	4.45	0.53987	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.52532	D	0.000063	T	0.33731	0.0873	N	0.14661	0.345	0.27302	N	0.957547	B	0.15141	0.012	B	0.10450	0.005	T	0.19128	-1.0315	10	0.37606	T	0.19	.	9.9313	0.41523	0.0946:0.0:0.9054:0.0	.	529	Q8WV44	TRI41_HUMAN	H	529;214	ENSP00000320869:R529H	ENSP00000320869:R529H	R	+	2	0	TRIM41	180594074	0.998000	0.40836	0.955000	0.39395	0.211000	0.24417	4.196000	0.58407	1.255000	0.44051	0.449000	0.29647	CGC	.	.	none		0.692	TRIM41-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253574.3	NM_201627		A	180661468	G	A	180661468	3	1	23	1	0	0	0	0	1	0	0	0	16531	1087	38	1	1608	1	TRIM41	5	180661468	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	2096562	180661468	253792	237	7681											
C6orf195	154386	hgsc.bcm.edu	37	chr6	2623960	2623960	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggctggcagagtggctccaTgccatcaaatgccctttctc	7	11	10	13	0	2	1	1	0	1	1	4	1	3	1	3	3	2	3	3	3	1	1	rs201134793	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:2623960T>C	ENST00000296847.3	-	3	620	c.97A>G	c.(97-99)Atg>Gtg	p.M33V		NM_152554.2	NP_689767.2	Q96MT4	CF195_HUMAN	chromosome 6 open reading frame 195	33										cervix(1)|endometrium(1)|lung(2)|skin(1)	5	Ovarian(93;0.0412)	all_hematologic(90;0.0895)				AGTGGCTCCATGCCATCAAAT	0.592													T|||	5	0.000998403	0.0	0.0043	5008	,	,		17886	0.0		0.002	False		,,,				2504	0.0				p.M33V		Atlas-SNP	.											.	C6orf195	10	.	0			c.A97G						PASS	.	T	VAL/MET	0,4034		0,0,2017	38	45	42		97	-0.6	0	6		42	25,8323		0,25,4149	yes	missense	C6orf195	NM_152554.2	21	0,25,6166	CC,CT,TT		0.2995,0.0,0.2019	benign	33/128	2623960	25,12357	2017	4174	6191	SO:0001583	missense	154386	exon3			GCTCCATGCCATC	AK056496	CCDS43416.1	6p25.2	2008-10-21			ENSG00000164385	ENSG00000164385			21600	protein-coding gene	gene with protein product							Standard	NM_152554		Approved	FLJ31934, bA145H9.2	uc003mtw.2	Q96MT4	OTTHUMG00000014122	ENST00000296847.3:c.97A>G	6.37:g.2623960T>C	ENSP00000296847:p.Met33Val	77	0	0		72	29	0.402778	NM_152554	Q3SY08|Q3SY09|Q3SY10|Q5TAW4	Missense_Mutation	SNP	ENST00000296847.3	37	CCDS43416.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	T	5.297	0.240255	0.10023	0.0	0.002995	ENSG00000164385	ENST00000296847	T	0.33438	1.41	3.3	-0.649	0.11461	.	.	.	.	.	T	0.04318	0.0119	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38222	-0.9671	9	0.87932	D	0	.	2.698	0.05140	0.2349:0.433:0.0:0.3322	.	33	Q96MT4	CF195_HUMAN	V	33	ENSP00000296847:M33V	ENSP00000296847:M33V	M	-	1	0	C6orf195	2568959	0.001000	0.12720	0.000000	0.03702	0.129000	0.20672	-0.866000	0.04245	-0.105000	0.12132	0.482000	0.46254	ATG	T|0.999;C|0.001	0.001	strong		0.592	C6orf195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039633.1	NM_152554		C	2623960	T	C	2623960	3	2	23	1	0	0	0	0	1	0	0	0	2352	1464	51	3	290	3	C6orf195	6	2623960	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10		2623960	168491107	238	7682											
ELOVL2	54898	hgsc.bcm.edu	37	chr6	11005776	11005776	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	taagagtccaacatgaaccaCcctctgactcgagaatctga	14	8	7	12	1	2	5	0	3	2	2	4	6	3	5	3	0	2	0	3	0	4	1	rs559223553		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:11005776C>T	ENST00000354666.3	-	3	167	c.84G>A	c.(82-84)ggG>ggA	p.G28G		NM_017770.3	NP_060240.3	Q9NXB9	ELOV2_HUMAN	ELOVL fatty acid elongase 2	28					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)			ACATGAACCACCCTCTGACTC	0.408													C|||	1	0.000199681	0.0	0.0	5008	,	,		23355	0.0		0.0	False		,,,				2504	0.001				p.G28G		Atlas-SNP	.											.	ELOVL2	40	.	0			c.G84A						PASS	.						107	82	90					6																	11005776		2203	4300	6503	SO:0001819	synonymous_variant	54898	exon3			GAACCACCCTCTG	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.84G>A	6.37:g.11005776C>T		72	0	0		101	51	0.504951	NM_017770	Q6P9E1|Q86W94	Silent	SNP	ENST00000354666.3	37	CCDS4518.1																																																																																			.	.	none		0.408	ELOVL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039849.1			T	11005776	C	T	11005776	2	4	23	1	0	0	0	0	0	0	0	1	5076	494	18	2		2	ELOVL2	6	11005776	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	8381816	11005776	160109291	239	7683											
RNF144B	255488	hgsc.bcm.edu	37	chr6	18457574	18457574	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagacagtcagcctattgtcCtgccaacagagcaccggtaa	12	7	10	12	1	1	2	1	0	0	2	2	3	2	2	4	1	4	2	4	1	3	3	rs75403847		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:18457574C>T	ENST00000259939.3	+	5	837	c.520C>T	c.(520-522)Ctg>Ttg	p.L174L	RNF144B_ENST00000429054.2_Silent_p.L85L	NM_182757.3	NP_877434.2	Q7Z419	R144B_HUMAN	ring finger protein 144B	174					apoptotic process (GO:0006915)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(7)	11	Ovarian(93;0.00365)|Breast(50;0.0145)	all_hematologic(90;0.0536)	OV - Ovarian serous cystadenocarcinoma(7;0.00165)|all cancers(50;0.0102)|Epithelial(50;0.0105)			GCCTATTGTCCTGCCAACAGA	0.453													C|||	1	0.000199681	0.0	0.0	5008	,	,		20281	0.0		0.001	False		,,,				2504	0.0				p.L174L		Atlas-SNP	.											.	RNF144B	18	.	0			c.C520T						PASS	.	C		0,4406		0,0,2203	184	170	175		520	3.3	1	6	dbSNP_132	175	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous	RNF144B	NM_182757.3		0,11,6492	TT,TC,CC		0.1279,0.0,0.0846		174/304	18457574	11,12995	2203	4300	6503	SO:0001819	synonymous_variant	255488	exon5			ATTGTCCTGCCAA	AK096832	CCDS34345.1	6p22.3	2011-05-23	2009-01-05	2007-08-20	ENSG00000137393	ENSG00000137393		"RING-type (C3HC4) zinc fingers"	21578	protein-coding gene	gene with protein product			"IBR domain containing 2"	IBRDC2			Standard	NM_182757		Approved	bA528A10.3	uc003ncs.3	Q7Z419	OTTHUMG00000014322	ENST00000259939.3:c.520C>T	6.37:g.18457574C>T		109	0	0		156	72	0.461538	NM_182757	B3KUA8|B4DZI2|Q5TB85|Q6P4Q0|Q8N3R7|Q9BX38	Silent	SNP	ENST00000259939.3	37	CCDS34345.1																																																																																			C|0.999;T|0.001	0.001	strong		0.453	RNF144B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039965.2	XM_172581		T	18457574	C	T	18457574	2	4	23	1	0	0	0	0	0	0	0	1	13461	680	24	2		2	RNF144B	6	18457574	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	7451798	18457574	152657493	240	7684											
KIAA0319	9856	hgsc.bcm.edu	37	chr6	24570151	24570151	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgacgtgctcccagtggtaGaagacaatgccgtggtcatc	9	9	12	11	2	1	3	1	1	0	2	3	3	2	3	2	2	2	2	2	2	3	1	rs41271797	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:24570151G>A	ENST00000378214.3	-	12	2495	c.1971C>T	c.(1969-1971)ttC>ttT	p.F657F	KIAA0319_ENST00000543707.1_Silent_p.F657F|KIAA0319_ENST00000430948.2_Silent_p.F612F|KIAA0319_ENST00000535378.1_Silent_p.F648F|KIAA0319_ENST00000537886.1_Silent_p.F657F	NM_001168375.1|NM_014809.3	NP_001161847.1|NP_055624.2	Q5VV43	K0319_HUMAN	KIAA0319	657	PKD 4. {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						CCCAGTGGTAGAAGACAATGC	0.537													G|||	2	0.000399361	0.0	0.0	5008	,	,		20249	0.0		0.002	False		,,,				2504	0.0				p.F657F		Atlas-SNP	.											KIAA0319,NS,carcinoma,0,1	KIAA0319	117	1	0			c.C1971T						PASS	.	G	,,,,	2,4404	4.2+/-10.8	0,2,2201	118	103	108		1944,1971,1836,1971,1971	2.1	0.8	6	dbSNP_127	108	15,8585	12.6+/-44.7	0,15,4285	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KIAA0319	NM_001168374.1,NM_001168375.1,NM_001168376.1,NM_001168377.1,NM_014809.3	,,,,	0,17,6486	AA,AG,GG		0.1744,0.0454,0.1307	,,,,	648/1064,657/1073,612/1028,657/1012,657/1073	24570151	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	9856	exon12			GTGGTAGAAGACA	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.1971C>T	6.37:g.24570151G>A		209	0	0		250	126	0.504	NM_001168377	A7MD37|B2RTU7|B4DHA7|B4DK75|B7ZML3|F5H123|Q9UJC8|Q9Y4G7	Silent	SNP	ENST00000378214.3	37	CCDS34348.1																																																																																			G|0.999;A|0.001	0.001	strong		0.537	KIAA0319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040009.1	NM_014809		A	24570151	G	A	24570151	2	1	23	1	0	0	0	0	0	0	0	1	8177	933	33	2		2	KIAA0319	6	24570151	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	6112577	24570151	146544916	241	7685											
TDP2	51567	hgsc.bcm.edu	37	chr6	24653283	24653283	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggagcctcttgcattttcttTaaaaccatttttaactgatt	10	18	5	8	0	2	1	0	1	2	0	2	2	2	2	2	1	4	1	2	1	3	9	rs11559067	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:24653283T>C	ENST00000378198.4	-	6	905	c.735A>G	c.(733-735)ttA>ttG	p.L245L	TDP2_ENST00000341060.3_Silent_p.L187L|TDP2_ENST00000545995.1_Silent_p.L275L|TDP2_ENST00000478285.1_5'Flank			O95551	TYDP2_HUMAN	tyrosyl-DNA phosphodiesterase 2	245					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						GCATTTTCTTTAAAACCATTT	0.428								Direct reversal of damage					T|||	60	0.0119808	0.003	0.0202	5008	,	,		17943	0.001		0.0318	False		,,,				2504	0.0092				p.L245L		Atlas-SNP	.											.	TDP2	29	.	0			c.A735G						PASS	.	T		39,4367	43.1+/-76.7	0,39,2164	212	222	219		735	-1.5	0	6	dbSNP_120	219	322,8278	113.5+/-173.5	7,308,3985	no	coding-synonymous	TDP2	NM_016614.2		7,347,6149	CC,CT,TT		3.7442,0.8852,2.7756		245/363	24653283	361,12645	2203	4300	6503	SO:0001819	synonymous_variant	51567	exon6			TTTCTTTAAAACC	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.735A>G	6.37:g.24653283T>C		80	0	0		120	61	0.508333	NM_016614	B4DKL8|B4DQ95|Q2TBE2|Q5JYM0|Q7Z6U5|Q9NUK5|Q9NYY9	Silent	SNP	ENST00000378198.4	37	CCDS4557.1																																																																																			T|0.977;C|0.023	0.023	strong		0.428	TDP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000040012.1			C	24653283	T	C	24653283	2	2	23	1	0	0	0	0	0	0	0	1	15744	1751	61	3		3	TDP2	6	24653283	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	83132	24653283	146461784	242	7686											
HIST1H1D	3007	hgsc.bcm.edu	37	chr6	26234923	26234923	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcttgaggccaagcttgataCggctgttgtttttttctaca	7	17	9	8	1	2	2	0	2	2	0	2	2	2	2	1	2	3	4	1	2	3	8			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26234923C>A	ENST00000244534.5	-	1	293	c.239G>T	c.(238-240)cGt>cTt	p.R80L		NM_005320.2	NP_005311.1	P16402	H13_HUMAN	histone cluster 1, H1d	80	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)	p.R80H(1)		breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				AAGCTTGATACGGCTGTTGTT	0.537																																					p.R80L		Atlas-SNP	.											HIST1H1D,NS,lymphoid_neoplasm,0,1	HIST1H1D	40	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G239T						PASS	.						88	96	93					6																	26234923		2203	4300	6503	SO:0001583	missense	3007	exon1			TTGATACGGCTGT	M60747	CCDS4597.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000124575	ENSG00000124575		"Histones / Replication-dependent"	4717	protein-coding gene	gene with protein product		142210	"H1 histone family, member 3", "histone 1, H1d"	H1F3		1916825, 12408966	Standard	NM_005320		Approved	H1.3, H1d, H1s-2	uc003nhd.3	P16402	OTTHUMG00000014432	ENST00000244534.5:c.239G>T	6.37:g.26234923C>A	ENSP00000244534:p.Arg80Leu	211	0	0		289	57	0.197232	NM_005320	B2R751|Q2M2I2	Missense_Mutation	SNP	ENST00000244534.5	37	CCDS4597.1	.	.	.	.	.	.	.	.	.	.	.	22.8	4.340881	0.81911	.	.	ENSG00000124575	ENST00000244534	T	0.09445	2.98	5.23	5.23	0.72850	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.18002	0.0432	L	0.56199	1.76	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.04509	-1.0946	10	0.15499	T	0.54	-17.6271	18.1633	0.89717	0.0:1.0:0.0:0.0	.	80	P16402	H13_HUMAN	L	80	ENSP00000244534:R80L	ENSP00000244534:R80L	R	-	2	0	HIST1H1D	26342902	1.000000	0.71417	1.000000	0.80357	0.221000	0.24807	4.921000	0.63397	2.623000	0.88846	0.655000	0.94253	CGT	.	.	none		0.537	HIST1H1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040095.1	NM_005320		A	26234923	C	A	26234923	3	1	23	1	0	0	0	0	1	0	0	0	7134	536	19	4	430	4	HIST1H1D	6	26234923	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1581640	26234923	144880144	243	7687											
BTN2A1	11120	hgsc.bcm.edu	37	chr6	26468637	26468637	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccccgttcagccttttccGtgcctgtgaggcccttcttc	2	14	9	16	2	2	1	1	1	1	0	5	1	4	1	6	1	2	1	6	1	0	5	rs142664900	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26468637G>A	ENST00000312541.5	+	8	1692	c.1444G>A	c.(1444-1446)Gtg>Atg	p.V482M	BTN2A1_ENST00000469185.1_Intron|BTN2A1_ENST00000429381.1_3'UTR|BTN2A1_ENST00000541522.1_Missense_Mutation_p.V421M	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	482	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						AGCCTTTTCCGTGCCTGTGAG	0.577																																					p.V482M		Atlas-SNP	.											.	BTN2A1	118	.	0			c.G1444A						PASS	.	G	MET/VAL,,MET/VAL,	2,4404	4.2+/-10.8	0,2,2201	173	135	148		1261,,1444,	1.8	0.1	6	dbSNP_134	148	1,8599	1.2+/-3.3	0,1,4299	yes	missense,intron,missense,utr-3	BTN2A1	NM_001197233.1,NM_001197234.1,NM_007049.3,NM_078476.2	21,,21,	0,3,6500	AA,AG,GG		0.0116,0.0454,0.0231	possibly-damaging,,possibly-damaging,	421/467,,482/528,	26468637	3,13003	2203	4300	6503	SO:0001583	missense	11120	exon8			TTTTCCGTGCCTG	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.1444G>A	6.37:g.26468637G>A	ENSP00000312158:p.Val482Met	347	1	0.00288184		515	263	0.51068	NM_007049	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Missense_Mutation	SNP	ENST00000312541.5	37	CCDS4613.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.773|7.773	0.707775|0.707775	0.15239|0.15239	4.54E-4|4.54E-4	1.16E-4|1.16E-4	ENSG00000112763|ENSG00000112763	ENST00000265424|ENST00000312541;ENST00000541522	.|T;T	.|0.60920	.|0.15;0.15	2.72|2.72	1.84|1.84	0.25277|0.25277	.|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	.|0.45617	.|0.1351	L|L	0.61218|0.61218	1.895|1.895	0.09310|0.09310	N|N	1|1	.|D	.|0.58620	.|0.983	.|P	.|0.51055	.|0.657	.|T	.|0.23655	.|-1.0182	.|9	.|0.59425	.|D	.|0.04	.|.	8.0041|8.0041	0.30315|0.30315	0.1317:0.0:0.8683:0.0|0.1317:0.0:0.8683:0.0	.|.	.|482	.|Q7KYR7	.|BT2A1_HUMAN	.|M	-1|482;421	.|ENSP00000312158:V482M;ENSP00000443909:V421M	.|ENSP00000312158:V482M	.|V	+|+	.|1	.|0	BTN2A1|BTN2A1	26576616|26576616	0.006000|0.006000	0.16342|0.16342	0.051000|0.051000	0.19133|0.19133	0.003000|0.003000	0.03518|0.03518	1.564000|1.564000	0.36375|0.36375	0.712000|0.712000	0.32039|0.32039	-0.424000|-0.424000	0.05967|0.05967	.|GTG	G|0.999;A|0.001	0.001	strong		0.577	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049		A	26468637	G	A	26468637	3	1	23	1	0	0	0	0	1	0	0	0	1562	1145	40	1	1497	1	BTN2A1	6	26468637	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	233714	26468637	144646430	244	7688											
ZNF193	7746	hgsc.bcm.edu	37	chr6	28195521	28195521	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtaaagagatggtgcctctAgcagagcagacaccactgac	13	7	11	10	0	1	4	0	1	1	3	1	5	1	4	2	1	3	3	2	1	3	2	rs12197427	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:28195521A>G	ENST00000252207.5	+	3	622	c.474A>G	c.(472-474)ctA>ctG	p.L158L	ZSCAN9_ENST00000425468.2_Silent_p.L158L|ZSCAN9_ENST00000527436.1_Silent_p.L158L|ZSCAN9_ENST00000531979.1_Silent_p.L158L|ZSCAN9_ENST00000531981.1_3'UTR	NM_006299.4	NP_006290.1	O15535	ZSC9_HUMAN	zinc finger and SCAN domain containing 9	158					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)										TGGTGCCTCTAGCAGAGCAGA	0.488													A|||	78	0.0155751	0.0	0.0274	5008	,	,		18815	0.0129		0.0278	False		,,,				2504	0.0184				p.L158L		Atlas-SNP	.											ZNF193,NS,carcinoma,+2,1	.	.	1	0			c.A474G						PASS	.	A	,,	26,4380	32.6+/-62.9	0,26,2177	70	64	66		474,474,474	-3.5	0	6	dbSNP_120	66	313,8287	112.0+/-172.2	8,297,3995	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF193	NM_001199479.1,NM_001199480.1,NM_006299.4	,,	8,323,6172	GG,GA,AA		3.6395,0.5901,2.6065	,,	158/446,158/395,158/395	28195521	339,12667	2203	4300	6503	SO:0001819	synonymous_variant	7746	exon3			GCCTCTAGCAGAG	U62392	CCDS4646.1, CCDS56407.1	6p21	2013-01-09	2013-01-09	2013-01-09	ENSG00000137185	ENSG00000137185		"-", "Zinc fingers, C2H2-type"	12984	protein-coding gene	gene with protein product		602246	"zinc finger protein 193"	ZNF193			Standard	NM_001199479		Approved	PRD51	uc003nkq.2	O15535	OTTHUMG00000014515	ENST00000252207.5:c.474A>G	6.37:g.28195521A>G		205	0	0		213	125	0.586854	NM_006299	B4E1W6|E7EVQ2|Q2TTR1	Silent	SNP	ENST00000252207.5	37	CCDS4646.1																																																																																			A|0.971;G|0.029	0.029	strong		0.488	ZSCAN9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000040183.2	NM_006299		G	28195521	A	G	28195521	2	3	23	1	0	0	0	0	0	0	0	1	17772	407	15	3		3	ZNF193	6	28195521	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	1726884	28195521	142919546	245	7689											
C6orf15	29113	hgsc.bcm.edu	37	chr6	31079310	31079310	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctgcctcctggataccgatTaatattcccccagctgcctc	7	11	7	16	1	0	0	0	0	0	0	3	2	2	1	6	1	4	2	6	1	3	4	rs560168888	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31079310T>G	ENST00000259870.3	-	2	829	c.826A>C	c.(826-828)Aat>Cat	p.N276H		NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	276	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						GGATACCGATTAATATTCCCC	0.502													T|||	2	0.000399361	0.0008	0.0	5008	,	,		16631	0.0		0.0	False		,,,				2504	0.001				p.N276H		Atlas-SNP	.											.	C6orf15	29	.	0			c.A826C						PASS	.						67	76	73					6																	31079310		1743	3414	5157	SO:0001583	missense	29113	exon2			ACCGATTAATATT	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.826A>C	6.37:g.31079310T>G	ENSP00000259870:p.Asn276His	123	0	0		137	9	0.0656934	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Missense_Mutation	SNP	ENST00000259870.3	37	CCDS4693.1	.	.	.	.	.	.	.	.	.	.	T	13.91	2.378711	0.42207	.	.	ENSG00000204542	ENST00000259870	T	0.06687	3.27	4.19	1.66	0.24008	.	0.372474	0.19119	U	0.122222	T	0.07143	0.0181	L	0.54323	1.7	0.09310	N	1	D	0.76494	0.999	D	0.65684	0.937	T	0.15954	-1.0419	10	0.45353	T	0.12	-12.0482	3.1014	0.06327	0.3753:0.1067:0.0:0.518	.	276	Q6UXA7	CF015_HUMAN	H	276	ENSP00000259870:N276H	ENSP00000259870:N276H	N	-	1	0	C6orf15	31187289	0.000000	0.05858	0.012000	0.15200	0.265000	0.26407	-0.001000	0.12947	0.149000	0.19098	0.372000	0.22366	AAT	.	.	none		0.502	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070		G	31079310	T	G	31079310	3	3	23	1	0	0	0	0	1	0	0	0	2338	1754	61	5	155	5	C6orf15	6	31079310	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	2883789	31079310	140035757	246	7690											
C6orf15	29113	hgsc.bcm.edu	37	chr6	31079350	31079350	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggataccgattaatattTccccagctgcctcctggata	9	12	7	13	1	0	0	0	0	0	0	2	3	2	2	6	2	3	1	6	2	4	5	rs146335336	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31079350T>C	ENST00000259870.3	-	2	789	c.786A>G	c.(784-786)ggA>ggG	p.G262G		NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	262	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						GATTAATATTTCCCCAGCTGC	0.502																																					p.G262G		Atlas-SNP	.											.	C6orf15	29	.	0			c.A786G						PASS	.						64	75	71					6																	31079350		1739	3348	5087	SO:0001819	synonymous_variant	29113	exon2			AATATTTCCCCAG	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.786A>G	6.37:g.31079350T>C		147	0	0		184	63	0.342391	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Silent	SNP	ENST00000259870.3	37	CCDS4693.1																																																																																			T|0.998;C|0.002	0.002	strong		0.502	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070		C	31079350	T	C	31079350	2	2	23	1	0	0	0	0	0	0	0	1	2338	1770	62	3		3	C6orf15	6	31079350	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	40	31079350	140035717	247	7691											
CDSN	170679	hgsc.bcm.edu	37	chr6	31085226	31085226	+	Intron	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggagtcacccttcccagtgaGgcaggggtcgttaggggagg	7	7	18	9	1	1	1	1	1	0	0	3	3	2	3	2	7	0	2	2	7	1	2	rs7742033	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31085226G>A	ENST00000259881.9	+	1	61				PSORS1C1_ENST00000467107.1_3'UTR|CDSN_ENST00000376288.2_Missense_Mutation_p.L56F	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						TTCCCAGTGAGGCAGGGGTCG	0.582													G|||	115	0.0229633	0.0598	0.013	5008	,	,		18022	0.003		0.0099	False		,,,				2504	0.0143				p.L56F		Atlas-SNP	.											.	CDSN	48	.	0			c.C166T						PASS	.	G	PHE/LEU,	134,3408		2,130,1639	13	10	11		166,	2	0.7	6	dbSNP_116	11	54,6800		0,54,3373	yes	missense,intron	CDSN,PSORS1C1	NM_001264.4,NM_014068.2	22,	2,184,5012	AA,AG,GG		0.7879,3.7832,1.8084	probably-damaging,	56/530,	31085226	188,10208	1771	3427	5198	SO:0001627	intron_variant	1041	exon2			CAGTGAGGCAGGG	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+2558G>A	6.37:g.31085226G>A		155	0	0		176	107	0.607955	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	37	CCDS34390.1	31	0.014194139194139194	23	0.046747967479674794	3	0.008287292817679558	2	0.0034965034965034965	3	0.00395778364116095	G	9.818	1.185048	0.21870	0.037832	0.007879	ENSG00000204539	ENST00000376288	T	0.07444	3.19	4.93	1.98	0.26296	.	0.486240	0.16016	N	0.233557	T	0.02649	0.0080	L	0.55990	1.75	0.09310	N	1	B	0.21225	0.053	B	0.21917	0.037	T	0.36407	-0.9749	10	0.44086	T	0.13	-14.2507	3.4184	0.07384	0.2129:0.0:0.5839:0.2031	rs7742033;rs52820068;rs7742033	56	Q15517	CDSN_HUMAN	F	56	ENSP00000365465:L56F	ENSP00000365465:L56F	L	-	1	0	CDSN	31193205	0.039000	0.19947	0.665000	0.29768	0.069000	0.16628	0.060000	0.14342	1.222000	0.43521	0.549000	0.68633	CTC	G|0.979;A|0.021	0.021	strong		0.582	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068		A	31085226	G	A	31085226	1	1	23	0	1	0	0	0	0	0	0	0	3181	1000	35	2		2	CDSN	6	31085226	Intron	SNP	G	TCGA-G8-6325-01A-11D-2210-10	5876	31085226	140029841	248	7692											
HLA-C	3107	hgsc.bcm.edu	37	chr6	31239622	31239622	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gggccgggacacggcggtgtCgaaatacctcatggagtggg	8	6	18	9	4	1	0	1	0	0	0	2	3	1	2	2	6	1	0	2	6	2	1	rs9264668	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31239622C>G	ENST00000376228.5	-	2	111	c.97G>C	c.(97-99)Gac>Cac	p.D33H	HLA-C_ENST00000383329.3_Missense_Mutation_p.D33H	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	33	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)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						ACGGCGGTGTCGAAATACCTC	0.726													a|||	20	0.00399361	0.0113	0.0	5008	,	,		11654	0.001		0.003	False		,,,				2504	0.001				p.D33H		Atlas-SNP	.											HLA-C_ENST00000383329,NS,neuroblastoma,0,2	HLA-C	92	2	0			c.G97C						scavenged	.						16	17	17					6																	31239622		1477	2676	4153	SO:0001583	missense	3107	exon2			CGGTGTCGAAATA	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4933	protein-coding gene	gene with protein product		142840	"psoriasis susceptibility 1"	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.97G>C	6.37:g.31239622C>G	ENSP00000365402:p.Asp33His	79	0	0		76	12	0.157895	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	0.003|0.003	-2.468672|-2.468672	0.00169|0.00169	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|.	0.00009|.	9.5;9.5|.	2.16|2.16	-4.32|-4.32	0.03688|0.03688	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);|.	10.311600|.	0.00879|.	N|.	0.002109|.	T|T	0.03390|0.03390	0.0098|0.0098	L|L	0.31578|0.31578	0.945|0.945	0.09310|0.09310	N|N	1|1	P;P;P;P|.	0.51351|.	0.944;0.822;0.822;0.888|.	P;P;P;D|.	0.68483|.	0.904;0.904;0.829;0.958|.	T|T	0.58504|0.58504	-0.7625|-0.7625	10|5	0.42905|.	T|.	0.14|.	.|.	0.4543|0.4543	0.00506|0.00506	0.2454:0.267:0.2544:0.2332|0.2454:0.267:0.2544:0.2332	.|.	33;33;33;33|.	A2AEA4;A6H578;A2AEA2;P10321|.	.;.;.;1C07_HUMAN|.	H|P	33;33;33;70|32	ENSP00000365402:D33H;ENSP00000372819:D33H|.	ENSP00000365402:D33H|.	D|R	-|-	1|2	0|0	HLA-C|HLA-C	31347601|31347601	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-13.217000|-13.217000	0.00001|0.00001	-7.736000|-7.736000	0.00000|0.00000	-4.008000|-4.008000	0.00013|0.00013	GAC|CGA	A|0.575;C|0.423;G|0.002	0.002	strong		0.726	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117		G	31239622	C	G	31239622	3	3	23	1	0	0	0	0	1	0	0	0	7206	884	31	4	1031	4	HLA-C	6	31239622	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	154396	31239622	139875445	249	7693											
MICA	100507436	hgsc.bcm.edu	37	chr6	31378928	31378928	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agctcccagcatttctactaCgatggggagctcttcctctc	7	12	8	14	1	3	0	0	0	3	0	6	2	5	1	2	2	5	3	2	2	2	4	rs41553614	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31378928C>T	ENST00000449934.2	+	3	459	c.405C>T	c.(403-405)taC>taT	p.Y135Y	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)				ATTTCTACTACGATGGGGAGC	0.552													c|||	77	0.0153754	0.0212	0.0245	5008	,	,		20471	0.003		0.0159	False		,,,				2504	0.0133				p.Y135Y		Atlas-SNP	.											.	MICA	21	.	0			c.C405T						PASS	.	C		38,1346		1,36,655	45	42	43		405	-3	0	6	dbSNP_127	43	49,3133		1,47,1543	no	coding-synonymous	MICA	NM_001177519.1		2,83,2198	TT,TC,CC		1.5399,2.7457,1.9054		135/333	31378928	87,4479	692	1591	2283	SO:0001819	synonymous_variant	100507436	exon3			CTACTACGATGGG	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	ENST00000449934.2:c.405C>T	6.37:g.31378928C>T		161	0	0		221	113	0.511312	NM_001177519		Silent	SNP	ENST00000449934.2	37	CCDS56412.1																																																																																			C|0.987;T|0.013	0.013	strong		0.552	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519		T	31378928	C	T	31378928	2	4	23	1	0	0	0	0	0	0	0	1	9577	547	19	1		1	MICA	6	31378928	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	139306	31378928	139736139	250	7694											
BAT1	7919	hgsc.bcm.edu	37	chr6	31503219	31503219	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacatcatgacctgcttctcGtggggggtcatgcgaaaaat	11	10	11	9	2	3	1	2	1	1	0	4	2	3	1	1	3	3	1	1	3	3	1	rs55799418	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31503219G>A	ENST00000396172.1	-	6	1290	c.660C>T	c.(658-660)caC>caT	p.H220H	DDX39B_ENST00000415382.2_Silent_p.H142H|DDX39B_ENST00000453105.2_Silent_p.H173H|DDX39B_ENST00000417556.2_Silent_p.H235H|DDX39B_ENST00000458640.1_Silent_p.H220H|SNORD117_ENST00000364915.1_RNA|DDX39B_ENST00000376177.2_Silent_p.H220H|ATP6V1G2-DDX39B_ENST00000376185.1_3'UTR	NM_004640.6	NP_004631.1	Q13838	DX39B_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	220	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						CCTGCTTCTCGTGGGGGGTCA	0.443													G|||	46	0.0091853	0.0098	0.0086	5008	,	,		19144	0.003		0.0089	False		,,,				2504	0.0153				p.H220H		Atlas-SNP	.											.	DDX39B	38	.	0			c.C660T						PASS	.	G	,	18,3004		0,18,1493	190	151	165		660,660	-3.5	1	6	dbSNP_129	165	45,5373		0,45,2664	no	coding-synonymous,coding-synonymous	DDX39B	NM_004640.6,NM_080598.5	,	0,63,4157	AA,AG,GG		0.8306,0.5956,0.7464	,	220/429,220/429	31503219	63,8377	1511	2709	4220	SO:0001819	synonymous_variant	7919	exon6			CTTCTCGTGGGGG	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.660C>T	6.37:g.31503219G>A		94	0	0		104	53	0.509615	NM_004640	B0S8C0|O43496|Q0EFA1|Q2L6F9|Q53GL9|Q5RJ64|Q5RJ66|Q5ST94|Q5STB4|Q5STB5|Q5STB7|Q5STB8|Q5STU4|Q5STU5|Q5STU6|Q5STU8|Q71V76	Silent	SNP	ENST00000396172.1	37	CCDS4697.1																																																																																			G|0.993;A|0.007	0.007	strong		0.443	DDX39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259083.1	NM_004640		A	31503219	G	A	31503219	2	1	23	1	0	0	0	0	0	0	0	1	1318	1136	40	1		1	BAT1	6	31503219	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	124291	31503219	139611848	251	7695											
LTA	4049	hgsc.bcm.edu	37	chr6	31541086	31541086	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agcaagcagaactcactgctCtggagagcaaacacggaccg	14	4	11	12	2	2	2	1	0	1	2	2	4	2	3	1	2	6	4	1	2	3	0			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31541086C>T	ENST00000454783.1	+	4	492	c.234C>T	c.(232-234)ctC>ctT	p.L78L	LTA_ENST00000418386.2_Silent_p.L78L|TNF_ENST00000449264.2_5'Flank	NM_001159740.2	NP_001153212.1	P01374	TNFB_HUMAN	lymphotoxin alpha	78					apoptotic process (GO:0006915)|cell-cell signaling (GO:0007267)|defense response to Gram-positive bacterium (GO:0050830)|humoral immune response (GO:0006959)|lymph node development (GO:0048535)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of growth of symbiont in host (GO:0044130)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chronic inflammatory response to antigenic stimulus (GO:0002876)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of interferon-gamma production (GO:0032729)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|membrane (GO:0016020)	receptor binding (GO:0005102)			endometrium(2)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9					Etanercept(DB00005)	ACTCACTGCTCTGGAGAGCAA	0.562																																					p.L78L		Atlas-SNP	.											.	LTA	18	.	0			c.C234T						PASS	.						73	63	67					6																	31541086		2203	4300	6503	SO:0001819	synonymous_variant	4049	exon4			ACTGCTCTGGAGA	X01393	CCDS4701.1	6p21.3	2013-05-22	2013-05-22		ENSG00000226979	ENSG00000226979		"Tumor necrosis factor (ligand) superfamily"	6709	protein-coding gene	gene with protein product	"TNF superfamily member 1"	153440	"lymphotoxin alpha (TNF superfamily, member 1)"	TNFB		2995927, 3001529	Standard	NM_001159740		Approved	TNFSF1, LT	uc011dnu.2	P01374	OTTHUMG00000031135	ENST00000454783.1:c.234C>T	6.37:g.31541086C>T		175	0	0		157	50	0.318471	NM_001159740	Q8N4C3|Q9UKS8	Silent	SNP	ENST00000454783.1	37	CCDS4701.1																																																																																			.	.	none		0.562	LTA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259097.1			T	31541086	C	T	31541086	2	4	23	1	0	0	0	0	0	0	0	1	9077	900	32	2		2	LTA	6	31541086	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	37867	31541086	139573981	252	7696											
BAT2	7916	hgsc.bcm.edu	37	chr6	31599556	31599556	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgagtattttgccagagggAggggttttcgggggacctat	7	11	17	6	2	0	1	0	0	0	1	1	4	0	3	2	5	1	2	2	5	2	6	rs78503551	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31599556A>C	ENST00000376033.2	+	16	3340	c.3106A>C	c.(3106-3108)Agg>Cgg	p.R1036R	PRRC2A_ENST00000376007.4_Silent_p.R1036R	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1036	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						TGCCAGAGGGAGGGGTTTTCG	0.622													A|||	42	0.00838658	0.0068	0.0072	5008	,	,		12527	0.003		0.0099	False		,,,				2504	0.0153				p.R1036R		Atlas-SNP	.											.	PRRC2A	152	.	0			c.A3106C						PASS	.	A	,	10,3000		0,10,1495	13	17	15		3106,3106	5	1	6	dbSNP_131	15	37,5373		0,37,2668	no	coding-synonymous,coding-synonymous	PRRC2A	NM_004638.3,NM_080686.2	,	0,47,4163	CC,CA,AA		0.6839,0.3322,0.5582	,	1036/2158,1036/2158	31599556	47,8373	1505	2705	4210	SO:0001819	synonymous_variant	7916	exon16			AGAGGGAGGGGTT	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.3106A>C	6.37:g.31599556A>C		43	0	0		55	33	0.6	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Silent	SNP	ENST00000376033.2	37	CCDS4708.1																																																																																			A|0.995;C|0.005	0.005	strong		0.622	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686		C	31599556	A	C	31599556	2	2	23	1	0	0	0	0	0	0	0	1	1319	295	11	5		5	BAT2	6	31599556	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	58470	31599556	139515511	253	7697											
BAT2	7916	hgsc.bcm.edu	37	chr6	31600430	31600430	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgggagactgcatcagagaGcagtgacttcaccagtgagc	12	7	13	9	0	2	4	2	2	0	2	2	6	2	4	1	1	3	2	1	1	0	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31600430G>A	ENST00000376033.2	+	16	4214	c.3980G>A	c.(3979-3981)aGc>aAc	p.S1327N	PRRC2A_ENST00000376007.4_Missense_Mutation_p.S1327N	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1327	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						GCATCAGAGAGCAGTGACTTC	0.602																																					p.S1327N		Atlas-SNP	.											.	PRRC2A	152	.	0			c.G3980A						PASS	.						76	79	78					6																	31600430		1509	2709	4218	SO:0001583	missense	7916	exon16			CAGAGAGCAGTGA	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.3980G>A	6.37:g.31600430G>A	ENSP00000365201:p.Ser1327Asn	132	0	0		156	91	0.583333	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	37	CCDS4708.1	.	.	.	.	.	.	.	.	.	.	G	11.25	1.584062	0.28268	.	.	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033;ENST00000376010	T;T	0.04234	3.67;3.67	5.22	5.22	0.72569	.	0.084158	0.52532	D	0.000067	T	0.11537	0.0281	L	0.60067	1.865	0.45747	D	0.99864	D	0.67145	0.996	P	0.62740	0.906	T	0.00717	-1.1596	10	0.87932	D	0	-14.4073	17.7172	0.88341	0.0:0.0:1.0:0.0	.	1327	P48634	PRC2A_HUMAN	N	1321;1310;1327;1327;552	ENSP00000365175:S1327N;ENSP00000365201:S1327N	ENSP00000365175:S1327N	S	+	2	0	PRRC2A	31708409	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.369000	0.79578	2.714000	0.92807	0.561000	0.74099	AGC	.	.	none		0.602	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686		A	31600430	G	A	31600430	3	1	23	1	0	0	0	0	1	0	0	0	1319	971	34	2	4038	2	BAT2	6	31600430	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	874	31600430	139514637	254	7698											
BAT2	7916	hgsc.bcm.edu	37	chr6	31605016	31605016	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccttcttcccttaggtcctTctctggcctcaattcccgtc	3	15	5	18	1	3	0	1	0	2	0	8	0	6	0	5	2	0	0	5	2	2	5	rs35595439	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31605016T>C	ENST00000376033.2	+	30	6482	c.6248T>C	c.(6247-6249)tTc>tCc	p.F2083S	PRRC2A_ENST00000376007.4_Missense_Mutation_p.F2083S	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	2083	3 X 50 AA type C 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						CTTAGGTCCTTCTCTGGCCTC	0.552													T|||	42	0.00838658	0.0068	0.0072	5008	,	,		17444	0.003		0.0099	False		,,,				2504	0.0153				p.F2083S		Atlas-SNP	.											.	PRRC2A	152	.	0			c.T6248C						PASS	.	T	SER/PHE,SER/PHE	10,3010		0,10,1500	86	81	83		6248,6248	5.6	1	6	dbSNP_126	83	41,5375		0,41,2667	yes	missense,missense	PRRC2A	NM_004638.3,NM_080686.2	155,155	0,51,4167	CC,CT,TT		0.757,0.3311,0.6046	probably-damaging,probably-damaging	2083/2158,2083/2158	31605016	51,8385	1510	2708	4218	SO:0001583	missense	7916	exon30			GGTCCTTCTCTGG	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.6248T>C	6.37:g.31605016T>C	ENSP00000365201:p.Phe2083Ser	104	0	0		100	52	0.52	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	37	CCDS4708.1	11	0.005036630036630037	2	0.0040650406504065045	3	0.008287292817679558	2	0.0034965034965034965	4	0.005277044854881266	T	11.20	1.569725	0.28003	0.003311	0.00757	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033;ENST00000376010	T;T	0.01871	4.59;4.59	5.63	5.63	0.86233	.	0.374635	0.24516	N	0.037848	T	0.01800	0.0057	N	0.19112	0.55	0.42923	D	0.994293	D	0.61697	0.99	P	0.51657	0.676	T	0.64193	-0.6465	10	0.87932	D	0	-0.0191	13.6537	0.62325	0.0:0.0:0.0:1.0	rs35595439	2083	P48634	PRC2A_HUMAN	S	2075;2064;2083;2083;1308	ENSP00000365175:F2083S;ENSP00000365201:F2083S	ENSP00000365175:F2083S	F	+	2	0	PRRC2A	31712995	1.000000	0.71417	0.999000	0.59377	0.774000	0.43823	2.456000	0.44997	2.271000	0.75665	0.533000	0.62120	TTC	T|0.993;C|0.007	0.007	strong		0.552	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686		C	31605016	T	C	31605016	3	2	23	1	0	0	0	0	1	0	0	0	1319	1783	62	3	6362	3	BAT2	6	31605016	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	4586	31605016	139510051	255	7699											
LY6G6F	259215	hgsc.bcm.edu	37	chr6	31677953	31677953	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gagggtccgtggggctccagGcagaggtgagtccctccctc	5	7	16	13	1	0	2	0	1	0	1	5	3	4	2	4	5	0	2	4	5	0	0	rs61740977	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31677953G>A	ENST00000375832.4	+	4	819	c.797G>A	c.(796-798)gGc>gAc	p.G266D	MEGT1_ENST00000503322.1_Missense_Mutation_p.G266D|LY6G6F_ENST00000556581.1_Missense_Mutation_p.G266D|XXbac-BPG32J3.20_ENST00000461287.1_Intron	NM_001003693.1	NP_001003693.1	Q5SQ64	LY66F_HUMAN	lymphocyte antigen 6 complex, locus G6F	266						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(4)	12						GGGGCTCCAGGCAGAGGTGAG	0.632													G|||	42	0.00838658	0.0068	0.0072	5008	,	,		19569	0.003		0.0099	False		,,,				2504	0.0153				p.G266D		Atlas-SNP	.											LY6G6F,colon,carcinoma,+1,1	LY6G6F	23	1	0			c.G797A						scavenged	.	G	ASP/GLY	10,3012		0,10,1501	60	62	61		797	-0.1	0	6	dbSNP_129	61	41,5373		0,41,2666	yes	missense	LY6G6F	NM_001003693.1	94	0,51,4167	AA,AG,GG		0.7573,0.3309,0.6046	probably-damaging	266/298	31677953	51,8385	1511	2707	4218	SO:0001583	missense	259215	exon4			CTCCAGGCAGAGG		CCDS34403.1	6p21	2013-01-11	2008-05-21	2008-05-21		ENSG00000204424		"Immunoglobulin superfamily / V-set domain containing"	13933	protein-coding gene	gene with protein product		611404	"chromosome 6 open reading frame 21"	LY6G6D, C6orf21		12852788	Standard	NM_001003693		Approved	G6f, NG32	uc003nwa.1	Q5SQ64	OTTHUMG00000031252	ENST00000375832.4:c.797G>A	6.37:g.31677953G>A	ENSP00000364992:p.Gly266Asp	117	1	0.00854701		112	53	0.473214	NM_001003693	B0UXB7|O95869|Q7Z5H2|Q96QC7|Q9NZJ1	Missense_Mutation	SNP	ENST00000375832.4	37	CCDS34403.1	11	0.005036630036630037	2	0.0040650406504065045	3	0.008287292817679558	2	0.0034965034965034965	4	0.005277044854881266	G	8.620	0.891217	0.17613	0.003309	0.007573	ENSG00000204424;ENSG00000204424;ENSG00000250641	ENST00000556581;ENST00000375832;ENST00000503322	T;T;T	0.16196	2.52;2.36;2.52	5.25	-0.08	0.13708	.	0.971401	0.08471	N	0.940953	T	0.01627	0.0052	N	0.02539	-0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.47560	-0.9108	10	0.27785	T	0.31	0.4188	5.858	0.18730	0.353:0.0:0.5128:0.1342	rs61740977	266;266	Q9NZJ1;Q5SQ64	.;LY66F_HUMAN	D	266	ENSP00000452432:G266D;ENSP00000364992:G266D;ENSP00000421232:G266D	ENSP00000364992:G266D	G	+	2	0	XXbac-BPG32J3.19;LY6G6F	31785932	0.007000	0.16637	0.020000	0.16555	0.036000	0.12997	0.191000	0.17076	-0.177000	0.10690	-1.491000	0.00971	GGC	G|0.994;A|0.006	0.006	strong		0.632	LY6G6F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076532.2	NM_001003693		A	31677953	G	A	31677953	3	1	23	1	0	0	0	0	1	0	0	0	9105	1203	42	2	811	2	LY6G6F	6	31677953	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	72937	31677953	139437114	256	7700											
DOM3Z	1797	hgsc.bcm.edu	37	chr6	31939319	31939319	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagcccagttccgaagggCgccggtagaaaggaaagggc	12	3	16	10	3	0	1	0	0	0	1	1	3	1	2	3	4	2	3	3	4	4	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31939319C>T	ENST00000375349.3	-	2	545	c.134G>A	c.(133-135)cGc>cAc	p.R45H	DXO_ENST00000478221.1_Intron|STK19_ENST00000375333.2_5'Flank|DXO_ENST00000375356.3_Missense_Mutation_p.R45H|DXO_ENST00000337523.5_Missense_Mutation_p.R45H|STK19_ENST00000375331.2_5'Flank			O77932	DXO_HUMAN	decapping exoribonuclease	45					metabolic process (GO:0008152)|mRNA catabolic process (GO:0006402)|nuclear mRNA surveillance (GO:0071028)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA destabilization (GO:0050779)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|magnesium ion binding (GO:0000287)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA pyrophosphohydrolase activity (GO:0034353)										TTCCGAAGGGCGCCGGTAGAA	0.602																																					p.R45H		Atlas-SNP	.											.	DOM3Z	20	.	0			c.G134A						PASS	.						88	95	93					6																	31939319		2203	4300	6503	SO:0001583	missense	1797	exon2			GAAGGGCGCCGGT	AF059252	CCDS4732.1	6p21.3	2013-09-11	2013-09-11	2013-09-11	ENSG00000204348	ENSG00000204348			2992	protein-coding gene	gene with protein product		605996	"DOM-3 (C. elegans) homolog Z", "dom-3 homolog Z (C. elegans)"	DOM3Z		9799600, 23523372	Standard	NM_005510		Approved		uc003nyp.1	O77932	OTTHUMG00000031272	ENST00000375349.3:c.134G>A	6.37:g.31939319C>T	ENSP00000364498:p.Arg45His	90	0	0		118	35	0.29661	NM_005510	A2CER3|B0UZ80|O15004|O78127|O78128|Q5ST60|Q6IPZ2|Q9NPK4	Missense_Mutation	SNP	ENST00000375349.3	37	CCDS4732.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.356161	0.82243	.	.	ENSG00000204348	ENST00000337523;ENST00000375349;ENST00000375356	T;T;T	0.21031	2.03;2.03;2.03	4.92	4.03	0.46877	.	0.198410	0.46442	D	0.000300	T	0.23806	0.0576	M	0.75884	2.315	0.80722	D	1	D;D	0.67145	0.996;0.994	P;P	0.52554	0.702;0.512	T	0.05484	-1.0882	10	0.66056	D	0.02	0.0351	11.4467	0.50127	0.3265:0.6735:0.0:0.0	.	45;45	F8WC68;O77932	.;DOM3Z_HUMAN	H	45	ENSP00000337759:R45H;ENSP00000364498:R45H;ENSP00000364505:R45H	ENSP00000337759:R45H	R	-	2	0	DOM3Z	32047298	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	2.796000	0.47869	1.234000	0.43709	0.561000	0.74099	CGC	.	.	none		0.602	DXO-006	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076592.3			T	31939319	C	T	31939319	3	4	23	1	0	0	0	0	1	0	0	0	4707	768	27	1	1080	1	DOM3Z	6	31939319	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	261366	31939319	139175748	257	7701											
HLA-DRB5	3127	hgsc.bcm.edu	37	chr6	32497986	32497986	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catgtaggaacctccagggaGcttcagacacaccatgctgg	11	7	11	12	0	1	1	1	0	0	1	2	3	2	3	3	3	3	3	3	3	2	2	rs200744795		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32497986G>A	ENST00000374975.3	-	1	78	c.16C>T	c.(16-18)Ctc>Ttc	p.L6F		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						CCTCCAGGGAGCTTCAGACAC	0.577																																					p.L6F		Atlas-SNP	.											HLA-DRB5,rectum,carcinoma,0,1	HLA-DRB5	31	1	0			c.C16T						scavenged	.						55	61	59					6																	32497986		2203	4296	6499	SO:0001583	missense	3127	exon1			CAGGGAGCTTCAG		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.16C>T	6.37:g.32497986G>A	ENSP00000364114:p.Leu6Phe	62	2	0.0322581		209	13	0.062201	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	4.629	0.117010	0.08881	.	.	ENSG00000198502	ENST00000374975	T	0.00281	8.32	4.42	-2.83	0.05769	MHC classes I/II-like antigen recognition protein (1);	.	.	.	.	T	0.00039	0.0001	L	0.27975	0.815	0.09310	N	1	B	0.06786	0.001	B	0.12156	0.007	T	0.28808	-1.0032	9	0.06891	T	0.86	.	5.2478	0.15506	0.2872:0.0:0.5657:0.1472	rs1059548;rs2308658;rs3200252;rs16822997	6	Q30154	DRB5_HUMAN	F	6	ENSP00000364114:L6F	ENSP00000364114:L6F	L	-	1	0	HLA-DRB5	32605964	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.163000	0.09997	-0.229000	0.09854	-0.350000	0.07774	CTC	.	.	weak		0.577	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125		A	32497986	G	A	32497986	3	1	23	1	0	0	0	0	1	0	0	0	7218	971	34	2	808	2	HLA-DRB5	6	32497986	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	558667	32497986	138617081	258	7702											
HLA-DRB1	3123	hgsc.bcm.edu	37	chr6	32549582	32549582	+	Missense_Mutation	SNP	G	G	T																															tgtggtgctgcaggggctggGtctttgaaggatatacagtc																								rs200516145		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32549582G>T	ENST00000360004.5	-	3	509	c.404C>A	c.(403-405)aCc>aAc	p.T135N		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	135	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)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						CAGGGGCTGGGTCTTTGAAGG	0.507										Multiple Myeloma(14;0.17)																											p.T135N		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.C404A						PASS	.						67	84	78					6																	32549582		1510	2709	4219	SO:0001583	missense	3123	exon3			GGCTGGGTCTTTG	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.404C>A	6.37:g.32549582G>T	ENSP00000353099:p.Thr135Asn	188	0	0		375	37	0.0986667	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	11.78	1.740603	0.30865	.	.	ENSG00000196126	ENST00000360004	T	0.02863	4.13	3.87	2.92	0.33932	Immunoglobulin-like (1);Immunoglobulin C1-set (1);Immunoglobulin-like fold (1);	0.480425	0.24686	N	0.036424	T	0.06781	0.0173	M	0.76574	2.34	0.26397	N	0.97649	D	0.76494	0.999	D	0.87578	0.998	T	0.02632	-1.1131	10	0.87932	D	0	.	10.9743	0.47456	0.0:0.0:0.8139:0.1861	.	135	P01911	2B1F_HUMAN	N	135	ENSP00000353099:T135N	ENSP00000353099:T135N	T	-	2	0	HLA-DRB1	32657560	0.030000	0.19436	0.762000	0.31397	0.139000	0.21198	1.809000	0.38922	1.883000	0.54544	0.453000	0.30009	ACC	.	.	weak		0.507	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124		T	32549582	G	T	32549582	3	4	23	1	0	0	0	0	1	0	0	0	7217	1261	44	4	412	4	HLA-DRB1	6	32549582	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	51596	32549582	138565485	259	7703	100	3									
HLA-DRB1	3123	hgsc.bcm.edu	37	chr6	32549583	32549583	+	Missense_Mutation	SNP	T	T	C																															gtggtgctgcaggggctgggTctttgaaggatatacagtca																								rs17433947		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32549583T>C	ENST00000360004.5	-	3	508	c.403A>G	c.(403-405)Acc>Gcc	p.T135A		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	135	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)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						AGGGGCTGGGTCTTTGAAGGA	0.507										Multiple Myeloma(14;0.17)																											p.T135A		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.A403G						PASS	.						66	82	76					6																	32549583		1510	2709	4219	SO:0001583	missense	3123	exon3			GCTGGGTCTTTGA	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.403A>G	6.37:g.32549583T>C	ENSP00000353099:p.Thr135Ala	185	0	0		372	37	0.0994624	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	10.80	1.451590	0.26074	.	.	ENSG00000196126	ENST00000360004	T	0.02787	4.16	3.87	1.14	0.20703	Immunoglobulin-like (1);Immunoglobulin C1-set (1);Immunoglobulin-like fold (1);	0.480425	0.24686	N	0.036424	T	0.03959	0.0111	M	0.62088	1.915	0.25150	N	0.990439	D	0.54964	0.969	D	0.73708	0.981	T	0.28170	-1.0052	10	0.72032	D	0.01	.	5.5797	0.17243	0.0:0.1048:0.1704:0.7249	.	135	P01911	2B1F_HUMAN	A	135	ENSP00000353099:T135A	ENSP00000353099:T135A	T	-	1	0	HLA-DRB1	32657561	0.000000	0.05858	0.754000	0.31244	0.116000	0.19942	-1.406000	0.02490	0.483000	0.27608	-0.639000	0.03973	ACC	.	.	weak		0.507	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124		C	32549583	T	C	32549583	3	2	23	1	0	0	0	0	1	0	0	0	7217	1667	58	3	413	3	HLA-DRB1	6	32549583	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	1	32549583	138565484	260	7704	100	3									
HLA-DRB1	3123	hgsc.bcm.edu	37	chr6	32549584	32549584	+	Silent	SNP	C	C	T																															tggtgctgcaggggctgggtCtttgaaggatatacagtcac																								rs200078051|rs35616319|rs200088269		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32549584C>T	ENST00000360004.5	-	3	507	c.402G>A	c.(400-402)aaG>aaA	p.K134K		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	134	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)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						GGGGCTGGGTCTTTGAAGGAT	0.507										Multiple Myeloma(14;0.17)																											p.K134K		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.G402A						PASS	.						64	80	74					6																	32549584		1510	2709	4219	SO:0001819	synonymous_variant	3123	exon3			CTGGGTCTTTGAA	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.402G>A	6.37:g.32549584C>T		183	0	0		368	36	0.0978261	NM_002124	P01914|Q9MYF5	Silent	SNP	ENST00000360004.5	37	CCDS47409.1																																																																																			.	.	weak		0.507	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124		T	32549584	C	T	32549584	2	4	23	1	0	0	0	0	0	0	0	1	7217	912	32	2		2	HLA-DRB1	6	32549584	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1	32549584	138565483	261	7705	100	3									
DAXX	1616	hgsc.bcm.edu	37	chr6	33287810	33287810	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgctgcttcttcctcttcGtcctcctcttcatcatcctc	2	17	4	18	1	5	0	2	0	3	0	11	0	9	0	4	0	2	3	4	0	0	4	rs370615019		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:33287810G>A	ENST00000374542.5	-	5	1647	c.1443C>T	c.(1441-1443)gaC>gaT	p.D481D	DAXX_ENST00000414083.2_Silent_p.D406D|ZBTB22_ENST00000418724.1_5'Flank|DAXX_ENST00000477162.1_5'UTR|DAXX_ENST00000266000.6_Silent_p.D481D|ZBTB22_ENST00000431845.2_5'Flank	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	481	Asp/Glu-rich (acidic).|Necessary for interaction with USP7.				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						cttcctcttcgtcctcctctt	0.502			"Mis, F, N"		Pancreatic neuroendocrine tumors. Paediatric GBM								G|||	1	0.000199681	0.0	0.0	5008	,	,		20984	0.001		0.0	False		,,,				2504	0.0				p.D493D		Atlas-SNP	.		Rec	yes		6	6p21.3	1616	death-domain associated protein		E	.	DAXX	111	.	0			c.C1479T						PASS	.	G	,,	0,4406		0,0,2203	238	162	188		1443,1479,1443	-2.5	0.2	6		188	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	DAXX	NM_001141969.1,NM_001141970.1,NM_001350.4	,,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,,	481/741,493/753,481/741	33287810	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	1616	exon5			CTCTTCGTCCTCC	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.1443C>T	6.37:g.33287810G>A		244	0	0		303	170	0.561056	NM_001141970	B4E1I3|F5H082|O14747|O15141|O15208|Q5STK9|Q9BWI3	Silent	SNP	ENST00000374542.5	37	CCDS4776.1																																																																																			.	.	weak		0.502	DAXX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076403.1			A	33287810	G	A	33287810	2	1	23	1	0	0	0	0	0	0	0	1	4245	1136	40	1		1	DAXX	6	33287810	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	738226	33287810	137827257	262	7706											
FKBP5	2289	hgsc.bcm.edu	37	chr6	35544942	35544942	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccttggctgactcaaactcGttcatgagcagctgggcttc	7	11	10	13	1	2	2	2	2	0	0	4	2	2	2	1	2	3	5	1	2	1	3	rs34866878	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:35544942G>A	ENST00000539068.1	-	10	1297	c.1095C>T	c.(1093-1095)aaC>aaT	p.N365N	FKBP5_ENST00000540787.1_Silent_p.N186N|FKBP5_ENST00000536438.1_Silent_p.N365N|FKBP5_ENST00000357266.4_Silent_p.N365N	NM_001145776.1	NP_001139248.1	Q13451	FKBP5_HUMAN	FK506 binding protein 5	365					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						ACTCAAACTCGTTCATGAGCA	0.483													G|||	334	0.0666933	0.2239	0.0245	5008	,	,		18453	0.001		0.0179	False		,,,				2504	0.002				p.N365N		Atlas-SNP	.											.	FKBP5	64	.	0			c.C1095T						PASS	.	G	,,	815,3591	326.1+/-299.4	68,679,1456	161	154	156		1095,1095,1095	-3.6	0.8	6	dbSNP_126	156	225,8375	92.8+/-154.8	5,215,4080	no	coding-synonymous,coding-synonymous,coding-synonymous	FKBP5	NM_001145775.1,NM_001145776.1,NM_004117.3	,,	73,894,5536	AA,AG,GG		2.6163,18.4975,7.9963	,,	365/458,365/458,365/458	35544942	1040,11966	2203	4300	6503	SO:0001819	synonymous_variant	2289	exon11			AAACTCGTTCATG	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.1095C>T	6.37:g.35544942G>A		198	0	0		206	82	0.398058	NM_001145775	F5H7R1|Q59EB8|Q5TGM6	Silent	SNP	ENST00000539068.1	37	CCDS4808.1																																																																																			G|0.928;A|0.072	0.072	strong		0.483	FKBP5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040309.2			A	35544942	G	A	35544942	2	1	23	1	0	0	0	0	0	0	0	1	5919	1136	40	1		1	FKBP5	6	35544942	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	2257132	35544942	135570125	263	7707											
DNAH8	1769	hgsc.bcm.edu	37	chr6	38805753	38805753	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgtggaggaaatttgttacGtattcatctggtgaacaact	11	14	10	6	1	2	1	1	1	1	0	2	3	2	3	0	3	3	2	0	3	5	4	rs45622336	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:38805753G>A	ENST00000359357.3	+	31	4004	c.3750G>A	c.(3748-3750)acG>acA	p.T1250T	DNAH8_ENST00000449981.2_Silent_p.T1467T|DNAH8_ENST00000441566.1_Silent_p.T1250T			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1250					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						AATTTGTTACGTATTCATCTG	0.313													A|||	11	0.00219649	0.0023	0.0	5008	,	,		17985	0.0		0.007	False		,,,				2504	0.001				p.T1467T		Atlas-SNP	.											DNAH8_ENST00000359357,head_neck,malignant_melanoma,+1,2	DNAH8	1239	2	0			c.G4401A						PASS	.	A		10,4396	824.8+/-416.5	0,10,2193	169	154	159		4401	-9.2	0.6	6	dbSNP_127	159	76,8524	815.6+/-407.0	1,74,4225	no	coding-synonymous	DNAH8	NM_001206927.1		1,84,6418	AA,AG,GG		0.8837,0.227,0.6612		1467/4708	38805753	86,12920	2203	4300	6503	SO:0001819	synonymous_variant	1769	exon33			TGTTACGTATTCA	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.3750G>A	6.37:g.38805753G>A		123	0	0		173	95	0.549133	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	37																																																																																				G|0.995;A|0.005	0.005	strong		0.313	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		A	38805753	G	A	38805753	2	1	23	1	0	0	0	0	0	0	0	1	4609	1132	40	1		1	DNAH8	6	38805753	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	3260811	38805753	132309314	264	7708											
DNAH8	1769	hgsc.bcm.edu	37	chr6	38903421	38903421	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gatgttacttttaataagcgGaagatgaaagaacttgaaga	17	11	10	3	1	0	5	0	2	0	3	0	7	0	6	0	1	3	1	0	1	7	5	rs61748646	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:38903421G>A	ENST00000359357.3	+	75	11114	c.10860G>A	c.(10858-10860)cgG>cgA	p.R3620R	RP1-207H1.3_ENST00000416948.1_RNA|DNAH8_ENST00000449981.2_Silent_p.R3837R|RP1-207H1.3_ENST00000453417.1_RNA|DNAH8_ENST00000441566.1_Silent_p.R3584R			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	3620	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						TTAATAAGCGGAAGATGAAAG	0.308													G|||	59	0.0117812	0.003	0.0144	5008	,	,		17584	0.006		0.0328	False		,,,				2504	0.0061				p.R3837R		Atlas-SNP	.											.	DNAH8	1239	.	0			c.G11511A						PASS	.	G		23,4383	29.9+/-59.1	0,23,2180	159	178	172		11511	5.1	1	6	dbSNP_129	172	286,8310	104.6+/-165.6	4,278,4016	no	coding-synonymous	DNAH8	NM_001206927.1		4,301,6196	AA,AG,GG		3.3271,0.522,2.3766		3837/4708	38903421	309,12693	2203	4298	6501	SO:0001819	synonymous_variant	1769	exon77			TAAGCGGAAGATG	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.10860G>A	6.37:g.38903421G>A		40	0	0		44	23	0.522727	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	37																																																																																				G|0.980;A|0.020	0.020	strong		0.308	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		A	38903421	G	A	38903421	2	1	23	1	0	0	0	0	0	0	0	1	4609	1161	41	2		2	DNAH8	6	38903421	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	97668	38903421	132211646	265	7709											
GUCA1B	2979	hgsc.bcm.edu	37	chr6	42152583	42152583	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacttttccgtctctgctgAgcgagccagctgctgggatt	5	12	12	12	2	1	1	0	1	1	0	3	3	2	2	2	1	5	4	2	1	0	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:42152583A>G	ENST00000230361.3	-	4	668	c.573T>C	c.(571-573)gcT>gcC	p.A191A		NM_002098.5	NP_002089.4	Q9UMX6	GUC1B_HUMAN	guanylate cyclase activator 1B (retina)	191					body fluid secretion (GO:0007589)|cell-cell signaling (GO:0007267)|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)	photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)			large_intestine(3)|lung(3)|skin(2)	8	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00154)|STAD - Stomach adenocarcinoma(11;0.00177)			GTCTCTGCTGAGCGAGCCAGC	0.587																																					p.A191A		Atlas-SNP	.											.	GUCA1B	19	.	0			c.T573C						PASS	.						117	99	105					6																	42152583		2203	4300	6503	SO:0001819	synonymous_variant	2979	exon4			CTGCTGAGCGAGC	AF173227	CCDS4865.1	6p21.1	2013-02-14			ENSG00000112599	ENSG00000112599		"EF-hand domain containing"	4679	protein-coding gene	gene with protein product		602275				9119368	Standard	NM_002098		Approved	GCAP2, RP48	uc003orz.3	Q9UMX6	OTTHUMG00000014697	ENST00000230361.3:c.573T>C	6.37:g.42152583A>G		74	0	0		98	4	0.0408163	NM_002098	Q9NU15	Silent	SNP	ENST00000230361.3	37	CCDS4865.1																																																																																			.	.	none		0.587	GUCA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040550.1	NM_002098		G	42152583	A	G	42152583	2	3	23	1	0	0	0	0	0	0	0	1	6898	291	11	3		3	GUCA1B	6	42152583	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	3249162	42152583	128962484	266	7710											
CUL7	9820	hgsc.bcm.edu	37	chr6	43006687	43006687	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagccacgtccactgcagtcGcctctgtgagcctcgctcaa	7	8	9	17	3	2	1	1	1	1	0	5	1	3	1	4	0	3	2	4	0	1	0	rs121918228		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:43006687G>A	ENST00000265348.3	-	23	4418	c.4333C>T	c.(4333-4335)Cga>Tga	p.R1445*	CUL7_ENST00000535468.1_Nonsense_Mutation_p.R1529*|RN7SL403P_ENST00000481783.2_RNA			Q14999	CUL7_HUMAN	cullin 7	1445					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)			CACTGCAGTCGCCTCTGTGAG	0.607													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19760	0.0		0.0	False		,,,				2504	0.0				p.R1529X		Atlas-SNP	.											.	CUL7	133	.	0			c.C4585T	GRCh37	CM053196	CUL7	M	rs121918228	PASS	.	G	stop/ARG,stop/ARG	0,4406		0,0,2203	61	54	56	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4585,4333	3.6	0	6	dbSNP_133	56	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained,stop-gained	CUL7	NM_001168370.1,NM_014780.4	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	1529/1783,1445/1699	43006687	1,13005	2203	4300	6503	SO:0001587	stop_gained	9820	exon23			GCAGTCGCCTCTG	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.4333C>T	6.37:g.43006687G>A	ENSP00000265348:p.Arg1445*	88	0	0		106	52	0.490566	NM_001168370	B4DYZ0|F5H0L1|Q5T654	Nonsense_Mutation	SNP	ENST00000265348.3	37	CCDS4881.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	45	11.398506	0.99556	0.0	1.16E-4	ENSG00000044090	ENST00000265348;ENST00000535468	.	.	.	4.52	3.63	0.41609	.	0.343472	0.30989	N	0.008461	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.7945	13.7801	0.63077	0.0:0.0:0.8456:0.1544	.	.	.	.	X	1445;1529	.	ENSP00000265348:R1445X	R	-	1	2	CUL7	43114665	0.819000	0.29175	0.030000	0.17652	0.998000	0.95712	4.557000	0.60782	1.087000	0.41251	0.650000	0.86243	CGA	G|1.000;A|0.000	0.000	strong		0.607	CUL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040575.1	NM_014780		A	43006687	G	A	43006687	4	1	23	1	0	0	0	0	0	1	0	0	4062	1095	38	1	779	1	CUL7	6	43006687	Nonsense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	854104	43006687	128108380	267	7711											
CUL9	23113	hgsc.bcm.edu	37	chr6	43154017	43154017	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtcaccacccccagaagaCaagggtgggtcttccgccag	9	7	11	14	1	2	2	1	0	1	2	3	2	3	2	5	2	0	0	5	2	2	2	rs150188923	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:43154017C>G	ENST00000252050.4	+	4	1159	c.1075C>G	c.(1075-1077)Caa>Gaa	p.Q359E	CUL9_ENST00000372647.2_Missense_Mutation_p.Q359E|CUL9_ENST00000354495.3_Missense_Mutation_p.Q359E	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	359					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						CCCCAGAAGACAAGGGTGGGT	0.587													C|||	15	0.00299521	0.0008	0.0029	5008	,	,		17488	0.0		0.0119	False		,,,				2504	0.0				p.Q359E		Atlas-SNP	.											.	CUL9	248	.	0			c.C1075G						PASS	.	C	GLU/GLN	8,4398	14.3+/-33.2	0,8,2195	78	82	81		1075	4.6	0.3	6	dbSNP_134	81	75,8525	44.5+/-102.8	1,73,4226	yes	missense	CUL9	NM_015089.2	29	1,81,6421	GG,GC,CC		0.8721,0.1816,0.6382	benign	359/2518	43154017	83,12923	2203	4300	6503	SO:0001583	missense	23113	exon4			AGAAGACAAGGGT	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.1075C>G	6.37:g.43154017C>G	ENSP00000252050:p.Gln359Glu	97	0	0		122	56	0.459016	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	37	CCDS4890.1	12	0.005494505494505495	0	0.0	0	0.0	0	0.0	12	0.0158311345646438	C	12.56	1.974769	0.34848	0.001816	0.008721	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.72942	-0.7;-0.69;-0.6	5.5	4.63	0.57726	.	1.075350	0.07089	N	0.838384	T	0.49457	0.1558	L	0.42245	1.32	0.22001	N	0.999429	B;B;B	0.23937	0.094;0.094;0.044	B;B;B	0.21360	0.034;0.034;0.019	T	0.52601	-0.8554	10	0.45353	T	0.12	0.0071	14.0214	0.64558	0.0:0.9271:0.0:0.0729	.	359;359;359	E9PEZ1;Q8IWT3;Q05C85	.;CUL9_HUMAN;.	E	359	ENSP00000252050:Q359E;ENSP00000346490:Q359E;ENSP00000361730:Q359E	ENSP00000252050:Q359E	Q	+	1	0	CUL9	43261995	1.000000	0.71417	0.272000	0.24630	0.923000	0.55619	2.022000	0.41030	1.317000	0.45149	0.467000	0.42956	CAA	C|0.995;G|0.005	0.005	strong		0.587	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		G	43154017	C	G	43154017	3	3	23	1	0	0	0	0	1	0	0	0	4063	479	17	4	1085	4	CUL9	6	43154017	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	147330	43154017	127961050	268	7712											
NFKBIE	4794	hgsc.bcm.edu	37	chr6	44232842	44232845	+	Frame_Shift_Del	DEL	GTGT	GTGT	-																															ggccccccagcaaggacaggGtgtaggtgagcgaggaggag																										TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	GTGT	GTGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:44232842_44232845delGTGT	ENST00000275015.5	-	1	655_658	c.656_659delACAC	c.(655-660)tacaccfs	p.YT219fs		NM_004556.2	NP_004547.2	O00221	IKBE_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, epsilon	219					cytoplasmic sequestering of transcription factor (GO:0042994)|D-serine transport (GO:0042942)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|urinary_tract(1)	10	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)			CAAGGACAGGGTGTAGGTGAGCGA	0.681																																					p.219_220del		Pindel,Atlas-Indel	.											.	NFKBIE	31	.	0			c.657_660del						PASS	.																																			SO:0001589	frameshift_variant	4794	exon1			.	U91616	CCDS34463.1	6p21.1	2013-01-10			ENSG00000146232	ENSG00000146232		"Ankyrin repeat domain containing"	7799	protein-coding gene	gene with protein product		604548				9135156	Standard	NM_004556		Approved	IKBE	uc003oxe.1	O00221	OTTHUMG00000014762	ENST00000275015.5:c.656_659delACAC	6.37:g.44232842_44232845delGTGT	ENSP00000275015:p.Tyr219fs	112	0	.		146	22	0.151	NM_004556	Q5T9V9	Frame_Shift_Del	DEL	ENST00000275015.5	37	CCDS34463.1																																																																																			.	.	none		0.681	NFKBIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040733.2			-	44232845	GTGT	-	44232842	7	5	23	1	0	1	0	1	0	0	0	0	10389	1261	44	0	867	0	NFKBIE	6	44232842	Frame_Shift_Del	DEL	GTGT	TCGA-G8-6325-01A-11D-2210-10	1078825	44232842	126882225	269	7713											
TFAP2B	7021	hgsc.bcm.edu	37	chr6	50791444	50791444	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgccccagctctcgggccttGacccccggagggactaccac	6	6	11	18	2	1	1	0	1	1	0	2	3	1	3	6	3	3	1	6	3	1	2	rs139904414		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:50791444G>C	ENST00000393655.3	+	2	575	c.406G>C	c.(406-408)Gac>Cac	p.D136H	TFAP2B_ENST00000263046.4_Missense_Mutation_p.D145H|TFAP2B_ENST00000489228.1_3'UTR	NM_003221.3	NP_003212.2	Q92481	AP2B_HUMAN	transcription factor AP-2 beta (activating enhancer binding protein 2 beta)	136					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)					CTCGGGCCTTGACCCCCGGAG	0.711																																					p.D136H	Pancreas(116;1373 2332 5475 10752)	Atlas-SNP	.											.	TFAP2B	91	.	0			c.G406C						PASS	.	G	HIS/ASP	0,4398		0,0,2199	13	16	15		406	5.6	0.9	6	dbSNP_134	15	1,8595		0,1,4297	no	missense	TFAP2B	NM_003221.3	81	0,1,6496	CC,CG,GG		0.0116,0.0,0.0077	possibly-damaging	136/461	50791444	1,12993	2199	4298	6497	SO:0001583	missense	7021	exon2			GGCCTTGACCCCC	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.406G>C	6.37:g.50791444G>C	ENSP00000377265:p.Asp136His	52	0	0		34	21	0.617647	NM_003221	Q5JYX6|Q9NQ63|Q9NU99|Q9UJI7|Q9Y214|Q9Y3K3	Missense_Mutation	SNP	ENST00000393655.3	37	CCDS4934.2	.	.	.	.	.	.	.	.	.	.	G	30	5.057098	0.93846	0.0	1.16E-4	ENSG00000008196	ENST00000393655;ENST00000344788;ENST00000263046	D;D;D	0.88201	-2.35;-2.35;-2.35	5.58	5.58	0.84498	.	0.145200	0.64402	D	0.000012	D	0.86264	0.5891	L	0.58428	1.81	0.80722	D	1	P	0.41041	0.736	B	0.41036	0.346	D	0.87780	0.2611	10	0.59425	D	0.04	-16.9265	19.5711	0.95419	0.0:0.0:1.0:0.0	.	136	Q92481	AP2B_HUMAN	H	136;134;145	ENSP00000377265:D136H;ENSP00000342252:D134H;ENSP00000263046:D145H	ENSP00000263046:D145H	D	+	1	0	TFAP2B	50899403	1.000000	0.71417	0.926000	0.36857	0.956000	0.61745	7.875000	0.87205	2.638000	0.89438	0.563000	0.77884	GAC	G|1.000;C|0.000	0.000	weak		0.711	TFAP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040886.3	NM_003221		C	50791444	G	C	50791444	3	2	23	1	0	0	0	0	1	0	0	0	15803	1290	45	4	412	4	TFAP2B	6	50791444	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	6558602	50791444	120323623	270	7714											
GCLC	2729	hgsc.bcm.edu	37	chr6	53387230	53387230	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tactttgggtttgtcctttcCcccttctcttgcagagtttc	3	19	7	12	0	1	1	0	0	1	1	5	1	3	1	3	1	2	3	3	1	1	7			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:53387230C>T	ENST00000229416.6	-	2	729	c.246G>A	c.(244-246)ggG>ggA	p.G82G	GCLC_ENST00000514004.1_Silent_p.G82G	NM_001197115.1|NM_001498.3	NP_001184044.1|NP_001489.1	P48506	GSH1_HUMAN	glutamate-cysteine ligase, catalytic subunit	82					apoptotic mitochondrial changes (GO:0008637)|cell redox homeostasis (GO:0045454)|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)|L-ascorbic acid metabolic process (GO:0019852)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|regulation of blood vessel size (GO:0050880)|regulation of mitochondrial depolarization (GO:0051900)|response to arsenic-containing substance (GO:0046685)|response to heat (GO:0009408)|response to hormone (GO:0009725)|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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|glutamate-cysteine ligase complex (GO:0017109)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|coenzyme binding (GO:0050662)|glutamate binding (GO:0016595)|glutamate-cysteine ligase activity (GO:0004357)|magnesium ion binding (GO:0000287)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22	Lung NSC(77;0.0137)				L-Cysteine(DB00151)|Vitamin E(DB00163)	TTGTCCTTTCCCCCTTCTCTT	0.378																																					p.G82G		Atlas-SNP	.											.	GCLC	58	.	0			c.G246A						PASS	.						115	112	113					6																	53387230		2203	4300	6503	SO:0001819	synonymous_variant	2729	exon2			CCTTTCCCCCTTC	M90656	CCDS4952.1, CCDS75471.1	6p12	2008-02-05				ENSG00000001084	6.3.2.2		4311	protein-coding gene	gene with protein product		606857		GLCLC, GLCL		1350904	Standard	NM_001498		Approved	GCS	uc003pbw.2	P48506		ENST00000229416.6:c.246G>A	6.37:g.53387230C>T		74	0	0		91	12	0.131868	NM_001197115	Q14399	Silent	SNP	ENST00000229416.6	37	CCDS4952.1	.	.	.	.	.	.	.	.	.	.	C	9.717	1.158655	0.21454	.	.	ENSG00000001084	ENST00000513939	T	0.72725	-0.68	5.67	1.4	0.22301	.	0.000000	0.85682	D	0.000000	T	0.19765	0.0475	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34925	-0.9809	7	0.02654	T	1	.	4.0727	0.09889	0.237:0.4463:0.0:0.3167	.	.	.	.	E	70	ENSP00000424211:G70E	ENSP00000424211:G70E	G	-	2	0	GCLC	53495189	0.003000	0.15002	1.000000	0.80357	0.995000	0.86356	-1.302000	0.02746	0.193000	0.20303	0.585000	0.79938	GGG	.	.	none		0.378	GCLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359710.2			T	53387230	C	T	53387230	2	4	23	1	0	0	0	0	0	0	0	1	6303	610	22	2		2	GCLC	6	53387230	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	2595786	53387230	117727837	271	7715											
EYS	346007	hgsc.bcm.edu	37	chr6	64488001	64488001	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgcgtccagcatttgggTggccctcaggatttcccagt	6	11	11	13	1	1	0	1	0	0	0	3	1	3	1	3	3	2	1	3	3	0	2	rs74636274	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:64488001T>C	ENST00000370621.3	-	40	8322	c.7796A>G	c.(7795-7797)cAc>cGc	p.H2599R	PHF3_ENST00000420043.1_3'UTR|EYS_ENST00000370616.2_Missense_Mutation_p.H2599R|EYS_ENST00000503581.1_Missense_Mutation_p.H2599R			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	2599	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.		H -> R (in dbSNP:rs74636274). {ECO:0000269|PubMed:20333770}.		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						AGCATTTGGGTGGCCCTCAGG	0.473													T|||	23	0.00459265	0.0	0.0043	5008	,	,		17905	0.0		0.0109	False		,,,				2504	0.0092				p.H2599R		Atlas-SNP	.											.	EYS	527	.	0			c.A7796G						PASS	.	T	ARG/HIS	1,1383		0,1,691	100	82	88		7796	1.5	0.5	6	dbSNP_131	88	35,3147		0,35,1556	yes	missense	EYS	NM_001142800.1	29	0,36,2247	CC,CT,TT		1.0999,0.0723,0.7884	benign	2599/3145	64488001	36,4530	692	1591	2283	SO:0001583	missense	346007	exon40			TTTGGGTGGCCCT		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.7796A>G	6.37:g.64488001T>C	ENSP00000359655:p.His2599Arg	270	0	0		250	114	0.456	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	37		9|9|9	0.004120879120879121|0.004120879120879121|0.004120879120879121	0|0|0	0.0|0.0|0.0	2|2|2	0.0055248618784530384|0.0055248618784530384|0.0055248618784530384	0|0|0	0.0|0.0|0.0	7|7|7	0.009234828496042216|0.009234828496042216|0.009234828496042216	T|T|T	9.321|9.321|9.321	1.057987|1.057987|1.057987	0.19987|0.19987|0.19987	7.23E-4|7.23E-4|7.23E-4	0.010999|0.010999|0.010999	ENSG00000188107|ENSG00000188107|ENSG00000118482	ENST00000503581;ENST00000370621;ENST00000370616|ENST00000398580|ENST00000505138	D;T;T|.|.	0.81659|.|.	-1.52;-1.49;-1.49|.|.	4.02|4.02|4.02	1.47|1.47|1.47	0.22746|0.22746|0.22746	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);|.|.	0.285145|.|.	0.21597|.|.	N|.|.	0.072010|.|.	T|T|T	0.14874|0.14874|0.14874	0.0359|0.0359|0.0359	N|N|N	0.11201|0.11201|0.11201	0.11|0.11|0.11	0.80722|0.80722|0.80722	D|D|D	1|1|1	B;B|.|.	0.23540|.|.	0.087;0.053|.|.	B;B|.|.	0.20384|.|.	0.029;0.013|.|.	T|T|T	0.05937|0.05937|0.05937	-1.0855|-1.0855|-1.0855	10|5|5	0.25106|.|.	T|.|.	0.35|.|.	.|.|.	7.1543|7.1543|7.1543	0.25628|0.25628|0.25628	0.0:0.1867:0.0:0.8133|0.0:0.1867:0.0:0.8133|0.0:0.1867:0.0:0.8133	.|.|.	2599;2599|.|.	Q5T1H1-1;Q5T1H1|.|.	.;EYS_HUMAN|.|.	R|A|R	2599|371|136	ENSP00000424243:H2599R;ENSP00000359655:H2599R;ENSP00000359650:H2599R|.|.	ENSP00000359650:H2599R|.|.	H|T|W	-|-|+	2|1|1	0|0|0	EYS|EYS|PHF3	64545960|64545960|64545960	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.475000|0.475000|0.475000	0.27278|0.27278|0.27278	0.032000|0.032000|0.032000	0.12392|0.12392|0.12392	1.000000|1.000000|1.000000	0.29770|0.29770|0.29770	0.020000|0.020000|0.020000	0.15106|0.15106|0.15106	0.533000|0.533000|0.533000	0.62120|0.62120|0.62120	CAC|ACC|TGG	T|0.996;C|0.004	0.004	strong		0.473	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		C	64488001	T	C	64488001	3	2	23	1	0	0	0	0	1	0	0	0	5334	1696	59	3	1654	3	EYS	6	64488001	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	11100771	64488001	106627066	272	7716											
RIMS1	22999	hgsc.bcm.edu	37	chr6	72892796	72892796	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggaggagggcgtgtcgacgcCcgagtacaccagctgcgagg	8	4	18	11	5	0	0	0	0	0	0	1	5	0	2	2	4	3	2	2	4	1	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:72892796C>T	ENST00000521978.1	+	6	1622	c.1622C>T	c.(1621-1623)cCc>cTc	p.P541L	RIMS1_ENST00000522291.1_Missense_Mutation_p.P541L|RIMS1_ENST00000264839.7_Missense_Mutation_p.P541L|RIMS1_ENST00000348717.5_Missense_Mutation_p.P541L|RIMS1_ENST00000520567.1_Missense_Mutation_p.P541L|RIMS1_ENST00000517960.1_Missense_Mutation_p.P541L|RIMS1_ENST00000518273.1_Missense_Mutation_p.P541L|RIMS1_ENST00000491071.2_Missense_Mutation_p.P541L	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	541					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)				GTGTCGACGCCCGAGTACACC	0.682																																					p.P541L		Atlas-SNP	.											RIMS1,caecum,carcinoma,0,1	RIMS1	278	1	0			c.C1622T						scavenged	.						9	10	10					6																	72892796		1995	4142	6137	SO:0001583	missense	22999	exon6			CGACGCCCGAGTA	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.1622C>T	6.37:g.72892796C>T	ENSP00000428417:p.Pro541Leu	73	0	0		56	3	0.0535714	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	37	CCDS47449.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.088952	0.76756	.	.	ENSG00000079841	ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978	T;T;T;T;T;T;T;T	0.30714	1.57;1.72;1.63;1.73;1.65;1.67;1.74;1.52	4.05	3.16	0.36331	.	0.200172	0.34110	N	0.004245	T	0.43166	0.1235	M	0.72894	2.215	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.94;0.966;0.999	T	0.49978	-0.8881	10	0.87932	D	0	-4.1408	13.4986	0.61440	0.0:0.8416:0.1584:0.0	.	541;541;541	E9PHR1;C9JNW6;Q86UR5	.;.;RIMS1_HUMAN	L	541	ENSP00000430101:P541L;ENSP00000275037:P541L;ENSP00000264839:P541L;ENSP00000429959:P541L;ENSP00000430408:P541L;ENSP00000430502:P541L;ENSP00000430932:P541L;ENSP00000428417:P541L	ENSP00000264839:P541L	P	+	2	0	RIMS1	72949517	1.000000	0.71417	0.681000	0.30009	0.907000	0.53573	7.468000	0.80943	0.657000	0.30906	-0.519000	0.04390	CCC	.	.	none		0.682	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			T	72892796	C	T	72892796	3	4	23	1	0	0	0	0	1	0	0	0	13382	623	22	2	1644	2	RIMS1	6	72892796	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	8404795	72892796	98222271	273	7717											
CYB5R4	51167	hgsc.bcm.edu	37	chr6	84618792	84618792	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggttggcagaatggccattaAacctgctgttctgaaaggta	11	11	12	7	0	1	2	0	1	1	1	1	2	1	2	2	4	2	5	2	4	5	4			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:84618792A>G	ENST00000369681.5	+	4	535	c.395A>G	c.(394-396)aAa>aGa	p.K132R	CYB5R4_ENST00000369679.4_Missense_Mutation_p.K98R	NM_016230.3	NP_057314.2	Q7L1T6	NB5R4_HUMAN	cytochrome b5 reductase 4	132					cell development (GO:0048468)|detection of oxygen (GO:0003032)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|NADP metabolic process (GO:0006739)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|superoxide metabolic process (GO:0006801)	endoplasmic reticulum (GO:0005783)|perinuclear region of cytoplasm (GO:0048471)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|NAD(P)H oxidase activity (GO:0016174)|NADPH-hemoprotein reductase activity (GO:0003958)|oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor (GO:0016653)			breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	23		all_cancers(76;7e-07)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00128)		BRCA - Breast invasive adenocarcinoma(397;0.0871)		ATGGCCATTAAACCTGCTGTT	0.398																																					p.K132R	Esophageal Squamous(86;1289 1332 25971 40349 52675)	Atlas-SNP	.											.	CYB5R4	72	.	0			c.A395G						PASS	.						133	118	123					6																	84618792		2203	4300	6503	SO:0001583	missense	51167	exon4			CCATTAAACCTGC	AF169803	CCDS5000.2	6q14.2	2012-09-19		2005-07-13	ENSG00000065615	ENSG00000065615	1.6.2.2		20147	protein-coding gene	gene with protein product		608343	"NADPH cytochrome B5 oxidoreductase"	NCB5OR		10611283	Standard	NM_016230		Approved	b5+b5R, dJ676J13.1	uc003pkf.3	Q7L1T6	OTTHUMG00000015118	ENST00000369681.5:c.395A>G	6.37:g.84618792A>G	ENSP00000358695:p.Lys132Arg	67	0	0		62	29	0.467742	NM_016230	B1AEM2|Q5TGI9|Q9NUE4|Q9UHI9	Missense_Mutation	SNP	ENST00000369681.5	37	CCDS5000.2	.	.	.	.	.	.	.	.	.	.	A	18.22	3.576672	0.65878	.	.	ENSG00000065615	ENST00000369681;ENST00000369679	D;D	0.84944	-1.92;-1.68	5.74	5.74	0.90152	Cytochrome b5 (1);	0.206931	0.48767	D	0.000169	T	0.62720	0.2451	N	0.19112	0.55	0.44862	D	0.99787	B	0.27910	0.193	B	0.22386	0.039	T	0.64689	-0.6348	10	0.31617	T	0.26	.	12.4249	0.55540	1.0:0.0:0.0:0.0	.	132	Q7L1T6	NB5R4_HUMAN	R	132;98	ENSP00000358695:K132R;ENSP00000358693:K98R	ENSP00000358693:K98R	K	+	2	0	CYB5R4	84675511	1.000000	0.71417	0.173000	0.22940	0.007000	0.05969	5.761000	0.68801	2.182000	0.69389	0.482000	0.46254	AAA	.	.	none		0.398	CYB5R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041362.4	NM_016230		G	84618792	A	G	84618792	3	3	23	1	0	0	0	0	1	0	0	0	4131	14	1	3	409	3	CYB5R4	6	84618792	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	11725996	84618792	86496275	274	7718											
C6orf165	154313	hgsc.bcm.edu	37	chr6	88173748	88173748	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctctttaggctaatttgcGccagaaagttactcactcag	10	14	7	10	1	3	1	2	0	1	1	4	1	3	1	1	1	2	2	1	1	4	6	rs139574881	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:88173748G>A	ENST00000507897.1	+	13	1732	c.1649G>A	c.(1648-1650)cGc>cAc	p.R550H	C6orf165_ENST00000506888.1_3'UTR|C6ORF165_ENST00000369562.4_Missense_Mutation_p.R550H			Q8IYR0	CF165_HUMAN	chromosome 6 open reading frame 165	550										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)		GCTAATTTGCGCCAGAAAGTT	0.358													.|||	4	0.000798722	0.0008	0.0	5008	,	,		18450	0.003		0.0	False		,,,				2504	0.0				p.R550H		Atlas-SNP	.											.	C6orf165	116	.	0			c.G1649A						PASS	.	G	HIS/ARG	3,4403	6.2+/-15.9	0,3,2200	39	40	40		1649	2.1	0.6	6	dbSNP_134	40	13,8587	9.8+/-36.6	0,13,4287	yes	missense	C6orf165	NM_001031743.2	29	0,16,6487	AA,AG,GG		0.1512,0.0681,0.123	possibly-damaging	550/623	88173748	16,12990	2203	4300	6503	SO:0001583	missense	154313	exon13			ATTTGCGCCAGAA	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.1649G>A	6.37:g.88173748G>A	ENSP00000426769:p.Arg550His	45	0	0		31	13	0.419355	NM_001031743	A8K969|E1P507|Q8N9U4	Missense_Mutation	SNP	ENST00000507897.1	37	CCDS34498.1	4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	G	9.169	1.020606	0.19433	6.81E-4	0.001512	ENSG00000213204	ENST00000369562	T	0.38560	1.13	5.78	2.06	0.26882	.	0.152890	0.64402	N	0.000017	T	0.26448	0.0646	M	0.70842	2.15	0.36551	D	0.871855	D	0.57257	0.979	B	0.41666	0.363	T	0.13683	-1.0500	10	0.33940	T	0.23	.	14.1357	0.65287	0.1855:0.0:0.8145:0.0	.	550	Q8IYR0	CF165_HUMAN	H	550	ENSP00000358575:R550H	ENSP00000358575:R550H	R	+	2	0	C6orf165	88230467	0.998000	0.40836	0.619000	0.29118	0.204000	0.24138	2.447000	0.44917	0.089000	0.17243	-1.332000	0.01269	CGC	G|0.999;A|0.001	0.001	strong		0.358	C6orf165-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000470406.1	NM_178823		A	88173748	G	A	88173748	3	1	23	1	0	0	0	0	1	0	0	0	2343	1087	38	1	1695	1	C6orf165	6	88173748	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	3554956	88173748	82941319	275	7719											
KLHL32	114792	hgsc.bcm.edu	37	chr6	97562207	97562207	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aactgccgggagcattttgtGctgggtgccatggaggaata	9	10	15	7	1	0	0	0	0	0	0	0	3	0	3	2	4	5	2	2	4	3	3	rs74787311	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:97562207G>T	ENST00000369261.4	+	7	1539	c.1176G>T	c.(1174-1176)gtG>gtT	p.V392V	KLHL32_ENST00000539200.1_Silent_p.V323V|KLHL32_ENST00000536676.1_Silent_p.V356V|KLHL32_ENST00000544166.1_Intron	NM_052904.3	NP_443136.2	Q96NJ5	KLH32_HUMAN	kelch-like family member 32	392										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)		AGCATTTTGTGCTGGGTGCCA	0.542													G|||	92	0.0183706	0.0023	0.0375	5008	,	,		19608	0.001		0.0517	False		,,,				2504	0.0102				p.V392V		Atlas-SNP	.											.	KLHL32	85	.	0			c.G1176T						PASS	.	G		55,4349	52.3+/-87.9	1,53,2148	44	42	43		1176	2.5	1	6	dbSNP_132	43	590,8010	157.0+/-210.8	23,544,3733	no	coding-synonymous	KLHL32	NM_052904.3		24,597,5881	TT,TG,GG		6.8605,1.2489,4.96		392/621	97562207	645,12359	2202	4300	6502	SO:0001819	synonymous_variant	114792	exon7			TTTTGTGCTGGGT	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.1176G>T	6.37:g.97562207G>T		70	0	0		82	32	0.390244	NM_052904	B7Z346|B7Z4E2|E1P528|Q5THT0|Q96PY7	Silent	SNP	ENST00000369261.4	37	CCDS5038.1																																																																																			G|0.960;T|0.040	0.040	strong		0.542	KLHL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041570.1	NM_052904		T	97562207	G	T	97562207	2	4	23	1	0	0	0	0	0	0	0	1	8395	1306	46	4		4	KLHL32	6	97562207	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	9388459	97562207	73552860	276	7720											
C6orf167	253714	hgsc.bcm.edu	37	chr6	97599674	97599674	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagaagtcagctgggaggaaGgttcttcttctgaccccact	9	10	11	11	0	4	2	1	1	3	1	4	4	4	4	2	3	1	2	2	3	2	3	rs138146580	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:97599674G>A	ENST00000275053.4	-	23	3720	c.3455C>T	c.(3454-3456)cCt>cTt	p.P1152L	MMS22L_ENST00000369251.2_Missense_Mutation_p.P1112L	NM_198468.2	NP_940870.2	Q6ZRQ5	MMS22_HUMAN	MMS22-like, DNA repair protein	1152					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						CTGGGAGGAAGGTTCTTCTTC	0.433													G|||	37	0.00738818	0.0023	0.0058	5008	,	,		15425	0.0		0.0239	False		,,,				2504	0.0061				p.P1152L		Atlas-SNP	.											.	MMS22L	102	.	0			c.C3455T						PASS	.	G	LEU/PRO	17,4389	24.3+/-50.5	0,17,2186	204	203	203		3455	3.6	1	6	dbSNP_134	203	155,8445	73.5+/-136.2	2,151,4147	yes	missense	MMS22L	NM_198468.2	98	2,168,6333	AA,AG,GG		1.8023,0.3858,1.3225	benign	1152/1244	97599674	172,12834	2203	4300	6503	SO:0001583	missense	253714	exon23			GAGGAAGGTTCTT		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.3455C>T	6.37:g.97599674G>A	ENSP00000275053:p.Pro1152Leu	189	0	0		184	109	0.592391	NM_198468	D6R9Y8|D6RBQ4|E1P529|Q5THT2|Q68CQ6|Q68D32	Missense_Mutation	SNP	ENST00000275053.4	37	CCDS5039.1	26	0.011904761904761904	3	0.006097560975609756	4	0.011049723756906077	0	0.0	19	0.025065963060686015	G	9.389	1.074903	0.20227	0.003858	0.018023	ENSG00000146263	ENST00000275053;ENST00000369251	T;T	0.29655	3.93;1.56	5.44	3.59	0.41128	.	0.290094	0.38492	N	0.001666	T	0.09202	0.0227	L	0.56769	1.78	0.44966	D	0.997984	B;B	0.31548	0.328;0.082	B;B	0.27380	0.079;0.036	T	0.13255	-1.0516	10	0.14252	T	0.57	.	3.4047	0.07336	0.1576:0.1261:0.5698:0.1465	.	1112;1152	E2QRD4;Q6ZRQ5	.;MMS22_HUMAN	L	1152;1112	ENSP00000275053:P1152L;ENSP00000358254:P1112L	ENSP00000275053:P1152L	P	-	2	0	MMS22L	97706395	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	1.175000	0.31944	0.606000	0.29965	0.650000	0.86243	CCT	G|0.987;A|0.013	0.013	strong		0.433	MMS22L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041573.3	NM_198468		A	97599674	G	A	97599674	3	1	23	1	0	0	0	0	1	0	0	0	2344	1000	35	2	288	2	C6orf167	6	97599674	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	37467	97599674	73515393	277	7721											
FOXO3	2309	hgsc.bcm.edu	37	chr6	108882915	108882915	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacgcggacctgatcacccgCgccatcgagagctccccgga	8	5	11	17	6	1	2	1	1	0	1	3	5	2	4	5	2	2	1	5	2	1	1	rs150320900	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:108882915C>T	ENST00000343882.6	+	2	808	c.504C>T	c.(502-504)cgC>cgT	p.R168R	FOXO3_ENST00000406360.1_Silent_p.R168R	NM_201559.2	NP_963853.1	O43524	FOXO3_HUMAN	forkhead box O3	168					antral ovarian follicle growth (GO:0001547)|cellular response to oxidative stress (GO:0034599)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|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)|glucose homeostasis (GO:0042593)|initiation of primordial ovarian follicle growth (GO:0001544)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|ovulation from ovarian follicle (GO:0001542)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of erythrocyte differentiation (GO:0045648)|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 transcription from RNA polymerase II promoter (GO:0006357)|regulation of translation (GO:0006417)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(5)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26		all_cancers(87;1.78e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;3.88e-05)|Colorectal(196;0.0294)|all_lung(197;0.0487)|Lung SC(18;0.152)		Epithelial(106;0.000759)|all cancers(137;0.00121)|BRCA - Breast invasive adenocarcinoma(108;0.00163)|OV - Ovarian serous cystadenocarcinoma(136;0.00718)		TGATCACCCGCGCCATCGAGA	0.657													C|||	12	0.00239617	0.0	0.0029	5008	,	,		13235	0.0		0.008	False		,,,				2504	0.002				p.R168R		Atlas-SNP	.											.	FOXO3	67	.	0			c.C504T						PASS	.	C	,	3,4403	6.2+/-15.9	0,3,2200	28	24	25		504,504	0.4	1	6	dbSNP_134	25	70,8530	42.2+/-99.7	0,70,4230	no	coding-synonymous,coding-synonymous	FOXO3	NM_001455.3,NM_201559.2	,	0,73,6430	TT,TC,CC		0.814,0.0681,0.5613	,	168/674,168/674	108882915	73,12933	2203	4300	6503	SO:0001819	synonymous_variant	2309	exon1			CACCCGCGCCATC	AF032886	CCDS5068.1	6q21	2008-09-08	2007-05-02	2007-05-02	ENSG00000118689	ENSG00000118689		"Forkhead boxes"	3821	protein-coding gene	gene with protein product		602681		FKHRL1, FOXO3A		9479491	Standard	NM_001455		Approved	AF6q21, FOXO2	uc003psm.2	O43524	OTTHUMG00000015327	ENST00000343882.6:c.504C>T	6.37:g.108882915C>T		125	0	0		127	65	0.511811	NM_001455	B4DVZ6|E1P5E6|O15171|Q5T2I7|Q9BZ04	Silent	SNP	ENST00000343882.6	37	CCDS5068.1																																																																																			C|0.995;T|0.005	0.005	strong		0.657	FOXO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041722.2			T	108882915	C	T	108882915	2	4	23	1	0	0	0	0	0	0	0	1	6032	755	27	1		1	FOXO3	6	108882915	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	11283241	108882915	62232152	278	7722											
REV3L	5980	hgsc.bcm.edu	37	chr6	111694124	111694124	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aaaagaggtattggctgagtCaagagactgtcccatttctt	12	12	10	7	0	2	3	1	1	1	2	3	4	3	3	1	2	0	2	1	2	4	4	rs3218599	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:111694124C>G	ENST00000358835.3	-	14	5888	c.5434G>C	c.(5434-5436)Gac>Cac	p.D1812H	REV3L_ENST00000368805.1_Missense_Mutation_p.D1812H|REV3L_ENST00000435970.1_Missense_Mutation_p.D1734H|REV3L_ENST00000368802.3_Missense_Mutation_p.D1812H			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	1812			D -> H (in dbSNP:rs3218599). {ECO:0000269|Ref.5}.		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)		TTGGCTGAGTCAAGAGACTGT	0.428								DNA polymerases (catalytic subunits)					C|||	46	0.0091853	0.0008	0.0245	5008	,	,		19961	0.0		0.0278	False		,,,				2504	0.0				p.D1812H		Atlas-SNP	.											.	REV3L	386	.	0			c.G5434C	GRCh37	CM065439	REV3L	M	rs3218599	PASS	.	C	HIS/ASP	23,4383	30.8+/-60.4	0,23,2180	149	136	140		5434	5.1	1	6	dbSNP_106	140	187,8413	84.2+/-146.7	6,175,4119	yes	missense	REV3L	NM_002912.3	81	6,198,6299	GG,GC,CC		2.1744,0.522,1.6146	benign	1812/3131	111694124	210,12796	2203	4300	6503	SO:0001583	missense	5980	exon13			CTGAGTCAAGAGA	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.5434G>C	6.37:g.111694124C>G	ENSP00000351697:p.Asp1812His	79	0	0		87	54	0.62069	NM_002912	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	37	CCDS5091.2	31	0.014194139194139194	0	0.0	7	0.019337016574585635	0	0.0	24	0.0316622691292876	C	10.13	1.266893	0.23136	0.00522	0.021744	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	T;T;T;T	0.01685	4.79;4.79;4.79;4.69	5.93	5.06	0.68205	Ribonuclease H-like (1);	0.336140	0.29383	N	0.012319	T	0.00967	0.0032	L	0.56769	1.78	0.35663	D	0.812702	B	0.23735	0.09	B	0.20184	0.028	T	0.50039	-0.8874	10	0.21540	T	0.41	-0.47	10.7403	0.46149	0.0:0.7996:0.1321:0.0684	rs3218599;rs17539658;rs17686344;rs52831072;rs3218599	1812	O60673	DPOLZ_HUMAN	H	1812;1812;1812;1734	ENSP00000357792:D1812H;ENSP00000357795:D1812H;ENSP00000351697:D1812H;ENSP00000402003:D1734H	ENSP00000351697:D1812H	D	-	1	0	REV3L	111800817	1.000000	0.71417	1.000000	0.80357	0.706000	0.40770	3.495000	0.53280	1.484000	0.48361	0.655000	0.94253	GAC	C|0.985;G|0.015	0.015	strong		0.428	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		G	111694124	C	G	111694124	3	3	23	1	0	0	0	0	1	0	0	0	13255	826	29	4	4038	4	REV3L	6	111694124	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	2811209	111694124	59420943	279	7723											
TRDN	10345	hgsc.bcm.edu	37	chr6	123703291	123703291	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtttttttgttttcttggaAtctgaaaacacaaagataaa	14	16	7	4	0	2	2	0	1	2	1	2	3	2	3	0	2	1	2	0	2	6	7	rs200706450		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:123703291A>C	ENST00000398178.3	-	15	1158	c.1137T>G	c.(1135-1137)gaT>gaG	p.D379E	TRDN_ENST00000334268.4_Splice_Site_p.D379E	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin	379					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)		TTTTCTTGGAATCTGAAAACA	0.284																																					p.D380E		Atlas-SNP	.											.	TRDN	88	.	0			c.T1140G						PASS	.						21	19	20					6																	123703291		1645	3752	5397	SO:0001630	splice_region_variant	10345	exon15			CTTGGAATCTGAA	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.1136-1T>G	6.37:g.123703291A>C		180	0	0		132	55	0.416667	NM_001251987	A5D6W5|F5H2W7|Q6NSB8	Missense_Mutation	SNP	ENST00000398178.3	37	CCDS55053.1	.	.	.	.	.	.	.	.	.	.	A	12.01	1.809011	0.31961	.	.	ENSG00000186439	ENST00000398178;ENST00000398161;ENST00000334268	T;T	0.21361	2.02;2.01	4.42	1.95	0.26073	.	0.317399	0.28420	N	0.015417	T	0.02230	0.0069	N	0.14661	0.345	0.80722	D	1	B;B;B	0.17667	0.023;0.023;0.023	B;B;B	0.12837	0.008;0.008;0.008	T	0.43669	-0.9377	10	0.02654	T	1	.	3.799	0.08751	0.7097:0.0:0.1035:0.1868	.	379;380;379	Q5SWK9;Q8IVK2;Q13061	.;.;TRDN_HUMAN	E	379;381;379	ENSP00000381240:D379E;ENSP00000333984:D379E	ENSP00000333984:D379E	D	-	3	2	TRDN	123744990	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.025000	0.30090	0.297000	0.22615	0.377000	0.23210	GAT	.	.	weak		0.284	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			Missense_Mutation	C	123703291	A	C	123703291	5	2	23	1	0	0	0	0	0	0	1	0	16483	115	4	5	1160	5	TRDN	6	123703291	Splice_Site	SNP	A	TCGA-G8-6325-01A-11D-2210-10	12009167	123703291	47411776	280	7724											
NCOA7	135112	hgsc.bcm.edu	37	chr6	126210797	126210797	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acctgactaagaacaaagaaGggccacaggtatctgaaaat	18	6	9	8	0	1	4	0	2	1	2	1	4	1	4	2	2	1	1	2	2	7	2	rs35223550	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:126210797G>A	ENST00000368357.3	+	10	1949	c.1597G>A	c.(1597-1599)Ggg>Agg	p.G533R	NCOA7_ENST00000392477.2_Missense_Mutation_p.G533R|NCOA7_ENST00000229634.9_Missense_Mutation_p.G418R	NM_001199619.1|NM_001199620.1	NP_001186548.1|NP_001186549.1	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7	533			G -> R (in dbSNP:rs35223550).		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)		GAACAAAGAAGGGCCACAGGT	0.373													G|||	6	0.00119808	0.0008	0.0043	5008	,	,		20188	0.0		0.0	False		,,,				2504	0.002				p.G533R		Atlas-SNP	.											.	NCOA7	92	.	0			c.G1597A						PASS	.	G	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	3,4401		0,3,2199	39	43	42		1564,1597,1597,1252,1597	3.7	0.5	6	dbSNP_126	42	50,8540		0,50,4245	yes	missense,missense,missense,missense,missense	NCOA7	NM_001122842.2,NM_001199619.1,NM_001199620.1,NM_001199621.1,NM_181782.4	125,125,125,125,125	0,53,6444	AA,AG,GG		0.5821,0.0681,0.4079	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	522/932,533/943,533/943,418/828,533/943	126210797	53,12941	2202	4295	6497	SO:0001583	missense	135112	exon10			AAAGAAGGGCCAC	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.1597G>A	6.37:g.126210797G>A	ENSP00000357341:p.Gly533Arg	62	0	0		56	32	0.571429	NM_001199619	B2RNS2|B7Z2C4|B9EH71|G8JL91|Q3LID6|Q4G0V1|Q5TF95|Q6IPQ4|Q6NE83|Q86T89|Q8N1W4	Missense_Mutation	SNP	ENST00000368357.3	37	CCDS5132.1	4	0.0018315018315018315	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	0	0.0	G	14.31	2.497726	0.44455	6.81E-4	0.005821	ENSG00000111912	ENST00000368357;ENST00000392477;ENST00000229634;ENST00000413085	T;T;T;T	0.37235	1.21;1.21;1.21;1.21	5.52	3.73	0.42828	.	0.382752	0.30277	N	0.009999	T	0.25494	0.0620	N	0.24115	0.695	0.24605	N	0.993753	B;D;D	0.76494	0.002;0.999;0.999	B;D;D	0.69479	0.004;0.964;0.922	T	0.09400	-1.0676	10	0.51188	T	0.08	-0.0117	9.3566	0.38171	0.0756:0.1447:0.7796:0.0	rs35223550	522;522;533	B3KXK4;Q8NI08-2;Q8NI08	.;.;NCOA7_HUMAN	R	533;533;418;331	ENSP00000357341:G533R;ENSP00000376269:G533R;ENSP00000229634:G418R;ENSP00000389186:G331R	ENSP00000229634:G418R	G	+	1	0	NCOA7	126252490	1.000000	0.71417	0.535000	0.28026	0.811000	0.45836	2.682000	0.46934	0.670000	0.31165	0.655000	0.94253	GGG	G|0.996;A|0.004	0.004	strong		0.373	NCOA7-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042083.4	XM_059748		A	126210797	G	A	126210797	3	1	23	1	0	0	0	0	1	0	0	0	10243	1000	35	2	1627	2	NCOA7	6	126210797	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	2507506	126210797	44904270	281	7725											
LAMA2	3908	hgsc.bcm.edu	37	chr6	129635920	129635920	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctactacccagtgctctgaaGcaaaaggactgatccggacg	12	7	10	12	2	1	2	0	2	1	0	2	4	2	4	2	2	4	2	2	2	5	2	rs34505698		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:129635920G>A	ENST00000421865.2	+	24	3581	c.3532G>A	c.(3532-3534)Gca>Aca	p.A1178T		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1178	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)		GTGCTCTGAAGCAAAAGGACT	0.527													G|||	1	0.000199681	0.0	0.0014	5008	,	,		18459	0.0		0.0	False		,,,				2504	0.0				p.A1178T		Atlas-SNP	.											.	LAMA2	481	.	0			c.G3532A						PASS	.	G	THR/ALA,THR/ALA	0,4406		0,0,2203	87	83	84		3532,3532	5.6	1	6	dbSNP_126	84	13,8587	9.8+/-36.6	0,13,4287	yes	missense,missense	LAMA2	NM_000426.3,NM_001079823.1	58,58	0,13,6490	AA,AG,GG		0.1512,0.0,0.1	benign,benign	1178/3123,1178/3119	129635920	13,12993	2203	4300	6503	SO:0001583	missense	3908	exon24			TCTGAAGCAAAAG	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.3532G>A	6.37:g.129635920G>A	ENSP00000400365:p.Ala1178Thr	73	0	0		59	27	0.457627	NM_000426	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	18.81	3.703093	0.68501	0.0	0.001512	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.36878	1.23	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.46151	0.1378	L	0.50333	1.59	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.09271	-1.0682	10	0.21540	T	0.41	.	19.5763	0.95446	0.0:0.0:1.0:0.0	rs34505698	1178;1178	A6NF00;P24043	.;LAMA2_HUMAN	T	1178	ENSP00000400365:A1178T	ENSP00000346769:A1178T	A	+	1	0	LAMA2	129677613	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.230000	0.95299	2.646000	0.89796	0.655000	0.94253	GCA	G|0.999;A|0.001	0.001	strong		0.527	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			A	129635920	G	A	129635920	3	1	23	1	0	0	0	0	1	0	0	0	8615	971	34	2	3626	2	LAMA2	6	129635920	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	3425123	129635920	41479147	282	7726											
VNN2	8875	hgsc.bcm.edu	37	chr6	133073844	133073844	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgttgaaagtcaccaactcCggcttttcagggacattaaa	12	11	9	9	1	2	1	2	1	0	0	3	2	3	2	2	2	1	2	2	2	4	4	rs33980664	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:133073844C>T	ENST00000326499.6	-	4	706	c.582G>A	c.(580-582)ccG>ccA	p.P194P	VNN2_ENST00000526192.1_5'Flank|VNN2_ENST00000525289.1_Intron|RP1-55C23.7_ENST00000430895.1_RNA|VNN2_ENST00000525270.1_Silent_p.P141P	NM_004665.2	NP_004656	O95498	VNN2_HUMAN	vanin 2	194	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				cellular component movement (GO:0006928)|pantothenate metabolic process (GO:0015939)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	pantetheine hydrolase activity (GO:0017159)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(155;0.00237)|GBM - Glioblastoma multiforme(226;0.0267)		TCACCAACTCCGGCTTTTCAG	0.408													C|||	85	0.0169728	0.0023	0.049	5008	,	,		19553	0.004		0.0278	False		,,,				2504	0.0164				p.P194P		Atlas-SNP	.											.	VNN2	83	.	0			c.G582A						PASS	.	C	,,	24,4382	29.0+/-57.7	0,24,2179	119	115	116		,582,423	-10.8	0	6	dbSNP_126	116	294,8306	108.0+/-168.7	6,282,4012	no	intron,coding-synonymous,coding-synonymous	VNN2	NM_001242350.1,NM_004665.2,NM_078488.1	,,	6,306,6191	TT,TC,CC		3.4186,0.5447,2.445	,,	,194/521,141/468	133073844	318,12688	2203	4300	6503	SO:0001819	synonymous_variant	8875	exon4			CAACTCCGGCTTT	AB026705	CCDS5161.1, CCDS5162.1, CCDS56451.1	6q23-q24	2013-02-13			ENSG00000112303	ENSG00000112303	3.5.1.92	"Vanins"	12706	protein-coding gene	gene with protein product	"pantetheinase"	603571				9790769, 11491533	Standard	NM_078488		Approved	FOAP-4, GPI-80	uc003qdt.3	O95498	OTTHUMG00000015588	ENST00000326499.6:c.582G>A	6.37:g.133073844C>T		89	0	0		81	37	0.45679	NM_004665	A0AUZ3|A6NDY1|A8K4E3|A8K7W0|B2DFZ0|B2DFZ1|B2DFZ2|B2DFZ3|F6XL73|Q2XUN1|Q9UJF3|Q9UMW2	Silent	SNP	ENST00000326499.6	37	CCDS5161.1																																																																																			C|0.976;T|0.024	0.024	strong		0.408	VNN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042264.2			T	133073844	C	T	133073844	2	4	23	1	0	0	0	0	0	0	0	1	17198	639	23	1		1	VNN2	6	133073844	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	3437924	133073844	38041223	283	7727											
HBS1L	10767	hgsc.bcm.edu	37	chr6	135287597	135287597	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gctctaccaatgcattctggCctttagtcaaaaacctatta	12	13	5	11	0	3	0	1	0	2	0	3	0	3	0	3	1	3	2	3	1	7	6			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:135287597C>T	ENST00000367837.5	-	17	2119	c.1913G>A	c.(1912-1914)gGc>gAc	p.G638D	HBS1L_ENST00000445176.2_Missense_Mutation_p.G362D|HBS1L_ENST00000415177.2_Missense_Mutation_p.G573D|HBS1L_ENST00000367826.2_Missense_Mutation_p.G596D|HBS1L_ENST00000367824.4_Missense_Mutation_p.G474D|HBS1L_ENST00000527578.1_Missense_Mutation_p.G474D	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase	638					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)		TGCATTCTGGCCTTTAGTCAA	0.328																																					p.G638D		Atlas-SNP	.											.	HBS1L	75	.	0			c.G1913A						PASS	.						106	105	106					6																	135287597		2203	4300	6503	SO:0001583	missense	10767	exon17			TTCTGGCCTTTAG	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.1913G>A	6.37:g.135287597C>T	ENSP00000356811:p.Gly638Asp	70	0	0		54	20	0.37037	NM_006620	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Missense_Mutation	SNP	ENST00000367837.5	37	CCDS5173.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.145634	0.77888	.	.	ENSG00000112339	ENST00000367837;ENST00000527578;ENST00000415177;ENST00000367826;ENST00000367824;ENST00000533274;ENST00000445176	T;T;T;T;T;T;T	0.69561	-0.38;-0.38;-0.34;-0.4;-0.38;-0.41;0.71	5.96	5.96	0.96718	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal (1);Translation elongation factor EFTu/EF1A, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.80008	0.4545	M	0.73319	2.225	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.79108	0.967;0.992	T	0.80279	-0.1449	10	0.87932	D	0	-8.0087	20.4008	0.98991	0.0:1.0:0.0:0.0	.	596;638	Q9Y450-4;Q9Y450	.;HBS1L_HUMAN	D	638;474;573;596;474;508;362	ENSP00000356811:G638D;ENSP00000436256:G474D;ENSP00000389826:G573D;ENSP00000356800:G596D;ENSP00000356798:G474D;ENSP00000434533:G508D;ENSP00000415305:G362D	ENSP00000356798:G474D	G	-	2	0	HBS1L	135329290	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.265000	0.78442	2.826000	0.97356	0.655000	0.94253	GGC	.	.	none		0.328	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2			T	135287597	C	T	135287597	3	4	23	1	0	0	0	0	1	0	0	0	6996	739	26	2	149	2	HBS1L	6	135287597	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	2213753	135287597	35827470	284	7728											
BCLAF1	9774	hgsc.bcm.edu	37	chr6	136599912	136599912	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgttctggaacgagacctaGaactaaaaatgaaataaata	20	9	7	5	1	1	3	0	1	1	2	1	5	1	4	1	1	2	1	1	1	10	5	rs200334350		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:136599912G>T	ENST00000531224.1	-	4	359	c.107C>A	c.(106-108)tCt>tAt	p.S36Y	BCLAF1_ENST00000392348.2_Intron|BCLAF1_ENST00000527536.1_Missense_Mutation_p.S36Y|BCLAF1_ENST00000530767.1_Missense_Mutation_p.S36Y|BCLAF1_ENST00000353331.4_Intron|BCLAF1_ENST00000527759.1_Intron	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	36					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)		ACGAGACCTAGAACTAAAAAT	0.318																																					p.S36Y	Colon(142;1534 1789 5427 7063 28491)	Atlas-SNP	.											BCLAF1_ENST00000531224,head_neck,carcinoma,-1,1	BCLAF1	203	1	0			c.C107A						scavenged	.						23	24	24					6																	136599912		2199	4289	6488	SO:0001583	missense	9774	exon4			GACCTAGAACTAA	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.107C>A	6.37:g.136599912G>T	ENSP00000435210:p.Ser36Tyr	29	1	0.0344828		20	2	0.1	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	37	CCDS5177.1	.	.	.	.	.	.	.	.	.	.	G	5.506	0.278344	0.10403	.	.	ENSG00000029363	ENST00000531224;ENST00000527536;ENST00000530767;ENST00000529826	T;T;T;T	0.46819	1.23;1.07;0.86;0.93	5.84	5.84	0.93424	.	0.000000	0.64402	D	0.000004	T	0.63295	0.2499	M	0.61703	1.905	0.80722	D	1	D;D	0.64830	0.994;0.994	D;D	0.74348	0.983;0.983	T	0.64245	-0.6453	10	0.87932	D	0	-6.9024	20.1392	0.98050	0.0:0.0:1.0:0.0	.	36;36	Q9NYF8;Q9NYF8-4	BCLF1_HUMAN;.	Y	36	ENSP00000435210:S36Y;ENSP00000435441:S36Y;ENSP00000436501:S36Y;ENSP00000431734:S36Y	ENSP00000435441:S36Y	S	-	2	0	BCLAF1	136641605	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.159000	0.77483	2.765000	0.95021	0.557000	0.71058	TCT	.	.	weak		0.318	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739		T	136599912	G	T	136599912	3	4	23	1	0	0	0	0	1	0	0	0	1383	942	33	4	2695	4	BCLAF1	6	136599912	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1312315	136599912	34515155	285	7729											
IL22RA2	116379	hgsc.bcm.edu	37	chr6	137482840	137482840	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acttacctgctacaccagtaAggaagaaactgatgaggaag	16	7	10	8	0	0	3	0	2	0	1	0	5	0	5	2	2	4	2	2	2	6	3	rs28385692	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:137482840A>G	ENST00000296980.2	-	2	347	c.47T>C	c.(46-48)cTt>cCt	p.L16P	IL22RA2_ENST00000339602.3_Missense_Mutation_p.L16P|IL22RA2_ENST00000349184.4_Missense_Mutation_p.L16P	NM_052962.2	NP_443194.1	Q969J5	I22R2_HUMAN	interleukin 22 receptor, alpha 2	16			L -> P (in dbSNP:rs28385692). {ECO:0000269|Ref.6}.		cytokine-mediated signaling pathway (GO:0019221)|negative regulation of inflammatory response (GO:0050728)|regulation of tyrosine phosphorylation of Stat3 protein (GO:0042516)	cytosol (GO:0005829)|extracellular space (GO:0005615)	interleukin-22 binding (GO:0042017)|interleukin-22 receptor activity (GO:0042018)			endometrium(1)|large_intestine(1)|lung(3)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000313)|OV - Ovarian serous cystadenocarcinoma(155;0.00407)		TACACCAGTAAGGAAGAAACT	0.428													A|||	89	0.0177716	0.0023	0.0159	5008	,	,		17508	0.001		0.0318	False		,,,				2504	0.0429				p.L16P		Atlas-SNP	.											IL22RA2,NS,malignant_melanoma,-1,1	IL22RA2	17	1	0			c.T47C						PASS	.	A	PRO/LEU,PRO/LEU,PRO/LEU	30,4376	36.0+/-67.5	0,30,2173	119	92	101		47,47,47	3.3	0.7	6	dbSNP_125	101	295,8305	106.0+/-166.9	8,279,4013	yes	missense,missense,missense	IL22RA2	NM_052962.2,NM_181309.1,NM_181310.1	98,98,98	8,309,6186	GG,GA,AA		3.4302,0.6809,2.4988	benign,benign,benign	16/264,16/232,16/131	137482840	325,12681	2203	4300	6503	SO:0001583	missense	116379	exon2			CCAGTAAGGAAGA	AY044429	CCDS5182.1, CCDS5183.1, CCDS5184.1	6q24.1-q24.2	2008-02-05			ENSG00000164485	ENSG00000164485		"Interleukins and interleukin receptors"	14901	protein-coding gene	gene with protein product		606648				11481447, 11390454	Standard	NM_181309		Approved	CRF2-S1, IL-22BP	uc003qhl.3	Q969J5	OTTHUMG00000015655	ENST00000296980.2:c.47T>C	6.37:g.137482840A>G	ENSP00000296980:p.Leu16Pro	133	0	0		104	36	0.346154	NM_181309	Q08AH7|Q6UWM1|Q96A41|Q96QR0	Missense_Mutation	SNP	ENST00000296980.2	37	CCDS5182.1	29	0.013278388278388278	0	0.0	4	0.011049723756906077	0	0.0	25	0.032981530343007916	A	11.51	1.659956	0.29515	0.006809	0.034302	ENSG00000164485	ENST00000349184;ENST00000296980;ENST00000339602	T;T;T	0.79653	-1.29;-1.29;-1.29	4.55	3.3	0.37823	.	.	.	.	.	T	0.71879	0.3392	M	0.83384	2.64	0.38674	D	0.952373	B;B;P	0.45634	0.125;0.224;0.863	B;B;B	0.42112	0.037;0.097;0.376	T	0.72593	-0.4246	9	0.33141	T	0.24	.	7.7806	0.29062	0.7873:0.2127:0.0:0.0	rs28385692;rs35818500;rs28385692	16;16;16	Q969J5-3;Q969J5-2;Q969J5	.;.;I22R2_HUMAN	P	16	ENSP00000296979:L16P;ENSP00000296980:L16P;ENSP00000340920:L16P	ENSP00000296980:L16P	L	-	2	0	IL22RA2	137524533	0.004000	0.15560	0.734000	0.30879	0.386000	0.30323	0.318000	0.19504	2.060000	0.61445	0.524000	0.50904	CTT	A|0.974;G|0.026	0.026	strong		0.428	IL22RA2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042399.1			G	137482840	A	G	137482840	3	3	23	1	0	0	0	0	1	0	0	0	7683	72	3	3	768	3	IL22RA2	6	137482840	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	882928	137482840	33632227	286	7730											
TNFAIP3	7128	hgsc.bcm.edu	37	chr6	138192494	138192501	+	Frame_Shift_Del	DEL	CACCGATA	CACCGATA	-																															ttcatcattttaaaaccatgCaccgatacacactggaaatg																										TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CACCGATA	CACCGATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:138192494_138192501delCACCGATA	ENST00000237289.4	+	2	196_203	c.130_137delCACCGATA	c.(130-138)caccgatacfs	p.HRY44fs		NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	44					apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|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 interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|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 protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)|p.M43fs*55(1)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		TAAAACCATGCACCGATACACACTGGAA	0.438			"D, N, F"		"marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"																																p.43_46del	GBM(130;153 1739 22295 28918 47987)	Atlas-Indel	.		Rec	yes		6	6q23	7128	"tumor necrosis factor, alpha-induced protein 3"		L	.	TNFAIP3	340	.	26	Whole gene deletion(25)|Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(26)	c.129_136del						PASS	.																																			SO:0001589	frameshift_variant	7128	exon2			.	M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"OTU domain containing"	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.130_137delCACCGATA	6.37:g.138192494_138192501delCACCGATA	ENSP00000237289:p.His44fs	148	0	0		114	12	0.105263	NM_006290	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Frame_Shift_Del	DEL	ENST00000237289.4	37	CCDS5187.1																																																																																			.	.	none		0.438	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1			-	138192501	CACCGATA	-	138192494	7	5	23	1	0	1	0	1	0	0	0	0	16289	710	25	0	132	0	TNFAIP3	6	138192494	Frame_Shift_Del	DEL	CACCGATA	TCGA-G8-6325-01A-11D-2210-10	709654	138192494	32922573	287	7731											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152730807	152730807	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgatttcaggttctgatattCtctcattaagtcaataagtc	11	17	6	7	0	5	2	3	2	2	0	7	2	5	2	0	1	0	1	0	1	4	6	rs374482089		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:152730807C>G	ENST00000367255.5	-	43	6869	c.6268G>C	c.(6268-6270)Gaa>Caa	p.E2090Q	SYNE1_ENST00000423061.1_Missense_Mutation_p.E2097Q|SYNE1_ENST00000265368.4_Missense_Mutation_p.E2090Q|SYNE1_ENST00000448038.1_Missense_Mutation_p.E2097Q|RNA5SP223_ENST00000365174.1_RNA|SYNE1_ENST00000341594.5_Missense_Mutation_p.E2127Q	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2090					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)		TTCTGATATTCTCTCATTAAG	0.368										HNSCC(10;0.0054)																											p.E2097Q		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G6289C						PASS	.	C	GLN/GLU,GLN/GLU	0,4406		0,0,2203	98	96	96		6268,6289	5.9	1	6		96	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	SYNE1	NM_182961.3,NM_033071.3	29,29	0,1,6502	GG,GC,CC		0.0116,0.0,0.0077	benign,benign	2090/8798,2097/8750	152730807	1,13005	2203	4300	6503	SO:0001583	missense	23345	exon43			GATATTCTCTCAT	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.6268G>C	6.37:g.152730807C>G	ENSP00000356224:p.Glu2090Gln	83	0	0		85	43	0.505882	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	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	14.85	2.658164	0.47467	0.0	1.16E-4	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.31510	1.49;1.49;1.49;1.49;1.49	5.92	5.92	0.95590	.	0.192526	0.36134	N	0.002765	T	0.18841	0.0452	L	0.59436	1.845	0.80722	D	1	P;B;B;B	0.38250	0.624;0.011;0.023;0.019	B;B;B;B	0.39706	0.307;0.005;0.008;0.011	T	0.02244	-1.1189	10	0.12430	T	0.62	.	14.4744	0.67537	0.0:0.9305:0.0:0.0695	.	2073;2090;2090;2097	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	Q	2090;2097;2090;2097;2127	ENSP00000356224:E2090Q;ENSP00000396024:E2097Q;ENSP00000265368:E2090Q;ENSP00000390975:E2097Q;ENSP00000341887:E2127Q	ENSP00000265368:E2090Q	E	-	1	0	SYNE1	152772500	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.922000	0.63404	2.822000	0.97130	0.650000	0.86243	GAA	.	.	weak		0.368	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		G	152730807	C	G	152730807	3	3	23	1	0	0	0	0	1	0	0	0	15460	922	32	4	20614	4	SYNE1	6	152730807	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	14538313	152730807	18384260	288	7732											
TCP10	6953	hgsc.bcm.edu	37	chr6	167786686	167786686	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	catgtcctgtctggagggagCggcgtgcagagctcctggaa	7	8	16	10	2	1	1	0	0	1	1	3	4	3	4	2	4	3	2	2	4	1	0	rs140649985	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:167786686C>T	ENST00000397829.4	-	8	1119	c.952G>A	c.(952-954)Gct>Act	p.A318T	TCP10_ENST00000366827.2_Intron	NM_004610.3	NP_004601.3	Q12799	TCP10_HUMAN	t-complex 10	345						cytosol (GO:0005829)				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)		CTGGAGGGAGCGGCGTGCAGA	0.532																																					p.A318T		Atlas-SNP	.											.	TCP10	35	.	0			c.G952A						PASS	.	C	THR/ALA	5,3699		0,5,1847	86	91	89		952	-3.3	0	6	dbSNP_134	89	45,8151		0,45,4053	no	missense	TCP10	NM_004610.3	58	0,50,5900	TT,TC,CC		0.549,0.135,0.4202	probably-damaging	318/327	167786686	50,11850	1852	4098	5950	SO:0001583	missense	6953	exon8			AGGGAGCGGCGTG	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.952G>A	6.37:g.167786686C>T	ENSP00000380929:p.Ala318Thr	173	0	0		188	49	0.260638	NM_004610	Q5JR60|Q6P4F4	Missense_Mutation	SNP	ENST00000397829.4	37	CCDS43527.1	18	0.008241758241758242	2	0.0040650406504065045	1	0.0027624309392265192	5	0.008741258741258742	10	0.013192612137203167	c	13.11	2.137893	0.37728	0.00135	0.00549	ENSG00000203690	ENST00000397829	T	0.27890	1.64	1.64	-3.29	0.05017	.	.	.	.	.	T	0.03178	0.0093	N	0.14661	0.345	0.09310	N	0.999998	P	0.45126	0.851	B	0.24848	0.056	T	0.23547	-1.0185	9	0.87932	D	0	.	4.2044	0.10481	0.3777:0.3043:0.3179:0.0	.	345	Q12799	TCP10_HUMAN	T	318	ENSP00000380929:A318T	ENSP00000380929:A318T	A	-	1	0	TCP10	167706676	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.523000	0.06230	-1.547000	0.01715	0.467000	0.42956	GCT	C|0.994;T|0.006	0.006	strong		0.532	TCP10-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365570.1	NM_004610		T	167786686	C	T	167786686	3	4	23	1	0	0	0	0	1	0	0	0	15725	768	27	1	32	1	TCP10	6	167786686	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	15055879	167786686	3328381	289	7733											
GPR146	115330	hgsc.bcm.edu	37	chr7	1097430	1097430	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccccgagctcccggtgggcGctgtggagtgtgggcggcga	3	6	19	13	5	0	0	0	0	0	0	1	3	1	1	3	5	1	2	3	5	0	0	rs61742514	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:1097430G>A	ENST00000397095.1	+	2	502	c.279G>A	c.(277-279)gcG>gcA	p.A93A	C7orf50_ENST00000397098.3_Intron|GPR146_ENST00000297468.3_Silent_p.A93A|C7orf50_ENST00000397100.2_Intron|C7orf50_ENST00000488073.1_Intron|RP11-449P15.1_ENST00000549241.1_RNA|C7orf50_ENST00000357429.6_Intron			Q96CH1	GP146_HUMAN	G protein-coupled receptor 146	93						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|ovary(1)|skin(1)	8		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.74e-15)		CCCGGTGGGCGCTGTGGAGTG	0.667													g|||	45	0.00898562	0.0	0.0029	5008	,	,		18213	0.0		0.0318	False		,,,				2504	0.0112				p.A93A		Atlas-SNP	.											.	GPR146	20	.	0			c.G279A						PASS	.		,,,	30,4376	34.3+/-65.2	0,30,2173	35	37	36		,,,279	-10.2	0	7	dbSNP_129	36	313,8285	110.2+/-170.6	9,295,3995	no	intron,intron,intron,coding-synonymous	C7orf50,GPR146	NM_001134395.1,NM_001134396.1,NM_032350.5,NM_138445.2	,,,	9,325,6168	AA,AG,GG		3.6404,0.6809,2.6376	,,,	,,,93/334	1097430	343,12661	2203	4299	6502	SO:0001819	synonymous_variant	115330	exon1			GTGGGCGCTGTGG	BC014241	CCDS5321.1	7p22.3	2012-08-21			ENSG00000164849	ENSG00000164849		"GPCR / Class A : Orphans"	21718	protein-coding gene	gene with protein product							Standard	NM_138445		Approved	PGR8	uc003sjy.1	Q96CH1	OTTHUMG00000023934	ENST00000397095.1:c.279G>A	7.37:g.1097430G>A		78	0	0		67	36	0.537313	NM_138445	Q86SP5	Silent	SNP	ENST00000397095.1	37	CCDS5321.1																																																																																			G|0.978;A|0.022	0.022	strong		0.667	GPR146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206855.1	NM_138445		A	1097430	G	A	1097430	2	1	23	1	0	0	0	0	0	0	0	1	6660	1074	38	1		1	GPR146	7	1097430	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10		1097430	158041233	290	7734											
C7orf27	221927	hgsc.bcm.edu	37	chr7	2582878	2582878	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccaaagccaggggtcccaTgtgggtgggacccaggcagc	8	4	15	14	0	0	0	0	0	0	0	1	1	1	1	5	5	2	1	5	5	1	0	rs151317339	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:2582878T>C	ENST00000340611.4	-	6	1139	c.883A>G	c.(883-885)Atg>Gtg	p.M295V	BRAT1_ENST00000473879.1_5'Flank	NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	295					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						AGGGGTCCCATGTGGGTGGGA	0.647													T|||	3	0.000599042	0.0023	0.0	5008	,	,		14712	0.0		0.0	False		,,,				2504	0.0				p.M295V		Atlas-SNP	.											.	BRAT1	57	.	0			c.A883G						PASS	.	T	VAL/MET	1,4405	2.1+/-5.4	0,1,2202	58	61	60		883	4	0	7	dbSNP_134	60	5,8595	3.7+/-12.6	0,5,4295	yes	missense	BRAT1	NM_152743.3	21	0,6,6497	CC,CT,TT		0.0581,0.0227,0.0461	benign	295/822	2582878	6,13000	2203	4300	6503	SO:0001583	missense	221927	exon6			GTCCCATGTGGGT	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.883A>G	7.37:g.2582878T>C	ENSP00000339637:p.Met295Val	82	0	0		94	47	0.5	NM_152743	A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	Missense_Mutation	SNP	ENST00000340611.4	37	CCDS5334.1	.	.	.	.	.	.	.	.	.	.	T	0.409	-0.914401	0.02415	2.27E-4	5.81E-4	ENSG00000106009	ENST00000340611	T	0.67698	-0.28	5.85	4.02	0.46733	Armadillo-type fold (1);	0.985177	0.08314	N	0.964822	T	0.43166	0.1235	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31916	-0.9926	10	0.19590	T	0.45	-0.4835	5.0952	0.14729	0.1497:0.6269:0.1447:0.0787	.	295	Q6PJG6	BRAT1_HUMAN	V	295	ENSP00000339637:M295V	ENSP00000339637:M295V	M	-	1	0	BRAT1	2549404	0.006000	0.16342	0.001000	0.08648	0.031000	0.12232	0.555000	0.23422	0.788000	0.33755	-0.146000	0.13790	ATG	T|1.000;C|0.000	0.000	strong		0.647	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239305.2	NM_152743		C	2582878	T	C	2582878	3	2	23	1	0	0	0	0	1	0	0	0	2384	1464	51	3	1618	3	C7orf27	7	2582878	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	1485448	2582878	156555785	291	7735											
USP42	84132	hgsc.bcm.edu	37	chr7	6175526	6175526	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaagcacatattacccaggCactcagtaatcctggggacg	12	7	10	12	1	1	0	1	0	0	0	2	1	2	1	2	3	2	4	2	3	4	3	rs61757573	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:6175526C>T	ENST00000306177.5	+	4	655	c.497C>T	c.(496-498)gCa>gTa	p.A166V		NM_032172.2	NP_115548.1	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	166	USP.				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)		ATTACCCAGGCACTCAGTAAT	0.348													C|||	8	0.00159744	0.0	0.0058	5008	,	,		16238	0.0		0.001	False		,,,				2504	0.0031				p.A166V		Atlas-SNP	.											.	USP42	138	.	0			c.C497T						PASS	.	C	VAL/ALA	2,3760		0,2,1879	119	110	113		497	5.2	1	7	dbSNP_129	113	42,8208		0,42,4083	yes	missense	USP42	NM_032172.2	64	0,44,5962	TT,TC,CC		0.5091,0.0532,0.3663	benign	166/1317	6175526	44,11968	1881	4125	6006	SO:0001583	missense	84132	exon4			CCCAGGCACTCAG	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.497C>T	7.37:g.6175526C>T	ENSP00000301962:p.Ala166Val	176	0	0		170	69	0.405882	NM_032172	A2RUE3|B5MDA5|Q0VIN8|Q3C166|Q6P9B4	Missense_Mutation	SNP	ENST00000306177.5	37	CCDS47535.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	19.15	3.771386	0.69992	5.32E-4	0.005091	ENSG00000106346	ENST00000306177;ENST00000465073;ENST00000426246	T;T;T	0.02709	4.19;4.19;4.19	5.19	5.19	0.71726	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.091899	0.47455	D	0.000230	T	0.03178	0.0093	N	0.21373	0.66	0.35910	D	0.831063	P;P;P	0.41597	0.712;0.756;0.756	P;P;P	0.49953	0.493;0.627;0.627	T	0.54330	-0.8310	10	0.40728	T	0.16	.	13.4431	0.61125	0.0:0.9214:0.0:0.0786	rs61757573	166;166;166	Q9H9J4-2;Q9H9J4;A4D2N6	.;UBP42_HUMAN;.	V	166;99;12	ENSP00000301962:A166V;ENSP00000430568:A99V;ENSP00000408217:A12V	ENSP00000301962:A166V	A	+	2	0	USP42	6142052	0.755000	0.28372	1.000000	0.80357	0.997000	0.91878	1.296000	0.33389	2.578000	0.87016	0.467000	0.42956	GCA	C|0.999;T|0.001	0.001	strong		0.348	USP42-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324262.3	XM_166526		T	6175526	C	T	6175526	3	4	23	1	0	0	0	0	1	0	0	0	17088	710	25	2	507	2	USP42	7	6175526	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	3592648	6175526	152963137	292	7736											
ETV1	2115	hgsc.bcm.edu	37	chr7	13950864	13950864	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcagtggtggacaacttaaCttctgttctgctgggatgag	8	14	12	7	0	3	1	1	1	2	0	3	3	3	3	0	3	3	2	0	3	2	4			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:13950864C>T	ENST00000430479.1	-	10	1538	c.871G>A	c.(871-873)Ggc>Agc	p.G291S	ETV1_ENST00000399357.3_Splice_Site_p.G188S|ETV1_ENST00000420159.2_Splice_Site_p.G233S|ETV1_ENST00000343495.5_Splice_Site_p.G273S|ETV1_ENST00000405192.2_Intron|ETV1_ENST00000403685.1_Splice_Site_p.G273S|ETV1_ENST00000403527.1_Splice_Site_p.G251S|ETV1_ENST00000242066.5_Splice_Site_p.G273S|ETV1_ENST00000476720.2_5'Flank|ETV1_ENST00000405358.4_Splice_Site_p.G305S|ETV1_ENST00000405218.2_Splice_Site_p.G291S	NM_004956.4	NP_004947.2	P50549	ETV1_HUMAN	ets variant 1	291					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						GACAACTTAACTTCTGTTCTG	0.383			T	"EWSR1, TMPRSS2, SLC45A3, C15orf21, HNRNPA2B1. ACSL3"	"Ewing sarcoma, prostate"																																p.G291S		Atlas-SNP	.		Dom	yes		7	7p22	2115	ets variant gene 1		"M, E"	.	ETV1	138	.	0			c.G871A						PASS	.						81	80	81					7																	13950864		1904	4108	6012	SO:0001630	splice_region_variant	2115	exon10			ACTTAACTTCTGT		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.871+1G>A	7.37:g.13950864C>T		134	0	0		115	14	0.121739	NM_004956	A4D118|B2R768|B7Z2I4|B7Z618|B7Z9P2|C9JT37|E9PHB1|F5GXR2|O75849|Q4KMQ6|Q59GA7|Q6AI30|Q9UQ71|Q9Y636	Missense_Mutation	SNP	ENST00000430479.1	37	CCDS55088.1	.	.	.	.	.	.	.	.	.	.	C	36	5.733116	0.96856	.	.	ENSG00000006468	ENST00000430479;ENST00000242066;ENST00000343495;ENST00000420159;ENST00000399357;ENST00000405358;ENST00000403527;ENST00000405218;ENST00000403685;ENST00000438956	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	5.26	5.26	0.73747	.	2.792530	0.00481	N	0.000121	T	0.54464	0.1860	L	0.60067	1.865	0.80722	D	1	.	.	.	.	.	.	T	0.39820	-0.9595	7	.	.	.	.	19.7471	0.96257	0.0:1.0:0.0:0.0	.	.	.	.	S	291;273;273;233;188;305;251;291;273;233	ENSP00000405327:G291S;ENSP00000242066:G273S;ENSP00000340853:G273S;ENSP00000411626:G233S;ENSP00000382293:G188S;ENSP00000384085:G305S;ENSP00000384138:G251S;ENSP00000385551:G291S;ENSP00000385686:G273S;ENSP00000393078:G233S	.	G	-	1	0	ETV1	13917389	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.776000	0.85560	2.838000	0.97847	0.591000	0.81541	GGC	.	.	none		0.383	ETV1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326111.1	NM_004956	Missense_Mutation	T	13950864	C	T	13950864	5	4	23	1	0	0	0	0	0	0	1	0	5279	579	20	2	582	2	ETV1	7	13950864	Splice_Site	SNP	C	TCGA-G8-6325-01A-11D-2210-10	7775338	13950864	145187799	293	7737											
GPNMB	10457	hgsc.bcm.edu	37	chr7	23313745	23313745	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtggtcagaagcaaaggcCtgagtgtctttctcaaccgt	10	11	11	9	1	3	2	2	1	2	1	4	2	3	2	2	2	2	1	2	2	3	1	rs78340800	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:23313745C>T	ENST00000381990.2	+	11	1782	c.1621C>T	c.(1621-1623)Ctg>Ttg	p.L541L	GPNMB_ENST00000478451.1_3'UTR|GPNMB_ENST00000258733.4_Silent_p.L529L|GPNMB_ENST00000539136.1_Silent_p.L430L|GPNMB_ENST00000453162.2_Silent_p.L483L	NM_001005340.1|NM_002510.2	NP_001005340.1|NP_002501.1	Q14956	GPNMB_HUMAN	glycoprotein (transmembrane) nmb	541					bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|negative regulation of cell proliferation (GO:0008285)|osteoblast differentiation (GO:0001649)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)			breast(5)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(3)|stomach(2)	41			GBM - Glioblastoma multiforme(13;0.154)			AAGCAAAGGCCTGAGTGTCTT	0.388													C|||	10	0.00199681	0.0	0.0	5008	,	,		17461	0.0		0.0099	False		,,,				2504	0.0				p.L541L		Atlas-SNP	.											.	GPNMB	88	.	0			c.C1621T						PASS	.	C	,	7,4399	12.9+/-30.5	0,7,2196	84	85	85		1621,1585	4.2	0.2	7	dbSNP_132	85	59,8541	35.9+/-90.5	0,59,4241	no	coding-synonymous,coding-synonymous	GPNMB	NM_001005340.1,NM_002510.2	,	0,66,6437	TT,TC,CC		0.686,0.1589,0.5075	,	541/573,529/561	23313745	66,12940	2203	4300	6503	SO:0001819	synonymous_variant	10457	exon11			AAAGGCCTGAGTG	X76534	CCDS5380.1, CCDS34610.1	7p	2008-07-18			ENSG00000136235	ENSG00000136235			4462	protein-coding gene	gene with protein product	"transmembrane glycoprotein", "glycoprotein NMB", "glycoprotein nmb-like protein", "osteoactivin"	604368				7814155	Standard	NM_002510		Approved	NMB, HGFIN	uc003swc.3	Q14956	OTTHUMG00000022811	ENST00000381990.2:c.1621C>T	7.37:g.23313745C>T		106	0	0		122	55	0.45082	NM_001005340	A4D155|Q6UVX1|Q8N1A1	Silent	SNP	ENST00000381990.2	37	CCDS34610.1																																																																																			C|0.995;T|0.005	0.005	strong		0.388	GPNMB-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327152.1	NM_001005340		T	23313745	C	T	23313745	2	4	23	1	0	0	0	0	0	0	0	1	6628	680	24	2		2	GPNMB	7	23313745	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	9362881	23313745	135824918	294	7738											
CHN2	1124	hgsc.bcm.edu	37	chr7	29539639	29539639	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtggtagacatatgcattcGggaaattgaagcaagaggtt	13	10	14	4	1	0	3	0	1	0	2	1	4	0	4	0	4	2	4	0	4	5	5			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:29539639G>A	ENST00000222792.6	+	9	1426	c.896G>A	c.(895-897)cGg>cAg	p.R299Q	CHN2_ENST00000539406.1_Missense_Mutation_p.R374Q|CHN2_ENST00000424025.2_Missense_Mutation_p.R118Q|CHN2_ENST00000421775.2_Intron|CHN2_ENST00000410098.1_3'UTR|CHN2_ENST00000439711.2_Missense_Mutation_p.R163Q|CHN2_ENST00000539389.1_Missense_Mutation_p.R155Q|CHN2_ENST00000409041.4_Missense_Mutation_p.R163Q|CHN2_ENST00000435288.2_Intron|CHN2_ENST00000546235.1_Missense_Mutation_p.R284Q|CHN2_ENST00000495789.2_Missense_Mutation_p.R312Q	NM_004067.2	NP_004058.1	P52757	CHIO_HUMAN	chimerin 2	299	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				positive regulation of GTPase activity (GO:0043547)|positive regulation of signal transduction (GO:0009967)|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)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(3)|large_intestine(2)|lung(12)|ovary(2)|urinary_tract(2)	23						ATATGCATTCGGGAAATTGAA	0.378																																					p.R299Q	Ovarian(1;44 48 13232 18918 31480)	Atlas-SNP	.											.	CHN2	98	.	0			c.G896A						PASS	.						69	63	65					7																	29539639		2203	4300	6503	SO:0001583	missense	1124	exon9			GCATTCGGGAAAT	L29126	CCDS5420.1	7p15.3	2013-02-14	2012-10-17		ENSG00000106069	ENSG00000106069		"Rho GTPase activating proteins", "SH2 domain containing"	1944	protein-coding gene	gene with protein product	"beta chimerin", "chimaerin 2"	602857	"chimerin (chimaerin) 2"			8175705	Standard	XM_005249602		Approved	ARHGAP3, RhoGAP3	uc003szz.3	P52757	OTTHUMG00000023063	ENST00000222792.6:c.896G>A	7.37:g.29539639G>A	ENSP00000222792:p.Arg299Gln	110	0	0		67	9	0.134328	NM_004067	A4D1A2|B3VCF1|B3VCF2|B3VCF3|B3VCF7|B3VCG1|C9J7B0|E9PGE0|F8QPL9|Q2M203|Q75MM2	Missense_Mutation	SNP	ENST00000222792.6	37	CCDS5420.1	.	.	.	.	.	.	.	.	.	.	G	13.24	2.177801	0.38413	.	.	ENSG00000106069	ENST00000539406;ENST00000222792;ENST00000495789;ENST00000539389;ENST00000546235;ENST00000446446;ENST00000409041;ENST00000424025;ENST00000439711	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	5.6	5.6	0.85130	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.109458	0.64402	D	0.000006	T	0.07458	0.0188	N	0.10945	0.07	0.80722	D	1	B;B;B;B;B;B;P;B;B;B;B;B;B;B	0.39665	0.031;0.006;0.046;0.206;0.051;0.104;0.682;0.051;0.224;0.055;0.014;0.083;0.224;0.014	B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.24006	0.002;0.004;0.002;0.015;0.01;0.037;0.05;0.015;0.016;0.006;0.002;0.016;0.01;0.002	T	0.36915	-0.9728	10	0.28530	T	0.3	.	12.8884	0.58057	0.0753:0.0:0.9247:0.0	.	92;284;312;374;118;118;163;163;163;155;299;69;163;299	B7Z215;B7Z1W9;B7Z1V0;F5H003;B3VCF1;B3VCF2;B3VCF5;B3VCF7;B3VCF6;B3VCG1;A4D1A2;B3VCF8;E9PGE0;P52757	.;.;.;.;.;.;.;.;.;.;.;.;.;CHIO_HUMAN	Q	374;299;312;155;284;124;163;118;163	ENSP00000444063:R374Q;ENSP00000222792:R299Q;ENSP00000438587:R312Q;ENSP00000440526:R155Q;ENSP00000442812:R284Q;ENSP00000396867:R124Q;ENSP00000386849:R163Q;ENSP00000406337:R118Q;ENSP00000387425:R163Q	ENSP00000222792:R299Q	R	+	2	0	CHN2	29506164	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	4.894000	0.63206	2.800000	0.96347	0.455000	0.32223	CGG	.	.	none		0.378	CHN2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214228.2	NM_004067		A	29539639	G	A	29539639	3	1	23	1	0	0	0	0	1	0	0	0	3365	1116	39	1	1098	1	CHN2	7	29539639	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	6225894	29539639	129599024	295	7739											
GARS	2617	hgsc.bcm.edu	37	chr7	30634548	30634548	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgcaggctcatgccctctcCgcgtccagtgctgcttagag	5	9	11	16	3	2	1	1	0	1	1	4	1	3	1	4	1	3	4	4	1	1	1	rs62636572	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:30634548C>T	ENST00000389266.3	+	1	252	c.11C>T	c.(10-12)cCg>cTg	p.P4L	AC005154.6_ENST00000579174.1_RNA|AC005154.6_ENST00000580440.1_RNA|AC005154.6_ENST00000583664.1_RNA|AC005154.6_ENST00000584372.1_RNA|AC005154.6_ENST00000578994.1_RNA|AC005154.6_ENST00000584199.1_RNA|AC005154.6_ENST00000582549.1_RNA|AC005154.6_ENST00000581665.1_RNA	NM_002047.2	NP_002038.2	P41250	SYG_HUMAN	glycyl-tRNA synthetase	4					cell death (GO:0008219)|diadenosine tetraphosphate biosynthetic process (GO:0015966)|gene expression (GO:0010467)|glycyl-tRNA aminoacylation (GO:0006426)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|secretory granule (GO:0030141)	ATP binding (GO:0005524)|glycine-tRNA ligase activity (GO:0004820)|protein dimerization activity (GO:0046983)			breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|urinary_tract(1)	24					Glycine(DB00145)	ATGCCCTCTCCGCGTCCAGTG	0.711													C|||	42	0.00838658	0.0	0.0245	5008	,	,		14101	0.0		0.0239	False		,,,				2504	0.001				p.P4L		Atlas-SNP	.											.	GARS	52	.	0			c.C11T						PASS	.	C	LEU/PRO	10,3978		0,10,1984	7	8	8		11	-1.4	0	7	dbSNP_129	8	113,8037		0,113,3962	yes	missense	GARS	NM_002047.2	98	0,123,5946	TT,TC,CC		1.3865,0.2508,1.0133	benign	4/740	30634548	123,12015	1994	4075	6069	SO:0001583	missense	2617	exon1			CCTCTCCGCGTCC	AK074524	CCDS43564.1	7p15	2014-09-17	2004-02-13		ENSG00000106105	ENSG00000106105	6.1.1.14	"Aminoacyl tRNA synthetases / Class II"	4162	protein-coding gene	gene with protein product	"glycine tRNA ligase"	600287	"Charcot-Marie-Tooth neuropathy 2D"	CMT2D		8595897, 8872480	Standard	NM_002047		Approved	GlyRS, DSMAV, SMAD1	uc003tbm.3	P41250	OTTHUMG00000152769	ENST00000389266.3:c.11C>T	7.37:g.30634548C>T	ENSP00000373918:p.Pro4Leu	23	0	0		9	7	0.777778	NM_002047	B3KQA2|B4DIA0|Q969Y1	Missense_Mutation	SNP	ENST00000389266.3	37	CCDS43564.1	29	0.013278388278388278	0	0.0	11	0.03038674033149171	0	0.0	18	0.023746701846965697	C	0.026	-1.372300	0.01214	0.002508	0.013865	ENSG00000106105	ENST00000389266	T	0.80566	-1.39	3.33	-1.39	0.08997	.	0.647368	0.15500	N	0.259091	T	0.29817	0.0745	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25641	-1.0126	10	0.10377	T	0.69	0.9595	7.0049	0.24830	0.0:0.4002:0.0:0.5998	rs62636572	4	P41250	SYG_HUMAN	L	4	ENSP00000373918:P4L	ENSP00000373918:P4L	P	+	2	0	GARS	30601073	0.000000	0.05858	0.011000	0.14972	0.317000	0.28152	-0.624000	0.05540	-0.325000	0.08577	-0.133000	0.14855	CCG	C|0.986;T|0.014	0.014	strong		0.711	GARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327735.1	NM_002047		T	30634548	C	T	30634548	3	4	23	1	0	0	0	0	1	0	0	0	6250	652	23	1	13	1	GARS	7	30634548	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1094909	30634548	128504115	296	7740											
HECW1	23072	hgsc.bcm.edu	37	chr7	43506113	43506113	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accttgctgctgcagtccccAgcggtcaagttcatcaccaa	9	9	8	15	1	3	0	3	0	0	0	4	0	4	0	4	1	4	4	4	1	2	2	rs138489968	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:43506113A>C	ENST00000395891.2	+	15	3464	c.2859A>C	c.(2857-2859)ccA>ccC	p.P953P	HECW1_ENST00000453890.1_Silent_p.P919P	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	953					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						TGCAGTCCCCAGCGGTCAAGT	0.498													A|||	29	0.00579073	0.0023	0.0058	5008	,	,		15535	0.001		0.0169	False		,,,				2504	0.0041				p.P953P		Atlas-SNP	.											.	HECW1	540	.	0			c.A2859C						PASS	.	A		12,3884		0,12,1936	113	107	109		2859	-4.4	0.8	7	dbSNP_134	109	186,8096		2,182,3957	no	coding-synonymous	HECW1	NM_015052.3		2,194,5893	CC,CA,AA		2.2458,0.308,1.6259		953/1607	43506113	198,11980	1948	4141	6089	SO:0001819	synonymous_variant	23072	exon15			GTCCCCAGCGGTC	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.2859A>C	7.37:g.43506113A>C		57	0	0		72	36	0.5	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	ENST00000395891.2	37	CCDS5469.2																																																																																			A|0.990;C|0.010	0.010	strong		0.498	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		C	43506113	A	C	43506113	2	2	23	1	0	0	0	0	0	0	0	1	7051	175	7	5		5	HECW1	7	43506113	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	12871565	43506113	115632550	297	7741											
ADCY1	107	hgsc.bcm.edu	37	chr7	45701762	45701762	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atgcactgccggaaaatgttCaaggccgagatccccttctc	10	9	9	13	2	2	1	1	0	1	1	4	3	3	2	4	2	2	2	4	2	3	2	rs61729596	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:45701762C>T	ENST00000297323.7	+	8	1576	c.1554C>T	c.(1552-1554)ttC>ttT	p.F518F	ADCY1_ENST00000432715.1_Silent_p.F293F	NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	518	Interaction with calmodulin. {ECO:0000250}.				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)	GGAAAATGTTCAAGGCCGAGA	0.542													C|||	50	0.00998403	0.0	0.0101	5008	,	,		19969	0.0		0.0239	False		,,,				2504	0.0194				p.F518F		Atlas-SNP	.											.	ADCY1	187	.	0			c.C1554T						PASS	.	C		20,4386	27.2+/-55.0	0,20,2183	84	70	75		1554	3.9	1	7	dbSNP_129	75	175,8425	79.2+/-141.9	3,169,4128	no	coding-synonymous	ADCY1	NM_021116.2		3,189,6311	TT,TC,CC		2.0349,0.4539,1.4993		518/1120	45701762	195,12811	2203	4300	6503	SO:0001819	synonymous_variant	107	exon8			AATGTTCAAGGCC	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.1554C>T	7.37:g.45701762C>T		106	0	0		94	43	0.457447	NM_021116	A4D2L8|Q75MI1	Silent	SNP	ENST00000297323.7	37	CCDS34631.1																																																																																			C|0.986;T|0.014	0.014	strong		0.542	ADCY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340055.2	NM_021116		T	45701762	C	T	45701762	2	4	23	1	0	0	0	0	0	0	0	1	292	825	29	2		2	ADCY1	7	45701762	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	2195649	45701762	113436901	298	7742											
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47851578	47851578	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tatagagagtgaagtgcacaGacacagccctggtgctgcgg	11	7	14	9	1	0	3	0	1	0	2	0	4	0	3	1	2	4	2	1	2	3	2	rs140456142		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:47851578G>A	ENST00000289672.2	-	50	7468	c.7418C>T	c.(7417-7419)tCt>tTt	p.S2473F	PKD1L1_ENST00000462350.1_5'Flank|C7orf69_ENST00000258776.4_Intron|C7orf69_ENST00000418326.2_Intron	NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2473					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						GAAGTGCACAGACACAGCCCT	0.592													G|||	1	0.000199681	0.0	0.0	5008	,	,		19929	0.0		0.0	False		,,,				2504	0.001				p.S2473F		Atlas-SNP	.											.	PKD1L1	328	.	0			c.C7418T						PASS	.	G	,PHE/SER	2,4404		0,2,2201	79	64	69		,7418	4.6	0.8	7	dbSNP_134	69	10,8588		0,10,4289	yes	intron,missense	C7orf69,PKD1L1	NM_025031.2,NM_138295.3	,155	0,12,6490	AA,AG,GG		0.1163,0.0454,0.0923	,probably-damaging	,2473/2850	47851578	12,12992	2203	4299	6502	SO:0001583	missense	168507	exon50			TGCACAGACACAG	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.7418C>T	7.37:g.47851578G>A	ENSP00000289672:p.Ser2473Phe	133	0	0		118	56	0.474576	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	G	8.910	0.958416	0.18507	4.54E-4	0.001163	ENSG00000158683	ENST00000289672	T	0.61742	0.08	5.49	4.55	0.56014	Polycystin cation channel, PKD1/PKD2 (1);	0.725348	0.12568	N	0.457613	T	0.34629	0.0904	N	0.10874	0.06	0.18873	N	0.999984	P	0.38922	0.651	B	0.39068	0.289	T	0.09357	-1.0678	10	0.09843	T	0.71	-19.6503	8.5081	0.33199	0.0:0.166:0.6623:0.1717	.	2473	Q8TDX9	PK1L1_HUMAN	F	2473	ENSP00000289672:S2473F	ENSP00000289672:S2473F	S	-	2	0	PKD1L1	47818103	0.001000	0.12720	0.800000	0.32199	0.787000	0.44495	0.791000	0.26915	2.573000	0.86826	0.453000	0.30009	TCT	G|0.999;A|0.001	0.001	strong		0.592	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		A	47851578	G	A	47851578	3	1	23	1	0	0	0	0	1	0	0	0	11973	942	33	2	1163	2	PKD1L1	7	47851578	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	2149816	47851578	111287085	299	7743											
C7orf57	136288	hgsc.bcm.edu	37	chr7	48086151	48086151	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	catccagaagagggcccttcGacttcgacatgaaaacagtt	13	8	9	11	2	0	3	0	1	0	2	3	5	1	3	2	1	1	1	2	1	3	3	rs111480809	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:48086151G>A	ENST00000348904.3	+	5	657	c.445G>A	c.(445-447)Gac>Aac	p.D149N	C7orf57_ENST00000430738.1_Missense_Mutation_p.D194N|C7orf57_ENST00000420324.1_Missense_Mutation_p.D194N|C7orf57_ENST00000539619.1_Missense_Mutation_p.D149N|C7orf57_ENST00000435376.1_Missense_Mutation_p.D27N	NM_001100159.2	NP_001093629.1	Q8NEG2	CG057_HUMAN	chromosome 7 open reading frame 57	149										breast(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	9						AGGGCCCTTCGACTTCGACAT	0.493													G|||	26	0.00519169	0.0	0.0101	5008	,	,		19923	0.0		0.0169	False		,,,				2504	0.002				p.D149N		Atlas-SNP	.											C7orf57_ENST00000348904,colon,carcinoma,0,2	C7orf57	59	2	0			c.G445A						PASS	.	G	ASN/ASP	5,3889		0,5,1942	61	57	59		445	4.6	1	7	dbSNP_132	59	103,8171		0,103,4034	yes	missense	C7orf57	NM_001100159.1	23	0,108,5976	AA,AG,GG		1.2449,0.1284,0.8876	probably-damaging	149/296	48086151	108,12060	1947	4137	6084	SO:0001583	missense	136288	exon5			CCCTTCGACTTCG	BC031107	CCDS47583.1, CCDS59054.1, CCDS75594.1	7p12.3	2011-11-25			ENSG00000164746	ENSG00000164746			22247	protein-coding gene	gene with protein product							Standard	NM_001100159		Approved		uc003toh.5	Q8NEG2	OTTHUMG00000155808	ENST00000348904.3:c.445G>A	7.37:g.48086151G>A	ENSP00000335500:p.Asp149Asn	75	0	0		91	43	0.472527	NM_001100159	C9JBJ8	Missense_Mutation	SNP	ENST00000348904.3	37	CCDS47583.1	16	0.007326007326007326	0	0.0	4	0.011049723756906077	0	0.0	12	0.0158311345646438	G	17.67	3.447949	0.63178	0.001284	0.012449	ENSG00000164746	ENST00000420324;ENST00000435376;ENST00000430738;ENST00000348904;ENST00000539619	T;T;T;T;T	0.58060	0.36;0.36;0.36;0.36;0.36	5.44	4.56	0.56223	.	0.056720	0.64402	D	0.000001	T	0.55016	0.1894	M	0.76574	2.34	0.40682	D	0.982317	D;P	0.89917	1.0;0.638	D;B	0.73380	0.98;0.167	T	0.69022	-0.5255	10	0.59425	D	0.04	-23.6274	12.28	0.54759	0.0829:0.0:0.9171:0.0	.	27;149	C9JBJ8;Q8NEG2	.;CG057_HUMAN	N	194;27;194;149;149	ENSP00000394648:D194N;ENSP00000391652:D27N;ENSP00000410944:D194N;ENSP00000335500:D149N;ENSP00000442474:D149N	ENSP00000335500:D149N	D	+	1	0	C7orf57	48052676	1.000000	0.71417	0.965000	0.40720	0.991000	0.79684	4.434000	0.59935	1.425000	0.47237	0.655000	0.94253	GAC	G|0.989;A|0.011	0.011	strong		0.493	C7orf57-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341745.1	NM_001100159		A	48086151	G	A	48086151	3	1	23	1	0	0	0	0	1	0	0	0	2406	1058	37	1	459	1	C7orf57	7	48086151	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	234573	48086151	111052512	300	7744											
CHCHD2	51142	hgsc.bcm.edu	37	chr7	56172086	56172086	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggggcgcagcagcagaagAgccaactgcagatgggggtg	10	3	18	10	2	0	3	0	0	0	3	0	3	0	3	2	4	5	4	2	4	2	0			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:56172086A>C	ENST00000395422.3	-	2	295	c.133T>G	c.(133-135)Tct>Gct	p.S45A		NM_016139.2	NP_057223.1	Q9Y6H1	CHCH2_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 2	45						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)			GCAGCAGAAGAGCCAACTGCA	0.637																																					p.S45A		Atlas-SNP	.											.	CHCHD2	10	.	0			c.T133G						PASS	.						13	16	15					7																	56172086		2196	4288	6484	SO:0001583	missense	51142	exon2			CAGAAGAGCCAAC	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.133T>G	7.37:g.56172086A>C	ENSP00000378812:p.Ser45Ala	204	0	0		200	94	0.47	NM_016139	Q498C3|Q6NZ50	Missense_Mutation	SNP	ENST00000395422.3	37	CCDS5526.1	.	.	.	.	.	.	.	.	.	.	A	10.83	1.459974	0.26248	.	.	ENSG00000106153	ENST00000395422	T	0.40225	1.04	5.09	2.66	0.31614	.	0.447785	0.23465	N	0.047899	T	0.20047	0.0482	N	0.21194	0.64	0.27295	N	0.957738	B	0.02656	0.0	B	0.01281	0.0	T	0.16988	-1.0384	10	0.07813	T	0.8	.	3.1841	0.06594	0.5928:0.2281:0.1791:0.0	.	45	Q9Y6H1	CHCH2_HUMAN	A	45	ENSP00000378812:S45A	ENSP00000378812:S45A	S	-	1	0	CHCHD2	56139580	0.246000	0.23909	0.544000	0.28141	0.931000	0.56810	0.333000	0.19768	0.936000	0.37367	0.533000	0.62120	TCT	.	.	none		0.637	CHCHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251589.1	NM_016139		C	56172086	A	C	56172086	3	2	23	1	0	0	0	0	1	0	0	0	3318	304	11	5	334	5	CHCHD2	7	56172086	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	8085935	56172086	102966577	301	7745											
CCDC146	57639	hgsc.bcm.edu	37	chr7	76891535	76891535	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gagagaaagaacgagattttCgaaatttaagaaagatggaa	20	8	11	2	2	0	5	0	0	0	5	1	10	0	6	0	1	1	0	0	1	6	4	rs371350411		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:76891535C>T	ENST00000285871.4	+	9	1211	c.1084C>T	c.(1084-1086)Cga>Tga	p.R362*	CCDC146_ENST00000431197.1_Nonsense_Mutation_p.R108*|CCDC146_ENST00000415740.2_3'UTR	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	362										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)				ACGAGATTTTCGAAATTTAAG	0.423																																					p.R362X		Atlas-SNP	.											CCDC146,NS,carcinoma,0,2	CCDC146	87	2	0			c.C1084T						PASS	.	C	stop/ARG	0,4406		0,0,2203	99	98	98		1084	4.8	1	7		98	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained	CCDC146	NM_020879.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		362/956	76891535	1,13005	2203	4300	6503	SO:0001587	stop_gained	57639	exon9			GATTTTCGAAATT	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.1084C>T	7.37:g.76891535C>T	ENSP00000285871:p.Arg362*	74	0	0		102	13	0.127451	NM_020879	A8K8X6|Q9P223	Nonsense_Mutation	SNP	ENST00000285871.4	37	CCDS34671.1	.	.	.	.	.	.	.	.	.	.	C	38	6.998870	0.97990	0.0	1.16E-4	ENSG00000135205	ENST00000285871;ENST00000431197	.	.	.	5.78	4.82	0.62117	.	0.207319	0.41823	D	0.000813	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.9971	13.1907	0.59709	0.2483:0.7517:0.0:0.0	.	.	.	.	X	362;108	.	ENSP00000285871:R362X	R	+	1	2	AC007000.1	76729471	1.000000	0.71417	1.000000	0.80357	0.735000	0.41995	1.811000	0.38942	2.744000	0.94065	0.563000	0.77884	CGA	.	.	weak		0.423	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879		T	76891535	C	T	76891535	4	4	23	1	0	0	0	0	0	1	0	0	2782	876	31	1	1114	1	CCDC146	7	76891535	Nonsense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	20719449	76891535	82247128	302	7746											
CACNA2D1	781	hgsc.bcm.edu	37	chr7	81593541	81593541	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accacatatgctgagcgatgTcctgctccttgttttggtgc	6	14	10	11	1	0	1	0	1	0	0	2	2	2	1	3	1	4	3	3	1	1	4			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:81593541T>C	ENST00000356253.5	-	33	3000	c.2745A>G	c.(2743-2745)ggA>ggG	p.G915G	CACNA2D1_ENST00000535308.1_Silent_p.G115G|CACNA2D1_ENST00000356860.3_Silent_p.G903G			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	915					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)	CTGAGCGATGTCCTGCTCCTT	0.408																																					p.G903G		Atlas-SNP	.											.	CACNA2D1	191	.	0			c.A2709G						PASS	.						128	128	128					7																	81593541		2203	4300	6503	SO:0001819	synonymous_variant	781	exon33			GCGATGTCCTGCT	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.2745A>G	7.37:g.81593541T>C		97	0	0		121	8	0.0661157	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Silent	SNP	ENST00000356253.5	37																																																																																				.	.	none		0.408	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding				C	81593541	T	C	81593541	2	2	23	1	0	0	0	0	0	0	0	1	2550	1654	58	3		3	CACNA2D1	7	81593541	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	4702006	81593541	77545122	303	7747											
SEMA3E	9723	hgsc.bcm.edu	37	chr7	82996931	82996931	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagcgtgtgcctgggcaggcGgtaatgctcaggtttggaac	7	9	16	9	2	1	0	1	0	0	0	1	1	1	1	1	5	4	4	1	5	2	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:82996931G>A	ENST00000307792.3	-	17	2766	c.2299C>T	c.(2299-2301)Cgc>Tgc	p.R767C	SEMA3E_ENST00000427262.1_Missense_Mutation_p.R707C	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	767	Arg/Lys-rich (basic).				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)				CTGGGCAGGCGGTAATGCTCA	0.418																																					p.R767C		Atlas-SNP	.											.	SEMA3E	125	.	0			c.C2299T						PASS	.						172	172	172					7																	82996931		2203	4300	6503	SO:0001583	missense	9723	exon17			GCAGGCGGTAATG	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.2299C>T	7.37:g.82996931G>A	ENSP00000303212:p.Arg767Cys	249	0	0		233	112	0.480687	NM_012431	B4E1P1|Q75M94|Q75M97	Missense_Mutation	SNP	ENST00000307792.3	37	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.281561	0.80692	.	.	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514	T;T	0.36157	1.31;1.27	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.65396	0.2687	M	0.81802	2.56	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68727	-0.5332	10	0.87932	D	0	.	19.7061	0.96072	0.0:0.0:1.0:0.0	.	767	O15041	SEM3E_HUMAN	C	767;707;758	ENSP00000303212:R767C;ENSP00000405052:R707C	ENSP00000303212:R767C	R	-	1	0	SEMA3E	82834867	1.000000	0.71417	0.986000	0.45419	0.664000	0.39144	4.641000	0.61375	2.660000	0.90430	0.585000	0.79938	CGC	.	.	none		0.418	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431		A	82996931	G	A	82996931	3	1	23	1	0	0	0	0	1	0	0	0	14043	1116	39	1	32	1	SEMA3E	7	82996931	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1403390	82996931	76141732	304	7748											
SLC25A40	55972	hgsc.bcm.edu	37	chr7	87476292	87476292	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtacatctctaagaacagtAggagcccagcccctccaaag	13	6	9	13	0	1	1	0	0	1	1	3	2	2	2	4	2	4	2	4	2	5	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:87476292A>G	ENST00000341119.5	-	8	949	c.603T>C	c.(601-603)ccT>ccC	p.P201P		NM_018843.3	NP_061331.2	Q8TBP6	S2540_HUMAN	solute carrier family 25, member 40	201					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				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)					TAAGAACAGTAGGAGCCCAGC	0.393																																					p.P201P		Atlas-SNP	.											.	SLC25A40	32	.	0			c.T603C						PASS	.						99	106	104					7																	87476292		2203	4300	6503	SO:0001819	synonymous_variant	55972	exon8			AACAGTAGGAGCC	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.603T>C	7.37:g.87476292A>G		52	0	0		74	4	0.0540541	NM_018843	A8K483|D6W5P6|Q53GB1|Q9UHR1	Silent	SNP	ENST00000341119.5	37	CCDS5610.1																																																																																			.	.	none		0.393	SLC25A40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253677.5	NM_018843		G	87476292	A	G	87476292	2	3	23	1	0	0	0	0	0	0	0	1	14520	407	15	3		3	SLC25A40	7	87476292	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	4479361	87476292	71662371	305	7749											
DBF4	10926	hgsc.bcm.edu	37	chr7	87537188	87537188	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaaaatacatcgaaaagtgAaaataatattaggacgaaat	22	9	7	3	2	0	1	0	1	0	0	1	4	0	2	0	1	1	1	0	1	11	5	rs61747462	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:87537188A>G	ENST00000265728.1	+	12	2239	c.1735A>G	c.(1735-1737)Aaa>Gaa	p.K579E		NM_006716.3	NP_006707.1	Q9UBU7	DBF4A_HUMAN	DBF4 zinc finger	579					DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)	nucleoplasm (GO:0005654)	enzyme activator activity (GO:0008047)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|skin(3)	28	Esophageal squamous(14;0.00202)	Breast(660;0.0334)				TCGAAAAGTGAAAATAATATT	0.333													A|||	29	0.00579073	0.0008	0.013	5008	,	,		19546	0.0		0.0169	False		,,,				2504	0.002				p.K579E		Atlas-SNP	.											.	DBF4	67	.	0			c.A1735G						PASS	.	A	GLU/LYS	16,4388		0,16,2186	46	53	51		1735	4	1	7	dbSNP_129	51	99,8435		1,97,4169	no	missense	DBF4	NM_006716.3	56	1,113,6355	GG,GA,AA		1.1601,0.3633,0.8889	possibly-damaging	579/675	87537188	115,12823	2202	4267	6469	SO:0001583	missense	10926	exon12			AAAGTGAAAATAA	AF160876	CCDS5611.1	7q21.3	2014-02-17	2014-02-17		ENSG00000006634	ENSG00000006634		"Zinc fingers, DBF-type"	17364	protein-coding gene	gene with protein product	"activator of S phase kinase", "chiffon homolog (Drosophila)", "zinc finger, DBF-type containing 1", "DBF4 zinc finger A"	604281	"DBF4 homolog (S. cerevisiae)"			10373557, 10517317	Standard	NM_006716		Approved	ASK, chif, ZDBF1, DBF4A	uc003ujf.1	Q9UBU7	OTTHUMG00000131034	ENST00000265728.1:c.1735A>G	7.37:g.87537188A>G	ENSP00000265728:p.Lys579Glu	250	0	0		269	130	0.483271	NM_006716	A4D1D8|A8K954|O75226|Q75MS6|Q75N01|Q9Y2M6	Missense_Mutation	SNP	ENST00000265728.1	37	CCDS5611.1	14	0.00641025641025641	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	10	0.013192612137203167	A	13.61	2.289011	0.40494	0.003633	0.011601	ENSG00000006634	ENST00000265728	T	0.37235	1.21	5.13	3.98	0.46160	.	0.088141	0.47852	D	0.000204	T	0.25005	0.0607	L	0.56769	1.78	0.30535	N	0.767027	B;B	0.26195	0.144;0.068	B;B	0.21708	0.036;0.036	T	0.35674	-0.9779	10	0.66056	D	0.02	-9.6101	8.964	0.35865	0.9161:0.0:0.0839:0.0	rs61747462	355;579	B7Z8C6;Q9UBU7	.;DBF4A_HUMAN	E	579	ENSP00000265728:K579E	ENSP00000265728:K579E	K	+	1	0	DBF4	87375124	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.387000	0.59626	1.934000	0.56057	0.528000	0.53228	AAA	A|0.992;G|0.008	0.008	strong		0.333	DBF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253678.1	NM_006716		G	87537188	A	G	87537188	3	3	23	1	0	0	0	0	1	0	0	0	4250	247	9	3	1781	3	DBF4	7	87537188	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	60896	87537188	71601475	306	7750											
AKAP9	10142	hgsc.bcm.edu	37	chr7	91632286	91632286	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgatactcaagtaagctctTtattagatggagttgtgacc	11	14	10	6	0	2	3	1	2	1	1	2	4	2	4	1	1	2	3	1	1	5	6			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:91632286T>G	ENST00000359028.2	+	9	3316	c.3091T>G	c.(3091-3093)Tta>Gta	p.L1031V	AKAP9_ENST00000356239.3_Missense_Mutation_p.L1019V|AKAP9_ENST00000358100.2_Missense_Mutation_p.L1031V			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	1031					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)			AGTAAGCTCTTTATTAGATGG	0.358			T	BRAF	papillary thyroid																																p.L1019V		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.T3055G						PASS	.						84	85	85					7																	91632286		2203	4300	6503	SO:0001583	missense	10142	exon8			AGCTCTTTATTAG	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.3091T>G	7.37:g.91632286T>G	ENSP00000351922:p.Leu1031Val	151	0	0		134	65	0.485075	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		.	.	.	.	.	.	.	.	.	.	T	12.35	1.911886	0.33721	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394565	T;T;T	0.03358	3.96;3.96;3.96	5.72	3.2	0.36748	.	0.556233	0.13630	N	0.373796	T	0.05364	0.0142	L	0.54323	1.7	0.09310	N	1	B;P;B;P	0.46220	0.094;0.874;0.152;0.493	B;B;B;B	0.41723	0.039;0.365;0.085;0.085	T	0.32348	-0.9910	10	0.56958	D	0.05	.	8.3792	0.32461	0.0:0.0687:0.1325:0.7988	.	1031;1019;1019;1031	Q99996;Q99996-2;Q99996-3;A4D1E4	AKAP9_HUMAN;.;.;.	V	1019;1031;1031;1031;1031	ENSP00000348573:L1019V;ENSP00000351922:L1031V;ENSP00000350813:L1031V	ENSP00000348573:L1019V	L	+	1	2	AKAP9	91470222	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	0.085000	0.14912	1.091000	0.41335	0.528000	0.53228	TTA	.	.	none		0.358	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		G	91632286	T	G	91632286	3	3	23	1	0	0	0	0	1	0	0	0	459	1838	64	5	3085	5	AKAP9	7	91632286	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	4095098	91632286	67506377	307	7751											
SAMD9	54809	hgsc.bcm.edu	37	chr7	92735154	92735154	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tactgggctttcccatcttaGatgtctgaatcgaatcttca	9	15	7	10	1	4	2	1	1	3	1	6	3	5	2	1	1	1	1	1	1	4	4	rs147157740	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:92735154G>A	ENST00000379958.2	-	3	526	c.257C>T	c.(256-258)tCt>tTt	p.S86F		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	86						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)			TCCCATCTTAGATGTCTGAAT	0.383													G|||	15	0.00299521	0.0	0.0072	5008	,	,		18338	0.0		0.0099	False		,,,				2504	0.0				p.S86F		Atlas-SNP	.											.	SAMD9	239	.	0			c.C257T						PASS	.	G	PHE/SER,PHE/SER	7,4399	12.9+/-30.5	0,7,2196	171	169	170		257,257	-2.1	0	7	dbSNP_134	170	58,8542	36.4+/-91.3	0,58,4242	yes	missense,missense	SAMD9	NM_001193307.1,NM_017654.3	155,155	0,65,6438	AA,AG,GG		0.6744,0.1589,0.4998	benign,benign	86/1590,86/1590	92735154	65,12941	2203	4300	6503	SO:0001583	missense	54809	exon2			ATCTTAGATGTCT	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.257C>T	7.37:g.92735154G>A	ENSP00000369292:p.Ser86Phe	161	0	0		217	105	0.483871	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	37	CCDS34680.1	14	0.00641025641025641	0	0.0	5	0.013812154696132596	0	0.0	9	0.011873350923482849	G	9.731	1.162254	0.21538	0.001589	0.006744	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.25250	1.81;2.63	4.6	-2.08	0.07254	.	1.711930	0.03721	N	0.251921	T	0.11922	0.0290	L	0.27053	0.805	0.09310	N	1	B	0.32653	0.379	B	0.30782	0.12	T	0.20605	-1.0270	10	0.62326	D	0.03	.	4.2849	0.10850	0.0861:0.4566:0.2508:0.2066	.	86	Q5K651	SAMD9_HUMAN	F	86	ENSP00000369292:S86F;ENSP00000414529:S86F	ENSP00000369292:S86F	S	-	2	0	SAMD9	92573090	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.011000	0.12721	-0.530000	0.06349	-1.368000	0.01194	TCT	G|0.995;A|0.005	0.005	strong		0.383	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		A	92735154	G	A	92735154	3	1	23	1	0	0	0	0	1	0	0	0	13841	942	33	2	4516	2	SAMD9	7	92735154	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1102868	92735154	66403509	308	7752											
CYP3A5	1577	hgsc.bcm.edu	37	chr7	99261643	99261643	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttctgtttacagatttacttAaaaaatttatggtatctttt	12	21	4	4	0	2	1	0	0	2	1	2	1	2	1	0	1	2	2	0	1	7	11	rs201260783		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:99261643A>T	ENST00000222982.4	-	8	845	c.746T>A	c.(745-747)tTa>tAa	p.L249*	CYP3A5_ENST00000343703.5_Nonsense_Mutation_p.L239*|CYP3A5_ENST00000339843.2_3'UTR|CYP3A5_ENST00000480723.1_5'Flank	NM_000777.3	NP_000768.1	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 5	249					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)	AGATTTACTTAAAAAATTTAT	0.318													A|||	1	0.000199681	0.0	0.0	5008	,	,		18056	0.001		0.0	False		,,,				2504	0.0				p.L249X		Atlas-SNP	.											.	CYP3A5	46	.	0			c.T746A						PASS	.						101	97	99					7																	99261643		2203	4300	6503	SO:0001587	stop_gained	1577	exon8			TTACTTAAAAAAT	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.746T>A	7.37:g.99261643A>T	ENSP00000222982:p.Leu249*	141	0	0		166	78	0.46988	NM_000777	A4D289|B7Z5I7|Q53WY8|Q75MV0|Q9HB56	Nonsense_Mutation	SNP	ENST00000222982.4	37	CCDS5672.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.424707	0.83667	.	.	ENSG00000106258	ENST00000222982;ENST00000343703	.	.	.	4.61	4.61	0.57282	.	0.204155	0.50627	D	0.000105	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	11.9716	0.53067	1.0:0.0:0.0:0.0	.	.	.	.	X	249;239	.	ENSP00000222982:L249X	L	-	2	0	CYP3A5	99099579	1.000000	0.71417	0.708000	0.30435	0.010000	0.07245	6.921000	0.75805	1.708000	0.51301	0.533000	0.62120	TTA	.	.	weak		0.318	CYP3A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345469.1			T	99261643	A	T	99261643	4	4	23	1	0	0	0	0	0	1	0	0	4182	372	13	5	786	5	CYP3A5	7	99261643	Nonsense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	6526489	99261643	59877020	309	7753											
C7orf51	222950	hgsc.bcm.edu	37	chr7	100086246	100086246	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttccgccccatgcccaccGccgcccagcttcagccctcc	4	6	6	25	3	1	0	1	0	0	0	3	0	3	0	10	0	3	1	10	0	0	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:100086246G>A	ENST00000300179.2	+	4	1061	c.902G>A	c.(901-903)cGc>cAc	p.R301H	NYAP1_ENST00000454988.1_Missense_Mutation_p.R244H|NYAP1_ENST00000423930.1_Missense_Mutation_p.R301H	NM_173564.2	NP_775835.2	Q6ZVC0	NYAP1_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 1	301	Pro-rich.				neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												CATGCCCACCGCCGCCCAGCT	0.692																																					p.R301H		Atlas-SNP	.											.	.	.	.	0			c.G902A						PASS	.						46	49	48					7																	100086246		2203	4296	6499	SO:0001583	missense	222950	exon4			CCCACCGCCGCCC	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.902G>A	7.37:g.100086246G>A	ENSP00000300179:p.Arg301His	150	0	0		91	13	0.142857	NM_173564	Q6U9Y3|Q8N1V0	Missense_Mutation	SNP	ENST00000300179.2	37	CCDS5696.1	.	.	.	.	.	.	.	.	.	.	G	7.182	0.589872	0.13812	.	.	ENSG00000166924	ENST00000300179;ENST00000423930;ENST00000454988	T;T;T	0.32988	1.43;1.43;1.45	4.9	4.02	0.46733	.	0.133388	0.34802	N	0.003671	T	0.21921	0.0528	L	0.34521	1.04	0.43719	D	0.996195	P;P	0.40834	0.68;0.73	B;B	0.38500	0.214;0.275	T	0.02371	-1.1169	10	0.33940	T	0.23	-13.797	9.197	0.37235	0.1022:0.0:0.8978:0.0	.	244;301	C9JS30;Q6ZVC0	.;CG051_HUMAN	H	301;301;244	ENSP00000300179:R301H;ENSP00000411861:R301H;ENSP00000394424:R244H	ENSP00000300179:R301H	R	+	2	0	C7orf51	99924182	0.929000	0.31497	0.990000	0.47175	0.190000	0.23558	1.581000	0.36558	1.055000	0.40461	0.407000	0.27541	CGC	.	.	none		0.692	NYAP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339335.2	NM_173564		A	100086246	G	A	100086246	3	1	23	1	0	0	0	0	1	0	0	0	2402	1087	38	1	912	1	C7orf51	7	100086246	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	824603	100086246	59052417	310	7754											
GIGYF1	64599	hgsc.bcm.edu	37	chr7	100279988	100279988	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agcgtgtgcagcatctgctcGcaccactgggtgaagccgtc	7	8	13	13	3	1	1	0	1	1	0	3	1	1	1	2	1	5	4	2	1	1	0	rs117477530	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:100279988G>A	ENST00000275732.5	-	21	3927	c.2718C>T	c.(2716-2718)tgC>tgT	p.C906C	GIGYF1_ENST00000471340.2_5'Flank	NM_022574.4	NP_072096.2	O75420	PERQ1_HUMAN	GRB10 interacting GYF protein 1	906					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)					GCATCTGCTCGCACCACTGGG	0.672													G|||	6	0.00119808	0.0	0.0058	5008	,	,		15974	0.0		0.002	False		,,,				2504	0.0				p.C906C		Atlas-SNP	.											.	GIGYF1	113	.	0			c.C2718T						PASS	.	G		3,4401		0,3,2199	54	46	49		2718	-2.7	0.9	7	dbSNP_132	49	27,8573		0,27,4273	yes	coding-synonymous	GIGYF1	NM_022574.4		0,30,6472	AA,AG,GG		0.314,0.0681,0.2307		906/1036	100279988	30,12974	2202	4300	6502	SO:0001819	synonymous_variant	64599	exon21			CTGCTCGCACCAC	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.2718C>T	7.37:g.100279988G>A		65	0	0		64	28	0.4375	NM_022574	Q6Y7W7|Q8WZ38	Silent	SNP	ENST00000275732.5	37	CCDS34708.1																																																																																			G|0.998;A|0.002	0.002	strong		0.672	GIGYF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347205.2	NM_022574		A	100279988	G	A	100279988	2	1	23	1	0	0	0	0	0	0	0	1	6385	1079	38	1		1	GIGYF1	7	100279988	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	193742	100279988	58858675	311	7755											
MUC17	140453	hgsc.bcm.edu	37	chr7	100696348	100696348	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agtctggtgtacggcctcgtGggggcaggggtcgtgctgat	4	10	19	8	3	1	1	0	1	1	0	3	1	1	1	1	6	2	3	1	6	1	1	rs200413820		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:100696348G>T	ENST00000306151.4	+	10	13249	c.13185G>T	c.(13183-13185)gtG>gtT	p.V4395V		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	4395					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)					ACGGCCTCGTGGGGGCAGGGG	0.597													G|||	1	0.000199681	0.0	0.0	5008	,	,		17902	0.0		0.001	False		,,,				2504	0.0				p.V4395V		Atlas-SNP	.											MUC17,right_lower_lobe,carcinoma,0,1	MUC17	804	1	0			c.G13185T						PASS	.						91	77	82					7																	100696348		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon10			CCTCGTGGGGGCA	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.13185G>T	7.37:g.100696348G>T		97	0	0		112	43	0.383929	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			G|1.000;T|0.000	0.000	strong		0.597	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		T	100696348	G	T	100696348	2	4	23	1	0	0	0	0	0	0	0	1	9983	1335	47	4		4	MUC17	7	100696348	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	416360	100696348	58442315	312	7756											
LAMB1	3912	hgsc.bcm.edu	37	chr7	107591763	107591763	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatgcactggcactgccccGtgaactgcggccagaacaca	10	5	11	15	2	0	2	0	1	0	1	0	2	0	2	3	2	5	3	3	2	2	0	rs145485632	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:107591763G>A	ENST00000222399.6	-	24	3529	c.3299C>T	c.(3298-3300)aCg>aTg	p.T1100M	LAMB1_ENST00000393561.1_Missense_Mutation_p.T1124M	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	1100	Laminin EGF-like 12. {ECO:0000255|PROSITE-ProRule:PRU00460}.				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						GCACTGCCCCGTGAACTGCGG	0.572													G|||	5	0.000998403	0.0	0.0029	5008	,	,		16910	0.0		0.003	False		,,,				2504	0.0				p.T1100M		Atlas-SNP	.											.	LAMB1	185	.	0			c.C3299T						PASS	.	G	MET/THR	3,4403	6.2+/-15.9	0,3,2200	42	38	39		3299	5	1	7	dbSNP_134	39	1,8599	1.2+/-3.3	0,1,4299	yes	missense	LAMB1	NM_002291.2	81	0,4,6499	AA,AG,GG		0.0116,0.0681,0.0308	possibly-damaging	1100/1787	107591763	4,13002	2203	4300	6503	SO:0001583	missense	3912	exon24			TGCCCCGTGAACT	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.3299C>T	7.37:g.107591763G>A	ENSP00000222399:p.Thr1100Met	104	0	0		116	54	0.465517	NM_002291	Q14D91	Missense_Mutation	SNP	ENST00000222399.6	37	CCDS5750.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	G	17.85	3.489271	0.64074	6.81E-4	1.16E-4	ENSG00000091136	ENST00000393561;ENST00000222399	T;T	0.66099	-0.19;-0.19	5.0	5.0	0.66597	EGF-like, laminin (3);	.	.	.	.	T	0.77532	0.4144	M	0.92507	3.315	0.80722	D	1	D;D	0.65815	0.995;0.991	P;B	0.59115	0.852;0.424	D	0.84831	0.0802	9	0.66056	D	0.02	.	18.8361	0.92164	0.0:0.0:1.0:0.0	.	1100;1124	P07942;G3XAI2	LAMB1_HUMAN;.	M	1124;1100	ENSP00000377191:T1124M;ENSP00000222399:T1100M	ENSP00000222399:T1100M	T	-	2	0	LAMB1	107378999	0.986000	0.35501	0.976000	0.42696	0.899000	0.52679	2.037000	0.41174	2.748000	0.94277	0.655000	0.94253	ACG	G|0.999;A|0.001	0.001	strong		0.572	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291		A	107591763	G	A	107591763	3	1	23	1	0	0	0	0	1	0	0	0	8619	1145	40	1	2105	1	LAMB1	7	107591763	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	6895415	107591763	51546900	313	7757											
PNPLA8	50640	hgsc.bcm.edu	37	chr7	108155377	108155377	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtgtaatgaaaaagactgcGtttacctatatcttcttctt	11	17	6	7	1	3	2	0	1	3	1	3	2	3	2	1	0	2	2	1	0	6	8	rs139626312	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:108155377G>A	ENST00000422087.1	-	4	965	c.559C>T	c.(559-561)Cgc>Tgc	p.R187C	PNPLA8_ENST00000257694.8_Missense_Mutation_p.R187C|PNPLA8_ENST00000483879.1_Intron|PNPLA8_ENST00000436062.1_Missense_Mutation_p.R187C|PNPLA8_ENST00000453144.1_Missense_Mutation_p.R87C|PNPLA8_ENST00000426128.2_Missense_Mutation_p.R187C|PNPLA8_ENST00000388728.5_Missense_Mutation_p.R187C	NM_015723.3	NP_056538.1	Q9NP80	PLPL8_HUMAN	patatin-like phospholipase domain containing 8	187					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						AAAAGACTGCGTTTACCTATA	0.294													G|||	7	0.00139776	0.0	0.0014	5008	,	,		18615	0.0		0.004	False		,,,				2504	0.002				p.R187C		Atlas-SNP	.											PNPLA8,caecum,carcinoma,+1,2	PNPLA8	82	2	0			c.C559T						PASS	.	G	CYS/ARG	6,4400	11.4+/-27.6	0,6,2197	52	55	54		559	3.8	0.1	7	dbSNP_134	54	43,8557	27.9+/-77.7	0,43,4257	yes	missense	PNPLA8	NM_015723.2	180	0,49,6454	AA,AG,GG		0.5,0.1362,0.3767	possibly-damaging	187/783	108155377	49,12957	2203	4300	6503	SO:0001583	missense	50640	exon2			GACTGCGTTTACC	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.559C>T	7.37:g.108155377G>A	ENSP00000410804:p.Arg187Cys	35	0	0		42	23	0.547619	NM_001256008	A4D0S1|C9JZI4|O95035|Q8N3I3|Q9H7T5|Q9NR17|Q9NUN2|Q9NZ79	Missense_Mutation	SNP	ENST00000422087.1	37	CCDS34733.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	10.38	1.334998	0.24253	0.001362	0.005	ENSG00000135241	ENST00000426128;ENST00000257694;ENST00000388728;ENST00000422087;ENST00000453144;ENST00000436062;ENST00000453085;ENST00000427008	D;D;D;D;D;D;D	0.97959	-3.43;-4.63;-3.43;-4.63;-4.62;-4.63;-4.62	5.78	3.83	0.44106	.	0.974744	0.08470	N	0.941087	D	0.90445	0.7008	N	0.08118	0	0.09310	N	1	P	0.47762	0.9	B	0.40009	0.316	D	0.86221	0.1631	10	0.66056	D	0.02	.	8.1982	0.31409	0.0:0.2353:0.4795:0.2852	.	187	Q9NP80	PLPL8_HUMAN	C	187;187;187;187;87;187;87;187	ENSP00000394988:R187C;ENSP00000257694:R187C;ENSP00000373380:R187C;ENSP00000410804:R187C;ENSP00000387789:R87C;ENSP00000406779:R187C;ENSP00000402274:R87C	ENSP00000257694:R187C	R	-	1	0	PNPLA8	107942613	0.537000	0.26386	0.086000	0.20670	0.523000	0.34469	0.688000	0.25422	1.406000	0.46857	0.591000	0.81541	CGC	G|0.997;A|0.003	0.003	strong		0.294	PNPLA8-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337475.1	NM_015723		A	108155377	G	A	108155377	3	1	23	1	0	0	0	0	1	0	0	0	12180	1145	40	1	1825	1	PNPLA8	7	108155377	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	563614	108155377	50983286	314	7758											
MDFIC	29969	hgsc.bcm.edu	37	chr7	114562638	114562639	+	In_Frame_Ins	INS	-	-	GAG																															gctaactttccggggcggaaINSgaggaggaggaggaggagga																										TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:114562638_114562639insGAG	ENST00000257724.3	+	1	430_431	c.167_168insGAG	c.(166-171)aagagg>aaGAGgagg	p.62_63insR	MDFIC_ENST00000423503.1_5'Flank|MDFIC_ENST00000393486.1_5'UTR|MDFIC_ENST00000448022.1_5'UTR					MyoD family inhibitor domain containing											breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	8						CCGGGGCggaagaggaggagga	0.703											OREG0003787	type=REGULATORY REGION|Gene=MDFIC|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.K56delinsKR		Pindel,Atlas-Indel	.											.	MDFIC	30	.	0			c.167_168insGAG						PASS	.																																			SO:0001652	inframe_insertion	29969	exon1			.	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.183_185dupGAG	7.37:g.114562645_114562647dupGAG	ENSP00000257724:p.Arg62_Arg62dup	40	0	.	1459	42	13	0.31	NM_001166346		In_Frame_Ins	INS	ENST00000257724.3	37	CCDS34737.1																																																																																			.	.	none		0.703	MDFIC-007	KNOWN	non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000366397.1	NM_199072		GAG	114562639	-	GAG	114562638	7	5	23	1	0	1	1	0	0	0	0	0	9414	72	3	0	169	0	MDFIC	7	114562638	In_Frame_Ins	INS	-	TCGA-G8-6325-01A-11D-2210-10	6407261	114562638	44576025	315	7759											
MET	4233	hgsc.bcm.edu	37	chr7	116339282	116339282	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagcttcccaacttcaccgcGgaaacacccatccagaatgt	12	7	6	16	2	1	1	1	0	0	1	3	2	3	2	4	1	3	1	4	1	3	2	rs11762213	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:116339282G>A	ENST00000318493.6	+	2	331	c.144G>A	c.(142-144)gcG>gcA	p.A48A	MET_ENST00000436117.2_Silent_p.A48A|MET_ENST00000397752.3_Silent_p.A48A			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0	SAP. {ECO:0000255|PROSITE- ProRule:PRU00186}.				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)			ACTTCACCGCGGAAACACCCA	0.433			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				G|||	77	0.0153754	0.0023	0.0346	5008	,	,		21839	0.0		0.0398	False		,,,				2504	0.0102				p.A48A		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,adenocarcinoma,+1,2	MET	412	2	0			c.G144A						PASS	.	G	,	42,3886		0,42,1922	100	99	99		144,144	-11.8	0	7	dbSNP_120	99	391,7915		6,379,3768	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	6,421,5690	AA,AG,GG		4.7074,1.0692,3.5393	,	48/1391,48/1409	116339282	433,11801	1964	4153	6117	SO:0001819	synonymous_variant	4233	exon2	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	CACCGCGGAAACA	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.144G>A	7.37:g.116339282G>A		159	0	0		174	98	0.563218	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			G|0.974;A|0.026	0.026	strong		0.433	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			A	116339282	G	A	116339282	2	1	23	1	0	0	0	0	0	0	0	1	9494	1103	39	1		1	MET	7	116339282	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1776644	116339282	42799381	316	7760											
MET	4233	hgsc.bcm.edu	37	chr7	116397572	116397572	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatggccacgggacaacacaAtacagtacattctcctatgt	14	9	7	11	1	1	0	0	0	1	0	2	1	1	1	2	2	3	1	2	2	6	4	rs13223756	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:116397572A>G	ENST00000318493.6	+	7	2131	c.1944A>G	c.(1942-1944)caA>caG	p.Q648Q	MET_ENST00000436117.2_Silent_p.Q648Q|MET_ENST00000397752.3_Silent_p.Q648Q			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0	Arg/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)			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)			GGACAACACAATACAGTACAT	0.318			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				A|||	941	0.187899	0.1089	0.1254	5008	,	,		17860	0.2728		0.2048	False		,,,				2504	0.2342				p.Q648Q		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.A1944G						PASS	.	A	,	486,3224		27,432,1396	93	92	92		1944,1944	-6.5	0	7	dbSNP_121	92	1521,6665		129,1263,2701	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	156,1695,4097	GG,GA,AA		18.5805,13.0997,16.8712	,	648/1391,648/1409	116397572	2007,9889	1855	4093	5948	SO:0001819	synonymous_variant	4233	exon7	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	AACACAATACAGT	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.1944A>G	7.37:g.116397572A>G		88	0	0		71	25	0.352113	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			A|0.817;G|0.183	0.183	strong		0.318	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			G	116397572	A	G	116397572	2	3	23	1	0	0	0	0	0	0	0	1	9494	98	4	3		3	MET	7	116397572	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	58290	116397572	42741091	317	7761											
WNT16	51384	hgsc.bcm.edu	37	chr7	120972016	120972016	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataacaatgaagctggaaggCaggtatgtattagaaaatgg	17	9	12	3	0	0	2	0	1	0	1	0	3	0	3	0	4	2	4	0	4	9	4	rs74389152	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:120972016C>A	ENST00000222462.2	+	3	921	c.631C>A	c.(631-633)Cag>Aag	p.Q211K	WNT16_ENST00000361301.2_Missense_Mutation_p.Q201K	NM_057168.1	NP_476509.1	Q9UBV4	WNT16_HUMAN	wingless-type MMTV integration site family, member 16	211					bone remodeling (GO:0046849)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell fate commitment (GO:0045165)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|negative regulation of cell death (GO:0060548)|neuron differentiation (GO:0030182)|optic cup formation involved in camera-type eye development (GO:0003408)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of gene expression (GO:0010628)|positive regulation of JNK cascade (GO:0046330)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|replicative senescence (GO:0090399)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)	18	all_neural(327;0.117)					AGCTGGAAGGCAGGTATGTAT	0.378													C|||	4	0.000798722	0.0	0.0	5008	,	,		19182	0.0		0.003	False		,,,				2504	0.001				p.Q211K		Atlas-SNP	.											.	WNT16	97	.	0			c.C631A						PASS	.	C	LYS/GLN,LYS/GLN	3,4403	6.2+/-15.9	0,3,2200	51	52	51		601,631	6	1	7	dbSNP_131	51	20,8580	14.6+/-50.1	0,20,4280	yes	missense,missense	WNT16	NM_016087.2,NM_057168.1	53,53	0,23,6480	AA,AC,CC		0.2326,0.0681,0.1768	benign,benign	201/356,211/366	120972016	23,12983	2203	4300	6503	SO:0001583	missense	51384	exon3			GGAAGGCAGGTAT	AF152584	CCDS5780.1, CCDS5781.1	7q31	2008-07-18			ENSG00000002745	ENSG00000002745		"Wingless-type MMTV integration sites"	16267	protein-coding gene	gene with protein product		606267				10500199	Standard	NM_016087		Approved		uc003vjw.3	Q9UBV4	OTTHUMG00000156963	ENST00000222462.2:c.631C>A	7.37:g.120972016C>A	ENSP00000222462:p.Gln211Lys	93	0	0		80	40	0.5	NM_057168	Q2M3G1|Q9Y5C0	Missense_Mutation	SNP	ENST00000222462.2	37	CCDS5781.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	7.287	0.610367	0.14066	6.81E-4	0.002326	ENSG00000002745	ENST00000361301;ENST00000222462	T;T	0.74632	-0.86;-0.86	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.60856	0.2301	N	0.13098	0.295	0.58432	D	0.999997	B;B	0.21688	0.059;0.059	B;B	0.29353	0.101;0.101	T	0.57723	-0.7762	10	0.05436	T	0.98	.	20.547	0.99278	0.0:1.0:0.0:0.0	.	211;201	Q9UBV4;E9PH60	WNT16_HUMAN;.	K	201;211	ENSP00000355065:Q201K;ENSP00000222462:Q211K	ENSP00000222462:Q211K	Q	+	1	0	WNT16	120759252	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	3.875000	0.56108	2.850000	0.98022	0.650000	0.86243	CAG	C|0.998;A|0.002	0.002	strong		0.378	WNT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346843.1	NM_057168		A	120972016	C	A	120972016	3	1	23	1	0	0	0	0	1	0	0	0	17400	711	25	4	710	4	WNT16	7	120972016	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	4574444	120972016	38166647	318	7762											
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121698871	121698871	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taggatgattatgtacttgaAgtgaggcactttcagtgtcc	10	14	11	6	0	1	3	1	3	0	0	2	4	2	4	1	2	1	2	1	2	4	5			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:121698871A>C	ENST00000393386.2	+	28	6957	c.6546A>C	c.(6544-6546)gaA>gaC	p.E2182D	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.E1315D	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	2182	Tyrosine-protein phosphatase 2. {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						ATGTACTTGAAGTGAGGCACT	0.358																																					p.E2182D		Atlas-SNP	.											PTPRZ1_ENST00000393386,NS,carcinoma,0,2	PTPRZ1	605	2	0			c.A6546C						PASS	.						104	103	103					7																	121698871		2203	4300	6503	SO:0001583	missense	5803	exon28			ACTTGAAGTGAGG	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.6546A>C	7.37:g.121698871A>C	ENSP00000377047:p.Glu2182Asp	80	0	0		87	8	0.091954	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	A	19.08	3.758217	0.69763	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	D;D	0.84146	-1.81;-1.81	6.07	6.07	0.98685	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	D	0.90960	0.7158	M	0.76938	2.355	0.52501	D	0.999957	B;B;P	0.47191	0.38;0.236;0.891	B;B;P	0.55667	0.229;0.173;0.781	D	0.91729	0.5395	10	0.72032	D	0.01	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	1321;1315;2182	P23471-2;C9JFM0;P23471	.;.;PTPRZ_HUMAN	D	2182;1315	ENSP00000377047:E2182D;ENSP00000410000:E1315D	ENSP00000377047:E2182D	E	+	3	2	PTPRZ1	121486107	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.621000	0.54210	2.326000	0.78906	0.533000	0.62120	GAA	.	.	none		0.358	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		C	121698871	A	C	121698871	3	2	23	1	0	0	0	0	1	0	0	0	12829	69	3	5	6656	5	PTPRZ1	7	121698871	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	726855	121698871	37439792	319	7763											
RNF133	168433	hgsc.bcm.edu	37	chr7	122338071	122338071	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttgaatccccaaaactttaAgaatatcacatttgcaaatg	16	12	4	9	0	1	2	1	1	0	1	2	2	2	2	2	0	2	1	2	0	7	5	rs113127267	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:122338071A>G	ENST00000340112.2	-	1	1139	c.902T>C	c.(901-903)cTt>cCt	p.L301P	CADPS2_ENST00000449022.2_Intron|CADPS2_ENST00000412584.2_Intron|CADPS2_ENST00000313070.7_Intron|CADPS2_ENST00000334010.7_Intron	NM_139175.1	NP_631914.1	Q8WVZ7	RN133_HUMAN	ring finger protein 133	301					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						CAAAACTTTAAGAATATCACA	0.383													A|||	9	0.00179712	0.0	0.0014	5008	,	,		20051	0.0		0.006	False		,,,				2504	0.002				p.L301P	Colon(198;1778 2057 7449 19869 45985)	Atlas-SNP	.											.	RNF133	41	.	0			c.T902C						PASS	.	A	,,,PRO/LEU	4,4402	8.1+/-20.4	0,4,2199	80	81	80		,,,902	5.5	1	7	dbSNP_132	80	55,8543	33.8+/-87.4	0,55,4244	yes	intron,intron,intron,missense	CADPS2,RNF133	NM_001009571.3,NM_001167940.1,NM_017954.10,NM_139175.1	,,,98	0,59,6443	GG,GA,AA		0.6397,0.0908,0.4537	,,,probably-damaging	,,,301/377	122338071	59,12945	2203	4299	6502	SO:0001583	missense	168433	exon1			ACTTTAAGAATAT	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.902T>C	7.37:g.122338071A>G	ENSP00000344489:p.Leu301Pro	120	0	0		134	69	0.514925	NM_139175	A4D0W2|Q8N7G7	Missense_Mutation	SNP	ENST00000340112.2	37	CCDS5784.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	A	14.28	2.489317	0.44249	9.08E-4	0.006397	ENSG00000188050	ENST00000340112	T	0.68479	-0.33	5.53	5.53	0.82687	.	0.000000	0.56097	U	0.000021	T	0.65709	0.2717	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.72377	-0.4312	10	0.66056	D	0.02	.	10.0982	0.42488	0.8506:0.0:0.0:0.1494	.	301	Q8WVZ7	RN133_HUMAN	P	301	ENSP00000344489:L301P	ENSP00000344489:L301P	L	-	2	0	RNF133	122125307	1.000000	0.71417	0.995000	0.50966	0.527000	0.34593	4.633000	0.61318	2.099000	0.63709	0.402000	0.26972	CTT	A|0.997;G|0.003	0.003	strong		0.383	RNF133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347413.1	NM_139175		G	122338071	A	G	122338071	3	3	23	1	0	0	0	0	1	0	0	0	13454	72	3	3	232	3	RNF133	7	122338071	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	639200	122338071	36800592	320	7764											
IRF5	3663	hgsc.bcm.edu	37	chr7	128588712	128588712	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tagtatccggctacagatctCaaacccagacctcaaagacc	14	7	6	14	1	2	3	2	0	1	3	4	3	3	3	4	1	2	2	4	1	5	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:128588712C>T	ENST00000402030.2	+	9	1409	c.1337C>T	c.(1336-1338)tCa>tTa	p.S446L	IRF5_ENST00000473745.1_Missense_Mutation_p.S446L|IRF5_ENST00000249375.4_Missense_Mutation_p.S446L|IRF5_ENST00000477535.1_Missense_Mutation_p.S360L|IRF5_ENST00000357234.5_Missense_Mutation_p.S462L	NM_001098629.1|NM_001098630.1	NP_001092099.1|NP_001092100.1	Q13568	IRF5_HUMAN	interferon regulatory factor 5	446					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|prostate(1)	15						CTACAGATCTCAAACCCAGAC	0.577																																					p.S462L		Atlas-SNP	.											.	IRF5	40	.	0			c.C1385T						PASS	.						123	128	126					7																	128588712		2203	4300	6503	SO:0001583	missense	3663	exon9			AGATCTCAAACCC		CCDS5808.1, CCDS43645.1, CCDS56512.1	7q32	2008-07-18			ENSG00000128604	ENSG00000128604			6120	protein-coding gene	gene with protein product		607218					Standard	XM_005250317		Approved		uc003vog.3	Q13568	OTTHUMG00000158410	ENST00000402030.2:c.1337C>T	7.37:g.128588712C>T	ENSP00000385352:p.Ser446Leu	93	0	0		99	16	0.161616	NM_001098629	A4D1J8|A8DUA8|A8DUA9|E7EQ16|E7EW54|Q1A7B4|Q64GA9|Q64GB1|Q64GB2|Q6RCM8|Q9BQF0	Missense_Mutation	SNP	ENST00000402030.2	37	CCDS5808.1	.	.	.	.	.	.	.	.	.	.	C	33	5.274132	0.95459	.	.	ENSG00000128604	ENST00000357234;ENST00000477535;ENST00000402030;ENST00000249375;ENST00000473745;ENST00000412326	D;D;D;D;D	0.96136	-3.92;-3.92;-3.92;-3.92;-3.92	5.88	5.88	0.94601	SMAD domain-like (1);SMAD/FHA domain (1);	0.000000	0.49916	D	0.000135	D	0.97445	0.9164	M	0.71036	2.16	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.993;0.993;0.999	D	0.97569	1.0103	10	0.62326	D	0.03	-6.6903	17.7218	0.88353	0.0:1.0:0.0:0.0	.	360;446;462	E7EW54;Q13568;Q13568-2	.;IRF5_HUMAN;.	L	462;360;446;446;446;436	ENSP00000349770:S462L;ENSP00000419950:S360L;ENSP00000385352:S446L;ENSP00000249375:S446L;ENSP00000419149:S446L	ENSP00000249375:S446L	S	+	2	0	IRF5	128375948	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	7.487000	0.81328	2.778000	0.95560	0.655000	0.94253	TCA	.	.	none		0.577	IRF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350934.1	NM_001098627		T	128588712	C	T	128588712	3	4	23	1	0	0	0	0	1	0	0	0	7842	838	29	2	1415	2	IRF5	7	128588712	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	6250641	128588712	30549951	321	7765											
SMO	6608	hgsc.bcm.edu	37	chr7	128846328	128846328	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gatggggactctgtgagtggGatttgttttgtgggctacaa	7	14	16	4	0	1	1	0	1	1	0	1	4	1	3	0	4	1	2	0	4	2	4	rs2228617	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:128846328G>C	ENST00000249373.3	+	6	1444	c.1164G>C	c.(1162-1164)ggG>ggC	p.G388G		NM_005631.4	NP_005622.1	Q99835	SMO_HUMAN	smoothened, frizzled class receptor	388					adenohypophysis development (GO:0021984)|anterior/posterior pattern specification (GO:0009952)|atrial septum morphogenesis (GO:0060413)|axon extension involved in axon guidance (GO:0048846)|canonical Wnt signaling pathway (GO:0060070)|cardioblast differentiation (GO:0010002)|cell fate specification (GO:0001708)|cellular response to cholesterol (GO:0071397)|central nervous system neuron differentiation (GO:0021953)|cerebellar cortex morphogenesis (GO:0021696)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|detection of cell density by contact stimulus involved in contact inhibition (GO:0060248)|determination of left/right asymmetry in lateral mesoderm (GO:0003140)|determination of left/right symmetry (GO:0007368)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|epithelial-mesenchymal cell signaling (GO:0060684)|exocrine pancreas development (GO:0031017)|facial nerve development (GO:0021561)|floor plate formation (GO:0021508)|forebrain morphogenesis (GO:0048853)|gonad development (GO:0008406)|hair follicle morphogenesis (GO:0031069)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mammary gland epithelial cell differentiation (GO:0060644)|mesenchymal to epithelial transition involved in metanephric renal vesicle formation (GO:0072285)|midgut development (GO:0007494)|multicellular organism growth (GO:0035264)|muscle cell fate commitment (GO:0042693)|myoblast migration (GO:0051451)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of gene expression (GO:0010629)|negative regulation of hair follicle development (GO:0051799)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate commitment (GO:0048663)|neuron projection regeneration (GO:0031102)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|otolith morphogenesis (GO:0032474)|pancreas morphogenesis (GO:0061113)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gene expression (GO:0010628)|positive regulation of hh target transcription factor activity (GO:0007228)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|protein stabilization (GO:0050821)|regulation of heart morphogenesis (GO:2000826)|regulation of stem cell maintenance (GO:2000036)|renal system development (GO:0072001)|semicircular canal morphogenesis (GO:0048752)|skeletal muscle fiber development (GO:0048741)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021910)|somite development (GO:0061053)|spermatogenesis (GO:0007283)|thalamus development (GO:0021794)|type B pancreatic cell development (GO:0003323)|vasculogenesis (GO:0001570)|ventral midline determination (GO:0007371)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	drug binding (GO:0008144)|G-protein coupled receptor activity (GO:0004930)|patched binding (GO:0005113)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			biliary_tract(1)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(14)|liver(1)|lung(11)|pancreas(2)|prostate(1)|skin(20)|upper_aerodigestive_tract(3)|urinary_tract(1)	64					Fluocinonide(DB01047)|Vismodegib(DB08828)	CTGTGAGTGGGATTTGTTTTG	0.597			Mis		skin basal cell								C|||	3787	0.75619	0.6687	0.7896	5008	,	,		19589	0.7718		0.8231	False		,,,				2504	0.7658				p.G388G		Atlas-SNP	.		Dom	yes		7	7q31-q32	6608	smoothened homolog (Drosophila)		E	.	SMO	145	.	0			c.G1164C						PASS	.	C		3054,1352	451.8+/-349.8	1066,922,215	231	190	204		1164	5.3	1	7	dbSNP_98	204	7216,1384	269.4+/-288.4	3025,1166,109	no	coding-synonymous	SMO	NM_005631.4		4091,2088,324	CC,CG,GG		16.093,30.6854,21.0364		388/788	128846328	10270,2736	2203	4300	6503	SO:0001819	synonymous_variant	6608	exon6			GAGTGGGATTTGT	U84401	CCDS5811.1	7q32.1	2014-01-29	2014-01-29	2003-01-17	ENSG00000128602	ENSG00000128602		"GPCR / Class F : Frizzled receptors"	11119	protein-coding gene	gene with protein product	"frizzled family member 11"	601500	"smoothened (Drosophila) homolog", "smoothened homolog (Drosophila)", "smoothened, seven transmembrane spanning receptor", "smoothened, frizzled family receptor"	SMOH		9628830	Standard	NM_005631		Approved	FZD11	uc003vor.3	Q99835	OTTHUMG00000158421	ENST00000249373.3:c.1164G>C	7.37:g.128846328G>C		133	0	0		147	146	0.993197	NM_005631	A4D1K5	Silent	SNP	ENST00000249373.3	37	CCDS5811.1																																																																																			G|0.216;C|0.784	0.784	strong		0.597	SMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350986.1	NM_005631		C	128846328	G	C	128846328	2	2	23	1	0	0	0	0	0	0	0	1	14815	1161	41	4		4	SMO	7	128846328	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	257616	128846328	30292335	322	7766											
MEST	4232	hgsc.bcm.edu	37	chr7	130140729	130140729	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacgggaacttagtcattgaCaggtaagaagttaccctttg	12	11	11	7	1	1	2	1	1	0	1	1	4	1	3	1	2	2	2	1	2	5	5			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:130140729C>T	ENST00000223215.4	+	9	968	c.747C>T	c.(745-747)gaC>gaT	p.D249D	MEST_ENST00000341441.5_Silent_p.D240D|MEST_ENST00000378576.4_Intron|MEST_ENST00000393187.1_Silent_p.D240D|MEST_ENST00000416162.2_Intron|MEST_ENST00000462132.1_3'UTR|MEST_ENST00000437945.1_Silent_p.D249D|hsa-mir-335_ENST00000604666.1_RNA	NM_001253900.1|NM_002402.3	NP_001240829.1|NP_002393.2	Q5EB52	MEST_HUMAN	mesoderm specific transcript	249					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)					TAGTCATTGACAGGTAAGAAG	0.512																																					p.D249D	Colon(126;2182 2305 6517 35181)	Atlas-SNP	.											.	MEST	28	.	0			c.C747T						PASS	.						98	78	85					7																	130140729		2203	4300	6503	SO:0001819	synonymous_variant	4232	exon9			CATTGACAGGTAA		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.747C>T	7.37:g.130140729C>T		79	0	0		95	46	0.484211	NM_002402	B2R6S1|O14973|O15007|Q6AI49|Q92571	Silent	SNP	ENST00000223215.4	37	CCDS5822.1																																																																																			.	.	none		0.512	MEST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345183.2	NM_002402		T	130140729	C	T	130140729	2	4	23	1	0	0	0	0	0	0	0	1	9493	477	17	2		2	MEST	7	130140729	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1294401	130140729	28997934	323	7767											
DGKI	9162	hgsc.bcm.edu	37	chr7	137150761	137150761	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atctcatcttgggaaatctcCatcacaaagtgcaaatgttc	13	12	6	10	0	4	0	2	0	3	0	7	1	4	1	1	1	1	2	1	1	3	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:137150761C>T	ENST00000288490.5	-	27	2529	c.2529G>A	c.(2527-2529)atG>atA	p.M843I	DGKI_ENST00000424189.2_Missense_Mutation_p.M856I|DGKI_ENST00000453654.2_Missense_Mutation_p.M553I|DGKI_ENST00000446122.1_Missense_Mutation_p.M825I	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	843					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						GGGAAATCTCCATCACAAAGT	0.448																																					p.M843I		Atlas-SNP	.											.	DGKI	335	.	0			c.G2529A						PASS	.						70	74	72					7																	137150761		2203	4300	6503	SO:0001583	missense	9162	exon27			AATCTCCATCACA	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.2529G>A	7.37:g.137150761C>T	ENSP00000288490:p.Met843Ile	104	0	0		98	4	0.0408163	NM_004717	A4D1Q9|Q9NZ49	Missense_Mutation	SNP	ENST00000288490.5	37	CCDS5845.1	.	.	.	.	.	.	.	.	.	.	C	13.45	2.240246	0.39598	.	.	ENSG00000157680	ENST00000453654;ENST00000540376;ENST00000424189;ENST00000288490;ENST00000446122	T;T;T	0.32023	2.02;1.47;1.67	5.82	5.82	0.92795	.	0.140824	0.64402	D	0.000004	T	0.17959	0.0431	N	0.08118	0	0.38820	D	0.955614	B;B	0.18968	0.004;0.032	B;B	0.17722	0.012;0.019	T	0.11012	-1.0605	10	0.27785	T	0.31	.	14.8811	0.70534	0.1434:0.8566:0.0:0.0	.	553;843	E9PFX6;O75912	.;DGKI_HUMAN	I	553;801;846;843;825	ENSP00000392161:M553I;ENSP00000288490:M843I;ENSP00000399131:M825I	ENSP00000288490:M843I	M	-	3	0	DGKI	136801301	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.836000	0.27545	2.767000	0.95098	0.655000	0.94253	ATG	.	.	none		0.448	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717		T	137150761	C	T	137150761	3	4	23	1	0	0	0	0	1	0	0	0	4473	594	21	2	700	2	DGKI	7	137150761	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	7010032	137150761	21987902	324	7768											
ARHGEF5	7984	hgsc.bcm.edu	37	chr7	144069807	144069807	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gagaacacagcctggctcctCggaggaggcagaggccacga	11	3	15	12	2	0	2	0	0	0	2	2	6	1	4	3	5	2	2	3	5	1	0			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:144069807C>T	ENST00000056217.5	+	9	4181	c.4007C>T	c.(4006-4008)tCg>tTg	p.S1336L	ARHGEF5_ENST00000471847.2_Missense_Mutation_p.S258L	NM_005435.3	NP_005426.2	Q12774	ARHG5_HUMAN	Rho guanine nucleotide exchange factor (GEF) 5	1336	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				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)					CCTGGCTCCTCGGAGGAGGCA	0.542																																					p.S1336L		Atlas-SNP	.											ARHGEF5,NS,carcinoma,-1,1	ARHGEF5	73	1	0			c.C4007T						scavenged	.						12	12	12					7																	144069807		2148	4221	6369	SO:0001583	missense	7984	exon9			GCTCCTCGGAGGA	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.4007C>T	7.37:g.144069807C>T	ENSP00000056217:p.Ser1336Leu	881	2	0.00227015		587	114	0.194208	NM_005435	A6NNJ2|Q6ZML7	Missense_Mutation	SNP	ENST00000056217.5	37	CCDS34771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.58|11.58	1.682337|1.682337	0.29872|0.29872	.|.	.|.	ENSG00000050327|ENSG00000050327	ENST00000474817|ENST00000056217;ENST00000344879;ENST00000471847	.|T;T	.|0.63913	.|-0.07;-0.07	5.1|5.1	5.1|5.1	0.69264|0.69264	.|Dbl homology (DH) domain (5);	.|0.925322	.|0.09085	.|N	.|0.850706	T|T	0.40448|0.40448	0.1117|0.1117	N|N	0.11255|0.11255	0.115|0.115	0.09310|0.09310	N|N	0.999996|0.999996	.|B;P	.|0.49307	.|0.0;0.922	.|B;B	.|0.36534	.|0.005;0.227	T|T	0.10451|0.10451	-1.0629|-1.0629	5|10	.|0.40728	.|T	.|0.16	0.254|0.254	9.6027|9.6027	0.39615|0.39615	0.0:0.9043:0.0:0.0957|0.0:0.9043:0.0:0.0957	.|.	.|191;1336	.|B3KQX6;Q12774	.|.;ARHG5_HUMAN	W|L	590|1336;191;258	.|ENSP00000056217:S1336L;ENSP00000418227:S258L	.|ENSP00000056217:S1336L	R|S	+|+	1|2	2|0	ARHGEF5|ARHGEF5	143700740|143700740	0.001000|0.001000	0.12720|0.12720	0.974000|0.974000	0.42286|0.42286	0.355000|0.355000	0.29361|0.29361	1.151000|1.151000	0.31651|0.31651	2.369000|2.369000	0.80426|0.80426	0.655000|0.655000	0.94253|0.94253	CGG|TCG	.	.	none		0.542	ARHGEF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349981.1	NM_005435		T	144069807	C	T	144069807	3	4	23	1	0	0	0	0	1	0	0	0	909	893	31	1	4037	1	ARHGEF5	7	144069807	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	6919046	144069807	15068856	325	7769											
EZH2	2146	hgsc.bcm.edu	37	chr7	148525904	148525904	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtctccatcatcatcatcgtCatcatcattatattgaccaa	12	14	3	12	1	7	1	6	1	1	0	9	1	7	1	2	0	0	0	2	0	3	3	rs2302427	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:148525904C>G	ENST00000460911.1	-	6	641	c.553G>C	c.(553-555)Gac>Cac	p.D185H	EZH2_ENST00000476773.1_Missense_Mutation_p.D176H|EZH2_ENST00000541220.1_Missense_Mutation_p.D176H|EZH2_ENST00000350995.2_Missense_Mutation_p.D146H|EZH2_ENST00000536783.1_Missense_Mutation_p.D76H|EZH2_ENST00000320356.2_Missense_Mutation_p.D185H|EZH2_ENST00000478654.1_Missense_Mutation_p.D176H|EZH2_ENST00000483967.1_Missense_Mutation_p.D176H			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	185	Interaction with DNMT1, DNMT3A and DNMT3B.		D -> H (in dbSNP:rs2302427).		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)			tcatcatcgtcatcatcatta	0.393			Mis		DLBCL								C|||	400	0.0798722	0.0038	0.0461	5008	,	,		19098	0.2063		0.0696	False		,,,				2504	0.0869				p.D185H		Atlas-SNP	.		Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	EZH2_ENST00000350995,NS,carcinoma,+2,2	EZH2	823	2	0			c.G553C						PASS	.	C	HIS/ASP,HIS/ASP,HIS/ASP,HIS/ASP,HIS/ASP	66,4340	60.5+/-97.4	0,66,2137	178	146	157		553,526,526,553,436	5.7	0.9	7	dbSNP_100	157	719,7881	175.3+/-225.4	30,659,3611	yes	missense,missense,missense,missense,missense	EZH2	NM_001203247.1,NM_001203248.1,NM_001203249.1,NM_004456.4,NM_152998.2	81,81,81,81,81	30,725,5748	GG,GC,CC		8.3605,1.498,6.0357	benign,benign,benign,benign,benign	185/747,176/738,176/696,185/752,146/708	148525904	785,12221	2203	4300	6503	SO:0001583	missense	2146	exon6			CATCGTCATCATC		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.553G>C	7.37:g.148525904C>G	ENSP00000419711:p.Asp185His	204	0	0		141	83	0.588652	NM_001203247	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Missense_Mutation	SNP	ENST00000460911.1	37	CCDS56516.1	161	0.07371794871794872	3	0.006097560975609756	21	0.058011049723756904	83	0.1451048951048951	54	0.0712401055408971	C	19.43	3.826662	0.71143	0.01498	0.083605	ENSG00000106462	ENST00000478654;ENST00000320356;ENST00000460911;ENST00000350995;ENST00000541220;ENST00000476773;ENST00000483967;ENST00000536783	D;D;D;D;D;D;D;T	0.94828	-3.46;-3.5;-3.46;-3.5;-3.46;-3.46;-3.53;0.81	5.69	5.69	0.88448	SANT domain, DNA binding (1);	0.168733	0.49916	D	0.000127	T	0.08980	0.0222	L	0.34521	1.04	0.09310	P	0.99999641944	P;B;B;B;P;P	0.47604	0.898;0.348;0.348;0.41;0.659;0.676	P;B;B;B;B;P	0.49226	0.553;0.393;0.393;0.299;0.393;0.603	T	0.59161	-0.7506	9	0.72032	D	0.01	.	19.4235	0.94732	0.0:1.0:0.0:0.0	rs2302427;rs52833659	185;176;176;185;146;185	B7Z8K5;Q15910-4;Q15910-5;Q15910;Q15910-3;Q15910-2	.;.;.;EZH2_HUMAN;.;.	H	176;185;185;146;176;176;176;76	ENSP00000417062:D176H;ENSP00000320147:D185H;ENSP00000419711:D185H;ENSP00000223193:D146H;ENSP00000443219:D176H;ENSP00000419050:D176H;ENSP00000419856:D176H;ENSP00000439305:D76H	ENSP00000320147:D185H	D	-	1	0	EZH2	148156837	1.000000	0.71417	0.919000	0.36401	0.821000	0.46438	7.538000	0.82048	2.682000	0.91365	0.585000	0.79938	GAC	C|0.926;G|0.074	0.074	strong		0.393	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456		G	148525904	C	G	148525904	3	3	23	1	0	0	0	0	1	0	0	0	5336	826	29	4	1762	4	EZH2	7	148525904	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	4456097	148525904	10612759	326	7770											
ACTR3C	653857	hgsc.bcm.edu	37	chr7	149981856	149981856	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcataccttatacagcggacGccgcacatcgatggggcagt	10	8	11	12	4	1	0	1	0	0	0	2	2	1	1	2	3	3	2	2	3	3	3	rs117425825	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:149981856G>A	ENST00000539352.1	-	6	801	c.550C>T	c.(550-552)Cgt>Tgt	p.R184C	ACTR3C_ENST00000252071.4_Missense_Mutation_p.R184C	NM_001164458.1	NP_001157930.1	Q9C0K3	ARP3C_HUMAN	ARP3 actin-related protein 3 homolog C (yeast)	184						extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)										TACAGCGGACGCCGCACATCG	0.403													G|||	105	0.0209665	0.003	0.0187	5008	,	,		13887	0.0		0.0457	False		,,,				2504	0.0429				p.R184C		Atlas-SNP	.											.	.	.	.	0			c.C550T						PASS	.	G	CYS/ARG,CYS/ARG	13,1371		0,13,679	85	73	77		550,550	2.2	0.9	7	dbSNP_132	77	125,3057		1,123,1467	yes	missense,missense	ACTR3C	NM_001164458.1,NM_001164459.1	180,180	1,136,2146	AA,AG,GG		3.9283,0.9393,3.0223	probably-damaging,probably-damaging	184/211,184/211	149981856	138,4428	692	1591	2283	SO:0001583	missense	653857	exon6			GCGGACGCCGCAC		CCDS47744.1	7q36.1	2009-09-23			ENSG00000106526	ENSG00000106526			37282	protein-coding gene	gene with protein product						11162478, 14651955	Standard	NM_001164458		Approved	ARP11	uc022aps.1	Q9C0K3	OTTHUMG00000158323	ENST00000539352.1:c.550C>T	7.37:g.149981856G>A	ENSP00000440990:p.Arg184Cys	84	0	0		95	40	0.421053	NM_001164459	Q5CZI4	Missense_Mutation	SNP	ENST00000539352.1	37	CCDS47744.1	43	0.019688644688644688	0	0.0	10	0.027624309392265192	1	0.0017482517482517483	32	0.04221635883905013	G	13.83	2.352944	0.41700	0.009393	0.039283	ENSG00000106526	ENST00000478393;ENST00000252071;ENST00000539352	T;T;T	0.09350	2.99;2.99;2.99	2.16	2.16	0.27623	.	0.221425	0.28151	N	0.016416	T	0.14141	0.0342	H	0.97587	4.035	0.39214	D	0.963377	D	0.89917	1.0	D	0.68943	0.961	T	0.52961	-0.8505	9	.	.	.	.	10.4552	0.44546	0.0:0.0:1.0:0.0	.	184	Q9C0K3	ARP3C_HUMAN	C	182;184;184	ENSP00000417426:R182C;ENSP00000252071:R184C;ENSP00000440990:R184C	.	R	-	1	0	ACTR3C	149612789	1.000000	0.71417	0.896000	0.35187	0.654000	0.38779	4.696000	0.61774	1.511000	0.48818	0.398000	0.26397	CGT	G|0.976;A|0.024	0.024	strong		0.403	ACTR3C-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350676.2			A	149981856	G	A	149981856	3	1	23	1	0	0	0	0	1	0	0	0	214	1087	38	1	90	1	ACTR3C	7	149981856	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1455952	149981856	9156807	327	7771											
KCNH2	3757	hgsc.bcm.edu	37	chr7	150644428	150644428	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccctcacctgttgagctggCgctggagggcatccagcctg	5	9	13	14	1	1	1	1	1	0	0	3	2	3	2	4	3	2	4	4	3	0	1	rs36210421	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:150644428C>A	ENST00000262186.5	-	13	3541	c.3140G>T	c.(3139-3141)cGc>cTc	p.R1047L	KCNH2_ENST00000330883.4_Missense_Mutation_p.R707L|KCNH2_ENST00000392968.2_Missense_Mutation_p.R951L	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2	1047					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)	GTTGAGCTGGCGCTGGAGGGC	0.716													C|||	45	0.00898562	0.0	0.0043	5008	,	,		8790	0.001		0.0378	False		,,,				2504	0.0031				p.R1047L	GBM(137;110 1844 13671 20123 45161)	Atlas-SNP	.											.	KCNH2	157	.	0			c.G3140T	GRCh37	CM045797	KCNH2	M	rs36210421	PASS	.	C	LEU/ARG,LEU/ARG	16,3806		0,16,1895	5	7	6		3140,2120	4.1	1	7	dbSNP_126	6	139,7661		0,139,3761	no	missense,missense	KCNH2	NM_000238.3,NM_172057.2	102,102	0,155,5656	AA,AC,CC		1.7821,0.4186,1.3337	possibly-damaging,possibly-damaging	1047/1160,707/820	150644428	155,11467	1911	3900	5811	SO:0001583	missense	3757	exon13			AGCTGGCGCTGGA	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.3140G>T	7.37:g.150644428C>A	ENSP00000262186:p.Arg1047Leu	7	0	0		15	10	0.666667	NM_000238	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Missense_Mutation	SNP	ENST00000262186.5	37	CCDS5910.1	37	0.01694139194139194	0	0.0	4	0.011049723756906077	0	0.0	33	0.04353562005277045	C	19.00	3.741960	0.69418	0.004186	0.017821	ENSG00000055118	ENST00000330883;ENST00000392968;ENST00000262186	D;D;D	0.87256	-2.23;-2.23;-2.23	4.97	4.09	0.47781	.	0.140191	0.45867	D	0.000324	T	0.52500	0.1738	L	0.40543	1.245	0.80722	D	1	B;B;B	0.22146	0.039;0.039;0.065	B;B;B	0.23275	0.028;0.02;0.045	T	0.64922	-0.6293	10	0.36615	T	0.2	.	7.6627	0.28413	0.0:0.8092:0.0:0.1908	rs36210421;rs41313758	951;1047;707	C4PFH9;Q12809;Q12809-2	.;KCNH2_HUMAN;.	L	707;951;1047	ENSP00000328531:R707L;ENSP00000376695:R951L;ENSP00000262186:R1047L	ENSP00000262186:R1047L	R	-	2	0	KCNH2	150275361	0.000000	0.05858	0.998000	0.56505	0.966000	0.64601	-0.090000	0.11163	1.094000	0.41399	0.555000	0.69702	CGC	C|0.983;A|0.017	0.017	strong		0.716	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2	NM_000238		A	150644428	C	A	150644428	3	1	23	1	0	0	0	0	1	0	0	0	8041	768	27	4	351	4	KCNH2	7	150644428	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	662572	150644428	8494235	328	7772											
GALNT11	63917	hgsc.bcm.edu	37	chr7	151791435	151791435	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagccacttaagaatgtgccCgtcaaggggtctgggcccca	9	7	12	13	1	2	1	1	0	1	1	2	1	2	1	4	3	2	0	4	3	3	1	rs138436495	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:151791435C>T	ENST00000434507.1	+	4	560	c.123C>T	c.(121-123)ccC>ccT	p.P41P	GALNT11_ENST00000422997.2_Silent_p.P41P|GALNT11_ENST00000320311.2_Silent_p.P41P|GALNT11_ENST00000415421.1_Silent_p.P41P|GALNT11_ENST00000452146.2_Intron|GALNT11_ENST00000482812.1_3'UTR|GALNT11_ENST00000430044.2_Silent_p.P41P			Q8NCW6	GLT11_HUMAN	polypeptide N-acetylgalactosaminyltransferase 11	41					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)		AGAATGTGCCCGTCAAGGGGT	0.473													C|||	4	0.000798722	0.0	0.0029	5008	,	,		16967	0.0		0.002	False		,,,				2504	0.0				p.P41P		Atlas-SNP	.											GALNT11,NS,carcinoma,+1,1	GALNT11	59	1	0			c.C123T						PASS	.	C		4,4402	8.1+/-20.4	0,4,2199	138	141	140		123	5.7	1	7	dbSNP_134	140	23,8577	16.6+/-54.9	0,23,4277	no	coding-synonymous	GALNT11	NM_022087.2		0,27,6476	TT,TC,CC		0.2674,0.0908,0.2076		41/609	151791435	27,12979	2203	4300	6503	SO:0001819	synonymous_variant	63917	exon2			TGTGCCCGTCAAG	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.123C>T	7.37:g.151791435C>T		93	0	0		122	72	0.590164	NM_022087	B3KWF4|Q6PCD1|Q9H6C2|Q9H6Z5|Q9UDR8	Silent	SNP	ENST00000434507.1	37	CCDS5930.1																																																																																			C|0.998;T|0.002	0.002	strong		0.473	GALNT11-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348184.1	NM_022087		T	151791435	C	T	151791435	2	4	23	1	0	0	0	0	0	0	0	1	6217	639	23	1		1	GALNT11	7	151791435	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1147007	151791435	7347228	329	7773											
ARHGEF10	9639	hgsc.bcm.edu	37	chr8	1893773	1893773	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcacacggaaactctcaagCacctgcaggacatcaacatc	14	7	6	14	1	3	0	3	0	1	0	5	2	3	2	1	2	4	2	1	2	3	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:1893773C>A	ENST00000398564.1	+	27	3424	c.3424C>A	c.(3424-3426)Cac>Aac	p.H1142N	ARHGEF10_ENST00000520359.1_Missense_Mutation_p.H1079N|ARHGEF10_ENST00000262112.6_Missense_Mutation_p.H1113N|ARHGEF10_ENST00000349830.3_Missense_Mutation_p.H1117N|ARHGEF10_ENST00000518288.1_Missense_Mutation_p.H1141N|ARHGEF10_ENST00000521927.1_3'UTR			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	1142					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)		AACTCTCAAGCACCTGCAGGA	0.617																																					p.H1117N		Atlas-SNP	.											.	ARHGEF10	255	.	0			c.C3349A						PASS	.						134	106	115					8																	1893773		2203	4300	6503	SO:0001583	missense	9639	exon27			CTCAAGCACCTGC	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.3424C>A	8.37:g.1893773C>A	ENSP00000381571:p.His1142Asn	112	0	0		139	71	0.510791	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Missense_Mutation	SNP	ENST00000398564.1	37		.	.	.	.	.	.	.	.	.	.	c	14.10	2.433766	0.43224	.	.	ENSG00000104728	ENST00000349830;ENST00000520359;ENST00000518288;ENST00000398564;ENST00000262112;ENST00000522435	T;T;T;T;T;T	0.62639	1.55;1.55;1.55;1.55;0.01;0.01	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	T	0.68668	0.3026	M	0.82823	2.61	0.80722	D	1	B;P	0.34892	0.047;0.474	B;B	0.36335	0.059;0.222	T	0.72757	-0.4197	10	0.48119	T	0.1	-35.744	18.2931	0.90137	0.0:1.0:0.0:0.0	.	1079;1117	O15013-7;O15013-5	.;.	N	1117;1079;1141;1142;1113;761	ENSP00000340297:H1117N;ENSP00000427909:H1079N;ENSP00000431012:H1141N;ENSP00000381571:H1142N;ENSP00000262112:H1113N;ENSP00000427768:H761N	ENSP00000262112:H1113N	H	+	1	0	ARHGEF10	1881180	1.000000	0.71417	0.927000	0.36925	0.343000	0.28985	6.849000	0.75414	2.302000	0.77476	0.431000	0.28591	CAC	.	.	none		0.617	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding				A	1893773	C	A	1893773	3	1	23	1	0	0	0	0	1	0	0	0	894	710	25	4	3451	4	ARHGEF10	8	1893773	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10		1893773	144470249	330	7774											
TNKS	8658	hgsc.bcm.edu	37	chr8	9605648	9605648	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggaaggacgcagctgtgcGccctcctcctagcgcatggt	8	7	13	13	3	0	0	0	0	0	0	2	2	2	2	3	3	3	3	3	3	3	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:9605648G>A	ENST00000310430.6	+	18	2784	c.2758G>A	c.(2758-2760)Gcc>Acc	p.A920T	TNKS_ENST00000518281.1_Missense_Mutation_p.A683T	NM_003747.2	NP_003738.2	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	920					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)	p.A920T(1)		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)		GCAGCTGTGCGCCCTCCTCCT	0.507																																					p.A920T		Atlas-SNP	.											TNKS_ENST00000310430,NS,carcinoma,0,3	TNKS	198	3	1	Substitution - Missense(1)	kidney(1)	c.G2758A						PASS	.						93	88	90					8																	9605648		2203	4300	6503	SO:0001583	missense	8658	exon18			CTGTGCGCCCTCC	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.2758G>A	8.37:g.9605648G>A	ENSP00000311579:p.Ala920Thr	112	0	0		113	16	0.141593	NM_003747	O95272|Q4G0F2	Missense_Mutation	SNP	ENST00000310430.6	37	CCDS5974.1	.	.	.	.	.	.	.	.	.	.	G	17.05	3.288784	0.59976	.	.	ENSG00000173273	ENST00000310430;ENST00000518281	T;T	0.65549	-0.16;-0.16	5.88	5.88	0.94601	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.53948	0.1828	N	0.21194	0.64	0.80722	D	1	B	0.27791	0.189	B	0.29716	0.106	T	0.49123	-0.8972	10	0.41790	T	0.15	.	20.2381	0.98363	0.0:0.0:1.0:0.0	.	920	O95271	TNKS1_HUMAN	T	920;683	ENSP00000311579:A920T;ENSP00000429890:A683T	ENSP00000311579:A920T	A	+	1	0	TNKS	9643058	1.000000	0.71417	1.000000	0.80357	0.041000	0.13682	9.623000	0.98386	2.779000	0.95612	0.650000	0.86243	GCC	.	.	none		0.507	TNKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206935.1	NM_003747		A	9605648	G	A	9605648	3	1	23	1	0	0	0	0	1	0	0	0	16334	1087	38	1	2828	1	TNKS	8	9605648	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	7711875	9605648	136758374	331	7775											
RP1L1	94137	hgsc.bcm.edu	37	chr8	10469292	10469292	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggaggtatgggggccggCgagcatgtcctggaccccgc	5	6	19	11	3	0	0	0	0	0	0	1	3	1	2	4	7	1	2	4	7	1	1	rs62490857	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:10469292C>T	ENST00000382483.3	-	4	2539	c.2316G>A	c.(2314-2316)tcG>tcA	p.S772S		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	772					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)		TGGGGGCCGGCGAGCATGTCC	0.662													C|||	152	0.0303514	0.0023	0.0288	5008	,	,		16095	0.001		0.1083	False		,,,				2504	0.0194				p.S772S		Atlas-SNP	.											.	RP1L1	453	.	0			c.G2316A						PASS	.	C		64,3840		0,64,1888	50	57	55		2316	-10.2	0	8	dbSNP_129	55	681,7581		25,631,3475	no	coding-synonymous	RP1L1	NM_178857.5		25,695,5363	TT,TC,CC		8.2426,1.6393,6.1236		772/2401	10469292	745,11421	1952	4131	6083	SO:0001819	synonymous_variant	94137	exon4			GGCCGGCGAGCAT	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.2316G>A	8.37:g.10469292C>T		141	0	0		123	65	0.528455	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																			C|0.945;T|0.055	0.055	strong		0.662	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			T	10469292	C	T	10469292	2	4	23	1	0	0	0	0	0	0	0	1	13548	755	27	1		1	RP1L1	8	10469292	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	863644	10469292	135894730	332	7776											
MTMR7	9108	hgsc.bcm.edu	37	chr8	17169039	17169039	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatgaagcccttcagagtcCggtagtgagggtccagcagc	9	7	13	12	1	1	3	1	2	0	1	3	3	3	3	4	2	3	2	4	2	2	2	rs147637471		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:17169039C>T	ENST00000180173.5	-	9	1116	c.1082G>A	c.(1081-1083)cGg>cAg	p.R361Q	MTMR7_ENST00000398099.3_5'UTR|MTMR7_ENST00000521857.1_Missense_Mutation_p.R361Q	NM_004686.4	NP_004677.3	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	361	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)		CTTCAGAGTCCGGTAGTGAGG	0.582																																					p.R361Q		Atlas-SNP	.											.	MTMR7	75	.	0			c.G1082A						PASS	.	C	GLN/ARG	0,4406		0,0,2203	214	209	211		1082	4.9	1	8	dbSNP_134	211	3,8597	3.0+/-9.4	0,3,4297	no	missense	MTMR7	NM_004686.4	43	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging	361/661	17169039	3,13003	2203	4300	6503	SO:0001583	missense	9108	exon9			AGAGTCCGGTAGT	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.1082G>A	8.37:g.17169039C>T	ENSP00000180173:p.Arg361Gln	73	0	0		84	38	0.452381	NM_004686	A1L4K9|B4DG87|Q68DX4	Missense_Mutation	SNP	ENST00000180173.5	37	CCDS34851.1	.	.	.	.	.	.	.	.	.	.	C	34	5.299020	0.95574	0.0	3.49E-4	ENSG00000003987	ENST00000180173;ENST00000521857	D;D	0.98135	-4.74;-4.74	4.86	4.86	0.63082	Myotubularin phosphatase domain (1);	0.047533	0.85682	D	0.000000	D	0.99405	0.9790	H	0.99516	4.605	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	D	0.98030	1.0376	10	0.87932	D	0	.	18.5539	0.91075	0.0:1.0:0.0:0.0	.	361;361	Q9Y216-2;Q9Y216	.;MTMR7_HUMAN	Q	361	ENSP00000180173:R361Q;ENSP00000429733:R361Q	ENSP00000180173:R361Q	R	-	2	0	MTMR7	17213410	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.651000	0.83577	2.697000	0.92050	0.655000	0.94253	CGG	C|1.000;T|0.000	0.000	weak		0.582	MTMR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375311.1	NM_004686		T	17169039	C	T	17169039	3	4	23	1	0	0	0	0	1	0	0	0	9957	652	23	1	924	1	MTMR7	8	17169039	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	6699747	17169039	129194983	333	7777											
MTUS1	57509	hgsc.bcm.edu	37	chr8	17503612	17503612	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	actttcgactccttctccagCgactcttgcagaacagcctg	8	11	7	15	2	2	1	0	0	2	1	5	3	3	1	3	0	4	1	3	0	1	3	rs61733704	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:17503612C>G	ENST00000262102.6	-	15	3860	c.3636G>C	c.(3634-3636)tcG>tcC	p.S1212S	MTUS1_ENST00000544260.1_Silent_p.S357S|MTUS1_ENST00000381861.3_Silent_p.S459S|MTUS1_ENST00000297488.6_Silent_p.S378S|MTUS1_ENST00000519263.1_Silent_p.S1158S|MTUS1_ENST00000400046.1_Silent_p.S284S|MTUS1_ENST00000381869.3_Silent_p.S1158S	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	1212					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)		CCTTCTCCAGCGACTCTTGCA	0.448													C|||	77	0.0153754	0.0015	0.0115	5008	,	,		14078	0.0		0.0388	False		,,,				2504	0.0286				p.S1212S		Atlas-SNP	.											.	MTUS1	144	.	0			c.G3636C						PASS	.	C	,,,,	21,3729		0,21,1854	38	39	39		3636,3474,1377,1071,1134	-8.9	0	8	dbSNP_129	39	329,7903		2,325,3789	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MTUS1	NM_001001924.2,NM_001001925.2,NM_001001931.2,NM_001166393.1,NM_020749.4	,,,,	2,346,5643	GG,GC,CC		3.9966,0.56,2.921	,,,,	1212/1271,1158/1217,459/518,357/416,378/437	17503612	350,11632	1875	4116	5991	SO:0001819	synonymous_variant	57509	exon15			CTCCAGCGACTCT	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.3636G>C	8.37:g.17503612C>G		68	0	0		76	41	0.539474	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Silent	SNP	ENST00000262102.6	37	CCDS43717.1																																																																																			C|0.956;G|0.044	0.044	strong		0.448	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		G	17503612	C	G	17503612	2	3	23	1	0	0	0	0	0	0	0	1	9974	755	27	4		4	MTUS1	8	17503612	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	334573	17503612	128860410	334	7778											
ADAM28	10863	hgsc.bcm.edu	37	chr8	24167700	24167700	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctccttgcaccaggctacacGgaaacatattataattccac	13	10	5	13	1	0	0	0	0	0	0	2	1	2	1	3	2	3	2	3	2	5	6	rs150620720	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:24167700G>A	ENST00000265769.4	+	4	362	c.252G>A	c.(250-252)acG>acA	p.T84T	RP11-624C23.1_ENST00000523578.1_RNA|ADAM28_ENST00000540823.1_5'UTR|RP11-624C23.1_ENST00000518988.1_RNA|ADAM28_ENST00000397649.3_5'UTR|RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523700.1_RNA|ADAM28_ENST00000437154.2_Silent_p.T84T	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	84					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)		CAGGCTACACGGAAACATATT	0.398													A|||	2	0.000399361	0.0	0.0	5008	,	,		18307	0.0		0.002	False		,,,				2504	0.0				p.T84T	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											ADAM28,NS,carcinoma,0,1	ADAM28	100	1	0			c.G252A						PASS	.	A	,	1,4405	825.4+/-416.5	0,1,2202	92	79	83		252,252	-9.1	0	8	dbSNP_134	83	1,8599	818.4+/-406.9	0,1,4299	no	coding-synonymous,coding-synonymous	ADAM28	NM_014265.4,NM_021777.3	,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	,	84/776,84/541	24167700	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	10863	exon4			CTACACGGAAACA	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.252G>A	8.37:g.24167700G>A		72	0	0		93	37	0.397849	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Silent	SNP	ENST00000265769.4	37	CCDS34865.1																																																																																			G|1.000;A|0.000	0.000	strong		0.398	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778		A	24167700	G	A	24167700	2	1	23	1	0	0	0	0	0	0	0	1	246	1103	39	1		1	ADAM28	8	24167700	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	6664088	24167700	122196322	335	7779											
NRG1	3084	hgsc.bcm.edu	37	chr8	32611970	32611970	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtggtcggcatcatgtgtGtggtggcctactgcaaaacc	7	12	13	9	1	1	0	1	0	0	0	2	0	1	0	2	4	3	2	2	4	3	2	rs74942016	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:32611970G>T	ENST00000405005.3	+	8	781	c.781G>T	c.(781-783)Gtg>Ttg	p.V261L	NRG1_ENST00000287845.5_Missense_Mutation_p.V232L|NRG1_ENST00000539990.1_Missense_Mutation_p.V104L|NRG1_ENST00000356819.4_Missense_Mutation_p.V266L|NRG1_ENST00000341377.5_3'UTR|NRG1_ENST00000519301.1_Missense_Mutation_p.V211L|NRG1_ENST00000338921.4_Missense_Mutation_p.V269L|NRG1_ENST00000521670.1_Missense_Mutation_p.V261L|NRG1_ENST00000523079.1_Missense_Mutation_p.V258L|NRG1_ENST00000287842.3_Missense_Mutation_p.V258L			Q02297	NRG1_HUMAN	neuregulin 1	261				V -> L (in Ref. 10; ABQ53540). {ECO:0000305}.	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)		CATCATGTGTGTGGTGGCCTA	0.527													G|||	72	0.014377	0.0008	0.0259	5008	,	,		17487	0.0		0.0467	False		,,,				2504	0.0061				p.V266L		Atlas-SNP	.											.	NRG1	260	.	0			c.G796T	GRCh37	CM066934	NRG1	M	rs74942016	PASS	.	G	LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL	47,4359	48.9+/-83.8	0,47,2156	226	165	186		682,319,733,631,772,772,796,772,781,781	5.6	1	8	dbSNP_131	186	405,8195	127.5+/-185.8	12,381,3907	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	NRG1	NM_001159995.1,NM_001159996.1,NM_001159999.1,NM_001160001.1,NM_001160004.1,NM_001160008.1,NM_013956.3,NM_013957.3,NM_013960.3,NM_013964.3	32,32,32,32,32,32,32,32,32,32	12,428,6063	TT,TG,GG		4.7093,1.0667,3.4753	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	228/608,107/309,245/625,211/591,258/460,258/421,266/646,258/638,261/463,261/641	32611970	452,12554	2203	4300	6503	SO:0001583	missense	3084	exon9			ATGTGTGTGGTGG	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.781G>T	8.37:g.32611970G>T	ENSP00000384620:p.Val261Leu	172	0	0		188	69	0.367021	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	37	CCDS6085.1	40	0.018315018315018316	0	0.0	9	0.024861878453038673	0	0.0	31	0.040897097625329816	G	35	5.558867	0.96514	0.010667	0.047093	ENSG00000157168	ENST00000518104;ENST00000519301;ENST00000523534;ENST00000523079;ENST00000338921;ENST00000356819;ENST00000287840;ENST00000287845;ENST00000287842;ENST00000405005;ENST00000521670;ENST00000522402;ENST00000519240;ENST00000539990	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.61040	0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;2.63;0.14	5.62	5.62	0.85841	Neuregulin 1-related, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.40932	0.1137	M	0.73962	2.25	0.80722	D	1	D;D;D;D;D;D;P;D;P;D;D	0.71674	0.979;0.998;0.995;0.979;0.983;0.995;0.599;0.962;0.946;0.979;0.994	D;D;D;P;D;D;B;P;P;P;D	0.85130	0.986;0.997;0.972;0.879;0.926;0.972;0.283;0.879;0.893;0.879;0.914	T	0.67722	-0.5597	10	0.72032	D	0.01	-36.9375	19.6569	0.95845	0.0:0.0:1.0:0.0	.	104;107;258;232;266;257;269;258;261;266;261	B7Z1E3;B7Z1D7;E9PHH4;F8W9E3;Q7RTW4;B0FYA9;Q02297-2;Q02297-7;Q02297;Q02297-6;Q02297-3	.;.;.;.;.;.;.;.;NRG1_HUMAN;.;.	L	228;211;334;258;269;266;261;232;258;261;261;107;104;104	ENSP00000430053:V228L;ENSP00000429582:V211L;ENSP00000429067:V334L;ENSP00000430120:V258L;ENSP00000343395:V269L;ENSP00000349275:V266L;ENSP00000287840:V261L;ENSP00000287845:V232L;ENSP00000287842:V258L;ENSP00000384620:V261L;ENSP00000428828:V261L;ENSP00000430862:V107L;ENSP00000428411:V104L;ENSP00000439276:V104L	ENSP00000287840:V261L	V	+	1	0	NRG1	32731512	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.639000	0.89480	0.650000	0.86243	GTG	G|0.968;T|0.032	0.032	strong		0.527	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1			T	32611970	G	T	32611970	3	4	23	1	0	0	0	0	1	0	0	0	10656	1377	48	4	2407	4	NRG1	8	32611970	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	8444270	32611970	113752052	336	7780											
C8orf41	80185	hgsc.bcm.edu	37	chr8	33361280	33361280	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcacctgttcacgaaagcCggcaggtttcttgcgtaggt	7	11	11	12	3	3	0	2	0	1	0	3	1	3	0	3	3	2	4	3	3	2	4	rs17850186	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:33361280C>T	ENST00000431156.2	-	5	1719	c.1101G>A	c.(1099-1101)ccG>ccA	p.P367P	TTI2_ENST00000519356.1_5'UTR|TTI2_ENST00000360742.5_Silent_p.P367P|TTI2_ENST00000520636.1_Silent_p.P336P	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	367																	TCACGAAAGCCGGCAGGTTTC	0.527													C|||	43	0.00858626	0.0023	0.0058	5008	,	,		17510	0.002		0.0229	False		,,,				2504	0.0112				p.P367P		Atlas-SNP	.											C8orf41,rectum,carcinoma,0,2	.	.	2	0			c.G1101A						PASS	.	C	,	17,4389	24.3+/-50.5	0,17,2186	33	31	32		1101,1101	-8.6	0.2	8	dbSNP_123	32	172,8428	78.4+/-141.0	3,166,4131	no	coding-synonymous,coding-synonymous	TTI2	NM_001102401.1,NM_025115.2	,	3,183,6317	TT,TC,CC		2.0,0.3858,1.4532	,	367/509,367/509	33361280	189,12817	2203	4300	6503	SO:0001819	synonymous_variant	80185	exon5			GAAAGCCGGCAGG	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.1101G>A	8.37:g.33361280C>T		96	0	0		51	23	0.45098	NM_001265581	D3DSV7|Q96IM2|Q9H5N4	Silent	SNP	ENST00000431156.2	37	CCDS6090.1																																																																																			C|0.986;T|0.014	0.014	strong		0.527	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115		T	33361280	C	T	33361280	2	4	23	1	0	0	0	0	0	0	0	1	2429	639	23	1		1	C8orf41	8	33361280	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	749310	33361280	113002742	337	7781											
MYST3	7994	hgsc.bcm.edu	37	chr8	41790866	41790866	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ctgcagttggcagcaggctgGacgctgctctgctgcatcat	6	10	13	12	1	2	0	1	0	1	0	2	1	2	1	0	3	5	9	0	3	0	1	rs2980901	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:41790866G>C	ENST00000396930.3	-	18	5415	c.4872C>G	c.(4870-4872)gtC>gtG	p.V1624V	KAT6A_ENST00000265713.2_Silent_p.V1624V|KAT6A_ENST00000406337.1_Silent_p.V1624V	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1624	Interaction with PML.|Interaction with RUNX1-2.				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)										CAGCAGGCTGGACGCTGCTCT	0.642													G|||	182	0.0363419	0.1074	0.0159	5008	,	,		16184	0.0089		0.0089	False		,,,				2504	0.0112				p.V1624V		Atlas-SNP	.											.	.	.	.	0			c.C4872G						PASS	.	G	,,	386,4016		16,354,1831	29	26	27		4872,4872,4872	1.7	1	8	dbSNP_101	27	123,8469		0,123,4173	no	coding-synonymous,coding-synonymous,coding-synonymous	KAT6A	NM_001099412.1,NM_001099413.1,NM_006766.3	,,	16,477,6004	CC,CG,GG		1.4316,8.7687,3.9172	,,	1624/2005,1624/2005,1624/2005	41790866	509,12485	2201	4296	6497	SO:0001819	synonymous_variant	7994	exon18			AGGCTGGACGCTG	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.4872C>G	8.37:g.41790866G>C		50	0	0		46	25	0.543478	NM_001099412	Q76L81	Silent	SNP	ENST00000396930.3	37	CCDS6124.1																																																																																			G|0.964;C|0.036	0.036	strong		0.642	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		C	41790866	G	C	41790866	2	2	23	1	0	0	0	0	0	0	0	1	10113	1161	41	4		4	MYST3	8	41790866	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	8429586	41790866	104573156	338	7782											
ARFGEF1	10565	hgsc.bcm.edu	37	chr8	68130265	68130265	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cacacaccagtagagctgagCaaaaatgtcatccaaaagta	18	6	7	10	0	1	2	1	1	0	1	2	2	2	2	2	0	2	4	2	0	6	2	rs142342517	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:68130265C>A	ENST00000262215.3	-	31	4836	c.4447G>T	c.(4447-4449)Gct>Tct	p.A1483S	ARFGEF1_ENST00000520381.1_Missense_Mutation_p.A937S|ARFGEF1_ENST00000518230.1_Missense_Mutation_p.A321S	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	1483					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)			TAGAGCTGAGCAAAAATGTCA	0.373													C|||	8	0.00159744	0.0	0.0014	5008	,	,		11866	0.0		0.007	False		,,,				2504	0.0				p.A1483S		Atlas-SNP	.											.	ARFGEF1	196	.	0			c.G4447T						PASS	.	C	SER/ALA	8,4398	12.9+/-30.5	0,8,2195	108	96	100		4447	4.6	1	8	dbSNP_134	100	79,8521	46.3+/-105.2	0,79,4221	yes	missense	ARFGEF1	NM_006421.4	99	0,87,6416	AA,AC,CC		0.9186,0.1816,0.6689	benign	1483/1850	68130265	87,12919	2203	4300	6503	SO:0001583	missense	10565	exon31			GCTGAGCAAAAAT	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.4447G>T	8.37:g.68130265C>A	ENSP00000262215:p.Ala1483Ser	112	0	0		128	62	0.484375	NM_006421	Q9NV46|Q9UFV2|Q9UNL0	Missense_Mutation	SNP	ENST00000262215.3	37	CCDS6199.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	10.81	1.455699	0.26161	0.001816	0.009186	ENSG00000066777	ENST00000520381;ENST00000262215;ENST00000518230	T;T;T	0.63913	0.07;-0.07;-0.03	5.48	4.59	0.56863	Armadillo-like helical (1);Armadillo-type fold (1);	0.052243	0.85682	D	0.000000	T	0.39784	0.1091	N	0.25890	0.77	0.44254	D	0.997101	B;B;B	0.12013	0.005;0.0;0.0	B;B;B	0.10450	0.005;0.001;0.002	T	0.34700	-0.9818	10	0.11182	T	0.66	.	15.9776	0.80083	0.136:0.864:0.0:0.0	.	1483;961;937	Q9Y6D6;Q59FY5;E5RIF2	BIG1_HUMAN;.;.	S	937;1483;321	ENSP00000428429:A937S;ENSP00000262215:A1483S;ENSP00000430891:A321S	ENSP00000262215:A1483S	A	-	1	0	ARFGEF1	68292819	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.366000	0.44204	1.427000	0.47276	0.655000	0.94253	GCT	C|0.995;A|0.005	0.005	strong		0.373	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421		A	68130265	C	A	68130265	3	1	23	1	0	0	0	0	1	0	0	0	852	710	25	4	1138	4	ARFGEF1	8	68130265	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	26339399	68130265	78233757	339	7783											
FABP9	646480	hgsc.bcm.edu	37	chr8	82370894	82370894	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gttgtctctttgccaagccaTttttggacgtgaatcattga	8	16	9	8	1	2	2	1	2	1	0	3	3	2	3	2	1	2	1	2	1	2	5	rs139486050	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:82370894T>C	ENST00000379071.2	-	3	346	c.291A>G	c.(289-291)aaA>aaG	p.K97K	RP11-157I4.4_ENST00000524085.2_RNA	NM_001080526.1	NP_001073995.1	Q0Z7S8	FABP9_HUMAN	fatty acid binding protein 9, testis	97					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)			TGCCAAGCCATTTTTGGACGT	0.328													T|||	2	0.000399361	0.0	0.0014	5008	,	,		18485	0.0		0.001	False		,,,				2504	0.0				p.K97K		Atlas-SNP	.											.	FABP9	15	.	0			c.A291G						PASS	.	T		5,4397	9.9+/-24.2	0,5,2196	103	95	98		291	2.7	1	8	dbSNP_134	98	20,8580	14.6+/-50.1	0,20,4280	no	coding-synonymous	FABP9	NM_001080526.1		0,25,6476	CC,CT,TT		0.2326,0.1136,0.1923		97/133	82370894	25,12977	2201	4300	6501	SO:0001819	synonymous_variant	646480	exon3			AAGCCATTTTTGG			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.291A>G	8.37:g.82370894T>C		224	0	0		254	127	0.5	NM_001080526		Silent	SNP	ENST00000379071.2	37																																																																																				T|0.999;C|0.001	0.001	strong		0.328	FABP9-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379367.2	NM_001080526		C	82370894	T	C	82370894	2	2	23	1	0	0	0	0	0	0	0	1	5368	1490	52	3		3	FABP9	8	82370894	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	14240629	82370894	63993128	340	7784											
CA13	377677	hgsc.bcm.edu	37	chr8	86180719	86180719	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggtaaacaaactcgattcAcaaattttgacctattgtct	14	13	6	8	1	2	1	1	1	1	0	3	2	2	1	1	1	2	1	1	1	5	6	rs75353219	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:86180719A>G	ENST00000321764.3	+	6	834	c.532A>G	c.(532-534)Aca>Gca	p.T178A	CA13_ENST00000517298.1_3'UTR	NM_198584.2	NP_940986.1	Q8N1Q1	CAH13_HUMAN	carbonic anhydrase XIII	178					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|myelin sheath (GO:0043209)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(6)	7					Zonisamide(DB00909)	AACTCGATTCACAAATTTTGA	0.413													A|||	24	0.00479233	0.0015	0.0058	5008	,	,		17595	0.0		0.0139	False		,,,				2504	0.0041				p.T178A		Atlas-SNP	.											.	CA13	26	.	0			c.A532G						PASS	.	A	ALA/THR	8,4398	12.9+/-30.5	0,8,2195	171	159	163		532	5.5	1	8	dbSNP_131	163	132,8468	68.0+/-130.5	1,130,4169	yes	missense	CA13	NM_198584.2	58	1,138,6364	GG,GA,AA		1.5349,0.1816,1.0764	benign	178/263	86180719	140,12866	2203	4300	6503	SO:0001583	missense	377677	exon6			CGATTCACAAATT	BC052602	CCDS6236.1	8q21	2004-05-10				ENSG00000185015		"Carbonic anhydrases"	14914	protein-coding gene	gene with protein product		611436				14600151	Standard	NM_198584		Approved	CAXIII, FLJ37995, MGC59868	uc003ydg.2	Q8N1Q1		ENST00000321764.3:c.532A>G	8.37:g.86180719A>G	ENSP00000318912:p.Thr178Ala	185	0	0		187	98	0.524064	NM_198584		Missense_Mutation	SNP	ENST00000321764.3	37	CCDS6236.1	13	0.005952380952380952	0	0.0	0	0.0	0	0.0	13	0.017150395778364115	A	14.11	2.436542	0.43224	0.001816	0.015349	ENSG00000185015	ENST00000321764	T	0.63580	-0.05	5.5	5.5	0.81552	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.144213	0.64402	D	0.000006	T	0.35885	0.0947	L	0.38953	1.18	0.46849	D	0.999224	B	0.21381	0.055	B	0.21917	0.037	T	0.38001	-0.9681	10	0.21540	T	0.41	-11.4932	14.5856	0.68322	1.0:0.0:0.0:0.0	.	178	Q8N1Q1	CAH13_HUMAN	A	178	ENSP00000318912:T178A	ENSP00000318912:T178A	T	+	1	0	CA13	86367971	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	2.135000	0.42112	2.104000	0.64026	0.383000	0.25322	ACA	A|0.992;G|0.008	0.008	strong		0.413	CA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381066.1	NM_198584		G	86180719	A	G	86180719	3	3	23	1	0	0	0	0	1	0	0	0	2516	159	6	3	554	3	CA13	8	86180719	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	3809825	86180719	60183303	341	7785											
VPS13B	157680	hgsc.bcm.edu	37	chr8	100454804	100454804	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gattattagtgctgggcacaAgtatatggaacctctgcagg	11	11	12	7	0	1	0	0	0	1	0	1	2	1	1	1	3	3	4	1	3	6	4	rs61759485	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:100454804A>G	ENST00000358544.2	+	23	3497	c.3386A>G	c.(3385-3387)aAg>aGg	p.K1129R	VPS13B_ENST00000357162.2_Missense_Mutation_p.K1129R|VPS13B_ENST00000395996.1_Missense_Mutation_p.K1129R	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	1129					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)			GCTGGGCACAAGTATATGGAA	0.398													A|||	7	0.00139776	0.0	0.0058	5008	,	,		17905	0.0		0.003	False		,,,				2504	0.0				p.K1129R	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.A3386G						PASS	.	A	ARG/LYS,ARG/LYS	16,4390	24.3+/-50.5	0,16,2187	100	96	97		3386,3386	3.3	0.9	8	dbSNP_129	97	35,8565	22.8+/-68.1	0,35,4265	yes	missense,missense	VPS13B	NM_017890.3,NM_152564.3	26,26	0,51,6452	GG,GA,AA		0.407,0.3631,0.3921	probably-damaging,probably-damaging	1129/4023,1129/3998	100454804	51,12955	2203	4300	6503	SO:0001583	missense	157680	exon23			GGCACAAGTATAT	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.3386A>G	8.37:g.100454804A>G	ENSP00000351346:p.Lys1129Arg	134	0	0		150	75	0.5	NM_152564	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	7	0.003205128205128205	0	0.0	4	0.011049723756906077	0	0.0	3	0.00395778364116095	A	19.74	3.883056	0.72410	0.003631	0.00407	ENSG00000132549	ENST00000357162;ENST00000358544;ENST00000395996	T;T;T	0.25912	1.77;1.77;1.77	5.71	3.34	0.38264	.	0.105634	0.64402	N	0.000012	T	0.32852	0.0843	L	0.49350	1.555	0.41967	D	0.990735	D;D;B;D	0.76494	0.999;0.998;0.125;0.989	D;D;B;D	0.78314	0.991;0.937;0.028;0.967	T	0.05321	-1.0892	10	0.51188	T	0.08	.	10.0017	0.41933	0.8633:0.0:0.1367:0.0	rs61759485	1128;1129;1129;1129	Q7Z7G8-6;Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3	.;.;VP13B_HUMAN;.	R	1129	ENSP00000349685:K1129R;ENSP00000351346:K1129R;ENSP00000379318:K1129R	ENSP00000349685:K1129R	K	+	2	0	VPS13B	100523980	1.000000	0.71417	0.933000	0.37362	0.815000	0.46073	4.769000	0.62300	0.447000	0.26695	-0.326000	0.08463	AAG	A|0.996;G|0.004	0.004	strong		0.398	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		G	100454804	A	G	100454804	3	3	23	1	0	0	0	0	1	0	0	0	17205	72	3	3	3595	3	VPS13B	8	100454804	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	14274085	100454804	45909218	342	7786											
MTBP	27085	hgsc.bcm.edu	37	chr8	121463425	121463425	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgttagttttgtagttctgaTtggcaagagatacattttga	10	18	10	3	0	1	3	0	2	1	1	1	4	1	3	0	1	1	5	0	1	4	9	rs61753755	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:121463425T>C	ENST00000305949.1	+	4	333	c.288T>C	c.(286-288)gaT>gaC	p.D96D		NM_022045.4	NP_071328.2	Q96DY7	MTBP_HUMAN	MDM2 binding protein	96					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)			GTAGTTCTGATTGGCAAGAGA	0.269													T|||	189	0.0377396	0.0847	0.0144	5008	,	,		15992	0.0		0.0288	False		,,,				2504	0.0389				p.D96D		Atlas-SNP	.											.	MTBP	77	.	0			c.T288C						PASS	.	T		360,4046	178.0+/-206.8	12,336,1855	60	61	61		288	-0.1	1	8	dbSNP_129	61	181,8409	80.9+/-143.5	2,177,4116	no	coding-synonymous	MTBP	NM_022045.3		14,513,5971	CC,CT,TT		2.1071,8.1707,4.1628		96/905	121463425	541,12455	2203	4295	6498	SO:0001819	synonymous_variant	27085	exon4			TTCTGATTGGCAA		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.288T>C	8.37:g.121463425T>C		86	0	0		54	24	0.444444	NM_022045	B4DUR5|Q9HA89	Silent	SNP	ENST00000305949.1	37	CCDS6333.1																																																																																			T|0.966;C|0.034	0.034	strong		0.269	MTBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381530.1	NM_022045		C	121463425	T	C	121463425	2	2	23	1	0	0	0	0	0	0	0	1	9921	1490	52	3		3	MTBP	8	121463425	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	21008621	121463425	24900597	343	7787											
NDRG1	10397	hgsc.bcm.edu	37	chr8	134296524	134296524	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caccaaaggcttcacctcagCgaggtctacatcctgcatct	10	9	7	15	1	4	0	2	0	2	0	5	1	5	0	3	2	3	2	3	2	2	2	rs145871479	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:134296524C>T	ENST00000414097.2	-	2	898	c.31G>A	c.(31-33)Gct>Act	p.A11T	NDRG1_ENST00000537882.1_5'UTR|NDRG1_ENST00000518066.1_Missense_Mutation_p.A11T|NDRG1_ENST00000354944.5_Missense_Mutation_p.A11T|NDRG1_ENST00000522476.1_Intron|NDRG1_ENST00000323851.7_Missense_Mutation_p.A11T|NDRG1_ENST00000518176.1_Missense_Mutation_p.A11T	NM_001135242.1	NP_001128714.1	Q92597	NDRG1_HUMAN	N-myc downstream regulated 1	11					cell death (GO:0008219)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|mast cell activation (GO:0045576)|peripheral nervous system myelin maintenance (GO:0032287)|positive regulation of spindle checkpoint (GO:0090232)|response to metal ion (GO:0010038)	cell-cell adherens junction (GO:0005913)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	cadherin binding (GO:0045296)|gamma-tubulin binding (GO:0043015)|microtubule binding (GO:0008017)|Rab GTPase binding (GO:0017137)		NDRG1/ERG(5)	endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(4)|prostate(1)|skin(1)	17	all_epithelial(106;4.26e-24)|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)			TTCACCTCAGCGAGGTCTACA	0.552			T	ERG	prostate								C|||	3	0.000599042	0.0	0.0014	5008	,	,		20508	0.0		0.002	False		,,,				2504	0.0				p.A11T		Atlas-SNP	.		Dom	yes		8	8q24.3	10397	N-myc downstream regulated 1		E	.	NDRG1	40	.	0			c.G31A						PASS	.	C	THR/ALA,THR/ALA	3,4403	6.2+/-15.9	0,3,2200	234	169	191		31,31	5	0.4	8	dbSNP_134	191	15,8585	11.2+/-40.8	0,15,4285	yes	missense,missense	NDRG1	NM_001135242.1,NM_006096.3	58,58	0,18,6485	TT,TC,CC		0.1744,0.0681,0.1384	probably-damaging,probably-damaging	11/395,11/395	134296524	18,12988	2203	4300	6503	SO:0001583	missense	10397	exon2			CCTCAGCGAGGTC	X92845	CCDS34945.1, CCDS59112.1, CCDS59113.1	8q24	2014-09-17	2008-09-12		ENSG00000104419	ENSG00000104419			7679	protein-coding gene	gene with protein product		605262		CAP43		9251681, 8939898, 18455888	Standard	NM_006096		Approved	DRG1, RTP, TDD5, NDR1	uc003yue.2	Q92597	OTTHUMG00000164441	ENST00000414097.2:c.31G>A	8.37:g.134296524C>T	ENSP00000404854:p.Ala11Thr	201	0	0		213	117	0.549296	NM_006096	B3KR80|B7Z446|O15207|Q6IBG2|Q9NYR6|Q9UK29	Missense_Mutation	SNP	ENST00000414097.2	37	CCDS34945.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	6.861	0.528153	0.13127	6.81E-4	0.001744	ENSG00000104419	ENST00000323851;ENST00000537144;ENST00000354944;ENST00000414097;ENST00000518176;ENST00000518066;ENST00000520230;ENST00000519228;ENST00000519580;ENST00000522890;ENST00000520943;ENST00000521544;ENST00000522738	T;T;T;T;T;T;T;T;T;T	0.17854	2.44;2.51;2.44;2.35;2.41;2.39;2.39;2.35;2.39;2.25	5.03	5.03	0.67393	.	0.055881	0.64402	D	0.000001	T	0.21387	0.0515	N	0.17800	0.525	0.80722	D	1	D;B	0.76494	0.999;0.027	D;B	0.77004	0.989;0.011	T	0.01791	-1.1273	10	0.02654	T	1	-24.0443	13.7228	0.62737	0.0:1.0:0.0:0.0	.	11;11	E7ESM1;Q92597	.;NDRG1_HUMAN	T	11;11;11;11;11;11;28;11;11;11;22;11;65	ENSP00000319977:A11T;ENSP00000347028:A11T;ENSP00000404854:A11T;ENSP00000428345:A28T;ENSP00000429994:A11T;ENSP00000429272:A11T;ENSP00000428384:A11T;ENSP00000429840:A22T;ENSP00000429524:A11T;ENSP00000428991:A65T	ENSP00000319977:A11T	A	-	1	0	NDRG1	134365706	0.868000	0.29978	0.417000	0.26559	0.896000	0.52359	3.701000	0.54793	2.609000	0.88269	0.650000	0.86243	GCT	C|0.999;T|0.001	0.001	strong		0.552	NDRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378805.1			T	134296524	C	T	134296524	3	4	23	1	0	0	0	0	1	0	0	0	10260	768	27	1	1213	1	NDRG1	8	134296524	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	12833099	134296524	12067498	344	7788											
LYPD2	137797	hgsc.bcm.edu	37	chr8	143833840	143833840	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccgcaggcagccagcaccagCgccaggagcgccagccgcgt	8	1	14	18	5	0	0	0	0	0	0	0	1	0	1	6	2	5	3	6	2	0	0	rs78400087	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:143833840C>G	ENST00000359228.3	-	1	112	c.30G>C	c.(28-30)gcG>gcC	p.A10A		NM_205545.1	NP_991108.1	Q6UXB3	LYPD2_HUMAN	LY6/PLAUR domain containing 2	10						anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(2)	7	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)					CCAGCACCAGCGCCAGGAGCG	0.687													C|||	46	0.0091853	0.0015	0.0159	5008	,	,		12658	0.0		0.0328	False		,,,				2504	0.0				p.A10A		Atlas-SNP	.											LYPD2,NS,carcinoma,0,1	LYPD2	18	1	0			c.G30C						PASS	.	C		20,4384	24.3+/-50.5	0,20,2182	44	50	48		30	-3.3	0	8	dbSNP_133	48	186,8406	78.4+/-141.0	4,178,4114	no	coding-synonymous	LYPD2	NM_205545.1		4,198,6296	GG,GC,CC		2.1648,0.4541,1.5851		10/126	143833840	206,12790	2202	4296	6498	SO:0001819	synonymous_variant	137797	exon1			CACCAGCGCCAGG	AY358432	CCDS6388.1	8q24.3	2005-08-30		2005-08-30	ENSG00000197353	ENSG00000197353			25215	protein-coding gene	gene with protein product				LYPDC2		12975309	Standard	NM_205545		Approved	RGTR430, UNQ430	uc003ywz.3	Q6UXB3	OTTHUMG00000164686	ENST00000359228.3:c.30G>C	8.37:g.143833840C>G		303	0	0		162	82	0.506173	NM_205545	A8K2R6|Q0VD64|Q0VF31	Silent	SNP	ENST00000359228.3	37	CCDS6388.1																																																																																			C|0.985;G|0.015	0.015	strong		0.687	LYPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379742.1	NM_205545		G	143833840	C	G	143833840	2	3	23	1	0	0	0	0	0	0	0	1	9119	755	27	4		4	LYPD2	8	143833840	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	9537316	143833840	2530182	345	7789											
ZFP41	286128	hgsc.bcm.edu	37	chr8	144332045	144332045	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcaggcagaaaaaagaagaCgccgaccccaagggaggagg	16	1	15	9	2	0	3	0	0	0	3	0	6	0	5	3	4	1	2	3	4	5	0			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144332045C>T	ENST00000330701.4	+	2	401	c.32C>T	c.(31-33)aCg>aTg	p.T11M	ZFP41_ENST00000522452.1_Missense_Mutation_p.T11M|ZFP41_ENST00000520584.1_Missense_Mutation_p.T11M	NM_173832.4	NP_776193.1	Q8N8Y5	ZFP41_HUMAN	ZFP41 zinc finger protein	11					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)			AAAAAGAAGACGCCGACCCCA	0.592																																					p.T11M		Atlas-SNP	.											ZFP41,NS,carcinoma,0,1	ZFP41	25	1	0			c.C32T						PASS	.						26	29	28					8																	144332045		2200	4299	6499	SO:0001583	missense	286128	exon2			AGAAGACGCCGAC		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.32C>T	8.37:g.144332045C>T	ENSP00000327427:p.Thr11Met	73	0	0		81	43	0.530864	NM_173832	D3DWJ5	Missense_Mutation	SNP	ENST00000330701.4	37	CCDS6397.1	.	.	.	.	.	.	.	.	.	.	C	9.340	1.062804	0.19987	.	.	ENSG00000181638	ENST00000520584;ENST00000330701;ENST00000522452	T;T;T	0.06371	3.31;3.31;3.31	2.64	-1.62	0.08372	.	.	.	.	.	T	0.03178	0.0093	N	0.19112	0.55	0.09310	N	1	B	0.27013	0.166	B	0.12837	0.008	T	0.42310	-0.9459	9	0.66056	D	0.02	-0.6933	0.4835	0.00552	0.1961:0.3496:0.1927:0.2616	.	11	Q8N8Y5	ZFP41_HUMAN	M	11	ENSP00000430465:T11M;ENSP00000327427:T11M;ENSP00000428966:T11M	ENSP00000327427:T11M	T	+	2	0	ZFP41	144403420	.	.	0.000000	0.03702	0.001000	0.01503	.	.	-0.428000	0.07339	-0.339000	0.08088	ACG	.	.	none		0.592	ZFP41-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381114.2	NM_173832		T	144332045	C	T	144332045	3	4	23	1	0	0	0	0	1	0	0	0	17664	536	19	1	34	1	ZFP41	8	144332045	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	498205	144332045	2031977	346	7790											
C8orf73	642475	hgsc.bcm.edu	37	chr8	144654730	144654730	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggtctgtggctcagcctcaGgtttgacctcccaggacttg	5	11	13	12	0	3	1	2	1	1	0	4	2	4	2	3	4	1	2	3	4	0	2	rs185255597	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144654730G>T	ENST00000398882.3	-	1	411	c.155C>A	c.(154-156)cCt>cAt	p.P52H	NAPRT1_ENST00000460623.1_5'Flank|MROH6_ENST00000533679.1_5'Flank|RP11-661A12.9_ENST00000531730.1_RNA	NM_001100878.1	NP_001094348.1	A6NGR9	MROH6_HUMAN	maestro heat-like repeat family member 6	52																	CTCAGCCTCAGGTTTGACCTC	0.682													g|||	4	0.000798722	0.0	0.0	5008	,	,		13956	0.0		0.004	False		,,,				2504	0.0				p.P52H		Atlas-SNP	.											.	.	.	.	0			c.C155A						PASS	.		HIS/PRO	6,3902		0,6,1948	16	20	19		155	0.3	0	8		19	28,8238		0,28,4105	yes	missense	C8orf73	NM_001100878.1	77	0,34,6053	TT,TG,GG		0.3387,0.1535,0.2793	probably-damaging	52/720	144654730	34,12140	1954	4133	6087	SO:0001583	missense	642475	exon1			GCCTCAGGTTTGA	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.155C>A	8.37:g.144654730G>T	ENSP00000381857:p.Pro52His	79	0	0		67	42	0.626866	NM_001100878	A8MWB1	Missense_Mutation	SNP	ENST00000398882.3	37	CCDS47928.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	g	16.46	3.129400	0.56721	0.001535	0.003387	ENSG00000204839	ENST00000398882;ENST00000529971	T;T	0.30981	3.71;1.51	4.54	0.342	0.15996	.	.	.	.	.	T	0.15262	0.0368	N	0.14661	0.345	0.09310	N	0.999998	D;P	0.54207	0.965;0.681	P;B	0.50378	0.639;0.371	T	0.09796	-1.0658	9	0.87932	D	0	-1.6263	2.8407	0.05528	0.1024:0.334:0.3925:0.1711	.	52;52	E9PPP7;A6NGR9	.;CH073_HUMAN	H	52	ENSP00000381857:P52H;ENSP00000436959:P52H	ENSP00000381857:P52H	P	-	2	0	C8orf73	144725873	0.000000	0.05858	0.000000	0.03702	0.131000	0.20780	0.024000	0.13555	0.449000	0.26747	0.461000	0.40582	CCT	G|0.998;T|0.002	0.002	strong		0.682	MROH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382330.3	NM_001100878		T	144654730	G	T	144654730	3	4	23	1	0	0	0	0	1	0	0	0	2437	1000	35	4	2060	4	C8orf73	8	144654730	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	322685	144654730	1709292	347	7791											
KIFC2	90990	hgsc.bcm.edu	37	chr8	145698758	145698758	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cggctctcgcgcccgcagagGgcctgcccctctagtcctgg	3	7	13	18	4	2	1	0	0	2	1	4	1	3	1	5	3	1	2	5	3	1	1	rs201074786	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:145698758G>A	ENST00000301332.2	+	17	2819	c.2442G>A	c.(2440-2442)agG>agA	p.R814R	FOXH1_ENST00000525197.1_5'Flank|KIFC2_ENST00000301331.5_3'UTR	NM_145754.2	NP_665697.1	Q96AC6	KIFC2_HUMAN	kinesin family member C2	814	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)			GCCCGCAGAGGGCCTGCCCCT	0.706													G|||	11	0.00219649	0.0	0.0072	5008	,	,		9786	0.0		0.006	False		,,,				2504	0.0				p.R814R		Atlas-SNP	.											.	KIFC2	53	.	0			c.G2442A						PASS	.	G		2,3926		0,2,1962	7	6	6		2442	1.7	0	8		6	61,7875		0,61,3907	no	coding-synonymous	KIFC2	NM_145754.2		0,63,5869	AA,AG,GG		0.7686,0.0509,0.531		814/839	145698758	63,11801	1964	3968	5932	SO:0001819	synonymous_variant	90990	exon17			GCAGAGGGCCTGC	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.2442G>A	8.37:g.145698758G>A		37	0	0		22	10	0.454545	NM_145754	E9PHB2|Q96NN6	Silent	SNP	ENST00000301332.2	37	CCDS6427.1	6	0.0027472527472527475	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	8.900	0.956047	0.18507	5.09E-4	0.007686	ENSG00000167702	ENST00000528415	.	.	.	3.48	1.66	0.24008	.	.	.	.	.	T	0.26738	0.0654	.	.	.	0.28321	N	0.922249	.	.	.	.	.	.	T	0.22103	-1.0226	4	.	.	.	-4.4999	7.859	0.29499	0.2172:0.0:0.7828:0.0	.	.	.	.	E	539	.	.	G	+	2	0	KIFC2	145669566	0.001000	0.12720	0.037000	0.18230	0.019000	0.09904	0.281000	0.18810	0.474000	0.27392	0.484000	0.47621	GGG	G|0.997;A|0.003	0.003	strong		0.706	KIFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382052.2	NM_145754		A	145698758	G	A	145698758	2	1	23	1	0	0	0	0	0	0	0	1	8322	1223	43	2		2	KIFC2	8	145698758	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1044028	145698758	665264	348	7792											
RLN1	6013	hgsc.bcm.edu	37	chr9	5335590	5335590	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctttgttgatgaaggatggTacaatttctgttaagtttaa	11	18	9	3	0	2	2	0	2	2	0	2	3	2	3	0	2	1	4	0	2	5	7	rs35426888	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:5335590T>G	ENST00000223862.1	-	2	345	c.219A>C	c.(217-219)gtA>gtC	p.V73V	RLN1_ENST00000487557.2_5'UTR|RLN1_ENST00000223858.4_Missense_Mutation_p.Y107S	NM_006911.2	NP_008842.1	P04808	REL1_HUMAN	relaxin 1	73					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)		TGAAGGATGGTACAATTTCTG	0.363													T|||	37	0.00738818	0.0	0.0173	5008	,	,		20846	0.0		0.0109	False		,,,				2504	0.0143				p.V73V		Atlas-SNP	.											.	RLN1	16	.	0			c.A219C						PASS	.						46	48	47					9																	5335590		2202	4300	6502	SO:0001819	synonymous_variant	6013	exon2			GGATGGTACAATT		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.219A>C	9.37:g.5335590T>G		64	0	0		40	15	0.375	NM_006911	Q99936|Q9UQJ1	Silent	SNP	ENST00000223862.1	37	CCDS6462.1	.	.	.	.	.	.	.	.	.	.	T	2.574	-0.298894	0.05532	.	.	ENSG00000107018	ENST00000223858	T	0.23348	1.91	2.21	0.163	0.14986	.	.	.	.	.	T	0.10035	0.0246	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.34527	-0.9825	6	0.12430	T	0.62	.	3.1868	0.06603	0.2517:0.5914:0.0:0.1569	rs35426888;rs61758132	.	.	.	S	107	ENSP00000223858:Y107S	ENSP00000223858:Y107S	Y	-	2	0	RLN1	5325590	0.000000	0.05858	0.009000	0.14445	0.005000	0.04900	-0.303000	0.08210	0.053000	0.16036	-1.550000	0.00899	TAC	C|0.005;G|0.002;T|0.993	0.002	strong		0.363	RLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051617.1			G	5335590	T	G	5335590	2	3	23	1	0	0	0	0	0	0	0	1	13406	1625	57	5		5	RLN1	9	5335590	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10		5335590	135877841	349	7793											
SNAPC3	6619	hgsc.bcm.edu	37	chr9	15422888	15422888	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tggggcgaacatggctgaagGaagccgaggtggccctacgt	9	6	17	9	3	0	1	0	1	0	0	0	4	0	2	2	6	3	1	2	6	4	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:15422888G>C	ENST00000380821.3	+	1	187	c.11G>C	c.(10-12)gGa>gCa	p.G4A		NM_001039697.1	NP_001034786.1	Q92966	SNPC3_HUMAN	small nuclear RNA activating complex, polypeptide 3, 50kDa	4					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)		ATGGCTGAAGGAAGCCGAGGT	0.632																																					p.G4A		Atlas-SNP	.											.	SNAPC3	28	.	0			c.G11C						PASS	.						27	24	25					9																	15422888		2093	4148	6241	SO:0001583	missense	6619	exon1			CTGAAGGAAGCCG	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.11G>C	9.37:g.15422888G>C	ENSP00000370200:p.Gly4Ala	53	0	0		36	12	0.333333	NM_001039697	D3DRI8|Q2VPI6|Q5T285	Missense_Mutation	SNP	ENST00000380821.3	37	CCDS6478.1	.	.	.	.	.	.	.	.	.	.	G	12.57	1.977930	0.34942	.	.	ENSG00000164975	ENST00000380821;ENST00000380807;ENST00000447670;ENST00000421710	T	0.41400	1.0	5.13	1.96	0.26148	.	0.722427	0.13995	N	0.348553	T	0.29620	0.0739	L	0.36672	1.1	0.18873	N	0.999989	B;B	0.19583	0.013;0.037	B;B	0.18561	0.022;0.02	T	0.22417	-1.0217	10	0.54805	T	0.06	-21.5863	5.523	0.16943	0.5091:0.0:0.4909:0.0	.	4;4	B4DDR9;Q92966	.;SNPC3_HUMAN	A	4	ENSP00000370200:G4A	ENSP00000370185:G4A	G	+	2	0	SNAPC3	15412888	0.013000	0.17824	0.128000	0.21923	0.010000	0.07245	1.978000	0.40598	0.594000	0.29761	0.462000	0.41574	GGA	.	.	none		0.632	SNAPC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051763.2	NM_001039697		C	15422888	G	C	15422888	3	2	23	1	0	0	0	0	1	0	0	0	14851	1174	41	4	13	4	SNAPC3	9	15422888	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	10087298	15422888	125790543	350	7794											
SNAPC3	6619	hgsc.bcm.edu	37	chr9	15459821	15459821	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaggcaacaaactgggggAattccttgcttatccttatg	12	11	10	8	0	0	1	0	0	0	1	2	2	2	2	2	3	3	2	2	3	6	4	rs3087653	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:15459821A>C	ENST00000380821.3	+	9	1369	c.1193A>C	c.(1192-1194)gAa>gCa	p.E398A		NM_001039697.1	NP_001034786.1	Q92966	SNPC3_HUMAN	small nuclear RNA activating complex, polypeptide 3, 50kDa	398			E -> A (in dbSNP:rs3087653).		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)		AAACTGGGGGAATTCCTTGCT	0.413													A|||	193	0.0385383	0.0416	0.0231	5008	,	,		16799	0.0		0.0596	False		,,,				2504	0.0634				p.E398A		Atlas-SNP	.											.	SNAPC3	28	.	0			c.A1193C						PASS	.	A	ALA/GLU	145,4261	101.2+/-139.8	0,145,2058	134	122	126		1193	5.9	1	9	dbSNP_102	126	425,8175	131.8+/-189.6	13,399,3888	yes	missense	SNAPC3	NM_001039697.1	107	13,544,5946	CC,CA,AA		4.9419,3.291,4.3826	probably-damaging	398/412	15459821	570,12436	2203	4300	6503	SO:0001583	missense	6619	exon9			TGGGGGAATTCCT	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.1193A>C	9.37:g.15459821A>C	ENSP00000370200:p.Glu398Ala	145	0	0		138	44	0.318841	NM_001039697	D3DRI8|Q2VPI6|Q5T285	Missense_Mutation	SNP	ENST00000380821.3	37	CCDS6478.1	78	0.03571428571428571	26	0.052845528455284556	11	0.03038674033149171	0	0.0	41	0.05408970976253298	A	31	5.081553	0.94050	0.03291	0.049419	ENSG00000164975	ENST00000380821	T	0.44083	0.93	5.86	5.86	0.93980	.	0.138414	0.64402	D	0.000005	T	0.17450	0.0419	M	0.65498	2.005	0.80722	D	1	D	0.57571	0.98	P	0.53224	0.721	T	0.31447	-0.9943	10	0.56958	D	0.05	-42.6534	16.5602	0.84551	1.0:0.0:0.0:0.0	rs3087653;rs3198208;rs52828246;rs3087653	398	Q92966	SNPC3_HUMAN	A	398	ENSP00000370200:E398A	ENSP00000370200:E398A	E	+	2	0	SNAPC3	15449821	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.283000	0.78640	2.367000	0.80283	0.528000	0.53228	GAA	A|0.956;C|0.044	0.044	strong		0.413	SNAPC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051763.2	NM_001039697		C	15459821	A	C	15459821	3	2	23	1	0	0	0	0	1	0	0	0	14851	246	9	5	1227	5	SNAPC3	9	15459821	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	36933	15459821	125753610	351	7795											
NOL6	65083	hgsc.bcm.edu	37	chr9	33467397	33467397	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gctggggtcccccacctcagGctggtctgcctctggaccca	4	8	12	17	0	3	0	1	0	2	0	4	1	4	1	5	5	1	2	5	5	0	0			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:33467397G>A	ENST00000379471.2	-	13	1807	c.1720C>T	c.(1720-1722)Cct>Tct	p.P574S	NOL6_ENST00000464829.1_Intron|NOL6_ENST00000455041.2_Missense_Mutation_p.P522S			Q9H6R4	NOL6_HUMAN	nucleolar protein 6 (RNA-associated)	574					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)		CCCACCTCAGGCTGGTCTGCC	0.617											OREG0019137	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P574S		Atlas-SNP	.											.	NOL6	85	.	0			c.C1720T						PASS	.						56	54	54					9																	33467397		2203	4300	6503	SO:0001583	missense	65083	exon13			CCTCAGGCTGGTC	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.1720C>T	9.37:g.33467397G>A	ENSP00000368784:p.Pro574Ser	153	0	0	840	165	30	0.181818	NM_022917	Q5T5M3|Q5T5M4|Q7L4G6|Q8N6I0|Q8TEY9|Q8TEZ0|Q8TEZ1|Q9H675	Missense_Mutation	SNP	ENST00000379471.2	37		.	.	.	.	.	.	.	.	.	.	G	16.58	3.162530	0.57368	.	.	ENSG00000165271	ENST00000353159;ENST00000297990;ENST00000379471;ENST00000541373;ENST00000325914;ENST00000455041	T;T;T;T	0.39997	1.05;1.05;1.05;1.05	5.06	4.12	0.48240	.	0.154190	0.64402	D	0.000013	T	0.37156	0.0993	L	0.45422	1.42	0.58432	D	0.999999	P;P;P;P;P	0.40398	0.716;0.499;0.499;0.708;0.555	B;B;B;B;B	0.42245	0.381;0.161;0.161;0.331;0.248	T	0.06006	-1.0851	10	0.19147	T	0.46	.	14.0961	0.65023	0.0:0.1492:0.8508:0.0	.	522;571;574;574;574	B4DF80;Q9H6R4-4;Q9H6R4-2;Q9H6R4-3;Q9H6R4	.;.;.;.;NOL6_HUMAN	S	574;574;574;130;574;522	ENSP00000313978:P574S;ENSP00000297990:P574S;ENSP00000368784:P574S;ENSP00000395915:P522S	ENSP00000297990:P574S	P	-	1	0	NOL6	33457397	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	3.752000	0.55172	2.638000	0.89438	0.655000	0.94253	CCT	.	.	none		0.617	NOL6-005	NOVEL	non_canonical_TEC|basic	protein_coding	protein_coding	OTTHUMT00000001019.2	NM_022917		A	33467397	G	A	33467397	3	1	23	1	0	0	0	0	1	0	0	0	10534	1203	42	2	1776	2	NOL6	9	33467397	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	18007576	33467397	107746034	352	7796											
CCDC107	203260	hgsc.bcm.edu	37	chr9	35660872	35660872	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggtgaaggctcgggaggCgagtctgctggaggtggaga	8	6	20	7	2	1	2	0	1	1	1	2	6	1	4	1	7	1	2	1	7	1	0	rs141349284	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:35660872C>T	ENST00000426546.2	+	5	606	c.540C>T	c.(538-540)ggC>ggT	p.G180G	ARHGEF39_ENST00000378395.2_3'UTR|CCDC107_ENST00000378406.1_3'UTR|RMRP_ENST00000602361.1_lincRNA|CCDC107_ENST00000327351.2_Intron|CCDC107_ENST00000378409.3_Intron|ARHGEF39_ENST00000490970.1_5'Flank|ARHGEF39_ENST00000378387.3_3'UTR|ARHGEF39_ENST00000343259.3_3'UTR|CCDC107_ENST00000378407.3_3'UTR|CCDC107_ENST00000421582.2_3'UTR	NM_001195200.1|NM_001195201.1|NM_001195217.1|NM_174923.2	NP_001182129.1|NP_001182130.1|NP_001182146.1|NP_777583.2	Q8WV48	CC107_HUMAN	coiled-coil domain containing 107	180						integral component of membrane (GO:0016021)				endometrium(1)|lung(3)|skin(1)	5	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			GCTCGGGAGGCGAGTCTGCTG	0.527													C|||	4	0.000798722	0.0	0.0029	5008	,	,		19570	0.001		0.001	False		,,,				2504	0.0				p.G180G		Atlas-SNP	.											.	CCDC107	12	.	0			c.C540T						PASS	.	C	,,,,	0,4406		0,0,2203	123	134	130		,,,,540	-4.9	0	9	dbSNP_134	130	2,8598	2.2+/-6.3	0,2,4298	no	intron,intron,utr-3,utr-3,coding-synonymous	C9orf100,CCDC107	NM_001195200.1,NM_001195201.1,NM_001195217.1,NM_032818.2,NM_174923.2	,,,,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,,,,	,,,,180/284	35660872	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	203260	exon5			GGGAGGCGAGTCT	AK075523	CCDS6583.1, CCDS56573.1, CCDS56574.1, CCDS56575.1	9q13.3	2008-02-05			ENSG00000159884	ENSG00000159884			28465	protein-coding gene	gene with protein product						12477932	Standard	NM_174923		Approved	MGC31967	uc011lox.2	Q8WV48	OTTHUMG00000019868	ENST00000426546.2:c.540C>T	9.37:g.35660872C>T		64	0	0		80	36	0.45	NM_174923	A6XND6|Q5T4R5|Q5T4R8|Q5T4R9|Q86VB6|Q8N2E4	Silent	SNP	ENST00000426546.2	37	CCDS6583.1																																																																																			C|1.000;T|0.000	0.000	strong		0.527	CCDC107-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052325.1	NM_174923		T	35660872	C	T	35660872	2	4	23	1	0	0	0	0	0	0	0	1	2744	755	27	1		1	CCDC107	9	35660872	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	2193475	35660872	105552559	353	7797											
CA9	768	hgsc.bcm.edu	37	chr9	35674059	35674059	+	Frame_Shift_Del	DEL	G	G	-																															cactgctgcttctggtgcctGtccatccccagaggttgccc																								rs565650695	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:35674059delG	ENST00000378357.4	+	1	207	c.103delG	c.(103-105)gtcfs	p.V35fs	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)	TCTGGTGCCTGTCCATCCCCA	0.652													G|G|-|deletion	3	0.000599042	0.0	0.0029	5008	,	,		18058	0.0		0.001	False		,,,				2504	0.0				p.P34fs		Pindel,Atlas-Indel	.											.	CA9	48	.	0			c.102delT						PASS	.						61	56	57					9																	35674059		2203	4300	6503	SO:0001589	frameshift_variant	768	exon1			.	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.103delG	9.37:g.35674059delG	ENSP00000367608:p.Val35fs	120	0	.		121	37	0.306	NM_001216	Q5T4R1	Frame_Shift_Del	DEL	ENST00000378357.4	37	CCDS6585.1																																																																																			.	.	none		0.652	CA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055479.1	NM_001216		-	35674059	G	-	35674059	7	5	23	1	0	1	0	1	0	0	0	0	2526	1377	48	0	105	0	CA9	9	35674059	Frame_Shift_Del	DEL	G	TCGA-G8-6325-01A-11D-2210-10	13187	35674059	105539372	354	7798											
MELK	9833	hgsc.bcm.edu	37	chr9	36597284	36597284	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tttggtctctgtgcaaaaccCaaggtaagtgcagaaataag	14	10	10	7	0	1	1	0	0	1	1	2	1	1	1	1	2	3	3	1	2	6	3	rs139481227	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:36597284C>G	ENST00000298048.2	+	6	655	c.471C>G	c.(469-471)ccC>ccG	p.P157P	MELK_ENST00000487398.1_3'UTR|MELK_ENST00000541717.1_Silent_p.P157P|MELK_ENST00000545008.1_Intron|MELK_ENST00000536860.1_Silent_p.P109P|MELK_ENST00000538311.1_5'UTR|MELK_ENST00000536329.1_Silent_p.P86P|MELK_ENST00000536987.1_Silent_p.P26P|MELK_ENST00000543751.1_Silent_p.P125P	NM_014791.3	NP_055606.1	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase	157	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)			GTGCAAAACCCAAGGTAAGTG	0.318																																					p.P157P	Ovarian(82;980 1317 7225 14391 18624)	Atlas-SNP	.											.	MELK	74	.	0			c.C471G						PASS	.	C		0,4406		0,0,2203	105	109	108		471	1.4	1	9	dbSNP_134	108	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	MELK	NM_014791.2		0,6,6497	GG,GC,CC		0.0698,0.0,0.0461		157/652	36597284	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	9833	exon6			AAAACCCAAGGTA	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.471C>G	9.37:g.36597284C>G		69	0	0		69	35	0.507246	NM_014791	A6P3A7|A6P3A8|B1AMQ6|B7Z1E6|B7Z5M5|B7Z6Q7|B7Z6R8|B7Z6Y0|B7Z7Q1|D3DRP8|F5H0Y0|F5H2R4|F5H689|Q7L3C3	Silent	SNP	ENST00000298048.2	37	CCDS6606.1																																																																																			C|0.999;G|0.001	0.001	strong		0.318	MELK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052428.3	NM_014791		G	36597284	C	G	36597284	2	3	23	1	0	0	0	0	0	0	0	1	9479	581	21	4		4	MELK	9	36597284	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	923225	36597284	104616147	355	7799											
ZCCHC7	84186	hgsc.bcm.edu	37	chr9	37304232	37304232	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggaagatggacccagcggtaCtattcagccaacaaaaacat	16	6	9	10	1	1	1	1	0	0	1	1	3	1	3	2	3	5	1	2	3	6	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:37304232C>T	ENST00000336755.5	+	4	808	c.702C>T	c.(700-702)taC>taT	p.Y234Y	ZCCHC7_ENST00000461038.1_3'UTR|ZCCHC7_ENST00000534928.1_5'UTR	NM_032226.2	NP_115602.2	Q8N3Z6	ZCHC7_HUMAN	zinc finger, CCHC domain containing 7	234						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)		CCCAGCGGTACTATTCAGCCA	0.363																																					p.Y234Y		Atlas-SNP	.											.	ZCCHC7	56	.	0			c.C702T						PASS	.						99	95	96					9																	37304232		2203	4300	6503	SO:0001819	synonymous_variant	84186	exon4			GCGGTACTATTCA	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.702C>T	9.37:g.37304232C>T		128	0	0		107	25	0.233645	NM_032226	B2RCI4|D3DRQ0|Q5T0Q8|Q5T0Q9|Q5T0R0|Q8N2M1|Q8N4J2|Q8TBK8|Q9H648|Q9P0F0	Silent	SNP	ENST00000336755.5	37	CCDS6608.2																																																																																			.	.	none		0.363	ZCCHC7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052453.2	NM_032226		T	37304232	C	T	37304232	2	4	23	1	0	0	0	0	0	0	0	1	17608	576	20	2		2	ZCCHC7	9	37304232	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	706948	37304232	103909199	356	7800											
GRHPR	9380	hgsc.bcm.edu	37	chr9	37436755	37436755	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctggcctgagaggggagccGatgcctagtgaactcaagct	9	7	15	10	1	1	2	1	2	0	1	1	5	1	3	3	3	4	2	3	3	3	1	rs76299266	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:37436755G>A	ENST00000318158.6	+	9	1048	c.963G>A	c.(961-963)ccG>ccA	p.P321P		NM_012203.1	NP_036335.1	Q9UBQ7	GRHPR_HUMAN	glyoxylate reductase/hydroxypyruvate reductase	321					cellular nitrogen compound metabolic process (GO:0034641)|dicarboxylic acid metabolic process (GO:0043648)|excretion (GO:0007588)|glyoxylate metabolic process (GO:0046487)|metabolic process (GO:0008152)|oxidation-reduction process (GO:0055114)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisomal matrix (GO:0005782)	carboxylic acid binding (GO:0031406)|glycerate dehydrogenase activity (GO:0008465)|glyoxylate reductase (NADP) activity (GO:0030267)|hydroxypyruvate reductase activity (GO:0016618)|NAD binding (GO:0051287)|NADPH binding (GO:0070402)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12				GBM - Glioblastoma multiforme(29;0.00687)		GAGGGGAGCCGATGCCTAGTG	0.557													G|||	60	0.0119808	0.0272	0.0029	5008	,	,		18599	0.001		0.005	False		,,,				2504	0.0164				p.P321P		Atlas-SNP	.											.	GRHPR	35	.	0			c.G963A						PASS	.	G		103,4303	81.4+/-119.9	2,99,2102	162	154	157	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	963	-4.3	1	9	dbSNP_132	157	45,8555	30.1+/-81.4	0,45,4255	no	coding-synonymous	GRHPR	NM_012203.1		2,144,6357	AA,AG,GG		0.5233,2.3377,1.1379		321/329	37436755	148,12858	2203	4300	6503	SO:0001819	synonymous_variant	9380	exon9			GGAGCCGATGCCT	AF134895	CCDS6609.1	9q12	2012-07-13			ENSG00000137106	ENSG00000137106	1.1.1.79, 1.1.1.81		4570	protein-coding gene	gene with protein product	"primary hyperoxaluria type 2"	604296		GLXR		10524214, 10484776	Standard	XM_005251631		Approved	PH2	uc003zzu.1	Q9UBQ7	OTTHUMG00000019914	ENST00000318158.6:c.963G>A	9.37:g.37436755G>A		80	0	0		91	37	0.406593	NM_012203	Q5T945|Q9H3E9|Q9H636|Q9UKX1	Silent	SNP	ENST00000318158.6	37	CCDS6609.1																																																																																			G|0.992;A|0.008	0.008	strong		0.557	GRHPR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052442.1	NM_012203		A	37436755	G	A	37436755	2	1	23	1	0	0	0	0	0	0	0	1	6775	1045	37	1		1	GRHPR	9	37436755	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	132523	37436755	103776676	357	7801											
C9orf40	55071	hgsc.bcm.edu	37	chr9	77567335	77567335	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gctgggcgaagccgagggctCtgccatggtccctgcgtcga	5	7	16	13	4	1	0	0	0	1	0	3	3	2	0	3	3	3	2	3	3	1	0			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:77567335C>T	ENST00000376854.5	-	1	467	c.193G>A	c.(193-195)Gag>Aag	p.E65K	RP11-197P3.4_ENST00000455609.1_RNA	NM_017998.2	NP_060468.2	Q8IXQ3	CI040_HUMAN	chromosome 9 open reading frame 40	65										lung(2)|stomach(1)	3						GCCGAGGGCTCTGCCATGGTC	0.706																																					p.E65K		Atlas-SNP	.											.	C9orf40	5	.	0			c.G193A						PASS	.						11	11	11					9																	77567335		2086	4155	6241	SO:0001583	missense	55071	exon1			AGGGCTCTGCCAT	AK000972	CCDS6648.1	9q21.31	2012-03-15			ENSG00000135045	ENSG00000135045			23433	protein-coding gene	gene with protein product							Standard	NM_017998		Approved	FLJ10110	uc004ajo.4	Q8IXQ3	OTTHUMG00000020031	ENST00000376854.5:c.193G>A	9.37:g.77567335C>T	ENSP00000366050:p.Glu65Lys	89	0	0		60	24	0.4	NM_017998	Q9NWD3	Missense_Mutation	SNP	ENST00000376854.5	37	CCDS6648.1	.	.	.	.	.	.	.	.	.	.	C	20.0	3.930235	0.73327	.	.	ENSG00000135045	ENST00000376854	.	.	.	5.21	4.25	0.50352	.	0.327978	0.21929	N	0.067058	T	0.50769	0.1635	M	0.61703	1.905	0.23620	N	0.997277	P	0.50156	0.932	P	0.53450	0.726	T	0.44034	-0.9354	9	0.56958	D	0.05	-11.2091	10.2293	0.43245	0.1977:0.8023:0.0:0.0	.	65	Q8IXQ3	CI040_HUMAN	K	65	.	ENSP00000366050:E65K	E	-	1	0	C9orf40	76757155	0.160000	0.22878	0.496000	0.27539	0.498000	0.33706	1.673000	0.37534	2.447000	0.82792	0.305000	0.20034	GAG	.	.	none		0.706	C9orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052702.1	NM_017998		T	77567335	C	T	77567335	3	4	23	1	0	0	0	0	1	0	0	0	2483	922	32	2	399	2	C9orf40	9	77567335	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	40130580	77567335	63646096	358	7802											
PCSK5	5125	hgsc.bcm.edu	37	chr9	78638797	78638797	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccagatctgatgcaaaactaCgtgagtgtatgctgtggtta	11	12	11	7	1	1	3	0	2	1	1	1	3	1	3	1	1	4	4	1	1	5	3	rs34417623	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:78638797C>T	ENST00000545128.1	+	4	1093	c.555C>T	c.(553-555)taC>taT	p.Y185Y	PCSK5_ENST00000376752.4_Splice_Site_p.Y185Y|PCSK5_ENST00000376767.3_Splice_Site_p.Y185Y	NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	185	Peptidase S8.				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						TGCAAAACTACGTGAGTGTAT	0.438													C|||	43	0.00858626	0.0174	0.0029	5008	,	,		19983	0.0		0.0129	False		,,,				2504	0.0051				p.Y185Y		Atlas-SNP	.											.	PCSK5	329	.	0			c.C555T						PASS	.	C	,	42,4364	46.0+/-80.4	1,40,2162	173	150	158		555,555	-11.3	0.3	9	dbSNP_126	158	110,8490	58.7+/-120.3	3,104,4193	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	PCSK5	NM_001190482.1,NM_006200.3	,	4,144,6355	TT,TC,CC		1.2791,0.9532,1.1687	,	185/1861,185/914	78638797	152,12854	2203	4300	6503	SO:0001630	splice_region_variant	5125	exon4			AAACTACGTGAGT		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.555+1C>T	9.37:g.78638797C>T		147	0	0		148	71	0.47973	NM_006200	F5H2G7|Q13527|Q96EP4	Silent	SNP	ENST00000545128.1	37	CCDS55320.1																																																																																			C|0.989;T|0.011	0.011	strong		0.438	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			Silent	T	78638797	C	T	78638797	5	4	23	1	0	0	0	0	0	0	1	0	11612	550	19	1	569	1	PCSK5	9	78638797	Splice_Site	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1071462	78638797	62574634	359	7803											
KIF27	55582	hgsc.bcm.edu	37	chr9	86518433	86518433	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttccgtgctctgttggcatAtttgagagaatttaaggact	9	15	11	6	1	1	2	0	1	1	1	2	4	2	3	1	2	1	4	1	2	3	6	rs144003628		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:86518433A>G	ENST00000297814.2	-	4	1143	c.1000T>C	c.(1000-1002)Tat>Cat	p.Y334H	KIF27_ENST00000334204.2_Missense_Mutation_p.Y334H|KIF27_ENST00000413982.1_Missense_Mutation_p.Y334H	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	334	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				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						CTGTTGGCATATTTGAGAGAA	0.433																																					p.Y334H		Atlas-SNP	.											.	KIF27	103	.	0			c.T1000C						PASS	.						95	95	95					9																	86518433		2203	4300	6503	SO:0001583	missense	55582	exon4			TGGCATATTTGAG	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.1000T>C	9.37:g.86518433A>G	ENSP00000297814:p.Tyr334His	149	0	0		108	48	0.444444	NM_017576	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Missense_Mutation	SNP	ENST00000297814.2	37	CCDS6665.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.979561	0.74360	.	.	ENSG00000165115	ENST00000297814;ENST00000413982;ENST00000334204	T;T;T	0.81415	-1.49;-1.49;-1.49	5.56	4.44	0.53790	Kinesin, motor domain (3);	0.000000	0.52532	D	0.000072	D	0.93475	0.7918	H	0.99156	4.45	0.40294	D	0.978531	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.987;0.998;0.999	D	0.95040	0.8177	10	0.87932	D	0	.	10.909	0.47097	0.9271:0.0:0.0729:0.0	.	334;334;334	Q86VH2-3;Q86VH2-2;Q86VH2	.;.;KIF27_HUMAN	H	334	ENSP00000297814:Y334H;ENSP00000401688:Y334H;ENSP00000333928:Y334H	ENSP00000297814:Y334H	Y	-	1	0	KIF27	85708253	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.531000	0.81973	2.125000	0.65367	0.533000	0.62120	TAT	A|1.000;T|0.000	.	alt		0.433	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576		G	86518433	A	G	86518433	3	3	23	1	0	0	0	0	1	0	0	0	8305	449	16	3	3265	3	KIF27	9	86518433	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	7879636	86518433	54694998	360	7804											
AGTPBP1	23287	hgsc.bcm.edu	37	chr9	88248239	88248239	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acaacaataggaccacgtacTtttccctcaaatacaaaagg	17	8	5	11	1	1	0	1	0	0	0	2	1	2	1	2	2	3	1	2	2	8	5	rs144890878	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:88248239T>C	ENST00000357081.3	-	14	1497	c.1353A>G	c.(1351-1353)aaA>aaG	p.K451K	AGTPBP1_ENST00000337006.4_3'UTR|AGTPBP1_ENST00000432218.1_Silent_p.K289K|AGTPBP1_ENST00000376083.3_Silent_p.K411K|AGTPBP1_ENST00000376109.3_Silent_p.K463K			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	451					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						GACCACGTACTTTTCCCTCAA	0.328													T|||	31	0.0061901	0.0015	0.0043	5008	,	,		17053	0.0		0.008	False		,,,				2504	0.0184				p.K411K		Atlas-SNP	.											.	AGTPBP1	128	.	0			c.A1233G						PASS	.	T		5,4387		0,5,2191	56	60	58		1233	-3	0	9	dbSNP_134	58	42,8514		0,42,4236	no	coding-synonymous	AGTPBP1	NM_015239.2		0,47,6427	CC,CT,TT		0.4909,0.1138,0.363		411/1187	88248239	47,12901	2196	4278	6474	SO:0001819	synonymous_variant	23287	exon14			ACGTACTTTTCCC	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.1353A>G	9.37:g.88248239T>C		154	0	0		133	57	0.428571	NM_015239	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Silent	SNP	ENST00000357081.3	37																																																																																				T|0.994;C|0.006	0.006	strong		0.328	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239		C	88248239	T	C	88248239	2	2	23	1	0	0	0	0	0	0	0	1	400	1606	56	3		3	AGTPBP1	9	88248239	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	1729806	88248239	52965192	361	7805											
TSTD2	158427	hgsc.bcm.edu	37	chr9	100364900	100364900	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgtcttgcatagggcctgAaactttcctgctccccttgt	5	14	9	13	0	1	1	0	1	1	0	3	1	3	1	4	1	3	3	4	1	2	4	rs145024955	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:100364900A>C	ENST00000341170.4	-	10	1784	c.1402T>G	c.(1402-1404)Tca>Gca	p.S468A		NM_139246.4	NP_640339.4	Q5T7W7	TSTD2_HUMAN	thiosulfate sulfurtransferase (rhodanese)-like domain containing 2	468										large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	15						ATAGGGCCTGAAACTTTCCTG	0.557													A|||	2	0.000399361	0.0	0.0	5008	,	,		20972	0.0		0.002	False		,,,				2504	0.0				p.S468A		Atlas-SNP	.											.	TSTD2	42	.	0			c.T1402G						PASS	.	A	ALA/SER	1,4405	2.1+/-5.4	0,1,2202	264	222	236		1402	1.8	0.2	9	dbSNP_134	236	14,8586	10.5+/-38.8	0,14,4286	yes	missense	TSTD2	NM_139246.4	99	0,15,6488	CC,CA,AA		0.1628,0.0227,0.1153	benign	468/517	100364900	15,12991	2203	4300	6503	SO:0001583	missense	158427	exon10			GGCCTGAAACTTT	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.1402T>G	9.37:g.100364900A>C	ENSP00000342499:p.Ser468Ala	252	0	0		228	111	0.486842	NM_139246	A6NMJ4|A8K584|Q6ZQZ6|Q8IYM3|Q8WY73|Q96ML6|Q96MU1	Missense_Mutation	SNP	ENST00000341170.4	37	CCDS6727.2	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	A	5.124	0.208479	0.09757	2.27E-4	0.001628	ENSG00000136925	ENST00000375173;ENST00000341170	T;T	0.28895	1.59;1.59	5.5	1.77	0.24775	.	0.830019	0.10733	N	0.640447	T	0.15478	0.0373	N	0.17872	0.535	0.26488	N	0.974986	B	0.06786	0.001	B	0.04013	0.001	T	0.29912	-0.9996	10	0.25106	T	0.35	-2.0967	1.4504	0.02373	0.4114:0.2983:0.1611:0.1292	.	468	Q5T7W7	TSTD2_HUMAN	A	64;468	ENSP00000364316:S64A;ENSP00000342499:S468A	ENSP00000342499:S468A	S	-	1	0	TSTD2	99404721	0.016000	0.18221	0.206000	0.23566	0.267000	0.26476	0.794000	0.26958	0.117000	0.18138	0.460000	0.39030	TCA	A|0.999;C|0.001	0.001	strong		0.557	TSTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053325.4	NM_139246		C	100364900	A	C	100364900	3	2	23	1	0	0	0	0	1	0	0	0	16690	246	9	5	152	5	TSTD2	9	100364900	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	12116661	100364900	40848531	362	7806											
COL15A1	1306	hgsc.bcm.edu	37	chr9	101797679	101797679	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctattgaatgaacccaaactCtccagaccaacggctgcaat	14	8	6	13	1	1	3	0	2	1	1	2	3	1	3	3	1	4	2	3	1	6	2	rs35494947	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:101797679C>G	ENST00000375001.3	+	19	2691	c.2268C>G	c.(2266-2268)ctC>ctG	p.L756L		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	756	Nonhelical region 3 (NC3).				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)				AACCCAAACTCTCCAGACCAA	0.512													C|||	21	0.00419329	0.0	0.0058	5008	,	,		19093	0.001		0.0129	False		,,,				2504	0.0031				p.L756L		Atlas-SNP	.											.	COL15A1	211	.	0			c.C2268G						PASS	.	C		13,4393	20.2+/-43.8	0,13,2190	100	95	97		2268	4.2	0.1	9	dbSNP_126	97	107,8493	58.3+/-119.8	0,107,4193	no	coding-synonymous	COL15A1	NM_001855.3		0,120,6383	GG,GC,CC		1.2442,0.2951,0.9227		756/1389	101797679	120,12886	2203	4300	6503	SO:0001819	synonymous_variant	1306	exon19			CAAACTCTCCAGA	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.2268C>G	9.37:g.101797679C>G		76	0	0		85	85	1	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Silent	SNP	ENST00000375001.3	37	CCDS35081.1																																																																																			C|0.992;G|0.008	0.008	strong		0.512	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855		G	101797679	C	G	101797679	2	3	23	1	0	0	0	0	0	0	0	1	3674	900	32	4		4	COL15A1	9	101797679	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1432779	101797679	39415752	363	7807											
ZNF462	58499	hgsc.bcm.edu	37	chr9	109692820	109692820	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taccagccttttggtcacttAgaagaggtgccaaagatcaa	13	10	9	9	0	2	3	2	0	0	3	2	3	2	3	3	2	3	0	3	2	5	4	rs139184113	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:109692820A>G	ENST00000277225.5	+	4	6151	c.5862A>G	c.(5860-5862)ttA>ttG	p.L1954L	ZNF462_ENST00000457913.1_Silent_p.L1954L|ZNF462_ENST00000497489.1_3'UTR|ZNF462_ENST00000441147.2_Silent_p.L799L|ZNF462_ENST00000542028.1_5'Flank			Q96JM2	ZN462_HUMAN	zinc finger protein 462	1954					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						TTGGTCACTTAGAAGAGGTGC	0.453																																					p.L1954L		Atlas-SNP	.											.	ZNF462	322	.	0			c.A5862G						PASS	.	A		2,4404	4.2+/-10.8	0,2,2201	102	95	97		5862	5.4	1	9	dbSNP_134	97	27,8573	19.2+/-60.6	0,27,4273	no	coding-synonymous	ZNF462	NM_021224.4		0,29,6474	GG,GA,AA		0.314,0.0454,0.223		1954/2507	109692820	29,12977	2203	4300	6503	SO:0001819	synonymous_variant	58499	exon4			TCACTTAGAAGAG	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.5862A>G	9.37:g.109692820A>G		100	0	0		149	67	0.449664	NM_021224	Q5T0T4|Q8N408	Silent	SNP	ENST00000277225.5	37	CCDS35096.1																																																																																			A|0.999;G|0.001	0.001	strong		0.453	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224		G	109692820	A	G	109692820	2	3	23	1	0	0	0	0	0	0	0	1	17941	417	15	3		3	ZNF462	9	109692820	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	7895141	109692820	31520611	364	7808											
SVEP1	79987	hgsc.bcm.edu	37	chr9	113169619	113169619	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tattctctagacaaagccttAagtcagagcctgctagaatg	13	11	8	9	0	2	3	1	0	1	3	3	3	2	3	2	0	3	1	2	0	6	5	rs199899670	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:113169619A>G	ENST00000401783.2	-	38	8597	c.8261T>C	c.(8260-8262)tTa>tCa	p.L2754S	SVEP1_ENST00000297826.5_Missense_Mutation_p.L680S|SVEP1_ENST00000374469.1_Missense_Mutation_p.L2731S	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2754	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						ACAAAGCCTTAAGTCAGAGCC	0.453													A|||	8	0.00159744	0.0	0.0	5008	,	,		22575	0.0		0.002	False		,,,				2504	0.0061				p.L2754S		Atlas-SNP	.											.	SVEP1	326	.	0			c.T8261C						PASS	.	A	SER/LEU	0,3978		0,0,1989	76	80	79		8261	1	0	9	dbSNP_132	79	12,8300		0,12,4144	yes	missense	SVEP1	NM_153366.3	145	0,12,6133	GG,GA,AA		0.1444,0.0,0.0976	benign	2754/3572	113169619	12,12278	1989	4156	6145	SO:0001583	missense	79987	exon38			AGCCTTAAGTCAG	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.8261T>C	9.37:g.113169619A>G	ENSP00000384917:p.Leu2754Ser	264	0	0		260	121	0.465385	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	0.008	-1.912475	0.00508	0.0	0.001444	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826;ENST00000374463	T;T;T	0.63255	-0.03;-0.03;-0.03	5.87	0.967	0.19674	Complement control module (2);Sushi/SCR/CCP (3);	0.805314	0.12128	N	0.497090	T	0.28134	0.0694	N	0.04387	-0.21	0.09310	N	1	B	0.20164	0.042	B	0.25506	0.061	T	0.30679	-0.9970	10	0.06494	T	0.89	.	0.0954	0.00043	0.2867:0.1649:0.2327:0.3157	.	2754	Q4LDE5	SVEP1_HUMAN	S	2754;2731;680;426	ENSP00000384917:L2754S;ENSP00000363593:L2731S;ENSP00000297826:L680S	ENSP00000297826:L680S	L	-	2	0	SVEP1	112209440	0.073000	0.21202	0.001000	0.08648	0.119000	0.20118	2.094000	0.41719	1.062000	0.40625	0.477000	0.44152	TTA	A|0.998;G|0.002	0.002	strong		0.453	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	113169619	A	G	113169619	3	3	23	1	0	0	0	0	1	0	0	0	15435	372	13	3	2498	3	SVEP1	9	113169619	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	3476799	113169619	28043812	365	7809											
ZNF483	158399	hgsc.bcm.edu	37	chr9	114305075	114305075	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgacttttagccattttacGtctgtgatttatcatcaaag	11	17	6	7	1	3	2	2	2	1	0	3	2	3	2	1	0	2	0	1	0	4	6	rs142830150		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:114305075G>A	ENST00000309235.5	+	6	2018	c.1860G>A	c.(1858-1860)acG>acA	p.T620T	ZNF483_ENST00000358151.4_Intron	NM_133464.2	NP_597721.2	Q8TF39	ZN483_HUMAN	zinc finger protein 483	620					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						GCCATTTTACGTCTGTGATTT	0.408																																					p.T620T		Atlas-SNP	.											ZNF483,NS,carcinoma,+1,1	ZNF483	78	1	0			c.G1860A						scavenged	.	G	,	1,4405	2.1+/-5.4	0,1,2202	65	67	66		,1860	-5.3	0.1	9	dbSNP_134	66	0,8600		0,0,4300	no	intron,coding-synonymous	ZNF483	NM_001007169.2,NM_133464.2	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	,620/745	114305075	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	158399	exon6			TTTTACGTCTGTG	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.1860G>A	9.37:g.114305075G>A		103	1	0.00970874		84	5	0.0595238	NM_133464	Q5VZN2|Q8NAE1	Silent	SNP	ENST00000309235.5	37	CCDS35106.1																																																																																			G|1.000;A|0.000	0.000	weak		0.408	ZNF483-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053641.1	XM_088567		A	114305075	G	A	114305075	2	1	23	1	0	0	0	0	0	0	0	1	17951	1132	40	1		1	ZNF483	9	114305075	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1135456	114305075	26908356	366	7810											
HSDL2	84263	hgsc.bcm.edu	37	chr9	115167994	115167994	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtggagaaagccatcaagaAatttggaggtaataccttca	16	9	10	6	0	2	2	2	0	0	2	2	4	2	3	2	3	2	1	2	3	5	4	rs41280175	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:115167994A>T	ENST00000398805.3	+	3	499	c.272A>T	c.(271-273)aAa>aTa	p.K91I	HSDL2_ENST00000539114.1_5'UTR|HSDL2_ENST00000488101.1_3'UTR|HSDL2_ENST00000262542.7_5'UTR|HSDL2_ENST00000398803.1_Missense_Mutation_p.K91I	NM_032303.4	NP_115679.2	Q6YN16	HSDL2_HUMAN	hydroxysteroid dehydrogenase like 2	91						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						GCCATCAAGAAATTTGGAGGT	0.318													A|||	10	0.00199681	0.0008	0.0058	5008	,	,		16111	0.0		0.005	False		,,,				2504	0.0				p.K91I		Atlas-SNP	.											.	HSDL2	24	.	0			c.A272T						PASS	.	A	ILE/LYS,ILE/LYS	7,3743		0,7,1868	128	126	126		272,272	3.2	1	9	dbSNP_127	126	107,8109		1,105,4002	yes	missense,missense	HSDL2	NM_001195822.1,NM_032303.4	102,102	1,112,5870	TT,TA,AA		1.3023,0.1867,0.9527	benign,benign	91/346,91/419	115167994	114,11852	1875	4108	5983	SO:0001583	missense	84263	exon3			TCAAGAAATTTGG	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.272A>T	9.37:g.115167994A>T	ENSP00000381785:p.Lys91Ile	65	0	0		46	32	0.695652	NM_032303	A8K1L4|A8K8X1|A8MSV3|Q658M8|Q9BT58	Missense_Mutation	SNP	ENST00000398805.3	37	CCDS43864.1	8	0.003663003663003663	0	0.0	3	0.008287292817679558	0	0.0	5	0.006596306068601583	A	12.14	1.848888	0.32699	0.001867	0.013023	ENSG00000119471	ENST00000398805;ENST00000398803	D;D	0.88431	-2.38;-2.38	5.57	3.15	0.36227	NAD(P)-binding domain (1);	0.456598	0.25677	N	0.029030	D	0.82296	0.5006	M	0.69823	2.125	0.80722	D	1	P;B	0.45902	0.868;0.064	B;B	0.42138	0.377;0.159	T	0.79027	-0.1971	10	0.39692	T	0.17	.	6.4508	0.21902	0.6281:0.2284:0.1434:0.0	rs41280175	91;91	Q6YN16-2;Q6YN16	.;HSDL2_HUMAN	I	91	ENSP00000381785:K91I;ENSP00000381783:K91I	ENSP00000381783:K91I	K	+	2	0	HSDL2	114207815	0.922000	0.31269	0.991000	0.47740	0.021000	0.10359	0.964000	0.29306	0.369000	0.24510	0.260000	0.18958	AAA	A|0.995;T|0.005	0.005	strong		0.318	HSDL2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053681.1	NM_032303		T	115167994	A	T	115167994	3	4	23	1	0	0	0	0	1	0	0	0	7403	14	1	5	282	5	HSDL2	9	115167994	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	862919	115167994	26045437	367	7811											
TLR4	7099	hgsc.bcm.edu	37	chr9	120474891	120474891	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taatgtggctcacaatcttaTccaatctttcaaattacctg	12	15	4	10	0	4	0	2	0	2	0	5	0	5	0	2	1	1	1	2	1	6	4	rs200168998		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:120474891T>C	ENST00000355622.6	+	3	586	c.485T>C	c.(484-486)aTc>aCc	p.I162T	TLR4_ENST00000394487.4_Missense_Mutation_p.I122T|TLR4_ENST00000472304.1_3'UTR	NM_138554.4|NM_138557.2	NP_612564.1|NP_612567.1	O00206	TLR4_HUMAN	toll-like receptor 4	162					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)	CACAATCTTATCCAATCTTTC	0.388																																					p.I162T		Atlas-SNP	.											.	TLR4	220	.	0			c.T485C						PASS	.	T	THR/ILE	0,4406		0,0,2203	94	98	97		485	5.1	0.3	9		97	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TLR4	NM_138554.3	89	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	probably-damaging	162/840	120474891	1,13005	2203	4300	6503	SO:0001583	missense	7099	exon3			ATCTTATCCAATC	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.485T>C	9.37:g.120474891T>C	ENSP00000363089:p.Ile162Thr	146	0	0		154	83	0.538961	NM_138554	A8K1Y8|A9XLP9|A9XLQ0|A9XLQ1|B4E194|D1CS52|D1CS53|Q5VZI8|Q5VZI9|Q9UK78|Q9UM57	Missense_Mutation	SNP	ENST00000355622.6	37	CCDS6818.1	.	.	.	.	.	.	.	.	.	.	T	14.73	2.622678	0.46840	0.0	1.16E-4	ENSG00000136869	ENST00000394487;ENST00000355622	T;T	0.21734	1.99;1.99	5.08	5.08	0.68730	.	0.000000	0.64402	D	0.000005	T	0.49236	0.1545	M	0.83012	2.62	0.40068	D	0.975989	D	0.76494	0.999	D	0.91635	0.999	T	0.53767	-0.8392	10	0.39692	T	0.17	.	14.8663	0.70419	0.0:0.0:0.0:1.0	.	162	O00206	TLR4_HUMAN	T	122;162	ENSP00000377997:I122T;ENSP00000363089:I162T	ENSP00000363089:I162T	I	+	2	0	TLR4	119514712	0.955000	0.32602	0.282000	0.24776	0.322000	0.28314	3.253000	0.51469	1.913000	0.55393	0.533000	0.62120	ATC	.	.	weak		0.388	TLR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055549.3	NM_138554		C	120474891	T	C	120474891	3	2	23	1	0	0	0	0	1	0	0	0	15968	1435	50	3	495	3	TLR4	9	120474891	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	5306897	120474891	20738540	368	7812											
CRB2	286204	hgsc.bcm.edu	37	chr9	126125327	126125327	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tccagatcccaccggcttccGctgctactgcgtgccgggtt	4	10	11	16	4	0	1	0	0	0	1	3	1	3	1	5	2	4	4	5	2	1	3	rs138381817	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:126125327G>A	ENST00000373631.3	+	2	279	c.278G>A	c.(277-279)cGc>cAc	p.R93H	CRB2_ENST00000359999.3_Missense_Mutation_p.R93H	NM_173689.5	NP_775960.4	Q5IJ48	CRUM2_HUMAN	crumbs family member 2	93	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cardiovascular system development (GO:0072358)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|mesoderm formation (GO:0001707)|negative regulation of endopeptidase activity (GO:0010951)|notochord formation (GO:0014028)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|somitogenesis (GO:0001756)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)			NS(2)|breast(1)|cervix(1)|endometrium(2)|lung(11)|ovary(1)|prostate(2)|skin(3)	23						ACCGGCTTCCGCTGCTACTGC	0.692													G|||	15	0.00299521	0.0	0.0101	5008	,	,		14806	0.0		0.008	False		,,,				2504	0.0				p.R93H		Atlas-SNP	.											.	CRB2	86	.	0			c.G278A						PASS	.	G	HIS/ARG	8,4398		0,8,2195	40	39	39		278	2.7	1	9	dbSNP_134	39	102,8494		2,98,4198	yes	missense	CRB2	NM_173689.5	29	2,106,6393	AA,AG,GG		1.1866,0.1816,0.846	probably-damaging	93/1286	126125327	110,12892	2203	4298	6501	SO:0001583	missense	286204	exon2			GCTTCCGCTGCTA	AK095783	CCDS6852.2	9q33.2	2014-02-06	2014-02-06		ENSG00000148204	ENSG00000148204			18688	protein-coding gene	gene with protein product		609720	"crumbs homolog 2 (Drosophila)"			14767562	Standard	XM_005251934		Approved	FLJ38464, FLJ16786	uc004bnx.1	Q5IJ48	OTTHUMG00000020638	ENST00000373631.3:c.278G>A	9.37:g.126125327G>A	ENSP00000362734:p.Arg93His	126	0	0		89	52	0.58427	NM_173689	A2A3N4|Q0QD46|Q5JS41|Q5JS43|Q6ZTA9|Q6ZWI6	Missense_Mutation	SNP	ENST00000373631.3	37	CCDS6852.2	9	0.004120879120879121	0	0.0	3	0.008287292817679558	0	0.0	6	0.0079155672823219	G	14.66	2.601296	0.46423	0.001816	0.011866	ENSG00000148204	ENST00000359999;ENST00000373631	T;T	0.61274	0.12;0.12	4.7	2.69	0.31865	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.172979	0.27841	N	0.017634	T	0.28366	0.0701	L	0.31664	0.95	0.80722	D	1	B;B	0.28971	0.013;0.229	B;B	0.21360	0.004;0.034	T	0.24440	-1.0160	10	0.51188	T	0.08	.	2.6651	0.05041	0.104:0.1689:0.5289:0.1981	.	93;93	Q5IJ48;Q5IJ48-2	CRUM2_HUMAN;.	H	93	ENSP00000353092:R93H;ENSP00000362734:R93H	ENSP00000353092:R93H	R	+	2	0	CRB2	125165148	0.035000	0.19736	1.000000	0.80357	0.834000	0.47266	0.452000	0.21795	1.214000	0.43395	0.448000	0.29417	CGC	G|0.993;A|0.007	0.007	strong		0.692	CRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053990.3	NM_173689		A	126125327	G	A	126125327	3	1	23	1	0	0	0	0	1	0	0	0	3851	1087	38	1	284	1	CRB2	9	126125327	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	5650436	126125327	15088104	369	7813											
DENND1A	57706	hgsc.bcm.edu	37	chr9	126144390	126144390	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgctgagcgggtccaggaggGcgagcagggcgtcactgctc	6	6	18	11	3	1	1	1	1	0	0	3	3	2	2	1	4	4	3	1	4	0	0	rs189947178	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:126144390G>T	ENST00000373624.2	-	22	2552	c.2351C>A	c.(2350-2352)gCc>gAc	p.A784D	DENND1A_ENST00000542603.1_Missense_Mutation_p.A569D|DENND1A_ENST00000394219.3_Missense_Mutation_p.A795D|DENND1A_ENST00000473039.1_5'UTR	NM_020946.1	NP_065997.1	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A	784	Pro-rich.				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						GTCCAGGAGGGCGAGCAGGGC	0.697													G|||	16	0.00319489	0.0	0.0101	5008	,	,		10971	0.0		0.0089	False		,,,				2504	0.0				p.A784D		Atlas-SNP	.											.	DENND1A	112	.	0			c.C2351A						PASS	.	G	ASP/ALA	8,4368		0,8,2180	10	14	13		2351	3.5	1	9		13	81,8467		1,79,4194	no	missense	DENND1A	NM_020946.1	126	1,87,6374	TT,TG,GG		0.9476,0.1828,0.6886	possibly-damaging	784/1010	126144390	89,12835	2188	4274	6462	SO:0001583	missense	57706	exon22			AGGAGGGCGAGCA	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.2351C>A	9.37:g.126144390G>T	ENSP00000362727:p.Ala784Asp	54	0	0		46	30	0.652174	NM_020946	A8MZA3|B1AM80|B7Z3C8|B7Z669|D3PFD3|Q05C88|Q5VWF0|Q6PJZ5|Q8IVD6|Q9H796	Missense_Mutation	SNP	ENST00000373624.2	37	CCDS35133.1	15	0.006868131868131868	5	0.01016260162601626	3	0.008287292817679558	0	0.0	7	0.009234828496042216	G	11.10	1.538370	0.27475	0.001828	0.009476	ENSG00000119522	ENST00000373624;ENST00000542603;ENST00000394219	T;T;T	0.23754	3.34;1.89;3.21	4.47	3.5	0.40072	.	0.251626	0.36101	N	0.002785	T	0.20210	0.0486	L	0.27053	0.805	0.80722	D	1	D;D;P;P	0.58970	0.984;0.984;0.926;0.483	P;P;P;B	0.55161	0.77;0.77;0.454;0.084	T	0.01405	-1.1363	10	0.56958	D	0.05	-15.6303	9.6391	0.39828	0.0:0.3391:0.5308:0.1301	.	795;785;784;647	Q8TEH3-6;Q8TEH3-7;Q8TEH3;Q9HCG4	.;.;DEN1A_HUMAN;.	D	784;569;795	ENSP00000362727:A784D;ENSP00000437457:A569D;ENSP00000377766:A795D	ENSP00000362727:A784D	A	-	2	0	DENND1A	125184211	1.000000	0.71417	0.982000	0.44146	0.008000	0.06430	2.369000	0.44231	2.029000	0.59856	0.557000	0.71058	GCC	G|0.993;T|0.007	0.007	strong		0.697	DENND1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053997.1	NM_024820		T	126144390	G	T	126144390	3	4	23	1	0	0	0	0	1	0	0	0	4428	1203	42	4	682	4	DENND1A	9	126144390	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	19063	126144390	15069041	370	7814											
TRUB2	26995	hgsc.bcm.edu	37	chr9	131073842	131073842	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgatgggagccttggataaCggccagaatgcggtccagct	9	8	14	10	2	0	2	0	1	0	1	1	4	1	4	3	4	4	1	3	4	2	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:131073842C>T	ENST00000372890.4	-	6	832	c.499G>A	c.(499-501)Gtt>Att	p.V167I	TRUB2_ENST00000460320.1_5'UTR|TRUB2_ENST00000546104.1_Missense_Mutation_p.V111I	NM_015679.1	NP_056494.1	O95900	TRUB2_HUMAN	TruB pseudouridine (psi) synthase family member 2	167					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						CCTTGGATAACGGCCAGAATG	0.577																																					p.V167I		Atlas-SNP	.											.	TRUB2	26	.	0			c.G499A						PASS	.						121	102	108					9																	131073842		2203	4300	6503	SO:0001583	missense	26995	exon6			GGATAACGGCCAG	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.499G>A	9.37:g.131073842C>T	ENSP00000361982:p.Val167Ile	126	0	0		137	20	0.145985	NM_015679	B7Z7G5	Missense_Mutation	SNP	ENST00000372890.4	37	CCDS6897.1	.	.	.	.	.	.	.	.	.	.	C	5.380	0.255372	0.10185	.	.	ENSG00000167112	ENST00000372890;ENST00000546104	T;T	0.51071	0.72;0.72	5.58	-2.46	0.06461	Pseudouridine synthase, catalytic domain (1);	0.527930	0.21014	N	0.081636	T	0.40398	0.1115	L	0.54323	1.7	0.21020	N	0.999806	B	0.10296	0.003	B	0.09377	0.004	T	0.25433	-1.0132	10	0.38643	T	0.18	-1.9214	15.1301	0.72517	0.0:0.7555:0.0944:0.1501	.	167	O95900	TRUB2_HUMAN	I	167;111	ENSP00000361982:V167I;ENSP00000438084:V111I	ENSP00000361982:V167I	V	-	1	0	TRUB2	130113663	0.001000	0.12720	0.009000	0.14445	0.593000	0.36681	-0.332000	0.07904	-0.900000	0.03896	-1.317000	0.01298	GTT	.	.	none		0.577	TRUB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054419.1	NM_015679		T	131073842	C	T	131073842	3	4	23	1	0	0	0	0	1	0	0	0	16618	536	19	1	508	1	TRUB2	9	131073842	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	4929452	131073842	10139589	371	7815											
SPTAN1	6709	hgsc.bcm.edu	37	chr9	131371241	131371241	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agacatttctagccggcgcaAtgaggtcttggacaggtggg	9	9	15	8	2	2	2	0	1	2	1	2	3	2	3	1	5	1	1	1	5	2	3	rs145038571		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:131371241A>G	ENST00000372731.4	+	35	4690	c.4580A>G	c.(4579-4581)aAt>aGt	p.N1527S	SPTAN1_ENST00000358161.5_Missense_Mutation_p.N1527S|SPTAN1_ENST00000372739.3_Missense_Mutation_p.N1527S	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1527					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						AGCCGGCGCAATGAGGTCTTG	0.572													A|||	1	0.000199681	0.0	0.0014	5008	,	,		20265	0.0		0.0	False		,,,				2504	0.0				p.N1527S	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.A4580G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN	0,4406		0,0,2203	118	121	120		4580,4520,4580	5.8	1	9	dbSNP_134	120	14,8586	10.5+/-38.8	0,14,4286	yes	missense,missense,missense	SPTAN1	NM_001130438.2,NM_001195532.1,NM_003127.3	46,46,46	0,14,6489	GG,GA,AA		0.1628,0.0,0.1076	benign,benign,benign	1527/2478,1507/2453,1527/2473	131371241	14,12992	2203	4300	6503	SO:0001583	missense	6709	exon35			GGCGCAATGAGGT	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.4580A>G	9.37:g.131371241A>G	ENSP00000361816:p.Asn1527Ser	140	0	0		160	75	0.46875	NM_003127	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Missense_Mutation	SNP	ENST00000372731.4	37	CCDS6905.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	A	13.35	2.209863	0.39003	0.0	0.001628	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719	T;T;T	0.46063	0.88;1.39;0.88	5.77	5.77	0.91146	.	0.141471	0.64402	D	0.000005	T	0.27900	0.0687	N	0.16266	0.395	0.54753	D	0.999983	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.11227	-1.0596	10	0.11485	T	0.65	.	16.383	0.83481	1.0:0.0:0.0:0.0	.	1507;1527;1527	Q13813-3;Q13813-2;Q13813	.;.;SPTA2_HUMAN	S	1527;1527;1527;1507	ENSP00000350882:N1527S;ENSP00000361816:N1527S;ENSP00000361824:N1527S	ENSP00000350882:N1527S	N	+	2	0	SPTAN1	130411062	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.013000	0.57138	2.326000	0.78906	0.533000	0.62120	AAT	A|0.999;G|0.001	0.001	strong		0.572	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127		G	131371241	A	G	131371241	3	3	23	1	0	0	0	0	1	0	0	0	15132	101	4	3	4714	3	SPTAN1	9	131371241	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	297399	131371241	9842190	372	7816											
LRRC8A	56262	hgsc.bcm.edu	37	chr9	131670217	131670217	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccatgtggaggagggggaCattgtgtaccgcctctacat	9	9	13	10	1	1	0	0	0	1	0	1	3	1	3	3	4	2	1	3	4	2	3	rs41275930	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:131670217C>T	ENST00000259324.5	+	3	1297	c.774C>T	c.(772-774)gaC>gaT	p.D258D	LRRC8A_ENST00000372600.4_Silent_p.D258D|LRRC8A_ENST00000372599.3_Silent_p.D258D	NM_001127244.1	NP_001120716.1	Q8IWT6	LRC8A_HUMAN	leucine rich repeat containing 8 family, member A	258					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						AGGAGGGGGACATTGTGTACC	0.547													C|||	76	0.0151757	0.0008	0.0115	5008	,	,		21421	0.0		0.0099	False		,,,				2504	0.0583				p.D258D		Atlas-SNP	.											.	LRRC8A	69	.	0			c.C774T						PASS	.	C	,,	9,4397	14.3+/-33.2	0,9,2194	200	172	182		774,774,774	2.3	1	9	dbSNP_127	182	127,8473	65.3+/-127.6	0,127,4173	no	coding-synonymous,coding-synonymous,coding-synonymous	LRRC8A	NM_001127244.1,NM_001127245.1,NM_019594.3	,,	0,136,6367	TT,TC,CC		1.4767,0.2043,1.0457	,,	258/811,258/811,258/811	131670217	136,12870	2203	4300	6503	SO:0001819	synonymous_variant	56262	exon3			GGGGGACATTGTG	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.774C>T	9.37:g.131670217C>T		134	0	0		147	67	0.455782	NM_001127244	Q6UXM2|Q8NCI0|Q9P2B1	Silent	SNP	ENST00000259324.5	37	CCDS35155.1																																																																																			C|0.991;T|0.009	0.009	strong		0.547	LRRC8A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054516.2	NM_019594		T	131670217	C	T	131670217	2	4	23	1	0	0	0	0	0	0	0	1	9030	477	17	2		2	LRRC8A	9	131670217	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	298976	131670217	9543214	373	7817											
EXOSC2	23404	hgsc.bcm.edu	37	chr9	133579152	133579152	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgccagaggcttttggaacaGgagggataaggaggtgctcc	10	7	16	8	1	0	1	0	0	0	1	1	5	1	5	2	6	2	2	2	6	2	3	rs34680820	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:133579152G>A	ENST00000372358.5	+	9	944	c.873G>A	c.(871-873)caG>caA	p.Q291Q	EXOSC2_ENST00000546165.1_Silent_p.Q265Q|EXOSC2_ENST00000372352.3_Silent_p.Q283Q|EXOSC2_ENST00000372351.3_Silent_p.Q261Q|EXOSC2_ENST00000467138.1_3'UTR			Q13868	EXOS2_HUMAN	exosome component 2	291					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)|positive regulation of cell growth (GO:0030307)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|7S RNA binding (GO:0008312)			breast(1)|endometrium(1)|large_intestine(3)|ovary(1)	6		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(13;0.0588)		OV - Ovarian serous cystadenocarcinoma(145;0.000324)		TTTTGGAACAGGAGGGATAAG	0.478													G|||	22	0.00439297	0.0023	0.0043	5008	,	,		20923	0.0		0.0109	False		,,,				2504	0.0051				p.Q291Q	Pancreas(134;1683 1824 10118 27928 31640)	Atlas-SNP	.											.	EXOSC2	15	.	0			c.G873A						PASS	.	G		24,4382	29.9+/-59.1	0,24,2179	119	128	125		873	4.1	1	9	dbSNP_126	125	230,8370	93.8+/-155.7	3,224,4073	no	coding-synonymous	EXOSC2	NM_014285.5		3,248,6252	AA,AG,GG		2.6744,0.5447,1.9529		291/294	133579152	254,12752	2203	4300	6503	SO:0001819	synonymous_variant	23404	exon9			GGAACAGGAGGGA	AK001916	CCDS6935.1, CCDS65160.1, CCDS65161.1	9q34	2008-02-05			ENSG00000130713	ENSG00000130713			17097	protein-coding gene	gene with protein product	"homolog of yeast RRP4 (ribosomal RNA processing 4), 3' 5' exoribonuclease (RRP4)"	602238				8600032, 1538749	Standard	XM_005272176		Approved	hRrp4p, Rrp4p, RRP4, p7	uc004bzu.2	Q13868	OTTHUMG00000020811	ENST00000372358.5:c.873G>A	9.37:g.133579152G>A		70	0	0		36	13	0.361111	NM_014285	A3KFL3|B4DKK6|Q9NUY4	Silent	SNP	ENST00000372358.5	37	CCDS6935.1																																																																																			G|0.986;A|0.014	0.014	strong		0.478	EXOSC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054673.1	NM_014285		A	133579152	G	A	133579152	2	1	23	1	0	0	0	0	0	0	0	1	5317	991	35	2		2	EXOSC2	9	133579152	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1908935	133579152	7634279	374	7818											
ABL1	25	hgsc.bcm.edu	37	chr9	133755528	133755528	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttgaaacaatgttccaggaAtccagtatctcagacggtaa	14	11	8	8	1	1	2	1	1	1	1	4	3	3	3	2	2	1	3	2	2	5	4	rs2227985	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:133755528A>G	ENST00000318560.5	+	9	1878	c.1497A>G	c.(1495-1497)gaA>gaG	p.E499E		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	499					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)	TGTTCCAGGAATCCAGTATCT	0.542			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"								A|||	429	0.0856629	0.2057	0.0836	5008	,	,		18557	0.001		0.0696	False		,,,				2504	0.0286				p.E518E		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.A1554G						PASS	.	A	,	757,3649	309.7+/-291.2	52,653,1498	106	106	106		1497,1554	-2.8	1	9	dbSNP_98	106	641,7959	164.3+/-216.7	27,587,3686	no	coding-synonymous,coding-synonymous	ABL1	NM_005157.4,NM_007313.2	,	79,1240,5184	GG,GA,AA		7.4535,17.1811,10.7489	,	499/1131,518/1150	133755528	1398,11608	2203	4300	6503	SO:0001819	synonymous_variant	25	exon9			CCAGGAATCCAGT	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.1497A>G	9.37:g.133755528A>G		100	0	0		89	39	0.438202	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																			A|0.898;G|0.102	0.102	strong		0.542	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		G	133755528	A	G	133755528	2	3	23	1	0	0	0	0	0	0	0	1	92	98	4	3		3	ABL1	9	133755528	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	176376	133755528	7457903	375	7819											
ABL1	25	hgsc.bcm.edu	37	chr9	133760029	133760029	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcacagtaacgcctcccccCaggctggtgaaaaagaatga	13	5	11	12	1	0	3	0	2	0	1	1	3	1	3	4	3	1	3	4	3	4	1	rs2229070	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:133760029C>G	ENST00000318560.5	+	11	2733	c.2352C>G	c.(2350-2352)ccC>ccG	p.P784P		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	784	Pro-rich.				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)	CGCCTCCCCCCAGGCTGGTGA	0.592			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"								C|||	534	0.106629	0.2821	0.0865	5008	,	,		18610	0.001		0.0696	False		,,,				2504	0.0307				p.P803P		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.C2409G						PASS	.	C	,	985,3415		107,771,1322	26	30	28		2352,2409	1.6	0.2	9	dbSNP_98	28	622,7976		27,568,3704	no	coding-synonymous,coding-synonymous	ABL1	NM_005157.4,NM_007313.2	,	134,1339,5026	GG,GC,CC		7.2342,22.3864,12.3634	,	784/1131,803/1150	133760029	1607,11391	2200	4299	6499	SO:0001819	synonymous_variant	25	exon11			TCCCCCCAGGCTG	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.2352C>G	9.37:g.133760029C>G		36	0	0		33	16	0.484848	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																			C|0.885;G|0.115	0.115	strong		0.592	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		G	133760029	C	G	133760029	2	3	23	1	0	0	0	0	0	0	0	1	92	581	21	4		4	ABL1	9	133760029	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	4501	133760029	7453402	376	7820											
ABL1	25	hgsc.bcm.edu	37	chr9	133760106	133760106	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccagcccgggctccagccCgcccaacctgactccaaaac	9	4	8	20	2	0	1	0	1	0	0	3	1	3	1	7	1	4	1	7	1	3	0	rs2229071	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:133760106C>T	ENST00000318560.5	+	11	2810	c.2429C>T	c.(2428-2430)cCg>cTg	p.P810L		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	810	Pro-rich.		P -> L (in dbSNP:rs2229071). {ECO:0000269|PubMed:17344846}.		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)	GGCTCCAGCCCGCCCAACCTG	0.627			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"								C|||	11	0.00219649	0.0	0.0072	5008	,	,		17189	0.0		0.004	False		,,,				2504	0.002				p.P829L		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.C2486T						PASS	.	C	LEU/PRO,LEU/PRO	6,4394		0,6,2194	16	20	18		2429,2486	4.8	0.9	9	dbSNP_98	18	80,8518		0,80,4219	yes	missense,missense	ABL1	NM_005157.4,NM_007313.2	98,98	0,86,6413	TT,TC,CC		0.9304,0.1364,0.6616	probably-damaging,probably-damaging	810/1131,829/1150	133760106	86,12912	2200	4299	6499	SO:0001583	missense	25	exon11			CCAGCCCGCCCAA	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.2429C>T	9.37:g.133760106C>T	ENSP00000323315:p.Pro810Leu	74	0	0		74	42	0.567568	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Missense_Mutation	SNP	ENST00000318560.5	37	CCDS35166.1	5	0.0022893772893772895	0	0.0	3	0.008287292817679558	0	0.0	2	0.002638522427440633	C	14.83	2.651718	0.47362	0.001364	0.009304	ENSG00000097007	ENST00000444970;ENST00000372348;ENST00000318560	T;T	0.23950	1.88;1.88	5.69	4.79	0.61399	.	0.000000	0.85682	D	0.000000	T	0.25606	0.0623	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.04128	-1.0975	10	0.08837	T	0.75	.	13.6197	0.62130	0.0:0.9257:0.0:0.0743	rs2229071	810;847	P00519;Q59FK4	ABL1_HUMAN;.	L	625;829;810	ENSP00000361423:P829L;ENSP00000323315:P810L	ENSP00000323315:P810L	P	+	2	0	ABL1	132749927	1.000000	0.71417	0.922000	0.36590	0.138000	0.21146	7.563000	0.82314	1.410000	0.46936	0.561000	0.74099	CCG	C|0.995;T|0.005	0.005	strong		0.627	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		T	133760106	C	T	133760106	3	4	23	1	0	0	0	0	1	0	0	0	92	652	23	1	2611	1	ABL1	9	133760106	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	77	133760106	7453325	377	7821											
ABL1	25	hgsc.bcm.edu	37	chr9	133760380	133760380	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctcaaacctgccccgccgccCccaccagcagcctctgcagg	7	4	8	22	2	2	0	1	0	1	0	2	0	2	0	8	1	5	2	8	1	1	0	rs56017837	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:133760380C>G	ENST00000318560.5	+	11	3084	c.2703C>G	c.(2701-2703)ccC>ccG	p.P901P		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	901	DNA-binding. {ECO:0000250}.|Poly-Pro.|Pro-rich.				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)	CCCCGCCGCCCCCACCAGCAG	0.672			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"								C|||	4	0.000798722	0.0	0.0014	5008	,	,		15690	0.0		0.002	False		,,,				2504	0.001				p.P920P		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.C2760G						PASS	.	C	,	0,4338		0,0,2169	8	11	10		2703,2760	-2	0.8	9	dbSNP_129	10	14,8502		0,14,4244	no	coding-synonymous,coding-synonymous	ABL1	NM_005157.4,NM_007313.2	,	0,14,6413	GG,GC,CC		0.1644,0.0,0.1089	,	901/1131,920/1150	133760380	14,12840	2169	4258	6427	SO:0001819	synonymous_variant	25	exon11			GCCGCCCCCACCA	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.2703C>G	9.37:g.133760380C>G		80	0	0		80	39	0.4875	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																			.	.	weak		0.672	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		G	133760380	C	G	133760380	2	3	23	1	0	0	0	0	0	0	0	1	92	610	22	4		4	ABL1	9	133760380	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	274	133760380	7453051	378	7822											
CEL	1056	hgsc.bcm.edu	37	chr9	135946483	135946483	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgggcagcagctccatgaagCggagcctgagaaccaacttc	11	6	12	12	1	0	2	0	2	0	1	2	4	1	3	3	2	6	3	3	2	3	1	rs200231984		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:135946483C>T	ENST00000372080.4	+	11	1619	c.1603C>T	c.(1603-1605)Cgg>Tgg	p.R535W	CEL_ENST00000351304.7_Missense_Mutation_p.R466W	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	532					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)		CTCCATGAAGCGGAGCCTGAG	0.622																																					p.R535W		Atlas-SNP	.											.	CEL	71	.	0			c.C1603T						PASS	.	C	TRP/ARG	2,3834		0,2,1916	30	35	33		1603	3.2	0	9		33	9,8191		0,9,4091	no	missense	CEL	NM_001807.3	101	0,11,6007	TT,TC,CC		0.1098,0.0521,0.0914	probably-damaging	535/757	135946483	11,12025	1918	4100	6018	SO:0001583	missense	1056	exon11			ATGAAGCGGAGCC	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.1603C>T	9.37:g.135946483C>T	ENSP00000361151:p.Arg535Trp	73	0	0		103	49	0.475728	NM_001807	Q16398|Q5T7U7|Q9UCH1|Q9UP41	Missense_Mutation	SNP	ENST00000372080.4	37	CCDS43896.1	.	.	.	.	.	.	.	.	.	.	C	12.66	2.003200	0.35320	5.21E-4	0.001098	ENSG00000170835	ENST00000372080;ENST00000351304;ENST00000303626	T;T	0.71341	-0.39;-0.56	5.2	3.23	0.37069	Carboxylesterase, type B (1);	0.713375	0.14331	N	0.326364	T	0.75568	0.3867	L	0.56769	1.78	0.09310	N	1	D	0.71674	0.998	P	0.56563	0.801	T	0.64740	-0.6336	10	0.72032	D	0.01	.	9.357	0.38173	0.0:0.7253:0.1927:0.082	.	532	P19835	CEL_HUMAN	W	535;466;534	ENSP00000361151:R535W;ENSP00000342217:R466W	ENSP00000304021:R534W	R	+	1	2	CEL	134936304	0.941000	0.31946	0.013000	0.15412	0.045000	0.14185	0.437000	0.21543	0.461000	0.27071	0.478000	0.44815	CGG	C|0.999;T|0.001	0.001	weak		0.622	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054823.1			T	135946483	C	T	135946483	3	4	23	1	0	0	0	0	1	0	0	0	3211	759	27	1	1645	1	CEL	9	135946483	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	2186103	135946483	5266948	379	7823											
SNAPC4	6621	hgsc.bcm.edu	37	chr9	139272045	139272045	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cggctgcccgtccctgtctgCaagttccagctcactcagga	6	9	10	16	2	3	0	2	0	1	0	5	1	5	1	3	2	3	4	3	2	1	1	rs79283598	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:139272045C>A	ENST00000298532.2	-	21	4602	c.4234G>T	c.(4234-4236)Gca>Tca	p.A1412S		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)		TCCCTGTCTGCAAGTTCCAGC	0.677													C|||	68	0.0135783	0.0023	0.0187	5008	,	,		15784	0.001		0.0477	False		,,,				2504	0.0031				p.A1412S		Atlas-SNP	.											.	SNAPC4	82	.	0			c.G4234T						PASS	.		SER/ALA	26,4380	29.0+/-57.7	0,26,2177	38	37	37		4234	-7.5	0	9	dbSNP_131	37	273,8317	100.3+/-161.8	4,265,4026	yes	missense	SNAPC4	NM_003086.2	99	4,291,6203	AA,AC,CC		3.1781,0.5901,2.3007	benign	1412/1470	139272045	299,12697	2203	4295	6498	SO:0001583	missense	6621	exon21			TGTCTGCAAGTTC	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.4234G>T	9.37:g.139272045C>A	ENSP00000298532:p.Ala1412Ser	59	0	0		71	37	0.521127	NM_003086		Missense_Mutation	SNP	ENST00000298532.2	37	CCDS6998.1	45	0.020604395604395604	2	0.0040650406504065045	6	0.016574585635359115	1	0.0017482517482517483	36	0.047493403693931395	c	0.796	-0.757231	0.03019	0.005901	0.031781	ENSG00000165684	ENST00000298532	T	0.21191	2.02	3.74	-7.47	0.01365	.	7.836560	0.00531	N	0.000204	T	0.01320	0.0043	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13255	-1.0516	10	0.40728	T	0.16	1.8076	1.6888	0.02847	0.3671:0.1135:0.0831:0.4363	.	1412	Q5SXM2	SNPC4_HUMAN	S	1412	ENSP00000298532:A1412S	ENSP00000298532:A1412S	A	-	1	0	SNAPC4	138391866	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.362000	0.01082	-3.382000	0.00175	-0.387000	0.06579	GCA	C|0.976;A|0.024	0.024	strong		0.677	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086		A	139272045	C	A	139272045	3	1	23	1	0	0	0	0	1	0	0	0	14852	710	25	4	183	4	SNAPC4	9	139272045	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	3325562	139272045	1941386	380	7824											
NOTCH1	4851	hgsc.bcm.edu	37	chr9	139407932	139407932	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagggttggattcacactcAttgttgttgatgtcacagtt	9	15	10	7	0	3	1	3	1	0	0	3	2	3	2	0	2	0	4	0	2	1	6	rs2229971|rs587778559	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:139407932A>G	ENST00000277541.6	-	14	2340	c.2265T>C	c.(2263-2265)aaT>aaC	p.N755N		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	755	EGF-like 20. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)		ATTCACACTCATTGTTGTTGA	0.602			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)			G|||	2643	0.527756	0.6997	0.4784	5008	,	,		19531	0.7768		0.335	False		,,,				2504	0.272				p.N755N		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	.	NOTCH1	1980	.	0			c.T2265C						PASS	.	G		2695,1683		864,967,358	109	123	118		2265	-2.3	0	9	dbSNP_98	118	2445,6109		358,1729,2190	no	coding-synonymous	NOTCH1	NM_017617.3		1222,2696,2548	GG,GA,AA		28.5831,38.4422,39.7464		755/2556	139407932	5140,7792	2189	4277	6466	SO:0001819	synonymous_variant	4851	exon14			ACACTCATTGTTG	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.2265T>C	9.37:g.139407932A>G		102	0	0		138	138	1	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			A|0.484;G|0.516	0.516	strong		0.602	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		G	139407932	A	G	139407932	2	3	23	1	0	0	0	0	0	0	0	1	10556	214	8	3		3	NOTCH1	9	139407932	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	135887	139407932	1805499	381	7825											
FBXW5	54461	hgsc.bcm.edu	37	chr9	139838414	139838414	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctccacaggaactcgtccCgcgacacggcctgccattgg	7	6	10	18	4	0	0	0	0	0	0	3	2	2	1	5	3	2	0	5	3	1	1	rs200423543		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:139838414C>T	ENST00000325285.3	-	2	201	c.122G>A	c.(121-123)cGg>cAg	p.R41Q	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	41	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				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)		GAACTCGTCCCGCGACACGGC	0.701																																					p.R41Q		Atlas-SNP	.											.	FBXW5	36	.	0			c.G122A						PASS	.		GLN/ARG	4,4272		0,4,2134	12	14	13		122	2.1	0.9	9		13	30,8458		0,30,4214	yes	missense	FBXW5	NM_018998.2	43	0,34,6348	TT,TC,CC		0.3534,0.0935,0.2664	probably-damaging	41/567	139838414	34,12730	2138	4244	6382	SO:0001583	missense	54461	exon2			TCGTCCCGCGACA	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.122G>A	9.37:g.139838414C>T	ENSP00000313034:p.Arg41Gln	98	0	0		30	21	0.7	NM_018998	B2RDZ6|Q59ET5|Q5SPZ8|Q5SPZ9|Q5SQ00|Q5SQ02|Q5SQ03|Q5SQ04|Q8WY79|Q96GJ6|Q9BSU8|Q9H6A8|Q9HBQ6|Q9NSZ3	Missense_Mutation	SNP	ENST00000325285.3	37	CCDS7014.1	.	.	.	.	.	.	.	.	.	.	c	19.18	3.777882	0.70107	9.35E-4	0.003534	ENSG00000159069	ENST00000325285;ENST00000428398;ENST00000443788	T;T;T	0.66460	-0.21;-0.21;-0.21	4.02	2.08	0.27032	F-box domain, cyclin-like (2);F-box domain, Skp2-like (1);	0.139015	0.47852	D	0.000201	T	0.67078	0.2855	L	0.35414	1.06	0.40830	D	0.983582	D	0.89917	1.0	D	0.68765	0.96	T	0.62334	-0.6876	10	0.33940	T	0.23	-1.4432	7.9151	0.29814	0.1841:0.6384:0.1775:0.0	.	41	Q969U6	FBXW5_HUMAN	Q	41	ENSP00000313034:R41Q;ENSP00000404829:R41Q;ENSP00000394011:R41Q	ENSP00000313034:R41Q	R	-	2	0	FBXW5	138958235	1.000000	0.71417	0.898000	0.35279	0.387000	0.30353	5.101000	0.64566	0.321000	0.23259	-0.529000	0.04317	CGG	.	.	weak		0.701	FBXW5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055227.1	NM_018998		T	139838414	C	T	139838414	3	4	23	1	0	0	0	0	1	0	0	0	5776	652	23	1	1610	1	FBXW5	9	139838414	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	430482	139838414	1375017	382	7826											
LCNL1	401562	hgsc.bcm.edu	37	chr9	139879196	139879196	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agtgacatccgagtggccttCtccgactaccagcactttgc	8	10	9	14	2	1	1	0	1	1	0	3	3	2	1	4	1	3	1	4	1	1	3	rs201494183		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:139879196C>T	ENST00000408973.2	+	3	822	c.228C>T	c.(226-228)ttC>ttT	p.F76F	LCNL1_ENST00000432827.1_Intron	NM_207510.3	NP_997393.3	Q6ZST4	LCNL1_HUMAN	lipocalin-like 1	76																	GAGTGGCCTTCTCCGACTACC	0.687													c|||	1	0.000199681	0.0	0.0	5008	,	,		13386	0.0		0.001	False		,,,				2504	0.0				p.F76F		Atlas-SNP	.											.	LCNL1	4	.	0			c.C228T						PASS	.			3,4273		0,3,2135	30	33	32		228	2	0	9		32	38,8454		0,38,4208	no	coding-synonymous	LCNL1	NM_207510.3		0,41,6343	TT,TC,CC		0.4475,0.0702,0.3211		76/165	139879196	41,12727	2138	4246	6384	SO:0001819	synonymous_variant	401562	exon3			GGCCTTCTCCGAC		CCDS43908.1	9q34.3	2014-01-22			ENSG00000214402	ENSG00000214402		"Lipocalins"	34436	protein-coding gene	gene with protein product							Standard	NM_207510		Approved	FLJ45224	uc004ckh.1	Q6ZST4	OTTHUMG00000159546	ENST00000408973.2:c.228C>T	9.37:g.139879196C>T		62	0	0		70	35	0.5	NM_207510		Silent	SNP	ENST00000408973.2	37	CCDS43908.1																																																																																			C|0.996;T|0.004	0.004	strong		0.687	LCNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356128.1	NM_207510		T	139879196	C	T	139879196	2	4	23	1	0	0	0	0	0	0	0	1	8697	912	32	2		2	LCNL1	9	139879196	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	40782	139879196	1334235	383	7827											
CLIC3	9022	hgsc.bcm.edu	37	chr9	139890105	139890105	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggatggggcctcacctgcgCgtgtccaccgtggtgagggt	5	8	17	11	3	1	1	1	1	0	0	2	2	2	2	4	5	1	0	4	5	0	0	rs141765089	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:139890105C>G	ENST00000494426.1	-	2	397	c.138G>C	c.(136-138)acG>acC	p.T46T	CLIC3_ENST00000480181.1_5'UTR	NM_004669.2	NP_004660.2	O95833	CLIC3_HUMAN	chloride intracellular channel 3	46	GST N-terminal.|Required for insertion into the membrane. {ECO:0000250}.				chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|signal transduction (GO:0007165)	chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			lung(1)|skin(1)	2	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		CTCACCTGCGCGTGTCCACCG	0.706													C|||	21	0.00419329	0.0015	0.0058	5008	,	,		10979	0.0		0.0149	False		,,,				2504	0.0				p.T46T		Atlas-SNP	.											.	CLIC3	13	.	0			c.G138C						PASS	.	C		19,4383	25.3+/-52.1	0,19,2182	40	37	38		138	-7.4	0	9	dbSNP_134	38	162,8434	69.4+/-131.9	2,158,4138	no	coding-synonymous	CLIC3	NM_004669.2		2,177,6320	GG,GC,CC		1.8846,0.4316,1.3925		46/237	139890105	181,12817	2201	4298	6499	SO:0001819	synonymous_variant	9022	exon2			CCTGCGCGTGTCC	AF102166	CCDS7021.1	9q34.3	2012-09-26			ENSG00000169583	ENSG00000169583		"Ion channels / Chloride channels : Intracellular"	2064	protein-coding gene	gene with protein product		606533				9880541	Standard	NM_004669		Approved		uc004ckj.1	O95833	OTTHUMG00000020954	ENST00000494426.1:c.138G>C	9.37:g.139890105C>G		75	0	0		68	44	0.647059	NM_004669	Q5SPZ7	Silent	SNP	ENST00000494426.1	37	CCDS7021.1																																																																																			C|0.991;G|0.009	0.009	strong		0.706	CLIC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055173.2	NM_004669		G	139890105	C	G	139890105	2	3	23	1	0	0	0	0	0	0	0	1	3529	755	27	4		4	CLIC3	9	139890105	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	10909	139890105	1323326	384	7828											
SLC34A3	142680	hgsc.bcm.edu	37	chr9	140127725	140127725	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtgctggtcctgctgccaCtggagagcgccacggccctg	5	7	14	15	2	0	1	0	0	0	1	1	2	1	1	4	3	4	2	4	3	0	0	rs34796681	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:140127725C>T	ENST00000538474.1	+	7	849	c.625C>T	c.(625-627)Ctg>Ttg	p.L209L	SLC34A3_ENST00000361134.2_Silent_p.L209L	NM_001177316.1|NM_001177317.1	NP_001170787|NP_001170788	Q8N130	NPT2C_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 3	209					cellular phosphate ion homeostasis (GO:0030643)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)			kidney(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		CCTGCTGCCACTGGAGAGCGC	0.682													c|||	2	0.000399361	0.0	0.0014	5008	,	,		11300	0.0		0.001	False		,,,				2504	0.0				p.L209L		Atlas-SNP	.											.	SLC34A3	32	.	0			c.C625T						PASS	.		,,	8,4304		0,8,2148	14	15	15		625,625,625	2.7	0.6	9	dbSNP_126	15	59,8433		0,59,4187	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC34A3	NM_001177316.1,NM_001177317.1,NM_080877.2	,,	0,67,6335	TT,TC,CC		0.6948,0.1855,0.5233	,,	209/600,209/600,209/600	140127725	67,12737	2156	4246	6402	SO:0001819	synonymous_variant	142680	exon7			CTGCCACTGGAGA	AB055000	CCDS7038.1	9q34.3	2013-07-17	2013-07-17		ENSG00000198569	ENSG00000198569		"Solute carriers"	20305	protein-coding gene	gene with protein product		609826	"solute carrier family 34 (sodium phosphate), member 3"			11880379, 16358215, 16358214	Standard	NM_080877		Approved	NPTIIc, FLJ38680	uc004cmf.1	Q8N130	OTTHUMG00000131780	ENST00000538474.1:c.625C>T	9.37:g.140127725C>T		46	0	0		58	31	0.534483	NM_001177317	A2BFA1	Silent	SNP	ENST00000538474.1	37	CCDS7038.1																																																																																			C|0.993;T|0.007	0.007	strong		0.682	SLC34A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254712.1	NM_080877		T	140127725	C	T	140127725	2	4	23	1	0	0	0	0	0	0	0	1	14584	564	20	2		2	SLC34A3	9	140127725	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	237620	140127725	1085706	385	7829											
PNPLA7	375775	hgsc.bcm.edu	37	chr9	140438216	140438216	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttggtcctcttcctggcccGctgccggggcagggcagtgt	2	10	15	14	2	1	0	0	0	1	0	3	0	3	0	4	5	1	3	4	5	0	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:140438216G>A	ENST00000277531.4	-	4	436	c.250C>T	c.(250-252)Cgg>Tgg	p.R84W	PNPLA7_ENST00000406427.1_Missense_Mutation_p.R109W|AL365502.1_ENST00000580317.1_RNA	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	84					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)		TTCCTGGCCCGCTGCCGGGGC	0.637																																					p.R109W		Atlas-SNP	.											.	PNPLA7	124	.	0			c.C325T						PASS	.						85	77	80					9																	140438216		2203	4300	6503	SO:0001583	missense	375775	exon5			TGGCCCGCTGCCG	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.250C>T	9.37:g.140438216G>A	ENSP00000277531:p.Arg84Trp	150	0	0		171	74	0.432749	NM_001098537	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Missense_Mutation	SNP	ENST00000277531.4	37	CCDS7045.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.306502	0.60305	.	.	ENSG00000130653	ENST00000277531;ENST00000406427;ENST00000371451;ENST00000434090;ENST00000371450	T;T;T	0.62364	0.05;0.03;0.06	3.41	2.4	0.29515	.	0.066594	0.56097	D	0.000027	T	0.74966	0.3786	M	0.77103	2.36	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	T	0.76767	-0.2838	10	0.87932	D	0	-14.0749	8.3027	0.32023	0.0:0.0:0.5617:0.4382	.	109;84	Q6ZV29-5;Q6ZV29	.;PLPL7_HUMAN	W	84;109;84;75;109	ENSP00000277531:R84W;ENSP00000384610:R109W;ENSP00000400582:R75W	ENSP00000277531:R84W	R	-	1	2	PNPLA7	139558037	1.000000	0.71417	0.954000	0.39281	0.848000	0.48234	1.656000	0.37355	1.907000	0.55213	0.462000	0.41574	CGG	.	.	none		0.637	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286		A	140438216	G	A	140438216	3	1	23	1	0	0	0	0	1	0	0	0	12179	1086	38	1	3827	1	PNPLA7	9	140438216	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	310491	140438216	775215	386	7830											
EHMT1	79813	hgsc.bcm.edu	37	chr9	140638534	140638534	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatgtcggaggctgatcgcGcccagaaggtatgtgttgct	7	10	15	9	3	0	2	0	1	0	1	2	3	0	3	1	3	1	5	1	3	2	2	rs11137198	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:140638534G>A	ENST00000460843.1	+	6	1189	c.1162G>A	c.(1162-1164)Gcc>Acc	p.A388T	EHMT1_ENST00000334856.6_Missense_Mutation_p.A357T|EHMT1_ENST00000371394.2_3'UTR|EHMT1_ENST00000462484.1_Missense_Mutation_p.A388T	NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	388			A -> T (in dbSNP:rs11137198).		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)		GGCTGATCGCGCCCAGAAGGT	0.567													G|||	34	0.00678914	0.0008	0.0058	5008	,	,		16838	0.0		0.0199	False		,,,				2504	0.0092				p.A388T		Atlas-SNP	.											.	EHMT1	196	.	0			c.G1162A						PASS	.	G	THR/ALA,THR/ALA	16,4390	23.3+/-48.9	0,16,2187	60	63	62		1162,1162	-0.3	0	9	dbSNP_120	62	187,8413	84.2+/-146.7	3,181,4116	yes	missense,missense	EHMT1	NM_001145527.1,NM_024757.4	58,58	3,197,6303	AA,AG,GG		2.1744,0.3631,1.5608	benign,benign	388/809,388/1299	140638534	203,12803	2203	4300	6503	SO:0001583	missense	79813	exon6			GATCGCGCCCAGA	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.1162G>A	9.37:g.140638534G>A	ENSP00000417980:p.Ala388Thr	40	0	0		50	31	0.62	NM_001145527	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Missense_Mutation	SNP	ENST00000460843.1	37	CCDS7050.2	19	0.0086996336996337	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	17	0.022427440633245383	G	4.068	0.010439	0.07912	0.003631	0.021744	ENSG00000181090	ENST00000334856;ENST00000371400;ENST00000462484;ENST00000460843	T;T;T	0.69685	1.67;0.91;-0.42	5.25	-0.306	0.12780	.	0.794414	0.11854	N	0.523050	T	0.26304	0.0642	N	0.22421	0.69	0.09310	N	0.999992	B;B;B	0.14012	0.002;0.009;0.009	B;B;B	0.13407	0.001;0.009;0.009	T	0.14952	-1.0454	10	0.09084	T	0.74	.	4.0512	0.09796	0.3854:0.0:0.3682:0.2464	rs11137198;rs11137198	388;357;388	Q9H9B1;Q9H9B1-2;Q9H9B1-4	EHMT1_HUMAN;.;.	T	357;357;388;388	ENSP00000334476:A357T;ENSP00000417328:A388T;ENSP00000417980:A388T	ENSP00000334476:A357T	A	+	1	0	EHMT1	139758355	0.022000	0.18835	0.021000	0.16686	0.026000	0.11368	0.074000	0.14662	-0.417000	0.07461	-1.036000	0.02392	GCC	G|0.986;A|0.014	0.014	strong		0.567	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757		A	140638534	G	A	140638534	3	1	23	1	0	0	0	0	1	0	0	0	4985	1087	38	1	1184	1	EHMT1	9	140638534	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	200318	140638534	574897	387	7831											
AKR1C3	8644	hgsc.bcm.edu	37	chr10	5138747	5138747	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatggcagtgtgaagagagAagacatattctacacttcaa	16	9	10	6	0	2	5	1	1	1	4	2	6	2	5	0	1	1	1	0	1	5	4	rs11551177	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:5138747A>G	ENST00000380554.3	+	2	882	c.230A>G	c.(229-231)gAa>gGa	p.E77G	AKR1C3_ENST00000470862.2_3'UTR|AKR1C3_ENST00000439082.2_5'UTR|AKR1C3_ENST00000605149.1_Missense_Mutation_p.E54G	NM_001253908.1|NM_003739.5	NP_001240837.1|NP_003730.4	P42330	AK1C3_HUMAN	aldo-keto reductase family 1, member C3	77			E -> G (in dbSNP:rs41306308).		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)	GTGAAGAGAGAAGACATATTC	0.423													A|||	184	0.0367412	0.028	0.0663	5008	,	,		22113	0.001		0.0825	False		,,,				2504	0.0174				p.E77G		Atlas-SNP	.											.	AKR1C3	21	.	0			c.A230G						PASS	.	A	GLY/GLU	111,4295	86.8+/-125.4	0,111,2092	175	138	151		230	2	0.5	10	dbSNP_120	151	543,8053	149.5+/-204.6	13,517,3768	no	missense	AKR1C3	NM_003739.4	98	13,628,5860	GG,GA,AA		6.3169,2.5193,5.03	benign	77/324	5138747	654,12348	2203	4298	6501	SO:0001583	missense	8644	exon2			AGAGAGAAGACAT	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.230A>G	10.37:g.5138747A>G	ENSP00000369927:p.Glu77Gly	285	1	0.00350877		328	157	0.478659	NM_001253908	A8K2V0|B4DL37|Q5T2L1|Q96DJ1|Q96KI8|Q99530|Q9UCX1|Q9UII3|Q9UKL9	Missense_Mutation	SNP	ENST00000380554.3	37	CCDS7063.1	103	0.04716117216117216	14	0.028455284552845527	25	0.06906077348066299	1	0.0017482517482517483	63	0.08311345646437995	A	17.28	3.349582	0.61183	0.025193	0.063169	ENSG00000196139	ENST00000380554	T	0.56611	0.45	2.0	2.0	0.26442	NADP-dependent oxidoreductase domain (3);	0.103283	0.39544	N	0.001339	T	0.04861	0.0131	M	0.78637	2.42	0.80722	D	1	B;B	0.20780	0.029;0.048	B;B	0.29598	0.096;0.104	T	0.36138	-0.9760	10	0.87932	D	0	.	7.9207	0.29843	1.0:0.0:0.0:0.0	rs41306308	77;77	B4DKT3;P42330	.;AK1C3_HUMAN	G	77	ENSP00000369927:E77G	ENSP00000369927:E77G	E	+	2	0	AKR1C3	5128747	1.000000	0.71417	0.478000	0.27316	0.756000	0.42949	6.896000	0.75665	1.168000	0.42723	0.260000	0.18958	GAA	A|0.950;G|0.050	0.050	strong		0.423	AKR1C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046533.2	NM_003739		G	5138747	A	G	5138747	3	3	23	1	0	0	0	0	1	0	0	0	471	246	9	3	236	3	AKR1C3	10	5138747	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10		5138747	130396000	388	7832											
FBXO18	84893	hgsc.bcm.edu	37	chr10	5948352	5948352	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagaagcagaggacagtacGtctcggctctctgcggagtc	10	7	13	11	3	2	2	0	0	2	2	5	4	2	4	0	3	3	3	0	3	3	1	rs138692839	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:5948352G>A	ENST00000362091.4	+	3	625	c.510G>A	c.(508-510)acG>acA	p.T170T	FBXO18_ENST00000397269.3_5'UTR|FBXO18_ENST00000379999.5_Silent_p.T221T|FBXO18_ENST00000470089.1_3'UTR	NM_001258453.1|NM_178150.2	NP_001245382.1|NP_835363.1	Q8NFZ0	FBX18_HUMAN	F-box protein, helicase, 18	170	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				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						AGGACAGTACGTCTCGGCTCT	0.572													G|||	6	0.00119808	0.0	0.0	5008	,	,		22855	0.0		0.006	False		,,,				2504	0.0				p.T221T		Atlas-SNP	.											.	FBXO18	108	.	0			c.G663A						PASS	.	G	,	4,4402	8.1+/-20.4	0,4,2199	60	52	55		663,510	0.3	0	10	dbSNP_134	55	42,8558	27.4+/-76.7	0,42,4258	no	coding-synonymous,coding-synonymous	FBXO18	NM_032807.3,NM_178150.1	,	0,46,6457	AA,AG,GG		0.4884,0.0908,0.3537	,	221/1095,170/1044	5948352	46,12960	2203	4300	6503	SO:0001819	synonymous_variant	84893	exon4			CAGTACGTCTCGG	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.510G>A	10.37:g.5948352G>A		157	0	0		140	78	0.557143	NM_032807	Q5JVB0|Q5JVB1|Q7Z4Q6|Q7Z4R0|Q8N1P5|Q8N586|Q96E82|Q96K67|Q96SW7|Q9UFB2	Silent	SNP	ENST00000362091.4	37	CCDS7072.1																																																																																			G|0.998;A|0.002	0.002	strong		0.572	FBXO18-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046596.1	NM_032807		A	5948352	G	A	5948352	2	1	23	1	0	0	0	0	0	0	0	1	5739	1132	40	1		1	FBXO18	10	5948352	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	809605	5948352	129586395	389	7833											
USP6NL	9712	hgsc.bcm.edu	37	chr10	11504687	11504687	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtccatgattgtccctgcGtctcaggtctgtatgtataa	7	14	11	9	1	2	1	1	1	2	0	5	1	4	1	2	2	1	2	2	2	3	4	rs41291253	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:11504687G>A	ENST00000609104.1	-	15	2634	c.2240C>T	c.(2239-2241)aCg>aTg	p.T747M	USP6NL_ENST00000379237.2_Missense_Mutation_p.T770M|USP6NL_ENST00000277575.5_Missense_Mutation_p.T764M	NM_014688.2	NP_055503.1	Q92738	US6NL_HUMAN	USP6 N-terminal like	747					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						TTGTCCCTGCGTCTCAGGTCT	0.468													G|||	6	0.00119808	0.0008	0.0014	5008	,	,		20911	0.0		0.004	False		,,,				2504	0.0				p.T764M		Atlas-SNP	.											.	USP6NL	57	.	0			c.C2291T						PASS	.	G	MET/THR,MET/THR	5,3907		0,5,1951	137	142	140		2291,2240	-1.2	0	10	dbSNP_127	140	35,8269		0,35,4117	yes	missense,missense	USP6NL	NM_001080491.2,NM_014688.2	81,81	0,40,6068	AA,AG,GG		0.4215,0.1278,0.3274	benign,benign	764/846,747/829	11504687	40,12176	1956	4152	6108	SO:0001583	missense	9712	exon14			CCCTGCGTCTCAG	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.2240C>T	10.37:g.11504687G>A	ENSP00000476462:p.Thr747Met	75	0	0		84	42	0.5	NM_001080491	A8KA79|Q15400|Q5VV10|Q7L0K9	Missense_Mutation	SNP	ENST00000609104.1	37	CCDS53492.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	3.027	-0.200380	0.06219	0.001278	0.004215	ENSG00000148429	ENST00000535316;ENST00000277575;ENST00000379237	T;T	0.03889	3.77;3.77	6.17	-1.16	0.09678	.	1.547390	0.03119	N	0.163470	T	0.02888	0.0086	N	0.02802	-0.49	0.09310	N	1	B;B	0.18968	0.019;0.032	B;B	0.11329	0.002;0.006	T	0.44360	-0.9333	10	0.31617	T	0.26	.	11.551	0.50721	0.5617:0.0:0.4383:0.0	rs41291253	747;764	Q92738;Q92738-2	US6NL_HUMAN;.	M	747;764;747	ENSP00000277575:T764M;ENSP00000368539:T747M	ENSP00000277575:T764M	T	-	2	0	USP6NL	11544693	0.000000	0.05858	0.003000	0.11579	0.002000	0.02628	-0.006000	0.12833	-0.047000	0.13423	-0.290000	0.09829	ACG	G|0.997;A|0.003	0.003	strong		0.468	USP6NL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046764.3	NM_014688		A	11504687	G	A	11504687	3	1	23	1	0	0	0	0	1	0	0	0	17102	1145	40	1	250	1	USP6NL	10	11504687	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	5556335	11504687	124030060	390	7834											
SUV39H2	79723	hgsc.bcm.edu	37	chr10	14939485	14939485	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gacccttgtgaagattaaaaGaatgagttttgtcatggaat	14	13	10	4	0	1	4	1	2	0	2	1	6	1	5	1	1	0	1	1	1	5	4			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:14939485G>A	ENST00000354919.6	+	3	818	c.818G>A	c.(817-819)aGa>aAa	p.R273K	SUV39H2_ENST00000313519.5_Missense_Mutation_p.R213K|SUV39H2_ENST00000378325.3_Intron|DCLRE1C_ENST00000378289.4_3'UTR	NM_001193424.1	NP_001180353.1	Q9H5I1	SUV92_HUMAN	suppressor of variegation 3-9 homolog 2 (Drosophila)	273	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				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)	p.R213I(1)		breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)	19						AAGATTAAAAGAATGAGTTTT	0.383																																					p.R273K		Atlas-SNP	.											SUV39H2,colon,carcinoma,0,1	SUV39H2	72	1	1	Substitution - Missense(1)	large_intestine(1)	c.G818A						PASS	.						73	69	71					10																	14939485		2203	4300	6503	SO:0001583	missense	79723	exon3			TTAAAAGAATGAG	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.818G>A	10.37:g.14939485G>A	ENSP00000346997:p.Arg273Lys	64	0	0		59	23	0.38983	NM_001193424	D3DRT4|Q5JSS4|Q5JSS5|Q6I9Y3|Q8ND06	Missense_Mutation	SNP	ENST00000354919.6	37	CCDS53494.1	.	.	.	.	.	.	.	.	.	.	G	4.956	0.177547	0.09443	.	.	ENSG00000152455	ENST00000354919;ENST00000313519;ENST00000420416	T;T;D	0.87103	-1.19;-1.19;-2.21	5.86	4.96	0.65561	SET domain (3);	0.200646	0.44688	N	0.000427	T	0.52885	0.1762	N	0.00226	-1.805	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.60682	-0.7215	10	0.02654	T	1	.	6.9776	0.24686	0.1531:0.1541:0.6928:0.0	.	273	Q9H5I1	SUV92_HUMAN	K	273;213;213	ENSP00000346997:R273K;ENSP00000319208:R213K;ENSP00000392201:R213K	ENSP00000319208:R213K	R	+	2	0	SUV39H2	14979491	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.691000	0.47010	1.631000	0.50456	0.650000	0.86243	AGA	.	.	none		0.383	SUV39H2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046947.2	NM_024670		A	14939485	G	A	14939485	3	1	23	1	0	0	0	0	1	0	0	0	15428	942	33	2	640	2	SUV39H2	10	14939485	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	3434798	14939485	120595262	391	7835											
RSU1	6251	hgsc.bcm.edu	37	chr10	16635400	16635402	+	In_Frame_Del	DEL	TTC	TTC	-																															gccaatcccttccttatctgTtcttggctgccaggggtttc																								rs575845875		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:16635400_16635402delTTC	ENST00000377921.3	-	8	1126_1128	c.825_827delGAA	c.(823-828)aagaac>aac	p.K275del	RSU1_ENST00000602389.1_In_Frame_Del_p.K222del|RSU1_ENST00000345264.5_In_Frame_Del_p.K275del|RSU1_ENST00000464074.2_5'UTR			Q15404	RSU1_HUMAN	Ras suppressor protein 1	275					cell junction assembly (GO:0034329)|positive regulation of neural precursor cell proliferation (GO:2000179)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(1;7.54e-08)		TCCTTATCTGTTCTTGGCTGCCA	0.507																																					p.276_276del		Pindel,Atlas-Indel	.											.	RSU1	31	.	0			c.826_828del						PASS	.																																			SO:0001651	inframe_deletion	6251	exon9			.	AK055596	CCDS7112.1, CCDS31157.1	10p13	2012-09-20			ENSG00000148484	ENSG00000148484			10464	protein-coding gene	gene with protein product		179555				8288261	Standard	NM_152724		Approved	RSP-1, FLJ31034	uc001iol.3	Q15404	OTTHUMG00000017740	ENST00000377921.3:c.825_827delGAA	10.37:g.16635400_16635402delTTC	ENSP00000367154:p.Lys275del	205	0	.		213	71	0.333	NM_012425	A8KA46|D3DRU3|Q6FI17	In_Frame_Del	DEL	ENST00000377921.3	37	CCDS7112.1																																																																																			.	.	none		0.507	RSU1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047006.1	NM_012425, NM_152724		-	16635402	TTC	-	16635400	7	5	23	1	0	1	0	1	0	0	0	0	13731	1725	60	0	10	0	RSU1	10	16635400	In_Frame_Del	DEL	TTC	TCGA-G8-6325-01A-11D-2210-10	1695915	16635400	118899347	392	7836											
KIAA1217	56243	hgsc.bcm.edu	37	chr10	24834980	24834980	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctgctcactctgcctccctCatcccttctgtctctaatgg	4	14	5	18	0	5	0	2	0	3	0	8	0	7	0	4	1	2	1	4	1	1	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:24834980C>T	ENST00000376454.3	+	21	5589	c.5559C>T	c.(5557-5559)ctC>ctT	p.L1853L	KIAA1217_ENST00000458595.1_Silent_p.L1259L|KIAA1217_ENST00000376452.3_Silent_p.L1284L|KIAA1217_ENST00000396445.1_3'UTR|KIAA1217_ENST00000376462.1_Silent_p.L1174L|KIAA1217_ENST00000376451.2_3'UTR	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	1853	Ser-rich. {ECO:0000255}.				embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)		p.L1853L(1)		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						CTGCCTCCCTCATCCCTTCTG	0.502																																					p.L1853L		Atlas-SNP	.											KIAA1217,NS,carcinoma,0,1	KIAA1217	235	1	1	Substitution - coding silent(1)	kidney(1)	c.C5559T						PASS	.						173	177	176					10																	24834980		2203	4300	6503	SO:0001819	synonymous_variant	56243	exon21			CTCCCTCATCCCT	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.5559C>T	10.37:g.24834980C>T		255	0	0		271	129	0.476015	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Silent	SNP	ENST00000376454.3	37	CCDS31165.1																																																																																			.	.	none		0.502	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		T	24834980	C	T	24834980	2	4	23	1	0	0	0	0	0	0	0	1	8225	813	29	2		2	KIAA1217	10	24834980	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	8199580	24834980	110699767	393	7837											
ARHGAP21	57584	hgsc.bcm.edu	37	chr10	24908668	24908668	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgctcagtttcagcctctTgtaaacttaaatcttgattc	10	17	5	9	0	4	1	2	1	2	0	5	1	4	1	1	0	3	3	1	0	4	7	rs142573508	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:24908668T>C	ENST00000396432.2	-	9	2642	c.2156A>G	c.(2155-2157)cAa>cGa	p.Q719R	ARHGAP21_ENST00000320481.6_Missense_Mutation_p.Q506R	NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	718					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						TTCAGCCTCTTGTAAACTTAA	0.453													T|||	11	0.00219649	0.0	0.0	5008	,	,		19618	0.0		0.0	False		,,,				2504	0.0112				p.Q719R		Atlas-SNP	.											.	ARHGAP21	185	.	0			c.A2156G						PASS	.	T	ARG/GLN	0,4406		0,0,2203	61	58	59		2156	-2.6	0	10	dbSNP_134	59	2,8598	2.2+/-6.3	0,2,4298	no	missense	ARHGAP21	NM_020824.3	43	0,2,6501	CC,CT,TT		0.0233,0.0,0.0154	benign	719/1959	24908668	2,13004	2203	4300	6503	SO:0001583	missense	57584	exon9			GCCTCTTGTAAAC	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.2156A>G	10.37:g.24908668T>C	ENSP00000379709:p.Gln719Arg	154	0	0		143	65	0.454545	NM_020824	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000396432.2	37	CCDS7144.2	.	.	.	.	.	.	.	.	.	.	T	4.856	0.159203	0.09236	0.0	2.33E-4	ENSG00000107863	ENST00000396432;ENST00000320481;ENST00000376410;ENST00000446003;ENST00000445703	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	5.1	-2.62	0.06152	.	1.071100	0.07121	N	0.843866	T	0.24774	0.0601	L	0.31294	0.92	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.24190	-1.0167	10	0.16420	T	0.52	.	5.0428	0.14467	0.1188:0.0718:0.4868:0.3226	.	709;718	F8W9U9;Q5T5U3	.;RHG21_HUMAN	R	719;506;709;719;554	ENSP00000379709:Q719R;ENSP00000365604:Q506R;ENSP00000365592:Q709R;ENSP00000405018:Q719R	ENSP00000365604:Q506R	Q	-	2	0	ARHGAP21	24948674	0.004000	0.15560	0.043000	0.18650	0.866000	0.49608	0.189000	0.17037	-0.256000	0.09473	0.533000	0.62120	CAA	T|1.000;C|0.000	0.000	strong		0.453	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824		C	24908668	T	C	24908668	3	2	23	1	0	0	0	0	1	0	0	0	871	1812	63	3	3792	3	ARHGAP21	10	24908668	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	73688	24908668	110626079	394	7838											
RET	5979	hgsc.bcm.edu	37	chr10	43610119	43610119	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggtcagctactcctcttccGgtgcccgccggccctcgctg	2	9	11	19	5	2	0	1	0	1	0	5	0	4	0	5	3	3	2	5	3	1	2	rs1799939	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:43610119G>A	ENST00000355710.3	+	11	2303	c.2071G>A	c.(2071-2073)Ggt>Agt	p.G691S	RET_ENST00000340058.5_Missense_Mutation_p.G691S	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	691			G -> S (in dbSNP:rs1799939). {ECO:0000269|PubMed:14566559, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9223675, ECO:0000269|PubMed:9497256}.		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)	CTCCTCTTCCGGTGCCCGCCG	0.647		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				G|||	847	0.169129	0.0923	0.2565	5008	,	,		18422	0.121		0.1889	False		,,,				2504	0.2403				p.G691S	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_ENST00000340058,adrenal_gland,pheochromocytoma,0,2	RET	916	2	0			c.G2071A	GRCh37	CM023821	RET	M	rs1799939	PASS	.	G	SER/GLY,SER/GLY	455,3951	216.4+/-235.1	19,417,1767	61	55	57	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2071,2071	-1.1	0	10	dbSNP_89	57	1587,7013	295.7+/-302.5	155,1277,2868	yes	missense,missense	RET	NM_020630.4,NM_020975.4	56,56	174,1694,4635	AA,AG,GG		18.4535,10.3268,15.7004	possibly-damaging,possibly-damaging	691/1073,691/1115	43610119	2042,10964	2203	4300	6503	SO:0001583	missense	5979	exon11	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	TCTTCCGGTGCCC	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.2071G>A	10.37:g.43610119G>A	ENSP00000347942:p.Gly691Ser	58	0	0		79	37	0.468354	NM_020630	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Missense_Mutation	SNP	ENST00000355710.3	37	CCDS7200.1	338	0.15476190476190477	45	0.09146341463414634	82	0.2265193370165746	60	0.1048951048951049	151	0.19920844327176782	G	8.525	0.869582	0.17322	0.103268	0.184535	ENSG00000165731	ENST00000355710;ENST00000340058	T;T	0.78246	-1.05;-1.16	4.75	-1.08	0.09936	.	0.349618	0.34603	N	0.003826	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.24426	0.062;0.062;0.103	B;B;B	0.16722	0.004;0.007;0.016	T	0.04128	-1.0975	9	0.07990	T	0.79	.	9.2584	0.37597	0.7374:0.0:0.2626:0.0	rs1799939;rs3781260;rs17362555;rs17845010;rs17857772;rs1799939	437;691;691	B4DGX8;P07949;P07949-2	.;RET_HUMAN;.	S	691	ENSP00000347942:G691S;ENSP00000344798:G691S	ENSP00000344798:G691S	G	+	1	0	RET	42930125	1.000000	0.71417	0.000000	0.03702	0.411000	0.31082	4.395000	0.59678	-0.060000	0.13132	0.462000	0.41574	GGT	G|0.839;A|0.161	0.161	strong		0.647	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975		A	43610119	G	A	43610119	3	1	23	1	0	0	0	0	1	0	0	0	13250	1116	39	1	2113	1	RET	10	43610119	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	18701451	43610119	91924628	395	7839											
FRMPD2	143162	hgsc.bcm.edu	37	chr10	49400730	49400730	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaatgtgtcacacccacctgCgcccgatgccttctgctcca	8	9	7	17	2	2	0	1	0	1	0	3	1	3	0	5	0	3	1	5	0	1	1	rs116034788	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:49400730C>T	ENST00000374201.3	-	16	2464	c.2162G>A	c.(2161-2163)cGc>cAc	p.R721H	FRMPD2_ENST00000407470.4_Missense_Mutation_p.R689H|FRMPD2_ENST00000305531.3_Missense_Mutation_p.R696H	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	721					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)		CACCCACCTGCGCCCGATGCC	0.493													C|||	14	0.00279553	0.0	0.0029	5008	,	,		20123	0.0089		0.003	False		,,,				2504	0.0				p.R721H		Atlas-SNP	.											FRMPD2,NS,carcinoma,-1,1	FRMPD2	157	1	0			c.G2162A						PASS	.	C	HIS/ARG	6,4400	11.4+/-27.6	0,6,2197	75	54	61		2162	0.9	0.7	10	dbSNP_132	61	19,8581	14.0+/-48.4	0,19,4281	yes	missense	FRMPD2	NM_001018071.3	29	0,25,6478	TT,TC,CC		0.2209,0.1362,0.1922	possibly-damaging	721/1310	49400730	25,12981	2203	4300	6503	SO:0001583	missense	143162	exon16			CACCTGCGCCCGA	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.2162G>A	10.37:g.49400730C>T	ENSP00000363317:p.Arg721His	121	0	0		131	60	0.458015	NM_001018071	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Missense_Mutation	SNP	ENST00000374201.3	37	CCDS31195.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	4	0.006993006993006993	1	0.0013192612137203166	C	9.151	1.016217	0.19355	0.001362	0.002209	ENSG00000170324	ENST00000374201;ENST00000305531;ENST00000407470	T;T;T	0.64803	-0.08;-0.12;-0.11	5.01	0.934	0.19477	.	.	.	.	.	T	0.29882	0.0747	N	0.14661	0.345	0.21184	N	0.999768	B;D;B	0.54207	0.024;0.965;0.024	B;B;B	0.38156	0.003;0.266;0.003	T	0.13818	-1.0495	9	0.45353	T	0.12	.	6.935	0.24461	0.0:0.5514:0.2905:0.1581	.	696;721;689	Q68DX3-2;Q68DX3;F8WCT2	.;FRPD2_HUMAN;.	H	721;696;689	ENSP00000363317:R721H;ENSP00000307079:R696H;ENSP00000384339:R689H	ENSP00000307079:R696H	R	-	2	0	FRMPD2	49070736	0.170000	0.23016	0.681000	0.30009	0.090000	0.18270	0.379000	0.20585	0.234000	0.21139	-0.211000	0.12701	CGC	C|0.998;T|0.002	0.002	strong		0.493	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428		T	49400730	C	T	49400730	3	4	23	1	0	0	0	0	1	0	0	0	6066	768	27	1	1823	1	FRMPD2	10	49400730	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	5790611	49400730	86134017	396	7840											
FRMPD2	143162	hgsc.bcm.edu	37	chr10	49431171	49431171	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtttgcagcactcactggagCagcccatagtggctgacaaa	11	8	11	11	0	1	1	1	1	0	0	1	2	1	2	1	2	4	5	1	2	2	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:49431171C>T	ENST00000374201.3	-	11	1613	c.1311G>A	c.(1309-1311)ctG>ctA	p.L437L	FRMPD2_ENST00000407470.4_Silent_p.L406L|FRMPD2_ENST00000305531.3_Silent_p.L413L	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	437	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				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)		CTCACTGGAGCAGCCCATAGT	0.473																																					p.L437L		Atlas-SNP	.											.	FRMPD2	157	.	0			c.G1311A						PASS	.						85	82	83					10																	49431171		2203	4300	6503	SO:0001819	synonymous_variant	143162	exon11			CTGGAGCAGCCCA	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.1311G>A	10.37:g.49431171C>T		83	0	0		84	51	0.607143	NM_001018071	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Silent	SNP	ENST00000374201.3	37	CCDS31195.1																																																																																			.	.	none		0.473	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428		T	49431171	C	T	49431171	2	4	23	1	0	0	0	0	0	0	0	1	6066	697	25	2		2	FRMPD2	10	49431171	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	30441	49431171	86103576	397	7841											
PRKG1	5592	hgsc.bcm.edu	37	chr10	52751177	52751177	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gactttgccaagattctcatGctcaaggaggagaggatcaa	13	9	11	8	0	3	2	3	0	1	2	4	6	3	4	1	3	2	1	1	3	3	2	rs202017913		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:52751177G>A	ENST00000401604.2	+	1	233	c.39G>A	c.(37-39)atG>atA	p.M13I	PRKG1_ENST00000373985.1_Start_Codon_SNP_p.M1I			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	13	Leucine-zipper.|Required for dimerization.				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)		AGATTCTCATGCTCAAGGAGG	0.567													G|||	1	0.000199681	0.0	0.0	5008	,	,		10226	0.0		0.001	False		,,,				2504	0.0				p.M13I		Atlas-SNP	.											.	PRKG1	167	.	0			c.G39A						PASS	.	G	ILE/MET	1,3781		0,1,1890	22	28	26		39	4.8	1	10		26	8,8204		0,8,4098	yes	missense	PRKG1	NM_001098512.2	10	0,9,5988	AA,AG,GG		0.0974,0.0264,0.075	benign	13/672	52751177	9,11985	1891	4106	5997	SO:0001583	missense	5592	exon1			TCTCATGCTCAAG		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.39G>A	10.37:g.52751177G>A	ENSP00000384200:p.Met13Ile	115	0	0		106	43	0.40566	NM_001098512	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Missense_Mutation	SNP	ENST00000401604.2	37	CCDS44399.1	.	.	.	.	.	.	.	.	.	.	G	12.50	1.956344	0.34565	2.64E-4	9.74E-4	ENSG00000185532	ENST00000401604;ENST00000373985	T;T	0.66638	-0.22;-0.13	4.76	4.76	0.60689	.	.	.	.	.	T	0.48466	0.1501	N	0.08118	0	0.27645	N	0.947607	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.001	T	0.33369	-0.9871	9	0.30854	T	0.27	.	15.5982	0.76602	0.0:0.0:1.0:0.0	.	13;13	B4DT93;Q13976	.;KGP1_HUMAN	I	13;1	ENSP00000384200:M13I;ENSP00000363097:M1I	ENSP00000363097:M1I	M	+	3	0	PRKG1	52421183	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.962000	0.63687	2.349000	0.79799	0.462000	0.41574	ATG	.	.	weak		0.567	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	52751177	G	A	52751177	3	1	23	1	0	0	0	0	1	0	0	0	12534	1319	46	2	41	2	PRKG1	10	52751177	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	3320006	52751177	82783570	398	7842											
JMJD1C	221037	hgsc.bcm.edu	37	chr10	64927837	64927837	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	catatcctctacttcatcctCgtgtatcttcaaggctctca	8	15	4	14	1	5	0	3	0	3	0	9	0	7	0	2	1	1	2	2	1	4	5	rs71508957	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:64927837C>T	ENST00000399262.2	-	26	7809	c.7591G>A	c.(7591-7593)Gag>Aag	p.E2531K	JMJD1C_ENST00000399251.1_3'UTR|JMJD1C_ENST00000542921.1_Missense_Mutation_p.E2349K|JMJD1C_ENST00000402544.1_Missense_Mutation_p.E2294K	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	2531					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)					ACTTCATCCTCGTGTATCTTC	0.333													C|||	10	0.00199681	0.0008	0.0	5008	,	,		18116	0.0		0.004	False		,,,				2504	0.0051				p.E2531K		Atlas-SNP	.											.	JMJD1C	347	.	0			c.G7591A						PASS	.	C	LYS/GLU,LYS/GLU	6,3716		0,6,1855	181	163	169		6880,7591	5.4	1	10	dbSNP_130	169	82,8102		1,80,4011	yes	missense,missense	JMJD1C	NM_004241.2,NM_032776.1	56,56	1,86,5866	TT,TC,CC		1.002,0.1612,0.7391	probably-damaging,probably-damaging	2294/2304,2531/2541	64927837	88,11818	1861	4092	5953	SO:0001583	missense	221037	exon26			CATCCTCGTGTAT	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.7591G>A	10.37:g.64927837C>T	ENSP00000382204:p.Glu2531Lys	102	0	0		112	45	0.401786	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	37	CCDS41532.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	17.89	3.499039	0.64298	0.001612	0.01002	ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000542921	T;T;T	0.67698	-0.28;-0.28;-0.28	5.42	5.42	0.78866	.	0.128349	0.53938	D	0.000055	T	0.62502	0.2433	L	0.34521	1.04	0.80722	D	1	D;B	0.69078	0.997;0.403	P;B	0.53450	0.726;0.17	T	0.70306	-0.4908	10	0.62326	D	0.03	-21.4168	19.2123	0.93760	0.0:1.0:0.0:0.0	.	2531;2349	Q15652;A0T124	JHD2C_HUMAN;.	K	2531;2294;2349	ENSP00000382204:E2531K;ENSP00000384990:E2294K;ENSP00000444682:E2349K	ENSP00000382204:E2531K	E	-	1	0	JMJD1C	64597843	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	2.593000	0.46180	2.528000	0.85240	0.591000	0.81541	GAG	C|0.998;T|0.002	0.002	strong		0.333	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		T	64927837	C	T	64927837	3	4	23	1	0	0	0	0	1	0	0	0	7959	893	31	1	35	1	JMJD1C	10	64927837	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	12176660	64927837	70606910	399	7843											
LRRTM3	347731	hgsc.bcm.edu	37	chr10	68687942	68687942	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tttccataaaatcatcgcggGcagcgtggcgcttttcctgt	7	13	10	11	4	1	0	1	0	0	0	4	0	3	0	2	2	1	2	2	2	2	4			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:68687942G>C	ENST00000361320.4	+	2	1846	c.1268G>C	c.(1267-1269)gGc>gCc	p.G423A	CTNNA3_ENST00000433211.2_Intron|CTNNA3_ENST00000373744.4_Intron	NM_178011.3	NP_821079.3	Q86VH5	LRRT3_HUMAN	leucine rich repeat transmembrane neuronal 3	423					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						ATCATCGCGGGCAGCGTGGCG	0.612																																					p.G423A		Atlas-SNP	.											.	LRRTM3	241	.	0			c.G1268C						PASS	.						70	68	69					10																	68687942		2203	4300	6503	SO:0001583	missense	347731	exon2			TCGCGGGCAGCGT	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.1268G>C	10.37:g.68687942G>C	ENSP00000355187:p.Gly423Ala	71	0	0		56	21	0.375	NM_178011	A8K2A3|Q2NKX7|Q6N0A3	Missense_Mutation	SNP	ENST00000361320.4	37	CCDS7270.1	.	.	.	.	.	.	.	.	.	.	G	18.76	3.692071	0.68271	.	.	ENSG00000198739	ENST00000361320;ENST00000373722	T	0.75367	-0.93	5.94	5.94	0.96194	.	0.000000	0.64402	D	0.000001	D	0.87525	0.6199	M	0.82056	2.57	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.87653	0.2529	10	0.62326	D	0.03	.	19.1373	0.93433	0.0:0.0:1.0:0.0	.	423;423	Q86VH5;Q86VH5-2	LRRT3_HUMAN;.	A	423	ENSP00000355187:G423A	ENSP00000355187:G423A	G	+	2	0	LRRTM3	68357948	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	9.869000	0.99810	2.820000	0.97059	0.650000	0.86243	GGC	.	.	none		0.612	LRRTM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048277.2	NM_178011		C	68687942	G	C	68687942	3	2	23	1	0	0	0	0	1	0	0	0	9050	1203	42	4	1274	4	LRRTM3	10	68687942	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	3760105	68687942	66846805	400	7844											
HKDC1	80201	hgsc.bcm.edu	37	chr10	71026433	71026433	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgatgtgacattcatgctgTcagaagatggcagtggaaaa	13	10	13	5	0	2	4	2	2	0	2	2	5	2	5	0	2	1	2	0	2	3	1	rs148418934	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:71026433T>C	ENST00000354624.5	+	18	2807	c.2674T>C	c.(2674-2676)Tca>Cca	p.S892P	RP11-227H15.5_ENST00000413220.1_RNA	NM_025130.3	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	892	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						ATTCATGCTGTCAGAAGATGG	0.478													T|||	3	0.000599042	0.0	0.0029	5008	,	,		19517	0.0		0.001	False		,,,				2504	0.0				p.S892P		Atlas-SNP	.											.	HKDC1	98	.	0			c.T2674C						PASS	.	T	PRO/SER	2,4404	4.2+/-10.8	0,2,2201	163	145	151		2674	5	1	10	dbSNP_134	151	16,8584	11.9+/-42.8	0,16,4284	yes	missense	HKDC1	NM_025130.3	74	0,18,6485	CC,CT,TT		0.186,0.0454,0.1384	probably-damaging	892/918	71026433	18,12988	2203	4300	6503	SO:0001583	missense	80201	exon18			ATGCTGTCAGAAG		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.2674T>C	10.37:g.71026433T>C	ENSP00000346643:p.Ser892Pro	113	0	0		128	63	0.492188	NM_025130	B5MDN9|Q2TB91|Q5VTC7|Q7Z373|Q8WU37|Q96EH2|Q9H5Y9	Missense_Mutation	SNP	ENST00000354624.5	37	CCDS7288.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	T	20.7	4.030350	0.75504	4.54E-4	0.00186	ENSG00000156510	ENST00000354624	D	0.97279	-4.32	4.96	4.96	0.65561	Hexokinase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98607	0.9534	H	0.97540	4.025	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96137	0.9097	10	0.87932	D	0	-5.87	15.069	0.72021	0.0:0.0:0.0:1.0	.	892	Q2TB90	HKDC1_HUMAN	P	892	ENSP00000346643:S892P	ENSP00000346643:S892P	S	+	1	0	HKDC1	70696439	1.000000	0.71417	1.000000	0.80357	0.605000	0.37080	7.387000	0.79785	2.206000	0.71126	0.533000	0.62120	TCA	T|0.998;C|0.002	0.002	strong		0.478	HKDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048389.1	NM_025130		C	71026433	T	C	71026433	3	2	23	1	0	0	0	0	1	0	0	0	7202	1667	58	3	2744	3	HKDC1	10	71026433	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	2338491	71026433	64508314	401	7845											
ECD	11319	hgsc.bcm.edu	37	chr10	74894526	74894526	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacagattctcccgtaccagAatcttcctcatctgaattgt	11	13	5	12	1	4	3	1	1	3	2	6	3	5	3	3	0	2	1	3	0	4	4	rs35331959	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:74894526A>C	ENST00000372979.4	-	14	1956	c.1750T>G	c.(1750-1752)Tct>Gct	p.S584A	ECD_ENST00000430082.2_Missense_Mutation_p.S617A|ECD_ENST00000454759.2_Missense_Mutation_p.S541A	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	584					cell proliferation (GO:0008283)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of glycolytic process (GO:0006110)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(51;0.0119)					CCCGTACCAGAATCTTCCTCA	0.428													A|||	14	0.00279553	0.0015	0.0029	5008	,	,		17074	0.0		0.0099	False		,,,				2504	0.0				p.S617A		Atlas-SNP	.											.	ECD	50	.	0			c.T1849G						PASS	.	A	ALA/SER,ALA/SER,ALA/SER	13,4393	20.2+/-43.8	0,13,2190	114	111	112		1849,1621,1750	4.3	1	10	dbSNP_126	112	136,8464	68.7+/-131.2	2,132,4166	yes	missense,missense,missense	ECD	NM_001135752.1,NM_001135753.1,NM_007265.2	99,99,99	2,145,6356	CC,CA,AA		1.5814,0.2951,1.1456	benign,benign,benign	617/678,541/602,584/645	74894526	149,12857	2203	4300	6503	SO:0001583	missense	11319	exon15			TACCAGAATCTTC	BC000721	CCDS7321.1, CCDS44433.1, CCDS44434.1	10q22.3	2006-02-07				ENSG00000122882			17029	protein-coding gene	gene with protein product						9928932, 15128659	Standard	NM_007265		Approved	hSGT1, GCR2	uc001jtn.3	O95905		ENST00000372979.4:c.1750T>G	10.37:g.74894526A>C	ENSP00000362070:p.Ser584Ala	169	0	0		160	67	0.41875	NM_001135752	C9JX46|E9PAW8	Missense_Mutation	SNP	ENST00000372979.4	37	CCDS7321.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	A	4.002	-0.002418	0.07819	0.002951	0.015814	ENSG00000122882	ENST00000372979;ENST00000430082;ENST00000454759	T;T;T	0.19394	2.15;2.15;2.15	5.48	4.29	0.51040	.	0.570097	0.19982	N	0.101760	T	0.04861	0.0131	N	0.12746	0.255	0.26648	N	0.972169	B;B;B	0.09022	0.002;0.002;0.001	B;B;B	0.15484	0.01;0.003;0.013	T	0.24297	-1.0164	10	0.09590	T	0.72	-0.8007	10.5006	0.44804	0.7883:0.2116:0.0:0.0	rs35331959	541;617;584	E9PAW8;C9JX46;O95905	.;.;SGT1_HUMAN	A	584;617;541	ENSP00000362070:S584A;ENSP00000401566:S617A;ENSP00000395786:S541A	ENSP00000362070:S584A	S	-	1	0	ECD	74564532	1.000000	0.71417	1.000000	0.80357	0.242000	0.25591	2.625000	0.46452	2.063000	0.61619	0.460000	0.39030	TCT	A|0.991;C|0.009	0.009	strong		0.428	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265		C	74894526	A	C	74894526	3	2	23	1	0	0	0	0	1	0	0	0	4890	246	9	5	188	5	ECD	10	74894526	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	3868093	74894526	60640221	402	7846											
CYP2C9	1559	hgsc.bcm.edu	37	chr10	96740981	96740981	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aacgtgtgattggcagaaacCggagcccctgcatgcaagac	12	6	12	11	2	0	3	0	1	0	2	0	4	0	4	3	2	5	3	3	2	3	1	rs28371685	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:96740981C>T	ENST00000260682.6	+	7	1015	c.1003C>T	c.(1003-1005)Cgg>Tgg	p.R335W		NM_000771.3	NP_000762.2	P11712	CP2C9_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 9	335			R -> W (in allele CYP2C9*11; dbSNP:rs28371685). {ECO:0000269|PubMed:11926893, ECO:0000269|PubMed:15469410}.		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)	TGGCAGAAACCGGAGCCCCTG	0.498													C|||	36	0.0071885	0.0242	0.0014	5008	,	,		17934	0.0		0.002	False		,,,				2504	0.001				p.R335W	Ovarian(54;1266 1406 16072 35076)	Atlas-SNP	.											CYP2C9,NS,carcinoma,-1,1	CYP2C9	82	1	0			c.C1003T	GRCh37	CM056574	CYP2C9	M	rs28371685	scavenged	.	C	TRP/ARG	84,4322		0,84,2119	164	146	152		1003	2.8	0.9	10	dbSNP_125	152	16,8584		0,16,4284	no	missense	CYP2C9	NM_000771.3	101	0,100,6403	TT,TC,CC		0.186,1.9065,0.7689	probably-damaging	335/491	96740981	100,12906	2203	4300	6503	SO:0001583	missense	1559	exon7			AGAAACCGGAGCC	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.1003C>T	10.37:g.96740981C>T	ENSP00000260682:p.Arg335Trp	158	1	0.00632911		199	107	0.537688	NM_000771	P11713|Q16756|Q16872|Q5VX92|Q6IRV8|Q8WW80	Missense_Mutation	SNP	ENST00000260682.6	37	CCDS7437.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	.	12.02	1.813765	0.32053	0.019065	0.00186	ENSG00000138109	ENST00000545448;ENST00000260682	T	0.71698	-0.59	3.78	2.85	0.33270	.	0.293574	0.27035	U	0.021241	T	0.74772	0.3760	H	0.97186	3.955	0.18873	N	0.999988	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.73905	-0.3835	10	0.87932	D	0	.	10.7287	0.46083	0.191:0.809:0.0:0.0	rs28371685;rs60219528	335;335	Q5VX92;P11712	.;CP2C9_HUMAN	W	335	ENSP00000260682:R335W	ENSP00000260682:R335W	R	+	1	2	CYP2C9	96730971	0.615000	0.27026	0.866000	0.34008	0.172000	0.22775	1.328000	0.33758	0.910000	0.36722	0.305000	0.20034	CGG	C|0.986;T|0.014	0.014	strong		0.498	CYP2C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049501.1	NM_000771		T	96740981	C	T	96740981	3	4	23	1	0	0	0	0	1	0	0	0	4170	643	23	1	1029	1	CYP2C9	10	96740981	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	21846455	96740981	38793766	403	7847											
SLC18A2	6571	hgsc.bcm.edu	37	chr10	119003546	119003546	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aatgctacagaaatccagacGgccaggccagtgcacactgc	13	5	10	13	1	0	2	0	0	0	2	1	2	1	2	3	2	4	2	3	2	3	1	rs11568722		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:119003546G>A	ENST00000298472.5	+	3	329	c.186G>A	c.(184-186)acG>acA	p.T62T	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	62					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)	AAATCCAGACGGCCAGGCCAG	0.498																																					p.T62T		Atlas-SNP	.											SLC18A2,NS,carcinoma,+1,1	SLC18A2	58	1	0			c.G186A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	88	76	80		186	-11.6	0	10	dbSNP_126	80	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	SLC18A2	NM_003054.4		0,7,6496	AA,AG,GG		0.0698,0.0227,0.0538		62/515	119003546	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	6571	exon3			CCAGACGGCCAGG	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.186G>A	10.37:g.119003546G>A		121	0	0		99	55	0.555556	NM_003054	B2RC96|D3DRC4|Q15876|Q4G147|Q5VW49|Q9H3P6	Silent	SNP	ENST00000298472.5	37	CCDS7599.1																																																																																			G|1.000;A|0.000	0.000	weak		0.498	SLC18A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050563.1	NM_003054		A	119003546	G	A	119003546	2	1	23	1	0	0	0	0	0	0	0	1	14441	1103	39	1		1	SLC18A2	10	119003546	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	22262565	119003546	16531201	404	7848											
FGFR2	2263	hgsc.bcm.edu	37	chr10	123239112	123239112	+	3'UTR	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcctactggtccacagccaGtacgcacggcaggtgagagg	9	6	14	12	2	0	1	0	1	0	1	2	2	2	1	3	4	3	3	3	4	2	2	rs1047057	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:123239112G>A	ENST00000358487.5	-	0	2997				FGFR2_ENST00000369061.4_3'UTR|FGFR2_ENST00000369060.4_3'UTR|FGFR2_ENST00000478859.1_3'UTR|FGFR2_ENST00000357555.5_Silent_p.L703L|FGFR2_ENST00000356226.4_3'UTR	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2						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)	p.L703L(1)		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)	TCCACAGCCAGTACGCACGGC	0.483		5	Mis		"gastric. NSCLC, endometrial"		"Crouzon, Pfeiffer, and Apert syndromes"		Saethre-Chotzen syndrome;Apert syndrome				G|||	2075	0.414337	0.0938	0.6873	5008	,	,		15689	0.3512		0.5099	False		,,,				2504	0.6207				p.L703L		Atlas-SNP	.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	FGFR2_ENST00000357555,NS,carcinoma,0,1	FGFR2	758	1	1	Substitution - coding silent(1)	stomach(1)	c.C2107T						PASS	.	G	,,,,,,	237,1147		19,199,474	86	84	85		,,2107,,,,	4.5	0.9	10	dbSNP_86	85	1747,1435		500,747,344	no	utr-3,utr-3,coding-synonymous,utr-3,utr-3,utr-3,utr-3	FGFR2	NM_000141.4,NM_001144914.1,NM_001144915.1,NM_001144916.1,NM_001144917.1,NM_001144918.1,NM_022970.3	,,,,,,	519,946,818	AA,AG,GG		45.0974,17.1243,43.4516	,,,,,,	,,703/708,,,,	123239112	1984,2582	692	1591	2283	SO:0001624	3_prime_UTR_variant	2263	exon17	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	CAGCCAGTACGCA	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.*259C>T	10.37:g.123239112G>A		86	0	0		90	47	0.522222	NM_001144915	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	Silent	SNP	ENST00000358487.5	37	CCDS31298.1																																																																																			G|0.609;A|0.391	0.391	strong		0.483	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141		A	123239112	G	A	123239112	1	1	23	0	1	0	0	0	0	0	0	0	5874	1020	36	2		2	FGFR2	10	123239112	3'UTR	SNP	G	TCGA-G8-6325-01A-11D-2210-10	4235566	123239112	12295635	405	7849											
BTBD16	118663	hgsc.bcm.edu	37	chr10	124036305	124036305	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctttctttgattaccaagcaGcacaaagctcggctggaacg	11	10	9	11	2	1	1	0	1	1	0	2	2	1	2	1	2	5	4	1	2	4	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:124036305G>T	ENST00000260723.4	+	3	269		c.e3-1		BTBD16_ENST00000368994.2_Missense_Mutation_p.Q7H	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16											breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(3)|skin(2)|stomach(1)|urinary_tract(1)	15		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)				TTACCAAGCAGCACAAAGCTC	0.448																																					.		Atlas-SNP	.											BTBD16,bladder,carcinoma,0,1	BTBD16	44	1	0			c.19-1G>T						PASS	.						84	87	86					10																	124036305		2203	4300	6503	SO:0001630	splice_region_variant	118663	exon3			CAAGCAGCACAAA	AK058088	CCDS31301.1	10q26.13	2013-01-24	2006-07-04	2006-07-04	ENSG00000138152	ENSG00000138152		"BTB/POZ domain containing"	26340	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 87"	C10orf87			Standard	NM_144587		Approved	FLJ25359, Em:AC061711.1	uc001lgc.1	Q32M84	OTTHUMG00000019182	ENST00000260723.4:c.19-1G>T	10.37:g.124036305G>T		125	0	0		134	18	0.134328	NM_144587	A6NM63|Q4VXL1|Q96LN0	Splice_Site	SNP	ENST00000260723.4	37	CCDS31301.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.139|9.139	1.013409|1.013409	0.19277|0.19277	.|.	.|.	ENSG00000138152|ENSG00000138152	ENST00000260723|ENST00000368994	.|T	.|0.19250	.|2.16	4.66|4.66	3.76|3.76	0.43208|0.43208	.|.	.|.	.|.	.|.	.|.	.|T	.|0.34571	.|0.0902	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|D	.|0.61697	.|0.99	.|P	.|0.58873	.|0.847	.|T	.|0.07139	.|-1.0788	.|8	.|0.44086	.|T	.|0.13	.|-0.0759	8.8669|8.8669	0.35291|0.35291	0.1013:0.0:0.8987:0.0|0.1013:0.0:0.8987:0.0	.|.	.|7	.|Q32M84-2	.|.	.|H	-1|7	.|ENSP00000357990:Q7H	.|ENSP00000357990:Q7H	.|Q	+|+	.|3	.|2	BTBD16|BTBD16	124026295|124026295	0.605000|0.605000	0.26941|0.26941	0.007000|0.007000	0.13788|0.13788	0.006000|0.006000	0.05464|0.05464	2.406000|2.406000	0.44557|0.44557	1.332000|1.332000	0.45431|0.45431	0.650000|0.650000	0.86243|0.86243	.|CAG	.	.	none		0.448	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587	Intron	T	124036305	G	T	124036305	5	4	23	1	0	0	0	0	0	0	1	0	1543	985	34	4	24	4	BTBD16	10	124036305	Splice_Site	SNP	G	TCGA-G8-6325-01A-11D-2210-10	797193	124036305	11498442	406	7850											
HTRA1	5654	hgsc.bcm.edu	37	chr10	124268261	124268261	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagattaaaaagttcctcacGgagtcccatgaccgacaggc	14	7	9	11	2	1	2	1	1	0	1	3	4	3	3	3	2	0	1	3	2	4	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:124268261G>A	ENST00000368984.3	+	6	1223	c.1095G>A	c.(1093-1095)acG>acA	p.T365T		NM_002775.4	NP_002766.1	Q92743	HTRA1_HUMAN	HtrA serine peptidase 1	365	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(1)|kidney(1)|large_intestine(8)|lung(7)	17		all_neural(114;0.0765)|Lung NSC(174;0.133)|all_lung(145;0.163)|Breast(234;0.238)				AGTTCCTCACGGAGTCCCATG	0.517																																					p.T365T		Atlas-SNP	.											HTRA1,colon,carcinoma,+2,2	HTRA1	40	2	0			c.G1095A						PASS	.						98	102	100					10																	124268261		2203	4300	6503	SO:0001819	synonymous_variant	5654	exon6			CCTCACGGAGTCC	AF097709	CCDS7630.1	10q26.3	2014-01-28	2005-08-18	2005-08-18	ENSG00000166033	ENSG00000166033		"Serine peptidases / Serine peptidases"	9476	protein-coding gene	gene with protein product		602194	"protease, serine, 11 (IGF binding)"	PRSS11		8977104	Standard	NM_002775		Approved	HtrA, IGFBP5-protease, ARMD7	uc001lgj.2	Q92743	OTTHUMG00000019186	ENST00000368984.3:c.1095G>A	10.37:g.124268261G>A		52	0	0		64	11	0.171875	NM_002775	D3DRE4|Q9UNS5	Silent	SNP	ENST00000368984.3	37	CCDS7630.1																																																																																			.	.	none		0.517	HTRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128327.1	NM_002775		A	124268261	G	A	124268261	2	1	23	1	0	0	0	0	0	0	0	1	7462	1103	39	1		1	HTRA1	10	124268261	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	231956	124268261	11266486	407	7851											
MKI67	4288	hgsc.bcm.edu	37	chr10	129904286	129904286	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctttaggagtttgtggccGtctcttgctgccaggtaaat	6	16	11	8	1	2	0	0	0	2	0	3	1	2	1	2	3	2	3	2	3	3	6	rs146273614	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:129904286G>A	ENST00000368654.3	-	13	6193	c.5818C>T	c.(5818-5820)Cgg>Tgg	p.R1940W	MKI67_ENST00000368653.3_Missense_Mutation_p.R1580W	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1940	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)				GTTTGTGGCCGTCTCTTGCTG	0.493													G|||	15	0.00299521	0.0	0.0072	5008	,	,		18668	0.0		0.0089	False		,,,				2504	0.001				p.R1940W		Atlas-SNP	.											.	MKI67	363	.	0			c.C5818T						PASS	.	G	TRP/ARG,TRP/ARG	7,4399	14.3+/-33.2	0,7,2196	173	179	177		4738,5818	-8.8	0	10	dbSNP_134	177	78,8522	46.7+/-105.8	0,78,4222	no	missense,missense	MKI67	NM_001145966.1,NM_002417.4	101,101	0,85,6418	AA,AG,GG		0.907,0.1589,0.6535	benign,benign	1580/2897,1940/3257	129904286	85,12921	2203	4300	6503	SO:0001583	missense	4288	exon13			GTGGCCGTCTCTT	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.5818C>T	10.37:g.129904286G>A	ENSP00000357643:p.Arg1940Trp	348	0	0		403	163	0.404467	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	9	0.004120879120879121	0	0.0	3	0.008287292817679558	0	0.0	6	0.0079155672823219	G	9.208	1.030151	0.19512	0.001589	0.00907	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02446	4.29;4.29	4.42	-8.82	0.00810	.	.	.	.	.	T	0.01320	0.0043	L	0.35854	1.095	0.09310	N	1	B;B;B	0.30104	0.006;0.268;0.012	B;B;B	0.21360	0.005;0.034;0.005	T	0.26950	-1.0088	9	0.59425	D	0.04	.	4.3783	0.11281	0.1014:0.0852:0.3233:0.4901	.	1939;1580;1940	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	W	1940;1580;1939	ENSP00000357643:R1940W;ENSP00000357642:R1580W	ENSP00000357642:R1580W	R	-	1	2	MKI67	129794276	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.725000	0.01863	-2.749000	0.00375	-2.677000	0.00143	CGG	G|0.994;A|0.006	0.006	strong		0.493	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		A	129904286	G	A	129904286	3	1	23	1	0	0	0	0	1	0	0	0	9607	1144	40	1	3964	1	MKI67	10	129904286	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	5636025	129904286	5630461	408	7852											
B4GALNT4	338707	hgsc.bcm.edu	37	chr11	380395	380395	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagggcaggctggccttcgCgcccgtggtcatgcgcctga	4	7	17	13	4	1	1	1	1	0	0	2	2	1	2	3	5	1	2	3	5	0	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:380395C>T	ENST00000329962.6	+	18	2819	c.2819C>T	c.(2818-2820)gCg>gTg	p.A940V		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	940					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)		CTGGCCTTCGCGCCCGTGGTC	0.687																																					p.A940V		Atlas-SNP	.											B4GALNT4,NS,carcinoma,+1,1	B4GALNT4	83	1	0			c.C2819T						scavenged	.						55	40	45					11																	380395		2202	4299	6501	SO:0001583	missense	338707	exon18			CCTTCGCGCCCGT	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.2819C>T	11.37:g.380395C>T	ENSP00000328277:p.Ala940Val	87	0	0		52	3	0.0576923	NM_178537	Q96LV2	Missense_Mutation	SNP	ENST00000329962.6	37	CCDS7694.1	.	.	.	.	.	.	.	.	.	.	c	25.9	4.682412	0.88542	.	.	ENSG00000182272	ENST00000329962	T	0.35236	1.32	3.81	3.81	0.43845	.	0.000000	0.85682	D	0.000000	T	0.41858	0.1177	M	0.67517	2.055	0.58432	D	0.99999	P	0.46512	0.879	P	0.45856	0.495	T	0.36432	-0.9748	10	0.20519	T	0.43	-32.7173	16.2551	0.82510	0.0:1.0:0.0:0.0	.	940	Q76KP1	B4GN4_HUMAN	V	940	ENSP00000328277:A940V	ENSP00000328277:A940V	A	+	2	0	B4GALNT4	370395	1.000000	0.71417	0.977000	0.42913	0.811000	0.45836	7.456000	0.80751	2.118000	0.64928	0.561000	0.74099	GCG	.	.	none		0.687	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537		T	380395	C	T	380395	3	4	23	1	0	0	0	0	1	0	0	0	1269	768	27	1	2889	1	B4GALNT4	11	380395	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10		380395	134626121	409	7853											
ANO9	338440	hgsc.bcm.edu	37	chr11	421036	421036	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccatcatgcagccgctggCgtggcactgcggggccagac	6	6	15	14	3	1	1	1	0	0	1	2	1	2	1	3	4	3	3	3	4	0	0			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:421036C>T	ENST00000332826.6	-	17	1483	c.1399G>A	c.(1399-1401)Gcc>Acc	p.A467T		NM_001012302.2	NP_001012302	A1A5B4	ANO9_HUMAN	anoctamin 9	467					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						CAGCCGCTGGCGTGGCACTGC	0.652																																					p.A467T		Atlas-SNP	.											.	ANO9	61	.	0			c.G1399A						PASS	.						24	26	26					11																	421036		2200	4297	6497	SO:0001583	missense	338440	exon17			CGCTGGCGTGGCA	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.1399G>A	11.37:g.421036C>T	ENSP00000332788:p.Ala467Thr	70	0	0		84	43	0.511905	NM_001012302	B3KUC4|B4E134|Q8TEN4	Missense_Mutation	SNP	ENST00000332826.6	37	CCDS31326.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.532417	0.85812	.	.	ENSG00000185101	ENST00000332826	T	0.63255	-0.03	3.99	3.06	0.35304	.	0.419080	0.22997	N	0.053128	T	0.56949	0.2020	L	0.46157	1.445	0.80722	D	1	P;P	0.49961	0.903;0.93	B;B	0.43194	0.215;0.411	T	0.61242	-0.7102	10	0.62326	D	0.03	.	13.5161	0.61541	0.0:0.1658:0.8342:0.0	.	168;467	A1A5B4-2;A1A5B4	.;ANO9_HUMAN	T	467	ENSP00000332788:A467T	ENSP00000332788:A467T	A	-	1	0	ANO9	411036	1.000000	0.71417	0.971000	0.41717	0.933000	0.57130	6.568000	0.73987	0.789000	0.33779	0.306000	0.20318	GCC	.	.	none		0.652	ANO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384116.1	NM_001012302		T	421036	C	T	421036	3	4	23	1	0	0	0	0	1	0	0	0	704	768	27	1	977	1	ANO9	11	421036	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	40641	421036	134585480	410	7854											
HRAS	3265	hgsc.bcm.edu	37	chr11	534242	534242	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggtcgtattcgtccacaaaAtggttctggatcagctggat	9	12	12	8	2	2	0	1	0	1	0	5	2	3	2	1	4	1	3	1	4	3	3	rs12628	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:534242A>G	ENST00000451590.1	-	2	268	c.81T>C	c.(79-81)caT>caC	p.H27H	HRAS_ENST00000397594.1_Silent_p.H27H|HRAS_ENST00000468682.2_5'UTR|HRAS_ENST00000417302.1_Silent_p.H27H|HRAS_ENST00000311189.7_Silent_p.H27H|HRAS_ENST00000397596.2_Silent_p.H27H	NM_001130442.1|NM_005343.2	NP_001123914.1|NP_005334.1	P01112	RASH_HUMAN	Harvey rat sarcoma viral oncogene homolog	27					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular senescence (GO:0090398)|chemotaxis (GO:0006935)|endocytosis (GO:0006897)|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)|intrinsic apoptotic signaling pathway (GO:0097193)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Rho GTPase activity (GO:0034259)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|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 DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of wound healing (GO:0090303)|protein heterooligomerization (GO:0051291)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein C-terminus binding (GO:0008022)	p.H27H(26)		adrenal_gland(1)|bone(3)|breast(7)|cervix(23)|endometrium(4)|haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|oesophagus(2)|penis(2)|pituitary(10)|prostate(31)|salivary_gland(24)|skin(184)|soft_tissue(38)|stomach(14)|testis(5)|thymus(1)|thyroid(173)|upper_aerodigestive_tract(122)|urinary_tract(225)	901		all_cancers(49;4.37e-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;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)		CGTCCACAAAATGGTTCTGGA	0.642		6	Mis		"infrequent sarcomas, rare other types"	"rhadomyosarcoma, ganglioneuroblastoma, bladder"			Costello syndrome	HNSCC(11;0.0054)			G|||	1488	0.297125	0.3729	0.3646	5008	,	,		18347	0.1726		0.3121	False		,,,				2504	0.2597				p.H27H		Atlas-SNP	.	yes	Dom	yes	Costello syndrome	11	11p15.5	3265	v-Ha-ras Harvey rat sarcoma viral oncogene homolog		"E, L, M"	HRAS,arm,benign_melanocytic_nevus,0,26	HRAS	1232	26	26	Substitution - coding silent(26)	urinary_tract(25)|skin(1)	c.T81C	GRCh37	CM035804	HRAS	M	rs12628	PASS	.	G	,,	1652,2754	653.2+/-399.5	309,1034,860	135	123	127	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	81,81,81	1	1	11	dbSNP_52	127	2959,5641	665.8+/-402.3	510,1939,1851	no	coding-synonymous,coding-synonymous,coding-synonymous	HRAS	NM_001130442.1,NM_005343.2,NM_176795.3	,,	819,2973,2711	GG,GA,AA		34.407,37.4943,35.4529	,,	27/190,27/190,27/171	534242	4611,8395	2203	4300	6503	SO:0001819	synonymous_variant	3265	exon2	Familial Cancer Database	incl.: Facio-Cutaneous-Skeletal syndrome	CACAAAATGGTTC	AJ437024	CCDS7698.1, CCDS7699.1	11p15.5	2014-09-17	2013-07-08		ENSG00000174775	ENSG00000174775			5173	protein-coding gene	gene with protein product		190020	"v-Ha-ras Harvey rat sarcoma viral oncogene homolog"	HRAS1			Standard	NM_176795		Approved		uc010qvx.2	P01112	OTTHUMG00000131919	ENST00000451590.1:c.81T>C	11.37:g.534242A>G		144	0	0		102	59	0.578431	NM_001130442	B5BUA0|Q14080|Q6FHV9|Q9BR65|Q9UCE2	Silent	SNP	ENST00000451590.1	37	CCDS7698.1																																																																																			A|0.663;G|0.337	0.337	strong		0.642	HRAS-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259403.2	NM_176795		G	534242	A	G	534242	2	3	23	1	0	0	0	0	0	0	0	1	7357	98	4	3		3	HRAS	11	534242	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	113206	534242	134472274	411	7855											
PHRF1	57661	hgsc.bcm.edu	37	chr11	582056	582056	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaagacgagggggcgtctgaGgaggaagacctggaagacag	13	3	19	6	2	1	4	0	1	1	3	1	9	1	7	1	5	0	0	1	5	3	0	rs117660271	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:582056G>A	ENST00000264555.5	+	3	317	c.189G>A	c.(187-189)gaG>gaA	p.E63E	PHRF1_ENST00000533464.1_Silent_p.E59E|PHRF1_ENST00000416188.2_Silent_p.E63E|PHRF1_ENST00000413872.2_Silent_p.E62E	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	63					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						GGGCGTCTGAGGAGGAAGACC	0.572													G|||	7	0.00139776	0.0	0.0014	5008	,	,		17686	0.0		0.005	False		,,,				2504	0.001				p.E63E		Atlas-SNP	.											.	PHRF1	188	.	0			c.G189A						PASS	.	G		4,4256		0,4,2126	50	67	62		189	-5.6	0	11	dbSNP_132	62	35,8479		0,35,4222	no	coding-synonymous	PHRF1	NM_020901.2		0,39,6348	AA,AG,GG		0.4111,0.0939,0.3053		63/1649	582056	39,12735	2130	4257	6387	SO:0001819	synonymous_variant	57661	exon3			GTCTGAGGAGGAA	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.189G>A	11.37:g.582056G>A		67	0	0		77	34	0.441558	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Silent	SNP	ENST00000264555.5	37																																																																																				G|0.997;A|0.003	0.003	strong		0.572	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901		A	582056	G	A	582056	2	1	23	1	0	0	0	0	0	0	0	1	11870	991	35	2		2	PHRF1	11	582056	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	47814	582056	134424460	412	7856											
MUC2	4583	hgsc.bcm.edu	37	chr11	1092971	1092971	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tacggtgaccccaaccccaaCacccaccggcacacagaccc	12	2	6	21	2	0	2	0	1	0	1	0	2	0	2	7	2	3	1	7	2	3	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:1092971C>T	ENST00000441003.2	+	30	4817	c.4790C>T	c.(4789-4791)aCa>aTa	p.T1597I	MUC2_ENST00000359061.5_Intron|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)	ccaaccccaacacccaccggc	0.632																																					p.T1597I		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,1	MUC2	614	1	0			c.C4790T						scavenged	.						47	82	70					11																	1092971		1782	3233	5015	SO:0001583	missense	4583	exon30			CCCCAACACCCAC	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.4790C>T	11.37:g.1092971C>T	ENSP00000415183:p.Thr1597Ile	114	1	0.00877193		121	6	0.0495868	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	2.395	-0.338980	0.05243	.	.	ENSG00000198788	ENST00000441003	T	0.14640	2.49	1.75	0.762	0.18454	.	.	.	.	.	T	0.07143	0.0181	.	.	.	0.09310	N	1	B	0.13145	0.007	B	0.04013	0.001	T	0.41520	-0.9504	8	0.22109	T	0.4	.	4.3366	0.11089	0.0:0.6142:0.0:0.3858	.	1597	E7EUV1	.	I	1597	ENSP00000415183:T1597I	ENSP00000415183:T1597I	T	+	2	0	MUC2	1082971	0.029000	0.19370	0.001000	0.08648	0.134000	0.20937	1.107000	0.31110	0.104000	0.17725	0.121000	0.15741	ACA	.	.	none		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1092971	C	T	1092971	3	4	23	1	0	0	0	0	1	0	0	0	9984	478	17	2	4908	2	MUC2	11	1092971	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	510915	1092971	133913545	413	7857											
TRIM21	6737	hgsc.bcm.edu	37	chr11	4411471	4411471	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagattcttgagcagaaagcGctgccggcacacaggacaga	13	5	13	10	2	1	4	0	1	1	3	1	6	1	5	1	2	3	3	1	2	1	2	rs200488796		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4411471G>A	ENST00000254436.7	-	2	281	c.169C>T	c.(169-171)Cgc>Tgc	p.R57C	TRIM21_ENST00000543625.1_Missense_Mutation_p.R57C	NM_003141.3	NP_003132.2	P19474	RO52_HUMAN	tripartite motif containing 21	57					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)		AGCAGAAAGCGCTGCCGGCAC	0.582													G|||	1	0.000199681	0.0	0.0014	5008	,	,		19735	0.0		0.0	False		,,,				2504	0.0				p.R57C		Atlas-SNP	.											.	TRIM21	45	.	0			c.C169T						PASS	.	G	CYS/ARG	0,4246		0,0,2123	90	94	93		169	-1.4	0	11		93	17,8461		0,17,4222	yes	missense	TRIM21	NM_003141.3	180	0,17,6345	AA,AG,GG		0.2005,0.0,0.1336	possibly-damaging	57/476	4411471	17,12707	2123	4239	6362	SO:0001583	missense	6737	exon2			GAAAGCGCTGCCG	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.169C>T	11.37:g.4411471G>A	ENSP00000254436:p.Arg57Cys	99	0	0		123	69	0.560976	NM_003141	Q5XPV5|Q96RF8	Missense_Mutation	SNP	ENST00000254436.7	37	CCDS44525.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	5.894	0.349073	0.11182	0.0	0.002005	ENSG00000132109	ENST00000254436;ENST00000543625	D;D	0.84223	-1.82;-1.82	4.46	-1.39	0.08997	Zinc finger, RING/FYVE/PHD-type (1);	4.312490	0.00166	N	0.000018	T	0.72228	0.3434	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.62224	-0.6899	10	0.62326	D	0.03	.	7.6016	0.28079	0.1865:0.0:0.6493:0.1642	.	57	P19474	RO52_HUMAN	C	57	ENSP00000254436:R57C;ENSP00000444045:R57C	ENSP00000254436:R57C	R	-	1	0	TRIM21	4368047	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.155000	0.03163	-0.237000	0.09739	0.655000	0.94253	CGC	G|1.000;A|0.000	0.000	strong		0.582	TRIM21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385842.1	NM_003141		A	4411471	G	A	4411471	3	1	23	1	0	0	0	0	1	0	0	0	16510	1087	38	1	1282	1	TRIM21	11	4411471	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	3318500	4411471	130595045	414	7858											
C11orf40	143501	hgsc.bcm.edu	37	chr11	4594648	4594648	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	ggcctggtgtatgaacacatCcttatctaagttaaaggctc	11	12	9	9	0	1	1	0	1	1	0	3	1	2	1	2	3	1	3	2	3	6	4			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4594648C>G	ENST00000307616.1	-	2	195	c.196G>C	c.(196-198)Gat>Cat	p.D66H		NM_144663.1	NP_653264.1	Q8WZ69	CK040_HUMAN	chromosome 11 open reading frame 40	66										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)		ATGAACACATCCTTATCTAAG	0.433																																					p.D66H		Atlas-SNP	.											C11orf40,NS,carcinoma,0,1	C11orf40	37	1	0			c.G196C						PASS	.						164	146	152					11																	4594648		2201	4298	6499	SO:0001583	missense	143501	exon2			ACACATCCTTATC		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.196G>C	11.37:g.4594648C>G	ENSP00000302918:p.Asp66His	154	0	0		150	78	0.52	NM_144663		Missense_Mutation	SNP	ENST00000307616.1	37	CCDS31354.1	.	.	.	.	.	.	.	.	.	.	C	5.540	0.284501	0.10513	.	.	ENSG00000171987	ENST00000307616	T	0.57107	0.42	1.49	-1.98	0.07480	.	.	.	.	.	T	0.30634	0.0771	N	0.08118	0	0.09310	N	1	D	0.58268	0.982	P	0.47603	0.551	T	0.17592	-1.0364	9	0.87932	D	0	.	1.9732	0.03410	0.2617:0.3567:0.0:0.3816	.	66	Q8WZ69	CK040_HUMAN	H	66	ENSP00000302918:D66H	ENSP00000302918:D66H	D	-	1	0	C11orf40	4551224	0.000000	0.05858	0.000000	0.03702	0.098000	0.18820	-1.399000	0.02506	-0.671000	0.05274	0.563000	0.77884	GAT	.	.	none		0.433	C11orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383529.1	NM_144663		G	4594648	C	G	4594648	3	3	23	1	0	0	0	0	1	0	0	0	1641	855	30	4	468	4	C11orf40	11	4594648	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	183177	4594648	130411868	415	7859											
OR52W1	120787	hgsc.bcm.edu	37	chr11	6221305	6221305	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgcacatccttctctccaaCatctacttgctgctgccacc	7	12	5	17	0	2	0	0	0	2	0	5	0	4	0	4	0	6	3	4	0	2	3	rs374054864		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6221305C>G	ENST00000311352.2	+	1	930	c.852C>G	c.(850-852)aaC>aaG	p.N284K	RP11-290F24.6_ENST00000600308.1_lincRNA	NM_001005178.1	NP_001005178.1	Q6IF63	O52W1_HUMAN	olfactory receptor, family 52, subfamily W, 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)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)	11		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;2.13e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTCTCTCCAACATCTACTTGC	0.527																																					p.N284K		Atlas-SNP	.											.	OR52W1	33	.	0			c.C852G						PASS	.	C	LYS/ASN	0,4402		0,0,2201	338	328	332		852	-0.5	1	11		332	1,8591	1.2+/-3.3	0,1,4295	no	missense	OR52W1	NM_001005178.1	94	0,1,6496	GG,GC,CC		0.0116,0.0,0.0077	possibly-damaging	284/321	6221305	1,12993	2201	4296	6497	SO:0001583	missense	120787	exon1			CTCCAACATCTAC	AB065511	CCDS31407.1	11p15.4	2012-08-09		2004-03-10	ENSG00000175485	ENSG00000175485		"GPCR / Class A : Olfactory receptors"	15239	protein-coding gene	gene with protein product				OR52W1P			Standard	NM_001005178		Approved		uc010qzz.2	Q6IF63	OTTHUMG00000165378	ENST00000311352.2:c.852C>G	11.37:g.6221305C>G	ENSP00000309673:p.Asn284Lys	97	0	0		105	46	0.438095	NM_001005178	Q8NH78	Missense_Mutation	SNP	ENST00000311352.2	37	CCDS31407.1	.	.	.	.	.	.	.	.	.	.	C	15.85	2.954305	0.53293	0.0	1.16E-4	ENSG00000175485	ENST00000311352	T	0.00115	8.71	5.11	-0.514	0.11958	GPCR, rhodopsin-like superfamily (1);	0.173838	0.27245	N	0.020242	T	0.00241	0.0007	M	0.87971	2.92	0.22226	N	0.999278	P	0.47191	0.891	P	0.45377	0.478	T	0.42632	-0.9440	10	0.87932	D	0	.	6.437	0.21829	0.0:0.5957:0.1217:0.2826	.	284	Q6IF63	O52W1_HUMAN	K	284	ENSP00000309673:N284K	ENSP00000309673:N284K	N	+	3	2	OR52W1	6177881	0.000000	0.05858	0.995000	0.50966	0.975000	0.68041	-0.511000	0.06321	0.003000	0.14656	-0.253000	0.11424	AAC	.	.	weak		0.527	OR52W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383758.1	NM_001005178		G	6221305	C	G	6221305	3	3	23	1	0	0	0	0	1	0	0	0	11141	477	17	4	854	4	OR52W1	11	6221305	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1626657	6221305	128785211	416	7860											
ST5	6764	hgsc.bcm.edu	37	chr11	8724191	8724191	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agattcggatgagctggcgcAcactgaggcaggtaaaaagg	13	6	15	7	2	0	3	0	2	0	1	1	4	0	4	0	5	1	4	0	5	3	2	rs113126215	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:8724191A>G	ENST00000534127.1	-	17	3033	c.2648T>C	c.(2647-2649)gTg>gCg	p.V883A	ST5_ENST00000534278.1_Missense_Mutation_p.V74A|ST5_ENST00000526099.1_Missense_Mutation_p.V396A|ST5_ENST00000530438.1_Missense_Mutation_p.V463A|ST5_ENST00000357665.1_Missense_Mutation_p.V883A|ST5_ENST00000313726.6_Missense_Mutation_p.V883A|ST5_ENST00000526757.1_Missense_Mutation_p.V463A|RPL27A_ENST00000531102.1_Intron|ST5_ENST00000530991.1_Missense_Mutation_p.V355A	NM_005418.3	NP_005409.3	P78524	ST5_HUMAN	suppression of tumorigenicity 5	883	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				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)		GAGCTGGCGCACACTGAGGCA	0.582													a|||	8	0.00159744	0.0008	0.0014	5008	,	,		19188	0.0		0.005	False		,,,				2504	0.001				p.V883A		Atlas-SNP	.											.	ST5	85	.	0			c.T2648C						PASS	.	A	ALA/VAL,ALA/VAL,ALA/VAL	9,4393	15.5+/-35.6	0,9,2192	86	79	81		2648,1388,2648	4.7	1	11	dbSNP_132	81	48,8544	31.2+/-83.2	0,48,4248	yes	missense,missense,missense	ST5	NM_005418.3,NM_139157.2,NM_213618.1	64,64,64	0,57,6440	GG,GA,AA		0.5587,0.2045,0.4387	benign,benign,benign	883/1138,463/718,883/1138	8724191	57,12937	2201	4296	6497	SO:0001583	missense	6764	exon17			TGGCGCACACTGA	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.2648T>C	11.37:g.8724191A>G	ENSP00000433528:p.Val883Ala	50	0	0		43	19	0.44186	NM_005418	B2R6X7|B3KXQ6|P78523|Q16492|Q7KYY2|Q7KZ12|Q8NE12|Q9BQQ6	Missense_Mutation	SNP	ENST00000534127.1	37	CCDS7791.1	4	0.0018315018315018315	1	0.0020325203252032522	0	0.0	0	0.0	3	0.00395778364116095	a	16.30	3.083512	0.55861	0.002045	0.005587	ENSG00000166444	ENST00000526757;ENST00000534127;ENST00000313726;ENST00000530991;ENST00000357665;ENST00000526099;ENST00000534278;ENST00000530438;ENST00000533081	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	4.72	4.72	0.59763	DENN (3);	0.000000	0.85682	D	0.000000	T	0.19406	0.0466	M	0.78801	2.425	0.53005	D	0.999961	B;B;B	0.28026	0.023;0.012;0.198	B;B;B	0.38755	0.202;0.038;0.281	T	0.05699	-1.0869	10	0.87932	D	0	-10.884	14.2346	0.65916	1.0:0.0:0.0:0.0	.	396;463;883	B4DDL8;P78524-2;P78524	.;.;ST5_HUMAN	A	463;883;883;355;883;396;74;463;73	ENSP00000435097:V463A;ENSP00000433528:V883A;ENSP00000319678:V883A;ENSP00000432887:V355A;ENSP00000350294:V883A;ENSP00000436808:V396A;ENSP00000433349:V74A;ENSP00000436802:V463A;ENSP00000436067:V73A	ENSP00000319678:V883A	V	-	2	0	ST5	8680767	0.990000	0.36364	1.000000	0.80357	0.992000	0.81027	7.573000	0.82421	1.760000	0.52011	0.398000	0.26397	GTG	A|0.996;G|0.004	0.004	strong		0.582	ST5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386518.1	NM_005418		G	8724191	A	G	8724191	3	3	23	1	0	0	0	0	1	0	0	0	15235	159	6	3	793	3	ST5	11	8724191	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	2502886	8724191	126282325	417	7861											
MPPED2	744	hgsc.bcm.edu	37	chr11	30433028	30433028	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tagagcttcaggaaccctgtGggtttggaaggtcaaatata	12	11	12	6	0	2	1	2	0	0	1	2	3	2	3	1	4	2	2	1	4	6	5	rs146268212		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:30433028G>A	ENST00000358117.5	-	6	994	c.872C>T	c.(871-873)cCa>cTa	p.P291L	MPPED2_ENST00000524667.1_5'UTR|MPPED2_ENST00000448418.2_Intron	NM_001584.2	NP_001575.1	Q15777	MPPD2_HUMAN	metallophosphoesterase domain containing 2	291					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						GGAACCCTGTGGGTTTGGAAG	0.418																																					p.P291L		Atlas-SNP	.											.	MPPED2	106	.	0			c.C872T						PASS	.	G	,LEU/PRO	0,4404		0,0,2202	112	97	102		,872	5.6	1	11	dbSNP_134	102	1,8597	1.2+/-3.3	0,1,4298	no	intron,missense	MPPED2	NM_001145399.1,NM_001584.2	,98	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	,probably-damaging	,291/295	30433028	1,13001	2202	4299	6501	SO:0001583	missense	744	exon6			CCCTGTGGGTTTG	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.872C>T	11.37:g.30433028G>A	ENSP00000350833:p.Pro291Leu	121	0	0		101	46	0.455446	NM_001584	D3DQZ5|E9PB10|Q59GE6	Missense_Mutation	SNP	ENST00000358117.5	37	CCDS7870.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.376204	0.82682	0.0	1.16E-4	ENSG00000066382	ENST00000358117	T	0.51325	0.71	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.73087	0.3542	M	0.82716	2.605	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.74352	-0.3693	10	0.52906	T	0.07	-7.0431	19.8808	0.96899	0.0:0.0:1.0:0.0	.	291	Q15777	MPPD2_HUMAN	L	291	ENSP00000350833:P291L	ENSP00000350833:P291L	P	-	2	0	MPPED2	30389604	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.813000	0.99286	2.771000	0.95319	0.561000	0.74099	CCA	G|1.000;A|0.000	0.000	weak		0.418	MPPED2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388155.2	NM_001584		A	30433028	G	A	30433028	3	1	23	1	0	0	0	0	1	0	0	0	9751	1348	47	2	88	2	MPPED2	11	30433028	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	21708837	30433028	104573488	418	7862											
APIP	8050	hgsc.bcm.edu	37	chr11	34937828	34937828	+	5'Flank	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcccgagcatcacagccagAcatggcccagaccagggacc	11	3	10	17	1	1	2	1	0	0	2	2	4	2	3	5	2	2	1	5	2	0	0			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:34937828A>G	ENST00000227868.4	+	0	0				APIP_ENST00000395787.3_Missense_Mutation_p.S2P|APIP_ENST00000278359.5_5'UTR|APIP_ENST00000527830.1_5'UTR|PDHX_ENST00000430469.2_5'Flank|PDHX_ENST00000448838.3_5'UTR			O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X						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)			TCACAGCCAGACATGGCCCAG	0.687																																					p.S2P		Atlas-SNP	.											.	APIP	21	.	0			c.T4C						PASS	.						16	18	17					11																	34937828		2197	4293	6490	SO:0001631	upstream_gene_variant	51074	exon1			AGCCAGACATGGC	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		11.37:g.34937828A>G	Exception_encountered	62	0	0		83	25	0.301205	NM_015957	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Missense_Mutation	SNP	ENST00000227868.4	37	CCDS7896.1	.	.	.	.	.	.	.	.	.	.	A	16.07	3.018048	0.54576	.	.	ENSG00000149089	ENST00000395787	T	0.19394	2.15	4.68	-0.69	0.11309	.	0.808144	0.11278	N	0.580708	T	0.09024	0.0223	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.14117	-1.0484	10	0.54805	T	0.06	.	4.192	0.10426	0.4606:0.3478:0.1917:0.0	.	2	Q96GX9	MTNB_HUMAN	P	2	ENSP00000379133:S2P	ENSP00000379133:S2P	S	-	1	0	APIP	34894404	0.998000	0.40836	0.865000	0.33974	0.003000	0.03518	0.450000	0.21762	0.064000	0.16427	-0.441000	0.05720	TCT	.	.	none		0.687	PDHX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390017.1	NM_003477		G	34937828	A	G	34937828	1	3	23	0	1	0	0	0	0	0	0	0	774	275	10	3		3	APIP	11	34937828	5'Flank	SNP	A	TCGA-G8-6325-01A-11D-2210-10	4504800	34937828	100068688	419	7863											
CD44	960	hgsc.bcm.edu	37	chr11	35211471	35211471	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	accccagcaaccctactgatGatgacgtgagcagcggctcc	10	6	10	15	2	0	4	0	4	0	0	1	4	1	4	4	1	5	3	4	1	2	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:35211471G>A	ENST00000428726.2	+	5	649	c.526G>A	c.(526-528)Gat>Aat	p.D176N	CD44_ENST00000360158.4_Missense_Mutation_p.D176N|CD44_ENST00000434472.2_Missense_Mutation_p.D176N|CD44_ENST00000278386.6_Intron|CD44_ENST00000526669.2_Intron|CD44_ENST00000263398.6_Missense_Mutation_p.D176N|CD44_ENST00000352818.4_Missense_Mutation_p.D176N|CD44_ENST00000433892.2_Missense_Mutation_p.D176N|CD44_ENST00000433354.2_Missense_Mutation_p.D176N|CD44_ENST00000415148.2_Missense_Mutation_p.D176N|CD44_ENST00000449691.2_Missense_Mutation_p.D176N|CD44_ENST00000437706.2_Missense_Mutation_p.D176N	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)	176					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)	CCCTACTGATGATGACGTGAG	0.502																																					p.D176N		Atlas-SNP	.											.	CD44	48	.	0			c.G526A						PASS	.						123	98	106					11																	35211471		2202	4298	6500	SO:0001583	missense	960	exon5			ACTGATGATGACG	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.526G>A	11.37:g.35211471G>A	ENSP00000398632:p.Asp176Asn	198	0	0		239	120	0.502092	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	Missense_Mutation	SNP	ENST00000428726.2	37	CCDS7897.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.4|21.4	4.140023|4.140023	0.77775|0.77775	.|.	.|.	ENSG00000026508|ENSG00000026508	ENST00000263398;ENST00000415148;ENST00000433354;ENST00000449691;ENST00000437706;ENST00000360158;ENST00000428726;ENST00000433892;ENST00000434472;ENST00000352818;ENST00000525211;ENST00000526000;ENST00000279452;ENST00000531110;ENST00000525688;ENST00000278385;ENST00000533222|ENST00000527889;ENST00000531873;ENST00000525685	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T|.	0.36699|.	1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24|.	5.82|5.82	5.82|5.82	0.92795|0.92795	.|.	0.411612|.	0.26136|.	N|.	0.026133|.	T|T	0.59702|0.59702	0.2213|0.2213	M|M	0.65975|0.65975	2.015|2.015	0.26051|0.26051	N|N	0.981485|0.981485	P;P;P;D;P;D|.	0.71674|.	0.453;0.614;0.798;0.998;0.867;0.993|.	B;P;P;D;P;D|.	0.76575|.	0.42;0.49;0.815;0.988;0.803;0.946|.	T|T	0.55366|0.55366	-0.8152|-0.8152	10|5	0.35671|.	T|.	0.21|.	-24.8201|-24.8201	15.6093|15.6093	0.76704|0.76704	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	176;176;176;176;176;176|.	B6EAT9;P16070-11;P16070-12;P16070-10;P16070-4;P16070|.	.;.;.;.;.;CD44_HUMAN|.	N|I	176;176;176;176;176;176;176;176;176;176;155;154;136;50;15;12;9|131;96;43	ENSP00000263398:D176N;ENSP00000389830:D176N;ENSP00000414567:D176N;ENSP00000391008:D176N;ENSP00000403990:D176N;ENSP00000353280:D176N;ENSP00000398632:D176N;ENSP00000392331:D176N;ENSP00000404447:D176N;ENSP00000309732:D176N;ENSP00000432405:D155N;ENSP00000434465:D154N;ENSP00000279452:D136N;ENSP00000436549:D50N;ENSP00000436980:D15N;ENSP00000278385:D12N;ENSP00000435321:D9N|.	ENSP00000263398:D176N|.	D|M	+|+	1|3	0|0	CD44|CD44	35168047|35168047	0.417000|0.417000	0.25432|0.25432	0.083000|0.083000	0.20561|0.20561	0.003000|0.003000	0.03518|0.03518	2.101000|2.101000	0.41787|0.41787	2.745000|2.745000	0.94114|0.94114	0.655000|0.655000	0.94253|0.94253	GAT|ATG	.	.	none		0.502	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	NM_000610		A	35211471	G	A	35211471	3	1	23	1	0	0	0	0	1	0	0	0	3019	1290	45	2	544	2	CD44	11	35211471	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	273643	35211471	99795045	420	7864											
TRAF6	7189	hgsc.bcm.edu	37	chr11	36518764	36518764	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatggaatttttggaagggaCgctggcattggggacaatcc	10	11	14	6	1	0	0	0	0	0	0	1	4	1	4	1	6	0	2	1	6	4	4	rs577802750		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:36518764C>T	ENST00000526995.1	-	4	746	c.500G>A	c.(499-501)cGt>cAt	p.R167H	TRAF6_ENST00000348124.5_Missense_Mutation_p.R167H|TRAF6_ENST00000529150.1_5'Flank	NM_004620.3	NP_004611.1	Q9Y4K3	TRAF6_HUMAN	TNF receptor-associated factor 6, E3 ubiquitin protein ligase	167	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)				TTGGAAGGGACGCTGGCATTG	0.378																																					p.R167H		Atlas-SNP	.											.	TRAF6	56	.	0			c.G500A						PASS	.						72	75	74					11																	36518764		2202	4298	6500	SO:0001583	missense	7189	exon4			AAGGGACGCTGGC		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.500G>A	11.37:g.36518764C>T	ENSP00000433623:p.Arg167His	68	0	0		42	19	0.452381	NM_004620	A6NKI7|A8KAB3|D3DR16|Q8NEH5	Missense_Mutation	SNP	ENST00000526995.1	37	CCDS7901.1	.	.	.	.	.	.	.	.	.	.	C	6.898	0.535263	0.13188	.	.	ENSG00000175104	ENST00000526995;ENST00000348124	T;T	0.25579	1.79;1.79	5.49	-1.99	0.07457	Zinc finger, TRAF-type (1);	0.684611	0.15781	N	0.244901	T	0.13586	0.0329	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.16928	-1.0386	10	0.42905	T	0.14	-4.1496	7.0542	0.25089	0.1248:0.5163:0.0:0.3588	.	167	Q9Y4K3	TRAF6_HUMAN	H	167	ENSP00000433623:R167H;ENSP00000337853:R167H	ENSP00000337853:R167H	R	-	2	0	TRAF6	36475340	0.055000	0.20627	0.000000	0.03702	0.226000	0.24999	1.129000	0.31381	-0.206000	0.10203	0.650000	0.86243	CGT	.	.	none		0.378	TRAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389530.1	NM_145803		T	36518764	C	T	36518764	3	4	23	1	0	0	0	0	1	0	0	0	16460	536	19	1	1084	1	TRAF6	11	36518764	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1307293	36518764	98487752	421	7865											
LRRC4C	57689	hgsc.bcm.edu	37	chr11	40136049	40136049	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagggagatttgtatgagttAtagtgatttaggtgctcatg	11	15	13	2	0	1	3	1	2	0	1	1	4	1	3	0	2	1	3	0	2	5	6			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:40136049A>G	ENST00000278198.2	-	2	3757	c.1794T>C	c.(1792-1794)taT>taC	p.Y598Y	LRRC4C_ENST00000527150.1_Silent_p.Y598Y|LRRC4C_ENST00000528697.1_Silent_p.Y598Y|LRRC4C_ENST00000530763.1_Silent_p.Y598Y			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	598					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)				TGTATGAGTTATAGTGATTTA	0.408																																					p.Y598Y		Atlas-SNP	.											LRRC4C,NS,carcinoma,0,1	LRRC4C	190	1	0			c.T1794C						PASS	.						230	222	225					11																	40136049		2203	4300	6503	SO:0001819	synonymous_variant	57689	exon7			TGAGTTATAGTGA	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.1794T>C	11.37:g.40136049A>G		265	0	0		295	133	0.450847	NM_001258419	A8K0T1|Q7L0N3	Silent	SNP	ENST00000278198.2	37	CCDS31464.1																																																																																			.	.	none		0.408	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929		G	40136049	A	G	40136049	2	3	23	1	0	0	0	0	0	0	0	1	9017	456	16	3		3	LRRC4C	11	40136049	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	3617285	40136049	94870467	422	7866											
CKAP5	9793	hgsc.bcm.edu	37	chr11	46789135	46789135	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gttaacatacctttgctttaGaggataatcctggagctttg	10	15	9	7	0	0	1	0	0	0	1	1	3	1	3	2	2	4	3	2	2	4	7			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:46789135G>C	ENST00000529230.1	-	27	3447	c.3401C>G	c.(3400-3402)tCt>tGt	p.S1134C	CKAP5_ENST00000312055.5_Missense_Mutation_p.S1134C|CKAP5_ENST00000415402.1_Missense_Mutation_p.S1134C|CKAP5_ENST00000354558.3_Missense_Mutation_p.S1134C			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	1134					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						CTTTGCTTTAGAGGATAATCC	0.328																																					p.S1134C	Ovarian(4;85 273 2202 4844 13323)	Atlas-SNP	.											.	CKAP5	134	.	0			c.C3401G						PASS	.						128	131	130					11																	46789135		2201	4299	6500	SO:0001583	missense	9793	exon27			GCTTTAGAGGATA		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.3401C>G	11.37:g.46789135G>C	ENSP00000432768:p.Ser1134Cys	39	0	0		48	23	0.479167	NM_001008938	Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	Missense_Mutation	SNP	ENST00000529230.1	37	CCDS31477.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.568689	0.86439	.	.	ENSG00000175216	ENST00000529230;ENST00000415402;ENST00000312055;ENST00000354558	T;T;T;T	0.52754	0.66;0.65;0.65;0.65	5.7	5.7	0.88788	Armadillo-type fold (1);	0.272597	0.42964	D	0.000632	T	0.68393	0.2996	M	0.63843	1.955	0.51767	D	0.999933	D;D;D	0.71674	0.996;0.998;0.98	D;D;P	0.79108	0.947;0.992;0.706	T	0.68887	-0.5290	10	0.66056	D	0.02	-10.0808	19.8276	0.96624	0.0:0.0:1.0:0.0	.	1134;1134;1134	Q14008-3;Q14008-2;Q14008	.;.;CKAP5_HUMAN	C	1134	ENSP00000432768:S1134C;ENSP00000395302:S1134C;ENSP00000310227:S1134C;ENSP00000346566:S1134C	ENSP00000310227:S1134C	S	-	2	0	CKAP5	46745711	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	7.176000	0.77643	2.697000	0.92050	0.585000	0.79938	TCT	.	.	none		0.328	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1	NM_014756		C	46789135	G	C	46789135	3	2	23	1	0	0	0	0	1	0	0	0	3447	942	33	4	2769	4	CKAP5	11	46789135	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	6653086	46789135	88217381	423	7867											
PTPRJ	5795	hgsc.bcm.edu	37	chr11	48145397	48145397	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcaaataagacaaagggagaCcccttgggcacagaaggtgg	15	5	13	8	0	1	3	1	0	0	3	1	4	1	3	2	4	0	1	2	4	4	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:48145397C>A	ENST00000418331.2	+	5	1201	c.849C>A	c.(847-849)gaC>gaA	p.D283E	PTPRJ_ENST00000440289.2_Missense_Mutation_p.D283E	NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	283	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Fibronectin type-III 3. {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						CAAAGGGAGACCCCTTGGGCA	0.433																																					p.D283E		Atlas-SNP	.											.	PTPRJ	225	.	0			c.C849A						PASS	.						67	64	65					11																	48145397		2201	4298	6499	SO:0001583	missense	5795	exon5			GGGAGACCCCTTG	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.849C>A	11.37:g.48145397C>A	ENSP00000400010:p.Asp283Glu	103	0	0		131	53	0.40458	NM_001098503	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Missense_Mutation	SNP	ENST00000418331.2	37	CCDS7945.1	.	.	.	.	.	.	.	.	.	.	C	9.966	1.224237	0.22457	.	.	ENSG00000149177	ENST00000278456;ENST00000418331;ENST00000440289	T;T	0.35236	2.65;1.32	4.27	-1.19	0.09585	Fibronectin, type III (2);	.	.	.	.	T	0.14098	0.0341	N	0.17082	0.46	0.09310	N	1	B;P	0.36874	0.004;0.572	B;B	0.33454	0.003;0.164	T	0.16541	-1.0399	9	0.10902	T	0.67	.	1.6576	0.02785	0.1508:0.3485:0.3127:0.188	.	283;283	Q12913;Q6P4H4	PTPRJ_HUMAN;.	E	283	ENSP00000400010:D283E;ENSP00000409733:D283E	ENSP00000278456:D283E	D	+	3	2	PTPRJ	48101973	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.779000	0.04659	-0.334000	0.08463	0.557000	0.71058	GAC	.	.	none		0.433	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1			A	48145397	C	A	48145397	3	1	23	1	0	0	0	0	1	0	0	0	12819	506	18	4	867	4	PTPRJ	11	48145397	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1356262	48145397	86861119	424	7868											
FOLH1	2346	hgsc.bcm.edu	37	chr11	49207398	49207398	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttggcccctgccagctgggCatttttaacctagaaaacac	10	11	8	12	0	0	1	0	0	0	1	0	1	0	1	4	2	4	2	4	2	4	5			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:49207398C>T	ENST00000256999.2	-	6	909	c.649G>A	c.(649-651)Gcc>Acc	p.A217T	FOLH1_ENST00000340334.7_Missense_Mutation_p.A202T|FOLH1_ENST00000343844.4_Intron|FOLH1_ENST00000533034.1_Missense_Mutation_p.A202T|FOLH1_ENST00000356696.3_Missense_Mutation_p.A217T	NM_004476.1	NP_004467.1	Q04609	FOLH1_HUMAN	folate hydrolase (prostate-specific membrane antigen) 1	217					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)	GCCAGCTGGGCATTTTTAACC	0.418																																					p.A217T		Atlas-SNP	.											.	FOLH1	141	.	0			c.G649A						PASS	.						37	44	42					11																	49207398		2201	4296	6497	SO:0001583	missense	2346	exon6			GCTGGGCATTTTT	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.649G>A	11.37:g.49207398C>T	ENSP00000256999:p.Ala217Thr	195	0	0		206	31	0.150485	NM_004476	A4UU12|A9CB79|B7Z312|B7Z343|D3DQS5|E9PDX8|O43748|Q16305|Q541A4|Q8TAY3|Q9NP15|Q9NYE2|Q9P1P8	Missense_Mutation	SNP	ENST00000256999.2	37	CCDS7946.1	.	.	.	.	.	.	.	.	.	.	C	18.98	3.737168	0.69304	.	.	ENSG00000086205	ENST00000256999;ENST00000356696;ENST00000340334;ENST00000533034;ENST00000389724	T;T;T;T	0.72167	-0.63;-0.63;-0.63;-0.63	3.01	2.06	0.26882	Protease-associated domain, PA (1);	0.126165	0.35407	N	0.003233	D	0.87822	0.6274	H	0.97516	4.02	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;0.993;0.999	D	0.88363	0.2989	10	0.87932	D	0	.	9.7982	0.40748	0.0:0.7869:0.2131:0.0	.	202;202;217;217	Q04609-9;Q04609-7;Q04609-8;Q04609	.;.;.;FOLH1_HUMAN	T	217;217;202;202;217	ENSP00000256999:A217T;ENSP00000349129:A217T;ENSP00000344131:A202T;ENSP00000431463:A202T	ENSP00000256999:A217T	A	-	1	0	FOLH1	49163974	1.000000	0.71417	0.992000	0.48379	0.974000	0.67602	5.974000	0.70465	0.593000	0.29745	0.400000	0.26472	GCC	.	.	none		0.418	FOLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390896.1	NM_004476		T	49207398	C	T	49207398	3	4	23	1	0	0	0	0	1	0	0	0	5987	710	25	2	1659	2	FOLH1	11	49207398	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1062001	49207398	85799118	425	7869											
SERPING1	710	hgsc.bcm.edu	37	chr11	57373646	57373646	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctagacagtctgccctcCgatacccgccttgtcctcct	5	11	7	18	2	1	1	0	0	1	1	4	2	4	1	6	0	3	1	6	0	2	3	rs143760635	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:57373646C>T	ENST00000278407.4	+	5	1076	c.849C>T	c.(847-849)tcC>tcT	p.S283S	SERPING1_ENST00000403558.1_Silent_p.S317S|SERPING1_ENST00000340687.6_Silent_p.S283S|SERPING1_ENST00000378323.4_Silent_p.S288S|SERPING1_ENST00000378324.2_Silent_p.S231S	NM_000062.2	NP_000053.2	P05155	IC1_HUMAN	serpin peptidase inhibitor, clade G (C1 inhibitor), member 1	283					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)	p.S283S(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(1)	27						GTCTGCCCTCCGATACCCGCC	0.542													C|||	2	0.000399361	0.0008	0.0	5008	,	,		20271	0.0		0.001	False		,,,				2504	0.0				p.S283S		Atlas-SNP	.											SERPING1,NS,carcinoma,0,1	SERPING1	57	1	1	Substitution - coding silent(1)	lung(1)	c.C849T						PASS	.	C	,	1,4401	2.1+/-5.4	0,1,2200	190	178	183		849,849	-10.3	0	11	dbSNP_134	183	22,8570	16.0+/-53.3	0,22,4274	no	coding-synonymous,coding-synonymous	SERPING1	NM_000062.2,NM_001032295.1	,	0,23,6474	TT,TC,CC		0.2561,0.0227,0.177	,	283/501,283/501	57373646	23,12971	2201	4296	6497	SO:0001819	synonymous_variant	710	exon4			GCCCTCCGATACC	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.849C>T	11.37:g.57373646C>T		219	1	0.00456621		239	124	0.518828	NM_001032295	A6NMU0|A8KAI9|B2R6L5|B4E1F0|B4E1H2|Q16304|Q547W3|Q59EI5|Q7Z455|Q96FE0|Q9UC49|Q9UCF9	Silent	SNP	ENST00000278407.4	37	CCDS7962.1																																																																																			C|0.999;T|0.001	0.001	strong		0.542	SERPING1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317465.1	NM_000062		T	57373646	C	T	57373646	2	4	23	1	0	0	0	0	0	0	0	1	14131	639	23	1		1	SERPING1	11	57373646	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	8166248	57373646	77632870	426	7870											
CTNND1	1500	hgsc.bcm.edu	37	chr11	57564451	57564451	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgggacaccctctgaccctCgtcggcgcctcaggtaggca	6	7	12	16	3	2	1	1	1	1	0	4	2	2	2	3	4	0	2	3	4	1	1	rs199813020		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:57564451C>T	ENST00000399050.4	+	6	1479	c.943C>T	c.(943-945)Cgt>Tgt	p.R315C	CTNND1_ENST00000428599.2_Missense_Mutation_p.R315C|CTNND1_ENST00000415361.2_Missense_Mutation_p.R214C|CTNND1_ENST00000360682.6_Missense_Mutation_p.R315C|CTNND1_ENST00000532245.1_Missense_Mutation_p.R214C|CTNND1_ENST00000361391.6_Missense_Mutation_p.R315C|CTNND1_ENST00000530748.1_Missense_Mutation_p.R261C|CTNND1_ENST00000528621.1_Missense_Mutation_p.R261C|CTNND1_ENST00000361332.4_Missense_Mutation_p.R315C|CTNND1_ENST00000399039.4_Missense_Mutation_p.R315C|CTNND1_ENST00000533667.1_Intron|CTNND1_ENST00000528232.1_Missense_Mutation_p.R214C|CTNND1_ENST00000526772.1_Intron|CTNND1_ENST00000529873.1_Missense_Mutation_p.R261C|CTNND1_ENST00000525902.1_Intron|CTNND1_ENST00000426142.2_Missense_Mutation_p.R214C|CTNND1_ENST00000358694.6_Missense_Mutation_p.R315C|CTNND1_ENST00000532463.1_Missense_Mutation_p.R214C|CTNND1_ENST00000532787.1_Missense_Mutation_p.R214C|CTNND1_ENST00000361796.4_Missense_Mutation_p.R315C|CTNND1_ENST00000526357.1_Missense_Mutation_p.R261C|CTNND1_ENST00000530094.1_Missense_Mutation_p.R214C|CTNND1_ENST00000529986.1_Missense_Mutation_p.R214C|CTNND1_ENST00000524630.1_Missense_Mutation_p.R315C|CTNND1_ENST00000527467.1_Intron|CTNND1_ENST00000534579.1_Missense_Mutation_p.R261C|CTNND1_ENST00000529526.1_Missense_Mutation_p.R261C|CTNND1_ENST00000532844.1_Missense_Mutation_p.R261C|CTNND1_ENST00000531014.1_Intron|CTNND1_ENST00000529919.1_Missense_Mutation_p.R315C|CTNND1_ENST00000532649.1_Missense_Mutation_p.R261C|CTNND1_ENST00000526938.1_Missense_Mutation_p.R315C	NM_001085458.1	NP_001078927.1	O60716	CTND1_HUMAN	catenin (cadherin-associated protein), delta 1	315					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)				CTCTGACCCTCGTCGGCGCCT	0.527													C|||	1	0.000199681	0.0	0.0	5008	,	,		13710	0.001		0.0	False		,,,				2504	0.0				p.R315C		Atlas-SNP	.											.	CTNND1	203	.	0			c.C943T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	1,3955		0,1,1977	60	62	61		943,943,943,943,943,640,640,640,640,640,640,640,781,781,943,781,781,781,781,640,781,943	5.8	1	11		61	2,8326		0,2,4162	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	CTNND1	NM_001085458.1,NM_001085459.1,NM_001085460.1,NM_001085461.1,NM_001085462.1,NM_001085463.1,NM_001085464.1,NM_001085465.1,NM_001085466.1,NM_001085467.1,NM_001085468.1,NM_001085469.1,NM_001206883.1,NM_001206884.1,NM_001206885.1,NM_001206886.1,NM_001206887.1,NM_001206888.1,NM_001206889.1,NM_001206890.1,NM_001206891.1,NM_001331.2	180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180	0,3,6139	TT,TC,CC		0.024,0.0253,0.0244	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	315/969,315/963,315/934,315/934,315/934,214/868,214/862,214/841,214/839,214/833,214/833,214/833,261/915,261/886,315/940,261/909,261/888,261/880,261/880,214/833,261/880,315/942	57564451	3,12281	1978	4164	6142	SO:0001583	missense	1500	exon6			GACCCTCGTCGGC	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.943C>T	11.37:g.57564451C>T	ENSP00000382004:p.Arg315Cys	89	0	0		96	42	0.4375	NM_001085461	A8K939|O15088|O60713|O60714|O60715|O60935|Q6DHZ7|Q6RBX8|Q9UP71|Q9UP72|Q9UP73	Missense_Mutation	SNP	ENST00000399050.4	37	CCDS44604.1	.	.	.	.	.	.	.	.	.	.	C	18.67	3.674466	0.67928	2.53E-4	2.4E-4	ENSG00000198561	ENST00000524630;ENST00000529919;ENST00000399039;ENST00000360682;ENST00000361796;ENST00000529526;ENST00000426142;ENST00000399050;ENST00000361391;ENST00000361332;ENST00000532463;ENST00000529986;ENST00000358694;ENST00000532787;ENST00000532649;ENST00000528621;ENST00000530748;ENST00000428599;ENST00000528232;ENST00000529873;ENST00000532844;ENST00000526357;ENST00000530094;ENST00000415361;ENST00000532245;ENST00000534579;ENST00000526938;ENST00000534647	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	0.73258	-0.36;-0.36;-0.36;-0.73;-0.36;-0.36;-0.27;-0.37;-0.73;-0.37;-0.27;-0.27;-0.36;-0.62;-0.36;-0.36;-0.37;-0.36;-0.28;-0.73;-0.38;-0.37;-0.36;-0.37;-0.27;-0.36;-0.73;2.06	5.82	5.82	0.92795	Armadillo-like helical (1);	0.158729	0.64402	D	0.000018	T	0.79269	0.4417	L	0.43152	1.355	0.53005	D	0.999967	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;P;D;D;D;D;P	0.65010	0.917;0.917;0.828;0.917;0.917;0.931;0.917;0.828	T	0.76556	-0.2916	10	0.39692	T	0.17	-4.6961	19.6883	0.95987	0.0:1.0:0.0:0.0	.	315;315;315;261;261;315;315;315	O60716-3;O60716-2;O60716;O60716-14;O60716-10;O60716-5;F8WA43;C9JZR2	.;.;CTND1_HUMAN;.;.;.;.;.	C	315;315;315;315;315;261;214;315;315;315;214;214;315;214;261;261;261;315;214;261;261;261;214;214;214;261;315;237	ENSP00000436543:R315C;ENSP00000434808:R315C;ENSP00000381996:R315C;ENSP00000353902:R315C;ENSP00000354907:R315C;ENSP00000436323:R261C;ENSP00000409930:R214C;ENSP00000382004:R315C;ENSP00000354785:R315C;ENSP00000354823:R315C;ENSP00000432075:R214C;ENSP00000437156:R214C;ENSP00000351527:R315C;ENSP00000434949:R214C;ENSP00000435379:R261C;ENSP00000432243:R261C;ENSP00000436744:R261C;ENSP00000413586:R315C;ENSP00000435266:R214C;ENSP00000435494:R261C;ENSP00000433276:R261C;ENSP00000433334:R261C;ENSP00000437327:R214C;ENSP00000403518:R214C;ENSP00000434017:R214C;ENSP00000435789:R261C;ENSP00000432041:R315C;ENSP00000434202:R237C	ENSP00000351527:R315C	R	+	1	0	CTNND1	57321027	0.996000	0.38824	1.000000	0.80357	0.974000	0.67602	2.279000	0.43435	2.747000	0.94245	0.655000	0.94253	CGT	.	.	weak		0.527	CTNND1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393944.1	NM_001331		T	57564451	C	T	57564451	3	4	23	1	0	0	0	0	1	0	0	0	4021	884	31	1	957	1	CTNND1	11	57564451	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	190805	57564451	77442065	427	7871											
OR5B12	390191	hgsc.bcm.edu	37	chr11	58207494	58207494	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtccagtagaatcaattcaAtcatccccaggttcccaacc	13	9	5	14	0	3	1	3	0	0	1	6	1	6	1	5	1	1	2	5	1	5	3	rs140525146	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:58207494A>G	ENST00000302572.2	-	1	152	c.131T>C	c.(130-132)aTt>aCt	p.I44T		NM_001004733.2	NP_001004733.1	Q96R08	OR5BC_HUMAN	olfactory receptor, family 5, subfamily B, member 12	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(6)|liver(1)|lung(28)|ovary(1)|prostate(3)|skin(1)	40	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				AATCAATTCAATCATCCCCAG	0.488													A|||	11	0.00219649	0.0076	0.0014	5008	,	,		18591	0.0		0.0	False		,,,				2504	0.0				p.I44T		Atlas-SNP	.											.	OR5B12	80	.	0			c.T131C						PASS	.	A	THR/ILE	53,4349	52.9+/-88.7	2,49,2150	76	85	82		131	1.1	0	11	dbSNP_134	82	4,8586	3.7+/-12.6	0,4,4291	yes	missense	OR5B12	NM_001004733.2	89	2,53,6441	GG,GA,AA		0.0466,1.204,0.4387	benign	44/315	58207494	57,12935	2201	4295	6496	SO:0001583	missense	390191	exon1			AATTCAATCATCC	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.131T>C	11.37:g.58207494A>G	ENSP00000306657:p.Ile44Thr	108	0	0		109	60	0.550459	NM_001004733	B2RNL2|Q6IEV5	Missense_Mutation	SNP	ENST00000302572.2	37	CCDS31551.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	A	5.557	0.287633	0.10513	0.01204	4.66E-4	ENSG00000172362	ENST00000302572	T	0.00640	6.03	4.74	1.11	0.20524	GPCR, rhodopsin-like superfamily (1);	1.336050	0.05196	N	0.503944	T	0.00815	0.0027	M	0.85777	2.775	0.09310	N	1	B	0.18741	0.03	B	0.24394	0.053	T	0.47328	-0.9126	10	0.62326	D	0.03	-6.3258	7.7035	0.28636	0.7459:0.0:0.254:0.0	.	44	Q96R08	OR5BC_HUMAN	T	44	ENSP00000306657:I44T	ENSP00000306657:I44T	I	-	2	0	OR5B12	57964070	0.014000	0.17966	0.049000	0.19019	0.222000	0.24845	2.799000	0.47892	0.087000	0.17167	0.459000	0.35465	ATT	A|0.995;G|0.005	0.005	strong		0.488	OR5B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394987.1	NM_001004733		G	58207494	A	G	58207494	3	3	23	1	0	0	0	0	1	0	0	0	11157	101	4	3	817	3	OR5B12	11	58207494	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	643043	58207494	76799022	428	7872											
TCN1	6947	hgsc.bcm.edu	37	chr11	59623479	59623479	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcactgtattcagagttTgttggcaattccagtcattt	9	16	9	7	0	2	2	2	1	0	1	3	2	3	2	1	1	1	5	1	1	2	6			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:59623479T>G	ENST00000257264.3	-	6	904	c.800A>C	c.(799-801)cAa>cCa	p.Q267P	TCN1_ENST00000532419.1_Intron	NM_001062.3	NP_001053.2	P20061	TCO1_HUMAN	transcobalamin I (vitamin B12 binding protein, R binder family)	267	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)	ATTCAGAGTTTGTTGGCAATT	0.473																																					p.Q267P		Atlas-SNP	.											.	TCN1	64	.	0			c.A800C						PASS	.						122	124	124					11																	59623479		2201	4295	6496	SO:0001583	missense	6947	exon6			AGAGTTTGTTGGC	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.800A>C	11.37:g.59623479T>G	ENSP00000257264:p.Gln267Pro	144	0	0		194	34	0.175258	NM_001062	A8KAC5|Q8WV77	Missense_Mutation	SNP	ENST00000257264.3	37	CCDS7978.1	.	.	.	.	.	.	.	.	.	.	t	11.77	1.737860	0.30774	.	.	ENSG00000134827	ENST00000257264	T	0.35973	1.28	4.44	3.21	0.36854	.	0.874076	0.09641	N	0.775035	T	0.29423	0.0733	L	0.29908	0.895	0.09310	N	1	B	0.33919	0.432	B	0.39119	0.291	T	0.23511	-1.0186	10	0.45353	T	0.12	.	6.5473	0.22412	0.2145:0.0:0.0:0.7855	.	267	P20061	TCO1_HUMAN	P	267	ENSP00000257264:Q267P	ENSP00000257264:Q267P	Q	-	2	0	TCN1	59380055	0.622000	0.27085	0.497000	0.27552	0.055000	0.15305	1.583000	0.36579	1.638000	0.50547	0.473000	0.43528	CAA	.	.	none		0.473	TCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394503.1	NM_001062		G	59623479	T	G	59623479	3	3	23	1	0	0	0	0	1	0	0	0	15721	1812	63	5	517	5	TCN1	11	59623479	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	1415985	59623479	75383037	429	7873											
MS4A4A	51338	hgsc.bcm.edu	37	chr11	60073626	60073626	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggaattctgcattgctgtGtccctctctgcctttggatg	4	16	10	11	0	2	0	0	0	2	0	4	2	3	2	2	2	3	2	2	2	1	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:60073626G>A	ENST00000337908.4	+	6	690	c.600G>A	c.(598-600)gtG>gtA	p.V200V	MS4A4A_ENST00000395016.3_Silent_p.V181V|MS4A4A_ENST00000355131.3_Silent_p.V181V|MS4A4A_ENST00000532114.1_Silent_p.V147V	NM_148975.2	NP_683876.1	Q96JQ5	M4A4A_HUMAN	membrane-spanning 4-domains, subfamily A, member 4A	200				V -> C (in Ref. 4; AAL56220). {ECO:0000305}.		integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(12)|prostate(1)|skin(4)	23						GCATTGCTGTGTCCCTCTCTG	0.453																																					p.V200V		Atlas-SNP	.											.	MS4A4A	76	.	0			c.G600A						PASS	.						335	284	301					11																	60073626		2203	4300	6503	SO:0001819	synonymous_variant	51338	exon6			TGCTGTGTCCCTC	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.600G>A	11.37:g.60073626G>A		408	1	0.00245098		377	179	0.474801	NM_148975	Q8TEZ6|Q96PG7|Q9BY18|Q9H3V3|Q9P1S3	Silent	SNP	ENST00000337908.4	37	CCDS7982.1																																																																																			.	.	none		0.453	MS4A4A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337774.2			A	60073626	G	A	60073626	2	1	23	1	0	0	0	0	0	0	0	1	9871	1364	48	2		2	MS4A4A	11	60073626	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	450147	60073626	74932890	430	7874											
C11orf48	79081	hgsc.bcm.edu	37	chr11	62437422	62437422	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gagagggttgggcagcctggGactttctggatgctgggagg	6	9	20	6	0	1	1	0	0	1	1	1	5	1	4	1	6	2	3	1	6	0	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:62437422G>A	ENST00000431002.2	-	1	1815	c.82C>T	c.(82-84)Ccc>Tcc	p.P28S	C11orf48_ENST00000532208.1_Missense_Mutation_p.P28S|C11orf83_ENST00000531323.1_5'Flank|C11orf48_ENST00000354588.3_Missense_Mutation_p.P28S|C11orf83_ENST00000377953.3_5'Flank			Q9BQE6	CK048_HUMAN	chromosome 11 open reading frame 48	28										endometrium(1)|lung(5)|urinary_tract(1)	7						GGCAGCCTGGGACTTTCTGGA	0.542																																					p.P28S		Atlas-SNP	.											.	C11orf48	18	.	0			c.C82T						PASS	.						101	94	96					11																	62437422		2202	4299	6501	SO:0001583	missense	79081	exon2			GCCTGGGACTTTC	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.82C>T	11.37:g.62437422G>A	ENSP00000416856:p.Pro28Ser	182	0	0		197	94	0.477157	NM_024099	Q96NA4	Missense_Mutation	SNP	ENST00000431002.2	37		.	.	.	.	.	.	.	.	.	.	G	13.80	2.346432	0.41599	.	.	ENSG00000162194	ENST00000354588;ENST00000431002;ENST00000532208;ENST00000377954;ENST00000526490	.	.	.	4.49	2.59	0.31030	.	0.201361	0.24988	N	0.034002	T	0.29288	0.0729	N	0.19112	0.55	0.32145	N	0.585027	P;B	0.46912	0.886;0.301	P;B	0.46275	0.51;0.184	T	0.37753	-0.9692	9	0.87932	D	0	-0.7818	5.6644	0.17687	0.1061:0.2021:0.6918:0.0	.	28;28	B4DYP8;Q9BQE6-2	.;.	S	28;28;28;53;28	.	ENSP00000346600:P28S	P	-	1	0	C11orf48	62193998	0.087000	0.21565	0.765000	0.31456	0.811000	0.45836	1.056000	0.30480	1.216000	0.43427	0.563000	0.77884	CCC	.	.	none		0.542	C11orf48-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000395233.1	NM_024099		A	62437422	G	A	62437422	3	1	23	1	0	0	0	0	1	0	0	0	1646	1174	41	2	733	2	C11orf48	11	62437422	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	2363796	62437422	72569094	431	7875											
ZBTB3	79842	hgsc.bcm.edu	37	chr11	62519806	62519806	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catagggtcgctcacgtgtgTgcaccgtggcatgtcgccgt	5	10	14	12	5	1	0	1	0	0	0	3	0	1	0	2	2	1	3	2	2	1	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:62519806T>C	ENST00000394807.3	-	2	1606	c.1481A>G	c.(1480-1482)cAc>cGc	p.H494R		NM_024784.3	NP_079060.1	Q9H5J0	ZBTB3_HUMAN	zinc finger and BTB domain containing 3	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)			breast(4)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(9)|ovary(2)|prostate(2)	24						CTCACGTGTGTGCACCGTGGC	0.572																																					p.H494R		Atlas-SNP	.											.	ZBTB3	47	.	0			c.A1481G						PASS	.						92	81	85					11																	62519806		2202	4299	6501	SO:0001583	missense	79842	exon2			CGTGTGTGCACCG	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.1481A>G	11.37:g.62519806T>C	ENSP00000378286:p.His494Arg	80	0	0		101	54	0.534653	NM_024784		Missense_Mutation	SNP	ENST00000394807.3	37	CCDS8034.1	.	.	.	.	.	.	.	.	.	.	T	18.58	3.654116	0.67472	.	.	ENSG00000185670	ENST00000394807	T	0.67523	-0.27	4.61	4.61	0.57282	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	0.83138	0.5189	M	0.89095	3.005	0.43777	D	0.996307	D	0.89917	1.0	D	0.91635	0.999	D	0.86175	0.1602	10	0.87932	D	0	.	11.9849	0.53142	0.0:0.0:0.0:1.0	.	494	Q9H5J0	ZBTB3_HUMAN	R	494	ENSP00000378286:H494R	ENSP00000378286:H494R	H	-	2	0	ZBTB3	62276382	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.698000	0.84413	1.724000	0.51502	0.459000	0.35465	CAC	.	.	none		0.572	ZBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395342.1	NM_024784		C	62519806	T	C	62519806	3	2	23	1	0	0	0	0	1	0	0	0	17549	1696	59	3	247	3	ZBTB3	11	62519806	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	82384	62519806	72486710	432	7876											
C11orf20	25858	hgsc.bcm.edu	37	chr11	64071272	64071272	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tgcccctgatggaactcatgGagaatgaagctctggaaatc	12	9	11	9	0	2	3	1	2	1	1	3	6	2	5	2	3	3	1	2	3	4	0	rs117629442	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64071272G>C	ENST00000328404.6	+	4	480	c.460G>C	c.(460-462)Gag>Cag	p.E154Q	RP11-783K16.10_ENST00000539086.1_RNA|ESRRA_ENST00000405666.1_5'Flank|ESRRA_ENST00000406310.1_5'Flank|ESRRA_ENST00000000442.6_5'Flank|TEX40_ENST00000539943.1_Missense_Mutation_p.E112Q	NM_001039496.1	NP_001034585.1	Q9NTU4	TEX40_HUMAN	testis expressed 40	154					cell differentiation (GO:0030154)|male meiosis (GO:0007140)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)											GGAACTCATGGAGAATGAAGC	0.567													G|||	27	0.00539137	0.0008	0.0101	5008	,	,		13275	0.0		0.0169	False		,,,				2504	0.002				p.E154Q		Atlas-SNP	.											.	.	.	.	0			c.G460C						PASS	.	G	GLN/GLU	13,3981		0,13,1984	33	36	35		460	2.3	1	11	dbSNP_132	35	123,8191		0,123,4034	yes	missense	C11orf20	NM_001039496.1	29	0,136,6018	CC,CG,GG		1.4794,0.3255,1.105	possibly-damaging	154/201	64071272	136,12172	1997	4157	6154	SO:0001583	missense	25858	exon4			CTCATGGAGAATG			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.460G>C	11.37:g.64071272G>C	ENSP00000330877:p.Glu154Gln	97	0	0		126	66	0.52381	NM_001039496		Missense_Mutation	SNP	ENST00000328404.6	37		18	0.008241758241758242	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	13	0.017150395778364115	G	13.31	2.198647	0.38806	0.003255	0.014794	ENSG00000219435	ENST00000328404;ENST00000539943	T;T	0.58210	0.35;0.37	4.22	2.3	0.28687	.	.	.	.	.	T	0.39572	0.1083	L	0.32530	0.975	0.25789	N	0.984643	D	0.76494	0.999	D	0.70487	0.969	T	0.28870	-1.0030	9	0.62326	D	0.03	-18.7303	5.3022	0.15783	0.1056:0.0:0.6949:0.1995	.	154	Q9NTU4	CK020_HUMAN	Q	154;112	ENSP00000330877:E154Q;ENSP00000443917:E112Q	ENSP00000330877:E154Q	E	+	1	0	C11orf20	63827848	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	2.823000	0.48081	0.528000	0.28580	-0.300000	0.09419	GAG	G|0.991;C|0.009	0.009	strong		0.567	TEX40-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001039496		C	64071272	G	C	64071272	3	2	23	1	0	0	0	0	1	0	0	0	1636	1175	41	4	474	4	C11orf20	11	64071272	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1551466	64071272	70935244	433	7877											
NRXN2	9379	hgsc.bcm.edu	37	chr11	64457892	64457892	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgaccttttgttggctggtGcacatcgccggctcctcctc	3	13	10	15	2	0	1	0	1	0	0	4	1	2	1	4	3	1	4	4	3	0	3	rs141807338		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64457892G>A	ENST00000377551.1	-	4	1046	c.835C>T	c.(835-837)Cac>Tac	p.H279Y	NRXN2_ENST00000377559.3_Intron|NRXN2_ENST00000409571.1_Missense_Mutation_p.H279Y|NRXN2_ENST00000265459.6_Missense_Mutation_p.H279Y			Q9P2S2	NRX2A_HUMAN	neurexin 2	279					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						GTTGGCTGGTGCACATCGCCG	0.627													G|||	1	0.000199681	0.0	0.0	5008	,	,		15787	0.0		0.001	False		,,,				2504	0.0				p.H279Y		Atlas-SNP	.											.	NRXN2	247	.	0			c.C835T						PASS	.	G	TYR/HIS,	0,4402		0,0,2201	58	53	54		835,	4.5	1	11	dbSNP_134	54	2,8592	2.2+/-6.3	0,2,4295	no	missense,intron	NRXN2	NM_015080.3,NM_138732.2	83,	0,2,6496	AA,AG,GG		0.0233,0.0,0.0154	benign,	279/1713,	64457892	2,12994	2201	4297	6498	SO:0001583	missense	9379	exon5			GCTGGTGCACATC		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.835C>T	11.37:g.64457892G>A	ENSP00000366774:p.His279Tyr	109	0	0		89	48	0.539326	NM_015080	A7E2C1|Q9Y2D6	Missense_Mutation	SNP	ENST00000377551.1	37	CCDS8077.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	G|G	3.483|3.483	-0.105541|-0.105541	0.06967|0.06967	0.0|0.0	2.33E-4|2.33E-4	ENSG00000110076|ENSG00000110076	ENST00000437746|ENST00000377551;ENST00000265459;ENST00000409571;ENST00000442300	.|T;T;T;T	.|0.59772	.|0.24;0.24;0.32;1.31	4.47|4.47	4.47|4.47	0.54385|0.54385	.|.	.|.	.|.	.|.	.|.	T|T	0.31040|0.31040	0.0784|0.0784	N|N	0.08118|0.08118	0|0	0.35143|0.35143	D|D	0.769073|0.769073	.|P	.|0.43909	.|0.821	.|B	.|0.38225	.|0.268	T|T	0.43343|0.43343	-0.9397|-0.9397	5|9	.|0.02654	.|T	.|1	.|.	12.9884|12.9884	0.58604|0.58604	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|279	.|Q9P2S2	.|NRX2A_HUMAN	V|Y	68|279;279;279;50	.|ENSP00000366774:H279Y;ENSP00000265459:H279Y;ENSP00000386416:H279Y;ENSP00000388971:H50Y	.|ENSP00000265459:H279Y	A|H	-|-	2|1	0|0	NRXN2|NRXN2	64214468|64214468	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	3.226000|3.226000	0.51254|0.51254	2.216000|2.216000	0.71823|0.71823	0.442000|0.442000	0.29010|0.29010	GCA|CAC	G|1.000;A|0.000	0.000	strong		0.627	NRXN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104967.3	NM_015080		A	64457892	G	A	64457892	3	1	23	1	0	0	0	0	1	0	0	0	10675	1319	46	2	4648	2	NRXN2	11	64457892	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	386620	64457892	70548624	434	7878											
SCYL1	57410	hgsc.bcm.edu	37	chr11	65293819	65293819	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagagtggtcagagagaaGtggtgggtgactgggggcag	9	6	22	4	0	1	4	1	1	0	3	1	5	1	4	0	6	0	2	0	6	1	0	rs75169347	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:65293819G>A	ENST00000270176.5	+	4	677	c.600G>A	c.(598-600)aaG>aaA	p.K200K	SCYL1_ENST00000279270.6_Silent_p.K200K|SCYL1_ENST00000525364.1_Silent_p.K200K|SCYL1_ENST00000420247.2_Silent_p.K200K|SCYL1_ENST00000533862.1_Silent_p.K200K|SCYL1_ENST00000527009.1_Silent_p.K57K|SCYL1_ENST00000524944.1_Silent_p.K200K	NM_020680.3	NP_065731.3	Q96KG9	NTKL_HUMAN	SCY1-like 1 (S. cerevisiae)	200	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						TCAGAGAGAAGTGGTGGGTGA	0.657													G|||	91	0.0181709	0.0015	0.0303	5008	,	,		16563	0.0		0.0616	False		,,,				2504	0.0061				p.K200K		Atlas-SNP	.											.	SCYL1	76	.	0			c.G600A						PASS	.	G	,	34,4166		0,34,2066	16	19	18		600,600	-1.8	0.8	11	dbSNP_131	18	504,7942		14,476,3733	no	coding-synonymous,coding-synonymous	SCYL1	NM_001048218.1,NM_020680.3	,	14,510,5799	AA,AG,GG		5.9673,0.8095,4.2543	,	200/792,200/809	65293819	538,12108	2100	4223	6323	SO:0001819	synonymous_variant	57410	exon4			AGAGAAGTGGTGG	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.600G>A	11.37:g.65293819G>A		119	0	0		110	44	0.4	NM_020680	A6NJF1|Q96G50|Q96KG8|Q96KH1|Q9HAW5|Q9HBL3|Q9NR53	Silent	SNP	ENST00000270176.5	37	CCDS41672.1																																																																																			G|0.968;A|0.032	0.032	strong		0.657	SCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389159.2	NM_020680		A	65293819	G	A	65293819	2	1	23	1	0	0	0	0	0	0	0	1	13962	1020	36	2		2	SCYL1	11	65293819	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	835927	65293819	69712697	435	7879											
MAP3K11	4296	hgsc.bcm.edu	37	chr11	65367223	65367223	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggctcctcgggctccaggctAggccgcggggggttacctgc	3	7	17	14	3	0	0	0	0	0	0	3	0	2	0	4	7	2	4	4	7	2	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:65367223A>G	ENST00000530153.1	-	9	1598	c.1077T>C	c.(1075-1077)ccT>ccC	p.P359P	MAP3K11_ENST00000534432.1_5'UTR|MAP3K11_ENST00000532507.1_Silent_p.P32P|MAP3K11_ENST00000309100.3_Silent_p.P616P					mitogen-activated protein kinase kinase kinase 11											breast(3)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(14)|skin(1)	24						GCTCCAGGCTAGGCCGCGGGG	0.697																																					p.P616P		Atlas-SNP	.											.	MAP3K11	67	.	0			c.T1848C						PASS	.						7	8	8					11																	65367223		2068	4080	6148	SO:0001819	synonymous_variant	4296	exon9			CAGGCTAGGCCGC		CCDS8107.1	11q13.1-q13.3	2011-06-09			ENSG00000173327	ENSG00000173327	2.7.10.1	"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6850	protein-coding gene	gene with protein product		600050		MLK3, PTK1		9267807, 8183572	Standard	NM_002419		Approved	SPRK, MEKK11	uc001oew.3	Q16584	OTTHUMG00000166529	ENST00000530153.1:c.1077T>C	11.37:g.65367223A>G		28	0	0		30	4	0.133333	NM_002419		Silent	SNP	ENST00000530153.1	37																																																																																				.	.	none		0.697	MAP3K11-004	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000390233.2			G	65367223	A	G	65367223	2	3	23	1	0	0	0	0	0	0	0	1	9254	407	15	3		3	MAP3K11	11	65367223	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	73404	65367223	69639293	436	7880											
GAL3ST3	89792	hgsc.bcm.edu	37	chr11	65811114	65811116	+	In_Frame_Del	DEL	GAG	GAG	-																															gcgcggcggcgagttccgcaGaggagggcagctcaagggga																										TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:65811114_65811116delGAG	ENST00000312006.4	-	3	439_441	c.158_160delCTC	c.(157-162)cctctg>ctg	p.P53del	GAL3ST3_ENST00000527878.1_In_Frame_Del_p.P53del	NM_033036.2	NP_149025.1	Q96A11	G3ST3_HUMAN	galactose-3-O-sulfotransferase 3	53					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						GAGTTCCGCAGAGGAGGGCAGCT	0.645																																					p.53_54del		Pindel,Atlas-Indel	.											.	GAL3ST3	40	.	0			c.159_161del						PASS	.																																			SO:0001651	inframe_deletion	89792	exon3			.	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.158_160delCTC	11.37:g.65811117_65811119delGAG	ENSP00000308591:p.Pro53del	185	0	.		161	55	0.342	NM_033036	Q14D05	In_Frame_Del	DEL	ENST00000312006.4	37	CCDS8128.1																																																																																			.	.	none		0.645	GAL3ST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391052.1	NM_033036		-	65811116	GAG	-	65811114	7	5	23	1	0	1	0	1	0	0	0	0	6207	933	33	0	1139	0	GAL3ST3	11	65811114	In_Frame_Del	DEL	GAG	TCGA-G8-6325-01A-11D-2210-10	443891	65811114	69195402	437	7881											
B3GNT1	11041	hgsc.bcm.edu	37	chr11	66113995	66113995	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgaagccgtactgccgaaagCgctcgtcgaaggtgggcacc	9	6	14	12	5	0	1	0	1	0	0	2	3	0	1	3	2	4	3	3	2	4	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:66113995C>T	ENST00000311181.4	-	1	1168	c.1022G>A	c.(1021-1023)cGc>cAc	p.R341H	RP11-867G23.8_ENST00000531602.1_5'Flank|BRMS1_ENST00000425825.2_5'Flank|BRMS1_ENST00000359957.3_5'Flank	NM_006876.2	NP_006867.1	O43505	B3GN1_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 1	341					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						CTGCCGAAAGCGCTCGTCGAA	0.627																																					p.R341H		Atlas-SNP	.											.	B3GNT1	28	.	0			c.G1022A						PASS	.						77	82	80					11																	66113995		2200	4291	6491	SO:0001583	missense	11041	exon1			CGAAAGCGCTCGT	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.1022G>A	11.37:g.66113995C>T	ENSP00000309096:p.Arg341His	87	0	0		86	34	0.395349	NM_006876	Q4TTN0	Missense_Mutation	SNP	ENST00000311181.4	37	CCDS8136.1	.	.	.	.	.	.	.	.	.	.	C	18.51	3.640477	0.67244	.	.	ENSG00000174684	ENST00000311181;ENST00000538757	T	0.32272	1.46	5.83	5.83	0.93111	.	0.165306	0.51477	D	0.000098	T	0.61627	0.2362	M	0.84846	2.72	0.46203	D	0.998928	D	0.89917	1.0	D	0.79784	0.993	T	0.65450	-0.6165	10	0.66056	D	0.02	-24.2929	17.6063	0.88039	0.0:1.0:0.0:0.0	.	341	O43505	B3GN1_HUMAN	H	341;112	ENSP00000309096:R341H	ENSP00000309096:R341H	R	-	2	0	B3GNT1	65870571	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.911000	0.48774	2.761000	0.94854	0.563000	0.77884	CGC	.	.	none		0.627	B3GNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392959.1	NM_006876		T	66113995	C	T	66113995	3	4	23	1	0	0	0	0	1	0	0	0	1256	768	27	1	233	1	B3GNT1	11	66113995	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	302881	66113995	68892521	438	7882											
GPR152	390212	hgsc.bcm.edu	37	chr11	67218787	67218787	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgtgttcctggaccctcacGtggggcctgcgcccggggcc	2	7	16	16	4	1	0	1	0	0	0	2	1	2	1	5	5	1	1	5	5	0	1	rs137906019		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:67218787G>A	ENST00000312457.2	-	1	1413	c.1409C>T	c.(1408-1410)aCg>aTg	p.T470M	CABP4_ENST00000438189.2_5'Flank	NM_206997.1	NP_996880.1	Q8TDT2	GP152_HUMAN	G protein-coupled receptor 152	470						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)			GGACCCTCACGTGGGGCCTGC	0.687													G|||	1	0.000199681	0.0008	0.0	5008	,	,		13832	0.0		0.0	False		,,,				2504	0.0				p.T470M	Pancreas(102;800 1581 2723 7382 33622)	Atlas-SNP	.											.	GPR152	41	.	0			c.C1409T						PASS	.	G	MET/THR	0,4364		0,0,2182	28	38	35		1409	2.4	0.5	11	dbSNP_134	35	18,8506		0,18,4244	yes	missense	GPR152	NM_206997.1	81	0,18,6426	AA,AG,GG		0.2112,0.0,0.1397	benign	470/471	67218787	18,12870	2182	4262	6444	SO:0001583	missense	390212	exon1			CCTCACGTGGGGC	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.1409C>T	11.37:g.67218787G>A	ENSP00000310255:p.Thr470Met	45	0	0		52	30	0.576923	NM_206997	Q0VD88|Q86SM0	Missense_Mutation	SNP	ENST00000312457.2	37	CCDS8165.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	12.15	1.853057	0.32699	0.0	0.002112	ENSG00000175514	ENST00000312457	T	0.19938	2.11	4.28	2.37	0.29283	.	0.439888	0.16902	N	0.194879	T	0.13756	0.0333	L	0.29908	0.895	0.20489	N	0.999897	B	0.17038	0.02	B	0.12156	0.007	T	0.21827	-1.0234	10	0.87932	D	0	.	5.1949	0.15232	0.1064:0.0:0.6923:0.2012	.	470	Q8TDT2	GP152_HUMAN	M	470	ENSP00000310255:T470M	ENSP00000310255:T470M	T	-	2	0	GPR152	66975363	0.706000	0.27856	0.469000	0.27204	0.026000	0.11368	0.692000	0.25482	0.423000	0.26033	-0.226000	0.12346	ACG	G|0.998;A|0.002	0.002	strong		0.687	GPR152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397623.1			A	67218787	G	A	67218787	3	1	23	1	0	0	0	0	1	0	0	0	6666	1145	40	1	7	1	GPR152	11	67218787	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1104792	67218787	67787729	439	7883											
KRTAP5-9	3846	hgsc.bcm.edu	37	chr11	71259841	71259841	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tactgctgcaagcccgtgtgCtgctgtgttccagcctgttc	4	13	11	13	1	0	0	0	0	0	0	2	0	1	0	3	0	7	6	3	0	2	3	rs189729045	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:71259841C>T	ENST00000528743.2	+	1	376	c.138C>T	c.(136-138)tgC>tgT	p.C46C		NM_005553.3	NP_005544.4	P26371	KRA59_HUMAN	keratin associated protein 5-9	46	8 X 4 AA repeats of C-C-X-P.				epidermis development (GO:0008544)	keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(6)|prostate(3)	11						AGCCCGTGTGCTGCTGTGTTC	0.652													c|||	16	0.00319489	0.0	0.0086	5008	,	,		18955	0.0		0.007	False		,,,				2504	0.0031				p.C46C		Atlas-SNP	.											.	KRTAP5-9	19	.	0			c.C138T						PASS	.	C		7,4393		0,7,2193	95	107	103		138	1.6	1	11		103	85,8503		0,85,4209	no	coding-synonymous	KRTAP5-9	NM_005553.3		0,92,6402	TT,TC,CC		0.9898,0.1591,0.7083		46/170	71259841	92,12896	2200	4294	6494	SO:0001819	synonymous_variant	3846	exon1			CGTGTGCTGCTGT	AB126078	CCDS53677.1	11q13.4	2008-02-05				ENSG00000254997		"Keratin associated proteins"	23604	protein-coding gene	gene with protein product		148021		KRN1		15144888	Standard	NM_005553		Approved	KRTAP5.9, KRTAP5-1	uc001oqs.1	P26371		ENST00000528743.2:c.138C>T	11.37:g.71259841C>T		290	0	0		355	159	0.447887	NM_005553	Q14564|Q3MIP8	Silent	SNP	ENST00000528743.2	37	CCDS53677.1																																																																																			C|0.996;T|0.004	0.004	strong		0.652	KRTAP5-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393901.2			T	71259841	C	T	71259841	2	4	23	1	0	0	0	0	0	0	0	1	8577	805	28	2		2	KRTAP5-9	11	71259841	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	4041054	71259841	63746675	440	7884											
NUMA1	4926	hgsc.bcm.edu	37	chr11	71720030	71720030	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tacctgtgcctccaggctgcGcacctgggcagtaaggtggc	6	8	14	13	1	0	0	0	0	0	0	1	0	1	0	4	4	3	4	4	4	2	2	rs74985106	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:71720030G>A	ENST00000393695.3	-	19	5372	c.5041C>T	c.(5041-5043)Cgc>Tgc	p.R1681C	NUMA1_ENST00000351960.6_Missense_Mutation_p.R545C|NUMA1_ENST00000358965.6_Missense_Mutation_p.R1667C	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						TCCAGGCTGCGCACCTGGGCA	0.612			T	RARA	APL								G|||	67	0.0133786	0.0008	0.0231	5008	,	,		13503	0.0188		0.0179	False		,,,				2504	0.0133				p.R1681C		Atlas-SNP	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1	142	.	0			c.C5041T						PASS	.	G	CYS/ARG	26,4374	31.7+/-61.6	0,26,2174	63	62	63		5041	5.6	1	11	dbSNP_131	63	203,8383	86.3+/-148.7	2,199,4092	yes	missense	NUMA1	NM_006185.2	180	2,225,6266	AA,AG,GG		2.3643,0.5909,1.7634	probably-damaging	1681/2116	71720030	229,12757	2200	4293	6493	SO:0001583	missense	4926	exon19			GGCTGCGCACCTG	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.5041C>T	11.37:g.71720030G>A	ENSP00000377298:p.Arg1681Cys	166	0	0		140	67	0.478571	NM_006185		Missense_Mutation	SNP	ENST00000393695.3	37	CCDS31633.1	36	0.016483516483516484	0	0.0	11	0.03038674033149171	14	0.024475524475524476	11	0.014511873350923483	G	21.4	4.145619	0.77888	0.005909	0.023643	ENSG00000137497	ENST00000351960;ENST00000358965;ENST00000393695;ENST00000359652;ENST00000536544	T;T;T	0.50001	2.07;0.76;2.52	5.56	5.56	0.83823	.	0.127189	0.36409	N	0.002604	T	0.31451	0.0797	L	0.32530	0.975	0.46586	D	0.999115	D;D;D;D;D	0.89917	0.998;0.998;0.996;0.998;1.0	P;P;P;P;D	0.65010	0.629;0.819;0.819;0.629;0.931	T	0.48103	-0.9064	10	0.72032	D	0.01	.	14.0441	0.64695	0.0:0.0:0.8489:0.1511	.	1687;1151;1667;1681;545	Q4LE64;Q59HB8;Q14980-2;Q14980;Q9BTE9	.;.;.;NUMA1_HUMAN;.	C	545;1667;1681;1230;636	ENSP00000260051:R545C;ENSP00000351851:R1667C;ENSP00000377298:R1681C	ENSP00000260051:R545C	R	-	1	0	NUMA1	71397678	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.624000	0.46444	2.618000	0.88619	0.561000	0.74099	CGC	G|0.982;A|0.018	0.018	strong		0.612	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1			A	71720030	G	A	71720030	3	1	23	1	0	0	0	0	1	0	0	0	10759	1087	38	1	1342	1	NUMA1	11	71720030	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	460189	71720030	63286486	441	7885											
NUMA1	4926	hgsc.bcm.edu	37	chr11	71724784	71724784	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctcttctctgactcggccatCaccagccgcttcaactcctt	6	12	5	18	2	4	1	2	1	2	0	7	1	5	1	4	1	2	1	4	1	1	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:71724784C>T	ENST00000393695.3	-	15	4096	c.3765G>A	c.(3763-3765)gtG>gtA	p.V1255V	NUMA1_ENST00000351960.6_Intron|NUMA1_ENST00000358965.6_Silent_p.V1255V|RP11-849H4.4_ENST00000502284.1_RNA	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						ACTCGGCCATCACCAGCCGCT	0.597			T	RARA	APL																																p.V1255V		Atlas-SNP	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1	142	.	0			c.G3765A						PASS	.						51	52	52					11																	71724784		2200	4293	6493	SO:0001819	synonymous_variant	4926	exon15			GGCCATCACCAGC	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.3765G>A	11.37:g.71724784C>T		64	0	0		58	29	0.5	NM_006185		Silent	SNP	ENST00000393695.3	37	CCDS31633.1																																																																																			.	.	none		0.597	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1			T	71724784	C	T	71724784	2	4	23	1	0	0	0	0	0	0	0	1	10759	813	29	2		2	NUMA1	11	71724784	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	4754	71724784	63281732	442	7886											
CAPN5	726	hgsc.bcm.edu	37	chr11	76796082	76796082	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	acgccggggcccgccgtcagGtggaagcgacccaaggtcag	8	3	16	14	5	2	0	2	0	0	0	2	2	2	1	4	5	1	0	4	5	2	0	rs368891933		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:76796082G>A	ENST00000278559.3	+	2	339	c.150G>A	c.(148-150)agG>agA	p.R50R	CAPN5_ENST00000456580.2_Silent_p.R50R|CAPN5_ENST00000531028.1_Splice_Site|CAPN5_ENST00000529629.1_Silent_p.R50R	NM_004055.4	NP_004046.2	O15484	CAN5_HUMAN	calpain 5	50	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				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						CCGCCGTCAGGTGGAAGCGAC	0.692																																					p.R50R		Atlas-SNP	.											.	CAPN5	67	.	0			c.G150A						PASS	.	G		0,4396		0,0,2198	21	24	23		150	3	0.9	11		23	1,8583		0,1,4291	no	coding-synonymous	CAPN5	NM_004055.4		0,1,6489	AA,AG,GG		0.0116,0.0,0.0077		50/641	76796082	1,12979	2198	4292	6490	SO:0001819	synonymous_variant	726	exon2			CGTCAGGTGGAAG		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.150G>A	11.37:g.76796082G>A		69	0	0		63	40	0.634921	NM_004055	O00263	Silent	SNP	ENST00000278559.3	37	CCDS8248.1																																																																																			.	.	weak		0.692	CAPN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382564.2	NM_004055		A	76796082	G	A	76796082	2	1	23	1	0	0	0	0	0	0	0	1	2631	1252	44	2		2	CAPN5	11	76796082	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	5071298	76796082	58210434	443	7887											
MYO7A	4647	hgsc.bcm.edu	37	chr11	76895787	76895787	+	Intron	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccgggaggcggggacaccaGggcctgaaagtcttttggtg	7	7	18	9	2	1	1	0	1	1	0	1	3	1	3	3	6	0	0	3	6	1	2	rs111033223|rs143953991	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:76895787G>A	ENST00000409709.3	+	27	3775				MYO7A_ENST00000458637.2_Intron|MYO7A_ENST00000409893.1_Missense_Mutation_p.R1177K|MYO7A_ENST00000409619.2_Intron	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA						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						GGGGACACCAGGGCCTGAAAG	0.602																																					p.R1177K		Atlas-SNP	.											.	MYO7A	164	.	0			c.G3530A						PASS	.						13	15	14					11																	76895787		1872	3718	5590	SO:0001627	intron_variant	4647	exon27			ACACCAGGGCCTG	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.3503+27G>A	11.37:g.76895787G>A		0	0	.		71	71	1	NM_001127179	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	37	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	.	1.085	-0.665772	0.03428	.	.	ENSG00000137474	ENST00000409893	D	0.87729	-2.29	4.38	0.879	0.19155	.	.	.	.	.	T	0.68705	0.3030	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.53851	-0.8380	8	.	.	.	.	3.7783	0.08669	0.2584:0.0:0.5575:0.1841	.	1177	B9A012	.	K	1177	ENSP00000386689:R1177K	.	R	+	2	0	MYO7A	76573435	0.001000	0.12720	0.009000	0.14445	0.011000	0.07611	0.416000	0.21198	0.304000	0.22809	-0.452000	0.05504	AGG	.	.	none		0.602	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		A	76895787	G	A	76895787	1	1	23	0	1	0	0	0	0	0	0	0	10091	1000	35	2		2	MYO7A	11	76895787	Intron	SNP	G	TCGA-G8-6325-01A-11D-2210-10	99705	76895787	58110729	444	7888											
NARS2	79731	hgsc.bcm.edu	37	chr11	78189653	78189653	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttggccaggtgctatgaatTtgtgacagagttcaacatct	10	14	10	7	0	2	3	1	2	1	1	2	3	2	3	1	2	2	2	1	2	3	4	rs116930926	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:78189653T>C	ENST00000281038.5	-	8	1274	c.899A>G	c.(898-900)aAa>aGa	p.K300R	NARS2_ENST00000528850.1_Missense_Mutation_p.K73R	NM_001243251.1|NM_024678.5	NP_001230180.1|NP_078954.4	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial (putative)	300					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)	TGCTATGAATTTGTGACAGAG	0.313													T|||	29	0.00579073	0.0038	0.0043	5008	,	,		15374	0.0		0.0199	False		,,,				2504	0.001				p.K300R		Atlas-SNP	.											.	NARS2	62	.	0			c.A899G						PASS	.	T	ARG/LYS	26,4374	31.7+/-61.6	0,26,2174	118	112	114		899	0.6	0.8	11	dbSNP_132	114	240,8344	96.1+/-157.9	2,236,4054	yes	missense	NARS2	NM_024678.5	26	2,262,6228	CC,CT,TT		2.7959,0.5909,2.0487	benign	300/478	78189653	266,12718	2200	4292	6492	SO:0001583	missense	79731	exon8			ATGAATTTGTGAC	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.899A>G	11.37:g.78189653T>C	ENSP00000281038:p.Lys300Arg	150	0	0		166	71	0.427711	NM_024678	G3V178	Missense_Mutation	SNP	ENST00000281038.5	37	CCDS8261.1	20	0.009157509157509158	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	15	0.01978891820580475	T	13.75	2.329174	0.41197	0.005909	0.027959	ENSG00000137513	ENST00000281038;ENST00000528850	T;T	0.77489	-1.1;0.92	5.38	0.559	0.17272	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (D/K/N) (1);	0.174888	0.64402	N	0.000011	T	0.41166	0.1147	L	0.37630	1.12	0.38330	D	0.943783	B	0.20459	0.045	B	0.23716	0.048	T	0.50996	-0.8761	10	0.62326	D	0.03	-6.9707	7.4242	0.27090	0.0:0.3544:0.0:0.6456	.	300	Q96I59	SYNM_HUMAN	R	300;73	ENSP00000281038:K300R;ENSP00000432635:K73R	ENSP00000281038:K300R	K	-	2	0	NARS2	77867301	0.997000	0.39634	0.798000	0.32154	0.997000	0.91878	1.180000	0.32005	-0.058000	0.13177	0.528000	0.53228	AAA	T|0.984;C|0.016	0.016	strong		0.313	NARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391138.2	NM_024678		C	78189653	T	C	78189653	3	2	23	1	0	0	0	0	1	0	0	0	10180	1841	64	3	562	3	NARS2	11	78189653	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	1293866	78189653	56816863	445	7889											
SYTL2	54843	hgsc.bcm.edu	37	chr11	85435805	85435805	+	Intron	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggctcgcctgggctcctcTgtactacctattaactttga	6	14	9	12	1	1	1	0	1	1	0	3	1	2	1	3	2	3	3	3	2	4	5	rs532374094		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:85435805T>C	ENST00000528231.1	-	7	1737				SYTL2_ENST00000524452.1_Intron|SYTL2_ENST00000527523.1_Intron|SYTL2_ENST00000316356.4_Intron|SYTL2_ENST00000389960.4_Intron|SYTL2_ENST00000354566.3_Silent_p.T565T|SYTL2_ENST00000525423.1_Silent_p.T565T|SYTL2_ENST00000359152.5_Silent_p.T1089T	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)		TGGGCTCCTCTGTACTACCTA	0.423													T|||	1	0.000199681	0.0	0.0	5008	,	,		16092	0.0		0.001	False		,,,				2504	0.0				p.T565T		Atlas-SNP	.											.	SYTL2	231	.	0			c.A1695G						PASS	.						66	67	67					11																	85435805		2203	4299	6502	SO:0001627	intron_variant	54843	exon1			CTCCTCTGTACTA	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+3133A>G	11.37:g.85435805T>C		131	0	0		155	74	0.477419	NM_206927	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Silent	SNP	ENST00000528231.1	37	CCDS53688.1																																																																																			.	.	none		0.423	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927		C	85435805	T	C	85435805	1	2	23	0	1	0	0	0	0	0	0	0	15498	1567	55	3		3	SYTL2	11	85435805	Intron	SNP	T	TCGA-G8-6325-01A-11D-2210-10	7246152	85435805	49570711	446	7890											
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103153765	103153765	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acaaaaaatacgtgatcagcTtccgtcttggatagatcagg	14	10	9	8	2	3	2	2	1	1	1	4	3	4	3	1	2	2	1	1	2	5	4			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:103153765T>G	ENST00000375735.2	+	73	10985	c.10841T>G	c.(10840-10842)cTt>cGt	p.L3614R	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.L3621R|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	3614					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)		CGTGATCAGCTTCCGTCTTGG	0.328																																					p.L3621R		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T10862G						PASS	.						69	68	68					11																	103153765		1829	4067	5896	SO:0001583	missense	79659	exon74			ATCAGCTTCCGTC	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.10841T>G	11.37:g.103153765T>G	ENSP00000364887:p.Leu3614Arg	100	0	0		136	29	0.213235	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	T	15.93	2.978729	0.53720	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.08634	3.07;3.07	5.44	5.44	0.79542	Dynein heavy chain (1);	2.073920	0.01925	N	0.040832	T	0.18173	0.0436	M	0.66297	2.02	0.37386	D	0.912237	B;B	0.24043	0.096;0.078	B;B	0.31442	0.13;0.116	T	0.44205	-0.9343	10	0.20046	T	0.44	.	14.4816	0.67587	0.0:0.0:0.0:1.0	.	3614;3621	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	R	3614;3621	ENSP00000364887:L3614R;ENSP00000381167:L3621R	ENSP00000364887:L3614R	L	+	2	0	DYNC2H1	102658975	1.000000	0.71417	0.989000	0.46669	0.970000	0.65996	3.813000	0.55636	2.062000	0.61559	0.377000	0.23210	CTT	.	.	none		0.328	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		G	103153765	T	G	103153765	3	3	23	1	0	0	0	0	1	0	0	0	4848	1609	56	5	11156	5	DYNC2H1	11	103153765	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	17717960	103153765	31852751	447	7891											
RAB39	54734	hgsc.bcm.edu	37	chr11	107833065	107833065	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actgtgcattcttctgaggaAgcagtaaagcccaggaaaga	14	8	11	8	0	2	2	0	1	2	1	2	4	2	4	1	2	3	3	1	2	4	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:107833065A>C	ENST00000320578.2	+	2	687	c.621A>C	c.(619-621)gaA>gaC	p.E207D		NM_017516.1	NP_059986.1	Q14964	RB39A_HUMAN	RAB39A, member RAS oncogene family	207					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)										CTTCTGAGGAAGCAGTAAAGC	0.383																																					p.E207D		Atlas-SNP	.											.	.	.	.	0			c.A621C						PASS	.						49	55	53					11																	107833065		2200	4298	6498	SO:0001583	missense	54734	exon2			TGAGGAAGCAGTA	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.621A>C	11.37:g.107833065A>C	ENSP00000322594:p.Glu207Asp	116	0	0		135	66	0.488889	NM_017516	A8KAA4|Q8N6W2	Missense_Mutation	SNP	ENST00000320578.2	37	CCDS8338.1	.	.	.	.	.	.	.	.	.	.	A	10.34	1.323277	0.24080	.	.	ENSG00000179331	ENST00000320578	T	0.66995	-0.24	5.55	3.27	0.37495	.	0.000000	0.64402	D	0.000010	T	0.45034	0.1322	N	0.19112	0.55	0.32971	D	0.52234	B	0.16166	0.016	B	0.12156	0.007	T	0.43766	-0.9371	10	0.13108	T	0.6	.	8.0299	0.30459	0.7816:0.0:0.2184:0.0	.	207	Q14964	RB39A_HUMAN	D	207	ENSP00000322594:E207D	ENSP00000322594:E207D	E	+	3	2	RAB39	107338275	0.984000	0.35163	1.000000	0.80357	0.984000	0.73092	0.350000	0.20079	0.553000	0.29044	0.482000	0.46254	GAA	.	.	none		0.383	RAB39A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389423.1	NM_017516		C	107833065	A	C	107833065	3	2	23	1	0	0	0	0	1	0	0	0	12944	69	3	5	627	5	RAB39	11	107833065	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	4679300	107833065	27173451	448	7892											
ATM	472	hgsc.bcm.edu	37	chr11	108124761	108124761	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcttctgaataattactcaTctgaggtgagattttttaaa	13	16	7	5	0	3	3	1	3	2	1	3	4	3	3	0	1	2	1	0	1	5	6	rs4986761	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:108124761T>C	ENST00000452508.2	+	14	2308	c.2119T>C	c.(2119-2121)Tct>Cct	p.S707P	ATM_ENST00000278616.4_Missense_Mutation_p.S707P			Q13315	ATM_HUMAN	ATM serine/threonine kinase	707			S -> P (in dbSNP:rs4986761). {ECO:0000269|PubMed:10534763, ECO:0000269|PubMed:17344846}.|YSS -> FIP (in AT; might be associated with susceptibility to cancer).		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.S707P(2)|p.S707fs*29(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)	TAATTACTCATCTGAGGTGAG	0.393			"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)			T|||	22	0.00439297	0.0	0.0101	5008	,	,		16199	0.0		0.0129	False		,,,				2504	0.002				p.S707P		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	ATM,NS,carcinoma,0,2	ATM	1657	2	3	Substitution - Missense(2)|Deletion - Frameshift(1)	breast(2)|haematopoietic_and_lymphoid_tissue(1)	c.T2119C	GRCh37	CM013692	ATM	M	rs4986761	PASS	.	T	PRO/SER	17,4383	21.2+/-45.6	0,17,2183	55	55	55		2119	3.8	1	11	dbSNP_111	55	94,8502	50.6+/-110.7	1,92,4205	yes	missense	ATM	NM_000051.3	74	1,109,6388	CC,CT,TT		1.0935,0.3864,0.8541	benign	707/3057	108124761	111,12885	2200	4298	6498	SO:0001583	missense	472	exon13	Familial Cancer Database	AT, Louis-Bar syndrome	TACTCATCTGAGG	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.2119T>C	11.37:g.108124761T>C	ENSP00000388058:p.Ser707Pro	63	0	0		67	35	0.522388	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	T	11.63	1.694897	0.30052	0.003864	0.010935	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.78364	-1.17;-1.17;-1.17	6.11	3.81	0.43845	Armadillo-type fold (1);	0.179298	0.50627	N	0.000119	T	0.52141	0.1716	N	0.17872	0.535	0.23076	N	0.998335	B	0.02656	0.0	B	0.01281	0.0	T	0.42565	-0.9444	10	0.31617	T	0.26	.	7.5463	0.27768	0.0:0.2362:0.0:0.7638	rs4986761;rs52832782;rs4986761	707	Q13315	ATM_HUMAN	P	707	ENSP00000435747:S707P;ENSP00000278616:S707P;ENSP00000388058:S707P	ENSP00000278616:S707P	S	+	1	0	ATM	107629971	0.015000	0.18098	0.999000	0.59377	0.911000	0.54048	-0.127000	0.10547	0.553000	0.29044	0.533000	0.62120	TCT	T|0.993;C|0.007	0.007	strong		0.393	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		C	108124761	T	C	108124761	3	2	23	1	0	0	0	0	1	0	0	0	1109	1435	50	3	2165	3	ATM	11	108124761	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	291696	108124761	26881755	449	7893											
ATM	472	hgsc.bcm.edu	37	chr11	108175462	108175462	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttcatgatattttactccaaGatacaaatgaatcatggaga	16	13	6	6	0	2	4	2	2	0	2	3	5	3	4	1	1	2	0	1	1	6	5	rs1801516	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:108175462G>A	ENST00000452508.2	+	38	5746	c.5557G>A	c.(5557-5559)Gat>Aat	p.D1853N	ATM_ENST00000278616.4_Missense_Mutation_p.D1853N			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1853			D -> N (common polymorphism; dbSNP:rs1801516). {ECO:0000269|PubMed:10397742, ECO:0000269|PubMed:10425038, ECO:0000269|PubMed:10534763, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9711876, ECO:0000269|PubMed:9887333}.|D -> V (might contribute to B-cell chronic lymphocytic leukemia; dbSNP:rs1801673). {ECO:0000269|PubMed:10397742, ECO:0000269|PubMed:10817650, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9872980, ECO:0000269|PubMed:9887333}.		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.D1853N(10)		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)	TTTACTCCAAGATACAAATGA	0.388			"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)			G|||	335	0.066893	0.0083	0.0965	5008	,	,		16727	0.0159		0.162	False		,,,				2504	0.0798				p.D1853N		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	ATM_ENST00000278616,colon,carcinoma,-1,17	ATM	1657	17	10	Substitution - Missense(10)	breast(9)|skin(1)	c.G5557A	GRCh37	CM077896	ATM	M	rs1801516	PASS	.	G	ASN/ASP	125,4277	92.5+/-131.2	3,119,2079	75	72	73	http://www.ncbi.nlm.nih.gov/pubmed?term	5557	5.5	1	11	dbSNP_89	73	1205,7391	241.8+/-272.0	99,1007,3192	yes	missense	ATM	NM_000051.3	23	102,1126,5271	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	14.0181,2.8396,10.2323	possibly-damaging	1853/3057	108175462	1330,11668	2201	4298	6499	SO:0001583	missense	472	exon37	Familial Cancer Database	AT, Louis-Bar syndrome	CTCCAAGATACAA	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.5557G>A	11.37:g.108175462G>A	ENSP00000388058:p.Asp1853Asn	120	0	0		111	54	0.486486	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	172	0.07875457875457875	5	0.01016260162601626	40	0.11049723756906077	7	0.012237762237762238	120	0.158311345646438	G	17.18	3.324076	0.60634	0.028396	0.140181	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.73152	-0.72;-0.72	5.52	5.52	0.82312	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.00580	0.0019	L	0.61036	1.89	0.19945	P	0.9999491241	B	0.20368	0.044	B	0.16289	0.015	T	0.10730	-1.0617	9	0.33940	T	0.23	.	19.8041	0.96521	0.0:0.0:1.0:0.0	rs1801516;rs17503060;rs52821794;rs60879649;rs1801516	1853	Q13315	ATM_HUMAN	N	1853	ENSP00000278616:D1853N;ENSP00000388058:D1853N	ENSP00000278616:D1853N	D	+	1	0	ATM	107680672	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.342000	0.72982	2.748000	0.94277	0.591000	0.81541	GAT	G|0.910;A|0.090	0.090	strong		0.388	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		A	108175462	G	A	108175462	3	1	23	1	0	0	0	0	1	0	0	0	1109	942	33	2	5699	2	ATM	11	108175462	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	50701	108175462	26831054	450	7894											
APOA4	337	hgsc.bcm.edu	37	chr11	116693871	116693871	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctactcaccggcgacagccaCcagggccagggtcaggacca	10	3	12	16	2	2	0	2	0	0	0	2	2	2	1	5	4	2	0	5	4	1	1	rs12721041	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:116693871C>T	ENST00000357780.3	-	1	151	c.37G>A	c.(37-39)Gtg>Atg	p.V13M		NM_000482.3	NP_000473.2	P06727	APOA4_HUMAN	apolipoprotein A-IV	13			V -> M (in allele APOA-IV*1D). {ECO:0000269|PubMed:1349197, ECO:0000269|PubMed:15108119}.		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)		GCGACAGCCACCAGGGCCAGG	0.582													C|||	15	0.00299521	0.0	0.0014	5008	,	,		19224	0.0		0.0129	False		,,,				2504	0.001				p.V13M		Atlas-SNP	.											.	APOA4	51	.	0			c.G37A						PASS	.	C	MET/VAL	12,4390	21.2+/-45.6	0,12,2189	138	133	135		37	3.4	1	11	dbSNP_126	135	144,8440	71.0+/-133.6	1,142,4149	yes	missense	APOA4	NM_000482.3	21	1,154,6338	TT,TC,CC		1.6775,0.2726,1.2013	benign	13/397	116693871	156,12830	2201	4292	6493	SO:0001583	missense	337	exon1			CAGCCACCAGGGC		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.37G>A	11.37:g.116693871C>T	ENSP00000350425:p.Val13Met	121	0	0		143	77	0.538462	NM_000482	A8MSL6|Q14CW8|Q6Q787	Missense_Mutation	SNP	ENST00000357780.3	37	CCDS31681.1	12	0.005494505494505495	0	0.0	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	C	13.60	2.286795	0.40494	0.002726	0.016775	ENSG00000110244	ENST00000357780	T	0.77098	-1.07	4.33	3.39	0.38822	.	0.512987	0.17527	N	0.171020	T	0.69672	0.3137	M	0.83012	2.62	0.22489	N	0.999052	B	0.29301	0.241	B	0.38880	0.284	T	0.72043	-0.4409	10	0.72032	D	0.01	-28.2212	10.1918	0.43030	0.0:0.798:0.202:0.0	rs12721041;rs45558133	13	P06727	APOA4_HUMAN	M	13	ENSP00000350425:V13M	ENSP00000350425:V13M	V	-	1	0	APOA4	116199081	0.999000	0.42202	1.000000	0.80357	0.774000	0.43823	0.411000	0.21115	1.383000	0.46405	0.655000	0.94253	GTG	C|0.990;T|0.010	0.010	strong		0.582	APOA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106279.2	NM_000482		T	116693871	C	T	116693871	3	4	23	1	0	0	0	0	1	0	0	0	783	507	18	2	1165	2	APOA4	11	116693871	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	8518409	116693871	18312645	451	7895											
PHLDB1	23187	hgsc.bcm.edu	37	chr11	118516274	118516274	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggggaggagggtgagcacGcctatgatacgctgagtctg	8	8	18	7	2	1	3	0	3	1	0	1	5	1	5	1	4	2	2	1	4	2	2	rs149914355	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:118516274G>A	ENST00000361417.2	+	17	3733	c.3322G>A	c.(3322-3324)Gcc>Acc	p.A1108T	PHLDB1_ENST00000356063.5_Missense_Mutation_p.A1061T|PHLDB1_ENST00000524713.1_Missense_Mutation_p.A251T|PHLDB1_ENST00000534672.1_3'UTR|PHLDB1_ENST00000527898.1_Missense_Mutation_p.A159T	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	1108										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)		GGGTGAGCACGCCTATGATAC	0.647													G|||	7	0.00139776	0.0	0.0014	5008	,	,		18185	0.0		0.005	False		,,,				2504	0.001				p.A1108T		Atlas-SNP	.											.	PHLDB1	103	.	0			c.G3322A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	3,4397	6.2+/-15.9	0,3,2197	95	92	93		3322,3181,3322	5.5	0.9	11	dbSNP_134	93	12,8578	9.1+/-34.3	0,12,4283	yes	missense,missense,missense	PHLDB1	NM_001144758.1,NM_001144759.1,NM_015157.2	58,58,58	0,15,6480	AA,AG,GG		0.1397,0.0682,0.1155	benign,benign,benign	1108/1378,1061/1320,1108/1378	118516274	15,12975	2200	4295	6495	SO:0001583	missense	23187	exon16			GAGCACGCCTATG		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.3322G>A	11.37:g.118516274G>A	ENSP00000354498:p.Ala1108Thr	91	0	0		126	61	0.484127	NM_001144758	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Missense_Mutation	SNP	ENST00000361417.2	37	CCDS8401.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	G	15.18	2.757205	0.49468	6.82E-4	0.001397	ENSG00000019144	ENST00000361417;ENST00000361465;ENST00000358191;ENST00000356063;ENST00000527898;ENST00000524713	T;T;T;T	0.61040	0.14;0.14;0.14;0.14	5.52	5.52	0.82312	.	0.223446	0.46758	D	0.000268	T	0.45498	0.1345	L	0.56280	1.765	0.29675	N	0.842181	P;P;P;P;P	0.48016	0.904;0.681;0.898;0.764;0.883	B;B;B;B;B	0.38296	0.23;0.216;0.27;0.151;0.27	T	0.56396	-0.7986	10	0.36615	T	0.2	-19.0047	18.4343	0.90638	0.0:0.0:1.0:0.0	.	251;472;867;1061;1108	B4DK17;B0YJ65;Q5W9G0;Q86UU1-2;Q86UU1	.;.;.;.;PHLB1_HUMAN	T	1108;882;472;1061;159;251	ENSP00000354498:A1108T;ENSP00000348359:A1061T;ENSP00000435388:A159T;ENSP00000434905:A251T	ENSP00000348359:A1061T	A	+	1	0	PHLDB1	118021484	0.998000	0.40836	0.928000	0.36995	0.654000	0.38779	2.954000	0.49113	2.596000	0.87737	0.655000	0.94253	GCC	G|0.998;A|0.002	0.002	strong		0.647	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157		A	118516274	G	A	118516274	3	1	23	1	0	0	0	0	1	0	0	0	11860	1087	38	1	3380	1	PHLDB1	11	118516274	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1822403	118516274	16490242	452	7896											
CXCR5	643	hgsc.bcm.edu	37	chr11	118764448	118764448	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcctcatcttcctcctgggCgtgatcggcaacgtcctggt	5	11	11	14	3	2	1	1	1	1	0	6	1	5	1	4	3	2	1	4	3	1	1	rs537787473		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:118764448C>T	ENST00000292174.4	+	2	371	c.195C>T	c.(193-195)ggC>ggT	p.G65G		NM_001716.4|NM_032966.2	NP_001707.1|NP_116743.1	P32302	CXCR5_HUMAN	chemokine (C-X-C motif) receptor 5	65					B cell activation (GO:0042113)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of cytokinesis (GO:0032467)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|G-protein coupled receptor activity (GO:0004930)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(5)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	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)		TCCTCCTGGGCGTGATCGGCA	0.642													C|||	1	0.000199681	0.0	0.0014	5008	,	,		19111	0.0		0.0	False		,,,				2504	0.0				p.G65G		Atlas-SNP	.											.	CXCR5	34	.	0			c.C195T						PASS	.						117	105	109					11																	118764448		2200	4295	6495	SO:0001819	synonymous_variant	643	exon2			CCTGGGCGTGATC	X68829	CCDS8402.1	11q23.3	2012-08-08	2008-01-22	2008-01-22	ENSG00000160683	ENSG00000160683		"CD molecules", "GPCR / Class A : Chemokine receptors : C-X-C motif"	1060	protein-coding gene	gene with protein product		601613	"Burkitt lymphoma receptor 1, GTP-binding protein", "Burkitt lymphoma receptor 1, GTP binding protein (chemokine (C-X-C motif) receptor 5)"	BLR1		1425907	Standard	NM_001716		Approved	MDR15, CD185	uc001pue.4	P32302	OTTHUMG00000166345	ENST00000292174.4:c.195C>T	11.37:g.118764448C>T		147	0	0		151	70	0.463576	NM_001716	Q14811	Silent	SNP	ENST00000292174.4	37	CCDS8402.1																																																																																			.	.	none		0.642	CXCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389309.1	NM_001716		T	118764448	C	T	118764448	2	4	23	1	0	0	0	0	0	0	0	1	4096	755	27	1		1	CXCR5	11	118764448	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	248174	118764448	16242068	453	7897											
TECTA	7007	hgsc.bcm.edu	37	chr11	121028666	121028666	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaggagtgtgcgctgcgcaaCggggtgcgcggctgcttcag	5	7	19	10	5	1	0	1	0	0	0	1	2	1	1	0	4	5	4	0	4	1	1	rs33981325	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:121028666C>T	ENST00000392793.1	+	14	4693	c.4422C>T	c.(4420-4422)aaC>aaT	p.N1474N	TECTA_ENST00000264037.2_Silent_p.N1474N			O75443	TECTA_HUMAN	tectorin alpha	1474					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)		CGCTGCGCAACGGGGTGCGCG	0.682													C|||	58	0.0115815	0.0015	0.0187	5008	,	,		10842	0.0		0.0348	False		,,,				2504	0.0082				p.N1474N		Atlas-SNP	.											TECTA,NS,carcinoma,+1,1	TECTA	329	1	0			c.C4422T						PASS	.	C		26,4380	32.6+/-62.9	1,24,2178	41	39	39		4422	-1.3	0.8	11	dbSNP_126	39	288,8308	105.2+/-166.2	4,280,4014	no	coding-synonymous	TECTA	NM_005422.2		5,304,6192	TT,TC,CC		3.3504,0.5901,2.415		1474/2156	121028666	314,12688	2203	4298	6501	SO:0001819	synonymous_variant	7007	exon13			GCGCAACGGGGTG	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.4422C>T	11.37:g.121028666C>T		64	0	0		53	35	0.660377	NM_005422		Silent	SNP	ENST00000392793.1	37	CCDS8434.1																																																																																			C|0.978;T|0.022	0.022	strong		0.682	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		T	121028666	C	T	121028666	2	4	23	1	0	0	0	0	0	0	0	1	15762	535	19	1		1	TECTA	11	121028666	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	2264218	121028666	13977850	454	7898											
ST14	6768	hgsc.bcm.edu	37	chr11	130060453	130060453	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctcatgcccgctgccagtggGccctgcggggggacgccgac	4	5	16	16	4	1	0	1	0	0	0	1	2	1	1	4	4	3	1	4	4	0	0	rs35230546|rs144266633	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:130060453G>A	ENST00000278742.5	+	7	1157	c.739G>A	c.(739-741)Gcc>Acc	p.A247T		NM_021978.3	NP_068813.1	Q9Y5Y6	ST14_HUMAN	suppression of tumorigenicity 14 (colon carcinoma)	247	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				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)	CTGCCAGTGGGCCCTGCGGGG	0.687																																					p.A247T		Atlas-SNP	.											.	ST14	82	.	0			c.G739A						PASS	.	G	THR/ALA	0,4400		0,0,2200	27	25	26		739	1.3	1	11	dbSNP_134	26	7,8583		0,7,4288	yes	missense	ST14	NM_021978.3	58	0,7,6488	AA,AG,GG		0.0815,0.0,0.0539	benign	247/856	130060453	7,12983	2200	4295	6495	SO:0001583	missense	6768	exon7			CAGTGGGCCCTGC	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.739G>A	11.37:g.130060453G>A	ENSP00000278742:p.Ala247Thr	106	0	0		45	29	0.644444	NM_021978	Q9BS01|Q9H3S0|Q9HB36|Q9HCA3	Missense_Mutation	SNP	ENST00000278742.5	37	CCDS8487.1	.	.	.	.	.	.	.	.	.	.	G	11.00	1.510543	0.27036	0.0	8.15E-4	ENSG00000149418	ENST00000278742;ENST00000525779	T	0.30714	1.52	5.45	1.26	0.21427	CUB (5);	1.014350	0.07937	N	0.978525	T	0.10035	0.0246	N	0.01188	-0.97	0.23271	N	0.998006	B;B	0.10296	0.003;0.002	B;B	0.12837	0.008;0.005	T	0.34625	-0.9821	10	0.08837	T	0.75	.	7.5637	0.27866	0.5136:0.0:0.4864:0.0	.	57;247	B4DYI7;Q9Y5Y6	.;ST14_HUMAN	T	247;149	ENSP00000278742:A247T	ENSP00000278742:A247T	A	+	1	0	ST14	129565663	0.025000	0.19082	0.997000	0.53966	0.915000	0.54546	0.259000	0.18405	-0.033000	0.13736	0.650000	0.86243	GCC	G|1.000;A|0.000	0.000	strong		0.687	ST14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386119.1			A	130060453	G	A	130060453	3	1	23	1	0	0	0	0	1	0	0	0	15226	1203	42	2	765	2	ST14	11	130060453	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	9031787	130060453	4946063	455	7899											
KCNA5	3741	hgsc.bcm.edu	37	chr12	5154064	5154064	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agagctctgggtccgcgcggGccatcgccatcgtctcggtc	4	8	14	15	6	2	1	0	0	2	1	7	1	3	1	3	3	1	1	3	3	0	0	rs12720442	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:5154064G>A	ENST00000252321.3	+	1	980	c.751G>A	c.(751-753)Gcc>Acc	p.A251T		NM_002234.3	NP_002225.2	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 5	251					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)	GTCCGCGCGGGCCATCGCCAT	0.587													G|||	41	0.0081869	0.0015	0.0274	5008	,	,		15304	0.0		0.0169	False		,,,				2504	0.0031				p.A251T		Atlas-SNP	.											KCNA5,brain,glioma,0,1	KCNA5	138	1	0			c.G751A						PASS	.	G	THR/ALA	14,4392	22.3+/-47.3	1,12,2190	109	118	115		751	4.8	0.9	12	dbSNP_126	115	109,8491	58.3+/-119.8	1,107,4192	yes	missense	KCNA5	NM_002234.2	58	2,119,6382	AA,AG,GG		1.2674,0.3177,0.9457	benign	251/614	5154064	123,12883	2203	4300	6503	SO:0001583	missense	3741	exon1			GCGCGGGCCATCG	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.751G>A	12.37:g.5154064G>A	ENSP00000252321:p.Ala251Thr	91	0	0		103	47	0.456311	NM_002234	Q4KKT8|Q4VAJ1|Q4VAJ2|Q9UDA4	Missense_Mutation	SNP	ENST00000252321.3	37	CCDS8536.1	22	0.010073260073260074	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	13	0.017150395778364115	G	10.28	1.305403	0.23736	0.003177	0.012674	ENSG00000130037	ENST00000252321	T	0.65178	-0.14	4.77	4.77	0.60923	.	0.227351	0.34484	U	0.003922	T	0.38480	0.1042	L	0.38175	1.15	0.28718	N	0.90318	B	0.13145	0.007	B	0.17722	0.019	T	0.48603	-0.9021	10	0.48119	T	0.1	.	16.9696	0.86295	0.0:0.0:1.0:0.0	rs12720442;rs45573135	251	P22460	KCNA5_HUMAN	T	251	ENSP00000252321:A251T	ENSP00000252321:A251T	A	+	1	0	KCNA5	5024325	0.948000	0.32251	0.932000	0.37286	0.982000	0.71751	5.267000	0.65530	2.478000	0.83669	0.561000	0.74099	GCC	G|0.990;A|0.010	0.010	strong		0.587	KCNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398925.2	NM_002234		A	5154064	G	A	5154064	3	1	23	1	0	0	0	0	1	0	0	0	8015	1203	42	2	753	2	KCNA5	12	5154064	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10		5154064	128697831	456	7900											
SCNN1A	6337	hgsc.bcm.edu	37	chr12	6472752	6472752	+	Missense_Mutation	SNP	G	G	A																															ggggtgcggcagagtcccccGcaggtcgcgacggctgcggg																								rs55797039	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:6472752G>A	ENST00000228916.2	-	3	639	c.541C>T	c.(541-543)Cgg>Tgg	p.R181W	SCNN1A_ENST00000540037.1_5'UTR|SCNN1A_ENST00000358945.3_Missense_Mutation_p.R181W|SCNN1A_ENST00000360168.3_Missense_Mutation_p.R240W|SCNN1A_ENST00000396966.2_Missense_Mutation_p.R181W|SCNN1A_ENST00000543768.1_Missense_Mutation_p.R204W|SCNN1A_ENST00000538979.1_Intron	NM_001038.5	NP_001029.1	P37088	SCNNA_HUMAN	sodium channel, non-voltage-gated 1 alpha subunit	181			R -> W (functional polymorphism; significant increase of amiloride- sensitive sodium currents; dbSNP:rs55797039). {ECO:0000269|PubMed:16207733, ECO:0000269|PubMed:19462466}.		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)	apical plasma membrane (GO:0016324)|ciliary membrane (GO:0060170)|cortical actin cytoskeleton (GO:0030864)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(2)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Amiloride(DB00594)|Triamterene(DB00384)	AGAGTCCCCCGCAGGTCGCGA	0.682													G|||	36	0.0071885	0.0	0.0072	5008	,	,		10784	0.0		0.0209	False		,,,				2504	0.0102				p.R240W		Atlas-SNP	.											.	SCNN1A	54	.	0			c.C718T	GRCh37	CM055536	SCNN1A	M	rs55797039	PASS	.	G	TRP/ARG,TRP/ARG,TRP/ARG	15,4385		0,15,2185	13	15	14		541,610,718	-3.5	0	12	dbSNP_129	14	141,8449		4,133,4158	no	missense,missense,missense	SCNN1A	NM_001038.5,NM_001159575.1,NM_001159576.1	101,101,101	4,148,6343	AA,AG,GG		1.6414,0.3409,1.2009	probably-damaging,probably-damaging,probably-damaging	181/670,204/693,240/729	6472752	156,12834	2200	4295	6495	SO:0001583	missense	6337	exon2			TCCCCCGCAGGTC	Z92978	CCDS8543.1, CCDS53738.1, CCDS53739.1	12p13	2012-02-28	2012-02-28		ENSG00000111319	ENSG00000111319		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10599	protein-coding gene	gene with protein product		600228	"sodium channel, nonvoltage-gated 1 alpha", "sodium channel, non-voltage-gated 1 alpha"	SCNN1		7896277	Standard	NM_001038		Approved	ENaCalpha	uc001qnw.3	P37088	OTTHUMG00000168268	ENST00000228916.2:c.541C>T	12.37:g.6472752G>A	ENSP00000228916:p.Arg181Trp	26	0	0		17	11	0.647059	NM_001159576	A5X2U9|B4E2Q5|C5HTZ0|O43271|Q6GSQ6|Q9UM64	Missense_Mutation	SNP	ENST00000228916.2	37	CCDS8543.1	17	0.007783882783882784	0	0.0	2	0.0055248618784530384	0	0.0	15	0.01978891820580475	G	14.54	2.565723	0.45694	0.003409	0.016414	ENSG00000111319	ENST00000360168;ENST00000358945;ENST00000228916;ENST00000396966;ENST00000543768	T;T;T;T;T	0.70986	-0.49;-0.53;-0.46;-0.13;-0.47	5.46	-3.48	0.04739	.	1.661160	0.03643	N	0.239873	T	0.62974	0.2472	L	0.32530	0.975	0.09310	N	1	D;D;D	0.76494	0.999;0.999;0.998	P;P;P	0.59703	0.862;0.809;0.827	T	0.69870	-0.5028	10	0.59425	D	0.04	-31.5772	17.9864	0.89157	0.0:0.7352:0.164:0.1009	rs55797039;rs61759925	204;181;240	B4E2Q5;P37088;P37088-2	.;SCNNA_HUMAN;.	W	240;181;181;181;204	ENSP00000353292:R240W;ENSP00000351825:R181W;ENSP00000228916:R181W;ENSP00000380166:R181W;ENSP00000438739:R204W	ENSP00000228916:R181W	R	-	1	2	SCNN1A	6343013	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-1.833000	0.01695	-0.647000	0.05444	0.561000	0.74099	CGG	G|0.986;A|0.014	0.014	strong		0.682	SCNN1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399055.1			A	6472752	G	A	6472752	3	1	23	1	0	0	0	0	1	0	0	0	13942	1086	38	1	1512	1	SCNN1A	12	6472752	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1318688	6472752	127379143	457	7901	101	2									
SCNN1A	6337	hgsc.bcm.edu	37	chr12	6472753	6472753	+	Silent	SNP	C	C	A																															gggtgcggcagagtcccccgCaggtcgcgacggctgcggga																								rs55859427	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:6472753C>A	ENST00000228916.2	-	3	638	c.540G>T	c.(538-540)ctG>ctT	p.L180L	SCNN1A_ENST00000540037.1_5'UTR|SCNN1A_ENST00000358945.3_Silent_p.L180L|SCNN1A_ENST00000360168.3_Silent_p.L239L|SCNN1A_ENST00000396966.2_Silent_p.L180L|SCNN1A_ENST00000543768.1_Silent_p.L203L|SCNN1A_ENST00000538979.1_Intron	NM_001038.5	NP_001029.1	P37088	SCNNA_HUMAN	sodium channel, non-voltage-gated 1 alpha subunit	180					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)	apical plasma membrane (GO:0016324)|ciliary membrane (GO:0060170)|cortical actin cytoskeleton (GO:0030864)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(2)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Amiloride(DB00594)|Triamterene(DB00384)	GAGTCCCCCGCAGGTCGCGAC	0.682													C|||	36	0.0071885	0.0	0.0072	5008	,	,		10426	0.0		0.0209	False		,,,				2504	0.0102				p.L239L		Atlas-SNP	.											.	SCNN1A	54	.	0			c.G717T						PASS	.	C	,,	17,4383		0,17,2183	13	15	14		540,609,717	-0.9	0	12	dbSNP_129	14	150,8444		5,140,4152	no	coding-synonymous,coding-synonymous,coding-synonymous	SCNN1A	NM_001038.5,NM_001159575.1,NM_001159576.1	,,	5,157,6335	AA,AC,CC		1.7454,0.3864,1.2852	,,	180/670,203/693,239/729	6472753	167,12827	2200	4297	6497	SO:0001819	synonymous_variant	6337	exon2			CCCCCGCAGGTCG	Z92978	CCDS8543.1, CCDS53738.1, CCDS53739.1	12p13	2012-02-28	2012-02-28		ENSG00000111319	ENSG00000111319		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10599	protein-coding gene	gene with protein product		600228	"sodium channel, nonvoltage-gated 1 alpha", "sodium channel, non-voltage-gated 1 alpha"	SCNN1		7896277	Standard	NM_001038		Approved	ENaCalpha	uc001qnw.3	P37088	OTTHUMG00000168268	ENST00000228916.2:c.540G>T	12.37:g.6472753C>A		26	0	0		17	11	0.647059	NM_001159576	A5X2U9|B4E2Q5|C5HTZ0|O43271|Q6GSQ6|Q9UM64	Silent	SNP	ENST00000228916.2	37	CCDS8543.1																																																																																			C|0.985;A|0.015	0.015	strong		0.682	SCNN1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399055.1			A	6472753	C	A	6472753	2	1	23	1	0	0	0	0	0	0	0	1	13942	697	25	4		4	SCNN1A	12	6472753	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1	6472753	127379142	458	7902	101	2									
LAG3	3902	hgsc.bcm.edu	37	chr12	6884585	6884585	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggccctgacctcctggtgActggagacaatggcgacttt	8	9	13	11	1	0	3	0	2	0	1	1	6	1	3	3	4	0	0	3	4	1	1	rs149434241	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:6884585A>T	ENST00000203629.2	+	5	1261	c.928A>T	c.(928-930)Act>Tct	p.T310S	LAG3_ENST00000441671.2_Missense_Mutation_p.T310S	NM_002286.5	NP_002277.4	P18627	LAG3_HUMAN	lymphocyte-activation gene 3	310	Ig-like C2-type 2.				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						CCTCCTGGTGACTGGAGACAA	0.627													A|||	10	0.00199681	0.0	0.0043	5008	,	,		17324	0.0		0.007	False		,,,				2504	0.0				p.T310S		Atlas-SNP	.											.	LAG3	35	.	0			c.A928T						PASS	.	A	SER/THR	5,4401	11.4+/-27.6	0,5,2198	96	88	91		928	-2.2	1	12	dbSNP_134	91	74,8526	44.5+/-102.8	1,72,4227	yes	missense	LAG3	NM_002286.5	58	1,77,6425	TT,TA,AA		0.8605,0.1135,0.6074	benign	310/526	6884585	79,12927	2203	4300	6503	SO:0001583	missense	3902	exon5			CTGGTGACTGGAG		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.928A>T	12.37:g.6884585A>T	ENSP00000203629:p.Thr310Ser	184	0	0		216	102	0.472222	NM_002286	A8K7T9|Q7Z643	Missense_Mutation	SNP	ENST00000203629.2	37	CCDS8561.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	A	6.623	0.483348	0.12581	0.001135	0.008605	ENSG00000089692	ENST00000441671;ENST00000203629	T;T	0.11169	2.8;2.8	5.55	-2.19	0.07015	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.731904	0.12659	N	0.449835	T	0.03390	0.0098	L	0.34521	1.04	0.09310	N	0.999994	B;B	0.06786	0.0;0.001	B;B	0.09377	0.001;0.004	T	0.43782	-0.9370	10	0.08599	T	0.76	-1.8946	2.0189	0.03505	0.235:0.2239:0.4154:0.1257	.	310;310	P18627;Q7Z643	LAG3_HUMAN;.	S	310	ENSP00000413825:T310S;ENSP00000203629:T310S	ENSP00000203629:T310S	T	+	1	0	LAG3	6754846	0.105000	0.21958	0.992000	0.48379	0.722000	0.41435	-0.198000	0.09505	-0.199000	0.10317	-1.741000	0.00685	ACT	A|0.994;T|0.006	0.006	strong		0.627	LAG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402846.1			T	6884585	A	T	6884585	3	4	23	1	0	0	0	0	1	0	0	0	8609	275	10	5	946	5	LAG3	12	6884585	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	411832	6884585	126967310	459	7903											
TAS2R8	50836	hgsc.bcm.edu	37	chr12	10958896	10958896	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttaatggctctcacatgaacTtctgtgctggggtctctact	7	15	9	10	0	3	1	1	1	3	0	5	1	3	1	0	3	3	2	0	3	3	3	rs143804727	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:10958896T>G	ENST00000240615.2	-	1	996	c.684A>C	c.(682-684)gaA>gaC	p.E228D		NM_023918.1	NP_076407.1	Q9NYW2	TA2R8_HUMAN	taste receptor, type 2, member 8	228					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						TCACATGAACTTCTGTGCTGG	0.333													T|||	42	0.00838658	0.0	0.0231	5008	,	,		18097	0.002		0.0129	False		,,,				2504	0.0112				p.E228D		Atlas-SNP	.											TAS2R8,colon,carcinoma,0,1	TAS2R8	42	1	0			c.A684C						PASS	.	T	ASP/GLU	14,4392	21.2+/-45.6	0,14,2189	82	86	84		684	-1.8	0	12	dbSNP_134	84	197,8401	84.8+/-147.2	2,193,4104	yes	missense	TAS2R8	NM_023918.1	45	2,207,6293	GG,GT,TT		2.2912,0.3177,1.6226	possibly-damaging	228/310	10958896	211,12793	2203	4299	6502	SO:0001583	missense	50836	exon1			ATGAACTTCTGTG	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.684A>C	12.37:g.10958896T>G	ENSP00000240615:p.Glu228Asp	80	0	0		78	44	0.564103	NM_023918	Q4KN29|Q645Y2	Missense_Mutation	SNP	ENST00000240615.2	37	CCDS8632.1	14	0.00641025641025641	0	0.0	8	0.022099447513812154	1	0.0017482517482517483	5	0.006596306068601583	T	11.29	1.595797	0.28445	0.003177	0.022912	ENSG00000121314	ENST00000240615	T	0.37752	1.18	5.38	-1.83	0.07833	GPCR, rhodopsin-like superfamily (1);	0.488214	0.16827	U	0.197913	T	0.35098	0.0920	M	0.80332	2.49	0.09310	N	1	D	0.63046	0.992	D	0.65573	0.936	T	0.36089	-0.9762	10	0.72032	D	0.01	.	5.7484	0.18132	0.1379:0.3212:0.0:0.5409	.	228	Q9NYW2	TA2R8_HUMAN	D	228	ENSP00000240615:E228D	ENSP00000240615:E228D	E	-	3	2	TAS2R8	10850163	0.000000	0.05858	0.032000	0.17829	0.008000	0.06430	-3.643000	0.00405	-0.700000	0.05070	-0.904000	0.02843	GAA	T|0.987;G|0.013	0.013	strong		0.333	TAS2R8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399932.1			G	10958896	T	G	10958896	3	3	23	1	0	0	0	0	1	0	0	0	15602	1606	56	5	248	5	TAS2R8	12	10958896	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	4074311	10958896	122892999	460	7904											
STRAP	11171	hgsc.bcm.edu	37	chr12	16042908	16042908	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atgaattgatgaccctggctCataaacacattgtcaagact	14	11	7	9	0	2	4	2	3	0	1	2	4	2	4	1	1	1	1	1	1	4	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:16042908C>T	ENST00000419869.2	+	3	608	c.295C>T	c.(295-297)Cat>Tat	p.H99Y	STRAP_ENST00000538352.1_Missense_Mutation_p.H5Y|STRAP_ENST00000025399.6_Missense_Mutation_p.H112Y	NM_007178.3	NP_009109.3	Q9Y3F4	STRAP_HUMAN	serine/threonine kinase receptor associated protein	99					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)				GACCCTGGCTCATAAACACAT	0.338																																					p.H99Y		Atlas-SNP	.											.	STRAP	33	.	0			c.C295T						PASS	.						112	105	107					12																	16042908		2203	4300	6503	SO:0001583	missense	11171	exon3			CTGGCTCATAAAC	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.295C>T	12.37:g.16042908C>T	ENSP00000392270:p.His99Tyr	309	0	0		325	45	0.138462	NM_007178	B2R5S5|B4DNJ6|Q5TZT4|Q9NTK0|Q9UQC8	Missense_Mutation	SNP	ENST00000419869.2	37	CCDS8676.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.221170	0.79464	.	.	ENSG00000023734	ENST00000538352;ENST00000025399;ENST00000419869	T;T;T	0.81415	-1.49;-1.49;-1.49	4.69	3.78	0.43462	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.047356	0.85682	D	0.000000	D	0.91429	0.7295	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	0.93213	0.6602	10	0.87932	D	0	-16.9887	14.0735	0.64874	0.1519:0.8481:0.0:0.0	.	112;99	B4DNJ6;Q9Y3F4	.;STRAP_HUMAN	Y	5;112;99	ENSP00000439761:H5Y;ENSP00000025399:H112Y;ENSP00000392270:H99Y	ENSP00000025399:H112Y	H	+	1	0	STRAP	15934175	1.000000	0.71417	0.965000	0.40720	0.996000	0.88848	5.453000	0.66645	1.143000	0.42306	0.655000	0.94253	CAT	.	.	none		0.338	STRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401114.1	NM_007178		T	16042908	C	T	16042908	3	4	23	1	0	0	0	0	1	0	0	0	15341	826	29	2	305	2	STRAP	12	16042908	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	5084012	16042908	117808987	461	7905											
DERA	51071	hgsc.bcm.edu	37	chr12	16189279	16189279	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagccagaactctttcgaatAggtgccagtactctgctctc	10	11	8	12	1	3	1	0	0	3	1	5	2	3	1	2	1	5	2	2	1	5	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:16189279A>G	ENST00000428559.2	+	8	1076	c.864A>G	c.(862-864)atA>atG	p.I288M	DERA_ENST00000526530.1_Missense_Mutation_p.I200M|DERA_ENST00000532964.1_Missense_Mutation_p.I245M	NM_015954.2	NP_057038.2	Q9Y315	DEOC_HUMAN	deoxyribose-phosphate aldolase (putative)	288					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)				TCTTTCGAATAGGTGCCAGTA	0.458																																					p.I288M		Atlas-SNP	.											.	DERA	20	.	0			c.A864G						PASS	.						101	99	99					12																	16189279		1867	4110	5977	SO:0001583	missense	51071	exon8			TCGAATAGGTGCC	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.864A>G	12.37:g.16189279A>G	ENSP00000416583:p.Ile288Met	88	0	0		77	33	0.428571	NM_015954	Q53HN9|Q6PHW2	Missense_Mutation	SNP	ENST00000428559.2	37	CCDS44838.1	.	.	.	.	.	.	.	.	.	.	A	16.36	3.102495	0.56183	.	.	ENSG00000023697	ENST00000428559;ENST00000532964;ENST00000526530	.	.	.	5.57	-0.0832	0.13695	Aldolase-type TIM barrel (1);	0.155772	0.56097	D	0.000032	T	0.67040	0.2851	M	0.91249	3.19	0.47407	D	0.99941	P	0.52577	0.954	P	0.52957	0.714	T	0.64685	-0.6349	9	0.72032	D	0.01	-25.8467	3.2921	0.06953	0.2024:0.4745:0.0912:0.2318	.	288	Q9Y315	DEOC_HUMAN	M	288;245;200	.	ENSP00000416583:I288M	I	+	3	3	DERA	16080546	0.982000	0.34865	0.979000	0.43373	0.913000	0.54294	0.125000	0.15749	0.039000	0.15632	-0.327000	0.08410	ATA	.	.	none		0.458	DERA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384731.1	NM_015954		G	16189279	A	G	16189279	3	3	23	1	0	0	0	0	1	0	0	0	4447	410	15	3	894	3	DERA	12	16189279	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	146371	16189279	117662616	462	7906											
CAPZA3	93661	hgsc.bcm.edu	37	chr12	18891318	18891318	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatctctgtctgcttatccGtgatgaaaaacttatgcacc	10	14	7	10	1	2	3	0	3	2	0	4	3	3	3	2	0	3	2	2	0	4	2	rs117330813	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:18891318G>A	ENST00000317658.3	+	1	274	c.116G>A	c.(115-117)cGt>cAt	p.R39H	PLCZ1_ENST00000266505.7_5'Flank|PLCZ1_ENST00000435379.1_5'Flank|PLCZ1_ENST00000447925.2_5'Flank|RP11-361I14.2_ENST00000536931.1_RNA|PLCZ1_ENST00000539875.1_5'Flank	NM_033328.2	NP_201585.1	Q96KX2	CAZA3_HUMAN	capping protein (actin filament) muscle Z-line, alpha 3	39					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cortical cytoskeleton (GO:0030863)|F-actin capping protein complex (GO:0008290)|membrane (GO:0016020)|nucleus (GO:0005634)|WASH complex (GO:0071203)		p.R39H(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|prostate(1)	19	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)	Hepatocellular(102;0.194)				CTGCTTATCCGTGATGAAAAA	0.458													G|||	11	0.00219649	0.0	0.0029	5008	,	,		19990	0.001		0.007	False		,,,				2504	0.001				p.R39H		Atlas-SNP	.											CAPZA3,NS,carcinoma,0,1	CAPZA3	51	1	1	Substitution - Missense(1)	breast(1)	c.G116A						scavenged	.	G	HIS/ARG	12,4394	19.1+/-41.9	0,12,2191	121	111	115		116	3.8	1	12	dbSNP_132	115	67,8531	41.2+/-98.3	0,67,4232	yes	missense	CAPZA3	NM_033328.2	29	0,79,6423	AA,AG,GG		0.7793,0.2724,0.6075	possibly-damaging	39/300	18891318	79,12925	2203	4299	6502	SO:0001583	missense	93661	exon1			TTATCCGTGATGA	AB053259	CCDS8681.1	12p12.3	2008-02-05			ENSG00000177938	ENSG00000177938			24205	protein-coding gene	gene with protein product		608722				12029070	Standard	NM_033328		Approved	Gsg3, CAPPA3	uc001rdy.3	Q96KX2	OTTHUMG00000169001	ENST00000317658.3:c.116G>A	12.37:g.18891318G>A	ENSP00000326238:p.Arg39His	171	1	0.00584795		181	77	0.425414	NM_033328	Q969J0	Missense_Mutation	SNP	ENST00000317658.3	37	CCDS8681.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	1	0.0017482517482517483	5	0.006596306068601583	G	13.90	2.375049	0.42105	0.002724	0.007793	ENSG00000177938	ENST00000317658	.	.	.	4.8	3.83	0.44106	.	0.346611	0.27415	N	0.019461	T	0.38506	0.1043	L	0.36672	1.1	0.34727	D	0.72938	D	0.60575	0.988	P	0.56916	0.809	T	0.55108	-0.8192	9	0.51188	T	0.08	-1.6784	5.836	0.18607	0.1725:0.0:0.8275:0.0	.	39	Q96KX2	CAZA3_HUMAN	H	39	.	ENSP00000326238:R39H	R	+	2	0	CAPZA3	18782585	0.150000	0.22732	1.000000	0.80357	0.998000	0.95712	1.795000	0.38784	2.498000	0.84270	0.563000	0.77884	CGT	G|0.995;A|0.005	0.005	strong		0.458	CAPZA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401902.1	NM_033328		A	18891318	G	A	18891318	3	1	23	1	0	0	0	0	1	0	0	0	2644	1145	40	1	118	1	CAPZA3	12	18891318	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	2702039	18891318	114960577	463	7907											
SLCO1B1	10599	hgsc.bcm.edu	37	chr12	21331940	21331940	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	taaaatgtacgtggatattgGatatgtagatctaagtaagt	15	14	10	2	1	1	1	0	0	1	1	1	3	1	3	0	2	1	3	0	2	8	8	rs374113543		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:21331940G>A	ENST00000256958.2	+	7	809	c.713G>A	c.(712-714)gGa>gAa	p.G238E		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	238					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)	GTGGATATTGGATATGTAGAT	0.333																																					p.G238E		Atlas-SNP	.											.	SLCO1B1	151	.	0			c.G713A						PASS	.	G	GLU/GLY	0,4406		0,0,2203	105	105	105		713	3.8	1	12		105	1,8593	1.2+/-3.3	0,1,4296	no	missense	SLCO1B1	NM_006446.4	98	0,1,6499	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	238/692	21331940	1,12999	2203	4297	6500	SO:0001583	missense	10599	exon7			ATATTGGATATGT		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.713G>A	12.37:g.21331940G>A	ENSP00000256958:p.Gly238Glu	74	0	0		56	20	0.357143	NM_006446	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Missense_Mutation	SNP	ENST00000256958.2	37	CCDS8685.1	.	.	.	.	.	.	.	.	.	.	G	15.15	2.747048	0.49257	0.0	1.16E-4	ENSG00000134538	ENST00000256958	T	0.71579	-0.58	3.76	3.76	0.43208	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.83751	0.5322	M	0.80028	2.48	0.53005	D	0.999961	D	0.71674	0.998	D	0.75484	0.986	D	0.85519	0.1202	10	0.46703	T	0.11	.	16.1164	0.81306	0.0:0.0:1.0:0.0	.	238	Q9Y6L6	SO1B1_HUMAN	E	238	ENSP00000256958:G238E	ENSP00000256958:G238E	G	+	2	0	SLCO1B1	21223207	1.000000	0.71417	1.000000	0.80357	0.470000	0.32858	7.186000	0.77722	2.096000	0.63516	0.305000	0.20034	GGA	.	.	weak		0.333	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446		A	21331940	G	A	21331940	3	1	23	1	0	0	0	0	1	0	0	0	14738	1174	41	2	735	2	SLCO1B1	12	21331940	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	2440622	21331940	112519955	464	7908											
BICD1	636	hgsc.bcm.edu	37	chr12	32458756	32458756	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caccaactggaagaagccctCgagactttaaaaaatgaaag	18	6	8	9	1	0	3	0	1	0	2	1	5	0	4	2	1	2	0	2	1	7	2	rs11051922	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:32458756C>T	ENST00000281474.5	+	4	808	c.705C>T	c.(703-705)ctC>ctT	p.L235L	BICD1_ENST00000548411.1_Silent_p.L235L	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	235					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)			AAGAAGCCCTCGAGACTTTAA	0.458													C|||	28	0.00559105	0.0008	0.0058	5008	,	,		16322	0.0		0.0189	False		,,,				2504	0.0041				p.L235L		Atlas-SNP	.											.	BICD1	89	.	0			c.C705T						PASS	.	C	,	19,4387	26.2+/-53.5	0,19,2184	63	60	61		705,705	-8.6	0	12	dbSNP_120	61	204,8396	87.9+/-150.2	5,194,4101	no	coding-synonymous,coding-synonymous	BICD1	NM_001003398.1,NM_001714.2	,	5,213,6285	TT,TC,CC		2.3721,0.4312,1.7146	,	235/836,235/976	32458756	223,12783	2203	4300	6503	SO:0001819	synonymous_variant	636	exon4			AGCCCTCGAGACT	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.705C>T	12.37:g.32458756C>T		69	0	0		52	28	0.538462	NM_001714	A8K2C3|F8W113|O43892|O43893	Silent	SNP	ENST00000281474.5	37	CCDS8726.1																																																																																			C|0.988;T|0.012	0.012	strong		0.458	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714		T	32458756	C	T	32458756	2	4	23	1	0	0	0	0	0	0	0	1	1428	871	31	1		1	BICD1	12	32458756	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	11126816	32458756	101393139	465	7909											
BICD1	636	hgsc.bcm.edu	37	chr12	32480886	32480886	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atagccaacgaaaatcacagTacccttaatacggcccagga	16	6	7	12	2	1	0	1	0	0	0	1	2	1	1	3	2	4	1	3	2	7	4	rs12369637	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:32480886T>C	ENST00000281474.5	+	5	1600	c.1497T>C	c.(1495-1497)agT>agC	p.S499S	BICD1_ENST00000548411.1_Silent_p.S499S	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	499					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)			AAAATCACAGTACCCTTAATA	0.468													T|||	27	0.00539137	0.0008	0.0058	5008	,	,		20862	0.0		0.0189	False		,,,				2504	0.0031				p.S499S		Atlas-SNP	.											.	BICD1	89	.	0			c.T1497C						PASS	.	T	,	21,4385	28.1+/-56.4	0,21,2182	143	119	127		1497,1497	-1.3	1	12	dbSNP_120	127	208,8392	89.2+/-151.4	5,198,4097	no	coding-synonymous,coding-synonymous	BICD1	NM_001003398.1,NM_001714.2	,	5,219,6279	CC,CT,TT		2.4186,0.4766,1.7607	,	499/836,499/976	32480886	229,12777	2203	4300	6503	SO:0001819	synonymous_variant	636	exon5			TCACAGTACCCTT	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.1497T>C	12.37:g.32480886T>C		165	0	0		174	69	0.396552	NM_001714	A8K2C3|F8W113|O43892|O43893	Silent	SNP	ENST00000281474.5	37	CCDS8726.1																																																																																			T|0.987;C|0.013	0.013	strong		0.468	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714		C	32480886	T	C	32480886	2	2	23	1	0	0	0	0	0	0	0	1	1428	1635	57	3		3	BICD1	12	32480886	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	22130	32480886	101371009	466	7910											
CNTN1	1272	hgsc.bcm.edu	37	chr12	41312471	41312471	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agacaaaggatttggaccaaTttttgaagagcagccaatca	16	9	9	7	0	1	3	1	1	0	2	1	5	1	5	2	2	2	1	2	2	4	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:41312471T>C	ENST00000551295.2	+	4	242	c.125T>C	c.(124-126)aTt>aCt	p.I42T	CNTN1_ENST00000547702.1_Missense_Mutation_p.I42T|CNTN1_ENST00000360099.3_Missense_Mutation_p.I42T|CNTN1_ENST00000547849.1_Missense_Mutation_p.I42T|CNTN1_ENST00000348761.2_Missense_Mutation_p.I31T|CNTN1_ENST00000347616.1_Missense_Mutation_p.I42T	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	42	Ig-like C2-type 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)				TTTGGACCAATTTTTGAAGAG	0.378																																					p.I42T		Atlas-SNP	.											.	CNTN1	207	.	0			c.T125C						PASS	.						73	79	77					12																	41312471		2203	4300	6503	SO:0001583	missense	1272	exon4			GACCAATTTTTGA	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.125T>C	12.37:g.41312471T>C	ENSP00000447006:p.Ile42Thr	184	0	0		205	34	0.165854	NM_001256063	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Missense_Mutation	SNP	ENST00000551295.2	37	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.707931	0.89018	.	.	ENSG00000018236	ENST00000547702;ENST00000551424;ENST00000551295;ENST00000548005;ENST00000552248;ENST00000547849;ENST00000552913;ENST00000347616;ENST00000360099;ENST00000348761	T;T;T;T;T;T;T;T	0.65178	-0.14;0.25;1.05;1.05;-0.14;0.25;-0.14;0.18	5.36	5.36	0.76844	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.059649	0.64402	D	0.000003	T	0.63331	0.2502	N	0.25957	0.775	0.41091	D	0.985594	P;P;P	0.50156	0.9;0.917;0.932	B;P;P	0.57009	0.39;0.637;0.811	T	0.60576	-0.7236	10	0.25106	T	0.35	.	15.6713	0.77279	0.0:0.0:0.0:1.0	.	42;31;42	Q12860-3;Q12860-2;Q12860	.;.;CNTN1_HUMAN	T	42;42;42;42;42;42;42;42;42;31	ENSP00000448004:I42T;ENSP00000447006:I42T;ENSP00000447862:I42T;ENSP00000447860:I42T;ENSP00000448653:I42T;ENSP00000325660:I42T;ENSP00000353213:I42T;ENSP00000261160:I31T	ENSP00000325660:I42T	I	+	2	0	CNTN1	39598738	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.314000	0.78988	2.167000	0.68274	0.477000	0.44152	ATT	.	.	none		0.378	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843		C	41312471	T	C	41312471	3	2	23	1	0	0	0	0	1	0	0	0	3642	1493	52	3	135	3	CNTN1	12	41312471	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	8831585	41312471	92539424	467	7911											
PDZRN4	29951	hgsc.bcm.edu	37	chr12	41966771	41966771	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcatggagcatccagaaaaGtctgacaaggacagttctag	15	8	10	8	0	3	2	1	1	2	1	4	4	4	4	1	2	1	2	1	2	4	2	rs113916113	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:41966771G>A	ENST00000402685.2	+	10	2198	c.2190G>A	c.(2188-2190)aaG>aaA	p.K730K	PDZRN4_ENST00000298919.7_Silent_p.K470K|PDZRN4_ENST00000539469.2_Silent_p.K472K	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	730							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)				ATCCAGAAAAGTCTGACAAGG	0.478													G|||	14	0.00279553	0.0008	0.0029	5008	,	,		22463	0.0		0.008	False		,,,				2504	0.0031				p.K730K		Atlas-SNP	.											.	PDZRN4	346	.	0			c.G2190A						PASS	.	G	,	11,4395	17.9+/-39.9	0,11,2192	114	116	115		2190,1416	3.1	1	12	dbSNP_132	115	98,8502	54.4+/-115.2	1,96,4203	no	coding-synonymous,coding-synonymous	PDZRN4	NM_001164595.1,NM_013377.3	,	1,107,6395	AA,AG,GG		1.1395,0.2497,0.8381	,	730/1037,472/779	41966771	109,12897	2203	4300	6503	SO:0001819	synonymous_variant	29951	exon10			AGAAAAGTCTGAC	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.2190G>A	12.37:g.41966771G>A		49	0	0		68	41	0.602941	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Silent	SNP	ENST00000402685.2	37	CCDS53777.1																																																																																			G|0.992;A|0.008	0.008	strong		0.478	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377		A	41966771	G	A	41966771	2	1	23	1	0	0	0	0	0	0	0	1	11719	1020	36	2		2	PDZRN4	12	41966771	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	654300	41966771	91885124	468	7912											
PPHLN1	51535	hgsc.bcm.edu	37	chr12	42840082	42840082	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctctctgttgtacattgcaActcacgcaaggtattggtcc	8	13	9	11	1	2	0	1	0	1	0	4	0	3	0	1	2	3	6	1	2	4	5	rs149559306	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:42840082A>C	ENST00000395568.2	+	12	1424	c.1340A>C	c.(1339-1341)aAc>aCc	p.N447T	PPHLN1_ENST00000317560.9_Intron|PPHLN1_ENST00000256678.8_Missense_Mutation_p.N352T|PPHLN1_ENST00000432191.2_Missense_Mutation_p.N423T	NM_016488.6	NP_057572.5	Q8NEY8	PPHLN_HUMAN	periphilin 1	447					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)		gtacattgcaactcacgcaag	0.433													A|||	11	0.00219649	0.0	0.0043	5008	,	,		17538	0.0		0.008	False		,,,				2504	0.0				p.N447T		Atlas-SNP	.											.	PPHLN1	101	.	0			c.A1340C						PASS	.	A	THR/ASN,THR/ASN	9,4163		0,9,2077	32	34	33		1268,1340	0.2	0.1	12	dbSNP_134	33	69,8029		0,69,3980	yes	missense,missense	PPHLN1	NM_001143787.1,NM_016488.6	65,65	0,78,6057	CC,CA,AA		0.8521,0.2157,0.6357	possibly-damaging,possibly-damaging	423/435,447/459	42840082	78,12192	2086	4049	6135	SO:0001583	missense	51535	exon12			ATTGCAACTCACG	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.1340A>C	12.37:g.42840082A>C	ENSP00000378935:p.Asn447Thr	14	0	0		18	6	0.333333	NM_016488	E9PAX8|Q86YT2|Q8IXN3|Q8TB09|Q96NB9|Q9NXL4|Q9P0P6|Q9P0R9	Missense_Mutation	SNP	ENST00000395568.2	37	CCDS31777.1	9	0.004120879120879121	0	0.0	3	0.008287292817679558	0	0.0	6	0.0079155672823219	A	7.021	0.558783	0.13436	0.002157	0.008521	ENSG00000134283	ENST00000395568;ENST00000256678;ENST00000432191	.	.	.	0.158	0.158	0.14942	.	.	.	.	.	T	0.23492	0.0568	N	0.22421	0.69	0.09310	N	1	P;P;P;P	0.42039	0.769;0.659;0.769;0.659	P;B;P;B	0.49332	0.607;0.403;0.607;0.403	T	0.18398	-1.0338	7	0.87932	D	0	.	.	.	.	.	352;398;423;447	F8W6A0;B7Z695;Q8NEY8-3;Q8NEY8	.;.;.;PPHLN_HUMAN	T	447;352;423	.	ENSP00000256678:N352T	N	+	2	0	PPHLN1	41126349	0.169000	0.23002	0.075000	0.20258	0.076000	0.17211	0.241000	0.18065	0.175000	0.19841	0.172000	0.16884	AAC	A|0.992;C|0.008	0.008	strong		0.433	PPHLN1-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404047.1	NM_201515		C	42840082	A	C	42840082	3	2	23	1	0	0	0	0	1	0	0	0	12324	43	2	5	1592	5	PPHLN1	12	42840082	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	873311	42840082	91011813	469	7913											
DDN	23109	hgsc.bcm.edu	37	chr12	49391682	49391682	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatggctgtcgctaccactgTtcaggtcagcagcagccagc	8	8	12	13	1	2	0	2	0	0	0	3	1	2	0	2	2	5	5	2	2	1	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:49391682T>C	ENST00000421952.2	-	2	998	c.977A>G	c.(976-978)aAc>aGc	p.N326S	RP11-386G11.5_ENST00000552284.1_RNA|RP11-386G11.5_ENST00000547395.1_RNA|RP11-386G11.5_ENST00000552933.1_RNA|RP11-386G11.3_ENST00000549516.1_RNA|RP11-386G11.5_ENST00000547866.1_RNA	NM_015086.1	NP_055901.2	O94850	DEND_HUMAN	dendrin	326						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						GCTACCACTGTTCAGGTCAGC	0.662																																					p.N326S		Atlas-SNP	.											.	DDN	54	.	0			c.A977G						PASS	.						45	53	50					12																	49391682		2203	4298	6501	SO:0001583	missense	23109	exon2			CCACTGTTCAGGT	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.977A>G	12.37:g.49391682T>C	ENSP00000390590:p.Asn326Ser	72	0	0		72	36	0.5	NM_015086		Missense_Mutation	SNP	ENST00000421952.2	37	CCDS31791.2	.	.	.	.	.	.	.	.	.	.	T	9.110	1.006312	0.19199	.	.	ENSG00000181418	ENST00000421952	T	0.47528	0.84	3.88	0.238	0.15480	.	0.712920	0.12723	N	0.444514	T	0.24044	0.0582	N	0.12182	0.205	0.09310	N	1	B	0.16396	0.017	B	0.10450	0.005	T	0.21415	-1.0246	10	0.18710	T	0.47	-24.1145	6.6688	0.23056	0.0:0.3358:0.0:0.6642	.	326	O94850	DEND_HUMAN	S	326	ENSP00000390590:N326S	ENSP00000390590:N326S	N	-	2	0	DDN	47677949	0.000000	0.05858	0.001000	0.08648	0.629000	0.37895	0.452000	0.21795	0.039000	0.15632	0.459000	0.35465	AAC	.	.	none		0.662	DDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343335.1			C	49391682	T	C	49391682	3	2	23	1	0	0	0	0	1	0	0	0	4335	1725	60	3	1162	3	DDN	12	49391682	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	6551600	49391682	84460213	470	7914											
MLL2	8085	hgsc.bcm.edu	37	chr12	49439900	49439900	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acacagtcaaagccttcatcGgctgcctgctccacatcgtc	9	9	7	16	2	2	0	2	0	0	0	6	0	3	0	3	1	3	2	3	1	1	1	rs377048725		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:49439900G>A	ENST00000301067.7	-	17	4640	c.4641C>T	c.(4639-4641)gcC>gcT	p.A1547A		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1547				EQAA -> DHAP (in Ref. 1; AAC51734/ AAC51735). {ECO:0000305}.	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)										AGCCTTCATCGGCTGCCTGCT	0.577																																					p.A1547A		Atlas-SNP	.											.	MLL2	1173	.	0			c.C4641T						PASS	.	G		1,4203		0,1,2101	39	47	44		4641	-10.7	0.2	12		44	1,8433		0,1,4216	no	coding-synonymous	MLL2	NM_003482.3		0,2,6317	AA,AG,GG		0.0119,0.0238,0.0158		1547/5538	49439900	2,12636	2102	4217	6319	SO:0001819	synonymous_variant	8085	exon17			TTCATCGGCTGCC	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.4641C>T	12.37:g.49439900G>A		151	0	0		175	83	0.474286	NM_003482	O14687	Silent	SNP	ENST00000301067.7	37	CCDS44873.1																																																																																			.	.	weak		0.577	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49439900	G	A	49439900	2	1	23	1	0	0	0	0	0	0	0	1	9630	1103	39	1		1	MLL2	12	49439900	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	48218	49439900	84411995	471	7915											
LIMA1	51474	hgsc.bcm.edu	37	chr12	50571221	50571221	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaagccttggcattttccaCttgtttcctttctgcaactc	7	16	6	12	0	1	1	0	0	1	1	4	1	3	1	3	1	3	3	3	1	2	6			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:50571221C>T	ENST00000341247.4	-	11	2055	c.1906G>A	c.(1906-1908)Gtg>Atg	p.V636M	LIMA1_ENST00000552823.1_Missense_Mutation_p.V476M|LIMA1_ENST00000547825.1_Missense_Mutation_p.V334M|LIMA1_ENST00000394943.3_Missense_Mutation_p.V637M|LIMA1_ENST00000552491.1_Missense_Mutation_p.V333M|LIMA1_ENST00000552909.1_Missense_Mutation_p.V475M|LIMA1_ENST00000552783.1_Missense_Mutation_p.V477M	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	636					actin filament bundle assembly (GO:0051017)|negative regulation of actin filament depolymerization (GO:0030835)|ruffle organization (GO:0031529)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(2)	44						GCATTTTCCACTTGTTTCCTT	0.463																																					p.V637M		Atlas-SNP	.											.	LIMA1	67	.	0			c.G1909A						PASS	.						284	292	289					12																	50571221		2203	4300	6503	SO:0001583	missense	51474	exon11			TTTCCACTTGTTT	AF198454	CCDS8802.1, CCDS44877.1, CCDS55826.1, CCDS58230.1	12q13.12	2006-04-12				ENSG00000050405			24636	protein-coding gene	gene with protein product	"epithelial protein lost in neoplasm beta"	608364				10806352, 10618726, 12566430	Standard	NM_016357		Approved	EPLIN	uc001rwk.4	Q9UHB6		ENST00000341247.4:c.1906G>A	12.37:g.50571221C>T	ENSP00000340184:p.Val636Met	269	0	0		277	125	0.451264	NM_001113546	B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Missense_Mutation	SNP	ENST00000341247.4	37	CCDS8802.1	.	.	.	.	.	.	.	.	.	.	C	6.055	0.378474	0.11466	.	.	ENSG00000050405	ENST00000552491;ENST00000547825;ENST00000552823;ENST00000394943;ENST00000341247;ENST00000552783;ENST00000552909;ENST00000420992	T;T;T;D;T;T;T	0.84146	-1.07;-1.07;-1.39;-1.81;-1.07;-1.39;-1.39	5.31	1.23	0.21249	.	0.834586	0.11054	N	0.604718	T	0.65312	0.2679	N	0.03115	-0.41	0.09310	N	1	B;B;B	0.14438	0.01;0.01;0.007	B;B;B	0.15052	0.002;0.002;0.012	T	0.52305	-0.8593	10	0.22109	T	0.4	.	7.9273	0.29883	0.0:0.4745:0.0:0.5255	.	646;636;475	Q59FE8;Q9UHB6;F8VQE1	.;LIMA1_HUMAN;.	M	333;334;476;637;636;477;475;555	ENSP00000448463:V333M;ENSP00000448706:V334M;ENSP00000450266:V476M;ENSP00000378400:V637M;ENSP00000340184:V636M;ENSP00000448779:V477M;ENSP00000450087:V475M	ENSP00000340184:V636M	V	-	1	0	LIMA1	48857488	0.000000	0.05858	0.036000	0.18154	0.640000	0.38277	0.484000	0.22308	0.399000	0.25367	0.650000	0.86243	GTG	.	.	none		0.463	LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357		T	50571221	C	T	50571221	3	4	23	1	0	0	0	0	1	0	0	0	8805	565	20	2	377	2	LIMA1	12	50571221	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1131321	50571221	83280674	472	7916											
SLC4A8	9498	hgsc.bcm.edu	37	chr12	51856159	51856159	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ctggcggggattgatgagttCctagaccaggtgacggtgct	7	10	16	8	2	0	4	0	3	0	1	1	5	1	5	2	5	1	2	2	5	1	3	rs71449805	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:51856159C>T	ENST00000453097.2	+	10	1384	c.1167C>T	c.(1165-1167)ttC>ttT	p.F389F	SLC4A8_ENST00000514353.3_Silent_p.F336F|SLC4A8_ENST00000535225.2_Silent_p.F336F|SLC4A8_ENST00000394856.1_Silent_p.F336F|SLC4A8_ENST00000358657.3_Silent_p.F416F	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)		TTGATGAGTTCCTAGACCAGG	0.473													C|||	48	0.00958466	0.0015	0.0187	5008	,	,		18122	0.0		0.0278	False		,,,				2504	0.0051				p.F389F		Atlas-SNP	.											.	SLC4A8	292	.	0			c.C1167T						PASS	.	C	,	36,4370	41.6+/-74.8	0,36,2167	123	118	120		1167,1167	4.3	1	12	dbSNP_130	120	351,8249	118.5+/-177.9	5,341,3954	no	coding-synonymous,coding-synonymous	SLC4A8	NM_001039960.1,NM_004858.2	,	5,377,6121	TT,TC,CC		4.0814,0.8171,2.9755	,	389/1094,389/1045	51856159	387,12619	2203	4300	6503	SO:0001819	synonymous_variant	9498	exon10			TGAGTTCCTAGAC	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.1167C>T	12.37:g.51856159C>T		104	0	0		130	61	0.469231	NM_001039960		Silent	SNP	ENST00000453097.2	37	CCDS44890.1																																																																																			C|0.974;T|0.026	0.026	strong		0.473	SLC4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404356.1	NM_004858		T	51856159	C	T	51856159	2	4	23	1	0	0	0	0	0	0	0	1	14674	854	30	2		2	SLC4A8	12	51856159	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1284938	51856159	81995736	473	7917											
KRT74	121391	hgsc.bcm.edu	37	chr12	52966368	52966368	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcaaggatgggctccaggttCttcttgcagttgttcaggtc	6	14	12	9	0	4	0	2	0	2	0	6	1	5	1	1	4	1	5	1	4	1	5	rs78832381	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52966368C>T	ENST00000305620.2	-	2	602	c.555G>A	c.(553-555)aaG>aaA	p.K185K	KRT74_ENST00000549343.1_Silent_p.K185K	NM_175053.3	NP_778223.2	Q7RTS7	K2C74_HUMAN	keratin 74	185	Linker 1.|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)		GCTCCAGGTTCTTCTTGCAGT	0.562													C|||	79	0.0157748	0.003	0.0389	5008	,	,		20869	0.0		0.0398	False		,,,				2504	0.0082				p.K185K		Atlas-SNP	.											.	KRT74	67	.	0			c.G555A						PASS	.	C		42,4364	46.0+/-80.4	1,40,2162	151	139	143		555	-3.5	0.8	12	dbSNP_132	143	310,8290	111.4+/-171.7	7,296,3997	no	coding-synonymous	KRT74	NM_175053.3		8,336,6159	TT,TC,CC		3.6047,0.9532,2.7064		185/530	52966368	352,12654	2203	4300	6503	SO:0001819	synonymous_variant	121391	exon2			CAGGTTCTTCTTG	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.555G>A	12.37:g.52966368C>T		224	0	0		270	116	0.42963	NM_175053	B5MD61|Q86Y45	Silent	SNP	ENST00000305620.2	37	CCDS8832.1																																																																																			C|0.974;T|0.026	0.026	strong		0.562	KRT74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405324.1	NM_175053		T	52966368	C	T	52966368	2	4	23	1	0	0	0	0	0	0	0	1	8496	912	32	2		2	KRT74	12	52966368	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1110209	52966368	80885527	474	7918											
KRT1	3848	hgsc.bcm.edu	37	chr12	53070174	53070174	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gcgggccaggtcttccttggCctgctgcagggcatcctcca	4	9	13	15	1	1	0	0	0	1	0	4	0	4	0	5	4	2	3	5	4	0	2	rs17678945	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:53070174C>A	ENST00000252244.3	-	7	1418	c.1360G>T	c.(1360-1362)Gcc>Tcc	p.A454S		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	454	Coil 2.|Rod.		A -> S (in dbSNP:rs17678945).		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						TCTTCCTTGGCCTGCTGCAGG	0.587													c|||	27	0.00539137	0.0	0.0101	5008	,	,		19137	0.0		0.0169	False		,,,				2504	0.0031				p.A454S		Atlas-SNP	.											.	KRT1	110	.	0			c.G1360T						PASS	.	C	SER/ALA	26,4380	31.7+/-61.6	0,26,2177	80	71	74		1360	3.2	1	12	dbSNP_123	74	231,8369	94.5+/-156.4	3,225,4072	no	missense	KRT1	NM_006121.3	99	3,251,6249	AA,AC,CC		2.686,0.5901,1.976	benign	454/645	53070174	257,12749	2203	4300	6503	SO:0001583	missense	3848	exon7			CCTTGGCCTGCTG	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.1360G>T	12.37:g.53070174C>A	ENSP00000252244:p.Ala454Ser	251	0	0		238	121	0.508403	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Missense_Mutation	SNP	ENST00000252244.3	37	CCDS8836.1	20	0.009157509157509158	0	0.0	4	0.011049723756906077	0	0.0	16	0.021108179419525065	c	17.21	3.332241	0.60853	0.005901	0.02686	ENSG00000167768	ENST00000252244	T	0.75589	-0.95	5.03	3.15	0.36227	Prefoldin (1);Filament (1);	.	.	.	.	T	0.62085	0.2399	M	0.73217	2.22	0.25099	N	0.990795	P	0.47350	0.894	D	0.63033	0.91	T	0.62895	-0.6757	9	0.59425	D	0.04	.	3.3536	0.07162	0.1474:0.5686:0.143:0.141	rs17678945;rs17678945	454	P04264	K2C1_HUMAN	S	454	ENSP00000252244:A454S	ENSP00000252244:A454S	A	-	1	0	KRT1	51356441	0.595000	0.26857	0.965000	0.40720	0.684000	0.39900	1.225000	0.32551	1.226000	0.43582	0.462000	0.41574	GCC	C|0.981;A|0.019	0.019	strong		0.587	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121		A	53070174	C	A	53070174	3	1	23	1	0	0	0	0	1	0	0	0	8456	739	26	4	586	4	KRT1	12	53070174	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	103806	53070174	80781721	475	7919											
NEUROD4	58158	hgsc.bcm.edu	37	chr12	55420785	55420785	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tcctcctggagaagcacgagGataaatctcctatttgtgac	11	11	9	10	1	1	2	0	1	1	1	4	5	3	3	3	2	1	1	3	2	4	3	rs151143558	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:55420785G>A	ENST00000242994.3	+	2	940	c.562G>A	c.(562-564)Gat>Aat	p.D188N		NM_021191.2	NP_067014.2	Q9HD90	NDF4_HUMAN	neuronal differentiation 4	188					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						GAAGCACGAGGATAAATCTCC	0.517													G|||	4	0.000798722	0.0	0.0014	5008	,	,		18905	0.0		0.003	False		,,,				2504	0.0				p.D188N		Atlas-SNP	.											.	NEUROD4	87	.	0			c.G562A						PASS	.	G	ASN/ASP	0,4406		0,0,2203	77	81	80		562	5.6	1	12	dbSNP_134	80	39,8561	24.6+/-71.5	0,39,4261	yes	missense	NEUROD4	NM_021191.2	23	0,39,6464	AA,AG,GG		0.4535,0.0,0.2999	benign	188/332	55420785	39,12967	2203	4300	6503	SO:0001583	missense	58158	exon2			CACGAGGATAAAT	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.562G>A	12.37:g.55420785G>A	ENSP00000242994:p.Asp188Asn	51	0	0		56	30	0.535714	NM_021191	B2RAC9	Missense_Mutation	SNP	ENST00000242994.3	37	CCDS8886.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	20.4	3.977793	0.74360	0.0	0.004535	ENSG00000123307	ENST00000242994	T	0.65178	-0.14	5.56	5.56	0.83823	Neurogenic differentiation factor, domain of unknown function (1);	0.214698	0.47455	D	0.000236	T	0.67739	0.2925	L	0.41492	1.28	0.37808	D	0.927932	B	0.24317	0.101	B	0.43809	0.432	T	0.70414	-0.4878	10	0.72032	D	0.01	-37.9711	17.4011	0.87459	0.0:0.0:1.0:0.0	.	188	Q9HD90	NDF4_HUMAN	N	188	ENSP00000242994:D188N	ENSP00000242994:D188N	D	+	1	0	NEUROD4	53707052	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	6.774000	0.75012	2.774000	0.95407	0.655000	0.94253	GAT	G|0.997;A|0.003	0.003	strong		0.517	NEUROD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406104.1			A	55420785	G	A	55420785	3	1	23	1	0	0	0	0	1	0	0	0	10359	1174	41	2	564	2	NEUROD4	12	55420785	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	2350611	55420785	78431110	476	7920											
OR10P1	121130	hgsc.bcm.edu	37	chr12	56031318	56031318	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttatgatccccttctctctgAttgtcacctcttacatccgc	6	16	4	15	1	4	2	1	2	3	0	7	2	6	2	4	0	1	0	4	0	2	4	rs76940436	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:56031318A>T	ENST00000309675.2	+	1	675	c.643A>T	c.(643-645)Att>Ttt	p.I215F	RP11-644F5.16_ENST00000556606.1_RNA	NM_206899.1	NP_996782.1	Q8NGE3	O10P1_HUMAN	olfactory receptor, family 10, subfamily P, member 1	215						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						CTTCTCTCTGATTGTCACCTC	0.567													A|||	53	0.0105831	0.0386	0.0029	5008	,	,		18931	0.0		0.0	False		,,,				2504	0.0				p.I215F		Atlas-SNP	.											.	OR10P1	48	.	0			c.A643T						PASS	.	A	PHE/ILE	209,4197	130.2+/-166.9	3,203,1997	133	112	119		643	4.4	0.2	12	dbSNP_131	119	3,8597	2.2+/-6.3	0,3,4297	yes	missense	OR10P1	NM_206899.1	21	3,206,6294	TT,TA,AA		0.0349,4.7435,1.63	probably-damaging	215/314	56031318	212,12794	2203	4300	6503	SO:0001583	missense	121130	exon1			TCTCTGATTGTCA	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.643A>T	12.37:g.56031318A>T	ENSP00000308082:p.Ile215Phe	91	0	0		103	52	0.504854	NM_206899	B9EGY4	Missense_Mutation	SNP	ENST00000309675.2	37	CCDS31828.1	19	0.0086996336996337	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	A	12.41	1.929041	0.34002	0.047435	3.49E-4	ENSG00000175398	ENST00000309675	T	0.00333	8.07	4.44	4.44	0.53790	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000194	T	0.00241	0.0007	H	0.97564	4.03	0.37082	D	0.899042	D	0.76494	0.999	D	0.75484	0.986	T	0.08452	-1.0721	10	0.87932	D	0	.	6.7619	0.23546	0.8955:0.0:0.1045:0.0	.	215	Q8NGE3	O10P1_HUMAN	F	215	ENSP00000308082:I215F	ENSP00000308082:I215F	I	+	1	0	OR10P1	54317585	0.728000	0.28080	0.178000	0.23040	0.033000	0.12548	2.073000	0.41519	1.999000	0.58509	0.459000	0.35465	ATT	A|0.985;T|0.015	0.015	strong		0.567	OR10P1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406680.1			T	56031318	A	T	56031318	3	4	23	1	0	0	0	0	1	0	0	0	10924	333	12	5	645	5	OR10P1	12	56031318	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	610533	56031318	77820577	477	7921											
SUOX	6821	hgsc.bcm.edu	37	chr12	56397802	56397802	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gacagaaaactacatcacacCcaaccctatcttcttcaccc	14	8	2	17	0	4	1	2	0	2	1	4	2	4	1	3	0	3	0	3	0	5	4	rs141735896	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:56397802C>T	ENST00000394109.3	+	3	1353	c.629C>T	c.(628-630)cCc>cTc	p.P210L	SUOX_ENST00000551841.2_Intron|SUOX_ENST00000356124.4_Missense_Mutation_p.P210L|SUOX_ENST00000266971.3_Missense_Mutation_p.P210L|SUOX_ENST00000394115.2_Missense_Mutation_p.P210L|SUOX_ENST00000548274.1_Missense_Mutation_p.P210L			P51687	SUOX_HUMAN	sulfite oxidase	210	Moco domain. {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)			TACATCACACCCAACCCTATC	0.552													C|||	9	0.00179712	0.0	0.0101	5008	,	,		20235	0.0		0.002	False		,,,				2504	0.0				p.P210L		Atlas-SNP	.											.	SUOX	33	.	0			c.C629T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO	5,4401	9.9+/-24.2	0,5,2198	114	106	109		629,629,629	5.1	1	12	dbSNP_134	109	31,8569	21.6+/-65.8	0,31,4269	yes	missense,missense,missense	SUOX	NM_000456.2,NM_001032386.1,NM_001032387.1	98,98,98	0,36,6467	TT,TC,CC		0.3605,0.1135,0.2768	probably-damaging,probably-damaging,probably-damaging	210/546,210/546,210/546	56397802	36,12970	2203	4300	6503	SO:0001583	missense	6821	exon6			TCACACCCAACCC	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.629C>T	12.37:g.56397802C>T	ENSP00000377668:p.Pro210Leu	263	0	0		270	131	0.485185	NM_000456		Missense_Mutation	SNP	ENST00000394109.3	37	CCDS8901.2	9	0.004120879120879121	0	0.0	6	0.016574585635359115	0	0.0	3	0.00395778364116095	C	23.2	4.384135	0.82792	0.001135	0.003605	ENSG00000139531	ENST00000356124;ENST00000266971;ENST00000394115;ENST00000548274;ENST00000394109	D;D;D;D;D	0.96041	-3.89;-3.89;-3.89;-3.89;-3.89	5.12	5.12	0.69794	Oxidoreductase, molybdopterin-binding domain (2);	0.000000	0.85682	D	0.000000	D	0.96185	0.8756	M	0.92317	3.295	0.80722	D	1	D	0.63880	0.993	P	0.60117	0.869	D	0.94083	0.7346	10	0.72032	D	0.01	-26.2213	17.8714	0.88812	0.0:1.0:0.0:0.0	.	210	P51687	SUOX_HUMAN	L	210	ENSP00000348440:P210L;ENSP00000266971:P210L;ENSP00000377674:P210L;ENSP00000450245:P210L;ENSP00000377668:P210L	ENSP00000266971:P210L	P	+	2	0	SUOX	54684069	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	6.994000	0.76251	2.837000	0.97791	0.591000	0.81541	CCC	C|0.997;T|0.003	0.003	strong		0.552	SUOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250309.1	NM_000456		T	56397802	C	T	56397802	3	4	23	1	0	0	0	0	1	0	0	0	15410	623	22	2	639	2	SUOX	12	56397802	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	366484	56397802	77454093	478	7922											
SMARCC2	6601	hgsc.bcm.edu	37	chr12	56558483	56558483	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgcccctggcatcattgaggGaggagtttgttggttgggga	6	12	17	6	0	1	1	1	1	0	0	1	4	1	4	2	6	1	4	2	6	0	4	rs76701112	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:56558483G>A	ENST00000267064.4	-	27	3258	c.3172C>T	c.(3172-3174)Ccc>Tcc	p.P1058S	SMARCC2_ENST00000347471.4_Missense_Mutation_p.P1089S|RP11-977G19.5_ENST00000553176.1_RNA|SMARCC2_ENST00000550164.1_Missense_Mutation_p.P1089S|SMARCC2_ENST00000394023.3_Missense_Mutation_p.P1089S	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	1058	Pro-rich.				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)			ATCATTGAGGGAGGAGTTTGT	0.522													G|||	26	0.00519169	0.0159	0.0072	5008	,	,		17586	0.0		0.0	False		,,,				2504	0.0				p.P1089S		Atlas-SNP	.											SMARCC2_ENST00000267064,NS,carcinoma,+1,2	SMARCC2	212	2	0			c.C3265T						PASS	.	G	SER/PRO,SER/PRO,SER/PRO	33,4373	36.8+/-68.6	1,31,2171	30	29	30		3265,3172,3265	4.7	1	12	dbSNP_131	30	6,8594	3.0+/-9.4	0,6,4294	yes	missense,missense,missense	SMARCC2	NM_139067.2,NM_003075.3,NM_001130420.1	74,74,74	1,37,6465	AA,AG,GG		0.0698,0.749,0.2999	benign,benign,benign	1089/1131,1058/1215,1089/1153	56558483	39,12967	2203	4300	6503	SO:0001583	missense	6601	exon28			TTGAGGGAGGAGT	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.3172C>T	12.37:g.56558483G>A	ENSP00000267064:p.Pro1058Ser	101	0	0		102	42	0.411765	NM_139067	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Missense_Mutation	SNP	ENST00000267064.4	37	CCDS8907.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	G	10.44	1.350723	0.24512	0.00749	6.98E-4	ENSG00000139613	ENST00000394023;ENST00000550164;ENST00000347471;ENST00000267064	T;T;T;T	0.55760	1.08;0.57;0.5;0.61	4.67	4.67	0.58626	.	0.000000	0.45126	D	0.000388	T	0.14787	0.0357	N	0.08118	0	0.41798	D	0.989902	B;B;B;B;B	0.06786	0.0;0.001;0.001;0.001;0.001	B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.001	T	0.08973	-1.0696	10	0.27082	T	0.32	-10.7152	6.6581	0.22998	0.0933:0.0:0.7261:0.1806	.	978;1089;1093;1058;1089	B4DF22;F8VTJ5;Q59G16;Q8TAQ2;Q8TAQ2-2	.;.;.;SMRC2_HUMAN;.	S	1089;1089;1089;1058	ENSP00000377591:P1089S;ENSP00000449396:P1089S;ENSP00000302919:P1089S;ENSP00000267064:P1058S	ENSP00000267064:P1058S	P	-	1	0	SMARCC2	54844750	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.937000	0.40193	2.528000	0.85240	0.557000	0.71058	CCC	G|0.995;A|0.005	0.005	strong		0.522	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1			A	56558483	G	A	56558483	3	1	23	1	0	0	0	0	1	0	0	0	14791	1174	41	2	480	2	SMARCC2	12	56558483	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	160681	56558483	77293412	479	7923											
SMARCC2	6601	hgsc.bcm.edu	37	chr12	56559415	56559415	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctgccgagccctcatctcCgcatacttcagctgctccat	6	11	7	17	2	3	0	2	0	1	0	5	1	4	0	4	0	6	4	4	0	1	2	rs116595430	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:56559415C>T	ENST00000267064.4	-	26	2912	c.2826G>A	c.(2824-2826)gcG>gcA	p.A942A	SMARCC2_ENST00000347471.4_Silent_p.A973A|RP11-977G19.5_ENST00000553176.1_RNA|SMARCC2_ENST00000550164.1_Silent_p.A973A|SMARCC2_ENST00000394023.3_Silent_p.A973A	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	942				A -> P (in Ref. 1; AAC50694). {ECO:0000305}.	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)			CCCTCATCTCCGCATACTTCA	0.587													C|||	26	0.00519169	0.0159	0.0072	5008	,	,		17950	0.0		0.0	False		,,,				2504	0.0				p.A973A		Atlas-SNP	.											.	SMARCC2	212	.	0			c.G2919A						PASS	.	C	,,	36,4370	40.8+/-73.8	1,34,2168	53	56	55		2919,2826,2919	-8.5	0.1	12	dbSNP_132	55	7,8593	6.4+/-24.3	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous	SMARCC2	NM_001130420.1,NM_003075.3,NM_139067.2	,,	1,41,6461	TT,TC,CC		0.0814,0.8171,0.3306	,,	973/1153,942/1215,973/1131	56559415	43,12963	2203	4300	6503	SO:0001819	synonymous_variant	6601	exon27			CATCTCCGCATAC	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.2826G>A	12.37:g.56559415C>T		142	0	0		149	78	0.52349	NM_139067	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Silent	SNP	ENST00000267064.4	37	CCDS8907.1																																																																																			C|0.996;T|0.004	0.004	strong		0.587	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1			T	56559415	C	T	56559415	2	4	23	1	0	0	0	0	0	0	0	1	14791	639	23	1		1	SMARCC2	12	56559415	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	932	56559415	77292480	480	7924											
RNF41	10193	hgsc.bcm.edu	37	chr12	56601998	56601998	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gacgtcttctccagctctgcGatgcgtgtctgctgctgctg	3	13	12	13	3	4	0	0	0	4	0	5	2	4	0	1	0	6	4	1	0	0	1	rs17118378	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:56601998G>A	ENST00000345093.4	-	5	816	c.447C>T	c.(445-447)atC>atT	p.I149I	RNF41_ENST00000552244.1_Silent_p.I149I|RNF41_ENST00000394013.2_Silent_p.I78I|RNF41_ENST00000552656.1_Silent_p.I149I	NM_005785.3|NM_194359.2	NP_005776.1|NP_919340.1	Q9H4P4	RNF41_HUMAN	ring finger protein 41, E3 ubiquitin protein ligase	149					extrinsic apoptotic signaling pathway (GO:0097191)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|proteasomal protein catabolic process (GO:0010498)|protein autoubiquitination (GO:0051865)|protein polyubiquitination (GO:0000209)|regulation of establishment of cell polarity (GO:2000114)|regulation of lymphocyte differentiation (GO:0045619)|regulation of MAPK cascade (GO:0043408)|regulation of myeloid cell differentiation (GO:0045637)|regulation of protein kinase B signaling (GO:0051896)|regulation of reactive oxygen species metabolic process (GO:2000377)	cytosol (GO:0005829)	acid-amino acid ligase activity (GO:0016881)|protein tag (GO:0031386)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|large_intestine(2)|lung(1)|skin(2)|urinary_tract(1)	11						CCAGCTCTGCGATGCGTGTCT	0.562													G|||	77	0.0153754	0.0424	0.0072	5008	,	,		19990	0.0		0.0	False		,,,				2504	0.0164				p.I149I		Atlas-SNP	.											.	RNF41	31	.	0			c.C447T						PASS	.	G	,,,	142,4264	101.6+/-140.2	6,130,2067	132	104	114		447,447,234,447	-4	0.9	12	dbSNP_123	114	9,8591	7.7+/-29.5	0,9,4291	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RNF41	NM_001242826.1,NM_005785.3,NM_194358.2,NM_194359.2	,,,	6,139,6358	AA,AG,GG		0.1047,3.2229,1.161	,,,	149/318,149/318,78/247,149/318	56601998	151,12855	2203	4300	6503	SO:0001819	synonymous_variant	10193	exon5			CTCTGCGATGCGT	AF077599	CCDS8909.1, CCDS8910.1	12q13.13	2014-03-24	2014-03-24		ENSG00000181852	ENSG00000181852		"RING-type (C3HC4) zinc fingers"	18401	protein-coding gene	gene with protein product			"ring finger protein 41"				Standard	NM_005785		Approved	SBBI03, NRDP1	uc001skg.2	Q9H4P4	OTTHUMG00000170328	ENST00000345093.4:c.447C>T	12.37:g.56601998G>A		160	0	0		214	96	0.448598	NM_005785	A6NFW0|B2RBT8|O75598	Silent	SNP	ENST00000345093.4	37	CCDS8909.1																																																																																			G|0.986;A|0.014	0.014	strong		0.562	RNF41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408525.1	NM_005785		A	56601998	G	A	56601998	2	1	23	1	0	0	0	0	0	0	0	1	13509	1048	37	1		1	RNF41	12	56601998	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	42583	56601998	77249897	481	7925											
NAB2	4665	hgsc.bcm.edu	37	chr12	57485291	57485291	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggaaaaggcaggcagtgcccGcagttttagccccaagagcc	11	5	13	12	1	0	1	0	0	0	1	0	2	0	2	4	3	3	4	4	3	4	2	rs140433833	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:57485291G>A	ENST00000300131.3	+	2	845	c.467G>A	c.(466-468)cGc>cAc	p.R156H	NAB2_ENST00000554718.1_3'UTR|NAB2_ENST00000357680.4_Missense_Mutation_p.R156H|NAB2_ENST00000342556.6_Missense_Mutation_p.R156H	NM_005967.3	NP_005958.1	Q15742	NAB2_HUMAN	NGFI-A binding protein 2 (EGR1 binding protein 2)	156					cell proliferation (GO:0008283)|endochondral ossification (GO:0001958)|myelination (GO:0042552)|negative regulation of transcription from RNA polymerase III promoter (GO:0016480)|nervous system development (GO:0007399)|regulation of epidermis development (GO:0045682)|Schwann cell differentiation (GO:0014037)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	20						GGCAGTGCCCGCAGTTTTAGC	0.632													G|||	12	0.00239617	0.0076	0.0029	5008	,	,		16784	0.0		0.0	False		,,,				2504	0.0				p.R156H		Atlas-SNP	.											NAB2,NS,carcinoma,-1,1	NAB2	47	1	0			c.G467A						PASS	.	G	HIS/ARG	13,4393	21.2+/-45.6	0,13,2190	55	56	56		467	4.2	1	12	dbSNP_134	56	5,8595	5.0+/-18.6	0,5,4295	yes	missense	NAB2	NM_005967.3	29	0,18,6485	AA,AG,GG		0.0581,0.2951,0.1384	probably-damaging	156/526	57485291	18,12988	2203	4300	6503	SO:0001583	missense	4665	exon2			GTGCCCGCAGTTT	BC065931	CCDS8930.1	12q13.3	2008-05-14				ENSG00000166886			7627	protein-coding gene	gene with protein product		602381				8668170, 8649813	Standard	XM_005268894		Approved	MADER	uc001smz.3	Q15742		ENST00000300131.3:c.467G>A	12.37:g.57485291G>A	ENSP00000300131:p.Arg156His	51	0	0		41	23	0.560976	NM_005967	B2RAK3|O76006|Q14797	Missense_Mutation	SNP	ENST00000300131.3	37	CCDS8930.1	9	0.004120879120879121	7	0.014227642276422764	2	0.0055248618784530384	0	0.0	0	0.0	G	16.63	3.176780	0.57692	0.002951	5.81E-4	ENSG00000166886	ENST00000300131;ENST00000342556;ENST00000357680	.	.	.	4.18	4.18	0.49190	.	0.433911	0.21867	N	0.067954	T	0.32315	0.0825	N	0.14661	0.345	0.49051	D	0.999745	D	0.59767	0.986	P	0.46299	0.511	T	0.35325	-0.9793	9	0.46703	T	0.11	-8.9058	14.0515	0.64739	0.0:0.0:1.0:0.0	.	156	Q15742	NAB2_HUMAN	H	156	.	ENSP00000300131:R156H	R	+	2	0	NAB2	55771558	0.991000	0.36638	0.997000	0.53966	0.957000	0.61999	1.829000	0.39121	2.156000	0.67533	0.462000	0.41574	CGC	G|0.997;A|0.003	0.003	strong		0.632	NAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412222.1	NM_005967		A	57485291	G	A	57485291	3	1	23	1	0	0	0	0	1	0	0	0	10141	1087	38	1	473	1	NAB2	12	57485291	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	883293	57485291	76366604	482	7926											
GRIP1	23426	hgsc.bcm.edu	37	chr12	66773075	66773075	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttacccactggctgtggacCggtcccagtcttcataactc	7	11	8	15	1	2	0	1	0	1	0	4	1	3	1	3	3	2	1	3	3	2	3	rs145115262	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:66773075C>T	ENST00000398016.3	-	19	2518	c.2450G>A	c.(2449-2451)cGg>cAg	p.R817Q	GRIP1_ENST00000359742.4_Missense_Mutation_p.R869Q|GRIP1_ENST00000286445.7_Missense_Mutation_p.R869Q	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)		GGCTGTGGACCGGTCCCAGTC	0.517													C|||	15	0.00299521	0.0008	0.0058	5008	,	,		17397	0.003		0.007	False		,,,				2504	0.0				p.R817Q		Atlas-SNP	.											.	GRIP1	106	.	0			c.G2450A						PASS	.	C	GLN/ARG,GLN/ARG	9,3877		0,9,1934	169	165	166		2450,2450	2	1	12	dbSNP_134	166	69,8193		0,69,4062	yes	missense,missense	GRIP1	NM_001178074.1,NM_021150.3	43,43	0,78,5996	TT,TC,CC		0.8351,0.2316,0.6421	benign,benign	817/1062,817/1077	66773075	78,12070	1943	4131	6074	SO:0001583	missense	23426	exon19			GTGGACCGGTCCC	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.2450G>A	12.37:g.66773075C>T	ENSP00000381098:p.Arg817Gln	215	0	0		182	87	0.478022	NM_001178074	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Missense_Mutation	SNP	ENST00000398016.3	37	CCDS41807.1	6|6	0.0027472527472527475|0.0027472527472527475	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0017482517482517483|0.0017482517482517483	5|5	0.006596306068601583|0.006596306068601583	C|C	13.77|13.77	2.337222|2.337222	0.41398|0.41398	0.002316|0.002316	0.008351|0.008351	ENSG00000155974|ENSG00000155974	ENST00000538164|ENST00000398016;ENST00000359742;ENST00000286445;ENST00000538211;ENST00000540433;ENST00000536215	.|T;T;T;T;T;T	.|0.81415	.|-1.49;-1.49;-1.49;-1.49;-1.49;-1.49	4.8|4.8	1.95|1.95	0.26073|0.26073	.|.	.|0.233910	.|0.42294	.|N	.|0.000731	T|T	0.69178|0.69178	0.3082|0.3082	M|M	0.62723|0.62723	1.935|1.935	0.44129|0.44129	D|D	0.996911|0.996911	.|P;P;P;D	.|0.54397	.|0.911;0.88;0.956;0.966	.|B;B;B;B	.|0.43018	.|0.173;0.108;0.297;0.405	T|T	0.69124|0.69124	-0.5228|-0.5228	5|9	.|.	.|.	.|.	-5.1095|-5.1095	9.3305|9.3305	0.38018|0.38018	0.0:0.7035:0.0:0.2965|0.0:0.7035:0.0:0.2965	.|.	.|817;869;817;869	.|F5H4N6;Q9Y3R0;Q9Y3R0-3;Q9Y3R0-2	.|.;GRIP1_HUMAN;.;.	S|Q	684|817;869;869;817;761;709	.|ENSP00000381098:R817Q;ENSP00000352780:R869Q;ENSP00000286445:R869Q;ENSP00000446047:R817Q;ENSP00000446024:R761Q;ENSP00000446011:R709Q	.|.	G|R	-|-	1|2	0|0	GRIP1|GRIP1	65059342|65059342	1.000000|1.000000	0.71417|0.71417	0.968000|0.968000	0.41197|0.41197	0.988000|0.988000	0.76386|0.76386	2.867000|2.867000	0.48428|0.48428	0.317000|0.317000	0.23160|0.23160	-0.258000|-0.258000	0.10820|0.10820	GGT|CGG	C|0.997;T|0.003	0.003	strong		0.517	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401975.2			T	66773075	C	T	66773075	3	4	23	1	0	0	0	0	1	0	0	0	6796	652	23	1	804	1	GRIP1	12	66773075	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	9287784	66773075	67078820	483	7927											
DYRK2	8445	hgsc.bcm.edu	37	chr12	68043643	68043643	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctcggtgcaggggccacccGgagcggagtggggactggcc	5	4	20	12	3	0	0	0	0	0	0	1	3	0	3	3	8	2	2	3	8	0	0			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:68043643G>A	ENST00000344096.3	+	2	529	c.116G>A	c.(115-117)cGg>cAg	p.R39Q	DYRK2_ENST00000537632.1_3'UTR|DYRK2_ENST00000393555.3_Intron	NM_006482.2	NP_006473.2	Q92630	DYRK2_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	39					cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of NFAT protein import into nucleus (GO:0051534)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of glycogen biosynthetic process (GO:0045725)|protein phosphorylation (GO:0006468)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	30			Lung(24;6.81e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(7;0.000573)		GGGGCCACCCGGAGCGGAGTG	0.741																																					p.R39Q		Atlas-SNP	.											.	DYRK2	63	.	0			c.G116A						PASS	.						12	14	13					12																	68043643		2187	4283	6470	SO:0001583	missense	8445	exon2			CCACCCGGAGCGG	Y09216	CCDS8978.1, CCDS8979.1	12q15	2008-07-03				ENSG00000127334			3093	protein-coding gene	gene with protein product		603496				9748265	Standard	NM_003583		Approved		uc001str.4	Q92630		ENST00000344096.3:c.116G>A	12.37:g.68043643G>A	ENSP00000342105:p.Arg39Gln	65	0	0		52	34	0.653846	NM_006482	B2R9V9|Q9BRB5	Missense_Mutation	SNP	ENST00000344096.3	37	CCDS8978.1	.	.	.	.	.	.	.	.	.	.	G	10.88	1.475230	0.26511	.	.	ENSG00000127334	ENST00000344096	T	0.66638	-0.22	3.91	3.01	0.34805	.	0.416053	0.21001	N	0.081872	T	0.47322	0.1439	N	0.19112	0.55	0.80722	D	1	B	0.11235	0.004	B	0.01281	0.0	T	0.28839	-1.0031	9	.	.	.	.	10.5729	0.45211	0.0975:0.0:0.9025:0.0	.	39	Q92630	DYRK2_HUMAN	Q	39	ENSP00000342105:R39Q	.	R	+	2	0	DYRK2	66329910	1.000000	0.71417	0.998000	0.56505	0.278000	0.26855	4.423000	0.59861	0.997000	0.38969	-0.258000	0.10820	CGG	.	.	none		0.741	DYRK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402218.1			A	68043643	G	A	68043643	3	1	23	1	0	0	0	0	1	0	0	0	4858	1116	39	1	122	1	DYRK2	12	68043643	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1270568	68043643	65808252	484	7928											
LGR5	8549	hgsc.bcm.edu	37	chr12	71977427	71977427	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgccttccttggacttctagGccccttcaaaccctgtgaac	7	12	7	15	0	2	1	1	1	1	0	3	2	3	2	5	2	3	0	5	2	3	5	rs200272164		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:71977427G>A	ENST00000266674.5	+	18	1948	c.1637G>A	c.(1636-1638)gGc>gAc	p.G546D	LGR5_ENST00000536515.1_Splice_Site_p.G474D|RP11-186F10.2_ENST00000546601.1_RNA|LGR5_ENST00000540815.2_Splice_Site_p.G522D			O75473	LGR5_HUMAN	leucine-rich repeat containing G protein-coupled receptor 5	546					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						GGACTTCTAGGCCCCTTCAAA	0.423													G|||	1	0.000199681	0.0	0.0	5008	,	,		22325	0.0		0.001	False		,,,				2504	0.0				p.G546D		Atlas-SNP	.											.	LGR5	103	.	0			c.G1637A						PASS	.						180	173	176					12																	71977427		2203	4300	6503	SO:0001630	splice_region_variant	8549	exon18			TTCTAGGCCCCTT	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.1637-1G>A	12.37:g.71977427G>A		281	0	0		268	123	0.458955	NM_003667	D8MCT0|Q4VAM0|Q4VAM2|Q9UP75	Missense_Mutation	SNP	ENST00000266674.5	37	CCDS9000.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	25.7	4.663054	0.88251	.	.	ENSG00000139292	ENST00000266674;ENST00000451585;ENST00000536515;ENST00000540815	D;D;D	0.90563	-2.69;-2.69;-2.69	5.69	5.69	0.88448	.	0.000000	0.64402	D	0.000005	D	0.92570	0.7640	L	0.31065	0.9	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.99;0.998	D	0.91262	0.5037	9	.	.	.	.	19.812	0.96551	0.0:0.0:1.0:0.0	.	522;546	O75473-2;O75473	.;LGR5_HUMAN	D	546;546;474;522	ENSP00000266674:G546D;ENSP00000443033:G474D;ENSP00000441035:G522D	.	G	+	2	0	LGR5	70263694	1.000000	0.71417	0.991000	0.47740	0.940000	0.58332	9.807000	0.99171	2.685000	0.91497	0.655000	0.94253	GGC	G|1.000;A|0.000	0.000	strong		0.423	LGR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404744.1	NM_003667	Missense_Mutation	A	71977427	G	A	71977427	5	1	23	1	0	0	0	0	0	0	1	0	8766	1217	42	2	1707	2	LGR5	12	71977427	Splice_Site	SNP	G	TCGA-G8-6325-01A-11D-2210-10	3933784	71977427	61874468	485	7929											
GLIPR1L2	144321	hgsc.bcm.edu	37	chr12	75804262	75804262	+	Frame_Shift_Del	DEL	T	T	-																															ctagagcatggggaaaaaaaTgtttgtttacgcataatatt																										TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:75804262delT	ENST00000550916.1	+	2	330	c.283delT	c.(283-285)tgtfs	p.C95fs	GLIPR1L2_ENST00000547164.1_Frame_Shift_Del_p.C95fs|GLIPR1L2_ENST00000441218.1_Frame_Shift_Del_p.C30fs|GLIPR1L2_ENST00000435775.1_Frame_Shift_Del_p.C95fs|GLIPR1L2_ENST00000320460.4_Frame_Shift_Del_p.C95fs|GLIPR1L2_ENST00000378692.3_5'UTR	NM_001270396.1	NP_001257325.1	Q4G1C9	GRPL2_HUMAN	GLI pathogenesis-related 1 like 2	95	SCP.					integral component of membrane (GO:0016021)				kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16						GGGAAAAAAATGTTTGTTTAC	0.323																																					p.K94fs		Pindel,Atlas-Indel	.											.	GLIPR1L2	54	.	0			c.282delA						PASS	.			0,4264		0,0,2132	87	87	87			0.1	1	12		87	3,8247		0,3,4122	no	frameshift	GLIPR1L2	NM_152436.1		0,3,6254	A1A1,A1R,RR		0.0364,0.0,0.024			75804262	3,12511	2203	4299	6502	SO:0001589	frameshift_variant	144321	exon2			.	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.283delT	12.37:g.75804262delT	ENSP00000448248:p.Cys95fs	134	0	.		136	43	0.316	NM_152436	Q6MZS1|Q8N6N0|Q8NA43	Frame_Shift_Del	DEL	ENST00000550916.1	37	CCDS58258.1																																																																																			.	.	none		0.323	GLIPR1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405718.1	NM_152436		-	75804262	T	-	75804262	7	5	23	1	0	1	0	1	0	0	0	0	6451	1464	51	0	289	0	GLIPR1L2	12	75804262	Frame_Shift_Del	DEL	T	TCGA-G8-6325-01A-11D-2210-10	3826835	75804262	58047633	486	7930											
BBS10	79738	hgsc.bcm.edu	37	chr12	76741341	76741341	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtactggtccataataccgtCtaatatttgtgtctgaaacg	11	14	8	8	2	2	1	0	1	2	0	3	1	3	1	2	1	3	1	2	1	6	6	rs142863601	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:76741341C>T	ENST00000393262.3	-	2	507	c.424G>A	c.(424-426)Gac>Aac	p.D142N		NM_024685.3	NP_078961.3	Q8TAM1	BBS10_HUMAN	Bardet-Biedl syndrome 10	142			D -> N (in dbSNP:rs142863601). {ECO:0000269|PubMed:20120035}.		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						ATAATACCGTCTAATATTTGT	0.388									Bardet-Biedl syndrome				C|||	14	0.00279553	0.0008	0.0029	5008	,	,		19235	0.0		0.0109	False		,,,				2504	0.0				p.D142N		Atlas-SNP	.											.	BBS10	46	.	0			c.G424A						PASS	.	C	ASN/ASP	11,4395	17.9+/-39.9	0,11,2192	72	68	70		424	5.3	0.9	12	dbSNP_134	70	92,8508	51.9+/-112.3	1,90,4209	yes	missense	BBS10	NM_024685.3	23	1,101,6401	TT,TC,CC		1.0698,0.2497,0.7919	possibly-damaging	142/724	76741341	103,12903	2203	4300	6503	SO:0001583	missense	79738	exon2	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	TACCGTCTAATAT	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.424G>A	12.37:g.76741341C>T	ENSP00000376946:p.Asp142Asn	115	0	0		104	56	0.538462	NM_024685	Q96CW2|Q9H5D2	Missense_Mutation	SNP	ENST00000393262.3	37	CCDS9014.2	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	C	25.9	4.683655	0.88639	0.002497	0.010698	ENSG00000179941	ENST00000393262;ENST00000547830	D	0.89050	-2.46	5.34	5.34	0.76211	.	0.128969	0.49916	D	0.000131	D	0.88948	0.6576	L	0.60455	1.87	0.40719	D	0.982642	D	0.58970	0.984	P	0.55303	0.773	D	0.89985	0.4103	10	0.56958	D	0.05	-8.0958	16.9217	0.86166	0.0:1.0:0.0:0.0	.	142	Q8TAM1	BBS10_HUMAN	N	142;76	ENSP00000376946:D142N	ENSP00000376946:D142N	D	-	1	0	BBS10	75265472	1.000000	0.71417	0.950000	0.38849	0.971000	0.66376	5.183000	0.65065	2.937000	0.99478	0.650000	0.86243	GAC	C|0.994;T|0.006	0.006	strong		0.388	BBS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303983.2	NM_024685		T	76741341	C	T	76741341	3	4	23	1	0	0	0	0	1	0	0	0	1336	913	32	2	1751	2	BBS10	12	76741341	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	937079	76741341	57110554	487	7931											
TMTC2	160335	hgsc.bcm.edu	37	chr12	83290083	83290083	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaaatggcattaaaaacgatGtatcacagagaacccagctt	18	8	7	8	1	1	1	1	0	0	1	1	3	1	1	1	1	3	3	1	1	7	3	rs35725509	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:83290083G>A	ENST00000321196.3	+	3	1848	c.1141G>A	c.(1141-1143)Gta>Ata	p.V381I	TMTC2_ENST00000549919.1_Missense_Mutation_p.V375I|TMTC2_ENST00000548305.1_Missense_Mutation_p.V381I	NM_152588.1	NP_689801.1	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat containing 2	381					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						TAAAAACGATGTATCACAGAG	0.408													G|||	58	0.0115815	0.0	0.0072	5008	,	,		20195	0.0		0.0089	False		,,,				2504	0.045				p.V381I		Atlas-SNP	.											.	TMTC2	100	.	0			c.G1141A						PASS	.	G	ILE/VAL	5,4401	11.4+/-27.6	0,5,2198	172	167	169		1141	5	0	12	dbSNP_126	169	66,8534	40.3+/-97.0	0,66,4234	yes	missense	TMTC2	NM_152588.1	29	0,71,6432	AA,AG,GG		0.7674,0.1135,0.5459	benign	381/837	83290083	71,12935	2203	4300	6503	SO:0001583	missense	160335	exon3			AACGATGTATCAC	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.1141G>A	12.37:g.83290083G>A	ENSP00000322300:p.Val381Ile	121	0	0		107	43	0.401869	NM_152588	B2RCU7|Q8N2K8	Missense_Mutation	SNP	ENST00000321196.3	37	CCDS9025.1	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	G	0.548	-0.850759	0.02651	0.001135	0.007674	ENSG00000179104	ENST00000321196;ENST00000548305;ENST00000549919;ENST00000546590	T;T;T	0.61274	0.77;0.12;0.67	5.86	4.98	0.66077	.	1.043000	0.07418	N	0.893502	T	0.27419	0.0673	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	0.26538	-1.0100	10	0.12766	T	0.61	-0.0418	6.9111	0.24335	0.1418:0.0:0.7159:0.1423	rs35725509	381;136;381	Q8N394;F8VRQ2;F8VSH2	TMTC2_HUMAN;.;.	I	381;381;375;136	ENSP00000322300:V381I;ENSP00000448292:V381I;ENSP00000447609:V375I	ENSP00000322300:V381I	V	+	1	0	TMTC2	81814214	0.028000	0.19301	0.014000	0.15608	0.171000	0.22731	1.832000	0.39151	1.494000	0.48533	-0.142000	0.14014	GTA	G|0.994;A|0.006	0.006	strong		0.408	TMTC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405663.1	NM_152588		A	83290083	G	A	83290083	3	1	23	1	0	0	0	0	1	0	0	0	16276	1377	48	2	1151	2	TMTC2	12	83290083	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	6548742	83290083	50561812	488	7932											
EEA1	8411	hgsc.bcm.edu	37	chr12	93172994	93172994	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttctcctgttcaacagctGccttcagggagtccgctttt	5	15	8	13	1	4	0	2	0	2	0	6	1	5	1	3	1	3	3	3	1	1	5	rs138526188	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:93172994G>A	ENST00000322349.8	-	25	3815	c.3551C>T	c.(3550-3552)gCa>gTa	p.A1184V		NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	1184	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						TTCAACAGCTGCCTTCAGGGA	0.388																																					p.A1184V		Atlas-SNP	.											.	EEA1	104	.	0			c.C3551T						PASS	.	G	VAL/ALA	0,4406		0,0,2203	132	128	129		3551	3.7	0	12	dbSNP_134	129	3,8597	3.0+/-9.4	0,3,4297	yes	missense	EEA1	NM_003566.3	64	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	benign	1184/1412	93172994	3,13003	2203	4300	6503	SO:0001583	missense	8411	exon25			ACAGCTGCCTTCA	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.3551C>T	12.37:g.93172994G>A	ENSP00000317955:p.Ala1184Val	260	0	0		258	139	0.53876	NM_003566	Q14221	Missense_Mutation	SNP	ENST00000322349.8	37	CCDS31874.1	.	.	.	.	.	.	.	.	.	.	G	7.333	0.619287	0.14129	0.0	3.49E-4	ENSG00000102189	ENST00000322349	T	0.65549	-0.16	5.63	3.74	0.42951	.	0.607873	0.14539	N	0.313361	T	0.46171	0.1379	N	0.19112	0.55	0.09310	N	1	B	0.24258	0.1	B	0.19148	0.024	T	0.24657	-1.0154	10	0.30078	T	0.28	.	12.553	0.56238	0.0:0.1276:0.7395:0.1329	.	1184	Q15075	EEA1_HUMAN	V	1184	ENSP00000317955:A1184V	ENSP00000317955:A1184V	A	-	2	0	EEA1	91697125	0.159000	0.22864	0.032000	0.17829	0.164000	0.22412	1.860000	0.39428	0.672000	0.31204	0.557000	0.71058	GCA	G|1.000;A|0.000	0.000	strong		0.388	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566		A	93172994	G	A	93172994	3	1	23	1	0	0	0	0	1	0	0	0	4923	1319	46	2	704	2	EEA1	12	93172994	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	9882911	93172994	40678901	489	7933											
ANKS1B	56899	hgsc.bcm.edu	37	chr12	99139559	99139559	+	Intron	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttggtattaatgcccctcttGgcttcttggcccggctccac	4	14	9	14	1	2	0	0	0	2	0	3	0	3	0	4	4	1	3	4	4	2	6	rs61932058	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:99139559G>T	ENST00000547776.2	-	25	3672				ANKS1B_ENST00000329257.7_Intron|ANKS1B_ENST00000547010.1_Intron|ANKS1B_ENST00000549025.2_Silent_p.A344A|ANKS1B_ENST00000549493.2_Silent_p.A497A|ANKS1B_ENST00000550693.2_Silent_p.A437A|ANKS1B_ENST00000546568.1_Silent_p.A413A|ANKS1B_ENST00000333732.7_Silent_p.A276A|ANKS1B_ENST00000547446.1_Silent_p.A381A|ANKS1B_ENST00000332712.7_Silent_p.A437A|ANKS1B_ENST00000341752.7_Intron|ANKS1B_ENST00000549558.2_Intron	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B							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)		TGCCCCTCTTGGCTTCTTGGC	0.537													G|||	57	0.0113818	0.0113	0.0101	5008	,	,		16338	0.001		0.0189	False		,,,				2504	0.0153				p.A497A		Atlas-SNP	.											.	ANKS1B	180	.	0			c.C1491A						PASS	.	G	,,,,,,,,,,,	63,3759		1,61,1849	104	108	107		831,1032,1143,,1311,1239,831,759,,,,1491	2.7	1	12	dbSNP_129	107	181,8087		1,179,3954	no	coding-synonymous,coding-synonymous,coding-synonymous,utr-3,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron,intron,intron,coding-synonymous	ANKS1B	NM_001204065.1,NM_001204066.1,NM_001204067.1,NM_001204068.1,NM_001204069.1,NM_001204070.1,NM_001204079.1,NM_001204080.1,NM_001204081.1,NM_020140.3,NM_152788.4,NM_181670.3	,,,,,,,,,,,	2,240,5803	TT,TG,GG		2.1892,1.6484,2.0182	,,,,,,,,,,,	277/291,344/358,381/395,,437/451,413/427,277/291,253/267,,,,497/511	99139559	244,11846	1911	4134	6045	SO:0001627	intron_variant	56899	exon13			CCTCTTGGCTTCT	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.3672+5573C>A	12.37:g.99139559G>T		106	0	0		114	59	0.517544	NM_181670	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Silent	SNP	ENST00000547776.2	37	CCDS55872.1	32	0.014652014652014652	10	0.02032520325203252	4	0.011049723756906077	0	0.0	18	0.023746701846965697	G	5.366	0.252738	0.10185	0.016484	0.021892	ENSG00000185046	ENST00000550778	.	.	.	4.66	2.65	0.31530	.	.	.	.	.	T	0.42585	0.1209	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47761	-0.9092	4	.	.	.	.	9.5531	0.39321	0.0:0.1547:0.685:0.1604	rs61932058	.	.	.	Q	519	.	.	P	-	2	0	ANKS1B	97663690	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	2.200000	0.42724	1.048000	0.40298	-0.326000	0.08463	CCA	G|0.984;T|0.016	0.016	strong		0.537	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140		T	99139559	G	T	99139559	1	4	23	0	1	0	0	0	0	0	0	0	689	1335	47	4		4	ANKS1B	12	99139559	Intron	SNP	G	TCGA-G8-6325-01A-11D-2210-10	5966565	99139559	34712336	490	7934											
ANKS1B	56899	hgsc.bcm.edu	37	chr12	100048924	100048924	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaagtcctgatggcccacacGtattttcatcatcatcctct	10	13	5	13	1	4	1	3	1	1	0	6	1	6	1	3	1	0	1	3	1	2	3	rs377459874		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:100048924G>A	ENST00000547776.2	-	9	1192	c.1193C>T	c.(1192-1194)aCg>aTg	p.T398M	ANKS1B_ENST00000329257.7_Missense_Mutation_p.T398M|ANKS1B_ENST00000547010.1_De_novo_Start_InFrame	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	398						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)		TGGCCCACACGTATTTTCATC	0.378													G|||	1	0.000199681	0.0	0.0	5008	,	,		16060	0.0		0.001	False		,,,				2504	0.0				p.T398M		Atlas-SNP	.											.	ANKS1B	180	.	0			c.C1193T						PASS	.	G	MET/THR	1,3821		0,1,1910	119	117	118		1193	3.5	0.2	12		118	1,8241		0,1,4120	no	missense	ANKS1B	NM_152788.4	81	0,2,6030	AA,AG,GG		0.0121,0.0262,0.0166	possibly-damaging	398/1249	100048924	2,12062	1911	4121	6032	SO:0001583	missense	56899	exon9			CCACACGTATTTT	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.1193C>T	12.37:g.100048924G>A	ENSP00000449629:p.Thr398Met	224	0	0		250	114	0.456	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Missense_Mutation	SNP	ENST00000547776.2	37	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	G	9.507	1.104632	0.20632	2.62E-4	1.21E-4	ENSG00000185046	ENST00000547776;ENST00000329257;ENST00000549866	T;T;T	0.51071	0.85;0.85;0.72	5.47	3.51	0.40186	.	0.251827	0.30959	N	0.008522	T	0.31104	0.0786	N	0.22421	0.69	0.46078	D	0.998858	P;P	0.51791	0.948;0.913	B;B	0.39876	0.312;0.165	T	0.05971	-1.0853	9	.	.	.	-4.2304	12.7356	0.57222	0.0:0.4365:0.5635:0.0	.	364;398	F8VVQ4;Q7Z6G8	.;ANS1B_HUMAN	M	398;398;364	ENSP00000449629:T398M;ENSP00000331381:T398M;ENSP00000449894:T364M	.	T	-	2	0	ANKS1B	98573055	1.000000	0.71417	0.180000	0.23079	0.246000	0.25737	2.677000	0.46892	1.292000	0.44672	-0.283000	0.09986	ACG	.	.	weak		0.378	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140		A	100048924	G	A	100048924	3	1	23	1	0	0	0	0	1	0	0	0	689	1145	40	1	2913	1	ANKS1B	12	100048924	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	909365	100048924	33802971	491	7935											
PAH	5053	hgsc.bcm.edu	37	chr12	103288554	103288554	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gtgaaagctcatggacagtgGcaccaatgtcatgcctcaag	12	8	11	10	0	3	1	3	1	0	0	3	2	3	2	2	2	2	2	2	2	3	0	rs398123291|rs62642929|rs199475570		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:103288554G>T	ENST00000553106.1	-	3	783	c.311C>A	c.(310-312)gCc>gAc	p.A104D	PAH_ENST00000307000.2_Missense_Mutation_p.A99D|PAH_ENST00000551988.1_5'UTR	NM_000277.1	NP_000268.1	P00439	PH4H_HUMAN	phenylalanine hydroxylase	104	ACT. {ECO:0000255|PROSITE- ProRule:PRU01007}.		A -> D (in PKU; mild; haplotype 1).		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)	ATGGACAGTGGCACCAATGTC	0.383																																					p.A104D		Atlas-SNP	.											.	PAH	77	.	0			c.C311A	GRCh37	CM920543	PAH	M	rs62642929	PASS	.						150	143	146					12																	103288554		2203	4300	6503	SO:0001583	missense	5053	exon3			ACAGTGGCACCAA	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.311C>A	12.37:g.103288554G>T	ENSP00000448059:p.Ala104Asp	96	0	0		123	49	0.398374	NM_000277	Q16717|Q8TC14	Missense_Mutation	SNP	ENST00000553106.1	37	CCDS9092.1	.	.	.	.	.	.	.	.	.	.	G	14.05	2.418471	0.42918	.	.	ENSG00000171759	ENST00000553106;ENST00000307000;ENST00000551337;ENST00000546844	D;D;D;D	0.98280	-4.84;-4.84;-4.84;-4.84	6.17	5.29	0.74685	.	0.098719	0.64402	D	0.000002	D	0.95153	0.8429	L	0.29908	0.895	0.49299	D	0.999774	B;B	0.15930	0.015;0.002	B;B	0.11329	0.006;0.002	D	0.92907	0.6344	10	0.19147	T	0.46	-15.3988	13.5379	0.61657	0.1288:0.0:0.8712:0.0	rs62642929	104;104	B4DPN2;P00439	.;PH4H_HUMAN	D	104;99;104;104	ENSP00000448059:A104D;ENSP00000303500:A99D;ENSP00000447620:A104D;ENSP00000446658:A104D	ENSP00000303500:A99D	A	-	2	0	PAH	101812684	1.000000	0.71417	0.996000	0.52242	0.829000	0.46940	2.755000	0.47540	1.625000	0.50366	0.655000	0.94253	GCC	.	.	weak		0.383	PAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406692.1			T	103288554	G	T	103288554	3	4	23	1	0	0	0	0	1	0	0	0	11403	1203	42	4	1091	4	PAH	12	103288554	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	3239630	103288554	30563341	492	7936											
SSH1	54434	hgsc.bcm.edu	37	chr12	109194652	109194652	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgttatgatatgcaaataagCcaggaaaaaaattatcgatt	18	12	7	4	1	0	1	0	1	0	0	1	3	0	2	1	1	2	2	1	1	8	5			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:109194652C>G	ENST00000326495.5	-	12	1145	c.1052G>C	c.(1051-1053)gGc>gCc	p.G351A	SSH1_ENST00000326470.5_Missense_Mutation_p.G362A|SSH1_ENST00000551165.1_Missense_Mutation_p.G351A|SSH1_ENST00000360239.3_Missense_Mutation_p.G39A	NM_018984.3	NP_061857.3	Q8WYL5	SSH1_HUMAN	slingshot protein phosphatase 1	351	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						TGCAAATAAGCCAGGAAAAAA	0.348																																					p.G362A		Atlas-SNP	.											SSH1_ENST00000326470,NS,carcinoma,0,2	SSH1	144	2	0			c.G1085C						PASS	.						93	101	98					12																	109194652		2203	4300	6503	SO:0001583	missense	54434	exon11			AATAAGCCAGGAA	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.1052G>C	12.37:g.109194652C>G	ENSP00000315713:p.Gly351Ala	97	0	0		130	74	0.569231	NM_001161331	Q6P6C0|Q8N9A7|Q8WYL3|Q8WYL4|Q9P2P8	Missense_Mutation	SNP	ENST00000326495.5	37	CCDS9121.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.811838	0.90707	.	.	ENSG00000084112	ENST00000360239;ENST00000326495;ENST00000551165;ENST00000326470	D;T;T;T	0.85556	-2.0;0.09;0.09;0.09	5.72	5.72	0.89469	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.000000	0.85682	D	0.000000	D	0.90800	0.7111	L	0.50919	1.6	0.80722	D	1	B;P;B;D	0.76494	0.068;0.562;0.084;0.999	B;B;B;D	0.80764	0.077;0.239;0.125;0.994	D	0.89849	0.4008	10	0.51188	T	0.08	-49.7361	20.2626	0.98452	0.0:1.0:0.0:0.0	.	362;351;351;39	Q8WYL5-5;Q8WYL5-2;Q8WYL5;Q8WYL5-4	.;.;SSH1_HUMAN;.	A	39;351;351;362	ENSP00000353374:G39A;ENSP00000315713:G351A;ENSP00000448824:G351A;ENSP00000326107:G362A	ENSP00000326107:G362A	G	-	2	0	SSH1	107718781	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	7.818000	0.86416	2.873000	0.98535	0.563000	0.77884	GGC	.	.	none		0.348	SSH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403724.1	NM_018984		G	109194652	C	G	109194652	3	3	23	1	0	0	0	0	1	0	0	0	15199	739	26	4	2299	4	SSH1	12	109194652	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	5906098	109194652	24657243	493	7937											
ACACB	32	hgsc.bcm.edu	37	chr12	109665242	109665242	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcaccggcagctcccggacGgcacctgcgtggtagaattc	8	6	13	14	4	0	1	0	0	0	1	2	2	1	2	3	4	3	5	3	4	2	2	rs60293430	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:109665242G>A	ENST00000338432.7	+	28	4068	c.3949G>A	c.(3949-3951)Ggc>Agc	p.G1317S	ACACB_ENST00000377854.5_Missense_Mutation_p.G1247S|ACACB_ENST00000377848.3_Missense_Mutation_p.G1317S			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	1317					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)	GCTCCCGGACGGCACCTGCGT	0.577													G|||	259	0.0517173	0.1074	0.0548	5008	,	,		17197	0.002		0.0586	False		,,,				2504	0.0184				p.G1317S		Atlas-SNP	.											.	ACACB	330	.	0			c.G3949A						PASS	.	G	SER/GLY	456,3950	214.8+/-234.0	23,410,1770	53	45	47		3949	5.4	1	12	dbSNP_129	47	522,8078	144.3+/-200.2	19,484,3797	yes	missense	ACACB	NM_001093.3	56	42,894,5567	AA,AG,GG		6.0698,10.3495,7.5196	benign	1317/2459	109665242	978,12028	2203	4300	6503	SO:0001583	missense	32	exon27			CCGGACGGCACCT	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.3949G>A	12.37:g.109665242G>A	ENSP00000341044:p.Gly1317Ser	91	0	0		120	64	0.533333	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	105	0.04807692307692308	45	0.09146341463414634	22	0.06077348066298342	0	0.0	38	0.05013192612137203	G	16.13	3.034855	0.54896	0.103495	0.060698	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854;ENST00000390027	T;T;T	0.44881	0.91;0.91;0.91	5.38	5.38	0.77491	Acetyl-CoA carboxylase, central domain (1);	0.053759	0.85682	D	0.000000	T	0.02342	0.0072	L	0.55213	1.73	0.09310	P	1.0	D	0.65815	0.995	P	0.62813	0.907	T	0.04128	-1.0975	9	0.17832	T	0.49	.	14.364	0.66792	0.0:0.0:0.852:0.148	rs60293430;rs61752506	1317	O00763	ACACB_HUMAN	S	1317;1317;1247;548	ENSP00000341044:G1317S;ENSP00000367079:G1317S;ENSP00000367085:G1247S	ENSP00000341044:G1317S	G	+	1	0	ACACB	108149625	1.000000	0.71417	0.985000	0.45067	0.984000	0.73092	4.727000	0.61993	2.679000	0.91253	0.655000	0.94253	GGC	G|0.932;A|0.068	0.068	strong		0.577	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		A	109665242	G	A	109665242	3	1	23	1	0	0	0	0	1	0	0	0	107	1116	39	1	4055	1	ACACB	12	109665242	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	470590	109665242	24186653	494	7938											
UBE3B	89910	hgsc.bcm.edu	37	chr12	109972462	109972462	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccgcaagcgggagccaggcGgccgcctgcccacctcctcc	5	4	12	20	4	0	0	0	0	0	0	3	1	3	1	8	3	3	1	8	3	1	0	rs374046452		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:109972462G>A	ENST00000342494.3	+	28	3677	c.3082G>A	c.(3082-3084)Ggc>Agc	p.G1028S	UBE3B_ENST00000434735.2_Missense_Mutation_p.G1028S	NM_130466.3	NP_569733.2	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B	1028	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						GGAGCCAGGCGGCCGCCTGCC	0.632																																					p.G1028S		Atlas-SNP	.											.	UBE3B	116	.	0			c.G3082A						PASS	.	G	SER/GLY,SER/GLY	1,4405	2.1+/-5.4	0,1,2202	64	59	60		3082,3082	5.3	1	12		60	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	UBE3B	NM_130466.2,NM_183415.1	56,56	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	benign,benign	1028/1069,1028/1069	109972462	2,13004	2203	4300	6503	SO:0001583	missense	89910	exon28			CCAGGCGGCCGCC	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.3082G>A	12.37:g.109972462G>A	ENSP00000340596:p.Gly1028Ser	147	0	0		174	37	0.212644	NM_130466	A5D8Z3|Q05BX9|Q659F7|Q7Z7Q1|Q9BXZ4	Missense_Mutation	SNP	ENST00000342494.3	37	CCDS9129.1	.	.	.	.	.	.	.	.	.	.	G	15.75	2.924638	0.52653	2.27E-4	1.16E-4	ENSG00000151148	ENST00000434735;ENST00000342494	T;T	0.41065	1.01;1.01	5.3	5.3	0.74995	HECT (4);	0.000000	0.85682	D	0.000000	T	0.21801	0.0525	N	0.02539	-0.55	0.80722	D	1	B	0.25105	0.118	B	0.22386	0.039	T	0.10086	-1.0645	10	0.25106	T	0.35	-23.3915	17.9631	0.89092	0.0:0.0:1.0:0.0	.	1028	Q7Z3V4	UBE3B_HUMAN	S	1028	ENSP00000391529:G1028S;ENSP00000340596:G1028S	ENSP00000340596:G1028S	G	+	1	0	UBE3B	108456845	1.000000	0.71417	0.956000	0.39512	0.961000	0.63080	9.385000	0.97223	2.474000	0.83562	0.563000	0.77884	GGC	.	.	weak		0.632	UBE3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403119.1	NM_183415		A	109972462	G	A	109972462	3	1	23	1	0	0	0	0	1	0	0	0	16895	1116	39	1	3184	1	UBE3B	12	109972462	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	307220	109972462	23879433	495	7939											
C12orf34	84915	hgsc.bcm.edu	37	chr12	110206760	110206760	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cccaccagcttcaccgtaggCcagtactttgcggccccgtg	6	8	10	17	3	1	0	1	0	0	0	1	0	1	0	6	2	3	3	6	2	2	4	rs79456911	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:110206760C>A	ENST00000538780.1	+	3	1742	c.1026C>A	c.(1024-1026)ggC>ggA	p.G342G	FAM222A-AS1_ENST00000541723.1_RNA|FAM222A-AS1_ENST00000541460.1_RNA|FAM222A_ENST00000358906.3_Silent_p.G342G	NM_032829.2	NP_116218.2	Q5U5X8	F222A_HUMAN	family with sequence similarity 222, member A	342																	TCACCGTAGGCCAGTACTTTG	0.701													C|||	29	0.00579073	0.0015	0.0043	5008	,	,		14090	0.0		0.0149	False		,,,				2504	0.0092				p.G342G		Atlas-SNP	.											.	.	.	.	0			c.C1026A						PASS	.	C		12,4352		0,12,2170	14	13	13		1026	0.1	1	12	dbSNP_131	13	56,8518		0,56,4231	no	coding-synonymous	C12orf34	NM_032829.2		0,68,6401	AA,AC,CC		0.6531,0.275,0.5256		342/453	110206760	68,12870	2182	4287	6469	SO:0001819	synonymous_variant	84915	exon3			CGTAGGCCAGTAC	AK027627	CCDS9133.1	12q24.11	2012-04-27	2012-04-27	2012-04-27	ENSG00000139438	ENSG00000139438			25915	protein-coding gene	gene with protein product			"chromosome 12 open reading frame 34"	C12orf34		12477932	Standard	NM_032829		Approved	FLJ14721	uc001tpd.2	Q5U5X8	OTTHUMG00000169260	ENST00000538780.1:c.1026C>A	12.37:g.110206760C>A		20	0	0		21	10	0.47619	NM_032829	Q8NCD5|Q96SP6	Silent	SNP	ENST00000538780.1	37	CCDS9133.1																																																																																			C|0.994;A|0.006	0.006	strong		0.701	FAM222A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403175.1	NM_032829		A	110206760	C	A	110206760	2	1	23	1	0	0	0	0	0	0	0	1	1683	726	26	4		4	C12orf34	12	110206760	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	234298	110206760	23645135	496	7940											
CIT	11113	hgsc.bcm.edu	37	chr12	120166407	120166407	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catgcttcttctccaggtcaTtgagctagacatttggaaag	10	13	9	9	0	3	2	1	1	2	1	4	3	3	3	1	2	2	2	1	2	2	5	rs145731510	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:120166407T>C	ENST00000261833.7	-	27	3417	c.3365A>G	c.(3364-3366)aAt>aGt	p.N1122S	CIT_ENST00000392521.2_Missense_Mutation_p.N1164S|CIT_ENST00000537607.1_5'UTR	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	1122	Interaction with Rho/Rac.				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)		CTCCAGGTCATTGAGCTAGAC	0.443																																					p.N1164S		Atlas-SNP	.											.	CIT	535	.	0			c.A3491G						PASS	.	T	SER/ASN,SER/ASN	0,4406		0,0,2203	170	159	163		3491,3365	4.1	1	12	dbSNP_134	163	14,8586	10.5+/-38.8	0,14,4286	yes	missense,missense	CIT	NM_001206999.1,NM_007174.2	46,46	0,14,6489	CC,CT,TT		0.1628,0.0,0.1076	probably-damaging,probably-damaging	1164/2070,1122/2028	120166407	14,12992	2203	4300	6503	SO:0001583	missense	11113	exon28			AGGTCATTGAGCT	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.3365A>G	12.37:g.120166407T>C	ENSP00000261833:p.Asn1122Ser	59	0	0		73	41	0.561644	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Missense_Mutation	SNP	ENST00000261833.7	37	CCDS9192.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.39|13.39	2.222469|2.222469	0.39300|0.39300	0.0|0.0	0.001628|0.001628	ENSG00000122966|ENSG00000122966	ENST00000392520|ENST00000392521;ENST00000261833	.|T;T	.|0.63913	.|-0.03;-0.07	5.29|5.29	4.14|4.14	0.48551|0.48551	.|.	.|0.052340	.|0.85682	.|N	.|0.000000	T|T	0.53769|0.53769	0.1817|0.1817	N|N	0.17082|0.17082	0.46|0.46	0.45791|0.45791	D|D	0.998671|0.998671	.|D;B;B	.|0.62365	.|0.991;0.0;0.023	.|P;B;B	.|0.52343	.|0.696;0.002;0.032	T|T	0.50792|0.50792	-0.8786|-0.8786	5|10	.|0.32370	.|T	.|0.25	.|.	11.2234|11.2234	0.48869|0.48869	0.0:0.0724:0.0:0.9276|0.0:0.0724:0.0:0.9276	.|.	.|1164;1122;655	.|Q2M5E1;O14578;O14578-3	.|.;CTRO_HUMAN;.	V|S	750|1164;1122	.|ENSP00000376306:N1164S;ENSP00000261833:N1122S	.|ENSP00000261833:N1122S	M|N	-|-	1|2	0|0	CIT|CIT	118650790|118650790	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	3.105000|3.105000	0.50314|0.50314	0.959000|0.959000	0.37980|0.37980	0.533000|0.533000	0.62120|0.62120	ATG|AAT	T|0.999;C|0.001	0.001	strong		0.443	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174		C	120166407	T	C	120166407	3	2	23	1	0	0	0	0	1	0	0	0	3440	1493	52	3	2802	3	CIT	12	120166407	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	9959647	120166407	13685488	497	7941											
HNF1A	6927	hgsc.bcm.edu	37	chr12	121437114	121437114	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtggcccagtacacccacacGggcctgctcccgcagactat	8	6	10	17	2	0	1	0	0	0	1	1	1	1	1	4	2	2	3	4	2	2	2	rs55834942	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:121437114G>A	ENST00000257555.6	+	8	1771	c.1545G>A	c.(1543-1545)acG>acA	p.T515T	HNF1A_ENST00000541395.1_Silent_p.T515T|RP11-216P16.2_ENST00000606238.1_RNA|HNF1A_ENST00000544413.1_Silent_p.T515T			P20823	HNF1A_HUMAN	HNF1 homeobox A	515					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)					ACACCCACACGGGCCTGCTCC	0.677									Hepatic Adenoma, Familial Clustering of				.|||	315	0.0628994	0.0121	0.1095	5008	,	,		16172	0.001		0.1988	False		,,,				2504	0.0225				p.T515T		Atlas-SNP	.											HNF1A,brain,glioma,0,4	HNF1A	302	4	0			c.G1545A						PASS	.	G		175,4231	113.3+/-151.4	4,167,2032	68	70	70		1545	-7.7	0.9	12	dbSNP_129	70	1654,6944	303.3+/-306.4	156,1342,2801	yes	coding-synonymous	HNF1A	NM_000545.5		160,1509,4833	AA,AG,GG		19.237,3.9719,14.0649		515/632	121437114	1829,11175	2203	4299	6502	SO:0001819	synonymous_variant	6927	exon8	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CCACACGGGCCTG	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.1545G>A	12.37:g.121437114G>A		189	0	0		207	112	0.541063	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Silent	SNP	ENST00000257555.6	37	CCDS9209.1																																																																																			G|0.860;A|0.140	0.140	strong		0.677	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		A	121437114	G	A	121437114	2	1	23	1	0	0	0	0	0	0	0	1	7260	1103	39	1		1	HNF1A	12	121437114	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1270707	121437114	12414781	498	7942											
GPR81	27198	hgsc.bcm.edu	37	chr12	123214372	123214372	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgtcatgccagccattggccGactccatgatgaagctctca	9	10	9	13	1	2	2	2	2	1	0	4	3	3	2	4	1	3	1	4	1	1	1	rs61742326	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:123214372G>A	ENST00000436083.2	-	1	1018	c.515C>T	c.(514-516)tCg>tTg	p.S172L	HCAR1_ENST00000432564.1_Missense_Mutation_p.S172L|HCAR1_ENST00000356987.2_Missense_Mutation_p.S172L			Q9BXC0	HCAR1_HUMAN	hydroxycarboxylic acid receptor 1	172					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						GCCATTGGCCGACTCCATGAT	0.532													G|||	12	0.00239617	0.0	0.0072	5008	,	,		20664	0.001		0.006	False		,,,				2504	0.0				p.S172L		Atlas-SNP	.											.	HCAR1	21	.	0			c.C515T						PASS	.	G	LEU/SER	5,4401	9.9+/-24.2	0,5,2198	56	57	57		515	5.5	1	12	dbSNP_129	57	31,8569	21.0+/-64.5	0,31,4269	yes	missense	HCAR1	NM_032554.3	145	0,36,6467	AA,AG,GG		0.3605,0.1135,0.2768	benign	172/347	123214372	36,12970	2203	4300	6503	SO:0001583	missense	27198	exon1			TTGGCCGACTCCA	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.515C>T	12.37:g.123214372G>A	ENSP00000409980:p.Ser172Leu	22	0	0		27	14	0.518519	NM_032554	B2R9X4|Q3Y5J3|Q4VBN1|Q6NXU5	Missense_Mutation	SNP	ENST00000436083.2	37	CCDS9236.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	G	12.54	1.968654	0.34754	0.001135	0.003605	ENSG00000196917	ENST00000356987;ENST00000432564;ENST00000436083	T;T;T	0.28255	1.62;1.62;1.62	5.52	5.52	0.82312	GPCR, rhodopsin-like superfamily (1);	0.194005	0.34802	N	0.003663	T	0.14570	0.0352	L	0.33710	1.025	0.33582	D	0.599988	B	0.32829	0.386	B	0.25884	0.064	T	0.23762	-1.0179	10	0.28530	T	0.3	-8.6437	10.379	0.44099	0.089:0.0:0.911:0.0	.	172	Q9BXC0	HCAR1_HUMAN	L	172	ENSP00000349478:S172L;ENSP00000389255:S172L;ENSP00000409980:S172L	ENSP00000349478:S172L	S	-	2	0	HCAR1	121780325	0.143000	0.22626	0.952000	0.39060	0.774000	0.43823	1.785000	0.38684	2.577000	0.86979	0.655000	0.94253	TCG	G|0.996;A|0.004	0.004	strong		0.532	HCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401415.1			A	123214372	G	A	123214372	3	1	23	1	0	0	0	0	1	0	0	0	6719	1059	37	1	529	1	GPR81	12	123214372	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1777258	123214372	10637523	499	7943											
SETD8	387893	hgsc.bcm.edu	37	chr12	123892235	123892235	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttccattgaagcccacccGtggctgaagcattaaccggt	9	9	10	13	2	0	2	0	2	0	0	1	2	1	2	4	2	3	3	4	2	3	3	rs61955128	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:123892235G>A	ENST00000402868.3	+	8	1470	c.1044G>A	c.(1042-1044)ccG>ccA	p.P348P	SETD8_ENST00000330479.4_Silent_p.P348P			Q9NQR1	SETD8_HUMAN	SET domain containing (lysine methyltransferase) 8	389	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				histone lysine methylation (GO:0034968)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|urinary_tract(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		AAGCCCACCCGTGGCTGAAGC	0.562													G|||	26	0.00519169	0.0083	0.0014	5008	,	,		14479	0.003		0.003	False		,,,				2504	0.0082				p.P348P		Atlas-SNP	.											SETD8,NS,neuroblastoma,0,1	SETD8	35	1	0			c.G1044A						scavenged	.						15	15	15					12																	123892235		2194	4279	6473	SO:0001819	synonymous_variant	387893	exon8			CCACCCGTGGCTG	AY102937	CCDS9247.1	12q24.31	2011-07-01			ENSG00000183955	ENSG00000183955		"Chromatin-modifying enzymes / K-methyltransferases"	29489	protein-coding gene	gene with protein product		607240				15933070, 12086618, 12121615	Standard	NM_020382		Approved	SET8, SET07, PR-Set7, KMT5A	uc001uew.3	Q9NQR1	OTTHUMG00000150477	ENST00000402868.3:c.1044G>A	12.37:g.123892235G>A		73	1	0.0136986		75	3	0.04	NM_020382	A8K9D0|Q86W83|Q8TD09	Silent	SNP	ENST00000402868.3	37	CCDS9247.1																																																																																			G|0.999;A|0.001	0.001	strong		0.562	SETD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318263.1	NM_020382		A	123892235	G	A	123892235	2	1	23	1	0	0	0	0	0	0	0	1	14152	1132	40	1		1	SETD8	12	123892235	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	677863	123892235	9959660	500	7944											
DNAH10	196385	hgsc.bcm.edu	37	chr12	124298030	124298030	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatagcttatgaggttatgcGccaccctctaattaaggatg	11	12	10	8	1	1	1	0	1	1	0	1	3	1	2	2	2	2	2	2	2	5	5	rs143713799	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:124298030G>A	ENST00000409039.3	+	19	3135	c.3110G>A	c.(3109-3111)cGc>cAc	p.R1037H		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1037	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)		GAGGTTATGCGCCACCCTCTA	0.438													G|||	65	0.0129792	0.0151	0.0058	5008	,	,		20812	0.0		0.008	False		,,,				2504	0.0337				p.R1037H		Atlas-SNP	.											DNAH10_ENST00000409039,colon,carcinoma,+1,7	DNAH10	888	7	0			c.G3110A						PASS	.	G	HIS/ARG	73,4333	64.7+/-102.0	1,71,2131	90	84	86		3110	0.7	0	12	dbSNP_134	86	125,8475	64.6+/-126.8	1,123,4176	yes	missense	DNAH10	NM_207437.3	29	2,194,6307	AA,AG,GG		1.4535,1.6568,1.5224	benign	1037/4472	124298030	198,12808	2203	4300	6503	SO:0001583	missense	196385	exon19			TTATGCGCCACCC	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.3110G>A	12.37:g.124298030G>A	ENSP00000386770:p.Arg1037His	103	0	0		134	65	0.485075	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	18	0.008241758241758242	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	G	5.489	0.275238	0.10403	0.016568	0.014535	ENSG00000197653	ENST00000409039	T	0.22134	1.97	5.83	0.742	0.18341	.	0.186131	0.36200	N	0.002740	T	0.04137	0.0115	N	0.04959	-0.14	0.09310	N	1	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.09377	0.004;0.001;0.001	T	0.25572	-1.0128	10	0.44086	T	0.13	.	8.8463	0.35172	0.5998:0.0:0.4002:0.0	.	1037;912;1037	Q8IVF4-2;C4IXU6;Q8IVF4	.;.;DYH10_HUMAN	H	1037	ENSP00000386770:R1037H	ENSP00000386770:R1037H	R	+	2	0	DNAH10	122863983	0.001000	0.12720	0.035000	0.18076	0.004000	0.04260	0.637000	0.24659	0.067000	0.16545	-0.244000	0.11960	CGC	G|0.987;A|0.013	0.013	strong		0.438	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			A	124298030	G	A	124298030	3	1	23	1	0	0	0	0	1	0	0	0	4600	1087	38	1	3184	1	DNAH10	12	124298030	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	405795	124298030	9553865	501	7945											
DNAH10	196385	hgsc.bcm.edu	37	chr12	124298380	124298380	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgcaacaattgcagaaattaGaagtaaatctctagtcatgg	16	11	8	6	0	2	2	1	0	1	2	3	2	2	2	0	1	3	3	0	1	8	4			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:124298380G>A	ENST00000409039.3	+	20	3372	c.3347G>A	c.(3346-3348)aGa>aAa	p.R1116K		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1116	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)		GCAGAAATTAGAAGTAAATCT	0.398																																					p.R1116K		Atlas-SNP	.											.	DNAH10	888	.	0			c.G3347A						PASS	.						73	72	72					12																	124298380		2044	4232	6276	SO:0001583	missense	196385	exon20			AAATTAGAAGTAA	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.3347G>A	12.37:g.124298380G>A	ENSP00000386770:p.Arg1116Lys	80	0	0		89	41	0.460674	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	14.43	2.531934	0.45073	.	.	ENSG00000197653	ENST00000409039	T	0.22134	1.97	5.72	2.94	0.34122	.	.	.	.	.	T	0.18882	0.0453	L	0.54323	1.7	0.36729	D	0.881622	B	0.14805	0.011	B	0.16722	0.016	T	0.11324	-1.0592	9	0.17832	T	0.49	.	9.9842	0.41832	0.2701:0.0:0.7299:0.0	.	1116	Q8IVF4	DYH10_HUMAN	K	1116	ENSP00000386770:R1116K	ENSP00000386770:R1116K	R	+	2	0	DNAH10	122864333	0.988000	0.35896	0.047000	0.18901	0.982000	0.71751	1.629000	0.37071	0.364000	0.24374	-0.136000	0.14681	AGA	.	.	none		0.398	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			A	124298380	G	A	124298380	3	1	23	1	0	0	0	0	1	0	0	0	4600	942	33	2	3425	2	DNAH10	12	124298380	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	350	124298380	9553515	502	7946											
NCOR2	9612	hgsc.bcm.edu	37	chr12	124824869	124824869	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatgggtgcgtgctccaccGtcgtggtggacgtgaggatg	6	9	18	8	4	0	2	0	1	0	1	2	4	1	4	2	4	2	1	2	4	0	0	rs61755988	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:124824869G>A	ENST00000405201.1	-	36	5459	c.5459C>T	c.(5458-5460)aCg>aTg	p.T1820M	NCOR2_ENST00000429285.2_Missense_Mutation_p.T1810M|NCOR2_ENST00000356219.3_Missense_Mutation_p.T1827M|NCOR2_ENST00000404121.2_Missense_Mutation_p.T1381M|NCOR2_ENST00000404621.1_Missense_Mutation_p.T1810M|NCOR2_ENST00000397355.1_Missense_Mutation_p.T1811M			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1828					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)		GTGCTCCACCGTCGTGGTGGA	0.672													G|||	6	0.00119808	0.0008	0.0014	5008	,	,		15239	0.0		0.004	False		,,,				2504	0.0				p.T1820M		Atlas-SNP	.											.	NCOR2	475	.	0			c.C5459T						PASS	.	G	MET/THR,MET/THR,MET/THR	7,4175		0,7,2084	54	65	61		5429,5429,5459	4.2	0.2	12	dbSNP_129	61	86,8354		0,86,4134	yes	missense,missense,missense	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	81,81,81	0,93,6218	AA,AG,GG		1.019,0.1674,0.7368	probably-damaging,probably-damaging,probably-damaging	1810/2459,1810/2505,1820/2515	124824869	93,12529	2091	4220	6311	SO:0001583	missense	9612	exon38			TCCACCGTCGTGG	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.5459C>T	12.37:g.124824869G>A	ENSP00000384018:p.Thr1820Met	45	0	0		48	26	0.541667	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	37	CCDS41858.2	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	8.853	0.944957	0.18356	0.001674	0.01019	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285	T;T;T;T;T;T	0.19394	2.15;2.42;2.16;2.42;2.16;2.42	4.18	4.18	0.49190	.	0.204758	0.40554	N	0.001069	T	0.30293	0.0760	L	0.40543	1.245	0.28417	N	0.917932	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.991;0.996;0.994	T	0.14671	-1.0464	10	0.72032	D	0.01	-13.5861	16.4861	0.84184	0.0:0.0:1.0:0.0	rs61755988	1810;1811;1820	C9J0Q5;C9J239;C9JFD3	.;.;.	M	1820;1810;1827;1811;1819;1381;1810	ENSP00000384018:T1820M;ENSP00000384202:T1810M;ENSP00000348551:T1827M;ENSP00000380513:T1811M;ENSP00000385618:T1381M;ENSP00000400281:T1810M	ENSP00000348551:T1827M	T	-	2	0	NCOR2	123390822	1.000000	0.71417	0.195000	0.23364	0.015000	0.08874	6.455000	0.73497	1.858000	0.53909	0.491000	0.48974	ACG	G|0.997;A|0.003	0.003	strong		0.672	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		A	124824869	G	A	124824869	3	1	23	1	0	0	0	0	1	0	0	0	10245	1145	40	1	2133	1	NCOR2	12	124824869	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	526489	124824869	9027026	503	7947											
NCOR2	9612	hgsc.bcm.edu	37	chr12	124831388	124831388	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgtgcctccacgtaggaccGagggatccctgccgggccga	6	6	14	15	4	0	0	0	0	0	0	2	4	2	2	6	3	2	1	6	3	1	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:124831388G>A	ENST00000405201.1	-	31	4081	c.4081C>T	c.(4081-4083)Cgg>Tgg	p.R1361W	NCOR2_ENST00000429285.2_Missense_Mutation_p.R1351W|NCOR2_ENST00000356219.3_Missense_Mutation_p.R1368W|NCOR2_ENST00000404121.2_Missense_Mutation_p.R922W|NCOR2_ENST00000404621.1_Missense_Mutation_p.R1351W|NCOR2_ENST00000397355.1_Missense_Mutation_p.R1352W			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1369					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)		ACGTAGGACCGAGGGATCCCT	0.687																																					p.R1361W		Atlas-SNP	.											.	NCOR2	475	.	0			c.C4081T						PASS	.						7	10	9					12																	124831388		2025	4146	6171	SO:0001583	missense	9612	exon33			AGGACCGAGGGAT	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.4081C>T	12.37:g.124831388G>A	ENSP00000384018:p.Arg1361Trp	44	0	0		46	24	0.521739	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	37	CCDS41858.2	.	.	.	.	.	.	.	.	.	.	G	12.13	1.846645	0.32606	.	.	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285;ENST00000458234	T;T;T;T;T;T;T	0.60920	0.15;0.15;0.15;0.15;0.15;0.15;0.15	5.2	2.19	0.27852	.	0.000000	0.85682	D	0.000000	T	0.73087	0.3542	M	0.71036	2.16	0.54753	D	0.999988	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.993;0.997	T	0.74544	-0.3630	10	0.87932	D	0	-29.7811	13.8264	0.63352	0.0:0.0:0.5877:0.4123	.	1351;1352;1361	C9J0Q5;C9J239;C9JFD3	.;.;.	W	1361;1351;1368;1352;1360;922;1351;1369	ENSP00000384018:R1361W;ENSP00000384202:R1351W;ENSP00000348551:R1368W;ENSP00000380513:R1352W;ENSP00000385618:R922W;ENSP00000400281:R1351W;ENSP00000402808:R1369W	ENSP00000348551:R1368W	R	-	1	2	NCOR2	123397341	1.000000	0.71417	0.020000	0.16555	0.346000	0.29079	3.614000	0.54160	0.144000	0.18951	-0.448000	0.05591	CGG	.	.	none		0.687	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		A	124831388	G	A	124831388	3	1	23	1	0	0	0	0	1	0	0	0	10245	1057	37	1	3531	1	NCOR2	12	124831388	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	6519	124831388	9020507	504	7948											
DHX37	57647	hgsc.bcm.edu	37	chr12	125438712	125438712	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ttcatctgggccacccgggcCcgcttgctcttcagcctggt	3	11	11	16	2	4	0	2	0	2	0	4	0	4	0	4	3	2	2	4	3	0	3	rs11829165	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:125438712C>A	ENST00000308736.2	-	19	2597	c.2499G>T	c.(2497-2499)cgG>cgT	p.R833R	DHX37_ENST00000544745.1_Silent_p.R620R	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	833							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)		CCACCCGGGCCCGCTTGCTCT	0.652													C|||	712	0.142173	0.4728	0.0605	5008	,	,		15886	0.0		0.0338	False		,,,				2504	0.0112				p.R833R		Atlas-SNP	.											DHX37,NS,carcinoma,0,1	DHX37	114	1	0			c.G2499T						PASS	.	C		1886,2520	527.8+/-372.2	401,1084,718	32	36	35		2499	2.4	1	12	dbSNP_120	35	342,8258	114.6+/-174.5	3,336,3961	no	coding-synonymous	DHX37	NM_032656.3		404,1420,4679	AA,AC,CC		3.9767,42.8053,17.1306		833/1158	125438712	2228,10778	2203	4300	6503	SO:0001819	synonymous_variant	57647	exon19			CCGGGCCCGCTTG	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.2499G>T	12.37:g.125438712C>A		118	0	0		147	79	0.537415	NM_032656	Q9BUI7|Q9P211	Silent	SNP	ENST00000308736.2	37	CCDS9261.1																																																																																			C|0.852;A|0.148	0.148	strong		0.652	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656		A	125438712	C	A	125438712	2	1	23	1	0	0	0	0	0	0	0	1	4512	610	22	4		4	DHX37	12	125438712	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	607324	125438712	8413183	505	7949											
PGAM5	192111	hgsc.bcm.edu	37	chr12	133294371	133294371	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccgcccgtgtctcattggaAgccggaagctgtggtaaaaa	10	8	12	11	3	1	0	1	0	1	0	2	2	1	2	3	3	2	2	3	3	5	2	rs117147264	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:133294371A>G	ENST00000498926.2	+	4	630	c.572A>G	c.(571-573)aAg>aGg	p.K191R	PXMP2_ENST00000545677.1_3'UTR|PGAM5_ENST00000543955.1_Missense_Mutation_p.K42R|PGAM5_ENST00000454808.2_Missense_Mutation_p.K42R|PGAM5_ENST00000317555.2_Missense_Mutation_p.K191R	NM_001170543.1|NM_001170544.1	NP_001164014.1|NP_001164015.1	Q96HS1	PGAM5_HUMAN	phosphoglycerate mutase family member 5	191					dephosphorylation (GO:0016311)|necroptotic process (GO:0070266)|positive regulation of GTPase activity (GO:0043547)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|phosphatase activity (GO:0016791)|phosphoprotein phosphatase activity (GO:0004721)|protein complex binding (GO:0032403)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.89e-08)|Epithelial(86;1.14e-07)|all cancers(50;3.57e-06)		TCTCATTGGAAGCCGGAAGCT	0.652													A|||	163	0.0325479	0.003	0.1671	5008	,	,		12769	0.0		0.0358	False		,,,				2504	0.0072				p.K191R		Atlas-SNP	.											PGAM5,NS,carcinoma,0,1	PGAM5	18	1	0			c.A572G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS	38,4320		0,38,2141	22	28	26		572,572,572	5.5	1	12	dbSNP_132	26	321,8239		3,315,3962	yes	missense,missense,missense	PGAM5	NM_001170543.1,NM_001170544.1,NM_138575.3	26,26,26	3,353,6103	GG,GA,AA		3.75,0.872,2.7791	benign,benign,benign	191/290,191/289,191/256	133294371	359,12559	2179	4280	6459	SO:0001583	missense	192111	exon4			ATTGGAAGCCGGA	BC008196	CCDS9280.1, CCDS53845.1	12q24.33	2011-07-28			ENSG00000247077	ENSG00000247077			28763	protein-coding gene	gene with protein product		614939				11283018	Standard	NM_001170543		Approved	MGC5352, BXLBv68	uc009zyv.3	Q96HS1	OTTHUMG00000168021	ENST00000498926.2:c.572A>G	12.37:g.133294371A>G	ENSP00000438465:p.Lys191Arg	56	0	0		52	15	0.288462	NM_138575	A9LN06|C9IZY7|Q96JB0	Missense_Mutation	SNP	ENST00000498926.2	37	CCDS53845.1	74	0.03388278388278388	2	0.0040650406504065045	48	0.13259668508287292	0	0.0	24	0.0316622691292876	A	11.76	1.734893	0.30774	0.00872	0.0375	ENSG00000247077	ENST00000317555;ENST00000498926;ENST00000543955;ENST00000454808	T;T	0.71817	-0.6;-0.6	5.5	5.5	0.81552	Histidine phosphatase superfamily, clade-1 (2);	0.000000	0.85682	D	0.000000	T	0.00724	0.0024	N	0.10760	0.04	0.09310	P	0.99999969864	B;B	0.22683	0.035;0.073	B;B	0.19148	0.024;0.019	T	0.10245	-1.0638	9	0.34782	T	0.22	-20.1292	15.6131	0.76744	1.0:0.0:0.0:0.0	.	191;191	Q96HS1;Q96HS1-2	PGAM5_HUMAN;.	R	191;191;42;42	ENSP00000321503:K191R;ENSP00000438465:K191R	ENSP00000321503:K191R	K	+	2	0	PGAM5	131804444	1.000000	0.71417	1.000000	0.80357	0.183000	0.23260	8.497000	0.90488	2.084000	0.62774	0.533000	0.62120	AAG	A|0.971;G|0.029	0.029	strong		0.652	PGAM5-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397562.1	NM_138575		G	133294371	A	G	133294371	3	3	23	1	0	0	0	0	1	0	0	0	11785	72	3	3	586	3	PGAM5	12	133294371	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	7855659	133294371	557524	506	7950											
ATP12A	479	hgsc.bcm.edu	37	chr13	25255705	25255705	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gggcttctctttcagaaaacCccagaaatttactccgtgga	11	11	8	11	1	2	2	1	0	1	2	4	3	3	3	3	2	2	1	3	2	4	4	rs41288276	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:25255705C>A	ENST00000381946.3	+	2	182	c.15C>A	c.(13-15)acC>acA	p.T5T	ATP12A_ENST00000218548.6_Silent_p.T5T			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	5					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)		TTCAGAAAACCCCAGAAATTT	0.542													C|||	256	0.0511182	0.1044	0.0303	5008	,	,		17355	0.001		0.0477	False		,,,				2504	0.0491				p.T5T	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.C15A						PASS	.	C	,	401,4005	199.8+/-223.2	18,365,1820	51	54	53		15,15	-6.3	0	13	dbSNP_127	53	391,8209	125.5+/-184.1	5,381,3914	no	coding-synonymous,coding-synonymous	ATP12A	NM_001185085.1,NM_001676.5	,	23,746,5734	AA,AC,CC		4.5465,9.1012,6.0895	,	5/1046,5/1040	25255705	792,12214	2203	4300	6503	SO:0001819	synonymous_variant	479	exon2			GAAAACCCCAGAA	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.15C>A	13.37:g.25255705C>A		77	0	0		56	25	0.446429	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Silent	SNP	ENST00000381946.3	37	CCDS31948.1																																																																																			C|0.942;A|0.058	0.058	strong		0.542	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		A	25255705	C	A	25255705	2	1	23	1	0	0	0	0	0	0	0	1	1122	610	22	4		4	ATP12A	13	25255705	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10		25255705	89914173	507	7951											
ATP12A	479	hgsc.bcm.edu	37	chr13	25267017	25267017	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agttcaagccaggacaggaaAatgtccccatcatgaaggta	15	7	10	9	0	2	1	2	1	0	0	3	3	3	3	3	3	1	2	3	3	5	2	rs56291145	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:25267017A>C	ENST00000381946.3	+	10	1527	c.1360A>C	c.(1360-1362)Aat>Cat	p.N454H	ATP12A_ENST00000218548.6_Missense_Mutation_p.N460H			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	454					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)		AGGACAGGAAAATGTCCCCAT	0.453													A|||	74	0.0147764	0.0023	0.0187	5008	,	,		21024	0.001		0.0388	False		,,,				2504	0.0184				p.N460H	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.A1378C						PASS	.	A	HIS/ASN,HIS/ASN	25,4381	33.5+/-64.1	0,25,2178	157	145	149		1378,1360	5.7	0.1	13	dbSNP_129	149	332,8268	116.6+/-176.3	5,322,3973	yes	missense,missense	ATP12A	NM_001185085.1,NM_001676.5	68,68	5,347,6151	CC,CA,AA		3.8605,0.5674,2.7449	benign,benign	460/1046,454/1040	25267017	357,12649	2203	4300	6503	SO:0001583	missense	479	exon10			CAGGAAAATGTCC	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.1360A>C	13.37:g.25267017A>C	ENSP00000371372:p.Asn454His	84	0	0		69	28	0.405797	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	37	CCDS31948.1	42	0.019230769230769232	3	0.006097560975609756	6	0.016574585635359115	1	0.0017482517482517483	32	0.04221635883905013	A	10.05	1.245297	0.22796	0.005674	0.038605	ENSG00000075673	ENST00000218548;ENST00000381946	T;T	0.80123	-1.34;-1.34	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);	0.486738	0.23874	N	0.043705	T	0.36963	0.0986	N	0.13198	0.31	0.09310	N	1	B;B	0.30889	0.242;0.299	B;B	0.38156	0.197;0.266	T	0.52472	-0.8571	10	0.40728	T	0.16	.	8.3857	0.32499	0.9132:0.0:0.0868:0.0	rs56291145;rs61729900	460;454	P54707-2;P54707	.;AT12A_HUMAN	H	460;454	ENSP00000218548:N460H;ENSP00000371372:N454H	ENSP00000218548:N460H	N	+	1	0	ATP12A	24165017	0.002000	0.14202	0.133000	0.22050	0.757000	0.42996	1.843000	0.39259	2.154000	0.67381	0.533000	0.62120	AAT	A|0.975;C|0.025	0.025	strong		0.453	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		C	25267017	A	C	25267017	3	2	23	1	0	0	0	0	1	0	0	0	1122	14	1	5	1416	5	ATP12A	13	25267017	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	11312	25267017	89902861	508	7952											
KATNAL1	84056	hgsc.bcm.edu	37	chr13	30784566	30784566	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggttgatcttcagaagctcAgctcttccttttgctgttac	7	16	8	10	0	4	2	2	1	2	1	5	2	5	2	1	1	4	5	1	1	2	6	rs11617724	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:30784566A>G	ENST00000380615.3	-	10	1328	c.1161T>C	c.(1159-1161)gcT>gcC	p.A387A	KATNAL1_ENST00000380617.3_Silent_p.A387A	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)		TCAGAAGCTCAGCTCTTCCTT	0.378													a|||	224	0.0447284	0.1233	0.036	5008	,	,		18073	0.0		0.0328	False		,,,				2504	0.0031				p.A387A		Atlas-SNP	.											.	KATNAL1	53	.	0			c.T1161C						PASS	.	A	,	483,3923	226.9+/-242.2	30,423,1750	181	170	174		1161,1161	-11.5	0.3	13	dbSNP_120	174	319,8281	113.3+/-173.4	3,313,3984	no	coding-synonymous,coding-synonymous	KATNAL1	NM_001014380.1,NM_032116.3	,	33,736,5734	GG,GA,AA		3.7093,10.9623,6.1664	,	387/491,387/491	30784566	802,12204	2203	4300	6503	SO:0001819	synonymous_variant	84056	exon10			AAGCTCAGCTCTT	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.1161T>C	13.37:g.30784566A>G		261	0	0		209	206	0.985646	NM_001014380		Silent	SNP	ENST00000380615.3	37	CCDS31956.1																																																																																			A|0.940;G|0.060	0.060	strong		0.378	KATNAL1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044346.2	NM_032116		G	30784566	A	G	30784566	2	3	23	1	0	0	0	0	0	0	0	1	7994	175	7	3		3	KATNAL1	13	30784566	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	5517549	30784566	84385312	509	7953											
WBP4	11193	hgsc.bcm.edu	37	chr13	41646958	41646958	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtagaaggtttaagtgaagAtggttttacctattactata	13	15	10	3	0	0	3	0	1	0	2	0	3	0	3	1	3	2	3	1	3	9	9			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:41646958A>G	ENST00000379487.3	+	7	927	c.527A>G	c.(526-528)gAt>gGt	p.D176G	WBP4_ENST00000542082.1_Missense_Mutation_p.D155G	NM_007187.3	NP_009118.1	O75554	WBP4_HUMAN	WW domain binding protein 4	176	WW 2. {ECO:0000255|PROSITE- ProRule:PRU00224}.				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)		TTAAGTGAAGATGGTTTTACC	0.343																																					p.D176G		Atlas-SNP	.											.	WBP4	40	.	0			c.A527G						PASS	.						136	137	137					13																	41646958		2203	4300	6503	SO:0001583	missense	11193	exon7			GTGAAGATGGTTT	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.527A>G	13.37:g.41646958A>G	ENSP00000368801:p.Asp176Gly	117	0	0		105	47	0.447619	NM_007187	B7Z4M2|Q32P29	Missense_Mutation	SNP	ENST00000379487.3	37	CCDS9375.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.704428	0.88924	.	.	ENSG00000120688	ENST00000379487;ENST00000542082	D;D	0.84223	-1.82;-1.82	5.6	5.6	0.85130	WW/Rsp5/WWP (6);	0.156971	0.56097	D	0.000034	D	0.90741	0.7094	M	0.72624	2.21	0.58432	D	0.999994	P;D	0.64830	0.865;0.994	P;D	0.64595	0.57;0.927	D	0.89758	0.3945	10	0.33940	T	0.23	-16.308	15.7909	0.78364	1.0:0.0:0.0:0.0	.	155;176	B7Z4M2;O75554	.;WBP4_HUMAN	G	176;155	ENSP00000368801:D176G;ENSP00000439301:D155G	ENSP00000368801:D176G	D	+	2	0	WBP4	40544958	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	7.627000	0.83176	2.121000	0.65114	0.460000	0.39030	GAT	.	.	none		0.343	WBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044655.2	NM_007187		G	41646958	A	G	41646958	3	3	23	1	0	0	0	0	1	0	0	0	17276	333	12	3	553	3	WBP4	13	41646958	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	10862392	41646958	73522920	510	7954											
LRCH1	23143	hgsc.bcm.edu	37	chr13	47279258	47279258	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acctatatcctatgggatcaGcagaagccttagaattacaa	15	10	7	9	0	1	2	1	0	0	2	2	3	2	3	3	1	3	1	3	1	8	5	rs11617392	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:47279258G>T	ENST00000389798.3	+	12	1653	c.1456G>T	c.(1456-1458)Gca>Tca	p.A486S	LRCH1_ENST00000311191.6_Missense_Mutation_p.A486S|LRCH1_ENST00000389797.3_Missense_Mutation_p.A486S	NM_015116.2	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 1	486			A -> S (in dbSNP:rs11617392).							breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)		TATGGGATCAGCAGAAGCCTT	0.294													G|||	39	0.00778754	0.0008	0.0072	5008	,	,		17206	0.0		0.0288	False		,,,				2504	0.0041				p.A486S		Atlas-SNP	.											.	LRCH1	104	.	0			c.G1456T						PASS	.	G	SER/ALA,SER/ALA,SER/ALA	26,4380	32.6+/-62.9	0,26,2177	112	124	120		1456,1456,1456	5.1	0.9	13	dbSNP_120	120	273,8327	102.5+/-163.7	4,265,4031	yes	missense,missense,missense	LRCH1	NM_001164211.1,NM_001164213.1,NM_015116.2	99,99,99	4,291,6208	TT,TG,GG		3.1744,0.5901,2.2989	benign,benign,benign	486/764,486/697,486/729	47279258	299,12707	2203	4300	6503	SO:0001583	missense	23143	exon12			GGATCAGCAGAAG	AB023233	CCDS31972.1, CCDS53865.1, CCDS53866.1	13q14.11	2008-02-05	2004-05-27	2004-05-28	ENSG00000136141	ENSG00000136141			20309	protein-coding gene	gene with protein product		610368	"calponin homology (CH) domain containing 1"	CHDC1		10231032	Standard	NM_015116		Approved	KIAA1016	uc001vbk.3	Q9Y2L9	OTTHUMG00000016877	ENST00000389798.3:c.1456G>T	13.37:g.47279258G>T	ENSP00000374448:p.Ala486Ser	239	0	0		214	93	0.434579	NM_015116	B7ZLL5|F8W6F0|Q17R43|Q2KHR1|Q5TBU9|Q7Z5F6|Q7Z5F7	Missense_Mutation	SNP	ENST00000389798.3	37	CCDS31972.1	30	0.013736263736263736	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	25	0.032981530343007916	G	7.774	0.708144	0.15239	0.005901	0.031744	ENSG00000136141	ENST00000311191;ENST00000389798;ENST00000389797	T;T;T	0.55052	0.54;0.59;0.59	5.95	5.1	0.69264	.	0.509560	0.21773	N	0.069329	T	0.24812	0.0602	M	0.67953	2.075	0.23186	N	0.998159	B;B;B;B	0.14805	0.0;0.011;0.001;0.011	B;B;B;B	0.17098	0.004;0.017;0.009;0.005	T	0.31806	-0.9930	10	0.09338	T	0.73	-1.0147	13.4916	0.61399	0.0:0.0:0.8433:0.1566	rs11617392;rs17281816;rs52819157;rs61459892;rs11617392	486;486;486;486	Q17R43;Q9Y2L9-2;F8W6F0;Q9Y2L9	.;.;.;LRCH1_HUMAN	S	486	ENSP00000308493:A486S;ENSP00000374448:A486S;ENSP00000374447:A486S	ENSP00000308493:A486S	A	+	1	0	LRCH1	46177259	0.993000	0.37304	0.907000	0.35723	0.457000	0.32468	1.831000	0.39141	1.490000	0.48466	0.655000	0.94253	GCA	G|0.982;T|0.018	0.018	strong		0.294	LRCH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044824.2	NM_015116		T	47279258	G	T	47279258	3	4	23	1	0	0	0	0	1	0	0	0	8941	971	34	4	1502	4	LRCH1	13	47279258	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	5632300	47279258	67890620	511	7955											
WDFY2	115825	hgsc.bcm.edu	37	chr13	52313253	52313253	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggcagttcagatcactctGtcatcatgtgggacatcggt	9	11	11	10	1	5	1	4	0	1	1	6	2	5	2	0	3	0	2	0	3	0	1	rs77486739	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:52313253G>A	ENST00000298125.5	+	7	847	c.667G>A	c.(667-669)Gtc>Atc	p.V223I		NM_052950.3	NP_443182.1	Q96P53	WDFY2_HUMAN	WD repeat and FYVE domain containing 2	223							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)		AGATCACTCTGTCATCATGTG	0.512													G|||	18	0.00359425	0.0106	0.0058	5008	,	,		18017	0.0		0.0	False		,,,				2504	0.0				p.V223I		Atlas-SNP	.											.	WDFY2	36	.	0			c.G667A						PASS	.	G	ILE/VAL	63,4343	59.3+/-96.0	0,63,2140	160	140	147		667	5.3	1	13	dbSNP_131	147	4,8596	3.7+/-12.6	0,4,4296	yes	missense	WDFY2	NM_052950.3	29	0,67,6436	AA,AG,GG		0.0465,1.4299,0.5151	benign	223/401	52313253	67,12939	2203	4300	6503	SO:0001583	missense	115825	exon7			CACTCTGTCATCA	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.667G>A	13.37:g.52313253G>A	ENSP00000298125:p.Val223Ile	142	0	0		149	75	0.503356	NM_052950	B1AL86|Q96CS1	Missense_Mutation	SNP	ENST00000298125.5	37	CCDS9429.1	4	0.0018315018315018315	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	G	9.675	1.147653	0.21288	0.014299	4.65E-4	ENSG00000139668	ENST00000298125	T	0.57107	0.42	6.17	5.32	0.75619	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.049499	0.85682	D	0.000000	T	0.25680	0.0625	L	0.35542	1.07	0.49798	D	0.999829	B;B	0.14805	0.011;0.001	B;B	0.14023	0.01;0.003	T	0.16482	-1.0401	10	0.02654	T	1	-25.4701	7.2469	0.26127	0.2059:0.0:0.7941:0.0	.	120;223	Q96LK4;Q96P53	.;WDFY2_HUMAN	I	223	ENSP00000298125:V223I	ENSP00000298125:V223I	V	+	1	0	WDFY2	51211254	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.740000	0.68629	2.941000	0.99782	0.655000	0.94253	GTC	G|0.996;A|0.004	0.004	strong		0.512	WDFY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045985.3	NM_052950		A	52313253	G	A	52313253	3	1	23	1	0	0	0	0	1	0	0	0	17284	1377	48	2	693	2	WDFY2	13	52313253	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	5033995	52313253	62856625	512	7956											
UPF3A	65110	hgsc.bcm.edu	37	chr13	115067419	115067419	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agccaggacagcggggctccGggggaggccatggagagact	9	3	19	10	2	0	1	0	0	0	1	1	5	1	4	3	7	2	1	3	7	0	0	rs146464930	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:115067419G>A	ENST00000375299.3	+	9	1277	c.1221G>A	c.(1219-1221)ccG>ccA	p.P407P	UPF3A_ENST00000351487.5_Silent_p.P374P|UPF3A_ENST00000475218.2_3'UTR	NM_023011.3	NP_075387.1	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A (yeast)	407					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)		GCGGGGCTCCGGGGGAGGCCA	0.567													G|||	14	0.00279553	0.0008	0.0043	5008	,	,		19212	0.0		0.0099	False		,,,				2504	0.0				p.P407P		Atlas-SNP	.											.	UPF3A	47	.	0			c.G1221A						PASS	.	G	,	13,4359		0,13,2173	14	19	17		1221,1122	-9.9	0	13	dbSNP_134	17	156,8366		2,152,4107	no	coding-synonymous,coding-synonymous	UPF3A	NM_023011.3,NM_080687.2	,	2,165,6280	AA,AG,GG		1.8306,0.2973,1.3107	,	407/477,374/444	115067419	169,12725	2186	4261	6447	SO:0001819	synonymous_variant	65110	exon9			GGCTCCGGGGGAG	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.1221G>A	13.37:g.115067419G>A		140	0	0		115	60	0.521739	NM_023011	A2A366|Q5T8C3|Q5T8C9|Q7Z6N3|Q86YK1|Q9BZI8	Silent	SNP	ENST00000375299.3	37	CCDS9543.1																																																																																			G|0.991;A|0.009	0.009	strong		0.567	UPF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045968.2			A	115067419	G	A	115067419	2	1	23	1	0	0	0	0	0	0	0	1	17020	1103	39	1		1	UPF3A	13	115067419	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	62754166	115067419	102459	513	7957											
METTL3	56339	hgsc.bcm.edu	37	chr14	21971694	21971694	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ttctgcaggaggctttctacCccatcttgagtggcaggagc	7	11	12	11	0	3	1	0	1	3	0	3	3	3	3	2	4	3	3	2	4	1	4	rs11540964	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:21971694C>G	ENST00000298717.4	-	3	496	c.345G>C	c.(343-345)ggG>ggC	p.G115G	METTL3_ENST00000538267.1_Silent_p.G115G	NM_019852.3	NP_062826.2	Q86U44	MTA70_HUMAN	methyltransferase like 3	115					circadian rhythm (GO:0007623)|gene expression (GO:0010467)|mRNA destabilization (GO:0061157)|mRNA methylation (GO:0080009)|mRNA processing (GO:0006397)|RNA methylation (GO:0001510)|stem cell maintenance (GO:0019827)	MIS complex (GO:0036396)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity (GO:0016422)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(95;0.000628)		Epithelial(56;6.61e-06)	GBM - Glioblastoma multiforme(265;0.0146)		GGCTTTCTACCCCATCTTGAG	0.478													C|||	2	0.000399361	0.0	0.0	5008	,	,		23416	0.0		0.002	False		,,,				2504	0.0				p.G115G		Atlas-SNP	.											.	METTL3	48	.	0			c.G345C						PASS	.	C		0,4406		0,0,2203	60	56	57		345	-4	0.9	14	dbSNP_120	57	25,8575	16.6+/-54.9	0,25,4275	no	coding-synonymous	METTL3	NM_019852.3		0,25,6478	GG,GC,CC		0.2907,0.0,0.1922		115/581	21971694	25,12981	2203	4300	6503	SO:0001819	synonymous_variant	56339	exon3			TTCTACCCCATCT	AF014837	CCDS32044.1	14q11.1	2012-06-12			ENSG00000165819	ENSG00000165819	2.1.1.62		17563	protein-coding gene	gene with protein product	"N6-adenosine-methyltransferase 70 kDa subunit"	612472					Standard	XM_006720206		Approved	Spo8, M6A, MT-A70	uc001wbc.3	Q86U44	OTTHUMG00000168825	ENST00000298717.4:c.345G>C	14.37:g.21971694C>G		54	0	0		59	27	0.457627	NM_019852	O14736|Q86V05|Q9HB32	Silent	SNP	ENST00000298717.4	37	CCDS32044.1																																																																																			C|0.998;G|0.002	0.002	strong		0.478	METTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401227.1	NM_019852		G	21971694	C	G	21971694	2	3	23	1	0	0	0	0	0	0	0	1	9510	610	22	4		4	METTL3	14	21971694	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10		21971694	85377846	514	7958											
CIDEB	27141	hgsc.bcm.edu	37	chr14	24775287	24775287	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acgtcaaaggtgaatcgggcGatgtccttgctgtgcttggg	7	11	15	8	3	1	1	1	1	0	0	3	2	2	1	1	3	2	2	1	3	2	2	rs139893717	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:24775287G>A	ENST00000336557.5	-	7	1695	c.393C>T	c.(391-393)atC>atT	p.I131I	CIDEB_ENST00000258807.5_Silent_p.I131I|CIDEB_ENST00000554411.1_Silent_p.I131I|NOP9_ENST00000267425.3_3'UTR|LTB4R2_ENST00000528054.1_5'Flank			Q9UHD4	CIDEB_HUMAN	cell death-inducing DFFA-like effector b	131					apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|regulation of apoptotic process (GO:0042981)	cytosol (GO:0005829)|lipid particle (GO:0005811)	identical protein binding (GO:0042802)			NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|urinary_tract(1)	7				GBM - Glioblastoma multiforme(265;0.0181)		TGAATCGGGCGATGTCCTTGC	0.527													G|||	8	0.00159744	0.0	0.0072	5008	,	,		21522	0.0		0.002	False		,,,				2504	0.001				p.I131I		Atlas-SNP	.											.	CIDEB	17	.	0			c.C393T						PASS	.	G		9,4397	15.5+/-35.6	0,9,2194	196	166	176		393	0.1	1	14	dbSNP_134	176	72,8528	43.1+/-100.9	1,70,4229	no	coding-synonymous	CIDEB	NM_014430.2		1,79,6423	AA,AG,GG		0.8372,0.2043,0.6228		131/220	24775287	81,12925	2203	4300	6503	SO:0001819	synonymous_variant	27141	exon6			TCGGGCGATGTCC	AF190901	CCDS32056.1	14q12	2012-09-20			ENSG00000136305	ENSG00000136305			1977	protein-coding gene	gene with protein product		604441				10619428, 10837461	Standard	XM_005267540		Approved		uc001woo.3	Q9UHD4	OTTHUMG00000171555	ENST00000336557.5:c.393C>T	14.37:g.24775287G>A		70	0	0		62	28	0.451613	NM_014430	D3DS73|Q546V8|Q9NNW9	Silent	SNP	ENST00000336557.5	37	CCDS32056.1																																																																																			G|0.995;A|0.005	0.005	strong		0.527	CIDEB-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414120.1			A	24775287	G	A	24775287	2	1	23	1	0	0	0	0	0	0	0	1	3428	1048	37	1		1	CIDEB	14	24775287	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	2803593	24775287	82574253	515	7959											
ADCY4	196883	hgsc.bcm.edu	37	chr14	24803710	24803710	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctcggctcaccctgccgctgGcccaggccactgcgagcagc	5	5	12	19	3	1	0	1	0	0	0	2	1	1	0	4	3	4	3	4	3	0	0	rs77202343	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:24803710G>A	ENST00000310677.4	-	2	262	c.149C>T	c.(148-150)gCc>gTc	p.A50V	ADCY4_ENST00000558563.1_5'UTR|ADCY4_ENST00000554068.2_Missense_Mutation_p.A50V|ADCY4_ENST00000418030.2_Missense_Mutation_p.A50V|RP11-934B9.3_ENST00000555591.1_Intron|ADCY4_ENST00000396747.3_5'UTR	NM_001198568.1|NM_001198592.1|NM_139247.3	NP_001185497.1|NP_001185521.1|NP_640340.2	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4	50					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)		CCTGCCGCTGGCCCAGGCCAC	0.637													G|||	42	0.00838658	0.0023	0.0101	5008	,	,		11094	0.0		0.0229	False		,,,				2504	0.0092				p.A50V		Atlas-SNP	.											.	ADCY4	86	.	0			c.C149T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA	21,4081		0,21,2030	5	5	5		149,149,149	5.4	1	14	dbSNP_131	5	159,7961		2,155,3903	no	missense,missense,missense	ADCY4	NM_001198568.1,NM_001198592.1,NM_139247.3	64,64,64	2,176,5933	AA,AG,GG		1.9581,0.5119,1.4728	benign,benign,benign	50/1078,50/1078,50/1078	24803710	180,12042	2051	4060	6111	SO:0001583	missense	196883	exon2			CCGCTGGCCCAGG	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.149C>T	14.37:g.24803710G>A	ENSP00000312126:p.Ala50Val	26	0	0		14	9	0.642857	NM_001198592	B3KV74|D3DS75|Q17R40|Q6ZTM6|Q96ML7	Missense_Mutation	SNP	ENST00000310677.4	37	CCDS9627.1	26	0.011904761904761904	3	0.006097560975609756	3	0.008287292817679558	0	0.0	20	0.026385224274406333	G	35	5.421899	0.96111	0.005119	0.019581	ENSG00000129467	ENST00000310677;ENST00000554068;ENST00000418030	T;T;T	0.76316	-1.01;-1.01;-1.01	5.45	5.45	0.79879	.	0.000000	0.46145	D	0.000314	T	0.66066	0.2752	L	0.50333	1.59	0.80722	D	1	D;D	0.63046	0.992;0.985	D;P	0.66602	0.945;0.771	T	0.71174	-0.4670	10	0.15499	T	0.54	.	16.8265	0.85933	0.0:0.0:1.0:0.0	.	50;50	G3V258;Q8NFM4	.;ADCY4_HUMAN	V	50	ENSP00000312126:A50V;ENSP00000452250:A50V;ENSP00000393177:A50V	ENSP00000312126:A50V	A	-	2	0	ADCY4	23873550	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.145000	0.71769	2.838000	0.97847	0.655000	0.94253	GCC	G|0.987;A|0.013	0.013	strong		0.637	ADCY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073200.4			A	24803710	G	A	24803710	3	1	23	1	0	0	0	0	1	0	0	0	296	1203	42	2	3184	2	ADCY4	14	24803710	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	28423	24803710	82545830	516	7960											
NUBPL	80224	hgsc.bcm.edu	37	chr14	32319354	32319354	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccttacaccttaatataaggGaagcttcagatacaggccag	14	9	8	10	0	1	1	1	0	0	1	1	2	1	2	3	2	3	1	3	2	6	6			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:32319354G>T	ENST00000281081.7	+	10	889	c.844G>T	c.(844-846)Gaa>Taa	p.E282*	NUBPL_ENST00000536705.1_Nonsense_Mutation_p.E186*|NUBPL_ENST00000418681.2_3'UTR	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	282					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)		TAATATAAGGGAAGCTTCAGA	0.358																																					p.E282X		Atlas-SNP	.											.	NUBPL	21	.	0			c.G844T						PASS	.						95	89	91					14																	32319354		1811	4084	5895	SO:0001587	stop_gained	80224	exon10			ATAAGGGAAGCTT	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.844G>T	14.37:g.32319354G>T	ENSP00000281081:p.Glu282*	137	0	0		138	10	0.0724638	NM_025152	B4DHZ1|Q86TZ4|Q9H9M2	Nonsense_Mutation	SNP	ENST00000281081.7	37	CCDS41940.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.524580	0.85600	.	.	ENSG00000151413	ENST00000550649;ENST00000281081;ENST00000536705	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-10.7882	18.1531	0.89682	0.0:0.0:1.0:0.0	.	.	.	.	X	148;282;186	.	ENSP00000281081:E282X	E	+	1	0	NUBPL	31389105	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	4.773000	0.62331	2.885000	0.99019	0.655000	0.94253	GAA	.	.	none		0.358	NUBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409519.1	NM_025152		T	32319354	G	T	32319354	4	4	23	1	0	0	0	0	0	1	0	0	10726	1175	41	4	882	4	NUBPL	14	32319354	Nonsense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	7515644	32319354	75030186	517	7961											
FBXO33	254170	hgsc.bcm.edu	37	chr14	39870594	39870594	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctatcaaaatgaatcctctcTagtggtatactgggtttcag	11	14	8	8	0	3	1	2	1	1	0	5	1	4	1	1	2	1	2	1	2	7	5	rs61754302		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:39870594T>C	ENST00000298097.7	-	3	1519	c.1182A>G	c.(1180-1182)ctA>ctG	p.L394L	FBXO33_ENST00000554190.1_Intron	NM_203301.3	NP_976046.1	Q7Z6M2	FBX33_HUMAN	F-box protein 33	394					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)		GAATCCTCTCTAGTGGTATAC	0.368																																					p.L394L		Atlas-SNP	.											.	FBXO33	21	.	0			c.A1182G						PASS	.	T		0,4406		0,0,2203	100	96	97		1182	0.4	1	14	dbSNP_129	97	3,8597	3.7+/-12.6	0,3,4297	no	coding-synonymous	FBXO33	NM_203301.3		0,3,6500	CC,CT,TT		0.0349,0.0,0.0231		394/556	39870594	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	254170	exon3			CCTCTCTAGTGGT	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.1182A>G	14.37:g.39870594T>C		125	0	0		143	70	0.48951	NM_203301	Q6PIR2|Q86TR2|Q86YE0	Silent	SNP	ENST00000298097.7	37	CCDS9677.1																																																																																			T|1.000;C|0.000	0.000	weak		0.368	FBXO33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276769.2			C	39870594	T	C	39870594	2	2	23	1	0	0	0	0	0	0	0	1	5751	1509	53	3		3	FBXO33	14	39870594	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	7551240	39870594	67478946	518	7962											
SOS2	6655	hgsc.bcm.edu	37	chr14	50626657	50626657	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgtttggcaccgattcttgtCaatggtccctccataatgaa	9	14	8	10	1	2	1	1	1	1	0	4	2	4	1	3	2	0	2	3	2	3	4	rs35530861	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:50626657C>T	ENST00000216373.5	-	10	1618	c.1344G>A	c.(1342-1344)ttG>ttA	p.L448L	SOS2_ENST00000543680.1_Silent_p.L415L|SOS2_ENST00000555794.1_5'UTR	NM_006939.2	NP_008870.2	Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	448	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)					CGATTCTTGTCAATGGTCCCT	0.383													C|||	6	0.00119808	0.0	0.0014	5008	,	,		19647	0.0		0.005	False		,,,				2504	0.0				p.L448L		Atlas-SNP	.											.	SOS2	195	.	0			c.G1344A						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	197	185	189		1344	3.7	1	14	dbSNP_126	189	41,8559	27.9+/-77.7	0,41,4259	no	coding-synonymous	SOS2	NM_006939.2		0,43,6460	TT,TC,CC		0.4767,0.0454,0.3306		448/1333	50626657	43,12963	2203	4300	6503	SO:0001819	synonymous_variant	6655	exon10			TCTTGTCAATGGT	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.1344G>A	14.37:g.50626657C>T		272	0	0		281	140	0.498221	NM_006939	B7ZKT6|D3DSB4|Q15503|Q17RN1	Silent	SNP	ENST00000216373.5	37	CCDS9697.1																																																																																			C|0.997;T|0.003	0.003	strong		0.383	SOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276878.2			T	50626657	C	T	50626657	2	4	23	1	0	0	0	0	0	0	0	1	14952	825	29	2		2	SOS2	14	50626657	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	10756063	50626657	56722883	519	7963											
SLC35F4	341880	hgsc.bcm.edu	37	chr14	58060707	58060707	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacaaactcctgaggatcctTggttttgaagttcaagaata	13	12	8	8	0	1	3	1	2	0	1	3	4	3	4	2	2	1	2	2	2	5	5	rs145246618	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:58060707T>C	ENST00000339762.6	-	2	346	c.347A>G	c.(346-348)cAa>cGa	p.Q116R	SLC35F4_ENST00000557430.1_5'Flank|SLC35F4_ENST00000554729.1_5'UTR|SLC35F4_ENST00000556826.1_Missense_Mutation_p.Q80R			A4IF30	S35F4_HUMAN	solute carrier family 35, member F4	116					transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|large_intestine(3)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						TGAGGATCCTTGGTTTTGAAG	0.478													C|||	9	0.00179712	0.0068	0.0	5008	,	,		18702	0.0		0.0	False		,,,				2504	0.0				p.Q80R		Atlas-SNP	.											SLC35F4_ENST00000339762,right_upper_lobe,carcinoma,0,2	SLC35F4	105	2	0			c.A239G						PASS	.	C	ARG/GLN	26,3862		0,26,1918	92	92	92		239	5.8	1	14	dbSNP_134	92	4,8274		0,4,4135	yes	missense	SLC35F4	NM_001206920.1	43	0,30,6053	CC,CT,TT		0.0483,0.6687,0.2466	benign	80/485	58060707	30,12136	1944	4139	6083	SO:0001583	missense	341880	exon2			GATCCTTGGTTTT			14q22.3	2013-05-22		2003-11-28	ENSG00000151812	ENSG00000151812		"Solute carriers"	19845	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 36"	C14orf36			Standard	NM_001206920		Approved	FLJ37712	uc021rtp.1	A4IF30	OTTHUMG00000171317	ENST00000339762.6:c.347A>G	14.37:g.58060707T>C	ENSP00000342518:p.Gln116Arg	231	0	0		186	94	0.505376	NM_001206920	A6NDQ3	Missense_Mutation	SNP	ENST00000339762.6	37		7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	7.347	0.622089	0.14193	0.006687	4.83E-4	ENSG00000151812	ENST00000556826;ENST00000339762	T;T	0.38722	1.15;1.12	5.83	5.83	0.93111	.	0.207799	0.41500	N	0.000877	T	0.10337	0.0253	N	0.01048	-1.04	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.16453	-1.0402	10	0.02654	T	1	-3.5905	13.5376	0.61655	0.0:0.928:0.0:0.072	.	116	A4IF30	S35F4_HUMAN	R	80;116	ENSP00000452086:Q80R;ENSP00000342518:Q116R	ENSP00000342518:Q116R	Q	-	2	0	SLC35F4	57130460	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	3.174000	0.50847	1.489000	0.48450	-0.197000	0.12766	CAA	T|0.997;C|0.003	0.003	strong		0.478	SLC35F4-201	KNOWN	basic	protein_coding	protein_coding		XM_292260		C	58060707	T	C	58060707	3	2	23	1	0	0	0	0	1	0	0	0	14606	1812	63	3	1246	3	SLC35F4	14	58060707	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	7434050	58060707	49288833	520	7964											
C14orf37	145407	hgsc.bcm.edu	37	chr14	58604730	58604730	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcattgtatttcccaacagTtggtctgcctcagactcata	9	15	6	11	0	4	1	3	0	1	1	5	1	5	1	2	1	2	2	2	1	3	6	rs137871178	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:58604730T>C	ENST00000267485.7	-	2	1541	c.1347A>G	c.(1345-1347)caA>caG	p.Q449Q	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	449						integral component of membrane (GO:0016021)		p.Q449Q(1)		breast(7)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|skin(1)	33						TTCCCAACAGTTGGTCTGCCT	0.343													T|||	22	0.00439297	0.0	0.0043	5008	,	,		18899	0.001		0.0109	False		,,,				2504	0.0072				p.Q449Q		Atlas-SNP	.											C14orf37,NS,carcinoma,0,1	C14orf37	87	1	1	Substitution - coding silent(1)	pancreas(1)	c.A1347G						PASS	.	T		3,4403	6.2+/-15.9	0,3,2200	71	73	73		1347	-7	0	14	dbSNP_134	73	101,8499	54.8+/-115.7	1,99,4200	no	coding-synonymous	C14orf37	NM_001001872.2		1,102,6400	CC,CT,TT		1.1744,0.0681,0.7996		449/775	58604730	104,12902	2203	4300	6503	SO:0001819	synonymous_variant	145407	exon2			CAACAGTTGGTCT		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.1347A>G	14.37:g.58604730T>C		64	0	0		68	36	0.529412	NM_001001872	A8K8Z8|Q6P5Q1|Q86TY1	Silent	SNP	ENST00000267485.7	37	CCDS32089.1																																																																																			T|0.992;C|0.008	0.008	strong		0.343	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872		C	58604730	T	C	58604730	2	2	23	1	0	0	0	0	0	0	0	1	1773	1722	60	3		3	C14orf37	14	58604730	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	544023	58604730	48744810	521	7965											
KCNH5	27133	hgsc.bcm.edu	37	chr14	63174700	63174700	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cccattgactcagctttagtGacattattccagtcttcctt	8	16	5	12	0	2	2	1	2	1	0	4	2	4	2	3	0	1	1	3	0	2	7	rs142813655		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:63174700G>A	ENST00000322893.7	-	11	2761	c.2493C>T	c.(2491-2493)gtC>gtT	p.V831V	KCNH5_ENST00000420622.2_3'UTR	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	831					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)		CAGCTTTAGTGACATTATTCC	0.433																																					p.V831V		Atlas-SNP	.											.	KCNH5	320	.	0			c.C2493T						PASS	.	G	,	0,4406		0,0,2203	158	148	151		2493,	5	1	14	dbSNP_134	151	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,utr-3	KCNH5	NM_139318.3,NM_172375.1	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	831/989,	63174700	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	27133	exon11			TTTAGTGACATTA	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.2493C>T	14.37:g.63174700G>A		359	0	0		425	210	0.494118	NM_139318	C9JP98	Silent	SNP	ENST00000322893.7	37	CCDS9756.1																																																																																			G|1.000;A|0.000	0.000	weak		0.433	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		A	63174700	G	A	63174700	2	1	23	1	0	0	0	0	0	0	0	1	8044	1277	45	2		2	KCNH5	14	63174700	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	4569970	63174700	44174840	522	7966											
KCNH5	27133	hgsc.bcm.edu	37	chr14	63175012	63175012	+	Silent	SNP	A	A	G																															agttggttcctctcagggtcAccctgtgttgagccctgatt																										TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:63175012A>G	ENST00000322893.7	-	11	2449	c.2181T>C	c.(2179-2181)ggT>ggC	p.G727G	KCNH5_ENST00000420622.2_3'UTR	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	727					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)		TCTCAGGGTCACCCTGTGTTG	0.557																																					p.G727G		Atlas-SNP	.											KCNH5,NS,carcinoma,-1,1	KCNH5	320	1	0			c.T2181C						PASS	.						114	106	109					14																	63175012		2203	4300	6503	SO:0001819	synonymous_variant	27133	exon11			AGGGTCACCCTGT	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.2181T>C	14.37:g.63175012A>G		156	0	0		160	67	0.41875	NM_139318	C9JP98	Silent	SNP	ENST00000322893.7	37	CCDS9756.1																																																																																			.	.	none		0.557	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		G	63175012	A	G	63175012	2	3	23	1	0	0	0	0	0	0	0	1	8044	146	6	3		3	KCNH5	14	63175012	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	312	63175012	44174528	523	7967	102	2									
KCNH5	27133	hgsc.bcm.edu	37	chr14	63175013	63175013	+	Missense_Mutation	SNP	C	C	T																															gttggttcctctcagggtcaCcctgtgttgagccctgattc																										TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:63175013C>T	ENST00000322893.7	-	11	2448	c.2180G>A	c.(2179-2181)gGt>gAt	p.G727D	KCNH5_ENST00000420622.2_3'UTR	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	727					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)		CTCAGGGTCACCCTGTGTTGA	0.557																																					p.G727D		Atlas-SNP	.											KCNH5,NS,carcinoma,0,1	KCNH5	320	1	0			c.G2180A						PASS	.						115	107	110					14																	63175013		2203	4300	6503	SO:0001583	missense	27133	exon11			GGGTCACCCTGTG	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.2180G>A	14.37:g.63175013C>T	ENSP00000321427:p.Gly727Asp	159	0	0		161	68	0.42236	NM_139318	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	37	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	C	0.402	-0.917791	0.02396	.	.	ENSG00000140015	ENST00000322893	D	0.98849	-5.18	5.52	2.7	0.31948	.	0.410001	0.25494	N	0.030283	D	0.95191	0.8441	L	0.34521	1.04	0.34981	D	0.754079	B	0.10296	0.003	B	0.17098	0.017	D	0.91085	0.4902	10	0.19147	T	0.46	.	6.6545	0.22981	0.3021:0.5555:0.0:0.1423	.	727	Q8NCM2	KCNH5_HUMAN	D	727	ENSP00000321427:G727D	ENSP00000321427:G727D	G	-	2	0	KCNH5	62244766	0.000000	0.05858	0.065000	0.19835	0.001000	0.01503	0.059000	0.14322	0.297000	0.22615	-0.181000	0.13052	GGT	.	.	none		0.557	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		T	63175013	C	T	63175013	3	4	23	1	0	0	0	0	1	0	0	0	8044	507	18	2	790	2	KCNH5	14	63175013	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1	63175013	44174527	524	7968	102	2									
AKAP5	9495	hgsc.bcm.edu	37	chr14	64935726	64935726	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgtgagcaatagcacaacttCtggagagaaagtgatttcag	14	10	11	6	0	2	3	1	2	1	1	2	5	2	4	0	1	3	2	0	1	4	3	rs2230492	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:64935726C>T	ENST00000394718.4	+	2	992	c.614C>T	c.(613-615)tCt>tTt	p.S205F	ZBTB25_ENST00000555424.1_Intron|AKAP5_ENST00000320636.5_Missense_Mutation_p.S205F|ZBTB25_ENST00000555220.1_Intron	NM_004857.3	NP_004848.3	P24588	AKAP5_HUMAN	A kinase (PRKA) anchor protein 5	205					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)		AGCACAACTTCTGGAGAGAAA	0.413													C|||	7	0.00139776	0.0	0.0	5008	,	,		21422	0.0		0.006	False		,,,				2504	0.001				p.S205F		Atlas-SNP	.											.	AKAP5	23	.	0			c.C614T						PASS	.	C	PHE/SER	7,4399	12.9+/-30.5	0,7,2196	97	101	100		614	6	1	14	dbSNP_98	100	56,8544	35.9+/-90.5	0,56,4244	yes	missense	AKAP5	NM_004857.3	155	0,63,6440	TT,TC,CC		0.6512,0.1589,0.4844	benign	205/428	64935726	63,12943	2203	4300	6503	SO:0001583	missense	9495	exon2			CAACTTCTGGAGA	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.614C>T	14.37:g.64935726C>T	ENSP00000378207:p.Ser205Phe	86	0	0		94	39	0.414894	NM_004857	A2RRB8	Missense_Mutation	SNP	ENST00000394718.4	37	CCDS9764.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	15.66	2.899719	0.52227	0.001589	0.006512	ENSG00000179841	ENST00000394718;ENST00000320636	T;T	0.32272	1.46;1.46	6.02	6.02	0.97574	.	0.341615	0.25383	N	0.031074	T	0.39860	0.1094	L	0.55481	1.735	0.37227	D	0.905491	D	0.65815	0.995	P	0.57371	0.819	T	0.46652	-0.9176	10	0.87932	D	0	-9.0253	17.454	0.87602	0.0:1.0:0.0:0.0	rs2230492;rs2230492	205	P24588	AKAP5_HUMAN	F	205	ENSP00000378207:S205F;ENSP00000315615:S205F	ENSP00000315615:S205F	S	+	2	0	AKAP5	64005479	0.035000	0.19736	0.957000	0.39632	0.717000	0.41224	1.428000	0.34892	2.857000	0.98124	0.650000	0.86243	TCT	C|0.996;T|0.004	0.004	strong		0.413	AKAP5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268070.3			T	64935726	C	T	64935726	3	4	23	1	0	0	0	0	1	0	0	0	454	913	32	2	616	2	AKAP5	14	64935726	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1760713	64935726	42413814	525	7969											
RAD51L1	5890	hgsc.bcm.edu	37	chr14	68353893	68353893	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagagaggcatcctccttgaAgtatttggctgaggagtttt	10	13	12	6	0	0	3	0	2	0	1	2	5	2	4	2	3	0	4	2	3	3	5	rs34594234	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:68353893A>G	ENST00000487270.1	+	7	776	c.728A>G	c.(727-729)aAg>aGg	p.K243R	RAD51B_ENST00000471583.1_Missense_Mutation_p.K243R|RAD51B_ENST00000488612.1_Missense_Mutation_p.K243R|RAD51B_ENST00000487861.1_Missense_Mutation_p.K243R|RAD51B_ENST00000469165.2_3'UTR|RAD51B_ENST00000390683.3_Missense_Mutation_p.K243R	NM_133509.3	NP_598193.2	O15315	RA51B_HUMAN	RAD51 paralog B	243			K -> R (in dbSNP:rs34594234). {ECO:0000269|Ref.5}.		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						TCCTCCTTGAAGTATTTGGCT	0.358								Direct reversal of damage					A|||	15	0.00299521	0.0	0.0043	5008	,	,		14243	0.0		0.0089	False		,,,				2504	0.0031				p.K243R		Atlas-SNP	.											.	RAD51B	80	.	0			c.A728G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS	17,4389	22.3+/-47.3	0,17,2186	74	76	76		728,728,728	5.9	1	14	dbSNP_126	76	97,8503	51.1+/-111.2	2,93,4205	yes	missense,missense,missense	RAD51B	NM_002877.5,NM_133509.3,NM_133510.3	26,26,26	2,110,6391	GG,GA,AA		1.1279,0.3858,0.8765	probably-damaging,probably-damaging,probably-damaging	243/351,243/385,243/351	68353893	114,12892	2203	4300	6503	SO:0001583	missense	5890	exon7			CCTTGAAGTATTT	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.728A>G	14.37:g.68353893A>G	ENSP00000419471:p.Lys243Arg	110	0	0		152	67	0.440789	NM_133509	O60914|O75210|Q3Y4F8|Q6FHX8|Q86SY3|Q86SY4|Q86TR0|Q86U92|Q86U93|Q86U94|Q8N6H4|Q9UPL5	Missense_Mutation	SNP	ENST00000487270.1	37	CCDS9789.1	9	0.004120879120879121	0	0.0	3	0.008287292817679558	0	0.0	6	0.0079155672823219	A	25.4	4.630716	0.87660	0.003858	0.011279	ENSG00000182185	ENST00000487861;ENST00000471583;ENST00000487270;ENST00000488612;ENST00000390683;ENST00000402498;ENST00000342389	T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29	5.9	5.9	0.94986	DNA recombination/repair protein RecA/RadB, ATP-binding domain (1);ATPase, AAA+ type, core (1);DNA recombination and repair protein Rad51, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.66819	0.2828	L	0.33293	1	0.44485	D	0.997423	D;D;D;D;D;P	0.89917	1.0;1.0;1.0;1.0;1.0;0.746	D;D;D;D;D;P	0.97110	1.0;1.0;1.0;1.0;1.0;0.8	T	0.69595	-0.5103	10	0.34782	T	0.22	-21.1874	14.8985	0.70661	1.0:0.0:0.0:0.0	rs34594234	243;243;243;243;243;243	C9JYJ0;C9JSP9;O15315-4;O15315;O15315-1;O15315-2	.;.;.;RA51B_HUMAN;.;.	R	243	ENSP00000419881:K243R;ENSP00000418859:K243R;ENSP00000419471:K243R;ENSP00000420061:K243R;ENSP00000375101:K243R	ENSP00000343531:K243R	K	+	2	0	RAD51B	67423646	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	6.799000	0.75160	2.266000	0.75297	0.528000	0.53228	AAG	A|0.992;G|0.008	0.008	strong		0.358	RAD51B-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000349063.1			G	68353893	A	G	68353893	3	3	23	1	0	0	0	0	1	0	0	0	13004	72	3	3	750	3	RAD51L1	14	68353893	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	3418167	68353893	38995647	526	7970											
ACTN1	87	hgsc.bcm.edu	37	chr14	69341653	69341653	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcacggagtcggggccggTgtagggggccatccgcgcga	5	5	20	11	6	0	0	0	0	0	0	2	2	1	1	3	7	0	2	3	7	1	1	rs11557769	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:69341653T>A	ENST00000193403.6	-	21	2985	c.2602A>T	c.(2602-2604)Acc>Tcc	p.T868S	ACTN1_ENST00000438964.2_Missense_Mutation_p.T863S|ACTN1_ENST00000376839.3_Missense_Mutation_p.T798S|ACTN1_ENST00000538545.2_Missense_Mutation_p.T906S|ACTN1_ENST00000394419.4_Missense_Mutation_p.T890S	NM_001102.3	NP_001093.1	P12814	ACTN1_HUMAN	actinin, alpha 1	868			T -> S (in dbSNP:rs11557769).		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)		TCGGGGCCGGTGTAGGGGGCC	0.662													t|||	31	0.0061901	0.0	0.0159	5008	,	,		14509	0.0		0.0189	False		,,,				2504	0.001				p.T890S		Atlas-SNP	.											ACTN1,NS,carcinoma,+2,1	ACTN1	77	1	0			c.A2668T						scavenged	.	T	SER/THR,SER/THR,SER/THR	16,4390	25.3+/-52.1	0,16,2187	42	41	41		2602,2668,2587	-2.7	0.9	14	dbSNP_120	41	142,8458	70.3+/-132.9	0,142,4158	yes	missense,missense,missense	ACTN1	NM_001102.3,NM_001130004.1,NM_001130005.1	58,58,58	0,158,6345	AA,AT,TT		1.6512,0.3631,1.2148	benign,benign,benign	868/893,890/915,863/888	69341653	158,12848	2203	4300	6503	SO:0001583	missense	87	exon22			GGCCGGTGTAGGG	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.2602A>T	14.37:g.69341653T>A	ENSP00000193403:p.Thr868Ser	66	1	0.0151515		80	32	0.4	NM_001130004	B3V8S3|B4DHH3|B7TY16|Q1HE25|Q9BTN1	Missense_Mutation	SNP	ENST00000193403.6	37	CCDS9792.1	18	0.008241758241758242	0	0.0	8	0.022099447513812154	0	0.0	10	0.013192612137203167	T	9.571	1.121108	0.20877	0.003631	0.016512	ENSG00000072110	ENST00000193403;ENST00000394419;ENST00000438964;ENST00000376839;ENST00000538545	T;T;T;T;T	0.39229	1.6;1.09;1.09;1.09;1.09	4.68	-2.72	0.05968	EF-hand, Ca insensitive (1);EF-hand-like domain (1);	0.656003	0.15664	N	0.250756	T	0.09642	0.0237	L	0.28556	0.865	0.22185	N	0.999308	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	0.21690	-1.0238	10	0.08381	T	0.77	.	2.1866	0.03888	0.1289:0.3501:0.1331:0.3879	rs11557769	863;890;868;510	P12814-2;Q1HE25;P12814;B4DFY0	.;.;ACTN1_HUMAN;.	S	868;890;863;798;906	ENSP00000193403:T868S;ENSP00000377941:T890S;ENSP00000414272:T863S;ENSP00000366035:T798S;ENSP00000439828:T906S	ENSP00000193403:T868S	T	-	1	0	ACTN1	68411406	0.003000	0.15002	0.930000	0.37139	0.998000	0.95712	-0.007000	0.12810	-0.578000	0.05959	0.528000	0.53228	ACC	T|0.988;A|0.012	0.012	strong		0.662	ACTN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413233.3	NM_001102		A	69341653	T	A	69341653	3	1	23	1	0	0	0	0	1	0	0	0	204	1696	59	5	80	5	ACTN1	14	69341653	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	987760	69341653	38007887	527	7971											
ADAM21	8747	hgsc.bcm.edu	37	chr14	70924432	70924432	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggtttgggggccagaaacaCgttgttcatatgagggtcaa	10	10	14	7	2	2	2	2	1	0	1	2	2	2	2	1	4	1	3	1	4	3	4	rs553149454		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:70924432C>T	ENST00000603540.1	+	2	474	c.216C>T	c.(214-216)caC>caT	p.H72H	ADAM21_ENST00000267499.3_Silent_p.H72H|RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	72					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)	p.H72H(2)		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)		GCCAGAAACACGTTGTTCATA	0.537													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20886	0.0		0.0	False		,,,				2504	0.0				p.H72H		Atlas-SNP	.											ADAM21_ENST00000267499,colon,carcinoma,0,2	ADAM21	181	2	2	Substitution - coding silent(2)	large_intestine(2)	c.C216T						scavenged	.						122	128	126					14																	70924432		2203	4300	6503	SO:0001819	synonymous_variant	8747	exon2			GAAACACGTTGTT	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.216C>T	14.37:g.70924432C>T		315	0	0		265	14	0.0528302	NM_003813	O43507|Q2VPC6|Q32MR0	Silent	SNP	ENST00000603540.1	37	CCDS9804.1																																																																																			.	.	none		0.537	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3			T	70924432	C	T	70924432	2	4	23	1	0	0	0	0	0	0	0	1	243	535	19	1		1	ADAM21	14	70924432	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1582779	70924432	36425108	528	7972											
SIPA1L1	26037	hgsc.bcm.edu	37	chr14	72090809	72090809	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctggaggacgccattccgtcGacagccaagcactcgacagc	10	5	11	15	4	0	0	0	0	0	0	3	4	1	2	3	2	3	1	3	2	1	1	rs113082664	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:72090809G>A	ENST00000555818.1	+	4	2022	c.1674G>A	c.(1672-1674)tcG>tcA	p.S558S	SIPA1L1_ENST00000358550.2_Silent_p.S558S|SIPA1L1_ENST00000537413.1_Silent_p.S33S|SIPA1L1_ENST00000381232.3_Silent_p.S558S	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	558					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)		CCATTCCGTCGACAGCCAAGC	0.577													G|||	26	0.00519169	0.0151	0.0029	5008	,	,		19331	0.0		0.004	False		,,,				2504	0.0				p.S558S		Atlas-SNP	.											.	SIPA1L1	219	.	0			c.G1674A						PASS	.	G		78,4328	69.2+/-107.0	1,76,2126	170	154	159		1674	-4.7	0.9	14	dbSNP_132	159	14,8586	11.2+/-40.8	0,14,4286	no	coding-synonymous	SIPA1L1	NM_015556.1		1,90,6412	AA,AG,GG		0.1628,1.7703,0.7074		558/1805	72090809	92,12914	2203	4300	6503	SO:0001819	synonymous_variant	26037	exon4			TCCGTCGACAGCC	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.1674G>A	14.37:g.72090809G>A		80	0	0		85	35	0.411765	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Silent	SNP	ENST00000555818.1	37	CCDS9807.1																																																																																			G|0.994;A|0.006	0.006	strong		0.577	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		A	72090809	G	A	72090809	2	1	23	1	0	0	0	0	0	0	0	1	14344	1045	37	1		1	SIPA1L1	14	72090809	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1166377	72090809	35258731	529	7973											
GSTZ1	2954	hgsc.bcm.edu	37	chr14	77793237	77793237	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccatcaatctcataaaggatGggggccaacaggtaagaagg	15	6	12	8	0	2	1	2	0	1	1	3	2	2	2	2	5	1	1	2	5	6	2	rs7972	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:77793237G>A	ENST00000556627.1	+	3	255	c.124G>A	c.(124-126)Ggg>Agg	p.G42R	GSTZ1_ENST00000554279.1_Missense_Mutation_p.G42R|GSTZ1_ENST00000557639.1_5'UTR|GSTZ1_ENST00000553586.1_Missense_Mutation_p.G43R|GSTZ1_ENST00000557053.1_5'UTR|GSTZ1_ENST00000216465.5_Missense_Mutation_p.G42R|GSTZ1_ENST00000349555.3_Missense_Mutation_p.G42R|GSTZ1_ENST00000361389.4_5'UTR|GSTZ1_ENST00000393734.1_5'UTR			O43708	MAAI_HUMAN	glutathione S-transferase zeta 1	42	GST N-terminal.		R -> G (in allele GSTZ1*B and allele GSTZ1*C; dbSNP:rs7972). {ECO:0000269|PubMed:10373324, ECO:0000269|PubMed:10739172, ECO:0000269|PubMed:12508121, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9417084, ECO:0000269|PubMed:9925947, ECO:0000269|Ref.6, ECO:0000269|Ref.7, ECO:0000269|Ref.9}.		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)	CATAAAGGATGGGGGCCAACA	0.567													G|||	153	0.0305511	0.0038	0.0274	5008	,	,		21279	0.0		0.1113	False		,,,				2504	0.0174				p.G42R		Atlas-SNP	.											.	GSTZ1	35	.	0			c.G124A						PASS	.	G	,ARG/GLY,ARG/GLY	78,4326	62.9+/-100.1	0,78,2124	43	35	37		,124,124	5.6	1	14	dbSNP_52	37	707,7893	164.3+/-216.7	41,625,3634	yes	utr-5,missense,missense	GSTZ1	NM_001513.3,NM_145870.2,NM_145871.2	,125,125	41,703,5758	AA,AG,GG		8.2209,1.7711,6.0366	,benign,benign	,42/217,42/175	77793237	785,12219	2202	4300	6502	SO:0001583	missense	2954	exon3			AAGGATGGGGGCC	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.124G>A	14.37:g.77793237G>A	ENSP00000450487:p.Gly42Arg	64	0	0		66	27	0.409091	NM_145871	A6NED0|A6NNB8|A8MWD7|B2RCK3|O15308|O75430|Q6IB17|Q7Z610|Q9BV63	Missense_Mutation	SNP	ENST00000556627.1	37		109	0.04990842490842491	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	96	0.1266490765171504	G	28.3	4.909294	0.92107	0.017711	0.082209	ENSG00000100577	ENST00000216465;ENST00000554279;ENST00000349555;ENST00000556627;ENST00000553586	T;T;T;T;T	0.18810	4.45;3.14;2.19;2.36;4.44	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.00637	0.0021	.	.	.	0.09310	P	1.0	D	0.89917	1.0	D	0.83275	0.996	T	0.00335	-1.1808	8	0.72032	D	0.01	-6.8373	16.4581	0.84029	0.0:0.0:1.0:0.0	rs7972;rs1128968;rs2266617;rs3177429;rs3186383;rs11551317;rs17353483;rs17750846;rs52835763;rs58270987;rs7972	42	A6NED0	.	R	42;42;42;42;43	ENSP00000216465:G42R;ENSP00000452498:G42R;ENSP00000314404:G42R;ENSP00000450487:G42R;ENSP00000451976:G43R	ENSP00000216465:G42R	G	+	1	0	GSTZ1	76862990	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	5.705000	0.68355	2.614000	0.88457	0.655000	0.94253	GGG	G|0.949;A|0.051	0.051	strong		0.567	GSTZ1-012	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000414090.1	NM_145870		A	77793237	G	A	77793237	3	1	23	1	0	0	0	0	1	0	0	0	6857	1348	47	2	134	2	GSTZ1	14	77793237	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	5702428	77793237	29556303	530	7974											
TSHR	7253	hgsc.bcm.edu	37	chr14	81558919	81558919	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gacgtcaatccctgtgaatgCttttcagggactatgcaatg	10	12	10	9	1	2	1	2	1	0	0	3	3	3	2	1	1	2	2	1	1	4	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:81558919C>G	ENST00000541158.2	+	7	834	c.512C>G	c.(511-513)gCt>gGt	p.A171G	TSHR_ENST00000298171.2_Missense_Mutation_p.A171G|TSHR_ENST00000554435.1_Missense_Mutation_p.A171G|TSHR_ENST00000554263.1_Missense_Mutation_p.A171G|TSHR_ENST00000342443.6_Missense_Mutation_p.A171G			P16473	TSHR_HUMAN	thyroid stimulating hormone receptor	171					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)	CCTGTGAATGCTTTTCAGGGA	0.388			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism																														p.A171G		Atlas-SNP	.	yes	Dom	yes		14	14q31	7253	thyroid stimulating hormone receptor	yes	E	TSHR_ENST00000554435,NS,carcinoma,+1,2	TSHR	462	2	0			c.C512G						PASS	.						204	181	189					14																	81558919		2203	4300	6503	SO:0001583	missense	7253	exon6			TGAATGCTTTTCA	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.512C>G	14.37:g.81558919C>G	ENSP00000441235:p.Ala171Gly	152	0	0		201	26	0.129353	NM_000369	A0PJU7|F5GYU5|G3V2A9|Q16503|Q8TB90|Q96GT6|Q9P1V4|Q9ULA3|Q9UPH3	Missense_Mutation	SNP	ENST00000541158.2	37	CCDS9872.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.074553	0.76415	.	.	ENSG00000165409	ENST00000541158;ENST00000342443;ENST00000298171;ENST00000554263;ENST00000554435	D;D;D;D;D	0.93659	-3.26;-3.26;-3.26;-3.26;-3.26	5.28	5.28	0.74379	.	0.104905	0.64402	D	0.000003	D	0.97235	0.9096	H	0.94264	3.515	0.58432	D	0.999992	P;D;P;P	0.54207	0.918;0.965;0.953;0.852	P;P;P;P	0.61533	0.88;0.789;0.89;0.502	D	0.98083	1.0405	10	0.87932	D	0	.	14.4086	0.67101	0.0:1.0:0.0:0.0	.	171;171;171;171	G3V2A9;F5GYU5;P16473-2;P16473	.;.;.;TSHR_HUMAN	G	171	ENSP00000441235:A171G;ENSP00000340113:A171G;ENSP00000298171:A171G;ENSP00000451202:A171G;ENSP00000450549:A171G	ENSP00000298171:A171G	A	+	2	0	TSHR	80628672	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.359000	0.52292	2.483000	0.83821	0.655000	0.94253	GCT	.	.	none		0.388	TSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413364.1	NM_000369		G	81558919	C	G	81558919	3	3	23	1	0	0	0	0	1	0	0	0	16637	797	28	4	534	4	TSHR	14	81558919	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	3765682	81558919	25790621	531	7975											
EML5	161436	hgsc.bcm.edu	37	chr14	89220874	89220874	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acctgtccatctaagtcaaaCgccaagcaagctataccatg	14	8	6	13	1	2	0	1	0	1	0	3	0	3	0	4	0	4	2	4	0	6	3	rs201072176		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:89220874C>T	ENST00000380664.5	-	2	338	c.339G>A	c.(337-339)gcG>gcA	p.A113A	EML5_ENST00000554922.1_Silent_p.A113A|EML5_ENST00000352093.5_Silent_p.A113A			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	113						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						CTAAGTCAAACGCCAAGCAAG	0.299													C|||	1	0.000199681	0.0	0.0	5008	,	,		15572	0.0		0.0	False		,,,				2504	0.001				p.A113A		Atlas-SNP	.											.	EML5	141	.	0			c.G339A						PASS	.	C		1,3729		0,1,1864	105	92	96		339	1	1	14		96	8,8200		0,8,4096	no	coding-synonymous	EML5	NM_183387.2		0,9,5960	TT,TC,CC		0.0975,0.0268,0.0754		113/1978	89220874	9,11929	1865	4104	5969	SO:0001819	synonymous_variant	161436	exon2			GTCAAACGCCAAG	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.339G>A	14.37:g.89220874C>T		93	0	0		95	53	0.557895	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Silent	SNP	ENST00000380664.5	37	CCDS45148.1																																																																																			C|0.999;T|0.001	0.001	weak		0.299	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1			T	89220874	C	T	89220874	2	4	23	1	0	0	0	0	0	0	0	1	5102	523	19	1		1	EML5	14	89220874	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	7661955	89220874	18128666	532	7976											
BTBD7	55727	hgsc.bcm.edu	37	chr14	93712290	93712290	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggtacaatcaggcggtgcagCtttcacactcggcaagtaga	11	8	12	10	2	2	1	2	0	0	1	3	1	2	1	0	4	3	5	0	4	4	3	rs61991737	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:93712290C>A	ENST00000334746.5	-	10	2771	c.2464G>T	c.(2464-2466)Gct>Tct	p.A822S	BTBD7_ENST00000393170.2_Missense_Mutation_p.A396S|BTBD7_ENST00000554565.1_Missense_Mutation_p.A471S	NM_001002860.2	NP_001002860.2	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7	822	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)		GGCGGTGCAGCTTTCACACTC	0.572													C|||	3	0.000599042	0.0	0.0	5008	,	,		17134	0.0		0.001	False		,,,				2504	0.002				p.A822S		Atlas-SNP	.											.	BTBD7	112	.	0			c.G2464T						PASS	.	C	SER/ALA	2,4404	4.2+/-10.8	0,2,2201	55	56	55		2464	5.9	0.3	14	dbSNP_129	55	10,8590	7.7+/-29.5	0,10,4290	yes	missense	BTBD7	NM_001002860.2	99	0,12,6491	AA,AC,CC		0.1163,0.0454,0.0923	possibly-damaging	822/1133	93712290	12,12994	2203	4300	6503	SO:0001583	missense	55727	exon10			GTGCAGCTTTCAC	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.2464G>T	14.37:g.93712290C>A	ENSP00000335615:p.Ala822Ser	71	0	0		77	34	0.441558	NM_001002860	A8K5V7|Q69Z05|Q7Z308|Q86TS0|Q9HAA4|Q9NVM0	Missense_Mutation	SNP	ENST00000334746.5	37	CCDS32146.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	15.21	2.766791	0.49574	4.54E-4	0.001163	ENSG00000011114	ENST00000334746;ENST00000554565;ENST00000553975;ENST00000393170	T;T	0.49139	1.14;0.79	5.94	5.94	0.96194	.	0.141339	0.64402	D	0.000004	T	0.41627	0.1167	N	0.19112	0.55	0.37849	D	0.929331	P;B;B	0.39480	0.675;0.449;0.058	B;B;B	0.41813	0.367;0.26;0.042	T	0.32241	-0.9914	10	0.34782	T	0.22	.	20.3517	0.98814	0.0:1.0:0.0:0.0	rs61991737	396;471;822	E7ERI4;Q9P203-5;Q9P203	.;.;BTBD7_HUMAN	S	822;471;437;396	ENSP00000335615:A822S;ENSP00000451010:A471S	ENSP00000335615:A822S	A	-	1	0	BTBD7	92782043	1.000000	0.71417	0.295000	0.24960	0.026000	0.11368	3.688000	0.54699	2.818000	0.97014	0.650000	0.86243	GCT	C|0.999;A|0.001	0.001	strong		0.572	BTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412701.1	NM_001002860		A	93712290	C	A	93712290	3	1	23	1	0	0	0	0	1	0	0	0	1548	797	28	4	942	4	BTBD7	14	93712290	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	4491416	93712290	13637250	533	7977											
ASB2	51676	hgsc.bcm.edu	37	chr14	94405616	94405616	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcagcgacaggcacttcatGgcgaacatgatggtggcggg	10	6	16	9	3	1	1	1	1	0	0	1	3	1	1	0	5	3	2	0	5	1	1	rs140791740		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:94405616G>A	ENST00000315988.4	-	6	1799	c.1311C>T	c.(1309-1311)gcC>gcT	p.A437A	ASB2_ENST00000555019.1_Silent_p.A485A|ASB2_ENST00000556337.1_5'Flank|RP11-131H24.4_ENST00000557646.1_5'Flank	NM_016150.4	NP_057234.2	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box containing 2	437					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)		GGCACTTCATGGCGAACATGA	0.667													G|||	1	0.000199681	0.0	0.0014	5008	,	,		15940	0.0		0.0	False		,,,				2504	0.0				p.A485A		Atlas-SNP	.											.	ASB2	71	.	0			c.C1455T						PASS	.	G	,	0,4406		0,0,2203	55	56	56		1455,1311	5.1	1	14	dbSNP_134	56	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous,coding-synonymous	ASB2	NM_001202429.1,NM_016150.4	,	0,5,6498	AA,AG,GG		0.0581,0.0,0.0384	,	485/636,437/588	94405616	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	51676	exon8			CTTCATGGCGAAC	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.1311C>T	14.37:g.94405616G>A		105	0	0		97	44	0.453608	NM_001202429	B2RDP9|B4E166|Q9NSU5|Q9Y567	Silent	SNP	ENST00000315988.4	37	CCDS9915.1																																																																																			G|1.000;A|0.000	0.000	strong		0.667	ASB2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412845.1			A	94405616	G	A	94405616	2	1	23	1	0	0	0	0	0	0	0	1	1023	1335	47	2		2	ASB2	14	94405616	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	693326	94405616	12943924	534	7978											
SERPINA9	327657	hgsc.bcm.edu	37	chr14	94936062	94936062	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aatacacctgtgaggcagggGtgctctttgtggaggaaggg	9	9	17	6	0	1	1	0	1	1	0	1	3	1	3	1	6	2	2	1	6	3	2	rs45438596	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:94936062G>A	ENST00000380365.3	-	2	194	c.116C>T	c.(115-117)aCc>aTc	p.T39I	SERPINA9_ENST00000424550.2_Intron|SERPINA9_ENST00000539349.1_5'Flank|SERPINA9_ENST00000546329.1_Intron|SERPINA9_ENST00000298845.7_Missense_Mutation_p.T57I|SERPINA9_ENST00000337425.5_Missense_Mutation_p.T57I|SERPINA9_ENST00000448305.2_Intron			Q86WD7	SPA9_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	39					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)		TGAGGCAGGGGTGCTCTTTGT	0.567													G|||	93	0.0185703	0.0393	0.0144	5008	,	,		17740	0.0		0.0278	False		,,,				2504	0.0031				p.T57I		Atlas-SNP	.											.	SERPINA9	105	.	0			c.C170T						PASS	.	G	ILE/THR,ILE/THR	176,3872		7,162,1855	86	89	88		170,170	-8	0	14	dbSNP_127	88	245,8115		2,241,3937	yes	missense,missense	SERPINA9	NM_001042518.1,NM_175739.3	89,89	9,403,5792	AA,AG,GG		2.9306,4.3478,3.393	possibly-damaging,possibly-damaging	57/336,57/436	94936062	421,11987	2024	4180	6204	SO:0001583	missense	327657	exon2			GCAGGGGTGCTCT	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.116C>T	14.37:g.94936062G>A	ENSP00000369723:p.Thr39Ile	97	0	0		92	51	0.554348	NM_175739	B4DVH4|B9ZVX3|Q2T9J2|Q6UWP9|Q86WD4|Q86WD5|Q86WD6|Q86YP6|Q86YP7	Missense_Mutation	SNP	ENST00000380365.3	37		40	0.018315018315018316	16	0.032520325203252036	4	0.011049723756906077	0	0.0	20	0.026385224274406333	G	11.98	1.800787	0.31869	0.043478	0.029306	ENSG00000170054	ENST00000298845;ENST00000337425;ENST00000380365	D;D;D	0.87571	-2.27;-2.27;-2.27	3.99	-7.98	0.01135	Serpin domain (1);	1.422810	0.05300	U	0.522890	T	0.41558	0.1164	N	0.08118	0	0.09310	N	1	B;B;B	0.18968	0.007;0.032;0.021	B;B;B	0.22386	0.01;0.039;0.025	T	0.57825	-0.7744	10	0.54805	T	0.06	.	9.7894	0.40697	0.0:0.3432:0.454:0.2028	rs45438596;rs61743375	39;57;57	Q86WD7;Q86WD7-7;Q86WD7-2	SPA9_HUMAN;.;.	I	57;57;39	ENSP00000298845:T57I;ENSP00000337133:T57I;ENSP00000369723:T39I	ENSP00000298845:T57I	T	-	2	0	SERPINA9	94005815	0.000000	0.05858	0.000000	0.03702	0.438000	0.31896	-1.284000	0.02793	-1.491000	0.01840	0.313000	0.20887	ACC	G|0.979;A|0.021	0.021	strong		0.567	SERPINA9-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395803.2	NM_175739		A	94936062	G	A	94936062	3	1	23	1	0	0	0	0	1	0	0	0	14110	1261	44	2	1153	2	SERPINA9	14	94936062	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	530446	94936062	12413478	535	7979											
ATG2B	55102	hgsc.bcm.edu	37	chr14	96800027	96800027	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagtttgagttgcttaccaCggctagaaggtgtacgagct	10	11	12	8	2	0	2	0	1	0	1	0	3	0	2	1	2	4	6	1	2	4	5	rs183527316	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:96800027C>T	ENST00000359933.4	-	8	2098	c.1205G>A	c.(1204-1206)cGt>cAt	p.R402H		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	402					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)		TTGCTTACCACGGCTAGAAGG	0.363													C|||	2	0.000399361	0.0	0.0	5008	,	,		16337	0.0		0.002	False		,,,				2504	0.0				p.R402H		Atlas-SNP	.											.	ATG2B	169	.	0			c.G1205A						PASS	.	C	HIS/ARG	4,3650		0,4,1823	77	70	72		1205	5.6	1	14		72	59,8131		0,59,4036	yes	missense	ATG2B	NM_018036.5	29	0,63,5859	TT,TC,CC		0.7204,0.1095,0.5319	benign	402/2079	96800027	63,11781	1827	4095	5922	SO:0001583	missense	55102	exon8			TTACCACGGCTAG	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.1205G>A	14.37:g.96800027C>T	ENSP00000353010:p.Arg402His	106	0	0		95	46	0.484211	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	37	CCDS9944.2	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	16.68	3.189548	0.57909	0.001095	0.007204	ENSG00000066739	ENST00000359933	T	0.10382	2.88	5.6	5.6	0.85130	.	0.423584	0.20315	U	0.094755	T	0.05640	0.0148	N	0.19112	0.55	0.47341	D	0.999394	B	0.22211	0.066	B	0.14023	0.01	T	0.24657	-1.0154	10	0.41790	T	0.15	.	13.2187	0.59875	0.0:0.9272:0.0:0.0728	.	402	Q96BY7	ATG2B_HUMAN	H	402	ENSP00000353010:R402H	ENSP00000353010:R402H	R	-	2	0	ATG2B	95869780	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.238000	0.65366	2.793000	0.96121	0.591000	0.81541	CGT	C|0.998;T|0.002	0.002	strong		0.363	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		T	96800027	C	T	96800027	3	4	23	1	0	0	0	0	1	0	0	0	1094	536	19	1	5171	1	ATG2B	14	96800027	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1863965	96800027	10549513	536	7980											
OTUD7A	161725	hgsc.bcm.edu	37	chr15	31776837	31776837	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gctgttagaattgctgcacaCcgaatcgcggtccgagtcca	9	9	11	12	4	0	1	0	0	0	1	3	3	2	1	3	1	2	4	3	1	3	2	rs76704217	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:31776837C>G	ENST00000307050.4	-	11	1533	c.1441G>C	c.(1441-1443)Gtg>Ctg	p.V481L	OTUD7A_ENST00000382902.1_Missense_Mutation_p.V488L	NM_130901.1	NP_570971.1	Q8TE49	OTU7A_HUMAN	OTU deubiquitinase 7A	481					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)		TTGCTGCACACCGAATCGCGG	0.642													C|||	57	0.0113818	0.0015	0.0173	5008	,	,		19876	0.001		0.0378	False		,,,				2504	0.0041				p.V481L		Atlas-SNP	.											.	OTUD7A	89	.	0			c.G1441C						PASS	.	C	LEU/VAL	30,4354		0,30,2162	80	57	64		1441	2.4	1	15	dbSNP_131	64	415,8183		14,387,3898	yes	missense	OTUD7A	NM_130901.1	32	14,417,6060	GG,GC,CC		4.8267,0.6843,3.4278	benign	481/927	31776837	445,12537	2192	4299	6491	SO:0001583	missense	161725	exon11			TGCACACCGAATC	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.1441G>C	15.37:g.31776837C>G	ENSP00000305926:p.Val481Leu	126	0	0		137	59	0.430657	NM_130901	Q8IWK5	Missense_Mutation	SNP	ENST00000307050.4	37	CCDS10026.1	45	0.020604395604395604	2	0.0040650406504065045	7	0.019337016574585635	1	0.0017482517482517483	35	0.04617414248021108	C	14.83	2.652700	0.47362	0.006843	0.048267	ENSG00000169918	ENST00000307050;ENST00000382902	T;T	0.34472	1.37;1.36	4.35	2.4	0.29515	.	0.175056	0.50627	D	0.000102	T	0.06005	0.0156	M	0.69823	2.125	0.28750	N	0.90147	B;B	0.12013	0.005;0.003	B;B	0.13407	0.009;0.004	T	0.12656	-1.0539	10	0.51188	T	0.08	-32.5726	3.9645	0.09424	0.0:0.5203:0.2199:0.2599	.	488;481	Q8TE49-2;Q8TE49	.;OTU7A_HUMAN	L	481;488	ENSP00000305926:V481L;ENSP00000372358:V488L	ENSP00000305926:V481L	V	-	1	0	OTUD7A	29564129	1.000000	0.71417	0.994000	0.49952	0.995000	0.86356	2.060000	0.41394	0.936000	0.37367	0.655000	0.94253	GTG	C|0.970;G|0.030	0.030	strong		0.642	OTUD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251393.2	NM_130901		G	31776837	C	G	31776837	3	3	23	1	0	0	0	0	1	0	0	0	11327	507	18	4	1343	4	OTUD7A	15	31776837	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10		31776837	70754555	537	7981											
DISP2	85455	hgsc.bcm.edu	37	chr15	40660043	40660043	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gagccagctgccgtcgggggGgctggcgcagcgcgtgggcc	3	4	21	13	5	0	0	0	0	0	0	1	1	0	0	3	5	4	3	3	5	0	0	rs76331864	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:40660043G>T	ENST00000267889.3	+	8	1817	c.1730G>T	c.(1729-1731)gGg>gTg	p.G577V	RP11-64K12.4_ENST00000558421.1_RNA	NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	577	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				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)		CCGTCGGGGGGGCTGGCGCAG	0.667													G|||	93	0.0185703	0.0469	0.0144	5008	,	,		13554	0.002		0.0159	False		,,,				2504	0.0031				p.G577V		Atlas-SNP	.											.	DISP2	86	.	0			c.G1730T						PASS	.	G	VAL/GLY	178,4228	105.2+/-143.6	4,170,2029	23	23	23		1730	4.7	1	15	dbSNP_131	23	113,8487	52.7+/-113.3	1,111,4188	yes	missense	DISP2	NM_033510.1	109	5,281,6217	TT,TG,GG		1.314,4.0399,2.2374	benign	577/1402	40660043	291,12715	2203	4300	6503	SO:0001583	missense	85455	exon8			CGGGGGGGCTGGC	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.1730G>T	15.37:g.40660043G>T	ENSP00000267889:p.Gly577Val	22	0	0		22	10	0.454545	NM_033510	Q6AHW3|Q9C0C1	Missense_Mutation	SNP	ENST00000267889.3	37	CCDS10056.1	46	0.021062271062271064	27	0.054878048780487805	10	0.027624309392265192	0	0.0	9	0.011873350923482849	G	13.16	2.155343	0.38021	0.040399	0.01314	ENSG00000140323	ENST00000267889	D	0.95377	-3.69	5.58	4.66	0.58398	Sterol-sensing domain (1);	0.166012	0.53938	D	0.000060	T	0.75882	0.3910	L	0.48362	1.52	0.80722	D	1	P	0.45715	0.865	B	0.42555	0.391	T	0.81671	-0.0827	10	0.31617	T	0.26	-15.0114	14.6339	0.68676	0.0703:0.0:0.9297:0.0	.	577	A7MBM2	DISP2_HUMAN	V	577	ENSP00000267889:G577V	ENSP00000267889:G577V	G	+	2	0	DISP2	38447335	1.000000	0.71417	0.998000	0.56505	0.741000	0.42261	5.783000	0.68982	1.357000	0.45904	0.561000	0.74099	GGG	G|0.977;T|0.023	0.023	strong		0.667	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510		T	40660043	G	T	40660043	3	4	23	1	0	0	0	0	1	0	0	0	4542	1232	43	4	1760	4	DISP2	15	40660043	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	8883206	40660043	61871349	538	7982											
PPP1R14D	54866	hgsc.bcm.edu	37	chr15	41120675	41120675	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tcatacttcactgtcaggcgGctgggtctccgggacctggg	5	10	14	12	2	4	0	3	0	1	0	5	1	4	1	2	5	1	1	2	5	1	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:41120675G>C	ENST00000299174.5	-	1	232	c.165C>G	c.(163-165)agC>agG	p.S55R	PPP1R14D_ENST00000427255.2_Missense_Mutation_p.S55R	NM_017726.7	NP_060196.1	Q9NXH3	PP14D_HUMAN	protein phosphatase 1, regulatory (inhibitor) subunit 14D	55					regulation of phosphorylation (GO:0042325)	cytoplasm (GO:0005737)	protein phosphatase inhibitor activity (GO:0004864)			breast(1)|large_intestine(2)|lung(2)|skin(1)	6		all_cancers(109;6.29e-14)|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;2.88e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		CTGTCAGGCGGCTGGGTCTCC	0.597																																					p.S55R		Atlas-SNP	.											.	PPP1R14D	8	.	0			c.C165G						PASS	.						77	75	76					15																	41120675		2203	4300	6503	SO:0001583	missense	54866	exon1			CAGGCGGCTGGGT	AK000258	CCDS10066.1, CCDS45230.1	15q11.2-q14	2012-04-17			ENSG00000166143	ENSG00000166143		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	14953	protein-coding gene	gene with protein product	"gut and brain phosphatase inhibitor 1", "PKC-dependent PP1 inhibitory protein"	613256				11948623	Standard	NM_017726		Approved	CPI17-like, FLJ20251, GBPI-1, MGC119014, MGC119016	uc001zmz.3	Q9NXH3	OTTHUMG00000130064	ENST00000299174.5:c.165C>G	15.37:g.41120675G>C	ENSP00000299174:p.Ser55Arg	143	0	0		149	69	0.463087	NM_017726	Q4V773	Missense_Mutation	SNP	ENST00000299174.5	37	CCDS10066.1	.	.	.	.	.	.	.	.	.	.	G	18.71	3.682021	0.68042	.	.	ENSG00000166143	ENST00000299174;ENST00000427255	.	.	.	5.82	4.91	0.64330	.	0.067227	0.64402	D	0.000004	T	0.50752	0.1634	N	0.24115	0.695	0.34284	D	0.682531	D;D	0.76494	0.999;0.983	D;P	0.69479	0.964;0.839	T	0.61845	-0.6979	9	0.38643	T	0.18	-11.6822	10.8969	0.47027	0.086:0.0:0.914:0.0	.	55;55	E9PAT1;Q9NXH3	.;PP14D_HUMAN	R	55	.	ENSP00000299174:S55R	S	-	3	2	PPP1R14D	38907967	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	2.421000	0.44688	1.490000	0.48466	-0.142000	0.14014	AGC	.	.	none		0.597	PPP1R14D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252355.2	NM_017726		C	41120675	G	C	41120675	3	2	23	1	0	0	0	0	1	0	0	0	12374	1194	42	4	457	4	PPP1R14D	15	41120675	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	460632	41120675	61410717	539	7983											
EXD1	161829	hgsc.bcm.edu	37	chr15	41488231	41488231	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agtaaactcggcaatttgtgGccacctacaatagaccatcc	13	9	7	12	1	0	1	0	0	0	1	2	1	1	1	4	2	2	2	4	2	6	4	rs139947718	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:41488231G>C	ENST00000314992.5	-	6	555	c.365C>G	c.(364-366)gCc>gGc	p.A122G	EXD1_ENST00000458580.2_Missense_Mutation_p.A180G	NM_152596.2	NP_689809.2	Q8NHP7	EXD1_HUMAN	exonuclease 3'-5' domain containing 1	122	3'-5' exonuclease.						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						GCAATTTGTGGCCACCTACAA	0.383													G|||	8	0.00159744	0.0	0.0043	5008	,	,		19008	0.0		0.004	False		,,,				2504	0.001				p.A122G		Atlas-SNP	.											.	EXD1	52	.	0			c.C365G						PASS	.	G	GLY/ALA	5,4401	4.2+/-10.8	0,5,2198	46	47	47		365	5.7	1	15	dbSNP_134	47	48,8552	26.3+/-74.7	0,48,4252	yes	missense	EXD1	NM_152596.2	60	0,53,6450	CC,CG,GG		0.5581,0.1135,0.4075	probably-damaging	122/515	41488231	53,12953	2203	4300	6503	SO:0001583	missense	161829	exon6			TTTGTGGCCACCT	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.365C>G	15.37:g.41488231G>C	ENSP00000321029:p.Ala122Gly	52	0	0		70	32	0.457143	NM_152596	A8K909|B7Z839|Q6ZW94	Missense_Mutation	SNP	ENST00000314992.5	37	CCDS10072.1	5	0.0022893772893772895	0	0.0	3	0.008287292817679558	0	0.0	2	0.002638522427440633	G	21.6	4.173271	0.78452	0.001135	0.005581	ENSG00000178997	ENST00000314992;ENST00000458580	T;T	0.61742	0.08;0.08	5.65	5.65	0.86999	-5&apos (2);Ribonuclease H-like (1); exonuclease (2);3&apos (2);	0.062205	0.64402	D	0.000008	T	0.63885	0.2549	L	0.46885	1.475	0.50813	D	0.999899	D;D	0.71674	0.998;0.998	D;D	0.74023	0.982;0.982	T	0.67887	-0.5554	10	0.52906	T	0.07	-8.9912	17.4865	0.87689	0.0:0.0:1.0:0.0	.	180;122	B7Z839;Q8NHP7	.;EXD1_HUMAN	G	122;180	ENSP00000321029:A122G;ENSP00000415056:A180G	ENSP00000321029:A122G	A	-	2	0	EXD1	39275523	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	5.633000	0.67825	2.665000	0.90641	0.462000	0.41574	GCC	G|0.996;C|0.004	0.004	strong		0.383	EXD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252553.2	NM_152596		C	41488231	G	C	41488231	3	2	23	1	0	0	0	0	1	0	0	0	5299	1203	42	4	1199	4	EXD1	15	41488231	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	367556	41488231	61043161	540	7984											
TYRO3	7301	hgsc.bcm.edu	37	chr15	41862436	41862436	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaatcctgggttttcctttAggcaagcctttgacagtgtc	8	14	9	10	0	0	1	0	1	0	0	3	1	2	1	3	2	1	2	3	2	3	5	rs201371674	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:41862436A>G	ENST00000263798.3	+	11	1606		c.e11-1		TYRO3_ENST00000559066.1_Splice_Site	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase						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)		GTTTTCCTTTAGGCAAGCCTT	0.587																																					.		Atlas-SNP	.											.	TYRO3	169	.	0			c.1383-2A>G						PASS	.																																			SO:0001630	splice_region_variant	7301	exon11			TCCTTTAGGCAAG	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.1383-1A>G	15.37:g.41862436A>G		79	0	0		86	8	0.0930233	NM_006293	O14953|Q86VR3	Splice_Site	SNP	ENST00000263798.3	37	CCDS10080.1	.	.	.	.	.	.	.	.	.	.	A	19.62	3.862477	0.71949	.	.	ENSG00000092445	ENST00000540218;ENST00000263798	.	.	.	5.26	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.0491	0.58944	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TYRO3	39649728	1.000000	0.71417	0.998000	0.56505	0.942000	0.58702	7.007000	0.76335	2.208000	0.71279	0.533000	0.62120	.	A|0.986;G|0.014	0.014	strong		0.587	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2		Intron	G	41862436	A	G	41862436	5	3	23	1	0	0	0	0	0	0	1	0	16829	434	15	3	1423	3	TYRO3	15	41862436	Splice_Site	SNP	A	TCGA-G8-6325-01A-11D-2210-10	374205	41862436	60668956	541	7985											
MGA	23269	hgsc.bcm.edu	37	chr15	41989091	41989091	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actctgtaaggcaggacgacCacctaagaacacaggaaagt	16	5	10	10	1	1	1	0	0	1	1	1	4	1	3	2	3	1	2	2	3	4	2	rs61736074	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:41989091C>A	ENST00000570161.1	+	2	1883	c.1883C>A	c.(1882-1884)cCa>cAa	p.P628Q	MGA_ENST00000566586.1_Missense_Mutation_p.P628Q|MGA_ENST00000389936.4_Missense_Mutation_p.P628Q|MGA_ENST00000545763.1_Missense_Mutation_p.P628Q|MGA_ENST00000219905.7_Missense_Mutation_p.P628Q			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)	GCAGGACGACCACCTAAGAAC	0.448													C|||	30	0.00599042	0.0008	0.0058	5008	,	,		19971	0.0		0.0209	False		,,,				2504	0.0041				p.P628Q		Atlas-SNP	.											.	MGA	264	.	0			c.C1883A						PASS	.	C	GLN/PRO,GLN/PRO	14,3724		0,14,1855	23	21	21		1883,1883	5.2	1	15	dbSNP_129	21	154,8048		2,150,3949	yes	missense,missense	MGA	NM_001080541.2,NM_001164273.1	76,76	2,164,5804	AA,AC,CC		1.8776,0.3745,1.407	probably-damaging,probably-damaging	628/2857,628/3066	41989091	168,11772	1869	4101	5970	SO:0001583	missense	23269	exon3			GACGACCACCTAA	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.1883C>A	15.37:g.41989091C>A	ENSP00000457035:p.Pro628Gln	100	0	0		134	75	0.559702	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	37	CCDS55959.1	22	0.010073260073260074	0	0.0	4	0.011049723756906077	0	0.0	18	0.023746701846965697	C	18.09	3.545802	0.65198	0.003745	0.018776	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	T;T;T	0.47528	0.84;0.84;0.84	5.21	5.21	0.72293	.	2.567660	0.01142	N	0.006237	T	0.44973	0.1319	N	0.24115	0.695	0.31046	N	0.715753	D;D	0.76494	0.999;0.999	D;D	0.77004	0.989;0.973	T	0.51513	-0.8696	10	0.87932	D	0	.	12.162	0.54109	0.0:0.9216:0.0:0.0784	rs61736074	628;628	F5H7K2;E7ENI0	.;.	Q	628	ENSP00000219905:P628Q;ENSP00000374586:P628Q;ENSP00000442467:P628Q	ENSP00000219905:P628Q	P	+	2	0	MGA	39776383	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	4.086000	0.57664	2.441000	0.82636	0.462000	0.41574	CCA	C|0.987;A|0.013	0.013	strong		0.448	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		A	41989091	C	A	41989091	3	1	23	1	0	0	0	0	1	0	0	0	9549	594	21	4	1889	4	MGA	15	41989091	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	126655	41989091	60542301	542	7986											
SPTBN5	51332	hgsc.bcm.edu	37	chr15	42162467	42162467	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcggtgcccacgagttctcGctccagcccctggtggcttc	3	10	11	17	3	1	0	0	0	1	0	5	1	2	0	4	3	2	3	4	3	0	2	rs61750839	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:42162467G>A	ENST00000320955.6	-	31	5874	c.5647C>T	c.(5647-5649)Cga>Tga	p.R1883*		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1883					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)		ACGAGTTCTCGCTCCAGCCCC	0.662													G|||	54	0.0107827	0.0	0.0101	5008	,	,		17221	0.0		0.0358	False		,,,				2504	0.0112				p.R1848X		Atlas-SNP	.											.	SPTBN5	171	.	0			c.C5542T						PASS	.	G	stop/ARG	20,3888		0,20,1934	10	12	12		5542	0.3	0.1	15	dbSNP_129	12	277,7857		7,263,3797	yes	stop-gained	SPTBN5	NM_016642.2		7,283,5731	AA,AG,GG		3.4055,0.5118,2.4664		1848/3640	42162467	297,11745	1954	4067	6021	SO:0001587	stop_gained	51332	exon31			GTTCTCGCTCCAG	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.5647C>T	15.37:g.42162467G>A	ENSP00000317790:p.Arg1883*	93	0	0		110	70	0.636364	NM_016642		Nonsense_Mutation	SNP	ENST00000320955.6	37		38	0.0173992673992674	0	0.0	6	0.016574585635359115	0	0.0	32	0.04221635883905013	.	44	10.798073	0.99469	0.005118	0.034055	ENSG00000137877	ENST00000320955	.	.	.	4.63	0.285	0.15705	.	0.608014	0.15586	N	0.254650	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.4729	0.11720	0.2652:0.0:0.5822:0.1526	.	.	.	.	X	1883	.	ENSP00000317790:R1883X	R	-	1	2	SPTBN5	39949759	0.002000	0.14202	0.057000	0.19452	0.159000	0.22180	0.862000	0.27899	0.057000	0.16193	0.655000	0.94253	CGA	G|0.982;A|0.018	0.018	strong		0.662	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		A	42162467	G	A	42162467	4	1	23	1	0	0	0	0	0	1	0	0	15137	1095	38	1	5529	1	SPTBN5	15	42162467	Nonsense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	173376	42162467	60368925	543	7987											
CDAN1	146059	hgsc.bcm.edu	37	chr15	43022868	43022868	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gaacaacatggtcagcaaagGagagaaactccaccagccag	17	3	10	11	0	1	1	1	0	0	1	2	4	2	2	3	2	5	1	3	2	4	0			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:43022868G>A	ENST00000356231.3	-	14	2125	c.2102C>T	c.(2101-2103)tCc>tTc	p.S701F		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	701					chromatin assembly (GO:0031497)|chromatin organization (GO:0006325)|negative regulation of DNA replication (GO:0008156)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	24		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		GTCAGCAAAGGAGAGAAACTC	0.622																																					p.S701F		Atlas-SNP	.											.	CDAN1	70	.	0			c.C2102T						PASS	.						38	41	40					15																	43022868		2203	4299	6502	SO:0001583	missense	146059	exon14			GCAAAGGAGAGAA	AF525398	CCDS32209.1	15q15.2	2012-04-25	2012-04-25			ENSG00000140326			1713	protein-coding gene	gene with protein product		607465	"congenital dyserythropoietic anemia, type I"			8634422, 12434312	Standard	XM_005254177		Approved	CDA-I, CDAI	uc001zql.3	Q8IWY9		ENST00000356231.3:c.2102C>T	15.37:g.43022868G>A	ENSP00000348564:p.Ser701Phe	179	0	0		186	10	0.0537634	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Missense_Mutation	SNP	ENST00000356231.3	37	CCDS32209.1	.	.	.	.	.	.	.	.	.	.	G	31	5.097079	0.94197	.	.	ENSG00000140326	ENST00000356231;ENST00000267892	D	0.86432	-2.12	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	D	0.93887	0.8044	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.93948	0.7229	10	0.87932	D	0	-20.6001	19.9915	0.97366	0.0:0.0:1.0:0.0	.	701	Q8IWY9	CDAN1_HUMAN	F	701;699	ENSP00000348564:S701F	ENSP00000267892:S699F	S	-	2	0	CDAN1	40810160	1.000000	0.71417	0.705000	0.30386	0.941000	0.58515	9.420000	0.97426	2.723000	0.93209	0.655000	0.94253	TCC	.	.	none		0.622	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300		A	43022868	G	A	43022868	3	1	23	1	0	0	0	0	1	0	0	0	3056	1174	41	2	1641	2	CDAN1	15	43022868	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	860401	43022868	59508524	544	7988											
UBR1	197131	hgsc.bcm.edu	37	chr15	43256191	43256191	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaagagcaggaacaaatttgTaggtaaagatagatagctac	18	8	11	4	0	0	3	0	0	0	3	0	5	0	4	0	2	4	4	0	2	9	6	rs3917223	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:43256191T>C	ENST00000290650.4	-	42	4720	c.4642A>G	c.(4642-4644)Aca>Gca	p.T1548A	UBR1_ENST00000382177.2_3'UTR	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	1548			T -> A (in dbSNP:rs3917223).		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)		AACAAATTTGTAGGTAAAGAT	0.373													T|||	166	0.033147	0.0023	0.0259	5008	,	,		18240	0.001		0.0736	False		,,,				2504	0.0716				p.T1548A		Atlas-SNP	.											.	UBR1	124	.	0			c.A4642G						PASS	.	T	ALA/THR	73,4333	65.3+/-102.7	1,71,2131	76	73	74		4642	4.7	1	15	dbSNP_108	74	632,7966	162.2+/-214.9	26,580,3693	yes	missense	UBR1	NM_174916.2	58	27,651,5824	CC,CT,TT		7.3505,1.6568,5.4214	benign	1548/1750	43256191	705,12299	2203	4299	6502	SO:0001583	missense	197131	exon42			AATTTGTAGGTAA		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.4642A>G	15.37:g.43256191T>C	ENSP00000290650:p.Thr1548Ala	85	0	0		116	71	0.612069	NM_174916	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	37	CCDS10091.1	71	0.03250915750915751	0	0.0	11	0.03038674033149171	1	0.0017482517482517483	59	0.07783641160949868	T	14.23	2.472063	0.43942	0.016568	0.073505	ENSG00000159459	ENST00000290650	T	0.48836	0.8	4.65	4.65	0.58169	.	0.113840	0.64402	D	0.000011	T	0.02012	0.0063	L	0.33245	0.995	0.80722	D	1	P	0.40083	0.702	B	0.36092	0.217	T	0.00878	-1.1530	10	0.28530	T	0.3	-28.0639	12.4581	0.55716	0.0:0.0:0.0:1.0	rs3917223;rs17719808;rs52813857;rs61722037;rs17719808	1548	Q8IWV7	UBR1_HUMAN	A	1548	ENSP00000290650:T1548A	ENSP00000290650:T1548A	T	-	1	0	UBR1	41043483	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	3.860000	0.55995	1.969000	0.57287	0.528000	0.53228	ACA	T|0.847;G|0.006;C|0.046;A|0.102	0.046	strong		0.373	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916		C	43256191	T	C	43256191	3	2	23	1	0	0	0	0	1	0	0	0	16916	1638	57	3	631	3	UBR1	15	43256191	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	233323	43256191	59275201	545	7989											
TGM5	9333	hgsc.bcm.edu	37	chr15	43527819	43527819	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaggacaaagcatatatccTggcccatgttgggcgggtcg	9	8	14	10	2	0	0	0	0	0	0	2	1	1	1	2	4	1	3	2	4	3	3	rs35985214	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:43527819T>C	ENST00000220420.5	-	10	1569	c.1562A>G	c.(1561-1563)cAg>cGg	p.Q521R	TGM5_ENST00000349114.4_Missense_Mutation_p.Q439R	NM_201631.3	NP_963925.2	O43548	TGM5_HUMAN	transglutaminase 5	521			Q -> R (in dbSNP:rs35985214).		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)	GCATATATCCTGGCCCATGTT	0.577													T|||	28	0.00559105	0.0008	0.0086	5008	,	,		21464	0.0		0.0179	False		,,,				2504	0.0031				p.Q521R		Atlas-SNP	.											TGM5,rectum,carcinoma,-1,1	TGM5	88	1	0			c.A1562G						PASS	.	T	ARG/GLN,ARG/GLN	17,4389	23.3+/-48.9	0,17,2186	99	81	87		1316,1562	1.7	1	15	dbSNP_126	87	146,8452	70.7+/-133.2	1,144,4154	yes	missense,missense	TGM5	NM_004245.3,NM_201631.3	43,43	1,161,6340	CC,CT,TT		1.6981,0.3858,1.2535	benign,benign	439/639,521/721	43527819	163,12841	2203	4299	6502	SO:0001583	missense	9333	exon10			ATATCCTGGCCCA	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.1562A>G	15.37:g.43527819T>C	ENSP00000220420:p.Gln521Arg	186	0	0		160	59	0.36875	NM_201631	O43549|Q0VF40|Q9UEZ4	Missense_Mutation	SNP	ENST00000220420.5	37	CCDS32212.1	14	0.00641025641025641	0	0.0	2	0.0055248618784530384	0	0.0	12	0.0158311345646438	T	7.086	0.571152	0.13623	0.003858	0.016981	ENSG00000104055	ENST00000220420;ENST00000349114;ENST00000396996	T;T	0.69561	-0.41;-0.41	5.58	1.73	0.24493	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.134279	0.47852	D	0.000201	T	0.37919	0.1021	L	0.50333	1.59	0.27114	N	0.962306	B;B	0.12630	0.004;0.006	B;B	0.19666	0.013;0.026	T	0.39502	-0.9611	10	0.42905	T	0.14	-8.616	4.8757	0.13655	0.1649:0.1715:0.0:0.6635	rs35985214	439;521	O43548-2;O43548	.;TGM5_HUMAN	R	521;439;520	ENSP00000220420:Q521R;ENSP00000220419:Q439R	ENSP00000220420:Q521R	Q	-	2	0	TGM5	41315111	1.000000	0.71417	0.997000	0.53966	0.029000	0.11900	1.138000	0.31491	0.387000	0.25024	-0.274000	0.10170	CAG	T|0.988;C|0.012	0.012	strong		0.577	TGM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432257.1	NM_004245		C	43527819	T	C	43527819	3	2	23	1	0	0	0	0	1	0	0	0	15848	1580	55	3	616	3	TGM5	15	43527819	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	271628	43527819	59003573	546	7990											
MAP1A	4130	hgsc.bcm.edu	37	chr15	43818959	43818959	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatttccaggaatcctcacCacagaaggggctagaggtgg	11	7	14	9	0	1	2	1	0	0	2	3	4	3	4	3	6	0	1	3	6	3	2	rs375898111		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:43818959C>G	ENST00000300231.5	+	4	5738	c.5288C>G	c.(5287-5289)cCa>cGa	p.P1763R	MAP1A_ENST00000399453.1_Missense_Mutation_p.P1763R|MAP1A_ENST00000382031.1_Missense_Mutation_p.P2001R			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1763					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)	GAATCCTCACCACAGAAGGGG	0.572																																					p.P1763R		Atlas-SNP	.											.	MAP1A	189	.	0			c.C5288G						PASS	.	C	ARG/PRO	0,3894		0,0,1947	74	76	76		5288	4.5	0.5	15		76	1,8265		0,1,4132	no	missense	MAP1A	NM_002373.5	103	0,1,6079	GG,GC,CC		0.0121,0.0,0.0082	benign	1763/2804	43818959	1,12159	1947	4133	6080	SO:0001583	missense	4130	exon4			CCTCACCACAGAA	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.5288C>G	15.37:g.43818959C>G	ENSP00000300231:p.Pro1763Arg	87	0	0		106	46	0.433962	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	37	CCDS42031.1	.	.	.	.	.	.	.	.	.	.	C	2.185	-0.386740	0.04966	0.0	1.21E-4	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.01854	4.6;4.61;4.61	4.46	4.46	0.54185	.	0.268702	0.20049	N	0.100342	T	0.03390	0.0098	L	0.32530	0.975	0.20563	N	0.999883	B	0.32467	0.372	B	0.36989	0.238	T	0.38672	-0.9650	10	0.66056	D	0.02	0.9333	15.0779	0.72090	0.0:1.0:0.0:0.0	.	1763	P78559	MAP1A_HUMAN	R	2001;1763;1763	ENSP00000371462:P2001R;ENSP00000382380:P1763R;ENSP00000300231:P1763R	ENSP00000300231:P1763R	P	+	2	0	MAP1A	41606251	0.953000	0.32496	0.451000	0.26982	0.145000	0.21501	2.451000	0.44952	2.321000	0.78463	0.455000	0.32223	CCA	.	.	weak		0.572	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373		G	43818959	C	G	43818959	3	3	23	1	0	0	0	0	1	0	0	0	9236	594	21	4	5290	4	MAP1A	15	43818959	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	291140	43818959	58712433	547	7991											
TRPM7	54822	hgsc.bcm.edu	37	chr15	50884289	50884294	+	In_Frame_Del	DEL	ATTTTT	ATTTTT	-																															gatgaactgcctaatttttgAtttttattaaatatttttaa																										TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	ATTTTT	ATTTTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:50884289_50884294delATTTTT	ENST00000313478.7	-	26	4419_4424	c.4138_4143delAAAAAT	c.(4138-4143)aaaaatdel	p.KN1380del	TRPM7_ENST00000560955.1_In_Frame_Del_p.KN1380del	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7	1380					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)		Ctaatttttgatttttattaaatatt	0.417																																					p.1380_1382del		Pindel,Atlas-Indel	.											.	TRPM7	145	.	0			c.4139_4144del						PASS	.			3,3465		1,1,1732						0.5	0.6			62	3,7803		0,3,3900	no	coding	TRPM7	NM_017672.4		1,4,5632	A1A1,A1R,RR		0.0384,0.0865,0.0532				6,11268				SO:0001651	inframe_deletion	54822	exon26			.	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.4138_4143delAAAAAT	15.37:g.50884289_50884294delATTTTT	ENSP00000320239:p.Lys1380_Asn1381del	35	0	.		35	10	0.286	NM_017672	Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	In_Frame_Del	DEL	ENST00000313478.7	37	CCDS42035.1																																																																																			.	.	none		0.417	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672		-	50884294	ATTTTT	-	50884289	7	5	23	1	0	1	0	1	0	0	0	0	16606	330	12	0	1510	0	TRPM7	15	50884289	In_Frame_Del	DEL	ATTTTT	TCGA-G8-6325-01A-11D-2210-10	7065330	50884289	51647103	548	7992											
PYGO1	26108	hgsc.bcm.edu	37	chr15	55838976	55838976	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgttgattaggcatgttgaCattctgacttagtgcattat	10	17	9	5	0	1	3	0	3	1	0	1	3	1	3	0	1	1	4	0	1	3	6	rs144876912	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:55838976C>G	ENST00000302000.6	-	3	599	c.505G>C	c.(505-507)Gtc>Ctc	p.V169L	PYGO1_ENST00000563719.1_Missense_Mutation_p.V169L	NM_015617.1	NP_056432.1	Q9Y3Y4	PYGO1_HUMAN	pygopus family PHD finger 1	169	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)		GGCATGTTGACATTCTGACTT	0.383																																					p.V169L		Atlas-SNP	.											PYGO1,NS,carcinoma,+2,1	PYGO1	56	1	0			c.G505C						PASS	.	C	LEU/VAL	2,4384	4.2+/-10.8	0,2,2191	114	116	115		505	3.3	1	15	dbSNP_134	115	16,8568	11.9+/-42.8	0,16,4276	yes	missense	PYGO1	NM_015617.1	32	0,18,6467	GG,GC,CC		0.1864,0.0456,0.1388	benign	169/420	55838976	18,12952	2193	4292	6485	SO:0001583	missense	26108	exon3			TGTTGACATTCTG	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.505G>C	15.37:g.55838976C>G	ENSP00000302327:p.Val169Leu	180	0	0		187	99	0.529412	NM_015617	A7Y2D6	Missense_Mutation	SNP	ENST00000302000.6	37	CCDS10155.1	.	.	.	.	.	.	.	.	.	.	C	9.561	1.118537	0.20877	4.56E-4	0.001864	ENSG00000171016	ENST00000302000;ENST00000401688	T	0.45668	0.89	5.23	3.33	0.38152	.	0.395337	0.23849	N	0.043976	T	0.23532	0.0569	N	0.19112	0.55	0.27105	N	0.962529	B;B	0.15473	0.013;0.013	B;B	0.17979	0.011;0.02	T	0.21484	-1.0244	10	0.11794	T	0.64	-7.226	8.1499	0.31134	0.0:0.7585:0.0:0.2415	.	169;169	A7Y2D6;Q9Y3Y4	.;PYGO1_HUMAN	L	169	ENSP00000302327:V169L	ENSP00000302327:V169L	V	-	1	0	PYGO1	53626268	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	0.943000	0.29030	0.685000	0.31468	0.585000	0.79938	GTC	C|0.998;G|0.002	0.002	strong		0.383	PYGO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254977.2	NM_015617		G	55838976	C	G	55838976	3	3	23	1	0	0	0	0	1	0	0	0	12878	478	17	4	758	4	PYGO1	15	55838976	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	4954687	55838976	46692416	549	7993											
CGNL1	84952	hgsc.bcm.edu	37	chr15	57731384	57731384	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggatagcgcctttccttttgGcctccaagggaactcggagt	7	11	12	11	2	0	0	0	0	0	0	3	3	2	3	4	4	2	0	4	4	3	4	rs148544821	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:57731384G>T	ENST00000281282.5	+	2	1265	c.1187G>T	c.(1186-1188)gGc>gTc	p.G396V		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	396	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)		TTTCCTTTTGGCCTCCAAGGG	0.527													G|||	4	0.000798722	0.0008	0.0014	5008	,	,		18234	0.0		0.002	False		,,,				2504	0.0				p.G396V		Atlas-SNP	.											.	CGNL1	125	.	0			c.G1187T						PASS	.	G	VAL/GLY	2,4382	4.2+/-10.8	0,2,2190	94	96	95		1187	5.8	0.3	15	dbSNP_134	95	14,8570	9.8+/-36.6	0,14,4278	yes	missense	CGNL1	NM_032866.3	109	0,16,6468	TT,TG,GG		0.1631,0.0456,0.1234	probably-damaging	396/1303	57731384	16,12952	2192	4292	6484	SO:0001583	missense	84952	exon2			CTTTTGGCCTCCA	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.1187G>T	15.37:g.57731384G>T	ENSP00000281282:p.Gly396Val	128	0	0		115	46	0.4	NM_032866	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Missense_Mutation	SNP	ENST00000281282.5	37	CCDS10161.1	4	0.0018315018315018315	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	17.89	3.498940	0.64298	4.56E-4	0.001631	ENSG00000128849	ENST00000281282	T	0.58940	0.3	5.79	5.79	0.91817	.	0.000000	0.52532	D	0.000073	T	0.68723	0.3032	L	0.54323	1.7	0.58432	D	0.999999	D	0.65815	0.995	P	0.59357	0.856	T	0.70733	-0.4791	10	0.87932	D	0	-28.2427	15.212	0.73230	0.0689:0.0:0.9311:0.0	.	396	Q0VF96	CGNL1_HUMAN	V	396	ENSP00000281282:G396V	ENSP00000281282:G396V	G	+	2	0	CGNL1	55518676	1.000000	0.71417	0.255000	0.24374	0.477000	0.33069	6.194000	0.72082	2.722000	0.93159	0.655000	0.94253	GGC	G|0.998;T|0.002	0.002	strong		0.527	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866		T	57731384	G	T	57731384	3	4	23	1	0	0	0	0	1	0	0	0	3306	1203	42	4	1189	4	CGNL1	15	57731384	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1892408	57731384	44800008	550	7994											
TPM1	7168	hgsc.bcm.edu	37	chr15	63363291	63363291	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctaatctcaccacagagAaagtggctcatgccaaagaa	15	9	7	10	0	3	2	2	0	2	2	4	3	3	2	2	1	1	1	2	1	4	2	rs144045691	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:63363291A>G	ENST00000357980.4	+	10	980	c.901A>G	c.(901-903)Aaa>Gaa	p.K301E	TPM1_ENST00000358278.3_Missense_Mutation_p.K259E|TPM1_ENST00000559397.1_Missense_Mutation_p.K259E|RP11-244F12.2_ENST00000558905.1_RNA|TPM1_ENST00000559556.1_Missense_Mutation_p.K259E|TPM1_ENST00000404484.4_Missense_Mutation_p.K223E|TPM1_ENST00000267996.7_Missense_Mutation_p.K259E			P09493	TPM1_HUMAN	tropomyosin 1 (alpha)	259					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						CACCACAGAGAAAGTGGCTCA	0.413													A|||	3	0.000599042	0.0	0.0	5008	,	,		23023	0.0		0.003	False		,,,				2504	0.0				p.K259E		Atlas-SNP	.											.	TPM1	59	.	0			c.A775G						PASS	.	A	GLU/LYS,GLU/LYS,GLU/LYS,GLU/LYS	0,4406		0,0,2203	122	113	116		775,775,775,775	6	1	15	dbSNP_134	116	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense,missense,missense	TPM1	NM_001018004.1,NM_001018006.1,NM_001018007.1,NM_001018020.1	56,56,56,56	0,4,6499	GG,GA,AA		0.0465,0.0,0.0308	benign,benign,benign,benign	259/285,259/285,259/285,259/285	63363291	4,13002	2203	4300	6503	SO:0001583	missense	7168	exon9			ACAGAGAAAGTGG	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	ENST00000357980.4:c.901A>G	15.37:g.63363291A>G	ENSP00000350667:p.Lys301Glu	110	0	0		128	66	0.515625	NM_001018007	B7Z5T7|D9YZV2|D9YZV3|D9YZV8|P09494|P10469|Q6DV89|Q6DV90|Q7Z6L8|Q86W64|Q96IK2|Q9UCI1|Q9UCI2|Q9UCY9|Q9Y427	Missense_Mutation	SNP	ENST00000357980.4	37		3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	10.44	1.350695	0.24512	0.0	4.65E-4	ENSG00000140416	ENST00000267996;ENST00000358278;ENST00000357980	T;T;T	0.73897	-0.79;-0.79;-0.79	6.02	6.02	0.97574	.	0.000000	0.56097	D	0.000039	T	0.52869	0.1761	N	0.05467	-0.045	0.80722	D	1	B;B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.15052	0.012;0.006;0.002;0.001;0.001;0.001	T	0.53858	-0.8379	10	0.02654	T	1	-4.6565	15.7258	0.77756	1.0:0.0:0.0:0.0	.	223;301;259;259;259;259	B7Z722;Q6ZN40;D9YZV8;D9YZV5;Q9Y427;D9YZV3	.;.;.;.;.;.	E	259;259;301	ENSP00000267996:K259E;ENSP00000351022:K259E;ENSP00000350667:K301E	ENSP00000267996:K259E	K	+	1	0	TPM1	61150344	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.122000	0.94380	2.311000	0.77944	0.533000	0.62120	AAA	A|0.999;G|0.001	0.001	strong		0.413	TPM1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000417087.2	NM_001018004		G	63363291	A	G	63363291	3	3	23	1	0	0	0	0	1	0	0	0	16420	247	9	3	1328	3	TPM1	15	63363291	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	5631907	63363291	39168101	551	7995											
STRA6	64220	hgsc.bcm.edu	37	chr15	74472525	74472525	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accccagcgagccctgccgcGgctggccccgggcctagctc	4	4	13	20	4	0	0	0	0	0	0	1	1	0	0	7	3	4	2	7	3	1	1	rs200178616		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:74472525G>A	ENST00000323940.5	-	19	2145	c.1900C>T	c.(1900-1902)Cgc>Tgc	p.R634C	STRA6_ENST00000574278.1_Missense_Mutation_p.R649C|STRA6_ENST00000535552.1_Missense_Mutation_p.R671C|STRA6_ENST00000395105.4_Missense_Mutation_p.R634C|STRA6_ENST00000574439.1_5'UTR|STRA6_ENST00000563965.1_Missense_Mutation_p.R673C|STRA6_ENST00000449139.2_Missense_Mutation_p.R634C|STRA6_ENST00000416286.3_Missense_Mutation_p.R626C|RP11-665J16.1_ENST00000561647.1_RNA|STRA6_ENST00000423167.2_Missense_Mutation_p.R625C	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	634					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						GCCCTGCCGCGGCTGGCCCCG	0.637													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19002	0.0		0.0	False		,,,				2504	0.0				p.R673C		Atlas-SNP	.											STRA6,NS,carcinoma,+1,1	STRA6	66	1	0			c.C2017T						scavenged	.						91	104	100					15																	74472525		2198	4297	6495	SO:0001583	missense	64220	exon19			TGCCGCGGCTGGC	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.1900C>T	15.37:g.74472525G>A	ENSP00000326085:p.Arg634Cys	147	1	0.00680272		158	77	0.487342	NM_001199042	A8K7F1|B7Z5M9|B7Z862|D3DW54|F5GYI8|I3L1G8|Q6PJF8|Q71RB9|Q7L9G1|Q7Z3U9|Q8TB21|Q9BX78|Q9H9U8	Missense_Mutation	SNP	ENST00000323940.5	37	CCDS10261.1	.	.	.	.	.	.	.	.	.	.	G	11.53	1.666348	0.29604	.	.	ENSG00000137868	ENST00000395105;ENST00000323940;ENST00000416286;ENST00000545137;ENST00000449139;ENST00000423167;ENST00000535552;ENST00000536129	D;D;D;D	0.85484	-1.99;-1.99;-1.99;-1.99	4.5	2.61	0.31194	.	0.757532	0.12544	N	0.459624	D	0.86205	0.5877	L	0.48642	1.525	0.21473	N	0.999671	D;D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.999;0.999	P;P;P;P;P;P	0.56916	0.804;0.804;0.736;0.736;0.804;0.809	T	0.75286	-0.3371	10	0.66056	D	0.02	-2.8476	8.8353	0.35109	0.1759:0.0:0.8241:0.0	.	671;672;625;634;673;443	F5GYI8;B7Z5G7;Q9BX79-3;Q9BX79;Q9BX79-4;B3KRT6	.;.;.;STRA6_HUMAN;.;.	C	634;634;566;443;673;625;671;524	ENSP00000378537:R634C;ENSP00000326085:R634C;ENSP00000413012:R625C;ENSP00000440238:R671C	ENSP00000326085:R634C	R	-	1	0	STRA6	72259578	0.075000	0.21258	0.004000	0.12327	0.013000	0.08279	2.732000	0.47352	0.351000	0.24027	-0.379000	0.06801	CGC	G|0.999;A|0.001	0.001	weak		0.637	STRA6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272891.1			A	74472525	G	A	74472525	3	1	23	1	0	0	0	0	1	0	0	0	15337	1116	39	1	107	1	STRA6	15	74472525	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	11109234	74472525	28058867	552	7996											
C15orf27	123591	hgsc.bcm.edu	37	chr15	76494569	76494569	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgatgaaggacgacatgaacAgctacatcagtcagtattac	15	8	9	9	2	2	2	2	2	0	0	2	5	2	3	0	1	4	2	0	1	5	3	rs62030189	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:76494569A>G	ENST00000388942.3	+	10	1261	c.985A>G	c.(985-987)Agc>Ggc	p.S329G		NM_152335.2	NP_689548.2	Q2M3C6	CO027_HUMAN	chromosome 15 open reading frame 27	329					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|membrane depolarization during action potential (GO:0086010)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	voltage-gated calcium channel activity (GO:0005245)			endometrium(1)|large_intestine(1)|lung(10)|pancreas(1)	13						CGACATGAACAGCTACATCAG	0.522													A|||	3	0.000599042	0.0	0.0	5008	,	,		21160	0.0		0.003	False		,,,				2504	0.0				p.S329G		Atlas-SNP	.											.	C15orf27	32	.	0			c.A985G						PASS	.	A	GLY/SER	4,4390	9.9+/-24.2	0,4,2193	191	141	158		985	3.3	1	15	dbSNP_129	158	47,8541	30.1+/-81.4	0,47,4247	yes	missense	C15orf27	NM_152335.2	56	0,51,6440	GG,GA,AA		0.5473,0.091,0.3929	benign	329/532	76494569	51,12931	2197	4294	6491	SO:0001583	missense	123591	exon10			ATGAACAGCTACA	AK095509	CCDS10289.2	15q23-q24.1	2012-09-27			ENSG00000169758	ENSG00000169758			26763	protein-coding gene	gene with protein product						14702039, 22020278	Standard	NM_152335		Approved	FLJ38190	uc002bbq.3	Q2M3C6	OTTHUMG00000142918	ENST00000388942.3:c.985A>G	15.37:g.76494569A>G	ENSP00000373594:p.Ser329Gly	140	0	0		151	80	0.529801	NM_152335	Q8N993|Q96LL5	Missense_Mutation	SNP	ENST00000388942.3	37	CCDS10289.2	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	A	14.79	2.640347	0.47153	9.1E-4	0.005473	ENSG00000169758	ENST00000388942	T	0.33865	1.39	4.48	3.31	0.37934	.	0.148543	0.64402	D	0.000016	T	0.19846	0.0477	L	0.40543	1.245	0.32431	N	0.548089	B;B	0.33171	0.4;0.03	B;B	0.30855	0.121;0.037	T	0.26087	-1.0113	10	0.44086	T	0.13	-11.903	9.2607	0.37610	0.8177:0.1823:0.0:0.0	rs62030189	293;329	Q2M3C6-2;Q2M3C6	.;CO027_HUMAN	G	329	ENSP00000373594:S329G	ENSP00000373594:S329G	S	+	1	0	C15orf27	74281624	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	6.533000	0.73829	0.630000	0.30394	0.379000	0.24179	AGC	A|0.996;G|0.004	0.004	strong		0.522	C15orf27-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286637.2	NM_152335		G	76494569	A	G	76494569	3	3	23	1	0	0	0	0	1	0	0	0	1790	188	7	3	1019	3	C15orf27	15	76494569	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	2022044	76494569	26036823	553	7997											
IREB2	3658	hgsc.bcm.edu	37	chr15	78789534	78789534	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcatttgattggaattggcAtagctccacttcagttcctt	9	16	7	9	0	2	1	2	1	0	0	4	2	4	2	2	2	1	3	2	2	2	7	rs140959198	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:78789534A>G	ENST00000258886.8	+	21	2811	c.2662A>G	c.(2662-2664)Ata>Gta	p.I888V		NM_004136.2	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2	888					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)		TGGAATTGGCATAGCTCCACT	0.393													A|||	8	0.00159744	0.0	0.0058	5008	,	,		16922	0.0		0.004	False		,,,				2504	0.0				p.I888V	NSCLC(200;764 2208 35157 49871 50830)	Atlas-SNP	.											.	IREB2	106	.	0			c.A2662G						PASS	.	A	VAL/ILE	2,4390	4.2+/-10.8	0,2,2194	114	106	109		2662	4.8	1	15	dbSNP_134	109	41,8545	27.4+/-76.7	0,41,4252	yes	missense	IREB2	NM_004136.2	29	0,43,6446	GG,GA,AA		0.4775,0.0455,0.3313	benign	888/964	78789534	43,12935	2196	4293	6489	SO:0001583	missense	3658	exon21			ATTGGCATAGCTC	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.2662A>G	15.37:g.78789534A>G	ENSP00000258886:p.Ile888Val	167	0	0		170	83	0.488235	NM_004136	A8KAC7|E1CJT9|H0YKU0|Q13095|Q1HE21|Q59FQ7|Q8WVK6|Q9UF17	Missense_Mutation	SNP	ENST00000258886.8	37	CCDS10302.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	A	12.03	1.814651	0.32053	4.55E-4	0.004775	ENSG00000136381	ENST00000258886	T	0.13657	2.57	5.87	4.75	0.60458	Aconitase/3-isopropylmalate dehydratase, swivel (2);Aconitase A/isopropylmalate dehydratase small subunit, swivel (1);	0.084546	0.85682	D	0.000000	T	0.06962	0.0177	L	0.28458	0.855	0.80722	D	1	B	0.12630	0.006	B	0.20184	0.028	T	0.10636	-1.0621	10	0.09843	T	0.71	.	12.1948	0.54290	0.9334:0.0:0.0666:0.0	.	888	P48200	IREB2_HUMAN	V	888	ENSP00000258886:I888V	ENSP00000258886:I888V	I	+	1	0	IREB2	76576589	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	6.693000	0.74582	1.148000	0.42385	0.533000	0.62120	ATA	A|0.998;G|0.002	0.002	strong		0.393	IREB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290109.3	NM_004136		G	78789534	A	G	78789534	3	3	23	1	0	0	0	0	1	0	0	0	7835	217	8	3	2744	3	IREB2	15	78789534	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	2294965	78789534	23741858	554	7998											
CHRNA3	1136	hgsc.bcm.edu	37	chr15	78893787	78893787	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcagtaaccacacatcccGtcctggcaggggtagccctc	8	7	11	15	1	0	0	0	0	0	0	3	0	2	0	4	4	2	4	4	4	2	2	rs56403513	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:78893787G>A	ENST00000326828.5	-	5	1581	c.1197C>T	c.(1195-1197)gaC>gaT	p.D399D	CHRNA3_ENST00000348639.3_Silent_p.D399D	NM_000743.4	NP_000734.2	P32297	ACHA3_HUMAN	cholinergic receptor, nicotinic, alpha 3 (neuronal)	399					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|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)|nervous system development (GO:0007399)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane potential (GO:0042391)|regulation of smooth muscle contraction (GO:0006940)|signal transduction (GO:0007165)|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)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|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)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18					Bupropion(DB01156)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Levomethadyl Acetate(DB01227)|Nicotine(DB00184)|Pentolinium(DB01090)|Varenicline(DB01273)	CACACATCCCGTCCTGGCAGG	0.542													G|||	5	0.000998403	0.0008	0.0	5008	,	,		19435	0.001		0.003	False		,,,				2504	0.0				p.D399D		Atlas-SNP	.											.	CHRNA3	56	.	0			c.C1197T						PASS	.	G	,	2,4390	4.2+/-10.8	0,2,2194	104	93	97		1197,1197	-12	0	15	dbSNP_129	97	33,8553	22.8+/-68.1	0,33,4260	no	coding-synonymous,coding-synonymous	CHRNA3	NM_000743.4,NM_001166694.1	,	0,35,6454	AA,AG,GG		0.3843,0.0455,0.2697	,	399/506,399/490	78893787	35,12943	2196	4293	6489	SO:0001819	synonymous_variant	1136	exon5			CATCCCGTCCTGG		CCDS10305.1, CCDS53964.1	15q24	2012-02-11	2012-02-07		ENSG00000080644	ENSG00000080644		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1957	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 3 (neuronal)"	118503	"cholinergic receptor, nicotinic, alpha polypeptide 3"			2004777	Standard	NM_000743		Approved		uc002bec.3	P32297	OTTHUMG00000143863	ENST00000326828.5:c.1197C>T	15.37:g.78893787G>A		239	0	0		243	115	0.473251	NM_000743	Q15823|Q4KMN8|Q86U77|Q96RH3|Q99553|Q9BQ93|Q9BRR4	Silent	SNP	ENST00000326828.5	37	CCDS10305.1																																																																																			G|0.996;A|0.004	0.004	strong		0.542	CHRNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290111.3			A	78893787	G	A	78893787	2	1	23	1	0	0	0	0	0	0	0	1	3386	1136	40	1		1	CHRNA3	15	78893787	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	104253	78893787	23637605	555	7999											
CHRNA3	1136	hgsc.bcm.edu	37	chr15	78894420	78894420	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagagccgatcaggaccagAtcgattttcgccttatcgta	11	10	10	10	4	1	2	1	0	0	2	4	6	1	3	3	1	1	1	3	1	3	4	rs8192480|rs74315118	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:78894420A>G	ENST00000326828.5	-	5	948	c.564T>C	c.(562-564)gaT>gaC	p.D188D	CHRNA3_ENST00000348639.3_Silent_p.D188D	NM_000743.4	NP_000734.2	P32297	ACHA3_HUMAN	cholinergic receptor, nicotinic, alpha 3 (neuronal)	188					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|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)|nervous system development (GO:0007399)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane potential (GO:0042391)|regulation of smooth muscle contraction (GO:0006940)|signal transduction (GO:0007165)|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)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|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)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18					Bupropion(DB01156)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Levomethadyl Acetate(DB01227)|Nicotine(DB00184)|Pentolinium(DB01090)|Varenicline(DB01273)	TCAGGACCAGATCGATTTTCG	0.488													A|||	14	0.00279553	0.0008	0.0	5008	,	,		18118	0.0		0.0099	False		,,,				2504	0.0031				p.D188D		Atlas-SNP	.											.	CHRNA3	56	.	0			c.T564C						PASS	.	A	,	3,4389	6.2+/-15.9	0,3,2193	180	160	167		564,564	0.9	1	15	dbSNP_117	167	39,8547	26.3+/-74.7	1,37,4255	no	coding-synonymous,coding-synonymous	CHRNA3	NM_000743.4,NM_001166694.1	,	1,40,6448	GG,GA,AA		0.4542,0.0683,0.3236	,	188/506,188/490	78894420	42,12936	2196	4293	6489	SO:0001819	synonymous_variant	1136	exon5			GACCAGATCGATT		CCDS10305.1, CCDS53964.1	15q24	2012-02-11	2012-02-07		ENSG00000080644	ENSG00000080644		"Cholinergic receptors", "Ligand-gated ion channels / Acetylcholine receptors, nicotinic"	1957	protein-coding gene	gene with protein product	"acetylcholine receptor, nicotinic, alpha 3 (neuronal)"	118503	"cholinergic receptor, nicotinic, alpha polypeptide 3"			2004777	Standard	NM_000743		Approved		uc002bec.3	P32297	OTTHUMG00000143863	ENST00000326828.5:c.564T>C	15.37:g.78894420A>G		223	0	0		189	93	0.492063	NM_000743	Q15823|Q4KMN8|Q86U77|Q96RH3|Q99553|Q9BQ93|Q9BRR4	Silent	SNP	ENST00000326828.5	37	CCDS10305.1																																																																																			A|0.995;G|0.005	0.005	strong		0.488	CHRNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290111.3			G	78894420	A	G	78894420	2	3	23	1	0	0	0	0	0	0	0	1	3386	330	12	3		3	CHRNA3	15	78894420	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	633	78894420	23636972	556	8000											
MTHFS	10588	hgsc.bcm.edu	37	chr15	80189277	80189277	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctcatcgcccgcagacgctgCttcagctctccccgcaggct	5	8	9	19	4	3	1	2	0	1	1	5	1	3	1	3	1	2	6	3	1	0	1	rs375170671	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:80189277C>T	ENST00000258874.3	-	1	114	c.54G>A	c.(52-54)aaG>aaA	p.K18K	ST20-MTHFS_ENST00000494999.1_Intron|ST20-MTHFS_ENST00000479961.1_Intron|MTHFS_ENST00000559722.1_Intron	NM_006441.3	NP_006432.1	P49914	MTHFS_HUMAN	5,10-methenyltetrahydrofolate synthetase (5-formyltetrahydrofolate cyclo-ligase)	18					formate metabolic process (GO:0015942)|tetrahydrofolate metabolic process (GO:0046653)	cytoplasm (GO:0005737)	5-formyltetrahydrofolate cyclo-ligase activity (GO:0030272)|ATP binding (GO:0005524)|folic acid binding (GO:0005542)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(1)|liver(1)	5				all cancers(203;0.00467)		GCAGACGCTGCTTCAGCTCTC	0.736													C|||	8	0.00159744	0.0	0.0029	5008	,	,		11491	0.0		0.004	False		,,,				2504	0.002				p.K18K		Atlas-SNP	.											.	MTHFS	11	.	0			c.G54A						PASS	.	C	,,	3,3811		0,3,1904	6	6	6		,,54	4	1	15		6	24,7530		0,24,3753	no	intron,intron,coding-synonymous	MTHFS,ST20-MTHFS	NM_001199758.1,NM_001199760.1,NM_006441.3	,,	0,27,5657	TT,TC,CC		0.3177,0.0787,0.2375	,,	,,18/204	80189277	27,11341	1907	3777	5684	SO:0001819	synonymous_variant	10588	exon1			ACGCTGCTTCAGC	L38928	CCDS10311.1	15q24.3	2014-05-15			ENSG00000136371	ENSG00000136371	6.3.3.2		7437	protein-coding gene	gene with protein product		604197				8522195	Standard	NM_006441		Approved	HsT19268	uc002bex.4	P49914	OTTHUMG00000144174	ENST00000258874.3:c.54G>A	15.37:g.80189277C>T		46	0	0		19	15	0.789474	NM_006441	H3BQ75	Silent	SNP	ENST00000258874.3	37	CCDS10311.1																																																																																			.	.	weak		0.736	MTHFS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291374.2	NM_006441		T	80189277	C	T	80189277	2	4	23	1	0	0	0	0	0	0	0	1	9941	796	28	2		2	MTHFS	15	80189277	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1294857	80189277	22342115	557	8001											
KIAA1199	57214	hgsc.bcm.edu	37	chr15	81173354	81173354	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctctcctggacatttctgaAcaagacccttcacccaggtg	9	10	8	14	0	3	2	1	1	2	1	4	3	3	3	3	2	1	1	3	2	2	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:81173354A>G	ENST00000394685.3	+	6	913	c.494A>G	c.(493-495)aAc>aGc	p.N165S	KIAA1199_ENST00000356249.5_Missense_Mutation_p.N165S|KIAA1199_ENST00000220244.3_Missense_Mutation_p.N165S			Q8WUJ3	CEMIP_HUMAN		165	G8. {ECO:0000255|PROSITE- ProRule:PRU00817}.				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						ACATTTCTGAACAAGACCCTT	0.488																																					p.N165S		Atlas-SNP	.											.	KIAA1199	118	.	0			c.A494G						PASS	.						131	126	128					15																	81173354		2203	4300	6503	SO:0001583	missense	57214	exon5			TTCTGAACAAGAC																												ENST00000394685.3:c.494A>G	15.37:g.81173354A>G	ENSP00000378177:p.Asn165Ser	195	0	0		187	78	0.417112	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Missense_Mutation	SNP	ENST00000394685.3	37	CCDS10315.1	.	.	.	.	.	.	.	.	.	.	A	7.211	0.595402	0.13875	.	.	ENSG00000103888	ENST00000220244;ENST00000394685;ENST00000356249;ENST00000394683	D;D;D	0.88509	-2.39;-2.39;-2.39	5.95	-0.988	0.10245	G8 domain (2);	0.111999	0.56097	N	0.000025	T	0.79191	0.4404	L	0.46157	1.445	0.41440	D	0.987918	B	0.02656	0.0	B	0.12156	0.007	T	0.61705	-0.7008	10	0.07813	T	0.8	-42.3377	6.5765	0.22569	0.6185:0.1162:0.2653:0.0	.	165	Q8WUJ3	K1199_HUMAN	S	165	ENSP00000220244:N165S;ENSP00000378177:N165S;ENSP00000348583:N165S	ENSP00000220244:N165S	N	+	2	0	KIAA1199	78960409	1.000000	0.71417	0.778000	0.31720	0.594000	0.36715	3.502000	0.53332	-0.411000	0.07530	0.533000	0.62120	AAC	.	.	none		0.488	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1			G	81173354	A	G	81173354	3	3	23	1	0	0	0	0	1	0	0	0	8222	43	2	3	508	3	KIAA1199	15	81173354	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	984077	81173354	21358038	558	8002											
FAM154B	283726	hgsc.bcm.edu	37	chr15	82574734	82574735	+	Frame_Shift_Del	DEL	AC	AC	-																															gtttacaaaccaactgaccaAcgctttgaggatctcacaac																								rs531481065	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:82574734_82574735delAC	ENST00000339465.5	+	3	597_598	c.528_529delAC	c.(526-531)caacgcfs	p.R177fs	FAM154B_ENST00000565501.1_3'UTR|FAM154B_ENST00000427381.2_Frame_Shift_Del_p.R162fs	NM_001008226.1	NP_001008227.1	Q658L1	F154B_HUMAN	family with sequence similarity 154, member B	177										autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(2)	19						CAACTGACCAACGCTTTGAGGA	0.441														6	0.00119808	0.0	0.0	5008	,	,		20560	0.0		0.006	False		,,,				2504	0.0				p.176_176del		Pindel,Atlas-Indel	.											.	FAM154B	50	.	0			c.527_528del						PASS	.			11,4253		0,11,2121						1.4	0			67	78,8176		1,76,4050	no	frameshift	FAM154B	NM_001008226.1		1,87,6171	A1A1,A1R,RR		0.945,0.258,0.711				89,12429				SO:0001589	frameshift_variant	283726	exon3			.	AL833762	CCDS32310.1	15q25.2	2008-02-21				ENSG00000188659			33727	protein-coding gene	gene with protein product							Standard	XM_005254317		Approved	DKFZp666G057	uc002bgv.3	Q658L1		ENST00000339465.5:c.528_529delAC	15.37:g.82574734_82574735delAC	ENSP00000340445:p.Arg177fs	87	0	.		91	34	0.374	NM_001008226	B4E2M2	Frame_Shift_Del	DEL	ENST00000339465.5	37	CCDS32310.1																																																																																			.	.	none		0.441	FAM154B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419644.1	NM_001008226		-	82574735	AC	-	82574734	7	5	23	1	0	1	0	1	0	0	0	0	5469	40	2	0	538	0	FAM154B	15	82574734	Frame_Shift_Del	DEL	AC	TCGA-G8-6325-01A-11D-2210-10	1401380	82574734	19956658	559	8003											
SEC11A	23478	hgsc.bcm.edu	37	chr15	85234858	85234858	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagacaatcattccaaaattTaggacttgataatagagctg	16	11	8	6	0	1	3	1	1	0	2	2	5	2	4	1	1	1	1	1	1	6	6	rs369852123		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:85234858T>C	ENST00000268220.7	-	2	709	c.69A>G	c.(67-69)ctA>ctG	p.L23L	SEC11A_ENST00000560266.1_Silent_p.L23L|SEC11A_ENST00000558134.1_Silent_p.L23L|SEC11A_ENST00000455959.3_5'UTR	NM_014300.2	NP_055115.1	P67812	SC11A_HUMAN	SEC11 homolog A (S. cerevisiae)	23					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)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	serine-type peptidase activity (GO:0008236)			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(143;0.199)			TTCCAAAATTTAGGACTTGAT	0.398																																					p.L23L		Atlas-SNP	.											.	SEC11A	8	.	0			c.A69G						PASS	.	T		0,3756		0,0,1878	75	69	71		69	-1.8	1	15		71	1,8227		0,1,4113	no	coding-synonymous	SEC11A	NM_014300.2		0,1,5991	CC,CT,TT		0.0122,0.0,0.0083		23/180	85234858	1,11983	1878	4114	5992	SO:0001819	synonymous_variant	23478	exon2			AAAATTTAGGACT	AF061737	CCDS45340.1, CCDS61742.1, CCDS61743.1, CCDS61744.1, CCDS73776.1	15q25.2	2006-11-07	2006-11-07	2006-11-07		ENSG00000140612			17718	protein-coding gene	gene with protein product			"SEC11-like 1 (S. cerevisiae)"	SEC11L1			Standard	NM_001271919		Approved	SPC18, sid2895, SPCS4A	uc031qtg.1	P67812		ENST00000268220.7:c.69A>G	15.37:g.85234858T>C		77	0	0		77	45	0.584416	NM_014300	B2RAD7|B4DUL4|H0YK72|H0YK83|O75957|P21378|Q53FQ8	Silent	SNP	ENST00000268220.7	37	CCDS45340.1																																																																																			.	.	weak		0.398	SEC11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418777.1	NM_014300		C	85234858	T	C	85234858	2	2	23	1	0	0	0	0	0	0	0	1	13993	1741	61	3		3	SEC11A	15	85234858	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	2660124	85234858	17296534	560	8004											
AKAP13	11214	hgsc.bcm.edu	37	chr15	86124861	86124861	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atgaagcacatcctgtcctaCtgcagcctgttgccaaggag	10	9	10	12	0	0	1	0	1	0	0	2	2	2	2	4	1	5	3	4	1	3	2	rs371702364		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:86124861C>A	ENST00000394518.2	+	7	3657	c.3562C>A	c.(3562-3564)Ctg>Atg	p.L1188M	RP11-815J21.2_ENST00000561409.1_RNA|AKAP13_ENST00000361243.2_Missense_Mutation_p.L1188M	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	1188					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						TCCTGTCCTACTGCAGCCTGT	0.582																																					p.L1188M	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.C3562A						PASS	.	C	MET/LEU,MET/LEU	0,4404		0,0,2202	71	69	69		3562,3562	2.5	0	15		69	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense	AKAP13	NM_006738.4,NM_007200.3	15,15	0,1,6500	AA,AC,CC		0.0116,0.0,0.0077	benign,benign	1188/2818,1188/2814	86124861	1,13001	2202	4299	6501	SO:0001583	missense	11214	exon7			GTCCTACTGCAGC	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.3562C>A	15.37:g.86124861C>A	ENSP00000378026:p.Leu1188Met	124	0	0		101	55	0.544554	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	37	CCDS32319.1	.	.	.	.	.	.	.	.	.	.	C	9.556	1.117178	0.20795	0.0	1.16E-4	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540	T;T	0.16196	2.36;2.36	5.49	2.49	0.30216	.	.	.	.	.	T	0.09024	0.0223	N	0.14661	0.345	0.09310	N	0.999999	B;B	0.28291	0.028;0.206	B;B	0.27170	0.014;0.077	T	0.31916	-0.9926	9	0.45353	T	0.12	.	4.1054	0.10035	0.1653:0.5884:0.1595:0.0867	.	1188;1188	Q12802;Q12802-2	AKP13_HUMAN;.	M	1188;1188;1187;1187	ENSP00000354718:L1188M;ENSP00000378026:L1188M	ENSP00000354718:L1188M	L	+	1	2	AKAP13	83925865	0.001000	0.12720	0.000000	0.03702	0.217000	0.24651	1.161000	0.31773	0.236000	0.21180	0.650000	0.86243	CTG	.	.	weak		0.582	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200		A	86124861	C	A	86124861	3	1	23	1	0	0	0	0	1	0	0	0	449	564	20	4	3584	4	AKAP13	15	86124861	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	890003	86124861	16406531	561	8005											
POLG	5428	hgsc.bcm.edu	37	chr15	89864987	89864987	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgggcattgctggcggtgaGccatgtgggctccacagccc	5	7	15	14	2	0	1	0	1	0	0	1	1	1	1	4	4	3	3	4	4	0	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:89864987G>A	ENST00000268124.5	-	16	2911	c.2578C>T	c.(2578-2580)Ctc>Ttc	p.L860F	POLG_ENST00000442287.2_Missense_Mutation_p.L860F	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma	860					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)			CTGGCGGTGAGCCATGTGGGC	0.617								DNA polymerases (catalytic subunits)																													p.L860F	Colon(73;648 1203 11348 18386 27782)	Atlas-SNP	.											.	POLG	75	.	0			c.C2578T						PASS	.						68	69	69					15																	89864987		2200	4299	6499	SO:0001583	missense	5428	exon16			CGGTGAGCCATGT	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.2578C>T	15.37:g.89864987G>A	ENSP00000268124:p.Leu860Phe	79	0	0		111	20	0.18018	NM_002693	Q8NFM2|Q92515	Missense_Mutation	SNP	ENST00000268124.5	37	CCDS10350.1	.	.	.	.	.	.	.	.	.	.	G	33	5.233367	0.95207	.	.	ENSG00000140521	ENST00000268124;ENST00000442287	D;D	0.99089	-5.41;-5.41	5.24	5.24	0.73138	DNA-directed DNA polymerase, family A, palm domain (1);	0.000000	0.85682	D	0.000000	D	0.99429	0.9798	M	0.90198	3.095	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98735	1.0714	10	0.72032	D	0.01	-22.7577	18.8187	0.92088	0.0:0.0:1.0:0.0	.	860	P54098	DPOG1_HUMAN	F	860	ENSP00000268124:L860F;ENSP00000399851:L860F	ENSP00000268124:L860F	L	-	1	0	POLG	87665991	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.553000	0.82203	2.448000	0.82819	0.655000	0.94253	CTC	.	.	none		0.617	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000312854.2	NM_002693		A	89864987	G	A	89864987	3	1	23	1	0	0	0	0	1	0	0	0	12209	971	34	2	1173	2	POLG	15	89864987	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	3740126	89864987	12666405	562	8006											
SV2B	9899	hgsc.bcm.edu	37	chr15	91827271	91827271	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctctacgagcacaagttcAtcaactgtcggtttatcaac	12	11	6	12	2	4	0	3	0	1	0	5	1	4	0	1	1	4	3	1	1	5	4	rs117361551	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:91827271A>G	ENST00000394232.1	+	11	1998	c.1528A>G	c.(1528-1530)Atc>Gtc	p.I510V	SV2B_ENST00000330276.4_Missense_Mutation_p.I510V|SV2B_ENST00000545111.2_Missense_Mutation_p.I359V	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	510					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)			GCACAAGTTCATCAACTGTCG	0.507													A|||	56	0.0111821	0.0008	0.013	5008	,	,		19869	0.0		0.0169	False		,,,				2504	0.0297				p.I510V		Atlas-SNP	.											.	SV2B	98	.	0			c.A1528G						PASS	.	A	VAL/ILE,VAL/ILE	12,4384	19.1+/-41.9	0,12,2186	192	184	187		1075,1528	5.6	1	15	dbSNP_132	187	127,8469	64.9+/-127.2	2,123,4173	yes	missense,missense	SV2B	NM_001167580.1,NM_014848.4	29,29	2,135,6359	GG,GA,AA		1.4774,0.273,1.0699	benign,benign	359/533,510/684	91827271	139,12853	2198	4298	6496	SO:0001583	missense	9899	exon12			AAGTTCATCAACT	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.1528A>G	15.37:g.91827271A>G	ENSP00000377779:p.Ile510Val	104	0	0		160	81	0.50625	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Missense_Mutation	SNP	ENST00000394232.1	37	CCDS10370.1	16	0.007326007326007326	0	0.0	4	0.011049723756906077	0	0.0	12	0.0158311345646438	A	10.16	1.274723	0.23307	0.00273	0.014774	ENSG00000185518	ENST00000545111;ENST00000394232;ENST00000330276	T;T;T	0.41400	1.0;1.0;1.0	5.61	5.61	0.85477	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.099589	0.64402	D	0.000004	T	0.21145	0.0509	L	0.39245	1.2	0.47584	D	0.999462	B	0.23937	0.094	B	0.31016	0.123	T	0.08911	-1.0699	10	0.12766	T	0.61	-31.4023	14.6867	0.69055	1.0:0.0:0.0:0.0	.	510	Q7L1I2	SV2B_HUMAN	V	359;510;510	ENSP00000443243:I359V;ENSP00000377779:I510V;ENSP00000332818:I510V	ENSP00000332818:I510V	I	+	1	0	SV2B	89628275	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.317000	0.43770	2.152000	0.67230	0.477000	0.44152	ATC	A|0.990;G|0.010	0.010	strong		0.507	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848		G	91827271	A	G	91827271	3	3	23	1	0	0	0	0	1	0	0	0	15433	217	8	3	1566	3	SV2B	15	91827271	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	1962284	91827271	10704121	563	8007											
DECR2	26063	hgsc.bcm.edu	37	chr16	461443	461443	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagaccgagatcgcccacagCgtgctctacctggccagccc	9	5	10	17	3	1	2	0	0	1	2	2	3	1	2	5	1	4	1	5	1	2	1	rs138044046	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:461443C>T	ENST00000219481.5	+	8	882	c.744C>T	c.(742-744)agC>agT	p.S248S	DECR2_ENST00000461947.1_Intron|DECR2_ENST00000424398.2_Silent_p.S236S	NM_020664.3	NP_065715.1	Q9NUI1	DECR2_HUMAN	2,4-dienoyl CoA reductase 2, peroxisomal	248					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)				TCGCCCACAGCGTGCTCTACC	0.667													C|||	4	0.000798722	0.0	0.0	5008	,	,		17246	0.0		0.004	False		,,,				2504	0.0				p.S248S		Atlas-SNP	.											.	DECR2	47	.	0			c.C744T						PASS	.	C		4,4400	8.1+/-20.4	0,4,2198	80	75	77		744	-5.8	0	16	dbSNP_134	77	51,8549	32.3+/-84.9	0,51,4249	no	coding-synonymous	DECR2	NM_020664.3		0,55,6447	TT,TC,CC		0.593,0.0908,0.4229		248/293	461443	55,12949	2202	4300	6502	SO:0001819	synonymous_variant	26063	exon8			CCACAGCGTGCTC	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.744C>T	16.37:g.461443C>T		94	0	0		106	60	0.566038	NM_020664	Q6ZRS7|Q96ET0	Silent	SNP	ENST00000219481.5	37	CCDS10409.1																																																																																			C|0.997;T|0.003	0.003	strong		0.667	DECR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109069.4	NM_020664		T	461443	C	T	461443	2	4	23	1	0	0	0	0	0	0	0	1	4385	767	27	1		1	DECR2	16	461443	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10		461443	89893310	564	8008											
SOLH	6650	hgsc.bcm.edu	37	chr16	602430	602430	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aagcgcgcggtcaagaagttCgtcagctgcgacgtcatgct	9	8	13	11	6	3	1	3	0	0	1	4	2	3	1	0	1	4	3	0	1	3	1	rs148358614	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:602430C>T	ENST00000219611.2	+	11	3000	c.2637C>T	c.(2635-2637)ttC>ttT	p.F879F	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	879					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)										TCAAGAAGTTCGTCAGCTGCG	0.701													t|||	29	0.00579073	0.0008	0.0014	5008	,	,		12936	0.005		0.002	False		,,,				2504	0.0204				p.F879F		Atlas-SNP	.											SOLH,NS,carcinoma,0,1	SOLH	47	1	0			c.C2637T						PASS	.	T		5,4343		0,5,2169	21	26	24		2637	-8.4	0.4	16	dbSNP_134	24	68,8490		0,68,4211	no	coding-synonymous	SOLH	NM_005632.2		0,73,6380	TT,TC,CC		0.7946,0.115,0.5656		879/1087	602430	73,12833	2174	4279	6453	SO:0001819	synonymous_variant	6650	exon11			GAAGTTCGTCAGC	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.2637C>T	16.37:g.602430C>T		34	0	0		16	10	0.625	NM_005632	B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Silent	SNP	ENST00000219611.2	37	CCDS10410.1																																																																																			C|0.995;T|0.005	0.005	strong		0.701	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1	NM_005632		T	602430	C	T	602430	2	4	23	1	0	0	0	0	0	0	0	1	14940	883	31	1		1	SOLH	16	602430	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	140987	602430	89752323	565	8009											
SOLH	6650	hgsc.bcm.edu	37	chr16	602647	602647	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgagagcctccccagagcCgccgggccacgtgctggctg	5	4	14	18	4	0	2	0	0	0	2	1	3	1	2	7	2	3	2	7	2	0	0	rs200960455	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:602647C>T	ENST00000219611.2	+	12	3143	c.2780C>T	c.(2779-2781)cCg>cTg	p.P927L	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	927					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)										TCCCCAGAGCCGCCGGGCCAC	0.711													c|||	4	0.000798722	0.0008	0.0	5008	,	,		10136	0.001		0.002	False		,,,				2504	0.0				p.P927L		Atlas-SNP	.											.	SOLH	47	.	0			c.C2780T						PASS	.	C	LEU/PRO	2,3806		0,2,1902	4	6	5		2780	4.7	0.6	16		5	19,7667		0,19,3824	yes	missense	SOLH	NM_005632.2	98	0,21,5726	TT,TC,CC		0.2472,0.0525,0.1827	benign	927/1087	602647	21,11473	1904	3843	5747	SO:0001583	missense	6650	exon12			CAGAGCCGCCGGG	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.2780C>T	16.37:g.602647C>T	ENSP00000219611:p.Pro927Leu	37	0	0		20	9	0.45	NM_005632	B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Missense_Mutation	SNP	ENST00000219611.2	37	CCDS10410.1	.	.	.	.	.	.	.	.	.	.	c	3.563	-0.089241	0.07097	5.25E-4	0.002472	ENSG00000103326	ENST00000219611	D	0.87887	-2.31	4.71	4.71	0.59529	.	0.247201	0.41938	D	0.000781	T	0.76800	0.4038	N	0.22421	0.69	0.44012	D	0.99672	B	0.30179	0.271	B	0.15870	0.014	T	0.73672	-0.3909	10	0.14656	T	0.56	.	16.7447	0.85469	0.0:1.0:0.0:0.0	.	927	O75808	CAN15_HUMAN	L	927	ENSP00000219611:P927L	ENSP00000219611:P927L	P	+	2	0	SOLH	542648	0.953000	0.32496	0.593000	0.28771	0.069000	0.16628	1.901000	0.39838	2.607000	0.88179	0.556000	0.70494	CCG	.	.	weak		0.711	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1	NM_005632		T	602647	C	T	602647	3	4	23	1	0	0	0	0	1	0	0	0	14940	652	23	1	2814	1	SOLH	16	602647	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	217	602647	89752106	566	8010											
WDR90	197335	hgsc.bcm.edu	37	chr16	711429	711429	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctggcggcctctgccagcatCtcattttcccccatagcacc	6	10	7	18	1	2	0	1	0	2	0	4	0	3	0	5	2	3	2	5	2	1	3	rs199527716	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:711429C>T	ENST00000293879.4	+	30	3601	c.3601C>T	c.(3601-3603)Ctc>Ttc	p.L1201F	WDR90_ENST00000549091.1_Missense_Mutation_p.L1201F			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1201										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CTGCCAGCATCTCATTTTCCC	0.642													C|||	4	0.000798722	0.0	0.0	5008	,	,		15642	0.0		0.003	False		,,,				2504	0.001				p.L1201F		Atlas-SNP	.											.	WDR90	107	.	0			c.C3601T						PASS	.	C	PHE/LEU	2,4106		0,2,2052	44	51	48		3601	2.3	0	16		48	33,8345		0,33,4156	yes	missense	WDR90	NM_145294.4	22	0,35,6208	TT,TC,CC		0.3939,0.0487,0.2803	probably-damaging	1201/1749	711429	35,12451	2054	4189	6243	SO:0001583	missense	197335	exon30			CAGCATCTCATTT	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.3601C>T	16.37:g.711429C>T	ENSP00000293879:p.Leu1201Phe	82	0	0		70	38	0.542857	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	37	CCDS42092.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	12.40	1.927260	0.34002	4.87E-4	0.003939	ENSG00000161996	ENST00000549091;ENST00000293879	T;T	0.29917	1.55;3.54	5.51	2.27	0.28462	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.521846	0.19207	N	0.120035	T	0.33702	0.0872	M	0.67953	2.075	0.09310	N	0.999991	D;D	0.56035	0.974;0.964	P;P	0.49140	0.601;0.504	T	0.20042	-1.0287	10	0.56958	D	0.05	.	3.7409	0.08530	0.1417:0.3854:0.3779:0.0949	.	1201;1201	F8VUX9;Q96KV7	.;WDR90_HUMAN	F	1201	ENSP00000448122:L1201F;ENSP00000293879:L1201F	ENSP00000293879:L1201F	L	+	1	0	WDR90	651430	0.002000	0.14202	0.002000	0.10522	0.026000	0.11368	1.451000	0.35145	0.647000	0.30713	0.555000	0.69702	CTC	C|0.998;T|0.002	0.002	strong		0.642	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294		T	711429	C	T	711429	3	4	23	1	0	0	0	0	1	0	0	0	17352	913	32	2	3719	2	WDR90	16	711429	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	108782	711429	89643324	567	8011											
RHBDL1	9028	hgsc.bcm.edu	37	chr16	726301	726301	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttggtccaggggtcgggcccGcactcaggccttggctggcg	3	8	17	13	3	1	0	1	0	0	0	3	0	2	0	3	7	0	2	3	7	0	2	rs139776304	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:726301G>A	ENST00000219551.2	+	1	227	c.200G>A	c.(199-201)cGc>cAc	p.R67H	LA16c-313D11.9_ENST00000567091.1_RNA|RHBDL1_ENST00000352681.3_Intron|LA16c-313D11.9_ENST00000571933.1_RNA			O75783	RHBL1_HUMAN	rhomboid, veinlet-like 1 (Drosophila)	67					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)				GGTCGGGCCCGCACTCAGGCC	0.667													G|||	3	0.000599042	0.0	0.0	5008	,	,		12129	0.0		0.003	False		,,,				2504	0.0				p.R67H		Atlas-SNP	.											.	RHBDL1	14	.	0			c.G200A						PASS	.	G	HIS/ARG	3,4303		0,3,2150	10	11	10		200	-5.9	0	16	dbSNP_134	10	33,8439		0,33,4203	yes	missense	RHBDL1	NM_003961.1	29	0,36,6353	AA,AG,GG		0.3895,0.0697,0.2817	benign	67/439	726301	36,12742	2153	4236	6389	SO:0001583	missense	9028	exon1			GGGCCCGCACTCA	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.200G>A	16.37:g.726301G>A	ENSP00000219551:p.Arg67His	168	0	0		160	86	0.5375	NM_003961	A2IDC0|A2IDC1|Q0VAX4|Q9NQ85	Missense_Mutation	SNP	ENST00000219551.2	37	CCDS10418.1	.	.	.	.	.	.	.	.	.	.	G	10.83	1.462076	0.26248	6.97E-4	0.003895	ENSG00000103269	ENST00000219551	T	0.33216	1.42	3.75	-5.92	0.02261	.	3.088160	0.01236	N	0.008493	T	0.12944	0.0314	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.14952	-1.0454	10	0.37606	T	0.19	-10.5783	1.9892	0.03442	0.1944:0.2915:0.3706:0.1436	.	67	O75783	RHBL1_HUMAN	H	67	ENSP00000219551:R67H	ENSP00000219551:R67H	R	+	2	0	RHBDL1	666302	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-0.123000	0.10611	-0.437000	0.07243	-0.672000	0.03802	CGC	G|0.999;A|0.001	0.001	strong		0.667	RHBDL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000241619.1	NM_003961		A	726301	G	A	726301	3	1	23	1	0	0	0	0	1	0	0	0	13336	1087	38	1	202	1	RHBDL1	16	726301	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	14872	726301	89628452	568	8012											
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1258033	1258033	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agctgaagatgtgttccctgGccgtgacccccaacgggcac	8	7	12	14	2	0	3	0	2	0	1	1	3	1	3	4	2	2	3	4	2	2	1	rs41292285	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:1258033G>T	ENST00000348261.5	+	16	3423	c.3175G>T	c.(3175-3177)Gcc>Tcc	p.A1059S	CACNA1H_ENST00000358590.4_Missense_Mutation_p.A1059S|RP11-616M22.3_ENST00000564700.1_RNA|CACNA1H_ENST00000565831.1_Missense_Mutation_p.A1059S	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1059					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)	GTGTTCCCTGGCCGTGACCCC	0.647													G|||	17	0.00339457	0.0008	0.0086	5008	,	,		15928	0.0		0.007	False		,,,				2504	0.0031				p.A1059S		Atlas-SNP	.											.	CACNA1H	317	.	0			c.G3175T	GRCh37	CM076048	CACNA1H	M	rs41292285	PASS	.	G	SER/ALA,SER/ALA	10,4036		0,10,2013	24	31	29		3175,3175	3	0.7	16	dbSNP_127	29	83,8211		0,83,4064	yes	missense,missense	CACNA1H	NM_001005407.1,NM_021098.2	99,99	0,93,6077	TT,TG,GG		1.0007,0.2472,0.7536	probably-damaging,probably-damaging	1059/2348,1059/2354	1258033	93,12247	2023	4147	6170	SO:0001583	missense	8912	exon16			TCCCTGGCCGTGA	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.3175G>T	16.37:g.1258033G>T	ENSP00000334198:p.Ala1059Ser	121	0	0		125	64	0.512	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	14	0.00641025641025641	0	0.0	7	0.019337016574585635	0	0.0	7	0.009234828496042216	G	4.225	0.040710	0.08196	0.002472	0.010007	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.96491	-4.03;-3.98	4.01	3.02	0.34903	.	1.003600	0.08028	N	0.992969	D	0.88865	0.6553	L	0.44542	1.39	0.29001	N	0.887463	P;P	0.48089	0.675;0.905	B;B	0.40825	0.311;0.341	T	0.82293	-0.0529	10	0.20046	T	0.44	.	11.9499	0.52948	0.0:0.0:0.8251:0.1749	rs41292285;rs61406959	1059;1059	O95180-2;O95180	.;CAC1H_HUMAN	S	1059	ENSP00000334198:A1059S;ENSP00000351401:A1059S	ENSP00000334198:A1059S	A	+	1	0	CACNA1H	1198034	1.000000	0.71417	0.742000	0.31022	0.188000	0.23474	5.661000	0.68025	0.876000	0.35872	0.650000	0.86243	GCC	G|0.992;T|0.008	0.008	strong		0.647	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		T	1258033	G	T	1258033	3	4	23	1	0	0	0	0	1	0	0	0	2547	1203	42	4	3233	4	CACNA1H	16	1258033	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	531732	1258033	89096720	569	8013											
GNPTG	84572	hgsc.bcm.edu	37	chr16	1411894	1411894	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tacaagtatgagttctgcccGttccacaacgtgacccagca	11	9	8	13	2	1	2	0	2	1	0	2	2	2	2	3	0	4	4	3	0	4	4	rs76594024	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:1411894G>A	ENST00000204679.4	+	5	298	c.255G>A	c.(253-255)ccG>ccA	p.P85P	LA16c-316G12.2_ENST00000569831.1_RNA	NM_032520.4	NP_115909.1	Q9UJJ9	GNPTG_HUMAN	N-acetylglucosamine-1-phosphate transferase, gamma subunit	85	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)				AGTTCTGCCCGTTCCACAACG	0.657													G|||	11	0.00219649	0.0015	0.0029	5008	,	,		15450	0.0		0.007	False		,,,				2504	0.0				p.P85P		Atlas-SNP	.											.	GNPTG	18	.	0			c.G255A						PASS	.	G		23,4375	29.9+/-59.1	0,23,2176	58	53	54		255	-10	0	16	dbSNP_131	54	71,8529	42.6+/-100.3	0,71,4229	no	coding-synonymous	GNPTG	NM_032520.4		0,94,6405	AA,AG,GG		0.8256,0.523,0.7232		85/306	1411894	94,12904	2199	4300	6499	SO:0001819	synonymous_variant	84572	exon5			CTGCCCGTTCCAC	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.255G>A	16.37:g.1411894G>A		64	0	0		76	42	0.552632	NM_032520	B2R556|Q6XYD7|Q96L13	Silent	SNP	ENST00000204679.4	37	CCDS10436.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	0.346	-0.947731	0.02304	0.00523	0.008256	ENSG00000090581	ENST00000529110	.	.	.	5.0	-10.0	0.00425	.	.	.	.	.	T	0.31231	0.0790	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56288	-0.8004	4	.	.	.	-13.0868	2.9834	0.05961	0.31:0.094:0.4001:0.1959	.	.	.	.	I	108	.	.	V	+	1	0	GNPTG	1351895	0.000000	0.05858	0.027000	0.17364	0.670000	0.39368	-3.271000	0.00532	-4.717000	0.00035	-1.021000	0.02439	GTT	G|0.994;A|0.006	0.006	strong		0.657	GNPTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109058.2	NM_032520		A	1411894	G	A	1411894	2	1	23	1	0	0	0	0	0	0	0	1	6554	1132	40	1		1	GNPTG	16	1411894	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	153861	1411894	88942859	570	8014											
RPL3L	6123	hgsc.bcm.edu	37	chr16	2002960	2002960	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccggagacctcgaggggtggCcacgtagcccaccacgccca	8	3	13	17	4	0	1	0	0	0	1	1	3	0	1	6	4	1	1	6	4	1	1	rs118144581	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:2002960C>T	ENST00000268661.7	-	3	374	c.280G>A	c.(280-282)Gcc>Acc	p.A94T	RPL3L_ENST00000566484.1_5'Flank	NM_005061.2	NP_005052.1	Q92901	RL3L_HUMAN	ribosomal protein L3-like	94					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)|ribosome (GO:0005840)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	17						CGAGGGGTGGCCACGTAGCCC	0.592													C|||	19	0.00379393	0.0015	0.0058	5008	,	,		17359	0.0		0.0129	False		,,,				2504	0.0				p.A94T		Atlas-SNP	.											.	RPL3L	42	.	0			c.G280A						PASS	.	C	THR/ALA	3,4395	6.2+/-15.9	0,3,2196	72	66	68		280	4.3	1	16	dbSNP_132	68	59,8541	37.8+/-93.5	0,59,4241	yes	missense	RPL3L	NM_005061.2	58	0,62,6437	TT,TC,CC		0.686,0.0682,0.477	benign	94/408	2002960	62,12936	2199	4300	6499	SO:0001583	missense	6123	exon3			GGGTGGCCACGTA	U65581	CCDS10450.1	16p13.3	2008-02-05			ENSG00000140986	ENSG00000140986		"L ribosomal proteins"	10351	protein-coding gene	gene with protein product						8921388	Standard	NM_005061		Approved		uc002cnh.3	Q92901	OTTHUMG00000128685	ENST00000268661.7:c.280G>A	16.37:g.2002960C>T	ENSP00000268661:p.Ala94Thr	80	0	0		81	50	0.617284	NM_005061		Missense_Mutation	SNP	ENST00000268661.7	37	CCDS10450.1	10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	C	11.69	1.713498	0.30413	6.82E-4	0.00686	ENSG00000140986	ENST00000268661	T	0.21932	1.98	5.28	4.33	0.51752	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.519934	0.20912	N	0.083458	T	0.14485	0.0350	L	0.44542	1.39	0.30156	N	0.802631	B	0.06786	0.001	B	0.06405	0.002	T	0.08086	-1.0739	10	0.72032	D	0.01	-24.4315	12.7616	0.57367	0.0:0.9211:0.0:0.0789	.	94	Q92901	RL3L_HUMAN	T	94	ENSP00000268661:A94T	ENSP00000268661:A94T	A	-	1	0	RPL3L	1942961	1.000000	0.71417	1.000000	0.80357	0.115000	0.19883	1.833000	0.39161	1.238000	0.43771	0.609000	0.83330	GCC	C|0.996;T|0.004	0.004	strong		0.592	RPL3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250582.2	NM_005061		T	2002960	C	T	2002960	3	4	23	1	0	0	0	0	1	0	0	0	13609	739	26	2	975	2	RPL3L	16	2002960	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	591066	2002960	88351793	571	8015											
TSC2	7249	hgsc.bcm.edu	37	chr16	2136842	2136842	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccattgtctacaatgactcCggtgaggacttcaagcttgg	9	12	10	10	1	2	2	1	2	1	0	4	3	4	3	2	3	2	1	2	3	3	4	rs45517384|rs137854272	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:2136842C>T	ENST00000219476.3	+	38	5589	c.4959C>T	c.(4957-4959)tcC>tcT	p.S1653S	TSC2_ENST00000350773.4_Silent_p.S1630S|TSC2_ENST00000568454.1_Silent_p.S1597S|TSC2_ENST00000353929.4_Silent_p.S1610S|TSC2_ENST00000382538.6_Silent_p.S1538S|TSC2_ENST00000439673.2_Silent_p.S1550S|TSC2_ENST00000401874.2_Silent_p.S1586S	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	1653	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.		S -> F (in TSC2). {ECO:0000269|PubMed:15024740}.		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)				ACAATGACTCCGGTGAGGACT	0.612			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis				c|||	17	0.00339457	0.0023	0.0086	5008	,	,		20855	0.0		0.008	False		,,,				2504	0.0				p.S1653S		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	.	TSC2	364	.	0			c.C4959T						PASS	.	T	,,	11,4377	16.8+/-37.8	0,11,2183	71	52	59	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4959,4758,4890	-9.4	0.2	16	dbSNP_127	59	127,8453	60.6+/-122.4	0,127,4163	no	coding-synonymous,coding-synonymous,coding-synonymous	TSC2	NM_000548.3,NM_001077183.1,NM_001114382.1	,,	0,138,6346	TT,TC,CC		1.4802,0.2507,1.0642	,,	1653/1808,1586/1741,1630/1785	2136842	138,12830	2194	4290	6484	SO:0001819	synonymous_variant	7249	exon38	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	TGACTCCGGTGAG	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.4959C>T	16.37:g.2136842C>T		84	0	0		85	43	0.505882	NM_000548	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Silent	SNP	ENST00000219476.3	37	CCDS10458.1																																																																																			C|0.992;T|0.008	0.008	strong		0.612	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		T	2136842	C	T	2136842	2	4	23	1	0	0	0	0	0	0	0	1	16621	639	23	1		1	TSC2	16	2136842	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	133882	2136842	88217911	572	8016											
ZNF174	7727	hgsc.bcm.edu	37	chr16	3454480	3454480	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggagaaaactggatctcagCttggagaacaggaactgcca	14	7	12	8	0	1	2	1	0	1	2	2	6	1	4	1	4	5	1	1	4	4	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:3454480C>T	ENST00000268655.4	+	2	1042	c.457C>T	c.(457-459)Ctt>Ttt	p.L153F	ZNF174_ENST00000344823.5_Missense_Mutation_p.L153F|ZNF174_ENST00000572544.1_Missense_Mutation_p.L153F|ZNF174_ENST00000575752.1_Missense_Mutation_p.L153F|ZNF174_ENST00000571936.1_Missense_Mutation_p.L153F	NM_003450.2	NP_003441.1	Q15697	ZN174_HUMAN	zinc finger protein 174	153					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase II promoter (GO:0006366)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|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)|large_intestine(3)|lung(3)|prostate(2)|urinary_tract(2)	12						TGGATCTCAGCTTGGAGAACA	0.537																																					p.L153F		Atlas-SNP	.											.	ZNF174	32	.	0			c.C457T						PASS	.						115	126	122					16																	3454480		2197	4300	6497	SO:0001583	missense	7727	exon2			TCTCAGCTTGGAG	U31248	CCDS10504.1, CCDS32380.1	16p13	2013-01-09			ENSG00000103343	ENSG00000103343		"-", "Zinc fingers, C2H2-type"	12963	protein-coding gene	gene with protein product		603900					Standard	NM_003450		Approved	ZSCAN8	uc002cvc.3	Q15697	OTTHUMG00000129358	ENST00000268655.4:c.457C>T	16.37:g.3454480C>T	ENSP00000268655:p.Leu153Phe	142	0	0		121	52	0.429752	NM_001032292	Q53Y68|Q9BQ34	Missense_Mutation	SNP	ENST00000268655.4	37	CCDS10504.1	.	.	.	.	.	.	.	.	.	.	C	14.35	2.508223	0.44660	.	.	ENSG00000103343	ENST00000344823;ENST00000268655	T;T	0.07444	4.06;3.19	5.32	3.34	0.38264	Transcription regulator SCAN (1);	0.161847	0.29631	N	0.011620	T	0.11153	0.0272	L	0.29908	0.895	0.29888	N	0.825478	P;D;P	0.53619	0.761;0.961;0.935	B;P;P	0.56700	0.36;0.804;0.642	T	0.02345	-1.1173	10	0.56958	D	0.05	.	5.9089	0.19016	0.1921:0.7141:0.0:0.0937	.	153;153;153	Q15697;Q15697-2;Q8IZN5	ZN174_HUMAN;.;.	F	153	ENSP00000339781:L153F;ENSP00000268655:L153F	ENSP00000268655:L153F	L	+	1	0	ZNF174	3394481	0.994000	0.37717	1.000000	0.80357	0.984000	0.73092	0.526000	0.22971	1.542000	0.49330	0.563000	0.77884	CTT	.	.	none		0.537	ZNF174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251510.1	NM_003450		T	3454480	C	T	3454480	3	4	23	1	0	0	0	0	1	0	0	0	17759	797	28	2	463	2	ZNF174	16	3454480	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1317638	3454480	86900273	573	8017											
C16orf71	146562	hgsc.bcm.edu	37	chr16	4790446	4790446	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agagcccctcagcactgcctCacaagaatctgtgaaccgcc	11	6	8	16	1	3	3	2	1	1	2	3	3	3	3	5	0	4	1	5	0	3	0	rs35599524	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:4790446C>T	ENST00000299320.5	+	4	1047	c.569C>T	c.(568-570)tCa>tTa	p.S190L	RP11-127I20.7_ENST00000588099.1_RNA|C16orf71_ENST00000590191.1_Missense_Mutation_p.S204L	NM_139170.2	NP_631909.2	Q8IYS4	CP071_HUMAN	chromosome 16 open reading frame 71	190			S -> L (in dbSNP:rs35599524).							breast(1)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(1)	11						AGCACTGCCTCACAAGAATCT	0.612													C|||	73	0.0145767	0.0061	0.0245	5008	,	,		17919	0.0069		0.0239	False		,,,				2504	0.0174				p.S190L		Atlas-SNP	.											.	C16orf71	46	.	0			c.C569T						PASS	.	C	LEU/SER	53,4341	53.6+/-89.4	1,51,2145	41	44	43		569	-0.2	0	16	dbSNP_126	43	218,8382	89.7+/-151.9	2,214,4084	yes	missense	C16orf71	NM_139170.2	145	3,265,6229	TT,TC,CC		2.5349,1.2062,2.0856	benign	190/521	4790446	271,12723	2197	4300	6497	SO:0001583	missense	146562	exon4			CTGCCTCACAAGA	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.569C>T	16.37:g.4790446C>T	ENSP00000299320:p.Ser190Leu	82	0	0		112	55	0.491071	NM_139170	Q8NCV0	Missense_Mutation	SNP	ENST00000299320.5	37	CCDS10521.1	32	0.014652014652014652	2	0.0040650406504065045	3	0.008287292817679558	6	0.01048951048951049	21	0.027704485488126648	C	10.63	1.404118	0.25291	0.012062	0.025349	ENSG00000166246	ENST00000299320	T	0.12147	2.71	4.18	-0.182	0.13287	.	1.917540	0.03379	N	0.200152	T	0.03390	0.0098	L	0.50333	1.59	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.28554	-1.0040	10	0.02654	T	1	0.8564	4.4743	0.11727	0.0:0.4558:0.2178:0.3264	rs35599524	190	Q8IYS4	CP071_HUMAN	L	190	ENSP00000299320:S190L	ENSP00000299320:S190L	S	+	2	0	C16orf71	4730447	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.499000	0.06413	-0.065000	0.13021	-0.232000	0.12228	TCA	C|0.981;T|0.019	0.019	strong		0.612	C16orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251644.1	NM_139170		T	4790446	C	T	4790446	3	4	23	1	0	0	0	0	1	0	0	0	1832	838	29	2	579	2	C16orf71	16	4790446	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1335966	4790446	85564307	574	8018											
CLEC16A	23274	hgsc.bcm.edu	37	chr16	11097155	11097155	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggcatcaagacgagtggggaGagtgaaggtgagtgtcccca	11	6	17	7	1	1	4	1	2	0	2	2	6	2	4	2	4	0	1	2	4	2	0	rs45464291	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:11097155G>A	ENST00000409790.1	+	11	1526	c.1296G>A	c.(1294-1296)gaG>gaA	p.E432E	CLEC16A_ENST00000409552.3_Intron	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A											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						CGAGTGGGGAGAGTGAAGGTG	0.617													G|||	4	0.000798722	0.0	0.0	5008	,	,		17429	0.0		0.004	False		,,,				2504	0.0				p.E432E		Atlas-SNP	.											.	CLEC16A	101	.	0			c.G1296A						PASS	.	G		5,4135		0,5,2065	76	87	83		1296	3.6	1	16	dbSNP_127	83	25,8389		0,25,4182	no	coding-synonymous	CLEC16A	NM_015226.2		0,30,6247	AA,AG,GG		0.2971,0.1208,0.239		432/1054	11097155	30,12524	2070	4207	6277	SO:0001819	synonymous_variant	23274	exon10			TGGGGAGAGTGAA	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.1296G>A	16.37:g.11097155G>A		154	0	0		136	57	0.419118	NM_015226		Silent	SNP	ENST00000409790.1	37	CCDS45409.1																																																																																			G|0.999;A|0.001	0.001	strong		0.617	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226		A	11097155	G	A	11097155	2	1	23	1	0	0	0	0	0	0	0	1	3502	933	33	2		2	CLEC16A	16	11097155	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	6306709	11097155	79257598	575	8019											
PDXDC1	23042	hgsc.bcm.edu	37	chr16	15100301	15100301	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agaggaaagagaaggacttgCaaagatatgtaggcttgcca	16	7	13	5	0	0	3	0	0	0	3	0	6	0	5	1	3	2	3	1	3	5	4	rs141901522	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:15100301C>T	ENST00000396410.4	+	6	537	c.440C>T	c.(439-441)gCa>gTa	p.A147V	PDXDC1_ENST00000447912.2_Missense_Mutation_p.A56V|PDXDC1_ENST00000325823.7_Missense_Mutation_p.A132V|PDXDC1_ENST00000569715.1_Missense_Mutation_p.A120V|PDXDC1_ENST00000455313.2_Missense_Mutation_p.A147V|PDXDC1_ENST00000563679.1_Missense_Mutation_p.A165V|PDXDC1_ENST00000535621.2_Missense_Mutation_p.A147V|PDXDC1_ENST00000450288.2_Missense_Mutation_p.A119V	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	147					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						GAAGGACTTGCAAAGATATGT	0.353													.|||	3	0.000599042	0.0	0.0	5008	,	,		33956	0.0		0.003	False		,,,				2504	0.0				p.A147V		Atlas-SNP	.											.	PDXDC1	59	.	0			c.C440T						PASS	.	C	VAL/ALA	2,4392	4.2+/-10.8	0,2,2195	149	150	150		440	4.8	1	16	dbSNP_134	150	21,8579	14.0+/-48.4	0,21,4279	no	missense	PDXDC1	NM_015027.2	64	0,23,6474	TT,TC,CC		0.2442,0.0455,0.177	benign	147/789	15100301	23,12971	2197	4300	6497	SO:0001583	missense	23042	exon6			GACTTGCAAAGAT	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.440C>T	16.37:g.15100301C>T	ENSP00000379691:p.Ala147Val	381	0	0		372	103	0.276882	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Missense_Mutation	SNP	ENST00000396410.4	37	CCDS32393.1	.	.	.	.	.	.	.	.	.	.	C	12.02	1.813847	0.32053	4.55E-4	0.002442	ENSG00000179889	ENST00000325823;ENST00000447912;ENST00000535621;ENST00000396410;ENST00000450288;ENST00000455313	T;T;T;T;T;T	0.36157	1.27;2.41;1.27;1.27;1.27;1.27	5.82	4.79	0.61399	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.260219	0.37178	N	0.002204	T	0.11153	0.0272	N	0.02539	-0.55	0.33168	D	0.547894	B;B;B;B;B;B;B	0.13145	0.005;0.002;0.005;0.007;0.005;0.005;0.003	B;B;B;B;B;B;B	0.15052	0.008;0.004;0.008;0.007;0.012;0.008;0.006	T	0.32428	-0.9907	10	0.06891	T	0.86	-0.0283	4.3523	0.11162	0.0:0.7219:0.0:0.2781	.	119;56;132;147;119;147;147	E7EPL4;E7EMH5;B4DHL7;Q86XE2;B4DR55;Q6P996;Q6P996-2	.;.;.;.;.;PDXD1_HUMAN;.	V	132;56;147;147;119;147	ENSP00000322807:A132V;ENSP00000400310:A56V;ENSP00000437835:A147V;ENSP00000379691:A147V;ENSP00000391147:A119V;ENSP00000406703:A147V	ENSP00000322807:A132V	A	+	2	0	PDXDC1	15007802	0.932000	0.31603	1.000000	0.80357	0.901000	0.52897	3.426000	0.52778	2.765000	0.95021	0.650000	0.86243	GCA	C|0.998;T|0.002	0.002	strong		0.353	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027		T	15100301	C	T	15100301	3	4	23	1	0	0	0	0	1	0	0	0	11705	710	25	2	462	2	PDXDC1	16	15100301	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	4003146	15100301	75254452	576	8020											
MYH11	4629	hgsc.bcm.edu	37	chr16	15808876	15808876	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggcgttgatgcgctgggaCtcctcctctgcctcctccag	3	12	11	15	2	1	1	0	1	1	0	5	2	5	2	5	2	2	2	5	2	0	2	rs113964173	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:15808876C>G	ENST00000300036.5	-	40	5785	c.5676G>C	c.(5674-5676)gaG>gaC	p.E1892D	NDE1_ENST00000396355.1_Intron|NDE1_ENST00000396354.1_Intron|MYH11_ENST00000396324.3_Missense_Mutation_p.E1899D|MYH11_ENST00000576790.2_Missense_Mutation_p.E1892D|MYH11_ENST00000452625.2_Missense_Mutation_p.E1899D|NDE1_ENST00000342673.5_Intron	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1892					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						TGCGCTGGGACTCCTCCTCTG	0.642			T	CBFB	AML								C|||	17	0.00339457	0.0015	0.0029	5008	,	,		13850	0.0		0.0109	False		,,,				2504	0.002				p.E1899D		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	.	MYH11	520	.	0			c.G5697C						PASS	.	C	ASP/GLU,ASP/GLU,,ASP/GLU,,ASP/GLU	7,4387	12.9+/-30.5	0,7,2190	128	121	123		5697,5697,,5676,,5676	1.1	1	16	dbSNP_132	123	61,8539	37.4+/-92.8	0,61,4239	yes	missense,missense,intron,missense,intron,missense	MYH11,NDE1	NM_001040113.1,NM_001040114.1,NM_001143979.1,NM_002474.2,NM_017668.2,NM_022844.2	45,45,,45,,45	0,68,6429	GG,GC,CC		0.7093,0.1593,0.5233	possibly-damaging,possibly-damaging,,possibly-damaging,,possibly-damaging	1899/1946,1899/1980,,1892/1973,,1892/1939	15808876	68,12926	2197	4300	6497	SO:0001583	missense	4629	exon41			CTGGGACTCCTCC	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.5676G>C	16.37:g.15808876C>G	ENSP00000300036:p.Glu1892Asp	127	0	0		152	76	0.5	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	10	0.004578754578754579	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	C	19.31	3.802956	0.70682	0.001593	0.007093	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	T;T;T;T	0.78816	-1.21;-1.21;-1.21;-1.21	4.76	1.09	0.20402	Myosin tail (1);	0.000000	0.85682	D	0.000000	T	0.81992	0.4940	M	0.91140	3.18	0.58432	D	0.999998	P;P;P;P;P	0.46784	0.884;0.884;0.884;0.884;0.884	P;P;P;P;P	0.55011	0.766;0.766;0.766;0.766;0.766	D	0.84056	0.0372	10	0.72032	D	0.01	.	9.1943	0.37217	0.0:0.6481:0.0:0.3519	.	1899;1892;1899;1892;1899	B1PS43;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;MYH11_HUMAN;.;.;.	D	1892;1892;1899;1899;1899	ENSP00000300036:E1892D;ENSP00000345136:E1892D;ENSP00000379616:E1899D;ENSP00000407821:E1899D	ENSP00000300036:E1892D	E	-	3	2	MYH11	15716377	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.567000	0.45956	0.401000	0.25424	0.455000	0.32223	GAG	C|0.993;G|0.007	0.007	strong		0.642	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		G	15808876	C	G	15808876	3	3	23	1	0	0	0	0	1	0	0	0	10040	564	20	4	285	4	MYH11	16	15808876	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	708575	15808876	74545877	577	8021											
TMC5	79838	hgsc.bcm.edu	37	chr16	19481020	19481020	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tagcatggccaagtatttccGgaacaacttcattaatcccc	12	11	6	12	1	1	0	1	0	0	0	3	1	3	1	4	2	3	2	4	2	6	5			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:19481020G>A	ENST00000396229.2	+	10	2404	c.1655G>A	c.(1654-1656)cGg>cAg	p.R552Q	TMC5_ENST00000381414.4_Missense_Mutation_p.R552Q|TMC5_ENST00000541464.1_Missense_Mutation_p.R552Q|TMC5_ENST00000561503.1_Missense_Mutation_p.R193Q|TMC5_ENST00000219821.5_Missense_Mutation_p.R306Q|TMC5_ENST00000564959.1_Missense_Mutation_p.R235Q|TMC5_ENST00000542583.2_Missense_Mutation_p.R552Q	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5	552					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						AAGTATTTCCGGAACAACTTC	0.473																																					p.R552Q		Atlas-SNP	.											TMC5_ENST00000396229,NS,malignant_melanoma,0,2	TMC5	169	2	0			c.G1655A						PASS	.						117	107	111					16																	19481020		2197	4300	6497	SO:0001583	missense	79838	exon10			ATTTCCGGAACAA	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.1655G>A	16.37:g.19481020G>A	ENSP00000379531:p.Arg552Gln	104	0	0		145	28	0.193103	NM_001105249	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	Missense_Mutation	SNP	ENST00000396229.2	37	CCDS45431.1	.	.	.	.	.	.	.	.	.	.	G	12.61	1.990463	0.35131	.	.	ENSG00000103534	ENST00000541464;ENST00000381414;ENST00000396229;ENST00000542583;ENST00000219821;ENST00000440743	T;T;T;T;T	0.55930	0.49;0.49;0.49;0.49;0.49	5.65	5.65	0.86999	.	0.249267	0.41605	D	0.000859	T	0.47154	0.1430	M	0.64260	1.97	0.29006	N	0.887155	P;P;P;P;P;P	0.45902	0.868;0.81;0.74;0.622;0.676;0.782	B;B;B;B;B;B	0.42386	0.386;0.372;0.218;0.109;0.216;0.386	T	0.52238	-0.8602	10	0.27082	T	0.32	-25.7205	6.6578	0.22996	0.0715:0.1292:0.6653:0.134	.	552;235;306;306;552;552	F5GYU8;E7EU57;Q6UXY8-3;B3KUQ8;Q6UXY8;Q6UXY8-2	.;.;.;.;TMC5_HUMAN;.	Q	552;552;552;552;306;235	ENSP00000441227:R552Q;ENSP00000370822:R552Q;ENSP00000379531:R552Q;ENSP00000446274:R552Q;ENSP00000219821:R306Q	ENSP00000219821:R306Q	R	+	2	0	TMC5	19388521	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	2.204000	0.42761	2.663000	0.90544	0.655000	0.94253	CGG	.	.	none		0.473	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	NM_024780		A	19481020	G	A	19481020	3	1	23	1	0	0	0	0	1	0	0	0	16003	1116	39	1	1999	1	TMC5	16	19481020	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	3672144	19481020	70873733	578	8022											
IQCK	124152	hgsc.bcm.edu	37	chr16	19775403	19775403	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattcacagaatttttctccAttccatttgtggaggagcgg	9	14	9	9	1	2	1	1	0	1	1	4	3	3	3	2	3	1	0	2	3	1	5	rs149444739	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:19775403A>C	ENST00000320394.6	+	7	1273	c.574A>C	c.(574-576)Att>Ctt	p.I192L	IQCK_ENST00000433597.2_Missense_Mutation_p.I104L|CTD-2380F24.1_ENST00000564490.1_RNA|CTD-2380F24.1_ENST00000568843.1_RNA|CTD-2380F24.1_ENST00000565817.1_RNA|IQCK_ENST00000541926.1_Missense_Mutation_p.I192L|IQCK_ENST00000564186.1_Missense_Mutation_p.I192L|IQCK_ENST00000562762.1_3'UTR	NM_153208.1	NP_694940.1	Q8N0W5	IQCK_HUMAN	IQ motif containing K	192										kidney(1)|large_intestine(2)|lung(2)|skin(1)	6						ATTTTTCTCCATTCCATTTGT	0.368																																					p.I192L		Atlas-SNP	.											.	IQCK	35	.	0			c.A574C						PASS	.	A	LEU/ILE	5,4389	8.1+/-20.4	0,5,2192	79	76	77		574	5.1	1	16	dbSNP_134	77	40,8560	26.8+/-75.7	0,40,4260	yes	missense	IQCK	NM_153208.1	5	0,45,6452	CC,CA,AA		0.4651,0.1138,0.3463	probably-damaging	192/288	19775403	45,12949	2197	4300	6497	SO:0001583	missense	124152	exon7			TTCTCCATTCCAT	AF520569	CCDS10580.1	16p12.3	2008-02-05			ENSG00000174628	ENSG00000174628			28556	protein-coding gene	gene with protein product						10493829	Standard	NM_153208		Approved	MGC35048, FLJ36575	uc002dgr.3	Q8N0W5	OTTHUMG00000131453	ENST00000320394.6:c.574A>C	16.37:g.19775403A>C	ENSP00000324901:p.Ile192Leu	157	0	0		124	66	0.532258	NM_153208	B2RDU0|O43327|Q8NFF4	Missense_Mutation	SNP	ENST00000320394.6	37	CCDS10580.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.314559	0.81358	0.001138	0.004651	ENSG00000174628	ENST00000320394;ENST00000541926;ENST00000433597	T;T;T	0.23348	1.91;1.91;1.91	5.11	5.11	0.69529	.	0.000000	0.51477	D	0.000092	T	0.49932	0.1586	M	0.74881	2.28	0.38431	D	0.94645	D;D	0.67145	0.996;0.996	D;D	0.80764	0.994;0.994	T	0.55186	-0.8180	9	.	.	.	-15.7553	13.6471	0.62288	1.0:0.0:0.0:0.0	.	192;192	B4DXE1;Q8N0W5	.;IQCK_HUMAN	L	192;192;104	ENSP00000324901:I192L;ENSP00000439344:I192L;ENSP00000406013:I104L	.	I	+	1	0	IQCK	19682904	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	5.500000	0.66943	2.152000	0.67230	0.528000	0.53228	ATT	A|0.996;C|0.004	0.004	strong		0.368	IQCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254273.2	NM_153208		C	19775403	A	C	19775403	3	2	23	1	0	0	0	0	1	0	0	0	7822	217	8	5	596	5	IQCK	16	19775403	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	294383	19775403	70579350	579	8023											
GGA2	23062	hgsc.bcm.edu	37	chr16	23504719	23504719	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gatcagttcgttcaggaaacGaaatttggccacctcgctgt	10	11	10	10	3	2	0	2	0	0	0	4	3	2	1	2	2	1	3	2	2	2	3	rs143003037		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:23504719G>C	ENST00000309859.4	-	4	395	c.313C>G	c.(313-315)Cgt>Ggt	p.R105G	GGA2_ENST00000567468.1_Missense_Mutation_p.R105G	NM_015044.4	NP_055859.1	Q9UJY4	GGA2_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 2	105	VHS. {ECO:0000255|PROSITE- ProRule:PRU00218}.				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)		TTCAGGAAACGAAATTTGGCC	0.552																																					p.R105G		Atlas-SNP	.											GGA2,mucosal,malignant_melanoma,0,3	GGA2	49	3	0			c.C313G						PASS	.	G	GLY/ARG	0,4394		0,0,2197	183	135	151		313	5.6	1	16	dbSNP_134	151	4,8596	3.7+/-12.6	0,4,4296	no	missense	GGA2	NM_015044.4	125	0,4,6493	CC,CG,GG		0.0465,0.0,0.0308	probably-damaging	105/614	23504719	4,12990	2197	4300	6497	SO:0001583	missense	23062	exon4			GGAAACGAAATTT	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.313C>G	16.37:g.23504719G>C	ENSP00000311962:p.Arg105Gly	76	0	0		85	34	0.4	NM_015044	D3DWF0|O14564|Q9NYN2|Q9UPS2	Missense_Mutation	SNP	ENST00000309859.4	37	CCDS10611.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.556060	0.86231	0.0	4.65E-4	ENSG00000103365	ENST00000309859	T	0.23348	1.91	5.58	5.58	0.84498	VHS subgroup (1);ENTH/VHS (2);VHS (2);	0.000000	0.85682	D	0.000000	T	0.56124	0.1964	M	0.83312	2.635	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.60657	-0.7220	10	0.72032	D	0.01	-16.2173	17.0743	0.86582	0.0:0.0:1.0:0.0	.	105	Q9UJY4	GGA2_HUMAN	G	105	ENSP00000311962:R105G	ENSP00000311962:R105G	R	-	1	0	GGA2	23412220	1.000000	0.71417	1.000000	0.80357	0.572000	0.35998	6.105000	0.71505	2.638000	0.89438	0.448000	0.29417	CGT	G|1.000;C|0.000	0.000	weak		0.552	GGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214019.1			C	23504719	G	C	23504719	3	2	23	1	0	0	0	0	1	0	0	0	6361	1058	37	4	1584	4	GGA2	16	23504719	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	3729316	23504719	66850034	580	8024											
NKD1	85407	hgsc.bcm.edu	37	chr16	50667299	50667299	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggctccggggcacccaggaCgggagcaagcactttgtgag	8	5	16	12	3	0	1	0	1	0	0	1	3	1	3	2	5	2	4	2	5	1	1	rs34100051	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:50667299C>T	ENST00000268459.3	+	10	1244	c.1020C>T	c.(1018-1020)gaC>gaT	p.D340D		NM_033119.4	NP_149110.1	Q969G9	NKD1_HUMAN	naked cuticle homolog 1 (Drosophila)	340					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)		GCACCCAGGACGGGAGCAAGC	0.657													C|||	55	0.0109824	0.0015	0.0245	5008	,	,		13464	0.0		0.0278	False		,,,				2504	0.0082				p.D340D		Atlas-SNP	.											.	NKD1	43	.	0			c.C1020T						PASS	.	C		18,4378	24.3+/-50.5	0,18,2180	64	74	71		1020	-2.4	1	16	dbSNP_126	71	258,8342	100.8+/-162.1	2,254,4044	no	coding-synonymous	NKD1	NM_033119.4		2,272,6224	TT,TC,CC		3.0,0.4095,2.1237		340/471	50667299	276,12720	2198	4300	6498	SO:0001819	synonymous_variant	85407	exon10			CCAGGACGGGAGC	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.1020C>T	16.37:g.50667299C>T		276	1	0.00362319		285	133	0.466667	NM_033119	B2RC39|Q8WZ08	Silent	SNP	ENST00000268459.3	37	CCDS10743.1																																																																																			C|0.981;T|0.019	0.019	strong		0.657	NKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256873.1			T	50667299	C	T	50667299	2	4	23	1	0	0	0	0	0	0	0	1	10450	535	19	1		1	NKD1	16	50667299	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	27162580	50667299	39687454	581	8025											
NOD2	64127	hgsc.bcm.edu	37	chr16	50746228	50746228	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagctggactacaactctgtGggtgacattggcgtggagca	9	9	14	9	1	1	1	0	1	1	0	1	3	1	3	0	4	4	2	0	4	2	2	rs104895495		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:50746228G>T	ENST00000300589.2	+	4	2511	c.2406G>T	c.(2404-2406)gtG>gtT	p.V802V	RP11-327F22.6_ENST00000602304.1_RNA	NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	802					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)				ACAACTCTGTGGGTGACATTG	0.602													G|||	1	0.000199681	0.0	0.0	5008	,	,		21477	0.0		0.001	False		,,,				2504	0.0				p.V802V		Atlas-SNP	.											.	NOD2	118	.	0			c.G2406T						PASS	.	G		2,4394	4.2+/-10.8	0,2,2196	113	115	114	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2406	3.3	1	16	dbSNP_132	114	16,8584	11.9+/-42.8	0,16,4284	no	coding-synonymous	NOD2	NM_022162.1		0,18,6480	TT,TG,GG		0.186,0.0455,0.1385		802/1041	50746228	18,12978	2198	4300	6498	SO:0001819	synonymous_variant	64127	exon4			CTCTGTGGGTGAC	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.2406G>T	16.37:g.50746228G>T		146	0	0		147	66	0.44898	NM_022162	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Silent	SNP	ENST00000300589.2	37	CCDS10746.1	.	.	.	.	.	.	.	.	.	.	G	6.792	0.515223	0.12944	4.55E-4	0.00186	ENSG00000167207	ENST00000534057	.	.	.	5.29	3.28	0.37604	.	.	.	.	.	T	0.54983	0.1892	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47262	-0.9131	4	.	.	.	.	6.42	0.21738	0.0846:0.0:0.5875:0.3279	.	.	.	.	W	42	.	.	G	+	1	0	NOD2	49303729	0.786000	0.28738	0.995000	0.50966	0.966000	0.64601	-0.179000	0.09768	0.575000	0.29434	0.555000	0.69702	GGG	G|0.998;T|0.002	0.002	strong		0.602	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162		T	50746228	G	T	50746228	2	4	23	1	0	0	0	0	0	0	0	1	10526	1335	47	4		4	NOD2	16	50746228	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	78929	50746228	39608525	582	8026											
CYLD	1540	hgsc.bcm.edu	37	chr16	50810149	50810149	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ttatgtcaagaggtgttgggGacaaaggttcatccagtcat	11	12	12	6	0	3	1	3	0	0	1	4	2	4	2	1	4	0	2	1	4	3	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:50810149G>A	ENST00000427738.3	+	6	1187	c.982G>A	c.(982-984)Gac>Aac	p.D328N	CYLD_ENST00000566206.1_Missense_Mutation_p.D325N|CYLD_ENST00000569418.1_Missense_Mutation_p.D325N|CYLD_ENST00000311559.9_Missense_Mutation_p.D328N|CYLD_ENST00000398568.2_Missense_Mutation_p.D325N|CYLD_ENST00000540145.1_Missense_Mutation_p.D328N|CYLD_ENST00000568704.2_Missense_Mutation_p.D325N|CYLD_ENST00000564326.1_Missense_Mutation_p.D325N			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	328	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)				AGGTGTTGGGGACAAAGGTTC	0.388			"Mis, N, F, S"		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis																												p.D328N		Atlas-SNP	.	yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	.	CYLD	150	.	0			c.G982A						PASS	.						102	102	102					16																	50810149		1861	4094	5955	SO:0001583	missense	1540	exon8	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	GTTGGGGACAAAG	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.982G>A	16.37:g.50810149G>A	ENSP00000392025:p.Asp328Asn	97	0	0		104	13	0.125	NM_015247	O94934|Q7L3N6|Q96EH0|Q9NZX9	Missense_Mutation	SNP	ENST00000427738.3	37	CCDS45482.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.299579	0.81136	.	.	ENSG00000083799	ENST00000540145;ENST00000311559;ENST00000427738;ENST00000398568	T;T;T	0.19669	2.13;2.13;2.13	6.17	6.17	0.99709	.	0.151321	0.64402	D	0.000010	T	0.17365	0.0417	N	0.14661	0.345	0.49582	D	0.999803	B;B;B;B	0.12013	0.003;0.005;0.005;0.003	B;B;B;B	0.11329	0.003;0.006;0.006;0.003	T	0.05937	-1.0855	10	0.48119	T	0.1	-20.1557	20.8794	0.99867	0.0:0.0:1.0:0.0	.	325;328;325;328	A8KAB0;F5H2R7;Q9NQC7-2;Q9NQC7	.;.;.;CYLD_HUMAN	N	328;328;325;325	ENSP00000445447:D328N;ENSP00000308928:D328N;ENSP00000381574:D325N	ENSP00000308928:D328N	D	+	1	0	CYLD	49367650	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.760000	0.74939	2.941000	0.99782	0.655000	0.94253	GAC	.	.	none		0.388	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2			A	50810149	G	A	50810149	3	1	23	1	0	0	0	0	1	0	0	0	4145	1174	41	2	1000	2	CYLD	16	50810149	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	63921	50810149	39544604	583	8027											
SLC12A3	6559	hgsc.bcm.edu	37	chr16	56928555	56928555	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atggaccaggagagaaaggcGtaagtgtggagggctggcct	11	6	18	6	1	0	1	0	0	0	1	0	5	0	4	2	6	0	2	2	6	2	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:56928555G>A	ENST00000563236.1	+	22	2658		c.e22+1		SLC12A3_ENST00000438926.2_Splice_Site|SLC12A3_ENST00000566786.1_Splice_Site|SLC12A3_ENST00000262502.5_Splice_Site			P55017	S12A3_HUMAN	solute carrier family 12 (sodium/chloride transporter), member 3						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)	AGAGAAAGGCGTAAGTGTGGA	0.577																																					.		Atlas-SNP	.											.	SLC12A3	99	.	0			c.2633+1G>A	GRCh37	CD077781|CS066650|CS076679	SLC12A3	D|S		PASS	.						111	82	92					16																	56928555		2198	4300	6498	SO:0001630	splice_region_variant	6559	exon22			AAAGGCGTAAGTG		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.2633+1G>A	16.37:g.56928555G>A		108	0	0		110	56	0.509091	NM_001126108	A8MSJ2|C9JNN9	Splice_Site	SNP	ENST00000563236.1	37	CCDS58464.1	.	.	.	.	.	.	.	.	.	.	G	13.07	2.126969	0.37533	.	.	ENSG00000070915	ENST00000438926;ENST00000262502	.	.	.	4.76	4.76	0.60689	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.6949	0.85333	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC12A3	55486056	1.000000	0.71417	1.000000	0.80357	0.110000	0.19582	7.659000	0.83766	2.350000	0.79820	0.561000	0.74099	.	.	.	none		0.577	SLC12A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432337.1		Intron	A	56928555	G	A	56928555	5	1	23	1	0	0	0	0	0	0	1	0	14399	1159	40	1	2747	1	SLC12A3	16	56928555	Splice_Site	SNP	G	TCGA-G8-6325-01A-11D-2210-10	6118406	56928555	33426198	584	8028											
HYDIN	54768	hgsc.bcm.edu	37	chr16	71054116	71054116	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agggatttatcagtctcacaTataaagaagggtccagatgt	14	11	10	6	0	2	2	2	0	1	2	4	3	3	3	1	2	0	0	1	2	5	4	rs183427172	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:71054116T>C	ENST00000393567.2	-	22	3441	c.3291A>G	c.(3289-3291)atA>atG	p.I1097M	HYDIN_ENST00000448089.2_Missense_Mutation_p.I1049M	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	1097					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)				CAGTCTCACATATAAAGAAGG	0.502													T|||	8	0.00159744	0.0	0.0014	5008	,	,		16126	0.0		0.005	False		,,,				2504	0.002				p.I1097M		Atlas-SNP	.											.	HYDIN	788	.	0			c.A3291G						PASS	.	T	MET/ILE	2,3636		0,2,1817	35	37	37		3291	-9.2	0	16		37	23,8143		0,23,4060	yes	missense	HYDIN	NM_032821.2	10	0,25,5877	CC,CT,TT		0.2817,0.055,0.2118	possibly-damaging	1097/5121	71054116	25,11779	1819	4083	5902	SO:0001583	missense	54768	exon22			CTCACATATAAAG	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.3291A>G	16.37:g.71054116T>C	ENSP00000377197:p.Ile1097Met	69	0	0		63	36	0.571429	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	14.02	2.410733	0.42817	5.5E-4	0.002817	ENSG00000157423	ENST00000393567;ENST00000316490;ENST00000448089	T;T	0.11063	2.81;2.81	4.61	-9.21	0.00678	.	0.254648	0.19540	U	0.111835	T	0.04363	0.0120	L	0.43923	1.385	0.51482	D	0.999923	P	0.40107	0.703	B	0.34385	0.181	T	0.38200	-0.9672	10	0.28530	T	0.3	.	1.6982	0.02866	0.2194:0.232:0.3592:0.1895	.	1097	F8WD23	.	M	1097;1097;1049	ENSP00000377197:I1097M;ENSP00000398544:I1049M	ENSP00000313052:I1097M	I	-	3	3	HYDIN	69611617	0.357000	0.24938	0.045000	0.18777	0.300000	0.27592	-0.549000	0.06041	-1.172000	0.02762	-0.394000	0.06481	ATA	T|0.998;C|0.002	0.002	strong		0.502	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			C	71054116	T	C	71054116	3	2	23	1	0	0	0	0	1	0	0	0	7476	1396	49	3	12331	3	HYDIN	16	71054116	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	14125561	71054116	19300637	585	8029											
HPR	3250	hgsc.bcm.edu	37	chr16	72110872	72110872	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggaggacacctggtacgcGgctgggatcctaagctttga	9	8	15	9	2	0	1	0	1	0	0	1	5	1	4	2	5	2	3	2	5	2	3	rs147707949	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:72110872G>A	ENST00000540303.2	+	5	971	c.939G>A	c.(937-939)gcG>gcA	p.A313A	HPR_ENST00000228226.8_Silent_p.A350A|HPR_ENST00000356967.5_Silent_p.A313A|HPR_ENST00000561690.1_Missense_Mutation_p.G112S	NM_020995.3	NP_066275.3	P00739	HPTR_HUMAN	haptoglobin-related protein	313	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)				CCTGGTACGCGGCTGGGATCC	0.547													G|||	8	0.00159744	0.0	0.0014	5008	,	,		25381	0.0		0.005	False		,,,				2504	0.002				p.A313A		Atlas-SNP	.											HPR,NS,carcinoma,+2,1	HPR	43	1	0			c.G939A						PASS	.	G		2,4190		0,2,2094	270	180	210		939	-0.2	1	16	dbSNP_134	210	21,8425		0,21,4202	no	coding-synonymous	HPR	NM_020995.3		0,23,6296	AA,AG,GG		0.2486,0.0477,0.182		313/349	72110872	23,12615	2096	4223	6319	SO:0001819	synonymous_variant	3250	exon5			GTACGCGGCTGGG	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.939G>A	16.37:g.72110872G>A		206	0	0		251	106	0.422311	NM_020995	Q7LE20|Q92658|Q92659|Q9ULB0	Silent	SNP	ENST00000540303.2	37	CCDS42193.1																																																																																			G|0.997;A|0.003	0.003	strong		0.547	HPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421696.1	NM_020995		A	72110872	G	A	72110872	2	1	23	1	0	0	0	0	0	0	0	1	7346	1103	39	1		1	HPR	16	72110872	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1056756	72110872	18243881	586	8030											
LDHD	84937	hgsc.bcm.edu	37	chr16	75146357	75146357	+	IGR	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacctcctcctgcagcagcTgccgcttgcccattccgatg	5	9	8	19	2	0	0	0	0	0	0	3	1	3	0	7	0	5	4	7	0	0	2	rs372986804		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:75146357T>G	ENST00000335325.4	+	0	4620				RP11-252E2.1_ENST00000499110.1_RNA|LDHD_ENST00000300051.4_Missense_Mutation_p.Q474P|LDHD_ENST00000450168.2_Missense_Mutation_p.Q451P	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						CTGCAGCAGCTGCCGCTTGCC	0.667																																					p.Q474P		Atlas-SNP	.											.	LDHD	34	.	0			c.A1421C						PASS	.	T	PRO/GLN,PRO/GLN	0,4396		0,0,2198	27	28	28		1421,1352	4.2	1	16		28	2,8598		0,2,4298	no	missense,missense	LDHD	NM_153486.3,NM_194436.2	76,76	0,2,6496	GG,GT,TT		0.0233,0.0,0.0154	benign,benign	474/508,451/485	75146357	2,12994	2198	4300	6498	SO:0001628	intergenic_variant	197257	exon11			AGCAGCTGCCGCT	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		16.37:g.75146357T>G		84	0	0		70	31	0.442857	NM_153486	D3DUJ9|Q9H083	Missense_Mutation	SNP	ENST00000335325.4	37	CCDS10912.1	.	.	.	.	.	.	.	.	.	.	T	14.78	2.636542	0.47049	0.0	2.33E-4	ENSG00000166816	ENST00000450168;ENST00000300051	D;D	0.87179	-2.22;-2.22	5.27	4.16	0.48862	Vanillyl-alcohol oxidase, C-terminal subdomain 2 (1);FAD-linked oxidase-like, C-terminal (1);FAD-linked oxidase, C-terminal (1);	0.450708	0.22902	N	0.054258	T	0.79741	0.4498	N	0.13003	0.285	0.30172	N	0.801213	P;P	0.41546	0.579;0.754	B;P	0.48089	0.43;0.566	T	0.74275	-0.3718	10	0.33141	T	0.24	-16.5283	6.5485	0.22420	0.2656:0.0:0.138:0.5963	.	451;474	Q86WU2-2;Q86WU2	.;LDHD_HUMAN	P	451;474	ENSP00000417011:Q451P;ENSP00000300051:Q474P	ENSP00000300051:Q474P	Q	-	2	0	LDHD	73703858	0.800000	0.28916	1.000000	0.80357	0.974000	0.67602	1.415000	0.34748	0.821000	0.34540	0.460000	0.39030	CAG	.	.	weak		0.667	ZNRF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269020.2			G	75146357	T	G	75146357	1	3	23	0	1	0	0	0	0	0	0	0	8712	1580	55	5		5	LDHD	16	75146357	IGR	SNP	T	TCGA-G8-6325-01A-11D-2210-10	3035485	75146357	15208396	587	8031											
ADAT1	23536	hgsc.bcm.edu	37	chr16	75642801	75642801	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttttgcctgcaccgcactgcGgctctgttcaaatagtaaat	9	13	8	11	2	2	0	1	0	1	0	2	0	2	0	2	1	3	5	2	1	4	5	rs77029992	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:75642801G>A	ENST00000307921.3	-	8	1274	c.1129C>T	c.(1129-1131)Cgc>Tgc	p.R377C	RP11-77K12.8_ENST00000564489.1_RNA	NM_012091.3	NP_036223.2	Q9BUB4	ADAT1_HUMAN	adenosine deaminase, tRNA-specific 1	377	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						ACCGCACTGCGGCTCTGTTCA	0.473													G|||	27	0.00539137	0.0008	0.0086	5008	,	,		21246	0.0		0.0189	False		,,,				2504	0.001				p.R377C		Atlas-SNP	.											.	ADAT1	45	.	0			c.C1129T						PASS	.	G	CYS/ARG	20,4376	27.2+/-55.0	0,20,2178	80	74	76		1129	5.1	1	16	dbSNP_131	76	240,8360	97.2+/-158.9	3,234,4063	yes	missense	ADAT1	NM_012091.3	180	3,254,6241	AA,AG,GG		2.7907,0.455,2.0006	probably-damaging	377/503	75642801	260,12736	2198	4300	6498	SO:0001583	missense	23536	exon8			CACTGCGGCTCTG	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.1129C>T	16.37:g.75642801G>A	ENSP00000310015:p.Arg377Cys	89	0	0		91	48	0.527473	NM_012091	Q9NVB7|Q9UNG3	Missense_Mutation	SNP	ENST00000307921.3	37	CCDS10922.1	22	0.010073260073260074	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	16	0.021108179419525065	G	14.21	2.467031	0.43839	0.00455	0.027907	ENSG00000065457	ENST00000307921;ENST00000542252	D	0.94184	-3.37	6.03	5.09	0.68999	Adenosine deaminase/editase (3);	0.476723	0.23298	N	0.049703	D	0.85124	0.5625	M	0.90542	3.125	0.58432	D	0.999999	B	0.27140	0.169	B	0.20767	0.031	D	0.87066	0.2156	10	0.56958	D	0.05	1.6221	8.8692	0.35305	0.0749:0.0:0.7765:0.1486	.	377	Q9BUB4	ADAT1_HUMAN	C	377;348	ENSP00000310015:R377C	ENSP00000310015:R377C	R	-	1	0	ADAT1	74200302	1.000000	0.71417	1.000000	0.80357	0.691000	0.40173	3.454000	0.52986	1.568000	0.49683	0.557000	0.71058	CGC	G|0.983;A|0.017	0.017	strong		0.473	ADAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269027.1	NM_012091		A	75642801	G	A	75642801	3	1	23	1	0	0	0	0	1	0	0	0	284	1116	39	1	395	1	ADAT1	16	75642801	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	496444	75642801	14711952	588	8032											
PKD1L2	114780	hgsc.bcm.edu	37	chr16	81232294	81232294	+	RNA	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggaacagccaggcggcaaaTcccaaatggctctccaaagc	13	4	10	14	2	1	0	0	0	1	0	3	1	2	1	3	4	3	2	3	4	4	0	rs61734110	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81232294T>C	ENST00000525539.1	-	0	1515				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						AGGCGGCAAATCCCAAATGGC	0.582													T|||	154	0.0307508	0.0325	0.0317	5008	,	,		20196	0.004		0.0716	False		,,,				2504	0.0133				p.I506V		Atlas-SNP	.											.	PKD1L2	361	.	0			c.A1516G						PASS	.	T	VAL/ILE,VAL/ILE	168,3844		1,166,1839	51	52	51		1516,1516	2.8	0.5	16	dbSNP_129	51	526,7782		17,492,3645	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	29,29	18,658,5484	CC,CT,TT		6.3312,4.1874,5.6331	benign,benign	506/992,506/2460	81232294	694,11626	2006	4154	6160			114780	exon7			GGCAAATCCCAAA	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		16.37:g.81232294T>C		102	0	0		101	60	0.594059	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		85|85	0.03891941391941392|0.03891941391941392	17|17	0.034552845528455285|0.034552845528455285	16|16	0.04419889502762431|0.04419889502762431	1|1	0.0017482517482517483|0.0017482517482517483	51|51	0.06728232189973615|0.06728232189973615	T|T	0.006|0.006	-2.058861|-2.058861	0.00390|0.00390	0.041874|0.041874	0.063312|0.063312	ENSG00000166473|ENSG00000166473	ENST00000526632|ENST00000337114	.|T	.|0.01279	.|5.06	5.08|5.08	2.75|2.75	0.32379|0.32379	.|Egg jelly receptor, REJ-like (1);	.|1.001100	.|0.08058	.|N	.|0.997623	T|T	0.00144|0.00144	0.0004|0.0004	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|B;B	.|0.16603	.|0.018;0.006	.|B;B	.|0.17722	.|0.019;0.004	T|T	0.50127|0.50127	-0.8864|-0.8864	4|9	.|0.22706	.|T	.|0.39	-3.0E-4|-3.0E-4	8.8296|8.8296	0.35076|0.35076	0.0:0.2087:0.0:0.7913|0.0:0.2087:0.0:0.7913	.|.	.|506;506	.|Q7Z442-3;Q7Z442	.|.;PK1L2_HUMAN	G|V	33|506	.|ENSP00000337397:I506V	.|ENSP00000337397:I506V	D|I	-|-	2|1	0|0	PKD1L2|PKD1L2	79789795|79789795	0.000000|0.000000	0.05858|0.05858	0.487000|0.487000	0.27428|0.27428	0.041000|0.041000	0.13682|0.13682	0.422000|0.422000	0.21296|0.21296	0.790000|0.790000	0.33803|0.33803	-0.398000|-0.398000	0.06409|0.06409	GAT|ATT	T|0.956;C|0.044	0.044	strong		0.582	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2			C	81232294	T	C	81232294	1	2	23	0	1	0	0	0	0	0	0	0	11974	1435	50	3		3	PKD1L2	16	81232294	RNA	SNP	T	TCGA-G8-6325-01A-11D-2210-10	5589493	81232294	9122459	589	8033											
OSGIN1	29948	hgsc.bcm.edu	37	chr16	83999548	83999548	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacaacttcgtgaggtttgTgcaggggggcgccttggctg	5	10	18	8	2	0	1	0	1	0	0	1	2	0	2	1	6	2	3	1	6	1	3	rs62640905	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:83999548T>C	ENST00000343939.2	+	7	2002	c.1619T>C	c.(1618-1620)gTg>gCg	p.V540A	OSGIN1_ENST00000393306.1_Missense_Mutation_p.V457A|OSGIN1_ENST00000361711.3_Missense_Mutation_p.V457A|NECAB2_ENST00000305202.4_5'Flank			Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	540					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						GTGAGGTTTGTGCAGGGGGGC	0.662													T|||	40	0.00798722	0.0	0.013	5008	,	,		17559	0.0		0.0278	False		,,,				2504	0.0031				p.V457A		Atlas-SNP	.											.	OSGIN1	33	.	0			c.T1370C						PASS	.	T	ALA/VAL,ALA/VAL,ALA/VAL	14,4370		0,14,2178	14	15	15		1619,1370,1370	4.4	1	16	dbSNP_129	15	218,8354		5,208,4073	yes	missense,missense,missense	OSGIN1	NM_013370.3,NM_182980.2,NM_182981.2	64,64,64	5,222,6251	CC,CT,TT		2.5432,0.3193,1.7907	possibly-damaging,possibly-damaging,possibly-damaging	540/561,457/478,457/478	83999548	232,12724	2192	4286	6478	SO:0001583	missense	29948	exon6			GGTTTGTGCAGGG	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.1619T>C	16.37:g.83999548T>C	ENSP00000343376:p.Val540Ala	69	0	0		57	20	0.350877	NM_182981	Q52M33|Q86UQ1|Q96S88|Q9BZ70	Missense_Mutation	SNP	ENST00000343939.2	37		27	0.012362637362637362	0	0.0	6	0.016574585635359115	0	0.0	21	0.027704485488126648	T	16.86	3.238732	0.58995	0.003193	0.025432	ENSG00000140961	ENST00000343939;ENST00000361711;ENST00000393306	T;T;T	0.37411	1.2;1.2;1.2	4.37	4.37	0.52481	.	0.065516	0.64402	D	0.000009	T	0.15739	0.0379	M	0.63428	1.95	0.80722	D	1	D	0.58268	0.982	B	0.44315	0.446	T	0.04811	-1.0925	10	0.24483	T	0.36	-26.2537	12.7349	0.57218	0.0:0.0:0.0:1.0	rs62640905	540	Q9UJX0	OSGI1_HUMAN	A	540;457;457	ENSP00000343376:V540A;ENSP00000355374:V457A;ENSP00000376983:V457A	ENSP00000343376:V540A	V	+	2	0	OSGIN1	82557049	1.000000	0.71417	0.954000	0.39281	0.681000	0.39784	7.645000	0.83430	1.606000	0.50161	0.260000	0.18958	GTG	T|0.985;C|0.015	0.015	strong		0.662	OSGIN1-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000269081.1	NM_013370		C	83999548	T	C	83999548	3	2	23	1	0	0	0	0	1	0	0	0	11298	1696	59	3	1645	3	OSGIN1	16	83999548	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	2767254	83999548	6355205	590	8034											
SLC38A8	146167	hgsc.bcm.edu	37	chr16	84063130	84063130	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagatggtggggaagacaCtgaacacagaggtccaggag	14	4	16	7	0	0	4	0	1	0	3	1	6	1	6	1	5	2	1	1	5	2	0	rs11862366	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:84063130C>G	ENST00000299709.3	-	5	658	c.659G>C	c.(658-660)aGt>aCt	p.S220T		NM_001080442.1	NP_001073911.1	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8	220			S -> T (in dbSNP:rs11862366).		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						GGGGAAGACACTGAACACAGA	0.522													C|||	279	0.0557109	0.171	0.0144	5008	,	,		18537	0.0		0.0189	False		,,,				2504	0.0245				p.S220T		Atlas-SNP	.											.	SLC38A8	60	.	0			c.G659C						PASS	.	C	THR/SER	624,3776	270.7+/-269.8	34,556,1610	93	89	91		659	4.1	0.7	16	dbSNP_120	91	174,8426	78.4+/-141.0	4,166,4130	yes	missense	SLC38A8	NM_001080442.1	58	38,722,5740	GG,GC,CC		2.0233,14.1818,6.1385	benign	220/436	84063130	798,12202	2200	4300	6500	SO:0001583	missense	146167	exon5			AAGACACTGAACA		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.659G>C	16.37:g.84063130C>G	ENSP00000299709:p.Ser220Thr	74	0	0		84	45	0.535714	NM_001080442		Missense_Mutation	SNP	ENST00000299709.3	37	CCDS32495.1	113	0.051739926739926737	92	0.18699186991869918	4	0.011049723756906077	0	0.0	17	0.022427440633245383	C	13.96	2.394329	0.42410	0.141818	0.020233	ENSG00000166558	ENST00000299709	T	0.02177	4.41	5.25	4.07	0.47477	.	0.087359	0.85682	D	0.000000	T	0.00012	0.0000	M	0.76002	2.32	0.20975	P	0.999818287	P	0.42620	0.785	B	0.43508	0.422	T	0.53251	-0.8465	9	0.28530	T	0.3	.	12.3155	0.54953	0.0:0.8818:0.0:0.1182	rs11862366	220	A6NNN8	S38A8_HUMAN	T	220	ENSP00000299709:S220T	ENSP00000299709:S220T	S	-	2	0	SLC38A8	82620631	0.263000	0.24083	0.730000	0.30809	0.806000	0.45545	0.840000	0.27600	2.621000	0.88768	0.643000	0.83706	AGT	C|0.939;G|0.061	0.061	strong		0.522	SLC38A8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432623.1	NM_001080442		G	84063130	C	G	84063130	3	3	23	1	0	0	0	0	1	0	0	0	14625	565	20	4	672	4	SLC38A8	16	84063130	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	63582	84063130	6291623	591	8035											
KIAA0182	23199	hgsc.bcm.edu	37	chr16	85702028	85702028	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcttaccaggaacacatagAaggtaagggggtgctgggga	13	6	16	6	0	0	1	0	0	0	1	0	3	0	3	1	6	4	3	1	6	5	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:85702028A>G	ENST00000253458.7	+	14	3589	c.3413A>G	c.(3412-3414)gAa>gGa	p.E1138G	GSE1_ENST00000405402.2_Missense_Mutation_p.E1034G|GSE1_ENST00000393243.1_Missense_Mutation_p.E1065G	NM_014615.2	NP_055430.1	Q14687	GSE1_HUMAN	Gse1 coiled-coil protein	1138																	GAACACATAGAAGGTAAGGGG	0.547																																					p.E1138G		Atlas-SNP	.											KIAA0182,NS,carcinoma,+1,1	.	.	1	0			c.A3413G						scavenged	.						27	31	29					16																	85702028		2196	4300	6496	SO:0001583	missense	23199	exon14			ACATAGAAGGTAA	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.3413A>G	16.37:g.85702028A>G	ENSP00000253458:p.Glu1138Gly	23	0	0		25	7	0.28	NM_014615	D3DUM4|Q8IY61|Q96GA4|Q9BW09	Missense_Mutation	SNP	ENST00000253458.7	37	CCDS10952.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.4|21.4	4.142274|4.142274	0.77775|0.77775	.|.	.|.	ENSG00000131149|ENSG00000131149	ENST00000405402;ENST00000253458;ENST00000393243|ENST00000412692;ENST00000438180	T;T;T|.	0.34472|.	1.36;1.36;1.36|.	5.14|5.14	5.14|5.14	0.70334|0.70334	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.71091|0.71091	0.3299|0.3299	M|M	0.64997|0.64997	1.995|1.995	0.58432|0.58432	D|D	0.999999|0.999999	D;D;D;D|.	0.89917|.	0.999;1.0;1.0;1.0|.	D;D;D;D|.	0.91635|.	0.995;0.999;0.999;0.998|.	T|T	0.70930|0.70930	-0.4738|-0.4738	10|5	0.72032|.	D|.	0.01|.	-11.1152|-11.1152	14.9832|14.9832	0.71327|0.71327	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	901;1034;1065;1138|.	Q59GZ0;Q14687-2;Q14687-3;Q14687|.	.;.;.;GSE1_HUMAN|.	G|E	1034;1138;1065|907;340	ENSP00000384839:E1034G;ENSP00000253458:E1138G;ENSP00000376934:E1065G|.	ENSP00000253458:E1138G|.	E|K	+|+	2|1	0|0	KIAA0182|KIAA0182	84259529|84259529	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.603000|0.603000	0.37013|0.37013	8.832000|8.832000	0.92079|0.92079	1.951000|1.951000	0.56629|0.56629	0.459000|0.459000	0.35465|0.35465	GAA|AAG	.	.	none		0.547	GSE1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325527.1	NM_014615		G	85702028	A	G	85702028	3	3	23	1	0	0	0	0	1	0	0	0	8168	246	9	3	3467	3	KIAA0182	16	85702028	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	1638898	85702028	4652725	592	8036											
MTHFSD	64779	hgsc.bcm.edu	37	chr16	86585743	86585743	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tttgatgttttggcaagccaGataagacccctagttaggca	11	12	10	8	0	0	3	0	1	0	2	0	3	0	3	3	2	1	4	3	2	4	6	rs34005514	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:86585743G>C	ENST00000360900.6	-	3	158	c.133C>G	c.(133-135)Ctg>Gtg	p.L45V	MTHFSD_ENST00000546093.1_Intron|MTHFSD_ENST00000568037.1_Intron|MTHFSD_ENST00000322911.6_Missense_Mutation_p.L44V|MTHFSD_ENST00000381214.5_Intron|MTHFSD_ENST00000543303.2_Intron	NM_001159380.1	NP_001152852.1	Q2M296	MTHSD_HUMAN	methenyltetrahydrofolate synthetase domain containing	45			L -> V (in dbSNP:rs34005514).				nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(3)|lung(6)|skin(1)	11						TGGCAAGCCAGATAAGACCCC	0.473													G|||	95	0.0189696	0.0053	0.0274	5008	,	,		19532	0.004		0.0517	False		,,,				2504	0.0133				p.L45V		Atlas-SNP	.											.	MTHFSD	52	.	0			c.C133G						PASS	.	G	VAL/LEU,,,VAL/LEU,VAL/LEU	43,3753		0,43,1855	151	153	152		133,,,73,130	-0.4	0.6	16	dbSNP_126	152	398,7840		14,370,3735	yes	missense,intron,intron,missense,missense	MTHFSD	NM_001159377.1,NM_001159378.1,NM_001159379.1,NM_001159380.1,NM_022764.2	32,,,32,32	14,413,5590	CC,CG,GG		4.8313,1.1328,3.6646	,,,,	45/384,,,25/364,44/383	86585743	441,11593	1898	4119	6017	SO:0001583	missense	64779	exon3			AAGCCAGATAAGA	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.133C>G	16.37:g.86585743G>C	ENSP00000354152:p.Leu45Val	115	0	0		121	61	0.504132	NM_001159377	A8MQ77|B7ZLC0|B7ZLC2|D3DUM9|E9PAM1|Q9H878|Q9H954	Missense_Mutation	SNP	ENST00000360900.6	37	CCDS54047.1	55	0.025183150183150184	2	0.0040650406504065045	8	0.022099447513812154	4	0.006993006993006993	41	0.05408970976253298	G	10.80	1.453214	0.26161	0.011328	0.048313	ENSG00000103248	ENST00000543303;ENST00000360900;ENST00000322911	T;T	0.41400	1.0;1.0	5.93	-0.438	0.12268	5-formyltetrahydrofolate cyclo-ligase-like domain (1);	1.474430	0.04126	N	0.317098	T	0.04724	0.0128	N	0.04297	-0.235	0.09310	N	1	B;B	0.17465	0.022;0.017	B;B	0.23852	0.049;0.029	T	0.23726	-1.0180	10	0.35671	T	0.21	-11.0693	14.9226	0.70851	0.0:0.419:0.4829:0.0981	rs34005514	45;44	Q2M296;Q2M296-2	MTHSD_HUMAN;.	V	43;45;44	ENSP00000354152:L45V;ENSP00000326777:L44V	ENSP00000326777:L44V	L	-	1	2	MTHFSD	85143244	0.057000	0.20700	0.564000	0.28396	0.964000	0.63967	0.453000	0.21811	0.070000	0.16634	0.655000	0.94253	CTG	G|0.968;C|0.032	0.032	strong		0.473	MTHFSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432182.1	NM_022764		C	86585743	G	C	86585743	3	2	23	1	0	0	0	0	1	0	0	0	9942	933	33	4	1042	4	MTHFSD	16	86585743	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	883715	86585743	3769010	593	8037											
CDT1	353	hgsc.bcm.edu	37	chr16	88873824	88873824	+	IGR	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tctttgtgtccgaacgcaagCctgcgctcagcatggaggtg	7	10	13	11	3	2	0	1	0	1	0	3	2	3	1	2	2	4	3	2	2	2	1	rs141663679	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:88873824C>G	ENST00000378364.3	-	0	947				CDT1_ENST00000301019.4_Missense_Mutation_p.P471A	NM_000485.2	NP_000476.1	P07741	APT_HUMAN	adenine phosphoribosyltransferase						adenine salvage (GO:0006168)|AMP salvage (GO:0044209)|cellular response to insulin stimulus (GO:0032869)|grooming behavior (GO:0007625)|lactation (GO:0007595)|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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	adenine binding (GO:0002055)|adenine phosphoribosyltransferase activity (GO:0003999)|AMP binding (GO:0016208)			cervix(1)|endometrium(1)|liver(1)	3				BRCA - Breast invasive adenocarcinoma(80;0.0477)	Adenine(DB00173)|Adenosine monophosphate(DB00131)	CGAACGCAAGCCTGCGCTCAG	0.667													C|||	5	0.000998403	0.0	0.0014	5008	,	,		17483	0.0		0.002	False		,,,				2504	0.002				p.P471A		Atlas-SNP	.											.	CDT1	30	.	0			c.C1411G						PASS	.	C	ALA/PRO	3,4391	6.2+/-15.9	0,3,2194	60	49	53		1411	3.5	0.8	16	dbSNP_134	53	44,8556	29.0+/-79.6	0,44,4256	yes	missense	CDT1	NM_030928.3	27	0,47,6450	GG,GC,CC		0.5116,0.0683,0.3617	benign	471/547	88873824	47,12947	2197	4300	6497	SO:0001628	intergenic_variant	81620	exon9			CGCAAGCCTGCGC		CCDS32511.1, CCDS45546.1	16q24	2012-10-02				ENSG00000198931	2.4.2.7		626	protein-coding gene	gene with protein product		102600					Standard	NM_000485		Approved		uc002flv.3	P07741			16.37:g.88873824C>G		121	0	0		147	87	0.591837	NM_030928	G5E9J2|Q3KP55|Q68DF9	Missense_Mutation	SNP	ENST00000378364.3	37	CCDS32511.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	9.456	1.091956	0.20471	6.83E-4	0.005116	ENSG00000167513	ENST00000301019	T	0.77098	-1.07	5.43	3.49	0.39957	.	0.056769	0.64402	D	0.000001	T	0.63838	0.2545	M	0.61703	1.905	0.53688	D	0.999975	B	0.26744	0.158	B	0.23419	0.046	T	0.60722	-0.7207	10	0.27785	T	0.31	-16.1815	8.6516	0.34038	0.0:0.7221:0.1338:0.144	.	471	Q9H211	CDT1_HUMAN	A	471	ENSP00000301019:P471A	ENSP00000301019:P471A	P	+	1	0	CDT1	87401325	1.000000	0.71417	0.843000	0.33291	0.003000	0.03518	2.711000	0.47177	0.667000	0.31107	-0.251000	0.11542	CCT	C|0.998;G|0.002	0.002	strong		0.667	APRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430000.2	NM_000485		G	88873824	C	G	88873824	1	3	23	0	1	0	0	0	0	0	0	0	3182	739	26	4		4	CDT1	16	88873824	IGR	SNP	C	TCGA-G8-6325-01A-11D-2210-10	2288081	88873824	1480929	594	8038											
PABPN1L	390748	hgsc.bcm.edu	37	chr16	88932857	88932857	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcctctgcatcctcttccTcctctttctcctccttccct	1	18	1	21	0	4	0	0	0	4	0	11	0	10	0	7	0	1	1	7	0	0	4	rs139390142	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:88932857T>C	ENST00000419291.2	-	1	169	c.158A>G	c.(157-159)gAg>gGg	p.E53G	PABPN1L_ENST00000378358.4_Missense_Mutation_p.E53G|PABPN1L_ENST00000427766.1_Missense_Mutation_p.E53G|PABPN1L_ENST00000411789.2_Missense_Mutation_p.E53G	NM_001080487.2	NP_001073956.2	A6NDY0	EPAB2_HUMAN	poly(A) binding protein, nuclear 1-like (cytoplasmic)	53						cytoplasm (GO:0005737)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			kidney(1)	1						atcctcttcctcctctttctc	0.607													t|||	11	0.00219649	0.0	0.0043	5008	,	,		19104	0.0		0.006	False		,,,				2504	0.002				p.E53G		Atlas-SNP	.											.	PABPN1L	25	.	0			c.A158G						PASS	.	T	GLY/GLU	3,3929		0,3,1963	51	57	55		158	-4.2	0	16	dbSNP_134	55	42,7942		0,42,3950	yes	missense	PABPN1L	NM_001080487.2	98	0,45,5913	CC,CT,TT		0.5261,0.0763,0.3776	benign	53/279	88932857	45,11871	1966	3992	5958	SO:0001583	missense	390748	exon1			TCTTCCTCCTCTT		CCDS45547.1, CCDS45547.2, CCDS73925.1	16q24.3	2013-02-12	2009-12-17		ENSG00000205022	ENSG00000205022		"RNA binding motif (RRM) containing"	37237	protein-coding gene	gene with protein product	"embryonic poly(A) binding protein 2"					18483763	Standard	NM_001080487		Approved	ePABP2	uc010vpe.2	A6NDY0		ENST00000419291.2:c.158A>G	16.37:g.88932857T>C	ENSP00000408598:p.Glu53Gly	98	0	0		106	52	0.490566	NM_001080487	A1L3B3|A2VDI2	Missense_Mutation	SNP	ENST00000419291.2	37	CCDS45547.2	9	0.004120879120879121	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	5	0.006596306068601583	T	7.862	0.726328	0.15439	7.63E-4	0.005261	ENSG00000205022	ENST00000378358;ENST00000419291;ENST00000427766;ENST00000411789;ENST00000547152	T;T	0.19250	2.16;2.42	3.52	-4.19	0.03835	.	2.185190	0.02057	N	0.050477	T	0.11324	0.0276	N	0.24115	0.695	0.09310	N	1	B;B;B;P	0.46512	0.0;0.0;0.0;0.879	B;B;B;P	0.45998	0.0;0.001;0.0;0.5	T	0.18935	-1.0321	10	0.44086	T	0.13	.	4.3382	0.11097	0.1664:0.4546:0.0:0.379	.	53;53;53;53	A6NDY0;A6NDY0-4;C9JEK9;A6NDY0-2	EPAB2_HUMAN;.;.;.	G	53	ENSP00000367609:E53G;ENSP00000408598:E53G	ENSP00000367609:E53G	E	-	2	0	PABPN1L	87460358	0.314000	0.24563	0.000000	0.03702	0.026000	0.11368	0.515000	0.22801	-0.355000	0.08199	0.172000	0.16884	GAG	T|0.996;C|0.004	0.004	strong		0.607	PABPN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407502.1	NM_001080487		C	88932857	T	C	88932857	3	2	23	1	0	0	0	0	1	0	0	0	11378	1551	54	3	738	3	PABPN1L	16	88932857	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	59033	88932857	1421896	595	8039											
GEMIN4	50628	hgsc.bcm.edu	37	chr17	649984	649984	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	caggctacccactcgtccgaGaaggcccacttcttctcaga	9	8	8	16	2	2	2	1	0	2	2	5	3	3	2	3	2	1	1	3	2	2	3	rs147516197	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:649984G>A	ENST00000319004.5	-	2	1417	c.1299C>T	c.(1297-1299)ttC>ttT	p.F433F	GEMIN4_ENST00000437269.1_3'UTR|GEMIN4_ENST00000576778.1_Silent_p.F422F	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	433					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		ACTCGTCCGAGAAGGCCCACT	0.547													G|||	46	0.0091853	0.0	0.0043	5008	,	,		19907	0.0149		0.0089	False		,,,				2504	0.0194				p.F433F		Atlas-SNP	.											.	GEMIN4	116	.	0			c.C1299T						PASS	.	G		1,3955		0,1,1977	53	55	55		1299	5.1	1	17	dbSNP_134	55	86,8214		1,84,4065	no	coding-synonymous	GEMIN4	NM_015721.2		1,85,6042	AA,AG,GG		1.0361,0.0253,0.7099		433/1059	649984	87,12169	1978	4150	6128	SO:0001819	synonymous_variant	50628	exon2			GTCCGAGAAGGCC	AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"HCC-associated protein 1", "component of gems 4"	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.1299C>T	17.37:g.649984G>A		89	0	0		99	52	0.525253	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Silent	SNP	ENST00000319004.5	37	CCDS45559.1																																																																																			G|0.991;A|0.009	0.009	strong		0.547	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721		A	649984	G	A	649984	2	1	23	1	0	0	0	0	0	0	0	1	6338	933	33	2		2	GEMIN4	17	649984	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10		649984	80545226	596	8040											
SMYD4	114826	hgsc.bcm.edu	37	chr17	1686737	1686737	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaggaagctctcggcgtcaCgctggcaccccgacagccgc	8	4	12	17	5	2	0	1	0	1	0	3	2	2	1	3	3	2	3	3	3	1	0	rs374639152		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:1686737C>T	ENST00000305513.7	-	9	2221	c.2054G>A	c.(2053-2055)cGt>cAt	p.R685H		NM_052928.2	NP_443160.2	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	685							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						CTCGGCGTCACGCTGGCACCC	0.607																																					p.R685H		Atlas-SNP	.											.	SMYD4	50	.	0			c.G2054A						PASS	.	C	HIS/ARG	0,4406		0,0,2203	24	24	24		2054	-10	0	17		24	1,8599		0,1,4299	no	missense	SMYD4	NM_052928.2	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	685/805	1686737	1,13005	2203	4300	6503	SO:0001583	missense	114826	exon9			GCGTCACGCTGGC	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.2054G>A	17.37:g.1686737C>T	ENSP00000304360:p.Arg685His	172	0	0		185	102	0.551351	NM_052928	Q8N1P2|Q8NAT0|Q96LV4|Q96PV2	Missense_Mutation	SNP	ENST00000305513.7	37	CCDS11013.1	.	.	.	.	.	.	.	.	.	.	C	9.257	1.042180	0.19748	0.0	1.16E-4	ENSG00000186532	ENST00000305513	T	0.64260	-0.09	5.75	-10.0	0.00425	Tetratricopeptide-like helical (1);	1.666840	0.02239	N	0.065610	T	0.29850	0.0746	N	0.01352	-0.895	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.34229	-0.9837	10	0.14252	T	0.57	1.9281	14.6337	0.68673	0.1008:0.6859:0.0:0.2133	.	685	Q8IYR2	SMYD4_HUMAN	H	685	ENSP00000304360:R685H	ENSP00000304360:R685H	R	-	2	0	SMYD4	1633487	0.000000	0.05858	0.000000	0.03702	0.078000	0.17371	-1.683000	0.01934	-2.027000	0.00932	-0.474000	0.04947	CGT	.	.	weak		0.607	SMYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207108.4	XM_056082		T	1686737	C	T	1686737	3	4	23	1	0	0	0	0	1	0	0	0	14839	536	19	1	372	1	SMYD4	17	1686737	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1036753	1686737	79508473	597	8041											
MYBBP1A	10514	hgsc.bcm.edu	37	chr17	4446217	4446217	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccctgctcacctgcgggccCgtgggcatgtggctggggtc	2	8	17	14	2	1	0	1	0	0	0	2	0	1	0	3	5	2	3	3	5	0	0	rs138864176	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4446217C>T	ENST00000254718.4	-	20	3189	c.2883G>A	c.(2881-2883)acG>acA	p.T961T	MYBBP1A_ENST00000381556.2_Silent_p.T961T			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	961					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						CCTGCGGGCCCGTGGGCATGT	0.657													C|||	11	0.00219649	0.0	0.0029	5008	,	,		16836	0.0		0.0089	False		,,,				2504	0.0				p.T961T		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.G2883A						PASS	.	C	,	4,4402	8.1+/-20.4	0,4,2199	38	43	42		2883,2883	-0.6	0	17	dbSNP_134	42	37,8563	24.6+/-71.5	0,37,4263	no	coding-synonymous,coding-synonymous	MYBBP1A	NM_001105538.1,NM_014520.3	,	0,41,6462	TT,TC,CC		0.4302,0.0908,0.3152	,	961/1333,961/1329	4446217	41,12965	2203	4300	6503	SO:0001819	synonymous_variant	10514	exon20			CGGGCCCGTGGGC	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.2883G>A	17.37:g.4446217C>T		116	0	0		96	49	0.510417	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Silent	SNP	ENST00000254718.4	37	CCDS11046.1																																																																																			C|0.997;T|0.003	0.003	strong		0.657	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520		T	4446217	C	T	4446217	2	4	23	1	0	0	0	0	0	0	0	1	10017	639	23	1		1	MYBBP1A	17	4446217	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	2759480	4446217	76748993	598	8042											
MYBBP1A	10514	hgsc.bcm.edu	37	chr17	4458515	4458515	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtcccagaagaagtccaaGaactcgcgactgtgcttcaa	13	8	9	11	2	1	3	1	0	0	3	4	4	3	3	2	0	2	1	2	0	5	1	rs117128211	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4458515G>T	ENST00000254718.4	-	1	411	c.105C>A	c.(103-105)ttC>ttA	p.F35L	MYBBP1A_ENST00000381556.2_Missense_Mutation_p.F35L			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	35	Interaction with MYB. {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						AGAAGTCCAAGAACTCGCGAC	0.637													G|||	74	0.0147764	0.0008	0.0086	5008	,	,		16072	0.0		0.0348	False		,,,				2504	0.0327				p.F35L		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.C105A						PASS	.	G	LEU/PHE,LEU/PHE	19,4383	20.2+/-43.8	0,19,2182	27	27	27		105,105	2.9	1	17	dbSNP_132	27	241,8351	93.1+/-155.1	5,231,4060	yes	missense,missense	MYBBP1A	NM_001105538.1,NM_014520.3	22,22	5,250,6242	TT,TG,GG		2.8049,0.4316,2.0009	probably-damaging,probably-damaging	35/1333,35/1329	4458515	260,12734	2201	4296	6497	SO:0001583	missense	10514	exon1			GTCCAAGAACTCG	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.105C>A	17.37:g.4458515G>T	ENSP00000254718:p.Phe35Leu	80	0	0		61	34	0.557377	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Missense_Mutation	SNP	ENST00000254718.4	37	CCDS11046.1	29	0.013278388278388278	0	0.0	3	0.008287292817679558	0	0.0	26	0.03430079155672823	G	19.15	3.772199	0.69992	0.004316	0.028049	ENSG00000132382	ENST00000381556;ENST00000254718;ENST00000426435	T;T	0.56103	0.48;0.48	4.94	2.93	0.34026	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.28532	0.0706	L	0.34521	1.04	0.35719	D	0.817008	D;D	0.71674	0.997;0.998	D;D	0.72982	0.954;0.979	T	0.49457	-0.8938	10	0.11794	T	0.64	-29.3099	7.6026	0.28085	0.2721:0.0:0.7279:0.0	.	35;35	Q9BQG0;Q9BQG0-2	MBB1A_HUMAN;.	L	35	ENSP00000370968:F35L;ENSP00000254718:F35L	ENSP00000254718:F35L	F	-	3	2	MYBBP1A	4405264	1.000000	0.71417	0.998000	0.56505	0.252000	0.25951	1.905000	0.39878	0.662000	0.31006	-0.191000	0.12829	TTC	G|0.983;T|0.017	0.017	strong		0.637	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520		T	4458515	G	T	4458515	3	4	23	1	0	0	0	0	1	0	0	0	10017	933	33	4	4025	4	MYBBP1A	17	4458515	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	12298	4458515	76736695	599	8043											
PELP1	27043	hgsc.bcm.edu	37	chr17	4576195	4576195	+	Silent	SNP	C	C	T																															gtgggaggtccagggcgtgcCgagggcacagggcctgctga																										TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4576195C>T	ENST00000574876.1	-	16	2108	c.2091G>A	c.(2089-2091)tcG>tcA	p.S697S	AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000269230.7_Silent_p.S607S|PELP1_ENST00000572293.1_Silent_p.S747S|PELP1_ENST00000301396.4_Silent_p.S841S|PELP1_ENST00000436683.2_Silent_p.S550S			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	697	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						CAGGGCGTGCCGAGGGCACAG	0.677																																					p.S697S		Atlas-SNP	.											PELP1_ENST00000301396,NS,carcinoma,-1,3	PELP1	102	3	0			c.G2091A						PASS	.						32	38	36					17																	4576195		1989	4144	6133	SO:0001819	synonymous_variant	27043	exon16			GCGTGCCGAGGGC		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.2091G>A	17.37:g.4576195C>T		141	0	0		129	19	0.147287	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Silent	SNP	ENST00000574876.1	37	CCDS58503.1																																																																																			.	.	none		0.677	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389		T	4576195	C	T	4576195	2	4	23	1	0	0	0	0	0	0	0	1	11734	639	23	1		1	PELP1	17	4576195	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	117680	4576195	76619015	600	8044	103	2									
PELP1	27043	hgsc.bcm.edu	37	chr17	4576203	4576203	+	Missense_Mutation	SNP	C	C	T																															tccagggcgtgccgagggcaCagggcctgctgagggcatgg																										TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4576203C>T	ENST00000574876.1	-	16	2100	c.2083G>A	c.(2083-2085)Gtg>Atg	p.V695M	AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000269230.7_Missense_Mutation_p.V605M|PELP1_ENST00000572293.1_Missense_Mutation_p.V745M|PELP1_ENST00000301396.4_Missense_Mutation_p.V839M|PELP1_ENST00000436683.2_Missense_Mutation_p.V548M			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	695	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						GCCGAGGGCACAGGGCCTGCT	0.687																																					p.V695M		Atlas-SNP	.											.	PELP1	102	.	0			c.G2083A						PASS	.						33	39	37					17																	4576203		1990	4145	6135	SO:0001583	missense	27043	exon16			AGGGCACAGGGCC		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.2083G>A	17.37:g.4576203C>T	ENSP00000461625:p.Val695Met	141	0	0		136	26	0.191176	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Missense_Mutation	SNP	ENST00000574876.1	37	CCDS58503.1	.	.	.	.	.	.	.	.	.	.	C	1.457	-0.563579	0.03939	.	.	ENSG00000141456	ENST00000301396;ENST00000269230;ENST00000436683	T;T;T	0.48201	0.82;0.88;1.48	4.54	-7.16	0.01516	.	0.654618	0.14932	N	0.290033	T	0.21468	0.0517	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	0.06303	-1.0834	10	0.37606	T	0.19	-2.13	6.9569	0.24576	0.0:0.2953:0.3218:0.3829	.	548;695	E7EV54;Q8IZL8	.;PELP1_HUMAN	M	839;605;548	ENSP00000301396:V839M;ENSP00000269230:V605M;ENSP00000416231:V548M	ENSP00000269230:V605M	V	-	1	0	AC091153.1	4522952	0.000000	0.05858	0.001000	0.08648	0.155000	0.21991	-1.525000	0.02231	-1.363000	0.02164	-0.136000	0.14681	GTG	.	.	none		0.687	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389		T	4576203	C	T	4576203	3	4	23	1	0	0	0	0	1	0	0	0	11734	478	17	2	1317	2	PELP1	17	4576203	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	8	4576203	76619007	601	8045	103	2									
PELP1	27043	hgsc.bcm.edu	37	chr17	4576216	4576217	+	In_Frame_Ins	INS	-	-	GGCATGGGGCCTGCTGAA																															agggcacagggcctgctgagINSggcatggggcctgctgaagg																								rs147763003	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4576216_4576217insGGCATGGGGCCTGCTGAA	ENST00000574876.1	-	16	2086_2087	c.2069_2070insTTCAGCAGGCCCCATGCC	c.(2068-2070)ccc>ccTTCAGCAGGCCCCATGCCc	p.690_690P>PSAGPMP	AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000269230.7_In_Frame_Ins_p.600_600P>PSAGPMP|PELP1_ENST00000572293.1_In_Frame_Ins_p.740_740P>PSAGPMP|PELP1_ENST00000301396.4_In_Frame_Ins_p.834_834P>PSAGPMP|PELP1_ENST00000436683.2_In_Frame_Ins_p.543_543P>PSAGPMP			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	690	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						GGCCTGCTGAGGGCATGGGGCC	0.688																																					p.P690delinsPSAGPMP		Pindel	.											.	PELP1	102	.	0			c.2070_2071insTTCAGCAGGCCCCATGCC						PASS	.																																			SO:0001652	inframe_insertion	27043	exon16			.		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.2052_2069dupTTCAGCAGGCCCCATGCC	17.37:g.4576216_4576217insGGCATGGGGCCTGCTGAA	ENSP00000461625:p.SerAlaGlyProMetPro690dup	147	0	.		146	33	0.226	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	In_Frame_Ins	INS	ENST00000574876.1	37	CCDS58503.1																																																																																			.	.	none		0.688	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389		GGCATGGGGCCTGCTGAA	4576217	-	GGCATGGGGCCTGCTGAA	4576216	7	5	23	1	0	1	1	0	0	0	0	0	11734	987	35	0	1330	0	PELP1	17	4576216	In_Frame_Ins	INS	-	TCGA-G8-6325-01A-11D-2210-10	13	4576216	76618994	602	8046											
NLRP1	22861	hgsc.bcm.edu	37	chr17	5442790	5442790	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccctcacagagcagtcgcaCgccaacgtcatccaggttgt	9	7	9	16	3	2	1	2	0	0	1	4	1	3	1	4	1	2	3	4	1	1	1	rs61754791	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:5442790C>T	ENST00000572272.1	-	7	2814	c.2815G>A	c.(2815-2817)Gtg>Atg	p.V939M	NLRP1_ENST00000262467.5_Missense_Mutation_p.V939M|NLRP1_ENST00000354411.3_Missense_Mutation_p.V939M|NLRP1_ENST00000269280.4_Missense_Mutation_p.V939M|NLRP1_ENST00000577119.1_Missense_Mutation_p.V939M|NLRP1_ENST00000345221.3_Missense_Mutation_p.V939M|NLRP1_ENST00000571307.1_5'UTR			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	939					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)				AGCAGTCGCACGCCAACGTCA	0.622													C|||	58	0.0115815	0.0318	0.0058	5008	,	,		18777	0.0		0.0109	False		,,,				2504	0.001				p.V939M		Atlas-SNP	.											.	NLRP1	358	.	0			c.G2815A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	105,4301	82.9+/-121.4	3,99,2101	79	62	67		2815,2815,2815,2815,2815	0.5	0	17	dbSNP_129	67	134,8466	67.7+/-130.1	2,130,4168	yes	missense,missense,missense,missense,missense	NLRP1	NM_001033053.2,NM_014922.4,NM_033004.3,NM_033006.3,NM_033007.3	21,21,21,21,21	5,229,6269	TT,TC,CC		1.5581,2.3831,1.8376	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	939/1376,939/1430,939/1474,939/1444,939/1400	5442790	239,12767	2203	4300	6503	SO:0001583	missense	22861	exon7			GTCGCACGCCAAC	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.2815G>A	17.37:g.5442790C>T	ENSP00000460475:p.Val939Met	83	0	0		77	34	0.441558	NM_033007	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	37	CCDS42246.1	26	0.011904761904761904	14	0.028455284552845527	3	0.008287292817679558	0	0.0	9	0.011873350923482849	C	14.12	2.440438	0.43326	0.023831	0.015581	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000354411;ENST00000345221;ENST00000537069	T;T;T;T;T	0.14766	2.48;2.48;2.48;2.48;2.48	3.7	0.477	0.16784	.	0.224064	0.22878	N	0.054551	T	0.10680	0.0261	M	0.74546	2.27	0.09310	N	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;0.997;1.0	D;D;D;D;P;D	0.91635	0.912;0.999;0.997;0.982;0.896;0.982	T	0.03641	-1.1017	10	0.87932	D	0	.	2.8517	0.05560	0.2212:0.5366:0.0:0.2423	rs61754791	205;939;939;939;939;939	F5H042;Q9C000-3;Q9C000-4;Q9C000;Q9C000-2;E9PE50	.;.;.;NALP1_HUMAN;.;.	M	939;939;939;939;939;205	ENSP00000442029:V939M;ENSP00000262467:V939M;ENSP00000269280:V939M;ENSP00000346390:V939M;ENSP00000324366:V939M	ENSP00000262467:V939M	V	-	1	0	NLRP1	5383514	0.000000	0.05858	0.004000	0.12327	0.009000	0.06853	0.004000	0.13106	0.155000	0.19261	0.650000	0.86243	GTG	A|0.000;C|0.986;T|0.014	0.014	strong		0.622	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004		T	5442790	C	T	5442790	3	4	23	1	0	0	0	0	1	0	0	0	10480	536	19	1	1725	1	NLRP1	17	5442790	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	866574	5442790	75752420	603	8047											
ASGR2	433	hgsc.bcm.edu	37	chr17	7004927	7004927	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccggtggcattccgccttttCtcacacacccagcggtacac	7	9	8	17	3	1	0	1	0	1	0	3	0	2	0	4	3	2	2	4	3	1	4	rs11653054	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7004927C>T	ENST00000380952.2	-	9	1167	c.903G>A	c.(901-903)gaG>gaA	p.E301E	ASGR2_ENST00000355035.5_Silent_p.E301E|ASGR2_ENST00000254850.7_Silent_p.E277E|ASGR2_ENST00000446679.2_Silent_p.E282E	NM_001181.4|NM_001201352.1|NM_080912.3	NP_001172|NP_001188281.1|NP_550434	P07307	ASGR2_HUMAN	asialoglycoprotein receptor 2	301	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				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)	TCCGCCTTTTCTCACACACCC	0.602													C|||	44	0.00878594	0.0008	0.0101	5008	,	,		18902	0.001		0.0328	False		,,,				2504	0.002				p.E301E		Atlas-SNP	.											.	ASGR2	38	.	0			c.G903A						PASS	.	C	,,,,	28,4378	34.3+/-65.2	0,28,2175	89	76	81		903,888,903,831,846	3.8	1	17	dbSNP_120	81	266,8334	102.7+/-163.9	6,254,4040	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ASGR2	NM_001181.4,NM_001201352.1,NM_080912.3,NM_080913.3,NM_080914.2	,,,,	6,282,6215	TT,TC,CC		3.093,0.6355,2.2605	,,,,	301/312,296/307,301/312,277/288,282/293	7004927	294,12712	2203	4300	6503	SO:0001819	synonymous_variant	433	exon9			CCTTTTCTCACAC	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.903G>A	17.37:g.7004927C>T		95	0	0		71	39	0.549296	NM_080912	A6NLV8|A8MT12|D3DTM9|D3DTN0|O00448|Q03969	Silent	SNP	ENST00000380952.2	37	CCDS32544.1																																																																																			C|0.980;T|0.020	0.020	strong		0.602	ASGR2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000220003.1	NM_080914		T	7004927	C	T	7004927	2	4	23	1	0	0	0	0	0	0	0	1	1040	912	32	2		2	ASGR2	17	7004927	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1562137	7004927	74190283	604	8048											
TNK1	8711	hgsc.bcm.edu	37	chr17	7287992	7287992	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccctctgctccagggccctCtactccctcgccttgcgctg	2	10	8	21	2	2	0	0	0	2	0	5	0	4	0	6	1	3	2	6	1	1	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7287992C>A	ENST00000576812.1	+	7	1425	c.1056C>A	c.(1054-1056)ctC>ctA	p.L352L	TNK1_ENST00000570896.1_Silent_p.L352L|TNK1_ENST00000311668.2_Silent_p.L352L	NM_001251902.1	NP_001238831.1			tyrosine kinase, non-receptor, 1											central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(2)|pancreas(1)	16		Prostate(122;0.157)				CCAGGGCCCTCTACTCCCTCG	0.711																																					p.L352L		Atlas-SNP	.											.	TNK1	31	.	0			c.C1056A						PASS	.						16	20	19					17																	7287992		1951	4129	6080	SO:0001819	synonymous_variant	8711	exon7			GGCCCTCTACTCC	U43408	CCDS45602.1, CCDS58510.1	17p13.1	2005-09-22				ENSG00000174292			11940	protein-coding gene	gene with protein product		608076				8632913	Standard	NM_003985		Approved		uc002ggi.4	Q13470		ENST00000576812.1:c.1056C>A	17.37:g.7287992C>A		68	0	0		48	25	0.520833	NM_003985		Silent	SNP	ENST00000576812.1	37	CCDS58510.1																																																																																			.	.	none		0.711	TNK1-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440832.2	NM_003985		A	7287992	C	A	7287992	2	1	23	1	0	0	0	0	0	0	0	1	16332	900	32	4		4	TNK1	17	7287992	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	283065	7287992	73907218	605	8049											
NLGN2	57555	hgsc.bcm.edu	37	chr17	7319124	7319124	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggccgaccgggacaatggCgaaatgcgccgcaaaaccct	11	4	13	13	5	0	0	0	0	0	0	0	3	0	1	4	3	2	1	4	3	4	0	rs145633225		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7319124C>T	ENST00000302926.2	+	6	1405	c.1332C>T	c.(1330-1332)ggC>ggT	p.G444G	NLGN2_ENST00000575301.1_Silent_p.G444G	NM_020795.2	NP_065846.1	Q8NFZ4	NLGN2_HUMAN	neuroligin 2	444					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)				GGGACAATGGCGAAATGCGCC	0.582													C|||	1	0.000199681	0.0	0.0	5008	,	,		18788	0.0		0.001	False		,,,				2504	0.0				p.G444G		Atlas-SNP	.											.	NLGN2	61	.	0			c.C1332T						PASS	.	C		0,4406		0,0,2203	85	82	83		1332	-0.8	1	17	dbSNP_134	83	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	NLGN2	NM_020795.2		0,14,6489	TT,TC,CC		0.1628,0.0,0.1076		444/836	7319124	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	57555	exon6			CAATGGCGAAATG	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.1332C>T	17.37:g.7319124C>T		60	0	0		85	49	0.576471	NM_020795	Q9P2I1	Silent	SNP	ENST00000302926.2	37	CCDS11103.1																																																																																			C|0.999;T|0.001	0.001	strong		0.582	NLGN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226941.2	NM_020795		T	7319124	C	T	7319124	2	4	23	1	0	0	0	0	0	0	0	1	10471	755	27	1		1	NLGN2	17	7319124	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	31132	7319124	73876086	606	8050											
DNAH9	1770	hgsc.bcm.edu	37	chr17	11511480	11511480	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggccaatgagaagaatcGcctaaactggccccacatga	13	6	9	13	1	0	3	0	2	0	2	1	4	0	3	5	2	1	0	5	2	5	1	rs17599639	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:11511480G>A	ENST00000262442.4	+	2	520	c.452G>A	c.(451-453)cGc>cAc	p.R151H	DNAH9_ENST00000454412.2_Missense_Mutation_p.R151H|DNAH9_ENST00000579828.1_Missense_Mutation_p.R151H	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	151	Stem. {ECO:0000250}.		R -> H (in dbSNP:rs17599639).		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)		GAGAAGAATCGCCTAAACTGG	0.488													G|||	117	0.0233626	0.0159	0.0216	5008	,	,		19075	0.0		0.0417	False		,,,				2504	0.0399				p.R151H		Atlas-SNP	.											DNAH9,NS,malignant_melanoma,+1,1	DNAH9	695	1	0			c.G452A						PASS	.	G	HIS/ARG	82,4324	69.8+/-107.6	0,82,2121	150	146	147		452	0.9	0	17	dbSNP_123	147	353,8247	119.9+/-179.2	8,337,3955	yes	missense	DNAH9	NM_001372.3	29	8,419,6076	AA,AG,GG		4.1047,1.8611,3.3446	benign	151/4487	11511480	435,12571	2203	4300	6503	SO:0001583	missense	1770	exon2			AGAATCGCCTAAA	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.452G>A	17.37:g.11511480G>A	ENSP00000262442:p.Arg151His	84	0	0		92	45	0.48913	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	54	0.024725274725274724	11	0.022357723577235773	9	0.024861878453038673	0	0.0	34	0.044854881266490766	G	0.021	-1.427313	0.01117	0.018611	0.041047	ENSG00000007174	ENST00000262442;ENST00000454412	T;T	0.25749	1.82;1.78	5.7	0.937	0.19494	.	0.633514	0.15787	N	0.244627	T	0.01124	0.0037	N	0.00321	-1.65	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.45366	-0.9266	10	0.02654	T	1	.	11.4204	0.49978	0.8892:0.0:0.1108:0.0	rs17599639;rs52801139;rs17599639	151;151	Q9NYC9;E7EP17	DYH9_HUMAN;.	H	151	ENSP00000262442:R151H;ENSP00000414874:R151H	ENSP00000262442:R151H	R	+	2	0	DNAH9	11452205	0.998000	0.40836	0.000000	0.03702	0.104000	0.19210	4.213000	0.58520	-0.114000	0.11936	-0.812000	0.03155	CGC	G|0.971;A|0.029	0.029	strong		0.488	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		A	11511480	G	A	11511480	3	1	23	1	0	0	0	0	1	0	0	0	4610	1087	38	1	458	1	DNAH9	17	11511480	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	4192356	11511480	69683730	607	8051											
RAI1	10743	hgsc.bcm.edu	37	chr17	17698023	17698023	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctcgacagcttctccaagttCgtggcgggtgagcgggactg	6	9	15	11	4	1	1	0	1	1	0	4	3	1	2	1	3	2	2	1	3	1	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:17698023C>T	ENST00000353383.1	+	3	2230	c.1761C>T	c.(1759-1761)ttC>ttT	p.F587F	RAI1_ENST00000261641.6_Silent_p.F587F	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	587					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)		TCTCCAAGTTCGTGGCGGGTG	0.632																																					p.F587F		Atlas-SNP	.											.	RAI1	121	.	0			c.C1761T						PASS	.						68	70	69					17																	17698023		2201	4293	6494	SO:0001819	synonymous_variant	10743	exon3			CAAGTTCGTGGCG	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.1761C>T	17.37:g.17698023C>T		70	0	0		50	25	0.5	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Silent	SNP	ENST00000353383.1	37	CCDS11188.1																																																																																			.	.	none		0.632	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665		T	17698023	C	T	17698023	2	4	23	1	0	0	0	0	0	0	0	1	13022	883	31	1		1	RAI1	17	17698023	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	6186543	17698023	63497187	608	8052											
SREBF1	6720	hgsc.bcm.edu	37	chr17	17723595	17723595	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggagaaagcgggcatggacGggtacatcttcaatggagtg	11	7	17	6	2	2	1	1	0	1	1	2	4	2	3	0	5	2	2	0	5	3	2	rs115855236	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:17723595G>A	ENST00000261646.5	-	2	516	c.332C>T	c.(331-333)cCg>cTg	p.P111L	SREBF1_ENST00000435530.2_Missense_Mutation_p.P111L|SREBF1_ENST00000395757.1_5'Flank|SREBF1_ENST00000355815.4_Missense_Mutation_p.P141L|SREBF1_ENST00000583732.1_Intron|SREBF1_ENST00000338854.5_Missense_Mutation_p.P111L	NM_004176.4	NP_004167.3	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription factor 1	111	Pro/Ser-rich.				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						GGGCATGGACGGGTACATCTT	0.647													G|||	3	0.000599042	0.0	0.0	5008	,	,		17350	0.0		0.003	False		,,,				2504	0.0				p.P141L		Atlas-SNP	.											.	SREBF1	47	.	0			c.C422T						PASS	.	G	LEU/PRO,LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	65	72	69		422,332	2.2	0.9	17	dbSNP_132	69	8,8592	6.4+/-24.3	0,8,4292	yes	missense,missense	SREBF1	NM_001005291.2,NM_004176.4	98,98	0,9,6494	AA,AG,GG		0.093,0.0227,0.0692	probably-damaging,probably-damaging	141/1178,111/1148	17723595	9,12997	2203	4300	6503	SO:0001583	missense	6720	exon3			ATGGACGGGTACA	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.332C>T	17.37:g.17723595G>A	ENSP00000261646:p.Pro111Leu	81	0	0		96	50	0.520833	NM_001005291	B0I4X3|B0I4X4|D3DXC4|Q16062|Q59F52|Q6P4R7|Q6PFW7|Q6PJ36|Q8TAK9	Missense_Mutation	SNP	ENST00000261646.5	37	CCDS11189.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	6.553	0.470364	0.12461	2.27E-4	9.3E-4	ENSG00000072310	ENST00000338854;ENST00000355815;ENST00000261646;ENST00000418712;ENST00000423161;ENST00000435530	T;T;T;T;T	0.79454	0.49;0.53;0.54;-0.11;-1.27	4.52	2.2	0.27929	.	0.352176	0.24580	N	0.037309	T	0.67449	0.2894	L	0.54323	1.7	0.09310	N	1	P;P;P;P	0.47545	0.897;0.897;0.725;0.82	B;B;B;B	0.41135	0.256;0.186;0.134;0.348	T	0.59037	-0.7529	10	0.31617	T	0.26	-8.4746	6.4826	0.22071	0.1164:0.1911:0.6925:0.0	.	111;87;111;141	B0I4X3;B0I4X4;P36956;P36956-4	.;.;SRBP1_HUMAN;.	L	111;141;111;87;37;111	ENSP00000345822:P111L;ENSP00000348069:P141L;ENSP00000261646:P111L;ENSP00000411516:P37L;ENSP00000413389:P111L	ENSP00000261646:P111L	P	-	2	0	SREBF1	17664320	0.781000	0.28676	0.877000	0.34402	0.264000	0.26372	2.529000	0.45632	2.081000	0.62600	0.555000	0.69702	CCG	G|0.999;A|0.001	0.001	strong		0.647	SREBF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131771.1	NM_004176		A	17723595	G	A	17723595	3	1	23	1	0	0	0	0	1	0	0	0	15156	1116	39	1	3183	1	SREBF1	17	17723595	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	25572	17723595	63471615	609	8053											
MYO15A	51168	hgsc.bcm.edu	37	chr17	18058468	18058468	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcctctggtaacggaaagcGtgaagcgggccgtggtcagc	9	6	16	10	4	2	1	1	1	1	0	2	2	2	2	2	4	5	1	2	4	3	1	rs140140417	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:18058468G>A	ENST00000205890.5	+	46	8607	c.8269G>A	c.(8269-8271)Gtg>Atg	p.V2757M	MYO15A_ENST00000585180.1_Missense_Mutation_p.V21M|MYO15A_ENST00000418233.3_Missense_Mutation_p.V21M	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2757	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)					AACGGAAAGCGTGAAGCGGGC	0.642													G|||	11	0.00219649	0.0015	0.0058	5008	,	,		18941	0.0		0.002	False		,,,				2504	0.0031				p.V2757M		Atlas-SNP	.											.	MYO15A	268	.	0			c.G8269A						PASS	.	G	MET/VAL	0,4188		0,0,2094	41	51	47		8269	-0.2	0.3	17	dbSNP_134	47	18,8416		0,18,4199	yes	missense	MYO15A	NM_016239.3	21	0,18,6293	AA,AG,GG		0.2134,0.0,0.1426	probably-damaging	2757/3531	18058468	18,12604	2094	4217	6311	SO:0001583	missense	51168	exon45			GAAAGCGTGAAGC	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.8269G>A	17.37:g.18058468G>A	ENSP00000205890:p.Val2757Met	96	0	0		93	35	0.376344	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	6	0.0027472527472527475	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	2	0.002638522427440633	G	4.445	0.082431	0.08533	0.0	0.002134	ENSG00000091536	ENST00000205890	D	0.90788	-2.73	5.2	-0.241	0.13043	.	.	.	.	.	D	0.83709	0.5313	M	0.71206	2.165	0.39248	D	0.963971	B;B	0.29341	0.242;0.149	B;B	0.29663	0.105;0.01	T	0.80765	-0.1236	9	0.87932	D	0	.	6.7414	0.23439	0.2809:0.0:0.5946:0.1245	.	21;2757	B4DFC7;Q9UKN7	.;MYO15_HUMAN	M	2757	ENSP00000205890:V2757M	ENSP00000205890:V2757M	V	+	1	0	MYO15A	17999193	0.906000	0.30813	0.279000	0.24732	0.136000	0.21042	1.276000	0.33156	0.104000	0.17725	0.561000	0.74099	GTG	G|0.998;A|0.002	0.002	strong		0.642	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239		A	18058468	G	A	18058468	3	1	23	1	0	0	0	0	1	0	0	0	10072	1145	40	1	8443	1	MYO15A	17	18058468	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	334873	18058468	63136742	610	8054											
FLII	2314	hgsc.bcm.edu	37	chr17	18156957	18156957	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gtgatctggttgctgctgagGttgaggcggcgcaggctggg	4	10	20	7	2	1	3	0	3	1	0	1	3	1	3	0	6	2	6	0	6	0	2	rs147128917		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:18156957G>A	ENST00000327031.4	-	8	981	c.756C>T	c.(754-756)aaC>aaT	p.N252N	FLII_ENST00000584444.1_Intron|FLII_ENST00000379450.4_Silent_p.N167N|FLII_ENST00000579294.1_Silent_p.N241N|FLII_ENST00000578558.1_Silent_p.N252N|FLII_ENST00000545457.2_Silent_p.N198N	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	252	Interaction with LRRFIP1 and LRRFIP2.				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)					TGCTGCTGAGGTTGAGGCGGC	0.617													G|||	1	0.000199681	0.0	0.0	5008	,	,		19548	0.0		0.001	False		,,,				2504	0.0				p.N252N		Atlas-SNP	.											.	FLII	79	.	0			c.C756T						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	87	77	80		756	5.4	1	17	dbSNP_134	80	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	FLII	NM_002018.2		0,4,6499	AA,AG,GG		0.0233,0.0454,0.0308		252/1270	18156957	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	2314	exon8			GCTGAGGTTGAGG	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.756C>T	17.37:g.18156957G>A		128	0	0		171	75	0.438596	NM_002018	B4DIL0|F5H407|J3QLG3	Silent	SNP	ENST00000327031.4	37	CCDS11192.1																																																																																			G|0.999;A|0.001	0.001	strong		0.617	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132032.2	NM_002018		A	18156957	G	A	18156957	2	1	23	1	0	0	0	0	0	0	0	1	5933	1252	44	2		2	FLII	17	18156957	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	98489	18156957	63038253	611	8055											
KCNJ12	3768	hgsc.bcm.edu	37	chr17	21318826	21318826	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagtgcaacattgagttcGccaacatggacgagaagtca	13	7	11	10	2	1	2	1	1	0	1	2	4	1	3	2	1	3	2	2	1	3	2	rs142399667	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:21318826G>A	ENST00000583088.1	+	3	1067	c.172G>A	c.(172-174)Gcc>Acc	p.A58T	KCNJ12_ENST00000331718.5_Missense_Mutation_p.A58T	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	58					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)	CATTGAGTTCGCCAACATGGA	0.597										Prostate(3;0.18)																											p.A58T		Atlas-SNP	.											KCNJ12,NS,carcinoma,0,1	.	.	1	0			c.G172A						scavenged	.	G	THR/ALA	69,4337	52.3+/-87.9	0,69,2134	197	131	153		172	5.3	1	17	dbSNP_134	153	62,8538	26.8+/-75.7	0,62,4238	yes	missense	KCNJ12	NM_021012.4	58	0,131,6372	AA,AG,GG		0.7209,1.566,1.0072	benign	58/434	21318826	131,12875	2203	4300	6503	SO:0001583	missense	100134444	exon3			GAGTTCGCCAACA	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.172G>A	17.37:g.21318826G>A	ENSP00000463778:p.Ala58Thr	246	1	0.00406504		259	45	0.173745	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	37	CCDS11219.1	.	.	.	.	.	.	.	.	.	.	G	11.62	1.692589	0.30052	0.01566	0.007209	ENSG00000184185	ENST00000331718	D	0.93859	-3.3	5.33	5.33	0.75918	Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);	0.248894	0.40908	D	0.000997	T	0.77631	0.4159	N	0.16233	0.39	0.36661	D	0.877951	B	0.12630	0.006	B	0.18263	0.021	T	0.80009	-0.1562	10	0.32370	T	0.25	.	10.2342	0.43273	0.1224:0.0:0.8776:0.0	.	58	Q14500	IRK12_HUMAN	T	58	ENSP00000328150:A58T	ENSP00000328150:A58T	A	+	1	0	KCNJ12	21259419	0.993000	0.37304	1.000000	0.80357	0.988000	0.76386	2.230000	0.42999	2.506000	0.84524	0.591000	0.81541	GCC	G|0.993;A|0.007	0.007	strong		0.597	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012		A	21318826	G	A	21318826	3	1	23	1	0	0	0	0	1	0	0	0	8055	1087	38	1	174	1	KCNJ12	17	21318826	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	3161869	21318826	59876384	612	8056											
SPAG5	10615	hgsc.bcm.edu	37	chr17	26919344	26919344	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actagatttggtgtcaggcaTgtggacagaatatcttccac	11	12	10	8	0	2	2	1	0	1	2	3	3	3	3	1	3	0	1	1	3	3	4	rs113667723	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:26919344T>C	ENST00000321765.5	-	3	1250	c.918A>G	c.(916-918)acA>acG	p.T306T		NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	306					chromosome segregation (GO:0007059)|mitotic sister chromatid segregation (GO:0000070)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|microtubule plus-end (GO:0035371)|mitotic spindle (GO:0072686)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43	Lung NSC(42;0.00431)					GTGTCAGGCATGTGGACAGAA	0.453													T|||	15	0.00299521	0.0008	0.0058	5008	,	,		22177	0.0		0.0099	False		,,,				2504	0.0				p.T306T		Atlas-SNP	.											.	SPAG5	92	.	0			c.A918G						PASS	.	T		11,4395	15.5+/-35.6	0,11,2192	135	121	126		918	-1.2	0	17	dbSNP_132	126	111,8489	59.8+/-121.6	1,109,4190	no	coding-synonymous	SPAG5	NM_006461.3		1,120,6382	CC,CT,TT		1.2907,0.2497,0.938		306/1194	26919344	122,12884	2203	4300	6503	SO:0001819	synonymous_variant	10615	exon3			CAGGCATGTGGAC	AF063308	CCDS32594.1	17q11.2	2008-07-18			ENSG00000076382	ENSG00000076382			13452	protein-coding gene	gene with protein product	"mitotic spindle coiled-coil related protein", "astrin", "mitotic spindle associated protein p126"	615562				11549262	Standard	NM_006461		Approved	DEEPEST, MAP126, hMAP126	uc002hbq.3	Q96R06	OTTHUMG00000166586	ENST00000321765.5:c.918A>G	17.37:g.26919344T>C		103	0	0		124	64	0.516129	NM_006461	O95213|Q9BWE8|Q9NT17|Q9UFE6	Silent	SNP	ENST00000321765.5	37	CCDS32594.1																																																																																			T|0.992;C|0.008	0.008	strong		0.453	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461		C	26919344	T	C	26919344	2	2	23	1	0	0	0	0	0	0	0	1	14996	1451	51	3		3	SPAG5	17	26919344	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	5600518	26919344	54275866	613	8057											
RHBDL3	162494	hgsc.bcm.edu	37	chr17	30615883	30615883	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaggctaagcagcaaggccCtgctggaggagaaggggctg	10	4	18	9	0	0	1	0	0	0	1	0	3	0	2	1	6	3	6	1	6	3	1	rs150485822	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:30615883C>T	ENST00000269051.4	+	4	381	c.367C>T	c.(367-369)Ctg>Ttg	p.L123L	RHBDL3_ENST00000538145.1_Silent_p.L115L|RHBDL3_ENST00000536287.1_Silent_p.L25L	NM_138328.2	NP_612201.1	P58872	RHBL3_HUMAN	rhomboid, veinlet-like 3 (Drosophila)	123						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)				CAGCAAGGCCCTGCTGGAGGA	0.597																																					p.L123L		Atlas-SNP	.											.	RHBDL3	49	.	0			c.C367T						PASS	.	C		0,4406		0,0,2203	50	46	47		367	4.9	1	17	dbSNP_134	47	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	RHBDL3	NM_138328.2		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		123/405	30615883	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	162494	exon4			AAGGCCCTGCTGG	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.367C>T	17.37:g.30615883C>T		210	0	0		232	110	0.474138	NM_138328	A6NMH1|Q495Y4|Q495Y5|Q495Y6	Silent	SNP	ENST00000269051.4	37	CCDS32613.1																																																																																			C|1.000;T|0.000	0.000	strong		0.597	RHBDL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447120.1	NM_138328		T	30615883	C	T	30615883	2	4	23	1	0	0	0	0	0	0	0	1	13338	680	24	2		2	RHBDL3	17	30615883	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	3696539	30615883	50579327	614	8058											
ZNF207	7756	hgsc.bcm.edu	37	chr17	30689985	30689985	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccaggaataccacctctgAtgcctggaatgccaccaggt	11	7	10	13	0	1	1	0	1	1	0	1	4	1	3	6	3	3	0	6	3	3	1	rs140641814		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:30689985A>G	ENST00000321233.6	+	6	758	c.604A>G	c.(604-606)Atg>Gtg	p.M202V	ZNF207_ENST00000341711.6_Missense_Mutation_p.M119V|ZNF207_ENST00000577908.1_Missense_Mutation_p.M218V|ZNF207_ENST00000394670.4_Missense_Mutation_p.M218V|ZNF207_ENST00000342555.6_Missense_Mutation_p.M221V|RP11-227G15.3_ENST00000581915.1_RNA|ZNF207_ENST00000394673.2_Missense_Mutation_p.M218V	NM_003457.3	NP_003448.1	O43670	ZN207_HUMAN	zinc finger protein 207	202					attachment of spindle microtubules to kinetochore (GO:0008608)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|protein stabilization (GO:0050821)|regulation of chromosome segregation (GO:0051983)|regulation of transcription, DNA-templated (GO:0006355)	kinetochore (GO:0000776)|microtubule (GO:0005874)|nucleus (GO:0005634)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|lung(3)|urinary_tract(2)	10		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			ACCACCTCTGATGCCTGGAAT	0.363																																					p.M218V		Atlas-SNP	.											.	ZNF207	32	.	0			c.A652G						PASS	.	A	VAL/MET,VAL/MET,VAL/MET	0,4406		0,0,2203	111	108	109		652,652,604	5.7	1	17	dbSNP_134	109	1,8599		0,1,4299	no	missense,missense,missense	ZNF207	NM_001032293.2,NM_001098507.1,NM_003457.3	21,21,21	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign,benign,benign	218/464,218/495,202/479	30689985	1,13005	2203	4300	6503	SO:0001583	missense	7756	exon7			CCTCTGATGCCTG	AF046001	CCDS11271.1, CCDS32614.1, CCDS42294.1	17q11.2	2008-07-10			ENSG00000010244	ENSG00000010244		"Zinc fingers, C2H2-type"	12998	protein-coding gene	gene with protein product		603428				9799612	Standard	NM_001098507		Approved		uc002hhj.4	O43670	OTTHUMG00000132810	ENST00000321233.6:c.604A>G	17.37:g.30689985A>G	ENSP00000322777:p.Met202Val	74	0	0		56	31	0.553571	NM_001098507	A8K6Y6|E1P660|E1P661|E1P662|Q53XS9|Q96HW5|Q9BUQ7	Missense_Mutation	SNP	ENST00000321233.6	37	CCDS11271.1	.	.	.	.	.	.	.	.	.	.	A	3.923	-0.017677	0.07681	0.0	1.16E-4	ENSG00000010244	ENST00000394670;ENST00000394673;ENST00000394679;ENST00000321233;ENST00000341711;ENST00000342555	T;T;T	0.54279	0.95;0.88;0.58	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.46464	0.1394	L	0.50333	1.59	0.80722	D	1	B;B;B;B;B	0.24576	0.106;0.106;0.106;0.039;0.106	B;B;B;B;B	0.15484	0.013;0.013;0.013;0.013;0.013	T	0.38286	-0.9668	10	0.17369	T	0.5	.	16.0101	0.80396	1.0:0.0:0.0:0.0	.	202;221;218;218;202	A8MTG3;Q59G94;E1P660;O43670-2;O43670	.;.;.;.;ZN207_HUMAN	V	218;202;221;218;119;202	ENSP00000378165:M218V;ENSP00000378168:M202V;ENSP00000344913:M119V	ENSP00000322777:M218V	M	+	1	0	ZNF207	27714098	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.267000	0.78462	2.171000	0.68590	0.533000	0.62120	ATG	A|1.000;G|0.000	0.000	weak		0.363	ZNF207-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256251.2			G	30689985	A	G	30689985	3	3	23	1	0	0	0	0	1	0	0	0	17780	333	12	3	678	3	ZNF207	17	30689985	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	74102	30689985	50505225	615	8059											
GAS2L2	246176	hgsc.bcm.edu	37	chr17	34072031	34072031	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tactgaagctccatccacccGggatgcctcccctcccttgc	6	9	7	19	1	0	1	0	1	0	0	4	2	4	2	7	1	4	1	7	1	2	2	rs56386706	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:34072031G>A	ENST00000254466.6	-	6	2512	c.2485C>T	c.(2485-2487)Cgg>Tgg	p.R829W	GAS2L2_ENST00000587565.1_Missense_Mutation_p.R813W	NM_139285.3	NP_644814.1	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	829			R -> W (in dbSNP:rs56386706).		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)		CCATCCACCCGGGATGCCTCC	0.642													G|||	130	0.0259585	0.0045	0.0375	5008	,	,		17817	0.0		0.0626	False		,,,				2504	0.0358				p.R829W		Atlas-SNP	.											.	GAS2L2	94	.	0			c.C2485T						PASS	.	G	TRP/ARG	56,4350	54.9+/-90.9	0,56,2147	56	60	59		2485	0.3	0	17	dbSNP_129	59	471,8129	138.3+/-195.1	9,453,3838	yes	missense	GAS2L2	NM_139285.3	101	9,509,5985	AA,AG,GG		5.4767,1.271,4.052	possibly-damaging	829/881	34072031	527,12479	2203	4300	6503	SO:0001583	missense	246176	exon6			CCACCCGGGATGC	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.2485C>T	17.37:g.34072031G>A	ENSP00000254466:p.Arg829Trp	96	0	0		104	51	0.490385	NM_139285	Q8NHY4	Missense_Mutation	SNP	ENST00000254466.6	37	CCDS11298.1	57	0.0260989010989011	5	0.01016260162601626	11	0.03038674033149171	0	0.0	41	0.05408970976253298	G	11.13	1.547655	0.27652	0.01271	0.054767	ENSG00000132139	ENST00000254466;ENST00000359507	T	0.18810	2.19	3.57	0.351	0.16042	.	3.764050	0.01567	N	0.020407	T	0.01287	0.0042	N	0.08118	0	0.09310	N	1	D	0.53885	0.963	B	0.34452	0.183	T	0.14200	-1.0481	10	0.66056	D	0.02	6.0647	4.358	0.11188	0.2131:0.3724:0.4144:0.0	rs56386706	829	Q8NHY3	GA2L2_HUMAN	W	829;243	ENSP00000254466:R829W	ENSP00000254466:R829W	R	-	1	2	GAS2L2	31096144	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.218000	0.17622	0.131000	0.18576	-0.304000	0.09214	CGG	G|0.964;A|0.036	0.036	strong		0.642	GAS2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256497.1	NM_139285		A	34072031	G	A	34072031	3	1	23	1	0	0	0	0	1	0	0	0	6255	1115	39	1	161	1	GAS2L2	17	34072031	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	3382046	34072031	47123179	616	8060											
DHRS11	79154	hgsc.bcm.edu	37	chr17	34951481	34951481	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacctatcaaatgaagaggaCatcctctccatgttctcagc	12	10	7	12	0	3	2	2	1	2	1	6	4	4	3	3	1	1	1	3	1	3	2	rs73993036	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:34951481C>T	ENST00000251312.5	+	2	440	c.228C>T	c.(226-228)gaC>gaT	p.D76D	DHRS11_ENST00000590554.1_5'UTR|DHRS11_ENST00000394445.1_3'UTR	NM_024308.3	NP_077284.2	Q6UWP2	DHR11_HUMAN	dehydrogenase/reductase (SDR family) member 11	76						extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			endometrium(1)|lung(4)	5						ATGAAGAGGACATCCTCTCCA	0.537													C|||	104	0.0207668	0.0734	0.0101	5008	,	,		20188	0.0		0.0	False		,,,				2504	0.0				p.D76D		Atlas-SNP	.											.	DHRS11	10	.	0			c.C228T						PASS	.	C		278,4128	154.4+/-187.8	10,258,1935	146	126	133		228	3.7	1	17	dbSNP_130	133	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	DHRS11	NM_024308.3		10,261,6232	TT,TC,CC		0.0349,6.3096,2.1605		76/261	34951481	281,12725	2203	4300	6503	SO:0001819	synonymous_variant	79154	exon2			AGAGGACATCCTC		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	ENST00000251312.5:c.228C>T	17.37:g.34951481C>T		138	0	0		123	65	0.528455	NM_024308	B2RDZ3|Q9BUC7|Q9H674	Silent	SNP	ENST00000251312.5	37	CCDS11315.2																																																																																			C|0.977;T|0.023	0.023	strong		0.537	DHRS11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256681.2	NM_024308		T	34951481	C	T	34951481	2	4	23	1	0	0	0	0	0	0	0	1	4489	477	17	2		2	DHRS11	17	34951481	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	879450	34951481	46243729	617	8061											
ERBB2	2064	hgsc.bcm.edu	37	chr17	37879588	37879588	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagccctctgacgtccatcAtctctgcggtggttggcatt	5	12	10	14	2	3	1	1	1	2	0	5	1	4	1	3	3	2	2	3	3	0	2	rs1136201	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:37879588A>G	ENST00000269571.5	+	17	2122	c.1963A>G	c.(1963-1965)Atc>Gtc	p.I655V	ERBB2_ENST00000406381.2_Missense_Mutation_p.I625V|ERBB2_ENST00000540147.1_Missense_Mutation_p.I625V|ERBB2_ENST00000445658.2_Missense_Mutation_p.I379V|ERBB2_ENST00000584601.1_Missense_Mutation_p.I625V|ERBB2_ENST00000541774.1_Missense_Mutation_p.I640V|ERBB2_ENST00000584450.1_Missense_Mutation_p.I655V			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	655			I -> V (in allele B2 and allele B3; dbSNP:rs1136201). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:8095488, ECO:0000269|Ref.3}.		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)	GACGTCCATCATCTCTGCGGT	0.612		1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)			A|||	608	0.121406	0.0098	0.1369	5008	,	,		13960	0.124		0.2455	False		,,,				2504	0.1309				p.I655V		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.A1963G	GRCh37	CM004332	ERBB2	M	rs1136201	PASS	.	A	VAL/ILE,VAL/ILE	212,4194	132.1+/-168.6	5,202,1996	113	103	106	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1873,1963	5	1	17	dbSNP_86	106	1980,6620	346.8+/-326.3	223,1534,2543	yes	missense,missense	ERBB2	NM_001005862.1,NM_004448.2	29,29	228,1736,4539	GG,GA,AA		23.0233,4.8116,16.8538	benign,benign	625/1226,655/1256	37879588	2192,10814	2203	4300	6503	SO:0001583	missense	2064	exon17			TCCATCATCTCTG	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.1963A>G	17.37:g.37879588A>G	ENSP00000269571:p.Ile655Val	249	0	0		238	93	0.390756	NM_004448	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	37	CCDS32642.1	339	0.15521978021978022	5	0.01016260162601626	58	0.16022099447513813	83	0.1451048951048951	193	0.2546174142480211	A	13.67	2.306999	0.40795	0.048116	0.230233	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147	T;T;T;T;T	0.76316	-1.01;-1.01;-0.99;-1.01;-1.01	4.97	4.97	0.65823	Cytochrome c1, transmembrane anchor, C-terminal (1);	.	.	.	.	T	0.00039	0.0001	N	0.25485	0.75	0.09310	P	1.0	B;P;B	0.39576	0.406;0.679;0.406	B;B;B	0.37650	0.108;0.255;0.108	T	0.05920	-1.0856	8	0.22706	T	0.39	.	8.987	0.35999	0.9164:0.0:0.0836:0.0	rs1136201;rs1801200;rs2006406;rs2230699;rs17606815;rs59955961;rs1801200	379;640;655	B4DTR1;P04626-4;P04626	.;.;ERBB2_HUMAN	V	625;640;379;655;625	ENSP00000385185:I625V;ENSP00000446466:I640V;ENSP00000404047:I379V;ENSP00000269571:I655V;ENSP00000443562:I625V	ENSP00000269571:I655V	I	+	1	0	ERBB2	35133114	1.000000	0.71417	0.995000	0.50966	0.892000	0.51952	4.008000	0.57103	1.880000	0.54463	0.459000	0.35465	ATC	A|0.845;G|0.155;N|0.000;T|0.000	0.155	strong		0.612	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			G	37879588	A	G	37879588	3	3	23	1	0	0	0	0	1	0	0	0	5208	217	8	3	2029	3	ERBB2	17	37879588	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	2928107	37879588	43315622	618	8062											
KRT25	147183	hgsc.bcm.edu	37	chr17	38910676	38910676	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gctgtaagcctggcattatcGatctgcagaacagcattagc	11	10	10	10	1	1	1	0	0	1	1	2	2	1	1	1	1	5	5	1	1	4	3	rs146092638	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:38910676G>C	ENST00000312150.4	-	2	534	c.474C>G	c.(472-474)atC>atG	p.I158M		NM_181534.3	NP_853512.1			keratin 25											endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(4)	16		Breast(137;0.00526)				TGGCATTATCGATCTGCAGAA	0.388																																					p.I158M		Atlas-SNP	.											.	KRT25	63	.	0			c.C474G						PASS	.	G	MET/ILE	0,4406		0,0,2203	137	130	133		474	-1.5	1	17	dbSNP_134	133	2,8598	2.2+/-6.3	0,2,4298	no	missense	KRT25	NM_181534.3	10	0,2,6501	CC,CG,GG		0.0233,0.0,0.0154	possibly-damaging	158/451	38910676	2,13004	2203	4300	6503	SO:0001583	missense	147183	exon2			ATTATCGATCTGC	AK129503	CCDS11373.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000204897	ENSG00000204897		"-", "Intermediate filaments type I, keratins (acidic)"	30839	protein-coding gene	gene with protein product			"keratin 25A"	KRT25A		16831889	Standard	NM_181534		Approved		uc002hve.3	Q7Z3Z0	OTTHUMG00000133373	ENST00000312150.4:c.474C>G	17.37:g.38910676G>C	ENSP00000310573:p.Ile158Met	141	0	0		145	56	0.386207	NM_181534		Missense_Mutation	SNP	ENST00000312150.4	37	CCDS11373.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.305005	0.60305	0.0	2.33E-4	ENSG00000204897	ENST00000394042;ENST00000312150	D	0.89810	-2.57	5.73	-1.51	0.08664	Filament (1);	0.088817	0.49305	D	0.000153	D	0.92760	0.7698	M	0.84156	2.68	0.39210	D	0.963294	D	0.67145	0.996	D	0.66196	0.942	D	0.91638	0.5324	10	0.72032	D	0.01	.	11.8009	0.52126	0.6185:0.0:0.3815:0.0	.	158	Q7Z3Z0	K1C25_HUMAN	M	158	ENSP00000310573:I158M	ENSP00000310573:I158M	I	-	3	3	KRT25	36164202	0.036000	0.19791	0.972000	0.41901	0.900000	0.52787	-0.494000	0.06451	-0.516000	0.06470	-0.136000	0.14681	ATC	A|0.000;C|0.000;G|1.000	0.000	strong		0.388	KRT25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257218.1	NM_181534		C	38910676	G	C	38910676	3	2	23	1	0	0	0	0	1	0	0	0	8471	1048	37	4	906	4	KRT25	17	38910676	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1031088	38910676	42284534	619	8063											
KRTAP1-1	81851	hgsc.bcm.edu	37	chr17	39197485	39197485	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgagaagctaggaaatccAcagaagctggtctggcagca	13	7	13	8	0	1	2	0	1	1	2	2	4	2	3	1	3	3	5	1	3	4	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:39197485A>G	ENST00000306271.4	-	1	228	c.165T>C	c.(163-165)tgT>tgC	p.C55C		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	55			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)			TAGGAAATCCACAGAAGCTGG	0.602																																					p.C55C		Atlas-SNP	.											.	KRTAP1-1	23	.	0			c.T165C						PASS	.						83	92	89					17																	39197485		2026	4210	6236	SO:0001819	synonymous_variant	81851	exon1			AAATCCACAGAAG	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.165T>C	17.37:g.39197485A>G		180	0	0		196	24	0.122449	NM_030967	A6NC32|Q96S60|Q96S67	Silent	SNP	ENST00000306271.4	37	CCDS42324.1																																																																																			.	.	none		0.602	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967		G	39197485	A	G	39197485	2	3	23	1	0	0	0	0	0	0	0	1	8511	157	6	3		3	KRTAP1-1	17	39197485	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	286809	39197485	41997725	620	8064											
HSD17B1	3292	hgsc.bcm.edu	37	chr17	40706596	40706596	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagaaccctgaggaggtggCggaggtgagcgccgggctgg	7	4	21	9	3	0	3	0	2	0	1	0	5	0	5	2	7	2	2	2	7	1	0	rs147402365	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:40706596C>T	ENST00000585807.1	+	5	4433	c.713C>T	c.(712-714)gCg>gTg	p.A238V	RP11-400F19.8_ENST00000585572.1_RNA|HSD17B1_ENST00000225929.5_Missense_Mutation_p.A239V|RP11-400F19.6_ENST00000590513.1_RNA	NM_000413.2	NP_000404.2	P14061	DHB1_HUMAN	hydroxysteroid (17-beta) dehydrogenase 1	238			A -> V. {ECO:0000269|PubMed:8389226}.		bone development (GO:0060348)|cellular response to metal ion (GO:0071248)|estrogen biosynthetic process (GO:0006703)|estrogen metabolic process (GO:0008210)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|estradiol 17-beta-dehydrogenase activity (GO:0004303)			NS(1)|endometrium(1)|kidney(1)|lung(2)	5		all_cancers(22;5.59e-08)|all_epithelial(22;7e-07)|Ovarian(249;0.0261)		BRCA - Breast invasive adenocarcinoma(366;0.129)	Equilin(DB02187)	GAGGAGGTGGCGGAGGTGAGC	0.687													C|||	14	0.00279553	0.0008	0.0	5008	,	,		12600	0.0		0.0129	False		,,,				2504	0.0				p.A238V		Atlas-SNP	.											.	HSD17B1	24	.	0			c.C713T						PASS	.	C	VAL/ALA	9,4395	15.5+/-35.6	0,9,2193	39	31	34		713	-0.4	0	17	dbSNP_134	34	70,8530	42.2+/-99.7	0,70,4230	yes	missense	HSD17B1	NM_000413.2	64	0,79,6423	TT,TC,CC		0.814,0.2044,0.6075	benign	238/329	40706596	79,12925	2202	4300	6502	SO:0001583	missense	3292	exon5			AGGTGGCGGAGGT		CCDS11428.1	17q11-q21	2011-09-14					1.1.1.62	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	5210	protein-coding gene	gene with protein product	"Estradiol 17-beta-dehydrogenase-1", "short chain dehydrogenase/reductase family 28CE, member 1"	109684		EDHB17, EDH17B2		2330005, 19027726	Standard	NM_000413		Approved	HSD17, MGC138140, SDR28C1	uc002hzw.3	P14061		ENST00000585807.1:c.713C>T	17.37:g.40706596C>T	ENSP00000466799:p.Ala238Val	29	0	0		36	16	0.444444	NM_000413	B3KXS1|Q2M2L8	Missense_Mutation	SNP	ENST00000585807.1	37	CCDS11428.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	C	8.655	0.899159	0.17686	0.002044	0.00814	ENSG00000108786	ENST00000225929	.	.	.	4.16	-0.383	0.12477	NAD(P)-binding domain (1);	1.163550	0.06218	N	0.686122	T	0.07503	0.0189	N	0.04636	-0.2	0.09310	N	1	B;P	0.41102	0.002;0.738	B;B	0.28553	0.002;0.091	T	0.15065	-1.0450	9	0.30854	T	0.27	.	6.1916	0.20528	0.0:0.5144:0.0:0.4856	.	269;238	B3RFR9;P14061	.;DHB1_HUMAN	V	238	.	ENSP00000225929:A238V	A	+	2	0	HSD17B1	37960122	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	0.067000	0.14510	0.095000	0.17434	-0.658000	0.03865	GCG	C|0.996;T|0.004	0.004	strong		0.687	HSD17B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450392.1	NM_000413		T	40706596	C	T	40706596	3	4	23	1	0	0	0	0	1	0	0	0	7387	768	27	1	731	1	HSD17B1	17	40706596	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1509111	40706596	40488614	621	8065											
SLC4A1	6521	hgsc.bcm.edu	37	chr17	42327847	42327847	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacacaggcatggccacttcGtcgtattcatcccgaccttc	8	10	7	16	3	1	0	1	0	0	0	5	1	2	0	3	2	0	2	3	2	1	4	rs377326869		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:42327847G>C	ENST00000262418.6	-	20	2870	c.2715C>G	c.(2713-2715)gaC>gaG	p.D905E	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)	905	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)		TGGCCACTTCGTCGTATTCAT	0.592																																					p.D905E		Atlas-SNP	.											.	SLC4A1	104	.	0			c.C2715G						PASS	.						109	75	86					17																	42327847		2203	4300	6503	SO:0001583	missense	6521	exon20			CACTTCGTCGTAT		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.2715C>G	17.37:g.42327847G>C	ENSP00000262418:p.Asp905Glu	45	0	0		51	26	0.509804	NM_000342	G4V2I6|P78487|Q1ZZ45|Q4KKW9|Q4VB84|Q9UCY7|Q9UDJ1	Missense_Mutation	SNP	ENST00000262418.6	37	CCDS11481.1	.	.	.	.	.	.	.	.	.	.	G	1.789	-0.479900	0.04383	.	.	ENSG00000004939	ENST00000262418	T	0.73363	-0.74	4.91	-5.15	0.02866	.	0.251137	0.30649	N	0.009173	T	0.58352	0.2116	L	0.40543	1.245	0.30038	N	0.81285	B	0.10296	0.003	B	0.08055	0.003	T	0.46076	-0.9217	10	0.20046	T	0.44	.	13.9273	0.63970	0.7677:0.0:0.2323:0.0	.	905	P02730	B3AT_HUMAN	E	905	ENSP00000262418:D905E	ENSP00000262418:D905E	D	-	3	2	SLC4A1	39683373	0.000000	0.05858	0.009000	0.14445	0.005000	0.04900	-1.941000	0.01542	-0.728000	0.04882	-0.224000	0.12420	GAC	.	.	alt		0.592	SLC4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346194.1	NM_000342		C	42327847	G	C	42327847	3	2	23	1	0	0	0	0	1	0	0	0	14665	1136	40	4	24	4	SLC4A1	17	42327847	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1621251	42327847	38867363	622	8066											
GPATCH8	23131	hgsc.bcm.edu	37	chr17	42477385	42477385	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagccttgtgtttacgtttgTgtttgctggattttttgtgc	3	21	11	6	1	0	0	0	0	0	0	0	1	0	1	1	1	4	4	1	1	1	8	rs61744303	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:42477385T>C	ENST00000591680.1	-	8	2090	c.2060A>G	c.(2059-2061)cAc>cGc	p.H687R	GPATCH8_ENST00000434000.1_Missense_Mutation_p.H609R	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	687	Lys-rich.						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)		TTTACGTTTGTGTTTGCTGGA	0.443													T|||	18	0.00359425	0.0	0.0058	5008	,	,		20906	0.0		0.0139	False		,,,				2504	0.0				p.H687R		Atlas-SNP	.											.	GPATCH8	114	.	0			c.A2060G						PASS	.	T	ARG/HIS	19,4387	26.2+/-53.5	0,19,2184	240	240	240		2060	5.1	1	17	dbSNP_129	240	130,8470	67.0+/-129.4	0,130,4170	yes	missense	GPATCH8	NM_001002909.2	29	0,149,6354	CC,CT,TT		1.5116,0.4312,1.1456	benign	687/1503	42477385	149,12857	2203	4300	6503	SO:0001583	missense	23131	exon8			CGTTTGTGTTTGC	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.2060A>G	17.37:g.42477385T>C	ENSP00000467556:p.His687Arg	140	0	0		153	63	0.411765	NM_001002909	B9EGP9|O60300|Q8TB99	Missense_Mutation	SNP	ENST00000591680.1	37	CCDS32666.1	11	0.005036630036630037	0	0.0	0	0.0	0	0.0	11	0.014511873350923483	T	6.634	0.485507	0.12641	0.004312	0.015116	ENSG00000186566	ENST00000335500;ENST00000434000	T	0.02258	4.37	5.11	5.11	0.69529	.	0.096415	0.64402	D	0.000001	T	0.00845	0.0028	N	0.17082	0.46	0.39216	D	0.963406	B	0.24920	0.114	B	0.24974	0.057	T	0.60047	-0.7339	10	0.16420	T	0.52	-16.2378	9.5574	0.39348	0.0:0.0782:0.0:0.9218	.	687	Q9UKJ3	GPTC8_HUMAN	R	687;609	ENSP00000395016:H609R	ENSP00000335486:H687R	H	-	2	0	GPATCH8	39832911	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	2.849000	0.48286	2.156000	0.67533	0.402000	0.26972	CAC	T|0.989;C|0.011	0.011	strong		0.443	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457797.1	NM_001002909		C	42477385	T	C	42477385	3	2	23	1	0	0	0	0	1	0	0	0	6602	1696	59	3	2452	3	GPATCH8	17	42477385	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	149538	42477385	38717825	623	8067											
B4GALNT2	124872	hgsc.bcm.edu	37	chr17	47246956	47246956	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgattataggtcaccagtctCggtctccagtggtggactca	8	12	11	10	1	4	1	2	1	2	0	6	2	4	2	2	4	0	0	2	4	2	2	rs61743617	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:47246956C>T	ENST00000300404.2	+	11	1626	c.1567C>T	c.(1567-1569)Cgg>Tgg	p.R523W	B4GALNT2_ENST00000504681.1_Missense_Mutation_p.R437W|B4GALNT2_ENST00000393354.2_Missense_Mutation_p.R463W|RP11-708H21.4_ENST00000575159.1_lincRNA	NM_153446.2	NP_703147.2	Q8NHY0	B4GN2_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 2	523					lipid glycosylation (GO:0030259)|negative regulation of cell-cell adhesion (GO:0022408)|protein glycosylation (GO:0006486)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)			endometrium(3)|large_intestine(6)|liver(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	24			all cancers(6;0.000316)			TCACCAGTCTCGGTCTCCAGT	0.542													C|||	24	0.00479233	0.0008	0.0101	5008	,	,		20911	0.0		0.0129	False		,,,				2504	0.0031				p.R523W	GBM(124;244 1635 8663 18097 33175)	Atlas-SNP	.											.	B4GALNT2	67	.	0			c.C1567T						PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG	12,4394	19.1+/-41.9	0,12,2191	96	93	94		1387,1309,1567	2.5	0	17	dbSNP_129	94	130,8470	67.3+/-129.8	0,130,4170	yes	missense,missense,missense	B4GALNT2	NM_001159387.1,NM_001159388.1,NM_153446.2	101,101,101	0,142,6361	TT,TC,CC		1.5116,0.2724,1.0918	probably-damaging,probably-damaging,probably-damaging	463/507,437/481,523/567	47246956	142,12864	2203	4300	6503	SO:0001583	missense	124872	exon11			CAGTCTCGGTCTC	AJ517770	CCDS11544.1, CCDS54139.1, CCDS54140.1	17q21.33	2013-02-22	2006-01-08	2006-01-08	ENSG00000167080	ENSG00000167080	2.4.1.-	"Beta 4-glycosyltransferases", "Glycosyltransferase family 2 domain containing"	24136	protein-coding gene	gene with protein product		111730	"UDP-GalNAc:Neu5Acalpha2-3Galbeta-R beta1,4-N-acetylgalactosaminyltransferase"	GALGT2		8782649, 12678917	Standard	NM_153446		Approved	Sda, Cad	uc002ion.2	Q8NHY0	OTTHUMG00000161307	ENST00000300404.2:c.1567C>T	17.37:g.47246956C>T	ENSP00000300404:p.Arg523Trp	44	0	0		29	19	0.655172	NM_153446	B4DZE4|Q14CP1|Q86Y40	Missense_Mutation	SNP	ENST00000300404.2	37	CCDS11544.1	13	0.005952380952380952	0	0.0	4	0.011049723756906077	0	0.0	9	0.011873350923482849	C	17.61	3.432031	0.62844	0.002724	0.015116	ENSG00000167080	ENST00000504681;ENST00000393354;ENST00000300404	T;T;T	0.22743	1.94;1.94;1.94	5.79	2.47	0.30058	.	0.829068	0.10702	N	0.643916	T	0.14141	0.0342	L	0.50333	1.59	0.09310	N	1	D;D	0.69078	0.996;0.997	P;P	0.50231	0.635;0.543	T	0.07481	-1.0770	10	0.66056	D	0.02	-1.4776	7.8032	0.29187	0.3935:0.5316:0.0:0.0749	rs61743617	463;523	Q8NHY0-2;Q8NHY0	.;B4GN2_HUMAN	W	437;463;523	ENSP00000425510:R437W;ENSP00000377022:R463W;ENSP00000300404:R523W	ENSP00000300404:R523W	R	+	1	2	B4GALNT2	44601955	0.000000	0.05858	0.000000	0.03702	0.178000	0.23041	0.599000	0.24089	0.757000	0.33036	0.561000	0.74099	CGG	C|0.989;T|0.011	0.011	strong		0.542	B4GALNT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364477.1	NM_153446		T	47246956	C	T	47246956	3	4	23	1	0	0	0	0	1	0	0	0	1267	875	31	1	1627	1	B4GALNT2	17	47246956	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	4769571	47246956	33948254	624	8068											
MTMR4	9110	hgsc.bcm.edu	37	chr17	56585593	56585593	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tccagctctttgtcagtgatCcacacaggaaccagcagctt	10	10	8	13	0	2	1	1	1	1	0	4	2	4	2	3	1	4	3	3	1	1	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:56585593C>T	ENST00000323456.5	-	8	718	c.594G>A	c.(592-594)tgG>tgA	p.W198*	MTMR4_ENST00000579925.1_Nonsense_Mutation_p.W198*	NM_004687.4	NP_004678.3	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	198	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)					TGTCAGTGATCCACACAGGAA	0.557																																					p.W198X		Atlas-SNP	.											.	MTMR4	91	.	0			c.G594A						PASS	.						79	74	75					17																	56585593		2203	4300	6503	SO:0001587	stop_gained	9110	exon8			AGTGATCCACACA	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.594G>A	17.37:g.56585593C>T	ENSP00000325285:p.Trp198*	35	0	0		42	4	0.0952381	NM_004687	D3DTZ6|Q8IV27|Q9Y4D5	Nonsense_Mutation	SNP	ENST00000323456.5	37	CCDS11608.1	.	.	.	.	.	.	.	.	.	.	C	36	5.881577	0.97062	.	.	ENSG00000108389	ENST00000323456	.	.	.	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.8095	0.92053	0.0:1.0:0.0:0.0	.	.	.	.	X	198	.	ENSP00000325285:W198X	W	-	3	0	MTMR4	53940592	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.942000	0.70203	2.775000	0.95449	0.650000	0.86243	TGG	.	.	none		0.557	MTMR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444721.1	NM_004687		T	56585593	C	T	56585593	4	4	23	1	0	0	0	0	0	1	0	0	9955	856	30	2	3041	2	MTMR4	17	56585593	Nonsense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	9338637	56585593	24609617	625	8069											
BRIP1	83990	hgsc.bcm.edu	37	chr17	59761336	59761336	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aggcactattctctgatgacCcgagctcaggtgttgccttc	7	12	10	12	1	2	2	1	2	1	0	4	3	2	2	2	2	2	3	2	2	1	4	rs587781744		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:59761336C>A	ENST00000259008.2	-	20	3338	c.3071G>T	c.(3070-3072)gGg>gTg	p.G1024V		NM_032043.2	NP_114432.2	Q9BX63	FANCJ_HUMAN	BRCA1 interacting protein C-terminal helicase 1	1024	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						CTCTGATGACCCGAGCTCAGG	0.403			"F, N, Mis"			"AML, leukemia, breast"		Involved in tolerance or repair of DNA crosslinks																													p.G1024V		Atlas-SNP	.	yes	Rec		"Fanconi anaemia J, breast cancer susceptiblity"	17	17q22	83990	BRCA1 interacting protein C-terminal helicase 1		"L, E"	BRIP1_ENST00000259008,NS,carcinoma,-1,4	BRIP1	237	4	0			c.G3071T						scavenged	.						114	109	110					17																	59761336		2203	4300	6503	SO:0001583	missense	83990	exon20			GATGACCCGAGCT	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.3071G>T	17.37:g.59761336C>A	ENSP00000259008:p.Gly1024Val	111	1	0.00900901		128	58	0.453125	NM_032043	Q3MJE2|Q8NCI5	Missense_Mutation	SNP	ENST00000259008.2	37	CCDS11631.1	.	.	.	.	.	.	.	.	.	.	C	2.733	-0.263935	0.05754	.	.	ENSG00000136492	ENST00000259008	T	0.73681	-0.77	5.33	2.23	0.28157	.	1.080930	0.06971	N	0.818190	T	0.56673	0.2001	N	0.14661	0.345	0.09310	N	1	B	0.14438	0.01	B	0.17722	0.019	T	0.40720	-0.9548	9	.	.	.	-0.8307	7.1819	0.25778	0.0:0.7123:0.0:0.2877	.	1024	Q9BX63	FANCJ_HUMAN	V	1024	ENSP00000259008:G1024V	.	G	-	2	0	BRIP1	57116118	0.000000	0.05858	0.016000	0.15963	0.065000	0.16274	-0.987000	0.03743	0.316000	0.23135	-0.145000	0.13849	GGG	.	.	none		0.403	BRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445362.1	NM_032043		A	59761336	C	A	59761336	3	1	23	1	0	0	0	0	1	0	0	0	1516	623	22	4	682	4	BRIP1	17	59761336	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	3175743	59761336	21433874	626	8070											
MED13	9969	hgsc.bcm.edu	37	chr17	60038404	60038404	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgtctgtttgtccttcacTggagccagaataaaaggagg	10	12	11	8	0	3	1	1	0	2	1	4	3	4	3	2	3	1	1	2	3	3	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:60038404T>C	ENST00000397786.2	-	23	5380	c.5304A>G	c.(5302-5304)ccA>ccG	p.P1768P		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1768					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						TGTCCTTCACTGGAGCCAGAA	0.338																																					p.P1768P		Atlas-SNP	.											MED13,NS,carcinoma,-1,1	MED13	181	1	0			c.A5304G						PASS	.						112	97	102					17																	60038404		1828	4074	5902	SO:0001819	synonymous_variant	9969	exon23			CTTCACTGGAGCC	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.5304A>G	17.37:g.60038404T>C		102	0	0		102	52	0.509804	NM_005121	B2RU05|O60334	Silent	SNP	ENST00000397786.2	37	CCDS42366.1																																																																																			.	.	none		0.338	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121		C	60038404	T	C	60038404	2	2	23	1	0	0	0	0	0	0	0	1	9439	1567	55	3		3	MED13	17	60038404	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	277068	60038404	21156806	627	8071											
METTL2A	339175	hgsc.bcm.edu	37	chr17	60525113	60525113	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggtgatggaaccagagtttActtcttcacacaaggtatga	13	11	10	7	0	2	3	1	2	1	1	2	4	2	4	1	3	2	2	1	3	4	5			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:60525113A>C	ENST00000311506.5	+	8	1004	c.968A>C	c.(967-969)tAc>tCc	p.Y323S		NM_181725.3	NP_859076.3	Q96IZ6	MET2A_HUMAN	methyltransferase like 2A	323					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)			ACCAGAGTTTACTTCTTCACA	0.408																																					p.Y323S		Atlas-SNP	.											.	METTL2A	31	.	0			c.A968C						PASS	.						268	272	271					17																	60525113		2203	4300	6503	SO:0001583	missense	339175	exon8			GAGTTTACTTCTT	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.968A>C	17.37:g.60525113A>C	ENSP00000309610:p.Tyr323Ser	268	1	0.00373134		274	134	0.489051	NM_181725	A6NNC4|Q9H9G9|Q9NUI8|Q9P0B5	Missense_Mutation	SNP	ENST00000311506.5	37	CCDS45752.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.102365	0.76983	.	.	ENSG00000087995	ENST00000311506	T	0.11821	2.74	4.26	4.26	0.50523	.	0.056321	0.64402	D	0.000001	T	0.50137	0.1598	H	0.97415	4	0.80722	D	1	D	0.69078	0.997	D	0.74348	0.983	T	0.66590	-0.5885	10	0.87932	D	0	-0.4554	11.69	0.51510	1.0:0.0:0.0:0.0	.	323	Q96IZ6	MTL2A_HUMAN	S	323	ENSP00000309610:Y323S	ENSP00000309610:Y323S	Y	+	2	0	METTL2A	57878845	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	8.901000	0.92560	1.712000	0.51347	0.397000	0.26171	TAC	.	.	none		0.408	METTL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445130.1	NM_181725		C	60525113	A	C	60525113	3	2	23	1	0	0	0	0	1	0	0	0	9508	391	14	5	998	5	METTL2A	17	60525113	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	486709	60525113	20670097	628	8072											
AXIN2	8313	hgsc.bcm.edu	37	chr17	63532528	63532528	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtggggtcaggggaggcatcGcagggtcctgggtgaacagg	7	6	21	7	1	1	1	1	1	0	0	3	2	2	2	1	8	1	2	1	8	1	0	rs138287857	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:63532528G>A	ENST00000375702.5	-	6	1964	c.1856C>T	c.(1855-1857)gCg>gTg	p.A619V	AXIN2_ENST00000307078.5_Missense_Mutation_p.A684V			Q9Y2T1	AXIN2_HUMAN	axin 2	668				Missing (in Ref. 2; AAF22799). {ECO:0000305}.	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						GGGAGGCATCGCAGGGTCCTG	0.687									Oligodontia, Ectodermal Dysplasia and Colorectal Polyp syndrome				G|||	2	0.000399361	0.0	0.0	5008	,	,		15448	0.0		0.002	False		,,,				2504	0.0				p.A684V		Atlas-SNP	.											.	AXIN2	92	.	0			c.C2051T						PASS	.	G	VAL/ALA	3,4399	6.2+/-15.9	0,3,2198	24	26	25		2051	4.4	0.8	17	dbSNP_134	25	15,8585	10.5+/-38.8	0,15,4285	yes	missense	AXIN2	NM_004655.3	64	0,18,6483	AA,AG,GG		0.1744,0.0682,0.1384	possibly-damaging	684/844	63532528	18,12984	2201	4300	6501	SO:0001583	missense	8313	exon8	Familial Cancer Database	Oligodontia-Colorectal Cancer syndrome, Tooth Agenesis-Colorectal Cancer Syndrome	GGCATCGCAGGGT	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.1856C>T	17.37:g.63532528G>A	ENSP00000364854:p.Ala619Val	146	0	0		124	68	0.548387	NM_004655	Q3MJ88|Q9H3M6|Q9UH84	Missense_Mutation	SNP	ENST00000375702.5	37		.	.	.	.	.	.	.	.	.	.	G	22.6	4.307951	0.81247	6.82E-4	0.001744	ENSG00000168646	ENST00000307078;ENST00000375702	T;T	0.66280	-0.2;-0.18	5.41	4.37	0.52481	.	0.262657	0.43579	D	0.000560	T	0.57388	0.2050	L	0.48642	1.525	0.46260	D	0.998951	P;P	0.52061	0.95;0.923	B;B	0.40782	0.298;0.34	T	0.66818	-0.5827	10	0.66056	D	0.02	-11.6392	17.7442	0.88415	0.0:0.1327:0.8673:0.0	.	684;619	Q9Y2T1;E7ES00	AXIN2_HUMAN;.	V	684;619	ENSP00000302625:A684V;ENSP00000364854:A619V	ENSP00000302625:A684V	A	-	2	0	AXIN2	60962990	1.000000	0.71417	0.795000	0.32087	0.951000	0.60555	7.302000	0.78861	2.516000	0.84829	0.650000	0.86243	GCG	G|0.998;A|0.002	0.002	strong		0.687	AXIN2-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000445901.1	NM_004655		A	63532528	G	A	63532528	3	1	23	1	0	0	0	0	1	0	0	0	1237	1087	38	1	496	1	AXIN2	17	63532528	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	3007415	63532528	17662682	629	8073											
CD300LB	124599	hgsc.bcm.edu	37	chr17	72521967	72521967	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accagtaaacatctgcgtcaTctcgcctgagcccctccatg	9	9	7	16	2	3	1	1	1	2	0	5	1	4	1	5	0	3	1	5	0	2	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:72521967T>C	ENST00000392621.1	-	2	405	c.401A>G	c.(400-402)gAt>gGt	p.D134G	CD300LB_ENST00000314401.3_Missense_Mutation_p.D134G	NM_174892.2	NP_777552	A8K4G0	CLM7_HUMAN	CD300 molecule-like family member b	97					cellular response to lipopolysaccharide (GO:0071222)|innate immune response (GO:0045087)|neutrophil mediated immunity (GO:0002446)|positive regulation of mast cell activation (GO:0033005)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(1)	21						ATCTGCGTCATCTCGCCTGAG	0.512																																					p.D134G		Atlas-SNP	.											.	CD300LB	38	.	0			c.A401G						PASS	.						247	222	231					17																	72521967		2203	4300	6503	SO:0001583	missense	124599	exon2			GCGTCATCTCGCC	AF427618	CCDS11700.1, CCDS11700.2	17q25.1	2013-01-11	2006-03-29		ENSG00000178789	ENSG00000178789		"Immunoglobulin superfamily / V-set domain containing"	30811	protein-coding gene	gene with protein product	"triggering receptor expressed on myeloid cells 5"	610705	"CD300 antigen like family member B"			12975309	Standard	NM_174892		Approved	TREM5, CLM7	uc002jkx.2	A8K4G0	OTTHUMG00000067606	ENST00000392621.1:c.401A>G	17.37:g.72521967T>C	ENSP00000376397:p.Asp134Gly	215	0	0		210	35	0.166667	NM_174892	Q1EG73|Q8IX40|Q8N6D1	Missense_Mutation	SNP	ENST00000392621.1	37	CCDS11700.1	.	.	.	.	.	.	.	.	.	.	T	8.070	0.770010	0.15983	.	.	ENSG00000178789	ENST00000392621;ENST00000314401	T	0.04454	3.62	5.17	2.93	0.34026	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.155110	0.06495	N	0.735307	T	0.08044	0.0201	L	0.58354	1.805	0.09310	N	1	B;B	0.19935	0.003;0.04	B;B	0.24006	0.015;0.05	T	0.35822	-0.9773	10	0.54805	T	0.06	-16.8791	7.7177	0.28715	0.0:0.1769:0.0:0.8231	.	134;97	B4DQ71;A8K4G0	.;CLM7_HUMAN	G	97;134	ENSP00000317337:D134G	ENSP00000317337:D134G	D	-	2	0	CD300LB	70033562	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-0.348000	0.07740	0.900000	0.36469	0.460000	0.39030	GAT	.	.	none		0.512	CD300LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145082.2	NM_174892		C	72521967	T	C	72521967	3	2	23	1	0	0	0	0	1	0	0	0	3001	1435	50	3	327	3	CD300LB	17	72521967	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	8989439	72521967	8673243	630	8074											
C17orf77	146723	hgsc.bcm.edu	37	chr17	72588438	72588438	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaacaccgcaaacctactcGaatctccttcaagtctcttg	11	11	4	15	2	4	0	2	0	2	0	7	1	4	0	3	0	3	1	3	0	5	3	rs79556281	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:72588438G>T	ENST00000392620.1	+	3	615	c.253G>T	c.(253-255)Gaa>Taa	p.E85*	C17orf77_ENST00000328023.2_Nonsense_Mutation_p.E85*|CD300LD_ENST00000375352.1_5'Flank	NM_152460.2	NP_689673.2	Q96MU5	CQ077_HUMAN	chromosome 17 open reading frame 77	85						extracellular region (GO:0005576)				breast(2)|large_intestine(2)|lung(5)|prostate(1)|stomach(1)	11						AAACCTACTCGAATCTCCTTC	0.453													g|||	23	0.00459265	0.0	0.0043	5008	,	,		22359	0.0		0.0179	False		,,,				2504	0.002				p.E85X		Atlas-SNP	.											.	C17orf77	31	.	0			c.G253T						PASS	.	A	stop/GLU	10,4396	16.8+/-37.8	0,10,2193	90	86	87		253	-8.1	0	17	dbSNP_131	87	85,8515	49.4+/-109.1	1,83,4216	yes	stop-gained	C17orf77	NM_152460.2		1,93,6409	TT,TG,GG		0.9884,0.227,0.7304		85/244	72588438	95,12911	2203	4300	6503	SO:0001587	stop_gained	146723	exon3			CTACTCGAATCTC		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.253G>T	17.37:g.72588438G>T	ENSP00000376396:p.Glu85*	46	0	0		62	38	0.612903	NM_152460		Nonsense_Mutation	SNP	ENST00000392620.1	37	CCDS32721.1	15	0.006868131868131868	0	0.0	2	0.0055248618784530384	0	0.0	13	0.017150395778364115	g	20.2	3.948429	0.73787	0.00227	0.009884	ENSG00000182352	ENST00000392620;ENST00000328023	.	.	.	4.07	-8.14	0.01069	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.7694	0.05329	0.489:0.2388:0.1618:0.1105	.	.	.	.	X	85	.	.	E	+	1	0	C17orf77	70100033	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.219000	0.02973	-1.873000	0.01135	-1.316000	0.01300	GAA	G|0.994;T|0.006	0.006	strong		0.453	C17orf77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145090.2	NM_152460		T	72588438	G	T	72588438	4	4	23	1	0	0	0	0	0	1	0	0	1884	1059	37	4	255	4	C17orf77	17	72588438	Nonsense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	66471	72588438	8606772	631	8075											
NT5C	30833	hgsc.bcm.edu	37	chr17	73127348	73127348	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccaggtccaggaaaaagcccGgggcttcgtacacactggcc	10	5	12	14	2	0	0	0	0	0	0	2	1	1	1	4	5	2	2	4	5	3	2	rs11541956	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:73127348G>A	ENST00000245552.2	-	2	290	c.203C>T	c.(202-204)cCg>cTg	p.P68L	NT5C_ENST00000582170.1_Missense_Mutation_p.P68L|NT5C_ENST00000579082.1_5'UTR|NT5C_ENST00000578337.1_5'UTR|NT5C_ENST00000582160.1_5'UTR	NM_014595.2	NP_055410.1	Q8TCD5	NT5C_HUMAN	5', 3'-nucleotidase, cytosolic	68			P -> L (in dbSNP:rs11541956). {ECO:0000269|PubMed:15489334}.		dephosphorylation (GO:0016311)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|pyrimidine deoxyribonucleotide catabolic process (GO:0009223)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	5'-nucleotidase activity (GO:0008253)|metal ion binding (GO:0046872)|nucleotidase activity (GO:0008252)|pyrimidine nucleotide binding (GO:0019103)					all_lung(278;0.14)|Lung NSC(278;0.168)		LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)		Lamivudine(DB00709)	GAAAAAGCCCGGGGCTTCGTA	0.652													G|||	40	0.00798722	0.0008	0.0159	5008	,	,		12233	0.0		0.0249	False		,,,				2504	0.0031				p.P68L		Atlas-SNP	.											.	NT5C	3	.	0			c.C203T						PASS	.	G	LEU/PRO	23,4383	25.3+/-52.1	0,23,2180	36	43	41		203	3.4	0.2	17	dbSNP_120	41	242,8358	94.7+/-156.6	4,234,4062	yes	missense	NT5C	NM_014595.1	98	4,257,6242	AA,AG,GG		2.814,0.522,2.0375	probably-damaging	68/202	73127348	265,12741	2203	4300	6503	SO:0001583	missense	30833	exon2			AAGCCCGGGGCTT	AF154829	CCDS11715.1	17q25	2011-03-29	2002-05-23		ENSG00000125458	ENSG00000125458	3.1.3.5		17144	protein-coding gene	gene with protein product		191720	"5' nucleotidase, deoxy (pyrimidine), cytosolic type C", "uridine 5-prime monophosphate hydrolase 2"	UMPH2		10899995	Standard	NM_014595		Approved	DNT1, DNT-1, PN-I, cdN, dNT-1	uc002jmx.3	Q8TCD5		ENST00000245552.2:c.203C>T	17.37:g.73127348G>A	ENSP00000245552:p.Pro68Leu	264	0	0		231	113	0.489177	NM_001252377	Q96HS6|Q9NP82	Missense_Mutation	SNP	ENST00000245552.2	37	CCDS11715.1	27	0.012362637362637362	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	21	0.027704485488126648	G	12.25	1.882990	0.33255	0.00522	0.02814	ENSG00000125458	ENST00000245552	T	0.48836	0.8	4.35	3.36	0.38483	HAD-like domain (2);	0.372569	0.27581	N	0.018735	T	0.34774	0.0909	M	0.68317	2.08	0.80722	D	1	D	0.71674	0.998	P	0.61070	0.883	T	0.51293	-0.8724	10	0.56958	D	0.05	-1.2806	9.557	0.39346	0.0:0.0:0.6178:0.3822	rs11541956;rs17851989	68	Q8TCD5	NT5C_HUMAN	L	68	ENSP00000245552:P68L	ENSP00000245552:P68L	P	-	2	0	NT5C	70638943	0.998000	0.40836	0.217000	0.23759	0.737000	0.42083	3.393000	0.52544	1.154000	0.42482	0.555000	0.69702	CCG	G|0.983;A|0.017	0.017	strong		0.652	NT5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445853.1			A	73127348	G	A	73127348	3	1	23	1	0	0	0	0	1	0	0	0	10693	1116	39	1	418	1	NT5C	17	73127348	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	538910	73127348	8067862	632	8076											
UNC13D	201294	hgsc.bcm.edu	37	chr17	73838639	73838639	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgccgggacccggggctgccCcctggcacacctaccccctg	4	5	12	20	2	0	0	0	0	0	0	0	1	0	1	7	4	3	2	7	4	1	1	rs373551579		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:73838639C>T	ENST00000207549.4	-	6	823	c.444G>A	c.(442-444)ggG>ggA	p.G148G	UNC13D_ENST00000412096.2_Silent_p.G148G|UNC13D_ENST00000587504.1_5'UTR	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	148	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				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)			CGGGGCTGCCCCCTGGCACAC	0.677									Familial Hemophagocytic Lymphohistiocytosis				C|||	1	0.000199681	0.0	0.0014	5008	,	,		16781	0.0		0.0	False		,,,				2504	0.0				p.G148G		Atlas-SNP	.											.	UNC13D	68	.	0			c.G444A						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	55	56	55		444	-0.2	0.6	17		55	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	UNC13D	NM_199242.2		0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231		148/1091	73838639	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	201294	exon6	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GCTGCCCCCTGGC	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.444G>A	17.37:g.73838639C>T		84	0	0		95	43	0.452632	NM_199242	B4DWG9|Q9H7K5	Silent	SNP	ENST00000207549.4	37	CCDS11730.1																																																																																			.	.	weak		0.677	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950		T	73838639	C	T	73838639	2	4	23	1	0	0	0	0	0	0	0	1	17002	610	22	2		2	UNC13D	17	73838639	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	711291	73838639	7356571	633	8077											
TRIM65	201292	hgsc.bcm.edu	37	chr17	73887089	73887089	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccctgacacccctgggaggCgctgggcttccccgttgtgc	3	8	14	16	2	0	1	0	1	0	0	1	2	1	2	5	3	1	3	5	3	0	2	rs61754864	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:73887089C>T	ENST00000269383.3	-	6	1390	c.1325G>A	c.(1324-1326)cGc>cAc	p.R442H		NM_001256124.1|NM_173547.3	NP_001243053.1|NP_775818.2	Q6PJ69	TRI65_HUMAN	tripartite motif containing 65	442	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					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)			CCCTGGGAGGCGCTGGGCTTC	0.687													C|||	4	0.000798722	0.0	0.0	5008	,	,		15760	0.0		0.004	False		,,,				2504	0.0				p.R442H		Atlas-SNP	.											.	TRIM65	23	.	0			c.G1325A						PASS	.	C	HIS/ARG	11,4369		0,11,2179	17	20	19		1325	3.4	1	17	dbSNP_129	19	97,8473		1,95,4189	yes	missense	TRIM65	NM_173547.2	29	1,106,6368	TT,TC,CC		1.1319,0.2511,0.834	benign	442/518	73887089	108,12842	2190	4285	6475	SO:0001583	missense	201292	exon6			GGGAGGCGCTGGG	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.1325G>A	17.37:g.73887089C>T	ENSP00000269383:p.Arg442His	56	0	0		55	28	0.509091	NM_173547	Q4G0F0|Q6DKJ6|Q9BRP6	Missense_Mutation	SNP	ENST00000269383.3	37	CCDS11732.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	14.58	2.578467	0.46006	0.002511	0.011319	ENSG00000141569	ENST00000269383	T	0.69175	-0.38	5.35	3.36	0.38483	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.248458	0.29113	N	0.013101	T	0.36054	0.0953	N	0.20483	0.58	0.21020	N	0.999809	B	0.18461	0.028	B	0.17098	0.017	T	0.11299	-1.0593	10	0.21014	T	0.42	.	5.3044	0.15795	0.0:0.6089:0.0:0.3911	.	442	Q6PJ69	TRI65_HUMAN	H	442	ENSP00000269383:R442H	ENSP00000269383:R442H	R	-	2	0	TRIM65	71398684	0.014000	0.17966	0.998000	0.56505	0.957000	0.61999	0.102000	0.15272	1.267000	0.44247	0.561000	0.74099	CGC	C|0.997;T|0.003	0.003	strong		0.687	TRIM65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255170.2	NM_173547		T	73887089	C	T	73887089	3	4	23	1	0	0	0	0	1	0	0	0	16554	768	27	1	232	1	TRIM65	17	73887089	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	48450	73887089	7308121	634	8078											
UBE2O	63893	hgsc.bcm.edu	37	chr17	74387455	74387455	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggccttctccagcagggCatgggtttccagccaggact	6	9	13	13	0	1	0	0	0	1	0	3	1	2	1	4	4	2	3	4	4	0	2	rs34070229	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:74387455C>T	ENST00000319380.7	-	18	3512	c.3448G>A	c.(3448-3450)Gcc>Acc	p.A1150T		NM_022066.3	NP_071349.3	Q9C0C9	UBE2O_HUMAN	ubiquitin-conjugating enzyme E2O	1150				A -> T (in Ref. 6; BAB14320). {ECO:0000305}.	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						TCCAGCAGGGCATGGGTTTCC	0.657													c|||	21	0.00419329	0.0008	0.0043	5008	,	,		14338	0.0		0.0099	False		,,,				2504	0.0072				p.A1150T		Atlas-SNP	.											.	UBE2O	207	.	0			c.G3448A						PASS	.		THR/ALA	9,4395		0,9,2193	32	31	31		3448	3.6	0.6	17	dbSNP_126	31	125,8473		0,125,4174	yes	missense	UBE2O	NM_022066.3	58	0,134,6367	TT,TC,CC		1.4538,0.2044,1.0306	benign	1150/1293	74387455	134,12868	2202	4299	6501	SO:0001583	missense	63893	exon18			GCAGGGCATGGGT	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.3448G>A	17.37:g.74387455C>T	ENSP00000323687:p.Ala1150Thr	69	0	0		107	48	0.448598	NM_022066	A6NDU5|Q69YP4|Q6PIZ2|Q86UA4|Q8N425|Q8TBN1|Q9BSW1|Q9H6E6|Q9H7E4|Q9H9B2	Missense_Mutation	SNP	ENST00000319380.7	37	CCDS32742.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	c	11.30	1.597943	0.28445	0.002044	0.014538	ENSG00000175931	ENST00000319380	T	0.72615	-0.67	4.58	3.62	0.41486	Ubiquitin-conjugating enzyme/RWD-like (1);	0.271361	0.30085	N	0.010460	T	0.42381	0.1200	N	0.22421	0.69	0.25600	N	0.986606	B	0.06786	0.001	B	0.04013	0.001	T	0.19614	-1.0300	10	0.14656	T	0.56	-14.1712	7.7518	0.28901	0.161:0.7564:0.0:0.0826	rs34070229	1150	Q9C0C9	UBE2O_HUMAN	T	1150	ENSP00000323687:A1150T	ENSP00000323687:A1150T	A	-	1	0	UBE2O	71899050	0.997000	0.39634	0.648000	0.29521	0.911000	0.54048	2.190000	0.42630	1.146000	0.42352	0.556000	0.70494	GCC	C|0.991;T|0.009	0.009	strong		0.657	UBE2O-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450123.1	NM_022066		T	74387455	C	T	74387455	3	4	23	1	0	0	0	0	1	0	0	0	16883	710	25	2	434	2	UBE2O	17	74387455	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	500366	74387455	6807755	635	8079											
UBE2O	63893	hgsc.bcm.edu	37	chr17	74392249	74392249	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagaagacctcgcccttggcGctggtgaaggtgacgccagg	8	6	16	11	3	0	4	0	2	0	2	1	5	0	4	3	4	0	1	3	4	2	1	rs76110889	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:74392249G>A	ENST00000319380.7	-	14	2833	c.2769C>T	c.(2767-2769)agC>agT	p.S923S	UBE2O_ENST00000587581.1_5'Flank	NM_022066.3	NP_071349.3	Q9C0C9	UBE2O_HUMAN	ubiquitin-conjugating enzyme E2O	923					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						CGCCCTTGGCGCTGGTGAAGG	0.642													G|||	16	0.00319489	0.0	0.0058	5008	,	,		17280	0.0		0.0119	False		,,,				2504	0.0				p.S923S		Atlas-SNP	.											.	UBE2O	207	.	0			c.C2769T						PASS	.	G		12,4394	17.9+/-39.9	0,12,2191	40	43	42		2769	-0.5	1	17	dbSNP_132	42	106,8494	59.1+/-120.7	0,106,4194	no	coding-synonymous	UBE2O	NM_022066.3		0,118,6385	AA,AG,GG		1.2326,0.2724,0.9073		923/1293	74392249	118,12888	2203	4300	6503	SO:0001819	synonymous_variant	63893	exon14			CTTGGCGCTGGTG	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.2769C>T	17.37:g.74392249G>A		78	0	0		80	38	0.475	NM_022066	A6NDU5|Q69YP4|Q6PIZ2|Q86UA4|Q8N425|Q8TBN1|Q9BSW1|Q9H6E6|Q9H7E4|Q9H9B2	Silent	SNP	ENST00000319380.7	37	CCDS32742.1																																																																																			G|0.992;A|0.008	0.008	strong		0.642	UBE2O-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450123.1	NM_022066		A	74392249	G	A	74392249	2	1	23	1	0	0	0	0	0	0	0	1	16883	1078	38	1		1	UBE2O	17	74392249	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	4794	74392249	6802961	636	8080											
TMC8	147138	hgsc.bcm.edu	37	chr17	76130576	76130576	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgcgggtcaacgtactcaaCgggctcctggtggttggggc	5	9	16	11	3	2	0	2	0	0	0	3	0	3	0	1	6	4	3	1	6	3	2	rs149203228		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:76130576C>T	ENST00000318430.5	+	8	1292	c.918C>T	c.(916-918)aaC>aaT	p.N306N	TMC8_ENST00000589691.1_Silent_p.N83N|TMC6_ENST00000322914.3_5'Flank	NM_152468.4	NP_689681.2	Q8IU68	TMC8_HUMAN	transmembrane channel-like 8	306			N -> I (in dbSNP:rs7208422). {ECO:0000269|Ref.3}.		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)	p.N306N(1)		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)			ACGTACTCAACGGGCTCCTGG	0.612													C|||	1	0.000199681	0.0	0.0	5008	,	,		17681	0.0		0.001	False		,,,				2504	0.0				p.N306N		Atlas-SNP	.											TMC8,NS,carcinoma,0,1	TMC8	44	1	1	Substitution - coding silent(1)	lung(1)	c.C918T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	51	56	54		918	-6.5	0.5	17	dbSNP_134	54	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous	TMC8	NM_152468.4		0,15,6488	TT,TC,CC		0.1512,0.0454,0.1153		306/727	76130576	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	147138	exon8			ACTCAACGGGCTC	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.918C>T	17.37:g.76130576C>T		82	0	0		87	42	0.482759	NM_152468	Q2YDC0|Q8IWU7|Q8N358|Q8NF04	Silent	SNP	ENST00000318430.5	37	CCDS32749.1																																																																																			C|0.998;T|0.002	0.002	strong		0.612	TMC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436900.3			T	76130576	C	T	76130576	2	4	23	1	0	0	0	0	0	0	0	1	16006	535	19	1		1	TMC8	17	76130576	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1738327	76130576	5064634	637	8081											
CBX2	84733	hgsc.bcm.edu	37	chr17	77758653	77758653	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gtagcagctcggactccgacCccgactccgcctcgccgccc	5	5	10	21	6	0	0	0	0	0	0	4	3	2	1	7	1	2	3	7	1	1	1	rs141957173	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:77758653C>G	ENST00000310942.4	+	5	1515	c.1411C>G	c.(1411-1413)Ccc>Gcc	p.P471A		NM_005189.2	NP_005180.1	Q14781	CBX2_HUMAN	chromobox homolog 2	471					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)			GGACTCCGACCCCGACTCCGC	0.667													C|||	6	0.00119808	0.0	0.0	5008	,	,		15360	0.0		0.006	False		,,,				2504	0.0				p.P471A		Atlas-SNP	.											.	CBX2	50	.	0			c.C1411G						PASS	.	C	ALA/PRO	3,4403	6.2+/-15.9	0,3,2200	38	36	37		1411	5.4	1	17	dbSNP_134	37	87,8513	47.6+/-106.9	0,87,4213	yes	missense	CBX2	NM_005189.2	27	0,90,6413	GG,GC,CC		1.0116,0.0681,0.692	possibly-damaging	471/533	77758653	90,12916	2203	4300	6503	SO:0001583	missense	84733	exon5			TCCGACCCCGACT	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.1411C>G	17.37:g.77758653C>G	ENSP00000308750:p.Pro471Ala	70	0	0		51	20	0.392157	NM_005189	Q0VDA5|Q9BTB1	Missense_Mutation	SNP	ENST00000310942.4	37	CCDS32757.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	9.419	1.082569	0.20309	6.81E-4	0.010116	ENSG00000173894	ENST00000310942	.	.	.	5.45	5.45	0.79879	.	1.949320	0.02055	N	0.050337	T	0.46347	0.1388	L	0.36672	1.1	0.80722	D	1	B	0.34015	0.435	B	0.27262	0.078	T	0.30208	-0.9986	9	0.54805	T	0.06	13.4368	14.9645	0.71182	0.1433:0.8567:0.0:0.0	.	471	Q14781	CBX2_HUMAN	A	471	.	ENSP00000308750:P471A	P	+	1	0	CBX2	75373248	1.000000	0.71417	0.987000	0.45799	0.018000	0.09664	5.777000	0.68931	2.568000	0.86640	0.650000	0.86243	CCC	C|0.996;G|0.004	0.004	strong		0.667	CBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437040.1	NM_032647		G	77758653	C	G	77758653	3	3	23	1	0	0	0	0	1	0	0	0	2720	623	22	4	1777	4	CBX2	17	77758653	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1628077	77758653	3436557	638	8082											
MRPL12	6182	hgsc.bcm.edu	37	chr17	79671298	79671298	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caggtgccatgtgtctgtgcCgtgcgacatatgaggagcag	8	9	15	9	2	1	1	0	1	1	0	1	3	1	2	2	2	4	1	2	2	1	1	rs148659191	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:79671298C>T	ENST00000333676.3	+	2	244	c.99C>T	c.(97-99)gcC>gcT	p.A33A	SLC25A10_ENST00000571730.1_Silent_p.A33A|RP13-1032I1.7_ENST00000575312.1_RNA|SLC25A10_ENST00000541223.1_Silent_p.A33A	NM_002949.3	NP_002940.2	P52815	RM12_HUMAN	mitochondrial ribosomal protein L12	33				A -> T (in Ref. 1; CAA56249). {ECO:0000305}.	positive regulation of transcription, DNA-templated (GO:0045893)|transcription from mitochondrial promoter (GO:0006390)|translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|lung(2)|urinary_tract(1)	4	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)			GTGTCTGTGCCGTGCGACATA	0.607													C|||	10	0.00199681	0.0	0.0029	5008	,	,		17178	0.0		0.005	False		,,,				2504	0.0031				p.A33A		Atlas-SNP	.											.	MRPL12	12	.	0			c.C99T						PASS	.	C		4,4400	6.2+/-15.9	0,4,2198	55	51	52		99	-9.1	0	17	dbSNP_134	52	63,8537	38.8+/-94.9	0,63,4237	no	coding-synonymous	MRPL12	NM_002949.3		0,67,6435	TT,TC,CC		0.7326,0.0908,0.5152		33/199	79671298	67,12937	2202	4300	6502	SO:0001819	synonymous_variant	6182	exon2			CTGTGCCGTGCGA	X79865	CCDS11785.1	17q25	2012-11-14			ENSG00000262814	ENSG00000262814		"Mitochondrial ribosomal proteins / large subunits"	10378	protein-coding gene	gene with protein product		602375		RPML12		8626705, 9169145	Standard	NM_002949		Approved	MRPL7/L12, MRPL7		P52815	OTTHUMG00000178171	ENST00000333676.3:c.99C>T	17.37:g.79671298C>T		91	0	0		100	60	0.6	NM_002949	Q969U0|Q9HCA2|Q9UQJ3	Silent	SNP	ENST00000333676.3	37	CCDS11785.1																																																																																			C|0.996;T|0.004	0.004	strong		0.607	MRPL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440812.1	NM_002949		T	79671298	C	T	79671298	2	4	23	1	0	0	0	0	0	0	0	1	9786	639	23	1		1	MRPL12	17	79671298	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1912645	79671298	1523912	639	8083											
FN3KRP	79672	hgsc.bcm.edu	37	chr17	80684843	80684843	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcttctttctacggccactcGgaatatgagctggcaatagc	9	11	10	11	2	2	1	0	1	2	0	3	2	2	2	1	3	3	3	1	3	5	5	rs146293327	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:80684843G>A	ENST00000269373.6	+	6	799	c.726G>A	c.(724-726)tcG>tcA	p.S242S	RP11-388C12.5_ENST00000570919.1_lincRNA|FN3KRP_ENST00000535965.1_Silent_p.S192S	NM_024619.3	NP_078895.2	Q9HA64	KT3K_HUMAN	fructosamine 3 kinase related protein	242							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)			ACGGCCACTCGGAATATGAGC	0.557													G|||	2	0.000399361	0.0008	0.0	5008	,	,		16728	0.0		0.001	False		,,,				2504	0.0				p.S242S		Atlas-SNP	.											FN3KRP,right_upper_lobe,carcinoma,+1,2	FN3KRP	31	2	0			c.G726A						PASS	.	G		0,4406		0,0,2203	61	64	63		726	-8.8	0.9	17	dbSNP_134	63	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	FN3KRP	NM_024619.3		0,5,6498	AA,AG,GG		0.0581,0.0,0.0384		242/310	80684843	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	79672	exon6			CCACTCGGAATAT	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.726G>A	17.37:g.80684843G>A		89	0	0		128	65	0.507812	NM_024619	Q969F4|Q9H0U7	Silent	SNP	ENST00000269373.6	37	CCDS11817.1																																																																																			G|0.999;A|0.001	0.001	strong		0.557	FN3KRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439219.1	NM_024619		A	80684843	G	A	80684843	2	1	23	1	0	0	0	0	0	0	0	1	5972	1103	39	1		1	FN3KRP	17	80684843	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1013545	80684843	510367	640	8084											
MYOM1	8736	hgsc.bcm.edu	37	chr18	3141939	3141939	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgattctagagtcttacctTttccacaaagtacataatgc	12	15	5	9	0	2	2	0	1	2	1	3	2	3	2	2	0	3	1	2	0	5	8	rs200179081	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:3141939T>C	ENST00000356443.4	-	14	2356	c.2023A>G	c.(2023-2025)Aag>Gag	p.K675E	MYOM1_ENST00000400569.3_Missense_Mutation_p.K675E|MYOM1_ENST00000261606.7_Missense_Mutation_p.K675E	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	675	Fibronectin type-III 2. {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						AGTCTTACCTTTTCCACAAAG	0.507													T|||	2	0.000399361	0.0	0.0	5008	,	,		19010	0.0		0.002	False		,,,				2504	0.0				p.K675E		Atlas-SNP	.											.	MYOM1	192	.	0			c.A2023G						PASS	.	T	GLU/LYS,GLU/LYS	0,3942		0,0,1971	91	93	93		2023,2023	5.8	1	18		93	4,8312		0,4,4154	yes	missense,missense	MYOM1	NM_003803.3,NM_019856.1	56,56	0,4,6125	CC,CT,TT		0.0481,0.0,0.0326	probably-damaging,probably-damaging	675/1686,675/1590	3141939	4,12254	1971	4158	6129	SO:0001583	missense	8736	exon14			TTACCTTTTCCAC	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.2023A>G	18.37:g.3141939T>C	ENSP00000348821:p.Lys675Glu	83	0	0		89	29	0.325843	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.336470	0.81801	0.0	4.81E-4	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.57752	0.38;0.38;0.38	5.8	5.8	0.92144	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.75824	0.3902	M	0.87758	2.905	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.76942	-0.2772	10	0.34782	T	0.22	.	16.1611	0.81712	0.0:0.0:0.0:1.0	.	675;675	P52179-2;P52179	.;MYOM1_HUMAN	E	675	ENSP00000348821:K675E;ENSP00000383413:K675E;ENSP00000261606:K675E	ENSP00000261606:K675E	K	-	1	0	MYOM1	3131939	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	8.040000	0.89188	2.213000	0.71641	0.477000	0.44152	AAG	.	.	weak		0.507	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		C	3141939	T	C	3141939	3	2	23	1	0	0	0	0	1	0	0	0	10100	1850	64	3	3134	3	MYOM1	18	3141939	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10		3141939	74935309	641	8085											
ZNF519	162655	hgsc.bcm.edu	37	chr18	14105770	14105770	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttttctccagtgttaattaTcttatgtccctttagatgtg	7	21	6	7	0	2	1	0	0	2	1	4	1	3	1	2	0	0	1	2	0	4	7	rs61730995	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:14105770T>C	ENST00000590202.1	-	3	921	c.769A>G	c.(769-771)Ata>Gta	p.I257V	ZNF519_ENST00000589203.1_Intron|ZNF519_ENST00000589498.1_Intron|RP11-411B10.3_ENST00000592926.1_RNA	NM_145287.3	NP_660330.2	Q8TB69	ZN519_HUMAN	zinc finger protein 519	257					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						GTGTTAATTATCTTATGTCCC	0.328													T|||	7	0.00139776	0.0008	0.0014	5008	,	,		18546	0.0		0.004	False		,,,				2504	0.001				p.I257V		Atlas-SNP	.											.	ZNF519	53	.	0			c.A769G						PASS	.	T	VAL/ILE	5,4399	9.9+/-24.2	0,5,2197	43	48	46		769	0.6	0	18	dbSNP_129	46	72,8524	41.7+/-99.0	1,70,4227	no	missense	ZNF519	NM_145287.3	29	1,75,6424	CC,CT,TT		0.8376,0.1135,0.5923	benign	257/541	14105770	77,12923	2202	4298	6500	SO:0001583	missense	162655	exon3			TAATTATCTTATG	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.769A>G	18.37:g.14105770T>C	ENSP00000464872:p.Ile257Val	94	0	0		66	31	0.469697	NM_145287		Missense_Mutation	SNP	ENST00000590202.1	37	CCDS32797.1	4	0.0018315018315018315	1	0.0020325203252032522	0	0.0	0	0.0	3	0.00395778364116095	T	0.378	-0.930146	0.02359	0.001135	0.008376	ENSG00000175322	ENST00000309305	.	.	.	0.646	0.646	0.17789	.	.	.	.	.	T	0.19087	0.0458	N	0.25890	0.77	0.09310	N	0.999993	B	0.13594	0.008	B	0.08055	0.003	T	0.16041	-1.0416	8	0.39692	T	0.17	.	5.6281	0.17495	0.0:1.0E-4:0.0:0.9999	.	257	Q8TB69	ZN519_HUMAN	V	257	.	ENSP00000307908:I257V	I	-	1	0	ZNF519	14095770	0.000000	0.05858	0.005000	0.12908	0.342000	0.28953	-0.164000	0.09983	0.552000	0.29026	0.076000	0.15429	ATA	T|0.996;C|0.004	0.004	strong		0.328	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287		C	14105770	T	C	14105770	3	2	23	1	0	0	0	0	1	0	0	0	17979	1435	50	3	857	3	ZNF519	18	14105770	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	10963831	14105770	63971478	642	8086											
LAMA3	3909	hgsc.bcm.edu	37	chr18	21492734	21492734	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gaagtccgactgccaaatgaCctggaagatttgaaaggata	15	8	11	7	1	0	3	0	2	0	1	1	7	1	5	3	2	1	0	3	2	5	2	rs62093184		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:21492734C>T	ENST00000313654.9	+	56	7459	c.7218C>T	c.(7216-7218)gaC>gaT	p.D2406D	LAMA3_ENST00000399516.3_Silent_p.D2350D|LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000269217.6_Silent_p.D797D|LAMA3_ENST00000587184.1_Silent_p.D741D	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2406	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)					TGCCAAATGACCTGGAAGATT	0.448													C|||	1	0.000199681	0.0	0.0	5008	,	,		22166	0.0		0.001	False		,,,				2504	0.0				p.D2406D		Atlas-SNP	.											.	LAMA3	397	.	0			c.C7218T						PASS	.	C	,,,	3,4403	6.2+/-15.9	0,3,2200	114	113	114		2391,7050,2223,7218	4.8	1	18	dbSNP_129	114	17,8583	12.6+/-44.7	0,17,4283	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LAMA3	NM_000227.3,NM_001127717.1,NM_001127718.1,NM_198129.1	,,,	0,20,6483	TT,TC,CC		0.1977,0.0681,0.1538	,,,	797/1725,2350/3278,741/1669,2406/3334	21492734	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	3909	exon56			AAATGACCTGGAA	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.7218C>T	18.37:g.21492734C>T		85	0	0		78	31	0.397436	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	37	CCDS42419.1																																																																																			C|0.999;T|0.001	0.001	strong		0.448	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		T	21492734	C	T	21492734	2	4	23	1	0	0	0	0	0	0	0	1	8616	506	18	2		2	LAMA3	18	21492734	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	7386964	21492734	56584514	643	8087											
LAMA3	3909	hgsc.bcm.edu	37	chr18	21496533	21496533	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaggaaggaagagtcagaCaaaaattattttgaaggtac	18	8	12	3	0	1	3	1	1	0	2	1	6	1	6	0	4	1	1	0	4	7	4	rs61751706	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:21496533C>T	ENST00000313654.9	+	60	8038	c.7797C>T	c.(7795-7797)gaC>gaT	p.D2599D	LAMA3_ENST00000399516.3_Silent_p.D2543D|LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000269217.6_Silent_p.D990D|LAMA3_ENST00000587184.1_Silent_p.D934D	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2599	Laminin G-like 2. {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)					AAGAGTCAGACAAAAATTATT	0.423													C|||	5	0.000998403	0.0	0.0014	5008	,	,		18308	0.0		0.004	False		,,,				2504	0.0				p.D2599D		Atlas-SNP	.											.	LAMA3	397	.	0			c.C7797T						PASS	.	C	,,,	5,4401	9.9+/-24.2	0,5,2198	161	149	153		2970,7629,2802,7797	5.2	1	18	dbSNP_129	153	60,8540	37.8+/-93.5	1,58,4241	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LAMA3	NM_000227.3,NM_001127717.1,NM_001127718.1,NM_198129.1	,,,	1,63,6439	TT,TC,CC		0.6977,0.1135,0.4998	,,,	990/1725,2543/3278,934/1669,2599/3334	21496533	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	3909	exon60			GTCAGACAAAAAT	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.7797C>T	18.37:g.21496533C>T		103	0	0		66	33	0.5	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	37	CCDS42419.1																																																																																			C|0.995;T|0.005	0.005	strong		0.423	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		T	21496533	C	T	21496533	2	4	23	1	0	0	0	0	0	0	0	1	8616	477	17	2		2	LAMA3	18	21496533	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	3799	21496533	56580715	644	8088											
FHOD3	80206	hgsc.bcm.edu	37	chr18	34289118	34289118	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggaagcagaggcaggggcggGgcaggttgctgatgaagctg	9	5	21	6	1	0	3	0	2	0	1	0	4	0	4	0	7	3	6	0	7	2	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:34289118G>T	ENST00000359247.4	+	14	1721	c.1721G>T	c.(1720-1722)gGg>gTg	p.G574V	FHOD3_ENST00000257209.4_Missense_Mutation_p.G591V|FHOD3_ENST00000445677.1_Missense_Mutation_p.G553V|FHOD3_ENST00000590592.1_Missense_Mutation_p.G766V|FHOD3_ENST00000587493.1_3'UTR|FHOD3_ENST00000591635.1_Intron	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	574					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)				GCAGGGGCGGGGCAGGTTGCT	0.572																																					p.G591V		Atlas-SNP	.											FHOD3,NS,carcinoma,+1,1	FHOD3	210	1	0			c.G1772T						PASS	.						69	86	80					18																	34289118		2203	4300	6503	SO:0001583	missense	80206	exon15			GGGCGGGGCAGGT	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.1721G>T	18.37:g.34289118G>T	ENSP00000352186:p.Gly574Val	248	0	0		225	89	0.395556	NM_025135	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Missense_Mutation	SNP	ENST00000359247.4	37		.	.	.	.	.	.	.	.	.	.	G	14.69	2.609383	0.46527	.	.	ENSG00000134775	ENST00000257209;ENST00000359247;ENST00000445677	T;T;T	0.19105	2.2;2.17;2.17	5.84	-2.56	0.06268	.	0.594819	0.18286	N	0.145873	T	0.12860	0.0312	L	0.34521	1.04	0.20489	N	0.999893	B;B;B;B	0.23735	0.078;0.09;0.078;0.047	B;B;B;B	0.23419	0.036;0.046;0.022;0.036	T	0.17379	-1.0371	10	0.49607	T	0.09	.	7.3434	0.26650	0.5464:0.1225:0.3311:0.0	.	553;574;591;766	Q2V2M9-2;Q2V2M9;Q2V2M9-3;E5F5Q0	.;FHOD3_HUMAN;.;.	V	591;574;553	ENSP00000257209:G591V;ENSP00000352186:G574V;ENSP00000411430:G553V	ENSP00000257209:G591V	G	+	2	0	FHOD3	32543116	0.966000	0.33281	0.000000	0.03702	0.001000	0.01503	1.014000	0.29950	-0.327000	0.08551	-1.202000	0.01658	GGG	.	.	none		0.572	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114		T	34289118	G	T	34289118	3	4	23	1	0	0	0	0	1	0	0	0	5891	1232	43	4	1830	4	FHOD3	18	34289118	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	12792585	34289118	43788130	645	8089											
ZNF532	55205	hgsc.bcm.edu	37	chr18	56620910	56620910	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaaaagaaatctccatctcCtgtgaaaaaatcaatggaaa	19	8	7	7	0	3	2	1	1	2	1	5	4	3	4	2	2	0	0	2	2	8	0			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56620910C>T	ENST00000336078.4	+	8	3805	c.3029C>T	c.(3028-3030)cCt>cTt	p.P1010L	ZNF532_ENST00000591230.1_Missense_Mutation_p.P1010L|ZNF532_ENST00000591083.1_Missense_Mutation_p.P1010L|ZNF532_ENST00000591808.1_Missense_Mutation_p.P1010L|ZNF532_ENST00000589288.1_Missense_Mutation_p.P1010L	NM_018181.4	NP_060651.2	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	1010					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						TCTCCATCTCCTGTGAAAAAA	0.433																																					p.P1010L		Atlas-SNP	.											.	ZNF532	108	.	0			c.C3029T						PASS	.						77	77	77					18																	56620910		2203	4300	6503	SO:0001583	missense	55205	exon8			CATCTCCTGTGAA	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.3029C>T	18.37:g.56620910C>T	ENSP00000338217:p.Pro1010Leu	292	0	0		253	139	0.549407	NM_018181	Q4G0V6|Q7L7Z7|Q96QR7|Q9NVJ6	Missense_Mutation	SNP	ENST00000336078.4	37	CCDS11969.1	.	.	.	.	.	.	.	.	.	.	C	16.36	3.102745	0.56183	.	.	ENSG00000074657	ENST00000336078	T	0.01705	4.68	5.23	5.23	0.72850	.	0.109437	0.64402	D	0.000006	T	0.03520	0.0101	M	0.63843	1.955	0.80722	D	1	B;B	0.17852	0.024;0.012	B;B	0.15052	0.012;0.009	T	0.51779	-0.8662	10	0.22706	T	0.39	-0.2311	18.7617	0.91855	0.0:1.0:0.0:0.0	.	1010;1010	B3KXW2;Q9HCE3	.;ZN532_HUMAN	L	1010	ENSP00000338217:P1010L	ENSP00000338217:P1010L	P	+	2	0	ZNF532	54771890	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.384000	0.66225	2.599000	0.87857	0.637000	0.83480	CCT	.	.	none		0.433	ZNF532-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256130.1	NM_018181		T	56620910	C	T	56620910	3	4	23	1	0	0	0	0	1	0	0	0	17987	681	24	2	3047	2	ZNF532	18	56620910	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	22331792	56620910	21456338	646	8090											
ZNF516	9658	hgsc.bcm.edu	37	chr18	74090864	74090864	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccctggtagagggtcgcaaAgtcctttggaatgtacgtct	8	12	12	9	2	1	1	0	0	1	1	4	2	3	2	2	3	1	3	2	3	4	3	rs140499406	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:74090864A>G	ENST00000443185.2	-	5	3522	c.3205T>C	c.(3205-3207)Ttt>Ctt	p.F1069L	ZNF516_ENST00000524431.2_5'UTR|RP11-504I13.3_ENST00000583287.1_RNA	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	1069					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)		AGGGTCGCAAAGTCCTTTGGA	0.602													A|||	14	0.00279553	0.0015	0.0043	5008	,	,		17438	0.0		0.008	False		,,,				2504	0.001				p.F1069L		Atlas-SNP	.											.	ZNF516	102	.	0			c.T3205C						PASS	.	A	LEU/PHE	5,4081		0,5,2038	41	48	46		3206	-0.6	1	18	dbSNP_134	46	77,8287		2,73,4107	yes	missense	ZNF516	NM_014643.3	22	2,78,6145	GG,GA,AA		0.9206,0.1224,0.6586	benign	1069/1164	74090864	82,12368	2043	4182	6225	SO:0001583	missense	9658	exon5			TCGCAAAGTCCTT	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.3205T>C	18.37:g.74090864A>G	ENSP00000394757:p.Phe1069Leu	104	0	0		77	26	0.337662	NM_014643		Missense_Mutation	SNP	ENST00000443185.2	37		7|7	0.003205128205128205|0.003205128205128205	0|0	0.0|0.0	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	5|5	0.006596306068601583|0.006596306068601583	a|a	3.367|3.367	-0.129188|-0.129188	0.06753|0.06753	0.001224|0.001224	0.009206|0.009206	ENSG00000101493|ENSG00000101493	ENST00000443185|ENST00000542818	T|.	0.05786|.	3.39|.	3.8|3.8	-0.563|-0.563	0.11778|0.11778	.|.	0.482470|.	0.19919|.	N|.	0.103134|.	T|T	0.14614|0.14614	0.0353|0.0353	N|N	0.08118|0.08118	0|0	0.31674|0.31674	N|N	0.643972|0.643972	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.34750|0.34750	-0.9816|-0.9816	10|5	0.02654|.	T|.	1|.	-0.2046|-0.2046	7.7942|7.7942	0.29138|0.29138	0.34:0.0:0.66:0.0|0.34:0.0:0.66:0.0	.|.	1069|.	Q92618|.	ZN516_HUMAN|.	L|P	1069|2	ENSP00000394757:F1069L|.	ENSP00000394757:F1069L|.	F|L	-|-	1|2	0|0	ZNF516|ZNF516	72219852|72219852	1.000000|1.000000	0.71417|0.71417	0.961000|0.961000	0.40146|0.40146	0.841000|0.841000	0.47740|0.47740	3.490000|3.490000	0.53245|0.53245	-0.197000|-0.197000	0.10350|0.10350	0.478000|0.478000	0.44815|0.44815	TTT|CTT	A|0.994;G|0.006	0.006	strong		0.602	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643		G	74090864	A	G	74090864	3	3	23	1	0	0	0	0	1	0	0	0	17975	72	3	3	302	3	ZNF516	18	74090864	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	17469954	74090864	3986384	647	8091											
GALR1	2587	hgsc.bcm.edu	37	chr18	74980553	74980553	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttttctagactgcacagacaGttctggtggtggttgtggtg	6	15	14	6	0	2	2	0	0	2	2	2	2	2	2	0	4	1	3	0	4	1	5	rs142216832	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:74980553G>A	ENST00000299727.3	+	3	745	c.745G>A	c.(745-747)Gtt>Att	p.V249I		NM_001480.3	NP_001471.2	P47211	GALR1_HUMAN	galanin receptor 1	249					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)		TGCACAGACAGTTCTGGTGGT	0.517													G|||	19	0.00379393	0.0136	0.0014	5008	,	,		13369	0.0		0.0	False		,,,				2504	0.0				p.V249I		Atlas-SNP	.											.	GALR1	53	.	0			c.G745A						PASS	.	G	ILE/VAL	89,4317	74.7+/-112.8	0,89,2114	100	107	104		745	3	0.1	18	dbSNP_134	104	0,8600		0,0,4300	yes	missense	GALR1	NM_001480.3	29	0,89,6414	AA,AG,GG		0.0,2.02,0.6843	probably-damaging	249/350	74980553	89,12917	2203	4300	6503	SO:0001583	missense	2587	exon3			CAGACAGTTCTGG	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.745G>A	18.37:g.74980553G>A	ENSP00000299727:p.Val249Ile	77	0	0		52	31	0.596154	NM_001480	Q4VBL7	Missense_Mutation	SNP	ENST00000299727.3	37	CCDS12012.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	G	7.358	0.624331	0.14193	0.0202	0.0	ENSG00000166573	ENST00000299727	T	0.36878	1.23	4.74	2.96	0.34315	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.32704	0.0838	L	0.58101	1.795	0.80722	D	1	D	0.76494	0.999	D	0.71656	0.974	T	0.21415	-1.0246	10	0.17369	T	0.5	.	10.7925	0.46440	0.152:0.0:0.848:0.0	.	249	P47211	GALR1_HUMAN	I	249	ENSP00000299727:V249I	ENSP00000299727:V249I	V	+	1	0	GALR1	73109541	1.000000	0.71417	0.071000	0.20095	0.026000	0.11368	4.647000	0.61418	0.446000	0.26666	-1.012000	0.02466	GTT	G|0.993;A|0.007	0.007	strong		0.517	GALR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256362.1			A	74980553	G	A	74980553	3	1	23	1	0	0	0	0	1	0	0	0	6235	1029	36	2	755	2	GALR1	18	74980553	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	889689	74980553	3096695	648	8092											
SALL3	27164	hgsc.bcm.edu	37	chr18	76757145	76757145	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcggcatcccccagctcccCgtgagtcttgggggcagcgc	4	6	15	16	3	1	1	0	1	1	0	3	1	3	1	4	4	2	3	4	4	0	1	rs148335210	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:76757145C>T	ENST00000537592.2	+	3	3726	c.3726C>T	c.(3724-3726)ccC>ccT	p.P1242P	SALL3_ENST00000575389.2_Silent_p.P1170P|SALL3_ENST00000536229.3_Silent_p.P1037P	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	1242					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)	p.P1242P(1)		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)		CCCAGCTCCCCGTGAGTCTTG	0.612													C|||	6	0.00119808	0.0	0.0029	5008	,	,		17088	0.0		0.003	False		,,,				2504	0.001				p.P1242P		Atlas-SNP	.											SALL3,NS,malignant_melanoma,+2,1	SALL3	162	1	1	Substitution - coding silent(1)	lung(1)	c.C3726T						PASS	.	C		4,4402	8.1+/-20.4	0,4,2199	94	90	92		3726	-10.8	0	18	dbSNP_134	92	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous	SALL3	NM_171999.2		0,14,6489	TT,TC,CC		0.1163,0.0908,0.1076		1242/1301	76757145	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	27164	exon3			GCTCCCCGTGAGT	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.3726C>T	18.37:g.76757145C>T		76	0	0		86	4	0.0465116	NM_171999	Q9UGH1	Silent	SNP	ENST00000537592.2	37	CCDS12013.1																																																																																			C|0.999;T|0.001	0.001	strong		0.612	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999		T	76757145	C	T	76757145	2	4	23	1	0	0	0	0	0	0	0	1	13827	639	23	1		1	SALL3	18	76757145	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1776592	76757145	1320103	649	8093											
C19orf20	91978	hgsc.bcm.edu	37	chr19	507731	507731	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cactacttcgagaacatgggCctgcgctcgcctgtaaacgg	9	8	11	13	4	0	1	0	0	0	1	2	2	0	1	2	2	4	2	2	2	4	3	rs16990489	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:507731C>T	ENST00000359315.5	+	1	433	c.225C>T	c.(223-225)ggC>ggT	p.G75G	AC005775.2_ENST00000592413.1_RNA	NM_033513.2	NP_277048.2	Q6ZTW0	TPGS1_HUMAN	tubulin polyglutamylase complex subunit 1	75					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)										AGAACATGGGCCTGCGCTCGC	0.711													C|||	93	0.0185703	0.0545	0.0173	5008	,	,		12412	0.0		0.0089	False		,,,				2504	0.0				p.G75G		Atlas-SNP	.											.	.	.	.	0			c.C225T						PASS	.	C		140,3414		1,138,1638	7	10	9		225	2.2	1	19	dbSNP_123	9	51,7895		0,51,3922	no	coding-synonymous	C19orf20	NM_033513.2		1,189,5560	TT,TC,CC		0.6418,3.9392,1.6609		75/291	507731	191,11309	1777	3973	5750	SO:0001819	synonymous_variant	91978	exon1			CATGGGCCTGCGC	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.225C>T	19.37:g.507731C>T		43	0	0		24	14	0.583333	NM_033513	Q96GE2	Silent	SNP	ENST00000359315.5	37	CCDS42454.1																																																																																			C|0.974;T|0.026	0.026	strong		0.711	TPGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451887.2	NM_033513		T	507731	C	T	507731	2	4	23	1	0	0	0	0	0	0	0	1	1914	726	26	2		2	C19orf20	19	507731	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10		507731	58621252	650	8094											
ABCA7	10347	hgsc.bcm.edu	37	chr19	1062285	1062285	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagctgcttgcgcgcctgcgCggtgtcccggaggcccaggt	3	7	17	14	5	0	0	0	0	0	0	1	2	1	1	3	4	4	2	3	4	0	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:1062285C>T	ENST00000263094.6	+	42	5916	c.5685C>T	c.(5683-5685)cgC>cgT	p.R1895R	ABCA7_ENST00000433129.1_Silent_p.R1895R|ABCA7_ENST00000435683.2_Silent_p.R1757R	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1895	ABC transporter 2. {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)		CGCGCCTGCGCGGTGTCCCGG	0.677																																					p.R1895R		Atlas-SNP	.											.	ABCA7	174	.	0			c.C5685T						PASS	.						84	91	89					19																	1062285		2203	4296	6499	SO:0001819	synonymous_variant	10347	exon42			CCTGCGCGGTGTC	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.5685C>T	19.37:g.1062285C>T		60	0	0		52	10	0.192308	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	37	CCDS12055.1																																																																																			.	.	none		0.677	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		T	1062285	C	T	1062285	2	4	23	1	0	0	0	0	0	0	0	1	37	755	27	1		1	ABCA7	19	1062285	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	554554	1062285	58066698	651	8095											
PCSK4	54760	hgsc.bcm.edu	37	chr19	1487981	1487981	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acgtagttggcccagaggtcCgggtggtccttctcgatgcc	5	10	14	12	3	1	1	0	0	1	1	4	2	3	1	4	4	1	2	4	4	1	3	rs151115553	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:1487981C>T	ENST00000300954.5	-	4	559	c.498G>A	c.(496-498)ccG>ccA	p.P166P	PCSK4_ENST00000587784.1_5'UTR|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)		CCCAGAGGTCCGGGTGGTCCT	0.692													C|||	3	0.000599042	0.0	0.0014	5008	,	,		14584	0.0		0.002	False		,,,				2504	0.0				p.P166P		Atlas-SNP	.											.	PCSK4	44	.	0			c.G498A						PASS	.	C		4,4402	8.1+/-20.4	0,4,2199	71	71	71		498	-5.3	1	19	dbSNP_134	71	68,8532	40.3+/-97.0	0,68,4232	no	coding-synonymous	PCSK4	NM_017573.3		0,72,6431	TT,TC,CC		0.7907,0.0908,0.5536		166/756	1487981	72,12934	2203	4300	6503	SO:0001819	synonymous_variant	54760	exon4			GAGGTCCGGGTGG	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.498G>A	19.37:g.1487981C>T		72	0	0		54	26	0.481481	NM_017573		Silent	SNP	ENST00000300954.5	37	CCDS12069.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	2.497	-0.316156	0.05422	9.08E-4	0.007907	ENSG00000115257	ENST00000441747	.	.	.	2.67	-5.34	0.02705	.	.	.	.	.	T	0.29491	0.0735	.	.	.	0.80722	D	1	B	0.06786	0.001	B	0.01281	0.0	T	0.04373	-1.0956	7	0.54805	T	0.06	.	3.7736	0.08652	0.2281:0.3213:0.0:0.4506	.	8	B3KQ28	.	Q	8	.	ENSP00000402772:R8Q	R	-	2	0	PCSK4	1438981	0.000000	0.05858	0.987000	0.45799	0.937000	0.57800	-7.956000	0.00027	-0.883000	0.03982	-0.658000	0.03865	CGG	C|0.996;T|0.004	0.004	strong		0.692	PCSK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449703.1	NM_017573		T	1487981	C	T	1487981	2	4	23	1	0	0	0	0	0	0	0	1	11611	639	23	1		1	PCSK4	19	1487981	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	425696	1487981	57641002	652	8096											
C19orf28	126321	hgsc.bcm.edu	37	chr19	3546264	3546264	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagccctaccgtgtggggacCgatgaggtcggccgtcatgg	6	7	16	12	4	1	1	1	1	0	0	2	3	1	2	4	5	2	0	4	5	1	1	rs34878396	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:3546264C>T	ENST00000355415.2	-	7	1352	c.1183G>A	c.(1183-1185)Ggt>Agt	p.G395S	AC005786.7_ENST00000589360.1_RNA|MFSD12_ENST00000398558.4_Missense_Mutation_p.G395S|MFSD12_ENST00000591878.1_5'Flank|MFSD12_ENST00000389395.3_Missense_Mutation_p.G395S	NM_174983.3	NP_778148.2	Q6NUT3	MFS12_HUMAN	major facilitator superfamily domain containing 12	395			G -> S (in dbSNP:rs34878396).		transport (GO:0006810)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				cervix(1)|endometrium(2)|lung(4)|urinary_tract(2)	9						GTGTGGGGACCGATGAGGTCG	0.682													C|||	10	0.00199681	0.0	0.0029	5008	,	,		13963	0.0		0.007	False		,,,				2504	0.001				p.G395S		Atlas-SNP	.											.	MFSD12	22	.	0			c.G1183A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY	6,4266		0,6,2130	17	22	20		1183,1183,1183	4.6	1	19	dbSNP_126	20	58,8420		0,58,4181	no	missense,missense,missense	C19orf28	NM_001042680.1,NM_021731.2,NM_174983.3	56,56,56	0,64,6311	TT,TC,CC		0.6841,0.1404,0.502	possibly-damaging,possibly-damaging,possibly-damaging	395/474,395/539,395/481	3546264	64,12686	2136	4239	6375	SO:0001583	missense	126321	exon7			GGGGACCGATGAG	AF218008	CCDS42465.1, CCDS74256.1	19p13.3	2012-03-09	2011-11-24	2011-11-24	ENSG00000161091	ENSG00000161091			28299	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 28"	C19orf28		12477932	Standard	NM_174983		Approved	MGC20700, PP3501	uc002lxw.3	Q6NUT3		ENST00000355415.2:c.1183G>A	19.37:g.3546264C>T	ENSP00000347583:p.Gly395Ser	94	0	0		56	31	0.553571	NM_001042680	A8MXP7|D6W615|E9PAJ8|Q8N459	Missense_Mutation	SNP	ENST00000355415.2	37	CCDS42465.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	32	5.162522	0.94727	0.001404	0.006841	ENSG00000161091	ENST00000389395;ENST00000398558;ENST00000355415	D;D;D	0.87029	-2.2;-2.2;-2.2	4.63	4.63	0.57726	Major facilitator superfamily domain, general substrate transporter (1);	0.053348	0.64402	D	0.000001	D	0.90466	0.7014	M	0.77616	2.38	0.54753	D	0.999988	D;D;D	0.76494	0.992;0.997;0.999	P;P;D	0.65874	0.889;0.828;0.939	D	0.91435	0.5169	10	0.51188	T	0.08	-25.4799	16.4799	0.84155	0.0:1.0:0.0:0.0	rs34878396	395;386;395	Q6NUT3;Q6NUT3-2;A8MXP7	CS028_HUMAN;.;.	S	395	ENSP00000374046:G395S;ENSP00000381566:G395S;ENSP00000347583:G395S	ENSP00000347583:G395S	G	-	1	0	C19orf28	3497264	1.000000	0.71417	0.999000	0.59377	0.923000	0.55619	7.195000	0.77798	2.126000	0.65437	0.561000	0.74099	GGT	C|0.996;T|0.004	0.004	strong		0.682	MFSD12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452949.2	NM_174983		T	3546264	C	T	3546264	3	4	23	1	0	0	0	0	1	0	0	0	1919	652	23	1	482	1	C19orf28	19	3546264	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	2058283	3546264	55582719	653	8097											
SEMA6B	10501	hgsc.bcm.edu	37	chr19	4555079	4555079	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcatcaatggctaggaagtcGgtaacagtagctgtgaagag	13	8	14	6	1	1	2	1	1	0	1	2	3	1	3	0	3	2	5	0	3	6	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:4555079G>A	ENST00000586582.1	-	8	901	c.591C>T	c.(589-591)acC>acT	p.T197T	SEMA6B_ENST00000301293.3_Silent_p.T197T|SEMA6B_ENST00000586965.1_Silent_p.T197T	NM_032108.3	NP_115484.2	Q9H3T3	SEM6B_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	197	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)		CTAGGAAGTCGGTAACAGTAG	0.592																																					p.T197T		Atlas-SNP	.											.	SEMA6B	51	.	0			c.C591T						PASS	.						111	89	96					19																	4555079		2202	4300	6502	SO:0001819	synonymous_variant	10501	exon8			GAAGTCGGTAACA	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.591C>T	19.37:g.4555079G>A		63	0	0		75	9	0.12	NM_032108	A5PKU4|F6IB19|Q9NRK9	Silent	SNP	ENST00000586582.1	37	CCDS12131.1																																																																																			.	.	none		0.592	SEMA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458656.2	NM_032108		A	4555079	G	A	4555079	2	1	23	1	0	0	0	0	0	0	0	1	14055	1103	39	1		1	SEMA6B	19	4555079	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1008815	4555079	54573904	654	8098											
CLEC4M	10332	hgsc.bcm.edu	37	chr19	7828277	7828277	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagctgatgtctgtcaattcAgaagaagatccaacaaccag	15	8	9	9	0	3	4	2	1	1	3	4	5	4	4	2	0	3	1	2	0	5	1	rs62623420	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:7828277A>G	ENST00000327325.5	+	2	164		c.e2-1		CLEC4M_ENST00000334806.5_Intron|CLEC4M_ENST00000597522.1_Splice_Site|CLEC4M_ENST00000595496.1_Splice_Site|CLEC4M_ENST00000596707.1_Splice_Site|CLEC4M_ENST00000357361.2_Splice_Site|CLEC4M_ENST00000359059.5_Splice_Site|CLEC4M_ENST00000394122.2_Splice_Site|CLEC4M_ENST00000596363.1_Intron|CLEC4M_ENST00000248228.4_Splice_Site	NM_001144909.1|NM_014257.4	NP_001138381.1|NP_055072.3	Q9H2X3	CLC4M_HUMAN	C-type lectin domain family 4, member M						antigen processing and presentation (GO:0019882)|cell-cell recognition (GO:0009988)|endocytosis (GO:0006897)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intracellular transport of virus (GO:0075733)|leukocyte cell-cell adhesion (GO:0007159)|modulation by virus of host morphology or physiology (GO:0019048)|peptide antigen transport (GO:0046968)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|viral genome replication (GO:0019079)|virion attachment to host cell (GO:0019062)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|ICAM-3 receptor activity (GO:0030369)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)|peptide antigen binding (GO:0042605)|receptor activity (GO:0004872)|virion binding (GO:0046790)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(1)	26						CTGTCAATTCAGAAGAAGATC	0.522													A|||	5	0.000998403	0.0	0.0	5008	,	,		18184	0.0		0.005	False		,,,				2504	0.0				.		Atlas-SNP	.											.	CLEC4M	58	.	0			c.47-2A>G						PASS	.	A	,,,,,,,,	6,4400	11.4+/-27.6	0,6,2197	129	124	126		,,,,,,,,	2.5	0.1	19	dbSNP_129	126	50,8550	31.7+/-84.0	0,50,4250	yes	intron,intron,splice-3,splice-3,splice-3,splice-3,splice-3,intron,splice-3	CLEC4M	NM_001144904.1,NM_001144905.1,NM_001144906.1,NM_001144907.1,NM_001144908.1,NM_001144909.1,NM_001144910.1,NM_001144911.1,NM_014257.4	,,,,,,,,	0,56,6447	GG,GA,AA		0.5814,0.1362,0.4306	,,,,,,,,	,,,,,,,,	7828277	56,12950	2203	4300	6503	SO:0001630	splice_region_variant	10332	exon2			CAATTCAGAAGAA	AB015629	CCDS12187.1, CCDS59346.1, CCDS59347.1, CCDS59348.1	19p13	2008-02-05	2005-02-04	2005-02-11		ENSG00000104938		"C-type lectin domain containing", "CD molecules"	13523	protein-coding gene	gene with protein product		605872	"CD299 antigen"	CD209L, CD299		10072769	Standard	NM_001144904		Approved	HP10347, DC-SIGNR, LSIGN, DCSIGNR, DC-SIGN2	uc010dvt.3	Q9H2X3		ENST00000327325.5:c.47-1A>G	19.37:g.7828277A>G		124	0	0		134	69	0.514925	NM_001144907	A6NKI4|A8K8B3|Q69F40|Q969M4|Q96QP3|Q96QP4|Q96QP5|Q96QP6|Q9BXS3|Q9H2Q9|Q9H8F0|Q9Y2A8	Splice_Site	SNP	ENST00000327325.5	37	CCDS12187.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	A	7.317	0.616157	0.14129	0.001362	0.005814	ENSG00000104938	ENST00000327325;ENST00000394122;ENST00000248228;ENST00000359059;ENST00000357361	.	.	.	2.5	2.5	0.30297	.	.	.	.	.	.	.	.	.	.	.	0.53688	D	0.99997	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.3238	0.26542	1.0:0.0:0.0:0.0	rs62623420	.	.	.	.	-1	.	.	.	+	.	.	CLEC4M	7734277	0.022000	0.18835	0.128000	0.21923	0.082000	0.17680	1.015000	0.29963	1.134000	0.42165	0.344000	0.21773	.	A|0.997;G|0.003	0.003	strong		0.522	CLEC4M-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461161.1	NM_014257	Intron	G	7828277	A	G	7828277	5	3	23	1	0	0	0	0	0	0	1	0	3520	202	7	3	51	3	CLEC4M	19	7828277	Splice_Site	SNP	A	TCGA-G8-6325-01A-11D-2210-10	3273198	7828277	51300706	655	8099											
LASS4	79603	hgsc.bcm.edu	37	chr19	8326672	8326672	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttgctgcagctgctgcacGtgttctggtcttgcctcatt	3	16	11	11	1	3	0	1	0	2	0	3	0	3	0	1	1	6	7	1	1	0	4	rs141592194		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:8326672G>A	ENST00000251363.5	+	11	1249	c.949G>A	c.(949-951)Gtg>Atg	p.V317M	CERS4_ENST00000595722.1_3'UTR|CERS4_ENST00000559450.1_Missense_Mutation_p.V317M|CERS4_ENST00000558331.1_Missense_Mutation_p.V266M|CERS4_ENST00000559336.1_Intron	NM_024552.2	NP_078828.2	Q9HA82	CERS4_HUMAN	ceramide synthase 4	317	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)										GCTGCTGCACGTGTTCTGGTC	0.567													G|||	1	0.000199681	0.0	0.0	5008	,	,		16989	0.0		0.0	False		,,,				2504	0.001				p.V317M		Atlas-SNP	.											.	.	.	.	0			c.G949A						PASS	.	G	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	105	88	94		949	0.6	0.7	19	dbSNP_134	94	6,8594	5.0+/-18.6	0,6,4294	yes	missense	CERS4	NM_024552.2	21	0,7,6496	AA,AG,GG		0.0698,0.0227,0.0538	probably-damaging	317/395	8326672	7,12999	2203	4300	6503	SO:0001583	missense	79603	exon11			CTGCACGTGTTCT		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.949G>A	19.37:g.8326672G>A	ENSP00000251363:p.Val317Met	304	0	0		269	110	0.408922	NM_024552	D6W665	Missense_Mutation	SNP	ENST00000251363.5	37	CCDS12197.1	.	.	.	.	.	.	.	.	.	.	G	17.70	3.454447	0.63290	2.27E-4	6.98E-4	ENSG00000090661	ENST00000251363	D	0.86164	-2.08	5.13	0.644	0.17776	TRAM/LAG1/CLN8 homology domain (3);	0.257428	0.39985	N	0.001212	D	0.90363	0.6984	M	0.71296	2.17	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	D	0.87521	0.2446	10	0.62326	D	0.03	-22.7678	6.9208	0.24387	0.4709:0.0:0.5291:0.0	.	317	Q9HA82	CERS4_HUMAN	M	317	ENSP00000251363:V317M	ENSP00000251363:V317M	V	+	1	0	CERS4	8232672	0.711000	0.27906	0.672000	0.29872	0.694000	0.40290	1.129000	0.31381	0.194000	0.20326	0.561000	0.74099	GTG	G|0.999;A|0.001	0.001	strong		0.567	CERS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419200.1	NM_024552		A	8326672	G	A	8326672	3	1	23	1	0	0	0	0	1	0	0	0	8650	1145	40	1	983	1	LASS4	19	8326672	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	498395	8326672	50802311	656	8100											
OR7G1	125962	hgsc.bcm.edu	37	chr19	9225662	9225662	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcagcaacagcagaactaaTgtacaccccaaaagctgtcc	15	6	6	14	0	1	1	1	0	0	1	2	1	2	1	3	0	6	4	3	0	6	2	rs138190811		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9225662T>C	ENST00000541538.1	-	1	777	c.778A>G	c.(778-780)Att>Gtt	p.I260V	OR7G1_ENST00000293614.1_Missense_Mutation_p.I260V	NM_001005192.2	NP_001005192.2	Q8NGA0	OR7G1_HUMAN	olfactory receptor, family 7, subfamily G, member 1	260						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)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	20						GCAGAACTAATGTACACCCCA	0.468													T|||	1	0.000199681	0.0	0.0	5008	,	,		18140	0.001		0.0	False		,,,				2504	0.0				p.I260V		Atlas-SNP	.											.	OR7G1	53	.	0			c.A778G						PASS	.	T	VAL/ILE	0,4406		0,0,2203	109	102	104		778	-7.6	0	19	dbSNP_134	104	4,8596	3.7+/-12.6	0,4,4296	yes	missense	OR7G1	NM_001005192.2	29	0,4,6499	CC,CT,TT		0.0465,0.0,0.0308	benign	260/312	9225662	4,13002	2203	4300	6503	SO:0001583	missense	125962	exon1			AACTAATGTACAC		CCDS32898.1, CCDS32898.2	19p13.2	2013-09-24			ENSG00000161807	ENSG00000161807		"GPCR / Class A : Olfactory receptors"	8465	protein-coding gene	gene with protein product				OR7G1P			Standard	NM_001005192		Approved	OR19-15	uc021uoi.1	Q8NGA0	OTTHUMG00000168067	ENST00000541538.1:c.778A>G	19.37:g.9225662T>C	ENSP00000444134:p.Ile260Val	77	0	0		95	51	0.536842	NM_001005192	Q6IFJ5|Q96RA1	Missense_Mutation	SNP	ENST00000541538.1	37	CCDS32898.2	.	.	.	.	.	.	.	.	.	.	t	9.233	1.036306	0.19669	0.0	4.65E-4	ENSG00000161807	ENST00000293614;ENST00000541538	T;T	0.37058	1.22;1.22	3.78	-7.55	0.01327	GPCR, rhodopsin-like superfamily (1);	0.478549	0.15276	U	0.270958	T	0.18509	0.0444	N	0.25825	0.765	0.09310	N	1	B	0.16603	0.018	B	0.30943	0.122	T	0.22277	-1.0221	10	0.72032	D	0.01	.	2.0374	0.03542	0.2085:0.2559:0.3872:0.1484	.	260	Q8NGA0	OR7G1_HUMAN	V	260	ENSP00000293614:I260V;ENSP00000444134:I260V	ENSP00000293614:I260V	I	-	1	0	OR7G1	9086662	0.000000	0.05858	0.012000	0.15200	0.016000	0.09150	-2.649000	0.00858	-1.542000	0.01725	-0.539000	0.04255	ATT	T|0.999;C|0.001	0.001	strong		0.468	OR7G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397912.1			C	9225662	T	C	9225662	3	2	23	1	0	0	0	0	1	0	0	0	11231	1464	51	3	231	3	OR7G1	19	9225662	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	898990	9225662	49903321	657	8101											
EIF3G	5032	hgsc.bcm.edu	37	chr19	10226686	10226686	+	IGR	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccccgcggcggctggccccGtcgcgcaggctcggcggcac	2	4	16	19	8	0	0	0	0	0	0	3	0	1	0	4	6	0	4	4	6	0	0	rs200490441	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:10226686G>A	ENST00000321826.4	+	0	1943				EIF3G_ENST00000253108.4_Silent_p.D220D|EIF3G_ENST00000587168.1_5'Flank	NM_002566.4	NP_002557.2	Q96G91	P2Y11_HUMAN	purinergic receptor P2Y, G-protein coupled, 11						activation of adenylate cyclase activity (GO:0007190)|adenosine receptor signaling pathway (GO:0001973)|calcium-mediated signaling (GO:0019722)|cellular response to ATP (GO:0071318)|defense response (GO:0006952)|G-protein coupled receptor signaling pathway (GO:0007186)|neuronal signal transduction (GO:0023041)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP-activated nucleotide receptor activity (GO:0045031)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|neurotransmitter receptor activity (GO:0030594)|receptor activity (GO:0004872)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)	16			OV - Ovarian serous cystadenocarcinoma(20;3.53e-09)|Epithelial(33;4.91e-06)|all cancers(31;1.1e-05)			GGCTGGCCCCGTCGCGCAGGC	0.662													G|||	2	0.000399361	0.0	0.0	5008	,	,		15153	0.002		0.0	False		,,,				2504	0.0				p.D220D		Atlas-SNP	.											.	EIF3G	16	.	0			c.C660T						PASS	.	G		0,4402		0,0,2201	26	27	27		660	-5.3	0.9	19		27	1,8593		0,1,4296	no	coding-synonymous	EIF3G	NM_003755.3		0,1,6497	AA,AG,GG		0.0116,0.0,0.0077		220/321	10226686	1,12995	2201	4297	6498	SO:0001628	intergenic_variant	8666	exon8			GGCCCCGTCGCGC	AF030335	CCDS12226.1	19p13.2	2012-08-08			ENSG00000244165	ENSG00000244165		"Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	8540	protein-coding gene	gene with protein product		602697				9405388	Standard	NM_002566		Approved	P2Y11		Q96G91	OTTHUMG00000150166		19.37:g.10226686G>A		68	0	0		61	34	0.557377	NM_003755	B2R8X9|O43190|Q9BYU4|Q9H170	Silent	SNP	ENST00000321826.4	37	CCDS12226.1																																																																																			G|0.999;A|0.001	0.001	strong		0.662	P2RY11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316664.2	NM_002566		A	10226686	G	A	10226686	1	1	23	0	1	0	0	0	0	0	0	0	5019	1136	40	1		1	EIF3G	19	10226686	IGR	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1001024	10226686	48902297	658	8102											
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11145752	11145752	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agatgttcggccgtggctccCgccaccgcaaggaggtggac	7	6	15	13	4	0	1	0	0	0	1	2	3	1	3	4	5	0	3	4	5	1	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:11145752C>T	ENST00000429416.3	+	30	4395	c.4114C>T	c.(4114-4116)Cgc>Tgc	p.R1372C	SMARCA4_ENST00000590574.1_Missense_Mutation_p.R1339C|SMARCA4_ENST00000413806.3_Missense_Mutation_p.R1339C|SMARCA4_ENST00000358026.2_Missense_Mutation_p.R1372C|SMARCA4_ENST00000589677.1_Missense_Mutation_p.R1339C|SMARCA4_ENST00000541122.2_Missense_Mutation_p.R1339C|SMARCA4_ENST00000538456.3_3'UTR|SMARCA4_ENST00000444061.3_Missense_Mutation_p.R1339C|SMARCA4_ENST00000450717.3_Missense_Mutation_p.R1339C|SMARCA4_ENST00000344626.4_Missense_Mutation_p.R1372C	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1372					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)				CCGTGGCTCCCGCCACCGCAA	0.652			"F, N, Mis"		NSCLC																																p.R1372C		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.C4114T						PASS	.						44	36	39					19																	11145752		2203	4299	6502	SO:0001583	missense	6597	exon29			GGCTCCCGCCACC	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.4114C>T	19.37:g.11145752C>T	ENSP00000395654:p.Arg1372Cys	174	0	0		163	28	0.171779	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	25.0|25.0	4.593820|4.593820	0.86953|0.86953	.|.	.|.	ENSG00000127616|ENSG00000127616	ENST00000538456|ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	.|D;D;D;D;D;D;D	.|0.95724	.|-3.77;-3.79;-3.77;-3.03;-3.0;-3.07;-3.03	4.59|4.59	3.56|3.56	0.40772|0.40772	.|.	.|0.065843	.|0.64402	.|D	.|0.000006	D|D	0.98239|0.98239	0.9417|0.9417	H|H	0.96239|0.96239	3.79|3.79	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;0.999;1.0;1.0	D|D	0.98554|0.98554	1.0638|1.0638	5|10	.|0.87932	.|D	.|0	-29.8756|-29.8756	11.6252|11.6252	0.51139|0.51139	0.0:0.9121:0.0:0.0879|0.0:0.9121:0.0:0.0879	.|.	.|1339;1339;1339;1372;1339;559;1372	.|B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;P51532	.|.;.;.;.;.;.;SMCA4_HUMAN	L|C	108|1372;1372;1403;1372;1339;1339;1339;1339	.|ENSP00000395654:R1372C;ENSP00000350720:R1372C;ENSP00000343896:R1372C;ENSP00000445036:R1339C;ENSP00000392837:R1339C;ENSP00000397783:R1339C;ENSP00000414727:R1339C	.|ENSP00000343896:R1372C	P|R	+|+	2|1	0|0	SMARCA4|SMARCA4	11006752|11006752	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.546000|7.546000	0.82137|0.82137	1.164000|1.164000	0.42652|0.42652	0.558000|0.558000	0.71614|0.71614	CCG|CGC	.	.	none		0.652	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		T	11145752	C	T	11145752	3	4	23	1	0	0	0	0	1	0	0	0	14785	652	23	1	4224	1	SMARCA4	19	11145752	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	919066	11145752	47983231	659	8103											
CCDC151	115948	hgsc.bcm.edu	37	chr19	11545690	11545690	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tcctcccttggaacggcctgGggtccacgcctgggctgtgc	3	9	14	15	2	0	0	0	0	0	0	3	1	3	1	5	5	2	1	5	5	1	1	rs143295007	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:11545690G>A	ENST00000356392.4	-	1	235	c.148C>T	c.(148-150)Cca>Tca	p.P50S	PRKCSH_ENST00000252455.2_5'Flank|PRKCSH_ENST00000592741.1_5'Flank|PRKCSH_ENST00000591462.1_5'Flank|PRKCSH_ENST00000589838.1_5'Flank|CCDC151_ENST00000586836.1_Intron|CCDC151_ENST00000591179.1_Missense_Mutation_p.P50S|PRKCSH_ENST00000412601.1_5'Flank|CCDC151_ENST00000545100.1_Intron|PRKCSH_ENST00000587327.1_5'Flank	NM_145045.4	NP_659482.3	A5D8V7	CC151_HUMAN	coiled-coil domain containing 151	50										endometrium(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	12						GAACGGCCTGGGGTCCACGCC	0.597											OREG0025257	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	13	0.00259585	0.0008	0.0058	5008	,	,		18177	0.0		0.008	False		,,,				2504	0.0				p.P50S		Atlas-SNP	.											.	CCDC151	44	.	0			c.C148T						PASS	.	G	SER/PRO	3,3943		0,3,1970	68	73	72		148	-2.5	0	19	dbSNP_134	72	34,8254		1,32,4111	yes	missense	CCDC151	NM_145045.4	74	1,35,6081	AA,AG,GG		0.4102,0.076,0.3024	benign	50/596	11545690	37,12197	1973	4144	6117	SO:0001583	missense	115948	exon1			GGCCTGGGGTCCA		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.148C>T	19.37:g.11545690G>A	ENSP00000348757:p.Pro50Ser	88	0	0	673	86	39	0.453488	NM_145045	B4DXT0|Q96CG5	Missense_Mutation	SNP	ENST00000356392.4	37	CCDS42501.1	10	0.004578754578754579	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	6	0.0079155672823219	G	10.12	1.263504	0.23136	7.6E-4	0.004102	ENSG00000198003	ENST00000356392;ENST00000543934	T	0.10192	2.9	4.54	-2.55	0.06288	.	0.428688	0.17419	N	0.174920	T	0.02727	0.0082	N	0.11560	0.145	0.18873	N	0.999989	B;B	0.12013	0.002;0.005	B;B	0.12837	0.008;0.003	T	0.45396	-0.9264	10	0.09338	T	0.73	-5.9352	9.2378	0.37477	0.1027:0.6325:0.2648:0.0	.	50;50	B3KPH7;A5D8V7	.;CC151_HUMAN	S	50;29	ENSP00000348757:P50S	ENSP00000348757:P50S	P	-	1	0	CCDC151	11406690	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.152000	0.10159	-0.084000	0.12595	0.655000	0.94253	CCA	G|0.997;A|0.003	0.003	strong		0.597	CCDC151-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458800.1	NM_145045		A	11545690	G	A	11545690	3	1	23	1	0	0	0	0	1	0	0	0	2788	1232	43	2	1691	2	CCDC151	19	11545690	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	399938	11545690	47583293	660	8104											
ZNF653	115950	hgsc.bcm.edu	37	chr19	11594928	11594928	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttcctcttgaaggacttgccGcaggtctcgcaggtgaattc	7	12	11	11	2	2	2	0	2	2	0	5	3	3	3	2	3	1	2	2	3	2	4			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:11594928G>A	ENST00000293771.5	-	8	1735	c.1599C>T	c.(1597-1599)tgC>tgT	p.C533C	CTC-398G3.6_ENST00000585656.1_Intron	NM_138783.3	NP_620138.2	Q96CK0	ZN653_HUMAN	zinc finger protein 653	533					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)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	17						AGGACTTGCCGCAGGTCTCGC	0.647																																					p.C533C	Pancreas(83;980 1446 4542 6441 43352)	Atlas-SNP	.											.	ZNF653	48	.	0			c.C1599T						PASS	.						42	34	37					19																	11594928		2189	4255	6444	SO:0001819	synonymous_variant	115950	exon8			CTTGCCGCAGGTC	AY072704	CCDS12261.1	19p13.2	2013-01-08						"Zinc fingers, C2H2-type"	25196	protein-coding gene	gene with protein product		611371				12477932	Standard	NM_138783		Approved	Zip67	uc002mrz.2	Q96CK0		ENST00000293771.5:c.1599C>T	19.37:g.11594928G>A		99	0	0		100	16	0.16	NM_138783	Q96AS7	Silent	SNP	ENST00000293771.5	37	CCDS12261.1																																																																																			.	.	none		0.647	ZNF653-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458836.2	NM_138783		A	11594928	G	A	11594928	2	1	23	1	0	0	0	0	0	0	0	1	18081	1079	38	1		1	ZNF653	19	11594928	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	49238	11594928	47534055	661	8105											
ZNF763	284390	hgsc.bcm.edu	37	chr19	12087921	12087921	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgggctttgctggatatttcGcagaggaaactctacaggga	10	11	13	7	1	1	1	0	0	1	1	2	4	1	4	0	4	3	3	0	4	3	4	rs376310072	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:12087921G>C	ENST00000358987.3	+	2	199	c.72G>C	c.(70-72)tcG>tcC	p.S24S	ZNF763_ENST00000591944.1_Silent_p.S93S|ZNF763_ENST00000545530.1_Intron|ZNF763_ENST00000343949.5_Silent_p.S27S|ZNF763_ENST00000590798.1_Silent_p.S44S|ZNF763_ENST00000592625.1_Silent_p.S24S|ZNF763_ENST00000538752.1_Silent_p.S44S			Q0D2J5	ZN763_HUMAN	zinc finger protein 763	24	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)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)	15						TGGATATTTCGCAGAGGAAAC	0.493													N|||	4	0.000798722	0.0023	0.0	5008	,	,		18630	0.0		0.001	False		,,,				2504	0.0				p.S27S		Atlas-SNP	.											ZNF763,NS,carcinoma,+1,2	ZNF763	31	2	0			c.G81C						scavenged	.						150	152	151					19																	12087921		2203	4300	6503	SO:0001819	synonymous_variant	284390	exon2			TATTTCGCAGAGG	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.72G>C	19.37:g.12087921G>C		216	0	0		256	12	0.046875	NM_001012753	B3KRU3|B4DRE7	Silent	SNP	ENST00000358987.3	37																																																																																				.	.	alt		0.493	ZNF763-002	KNOWN	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000344158.1	NM_001012753		C	12087921	G	C	12087921	2	2	23	1	0	0	0	0	0	0	0	1	18152	1074	38	4		4	ZNF763	19	12087921	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	492993	12087921	47041062	662	8106											
ZNF20	7568	hgsc.bcm.edu	37	chr19	12244656	12244656	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtattaagagatgaatgaccCgtgccaacttctccacacac	13	9	7	12	1	1	3	0	2	1	1	2	4	1	3	3	0	2	1	3	0	4	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:12244656C>T	ENST00000334213.5	-	4	569	c.345G>A	c.(343-345)acG>acA	p.T115T	ZNF20_ENST00000600335.1_Intron|ZNF20_ENST00000485451.1_5'UTR|ZNF625-ZNF20_ENST00000430024.1_3'UTR	NM_001203250.1|NM_021143.3	NP_001190179.1|NP_066966.2	P17024	ZNF20_HUMAN	zinc finger protein 20	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)			endometrium(1)|kidney(1)|lung(6)	8						ATGAATGACCCGTGCCAACTT	0.423																																					p.T115T		Atlas-SNP	.											.	ZNF20	86	.	0			c.G345A						PASS	.						259	260	259					19																	12244656		2117	4252	6369	SO:0001819	synonymous_variant	7568	exon4			ATGACCCGTGCCA	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.345G>A	19.37:g.12244656C>T		171	0	0		210	112	0.533333	NM_021143	Q8N457|Q9UG41	Silent	SNP	ENST00000334213.5	37	CCDS45986.1																																																																																			.	.	none		0.423	ZNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344101.1	NM_021143		T	12244656	C	T	12244656	2	4	23	1	0	0	0	0	0	0	0	1	17776	639	23	1		1	ZNF20	19	12244656	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	156735	12244656	46884327	663	8107											
TRMT1	55621	hgsc.bcm.edu	37	chr19	13220734	13220734	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttcctccctgctcaccggccGctggggactcctgacgcttt	3	11	10	17	3	1	1	1	1	0	0	4	2	4	2	5	3	1	3	5	3	0	2	rs142446751		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:13220734G>A	ENST00000592062.1	-	10	1671	c.1101C>T	c.(1099-1101)agC>agT	p.S367S	TRMT1_ENST00000437766.1_Silent_p.S367S|TRMT1_ENST00000221504.8_Intron|TRMT1_ENST00000357720.4_Silent_p.S367S			Q9NXH9	TRM1_HUMAN	tRNA methyltransferase 1 homolog (S. cerevisiae)	367	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)		CTCACCGGCCGCTGGGGACTC	0.642													G|||	1	0.000199681	0.0	0.0	5008	,	,		16571	0.0		0.0	False		,,,				2504	0.001				p.S367S		Atlas-SNP	.											.	TRMT1	31	.	0			c.C1101T						PASS	.	G	,,	0,4406		0,0,2203	58	66	64		1101,,1101	-8.5	0	19	dbSNP_134	64	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,intron,coding-synonymous	TRMT1	NM_001136035.2,NM_001142554.1,NM_017722.3	,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,	367/660,,367/660	13220734	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	55621	exon9			CCGGCCGCTGGGG	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.1101C>T	19.37:g.13220734G>A		65	0	0		60	21	0.35	NM_001136035	O76103|Q548Y5|Q8WVA6	Silent	SNP	ENST00000592062.1	37	CCDS12293.1																																																																																			G|1.000;A|0.000	0.000	weak		0.642	TRMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452780.2	NM_017722		A	13220734	G	A	13220734	2	1	23	1	0	0	0	0	0	0	0	1	16576	1078	38	1		1	TRMT1	19	13220734	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	976078	13220734	45908249	664	8108											
C19orf57	79173	hgsc.bcm.edu	37	chr19	14001206	14001206	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagctccgtggcctcctggaGggggacccccagggtctcca	5	6	14	16	1	1	0	0	0	1	0	4	2	3	2	6	5	1	1	6	5	0	0	rs144502446	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:14001206G>A	ENST00000586783.1	-	5	462	c.463C>T	c.(463-465)Ctc>Ttc	p.L155F	C19orf57_ENST00000454313.1_Missense_Mutation_p.L155F|C19orf57_ENST00000346736.2_Missense_Mutation_p.L155F|C19orf57_ENST00000591586.1_Intron			Q0VDD7	CS057_HUMAN	chromosome 19 open reading frame 57	155					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)			GCCTCCTGGAGGGGGACCCCC	0.677													G|||	14	0.00279553	0.0023	0.0014	5008	,	,		13636	0.0		0.0089	False		,,,				2504	0.001				p.L155F		Atlas-SNP	.											.	C19orf57	34	.	0			c.C463T						PASS	.	G	PHE/LEU	5,4397		0,5,2196	28	34	32		463	-5.3	0	19	dbSNP_134	32	55,8527		0,55,4236	yes	missense	C19orf57	NM_024323.3	22	0,60,6432	AA,AG,GG		0.6409,0.1136,0.4621	benign	155/638	14001206	60,12924	2201	4291	6492	SO:0001583	missense	79173	exon6			CCTGGAGGGGGAC	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.463C>T	19.37:g.14001206G>A	ENSP00000465822:p.Leu155Phe	45	0	0		38	28	0.736842	NM_024323	Q13411|Q8N825|Q96D63|Q9BU49	Missense_Mutation	SNP	ENST00000586783.1	37		10	0.004578754578754579	2	0.0040650406504065045	0	0.0	0	0.0	8	0.010554089709762533	G	0.447	-0.895879	0.02472	0.001136	0.006409	ENSG00000132016	ENST00000454313;ENST00000346736	T;T	0.27402	1.67;1.67	2.65	-5.29	0.02747	.	.	.	.	.	T	0.07818	0.0196	N	0.11560	0.145	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.09796	-1.0658	9	0.32370	T	0.25	5.6759	0.5749	0.00702	0.256:0.2127:0.323:0.2083	.	155;155	Q0VDD7-2;Q0VDD7	.;CS057_HUMAN	F	155	ENSP00000404382:L155F;ENSP00000254336:L155F	ENSP00000254336:L155F	L	-	1	0	C19orf57	13862206	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-4.466000	0.00229	-3.561000	0.00141	-1.672000	0.00744	CTC	G|0.994;A|0.006	0.006	strong		0.677	C19orf57-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000457947.1	NM_024323		A	14001206	G	A	14001206	3	1	23	1	0	0	0	0	1	0	0	0	1941	1000	35	2	1462	2	C19orf57	19	14001206	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	780472	14001206	45127777	665	8109											
OR1I1	126370	hgsc.bcm.edu	37	chr19	15198666	15198666	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtgtacttacagcccacaTcccccagctcctcccagaag	9	8	6	18	0	0	1	0	0	0	1	3	1	3	1	5	0	4	2	5	0	3	2	rs144766527	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15198666T>A	ENST00000209540.2	+	1	876	c.790T>A	c.(790-792)Tcc>Acc	p.S264T		NM_001004713.1	NP_001004713.1	O60431	OR1I1_HUMAN	olfactory receptor, family 1, subfamily I, member 1	264						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(3)|large_intestine(7)|lung(3)|ovary(2)|stomach(2)	20						ACAGCCCACATCCCCCAGCTC	0.537													T|||	28	0.00559105	0.0008	0.0101	5008	,	,		22065	0.0		0.0189	False		,,,				2504	0.001				p.S264T		Atlas-SNP	.											OR1I1,NS,malignant_melanoma,-1,1	OR1I1	58	1	0			c.T790A						PASS	.	T	THR/SER	10,4396	17.9+/-39.9	0,10,2193	112	91	98		790	-0.9	0	19	dbSNP_134	98	132,8468	67.3+/-129.8	3,126,4171	yes	missense	OR1I1	NM_001004713.1	58	3,136,6364	AA,AT,TT		1.5349,0.227,1.0918	possibly-damaging	264/356	15198666	142,12864	2203	4300	6503	SO:0001583	missense	126370	exon1			CCCACATCCCCCA	AC004794	CCDS32937.1	19p13.1	2012-08-09				ENSG00000094661		"GPCR / Class A : Olfactory receptors"	8207	protein-coding gene	gene with protein product							Standard	NM_001004713		Approved	OR1I1P, OR19-20, OR1I1Q	uc010xoe.2	O60431		ENST00000209540.2:c.790T>A	19.37:g.15198666T>A	ENSP00000209540:p.Ser264Thr	112	0	0		132	54	0.409091	NM_001004713	Q96R92	Missense_Mutation	SNP	ENST00000209540.2	37	CCDS32937.1	19	0.0086996336996337	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	15	0.01978891820580475	T	6.410	0.443810	0.12164	0.00227	0.015349	ENSG00000094661	ENST00000209540	T	0.00258	8.41	4.33	-0.906	0.10524	GPCR, rhodopsin-like superfamily (1);	0.721661	0.10719	U	0.641993	T	0.00073	0.0002	L	0.46567	1.45	0.09310	N	1	B	0.30914	0.3	B	0.28916	0.096	T	0.09796	-1.0658	10	0.30854	T	0.27	.	1.0468	0.01571	0.2892:0.0999:0.3283:0.2825	.	264	O60431	OR1I1_HUMAN	T	264	ENSP00000209540:S264T	ENSP00000209540:S264T	S	+	1	0	OR1I1	15059666	0.000000	0.05858	0.006000	0.13384	0.236000	0.25371	-0.466000	0.06672	-0.070000	0.12908	0.449000	0.29647	TCC	T|0.989;A|0.011	0.011	strong		0.537	OR1I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465665.1			A	15198666	T	A	15198666	3	1	23	1	0	0	0	0	1	0	0	0	10967	1435	50	5	792	5	OR1I1	19	15198666	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	1197460	15198666	43930317	666	8110											
KLF2	10365	hgsc.bcm.edu	37	chr19	16436775	16436775	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caccgccactcacacctgcaGctacgcgggctgcggcaaga	9	4	11	17	4	1	1	1	0	0	1	1	1	1	1	3	2	4	4	3	2	2	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:16436775G>A	ENST00000248071.5	+	2	931	c.824G>A	c.(823-825)aGc>aAc	p.S275N	KLF2_ENST00000592003.1_Intron|CTD-2562J15.6_ENST00000588799.1_RNA	NM_016270.2	NP_057354.1	Q9Y5W3	KLF2_HUMAN	Kruppel-like factor 2	275					cell morphogenesis (GO:0000902)|cellular response to cycloheximide (GO:0071409)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to peptide (GO:1901653)|cellular response to tumor necrosis factor (GO:0071356)|erythrocyte maturation (GO:0043249)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of interleukin-6 production (GO:0032715)|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 gene expression, epigenetic (GO:0040029)|transcription, DNA-templated (GO:0006351)|Type I pneumocyte differentiation (GO:0060509)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			haematopoietic_and_lymphoid_tissue(3)|lung(1)|skin(1)	5						CACACCTGCAGCTACGCGGGC	0.697																																					p.S275N		Atlas-SNP	.											.	KLF2	10	.	0			c.G824A						PASS	.						8	5	6					19																	16436775		2074	4072	6146	SO:0001583	missense	10365	exon2			CCTGCAGCTACGC	AF123344	CCDS12343.1	19p13.11	2013-10-15	2013-10-15		ENSG00000127528	ENSG00000127528		"Kruppel-like transcription factors", "Zinc fingers, C2H2-type"	6347	protein-coding gene	gene with protein product		602016	"Kruppel-like factor 2 (lung)"			10217429, 10458913	Standard	NM_016270		Approved	LKLF	uc002ndw.3	Q9Y5W3	OTTHUMG00000182330	ENST00000248071.5:c.824G>A	19.37:g.16436775G>A	ENSP00000248071:p.Ser275Asn	50	0	0		39	5	0.128205	NM_016270	Q6IPC4|Q9UJS5|Q9UKR6	Missense_Mutation	SNP	ENST00000248071.5	37	CCDS12343.1	.	.	.	.	.	.	.	.	.	.	G	12.34	1.908073	0.33721	.	.	ENSG00000127528	ENST00000248071	T	0.08634	3.07	3.44	2.39	0.29439	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13072	0.0317	L	0.58810	1.83	0.80722	D	1	P	0.50943	0.94	P	0.52159	0.691	T	0.11867	-1.0570	9	0.25751	T	0.34	.	6.8756	0.24145	0.1023:0.3171:0.5806:0.0	.	275	Q9Y5W3	KLF2_HUMAN	N	275	ENSP00000248071:S275N	ENSP00000248071:S275N	S	+	2	0	KLF2	16297775	1.000000	0.71417	0.997000	0.53966	0.014000	0.08584	2.573000	0.46007	0.553000	0.29044	-0.384000	0.06662	AGC	.	.	none		0.697	KLF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460562.1			A	16436775	G	A	16436775	3	1	23	1	0	0	0	0	1	0	0	0	8355	971	34	2	830	2	KLF2	19	16436775	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1238109	16436775	42692208	667	8111											
KCNN1	3780	hgsc.bcm.edu	37	chr19	18104350	18104350	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgaacgaccaggctaacacGcttaccgacctagccaaggt	12	6	9	14	3	0	1	0	1	0	0	0	3	0	1	4	2	4	2	4	2	5	3	rs376852061		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:18104350G>A	ENST00000222249.9	+	10	1678	c.1359G>A	c.(1357-1359)acG>acA	p.T453T		NM_002248.3	NP_002239.2	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	453	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)	AGGCTAACACGCTTACCGACC	0.662																																					p.T453T		Atlas-SNP	.											.	KCNN1	74	.	0			c.G1359A						PASS	.	G		0,4080		0,0,2040	46	51	49		1359	-9	0.1	19		49	1,8349		0,1,4174	no	coding-synonymous	KCNN1	NM_002248.3		0,1,6214	AA,AG,GG		0.012,0.0,0.0080		453/544	18104350	1,12429	2040	4175	6215	SO:0001819	synonymous_variant	3780	exon10			TAACACGCTTACC	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.1359G>A	19.37:g.18104350G>A		242	0	0		221	101	0.457014	NM_002248	Q5KR10|Q6DJU4	Silent	SNP	ENST00000222249.9	37																																																																																				.	.	weak		0.662	KCNN1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471896.2	NM_002248		A	18104350	G	A	18104350	2	1	23	1	0	0	0	0	0	0	0	1	8087	1074	38	1		1	KCNN1	19	18104350	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1667575	18104350	41024633	668	8112											
IFI30	10437	hgsc.bcm.edu	37	chr19	18286008	18286008	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atggagatcctcaatgtcacGctggtgccctacggaaacgc	10	8	11	12	3	2	1	2	0	0	1	3	3	3	2	2	3	3	1	2	3	3	1	rs200372	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:18286008G>C	ENST00000407280.3	+	2	466	c.291G>C	c.(289-291)acG>acC	p.T97T	PIK3R2_ENST00000593731.1_3'UTR	NM_006332.3	NP_006323.2	P13284	GILT_HUMAN	interferon, gamma-inducible protein 30	97					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						TCAATGTCACGCTGGTGCCCT	0.617													G|||	37	0.00738818	0.0265	0.0029	5008	,	,		19002	0.0		0.0	False		,,,				2504	0.0				p.T97T		Atlas-SNP	.											IFI30,NS,carcinoma,+1,1	IFI30	12	1	0			c.G291C						PASS	.	G		103,4063		2,99,1982	38	38	38		291	-9.9	0	19	dbSNP_79	38	5,8409		0,5,4202	no	coding-synonymous	IFI30	NM_006332.3		2,104,6184	CC,CG,GG		0.0594,2.4724,0.8585		97/251	18286008	108,12472	2083	4207	6290	SO:0001819	synonymous_variant	10437	exon2			TGTCACGCTGGTG	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.291G>C	19.37:g.18286008G>C		93	0	0		115	50	0.434783	NM_006332	Q76MF9|Q8NEI4|Q8WU77|Q9UL08	Silent	SNP	ENST00000407280.3	37	CCDS46015.1																																																																																			G|0.994;C|0.006	0.006	strong		0.617	IFI30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466396.3	NM_006332		C	18286008	G	C	18286008	2	2	23	1	0	0	0	0	0	0	0	1	7524	1074	38	4		4	IFI30	19	18286008	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	181658	18286008	40842975	669	8113											
PDE4C	5143	hgsc.bcm.edu	37	chr19	18333062	18333062	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggactggagcctgcataatcCggcccaggccagggctggac	8	5	15	13	1	0	0	0	0	0	0	1	3	1	3	4	6	2	2	4	6	1	1	rs146818532	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:18333062C>T	ENST00000355502.3	-	6	1185	c.314G>A	c.(313-315)cGg>cAg	p.R105Q	AC068499.10_ENST00000594805.3_RNA|PDE4C_ENST00000594465.3_Missense_Mutation_p.R105Q|PDE4C_ENST00000539010.1_5'Flank|PDE4C_ENST00000447275.3_5'UTR|PDE4C_ENST00000262805.12_Missense_Mutation_p.R73Q|PDE4C_ENST00000598111.2_5'Flank|PDE4C_ENST00000597297.1_5'Flank|PDE4C_ENST00000594617.3_Missense_Mutation_p.R105Q			Q08493	PDE4C_HUMAN	phosphodiesterase 4C, cAMP-specific	105					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)	CTGCATAATCCGGCCCAGGCC	0.617													C|||	4	0.000798722	0.0008	0.0	5008	,	,		18538	0.0		0.0	False		,,,				2504	0.0031				p.R105Q		Atlas-SNP	.											.	PDE4C	80	.	0			c.G314A						PASS	.	C	GLN/ARG,GLN/ARG,	4,4402	8.1+/-20.4	0,4,2199	49	49	49		314,218,	-1.8	0	19	dbSNP_134	49	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,utr-5	PDE4C	NM_000923.4,NM_001098818.2,NM_001098819.2	43,43,	0,7,6496	TT,TC,CC		0.0349,0.0908,0.0538	benign,benign,	105/713,73/681,	18333062	7,12999	2203	4300	6503	SO:0001583	missense	5143	exon3			ATAATCCGGCCCA		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.314G>A	19.37:g.18333062C>T	ENSP00000347689:p.Arg105Gln	79	0	0		93	46	0.494624	NM_000923	B3KTC4|Q9UN44|Q9UN45|Q9UN46|Q9UPJ6	Missense_Mutation	SNP	ENST00000355502.3	37	CCDS12373.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	11.09	1.537093	0.27475	9.08E-4	3.49E-4	ENSG00000105650	ENST00000536045;ENST00000355502;ENST00000536507;ENST00000262805;ENST00000543547	T;T	0.69926	0.96;-0.44	4.13	-1.8	0.07907	.	0.902683	0.09345	N	0.814920	T	0.48714	0.1515	L	0.33485	1.01	0.80722	D	1	B;B;B	0.21905	0.054;0.062;0.003	B;B;B	0.13407	0.006;0.007;0.009	T	0.41787	-0.9489	10	0.62326	D	0.03	.	3.6337	0.08141	0.3236:0.2868:0.0:0.3896	.	214;105;73	B7Z2S3;Q08493;Q08493-3	.;PDE4C_HUMAN;.	Q	184;105;93;73;214	ENSP00000347689:R105Q;ENSP00000262805:R73Q	ENSP00000262805:R73Q	R	-	2	0	PDE4C	18194062	0.995000	0.38212	0.032000	0.17829	0.140000	0.21249	3.332000	0.52083	-0.112000	0.11979	0.306000	0.20318	CGG	C|0.999;T|0.001	0.001	strong		0.617	PDE4C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466295.1			T	18333062	C	T	18333062	3	4	23	1	0	0	0	0	1	0	0	0	11650	652	23	1	1880	1	PDE4C	19	18333062	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	47054	18333062	40795921	670	8114											
RFXANK	8625	hgsc.bcm.edu	37	chr19	19307817	19307817	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cactctcaccaaccggcagcGagggaacgaggtgtcagctc	10	5	12	14	3	2	0	2	0	1	0	4	3	2	1	2	3	4	2	2	3	2	0	rs375541634		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:19307817G>A	ENST00000303088.4	+	4	707	c.233G>A	c.(232-234)cGa>cAa	p.R78Q	RFXANK_ENST00000456252.3_Missense_Mutation_p.R78Q|RFXANK_ENST00000392324.4_Missense_Mutation_p.R77Q|RFXANK_ENST00000407360.3_Missense_Mutation_p.R78Q|RFXANK_ENST00000353145.1_Missense_Mutation_p.R77Q	NM_003721.2	NP_003712.1	O14593	RFXK_HUMAN	regulatory factor X-associated ankyrin-containing protein	78					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Ras protein signal transduction (GO:0007265)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)			NS(1)|breast(1)|endometrium(1)|lung(8)|ovary(2)|prostate(1)	14			Epithelial(12;0.00228)			AACCGGCAGCGAGGGAACGAG	0.617																																					p.R78Q		Atlas-SNP	.											.	RFXANK	31	.	0			c.G233A						PASS	.	G	GLN/ARG,GLN/ARG	0,4406		0,0,2203	81	76	77		233,230	4.1	1	19		77	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	RFXANK	NM_003721.2,NM_134440.1	43,43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	78/261,77/238	19307817	1,13005	2203	4300	6503	SO:0001583	missense	8625	exon4			GGCAGCGAGGGAA	AF094760	CCDS12395.1, CCDS12396.1, CCDS62611.1	19p12	2014-09-17			ENSG00000064490	ENSG00000064490		"Ankyrin repeat domain containing"	9987	protein-coding gene	gene with protein product	"ankyrin repeat-containing regulatory factor X-associated protein", "regulatory factor X subunit B", "RFX-Bdelta4", "DNA-binding protein RFXANK"	603200				9806546, 10072068	Standard	NM_003721		Approved	BLS, RFX-B, ANKRA1, F14150_1, MGC138628	uc002nls.3	O14593	OTTHUMG00000169224	ENST00000303088.4:c.233G>A	19.37:g.19307817G>A	ENSP00000305071:p.Arg78Gln	40	0	0		47	18	0.382979	NM_003721	O95839|Q24JQ1|Q6FGA8	Missense_Mutation	SNP	ENST00000303088.4	37	CCDS12395.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.492551	0.84962	0.0	1.16E-4	ENSG00000064490	ENST00000353145;ENST00000456252;ENST00000303088;ENST00000407360;ENST00000543652;ENST00000540981;ENST00000541873;ENST00000392324;ENST00000535017	T;T;T;T;T;T;T;T	0.70869	-0.52;1.01;1.1;1.03;1.7;-0.28;-0.52;-0.28	5.16	4.13	0.48395	.	0.054459	0.85682	N	0.000000	T	0.80391	0.4614	M	0.78049	2.395	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;0.996	T	0.78275	-0.2267	10	0.09338	T	0.73	-18.4611	11.3832	0.49770	0.0888:0.0:0.9112:0.0	.	78;78;77;78	Q6IB23;Q24JQ1;O14593-2;O14593	.;.;.;RFXK_HUMAN	Q	77;78;78;77;78;78;77;77;43	ENSP00000262804:R77Q;ENSP00000409138:R78Q;ENSP00000305071:R78Q;ENSP00000384572:R77Q;ENSP00000439581:R78Q;ENSP00000440325:R78Q;ENSP00000376138:R77Q;ENSP00000444280:R43Q	ENSP00000305071:R78Q	R	+	2	0	RFXANK	19168817	1.000000	0.71417	0.968000	0.41197	0.456000	0.32438	9.574000	0.98184	1.184000	0.42957	0.561000	0.74099	CGA	.	.	weak		0.617	RFXANK-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402923.2	NM_003721		A	19307817	G	A	19307817	3	1	23	1	0	0	0	0	1	0	0	0	13284	1058	37	1	239	1	RFXANK	19	19307817	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	974755	19307817	39821166	671	8115											
ZNF737	100129842	hgsc.bcm.edu	37	chr19	20736639	20736639	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	acgtctctaaattgcaatggCccctgaaacacacacacaac	15	7	5	14	1	1	1	0	1	1	0	2	1	1	1	2	1	3	1	2	1	5	2	rs111988999	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:20736639C>T	ENST00000427401.4	-	2	100	c.6G>A	c.(4-6)ggG>ggA	p.G2G	ZNF737_ENST00000596797.1_Silent_p.G2G|CTC-513N18.7_ENST00000595094.1_lincRNA	NM_001159293.1	NP_001152765.1	O75373	ZN737_HUMAN	zinc finger protein 737	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(2)|kidney(1)|lung(7)|ovary(1)|stomach(1)|urinary_tract(1)	13						ATTGCAATGGCCCCTGAAACA	0.408													t|||	295	0.0589058	0.2118	0.0216	5008	,	,		14230	0.0		0.0	False		,,,				2504	0.0				p.G2G		Atlas-SNP	.											.	ZNF737	50	.	0			c.G6A						PASS	.	T		248,1136		23,202,467	30	27	28		6	-1.6	0	19	dbSNP_132	28	3,3179		0,3,1588	no	coding-synonymous	ZNF737	NM_001159293.1		23,205,2055	TT,TC,CC		0.0943,17.9191,5.4972		2/537	20736639	251,4315	692	1591	2283	SO:0001819	synonymous_variant	100129842	exon2			CAATGGCCCCTGA	BC015765	CCDS54238.1	19p12	2013-01-08						"Zinc fingers, C2H2-type", "-"	32468	protein-coding gene	gene with protein product		603984					Standard	NM_001159293		Approved	ZNF102	uc002npa.3	O75373		ENST00000427401.4:c.6G>A	19.37:g.20736639C>T		65	0	0		71	40	0.56338	NM_001159293	C9JHM3	Silent	SNP	ENST00000427401.4	37	CCDS54238.1																																																																																			C|0.940;T|0.060	0.060	strong		0.408	ZNF737-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447844.2	NM_145289		T	20736639	C	T	20736639	2	4	23	1	0	0	0	0	0	0	0	1	18141	726	26	2		2	ZNF737	19	20736639	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1428822	20736639	38392344	672	8116											
ZNF626	199777	hgsc.bcm.edu	37	chr19	20808414	20808414	+	Missense_Mutation	SNP	C	C	T																															tttggaaagaatctttcatgCtctgctctggccaaaggtct																								rs8110802	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:20808414C>T	ENST00000601440.1	-	4	415	c.269G>A	c.(268-270)aGc>aAc	p.S90N	CTC-513N18.7_ENST00000595094.1_lincRNA	NM_001076675.2	NP_001070143.1	Q68DY1	ZN626_HUMAN	zinc finger protein 626	90			S -> N (in dbSNP:rs8110802).		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						ATCTTTCATGCTCTGCTCTGG	0.323													N|||	363	0.072484	0.2436	0.0259	5008	,	,		17039	0.0		0.0139	False		,,,				2504	0.0092				p.S90N		Atlas-SNP	.											.	ZNF626	121	.	0			c.G269A						PASS	.	C	ASN/SER	774,3566		90,594,1486	51	57	55		269	1.1	0	19	dbSNP_116	55	84,8476		3,78,4199	no	missense	ZNF626	NM_001076675.2	46	93,672,5685	TT,TC,CC		0.9813,17.8341,6.6512	benign	90/529	20808414	858,12042	2170	4280	6450	SO:0001583	missense	199777	exon4			TTCATGCTCTGCT	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.269G>A	19.37:g.20808414C>T	ENSP00000469958:p.Ser90Asn	86	0	0		122	50	0.409836	NM_001076675	Q8N8T4|Q96QM1	Missense_Mutation	SNP	ENST00000601440.1	37	CCDS42535.1	140	0.0641025641025641	119	0.241869918699187	10	0.027624309392265192	0	0.0	11	0.014511873350923483	N	2.780	-0.253612	0.05829	0.178341	0.009813	ENSG00000188171	ENST00000392298;ENST00000453075;ENST00000305570	.	.	.	1.08	1.08	0.20341	.	.	.	.	.	T	0.00012	0.0000	N	0.20574	0.59	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.33752	-0.9856	7	0.14656	T	0.56	.	3.4203	0.07391	0.0:0.703:0.0:0.297	rs8110802;rs16996433;rs8110802	90	Q68DY1	ZN626_HUMAN	N	90;14;90	.	ENSP00000445201:S90N	S	-	2	0	ZNF626	20600254	0.000000	0.05858	0.012000	0.15200	0.263000	0.26337	-0.331000	0.07914	0.503000	0.28060	0.289000	0.19496	AGC	C|0.961;T|0.039	0.039	strong		0.323	ZNF626-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447845.2	NM_145297		T	20808414	C	T	20808414	3	4	23	1	0	0	0	0	1	0	0	0	18065	797	28	2	1321	2	ZNF626	19	20808414	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	71775	20808414	38320569	673	8117	104	2									
ZNF626	199777	hgsc.bcm.edu	37	chr19	20808418	20808418	+	Missense_Mutation	SNP	G	G	C																															gaaagaatctttcatgctctGctctggccaaaggtcttggg																								rs8111015	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:20808418G>C	ENST00000601440.1	-	4	411	c.265C>G	c.(265-267)Cag>Gag	p.Q89E	CTC-513N18.7_ENST00000595094.1_lincRNA	NM_001076675.2	NP_001070143.1	Q68DY1	ZN626_HUMAN	zinc finger protein 626	89			Q -> E (in dbSNP:rs8111015).		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						TTCATGCTCTGCTCTGGCCAA	0.313													N|||	363	0.072484	0.2436	0.0259	5008	,	,		17032	0.0		0.0139	False		,,,				2504	0.0092				p.Q89E		Atlas-SNP	.											.	ZNF626	121	.	0			c.C265G						PASS	.	G	GLU/GLN	758,3578		90,578,1500	50	56	54		265	1.1	0	19	dbSNP_116	54	82,8474		3,76,4199	no	missense	ZNF626	NM_001076675.2	29	93,654,5699	CC,CG,GG		0.9584,17.4815,6.5157	benign	89/529	20808418	840,12052	2168	4278	6446	SO:0001583	missense	199777	exon4			TGCTCTGCTCTGG	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.265C>G	19.37:g.20808418G>C	ENSP00000469958:p.Gln89Glu	85	0	0		118	48	0.40678	NM_001076675	Q8N8T4|Q96QM1	Missense_Mutation	SNP	ENST00000601440.1	37	CCDS42535.1	140	0.0641025641025641	119	0.241869918699187	10	0.027624309392265192	0	0.0	11	0.014511873350923483	N	7.931	0.740652	0.15642	0.174815	0.009584	ENSG00000188171	ENST00000392298;ENST00000453075;ENST00000305570	.	.	.	1.08	1.08	0.20341	.	.	.	.	.	T	0.00039	0.0001	M	0.91818	3.245	0.58432	P	1.999999999946489E-6	B	0.20780	0.048	B	0.29524	0.103	T	0.10474	-1.0628	7	0.37606	T	0.19	.	7.5639	0.27868	0.0:0.0:1.0:0.0	rs8111015;rs8111015	89	Q68DY1	ZN626_HUMAN	E	89;13;89	.	ENSP00000445201:Q89E	Q	-	1	0	ZNF626	20600258	0.000000	0.05858	0.014000	0.15608	0.369000	0.29798	-0.692000	0.05127	0.503000	0.28060	0.289000	0.19496	CAG	G|0.944;C|0.056	0.056	strong		0.313	ZNF626-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447845.2	NM_145297		C	20808418	G	C	20808418	3	2	23	1	0	0	0	0	1	0	0	0	18065	1328	46	4	1325	4	ZNF626	19	20808418	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	4	20808418	38320565	674	8118	104	2									
ZNF91	7644	hgsc.bcm.edu	37	chr19	23543078	23543078	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttctctctggtatgaattctCttatgttcagtaagggttga	8	18	9	6	0	4	2	1	2	3	0	6	2	4	2	0	2	0	4	0	2	4	7	rs117657695	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:23543078C>T	ENST00000300619.7	-	4	2908	c.2703G>A	c.(2701-2703)aaG>aaA	p.K901K	ZNF91_ENST00000397082.2_Silent_p.K869K|ZNF91_ENST00000596528.1_5'Flank|ZNF91_ENST00000599743.1_Intron	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	901					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)				TATGAATTCTCTTATGTTCAG	0.388													C|||	12	0.00239617	0.0023	0.0029	5008	,	,		21504	0.0		0.007	False		,,,				2504	0.0				p.K901K		Atlas-SNP	.											.	ZNF91	349	.	0			c.G2703A						PASS	.	C		6,4362	9.9+/-24.2	0,6,2178	59	65	63		2703	-1.5	0	19	dbSNP_132	63	70,8512	41.7+/-99.0	1,68,4222	no	coding-synonymous	ZNF91	NM_003430.2		1,74,6400	TT,TC,CC		0.8157,0.1374,0.5869		901/1192	23543078	76,12874	2184	4291	6475	SO:0001819	synonymous_variant	7644	exon4			AATTCTCTTATGT	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.2703G>A	19.37:g.23543078C>T		36	0	0		62	27	0.435484	NM_003430	A8K5E1|B7Z6G6	Silent	SNP	ENST00000300619.7	37	CCDS42541.1																																																																																			C|0.995;T|0.005	0.005	strong		0.388	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		T	23543078	C	T	23543078	2	4	23	1	0	0	0	0	0	0	0	1	18215	912	32	2		2	ZNF91	19	23543078	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	2734660	23543078	35585905	675	8119											
CCDC123	84902	hgsc.bcm.edu	37	chr19	33414392	33414392	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttatttaactcttggtgcaaTtcttcattttctttcaccac	8	20	3	10	0	5	0	2	0	3	0	5	0	5	0	1	1	2	1	1	1	3	9	rs17599843	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:33414392T>C	ENST00000305768.5	-	12	1309	c.1221A>G	c.(1219-1221)gaA>gaG	p.E407E		NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	407					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						CTTGGTGCAATTCTTCATTTT	0.373													T|||	38	0.00758786	0.0	0.0058	5008	,	,		18272	0.001		0.008	False		,,,				2504	0.0256				p.E407E		Atlas-SNP	.											.	CEP89	82	.	0			c.A1221G						PASS	.	T		12,4392	19.1+/-41.9	0,12,2190	250	221	231		1221	-2.9	0	19	dbSNP_123	231	70,8528	42.6+/-100.3	0,70,4229	no	coding-synonymous	CEP89	NM_032816.3		0,82,6419	CC,CT,TT		0.8141,0.2725,0.6307		407/784	33414392	82,12920	2202	4299	6501	SO:0001819	synonymous_variant	84902	exon12			GTGCAATTCTTCA	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.1221A>G	19.37:g.33414392T>C		213	0	0		216	97	0.449074	NM_032816	B9EGA6|Q8N5J8	Silent	SNP	ENST00000305768.5	37	CCDS32987.1																																																																																			T|0.995;C|0.005	0.005	strong		0.373	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816		C	33414392	T	C	33414392	2	2	23	1	0	0	0	0	0	0	0	1	2761	1490	52	3		3	CCDC123	19	33414392	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	9871314	33414392	25714591	676	8120											
SBSN	374897	hgsc.bcm.edu	37	chr19	36018272	36018272	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctcatttccggcctgcccCgcagcatggtgggccccctg	3	8	12	18	2	1	0	1	0	0	0	2	0	2	0	7	3	2	2	7	3	0	1	rs12461911	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:36018272C>T	ENST00000452271.2	-	1	940	c.912G>A	c.(910-912)gcG>gcA	p.A304A	SBSN_ENST00000518157.1_Intron	NM_001166034.1	NP_001159506.1	Q6UWP8	SBSN_HUMAN	suprabasin	304	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)			CGGCCTGCCCCGCAGCATGGT	0.652													c|||	1051	0.209864	0.0371	0.3401	5008	,	,		21069	0.3631		0.1392	False		,,,				2504	0.2658				p.A304A		Atlas-SNP	.											.	SBSN	58	.	0			c.G912A						PASS	.	A	,,	86,1298		3,80,609	29	37	34		912,,	-8.9	0	19	dbSNP_120	34	440,2742		33,374,1184	no	coding-synonymous,intron,intron	SBSN	NM_001166034.1,NM_001166035.1,NM_198538.3	,,	36,454,1793	TT,TC,CC		13.8278,6.2139,11.5199	,,	304/591,,	36018272	526,4040	692	1591	2283	SO:0001819	synonymous_variant	374897	exon1			CTGCCCCGCAGCA	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.912G>A	19.37:g.36018272C>T		1	0	0		4	4	1	NM_001166034	A8K5J0|E9PBV3	Silent	SNP	ENST00000452271.2	37	CCDS54253.1																																																																																			C|0.795;T|0.205	0.205	strong		0.652	SBSN-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109463.3	NM_198538		T	36018272	C	T	36018272	2	4	23	1	0	0	0	0	0	0	0	1	13879	639	23	1		1	SBSN	19	36018272	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	2603880	36018272	23110711	677	8121											
NPHS1	4868	hgsc.bcm.edu	37	chr19	36339247	36339247	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtcagaccgttgtcctccCgccgcgccaggaatgtcagg	6	7	14	14	4	2	1	2	0	0	1	4	2	4	2	5	3	0	1	5	3	1	1	rs33950747	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:36339247C>T	ENST00000378910.5	-	10	1222	c.1223G>A	c.(1222-1224)cGg>cAg	p.R408Q	NPHS1_ENST00000353632.6_Missense_Mutation_p.R408Q	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	408	Ig-like C2-type 4.		R -> Q (in NPHS1; uncertain pathological significance; does not affect protein expression on the cell surface; dbSNP:rs33950747). {ECO:0000269|PubMed:11317351, ECO:0000269|PubMed:20172850, ECO:0000269|PubMed:9915943}.		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)			GTTGTCCTCCCGCCGCGCCAG	0.577													C|||	103	0.0205671	0.0023	0.0403	5008	,	,		17854	0.0		0.0557	False		,,,				2504	0.0164				p.R408Q		Atlas-SNP	.											.	NPHS1	165	.	0			c.G1223A	GRCh37	CM990958	NPHS1	M	rs33950747	PASS	.	C	GLN/ARG	56,4350	53.6+/-89.4	0,56,2147	99	87	91		1223	5.5	0.9	19	dbSNP_126	91	545,8055	151.0+/-205.8	27,491,3782	yes	missense	NPHS1	NM_004646.3	43	27,547,5929	TT,TC,CC		6.3372,1.271,4.6209	probably-damaging	408/1242	36339247	601,12405	2203	4300	6503	SO:0001583	missense	4868	exon10			TCCTCCCGCCGCG		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.1223G>A	19.37:g.36339247C>T	ENSP00000368190:p.Arg408Gln	81	0	0		98	38	0.387755	NM_004646	A6NDH2|C3RX61	Missense_Mutation	SNP	ENST00000378910.5	37	CCDS32996.1	64	0.029304029304029304	2	0.0040650406504065045	15	0.04143646408839779	0	0.0	47	0.06200527704485488	C	20.4	3.982368	0.74474	0.01271	0.063372	ENSG00000161270	ENST00000378910;ENST00000353632	T;T	0.78003	-1.14;-1.14	5.53	5.53	0.82687	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.135150	0.49305	D	0.000144	T	0.51024	0.1650	M	0.72894	2.215	0.48901	D	0.999722	D	0.89917	1.0	D	0.85130	0.997	T	0.72297	-0.4335	10	0.35671	T	0.21	-25.372	16.9674	0.86290	0.0:1.0:0.0:0.0	rs33950747	408	O60500	NPHN_HUMAN	Q	408	ENSP00000368190:R408Q;ENSP00000343634:R408Q	ENSP00000343634:R408Q	R	-	2	0	NPHS1	41031087	0.795000	0.28851	0.933000	0.37362	0.485000	0.33311	5.506000	0.66993	2.596000	0.87737	0.591000	0.81541	CGG	C|0.958;T|0.042	0.042	strong		0.577	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1			T	36339247	C	T	36339247	3	4	23	1	0	0	0	0	1	0	0	0	10591	652	23	1	2582	1	NPHS1	19	36339247	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	320975	36339247	22789736	678	8122											
WDR62	284403	hgsc.bcm.edu	37	chr19	36594676	36594676	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagccccccgtggataccCagcctggcgtcaccgtccct	5	7	10	19	3	1	0	1	0	0	0	2	1	2	1	7	2	4	1	7	2	1	1	rs35811023	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:36594676C>G	ENST00000270301.7	+	30	3931	c.3931C>G	c.(3931-3933)Cag>Gag	p.Q1311E	WDR62_ENST00000401500.2_Missense_Mutation_p.Q1316E			O43379	WDR62_HUMAN	WD repeat domain 62	1311			Q -> E (in dbSNP:rs35811023).		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)			CGTGGATACCCAGCCTGGCGT	0.677													C|||	7	0.00139776	0.0008	0.0	5008	,	,		19234	0.0		0.006	False		,,,				2504	0.0				p.Q1316E		Atlas-SNP	.											.	WDR62	102	.	0			c.C3946G						PASS	.	C	GLU/GLN,GLU/GLN	9,4397	15.5+/-35.6	0,9,2194	71	62	65		3946,3931	1.5	0	19	dbSNP_126	65	54,8546	34.8+/-89.0	0,54,4246	yes	missense,missense	WDR62	NM_001083961.1,NM_173636.4	29,29	0,63,6440	GG,GC,CC		0.6279,0.2043,0.4844	benign,benign	1316/1524,1311/1519	36594676	63,12943	2203	4300	6503	SO:0001583	missense	284403	exon30			GATACCCAGCCTG	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.3931C>G	19.37:g.36594676C>G	ENSP00000270301:p.Gln1311Glu	57	0	0		52	27	0.519231	NM_001083961	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Missense_Mutation	SNP	ENST00000270301.7	37	CCDS33001.1	5	0.0022893772893772895	1	0.0020325203252032522	0	0.0	0	0.0	4	0.005277044854881266	C	6.239	0.412249	0.11812	0.002043	0.006279	ENSG00000075702	ENST00000401500;ENST00000270301	T;T	0.46451	0.96;0.87	5.06	1.47	0.22746	.	0.568333	0.16576	N	0.208382	T	0.13970	0.0338	N	0.17082	0.46	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.25882	-1.0119	10	0.02654	T	1	-5.5063	7.7082	0.28663	0.3295:0.5109:0.1597:0.0	rs35811023;rs62636634	1316;1311	O43379-4;O43379	.;WDR62_HUMAN	E	1316;1311	ENSP00000384792:Q1316E;ENSP00000270301:Q1311E	ENSP00000270301:Q1311E	Q	+	1	0	WDR62	41286516	0.003000	0.15002	0.007000	0.13788	0.008000	0.06430	0.484000	0.22308	0.689000	0.31550	0.555000	0.69702	CAG	C|0.995;G|0.005	0.005	strong		0.677	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671		G	36594676	C	G	36594676	3	3	23	1	0	0	0	0	1	0	0	0	17328	595	21	4	4064	4	WDR62	19	36594676	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	255429	36594676	22534307	679	8123											
ZNF529	57711	hgsc.bcm.edu	37	chr19	37038584	37038584	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgagtaagttgtgcatgcacTctaaaggatttcccacagaa	13	10	9	9	1	1	1	0	0	1	1	2	3	2	2	1	1	2	4	1	1	4	4	rs183728423	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:37038584T>C	ENST00000591340.1	-	5	1034	c.876A>G	c.(874-876)agA>agG	p.R292R	ZNF529_ENST00000334116.7_Silent_p.R187R	NM_020951.4	NP_066002.3	Q6P280	ZN529_HUMAN	zinc finger protein 529	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)			breast(1)	1	Esophageal squamous(110;0.198)					GTGCATGCACTCTAAAGGATT	0.383													T|||	10	0.00199681	0.0	0.0	5008	,	,		20320	0.0		0.007	False		,,,				2504	0.0031				p.R292R		Atlas-SNP	.											.	ZNF529	82	.	0			c.A876G						PASS	.	T	,,	3,4007		0,3,2002	144	144	144		876,822,876	-0.1	0.5	19		144	44,8372		0,44,4164	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF529	NM_001145649.1,NM_001145650.1,NM_020951.4	,,	0,47,6166	CC,CT,TT		0.5228,0.0748,0.3782	,,	292/564,274/546,292/564	37038584	47,12379	2005	4208	6213	SO:0001819	synonymous_variant	57711	exon6			ATGCACTCTAAAG	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.876A>G	19.37:g.37038584T>C		162	0	0		182	86	0.472527	NM_001145649	K7EKE1|Q9H731|Q9HCF7	Silent	SNP	ENST00000591340.1	37	CCDS54256.1																																																																																			T|0.998;C|0.002	0.002	strong		0.383	ZNF529-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452730.1	NM_020951		C	37038584	T	C	37038584	2	2	23	1	0	0	0	0	0	0	0	1	17985	1548	54	3		3	ZNF529	19	37038584	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	443908	37038584	22090399	680	8124											
FAM98C	147965	hgsc.bcm.edu	37	chr19	38896204	38896204	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctcagagatcagtaccgcTgccgccgctgcctcctcctc	5	8	9	19	3	2	1	2	0	0	1	5	2	4	1	7	0	3	3	7	0	1	1	rs117354953	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:38896204T>G	ENST00000252530.5	+	6	698	c.679T>G	c.(679-681)Tgc>Ggc	p.C227G	FAM98C_ENST00000343358.7_Missense_Mutation_p.C201G|FAM98C_ENST00000588262.1_Intron	NM_174905.3	NP_777565.3	Q17RN3	FA98C_HUMAN	family with sequence similarity 98, member C	227										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)			TCAGTACCGCTGCCGCCGCTG	0.592													T|||	24	0.00479233	0.0008	0.0058	5008	,	,		16729	0.0		0.0169	False		,,,				2504	0.002				p.C227G		Atlas-SNP	.											FAM98C,NS,carcinoma,-1,1	FAM98C	39	1	0			c.T679G						PASS	.	T	GLY/CYS	12,4366		0,12,2177	52	59	57		679	4	1	19	dbSNP_132	57	127,8463		0,127,4168	yes	missense	FAM98C	NM_174905.3	159	0,139,6345	GG,GT,TT		1.4785,0.2741,1.0719	benign	227/350	38896204	139,12829	2189	4295	6484	SO:0001583	missense	147965	exon6			TACCGCTGCCGCC		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.679T>G	19.37:g.38896204T>G	ENSP00000252530:p.Cys227Gly	66	0	0		85	42	0.494118	NM_174905	A6NMW3|Q66K45	Missense_Mutation	SNP	ENST00000252530.5	37	CCDS42562.1	19	0.0086996336996337	2	0.0040650406504065045	3	0.008287292817679558	1	0.0017482517482517483	13	0.017150395778364115	T	13.51	2.259355	0.39995	0.002741	0.014785	ENSG00000130244	ENST00000252530;ENST00000343358	T;T	0.45668	0.89;0.89	5.02	3.99	0.46301	.	0.548059	0.15348	N	0.267098	T	0.25457	0.0619	M	0.79926	2.475	0.44295	D	0.997163	P;B	0.47910	0.902;0.086	B;B	0.38225	0.268;0.056	T	0.13602	-1.0503	10	0.30854	T	0.27	-0.3593	8.8557	0.35227	0.0:0.0:0.1896:0.8104	.	201;227	Q17RN3-2;Q17RN3	.;FA98C_HUMAN	G	227;201	ENSP00000252530:C227G;ENSP00000340348:C201G	ENSP00000252530:C227G	C	+	1	0	FAM98C	43588044	0.998000	0.40836	0.969000	0.41365	0.832000	0.47134	2.019000	0.41001	0.738000	0.32606	0.456000	0.33151	TGC	T|0.989;G|0.011	0.011	strong		0.592	FAM98C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459222.1	NM_174905		G	38896204	T	G	38896204	3	3	23	1	0	0	0	0	1	0	0	0	5666	1580	55	5	701	5	FAM98C	19	38896204	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	1857620	38896204	20232779	681	8125											
PLEKHG2	64857	hgsc.bcm.edu	37	chr19	39909394	39909394	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgctgcaacctgagcgtgagCgagagtccccgagaccctct	8	7	12	14	3	1	4	0	2	1	2	2	6	2	4	4	0	5	2	4	0	1	0	rs146672674	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:39909394C>T	ENST00000409794.3	+	10	1954	c.1104C>T	c.(1102-1104)agC>agT	p.S368S	PLEKHG2_ENST00000458508.2_Silent_p.S309S|PLEKHG2_ENST00000425673.1_Silent_p.S368S|PLEKHG2_ENST00000409797.2_Silent_p.S368S|PLEKHG2_ENST00000378550.1_Silent_p.S368S	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	368	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)			TGAGCGTGAGCGAGAGTCCCC	0.577													C|||	2	0.000399361	0.0015	0.0	5008	,	,		18474	0.0		0.0	False		,,,				2504	0.0				p.S368S		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.C1104T						PASS	.	C		6,4400	11.4+/-27.6	0,6,2197	230	231	231		1104	-3.3	1	19	dbSNP_134	231	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	PLEKHG2	NM_022835.2		0,12,6491	TT,TC,CC		0.0698,0.1362,0.0923		368/1387	39909394	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	64857	exon10			CGTGAGCGAGAGT	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.1104C>T	19.37:g.39909394C>T		81	0	0		85	39	0.458824	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Silent	SNP	ENST00000409794.3	37	CCDS33022.2	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	9.421	1.082999	0.20309	0.001362	6.98E-4	ENSG00000090924	ENST00000205135	.	.	.	4.4	-3.26	0.05064	.	.	.	.	.	T	0.48537	0.1505	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44406	-0.9330	4	.	.	.	.	6.3348	0.21291	0.1262:0.3477:0.0:0.5261	.	.	.	.	V	265	.	.	A	+	2	0	PLEKHG2	44601234	0.000000	0.05858	0.990000	0.47175	0.799000	0.45148	-4.066000	0.00302	-0.329000	0.08527	0.462000	0.41574	GCG	C|0.999;T|0.001	0.001	strong		0.577	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835		T	39909394	C	T	39909394	2	4	23	1	0	0	0	0	0	0	0	1	12078	767	27	1		1	PLEKHG2	19	39909394	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1013190	39909394	19219589	682	8126											
PLEKHG2	64857	hgsc.bcm.edu	37	chr19	39914225	39914225	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcatcagccaatgccccgcGccgccggcctcgggttctgg	4	6	14	17	5	2	0	1	0	1	0	3	0	2	0	6	4	2	2	6	4	1	1	rs201914405	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:39914225G>C	ENST00000409794.3	+	18	3381	c.2531G>C	c.(2530-2532)cGc>cCc	p.R844P	PLEKHG2_ENST00000458508.2_Missense_Mutation_p.R785P|PLEKHG2_ENST00000425673.1_Missense_Mutation_p.R815P|PLEKHG2_ENST00000409797.2_Intron|CTB-60E11.4_ENST00000601124.1_lincRNA|PLEKHG2_ENST00000378550.1_Intron	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	844					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)			AATGCCCCGCGCCGCCGGCCT	0.697													G|||	3	0.000599042	0.0	0.0	5008	,	,		13101	0.0		0.001	False		,,,				2504	0.002				p.R844P		Atlas-SNP	.											PLEKHG2_ENST00000458508,colon,carcinoma,0,3	PLEKHG2	329	3	0			c.G2531C						PASS	.	G	PRO/ARG	0,4390		0,0,2195	12	13	13		2531	5.7	1	19		13	5,8565		0,5,4280	yes	missense	PLEKHG2	NM_022835.2	103	0,5,6475	CC,CG,GG		0.0583,0.0,0.0386	probably-damaging	844/1387	39914225	5,12955	2195	4285	6480	SO:0001583	missense	64857	exon18			CCCCGCGCCGCCG	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.2531G>C	19.37:g.39914225G>C	ENSP00000386733:p.Arg844Pro	78	0	0		43	23	0.534884	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	37	CCDS33022.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.2|22.2	4.264441|4.264441	0.80358|0.80358	0.0|0.0	5.83E-4|5.83E-4	ENSG00000090924|ENSG00000090924	ENST00000205135|ENST00000409794;ENST00000425673;ENST00000458508	.|T;T;T	.|0.73575	.|-0.62;-0.67;-0.76	5.7|5.7	5.7|5.7	0.88788|0.88788	.|.	.|0.000000	.|0.48767	.|D	.|0.000180	T|T	0.77864|0.77864	0.4194|0.4194	L|L	0.32530|0.32530	0.975|0.975	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.63880	.|0.993;0.988;0.988	.|P;P;P	.|0.62649	.|0.905;0.806;0.806	T|T	0.75428|0.75428	-0.3321|-0.3321	5|9	.|.	.|.	.|.	.|.	15.3419|15.3419	0.74303|0.74303	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|815;844;785	.|Q9H7P9-3;Q9H7P9;E7ESZ3	.|.;PKHG2_HUMAN;.	P|P	712|844;815;785	.|ENSP00000386733:R844P;ENSP00000392906:R815P;ENSP00000408857:R785P	.|.	A|R	+|+	1|2	0|0	PLEKHG2|PLEKHG2	44606065|44606065	0.911000|0.911000	0.30947|0.30947	1.000000|1.000000	0.80357|0.80357	0.765000|0.765000	0.43378|0.43378	1.287000|1.287000	0.33284|0.33284	2.694000|2.694000	0.91930|0.91930	0.655000|0.655000	0.94253|0.94253	GCC|CGC	.	.	weak		0.697	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835		C	39914225	G	C	39914225	3	2	23	1	0	0	0	0	1	0	0	0	12078	1087	38	4	2597	4	PLEKHG2	19	39914225	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	4831	39914225	19214758	683	8127											
ZNF780A	284323	hgsc.bcm.edu	37	chr19	40580545	40580545	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agtatgcaatttctgatgtcGaataagttgcatatgaagtc	13	14	9	5	1	1	2	0	2	1	0	3	3	1	2	0	0	2	4	0	0	6	5	rs149702621	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:40580545G>A	ENST00000595687.2	-	6	2013	c.1804C>T	c.(1804-1806)Cga>Tga	p.R602*	ZNF780A_ENST00000340963.5_Nonsense_Mutation_p.R602*|ZNF780A_ENST00000414720.2_Intron|ZNF780A_ENST00000455521.1_Nonsense_Mutation_p.R603*|AC005614.5_ENST00000595508.1_RNA|ZNF780A_ENST00000450241.2_Nonsense_Mutation_p.R568*|ZNF780A_ENST00000594395.1_Nonsense_Mutation_p.R603*	NM_001010880.2	NP_001010880.2	O75290	Z780A_HUMAN	zinc finger protein 780A	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)|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)					TTCTGATGTCGAATAAGTTGC	0.398													g|||	2	0.000399361	0.0	0.0	5008	,	,		23667	0.0		0.002	False		,,,				2504	0.0				p.R603X		Atlas-SNP	.											ZNF780A_ENST00000455521,NS,carcinoma,0,2	ZNF780A	156	2	0			c.C1807T						PASS	.	G	stop/ARG,stop/ARG,stop/ARG,	1,4405	2.1+/-5.4	0,1,2202	140	138	139		1804,1807,1804,	-0.8	0	19	dbSNP_134	139	11,8589	7.7+/-29.5	0,11,4289	no	stop-gained,stop-gained,stop-gained,intron	ZNF780A	NM_001010880.2,NM_001142577.1,NM_001142578.1,NM_001142579.1	,,,	0,12,6491	AA,AG,GG		0.1279,0.0227,0.0923	,,,	602/642,603/643,602/642,	40580545	12,12994	2203	4300	6503	SO:0001587	stop_gained	284323	exon6			GATGTCGAATAAG	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.1804C>T	19.37:g.40580545G>A	ENSP00000472189:p.Arg602*	192	0	0		158	72	0.455696	NM_001142577	E9PB48|Q6ZN87	Nonsense_Mutation	SNP	ENST00000595687.2	37	CCDS33026.2	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	g	36	5.627543	0.96671	2.27E-4	0.001279	ENSG00000197782	ENST00000450241;ENST00000455521;ENST00000340963	.	.	.	1.93	-0.836	0.10770	.	.	.	.	.	.	.	.	.	.	.	0.51482	D	0.999922	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	.	4.3525	0.11162	0.1631:0.4575:0.3794:0.0	.	.	.	.	X	602;603;602	.	ENSP00000341507:R602X	R	-	1	2	ZNF780A	45272385	0.000000	0.05858	0.000000	0.03702	0.504000	0.33889	-5.163000	0.00145	-0.286000	0.09076	0.313000	0.20887	CGA	G|0.999;A|0.001	0.001	strong		0.398	ZNF780A-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000470066.1	NM_001010880		A	40580545	G	A	40580545	4	1	23	1	0	0	0	0	0	1	0	0	18167	1066	37	1	252	1	ZNF780A	19	40580545	Nonsense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	666320	40580545	18548438	684	8128											
HIPK4	147746	hgsc.bcm.edu	37	chr19	40886987	40886987	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gcgcctcccggtcagggaagGttagccgactggccacactg	7	6	14	14	3	1	0	1	0	0	0	2	2	2	1	4	4	1	1	4	4	2	1	rs79330270	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:40886987G>T	ENST00000291823.2	-	3	1195	c.911C>A	c.(910-912)aCc>aAc	p.T304N		NM_144685.3	NP_653286.2	Q8NE63	HIPK4_HUMAN	homeodomain interacting protein kinase 4	304	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				histone phosphorylation (GO:0016572)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of signal transduction by p53 class mediator (GO:1901796)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	20			Lung(22;4.95e-05)|LUSC - Lung squamous cell carcinoma(20;0.000292)			GTCAGGGAAGGTTAGCCGACT	0.612													G|||	10	0.00199681	0.0	0.0043	5008	,	,		19961	0.0		0.006	False		,,,				2504	0.001				p.T304N		Atlas-SNP	.											.	HIPK4	100	.	0			c.C911A						PASS	.	G	ASN/THR	13,4391		0,13,2189	44	40	41		911	-2.1	1	19	dbSNP_131	41	76,8522		0,76,4223	yes	missense	HIPK4	NM_144685.3	65	0,89,6412	TT,TG,GG		0.8839,0.2952,0.6845	benign	304/617	40886987	89,12913	2202	4299	6501	SO:0001583	missense	147746	exon3			GGGAAGGTTAGCC	BC034501	CCDS12555.1	19q13.2	2008-02-05				ENSG00000160396			19007	protein-coding gene	gene with protein product		611712					Standard	NM_144685		Approved	FLJ32818	uc002onp.3	Q8NE63		ENST00000291823.2:c.911C>A	19.37:g.40886987G>T	ENSP00000291823:p.Thr304Asn	67	0	0		58	33	0.568965	NM_144685	A8K863|Q96M54	Missense_Mutation	SNP	ENST00000291823.2	37	CCDS12555.1	.	.	.	.	.	.	.	.	.	.	G	2.504	-0.314455	0.05422	0.002952	0.008839	ENSG00000160396	ENST00000291823;ENST00000452139	T	0.20200	2.09	5.67	-2.14	0.07123	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.892967	0.09630	N	0.776416	T	0.03564	0.0102	N	0.01140	-0.99	0.25057	N	0.9911	B	0.06786	0.001	B	0.09377	0.004	T	0.41770	-0.9490	10	0.10902	T	0.67	.	5.9158	0.19053	0.0701:0.4725:0.2585:0.1989	.	304	Q8NE63	HIPK4_HUMAN	N	304;269	ENSP00000291823:T304N	ENSP00000291823:T304N	T	-	2	0	HIPK4	45578827	0.005000	0.15991	0.958000	0.39756	0.028000	0.11728	0.266000	0.18534	-0.454000	0.07066	-1.140000	0.01884	ACC	A|0.001;G|0.993;T|0.006	0.006	strong		0.612	HIPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462593.1	NM_144685		T	40886987	G	T	40886987	3	4	23	1	0	0	0	0	1	0	0	0	7128	1261	44	4	947	4	HIPK4	19	40886987	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	306442	40886987	18241996	685	8129											
CYP2A6	1548	hgsc.bcm.edu	37	chr19	41351211	41351211	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gatagcaccttagggaggaaGaaatcccgaaacttggtgtc	13	8	12	8	1	0	1	0	0	0	1	2	5	1	3	2	3	2	1	2	3	5	3	rs150586234	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:41351211G>A	ENST00000301141.5	-	7	1169	c.1149C>T	c.(1147-1149)ttC>ttT	p.F383F	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	383					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)	TAGGGAGGAAGAAATCCCGAA	0.552													.|||	8	0.00159744	0.0	0.0029	5008	,	,		16324	0.0		0.006	False		,,,				2504	0.0				p.F383F		Atlas-SNP	.											.	CYP2A6	69	.	0			c.C1149T						PASS	.						101	99	100					19																	41351211		2203	4300	6503	SO:0001819	synonymous_variant	1548	exon7			GAGGAAGAAATCC	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.1149C>T	19.37:g.41351211G>A		213	0	0		235	18	0.0765957	NM_000762	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Silent	SNP	ENST00000301141.5	37	CCDS12568.1																																																																																			G|0.998;A|0.002	0.002	strong		0.552	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762		A	41351211	G	A	41351211	2	1	23	1	0	0	0	0	0	0	0	1	4164	933	33	2		2	CYP2A6	19	41351211	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	464224	41351211	17777772	686	8130											
CYP2A13	1553	hgsc.bcm.edu	37	chr19	41600311	41600311	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagggtcaacaaggacaccAagtttcgggatttcttcctc	11	10	9	11	1	2	0	1	0	1	0	5	2	3	2	2	3	1	1	2	3	3	3	rs115698903	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:41600311A>C	ENST00000330436.3	+	7	1135	c.1135A>C	c.(1135-1137)Aag>Cag	p.K379Q		NM_000766.4	NP_000757.2	Q16696	CP2AD_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 13	379					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)	CAAGGACACCAAGTTTCGGGA	0.567													a|||	83	0.0165735	0.0061	0.0	5008	,	,		19775	0.0069		0.008	False		,,,				2504	0.0613				p.K379Q		Atlas-SNP	.											CYP2A13,NS,carcinoma,-1,1	CYP2A13	90	1	0			c.A1135C						PASS	.	A	GLN/LYS	19,4387		0,19,2184	116	106	110		1135	2.2	1	19	dbSNP_132	110	46,8554		0,46,4254	yes	missense	CYP2A13	NM_000766.3	53	0,65,6438	CC,CA,AA		0.5349,0.4312,0.4998	benign	379/495	41600311	65,12941	2203	4300	6503	SO:0001583	missense	1553	exon7			GACACCAAGTTTC	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.1135A>C	19.37:g.41600311A>C	ENSP00000332679:p.Lys379Gln	229	0	0		213	108	0.507042	NM_000766	Q53YR8|Q6R569|Q6R570|Q9H2X2	Missense_Mutation	SNP	ENST00000330436.3	37	CCDS12571.1	12	0.005494505494505495	6	0.012195121951219513	0	0.0	1	0.0017482517482517483	5	0.006596306068601583	.	7.352	0.623028	0.14193	0.004312	0.005349	ENSG00000197838	ENST00000330436	T	0.70164	-0.46	4.36	2.18	0.27775	.	0.237828	0.34652	N	0.003790	T	0.35537	0.0935	N	0.17764	0.52	0.21652	N	0.99961	B	0.12630	0.006	B	0.12837	0.008	T	0.14476	-1.0471	10	0.30078	T	0.28	.	4.1933	0.10431	0.6726:0.0:0.1762:0.1512	.	379	Q16696	CP2AD_HUMAN	Q	379	ENSP00000332679:K379Q	ENSP00000332679:K379Q	K	+	1	0	CYP2A13	46292151	0.000000	0.05858	0.974000	0.42286	0.188000	0.23474	-0.232000	0.09055	0.193000	0.20303	0.397000	0.26171	AAG	A|0.995;C|0.005	0.005	strong		0.567	CYP2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463505.1	NM_000766		C	41600311	A	C	41600311	3	2	23	1	0	0	0	0	1	0	0	0	4163	131	5	5	1161	5	CYP2A13	19	41600311	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	249100	41600311	17528672	687	8131											
ZNF574	64763	hgsc.bcm.edu	37	chr19	42583743	42583743	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accagctacagcagcacctgCggagtcaccgggagggcgtc	9	4	14	14	3	1	0	1	0	0	0	2	2	1	2	3	3	5	3	3	3	1	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:42583743C>T	ENST00000600245.1	+	2	1640	c.985C>T	c.(985-987)Cgg>Tgg	p.R329W	CTB-59C6.3_ENST00000594531.1_RNA|ZNF574_ENST00000222339.7_Missense_Mutation_p.R419W|ZNF574_ENST00000359044.4_Missense_Mutation_p.R329W			Q6ZN55	ZN574_HUMAN	zinc finger protein 574	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)			endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20		Prostate(69;0.059)				GCAGCACCTGCGGAGTCACCG	0.607																																					p.R329W		Atlas-SNP	.											.	ZNF574	57	.	0			c.C985T						PASS	.						99	108	105					19																	42583743		2203	4300	6503	SO:0001583	missense	64763	exon2			CACCTGCGGAGTC	AK074788	CCDS12596.1	19q13.2	2013-09-20			ENSG00000105732	ENSG00000105732		"Zinc fingers, C2H2-type"	26166	protein-coding gene	gene with protein product						12477932	Standard	NM_022752		Approved	FLJ22059	uc002osm.4	Q6ZN55	OTTHUMG00000182751	ENST00000600245.1:c.985C>T	19.37:g.42583743C>T	ENSP00000469029:p.Arg329Trp	149	0	0		159	69	0.433962	NM_022752	Q6IPE0|Q6ZN10|Q7L5Z5|Q8NCE3|Q9H6N0	Missense_Mutation	SNP	ENST00000600245.1	37	CCDS12596.1	.	.	.	.	.	.	.	.	.	.	c	15.18	2.756649	0.49362	.	.	ENSG00000105732	ENST00000222339;ENST00000359044	T;T	0.26223	1.75;1.75	4.63	3.58	0.41010	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.141481	0.45361	D	0.000364	T	0.53190	0.1781	M	0.86502	2.82	0.26272	N	0.978409	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.992	T	0.50800	-0.8785	10	0.87932	D	0	-19.0607	11.469	0.50257	0.3259:0.6741:0.0:0.0	.	329;418	Q6ZN55;Q6ZN55-2	ZN574_HUMAN;.	W	419;329	ENSP00000222339:R419W;ENSP00000351939:R329W	ENSP00000222339:R419W	R	+	1	2	ZNF574	47275583	0.563000	0.26594	1.000000	0.80357	0.762000	0.43233	2.030000	0.41108	1.287000	0.44583	-0.174000	0.13273	CGG	.	.	none		0.607	ZNF574-002	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463458.1	NM_022752		T	42583743	C	T	42583743	3	4	23	1	0	0	0	0	1	0	0	0	18021	759	27	1	987	1	ZNF574	19	42583743	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	983432	42583743	16545240	688	8132											
ZNF526	116115	hgsc.bcm.edu	37	chr19	42729121	42729121	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actgcctccaccttctccccCatccgaagtcaagatggagc	9	8	7	17	1	2	1	1	0	1	1	5	3	4	2	6	1	2	0	6	1	2	1	rs150807158	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:42729121C>T	ENST00000301215.3	+	3	791	c.566C>T	c.(565-567)cCa>cTa	p.P189L		NM_133444.1	NP_597701.1	Q8TF50	ZN526_HUMAN	zinc finger protein 526	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)			autonomic_ganglia(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(9)|prostate(1)|skin(3)	22		Prostate(69;0.0704)				CCTTCTCCCCCATCCGAAGTC	0.597													C|||	13	0.00259585	0.0008	0.0	5008	,	,		19799	0.0		0.006	False		,,,				2504	0.0061				p.P189L		Atlas-SNP	.											.	ZNF526	51	.	0			c.C566T						PASS	.	C	LEU/PRO	9,4397	15.5+/-35.6	0,9,2194	135	127	130		566	4.4	0.1	19	dbSNP_134	130	124,8476	64.9+/-127.2	2,120,4178	yes	missense	ZNF526	NM_133444.1	98	2,129,6372	TT,TC,CC		1.4419,0.2043,1.0226	possibly-damaging	189/671	42729121	133,12873	2203	4300	6503	SO:0001583	missense	116115	exon3			CTCCCCCATCCGA	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.566C>T	19.37:g.42729121C>T	ENSP00000301215:p.Pro189Leu	149	0	0		139	72	0.517986	NM_133444	B3KV29|Q69YI2|Q96E24	Missense_Mutation	SNP	ENST00000301215.3	37	CCDS12598.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	6.077	0.382572	0.11524	0.002043	0.014419	ENSG00000167625	ENST00000437878;ENST00000301215	T	0.08634	3.07	4.4	4.4	0.53042	.	0.555420	0.16362	N	0.217738	T	0.06096	0.0158	L	0.44542	1.39	0.33667	D	0.61049	B	0.12013	0.005	B	0.10450	0.005	T	0.02683	-1.1124	10	0.72032	D	0.01	-4.7579	9.9765	0.41786	0.0:0.9038:0.0:0.0962	.	189	Q8TF50	ZN526_HUMAN	L	45;189	ENSP00000301215:P189L	ENSP00000301215:P189L	P	+	2	0	ZNF526	47420961	0.022000	0.18835	0.057000	0.19452	0.395000	0.30598	2.169000	0.42434	2.449000	0.82847	0.467000	0.42956	CCA	C|0.991;T|0.009	0.009	strong		0.597	ZNF526-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463681.2	XM_057401		T	42729121	C	T	42729121	3	4	23	1	0	0	0	0	1	0	0	0	17982	594	21	2	568	2	ZNF526	19	42729121	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	145378	42729121	16399862	689	8133											
KLC3	147700	hgsc.bcm.edu	37	chr19	45848869	45848869	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gcctgagccctgaggagctgGtgcggcagacgcggcaagtg	7	5	18	11	3	0	3	0	2	0	1	0	4	0	4	2	4	3	3	2	4	1	0	rs546355544		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:45848869G>A	ENST00000391946.2	+	2	172	c.70G>A	c.(70-72)Gtg>Atg	p.V24M	KLC3_ENST00000585434.1_Missense_Mutation_p.V24M|KLC3_ENST00000470402.1_Missense_Mutation_p.V38M	NM_177417.2	NP_803136.2	Q6P597	KLC3_HUMAN	kinesin light chain 3	24					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)		TGAGGAGCTGGTGCGGCAGAC	0.706													G|||	1	0.000199681	0.0	0.0014	5008	,	,		13844	0.0		0.0	False		,,,				2504	0.0				p.V24M		Atlas-SNP	.											.	KLC3	37	.	0			c.G70A						PASS	.						5	7	7					19																	45848869		1932	4073	6005	SO:0001583	missense	147700	exon2			GAGCTGGTGCGGC	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.70G>A	19.37:g.45848869G>A	ENSP00000375810:p.Val24Met	141	0	0		133	59	0.443609	NM_177417	A0AVM3|A2RUT6|Q6GMU2|Q8NAL1|Q8WWJ9	Missense_Mutation	SNP	ENST00000391946.2	37	CCDS12660.2	.	.	.	.	.	.	.	.	.	.	G	12.08	1.830370	0.32329	.	.	ENSG00000104892	ENST00000391946;ENST00000470402	D;D	0.85171	-1.93;-1.95	3.4	3.4	0.38934	.	0.110159	0.38272	N	0.001756	T	0.77356	0.4118	N	0.25485	0.75	0.36902	D	0.890437	P;P;P	0.49635	0.926;0.926;0.879	P;P;B	0.46825	0.528;0.528;0.328	T	0.80141	-0.1506	10	0.56958	D	0.05	.	6.7358	0.23409	0.1316:0.0:0.8684:0.0	.	24;38;24	Q6P597-2;Q6P597-3;Q6P597	.;.;KLC3_HUMAN	M	24;38	ENSP00000375810:V24M;ENSP00000436019:V38M	ENSP00000375810:V24M	V	+	1	0	KLC3	50540709	1.000000	0.71417	1.000000	0.80357	0.516000	0.34256	2.415000	0.44635	1.918000	0.55548	0.313000	0.20887	GTG	.	.	none		0.706	KLC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289776.1	NM_145275		A	45848869	G	A	45848869	3	1	23	1	0	0	0	0	1	0	0	0	8344	1261	44	2	72	2	KLC3	19	45848869	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	3119748	45848869	13280114	690	8134											
EML2	24139	hgsc.bcm.edu	37	chr19	46137712	46137712	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aaaggttggcccggcagtctCggccacggtagccatagctg	8	7	14	12	3	1	0	0	0	1	0	2	0	1	0	3	5	2	4	3	5	3	3	rs144104945	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:46137712C>T	ENST00000245925.3	-	4	247	c.197G>A	c.(196-198)cGa>cAa	p.R66Q	EML2_ENST00000589876.1_Missense_Mutation_p.R66Q|EML2_ENST00000536630.1_Missense_Mutation_p.R213Q|EML2_ENST00000587152.1_Missense_Mutation_p.R267Q|EML2_ENST00000586902.1_5'Flank	NM_012155.2	NP_036287.1	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like 2	66	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)		CCGGCAGTCTCGGCCACGGTA	0.488													C|||	11	0.00219649	0.0008	0.0014	5008	,	,		14049	0.0		0.008	False		,,,				2504	0.001				p.R267Q		Atlas-SNP	.											.	EML2	64	.	0			c.G800A						PASS	.		GLN/ARG,GLN/ARG,GLN/ARG	9,4397	15.5+/-35.6	0,9,2194	35	27	30		800,638,197	4.7	1	19	dbSNP_134	30	50,8550	26.3+/-74.7	1,48,4251	yes	missense,missense,missense	EML2	NM_001193268.1,NM_001193269.1,NM_012155.2	43,43,43	1,57,6445	TT,TC,CC		0.5814,0.2043,0.4536	probably-damaging,probably-damaging,probably-damaging	267/851,213/797,66/650	46137712	59,12947	2203	4300	6503	SO:0001583	missense	24139	exon7			CAGTCTCGGCCAC	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.197G>A	19.37:g.46137712C>T	ENSP00000245925:p.Arg66Gln	68	0	0		81	44	0.54321	NM_001193268	B7Z3I2|B7Z3Q9|K7ERL7|Q59EN8|Q8N5A2|Q9UG50	Missense_Mutation	SNP	ENST00000245925.3	37	CCDS12670.1	9	0.004120879120879121	1	0.0020325203252032522	0	0.0	0	0.0	8	0.010554089709762533	C	26.6	4.755325	0.89843	0.002043	0.005814	ENSG00000125746	ENST00000536630;ENST00000245925;ENST00000448055;ENST00000399594	T;T;T	0.32515	1.45;1.45;5.06	4.74	4.74	0.60224	HELP (1);Quinonprotein alcohol dehydrogenase-like (1);	0.000000	0.85682	D	0.000000	T	0.45418	0.1341	M	0.66378	2.025	0.51012	D	0.999905	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;0.998;0.999;1.0	T	0.49969	-0.8882	10	0.51188	T	0.08	-8.2435	15.2541	0.73571	0.0:1.0:0.0:0.0	.	66;232;213;224;66	B7Z918;B7Z3Q9;B7Z3I2;B7Z872;O95834	.;.;.;.;EMAL2_HUMAN	Q	213;66;267;224	ENSP00000442365:R213Q;ENSP00000245925:R66Q;ENSP00000382503:R224Q	ENSP00000245925:R66Q	R	-	2	0	EML2	50829552	1.000000	0.71417	0.994000	0.49952	0.924000	0.55760	5.478000	0.66806	2.475000	0.83589	0.462000	0.41574	CGA	C|0.996;T|0.004	0.004	strong		0.488	EML2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459608.1	NM_012155		T	46137712	C	T	46137712	3	4	23	1	0	0	0	0	1	0	0	0	5099	884	31	1	1816	1	EML2	19	46137712	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	288843	46137712	12991271	691	8135											
CCDC61	729440	hgsc.bcm.edu	37	chr19	46520069	46520069	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaggggacgcccctaaccgCtcccgaaaccgcagctcctc	8	4	10	19	5	0	0	0	0	0	0	3	3	2	1	6	2	3	3	6	2	2	1	rs144277506	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:46520069C>T	ENST00000595358.1	+	10	1258	c.1209C>T	c.(1207-1209)cgC>cgT	p.R403R	CCDC61_ENST00000536603.1_Silent_p.R223R|MIR769_ENST00000390225.1_RNA|CCDC61_ENST00000594087.1_Silent_p.R223R|CCDC61_ENST00000263284.2_Silent_p.R422R	NM_001267723.1	NP_001254652.1	Q9Y6R9	CCD61_HUMAN	coiled-coil domain containing 61	403						centrosome (GO:0005813)				endometrium(3)|kidney(3)|large_intestine(1)|lung(5)|ovary(1)	13		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00221)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.164)		CCCCTAACCGCTCCCGAAACC	0.726													C|||	37	0.00738818	0.0	0.0101	5008	,	,		8715	0.0		0.0219	False		,,,				2504	0.0082				p.R403R		Atlas-SNP	.											.	CCDC61	32	.	0			c.C1209T						PASS	.			12,3400		0,12,1694	6	8	7		1266	1.8	1	19	dbSNP_134	7	132,7592		0,132,3730	no	coding-synonymous	CCDC61	NM_001080402.1		0,144,5424	TT,TC,CC		1.709,0.3517,1.2931		422/532	46520069	144,10992	1706	3862	5568	SO:0001819	synonymous_variant	729440	exon10			TAACCGCTCCCGA		CCDS46120.1, CCDS46120.2	19q13.32	2014-09-04			ENSG00000104983	ENSG00000104983			33629	protein-coding gene	gene with protein product							Standard	NM_001267723		Approved		uc031rlj.1	Q9Y6R9	OTTHUMG00000182488	ENST00000595358.1:c.1209C>T	19.37:g.46520069C>T		69	0	0		77	47	0.61039	NM_001267723	C8CAP4|Q9HDB6	Silent	SNP	ENST00000595358.1	37	CCDS46120.2																																																																																			C|0.989;T|0.011	0.011	strong		0.726	CCDC61-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461689.1	NM_001080402		T	46520069	C	T	46520069	2	4	23	1	0	0	0	0	0	0	0	1	2834	784	28	2		2	CCDC61	19	46520069	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	382357	46520069	12608914	692	8136											
CCDC61	729440	hgsc.bcm.edu	37	chr19	46520506	46520506	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggttactcctttttctcaggGgtcaccgccgccgtgggaag	5	11	13	12	3	2	0	2	0	1	0	4	1	3	1	4	4	1	1	4	4	2	3	rs61742389	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:46520506G>C	ENST00000595358.1	+	12	1361	c.1312G>C	c.(1312-1314)Ggt>Cgt	p.G438R	CCDC61_ENST00000536603.1_Splice_Site_p.G258R|MIR769_ENST00000390225.1_RNA|CCDC61_ENST00000594087.1_Splice_Site_p.G258R|CCDC61_ENST00000263284.2_Splice_Site_p.G457R	NM_001267723.1	NP_001254652.1	Q9Y6R9	CCD61_HUMAN	coiled-coil domain containing 61	438						centrosome (GO:0005813)				endometrium(3)|kidney(3)|large_intestine(1)|lung(5)|ovary(1)	13		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00221)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.164)		TTTTCTCAGGGGTCACCGCCG	0.607											OREG0025565	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	40	0.00798722	0.0015	0.0101	5008	,	,		10932	0.0		0.0219	False		,,,				2504	0.0092				p.G438R		Atlas-SNP	.											.	CCDC61	32	.	0			c.G1312C						PASS	.		ARG/GLY	20,3958		0,20,1969	21	26	25		1369	-1.7	0	19	dbSNP_129	25	131,8161		0,131,4015	yes	missense-near-splice	CCDC61	NM_001080402.1	125	0,151,5984	CC,CG,GG		1.5798,0.5028,1.2306	benign	457/532	46520506	151,12119	1989	4146	6135	SO:0001630	splice_region_variant	729440	exon12			CTCAGGGGTCACC		CCDS46120.1, CCDS46120.2	19q13.32	2014-09-04			ENSG00000104983	ENSG00000104983			33629	protein-coding gene	gene with protein product							Standard	NM_001267723		Approved		uc031rlj.1	Q9Y6R9	OTTHUMG00000182488	ENST00000595358.1:c.1311-1G>C	19.37:g.46520506G>C		53	0	0	939	39	14	0.358974	NM_001267723	C8CAP4|Q9HDB6	Missense_Mutation	SNP	ENST00000595358.1	37	CCDS46120.2	24	0.01098901098901099	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	16	0.021108179419525065	G	8.859	0.946358	0.18356	0.005028	0.015798	ENSG00000104983	ENST00000263284;ENST00000536603	.	.	.	3.77	-1.73	0.08081	.	1.284800	0.05551	N	0.567480	T	0.04227	0.0117	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.24048	-1.0171	9	0.10636	T	0.68	5.2453	2.635	0.04955	0.1288:0.4667:0.2536:0.1509	rs61742389	400	Q9Y6R9	CCD61_HUMAN	R	457;258	.	ENSP00000263284:G457R	G	+	1	0	CCDC61	51212346	0.000000	0.05858	0.002000	0.10522	0.022000	0.10575	-0.122000	0.10627	-0.025000	0.13918	0.450000	0.29827	GGT	A|0.000;C|0.012;G|0.987	0.012	strong		0.607	CCDC61-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461689.1	NM_001080402	Missense_Mutation	C	46520506	G	C	46520506	5	2	23	1	0	0	0	0	0	0	1	0	2834	1246	43	4	1419	4	CCDC61	19	46520506	Splice_Site	SNP	G	TCGA-G8-6325-01A-11D-2210-10	437	46520506	12608477	693	8137											
ZC3H4	23211	hgsc.bcm.edu	37	chr19	47572395	47572395	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgctctcagccagcctcctCgctctctcctcctcctcctg	2	12	5	22	1	2	0	1	0	2	0	10	0	7	0	7	0	3	2	7	0	0	0	rs202116030	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:47572395C>T	ENST00000253048.5	-	14	2389	c.2352G>A	c.(2350-2352)gcG>gcA	p.A784A	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	784							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)		CCAGCCTCCTCGCTCTCTCCT	0.692													C|||	3	0.000599042	0.0015	0.0014	5008	,	,		17200	0.0		0.0	False		,,,				2504	0.0				p.A784A		Atlas-SNP	.											.	ZC3H4	96	.	0			c.G2352A						PASS	.	C		3,4171		0,3,2084	68	80	76		2352	-2.5	1	19		76	4,8412		0,4,4204	no	coding-synonymous	ZC3H4	NM_015168.1		0,7,6288	TT,TC,CC		0.0475,0.0719,0.0556		784/1304	47572395	7,12583	2087	4208	6295	SO:0001819	synonymous_variant	23211	exon14			CCTCCTCGCTCTC	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.2352G>A	19.37:g.47572395C>T		54	0	0		45	17	0.377778	NM_015168	Q9Y420	Silent	SNP	ENST00000253048.5	37	CCDS42582.1																																																																																			C|1.000;T|0.000	0.000	strong		0.692	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1			T	47572395	C	T	47572395	2	4	23	1	0	0	0	0	0	0	0	1	17585	871	31	1		1	ZC3H4	19	47572395	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1051889	47572395	11556588	694	8138											
LIG1	3978	hgsc.bcm.edu	37	chr19	48626236	48626236	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgatctcgtaggtggcatcAacatccagggtcttcaccat	9	10	10	12	2	4	0	2	0	2	0	6	1	5	0	2	3	1	2	2	3	2	2	rs116999747	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:48626236A>G	ENST00000263274.7	-	23	2606	c.2187T>C	c.(2185-2187)gtT>gtC	p.V729V	CTC-453G23.5_ENST00000596839.1_RNA|LIG1_ENST00000536218.1_Silent_p.V661V|LIG1_ENST00000427526.2_Silent_p.V698V|CTC-453G23.5_ENST00000596563.1_RNA	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	729					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)	AGGTGGCATCAACATCCAGGG	0.617								Nucleotide excision repair (NER)					A|||	6	0.00119808	0.0	0.0029	5008	,	,		18483	0.0		0.004	False		,,,				2504	0.0				p.V729V		Atlas-SNP	.											.	LIG1	151	.	0			c.T2187C						PASS	.	A		2,4404	4.2+/-10.8	0,2,2201	166	149	155		2187	-9.9	0.1	19	dbSNP_132	155	35,8565	24.0+/-70.4	0,35,4265	no	coding-synonymous	LIG1	NM_000234.1		0,37,6466	GG,GA,AA		0.407,0.0454,0.2845		729/920	48626236	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	3978	exon23			GGCATCAACATCC		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.2187T>C	19.37:g.48626236A>G		136	0	0		119	57	0.478992	NM_000234	B2RAI8|Q2TB12|Q32P23	Silent	SNP	ENST00000263274.7	37	CCDS12711.1																																																																																			A|0.997;G|0.003	0.003	strong		0.617	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1	NM_000234		G	48626236	A	G	48626236	2	3	23	1	0	0	0	0	0	0	0	1	8790	117	5	3		3	LIG1	19	48626236	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	1053841	48626236	10502747	695	8139											
IZUMO1	284359	hgsc.bcm.edu	37	chr19	49244260	49244260	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cagtgaggatttgatgaaatCgatcaccttccttcgacgaa	12	11	9	9	3	1	3	1	3	0	0	4	7	2	4	2	1	0	0	2	1	2	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49244260C>T	ENST00000332955.2	-	10	1505	c.958G>A	c.(958-960)Gat>Aat	p.D320N	RASIP1_ENST00000222145.4_5'Flank|RASIP1_ENST00000594232.1_5'Flank	NM_182575.2	NP_872381.2	Q8IYV9	IZUM1_HUMAN	izumo sperm-egg fusion 1	320					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)		TTGATGAAATCGATCACCTTC	0.517																																					p.D320N		Atlas-SNP	.											.	IZUMO1	30	.	0			c.G958A						PASS	.						118	104	109					19																	49244260		2203	4300	6503	SO:0001583	missense	284359	exon10			TGAAATCGATCAC	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.958G>A	19.37:g.49244260C>T	ENSP00000327786:p.Asp320Asn	79	0	0		94	4	0.0425532	NM_182575	Q6Q8P6|Q6Q8P7	Missense_Mutation	SNP	ENST00000332955.2	37	CCDS12732.1	.	.	.	.	.	.	.	.	.	.	C	9.996	1.232155	0.22626	.	.	ENSG00000182264	ENST00000332955	T	0.26660	1.72	3.11	-1.93	0.07594	.	3.286190	0.01067	N	0.004759	T	0.12860	0.0312	N	0.19112	0.55	0.09310	N	1	B	0.28470	0.213	B	0.15870	0.014	T	0.08351	-1.0726	10	0.12430	T	0.62	0.0495	3.5485	0.07837	0.0:0.4402:0.1948:0.365	.	320	Q8IYV9	IZUM1_HUMAN	N	320	ENSP00000327786:D320N	ENSP00000327786:D320N	D	-	1	0	IZUMO1	53936072	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-0.629000	0.05508	-0.218000	0.10018	-0.150000	0.13652	GAT	.	.	none		0.517	IZUMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466189.1	NM_182575		T	49244260	C	T	49244260	3	4	23	1	0	0	0	0	1	0	0	0	7942	884	31	1	98	1	IZUMO1	19	49244260	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	618024	49244260	9884723	696	8140											
FGF21	26291	hgsc.bcm.edu	37	chr19	49261218	49261218	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccctgaggcctgcagcttccGggagctgcttcttgaggacg	5	9	14	13	2	1	2	0	2	1	0	2	4	2	4	3	3	4	4	3	3	0	3	rs142980324		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49261218G>A	ENST00000593756.1	+	4	943	c.371G>A	c.(370-372)cGg>cAg	p.R124Q	FUT1_ENST00000310160.3_5'Flank|FGF21_ENST00000222157.3_Missense_Mutation_p.R124Q			Q9NSA1	FGF21_HUMAN	fibroblast growth factor 21	124					cell-cell signaling (GO:0007267)|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 low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|regulation of low-density lipoprotein particle clearance (GO:0010988)|signal transduction (GO:0007165)	extracellular region (GO:0005576)				breast(1)|cervix(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	8		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;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		TGCAGCTTCCGGGAGCTGCTT	0.582																																					p.R124Q		Atlas-SNP	.											.	FGF21	21	.	0			c.G371A						PASS	.	G	GLN/ARG	0,4402		0,0,2201	158	173	168		371	3.4	1	19	dbSNP_134	168	4,8592	3.7+/-12.6	0,4,4294	yes	missense	FGF21	NM_019113.2	43	0,4,6495	AA,AG,GG		0.0465,0.0,0.0308	probably-damaging	124/210	49261218	4,12994	2201	4298	6499	SO:0001583	missense	26291	exon3			GCTTCCGGGAGCT	AB021975	CCDS12734.1	19q13.33	2012-09-20			ENSG00000105550	ENSG00000105550			3678	protein-coding gene	gene with protein product		609436				10858549	Standard	XM_005258731		Approved		uc002pko.1	Q9NSA1		ENST00000593756.1:c.371G>A	19.37:g.49261218G>A	ENSP00000471477:p.Arg124Gln	153	0	0		132	57	0.431818	NM_019113	Q8N683	Missense_Mutation	SNP	ENST00000593756.1	37	CCDS12734.1	.	.	.	.	.	.	.	.	.	.	G	19.37	3.814192	0.70912	0.0	4.65E-4	ENSG00000105550	ENST00000222157	D	0.81579	-1.51	4.44	3.4	0.38934	.	0.076506	0.49916	D	0.000128	T	0.80969	0.4726	M	0.74258	2.255	0.37112	D	0.900381	D	0.53745	0.962	P	0.48270	0.572	T	0.82814	-0.0271	10	0.46703	T	0.11	-15.5157	8.3528	0.32312	0.1087:0.0:0.8913:0.0	.	124	Q9NSA1	FGF21_HUMAN	Q	124	ENSP00000222157:R124Q	ENSP00000222157:R124Q	R	+	2	0	FGF21	53953030	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	1.173000	0.31920	1.220000	0.43490	0.511000	0.50034	CGG	G|1.000;A|0.000	0.000	weak		0.582	FGF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466200.1			A	49261218	G	A	49261218	3	1	23	1	0	0	0	0	1	0	0	0	5858	1116	39	1	381	1	FGF21	19	49261218	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	16958	49261218	9867765	697	8141											
CPT1C	126129	hgsc.bcm.edu	37	chr19	50216050	50216050	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccctgttcagcaaatgcatCtgtttgacgtccacaattac	10	13	6	12	1	2	1	1	1	1	0	4	1	4	1	2	0	3	4	2	0	3	3	rs79488403	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:50216050C>A	ENST00000392518.4	+	18	2449	c.2077C>A	c.(2077-2079)Ctg>Atg	p.L693M	CPT1C_ENST00000405931.2_Missense_Mutation_p.L682M|CPT1C_ENST00000598293.1_Missense_Mutation_p.L693M|CPT1C_ENST00000354199.5_Intron|CPT1C_ENST00000323446.5_Missense_Mutation_p.L693M	NM_001199752.1	NP_001186681.1	Q8TCG5	CPT1C_HUMAN	carnitine palmitoyltransferase 1C	693					carnitine metabolic process (GO:0009437)|fatty acid beta-oxidation (GO:0006635)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|endoplasmic reticulum membrane (GO:0005789)|mitochondrial outer membrane (GO:0005741)|synapse (GO:0045202)	carnitine O-palmitoyltransferase activity (GO:0004095)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		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;0.0011)|GBM - Glioblastoma multiforme(134;0.00786)		GCAAATGCATCTGTTTGACGT	0.592													c|||	4	0.000798722	0.0	0.0	5008	,	,		15329	0.0		0.004	False		,,,				2504	0.0				p.L693M		Atlas-SNP	.											.	CPT1C	93	.	0			c.C2077A						PASS	.	C	MET/LEU,MET/LEU,MET/LEU,MET/LEU	4,4402	8.1+/-20.4	0,4,2199	103	80	88		2044,2077,2077,2077	3.5	1	19	dbSNP_131	88	63,8537	37.4+/-92.8	0,63,4237	yes	missense,missense,missense,missense	CPT1C	NM_001136052.2,NM_001199752.1,NM_001199753.1,NM_152359.2	15,15,15,15	0,67,6436	AA,AC,CC		0.7326,0.0908,0.5151	probably-damaging,probably-damaging,probably-damaging,probably-damaging	682/793,693/804,693/804,693/804	50216050	67,12939	2203	4300	6503	SO:0001583	missense	126129	exon18			ATGCATCTGTTTG	AF357970	CCDS12779.1, CCDS46147.1	19q13.33	2014-03-14				ENSG00000169169			18540	protein-coding gene	gene with protein product		608846				12376098, 11001805	Standard	NM_001136052		Approved	FLJ23809, CPTIC, CPT1P	uc010eng.3	Q8TCG5		ENST00000392518.4:c.2077C>A	19.37:g.50216050C>A	ENSP00000376303:p.Leu693Met	252	0	0		218	90	0.412844	NM_001199752	A8K0Z8|Q5K6N5|Q8N6Q9|Q8NDS6|Q8TE84	Missense_Mutation	SNP	ENST00000392518.4	37	CCDS12779.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	16.60	3.167352	0.57476	9.08E-4	0.007326	ENSG00000169169	ENST00000392518;ENST00000405931;ENST00000323446	D;D;D	0.86366	-2.11;-2.09;-2.11	4.59	3.55	0.40652	.	0.000000	0.35207	N	0.003375	D	0.84804	0.5553	L	0.45698	1.435	0.80722	D	1	P;P	0.42649	0.746;0.786	P;P	0.55222	0.561;0.771	D	0.84213	0.0457	10	0.34782	T	0.22	-14.6614	11.8375	0.52333	0.0:0.9125:0.0:0.0875	.	682;693	Q8TCG5-2;Q8TCG5	.;CPT1C_HUMAN	M	693;682;693	ENSP00000376303:L693M;ENSP00000384465:L682M;ENSP00000319343:L693M	ENSP00000319343:L693M	L	+	1	2	CPT1C	54907862	0.882000	0.30256	0.987000	0.45799	0.996000	0.88848	0.767000	0.26575	1.305000	0.44909	0.650000	0.86243	CTG	C|0.996;A|0.004	0.004	strong		0.592	CPT1C-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465873.1	NM_152359		A	50216050	C	A	50216050	3	1	23	1	0	0	0	0	1	0	0	0	3835	912	32	4	2139	4	CPT1C	19	50216050	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	954832	50216050	8912933	698	8142											
ZNF528	84436	hgsc.bcm.edu	37	chr19	52909200	52909200	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtggccatagagttctctcAggaagagtggaaatgcctgg	10	10	14	7	0	2	2	1	0	1	2	3	4	2	4	2	4	1	1	2	4	3	2	rs370656674		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:52909200A>G	ENST00000360465.3	+	5	482	c.56A>G	c.(55-57)cAg>cGg	p.Q19R	ZNF528_ENST00000391788.2_Missense_Mutation_p.Q9R|ZNF528_ENST00000594530.1_Missense_Mutation_p.Q19R|ZNF528_ENST00000598192.1_Missense_Mutation_p.Q19R	NM_032423.2	NP_115799.2	Q3MIS6	ZN528_HUMAN	zinc finger protein 528	19	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(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)		GAGTTCTCTCAGGAAGAGTGG	0.468																																					p.Q19R		Atlas-SNP	.											.	ZNF528	95	.	0			c.A56G						PASS	.	A	ARG/GLN	0,4406		0,0,2203	182	179	180		56	-0.7	0	19		180	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZNF528	NM_032423.2	43	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign	19/629	52909200	1,13005	2203	4300	6503	SO:0001583	missense	84436	exon5			TCTCTCAGGAAGA	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.56A>G	19.37:g.52909200A>G	ENSP00000353652:p.Gln19Arg	197	0	0		200	96	0.48	NM_032423	B3KPN4|Q86T88|Q96JK0	Missense_Mutation	SNP	ENST00000360465.3	37	CCDS33091.1	.	.	.	.	.	.	.	.	.	.	A	10.75	1.438395	0.25900	0.0	1.16E-4	ENSG00000167555	ENST00000391788;ENST00000391787;ENST00000360465	T;T;T	0.01963	4.53;4.53;4.53	1.93	-0.733	0.11144	Krueppel-associated box (4);	.	.	.	.	T	0.05777	0.0151	L	0.53729	1.69	0.19775	N	0.999957	D	0.76494	0.999	D	0.72338	0.977	T	0.35151	-0.9800	9	0.45353	T	0.12	.	0.995	0.01465	0.2762:0.3854:0.1474:0.1911	.	19	Q3MIS6	ZN528_HUMAN	R	9;19;19	ENSP00000375665:Q9R;ENSP00000375664:Q19R;ENSP00000353652:Q19R	ENSP00000353652:Q19R	Q	+	2	0	ZNF528	57601012	0.001000	0.12720	0.015000	0.15790	0.517000	0.34286	-0.590000	0.05760	-0.452000	0.07087	0.402000	0.26972	CAG	.	.	weak		0.468	ZNF528-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344336.1	NM_032423		G	52909200	A	G	52909200	3	3	23	1	0	0	0	0	1	0	0	0	17984	188	7	3	62	3	ZNF528	19	52909200	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	2693150	52909200	6219783	699	8143											
LILRA6	79168	hgsc.bcm.edu	37	chr19	54744919	54744919	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaatctgtcgtagccgacaTcagagccacactggagggtc	11	7	11	12	2	2	1	1	0	1	1	4	3	2	2	2	2	2	1	2	2	2	1	rs61734504	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:54744919T>A	ENST00000396365.2	-	5	782	c.743A>T	c.(742-744)gAt>gTt	p.D248V	LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000391735.3_3'UTR|LILRA6_ENST00000419410.2_Missense_Mutation_p.D248V|LILRA6_ENST00000270464.5_Intron|LILRA6_ENST00000440558.2_Missense_Mutation_p.D248V|LILRA6_ENST00000245621.5_Missense_Mutation_p.D248V	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	248	Ig-like C2-type 1.				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)		GTAGCCGACATCAGAGCCACA	0.637																																					p.D248V		Atlas-SNP	.											LILRA6,NS,carcinoma,-1,1	LILRA6	75	1	0			c.A743T						PASS	.	T	VAL/ASP	22,4384	23.3+/-48.9	0,22,2181	98	107	104		743	1.3	0	19	dbSNP_129	104	253,8347	85.0+/-147.5	0,253,4047	no	missense	LILRA6	NM_024318.2	152	0,275,6228	AA,AT,TT		2.9419,0.4993,2.1144		248/482	54744919	275,12731	2203	4300	6503	SO:0001583	missense	79168	exon5			CCGACATCAGAGC	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.743A>T	19.37:g.54744919T>A	ENSP00000379651:p.Asp248Val	655	1	0.00152672		666	171	0.256757	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	31	0.014194139194139194	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	28	0.036939313984168866	T	12.50	1.957220	0.34565	0.004993	0.029419	ENSG00000244482	ENST00000440558;ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T	0.13778	2.56;2.56;2.56;2.56	2.39	1.27	0.21489	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.862360	0.09874	N	0.744562	T	0.11367	0.0277	M	0.87547	2.89	0.09310	N	1	D;D;D;D	0.89917	0.999;0.999;0.994;1.0	D;D;D;D	0.87578	0.992;0.989;0.925;0.998	T	0.02821	-1.1106	10	0.87932	D	0	.	5.2029	0.15275	0.0:0.0:0.3054:0.6946	rs61734504	248;248;248;248	C9JFH3;Q6PI73;F8WCY4;D3YTC4	.;LIRA6_HUMAN;.;.	V	248	ENSP00000390120:D248V;ENSP00000411227:D248V;ENSP00000379651:D248V;ENSP00000245621:D248V	ENSP00000245621:D248V	D	-	2	0	LILRA6	59436731	0.003000	0.15002	0.006000	0.13384	0.043000	0.13939	0.447000	0.21710	0.312000	0.23038	0.155000	0.16302	GAT	T|0.968;A|0.032	0.032	strong		0.637	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318		A	54744919	T	A	54744919	3	1	23	1	0	0	0	0	1	0	0	0	8798	1435	50	5	718	5	LILRA6	19	54744919	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	1835719	54744919	4384064	700	8144											
LILRA6	79168	hgsc.bcm.edu	37	chr19	54745682	54745682	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atcccttctgtgagccacatCggagggtcatattcccccct	7	11	8	15	1	2	1	1	1	1	0	5	2	4	2	5	2	1	0	5	2	1	3	rs111666280	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:54745682C>T	ENST00000396365.2	-	4	467	c.428G>A	c.(427-429)cGa>cAa	p.R143Q	LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000391735.3_Missense_Mutation_p.R143Q|LILRA6_ENST00000419410.2_Missense_Mutation_p.R143Q|LILRA6_ENST00000270464.5_Missense_Mutation_p.R143Q|LILRA6_ENST00000440558.2_Missense_Mutation_p.R143Q|LILRA6_ENST00000245621.5_Missense_Mutation_p.R143Q	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	143					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)		TGAGCCACATCGGAGGGTCAT	0.567																																					p.R143Q		Atlas-SNP	.											.	LILRA6	75	.	0			c.G428A						PASS	.						29	50	43					19																	54745682		2122	4289	6411	SO:0001583	missense	79168	exon4			CCACATCGGAGGG	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.428G>A	19.37:g.54745682C>T	ENSP00000379651:p.Arg143Gln	719	0	0		768	101	0.13151	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	C	0.554	-0.848058	0.02651	.	.	ENSG00000244482	ENST00000440558;ENST00000270464;ENST00000419410;ENST00000391735;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T;T;T	0.12774	2.65;2.65;2.65;4.09;2.65;2.65	3.38	-6.77	0.01727	Immunoglobulin-like fold (1);	0.513077	0.18054	N	0.153187	T	0.02047	0.0064	N	0.01640	-0.785	0.09310	N	1	B;B;B;B;B;B	0.33000	0.046;0.003;0.332;0.049;0.046;0.393	B;B;B;B;B;B	0.32342	0.008;0.002;0.144;0.015;0.015;0.014	T	0.37454	-0.9705	10	0.02654	T	1	.	0.493	0.00567	0.2783:0.2174:0.3072:0.1971	.	143;143;143;143;143;143	C9JFH3;Q6PI73-2;Q6PI73;F8WCY4;D3YTC4;F8W6G6	.;.;LIRA6_HUMAN;.;.;.	Q	143	ENSP00000390120:R143Q;ENSP00000270464:R143Q;ENSP00000411227:R143Q;ENSP00000375615:R143Q;ENSP00000379651:R143Q;ENSP00000245621:R143Q	ENSP00000245621:R143Q	R	-	2	0	LILRA6	59437494	0.000000	0.05858	0.001000	0.08648	0.096000	0.18686	-1.554000	0.02172	-1.307000	0.02321	0.162000	0.16502	CGA	C|0.904;T|0.096	0.096	strong		0.567	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318		T	54745682	C	T	54745682	3	4	23	1	0	0	0	0	1	0	0	0	8798	884	31	1	1037	1	LILRA6	19	54745682	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	763	54745682	4383301	701	8145											
GP6	51206	hgsc.bcm.edu	37	chr19	55539094	55539094	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	taccatctctcgggattcttGtagggcgcagggtccccttc	5	12	11	13	2	2	0	0	0	2	0	6	1	3	1	3	3	1	2	3	3	2	5			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55539094G>A	ENST00000417454.1	-	4	489	c.462C>T	c.(460-462)taC>taT	p.Y154Y	CTC-550B14.7_ENST00000593060.1_RNA|GP6_ENST00000333884.2_Silent_p.Y154Y|CTC-550B14.7_ENST00000586961.1_RNA|GP6_ENST00000310373.3_Silent_p.Y154Y|CTC-550B14.7_ENST00000586845.1_RNA|CTC-550B14.6_ENST00000585492.1_RNA	NM_016363.4	NP_057447	Q9HCN6	GPVI_HUMAN	glycoprotein VI (platelet)	154	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)		CGGGATTCTTGTAGGGCGCAG	0.587																																					p.Y154Y		Atlas-SNP	.											.	GP6	55	.	0			c.C462T						PASS	.						77	86	83					19																	55539094		1985	4171	6156	SO:0001819	synonymous_variant	51206	exon4			ATTCTTGTAGGGC	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.462C>T	19.37:g.55539094G>A		98	0	0		92	50	0.543478	NM_016363	Q9HCN7|Q9UIF2	Silent	SNP	ENST00000417454.1	37	CCDS46184.1																																																																																			.	.	none		0.587	GP6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357006.1			A	55539094	G	A	55539094	2	1	23	1	0	0	0	0	0	0	0	1	6592	1372	48	2		2	GP6	19	55539094	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	793412	55539094	3589889	702	8146											
NAT14	57106	hgsc.bcm.edu	37	chr19	55998317	55998317	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gtgagggaattcagcaaagaCctgtgaagctacagactgac	14	7	12	8	0	1	5	1	3	0	2	1	6	1	6	1	1	3	2	1	1	4	2	rs118182626	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55998317C>A	ENST00000205194.4	+	3	918	c.615C>A	c.(613-615)gaC>gaA	p.D205E	NAT14_ENST00000592719.1_Intron|SSC5D_ENST00000587166.1_5'Flank|SSC5D_ENST00000389623.6_5'Flank|NAT14_ENST00000587400.1_Intron	NM_020378.3	NP_065111.1	Q8WUY8	NAT14_HUMAN	N-acetyltransferase 14 (GCN5-related, putative)	205	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				DNA-templated transcription, initiation (GO:0006352)|positive regulation of transcription, DNA-templated (GO:0045893)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|N-acetyltransferase activity (GO:0008080)			central_nervous_system(1)|large_intestine(1)|ovary(1)|pancreas(1)	4	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0527)		TCAGCAAAGACCTGTGAAGCT	0.652													c|||	78	0.0155751	0.0008	0.036	5008	,	,		12211	0.0		0.0328	False		,,,				2504	0.0194				p.D205E		Atlas-SNP	.											.	NAT14	11	.	0			c.C615A						PASS	.	C	GLU/ASP	22,4034		0,22,2006	9	10	9		615	0.6	1	19	dbSNP_132	9	279,7729		2,275,3727	yes	missense	NAT14	NM_020378.3	45	2,297,5733	AA,AC,CC		3.484,0.5424,2.495	benign	205/207	55998317	301,11763	2028	4004	6032	SO:0001583	missense	57106	exon3			CAAAGACCTGTGA	AB055059	CCDS12926.1	19q13.42	2011-11-25	2008-09-24		ENSG00000090971	ENSG00000090971			28918	protein-coding gene	gene with protein product	"K562 cells-derived leucine zipper-like protein 1"		"N-acetyltransferase 14"			10873651	Standard	NM_020378		Approved	KLP1	uc002qle.2	Q8WUY8		ENST00000205194.4:c.615C>A	19.37:g.55998317C>A	ENSP00000205194:p.Asp205Glu	4	0	0		8	7	0.875	NM_020378	Q8TDY7|Q9NS72	Missense_Mutation	SNP	ENST00000205194.4	37	CCDS12926.1	46	0.021062271062271064	1	0.0020325203252032522	16	0.04419889502762431	0	0.0	29	0.03825857519788918	.	16.91	3.253386	0.59212	0.005424	0.03484	ENSG00000090971	ENST00000205194	.	.	.	4.44	0.636	0.17729	GCN5-related N-acetyltransferase (GNAT) domain (1);	0.238192	0.30809	N	0.008836	T	0.14527	0.0351	L	0.34521	1.04	0.35928	D	0.8323	B	0.14012	0.009	B	0.12837	0.008	T	0.36016	-0.9765	9	0.48119	T	0.1	-29.4319	11.7987	0.52114	0.455:0.5449:0.0:0.0	.	205	Q8WUY8	NAT14_HUMAN	E	205	.	ENSP00000205194:D205E	D	+	3	2	NAT14	60690129	0.982000	0.34865	1.000000	0.80357	0.839000	0.47603	0.051000	0.14141	0.394000	0.25230	0.455000	0.32223	GAC	C|0.978;A|0.022	0.022	strong		0.652	NAT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453339.1	NM_020378		A	55998317	C	A	55998317	3	1	23	1	0	0	0	0	1	0	0	0	10184	506	18	4	621	4	NAT14	19	55998317	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	459223	55998317	3130666	703	8147											
U2AF2	11338	hgsc.bcm.edu	37	chr19	56181019	56181019	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gtcaagtccatcgagatcccCcggcctgtggacggcgtcga	7	7	13	14	5	1	1	1	0	0	1	5	4	3	2	4	3	0	0	4	3	1	0	rs147666260	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56181019C>T	ENST00000308924.4	+	11	1294	c.1254C>T	c.(1252-1254)ccC>ccT	p.P418P	CTD-2537I9.13_ENST00000592252.1_RNA|U2AF2_ENST00000450554.2_Silent_p.P414P|CTD-2537I9.12_ENST00000589456.1_RNA|U2AF2_ENST00000590551.1_Silent_p.P250P|CTD-2537I9.12_ENST00000585940.1_RNA			P26368	U2AF2_HUMAN	U2 small nuclear RNA auxiliary factor 2	418	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)			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)		TCGAGATCCCCCGGCCTGTGG	0.657													C|||	15	0.00299521	0.0	0.0101	5008	,	,		16186	0.0		0.008	False		,,,				2504	0.0				p.P418P		Atlas-SNP	.											.	U2AF2	62	.	0			c.C1254T						PASS	.	C	,	9,4397	15.5+/-35.6	0,9,2194	123	111	115		1242,1254	-0.6	1	19	dbSNP_134	115	87,8513	48.5+/-108.0	1,85,4214	no	coding-synonymous,coding-synonymous	U2AF2	NM_001012478.1,NM_007279.2	,	1,94,6408	TT,TC,CC		1.0116,0.2043,0.7381	,	414/472,418/476	56181019	96,12910	2203	4300	6503	SO:0001819	synonymous_variant	11338	exon11			GATCCCCCGGCCT	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.1254C>T	19.37:g.56181019C>T		125	0	0		156	76	0.487179	NM_007279	Q96HC5	Silent	SNP	ENST00000308924.4	37	CCDS12933.1																																																																																			C|0.994;T|0.006	0.006	strong		0.657	U2AF2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453599.1	NM_007279		T	56181019	C	T	56181019	2	4	23	1	0	0	0	0	0	0	0	1	16838	610	22	2		2	U2AF2	19	56181019	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	182702	56181019	2947964	704	8148											
NLRP5	126206	hgsc.bcm.edu	37	chr19	56538723	56538723	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctgtcctcaacaatgacaCaaagctctgcaaagactggg	13	8	8	12	0	3	2	1	1	2	1	4	2	4	2	1	1	3	2	1	1	4	0			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56538723C>T	ENST00000390649.3	+	7	1124	c.1124C>T	c.(1123-1125)aCa>aTa	p.T375I		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	375	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				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)		AACAATGACACAAAGCTCTGC	0.557																																					p.T375I		Atlas-SNP	.											.	NLRP5	217	.	0			c.C1124T						PASS	.						45	46	46					19																	56538723		2075	4215	6290	SO:0001583	missense	126206	exon7			ATGACACAAAGCT	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.1124C>T	19.37:g.56538723C>T	ENSP00000375063:p.Thr375Ile	57	0	0		48	11	0.229167	NM_153447	A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	37	CCDS12938.1	.	.	.	.	.	.	.	.	.	.	C	3.198	-0.164275	0.06502	.	.	ENSG00000171487	ENST00000390649	T	0.73897	-0.79	3.35	-6.71	0.01760	NACHT nucleoside triphosphatase (1);	5.357820	0.00397	N	0.000045	T	0.50973	0.1647	N	0.17082	0.46	0.09310	N	1	B	0.15719	0.014	B	0.21708	0.036	T	0.44375	-0.9332	10	0.17832	T	0.49	.	0.8494	0.01169	0.2606:0.2256:0.11:0.4037	.	375	P59047	NALP5_HUMAN	I	375	ENSP00000375063:T375I	ENSP00000375063:T375I	T	+	2	0	NLRP5	61230535	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.527000	0.00441	-2.083000	0.00867	0.655000	0.94253	ACA	.	.	none		0.557	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447		T	56538723	C	T	56538723	3	4	23	1	0	0	0	0	1	0	0	0	10489	478	17	2	1150	2	NLRP5	19	56538723	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	357704	56538723	2590260	705	8149											
ZNF606	80095	hgsc.bcm.edu	37	chr19	58491382	58491382	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgagatggaacaaagtttaaGttctggctaaactctgcccc	12	11	9	9	0	2	1	0	1	2	1	2	3	2	2	2	2	3	3	2	2	5	4	rs142503772	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:58491382G>A	ENST00000341164.4	-	7	1286	c.666C>T	c.(664-666)aaC>aaT	p.N222N	ZNF606_ENST00000536132.1_Silent_p.N132N	NM_025027.3	NP_079303.2	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	222					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)		CAAAGTTTAAGTTCTGGCTAA	0.423													G|||	17	0.00339457	0.0	0.0115	5008	,	,		19562	0.0		0.0089	False		,,,				2504	0.0				p.N222N		Atlas-SNP	.											.	ZNF606	155	.	0			c.C666T						PASS	.	G		12,4394	20.2+/-43.8	0,12,2191	103	101	101		666	-0.5	0.4	19	dbSNP_134	101	95,8505	52.7+/-113.3	1,93,4206	no	coding-synonymous	ZNF606	NM_025027.3		1,105,6397	AA,AG,GG		1.1047,0.2724,0.8227		222/793	58491382	107,12899	2203	4300	6503	SO:0001819	synonymous_variant	80095	exon7			GTTTAAGTTCTGG	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.666C>T	19.37:g.58491382G>A		73	0	0		81	33	0.407407	NM_025027	A8KAN2|Q8NE04|Q96JH5	Silent	SNP	ENST00000341164.4	37	CCDS12968.1																																																																																			G|0.991;A|0.009	0.009	strong		0.423	ZNF606-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405961.1	NM_025027		A	58491382	G	A	58491382	2	1	23	1	0	0	0	0	0	0	0	1	18047	1020	36	2		2	ZNF606	19	58491382	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1952659	58491382	637601	706	8150											
ZSCAN1	284312	hgsc.bcm.edu	37	chr19	58564863	58564863	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgaggaccttctcgcagggcCctcctcagacctgcgggcag	6	7	13	15	2	2	2	1	1	1	1	4	3	3	3	4	3	1	2	4	3	0	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:58564863C>T	ENST00000282326.1	+	6	918	c.671C>T	c.(670-672)cCc>cTc	p.P224L		NM_182572.3	NP_872378.3	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	224					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)		CTCGCAGGGCCCTCCTCAGAC	0.622																																					p.P224L		Atlas-SNP	.											.	ZSCAN1	102	.	0			c.C671T						PASS	.						48	51	50					19																	58564863		2203	4300	6503	SO:0001583	missense	284312	exon6			CAGGGCCCTCCTC	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.671C>T	19.37:g.58564863C>T	ENSP00000282326:p.Pro224Leu	71	0	0		63	10	0.15873	NM_182572	Q3B798|Q6WLH8|Q86WS8	Missense_Mutation	SNP	ENST00000282326.1	37	CCDS12969.1	.	.	.	.	.	.	.	.	.	.	C	6.071	0.381441	0.11524	.	.	ENSG00000152467	ENST00000282326	T	0.04862	3.54	1.04	-2.09	0.07232	.	.	.	.	.	T	0.03178	0.0093	N	0.19112	0.55	0.09310	N	0.999993	B	0.09022	0.002	B	0.06405	0.002	T	0.45934	-0.9227	9	0.23302	T	0.38	.	2.0317	0.03530	0.2546:0.35:0.0:0.3953	.	224	Q8NBB4	ZSCA1_HUMAN	L	224	ENSP00000282326:P224L	ENSP00000282326:P224L	P	+	2	0	ZSCAN1	63256675	0.004000	0.15560	0.005000	0.12908	0.357000	0.29423	0.275000	0.18698	-0.640000	0.05495	0.491000	0.48974	CCC	.	.	none		0.622	ZSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466427.1	NM_182572		T	58564863	C	T	58564863	3	4	23	1	0	0	0	0	1	0	0	0	18241	623	22	2	685	2	ZSCAN1	19	58564863	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	73481	58564863	564120	707	8151											
SOX12	6666	hgsc.bcm.edu	37	chr20	306733	306733	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gtgtggtcgcagcacgaacgGcggaagatcatggaccagtg	10	6	16	9	4	1	1	1	0	0	1	2	4	1	3	1	4	2	2	1	4	2	0	rs73071018	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:306733G>A	ENST00000342665.2	+	1	495	c.165G>A	c.(163-165)cgG>cgA	p.R55R	RP5-1103G7.4_ENST00000442637.1_RNA|RP5-1103G7.4_ENST00000414676.1_RNA|SOX12_ENST00000544632.1_Silent_p.R55R	NM_006943.2	NP_008874.2	O15370	SOX12_HUMAN	SRY (sex determining region Y)-box 12	55					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)	p.R55R(1)		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)			AGCACGAACGGCGGAAGATCA	0.672													G|||	29	0.00579073	0.0015	0.0115	5008	,	,		7149	0.0		0.0179	False		,,,				2504	0.001				p.R55R		Atlas-SNP	.											SOX12,NS,lymphoid_neoplasm,0,1	SOX12	8	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.G165A						PASS	.	G		15,4391		0,15,2188	35	29	31		165	3.6	1	20	dbSNP_130	31	188,8408		1,186,4111	no	coding-synonymous	SOX12	NM_006943.2		1,201,6299	AA,AG,GG		2.1871,0.3404,1.5613		55/316	306733	203,12799	2203	4298	6501	SO:0001819	synonymous_variant	6666	exon1			CGAACGGCGGAAG	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.165G>A	20.37:g.306733G>A		147	0	0		157	89	0.566879	NM_006943	Q5D038|Q9NUD4	Silent	SNP	ENST00000342665.2	37	CCDS12995.1																																																																																			G|0.985;A|0.015	0.015	strong		0.672	SOX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077435.2	NM_006943		A	306733	G	A	306733	2	1	23	1	0	0	0	0	0	0	0	1	14958	1190	42	2		2	SOX12	20	306733	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10		306733	62718787	708	8152											
TGM6	343641	hgsc.bcm.edu	37	chr20	2411657	2411658	+	In_Frame_Ins	INS	-	-	AAC																															gggcagcggccttctccaggINSaacagctcagcatcgagtaa																								rs557817405		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:2411657_2411658insAAC	ENST00000202625.2	+	12	2012_2013	c.1951_1952insAAC	c.(1951-1953)gaa>gAACaa	p.652_653insQ	TGM6_ENST00000381423.1_Intron	NM_198994.2	NP_945345.2	O95932	TGM3L_HUMAN	transglutaminase 6	652					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)	CCTTCTCCAGGAACAGCTCAGC	0.594																																					p.E651delinsEQ		Pindel,Atlas-Indel	.											.	TGM6	126	.	0			c.1951_1952insAAC						PASS	.			4,4260		0,4,2128						5.2	1			81	27,8227		0,27,4100	no	coding	TGM6	NM_198994.2		0,31,6228	A1A1,A1R,RR		0.3271,0.0938,0.2476				31,12487				SO:0001652	inframe_insertion	343641	exon12			.	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.1952_1954dupAAC	20.37:g.2411658_2411660dupAAC	ENSP00000202625:p.Gln652_Gln652dup	63	0	.		80	30	0.375	NM_198994	Q5JXU4|Q5JXU5|Q719M2|Q719M3|Q9Y4U8	In_Frame_Ins	INS	ENST00000202625.2	37	CCDS13025.1																																																																																			.	.	none		0.594	TGM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077581.2	NM_198994		AAC	2411658	-	AAC	2411657	7	5	23	1	0	1	1	0	0	0	0	0	15849	1175	41	0	1997	0	TGM6	20	2411657	In_Frame_Ins	INS	-	TCGA-G8-6325-01A-11D-2210-10	2104924	2411657	60613863	709	8153											
NOP56	10528	hgsc.bcm.edu	37	chr20	2636059	2636059	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgcccagtttattggaaacCgaagggaactgaatgaggac	13	9	12	7	1	0	2	0	2	0	0	0	6	0	5	2	3	3	1	2	3	5	4			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:2636059C>T	ENST00000329276.5	+	6	1174	c.658C>T	c.(658-660)Cga>Tga	p.R220*	SNORD110_ENST00000408189.1_RNA|SNORA51_ENST00000606420.1_RNA|MIR1292_ENST00000408135.1_RNA|SNORD86_ENST00000391196.1_RNA|SNORD57_ENST00000448188.1_RNA|SNORD56_ENST00000413522.1_RNA|IDH3B_ENST00000488299.1_5'Flank	NM_006392.3	NP_006383.2	O00567	NOP56_HUMAN	NOP56 ribonucleoprotein	220					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						TATTGGAAACCGAAGGGAACT	0.537																																					p.R220X		Atlas-SNP	.											NOP56,NS,carcinoma,-2,1	NOP56	73	1	0			c.C658T						PASS	.						127	122	124					20																	2636059		2203	4300	6503	SO:0001587	stop_gained	10528	exon6			GGAAACCGAAGGG	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.658C>T	20.37:g.2636059C>T	ENSP00000370589:p.Arg220*	141	0	0		131	19	0.145038	NM_006392	Q2M3T6|Q9NQ05	Nonsense_Mutation	SNP	ENST00000329276.5	37	CCDS13030.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.905811	0.92107	.	.	ENSG00000101361	ENST00000329276;ENST00000445139	.	.	.	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.0976	12.2785	0.54751	0.1695:0.8305:0.0:0.0	.	.	.	.	X	220;249	.	ENSP00000370589:R220X	R	+	1	2	NOP56	2584059	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	2.769000	0.47654	2.672000	0.90937	0.561000	0.74099	CGA	.	.	none		0.537	NOP56-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077631.2	NM_006392		T	2636059	C	T	2636059	4	4	23	1	0	0	0	0	0	1	0	0	10548	644	23	1	680	1	NOP56	20	2636059	Nonsense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	224402	2636059	60389461	710	8154											
MYH7B	57644	hgsc.bcm.edu	37	chr20	33586674	33586674	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcccagtggaggagcaagtaCgaagcagatgccatccagag	13	4	14	10	1	0	2	0	0	0	2	1	5	1	4	3	2	4	3	3	2	3	1	rs377482062		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:33586674C>T	ENST00000262873.7	+	33	4364	c.4272C>T	c.(4270-4272)taC>taT	p.Y1424Y		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	1382						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)			GGAGCAAGTACGAAGCAGATG	0.632																																					p.Y1424Y		Atlas-SNP	.											.	MYH7B	145	.	0			c.C4272T						PASS	.	C		3,4401	4.2+/-10.8	0,3,2199	26	30	28		4272	-6	0.8	20		28	0,8596		0,0,4298	no	coding-synonymous	MYH7B	NM_020884.3		0,3,6497	TT,TC,CC		0.0,0.0681,0.0231		1424/1984	33586674	3,12997	2202	4298	6500	SO:0001819	synonymous_variant	57644	exon35			CAAGTACGAAGCA	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.4272C>T	20.37:g.33586674C>T		131	0	0		121	50	0.413223	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Silent	SNP	ENST00000262873.7	37	CCDS42869.1																																																																																			.	.	weak		0.632	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884		T	33586674	C	T	33586674	2	4	23	1	0	0	0	0	0	0	0	1	10049	547	19	1		1	MYH7B	20	33586674	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	30950615	33586674	29438846	711	8155											
CEP250	11190	hgsc.bcm.edu	37	chr20	34092076	34092076	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcatcaggaggaggctgcccGggcccgggctgaggctctgc	5	5	18	13	2	2	1	1	1	1	0	2	3	2	3	2	6	2	4	2	6	0	0	rs56259282	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:34092076G>A	ENST00000397527.1	+	30	6599	c.5879G>A	c.(5878-5880)cGg>cAg	p.R1960Q	CEP250_ENST00000342580.4_Missense_Mutation_p.R1904Q	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	1960	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)			GAGGCTGCCCGGGCCCGGGCT	0.657													G|||	24	0.00479233	0.0008	0.0115	5008	,	,		18767	0.0		0.0119	False		,,,				2504	0.0031				p.R1960Q		Atlas-SNP	.											.	CEP250	141	.	0			c.G5879A						PASS	.	G	GLN/ARG	9,4369		0,9,2180	9	11	10		5879	-4	0	20	dbSNP_129	10	103,8479		2,99,4190	yes	missense	CEP250	NM_007186.3	43	2,108,6370	AA,AG,GG		1.2002,0.2056,0.8642	benign	1960/2443	34092076	112,12848	2189	4291	6480	SO:0001583	missense	11190	exon30			CTGCCCGGGCCCG	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.5879G>A	20.37:g.34092076G>A	ENSP00000380661:p.Arg1960Gln	48	0	0		54	21	0.388889	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	ENST00000397527.1	37	CCDS13255.1	15	0.006868131868131868	0	0.0	8	0.022099447513812154	0	0.0	7	0.009234828496042216	G	2.257	-0.370208	0.05069	0.002056	0.012002	ENSG00000126001	ENST00000397527;ENST00000342580;ENST00000422671	T;T;T	0.41065	3.05;3.04;1.01	4.95	-4.04	0.04010	.	1.940040	0.02640	N	0.105311	T	0.11836	0.0288	L	0.29908	0.895	0.09310	N	1	B	0.13594	0.008	B	0.08055	0.003	T	0.05550	-1.0878	10	0.12430	T	0.62	.	0.1713	0.00113	0.3233:0.1493:0.21:0.3175	rs56259282	1960	Q9BV73	CP250_HUMAN	Q	1960;1904;448	ENSP00000380661:R1960Q;ENSP00000341541:R1904Q;ENSP00000395992:R448Q	ENSP00000341541:R1904Q	R	+	2	0	CEP250	33555490	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.281000	0.08456	-0.484000	0.06763	-0.733000	0.03571	CGG	G|0.993;A|0.007	0.007	strong		0.657	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		A	34092076	G	A	34092076	3	1	23	1	0	0	0	0	1	0	0	0	3254	1116	39	1	5985	1	CEP250	20	34092076	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	505402	34092076	28933444	712	8156											
RALGAPB	57148	hgsc.bcm.edu	37	chr20	37199443	37199443	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctctcagagctgatgacagaGatcagtactggtgtggaaac	12	9	12	8	0	2	4	2	2	1	2	3	6	2	5	0	2	3	2	0	2	2	1	rs139543103	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:37199443G>A	ENST00000262879.6	+	28	4379	c.4095G>A	c.(4093-4095)gaG>gaA	p.E1365E	RALGAPB_ENST00000397038.1_Silent_p.E1144E|RALGAPB_ENST00000397040.1_Silent_p.E1365E|RALGAPB_ENST00000397042.3_Silent_p.E1362E			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	1365	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				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						TGATGACAGAGATCAGTACTG	0.358													G|||	14	0.00279553	0.0	0.0043	5008	,	,		17277	0.0		0.0109	False		,,,				2504	0.0				p.E1365E		Atlas-SNP	.											.	RALGAPB	134	.	0			c.G4095A						PASS	.	G		18,4388	24.3+/-50.5	0,18,2185	82	83	83		4095	1.1	1	20	dbSNP_134	83	118,8482	62.4+/-124.4	1,116,4183	no	coding-synonymous	RALGAPB	NM_020336.2		1,134,6368	AA,AG,GG		1.3721,0.4085,1.0457		1365/1495	37199443	136,12870	2203	4300	6503	SO:0001819	synonymous_variant	57148	exon28			GACAGAGATCAGT	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.4095G>A	20.37:g.37199443G>A		60	0	0		85	49	0.576471	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Silent	SNP	ENST00000262879.6	37	CCDS13305.1																																																																																			G|0.991;A|0.009	0.009	strong		0.358	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336		A	37199443	G	A	37199443	2	1	23	1	0	0	0	0	0	0	0	1	13030	933	33	2		2	RALGAPB	20	37199443	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	3107367	37199443	25826077	713	8157											
ACTR5	79913	hgsc.bcm.edu	37	chr20	37394988	37394988	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ataggagaagaacaggctggGattgcagagactcttcagta	14	8	13	6	0	2	3	1	0	1	3	2	6	2	4	0	3	2	3	0	3	4	4	rs151070334	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:37394988G>A	ENST00000243903.4	+	7	1438	c.1401G>A	c.(1399-1401)ggG>ggA	p.G467G		NM_024855.3	NP_079131.3	Q9H9F9	ARP5_HUMAN	ARP5 actin-related protein 5 homolog (yeast)	467					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)				AACAGGCTGGGATTGCAGAGA	0.428													G|||	7	0.00139776	0.0	0.0029	5008	,	,		19343	0.0		0.005	False		,,,				2504	0.0				p.G467G		Atlas-SNP	.											.	ACTR5	44	.	0			c.G1401A						PASS	.	G		10,4396	16.8+/-37.8	0,10,2193	109	111	110		1401	-0.5	0	20	dbSNP_134	110	43,8557	28.5+/-78.6	0,43,4257	no	coding-synonymous	ACTR5	NM_024855.3		0,53,6450	AA,AG,GG		0.5,0.227,0.4075		467/608	37394988	53,12953	2203	4300	6503	SO:0001819	synonymous_variant	79913	exon7			GGCTGGGATTGCA	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.1401G>A	20.37:g.37394988G>A		171	0	0		173	79	0.456647	NM_024855	Q86WF7|Q8IUY5|Q8N724|Q9BRN0|Q9BVB7	Silent	SNP	ENST00000243903.4	37	CCDS13308.1																																																																																			G|0.996;A|0.004	0.004	strong		0.428	ACTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079205.2	NM_024855		A	37394988	G	A	37394988	2	1	23	1	0	0	0	0	0	0	0	1	215	1161	41	2		2	ACTR5	20	37394988	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	195545	37394988	25630532	714	8158											
PTPRT	11122	hgsc.bcm.edu	37	chr20	40743945	40743945	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcatctggccagtatcgcAcacatttcacctgtggccaa	9	11	8	13	1	3	0	2	0	1	0	4	0	3	0	3	2	0	2	3	2	2	2	rs41310016	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:40743945A>G	ENST00000373187.1	-	22	2992	c.2993T>C	c.(2992-2994)gTg>gCg	p.V998A	PTPRT_ENST00000373184.1_Missense_Mutation_p.V1008A|PTPRT_ENST00000373193.3_Missense_Mutation_p.V1001A|PTPRT_ENST00000373201.1_Missense_Mutation_p.V988A|PTPRT_ENST00000356100.2_Missense_Mutation_p.V1007A|PTPRT_ENST00000373190.1_Missense_Mutation_p.V997A|PTPRT_ENST00000373198.4_Missense_Mutation_p.V1017A			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	998	Tyrosine-protein phosphatase 1. {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)				CCAGTATCGCACACATTTCAC	0.507													A|||	7	0.00139776	0.0	0.0	5008	,	,		21027	0.0		0.006	False		,,,				2504	0.001				p.V1017A		Atlas-SNP	.											.	PTPRT	372	.	0			c.T3050C						PASS	.	A	ALA/VAL,ALA/VAL	3,4193		0,3,2095	120	126	124		3050,2993	5.8	1	20	dbSNP_127	124	39,8425		0,39,4193	yes	missense,missense	PTPRT	NM_133170.3,NM_007050.5	64,64	0,42,6288	GG,GA,AA		0.4608,0.0715,0.3318	benign,benign	1017/1461,998/1442	40743945	42,12618	2098	4232	6330	SO:0001583	missense	11122	exon23			TATCGCACACATT	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.2993T>C	20.37:g.40743945A>G	ENSP00000362283:p.Val998Ala	109	0	0		134	68	0.507463	NM_133170	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Missense_Mutation	SNP	ENST00000373187.1	37	CCDS42874.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	A	14.50	2.553285	0.45487	7.15E-4	0.004608	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	D;D;D;D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53	5.85	5.85	0.93711	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	T	0.66277	0.2773	N	0.04636	-0.2	0.58432	D	0.999998	P;B	0.39782	0.688;0.349	P;P	0.50378	0.639;0.516	T	0.71699	-0.4514	10	0.23302	T	0.38	.	16.2303	0.82332	1.0:0.0:0.0:0.0	rs41310016	1020;998	O14522-1;O14522	.;PTPRT_HUMAN	A	997;998;1001;1007;1020;1008;988	ENSP00000362286:V997A;ENSP00000362283:V998A;ENSP00000362289:V1001A;ENSP00000348408:V1007A;ENSP00000362294:V1020A;ENSP00000362280:V1008A;ENSP00000362297:V988A	ENSP00000348408:V1007A	V	-	2	0	PTPRT	40177359	1.000000	0.71417	0.994000	0.49952	0.972000	0.66771	4.153000	0.58118	2.233000	0.73108	0.533000	0.62120	GTG	A|0.997;G|0.003	0.003	strong		0.507	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1			G	40743945	A	G	40743945	3	3	23	1	0	0	0	0	1	0	0	0	12827	159	6	3	1372	3	PTPRT	20	40743945	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	3348957	40743945	22281575	715	8159											
SDC4	6385	hgsc.bcm.edu	37	chr20	43956017	43956017	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcagtaggatcaggaagaCggcaaagaggatgcccacga	15	3	15	8	2	1	2	1	0	0	2	1	7	1	5	1	4	2	3	1	4	3	1	rs202142981		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:43956017C>T	ENST00000372733.3	-	5	523	c.484G>A	c.(484-486)Gtc>Atc	p.V162I	SDC4_ENST00000537976.1_Missense_Mutation_p.V90I	NM_002999.3	NP_002990.2	P31431	SDC4_HUMAN	syndecan 4	162					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)				ATCAGGAAGACGGCAAAGAGG	0.532			T	ROS1	NSCLC								C|||	1	0.000199681	0.0	0.0	5008	,	,		17406	0.0		0.001	False		,,,				2504	0.0				p.V162I		Atlas-SNP	.		Dom	yes		20	20q12	6385	syndecan 4		E	.	SDC4	16	.	0			c.G484A						PASS	.	C	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	95	85	89		484	-3.4	0	20		89	0,8600		0,0,4300	yes	missense	SDC4	NM_002999.3	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	162/199	43956017	1,13005	2203	4300	6503	SO:0001583	missense	6385	exon5			GGAAGACGGCAAA	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.484G>A	20.37:g.43956017C>T	ENSP00000361818:p.Val162Ile	103	0	0		116	55	0.474138	NM_002999	O00773|Q16833|Q53FN9|Q6FGN3	Missense_Mutation	SNP	ENST00000372733.3	37	CCDS13350.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.725885	0.00694	2.27E-4	0.0	ENSG00000124145	ENST00000372733;ENST00000537976	T	0.24350	1.86	5.24	-3.38	0.04883	.	0.925625	0.09152	N	0.841349	T	0.13372	0.0324	N	0.21194	0.64	0.19300	N	0.999978	B	0.29766	0.256	B	0.23150	0.044	T	0.31888	-0.9927	10	0.07482	T	0.82	-1.8487	13.6197	0.62130	0.0:0.4611:0.0:0.5389	.	162	P31431	SDC4_HUMAN	I	162;90	ENSP00000361818:V162I	ENSP00000361818:V162I	V	-	1	0	SDC4	43389431	0.000000	0.05858	0.004000	0.12327	0.064000	0.16182	-0.645000	0.05409	-0.505000	0.06568	-0.253000	0.11424	GTC	.	.	weak		0.532	SDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080515.1	NM_002999		T	43956017	C	T	43956017	3	4	23	1	0	0	0	0	1	0	0	0	13969	536	19	1	116	1	SDC4	20	43956017	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	3212072	43956017	19069503	716	8160											
ZMYND8	23613	hgsc.bcm.edu	37	chr20	45878118	45878118	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttgggagagatgagaggaaCaggggtggactgttgctgga	10	8	19	4	0	0	2	0	1	0	2	0	8	0	6	0	6	2	2	0	6	1	2	rs77137073	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:45878118C>G	ENST00000311275.7	-	13	1880	c.1627G>C	c.(1627-1629)Gtt>Ctt	p.V543L	ZMYND8_ENST00000471951.2_Missense_Mutation_p.V563L|ZMYND8_ENST00000355972.4_Missense_Mutation_p.V543L|ZMYND8_ENST00000352431.2_Missense_Mutation_p.V563L|ZMYND8_ENST00000468376.2_5'UTR|ZMYND8_ENST00000446994.2_Missense_Mutation_p.V480L|ZMYND8_ENST00000372023.3_Missense_Mutation_p.V538L|ZMYND8_ENST00000458360.2_Missense_Mutation_p.V538L|ZMYND8_ENST00000540497.1_Missense_Mutation_p.V491L|ZMYND8_ENST00000360911.3_Missense_Mutation_p.V538L|ZMYND8_ENST00000262975.4_Missense_Mutation_p.V543L|ZMYND8_ENST00000396281.4_Missense_Mutation_p.V543L|ZMYND8_ENST00000536340.1_Missense_Mutation_p.V570L|ZMYND8_ENST00000461685.1_Missense_Mutation_p.V563L	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	543					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)	p.V563L(1)		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)			ATGAGAGGAACAGGGGTGGAC	0.493													C|||	19	0.00379393	0.0	0.0043	5008	,	,		21570	0.0		0.0149	False		,,,				2504	0.001				p.V563L		Atlas-SNP	.											ZMYND8,NS,lymphoid_neoplasm,0,1	ZMYND8	166	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G1687C						PASS	.	C	LEU/VAL,LEU/VAL,LEU/VAL	15,4391	22.3+/-47.3	0,15,2188	148	129	136		1687,1687,1612	5.7	0.1	20	dbSNP_132	136	114,8486	61.0+/-122.8	3,108,4189	yes	missense,missense,missense	ZMYND8	NM_012408.3,NM_183047.1,NM_183048.1	32,32,32	3,123,6377	GG,GC,CC		1.3256,0.3404,0.9918	benign,benign,benign	563/1161,563/1189,538/1136	45878118	129,12877	2203	4300	6503	SO:0001583	missense	23613	exon13			GAGGAACAGGGGT	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.1627G>C	20.37:g.45878118C>G	ENSP00000312237:p.Val543Leu	124	0	0		135	62	0.459259	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	Missense_Mutation	SNP	ENST00000311275.7	37		14|14	0.00641025641025641|0.00641025641025641	0|0	0.0|0.0	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	10|10	0.013192612137203167|0.013192612137203167	C|C	8.782|8.782	0.928382|0.928382	0.18131|0.18131	0.003404|0.003404	0.013256|0.013256	ENSG00000101040|ENSG00000101040	ENST00000467200|ENST00000360911;ENST00000311275;ENST00000458360;ENST00000262975;ENST00000471951;ENST00000352431;ENST00000396281;ENST00000536340;ENST00000355972;ENST00000446994;ENST00000461685;ENST00000372023;ENST00000540497	.|D;D;D;D;D;D;D;D;D;D;D	.|0.90563	.|-1.84;-1.74;-1.87;-1.74;-1.85;-1.75;-1.74;-2.69;-1.73;-1.84;-1.8	5.7|5.7	5.7|5.7	0.88788|0.88788	.|.	.|0.203494	.|0.42294	.|D	.|0.000725	D|D	0.82953|0.82953	0.5149|0.5149	L|L	0.43152|0.43152	1.355|1.355	0.09310|0.09310	N|N	0.999992|0.999992	.|P;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	.|0.46621	.|0.881;0.243;0.078;0.078;0.0;0.277;0.112;0.0;0.0;0.0;0.0;0.078;0.0;0.0;0.078;0.073;0.0;0.078	.|B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	.|0.40702	.|0.338;0.138;0.217;0.217;0.009;0.314;0.138;0.005;0.005;0.005;0.005;0.217;0.012;0.012;0.217;0.053;0.006;0.217	T|T	0.79969|0.79969	-0.1579|-0.1579	5|10	.|0.42905	.|T	.|0.14	-17.669|-17.669	13.0828|13.0828	0.59123|0.59123	0.0:0.927:0.0:0.073|0.0:0.927:0.0:0.073	.|.	.|538;570;538;538;518;537;563;543;538;563;563;543;480;538;491;563;491;543	.|B7ZM62;F5H0X3;Q2HXV7;Q2HXV3;Q5TH11;Q5JV90;Q9ULU4-7;Q9ULU4-9;Q9ULU4-14;Q9ULU4-12;Q9ULU4-13;Q9ULU4;B3KVL2;Q2HXV9;Q2HXV1;Q9ULU4-8;Q2HXV4;B7Z2A8	.|.;.;.;.;.;.;.;.;.;.;.;PKCB1_HUMAN;.;.;.;.;.;.	S|L	470|538;543;538;544;564;563;543;570;543;480;563;538;491	.|ENSP00000354166:V538L;ENSP00000312237:V543L;ENSP00000392964:V538L;ENSP00000335537:V563L;ENSP00000379577:V543L;ENSP00000439800:V570L;ENSP00000348246:V543L;ENSP00000396725:V480L;ENSP00000418210:V563L;ENSP00000361093:V538L;ENSP00000443086:V491L	.|ENSP00000262975:V544L	C|V	-|-	2|1	0|0	ZMYND8|ZMYND8	45311525|45311525	0.952000|0.952000	0.32445|0.32445	0.053000|0.053000	0.19242|0.19242	0.055000|0.055000	0.15305|0.15305	3.209000|3.209000	0.51122|0.51122	2.683000|2.683000	0.91414|0.91414	0.650000|0.650000	0.86243|0.86243	TGT|GTT	C|0.991;G|0.009	0.009	strong		0.493	ZMYND8-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000079596.2	NM_183047		G	45878118	C	G	45878118	3	3	23	1	0	0	0	0	1	0	0	0	17726	478	17	4	1923	4	ZMYND8	20	45878118	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1922101	45878118	17147402	717	8161											
PTPN1	5770	hgsc.bcm.edu	37	chr20	49195749	49195749	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tccgttgatatcaagaaagtGctgttagaaatgaggaagtt	14	12	11	4	1	1	4	1	2	0	2	2	5	2	5	1	1	1	4	1	1	6	4			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:49195749G>A	ENST00000371621.3	+	7	921	c.747G>A	c.(745-747)gtG>gtA	p.V249V	RP4-530I15.9_ENST00000431019.1_RNA|PTPN1_ENST00000541713.1_Silent_p.V176V	NM_001278618.1|NM_002827.2	NP_001265547.1|NP_002818.1	P18031	PTN1_HUMAN	protein tyrosine phosphatase, non-receptor type 1	249	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|endoplasmic reticulum unfolded protein response (GO:0030968)|insulin receptor signaling pathway (GO:0008286)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|peptidyl-tyrosine dephosphorylation (GO:0035335)|peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity (GO:1990264)|platelet activation (GO:0030168)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|regulation of endocytosis (GO:0030100)|regulation of hepatocyte growth factor receptor signaling pathway (GO:1902202)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of signal transduction (GO:0009966)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|sorting endosome (GO:0097443)	enzyme binding (GO:0019899)|ephrin receptor binding (GO:0046875)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|skin(2)	16		Lung NSC(126;0.163)			Tiludronate(DB01133)	TCAAGAAAGTGCTGTTAGAAA	0.493																																					p.V249V		Atlas-SNP	.											.	PTPN1	36	.	0			c.G747A						PASS	.						148	149	148					20																	49195749		2203	4300	6503	SO:0001819	synonymous_variant	5770	exon7			GAAAGTGCTGTTA		CCDS13430.1, CCDS63309.1	20q13.1-q13.2	2011-06-09			ENSG00000196396	ENSG00000196396		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9642	protein-coding gene	gene with protein product		176885		PTP1B		2164224	Standard	NM_002827		Approved		uc002xvl.3	P18031	OTTHUMG00000032729	ENST00000371621.3:c.747G>A	20.37:g.49195749G>A		58	0	0		72	24	0.333333	NM_002827	Q5TGD8|Q9BQV9|Q9NQQ4	Silent	SNP	ENST00000371621.3	37	CCDS13430.1																																																																																			.	.	none		0.493	PTPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079694.2			A	49195749	G	A	49195749	2	1	23	1	0	0	0	0	0	0	0	1	12792	1306	46	2		2	PTPN1	20	49195749	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	3317631	49195749	13829771	718	8162											
C20orf107	388799	hgsc.bcm.edu	37	chr20	55108507	55108507	+	Missense_Mutation	SNP	C	C	A																															cgaaccccaggggaaggtgcCgtgtggagagcactttcgga																								rs200150839|rs386815438	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:55108507C>A	ENST00000371325.1	+	1	206	c.110C>A	c.(109-111)cCg>cAg	p.P37Q		NM_001013646.2	NP_001013668.2	Q5JX69	F209B_HUMAN	family with sequence similarity 209, member B	37				PC -> QY (in Ref. 2; AAI05793). {ECO:0000305}.		integral component of membrane (GO:0016021)|nucleus (GO:0005634)											GGGAAGGTGCCGTGTGGAGAG	0.537													C|||	49	0.00978435	0.0023	0.0086	5008	,	,		20353	0.003		0.0089	False		,,,				2504	0.0286				p.P37Q		Atlas-SNP	.											.	.	.	.	0			c.C110A						PASS	.						167	140	149					20																	55108507		2203	4290	6493	SO:0001583	missense	388799	exon1			AGGTGCCGTGTGG	AL109806	CCDS33494.1	20q13.31	2011-11-24	2011-11-24	2011-11-24	ENSG00000213714	ENSG00000213714			16101	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 107"	C20orf107			Standard	NM_001013646		Approved	dJ1153D9.4	uc002xxz.4	Q5JX69	OTTHUMG00000032800	ENST00000371325.1:c.110C>A	20.37:g.55108507C>A	ENSP00000360376:p.Pro37Gln	293	0	0		181	26	0.143646	NM_001013646	Q3KRB5	Missense_Mutation	SNP	ENST00000371325.1	37	CCDS33494.1	.	.	.	.	.	.	.	.	.	.	C	3.871	-0.027889	0.07589	.	.	ENSG00000213714	ENST00000371325	T	0.08720	3.06	2.8	2.8	0.32819	.	0.000000	0.49305	D	0.000143	T	0.15522	0.0374	L	0.36672	1.1	0.33241	D	0.557293	D	0.89917	1.0	D	0.91635	0.999	T	0.10200	-1.0640	10	0.30854	T	0.27	-19.843	9.141	0.36903	0.0:1.0:0.0:0.0	.	37	Q5JX69	CT107_HUMAN	Q	37	ENSP00000360376:P37Q	ENSP00000360376:P37Q	P	+	2	0	C20orf107	54541914	0.973000	0.33851	0.988000	0.46212	0.019000	0.09904	1.612000	0.36889	1.556000	0.49512	0.393000	0.25936	CCG	.	.	weak		0.537	FAM209B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079816.1			A	55108507	C	A	55108507	3	1	23	1	0	0	0	0	1	0	0	0	2079	652	23	4	112	4	C20orf107	20	55108507	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	5912758	55108507	7917013	719	8163	105	2									
C20orf107	388799	hgsc.bcm.edu	37	chr20	55108508	55108508	+	Silent	SNP	G	G	A																															gaaccccaggggaaggtgccGtgtggagagcactttcggat																								rs150517677|rs386815438	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:55108508G>A	ENST00000371325.1	+	1	207	c.111G>A	c.(109-111)ccG>ccA	p.P37P		NM_001013646.2	NP_001013668.2	Q5JX69	F209B_HUMAN	family with sequence similarity 209, member B	37				PC -> QY (in Ref. 2; AAI05793). {ECO:0000305}.		integral component of membrane (GO:0016021)|nucleus (GO:0005634)											GGAAGGTGCCGTGTGGAGAGC	0.537													G|||	51	0.0101837	0.003	0.0086	5008	,	,		20351	0.003		0.0099	False		,,,				2504	0.0286				p.P37P		Atlas-SNP	.											.	.	.	.	0			c.G111A						PASS	.						169	142	151					20																	55108508		2203	4286	6489	SO:0001819	synonymous_variant	388799	exon1			GGTGCCGTGTGGA	AL109806	CCDS33494.1	20q13.31	2011-11-24	2011-11-24	2011-11-24	ENSG00000213714	ENSG00000213714			16101	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 107"	C20orf107			Standard	NM_001013646		Approved	dJ1153D9.4	uc002xxz.4	Q5JX69	OTTHUMG00000032800	ENST00000371325.1:c.111G>A	20.37:g.55108508G>A		294	0	0		181	26	0.143646	NM_001013646	Q3KRB5	Silent	SNP	ENST00000371325.1	37	CCDS33494.1																																																																																			G|0.985;A|0.015	0.015	strong		0.537	FAM209B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079816.1			A	55108508	G	A	55108508	2	1	23	1	0	0	0	0	0	0	0	1	2079	1132	40	1		1	C20orf107	20	55108508	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1	55108508	7917012	720	8164	105	2									
ZNF831	128611	hgsc.bcm.edu	37	chr20	57766113	57766113	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acctgccctgcccctcctgcGagggaccagccagctcccac	6	5	9	21	1	0	0	0	0	0	0	2	2	2	1	8	1	5	1	8	1	0	0	rs148289392	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:57766113G>A	ENST00000371030.2	+	1	39	c.39G>A	c.(37-39)gcG>gcA	p.A13A		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	13	Pro-rich.						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)					CCCCTCCTGCGAGGGACCAGC	0.637													.|||	3	0.000599042	0.0	0.0014	5008	,	,		17085	0.0		0.002	False		,,,				2504	0.0				p.A13A		Atlas-SNP	.											.	ZNF831	287	.	0			c.G39A						PASS	.	G		0,3912		0,0,1956	27	32	30		39	2.5	1	20	dbSNP_134	30	6,8286		0,6,4140	no	coding-synonymous	ZNF831	NM_178457.1		0,6,6096	AA,AG,GG		0.0724,0.0,0.0492		13/1678	57766113	6,12198	1956	4146	6102	SO:0001819	synonymous_variant	128611	exon1			TCCTGCGAGGGAC	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.39G>A	20.37:g.57766113G>A		49	0	0		27	14	0.518519	NM_178457	Q5TDR4|Q8TCP0	Silent	SNP	ENST00000371030.2	37	CCDS42894.1																																																																																			G|0.999;A|0.001	0.001	strong		0.637	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		A	57766113	G	A	57766113	2	1	23	1	0	0	0	0	0	0	0	1	18200	1045	37	1		1	ZNF831	20	57766113	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	2657605	57766113	5259407	721	8165											
USP25	29761	hgsc.bcm.edu	37	chr21	17236674	17236674	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	atcgtttacatcatgtagtgGtctactttatccagaaccag	11	14	7	9	1	2	1	1	0	1	1	4	1	3	1	2	1	3	2	2	1	5	6	rs142929561	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:17236674G>C	ENST00000285679.6	+	19	2794	c.2425G>C	c.(2425-2427)Gtc>Ctc	p.V809L	USP25_ENST00000351097.5_Intron|USP25_ENST00000400183.2_Missense_Mutation_p.V879L|USP25_ENST00000285681.2_Missense_Mutation_p.V841L	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	809					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)		TCATGTAGTGGTCTACTTTAT	0.363													G|||	6	0.00119808	0.0	0.0029	5008	,	,		13115	0.0		0.004	False		,,,				2504	0.0				p.V809L		Atlas-SNP	.											USP25,NS,carcinoma,-1,1	USP25	156	1	0			c.G2425C						PASS	.	G	LEU/VAL	3,4403	6.2+/-15.9	0,3,2200	82	78	80		2425	5.6	1	21	dbSNP_134	80	6,8594	5.0+/-18.6	0,6,4294	yes	missense	USP25	NM_013396.3	32	0,9,6494	CC,CG,GG		0.0698,0.0681,0.0692	benign	809/1056	17236674	9,12997	2203	4300	6503	SO:0001583	missense	29761	exon19			GTAGTGGTCTACT	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.2425G>C	21.37:g.17236674G>C	ENSP00000285679:p.Val809Leu	42	0	0		73	26	0.356164	NM_013396	C0LSZ0|Q6DHZ9|Q9H9W1	Missense_Mutation	SNP	ENST00000285679.6	37	CCDS33515.1	5|5	0.0022893772893772895|0.0022893772893772895	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	4|4	0.005277044854881266|0.005277044854881266	G|G	21.6|21.6	4.175610|4.175610	0.78564|0.78564	6.81E-4|6.81E-4	6.98E-4|6.98E-4	ENSG00000155313|ENSG00000155313	ENST00000285681;ENST00000285679;ENST00000400183|ENST00000449491	T;T;T|.	0.33438|.	1.54;1.7;1.41|.	5.62|5.62	5.62|5.62	0.85841|0.85841	.|.	0.053961|.	0.64402|.	D|.	0.000001|.	T|T	0.68183|0.68183	0.2973|0.2973	M|M	0.62723|0.62723	1.935|1.935	0.50813|0.50813	D|D	0.999893|0.999893	D;P;B|.	0.55172|.	0.97;0.83;0.214|.	P;B;B|.	0.53224|.	0.721;0.202;0.055|.	T|T	0.68394|0.68394	-0.5420|-0.5420	10|5	0.72032|.	D|.	0.01|.	.|.	20.0114|20.0114	0.97452|0.97452	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	879;841;809|.	Q9UHP3-3;Q9UHP3-1;Q9UHP3|.	.;.;UBP25_HUMAN|.	L|C	841;809;879|107	ENSP00000285681:V841L;ENSP00000285679:V809L;ENSP00000383044:V879L|.	ENSP00000285679:V809L|.	V|W	+|+	1|3	0|0	USP25|USP25	16158545|16158545	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.987000|0.987000	0.75469|0.75469	6.352000|6.352000	0.73027|0.73027	2.795000|2.795000	0.96236|0.96236	0.655000|0.655000	0.94253|0.94253	GTC|TGG	G|0.999;C|0.001	0.001	strong		0.363	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			C	17236674	G	C	17236674	3	2	23	1	0	0	0	0	1	0	0	0	17071	1261	44	4	2499	4	USP25	21	17236674	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10		17236674	30893221	722	8166											
DOPEY2	9980	hgsc.bcm.edu	37	chr21	37584331	37584331	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atcgtgcgcattctctcagcCgccacccagaccctactgag	8	8	8	17	3	2	2	1	1	1	1	4	2	2	2	4	0	3	1	4	0	1	2	rs147659226	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:37584331C>T	ENST00000399151.3	+	7	925	c.840C>T	c.(838-840)gcC>gcT	p.A280A	DOPEY2_ENST00000492760.1_3'UTR|RN7SL73P_ENST00000585239.1_RNA	NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	280					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						TTCTCTCAGCCGCCACCCAGA	0.468													c|||	8	0.00159744	0.0045	0.0029	5008	,	,		20397	0.0		0.0	False		,,,				2504	0.0				p.A280A		Atlas-SNP	.											DOPEY2,NS,carcinoma,+2,1	DOPEY2	184	1	0			c.C840T						scavenged	.	T		14,4392	21.2+/-45.6	0,14,2189	101	89	93		840	-10.2	0	21	dbSNP_134	93	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DOPEY2	NM_005128.2		0,15,6488	TT,TC,CC		0.0116,0.3177,0.1153		280/2299	37584331	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	9980	exon7			CTCAGCCGCCACC	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.840C>T	21.37:g.37584331C>T		93	1	0.0107527		100	49	0.49	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Silent	SNP	ENST00000399151.3	37	CCDS13643.1																																																																																			C|0.999;T|0.001	0.001	strong		0.468	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128		T	37584331	C	T	37584331	2	4	23	1	0	0	0	0	0	0	0	1	4710	639	23	1		1	DOPEY2	21	37584331	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	20347657	37584331	10545564	723	8167											
TTC3	7267	hgsc.bcm.edu	37	chr21	38538736	38538736	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgcctctgaaacacagatccTtgagggctctttgggaatat	10	12	10	9	0	2	3	0	2	2	1	3	4	3	4	2	2	2	1	2	2	3	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:38538736T>G	ENST00000399017.2	+	33	6967	c.4220T>G	c.(4219-4221)cTt>cGt	p.L1407R	TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000355666.1_Missense_Mutation_p.L1407R|TTC3_ENST00000354749.2_Missense_Mutation_p.L1407R	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1407					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)				ACACAGATCCTTGAGGGCTCT	0.438																																					p.L1407R	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.T4220G						PASS	.						121	114	117					21																	38538736		2203	4300	6503	SO:0001583	missense	7267	exon33			AGATCCTTGAGGG	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.4220T>G	21.37:g.38538736T>G	ENSP00000381981:p.Leu1407Arg	192	0	0		193	90	0.466321	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	.	.	.	.	.	.	.	.	.	.	T	9.860	1.196029	0.22037	.	.	ENSG00000182670	ENST00000355666;ENST00000399017;ENST00000354749	T;T;T	0.08807	3.05;3.05;3.05	4.85	-5.58	0.02512	.	1.732930	0.03051	N	0.154594	T	0.06690	0.0171	L	0.51422	1.61	0.09310	N	1	B;B	0.13145	0.001;0.007	B;B	0.09377	0.004;0.003	T	0.37454	-0.9705	9	.	.	.	0.1757	0.2964	0.00266	0.2464:0.163:0.2518:0.3389	.	465;1407	Q5GIT6;P53804	.;TTC3_HUMAN	R	1407	ENSP00000347889:L1407R;ENSP00000381981:L1407R;ENSP00000346791:L1407R	.	L	+	2	0	TTC3	37460606	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.249000	0.02888	-0.672000	0.05266	-0.290000	0.09829	CTT	.	.	none		0.438	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			G	38538736	T	G	38538736	3	3	23	1	0	0	0	0	1	0	0	0	16712	1609	56	5	4346	5	TTC3	21	38538736	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	954405	38538736	9591159	724	8168											
DYRK1A	1859	hgsc.bcm.edu	37	chr21	38884589	38884589	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcaatcaggcctaccagaatCgcccagtggctgctaatacc	11	7	9	14	1	1	1	1	0	0	1	2	1	1	1	4	2	3	3	4	2	5	3	rs201554841		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:38884589C>T	ENST00000398960.2	+	11	2122	c.2047C>T	c.(2047-2049)Cgc>Tgc	p.R683C	DYRK1A_ENST00000338785.3_3'UTR|DYRK1A_ENST00000455387.2_Missense_Mutation_p.R455C|DYRK1A_ENST00000339659.4_Missense_Mutation_p.R674C	NM_001396.3|NM_130438.2	NP_001387.2|NP_569122.1	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A	683					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						CTACCAGAATCGCCCAGTGGC	0.517																																					p.R683C	Melanoma(114;464 1602 31203 43785 45765)	Atlas-SNP	.											DYRK1A,NS,malignant_melanoma,0,1	DYRK1A	85	1	0			c.C2047T						PASS	.						142	128	133					21																	38884589		2203	4300	6503	SO:0001583	missense	1859	exon11			CAGAATCGCCCAG	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.2047C>T	21.37:g.38884589C>T	ENSP00000381932:p.Arg683Cys	148	0	0		177	81	0.457627	NM_001396	O60769|Q92582|Q92810|Q9UNM5	Missense_Mutation	SNP	ENST00000398960.2	37	CCDS42925.1	.	.	.	.	.	.	.	.	.	.	C	16.99	3.272816	0.59649	.	.	ENSG00000157540	ENST00000339659;ENST00000398960;ENST00000455387	T;T;T	0.58652	0.32;0.35;0.88	5.73	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.45597	0.1350	N	0.24115	0.695	0.80722	D	1	B;B	0.17465	0.013;0.022	B;B	0.08055	0.001;0.003	T	0.40869	-0.9540	10	0.87932	D	0	.	14.9122	0.70767	0.0:0.9311:0.0:0.0689	.	683;674	Q13627;Q13627-2	DYR1A_HUMAN;.	C	674;683;455	ENSP00000340373:R674C;ENSP00000381932:R683C;ENSP00000407854:R455C	ENSP00000340373:R674C	R	+	1	0	DYRK1A	37806459	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.398000	0.79919	1.433000	0.47394	-0.150000	0.13652	CGC	C|0.999;T|0.001	0.001	weak		0.517	DYRK1A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194804.1	NM_001396		T	38884589	C	T	38884589	3	4	23	1	0	0	0	0	1	0	0	0	4856	884	31	1	2173	1	DYRK1A	21	38884589	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	345853	38884589	9245306	725	8169											
DSCR4	10281	hgsc.bcm.edu	37	chr21	39493232	39493232	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ggatcaatacctgtggagagGagaagctgaggcaggatcag	13	6	16	6	0	2	3	2	1	0	2	2	7	2	5	1	5	2	2	1	5	3	1	rs61731605	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:39493232G>A	ENST00000328264.3	-	1	222	c.118C>T	c.(118-120)Cct>Tct	p.P40S	DSCR4_ENST00000398948.1_Missense_Mutation_p.P40S|DSCR8_ENST00000400477.3_5'Flank|DSCR8_ENST00000357704.4_5'Flank	NM_005867.2	NP_005858.1	P56555	DSCR4_HUMAN	Down syndrome critical region gene 4	40										large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	6						ctgtggagaggagaagctgag	0.512													G|||	51	0.0101837	0.0	0.0245	5008	,	,		17151	0.002		0.0278	False		,,,				2504	0.0041				p.P40S		Atlas-SNP	.											.	DSCR4	20	.	0			c.C118T						PASS	.	G		30,4376	35.2+/-66.4	0,30,2173	75	69	71			1.3	0	21	dbSNP_129	71	256,8344	98.8+/-160.4	3,250,4047	yes	intergenic				3,280,6220	AA,AG,GG		2.9767,0.6809,2.199			39493232	286,12720	2203	4300	6503	SO:0001583	missense	10281	exon1			GGAGAGGAGAAGC	AB000099	CCDS33554.1	21q22.2	2012-04-19			ENSG00000184029	ENSG00000184029			3045	protein-coding gene	gene with protein product		604829				9455479	Standard	NM_005867		Approved	DCRB	uc002ywp.3	P56555	OTTHUMG00000086673	ENST00000328264.3:c.118C>T	21.37:g.39493232G>A	ENSP00000328676:p.Pro40Ser	67	0	0		55	25	0.454545	NM_005867	Q4VB31	Missense_Mutation	SNP	ENST00000328264.3	37	CCDS33554.1	37	0.01694139194139194	0	0.0	12	0.03314917127071823	2	0.0034965034965034965	23	0.030343007915567283	G	9.758	1.169279	0.21621	0.006809	0.029767	ENSG00000184029	ENST00000398948;ENST00000328264	.	.	.	1.33	1.33	0.21861	.	.	.	.	.	T	0.30355	0.0762	.	.	.	0.09310	N	1	D	0.65815	0.995	D	0.65323	0.934	T	0.13098	-1.0522	7	0.87932	D	0	.	6.0593	0.19828	0.0:0.0:1.0:0.0	rs61731605	40	P56555	DSCR4_HUMAN	S	40	.	ENSP00000328676:P40S	P	-	1	0	DSCR4	38415102	0.006000	0.16342	0.011000	0.14972	0.058000	0.15608	0.196000	0.17176	1.058000	0.40530	0.313000	0.20887	CCT	G|0.980;A|0.020	0.020	strong		0.512	DSCR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000194834.1	NM_005867		A	39493232	G	A	39493232	3	1	23	1	0	0	0	0	1	0	0	0	4774	1174	41	2	250	2	DSCR4	21	39493232	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	608643	39493232	8636663	726	8170											
PLAC4	25825	hgsc.bcm.edu	37	chr21	42551270	42551270	+	Intron	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccagggtgaggagtgagggtAtccagggtgagtgagggtgt	8	8	21	4	0	0	4	0	4	0	0	1	5	1	5	2	5	0	1	2	5	1	1	rs199893430		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:42551270A>G	ENST00000330333.6	+	1	775				BACE2_ENST00000328735.6_Intron|PLAC4_ENST00000440221.2_RNA|BACE2_ENST00000347667.5_Intron|PLAC4_ENST00000430327.2_RNA|PLAC4_ENST00000414699.1_RNA|PLAC4_ENST00000536486.1_RNA|BACE2-IT1_ENST00000433378.1_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)				gagtgagggtatccagggtga	0.607																																					p.Y96H		Atlas-SNP	.											.	.	.	.	0			c.T286C						PASS	.						147	128	134					21																	42551270		2184	4258	6442	SO:0001627	intron_variant	191585	exon1			GAGGGTATCCAGG	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+10768A>G	21.37:g.42551270A>G		244	0	0		283	21	0.0742049	NM_182832	A8K7P1|Q5DIH8|Q8N2D4|Q9H2V8|Q9NZL1|Q9NZL2|Q9UJT6	Missense_Mutation	SNP	ENST00000330333.6	37	CCDS13668.1																																																																																			.	.	weak		0.607	BACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195056.1			G	42551270	A	G	42551270	1	3	23	0	1	0	0	0	0	0	0	0	12023	449	16	3		3	PLAC4	21	42551270	Intron	SNP	A	TCGA-G8-6325-01A-11D-2210-10	3058038	42551270	5578625	727	8171											
ZNF295	49854	hgsc.bcm.edu	37	chr21	43413158	43413158	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaggtgaatagacaggaacCtggctatccatcgacaatga	15	7	11	8	1	0	3	0	2	0	1	2	6	1	4	2	3	1	1	2	3	6	2	rs147318145	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:43413158C>T	ENST00000310826.5	-	3	1230	c.1047G>A	c.(1045-1047)caG>caA	p.Q349Q	ZBTB21_ENST00000398499.1_Silent_p.Q349Q|ZBTB21_ENST00000398511.3_Silent_p.Q349Q|ZBTB21_ENST00000398505.3_Silent_p.Q349Q|ZBTB21_ENST00000465968.1_Intron	NM_001098402.1	NP_001091872.1	Q9ULJ3	ZBT21_HUMAN	zinc finger and BTB domain containing 21	349					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)										AGACAGGAACCTGGCTATCCA	0.478													C|||	38	0.00758786	0.0008	0.0144	5008	,	,		19466	0.0		0.0229	False		,,,				2504	0.0041				p.Q349Q		Atlas-SNP	.											.	.	.	.	0			c.G1047A						PASS	.	C	,,	27,4379	33.5+/-64.1	0,27,2176	99	98	99		1047,1047,1047	5.1	1	21	dbSNP_134	99	232,8368	94.2+/-156.2	3,226,4071	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF295	NM_001098402.1,NM_001098403.1,NM_020727.4	,,	3,253,6247	TT,TC,CC		2.6977,0.6128,1.9914	,,	349/1067,349/866,349/1067	43413158	259,12747	2203	4300	6503	SO:0001819	synonymous_variant	49854	exon3			AGGAACCTGGCTA	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.1047G>A	21.37:g.43413158C>T		119	0	0		107	53	0.495327	NM_001098402	Q5R2W1|Q5R2W2|Q6P4R0	Silent	SNP	ENST00000310826.5	37	CCDS13678.1																																																																																			C|0.983;T|0.017	0.017	strong		0.478	ZBTB21-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195308.1	NM_020727		T	43413158	C	T	43413158	2	4	23	1	0	0	0	0	0	0	0	1	17842	680	24	2		2	ZNF295	21	43413158	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	861888	43413158	4716737	728	8172											
C21orf56	84221	hgsc.bcm.edu	37	chr21	47581869	47581869	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgttggccaccgtgaagccGtagagccgcgtcacgcccgg	7	6	14	14	6	1	2	1	1	0	1	1	2	1	2	5	2	2	2	5	2	2	2	rs139199473	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:47581869G>A	ENST00000291672.5	-	4	1718	c.657C>T	c.(655-657)taC>taT	p.Y219Y	SPATC1L_ENST00000330205.6_Silent_p.Y65Y	NM_001142854.1	NP_001136326.1	Q9H0A9	SPC1L_HUMAN	spermatogenesis and centriole associated 1-like	219																	CCGTGAAGCCGTAGAGCCGCG	0.731																																					p.Y219Y		Atlas-SNP	.											.	.	.	.	0			c.C657T						PASS	.	G	,	2,4390		0,2,2194	32	28	29		657,195	-8.4	0.7	21	dbSNP_134	29	10,8576		0,10,4283	no	coding-synonymous,coding-synonymous	C21orf56	NM_001142854.1,NM_032261.4	,	0,12,6477	AA,AG,GG		0.1165,0.0455,0.0925	,	219/341,65/187	47581869	12,12966	2196	4293	6489	SO:0001819	synonymous_variant	84221	exon4			GAAGCCGTAGAGC	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.657C>T	21.37:g.47581869G>A		62	0	0		30	16	0.533333	NM_001142854	B4E323|Q52LS9|Q6FIH5|Q6P0L3|Q9NSE5	Silent	SNP	ENST00000291672.5	37	CCDS46653.1																																																																																			G|1.000;A|0.000	0.000	strong		0.731	SPATC1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376654.1	NM_032261		A	47581869	G	A	47581869	2	1	23	1	0	0	0	0	0	0	0	1	2129	1140	40	1		1	C21orf56	21	47581869	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	4168711	47581869	548026	729	8173											
LSS	4047	hgsc.bcm.edu	37	chr21	47626602	47626602	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tcaccgaagacctccgagggGttcagcagctccagcaagtg	10	6	12	13	2	2	1	2	0	0	1	4	3	4	1	4	2	3	4	4	2	2	1	rs111779817	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:47626602G>A	ENST00000397728.3	-	16	1626	c.1548C>T	c.(1546-1548)aaC>aaT	p.N516N	LSS_ENST00000356396.4_Silent_p.N516N|LSS_ENST00000457828.2_Silent_p.N436N|LSS_ENST00000522411.1_Silent_p.N505N	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	516					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)					CCTCCGAGGGGTTCAGCAGCT	0.612													G|||	30	0.00599042	0.0	0.0072	5008	,	,		17554	0.0		0.007	False		,,,				2504	0.0184				p.N516N	Pancreas(114;955 2313 34923 50507)	Atlas-SNP	.											.	LSS	50	.	0			c.C1548T						PASS	.	G	,,,	3,4403	6.2+/-15.9	0,3,2200	78	72	74		1548,1515,1308,1548	2.6	1	21	dbSNP_132	74	29,8571	20.4+/-63.3	0,29,4271	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LSS	NM_001001438.2,NM_001145436.1,NM_001145437.1,NM_002340.5	,,,	0,32,6471	AA,AG,GG		0.3372,0.0681,0.246	,,,	516/733,505/722,436/653,516/733	47626602	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	4047	exon16			CGAGGGGTTCAGC	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.1548C>T	21.37:g.47626602G>A		53	0	0		52	28	0.538462	NM_001001438	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Silent	SNP	ENST00000397728.3	37	CCDS13733.1																																																																																			G|0.997;A|0.003	0.003	strong		0.612	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2			A	47626602	G	A	47626602	2	1	23	1	0	0	0	0	0	0	0	1	9074	1252	44	2		2	LSS	21	47626602	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	44733	47626602	503293	730	8174											
CECR6	27439	hgsc.bcm.edu	37	chr22	17600420	17600420	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cggagggcggagcaccgtagCcccctctggcccgactcggg	5	4	16	16	5	1	0	0	0	1	0	2	3	1	2	4	5	2	2	4	5	1	1	rs184892903	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:17600420C>A	ENST00000331437.3	-	1	1723	c.1598G>T	c.(1597-1599)gGc>gTc	p.G533V	AC006946.15_ENST00000441544.1_5'Flank|CECR6_ENST00000399875.1_Missense_Mutation_p.G178V	NM_031890.3	NP_114096.1	Q9BXQ6	CECR6_HUMAN	cat eye syndrome chromosome region, candidate 6	533										haematopoietic_and_lymphoid_tissue(1)	1		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.221)		AGCACCGTAGCCCCCTCTGGC	0.706													C|||	3	0.000599042	0.0008	0.0014	5008	,	,		11413	0.0		0.001	False		,,,				2504	0.0				p.G533V		Atlas-SNP	.											.	CECR6	11	.	0			c.G1598T						PASS	.	C	VAL/GLY,VAL/GLY	2,4254		0,2,2126	9	9	9		533,1598	3.2	0.3	22		9	20,8360		0,20,4170	no	missense,missense	CECR6	NM_001163079.1,NM_031890.3	109,109	0,22,6296	AA,AC,CC		0.2387,0.047,0.1741	probably-damaging,probably-damaging	178/224,533/579	17600420	22,12614	2128	4190	6318	SO:0001583	missense	27439	exon1			CCGTAGCCCCCTC	AF307451	CCDS13740.1, CCDS54494.1	22q11.2	2008-06-12			ENSG00000183307	ENSG00000183307			1844	protein-coding gene	gene with protein product						11381032	Standard	NM_031890		Approved		uc002zmb.2	Q9BXQ6	OTTHUMG00000030471	ENST00000331437.3:c.1598G>T	22.37:g.17600420C>A	ENSP00000329318:p.Gly533Val	26	0	0		15	11	0.733333	NM_031890	A8MYY1	Missense_Mutation	SNP	ENST00000331437.3	37	CCDS13740.1	.	.	.	.	.	.	.	.	.	.	C	10.37	1.331834	0.24167	4.7E-4	0.002387	ENSG00000183307	ENST00000399875;ENST00000331437	.	.	.	4.26	3.22	0.36961	.	0.421699	0.17930	U	0.157200	T	0.33059	0.0850	N	0.19112	0.55	0.34394	D	0.6945	P	0.37207	0.587	B	0.37989	0.262	T	0.50189	-0.8857	9	0.59425	D	0.04	.	10.2222	0.43203	0.0:0.7984:0.2016:0.0	.	533	Q9BXQ6	CECR6_HUMAN	V	178;533	.	ENSP00000329318:G533V	G	-	2	0	CECR6	15980420	0.943000	0.32029	0.307000	0.25127	0.185000	0.23345	2.249000	0.43169	1.119000	0.41883	0.561000	0.74099	GGC	.	.	weak		0.706	CECR6-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000075359.4	NM_031890		A	17600420	C	A	17600420	3	1	23	1	0	0	0	0	1	0	0	0	3210	739	26	4	142	4	CECR6	22	17600420	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10		17600420	33704146	731	8175											
TUBA8	51807	hgsc.bcm.edu	37	chr22	18609703	18609703	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcctgctgcatgctctacCggggcgacgtggtgcccaag	5	8	15	13	3	1	0	0	0	1	0	1	1	1	0	3	4	5	3	3	4	2	1	rs140202346		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:18609703C>T	ENST00000330423.3	+	4	1031	c.958C>T	c.(958-960)Cgg>Tgg	p.R320W	TUBA8_ENST00000316027.6_Missense_Mutation_p.R254W	NM_018943.2	NP_061816.1	Q9NY65	TBA8_HUMAN	tubulin, alpha 8	320					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						CATGCTCTACCGGGGCGACGT	0.562													c|||	1	0.000199681	0.0	0.0	5008	,	,		20392	0.0		0.001	False		,,,				2504	0.0				p.R320W		Atlas-SNP	.											.	TUBA8	36	.	0			c.C958T						PASS	.	C	TRP/ARG,TRP/ARG	2,4404		0,2,2201	99	83	89		760,958	3.5	1	22	dbSNP_134	89	3,8597		0,3,4297	yes	missense,missense	TUBA8	NM_001193414.1,NM_018943.2	101,101	0,5,6498	TT,TC,CC		0.0349,0.0454,0.0384	probably-damaging,probably-damaging	254/384,320/450	18609703	5,13001	2203	4300	6503	SO:0001583	missense	51807	exon4			CTCTACCGGGGCG	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.958C>T	22.37:g.18609703C>T	ENSP00000333326:p.Arg320Trp	142	0	0		174	96	0.551724	NM_018943	B2RCX2|B3KPW9|B4DWG3|Q2M3N4	Missense_Mutation	SNP	ENST00000330423.3	37	CCDS13751.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	.	16.41	3.115564	0.56505	4.54E-4	3.49E-4	ENSG00000183785	ENST00000316027;ENST00000330423;ENST00000416740	D;D;D	0.84589	-1.87;-1.87;-1.87	5.67	3.48	0.39840	Tubulin/FtsZ, 2-layer sandwich domain (3);Tubulin/FtsZ, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.95853	0.8650	H	0.99815	4.805	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	0.95830	0.8857	10	0.87932	D	0	.	11.9598	0.53001	0.1374:0.7305:0.1321:0.0	.	254;344;320	B3KPW9;C9J2C0;Q9NY65	.;.;TBA8_HUMAN	W	254;320;344	ENSP00000318575:R254W;ENSP00000333326:R320W;ENSP00000412646:R344W	ENSP00000318575:R254W	R	+	1	2	TUBA8	16989703	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.755000	0.62198	0.782000	0.33613	0.655000	0.94253	CGG	C|0.999;T|0.001	0.001	strong		0.562	TUBA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316232.3	NM_018943		T	18609703	C	T	18609703	3	4	23	1	0	0	0	0	1	0	0	0	16765	643	23	1	972	1	TUBA8	22	18609703	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1009283	18609703	32694863	732	8176											
MED15	51586	hgsc.bcm.edu	37	chr22	20922809	20922809	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctctctttctccctcaaggTccgagctccgatggtggtgc	4	13	10	14	2	4	0	1	0	3	0	8	2	6	0	3	3	2	1	3	3	1	1			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:20922809T>C	ENST00000263205.7	+	8	1112	c.1043T>C	c.(1042-1044)gTc>gCc	p.V348A	MED15_ENST00000541476.1_Splice_Site_p.V322A|MED15_ENST00000382974.2_Splice_Site_p.V277A|MED15_ENST00000478831.1_3'UTR|MED15_ENST00000542773.1_Splice_Site_p.V153A|MED15_ENST00000292733.7_Splice_Site_p.V348A|MED15_ENST00000425759.2_Splice_Site_p.V237A|MED15_ENST00000406969.1_Splice_Site_p.V322A	NM_001003891.1	NP_001003891.1	Q96RN5	MED15_HUMAN	mediator complex subunit 15	348	Pro-rich.				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)			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)			TCCCTCAAGGTCCGAGCTCCG	0.582																																					p.V348A		Atlas-SNP	.											.	MED15	68	.	0			c.T1043C						PASS	.						29	29	29					22																	20922809		2199	4297	6496	SO:0001630	splice_region_variant	51586	exon8			TCAAGGTCCGAGC	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.1042-1T>C	22.37:g.20922809T>C		90	0	0		94	52	0.553191	NM_015889	D3DX31|D3DX32|O15413|Q6IC31|Q8NF16|Q96CT0|Q96IH7|Q9P1T3	Missense_Mutation	SNP	ENST00000263205.7	37	CCDS33602.1	.	.	.	.	.	.	.	.	.	.	T	13.54	2.268558	0.40095	.	.	ENSG00000099917	ENST00000425759;ENST00000292733;ENST00000542773;ENST00000263205;ENST00000406969;ENST00000382974;ENST00000541476;ENST00000542312	T	0.41400	1.0	5.4	5.4	0.78164	Mediator complex, subunit Med15, metazoa (1);	0.481828	0.21991	N	0.066154	T	0.47116	0.1428	L	0.36672	1.1	0.42239	D	0.991925	D;D;P;P;D	0.53885	0.963;0.963;0.954;0.954;0.963	D;D;D;D;D	0.71414	0.973;0.973;0.954;0.954;0.973	T	0.40251	-0.9573	10	0.02654	T	1	.	11.7332	0.51750	0.0:0.0:0.0:1.0	.	294;367;322;348;348	B4DGD6;Q6PKB8;G3V1P5;Q96RN5-2;Q96RN5	.;.;.;.;MED15_HUMAN	A	237;348;153;348;322;277;322;294	ENSP00000263205:V348A	ENSP00000263205:V348A	V	+	2	0	MED15	19252809	1.000000	0.71417	1.000000	0.80357	0.110000	0.19582	3.611000	0.54132	2.274000	0.75844	0.533000	0.62120	GTC	.	.	none		0.582	MED15-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320177.2	NM_015889	Missense_Mutation	C	20922809	T	C	20922809	5	2	23	1	0	0	0	0	0	0	1	0	9442	1681	58	3	1073	3	MED15	22	20922809	Splice_Site	SNP	T	TCGA-G8-6325-01A-11D-2210-10	2313106	20922809	30381757	733	8177											
SERPIND1	3053	hgsc.bcm.edu	37	chr22	21134023	21134023	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttcaacctctaccgagtgctGaaagaccaggtcaacacttt	12	10	7	12	1	3	2	2	1	1	1	3	3	3	2	3	1	4	1	3	1	4	3	rs35646566	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:21134023G>A	ENST00000215727.5	+	2	706	c.423G>A	c.(421-423)ctG>ctA	p.L141L	PI4KA_ENST00000572273.1_Intron|SERPIND1_ENST00000406799.1_Silent_p.L141L|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	141					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)	ACCGAGTGCTGAAAGACCAGG	0.493													G|||	52	0.0103834	0.0	0.013	5008	,	,		20876	0.0		0.0268	False		,,,				2504	0.0164				p.L141L		Atlas-SNP	.											.	SERPIND1	92	.	0			c.G423A						PASS	.	G	,	25,4381	31.7+/-61.6	0,25,2178	96	81	86		423,	-0.4	0.2	22	dbSNP_126	86	242,8358	96.6+/-158.3	5,232,4063	no	coding-synonymous,intron	SERPIND1,PI4KA	NM_000185.3,NM_058004.3	,	5,257,6241	AA,AG,GG		2.814,0.5674,2.0529	,	141/500,	21134023	267,12739	2203	4300	6503	SO:0001819	synonymous_variant	3053	exon2			AGTGCTGAAAGAC	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.423G>A	22.37:g.21134023G>A		168	0	0		185	92	0.497297	NM_000185	B2RAI1|D3DX34|Q6IBZ5	Silent	SNP	ENST00000215727.5	37	CCDS13783.1																																																																																			G|0.984;A|0.016	0.016	strong		0.493	SERPIND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319961.1	NM_000185		A	21134023	G	A	21134023	2	1	23	1	0	0	0	0	0	0	0	1	14125	1277	45	2		2	SERPIND1	22	21134023	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	211214	21134023	30170543	734	8178											
CRKL	1399	hgsc.bcm.edu	37	chr22	21272249	21272249	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccgccaggttcgactcctcGgaccgctccgcctggtatat	5	10	10	16	5	0	0	0	0	0	0	5	2	3	1	6	3	0	3	6	3	2	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:21272249G>A	ENST00000354336.3	+	1	536	c.27G>A	c.(25-27)tcG>tcA	p.S9S		NM_005207.3	NP_005198.1	P46109	CRKL_HUMAN	v-crk avian sarcoma virus CT10 oncogene homolog-like	9					activation of MAPKK activity (GO:0000186)|anterior/posterior pattern specification (GO:0009952)|blood vessel development (GO:0001568)|heart development (GO:0007507)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|parathyroid gland development (GO:0060017)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|thymus development (GO:0048538)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)	poly(A) RNA binding (GO:0044822)|SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)	14	all_cancers(11;1.16e-25)|all_epithelial(7;3.37e-24)|Lung NSC(8;7.25e-16)|all_lung(8;1.37e-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;0.000204)|Lung(15;0.00494)|Epithelial(17;0.176)			TCGACTCCTCGGACCGCTCCG	0.692																																					p.S9S	Pancreas(85;3 1441 23889 42519 42763)	Atlas-SNP	.											.	CRKL	28	.	0			c.G27A						PASS	.						27	27	27					22																	21272249		2202	4299	6501	SO:0001819	synonymous_variant	1399	exon1			CTCCTCGGACCGC		CCDS13785.1	22q11.21	2013-07-09	2013-07-09		ENSG00000099942	ENSG00000099942		"SH2 domain containing"	2363	protein-coding gene	gene with protein product		602007				8361759, 8798523	Standard	NM_005207		Approved		uc002ztf.2	P46109	OTTHUMG00000150807	ENST00000354336.3:c.27G>A	22.37:g.21272249G>A		44	0	0		42	22	0.52381	NM_005207	A8KA44|D3DX35	Silent	SNP	ENST00000354336.3	37	CCDS13785.1																																																																																			.	.	none		0.692	CRKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320158.1	NM_005207		A	21272249	G	A	21272249	2	1	23	1	0	0	0	0	0	0	0	1	3887	1103	39	1		1	CRKL	22	21272249	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	138226	21272249	30032317	735	8179											
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230309	23230311	+	In_Frame_Del	DEL	CTG	CTG	-																															gtcccaggcagcgctggcccCtgctgctgctgggtctggcc																								rs551962377	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CTG	CTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:23230309_23230311delCTG	ENST00000526893.1	+	1	350_352	c.76_78delCTG	c.(76-78)ctgdel	p.L29del	IGLL5_ENST00000532223.2_In_Frame_Del_p.L29del|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000531372.1_In_Frame_Del_p.L29del	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	29						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GCGCTGGCCCCTGCTGCTGCTGG	0.665																																					p.25_26del		Atlas-Indel	.											.	IGLL5	26	.	0			c.75_77del						PASS	.																																			SO:0001651	inframe_deletion	100423062	exon1			.	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.76_78delCTG	22.37:g.23230318_23230320delCTG	ENSP00000431254:p.Leu29del	151	0	0		146	19	0.130137	NM_001178126		In_Frame_Del	DEL	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.665	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		-	23230311	CTG	-	23230309	7	5	23	1	0	1	0	1	0	0	0	0	7603	680	24	0	78	0	IGLL5	22	23230309	In_Frame_Del	DEL	CTG	TCGA-G8-6325-01A-11D-2210-10	1958060	23230309	28074257	736	8180											
SGSM1	129049	hgsc.bcm.edu	37	chr22	25251027	25251027	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccccatccttgcatctttgTtgggtaagttgtcctgtgtg	4	16	11	10	0	1	0	0	0	1	0	3	0	3	0	4	1	1	4	4	1	1	5	rs201064977	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:25251027T>C	ENST00000400359.4	+	6	527	c.520T>C	c.(520-522)Ttg>Ctg	p.L174L	SGSM1_ENST00000400358.4_Silent_p.L174L	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	174	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						TGCATCTTTGTTGGGTAAGTT	0.532													T|||	4	0.000798722	0.0	0.0029	5008	,	,		19277	0.0		0.002	False		,,,				2504	0.0				p.L174L		Atlas-SNP	.											.	SGSM1	150	.	0			c.T520C						PASS	.	T	,,,	1,3963		0,1,1981	95	95	95		520,520,520,520	-0.5	0.9	22		95	41,8295		0,41,4127	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SGSM1	NM_001039948.2,NM_001098497.1,NM_001098498.1,NM_133454.2	,,,	0,42,6108	CC,CT,TT		0.4918,0.0252,0.3415	,,,	174/1149,174/1094,174/1033,174/1088	25251027	42,12258	1982	4168	6150	SO:0001819	synonymous_variant	129049	exon6			TCTTTGTTGGGTA	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.520T>C	22.37:g.25251027T>C		249	0	0		271	115	0.424354	NM_001098497	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Silent	SNP	ENST00000400359.4	37	CCDS46674.1																																																																																			T|0.998;C|0.002	0.002	strong		0.532	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	XM_059318		C	25251027	T	C	25251027	2	2	23	1	0	0	0	0	0	0	0	1	14237	1722	60	3		3	SGSM1	22	25251027	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	2020718	25251027	26053539	737	8181											
MYO18B	84700	hgsc.bcm.edu	37	chr22	26164408	26164408	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aagactcatccccatgacgcCcccccttgcaagacctctcc	9	7	5	20	1	2	3	1	1	1	2	4	3	3	3	7	0	1	1	7	0	2	1	rs575271363		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:26164408C>G	ENST00000407587.2	+	4	694	c.525C>G	c.(523-525)gcC>gcG	p.A175A	MYO18B_ENST00000335473.7_Silent_p.A175A|MYO18B_ENST00000536101.1_Silent_p.A175A			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	175						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						CCCATGACGCCCCCCCTTGCA	0.597													c|||	1	0.000199681	0.0	0.0	5008	,	,		13166	0.0		0.0	False		,,,				2504	0.001				p.A175A		Atlas-SNP	.											.	MYO18B	322	.	0			c.C525G						PASS	.						21	25	24					22																	26164408		1966	4142	6108	SO:0001819	synonymous_variant	84700	exon4			TGACGCCCCCCCT	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.525C>G	22.37:g.26164408C>G		85	0	0		83	38	0.457831	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37																																																																																				.	.	none		0.597	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		G	26164408	C	G	26164408	2	3	23	1	0	0	0	0	0	0	0	1	10075	610	22	4		4	MYO18B	22	26164408	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	913381	26164408	25140158	738	8182											
HPS4	89781	hgsc.bcm.edu	37	chr22	26864577	26864577	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gtgagggagggcgggagttgGgtgctgacaatcctaggagg	8	7	21	5	1	0	2	0	2	0	0	1	5	1	5	1	6	1	2	1	6	2	2			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:26864577G>C	ENST00000398145.2	-	8	1225	c.609C>G	c.(607-609)acC>acG	p.T203T	HPS4_ENST00000336873.5_Silent_p.T203T|HPS4_ENST00000402105.3_Silent_p.T198T|HPS4_ENST00000398141.1_Silent_p.T198T	NM_022081.5	NP_071364.4	Q9NQG7	HPS4_HUMAN	Hermansky-Pudlak syndrome 4	203					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						GCGGGAGTTGGGTGCTGACAA	0.532									Hermansky-Pudlak syndrome																												p.T203T		Atlas-SNP	.											.	HPS4	123	.	0			c.C609G						PASS	.						96	77	83					22																	26864577		2203	4300	6503	SO:0001819	synonymous_variant	89781	exon8	Familial Cancer Database	HPS, HPS1-8	GAGTTGGGTGCTG		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.609C>G	22.37:g.26864577G>C		142	0	0		174	88	0.505747	NM_022081	B1AHQ4|Q5H8V6|Q96LX6|Q9BY93|Q9UH37|Q9UH38	Silent	SNP	ENST00000398145.2	37	CCDS13835.1																																																																																			.	.	none		0.532	HPS4-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320778.1	NM_022081		C	26864577	G	C	26864577	2	2	23	1	0	0	0	0	0	0	0	1	7350	1219	43	4		4	HPS4	22	26864577	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	700169	26864577	24439989	739	8183											
TPST2	8459	hgsc.bcm.edu	37	chr22	26937198	26937198	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggcctgcatggcggcgtcCagcacctcatccgtcacccc	7	6	10	18	3	2	0	2	0	0	0	4	0	4	0	6	3	2	2	6	3	1	0	rs140525210	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:26937198C>G	ENST00000338754.4	-	3	669	c.399G>C	c.(397-399)ctG>ctC	p.L133L	TPST2_ENST00000403880.1_Silent_p.L133L|TPST2_ENST00000398110.2_Silent_p.L133L	NM_003595.3	NP_003586.3	O60704	TPST2_HUMAN	tyrosylprotein sulfotransferase 2	133					fusion of sperm to egg plasma membrane (GO:0007342)|peptidyl-tyrosine sulfation (GO:0006478)|prevention of polyspermy (GO:0060468)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein-tyrosine sulfotransferase activity (GO:0008476)			central_nervous_system(1)|large_intestine(1)|lung(5)	7						TGGCGGCGTCCAGCACCTCAT	0.662													C|||	32	0.00638978	0.0	0.0029	5008	,	,		14224	0.0		0.0189	False		,,,				2504	0.0112				p.L133L		Atlas-SNP	.											.	TPST2	23	.	0			c.G399C						PASS	.	C	,	20,4386	25.3+/-52.1	0,20,2183	43	34	37		399,399	3.2	1	22	dbSNP_134	37	182,8416	80.6+/-143.3	1,180,4118	no	coding-synonymous,coding-synonymous	TPST2	NM_001008566.1,NM_003595.3	,	1,200,6301	GG,GC,CC		2.1168,0.4539,1.5534	,	133/378,133/378	26937198	202,12802	2203	4299	6502	SO:0001819	synonymous_variant	8459	exon3			GGCGTCCAGCACC	AF049891	CCDS13839.1	22q12.1	2012-12-13			ENSG00000128294	ENSG00000128294	2.8.2.20	"Sulfotransferases, membrane-bound"	12021	protein-coding gene	gene with protein product	"transport and golgi organization 13 homolog B (Drosophila)"	603126				9736702, 9733778	Standard	NM_003595		Approved	TANGO13B	uc003acx.3	O60704	OTTHUMG00000150987	ENST00000338754.4:c.399G>C	22.37:g.26937198C>G		38	0	0		49	23	0.469388	NM_001008566	B3KQA7|Q6FI98|Q9H0V4	Silent	SNP	ENST00000338754.4	37	CCDS13839.1																																																																																			C|0.985;G|0.015	0.015	strong		0.662	TPST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320820.3	NM_003595		G	26937198	C	G	26937198	2	3	23	1	0	0	0	0	0	0	0	1	16443	581	21	4		4	TPST2	22	26937198	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	72621	26937198	24367368	740	8184											
NEFH	4744	hgsc.bcm.edu	37	chr22	29886354	29886354	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aagtccccaccccagagaagGaggctcctgccaaggtggag	11	4	13	13	0	0	1	0	0	0	1	2	4	2	3	6	4	1	1	6	4	3	0			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:29886354G>A	ENST00000310624.6	+	4	2758	c.2725G>A	c.(2725-2727)Gag>Aag	p.E909K		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	915	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						CCCAGAGAAGGAGGCTCCTGC	0.502																																					p.E909K		Atlas-SNP	.											.	NEFH	178	.	0			c.G2725A						PASS	.						57	62	60					22																	29886354		2203	4300	6503	SO:0001583	missense	4744	exon4			GAGAAGGAGGCTC		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.2725G>A	22.37:g.29886354G>A	ENSP00000311997:p.Glu909Lys	114	0	0		145	77	0.531034	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	37	CCDS13858.1	.	.	.	.	.	.	.	.	.	.	G	10.76	1.442446	0.25987	.	.	ENSG00000100285	ENST00000328842;ENST00000310624	D	0.84223	-1.82	5.48	4.4	0.53042	.	0.270105	0.26719	N	0.022846	T	0.79633	0.4479	L	0.59436	1.845	0.41319	D	0.98716	P	0.38020	0.615	B	0.33121	0.158	T	0.79137	-0.1927	10	0.40728	T	0.16	.	10.1869	0.43002	0.0756:0.1391:0.7853:0.0	.	915	P12036	NFH_HUMAN	K	860;909	ENSP00000311997:E909K	ENSP00000311997:E909K	E	+	1	0	NEFH	28216354	1.000000	0.71417	1.000000	0.80357	0.305000	0.27757	3.431000	0.52814	2.739000	0.93911	0.655000	0.94253	GAG	.	.	none		0.502	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		A	29886354	G	A	29886354	3	1	23	1	0	0	0	0	1	0	0	0	10323	1175	41	2	2739	2	NEFH	22	29886354	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	2949156	29886354	21418212	741	8185											
MTMR3	8897	hgsc.bcm.edu	37	chr22	30415983	30415983	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcagtgttctcctcagttctCtccaggtcccccccagggga	5	11	9	16	0	4	0	2	0	2	0	8	1	6	1	5	3	0	2	5	3	0	2	rs61737780	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:30415983C>T	ENST00000401950.2	+	17	2677	c.2335C>T	c.(2335-2337)Ctc>Ttc	p.L779F	MTMR3_ENST00000323630.5_Missense_Mutation_p.L643F|MTMR3_ENST00000406629.1_Missense_Mutation_p.L779F|CTA-85E5.10_ENST00000429350.1_RNA|MTMR3_ENST00000351488.3_Missense_Mutation_p.L779F|CTA-85E5.10_ENST00000453743.2_RNA|MTMR3_ENST00000333027.3_Missense_Mutation_p.L779F	NM_021090.3	NP_066576.1	Q13615	MTMR3_HUMAN	myotubularin related protein 3	779					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)			CCTCAGTTCTCTCCAGGTCCC	0.552													C|||	17	0.00339457	0.0	0.0043	5008	,	,		18968	0.0		0.0139	False		,,,				2504	0.0				p.L779F		Atlas-SNP	.											.	MTMR3	106	.	0			c.C2335T						PASS	.	C	PHE/LEU,PHE/LEU,PHE/LEU	7,4399	12.9+/-30.5	0,7,2196	73	77	76		2335,2335,2335	3.7	0.9	22	dbSNP_129	76	99,8501	55.2+/-116.2	0,99,4201	yes	missense,missense,missense	MTMR3	NM_021090.3,NM_153050.2,NM_153051.2	22,22,22	0,106,6397	TT,TC,CC		1.1512,0.1589,0.815	possibly-damaging,possibly-damaging,possibly-damaging	779/1199,779/1171,779/1162	30415983	106,12900	2203	4300	6503	SO:0001583	missense	8897	exon17			AGTTCTCTCCAGG	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.2335C>T	22.37:g.30415983C>T	ENSP00000384651:p.Leu779Phe	148	0	0		161	70	0.434783	NM_021090	A5PL26|A7MD32|Q9NYN5|Q9NYN6|Q9UDX6|Q9UEG3	Missense_Mutation	SNP	ENST00000401950.2	37	CCDS13870.1	12	0.005494505494505495	0	0.0	3	0.008287292817679558	0	0.0	9	0.011873350923482849	C	2.316	-0.356778	0.05138	0.001589	0.011512	ENSG00000100330	ENST00000401950;ENST00000333027;ENST00000323630;ENST00000351488;ENST00000406629	D;D;D;D;D	0.93763	-3.08;-3.05;-3.28;-3.1;-3.05	4.73	3.66	0.41972	.	1.991870	0.01826	N	0.034355	D	0.84826	0.5558	N	0.19112	0.55	0.09310	N	1	P;B;P	0.37636	0.603;0.257;0.603	B;B;B	0.36186	0.219;0.109;0.219	T	0.76208	-0.3043	10	0.10111	T	0.7	.	12.5279	0.56098	0.3353:0.6647:0.0:0.0	rs61737780	779;779;779	Q13615-3;Q13615;Q13615-2	.;MTMR3_HUMAN;.	F	779;779;643;779;779	ENSP00000384651:L779F;ENSP00000331649:L779F;ENSP00000318070:L643F;ENSP00000307271:L779F;ENSP00000384077:L779F	ENSP00000318070:L643F	L	+	1	0	MTMR3	28745983	0.000000	0.05858	0.924000	0.36721	0.812000	0.45895	-0.164000	0.09983	2.448000	0.82819	0.462000	0.41574	CTC	C|0.992;T|0.008	0.008	strong		0.552	MTMR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322066.1	NM_021090		T	30415983	C	T	30415983	3	4	23	1	0	0	0	0	1	0	0	0	9954	913	32	2	2393	2	MTMR3	22	30415983	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	529629	30415983	20888583	742	8186											
HORMAD2	150280	hgsc.bcm.edu	37	chr22	30489945	30489945	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cctgatacattcctacaatgGccactgctcagctttctcac	9	12	5	15	0	2	1	2	1	1	0	4	1	3	1	3	1	4	2	3	1	3	4	rs34150968	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:30489945G>A	ENST00000336726.6	+	2	359	c.4G>A	c.(4-6)Gcc>Acc	p.A2T	HORMAD2_ENST00000403975.1_Missense_Mutation_p.A2T	NM_152510.2	NP_689723.1	Q8N7B1	HORM2_HUMAN	HORMA domain containing 2	2			A -> T (in dbSNP:rs34150968).		meiotic nuclear division (GO:0007126)|meiotic sister chromatid cohesion (GO:0051177)	chromosome (GO:0005694)|nucleus (GO:0005634)				large_intestine(1)|lung(1)	2			Epithelial(10;0.125)			TCCTACAATGGCCACTGCTCA	0.328													G|||	16	0.00319489	0.0	0.0043	5008	,	,		15203	0.0		0.0129	False		,,,				2504	0.0				p.A2T		Atlas-SNP	.											.	HORMAD2	12	.	0			c.G4A						PASS	.	G	THR/ALA	7,3711		0,7,1852	74	66	69		4	1.6	1	22	dbSNP_126	69	94,8134		0,94,4020	yes	missense	HORMAD2	NM_152510.2	58	0,101,5872	AA,AG,GG		1.1424,0.1883,0.8455	possibly-damaging	2/308	30489945	101,11845	1859	4114	5973	SO:0001583	missense	150280	exon2			ACAATGGCCACTG	AK098703	CCDS46683.1	22q12.2	2014-01-21			ENSG00000176635	ENSG00000176635			28383	protein-coding gene	gene with protein product						12477932	Standard	NM_152510		Approved	MGC26710, CT46.2	uc003agy.3	Q8N7B1	OTTHUMG00000150881	ENST00000336726.6:c.4G>A	22.37:g.30489945G>A	ENSP00000336984:p.Ala2Thr	243	1	0.00411523		249	110	0.441767	NM_152510	B5MEB2|Q8NHR2	Missense_Mutation	SNP	ENST00000336726.6	37	CCDS46683.1	12	0.005494505494505495	0	0.0	3	0.008287292817679558	0	0.0	9	0.011873350923482849	G	11.81	1.748595	0.30955	0.001883	0.011424	ENSG00000176635	ENST00000336726;ENST00000403975	T;T	0.35973	1.28;1.28	5.02	1.62	0.23740	.	0.497968	0.20580	N	0.089551	T	0.25827	0.0629	M	0.74881	2.28	0.31316	N	0.686633	B	0.23540	0.087	B	0.17433	0.018	T	0.28933	-1.0028	10	0.56958	D	0.05	-7.1149	5.765	0.18221	0.0917:0.0:0.577:0.3313	rs34150968	2	Q8N7B1	HORM2_HUMAN	T	2	ENSP00000336984:A2T;ENSP00000385055:A2T	ENSP00000336984:A2T	A	+	1	0	HORMAD2	28819945	1.000000	0.71417	1.000000	0.80357	0.379000	0.30106	1.781000	0.38644	0.340000	0.23745	0.491000	0.48974	GCC	G|0.993;A|0.007	0.007	strong		0.328	HORMAD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320416.2	NM_152510		A	30489945	G	A	30489945	3	1	23	1	0	0	0	0	1	0	0	0	7296	1203	42	2	6	2	HORMAD2	22	30489945	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	73962	30489945	20814621	743	8187											
SLC35E4	339665	hgsc.bcm.edu	37	chr22	31042606	31042606	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgccctgctgcaggaggagaGgctggacgcggtgaccctgc	6	6	17	12	2	0	2	0	1	0	1	0	5	0	4	2	5	4	3	2	5	0	0	rs148304964	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:31042606G>A	ENST00000343605.4	+	2	1440	c.641G>A	c.(640-642)aGg>aAg	p.R214K	SLC35E4_ENST00000406566.1_Intron|SLC35E4_ENST00000300385.8_Intron	NM_001001479.2	NP_001001479.1	Q6ICL7	S35E4_HUMAN	solute carrier family 35, member E4	214	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						CAGGAGGAGAGGCTGGACGCG	0.672													G|||	7	0.00139776	0.0	0.0029	5008	,	,		15892	0.0		0.005	False		,,,				2504	0.0				p.R214K		Atlas-SNP	.											.	SLC35E4	22	.	0			c.G641A						PASS	.	C	LYS/ARG	4,4374		0,4,2185	47	44	45		641	0.6	0.9	22	dbSNP_134	45	44,8528		0,44,4242	yes	missense	SLC35E4	NM_001001479.2	26	0,48,6427	AA,AG,GG		0.5133,0.0914,0.3707	benign	214/351	31042606	48,12902	2189	4286	6475	SO:0001583	missense	339665	exon2			AGGAGAGGCTGGA		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.641G>A	22.37:g.31042606G>A	ENSP00000339626:p.Arg214Lys	60	0	0		40	15	0.375	NM_001001479	Q567P0	Missense_Mutation	SNP	ENST00000343605.4	37	CCDS13882.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	g	0.181	-1.061767	0.01950	9.14E-4	0.005133	ENSG00000100036	ENST00000343605	T	0.60672	0.17	5.02	0.588	0.17445	Domain of unknown function DUF250 (1);	0.168007	0.51477	D	0.000083	T	0.15089	0.0364	N	0.02357	-0.585	0.80722	D	1	B	0.10296	0.003	B	0.10450	0.005	T	0.26121	-1.0112	10	0.02654	T	1	-15.9629	4.9658	0.14089	0.3219:0.148:0.53:0.0	.	214	Q6ICL7	S35E4_HUMAN	K	214	ENSP00000339626:R214K	ENSP00000339626:R214K	R	+	2	0	SLC35E4	29372606	0.994000	0.37717	0.915000	0.36163	0.067000	0.16453	0.739000	0.26173	0.267000	0.21916	-0.217000	0.12591	AGG	G|0.997;A|0.003	0.003	strong		0.672	SLC35E4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321382.1	XM_290973		A	31042606	G	A	31042606	3	1	23	1	0	0	0	0	1	0	0	0	14602	1000	35	2	647	2	SLC35E4	22	31042606	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	552661	31042606	20261960	744	8188											
APOL3	80833	hgsc.bcm.edu	37	chr22	36537871	36537871	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggacatgatgccagaggcagCgccagtggagctggacacca	11	4	15	11	1	0	2	0	1	0	1	0	5	0	5	3	4	3	2	3	4	0	0	rs140252051	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:36537871C>T	ENST00000349314.2	-	3	623	c.586G>A	c.(586-588)Gct>Act	p.A196T	APOL3_ENST00000487423.1_5'UTR|APOL3_ENST00000361710.2_5'UTR|APOL3_ENST00000397293.2_Missense_Mutation_p.A125T|APOL3_ENST00000397287.2_5'UTR|APOL3_ENST00000424878.2_5'UTR	NM_145640.2	NP_663615.1	O95236	APOL3_HUMAN	apolipoprotein L, 3	196					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						CCAGAGGCAGCGCCAGTGGAG	0.562													C|||	5	0.000998403	0.0015	0.0014	5008	,	,		21116	0.0		0.002	False		,,,				2504	0.0				p.A196T		Atlas-SNP	.											APOL3_ENST00000349314,caecum,carcinoma,0,4	APOL3	60	4	0			c.G586A						PASS	.	C	THR/ALA,,	8,4398	14.3+/-33.2	0,8,2195	93	85	88		586,,	-0.3	0	22	dbSNP_134	88	44,8556	29.0+/-79.6	0,44,4256	yes	missense,utr-5,utr-5	APOL3	NM_145640.2,NM_145641.2,NM_145642.2	58,,	0,52,6451	TT,TC,CC		0.5116,0.1816,0.3998	benign,,	196/403,,	36537871	52,12954	2203	4300	6503	SO:0001583	missense	80833	exon3			AGGCAGCGCCAGT	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.586G>A	22.37:g.36537871C>T	ENSP00000344577:p.Ala196Thr	119	0	0		121	64	0.528926	NM_145640	B1AHI4|B1AHI5|Q5U5N4|Q9BQ82|Q9BQA3	Missense_Mutation	SNP	ENST00000349314.2	37	CCDS13922.1	5	0.0022893772893772895	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	9.409	1.080032	0.20309	0.001816	0.005116	ENSG00000128284	ENST00000397293;ENST00000349314	T;T	0.04156	3.69;3.69	4.3	-0.295	0.12828	.	0.919146	0.09404	N	0.806779	T	0.01558	0.0050	N	0.02708	-0.52	0.09310	N	0.999997	D;D	0.57571	0.98;0.975	P;B	0.44897	0.463;0.236	T	0.46275	-0.9203	10	0.16420	T	0.52	.	7.5658	0.27879	0.0:0.5334:0.0:0.4666	.	196;125	O95236;O95236-2	APOL3_HUMAN;.	T	125;196	ENSP00000380461:A125T;ENSP00000344577:A196T	ENSP00000344577:A196T	A	-	1	0	APOL3	34867817	0.000000	0.05858	0.000000	0.03702	0.050000	0.14768	-2.685000	0.00834	-0.030000	0.13804	-0.556000	0.04195	GCT	C|0.997;T|0.003	0.003	strong		0.562	APOL3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319268.1	NM_145641		T	36537871	C	T	36537871	3	4	23	1	0	0	0	0	1	0	0	0	807	768	27	1	626	1	APOL3	22	36537871	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	5495265	36537871	14766695	745	8189											
TST	7263	hgsc.bcm.edu	37	chr22	37414321	37414321	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccagtgtggctttgaagacGgccggttctgggcgtgaggg	5	10	18	8	3	1	3	0	2	1	1	2	3	2	3	2	5	0	2	2	5	1	2	rs61743068		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:37414321G>A	ENST00000403892.3	-	1	1187	c.453C>T	c.(451-453)gcC>gcT	p.A151A	MPST_ENST00000397129.1_5'Flank|MPST_ENST00000404393.1_5'Flank|MPST_ENST00000401419.3_5'Flank|MPST_ENST00000429360.2_5'Flank|MPST_ENST00000341116.3_5'Flank|MPST_ENST00000404802.3_5'Flank|TST_ENST00000249042.3_Silent_p.A151A	NM_001270483.1	NP_001257412.1	Q16762	THTR_HUMAN	thiosulfate sulfurtransferase (rhodanese)	151	Hinge.				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						CTTTGAAGACGGCCGGTTCTG	0.592																																					p.A151A		Atlas-SNP	.											.	TST	22	.	0			c.C453T						PASS	.						76	67	70					22																	37414321		2202	4300	6502	SO:0001819	synonymous_variant	7263	exon2			GAAGACGGCCGGT	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.453C>T	22.37:g.37414321G>A		187	0	0		167	37	0.221557	NM_003312	B3KRM1|Q6IB06	Silent	SNP	ENST00000403892.3	37	CCDS13938.1																																																																																			G|0.985;T|0.015	.	alt		0.592	TST-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318790.1			A	37414321	G	A	37414321	2	1	23	1	0	0	0	0	0	0	0	1	16688	1103	39	1		1	TST	22	37414321	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	876450	37414321	13890245	746	8190											
SH3BP1	23616	hgsc.bcm.edu	37	chr22	38051493	38051493	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cctgcccggcgccaaagccgGcgttcaccagcctcccccag	6	4	10	21	4	1	0	1	0	0	0	2	0	2	0	8	2	3	1	8	2	1	1	rs117382629	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:38051493G>T	ENST00000357436.4	+	18	2221	c.1908G>T	c.(1906-1908)cgG>cgT	p.R636R	Z83844.1_ENST00000456099.1_RNA|SH3BP1_ENST00000599616.1_Intron	NM_018957.3	NP_061830.3	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	636					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)					GCCAAAGCCGGCGTTCACCAG	0.711													G|||	40	0.00798722	0.0015	0.0101	5008	,	,		4118	0.0		0.0268	False		,,,				2504	0.0041				p.R636R		Atlas-SNP	.											.	SH3BP1	41	.	0			c.G1908T						PASS	.	G		23,3653		0,23,1815	3	4	4		1908	-1.4	0.5	22	dbSNP_132	4	149,7211		0,149,3531	no	coding-synonymous	SH3BP1	NM_018957.3		0,172,5346	TT,TG,GG		2.0245,0.6257,1.5585		636/702	38051493	172,10864	1838	3680	5518	SO:0001819	synonymous_variant	23616	exon18			AAGCCGGCGTTCA		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.1908G>T	22.37:g.38051493G>T		58	0	0		58	33	0.568965	NM_018957	Q5R3N0|Q6IBZ2|Q6ZVL9|Q96HQ5|Q9NSQ9	Silent	SNP	ENST00000357436.4	37	CCDS13952.2																																																																																			G|0.987;T|0.013	0.013	strong		0.711	SH3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075884.4	NM_018957		T	38051493	G	T	38051493	2	4	23	1	0	0	0	0	0	0	0	1	14259	1190	42	4		4	SH3BP1	22	38051493	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	637172	38051493	13253073	747	8191											
GALR3	8484	hgsc.bcm.edu	37	chr22	38219570	38219570	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gcccgagtgcctggcaggagCctggcagcaccacggacctg	7	4	15	15	2	0	0	0	0	0	0	0	3	0	2	5	4	3	3	5	4	0	0	rs78650836	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:38219570C>G	ENST00000249041.2	+	1	182	c.157C>G	c.(157-159)Cct>Gct	p.P53A		NM_003614.1	NP_003605.1	O60755	GALR3_HUMAN	galanin receptor 3	53					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|feeding behavior (GO:0007631)|learning or memory (GO:0007611)|negative regulation of adenylate cyclase activity (GO:0007194)|neuropeptide signaling pathway (GO:0007218)|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)			endometrium(1)|liver(2)|lung(1)	4	Melanoma(58;0.045)					CTGGCAGGAGCCTGGCAGCAC	0.632													C|||	5	0.000998403	0.0008	0.0029	5008	,	,		11722	0.0		0.001	False		,,,				2504	0.001				p.P53A		Atlas-SNP	.											.	GALR3	12	.	0			c.C157G						PASS	.	C	ALA/PRO	5,4401	9.9+/-24.2	0,5,2198	72	53	59		157	4.2	1	22	dbSNP_131	59	52,8548	33.3+/-86.6	0,52,4248	yes	missense	GALR3	NM_003614.1	27	0,57,6446	GG,GC,CC		0.6047,0.1135,0.4383	possibly-damaging	53/369	38219570	57,12949	2203	4300	6503	SO:0001583	missense	8484	exon1			CAGGAGCCTGGCA	AF073799	CCDS13958.1	22q113.1	2012-08-08			ENSG00000128310	ENSG00000128310		"GPCR / Class A : Galanin receptors"	4134	protein-coding gene	gene with protein product		603692				9722565, 9832121	Standard	NM_003614		Approved		uc003aub.1	O60755	OTTHUMG00000150658	ENST00000249041.2:c.157C>G	22.37:g.38219570C>G	ENSP00000249041:p.Pro53Ala	162	0	0		154	73	0.474026	NM_003614	Q53YJ4	Missense_Mutation	SNP	ENST00000249041.2	37	CCDS13958.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	11.45	1.643789	0.29246	0.001135	0.006047	ENSG00000128310	ENST00000249041	T	0.36878	1.23	5.25	4.24	0.50183	GPCR, rhodopsin-like superfamily (1);	0.253805	0.39274	N	0.001413	T	0.12860	0.0312	N	0.20610	0.595	0.25697	N	0.985627	B	0.25206	0.12	B	0.18871	0.023	T	0.12993	-1.0526	10	0.12766	T	0.61	.	6.6972	0.23205	0.2991:0.6141:0.0:0.0869	.	53	O60755	GALR3_HUMAN	A	53	ENSP00000249041:P53A	ENSP00000249041:P53A	P	+	1	0	GALR3	36549516	0.992000	0.36948	1.000000	0.80357	0.921000	0.55340	2.077000	0.41557	2.885000	0.99019	0.655000	0.94253	CCT	C|0.996;G|0.004	0.004	strong		0.632	GALR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319452.1			G	38219570	C	G	38219570	3	3	23	1	0	0	0	0	1	0	0	0	6237	739	26	4	159	4	GALR3	22	38219570	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	168077	38219570	13084996	748	8192											
SLC16A8	23539	hgsc.bcm.edu	37	chr22	38477275	38477275	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccatcaggaacttggtgacgGcgtacacggcgaaggcgcgg	9	5	16	11	6	1	1	1	1	0	0	1	3	1	2	1	6	2	1	1	6	3	2	rs75640043	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:38477275G>A	ENST00000320521.5	-	4	878	c.770C>T	c.(769-771)gCc>gTc	p.A257V	SLC16A8_ENST00000469516.1_Intron	NM_013356.2	NP_037488.2	O95907	MOT3_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 8	257					blood coagulation (GO:0007596)|cellular metabolic process (GO:0044237)|lactate transmembrane transport (GO:0035873)|lactate transport (GO:0015727)|leukocyte migration (GO:0050900)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lactate transmembrane transporter activity (GO:0015129)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			kidney(1)|large_intestine(1)|prostate(1)	3	Melanoma(58;0.045)				Pyruvic acid(DB00119)	CTTGGTGACGGCGTACACGGC	0.721													G|||	140	0.0279553	0.0053	0.0533	5008	,	,		11403	0.003		0.0785	False		,,,				2504	0.0143				p.A257V		Atlas-SNP	.											SLC16A8,NS,carcinoma,0,1	SLC16A8	13	1	0			c.C770T						PASS	.	G	VAL/ALA	70,4292		2,66,2113	18	17	17		770	-0.7	0.9	22	dbSNP_131	17	783,7775		28,727,3524	yes	missense	SLC16A8	NM_013356.2	64	30,793,5637	AA,AG,GG		9.1493,1.6048,6.6022	benign	257/505	38477275	853,12067	2181	4279	6460	SO:0001583	missense	23539	exon4			GTGACGGCGTACA	AF132610	CCDS13966.1	22q12.3-q13.2	2013-07-18	2013-07-18		ENSG00000100156	ENSG00000100156		"Solute carriers"	16270	protein-coding gene	gene with protein product	"monocarboxylate transporter 3"	610409	"solute carrier 16 (monocarboxylic acid transporters), member 8"			10493836	Standard	NM_013356		Approved	MCT3, REMP	uc003auu.3	O95907	OTTHUMG00000151196	ENST00000320521.5:c.770C>T	22.37:g.38477275G>A	ENSP00000321735:p.Ala257Val	46	0	0		38	28	0.736842	NM_013356	Q9UBE2	Missense_Mutation	SNP	ENST00000320521.5	37	CCDS13966.1	82	0.037545787545787544	5	0.01016260162601626	13	0.03591160220994475	2	0.0034965034965034965	62	0.08179419525065963	G	13.23	2.173754	0.38413	0.016048	0.091493	ENSG00000100156	ENST00000320521	T	0.55930	0.49	3.34	-0.715	0.11215	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.106640	0.06977	N	0.819091	T	0.01870	0.0059	L	0.41124	1.26	0.22975	N	0.998482	B	0.19583	0.037	B	0.24974	0.057	T	0.10428	-1.0630	10	0.20046	T	0.44	.	7.5375	0.27719	0.4057:0.0:0.5943:0.0	.	257	O95907	MOT3_HUMAN	V	257	ENSP00000321735:A257V	ENSP00000321735:A257V	A	-	2	0	SLC16A8	36807221	0.995000	0.38212	0.948000	0.38648	0.931000	0.56810	2.753000	0.47524	-0.042000	0.13535	0.313000	0.20887	GCC	G|0.951;A|0.049	0.049	strong		0.721	SLC16A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321724.1	NM_013356		A	38477275	G	A	38477275	3	1	23	1	0	0	0	0	1	0	0	0	14429	1203	42	2	752	2	SLC16A8	22	38477275	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	257705	38477275	12827291	749	8193											
CENPM	79019	hgsc.bcm.edu	37	chr22	42342462	42342462	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctctttgagcatcgagtcCgccagctgctgcagaagagc	8	9	11	13	2	1	3	0	1	1	2	4	4	3	3	3	0	5	4	3	0	1	1	rs34730141	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:42342462C>T	ENST00000215980.5	-	2	183	c.96G>A	c.(94-96)gcG>gcA	p.A32A	CENPM_ENST00000404067.1_5'UTR|CENPM_ENST00000407253.3_Silent_p.A32A|CENPM_ENST00000402420.1_5'UTR|CENPM_ENST00000402338.1_5'UTR	NM_024053.3	NP_076958.1	Q9NSP4	CENPM_HUMAN	centromere protein M	32					mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)				kidney(1)|large_intestine(1)|prostate(1)	3						GCATCGAGTCCGCCAGCTGCT	0.657											OREG0026600	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	73	0.0145767	0.0514	0.0072	5008	,	,		17483	0.0		0.0	False		,,,				2504	0.0				p.A32A		Atlas-SNP	.											.	CENPM	8	.	0			c.G96A						PASS	.	C	,	203,4203	121.7+/-159.2	7,189,2007	35	31	32		96,96	-1.8	1	22	dbSNP_126	32	2,8596	4.3+/-15.6	0,2,4297	no	coding-synonymous,coding-synonymous	CENPM	NM_001002876.1,NM_024053.3	,	7,191,6304	TT,TC,CC		0.0233,4.6074,1.5764	,	32/108,32/181	42342462	205,12799	2203	4299	6502	SO:0001819	synonymous_variant	79019	exon2			CGAGTCCGCCAGC	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.96G>A	22.37:g.42342462C>T		230	0	0	908	288	152	0.527778	NM_024053	A7LM22|B1AHQ9|Q6I9W3	Silent	SNP	ENST00000215980.5	37	CCDS14025.1																																																																																			C|0.983;T|0.017	0.017	strong		0.657	CENPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322058.1	NM_024053		T	42342462	C	T	42342462	2	4	23	1	0	0	0	0	0	0	0	1	3239	639	23	1		1	CENPM	22	42342462	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	3865187	42342462	8962104	750	8194											
CYB5R3	1727	hgsc.bcm.edu	37	chr22	43032811	43032811	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggaacagcttcatgagcagActgtacaggaaccagactgg	13	7	12	9	0	1	3	1	1	0	2	1	5	1	5	1	3	5	3	1	3	3	2	rs370253340		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:43032811A>T	ENST00000352397.5	-	2	315	c.63T>A	c.(61-63)agT>agA	p.S21R	CYB5R3_ENST00000407332.1_5'UTR|CYB5R3_ENST00000402438.1_5'UTR|CYB5R3_ENST00000407623.3_5'UTR|CYB5R3_ENST00000361740.4_Missense_Mutation_p.S54R|CYB5R3_ENST00000396303.3_5'UTR	NM_000398.6	NP_000389.1	P00387	NB5R3_HUMAN	cytochrome b5 reductase 3	21					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)	TCATGAGCAGACTGTACAGGA	0.622																																					p.S54R		Atlas-SNP	.											.	CYB5R3	31	.	0			c.T162A						PASS	.	A	,,,ARG/SER,ARG/SER	0,4406		0,0,2203	78	67	71		,,,162,63	0.2	0.9	22		71	1,8599	1.2+/-3.3	0,1,4299	no	utr-5,utr-5,utr-5,missense,missense	CYB5R3	NM_001129819.2,NM_001171661.1,NM_007326.4,NM_001171660.1,NM_000398.6	,,,110,110	0,1,6502	TT,TA,AA		0.0116,0.0,0.0077	,,,benign,benign	,,,54/335,21/302	43032811	1,13005	2203	4300	6503	SO:0001583	missense	1727	exon2			GAGCAGACTGTAC	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.63T>A	22.37:g.43032811A>T	ENSP00000338461:p.Ser21Arg	51	0	0		49	14	0.285714	NM_001171660	B1AHF2|B7Z7L3|O75675|Q8TDL8|Q8WTS8|Q9UEN4|Q9UEN5|Q9UL55|Q9UL56	Missense_Mutation	SNP	ENST00000352397.5	37	CCDS33658.1	.	.	.	.	.	.	.	.	.	.	A	12.25	1.881744	0.33255	0.0	1.16E-4	ENSG00000100243	ENST00000361740;ENST00000352397	D;D	0.87256	-2.23;-2.2	4.82	0.217	0.15264	.	0.474289	0.25037	N	0.033621	T	0.75982	0.3924	L	0.44542	1.39	0.80722	D	1	P;B	0.37864	0.61;0.007	B;B	0.29942	0.109;0.025	T	0.65191	-0.6228	10	0.25751	T	0.34	-14.0956	8.2667	0.31819	0.3607:0.0:0.6393:0.0	.	54;21	B7Z7L3;P00387	.;NB5R3_HUMAN	R	54;21	ENSP00000354468:S54R;ENSP00000338461:S21R	ENSP00000338461:S21R	S	-	3	2	CYB5R3	41362755	0.801000	0.28930	0.938000	0.37757	0.799000	0.45148	0.491000	0.22419	-0.057000	0.13199	0.260000	0.18958	AGT	.	.	weak		0.622	CYB5R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320439.1			T	43032811	A	T	43032811	3	4	23	1	0	0	0	0	1	0	0	0	4130	272	10	5	874	5	CYB5R3	22	43032811	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	690349	43032811	8271755	751	8195											
TTLL1	25809	hgsc.bcm.edu	37	chr22	43447891	43447891	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcttgtcattgttcatcacCggctggagagagagtgacca	9	11	12	9	1	3	3	3	1	0	2	3	5	3	3	2	2	1	3	2	2	0	3	rs9607998	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:43447891C>T	ENST00000266254.7	-	9	1134	c.894G>A	c.(892-894)ccG>ccA	p.P298P	TTLL1_ENST00000331018.7_Intron|AL022476.2_ENST00000443063.1_RNA	NM_012263.4	NP_036395.1	O95922	TTLL1_HUMAN	tubulin tyrosine ligase-like family, member 1	298	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)		TGTTCATCACCGGCTGGAGAG	0.577													C|||	78	0.0155751	0.0068	0.0216	5008	,	,		21914	0.0		0.0497	False		,,,				2504	0.0041				p.P298P		Atlas-SNP	.											TTLL1,NS,carcinoma,-2,1	TTLL1	41	1	0			c.G894A						PASS	.	C		46,4360	48.2+/-83.0	3,40,2160	263	185	212		894	-3.7	1	22	dbSNP_119	212	419,8181	130.0+/-188.0	10,399,3891	no	coding-synonymous	TTLL1	NM_012263.4		13,439,6051	TT,TC,CC		4.8721,1.044,3.5753		298/424	43447891	465,12541	2203	4300	6503	SO:0001819	synonymous_variant	25809	exon9			CATCACCGGCTGG	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.894G>A	22.37:g.43447891C>T		101	0	0		123	82	0.666667	NM_012263	B2RDS7|Q9BR27|Q9NRS9|Q9UMU0	Silent	SNP	ENST00000266254.7	37	CCDS14043.1	52	0.023809523809523808	6	0.012195121951219513	10	0.027624309392265192	0	0.0	36	0.047493403693931395	C	9.531	1.110796	0.20714	0.01044	0.048721	ENSG00000100271	ENST00000495814	.	.	.	5.97	-3.65	0.04502	.	.	.	.	.	T	0.07503	0.0189	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29941	-0.9995	4	.	.	.	.	0.9386	0.01351	0.3008:0.1773:0.3147:0.2072	rs9607998;rs52827145;rs9607998	.	.	.	Q	224	.	.	R	-	2	0	TTLL1	41777835	0.001000	0.12720	0.987000	0.45799	0.774000	0.43823	-1.617000	0.02051	-0.307000	0.08804	-0.126000	0.14955	CGG	C|0.971;T|0.029	0.029	strong		0.577	TTLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319659.1	NM_012263		T	43447891	C	T	43447891	2	4	23	1	0	0	0	0	0	0	0	1	16737	639	23	1		1	TTLL1	22	43447891	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	415080	43447891	7856675	752	8196											
PRR5	55615	hgsc.bcm.edu	37	chr22	45132853	45132853	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctcagggcttctccgaccCgcccggccagggccccaccg	4	4	12	21	4	2	0	1	0	1	0	3	1	2	0	8	3	0	1	8	3	0	1	rs187629442	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:45132853C>T	ENST00000336985.6	+	8	1170	c.893C>T	c.(892-894)cCg>cTg	p.P298L	ARHGAP8_ENST00000389773.5_Intron|PRR5-ARHGAP8_ENST00000361473.5_Intron|PRR5_ENST00000403581.1_Missense_Mutation_p.P321L|PRR5_ENST00000006251.7_Missense_Mutation_p.P289L|PRR5-ARHGAP8_ENST00000352766.7_Intron|PRR5_ENST00000477331.1_3'UTR|ARHGAP8_ENST00000517296.3_Intron	NM_181333.3	NP_851850.1	P85299	PRR5_HUMAN	proline rich 5 (renal)	298					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)		TTCTCCGACCCGCCCGGCCAG	0.741													C|||	19	0.00379393	0.0008	0.0086	5008	,	,		12627	0.0		0.0099	False		,,,				2504	0.002				p.P321L		Atlas-SNP	.											.	PRR5	75	.	0			c.C962T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,	7,4311		0,7,2152	10	12	11		866,608,608,962,866,893,	0.9	0	22		11	91,8381		0,91,4145	yes	missense,missense,missense,missense,missense,missense,intron	PRR5,PRR5-ARHGAP8	NM_001017528.2,NM_001017529.2,NM_001017530.1,NM_001198721.1,NM_015366.3,NM_181333.3,NM_181334.4	98,98,98,98,98,98,	0,98,6297	TT,TC,CC		1.0741,0.1621,0.7662	,,,,,,	289/380,203/294,203/294,321/412,289/380,298/389,	45132853	98,12692	2159	4236	6395	SO:0001583	missense	55615	exon10			CCGACCCGCCCGG	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.893C>T	22.37:g.45132853C>T	ENSP00000337464:p.Pro298Leu	17	0	0		9	6	0.666667	NM_001198721	B1AHF6|B1AHG5|B3KP73|O75983|O95695|Q5BIW2|Q5EAJ8|Q5EAJ9|Q5XKJ6|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Missense_Mutation	SNP	ENST00000336985.6	37	CCDS14058.1	9|9	0.004120879120879121|0.004120879120879121	0|0	0.0|0.0	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	5|5	0.006596306068601583|0.006596306068601583	C|C	4.489|4.489	0.090760|0.090760	0.08632|0.08632	0.001621|0.001621	0.010741|0.010741	ENSG00000186654|ENSG00000186654	ENST00000006251;ENST00000404016;ENST00000403581;ENST00000336985|ENST00000455389	T;T;T|.	0.27557|.	1.68;1.66;1.68|.	4.27|4.27	0.846|0.846	0.18955|0.18955	.|.	.|.	.|.	.|.	.|.	T|T	0.03095|0.03095	0.0091|0.0091	N|N	0.00368|0.00368	-1.59|-1.59	0.09310|0.09310	N|N	1|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|T	0.38045|0.38045	-0.9679|-0.9679	8|5	.|.	.|.	.|.	.|.	1.0823|1.0823	0.01645|0.01645	0.1926:0.4208:0.128:0.2586|0.1926:0.4208:0.128:0.2586	.|.	262;321;197;298;298|.	B1AHF5;B1AHF6;P85299-2;P85299;A8K699|.	.;.;.;PRR5_HUMAN;.|.	L|C	289;262;321;298|258	ENSP00000006251:P289L;ENSP00000384848:P321L;ENSP00000337464:P298L|.	.|.	P|R	+|+	2|1	0|0	PRR5|PRR5	43511517|43511517	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.040000|0.040000	0.13550|0.13550	0.061000|0.061000	0.14366|0.14366	0.270000|0.270000	0.21984|0.21984	-0.680000|-0.680000	0.03767|0.03767	CCG|CGC	C|0.996;T|0.004	0.004	strong		0.741	PRR5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318200.2	NM_001017528		T	45132853	C	T	45132853	3	4	23	1	0	0	0	0	1	0	0	0	12612	652	23	1	923	1	PRR5	22	45132853	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	1684962	45132853	6171713	753	8197											
ARHGAP8	23779	hgsc.bcm.edu	37	chr22	45255688	45255688	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcacaactacgtcgtcctcCgctacctcatgggcttcctg	7	10	8	16	3	1	0	1	0	0	0	5	0	4	0	4	1	4	3	4	1	3	3	rs73176189	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:45255688C>T	ENST00000389774.2	+	12	1189	c.1048C>T	c.(1048-1050)Cgc>Tgc	p.R350C	ARHGAP8_ENST00000389773.5_Missense_Mutation_p.R441C|PRR5-ARHGAP8_ENST00000361473.5_Missense_Mutation_p.R450C|ARHGAP8_ENST00000336963.4_Intron|PRR5-ARHGAP8_ENST00000352766.7_Missense_Mutation_p.R529C|ARHGAP8_ENST00000517296.3_Missense_Mutation_p.R529C|ARHGAP8_ENST00000356099.6_Missense_Mutation_p.R319C	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	350	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				positive regulation of ERK1 and ERK2 cascade (GO:0070374)|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)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(9)|prostate(1)|skin(7)	29		all_neural(38;0.00409)|Ovarian(80;0.00976)|Glioma(61;0.0649)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0204)		CGTCGTCCTCCGCTACCTCAT	0.652													c|||	16	0.00319489	0.0008	0.0014	5008	,	,		19710	0.001		0.0099	False		,,,				2504	0.0031				p.R441C		Atlas-SNP	.											PRR5-ARHGAP8,caecum,carcinoma,0,2	PRR5-ARHGAP8	53	2	0			c.C1321T						PASS	.	T	CYS/ARG,,CYS/ARG,CYS/ARG	5,4401	9.9+/-24.2	0,5,2198	80	67	71		1048,,1321,955	-5.2	0.5	22	dbSNP_130	71	18,8582	11.9+/-42.8	0,18,4282	yes	missense,intron,missense,missense	ARHGAP8,PRR5-ARHGAP8	NM_001017526.1,NM_001198726.1,NM_181334.4,NM_181335.2	180,,180,180	0,23,6480	TT,TC,CC		0.2093,0.1135,0.1768	benign,,benign,benign	350/465,,441/556,319/434	45255688	23,12983	2203	4300	6503	SO:0001583	missense	553158	exon14			GTCCTCCGCTACC	AF177331	CCDS14060.2, CCDS33664.1, CCDS56233.1	22q13.3	2010-05-11			ENSG00000241484	ENSG00000241484		"Rho GTPase activating proteins"	677	protein-coding gene	gene with protein product		609405				10591208	Standard	NM_001198726		Approved	FLJ20185, BPGAP1		P85298	OTTHUMG00000030234	ENST00000389774.2:c.1048C>T	22.37:g.45255688C>T	ENSP00000374424:p.Arg350Cys	85	0	0		78	43	0.551282	NM_181334	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Missense_Mutation	SNP	ENST00000389774.2	37	CCDS33664.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	c	5.988	0.366197	0.11352	0.001135	0.002093	ENSG00000248405;ENSG00000248405;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484	ENST00000361473;ENST00000352766;ENST00000517296;ENST00000389773;ENST00000389774;ENST00000356099	T;T;T;T;T;T	0.21361	2.01;2.01;2.01;2.01;2.01;2.01	4.14	-5.19	0.02832	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	1.659120	0.04129	N	0.317650	T	0.13200	0.0320	L	0.28014	0.82	0.29807	N	0.831972	B;D;B;D;P	0.76494	0.03;0.999;0.033;0.989;0.56	B;P;B;B;B	0.50617	0.008;0.646;0.013;0.337;0.032	T	0.27088	-1.0084	10	0.52906	T	0.07	.	5.1071	0.14790	0.4424:0.3917:0.0766:0.0893	.	372;355;350;529;450	B7ZMA4;A2RU51;P85298;B1AHC4;B1AHC3	.;.;RHG08_HUMAN;.;.	C	450;529;529;441;350;319	ENSP00000354732:R450C;ENSP00000262731:R529C;ENSP00000429240:R529C;ENSP00000374423:R441C;ENSP00000374424:R350C;ENSP00000348407:R319C	ENSP00000348407:R319C	R	+	1	0	PRR5-ARHGAP8;ARHGAP8	43634352	0.427000	0.25514	0.455000	0.27031	0.005000	0.04900	0.560000	0.23500	-1.150000	0.02840	-1.499000	0.00960	CGC	C|0.998;T|0.002	0.002	strong		0.652	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701		T	45255688	C	T	45255688	3	4	23	1	0	0	0	0	1	0	0	0	888	652	23	1	1090	1	ARHGAP8	22	45255688	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	122835	45255688	6048878	754	8198											
PIM3	415116	hgsc.bcm.edu	37	chr22	50354773	50354773	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ccgcccgcgcctccctgcagCcaaggcggacaaggagagct	8	3	13	17	4	0	1	0	0	0	1	1	3	1	2	5	3	3	2	5	3	2	0			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50354773C>T	ENST00000360612.4	+	2	521	c.86C>T	c.(85-87)gCc>gTc	p.A29V		NM_001001852.3	NP_001001852.2	Q86V86	PIM3_HUMAN	Pim-3 proto-oncogene, serine/threonine kinase	29					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|histone phosphorylation (GO:0016572)|negative regulation of apoptotic process (GO:0043066)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)						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;0.196)|LUAD - Lung adenocarcinoma(64;0.247)		CTCCCTGCAGCCAAGGCGGAC	0.786																																					p.A29V		Atlas-SNP	.											.	PIM3	15	.	0			c.C86T						PASS	.						5	5	5					22																	50354773		1996	4027	6023	SO:0001630	splice_region_variant	415116	exon2			CTGCAGCCAAGGC	BC052239	CCDS33678.1	22q13	2014-06-25	2014-06-25		ENSG00000198355	ENSG00000198355			19310	protein-coding gene	gene with protein product		610580	"pim-3 oncogene"			12477932	Standard	NM_001001852		Approved		uc003bjb.3	Q86V86	OTTHUMG00000150290	ENST00000360612.4:c.86-1C>T	22.37:g.50354773C>T		24	0	0		16	7	0.4375	NM_001001852	A5D8X8|A8K7J0|B1B0P0|Q68BM2	Missense_Mutation	SNP	ENST00000360612.4	37	CCDS33678.1	.	.	.	.	.	.	.	.	.	.	c	7.065	0.567090	0.13560	.	.	ENSG00000198355	ENST00000360612	T	0.56611	0.45	2.28	-0.308	0.12773	Protein kinase-like domain (1);	0.177323	0.37393	U	0.002107	T	0.19485	0.0468	N	0.02802	-0.49	0.36106	D	0.844454	B	0.06786	0.001	B	0.09377	0.004	T	0.03910	-1.0993	10	0.21540	T	0.41	.	3.0393	0.06133	0.0:0.3221:0.2312:0.4467	.	29	Q86V86	PIM3_HUMAN	V	29	ENSP00000353824:A29V	ENSP00000353824:A29V	A	+	2	0	PIM3	48740777	1.000000	0.71417	0.559000	0.28332	0.795000	0.44927	1.317000	0.33631	-0.287000	0.09064	0.291000	0.19559	GCC	.	.	none		0.786	PIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317406.1	NM_001001852	Missense_Mutation	T	50354773	C	T	50354773	5	4	23	1	0	0	0	0	0	0	1	0	11938	753	26	2	92	2	PIM3	22	50354773	Splice_Site	SNP	C	TCGA-G8-6325-01A-11D-2210-10	5099085	50354773	949793	755	8199											
TUBGCP6	85378	hgsc.bcm.edu	37	chr22	50660064	50660064	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accatgccagtctgcacggaCggctcagcccctgggcccac	7	5	11	18	2	2	0	1	0	1	0	2	1	2	1	5	3	3	2	5	3	0	0	rs140491142	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50660064C>T	ENST00000248846.5	-	16	2828	c.2724G>A	c.(2722-2724)ccG>ccA	p.P908P	TUBGCP6_ENST00000439308.2_Silent_p.P908P|TUBGCP6_ENST00000491449.1_5'UTR			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	908					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)		TCTGCACGGACGGCTCAGCCC	0.677																																					p.P908P		Atlas-SNP	.											TUBGCP6,NS,carcinoma,0,1	TUBGCP6	132	1	0			c.G2724A						scavenged	.	C		0,4406		0,0,2203	42	38	39		2724	-2.5	0	22	dbSNP_134	39	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	TUBGCP6	NM_020461.3		0,6,6497	TT,TC,CC		0.0698,0.0,0.0461		908/1820	50660064	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	85378	exon16			CACGGACGGCTCA	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.2724G>A	22.37:g.50660064C>T		226	1	0.00442478		220	89	0.404545	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Silent	SNP	ENST00000248846.5	37	CCDS14087.1																																																																																			C|0.999;T|0.001	0.001	strong		0.677	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461		T	50660064	C	T	50660064	2	4	23	1	0	0	0	0	0	0	0	1	16785	523	19	1		1	TUBGCP6	22	50660064	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	305291	50660064	644502	756	8200											
MAPK11	5600	hgsc.bcm.edu	37	chr22	50704028	50704028	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacccagggggttggctccaCggaagatgctgctcaggtcc	7	7	14	13	1	1	1	1	0	0	1	3	2	3	2	3	5	2	4	3	5	1	1	rs33932986	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50704028C>T	ENST00000330651.6	-	10	924	c.824G>A	c.(823-825)cGt>cAt	p.R275H	MAPK11_ENST00000495277.1_5'Flank	NM_002751.5	NP_002742.3	Q15759	MK11_HUMAN	mitogen-activated protein kinase 11	275	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> H (in dbSNP:rs33932986). {ECO:0000269|PubMed:17344846, ECO:0000269|Ref.9}.		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)	GTTGGCTCCACGGAAGATGCT	0.642													C|||	83	0.0165735	0.0151	0.0331	5008	,	,		16651	0.0		0.0219	False		,,,				2504	0.0184				p.R275H	GBM(9;634 739 50668)	Atlas-SNP	.											.	MAPK11	23	.	0			c.G824A						PASS	.	C	HIS/ARG	44,4362	45.3+/-79.5	0,44,2159	46	46	46		824	-5	0.1	22	dbSNP_126	46	167,8433	75.4+/-138.0	0,167,4133	yes	missense	MAPK11	NM_002751.5	29	0,211,6292	TT,TC,CC		1.9419,0.9986,1.6223	benign	275/365	50704028	211,12795	2203	4300	6503	SO:0001583	missense	5600	exon10			GCTCCACGGAAGA	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.824G>A	22.37:g.50704028C>T	ENSP00000333685:p.Arg275His	74	0	0		102	29	0.284314	NM_002751	A8K730|B0LPG1|B7Z630|E7ETQ1|L7RT27|O00284|O15472|Q2XNF2	Missense_Mutation	SNP	ENST00000330651.6	37	CCDS14090.1	37	0.01694139194139194	7	0.014227642276422764	16	0.04419889502762431	0	0.0	14	0.018469656992084433	C	11.81	1.750982	0.31046	0.009986	0.019419	ENSG00000185386	ENST00000330651	T	0.14022	2.54	4.29	-4.97	0.03029	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.391142	0.24262	N	0.040077	T	0.01765	0.0056	L	0.28504	0.86	0.36446	D	0.865812	B	0.09022	0.002	B	0.11329	0.006	T	0.13361	-1.0512	10	0.33141	T	0.24	.	14.0629	0.64810	0.0:0.8033:0.0:0.1967	rs33932986	275	Q15759	MK11_HUMAN	H	275	ENSP00000333685:R275H	ENSP00000333685:R275H	R	-	2	0	MAPK11	49046155	0.000000	0.05858	0.122000	0.21767	0.970000	0.65996	-1.513000	0.02256	-0.973000	0.03555	-0.458000	0.05436	CGT	C|0.985;T|0.015	0.015	strong		0.642	MAPK11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316900.1			T	50704028	C	T	50704028	3	4	23	1	0	0	0	0	1	0	0	0	9282	536	19	1	282	1	MAPK11	22	50704028	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	43964	50704028	600538	757	8201											
FAM116B	414918	hgsc.bcm.edu	37	chr22	50753263	50753263	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accatctccgaggacacgtcGggcgagggtgccaggactag	9	5	15	12	4	1	0	0	0	1	0	3	4	1	2	3	4	1	0	3	4	1	1	rs113856947	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50753263G>A	ENST00000413817.3	-	10	917	c.846C>T	c.(844-846)ccC>ccT	p.P282P	XX-C283C717.1_ENST00000453835.1_RNA	NM_001001794.3	NP_001001794.3	Q8NEG7	DEN6B_HUMAN	DENN/MADD domain containing 6B	282					positive regulation of Rab GTPase activity (GO:0032851)	endosome (GO:0005768)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)										AGGACACGTCGGGCGAGGGTG	0.682													G|||	23	0.00459265	0.0008	0.0072	5008	,	,		17171	0.0		0.0089	False		,,,				2504	0.0082				p.P282P		Atlas-SNP	.											.	.	.	.	0			c.C846T						PASS	.	G		11,4179		0,11,2084	26	35	32		846	-7.3	0.3	22	dbSNP_132	32	70,8310		0,70,4120	no	coding-synonymous	FAM116B	NM_001001794.3		0,81,6204	AA,AG,GG		0.8353,0.2625,0.6444		282/586	50753263	81,12489	2095	4190	6285	SO:0001819	synonymous_variant	414918	exon10			CACGTCGGGCGAG	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.846C>T	22.37:g.50753263G>A		227	0	0		186	76	0.408602	NM_001001794	A6X8I5	Silent	SNP	ENST00000413817.3	37	CCDS46732.1	12	0.005494505494505495	0	0.0	5	0.013812154696132596	0	0.0	7	0.009234828496042216	G	11.25	1.583626	0.28268	0.002625	0.008353	ENSG00000205593	ENST00000433760	.	.	.	5.01	-7.27	0.01461	.	0.000000	0.85682	D	0.000000	T	0.34106	0.0886	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49214	-0.8963	6	0.87932	D	0	-21.3129	0.6044	0.00750	0.3433:0.203:0.2759:0.1779	.	.	.	.	L	303	.	ENSP00000414072:P303L	P	-	2	0	FAM116B	49095835	0.000000	0.05858	0.317000	0.25265	0.735000	0.41995	-3.056000	0.00625	-0.646000	0.05452	0.305000	0.20034	CCG	G|0.994;A|0.006	0.006	strong		0.682	DENND6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316845.3	NM_001001794		A	50753263	G	A	50753263	2	1	23	1	0	0	0	0	0	0	0	1	5413	1103	39	1		1	FAM116B	22	50753263	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	49235	50753263	551303	758	8202											
ARSF	416	hgsc.bcm.edu	37	chrX	2990197	2990197	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtattggagatctgggctgcTacggcaatgacaccatgagg	10	9	14	8	1	1	3	0	2	1	1	1	4	1	3	1	4	2	4	1	4	3	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2990197T>C	ENST00000381127.1	+	3	363	c.142T>C	c.(142-144)Tac>Cac	p.Y48H	ARSF_ENST00000359361.2_Missense_Mutation_p.Y48H|ARSF_ENST00000537104.1_Missense_Mutation_p.Y48H	NM_001201538.1|NM_001201539.1	NP_001188467.1|NP_001188468.1	P54793	ARSF_HUMAN	arylsulfatase F	48					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)				TCTGGGCTGCTACGGCAATGA	0.517																																					p.Y48H		Atlas-SNP	.											.	ARSF	97	.	0			c.T142C						PASS	.						207	172	184					X																	2990197		2203	4300	6503	SO:0001583	missense	416	exon3			GGCTGCTACGGCA	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.142T>C	X.37:g.2990197T>C	ENSP00000370519:p.Tyr48His	174	0	0		83	4	0.0481928	NM_004042	Q8TCC5	Missense_Mutation	SNP	ENST00000381127.1	37	CCDS14123.1	.	.	.	.	.	.	.	.	.	.	t	12.11	1.838448	0.32513	.	.	ENSG00000062096	ENST00000381127;ENST00000537104;ENST00000359361	D;D;D	0.95069	-3.6;-3.6;-3.6	2.46	2.46	0.29980	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.155495	0.44285	U	0.000472	D	0.96185	0.8756	M	0.89785	3.06	0.44862	D	0.997877	P	0.40000	0.698	P	0.50490	0.642	D	0.95657	0.8712	10	0.72032	D	0.01	.	9.9827	0.41824	0.0:0.0:0.0:1.0	.	48	P54793	ARSF_HUMAN	H	48	ENSP00000370519:Y48H;ENSP00000445594:Y48H;ENSP00000352319:Y48H	ENSP00000352319:Y48H	Y	+	1	0	ARSF	3000197	1.000000	0.71417	0.023000	0.16930	0.074000	0.17049	5.704000	0.68347	0.805000	0.34159	0.339000	0.21740	TAC	.	.	none		0.517	ARSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055652.1			C	2990197	T	C	2990197	3	2	23	1	0	0	0	0	1	0	0	0	991	1522	53	3	148	3	ARSF	23	2990197	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10		2990197	152280363	759	8203											
RPGR	6103	hgsc.bcm.edu	37	chrX	38145632	38145646	+	Intron	DEL	CTTCCTCCCCTTCTT	CTTCCTCCCCTTCTT	-																															ctcttccccctccccttctcCttcctccccttcttcctccc																								rs201131185|rs200824587		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CTTCCTCCCCTTCTT	CTTCCTCCCCTTCTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:38145632_38145646delCTTCCTCCCCTTCTT	ENST00000339363.3	-	14	2688				RPGR_ENST00000318842.7_Intron|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000338898.3_Intron|RPGR_ENST00000378505.2_In_Frame_Del_p.EEGEE869del|RPGR_ENST00000342811.3_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						tccccttctccttcctccccttcttcctccccttc	0.6																																					p.869_874del		Atlas-Indel	.											.	RPGR	175	.	0			c.2607_2621del	GRCh37	CD033265|CD064604|CI013682|CM074396	orf15	D|I|M		PASS	.		,	43,2971		2,33,6,1315,308					,	-0.2	0			10	195,4756		24,97,50,1779,1101	no	coding,intron	RPGR	NM_001034853.1,NM_000328.2	,	26,130,56,3094,1409	A1A1,A1R,A1,RR,R		3.9386,1.4267,2.9881	,	,		238,7727				SO:0001627	intron_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.2520+700AAGAAGGGGAGGAAG>-	X.37:g.38145632_38145646delCTTCCTCCCCTTCTT		44	0	0		27	20	0.740741	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	In_Frame_Del	DEL	ENST00000339363.3	37																																																																																				CTTCCTCCCCTTCTT|0.987;-|0.013	0.013	strong		0.6	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328		-	38145646	CTTCCTCCCCTTCTT	-	38145632	6	5	23	0	1	1	0	1	0	0	0	0	13563	690	24	0		0	RPGR	23	38145632	Intron	DEL	CTTCCTCCCCTTCTT	TCGA-G8-6325-01A-11D-2210-10	35155435	38145632	117124928	760	8204											
CCNB3	85417	hgsc.bcm.edu	37	chrX	50085217	50085217	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccaggtgtcctttgagatgaCccatgagaccctgtacttgg	8	11	11	11	0	0	3	0	3	0	2	1	5	1	3	4	2	1	1	4	2	1	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:50085217C>T	ENST00000376042.1	+	9	3831	c.3533C>T	c.(3532-3534)aCc>aTc	p.T1178I	CCNB3_ENST00000276014.7_Missense_Mutation_p.T1178I|CCNB3_ENST00000348603.2_Missense_Mutation_p.T74I|CCNB3_ENST00000376038.1_Missense_Mutation_p.T74I			Q8WWL7	CCNB3_HUMAN	cyclin B3	1178					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)					TTTGAGATGACCCATGAGACC	0.493																																					p.T1178I		Atlas-SNP	.											.	CCNB3	367	.	0			c.C3533T						PASS	.						221	179	194					X																	50085217		2203	4300	6503	SO:0001583	missense	85417	exon8			AGATGACCCATGA	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.3533C>T	X.37:g.50085217C>T	ENSP00000365210:p.Thr1178Ile	166	0	0		87	26	0.298851	NM_033031	B1AQI5|B1AQI6|Q96SB5|Q96SB6|Q96SB7|Q9NT38	Missense_Mutation	SNP	ENST00000376042.1	37	CCDS14331.1	.	.	.	.	.	.	.	.	.	.	C	4.077	0.012091	0.07912	.	.	ENSG00000147082	ENST00000376042;ENST00000376038;ENST00000348603;ENST00000276014	T;T;T;T	0.12465	2.68;2.75;2.75;2.68	5.11	-1.37	0.09056	Cyclin, N-terminal (1);Cyclin-like (3);	0.889284	0.09724	N	0.764028	T	0.14614	0.0353	L	0.41710	1.295	0.23820	N	0.996759	P;B;P	0.37688	0.605;0.411;0.605	P;B;B	0.45946	0.498;0.176;0.37	T	0.37502	-0.9703	9	.	.	.	.	7.004	0.24826	0.328:0.4757:0.1963:0.0	.	1178;74;1178	A8K8T9;Q8WWL7-2;Q8WWL7	.;.;CCNB3_HUMAN	I	1178;74;74;1178	ENSP00000365210:T1178I;ENSP00000365206:T74I;ENSP00000338682:T74I;ENSP00000276014:T1178I	.	T	+	2	0	CCNB3	50101957	0.933000	0.31639	0.312000	0.25196	0.443000	0.32047	-0.013000	0.12678	-0.093000	0.12396	-0.568000	0.04159	ACC	.	.	none		0.493	CCNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056558.1			T	50085217	C	T	50085217	3	4	23	1	0	0	0	0	1	0	0	0	2916	507	18	2	3559	2	CCNB3	23	50085217	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	11939585	50085217	105185343	761	8205											
HUWE1	10075	hgsc.bcm.edu	37	chrX	53654402	53654402	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctctccttcttgtgtagtaTtgggtctctggatctttggc	3	18	10	10	0	4	0	0	0	4	0	6	1	4	1	2	3	0	2	2	3	2	6	rs41307640	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:53654402T>C	ENST00000342160.3	-	16	1905	c.1448A>G	c.(1447-1449)aAt>aGt	p.N483S	HUWE1_ENST00000218328.8_Missense_Mutation_p.N483S|HUWE1_ENST00000262854.6_Missense_Mutation_p.N483S			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	483			N -> S (in dbSNP:rs41307640).		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						TTGTGTAGTATTGGGTCTCTG	0.368													t|||	34	0.00900662	0.003	0.0173	3775	,	,		10299	0.0		0.0179	False		,,,				2504	0.0				p.N483S		Atlas-SNP	.											.	HUWE1	724	.	0			c.A1448G						PASS	.		SER/ASN	15,3820		0,12,3,1620,568	191	160	171		1448	3.1	1	X	dbSNP_127	171	185,6543		4,127,50,2297,1822	yes	missense	HUWE1	NM_031407.4	46	4,139,53,3917,2390	CC,CT,C,TT,T		2.7497,0.3911,1.8934	benign	483/4375	53654402	200,10363	2203	4300	6503	SO:0001583	missense	10075	exon17			GTAGTATTGGGTC	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.1448A>G	X.37:g.53654402T>C	ENSP00000340648:p.Asn483Ser	252	0	0		136	136	1	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	37	CCDS35301.1	22	0.013261000602772756	2	0.0040650406504065045	4	0.0111731843575419	0	0.0	11	0.014627659574468085	t	0.090	-1.169288	0.01660	0.003911	0.027497	ENSG00000086758	ENST00000342160;ENST00000262854;ENST00000218328;ENST00000396323	T;T;T	0.42900	0.96;0.96;0.96	4.89	3.09	0.35607	E3 ubiquitin ligase, domain of unknown function DUF913 (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.291697	0.30979	N	0.008486	T	0.04724	0.0128	N	0.02960	-0.455	0.21697	N	0.999585	B	0.06786	0.001	B	0.06405	0.002	T	0.29579	-1.0007	10	0.02654	T	1	.	7.9684	0.30113	0.0:0.4667:0.4405:0.0928	rs41307640;rs61752441	483	Q7Z6Z7	HUWE1_HUMAN	S	483;483;483;109	ENSP00000340648:N483S;ENSP00000262854:N483S;ENSP00000218328:N483S	ENSP00000218328:N483S	N	-	2	0	HUWE1	53671127	1.000000	0.71417	0.999000	0.59377	0.739000	0.42172	0.945000	0.29056	0.327000	0.23409	-1.244000	0.01528	AAT	T|0.984;C|0.016	0.016	strong		0.368	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119		C	53654402	T	C	53654402	3	2	23	1	0	0	0	0	1	0	0	0	7470	1493	52	3	11948	3	HUWE1	23	53654402	Missense_Mutation	SNP	T	TCGA-G8-6325-01A-11D-2210-10	3569185	53654402	101616158	762	8206											
MED12	9968	hgsc.bcm.edu	37	chrX	70354254	70354254	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgcagcacccagcagaccacGgagtgggccatgctcctcct	8	5	11	17	2	0	1	0	0	0	1	2	2	2	2	5	2	3	4	5	2	0	0	rs375001801		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:70354254G>A	ENST00000374080.3	+	34	4697	c.4665G>A	c.(4663-4665)acG>acA	p.T1555T	MED12_ENST00000374102.1_Silent_p.T1555T|MED12_ENST00000333646.6_Silent_p.T1555T			Q93074	MED12_HUMAN	mediator complex subunit 12	1555					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)	p.T1555T(2)		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)					AGCAGACCACGGAGTGGGCCA	0.592			"M, S"		uterine leiomyoma		Opitz-Kaveggia Syndrome																														p.T1555T		Atlas-SNP	.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12	984	.	2	Substitution - coding silent(2)	endometrium(2)	c.G4665A						PASS	.			0,3706		0,0,1571,564	40	38	39		4665	-8.9	0.5	X		39	1,6607		0,1,2401,1804	no	coding-synonymous	MED12	NM_005120.2		0,1,3972,2368	AA,AG,GG,G		0.0151,0.0,0.0097		1555/2178	70354254	1,10313	2135	4206	6341	SO:0001819	synonymous_variant	9968	exon34			GACCACGGAGTGG	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.4665G>A	X.37:g.70354254G>A		166	0	0		92	92	1	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Silent	SNP	ENST00000374080.3	37	CCDS43970.1																																																																																			.	.	weak		0.592	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120		A	70354254	G	A	70354254	2	1	23	1	0	0	0	0	0	0	0	1	9437	1103	39	1		1	MED12	23	70354254	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	16699852	70354254	84916306	763	8207											
TEX13A	56157	hgsc.bcm.edu	37	chrX	104464360	104464360	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctcttcttcctcctcagctGctccttctgtgcaaacccct	4	14	4	19	0	4	0	1	0	3	0	7	0	7	0	6	0	4	3	6	0	1	3			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:104464360G>A	ENST00000413579.1	-	3	629	c.518C>T	c.(517-519)gCa>gTa	p.A173V	TEX13A_ENST00000372575.1_Missense_Mutation_p.A173V|TEX13A_ENST00000372578.3_Missense_Mutation_p.A173V|IL1RAPL2_ENST00000344799.4_Intron|IL1RAPL2_ENST00000372582.1_Intron			Q9BXU3	TX13A_HUMAN	testis expressed 13A	173							zinc ion binding (GO:0008270)			large_intestine(5)|ovary(2)|upper_aerodigestive_tract(1)	8						CTCCTCAGCTGCTCCTTCTGT	0.642																																					p.A173V		Atlas-SNP	.											.	TEX13A	55	.	0			c.C518T						PASS	.						28	33	32					X																	104464360		2123	4174	6297	SO:0001583	missense	56157	exon3			TCAGCTGCTCCTT	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.518C>T	X.37:g.104464360G>A	ENSP00000399753:p.Ala173Val	60	0	0		38	8	0.210526	NM_031274	B1B1G8|Q32NB6	Missense_Mutation	SNP	ENST00000413579.1	37		.	.	.	.	.	.	.	.	.	.	G	14.16	2.452266	0.43531	.	.	ENSG00000133149	ENST00000372578;ENST00000372575;ENST00000413579	.	.	.	3.02	-0.0125	0.13988	.	2.067560	0.02469	N	0.087303	T	0.29256	0.0728	.	.	.	0.09310	N	1	B;B	0.17852	0.024;0.024	B;B	0.15052	0.012;0.012	T	0.16897	-1.0387	8	0.49607	T	0.09	.	2.3339	0.04242	0.3036:0.0:0.4237:0.2727	.	173;173	C9JWK0;Q9BXU3	.;TX13A_HUMAN	V	173	.	ENSP00000361656:A173V	A	-	2	0	TEX13A	104351016	0.011000	0.17503	0.000000	0.03702	0.009000	0.06853	1.241000	0.32743	-0.119000	0.11830	-0.312000	0.09012	GCA	.	.	none		0.642	TEX13A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_031274		A	104464360	G	A	104464360	3	1	23	1	0	0	0	0	1	0	0	0	15791	1319	46	2	717	2	TEX13A	23	104464360	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	34110106	104464360	50806200	764	8208											
COL4A5	1287	hgsc.bcm.edu	37	chrX	107867476	107867476	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcttggaaggtatacctggAgtttcagggccaaaaggtta	11	12	12	6	0	2	0	1	0	1	0	2	2	2	2	2	5	1	3	2	5	6	6	rs104886373		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:107867476A>T	ENST00000361603.2	+	34	3172	c.2928A>T	c.(2926-2928)ggA>ggT	p.G976G	COL4A5_ENST00000328300.6_Silent_p.G976G	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	976	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						GTATACCTGGAGTTTCAGGGC	0.448									Alport syndrome with Diffuse Leiomyomatosis																												p.G976G		Atlas-SNP	.											.	COL4A5	262	.	0			c.A2928T						PASS	.						103	82	89					X																	107867476		2203	4300	6503	SO:0001819	synonymous_variant	1287	exon34	Familial Cancer Database		ACCTGGAGTTTCA	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.2928A>T	X.37:g.107867476A>T		110	0	0		44	16	0.363636	NM_000495	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Silent	SNP	ENST00000361603.2	37	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	A	3.794	-0.043138	0.07452	.	.	ENSG00000188153	ENST00000505728	.	.	.	5.5	2.99	0.34606	.	.	.	.	.	T	0.45716	0.1356	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34354	-0.9832	4	.	.	.	.	2.442	0.04497	0.5622:0.1178:0.0786:0.2414	.	.	.	.	V	54	.	.	E	+	2	0	COL4A5	107754132	0.702000	0.27816	0.732000	0.30844	0.498000	0.33706	1.305000	0.33493	0.715000	0.32103	0.441000	0.28932	GAG	.	.	none		0.448	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2			T	107867476	A	T	107867476	2	4	23	1	0	0	0	0	0	0	0	1	3696	291	11	5		5	COL4A5	23	107867476	Silent	SNP	A	TCGA-G8-6325-01A-11D-2210-10	3403116	107867476	47403084	765	8209											
PLS3	5358	hgsc.bcm.edu	37	chrX	114863593	114863593	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaggtatttgtgctctgggTggaacttcagagttgtccag	8	13	14	6	0	2	1	1	0	1	1	3	3	3	2	1	3	2	3	1	3	3	4	rs140121121	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:114863593T>A	ENST00000420625.2	+	4	455	c.321T>A	c.(319-321)ggT>ggA	p.G107G	PLS3_ENST00000537301.1_Silent_p.G85G|PLS3_ENST00000355899.3_Silent_p.G107G|PLS3_ENST00000539310.1_Silent_p.G62G|PLS3_ENST00000289290.3_Silent_p.G62G	NM_001136025.3|NM_001172335.1|NM_001282338.1	NP_001129497.1|NP_001165806.1|NP_001269267.1	P13797	PLST_HUMAN	plastin 3	107					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						GTGCTCTGGGTGGAACTTCAG	0.378													T|||	23	0.00609272	0.0	0.0029	3775	,	,		12691	0.0		0.0169	False		,,,				2504	0.0041				p.G107G	Colon(160;1047 1864 8490 12969 29601)	Atlas-SNP	.											.	PLS3	60	.	0			c.T321A						PASS	.	T	,,	10,3825		0,9,1,1623,570	130	115	120		321,240,321	-0.8	1	X	dbSNP_134	120	99,6629		2,75,20,2351,1852	no	coding-synonymous,coding-synonymous,coding-synonymous	PLS3	NM_001136025.3,NM_001172335.1,NM_005032.5	,,	2,84,21,3974,2422	AA,AT,A,TT,T		1.4715,0.2608,1.0319	,,	107/631,80/604,107/631	114863593	109,10454	2203	4300	6503	SO:0001819	synonymous_variant	5358	exon4			TCTGGGTGGAACT	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.321T>A	X.37:g.114863593T>A		265	1	0.00377358		128	128	1	NM_005032	A8K579|B1AQ09|B4DGB4|B7Z6M1|Q86YI6	Silent	SNP	ENST00000420625.2	37	CCDS14568.1																																																																																			T|0.990;A|0.010	0.010	strong		0.378	PLS3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057976.2			A	114863593	T	A	114863593	2	1	23	1	0	0	0	0	0	0	0	1	12117	1683	59	5		5	PLS3	23	114863593	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	6996117	114863593	40406967	766	8210											
AGTR2	186	hgsc.bcm.edu	37	chrX	115303837	115303837	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctactcttcctctatgggcaAcctattattcttatagatat	10	17	4	10	0	3	1	0	0	3	1	4	1	4	1	2	1	2	1	2	1	8	9			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:115303837A>C	ENST00000371906.4	+	3	494	c.304A>C	c.(304-306)Acc>Ccc	p.T102P		NM_000686.4	NP_000677.2	P50052	AGTR2_HUMAN	angiotensin II receptor, type 2	102					aldosterone secretion (GO:0035932)|angiotensin-activated signaling pathway (GO:0038166)|blood vessel remodeling (GO:0001974)|brain development (GO:0007420)|brain renin-angiotensin system (GO:0002035)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell surface receptor signaling pathway (GO:0007166)|cellular response to dexamethasone stimulus (GO:0071549)|cellular sodium ion homeostasis (GO:0006883)|cerebellar cortex development (GO:0021695)|dopamine biosynthetic process (GO:0042416)|exploration behavior (GO:0035640)|extracellular negative regulation of signal transduction (GO:1900116)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell growth (GO:0030308)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of heart rate (GO:0010459)|negative regulation of icosanoid secretion (GO:0032304)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of norepinephrine secretion (GO:0010700)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasodilation (GO:0045909)|regulation of blood pressure (GO:0008217)|regulation of metanephros size (GO:0035566)|regulation of systemic arterial blood pressure by circulatory renin-angiotensin (GO:0001991)|regulation of transcription factor import into nucleus (GO:0042990)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to organonitrogen compound (GO:0010243)|vasodilation by angiotensin involved in regulation of systemic arterial blood pressure (GO:0002033)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	angiotensin type II receptor activity (GO:0004945)|peptide hormone binding (GO:0017046)|receptor antagonist activity (GO:0048019)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|skin(1)	24					Tasosartan(DB01349)	TCTATGGGCAACCTATTATTC	0.378																																					p.T102P		Atlas-SNP	.											.	AGTR2	62	.	0			c.A304C						PASS	.						177	172	174					X																	115303837		2203	4300	6503	SO:0001583	missense	186	exon3			TGGGCAACCTATT	AY324607	CCDS14569.1	Xq22-q23	2012-08-08			ENSG00000180772	ENSG00000180772		"GPCR / Class A : Angiotensin receptors"	338	protein-coding gene	gene with protein product		300034	"angiotensin receptor 2"			1550596	Standard	NM_000686		Approved	AT2, MRX88	uc004eqh.4	P50052	OTTHUMG00000022243	ENST00000371906.4:c.304A>C	X.37:g.115303837A>C	ENSP00000360973:p.Thr102Pro	343	0	0		181	52	0.287293	NM_000686	B2R9V1|Q13016|Q6FGY7	Missense_Mutation	SNP	ENST00000371906.4	37	CCDS14569.1	.	.	.	.	.	.	.	.	.	.	A	13.43	2.235143	0.39498	.	.	ENSG00000180772	ENST00000371906	T	0.37584	1.19	4.48	2.01	0.26516	GPCR, rhodopsin-like superfamily (1);	0.327695	0.32459	N	0.006071	T	0.47838	0.1467	M	0.82630	2.6	0.29718	N	0.8389	B	0.33777	0.425	P	0.48227	0.571	T	0.48525	-0.9028	10	0.37606	T	0.19	-0.9265	4.2699	0.10782	0.7194:0.0:0.1019:0.1787	.	102	P50052	AGTR2_HUMAN	P	102	ENSP00000360973:T102P	ENSP00000360973:T102P	T	+	1	0	AGTR2	115217865	0.000000	0.05858	0.995000	0.50966	0.995000	0.86356	0.792000	0.26929	0.122000	0.18314	0.412000	0.27726	ACC	.	.	none		0.378	AGTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057984.1	NM_000686		C	115303837	A	C	115303837	3	2	23	1	0	0	0	0	1	0	0	0	402	43	2	5	306	5	AGTR2	23	115303837	Missense_Mutation	SNP	A	TCGA-G8-6325-01A-11D-2210-10	440244	115303837	39966723	767	8211											
USP26	83844	hgsc.bcm.edu	37	chrX	132161159	132161159	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgctgaaatggcctttttaaGattcaagagtaacatctcct	12	14	7	8	0	2	3	1	1	1	2	3	3	2	3	2	1	2	2	2	1	4	5	rs35397110	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:132161159G>A	ENST00000511190.1	-	6	1559	c.1090C>T	c.(1090-1092)Ctt>Ttt	p.L364F	USP26_ENST00000406273.1_Missense_Mutation_p.L364F|USP26_ENST00000370832.1_Missense_Mutation_p.L364F	NM_031907.1	NP_114113.1	Q9BXU7	UBP26_HUMAN	ubiquitin specific peptidase 26	364	USP.		L -> F (in dbSNP:rs35397110). {ECO:0000269|PubMed:15970005, ECO:0000269|PubMed:18377898, ECO:0000269|PubMed:18927127}.		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)					GCCTTTTTAAGATTCAAGAGT	0.373													g|||	61	0.0161589	0.0038	0.0101	3775	,	,		13219	0.0		0.0457	False		,,,				2504	0.0031				p.L364F	NSCLC(104;342 1621 36940 47097 52632)	Atlas-SNP	.											.	USP26	135	.	0			c.C1090T	GRCh37	CM056721	USP26	M	rs35397110	PASS	.		PHE/LEU	34,3801		0,29,5,1603,566	64	63	63		1090	-4	0	X	dbSNP_126	63	421,6305		8,297,108,2122,1764	yes	missense	USP26	NM_031907.1	22	8,326,113,3725,2330	AA,AG,A,GG,G		6.2593,0.8866,4.3083	benign	364/914	132161159	455,10106	2203	4299	6502	SO:0001583	missense	83844	exon1			TTTTAAGATTCAA	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.1090C>T	X.37:g.132161159G>A	ENSP00000423390:p.Leu364Phe	265	0	0		136	133	0.977941	NM_031907	B9WRT6|Q5H9H4	Missense_Mutation	SNP	ENST00000511190.1	37	CCDS14635.1	47	0.028330319469559977	1	0.0020325203252032522	4	0.0111731843575419	0	0.0	28	0.03814713896457766	g	9.121	1.009071	0.19199	0.008866	0.062593	ENSG00000134588	ENST00000370832;ENST00000511190;ENST00000406273	T;T;T	0.74526	-0.85;-0.85;-0.85	3.78	-4.02	0.04034	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.458295	0.16597	N	0.207518	T	0.05914	0.0154	N	0.05124	-0.11	0.80722	P	0.0	B	0.10296	0.003	B	0.12156	0.007	T	0.15122	-1.0448	9	0.11794	T	0.64	-4.0857	2.0978	0.03672	0.1422:0.1889:0.4345:0.2344	rs35397110;rs61751330	364	Q9BXU7	UBP26_HUMAN	F	364	ENSP00000359869:L364F;ENSP00000423390:L364F;ENSP00000384360:L364F	ENSP00000359869:L364F	L	-	1	0	USP26	131988825	0.086000	0.21541	0.001000	0.08648	0.015000	0.08874	0.254000	0.18314	-0.932000	0.03742	-0.432000	0.05891	CTT	G|0.963;A|0.037	0.037	strong		0.373	USP26-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359441.1	NM_031907		A	132161159	G	A	132161159	3	1	23	1	0	0	0	0	1	0	0	0	17072	942	33	2	1654	2	USP26	23	132161159	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	16857322	132161159	23109401	768	8212											
ZNF449	203523	hgsc.bcm.edu	37	chrX	134494878	134494878	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tttagacagagaccaagcctCgttattcatttaagaatcca	14	12	6	9	1	1	3	1	0	0	3	3	4	2	3	3	0	1	1	3	0	5	6	rs141878135	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:134494878C>T	ENST00000339249.4	+	5	1574	c.1434C>T	c.(1432-1434)ctC>ctT	p.L478L		NM_152695.5	NP_689908.3	Q6P9G9	ZN449_HUMAN	zinc finger protein 449	478					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)					GACCAAGCCTCGTTATTCATT	0.423																																					p.L478L		Atlas-SNP	.											.	ZNF449	68	.	0			c.C1434T						PASS	.	C		2,3833		0,2,0,1630,571	121	120	121		1434	0.2	1	X	dbSNP_134	121	10,6716		0,7,3,2420,1869	no	coding-synonymous	ZNF449	NM_152695.5		0,9,3,4050,2440	TT,TC,T,CC,C		0.1487,0.0522,0.1136		478/519	134494878	12,10549	2203	4299	6502	SO:0001819	synonymous_variant	203523	exon5			AAGCCTCGTTATT	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.1434C>T	X.37:g.134494878C>T		127	0	0		70	69	0.985714	NM_152695	Q5JRZ7|Q5JRZ8|Q6NZX2|Q8N3Q1|Q8TED7	Silent	SNP	ENST00000339249.4	37	CCDS14649.1																																																																																			C|0.999;T|0.001	0.001	strong		0.423	ZNF449-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058411.1	NM_152695		T	134494878	C	T	134494878	2	4	23	1	0	0	0	0	0	0	0	1	17935	871	31	1		1	ZNF449	23	134494878	Silent	SNP	C	TCGA-G8-6325-01A-11D-2210-10	2333719	134494878	20775682	769	8213											
MAGEC1	9947	hgsc.bcm.edu	37	chrX	140993885	140993885	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagggttttgcccagtctcCtctccagattcctgtgagcc	5	13	10	13	0	2	3	0	2	2	1	5	3	3	3	5	1	2	1	5	1	0	3	rs74847167	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:140993885C>T	ENST00000285879.4	+	4	981	c.695C>T	c.(694-696)cCt>cTt	p.P232L	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	232								p.P232L(1)		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)					GCCCAGTCTCCTCTCCAGATT	0.488										HNSCC(15;0.026)																											p.P232L		Atlas-SNP	.											.	MAGEC1	317	.	1	Substitution - Missense(1)	skin(1)	c.C695T						PASS	.	C	LEU/PRO	12,3823		0,11,1,1621,570	100	96	98		695		0.1	X	dbSNP_131	98	74,6638		0,69,5,2359,1851	no	missense	MAGEC1	NM_005462.4	98	0,80,6,3980,2421	TT,TC,T,CC,C		1.1025,0.3129,0.8154	benign	232/1143	140993885	86,10461	2203	4284	6487	SO:0001583	missense	9947	exon4			AGTCTCCTCTCCA	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.695C>T	X.37:g.140993885C>T	ENSP00000285879:p.Pro232Leu	822	2	0.00243309		327	215	0.657492	NM_005462	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	17	0.010247136829415311	0	0.0	5	0.013812154696132596	0	0.0	13	0.017195767195767195	c	5.440	0.266208	0.10294	0.003129	0.011025	ENSG00000155495	ENST00000285879;ENST00000370510	T	0.02216	4.39	.	.	.	.	.	.	.	.	T	0.00637	0.0021	N	0.08118	0	0.23341	N	0.997875	B	0.06786	0.001	B	0.01281	0.0	T	0.47947	-0.9077	8	0.87932	D	0	.	2.6694	0.05063	0.0:0.5025:0.0:0.4974	.	232	O60732	MAGC1_HUMAN	L	232;33	ENSP00000285879:P232L	ENSP00000285879:P232L	P	+	2	0	MAGEC1	140821551	0.002000	0.14202	0.066000	0.19879	0.066000	0.16364	0.991000	0.29654	0.054000	0.16065	0.054000	0.15206	CCT	C|0.989;T|0.011	0.011	strong		0.488	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462		T	140993885	C	T	140993885	3	4	23	1	0	0	0	0	1	0	0	0	9189	681	24	2	701	2	MAGEC1	23	140993885	Missense_Mutation	SNP	C	TCGA-G8-6325-01A-11D-2210-10	6499007	140993885	14276675	770	8214											
SLITRK4	139065	hgsc.bcm.edu	37	chrX	142718181	142718181	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttttaaaagccttccataTaagtcactgggagtttcaca	12	14	6	9	0	3	0	2	0	1	0	4	1	4	1	2	1	1	1	2	1	4	6			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:142718181T>C	ENST00000381779.4	-	2	969	c.744A>G	c.(742-744)ttA>ttG	p.L248L	SLITRK4_ENST00000356928.1_Silent_p.L248L|SLITRK4_ENST00000338017.4_Silent_p.L248L	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	248	LRRCT 1.					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)					GCCTTCCATATAAGTCACTGG	0.443																																					p.L248L		Atlas-SNP	.											.	SLITRK4	162	.	0			c.A744G						PASS	.						66	61	63					X																	142718181		2203	4300	6503	SO:0001819	synonymous_variant	139065	exon2			TCCATATAAGTCA	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.744A>G	X.37:g.142718181T>C		214	0	0		94	93	0.989362	NM_001184750	Q5JXG3|Q8TCM8|Q96DL3	Silent	SNP	ENST00000381779.4	37	CCDS14679.1																																																																																			.	.	none		0.443	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078		C	142718181	T	C	142718181	2	2	23	1	0	0	0	0	0	0	0	1	14760	1403	49	3		3	SLITRK4	23	142718181	Silent	SNP	T	TCGA-G8-6325-01A-11D-2210-10	1724296	142718181	12552379	771	8215											
PNMA3	29944	hgsc.bcm.edu	37	chrX	152226189	152226189	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttgtgtaaagcctatcaggaGgcaggagagaaagtatctag	14	9	13	5	0	2	1	1	0	1	1	2	4	2	3	1	3	1	3	1	3	6	5	rs141778950	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:152226189G>A	ENST00000370264.4	+	1	803	c.777G>A	c.(775-777)gaG>gaA	p.E259E	PNMA3_ENST00000370265.4_Silent_p.E259E|PNMA3_ENST00000447306.1_Silent_p.E259E			Q9UL41	PNMA3_HUMAN	paraneoplastic Ma antigen 3	259					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)					cctatcaggaggcaggagaga	0.488													G|||	4	0.0010596	0.0	0.0	3775	,	,		15718	0.0		0.004	False		,,,				2504	0.0				p.E259E		Atlas-SNP	.											.	PNMA3	81	.	0			c.G777A						PASS	.	G		3,3832		0,3,0,1629,571	166	157	160		777	-0.1	0	X	dbSNP_134	160	12,6716		0,10,2,2418,1870	no	coding-synonymous	PNMA3	NM_013364.4		0,13,2,4047,2441	AA,AG,A,GG,G		0.1784,0.0782,0.142		259/464	152226189	15,10548	2203	4300	6503	SO:0001819	synonymous_variant	29944	exon2			TCAGGAGGCAGGA	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.777G>A	X.37:g.152226189G>A		245	0	0		110	108	0.981818	NM_013364	D3DWT7|Q9H0A4	Silent	SNP	ENST00000370264.4	37	CCDS35435.2																																																																																			G|0.999;A|0.001	0.001	strong		0.488	PNMA3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060946.2	NM_013364		A	152226189	G	A	152226189	2	1	23	1	0	0	0	0	0	0	0	1	12164	991	35	2		2	PNMA3	23	152226189	Silent	SNP	G	TCGA-G8-6325-01A-11D-2210-10	9508008	152226189	3044371	772	8216											
PLXNA3	55558	hgsc.bcm.edu	37	chrX	153689643	153689643	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaagatcgtgcgcatgtgcGcgggagactcagagttctac	9	8	13	11	4	2	3	1	0	1	3	3	4	2	3	1	1	3	2	1	1	2	2	rs145244142	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:153689643G>A	ENST00000369682.3	+	3	974	c.799G>A	c.(799-801)Gcg>Acg	p.A267T		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	267	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)					GCGCATGTGCGCGGGAGACTC	0.607																																					p.A267T		Atlas-SNP	.											.	PLXNA3	156	.	0			c.G799A						PASS	.	G	THR/ALA	3,3832		0,3,1629,571	95	88	90		799	3.5	0	X	dbSNP_134	90	2,6726		0,2,2426,1872	yes	missense	PLXNA3	NM_017514.3	58	0,5,4055,2443	AA,AG,GG,G		0.0297,0.0782,0.0473	benign	267/1872	153689643	5,10558	2203	4300	6503	SO:0001583	missense	55558	exon3			ATGTGCGCGGGAG	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.799G>A	X.37:g.153689643G>A	ENSP00000358696:p.Ala267Thr	121	0	0		49	49	1	NM_017514	Q5HY36	Missense_Mutation	SNP	ENST00000369682.3	37	CCDS14752.1	.	.	.	.	.	.	.	.	.	.	G	8.118	0.780273	0.16120	7.82E-4	2.97E-4	ENSG00000130827	ENST00000369682	T	0.10960	2.82	5.29	3.5	0.40072	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.124679	0.56097	D	0.000036	T	0.08133	0.0203	L	0.43152	1.355	0.23816	N	0.996762	B	0.24258	0.1	B	0.26202	0.067	T	0.40534	-0.9558	10	0.09338	T	0.73	.	6.5277	0.22310	0.087:0.0:0.5809:0.3321	.	267	P51805	PLXA3_HUMAN	T	267	ENSP00000358696:A267T	ENSP00000358696:A267T	A	+	1	0	PLXNA3	153342837	0.000000	0.05858	0.019000	0.16419	0.256000	0.26092	0.639000	0.24690	0.584000	0.29591	0.594000	0.82650	GCG	G|0.999;A|0.001	0.001	strong		0.607	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514		A	153689643	G	A	153689643	3	1	23	1	0	0	0	0	1	0	0	0	12130	1087	38	1	805	1	PLXNA3	23	153689643	Missense_Mutation	SNP	G	TCGA-G8-6325-01A-11D-2210-10	1463454	153689643	1580917	773	8217											
NOC2L	26155	hgsc.bcm.edu	37	chr1	880502	880502	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	catcgtcttccaccccatgcCgagtgctcaggggcctcagt	6	9	10	16	2	3	0	2	0	1	0	5	1	4	0	5	2	2	1	5	2	0	1	rs74047418	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:880502C>T	ENST00000327044.6	-	18	2127	c.2078G>A	c.(2077-2079)cGg>cAg	p.R693Q		NM_015658.3	NP_056473	Q9Y3T9	NOC2L_HUMAN	nucleolar complex associated 2 homolog (S. cerevisiae)	693	Asp/Glu-rich (acidic).				apoptotic process (GO:0006915)|cellular response to UV (GO:0034644)|chromatin assembly (GO:0031497)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of histone acetylation (GO:0035067)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleolus to nucleoplasm transport (GO:0032066)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|nucleosome binding (GO:0031491)|poly(A) RNA binding (GO:0044822)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	16	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;1.86e-38)|OV - Ovarian serous cystadenocarcinoma(86;6.08e-23)|Colorectal(212;0.000161)|COAD - Colon adenocarcinoma(227;0.000194)|BRCA - Breast invasive adenocarcinoma(365;0.000475)|Kidney(185;0.00231)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0344)|Lung(427;0.2)		caccccATGCCGAGTGCTCAG	0.607													c|||	6	0.00119808	0.003	0.0014	5008	,	,		17544	0.0		0.001	False		,,,				2504	0.0				p.R693Q		Atlas-SNP	.											.	NOC2L	42	.	0			c.G2078A						PASS	.	C	GLN/ARG	9,4395	15.5+/-35.6	0,9,2193	88	81	84		2078	-6.8	0	1	dbSNP_130	84	15,8585	9.8+/-36.6	0,15,4285	yes	missense	NOC2L	NM_015658.3	43	0,24,6478	TT,TC,CC		0.1744,0.2044,0.1846	possibly-damaging	693/750	880502	24,12980	2202	4300	6502	SO:0001583	missense	26155	exon18			CCATGCCGAGTGC	AL050019	CCDS3.1	1p36.33	2014-06-12			ENSG00000188976	ENSG00000188976			24517	protein-coding gene	gene with protein product	"novel INHAT repressor", "protein phosphatase 1, regulatory subunit 12"	610770					Standard	NM_015658		Approved	DKFZP564C186, NET7, NET15, NIR, PPP1R112	uc001abz.4	Q9Y3T9	OTTHUMG00000040720	ENST00000327044.6:c.2078G>A	1.37:g.880502C>T	ENSP00000317992:p.Arg693Gln	99	0	0		101	52	0.514852	NM_015658	Q5SVA3|Q9BTN6	Missense_Mutation	SNP	ENST00000327044.6	37	CCDS3.1	5	0.0022893772893772895	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	4.022	0.001552	0.07819	0.002044	0.001744	ENSG00000188976	ENST00000327044	T	0.22134	1.97	3.39	-6.79	0.01715	Armadillo-type fold (1);	2.092900	0.02013	N	0.047121	T	0.06735	0.0172	N	0.22421	0.69	0.09310	N	1	B;B;B	0.12630	0.005;0.005;0.006	B;B;B	0.04013	0.001;0.001;0.001	T	0.28996	-1.0026	10	0.11485	T	0.65	0.8905	0.9663	0.01406	0.221:0.1346:0.2196:0.4248	.	693;693;460	B3KNC3;Q9Y3T9;Q9H9J5	.;NOC2L_HUMAN;.	Q	693	ENSP00000317992:R693Q	ENSP00000317992:R693Q	R	-	2	0	NOC2L	870365	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.544000	0.00933	-2.506000	0.00507	0.448000	0.29417	CGG	C|0.998;T|0.002	0.002	strong		0.607	NOC2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097869.1	NM_015658		T	880502	C	T	880502	3	4	24	1	0	0	0	0	1	0	0	0	10522	652	23	1	179	1	NOC2L	1	880502	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10		880502	248370119	1	8218											
AURKAIP1	54998	hgsc.bcm.edu	37	chr1	1309803	1309803	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cggctgcccagcactccagaGacgggccaaggcgggcggcc	7	2	16	16	4	0	1	0	0	0	1	1	2	1	1	4	5	2	2	4	5	1	0	rs9554		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:1309803G>A	ENST00000338370.3	-	2	475	c.75C>T	c.(73-75)gtC>gtT	p.V25V	AURKAIP1_ENST00000489799.1_5'UTR|AURKAIP1_ENST00000321751.5_Silent_p.V25V|AURKAIP1_ENST00000378853.3_Silent_p.V25V|AURKAIP1_ENST00000338338.5_Silent_p.V25V			Q9NWT8	AKIP_HUMAN	aurora kinase A interacting protein 1	25					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)		GCACTCCAGAGACGGGCCAAG	0.716																																					p.V25V		Atlas-SNP	.											.	AURKAIP1	12	.	0			c.C75T						PASS	.						2	4	3					1																	1309803		1684	3642	5326	SO:0001819	synonymous_variant	54998	exon3			TCCAGAGACGGGC		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.75C>T	1.37:g.1309803G>A		11	0	0		10	9	0.9	NM_001127230	Q5TA36|Q8TBD3	Silent	SNP	ENST00000338370.3	37	CCDS25.1																																																																																			.	.	weak		0.716	AURKAIP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008273.1	NM_017900		A	1309803	G	A	1309803	2	1	24	1	0	0	0	0	0	0	0	1	1222	929	33	2		2	AURKAIP1	1	1309803	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	429301	1309803	247940818	2	8219											
PANK4	55229	hgsc.bcm.edu	37	chr1	2445832	2445832	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctgaagcttgttccagtacTtctgccggaacttctccgcc	6	13	8	14	2	3	1	0	1	3	0	5	2	4	2	4	1	4	3	4	1	3	5			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:2445832T>C	ENST00000378466.3	-	11	1460	c.1448A>G	c.(1447-1449)aAg>aGg	p.K483R	PANK4_ENST00000435556.3_Missense_Mutation_p.K444R	NM_018216.1	NP_060686.1	Q9NVE7	PANK4_HUMAN	pantothenate kinase 4	483					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)		GTTCCAGTACTTCTGCCGGAA	0.627																																					p.K483R		Atlas-SNP	.											.	PANK4	64	.	0			c.A1448G						PASS	.						72	75	74					1																	2445832		2203	4300	6503	SO:0001583	missense	55229	exon11			CAGTACTTCTGCC	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.1448A>G	1.37:g.2445832T>C	ENSP00000367727:p.Lys483Arg	66	0	0		79	44	0.556962	NM_018216	B9DI84|Q53EU3|Q5TA84|Q7RTX3|Q9H3X5	Missense_Mutation	SNP	ENST00000378466.3	37	CCDS42.1	.	.	.	.	.	.	.	.	.	.	t	14.68	2.609185	0.46527	.	.	ENSG00000157881	ENST00000378466;ENST00000435556	T;T	0.18810	2.19;2.19	5.1	5.1	0.69264	Domain of unknown function DUF89 (2);	0.000000	0.85682	D	0.000000	T	0.32912	0.0845	L	0.33485	1.01	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.99	T	0.03503	-1.1030	10	0.22109	T	0.4	-33.6939	14.0447	0.64698	0.0:0.0:0.0:1.0	.	444;483	E9PHT6;Q9NVE7	.;PANK4_HUMAN	R	483;444	ENSP00000367727:K483R;ENSP00000421433:K444R	ENSP00000367727:K483R	K	-	2	0	PANK4	2435692	1.000000	0.71417	1.000000	0.80357	0.036000	0.12997	5.751000	0.68720	1.933000	0.56026	0.454000	0.30748	AAG	.	.	none		0.627	PANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002082.1			C	2445832	T	C	2445832	3	2	24	1	0	0	0	0	1	0	0	0	11428	1609	56	3	909	3	PANK4	1	2445832	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	1136029	2445832	246804789	3	8220											
PRDM16	63976	hgsc.bcm.edu	37	chr1	3102852	3102852	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acccccaaggagggctcgccGtacgaggcccctgtctacat	8	6	11	16	3	1	0	0	0	1	0	2	2	1	1	5	3	2	2	5	3	3	2	rs199614349	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:3102852G>A	ENST00000270722.5	+	2	250	c.201G>A	c.(199-201)ccG>ccA	p.P67P	PRDM16_ENST00000378391.2_Silent_p.P67P|PRDM16_ENST00000511072.1_Silent_p.P67P|PRDM16_ENST00000442529.2_Silent_p.P67P|PRDM16_ENST00000441472.2_Silent_p.P67P|PRDM16_ENST00000378398.3_Silent_p.P67P|PRDM16_ENST00000514189.1_Silent_p.P67P			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	67					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)		AGGGCTCGCCGTACGAGGCCC	0.672			T	EVI1	"MDS, AML"								G|||	6	0.00119808	0.0	0.0029	5008	,	,		14984	0.0		0.003	False		,,,				2504	0.001				p.P67P		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.G201A						PASS	.	G	,	0,4074		0,0,2037	49	60	56		201,201	-2.7	1	1		56	24,8284		0,24,4130	no	coding-synonymous,coding-synonymous	PRDM16	NM_022114.3,NM_199454.2	,	0,24,6167	AA,AG,GG		0.2889,0.0,0.1938	,	67/1277,67/1258	3102852	24,12358	2037	4154	6191	SO:0001819	synonymous_variant	63976	exon2			CTCGCCGTACGAG	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.201G>A	1.37:g.3102852G>A		198	0	0		240	123	0.5125	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Silent	SNP	ENST00000270722.5	37	CCDS41236.2																																																																																			G|0.989;A|0.011	0.011	strong		0.672	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114		A	3102852	G	A	3102852	2	1	24	1	0	0	0	0	0	0	0	1	12469	1132	40	1		1	PRDM16	1	3102852	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	657020	3102852	246147769	4	8221											
PRDM16	63976	hgsc.bcm.edu	37	chr1	3319541	3319541	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgagtgcaaggactgcgagcGgatgttccccaacaagtaca	12	6	12	11	3	0	0	0	0	0	0	1	4	1	2	2	2	5	3	2	2	4	2	rs141374404		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:3319541G>A	ENST00000270722.5	+	6	912	c.863G>A	c.(862-864)cGg>cAg	p.R288Q	PRDM16_ENST00000378391.2_Missense_Mutation_p.R288Q|PRDM16_ENST00000511072.1_Missense_Mutation_p.R289Q|PRDM16_ENST00000442529.2_Missense_Mutation_p.R288Q|PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000441472.2_Missense_Mutation_p.R288Q|PRDM16_ENST00000378398.3_Missense_Mutation_p.R289Q|PRDM16_ENST00000514189.1_Missense_Mutation_p.R289Q			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	288					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)		GACTGCGAGCGGATGTTCCCC	0.657			T	EVI1	"MDS, AML"								G|||	1	0.000199681	0.0	0.0	5008	,	,		15244	0.0		0.001	False		,,,				2504	0.0				p.R288Q		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.G863A						PASS	.						44	56	52					1																	3319541		2186	4274	6460	SO:0001583	missense	63976	exon6			GCGAGCGGATGTT	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.863G>A	1.37:g.3319541G>A	ENSP00000270722:p.Arg288Gln	225	0	0		266	115	0.432331	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Missense_Mutation	SNP	ENST00000270722.5	37	CCDS41236.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	6.953	0.545736	0.13312	.	.	ENSG00000142611	ENST00000511072;ENST00000378398;ENST00000441472;ENST00000442529;ENST00000378391;ENST00000514189;ENST00000270722;ENST00000512462;ENST00000408992;ENST00000509860	T;T;T;T;T;T;T;T;T	0.07567	3.18;3.18;3.18;3.18;3.18;3.18;3.18;3.18;3.18	4.32	3.39	0.38822	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.336202	0.19830	U	0.105113	T	0.09862	0.0242	L	0.29908	0.895	0.27992	N	0.935619	P;D;P;B	0.62365	0.85;0.991;0.636;0.39	B;P;B;B	0.49708	0.115;0.62;0.089;0.019	T	0.15607	-1.0431	10	0.21014	T	0.42	.	13.2179	0.59871	0.0:0.0:0.8395:0.1605	.	288;288;288;288	Q9HAZ2;Q9HAZ2-2;F8WEV3;D3YTA5	PRD16_HUMAN;.;.;.	Q	289;289;288;288;288;289;288;104;104;97	ENSP00000426975:R289Q;ENSP00000367651:R289Q;ENSP00000407968:R288Q;ENSP00000405253:R288Q;ENSP00000367643:R288Q;ENSP00000421400:R289Q;ENSP00000270722:R288Q;ENSP00000422504:R104Q;ENSP00000425796:R97Q	ENSP00000270722:R288Q	R	+	2	0	PRDM16	3309401	1.000000	0.71417	1.000000	0.80357	0.632000	0.37999	5.777000	0.68931	0.788000	0.33755	0.561000	0.74099	CGG	G|1.000;A|0.000	0.000	strong		0.657	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114		A	3319541	G	A	3319541	3	1	24	1	0	0	0	0	1	0	0	0	12469	1116	39	1	885	1	PRDM16	1	3319541	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	216689	3319541	245931080	5	8222											
TAS1R1	80835	hgsc.bcm.edu	37	chr1	6639073	6639073	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctgtcctgcctgacagttcGctcattccaactaatcatca	9	12	5	15	1	3	1	3	1	0	0	6	1	5	1	4	0	2	2	4	0	2	3	rs149418903	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:6639073G>A	ENST00000333172.6	+	6	2148	c.1955G>A	c.(1954-1956)cGc>cAc	p.R652H	ZBTB48_ENST00000377674.4_5'Flank|TAS1R1_ENST00000328191.4_3'UTR|TAS1R1_ENST00000351136.3_Missense_Mutation_p.R398H	NM_138697.3	NP_619642.2	Q7RTX1	TS1R1_HUMAN	taste receptor, type 1, member 1	652					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)		CTGACAGTTCGCTCATTCCAA	0.522													G|||	4	0.000798722	0.0	0.0014	5008	,	,		22421	0.0		0.001	False		,,,				2504	0.002				p.R652H		Atlas-SNP	.											TAS1R1,colon,carcinoma,0,1	TAS1R1	76	1	0			c.G1955A						scavenged	.	G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	129	128	128		1955,1193	4.8	1	1	dbSNP_134	128	14,8586	10.5+/-38.8	0,14,4286	yes	missense,missense	TAS1R1	NM_138697.3,NM_177540.2	29,29	0,14,6489	AA,AG,GG		0.1628,0.0,0.1076	probably-damaging,probably-damaging	652/842,398/588	6639073	14,12992	2203	4300	6503	SO:0001583	missense	80835	exon6			CAGTTCGCTCATT		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.1955G>A	1.37:g.6639073G>A	ENSP00000331867:p.Arg652His	169	1	0.00591716		220	115	0.522727	NM_138697	B2RMX0|Q5SY22|Q5SY24|Q8NGZ7|Q8TDJ7|Q8TDJ8|Q8TDJ9|Q8TDK0	Missense_Mutation	SNP	ENST00000333172.6	37	CCDS81.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.031876	0.93575	0.0	0.001628	ENSG00000173662	ENST00000333172;ENST00000351136	D;D	0.88664	-2.41;-2.41	4.85	4.85	0.62838	GPCR, family 3, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.94532	0.8239	M	0.81614	2.55	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.989;0.999	D	0.95172	0.8291	10	0.87932	D	0	.	17.1499	0.86775	0.0:0.0:1.0:0.0	.	398;652	Q7RTX1-2;Q7RTX1	.;TS1R1_HUMAN	H	652;398	ENSP00000331867:R652H;ENSP00000312558:R398H	ENSP00000331867:R652H	R	+	2	0	TAS1R1	6561660	0.885000	0.30320	0.994000	0.49952	0.998000	0.95712	2.584000	0.46102	2.505000	0.84491	0.655000	0.94253	CGC	G|0.999;A|0.001	0.001	strong		0.522	TAS1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004211.1			A	6639073	G	A	6639073	3	1	24	1	0	0	0	0	1	0	0	0	15577	1087	38	1	1977	1	TAS1R1	1	6639073	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	3319532	6639073	242611548	6	8223											
PER3	8863	hgsc.bcm.edu	37	chr1	7890153	7890153	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caggactccatcccatcctaCtgccactgttctgtccacgg	7	10	7	17	1	1	0	0	0	1	0	5	1	5	1	5	2	2	1	5	2	1	2	rs144178755	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:7890153C>T	ENST00000361923.2	+	18	3294	c.3119C>T	c.(3118-3120)aCt>aTt	p.T1040I	RP3-467L1.4_ENST00000451646.1_RNA|PER3_ENST00000377532.3_Missense_Mutation_p.T1049I	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	1040	5 X 18 AA tandem repeats of S-[HP]-[AP]- T-[AT]-[GST]-[ATV]-L-S-[MT]-G-[LS]-P-P- [MRS]-[EKR]-[NST]-P.|Ser-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)		TCCCATCCTACTGCCACTGTT	0.547													C|||	2	0.000399361	0.0	0.0029	5008	,	,		18916	0.0		0.0	False		,,,				2504	0.0				p.T1040I		Atlas-SNP	.											.	PER3	95	.	0			c.C3119T						PASS	.	C	ILE/THR	0,4406		0,0,2203	142	115	124		3119	0.4	0	1	dbSNP_134	124	24,8576	17.3+/-56.4	0,24,4276	yes	missense	PER3	NM_016831.1	89	0,24,6479	TT,TC,CC		0.2791,0.0,0.1845	benign	1040/1202	7890153	24,12982	2203	4300	6503	SO:0001583	missense	8863	exon18			ATCCTACTGCCAC	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.3119C>T	1.37:g.7890153C>T	ENSP00000355031:p.Thr1040Ile	97	0	0		141	74	0.524823	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	7.381	0.628779	0.14257	0.0	0.002791	ENSG00000049246	ENST00000377532;ENST00000361923;ENST00000539773	T;T	0.11495	2.77;2.83	1.61	0.359	0.16088	Period circadian-like, C-terminal (1);	7.092960	0.01606	U	0.022261	T	0.08891	0.0220	L	0.34521	1.04	0.09310	N	1	B;B;B;B;B	0.30889	0.075;0.054;0.299;0.248;0.054	B;B;B;B;B	0.27500	0.013;0.05;0.08;0.067;0.05	T	0.31166	-0.9953	10	0.52906	T	0.07	.	2.8786	0.05640	0.0:0.6047:0.0:0.3953	.	89;1040;1049;1049;1040	B4DR65;A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;.;PER3_HUMAN	I	1049;1040;233	ENSP00000366755:T1049I;ENSP00000355031:T1040I	ENSP00000355031:T1040I	T	+	2	0	PER3	7812740	0.086000	0.21541	0.017000	0.16124	0.014000	0.08584	-0.079000	0.11357	0.692000	0.31613	0.305000	0.20034	ACT	C|0.998;T|0.002	0.002	strong		0.547	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831		T	7890153	C	T	7890153	3	4	24	1	0	0	0	0	1	0	0	0	11740	565	20	2	3189	2	PER3	1	7890153	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1251080	7890153	241360468	7	8224											
APITD1	1325	hgsc.bcm.edu	37	chr1	10511534	10511534	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cagtgccgggcccctcatagGagaggaagcccgggaggtgg	8	4	18	11	2	1	1	1	0	0	1	1	4	1	3	4	6	2	0	4	6	2	1	rs201163116		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:10511534G>T	ENST00000377049.3	+	2	705	c.200G>T	c.(199-201)gGa>gTa	p.G67V	APITD1-CORT_ENST00000470413.2_3'UTR|APITD1_ENST00000602787.1_Missense_Mutation_p.G126V|APITD1_ENST00000602296.1_3'UTR|APITD1-CORT_ENST00000465026.1_3'UTR|APITD1-CORT_ENST00000400900.2_Missense_Mutation_p.G126V|CORT_ENST00000320498.4_Missense_Mutation_p.G117V	NM_001302.4	NP_001293.3	O00230	CORT_HUMAN	cortistatin	67					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|synaptic transmission (GO:0007268)	extracellular space (GO:0005615)	G-protein coupled receptor binding (GO:0001664)|neuropeptide hormone activity (GO:0005184)			breast(1)|endometrium(1)|stomach(1)	3	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;3.12e-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)|STAD - Stomach adenocarcinoma(132;0.0165)|READ - Rectum adenocarcinoma(331;0.0487)		CCCCTCATAGGAGAGGAAGCC	0.627																																					p.G126V		Atlas-SNP	.											.	.	.	.	0			c.G377T						PASS	.						26	32	30					1																	10511534		2200	4298	6498	SO:0001583	missense	100526739	exon5			TCATAGGAGAGGA	AF013252	CCDS117.1, CCDS117.2	1p36.22	2013-02-25			ENSG00000241563	ENSG00000241563		"Endogenous ligands"	2257	protein-coding gene	gene with protein product	"prepro-cortistatin"	602784				9205124	Standard	NM_001302		Approved	MGC32686		O00230	OTTHUMG00000001906	ENST00000377049.3:c.200G>T	1.37:g.10511534G>T	ENSP00000366248:p.Gly67Val	175	0	0		191	82	0.429319	NM_198544	Q5T6G0|Q6UX11	Missense_Mutation	SNP	ENST00000377049.3	37	CCDS117.2	.	.	.	.	.	.	.	.	.	.	G	16.62	3.173907	0.57692	.	.	ENSG00000175279;ENSG00000251503;ENSG00000241563;ENSG00000241563	ENST00000556104;ENST00000400900;ENST00000377049;ENST00000320498	.	.	.	5.39	2.33	0.28932	.	0.777718	0.12758	N	0.441634	T	0.24586	0.0596	L	0.50333	1.59	0.09310	N	0.999994	P;B	0.37781	0.608;0.019	B;B	0.31290	0.127;0.015	T	0.13098	-1.0522	9	0.23302	T	0.38	-15.679	4.4404	0.11572	0.0813:0.2856:0.4862:0.1469	.	67;126	O00230;Q8N2Z9-2	CORT_HUMAN;.	V	126;126;67;117	.	ENSP00000383692:G126V	G	+	2	0	APITD1-CORT;APITD1;CORT	10434121	0.005000	0.15991	0.006000	0.13384	0.188000	0.23474	0.349000	0.20055	0.196000	0.20367	0.591000	0.81541	GGA	G|0.999;T|0.001	0.001	weak		0.627	CORT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005410.3	NM_001302		T	10511534	G	T	10511534	3	4	24	1	0	0	0	0	1	0	0	0	775	1174	41	4	540	4	APITD1	1	10511534	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	2621381	10511534	238739087	8	8225											
CASZ1	54897	hgsc.bcm.edu	37	chr1	10720305	10720305	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcccaccacctccttgcccAcccgctcctcggtcttggtg	3	10	8	20	2	1	0	0	0	1	0	4	0	3	0	7	2	2	1	7	2	0	2	rs138985539	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:10720305A>G	ENST00000377022.3	-	6	1111	c.794T>C	c.(793-795)gTg>gCg	p.V265A	CASZ1_ENST00000344008.5_Missense_Mutation_p.V265A|CASZ1_ENST00000478728.2_5'Flank	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	265					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)		CTCCTTGCCCACCCGCTCCTC	0.692													A|||	15	0.00299521	0.0	0.0072	5008	,	,		13239	0.0		0.005	False		,,,				2504	0.0051				p.V265A		Atlas-SNP	.											.	CASZ1	150	.	0			c.T794C						PASS	.	A	ALA/VAL,ALA/VAL	6,4396	11.4+/-27.6	0,6,2195	28	33	31		794,794	1.3	0	1	dbSNP_134	31	84,8516	48.1+/-107.5	0,84,4216	no	missense,missense	CASZ1	NM_001079843.1,NM_017766.3	64,64	0,90,6411	GG,GA,AA		0.9767,0.1363,0.6922	benign,benign	265/1760,265/1167	10720305	90,12912	2201	4300	6501	SO:0001583	missense	54897	exon6			TTGCCCACCCGCT	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.794T>C	1.37:g.10720305A>G	ENSP00000366221:p.Val265Ala	31	0	0		23	11	0.478261	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	37	CCDS41246.1	8	0.003663003663003663	0	0.0	4	0.011049723756906077	0	0.0	4	0.005277044854881266	A	0.003	-2.556568	0.00138	0.001363	0.009767	ENSG00000130940	ENST00000377022;ENST00000344008	.	.	.	4.38	1.3	0.21679	.	0.492755	0.20891	N	0.083835	T	0.05502	0.0145	N	0.02539	-0.55	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	0.33803	-0.9854	9	0.02654	T	1	-4.3668	3.9612	0.09412	0.4216:0.0:0.4186:0.1597	.	289;265;265;265	B7Z1S3;B3KRV8;Q86V15-2;Q86V15	.;.;.;CASZ1_HUMAN	A	265	.	ENSP00000339445:V265A	V	-	2	0	CASZ1	10642892	0.454000	0.25728	0.020000	0.16555	0.084000	0.17831	0.831000	0.27476	0.082000	0.17018	-0.589000	0.04120	GTG	A|0.994;G|0.006	0.006	strong		0.692	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766		G	10720305	A	G	10720305	3	3	24	1	0	0	0	0	1	0	0	0	2687	159	6	3	4553	3	CASZ1	1	10720305	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	208771	10720305	238530316	9	8226											
MTOR	2475	hgsc.bcm.edu	37	chr1	11188142	11188142	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctgcattgtgccgggctgtCgtggtagacttagaagccac	7	10	14	10	2	0	2	0	0	0	2	1	2	0	2	2	2	3	4	2	2	3	3	rs192740864	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:11188142C>T	ENST00000361445.4	-	43	6028	c.5952G>A	c.(5950-5952)acG>acA	p.T1984T	MTOR_ENST00000376838.1_Silent_p.T189T	NM_004958.3	NP_004949.1	P42345	MTOR_HUMAN	mechanistic target of rapamycin (serine/threonine kinase)	1984					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)	GCCGGGCTGTCGTGGTAGACT	0.522													C|||	5	0.000998403	0.0	0.0014	5008	,	,		18279	0.0		0.001	False		,,,				2504	0.0031				p.T1984T		Atlas-SNP	.											.	MTOR	327	.	0			c.G5952A						PASS	.	C		0,4406		0,0,2203	125	130	128		5952	-8.4	0.5	1		128	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MTOR	NM_004958.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		1984/2550	11188142	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2475	exon43			GGCTGTCGTGGTA	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.5952G>A	1.37:g.11188142C>T		108	0	0		98	48	0.489796	NM_004958	Q4LE76|Q5TER1|Q6LE87|Q96QG3|Q9Y4I3	Silent	SNP	ENST00000361445.4	37	CCDS127.1																																																																																			C|1.000;T|0.000	0.000	strong		0.522	MTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005558.1	NM_004958		T	11188142	C	T	11188142	2	4	24	1	0	0	0	0	0	0	0	1	9963	871	31	1		1	MTOR	1	11188142	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	467837	11188142	238062479	10	8227											
PLOD1	5351	hgsc.bcm.edu	37	chr1	12012748	12012748	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	agggccaggacagcgacagcGatcagctgttttacaccaag	12	6	12	11	2	1	0	1	0	0	0	1	3	1	1	2	2	4	2	2	2	2	2	rs188165334		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:12012748G>C	ENST00000196061.4	+	5	562	c.535G>C	c.(535-537)Gat>Cat	p.D179H	PLOD1_ENST00000376369.3_Missense_Mutation_p.D226H|PLOD1_ENST00000485046.1_3'UTR	NM_000302.3	NP_000293.2	Q02809	PLOD1_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1	179					cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|extracellular matrix organization (GO:0030198)|hydroxylysine biosynthetic process (GO:0046947)|oxidation-reduction process (GO:0055114)|response to hypoxia (GO:0001666)	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)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	29	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;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000809)|KIRC - Kidney renal clear cell carcinoma(229;0.00267)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)	Succinic acid(DB00139)|Vitamin C(DB00126)	CAGCGACAGCGATCAGCTGTT	0.622																																					p.D179H		Atlas-SNP	.											PLOD1_ENST00000429000,colon,carcinoma,0,2	PLOD1	75	2	0			c.G535C						PASS	.						97	89	92					1																	12012748		2203	4300	6503	SO:0001583	missense	5351	exon5			GACAGCGATCAGC	BC016657	CCDS142.1	1p36.22	2011-08-25	2011-08-24	2004-12-14	ENSG00000083444	ENSG00000083444	1.14.11.4		9081	protein-coding gene	gene with protein product	"lysyl hydroxlase 1"	153454	"procollagen-lysine 1, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase, Ehlers-Danlos syndrome type VI)"	LLH, PLOD		1577494	Standard	NM_000302		Approved	LH1	uc001atm.3	Q02809	OTTHUMG00000002393	ENST00000196061.4:c.535G>C	1.37:g.12012748G>C	ENSP00000196061:p.Asp179His	105	0	0		96	42	0.4375	NM_000302	B4DR87|Q96AV9|Q9H132	Missense_Mutation	SNP	ENST00000196061.4	37	CCDS142.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.629555	0.87660	.	.	ENSG00000083444	ENST00000358133;ENST00000376369;ENST00000429000;ENST00000196061	T;T;T	0.40756	1.02;1.02;1.02	4.61	4.61	0.57282	.	0.000000	0.85682	D	0.000000	T	0.71005	0.3289	M	0.90425	3.115	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.78807	-0.2059	10	0.87932	D	0	.	16.5981	0.84802	0.0:0.0:1.0:0.0	.	226;179	B4DR87;Q02809	.;PLOD1_HUMAN	H	179;226;179;179	ENSP00000365548:D226H;ENSP00000405372:D179H;ENSP00000196061:D179H	ENSP00000196061:D179H	D	+	1	0	PLOD1	11935335	1.000000	0.71417	0.945000	0.38365	0.821000	0.46438	9.585000	0.98223	2.380000	0.81148	0.555000	0.69702	GAT	G|1.000;T|0.000	.	alt		0.622	PLOD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006865.1	NM_000302		C	12012748	G	C	12012748	3	2	24	1	0	0	0	0	1	0	0	0	12110	1058	37	4	553	4	PLOD1	1	12012748	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	824606	12012748	237237873	11	8228											
SPEN	23013	hgsc.bcm.edu	37	chr1	16255799	16255799	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcaaaaaagcagcctgacGtgtcctctagagaggtcatt	12	11	9	9	1	3	2	2	1	1	1	4	3	4	2	2	1	2	1	2	1	4	3	rs115566585	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:16255799G>A	ENST00000375759.3	+	11	3268	c.3064G>A	c.(3064-3066)Gtg>Atg	p.V1022M		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1022					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)		GCAGCCTGACGTGTCCTCTAG	0.423													G|||	12	0.00239617	0.0	0.0115	5008	,	,		20147	0.0		0.004	False		,,,				2504	0.0				p.V1022M		Atlas-SNP	.											.	SPEN	374	.	0			c.G3064A						PASS	.	G	MET/VAL	2,4404	2.1+/-5.4	0,2,2201	46	53	51		3064	-5.8	0	1	dbSNP_132	51	31,8569	18.5+/-59.3	0,31,4269	yes	missense	SPEN	NM_015001.2	21	0,33,6470	AA,AG,GG		0.3605,0.0454,0.2537	benign	1022/3665	16255799	33,12973	2203	4300	6503	SO:0001583	missense	23013	exon11			CCTGACGTGTCCT		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.3064G>A	1.37:g.16255799G>A	ENSP00000364912:p.Val1022Met	99	0	0		129	57	0.44186	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	5	0.0022893772893772895	0	0.0	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	0.012	-1.676123	0.00751	4.54E-4	0.003605	ENSG00000065526	ENST00000375759	T	0.09445	2.98	5.13	-5.85	0.02311	.	.	.	.	.	T	0.02304	0.0071	N	0.03608	-0.345	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.41233	-0.9520	9	0.42905	T	0.14	6.4781	3.6799	0.08306	0.2371:0.3302:0.3421:0.0907	.	1022	Q96T58	MINT_HUMAN	M	1022	ENSP00000364912:V1022M	ENSP00000364912:V1022M	V	+	1	0	SPEN	16128386	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	-1.308000	0.02730	-0.807000	0.04393	-0.150000	0.13652	GTG	G|0.998;A|0.002	0.002	strong		0.423	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		A	16255799	G	A	16255799	3	1	24	1	0	0	0	0	1	0	0	0	15053	1145	40	1	3106	1	SPEN	1	16255799	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	4243051	16255799	232994822	12	8229											
TAS1R2	80834	hgsc.bcm.edu	37	chr1	19180860	19180860	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgttgaaggacaaggtggcGttcaggcagttgtcgcactc	8	10	15	8	2	1	1	1	1	0	0	3	2	1	2	0	4	0	5	0	4	2	3	rs528216046		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:19180860G>A	ENST00000375371.3	-	3	1125	c.1104C>T	c.(1102-1104)aaC>aaT	p.N368N	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	368					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)	ACAAGGTGGCGTTCAGGCAGT	0.622																																					p.N368N		Atlas-SNP	.											.	TAS1R2	134	.	0			c.C1104T						PASS	.						128	114	119					1																	19180860		2203	4300	6503	SO:0001819	synonymous_variant	80834	exon3			GGTGGCGTTCAGG		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.1104C>T	1.37:g.19180860G>A		170	0	0		155	76	0.490323	NM_152232	Q5TZ19	Silent	SNP	ENST00000375371.3	37	CCDS187.1																																																																																			.	.	none		0.622	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1			A	19180860	G	A	19180860	2	1	24	1	0	0	0	0	0	0	0	1	15578	1136	40	1		1	TAS1R2	1	19180860	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	2925061	19180860	230069761	13	8230											
USP48	84196	hgsc.bcm.edu	37	chr1	22084201	22084201	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcatcgatgttatgaaaactAttttcatctatttctcctaa	12	18	3	8	1	4	1	2	1	2	0	6	2	4	1	1	0	1	1	1	0	6	7	rs150521027	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:22084201A>G	ENST00000308271.9	-	2	858	c.210T>C	c.(208-210)aaT>aaC	p.N70N	USP48_ENST00000400301.1_Silent_p.N70N|USP48_ENST00000529637.1_Silent_p.N70N|USP48_ENST00000421625.2_Silent_p.N70N	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	70					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)		TATGAAAACTATTTTCATCTA	0.333													A|||	6	0.00119808	0.0	0.0	5008	,	,		19681	0.0		0.006	False		,,,				2504	0.0				p.N70N		Atlas-SNP	.											.	USP48	91	.	0			c.T210C						PASS	.	A	,	5,4401	9.9+/-24.2	0,5,2198	108	102	104		210,210	1.8	1	1	dbSNP_134	104	55,8545	35.9+/-90.5	0,55,4245	no	coding-synonymous,coding-synonymous	USP48	NM_001032730.1,NM_032236.5	,	0,60,6443	GG,GA,AA		0.6395,0.1135,0.4613	,	70/486,70/1036	22084201	60,12946	2203	4300	6503	SO:0001819	synonymous_variant	84196	exon2			AAAACTATTTTCA	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.210T>C	1.37:g.22084201A>G		120	0	0		89	47	0.52809	NM_001032730	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Silent	SNP	ENST00000308271.9	37	CCDS30623.1																																																																																			A|0.996;G|0.004	0.004	strong		0.333	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236		G	22084201	A	G	22084201	2	3	24	1	0	0	0	0	0	0	0	1	17094	446	16	3		3	USP48	1	22084201	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	2903341	22084201	227166420	14	8231											
SRRM1	10250	hgsc.bcm.edu	37	chr1	24979487	24979487	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaagaagaatgcctcctcCaccaaggcatagaaggagta	15	5	10	11	0	0	3	0	0	0	3	2	4	2	4	5	2	1	2	5	2	7	2	rs144082896	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24979487C>T	ENST00000323848.9	+	8	1319	c.1004C>T	c.(1003-1005)cCa>cTa	p.P335L	SRRM1_ENST00000479034.1_3'UTR|SRRM1_ENST00000374389.4_Missense_Mutation_p.P330L|SRRM1_ENST00000537199.1_Missense_Mutation_p.P204L|SRRM1_ENST00000447431.2_Missense_Mutation_p.P335L	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	335	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)		ATGCCTCCTCCACCAAGGCAT	0.448													C|||	7	0.00139776	0.0	0.0	5008	,	,		17867	0.0		0.004	False		,,,				2504	0.0031				p.P335L	Ovarian(68;897 1494 3282 17478)	Atlas-SNP	.											.	SRRM1	81	.	0			c.C1004T						PASS	.	C	LEU/PRO	3,4403	6.2+/-15.9	0,3,2200	58	55	56		1004	5.4	1	1	dbSNP_134	56	33,8567	23.4+/-69.3	0,33,4267	yes	missense	SRRM1	NM_005839.3	98	0,36,6467	TT,TC,CC		0.3837,0.0681,0.2768	possibly-damaging	335/905	24979487	36,12970	2203	4300	6503	SO:0001583	missense	10250	exon8			CTCCTCCACCAAG	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.1004C>T	1.37:g.24979487C>T	ENSP00000326261:p.Pro335Leu	232	0	0		237	100	0.421941	NM_005839	O60585|Q5VVN4	Missense_Mutation	SNP	ENST00000323848.9	37	CCDS255.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	17.19	3.326020	0.60743	6.81E-4	0.003837	ENSG00000133226	ENST00000323848;ENST00000447431;ENST00000374389;ENST00000537199	T;T;T;T	0.53206	0.84;0.86;0.86;0.63	5.36	5.36	0.76844	.	0.000000	0.64402	D	0.000009	T	0.50120	0.1597	L	0.54323	1.7	0.53688	D	0.999977	P;P	0.50528	0.936;0.895	P;B	0.44477	0.451;0.264	T	0.50338	-0.8840	10	0.39692	T	0.17	.	19.065	0.93106	0.0:1.0:0.0:0.0	.	335;335	E9PCT1;Q8IYB3	.;SRRM1_HUMAN	L	335;335;330;204	ENSP00000326261:P335L;ENSP00000391430:P335L;ENSP00000363510:P330L;ENSP00000441776:P204L	ENSP00000326261:P335L	P	+	2	0	SRRM1	24852074	0.997000	0.39634	1.000000	0.80357	0.982000	0.71751	3.240000	0.51368	2.500000	0.84329	0.585000	0.79938	CCA	C|0.997;T|0.003	0.003	strong		0.448	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839		T	24979487	C	T	24979487	3	4	24	1	0	0	0	0	1	0	0	0	15183	594	21	2	1034	2	SRRM1	1	24979487	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	2895286	24979487	224271134	15	8232											
SRRM1	10250	hgsc.bcm.edu	37	chr1	24995933	24995933	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacggcattcgccctcaccaCggcctcgagctcctcagacc	8	6	8	19	4	2	1	2	0	0	1	5	2	3	1	5	2	2	2	5	2	1	1	rs149689871		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:24995933C>T	ENST00000323848.9	+	14	2374	c.2059C>T	c.(2059-2061)Cgg>Tgg	p.R687W	SRRM1_ENST00000479034.1_3'UTR|SRRM1_ENST00000374389.4_Missense_Mutation_p.R696W|snoU13_ENST00000459464.1_RNA|SRRM1_ENST00000447431.2_Missense_Mutation_p.R699W	NM_005839.3	NP_005830.2	Q8IYB3	SRRM1_HUMAN	serine/arginine repetitive matrix 1	687	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)		GCCCTCACCACGGCCTCGAGC	0.582																																					p.R687W	Ovarian(68;897 1494 3282 17478)	Atlas-SNP	.											.	SRRM1	81	.	0			c.C2059T						PASS	.	C	TRP/ARG	0,4406		0,0,2203	73	68	70		2059	5.8	1	1	dbSNP_134	70	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SRRM1	NM_005839.3	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	687/905	24995933	1,13005	2203	4300	6503	SO:0001583	missense	10250	exon14			TCACCACGGCCTC	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.2059C>T	1.37:g.24995933C>T	ENSP00000326261:p.Arg687Trp	115	0	0		120	55	0.458333	NM_005839	O60585|Q5VVN4	Missense_Mutation	SNP	ENST00000323848.9	37	CCDS255.1	.	.	.	.	.	.	.	.	.	.	C	18.70	3.681006	0.68042	0.0	1.16E-4	ENSG00000133226	ENST00000323848;ENST00000447431;ENST00000374389	T;T;T	0.37752	1.18;1.18;1.18	5.75	5.75	0.90469	.	0.000000	0.56097	D	0.000035	T	0.43433	0.1247	N	0.08118	0	0.80722	D	1	D;D	0.76494	0.999;0.993	D;B	0.74348	0.983;0.265	T	0.55244	-0.8171	10	0.72032	D	0.01	-1.1771	19.9382	0.97149	0.0:1.0:0.0:0.0	.	699;687	E9PCT1;Q8IYB3	.;SRRM1_HUMAN	W	687;699;696	ENSP00000326261:R687W;ENSP00000391430:R699W;ENSP00000363510:R696W	ENSP00000326261:R687W	R	+	1	2	SRRM1	24868520	0.999000	0.42202	0.999000	0.59377	0.987000	0.75469	3.471000	0.53107	2.720000	0.93068	0.563000	0.77884	CGG	C|1.000;T|0.000	0.000	weak		0.582	SRRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009292.2	NM_005839		T	24995933	C	T	24995933	3	4	24	1	0	0	0	0	1	0	0	0	15183	527	19	1	2113	1	SRRM1	1	24995933	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	16446	24995933	224254688	16	8233											
UBXN11	91544	hgsc.bcm.edu	37	chr1	26608867	26608867	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actggggccgggaccgggacCgggactggggccgggaccgg	5	2	22	12	5	0	0	0	0	0	0	0	4	0	4	5	9	0	0	5	9	0	0	rs193142354		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:26608867C>A	ENST00000374222.1	-	16	1950	c.1486G>T	c.(1486-1488)Ggt>Tgt	p.G496C	UBXN11_ENST00000374217.2_Missense_Mutation_p.G463C|UBXN11_ENST00000357089.4_Missense_Mutation_p.G463C|UBXN11_ENST00000374221.3_Missense_Mutation_p.G496C|UBXN11_ENST00000314675.7_Missense_Mutation_p.G376C|UBXN11_ENST00000374223.1_Missense_Mutation_p.G253C			Q5T124	UBX11_HUMAN	UBX domain protein 11	496	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						ggaccgggaccgggactgggg	0.721																																					p.G496C		Atlas-SNP	.											UBXN11,colon,carcinoma,0,2	UBXN11	54	2	1	Deletion - In frame(1)	ovary(1)	c.G1486T						PASS	.						25	29	28					1																	26608867		1765	4016	5781	SO:0001583	missense	91544	exon16			CGGGACCGGGACT	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.1486G>T	1.37:g.26608867C>A	ENSP00000363339:p.Gly496Cys	24	0	0		36	8	0.222222	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Missense_Mutation	SNP	ENST00000374222.1	37	CCDS41288.1	261	0.11950549450549451	72	0.14634146341463414	35	0.09668508287292818	16	0.027972027972027972	138	0.1820580474934037	A	8.132	0.783217	0.16189	.	.	ENSG00000158062	ENST00000314675;ENST00000374223;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217	T;T;T;T;T;T	0.23950	1.88;1.96;2.3;2.24;2.24;2.3	.	.	.	.	.	.	.	.	T	0.00073	0.0002	N	0.22421	0.69	0.58432	P	2.9999999999752447E-6	D;D;D;D	0.76494	0.999;0.999;0.999;0.998	D;D;D;P	0.65323	0.934;0.934;0.934;0.861	T	0.12578	-1.0542	7	0.66056	D	0.02	.	6.1326	0.20213	0.0:0.6805:0.3194:0.0	.	463;458;376;496	Q5T124-2;Q5T124-4;Q5T124-3;Q5T124	.;.;.;UBX11_HUMAN	C	376;253;463;496;496;463	ENSP00000324721:G376C;ENSP00000363340:G253C;ENSP00000349601:G463C;ENSP00000363338:G496C;ENSP00000363339:G496C;ENSP00000363334:G463C	ENSP00000324721:G376C	G	-	1	0	UBXN11	26481454	0.000000	0.05858	0.121000	0.21740	0.128000	0.20619	-1.193000	0.03049	0.392000	0.25172	0.391000	0.25812	GGT	C|0.880;A|0.120	0.120	strong		0.721	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345		A	26608867	C	A	26608867	3	1	24	1	0	0	0	0	1	0	0	0	16928	652	23	4	80	4	UBXN11	1	26608867	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1612934	26608867	222641754	17	8234											
AK2	204	hgsc.bcm.edu	37	chr1	33478841	33478841	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaaggctgctaggatgcttgCgaacacgacatcgggggtct	9	8	15	9	3	1	0	0	0	1	0	2	4	1	1	0	4	4	3	0	4	3	2	rs201817938		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:33478841C>T	ENST00000373449.2	-	6	702	c.661G>A	c.(661-663)Gca>Aca	p.A221T	AK2_ENST00000480134.1_3'UTR|AK2_ENST00000467905.1_Missense_Mutation_p.A221T|AK2_ENST00000354858.6_Missense_Mutation_p.A221T|AK2_ENST00000491241.1_5'UTR|RP1-117O3.2_ENST00000427524.1_RNA|AK2_ENST00000548033.1_Missense_Mutation_p.A179T	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)				AGGATGCTTGCGAACACGACA	0.507																																					p.A221T		Atlas-SNP	.											.	AK2	27	.	0			c.G661A						PASS	.						161	147	152					1																	33478841		2203	4300	6503	SO:0001583	missense	204	exon6			TGCTTGCGAACAC	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.661G>A	1.37:g.33478841C>T	ENSP00000362548:p.Ala221Thr	157	0	0		147	54	0.367347	NM_013411		Missense_Mutation	SNP	ENST00000373449.2	37	CCDS373.1	.	.	.	.	.	.	.	.	.	.	C	14.94	2.685133	0.47991	.	.	ENSG00000004455	ENST00000373449;ENST00000548033;ENST00000467905;ENST00000354858	T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1	5.17	4.26	0.50523	.	0.000000	0.85682	D	0.000000	T	0.66257	0.2771	N	0.24115	0.695	0.80722	D	1	B;B;B;B	0.22480	0.006;0.07;0.004;0.003	B;B;B;B	0.19148	0.003;0.024;0.001;0.002	T	0.64433	-0.6409	10	0.51188	T	0.08	-11.7289	14.769	0.69662	0.0:0.9289:0.0:0.0711	.	213;179;221;221	P54819-5;F8VY04;P54819;P54819-2	.;.;KAD2_HUMAN;.	T	221;179;221;221	ENSP00000362548:A221T;ENSP00000449003:A179T;ENSP00000447082:A221T;ENSP00000346921:A221T	ENSP00000346921:A221T	A	-	1	0	AK2	33251428	1.000000	0.71417	0.957000	0.39632	0.542000	0.35054	6.063000	0.71162	1.499000	0.48617	0.563000	0.77884	GCA	.	.	weak		0.507	AK2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011884.1	NM_001625		T	33478841	C	T	33478841	3	4	24	1	0	0	0	0	1	0	0	0	440	768	27	1	71	1	AK2	1	33478841	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	6869974	33478841	215771780	18	8235											
MAP7D1	55700	hgsc.bcm.edu	37	chr1	36644874	36644874	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tccaaacagcgtctggaggaGatcatgaagaggactcggaa	14	6	13	8	2	2	3	1	1	1	2	4	7	3	6	1	4	2	0	1	4	3	0			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:36644874G>A	ENST00000373151.2	+	13	2358	c.2142G>A	c.(2140-2142)gaG>gaA	p.E714E	MAP7D1_ENST00000373150.4_Silent_p.E682E|MAP7D1_ENST00000316156.4_Silent_p.E677E|MAP7D1_ENST00000373148.4_Silent_p.E251E	NM_018067.3	NP_060537.3	Q3KQU3	MA7D1_HUMAN	MAP7 domain containing 1	714					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)				GTCTGGAGGAGATCATGAAGA	0.597																																					p.E714E		Atlas-SNP	.											.	MAP7D1	62	.	0			c.G2142A						PASS	.						31	35	34					1																	36644874		2203	4300	6503	SO:0001819	synonymous_variant	55700	exon13			GGAGGAGATCATG	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.2142G>A	1.37:g.36644874G>A		125	0	0		138	75	0.543478	NM_018067	D3DPS4|Q7L8J5|Q8N905|Q8TAK0|Q9HBQ2|Q9NW29|Q9ULN3	Silent	SNP	ENST00000373151.2	37	CCDS30673.1																																																																																			.	.	none		0.597	MAP7D1-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382095.1	NM_018067		A	36644874	G	A	36644874	2	1	24	1	0	0	0	0	0	0	0	1	9276	933	33	2		2	MAP7D1	1	36644874	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	3166033	36644874	212605747	19	8236											
EPHA10	284656	hgsc.bcm.edu	37	chr1	38184343	38184343	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggactcactgggcagtcaTctcggccacggcctccaggc	6	8	12	15	2	3	0	2	0	1	0	5	1	4	1	3	5	0	1	3	5	0	1	rs201769517	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:38184343T>C	ENST00000373048.4	-	16	2901	c.2902A>G	c.(2902-2904)Atg>Gtg	p.M968V	EPHA10_ENST00000540011.1_3'UTR|EPHA10_ENST00000330210.7_Missense_Mutation_p.M463V|EPHA10_ENST00000446149.2_5'UTR|EPHA10_ENST00000427468.2_Missense_Mutation_p.M968V	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	968	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				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)				TGGGCAGTCATCTCGGCCACG	0.662													T|||	4	0.000798722	0.0	0.0029	5008	,	,		17173	0.001		0.001	False		,,,				2504	0.0				p.M968V		Atlas-SNP	.											.	EPHA10	120	.	0			c.A2902G						PASS	.	T	VAL/MET	0,3998		0,0,1999	24	28	26		2902	3.7	1	1		26	4,8338		0,4,4167	no	missense	EPHA10	NM_001099439.1	21	0,4,6166	CC,CT,TT		0.048,0.0,0.0324	possibly-damaging	968/1009	38184343	4,12336	1999	4171	6170	SO:0001583	missense	284656	exon16			CAGTCATCTCGGC	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.2902A>G	1.37:g.38184343T>C	ENSP00000362139:p.Met968Val	138	0	0		149	83	0.557047	NM_001099439	A4FU89|J3KPB5|Q6NW42	Missense_Mutation	SNP	ENST00000373048.4	37	CCDS41305.1	.	.	.	.	.	.	.	.	.	.	T	13.81	2.348125	0.41599	0.0	4.8E-4	ENSG00000183317	ENST00000330210;ENST00000427468;ENST00000373048	T;T;T	0.52295	0.67;0.67;0.67	4.88	3.67	0.42095	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.000000	0.47455	D	0.000232	T	0.54919	0.1888	L	0.56199	1.76	0.80722	D	1	P	0.52170	0.951	P	0.57679	0.825	T	0.53187	-0.8474	10	0.38643	T	0.18	.	10.8344	0.46679	0.0:0.0:0.158:0.842	.	968	Q5JZY3	EPHAA_HUMAN	V	463;968;968	ENSP00000330379:M463V;ENSP00000397746:M968V;ENSP00000362139:M968V	ENSP00000330379:M463V	M	-	1	0	EPHA10	37956930	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	4.864000	0.62990	1.969000	0.57287	0.402000	0.26972	ATG	T|0.998;C|0.002	0.002	strong		0.662	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641		C	38184343	T	C	38184343	3	2	24	1	0	0	0	0	1	0	0	0	5168	1435	50	3	132	3	EPHA10	1	38184343	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	1539469	38184343	211066278	20	8237											
ZNF643	65243	hgsc.bcm.edu	37	chr1	40929087	40929087	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggagtaaaaccttatgaatgCagtcattgtgggaaagcctt	13	11	11	6	0	1	1	1	1	0	0	1	3	1	3	2	2	3	2	2	2	5	4	rs142494383	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:40929087C>T	ENST00000411995.2	+	6	1806	c.1431C>T	c.(1429-1431)tgC>tgT	p.C477C	ZFP69B_ENST00000361584.3_Silent_p.C375C|ZFP69B_ENST00000484445.1_3'UTR|RP1-228H13.5_ENST00000565390.1_RNA	NM_023070.2	NP_075558.2	Q9UJL9	ZF69B_HUMAN	ZFP69 zinc finger protein B	477					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)										CTTATGAATGCAGTCATTGTG	0.373													C|||	17	0.00339457	0.0023	0.0086	5008	,	,		21479	0.0		0.007	False		,,,				2504	0.001				p.C477C		Atlas-SNP	.											.	.	.	.	0			c.C1431T						PASS	.	C		9,4397		0,9,2194	92	89	90		1431	0.4	0.9	1	dbSNP_134	90	93,8507		0,93,4207	no	coding-synonymous	ZNF643	NM_023070.2		0,102,6401	TT,TC,CC		1.0814,0.2043,0.7843		477/535	40929087	102,12904	2203	4300	6503	SO:0001819	synonymous_variant	65243	exon5			TGAATGCAGTCAT	BC017498	CCDS452.1, CCDS452.2	1p34.2	2013-01-09	2012-11-27	2012-11-27	ENSG00000187801	ENSG00000187801		"Zinc fingers, C2H2-type", "-", "-", "-"	28053	protein-coding gene	gene with protein product			"zinc finger protein 643"	ZNF643			Standard	NM_023070		Approved	ZKSCAN23B, FLJ34293, ZSCAN54B	uc001cfn.2	Q9UJL9	OTTHUMG00000007302	ENST00000411995.2:c.1431C>T	1.37:g.40929087C>T		93	0	0		73	33	0.452055	NM_023070	Q5QPL4	Silent	SNP	ENST00000411995.2	37	CCDS452.2																																																																																			C|0.991;T|0.009	0.009	strong		0.373	ZFP69B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019078.2	NM_023070		T	40929087	C	T	40929087	2	4	24	1	0	0	0	0	0	0	0	1	18074	718	25	2		2	ZNF643	1	40929087	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	2744744	40929087	208321534	21	8238											
DEM1	64789	hgsc.bcm.edu	37	chr1	40981245	40981246	+	Frame_Shift_Ins	INS	-	-	G																															tggaggaggcttggaagtgcINScggacgtgtacctatgcaga																								rs150018949	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:40981245_40981246insG	ENST00000372703.1	+	2	2103_2104	c.1029_1030insG	c.(1030-1032)cggfs	p.R344fs	RP11-656D10.6_ENST00000437060.1_RNA|EXO5_ENST00000296380.4_Frame_Shift_Ins_p.R344fs|RP11-656D10.5_ENST00000453437.1_RNA|EXO5_ENST00000358527.2_Frame_Shift_Ins_p.R344fs			Q9H790	EXO5_HUMAN	exonuclease 5	344					DNA catabolic process, exonucleolytic (GO:0000738)|interstrand cross-link repair (GO:0036297)	cytosol (GO:0005829)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|single-stranded DNA 5'-3' exodeoxyribonuclease activity (GO:0045145)										CTTGGAAGTGCCGGACGTGTAC	0.54													-|-|G|insertion	42	0.00838658	0.0015	0.0144	5008	,	,		19343	0.0		0.0209	False		,,,				2504	0.0092				p.C343fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.1029_1030insG						PASS	.			17,4249		0,17,2116						0.4	0.4		dbSNP_134	52	186,8064		3,180,3942	no	frameshift	DEM1	NM_022774.1		3,197,6058	A1A1,A1R,RR		2.2545,0.3985,1.6219				203,12313				SO:0001589	frameshift_variant	64789	exon3			.	AK024797	CCDS453.1	1p34.2	2012-11-02	2012-10-30	2012-10-30	ENSG00000164002	ENSG00000164002			26115	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 176", "defects in morphology 1 homolog (S. cerevisiae)"	C1orf176, DEM1		23095756	Standard	NM_022774		Approved	FLJ21144	uc001cfp.3	Q9H790	OTTHUMG00000007305	Exception_encountered	1.37:g.40981245_40981246insG	ENSP00000361788:p.Arg344fs	114	0	.		89	29	0.326	NM_022774	D3DPV4|Q5SWM7|Q5SWM8|Q5SWM9|Q5SWN0|Q5SWN1|Q8WTW9	Frame_Shift_Ins	INS	ENST00000372703.1	37	CCDS453.1																																																																																			-|0.989;G|0.011	0.011	strong		0.54	EXO5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019087.1	NM_022774		G	40981246	-	G	40981245	7	5	24	1	0	1	1	0	0	0	0	0	4427	747	26	0	1031	0	DEM1	1	40981245	Frame_Shift_Ins	INS	-	TCGA-G8-6326-01A-11D-2210-10	52158	40981245	208269376	22	8239											
PTCH2	8643	hgsc.bcm.edu	37	chr1	45292926	45292926	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcctcagagccattgcggtaCgagtggcgggtgatgcgccc	6	8	15	12	4	1	2	1	1	0	1	2	3	2	2	3	3	4	1	3	3	1	2	rs111471526	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:45292926C>G	ENST00000372192.3	-	16	2557	c.2427G>C	c.(2425-2427)tcG>tcC	p.S809S	PTCH2_ENST00000447098.2_Silent_p.S809S	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2	809					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)					CATTGCGGTACGAGTGGCGGG	0.627									Basal Cell Nevus syndrome				C|||	34	0.00678914	0.0008	0.0086	5008	,	,		17933	0.0		0.0249	False		,,,				2504	0.002				p.S809S		Atlas-SNP	.											.	PTCH2	96	.	0			c.G2427C						PASS	.	C	,	10,4396	16.8+/-37.8	0,10,2193	69	77	74		2427,2427	-9.9	0.8	1	dbSNP_132	74	153,8447	74.8+/-137.4	3,147,4150	no	coding-synonymous,coding-synonymous	PTCH2	NM_001166292.1,NM_003738.4	,	3,157,6343	GG,GC,CC		1.7791,0.227,1.2533	,	809/1147,809/1204	45292926	163,12843	2203	4300	6503	SO:0001819	synonymous_variant	8643	exon16	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	GCGGTACGAGTGG	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.2427G>C	1.37:g.45292926C>G		87	0	0		92	37	0.402174	NM_001166292	O95341|O95856|Q53Z57|Q5QP87|Q6UX14	Silent	SNP	ENST00000372192.3	37	CCDS516.1																																																																																			C|0.988;G|0.012	0.012	strong		0.627	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023428.4	NM_003738		G	45292926	C	G	45292926	2	3	24	1	0	0	0	0	0	0	0	1	12743	523	19	4		4	PTCH2	1	45292926	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	4311681	45292926	203957695	23	8240											
GPBP1L1	60313	hgsc.bcm.edu	37	chr1	46105889	46105889	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttctaaatcataccttggaaGgaggtggtacaggcttagga	12	11	12	6	0	2	0	1	0	1	0	2	3	2	3	1	6	2	2	1	6	6	6			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:46105889G>A	ENST00000290795.3	-	7	1958	c.737C>T	c.(736-738)cCt>cTt	p.P246L	GPBP1L1_ENST00000355105.3_Missense_Mutation_p.P246L			Q9HC44	GPBL1_HUMAN	GC-rich promoter binding protein 1-like 1	246					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)					TACCTTGGAAGGAGGTGGTAC	0.408																																					p.P246L		Atlas-SNP	.											.	GPBP1L1	43	.	0			c.C737T						PASS	.						114	110	111					1																	46105889		2203	4300	6503	SO:0001583	missense	60313	exon8			TTGGAAGGAGGTG		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.737C>T	1.37:g.46105889G>A	ENSP00000290795:p.Pro246Leu	78	0	0		93	45	0.483871	NM_021639	D3DQ10|Q9H751	Missense_Mutation	SNP	ENST00000290795.3	37	CCDS528.1	.	.	.	.	.	.	.	.	.	.	G	19.85	3.903432	0.72754	.	.	ENSG00000159592	ENST00000290795;ENST00000355105	T;T	0.28069	1.63;1.63	5.85	4.94	0.65067	.	0.053159	0.85682	D	0.000000	T	0.33469	0.0864	M	0.66939	2.045	0.58432	D	0.999999	P	0.35155	0.487	B	0.30943	0.122	T	0.25882	-1.0119	10	0.87932	D	0	-24.6457	15.1693	0.72858	0.0678:0.0:0.9322:0.0	.	246	Q9HC44	GPBL1_HUMAN	L	246	ENSP00000290795:P246L;ENSP00000347224:P246L	ENSP00000290795:P246L	P	-	2	0	GPBP1L1	45878476	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	9.439000	0.97543	1.478000	0.48253	0.655000	0.94253	CCT	.	.	none		0.408	GPBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098375.1	NM_021639		A	46105889	G	A	46105889	3	1	24	1	0	0	0	0	1	0	0	0	6604	1000	35	2	711	2	GPBP1L1	1	46105889	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	812963	46105889	203144732	24	8241											
OSBPL9	114883	hgsc.bcm.edu	37	chr1	52250216	52250216	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atcttccacactaaacccttCtatgggggcaagaagcacag	13	8	8	12	0	2	1	0	0	2	1	3	1	3	1	2	2	2	2	2	2	5	4	rs144748323		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:52250216C>T	ENST00000428468.1	+	20	1793	c.1791C>T	c.(1789-1791)ttC>ttT	p.F597F	OSBPL9_ENST00000462759.1_Silent_p.F419F|OSBPL9_ENST00000453295.1_Silent_p.F580F|OSBPL9_ENST00000337809.4_Silent_p.F602F|OSBPL9_ENST00000371710.3_Silent_p.F615F|OSBPL9_ENST00000530544.1_Silent_p.F516F|OSBPL9_ENST00000435686.2_Silent_p.F432F|OSBPL9_ENST00000371714.1_Silent_p.F584F|OSBPL9_ENST00000531828.1_Silent_p.F432F|OSBPL9_ENST00000447887.1_Silent_p.F607F|OSBPL9_ENST00000486942.1_Silent_p.F419F|OSBPL9_ENST00000361556.5_Silent_p.F487F			Q96SU4	OSBL9_HUMAN	oxysterol binding protein-like 9	597					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						CTAAACCCTTCTATGGGGGCA	0.403																																					p.F607F		Atlas-SNP	.											.	OSBPL9	192	.	0			c.C1821T						PASS	.	T	,,,,,,	0,4406		0,0,2203	87	90	89		1791,1257,1257,1740,1461,1752,1821	2.7	1	1	dbSNP_134	89	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OSBPL9	NM_024586.5,NM_148904.3,NM_148905.3,NM_148906.2,NM_148907.2,NM_148908.3,NM_148909.3	,,,,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,,,,	597/737,419/559,419/559,580/720,487/627,584/724,607/747	52250216	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	114883	exon20			ACCCTTCTATGGG	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	ENST00000428468.1:c.1791C>T	1.37:g.52250216C>T		94	0	0		141	74	0.524823	NM_148909	B1AKJ8|B3KPQ4|D3DQ31|Q5TFC0|Q6IA67|Q86YQ3|Q8NB17|Q8TAS8|Q96SK4|Q9H9X2	Silent	SNP	ENST00000428468.1	37	CCDS41332.3																																																																																			C|1.000;T|0.000	0.000	weak		0.403	OSBPL9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022584.4			T	52250216	C	T	52250216	2	4	24	1	0	0	0	0	0	0	0	1	11293	912	32	2		2	OSBPL9	1	52250216	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	6144327	52250216	197000405	25	8242											
PCSK9	255738	hgsc.bcm.edu	37	chr1	55505651	55505651	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggtgctagccttgcgttcCgaggaggacggcctggccga	5	8	16	12	4	0	0	0	0	0	0	1	4	1	2	4	5	3	2	4	5	1	3	rs28385701	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:55505651C>T	ENST00000302118.5	+	1	431	c.141C>T	c.(139-141)tcC>tcT	p.S47S	PCSK9_ENST00000452118.2_Silent_p.S47S|PCSK9_ENST00000543384.1_5'Flank	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	47					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						CCTTGCGTTCCGAGGAGGACG	0.706													C|||	20	0.00399361	0.0	0.0043	5008	,	,		14828	0.0		0.0099	False		,,,				2504	0.0072				p.S47S	Pancreas(137;1454 1827 5886 22361 42375)	Atlas-SNP	.											.	PCSK9	76	.	0			c.C141T						PASS	.	C		8,4366		0,8,2179	35	28	30		141	-6.4	0	1	dbSNP_125	30	80,8460		0,80,4190	no	coding-synonymous	PCSK9	NM_174936.3		0,88,6369	TT,TC,CC		0.9368,0.1829,0.6814		47/693	55505651	88,12826	2187	4270	6457	SO:0001819	synonymous_variant	255738	exon1			GCGTTCCGAGGAG	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.141C>T	1.37:g.55505651C>T		73	0	0		112	68	0.607143	NM_174936	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Silent	SNP	ENST00000302118.5	37	CCDS603.1																																																																																			C|0.993;T|0.007	0.007	strong		0.706	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936		T	55505651	C	T	55505651	2	4	24	1	0	0	0	0	0	0	0	1	11615	639	23	1		1	PCSK9	1	55505651	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	3255435	55505651	193744970	26	8243											
C1orf168	199920	hgsc.bcm.edu	37	chr1	57257914	57257914	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tctgggaaggaagagtctggGctccttttgtttccagcttt	6	15	12	8	0	2	1	0	0	2	1	4	3	4	3	2	3	1	3	2	3	2	4			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:57257914G>A	ENST00000343433.6	-	2	652	c.572C>T	c.(571-573)gCc>gTc	p.A191V	C1orf168_ENST00000484327.1_5'UTR	NM_001004303.4	NP_001004303.3	Q5VWT5	CA168_HUMAN	chromosome 1 open reading frame 168	191										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						AAGAGTCTGGGCTCCTTTTGT	0.468																																					p.A191V		Atlas-SNP	.											C1orf168,caecum,carcinoma,+1,1	C1orf168	102	1	0			c.C572T						PASS	.						102	104	104					1																	57257914		2203	4300	6503	SO:0001583	missense	199920	exon2			GTCTGGGCTCCTT	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.572C>T	1.37:g.57257914G>A	ENSP00000345972:p.Ala191Val	80	0	0		95	46	0.484211	NM_001004303	Q63HM3|Q6ZUY6	Missense_Mutation	SNP	ENST00000343433.6	37	CCDS30729.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.949546	0.73787	.	.	ENSG00000187889	ENST00000343433	T	0.32988	1.43	4.55	1.41	0.22369	.	0.483859	0.18959	N	0.126441	T	0.18882	0.0453	L	0.32530	0.975	0.09310	N	1	P;B	0.37955	0.612;0.176	B;B	0.37692	0.256;0.067	T	0.09997	-1.0649	10	0.49607	T	0.09	0.0321	2.8636	0.05594	0.1004:0.1808:0.5323:0.1865	.	191;191	Q5VWT5-2;Q5VWT5	.;CA168_HUMAN	V	191	ENSP00000345972:A191V	ENSP00000345972:A191V	A	-	2	0	C1orf168	57030502	0.000000	0.05858	0.213000	0.23690	0.813000	0.45954	0.139000	0.16036	0.642000	0.30620	0.563000	0.77884	GCC	.	.	none		0.468	C1orf168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022751.2	NM_001004303		A	57257914	G	A	57257914	3	1	24	1	0	0	0	0	1	0	0	0	2014	1203	42	2	1690	2	C1orf168	1	57257914	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1752263	57257914	191992707	27	8244											
MYSM1	114803	hgsc.bcm.edu	37	chr1	59126851	59126851	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agacagcttactttctgcaaAcaagtcaggtcagaatcccg	13	9	8	11	1	3	2	2	0	1	2	4	2	4	2	1	1	4	2	1	1	4	2	rs376987710		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:59126851A>G	ENST00000472487.1	-	19	2358	c.2319T>C	c.(2317-2319)tgT>tgC	p.C773C	MYSM1_ENST00000493821.1_5'UTR	NM_001085487.2	NP_001078956.1	Q5VVJ2	MYSM1_HUMAN	Myb-like, SWIRM and MPN domains 1	773					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)					CTTTCTGCAAACAAGTCAGGT	0.373																																					p.C773C		Atlas-SNP	.											.	MYSM1	50	.	0			c.T2319C						PASS	.	A		0,3664		0,0,1832	94	88	90		2319	4.1	1	1		90	2,8168		0,2,4083	no	coding-synonymous	MYSM1	NM_001085487.2		0,2,5915	GG,GA,AA		0.0245,0.0,0.0169		773/829	59126851	2,11832	1832	4085	5917	SO:0001819	synonymous_variant	114803	exon19			CTGCAAACAAGTC	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.2319T>C	1.37:g.59126851A>G		54	0	0		59	27	0.457627	NM_001085487	A8KA54|B3KX65|Q68DD3|Q6AI53|Q7Z3G8|Q96PX3	Silent	SNP	ENST00000472487.1	37	CCDS41343.1																																																																																			.	.	none		0.373	MYSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026343.2	XM_055481		G	59126851	A	G	59126851	2	3	24	1	0	0	0	0	0	0	0	1	10110	41	2	3		3	MYSM1	1	59126851	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	1868937	59126851	190123770	28	8245											
ALG6	29929	hgsc.bcm.edu	37	chr1	63881583	63881583	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcctgcttcctgcatgcatAaaattaatacttcagccctc	11	12	5	13	0	1	0	1	0	0	0	3	0	2	0	3	0	6	3	3	0	4	5			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:63881583A>G	ENST00000371108.4	+	11	1247	c.942A>G	c.(940-942)atA>atG	p.I314M	ALG6_ENST00000263440.4_Missense_Mutation_p.I316M	NM_013339.3	NP_037471.2	Q9Y672	ALG6_HUMAN	ALG6, alpha-1,3-glucosyltransferase	314					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						CTGCATGCATAAAATTAATAC	0.294																																					p.I314M		Atlas-SNP	.											.	ALG6	33	.	0			c.A942G						PASS	.						63	67	66					1																	63881583		2202	4297	6499	SO:0001583	missense	29929	exon11			ATGCATAAAATTA	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.942A>G	1.37:g.63881583A>G	ENSP00000360149:p.Ile314Met	285	0	0		294	138	0.469388	NM_013339	B3KMU2|Q5SXR9|Q9H3I0	Missense_Mutation	SNP	ENST00000371108.4	37	CCDS30735.1	.	.	.	.	.	.	.	.	.	.	A	11.01	1.513855	0.27123	.	.	ENSG00000088035	ENST00000371108;ENST00000263440	D;D	0.85339	-1.97;-1.97	5.06	2.55	0.30701	.	0.276621	0.39615	N	0.001314	T	0.78065	0.4225	M	0.86502	2.82	0.41346	D	0.987339	B	0.13145	0.007	B	0.21360	0.034	T	0.76713	-0.2858	10	0.45353	T	0.12	-4.5375	8.1541	0.31158	0.566:0.3205:0.0:0.1136	.	316	A2A2G4	.	M	314;316	ENSP00000360149:I314M;ENSP00000263440:I316M	ENSP00000263440:I316M	I	+	3	3	ALG6	63654171	0.999000	0.42202	0.266000	0.24541	0.836000	0.47400	0.610000	0.24253	0.870000	0.35726	0.533000	0.62120	ATA	.	.	none		0.294	ALG6-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025330.2	NM_013339		G	63881583	A	G	63881583	3	3	24	1	0	0	0	0	1	0	0	0	522	352	13	3	980	3	ALG6	1	63881583	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	4754732	63881583	185369038	29	8246											
BCL10	8915	hgsc.bcm.edu	37	chr1	85733328	85733328	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtcattgtcgtgaaacagtAcgtgatcttaagggaagaaa	14	11	11	5	2	2	3	1	2	1	1	3	4	2	4	0	1	2	1	0	1	5	3			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:85733328A>G	ENST00000370580.1	-	3	1421	c.684T>C	c.(682-684)cgT>cgC	p.R228R		NM_003921.4	NP_003912.1	O95999	BCL10_HUMAN	B-cell CLL/lymphoma 10	228					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)		GTGAAACAGTACGTGATCTTA	0.363			T	IGH@	MALT																																p.R228R	NSCLC(34;993 1034 12176 32621 50182)	Atlas-SNP	.		Dom	yes		1	1p22	8915	B-cell CLL/lymphoma 10		L	.	BCL10	39	.	0			c.T684C						PASS	.						62	65	64					1																	85733328		2203	4300	6503	SO:0001819	synonymous_variant	8915	exon3			AACAGTACGTGAT	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.684T>C	1.37:g.85733328A>G		63	0	0		67	4	0.0597015	NM_003921	Q5VUF1	Silent	SNP	ENST00000370580.1	37	CCDS704.1																																																																																			.	.	none		0.363	BCL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027612.1	NM_003921		G	85733328	A	G	85733328	2	3	24	1	0	0	0	0	0	0	0	1	1362	378	14	3		3	BCL10	1	85733328	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	21851745	85733328	163517293	30	8247											
GBP6	163351	hgsc.bcm.edu	37	chr1	89835209	89835209	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccctggtccttctggacaccGaaggtctgggcgatgtggaa	7	9	14	11	2	2	0	0	0	2	0	3	4	3	2	3	5	0	0	3	5	2	1	rs75966734	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:89835209G>A	ENST00000370456.4	+	3	388	c.295G>A	c.(295-297)Gaa>Aaa	p.E99K	GBP6_ENST00000535065.1_Intron	NM_198460.2	NP_940862.2	Q6ZN66	GBP6_HUMAN	guanylate binding protein family, member 6	99	GB1/RHD3-type G.|GTPase domain (Globular). {ECO:0000250}.				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)		TCTGGACACCGAAGGTCTGGG	0.512													G|||	26	0.00519169	0.0015	0.0014	5008	,	,		20562	0.0		0.0199	False		,,,				2504	0.0031				p.E99K		Atlas-SNP	.											.	GBP6	87	.	0			c.G295A						PASS	.	G	LYS/GLU	7,4399	12.9+/-30.5	0,7,2196	81	75	77		295	4.6	0.9	1	dbSNP_132	77	74,8526	44.5+/-102.8	0,74,4226	yes	missense	GBP6	NM_198460.2	56	0,81,6422	AA,AG,GG		0.8605,0.1589,0.6228	probably-damaging	99/634	89835209	81,12925	2203	4300	6503	SO:0001583	missense	163351	exon3			GACACCGAAGGTC	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.295G>A	1.37:g.89835209G>A	ENSP00000359485:p.Glu99Lys	156	0	0		148	59	0.398649	NM_198460	A2RRM3|Q6ZN86|Q7Z3F0	Missense_Mutation	SNP	ENST00000370456.4	37	CCDS723.1	17	0.007783882783882784	1	0.0020325203252032522	0	0.0	0	0.0	16	0.021108179419525065	G	20.9	4.059633	0.76074	0.001589	0.008605	ENSG00000183347	ENST00000544311;ENST00000370456	T	0.64803	-0.12	4.55	4.55	0.56014	Guanylate-binding protein, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.85487	0.5708	H	0.98786	4.33	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91319	0.5080	10	0.87932	D	0	-32.7322	14.7834	0.69784	0.0:0.0:1.0:0.0	.	99	Q6ZN66	GBP6_HUMAN	K	70;99	ENSP00000359485:E99K	ENSP00000359485:E99K	E	+	1	0	GBP6	89607797	1.000000	0.71417	0.911000	0.35937	0.426000	0.31534	6.781000	0.75068	2.079000	0.62486	0.585000	0.79938	GAA	G|0.993;A|0.007	0.007	strong		0.512	GBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028001.1	NM_198460		A	89835209	G	A	89835209	3	1	24	1	0	0	0	0	1	0	0	0	6286	1059	37	1	301	1	GBP6	1	89835209	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	4101881	89835209	159415412	31	8248											
LRRC8B	23507	hgsc.bcm.edu	37	chr1	90049577	90049577	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atcccagaggtgaagctgccCtctgcagtctcacagctggt	8	9	11	13	0	2	2	1	1	2	1	4	2	3	2	2	2	4	3	2	2	1	0	rs140158391		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:90049577C>T	ENST00000330947.2	+	5	1728	c.1368C>T	c.(1366-1368)ccC>ccT	p.P456P	LRRC8B_ENST00000439853.1_Silent_p.P456P|RP5-1007M22.2_ENST00000443562.1_RNA|LRRC8B_ENST00000358200.4_Silent_p.P456P	NM_001134476.1	NP_001127948.1	Q6P9F7	LRC8B_HUMAN	leucine rich repeat containing 8 family, member B	456					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)		TGAAGCTGCCCTCTGCAGTCT	0.473																																					p.P456P		Atlas-SNP	.											.	LRRC8B	49	.	0			c.C1368T						PASS	.	C	,	4,4402	8.1+/-20.4	0,4,2199	52	52	52		1368,1368	0.8	1	1	dbSNP_134	52	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	LRRC8B	NM_001134476.1,NM_015350.2	,	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	,	456/804,456/804	90049577	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	23507	exon5			GCTGCCCTCTGCA	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.1368C>T	1.37:g.90049577C>T		50	0	0		64	4	0.0625	NM_015350	D3DT28|Q6UY21|Q8N106|Q92627	Silent	SNP	ENST00000330947.2	37	CCDS724.1																																																																																			C|1.000;T|0.000	0.000	weak		0.473	LRRC8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028008.1	NM_015350		T	90049577	C	T	90049577	2	4	24	1	0	0	0	0	0	0	0	1	9031	668	24	2		2	LRRC8B	1	90049577	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	214368	90049577	159201044	32	8249											
ZNF326	284695	hgsc.bcm.edu	37	chr1	90482944	90482944	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatattgaactgcatctggAaagttcttcacatcaggaaa	15	11	8	7	0	4	2	2	1	2	1	4	4	4	4	0	2	2	2	0	2	4	4	rs200399673		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:90482944A>G	ENST00000340281.4	+	8	1138	c.995A>G	c.(994-996)gAa>gGa	p.E332G	ZNF326_ENST00000370447.3_Missense_Mutation_p.E243G|ZNF326_ENST00000455342.2_Missense_Mutation_p.E126G	NM_182976.2	NP_892021.1	Q5BKZ1	ZN326_HUMAN	zinc finger protein 326	332					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)		CTGCATCTGGAAAGTTCTTCA	0.284																																					p.E332G		Atlas-SNP	.											.	ZNF326	60	.	0			c.A995G						PASS	.	A	GLY/GLU	0,4402		0,0,2201	61	62	62		995	5.5	1	1		62	2,8584		0,2,4291	yes	missense	ZNF326	NM_182976.2	98	0,2,6492	GG,GA,AA		0.0233,0.0,0.0154	benign	332/583	90482944	2,12986	2201	4293	6494	SO:0001583	missense	284695	exon8			ATCTGGAAAGTTC	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.995A>G	1.37:g.90482944A>G	ENSP00000340796:p.Glu332Gly	141	0	0		121	48	0.396694	NM_182976	A8MYX1|B4DLN0|B4E179|Q5VW93|Q5VW94|Q5VW96|Q5VW97|Q6NSA2|Q7Z638|Q7Z6C2	Missense_Mutation	SNP	ENST00000340281.4	37	CCDS727.1	.	.	.	.	.	.	.	.	.	.	A	13.17	2.156916	0.38119	0.0	2.33E-4	ENSG00000162664	ENST00000394590;ENST00000340281;ENST00000370447;ENST00000455342	T;T;T	0.46063	0.88;0.88;0.88	5.48	5.48	0.80851	Zinc finger, C2H2-like (1);	0.187115	0.46758	D	0.000280	T	0.17152	0.0412	L	0.29908	0.895	0.33497	D	0.589491	P;B	0.39094	0.659;0.449	B;B	0.36567	0.228;0.191	T	0.11108	-1.0601	10	0.41790	T	0.15	-16.081	11.5747	0.50854	0.8508:0.1492:0.0:0.0	.	332;332	A8MYX1;Q5BKZ1	.;ZN326_HUMAN	G	332;332;243;126	ENSP00000340796:E332G;ENSP00000359476:E243G;ENSP00000403470:E126G	ENSP00000340796:E332G	E	+	2	0	ZNF326	90255532	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.363000	0.52321	2.082000	0.62665	0.529000	0.55759	GAA	A|0.999;G|0.001	0.001	weak		0.284	ZNF326-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029428.2	NM_181781		G	90482944	A	G	90482944	3	3	24	1	0	0	0	0	1	0	0	0	17861	246	9	3	1029	3	ZNF326	1	90482944	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	433367	90482944	158767677	33	8250											
ZNF644	84146	hgsc.bcm.edu	37	chr1	91404352	91404352	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaactttcatcttctgtttcAtaactatctttcttttcagc	8	20	3	10	0	7	0	3	0	4	0	7	1	7	0	0	0	3	1	0	0	3	8	rs149082287	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:91404352A>G	ENST00000370440.1	-	3	2776	c.2559T>C	c.(2557-2559)taT>taC	p.Y853Y	ZNF644_ENST00000361321.5_Intron|ZNF644_ENST00000347275.5_Intron|ZNF644_ENST00000467231.1_Intron|ZNF644_ENST00000337393.5_Silent_p.Y853Y			Q9H582	ZN644_HUMAN	zinc finger protein 644	853					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)		CTTCTGTTTCATAACTATCTT	0.363																																					p.Y853Y		Atlas-SNP	.											.	ZNF644	120	.	0			c.T2559C						PASS	.	A	,,	0,4406		0,0,2203	77	80	79		,,2559	2	1	1	dbSNP_134	79	4,8594	3.7+/-12.6	0,4,4295	no	intron,intron,coding-synonymous	ZNF644	NM_016620.3,NM_032186.4,NM_201269.2	,,	0,4,6498	GG,GA,AA		0.0465,0.0,0.0308	,,	,,853/1328	91404352	4,13000	2203	4299	6502	SO:0001819	synonymous_variant	84146	exon3			TGTTTCATAACTA	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.2559T>C	1.37:g.91404352A>G		88	0	0		82	42	0.512195	NM_201269	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Silent	SNP	ENST00000370440.1	37	CCDS731.1																																																																																			A|0.999;G|0.001	0.001	strong		0.363	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186		G	91404352	A	G	91404352	2	3	24	1	0	0	0	0	0	0	0	1	18075	224	8	3		3	ZNF644	1	91404352	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	921408	91404352	157846269	34	8251											
CELSR2	1952	hgsc.bcm.edu	37	chr1	109811522	109811522	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tcatctccgtagtgcgcttgGacaaagggaactttgctggg	8	11	13	9	2	2	0	1	0	1	0	3	2	2	2	1	3	3	3	1	3	3	3	rs148006855	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:109811522G>A	ENST00000271332.3	+	19	6584	c.6523G>A	c.(6523-6525)Gac>Aac	p.D2175N		NM_001408.2	NP_001399.1	Q9HCU4	CELR2_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 2	2175					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)		AGTGCGCTTGGACAAAGGGAA	0.622													G|||	25	0.00499201	0.0	0.0	5008	,	,		19345	0.0		0.002	False		,,,				2504	0.0235				p.D2175N	NSCLC(158;1285 2011 34800 34852 42084)	Atlas-SNP	.											CELSR2,NS,neuroblastoma,-2,1	CELSR2	228	1	0			c.G6523A						PASS	.	G	ASN/ASP	2,4404	4.2+/-10.8	0,2,2201	71	76	74		6523	4.4	1	1	dbSNP_134	74	9,8591	7.1+/-27.0	0,9,4291	yes	missense	CELSR2	NM_001408.2	23	0,11,6492	AA,AG,GG		0.1047,0.0454,0.0846	benign	2175/2924	109811522	11,12995	2203	4300	6503	SO:0001583	missense	1952	exon19			CGCTTGGACAAAG	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.6523G>A	1.37:g.109811522G>A	ENSP00000271332:p.Asp2175Asn	157	0	0		168	68	0.404762	NM_001408	Q5T2Y7|Q92566	Missense_Mutation	SNP	ENST00000271332.3	37	CCDS796.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	13.84	2.356070	0.41700	4.54E-4	0.001047	ENSG00000143126	ENST00000271332	T	0.10860	2.83	4.36	4.36	0.52297	Domain of unknown function DUF3497 (1);	.	.	.	.	T	0.05410	0.0143	L	0.48642	1.525	0.34853	D	0.741849	B	0.26935	0.164	B	0.28709	0.093	T	0.09443	-1.0674	9	0.52906	T	0.07	.	10.689	0.45860	0.0898:0.0:0.9102:0.0	.	2175	Q9HCU4	CELR2_HUMAN	N	2175	ENSP00000271332:D2175N	ENSP00000271332:D2175N	D	+	1	0	CELSR2	109613045	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	3.180000	0.50895	2.430000	0.82344	0.462000	0.41574	GAC	G|0.999;A|0.001	0.001	strong		0.622	CELSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033200.1	NM_001408		A	109811522	G	A	109811522	3	1	24	1	0	0	0	0	1	0	0	0	3224	1174	41	2	6597	2	CELSR2	1	109811522	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	18407170	109811522	139439099	35	8252											
IGSF3	3321	hgsc.bcm.edu	37	chr1	117156603	117156603	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggcatattcgctgctggAgtgaagcatgaaatctcggc	9	10	13	9	2	1	2	0	2	1	0	3	3	1	3	0	3	2	4	0	3	3	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:117156603A>T	ENST00000369486.3	-	4	1381	c.616T>A	c.(616-618)Tcc>Acc	p.S206T	IGSF3_ENST00000318837.6_Missense_Mutation_p.S206T|IGSF3_ENST00000369483.1_Missense_Mutation_p.S206T	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	206	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)		TCGCTGCTGGAGTGAAGCATG	0.617																																					p.S206T		Atlas-SNP	.											.	IGSF3	294	.	0			c.T616A						PASS	.						56	57	57					1																	117156603		2203	4300	6503	SO:0001583	missense	3321	exon4			TGCTGGAGTGAAG	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.616T>A	1.37:g.117156603A>T	ENSP00000358498:p.Ser206Thr	161	0	0		174	89	0.511494	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	A	13.46	2.243549	0.39697	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.23552	1.9;1.9;1.9	5.02	5.02	0.67125	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.061231	0.64402	D	0.000002	T	0.13543	0.0328	L	0.27053	0.805	0.42061	D	0.991163	B;P	0.36183	0.387;0.542	P;B	0.45660	0.489;0.388	T	0.05451	-1.0884	10	0.66056	D	0.02	-47.2567	7.3497	0.26684	0.9046:0.0:0.0954:0.0	.	206;206	O75054;A6NJZ6	IGSF3_HUMAN;.	T	206	ENSP00000358498:S206T;ENSP00000358495:S206T;ENSP00000321184:S206T	ENSP00000321184:S206T	S	-	1	0	IGSF3	116958126	1.000000	0.71417	1.000000	0.80357	0.616000	0.37450	3.342000	0.52159	2.101000	0.63845	0.528000	0.53228	TCC	.	.	none		0.617	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542		T	117156603	A	T	117156603	3	4	24	1	0	0	0	0	1	0	0	0	7610	304	11	5	3064	5	IGSF3	1	117156603	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	7345081	117156603	132094018	36	8253											
HSD3B2	3284	hgsc.bcm.edu	37	chr1	119964933	119964933	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctatgataaccttaattacaTcctgagcaaagagtttggcc	13	12	7	9	0	0	3	0	2	0	1	1	3	1	3	3	1	3	2	3	1	5	5	rs75429891	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:119964933T>C	ENST00000543831.1	+	4	1058	c.809T>C	c.(808-810)aTc>aCc	p.I270T	HSD3B2_ENST00000369416.3_Missense_Mutation_p.I270T	NM_001166120.1	NP_001159592.1	P26439	3BHS2_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2	270					androgen biosynthetic process (GO:0006702)|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 (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial membrane (GO:0031966)|smooth endoplasmic reticulum membrane (GO:0030868)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|steroid delta-isomerase activity (GO:0004769)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(19)|ovary(2)|skin(1)	27	all_neural(166;0.187)	all_lung(203;1.06e-06)|Lung NSC(69;7.5e-06)|all_epithelial(167;0.000284)		Lung(183;0.015)|LUSC - Lung squamous cell carcinoma(189;0.0836)	Corticotropin(DB01285)|Medroxyprogesterone Acetate(DB00603)|Trilostane(DB01108)	CTTAATTACATCCTGAGCAAA	0.498													T|||	2	0.000399361	0.0	0.0	5008	,	,		20150	0.0		0.002	False		,,,				2504	0.0				p.I270T		Atlas-SNP	.											.	HSD3B2	48	.	0			c.T809C						PASS	.	T	THR/ILE,THR/ILE	1,4405		0,1,2202	75	79	77		809,809	-8	0	1	dbSNP_131	77	6,8594		0,6,4294	no	missense,missense	HSD3B2	NM_000198.3,NM_001166120.1	89,89	0,7,6496	CC,CT,TT		0.0698,0.0227,0.0538	benign,benign	270/373,270/373	119964933	7,12999	2203	4300	6503	SO:0001583	missense	3284	exon4			ATTACATCCTGAG	BC038419	CCDS902.1	1p12	2014-06-03			ENSG00000203859	ENSG00000203859	1.1.1.145, 5.3.3.1	"Short chain dehydrogenase/reductase superfamily / Extended SDR fold"	5218	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 11E, member 2"	613890				1363812, 19027726	Standard	NM_000198		Approved	SDR11E2	uc001eht.3	P26439	OTTHUMG00000012526	ENST00000543831.1:c.809T>C	1.37:g.119964933T>C	ENSP00000445122:p.Ile270Thr	154	0	0		170	72	0.423529	NM_001166120	A2RRA5|Q16010|Q53GD4|Q6AI10|Q6LDB9|Q99890|Q9UD08	Missense_Mutation	SNP	ENST00000543831.1	37	CCDS902.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	-	0.003	-2.490832	0.00161	2.27E-4	6.98E-4	ENSG00000203859	ENST00000543831;ENST00000369416	D;D	0.88124	-2.34;-2.34	3.98	-7.97	0.01139	3-beta hydroxysteroid dehydrogenase/isomerase (1);NAD(P)-binding domain (1);	0.703655	0.13486	N	0.384300	T	0.28101	0.0693	N	0.00496	-1.435	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.55976	-0.8055	9	.	.	.	-2.0251	7.6517	0.28352	0.592:0.2386:0.0:0.1694	.	270	P26439	3BHS2_HUMAN	T	270	ENSP00000445122:I270T;ENSP00000358424:I270T	.	I	+	2	0	HSD3B2	119766456	0.000000	0.05858	0.034000	0.17996	0.257000	0.26127	-0.688000	0.05150	-1.777000	0.01283	-0.782000	0.03352	ATC	T|1.000;C|0.000	0.000	strong		0.498	HSD3B2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034994.1	NM_000198		C	119964933	T	C	119964933	3	2	24	1	0	0	0	0	1	0	0	0	7400	1435	50	3	819	3	HSD3B2	1	119964933	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	2808330	119964933	129285688	37	8254											
BCL9	607	hgsc.bcm.edu	37	chr1	147091689	147091689	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aactctgaaatggaagggccGaatgtccccaaccctgcatc	12	7	9	13	1	1	1	0	1	1	0	3	3	2	2	4	2	3	1	4	2	5	0	rs61751617	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:147091689G>A	ENST00000234739.3	+	8	2468	c.1728G>A	c.(1726-1728)ccG>ccA	p.P576P		NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	576	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)					TGGAAGGGCCGAATGTCCCCA	0.567			T	"IGH@, IGL@"	B-ALL								G|||	75	0.014976	0.0045	0.0303	5008	,	,		19654	0.001		0.0348	False		,,,				2504	0.0123				p.P576P		Atlas-SNP	.		Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	BCL9_ENST00000234739,NS,carcinoma,+1,1	BCL9	150	1	0			c.G1728A						scavenged	.	G		24,4382	31.7+/-61.6	0,24,2179	82	89	86		1728	-10.8	0	1	dbSNP_129	86	333,8267	113.1+/-173.2	7,319,3974	no	coding-synonymous	BCL9	NM_004326.2		7,343,6153	AA,AG,GG		3.8721,0.5447,2.7449		576/1427	147091689	357,12649	2203	4300	6503	SO:0001819	synonymous_variant	607	exon8			AGGGCCGAATGTC	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.1728G>A	1.37:g.147091689G>A		68	1	0.0147059		84	49	0.583333	NM_004326	Q5T489	Silent	SNP	ENST00000234739.3	37	CCDS30833.1																																																																																			G|0.973;A|0.027	0.027	strong		0.567	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326		A	147091689	G	A	147091689	2	1	24	1	0	0	0	0	0	0	0	1	1381	1045	37	1		1	BCL9	1	147091689	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	27126756	147091689	102158932	38	8255											
NBPF14	25832	hgsc.bcm.edu	37	chr1	148009437	148009437	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcagtcagttcaagacaacCtgaaggagttgaatagcatc	14	9	10	8	0	3	3	3	2	0	1	4	4	3	4	1	1	2	3	1	1	5	3			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:148009437C>T	ENST00000369219.1	-	16	1886	c.1870G>A	c.(1870-1872)Ggt>Agt	p.G624S				Q5TI25	NBPFE_HUMAN	neuroblastoma breakpoint family, member 14	624	NBPF 7. {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)					TCAAGACAACCTGAAGGAGTT	0.483																																					p.G624S		Atlas-SNP	.											.	NBPF14	107	.	0			c.G1870A						PASS	.						128	260	221					1																	148009437		1703	4065	5768	SO:0001583	missense	25832	exon16			GACAACCTGAAGG	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.1870G>A	1.37:g.148009437C>T	ENSP00000358221:p.Gly624Ser	172	0	0		262	17	0.0648855	NM_015383	Q5TI23|Q8IX76|Q9UJI9	Missense_Mutation	SNP	ENST00000369219.1	37		.	.	.	.	.	.	.	.	.	.	c	1.168	-0.641686	0.03531	.	.	ENSG00000122497	ENST00000369219;ENST00000434489	T	0.05382	3.45	.	.	.	DUF1220 (2);	.	.	.	.	T	0.01124	0.0037	L	0.33792	1.035	0.09310	N	1	.	.	.	.	.	.	T	0.46247	-0.9205	4	0.06625	T	0.88	.	.	.	.	.	624	Q5TI25	NBPFE_HUMAN	S	624;214	ENSP00000358221:G624S	ENSP00000358221:G624S	G	-	1	0	NBPF14	146476061	0.982000	0.34865	.	.	.	.	-1.256000	0.02869	.	.	.	.	GGT	.	.	none		0.483	NBPF14-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_015383		T	148009437	C	T	148009437	3	4	24	1	0	0	0	0	1	0	0	0	10203	681	24	2	923	2	NBPF14	1	148009437	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	917748	148009437	101241184	39	8256											
NUP210L	91181	hgsc.bcm.edu	37	chr1	154115962	154115962	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	accatcagttccagtggcgaAtcatctacataaagttcccg	12	10	7	12	2	3	0	2	0	1	0	5	1	5	0	3	1	1	2	3	1	4	4			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:154115962A>G	ENST00000368559.3	-	3	503	c.432T>C	c.(430-432)gaT>gaC	p.D144D	NUP210L_ENST00000271854.3_Silent_p.D144D	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	144					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)			CCAGTGGCGAATCATCTACAT	0.393																																					p.D144D		Atlas-SNP	.											.	NUP210L	181	.	0			c.T432C						PASS	.						125	126	126					1																	154115962		2069	4212	6281	SO:0001819	synonymous_variant	91181	exon3			TGGCGAATCATCT	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.432T>C	1.37:g.154115962A>G		197	0	0		199	105	0.527638	NM_001159484	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Silent	SNP	ENST00000368559.3	37	CCDS41399.1																																																																																			.	.	none		0.393	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308		G	154115962	A	G	154115962	2	3	24	1	0	0	0	0	0	0	0	1	10770	98	4	3		3	NUP210L	1	154115962	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	6106525	154115962	95134659	40	8257											
TTC24	164118	hgsc.bcm.edu	37	chr1	156551248	156551248	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaagaaaagaaagtggctgcGgcaagaagccagcatccaag	17	3	13	8	1	0	3	0	0	0	3	1	4	1	3	2	2	3	3	2	2	7	0	rs192869620	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:156551248G>A	ENST00000368237.3	+	1	92	c.92G>A	c.(91-93)cGg>cAg	p.R31Q	TTC24_ENST00000368236.3_Missense_Mutation_p.R31Q			A2A3L6	TTC24_HUMAN	tetratricopeptide repeat domain 24	31										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)					AAGTGGCTGCGGCAAGAAGCC	0.572													G|||	26	0.00519169	0.0	0.0173	5008	,	,		17596	0.0		0.0129	False		,,,				2504	0.001				p.R31Q		Atlas-SNP	.											TTC24,NS,carcinoma,0,2	TTC24	46	2	0			c.G92A						PASS	.						26	27	27					1																	156551248		692	1591	2283	SO:0001583	missense	164118	exon2			GGCTGCGGCAAGA		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.92G>A	1.37:g.156551248G>A	ENSP00000357220:p.Arg31Gln	120	0	0		122	67	0.54918	NM_001105669	Q5T3H7	Missense_Mutation	SNP	ENST00000368237.3	37	CCDS53379.1	13	0.005952380952380952	0	0.0	7	0.019337016574585635	0	0.0	6	0.0079155672823219	G	2.638	-0.284842	0.05605	.	.	ENSG00000187862	ENST00000368236;ENST00000368237	T;T	0.76968	-1.06;-1.06	4.23	-1.72	0.08107	.	0.820698	0.10269	N	0.694981	T	0.19805	0.0476	N	0.02916	-0.46	0.09310	N	1	.	.	.	.	.	.	T	0.15321	-1.0441	8	0.11794	T	0.64	-1.6385	1.4317	0.02335	0.3363:0.1592:0.3497:0.1549	.	.	.	.	Q	31	ENSP00000357219:R31Q;ENSP00000357220:R31Q	ENSP00000357219:R31Q	R	+	2	0	TTC24	154817872	0.000000	0.05858	0.000000	0.03702	0.312000	0.27988	-0.224000	0.09164	-0.319000	0.08652	-0.672000	0.03802	CGG	G|0.994;A|0.006	0.006	strong		0.572	TTC24-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158547.1	XM_089384		A	156551248	G	A	156551248	3	1	24	1	0	0	0	0	1	0	0	0	16707	1116	39	1	94	1	TTC24	1	156551248	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	2435286	156551248	92699373	41	8258											
SPTA1	6708	hgsc.bcm.edu	37	chr1	158592781	158592781	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atttttttaaaccttctgtaGaggcagctgtttctccagca	9	16	7	9	0	2	1	0	0	2	1	3	1	2	1	2	1	3	5	2	1	3	7	rs75931146	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:158592781G>A	ENST00000368147.4	-	43	6292	c.6112C>T	c.(6112-6114)Cta>Tta	p.L2038L		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2038					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)					ACCTTCTGTAGAGGCAGCTGT	0.443													G|||	270	0.0539137	0.1407	0.0303	5008	,	,		18220	0.0		0.0229	False		,,,				2504	0.0409				p.L2038L		Atlas-SNP	.											.	SPTA1	720	.	0			c.C6112T						PASS	.	G		527,3225		26,475,1375	139	139	139		6112	2.9	0.3	1	dbSNP_132	139	125,8097		2,121,3988	no	coding-synonymous	SPTA1	NM_003126.2		28,596,5363	AA,AG,GG		1.5203,14.0458,5.4451		2038/2420	158592781	652,11322	1876	4111	5987	SO:0001819	synonymous_variant	6708	exon43			TCTGTAGAGGCAG	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.6112C>T	1.37:g.158592781G>A		162	0	0		167	70	0.419162	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	37	CCDS41423.1																																																																																			G|0.961;A|0.039	0.039	strong		0.443	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		A	158592781	G	A	158592781	2	1	24	1	0	0	0	0	0	0	0	1	15131	933	33	2		2	SPTA1	1	158592781	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	2041533	158592781	90657840	42	8259			1	39		3	3	121	N	G_C	3.500081e-06
SPTA1	6708	hgsc.bcm.edu	37	chr1	158592847	158592847	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttccagcaactgttcccagcGcttcagcagagcggcataac	10	8	9	14	2	1	1	1	0	0	1	3	1	3	1	2	1	6	5	2	1	2	4	rs78394850	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:158592847G>A	ENST00000368147.4	-	43	6226	c.6046C>T	c.(6046-6048)Cgc>Tgc	p.R2016C		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2016					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)					TGTTCCCAGCGCTTCAGCAGA	0.478													G|||	272	0.0543131	0.1407	0.0317	5008	,	,		16998	0.0		0.0239	False		,,,				2504	0.0409				p.R2016C		Atlas-SNP	.											SPTA1,colon,carcinoma,+1,3	SPTA1	720	3	0			c.C6046T						PASS	.	G	CYS/ARG	541,3327		26,489,1419	237	236	236		6046	4.8	0.6	1	dbSNP_132	236	131,8137		2,127,4005	yes	missense	SPTA1	NM_003126.2	180	28,616,5424	AA,AG,GG		1.5844,13.9866,5.5372	probably-damaging	2016/2420	158592847	672,11464	1934	4134	6068	SO:0001583	missense	6708	exon43			CCCAGCGCTTCAG	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.6046C>T	1.37:g.158592847G>A	ENSP00000357129:p.Arg2016Cys	206	0	0		204	86	0.421569	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	103	0.04716117216117216	75	0.1524390243902439	11	0.03038674033149171	0	0.0	17	0.022427440633245383	G	17.61	3.432615	0.62844	0.139866	0.015844	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.41758	0.99;0.99	4.78	4.78	0.61160	.	.	.	.	.	T	0.60728	0.2291	M	0.79693	2.465	0.58432	D	0.999993	D	0.89917	1.0	D	0.83275	0.996	T	0.64918	-0.6294	9	0.56958	D	0.05	.	16.5446	0.84426	0.0:0.0:1.0:0.0	.	2016	P02549	SPTA1_HUMAN	C	2016;2013	ENSP00000357130:R2016C;ENSP00000357129:R2013C	ENSP00000357129:R2013C	R	-	1	0	SPTA1	156859471	1.000000	0.71417	0.631000	0.29282	0.015000	0.08874	8.964000	0.93389	2.481000	0.83766	0.655000	0.94253	CGC	G|0.959;A|0.041	0.041	strong		0.478	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		A	158592847	G	A	158592847	3	1	24	1	0	0	0	0	1	0	0	0	15131	1087	38	1	1253	1	SPTA1	1	158592847	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	66	158592847	90657774	43	8260			1	39		3	3	121	N	G_C	3.500081e-06
SPTA1	6708	hgsc.bcm.edu	37	chr1	158592901	158592901	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttagactggttgtgttgagCagaaatcagtttgtccttca	9	16	10	6	0	2	3	2	1	0	2	3	3	3	3	1	1	1	4	1	1	2	6	rs77877855	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:158592901C>G	ENST00000368147.4	-	43	6172	c.5992G>C	c.(5992-5994)Gct>Cct	p.A1998P		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1998					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)					TTGTGTTGAGCAGAAATCAGT	0.507													C|||	270	0.0539137	0.1407	0.0303	5008	,	,		16400	0.0		0.0229	False		,,,				2504	0.0409				p.A1998P		Atlas-SNP	.											.	SPTA1	720	.	0			c.G5992C						PASS	.	C	PRO/ALA	550,3340		26,498,1421	323	325	324		5992	3.9	0.4	1	dbSNP_131	324	126,8146		2,122,4012	yes	missense	SPTA1	NM_003126.2	27	28,620,5433	GG,GC,CC		1.5232,14.1388,5.5583	probably-damaging	1998/2420	158592901	676,11486	1945	4136	6081	SO:0001583	missense	6708	exon43			GTTGAGCAGAAAT	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.5992G>C	1.37:g.158592901C>G	ENSP00000357129:p.Ala1998Pro	260	0	0		221	100	0.452489	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	101	0.04624542124542125	75	0.1524390243902439	10	0.027624309392265192	0	0.0	16	0.021108179419525065	C	15.33	2.800750	0.50315	0.141388	0.015232	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.53423	0.62;0.62	4.78	3.86	0.44501	.	.	.	.	.	T	0.54175	0.1842	M	0.72118	2.19	0.36867	D	0.888732	D	0.53462	0.96	P	0.62885	0.908	T	0.60944	-0.7162	9	0.54805	T	0.06	.	13.0889	0.59156	0.1622:0.8378:0.0:0.0	.	1998	P02549	SPTA1_HUMAN	P	1998;1995	ENSP00000357130:A1998P;ENSP00000357129:A1995P	ENSP00000357129:A1995P	A	-	1	0	SPTA1	156859525	0.996000	0.38824	0.362000	0.25862	0.025000	0.11179	3.441000	0.52893	1.203000	0.43233	0.655000	0.94253	GCT	C|0.961;G|0.039	0.039	strong		0.507	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		G	158592901	C	G	158592901	3	3	24	1	0	0	0	0	1	0	0	0	15131	710	25	4	1307	4	SPTA1	1	158592901	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	54	158592901	90657720	44	8261			1	39		3	3	121	N	G_C	3.500081e-06
SPTA1	6708	hgsc.bcm.edu	37	chr1	158604391	158604391	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagccaaagcattcttttcaTtgatccaagcttcctcttcc	9	14	4	14	0	3	1	1	1	2	0	6	1	6	1	4	0	3	2	4	0	2	6	rs16830483	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:158604391T>C	ENST00000368147.4	-	39	5687	c.5507A>G	c.(5506-5508)aAt>aGt	p.N1836S		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1836			N -> S (in dbSNP:rs16830483).		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)					ATTCTTTTCATTGATCCAAGC	0.423													T|||	270	0.0539137	0.1407	0.0303	5008	,	,		22090	0.0		0.0229	False		,,,				2504	0.0409				p.N1836S		Atlas-SNP	.											.	SPTA1	720	.	0			c.A5507G						PASS	.	T	SER/ASN	544,3370		27,490,1440	197	180	185		5507	1.4	0.1	1	dbSNP_123	185	125,8155		2,121,4017	yes	missense	SPTA1	NM_003126.2	46	29,611,5457	CC,CT,TT		1.5097,13.8988,5.4863	benign	1836/2420	158604391	669,11525	1957	4140	6097	SO:0001583	missense	6708	exon39			TTTTCATTGATCC	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.5507A>G	1.37:g.158604391T>C	ENSP00000357129:p.Asn1836Ser	134	0	0		135	68	0.503704	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	101	0.04624542124542125	75	0.1524390243902439	10	0.027624309392265192	0	0.0	16	0.021108179419525065	T	10.38	1.332942	0.24167	0.138988	0.015097	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.48836	0.8;0.8	5.64	1.39	0.22231	.	1.056520	0.07576	N	0.919371	T	0.05273	0.0140	N	0.03016	-0.435	0.19575	N	0.999963	B	0.09022	0.002	B	0.12156	0.007	T	0.36648	-0.9739	10	0.06365	T	0.9	.	3.7159	0.08438	0.0:0.4471:0.1822:0.3708	rs16830483;rs52794569;rs61613472;rs16830483	1836	P02549	SPTA1_HUMAN	S	1836	ENSP00000357130:N1836S;ENSP00000357129:N1836S	ENSP00000357129:N1836S	N	-	2	0	SPTA1	156871015	0.982000	0.34865	0.086000	0.20670	0.956000	0.61745	0.751000	0.26348	0.447000	0.26695	-0.248000	0.11899	AAT	T|0.947;C|0.053	0.053	strong		0.423	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		C	158604391	T	C	158604391	3	2	24	1	0	0	0	0	1	0	0	0	15131	1493	52	3	1808	3	SPTA1	1	158604391	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	11490	158604391	90646230	45	8262											
ITLN1	55600	hgsc.bcm.edu	37	chr1	160853312	160853312	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccttgaagtaagtattagcCtcatctagggaatacacagg	13	11	9	8	0	2	1	1	1	1	0	3	2	3	2	2	2	2	2	2	2	7	6	rs79969862	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:160853312C>T	ENST00000326245.3	-	3	178	c.63G>A	c.(61-63)gaG>gaA	p.E21E	ITLN1_ENST00000487531.1_5'Flank	NM_017625.2	NP_060095.2	Q8WWA0	ITLN1_HUMAN	intelectin 1 (galactofuranose binding)	21					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)			AAGTATTAGCCTCATCTAGGG	0.463													C|||	89	0.0177716	0.0461	0.0043	5008	,	,		18185	0.0		0.0	False		,,,				2504	0.0256				p.E21E		Atlas-SNP	.											.	ITLN1	45	.	0			c.G63A						PASS	.	C		182,4224	117.1+/-155.0	5,172,2026	159	145	150		63	-3	0	1	dbSNP_132	150	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ITLN1	NM_017625.2		5,173,6325	TT,TC,CC		0.0116,4.1307,1.407		21/314	160853312	183,12823	2203	4300	6503	SO:0001819	synonymous_variant	55600	exon3			ATTAGCCTCATCT	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.63G>A	1.37:g.160853312C>T		155	0	0		139	49	0.352518	NM_017625	Q5IWS4|Q5VYI4|Q6YDJ3|Q9NP67	Silent	SNP	ENST00000326245.3	37	CCDS1211.1																																																																																			C|0.984;T|0.016	0.016	strong		0.463	ITLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071462.1	NM_017625		T	160853312	C	T	160853312	2	4	24	1	0	0	0	0	0	0	0	1	7919	680	24	2		2	ITLN1	1	160853312	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	2248921	160853312	88397309	46	8263											
ITLN2	142683	hgsc.bcm.edu	37	chr1	160922421	160922421	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attactcaccacctgcactaTggcagcgttccttgatttct	8	14	6	13	1	2	1	1	1	1	0	3	1	3	1	3	1	3	3	3	1	2	5	rs145457015	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:160922421T>G	ENST00000368029.3	-	3	239	c.182A>C	c.(181-183)cAt>cCt	p.H61P	ITLN2_ENST00000494442.1_5'Flank|RP11-544M22.1_ENST00000356006.3_RNA	NM_080878.2	NP_543154.1	Q8WWU7	ITLN2_HUMAN	intelectin 2	61	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)			ACCTGCACTATGGCAGCGTTC	0.483													T|||	44	0.00878594	0.0	0.0029	5008	,	,		21066	0.0		0.0	False		,,,				2504	0.0429				p.H61P		Atlas-SNP	.											.	ITLN2	35	.	0			c.A182C						PASS	.	T	PRO/HIS	5,4401	9.9+/-24.2	0,5,2198	101	95	97		182	-7.9	0	1	dbSNP_134	97	17,8583	11.9+/-42.8	0,17,4283	yes	missense	ITLN2	NM_080878.2	77	0,22,6481	GG,GT,TT		0.1977,0.1135,0.1692	benign	61/326	160922421	22,12984	2203	4300	6503	SO:0001583	missense	142683	exon3			GCACTATGGCAGC	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.182A>C	1.37:g.160922421T>G	ENSP00000357008:p.His61Pro	67	0	0		67	30	0.447761	NM_080878	Q17RR2|Q5VYI0	Missense_Mutation	SNP	ENST00000368029.3	37	CCDS1212.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	T	3.839	-0.034106	0.07543	0.001135	0.001977	ENSG00000158764	ENST00000368029	D	0.91631	-2.88	3.95	-7.9	0.01169	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	1.289890	0.06467	N	0.730523	T	0.52549	0.1741	N	0.02181	-0.65	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.004	T	0.57189	-0.7854	10	0.13470	T	0.59	0.3882	10.3753	0.44079	0.0:0.1869:0.1496:0.6635	.	60;61	A6NI51;Q8WWU7	.;ITLN2_HUMAN	P	61	ENSP00000357008:H61P	ENSP00000357008:H61P	H	-	2	0	ITLN2	159189045	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-6.326000	0.00070	-2.805000	0.00350	-0.396000	0.06452	CAT	T|0.999;G|0.001	0.001	strong		0.483	ITLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071465.1	NM_080878		G	160922421	T	G	160922421	3	3	24	1	0	0	0	0	1	0	0	0	7920	1464	51	5	819	5	ITLN2	1	160922421	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	69109	160922421	88328200	47	8264											
FCRLA	84824	hgsc.bcm.edu	37	chr1	161680617	161680617	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagagcagctgccacacggaGgatgacttgactgatgcaag	12	6	14	9	1	0	4	0	3	0	1	0	7	0	6	1	2	4	3	1	2	1	1			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:161680617G>A	ENST00000236938.6	+	2	440	c.198G>A	c.(196-198)gaG>gaA	p.E66E	FCRLA_ENST00000367953.3_Silent_p.E55E|FCRLA_ENST00000470841.1_3'UTR|FCRLA_ENST00000540926.1_Silent_p.E55E|FCRLA_ENST00000349527.4_Silent_p.E49E|FCRLA_ENST00000350710.3_Intron|FCRLA_ENST00000546024.1_Silent_p.E66E|FCRLA_ENST00000309691.6_Silent_p.E49E|FCRLA_ENST00000540521.1_Intron|FCRLA_ENST00000367957.2_Intron|FCRLA_ENST00000367949.2_Silent_p.E66E|FCRLA_ENST00000294796.4_Intron|FCRLA_ENST00000367950.1_Silent_p.E26E|FCRLA_ENST00000367959.2_Silent_p.E72E	NM_032738.3	NP_116127.3	Q7L513	FCRLA_HUMAN	Fc receptor-like A	49					cell differentiation (GO:0030154)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)				breast(1)|kidney(12)|large_intestine(4)|lung(13)|prostate(1)|skin(2)|stomach(1)	34	all_cancers(52;2.55e-15)|all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00301)			GCCACACGGAGGATGACTTGA	0.557																																					p.E72E		Atlas-SNP	.											.	FCRLA	101	.	0			c.G216A						PASS	.						108	81	90					1																	161680617		2203	4300	6503	SO:0001819	synonymous_variant	84824	exon3			CACGGAGGATGAC	AF531423	CCDS30926.1, CCDS53415.1, CCDS53416.1, CCDS53417.1, CCDS53418.1, CCDS53419.1, CCDS53420.1	1q23.3	2014-01-28	2006-09-26	2006-09-26	ENSG00000132185	ENSG00000132185		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18504	protein-coding gene	gene with protein product		606891	"Fc receptor-like and mucin-like 1"	FCRLM1		11754007	Standard	NM_001184866		Approved	MGC4595, FCRLc2, FCRLb, FCRLc1, FCRLd, FCRLe, FCRL, FCRLa, FREB, FCRLX	uc001gbe.3	Q7L513	OTTHUMG00000034537	ENST00000236938.6:c.198G>A	1.37:g.161680617G>A		90	0	0		77	33	0.428571	NM_001184866	A0N0M1|A6NC03|A6NL20|F5H720|F8W743|G3V1J2|Q5VXA1|Q5VXA2|Q5VXA3|Q5VXA4|Q5VXB0|Q5VXB1|Q8NEW4|Q8WXH3|Q96PC6|Q96PJ0|Q96PJ1|Q96PJ2|Q96PJ4|Q9BR57	Silent	SNP	ENST00000236938.6	37	CCDS30926.1																																																																																			.	.	none		0.557	FCRLA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083574.1	NM_032738		A	161680617	G	A	161680617	2	1	24	1	0	0	0	0	0	0	0	1	5808	991	35	2		2	FCRLA	1	161680617	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	758196	161680617	87570004	48	8265											
F5	2153	hgsc.bcm.edu	37	chr1	169526019	169526019	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gttctgctccaggacctggcCgttgaaatgaatggagaata	11	10	12	8	1	1	3	0	2	1	1	2	5	2	4	3	3	1	3	3	3	4	3			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:169526019C>T	ENST00000367797.3	-	6	1018	c.817G>A	c.(817-819)Ggc>Agc	p.G273S	F5_ENST00000367796.3_Missense_Mutation_p.G273S|F5_ENST00000546081.1_Missense_Mutation_p.G136S	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	273	F5/8 type A 1.|Plastocyanin-like 2.				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)	AGGACCTGGCCGTTGAAATGA	0.507																																					p.G273S		Atlas-SNP	.											F5,colon,carcinoma,0,1	F5	301	1	0			c.G817A						PASS	.						139	112	121					1																	169526019		2203	4300	6503	SO:0001583	missense	2153	exon6			CCTGGCCGTTGAA	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.817G>A	1.37:g.169526019C>T	ENSP00000356771:p.Gly273Ser	196	0	0		208	95	0.456731	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	37	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	C	36	5.703228	0.96812	.	.	ENSG00000198734	ENST00000367797;ENST00000367796;ENST00000546081	D;D;D	0.99894	-7.58;-7.58;-7.58	6.07	6.07	0.98685	Cupredoxin (2);	0.090272	0.85682	D	0.000000	D	0.99921	0.9963	M	0.90369	3.11	0.44018	D	0.996733	D	0.89917	1.0	D	0.91635	0.999	D	0.96555	0.9411	9	0.87932	D	0	-22.8868	20.6439	0.99570	0.0:1.0:0.0:0.0	.	273	P12259	FA5_HUMAN	S	273;273;136	ENSP00000356771:G273S;ENSP00000356770:G273S;ENSP00000439664:G136S	ENSP00000356770:G273S	G	-	1	0	F5	167792643	1.000000	0.71417	0.983000	0.44433	0.973000	0.67179	7.456000	0.80751	2.890000	0.99128	0.650000	0.86243	GGC	.	.	none		0.507	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130		T	169526019	C	T	169526019	3	4	24	1	0	0	0	0	1	0	0	0	5350	652	23	1	5937	1	F5	1	169526019	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	7845402	169526019	79724602	49	8266											
TNFSF4	7292	hgsc.bcm.edu	37	chr1	173155860	173155860	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catccttctggtaatgaaggCtaatgttgacttcctgggag	9	13	11	8	0	1	2	0	2	1	0	3	3	3	3	2	3	0	3	2	3	3	5	rs146261831		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:173155860C>T	ENST00000281834.3	-	3	483	c.347G>A	c.(346-348)aGc>aAc	p.S116N	TNFSF4_ENST00000367718.1_Missense_Mutation_p.S66N|TNFSF4_ENST00000488053.1_5'Flank	NM_003326.3	NP_003317.1	P23510	TNFL4_HUMAN	tumor necrosis factor (ligand) superfamily, member 4	116					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						GTAATGAAGGCTAATGTTGAC	0.463																																					p.S116N		Atlas-SNP	.											.	TNFSF4	29	.	0			c.G347A						PASS	.	C	ASN/SER	0,4406		0,0,2203	98	101	100		347	-0.7	0	1	dbSNP_134	100	5,8595	4.3+/-15.6	0,5,4295	yes	missense	TNFSF4	NM_003326.3	46	0,5,6498	TT,TC,CC		0.0581,0.0,0.0384	benign	116/184	173155860	5,13001	2203	4300	6503	SO:0001583	missense	7292	exon3			TGAAGGCTAATGT	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.347G>A	1.37:g.173155860C>T	ENSP00000281834:p.Ser116Asn	205	0	0		178	79	0.44382	NM_003326	Q5JZA5|Q8IV74|Q9HCN9	Missense_Mutation	SNP	ENST00000281834.3	37	CCDS1306.1	.	.	.	.	.	.	.	.	.	.	C	11.24	1.581728	0.28180	0.0	5.81E-4	ENSG00000117586	ENST00000367718;ENST00000281834;ENST00000545292	D;D	0.94613	-3.47;-3.47	5.91	-0.7	0.11273	Tumour necrosis factor (2);Tumour necrosis factor-like (1);	1.170620	0.05958	N	0.640076	T	0.81503	0.4836	L	0.41236	1.265	0.09310	N	1	B;B	0.12630	0.001;0.006	B;B	0.13407	0.009;0.009	T	0.69639	-0.5091	10	0.30078	T	0.28	-0.9441	4.6924	0.12786	0.0:0.2516:0.3912:0.3572	.	116;66	P23510;Q8IV74	TNFL4_HUMAN;.	N	66;116;66	ENSP00000356691:S66N;ENSP00000281834:S116N	ENSP00000281834:S116N	S	-	2	0	TNFSF4	171422483	0.000000	0.05858	0.001000	0.08648	0.055000	0.15305	-1.057000	0.03486	0.221000	0.20879	0.655000	0.94253	AGC	C|1.000;T|0.000	0.000	weak		0.463	TNFSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084271.1			T	173155860	C	T	173155860	3	4	24	1	0	0	0	0	1	0	0	0	16325	797	28	2	208	2	TNFSF4	1	173155860	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	3629841	173155860	76094761	50	8267											
TPR	7175	hgsc.bcm.edu	37	chr1	186314809	186314809	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cattctgaacactagaaagtGttttcttcaattcagataac	14	14	5	8	0	4	3	2	1	2	2	4	3	4	3	0	0	2	1	0	0	5	7	rs200209324	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:186314809G>A	ENST00000367478.4	-	24	3412	c.3116C>T	c.(3115-3117)aCa>aTa	p.T1039I		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	1039					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)		ACTAGAAAGTGTTTTCTTCAA	0.348			T	NTRK1	papillary thyroid																																p.T1039I		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.C3116T						PASS	.	G	ILE/THR	2,3686		0,2,1842	107	94	99		3116	4.3	1	1		99	16,8154		0,16,4069	yes	missense	TPR	NM_003292.2	89	0,18,5911	AA,AG,GG		0.1958,0.0542,0.1518	benign	1039/2364	186314809	18,11840	1844	4085	5929	SO:0001583	missense	7175	exon24			GAAAGTGTTTTCT	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.3116C>T	1.37:g.186314809G>A	ENSP00000356448:p.Thr1039Ile	64	0	0		72	35	0.486111	NM_003292	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	37	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	G	15.03	2.713644	0.48517	5.42E-4	0.001958	ENSG00000047410	ENST00000367478	T	0.23348	1.91	5.31	4.34	0.51931	Prefoldin (1);Tetratricopeptide, MLP1/MLP2-like (1);	0.083000	0.85682	D	0.000000	T	0.16769	0.0403	N	0.08118	0	0.28533	N	0.912504	P	0.35821	0.523	B	0.42798	0.398	T	0.07252	-1.0782	10	0.56958	D	0.05	.	9.3043	0.37865	0.0:0.3079:0.566:0.1261	.	1039	P12270	TPR_HUMAN	I	1039	ENSP00000356448:T1039I	ENSP00000356448:T1039I	T	-	2	0	TPR	184581432	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.135000	0.50546	2.630000	0.89119	0.650000	0.86243	ACA	G|0.998;A|0.002	0.002	strong		0.348	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		A	186314809	G	A	186314809	3	1	24	1	0	0	0	0	1	0	0	0	16431	1377	48	2	4087	2	TPR	1	186314809	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	13158949	186314809	62935812	51	8268											
C1orf106	55765	hgsc.bcm.edu	37	chr1	200867572	200867572	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgacaccgacagtggcatcaTcctgcagtctggtgagtgtt	8	10	12	11	2	2	1	1	1	1	0	3	3	3	1	2	2	1	3	2	2	0	1	rs41269923	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:200867572T>A	ENST00000367342.4	+	2	499	c.299T>A	c.(298-300)aTc>aAc	p.I100N	C1orf106_ENST00000413687.2_Missense_Mutation_p.I15N	NM_018265.3	NP_060735.3	Q3KP66	CA106_HUMAN	chromosome 1 open reading frame 106	100										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(2)	21						AGTGGCATCATCCTGCAGTCT	0.617													T|||	22	0.00439297	0.0	0.0101	5008	,	,		18319	0.0		0.0149	False		,,,				2504	0.0				p.I114N		Atlas-SNP	.											.	C1orf106	59	.	0			c.T341A						PASS	.	T	ASN/ILE,ASN/ILE	7,4399	12.9+/-30.5	0,7,2196	124	106	112		44,299	5	1	1	dbSNP_127	112	99,8501	55.2+/-116.2	1,97,4202	yes	missense,missense	C1orf106	NM_001142569.2,NM_018265.3	149,149	1,104,6398	AA,AT,TT		1.1512,0.1589,0.815	probably-damaging,probably-damaging	15/579,100/664	200867572	106,12900	2203	4300	6503	SO:0001583	missense	55765	exon2			GCATCATCCTGCA	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.299T>A	1.37:g.200867572T>A	ENSP00000356311:p.Ile100Asn	69	0	0		83	49	0.590361	NM_018265	B4E1K9|E9PFY0|Q9NV65|Q9NVI0	Missense_Mutation	SNP	ENST00000367342.4	37		12	0.005494505494505495	0	0.0	4	0.011049723756906077	0	0.0	8	0.010554089709762533	T	20.4	3.991502	0.74703	0.001589	0.011512	ENSG00000163362	ENST00000532631;ENST00000451872;ENST00000367342;ENST00000413687	T;T	0.58358	0.34;0.47	4.97	4.97	0.65823	.	0.128098	0.50627	D	0.000103	T	0.59582	0.2204	L	0.60455	1.87	0.42617	D	0.993332	D	0.71674	0.998	D	0.79784	0.993	T	0.67245	-0.5719	10	0.59425	D	0.04	-13.828	12.1482	0.54036	0.0:0.0:0.0:1.0	rs41269923	100	Q3KP66	CA106_HUMAN	N	15;15;100;15	ENSP00000356311:I100N;ENSP00000392105:I15N	ENSP00000356311:I100N	I	+	2	0	C1orf106	199134195	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.875000	0.69660	1.884000	0.54569	0.482000	0.46254	ATC	T|0.993;A|0.007	0.007	strong		0.617	C1orf106-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000087057.2	NM_018265		A	200867572	T	A	200867572	3	1	24	1	0	0	0	0	1	0	0	0	1982	1435	50	5	305	5	C1orf106	1	200867572	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	14552763	200867572	48383049	52	8269											
TMEM9	252839	hgsc.bcm.edu	37	chr1	201115964	201115964	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actggcatgggctccaccacGtgcaggcagttgctacaaca	10	7	11	13	1	0	0	0	0	0	0	1	0	1	0	2	3	4	6	2	3	2	2	rs139286836	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:201115964G>A	ENST00000367330.1	-	3	687	c.171C>T	c.(169-171)caC>caT	p.H57H	TMEM9_ENST00000472411.1_5'Flank|TMEM9_ENST00000367332.1_Silent_p.H60H|TMEM9_ENST00000367334.5_Silent_p.H57H|TMEM9_ENST00000367333.2_Silent_p.H57H|TMEM9_ENST00000485839.2_Silent_p.H57H			Q9P0T7	TMEM9_HUMAN	transmembrane protein 9	57					transport (GO:0006810)	integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)				liver(1)|lung(1)|stomach(1)	3		Breast(1374;0.000301)				GCTCCACCACGTGCAGGCAGT	0.612													G|||	20	0.00399361	0.0	0.0144	5008	,	,		19530	0.0		0.005	False		,,,				2504	0.0051				p.H57H		Atlas-SNP	.											.	TMEM9	12	.	0			c.C171T						PASS	.	G		3,4403	6.2+/-15.9	0,3,2200	95	74	81		171	-1.5	1	1	dbSNP_134	81	83,8517	47.6+/-106.9	0,83,4217	no	coding-synonymous	TMEM9	NM_016456.3		0,86,6417	AA,AG,GG		0.9651,0.0681,0.6612		57/184	201115964	86,12920	2203	4300	6503	SO:0001819	synonymous_variant	252839	exon4			CACCACGTGCAGG		CCDS1408.1, CCDS73001.1	1q41	2008-02-05			ENSG00000116857	ENSG00000116857			18823	protein-coding gene	gene with protein product							Standard	NM_001288565		Approved	TMEM9A	uc001gvy.3	Q9P0T7	OTTHUMG00000035831	ENST00000367330.1:c.171C>T	1.37:g.201115964G>A		91	0	0		80	42	0.525	NM_016456	B1ALM6|Q96NQ9|Q9BQF5	Silent	SNP	ENST00000367330.1	37	CCDS1408.1																																																																																			G|0.994;A|0.006	0.006	strong		0.612	TMEM9-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000087160.1	NM_016456		A	201115964	G	A	201115964	2	1	24	1	0	0	0	0	0	0	0	1	16232	1136	40	1		1	TMEM9	1	201115964	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	248392	201115964	48134657	53	8270											
IGFN1	91156	hgsc.bcm.edu	37	chr1	201193964	201193964	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggtgctgaggaccctgcaggGgaaggaggttgcccacagct	8	6	17	10	0	0	1	0	1	0	0	0	4	0	4	2	6	4	4	2	6	1	1			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:201193964G>C	ENST00000335211.4	+	21	10578	c.10448G>C	c.(10447-10449)gGg>gCg	p.G3483A	IGFN1_ENST00000295591.8_Intron|RP11-567E21.3_ENST00000453155.1_RNA	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	1026						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						ACCCTGCAGGGGAAGGAGGTT	0.602																																					p.G3483A		Atlas-SNP	.											IGFN1_ENST00000335211,NS,carcinoma,+1,2	IGFN1	220	2	0			c.G10448C						PASS	.						68	54	59					1																	201193964		2203	4300	6503	SO:0001583	missense	91156	exon21			TGCAGGGGAAGGA	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.10448G>C	1.37:g.201193964G>C	ENSP00000334714:p.Gly3483Ala	145	0	0		123	58	0.471545	NM_001164586	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000335211.4	37	CCDS53455.1	.	.	.	.	.	.	.	.	.	.	G	17.30	3.355022	0.61293	.	.	ENSG00000163395	ENST00000335211	T	0.81247	-1.47	4.11	3.16	0.36331	.	0.071084	0.56097	N	0.000031	D	0.89619	0.6767	M	0.86343	2.81	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	D	0.90409	0.4408	10	0.87932	D	0	.	11.9403	0.52896	0.0:0.1757:0.8242:0.0	.	3483	F8WAI1	.	A	3483	ENSP00000334714:G3483A	ENSP00000334714:G3483A	G	+	2	0	IGFN1	199460587	1.000000	0.71417	0.112000	0.21494	0.893000	0.52053	5.952000	0.70282	0.878000	0.35920	0.491000	0.48974	GGG	.	.	none		0.602	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275		C	201193964	G	C	201193964	3	2	24	1	0	0	0	0	1	0	0	0	7599	1232	43	4	10526	4	IGFN1	1	201193964	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	78000	201193964	48056657	54	8271											
TMEM81	388730	hgsc.bcm.edu	37	chr1	205052998	205052998	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcccagagtcatactcctGagcatatttaaacttcacaa	13	12	5	11	0	2	2	2	1	0	1	4	2	4	2	2	0	3	1	2	0	5	5	rs369137007		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:205052998G>T	ENST00000367167.3	-	1	647	c.451C>A	c.(451-453)Cag>Aag	p.Q151K		NM_203376.1	NP_976310.1	Q6P7N7	TMM81_HUMAN	transmembrane protein 81	151	Ig-like.					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)			TCATACTCCTGAGCATATTTA	0.478																																					p.Q151K		Atlas-SNP	.											TMEM81,NS,carcinoma,+2,1	TMEM81	23	1	0			c.C451A						scavenged	.	G	LYS/GLN	0,4406		0,0,2203	77	84	82		451	2.8	0	1		82	1,8599	1.2+/-3.3	0,1,4299	no	missense	TMEM81	NM_203376.1	53	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	benign	151/256	205052998	1,13005	2203	4300	6503	SO:0001583	missense	388730	exon1			ACTCCTGAGCATA	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.451C>A	1.37:g.205052998G>T	ENSP00000356135:p.Gln151Lys	155	1	0.00645161		138	61	0.442029	NM_203376	Q6UVZ4	Missense_Mutation	SNP	ENST00000367167.3	37	CCDS1450.1	.	.	.	.	.	.	.	.	.	.	G	3.064	-0.192683	0.06259	0.0	1.16E-4	ENSG00000174529	ENST00000367167	T	0.42900	0.96	5.93	2.81	0.32909	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.586479	0.17141	N	0.185438	T	0.23572	0.0570	L	0.43152	1.355	0.09310	N	1	B	0.21225	0.053	B	0.13407	0.009	T	0.28459	-1.0043	10	0.05436	T	0.98	-10.0286	1.3267	0.02127	0.183:0.1403:0.435:0.2417	.	151	Q6P7N7	TMM81_HUMAN	K	151	ENSP00000356135:Q151K	ENSP00000356135:Q151K	Q	-	1	0	TMEM81	203319621	0.004000	0.15560	0.012000	0.15200	0.685000	0.39939	1.419000	0.34793	0.793000	0.33875	0.655000	0.94253	CAG	.	.	none		0.478	TMEM81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090076.1	NM_203376		T	205052998	G	T	205052998	3	4	24	1	0	0	0	0	1	0	0	0	16220	1299	45	4	320	4	TMEM81	1	205052998	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	3859034	205052998	44197623	55	8272											
DUSP10	11221	hgsc.bcm.edu	37	chr1	221912334	221912334	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gactcgaggactatgtgaagTggctgggagggcatcactcg	9	8	16	8	2	1	1	1	1	0	0	3	5	1	3	0	4	0	2	0	4	2	1	rs35552569	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:221912334T>G	ENST00000366899.3	-	2	991	c.753A>C	c.(751-753)ccA>ccC	p.P251P	DUSP10_ENST00000323825.3_Intron|DUSP10_ENST00000544095.1_5'Flank|DUSP10_ENST00000468085.1_5'Flank	NM_007207.4	NP_009138.1	Q9Y6W6	DUS10_HUMAN	dual specificity phosphatase 10	251	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)		CTATGTGAAGTGGCTGGGAGG	0.483													T|||	4	0.000798722	0.0	0.0	5008	,	,		21697	0.0		0.004	False		,,,				2504	0.0				p.P251P		Atlas-SNP	.											.	DUSP10	64	.	0			c.A753C						PASS	.	T	,	5,4401	9.9+/-24.2	0,5,2198	162	167	165		753,	-1.2	0.9	1	dbSNP_126	165	52,8548	32.8+/-85.7	1,50,4249	no	coding-synonymous,intron	DUSP10	NM_007207.4,NM_144729.2	,	1,55,6447	GG,GT,TT		0.6047,0.1135,0.4383	,	251/483,	221912334	57,12949	2203	4300	6503	SO:0001819	synonymous_variant	11221	exon2			GTGAAGTGGCTGG	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.753A>C	1.37:g.221912334T>G		230	0	0		235	102	0.434043	NM_007207	D3DTB4|Q6GSI4|Q9H9Z5	Silent	SNP	ENST00000366899.3	37	CCDS1528.1																																																																																			T|0.997;G|0.003	0.003	strong		0.483	DUSP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090716.1	NM_007207		G	221912334	T	G	221912334	2	3	24	1	0	0	0	0	0	0	0	1	4812	1683	59	5		5	DUSP10	1	221912334	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	16859336	221912334	27338287	56	8273											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228537608	228537608	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cagatgggaaagcagtgcagGtggacccccaccacatcctc	11	5	11	14	0	0	1	0	0	0	1	2	3	1	3	4	3	2	2	4	3	1	0	rs375733623		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:228537608G>A	ENST00000422127.1	+	76	18210	c.18166G>A	c.(18166-18168)Gtg>Atg	p.V6056M	OBSCN_ENST00000366709.4_Missense_Mutation_p.V3175M|OBSCN_ENST00000570156.2_Missense_Mutation_p.V7013M|OBSCN_ENST00000366707.4_Missense_Mutation_p.V3690M|OBSCN_ENST00000284548.11_Missense_Mutation_p.V6056M	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	6056	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)				AGCAGTGCAGGTGGACCCCCA	0.632																																					p.V7013M		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G21037A						PASS	.	G	MET/VAL,MET/VAL	0,4170		0,0,2085	32	39	36		18166,18166	5.4	1	1		36	1,8301		0,1,4150	no	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	21,21	0,1,6235	AA,AG,GG		0.012,0.0,0.0080	probably-damaging,probably-damaging	6056/7969,6056/6621	228537608	1,12471	2085	4151	6236	SO:0001583	missense	84033	exon87			GTGCAGGTGGACC	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.18166G>A	1.37:g.228537608G>A	ENSP00000409493:p.Val6056Met	78	0	0		106	59	0.556604	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	37	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.205199|5.205199	0.95033|0.95033	0.0|0.0	1.2E-4|1.2E-4	ENSG00000154358|ENSG00000154358	ENST00000441106|ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	.|T;T;T;T	.|0.67345	.|-0.26;-0.26;-0.26;-0.26	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);	.|0.168788	.|0.38837	.|N	.|0.001548	T|T	0.68686|0.68686	0.3028|0.3028	N|N	0.10945|0.10945	0.07|0.07	0.48571|0.48571	D|D	0.999676|0.999676	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.77004	.|0.989;0.98	T|T	0.72520|0.72520	-0.4268|-0.4268	5|10	.|0.39692	.|T	.|0.17	.|.	19.1538|19.1538	0.93502|0.93502	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|6056;6056	.|Q5VST9;Q5VST9-3	.|OBSCN_HUMAN;.	D|M	672|6056;6056;3690;3175	.|ENSP00000284548:V6056M;ENSP00000409493:V6056M;ENSP00000355668:V3690M;ENSP00000355670:V3175M	.|ENSP00000284548:V6056M	G|V	+|+	2|1	0|0	OBSCN|OBSCN	226604231|226604231	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.810000|0.810000	0.45777|0.45777	7.813000|7.813000	0.86123|0.86123	2.517000|2.517000	0.84864|0.84864	0.491000|0.491000	0.48974|0.48974	GGT|GTG	.	.	none		0.632	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228537608	G	A	228537608	3	1	24	1	0	0	0	0	1	0	0	0	10821	1261	44	2	18464	2	OBSCN	1	228537608	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	6625274	228537608	20713013	57	8274											
FAM89A	375061	hgsc.bcm.edu	37	chr1	231155682	231155682	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acaagtcccgaggagggcctCggtccctcctgtcgtgcagg	6	7	14	14	3	0	0	0	0	0	0	5	2	3	1	4	4	1	1	4	4	1	0	rs141463019	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:231155682C>T	ENST00000366654.4	-	2	516	c.482G>A	c.(481-483)cGa>cAa	p.R161Q	MIR1182_ENST00000408363.1_RNA|FAM89A_ENST00000494111.1_5'UTR	NM_198552.2	NP_940954.1	Q96GI7	FA89A_HUMAN	family with sequence similarity 89, member A	161										endometrium(1)|upper_aerodigestive_tract(1)	2	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				AGGAGGGCCTCGGTCCCTCCT	0.582													C|||	4	0.000798722	0.0015	0.0	5008	,	,		20019	0.0		0.002	False		,,,				2504	0.0				p.R161Q		Atlas-SNP	.											.	FAM89A	8	.	0			c.G482A						PASS	.	C	GLN/ARG	6,4400	11.4+/-27.6	0,6,2197	81	79	80		482	-0.1	0	1	dbSNP_134	80	16,8584	11.9+/-42.8	0,16,4284	yes	missense	FAM89A	NM_198552.2	43	0,22,6481	TT,TC,CC		0.186,0.1362,0.1692	benign	161/185	231155682	22,12984	2203	4300	6503	SO:0001583	missense	375061	exon2			GGGCCTCGGTCCC	BC009447	CCDS1590.1	1q42.2	2008-02-05	2005-09-13	2005-09-13	ENSG00000182118	ENSG00000182118			25057	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 153"	C1orf153		12477932	Standard	NM_198552		Approved	MGC15887	uc001hui.2	Q96GI7	OTTHUMG00000037960	ENST00000366654.4:c.482G>A	1.37:g.231155682C>T	ENSP00000355614:p.Arg161Gln	75	0	0		91	47	0.516484	NM_198552		Missense_Mutation	SNP	ENST00000366654.4	37	CCDS1590.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	17.03	3.285071	0.59867	0.001362	0.00186	ENSG00000182118	ENST00000366654	.	.	.	5.6	-0.0557	0.13808	.	1.086610	0.07184	N	0.854580	T	0.26159	0.0638	N	0.19112	0.55	0.09310	N	1	B	0.22346	0.068	B	0.12837	0.008	T	0.22871	-1.0204	9	0.19147	T	0.46	5.0E-4	9.7002	0.40182	0.0:0.4293:0.0:0.5707	.	161	Q96GI7	FA89A_HUMAN	Q	161	.	ENSP00000355614:R161Q	R	-	2	0	FAM89A	229222305	0.000000	0.05858	0.001000	0.08648	0.968000	0.65278	-0.990000	0.03732	0.163000	0.19507	0.453000	0.30009	CGA	C|0.999;T|0.001	0.001	strong		0.582	FAM89A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092652.1	NM_198552		T	231155682	C	T	231155682	3	4	24	1	0	0	0	0	1	0	0	0	5655	884	31	1	76	1	FAM89A	1	231155682	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	2618074	231155682	18094939	58	8275											
EGLN1	54583	hgsc.bcm.edu	37	chr1	231557164	231557164	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtacaggttcgccttctcCtggaacagcgatgagcgggc	7	8	15	11	3	1	1	0	1	1	0	3	3	1	2	2	4	4	2	2	4	2	3	rs61750991	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:231557164C>G	ENST00000366641.3	-	1	3626	c.471G>C	c.(469-471)caG>caC	p.Q157H	EGLN1_ENST00000476717.1_5'Flank	NM_022051.2	NP_071334.1			egl-9 family hypoxia-inducible factor 1											breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|urinary_tract(1)	16		Prostate(94;0.194)|Acute lymphoblastic leukemia(190;0.244)				TCGCCTTCTCCTGGAACAGCG	0.766													C|||	33	0.00658946	0.0	0.0029	5008	,	,		9987	0.001		0.0268	False		,,,				2504	0.0031				p.Q157H		Atlas-SNP	.											.	EGLN1	38	.	0			c.G471C						PASS	.	C	HIS/GLN	17,3709		0,17,1846	6	6	6		471	-2.4	0	1	dbSNP_129	6	157,7197		2,153,3522	yes	missense	EGLN1	NM_022051.2	24	2,170,5368	GG,GC,CC		2.1349,0.4563,1.5704	possibly-damaging	157/427	231557164	174,10906	1863	3677	5540	SO:0001583	missense	54583	exon1			CTTCTCCTGGAAC	AJ310543	CCDS1595.1	1q42.1	2013-08-21	2013-08-21	2001-08-24	ENSG00000135766	ENSG00000135766		"Zinc fingers, MYND-type"	1232	protein-coding gene	gene with protein product	"HIF prolyl hydroxylase 2"	606425	"EGL nine (C.elegans) homolog 1", "egl nine homolog 1 (C. elegans)"	C1orf12		11056053	Standard	NM_022051		Approved	SM-20, PHD2, ZMYND6, HIFPH2	uc001huv.2	Q9GZT9	OTTHUMG00000038027	ENST00000366641.3:c.471G>C	1.37:g.231557164C>G	ENSP00000355601:p.Gln157His	17	0	0		13	11	0.846154	NM_022051		Missense_Mutation	SNP	ENST00000366641.3	37	CCDS1595.1	27	0.012362637362637362	4	0.008130081300813009	2	0.0055248618784530384	0	0.0	21	0.027704485488126648	C	14.92	2.680157	0.47886	0.004563	0.021349	ENSG00000135766	ENST00000366641	D	0.86164	-2.08	4.06	-2.39	0.06602	.	.	.	.	.	T	0.49201	0.1543	N	0.14661	0.345	0.09310	N	1	B	0.30664	0.289	B	0.28916	0.096	T	0.53788	-0.8389	9	0.38643	T	0.18	0.2922	5.8621	0.18754	0.1263:0.41:0.3885:0.0752	rs61750991	157	Q9GZT9	EGLN1_HUMAN	H	157	ENSP00000355601:Q157H	ENSP00000355601:Q157H	Q	-	3	2	EGLN1	229623787	0.007000	0.16637	0.000000	0.03702	0.015000	0.08874	0.147000	0.16202	-0.278000	0.09180	0.557000	0.71058	CAG	C|0.988;G|0.012	0.012	strong		0.766	EGLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092879.1	NM_022051		G	231557164	C	G	231557164	3	3	24	1	0	0	0	0	1	0	0	0	4970	680	24	4	829	4	EGLN1	1	231557164	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	401482	231557164	17693457	59	8276											
SIPA1L2	57568	hgsc.bcm.edu	37	chr1	232596859	232596859	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagccaagctggcccagccCgttcctcctcagggtcattt	7	9	10	15	1	2	0	2	0	0	0	4	1	4	0	5	2	3	2	5	2	2	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:232596859C>T	ENST00000366630.1	-	9	3227	c.2869G>A	c.(2869-2871)Ggg>Agg	p.G957R	SIPA1L2_ENST00000308942.4_Missense_Mutation_p.G31R|SIPA1L2_ENST00000262861.4_Missense_Mutation_p.G957R			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	957	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)				TGGCCCAGCCCGTTCCTCCTC	0.562																																					p.G957R		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.G2869A						PASS	.						129	137	135					1																	232596859		2130	4269	6399	SO:0001583	missense	57568	exon8			CCAGCCCGTTCCT	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.2869G>A	1.37:g.232596859C>T	ENSP00000355589:p.Gly957Arg	186	0	0		173	90	0.520231	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	37	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.424498	0.83667	.	.	ENSG00000116991	ENST00000366630;ENST00000262861;ENST00000308942	T;T;T	0.28069	1.63;1.63;1.63	5.94	5.94	0.96194	PDZ/DHR/GLGF (3);	0.108992	0.64402	D	0.000005	T	0.55465	0.1922	L	0.59436	1.845	0.54753	D	0.999985	D;D	0.89917	1.0;0.996	D;D	0.80764	0.994;0.927	T	0.52132	-0.8616	10	0.66056	D	0.02	-32.9946	20.3594	0.98849	0.0:1.0:0.0:0.0	.	957;31	Q9P2F8;Q9P2F8-2	SI1L2_HUMAN;.	R	957;957;31	ENSP00000355589:G957R;ENSP00000262861:G957R;ENSP00000309102:G31R	ENSP00000262861:G957R	G	-	1	0	SIPA1L2	230663482	0.997000	0.39634	0.993000	0.49108	0.957000	0.61999	3.845000	0.55880	2.816000	0.96949	0.563000	0.77884	GGG	.	.	none		0.562	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839		T	232596859	C	T	232596859	3	4	24	1	0	0	0	0	1	0	0	0	14345	652	23	1	2355	1	SIPA1L2	1	232596859	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1039695	232596859	16653762	60	8277											
RYR2	6262	hgsc.bcm.edu	37	chr1	237947171	237947171	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gacttccacaaagcgatggaGagccataagcactacacgca	15	5	9	12	2	0	1	0	0	0	1	1	4	1	1	2	1	4	2	2	1	3	3	rs41267517		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:237947171G>A	ENST00000366574.2	+	90	12476	c.12159G>A	c.(12157-12159)gaG>gaA	p.E4053E	RYR2_ENST00000360064.6_Silent_p.E4059E|RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000542537.1_Silent_p.E4037E	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	4053					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.E4051D(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)			AAGCGATGGAGAGCCATAAGC	0.448													G|||	1	0.000199681	0.0	0.0	5008	,	,		19393	0.0		0.001	False		,,,				2504	0.0				p.E4053E		Atlas-SNP	.											RYR2,NS,carcinoma,0,1	RYR2	1273	1	1	Substitution - Missense(1)	lung(1)	c.G12159A						PASS	.	G		1,3925		0,1,1962	45	44	44		12159	4.2	1	1	dbSNP_127	44	15,8295		0,15,4140	no	coding-synonymous	RYR2	NM_001035.2		0,16,6102	AA,AG,GG		0.1805,0.0255,0.1308		4053/4968	237947171	16,12220	1963	4155	6118	SO:0001819	synonymous_variant	6262	exon90			GATGGAGAGCCAT	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.12159G>A	1.37:g.237947171G>A		94	0	0		110	44	0.4	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	37	CCDS55691.1																																																																																			G|0.999;A|0.001	0.001	weak		0.448	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237947171	G	A	237947171	2	1	24	1	0	0	0	0	0	0	0	1	13784	933	33	2		2	RYR2	1	237947171	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	5350312	237947171	11303450	61	8278											
FMN2	56776	hgsc.bcm.edu	37	chr1	240371502	240371502	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctacccggagcgggcataccCcctcctccccctcttcccgg	4	7	8	22	3	1	0	0	0	1	0	4	1	4	1	7	3	3	1	7	3	2	3	rs200984130		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:240371502C>T	ENST00000319653.9	+	5	3620	c.3390C>T	c.(3388-3390)ccC>ccT	p.P1130P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1130	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)			CGGGCATACCCCCTCCTCCCC	0.721																																					p.P1130P		Atlas-SNP	.											.	FMN2	451	.	0			c.C3390T						PASS	.						7	8	8					1																	240371502		2106	4124	6230	SO:0001819	synonymous_variant	56776	exon5			CATACCCCCTCCT	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.3390C>T	1.37:g.240371502C>T		71	0	0		82	6	0.0731707	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			C|0.999;T|0.001	0.001	weak		0.721	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		T	240371502	C	T	240371502	2	4	24	1	0	0	0	0	0	0	0	1	5958	610	22	2		2	FMN2	1	240371502	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	2424331	240371502	8879119	62	8279											
RGS7	6000	hgsc.bcm.edu	37	chr1	240975229	240975229	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgttttaccttaaattttcCgagctgaattctgactctag	9	17	7	8	1	2	2	0	2	2	0	3	3	3	2	2	0	2	2	2	0	5	7			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:240975229C>T	ENST00000407727.1	-	13	1070	c.1071G>A	c.(1069-1071)tcG>tcA	p.S357S	RGS7_ENST00000331110.7_Silent_p.S331S|RGS7_ENST00000348120.2_Silent_p.S304S|RGS7_ENST00000366563.1_Silent_p.S357S|RGS7_ENST00000401882.1_Silent_p.S304S|RGS7_ENST00000366565.1_Silent_p.S357S|RGS7_ENST00000366562.4_Silent_p.S357S|RGS7_ENST00000446183.2_Silent_p.S273S|RGS7_ENST00000366564.1_Silent_p.S357S			P49802	RGS7_HUMAN	regulator of G-protein signaling 7	357	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)			TTAAATTTTCCGAGCTGAATT	0.393																																					p.S357S		Atlas-SNP	.											RGS7_ENST00000366565,right_upper_lobe,carcinoma,-1,2	RGS7	308	2	0			c.G1071A						PASS	.						68	72	71					1																	240975229		2203	4299	6502	SO:0001819	synonymous_variant	6000	exon14			ATTTTCCGAGCTG	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.1071G>A	1.37:g.240975229C>T		69	0	0		76	30	0.394737	NM_002924	Q5T3H4|Q8TD66|Q8TD67|Q8WW09|Q9UNU7|Q9Y6B9	Silent	SNP	ENST00000407727.1	37																																																																																				.	.	none		0.393	RGS7-204	KNOWN	basic	protein_coding	protein_coding		NM_002924		T	240975229	C	T	240975229	2	4	24	1	0	0	0	0	0	0	0	1	13325	639	23	1		1	RGS7	1	240975229	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	603727	240975229	8275392	63	8280											
CHML	1122	hgsc.bcm.edu	37	chr1	241797791	241797791	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatttagcatttattctttgAccaaagtgatctataattgc	12	18	5	6	0	2	2	0	2	2	0	2	2	2	2	1	0	2	1	1	0	6	10	rs372360469		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr1:241797791A>G	ENST00000366553.1	-	1	1441	c.1278T>C	c.(1276-1278)ggT>ggC	p.G426G	OPN3_ENST00000331838.5_Intron|OPN3_ENST00000469376.1_Intron|OPN3_ENST00000366554.2_Intron	NM_001821.3	NP_001812.2	P26374	RAE2_HUMAN	choroideremia-like (Rab escort protein 2)	426					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)			TTATTCTTTGACCAAAGTGAT	0.363																																					p.G426G		Atlas-SNP	.											.	CHML	82	.	0			c.T1278C						PASS	.	A	,	0,4406		0,0,2203	75	79	78		1278,	-0.2	1	1		78	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous,intron	CHML,OPN3	NM_001821.3,NM_014322.2	,	0,1,6500	GG,GA,AA		0.0116,0.0,0.0077	,	426/657,	241797791	1,13001	2203	4298	6501	SO:0001819	synonymous_variant	1122	exon1			TCTTTGACCAAAG	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.1278T>C	1.37:g.241797791A>G		55	0	0		52	23	0.442308	NM_001821	B2RAB9|Q17RE0|Q9H1Y4	Silent	SNP	ENST00000366553.1	37	CCDS31073.1																																																																																			.	.	none		0.363	CHML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095712.1	NM_001821		G	241797791	A	G	241797791	2	3	24	1	0	0	0	0	0	0	0	1	3353	262	10	3		3	CHML	1	241797791	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	822562	241797791	7452830	64	8281											
FAM150B	285016	hgsc.bcm.edu	37	chr2	287646	287646	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggcccagggcgcagtcccGcccgaggagctgcaggccct	5	3	16	17	4	0	0	0	0	0	0	1	2	1	1	4	4	2	3	4	4	0	0			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:287646G>T	ENST00000403610.4	-	2	530	c.190C>A	c.(190-192)Cgg>Agg	p.R64R	FAM150B_ENST00000401503.1_5'Flank|FAM150B_ENST00000405290.1_5'Flank|AC079779.4_ENST00000427831.1_RNA|FAM150B_ENST00000344414.5_5'Flank	NM_001002919.2	NP_001002919.2	Q6UX46	F150B_HUMAN	family with sequence similarity 150, member B	64						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)		GCGCAGTCCCGCCCGAGGAGC	0.776																																					p.R64R		Atlas-SNP	.											.	FAM150B	12	.	0			c.C190A						PASS	.						1	1	1					2																	287646		772	1574	2346	SO:0001819	synonymous_variant	285016	exon2			AGTCCCGCCCGAG		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.190C>A	2.37:g.287646G>T		4	0	0		4	4	1	NM_001002919	B5MC76	Silent	SNP	ENST00000403610.4	37	CCDS46218.1																																																																																			.	.	none		0.776	FAM150B-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322394.2	NM_001002919		T	287646	G	T	287646	2	4	24	1	0	0	0	0	0	0	0	1	5462	1086	38	4		4	FAM150B	2	287646	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10		287646	242911727	65	8282											
C2orf43	60526	hgsc.bcm.edu	37	chr2	20974586	20974586	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttaccgggagctcagggactCgcttcagcatctgaagtgtg	8	10	13	10	2	3	1	2	1	1	0	4	3	3	3	1	2	3	3	1	2	2	2	rs114010802	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:20974586C>T	ENST00000237822.3	-	4	531	c.452G>A	c.(451-453)cGa>cAa	p.R151Q	C2orf43_ENST00000381090.3_Missense_Mutation_p.R151Q|C2orf43_ENST00000435420.2_Missense_Mutation_p.R103Q|C2orf43_ENST00000541941.1_Missense_Mutation_p.R21Q|C2orf43_ENST00000403006.2_Missense_Mutation_p.R21Q|C2orf43_ENST00000440866.2_Missense_Mutation_p.R151Q	NM_001282721.1|NM_021925.2	NP_001269650.1|NP_068744.1	Q9H6V9	CB043_HUMAN	chromosome 2 open reading frame 43	151										endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTCAGGGACTCGCTTCAGCAT	0.483													C|||	20	0.00399361	0.0008	0.0043	5008	,	,		19497	0.0		0.0159	False		,,,				2504	0.0				p.R151Q		Atlas-SNP	.											.	C2orf43	28	.	0			c.G452A						PASS	.	C	GLN/ARG	10,4396	16.8+/-37.8	0,10,2193	169	155	160		452	-5.1	0	2	dbSNP_132	160	71,8529	42.6+/-100.3	0,71,4229	yes	missense	C2orf43	NM_021925.2	43	0,81,6422	TT,TC,CC		0.8256,0.227,0.6228	probably-damaging	151/326	20974586	81,12925	2203	4300	6503	SO:0001583	missense	60526	exon4			GGGACTCGCTTCA	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.452G>A	2.37:g.20974586C>T	ENSP00000237822:p.Arg151Gln	203	0	0		202	102	0.504951	NM_021925	B7ZA47|B7ZAJ5|D6W530|E7ESN0|Q53T37|Q53T58	Missense_Mutation	SNP	ENST00000237822.3	37	CCDS1702.1	17	0.007783882783882784	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	12	0.0158311345646438	C	11.34	1.610511	0.28712	0.00227	0.008256	ENSG00000118961	ENST00000403006;ENST00000381090;ENST00000237822;ENST00000435420;ENST00000440866;ENST00000541941;ENST00000432947;ENST00000412261	T;T;T;T	0.71817	0.86;1.47;0.86;-0.6	5.73	-5.05	0.02955	.	0.589533	0.17377	N	0.176450	T	0.34832	0.0911	L	0.52759	1.655	0.24725	N	0.99312	P;P;B;B;P;P	0.45396	0.857;0.798;0.141;0.141;0.485;0.636	B;B;B;B;B;B	0.35859	0.176;0.179;0.013;0.013;0.212;0.206	T	0.45234	-0.9275	10	0.48119	T	0.1	-0.0561	5.7365	0.18069	0.3052:0.4799:0.0:0.2149	.	109;151;103;109;151;151	B4DS38;B4DRG3;B7ZAJ5;B4DWE2;Q9H6V9;B5MDU6	.;.;.;.;CB043_HUMAN;.	Q	21;151;151;103;151;21;21;103	ENSP00000384267:R21Q;ENSP00000388635:R103Q;ENSP00000440570:R21Q;ENSP00000396911:R21Q	ENSP00000237822:R151Q	R	-	2	0	C2orf43	20838067	0.000000	0.05858	0.001000	0.08648	0.035000	0.12851	-0.373000	0.07494	-1.306000	0.02324	-0.157000	0.13467	CGA	C|0.993;T|0.007	0.007	strong		0.483	C2orf43-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242861.1	NM_021925		T	20974586	C	T	20974586	3	4	24	1	0	0	0	0	1	0	0	0	2169	884	31	1	541	1	C2orf43	2	20974586	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	20686940	20974586	222224787	66	8283											
DTNB	1838	hgsc.bcm.edu	37	chr2	25754393	25754393	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgctcaggaaaaacaggaTgcgggggttctctcgtgggt	8	10	16	7	2	2	0	1	0	1	0	4	2	2	2	0	5	3	3	0	5	2	2	rs199811406		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:25754393T>C	ENST00000406818.3	-	9	1199	c.950A>G	c.(949-951)cAt>cGt	p.H317R	DTNB_ENST00000496972.2_Missense_Mutation_p.H260R|DTNB_ENST00000407186.1_Missense_Mutation_p.H317R|DTNB_ENST00000407038.3_Missense_Mutation_p.H317R|DTNB_ENST00000405222.1_Missense_Mutation_p.H317R|DTNB_ENST00000545439.1_Missense_Mutation_p.H113R|DTNB_ENST00000404103.3_Missense_Mutation_p.H317R|DTNB_ENST00000288642.8_Missense_Mutation_p.H317R|DTNB_ENST00000407661.3_Missense_Mutation_p.H317R	NM_001256303.1|NM_021907.4	NP_001243232.1|NP_068707.1	O60941	DTNB_HUMAN	dystrobrevin, beta	317						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)					AAAAACAGGATGCGGGGGTTC	0.463																																					p.H317R		Atlas-SNP	.											.	DTNB	43	.	0			c.A950G						PASS	.	T	ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS	2,3750		0,2,1874	142	141	141		950,950,950,950,950	5.2	1	2		141	2,8196		0,2,4097	yes	missense,missense,missense,missense,missense	DTNB	NM_021907.3,NM_033147.2,NM_033148.2,NM_183360.1,NM_183361.1	29,29,29,29,29	0,4,5971	CC,CT,TT		0.0244,0.0533,0.0335	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	317/628,317/598,317/568,317/610,317/561	25754393	4,11946	1876	4099	5975	SO:0001583	missense	1838	exon9			ACAGGATGCGGGG	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.950A>G	2.37:g.25754393T>C	ENSP00000384084:p.His317Arg	139	0	0		126	63	0.5	NM_021907	B7Z733|F5GZG4|G5E9F6|O43782|O60881|O75538|Q86VR4|Q96AW0|Q9UE14|Q9UE15|Q9UE16	Missense_Mutation	SNP	ENST00000406818.3	37	CCDS46237.1	.	.	.	.	.	.	.	.	.	.	T	14.61	2.586513	0.46110	5.33E-4	2.44E-4	ENSG00000138101	ENST00000496972;ENST00000406818;ENST00000404103;ENST00000407661;ENST00000407038;ENST00000405222;ENST00000407186;ENST00000288642;ENST00000545439;ENST00000535791	T;T;T;T;T;T;T;T;T	0.44083	2.28;2.28;2.28;2.28;2.31;2.31;2.31;2.28;0.93	5.15	5.15	0.70609	.	0.094216	0.64402	D	0.000001	T	0.46521	0.1397	M	0.80847	2.515	0.53005	D	0.99996	B;B;B;B;B;B;B;B;B;B;B;B	0.09022	0.001;0.001;0.002;0.002;0.001;0.001;0.0;0.001;0.0;0.002;0.002;0.001	B;B;B;B;B;B;B;B;B;B;B;B	0.17722	0.005;0.003;0.007;0.019;0.003;0.005;0.001;0.003;0.012;0.012;0.018;0.005	T	0.43523	-0.9386	10	0.34782	T	0.22	-16.4358	12.9424	0.58352	0.0:0.0:0.0:1.0	.	317;113;260;317;317;260;317;317;317;317;317;317	E7EVB6;B7Z202;F5GZG4;O60941-3;B7Z6A9;B7Z733;E9PEY4;Q96AW0;O60941-2;O60941-4;G5E9F6;O60941	.;.;.;.;.;.;.;.;.;.;.;DTNB_HUMAN	R	260;317;317;317;317;317;317;317;113;170	ENSP00000444463:H260R;ENSP00000384084:H317R;ENSP00000385482:H317R;ENSP00000385193:H317R;ENSP00000384767:H317R;ENSP00000384787:H317R;ENSP00000385784:H317R;ENSP00000288642:H317R;ENSP00000444961:H113R	ENSP00000288642:H317R	H	-	2	0	DTNB	25607897	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	5.025000	0.64097	1.930000	0.55929	0.383000	0.25322	CAT	.	.	weak		0.463	DTNB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325361.1	NM_033147		C	25754393	T	C	25754393	3	2	24	1	0	0	0	0	1	0	0	0	4791	1464	51	3	981	3	DTNB	2	25754393	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	4779807	25754393	217444980	67	8284											
ALK	238	hgsc.bcm.edu	37	chr2	29497967	29497967	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtgagctgaacccttacctGtagggtcaaagatgggggtc	9	10	14	8	0	1	3	1	2	0	1	2	3	1	3	2	3	3	2	2	3	4	2	rs35228363	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:29497967G>A	ENST00000389048.3	-	11	2945	c.2039C>T	c.(2038-2040)aCa>aTa	p.T680I	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	680			T -> I (in dbSNP:rs35228363). {ECO:0000269|PubMed:17344846}.		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)	ACCCTTACCTGTAGGGTCAAA	0.463			"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				G|||	50	0.00998403	0.0	0.0288	5008	,	,		19632	0.001		0.0268	False		,,,				2504	0.002				p.T680I		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	.	ALK	533	.	0			c.C2039T						PASS	.	G	ILE/THR	23,4383	29.0+/-57.7	0,23,2180	91	92	91		2039	5.2	1	2	dbSNP_126	91	250,8350	99.0+/-160.6	4,242,4054	yes	missense	ALK	NM_004304.4	89	4,265,6234	AA,AG,GG		2.907,0.522,2.099	benign	680/1621	29497967	273,12733	2203	4300	6503	SO:0001583	missense	238	exon11	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	TTACCTGTAGGGT	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.2039C>T	2.37:g.29497967G>A	ENSP00000373700:p.Thr680Ile	207	0	0		224	113	0.504464	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	ENST00000389048.3	37	CCDS33172.1	21	0.009615384615384616	0	0.0	9	0.024861878453038673	0	0.0	12	0.0158311345646438	G	14.36	2.511497	0.44660	0.00522	0.02907	ENSG00000171094	ENST00000389048	T	0.78246	-1.16	5.21	5.21	0.72293	.	0.304589	0.23175	U	0.051094	T	0.49677	0.1571	L	0.53249	1.67	0.80722	D	1	B	0.22983	0.078	B	0.15484	0.013	T	0.60905	-0.7170	9	.	.	.	.	14.2919	0.66284	0.0:0.0:1.0:0.0	rs35228363;rs61730441	680	Q9UM73	ALK_HUMAN	I	680	ENSP00000373700:T680I	.	T	-	2	0	ALK	29351471	1.000000	0.71417	1.000000	0.80357	0.443000	0.32047	4.489000	0.60309	2.433000	0.82419	0.561000	0.74099	ACA	G|0.984;A|0.016	0.016	strong		0.463	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		A	29497967	G	A	29497967	3	1	24	1	0	0	0	0	1	0	0	0	525	1377	48	2	2899	2	ALK	2	29497967	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	3743574	29497967	213701406	68	8285											
ALK	238	hgsc.bcm.edu	37	chr2	29543699	29543699	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacagtgtgccttgggtccaGccacagaagccatcttcaaa	11	8	10	12	0	2	1	1	0	1	1	3	2	3	1	4	1	3	0	4	1	2	2	rs56165377	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:29543699G>A	ENST00000389048.3	-	7	2370	c.1464C>T	c.(1462-1464)ggC>ggT	p.G488G	ALK_ENST00000498037.1_5'Flank|ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	488	MAM 2. {ECO:0000255|PROSITE- ProRule:PRU00128}.				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)	CTTGGGTCCAGCCACAGAAGC	0.532			"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				G|||	20	0.00399361	0.0	0.0202	5008	,	,		18892	0.0		0.006	False		,,,				2504	0.0				p.G488G		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	.	ALK	533	.	0			c.C1464T						PASS	.	G		6,4400	11.4+/-27.6	0,6,2197	189	167	175		1464	5.9	1	2	dbSNP_129	175	88,8512	49.4+/-109.1	0,88,4212	no	coding-synonymous	ALK	NM_004304.4		0,94,6409	AA,AG,GG		1.0233,0.1362,0.7227		488/1621	29543699	94,12912	2203	4300	6503	SO:0001819	synonymous_variant	238	exon7	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	GGTCCAGCCACAG	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.1464C>T	2.37:g.29543699G>A		136	0	0		149	85	0.57047	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			G|0.995;A|0.005	0.005	strong		0.532	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		A	29543699	G	A	29543699	2	1	24	1	0	0	0	0	0	0	0	1	525	958	34	2		2	ALK	2	29543699	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	45732	29543699	213655674	69	8286											
LTBP1	4052	hgsc.bcm.edu	37	chr2	33567971	33567971	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ttgtgacaatacagctggctCcttccgctgcctctgttatc	6	14	8	13	1	1	1	0	1	1	0	4	1	3	1	3	1	3	4	3	1	3	4	rs61751742	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:33567971C>T	ENST00000404816.2	+	25	4150	c.3797C>T	c.(3796-3798)tCc>tTc	p.S1266F	LTBP1_ENST00000402934.1_Missense_Mutation_p.S887F|LTBP1_ENST00000404525.1_Missense_Mutation_p.S887F|LTBP1_ENST00000390003.4_Missense_Mutation_p.S941F|LTBP1_ENST00000418533.2_Intron|LTBP1_ENST00000354476.3_Missense_Mutation_p.S1267F|LTBP1_ENST00000407925.1_Missense_Mutation_p.S940F|LTBP1_ENST00000272273.5_Intron			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1266	EGF-like 13; 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)				ACAGCTGGCTCCTTCCGCTGC	0.453													C|||	20	0.00399361	0.0	0.0072	5008	,	,		17041	0.0		0.0129	False		,,,				2504	0.002				p.S1266F		Atlas-SNP	.											LTBP1_ENST00000407925,NS,carcinoma,-1,2	LTBP1	317	2	0			c.C3797T						PASS	.	C	PHE/SER,,PHE/SER,,PHE/SER	15,4391	22.3+/-47.3	0,15,2188	124	105	111		2819,,2660,,3797	5.9	1	2	dbSNP_129	111	79,8521	46.7+/-105.8	0,79,4221	yes	missense,intron,missense,intron,missense	LTBP1	NM_000627.3,NM_001166264.1,NM_001166265.1,NM_001166266.1,NM_206943.2	155,,155,,155	0,94,6409	TT,TC,CC		0.9186,0.3404,0.7227	probably-damaging,,probably-damaging,,probably-damaging	940/1396,,887/1343,,1266/1722	33567971	94,12912	2203	4300	6503	SO:0001583	missense	4052	exon25			CTGGCTCCTTCCG		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.3797C>T	2.37:g.33567971C>T	ENSP00000386043:p.Ser1266Phe	105	0	0		102	45	0.441176	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	37	CCDS33177.2	13|13	0.005952380952380952|0.005952380952380952	0|0	0.0|0.0	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	11|11	0.014511873350923483|0.014511873350923483	C|C	29.1|29.1	4.974955|4.974955	0.92919|0.92919	0.003404|0.003404	0.009186|0.009186	ENSG00000049323|ENSG00000049323	ENST00000415140|ENST00000404816;ENST00000354476;ENST00000390003;ENST00000402934;ENST00000404525;ENST00000407925	.|D;D;D;D;D;D	.|0.95412	.|-3.7;-3.7;-3.7;-3.7;-3.7;-3.7	5.91|5.91	5.91|5.91	0.95273|0.95273	.|.	.|.	.|.	.|.	.|.	D|D	0.97961|0.97961	0.9329|0.9329	H|H	0.94264|0.94264	3.515|3.515	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|0.994;1.0;1.0;1.0	.|P;D;D;D	.|0.91635	.|0.88;0.999;0.999;0.999	D|D	0.96283|0.96283	0.9208|0.9208	5|9	.|0.87932	.|D	.|0	.|.	20.3045|20.3045	0.98621|0.98621	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs61751742|rs61751742	.|887;940;941;1267	.|Q14766-3;Q14766-2;Q14766-5;Q14766-4	.|.;.;.;.	S|F	228|1266;1267;941;887;887;940	.|ENSP00000386043:S1266F;ENSP00000346467:S1267F;ENSP00000374653:S941F;ENSP00000384373:S887F;ENSP00000385359:S887F;ENSP00000384091:S940F	.|ENSP00000346467:S1267F	P|S	+|+	1|2	0|0	LTBP1|LTBP1	33421475|33421475	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.485000|7.485000	0.81204|0.81204	2.807000|2.807000	0.96579|0.96579	0.557000|0.557000	0.71058|0.71058	CCT|TCC	C|0.991;T|0.009	0.009	strong		0.453	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		T	33567971	C	T	33567971	3	4	24	1	0	0	0	0	1	0	0	0	9082	855	30	2	3950	2	LTBP1	2	33567971	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	4024272	33567971	209631402	70	8287											
C2orf56	55471	hgsc.bcm.edu	37	chr2	37459326	37459326	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acccggtgacgccgatgctgCggcatcttatgtacaaaata	11	9	10	11	4	1	1	0	1	1	0	1	2	1	1	2	2	3	3	2	2	5	3	rs146409773		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:37459326C>T	ENST00000002125.4	+	2	173	c.133C>T	c.(133-135)Cgg>Tgg	p.R45W	NDUFAF7_ENST00000483999.1_Intron|CEBPZ_ENST00000234170.5_5'Flank|NDUFAF7_ENST00000336237.6_Missense_Mutation_p.R45W	NM_144736.4	NP_653337.1	Q7L592	NDUF7_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 7	45					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)										GCCGATGCTGCGGCATCTTAT	0.483																																					p.R45W		Atlas-SNP	.											.	.	.	.	0			c.C133T						PASS	.	C	TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	110	103	105		133,133	3.7	1	2	dbSNP_134	105	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	C2orf56	NM_001083946.1,NM_144736.4	101,101	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging,probably-damaging	45/344,45/442	37459326	2,13004	2203	4300	6503	SO:0001583	missense	55471	exon2			ATGCTGCGGCATC		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.133C>T	2.37:g.37459326C>T	ENSP00000002125:p.Arg45Trp	115	0	0		133	65	0.488722	NM_001083946	Q7Z399|Q9P1G3	Missense_Mutation	SNP	ENST00000002125.4	37	CCDS1788.1	.	.	.	.	.	.	.	.	.	.	C	19.76	3.887012	0.72410	2.27E-4	1.16E-4	ENSG00000003509	ENST00000002125;ENST00000336237;ENST00000416653;ENST00000439218;ENST00000432075	T;T	0.76448	-1.02;-1.02	5.51	3.7	0.42460	.	0.339095	0.29631	N	0.011611	D	0.88392	0.6424	M	0.86864	2.845	0.21499	N	0.999661	D;D;D;D	0.89917	0.999;1.0;1.0;0.999	D;D;D;D	0.68765	0.929;0.913;0.96;0.929	T	0.82281	-0.0535	10	0.87932	D	0	-12.9679	13.9833	0.64317	0.5203:0.4797:0.0:0.0	.	45;45;45;45	E7EUC2;B4DQY3;Q7L592-2;Q7L592	.;.;.;MIDA_HUMAN	W	45;45;3;3;3	ENSP00000002125:R45W;ENSP00000337431:R45W	ENSP00000002125:R45W	R	+	1	2	C2orf56	37312830	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	1.134000	0.31442	0.677000	0.31305	-0.270000	0.10280	CGG	C|1.000;T|0.000	0.000	weak		0.483	NDUFAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250267.1	NM_144736		T	37459326	C	T	37459326	3	4	24	1	0	0	0	0	1	0	0	0	2179	759	27	1	139	1	C2orf56	2	37459326	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	3891355	37459326	205740047	71	8288											
PRKD3	23683	hgsc.bcm.edu	37	chr2	37518105	37518105	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taagaatgtacatagagagtAtgtggacgaatctggaagtc	15	10	12	4	1	1	2	0	0	1	2	2	6	1	4	0	2	1	2	0	2	7	4	rs138302731	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:37518105A>G	ENST00000379066.1	-	4	1227	c.465T>C	c.(463-465)caT>caC	p.H155H	PRKD3_ENST00000234179.2_Silent_p.H155H			O94806	KPCD3_HUMAN	protein kinase D3	155					intracellular signal transduction (GO:0035556)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)			breast(3)|central_nervous_system(2)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33		all_hematologic(82;0.21)				CATAGAGAGTATGTGGACGAA	0.388													A|||	2	0.000399361	0.0	0.0	5008	,	,		19716	0.0		0.0	False		,,,				2504	0.002				p.H155H	Melanoma(80;621 1355 8613 11814 51767)	Atlas-SNP	.											.	PRKD3	170	.	0			c.T465C						PASS	.	A		1,4405	2.1+/-5.4	0,1,2202	163	158	159		465	1	1	2	dbSNP_134	159	3,8597	2.2+/-6.3	0,3,4297	yes	coding-synonymous	PRKD3	NM_005813.3		0,4,6499	GG,GA,AA		0.0349,0.0227,0.0308		155/891	37518105	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	23683	exon3			GAGAGTATGTGGA	AB015982	CCDS1789.1	2p21	2013-01-10	2004-10-28	2004-10-30	ENSG00000115825	ENSG00000115825		"Pleckstrin homology (PH) domain containing"	9408	protein-coding gene	gene with protein product		607077	"protein kinase C, nu"	PRKCN		10231560	Standard	NM_005813		Approved	EPK2	uc002rqd.3	O94806	OTTHUMG00000100961	ENST00000379066.1:c.465T>C	2.37:g.37518105A>G		91	0	0		91	43	0.472527	NM_005813	D6W587|Q53TR7|Q8NEL8	Silent	SNP	ENST00000379066.1	37	CCDS1789.1																																																																																			A|1.000;G|0.000	0.000	strong		0.388	PRKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218570.3	NM_005813		G	37518105	A	G	37518105	2	3	24	1	0	0	0	0	0	0	0	1	12532	446	16	3		3	PRKD3	2	37518105	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	58779	37518105	205681268	72	8289											
MAP4K3	8491	hgsc.bcm.edu	37	chr2	39494378	39494378	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcagggatttttgctgataCagaaaatttcctaaatgtaa	14	15	7	5	0	1	2	1	1	0	1	2	3	2	3	1	1	2	2	1	1	6	7			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:39494378C>T	ENST00000263881.3	-	27	2308	c.1984G>A	c.(1984-1986)Gta>Ata	p.V662I	MAP4K3_ENST00000536018.1_Missense_Mutation_p.V215I|MAP4K3_ENST00000341681.5_Missense_Mutation_p.V641I|MAP4K3_ENST00000437545.1_Missense_Mutation_p.V578I	NM_003618.3	NP_003609.2	Q8IVH8	M4K3_HUMAN	mitogen-activated protein kinase kinase kinase kinase 3	662	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)				TTTGCTGATACAGAAAATTTC	0.348																																					p.V662I		Atlas-SNP	.											MAP4K3,right_lower_lobe,carcinoma,0,1	MAP4K3	109	1	0			c.G1984A						scavenged	.						109	110	110					2																	39494378		2203	4300	6503	SO:0001583	missense	8491	exon27			CTGATACAGAAAA	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.1984G>A	2.37:g.39494378C>T	ENSP00000263881:p.Val662Ile	53	0	0		71	3	0.0422535	NM_003618	Q6IQ39|Q8IVH7|Q9UDM5|Q9Y6R5	Missense_Mutation	SNP	ENST00000263881.3	37	CCDS1803.1	.	.	.	.	.	.	.	.	.	.	C	17.37	3.371764	0.61624	.	.	ENSG00000011566	ENST00000263881;ENST00000437545;ENST00000341681;ENST00000536018	T;T;T;T	0.04862	3.54;3.54;3.54;3.54	5.42	5.42	0.78866	Citron-like (3);	0.000000	0.85682	D	0.000000	T	0.10680	0.0261	L	0.33485	1.01	0.58432	D	0.999997	P;P	0.39903	0.694;0.624	P;P	0.46718	0.452;0.525	T	0.32214	-0.9915	10	0.21540	T	0.41	.	19.6002	0.95559	0.0:1.0:0.0:0.0	.	641;662	Q8IVH8-3;Q8IVH8	.;M4K3_HUMAN	I	662;578;641;215	ENSP00000263881:V662I;ENSP00000416958:V578I;ENSP00000345434:V641I;ENSP00000440580:V215I	ENSP00000263881:V662I	V	-	1	0	MAP4K3	39347882	0.999000	0.42202	1.000000	0.80357	0.983000	0.72400	3.286000	0.51724	2.691000	0.91804	0.655000	0.94253	GTA	.	.	none		0.348	MAP4K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219966.2	NM_003618		T	39494378	C	T	39494378	3	4	24	1	0	0	0	0	1	0	0	0	9270	478	17	2	732	2	MAP4K3	2	39494378	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1976273	39494378	203704995	73	8290											
THADA	63892	hgsc.bcm.edu	37	chr2	43571347	43571347	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaattcgttccgtgtttggaGtctgagtaggcttgcaacaa	9	13	12	7	2	1	1	0	1	1	0	3	3	2	2	1	2	2	5	1	2	4	5	rs35422033	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:43571347G>A	ENST00000405006.4	-	30	4608	c.4257C>T	c.(4255-4257)gaC>gaT	p.D1419D	THADA_ENST00000485353.1_5'UTR|THADA_ENST00000405975.2_Silent_p.D1419D|THADA_ENST00000415080.2_Silent_p.D1100D|THADA_ENST00000330266.7_Intron	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	1419										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)				CGTGTTTGGAGTCTGAGTAGG	0.398													G|||	91	0.0181709	0.0484	0.0187	5008	,	,		19017	0.0		0.006	False		,,,				2504	0.0082				p.D1419D		Atlas-SNP	.											.	THADA	131	.	0			c.C4257T						PASS	.	G	,	136,3678		3,130,1774	75	68	70		4257,4257	4.8	1	2	dbSNP_126	70	54,8200		0,54,4073	no	coding-synonymous,coding-synonymous	THADA	NM_001083953.1,NM_022065.4	,	3,184,5847	AA,AG,GG		0.6542,3.5658,1.5744	,	1419/1954,1419/1954	43571347	190,11878	1907	4127	6034	SO:0001819	synonymous_variant	63892	exon30			TTTGGAGTCTGAG	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.4257C>T	2.37:g.43571347G>A		167	0	0		166	87	0.524096	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Silent	SNP	ENST00000405006.4	37	CCDS46268.1	43	0.019688644688644688	31	0.06300813008130081	7	0.019337016574585635	0	0.0	5	0.006596306068601583	G	8.144	0.785827	0.16189	0.035658	0.006542	ENSG00000115970	ENST00000407351	.	.	.	4.8	4.8	0.61643	.	.	.	.	.	T	0.13543	0.0328	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.18650	-1.0330	4	.	.	.	-20.2203	8.2927	0.31967	0.0846:0.1598:0.7556:0.0	rs35422033	.	.	.	I	659	.	.	T	-	2	0	THADA	43424851	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.449000	0.35123	2.494000	0.84150	0.585000	0.79938	ACT	G|0.983;A|0.017	0.017	strong		0.398	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065		A	43571347	G	A	43571347	2	1	24	1	0	0	0	0	0	0	0	1	15855	1020	36	2		2	THADA	2	43571347	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	4076969	43571347	199628026	74	8291											
PREPL	9581	hgsc.bcm.edu	37	chr2	44566479	44566479	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgaggaaacgactgtcttttGtaagataaaggaaaacaaag	18	9	10	4	1	1	2	0	1	1	1	1	5	1	4	0	2	2	1	0	2	7	4			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:44566479G>T	ENST00000409936.1	-	7	1213	c.776C>A	c.(775-777)aCa>aAa	p.T259K	PREPL_ENST00000378520.3_Missense_Mutation_p.T259K|PREPL_ENST00000409272.1_Missense_Mutation_p.T259K|PREPL_ENST00000260648.6_Missense_Mutation_p.T259K|PREPL_ENST00000409411.1_Missense_Mutation_p.T170K|PREPL_ENST00000541738.1_Missense_Mutation_p.T170K|PREPL_ENST00000410081.1_Missense_Mutation_p.T259K|PREPL_ENST00000378511.3_Missense_Mutation_p.T259K|PREPL_ENST00000409957.1_Missense_Mutation_p.T170K	NM_001171606.1	NP_001165077.1	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like	259						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)				ACTGTCTTTTGTAAGATAAAG	0.408																																					p.T259K		Atlas-SNP	.											.	PREPL	69	.	0			c.C776A						PASS	.						60	58	59					2																	44566479		2203	4300	6503	SO:0001583	missense	9581	exon7			TCTTTTGTAAGAT	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.776C>A	2.37:g.44566479G>T	ENSP00000386543:p.Thr259Lys	109	0	0		120	60	0.5	NM_001171603	A7E2X6|D6W5A3|O43163|Q4J6C3|Q4J6C4|Q4ZG39|Q6ZMW7|Q96DW7	Missense_Mutation	SNP	ENST00000409936.1	37	CCDS33190.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.475698	0.84640	.	.	ENSG00000138078	ENST00000541738;ENST00000409411;ENST00000409957;ENST00000409936;ENST00000260648;ENST00000409272;ENST00000410081;ENST00000378520;ENST00000378511	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	5.37	5.37	0.77165	Peptidase S9A/B/C, oligopeptidase, N-terminal beta-propeller (2);	0.055903	0.64402	D	0.000001	T	0.66336	0.2779	L	0.55481	1.735	0.52501	D	0.999955	D;D;D	0.89917	0.996;1.0;0.999	D;D;D	0.77557	0.99;0.983;0.984	T	0.68603	-0.5365	10	0.87932	D	0	-16.2408	19.0981	0.93263	0.0:0.0:1.0:0.0	.	259;259;259	Q4J6C6-3;Q4J6C6-2;Q4J6C6	.;.;PPCEL_HUMAN	K	170;170;170;259;259;259;259;259;259	ENSP00000439626:T170K;ENSP00000387095:T170K;ENSP00000387241:T170K;ENSP00000386543:T259K;ENSP00000260648:T259K;ENSP00000386909:T259K;ENSP00000386509:T259K;ENSP00000367781:T259K;ENSP00000367772:T259K	ENSP00000260648:T259K	T	-	2	0	PREPL	44419983	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.733000	0.74796	2.491000	0.84063	0.585000	0.79938	ACA	.	.	none		0.408	PREPL-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327900.1	NM_006036		T	44566479	G	T	44566479	3	4	24	1	0	0	0	0	1	0	0	0	12487	1377	48	4	1443	4	PREPL	2	44566479	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	995132	44566479	198632894	75	8292											
FBXO11	80204	hgsc.bcm.edu	37	chr2	48059539	48059539	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacgtccatgatgaatatgAttccgtctaataattgggtt	11	15	8	7	2	2	3	1	3	1	0	4	3	4	3	2	1	0	1	2	1	4	6	rs141756242		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:48059539A>G	ENST00000403359.3	-	11	1419	c.1347T>C	c.(1345-1347)aaT>aaC	p.N449N	FBXO11_ENST00000316377.4_Silent_p.N365N|FBXO11_ENST00000434523.2_5'UTR|FBXO11_ENST00000402508.1_Silent_p.N365N	NM_001190274.1	NP_001177203.1	Q86XK2	FBX11_HUMAN	F-box protein 11	449					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)			GATGAATATGATTCCGTCTAA	0.333			"Mis, F, D"		DLBCL								A|||	1	0.000199681	0.0	0.0014	5008	,	,		16143	0.0		0.0	False		,,,				2504	0.0				p.N449N		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.T1347C						PASS	.	A	,	2,4402	4.2+/-10.8	0,2,2200	87	89	88		1347,1095	4.8	1	2	dbSNP_134	88	21,8577	16.0+/-53.3	0,21,4278	no	coding-synonymous,coding-synonymous	FBXO11	NM_001190274.1,NM_025133.4	,	0,23,6478	GG,GA,AA		0.2442,0.0454,0.1769	,	449/928,365/844	48059539	23,12979	2202	4299	6501	SO:0001819	synonymous_variant	80204	exon11			AATATGATTCCGT	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.1347T>C	2.37:g.48059539A>G		130	0	0		102	35	0.343137	NM_001190274	A1L491|Q52ZP1|Q53EP7|Q53RT5|Q8IXG3|Q96E90|Q9H6V8|Q9H9L1|Q9NR14|Q9UFK1|Q9UHI1|Q9UKC2	Silent	SNP	ENST00000403359.3	37	CCDS54357.1	.	.	.	.	.	.	.	.	.	.	A	7.851	0.724018	0.15439	4.54E-4	0.002442	ENSG00000138081	ENST00000493962	.	.	.	5.95	4.8	0.61643	.	.	.	.	.	T	0.63640	0.2528	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61187	-0.7113	4	.	.	.	-19.7747	11.946	0.52928	0.9324:0.0:0.0676:0.0	.	.	.	.	P	241	.	.	S	-	1	0	FBXO11	47913043	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.794000	0.55492	1.076000	0.40961	0.460000	0.39030	TCA	A|0.998;G|0.002	0.002	strong		0.333	FBXO11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251181.3	NM_012167, NM_018693, NM_025133		G	48059539	A	G	48059539	2	3	24	1	0	0	0	0	0	0	0	1	5735	330	12	3		3	FBXO11	2	48059539	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	3493060	48059539	195139834	76	8293											
USP34	9736	hgsc.bcm.edu	37	chr2	61450409	61450409	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcctgttaatgctgccatgtCagtctgtgataatgtcaaat	10	15	8	8	0	3	1	2	1	1	0	4	1	4	1	2	0	2	2	2	0	3	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:61450409C>G	ENST00000398571.2	-	63	7694	c.7618G>C	c.(7618-7620)Gac>Cac	p.D2540H	USP34_ENST00000472689.1_5'Flank	NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	2540					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)			GCTGCCATGTCAGTCTGTGAT	0.308																																					p.D2540H		Atlas-SNP	.											USP34,NS,carcinoma,+2,1	USP34	334	1	0			c.G7618C						PASS	.						137	128	131					2																	61450409		1847	4096	5943	SO:0001583	missense	9736	exon63			CCATGTCAGTCTG	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.7618G>C	2.37:g.61450409C>G	ENSP00000381577:p.Asp2540His	90	0	0		78	5	0.0641026	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	37	CCDS42686.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.5|25.5	4.646274|4.646274	0.87958|0.87958	.|.	.|.	ENSG00000115464|ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571|ENST00000411912	T|.	0.11169|.	2.8|.	5.72|5.72	5.72|5.72	0.89469|0.89469	Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.74473|.	0.3721|.	L|L	0.61218|0.61218	1.895|1.895	0.80722|0.80722	D|D	1|1	D|.	0.69078|.	0.997|.	D|.	0.71870|.	0.975|.	T|.	0.71062|.	-0.4701|.	10|.	0.72032|.	D|.	0.01|.	.|.	19.8938|19.8938	0.96942|0.96942	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	2540|.	Q70CQ2|.	UBP34_HUMAN|.	H|S	2388;2388;2540|299	ENSP00000381577:D2540H|.	ENSP00000263989:D2388H|.	D|X	-|-	1|2	0|2	USP34|USP34	61303913|61303913	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.946000|0.946000	0.59487|0.59487	7.348000|7.348000	0.79366|0.79366	2.703000|2.703000	0.92315|0.92315	0.460000|0.460000	0.39030|0.39030	GAC|TGA	.	.	none		0.308	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4			G	61450409	C	G	61450409	3	3	24	1	0	0	0	0	1	0	0	0	17080	826	29	4	3094	4	USP34	2	61450409	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	13390870	61450409	181748964	77	8294											
FAM161A	84140	hgsc.bcm.edu	37	chr2	62053677	62053677	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatcctggctgttggtatcAataaaataattttcttcccc	11	15	6	9	0	2	0	1	0	1	0	4	1	4	0	3	2	0	3	3	2	6	7	rs138464813	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:62053677A>G	ENST00000405894.3	-	6	1997	c.1896T>C	c.(1894-1896)atT>atC	p.I632I	FAM161A_ENST00000404929.1_Silent_p.I688I	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	632	Glu-rich.				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						TGTTGGTATCAATAAAATAAT	0.328													A|||	6	0.00119808	0.0	0.0029	5008	,	,		19015	0.0		0.003	False		,,,				2504	0.001				p.I688I		Atlas-SNP	.											.	FAM161A	200	.	0			c.T2064C						PASS	.	A	,	3,3635		0,3,1816	107	98	101		2064,1896	3	1	2	dbSNP_134	101	33,8127		0,33,4047	yes	coding-synonymous,coding-synonymous	FAM161A	NM_001201543.1,NM_032180.2	,	0,36,5863	GG,GA,AA		0.4044,0.0825,0.3051	,	688/717,632/661	62053677	36,11762	1819	4080	5899	SO:0001819	synonymous_variant	84140	exon7			GGTATCAATAAAA		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.1896T>C	2.37:g.62053677A>G		224	0	0		215	95	0.44186	NM_001201543	B4DJV7|Q9H8R2	Silent	SNP	ENST00000405894.3	37	CCDS42687.2																																																																																			A|0.998;G|0.002	0.002	strong		0.328	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180		G	62053677	A	G	62053677	2	3	24	1	0	0	0	0	0	0	0	1	5477	126	5	3		3	FAM161A	2	62053677	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	603268	62053677	181145696	78	8295											
ZNF638	27332	hgsc.bcm.edu	37	chr2	71650236	71650236	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcactgaaaatgccgaggagTgtgctttaaatcagcagatg	13	10	11	7	1	2	2	2	1	0	1	2	4	2	3	1	1	3	2	1	1	4	2	rs79157966	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:71650236T>C	ENST00000409544.1	+	22	4222	c.3592T>C	c.(3592-3594)Tgt>Cgt	p.C1198R	ZNF638_ENST00000355812.3_Intron|ZNF638_ENST00000264447.4_Missense_Mutation_p.C1198R|ZNF638_ENST00000409407.1_Missense_Mutation_p.C138R	NM_001252612.1	NP_001239541.1	Q14966	ZN638_HUMAN	zinc finger protein 638	1198	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						TGCCGAGGAGTGTGCTTTAAA	0.408													T|||	9	0.00179712	0.0	0.0014	5008	,	,		19971	0.0		0.008	False		,,,				2504	0.0				p.C1198R		Atlas-SNP	.											.	ZNF638	179	.	0			c.T3592C						PASS	.	T	ARG/CYS,ARG/CYS	4,4402	8.1+/-20.4	0,4,2199	96	96	96		3592,3592	4.4	1	2	dbSNP_131	96	74,8526	44.5+/-102.8	0,74,4226	yes	missense,missense	ZNF638	NM_001014972.1,NM_014497.3	180,180	0,78,6425	CC,CT,TT		0.8605,0.0908,0.5997	benign,benign	1198/1979,1198/1979	71650236	78,12928	2203	4300	6503	SO:0001583	missense	27332	exon22			GAGGAGTGTGCTT	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.3592T>C	2.37:g.71650236T>C	ENSP00000386433:p.Cys1198Arg	99	0	0		101	59	0.584158	NM_014497	B5MDV1|B7ZLD1|Q53R34|Q5XJ05|Q68DP3|Q6P2H2|Q7Z3T7|Q8NF92|Q8TCA1|Q9H2G1|Q9NP37	Missense_Mutation	SNP	ENST00000409544.1	37	CCDS1917.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	T	9.920	1.211800	0.22289	9.08E-4	0.008605	ENSG00000075292	ENST00000394137;ENST00000264447;ENST00000409544;ENST00000409407;ENST00000462695	T;T;T	0.30182	1.54;1.54;1.82	5.55	4.36	0.52297	.	0.556954	0.16511	N	0.211226	T	0.12305	0.0299	N	0.24115	0.695	0.80722	D	1	B;B;B	0.29432	0.244;0.144;0.089	B;B;B	0.21151	0.032;0.033;0.032	T	0.05209	-1.0899	10	0.15499	T	0.54	-1.0544	8.8782	0.35358	0.1665:0.0:0.0:0.8335	.	1198;1198;1198	A8K583;Q14966-3;Q14966	.;.;ZN638_HUMAN	R	777;1198;1198;138;138	ENSP00000264447:C1198R;ENSP00000386433:C1198R;ENSP00000386813:C138R	ENSP00000264447:C1198R	C	+	1	0	ZNF638	71503744	0.997000	0.39634	0.998000	0.56505	0.476000	0.33039	1.649000	0.37281	0.991000	0.38814	0.533000	0.62120	TGT	T|0.994;C|0.006	0.006	strong		0.408	ZNF638-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327431.1	NM_014497		C	71650236	T	C	71650236	3	2	24	1	0	0	0	0	1	0	0	0	18070	1696	59	3	3674	3	ZNF638	2	71650236	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	9596559	71650236	171549137	79	8296											
PTCD3	55037	hgsc.bcm.edu	37	chr2	86352925	86352925	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tattattttacagctgatgtAtacacatttaatgcattgat	13	18	5	5	0	0	2	0	2	0	0	0	2	0	2	0	0	4	3	0	0	6	9	rs139474497	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:86352925A>G	ENST00000254630.7	+	12	939	c.873A>G	c.(871-873)gtA>gtG	p.V291V	PTCD3_ENST00000409277.3_3'UTR	NM_017952.5	NP_060422.4	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3	291					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						CAGCTGATGTATACACATTTA	0.338													A|||	28	0.00559105	0.0	0.0086	5008	,	,		20926	0.0		0.0219	False		,,,				2504	0.0				p.V291V		Atlas-SNP	.											.	PTCD3	51	.	0			c.A873G						PASS	.	A		6,4400	11.4+/-27.6	0,6,2197	44	49	47		873	-11.5	0	2	dbSNP_134	47	127,8473	64.6+/-126.8	1,125,4174	no	coding-synonymous	PTCD3	NM_017952.5		1,131,6371	GG,GA,AA		1.4767,0.1362,1.0226		291/690	86352925	133,12873	2203	4300	6503	SO:0001819	synonymous_variant	55037	exon12			TGATGTATACACA		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.873A>G	2.37:g.86352925A>G		93	0	0		101	55	0.544554	NM_017952	A6NHD2|D6W5M1|Q597H0|Q658Y9|Q9BUZ8|Q9NWL0	Silent	SNP	ENST00000254630.7	37	CCDS33235.1																																																																																			A|0.991;G|0.009	0.009	strong		0.338	PTCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329854.1	NM_017952		G	86352925	A	G	86352925	2	3	24	1	0	0	0	0	0	0	0	1	12741	436	16	3		3	PTCD3	2	86352925	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	14702689	86352925	156846448	80	8297											
TEKT4	150483	hgsc.bcm.edu	37	chr2	95537330	95537330	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgggcggcaggcaccatggcGcagacagtgccgccctgcga	7	4	16	14	4	0	1	0	0	0	1	0	2	0	1	3	4	2	3	3	4	0	0	rs140196891	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:95537330G>A	ENST00000295201.4	+	1	143	c.6G>A	c.(4-6)gcG>gcA	p.A2A	AC097374.2_ENST00000568768.1_RNA|TEKT4_ENST00000427593.2_Silent_p.A2A	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	2					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						GCACCATGGCGCAGACAGTGC	0.697													.|||	17	0.00339457	0.0015	0.0043	5008	,	,		17151	0.0		0.007	False		,,,				2504	0.0051				p.A2A		Atlas-SNP	.											.	TEKT4	72	.	0			c.G6A						PASS	.	G		5,4261		0,5,2128	9	10	10		6	0.6	0.3	2	dbSNP_134	10	48,8290		0,48,4121	no	coding-synonymous	TEKT4	NM_144705.2		0,53,6249	AA,AG,GG		0.5757,0.1172,0.4205		2/436	95537330	53,12551	2133	4169	6302	SO:0001819	synonymous_variant	150483	exon1			CATGGCGCAGACA	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.6G>A	2.37:g.95537330G>A		47	0	0		55	28	0.509091	NM_144705		Silent	SNP	ENST00000295201.4	37	CCDS2005.1																																																																																			G|0.995;A|0.005	0.005	strong		0.697	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705		A	95537330	G	A	95537330	2	1	24	1	0	0	0	0	0	0	0	1	15770	1074	38	1		1	TEKT4	2	95537330	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	9184405	95537330	147662043	81	8298											
CNNM4	26504	hgsc.bcm.edu	37	chr2	97465379	97465379	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctatggccctgacctcggtcCcctccggtgagttgttgggc	3	11	13	14	2	0	2	0	2	0	0	3	2	2	2	5	4	0	2	5	4	1	3	rs144495984		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:97465379C>T	ENST00000377075.2	+	5	2040	c.1942C>T	c.(1942-1944)Ccc>Tcc	p.P648S	MIR3127_ENST00000583925.1_RNA|CNNM4_ENST00000540067.1_Missense_Mutation_p.P135S|CNNM4_ENST00000496186.1_3'UTR	NM_020184.3	NP_064569.3	Q6P4Q7	CNNM4_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 4	648					biomineral tissue development (GO:0031214)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	20						GACCTCGGTCCCCTCCGGTGA	0.602																																					p.P648S		Atlas-SNP	.											.	CNNM4	48	.	0			c.C1942T						PASS	.	C	SER/PRO	0,4340		0,0,2170	85	72	77		1942	-1.7	0	2	dbSNP_134	77	2,8374		0,2,4186	yes	missense	CNNM4	NM_020184.3	74	0,2,6356	TT,TC,CC		0.0239,0.0,0.0157	benign	648/776	97465379	2,12714	2170	4188	6358	SO:0001583	missense	26504	exon5			TCGGTCCCCTCCG	AB046812	CCDS2024.2	2q11.2	2014-08-08	2014-08-07		ENSG00000158158	ENSG00000158158			105	protein-coding gene	gene with protein product		607805	"cyclin M4"	ACDP4		21393841, 24194943	Standard	XM_005263914		Approved	KIAA1592	uc002swx.3	Q6P4Q7	OTTHUMG00000130532	ENST00000377075.2:c.1942C>T	2.37:g.97465379C>T	ENSP00000366275:p.Pro648Ser	161	0	0		174	84	0.482759	NM_020184	B7Z1U0|C7SQM3|C7SQM4|C7SQM5|Q53RE5|Q9H9G3|Q9HCI0|Q9NRN1	Missense_Mutation	SNP	ENST00000377075.2	37	CCDS2024.2	.	.	.	.	.	.	.	.	.	.	C	11.98	1.800104	0.31869	0.0	2.39E-4	ENSG00000158158	ENST00000377075;ENST00000540067	T	0.73047	-0.71	4.78	-1.71	0.08133	RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (2);	0.773363	0.12569	N	0.457447	T	0.36082	0.0954	N	0.03281	-0.365	0.18873	N	0.999989	B;B	0.14438	0.01;0.0	B;B	0.17433	0.018;0.0	T	0.18053	-1.0349	10	0.17369	T	0.5	-9.342	0.8361	0.01140	0.2255:0.3422:0.2194:0.2129	.	135;648	B7Z1U0;Q6P4Q7	.;CNNM4_HUMAN	S	648;135	ENSP00000366275:P648S	ENSP00000366275:P648S	P	+	1	0	CNNM4	96829106	0.000000	0.05858	0.000000	0.03702	0.230000	0.25150	-1.945000	0.01537	-0.484000	0.06763	-0.291000	0.09656	CCC	C|1.000;T|0.000	0.000	weak		0.602	CNNM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252954.1	NM_020184		T	97465379	C	T	97465379	3	4	24	1	0	0	0	0	1	0	0	0	3617	623	22	2	1960	2	CNNM4	2	97465379	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1928049	97465379	145733994	82	8299											
IL1R1	3554	hgsc.bcm.edu	37	chr2	102781629	102781629	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaaaatttgtggagaatgaGcctaacttatgttataatgc	14	13	9	5	0	0	2	0	1	0	1	0	3	0	2	1	1	3	2	1	1	7	5	rs3917286	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:102781629G>A	ENST00000410023.1	+	5	669	c.351G>A	c.(349-351)gaG>gaA	p.E117E	IL1R1_ENST00000409589.1_Silent_p.E117E|IL1R1_ENST00000409288.1_Silent_p.E117E|IL1R1_ENST00000409929.1_Silent_p.E117E|IL1R1_ENST00000233946.3_Silent_p.E117E|IL1R1_ENST00000424272.1_Silent_p.E117E|IL1R1_ENST00000409329.1_Silent_p.E117E			P14778	IL1R1_HUMAN	interleukin 1 receptor, type I	117					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)	TGGAGAATGAGCCTAACTTAT	0.313													G|||	225	0.0449281	0.0083	0.0072	5008	,	,		12413	0.0714		0.006	False		,,,				2504	0.1339				p.E117E		Atlas-SNP	.											.	IL1R1	52	.	0			c.G351A						PASS	.	G		47,4359	48.9+/-83.8	0,47,2156	50	51	50		351	-10	0.1	2	dbSNP_108	50	43,8555	27.4+/-76.7	0,43,4256	no	coding-synonymous	IL1R1	NM_000877.2		0,90,6412	AA,AG,GG		0.5001,1.0667,0.6921		117/570	102781629	90,12914	2203	4299	6502	SO:0001819	synonymous_variant	3554	exon4			GAATGAGCCTAAC	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.351G>A	2.37:g.102781629G>A		198	0	0		186	89	0.478495	NM_000877	Q587I7	Silent	SNP	ENST00000410023.1	37	CCDS2055.1																																																																																			G|0.984;A|0.016	0.016	strong		0.313	IL1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253299.1			A	102781629	G	A	102781629	2	1	24	1	0	0	0	0	0	0	0	1	7667	962	34	2		2	IL1R1	2	102781629	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	5316250	102781629	140417744	83	8300											
IL1R1	3554	hgsc.bcm.edu	37	chr2	102791086	102791086	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgattggtatatgtgtcaCgttgacagtcataattgtgt	10	16	10	5	1	2	2	2	2	0	0	2	2	2	2	0	1	0	2	0	1	3	6	rs28362304	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:102791086C>T	ENST00000410023.1	+	10	1349	c.1031C>T	c.(1030-1032)aCg>aTg	p.T344M	IL1R1_ENST00000409589.1_Intron|IL1R1_ENST00000409288.1_Missense_Mutation_p.T344M|IL1R1_ENST00000409929.1_Missense_Mutation_p.T344M|IL1R1_ENST00000233946.3_Missense_Mutation_p.T344M|AC007271.3_ENST00000428188.1_RNA|IL1R1_ENST00000424272.1_Missense_Mutation_p.T344M|IL1R1_ENST00000409329.1_Missense_Mutation_p.T344M			P14778	IL1R1_HUMAN	interleukin 1 receptor, type I	344			T -> M (in dbSNP:rs28362304).		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)	ATATGTGTCACGTTGACAGTC	0.313													C|||	228	0.0455272	0.0083	0.0072	5008	,	,		17379	0.0714		0.006	False		,,,				2504	0.137				p.T344M		Atlas-SNP	.											.	IL1R1	52	.	0			c.C1031T						PASS	.	C	MET/THR	49,4355	50.2+/-85.5	0,49,2153	185	167	173		1031	-3.8	0	2	dbSNP_125	173	43,8551	28.5+/-78.6	0,43,4254	yes	missense	IL1R1	NM_000877.2	81	0,92,6407	TT,TC,CC		0.5003,1.1126,0.7078	benign	344/570	102791086	92,12906	2202	4297	6499	SO:0001583	missense	3554	exon9			GTGTCACGTTGAC	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.1031C>T	2.37:g.102791086C>T	ENSP00000386380:p.Thr344Met	112	0	0		92	34	0.369565	NM_000877	Q587I7	Missense_Mutation	SNP	ENST00000410023.1	37	CCDS2055.1	50	0.022893772893772892	2	0.0040650406504065045	3	0.008287292817679558	40	0.06993006993006994	5	0.006596306068601583	C	9.085	1.000223	0.19121	0.011126	0.005003	ENSG00000115594	ENST00000409929;ENST00000424272;ENST00000409329;ENST00000428279;ENST00000409288;ENST00000410023;ENST00000233946	T;T;T;T;T;T;T	0.05447	4.36;3.75;3.75;3.44;3.75;4.38;4.38	5.57	-3.75	0.04372	.	1.033190	0.07574	N	0.919117	T	0.00328	0.0010	N	0.04880	-0.145	0.09310	N	1	B;B;B	0.13145	0.003;0.002;0.007	B;B;B	0.09377	0.001;0.002;0.004	T	0.42882	-0.9425	10	0.37606	T	0.19	.	14.2823	0.66221	0.0:0.7461:0.0:0.2539	rs28362304;rs28362304	344;344;344	B8ZZW4;P14778;B8ZZ73	.;IL1R1_HUMAN;.	M	344;344;344;200;344;344;344	ENSP00000386776:T344M;ENSP00000415366:T344M;ENSP00000387131:T344M;ENSP00000410461:T200M;ENSP00000386478:T344M;ENSP00000386380:T344M;ENSP00000233946:T344M	ENSP00000233946:T344M	T	+	2	0	IL1R1	102157518	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.517000	0.22832	-0.397000	0.07691	-0.982000	0.02568	ACG	C|0.985;T|0.015	0.015	strong		0.313	IL1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253299.1			T	102791086	C	T	102791086	3	4	24	1	0	0	0	0	1	0	0	0	7667	536	19	1	1061	1	IL1R1	2	102791086	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	9457	102791086	140408287	84	8301											
IL1RL2	8808	hgsc.bcm.edu	37	chr2	102851470	102851470	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctgtcagaagaacaaatcGcggtctacagtgccctgatc	12	8	9	12	2	2	3	1	1	1	2	4	3	2	3	2	1	3	0	2	1	4	1	rs75091099	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:102851470G>A	ENST00000264257.2	+	11	1537	c.1411G>A	c.(1411-1413)Gcg>Acg	p.A471T	IL1RL2_ENST00000539491.1_Missense_Mutation_p.A471T|IL1RL2_ENST00000441515.2_Missense_Mutation_p.A353T|IL1RL2_ENST00000481806.1_3'UTR	NM_003854.2	NP_003845.2	Q9HB29	ILRL2_HUMAN	interleukin 1 receptor-like 2	471	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				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						AGAACAAATCGCGGTCTACAG	0.488													G|||	144	0.028754	0.0	0.0072	5008	,	,		19953	0.0724		0.006	False		,,,				2504	0.0613				p.A471T		Atlas-SNP	.											IL1RL2,NS,carcinoma,-1,1	IL1RL2	118	1	0			c.G1411A						PASS	.	G	THR/ALA	9,4397	15.5+/-35.6	0,9,2194	132	120	124		1411	3.4	0.2	2	dbSNP_132	124	38,8562	25.1+/-72.6	0,38,4262	yes	missense	IL1RL2	NM_003854.2	58	0,47,6456	AA,AG,GG		0.4419,0.2043,0.3614	possibly-damaging	471/576	102851470	47,12959	2203	4300	6503	SO:0001583	missense	8808	exon11			CAAATCGCGGTCT	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.1411G>A	2.37:g.102851470G>A	ENSP00000264257:p.Ala471Thr	155	0	0		160	73	0.45625	NM_003854	A4FU63|Q13525|Q45H74|Q53TU8|Q587I8	Missense_Mutation	SNP	ENST00000264257.2	37	CCDS2056.1	49	0.022435897435897436	0	0.0	3	0.008287292817679558	42	0.07342657342657342	4	0.005277044854881266	G	17.94	3.510555	0.64522	0.002043	0.004419	ENSG00000115598	ENST00000264257;ENST00000441515;ENST00000539491	T;T;T	0.11712	2.75;2.75;2.75	5.43	3.4	0.38934	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.467616	0.23395	N	0.048647	T	0.01353	0.0044	M	0.69823	2.125	0.32198	N	0.57825	P;D	0.54047	0.924;0.964	P;P	0.48921	0.495;0.595	T	0.04115	-1.0976	10	0.59425	D	0.04	.	12.4276	0.55556	0.1128:0.0:0.8872:0.0	.	353;471	A4FU63;Q9HB29	.;ILRL2_HUMAN	T	471;353;471	ENSP00000264257:A471T;ENSP00000413348:A353T;ENSP00000442184:A471T	ENSP00000264257:A471T	A	+	1	0	IL1RL2	102217902	0.568000	0.26635	0.238000	0.24106	0.767000	0.43475	3.205000	0.51090	1.140000	0.42260	0.591000	0.81541	GCG	G|0.991;A|0.009	0.009	strong		0.488	IL1RL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253290.1	NM_003854		A	102851470	G	A	102851470	3	1	24	1	0	0	0	0	1	0	0	0	7673	1087	38	1	1449	1	IL1RL2	2	102851470	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	60384	102851470	140347903	85	8302											
ACOXL	55289	hgsc.bcm.edu	37	chr2	111666368	111666368	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctgttgattccctctagccGgaggcagtttgggcccaaaa	8	11	11	11	1	2	1	0	1	2	0	3	2	3	2	3	3	1	3	3	3	3	4	rs116012262	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:111666368G>A	ENST00000389811.4	+	11	1015	c.791G>A	c.(790-792)cGg>cAg	p.R264Q	ACOXL_ENST00000439055.1_Missense_Mutation_p.R264Q			Q9NUZ1	ACOXL_HUMAN	acyl-CoA oxidase-like	264					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						CCCTCTAGCCGGAGGCAGTTT	0.527													g|||	4	0.000798722	0.0	0.0	5008	,	,		19159	0.001		0.003	False		,,,				2504	0.0				p.R264Q		Atlas-SNP	.											.	ACOXL	93	.	0			c.G791A						PASS	.		GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	89	86	87		791	3.2	1	2	dbSNP_132	87	25,8575	17.9+/-57.8	0,25,4275	yes	missense	ACOXL	NM_001142807.1	43	0,27,6476	AA,AG,GG		0.2907,0.0454,0.2076	probably-damaging	264/581	111666368	27,12979	2203	4300	6503	SO:0001583	missense	55289	exon11			CTAGCCGGAGGCA		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.791G>A	2.37:g.111666368G>A	ENSP00000374461:p.Arg264Gln	168	0	0		124	67	0.540323	NM_001142807	A2RRB7|B7WPB3|B7WPP7|E9PB20|Q53R27|Q53R31|Q53SC6|Q8TCE7	Missense_Mutation	SNP	ENST00000389811.4	37		2	9.157509157509158E-4	0	0.0	0	0.0	1	0.0017482517482517483	1	0.0013192612137203166	g	15.47	2.842370	0.51057	4.54E-4	0.002907	ENSG00000153093	ENST00000389811;ENST00000439055;ENST00000422487;ENST00000417074	D;D;D	0.89810	-2.57;-2.57;-2.57	5.02	3.2	0.36748	Acyl-CoA dehydrogenase/oxidase C-terminal (2);Acyl-CoA oxidase/dehydrogenase, type 1 (1);	0.339475	0.23160	N	0.051250	D	0.94122	0.8115	M	0.87097	2.86	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.968;0.947;1.0	D	0.93087	0.6496	10	0.87932	D	0	-44.5563	9.5964	0.39576	0.1755:0.0:0.8245:0.0	.	264;264;264	E9PB20;Q9NUZ1-2;Q9NUZ1	.;.;ACOXL_HUMAN	Q	264;264;115;102	ENSP00000374461:R264Q;ENSP00000407761:R264Q;ENSP00000387832:R102Q	ENSP00000374461:R264Q	R	+	2	0	ACOXL	111382839	1.000000	0.71417	0.993000	0.49108	0.173000	0.22820	3.379000	0.52440	0.509000	0.28195	0.558000	0.71614	CGG	G|0.999;A|0.001	0.001	strong		0.527	ACOXL-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000254024.2	NM_018308		A	111666368	G	A	111666368	3	1	24	1	0	0	0	0	1	0	0	0	161	1116	39	1	829	1	ACOXL	2	111666368	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	8814898	111666368	131533005	86	8303											
DPP10	57628	hgsc.bcm.edu	37	chr2	115822349	115822349	+	Intron	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttagcaatggtcatcacagaGgtggctgagggaccagtaga	12	8	14	7	0	2	3	2	1	0	2	2	4	2	4	1	4	1	3	1	4	3	2	rs114821649	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:115822349G>T	ENST00000410059.1	+	2	540				DPP10_ENST00000409163.1_Intron	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						TCATCACAGAGGTGGCTGAGG	0.428													G|||	16	0.00319489	0.0023	0.0014	5008	,	,		17880	0.0		0.0099	False		,,,				2504	0.002				p.E5D		Atlas-SNP	.											.	DPP10	415	.	0			c.G15T						PASS	.																																			SO:0001627	intron_variant	57628	exon1			CACAGAGGTGGCT	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.61-244466G>T	2.37:g.115822349G>T		301	1	0.00332226		268	131	0.488806	NM_001178037	A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	37	CCDS46400.1	9	0.004120879120879121	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	G	0.476	-0.882031	0.02530	.	.	ENSG00000175497	ENST00000393146	.	.	.	2.54	-1.69	0.08186	.	.	.	.	.	T	0.09905	0.0243	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18053	-1.0349	8	0.27785	T	0.31	.	1.6277	0.02726	0.2314:0.1609:0.448:0.1596	.	5	Q0GLB9	.	D	5	.	ENSP00000376854:E5D	E	+	3	2	DPP10	115538819	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.978000	0.03778	-0.884000	0.03976	-2.947000	0.00085	GAG	G|0.996;T|0.004	0.004	strong		0.428	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868		T	115822349	G	T	115822349	1	4	24	0	1	0	0	0	0	0	0	0	4729	991	35	4		4	DPP10	2	115822349	Intron	SNP	G	TCGA-G8-6326-01A-11D-2210-10	4155981	115822349	127377024	87	8304											
TMEM37	6344	hgsc.bcm.edu	37	chr2	120194674	120194674	+	IGR	SNP	C	C	T																															atctgcttcagagacctgggCcaggcccatgtgcccgggct																								rs72833258	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:120194674C>T	ENST00000019103.5	-	0	1865				TMEM37_ENST00000465296.1_3'UTR|TMEM37_ENST00000409826.1_Silent_p.G89G|TMEM37_ENST00000306406.4_Silent_p.G77G	NM_002980.2	NP_002971.2	P47872	SCTR_HUMAN	secretin receptor						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)	GAGACCTGGGCCAGGCCCATG	0.657													C|||	72	0.014377	0.003	0.0144	5008	,	,		14624	0.001		0.0209	False		,,,				2504	0.0368				p.G77G		Atlas-SNP	.											.	TMEM37	40	.	0			c.C231T						PASS	.	C		21,4383	28.1+/-56.4	0,21,2181	50	53	52		231	-4.2	0.1	2	dbSNP_130	52	232,8366	94.2+/-156.2	2,228,4069	no	coding-synonymous	TMEM37	NM_183240.2		2,249,6250	TT,TC,CC		2.6983,0.4768,1.9459		77/191	120194674	253,12749	2202	4299	6501	SO:0001628	intergenic_variant	140738	exon2			CCTGGGCCAGGCC		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		2.37:g.120194674C>T		37	0	0		44	28	0.636364	NM_183240	Q12961|Q13213|Q53T00	Silent	SNP	ENST00000019103.5	37	CCDS2127.1																																																																																			C|0.983;T|0.017	0.017	strong		0.657	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2			T	120194674	C	T	120194674	1	4	24	0	1	0	0	0	0	0	0	0	16173	726	26	2		2	TMEM37	2	120194674	IGR	SNP	C	TCGA-G8-6326-01A-11D-2210-10	4372325	120194674	123004699	88	8305	106	2									
TMEM37	6344	hgsc.bcm.edu	37	chr2	120194680	120194680	+	IGR	SNP	C	C	G																															ttcagagacctgggccaggcCcatgtgcccgggctggccgt																								rs72833259	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:120194680C>G	ENST00000019103.5	-	0	1865				TMEM37_ENST00000465296.1_3'UTR|TMEM37_ENST00000409826.1_Silent_p.A91A|TMEM37_ENST00000306406.4_Silent_p.A79A	NM_002980.2	NP_002971.2	P47872	SCTR_HUMAN	secretin receptor						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)	TGGGCCAGGCCCATGTGCCCG	0.667													C|||	71	0.0141773	0.003	0.0144	5008	,	,		14497	0.001		0.0209	False		,,,				2504	0.0358				p.A79A		Atlas-SNP	.											.	TMEM37	40	.	0			c.C237G						PASS	.	C		21,4383	28.1+/-56.4	0,21,2181	50	53	52		237	1.8	0	2	dbSNP_130	52	234,8366	95.2+/-157.0	2,230,4068	no	coding-synonymous	TMEM37	NM_183240.2		2,251,6249	GG,GC,CC		2.7209,0.4768,1.9609		79/191	120194680	255,12749	2202	4300	6502	SO:0001628	intergenic_variant	140738	exon2			CCAGGCCCATGTG		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		2.37:g.120194680C>G		35	0	0		42	27	0.642857	NM_183240	Q12961|Q13213|Q53T00	Silent	SNP	ENST00000019103.5	37	CCDS2127.1																																																																																			C|0.983;G|0.017	0.017	strong		0.667	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2			G	120194680	C	G	120194680	1	3	24	0	1	0	0	0	0	0	0	0	16173	610	22	4		4	TMEM37	2	120194680	IGR	SNP	C	TCGA-G8-6326-01A-11D-2210-10	6	120194680	123004693	89	8306	106	2									
TTN	7273	hgsc.bcm.edu	37	chr2	179429612	179429612	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catctgatcttttgagattgAtgtcacaaaaggagttccag	12	13	9	7	0	3	3	1	3	2	1	4	5	4	4	1	1	0	1	1	1	2	4	rs186273940	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179429612A>G	ENST00000591111.1	-	276	76548	c.76324T>C	c.(76324-76326)Tca>Cca	p.S25442P	TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.S18210P|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.S18143P|TTN_ENST00000460472.2_Missense_Mutation_p.S18018P|TTN-AS1_ENST00000592600.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.S27083P|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.S24515P|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA			Q8WZ42	TITIN_HUMAN	titin	25442	Fibronectin type-III 85. {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)			TTTGAGATTGATGTCACAAAA	0.408													A|||	3	0.000599042	0.0	0.0	5008	,	,		21196	0.0		0.003	False		,,,				2504	0.0				p.S27083P		Atlas-SNP	.											.	TTN	18412	.	0			c.T81247C						PASS	.	A	PRO/SER,PRO/SER,PRO/SER,PRO/SER	0,3750		0,0,1875	77	73	74		54052,73543,54427,54628	4.8	1	2		74	6,8210		1,4,4103	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	74,74,74,74	1,4,5978	GG,GA,AA		0.073,0.0,0.0501	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	18018/26927,24515/33424,18143/27052,18210/27119	179429612	6,11960	1875	4108	5983	SO:0001583	missense	7273	exon326			AGATTGATGTCAC	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.76324T>C	2.37:g.179429612A>G	ENSP00000465570:p.Ser25442Pro	96	0	0		122	73	0.598361	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	37		3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	8.744	0.919583	0.17982	0.0	7.3E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	6.02	4.85	0.62838	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.51907	0.1702	L	0.53617	1.68	0.44207	D	0.997039	P;P;P;P	0.42584	0.784;0.784;0.784;0.662	P;P;P;P	0.48368	0.575;0.575;0.575;0.478	T	0.55617	-0.8113	9	0.87932	D	0	.	4.0826	0.09932	0.5754:0.2427:0.0654:0.1165	.	18018;18143;18210;25442	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	P	24515;18018;18210;18143;18016	ENSP00000343764:S24515P;ENSP00000434586:S18018P;ENSP00000340554:S18210P;ENSP00000352154:S18143P	ENSP00000340554:S18210P	S	-	1	0	TTN	179137858	1.000000	0.71417	0.960000	0.40013	0.993000	0.82548	1.448000	0.35112	1.063000	0.40649	0.528000	0.53228	TCA	A|0.999;G|0.001	0.001	strong		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179429612	A	G	179429612	3	3	24	1	0	0	0	0	1	0	0	0	16750	333	12	3	26880	3	TTN	2	179429612	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	59234932	179429612	63769761	90	8307											
TTN	7273	hgsc.bcm.edu	37	chr2	179606590	179606590	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtttcatttattttagataaTtgaagttcggcgctatgaag	11	17	9	4	2	1	3	1	2	0	1	2	3	1	3	0	1	0	3	0	1	6	9	rs72648918	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:179606590T>C	ENST00000591111.1	-	46	10643	c.10419A>G	c.(10417-10419)caA>caG	p.Q3473Q	TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000342175.6_Silent_p.Q3619Q|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Silent_p.Q3552Q|TTN_ENST00000460472.2_Silent_p.Q3427Q|TTN_ENST00000589042.1_Silent_p.Q3790Q|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron|TTN-AS1_ENST00000582847.1_RNA			Q8WZ42	TITIN_HUMAN	titin	13796					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)			TTTTAGATAATTGAAGTTCGG	0.338													T|||	3	0.000599042	0.0	0.0014	5008	,	,		14760	0.0		0.002	False		,,,				2504	0.0				p.Q3790Q		Atlas-SNP	.											.	TTN	18412	.	0			c.A11370G						PASS	.	T	,,,	0,3592		0,0,1796	41	37	39		10281,,10656,10857	-1.6	0	2	dbSNP_130	39	8,8112		1,6,4053	no	coding-synonymous,intron,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	1,6,5849	CC,CT,TT		0.0985,0.0,0.0683	,,,	3427/26927,,3552/27052,3619/27119	179606590	8,11704	1796	4060	5856	SO:0001819	synonymous_variant	7273	exon48			AGATAATTGAAGT	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.10419A>G	2.37:g.179606590T>C		50	0	0		63	31	0.492063	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	37																																																																																				T|0.999;C|0.001	0.001	strong		0.338	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179606590	T	C	179606590	2	2	24	1	0	0	0	0	0	0	0	1	16750	1490	52	3		3	TTN	2	179606590	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	176978	179606590	63592783	91	8308											
DUSP19	142679	hgsc.bcm.edu	37	chr2	183951888	183951888	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctgtcttattttccagaaTgttttgaatttattgaagaa	11	19	6	5	0	1	4	0	2	1	2	3	4	3	4	2	0	0	1	2	0	6	8			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:183951888T>C	ENST00000354221.4	+	3	569	c.394T>C	c.(394-396)Tgt>Cgt	p.C132R	AC064871.3_ENST00000444562.1_RNA|DUSP19_ENST00000469344.1_3'UTR|DUSP19_ENST00000342619.6_Intron	NM_080876.3	NP_543152.1	Q8WTR2	DUS19_HUMAN	dual specificity phosphatase 19	132					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 protein kinase activity (GO:0006469)|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 protein kinase activity (GO:0045860)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	JUN kinase phosphatase activity (GO:0008579)|MAP-kinase scaffold activity (GO:0005078)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein kinase activator activity (GO:0030295)|protein kinase inhibitor activity (GO:0004860)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/threonine phosphatase activity (GO:0008330)			breast(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(4)|pancreas(1)	17						TTTTCCAGAATGTTTTGAATT	0.343																																					p.C132R		Atlas-SNP	.											.	DUSP19	41	.	0			c.T394C						PASS	.						93	92	92					2																	183951888		2202	4299	6501	SO:0001583	missense	142679	exon3			CCAGAATGTTTTG	AB038770	CCDS2289.1, CCDS46469.1	2q32.1	2011-06-09			ENSG00000162999	ENSG00000162999		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	18894	protein-coding gene	gene with protein product		611437					Standard	NM_080876		Approved	SKRP1, DUSP17	uc002upd.3	Q8WTR2	OTTHUMG00000132622	ENST00000354221.4:c.394T>C	2.37:g.183951888T>C	ENSP00000346160:p.Cys132Arg	70	0	0		63	34	0.539683	NM_080876	B2RA79|Q547H4|Q8WYN4	Missense_Mutation	SNP	ENST00000354221.4	37	CCDS2289.1	.	.	.	.	.	.	.	.	.	.	t	19.13	3.768014	0.69878	.	.	ENSG00000162999	ENST00000354221	T	0.60424	0.19	5.37	4.18	0.49190	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.082767	0.85682	D	0.000000	T	0.81432	0.4821	H	0.95079	3.62	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	D	0.85083	0.0947	10	0.72032	D	0.01	.	11.6994	0.51562	0.1327:0.0:0.0:0.8673	.	132	Q8WTR2	DUS19_HUMAN	R	132	ENSP00000346160:C132R	ENSP00000346160:C132R	C	+	1	0	DUSP19	183660133	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.113000	0.77095	0.934000	0.37316	0.520000	0.50463	TGT	.	.	none		0.343	DUSP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255866.1			C	183951888	T	C	183951888	3	2	24	1	0	0	0	0	1	0	0	0	4820	1464	51	3	404	3	DUSP19	2	183951888	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	4345298	183951888	59247485	92	8309											
COL3A1	1281	hgsc.bcm.edu	37	chr2	189858790	189858790	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgggattaatggtagtccTggtggtaaaggcgaaatggt	10	11	15	5	1	0	0	0	0	0	0	1	2	1	1	2	6	0	2	2	6	5	3			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:189858790T>C	ENST00000304636.3	+	17	1346	c.1176T>C	c.(1174-1176)ccT>ccC	p.P392P	COL3A1_ENST00000317840.5_Silent_p.P392P	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	392	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)	ATGGTAGTCCTGGTGGTAAAG	0.383																																					p.P392P		Atlas-SNP	.											.	COL3A1	292	.	0			c.T1176C						PASS	.						129	127	128					2																	189858790		2203	4300	6503	SO:0001819	synonymous_variant	1281	exon17			TAGTCCTGGTGGT	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.1176T>C	2.37:g.189858790T>C		96	0	0		80	36	0.45	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Silent	SNP	ENST00000304636.3	37	CCDS2297.1	.	.	.	.	.	.	.	.	.	.	T	9.959	1.222154	0.22457	.	.	ENSG00000168542	ENST00000450867	.	.	.	5.86	3.44	0.39384	.	.	.	.	.	T	0.54549	0.1865	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46830	-0.9163	4	.	.	.	.	5.9517	0.19250	0.1242:0.1382:0.0:0.7376	.	.	.	.	R	59	.	.	W	+	1	0	COL3A1	189567035	0.989000	0.36119	1.000000	0.80357	0.974000	0.67602	0.128000	0.15810	0.540000	0.28808	0.528000	0.53228	TGG	.	.	none		0.383	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090		C	189858790	T	C	189858790	2	2	24	1	0	0	0	0	0	0	0	1	3690	1567	55	3		3	COL3A1	2	189858790	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	5906902	189858790	53340583	93	8310											
COL3A1	1281	hgsc.bcm.edu	37	chr2	189862995	189862995	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatatgattctttctagggcTtgcctggtacaggtggtcct	7	15	11	8	0	2	1	0	1	2	0	3	1	3	1	2	4	2	2	2	4	4	6	rs41263757	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:189862995T>C	ENST00000304636.3	+	28	2097	c.1927T>C	c.(1927-1929)Ttg>Ctg	p.L643L	COL3A1_ENST00000317840.5_Silent_p.L643L	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	643	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)	TTTCTAGGGCTTGCCTGGTAC	0.353													T|||	9	0.00179712	0.0	0.0014	5008	,	,		15368	0.0		0.008	False		,,,				2504	0.0				p.L643L		Atlas-SNP	.											.	COL3A1	292	.	0			c.T1927C						PASS	.	T		0,4406		0,0,2203	65	68	67		1927	-3.8	0.6	2	dbSNP_127	67	20,8580	14.0+/-48.4	0,20,4280	no	coding-synonymous	COL3A1	NM_000090.3		0,20,6483	CC,CT,TT		0.2326,0.0,0.1538		643/1467	189862995	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	1281	exon28			TAGGGCTTGCCTG	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.1927T>C	2.37:g.189862995T>C		76	0	0		102	47	0.460784	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Silent	SNP	ENST00000304636.3	37	CCDS2297.1																																																																																			T|0.998;C|0.002	0.002	strong		0.353	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090		C	189862995	T	C	189862995	2	2	24	1	0	0	0	0	0	0	0	1	3690	1606	56	3		3	COL3A1	2	189862995	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	4205	189862995	53336378	94	8311											
DNAH7	56171	hgsc.bcm.edu	37	chr2	196922836	196922836	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atttttctttgctggccgatTtatcctgtatgaaaaacatg	10	17	7	7	1	1	1	0	1	1	0	2	2	2	1	2	1	2	2	2	1	4	6	rs72917299	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:196922836T>A	ENST00000312428.6	-	2	120	c.20A>T	c.(19-21)aAa>aTa	p.K7I	DNAH7_ENST00000410072.1_Missense_Mutation_p.K7I	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	7	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						GCTGGCCGATTTATCCTGTAT	0.313													T|||	16	0.00319489	0.0008	0.0029	5008	,	,		16097	0.0		0.0129	False		,,,				2504	0.0				p.K7I		Atlas-SNP	.											.	DNAH7	512	.	0			c.A20T						PASS	.	T	ILE/LYS	10,3592		0,10,1791	181	174	176		20	4.3	0.9	2	dbSNP_130	176	108,8028		1,106,3961	yes	missense	DNAH7	NM_018897.2	102	1,116,5752	AA,AT,TT		1.3274,0.2776,1.0053	possibly-damaging	7/4025	196922836	118,11620	1801	4068	5869	SO:0001583	missense	56171	exon2			GCCGATTTATCCT	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.20A>T	2.37:g.196922836T>A	ENSP00000311273:p.Lys7Ile	131	0	0		98	46	0.469388	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	13	0.005952380952380952	0	0.0	2	0.0055248618784530384	1	0.0017482517482517483	10	0.013192612137203167	T	13.85	2.361068	0.41801	0.002776	0.013274	ENSG00000118997	ENST00000312428;ENST00000410072;ENST00000312446	T;T	0.23754	1.89;2.52	4.29	4.29	0.51040	.	.	.	.	.	T	0.26919	0.0659	N	0.22421	0.69	0.31255	N	0.693556	D	0.65815	0.995	D	0.75484	0.986	T	0.19712	-1.0297	9	0.87932	D	0	.	10.1288	0.42665	0.0:0.0:0.0:1.0	.	7	Q8WXX0	DYH7_HUMAN	I	7	ENSP00000311273:K7I;ENSP00000386260:K7I	ENSP00000311273:K7I	K	-	2	0	DNAH7	196631081	0.996000	0.38824	0.876000	0.34364	0.572000	0.35998	3.399000	0.52586	2.155000	0.67459	0.460000	0.39030	AAA	T|0.991;A|0.009	0.009	strong		0.313	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		A	196922836	T	A	196922836	3	1	24	1	0	0	0	0	1	0	0	0	4608	1841	64	5	12310	5	DNAH7	2	196922836	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	7059841	196922836	46276537	95	8312											
NBEAL1	65065	hgsc.bcm.edu	37	chr2	203922075	203922075	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcaaaaaaaaagagaaggaAatggcagatcagacatgtat	22	5	10	4	0	1	3	1	0	0	3	1	5	1	4	0	2	1	3	0	2	7	1	rs146121994	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:203922075A>G	ENST00000449802.1	+	6	747	c.414A>G	c.(412-414)gaA>gaG	p.E138E	NBEAL1_ENST00000478884.1_3'UTR	NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	138										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						AAGAGAAGGAAATGGCAGATC	0.313													A|||	7	0.00139776	0.0	0.0	5008	,	,		17801	0.0		0.006	False		,,,				2504	0.001				p.E138E		Atlas-SNP	.											.	NBEAL1	266	.	0			c.A414G						PASS	.	A		2,1382		0,2,690	169	146	153		414	2.5	1	2	dbSNP_134	153	29,3151		0,29,1561	no	coding-synonymous	NBEAL1	NM_001114132.1		0,31,2251	GG,GA,AA		0.9119,0.1445,0.6792		138/2695	203922075	31,4533	692	1590	2282	SO:0001819	synonymous_variant	65065	exon6			GAAGGAAATGGCA	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.414A>G	2.37:g.203922075A>G		53	0	0		49	28	0.571429	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Silent	SNP	ENST00000449802.1	37	CCDS46495.1																																																																																			A|0.997;G|0.003	0.003	strong		0.313	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4			G	203922075	A	G	203922075	2	3	24	1	0	0	0	0	0	0	0	1	10197	11	1	3		3	NBEAL1	2	203922075	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	6999239	203922075	39277298	96	8313											
NBEAL1	65065	hgsc.bcm.edu	37	chr2	204058557	204058557	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tatcagcagaagaagcagtgCagaagccaaccaaaatagac	19	4	9	9	0	1	4	1	0	0	4	1	4	1	4	2	0	5	3	2	0	8	2	rs114408639	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:204058557C>G	ENST00000449802.1	+	46	7207	c.6874C>G	c.(6874-6876)Cag>Gag	p.Q2292E		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	2292										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						AGAAGCAGTGCAGAAGCCAAC	0.348													C|||	8	0.00159744	0.0	0.0	5008	,	,		15075	0.0		0.006	False		,,,				2504	0.002				p.Q2292E		Atlas-SNP	.											.	NBEAL1	266	.	0			c.C6874G						PASS	.	C	GLU/GLN	3,3747		0,3,1872	156	155	155		6874	5.4	1	2	dbSNP_132	155	81,8123		0,81,4021	yes	missense	NBEAL1	NM_001114132.1	29	0,84,5893	GG,GC,CC		0.9873,0.08,0.7027	benign	2292/2695	204058557	84,11870	1875	4102	5977	SO:0001583	missense	65065	exon46			GCAGTGCAGAAGC	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.6874C>G	2.37:g.204058557C>G	ENSP00000399903:p.Gln2292Glu	101	0	0		95	45	0.473684	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Missense_Mutation	SNP	ENST00000449802.1	37	CCDS46495.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	13.17	2.158032	0.38119	8.0E-4	0.009873	ENSG00000144426	ENST00000449802;ENST00000414576	T;T	0.52526	0.66;1.25	5.43	5.43	0.79202	.	0.155623	0.40818	U	0.001008	T	0.34279	0.0892	L	0.54323	1.7	0.30447	N	0.775613	B	0.27450	0.179	B	0.27170	0.077	T	0.37979	-0.9682	10	0.27785	T	0.31	.	12.2442	0.54560	0.0:0.9212:0.0:0.0788	.	2292	Q6ZS30	NBEL1_HUMAN	E	2292;307	ENSP00000399903:Q2292E;ENSP00000388466:Q307E	ENSP00000388466:Q307E	Q	+	1	0	NBEAL1	203766802	1.000000	0.71417	0.957000	0.39632	0.991000	0.79684	4.345000	0.59360	2.550000	0.86006	0.650000	0.86243	CAG	C|0.997;G|0.003	0.003	strong		0.348	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4			G	204058557	C	G	204058557	3	3	24	1	0	0	0	0	1	0	0	0	10197	711	25	4	7052	4	NBEAL1	2	204058557	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	136482	204058557	39140816	97	8314											
ATG9A	79065	hgsc.bcm.edu	37	chr2	220088468	220088468	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtgacaatggggctcagcaActcttccaaaatgaacacct	13	9	8	11	0	2	2	1	2	1	0	3	2	3	2	2	2	3	2	2	2	5	1			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:220088468A>G	ENST00000409618.1	-	10	1877	c.1438T>C	c.(1438-1440)Ttg>Ctg	p.L480L	ATG9A_ENST00000396761.2_Silent_p.L480L|ATG9A_ENST00000361242.4_Silent_p.L480L|ATG9A_ENST00000409422.1_Silent_p.L419L|AC068946.1_ENST00000408417.1_RNA			Q7Z3C6	ATG9A_HUMAN	autophagy related 9A	480					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)		GGGCTCAGCAACTCTTCCAAA	0.577																																					p.L480L		Atlas-SNP	.											.	ATG9A	50	.	0			c.T1438C						PASS	.						57	66	63					2																	220088468		2035	4206	6241	SO:0001819	synonymous_variant	79065	exon10			TCAGCAACTCTTC	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.1438T>C	2.37:g.220088468A>G		61	0	0		91	44	0.483516	NM_001077198	Q3ZAQ6|Q6P0N7|Q7Z317|Q7Z320|Q8NDK6|Q8WU65|Q9BVL5|Q9H6L1|Q9HAG7	Silent	SNP	ENST00000409618.1	37	CCDS42820.1																																																																																			.	.	none		0.577	ATG9A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335930.1	NM_024085		G	220088468	A	G	220088468	2	3	24	1	0	0	0	0	0	0	0	1	1102	40	2	3		3	ATG9A	2	220088468	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	16029911	220088468	23110905	98	8315											
INHA	3623	hgsc.bcm.edu	37	chr2	220439634	220439634	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgtcaccgggaggacccGtggctgtgcccatgtctttg	5	10	13	13	2	2	0	1	0	1	0	2	2	2	2	3	3	1	1	3	3	0	1	rs149916845	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:220439634G>A	ENST00000243786.2	+	2	667	c.487G>A	c.(487-489)Gtg>Atg	p.V163M	INHA_ENST00000489456.1_3'UTR	NM_002191.3	NP_002182.1	P05111	INHA_HUMAN	inhibin, alpha	163					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)		GGGAGGACCCGTGGCTGTGCC	0.667													G|||	4	0.000798722	0.0	0.0	5008	,	,		19117	0.0		0.004	False		,,,				2504	0.0				p.V163M		Atlas-SNP	.											INHA,NS,carcinoma,-1,1	INHA	30	1	0			c.G487A						PASS	.	G	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	65	59	61		487	-0.8	0	2	dbSNP_134	61	16,8584	11.2+/-40.8	0,16,4284	yes	missense	INHA	NM_002191.3	21	0,17,6486	AA,AG,GG		0.186,0.0227,0.1307	benign	163/367	220439634	17,12989	2203	4300	6503	SO:0001583	missense	3623	exon2			GGACCCGTGGCTG		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.487G>A	2.37:g.220439634G>A	ENSP00000243786:p.Val163Met	133	0	0		147	74	0.503401	NM_002191	A8K8H5	Missense_Mutation	SNP	ENST00000243786.2	37	CCDS2444.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	0.133	-1.111751	0.01813	2.27E-4	0.00186	ENSG00000123999	ENST00000243786	D	0.85556	-2.0	4.84	-0.764	0.11027	.	0.785011	0.12700	N	0.446402	T	0.65883	0.2734	N	0.05608	-0.01	0.09310	N	1	B	0.14012	0.009	B	0.09377	0.004	T	0.53809	-0.8386	10	0.40728	T	0.16	0.0079	5.5726	0.17204	0.3651:0.1689:0.4659:0.0	.	163	P05111	INHA_HUMAN	M	163	ENSP00000243786:V163M	ENSP00000243786:V163M	V	+	1	0	INHA	220147878	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.549000	0.06041	0.025000	0.15241	-0.459000	0.05422	GTG	G|0.998;A|0.002	0.002	strong		0.667	INHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131425.1			A	220439634	G	A	220439634	3	1	24	1	0	0	0	0	1	0	0	0	7749	1145	40	1	493	1	INHA	2	220439634	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	351166	220439634	22759739	99	8316											
MOGAT1	116255	hgsc.bcm.edu	37	chr2	223574546	223574546	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tatatggaggaacttaggaaAttgtttgaggaacacaaagg	16	10	12	3	0	0	1	0	1	0	0	0	5	0	5	0	5	2	1	0	5	7	5	rs142300173	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:223574546A>G	ENST00000446656.3	+	6	945	c.945A>G	c.(943-945)aaA>aaG	p.K315K		NM_058165.2	NP_477513.2	Q96PD6	MOGT1_HUMAN	monoacylglycerol O-acyltransferase 1	315					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)		AACTTAGGAAATTGTTTGAGG	0.393													A|||	17	0.00339457	0.0113	0.0029	5008	,	,		17048	0.0		0.0	False		,,,				2504	0.0				p.K315K	Ovarian(93;205 1446 2385 11581 25911)	Atlas-SNP	.											.	MOGAT1	47	.	0			c.A945G						PASS	.	A		46,3662		0,46,1808	102	101	101		945	-4.6	0	2	dbSNP_134	101	0,8196		0,0,4098	no	coding-synonymous	MOGAT1	NM_058165.2		0,46,5906	GG,GA,AA		0.0,1.2406,0.3864		315/336	223574546	46,11858	1854	4098	5952	SO:0001819	synonymous_variant	116255	exon6			TAGGAAATTGTTT	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.945A>G	2.37:g.223574546A>G		158	0	0		117	57	0.487179	NM_058165	Q6IEE5	Silent	SNP	ENST00000446656.3	37	CCDS46524.1																																																																																			A|0.998;G|0.002	0.002	strong		0.393	MOGAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331010.3	NM_058165		G	223574546	A	G	223574546	2	3	24	1	0	0	0	0	0	0	0	1	9703	98	4	3		3	MOGAT1	2	223574546	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	3134912	223574546	19624827	100	8317											
SPHKAP	80309	hgsc.bcm.edu	37	chr2	228884530	228884530	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gtacatctttatccatcatgGagaaataagcatcttttgga	13	14	7	7	0	3	1	1	0	2	1	4	3	4	2	1	2	2	2	1	2	4	6	rs61752225	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:228884530G>A	ENST00000392056.3	-	7	1086	c.1040C>T	c.(1039-1041)tCc>tTc	p.S347F	SPHKAP_ENST00000344657.5_Missense_Mutation_p.S347F	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	347						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)		ATCCATCATGGAGAAATAAGC	0.428													G|||	12	0.00239617	0.0015	0.0058	5008	,	,		11672	0.0		0.004	False		,,,				2504	0.002				p.S347F		Atlas-SNP	.											SPHKAP_ENST00000392056,NS,carcinoma,-1,4	SPHKAP	750	4	0			c.C1040T						PASS	.	G	PHE/SER,PHE/SER	1,4405	2.1+/-5.4	0,1,2202	140	133	135		1040,1040	3.8	0.5	2	dbSNP_129	135	40,8560	26.8+/-75.7	0,40,4260	yes	missense,missense	SPHKAP	NM_001142644.1,NM_030623.3	155,155	0,41,6462	AA,AG,GG		0.4651,0.0227,0.3152	benign,benign	347/1701,347/1672	228884530	41,12965	2203	4300	6503	SO:0001583	missense	80309	exon7			ATCATGGAGAAAT		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.1040C>T	2.37:g.228884530G>A	ENSP00000375909:p.Ser347Phe	290	0	0		264	119	0.450758	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	11	0.005036630036630037	4	0.008130081300813009	3	0.008287292817679558	0	0.0	4	0.005277044854881266	G	10.13	1.267055	0.23136	2.27E-4	0.004651	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.12984	2.63;2.63	5.78	3.84	0.44239	.	1.477610	0.03572	N	0.228681	T	0.20007	0.0481	M	0.62723	1.935	0.09310	N	1	P;P	0.42993	0.612;0.797	B;P	0.47528	0.259;0.549	T	0.25293	-1.0136	10	0.72032	D	0.01	.	10.8001	0.46483	0.0:0.1313:0.7185:0.1502	rs61752225	347;347	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	F	347	ENSP00000375909:S347F;ENSP00000339886:S347F	ENSP00000339886:S347F	S	-	2	0	SPHKAP	228592774	0.820000	0.29190	0.537000	0.28052	0.062000	0.15995	2.710000	0.47169	2.742000	0.94016	0.650000	0.86243	TCC	G|0.997;A|0.003	0.003	strong		0.428	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		A	228884530	G	A	228884530	3	1	24	1	0	0	0	0	1	0	0	0	15063	1174	41	2	4086	2	SPHKAP	2	228884530	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	5309984	228884530	14314843	101	8318											
SP140L	93349	hgsc.bcm.edu	37	chr2	231256814	231256814	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcttacaggaaccttggcaaAgtgtatacagactgaggatg	13	10	11	7	0	1	2	0	1	1	1	1	4	1	4	1	3	3	2	1	3	5	4	rs183267141	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:231256814A>G	ENST00000415673.2	+	12	1063	c.977A>G	c.(976-978)aAg>aGg	p.K326R	SP140L_ENST00000243810.6_Missense_Mutation_p.K326R|SP140L_ENST00000444636.1_Missense_Mutation_p.K326R|SP140L_ENST00000396563.4_Missense_Mutation_p.K291R	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	326	SAND. {ECO:0000255|PROSITE- ProRule:PRU00185}.					nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|skin(1)	20						ACCTTGGCAAAGTGTATACAG	0.502													A|||	8	0.00159744	0.0	0.0029	5008	,	,		19306	0.0		0.006	False		,,,				2504	0.0				p.K326R		Atlas-SNP	.											.	SP140L	68	.	0			c.A977G						PASS	.	A	ARG/LYS	1,3985		0,1,1992	106	112	110		977	-0.4	0	2		110	42,8344		0,42,4151	no	missense	SP140L	NM_138402.4	26	0,43,6143	GG,GA,AA		0.5008,0.0251,0.3476	benign	326/581	231256814	43,12329	1993	4193	6186	SO:0001583	missense	93349	exon12			TGGCAAAGTGTAT	BC004921	CCDS46538.1	2q37.1	2013-01-28			ENSG00000185404	ENSG00000185404		"Zinc fingers, PHD-type"	25105	protein-coding gene	gene with protein product						12477932	Standard	NM_138402		Approved		uc010fxm.1	Q9H930	OTTHUMG00000153730	ENST00000415673.2:c.977A>G	2.37:g.231256814A>G	ENSP00000397911:p.Lys326Arg	150	0	0		155	78	0.503226	NM_138402	Q2M375|Q4ZG65|Q9BSP3	Missense_Mutation	SNP	ENST00000415673.2	37	CCDS46538.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	A	11.98	1.800033	0.31869	2.51E-4	0.005008	ENSG00000185404	ENST00000444636;ENST00000415673;ENST00000243810;ENST00000396563	T;T;T;T	0.74842	-0.88;-0.88;-0.88;-0.88	3.44	-0.423	0.12325	.	.	.	.	.	T	0.55386	0.1917	L	0.31420	0.93	0.09310	N	1	P;P	0.48230	0.811;0.907	P;P	0.49665	0.618;0.615	T	0.50651	-0.8803	9	0.35671	T	0.21	.	2.4941	0.04617	0.5579:0.0:0.2383:0.2038	.	291;326	Q9H930-2;Q9H930-4	.;.	R	326;326;326;291	ENSP00000395195:K326R;ENSP00000397911:K326R;ENSP00000243810:K326R;ENSP00000379811:K291R	ENSP00000243810:K326R	K	+	2	0	SP140L	230965058	0.259000	0.24043	0.000000	0.03702	0.011000	0.07611	0.573000	0.23699	-0.079000	0.12707	-0.326000	0.08463	AAG	A|0.997;G|0.003	0.003	strong		0.502	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402		G	231256814	A	G	231256814	3	3	24	1	0	0	0	0	1	0	0	0	14978	72	3	3	1023	3	SP140L	2	231256814	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	2372284	231256814	11942559	102	8319											
KLHL30	377007	hgsc.bcm.edu	37	chr2	239049537	239049537	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgggagctgccatgccacCgcggcctcctggcgctcagc	4	5	14	18	4	1	0	1	0	0	0	2	1	2	1	6	3	4	2	6	3	0	0	rs573206585		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:239049537C>T	ENST00000409223.1	+	2	249	c.142C>T	c.(142-144)Cgc>Tgc	p.R48C	KLHL30_ENST00000305959.4_Missense_Mutation_p.R30C			Q0D2K2	KLH30_HUMAN	kelch-like family member 30	48	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.									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)		GCCATGCCACCGCGGCCTCCT	0.692													C|||	1	0.000199681	0.0	0.0	5008	,	,		17775	0.0		0.0	False		,,,				2504	0.001				p.R48C		Atlas-SNP	.											.	KLHL30	79	.	0			c.C142T						PASS	.						36	43	41					2																	239049537		2132	4219	6351	SO:0001583	missense	377007	exon2			TGCCACCGCGGCC		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.142C>T	2.37:g.239049537C>T	ENSP00000386389:p.Arg48Cys	102	0	0		68	44	0.647059	NM_198582	Q6ZUS1	Missense_Mutation	SNP	ENST00000409223.1	37	CCDS46555.2	.	.	.	.	.	.	.	.	.	.	C	24.7	4.563511	0.86335	.	.	ENSG00000168427	ENST00000409223;ENST00000305959	T;T	0.75477	-0.94;-0.94	5.75	5.75	0.90469	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.90511	0.7027	H	0.94771	3.58	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92575	0.6069	10	0.87932	D	0	.	18.7132	0.91666	0.0:1.0:0.0:0.0	.	48	Q0D2K2	KLH30_HUMAN	C	48;30	ENSP00000386389:R48C;ENSP00000302386:R30C	ENSP00000302386:R30C	R	+	1	0	KLHL30	238714276	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	4.627000	0.61276	2.720000	0.93068	0.655000	0.94253	CGC	.	.	none		0.692	KLHL30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328518.1	NM_198582		T	239049537	C	T	239049537	3	4	24	1	0	0	0	0	1	0	0	0	8393	652	23	1	144	1	KLHL30	2	239049537	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	7792723	239049537	4149836	103	8320											
GPR35	2859	hgsc.bcm.edu	37	chr2	241569492	241569492	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgctgctcaacagcctggcGctctgggtgttctgctgccg	3	11	13	14	2	3	0	1	0	2	0	3	0	3	0	2	2	6	5	2	2	1	1	rs61734451	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:241569492G>C	ENST00000319838.5	+	6	1065	c.123G>C	c.(121-123)gcG>gcC	p.A41A	GPR35_ENST00000438013.2_Silent_p.A72A|GPR35_ENST00000430267.1_Silent_p.A41A|GPR35_ENST00000407714.1_Silent_p.A41A|GPR35_ENST00000403859.1_Silent_p.A41A	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)		ACAGCCTGGCGCTCTGGGTGT	0.652													g|||	22	0.00439297	0.0008	0.0043	5008	,	,		17820	0.0		0.0139	False		,,,				2504	0.0041				p.A72A		Atlas-SNP	.											.	GPR35	43	.	0			c.G216C						PASS	.	G	,,	25,4381	31.7+/-61.6	0,25,2178	75	69	71		216,216,123	-3.3	1	2	dbSNP_129	71	145,8455	71.3+/-133.9	2,141,4157	no	coding-synonymous,coding-synonymous,coding-synonymous	GPR35	NM_001195381.1,NM_001195382.1,NM_005301.3	,,	2,166,6335	CC,CG,GG		1.686,0.5674,1.3071	,,	72/341,72/341,41/310	241569492	170,12836	2203	4300	6503	SO:0001819	synonymous_variant	2859	exon6			CCTGGCGCTCTGG		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.123G>C	2.37:g.241569492G>C		79	0	0		80	36	0.45	NM_001195382	J3KR30|O43495|Q17R58|Q4VBN5|Q4ZFV2|Q6FHI8|Q86UH4	Silent	SNP	ENST00000319838.5	37	CCDS2541.1																																																																																			G|0.990;C|0.010	0.010	strong		0.652	GPR35-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325631.1	NM_001195382		C	241569492	G	C	241569492	2	2	24	1	0	0	0	0	0	0	0	1	6698	1074	38	4		4	GPR35	2	241569492	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	2519955	241569492	1629881	104	8321											
BOK	666	hgsc.bcm.edu	37	chr2	242501765	242501765	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctcttgtgaccacacaggcGatgagctggagatgatccgg	9	8	14	10	2	1	4	0	3	1	1	2	6	2	4	2	3	1	2	2	3	0	1			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr2:242501765G>A	ENST00000318407.3	+	3	525	c.223G>A	c.(223-225)Gat>Aat	p.D75N		NM_032515.4	NP_115904.1	Q9UMX3	BOK_HUMAN	BCL2-related ovarian killer	75					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cell proliferation (GO:0008283)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|male gonad development (GO:0008584)|neuron apoptotic process (GO:0051402)|oligodendrocyte differentiation (GO:0048709)|positive regulation of apoptotic process (GO:0043065)|positive regulation of execution phase of apoptosis (GO:1900119)	cytoplasm (GO:0005737)|mitochondrial membrane (GO:0031966)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			large_intestine(1)|lung(3)|ovary(1)	5		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;2.04e-33)|all cancers(36;7.87e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.52e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.64e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0835)		CCACACAGGCGATGAGCTGGA	0.647																																					p.D75N		Atlas-SNP	.											.	BOK	16	.	0			c.G223A						PASS	.						84	66	72					2																	242501765		2203	4300	6503	SO:0001583	missense	666	exon3			ACAGGCGATGAGC	AF174487	CCDS2550.1	2q37.3	2008-05-22			ENSG00000176720	ENSG00000176720			1087	protein-coding gene	gene with protein product		605404				9356461, 11034351, 15102863	Standard	NM_032515		Approved	BCL2L9, BOKL, MGC4631	uc002wbq.3	Q9UMX3	OTTHUMG00000133411	ENST00000318407.3:c.223G>A	2.37:g.242501765G>A	ENSP00000314132:p.Asp75Asn	56	0	0		52	26	0.5	NM_032515		Missense_Mutation	SNP	ENST00000318407.3	37	CCDS2550.1	.	.	.	.	.	.	.	.	.	.	G	31	5.087479	0.94100	.	.	ENSG00000176720	ENST00000318407	T	0.55588	0.51	4.97	4.97	0.65823	Apoptosis regulator, Bcl2-like (1);Apoptosis regulator, Bcl-2, BH (2);	0.116231	0.56097	D	0.000026	T	0.74222	0.3688	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.71414	0.973	T	0.78360	-0.2234	10	0.62326	D	0.03	-17.3648	18.2203	0.89899	0.0:0.0:1.0:0.0	.	75	Q9UMX3	BOK_HUMAN	N	75	ENSP00000314132:D75N	ENSP00000314132:D75N	D	+	1	0	BOK	242150438	1.000000	0.71417	0.978000	0.43139	0.758000	0.43043	9.034000	0.93747	2.283000	0.76528	0.655000	0.94253	GAT	.	.	none		0.647	BOK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257268.2	NM_032515		A	242501765	G	A	242501765	3	1	24	1	0	0	0	0	1	0	0	0	1484	1058	37	1	229	1	BOK	2	242501765	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	932273	242501765	697608	105	8322											
CHL1	10752	hgsc.bcm.edu	37	chr3	361493	361493	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tacttggaagaggactaatcGtatatctaatgttcctcctg	11	14	8	8	1	1	1	0	0	1	1	4	3	3	3	2	2	1	2	2	2	6	7	rs142251617	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:361493G>A	ENST00000256509.2	+	3	676	c.34G>A	c.(34-36)Gta>Ata	p.V12I	CHL1_ENST00000397491.2_Missense_Mutation_p.V12I	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	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)		AGGACTAATCGTATATCTAAT	0.348													G|||	66	0.0131789	0.0015	0.0634	5008	,	,		16221	0.001		0.0089	False		,,,				2504	0.0102				p.V12I		Atlas-SNP	.											.	CHL1	242	.	0			c.G34A						PASS	.	G	ILE/VAL	13,4391	20.2+/-43.8	0,13,2189	65	68	67		34	-9.8	0	3	dbSNP_134	67	106,8494	57.9+/-119.4	0,106,4194	yes	missense	CHL1	NM_006614.2	29	0,119,6383	AA,AG,GG		1.2326,0.2952,0.9151	benign	12/1225	361493	119,12885	2202	4300	6502	SO:0001583	missense	10752	exon1			CTAATCGTATATC	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.34G>A	3.37:g.361493G>A	ENSP00000256509:p.Val12Ile	43	0	0		41	18	0.439024	NM_001253388	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	37	CCDS2556.1	29	0.013278388278388278	3	0.006097560975609756	18	0.049723756906077346	1	0.0017482517482517483	7	0.009234828496042216	G	2.914	-0.224798	0.06022	0.002952	0.012326	ENSG00000134121	ENST00000256509;ENST00000397491;ENST00000427688;ENST00000421198;ENST00000435603;ENST00000449294	T;T;T;T;T;T	0.61627	0.34;0.34;1.06;0.43;0.31;0.09	4.91	-9.82	0.00484	.	2.380520	0.01454	N	0.015608	T	0.04861	0.0131	N	0.08118	0	0.09310	N	1	B;B;B	0.09022	0.0;0.001;0.002	B;B;B	0.04013	0.0;0.001;0.001	T	0.10941	-1.0608	10	0.11794	T	0.64	.	4.8623	0.13590	0.1328:0.4054:0.0618:0.4	.	12;12;12	B3KX75;O00533;O00533-2	.;CHL1_HUMAN;.	I	12	ENSP00000256509:V12I;ENSP00000380628:V12I;ENSP00000403311:V12I;ENSP00000413628:V12I;ENSP00000397445:V12I;ENSP00000390440:V12I	ENSP00000256509:V12I	V	+	1	0	CHL1	336493	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.238000	0.01199	-3.536000	0.00145	-0.238000	0.12139	GTA	G|0.990;A|0.010	0.010	strong		0.348	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614		A	361493	G	A	361493	3	1	24	1	0	0	0	0	1	0	0	0	3351	1145	40	1	36	1	CHL1	3	361493	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10		361493	197660937	106	8323											
SETMAR	6419	hgsc.bcm.edu	37	chr3	4358476	4358476	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaaaaaaggtcatggtcaCtatttggtggtctgctgctg	9	12	11	9	0	3	0	2	0	1	0	3	0	3	0	1	4	2	2	1	4	4	2	rs115195721	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:4358476C>T	ENST00000358065.4	+	3	1668	c.1601C>T	c.(1600-1602)aCt>aTt	p.T534I	SUMF1_ENST00000534863.1_Intron|SETMAR_ENST00000425863.1_Missense_Mutation_p.T395I	NM_006515.3	NP_006506.3	Q53H47	SETMR_HUMAN	SET domain and mariner transposase fusion gene	534	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)		gtcatggtcactatttggtgg	0.463								Chromatin Structure					C|||	43	0.00858626	0.0008	0.0144	5008	,	,		19453	0.0		0.0258	False		,,,				2504	0.0061				p.T534I		Atlas-SNP	.											SETMAR,NS,carcinoma,0,1	SETMAR	30	1	0			c.C1601T						PASS	.	C	ILE/THR	13,3159		0,13,1573	9	6	7		1601	0.2	0.8	3	dbSNP_132	7	122,5474		0,122,2676	no	missense	SETMAR	NM_006515.3	89	0,135,4249	TT,TC,CC		2.1801,0.4098,1.5397	possibly-damaging	534/685	4358476	135,8633	1586	2798	4384	SO:0001583	missense	6419	exon3			TGGTCACTATTTG	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.1601C>T	3.37:g.4358476C>T	ENSP00000373354:p.Thr534Ile	37	0	0		31	8	0.258065	NM_006515	B4DY74|E7EN68|Q13579|Q1G668|Q96F41	Missense_Mutation	SNP	ENST00000358065.4	37	CCDS2563.2	20	0.009157509157509158	0	0.0	8	0.022099447513812154	0	0.0	12	0.0158311345646438	C	11.57	1.678774	0.29783	0.004098	0.021801	ENSG00000170364	ENST00000358065;ENST00000425863	D;T	0.94931	-3.56;0.57	0.235	0.235	0.15431	.	.	.	.	.	D	0.90820	0.7117	M	0.65975	2.015	0.20926	N	0.999826	P;P;P;D	0.52996	0.908;0.898;0.91;0.957	P;P;P;P	0.56648	0.796;0.775;0.803;0.803	D	0.84476	0.0602	8	0.56958	D	0.05	.	.	.	.	.	278;395;521;279	B4DND2;E7EN68;Q53H47;Q96H41	.;.;SETMR_HUMAN;.	I	534;395	ENSP00000373354:T534I;ENSP00000403145:T395I	ENSP00000373354:T534I	T	+	2	0	SETMAR	4333476	0.851000	0.29673	0.754000	0.31244	0.760000	0.43138	0.305000	0.19254	0.308000	0.22923	0.313000	0.20887	ACT	C|0.991;T|0.009	0.009	strong		0.463	SETMAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206587.4	NM_006515		T	4358476	C	T	4358476	3	4	24	1	0	0	0	0	1	0	0	0	14155	565	20	2	1611	2	SETMAR	3	4358476	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	3996983	4358476	193663954	107	8324											
ITPR1	3708	hgsc.bcm.edu	37	chr3	4714929	4714929	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttctccgctgcatgtctgacGagaacctgccctatgacctc	7	11	8	15	2	2	3	0	2	2	1	4	4	2	3	4	0	3	2	4	0	2	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:4714929G>A	ENST00000443694.2	+	18	2269	c.2269G>A	c.(2269-2271)Gag>Aag	p.E757K	ITPR1_ENST00000357086.4_Missense_Mutation_p.E772K|ITPR1_ENST00000423119.2_Missense_Mutation_p.E772K|ITPR1_ENST00000302640.8_Missense_Mutation_p.E757K|ITPR1_ENST00000354582.6_Missense_Mutation_p.E772K|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000456211.2_Missense_Mutation_p.E757K			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	772					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)	CATGTCTGACGAGAACCTGCC	0.557																																					p.E772K		Atlas-SNP	.											ITPR1_ENST00000357086,NS,carcinoma,0,3	ITPR1	659	3	0			c.G2314A						scavenged	.						67	70	69					3																	4714929		2082	4212	6294	SO:0001583	missense	3708	exon21			TCTGACGAGAACC	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.2269G>A	3.37:g.4714929G>A	ENSP00000401671:p.Glu757Lys	91	1	0.010989		93	44	0.473118	NM_001099952	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	37	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	G	14.31	2.495999	0.44352	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.91686	-2.89;-2.89;-2.88;-2.88;-2.89;-2.89	4.74	3.85	0.44370	.	0.000000	0.85682	D	0.000000	D	0.92763	0.7699	L	0.45051	1.395	0.80722	D	1	P;B;D	0.76494	0.603;0.443;0.999	B;B;D	0.63597	0.142;0.06;0.916	D	0.90586	0.4533	10	0.22706	T	0.39	.	14.273	0.66162	0.0:0.0:0.8496:0.1504	.	757;772;772	E7EPX7;Q14643;G5E9P1	.;ITPR1_HUMAN;.	K	772;757;772;772;772;757;757	ENSP00000306253:E757K;ENSP00000346595:E772K;ENSP00000405934:E772K;ENSP00000349597:E772K;ENSP00000397885:E757K;ENSP00000401671:E757K	ENSP00000306253:E757K	E	+	1	0	ITPR1	4689929	1.000000	0.71417	0.797000	0.32132	0.308000	0.27856	9.511000	0.98006	1.327000	0.45338	-0.282000	0.10007	GAG	.	.	none		0.557	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222		A	4714929	G	A	4714929	3	1	24	1	0	0	0	0	1	0	0	0	7929	1059	37	1	2388	1	ITPR1	3	4714929	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	356453	4714929	193307501	108	8325											
SLC6A1	6529	hgsc.bcm.edu	37	chr3	11064091	11064091	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgctggccactggccatcacGctggccatcgcctggatcct	5	8	11	17	3	1	0	1	0	0	0	3	1	2	1	5	4	0	2	5	4	0	0	rs6344	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:11064091G>A	ENST00000287766.4	+	7	1072	c.651G>A	c.(649-651)acG>acA	p.T217T	SLC6A1_ENST00000536032.1_Silent_p.T39T	NM_003042.3	NP_003033.3	P30531	SC6A1_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 1	217					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)	TGGCCATCACGCTGGCCATCG	0.552													G|||	9	0.00179712	0.0008	0.0058	5008	,	,		20511	0.0		0.004	False		,,,				2504	0.0				p.T217T		Atlas-SNP	.											.	SLC6A1	88	.	0			c.G651A						PASS	.						85	76	79					3																	11064091		2203	4300	6503	SO:0001819	synonymous_variant	6529	exon7			CATCACGCTGGCC		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.651G>A	3.37:g.11064091G>A		101	0	0		104	59	0.567308	NM_003042	Q8N4K8	Silent	SNP	ENST00000287766.4	37	CCDS2603.1																																																																																			A|0.000;G|0.954;T|0.046	0.000	strong		0.552	SLC6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102767.2	NM_003042		A	11064091	G	A	11064091	2	1	24	1	0	0	0	0	0	0	0	1	14688	1074	38	1		1	SLC6A1	3	11064091	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	6349162	11064091	186958339	109	8326											
TIMP4	7079	hgsc.bcm.edu	37	chr3	12198336	12198336	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttaccagtcaagagatactgCttctggctgttggcttctag	8	14	10	9	0	3	1	1	0	2	1	3	2	3	1	1	2	3	4	1	2	4	6			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:12198336C>G	ENST00000287814.4	-	3	846	c.336G>C	c.(334-336)aaG>aaC	p.K112N	SYN2_ENST00000432424.2_RNA	NM_003256.3	NP_003247.1	Q99727	TIMP4_HUMAN	TIMP metallopeptidase inhibitor 4	112	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				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						AGAGATACTGCTTCTGGCTGT	0.433																																					p.K112N	Melanoma(199;1446 2144 30617 38794 51714)	Atlas-SNP	.											.	TIMP4	21	.	0			c.G336C						PASS	.						122	111	115					3																	12198336		2203	4300	6503	SO:0001583	missense	7079	exon3			ATACTGCTTCTGG	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.336G>C	3.37:g.12198336C>G	ENSP00000287814:p.Lys112Asn	188	0	0		192	88	0.458333	NM_003256	B2R7K6	Missense_Mutation	SNP	ENST00000287814.4	37	CCDS2608.1	.	.	.	.	.	.	.	.	.	.	C	12.04	1.819542	0.32145	.	.	ENSG00000157150	ENST00000287814	D	0.94184	-3.37	4.85	1.79	0.24919	Tissue inhibitor of metalloproteinases-like, OB-fold (1);Netrin domain (1);	0.246504	0.42172	D	0.000755	D	0.92391	0.7585	M	0.74467	2.265	0.43156	D	0.994932	P	0.43857	0.819	P	0.47402	0.546	D	0.89472	0.3744	10	0.56958	D	0.05	.	5.3067	0.15807	0.1289:0.5526:0.0:0.3185	.	112	Q99727	TIMP4_HUMAN	N	112	ENSP00000287814:K112N	ENSP00000287814:K112N	K	-	3	2	TIMP4	12173336	0.131000	0.22433	1.000000	0.80357	0.952000	0.60782	-0.631000	0.05496	0.541000	0.28827	-0.150000	0.13652	AAG	.	.	none		0.433	TIMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251978.1	NM_003256		G	12198336	C	G	12198336	3	3	24	1	0	0	0	0	1	0	0	0	15935	796	28	4	350	4	TIMP4	3	12198336	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1134245	12198336	185824094	110	8327											
TSEN2	80746	hgsc.bcm.edu	37	chr3	12538040	12538040	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagacaaacatgcctatcAtcacatcaaagaggtaagtc	17	8	7	9	0	3	3	3	1	0	2	4	3	3	3	1	1	2	1	1	1	5	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:12538040A>G	ENST00000284995.6	+	4	682	c.295A>G	c.(295-297)Atc>Gtc	p.I99V	TSEN2_ENST00000444864.1_Missense_Mutation_p.I99V|TSEN2_ENST00000314571.7_Missense_Mutation_p.I99V|TSEN2_ENST00000454502.2_Missense_Mutation_p.I99V|TSEN2_ENST00000402228.3_Missense_Mutation_p.I99V|TSEN2_ENST00000415684.1_Missense_Mutation_p.I99V|TSEN2_ENST00000383797.5_Missense_Mutation_p.I99V	NM_025265.3	NP_079541.1	Q8NCE0	SEN2_HUMAN	TSEN2 tRNA splicing endonuclease subunit	99					mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-intron endonuclease complex (GO:0000214)	lyase activity (GO:0016829)|nucleic acid binding (GO:0003676)|tRNA-intron endonuclease activity (GO:0000213)			central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)	19						CATGCCTATCATCACATCAAA	0.368																																					p.I99V		Atlas-SNP	.											.	TSEN2	46	.	0			c.A295G						PASS	.						201	190	194					3																	12538040		2203	4300	6503	SO:0001583	missense	80746	exon4			CCTATCATCACAT	BC019582	CCDS2611.1, CCDS46757.1, CCDS46758.1, CCDS46759.1	3p25.2	2013-08-06	2013-08-06		ENSG00000154743	ENSG00000154743		"tRNA splicing endonuclease subunits"	28422	protein-coding gene	gene with protein product		608753	"tRNA splicing endonuclease 2 homolog (SEN2, S. cerevisiae)", "tRNA splicing endonuclease 2 homolog (S. cerevisiae)"			15109492	Standard	NM_025265		Approved	SEN2, SEN2L, MGC2776	uc003bxb.3	Q8NCE0	OTTHUMG00000129765	ENST00000284995.6:c.295A>G	3.37:g.12538040A>G	ENSP00000284995:p.Ile99Val	118	0	0		121	50	0.413223	NM_001145394	B7Z6K1|C9IZI7|G5E9Q3|Q8WTW7|Q9BPU7	Missense_Mutation	SNP	ENST00000284995.6	37	CCDS2611.1	.	.	.	.	.	.	.	.	.	.	A	13.07	2.128557	0.37533	.	.	ENSG00000154743	ENST00000446004;ENST00000314571;ENST00000454502;ENST00000383797;ENST00000402228;ENST00000284995;ENST00000444864;ENST00000537959;ENST00000415684	T;T;T;T;T;T;T;T	0.59364	0.29;0.3;0.39;0.29;0.35;0.35;0.27;0.3	5.12	1.92	0.25849	.	0.308783	0.32935	N	0.005479	T	0.48466	0.1501	M	0.71581	2.175	0.27073	N	0.963277	B;B;B;B	0.32283	0.362;0.03;0.066;0.003	B;B;B;B	0.33121	0.158;0.047;0.094;0.003	T	0.32693	-0.9897	10	0.30854	T	0.27	-16.8333	3.9504	0.09366	0.4827:0.3484:0.1689:0.0	.	99;99;99;99	G5E9Q3;Q8NCE0;Q8NCE0-3;C9IZI7	.;SEN2_HUMAN;.;.	V	99;99;99;99;99;99;99;72;99	ENSP00000406238:I99V;ENSP00000323188:I99V;ENSP00000392029:I99V;ENSP00000373307:I99V;ENSP00000385976:I99V;ENSP00000284995:I99V;ENSP00000407974:I99V;ENSP00000416510:I99V	ENSP00000284995:I99V	I	+	1	0	TSEN2	12513040	0.985000	0.35326	0.991000	0.47740	0.982000	0.71751	0.964000	0.29306	1.943000	0.56356	0.529000	0.55759	ATC	.	.	none		0.368	TSEN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251981.1	NM_025265		G	12538040	A	G	12538040	3	3	24	1	0	0	0	0	1	0	0	0	16627	217	8	3	305	3	TSEN2	3	12538040	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	339704	12538040	185484390	111	8328											
DCLK3	85443	hgsc.bcm.edu	37	chr3	36779992	36779992	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggtctcggtctccccacaGcggtggtctcctttcagagc	4	10	13	14	2	4	1	1	0	3	1	7	1	4	1	3	5	2	0	3	5	0	1	rs55888784	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:36779992G>A	ENST00000416516.2	-	2	649	c.159C>T	c.(157-159)cgC>cgT	p.R53R		NM_033403.1	NP_208382.1	Q9C098	DCLK3_HUMAN	doublecortin-like kinase 3	53						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						TCTCCCCACAGCGGTGGTCTC	0.617													G|||	44	0.00878594	0.0008	0.013	5008	,	,		16590	0.001		0.0298	False		,,,				2504	0.0031				p.R53R		Atlas-SNP	.											DCLK3,NS,carcinoma,-2,1	DCLK3	95	1	0			c.C159T						PASS	.	G		12,3870		0,12,1929	75	78	77		159	1.1	0.1	3	dbSNP_129	77	220,8064		4,212,3926	no	coding-synonymous	DCLK3	NM_033403.1		4,224,5855	AA,AG,GG		2.6557,0.3091,1.907		53/649	36779992	232,11934	1941	4142	6083	SO:0001819	synonymous_variant	85443	exon2			CCCACAGCGGTGG	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.159C>T	3.37:g.36779992G>A		113	0	0		106	58	0.54717	NM_033403		Silent	SNP	ENST00000416516.2	37	CCDS43064.1																																																																																			G|0.982;A|0.018	0.018	strong		0.617	DCLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341727.1	XM_047355		A	36779992	G	A	36779992	2	1	24	1	0	0	0	0	0	0	0	1	4295	958	34	2		2	DCLK3	3	36779992	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	24241952	36779992	161242438	112	8329											
C3orf75	54859	hgsc.bcm.edu	37	chr3	47545911	47545911	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaggaacacaagctgcccacGctcccgcgccatggtcaggc	10	4	11	16	3	1	0	1	0	0	0	2	1	2	1	3	3	3	2	3	3	3	0	rs377204125		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:47545911G>A	ENST00000296149.4	-	4	402	c.232C>T	c.(232-234)Cgt>Tgt	p.R78C	ELP6_ENST00000446787.1_Missense_Mutation_p.R5C|ELP6_ENST00000439305.1_Missense_Mutation_p.R5C	NM_001031703.2	NP_001026873.2	Q0PNE2	ELP6_HUMAN	elongator acetyltransferase complex subunit 6	78					chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Elongator holoenzyme complex (GO:0033588)											AGCTGCCCACGCTCCCGCGCC	0.542																																					p.R78C		Atlas-SNP	.											.	.	.	.	0			c.C232T						PASS	.	G	CYS/ARG	0,4072		0,0,2036	57	61	60		232	2.1	0	3		60	1,8375		0,1,4187	no	missense	C3orf75	NM_001031703.2	180	0,1,6223	AA,AG,GG		0.0119,0.0,0.0080	benign	78/267	47545911	1,12447	2036	4188	6224	SO:0001583	missense	54859	exon4			GCCCACGCTCCCG	AK000218	CCDS43082.1	3p21.31	2012-08-14	2012-08-08	2012-08-08	ENSG00000163832	ENSG00000163832		"Elongator acetyltransferase complex subunits"	25976	protein-coding gene	gene with protein product		615020	"transmembrane protein 103", "chromosome 3 open reading frame 75"	TMEM103, C3orf75		22854966	Standard	XM_005265241		Approved	FLJ20211	uc003crk.3	Q0PNE2	OTTHUMG00000133521	ENST00000296149.4:c.232C>T	3.37:g.47545911G>A	ENSP00000296149:p.Arg78Cys	25	0	0		33	13	0.393939	NM_001031703	Q9BW57|Q9NXJ3	Missense_Mutation	SNP	ENST00000296149.4	37	CCDS43082.1	.	.	.	.	.	.	.	.	.	.	G	12.69	2.012549	0.35511	0.0	1.19E-4	ENSG00000163832	ENST00000296149;ENST00000450051;ENST00000446787;ENST00000439305;ENST00000412761;ENST00000444760;ENST00000425291;ENST00000449409;ENST00000414236	.	.	.	6.06	2.13	0.27403	.	0.296215	0.40064	N	0.001181	T	0.27489	0.0675	L	0.41027	1.25	0.09310	N	0.999998	B;B;B	0.25351	0.061;0.124;0.052	B;B;B	0.23018	0.019;0.043;0.027	T	0.21381	-1.0247	9	0.56958	D	0.05	-0.5247	2.3576	0.04300	0.2284:0.1263:0.5154:0.1298	.	54;78;78	B4DP60;C9JAS1;Q0PNE2	.;.;CC075_HUMAN	C	78;54;5;5;5;5;5;5;5	.	ENSP00000296149:R78C	R	-	1	0	C3orf75	47520915	0.001000	0.12720	0.012000	0.15200	0.638000	0.38207	0.871000	0.28023	0.398000	0.25338	0.655000	0.94253	CGT	.	.	weak		0.542	ELP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257493.1	NM_017713		A	47545911	G	A	47545911	3	1	24	1	0	0	0	0	1	0	0	0	2247	1087	38	1	584	1	C3orf75	3	47545911	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	10765919	47545911	150476519	113	8330											
USP19	10869	hgsc.bcm.edu	37	chr3	49148980	49148980	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctggcaaggagccaacctcaAtgggcccactggccagcatc	10	5	11	15	0	1	0	1	0	0	0	2	1	1	1	4	4	3	2	4	4	3	0			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:49148980A>G	ENST00000398888.2	-	20	3179	c.2861T>C	c.(2860-2862)aTt>aCt	p.I954T	USP19_ENST00000434032.2_Missense_Mutation_p.I1055T|USP19_ENST00000398898.2_Missense_Mutation_p.I994T|USP19_ENST00000398896.1_Missense_Mutation_p.I762T|USP19_ENST00000417901.1_Missense_Mutation_p.I1057T|USP19_ENST00000398892.3_Missense_Mutation_p.I994T|USP19_ENST00000453664.1_Missense_Mutation_p.I1045T	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	954	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)		GCCAACCTCAATGGGCCCACT	0.627																																					p.I1057T		Atlas-SNP	.											.	USP19	158	.	0			c.T3170C						PASS	.						35	36	36					3																	49148980		1888	4115	6003	SO:0001583	missense	10869	exon21			ACCTCAATGGGCC	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.2861T>C	3.37:g.49148980A>G	ENSP00000381863:p.Ile954Thr	49	0	0		41	16	0.390244	NM_001199161	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Missense_Mutation	SNP	ENST00000398888.2	37	CCDS43090.1	.	.	.	.	.	.	.	.	.	.	A	2.782	-0.253241	0.05829	.	.	ENSG00000172046	ENST00000398896;ENST00000398898;ENST00000417901;ENST00000453664;ENST00000398892;ENST00000398888;ENST00000434032	T;T;T;T;T;T;T	0.18174	2.23;2.24;2.34;2.34;2.24;2.33;2.34	6.04	-9.85	0.00476	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	1.404660	0.03866	N	0.274854	T	0.05640	0.0148	N	0.05414	-0.055	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	0.001;0.001;0.002;0.0;0.0	T	0.24977	-1.0145	10	0.14252	T	0.57	11.2509	3.8486	0.08945	0.2931:0.3067:0.3169:0.0833	.	1055;1045;954;994;762	E9PEG8;E7EN22;O94966;B5MEG5;E7ESU0	.;.;UBP19_HUMAN;.;.	T	762;994;1057;1045;994;954;1055	ENSP00000381870:I762T;ENSP00000381872:I994T;ENSP00000395260:I1057T;ENSP00000400090:I1045T;ENSP00000381867:I994T;ENSP00000381863:I954T;ENSP00000401197:I1055T	ENSP00000381863:I954T	I	-	2	0	USP19	49123984	0.000000	0.05858	0.000000	0.03702	0.819000	0.46315	-1.946000	0.01536	-1.572000	0.01661	-0.450000	0.05554	ATT	.	.	none		0.627	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677		G	49148980	A	G	49148980	3	3	24	1	0	0	0	0	1	0	0	0	17065	101	4	3	1123	3	USP19	3	49148980	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	1603069	49148980	148873450	114	8331											
CDHR4	389118	hgsc.bcm.edu	37	chr3	49831032	49831032	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttacctcaacctcgatggtaAtggtacaggagcctgagagg	11	9	12	9	1	1	1	1	1	0	1	2	4	1	2	3	4	4	2	3	4	4	3	rs115485248	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:49831032A>G	ENST00000412678.2	-	12	1615	c.1607T>C	c.(1606-1608)aTt>aCt	p.I536T	CDHR4_ENST00000462108.1_5'Flank	NM_001007540.2	NP_001007541.2	A6H8M9	CDHR4_HUMAN	cadherin-related family member 4	536	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						CTCGATGGTAATGGTACAGGA	0.488													A|||	3	0.000599042	0.0	0.0	5008	,	,		22546	0.0		0.003	False		,,,				2504	0.0				p.I536T		Atlas-SNP	.											.	CDHR4	37	.	0			c.T1607C						PASS	.	A	THR/ILE	0,1384		0,0,692	186	175	178		1607	5.7	1	3	dbSNP_132	178	9,3173		0,9,1582	yes	missense	CDHR4	NM_001007540.2	89	0,9,2274	GG,GA,AA		0.2828,0.0,0.1971	probably-damaging	536/789	49831032	9,4557	692	1591	2283	SO:0001583	missense	389118	exon12			ATGGTAATGGTAC		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.1607T>C	3.37:g.49831032A>G	ENSP00000391409:p.Ile536Thr	127	0	0		100	44	0.44	NM_001007540	Q6UXT0	Missense_Mutation	SNP	ENST00000412678.2	37	CCDS46829.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	17.57	3.423523	0.62733	0.0	0.002828	ENSG00000187492	ENST00000412678	T	0.43688	0.94	5.67	5.67	0.87782	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.66396	0.2785	M	0.84511	2.7	0.80722	D	1	D	0.76494	0.999	D	0.70487	0.969	T	0.72253	-0.4347	9	0.87932	D	0	.	12.3323	0.55046	1.0:0.0:0.0:0.0	.	536	A6H8M9	CDHR4_HUMAN	T	536	ENSP00000391409:I536T	ENSP00000391409:I536T	I	-	2	0	CDHR4	49806036	0.899000	0.30636	0.997000	0.53966	0.981000	0.71138	4.401000	0.59716	2.170000	0.68504	0.529000	0.55759	ATT	A|0.999;G|0.001	0.001	strong		0.488	CDHR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350387.1	NM_001007540		G	49831032	A	G	49831032	3	3	24	1	0	0	0	0	1	0	0	0	3123	101	4	3	791	3	CDHR4	3	49831032	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	682052	49831032	148191398	115	8332											
DOCK3	1795	hgsc.bcm.edu	37	chr3	51386357	51386357	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctctatgattaccagagcctCagctggattcgggtgagctg	8	11	12	10	1	2	3	1	2	1	1	3	4	2	4	2	2	4	2	2	2	2	3			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:51386357C>T	ENST00000266037.9	+	39	4013	c.3990C>T	c.(3988-3990)ctC>ctT	p.L1330L		NM_004947.4	NP_004938.1	Q8IZD9	DOCK3_HUMAN	dedicator of cytokinesis 3	1330	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)		ACCAGAGCCTCAGCTGGATTC	0.562																																					p.L1330L		Atlas-SNP	.											.	DOCK3	397	.	0			c.C3990T						PASS	.						67	67	67					3																	51386357		1965	4145	6110	SO:0001819	synonymous_variant	1795	exon39			GAGCCTCAGCTGG	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.3990C>T	3.37:g.51386357C>T		114	0	0		120	63	0.525	NM_004947	O15017	Silent	SNP	ENST00000266037.9	37	CCDS46835.1																																																																																			.	.	none		0.562	DOCK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346478.5	NM_004947		T	51386357	C	T	51386357	2	4	24	1	0	0	0	0	0	0	0	1	4690	813	29	2		2	DOCK3	3	51386357	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1555325	51386357	146636073	116	8333											
RRP9	9136	hgsc.bcm.edu	37	chr3	51969389	51969389	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaagacaagctgggactcctCggggatcttccacacacgta	11	7	11	12	2	1	1	0	0	1	1	4	4	3	3	2	3	1	2	2	3	3	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:51969389C>T	ENST00000232888.6	-	10	1013	c.940G>A	c.(940-942)Gag>Aag	p.E314K		NM_004704.3	NP_004695.1	O43818	U3IP2_HUMAN	ribosomal RNA processing 9, small subunit (SSU) processome component, homolog (yeast)	314					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)		TGGGACTCCTCGGGGATCTTC	0.652																																					p.E314K		Atlas-SNP	.											.	RRP9	40	.	0			c.G940A						PASS	.						40	40	40					3																	51969389		2203	4300	6503	SO:0001583	missense	9136	exon10			ACTCCTCGGGGAT	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.940G>A	3.37:g.51969389C>T	ENSP00000232888:p.Glu314Lys	91	0	0		95	40	0.421053	NM_004704	B2R996|Q8IZ30	Missense_Mutation	SNP	ENST00000232888.6	37	CCDS2837.1	.	.	.	.	.	.	.	.	.	.	C	32	5.146212	0.94603	.	.	ENSG00000114767	ENST00000232888	T	0.80909	-1.43	4.36	4.36	0.52297	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.051372	0.85682	D	0.000000	D	0.90748	0.7096	M	0.90759	3.145	0.80722	D	1	D	0.89917	1.0	D	0.70227	0.968	D	0.91266	0.5040	10	0.38643	T	0.18	-33.3696	16.7078	0.85377	0.0:1.0:0.0:0.0	.	314	O43818	U3IP2_HUMAN	K	314	ENSP00000232888:E314K	ENSP00000232888:E314K	E	-	1	0	RRP9	51944429	1.000000	0.71417	0.936000	0.37596	0.950000	0.60333	7.083000	0.76859	2.278000	0.76064	0.561000	0.74099	GAG	.	.	none		0.652	RRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346637.1	NM_004704		T	51969389	C	T	51969389	3	4	24	1	0	0	0	0	1	0	0	0	13706	893	31	1	511	1	RRP9	3	51969389	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	583032	51969389	146053041	117	8334											
PXK	54899	hgsc.bcm.edu	37	chr3	58376938	58376938	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagccaaaggaacggctagtGttaagctgggtaagctagct	12	8	13	8	1	0	0	0	0	0	0	0	1	0	1	1	3	5	6	1	3	6	4	rs55962533	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:58376938G>A	ENST00000356151.2	+	6	640	c.531G>A	c.(529-531)gtG>gtA	p.V177V	PXK_ENST00000463280.1_Silent_p.V144V|PXK_ENST00000302779.5_Silent_p.V160V|PXK_ENST00000484288.1_Silent_p.V177V|PXK_ENST00000536660.1_Silent_p.V40V|PXK_ENST00000383715.4_Silent_p.V160V|PXK_ENST00000479241.1_Silent_p.V160V|PXK_ENST00000383716.3_Silent_p.V144V	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)		AACGGCTAGTGTTAAGCTGGG	0.373													G|||	16	0.00319489	0.0	0.0029	5008	,	,		17947	0.0		0.0129	False		,,,				2504	0.001				p.V177V		Atlas-SNP	.											.	PXK	89	.	0			c.G531A						PASS	.	G		19,4387	26.2+/-53.5	0,19,2184	90	95	93		531	1.8	1	3	dbSNP_129	93	110,8490	59.5+/-121.1	1,108,4191	no	coding-synonymous	PXK	NM_017771.3		1,127,6375	AA,AG,GG		1.2791,0.4312,0.9918		177/579	58376938	129,12877	2203	4300	6503	SO:0001819	synonymous_variant	54899	exon6			GCTAGTGTTAAGC	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.531G>A	3.37:g.58376938G>A		65	0	0		68	36	0.529412	NM_017771		Silent	SNP	ENST00000356151.2	37	CCDS2889.1																																																																																			G|0.991;A|0.009	0.009	strong		0.373	PXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353499.1	NM_017771		A	58376938	G	A	58376938	2	1	24	1	0	0	0	0	0	0	0	1	12864	1364	48	2		2	PXK	3	58376938	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	6407549	58376938	139645492	118	8335											
ACOX2	8309	hgsc.bcm.edu	37	chr3	58494661	58494661	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgagcccactggaacaggcGttcgtagacgtttccatcat	9	10	10	12	3	1	2	1	1	0	1	3	3	2	3	2	2	2	3	2	2	2	3			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:58494661G>A	ENST00000302819.5	-	14	2233	c.1942C>T	c.(1942-1944)Cgc>Tgc	p.R648C	ACOX2_ENST00000459701.2_Missense_Mutation_p.R634C|ACOX2_ENST00000481527.1_5'UTR	NM_003500.3	NP_003491.1	Q99424	ACOX2_HUMAN	acyl-CoA oxidase 2, branched chain	648					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)		TGGAACAGGCGTTCGTAGACG	0.433																																					p.R648C		Atlas-SNP	.											.	ACOX2	53	.	0			c.C1942T						PASS	.						130	114	119					3																	58494661		2203	4300	6503	SO:0001583	missense	8309	exon14			ACAGGCGTTCGTA	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.1942C>T	3.37:g.58494661G>A	ENSP00000307697:p.Arg648Cys	91	0	0		103	49	0.475728	NM_003500	A6NF16|B2R8U5	Missense_Mutation	SNP	ENST00000302819.5	37	CCDS33775.1	.	.	.	.	.	.	.	.	.	.	G	19.75	3.885004	0.72410	.	.	ENSG00000168306	ENST00000459701;ENST00000302819	T;T	0.47528	0.84;0.84	5.43	4.52	0.55395	Acyl-CoA oxidase, C-terminal (1);Acyl-CoA dehydrogenase/oxidase C-terminal (1);	0.198277	0.34959	N	0.003549	T	0.71022	0.3291	M	0.87682	2.9	0.48571	D	0.999672	D	0.89917	1.0	D	0.79784	0.993	T	0.76408	-0.2970	10	0.87932	D	0	-16.8637	13.3882	0.60807	0.0:0.0:0.7178:0.2822	.	648	Q99424	ACOX2_HUMAN	C	634;648	ENSP00000418562:R634C;ENSP00000307697:R648C	ENSP00000307697:R648C	R	-	1	0	ACOX2	58469701	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	2.978000	0.49305	2.583000	0.87209	0.579000	0.79373	CGC	.	.	none		0.433	ACOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353541.1			A	58494661	G	A	58494661	3	1	24	1	0	0	0	0	1	0	0	0	159	1145	40	1	111	1	ACOX2	3	58494661	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	117723	58494661	139527769	119	8336											
PTPRG	5793	hgsc.bcm.edu	37	chr3	61989028	61989028	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttgtttcacacagtcgccAtccttctgaaagacgactat	11	13	6	11	2	2	2	1	1	1	1	4	3	3	2	2	0	0	1	2	0	2	4	rs140777402		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:61989028A>G	ENST00000474889.1	+	4	753	c.376A>G	c.(376-378)Atc>Gtc	p.I126V	PTPRG_ENST00000295874.10_Missense_Mutation_p.I126V	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	126	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)		CACAGTCGCCATCCTTCTGAA	0.428													A|||	1	0.000199681	0.0	0.0	5008	,	,		20437	0.0		0.001	False		,,,				2504	0.0				p.I126V		Atlas-SNP	.											PTPRG,NS,malignant_melanoma,-2,1	PTPRG	153	1	0			c.A376G						PASS	.	A	VAL/ILE	0,4406		0,0,2203	89	89	89		376	5	1	3	dbSNP_134	89	5,8595	3.7+/-12.6	0,5,4295	yes	missense	PTPRG	NM_002841.3	29	0,5,6498	GG,GA,AA		0.0581,0.0,0.0384	benign	126/1446	61989028	5,13001	2203	4300	6503	SO:0001583	missense	5793	exon4			GTCGCCATCCTTC	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.376A>G	3.37:g.61989028A>G	ENSP00000418112:p.Ile126Val	103	0	0		87	40	0.45977	NM_002841	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Missense_Mutation	SNP	ENST00000474889.1	37	CCDS2895.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	19.50	3.839240	0.71373	0.0	5.81E-4	ENSG00000144724	ENST00000474889;ENST00000295874	T;T	0.61742	0.08;0.08	6.16	5.0	0.66597	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.052424	0.85682	D	0.000000	T	0.41213	0.1149	N	0.12637	0.245	0.53688	D	0.999973	B;B	0.25272	0.1;0.122	B;B	0.27380	0.047;0.079	T	0.43261	-0.9402	10	0.87932	D	0	.	12.6615	0.56815	0.9349:0.0:0.0651:0.0	.	126;126	P23470-2;P23470	.;PTPRG_HUMAN	V	126	ENSP00000418112:I126V;ENSP00000295874:I126V	ENSP00000295874:I126V	I	+	1	0	PTPRG	61964068	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	4.799000	0.62517	2.367000	0.80283	0.528000	0.53228	ATC	A|1.000;G|0.000	0.000	strong		0.428	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841		G	61989028	A	G	61989028	3	3	24	1	0	0	0	0	1	0	0	0	12817	217	8	3	390	3	PTPRG	3	61989028	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	3494367	61989028	136033402	120	8337											
LRIG1	26018	hgsc.bcm.edu	37	chr3	66431280	66431280	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actgcatacgacccggccacCgtgttctgaaggacagcgcc	9	6	11	15	4	1	1	0	1	1	0	1	3	1	2	4	2	3	2	4	2	2	2	rs9877201	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:66431280C>T	ENST00000273261.3	-	18	3300	c.2776G>A	c.(2776-2778)Ggt>Agt	p.G926S	LRIG1_ENST00000496559.2_5'UTR|SLC25A26_ENST00000536651.1_3'UTR|LRIG1_ENST00000383703.3_Missense_Mutation_p.G903S	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	926			G -> S (in dbSNP:rs9877201).		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)		ACCCGGCCACCGTGTTCTGAA	0.597													C|||	554	0.110623	0.3873	0.0346	5008	,	,		18811	0.0		0.0179	False		,,,				2504	0.0				p.G926S		Atlas-SNP	.											LRIG1,NS,carcinoma,0,1	LRIG1	138	1	0			c.G2776A						PASS	.	C	SER/GLY	1492,2914	473.5+/-356.7	259,974,970	49	52	51		2776	-3.4	0	3	dbSNP_119	51	84,8516	48.9+/-108.6	1,82,4217	yes	missense	LRIG1	NM_015541.2	56	260,1056,5187	TT,TC,CC		0.9767,33.8629,12.1175	benign	926/1094	66431280	1576,11430	2203	4300	6503	SO:0001583	missense	26018	exon18			GGCCACCGTGTTC	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.2776G>A	3.37:g.66431280C>T	ENSP00000273261:p.Gly926Ser	69	0	0		81	40	0.493827	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Missense_Mutation	SNP	ENST00000273261.3	37	CCDS33783.1	210	0.09615384615384616	187	0.3800813008130081	8	0.022099447513812154	0	0.0	15	0.01978891820580475	C	10.82	1.457361	0.26161	0.338629	0.009767	ENSG00000144749	ENST00000273261;ENST00000383703;ENST00000383702	T;T	0.69040	-0.18;-0.37	5.34	-3.41	0.04839	.	0.402609	0.28016	N	0.016939	T	0.00012	0.0000	N	0.02315	-0.6	0.80722	P	0.0	B;B;B	0.24651	0.012;0.108;0.007	B;B;B	0.15870	0.014;0.014;0.002	T	0.38908	-0.9639	9	0.18710	T	0.47	.	8.9885	0.36008	0.145:0.5962:0.0:0.2587	rs9877201;rs52813156;rs59347115;rs9877201	903;926;926	Q96JA1-2;Q5XWD3;Q96JA1	.;.;LRIG1_HUMAN	S	926;903;829	ENSP00000273261:G926S;ENSP00000373208:G903S	ENSP00000273261:G926S	G	-	1	0	LRIG1	66513970	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	-0.284000	0.08422	-0.442000	0.07190	-0.794000	0.03295	GGT	C|0.879;T|0.121	0.121	strong		0.597	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541		T	66431280	C	T	66431280	3	4	24	1	0	0	0	0	1	0	0	0	8953	652	23	1	513	1	LRIG1	3	66431280	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	4442252	66431280	131591150	121	8338											
CRYBG3	131544	hgsc.bcm.edu	37	chr3	97634465	97634465	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcttttagctggctcctctAttaccaagaagacatgtttg	9	14	9	9	0	1	2	0	0	1	2	2	2	2	2	2	2	2	4	2	2	5	5	rs17302349	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:97634465A>G	ENST00000182096.4	+	14	2346	c.2282A>G	c.(2281-2283)tAt>tGt	p.Y761C		NM_153605.3	NP_705833.3	Q68DQ2	CRBG3_HUMAN	beta-gamma crystallin domain containing 3	2709							carbohydrate binding (GO:0030246)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(10)|stomach(1)|upper_aerodigestive_tract(2)	32						TGGCTCCTCTATTACCAAGAA	0.438													A|||	18	0.00359425	0.0	0.0014	5008	,	,		18952	0.0		0.0169	False		,,,				2504	0.0				p.Y2709C		Atlas-SNP	.											.	CRYBG3	86	.	0			c.A8126G						PASS	.	A	CYS/TYR	13,3869		0,13,1928	131	124	127		8126	-0.7	0.7	3	dbSNP_123	127	101,8169		2,97,4036	no	missense	CRYBG3	XM_003118522.2	194	2,110,5964	GG,GA,AA		1.2213,0.3349,0.9381	benign	2709/2971	97634465	114,12038	1941	4135	6076	SO:0001583	missense	131544	exon17			TCCTCTATTACCA			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.2282A>G	3.37:g.97634465A>G	ENSP00000182096:p.Tyr761Cys	126	0	0		125	57	0.456	NM_153605	B4DLE8|F6VHI2|Q4G0V8|Q7Z4R9|Q86VD0|Q8N262|Q8N7F1|Q8NDQ8	Missense_Mutation	SNP	ENST00000182096.4	37		15	0.006868131868131868	0	0.0	1	0.0027624309392265192	0	0.0	14	0.018469656992084433	A	4.996	0.184921	0.09495	0.003349	0.012213	ENSG00000080200	ENST00000182096	D	0.85702	-2.02	5.87	-0.682	0.11339	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.997902	0.08115	N	0.995570	T	0.66076	0.2753	L	0.60845	1.875	0.52501	D	0.999956	B	0.11235	0.004	B	0.09377	0.004	T	0.65919	-0.6051	10	0.51188	T	0.08	.	1.6488	0.02767	0.4574:0.1336:0.2803:0.1287	rs17302349;rs52818309;rs17302349	761	Q68DQ2	CRBG3_HUMAN	C	761	ENSP00000182096:Y761C	ENSP00000182096:Y761C	Y	+	2	0	CRYBG3	99117155	0.999000	0.42202	0.672000	0.29872	0.069000	0.16628	0.555000	0.23422	-0.105000	0.12132	-1.437000	0.01076	TAT	A|0.994;G|0.006	0.006	strong		0.438	CRYBG3-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353751.1	NM_153605		G	97634465	A	G	97634465	3	3	24	1	0	0	0	0	1	0	0	0	3915	449	16	3	2336	3	CRYBG3	3	97634465	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	31203185	97634465	100387965	122	8339											
MYLK	4638	hgsc.bcm.edu	37	chr3	123419782	123419782	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggcctcagggacccatagcGgtcactaccaccaccatcag	11	5	9	16	1	3	0	3	0	0	0	3	1	3	1	5	3	2	0	5	3	2	2	rs3732485	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:123419782G>A	ENST00000475616.1	-	15	2532	c.2533C>T	c.(2533-2535)Cgc>Tgc	p.R845C	MYLK_ENST00000360772.3_Missense_Mutation_p.R845C|MYLK_ENST00000510775.1_5'Flank|MYLK_ENST00000346322.5_Missense_Mutation_p.R776C|MYLK_ENST00000359169.1_Missense_Mutation_p.R845C|MYLK_ENST00000360304.3_Missense_Mutation_p.R845C			Q15746	MYLK_HUMAN	myosin light chain kinase	845			R -> C (in dbSNP:rs3732485).		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)		GACCCATAGCGGTCACTACCA	0.627													G|||	226	0.0451278	0.0318	0.0101	5008	,	,		13765	0.0526		0.0189	False		,,,				2504	0.1074				p.R845C		Atlas-SNP	.											.	MYLK	224	.	0			c.C2533T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	61,4341		0,61,2140	37	42	40		2533,2326,2533,2326	1.3	0	3	dbSNP_107	40	21,8569		0,21,4274	no	missense,missense,missense,missense	MYLK	NM_053025.3,NM_053026.3,NM_053027.3,NM_053028.3	180,180,180,180	0,82,6414	AA,AG,GG		0.2445,1.3857,0.6312	benign,benign,benign,benign	845/1915,776/1846,845/1864,776/1795	123419782	82,12910	2201	4295	6496	SO:0001583	missense	4638	exon18			CATAGCGGTCACT	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.2533C>T	3.37:g.123419782G>A	ENSP00000418335:p.Arg845Cys	23	0	0		43	22	0.511628	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	37	CCDS46896.1	61	0.027930402930402932	16	0.032520325203252036	4	0.011049723756906077	24	0.04195804195804196	17	0.022427440633245383	G	6.688	0.495469	0.12762	0.013857	0.002445	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000475616	T;T;T;T;T	0.67698	-0.28;-0.23;-0.28;-0.22;-0.23	5.45	1.3	0.21679	.	.	.	.	.	T	0.14056	0.0340	N	0.17082	0.46	0.09310	N	0.999992	B;B;B;B;B	0.17268	0.001;0.002;0.021;0.005;0.0	B;B;B;B;B	0.06405	0.001;0.002;0.002;0.002;0.0	T	0.13926	-1.0491	9	0.45353	T	0.12	.	0.6904	0.00890	0.2428:0.1873:0.3784:0.1914	rs3732485;rs52814293;rs3732485	845;776;845;776;845	Q15746-6;Q15746-4;Q15746-3;Q15746-2;Q15746	.;.;.;.;MYLK_HUMAN	C	845;845;845;776;845	ENSP00000354004:R845C;ENSP00000353452:R845C;ENSP00000352088:R845C;ENSP00000320622:R776C;ENSP00000418335:R845C	ENSP00000320622:R776C	R	-	1	0	MYLK	124902472	0.005000	0.15991	0.002000	0.10522	0.625000	0.37756	-0.063000	0.11655	-0.056000	0.13221	-0.314000	0.08810	CGC	G|0.987;A|0.013	0.013	strong		0.627	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025		A	123419782	G	A	123419782	3	1	24	1	0	0	0	0	1	0	0	0	10065	1116	39	1	3279	1	MYLK	3	123419782	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	25785317	123419782	74602648	123	8340											
KALRN	8997	hgsc.bcm.edu	37	chr3	124201699	124201699	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gccaactccatctcttcctaCctaattaagcctgtccaaag	11	11	4	15	0	1	0	0	0	1	0	5	0	4	0	6	0	3	0	6	0	5	4	rs61740058	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:124201699C>T	ENST00000240874.3	+	28	4387	c.4230C>T	c.(4228-4230)taC>taT	p.Y1410Y	KALRN_ENST00000360013.3_Silent_p.Y1410Y|KALRN_ENST00000460856.1_Silent_p.Y1401Y	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1410	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						TCTCTTCCTACCTAATTAAGC	0.527													C|||	38	0.00758786	0.0008	0.0144	5008	,	,		19189	0.0		0.0179	False		,,,				2504	0.0092				p.Y1410Y		Atlas-SNP	.											.	KALRN	556	.	0			c.C4230T						PASS	.	C	,	45,4361	46.7+/-81.2	0,45,2158	247	197	214		4230,4230	3.5	1	3	dbSNP_129	214	323,8277	113.7+/-173.7	7,309,3984	no	coding-synonymous,coding-synonymous	KALRN	NM_001024660.3,NM_003947.4	,	7,354,6142	TT,TC,CC		3.7558,1.0213,2.8295	,	1410/2987,1410/1664	124201699	368,12638	2203	4300	6503	SO:0001819	synonymous_variant	8997	exon28			TTCCTACCTAATT	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.4230C>T	3.37:g.124201699C>T		210	0	0		169	88	0.52071	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	37	CCDS3027.1	23	0.010531135531135532	0	0.0	8	0.022099447513812154	0	0.0	15	0.01978891820580475	C	8.830	0.939650	0.18281	0.010213	0.037558	ENSG00000160145	ENST00000354186	.	.	.	5.31	3.53	0.40419	.	.	.	.	.	T	0.25754	0.0627	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27938	-1.0059	4	.	.	.	.	8.0382	0.30506	0.0:0.7055:0.0:0.2945	rs61740058	.	.	.	I	1379	.	.	T	+	2	0	KALRN	125684389	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.928000	0.40104	0.819000	0.34492	0.655000	0.94253	ACC	C|0.979;T|0.021	0.021	strong		0.527	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		T	124201699	C	T	124201699	2	4	24	1	0	0	0	0	0	0	0	1	7984	518	18	2		2	KALRN	3	124201699	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	781917	124201699	73820731	124	8341											
GATA2	2624	hgsc.bcm.edu	37	chr3	128204960	128204960	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gccagagtgggctgctgtagGggtgagggaggccactgagc	7	6	20	8	0	0	3	0	2	0	1	0	4	0	4	2	5	2	3	2	5	1	1	rs34799090	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:128204960G>C	ENST00000341105.2	-	3	812	c.481C>G	c.(481-483)Cct>Gct	p.P161A	GATA2_ENST00000487848.1_Missense_Mutation_p.P161A|GATA2_ENST00000430265.2_Missense_Mutation_p.P161A	NM_032638.4	NP_116027.2	P23769	GATA2_HUMAN	GATA binding protein 2	161					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)		GCTGCTGTAGGGGTGAGGGAG	0.687			Mis		AML(CML blast transformation)								G|||	8	0.00159744	0.0008	0.0043	5008	,	,		13302	0.0		0.003	False		,,,				2504	0.001				p.P161A		Atlas-SNP	.		Dom	yes		3	3q21.3	2624	GATA binding protein 2		L	.	GATA2	122	.	0			c.C481G						PASS	.	G	ALA/PRO,ALA/PRO,ALA/PRO	14,4392	21.2+/-45.6	0,14,2189	38	36	36		481,481,481	4.5	1	3	dbSNP_126	36	108,8492	52.3+/-112.8	0,108,4192	yes	missense,missense,missense	GATA2	NM_001145661.1,NM_001145662.1,NM_032638.4	27,27,27	0,122,6381	CC,CG,GG		1.2558,0.3177,0.938	probably-damaging,probably-damaging,probably-damaging	161/481,161/467,161/481	128204960	122,12884	2203	4300	6503	SO:0001583	missense	2624	exon3			CTGTAGGGGTGAG	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.481C>G	3.37:g.128204960G>C	ENSP00000345681:p.Pro161Ala	105	0	0		129	76	0.589147	NM_001145662	D3DNB3|Q53YE0|Q96BH0|Q96BH8|Q9BUJ6	Missense_Mutation	SNP	ENST00000341105.2	37	CCDS3049.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	12.68	2.010340	0.35511	0.003177	0.012558	ENSG00000179348	ENST00000341105;ENST00000430265;ENST00000487848	D;D;D	0.97114	-4.25;-4.23;-4.25	4.46	4.46	0.54185	.	0.568431	0.17408	N	0.175271	D	0.93864	0.8037	N	0.08118	0	0.48452	D	0.999652	D;B	0.76494	0.999;0.03	D;B	0.83275	0.996;0.014	D	0.91294	0.5061	10	0.08599	T	0.76	-26.4928	16.6918	0.85323	0.0:0.0:1.0:0.0	rs34799090	161;161	P23769-2;P23769	.;GATA2_HUMAN	A	161	ENSP00000345681:P161A;ENSP00000400259:P161A;ENSP00000417074:P161A	ENSP00000345681:P161A	P	-	1	0	GATA2	129687650	1.000000	0.71417	0.988000	0.46212	0.945000	0.59286	5.112000	0.64634	2.022000	0.59522	0.484000	0.47621	CCT	G|0.992;C|0.008	0.008	strong		0.687	GATA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356925.1	NM_032638		C	128204960	G	C	128204960	3	2	24	1	0	0	0	0	1	0	0	0	6262	1232	43	4	977	4	GATA2	3	128204960	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	4003261	128204960	69817470	125	8342											
STAG1	10274	hgsc.bcm.edu	37	chr3	136062724	136062724	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcagactcaggttcttgaatCtggtctcccatgggccgact	7	12	10	12	1	5	2	2	1	3	1	6	3	5	2	2	3	0	1	2	3	1	2	rs34149860	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:136062724C>G	ENST00000383202.2	-	30	3652	c.3396G>C	c.(3394-3396)caG>caC	p.Q1132H	STAG1_ENST00000434713.2_Missense_Mutation_p.Q872H|STAG1_ENST00000236698.5_Missense_Mutation_p.Q1132H|STAG1_ENST00000536929.1_Missense_Mutation_p.Q716H	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	1132			Q -> H (in dbSNP:rs34149860).		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						GTTCTTGAATCTGGTCTCCCA	0.448													C|||	436	0.0870607	0.3124	0.0303	5008	,	,		20341	0.0		0.002	False		,,,				2504	0.0				p.Q1132H		Atlas-SNP	.											.	STAG1	135	.	0			c.G3396C						PASS	.	C	HIS/GLN	1218,3188	421.7+/-339.5	170,878,1155	100	99	99		3396	3.5	1	3	dbSNP_126	99	12,8588	8.4+/-32.0	0,12,4288	yes	missense	STAG1	NM_005862.2	24	170,890,5443	GG,GC,CC		0.1395,27.6441,9.4572	benign	1132/1259	136062724	1230,11776	2203	4300	6503	SO:0001583	missense	10274	exon30			TTGAATCTGGTCT	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.3396G>C	3.37:g.136062724C>G	ENSP00000372689:p.Gln1132His	155	0	0		164	73	0.445122	NM_005862	O00539|Q6P275	Missense_Mutation	SNP	ENST00000383202.2	37	CCDS3090.1	157	0.07188644688644688	145	0.29471544715447157	11	0.03038674033149171	0	0.0	1	0.0013192612137203166	C	8.880	0.951348	0.18431	0.276441	0.001395	ENSG00000118007	ENST00000383202;ENST00000236698;ENST00000434713;ENST00000536929	T;T;T;T	0.32272	1.87;1.9;1.85;1.46	5.48	3.45	0.39498	.	0.196262	0.47455	D	0.000221	T	0.00012	0.0000	N	0.11201	0.11	0.26204	P	0.9793941	B;B	0.06786	0.001;0.001	B;B	0.10450	0.005;0.002	T	0.34725	-0.9817	9	0.41790	T	0.15	.	9.8937	0.41304	0.0:0.7454:0.0:0.2546	rs34149860	1132;1132	Q6P275;Q8WVM7	.;STAG1_HUMAN	H	1132;1132;872;716	ENSP00000372689:Q1132H;ENSP00000236698:Q1132H;ENSP00000404396:Q872H;ENSP00000445787:Q716H	ENSP00000236698:Q1132H	Q	-	3	2	STAG1	137545414	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.602000	0.36783	1.316000	0.45131	-0.137000	0.14449	CAG	C|0.914;G|0.086	0.086	strong		0.448	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862		G	136062724	C	G	136062724	3	3	24	1	0	0	0	0	1	0	0	0	15257	912	32	4	400	4	STAG1	3	136062724	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	7857764	136062724	61959706	126	8343											
PCOLCE2	26577	hgsc.bcm.edu	37	chr3	142548681	142548681	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagttcatttctctcagacaCaattggcctaaaaaaagaaa	18	10	5	8	0	3	2	2	0	1	2	4	2	3	2	1	1	0	1	1	1	7	4	rs140721173	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:142548681C>T	ENST00000295992.3	-	6	1024	c.718G>A	c.(718-720)Gtg>Atg	p.V240M	PCOLCE2_ENST00000485766.1_Intron	NM_013363.3	NP_037495.1	Q9UKZ9	PCOC2_HUMAN	procollagen C-endopeptidase enhancer 2	240	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				positive regulation of peptidase activity (GO:0010952)	extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|peptidase activator activity (GO:0016504)			NS(1)|endometrium(1)|large_intestine(11)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	32						CTCTCAGACACAATTGGCCTA	0.313													C|||	4	0.000798722	0.0	0.0014	5008	,	,		16702	0.0		0.001	False		,,,				2504	0.002				p.V240M		Atlas-SNP	.											.	PCOLCE2	63	.	0			c.G718A						PASS	.	C	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	75	78	77		718	3.5	1	3	dbSNP_134	77	8,8592	6.4+/-24.3	0,8,4292	yes	missense	PCOLCE2	NM_013363.3	21	0,9,6494	TT,TC,CC		0.093,0.0227,0.0692	possibly-damaging	240/416	142548681	9,12997	2203	4300	6503	SO:0001583	missense	26577	exon6			CAGACACAATTGG	AF098269	CCDS3127.1	3q21-q24	2008-07-18			ENSG00000163710	ENSG00000163710			8739	protein-coding gene	gene with protein product		607064				10873381	Standard	NM_013363		Approved	PCPE2	uc003evd.3	Q9UKZ9	OTTHUMG00000159312	ENST00000295992.3:c.718G>A	3.37:g.142548681C>T	ENSP00000295992:p.Val240Met	55	0	0		64	34	0.53125	NM_013363	B2RCH9|D3DNG4|Q9BRH3	Missense_Mutation	SNP	ENST00000295992.3	37	CCDS3127.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	13.63	2.294192	0.40594	2.27E-4	9.3E-4	ENSG00000163710	ENST00000295992	T	0.30714	1.52	5.3	3.5	0.40072	CUB (5);	0.127288	0.51477	D	0.000085	T	0.37652	0.1011	M	0.69823	2.125	0.80722	D	1	P	0.48407	0.91	P	0.49561	0.615	T	0.10800	-1.0614	10	0.44086	T	0.13	-4.6795	6.5558	0.22460	0.125:0.5656:0.2418:0.0675	.	240	Q9UKZ9	PCOC2_HUMAN	M	240	ENSP00000295992:V240M	ENSP00000295992:V240M	V	-	1	0	PCOLCE2	144031371	0.876000	0.30132	0.999000	0.59377	0.724000	0.41520	-0.015000	0.12634	0.618000	0.30179	-0.226000	0.12346	GTG	C|0.999;T|0.001	0.001	strong		0.313	PCOLCE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354509.1	NM_013363		T	142548681	C	T	142548681	3	4	24	1	0	0	0	0	1	0	0	0	11604	478	17	2	545	2	PCOLCE2	3	142548681	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	6485957	142548681	55473749	127	8344											
AGTR1	185	hgsc.bcm.edu	37	chr3	148459129	148459129	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggcaattacctatgtaagAttgcttcagccagcgtcagt	10	13	9	9	1	2	1	2	0	0	1	2	1	2	1	2	1	4	3	2	1	4	6	rs201745152		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:148459129A>T	ENST00000497524.1	+	2	698	c.307A>T	c.(307-309)Att>Ttt	p.I103F	AGTR1_ENST00000404754.2_Missense_Mutation_p.I103F|AGTR1_ENST00000402260.1_Missense_Mutation_p.I103F|AGTR1_ENST00000475347.1_Missense_Mutation_p.I103F|AGTR1_ENST00000461609.1_Missense_Mutation_p.I103F|AGTR1_ENST00000542281.1_Missense_Mutation_p.I103F|AGTR1_ENST00000349243.3_Missense_Mutation_p.I103F|AGTR1_ENST00000418473.2_Missense_Mutation_p.I103F|AGTR1_ENST00000474935.1_Missense_Mutation_p.I103F	NM_009585.3	NP_033611.1	P30556	AGTR1_HUMAN	angiotensin II receptor, type 1	103					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)	CCTATGTAAGATTGCTTCAGC	0.458																																					p.I138F		Atlas-SNP	.											.	AGTR1	63	.	0			c.A412T						PASS	.						84	81	82					3																	148459129		2203	4300	6503	SO:0001583	missense	185	exon4			TGTAAGATTGCTT	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.307A>T	3.37:g.148459129A>T	ENSP00000419422:p.Ile103Phe	28	0	0		42	17	0.404762	NM_031850	Q13725|Q8TBK4	Missense_Mutation	SNP	ENST00000497524.1	37	CCDS3137.1	.	.	.	.	.	.	.	.	.	.	A	12.88	2.069842	0.36566	.	.	ENSG00000144891	ENST00000497524;ENST00000349243;ENST00000542281;ENST00000418473;ENST00000404754;ENST00000475347;ENST00000474935;ENST00000461609;ENST00000402260	T;T;T;T;T;T;T;T;T	0.38077	1.16;1.16;1.16;1.16;1.16;1.16;1.16;1.16;1.16	5.48	5.48	0.80851	GPCR, rhodopsin-like superfamily (1);	0.326257	0.29616	N	0.011648	T	0.26195	0.0639	N	0.17345	0.48	0.36625	D	0.875957	B	0.29270	0.24	B	0.38921	0.285	T	0.31943	-0.9925	10	0.48119	T	0.1	-17.5731	6.1718	0.20421	0.5754:0.1271:0.0:0.2975	.	103	P30556	AGTR1_HUMAN	F	103	ENSP00000419422:I103F;ENSP00000273430:I103F;ENSP00000443186:I103F;ENSP00000398832:I103F;ENSP00000385612:I103F;ENSP00000419783:I103F;ENSP00000418084:I103F;ENSP00000418851:I103F;ENSP00000385641:I103F	ENSP00000273430:I103F	I	+	1	0	AGTR1	149941819	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	1.369000	0.34227	2.071000	0.62044	0.533000	0.62120	ATT	A|0.999;T|0.001	0.001	weak		0.458	AGTR1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355807.1			T	148459129	A	T	148459129	3	4	24	1	0	0	0	0	1	0	0	0	401	333	12	5	309	5	AGTR1	3	148459129	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	5910448	148459129	49563301	128	8345											
HPS3	84343	hgsc.bcm.edu	37	chr3	148858267	148858267	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacataagaccaacaatcgaAtaagacggacagaagaaggt	20	4	9	8	2	0	4	0	0	0	4	1	6	0	5	1	2	1	0	1	2	7	2	rs199722122		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:148858267A>G	ENST00000296051.2	+	2	834	c.694A>G	c.(694-696)Ata>Gta	p.I232V	HPS3_ENST00000460120.1_Intron	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	232					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)			CAACAATCGAATAAGACGGAC	0.393									Hermansky-Pudlak syndrome																												p.I232V		Atlas-SNP	.											.	HPS3	104	.	0			c.A694G						PASS	.						82	80	81					3																	148858267		2168	4282	6450	SO:0001583	missense	84343	exon2	Familial Cancer Database	HPS, HPS1-8	AATCGAATAAGAC	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.694A>G	3.37:g.148858267A>G	ENSP00000296051:p.Ile232Val	125	0	0		133	79	0.593985	NM_032383	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Missense_Mutation	SNP	ENST00000296051.2	37	CCDS3140.1	.	.	.	.	.	.	.	.	.	.	A	5.521	0.281147	0.10458	.	.	ENSG00000163755	ENST00000296051	T	0.62498	0.02	5.46	-7.86	0.01187	.	2.003110	0.01674	N	0.025777	T	0.28962	0.0719	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30119	-0.9989	10	0.28530	T	0.3	2.052	7.5676	0.27887	0.0972:0.071:0.7585:0.0733	.	232	Q969F9	HPS3_HUMAN	V	232	ENSP00000296051:I232V	ENSP00000296051:I232V	I	+	1	0	HPS3	150340957	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.081000	0.11321	-2.013000	0.00949	-0.263000	0.10527	ATA	A|0.999;G|0.001	0.001	weak		0.393	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383		G	148858267	A	G	148858267	3	3	24	1	0	0	0	0	1	0	0	0	7349	101	4	3	700	3	HPS3	3	148858267	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	399138	148858267	49164163	129	8346											
GFM1	85476	hgsc.bcm.edu	37	chr3	158408032	158408032	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caaatgaatttcagggacaaGtaattgcaggaattaaccga	17	9	9	6	1	1	1	1	1	0	0	1	4	1	3	1	2	2	2	1	2	6	4	rs62288347	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:158408032G>A	ENST00000486715.1	+	16	2347	c.1990G>A	c.(1990-1992)Gta>Ata	p.V664I	GFM1_ENST00000264263.5_Missense_Mutation_p.V683I|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)			TCAGGGACAAGTAATTGCAGG	0.393													G|||	35	0.00698882	0.0	0.0058	5008	,	,		17035	0.0		0.0258	False		,,,				2504	0.0051				p.V664I		Atlas-SNP	.											.	GFM1	83	.	0			c.G1990A						PASS	.	G	ILE/VAL	10,4396	19.1+/-41.9	0,10,2193	167	167	167		1990	5.8	0.4	3	dbSNP_129	167	175,8425	80.4+/-143.0	0,175,4125	yes	missense	GFM1	NM_024996.5	29	0,185,6318	AA,AG,GG		2.0349,0.227,1.4224	possibly-damaging	664/752	158408032	185,12821	2203	4300	6503	SO:0001583	missense	85476	exon16			GGACAAGTAATTG	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.1990G>A	3.37:g.158408032G>A	ENSP00000419038:p.Val664Ile	95	0	0		101	49	0.485149	NM_024996		Missense_Mutation	SNP	ENST00000486715.1	37	CCDS33885.1	27	0.012362637362637362	0	0.0	3	0.008287292817679558	0	0.0	24	0.0316622691292876	G	19.54	3.846986	0.71603	0.00227	0.020349	ENSG00000168827	ENST00000486715;ENST00000264263	T;T	0.60299	0.2;0.2	5.8	5.8	0.92144	Elongation factor G/III/V (1);Translation elongation factor EFG/EF2, C-terminal (3);	0.063724	0.64402	D	0.000007	T	0.31702	0.0805	N	0.26092	0.79	0.80722	D	1	P;P	0.41848	0.72;0.763	B;P	0.45946	0.365;0.498	T	0.48536	-0.9027	10	0.54805	T	0.06	-5.1032	20.0589	0.97667	0.0:0.0:1.0:0.0	rs62288347	683;664	Q96RP9-2;Q96RP9	.;EFGM_HUMAN	I	664;683	ENSP00000419038:V664I;ENSP00000264263:V683I	ENSP00000264263:V683I	V	+	1	0	GFM1	159890726	1.000000	0.71417	0.420000	0.26596	0.975000	0.68041	7.491000	0.81471	2.732000	0.93576	0.650000	0.86243	GTA	G|0.986;A|0.014	0.014	strong		0.393	GFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352271.1	NM_024996		A	158408032	G	A	158408032	3	1	24	1	0	0	0	0	1	0	0	0	6349	1029	36	2	2052	2	GFM1	3	158408032	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	9549765	158408032	39614398	130	8347											
WDR49	151790	hgsc.bcm.edu	37	chr3	167217971	167217971	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgacggggcctccagaatttGgggacgctcttcctctggtt	5	12	13	11	2	2	2	0	1	2	1	4	3	4	3	3	5	0	2	3	5	1	3			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:167217971G>T	ENST00000308378.3	-	14	2250	c.1945C>A	c.(1945-1947)Caa>Aaa	p.Q649K	WDR49_ENST00000479765.1_Intron|WDR49_ENST00000476376.1_Missense_Mutation_p.Q474K|WDR49_ENST00000453925.2_Missense_Mutation_p.Q614K	NM_178824.3	NP_849146.1	Q8IV35	WDR49_HUMAN	WD repeat domain 49	649										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						TCCAGAATTTGGGGACGCTCT	0.423																																					p.Q649K		Atlas-SNP	.											.	WDR49	188	.	0			c.C1945A						PASS	.						131	149	143					3																	167217971		2203	4300	6503	SO:0001583	missense	151790	exon14			GAATTTGGGGACG	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.1945C>A	3.37:g.167217971G>T	ENSP00000311343:p.Gln649Lys	66	0	0		49	24	0.489796	NM_178824	Q8N297	Missense_Mutation	SNP	ENST00000308378.3	37	CCDS3201.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.588097	0.00128	.	.	ENSG00000174776	ENST00000308378;ENST00000476376;ENST00000453925	T;T;T	0.47177	0.85;2.16;1.33	5.13	0.462	0.16695	.	0.427611	0.20451	N	0.092100	T	0.28632	0.0709	L	0.39898	1.24	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30794	-0.9966	10	0.02654	T	1	.	7.4361	0.27156	0.0:0.2474:0.2598:0.4928	.	614;649	E7EQK3;Q8IV35	.;WDR49_HUMAN	K	649;474;614	ENSP00000311343:Q649K;ENSP00000420508:Q474K;ENSP00000410863:Q614K	ENSP00000311343:Q649K	Q	-	1	0	WDR49	168700665	0.002000	0.14202	0.000000	0.03702	0.004000	0.04260	0.770000	0.26618	0.135000	0.18707	0.467000	0.42956	CAA	.	.	none		0.423	WDR49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350592.3	NM_178824		T	167217971	G	T	167217971	3	4	24	1	0	0	0	0	1	0	0	0	17317	1357	47	4	156	4	WDR49	3	167217971	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	8809939	167217971	30804459	131	8348											
CCDC39	339829	hgsc.bcm.edu	37	chr3	180359790	180359790	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaaaattaccttatgtttTcccgttcttgatcaacatat	11	17	4	9	1	2	2	1	2	1	0	3	2	3	2	2	0	2	2	2	0	6	7	rs200277460	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:180359790T>C	ENST00000442201.2	-	13	1984	c.1865A>G	c.(1864-1866)gAa>gGa	p.E622G	CCDC39_ENST00000273654.4_Missense_Mutation_p.E706G	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	622					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)			CCTTATGTTTTCCCGTTCTTG	0.378													T|||	3	0.000599042	0.0	0.0	5008	,	,		17354	0.0		0.003	False		,,,				2504	0.0				p.E622G		Atlas-SNP	.											.	CCDC39	242	.	0			c.A1865G						PASS	.	T	GLY/GLU	0,3678		0,0,1839	129	119	122		1865	4.9	1	3		122	11,8175		0,11,4082	yes	missense	CCDC39	NM_181426.1	98	0,11,5921	CC,CT,TT		0.1344,0.0,0.0927	benign	622/942	180359790	11,11853	1839	4093	5932	SO:0001583	missense	339829	exon13			ATGTTTTCCCGTT	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.1865A>G	3.37:g.180359790T>C	ENSP00000405708:p.Glu622Gly	205	0	0		207	95	0.458937	NM_181426	B4E2H1	Missense_Mutation	SNP	ENST00000442201.2	37	CCDS46964.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	16.10	3.028257	0.54790	0.0	0.001344	ENSG00000145075	ENST00000273654;ENST00000442201	.	.	.	4.9	4.9	0.64082	.	0.169998	0.52532	D	0.000067	T	0.26412	0.0645	N	0.08118	0	0.26248	N	0.978768	B	0.24882	0.113	B	0.26094	0.066	T	0.24154	-1.0168	9	0.48119	T	0.1	-11.3381	14.5324	0.67936	0.0:0.0:0.0:1.0	.	622	Q9UFE4	CCD39_HUMAN	G	706;622	.	ENSP00000273654:E706G	E	-	2	0	CCDC39	181842484	1.000000	0.71417	0.990000	0.47175	0.975000	0.68041	6.020000	0.70826	1.961000	0.56991	0.472000	0.43445	GAA	T|0.999;C|0.001	0.001	strong		0.378	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028		C	180359790	T	C	180359790	3	2	24	1	0	0	0	0	1	0	0	0	2813	1783	62	3	992	3	CCDC39	3	180359790	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	13141819	180359790	17662640	132	8349											
ECE2	9718	hgsc.bcm.edu	37	chr3	183995839	183995839	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagagacctcattgagaaggTagggccactgagccggttga	11	7	15	8	1	1	4	1	3	0	2	1	7	1	4	3	3	1	2	3	3	2	3	rs56080981		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:183995839T>C	ENST00000402825.3	+	5	957		c.e5+2		ECE2_ENST00000359140.4_Splice_Site|EIF2B5_ENST00000444495.1_Intron|ECE2_ENST00000404464.3_Splice_Site|ECE2_ENST00000357474.5_Splice_Site	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2						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)			ATTGAGAAGGTAGGGCCACTG	0.577																																					.		Atlas-SNP	.											.	ECE2	303	.	0			c.957+2T>C						PASS	.						56	53	54					3																	183995839		2203	4300	6503	SO:0001630	splice_region_variant	9718	exon5			AGAAGGTAGGGCC	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.957+2T>C	3.37:g.183995839T>C		83	0	0		82	35	0.426829	NM_014693	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Splice_Site	SNP	ENST00000402825.3	37	CCDS3256.2	.	.	.	.	.	.	.	.	.	.	T	6.303	0.424006	0.11928	.	.	ENSG00000145194	ENST00000402825;ENST00000359140;ENST00000404464;ENST00000357474;ENST00000430587	.	.	.	4.96	1.22	0.21188	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.2333	0.10613	0.0:0.2167:0.1723:0.6111	rs56080981;rs62619887	.	.	.	.	-1	.	.	.	+	.	.	ECE2	185478533	0.998000	0.40836	0.167000	0.22817	0.190000	0.23558	2.513000	0.45494	0.060000	0.16281	0.459000	0.35465	.	.	.	weak		0.577	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693	Intron	C	183995839	T	C	183995839	5	2	24	1	0	0	0	0	0	0	1	0	4892	1652	57	3	1541	3	ECE2	3	183995839	Splice_Site	SNP	T	TCGA-G8-6326-01A-11D-2210-10	3636049	183995839	14026591	133	8350											
EIF4G1	1981	hgsc.bcm.edu	37	chr3	184049807	184049807	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcagaaatacctgtgtgaCgagcagaaggagctacaggc	13	6	13	9	1	0	3	0	1	0	2	0	5	0	4	1	2	5	3	1	2	4	2	rs11559218	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr3:184049807C>T	ENST00000346169.2	+	32	4822	c.4551C>T	c.(4549-4551)gaC>gaT	p.D1517D	EIF4G1_ENST00000319274.6_Silent_p.D1517D|EIF4G1_ENST00000342981.4_Silent_p.D1518D|EIF4G1_ENST00000411531.1_Silent_p.D1478D|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000441154.1_Silent_p.D1354D|EIF4G1_ENST00000392537.2_Silent_p.D1430D|EIF4G1_ENST00000424196.1_Silent_p.D1524D|EIF4G1_ENST00000352767.3_Silent_p.D1524D|EIF4G1_ENST00000382330.3_Silent_p.D1524D|EIF4G1_ENST00000427845.1_Silent_p.D1431D|EIF4G1_ENST00000350481.5_Silent_p.D1353D|EIF4G1_ENST00000414031.1_Silent_p.D1477D|EIF4G1_ENST00000434061.2_Silent_p.D1322D|EIF4G1_ENST00000435046.2_Silent_p.D1321D	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	1517	EIF4A-binding.|W2. {ECO:0000255|PROSITE- ProRule:PRU00695}.				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)			ACCTGTGTGACGAGCAGAAGG	0.587													C|||	12	0.00239617	0.0	0.0072	5008	,	,		20060	0.0		0.006	False		,,,				2504	0.001				p.D1524D		Atlas-SNP	.											.	EIF4G1	151	.	0			c.C4572T						PASS	.	C	,,,,,,	9,4397	15.5+/-35.6	0,9,2194	64	61	62		4572,4572,3966,4554,4551,4059,4290	-9.6	0.7	3	dbSNP_120	62	69,8531	42.2+/-99.7	0,69,4231	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	EIF4G1	NM_001194946.1,NM_001194947.1,NM_004953.4,NM_182917.4,NM_198241.2,NM_198242.2,NM_198244.2	,,,,,,	0,78,6425	TT,TC,CC		0.8023,0.2043,0.5997	,,,,,,	1524/1607,1524/1607,1322/1405,1518/1601,1517/1600,1353/1436,1430/1513	184049807	78,12928	2203	4300	6503	SO:0001819	synonymous_variant	1981	exon33			GTGTGACGAGCAG	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.4551C>T	3.37:g.184049807C>T		114	0	0		107	44	0.411215	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Silent	SNP	ENST00000346169.2	37	CCDS3259.1																																																																																			C|0.995;T|0.005	0.005	strong		0.587	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917		T	184049807	C	T	184049807	2	4	24	1	0	0	0	0	0	0	0	1	5038	535	19	1		1	EIF4G1	3	184049807	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	53968	184049807	13972623	134	8351											
PDE6B	5158	hgsc.bcm.edu	37	chr4	663878	663878	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcccagcacccaagtcttcAacctgctgtatcctgtgagc	8	9	9	15	0	2	1	1	1	1	0	3	1	3	1	4	1	4	3	4	1	3	2	rs137864502		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:663878A>G	ENST00000496514.1	+	22	2568	c.2547A>G	c.(2545-2547)tcA>tcG	p.S849S	ATP5I_ENST00000506525.1_5'Flank|PDE6B_ENST00000429163.2_Silent_p.S570S|PDE6B_ENST00000255622.6_Silent_p.S848S			P35913	PDE6B_HUMAN	phosphodiesterase 6B, cGMP-specific, rod, beta	849					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)	CCAAGTCTTCAACCTGCTGTA	0.527																																					p.S849S	GBM(71;463 1194 9848 25922 46834)	Atlas-SNP	.											.	PDE6B	80	.	0			c.A2547G						PASS	.	A	,,	1,4405	2.1+/-5.4	0,1,2202	165	163	164		2547,2544,1710	-8.7	0.5	4	dbSNP_134	164	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	PDE6B	NM_000283.3,NM_001145291.1,NM_001145292.1	,,	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	,,	849/855,848/854,570/576	663878	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	5158	exon22			GTCTTCAACCTGC	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.2547A>G	4.37:g.663878A>G		150	0	0		111	60	0.540541	NM_000283	B7Z9T9|E7ETT3|Q53XN5|Q9BWH5|Q9UD49	Silent	SNP	ENST00000496514.1	37	CCDS33932.1																																																																																			A|1.000;G|0.000	0.000	weak		0.527	PDE6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358109.1	NM_000283		G	663878	A	G	663878	2	3	24	1	0	0	0	0	0	0	0	1	11655	117	5	3		3	PDE6B	4	663878	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10		663878	190490398	135	8352											
STK32B	55351	hgsc.bcm.edu	37	chr4	5333091	5333091	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagctggcactggccctggaGtatcttcagaggtaccacat	9	9	12	11	0	2	1	1	0	1	1	2	3	2	2	2	4	2	4	2	4	2	3	rs16837029	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:5333091G>A	ENST00000282908.5	+	4	827	c.405G>A	c.(403-405)gaG>gaA	p.E135E	STK32B_ENST00000512636.1_Silent_p.E88E|STK32B_ENST00000510398.1_Silent_p.E88E	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						TGGCCCTGGAGTATCTTCAGA	0.577													G|||	422	0.0842652	0.2171	0.0245	5008	,	,		19648	0.0397		0.0328	False		,,,				2504	0.046				p.E135E		Atlas-SNP	.											.	STK32B	87	.	0			c.G405A						PASS	.	G		741,3665	304.9+/-288.7	63,615,1525	79	72	75		405	-1.6	0.9	4	dbSNP_123	75	222,8378	92.6+/-154.6	6,210,4084	no	coding-synonymous	STK32B	NM_018401.1		69,825,5609	AA,AG,GG		2.5814,16.818,7.4043		135/415	5333091	963,12043	2203	4300	6503	SO:0001819	synonymous_variant	55351	exon4			CCTGGAGTATCTT	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.405G>A	4.37:g.5333091G>A		70	0	0		52	28	0.538462	NM_018401		Silent	SNP	ENST00000282908.5	37	CCDS3380.1																																																																																			G|0.926;A|0.074	0.074	strong		0.577	STK32B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206854.4	NM_018401		A	5333091	G	A	5333091	2	1	24	1	0	0	0	0	0	0	0	1	15313	1020	36	2		2	STK32B	4	5333091	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	4669213	5333091	185821185	136	8353											
S100P	6286	hgsc.bcm.edu	37	chr4	6698664	6698664	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gataaattgctcaaggacctGgatgccaatggagatgccca	13	8	11	9	0	1	1	1	0	0	1	1	5	1	3	3	3	3	1	3	3	4	2	rs11737783	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:6698664G>A	ENST00000296370.3	+	2	1047	c.183G>A	c.(181-183)ctG>ctA	p.L61L	S100P_ENST00000513778.1_3'UTR	NM_005980.2	NP_005971.1	P25815	S100P_HUMAN	S100 calcium binding protein P	61	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				endothelial cell migration (GO:0043542)|response to organic substance (GO:0010033)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|magnesium ion binding (GO:0000287)			prostate(1)	1		Myeloproliferative disorder(84;0.0255)		Colorectal(103;0.011)	Cromoglicic acid(DB01003)	TCAAGGACCTGGATGCCAATG	0.532													G|||	144	0.028754	0.0023	0.0331	5008	,	,		21956	0.001		0.0427	False		,,,				2504	0.0757				p.L61L		Atlas-SNP	.											.	S100P	7	.	0			c.G183A						PASS	.	G		34,4372	40.8+/-73.8	0,34,2169	242	226	231		183	-0.2	0.5	4	dbSNP_120	231	340,8260	116.3+/-176.0	1,338,3961	no	coding-synonymous	S100P	NM_005980.2		1,372,6130	AA,AG,GG		3.9535,0.7717,2.8756		61/96	6698664	374,12632	2203	4300	6503	SO:0001819	synonymous_variant	6286	exon2			GGACCTGGATGCC	X65614	CCDS3391.1	4p16	2013-01-10	2001-11-28		ENSG00000163993	ENSG00000163993		"S100 calcium binding proteins", "EF-hand domain containing"	10504	protein-coding gene	gene with protein product		600614	"S100 calcium-binding protein P"			8341667, 7759097	Standard	NM_005980		Approved		uc003gjl.3	P25815	OTTHUMG00000090491	ENST00000296370.3:c.183G>A	4.37:g.6698664G>A		213	0	0		172	80	0.465116	NM_005980	Q5J7W2	Silent	SNP	ENST00000296370.3	37	CCDS3391.1																																																																																			G|0.972;A|0.028	0.028	strong		0.532	S100P-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206979.1	NM_005980		A	6698664	G	A	6698664	2	1	24	1	0	0	0	0	0	0	0	1	13805	1335	47	2		2	S100P	4	6698664	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1365573	6698664	184455612	137	8354											
CLNK	116449	hgsc.bcm.edu	37	chr4	10586571	10586571	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgtggcactattgatgcgaGgccatgacctagggcagaaa	11	8	13	9	1	0	3	0	2	0	1	0	4	0	3	2	3	1	2	2	3	3	3	rs61759824	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:10586571G>A	ENST00000226951.6	-	4	331	c.92C>T	c.(91-93)cCt>cTt	p.P31L	CLNK_ENST00000442825.2_5'UTR|CLNK_ENST00000507719.1_5'UTR	NM_052964.2	NP_443196.2	Q7Z7G1	CLNK_HUMAN	cytokine-dependent hematopoietic cell linker	31					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						ATTGATGCGAGGCCATGACCT	0.507													G|||	130	0.0259585	0.0091	0.0389	5008	,	,		16233	0.0		0.0567	False		,,,				2504	0.0348				p.P31L	GBM(87;402 1286 6949 13902 35851)	Atlas-SNP	.											.	CLNK	85	.	0			c.C92T						PASS	.	G	LEU/PRO	48,4018		1,46,1986	98	106	103		92	3.9	0.8	4	dbSNP_129	103	515,7829		15,485,3672	yes	missense	CLNK	NM_052964.2	98	16,531,5658	AA,AG,GG		6.1721,1.1805,4.5367	probably-damaging	31/429	10586571	563,11847	2033	4172	6205	SO:0001583	missense	116449	exon4			ATGCGAGGCCATG	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.92C>T	4.37:g.10586571G>A	ENSP00000226951:p.Pro31Leu	50	0	0		45	20	0.444444	NM_052964	Q05C27|Q9P2U9	Missense_Mutation	SNP	ENST00000226951.6	37	CCDS47024.1	65	0.02976190476190476	7	0.014227642276422764	12	0.03314917127071823	0	0.0	46	0.06068601583113457	G	10.66	1.412027	0.25465	0.011805	0.061721	ENSG00000109684	ENST00000226951;ENST00000429087	T	0.26660	1.72	4.79	3.94	0.45596	.	0.000000	0.44902	D	0.000411	T	0.03477	0.0100	L	0.29908	0.895	0.80722	D	1	D	0.60160	0.987	P	0.55011	0.766	T	0.00389	-1.1770	10	0.87932	D	0	-2.6544	10.4696	0.44629	0.0:0.0:0.8061:0.1939	rs61759824	31	Q7Z7G1	CLNK_HUMAN	L	31	ENSP00000226951:P31L	ENSP00000226951:P31L	P	-	2	0	CLNK	10195669	0.974000	0.33945	0.843000	0.33291	0.044000	0.14063	1.881000	0.39638	1.357000	0.45904	0.563000	0.77884	CCT	G|0.967;A|0.033	0.033	strong		0.507	CLNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359047.1	NM_052964		A	10586571	G	A	10586571	3	1	24	1	0	0	0	0	1	0	0	0	3549	1000	35	2	1258	2	CLNK	4	10586571	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	3887907	10586571	180567705	138	8355											
ZCCHC4	29063	hgsc.bcm.edu	37	chr4	25314478	25314478	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccgtggaggcagagggcaGcgcagggtgccggggaagct	8	3	21	9	3	0	1	0	0	0	1	0	3	0	3	2	6	4	4	2	6	1	0	rs201763036	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:25314478G>C	ENST00000302874.4	+	1	71	c.47G>C	c.(46-48)aGc>aCc	p.S16T	ZCCHC4_ENST00000505451.1_3'UTR	NM_024936.2	NP_079212.2	Q9H5U6	ZCHC4_HUMAN	zinc finger, CCHC domain containing 4	16							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)				GCAGAGGGCAGCGCAGGGTGC	0.642											OREG0016141	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2	0.000399361	0.0	0.0	5008	,	,		14396	0.0		0.002	False		,,,				2504	0.0				p.S16T		Atlas-SNP	.											.	ZCCHC4	34	.	0			c.G47C						PASS	.	G	THR/SER	2,4098		0,2,2048	70	89	83		47	-5.7	0	4		83	6,8382		0,6,4188	yes	missense	ZCCHC4	NM_024936.2	58	0,8,6236	CC,CG,GG		0.0715,0.0488,0.0641	benign	16/514	25314478	8,12480	2050	4194	6244	SO:0001583	missense	29063	exon1			AGGGCAGCGCAGG	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.47G>C	4.37:g.25314478G>C	ENSP00000303468:p.Ser16Thr	95	0	0	778	83	32	0.385542	NM_024936	B2RXF6|B4DRD8|B7ZW20|Q5IW78|Q96AN7	Missense_Mutation	SNP	ENST00000302874.4	37	CCDS43218.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	11.08	1.534797	0.27475	4.88E-4	7.15E-4	ENSG00000168228	ENST00000302874	T	0.30981	1.51	5.18	-5.71	0.02413	.	1.862370	0.01786	N	0.032033	T	0.14270	0.0345	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.16897	-1.0387	10	0.11182	T	0.66	-5.9509	1.3284	0.02130	0.2451:0.1002:0.2206:0.4341	.	16	Q9H5U6	ZCHC4_HUMAN	T	16	ENSP00000303468:S16T	ENSP00000303468:S16T	S	+	2	0	ZCCHC4	24923576	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.725000	0.01863	-1.763000	0.01307	0.655000	0.94253	AGC	G|0.999;C|0.001	0.001	strong		0.642	ZCCHC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361151.1			C	25314478	G	C	25314478	3	2	24	1	0	0	0	0	1	0	0	0	17605	971	34	4	49	4	ZCCHC4	4	25314478	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	14727907	25314478	165839798	139	8356											
ATP8A1	10396	hgsc.bcm.edu	37	chr4	42576646	42576646	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaaaactcacccataagcaaCtcccgctatggtgcacttct	13	9	5	14	1	2	0	1	0	1	0	3	0	3	0	2	1	4	3	2	1	5	3	rs61755862	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:42576646C>T	ENST00000381668.5	-	14	1516	c.1285G>A	c.(1285-1287)Gtt>Att	p.V429I	ATP8A1_ENST00000264449.10_Missense_Mutation_p.V429I	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	429					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)	CCATAAGCAACTCCCGCTATG	0.343													C|||	126	0.0251597	0.0923	0.0058	5008	,	,		17551	0.0		0.0	False		,,,				2504	0.0				p.V429I		Atlas-SNP	.											ATP8A1_ENST00000264449,NS,carcinoma,+1,2	ATP8A1	206	2	0			c.G1285A						PASS	.	C	ILE/VAL,ILE/VAL	297,4109	159.6+/-192.1	13,271,1919	55	56	56		1285,1285	3.4	1	4	dbSNP_129	56	2,8596	1.2+/-3.3	0,2,4297	yes	missense,missense	ATP8A1	NM_001105529.1,NM_006095.2	29,29	13,273,6216	TT,TC,CC		0.0233,6.7408,2.2993	benign,benign	429/1150,429/1165	42576646	299,12705	2203	4299	6502	SO:0001583	missense	10396	exon14			AAGCAACTCCCGC	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.1285G>A	4.37:g.42576646C>T	ENSP00000371084:p.Val429Ile	198	0	0		218	110	0.504587	NM_001105529	Q32M35|Q32M36|Q4W5J7|Q4W5P2	Missense_Mutation	SNP	ENST00000381668.5	37	CCDS3466.1	40	0.018315018315018316	38	0.07723577235772358	2	0.0055248618784530384	0	0.0	0	0.0	C	4.770	0.143139	0.09083	0.067408	2.33E-4	ENSG00000124406	ENST00000381668;ENST00000264449	T;T	0.74947	-0.89;-0.89	5.27	3.4	0.38934	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.068109	0.64402	D	0.000017	T	0.04137	0.0115	N	0.11845	0.185	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.001;0.003;0.001	T	0.03325	-1.1048	10	0.09338	T	0.73	.	6.9831	0.24713	0.0:0.6446:0.0:0.3554	.	429;429;429	B4DII6;Q32M35;Q9Y2Q0	.;.;AT8A1_HUMAN	I	429	ENSP00000371084:V429I;ENSP00000264449:V429I	ENSP00000264449:V429I	V	-	1	0	ATP8A1	42271403	0.999000	0.42202	1.000000	0.80357	0.986000	0.74619	0.657000	0.24963	1.459000	0.47892	0.591000	0.81541	GTT	C|0.975;T|0.025	0.025	strong		0.343	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	NM_006095		T	42576646	C	T	42576646	3	4	24	1	0	0	0	0	1	0	0	0	1192	565	20	2	2305	2	ATP8A1	4	42576646	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	17262168	42576646	148577630	140	8357											
KDR	3791	hgsc.bcm.edu	37	chr4	55972946	55972946	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacacttctccattcttcacAagggtatgggtttgtcactg	8	14	8	11	0	4	0	2	0	2	0	5	0	4	0	1	2	0	2	1	2	2	5	rs34231037	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:55972946A>G	ENST00000263923.4	-	11	1739	c.1444T>C	c.(1444-1446)Tgt>Cgt	p.C482R		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	482	Ig-like C2-type 5.		C -> R (in HCI susceptibility; expression of FLT1 in hemangioma endothelial cells is markedly reduced and KDR activity is increased compared to controls; low FLT1 expression in hemangioma cells is caused by reduced activity of a pathway involving ITGB1, ANTXR1, KDR and NFATC2IP; the mutation predicts to result in loss-of-function and disruption of the normal association of these molecules; dbSNP:rs34231037). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:18931684}.		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)	CATTCTTCACAAGGGTATGGG	0.333			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)			A|||	45	0.00898562	0.0015	0.0144	5008	,	,		18156	0.0		0.0308	False		,,,				2504	0.002				p.C482R		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	KDR,middle_lobe,carcinoma,+2,1	KDR	307	1	0			c.T1444C						PASS	.	A	ARG/CYS	23,4383	31.7+/-61.6	0,23,2180	81	85	83	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1444	5.7	0.9	4	dbSNP_126	83	242,8358	97.2+/-158.9	4,234,4062	yes	missense	KDR	NM_002253.2	180	4,257,6242	GG,GA,AA		2.814,0.522,2.0375	probably-damaging	482/1357	55972946	265,12741	2203	4300	6503	SO:0001583	missense	3791	exon11			CTTCACAAGGGTA	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.1444T>C	4.37:g.55972946A>G	ENSP00000263923:p.Cys482Arg	210	0	0		224	100	0.446429	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	37	CCDS3497.1	30	0.013736263736263736	0	0.0	6	0.016574585635359115	0	0.0	24	0.0316622691292876	A	13.84	2.356951	0.41801	0.00522	0.02814	ENSG00000128052	ENST00000263923	T	0.76839	-1.05	5.67	5.67	0.87782	Immunoglobulin subtype (1);Immunoglobulin-like (1);	0.000000	0.85682	D	0.000000	T	0.75436	0.3849	M	0.81497	2.545	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.82382	-0.0485	10	0.40728	T	0.16	.	15.905	0.79419	1.0:0.0:0.0:0.0	rs34231037	482;482	P35968-2;P35968	.;VGFR2_HUMAN	R	482	ENSP00000263923:C482R	ENSP00000263923:C482R	C	-	1	0	KDR	55667703	1.000000	0.71417	0.927000	0.36925	0.088000	0.18126	6.349000	0.73013	2.150000	0.67090	0.533000	0.62120	TGT	A|0.980;G|0.020	0.020	strong		0.333	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			G	55972946	A	G	55972946	3	3	24	1	0	0	0	0	1	0	0	0	8148	130	5	3	2706	3	KDR	4	55972946	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	13396300	55972946	135181330	141	8358											
KDR	3791	hgsc.bcm.edu	37	chr4	55972974	55972974	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggtttgtcactgagacagcTtggctataagaaagagataa	14	10	12	5	0	1	3	1	1	0	3	1	5	1	3	0	2	1	3	0	2	4	5	rs1870377	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:55972974T>A	ENST00000263923.4	-	11	1711	c.1416A>T	c.(1414-1416)caA>caT	p.Q472H		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	472	Ig-like C2-type 5.		Q -> H (in dbSNP:rs1870377). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		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)	p.Q472H(1)		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)	CTGAGACAGCTTGGCTATAAG	0.343			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)			T|||	1061	0.211861	0.09	0.1311	5008	,	,		17888	0.4653		0.2346	False		,,,				2504	0.1493				p.Q472H		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	KDR,NS,carcinoma,0,1	KDR	307	1	1	Substitution - Missense(1)	stomach(1)	c.A1416T	GRCh37	CM074306	KDR	M	rs1870377	PASS	.	T	HIS/GLN	485,3921	221.0+/-238.3	28,429,1746	79	82	81		1416	-1.8	0	4	dbSNP_92	81	2037,6563	353.6+/-329.2	246,1545,2509	yes	missense	KDR	NM_002253.2	24	274,1974,4255	AA,AT,TT		23.686,11.0077,19.3911	benign	472/1357	55972974	2522,10484	2203	4300	6503	SO:0001583	missense	3791	exon11			GACAGCTTGGCTA	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.1416A>T	4.37:g.55972974T>A	ENSP00000263923:p.Gln472His	170	0	0		190	81	0.426316	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	37	CCDS3497.1	513	0.2348901098901099	41	0.08333333333333333	52	0.143646408839779	248	0.43356643356643354	172	0.22691292875989447	T	4.227	0.041015	0.08196	0.110077	0.23686	ENSG00000128052	ENST00000263923	T	0.76448	-1.02	5.67	-1.82	0.07857	Immunoglobulin subtype (1);Immunoglobulin-like (1);	0.974058	0.08489	N	0.938324	T	0.00012	0.0000	L	0.49350	1.555	0.80722	P	0.0	P;B	0.52692	0.955;0.003	P;B	0.56514	0.8;0.011	T	0.14699	-1.0463	9	0.25106	T	0.35	.	5.5298	0.16978	0.0:0.2646:0.2451:0.4903	rs1870377;rs52810770;rs1870377	472;472	P35968-2;P35968	.;VGFR2_HUMAN	H	472	ENSP00000263923:Q472H	ENSP00000263923:Q472H	Q	-	3	2	KDR	55667731	0.011000	0.17503	0.005000	0.12908	0.006000	0.05464	-0.046000	0.11983	-0.160000	0.11002	-0.290000	0.09829	CAA	T|0.781;A|0.219	0.219	strong		0.343	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			A	55972974	T	A	55972974	3	1	24	1	0	0	0	0	1	0	0	0	8148	1606	56	5	2734	5	KDR	4	55972974	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	28	55972974	135181302	142	8359											
TMPRSS11F	389208	hgsc.bcm.edu	37	chr4	68925094	68925094	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tccagcacataacattcctgGagttatcaggccatcataca	13	10	6	12	0	2	0	2	0	0	0	4	1	4	1	3	2	3	2	3	2	3	4	rs142412240	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:68925094G>A	ENST00000356291.2	-	9	1167	c.1108C>T	c.(1108-1110)Cca>Tca	p.P370S	UBA6-AS1_ENST00000500538.2_RNA|RP11-35D5.1_ENST00000600441.1_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	370	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						AACATTCCTGGAGTTATCAGG	0.393													G|||	2	0.000399361	0.0	0.0014	5008	,	,		18312	0.0		0.001	False		,,,				2504	0.0				p.P370S		Atlas-SNP	.											.	TMPRSS11F	79	.	0			c.C1108T						PASS	.	G	SER/PRO	1,4405	2.1+/-5.4	0,1,2202	216	188	197		1108	0.3	1	4	dbSNP_134	197	14,8586	10.5+/-38.8	0,14,4286	yes	missense	TMPRSS11F	NM_207407.2	74	0,15,6488	AA,AG,GG		0.1628,0.0227,0.1153	benign	370/439	68925094	15,12991	2203	4300	6503	SO:0001583	missense	389208	exon9			TTCCTGGAGTTAT	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.1108C>T	4.37:g.68925094G>A	ENSP00000348639:p.Pro370Ser	177	0	0		201	87	0.432836	NM_207407	A8MXX2	Missense_Mutation	SNP	ENST00000356291.2	37	CCDS3520.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	3.434	-0.115545	0.06881	2.27E-4	0.001628	ENSG00000198092	ENST00000356291	D	0.92545	-3.06	5.2	0.258	0.15578	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.014630	0.07912	N	0.974403	T	0.81754	0.4889	N	0.16903	0.455	0.29686	N	0.841319	B	0.02656	0.0	B	0.06405	0.002	T	0.68303	-0.5444	10	0.18276	T	0.48	.	4.0738	0.09894	0.2767:0.0:0.4486:0.2746	.	370	Q6ZWK6	TM11F_HUMAN	S	370	ENSP00000348639:P370S	ENSP00000348639:P370S	P	-	1	0	TMPRSS11F	68607689	0.878000	0.30173	0.997000	0.53966	0.986000	0.74619	0.300000	0.19156	0.093000	0.17368	0.591000	0.81541	CCA	G|0.999;A|0.001	0.001	strong		0.393	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407		A	68925094	G	A	68925094	3	1	24	1	0	0	0	0	1	0	0	0	16258	1174	41	2	216	2	TMPRSS11F	4	68925094	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	12952120	68925094	122229182	143	8360											
C4orf40	401137	hgsc.bcm.edu	37	chr4	71024463	71024463	+	Missense_Mutation	SNP	G	G	C																															tgctgcagaggcacctgttgGagctgagcctgctgcagagg																								rs142405912	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:71024463G>C	ENST00000344526.5	+	3	683	c.494G>C	c.(493-495)gGa>gCa	p.G165A	C4orf40_ENST00000502294.1_Missense_Mutation_p.G165A|C4orf40_ENST00000502441.2_3'UTR	NM_214711.3	NP_999876.2	Q6MZM9	PRR27_HUMAN		165	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						GCACCTGTTGGAGCTGAGCCT	0.632													G|||	26	0.00519169	0.0038	0.0043	5008	,	,		16092	0.001		0.0139	False		,,,				2504	0.0031				p.G165A		Atlas-SNP	.											.	C4orf40	19	.	0			c.G494C						PASS	.	G	ALA/GLY	8,4398		0,8,2195	29	30	30		494	1.3	0	4	dbSNP_134	30	114,8482		2,110,4186	no	missense	C4orf40	NM_214711.3	60	2,118,6381	CC,CG,GG		1.3262,0.1816,0.9383	benign	165/220	71024463	122,12880	2203	4298	6501	SO:0001583	missense	401137	exon3			CTGTTGGAGCTGA																												ENST00000344526.5:c.494G>C	4.37:g.71024463G>C	ENSP00000343172:p.Gly165Ala	135	0	0		107	9	0.0841122	NM_214711	A8MXP0|Q6MZR6	Missense_Mutation	SNP	ENST00000344526.5	37	CCDS3535.1	12	0.005494505494505495	0	0.0	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	G	6.439	0.449185	0.12223	0.001816	0.013262	ENSG00000187533	ENST00000502294;ENST00000344526	T;T	0.29917	1.55;1.55	4.43	1.28	0.21552	.	.	.	.	.	T	0.05318	0.0141	N	0.01874	-0.695	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.33343	-0.9872	9	0.02654	T	1	0.4193	1.7036	0.02877	0.1887:0.2762:0.391:0.1441	.	165	Q6MZM9	CD040_HUMAN	A	165	ENSP00000426249:G165A;ENSP00000343172:G165A	ENSP00000343172:G165A	G	+	2	0	C4orf40	71059052	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.053000	0.11846	-0.013000	0.14199	-0.241000	0.12123	GGA	G|0.993;C|0.007	0.007	strong		0.632	C4orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251558.1			C	71024463	G	C	71024463	3	2	24	1	0	0	0	0	1	0	0	0	2271	1174	41	4	504	4	C4orf40	4	71024463	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	2099369	71024463	120129813	144	8361	107	4									
C4orf40	401137	hgsc.bcm.edu	37	chr4	71024466	71024466	+	Missense_Mutation	SNP	C	C	T																															tgcagaggcacctgttggagCtgagcctgctgcagaggcac																								rs201012961		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:71024466C>T	ENST00000344526.5	+	3	686	c.497C>T	c.(496-498)gCt>gTt	p.A166V	C4orf40_ENST00000502294.1_Missense_Mutation_p.A166V|C4orf40_ENST00000502441.2_3'UTR	NM_214711.3	NP_999876.2	Q6MZM9	PRR27_HUMAN		166	Ala/Pro-rich.					extracellular vesicular exosome (GO:0070062)		p.A166V(1)		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						CCTGTTGGAGCTGAGCCTGCT	0.632																																					p.A166V		Atlas-SNP	.											.	C4orf40	19	.	1	Substitution - Missense(1)	lung(1)	c.C497T						PASS	.						30	30	30					4																	71024466		2203	4298	6501	SO:0001583	missense	401137	exon3			TTGGAGCTGAGCC																												ENST00000344526.5:c.497C>T	4.37:g.71024466C>T	ENSP00000343172:p.Ala166Val	139	0	0		113	26	0.230089	NM_214711	A8MXP0|Q6MZR6	Missense_Mutation	SNP	ENST00000344526.5	37	CCDS3535.1	.	.	.	.	.	.	.	.	.	.	C	10.07	1.250256	0.22880	.	.	ENSG00000187533	ENST00000502294;ENST00000344526	T;T	0.33654	1.4;1.4	4.45	-4.02	0.04034	.	.	.	.	.	T	0.14874	0.0359	N	0.14661	0.345	0.09310	N	1	B	0.28713	0.22	B	0.22880	0.042	T	0.14952	-1.0454	9	0.45353	T	0.12	-4.1741	1.4635	0.02401	0.1179:0.3066:0.2443:0.3312	.	166	Q6MZM9	CD040_HUMAN	V	166	ENSP00000426249:A166V;ENSP00000343172:A166V	ENSP00000343172:A166V	A	+	2	0	C4orf40	71059055	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-1.976000	0.01497	-0.789000	0.04498	0.609000	0.83330	GCT	C|0.999;T|0.001	0.001	weak		0.632	C4orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251558.1			T	71024466	C	T	71024466	3	4	24	1	0	0	0	0	1	0	0	0	2271	797	28	2	507	2	C4orf40	4	71024466	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	3	71024466	120129810	145	8362	107	4									
C4orf40	401137	hgsc.bcm.edu	37	chr4	71024467	71024467	+	Silent	SNP	T	T	G																															gcagaggcacctgttggagcTgagcctgctgcagaggcacc																								rs201990073		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:71024467T>G	ENST00000344526.5	+	3	687	c.498T>G	c.(496-498)gcT>gcG	p.A166A	C4orf40_ENST00000502294.1_Silent_p.A166A|C4orf40_ENST00000502441.2_3'UTR	NM_214711.3	NP_999876.2	Q6MZM9	PRR27_HUMAN		166	Ala/Pro-rich.					extracellular vesicular exosome (GO:0070062)		p.A166V(1)		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						CTGTTGGAGCTGAGCCTGCTG	0.627																																					p.A166A		Atlas-SNP	.											.	C4orf40	19	.	1	Substitution - Missense(1)	lung(1)	c.T498G						PASS	.						30	31	30					4																	71024467		2203	4297	6500	SO:0001819	synonymous_variant	401137	exon3			TGGAGCTGAGCCT																												ENST00000344526.5:c.498T>G	4.37:g.71024467T>G		142	0	0		114	26	0.22807	NM_214711	A8MXP0|Q6MZR6	Silent	SNP	ENST00000344526.5	37	CCDS3535.1																																																																																			T|0.999;G|0.001	0.001	weak		0.627	C4orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251558.1			G	71024467	T	G	71024467	2	3	24	1	0	0	0	0	0	0	0	1	2271	1567	55	5		5	C4orf40	4	71024467	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	1	71024467	120129809	146	8363	107	4									
C4orf40	401137	hgsc.bcm.edu	37	chr4	71024473	71024473	+	Silent	SNP	T	T	A																															gcacctgttggagctgagccTgctgcagaggcacctgttgc																								rs542201615		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:71024473T>A	ENST00000344526.5	+	3	693	c.504T>A	c.(502-504)ccT>ccA	p.P168P	C4orf40_ENST00000502294.1_Silent_p.P168P|C4orf40_ENST00000502441.2_3'UTR	NM_214711.3	NP_999876.2	Q6MZM9	PRR27_HUMAN		168	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						GAGCTGAGCCTGCTGCAGAGG	0.627																																					p.P168P		Atlas-SNP	.											.	C4orf40	19	.	0			c.T504A						PASS	.																																			SO:0001819	synonymous_variant	401137	exon3			TGAGCCTGCTGCA																												ENST00000344526.5:c.504T>A	4.37:g.71024473T>A		151	0	0		125	20	0.16	NM_214711	A8MXP0|Q6MZR6	Silent	SNP	ENST00000344526.5	37	CCDS3535.1																																																																																			.	.	none		0.627	C4orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251558.1			A	71024473	T	A	71024473	2	1	24	1	0	0	0	0	0	0	0	1	2271	1567	55	5		5	C4orf40	4	71024473	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	6	71024473	120129803	147	8364	107	4									
PPEF2	5470	hgsc.bcm.edu	37	chr4	76797739	76797739	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaccatgggatgggtccctGtgcagagctcttctggttgg	7	11	14	9	0	2	1	0	0	2	1	3	2	3	2	2	4	3	3	2	4	1	2	rs149631239		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:76797739G>A	ENST00000286719.7	-	11	1377	c.1021C>T	c.(1021-1023)Cag>Tag	p.Q341*		NM_006239.2	NP_006230.2	O14830	PPE2_HUMAN	protein phosphatase, EF-hand calcium binding domain 2	341	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)			ATGGGTCCCTGTGCAGAGCTC	0.547													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18236	0.0		0.0	False		,,,				2504	0.0				p.Q341X	NSCLC(105;1359 1603 15961 44567 47947)	Atlas-SNP	.											.	PPEF2	108	.	0			c.C1021T						PASS	.	G	stop/GLN	1,4405	2.1+/-5.4	0,1,2202	95	98	97		1021	0.9	0	4	dbSNP_134	97	9,8591	7.1+/-27.0	0,9,4291	yes	stop-gained	PPEF2	NM_006239.2		0,10,6493	AA,AG,GG		0.1047,0.0227,0.0769		341/754	76797739	10,12996	2203	4300	6503	SO:0001587	stop_gained	5470	exon11			GTCCCTGTGCAGA	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.1021C>T	4.37:g.76797739G>A	ENSP00000286719:p.Gln341*	312	0	0		289	144	0.49827	NM_006239	O14831	Nonsense_Mutation	SNP	ENST00000286719.7	37	CCDS34013.1	.	.	.	.	.	.	.	.	.	.	G	34	5.301613	0.95601	2.27E-4	0.001047	ENSG00000156194	ENST00000286719;ENST00000337500	.	.	.	3.63	0.893	0.19236	.	2.033460	0.02299	N	0.070992	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	-0.1914	5.7028	0.17891	0.2626:0.4639:0.2735:0.0	.	.	.	.	X	341	.	ENSP00000286719:Q341X	Q	-	1	0	PPEF2	77016763	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.043000	0.13971	0.162000	0.19483	-0.339000	0.08088	CAG	G|0.999;A|0.001	0.001	strong		0.547	PPEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362929.1	NM_006239		A	76797739	G	A	76797739	4	1	24	1	0	0	0	0	0	1	0	0	12317	1386	48	2	1268	2	PPEF2	4	76797739	Nonsense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	5773266	76797739	114356537	148	8365											
CCDC158	339965	hgsc.bcm.edu	37	chr4	77255210	77255210	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gttcttccatcttcctctgtCttgctcagagacacagctgg	6	14	8	13	0	5	1	1	0	4	1	7	2	7	1	2	1	2	3	2	1	0	4	rs113022439	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:77255210C>T	ENST00000388914.3	-	18	2927	c.2775G>A	c.(2773-2775)aaG>aaA	p.K925K		NM_001042784.1	NP_001036249.1	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	925										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						CTTCCTCTGTCTTGCTCAGAG	0.483													C|||	32	0.00638978	0.0015	0.0072	5008	,	,		17210	0.0		0.0239	False		,,,				2504	0.001				p.K925K		Atlas-SNP	.											.	CCDC158	114	.	0			c.G2775A						PASS	.	C		15,4101		0,15,2043	158	159	159		2775	3.8	0.6	4	dbSNP_132	159	300,8128		4,292,3918	no	coding-synonymous	CCDC158	NM_001042784.1		4,307,5961	TT,TC,CC		3.5596,0.3644,2.5112		925/1114	77255210	315,12229	2058	4214	6272	SO:0001819	synonymous_variant	339965	exon18			CTCTGTCTTGCTC	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.2775G>A	4.37:g.77255210C>T		171	0	0		177	93	0.525424	NM_001042784	Q8IYQ1|Q8N7D4|Q8N7E3	Silent	SNP	ENST00000388914.3	37	CCDS43242.1																																																																																			C|0.984;T|0.016	0.016	strong		0.483	CCDC158-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362694.2	NM_001042784		T	77255210	C	T	77255210	2	4	24	1	0	0	0	0	0	0	0	1	2792	912	32	2		2	CCDC158	4	77255210	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	457471	77255210	113899066	149	8366											
SHROOM3	57619	hgsc.bcm.edu	37	chr4	77661017	77661017	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatttctgttcagtgcctgAaaatgaggaggatgcctccc	9	11	10	11	0	2	2	1	2	1	0	3	4	3	4	4	2	2	1	4	2	2	2	rs76656494	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:77661017A>C	ENST00000296043.6	+	5	2644	c.1691A>C	c.(1690-1692)gAa>gCa	p.E564A		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	564					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)			TCAGTGCCTGAAAATGAGGAG	0.502													A|||	33	0.00658946	0.0	0.013	5008	,	,		21550	0.0		0.0229	False		,,,				2504	0.001				p.E564A		Atlas-SNP	.											.	SHROOM3	134	.	0			c.A1691C						PASS	.	A	ALA/GLU	14,4392	22.3+/-47.3	0,14,2189	168	168	168		1691	4.4	1	4	dbSNP_131	168	145,8455	70.7+/-133.2	2,141,4157	yes	missense	SHROOM3	NM_020859.3	107	2,155,6346	CC,CA,AA		1.686,0.3177,1.2225	probably-damaging	564/1997	77661017	159,12847	2203	4300	6503	SO:0001583	missense	57619	exon5			TGCCTGAAAATGA	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.1691A>C	4.37:g.77661017A>C	ENSP00000296043:p.Glu564Ala	58	0	0		62	28	0.451613	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Missense_Mutation	SNP	ENST00000296043.6	37	CCDS3579.2	23	0.010531135531135532	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	17	0.022427440633245383	A	15.10	2.733513	0.48939	0.003177	0.01686	ENSG00000138771	ENST00000296043	T	0.26660	1.72	5.59	4.39	0.52855	.	0.093877	0.44902	D	0.000410	T	0.31009	0.0783	M	0.71581	2.175	0.35431	D	0.794093	D;P;P	0.76494	0.999;0.89;0.8	D;B;B	0.65987	0.94;0.382;0.153	T	0.57688	-0.7768	10	0.72032	D	0.01	-7.8779	12.7677	0.57401	0.8629:0.1371:0.0:0.0	.	388;564;342	B4E244;Q8TF72;B3KY47	.;SHRM3_HUMAN;.	A	564	ENSP00000296043:E564A	ENSP00000296043:E564A	E	+	2	0	SHROOM3	77880041	1.000000	0.71417	1.000000	0.80357	0.414000	0.31173	1.907000	0.39897	0.925000	0.37094	0.460000	0.39030	GAA	A|0.988;C|0.012	0.012	strong		0.502	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859		C	77661017	A	C	77661017	3	2	24	1	0	0	0	0	1	0	0	0	14310	246	9	5	1709	5	SHROOM3	4	77661017	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	405807	77661017	113493259	150	8367											
BMP2K	55589	hgsc.bcm.edu	37	chr4	79832488	79832488	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctggttatcccaaaagtgtAgatgtatttggctccactcc	9	13	8	11	0	0	1	0	0	0	1	3	1	3	1	4	2	0	4	4	2	5	4	rs574665641	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:79832488A>G	ENST00000335016.5	+	16	2953	c.2787A>G	c.(2785-2787)gtA>gtG	p.V929V	PAQR3_ENST00000295462.3_Intron	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	929					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)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						CCAAAAGTGTAGATGTATTTG	0.438													A|||	2	0.000399361	0.0	0.0	5008	,	,		21116	0.0		0.0	False		,,,				2504	0.002				p.V929V		Atlas-SNP	.											.	BMP2K	169	.	0			c.A2787G						PASS	.						60	54	56					4																	79832488		1946	4127	6073	SO:0001819	synonymous_variant	55589	exon16			AAGTGTAGATGTA	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.2787A>G	4.37:g.79832488A>G		289	1	0.00346021		306	155	0.506536	NM_198892	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Silent	SNP	ENST00000335016.5	37	CCDS47083.1	.	.	.	.	.	.	.	.	.	.	A	5.217	0.225527	0.09916	.	.	ENSG00000138756	ENST00000502613	.	.	.	5.3	-4.97	0.03029	.	.	.	.	.	T	0.46964	0.1420	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44892	-0.9298	4	.	.	.	-9.7415	5.8121	0.18471	0.1496:0.2279:0.5104:0.1121	.	.	.	.	G	622	.	.	R	+	1	2	BMP2K	80051512	0.006000	0.16342	0.843000	0.33291	0.837000	0.47467	-1.136000	0.03222	-0.932000	0.03742	0.397000	0.26171	AGA	.	.	none		0.438	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593		G	79832488	A	G	79832488	2	3	24	1	0	0	0	0	0	0	0	1	1460	407	15	3		3	BMP2K	4	79832488	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	2171471	79832488	111321788	151	8368											
DSPP	1834	hgsc.bcm.edu	37	chr4	88537288	88537288	+	Silent	SNP	C	C	T																															gacagcagtgacagcagcgaCagcagtgacagcagcgatag																								rs368208607		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:88537288C>T	ENST00000282478.7	+	4	3507	c.3474C>T	c.(3472-3474)gaC>gaT	p.D1158D	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.D1158D			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1158	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)		acagcagcgacagcagtgaca	0.557																																					p.D1158D		Atlas-SNP	.											.	DSPP	174	.	0			c.C3474T						PASS	.						46	59	54					4																	88537288		1591	2859	4450	SO:0001819	synonymous_variant	1834	exon5			CAGCGACAGCAGT	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.3474C>T	4.37:g.88537288C>T		217	0	0		175	9	0.0514286	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.557	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		T	88537288	C	T	88537288	2	4	24	1	0	0	0	0	0	0	0	1	4784	477	17	2		2	DSPP	4	88537288	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	8704800	88537288	102616988	152	8369	108	2									
DSPP	1834	hgsc.bcm.edu	37	chr4	88537294	88537294	+	Silent	SNP	T	T	C																															agtgacagcagcgacagcagTgacagcagcgatagcagcga																								rs111216206		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:88537294T>C	ENST00000282478.7	+	4	3513	c.3480T>C	c.(3478-3480)agT>agC	p.S1160S	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.S1160S			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1160	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)		gcgacagcagtgacagcagcg	0.567																																					p.S1160S		Atlas-SNP	.											.	DSPP	174	.	0			c.T3480C						PASS	.						43	58	53					4																	88537294		1580	2849	4429	SO:0001819	synonymous_variant	1834	exon5			CAGCAGTGACAGC	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.3480T>C	4.37:g.88537294T>C		216	0	0		177	17	0.0960452	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	weak		0.567	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		C	88537294	T	C	88537294	2	2	24	1	0	0	0	0	0	0	0	1	4784	1693	59	3		3	DSPP	4	88537294	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	6	88537294	102616982	153	8370	108	2									
DSPP	1834	hgsc.bcm.edu	37	chr4	88537324	88537324	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatagcagcgacagcagcgaCagcagcgatagcagtgacag	14	3	14	10	3	0	1	0	1	0	0	0	5	0	1	0	0	7	4	0	0	2	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:88537324C>T	ENST00000282478.7	+	4	3543	c.3510C>T	c.(3508-3510)gaC>gaT	p.D1170D	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.D1170D			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1170	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)		acagcagcgacagcagcgata	0.567																																					p.D1170D		Atlas-SNP	.											DSPP,NS,carcinoma,0,2	DSPP	174	2	0			c.C3510T						PASS	.						44	63	56					4																	88537324		1605	2847	4452	SO:0001819	synonymous_variant	1834	exon5			CAGCGACAGCAGC	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.3510C>T	4.37:g.88537324C>T		236	0	0		183	11	0.0601093	NM_014208	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.	.	none		0.567	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		T	88537324	C	T	88537324	2	4	24	1	0	0	0	0	0	0	0	1	4784	477	17	2		2	DSPP	4	88537324	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	30	88537324	102616952	154	8371											
HERC5	51191	hgsc.bcm.edu	37	chr4	89380540	89380540	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgaagatacattccgtggAccaaggagcagagcacatgc	14	6	11	10	1	0	3	0	1	0	2	1	5	1	5	2	2	4	2	2	2	3	2	rs75070724	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:89380540A>G	ENST00000264350.3	+	2	461	c.308A>G	c.(307-309)gAc>gGc	p.D103G	HERC5_ENST00000508695.1_3'UTR	NM_016323.3	NP_057407.2	Q9UII4	HERC5_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 5	103					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)		CATTCCGTGGACCAAGGAGCA	0.368													a|||	6	0.00119808	0.0	0.0014	5008	,	,		15874	0.0		0.005	False		,,,				2504	0.0				p.D103G	Esophageal Squamous(39;887 1012 34045 50514)	Atlas-SNP	.											.	HERC5	114	.	0			c.A308G						PASS	.	A	GLY/ASP	4,4402	8.1+/-20.4	0,4,2199	133	127	129		308	2.4	1	4	dbSNP_131	129	24,8576	17.3+/-56.4	0,24,4276	yes	missense	HERC5	NM_016323.2	94	0,28,6475	GG,GA,AA		0.2791,0.0908,0.2153	benign	103/1025	89380540	28,12978	2203	4300	6503	SO:0001583	missense	51191	exon2			CCGTGGACCAAGG	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.308A>G	4.37:g.89380540A>G	ENSP00000264350:p.Asp103Gly	483	0	0		490	258	0.526531	NM_016323	B2RTQ1|Q69G20	Missense_Mutation	SNP	ENST00000264350.3	37	CCDS3630.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	a	10.19	1.281261	0.23392	9.08E-4	0.002791	ENSG00000138646	ENST00000264350	T	0.80123	-1.34	3.62	2.4	0.29515	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.115379	0.34088	N	0.004267	T	0.59528	0.2200	N	0.25890	0.77	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.60037	-0.7341	10	0.59425	D	0.04	.	8.5302	0.33329	0.8048:0.1952:0.0:0.0	.	103	Q9UII4	HERC5_HUMAN	G	103	ENSP00000264350:D103G	ENSP00000264350:D103G	D	+	2	0	HERC5	89599563	1.000000	0.71417	1.000000	0.80357	0.667000	0.39255	2.018000	0.40991	0.730000	0.32425	0.529000	0.55759	GAC	A|0.998;G|0.002	0.002	strong		0.368	HERC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253554.2	NM_016323		G	89380540	A	G	89380540	3	3	24	1	0	0	0	0	1	0	0	0	7070	275	10	3	314	3	HERC5	4	89380540	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	843216	89380540	101773736	155	8372											
MTTP	4547	hgsc.bcm.edu	37	chr4	100532602	100532602	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttgggaaggctggtcttcacGgtagccaggtaactcacttc	8	11	12	10	1	3	0	2	0	1	0	4	1	3	1	1	5	2	3	1	5	3	5	rs113337987	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:100532602G>A	ENST00000265517.5	+	14	2184	c.1981G>A	c.(1981-1983)Ggt>Agt	p.G661S	RP11-766F14.1_ENST00000508578.1_RNA|MTTP_ENST00000457717.1_Missense_Mutation_p.G661S|MTTP_ENST00000511045.1_Missense_Mutation_p.G688S			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	661					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)	TGGTCTTCACGGTAGCCAGGT	0.413													G|||	49	0.00978435	0.0	0.036	5008	,	,		19260	0.001		0.0209	False		,,,				2504	0.002				p.G661S		Atlas-SNP	.											MTTP,caecum,carcinoma,0,1	MTTP	127	1	0			c.G1981A						PASS	.	G	SER/GLY	26,4380	31.7+/-61.6	0,26,2177	144	132	136		1981	3.7	0	4	dbSNP_132	136	305,8295	110.0+/-170.5	11,283,4006	yes	missense	MTTP	NM_000253.2	56	11,309,6183	AA,AG,GG		3.5465,0.5901,2.545	benign	661/895	100532602	331,12675	2203	4300	6503	SO:0001583	missense	4547	exon15			CTTCACGGTAGCC		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.1981G>A	4.37:g.100532602G>A	ENSP00000265517:p.Gly661Ser	116	0	0		104	64	0.615385	NM_000253	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	38	0.0173992673992674	0	0.0	22	0.06077348066298342	0	0.0	16	0.021108179419525065	G	7.432	0.639007	0.14386	0.005901	0.035465	ENSG00000138823	ENST00000511045;ENST00000457717;ENST00000265517	T;T;T	0.60299	0.2;0.21;0.21	5.62	3.68	0.42216	.	0.320705	0.36703	N	0.002460	T	0.07503	0.0189	L	0.34521	1.04	0.34748	D	0.731457	B;B	0.17852	0.024;0.008	B;B	0.09377	0.003;0.004	T	0.21895	-1.0232	10	0.36615	T	0.2	-11.0583	11.7253	0.51706	0.1287:0.0:0.8713:0.0	.	688;661	E9PBP6;P55157	.;MTP_HUMAN	S	688;661;661	ENSP00000427679:G688S;ENSP00000400821:G661S;ENSP00000265517:G661S	ENSP00000265517:G661S	G	+	1	0	MTTP	100751625	1.000000	0.71417	0.004000	0.12327	0.011000	0.07611	4.409000	0.59768	0.533000	0.28675	0.655000	0.94253	GGT	G|0.970;A|0.030	0.030	strong		0.413	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3			A	100532602	G	A	100532602	3	1	24	1	0	0	0	0	1	0	0	0	9973	1116	39	1	2035	1	MTTP	4	100532602	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	11152062	100532602	90621674	156	8373											
NFKB1	4790	hgsc.bcm.edu	37	chr4	103505961	103505961	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaaccaaaacctttcctctaCtatcctgaaatcaaaggtaa	16	10	4	11	0	2	1	1	1	1	0	4	2	4	1	4	1	3	1	4	1	8	4	rs4648039	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:103505961C>T	ENST00000505458.1	+	11	1324	c.1047C>T	c.(1045-1047)taC>taT	p.Y349Y	NFKB1_ENST00000394820.4_Silent_p.Y349Y|NFKB1_ENST00000600343.1_Silent_p.Y169Y|NFKB1_ENST00000226574.4_Silent_p.Y350Y			P19838	NFKB1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	349	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)	CTTTCCTCTACTATCCTGAAA	0.303													C|||	26	0.00519169	0.0	0.0014	5008	,	,		18222	0.0		0.0219	False		,,,				2504	0.0031				p.Y350Y		Atlas-SNP	.											.	NFKB1	78	.	0			c.C1050T						PASS	.	C	,	27,4379	33.5+/-64.1	0,27,2176	55	57	56		1047,1050	4	1	4	dbSNP_111	56	211,8389	89.7+/-151.9	2,207,4091	no	coding-synonymous,coding-synonymous	NFKB1	NM_001165412.1,NM_003998.3	,	2,234,6267	TT,TC,CC		2.4535,0.6128,1.8299	,	349/969,350/970	103505961	238,12768	2203	4300	6503	SO:0001819	synonymous_variant	4790	exon11			CCTCTACTATCCT	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.1047C>T	4.37:g.103505961C>T		106	0	0		134	70	0.522388	NM_003998	A8K5Y5|B3KVE8|Q68D84|Q86V43|Q8N4X7|Q9NZC0	Silent	SNP	ENST00000505458.1	37	CCDS54783.1																																																																																			C|0.983;T|0.017	0.017	strong		0.303	NFKB1-003	KNOWN	alternative_5_UTR|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363411.1			T	103505961	C	T	103505961	2	4	24	1	0	0	0	0	0	0	0	1	10384	576	20	2		2	NFKB1	4	103505961	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	2973359	103505961	87648315	157	8374											
LRIT3	345193	hgsc.bcm.edu	37	chr4	110791526	110791526	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagcaagaaccaagtaaccAtagatggcttggaacccggt	14	6	10	11	1	0	2	0	0	0	2	0	3	0	3	4	3	4	3	4	3	6	3	rs35997283	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:110791526A>G	ENST00000594814.1	+	4	1621	c.1621A>G	c.(1621-1623)Ata>Gta	p.I541V	LRIT3_ENST00000379920.3_Missense_Mutation_p.I496V|LRIT3_ENST00000327908.3_Missense_Mutation_p.I358V|LRIT3_ENST00000409621.2_Missense_Mutation_p.I358V	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	541	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)		CCAAGTAACCATAGATGGCTT	0.488													A|||	8	0.00159744	0.0015	0.0029	5008	,	,		20846	0.0		0.002	False		,,,				2504	0.002				p.I541V		Atlas-SNP	.											.	LRIT3	107	.	0			c.A1621G						PASS	.	A	VAL/ILE	3,4403	6.2+/-15.9	0,3,2200	104	99	101		1486	2.6	1	4	dbSNP_126	101	59,8541	36.4+/-91.3	0,59,4241	yes	missense	LRIT3	NM_198506.2	29	0,62,6441	GG,GA,AA		0.686,0.0681,0.4767	benign	496/635	110791526	62,12944	2203	4300	6503	SO:0001583	missense	345193	exon4			GTAACCATAGATG	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.1621A>G	4.37:g.110791526A>G	ENSP00000469759:p.Ile541Val	122	0	0		142	71	0.5	NM_198506	C9J1C2|Q6ZTG1	Missense_Mutation	SNP	ENST00000594814.1	37	CCDS3688.3	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	A	13.22	2.171157	0.38315	6.81E-4	0.00686	ENSG00000183423	ENST00000327908;ENST00000379920;ENST00000409621	T;T;T	0.27557	1.66;1.66;1.66	5.16	2.63	0.31362	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.106920	0.64402	D	0.000004	T	0.31136	0.0787	M	0.76838	2.35	0.40389	D	0.979528	P;P	0.46277	0.802;0.875	B;P	0.45037	0.206;0.467	T	0.36286	-0.9754	10	0.72032	D	0.01	.	11.922	0.52797	0.7234:0.2765:0.0:0.0	rs35997283	496;358	Q3SXY7;Q3SXY7-2	LRIT3_HUMAN;.	V	358;496;358	ENSP00000328222:I358V;ENSP00000369252:I496V;ENSP00000386734:I358V	ENSP00000328222:I358V	I	+	1	0	LRIT3	111010975	1.000000	0.71417	0.982000	0.44146	0.969000	0.65631	1.641000	0.37197	0.266000	0.21894	-0.313000	0.08912	ATA	A|0.996;G|0.004	0.004	strong		0.488	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506		G	110791526	A	G	110791526	3	3	24	1	0	0	0	0	1	0	0	0	8958	217	8	3	1496	3	LRIT3	4	110791526	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	7285565	110791526	80362750	158	8375											
PLK4	10733	hgsc.bcm.edu	37	chr4	128811038	128811038	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tagctcatttaagaaaaactActgaatatgacagcatcagc	17	10	6	8	0	2	3	2	2	0	1	2	3	2	3	0	0	5	2	0	0	7	5			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:128811038A>G	ENST00000270861.5	+	7	1751	c.1477A>G	c.(1477-1479)Act>Gct	p.T493A	PLK4_ENST00000514379.1_Missense_Mutation_p.T452A|PLK4_ENST00000507249.1_Missense_Mutation_p.T459A|PLK4_ENST00000515069.1_Intron|PLK4_ENST00000513090.1_Missense_Mutation_p.T461A|RNU6-583P_ENST00000516012.1_RNA	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	493					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						AAGAAAAACTACTGAATATGA	0.358																																					p.T493A	Colon(135;508 1718 19061 31832 42879)	Atlas-SNP	.											.	PLK4	65	.	0			c.A1477G						PASS	.						36	38	37					4																	128811038		2201	4296	6497	SO:0001583	missense	10733	exon7			AAAACTACTGAAT	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.1477A>G	4.37:g.128811038A>G	ENSP00000270861:p.Thr493Ala	158	0	0		122	61	0.5	NM_014264	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Missense_Mutation	SNP	ENST00000270861.5	37	CCDS3735.1	.	.	.	.	.	.	.	.	.	.	A	0.176	-1.066534	0.01934	.	.	ENSG00000142731	ENST00000270861;ENST00000513090;ENST00000507249;ENST00000514379	T;T;T;T	0.32023	1.47;1.47;1.47;1.47	4.57	0.741	0.18336	.	0.520099	0.21520	N	0.073224	T	0.11110	0.0271	N	0.12182	0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.29336	-1.0015	10	0.06625	T	0.88	-2.5911	3.9503	0.09366	0.3168:0.399:0.2842:0.0	.	461;493	O00444-2;O00444	.;PLK4_HUMAN	A	493;461;459;452	ENSP00000270861:T493A;ENSP00000427554:T461A;ENSP00000423412:T459A;ENSP00000423582:T452A	ENSP00000270861:T493A	T	+	1	0	PLK4	129030488	0.335000	0.24748	0.921000	0.36526	0.022000	0.10575	0.100000	0.15231	0.787000	0.33731	0.482000	0.46254	ACT	.	.	none		0.358	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257095.3			G	128811038	A	G	128811038	3	3	24	1	0	0	0	0	1	0	0	0	12107	391	14	3	1503	3	PLK4	4	128811038	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	18019512	128811038	62343238	159	8376											
ELMOD2	255520	hgsc.bcm.edu	37	chr4	141464666	141464666	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcttatagcttactgaagaGtgaagctttgaagtttcatc	11	14	10	6	0	1	4	1	3	0	1	2	4	1	4	0	1	3	4	0	1	6	5	rs148286208	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:141464666G>A	ENST00000323570.3	+	8	794	c.662G>A	c.(661-663)aGt>aAt	p.S221N		NM_153702.3	NP_714913.1	Q8IZ81	ELMD2_HUMAN	ELMO/CED-12 domain containing 2	221	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)					TTACTGAAGAGTGAAGCTTTG	0.338													G|||	3	0.000599042	0.0	0.0	5008	,	,		14795	0.0		0.003	False		,,,				2504	0.0				p.S221N		Atlas-SNP	.											.	ELMOD2	16	.	0			c.G662A						PASS	.	G	ASN/SER	3,4403	6.2+/-15.9	0,3,2200	114	114	114		662	5.3	1	4	dbSNP_134	114	11,8573	7.7+/-29.5	0,11,4281	yes	missense	ELMOD2	NM_153702.3	46	0,14,6481	AA,AG,GG		0.1281,0.0681,0.1078	benign	221/294	141464666	14,12976	2203	4292	6495	SO:0001583	missense	255520	exon8			TGAAGAGTGAAGC	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.662G>A	4.37:g.141464666G>A	ENSP00000326342:p.Ser221Asn	81	0	0		94	36	0.382979	NM_153702	B2R712|D3DNZ0	Missense_Mutation	SNP	ENST00000323570.3	37	CCDS3752.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	15.68	2.905457	0.52333	6.81E-4	0.001281	ENSG00000179387	ENST00000323570	T	0.30448	1.53	6.16	5.33	0.75918	Engulfment/cell motility, ELMO (2);	0.159239	0.64402	N	0.000001	T	0.26991	0.0661	L	0.51914	1.62	0.42822	D	0.993998	B	0.17038	0.02	B	0.22601	0.04	T	0.08493	-1.0719	10	0.18276	T	0.48	-4.9602	10.0032	0.41942	0.1887:0.0:0.8113:0.0	.	221	Q8IZ81	ELMD2_HUMAN	N	221	ENSP00000326342:S221N	ENSP00000326342:S221N	S	+	2	0	ELMOD2	141684116	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.898000	0.39809	1.631000	0.50456	0.650000	0.86243	AGT	A|0.001;G|0.999	0.001	strong		0.338	ELMOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257277.2	NM_153702		A	141464666	G	A	141464666	3	1	24	1	0	0	0	0	1	0	0	0	5071	1029	36	2	688	2	ELMOD2	4	141464666	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	12653628	141464666	49689610	160	8377											
LRBA	987	hgsc.bcm.edu	37	chr4	151388906	151388906	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgatgacccaaggaaacacTggatactgatttaagtcatt	14	11	9	7	0	1	3	1	3	0	0	1	5	1	5	1	2	2	0	1	2	4	4			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:151388906T>C	ENST00000357115.3	-	45	6975	c.6732A>G	c.(6730-6732)ccA>ccG	p.P2244P	LRBA_ENST00000535741.1_Silent_p.P2233P|LRBA_ENST00000503716.1_5'UTR|LRBA_ENST00000507224.1_Silent_p.P2233P|LRBA_ENST00000510413.1_Silent_p.P2233P	NM_006726.4	NP_006717.2	P50851	LRBA_HUMAN	LPS-responsive vesicle trafficking, beach and anchor containing	2244	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.					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)					AAGGAAACACTGGATACTGAT	0.323																																					p.P2244P		Atlas-SNP	.											.	LRBA	253	.	0			c.A6732G						PASS	.						117	110	113					4																	151388906		2203	4297	6500	SO:0001819	synonymous_variant	987	exon45			AAACACTGGATAC	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.6732A>G	4.37:g.151388906T>C		226	0	0		241	101	0.419087	NM_006726	Q4W5J4|Q4W5L6|Q8NFQ0|Q9H2U3|Q9H2U4	Silent	SNP	ENST00000357115.3	37	CCDS3773.1	.	.	.	.	.	.	.	.	.	.	T	10.20	1.283943	0.23392	.	.	ENSG00000198589	ENST00000509835	.	.	.	4.98	-2.12	0.07165	.	.	.	.	.	T	0.51143	0.1657	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47129	-0.9141	4	.	.	.	.	7.1251	0.25467	0.4743:0.0795:0.0:0.4462	.	.	.	.	R	886	.	.	Q	-	2	0	LRBA	151608356	0.547000	0.26465	0.999000	0.59377	0.998000	0.95712	-0.270000	0.08584	-0.014000	0.14175	0.477000	0.44152	CAG	.	.	none		0.323	LRBA-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364939.1			C	151388906	T	C	151388906	2	2	24	1	0	0	0	0	0	0	0	1	8940	1567	55	3		3	LRBA	4	151388906	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	9924240	151388906	39765370	161	8378											
FGG	2266	hgsc.bcm.edu	37	chr4	155533035	155533035	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttttcctggacttcaaagtaGcagcgtctatcatatctgta	10	15	7	9	1	4	0	2	0	2	0	5	1	5	1	1	1	2	3	1	1	5	7	rs148685782	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:155533035G>C	ENST00000336098.3	-	4	361	c.323C>G	c.(322-324)gCt>gGt	p.A108G	FGG_ENST00000405164.1_Missense_Mutation_p.A108G|FGG_ENST00000407946.1_Missense_Mutation_p.A108G|FGG_ENST00000404648.3_Missense_Mutation_p.A108G	NM_021870.2	NP_068656.2	P02679	FIBG_HUMAN	fibrinogen gamma chain	108					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|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)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|structural molecule activity (GO:0005198)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)	CTTCAAAGTAGCAGCGTCTAT	0.294													G|||	8	0.00159744	0.0	0.0	5008	,	,		16621	0.0		0.006	False		,,,				2504	0.002				p.A108G		Atlas-SNP	.											.	FGG	71	.	0			c.C323G	GRCh37	CM000383	FGG	M	rs148685782	PASS	.	G	GLY/ALA,GLY/ALA	4,4398	8.1+/-20.4	0,4,2197	74	75	75		323,323	5.1	0.7	4	dbSNP_134	75	30,8564	21.0+/-64.5	0,30,4267	yes	missense,missense	FGG	NM_000509.4,NM_021870.2	60,60	0,34,6464	CC,CG,GG		0.3491,0.0909,0.2616	benign,benign	108/438,108/454	155533035	34,12962	2201	4297	6498	SO:0001583	missense	2266	exon4			AAAGTAGCAGCGT		CCDS3788.1, CCDS47153.1	4q28	2014-09-17			ENSG00000171557	ENSG00000171557		"Fibrinogen C domain containing", "Endogenous ligands"	3694	protein-coding gene	gene with protein product		134850	"fibrinogen, gamma polypeptide"				Standard	NM_000509		Approved		uc003ioj.3	P02679	OTTHUMG00000150329	ENST00000336098.3:c.323C>G	4.37:g.155533035G>C	ENSP00000336829:p.Ala108Gly	89	0	0		72	27	0.375	NM_000509	A8K057|P04469|P04470|Q53Y18|Q96A14|Q96KJ3|Q9UC62|Q9UC63|Q9UCF3	Missense_Mutation	SNP	ENST00000336098.3	37	CCDS3788.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	G	11.32	1.605287	0.28623	9.09E-4	0.003491	ENSG00000171557	ENST00000404648;ENST00000405164;ENST00000336098;ENST00000407946;ENST00000443553;ENST00000393846	D;D;D;D;D;D	0.82893	-1.66;-1.66;-1.66;-1.66;-1.66;-1.66	6.02	5.07	0.68467	Fibrinogen, alpha/beta/gamma chain, coiled coil domain (2);	0.481885	0.23983	N	0.042648	T	0.69513	0.3119	M	0.69463	2.115	0.25585	N	0.986755	B;B;B;B	0.06786	0.001;0.001;0.001;0.001	B;B;B;B	0.08055	0.002;0.003;0.003;0.001	T	0.56378	-0.7989	10	0.25751	T	0.34	.	2.5551	0.04758	0.2099:0.0:0.5124:0.2777	.	108;108;108;108	C9JC84;P02679;C9JEU5;P02679-2	.;FIBG_HUMAN;.;.	G	108;108;108;108;5;5	ENSP00000384860:A108G;ENSP00000384101:A108G;ENSP00000336829:A108G;ENSP00000384552:A108G;ENSP00000407562:A5G;ENSP00000377429:A5G	ENSP00000336829:A108G	A	-	2	0	FGG	155752485	0.594000	0.26849	0.681000	0.30009	0.005000	0.04900	2.105000	0.41825	2.857000	0.98124	0.650000	0.86243	GCT	G|0.998;C|0.002	0.002	strong		0.294	FGG-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317581.1	NM_021870		C	155533035	G	C	155533035	3	2	24	1	0	0	0	0	1	0	0	0	5878	971	34	4	1081	4	FGG	4	155533035	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	4144129	155533035	35621241	162	8379											
DDX60	55601	hgsc.bcm.edu	37	chr4	169146815	169146815	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	actaaaatcctcagggagatCatcaaggaacacctagaagc	17	6	8	10	0	3	2	3	0	0	2	4	4	4	3	2	2	2	0	2	2	6	2	rs146255632	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:169146815C>T	ENST00000393743.3	-	34	4837	c.4546G>A	c.(4546-4548)Gat>Aat	p.D1516N		NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	1516					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)		TCAGGGAGATCATCAAGGAAC	0.353																																					p.D1516N		Atlas-SNP	.											.	DDX60	304	.	0			c.G4546A						PASS	.	C	ASN/ASP	0,4406		0,0,2203	79	81	80		4546	5	0.5	4	dbSNP_134	80	14,8584	10.5+/-38.8	0,14,4285	yes	missense	DDX60	NM_017631.5	23	0,14,6488	TT,TC,CC		0.1628,0.0,0.1077	probably-damaging	1516/1713	169146815	14,12990	2203	4299	6502	SO:0001583	missense	55601	exon34			GGAGATCATCAAG	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.4546G>A	4.37:g.169146815C>T	ENSP00000377344:p.Asp1516Asn	74	0	0		59	24	0.40678	NM_017631	Q6PK35|Q9NVE3	Missense_Mutation	SNP	ENST00000393743.3	37	CCDS34097.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.89|15.89	2.966660|2.966660	0.53507|0.53507	0.0|0.0	0.001628|0.001628	ENSG00000137628|ENSG00000137628	ENST00000393743|ENST00000511317	T|.	0.18810|.	2.19|.	5.82|5.82	4.97|4.97	0.65823|0.65823	.|.	0.190110|.	0.37012|.	N|.	0.002284|.	T|T	0.64136|0.64136	0.2571|0.2571	M|M	0.80982|0.80982	2.52|2.52	0.26026|0.26026	N|N	0.981803|0.981803	D|.	0.56287|.	0.975|.	P|.	0.50754|.	0.649|.	T|T	0.58847|0.58847	-0.7564|-0.7564	10|5	0.35671|.	T|.	0.21|.	.|.	14.3138|14.3138	0.66434|0.66434	0.0:0.9259:0.0:0.0741|0.0:0.9259:0.0:0.0741	.|.	1516|.	Q8IY21|.	DDX60_HUMAN|.	N|I	1516|8	ENSP00000377344:D1516N|.	ENSP00000377344:D1516N|.	D|M	-|-	1|3	0|0	DDX60|DDX60	169383390|169383390	0.995000|0.995000	0.38212|0.38212	0.540000|0.540000	0.28089|0.28089	0.111000|0.111000	0.19643|0.19643	2.338000|2.338000	0.43957|0.43957	2.755000|2.755000	0.94549|0.94549	0.563000|0.563000	0.77884|0.77884	GAT|ATG	C|0.999;T|0.001	0.001	strong		0.353	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631		T	169146815	C	T	169146815	3	4	24	1	0	0	0	0	1	0	0	0	4380	826	29	2	612	2	DDX60	4	169146815	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	13613780	169146815	22007461	163	8380											
NEIL3	55247	hgsc.bcm.edu	37	chr4	178256864	178256864	+	Frame_Shift_Del	DEL	T	T	-																															ttcatttcggaatgaaaggcTtcatcatgattaatccactt																										TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:178256864delT	ENST00000264596.3	+	3	419	c.301delT	c.(301-303)ttcfs	p.F101fs		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	101					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)		AATGAAAGGCTTCATCATGAT	0.323								Base excision repair (BER), DNA glycosylases																													p.G100fs		Pindel,Atlas-Indel	.											.	NEIL3	89	.	0			c.300delC						PASS	.						61	69	66					4																	178256864		2200	4300	6500	SO:0001589	frameshift_variant	55247	exon3			.	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.301delT	4.37:g.178256864delT	ENSP00000264596:p.Phe101fs	157	0	.		178	53	0.298	NM_018248	Q2PPJ3|Q8NG51|Q9NV95	Frame_Shift_Del	DEL	ENST00000264596.3	37	CCDS3828.1																																																																																			.	.	none		0.323	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248		-	178256864	T	-	178256864	7	5	24	1	0	1	0	1	0	0	0	0	10329	1609	56	0	311	0	NEIL3	4	178256864	Frame_Shift_Del	DEL	T	TCGA-G8-6326-01A-11D-2210-10	9110049	178256864	12897412	164	8381											
FAT1	2195	hgsc.bcm.edu	37	chr4	187518874	187518874	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatcacactgacaaacggcGccatccaaactgtcaaagca	16	5	7	13	2	2	1	2	1	0	0	3	2	3	1	2	1	3	1	2	1	4	0	rs116628547	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr4:187518874G>A	ENST00000441802.2	-	24	12539	c.12330C>T	c.(12328-12330)ggC>ggT	p.G4110G	FAT1_ENST00000512347.1_5'Flank	NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	4110	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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						GACAAACGGCGCCATCCAAAC	0.418										HNSCC(5;0.00058)			G|||	15	0.00299521	0.0008	0.0014	5008	,	,		18073	0.0		0.008	False		,,,				2504	0.0051				p.G4110G	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C12330T						PASS	.	G		7,3819		0,7,1906	74	66	68		12330	-3.1	1	4	dbSNP_132	68	51,8225		0,51,4087	no	coding-synonymous	FAT1	NM_005245.3		0,58,5993	AA,AG,GG		0.6162,0.183,0.4793		4110/4589	187518874	58,12044	1913	4138	6051	SO:0001819	synonymous_variant	2195	exon24			AACGGCGCCATCC	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.12330C>T	4.37:g.187518874G>A		158	0	0		147	81	0.55102	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			G|0.995;A|0.005	0.005	strong		0.418	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		A	187518874	G	A	187518874	2	1	24	1	0	0	0	0	0	0	0	1	5697	1074	38	1		1	FAT1	4	187518874	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	9262010	187518874	3635402	165	8382											
PLEKHG4B	153478	hgsc.bcm.edu	37	chr5	163099	163099	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ccccagcttaccgccccttgCccagagccccccaaagcatg	8	5	7	21	1	0	1	0	0	0	1	0	1	0	1	9	0	5	2	9	0	2	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:163099C>T	ENST00000283426.6	+	11	1894	c.1844C>T	c.(1843-1845)gCc>gTc	p.A615V		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	615							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)		CCGCCCCTTGCCCAGAGCCCC	0.657																																					p.A615V		Atlas-SNP	.											.	PLEKHG4B	167	.	0			c.C1844T						PASS	.						14	14	14					5																	163099		2168	4267	6435	SO:0001583	missense	153478	exon11			CCCTTGCCCAGAG	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.1844C>T	5.37:g.163099C>T	ENSP00000283426:p.Ala615Val	147	0	0		138	76	0.550725	NM_052909		Missense_Mutation	SNP	ENST00000283426.6	37	CCDS34124.1	.	.	.	.	.	.	.	.	.	.	C	7.808	0.715147	0.15306	.	.	ENSG00000153404	ENST00000283426	D	0.92099	-2.97	2.71	-5.43	0.02632	.	.	.	.	.	T	0.75874	0.3909	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.62671	-0.6805	9	0.27785	T	0.31	.	0.5644	0.00684	0.2612:0.3176:0.2217:0.1994	.	615	Q96PX9	PKH4B_HUMAN	V	615	ENSP00000283426:A615V	ENSP00000283426:A615V	A	+	2	0	PLEKHG4B	216099	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.238000	0.01199	-1.825000	0.01207	-0.670000	0.03821	GCC	.	.	none		0.657	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		T	163099	C	T	163099	3	4	24	1	0	0	0	0	1	0	0	0	12081	739	26	2	1886	2	PLEKHG4B	5	163099	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10		163099	180752161	166	8383											
FASTKD3	79072	hgsc.bcm.edu	37	chr5	7867027	7867027	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaaaagtttctgccactgcAttgaggatgggttttgaaag	12	12	11	6	0	1	2	0	2	1	0	1	3	1	3	1	2	2	3	1	2	3	4	rs77130393	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:7867027A>G	ENST00000264669.5	-	2	1306	c.1170T>C	c.(1168-1170)aaT>aaC	p.N390N	MTRR_ENST00000341013.6_5'Flank|MTRR_ENST00000264668.2_5'Flank|FASTKD3_ENST00000513658.1_Intron|MTRR_ENST00000440940.2_5'Flank|MTRR_ENST00000502509.1_Intron	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	390					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						CTGCCACTGCATTGAGGATGG	0.438													A|||	32	0.00638978	0.0	0.0173	5008	,	,		18240	0.0		0.0189	False		,,,				2504	0.001				p.N390N		Atlas-SNP	.											.	FASTKD3	88	.	0			c.T1170C						PASS	.	A		24,4382	30.8+/-60.4	0,24,2179	63	64	63		1170	-5.6	0	5	dbSNP_134	63	199,8401	87.1+/-149.5	1,197,4102	no	coding-synonymous	FASTKD3	NM_024091.3		1,221,6281	GG,GA,AA		2.314,0.5447,1.7146		390/663	7867027	223,12783	2203	4300	6503	SO:0001819	synonymous_variant	79072	exon2			CACTGCATTGAGG	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.1170T>C	5.37:g.7867027A>G		165	0	0		151	68	0.450331	NM_024091	Q9BVD3	Silent	SNP	ENST00000264669.5	37	CCDS3873.1																																																																																			A|0.984;G|0.016	0.016	strong		0.438	FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1	NM_024091		G	7867027	A	G	7867027	2	3	24	1	0	0	0	0	0	0	0	1	5695	214	8	3		3	FASTKD3	5	7867027	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	7703928	7867027	173048233	167	8384											
MTRR	4552	hgsc.bcm.edu	37	chr5	7892933	7892933	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaggttctgcggaagggagtAtgtacaggctggctggcctt	7	10	17	7	1	1	0	0	0	1	0	1	3	1	2	1	6	2	5	1	6	3	4	rs35890938	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:7892933A>G	ENST00000264668.2	+	11	1575	c.1545A>G	c.(1543-1545)gtA>gtG	p.V515V	MTRR_ENST00000440940.2_Silent_p.V488V	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	515	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				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)	GGAAGGGAGTATGTACAGGCT	0.473													G|||	40	0.00798722	0.0015	0.0245	5008	,	,		18051	0.0		0.0189	False		,,,				2504	0.002				p.V515V		Atlas-SNP	.											.	MTRR	74	.	0			c.A1545G						PASS	.	G	,	46,4360	822.1+/-416.4	0,46,2157	150	129	136		1464,1545	0.7	0.5	5	dbSNP_126	136	207,8393	810.1+/-407.1	2,203,4095	no	coding-synonymous,coding-synonymous	MTRR	NM_002454.2,NM_024010.2	,	2,249,6252	GG,GA,AA		2.407,1.044,1.9453	,	488/699,515/726	7892933	253,12753	2203	4300	6503	SO:0001819	synonymous_variant	4552	exon11			GGGAGTATGTACA	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.1545A>G	5.37:g.7892933A>G		131	0	0		158	72	0.455696	NM_024010	O60471|Q32MA9|Q7Z4M8	Silent	SNP	ENST00000264668.2	37	CCDS3874.1																																																																																			A|0.981;G|0.019	0.019	strong		0.473	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1			G	7892933	A	G	7892933	2	3	24	1	0	0	0	0	0	0	0	1	9970	436	16	3		3	MTRR	5	7892933	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	25906	7892933	173022327	168	8385											
MTRR	4552	hgsc.bcm.edu	37	chr5	7893005	7893005	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	catgcatcccatgaagacagCgggaaagccctggctcctaa	12	6	10	13	1	0	2	0	1	0	1	2	3	2	3	3	2	3	2	3	2	3	1	rs34172797	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:7893005C>T	ENST00000264668.2	+	11	1647	c.1617C>T	c.(1615-1617)agC>agT	p.S539S	MTRR_ENST00000440940.2_Silent_p.S512S	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	539	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				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)	ATGAAGACAGCGGGAAAGCCC	0.458													C|||	45	0.00898562	0.0045	0.0259	5008	,	,		18337	0.0		0.0189	False		,,,				2504	0.002				p.S539S		Atlas-SNP	.											.	MTRR	74	.	0			c.C1617T						PASS	.	C	,	66,4340	61.7+/-98.7	0,66,2137	84	71	75		1536,1617	0.2	0	5	dbSNP_126	75	207,8393	89.4+/-151.6	2,203,4095	no	coding-synonymous,coding-synonymous	MTRR	NM_002454.2,NM_024010.2	,	2,269,6232	TT,TC,CC		2.407,1.498,2.099	,	512/699,539/726	7893005	273,12733	2203	4300	6503	SO:0001819	synonymous_variant	4552	exon11			AGACAGCGGGAAA	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.1617C>T	5.37:g.7893005C>T		82	0	0		81	39	0.481481	NM_024010	O60471|Q32MA9|Q7Z4M8	Silent	SNP	ENST00000264668.2	37	CCDS3874.1																																																																																			C|0.981;T|0.019	0.019	strong		0.458	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1			T	7893005	C	T	7893005	2	4	24	1	0	0	0	0	0	0	0	1	9970	767	27	1		1	MTRR	5	7893005	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	72	7893005	173022255	169	8386											
DNAH5	1767	hgsc.bcm.edu	37	chr5	13867949	13867949	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tccacagcactaataagctcTttcttgaaactgggctgcag	11	11	8	11	0	2	1	0	1	2	0	3	1	3	1	1	1	4	4	1	1	3	4	rs146191243	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:13867949T>C	ENST00000265104.4	-	25	4091	c.3987A>G	c.(3985-3987)aaA>aaG	p.K1329K	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1329	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)					TAATAAGCTCTTTCTTGAAAC	0.453									Kartagener syndrome				T|||	16	0.00319489	0.0	0.0058	5008	,	,		17132	0.0		0.008	False		,,,				2504	0.0041				p.K1329K		Atlas-SNP	.											.	DNAH5	868	.	0			c.A3987G						PASS	.	T		12,4394	19.1+/-41.9	1,10,2192	131	124	126		3987	-0.1	1	5	dbSNP_134	126	158,8442	74.5+/-137.1	0,158,4142	no	coding-synonymous	DNAH5	NM_001369.2		1,168,6334	CC,CT,TT		1.8372,0.2724,1.3071		1329/4625	13867949	170,12836	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon25	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AAGCTCTTTCTTG	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.3987A>G	5.37:g.13867949T>C		158	0	0		174	96	0.551724	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			T|0.990;C|0.010	0.010	strong		0.453	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		C	13867949	T	C	13867949	2	2	24	1	0	0	0	0	0	0	0	1	4606	1606	56	3		3	DNAH5	5	13867949	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	5974944	13867949	167047311	170	8387											
CDH9	1007	hgsc.bcm.edu	37	chr5	26885964	26885964	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctttccgagtcatgattccTgctgtattatctgggggaga	7	15	11	8	1	3	2	1	1	2	1	5	4	5	2	2	2	1	2	2	2	2	4	rs35328154	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:26885964T>G	ENST00000231021.4	-	11	1813	c.1641A>C	c.(1639-1641)gcA>gcC	p.A547A		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	547	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						TCATGATTCCTGCTGTATTAT	0.318													T|||	49	0.00978435	0.0	0.0187	5008	,	,		17688	0.0		0.0109	False		,,,				2504	0.0256				p.A547A	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.A1641C						PASS	.	T		7,4399	11.4+/-27.6	0,7,2196	55	58	57		1641	-4.3	1	5	dbSNP_126	57	82,8518	44.0+/-102.2	0,82,4218	no	coding-synonymous	CDH9	NM_016279.3		0,89,6414	GG,GT,TT		0.9535,0.1589,0.6843		547/790	26885964	89,12917	2203	4300	6503	SO:0001819	synonymous_variant	1007	exon11			GATTCCTGCTGTA	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.1641A>C	5.37:g.26885964T>G		67	0	0		60	28	0.466667	NM_016279	Q3B7I5	Silent	SNP	ENST00000231021.4	37	CCDS3893.1																																																																																			T|0.992;G|0.008	0.008	strong		0.318	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		G	26885964	T	G	26885964	2	3	24	1	0	0	0	0	0	0	0	1	3119	1567	55	5		5	CDH9	5	26885964	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	13018015	26885964	154029296	171	8388											
UGT3A2	167127	hgsc.bcm.edu	37	chr5	36037933	36037933	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gatttgtttcatcttaagagCcaatgtctctgccttgagct	8	16	8	9	0	3	2	1	1	2	1	4	3	3	2	2	0	3	2	2	0	2	4			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:36037933C>T	ENST00000282507.3	-	6	1362	c.1261G>A	c.(1261-1263)Gct>Act	p.A421T	UGT3A2_ENST00000513300.1_Missense_Mutation_p.A387T|UGT3A2_ENST00000545528.1_Missense_Mutation_p.A119T|UGT3A2_ENST00000504954.1_5'Flank	NM_174914.3	NP_777574.2	Q3SY77	UD3A2_HUMAN	UDP glycosyltransferase 3 family, polypeptide A2	421					cellular response to genistein (GO:0071412)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)|UDP-glycosyltransferase activity (GO:0008194)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	43	all_lung(31;0.000179)		Lung(74;0.111)|Epithelial(62;0.113)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ATCTTAAGAGCCAATGTCTCT	0.438																																					p.A421T		Atlas-SNP	.											.	UGT3A2	117	.	0			c.G1261A						PASS	.						174	160	165					5																	36037933		2203	4300	6503	SO:0001583	missense	167127	exon6			TAAGAGCCAATGT		CCDS3914.1, CCDS54842.1	5p13.2	2014-05-20			ENSG00000168671	ENSG00000168671		"UDP glucuronosyltransferases"	27266	protein-coding gene	gene with protein product						12975309	Standard	NM_174914		Approved		uc003jjz.2	Q3SY77	OTTHUMG00000131108	ENST00000282507.3:c.1261G>A	5.37:g.36037933C>T	ENSP00000282507:p.Ala421Thr	96	0	0		128	57	0.445312	NM_174914	B4DUQ7|E9PFK7|Q6UXC4|Q8NBP2	Missense_Mutation	SNP	ENST00000282507.3	37	CCDS3914.1	.	.	.	.	.	.	.	.	.	.	C	8.741	0.918940	0.17982	.	.	ENSG00000168671	ENST00000282507;ENST00000513300;ENST00000545528	T;T;T	0.63580	-0.05;-0.05;3.2	3.18	0.239	0.15484	.	0.283721	0.27802	U	0.017798	T	0.48677	0.1513	L	0.42581	1.335	0.09310	N	1	B;B	0.26400	0.009;0.148	B;B	0.31191	0.024;0.125	T	0.36939	-0.9727	10	0.37606	T	0.19	.	6.4334	0.21809	0.3166:0.5888:0.0:0.0946	.	387;421	E9PFK7;Q3SY77	.;UD3A2_HUMAN	T	421;387;119	ENSP00000282507:A421T;ENSP00000427404:A387T;ENSP00000445367:A119T	ENSP00000282507:A421T	A	-	1	0	UGT3A2	36073690	0.000000	0.05858	0.014000	0.15608	0.623000	0.37688	-0.069000	0.11542	0.018000	0.15052	0.563000	0.77884	GCT	.	.	none		0.438	UGT3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253771.2	NM_174914		T	36037933	C	T	36037933	3	4	24	1	0	0	0	0	1	0	0	0	16979	739	26	2	318	2	UGT3A2	5	36037933	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	9151969	36037933	144877327	172	8389											
DAB2	1601	hgsc.bcm.edu	37	chr5	39381651	39381651	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taggttgtcctgtgggtgacGcctggcctgaaggttctgag	5	12	16	8	1	1	3	0	3	1	0	2	3	2	3	3	4	0	2	3	4	2	3			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:39381651G>A	ENST00000320816.6	-	11	1876	c.1409C>T	c.(1408-1410)gCg>gTg	p.A470V	DAB2_ENST00000509337.1_Missense_Mutation_p.A449V|DAB2_ENST00000545653.1_Missense_Mutation_p.A449V|DAB2_ENST00000339788.6_Missense_Mutation_p.A252V	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	470					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)			TGTGGGTGACGCCTGGCCTGA	0.582																																					p.A470V		Atlas-SNP	.											.	DAB2	124	.	0			c.C1409T						PASS	.						129	126	127					5																	39381651		2203	4300	6503	SO:0001583	missense	1601	exon11			GGTGACGCCTGGC	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.1409C>T	5.37:g.39381651G>A	ENSP00000313391:p.Ala470Val	167	0	0		137	52	0.379562	NM_001343	A6NES5|Q13598|Q9BTY0|Q9UK04	Missense_Mutation	SNP	ENST00000320816.6	37	CCDS34149.1	.	.	.	.	.	.	.	.	.	.	G	8.024	0.760343	0.15914	.	.	ENSG00000153071	ENST00000320816;ENST00000339788;ENST00000545653;ENST00000509337	T;T;T;T	0.38240	1.24;1.15;1.21;1.21	5.96	-0.00481	0.14020	.	1.030630	0.07591	N	0.921918	T	0.12008	0.0292	N	0.02539	-0.55	0.09310	N	1	B;B	0.12013	0.005;0.005	B;B	0.06405	0.001;0.002	T	0.27938	-1.0059	10	0.02654	T	1	11.0513	6.3792	0.21525	0.5083:0.0:0.3716:0.12	.	470;449	P98082;P98082-3	DAB2_HUMAN;.	V	470;252;449;449	ENSP00000313391:A470V;ENSP00000345508:A252V;ENSP00000439919:A449V;ENSP00000426245:A449V	ENSP00000313391:A470V	A	-	2	0	DAB2	39417408	0.296000	0.24398	0.041000	0.18516	0.818000	0.46254	0.497000	0.22514	-0.303000	0.08856	-0.345000	0.07892	GCG	.	.	none		0.582	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343		A	39381651	G	A	39381651	3	1	24	1	0	0	0	0	1	0	0	0	4220	1087	38	1	919	1	DAB2	5	39381651	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	3343718	39381651	141533609	173	8390											
FBXO4	26272	hgsc.bcm.edu	37	chr5	41925431	41925431	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catggcgggaagcgagccgcGcagcggaacaaactcgccgc	10	2	15	14	7	0	0	0	0	0	0	1	3	0	2	2	3	5	1	2	3	3	0	rs2231916		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:41925431G>A	ENST00000281623.3	+	1	76	c.20G>A	c.(19-21)cGc>cAc	p.R7H	FBXO4_ENST00000509134.1_Missense_Mutation_p.R7H|FBXO4_ENST00000296812.2_Missense_Mutation_p.R7H	NM_012176.2	NP_036308.1	Q9UKT5	FBX4_HUMAN	F-box protein 4	7					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)				AGCGAGCCGCGCAGCGGAACA	0.706																																					p.R7H		Atlas-SNP	.											.	FBXO4	42	.	0			c.G20A						PASS	.						3	5	4					5																	41925431		1448	2780	4228	SO:0001583	missense	26272	exon1			AGCCGCGCAGCGG	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.20G>A	5.37:g.41925431G>A	ENSP00000281623:p.Arg7His	16	0	0		20	10	0.5	NM_033484	Q68CU8|Q86VT8|Q9UK98	Missense_Mutation	SNP	ENST00000281623.3	37	CCDS3938.1	.	.	.	.	.	.	.	.	.	.	G	18.34	3.601780	0.66445	.	.	ENSG00000151876	ENST00000296812;ENST00000281623;ENST00000509134	T;T;T	0.65364	-0.15;-0.15;-0.15	4.14	4.14	0.48551	.	0.532611	0.20854	N	0.084478	T	0.41789	0.1174	N	0.14661	0.345	0.09310	N	1	B;B;B	0.10296	0.001;0.003;0.001	B;B;B	0.04013	0.0;0.001;0.001	T	0.24440	-1.0160	10	0.49607	T	0.09	-12.9866	8.033	0.30476	0.1107:0.0:0.8893:0.0	.	7;7;7	D6RAJ6;Q9UKT5;Q9UKT5-2	.;FBX4_HUMAN;.	H	7	ENSP00000296812:R7H;ENSP00000281623:R7H;ENSP00000421749:R7H	ENSP00000281623:R7H	R	+	2	0	FBXO4	41961188	0.010000	0.17322	0.037000	0.18230	0.752000	0.42762	1.241000	0.32743	2.311000	0.77944	0.563000	0.77884	CGC	.	.	alt		0.706	FBXO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211614.1			A	41925431	G	A	41925431	3	1	24	1	0	0	0	0	1	0	0	0	5756	1087	38	1	22	1	FBXO4	5	41925431	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	2543780	41925431	138989829	174	8391											
SKIV2L2	23517	hgsc.bcm.edu	37	chr5	54674963	54674963	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttctttttaggtaaagaaTgaaggagatgactttggctg	11	15	11	4	0	1	4	0	2	1	2	1	5	1	4	0	3	0	2	0	3	5	6	rs139182599	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:54674963T>C	ENST00000230640.5	+	18	2246	c.1992T>C	c.(1990-1992)aaT>aaC	p.N664N	SKIV2L2_ENST00000545714.1_Silent_p.N563N	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	664					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)				AGGTAAAGAATGAAGGAGATG	0.308													T|||	6	0.00119808	0.0	0.0	5008	,	,		15869	0.0		0.005	False		,,,				2504	0.001				p.N664N	Melanoma(2;92 134 23744 29976 33782)	Atlas-SNP	.											.	SKIV2L2	104	.	0			c.T1992C						PASS	.	T		6,4400	11.4+/-27.6	0,6,2197	46	51	50		1992	5.6	1	5	dbSNP_134	50	42,8552	26.8+/-75.7	0,42,4255	no	coding-synonymous	SKIV2L2	NM_015360.4		0,48,6452	CC,CT,TT		0.4887,0.1362,0.3692		664/1043	54674963	48,12952	2203	4297	6500	SO:0001819	synonymous_variant	23517	exon18			AAAGAATGAAGGA	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.1992T>C	5.37:g.54674963T>C		11	0	0		9	8	0.888889	NM_015360	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Silent	SNP	ENST00000230640.5	37	CCDS3967.1																																																																																			T|0.997;C|0.003	0.003	strong		0.308	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1			C	54674963	T	C	54674963	2	2	24	1	0	0	0	0	0	0	0	1	14375	1461	51	3		3	SKIV2L2	5	54674963	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	12749532	54674963	126240297	175	8392											
TMEM171	134285	hgsc.bcm.edu	37	chr5	72424269	72424269	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccaccttactttcctgaatcTtcagcttctgcggtcgctga	6	14	7	14	2	3	2	1	2	2	0	5	2	4	2	3	1	3	2	3	1	2	4	rs34728034	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:72424269T>G	ENST00000454765.2	+	3	1166	c.693T>G	c.(691-693)tcT>tcG	p.S231S	TMEM171_ENST00000287773.5_Silent_p.S231S			Q8WVE6	TM171_HUMAN	transmembrane protein 171	231						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)		TTCCTGAATCTTCAGCTTCTG	0.418													T|||	82	0.0163738	0.0545	0.0144	5008	,	,		17554	0.0		0.0	False		,,,				2504	0.0				p.S231S	NSCLC(112;638 2280 27369 30736)	Atlas-SNP	.											.	TMEM171	41	.	0			c.T693G						PASS	.	T	,	229,4177	138.0+/-173.8	6,217,1980	193	194	194		693,693	4.1	1	5	dbSNP_126	194	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous,coding-synonymous	TMEM171	NM_001161342.1,NM_173490.6	,	6,219,6278	GG,GT,TT		0.0233,5.1975,1.7761	,	231/324,231/325	72424269	231,12775	2203	4300	6503	SO:0001819	synonymous_variant	134285	exon3			TGAATCTTCAGCT	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.693T>G	5.37:g.72424269T>G		176	0	0		187	95	0.508021	NM_173490	Q8N0S1|Q8TDT7	Silent	SNP	ENST00000454765.2	37	CCDS4017.1																																																																																			T|0.980;G|0.020	0.020	strong		0.418	TMEM171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254037.2	NM_173490		G	72424269	T	G	72424269	2	3	24	1	0	0	0	0	0	0	0	1	16103	1596	56	5		5	TMEM171	5	72424269	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	17749306	72424269	108490991	176	8393											
RGNEF	64283	hgsc.bcm.edu	37	chr5	73205382	73205382	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcggacaggcagcatgaggAgctggccaatgtgcaccagc	10	4	15	12	2	0	1	0	1	0	0	0	3	0	3	2	4	4	4	2	4	1	0	rs200976886	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:73205382A>G	ENST00000426542.2	+	33	4327	c.4307A>G	c.(4306-4308)gAg>gGg	p.E1436G	ARHGEF28_ENST00000513042.2_Missense_Mutation_p.E1436G|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.E1123G|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.E1392G|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.E1436G|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.E1436G|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.E1436G|ARHGEF28_ENST00000512883.1_Missense_Mutation_p.E356G			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	1436	Interaction with microtubules. {ECO:0000250}.				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)										CAGCATGAGGAGCTGGCCAAT	0.677													A|||	6	0.00119808	0.0	0.0014	5008	,	,		17397	0.0		0.005	False		,,,				2504	0.0				p.E1436G		Atlas-SNP	.											.	.	.	.	0			c.A4307G						PASS	.	A	GLY/GLU,GLY/GLU	0,4202		0,0,2101	10	11	11		4307,4307	2.7	1	5		11	4,8440		0,4,4218	yes	missense,missense	RGNEF	NM_001080479.2,NM_001177693.1	98,98	0,4,6319	GG,GA,AA		0.0474,0.0,0.0316	probably-damaging,probably-damaging	1436/1732,1436/1706	73205382	4,12642	2101	4222	6323	SO:0001583	missense	64283	exon34			ATGAGGAGCTGGC		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.4307A>G	5.37:g.73205382A>G	ENSP00000412175:p.Glu1436Gly	122	0	0		166	92	0.554217	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	37	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	A	16.75	3.209869	0.58343	0.0	4.74E-4	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799;ENST00000512883	T;T;T;T;T;T;T;T	0.38077	1.16;1.16;1.16;1.16;1.16;1.16;1.16;1.16	5.34	2.73	0.32206	.	1.144270	0.07072	U	0.835626	T	0.62109	0.2401	M	0.81942	2.565	0.42236	D	0.991911	D;D;D;D;D	0.71674	0.996;0.998;0.997;0.997;0.998	P;D;D;D;D	0.67382	0.894;0.947;0.947;0.951;0.944	T	0.55698	-0.8100	10	0.87932	D	0	.	11.6878	0.51497	0.7192:0.2808:0.0:0.0	.	1123;1436;1436;356;1436	B5MDA3;Q8N1W1;E9PC75;D6RGZ3;Q8N1W1-4	.;RGNEF_HUMAN;.;.;.	G	1436;1436;1436;1392;1436;1436;1123;356	ENSP00000296794:E1436G;ENSP00000441913:E1436G;ENSP00000441436:E1436G;ENSP00000287898:E1392G;ENSP00000411459:E1436G;ENSP00000412175:E1436G;ENSP00000296799:E1123G;ENSP00000421081:E356G	ENSP00000287898:E1392G	E	+	2	0	RP11-428C6.1	73241138	1.000000	0.71417	1.000000	0.80357	0.282000	0.26991	4.810000	0.62598	0.841000	0.35020	0.454000	0.30748	GAG	A|0.997;G|0.003	0.003	weak		0.677	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			G	73205382	A	G	73205382	3	3	24	1	0	0	0	0	1	0	0	0	13298	304	11	3	4437	3	RGNEF	5	73205382	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	781113	73205382	107709878	177	8394											
GCNT4	51301	hgsc.bcm.edu	37	chr5	74325101	74325101	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttactgtttgggggtttcacCgtctccaacatatttgctcc	6	16	8	11	1	2	0	1	0	1	0	4	0	3	0	3	2	3	3	3	2	3	5			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:74325101C>T	ENST00000322348.4	-	1	1623	c.762G>A	c.(760-762)acG>acA	p.T254T		NM_016591.2	NP_057675.1	Q9P109	GCNT4_HUMAN	glucosaminyl (N-acetyl) transferase 4, core 2	254					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|homeostasis of number of cells (GO:0048872)|inter-male aggressive behavior (GO:0002121)|kidney morphogenesis (GO:0060993)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|thyroid hormone metabolic process (GO:0042403)|tissue morphogenesis (GO:0048729)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	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)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(2)|skin(1)|stomach(2)	19		all_lung(232;0.0131)|Lung NSC(167;0.0282)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;8.44e-57)		GGGGTTTCACCGTCTCCAACA	0.378																																					p.T254T		Atlas-SNP	.											GCNT4,NS,carcinoma,-2,1	GCNT4	46	1	0			c.G762A						PASS	.						85	88	87					5																	74325101		2203	4300	6503	SO:0001819	synonymous_variant	51301	exon1			TTTCACCGTCTCC	AF132035	CCDS4026.1	5q12	2013-02-25	2010-03-16		ENSG00000176928	ENSG00000176928	2.4.1.102	"Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	17973	protein-coding gene	gene with protein product	"core 2 beta-1,6-N-acetylglucosaminyltransferase 3", "beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase 4"		"glucosaminyl (N-acetyl) transferase 4, core 2 (beta-1,6-N-acetylglucosaminyltransferase)"			10753916	Standard	NM_016591		Approved	C2GNT3	uc003kdn.3	Q9P109	OTTHUMG00000131272	ENST00000322348.4:c.762G>A	5.37:g.74325101C>T		103	0	0		106	52	0.490566	NM_016591		Silent	SNP	ENST00000322348.4	37	CCDS4026.1																																																																																			.	.	none		0.378	GCNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254040.1	NM_016591		T	74325101	C	T	74325101	2	4	24	1	0	0	0	0	0	0	0	1	6311	639	23	1		1	GCNT4	5	74325101	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1119719	74325101	106590159	178	8395											
SPZ1	84654	hgsc.bcm.edu	37	chr5	79616400	79616400	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttgacaaaatcaatgaaatGttatcaacaaacctgcctgt	16	11	5	9	0	2	2	2	2	0	0	2	2	2	2	2	0	3	1	2	0	7	2	rs200562315	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:79616400G>A	ENST00000296739.4	+	1	611	c.366G>A	c.(364-366)atG>atA	p.M122I		NM_032567.3	NP_115956.3	Q9BXG8	SPZ1_HUMAN	spermatogenic leucine zipper 1	122					transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.M122I(1)		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)		TCAATGAAATGTTATCAACAA	0.368																																					p.M122I		Atlas-SNP	.											SPZ1,trunk,malignant_melanoma,0,1	SPZ1	60	1	1	Substitution - Missense(1)	skin(1)	c.G366A						scavenged	.						49	44	45					5																	79616400		1799	4058	5857	SO:0001583	missense	84654	exon1			TGAAATGTTATCA		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.366G>A	5.37:g.79616400G>A	ENSP00000369611:p.Met122Ile	275	0	0		265	12	0.045283	NM_032567	B2RA21|Q8N4P1|Q8N7E9	Missense_Mutation	SNP	ENST00000296739.4	37	CCDS43336.1	.	.	.	.	.	.	.	.	.	.	G	8.567	0.879064	0.17395	.	.	ENSG00000164299	ENST00000511881;ENST00000296739	T;T	0.39787	1.06;1.62	2.92	-2.42	0.06542	.	.	.	.	.	T	0.17238	0.0414	N	0.05078	-0.115	0.09310	N	1	B	0.20988	0.05	B	0.10450	0.005	T	0.15178	-1.0446	9	0.33940	T	0.23	.	4.398	0.11372	0.5786:0.0:0.2498:0.1716	.	122	Q9BXG8	SPZ1_HUMAN	I	122	ENSP00000426530:M122I;ENSP00000369611:M122I	ENSP00000369611:M122I	M	+	3	0	SPZ1	79652156	0.000000	0.05858	0.000000	0.03702	0.514000	0.34195	-1.754000	0.01816	-0.613000	0.05694	0.313000	0.20887	ATG	G|0.998;A|0.002	0.002	strong		0.368	SPZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369322.1	NM_032567		A	79616400	G	A	79616400	3	1	24	1	0	0	0	0	1	0	0	0	15142	1377	48	2	368	2	SPZ1	5	79616400	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	5291299	79616400	101298860	179	8396											
SPZ1	84654	hgsc.bcm.edu	37	chr5	79617039	79617039	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaatcttacagcagagagtAgagattctcaaggaactcca	16	8	8	9	0	2	2	1	0	2	2	4	5	3	3	1	1	3	2	1	1	5	3	rs374023153		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:79617039A>G	ENST00000296739.4	+	1	1250	c.1005A>G	c.(1003-1005)gtA>gtG	p.V335V		NM_032567.3	NP_115956.3	Q9BXG8	SPZ1_HUMAN	spermatogenic leucine zipper 1	335					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)		AGCAGAGAGTAGAGATTCTCA	0.423													A|||	1	0.000199681	0.0	0.0014	5008	,	,		19001	0.0		0.0	False		,,,				2504	0.0				p.V335V		Atlas-SNP	.											.	SPZ1	60	.	0			c.A1005G						PASS	.	A		0,3766		0,0,1883	112	106	108		1005	-6.3	0	5		108	3,8245		0,3,4121	no	coding-synonymous	SPZ1	NM_032567.3		0,3,6004	GG,GA,AA		0.0364,0.0,0.025		335/431	79617039	3,12011	1883	4124	6007	SO:0001819	synonymous_variant	84654	exon1			GAGAGTAGAGATT		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.1005A>G	5.37:g.79617039A>G		136	0	0		145	70	0.482759	NM_032567	B2RA21|Q8N4P1|Q8N7E9	Silent	SNP	ENST00000296739.4	37	CCDS43336.1																																																																																			.	.	weak		0.423	SPZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369322.1	NM_032567		G	79617039	A	G	79617039	2	3	24	1	0	0	0	0	0	0	0	1	15142	407	15	3		3	SPZ1	5	79617039	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	639	79617039	101298221	180	8397											
ZFYVE16	9765	hgsc.bcm.edu	37	chr5	79741086	79741086	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttcaattgattctaggactAtgttccaaagaacagaagag	15	12	8	6	0	2	4	1	1	1	3	3	5	3	5	1	1	1	1	1	1	6	6	rs150392926	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:79741086A>G	ENST00000338008.5	+	6	2766	c.2586A>G	c.(2584-2586)ctA>ctG	p.L862L	ZFYVE16_ENST00000510158.1_Silent_p.L862L|ZFYVE16_ENST00000505560.1_Silent_p.L862L	NM_001284236.1|NM_014733.3	NP_001271165.1|NP_055548	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	862					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)		TTCTAGGACTATGTTCCAAAG	0.318													a|||	10	0.00199681	0.0	0.0014	5008	,	,		18816	0.0		0.002	False		,,,				2504	0.0072				p.L862L	Melanoma(150;1452 1854 16018 17851 37292)	Atlas-SNP	.											.	ZFYVE16	100	.	0			c.A2586G						PASS	.	G	,	0,4406		0,0,2203	112	108	109		2586,2586	-4.7	0	5	dbSNP_134	109	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous,coding-synonymous	ZFYVE16	NM_001105251.1,NM_014733.3	,	0,14,6489	GG,GA,AA		0.1628,0.0,0.1076	,	862/1540,862/1540	79741086	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	9765	exon7			AGGACTATGTTCC	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.2586A>G	5.37:g.79741086A>G		75	0	0		97	53	0.546392	NM_001105251	O15023|Q5H9U2|Q7LAU7|Q86T69|Q8N5L3|Q8NEK3	Silent	SNP	ENST00000338008.5	37	CCDS4050.1																																																																																			A|0.999;G|0.001	0.001	strong		0.318	ZFYVE16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226982.2	NM_014733		G	79741086	A	G	79741086	2	3	24	1	0	0	0	0	0	0	0	1	17679	436	16	3		3	ZFYVE16	5	79741086	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	124047	79741086	101174174	181	8398											
GPR98	84059	hgsc.bcm.edu	37	chr5	90151620	90151620	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgcagactatgtggaatgtgCctgttcacacatgtctgtgt	8	14	11	8	0	2	1	1	0	1	1	2	2	2	2	1	1	2	2	1	1	2	2	rs201254386		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:90151620C>A	ENST00000405460.2	+	82	17753	c.17657C>A	c.(17656-17658)gCc>gAc	p.A5886D	GPR98_ENST00000425867.2_Missense_Mutation_p.A1547D	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	5886	GPS. {ECO:0000255|PROSITE- ProRule:PRU00098}.				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)		GTGGAATGTGCCTGTTCACAC	0.413																																					p.A5886D		Atlas-SNP	.											.	GPR98	605	.	0			c.C17657A						PASS	.	C	ASP/ALA	0,3922		0,0,1961	292	273	279		17657	5.5	1	5		279	2,8298		0,2,4148	yes	missense	GPR98	NM_032119.3	126	0,2,6109	AA,AC,CC		0.0241,0.0,0.0164	benign	5886/6307	90151620	2,12220	1961	4150	6111	SO:0001583	missense	84059	exon82			AATGTGCCTGTTC	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.17657C>A	5.37:g.90151620C>A	ENSP00000384582:p.Ala5886Asp	257	0	0		226	96	0.424779	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.039679	0.93630	0.0	2.41E-4	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.69306	-0.39;-0.39	5.5	5.5	0.81552	GPS domain (3);	0.000000	0.85682	D	0.000000	T	0.81955	0.4932	M	0.76574	2.34	0.80722	D	1	D;D;D	0.71674	0.975;0.998;0.968	P;D;P	0.71656	0.776;0.974;0.667	T	0.81193	-0.1044	9	.	.	.	.	19.7578	0.96301	0.0:1.0:0.0:0.0	.	1547;5886;1547	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	D	5886;5886;1547	ENSP00000384582:A5886D;ENSP00000392618:A1547D	.	A	+	2	0	GPR98	90187376	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.083000	0.76859	2.746000	0.94184	0.591000	0.81541	GCC	.	.	weak		0.413	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		A	90151620	C	A	90151620	3	1	24	1	0	0	0	0	1	0	0	0	6730	739	26	4	17983	4	GPR98	5	90151620	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	10410534	90151620	90763640	182	8399											
LNPEP	4012	hgsc.bcm.edu	37	chr5	96315320	96315320	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttgtttccatgggcacagatCaggcttcccactgccgttgt	6	13	10	12	1	1	1	1	0	0	1	3	1	3	1	3	2	1	4	3	2	0	4	rs61752351	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:96315320C>G	ENST00000231368.5	+	2	1190	c.498C>G	c.(496-498)atC>atG	p.I166M	LNPEP_ENST00000395770.3_Missense_Mutation_p.I152M	NM_005575.2	NP_005566.2	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase	166					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)		GGGCACAGATCAGGCTTCCCA	0.458													C|||	33	0.00658946	0.0008	0.0115	5008	,	,		21134	0.0		0.0209	False		,,,				2504	0.0031				p.I166M		Atlas-SNP	.											.	LNPEP	80	.	0			c.C498G						PASS	.	C	MET/ILE,MET/ILE	19,4387	26.2+/-53.5	0,19,2184	94	92	93		498,456	-1.4	0.2	5	dbSNP_129	93	168,8432	78.9+/-141.6	2,164,4134	yes	missense,missense	LNPEP	NM_005575.2,NM_175920.3	10,10	2,183,6318	GG,GC,CC		1.9535,0.4312,1.4378	benign,benign	166/1026,152/1012	96315320	187,12819	2203	4300	6503	SO:0001583	missense	4012	exon2			ACAGATCAGGCTT	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.498C>G	5.37:g.96315320C>G	ENSP00000231368:p.Ile166Met	118	0	0		114	58	0.508772	NM_005575	O00769|Q15145|Q59H76|Q9TNQ2|Q9TNQ3|Q9UIQ7	Missense_Mutation	SNP	ENST00000231368.5	37	CCDS4087.1	23	0.010531135531135532	0	0.0	5	0.013812154696132596	0	0.0	18	0.023746701846965697	C	0.007	-1.961172	0.00465	0.004312	0.019535	ENSG00000113441	ENST00000231368;ENST00000395770	T;T	0.04275	3.66;3.66	5.78	-1.36	0.09085	.	1.298990	0.04688	N	0.413675	T	0.01222	0.0040	N	0.08118	0	0.09310	N	0.999999	B	0.06786	0.001	B	0.17098	0.017	T	0.45833	-0.9234	10	0.25751	T	0.34	.	3.8746	0.09051	0.1147:0.1325:0.4957:0.2571	rs61752351	166	Q9UIQ6	LCAP_HUMAN	M	166;152	ENSP00000231368:I166M;ENSP00000379117:I152M	ENSP00000231368:I166M	I	+	3	3	LNPEP	96341076	0.048000	0.20356	0.200000	0.23457	0.089000	0.18198	-0.030000	0.12308	0.047000	0.15862	-0.226000	0.12346	ATC	C|0.986;G|0.014	0.014	strong		0.458	LNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250624.1	NM_005575		G	96315320	C	G	96315320	3	3	24	1	0	0	0	0	1	0	0	0	8873	816	29	4	504	4	LNPEP	5	96315320	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	6163700	96315320	84599940	183	8400											
SLCO6A1	133482	hgsc.bcm.edu	37	chr5	101815888	101815888	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttaaaaccttaccttcaatTcctaccttactttgtttatt	10	20	1	10	0	1	0	1	0	0	0	2	0	2	0	4	0	4	1	4	0	7	11	rs150189521	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:101815888T>C	ENST00000506729.1	-	2	780	c.609A>G	c.(607-609)ggA>ggG	p.G203G	SLCO6A1_ENST00000379807.3_Silent_p.G203G|SLCO6A1_ENST00000389019.3_Silent_p.G203G|SLCO6A1_ENST00000514551.1_Intron|SLCO6A1_ENST00000513675.1_Silent_p.G203G|SLCO6A1_ENST00000379810.1_Silent_p.G203G			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	203						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)		TACCTTCAATTCCTACCTTAC	0.299													T|||	12	0.00239617	0.0008	0.0029	5008	,	,		18321	0.0		0.0089	False		,,,				2504	0.0				p.G203G		Atlas-SNP	.											.	SLCO6A1	153	.	0			c.A609G						PASS	.	T		8,4394	11.4+/-27.6	0,8,2193	66	68	68		609	0.4	0	5	dbSNP_134	68	81,8513	37.8+/-93.5	0,81,4216	no	coding-synonymous	SLCO6A1	NM_173488.3		0,89,6409	CC,CT,TT		0.9425,0.1817,0.6848		203/720	101815888	89,12907	2201	4297	6498	SO:0001819	synonymous_variant	133482	exon2			TTCAATTCCTACC	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.609A>G	5.37:g.101815888T>C		73	0	0		69	31	0.449275	NM_173488	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Silent	SNP	ENST00000506729.1	37	CCDS34206.1																																																																																			T|0.994;C|0.006	0.006	strong		0.299	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488		C	101815888	T	C	101815888	2	2	24	1	0	0	0	0	0	0	0	1	14747	1770	62	3		3	SLCO6A1	5	101815888	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	5500568	101815888	79099372	184	8401											
FAM13B	51306	hgsc.bcm.edu	37	chr5	137354665	137354665	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgttcctcaatatagtccaCaacgtggcggactatgaatg	12	11	9	9	2	1	1	1	1	0	0	3	2	3	2	2	2	1	1	2	2	6	4	rs79543971	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:137354665C>T	ENST00000033079.3	-	3	587	c.136G>A	c.(136-138)Gtg>Atg	p.V46M	FAM13B_ENST00000420893.2_Missense_Mutation_p.V46M|FAM13B_ENST00000425075.2_Intron	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	46	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						ATATAGTCCACAACGTGGCGG	0.393													C|||	2	0.000399361	0.0	0.0	5008	,	,		19229	0.0		0.002	False		,,,				2504	0.0				p.V46M		Atlas-SNP	.											.	FAM13B	46	.	0			c.G136A						PASS	.	C	MET/VAL,,MET/VAL	3,4403	4.2+/-10.8	0,3,2200	92	88	89		136,,136	6.1	1	5	dbSNP_131	89	16,8584	11.9+/-42.8	0,16,4284	yes	missense,intron,missense	FAM13B	NM_001101800.1,NM_001101801.1,NM_016603.2	21,,21	0,19,6484	TT,TC,CC		0.186,0.0681,0.1461	probably-damaging,,probably-damaging	46/888,,46/916	137354665	19,12987	2203	4300	6503	SO:0001583	missense	51306	exon3			AGTCCACAACGTG	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.136G>A	5.37:g.137354665C>T	ENSP00000033079:p.Val46Met	159	0	0		153	82	0.535948	NM_001101800	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Missense_Mutation	SNP	ENST00000033079.3	37	CCDS4195.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	27.0	4.793716	0.90453	6.81E-4	0.00186	ENSG00000031003	ENST00000033079;ENST00000420893;ENST00000514310;ENST00000502471;ENST00000509596;ENST00000508403;ENST00000505961	T;T;T;T;T;T;T	0.46819	1.88;1.88;1.88;1.88;1.88;0.86;0.86	6.08	6.08	0.98989	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.72534	0.3472	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.73275	-0.4034	10	0.87932	D	0	-7.2121	20.6634	0.99662	0.0:1.0:0.0:0.0	.	46;46	Q9NYF5-2;Q9NYF5	.;FA13B_HUMAN	M	46	ENSP00000033079:V46M;ENSP00000388521:V46M;ENSP00000425326:V46M;ENSP00000424785:V46M;ENSP00000422311:V46M;ENSP00000426863:V46M;ENSP00000422673:V46M	ENSP00000033079:V46M	V	-	1	0	FAM13B	137382564	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.120000	0.77153	2.894000	0.99253	0.655000	0.94253	GTG	C|0.999;T|0.001	0.001	strong		0.393	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1			T	137354665	C	T	137354665	3	4	24	1	0	0	0	0	1	0	0	0	5458	478	17	2	2765	2	FAM13B	5	137354665	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	35538777	137354665	43560595	185	8402											
CDC25C	995	hgsc.bcm.edu	37	chr5	137621421	137621421	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagaagggcaatctgctccCgcagctgccgctccccttcc	6	7	9	19	2	1	1	0	0	1	1	4	1	4	1	6	1	3	5	6	1	2	1	rs139145068	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:137621421C>T	ENST00000323760.6	-	14	1660	c.1382G>A	c.(1381-1383)cGg>cAg	p.R461Q	CDC25C_ENST00000415130.2_Missense_Mutation_p.R388Q|CDC25C_ENST00000513970.1_Missense_Mutation_p.R461Q|CDC25C_ENST00000348983.3_Missense_Mutation_p.R388Q|CDC25C_ENST00000357274.3_Missense_Mutation_p.R418Q|CDC25C_ENST00000514555.1_Missense_Mutation_p.R431Q|CDC25C_ENST00000356505.3_Missense_Mutation_p.R431Q	NM_001790.3	NP_001781.2	P30307	MPIP3_HUMAN	cell division cycle 25C	461					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)	p.R461Q(1)		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)			AATCTGCTCCCGCAGCTGCCG	0.542													C|||	7	0.00139776	0.0	0.0043	5008	,	,		18171	0.0		0.001	False		,,,				2504	0.0031				p.R461Q		Atlas-SNP	.											CDC25C,NS,carcinoma,0,1	CDC25C	37	1	1	Substitution - Missense(1)	lung(1)	c.G1382A						PASS	.	C	GLN/ARG,GLN/ARG	5,4401	8.1+/-20.4	0,5,2198	92	83	86		1382,1163	-0.7	0.3	5	dbSNP_134	86	41,8559	27.9+/-77.7	0,41,4259	yes	missense,missense	CDC25C	NM_001790.3,NM_022809.2	43,43	0,46,6457	TT,TC,CC		0.4767,0.1135,0.3537	benign,benign	461/474,388/401	137621421	46,12960	2203	4300	6503	SO:0001583	missense	995	exon14			TGCTCCCGCAGCT	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.1382G>A	5.37:g.137621421C>T	ENSP00000321656:p.Arg461Gln	155	0	0		142	82	0.577465	NM_001790	D3DQB8|Q96PL3|Q9H168|Q9H2E8|Q9H2E9|Q9H2F1	Missense_Mutation	SNP	ENST00000323760.6	37	CCDS4202.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	C	12.41	1.928653	0.34002	0.001135	0.004767	ENSG00000158402	ENST00000323760;ENST00000356505;ENST00000357274;ENST00000348983;ENST00000415130;ENST00000513970;ENST00000534892;ENST00000514555	T;T;T;T;T;T;T	0.27256	2.26;2.28;1.68;1.68;1.68;2.26;2.28	5.08	-0.722	0.11184	.	0.630192	0.14121	N	0.340066	T	0.10895	0.0266	N	0.22421	0.69	0.19575	N	0.999965	B;B;B;B	0.20261	0.043;0.024;0.03;0.014	B;B;B;B	0.10450	0.005;0.003;0.005;0.002	T	0.17776	-1.0358	10	0.38643	T	0.18	0.8534	10.1514	0.42796	0.0:0.4294:0.0:0.5706	.	478;431;388;461	G3V1P6;P30307-2;P30307-4;P30307	.;.;.;MPIP3_HUMAN	Q	461;431;418;388;388;461;478;431	ENSP00000321656:R461Q;ENSP00000348898:R431Q;ENSP00000349821:R418Q;ENSP00000345205:R388Q;ENSP00000392631:R388Q;ENSP00000424795:R461Q;ENSP00000425470:R431Q	ENSP00000321656:R461Q	R	-	2	0	CDC25C	137649320	0.009000	0.17119	0.268000	0.24571	0.929000	0.56500	-0.472000	0.06623	-0.288000	0.09051	0.655000	0.94253	CGG	C|0.997;T|0.003	0.003	strong		0.542	CDC25C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251280.1			T	137621421	C	T	137621421	3	4	24	1	0	0	0	0	1	0	0	0	3066	652	23	1	43	1	CDC25C	5	137621421	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	266756	137621421	43293839	186	8403											
CDC25C	995	hgsc.bcm.edu	37	chr5	137654980	137654980	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tctgcctggtcttctcctagGtttggatttttatccaattt	5	20	7	9	0	3	0	0	0	3	0	5	1	4	1	3	3	1	1	3	3	3	7	rs111911741	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:137654980G>A	ENST00000323760.6	-	7	821	c.543C>T	c.(541-543)aaC>aaT	p.N181N	CDC25C_ENST00000415130.2_Silent_p.N108N|CDC25C_ENST00000513970.1_Silent_p.N181N|CDC25C_ENST00000348983.3_Silent_p.N108N|CDC25C_ENST00000357274.3_Silent_p.N138N|CDC25C_ENST00000514555.1_Silent_p.N151N|CDC25C_ENST00000356505.3_Silent_p.N151N	NM_001790.3	NP_001781.2	P30307	MPIP3_HUMAN	cell division cycle 25C	181					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)			CTTCTCCTAGGTTTGGATTTT	0.378													G|||	2	0.000399361	0.0	0.0029	5008	,	,		16400	0.0		0.0	False		,,,				2504	0.0				p.N181N		Atlas-SNP	.											.	CDC25C	37	.	0			c.C543T						PASS	.	G	,	3,4403	4.2+/-10.8	0,3,2200	136	133	134		543,324	-4.2	0	5	dbSNP_132	134	26,8574	19.2+/-60.6	0,26,4274	no	coding-synonymous,coding-synonymous	CDC25C	NM_001790.3,NM_022809.2	,	0,29,6474	AA,AG,GG		0.3023,0.0681,0.223	,	181/474,108/401	137654980	29,12977	2203	4300	6503	SO:0001819	synonymous_variant	995	exon7			TCCTAGGTTTGGA	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.543C>T	5.37:g.137654980G>A		131	0	0		155	67	0.432258	NM_001790	D3DQB8|Q96PL3|Q9H168|Q9H2E8|Q9H2E9|Q9H2F1	Silent	SNP	ENST00000323760.6	37	CCDS4202.1																																																																																			G|0.999;A|0.001	0.001	strong		0.378	CDC25C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251280.1			A	137654980	G	A	137654980	2	1	24	1	0	0	0	0	0	0	0	1	3066	1252	44	2		2	CDC25C	5	137654980	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	33559	137654980	43260280	187	8404											
DND1	373863	hgsc.bcm.edu	37	chr5	140050907	140050907	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aaccatggtacctgcctcagCcccagcagaccacaggaggt	11	5	10	15	0	1	1	1	0	0	1	1	2	1	2	6	3	5	2	6	3	2	1	rs148639416	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:140050907C>T	ENST00000542735.1	-	4	1076	c.1033G>A	c.(1033-1035)Gct>Act	p.A345T	WDR55_ENST00000520764.1_3'UTR|WDR55_ENST00000358337.5_3'UTR	NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	345					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)			CCTGCCTCAGCCCCAGCAGAC	0.602																																					p.A345T		Atlas-SNP	.											.	DND1	15	.	0			c.G1033A						PASS	.						77	65	69					5																	140050907		1940	3940	5880	SO:0001583	missense	373863	exon4			CCTCAGCCCCAGC	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.1033G>A	5.37:g.140050907C>T	ENSP00000445366:p.Ala345Thr	490	0	0		764	132	0.172775	NM_194249		Missense_Mutation	SNP	ENST00000542735.1	37	CCDS4236.1	.	.	.	.	.	.	.	.	.	.	C	11.05	1.525451	0.27299	.	.	ENSG00000256453	ENST00000542735	T	0.34859	1.34	4.97	4.97	0.65823	.	0.357138	0.23704	N	0.045400	T	0.26268	0.0641	N	0.19112	0.55	0.27565	N	0.950072	B	0.26635	0.155	B	0.25759	0.063	T	0.24764	-1.0151	10	0.72032	D	0.01	-6.3441	13.9714	0.64242	0.0:1.0:0.0:0.0	.	345	Q8IYX4	DND1_HUMAN	T	345	ENSP00000445366:A345T	ENSP00000445366:A345T	A	-	1	0	DND1	140031091	0.814000	0.29104	1.000000	0.80357	0.382000	0.30200	0.973000	0.29422	2.750000	0.94351	0.551000	0.68910	GCT	.	.	weak		0.602	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249		T	140050907	C	T	140050907	3	4	24	1	0	0	0	0	1	0	0	0	4668	739	26	2	32	2	DND1	5	140050907	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	2395927	140050907	40864353	188	8405											
PCDHGA7	56108	hgsc.bcm.edu	37	chr5	140763339	140763339	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	actcctaaacttccaaagatGtttcatctgaactcgcttac	12	13	4	12	1	2	2	1	1	1	1	5	2	4	2	2	0	3	2	2	0	5	4	rs187406135	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:140763339G>A	ENST00000518325.1	+	1	873	c.873G>A	c.(871-873)atG>atA	p.M291I	PCDHGA6_ENST00000517434.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018920.2	NP_061743.1	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7	291	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(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)			TTCCAAAGATGTTTCATCTGA	0.413													.|||	2	0.000399361	0.0	0.0029	5008	,	,		22196	0.0		0.0	False		,,,				2504	0.0				p.M291I		Atlas-SNP	.											.	PCDHGA7	130	.	0			c.G873A						PASS	.						56	56	56					5																	140763339		1866	4110	5976	SO:0001583	missense	56108	exon1			AAAGATGTTTCAT	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.873G>A	5.37:g.140763339G>A	ENSP00000430024:p.Met291Ile	104	0	0		103	41	0.398058	NM_032087	B2RN87|Q9Y5D0	Missense_Mutation	SNP	ENST00000518325.1	37	CCDS54927.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	.	0.004	-2.295701	0.00245	.	.	ENSG00000253537	ENST00000518325	T	0.51574	0.7	5.15	-3.98	0.04082	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.12646	0.0307	N	0.01048	-1.04	0.09310	N	0.999997	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.25363	-1.0134	9	0.13108	T	0.6	.	2.6961	0.05135	0.189:0.2096:0.4053:0.1961	.	291;291	Q9Y5G6;Q9Y5G6-2	PCDG7_HUMAN;.	I	291	ENSP00000430024:M291I	ENSP00000430024:M291I	M	+	3	0	PCDHGA7	140743523	0.000000	0.05858	0.081000	0.20488	0.030000	0.12068	-1.451000	0.02387	-0.495000	0.06659	-0.302000	0.09304	ATG	G|1.000;A|0.000	0.000	strong		0.413	PCDHGA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374744.1	NM_018920		A	140763339	G	A	140763339	3	1	24	1	0	0	0	0	1	0	0	0	11568	1377	48	2	875	2	PCDHGA7	5	140763339	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	712432	140763339	40151921	189	8406											
PRELID2	153768	hgsc.bcm.edu	37	chr5	145199531	145199531	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttaaaatttctggaaccaCgttctgacagattgcaatcc	12	12	6	11	1	2	2	0	1	2	1	3	3	3	3	3	1	2	2	3	1	4	4	rs142301961		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:145199531C>T	ENST00000334744.4	-	3	236	c.184G>A	c.(184-186)Gtg>Atg	p.V62M	PRELID2_ENST00000511435.1_Missense_Mutation_p.V62M|PRELID2_ENST00000505416.1_Missense_Mutation_p.V62M|PRELID2_ENST00000358004.2_Missense_Mutation_p.V62M|PRELID2_ENST00000394450.2_Missense_Mutation_p.V33M	NM_182960.2	NP_892005.1	Q8N945	PRLD2_HUMAN	PRELI domain containing 2	62	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)			TCTGGAACCACGTTCTGACAG	0.289													C|||	1	0.000199681	0.0	0.0	5008	,	,		16776	0.0		0.001	False		,,,				2504	0.0				p.V62M		Atlas-SNP	.											.	PRELID2	16	.	0			c.G184A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL	1,4405	2.1+/-5.4	0,1,2202	88	95	93		97,184,184	5.3	1	5	dbSNP_134	93	10,8590	7.7+/-29.5	0,10,4290	yes	missense,missense,missense	PRELID2	NM_138492.4,NM_182960.2,NM_205846.1	21,21,21	0,11,6492	TT,TC,CC		0.1163,0.0227,0.0846	probably-damaging,probably-damaging,probably-damaging	33/149,62/190,62/178	145199531	11,12995	2203	4300	6503	SO:0001583	missense	153768	exon3			GAACCACGTTCTG	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.184G>A	5.37:g.145199531C>T	ENSP00000335675:p.Val62Met	216	0	0		190	95	0.5	NM_182960	G5EA01|Q96EQ3	Missense_Mutation	SNP	ENST00000334744.4	37	CCDS34262.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	21.1	4.095855	0.76870	2.27E-4	0.001163	ENSG00000186314	ENST00000358004;ENST00000334744;ENST00000394450;ENST00000505416;ENST00000511435	T;T;T;T;T	0.17528	2.27;2.27;2.27;2.27;2.27	5.3	5.3	0.74995	PRELI/MSF1 (2);	0.000000	0.64402	D	0.000014	T	0.40956	0.1138	M	0.67953	2.075	0.43480	D	0.995704	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.995;0.992;0.998	T	0.07578	-1.0765	10	0.46703	T	0.11	-0.5438	16.2362	0.82377	0.0:1.0:0.0:0.0	.	62;62;62	D6RAB6;G5EA01;Q8N945	.;.;PRLD2_HUMAN	M	62;62;33;62;62	ENSP00000350694:V62M;ENSP00000335675:V62M;ENSP00000377965:V33M;ENSP00000424730:V62M;ENSP00000422789:V62M	ENSP00000335675:V62M	V	-	1	0	PRELID2	145179724	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.798000	0.47884	2.627000	0.88993	0.650000	0.86243	GTG	C|0.999;T|0.001	0.001	strong		0.289	PRELID2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000372970.1	NM_182960		T	145199531	C	T	145199531	3	4	24	1	0	0	0	0	1	0	0	0	12484	536	19	1	405	1	PRELID2	5	145199531	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	4436192	145199531	35715729	190	8407											
PPARGC1B	133522	hgsc.bcm.edu	37	chr5	149212614	149212614	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tcccagcaggtcagatcccgGccctggtcccggcaccactc	6	6	10	19	2	1	1	1	0	0	1	5	1	4	1	5	4	1	2	5	4	0	0	rs115557257	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:149212614G>T	ENST00000309241.5	+	5	1010	c.978G>T	c.(976-978)cgG>cgT	p.R326R	PPARGC1B_ENST00000360453.4_Silent_p.R287R|PPARGC1B_ENST00000403750.1_Silent_p.R262R|PPARGC1B_ENST00000394320.3_Silent_p.R326R	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	326					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)			TCAGATCCCGGCCCTGGTCCC	0.622													G|||	44	0.00878594	0.0061	0.0202	5008	,	,		16385	0.0		0.0149	False		,,,				2504	0.0072				p.R326R		Atlas-SNP	.											.	PPARGC1B	74	.	0			c.G978T						PASS	.	G	,,	43,4363	45.3+/-79.5	0,43,2160	51	57	55		861,786,978	2.7	0	5	dbSNP_132	55	200,8400	87.4+/-149.7	2,196,4102	no	coding-synonymous,coding-synonymous,coding-synonymous	PPARGC1B	NM_001172698.1,NM_001172699.1,NM_133263.3	,,	2,239,6262	TT,TG,GG		2.3256,0.9759,1.8684	,,	287/985,262/960,326/1024	149212614	243,12763	2203	4300	6503	SO:0001819	synonymous_variant	133522	exon5			ATCCCGGCCCTGG	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.978G>T	5.37:g.149212614G>T		175	0	0		166	89	0.536145	NM_133263	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Silent	SNP	ENST00000309241.5	37	CCDS4298.1	21	0.009615384615384616	3	0.006097560975609756	8	0.022099447513812154	0	0.0	10	0.013192612137203167	G	0.025	-1.378899	0.01204	0.009759	0.023256	ENSG00000155846	ENST00000434684	.	.	.	5.61	2.74	0.32292	.	.	.	.	.	T	0.14399	0.0348	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.16660	-1.0395	4	.	.	.	-0.718	5.3707	0.16138	0.07:0.1258:0.5442:0.26	.	.	.	.	S	13	.	.	A	+	1	0	PPARGC1B	149192807	0.001000	0.12720	0.001000	0.08648	0.105000	0.19272	0.072000	0.14617	0.264000	0.21851	0.655000	0.94253	GCC	G|0.985;T|0.015	0.015	strong		0.622	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263		T	149212614	G	T	149212614	2	4	24	1	0	0	0	0	0	0	0	1	12310	1190	42	4		4	PPARGC1B	5	149212614	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	4013083	149212614	31702646	191	8408											
CSF1R	1436	hgsc.bcm.edu	37	chr5	149457678	149457678	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatctgcagggactgaccttGgtgttgttgtgttggaggaa	7	13	16	5	0	1	1	0	1	1	0	1	5	1	4	1	4	1	4	1	4	1	4	rs2228422	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:149457678G>A	ENST00000286301.3	-	5	1017	c.726C>T	c.(724-726)acC>acT	p.T242T	CSF1R_ENST00000543093.1_Silent_p.T242T	NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	242	Ig-like C2-type 3.				cell proliferation (GO:0008283)|cell-cell junction maintenance (GO:0045217)|cellular response to cytokine stimulus (GO:0071345)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cytokine-mediated signaling pathway (GO:0019221)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary gland duct morphogenesis (GO:0060603)|monocyte differentiation (GO:0030224)|multicellular organismal development (GO:0007275)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of bone resorption (GO:0045124)|regulation of cell shape (GO:0008360)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|macrophage colony-stimulating factor receptor activity (GO:0005011)|protein homodimerization activity (GO:0042803)	p.T242T(1)		NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(38)|kidney(2)|large_intestine(6)|liver(3)|lung(23)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	93			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	GACTGACCTTGGTGTTGTTGT	0.572													G|||	1940	0.38738	0.2799	0.366	5008	,	,		20014	0.2113		0.5457	False		,,,				2504	0.5665				p.T242T		Atlas-SNP	.											CSF1R_ENST00000286301,NS,carcinoma,0,1	CSF1R	250	1	1	Substitution - coding silent(1)	stomach(1)	c.C726T						scavenged	.	G		1388,3018	457.5+/-351.6	220,948,1035	224	186	199		726	-0.9	1	5	dbSNP_98	199	4864,3736	618.2+/-396.8	1391,2082,827	no	coding-synonymous	CSF1R	NM_005211.3		1611,3030,1862	AA,AG,GG		43.4419,31.5025,48.0701		242/973	149457678	6252,6754	2203	4300	6503	SO:0001819	synonymous_variant	1436	exon5			GACCTTGGTGTTG	U63963	CCDS4302.1	5q32	2013-01-11	2008-08-01		ENSG00000182578	ENSG00000182578		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	2433	protein-coding gene	gene with protein product		164770	"McDonough feline sarcoma viral (v-fms) oncogene homolog"	FMS		1611909	Standard	NM_005211		Approved	C-FMS, CSFR, CD115	uc003lrm.3	P07333	OTTHUMG00000130050	ENST00000286301.3:c.726C>T	5.37:g.149457678G>A		188	1	0.00531915		195	80	0.410256	NM_005211	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Silent	SNP	ENST00000286301.3	37	CCDS4302.1																																																																																			G|0.561;A|0.439	0.439	strong		0.572	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2	NM_005211		A	149457678	G	A	149457678	2	1	24	1	0	0	0	0	0	0	0	1	3934	1335	47	2		2	CSF1R	5	149457678	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	245064	149457678	31457582	192	8409											
CSF1R	1436	hgsc.bcm.edu	37	chr5	149460553	149460553	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggcttcacgaccagctcAgggacactgggctctatcac	8	8	10	15	1	4	0	3	0	1	0	4	2	4	1	2	3	1	3	2	3	1	2	rs216123	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:149460553A>G	ENST00000286301.3	-	3	375	c.84T>C	c.(82-84)ccT>ccC	p.P28P	CSF1R_ENST00000543093.1_Silent_p.P28P	NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	28	Ig-like C2-type 1.				cell proliferation (GO:0008283)|cell-cell junction maintenance (GO:0045217)|cellular response to cytokine stimulus (GO:0071345)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cytokine-mediated signaling pathway (GO:0019221)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary gland duct morphogenesis (GO:0060603)|monocyte differentiation (GO:0030224)|multicellular organismal development (GO:0007275)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of bone resorption (GO:0045124)|regulation of cell shape (GO:0008360)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|macrophage colony-stimulating factor receptor activity (GO:0005011)|protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(38)|kidney(2)|large_intestine(6)|liver(3)|lung(23)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	93			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	CGACCAGCTCAGGGACACTGG	0.607													A|||	1679	0.335264	0.2587	0.353	5008	,	,		21664	0.0893		0.5527	False		,,,				2504	0.456				p.P28P		Atlas-SNP	.											.	CSF1R	250	.	0			c.T84C						PASS	.	A		1287,3119	437.2+/-344.9	183,921,1099	86	61	69		84	-8.2	0.9	5	dbSNP_79	69	4874,3726	618.5+/-396.8	1407,2060,833	no	coding-synonymous	CSF1R	NM_005211.3		1590,2981,1932	GG,GA,AA		43.3256,29.2102,47.3704		28/973	149460553	6161,6845	2203	4300	6503	SO:0001819	synonymous_variant	1436	exon3			CAGCTCAGGGACA	U63963	CCDS4302.1	5q32	2013-01-11	2008-08-01		ENSG00000182578	ENSG00000182578		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	2433	protein-coding gene	gene with protein product		164770	"McDonough feline sarcoma viral (v-fms) oncogene homolog"	FMS		1611909	Standard	NM_005211		Approved	C-FMS, CSFR, CD115	uc003lrm.3	P07333	OTTHUMG00000130050	ENST00000286301.3:c.84T>C	5.37:g.149460553A>G		168	0	0		159	158	0.993711	NM_005211	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Silent	SNP	ENST00000286301.3	37	CCDS4302.1																																																																																			A|0.588;G|0.411	0.411	strong		0.607	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2	NM_005211		G	149460553	A	G	149460553	2	3	24	1	0	0	0	0	0	0	0	1	3934	175	7	3		3	CSF1R	5	149460553	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	2875	149460553	31454707	193	8410											
FAT2	2196	hgsc.bcm.edu	37	chr5	150901209	150901209	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggaacctctgcaggttccGccagtggtcactcaccagct	8	8	11	14	1	3	0	2	0	1	0	4	2	4	1	4	3	3	3	4	3	1	1	rs142359154		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:150901209G>T	ENST00000261800.5	-	18	10957	c.10945C>A	c.(10945-10947)Cgg>Agg	p.R3649R		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3649					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)			TGCAGGTTCCGCCAGTGGTCA	0.607																																					p.R3649R		Atlas-SNP	.											.	FAT2	465	.	0			c.C10945A						PASS	.						34	30	32					5																	150901209		2203	4299	6502	SO:0001819	synonymous_variant	2196	exon18			GGTTCCGCCAGTG	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.10945C>A	5.37:g.150901209G>T		53	0	0		89	44	0.494382	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	8.154	0.788009	0.16258	.	.	ENSG00000086570	ENST00000520200	.	.	.	5.71	2.8	0.32819	.	.	.	.	.	T	0.68979	0.3060	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.65821	-0.6075	4	.	.	.	.	14.5588	0.68120	0.0:0.0:0.5656:0.4344	.	.	.	.	E	507	.	.	A	-	2	0	FAT2	150881402	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	2.794000	0.47853	0.264000	0.21851	-0.475000	0.04921	GCG	G|0.999;A|0.001	.	alt		0.607	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		T	150901209	G	T	150901209	2	4	24	1	0	0	0	0	0	0	0	1	5698	1086	38	4		4	FAT2	5	150901209	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1440656	150901209	30014051	194	8411											
IL12B	3593	hgsc.bcm.edu	37	chr5	158750329	158750329	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cggataccaatccaattctaCgacataaactggaatgcaca	16	8	6	11	2	1	0	0	0	1	0	2	3	2	2	2	2	4	1	2	2	7	4	rs3213096	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:158750329C>T	ENST00000231228.2	-	3	552	c.97G>A	c.(97-99)Gta>Ata	p.V33I		NM_002187.2	NP_002178.2	P29460	IL12B_HUMAN	interleukin 12B	33	Ig-like C2-type.		V -> I (in dbSNP:rs3213096). {ECO:0000269|Ref.5}.		cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|defense response to Gram-negative bacterium (GO:0050829)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|interferon-gamma biosynthetic process (GO:0042095)|natural killer cell activation (GO:0030101)|natural killer cell activation involved in immune response (GO:0002323)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of cell adhesion (GO:0045785)|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 biosynthetic process (GO:0045078)|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 lymphocyte proliferation (GO:0050671)|positive regulation of memory T cell differentiation (GO:0043382)|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 directed against tumor cell target (GO:0002860)|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 activation (GO:0051135)|positive regulation of NK T cell proliferation (GO:0051142)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|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 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 cytokine biosynthetic process (GO:0042035)|regulation of tyrosine phosphorylation of Stat1 protein (GO:0042510)|response to UV-B (GO:0010224)|sensory perception of pain (GO:0019233)|sexual reproduction (GO:0019953)|T-helper 1 type immune response (GO:0042088)|T-helper cell differentiation (GO:0042093)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|interleukin-12 complex (GO:0043514)|interleukin-23 complex (GO:0070743)|membrane (GO:0016020)	cytokine receptor activity (GO:0004896)|identical protein binding (GO:0042802)|interleukin-12 alpha subunit binding (GO:0042164)|interleukin-12 receptor binding (GO:0005143)|protein heterodimerization activity (GO:0046982)			cervix(1)|endometrium(1)|large_intestine(5)|lung(4)	11	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)			TCCAATTCTACGACATAAACT	0.502													C|||	19	0.00379393	0.0	0.0043	5008	,	,		20539	0.0		0.0099	False		,,,				2504	0.0061				p.V33I		Atlas-SNP	.											.	IL12B	30	.	0			c.G97A						PASS	.	C	ILE/VAL	7,4399	12.9+/-30.5	0,7,2196	61	56	58		97	5.2	0.9	5	dbSNP_106	58	49,8551	31.2+/-83.2	0,49,4251	yes	missense	IL12B	NM_002187.2	29	0,56,6447	TT,TC,CC		0.5698,0.1589,0.4306	benign	33/329	158750329	56,12950	2203	4300	6503	SO:0001583	missense	3593	exon3			ATTCTACGACATA	M65290	CCDS4346.1	5q31.1-q33.1	2014-09-17	2014-04-04		ENSG00000113302	ENSG00000113302		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5970	protein-coding gene	gene with protein product	"natural killer cell stimulatory factor-2", "cytotoxic lymphocyte maturation factor 2, p40", "interleukin 12, p40", "natural killer cell stimulatory factor, 40 kD subunit", "interleukin-12 beta chain", "IL12, subunit p40"	161561	"interleukin 12B (natural killer cell stimulatory factor 2, cytotoxic lymphocyte maturation factor 2, p40)"	NKSF2		1673147	Standard	NM_002187		Approved	CLMF, IL-12B, NKSF, CLMF2	uc003lxr.1	P29460	OTTHUMG00000130307	ENST00000231228.2:c.97G>A	5.37:g.158750329C>T	ENSP00000231228:p.Val33Ile	45	0	0		65	34	0.523077	NM_002187		Missense_Mutation	SNP	ENST00000231228.2	37	CCDS4346.1	13	0.005952380952380952	0	0.0	3	0.008287292817679558	0	0.0	10	0.013192612137203167	C	9.248	1.040122	0.19669	0.001589	0.005698	ENSG00000113302	ENST00000231228	T	0.22743	1.94	6.02	5.16	0.70880	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.054974	0.64402	D	0.000001	T	0.20210	0.0486	M	0.79475	2.455	0.45791	D	0.998676	B	0.09022	0.002	B	0.12156	0.007	T	0.03473	-1.1033	10	0.46703	T	0.11	-3.6912	11.4605	0.50208	0.0:0.9177:0.0:0.0823	rs3213096;rs17056679;rs17875310;rs52806839;rs56592501;rs3213096	33	P29460	IL12B_HUMAN	I	33	ENSP00000231228:V33I	ENSP00000231228:V33I	V	-	1	0	IL12B	158682907	0.822000	0.29219	0.877000	0.34402	0.087000	0.18053	1.240000	0.32731	1.568000	0.49683	-0.137000	0.14449	GTA	C|0.994;T|0.006	0.006	strong		0.502	IL12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252652.2	NM_002187		T	158750329	C	T	158750329	3	4	24	1	0	0	0	0	1	0	0	0	7634	536	19	1	909	1	IL12B	5	158750329	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	7849120	158750329	22164931	195	8412											
ODZ2	57451	hgsc.bcm.edu	37	chr5	167631599	167631599	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccgacgcatctttccctctcGaaatgtgaccagcatcttgg	8	11	8	14	3	3	1	0	1	3	0	5	3	4	1	3	1	1	2	3	1	1	2	rs141103827	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:167631599G>A	ENST00000518659.1	+	19	3836	c.3797G>A	c.(3796-3798)cGa>cAa	p.R1266Q	TENM2_ENST00000403607.2_Missense_Mutation_p.R1090Q|TENM2_ENST00000545108.1_Missense_Mutation_p.R1266Q|TENM2_ENST00000519204.1_Missense_Mutation_p.R1145Q|TENM2_ENST00000520394.1_Missense_Mutation_p.R1034Q	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	1266					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)										TTTCCCTCTCGAAATGTGACC	0.522													g|||	25	0.00499201	0.0008	0.0014	5008	,	,		18911	0.0		0.004	False		,,,				2504	0.0194				p.R1257Q		Atlas-SNP	.											.	.	.	.	0			c.G3770A						PASS	.	G	GLN/ARG	3,3911		0,3,1954	93	89	90		3770	4	1	5	dbSNP_134	90	38,8266		0,38,4114	yes	missense	ODZ2	NM_001122679.1	43	0,41,6068	AA,AG,GG		0.4576,0.0766,0.3356	possibly-damaging	1257/2766	167631599	41,12177	1957	4152	6109	SO:0001583	missense	57451	exon19			CCTCTCGAAATGT	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.3797G>A	5.37:g.167631599G>A	ENSP00000429430:p.Arg1266Gln	154	0	0		154	89	0.577922	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	37		4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	g	22.9	4.353549	0.82243	7.66E-4	0.004576	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.90069	-2.61;-2.61;-2.61;-2.61;-2.61	4.9	4.01	0.46588	Six-bladed beta-propeller, TolB-like (1);	0.229981	0.43579	D	0.000549	T	0.77164	0.4090	N	0.08118	0	0.32750	N	0.506584	D;P;P	0.53885	0.963;0.785;0.942	P;B;B	0.46850	0.529;0.166;0.149	D	0.85392	0.1126	10	0.87932	D	0	.	15.0945	0.72223	0.0:0.1425:0.8575:0.0	.	1266;1266;1034	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	Q	1266;1266;1145;1034;1090	ENSP00000429430:R1266Q;ENSP00000438635:R1266Q;ENSP00000428964:R1145Q;ENSP00000427874:R1034Q;ENSP00000384905:R1090Q	ENSP00000384905:R1090Q	R	+	2	0	ODZ2	167564177	1.000000	0.71417	0.986000	0.45419	0.986000	0.74619	5.887000	0.69751	1.025000	0.39708	0.550000	0.68814	CGA	G|0.997;A|0.003	0.003	strong		0.522	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		A	167631599	G	A	167631599	3	1	24	1	0	0	0	0	1	0	0	0	10844	1058	37	1	3844	1	ODZ2	5	167631599	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	8881270	167631599	13283661	196	8413											
SLIT3	6586	hgsc.bcm.edu	37	chr5	168114030	168114030	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagccattgattgtgtccaCgcactgggccccgtggcggc	5	9	14	13	3	0	1	0	1	0	0	1	1	1	1	4	3	1	2	4	3	1	3	rs148887706	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:168114030C>T	ENST00000519560.1	-	30	3687	c.3268G>A	c.(3268-3270)Gtg>Atg	p.V1090M	SLIT3_ENST00000404867.3_Missense_Mutation_p.V1090M|SLIT3_ENST00000332966.8_Missense_Mutation_p.V1097M	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	1090	EGF-like 5. {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)			ATTGTGTCCACGCACTGGGCC	0.622													c|||	4	0.000798722	0.0	0.0043	5008	,	,		20234	0.0		0.0	False		,,,				2504	0.001				p.V1097M	Ovarian(29;311 847 10864 17279 24903)	Atlas-SNP	.											.	SLIT3	224	.	0			c.G3289A						PASS	.	T	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	75	68	70		3268	0.6	0.9	5	dbSNP_134	70	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SLIT3	NM_003062.2	21	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	possibly-damaging	1090/1524	168114030	2,13004	2203	4300	6503	SO:0001583	missense	6586	exon30			TGTCCACGCACTG	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.3268G>A	5.37:g.168114030C>T	ENSP00000430333:p.Val1090Met	308	0	0		326	165	0.506135	NM_001271946	A6H8U9|J3KNP3|O95804|Q9UFH5	Missense_Mutation	SNP	ENST00000519560.1	37	CCDS4369.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	c	2.527	-0.309415	0.05458	2.27E-4	1.16E-4	ENSG00000184347	ENST00000519560;ENST00000332966;ENST00000404867	D;D;D	0.95103	-3.61;-3.61;-3.61	4.59	0.628	0.17681	EGF-like calcium-binding, conserved site (1);EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.373727	0.29707	N	0.011409	D	0.92264	0.7546	M	0.76574	2.34	0.38397	D	0.945565	P	0.43352	0.804	B	0.42163	0.378	D	0.87702	0.2561	10	0.42905	T	0.14	.	7.0594	0.25117	0.1166:0.6:0.0:0.2834	.	1090	O75094	SLIT3_HUMAN	M	1090;1097;1090	ENSP00000430333:V1090M;ENSP00000332164:V1097M;ENSP00000384890:V1090M	ENSP00000332164:V1097M	V	-	1	0	SLIT3	168046608	0.000000	0.05858	0.949000	0.38748	0.003000	0.03518	-0.190000	0.09615	-0.086000	0.12550	-4.011000	0.00013	GTG	C|1.000;T|0.000	0.000	strong		0.622	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062		T	168114030	C	T	168114030	3	4	24	1	0	0	0	0	1	0	0	0	14756	536	19	1	1331	1	SLIT3	5	168114030	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	482431	168114030	12801230	197	8414											
BNIP1	662	hgsc.bcm.edu	37	chr5	172578595	172578595	+	Intron	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctctatcaaagggcatttatTtggactgcttccacattttt	9	17	6	9	0	2	0	1	0	1	0	3	1	3	1	1	2	1	2	1	2	3	7	rs180928619	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:172578595T>C	ENST00000351486.5	+	3	208				BNIP1_ENST00000352523.6_Silent_p.I68I|BNIP1_ENST00000393770.4_Intron|BNIP1_ENST00000231668.9_Silent_p.I68I	NM_001205.2	NP_001196.2	Q12981	SEC20_HUMAN	BCL2/adenovirus E1B 19kDa interacting protein 1						apoptotic process (GO:0006915)|autophagy (GO:0006914)|endoplasmic reticulum membrane fusion (GO:0016320)|endoplasmic reticulum organization (GO:0007029)|execution phase of apoptosis (GO:0097194)|negative regulation of apoptotic process (GO:0043066)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			breast(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|skin(1)	11	Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GGGCATTTATTTGGACTGCTT	0.368													T|||	2	0.000399361	0.0015	0.0	5008	,	,		16395	0.0		0.0	False		,,,				2504	0.0				p.I68I		Atlas-SNP	.											.	BNIP1	30	.	0			c.T204C						PASS	.						108	103	105					5																	172578595		2203	4300	6503	SO:0001627	intron_variant	662	exon3			ATTTATTTGGACT	AF083957	CCDS4384.1, CCDS4385.1, CCDS4386.1, CCDS43400.1	5q33-q34	2008-02-05	2002-08-29		ENSG00000113734	ENSG00000113734			1082	protein-coding gene	gene with protein product		603291	"BCL2/adenovirus E1B 19kD-interacting protein 1"			7954800, 15272311	Standard	NM_013979		Approved	Nip1, SEC20	uc003mcj.4	Q12981	OTTHUMG00000130521	ENST00000351486.5:c.178-2730T>C	5.37:g.172578595T>C		98	0	0		121	55	0.454545	NM_013979	D3DQM3|D3DQM4|D3DQM5|D3DQM6|O75622|O75623|O75624|Q6K044|Q96FG4	Silent	SNP	ENST00000351486.5	37	CCDS4384.1																																																																																			T|0.999;C|0.001	0.001	strong		0.368	BNIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252939.1	NM_013979		C	172578595	T	C	172578595	1	2	24	0	1	0	0	0	0	0	0	0	1476	1829	64	3		3	BNIP1	5	172578595	Intron	SNP	T	TCGA-G8-6326-01A-11D-2210-10	4464565	172578595	8336665	198	8415											
BNIP1	662	hgsc.bcm.edu	37	chr5	172581387	172581387	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaacaacttctactccaggaAgtggagaatcacaaaaagca	19	6	7	9	0	2	1	1	0	1	1	3	3	3	2	1	2	4	1	1	2	7	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:172581387A>G	ENST00000351486.5	+	3	271	c.240A>G	c.(238-240)gaA>gaG	p.E80E	BNIP1_ENST00000352523.6_Silent_p.E123E|BNIP1_ENST00000393770.4_Silent_p.E80E|BNIP1_ENST00000231668.9_Silent_p.E123E	NM_001205.2	NP_001196.2	Q12981	SEC20_HUMAN	BCL2/adenovirus E1B 19kDa interacting protein 1	80					apoptotic process (GO:0006915)|autophagy (GO:0006914)|endoplasmic reticulum membrane fusion (GO:0016320)|endoplasmic reticulum organization (GO:0007029)|execution phase of apoptosis (GO:0097194)|negative regulation of apoptotic process (GO:0043066)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			breast(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|skin(1)	11	Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			TACTCCAGGAAGTGGAGAATC	0.478																																					p.E123E		Atlas-SNP	.											.	BNIP1	30	.	0			c.A369G						PASS	.						68	66	67					5																	172581387		2203	4300	6503	SO:0001819	synonymous_variant	662	exon4			CCAGGAAGTGGAG	AF083957	CCDS4384.1, CCDS4385.1, CCDS4386.1, CCDS43400.1	5q33-q34	2008-02-05	2002-08-29		ENSG00000113734	ENSG00000113734			1082	protein-coding gene	gene with protein product		603291	"BCL2/adenovirus E1B 19kD-interacting protein 1"			7954800, 15272311	Standard	NM_013979		Approved	Nip1, SEC20	uc003mcj.4	Q12981	OTTHUMG00000130521	ENST00000351486.5:c.240A>G	5.37:g.172581387A>G		206	0	0		240	119	0.495833	NM_013979	D3DQM3|D3DQM4|D3DQM5|D3DQM6|O75622|O75623|O75624|Q6K044|Q96FG4	Silent	SNP	ENST00000351486.5	37	CCDS4384.1																																																																																			.	.	none		0.478	BNIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252939.1	NM_013979		G	172581387	A	G	172581387	2	3	24	1	0	0	0	0	0	0	0	1	1476	69	3	3		3	BNIP1	5	172581387	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	2792	172581387	8333873	199	8416											
F12	2161	hgsc.bcm.edu	37	chr5	176831085	176831085	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcggctgctcccgcttcgccGgcaaggctgtggaggagcag	5	6	17	13	4	0	0	0	0	0	0	2	2	1	2	2	5	2	6	2	5	1	1	rs2230939	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:176831085G>A	ENST00000253496.3	-	10	1073	c.1025C>T	c.(1024-1026)cCg>cTg	p.P342L	F12_ENST00000514943.1_5'Flank	NM_000505.3	NP_000496.2	P00748	FA12_HUMAN	coagulation factor XII (Hageman factor)	342	Pro-rich.		P -> Q (in dbSNP:rs2230939).		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)	CCGCTTCGCCGGCAAGGCTGT	0.721									Hereditary Angioedema		OREG0017088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	4	0.000798722	0.0008	0.0014	5008	,	,		12509	0.0		0.002	False		,,,				2504	0.0				p.P342L		Atlas-SNP	.											.	F12	35	.	0			c.C1025T						PASS	.	G	LEU/PRO	0,4194		0,0,2097	9	12	11		1025	-5.3	0	5	dbSNP_98	11	13,8427		0,13,4207	yes	missense	F12	NM_000505.3	98	0,13,6304	AA,AG,GG		0.154,0.0,0.1029	benign	342/616	176831085	13,12621	2097	4220	6317	SO:0001583	missense	2161	exon10	Familial Cancer Database	HAE, type I-III, Hereditary Angioneurotic Edema, HANE,	TTCGCCGGCAAGG	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.1025C>T	5.37:g.176831085G>A	ENSP00000253496:p.Pro342Leu	5	0	0	1934	15	11	0.733333	NM_000505	P78339	Missense_Mutation	SNP	ENST00000253496.3	37	CCDS34302.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	9.062	0.994618	0.19043	0.0	0.00154	ENSG00000131187	ENST00000253496	D	0.88975	-2.45	4.9	-5.28	0.02755	.	3.606630	0.00899	N	0.002331	T	0.76898	0.4052	L	0.29908	0.895	0.09310	N	0.999996	B	0.06786	0.001	B	0.04013	0.001	T	0.65776	-0.6086	10	0.10902	T	0.67	.	0.9191	0.01311	0.1778:0.1964:0.325:0.3008	.	342	P00748	FA12_HUMAN	L	342	ENSP00000253496:P342L	ENSP00000253496:P342L	P	-	2	0	F12	176763691	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.303000	0.00519	-1.202000	0.02655	-0.367000	0.07326	CCG	T|0.005;G|0.993;A|0.001	0.001	strong		0.721	F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373217.1			A	176831085	G	A	176831085	3	1	24	1	0	0	0	0	1	0	0	0	5341	1116	39	1	842	1	F12	5	176831085	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	4249698	176831085	4084175	200	8417											
COL23A1	91522	hgsc.bcm.edu	37	chr5	177674821	177674821	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccagggggccctggctccacTatgagctgagcctagggagg	7	6	16	12	0	0	2	0	2	0	0	1	3	1	3	4	5	2	2	4	5	2	2	rs200475672	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr5:177674821T>C	ENST00000390654.3	-	21	1581	c.1224A>G	c.(1222-1224)atA>atG	p.I408M		NM_173465.3	NP_775736.2	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1	408	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)		CTGGCTCCACTATGAGCTGAG	0.632													T|||	2	0.000399361	0.0	0.0	5008	,	,		17262	0.0		0.002	False		,,,				2504	0.0				p.I408M		Atlas-SNP	.											.	COL23A1	47	.	0			c.A1224G						PASS	.	T	MET/ILE	0,3916		0,0,1958	19	22	21		1224	3.6	1	5		21	4,8254		0,4,4125	yes	missense	COL23A1	NM_173465.3	10	0,4,6083	CC,CT,TT		0.0484,0.0,0.0329	probably-damaging	408/541	177674821	4,12170	1958	4129	6087	SO:0001583	missense	91522	exon21			CTCCACTATGAGC	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.1224A>G	5.37:g.177674821T>C	ENSP00000375069:p.Ile408Met	157	0	0		146	68	0.465753	NM_173465	Q8IVR4|Q9NT93	Missense_Mutation	SNP	ENST00000390654.3	37	CCDS4436.1	.	.	.	.	.	.	.	.	.	.	T	7.999	0.754912	0.15846	0.0	4.84E-4	ENSG00000050767	ENST00000390654	D	0.93307	-3.2	4.76	3.57	0.40892	.	0.273854	0.26496	N	0.024047	D	0.89812	0.6823	L	0.47716	1.5	0.80722	D	1	P	0.44877	0.845	B	0.42522	0.39	D	0.86541	0.1828	10	0.48119	T	0.1	-4.3929	8.4416	0.32818	0.0:0.0:0.1982:0.8018	.	408	Q86Y22	CONA1_HUMAN	M	408	ENSP00000375069:I408M	ENSP00000375069:I408M	I	-	3	3	COL23A1	177607427	0.998000	0.40836	0.999000	0.59377	0.010000	0.07245	1.567000	0.36407	0.642000	0.30620	-0.460000	0.05396	ATA	.	.	weak		0.632	COL23A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253475.1	NM_173465		C	177674821	T	C	177674821	3	2	24	1	0	0	0	0	1	0	0	0	3684	1512	53	3	434	3	COL23A1	5	177674821	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	843736	177674821	3240439	201	8418											
EXOC2	55770	hgsc.bcm.edu	37	chr6	592566	592566	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccaagcagggtcaccagaCgcatgaaggtcagacaggta	13	5	13	10	1	2	3	2	1	0	2	2	3	2	3	2	3	2	3	2	3	3	1	rs62385137		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:592566C>T	ENST00000230449.4	-	11	1230	c.1095G>A	c.(1093-1095)gcG>gcA	p.A365A	EXOC2_ENST00000448181.3_Intron	NM_018303.5	NP_060773.3	Q96KP1	EXOC2_HUMAN	exocyst complex component 2	365					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)		GGTCACCAGACGCATGAAGGT	0.448																																					p.A365A		Atlas-SNP	.											EXOC2,colon,carcinoma,-1,1	EXOC2	81	1	0			c.G1095A						PASS	.	G		0,4406		0,0,2203	110	94	99		1095	-11.2	0	6	dbSNP_129	99	2,8598		0,2,4298	no	coding-synonymous	EXOC2	NM_018303.4		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		365/925	592566	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	55770	exon11			ACCAGACGCATGA	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.1095G>A	6.37:g.592566C>T		72	0	0		95	47	0.494737	NM_018303	B2RBE6|Q5JPC8|Q96AN6|Q9NUZ8|Q9UJM7	Silent	SNP	ENST00000230449.4	37	CCDS34327.1																																																																																			C|1.000;T|0.000	0.000	weak		0.448	EXOC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039627.1	NM_018303		T	592566	C	T	592566	2	4	24	1	0	0	0	0	0	0	0	1	5304	523	19	1		1	EXOC2	6	592566	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10		592566	170522501	202	8419											
RIPK1	8737	hgsc.bcm.edu	37	chr6	3083369	3083369	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtggagcaaactgaataaTgaagagcacaatgagctgag	17	7	12	5	0	0	5	0	4	0	1	0	6	0	6	0	1	4	3	0	1	5	1			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:3083369T>C	ENST00000259808.4	+	5	808	c.510T>C	c.(508-510)aaT>aaC	p.N170N	RIPK1_ENST00000380409.2_Silent_p.N170N|RIPK1_ENST00000479389.1_3'UTR|RIPK1_ENST00000541791.1_Silent_p.N124N			Q13546	RIPK1_HUMAN	receptor (TNFRSF)-interacting serine-threonine kinase 1	170	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)				AACTGAATAATGAAGAGCACA	0.527																																					p.N170N		Atlas-SNP	.											.	RIPK1	56	.	0			c.T510C						PASS	.						133	117	123					6																	3083369		2203	4300	6503	SO:0001819	synonymous_variant	8737	exon4			GAATAATGAAGAG	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.510T>C	6.37:g.3083369T>C		67	0	0		108	69	0.638889	NM_003804	A0AV89|B2RAG1|B4E3F9|Q13180|Q59H33	Silent	SNP	ENST00000259808.4	37	CCDS4482.1																																																																																			.	.	none		0.527	RIPK1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039659.2	NM_003804		C	3083369	T	C	3083369	2	2	24	1	0	0	0	0	0	0	0	1	13395	1461	51	3		3	RIPK1	6	3083369	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	2490803	3083369	168031698	203	8420											
SLC22A23	63027	hgsc.bcm.edu	37	chr6	3284097	3284097	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atgacgcaccttatcaccgtCggggtgatctccgcacagaa	10	8	10	13	4	2	3	1	2	1	1	4	3	2	3	3	2	0	2	3	2	2	1	rs142838841	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:3284097C>T	ENST00000406686.3	-	9	1691	c.1692G>A	c.(1690-1692)ccG>ccA	p.P564P	SLC22A23_ENST00000380302.4_Silent_p.P283P|SLC22A23_ENST00000436008.2_Silent_p.P572P|PSMG4_ENST00000451246.2_Intron|SLC22A23_ENST00000490273.1_Silent_p.P283P	NM_015482.1	NP_056297.1	A1A5C7	S22AN_HUMAN	solute carrier family 22, member 23	564					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)				TTATCACCGTCGGGGTGATCT	0.587													c|||	4	0.000798722	0.0	0.0	5008	,	,		19259	0.0		0.004	False		,,,				2504	0.0				p.P564P		Atlas-SNP	.											.	SLC22A23	89	.	0			c.G1692A						PASS	.	T	,	4,4402	8.1+/-20.4	0,4,2199	74	67	69		1692,849	0.3	0.9	6	dbSNP_134	69	39,8561	26.3+/-74.7	0,39,4261	no	coding-synonymous,coding-synonymous	SLC22A23	NM_015482.1,NM_021945.5	,	0,43,6460	TT,TC,CC		0.4535,0.0908,0.3306	,	564/687,283/406	3284097	43,12963	2203	4300	6503	SO:0001819	synonymous_variant	63027	exon9			CACCGTCGGGGTG	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.1692G>A	6.37:g.3284097C>T		57	0	0		44	19	0.431818	NM_015482	A1A5C8|Q5T8B8|Q6ZMH3|Q8IW73	Silent	SNP	ENST00000406686.3	37	CCDS47363.1																																																																																			C|0.997;T|0.003	0.003	strong		0.587	SLC22A23-006	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353059.1	NM_021945		T	3284097	C	T	3284097	2	4	24	1	0	0	0	0	0	0	0	1	14467	871	31	1		1	SLC22A23	6	3284097	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	200728	3284097	167830970	204	8421											
DEK	7913	hgsc.bcm.edu	37	chr6	18258286	18258286	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tcaatttcacaaagtttctgCccctttcctggggaaaaaaa	13	12	6	10	0	3	0	2	0	1	0	4	1	4	1	3	2	1	1	3	2	5	3	rs144486575	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:18258286C>T	ENST00000397239.3	-	4	702	c.255G>A	c.(253-255)ggG>ggA	p.G85G	DEK_ENST00000244776.7_Silent_p.G51G	NM_003472.3	NP_003463.1	P35659	DEK_HUMAN	DEK proto-oncogene	85					chromatin modification (GO:0016568)|regulation of double-strand break repair (GO:2000779)|regulation of double-strand break repair via nonhomologous end joining (GO:2001032)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	7	Ovarian(93;0.00769)|Breast(50;0.0495)	all_hematologic(90;0.053)	OV - Ovarian serous cystadenocarcinoma(7;0.00291)|all cancers(50;0.031)|Epithelial(50;0.0332)			AAAGTTTCTGCCCCTTTCCTG	0.308			T	NUP214	AML																																p.G85G		Atlas-SNP	.		Dom	yes		6	6p23	7913	DEK oncogene (DNA binding)		L	.	DEK	31	.	0			c.G255A						PASS	.	C	,	2,4402	4.2+/-10.8	0,2,2200	59	58	58		153,255	-7.4	0.6	6	dbSNP_134	58	4,8594	3.0+/-9.4	0,4,4295	no	coding-synonymous,coding-synonymous	DEK	NM_001134709.1,NM_003472.3	,	0,6,6495	TT,TC,CC		0.0465,0.0454,0.0461	,	51/342,85/376	18258286	6,12996	2202	4299	6501	SO:0001819	synonymous_variant	7913	exon4			TTTCTGCCCCTTT	X64229	CCDS34344.1, CCDS47382.1	6p23	2014-06-25	2014-06-25		ENSG00000124795	ENSG00000124795			2768	protein-coding gene	gene with protein product		125264	"DEK oncogene (DNA binding)", "DEK oncogene"			1549122	Standard	NM_003472		Approved	D6S231E	uc003ncr.1	P35659	OTTHUMG00000014319	ENST00000397239.3:c.255G>A	6.37:g.18258286C>T		35	0	0		42	20	0.47619	NM_003472	B2R6K6|B4DN37|Q5TGV4|Q5TGV5	Silent	SNP	ENST00000397239.3	37	CCDS34344.1																																																																																			C|0.999;T|0.001	0.001	strong		0.308	DEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039962.4			T	18258286	C	T	18258286	2	4	24	1	0	0	0	0	0	0	0	1	4426	726	26	2		2	DEK	6	18258286	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	14974189	18258286	152856781	205	8422											
E2F3	1871	hgsc.bcm.edu	37	chr6	20490428	20490428	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caaccaactcaggacatagcGattgctcagtttctatggga	12	10	9	10	1	3	0	2	0	1	0	3	3	3	2	1	2	4	2	1	2	4	4	rs4134982	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:20490428G>A	ENST00000346618.3	+	7	1231	c.1165G>A	c.(1165-1167)Gat>Aat	p.D389N	E2F3_ENST00000535432.1_Missense_Mutation_p.D258N	NM_001949.4	NP_001940.1	O00716	E2F3_HUMAN	E2F transcription factor 3	389			D -> N (in dbSNP:rs4134982). {ECO:0000269|Ref.2}.		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)			AGGACATAGCGATTGCTCAGT	0.408													G|||	15	0.00299521	0.0	0.0043	5008	,	,		19775	0.0		0.0119	False		,,,				2504	0.0				p.D389N		Atlas-SNP	.											E2F3,NS,carcinoma,-2,1	E2F3	30	1	0			c.G1165A						PASS	.	G	ASN/ASP	12,4394	17.9+/-39.9	0,12,2191	75	75	75		1165	5.5	0.8	6	dbSNP_108	75	99,8501	54.0+/-114.7	0,99,4201	yes	missense	E2F3	NM_001949.4	23	0,111,6392	AA,AG,GG		1.1512,0.2724,0.8535	benign	389/466	20490428	111,12895	2203	4300	6503	SO:0001583	missense	1871	exon7			CATAGCGATTGCT	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.1165G>A	6.37:g.20490428G>A	ENSP00000262904:p.Asp389Asn	176	0	0		137	57	0.416058	NM_001949	Q15000|Q68DT0|Q9BZ44	Missense_Mutation	SNP	ENST00000346618.3	37	CCDS4545.1	12	0.005494505494505495	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	8	0.010554089709762533	G	9.602	1.129011	0.21041	0.002724	0.011512	ENSG00000112242	ENST00000346618;ENST00000535432	T;T	0.06933	3.24;3.26	5.49	5.49	0.81192	.	0.338236	0.35378	N	0.003255	T	0.02304	0.0071	N	0.21097	0.63	0.42665	D	0.993494	B	0.16396	0.017	B	0.08055	0.003	T	0.45760	-0.9239	10	0.27082	T	0.32	.	9.5533	0.39324	0.0743:0.1436:0.782:0.0	rs4134982;rs52820498;rs4134982	389	O00716	E2F3_HUMAN	N	389;258	ENSP00000262904:D389N;ENSP00000443418:D258N	ENSP00000262904:D389N	D	+	1	0	E2F3	20598407	1.000000	0.71417	0.808000	0.32385	0.973000	0.67179	3.942000	0.56614	2.746000	0.94184	0.561000	0.74099	GAT	G|0.993;A|0.007	0.007	strong		0.408	E2F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043828.1			A	20490428	G	A	20490428	3	1	24	1	0	0	0	0	1	0	0	0	4870	1058	37	1	1191	1	E2F3	6	20490428	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	2232142	20490428	150624639	206	8423											
TRIM38	10475	hgsc.bcm.edu	37	chr6	25966909	25966909	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ccaagccaaaagcaactgagGcaggagacattctgctgtcc	13	6	10	12	0	1	2	0	1	1	1	2	3	2	2	3	2	4	3	3	2	4	1	rs41266771	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:25966909G>T	ENST00000357085.3	+	3	635	c.159G>T	c.(157-159)agG>agT	p.R53S	TRIM38_ENST00000349458.3_Missense_Mutation_p.R53S	NM_006355.3	NP_006346.1	O00635	TRI38_HUMAN	tripartite motif containing 38	53					negative regulation of defense response to virus (GO:0050687)|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)|positive regulation of viral entry into host cell (GO:0046598)|positive regulation of viral genome replication (GO:0045070)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|regulation of interferon-beta production (GO:0032648)|signal transduction (GO:0007165)	intracellular (GO:0005622)	signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	23						AGCAACTGAGGCAGGAGACAT	0.498													G|||	11	0.00219649	0.0	0.0072	5008	,	,		20263	0.0		0.006	False		,,,				2504	0.0				p.R53S		Atlas-SNP	.											.	TRIM38	50	.	0			c.G159T						PASS	.	G	SER/ARG	7,4399	12.9+/-30.5	0,7,2196	83	80	81		159	-1	0	6	dbSNP_127	81	73,8527	44.0+/-102.2	0,73,4227	yes	missense	TRIM38	NM_006355.2	110	0,80,6423	TT,TG,GG		0.8488,0.1589,0.6151	benign	53/466	25966909	80,12926	2203	4300	6503	SO:0001583	missense	10475	exon3			ACTGAGGCAGGAG	U90547	CCDS4568.1	6p21.3	2011-04-20	2011-01-25	2002-06-07	ENSG00000112343	ENSG00000112343		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	10059	protein-coding gene	gene with protein product			"ring finger protein 15", "tripartite motif-containing 38"	RNF15			Standard	XR_241880		Approved	RORET	uc003nfm.4	O00635	OTTHUMG00000014414	ENST00000357085.3:c.159G>T	6.37:g.25966909G>T	ENSP00000349596:p.Arg53Ser	71	0	0		78	33	0.423077	NM_006355	B2R862	Missense_Mutation	SNP	ENST00000357085.3	37	CCDS4568.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	g	7.501	0.652721	0.14580	0.001589	0.008488	ENSG00000112343	ENST00000540262;ENST00000349458;ENST00000357085	T;T;T	0.53423	0.62;0.62;0.62	3.88	-0.956	0.10353	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	3.891910	0.00698	N	0.000762	T	0.07007	0.0178	N	0.12502	0.225	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.05241	-1.0897	10	0.07482	T	0.82	.	1.1526	0.01789	0.3016:0.152:0.392:0.1543	rs41266771	53;53	B2R862;O00635	.;TRI38_HUMAN	S	53	ENSP00000443976:R53S;ENSP00000230099:R53S;ENSP00000349596:R53S	ENSP00000230099:R53S	R	+	3	2	TRIM38	26074888	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.076000	0.14712	-0.198000	0.10333	0.585000	0.79938	AGG	G|0.995;T|0.005	0.005	strong		0.498	TRIM38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040076.2			T	25966909	G	T	25966909	3	4	24	1	0	0	0	0	1	0	0	0	16527	1194	42	4	161	4	TRIM38	6	25966909	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	5476481	25966909	145148158	207	8424											
HIST1H2AC	8334	hgsc.bcm.edu	37	chr6	26124781	26124781	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgaccattgctcagggcggCgtccttcctaacatccaggc	7	9	11	14	2	1	1	1	1	0	0	4	1	4	1	4	3	2	1	4	3	1	3	rs143405410	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:26124781C>T	ENST00000602637.1	+	1	351	c.321C>T	c.(319-321)ggC>ggT	p.G107G	HIST1H2AC_ENST00000377791.2_Silent_p.G107G|HIST1H2BC_ENST00000396984.1_5'Flank|HIST1H2BC_ENST00000314332.5_5'Flank			Q93077	H2A1C_HUMAN	histone cluster 1, H2ac	107						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(5)	12						CTCAGGGCGGCGTCCTTCCTA	0.577													C|||	3	0.000599042	0.0	0.0	5008	,	,		19312	0.0		0.003	False		,,,				2504	0.0				p.G107G		Atlas-SNP	.											HIST1H2AC,colon,carcinoma,0,1	HIST1H2AC	29	1	0			c.C321T						scavenged	.	C		2,4404		0,2,2201	93	92	92		321	0.6	1	6	dbSNP_134	92	26,8574		0,26,4274	no	coding-synonymous	HIST1H2AC	NM_003512.3		0,28,6475	TT,TC,CC		0.3023,0.0454,0.2153		107/131	26124781	28,12978	2203	4300	6503	SO:0001819	synonymous_variant	8334	exon1			GGGCGGCGTCCTT	Z80778	CCDS4585.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000180573	ENSG00000180573		"Histones / Replication-dependent"	4733	protein-coding gene	gene with protein product		602794	"H2A histone family, member L", "histone 1, H2ac"	H2AFL		9119399, 12408966	Standard	NM_003512		Approved		uc003ngm.3	Q93077	OTTHUMG00000014428	ENST00000602637.1:c.321C>T	6.37:g.26124781C>T		169	1	0.00591716		190	95	0.5	NM_003512	B2R4F7|O00775|O00776|O00777|O00778|Q540R1	Silent	SNP	ENST00000602637.1	37	CCDS4585.1																																																																																			C|0.998;T|0.002	0.002	strong		0.577	HIST1H2AC-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468023.1	NM_003512		T	26124781	C	T	26124781	2	4	24	1	0	0	0	0	0	0	0	1	7139	755	27	1		1	HIST1H2AC	6	26124781	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	157872	26124781	144990286	208	8425											
HIST1H1B	3009	hgsc.bcm.edu	37	chr6	27834877	27834877	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctttttcgcccctgcagccTtcttggccttcttaggcgtg	2	15	9	15	2	2	0	0	0	2	0	3	0	2	0	5	2	2	1	5	2	1	6	rs11970638	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:27834877T>C	ENST00000331442.3	-	1	482	c.431A>G	c.(430-432)aAg>aGg	p.K144R		NM_005322.2	NP_005313.1	P16401	H15_HUMAN	histone cluster 1, H1b	144			K -> R (in dbSNP:rs11970638).		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						CCCTGCAGCCTTCTTGGCCTT	0.617													T|||	136	0.0271565	0.0802	0.0144	5008	,	,		15536	0.005		0.0119	False		,,,				2504	0.0031				p.K144R		Atlas-SNP	.											.	HIST1H1B	54	.	0			c.A431G						PASS	.	T	ARG/LYS	380,4026		14,352,1837	95	111	106		431	5.2	0.9	6	dbSNP_120	106	51,8547		1,49,4249	yes	missense	HIST1H1B	NM_005322.2	26	15,401,6086	CC,CT,TT		0.5932,8.6246,3.3144	probably-damaging	144/227	27834877	431,12573	2203	4299	6502	SO:0001583	missense	3009	exon1			GCAGCCTTCTTGG	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.431A>G	6.37:g.27834877T>C	ENSP00000330074:p.Lys144Arg	106	0	0		111	48	0.432432	NM_005322	Q14529|Q3MJ42	Missense_Mutation	SNP	ENST00000331442.3	37	CCDS4635.1	61	0.027930402930402932	40	0.08130081300813008	8	0.022099447513812154	4	0.006993006993006993	9	0.011873350923482849	T	15.08	2.726408	0.48833	0.086246	0.005932	ENSG00000184357	ENST00000331442	T	0.24538	1.85	5.19	5.19	0.71726	.	0.587579	0.17333	N	0.178040	T	0.20577	0.0495	N	0.08118	0	0.80722	D	1	D	0.63880	0.993	D	0.72625	0.978	T	0.29088	-1.0023	10	0.51188	T	0.08	-5.6028	14.5461	0.68032	0.0:0.0:0.0:1.0	rs11970638;rs11970638	144	P16401	H15_HUMAN	R	144	ENSP00000330074:K144R	ENSP00000330074:K144R	K	-	2	0	HIST1H1B	27942856	1.000000	0.71417	0.944000	0.38274	0.103000	0.19146	3.084000	0.50143	2.103000	0.63969	0.533000	0.62120	AAG	T|0.968;C|0.032	0.032	strong		0.617	HIST1H1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043371.1	NM_005322		C	27834877	T	C	27834877	3	2	24	1	0	0	0	0	1	0	0	0	7132	1609	56	3	253	3	HIST1H1B	6	27834877	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	1710096	27834877	143280190	209	8426											
ZKSCAN4	387032	hgsc.bcm.edu	37	chr6	28219695	28219695	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccaccttcacggtcaggaGccccgtctggtcttctgcag	5	10	10	16	2	5	0	2	0	3	0	6	1	6	1	4	3	2	1	4	3	0	2	rs62638680	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:28219695G>A	ENST00000377294.2	-	1	307	c.64C>T	c.(64-66)Ctc>Ttc	p.L22F	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						ACGGTCAGGAGCCCCGTCTGG	0.637													G|||	179	0.0357428	0.1082	0.0187	5008	,	,		15084	0.006		0.0139	False		,,,				2504	0.0031				p.L22F		Atlas-SNP	.											.	ZKSCAN4	42	.	0			c.C64T						PASS	.	G	PHE/LEU	433,3917		24,385,1766	63	69	67		64	-0.6	0.1	6	dbSNP_129	67	51,8447		0,51,4198	yes	missense	ZKSCAN4	NM_019110.3	22	24,436,5964	AA,AG,GG		0.6001,9.954,3.7671	benign	22/546	28219695	484,12364	2175	4249	6424	SO:0001583	missense	387032	exon1			TCAGGAGCCCCGT	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.64C>T	6.37:g.28219695G>A	ENSP00000366509:p.Leu22Phe	65	0	0		97	39	0.402062	NM_019110	B2RE32|Q5U7L4	Missense_Mutation	SNP	ENST00000377294.2	37	CCDS4647.1	77	0.035256410256410256	52	0.10569105691056911	9	0.024861878453038673	5	0.008741258741258742	11	0.014511873350923483	G	16.83	3.231677	0.58777	0.09954	0.006001	ENSG00000187626	ENST00000377294	T	0.08896	3.04	4.21	-0.602	0.11634	.	.	.	.	.	T	0.02047	0.0064	L	0.27053	0.805	0.09310	N	0.999995	P	0.46706	0.883	P	0.44732	0.459	T	0.39901	-0.9591	9	0.46703	T	0.11	.	3.0342	0.06116	0.0972:0.1668:0.458:0.278	.	22	Q969J2	ZKSC4_HUMAN	F	22	ENSP00000366509:L22F	ENSP00000366509:L22F	L	-	1	0	ZKSCAN4	28327674	0.000000	0.05858	0.050000	0.19076	0.678000	0.39670	-0.612000	0.05616	0.044000	0.15775	0.563000	0.77884	CTC	G|0.968;A|0.032	0.032	strong		0.637	ZKSCAN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040179.1	NM_019110		A	28219695	G	A	28219695	3	1	24	1	0	0	0	0	1	0	0	0	17704	971	34	2	1593	2	ZKSCAN4	6	28219695	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	384818	28219695	142895372	210	8427											
ZKSCAN3	80317	hgsc.bcm.edu	37	chr6	28331573	28331573	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgaaaagcaggagaaccaTggcagcctggtctccctggg	11	6	14	10	0	1	2	0	1	1	1	2	4	1	2	3	4	3	2	3	4	3	0	rs213227	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:28331573T>A	ENST00000377255.3	+	6	1035	c.738T>A	c.(736-738)caT>caA	p.H246Q	ZKSCAN3_ENST00000341464.5_Missense_Mutation_p.H98Q|ZKSCAN3_ENST00000252211.2_Missense_Mutation_p.H246Q	NM_001242894.1	NP_001229823.1	Q9BRR0	ZKSC3_HUMAN	zinc finger with KRAB and SCAN domains 3	246	KRAB.		H -> Q (in dbSNP:rs213227).		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						AGGAGAACCATGGCAGCCTGG	0.463													T|||	244	0.048722	0.1278	0.0346	5008	,	,		18669	0.0119		0.0189	False		,,,				2504	0.0204				p.H246Q		Atlas-SNP	.											.	ZKSCAN3	50	.	0			c.T738A						PASS	.	T	GLN/HIS,GLN/HIS,GLN/HIS	459,3947		25,409,1769	81	74	76		738,294,738	0.5	0	6	dbSNP_79	76	135,8465		1,133,4166	yes	missense,missense,missense	ZKSCAN3	NM_001242894.1,NM_001242895.1,NM_024493.3	24,24,24	26,542,5935	AA,AT,TT		1.5698,10.4176,4.5671	benign,benign,benign	246/539,98/391,246/539	28331573	594,12412	2203	4300	6503	SO:0001583	missense	80317	exon5			GAACCATGGCAGC	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.738T>A	6.37:g.28331573T>A	ENSP00000366465:p.His246Gln	75	0	0		77	34	0.441558	NM_024493	B2R8W2|B3KVC0|H7BXX1|Q5VXH3|Q92972|Q9H4T3	Missense_Mutation	SNP	ENST00000377255.3	37	CCDS4650.1	90	0.04120879120879121	53	0.10772357723577236	14	0.03867403314917127	11	0.019230769230769232	12	0.0158311345646438	.	12.65	2.001597	0.35320	0.104176	0.015698	ENSG00000189298	ENST00000252211;ENST00000341464;ENST00000377255	T;T;T	0.01725	4.67;4.67;4.67	2.98	0.46	0.16684	Krueppel-associated box (3);	.	.	.	.	T	0.00468	0.0015	L	0.29908	0.895	0.80722	P	0.0	P	0.35821	0.523	B	0.33392	0.163	T	0.47983	-0.9074	8	0.25751	T	0.34	.	3.8184	0.08825	0.0:0.2424:0.4061:0.3515	rs213227;rs61181430;rs213227	246	Q9BRR0	ZKSC3_HUMAN	Q	246;98;246	ENSP00000252211:H246Q;ENSP00000341883:H98Q;ENSP00000366465:H246Q	ENSP00000252211:H246Q	H	+	3	2	ZKSCAN3	28439552	0.000000	0.05858	0.002000	0.10522	0.920000	0.55202	-0.612000	0.05616	0.086000	0.17137	0.460000	0.39030	CAT	T|0.958;A|0.042	0.042	strong		0.463	ZKSCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040189.3	NM_024493		A	28331573	T	A	28331573	3	1	24	1	0	0	0	0	1	0	0	0	17703	1461	51	5	752	5	ZKSCAN3	6	28331573	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	111878	28331573	142783494	211	8428											
OR2J3	442186	hgsc.bcm.edu	37	chr6	29080386	29080386	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaccactgggcttcagaaagTgtttggaacatgtggagctc	11	10	12	8	0	1	1	1	0	0	1	2	3	1	3	1	3	3	3	1	3	3	2	rs79293918	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:29080386T>C	ENST00000377169.1	+	1	719	c.719T>C	c.(718-720)gTg>gCg	p.V240A		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	240						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						CTTCAGAAAGTGTTTGGAACA	0.448													T|||	116	0.0231629	0.0651	0.0101	5008	,	,		22544	0.0079		0.0119	False		,,,				2504	0.0031				p.V240A		Atlas-SNP	.											.	OR2J3	53	.	0			c.T719C						PASS	.	T	ALA/VAL	185,2355		4,177,1089	118	123	121		719	1.6	0.9	6	dbSNP_131	121	26,5120		0,26,2547	yes	missense	OR2J3	NM_001005216.2	64	4,203,3636	CC,CT,TT		0.5052,7.2835,2.7453	possibly-damaging	240/312	29080386	211,7475	1270	2573	3843	SO:0001583	missense	442186	exon1			AGAAAGTGTTTGG		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.719T>C	6.37:g.29080386T>C	ENSP00000366374:p.Val240Ala	318	1	0.00314465		345	152	0.44058	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Missense_Mutation	SNP	ENST00000377169.1	37	CCDS43433.1	54	0.024725274725274724	32	0.06504065040650407	6	0.016574585635359115	6	0.01048951048951049	10	0.013192612137203167	T	0.005	-2.139654	0.00335	0.072835	0.005052	ENSG00000204701	ENST00000377169	T	0.00009	9.47	2.78	1.63	0.23807	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.00123	-2.06	0.40080	D	0.976121	B	0.09022	0.002	B	0.13407	0.009	T	0.00849	-1.1541	9	0.02654	T	1	.	3.5019	0.07676	0.0:0.4818:0.0:0.5182	.	240	O76001	OR2J3_HUMAN	A	240	ENSP00000366374:V240A	ENSP00000366374:V240A	V	+	2	0	OR2J3	29188365	0.981000	0.34729	0.937000	0.37676	0.020000	0.10135	1.790000	0.38734	1.268000	0.44264	0.358000	0.22013	GTG	T|0.981;C|0.019	0.019	strong		0.448	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2			C	29080386	T	C	29080386	3	2	24	1	0	0	0	0	1	0	0	0	11013	1696	59	3	721	3	OR2J3	6	29080386	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	748813	29080386	142034681	212	8429											
OR11A1	26531	hgsc.bcm.edu	37	chr6	29395180	29395180	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccctccagcatttttggcAtcactgcggaggtgtagaga	9	10	12	10	1	1	1	1	0	0	1	2	3	2	2	2	3	3	3	2	3	1	3	rs61978565	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:29395180A>G	ENST00000377149.1	-	5	711	c.239T>C	c.(238-240)aTg>aCg	p.M80T	OR11A1_ENST00000377147.2_Missense_Mutation_p.M80T|OR5V1_ENST00000377154.1_Intron|OR11A1_ENST00000377148.1_Missense_Mutation_p.M80T			Q9GZK7	O11A1_HUMAN	olfactory receptor, family 11, subfamily A, 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)	p.M80T(1)		cervix(1)|large_intestine(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	19						CATTTTTGGCATCACTGCGGA	0.483													A|||	219	0.04373	0.1384	0.0115	5008	,	,		19957	0.0119		0.0129	False		,,,				2504	0.0031				p.M80T		Atlas-SNP	.											OR11A1,NS,carcinoma,0,1	OR11A1	30	1	1	Substitution - Missense(1)	pancreas(1)	c.T239C						PASS	.	A	THR/MET	369,2651		26,317,1167	70	63	66		239	3.8	0.9	6	dbSNP_129	66	34,5384		0,34,2675	yes	missense	OR11A1	NM_013937.2	81	26,351,3842	GG,GA,AA		0.6275,12.2185,4.776	benign	80/316	29395180	403,8035	1510	2709	4219	SO:0001583	missense	26531	exon1			TTTGGCATCACTG		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.239T>C	6.37:g.29395180A>G	ENSP00000366354:p.Met80Thr	63	0	0		50	28	0.56	NM_013937	A2BF33|A6NFQ3|B0S7T2|Q5ST16|Q9GZK8	Missense_Mutation	SNP	ENST00000377149.1	37	CCDS34363.1	102	0.046703296703296704	74	0.15040650406504066	7	0.019337016574585635	10	0.017482517482517484	11	0.014511873350923483	A	8.985	0.976299	0.18736	0.122185	0.006275	ENSG00000204694	ENST00000377148;ENST00000377149;ENST00000377147	T;T;T	0.02974	4.09;4.09;4.09	3.78	3.78	0.43462	GPCR, rhodopsin-like superfamily (1);	0.297272	0.18047	U	0.153413	T	0.00524	0.0017	N	0.01209	-0.955	0.18873	N	0.999989	B	0.13594	0.008	B	0.14578	0.011	T	0.51028	-0.8757	10	0.56958	D	0.05	-9.2563	11.5265	0.50582	1.0:0.0:0.0:0.0	.	80	Q9GZK7	O11A1_HUMAN	T	80	ENSP00000366353:M80T;ENSP00000366354:M80T;ENSP00000366352:M80T	ENSP00000366352:M80T	M	-	2	0	OR11A1	29503159	0.000000	0.05858	0.925000	0.36789	0.702000	0.40608	0.971000	0.29396	1.569000	0.49696	0.333000	0.21579	ATG	A|0.957;G|0.043	0.043	strong		0.483	OR11A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000193778.1			G	29395180	A	G	29395180	3	3	24	1	0	0	0	0	1	0	0	0	10933	217	8	3	712	3	OR11A1	6	29395180	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	314794	29395180	141719887	213	8430											
OR2H1	26716	hgsc.bcm.edu	37	chr6	29429732	29429732	+	Silent	SNP	T	T	C																															ccaatgtactttttcctctcTgacctctccttcttggacct																								rs61732184	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:29429732T>C	ENST00000377136.1	+	4	651	c.186T>C	c.(184-186)tcT>tcC	p.S62S	OR2H1_ENST00000442615.1_Silent_p.S62S|OR2H1_ENST00000396792.2_Silent_p.S62S|OR2H1_ENST00000377133.1_Silent_p.S62S|OR2H1_ENST00000473369.1_Intron|OR2H1_ENST00000377132.1_Silent_p.S62S			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, 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)			large_intestine(5)|lung(12)	17						TTTTCCTCTCTGACCTCTCCT	0.527													T|||	174	0.0347444	0.1044	0.013	5008	,	,		20433	0.0119		0.0119	False		,,,				2504	0.0031				p.S62S		Atlas-SNP	.											.	OR2H1	38	.	0			c.T186C						PASS	.	T		301,2721		17,267,1227	138	135	136		186	0	1	6	dbSNP_129	136	33,5385		0,33,2676	no	coding-synonymous	OR2H1	NM_030883.3		17,300,3903	CC,CT,TT		0.6091,9.9603,3.9573		62/317	29429732	334,8106	1511	2709	4220	SO:0001819	synonymous_variant	26716	exon3			CCTCTCTGACCTC	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.186T>C	6.37:g.29429732T>C		231	0	0		253	121	0.478261	NM_030883	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Silent	SNP	ENST00000377136.1	37	CCDS4660.1																																																																																			T|0.964;C|0.036	0.036	strong		0.527	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3			C	29429732	T	C	29429732	2	2	24	1	0	0	0	0	0	0	0	1	11010	1567	55	3		3	OR2H1	6	29429732	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	34552	29429732	141685335	214	8431	109	2									
OR2H1	26716	hgsc.bcm.edu	37	chr6	29429733	29429733	+	Missense_Mutation	SNP	G	G	A																															caatgtactttttcctctctGacctctccttcttggacctc																								rs61732185	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:29429733G>A	ENST00000377136.1	+	4	652	c.187G>A	c.(187-189)Gac>Aac	p.D63N	OR2H1_ENST00000442615.1_Missense_Mutation_p.D63N|OR2H1_ENST00000396792.2_Missense_Mutation_p.D63N|OR2H1_ENST00000377133.1_Missense_Mutation_p.D63N|OR2H1_ENST00000473369.1_Intron|OR2H1_ENST00000377132.1_Missense_Mutation_p.D63N			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, member 1	63			D -> N (in allele 6M1-16*02; dbSNP:rs61732185). {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)			large_intestine(5)|lung(12)	17						TTTCCTCTCTGACCTCTCCTT	0.532													G|||	174	0.0347444	0.1044	0.013	5008	,	,		20350	0.0119		0.0119	False		,,,				2504	0.0031				p.D63N		Atlas-SNP	.											.	OR2H1	38	.	0			c.G187A						PASS	.	G	ASN/ASP	301,2721		17,267,1227	137	134	135		187	0.4	1	6	dbSNP_129	135	33,5385		0,33,2676	yes	missense	OR2H1	NM_030883.3	23	17,300,3903	AA,AG,GG		0.6091,9.9603,3.9573	benign	63/317	29429733	334,8106	1511	2709	4220	SO:0001583	missense	26716	exon3			CTCTCTGACCTCT	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.187G>A	6.37:g.29429733G>A	ENSP00000366340:p.Asp63Asn	230	1	0.00434783		253	120	0.474308	NM_030883	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Missense_Mutation	SNP	ENST00000377136.1	37	CCDS4660.1	88	0.040293040293040296	60	0.12195121951219512	8	0.022099447513812154	10	0.017482517482517484	10	0.013192612137203167	G	1.564	-0.535865	0.04082	0.099603	0.006091	ENSG00000204688	ENST00000377136;ENST00000377133;ENST00000442615;ENST00000377132;ENST00000396792	T;T;T;T;T	0.00940	5.52;5.52;5.52;5.52;5.52	2.88	0.407	0.16371	GPCR, rhodopsin-like superfamily (1);	0.156786	0.30126	N	0.010354	T	0.00039	0.0001	N	0.00003	-3.425	0.24176	N	0.995605	B	0.02656	0.0	B	0.01281	0.0	T	0.12604	-1.0541	10	0.02654	T	1	.	4.2744	0.10802	0.6269:0.1713:0.2018:0.0	rs61732185	63	Q9GZK4	OR2H1_HUMAN	N	63	ENSP00000366340:D63N;ENSP00000366337:D63N;ENSP00000393254:D63N;ENSP00000366336:D63N;ENSP00000380010:D63N	ENSP00000366336:D63N	D	+	1	0	OR2H1	29537712	0.036000	0.19791	0.986000	0.45419	0.919000	0.55068	1.592000	0.36676	0.072000	0.16694	-0.354000	0.07668	GAC	G|0.964;A|0.036	0.036	strong		0.532	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3			A	29429733	G	A	29429733	3	1	24	1	0	0	0	0	1	0	0	0	11010	1290	45	2	189	2	OR2H1	6	29429733	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1	29429733	141685334	215	8432	109	2									
HLA-G	3135	hgsc.bcm.edu	37	chr6	29796435	29796435	+	Frame_Shift_Del	DEL	C	C	-																															tacctcgccctgaacgaggaCctgcgctcctggaccgcagc																								rs41557518	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:29796435delC	ENST00000360323.6	+	3	483	c.459delC	c.(457-459)gacfs	p.D153fs	HLA-G_ENST00000428701.1_Frame_Shift_Del_p.D153fs|HLA-G_ENST00000376828.2_Frame_Shift_Del_p.D158fs|HLA-G_ENST00000376815.3_Intron|HLA-G_ENST00000376818.3_Intron			P17693	HLAG_HUMAN	major histocompatibility complex, class I, G	153	Alpha-2.				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)	p.L154fs*60(1)		central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(4)|ovary(3)|pancreas(1)|prostate(5)|skin(1)	21						TGAACGAGGACCTGCGCTCCT	0.617													cc|CC|C|deletion	142	0.0283546	0.0741	0.013	5008	,	,		16865	0.0149		0.0119	False		,,,				2504	0.0082				p.D153fs		Pindel,Atlas-Indel	.											.	HLA-G	90	.	1	Deletion - Frameshift(1)	pancreas(1)	c.458delA						PASS	.			272,3948		19,234,1857	107	99	102			1.7	0.8	6	dbSNP_134	105	112,8078		11,90,3994	no	frameshift	HLA-G	NM_002127.5		30,324,5851	A1A1,A1R,RR		1.3675,6.4455,3.0943			29796435	384,12026	1510	2709	4219	SO:0001589	frameshift_variant	3135	exon4			.		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.459delC	6.37:g.29796435delC	ENSP00000353472:p.Asp153fs	177	0	.		226	74	0.327	NM_002127		Frame_Shift_Del	DEL	ENST00000360323.6	37	CCDS4668.1																																																																																			C|0.967;-|0.033	0.033	strong		0.617	HLA-G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076286.2	NM_002127		-	29796435	C	-	29796435	7	5	24	1	0	1	0	1	0	0	0	0	7221	506	18	0	469	0	HLA-G	6	29796435	Frame_Shift_Del	DEL	C	TCGA-G8-6326-01A-11D-2210-10	366702	29796435	141318632	216	8433											
HLA-A	3105	hgsc.bcm.edu	37	chr6	29911227	29911227	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaagtgggaggcggcccatGaggcggagcagttgagagcc	9	4	19	9	2	0	2	0	2	0	1	0	5	0	4	2	5	2	3	2	5	1	1	rs1059537	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:29911227G>T	ENST00000396634.1	+	5	867	c.526G>T	c.(526-528)Gag>Tag	p.E176*	HLA-A_ENST00000376806.5_Nonsense_Mutation_p.E176*|HLA-A_ENST00000376802.2_Nonsense_Mutation_p.E176*|HLA-A_ENST00000376809.5_Nonsense_Mutation_p.E176*			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	176	Alpha-2.				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						GGCGGCCCATGAGGCGGAGCA	0.647									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)			g|||	141	0.028155	0.0741	0.013	5008	,	,		12195	0.0149		0.0109	False		,,,				2504	0.0082				p.E176X		Atlas-SNP	.											.	HLA-A	89	.	0			c.G526T						PASS	.						37	29	31					6																	29911227		1506	2704	4210	SO:0001587	stop_gained	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GCCCATGAGGCGG	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.526G>T	6.37:g.29911227G>T	ENSP00000379873:p.Glu176*	192	0	0		220	94	0.427273	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Nonsense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	35|35	5.554389|5.554389	0.96501|0.96501	.|.	.|.	ENSG00000206503|ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802|ENST00000355767	.|.	.|.	.|.	3.78|3.78	-0.78|-0.78	0.10969|0.10969	.|.	17.376800|.	0.00944|.	U|.	0.002869|.	.|T	.|0.45175	.|0.1329	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.53287	.|-0.8460	.|4	0.59425|0.87932	D|D	0.04|0	.|.	11.7413|11.7413	0.51794|0.51794	0.0:0.0:0.4323:0.5677|0.0:0.0:0.4323:0.5677	rs1059537;rs41560012|rs1059537;rs41560012	.|.	.|.	.|.	X|I	176|150	.|.	ENSP00000365998:E176X|ENSP00000348012:M150I	E|M	+|+	1|3	0|0	HLA-A|HLA-A	30019206|30019206	0.268000|0.268000	0.24133|0.24133	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	1.211000|1.211000	0.32382|0.32382	0.028000|0.028000	0.15324|0.15324	-0.335000|-0.335000	0.08231|0.08231	GAG|ATG	C|0.002;G|0.992;T|0.006	0.006	strong		0.647	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116		T	29911227	G	T	29911227	4	4	24	1	0	0	0	0	0	1	0	0	7204	1291	45	4	536	4	HLA-A	6	29911227	Nonsense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	114792	29911227	141203840	217	8434											
TRIM15	89870	hgsc.bcm.edu	37	chr6	30131527	30131527	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtaccctctgtgcggggccGctggaggatgcggtgaccat	5	9	16	11	3	1	1	0	1	1	0	1	3	1	3	3	5	3	2	3	5	1	1	rs11961941	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:30131527G>T	ENST00000376694.4	+	1	535	c.66G>T	c.(64-66)ccG>ccT	p.P22P	TRIM10_ENST00000449742.2_5'Flank|TRIM15_ENST00000376688.1_Silent_p.P22P|TRIM10_ENST00000376704.3_5'Flank	NM_033229.2	NP_150232.2	Q9C019	TRI15_HUMAN	tripartite motif containing 15	22					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						GTGCGGGGCCGCTGGAGGATG	0.677													G|||	137	0.0273562	0.0688	0.0144	5008	,	,		16858	0.0139		0.0139	False		,,,				2504	0.0082				p.P22P		Atlas-SNP	.											.	TRIM15	34	.	0			c.G66T						PASS	.	G		195,2827		5,185,1321	55	48	50		66	3.1	0.4	6	dbSNP_120	50	74,5342		0,74,2634	no	coding-synonymous	TRIM15	NM_033229.2		5,259,3955	TT,TG,GG		1.3663,6.4527,3.188		22/466	30131527	269,8169	1511	2708	4219	SO:0001819	synonymous_variant	89870	exon1			GGGGCCGCTGGAG	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.66G>T	6.37:g.30131527G>T		100	0	0		105	45	0.428571	NM_033229	A2BEC9|O95604|Q8IUX9|Q9C018	Silent	SNP	ENST00000376694.4	37	CCDS4677.1																																																																																			G|0.964;T|0.036	0.036	strong		0.677	TRIM15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076026.2	NM_033229		T	30131527	G	T	30131527	2	4	24	1	0	0	0	0	0	0	0	1	16505	1074	38	4		4	TRIM15	6	30131527	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	220300	30131527	140983540	218	8435											
GTF2H4	2968	hgsc.bcm.edu	37	chr6	30881103	30881103	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagacacctgtgctgcccccCaccatcaccgaccagatccg	9	5	7	20	2	1	2	1	0	0	2	2	3	2	2	8	0	2	1	8	0	0	0	rs1132408	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:30881103C>A	ENST00000259895.4	+	13	1378	c.1155C>A	c.(1153-1155)ccC>ccA	p.P385P	GTF2H4_ENST00000376316.2_Silent_p.P385P|VARS2_ENST00000416670.2_5'Flank|VARS2_ENST00000542001.1_5'Flank|VARS2_ENST00000541562.1_5'Flank|VARS2_ENST00000321897.5_5'Flank	NM_001517.4	NP_001508.1	Q92759	TF2H4_HUMAN	general transcription factor IIH, polypeptide 4, 52kDa	385					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						TGCTGCCCCCCACCATCACCG	0.577								Nucleotide excision repair (NER)					C|||	69	0.013778	0.0166	0.0072	5008	,	,		16179	0.0149		0.0179	False		,,,				2504	0.0092				p.P385P		Atlas-SNP	.											.	GTF2H4	38	.	0			c.C1155A						PASS	.	C		92,2930		0,92,1419	77	87	83		1155	4.7	1	6	dbSNP_86	83	85,5331		0,85,2623	no	coding-synonymous	GTF2H4	NM_001517.4		0,177,4042	AA,AC,CC		1.5694,3.0443,2.0977		385/463	30881103	177,8261	1511	2708	4219	SO:0001819	synonymous_variant	2968	exon13			GCCCCCCACCATC	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.1155C>A	6.37:g.30881103C>A		200	1	0.005		220	218	0.990909	NM_001517	B4DTJ5|Q76KU4	Silent	SNP	ENST00000259895.4	37	CCDS34386.1																																																																																			C|0.980;A|0.020	0.020	strong		0.577	GTF2H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076044.3	NM_001517		A	30881103	C	A	30881103	2	1	24	1	0	0	0	0	0	0	0	1	6874	581	21	4		4	GTF2H4	6	30881103	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	749576	30881103	140233964	219	8436											
CDSN	170679	hgsc.bcm.edu	37	chr6	31084191	31084191	+	Intron	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgctggaaatgctagaacTgctggggactcgagaactgg	10	8	15	8	1	0	2	0	0	0	2	1	5	0	4	0	4	5	4	0	4	4	1	rs33941312	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:31084191T>C	ENST00000259881.9	+	1	61				PSORS1C1_ENST00000467107.1_3'UTR|CDSN_ENST00000376288.2_Missense_Mutation_p.S401G	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						ATGCTAGAACTGCTGGGGACT	0.647													T|||	60	0.0119808	0.0008	0.0058	5008	,	,		15616	0.0149		0.0288	False		,,,				2504	0.0112				p.S401G		Atlas-SNP	.											.	CDSN	48	.	0			c.A1201G						PASS	.	T	GLY/SER,	18,4382		0,18,2182	36	42	40		1201,	3.7	0.3	6	dbSNP_126	40	169,8425		3,163,4131	yes	missense,intron	CDSN,PSORS1C1	NM_001264.4,NM_014068.2	56,	3,181,6313	CC,CT,TT		1.9665,0.4091,1.4391	possibly-damaging,	401/530,	31084191	187,12807	2200	4297	6497	SO:0001627	intron_variant	1041	exon2			TAGAACTGCTGGG	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+1523T>C	6.37:g.31084191T>C		38	0	0		35	35	1	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	37	CCDS34390.1	40	0.018315018315018316	0	0.0	2	0.0055248618784530384	14	0.024475524475524476	24	0.0316622691292876	T	9.761	1.170009	0.21621	0.004091	0.019665	ENSG00000204539	ENST00000376288	T	0.08807	3.05	3.74	3.74	0.42951	.	0.140133	0.32901	N	0.005510	T	0.06690	0.0171	N	0.24115	0.695	0.09310	N	0.999995	P	0.49696	0.927	D	0.67725	0.953	T	0.14755	-1.0461	10	0.52906	T	0.07	-3.9289	8.9816	0.35968	0.0:0.0:0.0:1.0	rs33941312	401	Q15517	CDSN_HUMAN	G	401	ENSP00000365465:S401G	ENSP00000365465:S401G	S	-	1	0	CDSN	31192170	0.006000	0.16342	0.252000	0.24328	0.287000	0.27160	-0.141000	0.10327	1.683000	0.51011	0.386000	0.25728	AGT	T|0.985;C|0.015	0.015	strong		0.647	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068		C	31084191	T	C	31084191	1	2	24	0	1	0	0	0	0	0	0	0	3181	1580	55	3		3	CDSN	6	31084191	Intron	SNP	T	TCGA-G8-6326-01A-11D-2210-10	203088	31084191	140030876	220	8437											
POU5F1	5460	hgsc.bcm.edu	37	chr6	31138310	31138310	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tagccaggtccgaggatcaaCccagcccggctccggccccc	7	4	11	19	3	1	0	1	0	0	0	3	2	3	1	7	4	3	1	7	4	2	1	rs41257954	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:31138310C>T	ENST00000259915.8	-	1	160	c.88G>A	c.(88-90)Gtt>Att	p.V30I	POU5F1_ENST00000441888.3_Intron	NM_002701.4	NP_002692.2	Q01860	PO5F1_HUMAN	POU class 5 homeobox 1	30					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)	CGAGGATCAACCCAGCCCGGC	0.687			T	EWSR1	sarcoma								C|||	59	0.0117812	0.0015	0.0043	5008	,	,		13351	0.0149		0.0278	False		,,,				2504	0.0112				p.V30I		Atlas-SNP	.		Dom	yes		6	6p21.31	5460	"POU domain, class 5, transcription factor 1"		M	.	POU5F1	25	.	0			c.G88A						PASS	.	C	ILE/VAL	10,2778		0,10,1384	4	5	5		88	1.9	1	6	dbSNP_127	5	72,4952		0,72,2440	no	missense	POU5F1	NM_002701.4	29	0,82,3824	TT,TC,CC		1.4331,0.3587,1.0497	benign	30/361	31138310	82,7730	1394	2512	3906	SO:0001583	missense	5460	exon1			GATCAACCCAGCC	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.88G>A	6.37:g.31138310C>T	ENSP00000259915:p.Val30Ile	67	0	0		77	76	0.987013	NM_002701	A6NCS1|A6NLL8|D2IYK4|P31359|Q15167|Q15168|Q16422|Q5STF3|Q5STF4	Missense_Mutation	SNP	ENST00000259915.8	37	CCDS34391.1	42	0.019230769230769232	2	0.0040650406504065045	2	0.0055248618784530384	14	0.024475524475524476	24	0.0316622691292876	C	15.63	2.891065	0.52014	0.003587	0.014331	ENSG00000204531	ENST00000259915;ENST00000448657	T	0.61742	0.08	3.7	1.92	0.25849	.	0.791726	0.10706	N	0.643431	T	0.34600	0.0903	M	0.61703	1.905	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43163	-0.9408	10	0.66056	D	0.02	.	5.9515	0.19248	0.0:0.7594:0.0:0.2406	rs41257954	30	Q01860	PO5F1_HUMAN	I	30	ENSP00000259915:V30I	ENSP00000259915:V30I	V	-	1	0	POU5F1	31246289	0.985000	0.35326	0.998000	0.56505	0.952000	0.60782	0.124000	0.15728	0.553000	0.29044	0.549000	0.68633	GTT	C|0.974;T|0.026	0.026	strong		0.687	POU5F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076413.4	NM_002701		T	31138310	C	T	31138310	3	4	24	1	0	0	0	0	1	0	0	0	12290	507	18	2	1014	2	POU5F1	6	31138310	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	54119	31138310	139976757	221	8438											
EHMT2	10919	hgsc.bcm.edu	37	chr6	31851172	31851172	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caccggatgctgagctggccGcacaggcagttggagctaga	9	6	15	11	2	0	2	0	1	0	1	0	4	0	4	2	4	3	6	2	4	1	2	rs148424397	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:31851172G>A	ENST00000375537.4	-	23	2967	c.2961C>T	c.(2959-2961)tgC>tgT	p.C987C	EHMT2_ENST00000375530.4_Silent_p.C953C|EHMT2_ENST00000395728.3_Silent_p.C1044C|EHMT2-AS1_ENST00000434689.1_RNA|EHMT2_ENST00000480912.1_5'UTR|EHMT2_ENST00000375528.4_Silent_p.C1010C	NM_006709.3	NP_006700.3	Q96KQ7	EHMT2_HUMAN	euchromatic histone-lysine N-methyltransferase 2	987	Pre-SET. {ECO:0000255|PROSITE- ProRule:PRU00157}.				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						TGAGCTGGCCGCACAGGCAGT	0.632													G|||	6	0.00119808	0.0	0.0043	5008	,	,		20855	0.0		0.003	False		,,,				2504	0.0				p.C987C		Atlas-SNP	.											.	EHMT2	45	.	0			c.C2961T						PASS	.	G	,	0,3018		0,0,1509	51	39	43		2961,2859	-9	0.7	6	dbSNP_134	43	8,5410		0,8,2701	yes	coding-synonymous,coding-synonymous	EHMT2	NM_006709.3,NM_025256.5	,	0,8,4210	AA,AG,GG		0.1477,0.0,0.0948	,	987/1211,953/1177	31851172	8,8428	1509	2709	4218	SO:0001819	synonymous_variant	10919	exon23			CTGGCCGCACAGG	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.2961C>T	6.37:g.31851172G>A		252	0	0		269	145	0.539033	NM_006709	B0UZY2|Q14349|Q5JP83|Q5JQ92|Q5JQA1|Q5JQG3|Q6PK06|Q96MH5|Q96QD0|Q9UQL8|Q9Y331	Silent	SNP	ENST00000375537.4	37	CCDS4725.1																																																																																			G|0.999;A|0.001	0.001	strong		0.632	EHMT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076355.5	NM_006709		A	31851172	G	A	31851172	2	1	24	1	0	0	0	0	0	0	0	1	4986	1079	38	1		1	EHMT2	6	31851172	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	712862	31851172	139263895	222	8439											
NOTCH4	4855	hgsc.bcm.edu	37	chr6	32163541	32163541	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgagaggctccggcaatgAgaataggccccgcccccccg	8	3	12	18	4	0	2	0	1	0	2	1	4	1	2	7	3	0	2	7	3	3	1	rs1044507	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:32163541A>C	ENST00000375023.3	-	30	5823	c.5685T>G	c.(5683-5685)tcT>tcG	p.S1895S	GPSM3_ENST00000375043.3_5'Flank|NOTCH4_ENST00000443903.2_3'UTR|GPSM3_ENST00000375040.3_5'Flank|GPSM3_ENST00000487761.1_5'Flank	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	1895					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						TCCGGCAATGAGAATAGGCCC	0.701													A|||	179	0.0357428	0.0144	0.0187	5008	,	,		13590	0.0278		0.0258	False		,,,				2504	0.0951				p.S1895S		Atlas-SNP	.											.	NOTCH4	201	.	0			c.T5685G						PASS	.	A		53,2953		0,53,1450	15	20	18		5685	-5.5	0	6	dbSNP_86	18	135,5251		3,129,2561	no	coding-synonymous	NOTCH4	NM_004557.3		3,182,4011	CC,CA,AA		2.5065,1.7631,2.2402		1895/2004	32163541	188,8204	1503	2693	4196	SO:0001819	synonymous_variant	4855	exon30			GCAATGAGAATAG		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.5685T>G	6.37:g.32163541A>C		20	0	0		31	30	0.967742	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Silent	SNP	ENST00000375023.3	37	CCDS34420.1																																																																																			A|0.974;C|0.026	0.026	strong		0.701	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2			C	32163541	A	C	32163541	2	2	24	1	0	0	0	0	0	0	0	1	10560	291	11	5		5	NOTCH4	6	32163541	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	312369	32163541	138951526	223	8440											
VPS52	6293	hgsc.bcm.edu	37	chr6	33234454	33234454	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caggaattgtctaggagggcGtagtgctggctgcggaagag	9	8	18	6	2	1	1	0	0	1	1	1	4	1	4	0	5	2	3	0	5	4	3	rs34933266	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33234454G>A	ENST00000445902.2	-	12	1379	c.1161C>T	c.(1159-1161)taC>taT	p.Y387Y	VPS52_ENST00000478934.1_5'UTR|VPS52_ENST00000436044.2_Silent_p.Y262Y|VPS52_ENST00000482399.1_3'UTR	NM_022553.4	NP_072047.4	Q8N1B4	VPS52_HUMAN	vacuolar protein sorting 52 homolog (S. cerevisiae)	387					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						CTAGGAGGGCGTAGTGCTGGC	0.517													G|||	33	0.00658946	0.003	0.0014	5008	,	,		18785	0.0129		0.008	False		,,,				2504	0.0072				p.Y387Y		Atlas-SNP	.											.	VPS52	56	.	0			c.C1161T						PASS	.	G		13,3007		0,13,1497	61	64	63		1161	-5.7	1	6	dbSNP_126	63	31,5387		0,31,2678	no	coding-synonymous	VPS52	NM_022553.4		0,44,4175	AA,AG,GG		0.5722,0.4305,0.5215		387/724	33234454	44,8394	1510	2709	4219	SO:0001819	synonymous_variant	6293	exon12			GAGGGCGTAGTGC	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.1161C>T	6.37:g.33234454G>A		86	0	0		83	45	0.542169	NM_022553	A2BF38|B0UZZ4|B4DNI9|Q53GR4|Q5JPA0|Q5SQW1|Q8IUN6|Q9NPT5	Silent	SNP	ENST00000445902.2	37	CCDS4770.2																																																																																			G|0.994;A|0.006	0.006	strong		0.517	VPS52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076598.2	NM_022553		A	33234454	G	A	33234454	2	1	24	1	0	0	0	0	0	0	0	1	17229	1140	40	1		1	VPS52	6	33234454	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1070913	33234454	137880613	224	8441											
KIFC1	3833	hgsc.bcm.edu	37	chr6	33373341	33373341	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgagtgtgagattcgccgtgCagggccagggagtgaggagc	8	6	19	8	3	0	2	0	2	0	1	1	6	0	4	2	3	2	1	2	3	0	1	rs7770412	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33373341C>T	ENST00000428849.2	+	7	1919	c.1469C>T	c.(1468-1470)gCa>gTa	p.A490V		NM_002263.3	NP_002254.2	Q9BW19	KIFC1_HUMAN	kinesin family member C1	490	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic sister chromatid segregation (GO:0000070)|spindle assembly (GO:0051225)	endosome (GO:0005768)|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)|minus-end-directed microtubule motor activity (GO:0008569)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(3)|skin(1)	13						ATTCGCCGTGCAGGGCCAGGG	0.562													C|||	43	0.00858626	0.0098	0.0014	5008	,	,		19788	0.0099		0.0109	False		,,,				2504	0.0082				p.A490V		Atlas-SNP	.											.	KIFC1	47	.	0			c.C1469T						PASS	.	C	VAL/ALA	21,4385	25.3+/-52.1	0,21,2182	28	29	29		1469	5.2	1	6	dbSNP_116	29	72,8528	42.6+/-100.3	0,72,4228	yes	missense	KIFC1	NM_002263.3	64	0,93,6410	TT,TC,CC		0.8372,0.4766,0.7151	benign	490/674	33373341	93,12913	2203	4300	6503	SO:0001583	missense	3833	exon7			GCCGTGCAGGGCC	D14678	CCDS34430.1	6p21.32	2014-05-15	2003-01-09	2003-01-10	ENSG00000237649	ENSG00000237649		"Kinesins"	6389	protein-coding gene	gene with protein product		603763	"kinesin-like 2"	KNSL2		8276466	Standard	NM_002263		Approved	HSET	uc003oef.4	Q9BW19	OTTHUMG00000031209	ENST00000428849.2:c.1469C>T	6.37:g.33373341C>T	ENSP00000393963:p.Ala490Val	24	0	0		24	9	0.375	NM_002263	O60887|Q14834|Q4KMP0|Q5SU09|Q6GMS7|Q6P4A5|Q9UQP7	Missense_Mutation	SNP	ENST00000428849.2	37	CCDS34430.1	23	0.010531135531135532	8	0.016260162601626018	1	0.0027624309392265192	8	0.013986013986013986	6	0.0079155672823219	C	10.18	1.279858	0.23392	0.004766	0.008372	ENSG00000237649	ENST00000428849	T	0.75367	-0.93	5.22	5.22	0.72569	Kinesin, motor domain (4);	0.346115	0.29900	N	0.010904	T	0.41650	0.1168	N	0.20610	0.595	0.45502	D	0.998463	B;B	0.28400	0.21;0.21	B;B	0.26094	0.066;0.066	T	0.39143	-0.9628	10	0.22109	T	0.4	-17.1298	9.6556	0.39923	0.0:0.9081:0.0:0.0919	rs7770412	482;490	B4E063;Q9BW19	.;KIFC1_HUMAN	V	490	ENSP00000393963:A490V	ENSP00000393963:A490V	A	+	2	0	KIFC1	33481319	0.997000	0.39634	1.000000	0.80357	0.952000	0.60782	2.994000	0.49433	2.720000	0.93068	0.655000	0.94253	GCA	C|0.993;T|0.007	0.007	strong		0.562	KIFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076417.1	NM_002263		T	33373341	C	T	33373341	3	4	24	1	0	0	0	0	1	0	0	0	8321	710	25	2	1495	2	KIFC1	6	33373341	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	138887	33373341	137741726	225	8442											
SYNGAP1	8831	hgsc.bcm.edu	37	chr6	33419593	33419593	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtgtgacgctggccccaccGtggaatggcctggccccccc	4	6	13	18	3	0	1	0	1	0	0	0	2	0	2	7	4	0	1	7	4	1	0	rs372190836		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:33419593G>A	ENST00000418600.2	+	19	4043	c.3942G>A	c.(3940-3942)ccG>ccA	p.P1314P	SYNGAP1_ENST00000428982.2_Silent_p.P1255P|ZBTB9_ENST00000395064.2_5'Flank|SYNGAP1_ENST00000496374.1_3'UTR	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	1314					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						TGGCCCCACCGTGGAATGGCC	0.642																																					p.P1314P		Atlas-SNP	.											SYNGAP1,caecum,carcinoma,0,1	SYNGAP1	202	1	0			c.G3942A						scavenged	.	A		0,4406		0,0,2203	16	15	15		3942	-0.8	1	6		15	1,8597		0,1,4298	no	coding-synonymous	SYNGAP1	NM_006772.2		0,1,6501	AA,AG,GG		0.0116,0.0,0.0077		1314/1344	33419593	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	8831	exon19			CCCACCGTGGAAT	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.3942G>A	6.37:g.33419593G>A		54	1	0.0185185		83	46	0.554217	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Silent	SNP	ENST00000418600.2	37	CCDS34434.2																																																																																			.	.	weak		0.642	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407		A	33419593	G	A	33419593	2	1	24	1	0	0	0	0	0	0	0	1	15462	1132	40	1		1	SYNGAP1	6	33419593	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	46252	33419593	137695474	226	8443											
TEAD3	7005	hgsc.bcm.edu	37	chr6	35446225	35446225	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtacccgcgaggaagtggAgaagacggcctggggcagag	11	4	18	8	3	0	3	0	0	0	3	0	6	0	4	2	5	1	2	2	5	3	1	rs144697750	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:35446225A>G	ENST00000402886.3	-	4	439	c.286T>C	c.(286-288)Tcc>Ccc	p.S96P	TEAD3_ENST00000338863.7_Missense_Mutation_p.S156P			Q99594	TEAD3_HUMAN	TEA domain family member 3	156					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						GAGGAAGTGGAGAAGACGGCC	0.612													a|||	16	0.00319489	0.0008	0.0072	5008	,	,		17840	0.0		0.008	False		,,,				2504	0.002				p.S156P		Atlas-SNP	.											.	TEAD3	52	.	0			c.T466C						PASS	.		PRO/SER	7,4137		0,7,2065	54	65	62		466	3.3	1	6	dbSNP_134	62	49,8365		0,49,4158	yes	missense	TEAD3	NM_003214.3	74	0,56,6223	GG,GA,AA		0.5824,0.1689,0.4459	benign	156/436	35446225	56,12502	2072	4207	6279	SO:0001583	missense	7005	exon6			AAGTGGAGAAGAC	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.286T>C	6.37:g.35446225A>G	ENSP00000384577:p.Ser96Pro	60	0	0		76	34	0.447368	NM_003214	O95910|Q5BJG7|Q8N6Y4	Missense_Mutation	SNP	ENST00000402886.3	37		8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	a	3.061	-0.193152	0.06259	0.001689	0.005824	ENSG00000007866	ENST00000338863;ENST00000402886;ENST00000373905;ENST00000433586	T;T;T	0.56275	0.48;0.47;0.91	4.46	3.26	0.37387	.	0.213980	0.41097	N	0.000949	T	0.19485	0.0468	N	0.17082	0.46	0.35183	D	0.77268	B;B;P	0.41748	0.002;0.0;0.761	B;B;P	0.45377	0.011;0.001;0.478	T	0.03473	-1.1033	10	0.09843	T	0.71	-16.0678	9.8736	0.41189	0.847:0.0:0.0:0.153	.	96;172;156	B5MCM0;Q7Z6V0;Q99594	.;.;TEAD3_HUMAN	P	156;96;172;67	ENSP00000345772:S156P;ENSP00000384577:S96P;ENSP00000416400:S67P	ENSP00000345772:S156P	S	-	1	0	TEAD3	35554203	1.000000	0.71417	0.997000	0.53966	0.915000	0.54546	2.068000	0.41471	0.826000	0.34661	0.444000	0.29173	TCC	A|0.995;G|0.005	0.005	strong		0.612	TEAD3-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316961.2			G	35446225	A	G	35446225	3	3	24	1	0	0	0	0	1	0	0	0	15755	304	11	3	873	3	TEAD3	6	35446225	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	2026632	35446225	135668842	227	8444											
SRPK1	6732	hgsc.bcm.edu	37	chr6	35803103	35803103	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagttaagccaagggtgcCggagacactcggcggcagtg	10	5	17	9	3	0	1	0	0	0	1	1	3	0	2	2	5	2	2	2	5	2	1	rs35124200	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:35803103C>T	ENST00000373825.2	-	16	2231	c.1946G>A	c.(1945-1947)cGg>cAg	p.R649Q	SRPK1_ENST00000373822.1_Missense_Mutation_p.R541Q|SRPK1_ENST00000423325.2_Missense_Mutation_p.R633Q					SRSF protein kinase 1											endometrium(2)|large_intestine(10)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21						CCAAGGGTGCCGGAGACACTC	0.562													C|||	15	0.00299521	0.0008	0.0043	5008	,	,		17497	0.002		0.006	False		,,,				2504	0.0031				p.R649Q	NSCLC(31;67 978 16289 24856 26454)	Atlas-SNP	.											.	SRPK1	61	.	0			c.G1946A						PASS	.	C	GLN/ARG	11,4087		0,11,2038	48	56	54		1946	4.8	1	6	dbSNP_126	54	98,8296		1,96,4100	yes	missense	SRPK1	NM_003137.4	43	1,107,6138	TT,TC,CC		1.1675,0.2684,0.8726	benign	649/656	35803103	109,12383	2049	4197	6246	SO:0001583	missense	6732	exon16			GGGTGCCGGAGAC	U09564	CCDS47415.1	6p21.31	2010-06-23	2010-06-23		ENSG00000096063	ENSG00000096063			11305	protein-coding gene	gene with protein product	"SR protein kinase 1", "serine/arginine-rich splicing factor kinase 1"	601939	"SFRS protein kinase 1"			8208298, 10198174	Standard	NM_003137		Approved	SFRSK1	uc003olj.3	Q96SB4	OTTHUMG00000014583	ENST00000373825.2:c.1946G>A	6.37:g.35803103C>T	ENSP00000362931:p.Arg649Gln	110	0	0		120	65	0.541667	NM_003137		Missense_Mutation	SNP	ENST00000373825.2	37	CCDS47415.1	8	0.003663003663003663	1	0.0020325203252032522	1	0.0027624309392265192	2	0.0034965034965034965	4	0.005277044854881266	C	10.84	1.464011	0.26335	0.002684	0.011675	ENSG00000096063	ENST00000373825;ENST00000361690;ENST00000423325;ENST00000373822	T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07	5.64	4.77	0.60923	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.10252	0.0251	N	0.01146	-0.985	0.50039	D	0.999849	P;B	0.45240	0.854;0.093	B;B	0.32393	0.145;0.007	T	0.22800	-1.0206	9	0.08179	T	0.78	-5.1123	10.6703	0.45755	0.0:0.8541:0.0:0.1459	rs35124200	633;649	B4DS61;Q96SB4	.;SRPK1_HUMAN	Q	649;665;633;541	ENSP00000362931:R649Q;ENSP00000354674:R665Q;ENSP00000391069:R633Q;ENSP00000362928:R541Q	ENSP00000354674:R665Q	R	-	2	0	SRPK1	35911081	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	2.142000	0.42177	1.381000	0.46364	0.655000	0.94253	CGG	C|0.996;T|0.004	0.004	strong		0.562	SRPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040319.3	NM_003137		T	35803103	C	T	35803103	3	4	24	1	0	0	0	0	1	0	0	0	15174	652	23	1	25	1	SRPK1	6	35803103	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	356878	35803103	135311964	228	8445											
SLC26A8	116369	hgsc.bcm.edu	37	chr6	35911856	35911856	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tggcctagatttggggttggGctccatctcaggctcagtct	5	13	13	10	0	3	1	2	0	2	1	5	1	4	1	2	5	0	3	2	5	1	3	rs61741366	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:35911856G>A	ENST00000490799.1	-	20	3087	c.2734C>T	c.(2734-2736)Ccc>Tcc	p.P912S	SLC26A8_ENST00000394602.2_Missense_Mutation_p.P807S|SLC26A8_ENST00000355574.2_Missense_Mutation_p.P912S	NM_052961.3	NP_443193.1			solute carrier family 26 (anion exchanger), member 8											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(16)|ovary(3)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	46						TTGGGGTTGGGCTCCATCTCA	0.572													G|||	13	0.00259585	0.0008	0.0043	5008	,	,		18402	0.0		0.006	False		,,,				2504	0.0031				p.P912S		Atlas-SNP	.											.	SLC26A8	95	.	0			c.C2734T						PASS	.	G	SER/PRO,SER/PRO,SER/PRO	13,4393	20.2+/-43.8	0,13,2190	179	156	164		2734,2734,2419	0.5	0	6	dbSNP_129	164	101,8499	56.0+/-117.1	1,99,4200	yes	missense,missense,missense	SLC26A8	NM_001193476.1,NM_052961.3,NM_138718.2	74,74,74	1,112,6390	AA,AG,GG		1.1744,0.2951,0.8765	probably-damaging,probably-damaging,probably-damaging	912/971,912/971,807/866	35911856	114,12892	2203	4300	6503	SO:0001583	missense	116369	exon20			GGTTGGGCTCCAT	AF331522	CCDS4813.1, CCDS4814.1	6p21	2013-07-18	2013-07-18		ENSG00000112053	ENSG00000112053		"Solute carriers"	14468	protein-coding gene	gene with protein product		608480	"solute carrier family 26, member 8"			11834742, 11829495	Standard	NM_001193476		Approved		uc003olm.3	Q96RN1	OTTHUMG00000014586	ENST00000490799.1:c.2734C>T	6.37:g.35911856G>A	ENSP00000417638:p.Pro912Ser	275	0	0		303	138	0.455446	NM_052961		Missense_Mutation	SNP	ENST00000490799.1	37	CCDS4813.1	6	0.0027472527472527475	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	G	9.857	1.195367	0.22037	0.002951	0.011744	ENSG00000112053	ENST00000490799;ENST00000394602;ENST00000355574	T;T;T	0.61274	0.12;0.12;0.12	3.3	0.505	0.16953	.	0.691418	0.12766	N	0.440964	T	0.19005	0.0456	L	0.29908	0.895	0.09310	N	1	B;B;B	0.26602	0.079;0.06;0.154	B;B;B	0.28784	0.014;0.056;0.094	T	0.24083	-1.0170	10	0.24483	T	0.36	.	5.426	0.16425	0.3874:0.0:0.6126:0.0	.	912;807;494	Q96RN1;Q96RN1-2;Q96RN1-3	S26A8_HUMAN;.;.	S	912;807;912	ENSP00000417638:P912S;ENSP00000378100:P807S;ENSP00000347778:P912S	ENSP00000347778:P912S	P	-	1	0	SLC26A8	36019834	0.365000	0.25006	0.009000	0.14445	0.037000	0.13140	1.727000	0.38095	0.080000	0.16959	-0.150000	0.13652	CCC	G|0.993;A|0.007	0.007	strong		0.572	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040325.2			A	35911856	G	A	35911856	3	1	24	1	0	0	0	0	1	0	0	0	14538	1203	42	2	182	2	SLC26A8	6	35911856	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	108753	35911856	135203211	229	8446											
PGC	5225	hgsc.bcm.edu	37	chr6	41710111	41710111	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgtggtggcctcatccacGgacagagcagggtaggccag	8	6	16	11	1	1	1	1	0	0	1	2	2	2	2	3	5	1	3	3	5	1	1	rs61731757	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:41710111G>A	ENST00000373025.3	-	5	626	c.564C>T	c.(562-564)tcC>tcT	p.S188S	PGC_ENST00000425343.2_Silent_p.S188S	NM_002630.3	NP_002621.1	P20142	PEPC_HUMAN	progastricsin (pepsinogen C)	188					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)			CCTCATCCACGGACAGAGCAG	0.602													G|||	12	0.00239617	0.0	0.0043	5008	,	,		18988	0.0		0.0089	False		,,,				2504	0.0				p.S188S		Atlas-SNP	.											.	PGC	56	.	0			c.C564T						PASS	.	G	,	7,4399	12.9+/-30.5	0,7,2196	130	94	106		564,564	-3.7	0	6	dbSNP_129	106	81,8519	47.2+/-106.3	0,81,4219	no	coding-synonymous,coding-synonymous	PGC	NM_001166424.1,NM_002630.3	,	0,88,6415	AA,AG,GG		0.9419,0.1589,0.6766	,	188/316,188/389	41710111	88,12918	2203	4300	6503	SO:0001819	synonymous_variant	5225	exon5			ATCCACGGACAGA		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.564C>T	6.37:g.41710111G>A		116	0	0		120	59	0.491667	NM_002630	B4DVZ3|Q5T3D7|Q5T3D8	Silent	SNP	ENST00000373025.3	37	CCDS4859.1																																																																																			G|0.994;A|0.006	0.006	strong		0.602	PGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040521.2			A	41710111	G	A	41710111	2	1	24	1	0	0	0	0	0	0	0	1	11794	1103	39	1		1	PGC	6	41710111	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	5798255	41710111	129404956	230	8447											
CUL9	23113	hgsc.bcm.edu	37	chr6	43152366	43152366	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tttcctcgagatccaggaggCctggatgaagtggcaatggg	9	9	15	8	1	0	2	0	1	0	1	3	5	2	4	3	5	0	1	3	5	2	1	rs41274928	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:43152366C>A	ENST00000252050.4	+	2	402	c.318C>A	c.(316-318)ggC>ggA	p.G106G	CUL9_ENST00000372647.2_Silent_p.G106G|CUL9_ENST00000354495.3_Silent_p.G106G	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	106					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						ATCCAGGAGGCCTGGATGAAG	0.607													C|||	248	0.0495208	0.1112	0.0288	5008	,	,		20915	0.003		0.0288	False		,,,				2504	0.0501				p.G106G		Atlas-SNP	.											.	CUL9	248	.	0			c.C318A						PASS	.	C		459,3947	217.1+/-235.6	32,395,1776	89	96	94		318	0.7	1	6	dbSNP_127	94	267,8333	101.9+/-163.1	2,263,4035	no	coding-synonymous	CUL9	NM_015089.2		34,658,5811	AA,AC,CC		3.1047,10.4176,5.582		106/2518	43152366	726,12280	2203	4300	6503	SO:0001819	synonymous_variant	23113	exon2			AGGAGGCCTGGAT	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.318C>A	6.37:g.43152366C>A		154	0	0		185	84	0.454054	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	37	CCDS4890.1																																																																																			C|0.948;A|0.052	0.052	strong		0.607	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		A	43152366	C	A	43152366	2	1	24	1	0	0	0	0	0	0	0	1	4063	726	26	4		4	CUL9	6	43152366	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1442255	43152366	127962701	231	8448											
DST	667	hgsc.bcm.edu	37	chr6	56373536	56373536	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccaaatgaaaaccatttggtCaagcttatcctgaacagcta	15	10	6	10	0	1	2	1	2	0	0	2	2	2	2	3	1	4	2	3	1	7	3	rs41271862	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:56373536C>T	ENST00000361203.3	-	70	18077	c.18070G>A	c.(18070-18072)Gac>Aac	p.D6024N	DST_ENST00000244364.6_Missense_Mutation_p.D3721N|DST_ENST00000370754.5_Missense_Mutation_p.D6313N|DST_ENST00000340834.4_5'UTR|DST_ENST00000370788.2_Missense_Mutation_p.D3938N|DST_ENST00000312431.6_3'UTR|DST_ENST00000421834.2_Missense_Mutation_p.D4047N|DST_ENST00000370769.4_Missense_Mutation_p.D6135N|DST_ENST00000446842.2_Missense_Mutation_p.D5809N			Q03001	DYST_HUMAN	dystonin	6020					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)			ACCATTTGGTCAAGCTTATCC	0.438													C|||	80	0.0159744	0.0	0.013	5008	,	,		21172	0.0		0.0557	False		,,,				2504	0.0153				p.D3721N		Atlas-SNP	.											.	DST	1427	.	0			c.G11161A						PASS	.	C	ASN/ASP	39,3815		0,39,1888	118	116	117		11161	5.5	1	6	dbSNP_127	117	407,7869		12,383,3743	yes	missense	DST	NM_015548.4	23	12,422,5631	TT,TC,CC		4.9178,1.0119,3.6768	probably-damaging	3721/5172	56373536	446,11684	1927	4138	6065	SO:0001583	missense	667	exon56			TTTGGTCAAGCTT	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.18070G>A	6.37:g.56373536C>T	ENSP00000354508:p.Asp6024Asn	165	0	0		175	81	0.462857	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	37		51	0.023351648351648352	0	0.0	4	0.011049723756906077	0	0.0	47	0.06200527704485488	C	20.9	4.070212	0.76301	0.010119	0.049178	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203;ENST00000537444	T;T;T;T;T;T;T	0.51071	1.26;1.26;1.26;1.26;1.26;1.26;0.72	5.54	5.54	0.83059	.	0.000000	0.56097	D	0.000022	T	0.57272	0.2042	L	0.53249	1.67	0.32212	N	0.576451	D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;0.963	D;D;D;D;P	0.97110	0.999;1.0;0.999;0.966;0.792	T	0.42430	-0.9452	9	0.23302	T	0.38	.	19.8426	0.96695	0.0:1.0:0.0:0.0	rs41271862	4047;6135;6313;6133;3721	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	N	3721;6313;6135;4047;5809;3938;6024;137	ENSP00000244364:D3721N;ENSP00000359790:D6313N;ENSP00000359805:D6135N;ENSP00000400883:D4047N;ENSP00000393645:D5809N;ENSP00000359824:D3938N;ENSP00000354508:D6024N	ENSP00000244364:D3721N	D	-	1	0	DST	56481495	1.000000	0.71417	0.999000	0.59377	0.976000	0.68499	6.039000	0.70972	2.765000	0.95021	0.557000	0.71058	GAC	C|0.967;T|0.033	0.033	strong		0.438	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		T	56373536	C	T	56373536	3	4	24	1	0	0	0	0	1	0	0	0	4785	826	29	2	4470	2	DST	6	56373536	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	13221170	56373536	114741531	232	8449											
PHF3	23469	hgsc.bcm.edu	37	chr6	64394121	64394121	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaagcatctgggaagactgtAtctactgctaaagcaggagt	14	9	11	7	0	2	1	0	0	2	1	2	3	2	3	0	2	4	4	0	2	6	3	rs35294942	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:64394121A>G	ENST00000262043.3	+	4	838	c.498A>G	c.(496-498)gtA>gtG	p.V166V	PHF3_ENST00000393387.1_Silent_p.V166V|PHF3_ENST00000509330.1_Silent_p.V166V			Q92576	PHF3_HUMAN	PHD finger protein 3	166					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)			GGAAGACTGTATCTACTGCTA	0.403													A|||	45	0.00898562	0.031	0.0029	5008	,	,		17216	0.0		0.002	False		,,,				2504	0.0				p.V166V	GBM(135;136 1820 29512 34071 46235)	Atlas-SNP	.											.	PHF3	191	.	0			c.A498G						PASS	.	A		118,4288	87.8+/-126.4	2,114,2087	176	183	180		498	-4.4	0.5	6	dbSNP_126	180	0,8600	1.2+/-3.3	0,0,4300	no	coding-synonymous	PHF3	NM_015153.2		2,114,6387	GG,GA,AA		0.0,2.6782,0.9073		166/2040	64394121	118,12888	2203	4300	6503	SO:0001819	synonymous_variant	23469	exon3			GACTGTATCTACT	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.498A>G	6.37:g.64394121A>G		129	0	0		113	59	0.522124	NM_015153	A3KFI8|Q14CR5|Q5CZI1|Q5T1T6|Q9NQ16|Q9UI45	Silent	SNP	ENST00000262043.3	37	CCDS4966.1																																																																																			A|0.990;G|0.010	0.010	strong		0.403	PHF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041086.2			G	64394121	A	G	64394121	2	3	24	1	0	0	0	0	0	0	0	1	11845	436	16	3		3	PHF3	6	64394121	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	8020585	64394121	106720946	233	8450											
KIAA0776	23376	hgsc.bcm.edu	37	chr6	96985311	96985311	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agctacataaagaaaagataTaagactacacaactcttgtt	19	10	5	7	0	1	3	0	0	1	3	1	3	1	3	0	0	4	2	0	0	9	7	rs55792562	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:96985311T>C	ENST00000369278.4	+	9	930	c.864T>C	c.(862-864)taT>taC	p.Y288Y		NM_015323.4	NP_056138.1	O94874	UFL1_HUMAN	UFM1-specific ligase 1	288					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)										AGAAAAGATATAAGACTACAC	0.373													T|||	65	0.0129792	0.0166	0.0259	5008	,	,		17079	0.0		0.0229	False		,,,				2504	0.002				p.Y288Y		Atlas-SNP	.											.	.	.	.	0			c.T864C						PASS	.	T		61,4345	58.1+/-94.6	0,61,2142	159	159	159		864	-6.8	0.9	6	dbSNP_129	159	247,8351	99.7+/-161.2	4,239,4056	no	coding-synonymous	UFL1	NM_015323.4		4,300,6198	CC,CT,TT		2.8728,1.3845,2.3685		288/795	96985311	308,12696	2203	4299	6502	SO:0001819	synonymous_variant	23376	exon9			AAGATATAAGACT	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.864T>C	6.37:g.96985311T>C		128	0	0		141	76	0.539007	NM_015323	A0PJ53|B4DJ57|C0H5X5|Q8N765|Q9NTQ0	Silent	SNP	ENST00000369278.4	37	CCDS5034.1																																																																																			T|0.978;C|0.022	0.022	strong		0.373	UFL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041557.1	NM_015323		C	96985311	T	C	96985311	2	2	24	1	0	0	0	0	0	0	0	1	8202	1413	49	3		3	KIAA0776	6	96985311	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	32591190	96985311	74129756	234	8451											
LAMA2	3908	hgsc.bcm.edu	37	chr6	129833568	129833568	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgaattccgcacaactacaaCgactggagttcttctgggga	11	10	10	10	2	2	1	0	1	2	0	3	4	3	3	1	3	3	2	1	3	4	4	rs145842163	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr6:129833568C>A	ENST00000421865.2	+	63	8967	c.8918C>A	c.(8917-8919)aCg>aAg	p.T2973K		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2973	Laminin G-like 5. {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)		ACAACTACAACGACTGGAGTT	0.363																																					p.T2973K		Atlas-SNP	.											.	LAMA2	481	.	0			c.C8918A						PASS	.	C	LYS/THR,LYS/THR	0,4406		0,0,2203	151	148	149		8918,8906	3.9	0.5	6	dbSNP_134	149	3,8597	3.0+/-9.4	0,3,4297	no	missense,missense	LAMA2	NM_000426.3,NM_001079823.1	78,78	0,3,6500	AA,AC,CC		0.0349,0.0,0.0231	probably-damaging,probably-damaging	2973/3123,2969/3119	129833568	3,13003	2203	4300	6503	SO:0001583	missense	3908	exon63			CTACAACGACTGG	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.8918C>A	6.37:g.129833568C>A	ENSP00000400365:p.Thr2973Lys	149	0	0		172	78	0.453488	NM_000426	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	C	0.026	-1.373086	0.01214	0.0	3.49E-4	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865;ENST00000443169	T	0.76839	-1.05	5.73	3.93	0.45458	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.207503	0.48767	D	0.000175	T	0.47655	0.1457	N	0.17674	0.51	0.09310	N	1	P;P	0.47484	0.896;0.896	P;P	0.44696	0.458;0.458	T	0.37820	-0.9689	9	.	.	.	.	7.8481	0.29437	0.1468:0.7266:0.0:0.1266	.	2974;2973	A6NF00;P24043	.;LAMA2_HUMAN	K	2973;2972;2973;991	ENSP00000400365:T2973K	.	T	+	2	0	LAMA2	129875261	0.986000	0.35501	0.534000	0.28014	0.194000	0.23727	1.787000	0.38704	1.406000	0.46857	0.655000	0.94253	ACG	C|1.000;A|0.000	0.000	strong		0.363	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			A	129833568	C	A	129833568	3	1	24	1	0	0	0	0	1	0	0	0	8615	536	19	4	9168	4	LAMA2	6	129833568	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	32848257	129833568	41281499	235	8452											
MICALL2	79778	hgsc.bcm.edu	37	chr7	1478525	1478525	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcctcctccttccagctctgCactcgggcttcctggccagg	3	11	9	18	1	1	0	0	0	1	0	7	0	6	0	6	3	2	3	6	3	0	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:1478525C>T	ENST00000297508.7	-	10	2248	c.2073G>A	c.(2071-2073)gtG>gtA	p.V691V	MICALL2_ENST00000471899.1_5'UTR|MICALL2_ENST00000405088.4_Silent_p.V479V	NM_182924.3	NP_891554.1	Q8IY33	MILK2_HUMAN	MICAL-like 2	691	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)			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)		TCCAGCTCTGCACTCGGGCTT	0.652																																					p.V691V		Atlas-SNP	.											.	MICALL2	63	.	0			c.G2073A						PASS	.						61	61	61					7																	1478525		2203	4300	6503	SO:0001819	synonymous_variant	79778	exon10			GCTCTGCACTCGG	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.2073G>A	7.37:g.1478525C>T		45	0	0		36	18	0.5	NM_182924	D3YTD2|Q7RTP4|Q7Z655|Q8TEQ4|Q9H5F9	Silent	SNP	ENST00000297508.7	37	CCDS5324.1																																																																																			.	.	none		0.652	MICALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239223.2	NM_182924		T	1478525	C	T	1478525	2	4	24	1	0	0	0	0	0	0	0	1	9583	697	25	2		2	MICALL2	7	1478525	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10		1478525	157660138	236	8453											
HOXA1	3198	hgsc.bcm.edu	37	chr7	27135317	27135319	+	In_Frame_Del	DEL	TGG	TGG	-																															tagccggctgggggtggcgaTggtggtggtggtggtggtgg																								rs2074398|rs587777901|rs544314279	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	TGG	TGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:27135317_27135319delTGG	ENST00000343060.4	-	1	274_276	c.213_215delCCA	c.(211-216)caccat>cat	p.71_72HH>H	HOXA1_ENST00000355633.5_In_Frame_Del_p.71_72HH>H|HOTAIRM1_ENST00000429611.3_RNA|HOTAIRM1_ENST00000425358.2_RNA|HOTAIRM1_ENST00000434063.3_RNA|HOTAIRM1_ENST00000495032.1_RNA	NM_005522.4	NP_005513	P49639	HXA1_HUMAN	homeobox A1	71	Poly-His.				abducens nerve formation (GO:0021599)|anatomical structure morphogenesis (GO:0009653)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|artery morphogenesis (GO:0048844)|central nervous system neuron differentiation (GO:0021953)|cochlea development (GO:0090102)|cochlea morphogenesis (GO:0090103)|cognition (GO:0050890)|embryonic neurocranium morphogenesis (GO:0048702)|facial nerve structural organization (GO:0021612)|facial nucleus development (GO:0021754)|inner ear development (GO:0048839)|motor neuron axon guidance (GO:0008045)|multicellular organismal development (GO:0007275)|neuromuscular process (GO:0050905)|optokinetic behavior (GO:0007634)|outer ear morphogenesis (GO:0042473)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of behavior (GO:0050795)|rhombomere 3 development (GO:0021569)|rhombomere 4 development (GO:0021570)|rhombomere 5 development (GO:0021571)|semicircular canal formation (GO:0060876)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(14)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						ggggtggcgatggtggtggtggt	0.64											OREG0003750	type=REGULATORY REGION|Gene=BC031342|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.72_72del		Pindel	.											.	HOXA1	64	.	0			c.214_216del						PASS	.																																			SO:0001651	inframe_deletion	3198	exon1			.		CCDS5401.1, CCDS5402.2	7p15.2	2011-06-20	2005-12-22		ENSG00000105991	ENSG00000105991		"Homeoboxes / ANTP class : HOXL subclass"	5099	protein-coding gene	gene with protein product		142955	"homeo box A1"	HOX1F, HOX1		1973146	Standard	NM_153620		Approved		uc003sye.3	P49639	OTTHUMG00000023207	ENST00000343060.4:c.213_215delCCA	7.37:g.27135326_27135328delTGG	ENSP00000343246:p.His72del	42	0	.	792	61	26	0.426	NM_005522	A4D184|B2R8U7|O43363	In_Frame_Del	DEL	ENST00000343060.4	37	CCDS5401.1																																																																																			.	.	none		0.64	HOXA1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358454.1			-	27135319	TGG	-	27135317	7	5	24	1	0	1	0	1	0	0	0	0	7297	1464	51	0	800	0	HOXA1	7	27135317	In_Frame_Del	DEL	TGG	TCGA-G8-6326-01A-11D-2210-10	25656792	27135317	132003346	237	8454											
CPVL	54504	hgsc.bcm.edu	37	chr7	29111950	29111950	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatatccatctccaatagcAattccgttcaggttgatctt	11	14	6	10	1	3	1	1	1	2	0	6	2	5	1	3	1	1	3	3	1	5	6	rs62442642	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:29111950A>G	ENST00000409850.1	-	12	1345	c.699T>C	c.(697-699)atT>atC	p.I233I	CPVL_ENST00000265394.5_Silent_p.I233I|CPVL_ENST00000396276.3_Silent_p.I233I			Q9H3G5	CPVL_HUMAN	carboxypeptidase, vitellogenic-like	233						extracellular vesicular exosome (GO:0070062)	serine-type carboxypeptidase activity (GO:0004185)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(1)	28						CTCCAATAGCAATTCCGTTCA	0.438													A|||	15	0.00299521	0.0015	0.0058	5008	,	,		20173	0.001		0.007	False		,,,				2504	0.001				p.I233I		Atlas-SNP	.											.	CPVL	60	.	0			c.T699C						PASS	.	A	,	9,4397	15.5+/-35.6	0,9,2194	154	129	138		699,699	-3.6	0.9	7	dbSNP_129	138	58,8542	36.4+/-91.3	0,58,4242	no	coding-synonymous,coding-synonymous	CPVL	NM_019029.2,NM_031311.3	,	0,67,6436	GG,GA,AA		0.6744,0.2043,0.5151	,	233/477,233/477	29111950	67,12939	2203	4300	6503	SO:0001819	synonymous_variant	54504	exon8			AATAGCAATTCCG	AF106704	CCDS5419.1	7p15.1	2012-02-10			ENSG00000106066	ENSG00000106066			14399	protein-coding gene	gene with protein product	"carboxypeptidase WUG", "vitellogenic carboxypeptidase-like protein", "CP-Mac carboxypeptidase"	609780				11401439	Standard	XM_005249786		Approved		uc003szw.3	Q9H3G5	OTTHUMG00000023669	ENST00000409850.1:c.699T>C	7.37:g.29111950A>G		124	0	0		120	59	0.491667	NM_019029	A4D1A4|Q6UX20|Q8NBL7|Q96AR7|Q9HB41	Silent	SNP	ENST00000409850.1	37	CCDS5419.1																																																																																			A|0.995;G|0.005	0.005	strong		0.438	CPVL-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328305.1	NM_019029		G	29111950	A	G	29111950	2	3	24	1	0	0	0	0	0	0	0	1	3837	126	5	3		3	CPVL	7	29111950	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	1976633	29111950	130026713	238	8455											
KIAA0895	23366	hgsc.bcm.edu	37	chr7	36396735	36396735	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	cagctgaggctttggctttgGaagagtggagaaatggcacc	10	9	15	7	0	0	3	0	1	0	2	0	5	0	4	1	5	1	4	1	5	2	2	rs199774798	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:36396735G>C	ENST00000297063.6	-	3	693	c.643C>G	c.(643-645)Cca>Gca	p.P215A	KIAA0895_ENST00000453212.1_Intron|KIAA0895_ENST00000436884.1_Missense_Mutation_p.P64A|KIAA0895_ENST00000480192.1_Intron|KIAA0895_ENST00000440378.1_Missense_Mutation_p.P164A|KIAA0895_ENST00000317020.6_Missense_Mutation_p.P164A|KIAA0895_ENST00000415803.2_Missense_Mutation_p.P202A|KIAA0895_ENST00000338533.5_Missense_Mutation_p.P202A	NM_001100425.1	NP_001093895.1	Q8NCT3	K0895_HUMAN	KIAA0895	215										breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						TTTGGCTTTGGAAGAGTGGAG	0.413													G|||	2	0.000399361	0.0008	0.0	5008	,	,		21233	0.0		0.001	False		,,,				2504	0.0				p.P215A		Atlas-SNP	.											.	KIAA0895	89	.	0			c.C643G						PASS	.	G	ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO	3,3749		0,3,1873	93	88	90		643,490,604,190,490	3.7	0.4	7		90	0,8236		0,0,4118	yes	missense,missense,missense,missense,missense	KIAA0895	NM_001100425.1,NM_001199706.1,NM_001199707.1,NM_001199708.1,NM_015314.2	27,27,27,27,27	0,3,5991	CC,CG,GG		0.0,0.08,0.025	benign,benign,benign,benign,benign	215/521,164/518,202/508,64/418,164/470	36396735	3,11985	1876	4118	5994	SO:0001583	missense	23366	exon3			GCTTTGGAAGAGT	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.643C>G	7.37:g.36396735G>C	ENSP00000297063:p.Pro215Ala	217	0	0		235	105	0.446809	NM_001100425	B4DF35|B7ZLT4|B9EGB9|O94969|Q0VGC1|Q7Z4L2	Missense_Mutation	SNP	ENST00000297063.6	37	CCDS43570.1	.	.	.	.	.	.	.	.	.	.	G	2.506	-0.314008	0.05422	8.0E-4	0.0	ENSG00000164542	ENST00000297063;ENST00000338533;ENST00000317020;ENST00000440378;ENST00000436884;ENST00000415803;ENST00000429651	.	.	.	5.65	3.69	0.42338	.	0.385185	0.30028	N	0.010586	T	0.24236	0.0587	N	0.15975	0.35	0.09310	N	1	B;B;B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.04013	0.001;0.0;0.0;0.001;0.001;0.001;0.0	T	0.13124	-1.0521	9	0.20046	T	0.44	-27.7009	11.557	0.50755	0.0:0.2899:0.5506:0.1596	.	164;164;64;202;215;202;164	B4DGN6;B7ZLT4;B4DF35;Q8NCT3-4;Q8NCT3;Q8NCT3-2;Q8NCT3-3	.;.;.;.;K0895_HUMAN;.;.	A	215;202;164;164;64;202;82	.	ENSP00000297063:P215A	P	-	1	0	KIAA0895	36363260	0.003000	0.15002	0.448000	0.26945	0.245000	0.25701	0.026000	0.13599	1.365000	0.46057	0.563000	0.77884	CCA	.	.	weak		0.413	KIAA0895-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337717.1	NM_015314		C	36396735	G	C	36396735	3	2	24	1	0	0	0	0	1	0	0	0	8206	1174	41	4	939	4	KIAA0895	7	36396735	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	7284785	36396735	122741928	239	8456											
VPS41	27072	hgsc.bcm.edu	37	chr7	38785204	38785204	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagtttctctgttgacagaTctcaagagccttcaattaaa	14	13	6	8	0	3	3	2	1	2	2	5	3	3	3	1	0	1	2	1	0	5	4			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:38785204T>C	ENST00000310301.4	-	23	1990	c.1936A>G	c.(1936-1938)Atc>Gtc	p.I646V	VPS41_ENST00000395969.2_Missense_Mutation_p.I621V	NM_014396.3	NP_055211.2	P49754	VPS41_HUMAN	vacuolar protein sorting 41 homolog (S. cerevisiae)	646					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						TGTTGACAGATCTCAAGAGCC	0.328																																					p.I646V		Atlas-SNP	.											.	VPS41	102	.	0			c.A1936G						PASS	.						112	114	113					7																	38785204		2203	4300	6503	SO:0001583	missense	27072	exon23			GACAGATCTCAAG	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.1936A>G	7.37:g.38785204T>C	ENSP00000309457:p.Ile646Val	89	0	0		101	44	0.435644	NM_014396	E9PF36|Q86TP8|Q99851|Q99852	Missense_Mutation	SNP	ENST00000310301.4	37	CCDS5457.1	.	.	.	.	.	.	.	.	.	.	T	13.62	2.290379	0.40494	.	.	ENSG00000006715	ENST00000310301;ENST00000395969	T;T	0.19105	2.17;2.17	5.35	5.35	0.76521	Tetratricopeptide-like helical (1);	0.252290	0.45126	D	0.000390	T	0.19725	0.0474	L	0.41236	1.265	0.58432	D	0.999996	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.02617	-1.1133	10	0.30078	T	0.28	-15.5727	15.6427	0.77020	0.0:0.0:0.0:1.0	.	646;621;646	B2RB94;E9PF36;P49754	.;.;VPS41_HUMAN	V	646;621	ENSP00000309457:I646V;ENSP00000379297:I621V	ENSP00000309457:I646V	I	-	1	0	VPS41	38751729	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.923000	0.63412	2.152000	0.67230	0.455000	0.32223	ATC	.	.	none		0.328	VPS41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226986.3			C	38785204	T	C	38785204	3	2	24	1	0	0	0	0	1	0	0	0	17225	1435	50	3	656	3	VPS41	7	38785204	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	2388469	38785204	120353459	240	8457											
EGFR	1956	hgsc.bcm.edu	37	chr7	55238087	55238087	+	Intron	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aatgatggcagcgtgtcccaCcagagcgggagcccagctgc	9	5	14	13	2	0	2	0	1	0	1	1	3	1	3	3	2	5	2	3	2	1	0	rs10258429	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:55238087C>T	ENST00000275493.2	+	16	2057				EGFR_ENST00000455089.1_Intron|EGFR_ENST00000344576.2_Silent_p.H656H|EGFR_ENST00000442591.1_Intron|EGFR_ENST00000454757.2_Intron	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor						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)	GCGTGTCCCACCAGAGCGGGA	0.512		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			C|||	563	0.11242	0.2398	0.049	5008	,	,		20745	0.0496		0.0736	False		,,,				2504	0.09				p.H656H		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.C1968T						PASS	.	C	,	922,3484	352.1+/-311.5	101,720,1382	108	89	95		,1968	2.4	0	7	dbSNP_119	95	606,7994	158.6+/-212.1	23,560,3717	no	intron,coding-synonymous	EGFR	NM_005228.3,NM_201284.1	,	124,1280,5099	TT,TC,CC		7.0465,20.926,11.7484	,	,656/706	55238087	1528,11478	2203	4300	6503	SO:0001627	intron_variant	1956	exon16	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	GTCCCACCAGAGC		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.1881-781C>T	7.37:g.55238087C>T		160	0	0		189	93	0.492063	NM_201284	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																			C|0.889;T|0.111	0.111	strong		0.512	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		T	55238087	C	T	55238087	1	4	24	0	1	0	0	0	0	0	0	0	4969	506	18	2		2	EGFR	7	55238087	Intron	SNP	C	TCGA-G8-6326-01A-11D-2210-10	16452883	55238087	103900576	241	8458											
EGFR	1956	hgsc.bcm.edu	37	chr7	55268916	55268916	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catttgccaagtcctacagaCtccaacttctaccgtgccct	9	11	5	16	1	1	1	0	0	1	1	3	1	3	1	5	0	5	0	5	0	4	4	rs2293347|rs587778251	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:55268916C>T	ENST00000275493.2	+	25	3159	c.2982C>T	c.(2980-2982)gaC>gaT	p.D994D	EGFR_ENST00000455089.1_Silent_p.D949D|EGFR_ENST00000442591.1_Intron|EGFR_ENST00000454757.2_Silent_p.D941D	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	994					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)	GTCCTACAGACTCCAACTTCT	0.512		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			t|||	710	0.141773	0.0129	0.1542	5008	,	,		18651	0.247		0.1113	False		,,,				2504	0.2301				p.D994D		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.C2982T						PASS	.	T		121,4285	90.6+/-129.3	1,119,2083	151	139	143		2982	3.8	1	7	dbSNP_100	143	795,7805	185.7+/-233.4	42,711,3547	no	coding-synonymous	EGFR	NM_005228.3		43,830,5630	TT,TC,CC		9.2442,2.7463,7.0429		994/1211	55268916	916,12090	2203	4300	6503	SO:0001819	synonymous_variant	1956	exon25	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	TACAGACTCCAAC		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.2982C>T	7.37:g.55268916C>T		135	0	0		158	72	0.455696	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																			C|0.894;T|0.106	0.106	strong		0.512	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		T	55268916	C	T	55268916	2	4	24	1	0	0	0	0	0	0	0	1	4969	564	20	2		2	EGFR	7	55268916	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	30829	55268916	103869747	242	8459											
UPK3B	80761	hgsc.bcm.edu	37	chr7	76140315	76140315	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agcagccgcgctgtgtcttcGatgggcttgccagcgccagc	5	8	14	14	4	1	0	0	0	1	0	2	1	1	0	3	1	5	3	3	1	0	2	rs144609046	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:76140315G>A	ENST00000257632.5	+	1	474	c.346G>A	c.(346-348)Gat>Aat	p.D116N	UPK3B_ENST00000334348.3_Missense_Mutation_p.D61N|UPK3B_ENST00000448265.3_Missense_Mutation_p.D116N|UPK3B_ENST00000394849.1_Missense_Mutation_p.D61N|UPK3B_ENST00000443097.2_Missense_Mutation_p.D61N|UPK3B_ENST00000419923.2_Missense_Mutation_p.D116N			Q9BT76	UPK3B_HUMAN	uroplakin 3B	116					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)				CTGTGTCTTCGATGGGCTTGC	0.632													.|||	3	0.000599042	0.0	0.0	5008	,	,		18847	0.0		0.001	False		,,,				2504	0.002				p.D116N		Atlas-SNP	.											.	UPK3B	15	.	0			c.G346A						PASS	.	G	ASN/ASP,ASN/ASP	0,4310		0,0,2155	9	8	9		346,181	3	0.2	7	dbSNP_134	9	10,8410		0,10,4200	no	missense,missense	UPK3B	NM_030570.2,NM_182684.1	23,23	0,10,6355	AA,AG,GG		0.1188,0.0,0.0786	possibly-damaging,possibly-damaging	116/321,61/277	76140315	10,12720	2155	4210	6365	SO:0001583	missense	80761	exon1			GTCTTCGATGGGC	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.346G>A	7.37:g.76140315G>A	ENSP00000257632:p.Asp116Asn	649	1	0.00154083		535	226	0.42243	NM_030570	A6NHH5|A8K231|A8MZA8|B3KPU5|Q75MM5|Q86W06	Missense_Mutation	SNP	ENST00000257632.5	37	CCDS5588.1	.	.	.	.	.	.	.	.	.	.	.	12.85	2.061280	0.36373	0.0	0.001188	ENSG00000243566	ENST00000334348;ENST00000419923;ENST00000448265;ENST00000443097;ENST00000257632;ENST00000394849	T;T;T;T;T;T	0.58358	0.34;1.28;1.28;0.34;1.28;1.29	4.93	2.99	0.34606	.	0.412335	0.23849	N	0.043977	T	0.48554	0.1506	N	0.17474	0.49	0.09310	N	1	D;D;D	0.76494	0.999;0.999;0.991	D;P;P	0.63381	0.914;0.9;0.539	T	0.22941	-1.0202	10	0.46703	T	0.11	-8.2617	7.7594	0.28944	0.0919:0.0:0.7447:0.1633	.	61;116;61	Q9BT76-2;Q9BT76;A6NHH5	.;UPK3B_HUMAN;.	N	61;116;116;61;116;61	ENSP00000334938:D61N;ENSP00000441602:D116N;ENSP00000441284:D116N;ENSP00000444585:D61N;ENSP00000257632:D116N;ENSP00000378319:D61N	ENSP00000257632:D116N	D	+	1	0	UPK3B	75978251	0.037000	0.19845	0.162000	0.22713	0.010000	0.07245	0.841000	0.27613	2.281000	0.76405	0.400000	0.26472	GAT	G|0.999;A|0.001	0.001	strong		0.632	UPK3B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000313978.2	NM_030570		A	76140315	G	A	76140315	3	1	24	1	0	0	0	0	1	0	0	0	17026	1058	37	1	348	1	UPK3B	7	76140315	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	20871399	76140315	82998348	243	8460											
KRIT1	889	hgsc.bcm.edu	37	chr7	91864857	91864857	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttctgtctgacctgattcagTagcatatgcaggatttatga	10	15	9	7	0	3	3	1	3	2	0	3	4	3	4	1	1	2	3	1	1	3	6	rs140396626		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:91864857T>C	ENST00000340022.2	-	8	1607	c.589A>G	c.(589-591)Act>Gct	p.T197A	KRIT1_ENST00000394503.2_Missense_Mutation_p.T197A|KRIT1_ENST00000394507.1_Missense_Mutation_p.T197A|KRIT1_ENST00000412043.2_Missense_Mutation_p.T197A|KRIT1_ENST00000394505.2_Missense_Mutation_p.T197A	NM_004912.3|NM_194455.1	NP_004903.2|NP_919437.1	O00522	KRIT1_HUMAN	KRIT1, ankyrin repeat containing	197					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)			CCTGATTCAGTAGCATATGCA	0.378																																					p.T197A		Atlas-SNP	.											.	KRIT1	66	.	0			c.A589G						PASS	.	T	ALA/THR,ALA/THR,ALA/THR,ALA/THR,ALA/THR	0,4406		0,0,2203	185	179	181		589,589,589,589,589	1.4	1	7	dbSNP_134	181	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense,missense,missense	KRIT1	NM_001013406.1,NM_004912.3,NM_194454.1,NM_194455.1,NM_194456.1	58,58,58,58,58	0,2,6501	CC,CT,TT		0.0233,0.0,0.0154	benign,benign,benign,benign,benign	197/689,197/737,197/737,197/737,197/737	91864857	2,13004	2203	4300	6503	SO:0001583	missense	889	exon9			ATTCAGTAGCATA	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.589A>G	7.37:g.91864857T>C	ENSP00000344668:p.Thr197Ala	110	0	0		118	61	0.516949	NM_194456	A6NNU0|O43894|Q506L6|Q6U276|Q75N19|Q9H180|Q9H264|Q9HAX5	Missense_Mutation	SNP	ENST00000340022.2	37	CCDS5624.1	.	.	.	.	.	.	.	.	.	.	T	9.752	1.167806	0.21621	0.0	2.33E-4	ENSG00000001631	ENST00000394507;ENST00000340022;ENST00000412043;ENST00000394505;ENST00000394503;ENST00000415227;ENST00000458177	T;T;T;T;T;D	0.85258	1.03;1.03;1.03;1.03;-0.48;-1.96	5.21	1.36	0.22044	.	0.546663	0.21326	N	0.076374	T	0.64405	0.2595	N	0.12182	0.205	0.24873	N	0.992278	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46707	-0.9172	10	0.09843	T	0.71	3.0499	4.3536	0.11167	0.1369:0.247:0.0:0.6161	.	197;197	A6NNU0;O00522	.;KRIT1_HUMAN	A	197	ENSP00000378015:T197A;ENSP00000344668:T197A;ENSP00000410909:T197A;ENSP00000378013:T197A;ENSP00000378011:T197A;ENSP00000391675:T197A	ENSP00000344668:T197A	T	-	1	0	KRIT1	91702793	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	1.687000	0.37680	-0.014000	0.14175	0.377000	0.23210	ACT	T|1.000;C|0.000	0.000	weak		0.378	KRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253910.1			C	91864857	T	C	91864857	3	2	24	1	0	0	0	0	1	0	0	0	8454	1638	57	3	1669	3	KRIT1	7	91864857	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	15724542	91864857	67273806	244	8461											
CALCR	799	hgsc.bcm.edu	37	chr7	93108763	93108763	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acgacgtaaagaaatggcttGggctctattgttggataggt	11	12	13	5	2	1	1	0	0	1	1	1	3	1	2	0	4	0	4	0	4	5	6	rs144326254	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:93108763G>C	ENST00000394441.1	-	3	423	c.108C>G	c.(106-108)ccC>ccG	p.P36P	CALCR_ENST00000359558.2_Silent_p.P54P|CALCR_ENST00000421592.1_Silent_p.P36P|CALCR_ENST00000360249.4_Silent_p.P36P|CALCR_ENST00000426151.1_Silent_p.P36P	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor	54					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)	GAAATGGCTTGGGCTCTATTG	0.418													G|||	27	0.00539137	0.0121	0.0072	5008	,	,		16950	0.0		0.006	False		,,,				2504	0.0				p.P54P		Atlas-SNP	.											.	CALCR	200	.	0			c.C162G						PASS	.	G	,,	35,4371	40.0+/-72.8	0,35,2168	179	168	171		162,108,108	-7.4	0	7	dbSNP_134	171	30,8570	21.6+/-65.8	0,30,4270	no	coding-synonymous,coding-synonymous,coding-synonymous	CALCR	NM_001164737.1,NM_001164738.1,NM_001742.3	,,	0,65,6438	CC,CG,GG		0.3488,0.7944,0.4998	,,	54/509,36/475,36/475	93108763	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	799	exon5			TGGCTTGGGCTCT	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.108C>G	7.37:g.93108763G>C		266	1	0.0037594		276	132	0.478261	NM_001164737	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Silent	SNP	ENST00000394441.1	37	CCDS5631.1																																																																																			G|0.995;C|0.005	0.005	strong		0.418	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742		C	93108763	G	C	93108763	2	2	24	1	0	0	0	0	0	0	0	1	2581	1335	47	4		4	CALCR	7	93108763	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1243906	93108763	66029900	245	8462											
TECPR1	25851	hgsc.bcm.edu	37	chr7	97852443	97852443	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccctgagggcgatggggggCacctccagccagggcccact	6	5	15	15	1	0	1	0	1	0	0	2	2	2	1	5	5	1	1	5	5	0	0	rs61745947	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:97852443C>T	ENST00000447648.2	-	21	3086	c.2787G>A	c.(2785-2787)gtG>gtA	p.V929V	TECPR1_ENST00000479975.1_5'UTR|TECPR1_ENST00000379795.3_Silent_p.V931V			Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	929					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						CGATGGGGGGCACCTCCAGCC	0.682													C|||	81	0.0161741	0.0008	0.0101	5008	,	,		10604	0.001		0.0219	False		,,,				2504	0.0511				p.V929V		Atlas-SNP	.											.	TECPR1	77	.	0			c.G2787A						PASS	.	C		16,4018		0,16,2001	20	26	24		2787	4	1	7	dbSNP_129	24	238,8088		4,230,3929	no	coding-synonymous	TECPR1	NM_015395.1		4,246,5930	TT,TC,CC		2.8585,0.3966,2.055		929/1166	97852443	254,12106	2017	4163	6180	SO:0001819	synonymous_variant	25851	exon21			GGGGGGCACCTCC		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.2787G>A	7.37:g.97852443C>T		118	0	0		96	50	0.520833	NM_015395	A8KAD1|B3KPZ1|C9J024|F5GX57|Q96EB0|Q9P2I9|Q9UFR6	Silent	SNP	ENST00000447648.2	37	CCDS47648.1																																																																																			C|0.985;T|0.015	0.015	strong		0.682	TECPR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334661.1	NM_015395		T	97852443	C	T	97852443	2	4	24	1	0	0	0	0	0	0	0	1	15758	697	25	2		2	TECPR1	7	97852443	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	4743680	97852443	61286220	246	8463											
PDAP1	11333	hgsc.bcm.edu	37	chr7	98997955	98997955	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcgaaagctcctttggcccGtccagatccagttgtgtgac	7	11	10	13	2	0	2	0	1	0	1	4	3	3	2	4	1	1	2	4	1	1	2	rs148987199		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:98997955G>A	ENST00000350498.3	-	4	586	c.306C>T	c.(304-306)gaC>gaT	p.D102D	PDAP1_ENST00000496335.1_5'Flank	NM_014891.6	NP_055706.1	Q13442	HAP28_HUMAN	PDGFA associated protein 1	102					cell proliferation (GO:0008283)|signal transduction (GO:0007165)		poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|ovary(2)|prostate(1)|skin(1)	9	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)			CCTTTGGCCCGTCCAGATCCA	0.552													G|||	1	0.000199681	0.0	0.0	5008	,	,		20454	0.0		0.001	False		,,,				2504	0.0				p.D102D		Atlas-SNP	.											.	PDAP1	17	.	0			c.C306T						PASS	.	G		0,4406		0,0,2203	168	123	138		306	-10.5	0.8	7	dbSNP_134	138	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PDAP1	NM_014891.6		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		102/182	98997955	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	11333	exon4			TGGCCCGTCCAGA	U41745	CCDS5662.1	7q	2008-07-18			ENSG00000106244	ENSG00000106244			14634	protein-coding gene	gene with protein product	"PDGF associated protein"	607075				8780057	Standard	NM_014891		Approved	PAP1, PAP, HASPP28	uc003uqe.3	Q13442	OTTHUMG00000154629	ENST00000350498.3:c.306C>T	7.37:g.98997955G>A		394	1	0.00253807		369	175	0.474255	NM_014891	D6W5S5|Q92906	Silent	SNP	ENST00000350498.3	37	CCDS5662.1																																																																																			G|1.000;A|0.000	0.000	strong		0.552	PDAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336388.2	NM_014891		A	98997955	G	A	98997955	2	1	24	1	0	0	0	0	0	0	0	1	11622	1136	40	1		1	PDAP1	7	98997955	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1145512	98997955	60140708	247	8464											
TFR2	7036	hgsc.bcm.edu	37	chr7	100226937	100226937	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agtatagccgtccccacagcGgatttagctgctcctgggcc	7	9	11	14	2	0	0	0	0	0	0	2	1	2	1	5	2	4	3	5	2	3	4	rs368298121		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:100226937G>A	ENST00000462107.1	-	11	1616	c.1329C>T	c.(1327-1329)tcC>tcT	p.S443S	TFR2_ENST00000431692.1_3'UTR|TFR2_ENST00000544242.1_5'UTR|TFR2_ENST00000223051.3_Silent_p.S443S			Q9UP52	TFR2_HUMAN	transferrin receptor 2	443					cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	transferrin receptor activity (GO:0004998)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(1)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	23	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)				Gallium nitrate(DB05260)	TCCCCACAGCGGATTTAGCTG	0.627																																					p.S443S		Atlas-SNP	.											TFR2,NS,carcinoma,-1,1	TFR2	53	1	0			c.C1329T						PASS	.	G	,	0,4406		0,0,2203	104	91	95		816,1329	-8.8	0.5	7		95	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	TFR2	NM_001206855.1,NM_003227.3	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	272/631,443/802	100226937	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	7036	exon10			CACAGCGGATTTA	AF053356	CCDS34707.1	7q22	2003-01-27			ENSG00000106327	ENSG00000106327			11762	protein-coding gene	gene with protein product		604720				9799793, 12130528	Standard	NM_003227		Approved	HFE3, TFRC2	uc003uvv.1	Q9UP52	OTTHUMG00000159598	ENST00000462107.1:c.1329C>T	7.37:g.100226937G>A		50	0	0		49	29	0.591837	NM_003227	A6NGM7|O75422|Q1HE13|Q9HA99|Q9NX67	Silent	SNP	ENST00000462107.1	37	CCDS34707.1																																																																																			.	.	weak		0.627	TFR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356392.3	NM_003227		A	100226937	G	A	100226937	2	1	24	1	0	0	0	0	0	0	0	1	15826	1103	39	1		1	TFR2	7	100226937	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1228982	100226937	58911726	248	8465											
RELN	5649	hgsc.bcm.edu	37	chr7	103205779	103205779	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tccaattctggaatctttccGaggtgtaaattgaactttcc	10	15	7	9	1	2	1	0	1	2	0	5	3	5	2	3	2	1	1	3	2	5	5	rs115913736	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:103205779G>A	ENST00000428762.1	-	34	5315	c.5156C>T	c.(5155-5157)tCg>tTg	p.S1719L	RELN_ENST00000343529.5_Missense_Mutation_p.S1719L|RELN_ENST00000424685.2_Missense_Mutation_p.S1719L	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1719					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)		GAATCTTTCCGAGGTGTAAAT	0.463													G|||	17	0.00339457	0.0008	0.0	5008	,	,		19094	0.0		0.0089	False		,,,				2504	0.0072				p.S1719L	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											RELN,NS,lymphoid_neoplasm,+1,1	RELN	593	1	0			c.C5156T						PASS	.	G	LEU/SER,LEU/SER	3,4403	6.2+/-15.9	0,3,2200	129	114	119		5156,5156	5.2	0.9	7	dbSNP_132	119	70,8530	42.2+/-99.7	2,66,4232	yes	missense,missense	RELN	NM_005045.3,NM_173054.2	145,145	2,69,6432	AA,AG,GG		0.814,0.0681,0.5613	probably-damaging,probably-damaging	1719/3461,1719/3459	103205779	73,12933	2203	4300	6503	SO:0001583	missense	5649	exon34			CTTTCCGAGGTGT		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.5156C>T	7.37:g.103205779G>A	ENSP00000392423:p.Ser1719Leu	127	0	0		110	45	0.409091	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	G	23.4	4.410786	0.83340	6.81E-4	0.00814	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.43688	1.75;0.94;1.75	6.02	5.15	0.70609	Neuraminidase (1);	0.066420	0.64402	N	0.000006	T	0.51261	0.1664	L	0.60455	1.87	0.54753	D	0.999988	D;D	0.76494	0.999;0.998	P;D	0.69307	0.889;0.963	T	0.56486	-0.7971	10	0.42905	T	0.14	.	15.254	0.73571	0.0668:0.0:0.9332:0.0	.	1719;1719	P78509-2;P78509	.;RELN_HUMAN	L	1719	ENSP00000392423:S1719L;ENSP00000345694:S1719L;ENSP00000388446:S1719L	ENSP00000345694:S1719L	S	-	2	0	RELN	102993015	1.000000	0.71417	0.913000	0.36048	0.978000	0.69477	9.139000	0.94554	1.569000	0.49696	0.655000	0.94253	TCG	G|0.994;A|0.006	0.006	strong		0.463	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		A	103205779	G	A	103205779	3	1	24	1	0	0	0	0	1	0	0	0	13235	1059	37	1	5354	1	RELN	7	103205779	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	2978842	103205779	55932884	249	8466											
PUS7	54517	hgsc.bcm.edu	37	chr7	105148683	105148683	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctgattcctcctcctcgcActcctctgaaagtccatctt	6	14	4	17	1	3	2	0	2	3	0	9	2	8	2	5	0	0	1	5	0	1	2	rs139058270	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:105148683A>G	ENST00000356362.2	-	2	491	c.277T>C	c.(277-279)Tgc>Cgc	p.C93R	PUS7_ENST00000469408.1_Missense_Mutation_p.C93R	NM_019042.3	NP_061915.2	Q96PZ0	PUS7_HUMAN	pseudouridylate synthase 7 (putative)	93					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						TCCTCCTCGCACTCCTCTGAA	0.493													A|||	8	0.00159744	0.0008	0.0014	5008	,	,		17461	0.0		0.006	False		,,,				2504	0.0				p.C93R	Colon(138;2387 3051 17860)	Atlas-SNP	.											.	PUS7	59	.	0			c.T277C						PASS	.	A	ARG/CYS	6,4400	11.4+/-27.6	0,6,2197	212	178	190		277	4.7	0.1	7	dbSNP_134	190	61,8539	38.3+/-94.2	0,61,4239	yes	missense	PUS7	NM_019042.3	180	0,67,6436	GG,GA,AA		0.7093,0.1362,0.5151	benign	93/662	105148683	67,12939	2203	4300	6503	SO:0001583	missense	54517	exon2			CCTCGCACTCCTC	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.277T>C	7.37:g.105148683A>G	ENSP00000348722:p.Cys93Arg	246	0	0		244	112	0.459016	NM_019042	Q75MG4|Q9NX19	Missense_Mutation	SNP	ENST00000356362.2	37	CCDS34725.1	6	0.0027472527472527475	1	0.0020325203252032522	0	0.0	0	0.0	5	0.006596306068601583	A	1.729	-0.494708	0.04322	0.001362	0.007093	ENSG00000091127	ENST00000356362;ENST00000544995;ENST00000469408	T;T	0.39592	1.07;1.07	5.58	4.69	0.59074	.	0.706924	0.14641	N	0.307220	T	0.15089	0.0364	N	0.08118	0	0.29644	N	0.844509	B;B	0.12630	0.006;0.006	B;B	0.09377	0.004;0.004	T	0.16424	-1.0403	10	0.16420	T	0.52	-6.8005	8.3068	0.32047	0.1631:0.759:0.0:0.0779	.	93;93	B3KY42;Q96PZ0	.;PUS7_HUMAN	R	93	ENSP00000348722:C93R;ENSP00000417402:C93R	ENSP00000348722:C93R	C	-	1	0	PUS7	104935919	0.000000	0.05858	0.097000	0.21041	0.261000	0.26267	0.758000	0.26447	1.326000	0.45319	-0.648000	0.03929	TGC	A|0.995;G|0.005	0.005	strong		0.493	PUS7-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348681.1	NM_019042		G	105148683	A	G	105148683	3	3	24	1	0	0	0	0	1	0	0	0	12848	159	6	3	1768	3	PUS7	7	105148683	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	1942904	105148683	53989980	250	8467											
CFTR	1080	hgsc.bcm.edu	37	chr7	117306991	117306991	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagaacaaagtgcggcagtaCgattccatccagaaactgct	14	7	10	10	2	0	2	0	0	0	2	2	4	2	2	2	1	5	3	2	1	4	2	rs1800135	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:117306991C>T	ENST00000003084.6	+	27	4404	c.4272C>T	c.(4270-4272)taC>taT	p.Y1424Y	CFTR_ENST00000454343.1_Silent_p.Y1363Y	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	1424	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				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)	TGCGGCAGTACGATTCCATCC	0.542									Cystic Fibrosis				C|||	21	0.00419329	0.0	0.0058	5008	,	,		17076	0.0		0.0139	False		,,,				2504	0.0031				p.Y1424Y		Atlas-SNP	.											.	CFTR	171	.	0			c.C4272T						PASS	.	C		9,4397	15.5+/-35.6	0,9,2194	59	51	54		4272	-9.6	0	7	dbSNP_89	54	58,8542	36.9+/-92.0	1,56,4243	no	coding-synonymous	CFTR	NM_000492.3		1,65,6437	TT,TC,CC		0.6744,0.2043,0.5151		1424/1481	117306991	67,12939	2203	4300	6503	SO:0001819	synonymous_variant	1080	exon27	Familial Cancer Database	CF	GCAGTACGATTCC	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.4272C>T	7.37:g.117306991C>T		218	1	0.00458716		191	92	0.481675	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Silent	SNP	ENST00000003084.6	37	CCDS5773.1																																																																																			C|0.994;T|0.006	0.006	strong		0.542	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492		T	117306991	C	T	117306991	2	4	24	1	0	0	0	0	0	0	0	1	3296	547	19	1		1	CFTR	7	117306991	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	12158308	117306991	41831672	251	8468											
RNF133	168433	hgsc.bcm.edu	37	chr7	122338664	122338664	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacctccccgttcaataagTgcaagccaggtctctgagta	11	9	8	13	1	2	1	1	1	1	0	4	1	3	1	4	1	3	3	4	1	5	3	rs373664210		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:122338664T>C	ENST00000340112.2	-	1	546	c.309A>G	c.(307-309)gcA>gcG	p.A103A	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	103	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						GTTCAATAAGTGCAAGCCAGG	0.458																																					p.A103A	Colon(198;1778 2057 7449 19869 45985)	Atlas-SNP	.											.	RNF133	41	.	0			c.A309G						PASS	.	T	,,,	0,4406		0,0,2203	155	165	162		,,,309	-5.2	0.7	7		162	2,8596	2.2+/-6.3	0,2,4297	no	intron,intron,intron,coding-synonymous	CADPS2,RNF133	NM_001009571.3,NM_001167940.1,NM_017954.10,NM_139175.1	,,,	0,2,6500	CC,CT,TT		0.0233,0.0,0.0154	,,,	,,,103/377	122338664	2,13002	2203	4299	6502	SO:0001819	synonymous_variant	168433	exon1			AATAAGTGCAAGC	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.309A>G	7.37:g.122338664T>C		167	0	0		153	69	0.45098	NM_139175	A4D0W2|Q8N7G7	Silent	SNP	ENST00000340112.2	37	CCDS5784.1																																																																																			.	.	weak		0.458	RNF133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347413.1	NM_139175		C	122338664	T	C	122338664	2	2	24	1	0	0	0	0	0	0	0	1	13454	1683	59	3		3	RNF133	7	122338664	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	5031673	122338664	36799999	252	8469											
TSGA14	95681	hgsc.bcm.edu	37	chr7	130038814	130038814	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cggggccgccacctggcagaTtctgagcgcttcgggcacca	6	6	14	15	4	1	2	0	1	1	1	2	2	1	2	4	4	1	3	4	4	0	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:130038814T>C	ENST00000223208.5	-	11	1310	c.1040A>G	c.(1039-1041)aAt>aGt	p.N347S	CEP41_ENST00000541543.1_Missense_Mutation_p.N259S|CEP41_ENST00000343969.5_Missense_Mutation_p.N275S	NM_001257158.1|NM_018718.2	NP_001244087.1|NP_061188.1	Q9BYV8	CEP41_HUMAN	centrosomal protein 41kDa	347					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)											ACCTGGCAGATTCTGAGCGCT	0.582																																					p.N347S		Atlas-SNP	.											.	.	.	.	0			c.A1040G						PASS	.						104	120	115					7																	130038814		2203	4300	6503	SO:0001583	missense	95681	exon11			GGCAGATTCTGAG	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.1040A>G	7.37:g.130038814T>C	ENSP00000223208:p.Asn347Ser	49	0	0		89	49	0.550562	NM_018718	A4D1M0|B4DQ35|F5H0V6|Q7Z496|Q86TM1|Q8NFU8|Q9H6A3|Q9NPV3	Missense_Mutation	SNP	ENST00000223208.5	37	CCDS5821.1	.	.	.	.	.	.	.	.	.	.	T	0.124	-1.121417	0.01785	.	.	ENSG00000106477	ENST00000223208;ENST00000541543;ENST00000343969	D;D;D	0.88586	-2.27;-2.08;-2.4	4.97	-6.65	0.01795	.	0.854162	0.10676	N	0.646990	T	0.67306	0.2879	N	0.04203	-0.255	0.09310	N	1	B;B;B	0.09022	0.001;0.002;0.0	B;B;B	0.06405	0.0;0.002;0.0	T	0.61647	-0.7020	10	0.08599	T	0.76	-0.4038	8.3272	0.32165	0.0:0.5135:0.2736:0.2129	.	259;275;347	F5H0V6;Q9BYV8-2;Q9BYV8	.;.;CEP41_HUMAN	S	347;259;275	ENSP00000223208:N347S;ENSP00000445888:N259S;ENSP00000342738:N275S	ENSP00000223208:N347S	N	-	2	0	TSGA14	129826050	0.807000	0.29009	0.020000	0.16555	0.048000	0.14542	-0.534000	0.06150	-0.868000	0.04058	-0.250000	0.11733	AAT	.	.	none		0.582	CEP41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349702.2	NM_018718		C	130038814	T	C	130038814	3	2	24	1	0	0	0	0	1	0	0	0	16635	1493	52	3	85	3	TSGA14	7	130038814	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	7700150	130038814	29099849	253	8470											
LRGUK	136332	hgsc.bcm.edu	37	chr7	133884016	133884016	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tattttgagcctcgttatatCctggtggtgcccatgaacaa	9	14	9	9	1	0	2	0	2	0	0	2	2	1	2	3	2	3	1	3	2	5	5	rs61749958		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:133884016C>T	ENST00000285928.2	+	14	1659	c.1590C>T	c.(1588-1590)atC>atT	p.I530I		NM_144648.1	NP_653249.1	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain containing	530	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.					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						CTCGTTATATCCTGGTGGTGC	0.368																																					p.I530I		Atlas-SNP	.											.	LRGUK	113	.	0			c.C1590T						PASS	.	C		0,4406		0,0,2203	93	98	96		1590	5.2	1	7	dbSNP_129	96	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	LRGUK	NM_144648.1		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		530/826	133884016	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	136332	exon14			TTATATCCTGGTG	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.1590C>T	7.37:g.133884016C>T		158	0	0		180	80	0.444444	NM_144648	Q2M3I1	Silent	SNP	ENST00000285928.2	37	CCDS5830.1																																																																																			C|1.000;T|0.000	0.000	weak		0.368	LRGUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339442.1	NM_144648		T	133884016	C	T	133884016	2	4	24	1	0	0	0	0	0	0	0	1	8952	845	30	2		2	LRGUK	7	133884016	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	3845202	133884016	25254647	254	8471											
AKR1B15	441282	hgsc.bcm.edu	37	chr7	134260595	134260595	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagtgtcacccatacctcaCgcaggagaaactgatccagt	12	8	9	12	1	2	3	2	2	0	1	3	4	3	3	3	1	2	1	3	1	2	1	rs141101327	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:134260595C>T	ENST00000457545.2	+	8	919	c.659C>T	c.(658-660)aCg>aTg	p.T220M	AKR1B15_ENST00000423958.1_Missense_Mutation_p.T192M	NM_001080538.2	NP_001074007.2	C9JRZ8	AK1BF_HUMAN	aldo-keto reductase family 1, member B15	220							oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|urinary_tract(1)	18						CCATACCTCACGCAGGAGAAA	0.537													C|||	31	0.0061901	0.0015	0.0072	5008	,	,		18433	0.0		0.0179	False		,,,				2504	0.0061				p.T220M		Atlas-SNP	.											.	AKR1B15	105	.	0			c.C659T						PASS	.	C	MET/THR	15,4391	20.2+/-43.8	0,15,2188	152	118	129		659	3	0.7	7	dbSNP_134	129	137,8463	67.7+/-130.1	0,137,4163	no	missense	AKR1B15	NM_001080538.2	81	0,152,6351	TT,TC,CC		1.593,0.3404,1.1687	probably-damaging	220/345	134260595	152,12854	2203	4300	6503	SO:0001583	missense	441282	exon8			ACCTCACGCAGGA		CCDS47715.1, CCDS47715.2	7q33	2009-09-09			ENSG00000227471	ENSG00000227471		"Aldo-keto reductases"	37281	protein-coding gene	gene with protein product							Standard	NM_001080538		Approved		uc011kpr.2	C9JRZ8	OTTHUMG00000155376	ENST00000457545.2:c.659C>T	7.37:g.134260595C>T	ENSP00000389289:p.Thr220Met	598	0	0		616	220	0.357143	NM_001080538	C9J3V2	Missense_Mutation	SNP	ENST00000457545.2	37	CCDS47715.2	19	0.0086996336996337	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	16	0.021108179419525065	C	11.82	1.754067	0.31046	0.003404	0.01593	ENSG00000227471	ENST00000457545;ENST00000423958	T;T	0.17854	2.25;2.25	3.87	2.98	0.34508	NADP-dependent oxidoreductase domain (3);	.	.	.	.	T	0.18173	0.0436	L	0.56199	1.76	0.39942	D	0.974421	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.01810	-1.1269	9	0.72032	D	0.01	.	8.189	0.31357	0.0:0.7958:0.0:0.2042	.	192;220	C9JRZ8-2;C9JRZ8	.;AK1BF_HUMAN	M	220;192	ENSP00000389289:T220M;ENSP00000397009:T192M	ENSP00000397009:T192M	T	+	2	0	AKR1B15	133911135	0.025000	0.19082	0.699000	0.30290	0.184000	0.23303	0.640000	0.24705	0.810000	0.34279	0.537000	0.68136	ACG	C|0.991;T|0.009	0.009	strong		0.537	AKR1B15-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339726.2			T	134260595	C	T	134260595	3	4	24	1	0	0	0	0	1	0	0	0	468	536	19	1	681	1	AKR1B15	7	134260595	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	376579	134260595	24878068	255	8472											
CNOT4	4850	hgsc.bcm.edu	37	chr7	135123060	135123060	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	actccacagggtcttccttcGcatcaggactgcgagacatc	9	9	9	14	2	2	1	1	0	1	1	6	3	4	2	2	2	1	1	2	2	0	2	rs17480616	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:135123060G>C	ENST00000315544.5	-	2	299	c.20C>G	c.(19-21)gCg>gGg	p.A7G	CNOT4_ENST00000423368.2_Missense_Mutation_p.A7G|CNOT4_ENST00000451834.1_Missense_Mutation_p.A7G|CNOT4_ENST00000541284.1_Missense_Mutation_p.A7G|CNOT4_ENST00000356162.4_Missense_Mutation_p.A7G|CNOT4_ENST00000361528.4_Missense_Mutation_p.A7G|CNOT4_ENST00000428680.2_Missense_Mutation_p.A7G|CNOT4_ENST00000414802.1_Missense_Mutation_p.A7G	NM_001190848.1	NP_001177777.1	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	7			A -> G (in dbSNP:rs17480616). {ECO:0000269|Ref.3}.		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						GTCTTCCTTCGCATCAGGACT	0.433													G|||	37	0.00738818	0.0023	0.0173	5008	,	,		17128	0.0		0.0209	False		,,,				2504	0.001				p.A7G	Ovarian(51;766 1130 5502 35047 50875)	Atlas-SNP	.											.	CNOT4	146	.	0			c.C20G						PASS	.	G	GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA	17,3759		0,17,1871	67	63	65		20,20,20,20,20,20	1.5	1	7	dbSNP_123	65	228,7992		4,220,3886	yes	missense,missense,missense,missense,missense,missense	CNOT4	NM_001008225.2,NM_001190847.1,NM_001190848.1,NM_001190849.1,NM_001190850.1,NM_013316.3	60,60,60,60,60,60	4,237,5757	CC,CG,GG		2.7737,0.4502,2.0423	benign,benign,benign,benign,benign,benign	7/573,7/643,7/576,7/711,7/714,7/640	135123060	245,11751	1888	4110	5998	SO:0001583	missense	4850	exon2			TCCTTCGCATCAG	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.20C>G	7.37:g.135123060G>C	ENSP00000326731:p.Ala7Gly	133	0	0		105	49	0.466667	NM_001190850	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Missense_Mutation	SNP	ENST00000315544.5	37	CCDS55166.1	27	0.012362637362637362	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	14	0.018469656992084433	G	12.53	1.964625	0.34659	0.004502	0.027737	ENSG00000080802	ENST00000541284;ENST00000451834;ENST00000423368;ENST00000262563;ENST00000361528;ENST00000414802;ENST00000356162;ENST00000428680;ENST00000315544	D;D;D;D;D;D;D;D	0.86164	-2.08;-2.08;-2.08;-2.08;-2.08;-2.08;-2.08;-2.08	5.87	1.55	0.23275	Zinc finger, RING/FYVE/PHD-type (1);	0.373548	0.33938	N	0.004417	T	0.50103	0.1596	N	0.14661	0.345	0.21290	N	0.999735	B;B;B;P;B;B	0.34997	0.211;0.315;0.405;0.479;0.019;0.019	B;B;B;B;B;B	0.31946	0.071;0.138;0.102;0.119;0.022;0.022	T	0.54063	-0.8349	10	0.32370	T	0.25	0.5143	9.3711	0.38254	0.4834:0.0:0.5166:0.0	rs17480616;rs52814664;rs17480616	7;7;7;7;7;7	E7ET38;F8VQP3;O95628;O95628-2;O95628-4;O95628-8	.;.;CNOT4_HUMAN;.;.;.	G	7	ENSP00000445508:A7G;ENSP00000388491:A7G;ENSP00000406777:A7G;ENSP00000354673:A7G;ENSP00000416532:A7G;ENSP00000348485:A7G;ENSP00000399108:A7G;ENSP00000326731:A7G	ENSP00000262563:A7G	A	-	2	0	CNOT4	134773600	0.999000	0.42202	0.976000	0.42696	0.929000	0.56500	1.442000	0.35046	-0.007000	0.14345	0.655000	0.94253	GCG	G|0.983;C|0.017	0.017	strong		0.433	CNOT4-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_013316		C	135123060	G	C	135123060	3	2	24	1	0	0	0	0	1	0	0	0	3623	1087	38	4	2044	4	CNOT4	7	135123060	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	862465	135123060	24015603	256	8473											
TBXAS1	6916	hgsc.bcm.edu	37	chr7	139717523	139717523	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccttcacgtacctgcccttcGgggccggcccacggagctgc	4	7	12	18	4	1	0	1	0	0	0	2	1	1	1	5	4	4	2	5	4	1	3	rs561266357|rs149988492	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:139717523G>T	ENST00000336425.5	+	16	1806	c.1417G>T	c.(1417-1419)Ggg>Tgg	p.G473W	TBXAS1_ENST00000263552.6_Missense_Mutation_p.G474W|TBXAS1_ENST00000436047.2_Missense_Mutation_p.G474W|TBXAS1_ENST00000458722.1_Missense_Mutation_p.G519W|TBXAS1_ENST00000416849.2_Missense_Mutation_p.G520W|TBXAS1_ENST00000414508.2_Intron|TBXAS1_ENST00000425687.1_Missense_Mutation_p.G406W|TBXAS1_ENST00000448866.1_Missense_Mutation_p.G473W|TBXAS1_ENST00000411653.1_Intron			P24557	THAS_HUMAN	thromboxane A synthase 1 (platelet)	473					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)	CCTGCCCTTCGGGGCCGGCCC	0.682																																					p.G520W		Atlas-SNP	.											.	TBXAS1	121	.	0			c.G1558T						PASS	.	G	TRP/GLY,TRP/GLY,TRP/GLY,TRP/GLY,	1,4405	2.1+/-5.4	0,1,2202	41	46	44		1420,1420,1558,1216,	4.7	0.3	7	dbSNP_134	44	0,8598		0,0,4299	no	missense,missense,missense,missense,intron	TBXAS1	NM_001061.4,NM_001130966.2,NM_001166253.1,NM_001166254.1,NM_030984.3	184,184,184,184,	0,1,6501	TT,TG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,	474/535,474/535,520/581,406/467,	139717523	1,13003	2203	4299	6502	SO:0001583	missense	6916	exon13			CCCTTCGGGGCCG	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.1417G>T	7.37:g.139717523G>T	ENSP00000338087:p.Gly473Trp	246	0	0		324	182	0.561728	NM_001166253	B4DJG6|E7EMU9|E7EP08|E7ESB5|O14987|Q16843|Q16844|Q8IUN1|Q96CN2|Q9GZW4|Q9HD77|Q9HD78|Q9HD79|Q9HD80|Q9HD81|Q9HD82|Q9HD83|Q9HD84	Missense_Mutation	SNP	ENST00000336425.5	37		.	.	.	.	.	.	.	.	.	.	G	22.0	4.228603	0.79576	2.27E-4	0.0	ENSG00000059377	ENST00000425687;ENST00000263552;ENST00000336425;ENST00000416849;ENST00000436047;ENST00000448866;ENST00000458722	T;T;T;T;T;T;T	0.80304	-1.36;-1.36;-1.36;-1.36;-1.36;-1.36;-1.36	4.69	4.69	0.59074	Cytochrome P450, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.93242	0.7847	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;1.0;1.0	D	0.95589	0.8653	10	0.87932	D	0	.	15.4076	0.74890	0.0:0.0:1.0:0.0	.	454;520;406;474;473	B4DVP1;E7EP08;E7ESB5;Q53F23;P24557	.;.;.;.;THAS_HUMAN	W	406;474;473;520;474;473;519	ENSP00000388736:G406W;ENSP00000263552:G474W;ENSP00000338087:G473W;ENSP00000389414:G520W;ENSP00000392361:G474W;ENSP00000402536:G473W;ENSP00000411274:G519W	ENSP00000263552:G474W	G	+	1	0	TBXAS1	139363992	1.000000	0.71417	0.334000	0.25495	0.882000	0.50991	6.773000	0.75006	2.162000	0.67917	0.561000	0.74099	GGG	G|1.000;T|0.000	0.000	strong		0.682	TBXAS1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000348373.1			T	139717523	G	T	139717523	3	4	24	1	0	0	0	0	1	0	0	0	15679	1116	39	4	1608	4	TBXAS1	7	139717523	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	4594463	139717523	19421140	257	8474											
BRAF	673	hgsc.bcm.edu	37	chr7	140449150	140449150	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcaattcatacagaacaatTccaaatgcatatacatctga	18	11	3	9	0	3	2	2	1	1	1	4	2	4	2	1	0	4	1	1	0	7	5	rs9648696	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:140449150T>C	ENST00000288602.6	-	16	1989	c.1929A>G	c.(1927-1929)ggA>ggG	p.G643G		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	643	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|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 stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	ACAGAACAATTCCAAATGCAT	0.348		61	"Mis, T, O"	"AKAP9, KIAA1549"	"melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome				C|||	1758	0.351038	0.7451	0.1585	5008	,	,		17576	0.1825		0.1531	False		,,,				2504	0.3323				p.G643G	Colon(40;35 892 2973 5743 27438)	Atlas-SNP	.		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	.	BRAF	36346	.	0			c.A1929G						PASS	.	C		2904,1502	476.8+/-357.7	963,978,262	105	108	107		1929	2.1	1	7	dbSNP_119	107	1258,7342	758.6+/-407.5	114,1030,3156	no	coding-synonymous	BRAF	NM_004333.4		1077,2008,3418	CC,CT,TT		14.6279,34.0899,32.0006		643/767	140449150	4162,8844	2203	4300	6503	SO:0001819	synonymous_variant	673	exon16	Familial Cancer Database	CFC, CFCS	AACAATTCCAAAT	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1929A>G	7.37:g.140449150T>C		167	0	0		138	65	0.471014	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Silent	SNP	ENST00000288602.6	37	CCDS5863.1	611	0.27976190476190477	355	0.7215447154471545	58	0.16022099447513813	91	0.1590909090909091	107	0.14116094986807387	C	9.723	1.160251	0.21454	0.659101	0.146279	ENSG00000157764	ENST00000496384	.	.	.	5.02	2.11	0.27256	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.33317	-0.9873	3	.	.	.	.	5.8585	0.18732	0.0:0.5864:0.1264:0.2872	rs9648696;rs10238189;rs60896634	.	.	.	G	251	.	.	E	-	2	0	BRAF	140095619	1.000000	0.71417	0.998000	0.56505	0.947000	0.59692	1.503000	0.35715	-0.010000	0.14271	-0.355000	0.07637	GAA	T|0.696;C|0.304	0.304	strong		0.348	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		C	140449150	T	C	140449150	2	2	24	1	0	0	0	0	0	0	0	1	1498	1770	62	3		3	BRAF	7	140449150	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	731627	140449150	18689513	258	8475											
TRPV6	55503	hgsc.bcm.edu	37	chr7	142574544	142574544	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgctcaatgagcagccgcacGatctcctcactgttcacaca	10	9	7	15	2	4	1	3	1	1	0	5	2	4	1	2	0	3	4	2	0	1	1	rs138110961	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:142574544G>A	ENST00000359396.3	-	5	779	c.534C>T	c.(532-534)atC>atT	p.I178I	RP11-114L10.2_ENST00000438839.1_RNA	NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	178					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)					GCAGCCGCACGATCTCCTCAC	0.597													G|||	3	0.000599042	0.0	0.0029	5008	,	,		20351	0.0		0.001	False		,,,				2504	0.0				p.I178I		Atlas-SNP	.											.	TRPV6	108	.	0			c.C534T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	101	86	91		534	-9.3	0	7	dbSNP_134	91	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	TRPV6	NM_018646.2		0,7,6496	AA,AG,GG		0.0698,0.0227,0.0538		178/726	142574544	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	55503	exon5			CCGCACGATCTCC	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.534C>T	7.37:g.142574544G>A		152	0	0		167	86	0.51497	NM_018646	A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Silent	SNP	ENST00000359396.3	37	CCDS5874.1																																																																																			G|0.999;A|0.001	0.001	strong		0.597	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274		A	142574544	G	A	142574544	2	1	24	1	0	0	0	0	0	0	0	1	16615	1048	37	1		1	TRPV6	7	142574544	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	2125394	142574544	16564119	259	8476											
CASP2	835	hgsc.bcm.edu	37	chr7	142988726	142988726	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagctgttgttgagcgaattGttagaacatcttctggagaa	11	13	11	6	1	2	3	0	1	2	2	2	5	2	3	0	1	3	4	0	1	4	5	rs4647288	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:142988726G>A	ENST00000310447.5	+	2	409	c.168G>A	c.(166-168)ttG>ttA	p.L56L	CASP2_ENST00000392925.2_Silent_p.L56L|CASP2_ENST00000493642.1_3'UTR|RN7SL535P_ENST00000479087.2_RNA	NM_032982.3|NM_032983.3	NP_116764.2|NP_116765.2	P42575	CASP2_HUMAN	caspase 2, apoptosis-related cysteine peptidase	56	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				aging (GO:0007568)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|brain development (GO:0007420)|cellular response to mechanical stimulus (GO:0071260)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|ectopic germ cell programmed cell death (GO:0035234)|execution phase of apoptosis (GO:0097194)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|luteolysis (GO:0001554)|neural retina development (GO:0003407)|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 neuron apoptotic process (GO:0043525)|protein processing (GO:0016485)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type endopeptidase activity involved in apoptotic process (GO:0097153)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)	21	Melanoma(164;0.059)					TGAGCGAATTGTTAGAACATC	0.448													G|||	58	0.0115815	0.0008	0.0202	5008	,	,		17867	0.0		0.0328	False		,,,				2504	0.0102				p.L56L		Atlas-SNP	.											.	CASP2	55	.	0			c.G168A						PASS	.	G	,,	35,4371	40.8+/-73.8	0,35,2168	189	191	190		75,168,168	2.8	1	7	dbSNP_111	190	272,8328	103.8+/-164.8	4,264,4032	no	coding-synonymous,coding-synonymous,coding-synonymous	CASP2	NM_001224.4,NM_032982.3,NM_032983.3	,,	4,299,6200	AA,AG,GG		3.1628,0.7944,2.3604	,,	25/313,56/453,56/109	142988726	307,12699	2203	4300	6503	SO:0001819	synonymous_variant	835	exon2			CGAATTGTTAGAA	AK096245, BC002427, BM998653, BX537669, CB988674, U13021	CCDS5879.1, CCDS47733.1	7q34-q35	2014-01-20	2008-08-01		ENSG00000106144	ENSG00000106144		"Caspases", "Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	1503	protein-coding gene	gene with protein product	"protein phosphatase 1, regulatory subunit 57"	600639	"neural precursor cell expressed, developmentally down-regulated 2"	NEDD2		7789948, 8780721	Standard	NM_032982		Approved	ICH1, PPP1R57, MGC2181	uc003wco.3	P42575	OTTHUMG00000023641	ENST00000310447.5:c.168G>A	7.37:g.142988726G>A		96	0	0		114	47	0.412281	NM_032982	A8K5F9|D3DXD6|E9PDN0|P42576|Q59F21|Q7KZL6|Q86UJ3|Q9BUP7|Q9BZK9|Q9BZL0	Silent	SNP	ENST00000310447.5	37	CCDS5879.1																																																																																			G|0.981;A|0.019	0.019	strong		0.448	CASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059962.3	NM_032982		A	142988726	G	A	142988726	2	1	24	1	0	0	0	0	0	0	0	1	2673	1368	48	2		2	CASP2	7	142988726	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	414182	142988726	16149937	260	8477											
C7orf29	113763	hgsc.bcm.edu	37	chr7	150027802	150027802	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaccactggaagcaagtcctCgtgtacaaggtgaaggagat	13	7	13	8	1	0	2	0	1	0	1	2	5	1	3	2	3	2	2	2	3	5	1	rs75555338	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:150027802C>T	ENST00000343855.4	+	1	865	c.309C>T	c.(307-309)ctC>ctT	p.L103L	LRRC61_ENST00000323078.7_Intron|LRRC61_ENST00000493307.1_Intron|LRRC61_ENST00000359623.4_Intron	NM_138434.2	NP_612443.1	Q96FA7	ZB6CL_HUMAN	ZBED6 C-terminal like	103																	AGCAAGTCCTCGTGTACAAGG	0.567													C|||	12	0.00239617	0.0008	0.0014	5008	,	,		19715	0.0		0.0099	False		,,,				2504	0.0				p.L103L		Atlas-SNP	.											.	C7orf29	18	.	0			c.C309T						PASS	.	C	,,	7,4399	12.9+/-30.5	0,7,2196	74	75	75		,,309	-7.5	0	7	dbSNP_133	75	138,8462	68.4+/-130.8	2,134,4164	no	intron,intron,coding-synonymous	LRRC61,C7orf29	NM_001142928.1,NM_023942.2,NM_138434.2	,,	2,141,6360	TT,TC,CC		1.6047,0.1589,1.1149	,,	,,103/237	150027802	145,12861	2203	4300	6503	SO:0001819	synonymous_variant	113763	exon1			AGTCCTCGTGTAC	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.309C>T	7.37:g.150027802C>T		82	0	0		111	53	0.477477	NM_138434		Silent	SNP	ENST00000343855.4	37	CCDS5900.1																																																																																			C|0.990;T|0.010	0.010	strong		0.567	ZBED6CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350702.1	NM_138434		T	150027802	C	T	150027802	2	4	24	1	0	0	0	0	0	0	0	1	2387	871	31	1		1	C7orf29	7	150027802	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	7039076	150027802	9110861	261	8478											
SLC4A2	6522	hgsc.bcm.edu	37	chr7	150768280	150768280	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcagggcgaggagctgctgcGctctgtggcccacttccagc	5	7	15	14	2	1	0	0	0	1	0	2	2	2	1	2	3	4	4	2	3	0	1	rs201086697		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:150768280G>A	ENST00000485713.1	+	13	2911	c.1871G>A	c.(1870-1872)cGc>cAc	p.R624H	SLC4A2_ENST00000310317.5_Missense_Mutation_p.R542H|SLC4A2_ENST00000413384.2_Missense_Mutation_p.R624H|SLC4A2_ENST00000392826.2_Missense_Mutation_p.R615H|SLC4A2_ENST00000461735.1_Missense_Mutation_p.R610H	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	624					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)		GAGCTGCTGCGCTCTGTGGCC	0.652													G|||	1	0.000199681	0.0	0.0	5008	,	,		15698	0.0		0.0	False		,,,				2504	0.001				p.R624H		Atlas-SNP	.											SLC4A2,NS,carcinoma,0,1	SLC4A2	98	1	0			c.G1871A						PASS	.						24	24	24					7																	150768280		2203	4299	6502	SO:0001583	missense	6522	exon13			TGCTGCGCTCTGT		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.1871G>A	7.37:g.150768280G>A	ENSP00000419412:p.Arg624His	132	0	0		106	48	0.45283	NM_003040	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Missense_Mutation	SNP	ENST00000485713.1	37	CCDS5917.1	.	.	.	.	.	.	.	.	.	.	G	13.93	2.382529	0.42207	.	.	ENSG00000164889	ENST00000485713;ENST00000413384;ENST00000310317;ENST00000392826;ENST00000461735	T;T;T;T;T	0.80214	-1.35;-1.35;-1.35;-1.35;-1.35	5.21	2.16	0.27623	Bicarbonate transporter, cytoplasmic (1);Phosphotransferase/anion transporter (1);	0.063739	0.64402	N	0.000005	T	0.67002	0.2847	L	0.38175	1.15	0.54753	D	0.999986	B;B;B	0.22480	0.07;0.031;0.031	B;B;B	0.18561	0.022;0.013;0.006	T	0.59925	-0.7362	10	0.46703	T	0.11	.	5.0009	0.14264	0.0834:0.1465:0.6191:0.151	.	615;610;624	F8W682;P04920-2;P04920	.;.;B3A2_HUMAN	H	624;624;542;615;610	ENSP00000419412:R624H;ENSP00000405600:R624H;ENSP00000311402:R542H;ENSP00000376571:R615H;ENSP00000419164:R610H	ENSP00000311402:R542H	R	+	2	0	SLC4A2	150399213	0.537000	0.26386	0.656000	0.29637	0.780000	0.44128	1.414000	0.34736	0.668000	0.31126	-0.145000	0.13849	CGC	.	.	weak		0.652	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040		A	150768280	G	A	150768280	3	1	24	1	0	0	0	0	1	0	0	0	14669	1087	38	1	1917	1	SLC4A2	7	150768280	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	740478	150768280	8370383	262	8479											
MLL3	58508	hgsc.bcm.edu	37	chr7	151970899	151970899	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taatgatacatctgggtacaTttctcttcacagcatttgat	11	16	6	8	0	3	2	1	2	2	0	4	2	3	2	0	1	3	2	0	1	3	6	rs577540910		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr7:151970899T>C	ENST00000262189.6	-	7	1121	c.903A>G	c.(901-903)aaA>aaG	p.K301K	KMT2C_ENST00000355193.2_Silent_p.K301K	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	301					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)										TCTGGGTACATTTCTCTTCAC	0.438													T|||	1	0.000199681	0.0	0.0	5008	,	,		26142	0.0		0.0	False		,,,				2504	0.001				p.K301K		Atlas-SNP	.											.	MLL3	1564	.	0			c.A903G						PASS	.						135	129	131					7																	151970899		2203	4300	6503	SO:0001819	synonymous_variant	58508	exon7			GGTACATTTCTCT	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.903A>G	7.37:g.151970899T>C		385	0	0		360	23	0.0638889	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Silent	SNP	ENST00000262189.6	37	CCDS5931.1																																																																																			.	.	none		0.438	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			C	151970899	T	C	151970899	2	2	24	1	0	0	0	0	0	0	0	1	9631	1490	52	3		3	MLL3	7	151970899	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	1202619	151970899	7167764	263	8480											
SOX7	83595	hgsc.bcm.edu	37	chr8	10583616	10583616	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggggacatcatggagacgcCgggggactggccaagggcca	10	3	18	10	2	1	1	1	0	0	1	1	4	1	3	3	7	0	0	3	7	1	0	rs180762782	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:10583616C>T	ENST00000304501.1	-	2	877	c.799G>A	c.(799-801)Ggc>Agc	p.G267S	SOX7_ENST00000554914.1_Missense_Mutation_p.G319S|SOX7_ENST00000553390.1_Missense_Mutation_p.G319S	NM_031439.2	NP_113627.1	Q9BT81	SOX7_HUMAN	SRY (sex determining region Y)-box 7	267					endoderm formation (GO:0001706)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|regulation of canonical Wnt signaling pathway (GO:0060828)|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)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20				COAD - Colon adenocarcinoma(149;0.0732)		ATGGAGACGCCGGGGGACTGG	0.672													C|||	6	0.00119808	0.0	0.0	5008	,	,		13618	0.0		0.006	False		,,,				2504	0.0				p.G267S		Atlas-SNP	.											.	SOX7	50	.	0			c.G799A						PASS	.	C	SER/GLY	5,4381		0,5,2188	23	30	27		799	2.9	0.4	8		27	73,8499		0,73,4213	yes	missense	SOX7	NM_031439.2	56	0,78,6401	TT,TC,CC		0.8516,0.114,0.6019	benign	267/389	10583616	78,12880	2193	4286	6479	SO:0001583	missense	83595	exon2			AGACGCCGGGGGA	AJ409320	CCDS5977.1	8p22	2013-01-25			ENSG00000171056	ENSG00000171056		"SRY (sex determining region Y)-boxes"	18196	protein-coding gene	gene with protein product		612202				11691915	Standard	NM_031439		Approved		uc003wtf.3	Q9BT81	OTTHUMG00000090585	ENST00000304501.1:c.799G>A	8.37:g.10583616C>T	ENSP00000301921:p.Gly267Ser	65	0	0		78	34	0.435897	NM_031439	B4DKV0|Q53YD0	Missense_Mutation	SNP	ENST00000304501.1	37	CCDS5977.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	6.489	0.458490	0.12342	0.00114	0.008516	ENSG00000171056;ENSG00000171056;ENSG00000258724	ENST00000304501;ENST00000553390;ENST00000554914	T;T;T	0.75477	-0.94;-0.94;-0.94	4.84	2.92	0.33932	.	0.176595	0.48286	N	0.000186	T	0.47192	0.1432	L	0.38531	1.155	0.20074	N	0.999936	P;B	0.52170	0.951;0.205	B;B	0.40134	0.32;0.023	T	0.49606	-0.8922	10	0.07644	T	0.81	.	7.2334	0.26055	0.0:0.6938:0.1419:0.1643	.	319;267	B4DKV0;Q9BT81	.;SOX7_HUMAN	S	267;319;319	ENSP00000301921:G267S;ENSP00000452017:G319S;ENSP00000451145:G319S	ENSP00000346908:G319S	G	-	1	0	SOX7;CTD-2135J3.4	10621026	0.000000	0.05858	0.377000	0.26055	0.354000	0.29330	-0.036000	0.12185	1.021000	0.39600	-0.379000	0.06801	GGC	C|0.997;T|0.003	0.003	strong		0.672	SOX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207131.1			T	10583616	C	T	10583616	3	4	24	1	0	0	0	0	1	0	0	0	14971	652	23	1	371	1	SOX7	8	10583616	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10		10583616	135780406	264	8481											
FAM86B1	85002	hgsc.bcm.edu	37	chr8	12044264	12044264	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctgcaaggtagagggcggCatcccatgtgaccaggcctg	8	8	14	11	1	1	2	0	1	1	1	2	2	2	2	3	4	1	3	3	4	2	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:12044264C>T	ENST00000448228.2	-	4	368	c.319G>A	c.(319-321)Gcc>Acc	p.A107T	FAM86B1_ENST00000534520.1_Missense_Mutation_p.A107T|FAM86B1_ENST00000321602.8_Start_Codon_SNP_p.M1I|FAM86B1_ENST00000533852.2_Missense_Mutation_p.A141T|FAM86B1_ENST00000533513.1_Missense_Mutation_p.A141T	NM_001083537.1	NP_001077006.1	Q8N7N1	F86B1_HUMAN	family with sequence similarity 86, member B1	107										kidney(1)|prostate(1)|stomach(1)	3			STAD - Stomach adenocarcinoma(15;0.033)	COAD - Colon adenocarcinoma(149;0.0965)		TAGAGGGCGGCATCCCATGTG	0.612																																					p.A107T		Atlas-SNP	.											FAM86B1,NS,carcinoma,+2,1	FAM86B1	7	1	0			c.G319A						scavenged	.						1	1	1					8																	12044264		461	1070	1531	SO:0001583	missense	85002	exon4			GGGCGGCATCCCA	BC007983	CCDS59512.1	8p23.1	2014-02-12	2005-08-19		ENSG00000186523	ENSG00000186523			28268	protein-coding gene	gene with protein product						12477932	Standard	NM_001083537		Approved	MGC16279	uc010lse.3	Q8N7N1	OTTHUMG00000165298	ENST00000448228.2:c.319G>A	8.37:g.12044264C>T	ENSP00000407067:p.Ala107Thr	533	0	0		559	35	0.0626118	NM_001083537		Missense_Mutation	SNP	ENST00000448228.2	37	CCDS59512.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	11.97|11.97	1.796969|1.796969	0.31777|0.31777	.|.	.|.	ENSG00000186523|ENSG00000186523	ENST00000431227;ENST00000340537;ENST00000448228;ENST00000534520;ENST00000526708;ENST00000524571;ENST00000533513|ENST00000321602;ENST00000526802	T;T;T;T;T|T	0.36340|0.24350	1.26;2.52;1.26;1.56;4.06|1.86	1.17|1.17	1.17|1.17	0.20885|0.20885	.|.	10.022600|.	0.01570|.	U|.	0.020538|.	T|T	0.33731|0.33731	0.0873|0.0873	M|M	0.90309|0.90309	3.105|3.105	0.80722|0.80722	D|D	1|1	P;P|B;B	0.46457|0.15719	0.878;0.749|0.014;0.003	D;P|B;B	0.64144|0.08055	0.922;0.624|0.003;0.002	T|T	0.42050|0.42050	-0.9474|-0.9474	10|9	0.72032|0.87932	D|D	0.01|0	.|.	8.2654|8.2654	0.31810|0.31810	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	107;141|1;38	Q8N7N1;E9PN63|F6QN85;Q4KMP3	F86B1_HUMAN;.|.;.	T|I	141;107;107;107;141;79;141|1;102	ENSP00000342610:A107T;ENSP00000407067:A107T;ENSP00000431362:A107T;ENSP00000432790:A79T;ENSP00000435201:A141T|ENSP00000439686:M1I	ENSP00000342610:A107T|ENSP00000439686:M1I	A|M	-|-	1|3	0|0	FAM86B1|FAM86B1	12081673|12081673	1.000000|1.000000	0.71417|0.71417	0.088000|0.088000	0.20740|0.20740	0.049000|0.049000	0.14656|0.14656	6.283000|6.283000	0.72646|0.72646	0.950000|0.950000	0.37743|0.37743	0.173000|0.173000	0.16961|0.16961	GCC|ATG	.	.	none		0.612	FAM86B1-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000383317.1	NM_032916		T	12044264	C	T	12044264	3	4	24	1	0	0	0	0	1	0	0	0	5652	710	25	2	587	2	FAM86B1	8	12044264	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1460648	12044264	134319758	265	8482											
DOK2	9046	hgsc.bcm.edu	37	chr8	21767042	21767042	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	catcgtatatgtggtcaggtCgagggggcagggtctcctca	7	10	15	9	2	3	0	2	0	1	0	6	1	3	0	1	5	0	2	1	5	2	2	rs372534431		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:21767042C>T	ENST00000276420.4	-	5	1277	c.1019G>A	c.(1018-1020)cGa>cAa	p.R340Q	DOK2_ENST00000544659.1_Missense_Mutation_p.R186Q	NM_003974.2	NP_003965.2	O60496	DOK2_HUMAN	docking protein 2, 56kDa	340	Pro-rich.				blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|leukocyte migration (GO:0050900)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)	receptor signaling protein activity (GO:0005057)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(3)|skin(1)	26				Colorectal(74;0.0145)|COAD - Colon adenocarcinoma(73;0.0608)		GTGGTCAGGTCGAGGGGGCAG	0.642																																					p.R340Q		Atlas-SNP	.											.	DOK2	51	.	0			c.G1019A						PASS	.	C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	54	51	52		1019	-7.8	0	8		52	0,8600		0,0,4300	no	missense	DOK2	NM_003974.2	43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	340/413	21767042	1,13005	2203	4300	6503	SO:0001583	missense	9046	exon5			TCAGGTCGAGGGG	AF034970	CCDS6016.1	8p21.3	2008-08-07	2002-08-29		ENSG00000147443	ENSG00000147443			2991	protein-coding gene	gene with protein product		604997	"docking protein 2, 56kD"			9478921, 14645010	Standard	NM_003974		Approved	p56dok-2, Dok-2	uc003wzy.1	O60496	OTTHUMG00000131075	ENST00000276420.4:c.1019G>A	8.37:g.21767042C>T	ENSP00000276420:p.Arg340Gln	100	0	0		94	40	0.425532	NM_003974	Q8N5A4	Missense_Mutation	SNP	ENST00000276420.4	37	CCDS6016.1	.	.	.	.	.	.	.	.	.	.	C	6.665	0.491294	0.12702	2.27E-4	0.0	ENSG00000147443	ENST00000276420;ENST00000544659	T;T	0.31247	1.91;1.5	5.42	-7.8	0.01214	.	2.171590	0.01745	N	0.029603	T	0.15522	0.0374	L	0.27053	0.805	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.04013	0.001;0.001	T	0.10823	-1.0613	10	0.27785	T	0.31	.	0.8219	0.01113	0.2645:0.1123:0.2445:0.3787	.	340;340	O60496;A8K7W1	DOK2_HUMAN;.	Q	340;186	ENSP00000276420:R340Q;ENSP00000443602:R186Q	ENSP00000276420:R340Q	R	-	2	0	DOK2	21822988	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.338000	0.07842	-1.129000	0.02918	-0.345000	0.07892	CGA	.	.	weak		0.642	DOK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253735.3	NM_003974		T	21767042	C	T	21767042	3	4	24	1	0	0	0	0	1	0	0	0	4699	884	31	1	223	1	DOK2	8	21767042	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	9722778	21767042	124596980	266	8483											
DUSP4	1846	hgsc.bcm.edu	37	chr8	29207692	29207692	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cgctcggcagccccagggtgCcgtggctgccgctgccgccc	2	5	15	19	5	0	0	0	0	0	0	1	0	0	0	6	3	4	4	6	3	0	0	rs527419472		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:29207692C>T	ENST00000240100.2	-	1	493	c.104G>A	c.(103-105)gGc>gAc	p.G35D	RP4-676L2.1_ENST00000567818.1_RNA|DUSP4_ENST00000240101.2_5'Flank	NM_001394.6	NP_001385.1	Q13115	DUS4_HUMAN	dual specificity phosphatase 4	35					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)		CCCCAGGGTGCCGTGGCTGCC	0.682																																					p.G35D		Atlas-SNP	.											.	DUSP4	58	.	0			c.G104A						PASS	.						11	15	14					8																	29207692		1933	3796	5729	SO:0001583	missense	1846	exon1			AGGGTGCCGTGGC	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.104G>A	8.37:g.29207692C>T	ENSP00000240100:p.Gly35Asp	12	0	0		17	9	0.529412	NM_001394	B2RBU5|D3DSU4|G5E930|Q13524	Missense_Mutation	SNP	ENST00000240100.2	37	CCDS6072.1	.	.	.	.	.	.	.	.	.	.	C	10.20	1.284687	0.23392	.	.	ENSG00000120875	ENST00000240100	T	0.02552	4.25	3.26	3.26	0.37387	Rhodanese-like (3);	0.000000	0.51477	D	0.000081	T	0.01523	0.0049	N	0.08118	0	0.80722	D	1	P	0.37233	0.588	B	0.19946	0.027	T	0.65841	-0.6070	10	0.51188	T	0.08	.	12.7539	0.57323	0.0:1.0:0.0:0.0	.	35	Q13115	DUS4_HUMAN	D	35	ENSP00000240100:G35D	ENSP00000240100:G35D	G	-	2	0	DUSP4	29263611	0.826000	0.29277	1.000000	0.80357	0.425000	0.31504	-0.265000	0.08644	2.101000	0.63845	0.491000	0.48974	GGC	.	.	none		0.682	DUSP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257249.1	NM_001394		T	29207692	C	T	29207692	3	4	24	1	0	0	0	0	1	0	0	0	4829	739	26	2	1260	2	DUSP4	8	29207692	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	7440650	29207692	117156330	267	8484											
TEX15	56154	hgsc.bcm.edu	37	chr8	30702739	30702739	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctaagactgatataagtacGtcagttttcgcctttgtgtg	9	16	9	7	2	2	2	1	1	1	1	3	2	2	2	1	0	1	2	1	0	4	7	rs117362953	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:30702739G>C	ENST00000256246.2	-	1	3869	c.3795C>G	c.(3793-3795)gaC>gaG	p.D1265E		NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	1265					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.D1265D(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)		ATATAAGTACGTCAGTTTTCG	0.333													G|||	9	0.00179712	0.0	0.0	5008	,	,		19980	0.0		0.008	False		,,,				2504	0.001				p.D1265E		Atlas-SNP	.											TEX15,NS,carcinoma,0,1	TEX15	350	1	1	Substitution - coding silent(1)	prostate(1)	c.C3795G						PASS	.	G	GLU/ASP	3,4403	6.2+/-15.9	0,3,2200	96	92	94		3795	-2.4	0	8	dbSNP_132	94	39,8559	25.7+/-73.6	0,39,4260	yes	missense	TEX15	NM_031271.3	45	0,42,6460	CC,CG,GG		0.4536,0.0681,0.323	possibly-damaging	1265/2790	30702739	42,12962	2203	4299	6502	SO:0001583	missense	56154	exon1			AAGTACGTCAGTT	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.3795C>G	8.37:g.30702739G>C	ENSP00000256246:p.Asp1265Glu	130	0	0		134	58	0.432836	NM_031271		Missense_Mutation	SNP	ENST00000256246.2	37	CCDS6080.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	G	10.11	1.259447	0.23051	6.81E-4	0.004536	ENSG00000133863	ENST00000256246	T	0.21932	1.98	5.92	-2.44	0.06502	.	0.178401	0.39759	N	0.001263	T	0.27313	0.0670	L	0.55481	1.735	0.09310	N	0.999999	D	0.89917	1.0	D	0.74674	0.984	T	0.19289	-1.0310	10	0.87932	D	0	.	12.5257	0.56085	0.5481:0.0:0.4519:0.0	.	1265	Q9BXT5	TEX15_HUMAN	E	1265	ENSP00000256246:D1265E	ENSP00000256246:D1265E	D	-	3	2	TEX15	30822281	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-1.182000	0.03082	-0.565000	0.06061	-0.797000	0.03246	GAC	G|0.997;C|0.003	0.003	strong		0.333	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1			C	30702739	G	C	30702739	3	2	24	1	0	0	0	0	1	0	0	0	15794	1136	40	4	4590	4	TEX15	8	30702739	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1495047	30702739	115661283	268	8485											
CHD7	55636	hgsc.bcm.edu	37	chr8	61767070	61767070	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaaagaacatttgccttctcGttttggcctaaggttggcag	9	13	11	8	1	1	1	0	0	1	1	2	2	1	1	2	3	2	3	2	3	3	6	rs61733338	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:61767070G>A	ENST00000423902.2	+	32	7403	c.6924G>A	c.(6922-6924)tcG>tcA	p.S2308S	CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	2308					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)	p.S2308S(2)		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)			TTGCCTTCTCGTTTTGGCCTA	0.423													G|||	12	0.00239617	0.0091	0.0	5008	,	,		19366	0.0		0.0	False		,,,				2504	0.0				p.S2308S		Atlas-SNP	.											CHD7_ENST00000423902,NS,carcinoma,0,2	CHD7	534	2	2	Substitution - coding silent(2)	prostate(2)	c.G6924A						PASS	.	G		22,3776		0,22,1877	220	199	206		6924	-4.3	1	8	dbSNP_129	206	0,8224		0,0,4112	no	coding-synonymous	CHD7	NM_017780.3		0,22,5989	AA,AG,GG		0.0,0.5793,0.183		2308/2998	61767070	22,12000	1899	4112	6011	SO:0001819	synonymous_variant	55636	exon32			CTTCTCGTTTTGG	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.6924G>A	8.37:g.61767070G>A		76	0	0		90	37	0.411111	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Silent	SNP	ENST00000423902.2	37	CCDS47865.1																																																																																			G|0.997;A|0.003	0.003	strong		0.423	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762		A	61767070	G	A	61767070	2	1	24	1	0	0	0	0	0	0	0	1	3332	1132	40	1		1	CHD7	8	61767070	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	31064331	61767070	84596952	269	8486											
PSKH2	85481	hgsc.bcm.edu	37	chr8	87060927	87060927	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggcctggccagctgacatgcGatgaccagcctccaaaatca	11	6	10	14	1	1	2	1	2	0	0	2	3	2	2	5	2	3	1	5	2	2	0			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:87060927G>A	ENST00000276616.2	-	3	996	c.922C>T	c.(922-924)Cgc>Tgc	p.R308C		NM_033126.1	NP_149117.1	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	308	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)			GCTGACATGCGATGACCAGCC	0.478																																					p.R308C		Atlas-SNP	.											PSKH2,caecum,carcinoma,+1,2	PSKH2	79	2	0			c.C922T						PASS	.						75	82	80					8																	87060927		2203	4300	6503	SO:0001583	missense	85481	exon3			ACATGCGATGACC	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.922C>T	8.37:g.87060927G>A	ENSP00000276616:p.Arg308Cys	131	0	0		127	61	0.480315	NM_033126	A0AV22	Missense_Mutation	SNP	ENST00000276616.2	37	CCDS6240.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.178342	0.78564	.	.	ENSG00000147613	ENST00000276616	T	0.80738	-1.41	4.94	4.05	0.47172	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.92938	0.7753	H	0.98646	4.29	0.46260	D	0.998955	D	0.89917	1.0	D	0.97110	1.0	D	0.93418	0.6774	9	0.87932	D	0	.	10.2011	0.43084	0.1009:0.0:0.8991:0.0	.	308	Q96QS6	KPSH2_HUMAN	C	308	ENSP00000276616:R308C	ENSP00000276616:R308C	R	-	1	0	PSKH2	87130043	1.000000	0.71417	0.998000	0.56505	0.986000	0.74619	3.946000	0.56644	1.034000	0.39945	0.555000	0.69702	CGC	.	.	none		0.478	PSKH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374628.1	NM_033126		A	87060927	G	A	87060927	3	1	24	1	0	0	0	0	1	0	0	0	12677	1058	37	1	237	1	PSKH2	8	87060927	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	25293857	87060927	59303095	270	8487											
POP1	10940	hgsc.bcm.edu	37	chr8	99146261	99146261	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggaatgtgtaacatagacAcaggtaaacttgttttaaag	15	12	9	5	0	0	1	0	0	0	1	0	2	0	2	0	2	2	3	0	2	7	6			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:99146261A>G	ENST00000401707.2	+	6	901	c.820A>G	c.(820-822)Aca>Gca	p.T274A	POP1_ENST00000349693.3_Missense_Mutation_p.T274A	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)	274					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)			TAACATAGACACAGGTAAACT	0.338																																					p.T274A		Atlas-SNP	.											POP1,NS,carcinoma,0,1	POP1	85	1	0			c.A820G						PASS	.						136	133	134					8																	99146261		2203	4300	6503	SO:0001583	missense	10940	exon6			ATAGACACAGGTA	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.820A>G	8.37:g.99146261A>G	ENSP00000385787:p.Thr274Ala	70	0	0		73	39	0.534247	NM_001145860	A8K5W9|Q15037	Missense_Mutation	SNP	ENST00000401707.2	37	CCDS6277.1	.	.	.	.	.	.	.	.	.	.	A	7.548	0.662067	0.14645	.	.	ENSG00000104356	ENST00000401707;ENST00000349693	T;T	0.35236	1.32;1.32	5.51	0.307	0.15811	.	0.441525	0.24174	N	0.040879	T	0.15912	0.0383	N	0.13235	0.315	0.36378	D	0.861726	B	0.02656	0.0	B	0.04013	0.001	T	0.37407	-0.9707	10	0.05525	T	0.97	0.0715	9.807	0.40799	0.6459:0.0:0.3541:0.0	.	274	Q99575	POP1_HUMAN	A	274	ENSP00000385787:T274A;ENSP00000339529:T274A	ENSP00000339529:T274A	T	+	1	0	POP1	99215437	0.205000	0.23458	0.931000	0.37212	0.838000	0.47535	0.840000	0.27600	-0.165000	0.10908	0.260000	0.18958	ACA	.	.	none		0.338	POP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379470.1	NM_015029		G	99146261	A	G	99146261	3	3	24	1	0	0	0	0	1	0	0	0	12260	159	6	3	838	3	POP1	8	99146261	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	12085334	99146261	47217761	271	8488											
TM7SF4	81501	hgsc.bcm.edu	37	chr8	105360994	105360994	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggattatcacgtgtgttctgCtgtgttgctccaagcatgca	7	14	11	9	1	2	0	1	0	1	0	3	1	3	1	1	1	4	6	1	1	2	3	rs61682032	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:105360994C>A	ENST00000297581.2	+	2	263	c.214C>A	c.(214-216)Ctg>Atg	p.L72M	DCSTAMP_ENST00000517991.1_Missense_Mutation_p.L72M|DPYS_ENST00000521601.1_Intron	NM_030788.3	NP_110415.1	Q9H295	DCSTP_HUMAN	dendrocyte expressed seven transmembrane protein	72					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)											GTGTGTTCTGCTGTGTTGCTC	0.522													C|||	179	0.0357428	0.0794	0.0144	5008	,	,		18689	0.0288		0.0189	False		,,,				2504	0.0164				p.L72M		Atlas-SNP	.											.	.	.	.	0			c.C214A						PASS	.	C	MET/LEU	252,4154	145.7+/-180.5	5,242,1956	129	117	121		214	4.1	0.8	8	dbSNP_129	121	73,8527	43.1+/-100.9	1,71,4228	yes	missense	TM7SF4	NM_030788.2	15	6,313,6184	AA,AC,CC		0.8488,5.7195,2.4988	probably-damaging	72/471	105360994	325,12681	2203	4300	6503	SO:0001583	missense	81501	exon2			GTTCTGCTGTGTT	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.214C>A	8.37:g.105360994C>A	ENSP00000297581:p.Leu72Met	157	0	0		172	81	0.47093	NM_001257317	B7ZVW2|E7ESG0|Q2M2D5	Missense_Mutation	SNP	ENST00000297581.2	37	CCDS6301.1	68	0.031135531135531136	32	0.06504065040650407	5	0.013812154696132596	19	0.033216783216783216	12	0.0158311345646438	C	14.48	2.548417	0.45383	0.057195	0.008488	ENSG00000164935	ENST00000297581;ENST00000517991	T	0.39229	1.09	5.84	4.05	0.47172	.	0.138356	0.49305	D	0.000154	T	0.08980	0.0222	M	0.64997	1.995	0.22779	N	0.998749	D	0.89917	1.0	D	0.79108	0.992	T	0.02437	-1.1159	9	.	.	.	-11.7717	8.7709	0.34731	0.0:0.7774:0.0:0.2226	rs61682032	72	Q9H295	TM7S4_HUMAN	M	72	ENSP00000297581:L72M	.	L	+	1	2	TM7SF4	105430170	.	.	0.761000	0.31378	0.580000	0.36256	.	.	1.496000	0.48567	0.655000	0.94253	CTG	C|0.973;A|0.027	0.027	strong		0.522	DCSTAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380810.1	NM_030788		A	105360994	C	A	105360994	3	1	24	1	0	0	0	0	1	0	0	0	15991	796	28	4	216	4	TM7SF4	8	105360994	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	6214733	105360994	41003028	272	8489											
TM7SF4	81501	hgsc.bcm.edu	37	chr8	105361803	105361803	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggttcacttgaaactgcaCggagaggtagggcccacagg	11	6	15	9	1	1	2	1	1	0	1	1	4	1	2	1	5	2	3	1	5	2	3	rs117086639	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:105361803C>T	ENST00000297581.2	+	2	1072	c.1023C>T	c.(1021-1023)caC>caT	p.H341H	DCSTAMP_ENST00000517991.1_Intron|DPYS_ENST00000521601.1_Intron	NM_030788.3	NP_110415.1	Q9H295	DCSTP_HUMAN	dendrocyte expressed seven transmembrane protein	341					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)											TGAAACTGCACGGAGAGGTAG	0.502													C|||	94	0.01877	0.0182	0.0086	5008	,	,		19755	0.0288		0.0169	False		,,,				2504	0.0184				p.H341H		Atlas-SNP	.											.	.	.	.	0			c.C1023T						PASS	.	C		39,4367	43.1+/-76.7	0,39,2164	99	100	100		1023	-2	0.6	8	dbSNP_132	100	69,8531	39.8+/-96.3	1,67,4232	no	coding-synonymous	TM7SF4	NM_030788.2		1,106,6396	TT,TC,CC		0.8023,0.8852,0.8304		341/471	105361803	108,12898	2203	4300	6503	SO:0001819	synonymous_variant	81501	exon2			ACTGCACGGAGAG	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.1023C>T	8.37:g.105361803C>T		84	0	0		80	45	0.5625	NM_030788	B7ZVW2|E7ESG0|Q2M2D5	Silent	SNP	ENST00000297581.2	37	CCDS6301.1																																																																																			C|0.989;T|0.011	0.011	strong		0.502	DCSTAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380810.1	NM_030788		T	105361803	C	T	105361803	2	4	24	1	0	0	0	0	0	0	0	1	15991	535	19	1		1	TM7SF4	8	105361803	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	809	105361803	41002219	273	8490											
CSMD3	114788	hgsc.bcm.edu	37	chr8	113364697	113364697	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atactacatctccaaccataTatctgtctccaattttaatt	13	16	1	11	0	3	0	0	0	3	0	5	0	3	0	3	0	3	0	3	0	7	7	rs139786530	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:113364697T>C	ENST00000297405.5	-	39	6447	c.6203A>G	c.(6202-6204)tAt>tGt	p.Y2068C	CSMD3_ENST00000352409.3_Missense_Mutation_p.Y1998C|CSMD3_ENST00000343508.3_Missense_Mutation_p.Y2028C|CSMD3_ENST00000455883.2_Missense_Mutation_p.Y1964C	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2068	Sushi 11. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.Y2028C(1)|p.Y2068C(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						TCCAACCATATATCTGTCTCC	0.343										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			T|||	3	0.000599042	0.0	0.0014	5008	,	,		16755	0.0		0.002	False		,,,				2504	0.0				p.Y2068C		Atlas-SNP	.											CSMD3_ENST00000343508,NS,carcinoma,0,2	CSMD3	2325	2	2	Substitution - Missense(2)	lung(2)	c.A6203G						PASS	.	T	CYS/TYR,CYS/TYR,CYS/TYR	2,4404	4.2+/-10.8	0,2,2201	110	103	105		5891,6203,6083	5	1	8	dbSNP_134	105	16,8582	11.2+/-40.8	0,16,4283	yes	missense,missense,missense	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	194,194,194	0,18,6484	CC,CT,TT		0.1861,0.0454,0.1384	probably-damaging,probably-damaging,probably-damaging	1964/3539,2068/3708,2028/3668	113364697	18,12986	2203	4299	6502	SO:0001583	missense	114788	exon39			ACCATATATCTGT	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.6203A>G	8.37:g.113364697T>C	ENSP00000297405:p.Tyr2068Cys	135	0	0		141	48	0.340426	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	18.72	3.684011	0.68157	4.54E-4	0.001861	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.69926	-0.44;-0.44;-0.44;-0.44;-0.44	4.96	4.96	0.65561	Complement control module (2);Sushi/SCR/CCP (3);	0.084638	0.49305	D	0.000151	D	0.85652	0.5746	M	0.93808	3.46	0.50467	D	0.999878	D;D;D	0.76494	0.999;0.996;0.999	D;D;D	0.72625	0.959;0.926;0.978	D	0.89488	0.3755	10	0.72032	D	0.01	.	15.0773	0.72087	0.0:0.0:0.0:1.0	.	1964;2068;2028	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	C	2028;2068;1338;1964;1998	ENSP00000345799:Y2028C;ENSP00000297405:Y2068C;ENSP00000341558:Y1338C;ENSP00000412263:Y1964C;ENSP00000343124:Y1998C	ENSP00000297405:Y2068C	Y	-	2	0	CSMD3	113433873	1.000000	0.71417	0.980000	0.43619	0.996000	0.88848	5.007000	0.63984	2.205000	0.71048	0.533000	0.62120	TAT	T|0.999;C|0.001	0.001	strong		0.343	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		C	113364697	T	C	113364697	3	2	24	1	0	0	0	0	1	0	0	0	3948	1406	49	3	5052	3	CSMD3	8	113364697	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	8002894	113364697	32999325	274	8491											
CSMD3	114788	hgsc.bcm.edu	37	chr8	113395826	113395826	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaagtcttggagcattgtTgtctcccccatcataaaagt	10	13	7	11	0	3	0	1	0	2	0	5	1	4	1	3	1	1	2	3	1	3	4			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:113395826T>C	ENST00000297405.5	-	37	6245	c.6001A>G	c.(6001-6003)Aac>Gac	p.N2001D	CSMD3_ENST00000352409.3_Missense_Mutation_p.N1931D|CSMD3_ENST00000343508.3_Missense_Mutation_p.N1961D|CSMD3_ENST00000455883.2_Missense_Mutation_p.N1897D	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2001	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						GGAGCATTGTTGTCTCCCCCA	0.323										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.N2001D		Atlas-SNP	.											.	CSMD3	2325	.	0			c.A6001G						PASS	.						84	82	83					8																	113395826		2203	4300	6503	SO:0001583	missense	114788	exon37			CATTGTTGTCTCC	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.6001A>G	8.37:g.113395826T>C	ENSP00000297405:p.Asn2001Asp	173	0	0		200	102	0.51	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	T	18.08	3.543166	0.65198	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.17054	2.3;2.3;2.3;2.3;2.3	4.42	4.42	0.53409	CUB (5);	0.269490	0.36409	N	0.002617	T	0.19046	0.0457	N	0.15975	0.35	0.39770	D	0.972152	P;B;D	0.60575	0.913;0.083;0.988	B;B;P	0.61201	0.431;0.174;0.885	T	0.07328	-1.0778	10	0.10636	T	0.68	.	14.1168	0.65159	0.0:0.0:0.0:1.0	.	1897;2001;1961	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	D	1961;2001;1271;1897;1931	ENSP00000345799:N1961D;ENSP00000297405:N2001D;ENSP00000341558:N1271D;ENSP00000412263:N1897D;ENSP00000343124:N1931D	ENSP00000297405:N2001D	N	-	1	0	CSMD3	113465002	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.040000	0.57333	1.975000	0.57531	0.383000	0.25322	AAC	.	.	none		0.323	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		C	113395826	T	C	113395826	3	2	24	1	0	0	0	0	1	0	0	0	3948	1812	63	3	5262	3	CSMD3	8	113395826	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	31129	113395826	32968196	275	8492											
ZHX2	22882	hgsc.bcm.edu	37	chr8	123964011	123964011	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaatactgcccctactccacGcaaaacctgaacgagttcac	14	7	5	15	2	1	1	1	1	0	0	2	2	2	1	4	0	5	2	4	0	6	3	rs61752912	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:123964011G>A	ENST00000314393.4	+	3	1096	c.261G>A	c.(259-261)acG>acA	p.T87T		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	87					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)			CCTACTCCACGCAAAACCTGA	0.468													G|||	115	0.0229633	0.0424	0.0331	5008	,	,		20913	0.0		0.0298	False		,,,				2504	0.0061				p.T87T	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											.	ZHX2	106	.	0			c.G261A						PASS	.	G		174,4232	114.6+/-152.6	5,164,2034	89	81	84		261	-6.5	0.7	8	dbSNP_129	84	278,8322	105.6+/-166.5	6,266,4028	no	coding-synonymous	ZHX2	NM_014943.3		11,430,6062	AA,AG,GG		3.2326,3.9492,3.4753		87/838	123964011	452,12554	2203	4300	6503	SO:0001819	synonymous_variant	22882	exon3			CTCCACGCAAAAC	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.261G>A	8.37:g.123964011G>A		41	0	0		52	18	0.346154	NM_014943		Silent	SNP	ENST00000314393.4	37	CCDS6336.1																																																																																			G|0.965;A|0.035	0.035	strong		0.468	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943		A	123964011	G	A	123964011	2	1	24	1	0	0	0	0	0	0	0	1	17691	1074	38	1		1	ZHX2	8	123964011	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	10568185	123964011	22400011	276	8493											
ZHX2	22882	hgsc.bcm.edu	37	chr8	123965193	123965193	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgactggccttgccaggagCgagatcaagaagtggttcag	10	8	15	8	1	2	3	2	1	0	2	2	5	2	4	2	3	2	1	2	3	2	2	rs111726812	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:123965193C>T	ENST00000314393.4	+	3	2278	c.1443C>T	c.(1441-1443)agC>agT	p.S481S		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	481	Required for interaction with NFYA.				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)			TTGCCAGGAGCGAGATCAAGA	0.567													C|||	116	0.0231629	0.0439	0.0317	5008	,	,		18163	0.0		0.0298	False		,,,				2504	0.0061				p.S481S	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											ZHX2,caecum,carcinoma,0,1	ZHX2	106	1	0			c.C1443T						scavenged	.	C		179,4227	116.7+/-154.6	5,169,2029	88	82	84		1443	-8.1	0.7	8	dbSNP_132	84	278,8322	105.4+/-166.3	6,266,4028	no	coding-synonymous	ZHX2	NM_014943.3		11,435,6057	TT,TC,CC		3.2326,4.0626,3.5138		481/838	123965193	457,12549	2203	4300	6503	SO:0001819	synonymous_variant	22882	exon3			CAGGAGCGAGATC	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.1443C>T	8.37:g.123965193C>T		70	1	0.0142857		70	32	0.457143	NM_014943		Silent	SNP	ENST00000314393.4	37	CCDS6336.1																																																																																			C|0.965;T|0.035	0.035	strong		0.567	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943		T	123965193	C	T	123965193	2	4	24	1	0	0	0	0	0	0	0	1	17691	767	27	1		1	ZHX2	8	123965193	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1182	123965193	22398829	277	8494											
COL22A1	169044	hgsc.bcm.edu	37	chr8	139712355	139712355	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggcaccgctactacttacGggcatccgtggatgtggtgt	7	10	14	10	3	0	0	0	0	0	0	1	2	1	1	2	4	3	3	2	4	3	3	rs77613350	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:139712355G>A	ENST00000303045.6	-	32	3038	c.2592C>T	c.(2590-2592)ccC>ccT	p.P864P	COL22A1_ENST00000435777.1_Splice_Site_p.P864P|COL22A1_ENST00000341807.4_5'UTR	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	864	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)			TACTACTTACGGGCATCCGTG	0.552										HNSCC(7;0.00092)			G|||	168	0.0335463	0.0787	0.0187	5008	,	,		17017	0.0278		0.0189	False		,,,				2504	0.0041				p.P864P		Atlas-SNP	.											.	COL22A1	390	.	0			c.C2592T						PASS	.	G		268,4138	151.4+/-185.3	5,258,1940	80	69	73		2592	-8.3	0	8	dbSNP_131	73	138,8462	68.0+/-130.5	1,136,4163	yes	coding-synonymous-near-splice	COL22A1	NM_152888.1		6,394,6103	AA,AG,GG		1.6047,6.0826,3.1216		864/1627	139712355	406,12600	2203	4300	6503	SO:0001630	splice_region_variant	169044	exon32			ACTTACGGGCATC	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.2592+1C>T	8.37:g.139712355G>A		52	0	0		56	26	0.464286	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Silent	SNP	ENST00000303045.6	37	CCDS6376.1																																																																																			G|0.967;A|0.033	0.033	strong		0.552	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	Silent	A	139712355	G	A	139712355	5	1	24	1	0	0	0	0	0	0	1	0	3683	1130	39	1	2424	1	COL22A1	8	139712355	Splice_Site	SNP	G	TCGA-G8-6326-01A-11D-2210-10	15747162	139712355	6651667	278	8495											
SLURP1	57152	hgsc.bcm.edu	37	chr8	143823241	143823241	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcctccaccgtcaccagcGtggtcatgcaggctgtgtcc	5	9	11	16	2	2	0	2	0	0	0	4	0	4	0	5	2	3	2	5	2	0	0			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:143823241G>A	ENST00000246515.1	-	2	183	c.158C>T	c.(157-159)aCg>aTg	p.T53M		NM_020427.2	NP_065160.1	P55000	SLUR1_HUMAN	secreted LY6/PLAUR domain containing 1	53	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)					CGTCACCAGCGTGGTCATGCA	0.652																																					p.T53M		Atlas-SNP	.											SLURP1,NS,carcinoma,0,1	SLURP1	16	1	0			c.C158T						PASS	.						100	87	91					8																	143823241		2203	4299	6502	SO:0001583	missense	57152	exon2			ACCAGCGTGGTCA	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.158C>T	8.37:g.143823241G>A	ENSP00000246515:p.Thr53Met	56	0	0		53	26	0.490566	NM_020427	Q53YJ6|Q6PUA6|Q92483	Missense_Mutation	SNP	ENST00000246515.1	37	CCDS6387.1	.	.	.	.	.	.	.	.	.	.	G	13.36	2.212927	0.39102	.	.	ENSG00000126233	ENST00000246515	T	0.70749	-0.51	4.17	-1.92	0.07618	Ly-6 antigen / uPA receptor -like (1);CD59 antigen (1);	1.602070	0.04459	N	0.374005	T	0.66137	0.2759	M	0.78456	2.415	0.09310	N	1	B	0.34313	0.448	B	0.29440	0.102	T	0.55623	-0.8112	10	0.72032	D	0.01	-20.1734	3.9364	0.09307	0.2058:0.0:0.356:0.4382	.	53	P55000	SLUR1_HUMAN	M	53	ENSP00000246515:T53M	ENSP00000246515:T53M	T	-	2	0	SLURP1	143820243	0.000000	0.05858	0.001000	0.08648	0.057000	0.15508	-0.051000	0.11885	-0.259000	0.09432	-0.704000	0.03662	ACG	.	.	none		0.652	SLURP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379741.1	NM_020427		A	143823241	G	A	143823241	3	1	24	1	0	0	0	0	1	0	0	0	14771	1145	40	1	161	1	SLURP1	8	143823241	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	4110886	143823241	2540781	279	8496											
EPPK1	83481	hgsc.bcm.edu	37	chr8	144944379	144944379	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agacacctgcttcccagagaAggggtctctgaagccagcaa	12	6	11	12	0	1	3	0	1	1	2	3	4	2	3	3	2	3	2	3	2	3	1			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:144944379A>G	ENST00000525985.1	-	2	3114	c.3043T>C	c.(3043-3045)Ttc>Ctc	p.F1015L				P58107	EPIPL_HUMAN	epiplakin 1	1015						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)			TTCCCAGAGAAGGGGTCTCTG	0.637																																					p.F1015L		Atlas-SNP	.											.	EPPK1	199	.	0			c.T3043C						PASS	.						14	17	16					8																	144944379		2067	4201	6268	SO:0001583	missense	83481	exon1			CAGAGAAGGGGTC	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.3043T>C	8.37:g.144944379A>G	ENSP00000436337:p.Phe1015Leu	68	0	0		68	32	0.470588	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		.	.	.	.	.	.	.	.	.	.	A	22.5	4.295045	0.81025	.	.	ENSG00000227184	ENST00000525985	T	0.67523	-0.27	4.67	3.52	0.40303	.	.	.	.	.	T	0.51890	0.1701	L	0.39898	1.24	0.24399	N	0.994711	B	0.16166	0.016	B	0.10450	0.005	T	0.35649	-0.9780	9	0.09843	T	0.71	.	8.3157	0.32100	0.9051:0.0:0.0949:0.0	.	1015	E9PPU0	.	L	1015	ENSP00000436337:F1015L	ENSP00000436337:F1015L	F	-	1	0	EPPK1	145016367	1.000000	0.71417	0.481000	0.27354	0.918000	0.54935	6.916000	0.75776	0.809000	0.34255	0.533000	0.62120	TTC	.	.	none		0.637	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		G	144944379	A	G	144944379	3	3	24	1	0	0	0	0	1	0	0	0	5192	72	3	3	4223	3	EPPK1	8	144944379	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	1121138	144944379	1419643	280	8497											
NFKBIL2	4796	hgsc.bcm.edu	37	chr8	145657840	145657840	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acagggtcttcaggtgctcaGcatctgcaccggggccagaa	9	7	13	12	1	4	1	2	0	2	1	4	1	4	1	2	4	3	3	2	4	1	1	rs146566654	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr8:145657840G>A	ENST00000409379.3	-	23	3592	c.3563C>T	c.(3562-3564)gCt>gTt	p.A1188V	AC084125.4_ENST00000544423.1_RNA	NM_013432.4	NP_038460.4	Q96HA7	TONSL_HUMAN	tonsoku-like, DNA repair protein	1188					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						CAGGTGCTCAGCATCTGCACC	0.667													G|||	2	0.000399361	0.0	0.0	5008	,	,		15419	0.0		0.0	False		,,,				2504	0.002				p.A1188V		Atlas-SNP	.											.	TONSL	128	.	0			c.C3563T						PASS	.	G	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	49	56	54		3563	5	0.9	8	dbSNP_134	54	8,8592	6.4+/-24.3	0,8,4292	yes	missense	TONSL	NM_013432.4	64	0,9,6494	AA,AG,GG		0.093,0.0227,0.0692	possibly-damaging	1188/1379	145657840	9,12997	2203	4300	6503	SO:0001583	missense	4796	exon23			TGCTCAGCATCTG		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.3563C>T	8.37:g.145657840G>A	ENSP00000386239:p.Ala1188Val	113	0	0		114	55	0.482456	NM_013432	B5MDP0|C9JKB1|C9JNV8|Q13006|Q9UGJ2	Missense_Mutation	SNP	ENST00000409379.3	37	CCDS34968.2	.	.	.	.	.	.	.	.	.	.	g	0.591	-0.833165	0.02713	2.27E-4	9.3E-4	ENSG00000160949	ENST00000409379;ENST00000422691	T	0.52526	0.66	4.99	4.99	0.66335	.	0.277567	0.33650	N	0.004684	T	0.44953	0.1318	L	0.51853	1.615	0.40916	D	0.984272	B	0.25390	0.125	B	0.22753	0.041	T	0.48175	-0.9058	10	0.66056	D	0.02	-9.63	15.8111	0.78565	0.0:0.0:1.0:0.0	.	1188	Q96HA7	TONSL_HUMAN	V	1188;1187	ENSP00000386239:A1188V	ENSP00000386239:A1188V	A	-	2	0	TONSL	145628648	0.970000	0.33590	0.868000	0.34077	0.114000	0.19823	2.838000	0.48199	2.324000	0.78689	0.456000	0.33151	GCT	G|1.000;A|0.000	0.000	strong		0.667	TONSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329668.2	NM_013432		A	145657840	G	A	145657840	3	1	24	1	0	0	0	0	1	0	0	0	10391	971	34	2	589	2	NFKBIL2	8	145657840	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	713461	145657840	706182	281	8498											
KANK1	23189	hgsc.bcm.edu	37	chr9	738503	738503	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgaagctgctgttagatgcCggtatgttggctgcccttcc	5	13	13	10	1	0	2	0	1	0	1	1	2	1	2	3	2	4	6	3	2	3	4			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:738503C>T	ENST00000382303.1	+	12	4204	c.3552C>T	c.(3550-3552)gcC>gcT	p.A1184A	KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382293.3_Splice_Site_p.A1026A|KANK1_ENST00000382297.2_Splice_Site_p.A1184A	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	1184	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)		TGTTAGATGCCGGTATGTTGG	0.517																																					p.A1184A		Atlas-SNP	.											.	KANK1	231	.	0			c.C3552T						PASS	.						103	78	87					9																	738503		2203	4300	6503	SO:0001630	splice_region_variant	23189	exon12			AGATGCCGGTATG	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.3553+1C>T	9.37:g.738503C>T		134	0	0		118	52	0.440678	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Silent	SNP	ENST00000382303.1	37	CCDS34976.1																																																																																			.	.	none		0.517	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158	Silent	T	738503	C	T	738503	5	4	24	1	0	0	0	0	0	0	1	0	7985	666	23	1	3578	1	KANK1	9	738503	Splice_Site	SNP	C	TCGA-G8-6326-01A-11D-2210-10		738503	140474928	282	8499											
DMRT2	10655	hgsc.bcm.edu	37	chr9	1056569	1056569	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taatttcttctaatgtcagcGtggccacaacttatagacag	12	13	7	9	1	3	1	1	0	2	1	3	1	3	1	1	1	2	0	1	1	5	6	rs140004479	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:1056569G>A	ENST00000358146.2	+	3	982	c.982G>A	c.(982-984)Gtg>Atg	p.V328M	DMRT2_ENST00000259622.6_3'UTR|DMRT2_ENST00000382255.3_3'UTR|DMRT2_ENST00000302441.6_Missense_Mutation_p.V328M|DMRT2_ENST00000382251.3_Missense_Mutation_p.V328M			Q9Y5R5	DMRT2_HUMAN	doublesex and mab-3 related transcription factor 2	328					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)		TAATGTCAGCGTGGCCACAAC	0.458													G|||	7	0.00139776	0.0008	0.0014	5008	,	,		21074	0.0		0.005	False		,,,				2504	0.0				p.V328M		Atlas-SNP	.											.	DMRT2	70	.	0			c.G982A						PASS	.	G	,,MET/VAL	5,4401	9.9+/-24.2	0,5,2198	96	101	99		,,982	5.6	1	9	dbSNP_134	99	35,8565	23.4+/-69.3	0,35,4265	yes	utr-3,utr-3,missense	DMRT2	NM_001130865.2,NM_006557.6,NM_181872.4	,,21	0,40,6463	AA,AG,GG		0.407,0.1135,0.3076	,,probably-damaging	,,328/562	1056569	40,12966	2203	4300	6503	SO:0001583	missense	10655	exon4			GTCAGCGTGGCCA	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.982G>A	9.37:g.1056569G>A	ENSP00000350865:p.Val328Met	99	0	0		129	75	0.581395	NM_181872	B1ANC0|B9EGJ1|Q9NPG6|Q9NQR6	Missense_Mutation	SNP	ENST00000358146.2	37	CCDS6444.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	20.8	4.048378	0.75846	0.001135	0.00407	ENSG00000173253	ENST00000382251;ENST00000302441;ENST00000358146	T;T;T	0.38240	1.15;1.15;1.15	5.62	5.62	0.85841	.	0.121836	0.56097	D	0.000039	T	0.60483	0.2272	M	0.64404	1.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.61579	-0.7034	10	0.87932	D	0	-22.0227	19.2806	0.94051	0.0:0.0:1.0:0.0	.	328;172	Q9Y5R5;Q5HYK2	DMRT2_HUMAN;.	M	328	ENSP00000371686:V328M;ENSP00000305785:V328M;ENSP00000350865:V328M	ENSP00000305785:V328M	V	+	1	0	DMRT2	1046569	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	9.230000	0.95299	2.665000	0.90641	0.650000	0.86243	GTG	G|0.997;A|0.003	0.003	strong		0.458	DMRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051492.1	NM_006557		A	1056569	G	A	1056569	3	1	24	1	0	0	0	0	1	0	0	0	4588	1145	40	1	1049	1	DMRT2	9	1056569	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	318066	1056569	140156862	283	8500											
JAK2	3717	hgsc.bcm.edu	37	chr9	5065003	5065003	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagtagcacctccagccgtgCttgaaaatatacaaagcaac	16	7	7	11	1	0	1	0	1	0	0	1	1	1	1	3	0	6	4	3	0	8	4	rs2230723	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:5065003C>G	ENST00000381652.3	+	9	1671	c.1177C>G	c.(1177-1179)Ctt>Gtt	p.L393V	JAK2_ENST00000544510.1_Missense_Mutation_p.L244V|JAK2_ENST00000539801.1_Missense_Mutation_p.L393V	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	393			L -> V (in dbSNP:rs2230723). {ECO:0000269|PubMed:17344846}.		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)	TCCAGCCGTGCTTGAAAATAT	0.343		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial				C|||	60	0.0119808	0.0272	0.0202	5008	,	,		17562	0.0		0.0099	False		,,,				2504	0.0				p.L393V		Atlas-SNP	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	35466	.	0			c.C1177G						PASS	.	C	VAL/LEU	132,4274	94.8+/-133.5	4,124,2075	74	71	72		1177	5.2	0.9	9	dbSNP_98	72	52,8548	33.3+/-86.6	0,52,4248	yes	missense	JAK2	NM_004972.3	32	4,176,6323	GG,GC,CC		0.6047,2.9959,1.4147	benign	393/1133	5065003	184,12822	2203	4300	6503	SO:0001583	missense	3717	exon9	Familial Cancer Database		GCCGTGCTTGAAA		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.1177C>G	9.37:g.5065003C>G	ENSP00000371067:p.Leu393Val	63	0	0		73	26	0.356164	NM_004972	O14636|O75297	Missense_Mutation	SNP	ENST00000381652.3	37	CCDS6457.1	29	0.013278388278388278	20	0.04065040650406504	7	0.019337016574585635	0	0.0	2	0.002638522427440633	C	7.763	0.705753	0.15172	0.029959	0.006047	ENSG00000096968	ENST00000539801;ENST00000381652;ENST00000544510	T;T;T	0.59083	0.29;0.29;0.29	5.15	5.15	0.70609	.	0.221618	0.39020	N	0.001490	T	0.10809	0.0264	N	0.17764	0.52	0.53005	D	0.999966	B	0.29612	0.251	B	0.23150	0.044	T	0.08330	-1.0727	10	0.08599	T	0.76	-14.3001	12.0387	0.53440	0.0:0.9205:0.0:0.0795	rs2230723;rs35844880	393	O60674	JAK2_HUMAN	V	393;393;244	ENSP00000440387:L393V;ENSP00000371067:L393V;ENSP00000443103:L244V	ENSP00000371067:L393V	L	+	1	0	JAK2	5055003	0.633000	0.27181	0.933000	0.37362	0.824000	0.46624	1.199000	0.32235	2.412000	0.81896	0.313000	0.20887	CTT	C|0.986;G|0.014	0.014	strong		0.343	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			G	5065003	C	G	5065003	3	3	24	1	0	0	0	0	1	0	0	0	7947	797	28	4	1203	4	JAK2	9	5065003	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	4008434	5065003	136148428	284	8501											
ERMP1	79956	hgsc.bcm.edu	37	chr9	5805741	5805741	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaacagcaatggacaaacagCgaaatgtcaaaaaatacttc	21	6	6	8	1	1	0	1	0	0	0	2	2	1	1	0	1	5	1	0	1	8	2	rs35643913	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:5805741C>T	ENST00000339450.5	-	9	1682	c.1593G>A	c.(1591-1593)tcG>tcA	p.S531S	ERMP1_ENST00000214893.5_5'UTR|ERMP1_ENST00000381506.3_Silent_p.S307S|ERMP1_ENST00000543230.1_Silent_p.S109S	NM_024896.2	NP_079172.2	Q7Z2K6	ERMP1_HUMAN	endoplasmic reticulum metallopeptidase 1	531						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)		GGACAAACAGCGAAATGTCAA	0.423													C|||	35	0.00698882	0.0	0.0029	5008	,	,		18923	0.0		0.006	False		,,,				2504	0.0276				p.S531S		Atlas-SNP	.											.	ERMP1	63	.	0			c.G1593A						PASS	.	C		5,4401	9.9+/-24.2	0,5,2198	90	81	84		1593	-1.9	0.5	9	dbSNP_126	84	67,8533	40.3+/-97.0	0,67,4233	no	coding-synonymous	ERMP1	NM_024896.2		0,72,6431	TT,TC,CC		0.7791,0.1135,0.5536		531/905	5805741	72,12934	2203	4300	6503	SO:0001819	synonymous_variant	79956	exon9			AAACAGCGAAATG	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.1593G>A	9.37:g.5805741C>T		74	0	0		106	45	0.424528	NM_024896	B2RNA4|B3KSB1|Q8N5T5|Q9H5M1	Silent	SNP	ENST00000339450.5	37	CCDS34983.1																																																																																			C|0.995;T|0.005	0.005	strong		0.423	ERMP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354877.1	NM_024896		T	5805741	C	T	5805741	2	4	24	1	0	0	0	0	0	0	0	1	5238	755	27	1		1	ERMP1	9	5805741	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	740738	5805741	135407690	285	8502											
KIAA1797	54914	hgsc.bcm.edu	37	chr9	20885216	20885216	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttcaagcagacttcacttgCtcttgtacatgaggtaggtt	9	15	9	8	0	3	2	2	1	1	1	3	2	3	2	0	2	3	5	0	2	3	7	rs187654100		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:20885216C>T	ENST00000380249.1	+	23	2976	c.2612C>T	c.(2611-2613)gCt>gTt	p.A871V	FOCAD_ENST00000338382.6_Missense_Mutation_p.A871V|FOCAD_ENST00000605086.1_Missense_Mutation_p.A307V	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	871						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											ACTTCACTTGCTCTTGTACAT	0.368													C|||	1	0.000199681	0.0	0.0014	5008	,	,		13975	0.0		0.0	False		,,,				2504	0.0				p.A871V		Atlas-SNP	.											.	.	.	.	0			c.C2612T						PASS	.						231	199	209					9																	20885216		2203	4300	6503	SO:0001583	missense	54914	exon23			CACTTGCTCTTGT	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.2612C>T	9.37:g.20885216C>T	ENSP00000369599:p.Ala871Val	263	0	0		260	128	0.492308	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	37	CCDS34993.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	14.10	2.435384	0.43224	.	.	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.08370	3.1;3.1	5.3	5.3	0.74995	Armadillo-type fold (1);	0.224065	0.46145	D	0.000317	T	0.09686	0.0238	L	0.53249	1.67	0.53005	D	0.999965	P	0.43412	0.806	B	0.32393	0.145	T	0.21895	-1.0232	10	0.29301	T	0.29	-28.1342	19.3232	0.94250	0.0:1.0:0.0:0.0	.	871	Q5VW36	K1797_HUMAN	V	871	ENSP00000369599:A871V;ENSP00000344307:A871V	ENSP00000344307:A871V	A	+	2	0	KIAA1797	20875216	1.000000	0.71417	0.526000	0.27913	0.138000	0.21146	5.289000	0.65656	2.633000	0.89246	0.650000	0.86243	GCT	C|1.000;T|0.000	0.000	strong		0.368	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794		T	20885216	C	T	20885216	3	4	24	1	0	0	0	0	1	0	0	0	8267	797	28	2	2690	2	KIAA1797	9	20885216	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	15079475	20885216	120328215	286	8503											
IFNA10	3446	hgsc.bcm.edu	37	chr9	21206605	21206605	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	atttctgctctgacaacctcCcaggcacaagggctgtattt	9	12	8	12	0	2	1	0	1	2	0	3	1	3	1	2	2	2	4	2	2	3	3	rs28368148	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:21206605C>G	ENST00000357374.2	-	1	537	c.492G>C	c.(490-492)tgG>tgC	p.W164C		NM_002171.1	NP_002162.1	P01566	IFN10_HUMAN	interferon, alpha 10	164					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)			endometrium(1)|large_intestine(3)|liver(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	16				Lung(24;1.26e-23)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.17)		TGACAACCTCCCAGGCACAAG	0.428													c|||	23	0.00459265	0.0008	0.0058	5008	,	,		18519	0.0		0.0129	False		,,,				2504	0.0051				p.W164C		Atlas-SNP	.											.	IFNA10	29	.	0			c.G492C						PASS	.	C	CYS/TRP	8,4398		0,8,2195	250	255	253		492	3.8	1	9	dbSNP_125	253	119,8481		1,117,4182	no	missense	IFNA10	NM_002171.1	215	1,125,6377	GG,GC,CC		1.3837,0.1816,0.9765	probably-damaging	164/190	21206605	127,12879	2203	4300	6503	SO:0001583	missense	3446	exon1			AACCTCCCAGGCA		CCDS6499.1	9p22	2010-08-24			ENSG00000186803	ENSG00000186803		"Interferons"	5418	protein-coding gene	gene with protein product		147577				1385305	Standard	NM_002171		Approved	IFN-alphaC	uc003zoq.1	P01566	OTTHUMG00000019658	ENST00000357374.2:c.492G>C	9.37:g.21206605C>G	ENSP00000369566:p.Trp164Cys	475	0	0		564	265	0.469858	NM_002171	Q5VV13	Missense_Mutation	SNP	ENST00000357374.2	37	CCDS6499.1	13	0.005952380952380952	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	8	0.010554089709762533	-	15.33	2.801079	0.50315	0.001816	0.013837	ENSG00000186803	ENST00000357374	T	0.43294	0.95	3.75	3.75	0.43078	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.000000	0.85682	D	0.000000	T	0.64472	0.2601	M	0.93678	3.445	0.58432	D	0.999991	D	0.89917	1.0	D	0.97110	1.0	T	0.77789	-0.2456	10	0.87932	D	0	.	12.9165	0.58209	0.0:1.0:0.0:0.0	rs28368148	164	P01566	IFN10_HUMAN	C	164	ENSP00000369566:W164C	ENSP00000369566:W164C	W	-	3	0	IFNA10	21196605	1.000000	0.71417	0.988000	0.46212	0.926000	0.56050	2.348000	0.44045	1.806000	0.52798	0.499000	0.49734	TGG	C|0.991;G|0.009	0.009	strong		0.428	IFNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051887.1	NM_002171		G	21206605	C	G	21206605	3	3	24	1	0	0	0	0	1	0	0	0	7541	624	22	4	81	4	IFNA10	9	21206605	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	321389	21206605	120006826	287	8504											
IFNA8	3445	hgsc.bcm.edu	37	chr9	21409439	21409439	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gagatgatccagcagaccttCaacctcttcagcacaaagga	14	7	8	12	0	3	3	2	1	1	2	4	5	4	4	3	1	3	2	3	1	2	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:21409439C>T	ENST00000380205.1	+	1	294	c.264C>T	c.(262-264)ttC>ttT	p.F88F		NM_002170.3	NP_002161.2	P32881	IFNA8_HUMAN	interferon, alpha 8	88					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)		AGCAGACCTTCAACCTCTTCA	0.473																																					p.F88F		Atlas-SNP	.											.	IFNA8	19	.	0			c.C264T						PASS	.						102	95	98					9																	21409439		2203	4300	6503	SO:0001819	synonymous_variant	3445	exon1			GACCTTCAACCTC		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.264C>T	9.37:g.21409439C>T		192	0	0		205	81	0.395122	NM_002170	P01565|P09236|Q5VWV7|Q5VYQ3	Silent	SNP	ENST00000380205.1	37	CCDS6507.1																																																																																			.	.	none		0.473	IFNA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051906.1	NM_002170		T	21409439	C	T	21409439	2	4	24	1	0	0	0	0	0	0	0	1	7552	825	29	2		2	IFNA8	9	21409439	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	202834	21409439	119803992	288	8505											
CDKN2B	1030	hgsc.bcm.edu	37	chr9	22006147	22006147	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaagccctcccgggcagcatCatgcaccggtcgggtgagag	8	5	15	13	3	1	1	1	1	0	1	3	3	2	1	3	3	3	3	3	3	1	0	rs148421170	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:22006147C>T	ENST00000276925.6	-	2	665	c.256G>A	c.(256-258)Gat>Aat	p.D86N	CDKN2B-AS1_ENST00000428597.1_RNA|CDKN2B-AS1_ENST00000582301.1_RNA|CDKN2B-AS1_ENST00000580576.1_RNA|CDKN2B_ENST00000380142.4_3'UTR|CDKN2B-AS1_ENST00000584816.1_RNA|CDKN2B-AS1_ENST00000583719.1_RNA|CDKN2B-AS1_ENST00000468603.2_RNA|CDKN2B-AS1_ENST00000584351.1_RNA|CDKN2B-AS1_ENST00000584020.1_RNA|CDKN2B-AS1_ENST00000455933.2_RNA|CDKN2B-AS1_ENST00000580467.1_RNA|CDKN2B-AS1_ENST00000584637.1_RNA|CDKN2B-AS1_ENST00000585267.1_RNA|CDKN2B-AS1_ENST00000577551.1_RNA|CDKN2B-AS1_ENST00000582072.1_RNA|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2B-AS1_ENST00000581051.1_RNA	NM_004936.3|NM_078487.2	NP_004927.2|NP_511042.1	P42772	CDN2B_HUMAN	cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4)	86					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)		CGGGCAGCATCATGCACCGGT	0.716													C|||	2	0.000399361	0.0	0.0	5008	,	,		14208	0.0		0.002	False		,,,				2504	0.0				p.D86N		Atlas-SNP	.											.	CDKN2B	12	.	2	Whole gene deletion(2)	lung(2)	c.G256A						PASS	.	C	ASN/ASP,	1,4381		0,1,2190	19	23	22		256,	4.8	1	9	dbSNP_134	22	26,8552		0,26,4263	no	missense,utr-3	CDKN2B	NM_004936.3,NM_078487.2	23,	0,27,6453	TT,TC,CC		0.3031,0.0228,0.2083	probably-damaging,	86/139,	22006147	27,12933	2191	4289	6480	SO:0001583	missense	1030	exon2			CAGCATCATGCAC	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.256G>A	9.37:g.22006147C>T	ENSP00000276925:p.Asp86Asn	52	0	0		46	27	0.586957	NM_004936	O15125|Q6FI09	Missense_Mutation	SNP	ENST00000276925.6	37	CCDS6512.1	.	.	.	.	.	.	.	.	.	.	C	33	5.278680	0.95459	2.28E-4	0.003031	ENSG00000147883	ENST00000276925	D	0.93906	-3.31	4.78	4.78	0.61160	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.93893	0.8046	L	0.28400	0.85	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93080	0.6490	10	0.35671	T	0.21	-31.5885	15.3443	0.74324	0.0:1.0:0.0:0.0	.	86	P42772	CDN2B_HUMAN	N	86	ENSP00000276925:D86N	ENSP00000276925:D86N	D	-	1	0	CDKN2B	21996147	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	4.857000	0.62939	2.472000	0.83506	0.655000	0.94253	GAT	C|0.998;T|0.002	0.002	strong		0.716	CDKN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051932.2	NM_004936		T	22006147	C	T	22006147	3	4	24	1	0	0	0	0	1	0	0	0	3166	826	29	2	164	2	CDKN2B	9	22006147	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	596708	22006147	119207284	289	8506											
SMU1	55234	hgsc.bcm.edu	37	chr9	33071879	33071879	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aattcacggagctctatcaaTtccagaacaacctggacaat	15	9	6	11	1	3	1	2	0	1	1	4	3	4	3	2	2	3	1	2	2	6	3			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:33071879T>C	ENST00000397149.3	-	3	299	c.249A>G	c.(247-249)gaA>gaG	p.E83E	SMU1_ENST00000536631.1_Intron	NM_018225.2	NP_060695.2	Q2TAY7	SMU1_HUMAN	smu-1 suppressor of mec-8 and unc-52 homolog (C. elegans)	83	CTLH. {ECO:0000255|PROSITE- ProRule:PRU00058}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|lung(4)|ovary(2)|prostate(1)	9			LUSC - Lung squamous cell carcinoma(29;0.0227)	GBM - Glioblastoma multiforme(74;0.11)		GCTCTATCAATTCCAGAACAA	0.368																																					p.E83E		Atlas-SNP	.											.	SMU1	29	.	0			c.A249G						PASS	.						74	72	73					9																	33071879		2203	4300	6503	SO:0001819	synonymous_variant	55234	exon3			TATCAATTCCAGA	AK001667	CCDS6534.1	9p12	2013-01-10			ENSG00000122692	ENSG00000122692		"WD repeat domain containing"	18247	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 57"					11438655, 11410362	Standard	NM_018225		Approved	SMU-1, FLJ10805, BWD, fSAP57	uc003zsf.1	Q2TAY7	OTTHUMG00000019757	ENST00000397149.3:c.249A>G	9.37:g.33071879T>C		113	0	0		122	51	0.418033	NM_018225	B4E3L0|Q9BU59|Q9HA96|Q9NVD1	Silent	SNP	ENST00000397149.3	37	CCDS6534.1																																																																																			.	.	none		0.368	SMU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052022.1	NM_018225		C	33071879	T	C	33071879	2	2	24	1	0	0	0	0	0	0	0	1	14832	1490	52	3		3	SMU1	9	33071879	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	11065732	33071879	108141552	290	8507											
TLN1	7094	hgsc.bcm.edu	37	chr9	35708425	35708425	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcaaactgtgtgggctccacTagcccttgctgtccagcttg	6	11	11	13	0	0	0	0	0	0	0	2	0	2	0	3	1	4	4	3	1	2	3	rs35461988	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:35708425T>C	ENST00000314888.9	-	34	4736	c.4383A>G	c.(4381-4383)ctA>ctG	p.L1461L	TLN1_ENST00000540444.1_Silent_p.L1461L|TLN1_ENST00000464379.1_5'Flank	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1461	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)			TGGGCTCCACTAGCCCTTGCT	0.562													T|||	40	0.00798722	0.0008	0.013	5008	,	,		19074	0.0		0.0288	False		,,,				2504	0.001				p.L1461L		Atlas-SNP	.											.	TLN1	185	.	0			c.A4383G						PASS	.	T		28,4378	35.2+/-66.4	0,28,2175	79	72	75		4383	0.9	1	9	dbSNP_126	75	302,8298	109.8+/-170.3	2,298,4000	no	coding-synonymous	TLN1	NM_006289.3		2,326,6175	CC,CT,TT		3.5116,0.6355,2.5373		1461/2542	35708425	330,12676	2203	4300	6503	SO:0001819	synonymous_variant	7094	exon34			CTCCACTAGCCCT	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.4383A>G	9.37:g.35708425T>C		61	0	0		48	20	0.416667	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Silent	SNP	ENST00000314888.9	37	CCDS35009.1																																																																																			T|0.978;C|0.022	0.022	strong		0.562	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		C	35708425	T	C	35708425	2	2	24	1	0	0	0	0	0	0	0	1	15962	1509	53	3		3	TLN1	9	35708425	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	2636546	35708425	105505006	291	8508											
GRHPR	9380	hgsc.bcm.edu	37	chr9	37422763	37422763	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcggatgagaccggtgcgaCtcatgaaggtgttcgtcacc	8	9	14	10	4	2	2	2	2	0	1	3	5	2	3	2	3	2	1	2	3	1	1	rs147185003	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:37422763C>T	ENST00000318158.6	+	1	101	c.16C>T	c.(16-18)Ctc>Ttc	p.L6F	GRHPR_ENST00000493368.1_3'UTR|GRHPR_ENST00000607784.1_Missense_Mutation_p.L6F	NM_012203.1	NP_036335.1	Q9UBQ7	GRHPR_HUMAN	glyoxylate reductase/hydroxypyruvate reductase	6					cellular nitrogen compound metabolic process (GO:0034641)|dicarboxylic acid metabolic process (GO:0043648)|excretion (GO:0007588)|glyoxylate metabolic process (GO:0046487)|metabolic process (GO:0008152)|oxidation-reduction process (GO:0055114)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisomal matrix (GO:0005782)	carboxylic acid binding (GO:0031406)|glycerate dehydrogenase activity (GO:0008465)|glyoxylate reductase (NADP) activity (GO:0030267)|hydroxypyruvate reductase activity (GO:0016618)|NAD binding (GO:0051287)|NADPH binding (GO:0070402)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12				GBM - Glioblastoma multiforme(29;0.00687)		ACCGGTGCGACTCATGAAGGT	0.701													C|||	17	0.00339457	0.0	0.0	5008	,	,		11840	0.0		0.001	False		,,,				2504	0.0164				p.L6F		Atlas-SNP	.											.	GRHPR	35	.	0			c.C16T						PASS	.	C	PHE/LEU	0,4382		0,0,2191	15	16	16		16	4	0.9	9	dbSNP_134	16	15,8557		0,15,4271	yes	missense	GRHPR	NM_012203.1	22	0,15,6462	TT,TC,CC		0.175,0.0,0.1158	possibly-damaging	6/329	37422763	15,12939	2191	4286	6477	SO:0001583	missense	9380	exon1			GTGCGACTCATGA	AF134895	CCDS6609.1	9q12	2012-07-13			ENSG00000137106	ENSG00000137106	1.1.1.79, 1.1.1.81		4570	protein-coding gene	gene with protein product	"primary hyperoxaluria type 2"	604296		GLXR		10524214, 10484776	Standard	XM_005251631		Approved	PH2	uc003zzu.1	Q9UBQ7	OTTHUMG00000019914	ENST00000318158.6:c.16C>T	9.37:g.37422763C>T	ENSP00000313432:p.Leu6Phe	41	0	0		65	23	0.353846	NM_012203	Q5T945|Q9H3E9|Q9H636|Q9UKX1	Missense_Mutation	SNP	ENST00000318158.6	37	CCDS6609.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	17.32	3.359027	0.61403	0.0	0.00175	ENSG00000137106	ENST00000377824;ENST00000318158	D;D	0.89050	-1.61;-2.46	4.9	3.99	0.46301	.	0.629307	0.15669	N	0.250520	D	0.86117	0.5856	L	0.40543	1.245	0.35594	D	0.807311	B	0.30664	0.289	B	0.36030	0.216	D	0.86917	0.2064	10	0.40728	T	0.16	.	14.397	0.67018	0.0:0.8509:0.1491:0.0	.	6	Q9UBQ7	GRHPR_HUMAN	F	6	ENSP00000367055:L6F;ENSP00000313432:L6F	ENSP00000313432:L6F	L	+	1	0	GRHPR	37412763	0.994000	0.37717	0.871000	0.34182	0.043000	0.13939	1.025000	0.30090	1.422000	0.47177	-0.518000	0.04402	CTC	C|0.999;T|0.001	0.001	strong		0.701	GRHPR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052442.1	NM_012203		T	37422763	C	T	37422763	3	4	24	1	0	0	0	0	1	0	0	0	6775	565	20	2	18	2	GRHPR	9	37422763	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1714338	37422763	103790668	292	8509											
POLR1E	64425	hgsc.bcm.edu	37	chr9	37501752	37501752	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctatgaaggcgaagattacTgcatatgtgatcatacttgc	12	13	9	7	1	2	3	1	2	1	1	2	4	2	3	0	1	4	1	0	1	6	5	rs17412622	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:37501752T>C	ENST00000377798.4	+	11	1124	c.1011T>C	c.(1009-1011)acT>acC	p.T337T	POLR1E_ENST00000377792.3_Silent_p.T399T|POLR1E_ENST00000442009.2_Silent_p.T267T	NM_022490.1	NP_071935.1	O15160	RPAC1_HUMAN	polymerase (RNA) I polypeptide E, 53kDa	0					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)			autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|skin(1)|stomach(1)	12				GBM - Glioblastoma multiforme(29;0.00851)|Lung(182;0.229)		CGAAGATTACTGCATATGTGA	0.388													T|||	112	0.0223642	0.003	0.036	5008	,	,		23063	0.0		0.0676	False		,,,				2504	0.0153				p.T337T	Ovarian(116;843 1620 18506 32459 34463)	Atlas-SNP	.											.	POLR1E	28	.	0			c.T1011C						PASS	.	T		77,4329	67.6+/-105.2	1,75,2127	148	135	139		1011	-11.6	0	9	dbSNP_123	139	659,7941	167.1+/-218.9	23,613,3664	no	coding-synonymous	POLR1E	NM_022490.1		24,688,5791	CC,CT,TT		7.6628,1.7476,5.6589		337/420	37501752	736,12270	2203	4300	6503	SO:0001819	synonymous_variant	64425	exon11			GATTACTGCATAT	AK091294	CCDS6611.1	9p13.1	2013-01-21	2006-03-09	2006-03-09	ENSG00000137054	ENSG00000137054		"RNA polymerase subunits"	17631	protein-coding gene	gene with protein product	"RNA polymerase I associated factor 53"		"polymerase (RNA) I associated factor 1"	PRAF1		8641287	Standard	XM_005251547		Approved	FLJ13390, PAF53, FLJ13970	uc003zzy.1	Q9GZS1	OTTHUMG00000019920	ENST00000377798.4:c.1011T>C	9.37:g.37501752T>C		132	0	0		114	63	0.552632	NM_022490	O75395|Q5JTE3	Silent	SNP	ENST00000377798.4	37	CCDS6611.1																																																																																			T|0.952;C|0.048	0.048	strong		0.388	POLR1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052464.1	NM_022490		C	37501752	T	C	37501752	2	2	24	1	0	0	0	0	0	0	0	1	12222	1567	55	3		3	POLR1E	9	37501752	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	78989	37501752	103711679	293	8510											
TJP2	9414	hgsc.bcm.edu	37	chr9	71864319	71864319	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaaacccagcccagagccacGagctcagatgaggagggctg	12	3	14	12	1	1	3	1	1	0	2	1	6	1	4	3	2	4	2	3	2	1	0	rs150494393		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:71864319G>A	ENST00000377245.4	+	20	3117	c.2909G>A	c.(2908-2910)cGa>cAa	p.R970Q	TJP2_ENST00000535702.1_Intron|TJP2_ENST00000453658.2_Intron|TJP2_ENST00000348208.4_Intron|TJP2_ENST00000539225.1_Missense_Mutation_p.R1001Q	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	970					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						CCAGAGCCACGAGCTCAGATG	0.542																																					p.R1001Q		Atlas-SNP	.											TJP2,caecum,carcinoma,0,1	TJP2	120	1	0			c.G3002A						PASS	.	G	,,GLN/ARG,,GLN/ARG,	0,4406		0,0,2203	40	33	35		,,3002,,2909,	3	1	9	dbSNP_134	35	2,8598	2.2+/-6.3	0,2,4298	no	intron,intron,missense,utr-3,missense,intron	TJP2	NM_001170414.1,NM_001170415.1,NM_001170416.1,NM_001170630.1,NM_004817.3,NM_201629.3	,,43,,43,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,,probably-damaging,,probably-damaging,	,,1001/1222,,970/1191,	71864319	2,13004	2203	4300	6503	SO:0001583	missense	9414	exon20			AGCCACGAGCTCA	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.2909G>A	9.37:g.71864319G>A	ENSP00000366453:p.Arg970Gln	78	0	0		103	70	0.679612	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Missense_Mutation	SNP	ENST00000377245.4	37	CCDS6627.1	.	.	.	.	.	.	.	.	.	.	G	17.44	3.390626	0.62066	0.0	2.33E-4	ENSG00000119139	ENST00000377245;ENST00000539225	T;T	0.09350	2.99;3.03	5.82	2.96	0.34315	.	0.136502	0.47093	N	0.000255	T	0.17152	0.0412	L	0.53249	1.67	0.80722	D	1	D;D	0.67145	0.996;0.985	P;P	0.55871	0.786;0.638	T	0.07424	-1.0773	10	0.16896	T	0.51	.	9.3062	0.37876	0.1309:0.1201:0.749:0.0	.	1001;970	F5H301;Q9UDY2	.;ZO2_HUMAN	Q	970;1001	ENSP00000366453:R970Q;ENSP00000438262:R1001Q	ENSP00000366453:R970Q	R	+	2	0	TJP2	71054139	1.000000	0.71417	0.968000	0.41197	0.993000	0.82548	1.825000	0.39081	0.363000	0.24346	0.563000	0.77884	CGA	G|1.000;A|0.000	0.000	weak		0.542	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629		A	71864319	G	A	71864319	3	1	24	1	0	0	0	0	1	0	0	0	15945	1058	37	1	3246	1	TJP2	9	71864319	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	34362567	71864319	69349112	294	8511											
GCNT1	2650	hgsc.bcm.edu	37	chr9	79118400	79118400	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgatgtttccaagggtgctcCctacccgccctgcgatggag	6	10	12	13	2	0	1	0	1	0	0	2	3	2	2	4	2	3	2	4	2	2	2	rs147866228	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:79118400C>T	ENST00000376730.4	+	4	1586	c.1103C>T	c.(1102-1104)cCc>cTc	p.P368L	GCNT1_ENST00000444201.2_Missense_Mutation_p.P368L|GCNT1_ENST00000536223.1_Missense_Mutation_p.P368L|GCNT1_ENST00000442371.1_Missense_Mutation_p.P368L	NM_001097636.1|NM_001490.4	NP_001091105.1|NP_001481.2	Q02742	GCNT1_HUMAN	glucosaminyl (N-acetyl) transferase 1, core 2	368	Catalytic. {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						AAGGGTGCTCCCTACCCGCCC	0.522													C|||	10	0.00199681	0.0015	0.0029	5008	,	,		13880	0.0		0.006	False		,,,				2504	0.0				p.P368L		Atlas-SNP	.											.	GCNT1	52	.	0			c.C1103T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	6,4400	12.9+/-30.5	0,6,2197	110	92	98		1103,1103,1103,1103,1103	5.3	1	9	dbSNP_134	98	89,8511	50.6+/-110.7	0,89,4211	yes	missense,missense,missense,missense,missense	GCNT1	NM_001097633.1,NM_001097634.1,NM_001097635.1,NM_001097636.1,NM_001490.4	98,98,98,98,98	0,95,6408	TT,TC,CC		1.0349,0.1362,0.7304	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	368/429,368/429,368/429,368/429,368/429	79118400	95,12911	2203	4300	6503	SO:0001583	missense	2650	exon4			GTGCTCCCTACCC	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.1103C>T	9.37:g.79118400C>T	ENSP00000365920:p.Pro368Leu	182	0	0		258	129	0.5	NM_001490	Q6DJZ4	Missense_Mutation	SNP	ENST00000376730.4	37	CCDS6653.1	8	0.003663003663003663	2	0.0040650406504065045	0	0.0	0	0.0	6	0.0079155672823219	c	14.65	2.600144	0.46423	0.001362	0.010349	ENSG00000187210	ENST00000536223;ENST00000442371;ENST00000444201;ENST00000376730	T;T;T;T	0.11169	2.8;2.8;2.8;2.8	6.17	5.28	0.74379	.	0.179527	0.50627	D	0.000111	T	0.28995	0.0720	M	0.82823	2.61	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	T	0.16070	-1.0415	9	.	.	.	1.2848	15.5517	0.76158	0.0:0.9345:0.0:0.0655	.	368	Q02742	GCNT1_HUMAN	L	368	ENSP00000440883:P368L;ENSP00000415454:P368L;ENSP00000390703:P368L;ENSP00000365920:P368L	.	P	+	2	0	GCNT1	78308220	0.432000	0.25554	0.987000	0.45799	0.047000	0.14425	2.020000	0.41010	1.635000	0.50512	0.655000	0.94253	CCC	C|0.994;T|0.006	0.006	strong		0.522	GCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052725.1	NM_001097634		T	79118400	C	T	79118400	3	4	24	1	0	0	0	0	1	0	0	0	6308	623	22	2	1105	2	GCNT1	9	79118400	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	7254081	79118400	62095031	295	8512											
CDK20	23552	hgsc.bcm.edu	37	chr9	90588970	90588970	+	Intron	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgcaggatagaaggcagaCactgccagcccaccctcggc	10	5	11	15	1	1	2	0	0	1	2	2	3	1	3	3	3	3	2	3	3	2	1	rs28364935	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:90588970C>A	ENST00000325303.8	-	2	381				CDK20_ENST00000605159.1_Intron|CDK20_ENST00000375883.3_Intron|CDK20_ENST00000375871.4_Intron|CDK20_ENST00000336654.5_Missense_Mutation_p.C32F	NM_001039803.2	NP_001034892.1	Q8IZL9	CDK20_HUMAN	cyclin-dependent kinase 20						cell cycle (GO:0007049)|cell division (GO:0051301)|multicellular organismal development (GO:0007275)	cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			skin(1)	1						AGAAGGCAGACACTGCCAGCC	0.632													.|||	371	0.0740815	0.2141	0.0447	5008	,	,		17061	0.0		0.0507	False		,,,				2504	0.0061				p.C32F		Atlas-SNP	.											.	CDK20	52	.	0			c.G95T						PASS	.	C	,,,,PHE/CYS	813,3593		77,659,1467	47	47	47		,,,,95	1.6	0	9	dbSNP_125	47	365,8235		8,349,3943	yes	intron,intron,intron,intron,missense	CDK20	NM_001039803.2,NM_001170639.1,NM_001170640.1,NM_012119.4,NM_178432.3	,,,,205	85,1008,5410	AA,AC,CC		4.2442,18.4521,9.0574	,,,,	,,,,32/339	90588970	1178,11828	2203	4300	6503	SO:0001627	intron_variant	23552	exon2			GGCAGACACTGCC	AF035013	CCDS6677.1, CCDS6678.1, CCDS35060.1, CCDS55324.1, CCDS65075.1	9q22.1	2011-11-08	2009-12-16	2009-12-16	ENSG00000156345	ENSG00000156345		"Cyclin-dependent kinases"	21420	protein-coding gene	gene with protein product		610076	"cell cycle related kinase"	CCRK		19884882	Standard	NM_178432		Approved	p42	uc004apr.3	Q8IZL9	OTTHUMG00000020161	ENST00000325303.8:c.76-20G>T	9.37:g.90588970C>A		49	0	0		64	32	0.5	NM_178432	A2A389|A2A390|B4DQX1|O95137|Q5EDC4|Q5VYW1|Q9BUF4	Missense_Mutation	SNP	ENST00000325303.8	37	CCDS35060.1	168	0.07692307692307693	104	0.21138211382113822	22	0.06077348066298342	0	0.0	42	0.055408970976253295	.	1.147	-0.647886	0.03506	0.184521	0.042442	ENSG00000156345	ENST00000336654	T	0.66815	-0.23	4.55	1.56	0.23342	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.06250	-1.0837	6	.	.	.	.	3.4873	0.07625	0.1726:0.5644:0.1672:0.0957	rs28364935	32	A2A390	.	F	32	ENSP00000338975:C32F	.	C	-	2	0	CDK20	89778790	0.014000	0.17966	0.002000	0.10522	0.013000	0.08279	0.096000	0.15147	0.099000	0.17552	-1.293000	0.01348	TGT	C|0.916;A|0.084	0.084	strong		0.632	CDK20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214996.1	NM_012119		A	90588970	C	A	90588970	1	1	24	0	1	0	0	0	0	0	0	0	3139	478	17	4		4	CDK20	9	90588970	Intron	SNP	C	TCGA-G8-6326-01A-11D-2210-10	11470570	90588970	50624461	296	8513											
PHF2	5253	hgsc.bcm.edu	37	chr9	96407953	96407953	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgccaggaagtcagctcacGctgggctacatggaggagca	10	6	15	10	1	2	0	2	0	0	0	2	3	2	3	1	4	4	4	1	4	2	1	rs35505758	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:96407953G>A	ENST00000359246.4	+	4	709	c.342G>A	c.(340-342)acG>acA	p.T114T	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	114					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)		GTCAGCTCACGCTGGGCTACA	0.642													G|||	88	0.0175719	0.0227	0.0058	5008	,	,		19930	0.0139		0.0268	False		,,,				2504	0.0133				p.T114T		Atlas-SNP	.											.	PHF2	113	.	0			c.G342A						PASS	.	G		95,4311	78.8+/-117.2	1,93,2109	87	80	82		342	-9.2	0	9	dbSNP_126	82	166,8434	77.5+/-140.1	3,160,4137	no	coding-synonymous	PHF2	NM_005392.3		4,253,6246	AA,AG,GG		1.9302,2.1562,2.0068		114/1097	96407953	261,12745	2203	4300	6503	SO:0001819	synonymous_variant	5253	exon4			GCTCACGCTGGGC	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.342G>A	9.37:g.96407953G>A		42	0	0		69	34	0.492754	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Silent	SNP	ENST00000359246.4	37	CCDS35069.1																																																																																			G|0.980;A|0.020	0.020	strong		0.642	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392		A	96407953	G	A	96407953	2	1	24	1	0	0	0	0	0	0	0	1	11839	1074	38	1		1	PHF2	9	96407953	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	5818983	96407953	44805478	297	8514											
PHF2	5253	hgsc.bcm.edu	37	chr9	96411414	96411414	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaggactgcaagatgaagctGaaggagtttgtggactatta	14	10	13	4	0	0	3	0	2	0	1	0	6	0	6	0	3	2	3	0	3	6	3	rs16912641	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:96411414G>A	ENST00000359246.4	+	5	889	c.522G>A	c.(520-522)ctG>ctA	p.L174L	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	174					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)		AGATGAAGCTGAAGGAGTTTG	0.572													G|||	177	0.0353435	0.0862	0.0101	5008	,	,		14042	0.0139		0.0298	False		,,,				2504	0.0123				p.L174L		Atlas-SNP	.											.	PHF2	113	.	0			c.G522A						PASS	.	G		330,3782		6,318,1732	110	71	84		522	3.7	1	9	dbSNP_123	84	140,7862		1,138,3862	no	coding-synonymous	PHF2	NM_005392.3		7,456,5594	AA,AG,GG		1.7496,8.0253,3.8798		174/1097	96411414	470,11644	2056	4001	6057	SO:0001819	synonymous_variant	5253	exon5			GAAGCTGAAGGAG	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.522G>A	9.37:g.96411414G>A		201	0	0		194	81	0.417526	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Silent	SNP	ENST00000359246.4	37	CCDS35069.1																																																																																			G|0.954;A|0.046	0.046	strong		0.572	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392		A	96411414	G	A	96411414	2	1	24	1	0	0	0	0	0	0	0	1	11839	1277	45	2		2	PHF2	9	96411414	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	3461	96411414	44802017	298	8515											
PHF2	5253	hgsc.bcm.edu	37	chr9	96436037	96436037	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggggtggcagtggcaagaGtgcaggcaaacgactgctga	10	6	18	7	1	0	2	0	1	0	1	0	3	0	2	0	5	3	5	0	5	2	0	rs41276200	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:96436037G>A	ENST00000359246.4	+	18	2886	c.2519G>A	c.(2518-2520)aGt>aAt	p.S840N	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	840				SGKSA -> NKGT (in Ref. 1; AAD21791). {ECO:0000305}.	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)		AGTGGCAAGAGTGCAGGCAAA	0.627													G|||	36	0.0071885	0.0	0.0029	5008	,	,		19197	0.0129		0.0169	False		,,,				2504	0.0041				p.S840N		Atlas-SNP	.											.	PHF2	113	.	0			c.G2519A						PASS	.	G	ASN/SER	11,4395	20.2+/-43.8	0,11,2192	88	74	78		2519	3.3	0	9	dbSNP_127	78	120,8480	62.4+/-124.4	2,116,4182	yes	missense	PHF2	NM_005392.3	46	2,127,6374	AA,AG,GG		1.3953,0.2497,1.0072	benign	840/1097	96436037	131,12875	2203	4300	6503	SO:0001583	missense	5253	exon18			GCAAGAGTGCAGG	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.2519G>A	9.37:g.96436037G>A	ENSP00000352185:p.Ser840Asn	119	0	0		150	75	0.5	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Missense_Mutation	SNP	ENST00000359246.4	37	CCDS35069.1	21	0.009615384615384616	1	0.0020325203252032522	1	0.0027624309392265192	6	0.01048951048951049	13	0.017150395778364115	G	10.03	1.237840	0.22711	0.002497	0.013953	ENSG00000197724	ENST00000359246	T	0.18502	2.21	5.18	3.32	0.38043	.	0.515497	0.21501	N	0.073536	T	0.02807	0.0084	N	0.11560	0.145	0.80722	D	1	B;B	0.13594	0.008;0.001	B;B	0.14578	0.011;0.003	T	0.22871	-1.0204	10	0.07990	T	0.79	-3.0171	3.472	0.07570	0.1562:0.0:0.4214:0.4224	rs41276200;rs61739260	259;840	Q8N359;O75151	.;PHF2_HUMAN	N	840	ENSP00000352185:S840N	ENSP00000352185:S840N	S	+	2	0	PHF2	95475858	0.998000	0.40836	0.019000	0.16419	0.398000	0.30690	2.824000	0.48088	1.149000	0.42402	0.561000	0.74099	AGT	G|0.990;A|0.010	0.010	strong		0.627	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392		A	96436037	G	A	96436037	3	1	24	1	0	0	0	0	1	0	0	0	11839	1029	36	2	2589	2	PHF2	9	96436037	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	24623	96436037	44777394	299	8516											
TRIM14	9830	hgsc.bcm.edu	37	chr9	100857170	100857170	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttccttaaggcgaatgtccaAtggcgtctgtaatgtactct	9	14	9	9	2	2	0	0	0	2	0	4	1	4	0	2	2	1	2	2	2	5	4	rs150211153	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:100857170A>G	ENST00000341469.2	-	4	688	c.679T>C	c.(679-681)Ttg>Ctg	p.L227L	TRIM14_ENST00000342043.3_Silent_p.L227L|TRIM14_ENST00000375098.3_Silent_p.L227L|TRIM14_ENST00000538344.1_5'Flank	NM_014788.2	NP_055603.2	Q14142	TRI14_HUMAN	tripartite motif containing 14	227					innate immune response (GO:0045087)|negative regulation of viral transcription (GO:0032897)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)|intracellular (GO:0005622)	zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(62;0.0559)				CGAATGTCCAATGGCGTCTGT	0.532													A|||	2	0.000399361	0.0	0.0	5008	,	,		22256	0.0		0.002	False		,,,				2504	0.0				p.L227L	Colon(14;460 597 13826 51781)	Atlas-SNP	.											.	TRIM14	24	.	0			c.T679C						PASS	.	A	,,	2,4404	4.2+/-10.8	0,2,2201	128	111	117		679,679,679	0	0.3	9	dbSNP_134	117	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous,coding-synonymous,coding-synonymous	TRIM14	NM_014788.2,NM_033219.1,NM_033220.1	,,	0,13,6490	GG,GA,AA		0.1279,0.0454,0.1	,,	227/443,227/443,227/443	100857170	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	9830	exon4			TGTCCAATGGCGT	AF220130	CCDS6734.1	9q31.1	2011-04-20	2011-01-25		ENSG00000106785	ENSG00000106785		"Tripartite motif containing / Tripartite motif containing"	16283	protein-coding gene	gene with protein product		606556	"tripartite motif-containing 14"			11331580	Standard	XM_005252320		Approved	KIAA0129	uc004ayd.2	Q14142	OTTHUMG00000020339	ENST00000341469.2:c.679T>C	9.37:g.100857170A>G		123	0	0		113	57	0.504425	NM_033219	A8K9W0|E7EQC4|F8W956|Q548W9|Q5TBQ8|Q6ZWL7|Q9BRD8|Q9C020	Silent	SNP	ENST00000341469.2	37	CCDS6734.1																																																																																			A|0.999;G|0.001	0.001	strong		0.532	TRIM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053350.1	NM_014788		G	100857170	A	G	100857170	2	3	24	1	0	0	0	0	0	0	0	1	16504	98	4	3		3	TRIM14	9	100857170	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	4421133	100857170	40356261	300	8517											
TRIM14	9830	hgsc.bcm.edu	37	chr9	100862339	100862339	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tacacctggagggtaagctgCgtgtttttatcaatgaattt	10	15	10	6	1	1	1	1	1	0	0	1	2	1	2	1	2	3	3	1	2	5	6	rs35830621	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:100862339C>A	ENST00000341469.2	-	3	420	c.411G>T	c.(409-411)acG>acT	p.T137T	TRIM14_ENST00000342043.3_Silent_p.T137T|TRIM14_ENST00000375098.3_Silent_p.T137T	NM_014788.2	NP_055603.2	Q14142	TRI14_HUMAN	tripartite motif containing 14	137					innate immune response (GO:0045087)|negative regulation of viral transcription (GO:0032897)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)	cytoplasm (GO:0005737)|intracellular (GO:0005622)	zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	9		Acute lymphoblastic leukemia(62;0.0559)				GGGTAAGCTGCGTGTTTTTAT	0.468													C|||	176	0.0351438	0.0711	0.0288	5008	,	,		19176	0.001		0.0527	False		,,,				2504	0.0082				p.T137T	Colon(14;460 597 13826 51781)	Atlas-SNP	.											.	TRIM14	24	.	0			c.G411T						PASS	.	C	,,	251,4155	145.7+/-180.5	6,239,1958	135	128	131		411,411,411	-9.1	0	9	dbSNP_126	131	465,8135	137.9+/-194.8	8,449,3843	no	coding-synonymous,coding-synonymous,coding-synonymous	TRIM14	NM_014788.2,NM_033219.1,NM_033220.1	,,	14,688,5801	AA,AC,CC		5.407,5.6968,5.5052	,,	137/443,137/443,137/443	100862339	716,12290	2203	4300	6503	SO:0001819	synonymous_variant	9830	exon3			AAGCTGCGTGTTT	AF220130	CCDS6734.1	9q31.1	2011-04-20	2011-01-25		ENSG00000106785	ENSG00000106785		"Tripartite motif containing / Tripartite motif containing"	16283	protein-coding gene	gene with protein product		606556	"tripartite motif-containing 14"			11331580	Standard	XM_005252320		Approved	KIAA0129	uc004ayd.2	Q14142	OTTHUMG00000020339	ENST00000341469.2:c.411G>T	9.37:g.100862339C>A		180	0	0		165	75	0.454545	NM_033219	A8K9W0|E7EQC4|F8W956|Q548W9|Q5TBQ8|Q6ZWL7|Q9BRD8|Q9C020	Silent	SNP	ENST00000341469.2	37	CCDS6734.1																																																																																			C|0.951;A|0.049	0.049	strong		0.468	TRIM14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053350.1	NM_014788		A	100862339	C	A	100862339	2	1	24	1	0	0	0	0	0	0	0	1	16504	755	27	4		4	TRIM14	9	100862339	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	5169	100862339	40351092	301	8518											
GABBR2	9568	hgsc.bcm.edu	37	chr9	101151234	101151234	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atgctgtagagaggtagggaGatcttccgcagctgctccag	9	9	14	9	1	1	2	0	0	1	2	3	4	3	2	2	2	3	6	2	2	2	3			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:101151234G>C	ENST00000259455.2	-	10	1890	c.1431C>G	c.(1429-1431)atC>atG	p.I477M		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	477					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)	GAGGTAGGGAGATCTTCCGCA	0.502																																					p.I477M		Atlas-SNP	.											.	GABBR2	126	.	0			c.C1431G						PASS	.						336	253	281					9																	101151234		2203	4300	6503	SO:0001583	missense	9568	exon10			TAGGGAGATCTTC	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.1431C>G	9.37:g.101151234G>C	ENSP00000259455:p.Ile477Met	284	1	0.00352113		273	118	0.432234	NM_005458	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Missense_Mutation	SNP	ENST00000259455.2	37	CCDS6736.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.399282	0.62177	.	.	ENSG00000136928	ENST00000259455	T	0.80304	-1.36	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.81044	0.4741	M	0.63843	1.955	0.80722	D	1	P	0.50617	0.937	P	0.49276	0.605	T	0.82902	-0.0227	10	0.87932	D	0	.	9.4371	0.38646	0.0978:0.0:0.9022:0.0	.	477	O75899	GABR2_HUMAN	M	477	ENSP00000259455:I477M	ENSP00000259455:I477M	I	-	3	3	GABBR2	100191055	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.035000	0.41155	2.389000	0.81357	0.655000	0.94253	ATC	.	.	none		0.502	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1			C	101151234	G	C	101151234	3	2	24	1	0	0	0	0	1	0	0	0	6164	932	33	4	1434	4	GABBR2	9	101151234	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	288895	101151234	40062197	302	8519											
ZNF189	7743	hgsc.bcm.edu	37	chr9	104162272	104162272	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agatgtcatgatggagaattAtggaaacctggtctcactgg	12	11	12	6	0	2	3	2	1	1	2	3	5	2	4	1	4	1	0	1	4	3	1			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:104162272A>G	ENST00000339664.2	+	2	269	c.140A>G	c.(139-141)tAt>tGt	p.Y47C	ZNF189_ENST00000259395.4_Missense_Mutation_p.Y5C|MRPL50_ENST00000539624.1_5'Flank|MRPL50_ENST00000374865.4_5'Flank|ZNF189_ENST00000374861.3_Missense_Mutation_p.Y33C	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	47	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)				ATGGAGAATTATGGAAACCTG	0.413																																					p.Y47C		Atlas-SNP	.											ZNF189,NS,carcinoma,+1,1	ZNF189	79	1	0			c.A140G						PASS	.						125	126	126					9																	104162272		2203	4300	6503	SO:0001583	missense	7743	exon2			AGAATTATGGAAA	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.140A>G	9.37:g.104162272A>G	ENSP00000342019:p.Tyr47Cys	78	0	0		63	26	0.412698	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Missense_Mutation	SNP	ENST00000339664.2	37	CCDS6754.1	.	.	.	.	.	.	.	.	.	.	A	17.28	3.348923	0.61183	.	.	ENSG00000136870	ENST00000374861;ENST00000339664;ENST00000259395	T;T;T	0.08193	4.26;4.26;3.12	4.79	3.61	0.41365	Krueppel-associated box (4);	0.191487	0.25958	N	0.027201	T	0.22627	0.0546	M	0.74467	2.265	0.34073	D	0.65865	P;D;D	0.63046	0.946;0.966;0.992	P;B;P	0.62184	0.749;0.338;0.899	T	0.29119	-1.0022	10	0.59425	D	0.04	.	9.0762	0.36522	0.8355:0.0:0.0:0.1645	.	32;33;47	B7ZLK9;Q5T7D8;O75820	.;.;ZN189_HUMAN	C	33;47;5	ENSP00000363995:Y33C;ENSP00000342019:Y47C;ENSP00000259395:Y5C	ENSP00000259395:Y5C	Y	+	2	0	ZNF189	103202093	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.826000	0.62715	0.924000	0.37069	0.528000	0.53228	TAT	.	.	none		0.413	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452		G	104162272	A	G	104162272	3	3	24	1	0	0	0	0	1	0	0	0	17769	449	16	3	146	3	ZNF189	9	104162272	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	3011038	104162272	37051159	303	8520											
DBC1	1620	hgsc.bcm.edu	37	chr9	121930416	121930416	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccgtggcacacgcagctcCgctggctctccaggaaggtt	6	8	13	14	3	1	0	0	0	1	0	3	1	2	1	3	4	2	6	3	4	1	1	rs141766717	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:121930416C>T	ENST00000265922.3	-	8	1693	c.1232G>A	c.(1231-1233)cGg>cAg	p.R411Q	BRINP1_ENST00000482797.1_Intron	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	411					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)		p.R411Q(1)									CACGCAGCTCCGCTGGCTCTC	0.597													C|||	5	0.000998403	0.0015	0.0	5008	,	,		19155	0.002		0.0	False		,,,				2504	0.001				p.R411Q		Atlas-SNP	.											DBC1,NS,carcinoma,0,2	DBC1	194	2	1	Substitution - Missense(1)	lung(1)	c.G1232A						PASS	.	C	GLN/ARG	6,4400	11.4+/-27.6	0,6,2197	20	18	19		1232	5.7	1	9	dbSNP_134	19	9,8591	7.1+/-27.0	0,9,4291	yes	missense	DBC1	NM_014618.2	43	0,15,6488	TT,TC,CC		0.1047,0.1362,0.1153	probably-damaging	411/762	121930416	15,12991	2203	4300	6503	SO:0001583	missense	1620	exon8			CAGCTCCGCTGGC	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.1232G>A	9.37:g.121930416C>T	ENSP00000265922:p.Arg411Gln	90	0	0		125	62	0.496	NM_014618	Q6IPV6|Q6P1A0|Q8WU22	Missense_Mutation	SNP	ENST00000265922.3	37	CCDS6822.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	24.4	4.525548	0.85600	0.001362	0.001047	ENSG00000078725	ENST00000373969;ENST00000265922	T	0.62364	0.03	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.62588	0.2440	L	0.41824	1.3	0.80722	D	1	D	0.63880	0.993	P	0.47134	0.539	T	0.63296	-0.6669	10	0.46703	T	0.11	-21.7784	19.8211	0.96595	0.0:1.0:0.0:0.0	.	411	O60477	DBC1_HUMAN	Q	411	ENSP00000265922:R411Q	ENSP00000265922:R411Q	R	-	2	0	DBC1	120970237	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.890000	0.63178	2.687000	0.91594	0.655000	0.94253	CGG	C|0.999;T|0.001	0.001	strong		0.597	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618		T	121930416	C	T	121930416	3	4	24	1	0	0	0	0	1	0	0	0	4249	652	23	1	1057	1	DBC1	9	121930416	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	17768144	121930416	19283015	304	8521											
STRBP	55342	hgsc.bcm.edu	37	chr9	125895238	125895238	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agacacagctgtattcacaaCgccctttgcctgttaaaata	13	11	6	11	1	1	1	1	0	0	1	1	1	1	1	2	0	3	3	2	0	5	5	rs79286922	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:125895238C>T	ENST00000348403.5	-	17	2212	c.1783G>A	c.(1783-1785)Gtt>Att	p.V595I	STRBP_ENST00000447404.2_Missense_Mutation_p.V595I|STRBP_ENST00000360998.3_Missense_Mutation_p.V581I	NM_018387.4	NP_060857.2	Q96SI9	STRBP_HUMAN	spermatid perinuclear RNA binding protein	595					cellular component movement (GO:0006928)|mechanosensory behavior (GO:0007638)|multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(6)|prostate(1)|skin(2)	26						GTATTCACAACGCCCTTTGCC	0.438													C|||	28	0.00559105	0.0061	0.0072	5008	,	,		20536	0.0		0.0129	False		,,,				2504	0.002				p.V595I		Atlas-SNP	.											.	STRBP	73	.	0			c.G1783A						PASS	.	C	ILE/VAL,ILE/VAL	30,4376	36.0+/-67.5	0,30,2173	90	84	86		1741,1783	4	1	9	dbSNP_131	86	160,8440	76.3+/-139.0	1,158,4141	yes	missense,missense	STRBP	NM_001171137.1,NM_018387.4	29,29	1,188,6314	TT,TC,CC		1.8605,0.6809,1.4609	benign,benign	581/659,595/673	125895238	190,12816	2203	4300	6503	SO:0001583	missense	55342	exon17			TCACAACGCCCTT	AK002169	CCDS6851.1, CCDS55337.1	9q33.1-q33.3	2008-08-29	2001-11-28		ENSG00000165209	ENSG00000165209			16462	protein-coding gene	gene with protein product		611138	"spermatid perinuclear RNA-binding protein", "interleukin enhancer binding factor 3-like"	ILF3L			Standard	NM_018387		Approved	FLJ11307, SPNR	uc004bns.3	Q96SI9	OTTHUMG00000020636	ENST00000348403.5:c.1783G>A	9.37:g.125895238C>T	ENSP00000321347:p.Val595Ile	139	0	0		130	61	0.469231	NM_018387	Q32NB9|Q9BUE1|Q9BXG4|Q9H0B4|Q9H7V1|Q9NUK4	Missense_Mutation	SNP	ENST00000348403.5	37	CCDS6851.1	18	0.008241758241758242	5	0.01016260162601626	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	C	15.15	2.746549	0.49257	0.006809	0.018605	ENSG00000165209	ENST00000447404;ENST00000348403;ENST00000360998	T;T;T	0.17054	2.56;2.56;2.3	5.96	4.03	0.46877	.	0.336970	0.34750	N	0.003716	T	0.05273	0.0140	N	0.24115	0.695	0.35920	D	0.831777	B;B	0.13145	0.004;0.007	B;B	0.08055	0.001;0.003	T	0.15752	-1.0426	10	0.30854	T	0.27	-1.5899	10.2451	0.43336	0.0:0.7752:0.0:0.2248	.	595;581	Q96SI9;Q96SI9-2	STRBP_HUMAN;.	I	595;595;581	ENSP00000415968:V595I;ENSP00000321347:V595I;ENSP00000354271:V581I	ENSP00000321347:V595I	V	-	1	0	STRBP	124935059	0.950000	0.32346	0.993000	0.49108	0.977000	0.68977	1.691000	0.37721	0.757000	0.33036	0.579000	0.79373	GTT	C|0.988;T|0.012	0.012	strong		0.438	STRBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053982.1			T	125895238	C	T	125895238	3	4	24	1	0	0	0	0	1	0	0	0	15342	536	19	1	247	1	STRBP	9	125895238	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	3964822	125895238	15318193	305	8522											
DENND1A	57706	hgsc.bcm.edu	37	chr9	126144441	126144441	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccccggggccagggctgagcGgctggagcagttcagtgggg	5	5	20	11	2	1	1	1	1	0	0	1	2	1	2	3	7	2	4	3	7	0	1	rs200503663		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:126144441G>A	ENST00000373624.2	-	22	2501	c.2300C>T	c.(2299-2301)cCg>cTg	p.P767L	DENND1A_ENST00000473039.1_5'UTR|DENND1A_ENST00000542603.1_Missense_Mutation_p.P552L|DENND1A_ENST00000394219.3_Missense_Mutation_p.P778L	NM_020946.1	NP_065997.1	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A	767	Pro-rich.				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						AGGGCTGAGCGGCTGGAGCAG	0.701																																					p.P767L		Atlas-SNP	.											DENND1A,colon,carcinoma,-1,1	DENND1A	112	1	0			c.C2300T						PASS	.	G	LEU/PRO	0,4364		0,0,2182	11	16	15		2300	4.8	0.9	9		15	1,8551		0,1,4275	yes	missense	DENND1A	NM_020946.1	98	0,1,6457	AA,AG,GG		0.0117,0.0,0.0077	probably-damaging	767/1010	126144441	1,12915	2182	4276	6458	SO:0001583	missense	57706	exon22			CTGAGCGGCTGGA	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.2300C>T	9.37:g.126144441G>A	ENSP00000362727:p.Pro767Leu	34	0	0		28	15	0.535714	NM_020946	A8MZA3|B1AM80|B7Z3C8|B7Z669|D3PFD3|Q05C88|Q5VWF0|Q6PJZ5|Q8IVD6|Q9H796	Missense_Mutation	SNP	ENST00000373624.2	37	CCDS35133.1	.	.	.	.	.	.	.	.	.	.	G	16.96	3.267066	0.59540	0.0	1.17E-4	ENSG00000119522	ENST00000373624;ENST00000542603;ENST00000394219	T;T;T	0.28895	2.99;1.59;2.9	4.83	4.83	0.62350	.	0.133128	0.51477	D	0.000095	T	0.47358	0.1441	M	0.63843	1.955	0.80722	D	1	D;D;D;D	0.67145	0.996;0.996;0.993;0.979	P;P;P;P	0.56398	0.742;0.797;0.557;0.481	T	0.49466	-0.8937	10	0.56958	D	0.05	-7.2386	16.1301	0.81422	0.0:0.0:1.0:0.0	.	778;768;767;630	Q8TEH3-6;Q8TEH3-7;Q8TEH3;Q9HCG4	.;.;DEN1A_HUMAN;.	L	767;552;778	ENSP00000362727:P767L;ENSP00000437457:P552L;ENSP00000377766:P778L	ENSP00000362727:P767L	P	-	2	0	DENND1A	125184262	1.000000	0.71417	0.906000	0.35671	0.485000	0.33311	6.349000	0.73013	2.224000	0.72417	0.557000	0.71058	CCG	.	.	weak		0.701	DENND1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053997.1	NM_024820		A	126144441	G	A	126144441	3	1	24	1	0	0	0	0	1	0	0	0	4428	1116	39	1	733	1	DENND1A	9	126144441	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	249203	126144441	15068990	306	8523											
ST6GALNAC6	30815	hgsc.bcm.edu	37	chr9	130656800	130656800	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agctgcgctaccttgttgccGagaatggggacatagccgtc	8	9	13	11	3	0	1	0	0	0	1	1	3	0	2	3	2	5	3	3	2	3	4	rs11552227	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:130656800G>A	ENST00000373146.1	-	4	467	c.288C>T	c.(286-288)ctC>ctT	p.L96L	ST6GALNAC6_ENST00000291839.5_Silent_p.L96L|ST6GALNAC6_ENST00000542456.1_Missense_Mutation_p.S32L|ST6GALNAC6_ENST00000373141.1_Silent_p.L62L|ST6GALNAC6_ENST00000485320.1_5'UTR|ST6GALNAC6_ENST00000373144.3_Silent_p.L62L|ST6GALNAC6_ENST00000373142.1_Silent_p.L96L			Q969X2	SIA7F_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 6	96					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						CCTTGTTGCCGAGAATGGGGA	0.587																																					p.L96L		Atlas-SNP	.											.	ST6GALNAC6	36	.	0			c.C288T						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	88	84	85		288	-9.8	0.1	9	dbSNP_120	85	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ST6GALNAC6	NM_013443.3		0,4,6499	AA,AG,GG		0.0233,0.0454,0.0308		96/334	130656800	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	30815	exon4			GTTGCCGAGAATG	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.288C>T	9.37:g.130656800G>A		34	0	0		40	18	0.45	NM_013443	B3KQ01|Q5T9C4|Q5T9C5|Q9H8A2|Q9ULB8	Silent	SNP	ENST00000373146.1	37	CCDS6882.1	.	.	.	.	.	.	.	.	.	.	G	11.08	1.533692	0.27387	4.54E-4	2.33E-4	ENSG00000160408	ENST00000542456	T	0.42900	0.96	4.88	-9.76	0.00503	.	.	.	.	.	T	0.21881	0.0527	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19160	-1.0314	7	.	.	.	-18.7556	10.2126	0.43150	0.5137:0.3211:0.1652:0.0	rs11552227	32	B4DU80	.	L	32	ENSP00000438109:S32L	.	S	-	2	0	ST6GALNAC6	129696621	0.000000	0.05858	0.082000	0.20525	0.589000	0.36550	-2.451000	0.01006	-3.649000	0.00126	-1.224000	0.01588	TCG	G|0.999;A|0.001	0.001	strong		0.587	ST6GALNAC6-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054278.1	NM_013443		A	130656800	G	A	130656800	2	1	24	1	0	0	0	0	0	0	0	1	15243	1045	37	1		1	ST6GALNAC6	9	130656800	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	4512359	130656800	10556631	307	8524											
QRFP	347148	hgsc.bcm.edu	37	chr9	133768827	133768827	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctggcccttcaccgccgaccGaagcggaagctgaagccgcc	8	4	12	17	5	1	1	1	1	0	0	1	4	1	2	6	2	3	1	6	2	3	1	rs139926605	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:133768827G>A	ENST00000343079.1	-	1	398	c.399C>T	c.(397-399)ttC>ttT	p.F133F		NM_198180.1	NP_937823.1			pyroglutamylated RFamide peptide											cervix(1)|endometrium(3)|lung(1)|skin(2)	7	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.17e-05)|Epithelial(140;0.000267)		ACCGCCGACCGAAGCGGAAGC	0.607													G|||	23	0.00459265	0.0068	0.0043	5008	,	,		18715	0.0		0.001	False		,,,				2504	0.0102				p.F133F		Atlas-SNP	.											.	QRFP	14	.	0			c.C399T						PASS	.	G		16,4388		0,16,2186	57	68	64		399	-7.2	0.6	9	dbSNP_134	64	10,8588		0,10,4289	no	coding-synonymous	QRFP	NM_198180.1		0,26,6475	AA,AG,GG		0.1163,0.3633,0.2		133/137	133768827	26,12976	2202	4299	6501	SO:0001819	synonymous_variant	347148	exon1			CCGACCGAAGCGG	AB109625	CCDS6936.1	9q34.12	2013-02-28			ENSG00000188710	ENSG00000188710		"Endogenous ligands"	29982	protein-coding gene	gene with protein product	"prepro-QRFP"	609795				12714592, 15808908	Standard	NM_198180		Approved	26RFa, P518	uc011mcb.2	P83859	OTTHUMG00000131663	ENST00000343079.1:c.399C>T	9.37:g.133768827G>A		68	0	0		79	40	0.506329	NM_198180		Silent	SNP	ENST00000343079.1	37	CCDS6936.1																																																																																			G|0.998;A|0.002	0.002	strong		0.607	QRFP-001	KNOWN	mRNA_start_NF|mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254566.1	NM_198180		A	133768827	G	A	133768827	2	1	24	1	0	0	0	0	0	0	0	1	12892	1049	37	1		1	QRFP	9	133768827	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	3112027	133768827	7444604	308	8525											
FIBCD1	84929	hgsc.bcm.edu	37	chr9	133779563	133779563	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cataggaggcgtgcgcaccgCgcaggtactgcccattgagg	8	6	15	12	4	0	1	0	1	0	0	0	2	0	2	2	4	3	3	2	4	2	3	rs138892175		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:133779563C>T	ENST00000372338.4	-	7	1516	c.1274G>A	c.(1273-1275)cGc>cAc	p.R425H	FIBCD1_ENST00000372337.2_Missense_Mutation_p.R267H|FIBCD1_ENST00000448616.1_Missense_Mutation_p.R425H|FIBCD1_ENST00000253018.4_Intron	NM_032843.4	NP_116232.3	Q8N539	FBCD1_HUMAN	fibrinogen C domain containing 1	425	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)		GTGCGCACCGCGCAGGTACTG	0.627																																					p.R425H		Atlas-SNP	.											FIBCD1,NS,carcinoma,+1,2	FIBCD1	34	2	0			c.G1274A						PASS	.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	133	112	119		1274,1274	3.8	0.9	9	dbSNP_134	119	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	FIBCD1	NM_001145106.1,NM_032843.4	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	425/462,425/462	133779563	1,13005	2203	4300	6503	SO:0001583	missense	84929	exon8			GCACCGCGCAGGT	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.1274G>A	9.37:g.133779563C>T	ENSP00000361413:p.Arg425His	96	0	0		117	61	0.521368	NM_001145106	A3KFK0|Q6UXK6|Q96SJ7	Missense_Mutation	SNP	ENST00000372338.4	37	CCDS6937.1	.	.	.	.	.	.	.	.	.	.	C	17.08	3.298660	0.60195	0.0	1.16E-4	ENSG00000130720	ENST00000448616;ENST00000372338;ENST00000372337	T;T;T	0.76060	-0.99;-0.99;-0.99	4.66	3.75	0.43078	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2 (1);	0.108817	0.56097	D	0.000024	T	0.58566	0.2131	L	0.46614	1.455	0.48288	D	0.999625	P	0.40619	0.724	B	0.25291	0.059	T	0.64309	-0.6438	10	0.54805	T	0.06	.	8.3984	0.32570	0.0:0.8277:0.0:0.1723	.	425	Q8N539	FBCD1_HUMAN	H	425;425;267	ENSP00000414501:R425H;ENSP00000361413:R425H;ENSP00000361412:R267H	ENSP00000361412:R267H	R	-	2	0	FIBCD1	132769384	0.842000	0.29525	0.881000	0.34555	0.103000	0.19146	1.528000	0.35985	2.138000	0.66242	0.455000	0.32223	CGC	C|1.000;T|0.000	0.000	weak		0.627	FIBCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054687.2	NM_032843		T	133779563	C	T	133779563	3	4	24	1	0	0	0	0	1	0	0	0	5892	768	27	1	115	1	FIBCD1	9	133779563	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	10736	133779563	7433868	309	8526											
BAT2L1	84726	hgsc.bcm.edu	37	chr9	134340174	134340174	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	catcaatgggcagcatgttcCggcaacagtccatcgaggac	11	7	11	12	2	1	0	1	0	0	0	4	2	3	1	2	3	2	4	2	3	2	1			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:134340174C>T	ENST00000357304.4	+	11	1484	c.1429C>T	c.(1429-1431)Cgg>Tgg	p.R477W	PRRC2B_ENST00000458550.1_Missense_Mutation_p.R477W|PRRC2B_ENST00000405995.1_Missense_Mutation_p.R477W|PRRC2B_ENST00000372249.1_5'UTR	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	477							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						CAGCATGTTCCGGCAACAGTC	0.582																																					p.R477W		Atlas-SNP	.											.	PRRC2B	266	.	0			c.C1429T						PASS	.						30	32	32					9																	134340174		2030	4175	6205	SO:0001583	missense	84726	exon11			ATGTTCCGGCAAC	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.1429C>T	9.37:g.134340174C>T	ENSP00000349856:p.Arg477Trp	115	0	0		125	55	0.44	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	37	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	C	19.33	3.806464	0.70682	.	.	ENSG00000130723	ENST00000405995;ENST00000357304;ENST00000458550;ENST00000422467	T;T;T;T	0.26373	4.12;4.46;4.12;1.74	5.61	3.64	0.41730	.	0.000000	0.39210	U	0.001428	T	0.45478	0.1344	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.45991	-0.9223	10	0.66056	D	0.02	-3.5568	13.2394	0.59987	0.3749:0.6251:0.0:0.0	.	477	Q5JSZ5	PRC2B_HUMAN	W	477;477;477;17	ENSP00000384606:R477W;ENSP00000349856:R477W;ENSP00000398853:R477W;ENSP00000391063:R17W	ENSP00000349856:R477W	R	+	1	2	PRRC2B	133329995	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	1.986000	0.40677	1.355000	0.45865	0.655000	0.94253	CGG	.	.	none		0.582	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	134340174	C	T	134340174	3	4	24	1	0	0	0	0	1	0	0	0	1320	643	23	1	1471	1	BAT2L1	9	134340174	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	560611	134340174	6873257	310	8527											
BAT2L1	84726	hgsc.bcm.edu	37	chr9	134351655	134351655	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgggagacggcctccgaaaGcagcgacttcagcgagcggc	9	4	16	12	5	1	1	1	0	0	1	2	5	2	1	2	3	4	1	2	3	1	1			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:134351655G>A	ENST00000357304.4	+	15	4194	c.4139G>A	c.(4138-4140)aGc>aAc	p.S1380N	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	1380							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						GCCTCCGAAAGCAGCGACTTC	0.662											OREG0019561	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S1380N		Atlas-SNP	.											.	PRRC2B	266	.	0			c.G4139A						PASS	.						16	19	18					9																	134351655		1954	4134	6088	SO:0001583	missense	84726	exon15			CCGAAAGCAGCGA	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.4139G>A	9.37:g.134351655G>A	ENSP00000349856:p.Ser1380Asn	78	0	0	1610	94	50	0.531915	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	37	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	G	18.55	3.647371	0.67358	.	.	ENSG00000130723	ENST00000357304;ENST00000418650	T	0.05447	3.44	5.93	5.93	0.95920	.	.	.	.	.	T	0.11537	0.0281	M	0.73962	2.25	0.80722	D	1	P;B;B	0.40970	0.734;0.347;0.236	B;B;B	0.35470	0.203;0.12;0.056	T	0.04565	-1.0942	9	0.33940	T	0.23	.	19.3291	0.94278	0.0:0.0:1.0:0.0	.	676;113;1380	Q5H9R5;Q5JSZ8;Q5JSZ5	.;.;PRC2B_HUMAN	N	1380;676	ENSP00000349856:S1380N	ENSP00000349856:S1380N	S	+	2	0	PRRC2B	133341476	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.145000	0.58065	2.814000	0.96858	0.655000	0.94253	AGC	.	.	none		0.662	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	134351655	G	A	134351655	3	1	24	1	0	0	0	0	1	0	0	0	1320	971	34	2	4197	2	BAT2L1	9	134351655	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	11481	134351655	6861776	311	8528											
SEC16A	9919	hgsc.bcm.edu	37	chr9	139347953	139347953	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttccaacaggcgcctcctgcGgcactatccctgtcaacggg	7	8	10	16	3	1	0	1	0	0	0	4	0	4	0	4	3	3	1	4	3	3	2	rs202042941		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139347953G>A	ENST00000371706.3	-	20	5585	c.5552C>T	c.(5551-5553)cCg>cTg	p.P1851L	SEC16A_ENST00000290037.6_Missense_Mutation_p.P1851L|SEC16A_ENST00000431893.2_Missense_Mutation_p.P1851L|SEC16A_ENST00000313050.7_Missense_Mutation_p.P2029L|SEC16A_ENST00000398335.1_5'Flank			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	1851	Pro-rich.				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)		CGCCTCCTGCGGCACTATCCC	0.483																																					p.P2029L		Atlas-SNP	.											.	SEC16A	249	.	0			c.C6086T						PASS	.	G	LEU/PRO	4,3968		0,4,1982	75	79	78		6086	2	0	9		78	6,8312		0,6,4153	yes	missense	SEC16A	NM_014866.1	98	0,10,6135	AA,AG,GG		0.0721,0.1007,0.0814	benign	2029/2358	139347953	10,12280	1986	4159	6145	SO:0001583	missense	9919	exon22			TCCTGCGGCACTA	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.5552C>T	9.37:g.139347953G>A	ENSP00000360771:p.Pro1851Leu	29	0	0		28	9	0.321429	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Missense_Mutation	SNP	ENST00000371706.3	37		.	.	.	.	.	.	.	.	.	.	G	15.41	2.825603	0.50739	0.001007	7.21E-4	ENSG00000148396	ENST00000313050;ENST00000277537;ENST00000453963;ENST00000371706;ENST00000290037;ENST00000431893;ENST00000404925;ENST00000398348	T;T;T;T;T;T	0.44482	1.89;0.92;1.51;1.88;1.88;1.87	4.84	1.96	0.26148	.	0.491778	0.21508	N	0.073403	T	0.56321	0.1977	M	0.71581	2.175	0.25198	N	0.990071	D;D;P;B;P	0.76494	0.997;0.999;0.573;0.278;0.769	D;D;B;B;B	0.71870	0.926;0.975;0.213;0.035;0.106	T	0.44772	-0.9306	10	0.45353	T	0.12	-0.9711	7.4567	0.27270	0.278:0.0:0.722:0.0	.	2029;1851;1851;1419;1851	F1T0I1;O15027-5;O15027-4;A4QN19;O15027	.;.;.;.;SC16A_HUMAN	L	2029;423;751;1851;1851;1851;1419;387	ENSP00000325827:P2029L;ENSP00000277537:P423L;ENSP00000403525:P751L;ENSP00000360771:P1851L;ENSP00000290037:P1851L;ENSP00000387583:P1851L	ENSP00000277537:P423L	P	-	2	0	SEC16A	138467774	0.128000	0.22383	0.002000	0.10522	0.019000	0.09904	1.080000	0.30779	0.191000	0.20236	0.561000	0.74099	CCG	.	.	weak		0.483	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459		A	139347953	G	A	139347953	3	1	24	1	0	0	0	0	1	0	0	0	14001	1116	39	1	1031	1	SEC16A	9	139347953	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	4996298	139347953	1865478	312	8529											
MAMDC4	158056	hgsc.bcm.edu	37	chr9	139748690	139748690	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccaactgtcccccgggacAccaccactgccagaacaagg	11	3	10	17	1	0	1	0	0	0	1	1	2	1	2	6	3	3	0	6	3	3	0	rs151266186	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139748690A>G	ENST00000317446.2	+	7	748	c.698A>G	c.(697-699)cAc>cGc	p.H233R	MAMDC4_ENST00000485732.1_3'UTR|MAMDC4_ENST00000445819.1_Missense_Mutation_p.H233R	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)		CCCCCGGGACACCACCACTGC	0.657													A|||	2	0.000399361	0.0	0.0	5008	,	,		13727	0.0		0.002	False		,,,				2504	0.0				p.H233R		Atlas-SNP	.											.	MAMDC4	117	.	0			c.A698G						PASS	.	A	ARG/HIS	1,4379		0,1,2189	24	26	25		698	4.3	0	9	dbSNP_134	25	14,8574		0,14,4280	yes	missense	MAMDC4	NM_206920.2	29	0,15,6469	GG,GA,AA		0.163,0.0228,0.1157	probably-damaging	233/1138	139748690	15,12953	2190	4294	6484	SO:0001583	missense	158056	exon7			CGGGACACCACCA	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.698A>G	9.37:g.139748690A>G	ENSP00000319388:p.His233Arg	109	0	0		95	34	0.357895	NM_206920		Missense_Mutation	SNP	ENST00000317446.2	37	CCDS7010.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	.	8.328	0.825771	0.16749	2.28E-4	0.00163	ENSG00000177943	ENST00000317446;ENST00000445819	D;D	0.95272	-3.66;-3.66	4.34	4.34	0.51931	.	0.426385	0.21311	N	0.076630	D	0.91236	0.7238	L	0.48935	1.535	0.09310	N	1	B	0.28636	0.218	B	0.31101	0.124	T	0.82218	-0.0566	10	0.25106	T	0.35	-8.7896	12.4851	0.55868	1.0:0.0:0.0:0.0	.	233	Q6UXC1-2	.	R	233	ENSP00000319388:H233R;ENSP00000411339:H233R	ENSP00000319388:H233R	H	+	2	0	MAMDC4	138868511	0.004000	0.15560	0.013000	0.15412	0.461000	0.32589	1.047000	0.30367	1.818000	0.53035	0.459000	0.35465	CAC	A|0.999;G|0.001	0.001	strong		0.657	MAMDC4-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254642.3	NM_206920		G	139748690	A	G	139748690	3	3	24	1	0	0	0	0	1	0	0	0	9213	159	6	3	724	3	MAMDC4	9	139748690	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	400737	139748690	1464741	313	8530											
FBXW5	54461	hgsc.bcm.edu	37	chr9	139835725	139835725	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccacgaagtccctgctgaCgtccaggaagatgaagaagc	12	5	13	11	2	0	4	0	2	0	2	2	6	2	5	3	2	2	1	3	2	4	0	rs374757784		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:139835725C>T	ENST00000325285.3	-	8	1514	c.1435G>A	c.(1435-1437)Gtc>Atc	p.V479I	FBXW5_ENST00000483559.1_5'UTR	NM_018998.3	NP_061871.1	Q969U6	FBXW5_HUMAN	F-box and WD repeat domain containing 5	479					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)		TCCCTGCTGACGTCCAGGAAG	0.697																																					p.V479I		Atlas-SNP	.											.	FBXW5	36	.	0			c.G1435A						PASS	.	C	ILE/VAL	0,4404		0,0,2202	32	27	29		1435	4.2	1	9		29	1,8595	1.2+/-3.3	0,1,4297	no	missense	FBXW5	NM_018998.2	29	0,1,6499	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	479/567	139835725	1,12999	2202	4298	6500	SO:0001583	missense	54461	exon8			TGCTGACGTCCAG	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.1435G>A	9.37:g.139835725C>T	ENSP00000313034:p.Val479Ile	16	0	0		24	13	0.541667	NM_018998	B2RDZ6|Q59ET5|Q5SPZ8|Q5SPZ9|Q5SQ00|Q5SQ02|Q5SQ03|Q5SQ04|Q8WY79|Q96GJ6|Q9BSU8|Q9H6A8|Q9HBQ6|Q9NSZ3	Missense_Mutation	SNP	ENST00000325285.3	37	CCDS7014.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.002574	0.74932	0.0	1.16E-4	ENSG00000159069	ENST00000325285	T	0.65732	-0.17	4.24	4.24	0.50183	WD40/YVTN repeat-like-containing domain (1);Soluble quinoprotein glucose/sorbosone dehydrogenase (1);	0.000000	0.85682	D	0.000000	T	0.73118	0.3546	L	0.54323	1.7	0.80722	D	1	D;P	0.76494	0.999;0.751	D;B	0.72982	0.979;0.106	T	0.69401	-0.5155	10	0.21540	T	0.41	-10.464	16.8298	0.85941	0.0:1.0:0.0:0.0	.	344;479	Q59ET5;Q969U6	.;FBXW5_HUMAN	I	479	ENSP00000313034:V479I	ENSP00000313034:V479I	V	-	1	0	FBXW5	138955546	1.000000	0.71417	0.985000	0.45067	0.964000	0.63967	7.002000	0.76304	2.204000	0.70986	0.561000	0.74099	GTC	.	.	weak		0.697	FBXW5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055227.1	NM_018998		T	139835725	C	T	139835725	3	4	24	1	0	0	0	0	1	0	0	0	5776	536	19	1	273	1	FBXW5	9	139835725	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	87035	139835725	1377706	314	8531											
EXD3	54932	hgsc.bcm.edu	37	chr9	140250749	140250749	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccgtaccgctcctgcagaCgcaagacctgcctgctcagc	7	6	10	18	4	1	2	1	0	0	2	2	2	2	2	5	0	5	5	5	0	2	1	rs180687197	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr9:140250749C>T	ENST00000340951.4	-	8	923	c.728G>A	c.(727-729)cGt>cAt	p.R243H	EXD3_ENST00000342129.4_5'UTR	NM_017820.3	NP_060290.3	Q9NX53	MUT7B_HUMAN	exonuclease 3'-5' domain containing 3	0										NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)	12						CTCCTGCAGACGCAAGACCTG	0.652													C|||	3	0.000599042	0.0008	0.0014	5008	,	,		16664	0.0		0.001	False		,,,				2504	0.0				p.R243H		Atlas-SNP	.											.	EXD3	86	.	0			c.G728A						PASS	.	C	HIS/ARG	1,4219		0,1,2109	28	33	31		728	1.4	0	9		31	7,8453		0,7,4223	yes	missense	EXD3	NM_017820.3	29	0,8,6332	TT,TC,CC		0.0827,0.0237,0.0631	benign	243/877	140250749	8,12672	2110	4230	6340	SO:0001583	missense	54932	exon8			TGCAGACGCAAGA		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.728G>A	9.37:g.140250749C>T	ENSP00000340474:p.Arg243His	27	0	0		45	25	0.555556	NM_017820	Q6P1M1|Q8IXT8	Missense_Mutation	SNP	ENST00000340951.4	37	CCDS48066.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	13.54	2.267912	0.40095	2.37E-4	8.27E-4	ENSG00000187609	ENST00000340951	T	0.63580	-0.05	2.34	1.41	0.22369	.	0.270733	0.24044	N	0.042075	T	0.43567	0.1253	L	0.35854	1.095	0.80722	D	1	B	0.30179	0.271	B	0.19148	0.024	T	0.31166	-0.9953	10	0.72032	D	0.01	.	5.0914	0.14710	0.0:0.6764:0.0:0.3236	.	243	Q8N9H8	MUT7_HUMAN	H	243	ENSP00000340474:R243H	ENSP00000340474:R243H	R	-	2	0	EXD3	139370570	0.005000	0.15991	0.019000	0.16419	0.567000	0.35839	1.383000	0.34385	0.294000	0.22547	0.306000	0.20318	CGT	C|0.999;T|0.001	0.001	strong		0.652	EXD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343182.1	NM_017820		T	140250749	C	T	140250749	3	4	24	1	0	0	0	0	1	0	0	0	5301	536	19	1	1962	1	EXD3	9	140250749	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	415024	140250749	962682	315	8532											
AKR1C2	1646	hgsc.bcm.edu	37	chr10	5043747	5043747	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttctctcttcacactgccatCtgcaatcttgcttcggatgg	6	15	7	13	1	5	0	1	0	4	0	7	1	5	1	1	2	3	2	1	2	1	4	rs142672563	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:5043747C>G	ENST00000380753.4	-	2	398	c.211G>C	c.(211-213)Gat>Cat	p.D71H	AKR1C2_ENST00000455190.1_Missense_Mutation_p.D71H|AKR1C2_ENST00000407674.1_Missense_Mutation_p.D71H|AKR1C2_ENST00000421196.3_Missense_Mutation_p.D71H	NM_205845.2	NP_995317.1	P52895	AK1C2_HUMAN	aldo-keto reductase family 1, member C2	71					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)	ACACTGCCATCTGCAATCTTG	0.443													C|||	13	0.00259585	0.0008	0.0043	5008	,	,		21249	0.0		0.001	False		,,,				2504	0.0082				p.D71H		Atlas-SNP	.											.	AKR1C2	68	.	0			c.G211C						PASS	.	C	HIS/ASP,HIS/ASP,HIS/ASP	0,4406		0,0,2203	133	114	120		211,211,211	2.3	1	10	dbSNP_134	120	11,8583	8.4+/-32.0	0,11,4286	no	missense,missense,missense	AKR1C2	NM_001135241.1,NM_001354.4,NM_205845.1	81,81,81	0,11,6489	GG,GC,CC		0.128,0.0,0.0846	probably-damaging,probably-damaging,probably-damaging	71/140,71/324,71/324	5043747	11,12989	2203	4297	6500	SO:0001583	missense	1646	exon4			TGCCATCTGCAAT	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.211G>C	10.37:g.5043747C>G	ENSP00000370129:p.Asp71His	274	0	0		327	158	0.48318	NM_001354	A8K2N9|B4DKR9|Q14133|Q5SR16|Q7M4N1|Q96A71	Missense_Mutation	SNP	ENST00000380753.4	37	CCDS7062.1	4	0.0018315018315018315	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	0	0.0	C	12.09	1.834056	0.32421	0.0	0.00128	ENSG00000151632	ENST00000380753;ENST00000421196;ENST00000407674;ENST00000455190	T;T;T;T	0.53206	0.63;0.63;0.63;0.63	2.35	2.35	0.29111	NADP-dependent oxidoreductase domain (3);	0.000000	0.56097	D	0.000030	T	0.53769	0.1817	M	0.72894	2.215	0.35214	D	0.775386	D;D;D	0.64830	0.989;0.994;0.988	D;P;P	0.65010	0.931;0.846;0.908	T	0.71735	-0.4503	10	0.87932	D	0	.	10.778	0.46361	0.0:1.0:0.0:0.0	.	71;71;71	B4DKR9;B4DK69;P52895	.;.;AK1C2_HUMAN	H	71	ENSP00000370129:D71H;ENSP00000392694:D71H;ENSP00000385221:D71H;ENSP00000408440:D71H	ENSP00000370129:D71H	D	-	1	0	AKR1C2	5033747	0.999000	0.42202	0.971000	0.41717	0.309000	0.27889	4.461000	0.60115	1.601000	0.50113	0.205000	0.17691	GAT	C|0.998;G|0.002	0.002	strong		0.443	AKR1C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046531.1	NM_001354		G	5043747	C	G	5043747	3	3	24	1	0	0	0	0	1	0	0	0	470	913	32	4	847	4	AKR1C2	10	5043747	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10		5043747	130491000	316	8533											
FRMD4A	55691	hgsc.bcm.edu	37	chr10	13779898	13779898	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tggaagatccctttgtagctCaggcccagccaccatggtat	9	10	10	12	0	1	1	1	0	0	1	2	2	2	2	4	3	2	3	4	3	3	3	rs61755072	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:13779898C>T	ENST00000357447.2	-	12	1073	c.705G>A	c.(703-705)ctG>ctA	p.L235L	FRMD4A_ENST00000358621.4_Silent_p.L220L|RP11-353M9.1_ENST00000449462.1_RNA|FRMD4A_ENST00000378503.1_Silent_p.L235L|FRMD4A_ENST00000342409.2_Silent_p.L251L	NM_018027.3	NP_060497.3	Q9P2Q2	FRM4A_HUMAN	FERM domain containing 4A	235	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						CTTTGTAGCTCAGGCCCAGCC	0.468													C|||	8	0.00159744	0.0008	0.0014	5008	,	,		19078	0.0		0.006	False		,,,				2504	0.0				p.L235L		Atlas-SNP	.											.	FRMD4A	108	.	0			c.G705A						PASS	.	C		9,4397	15.5+/-35.6	0,9,2194	156	116	130		705	1.5	1	10	dbSNP_129	130	90,8510	51.1+/-111.2	0,90,4210	no	coding-synonymous	FRMD4A	NM_018027.3		0,99,6404	TT,TC,CC		1.0465,0.2043,0.7612		235/1040	13779898	99,12907	2203	4300	6503	SO:0001819	synonymous_variant	55691	exon12			GTAGCTCAGGCCC	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.705G>A	10.37:g.13779898C>T		147	0	0		138	68	0.492754	NM_018027	A7E2Y3|Q5T377	Silent	SNP	ENST00000357447.2	37	CCDS7101.1																																																																																			C|0.994;T|0.006	0.006	strong		0.468	FRMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046889.1	NM_018027		T	13779898	C	T	13779898	2	4	24	1	0	0	0	0	0	0	0	1	6059	813	29	2		2	FRMD4A	10	13779898	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	8736151	13779898	121754849	317	8534											
THNSL1	79896	hgsc.bcm.edu	37	chr10	25313254	25313254	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tttttgcacactgtatcccaCcaagttgcaattatatgata	12	15	5	9	0	0	1	0	1	0	0	1	1	1	1	2	0	2	4	2	0	6	7	rs41279892	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:25313254C>A	ENST00000524413.1	+	3	1449	c.1102C>A	c.(1102-1104)Cca>Aca	p.P368T	THNSL1_ENST00000376356.4_Missense_Mutation_p.P368T			Q8IYQ7	THNS1_HUMAN	threonine synthase-like 1 (S. cerevisiae)	368						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)	CTGTATCCCACCAAGTTGCAA	0.383													C|||	51	0.0101837	0.0023	0.0187	5008	,	,		19468	0.0		0.0258	False		,,,				2504	0.0092				p.P368T		Atlas-SNP	.											.	THNSL1	70	.	0			c.C1102A						PASS	.	C	THR/PRO	19,4387	25.3+/-52.1	0,19,2184	93	91	92		1102	3.9	0.3	10	dbSNP_127	92	198,8402	86.9+/-149.2	0,198,4102	yes	missense	THNSL1	NM_024838.4	38	0,217,6286	AA,AC,CC		2.3023,0.4312,1.6685	benign	368/744	25313254	217,12789	2203	4300	6503	SO:0001583	missense	79896	exon3			ATCCCACCAAGTT	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.1102C>A	10.37:g.25313254C>A	ENSP00000434887:p.Pro368Thr	84	0	0		96	42	0.4375	NM_024838	B3KWL1|D3DRV3|Q5VV21	Missense_Mutation	SNP	ENST00000524413.1	37	CCDS7147.1	29	0.013278388278388278	1	0.0020325203252032522	10	0.027624309392265192	0	0.0	18	0.023746701846965697	C	2.420	-0.333296	0.05278	0.004312	0.023023	ENSG00000185875	ENST00000524413;ENST00000376356	T;T	0.10860	2.83;2.83	5.71	3.88	0.44766	Threonine synthase (1);Pyridoxal phosphate-dependent enzyme, beta subunit (2);	0.324845	0.30269	N	0.010010	T	0.02304	0.0071	N	0.25789	0.76	0.09310	N	1	B	0.19445	0.036	B	0.21546	0.035	T	0.29366	-1.0014	10	0.72032	D	0.01	-24.6105	6.0648	0.19858	0.2421:0.6037:0.0:0.1541	rs41279892	368	Q8IYQ7	THNS1_HUMAN	T	368	ENSP00000434887:P368T;ENSP00000365534:P368T	ENSP00000365534:P368T	P	+	1	0	THNSL1	25353260	0.056000	0.20664	0.287000	0.24848	0.804000	0.45430	3.083000	0.50136	0.783000	0.33636	-0.143000	0.13931	CCA	C|0.984;A|0.016	0.016	strong		0.383	THNSL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394913.1	NM_024838		A	25313254	C	A	25313254	3	1	24	1	0	0	0	0	1	0	0	0	15877	507	18	4	1104	4	THNSL1	10	25313254	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	11533356	25313254	110221493	318	8535											
ANKRD26	22852	hgsc.bcm.edu	37	chr10	27322306	27322306	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttgaagttgtctcacaacaaCctgataagacattttgttac	13	14	6	8	0	1	3	1	2	1	1	2	3	1	3	1	0	3	2	1	0	5	6	rs146819984	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:27322306C>T	ENST00000376087.4	-	25	3820	c.3655G>A	c.(3655-3657)Gtt>Att	p.V1219I	ANKRD26_ENST00000376070.3_Splice_Site_p.V776I|ANKRD26_ENST00000436985.2_Splice_Site_p.V1235I	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1218			V -> L (in dbSNP:rs12572862).		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						CTCACAACAACCTGATAAGAC	0.279													C|||	42	0.00838658	0.0045	0.0058	5008	,	,		14044	0.0		0.0129	False		,,,				2504	0.0194				p.V1219I		Atlas-SNP	.											.	ANKRD26	179	.	0			c.G3655A						PASS	.	C	ILE/VAL	8,3660		0,8,1826	136	120	125		3655	4.5	0.5	10	dbSNP_134	125	90,8082		1,88,3997	no	missense-near-splice	ANKRD26	NM_014915.2	29	1,96,5823	TT,TC,CC		1.1013,0.2181,0.8277	benign	1219/1711	27322306	98,11742	1834	4086	5920	SO:0001630	splice_region_variant	22852	exon25			CAACAACCTGATA	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.3655-1G>A	10.37:g.27322306C>T		65	0	0		88	53	0.602273	NM_014915	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Missense_Mutation	SNP	ENST00000376087.4	37	CCDS41499.1	17	0.007783882783882784	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	11	0.014511873350923483	C	11.08	1.534978	0.27475	0.002181	0.011013	ENSG00000107890	ENST00000376070;ENST00000376087;ENST00000436985	T;T;T	0.34667	3.83;1.35;1.36	5.41	4.51	0.55191	.	0.433404	0.18085	N	0.152181	T	0.26919	0.0659	M	0.62209	1.925	0.28550	N	0.911682	B;B;B	0.11235	0.003;0.001;0.004	B;B;B	0.10450	0.005;0.002;0.004	T	0.23154	-1.0196	10	0.48119	T	0.1	.	8.3454	0.32270	0.0:0.8224:0.0:0.1776	.	1219;1218;1235	Q9UPS8-3;Q9UPS8;A1L497	.;ANR26_HUMAN;.	I	776;1219;1235	ENSP00000365238:V776I;ENSP00000365255:V1219I;ENSP00000405112:V1235I	ENSP00000365238:V776I	V	-	1	0	ANKRD26	27362312	0.551000	0.26497	0.507000	0.27676	0.934000	0.57294	1.015000	0.29963	1.320000	0.45209	0.586000	0.80456	GTT	C|0.991;T|0.009	0.009	strong		0.279	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1		Missense_Mutation	T	27322306	C	T	27322306	5	4	24	1	0	0	0	0	0	0	1	0	654	521	18	2	1517	2	ANKRD26	10	27322306	Splice_Site	SNP	C	TCGA-G8-6326-01A-11D-2210-10	2009052	27322306	108212441	319	8536											
LYZL2	119180	hgsc.bcm.edu	37	chr10	30915078	30915078	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttctccttcagctttccgCgtctgcaccacgcgaagctg	5	12	9	15	4	3	0	1	0	2	0	5	1	4	0	3	0	3	4	3	0	1	3			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:30915078C>T	ENST00000375318.2	-	3	448	c.392G>A	c.(391-393)cGc>cAc	p.R131H		NM_183058.2	NP_898881.2	Q7Z4W2	LYZL2_HUMAN	lysozyme-like 2	85					cell wall macromolecule catabolic process (GO:0016998)	extracellular region (GO:0005576)	lysozyme activity (GO:0003796)			NS(2)|central_nervous_system(1)|large_intestine(1)|lung(14)|prostate(1)	19		Prostate(175;0.151)				CAGCTTTCCGCGTCTGCACCA	0.567																																					p.R131H		Atlas-SNP	.											.	LYZL2	33	.	0			c.G392A						PASS	.						173	144	154					10																	30915078		2203	4300	6503	SO:0001583	missense	119180	exon3			TTTCCGCGTCTGC	AF139543	CCDS7167.2	10p11.23	2009-12-04			ENSG00000151033	ENSG00000151033			29613	protein-coding gene	gene with protein product		612748					Standard	NM_183058		Approved		uc001ivk.3	Q7Z4W2	OTTHUMG00000017898	ENST00000375318.2:c.392G>A	10.37:g.30915078C>T	ENSP00000364467:p.Arg131His	164	0	0		210	93	0.442857	NM_183058	Q6NZ69	Missense_Mutation	SNP	ENST00000375318.2	37	CCDS7167.2	.	.	.	.	.	.	.	.	.	.	c	6.169	0.399451	0.11696	.	.	ENSG00000151033	ENST00000375318	T	0.69435	-0.4	2.27	-4.53	0.03462	.	1.768140	0.03329	N	0.193126	T	0.43211	0.1237	N	0.04148	-0.265	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.39840	-0.9594	10	0.59425	D	0.04	-18.6248	8.4711	0.32986	0.0:0.4079:0.0:0.5921	.	131	Q7Z4W2-2	.	H	131	ENSP00000364467:R131H	ENSP00000364467:R131H	R	-	2	0	LYZL2	30955084	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.771000	0.00779	-1.432000	0.01979	-2.148000	0.00335	CGC	.	.	none		0.567	LYZL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047434.1	NM_183058		T	30915078	C	T	30915078	3	4	24	1	0	0	0	0	1	0	0	0	9141	768	27	1	204	1	LYZL2	10	30915078	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	3592772	30915078	104619669	320	8537											
GJD4	219770	hgsc.bcm.edu	37	chr10	35896700	35896700	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagggcgtgtgcgtcctcCtcccctccgccgtcttcagc	2	10	10	19	4	2	0	1	0	1	0	7	0	7	0	7	1	2	0	7	1	0	1	rs76906304	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:35896700C>T	ENST00000321660.1	+	2	417	c.259C>T	c.(259-261)Ctc>Ttc	p.L87F	RP11-425A6.5_ENST00000609313.1_RNA	NM_153368.2	NP_699199.2	Q96KN9	CXD4_HUMAN	gap junction protein, delta 4, 40.1kDa	87					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						GTGCGTCCTCCTCCCCTCCGC	0.706													C|||	33	0.00658946	0.0	0.013	5008	,	,		11126	0.0		0.0119	False		,,,				2504	0.0123				p.L87F		Atlas-SNP	.											GJD4,NS,carcinoma,0,1	GJD4	38	1	0			c.C259T						PASS	.	C	PHE/LEU	16,4390	21.2+/-45.6	0,16,2187	148	122	131		259	4.3	0.1	10	dbSNP_131	131	148,8452	70.7+/-133.2	1,146,4153	yes	missense	GJD4	NM_153368.2	22	1,162,6340	TT,TC,CC		1.7209,0.3631,1.261	probably-damaging	87/371	35896700	164,12842	2203	4300	6503	SO:0001583	missense	219770	exon2			GTCCTCCTCCCCT	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.259C>T	10.37:g.35896700C>T	ENSP00000315070:p.Leu87Phe	58	0	0		64	30	0.46875	NM_153368	Q8N2R7	Missense_Mutation	SNP	ENST00000321660.1	37	CCDS7191.1	12	0.005494505494505495	0	0.0	5	0.013812154696132596	0	0.0	7	0.009234828496042216	C	15.31	2.795160	0.50208	0.003631	0.017209	ENSG00000177291	ENST00000321660	D	0.99129	-5.46	6.11	4.27	0.50696	Connexin, N-terminal (1);	0.215706	0.41938	N	0.000797	D	0.97228	0.9094	L	0.56769	1.78	0.51233	D	0.999916	D	0.52996	0.957	P	0.55087	0.768	D	0.93664	0.6984	10	0.62326	D	0.03	.	13.6296	0.62188	0.0:0.8795:0.0:0.1205	.	87	Q96KN9	CXD4_HUMAN	F	87	ENSP00000315070:L87F	ENSP00000315070:L87F	L	+	1	0	GJD4	35936706	0.680000	0.27605	0.144000	0.22314	0.036000	0.12997	1.246000	0.32803	0.916000	0.36871	0.655000	0.94253	CTC	C|0.989;T|0.011	0.011	strong		0.706	GJD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047576.1	NM_153368		T	35896700	C	T	35896700	3	4	24	1	0	0	0	0	1	0	0	0	6427	681	24	2	265	2	GJD4	10	35896700	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	4981622	35896700	99638047	321	8538											
ZNF37A	7587	hgsc.bcm.edu	37	chr10	38406359	38406359	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actattcaataatgaagttcAatgagtttaacaaaggtgga	17	12	8	4	0	2	2	2	2	0	0	2	3	2	3	0	2	1	2	0	2	7	6	rs150470434	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:38406359A>C	ENST00000361085.5	+	7	625	c.280A>C	c.(280-282)Aat>Cat	p.N94H	ZNF37A_ENST00000351773.3_Missense_Mutation_p.N94H	NM_001178101.1|NM_003421.2	NP_001171572.1|NP_003412.1	P17032	ZN37A_HUMAN	zinc finger protein 37A	94					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						AATGAAGTTCAATGAGTTTAA	0.294													A|||	4	0.000798722	0.0	0.0	5008	,	,		18981	0.0		0.004	False		,,,				2504	0.0				p.N94H		Atlas-SNP	.											.	ZNF37A	118	.	0			c.A280C						PASS	.	A	HIS/ASN,HIS/ASN,HIS/ASN	0,4396		0,0,2198	65	77	73		280,280,280	-4.3	0.1	10	dbSNP_134	73	17,8563	9.8+/-36.6	0,17,4273	yes	missense,missense,missense	ZNF37A	NM_001007094.2,NM_001178101.1,NM_003421.2	68,68,68	0,17,6471	CC,CA,AA		0.1981,0.0,0.131	benign,benign,benign	94/562,94/562,94/562	38406359	17,12959	2198	4290	6488	SO:0001583	missense	7587	exon7			AAGTTCAATGAGT	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.280A>C	10.37:g.38406359A>C	ENSP00000354377:p.Asn94His	163	0	0		187	81	0.433155	NM_003421	B3KRQ3|D3DRZ3|Q96B88	Missense_Mutation	SNP	ENST00000361085.5	37	CCDS31183.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	0.012	-1.647092	0.00792	0.0	0.001981	ENSG00000075407	ENST00000351773;ENST00000361085	T;T	0.07021	3.23;3.23	2.16	-4.33	0.03677	.	.	.	.	.	T	0.02571	0.0078	N	0.02213	-0.635	0.09310	N	1	B	0.23442	0.085	B	0.28011	0.085	T	0.46816	-0.9164	9	0.19147	T	0.46	.	4.1301	0.10146	0.3936:0.0:0.4349:0.1715	.	94	P17032	ZN37A_HUMAN	H	94	ENSP00000329141:N94H;ENSP00000354377:N94H	ENSP00000329141:N94H	N	+	1	0	ZNF37A	38446365	0.000000	0.05858	0.149000	0.22428	0.397000	0.30659	-1.717000	0.01876	-0.782000	0.04541	-0.376000	0.06991	AAT	A|0.998;C|0.002	0.002	strong		0.294	ZNF37A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047624.2	NM_003421		C	38406359	A	C	38406359	3	2	24	1	0	0	0	0	1	0	0	0	17887	130	5	5	294	5	ZNF37A	10	38406359	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	2509659	38406359	97128388	322	8539											
ASAH2	56624	hgsc.bcm.edu	37	chr10	52005057	52005057	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tagccactgaagttctgaaaTagaggagactctggggttaa	13	10	12	6	0	2	4	0	2	2	2	2	5	2	4	1	3	1	2	1	3	5	4	rs201282742		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:52005057T>C	ENST00000395526.4	-	2	284	c.285A>G	c.(283-285)ctA>ctG	p.L95L	ASAH2_ENST00000447815.1_Silent_p.L95L|ASAH2_ENST00000329428.6_Silent_p.L76L	NM_019893.2	NP_063946.2	Q9NR71	ASAH2_HUMAN	N-acylsphingosine amidohydrolase (non-lysosomal ceramidase) 2	95					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						AGTTCTGAAATAGAGGAGACT	0.517																																					p.L95L		Atlas-SNP	.											.	ASAH2	69	.	0			c.A285G						PASS	.	T	,	0,4406		0,0,2203	176	181	179		285,285	-10.3	0	10		179	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	ASAH2	NM_001143974.1,NM_019893.2	,	0,2,6501	CC,CT,TT		0.0233,0.0,0.0154	,	95/746,95/781	52005057	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	56624	exon2			CTGAAATAGAGGA	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.285A>G	10.37:g.52005057T>C		195	0	0		173	85	0.491329	NM_019893	Q3KNU1|Q5SNT7|Q5SZP6|Q5SZP7|Q5T1D5|Q71ME6	Silent	SNP	ENST00000395526.4	37	CCDS7239.2																																																																																			T|0.999;C|0.001	0.001	weak		0.517	ASAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048061.3	NM_019893		C	52005057	T	C	52005057	2	2	24	1	0	0	0	0	0	0	0	1	1007	1393	49	3		3	ASAH2	10	52005057	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	13598698	52005057	83529690	323	8540											
A1CF	29974	hgsc.bcm.edu	37	chr10	52601702	52601702	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttacaaatgcatatcctctAttgttgccattaaaatccat	13	15	4	9	0	1	0	0	0	1	0	3	0	3	0	3	0	3	3	3	0	6	6	rs141891504		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:52601702A>G	ENST00000373993.1	-	3	329	c.285T>C	c.(283-285)aaT>aaC	p.N95N	A1CF_ENST00000395495.1_Silent_p.N95N|A1CF_ENST00000282641.2_Silent_p.N95N|A1CF_ENST00000374001.2_Silent_p.N95N|A1CF_ENST00000373995.3_Silent_p.N103N|A1CF_ENST00000395489.2_Silent_p.N88N|A1CF_ENST00000373997.3_Silent_p.N95N			Q9NQ94	A1CF_HUMAN	APOBEC1 complementation factor	95	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						CATATCCTCTATTGTTGCCAT	0.303													A|||	1	0.000199681	0.0	0.0	5008	,	,		19096	0.0		0.001	False		,,,				2504	0.0				p.N103N		Atlas-SNP	.											.	A1CF	190	.	0			c.T309C						PASS	.	A	,,,,,	2,4402	2.1+/-5.4	0,2,2200	141	135	137		285,309,309,285,285,309	0.4	1	10	dbSNP_134	137	14,8584	10.5+/-38.8	0,14,4285	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	A1CF	NM_001198818.1,NM_001198819.1,NM_001198820.1,NM_014576.3,NM_138932.2,NM_138933.2	,,,,,	0,16,6485	GG,GA,AA		0.1628,0.0454,0.1231	,,,,,	95/587,103/603,103/595,95/587,95/595,103/595	52601702	16,12986	2202	4299	6501	SO:0001819	synonymous_variant	29974	exon6			TCCTCTATTGTTG	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.285T>C	10.37:g.52601702A>G		75	0	0		77	32	0.415584	NM_001198820	A1L4F2|A8K7G7|B7ZM14|Q5SZQ0|Q9NQ93|Q9NQX8|Q9NQX9|Q9NXC9|Q9NZD3	Silent	SNP	ENST00000373993.1	37	CCDS7242.1																																																																																			A|0.999;G|0.001	0.001	strong		0.303	A1CF-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048086.2	NM_014576		G	52601702	A	G	52601702	2	3	24	1	0	0	0	0	0	0	0	1	2	446	16	3		3	A1CF	10	52601702	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	596645	52601702	82933045	324	8541											
TFAM	7019	hgsc.bcm.edu	37	chr10	60145363	60145363	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgccctgggaaggtctggagCagagctgtgcaccggctgtg	6	8	17	10	1	1	1	0	0	1	1	1	3	1	3	2	4	4	4	2	4	1	0			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:60145363C>T	ENST00000487519.1	+	1	582	c.56C>T	c.(55-57)gCa>gTa	p.A19V	TFAM_ENST00000373899.3_3'UTR|TFAM_ENST00000373895.3_Missense_Mutation_p.A19V	NM_001270782.1|NM_003201.2	NP_001257711.1|NP_003192.1	Q00059	TFAM_HUMAN	transcription factor A, mitochondrial	19					DNA-dependent DNA replication (GO:0006261)|gene expression (GO:0010467)|mitochondrial respiratory chain complex assembly (GO:0033108)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|mitochondrial light strand promoter sense binding (GO:0070363)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(1)|lung(4)|prostate(1)	7						AGGTCTGGAGCAGAGCTGTGC	0.667											OREG0020196	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A19V		Atlas-SNP	.											.	TFAM	52	.	0			c.C56T						PASS	.						75	62	66					10																	60145363		2201	4289	6490	SO:0001583	missense	7019	exon1			CTGGAGCAGAGCT	BC018628	CCDS7253.1, CCDS59217.1	10q21	2010-09-24			ENSG00000108064	ENSG00000108064			11741	protein-coding gene	gene with protein product		600438		TCF6, TCF6L2		7789991	Standard	NM_003201		Approved		uc001jkf.4	Q00059	OTTHUMG00000018270	ENST00000487519.1:c.56C>T	10.37:g.60145363C>T	ENSP00000420588:p.Ala19Val	78	0	0	1043	95	43	0.452632	NM_003201	A8MRB2|A9QXC6|B5BU05|Q5U0C6	Missense_Mutation	SNP	ENST00000487519.1	37	CCDS7253.1	.	.	.	.	.	.	.	.	.	.	C	9.457	1.092160	0.20471	.	.	ENSG00000108064	ENST00000487519;ENST00000373895	T;T	0.14516	2.53;2.5	4.31	1.43	0.22495	.	0.907854	0.09398	N	0.807600	T	0.09598	0.0236	L	0.32530	0.975	0.09310	N	0.999999	B;B	0.10296	0.003;0.003	B;B	0.10450	0.005;0.003	T	0.42965	-0.9420	10	0.17832	T	0.49	.	6.2181	0.20665	0.0:0.6834:0.0:0.3166	.	19;19	A8MRB2;Q00059	.;TFAM_HUMAN	V	19	ENSP00000420588:A19V;ENSP00000363002:A19V	ENSP00000363002:A19V	A	+	2	0	TFAM	59815369	0.048000	0.20356	0.198000	0.23420	0.309000	0.27889	0.110000	0.15437	0.333000	0.23563	-0.123000	0.14984	GCA	.	.	none		0.667	TFAM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048146.1	NM_003201		T	60145363	C	T	60145363	3	4	24	1	0	0	0	0	1	0	0	0	15801	710	25	2	58	2	TFAM	10	60145363	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	7543661	60145363	75389384	325	8542											
MYPN	84665	hgsc.bcm.edu	37	chr10	69934012	69934012	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tcacagacgttcagcttggcCcggccgaagtatttcttccc	7	11	9	14	3	3	1	2	0	1	1	4	2	4	1	3	2	1	3	3	2	2	5	rs71584491	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:69934012C>A	ENST00000358913.5	+	11	2651	c.2163C>A	c.(2161-2163)gcC>gcA	p.A721A	MYPN_ENST00000540630.1_Silent_p.A721A|MYPN_ENST00000354393.2_Silent_p.A446A	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	721					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						TCAGCTTGGCCCGGCCGAAGT	0.537													C|||	215	0.0429313	0.1331	0.0173	5008	,	,		18309	0.0		0.0109	False		,,,				2504	0.0164				p.A721A		Atlas-SNP	.											.	MYPN	189	.	0			c.C2163A						PASS	.	C		458,3948	218.4+/-236.5	22,414,1767	117	120	119		2163	4.1	1	10	dbSNP_130	119	106,8494	57.2+/-118.5	0,106,4194	no	coding-synonymous	MYPN	NM_032578.2		22,520,5961	AA,AC,CC		1.2326,10.3949,4.3365		721/1321	69934012	564,12442	2203	4300	6503	SO:0001819	synonymous_variant	84665	exon11			CTTGGCCCGGCCG	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.2163C>A	10.37:g.69934012C>A		150	0	0		175	88	0.502857	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Silent	SNP	ENST00000358913.5	37	CCDS7275.1																																																																																			C|0.956;A|0.044	0.044	strong		0.537	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578		A	69934012	C	A	69934012	2	1	24	1	0	0	0	0	0	0	0	1	10107	610	22	4		4	MYPN	10	69934012	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	9788649	69934012	65600735	326	8543											
COL13A1	1305	hgsc.bcm.edu	37	chr10	71640267	71640267	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctccccgcaggggtccccCggagacgctgggctgtccat	4	7	13	17	3	1	1	0	0	1	1	4	2	3	1	5	4	0	3	5	4	0	0			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:71640267C>A	ENST00000398978.3	+	6	936	c.444C>A	c.(442-444)ccC>ccA	p.P148P	COL13A1_ENST00000522165.1_Silent_p.P148P|COL13A1_ENST00000354547.3_Silent_p.P148P|COL13A1_ENST00000398972.3_Silent_p.P148P|COL13A1_ENST00000398971.3_Silent_p.P148P|COL13A1_ENST00000357811.3_Silent_p.P148P|COL13A1_ENST00000398966.3_Silent_p.P148P|COL13A1_ENST00000520267.1_Intron|COL13A1_ENST00000398964.3_Intron|COL13A1_ENST00000356340.3_Silent_p.P148P|COL13A1_ENST00000398969.3_Intron|COL13A1_ENST00000398968.3_Silent_p.P148P|COL13A1_ENST00000517713.1_Silent_p.P148P|COL13A1_ENST00000398974.3_Silent_p.P136P|COL13A1_ENST00000520133.1_Intron|COL13A1_ENST00000398973.3_Silent_p.P148P	NM_001130103.1	NP_001123575.1			collagen, type XIII, alpha 1									p.P148P(1)		endometrium(5)|large_intestine(3)|lung(15)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	28						AGGGGTCCCCCGGAGACGCTG	0.622																																					p.P148P		Atlas-SNP	.											COL13A1_ENST00000398978,NS,carcinoma,0,1	COL13A1	133	1	1	Substitution - coding silent(1)	endometrium(1)	c.C444A						PASS	.						33	34	34					10																	71640267		1821	4077	5898	SO:0001819	synonymous_variant	1305	exon6			GTCCCCCGGAGAC	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.444C>A	10.37:g.71640267C>A		115	0	0		137	63	0.459854	NM_080802		Silent	SNP	ENST00000398978.3	37	CCDS44419.1																																																																																			.	.	none		0.622	COL13A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048468.1	NM_005203		A	71640267	C	A	71640267	2	1	24	1	0	0	0	0	0	0	0	1	3672	639	23	4		4	COL13A1	10	71640267	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1706255	71640267	63894480	327	8544											
SLC29A3	55315	hgsc.bcm.edu	37	chr10	73122284	73122284	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agggagctggctgaggccacGggagtggtgatgtcctttta	7	10	17	7	1	0	2	0	2	0	0	1	4	1	4	2	5	1	2	2	5	1	2	rs373404056		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:73122284G>A	ENST00000373189.5	+	6	1399	c.1347G>A	c.(1345-1347)acG>acA	p.T449T		NM_001174098.1|NM_018344.5	NP_001167569.1|NP_060814.4	Q9BZD2	S29A3_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 3	449			T -> R (in HLAS; results in reduced nucleoside transport). {ECO:0000269|PubMed:19336477}.		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						CTGAGGCCACGGGAGTGGTGA	0.602																																					p.T449T	Esophageal Squamous(200;1319 2142 18949 31248 39672)	Atlas-SNP	.											SLC29A3,NS,carcinoma,+1,1	SLC29A3	51	1	0			c.G1347A						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	86	60	69		,1347	-11.1	0	10		69	0,8600		0,0,4300	no	utr-3,coding-synonymous	SLC29A3	NM_001174098.1,NM_018344.5	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	,449/476	73122284	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	55315	exon6			GGCCACGGGAGTG	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.1347G>A	10.37:g.73122284G>A		137	0	0		144	79	0.548611	NM_018344	B2RB50|B4E2Z9|B7ZA37|Q0VAM9|Q5T465|Q7RTT8|Q8IVZ0|Q9BWI2|Q9NUS9	Silent	SNP	ENST00000373189.5	37	CCDS7310.1																																																																																			.	.	none		0.602	SLC29A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048544.1	NM_018344		A	73122284	G	A	73122284	2	1	24	1	0	0	0	0	0	0	0	1	14551	1103	39	1		1	SLC29A3	10	73122284	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1482017	73122284	62412463	328	8545											
CDH23	414152	hgsc.bcm.edu	37	chr10	73492027	73492027	+	Intron	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcactgggtactgagattgtGcgggtccaggcctactccat	7	10	13	11	1	0	1	0	1	0	1	2	2	2	1	3	3	3	2	3	3	2	3	rs111033453	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:73492027G>A	ENST00000398786.2	-	1	97				CDH23_ENST00000224721.6_Silent_p.V1338V	NM_001168390.1	NP_001161862.1	Q8TEF2	CJ105_HUMAN	chromosome 10 open reading frame 105							integral component of membrane (GO:0016021)											CTGAGATTGTGCGGGTCCAGG	0.562													G|||	5	0.000998403	0.0	0.0043	5008	,	,		21580	0.0		0.002	False		,,,				2504	0.0				p.V1333V		Atlas-SNP	.											.	CDH23	365	.	0			c.G3999A						PASS	.	G	,,	2,4110		0,2,2054	68	70	69	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,3999,3999	4.8	1	10	dbSNP_132	69	24,8384		0,24,4180	no	intron,coding-synonymous,coding-synonymous	CDH23,C10orf105	NM_001168390.1,NM_001171930.1,NM_022124.5	,,	0,26,6234	AA,AG,GG		0.2854,0.0486,0.2077	,,	,1333/1382,1333/3355	73492027	26,12494	2056	4204	6260	SO:0001627	intron_variant	64072	exon31			GATTGTGCGGGTC	AK074172	CCDS44430.1	10q22.1	2012-06-01			ENSG00000214688	ENSG00000214688			20304	protein-coding gene	gene with protein product							Standard	NM_001164375		Approved	FLJ00245	uc001jsa.2	Q8TEF2	OTTHUMG00000018427	ENST00000398786.2:c.4+5457C>T	10.37:g.73492027G>A		117	0	0		110	51	0.463636	NM_022124		Silent	SNP	ENST00000398786.2	37	CCDS44430.1																																																																																			G|0.998;A|0.002	0.002	strong		0.562	C10orf105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048551.2	NM_001164375		A	73492027	G	A	73492027	1	1	24	0	1	0	0	0	0	0	0	0	3110	1306	46	2		2	CDH23	10	73492027	Intron	SNP	G	TCGA-G8-6326-01A-11D-2210-10	369743	73492027	62042720	329	8546											
C10orf54	64115	hgsc.bcm.edu	37	chr10	73533124	73533124	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgaccttacctagggacgCagccaggaagagagcgaaga	13	3	13	12	3	0	2	0	0	0	2	0	7	0	4	4	2	3	1	4	2	4	2	rs146887444		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:73533124C>T	ENST00000394957.3	-	1	131	c.73G>A	c.(73-75)Gcg>Acg	p.A25T	CDH23_ENST00000224721.6_Intron	NM_022153.1	NP_071436.1	Q9H7M9	GI24_HUMAN	chromosome 10 open reading frame 54	25					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						CCTAGGGACGCAGCCAGGAAG	0.687													C|||	1	0.000199681	0.0	0.0014	5008	,	,		14034	0.0		0.0	False		,,,				2504	0.0				p.A25T		Atlas-SNP	.											.	C10orf54	29	.	0			c.G73A						PASS	.	C	,THR/ALA	1,4385		0,1,2192	13	17	16		,73	3	1	10	dbSNP_134	16	5,8581		0,5,4288	yes	intron,missense	CDH23,C10orf54	NM_022124.5,NM_022153.1	,58	0,6,6480	TT,TC,CC		0.0582,0.0228,0.0463	,probably-damaging	,25/312	73533124	6,12966	2193	4293	6486	SO:0001583	missense	64115	exon1			GGGACGCAGCCAG	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.73G>A	10.37:g.73533124C>T	ENSP00000378409:p.Ala25Thr	284	0	0		285	145	0.508772	NM_022153	A1L0X9|A4ZYV1|A8MVH5|Q6UXF3|Q8WUG3|Q8WYZ8	Missense_Mutation	SNP	ENST00000394957.3	37	CCDS31218.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	C|C	21.8|21.8	4.199161|4.199161	0.79015|0.79015	2.28E-4|2.28E-4	5.82E-4|5.82E-4	ENSG00000107738|ENSG00000107738	ENST00000394957|ENST00000263569	T|.	0.47528|.	0.84|.	3.91|3.91	3.0|3.0	0.34707|0.34707	.|.	0.571467|.	0.17287|.	N|.	0.179798|.	T|T	0.34948|0.34948	0.0915|0.0915	N|N	0.24115|0.24115	0.695|0.695	0.28462|0.28462	N|N	0.915816|0.915816	B|.	0.30482|.	0.281|.	B|.	0.29440|.	0.102|.	T|T	0.32745|0.32745	-0.9895|-0.9895	10|6	0.29301|0.87932	T|D	0.29|0	-0.9608|-0.9608	9.7011|9.7011	0.40187|0.40187	0.0:0.7891:0.2109:0.0|0.0:0.7891:0.2109:0.0	.|.	25|.	Q9H7M9|.	GI24_HUMAN|.	T|Y	25|48	ENSP00000378409:A25T|.	ENSP00000378409:A25T|ENSP00000263569:C48Y	A|C	-|-	1|2	0|0	C10orf54|C10orf54	73203130|73203130	0.018000|0.018000	0.18449|0.18449	1.000000|1.000000	0.80357|0.80357	0.974000|0.974000	0.67602|0.67602	0.381000|0.381000	0.20619|0.20619	1.226000|1.226000	0.43582|0.43582	0.455000|0.455000	0.32223|0.32223	GCG|TGC	C|0.999;T|0.001	0.001	strong		0.687	C10orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048548.1	NM_022153		T	73533124	C	T	73533124	3	4	24	1	0	0	0	0	1	0	0	0	1609	710	25	2	890	2	C10orf54	10	73533124	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	41097	73533124	62001623	330	8547											
DNAJB12	54788	hgsc.bcm.edu	37	chr10	74098037	74098037	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acgagaatcaggatgaggatAggcatcagctgcacaaacac	16	5	11	9	1	2	2	2	1	0	1	2	5	2	4	0	3	3	3	0	3	3	1	rs138477026	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:74098037A>G	ENST00000444643.2	-	6	1088	c.756T>C	c.(754-756)ccT>ccC	p.P252P	DNAJB12_ENST00000461919.1_Silent_p.P47P|DNAJB12_ENST00000394903.2_Silent_p.P286P|DNAJB12_ENST00000338820.3_Silent_p.P286P			Q9NXW2	DJB12_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 12	252						integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|skin(1)	4						GGATGAGGATAGGCATCAGCT	0.582													A|||	8	0.00159744	0.0	0.0014	5008	,	,		18106	0.0		0.001	False		,,,				2504	0.0061				p.P286P		Atlas-SNP	.											.	DNAJB12	22	.	0			c.T858C						PASS	.	A	,	0,4406		0,0,2203	111	96	101		858,858	4.9	1	10	dbSNP_134	101	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous,coding-synonymous	DNAJB12	NM_001002762.2,NM_017626.4	,	0,7,6496	GG,GA,AA		0.0814,0.0,0.0538	,	286/410,286/410	74098037	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	54788	exon6			GAGGATAGGCATC	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.756T>C	10.37:g.74098037A>G		71	0	0		82	34	0.414634	NM_017626	B7Z7I3|Q9H6H0	Silent	SNP	ENST00000444643.2	37																																																																																				A|1.000;G|0.000	0.000	strong		0.582	DNAJB12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048581.2			G	74098037	A	G	74098037	2	3	24	1	0	0	0	0	0	0	0	1	4619	407	15	3		3	DNAJB12	10	74098037	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	564913	74098037	61436710	331	8548											
SFTPA1	653509	hgsc.bcm.edu	37	chr10	81373810	81373810	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agtgtgtggagatgtacacaGatgggcagtggaatgacagg	12	8	17	4	0	0	3	0	1	0	2	0	5	0	4	0	4	1	2	0	4	2	1	rs548998131		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:81373810G>A	ENST00000398636.3	+	6	826	c.688G>A	c.(688-690)Gat>Aat	p.D230N	SFTPA1_ENST00000372313.5_Missense_Mutation_p.D171N|SFTPA1_ENST00000419470.2_Missense_Mutation_p.D245N|SFTPA1_ENST00000428376.2_Missense_Mutation_p.D230N|SFTPA1_ENST00000372308.3_Missense_Mutation_p.D230N	NM_001164644.1|NM_001164646.1|NM_005411.4	NP_001158116.1|NP_001158118.1|NP_005402.3	Q8IWL2	SFTA1_HUMAN	surfactant protein A1	230	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				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)			GATGTACACAGATGGGCAGTG	0.572													g|||	1	0.000199681	0.0	0.0	5008	,	,		19728	0.0		0.001	False		,,,				2504	0.0				p.D245N		Atlas-SNP	.											.	SFTPA1	23	.	0			c.G733A						PASS	.						141	128	132					10																	81373810		2203	4296	6499	SO:0001583	missense	653509	exon6			TACACAGATGGGC	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		ENST00000398636.3:c.688G>A	10.37:g.81373810G>A	ENSP00000381633:p.Asp230Asn	419	0	0		432	218	0.50463	NM_001093770	A8K3T8|B7ZW50|E3VLD8|E3VLD9|E3VLE0|E3VLE1|G5E9J3|P07714|Q14DV4|Q5RIR5|Q5RIR7|Q6PIT0|Q8TC19	Missense_Mutation	SNP	ENST00000398636.3	37	CCDS44445.1	.	.	.	.	.	.	.	.	.	.	.	11.71	1.719016	0.30503	.	.	ENSG00000122852	ENST00000372308;ENST00000398636;ENST00000428376;ENST00000372313;ENST00000419470;ENST00000394569	T;T;T;T;T	0.56776	0.44;0.44;0.44;0.44;0.44	2.89	1.98	0.26296	C-type lectin fold (2);C-type lectin, conserved site (2);C-type lectin-like (2);C-type lectin (6);	0.072464	0.56097	N	0.000034	T	0.61714	0.2369	L	0.52823	1.66	0.40129	D	0.976696	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	T	0.59337	-0.7473	10	0.40728	T	0.16	-9.4297	7.9528	0.30025	0.1308:0.0:0.8692:0.0	.	230;245;230	Q8IWL1;G5E9J3;Q8IWL2	SFPA2_HUMAN;.;SFTA1_HUMAN	N	230;230;230;171;245;230	ENSP00000361382:D230N;ENSP00000381633:D230N;ENSP00000411102:D230N;ENSP00000361387:D171N;ENSP00000397082:D245N	ENSP00000361382:D230N	D	+	1	0	SFTPA1	81043816	0.998000	0.40836	0.905000	0.35620	0.045000	0.14185	2.629000	0.46485	0.783000	0.33636	0.297000	0.19635	GAT	.	.	none		0.572	SFTPA1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_005411		A	81373810	G	A	81373810	3	1	24	1	0	0	0	0	1	0	0	0	14204	942	33	2	751	2	SFTPA1	10	81373810	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	7275773	81373810	54160937	332	8549											
CDHR1	92211	hgsc.bcm.edu	37	chr10	85978958	85978958	+	IGR	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgttcttgcatccccactgcGaaattgccttattcaatctg	8	15	6	12	1	3	0	1	0	2	0	4	1	4	0	3	0	3	2	3	0	3	5	rs529093147	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:85978958G>A	ENST00000372117.3	+	0	5428				CDHR1_ENST00000332904.3_Missense_Mutation_p.E722K	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1						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						TCCCCACTGCGAAATTGCCTT	0.403													G|||	6	0.00119808	0.0	0.0	5008	,	,		18511	0.0		0.0	False		,,,				2504	0.0061				p.E722K		Atlas-SNP	.											CDHR1_ENST00000332904,colon,carcinoma,0,3	CDHR1	122	3	0			c.G2164A						PASS	.																																			SO:0001628	intergenic_variant	92211	exon17			CACTGCGAAATTG	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		10.37:g.85978958G>A		117	0	0		80	36	0.45	NM_001171971	Q69YZ8|Q8IXY5	Missense_Mutation	SNP	ENST00000372117.3	37	CCDS7372.1	.	.	.	.	.	.	.	.	.	.	G	8.654	0.898947	0.17686	.	.	ENSG00000148600	ENST00000332904	T	0.56776	0.44	2.11	1.17	0.20885	.	.	.	.	.	T	0.24392	0.0591	.	.	.	0.09310	N	1	B	0.13145	0.007	B	0.04013	0.001	T	0.24728	-1.0152	8	0.06099	T	0.92	.	6.5893	0.22638	0.0:0.6863:0.3137:0.0	.	722	Q96JP9-2	.	K	722	ENSP00000331063:E722K	ENSP00000331063:E722K	E	+	1	0	CDHR1	85968938	0.000000	0.05858	0.002000	0.10522	0.011000	0.07611	-0.065000	0.11617	0.445000	0.26639	-0.147000	0.13772	GAA	.	.	none		0.403	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100		A	85978958	G	A	85978958	1	1	24	0	1	0	0	0	0	0	0	0	3120	1059	37	1		1	CDHR1	10	85978958	IGR	SNP	G	TCGA-G8-6326-01A-11D-2210-10	4605148	85978958	49555789	333	8550											
PDZD7	79955	hgsc.bcm.edu	37	chr10	102783354	102783354	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgatcttgtcccccacgcaCaggccagcccgctctgcacc	6	7	9	19	2	2	1	0	1	2	0	3	1	3	1	5	1	2	3	5	1	0	1			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:102783354C>G	ENST00000370215.3	-	4	606	c.381G>C	c.(379-381)ctG>ctC	p.L127L	PDZD7_ENST00000470414.1_Silent_p.L127L	NM_024895.4	NP_079171.1	Q9H5P4	PDZD7_HUMAN	PDZ domain containing 7	127	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.					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)		CCCCCACGCACAGGCCAGCCC	0.652																																					p.L127L		Atlas-SNP	.											.	PDZD7	101	.	0			c.G381C						PASS	.						63	54	57					10																	102783354		2203	4300	6503	SO:0001819	synonymous_variant	79955	exon4			CACGCACAGGCCA	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.381G>C	10.37:g.102783354C>G		48	0	0		60	33	0.55	NM_001195263	D5FJ77|Q8N321	Silent	SNP	ENST00000370215.3	37	CCDS31269.1																																																																																			.	.	none		0.652	PDZD7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049883.1	NM_024895		G	102783354	C	G	102783354	2	3	24	1	0	0	0	0	0	0	0	1	11713	465	17	4		4	PDZD7	10	102783354	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	16804396	102783354	32751393	334	8551											
MGEA5	10724	hgsc.bcm.edu	37	chr10	103577629	103577629	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	agcccctcctgcagccccggCcaccgccgctcccccagccc	4	3	8	26	3	0	0	0	0	0	0	2	0	2	0	11	1	4	2	11	1	0	0	rs35402016	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:103577629C>T	ENST00000361464.3	-	1	546	c.151G>A	c.(151-153)Gcc>Acc	p.A51T	MGEA5_ENST00000419011.2_Missense_Mutation_p.A51T|MGEA5_ENST00000439817.1_Missense_Mutation_p.A51T|MGEA5_ENST00000357797.5_Missense_Mutation_p.A51T|KCNIP2-AS1_ENST00000412353.1_RNA|MGEA5_ENST00000370094.3_Missense_Mutation_p.A51T	NM_012215.3	NP_036347.1	O60502	OGA_HUMAN	meningioma expressed antigen 5 (hyaluronidase)	51					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)		GCAGCCCCGGCCACCGCCGCT	0.721													C|||	10	0.00199681	0.0	0.0014	5008	,	,		11090	0.0		0.006	False		,,,				2504	0.0031				p.A51T		Atlas-SNP	.											.	MGEA5	53	.	0			c.G151A						PASS	.	C	THR/ALA,THR/ALA	2,3740		0,2,1869	6	7	6		151,151	1.8	0.2	10	dbSNP_126	6	38,7546		0,38,3754	no	missense,missense	MGEA5	NM_001142434.1,NM_012215.3	58,58	0,40,5623	TT,TC,CC		0.5011,0.0534,0.3532	benign,benign	51/864,51/917	103577629	40,11286	1871	3792	5663	SO:0001583	missense	10724	exon1			CCCCGGCCACCGC	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.151G>A	10.37:g.103577629C>T	ENSP00000354850:p.Ala51Thr	13	0	0		21	11	0.52381	NM_001142434	B7WPB9|D3DR79|E9PGF9|O75166|Q86WV0|Q8IV98|Q9BVA5|Q9HAR0	Missense_Mutation	SNP	ENST00000361464.3	37	CCDS7520.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	10.90	1.481501	0.26598	5.34E-4	0.005011	ENSG00000198408	ENST00000439817;ENST00000361464;ENST00000357797;ENST00000370094;ENST00000419011	T;T;T;T;T	0.47869	1.49;1.5;1.5;1.49;0.83	4.71	1.76	0.24704	.	0.766530	0.11933	N	0.515498	T	0.18173	0.0436	N	0.14661	0.345	0.21020	N	0.999804	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.06405	0.0;0.001;0.002;0.0	T	0.22417	-1.0217	10	0.13853	T	0.58	-0.0165	5.4435	0.16521	0.0:0.5247:0.1481:0.3272	rs35402016	51;51;51;51	E9PGF9;O60502-2;O60502-3;O60502	.;.;.;NCOAT_HUMAN	T	51	ENSP00000409973:A51T;ENSP00000354850:A51T;ENSP00000350445:A51T;ENSP00000359112:A51T;ENSP00000407081:A51T	ENSP00000350445:A51T	A	-	1	0	MGEA5	103567619	0.070000	0.21116	0.189000	0.23252	0.328000	0.28507	-0.171000	0.09883	0.141000	0.18875	0.561000	0.74099	GCC	C|0.996;T|0.004	0.004	strong		0.721	MGEA5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049987.1	NM_012215		T	103577629	C	T	103577629	3	4	24	1	0	0	0	0	1	0	0	0	9564	739	26	2	2663	2	MGEA5	10	103577629	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	794275	103577629	31957118	335	8552											
C10orf118	55088	hgsc.bcm.edu	37	chr10	115905428	115905428	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctcaagtgtctctttttcCtttcgaagatctaaagattc	9	18	5	9	1	3	2	1	0	3	2	8	3	4	2	1	0	0	0	1	0	4	6	rs367843443		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:115905428C>A	ENST00000369287.3	-	5	1247	c.981G>T	c.(979-981)aaG>aaT	p.K327N	C10orf118_ENST00000543782.1_5'Flank	NM_018017.2	NP_060487.2	Q7Z3E2	CC186_HUMAN		327										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)		TCTCTTTTTCCTTTCGAAGAT	0.368																																					p.K327N		Atlas-SNP	.											.	C10orf118	70	.	0			c.G981T						PASS	.	C	ASN/LYS	0,4406		0,0,2203	196	183	187		981	2.3	1	10		187	1,8599	1.2+/-3.3	0,1,4299	no	missense	C10orf118	NM_018017.2	94	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	probably-damaging	327/899	115905428	1,13005	2203	4300	6503	SO:0001583	missense	55088	exon5			TTTTTCCTTTCGA																												ENST00000369287.3:c.981G>T	10.37:g.115905428C>A	ENSP00000358293:p.Lys327Asn	144	0	0		156	91	0.583333	NM_018017	Q2M2V6|Q3ZB81|Q6NS91|Q7RTP1|Q8N117|Q8N3G3|Q8N6C2|Q9NWA3	Missense_Mutation	SNP	ENST00000369287.3	37	CCDS7587.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.075041	0.76415	0.0	1.16E-4	ENSG00000165813	ENST00000369287;ENST00000430353	T	0.53857	0.6	5.52	2.29	0.28610	.	0.099180	0.64402	D	0.000002	T	0.60248	0.2254	M	0.68593	2.085	0.80722	D	1	D	0.56746	0.977	P	0.55923	0.787	T	0.60900	-0.7171	10	0.72032	D	0.01	.	8.5338	0.33351	0.0:0.7277:0.0:0.2723	.	327	Q7Z3E2	CJ118_HUMAN	N	327;433	ENSP00000358293:K327N	ENSP00000358293:K327N	K	-	3	2	C10orf118	115895418	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.972000	0.29409	0.518000	0.28383	0.650000	0.86243	AAG	.	.	none		0.368	C10orf118-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050455.1			A	115905428	C	A	115905428	3	1	24	1	0	0	0	0	1	0	0	0	1589	680	24	4	1763	4	C10orf118	10	115905428	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	12327799	115905428	19629319	336	8553											
ATE1	11101	hgsc.bcm.edu	37	chr10	123662023	123662023	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggtgggtgaccttgagcctgGaaaccctcaagttctccagc	8	9	12	12	0	2	2	1	2	1	0	3	3	2	3	4	3	3	1	4	3	2	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:123662023G>T	ENST00000224652.6	-	6	781	c.696C>A	c.(694-696)ttC>ttA	p.F232L	ATE1_ENST00000540606.1_Missense_Mutation_p.F225L|ATE1_ENST00000535655.1_Intron|ATE1_ENST00000481784.1_5'UTR|ATE1_ENST00000369043.3_Missense_Mutation_p.F232L|ATE1_ENST00000543447.1_Missense_Mutation_p.F117L|ATE1_ENST00000369040.3_Missense_Mutation_p.F136L	NM_001001976.1	NP_001001976.1	O95260	ATE1_HUMAN	arginyltransferase 1	232					protein arginylation (GO:0016598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	arginyltransferase activity (GO:0004057)			endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		all_neural(114;0.061)|Lung NSC(174;0.095)|all_lung(145;0.124)|Breast(234;0.212)				CTTGAGCCTGGAAACCCTCAA	0.423																																					p.F232L		Atlas-SNP	.											.	ATE1	67	.	0			c.C696A						PASS	.						162	146	151					10																	123662023		2203	4300	6503	SO:0001583	missense	11101	exon6			AGCCTGGAAACCC	AF079098	CCDS31299.1, CCDS31300.1, CCDS73211.1, CCDS73212.1, CCDS73213.1	10q26	2013-05-08			ENSG00000107669	ENSG00000107669	2.3.2.8		782	protein-coding gene	gene with protein product		607103				16002466, 16943202	Standard	XM_005269458		Approved		uc001lfq.3	O95260	OTTHUMG00000019178	ENST00000224652.6:c.696C>A	10.37:g.123662023G>T	ENSP00000224652:p.Phe232Leu	158	0	0		166	77	0.463855	NM_001001976	O95261|Q5SQQ3|Q8WW04	Missense_Mutation	SNP	ENST00000224652.6	37	CCDS31300.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.679|0.679	-0.798913|-0.798913	0.02841|0.02841	.|.	.|.	ENSG00000107669|ENSG00000107669	ENST00000369043;ENST00000224652;ENST00000369040;ENST00000540606;ENST00000543447|ENST00000423243	.|.	.|.	.|.	4.58|4.58	3.66|3.66	0.41972|0.41972	.|.	0.913149|.	0.09305|.	N|.	0.820356|.	T|T	0.33644|0.33644	0.0870|0.0870	L|L	0.36672|0.36672	1.1|1.1	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|.	0.09377|.	0.004;0.001;0.002;0.001|.	T|T	0.20371|0.20371	-1.0277|-1.0277	9|5	0.23891|.	T|.	0.37|.	-7.5611|-7.5611	5.5146|5.5146	0.16900|0.16900	0.124:0.3975:0.4785:0.0|0.124:0.3975:0.4785:0.0	.|.	225;136;232;232|.	F5GXE4;B4E107;O95260;O95260-2|.	.;.;ATE1_HUMAN;.|.	L|T	232;232;136;225;117|229	.|.	ENSP00000224652:F232L|.	F|P	-|-	3|1	2|0	ATE1|ATE1	123652013|123652013	0.152000|0.152000	0.22762|0.22762	0.920000|0.920000	0.36463|0.36463	0.774000|0.774000	0.43823|0.43823	0.524000|0.524000	0.22940|0.22940	1.128000|1.128000	0.42052|0.42052	0.557000|0.557000	0.71058|0.71058	TTC|CCA	.	.	none		0.423	ATE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001001976		T	123662023	G	T	123662023	3	4	24	1	0	0	0	0	1	0	0	0	1078	1165	41	4	1021	4	ATE1	10	123662023	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	7756595	123662023	11872724	337	8554											
FAM175B	23172	hgsc.bcm.edu	37	chr10	126515249	126515249	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcttcacaagcagctcacccGcatcctcggcgtgcccgacc	7	7	8	19	4	3	0	2	0	1	0	5	1	4	0	4	1	3	3	4	1	1	1	rs140695652	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:126515249G>A	ENST00000298492.5	+	5	398	c.353G>A	c.(352-354)cGc>cAc	p.R118H		NM_032182.3	NP_115558.3	Q15018	F175B_HUMAN	family with sequence similarity 175, member B	118					cellular response to freezing (GO:0071497)	BRISC complex (GO:0070552)|cytoplasm (GO:0005737)	polyubiquitin binding (GO:0031593)			NS(1)	1						CAGCTCACCCGCATCCTCGGC	0.498													G|||	2	0.000399361	0.0	0.0014	5008	,	,		20576	0.0		0.001	False		,,,				2504	0.0				p.R118H		Atlas-SNP	.											.	FAM175B	39	.	0			c.G353A						PASS	.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	195	173	180		353	3.8	1	10	dbSNP_134	180	5,8595	4.3+/-15.6	0,5,4295	yes	missense	FAM175B	NM_032182.3	29	0,6,6497	AA,AG,GG		0.0581,0.0227,0.0461	benign	118/416	126515249	6,13000	2203	4300	6503	SO:0001583	missense	23172	exon5			TCACCCGCATCCT	D63877	CCDS31308.2	10q26.2	2013-01-24	2008-07-02	2008-07-02	ENSG00000165660	ENSG00000165660			28975	protein-coding gene	gene with protein product	"Abraxas brother"	611144	"KIAA0157"	KIAA0157		8590280	Standard	NM_032182		Approved	Em:AC068896.4, ABRO1	uc001lib.4	Q15018	OTTHUMG00000019218	ENST00000298492.5:c.353G>A	10.37:g.126515249G>A	ENSP00000298492:p.Arg118His	138	0	0		132	60	0.454545	NM_032182	B4DKR2|Q96H11	Missense_Mutation	SNP	ENST00000298492.5	37	CCDS31308.2	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	14.64	2.596729	0.46318	2.27E-4	5.81E-4	ENSG00000165660	ENST00000298492	T	0.43294	0.95	5.82	3.76	0.43208	.	0.413144	0.28459	N	0.015269	T	0.21267	0.0512	N	0.11560	0.145	0.35051	D	0.760609	B	0.12630	0.006	B	0.08055	0.003	T	0.13629	-1.0502	10	0.40728	T	0.16	-9.0446	6.6535	0.22975	0.3087:0.0:0.6913:0.0	.	118	Q15018	F175B_HUMAN	H	118	ENSP00000298492:R118H	ENSP00000298492:R118H	R	+	2	0	FAM175B	126505239	1.000000	0.71417	0.999000	0.59377	0.982000	0.71751	4.660000	0.61511	1.470000	0.48102	0.557000	0.71058	CGC	G|1.000;A|0.000	0.000	strong		0.498	FAM175B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050891.2	NM_032182		A	126515249	G	A	126515249	3	1	24	1	0	0	0	0	1	0	0	0	5503	1087	38	1	371	1	FAM175B	10	126515249	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	2853226	126515249	9019498	338	8555											
MKI67	4288	hgsc.bcm.edu	37	chr10	129902131	129902131	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctcctgctgggttcctctTctactgggtttggtttcttc	1	20	9	11	0	4	0	0	0	4	0	7	0	5	0	2	3	2	4	2	3	1	7	rs146439186		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:129902131T>C	ENST00000368654.3	-	13	8348	c.7973A>G	c.(7972-7974)gAa>gGa	p.E2658G	MKI67_ENST00000368653.3_Missense_Mutation_p.E2298G	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2658	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)				GGGTTCCTCTTCTACTGGGTT	0.517													T|||	1	0.000199681	0.0	0.0	5008	,	,		19173	0.0		0.0	False		,,,				2504	0.001				p.E2658G		Atlas-SNP	.											.	MKI67	363	.	0			c.A7973G						PASS	.	T	GLY/GLU,GLY/GLU	3,4403	6.2+/-15.9	0,3,2200	163	171	168		6893,7973	-7.3	0	10	dbSNP_134	168	18,8582	13.3+/-46.6	0,18,4282	yes	missense,missense	MKI67	NM_001145966.1,NM_002417.4	98,98	0,21,6482	CC,CT,TT		0.2093,0.0681,0.1615	possibly-damaging,possibly-damaging	2298/2897,2658/3257	129902131	21,12985	2203	4300	6503	SO:0001583	missense	4288	exon13			TCCTCTTCTACTG	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.7973A>G	10.37:g.129902131T>C	ENSP00000357643:p.Glu2658Gly	157	0	0		213	88	0.413146	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	T	4.259	0.047198	0.08243	6.81E-4	0.002093	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02216	4.39;4.39	3.68	-7.35	0.01422	.	0.726931	0.11842	N	0.524155	T	0.02156	0.0067	M	0.62723	1.935	0.09310	N	1	B;B;B	0.34290	0.11;0.11;0.447	B;B;B	0.33846	0.027;0.075;0.171	T	0.06373	-1.0830	10	0.33141	T	0.24	.	2.5101	0.04654	0.1564:0.0851:0.3995:0.3589	.	2657;2298;2658	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	G	2658;2298;2657	ENSP00000357643:E2658G;ENSP00000357642:E2298G	ENSP00000357642:E2298G	E	-	2	0	MKI67	129792121	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.059000	0.11731	-4.528000	0.00044	-1.301000	0.01330	GAA	T|0.998;C|0.002	0.002	strong		0.517	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		C	129902131	T	C	129902131	3	2	24	1	0	0	0	0	1	0	0	0	9607	1783	62	3	1809	3	MKI67	10	129902131	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	3386882	129902131	5632616	339	8556											
MKI67	4288	hgsc.bcm.edu	37	chr10	129914162	129914162	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcaacactgtcttttgaGtcatctgcggtactgtcttc	7	15	9	10	1	4	2	1	2	3	0	5	2	4	2	0	1	4	2	0	1	2	4	rs143381225	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr10:129914162G>C	ENST00000368654.3	-	7	885	c.510C>G	c.(508-510)gaC>gaG	p.D170E	MKI67_ENST00000368653.3_Intron	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	170					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)				TGTCTTTTGAGTCATCTGCGG	0.413													G|||	4	0.000798722	0.0	0.0014	5008	,	,		18963	0.0		0.003	False		,,,				2504	0.0				p.D170E		Atlas-SNP	.											.	MKI67	363	.	0			c.C510G						PASS	.	G	,GLU/ASP	3,4403	6.2+/-15.9	0,3,2200	202	190	194		,510	2.6	0	10	dbSNP_134	194	21,8579	16.0+/-53.3	0,21,4279	yes	intron,missense	MKI67	NM_001145966.1,NM_002417.4	,45	0,24,6479	CC,CG,GG		0.2442,0.0681,0.1845	,possibly-damaging	,170/3257	129914162	24,12982	2203	4300	6503	SO:0001583	missense	4288	exon7			TTTTGAGTCATCT	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.510C>G	10.37:g.129914162G>C	ENSP00000357643:p.Asp170Glu	41	0	0		40	20	0.5	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	13.09	2.133471	0.37630	6.81E-4	0.002442	ENSG00000148773	ENST00000368654;ENST00000537609	T	0.21543	2.0	3.54	2.64	0.31445	.	1.326700	0.05140	N	0.494199	T	0.12263	0.0298	N	0.19112	0.55	0.09310	N	0.999994	P	0.37864	0.61	B	0.29353	0.101	T	0.20505	-1.0273	9	.	.	.	.	6.9772	0.24683	0.1232:0.0:0.8768:0.0	.	170	P46013	KI67_HUMAN	E	170	ENSP00000357643:D170E	.	D	-	3	2	MKI67	129804152	0.001000	0.12720	0.005000	0.12908	0.042000	0.13812	0.408000	0.21065	1.097000	0.41459	0.655000	0.94253	GAC	G|0.998;C|0.002	0.002	strong		0.413	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		C	129914162	G	C	129914162	3	2	24	1	0	0	0	0	1	0	0	0	9607	1020	36	4	9296	4	MKI67	10	129914162	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	12031	129914162	5620585	340	8557											
MUC2	4583	hgsc.bcm.edu	37	chr11	1093054	1093054	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccaacacccactggcacaCagaccccaaccccaacagcc	13	1	4	23	0	0	1	0	0	0	1	0	1	0	1	8	1	4	1	8	1	3	0			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1093054C>G	ENST00000441003.2	+	30	4900	c.4873C>G	c.(4873-4875)Cag>Gag	p.Q1625E	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Intron	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)	cactggcacacagaccccaac	0.637																																					p.Q1625E		Atlas-SNP	.											.	MUC2	614	.	0			c.C4873G						PASS	.						130	168	155					11																	1093054		1880	3616	5496	SO:0001583	missense	4583	exon30			GGCACACAGACCC	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.4873C>G	11.37:g.1093054C>G	ENSP00000415183:p.Gln1625Glu	49	0	0		46	4	0.0869565	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	0.029	-1.348877	0.01266	.	.	ENSG00000198788	ENST00000441003	T	0.11277	2.79	1.61	-3.22	0.05125	.	.	.	.	.	T	0.02888	0.0086	.	.	.	0.09310	N	1	B	0.12013	0.005	B	0.06405	0.002	T	0.35450	-0.9788	8	0.02654	T	1	.	0.7509	0.00990	0.2924:0.2671:0.2831:0.1573	.	1625	E7EUV1	.	E	1625	ENSP00000415183:Q1625E	ENSP00000415183:Q1625E	Q	+	1	0	MUC2	1083054	0.000000	0.05858	0.000000	0.03702	0.080000	0.17528	-0.356000	0.07661	-2.888000	0.00316	0.121000	0.15741	CAG	.	.	none		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		G	1093054	C	G	1093054	3	3	24	1	0	0	0	0	1	0	0	0	9984	479	17	4	4991	4	MUC2	11	1093054	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10		1093054	133913462	341	8558											
MUC2	4583	hgsc.bcm.edu	37	chr11	1093778	1093778	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcagacctctcggtccacctCttcccctctcacggagtcaa	7	10	6	18	2	5	1	3	0	3	1	9	2	7	2	5	2	0	0	5	2	1	1			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1093778C>G	ENST00000441003.2	+	30	5624	c.5597C>G	c.(5596-5598)tCt>tGt	p.S1866C	MUC2_ENST00000333592.6_Missense_Mutation_p.S154C|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4228					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)	CGGTCCACCTCTTCCCCTCTC	0.627																																					p.S1862C		Atlas-SNP	.											.	MUC2	614	.	0			c.C5585G						PASS	.						240	285	270					11																	1093778		2162	4255	6417	SO:0001583	missense	4583	exon31			CCACCTCTTCCCC	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.5597C>G	11.37:g.1093778C>G	ENSP00000415183:p.Ser1866Cys	81	0	0		87	4	0.045977	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	8.146	0.786373	0.16189	.	.	ENSG00000198788	ENST00000441003;ENST00000333592	T;T	0.12984	2.63;3.09	1.81	-0.426	0.12314	.	.	.	.	.	T	0.07503	0.0189	N	0.14661	0.345	0.09310	N	1	P	0.52463	0.953	B	0.43783	0.431	T	0.22487	-1.0215	9	0.59425	D	0.04	.	3.1045	0.06337	0.2592:0.5749:0.0:0.1658	.	1866	E7EUV1	.	C	1866;154	ENSP00000415183:S1866C;ENSP00000331373:S154C	ENSP00000331373:S154C	S	+	2	0	MUC2	1083778	0.000000	0.05858	0.002000	0.10522	0.152000	0.21847	-0.239000	0.08965	-0.281000	0.09141	0.305000	0.20034	TCT	.	.	none		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		G	1093778	C	G	1093778	3	3	24	1	0	0	0	0	1	0	0	0	9984	913	32	4	5707	4	MUC2	11	1093778	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	724	1093778	133912738	342	8559											
KRTAP5-1	387264	hgsc.bcm.edu	37	chr11	1605957	1605957	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tccacaggagccacagccccCcttggagcccccacaagaac	11	3	8	19	0	0	1	0	0	0	1	1	3	1	3	7	2	4	0	7	2	2	1	rs151275365	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1605957C>T	ENST00000382171.2	-	1	556	c.523G>A	c.(523-525)Ggg>Agg	p.G175R	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	175	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)		CCACAGCCCCCCTTGGAGCCC	0.677																																					p.G175R		Atlas-SNP	.											.	KRTAP5-1	74	.	0			c.G523A						PASS	.	C	ARG/GLY	12,4390		0,12,2189	46	62	57		523	2.9	1	11	dbSNP_134	57	111,8487		1,109,4189	no	missense	KRTAP5-1	NM_001005922.1	125	1,121,6378	TT,TC,CC		1.291,0.2726,0.9462	possibly-damaging	175/279	1605957	123,12877	2201	4299	6500	SO:0001583	missense	387264	exon1			AGCCCCCCTTGGA	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.523G>A	11.37:g.1605957C>T	ENSP00000371606:p.Gly175Arg	142	0	0		163	57	0.349693	NM_001005922		Missense_Mutation	SNP	ENST00000382171.2	37	CCDS31330.1	12	0.005494505494505495	0	0.0	0	0.0	0	0.0	12	0.0158311345646438	c	0.039	-1.291524	0.01375	0.002726	0.01291	ENSG00000205869	ENST00000382171	T	0.05199	3.48	2.91	2.91	0.33838	.	.	.	.	.	T	0.03263	0.0095	M	0.62266	1.93	0.26033	N	0.981718	P	0.40332	0.713	B	0.40375	0.327	T	0.17592	-1.0364	9	0.12103	T	0.63	.	5.9746	0.19371	0.0:0.8455:0.0:0.1545	.	175	Q6L8H4	KRA51_HUMAN	R	175	ENSP00000371606:G175R	ENSP00000371606:G175R	G	-	1	0	KRTAP5-1	1562533	0.000000	0.05858	0.998000	0.56505	0.319000	0.28217	-1.117000	0.03283	1.185000	0.42971	0.271000	0.19318	GGG	C|0.989;T|0.011	0.011	strong		0.677	KRTAP5-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127922.1	NM_001005922		T	1605957	C	T	1605957	3	4	24	1	0	0	0	0	1	0	0	0	8567	623	22	2	317	2	KRTAP5-1	11	1605957	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	512179	1605957	133400559	343	8560											
SYT8	90019	hgsc.bcm.edu	37	chr11	1857207	1857207	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggagttcgactttggaaGccaggaggtgaagggccccg	8	7	16	10	2	0	1	0	1	0	0	1	5	0	4	4	5	1	1	4	5	2	2	rs139074200		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:1857207G>A	ENST00000381968.3	+	4	520	c.392G>A	c.(391-393)aGc>aAc	p.S131N	SYT8_ENST00000436964.2_Missense_Mutation_p.S117N|SYT8_ENST00000341958.3_Missense_Mutation_p.S117N|SYT8_ENST00000483280.1_3'UTR|SYT8_ENST00000535046.1_Missense_Mutation_p.S269N	NM_138567.3	NP_612634	Q8NBV8	SYT8_HUMAN	synaptotagmin VIII	131	C2 1. {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)		GACTTTGGAAGCCAGGAGGTG	0.652													G|||	1	0.000199681	0.0	0.0	5008	,	,		15882	0.0		0.001	False		,,,				2504	0.0				p.S131N		Atlas-SNP	.											.	SYT8	29	.	0			c.G392A						PASS	.						43	48	46					11																	1857207		2202	4299	6501	SO:0001583	missense	90019	exon4			TTGGAAGCCAGGA	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.392G>A	11.37:g.1857207G>A	ENSP00000371394:p.Ser131Asn	91	0	0		73	32	0.438356	NM_138567	A6NFJ4|Q9NSV9	Missense_Mutation	SNP	ENST00000381968.3	37	CCDS7726.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	g	4.933	0.173312	0.09391	.	.	ENSG00000149043	ENST00000436964;ENST00000535046;ENST00000381968;ENST00000341958	T;T;T;T	0.19669	2.13;2.13;3.08;3.08	3.01	0.926	0.19430	C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	T	0.12008	0.0292	L	0.28740	0.885	0.09310	N	0.999999	B;B;B	0.19583	0.037;0.031;0.031	B;B;B	0.15052	0.012;0.009;0.009	T	0.32587	-0.9901	9	0.26408	T	0.33	.	3.0174	0.06064	0.1045:0.3185:0.4148:0.1622	.	117;131;117	C9JSK3;Q8NBV8;A6NCR4	.;SYT8_HUMAN;.	N	117;269;131;117	ENSP00000414626:S117N;ENSP00000443325:S269N;ENSP00000371394:S131N;ENSP00000343691:S117N	ENSP00000343691:S117N	S	+	2	0	SYT8	1813783	0.003000	0.15002	0.654000	0.29608	0.166000	0.22503	0.440000	0.21592	0.108000	0.17862	0.305000	0.20034	AGC	G|1.000;A|0.000	0.000	strong		0.652	SYT8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025013.4			A	1857207	G	A	1857207	3	1	24	1	0	0	0	0	1	0	0	0	15495	971	34	2	406	2	SYT8	11	1857207	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	251250	1857207	133149309	344	8561											
OR51T1	401665	hgsc.bcm.edu	37	chr11	4903219	4903219	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgctcatgtctggatctcCattccagtctgctgtctcta	5	16	8	12	0	5	0	1	0	4	0	8	1	6	1	2	1	2	2	2	1	1	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:4903219C>T	ENST00000322049.1	+	1	90	c.90C>T	c.(88-90)tcC>tcT	p.S30S	MMP26_ENST00000380390.1_Intron|OR51T1_ENST00000380378.1_Silent_p.S57S|MMP26_ENST00000477339.1_Intron			Q8NGJ9	O51T1_HUMAN	olfactory receptor, family 51, subfamily T, member 1	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)|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)		TCTGGATCTCCATTCCAGTCT	0.448																																					p.S57S		Atlas-SNP	.											.	OR51T1	92	.	0			c.C171T						PASS	.						208	170	183					11																	4903219		2201	4298	6499	SO:0001819	synonymous_variant	401665	exon1			GATCTCCATTCCA	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.90C>T	11.37:g.4903219C>T		178	0	0		139	63	0.453237	NM_001004759	Q6IFH9	Silent	SNP	ENST00000322049.1	37																																																																																				.	.	none		0.448	OR51T1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000142180.1	NM_001004759		T	4903219	C	T	4903219	2	4	24	1	0	0	0	0	0	0	0	1	11115	581	21	2		2	OR51T1	11	4903219	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	3046012	4903219	130103297	345	8562											
OR51B5	282763	hgsc.bcm.edu	37	chr11	5364431	5364431	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcaagcagaatgccagactcGagaaaggaaagtgagtgtat	16	6	13	6	1	0	4	0	1	0	3	1	6	0	5	1	1	2	3	1	1	5	1	rs58233587	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5364431G>A	ENST00000300773.2	-	1	378	c.324C>T	c.(322-324)ctC>ctT	p.L108L	HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	108					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)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGCCAGACTCGAGAAAGGAAA	0.493													G|||	486	0.0970447	0.3041	0.0476	5008	,	,		20358	0.0		0.0457	False		,,,				2504	0.0051				p.L108L		Atlas-SNP	.											OR51B5,NS,carcinoma,-1,1	OR51B5	60	1	0			c.C324T						PASS	.	G		1214,3188	413.5+/-336.5	164,886,1151	46	45	46		324	-8.8	0.1	11	dbSNP_129	46	454,8140	135.6+/-192.8	13,428,3856	no	coding-synonymous	OR51B5	NM_001005567.2		177,1314,5007	AA,AG,GG		5.2828,27.5784,12.8347		108/313	5364431	1668,11328	2201	4297	6498	SO:0001819	synonymous_variant	282763	exon5			AGACTCGAGAAAG	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"GPCR / Class A : Olfactory receptors"	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.324C>T	11.37:g.5364431G>A		31	0	0		39	18	0.461538	NM_001005567	B2RN59	Silent	SNP	ENST00000300773.2	37	CCDS31378.1																																																																																			G|0.886;A|0.114	0.114	strong		0.493	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567		A	5364431	G	A	5364431	2	1	24	1	0	0	0	0	0	0	0	1	11100	1045	37	1		1	OR51B5	11	5364431	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	461212	5364431	129642085	346	8563			2	40		4	4	92	N	T_G_C	1.320057e-09
OR51B5	282763	hgsc.bcm.edu	37	chr11	5364476	5364476	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	taggcctgggaaaagcaggcCgcacttccaatctccctgtg	9	8	11	13	1	1	0	0	0	1	0	3	1	2	1	4	3	1	2	4	3	4	2	rs61738485	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5364476C>T	ENST00000300773.2	-	1	333	c.279G>A	c.(277-279)gcG>gcA	p.A93A	HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	93					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)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AAAAGCAGGCCGCACTTCCAA	0.562													T|||	491	0.0980431	0.3071	0.049	5008	,	,		18817	0.0		0.0457	False		,,,				2504	0.0051				p.A93A		Atlas-SNP	.											OR51B5,NS,carcinoma,-1,1	OR51B5	60	1	0			c.G279A						PASS	.	T		1240,3162	701.9+/-406.8	168,904,1129	43	42	42		279	-8.9	0	11	dbSNP_129	42	455,8139	796.1+/-407.5	13,429,3855	no	coding-synonymous	OR51B5	NM_001005567.2		181,1333,4984	TT,TC,CC		5.2944,28.169,13.0425		93/313	5364476	1695,11301	2201	4297	6498	SO:0001819	synonymous_variant	282763	exon5			GCAGGCCGCACTT	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"GPCR / Class A : Olfactory receptors"	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.279G>A	11.37:g.5364476C>T		35	0	0		51	25	0.490196	NM_001005567	B2RN59	Silent	SNP	ENST00000300773.2	37	CCDS31378.1																																																																																			C|0.885;T|0.115	0.115	strong		0.562	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567		T	5364476	C	T	5364476	2	4	24	1	0	0	0	0	0	0	0	1	11100	639	23	1		1	OR51B5	11	5364476	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	45	5364476	129642040	347	8564			2	40		4	4	92	N	T_G_C	1.320057e-09
OR51B5	282763	hgsc.bcm.edu	37	chr11	5364493	5364493	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccgcacttccaatctcccTgtgatccagccagaggactc	8	8	9	16	1	1	2	0	1	1	1	5	3	3	3	5	2	1	1	5	2	1	1	rs57900141	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5364493T>C	ENST00000300773.2	-	1	316	c.262A>G	c.(262-264)Agg>Ggg	p.R88G	HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	88			R -> G (in dbSNP:rs57900141).		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)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCAATCTCCCTGTGATCCAGC	0.562													T|||	528	0.105431	0.3306	0.0519	5008	,	,		18694	0.0		0.0497	False		,,,				2504	0.0051				p.R88G		Atlas-SNP	.											.	OR51B5	60	.	0			c.A262G						PASS	.	T	GLY/ARG	1300,3102	434.3+/-343.9	182,936,1083	42	42	42		262	4.8	0.9	11	dbSNP_129	42	458,8136	134.7+/-192.1	14,430,3853	yes	missense	OR51B5	NM_001005567.2	125	196,1366,4936	CC,CT,TT		5.3293,29.532,13.5272	probably-damaging	88/313	5364493	1758,11238	2201	4297	6498	SO:0001583	missense	282763	exon5			TCTCCCTGTGATC	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"GPCR / Class A : Olfactory receptors"	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.262A>G	11.37:g.5364493T>C	ENSP00000300773:p.Arg88Gly	42	0	0		64	30	0.46875	NM_001005567	B2RN59	Missense_Mutation	SNP	ENST00000300773.2	37	CCDS31378.1	209	0.09569597069597069	150	0.3048780487804878	23	0.06353591160220995	0	0.0	36	0.047493403693931395	T	14.56	2.573102	0.45902	0.29532	0.053293	ENSG00000242180	ENST00000300773	T	0.37752	1.18	4.76	4.76	0.60689	GPCR, rhodopsin-like superfamily (1);	0.186059	0.26532	N	0.023845	T	0.00012	0.0000	L	0.60845	1.875	0.80722	P	0.0	D	0.89917	1.0	D	0.91635	0.999	T	0.18777	-1.0326	9	0.87932	D	0	.	9.6048	0.39626	0.0:0.0:0.1761:0.8239	rs57900141;rs61738479	88	Q9H339	O51B5_HUMAN	G	88	ENSP00000300773:R88G	ENSP00000300773:R88G	R	-	1	2	OR51B5	5321069	0.000000	0.05858	0.874000	0.34290	0.601000	0.36947	-0.007000	0.12810	2.017000	0.59298	0.529000	0.55759	AGG	T|0.879;C|0.121	0.121	strong		0.562	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567		C	5364493	T	C	5364493	3	2	24	1	0	0	0	0	1	0	0	0	11100	1579	55	3	680	3	OR51B5	11	5364493	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	17	5364493	129642023	348	8565			2	40		4	4	92	N	T_G_C	1.320057e-09
OR51B5	282763	hgsc.bcm.edu	37	chr11	5364522	5364522	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagaggactcccagcaccGtgggcattgtggtcagggcc	7	6	15	13	1	1	1	1	0	0	1	2	2	2	2	4	4	1	2	4	4	0	1	rs57273781	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5364522G>T	ENST00000300773.2	-	1	287	c.233C>A	c.(232-234)aCg>aAg	p.T78K	HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	78			T -> K (in dbSNP:rs57273781).		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)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCCCAGCACCGTGGGCATTGT	0.542													G|||	487	0.0972444	0.3048	0.0476	5008	,	,		18344	0.0		0.0457	False		,,,				2504	0.0051				p.T78K		Atlas-SNP	.											OR51B5,NS,malignant_melanoma,+1,2	OR51B5	60	2	0			c.C233A						PASS	.	G	LYS/THR	1219,3183	416.7+/-337.7	164,891,1146	44	46	45		233	3.9	0.3	11	dbSNP_129	45	445,8149	132.5+/-190.1	13,419,3865	yes	missense	OR51B5	NM_001005567.2	78	177,1310,5011	TT,TG,GG		5.178,27.692,12.8039	probably-damaging	78/313	5364522	1664,11332	2201	4297	6498	SO:0001583	missense	282763	exon5			AGCACCGTGGGCA	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"GPCR / Class A : Olfactory receptors"	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.233C>A	11.37:g.5364522G>T	ENSP00000300773:p.Thr78Lys	54	0	0		68	29	0.426471	NM_001005567	B2RN59	Missense_Mutation	SNP	ENST00000300773.2	37	CCDS31378.1	188	0.08608058608058608	135	0.27439024390243905	20	0.055248618784530384	0	0.0	33	0.04353562005277045	G	17.13	3.311894	0.60414	0.27692	0.05178	ENSG00000242180	ENST00000300773	T	0.01538	4.79	4.76	3.86	0.44501	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42420	D	0.000713	T	0.00012	0.0000	L	0.27944	0.81	0.58432	P	1.0000000000287557E-6	D	0.67145	0.996	P	0.57846	0.828	T	0.61720	-0.7005	9	0.52906	T	0.07	.	11.866	0.52493	0.0855:0.0:0.9145:0.0	rs57273781;rs61738468	78	Q9H339	O51B5_HUMAN	K	78	ENSP00000300773:T78K	ENSP00000300773:T78K	T	-	2	0	OR51B5	5321098	0.000000	0.05858	0.313000	0.25210	0.802000	0.45316	0.385000	0.20685	1.255000	0.44051	0.650000	0.86243	ACG	G|0.889;T|0.111	0.111	strong		0.542	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567		T	5364522	G	T	5364522	3	4	24	1	0	0	0	0	1	0	0	0	11100	1145	40	4	709	4	OR51B5	11	5364522	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	29	5364522	129641994	349	8566			2	40		4	4	92	N	T_G_C	1.320057e-09
OR51I2	390064	hgsc.bcm.edu	37	chr11	5475505	5475505	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggggtctccacagtgcacCgctttgggaagcatgtccca	7	10	12	12	1	1	0	0	0	1	0	3	1	2	1	3	3	2	3	3	3	1	2	rs75620804	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:5475505C>T	ENST00000341449.2	+	1	868	c.787C>T	c.(787-789)Cgc>Tgc	p.R263C	HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001004754.2	NP_001004754.1	Q9H344	O51I2_HUMAN	olfactory receptor, family 51, subfamily I, member 2	263			R -> H (in dbSNP:rs11037502).		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)		CACAGTGCACCGCTTTGGGAA	0.483													C|||	38	0.00758786	0.0	0.0101	5008	,	,		22942	0.001		0.0239	False		,,,				2504	0.0061				p.R263C		Atlas-SNP	.											.	OR51I2	76	.	0			c.C787T						PASS	.	C	CYS/ARG	18,4384	25.3+/-52.1	0,18,2183	221	187	198		787	4.7	1	11	dbSNP_131	198	242,8352	96.6+/-158.3	2,238,4057	yes	missense	OR51I2	NM_001004754.2	180	2,256,6240	TT,TC,CC		2.8159,0.4089,2.0006	probably-damaging	263/313	5475505	260,12736	2201	4297	6498	SO:0001583	missense	390064	exon1			GTGCACCGCTTTG	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.787C>T	11.37:g.5475505C>T	ENSP00000341987:p.Arg263Cys	207	0	0		229	113	0.49345	NM_001004754	Q6IF81	Missense_Mutation	SNP	ENST00000341449.2	37	CCDS31383.1	30	0.013736263736263736	0	0.0	7	0.019337016574585635	1	0.0017482517482517483	22	0.029023746701846966	C	11.07	1.529354	0.27387	0.004089	0.028159	ENSG00000187918	ENST00000341449	T	0.37411	1.2	5.58	4.68	0.58851	GPCR, rhodopsin-like superfamily (1);	0.096182	0.46758	N	0.000280	T	0.38054	0.1026	M	0.91354	3.2	0.40176	D	0.977235	D	0.89917	1.0	D	0.87578	0.998	T	0.61520	-0.7046	10	0.72032	D	0.01	.	5.4856	0.16747	0.1603:0.6806:0.0:0.1591	.	263	Q9H344	O51I2_HUMAN	C	263	ENSP00000341987:R263C	ENSP00000341987:R263C	R	+	1	0	OR51I2	5432081	0.002000	0.14202	0.985000	0.45067	0.048000	0.14542	0.094000	0.15107	1.610000	0.50200	-0.126000	0.14955	CGC	C|0.983;T|0.017	0.017	strong		0.483	OR51I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143385.1	NM_001004754		T	5475505	C	T	5475505	3	4	24	1	0	0	0	0	1	0	0	0	11110	652	23	1	789	1	OR51I2	11	5475505	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	110983	5475505	129531011	350	8567											
OR52W1	120787	hgsc.bcm.edu	37	chr11	6220596	6220596	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gctggccctgctgggcaatgGagcactgccggcagtggtgt	5	8	17	11	1	0	0	0	0	0	0	0	1	0	1	2	5	3	5	2	5	1	0			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:6220596G>C	ENST00000311352.2	+	1	221	c.143G>C	c.(142-144)gGa>gCa	p.G48A	RP11-290F24.6_ENST00000600308.1_lincRNA	NM_001005178.1	NP_001005178.1	Q6IF63	O52W1_HUMAN	olfactory receptor, family 52, subfamily W, member 1	48						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(2)|large_intestine(1)|lung(6)	11		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;2.13e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTGGGCAATGGAGCACTGCCG	0.562																																					p.G48A		Atlas-SNP	.											.	OR52W1	33	.	0			c.G143C						PASS	.						58	51	53					11																	6220596		2201	4296	6497	SO:0001583	missense	120787	exon1			GCAATGGAGCACT	AB065511	CCDS31407.1	11p15.4	2012-08-09		2004-03-10	ENSG00000175485	ENSG00000175485		"GPCR / Class A : Olfactory receptors"	15239	protein-coding gene	gene with protein product				OR52W1P			Standard	NM_001005178		Approved		uc010qzz.2	Q6IF63	OTTHUMG00000165378	ENST00000311352.2:c.143G>C	11.37:g.6220596G>C	ENSP00000309673:p.Gly48Ala	172	0	0		165	81	0.490909	NM_001005178	Q8NH78	Missense_Mutation	SNP	ENST00000311352.2	37	CCDS31407.1	.	.	.	.	.	.	.	.	.	.	G	8.442	0.851009	0.17034	.	.	ENSG00000175485	ENST00000311352	T	0.02050	4.48	5.92	2.93	0.34026	GPCR, rhodopsin-like superfamily (1);	0.580151	0.13011	N	0.420892	T	0.02380	0.0073	L	0.41492	1.28	0.09310	N	1	B	0.12630	0.006	B	0.06405	0.002	T	0.44757	-0.9307	10	0.25106	T	0.35	.	7.8661	0.29539	0.0:0.307:0.328:0.365	.	48	Q6IF63	O52W1_HUMAN	A	48	ENSP00000309673:G48A	ENSP00000309673:G48A	G	+	2	0	OR52W1	6177172	0.000000	0.05858	0.759000	0.31340	0.903000	0.53119	-0.313000	0.08103	0.819000	0.34492	0.655000	0.94253	GGA	.	.	none		0.562	OR52W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383758.1	NM_001005178		C	6220596	G	C	6220596	3	2	24	1	0	0	0	0	1	0	0	0	11141	1174	41	4	145	4	OR52W1	11	6220596	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	745091	6220596	128785920	351	8568											
OR10A6	390093	hgsc.bcm.edu	37	chr11	7949707	7949707	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taatttcattaaggccacaaAagggaaaactagatacccat	18	9	6	8	0	1	1	1	0	0	1	1	2	1	2	2	2	2	0	2	2	8	5	rs111488559	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:7949707A>G	ENST00000309838.2	-	1	502	c.503T>C	c.(502-504)tTt>tCt	p.F168S		NM_001004461.1	NP_001004461.1	Q8NH74	O10A6_HUMAN	olfactory receptor, family 10, subfamily A, member 6	168						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)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	22				Epithelial(150;1.38e-07)|BRCA - Breast invasive adenocarcinoma(625;0.189)		AAGGCCACAAAAGGGAAAACT	0.328													A|||	92	0.0183706	0.0015	0.0648	5008	,	,		19130	0.0		0.0258	False		,,,				2504	0.0194				p.F168S		Atlas-SNP	.											.	OR10A6	49	.	0			c.T503C						PASS	.	A	SER/PHE	43,4359	41.6+/-74.8	0,43,2158	41	44	43		503	3.2	1	11	dbSNP_132	43	338,8252	113.1+/-173.2	14,310,3971	yes	missense	OR10A6	NM_001004461.1	155	14,353,6129	GG,GA,AA		3.9348,0.9768,2.9326	possibly-damaging	168/315	7949707	381,12611	2201	4295	6496	SO:0001583	missense	390093	exon1			CCACAAAAGGGAA	AB065515	CCDS31420.1	11p15.4	2012-08-09			ENSG00000175393	ENSG00000175393		"GPCR / Class A : Olfactory receptors"	15132	protein-coding gene	gene with protein product							Standard	NM_001004461		Approved		uc010rbh.2	Q8NH74	OTTHUMG00000165671	ENST00000309838.2:c.503T>C	11.37:g.7949707A>G	ENSP00000312470:p.Phe168Ser	160	0	0		136	63	0.463235	NM_001004461	Q6IF59	Missense_Mutation	SNP	ENST00000309838.2	37	CCDS31420.1	34	0.015567765567765568	2	0.0040650406504065045	16	0.04419889502762431	0	0.0	16	0.021108179419525065	A	12.07	1.828003	0.32329	0.009768	0.039348	ENSG00000175393	ENST00000309838	T	0.00193	8.58	4.41	3.24	0.37175	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44688	D	0.000440	T	0.00178	0.0005	H	0.94183	3.505	0.28076	N	0.93237	D	0.57899	0.981	P	0.58077	0.832	T	0.17018	-1.0383	10	0.87932	D	0	.	7.0241	0.24930	0.615:0.0:0.0:0.3849	.	168	Q8NH74	O10A6_HUMAN	S	168	ENSP00000312470:F168S	ENSP00000312470:F168S	F	-	2	0	OR10A6	7906283	0.999000	0.42202	0.997000	0.53966	0.171000	0.22731	1.052000	0.30429	0.792000	0.33850	0.533000	0.62120	TTT	A|0.976;G|0.024	0.024	strong		0.328	OR10A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385703.1	NM_001004461		G	7949707	A	G	7949707	3	3	24	1	0	0	0	0	1	0	0	0	10903	14	1	3	444	3	OR10A6	11	7949707	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	1729111	7949707	127056809	352	8569											
RIC3	79608	hgsc.bcm.edu	37	chr11	8159884	8159884	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	catcctctgcagttgttttcCcctttgagagctgagaattg	7	15	9	10	0	1	2	0	2	1	2	3	4	3	2	3	0	2	4	3	0	1	5	rs80168649	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:8159884C>G	ENST00000309737.6	-	3	361	c.362G>C	c.(361-363)gGg>gCg	p.G121A	RIC3_ENST00000425599.2_Missense_Mutation_p.G121A|RIC3_ENST00000530060.1_5'UTR|RIC3_ENST00000343202.4_Missense_Mutation_p.G121A|RIC3_ENST00000539720.1_Missense_Mutation_p.G72A|RIC3_ENST00000335425.7_Intron			Q7Z5B4	RIC3_HUMAN	RIC3 acetylcholine receptor chaperone	121					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)				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)		AGTTGTTTTCCCCTTTGAGAG	0.438													C|||	17	0.00339457	0.0008	0.0014	5008	,	,		16568	0.0		0.0149	False		,,,				2504	0.0				p.G121A		Atlas-SNP	.											.	RIC3	42	.	0			c.G362C						PASS	.	C	,ALA/GLY,ALA/GLY,ALA/GLY	12,4390	19.1+/-41.9	0,12,2189	224	215	218		,362,362,362	5.8	1	11	dbSNP_131	218	114,8478	60.6+/-122.4	0,114,4182	yes	intron,missense,missense,missense	RIC3	NM_001135109.1,NM_001206671.1,NM_001206672.1,NM_024557.3	,60,60,60	0,126,6371	GG,GC,CC		1.3268,0.2726,0.9697	,probably-damaging,probably-damaging,probably-damaging	,121/370,121/289,121/369	8159884	126,12868	2201	4296	6497	SO:0001583	missense	79608	exon3			GTTTTCCCCTTTG		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.362G>C	11.37:g.8159884C>G	ENSP00000308820:p.Gly121Ala	106	0	0		113	50	0.442478	NM_001206672	B0B1U0|B2RD25|D3DQU5|Q6UX78|Q7Z5B3|Q86T94|Q8TBJ9|Q9HAH8	Missense_Mutation	SNP	ENST00000309737.6	37	CCDS55742.1	15	0.006868131868131868	1	0.0020325203252032522	0	0.0	0	0.0	14	0.018469656992084433	C	21.8	4.195192	0.78902	0.002726	0.013268	ENSG00000166405	ENST00000343202;ENST00000309737;ENST00000543346;ENST00000539720;ENST00000425599;ENST00000531450	T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.38639	0.1048	M	0.68317	2.08	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	0.25606	-1.0127	10	0.32370	T	0.25	.	18.1955	0.89820	0.0:1.0:0.0:0.0	.	121;121;121;121	B7Z1U4;B0B1U0;Q7Z5B4;Q7Z5B4-5	.;.;RIC3_HUMAN;.	A	121;121;121;72;121;121	ENSP00000344904:G121A;ENSP00000308820:G121A;ENSP00000443871:G72A;ENSP00000395320:G121A;ENSP00000431658:G121A	ENSP00000308820:G121A	G	-	2	0	RIC3	8116460	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.457000	0.53007	2.738000	0.93877	0.609000	0.83330	GGG	C|0.992;G|0.008	0.008	strong		0.438	RIC3-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385900.1	NM_024557		G	8159884	C	G	8159884	3	3	24	1	0	0	0	0	1	0	0	0	13369	623	22	4	760	4	RIC3	11	8159884	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	210177	8159884	126846632	353	8570											
MICAL2	9645	hgsc.bcm.edu	37	chr11	12247813	12247813	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggatccctccagtgaccaCgggcaaagagatggcatctg	10	7	13	11	1	1	2	0	1	1	1	3	4	3	3	3	3	0	2	3	3	1	0			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:12247813C>T	ENST00000256194.4	+	14	2072	c.1784C>T	c.(1783-1785)aCg>aTg	p.T595M	MICAL2_ENST00000379612.3_Missense_Mutation_p.T595M|MICAL2_ENST00000527546.1_Missense_Mutation_p.T595M|MICAL2_ENST00000537344.1_Missense_Mutation_p.T595M|MICAL2_ENST00000342902.5_Missense_Mutation_p.T595M	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	595	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				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)		CCAGTGACCACGGGCAAAGAG	0.547																																					p.T595M		Atlas-SNP	.											MICAL2,NS,haematopoietic_neoplasm,0,1	MICAL2	114	1	0			c.C1784T						PASS	.						135	123	127					11																	12247813		2201	4294	6495	SO:0001583	missense	9645	exon14			TGACCACGGGCAA	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.1784C>T	11.37:g.12247813C>T	ENSP00000256194:p.Thr595Met	95	0	0		124	5	0.0403226	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Missense_Mutation	SNP	ENST00000256194.4	37	CCDS7809.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.684033	0.88639	.	.	ENSG00000133816	ENST00000537344;ENST00000544073;ENST00000256194;ENST00000527546;ENST00000342902;ENST00000379612	D;D;D;D;D	0.95588	-3.75;-3.75;-3.75;-3.75;-3.75	5.28	5.28	0.74379	Calponin homology domain (5);	0.062767	0.64402	D	0.000008	D	0.98074	0.9365	M	0.88450	2.955	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999	D;D;D;D;D	0.76575	0.98;0.979;0.984;0.983;0.988	D	0.99019	1.0817	10	0.87932	D	0	.	18.526	0.90973	0.0:1.0:0.0:0.0	.	595;595;595;595;595	G3XAC8;B7Z849;Q5KTR3;Q5KTR4;O94851	.;.;.;.;MICA2_HUMAN	M	595;128;595;595;595;595	ENSP00000441689:T595M;ENSP00000256194:T595M;ENSP00000433965:T595M;ENSP00000344894:T595M;ENSP00000368932:T595M	ENSP00000256194:T595M	T	+	2	0	MICAL2	12204389	1.000000	0.71417	0.968000	0.41197	0.895000	0.52256	7.818000	0.86416	2.466000	0.83321	0.563000	0.77884	ACG	.	.	none		0.547	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632		T	12247813	C	T	12247813	3	4	24	1	0	0	0	0	1	0	0	0	9579	536	19	1	1830	1	MICAL2	11	12247813	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	4087929	12247813	122758703	354	8571											
PHF21A	51317	hgsc.bcm.edu	37	chr11	45987091	45987091	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcctctggataagctgaggAgctgcgagcatgggaggtgg	8	7	19	7	1	1	1	0	1	1	0	1	5	1	4	1	6	4	3	1	6	1	1	rs151169176	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:45987091A>T	ENST00000418153.2	-	9	967	c.768T>A	c.(766-768)gcT>gcA	p.A256A	PHF21A_ENST00000323180.6_Silent_p.A257A|PHF21A_ENST00000257821.4_Silent_p.A257A|PHF21A_ENST00000527753.1_5'Flank			Q96BD5	PF21A_HUMAN	PHD finger protein 21A	256					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						TAAGCTGAGGAGCTGCGAGCA	0.537											OREG0020936	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	15	0.00299521	0.0	0.0072	5008	,	,		19319	0.0		0.004	False		,,,				2504	0.0061				p.A257A		Atlas-SNP	.											.	PHF21A	107	.	0			c.T771A						PASS	.	A	,	6,4398	11.4+/-27.6	0,6,2196	72	57	62		768,771	3.7	1	11	dbSNP_134	62	61,8537	38.8+/-94.9	1,59,4239	no	coding-synonymous,coding-synonymous	PHF21A	NM_001101802.1,NM_016621.3	,	1,65,6435	TT,TA,AA		0.7095,0.1362,0.5153	,	256/681,257/635	45987091	67,12935	2202	4299	6501	SO:0001819	synonymous_variant	51317	exon9			CTGAGGAGCTGCG	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.768T>A	11.37:g.45987091A>T		186	0	0	935	230	128	0.556522	NM_016621	D3DQP5|Q6AWA2|Q9C0G7|Q9H8V9|Q9HAK6|Q9NZE9	Silent	SNP	ENST00000418153.2	37	CCDS44578.1																																																																																			A|0.994;T|0.006	0.006	strong		0.537	PHF21A-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392583.1	NM_016621		T	45987091	A	T	45987091	2	4	24	1	0	0	0	0	0	0	0	1	11842	291	11	5		5	PHF21A	11	45987091	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	33739278	45987091	89019425	355	8572											
OR4A47	403253	hgsc.bcm.edu	37	chr11	48511050	48511050	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagggaggcaaaaagccctcTcaacctgcagttcccacatg	13	6	9	13	0	1	0	1	0	1	0	3	1	2	1	3	2	3	3	3	2	4	1	rs76991989	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:48511050T>C	ENST00000446524.1	+	1	782	c.706T>C	c.(706-708)Tca>Cca	p.S236P		NM_001005512.2	NP_001005512.2	Q6IF82	O4A47_HUMAN	olfactory receptor, family 4, subfamily A, member 47	236						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						AAAAGCCCTCTCAACCTGCAG	0.428													T|||	41	0.0081869	0.0015	0.0086	5008	,	,		18021	0.0		0.0268	False		,,,				2504	0.0061				p.S236P		Atlas-SNP	.											OR4A47,bladder,carcinoma,-1,1	OR4A47	72	1	0			c.T706C						PASS	.	T	PRO/SER	23,4379		0,23,2178	148	144	145		706	2.4	0.1	11	dbSNP_131	145	217,8379		3,211,4084	yes	missense	OR4A47	NM_001005512.2	74	3,234,6262	CC,CT,TT		2.5244,0.5225,1.8464	benign	236/310	48511050	240,12758	2201	4298	6499	SO:0001583	missense	403253	exon1			GCCCTCTCAACCT	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.706T>C	11.37:g.48511050T>C	ENSP00000412752:p.Ser236Pro	150	0	0		140	62	0.442857	NM_001005512		Missense_Mutation	SNP	ENST00000446524.1	37	CCDS31490.1	23	0.010531135531135532	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	17	0.022427440633245383	N	11.71	1.719811	0.30503	0.005225	0.025244	ENSG00000237388	ENST00000446524	T	0.00309	8.16	4.59	2.36	0.29203	GPCR, rhodopsin-like superfamily (1);	0.553031	0.16377	N	0.217096	T	0.00300	0.0009	H	0.98407	4.225	0.09310	N	0.999997	D	0.53462	0.96	P	0.54965	0.765	T	0.40098	-0.9581	10	0.87932	D	0	.	5.4392	0.16498	0.0:0.2998:0.0:0.7002	.	236	Q6IF82	O4A47_HUMAN	P	236	ENSP00000412752:S236P	ENSP00000412752:S236P	S	+	1	0	OR4A47	48467626	0.000000	0.05858	0.139000	0.22197	0.222000	0.24845	0.081000	0.14823	0.225000	0.20959	0.172000	0.16884	TCA	T|0.981;C|0.019	0.019	strong		0.428	OR4A47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390559.1	NM_001005512		C	48511050	T	C	48511050	3	2	24	1	0	0	0	0	1	0	0	0	11051	1551	54	3	708	3	OR4A47	11	48511050	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	2523959	48511050	86495466	356	8573											
OR5T2	219464	hgsc.bcm.edu	37	chr11	56000079	56000079	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agccactgtatgtatagtagCatgtaaaatgccagcaacat	15	10	8	8	0	0	0	0	0	0	0	0	0	0	0	2	0	5	6	2	0	7	5	rs77295387	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:56000079C>T	ENST00000313264.4	-	1	658	c.583G>A	c.(583-585)Gct>Act	p.A195T		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	195						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)					TGTATAGTAGCATGTAAAATG	0.433													c|||	34	0.00678914	0.0015	0.0029	5008	,	,		23389	0.0		0.0268	False		,,,				2504	0.0031				p.A195T		Atlas-SNP	.											.	OR5T2	107	.	0			c.G583A						PASS	.	C	THR/ALA	21,4381	26.2+/-53.5	0,21,2180	193	169	177		583	4.1	0.1	11	dbSNP_131	177	237,8355	96.6+/-158.3	1,235,4060	yes	missense	OR5T2	NM_001004746.1	58	1,256,6240	TT,TC,CC		2.7584,0.4771,1.9855	probably-damaging	195/360	56000079	258,12736	2201	4296	6497	SO:0001583	missense	219464	exon1			TAGTAGCATGTAA	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.583G>A	11.37:g.56000079C>T	ENSP00000323688:p.Ala195Thr	207	0	0		255	118	0.462745	NM_001004746	B9EGX5|Q6IFC8	Missense_Mutation	SNP	ENST00000313264.4	37	CCDS31523.1	21	0.009615384615384616	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	19	0.025065963060686015	C	12.15	1.852226	0.32699	0.004771	0.027584	ENSG00000181718	ENST00000313264	T	0.39056	1.1	5.07	4.13	0.48395	GPCR, rhodopsin-like superfamily (1);	0.184659	0.26013	U	0.026862	T	0.23054	0.0557	L	0.41356	1.27	0.09310	N	1	P	0.45986	0.87	P	0.53102	0.718	T	0.11155	-1.0599	10	0.49607	T	0.09	.	12.8779	0.57999	0.3516:0.6484:0.0:0.0	.	195	Q8NGG2	OR5T2_HUMAN	T	195	ENSP00000323688:A195T	ENSP00000323688:A195T	A	-	1	0	OR5T2	55756655	0.000000	0.05858	0.078000	0.20375	0.029000	0.11900	-0.966000	0.03825	1.207000	0.43291	0.478000	0.44815	GCT	C|0.981;T|0.019	0.019	strong		0.433	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746		T	56000079	C	T	56000079	3	4	24	1	0	0	0	0	1	0	0	0	11191	710	25	2	495	2	OR5T2	11	56000079	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	7489029	56000079	79006437	357	8574											
OR5AR1	219493	hgsc.bcm.edu	37	chr11	56431618	56431618	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgggctcttacctggctggtCtagtgagtttagtagcccac	6	13	12	10	0	2	1	0	1	2	0	2	1	2	1	2	3	2	4	2	3	4	5	rs77272836	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:56431618C>T	ENST00000302969.2	+	1	481	c.457C>T	c.(457-459)Cta>Tta	p.L153L		NM_001004730.1	NP_001004730.1	Q8NGP9	O5AR1_HUMAN	olfactory receptor, family 5, subfamily AR, member 1 (gene/pseudogene)	153						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L153I(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(12)|prostate(1)|skin(3)|stomach(1)	26						CCTGGCTGGTCTAGTGAGTTT	0.502													C|||	18	0.00359425	0.0008	0.0058	5008	,	,		21429	0.0		0.0129	False		,,,				2504	0.0				p.L153L		Atlas-SNP	.											OR5AR1,NS,carcinoma,0,1	OR5AR1	68	1	1	Substitution - Missense(1)	lung(1)	c.C457T						scavenged	.	C		14,4388	21.2+/-45.6	0,14,2187	204	181	189		457	4	1	11	dbSNP_132	189	100,8492	55.6+/-116.7	2,96,4198	no	coding-synonymous	OR5AR1	NM_001004730.1		2,110,6385	TT,TC,CC		1.1639,0.318,0.8773		153/311	56431618	114,12880	2201	4296	6497	SO:0001819	synonymous_variant	219493	exon1			GCTGGTCTAGTGA	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.457C>T	11.37:g.56431618C>T		180	1	0.00555556		209	102	0.488038	NM_001004730	Q6IF61	Silent	SNP	ENST00000302969.2	37	CCDS31535.1																																																																																			C|0.990;T|0.010	0.010	strong		0.502	OR5AR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334434.1	NM_001004730		T	56431618	C	T	56431618	2	4	24	1	0	0	0	0	0	0	0	1	11154	912	32	2		2	OR5AR1	11	56431618	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	431539	56431618	78574898	358	8575											
OR9G1	390174	hgsc.bcm.edu	37	chr11	56468258	56468258	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctccaagcccctgctttatgCccaggccatgtccataaagc	9	9	7	16	0	0	0	0	0	0	0	2	0	2	0	6	1	4	1	6	1	4	3	rs78340277	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:56468258C>T	ENST00000312153.1	+	1	395	c.395C>T	c.(394-396)gCc>gTc	p.A132V		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	132						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						CTGCTTTATGCCCAGGCCATG	0.498													C|||	31	0.0061901	0.0015	0.0029	5008	,	,		19708	0.0		0.0239	False		,,,				2504	0.0031				p.A132V		Atlas-SNP	.											.	.	.	.	0			c.C395T						PASS	.	C	VAL/ALA	16,4386	21.2+/-45.6	0,16,2185	186	171	176		395	4.4	0.8	11	dbSNP_131	176	171,8421	67.7+/-130.1	0,171,4125	yes	missense	OR9G1	NM_001005213.1	64	0,187,6310	TT,TC,CC		1.9902,0.3635,1.4391	possibly-damaging	132/306	56468258	187,12807	2201	4296	6497	SO:0001583	missense	504191	exon1			TTTATGCCCAGGC	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.395C>T	11.37:g.56468258C>T	ENSP00000309012:p.Ala132Val	315	0	0		305	72	0.236066	NM_001013358	Q6IEU9|Q8NGQ0	Missense_Mutation	SNP	ENST00000312153.1	37	CCDS31536.1	16	0.007326007326007326	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	14	0.018469656992084433	C	11.81	1.748637	0.30955	0.003635	0.019902	ENSG00000174914	ENST00000312153	T	0.01572	4.76	4.43	4.43	0.53597	GPCR, rhodopsin-like superfamily (1);	0.696787	0.13040	N	0.418614	T	0.00998	0.0033	L	0.31120	0.905	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.40117	-0.9580	10	0.66056	D	0.02	-6.4294	10.827	0.46638	0.0:0.9106:0.0:0.0894	.	132	Q8NH87	OR9G1_HUMAN	V	132	ENSP00000309012:A132V	ENSP00000309012:A132V	A	+	2	0	OR9G1	56224834	0.000000	0.05858	0.813000	0.32504	0.681000	0.39784	-0.197000	0.09518	2.430000	0.82344	0.585000	0.79938	GCC	C|0.987;T|0.013	0.013	strong		0.498	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213		T	56468258	C	T	56468258	3	4	24	1	0	0	0	0	1	0	0	0	11259	739	26	2	397	2	OR9G1	11	56468258	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	36640	56468258	78538258	359	8576											
MPEG1	219972	hgsc.bcm.edu	37	chr11	58978434	58978434	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atggccctccgcagctctatCggttctcccagcctccactg	5	10	8	18	2	2	0	0	0	2	0	6	0	4	0	5	2	2	3	5	2	1	2	rs180770562	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:58978434C>A	ENST00000361050.3	-	1	1990	c.1905G>T	c.(1903-1905)ccG>ccT	p.P635P		NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	635						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)				GCAGCTCTATCGGTTCTCCCA	0.567													C|||	10	0.00199681	0.0023	0.0014	5008	,	,		17979	0.0		0.005	False		,,,				2504	0.001				p.P635P		Atlas-SNP	.											.	MPEG1	72	.	0			c.G1905T						PASS	.	C		7,3897		0,7,1945	95	104	101		1905	-11.4	0	11	dbSNP_134	101	66,8194		0,66,4064	no	coding-synonymous	MPEG1	NM_001039396.1		0,73,6009	AA,AC,CC		0.799,0.1793,0.6001		635/717	58978434	73,12091	1952	4130	6082	SO:0001819	synonymous_variant	219972	exon1			CTCTATCGGTTCT	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.1905G>T	11.37:g.58978434C>A		113	0	0		133	59	0.443609	NM_001039396	Q2M1T6|Q8TEF8	Silent	SNP	ENST00000361050.3	37	CCDS41650.1																																																																																			C|0.996;A|0.004	0.004	strong		0.567	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396		A	58978434	C	A	58978434	2	1	24	1	0	0	0	0	0	0	0	1	9732	871	31	4		4	MPEG1	11	58978434	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	2510176	58978434	76028082	360	8577											
TMEM132A	54972	hgsc.bcm.edu	37	chr11	60696399	60696399	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tagtgctaccctcctgcttcGgcacaacttcacagccagcc	8	9	7	17	1	1	0	1	0	0	0	3	0	2	0	4	1	6	3	4	1	3	4	rs61751216	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:60696399G>A	ENST00000453848.2	+	4	991	c.833G>A	c.(832-834)cGg>cAg	p.R278Q	TMEM132A_ENST00000005286.4_Missense_Mutation_p.R278Q			Q24JP5	T132A_HUMAN	transmembrane protein 132A	278						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						CTCCTGCTTCGGCACAACTTC	0.637													G|||	50	0.00998403	0.003	0.013	5008	,	,		17378	0.0		0.0328	False		,,,				2504	0.0041				p.R278Q		Atlas-SNP	.											.	TMEM132A	135	.	0			c.G833A						PASS	.	G	GLN/ARG,GLN/ARG	27,4375		0,27,2174	39	39	39		833,833	2.8	0.8	11	dbSNP_129	39	347,8245		9,329,3958	yes	missense,missense	TMEM132A	NM_017870.3,NM_178031.2	43,43	9,356,6132	AA,AG,GG		4.0386,0.6134,2.8783	possibly-damaging,possibly-damaging	278/1025,278/1024	60696399	374,12620	2201	4296	6497	SO:0001583	missense	54972	exon4			TGCTTCGGCACAA	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.833G>A	11.37:g.60696399G>A	ENSP00000405823:p.Arg278Gln	83	0	0		84	35	0.416667	NM_178031	Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Missense_Mutation	SNP	ENST00000453848.2	37	CCDS44618.1	34	0.015567765567765568	3	0.006097560975609756	6	0.016574585635359115	0	0.0	25	0.032981530343007916	G	16.23	3.064526	0.55432	0.006134	0.040386	ENSG00000006118	ENST00000544065;ENST00000453848;ENST00000005286	T;T;T	0.13538	2.7;2.58;2.58	4.66	2.77	0.32553	.	0.000000	0.43110	D	0.000618	T	0.03739	0.0106	L	0.47716	1.5	0.19575	N	0.999969	D;D;D	0.60575	0.988;0.976;0.976	P;P;P	0.50934	0.654;0.465;0.465	T	0.04281	-1.0963	10	0.87932	D	0	.	7.0037	0.24823	0.3377:0.0:0.6623:0.0	rs61751216	267;278;278	Q24JP5-3;Q24JP5;Q24JP5-2	.;T132A_HUMAN;.	Q	16;278;278	ENSP00000442754:R16Q;ENSP00000405823:R278Q;ENSP00000005286:R278Q	ENSP00000005286:R278Q	R	+	2	0	TMEM132A	60452975	0.001000	0.12720	0.809000	0.32408	0.955000	0.61496	0.300000	0.19156	0.521000	0.28445	0.484000	0.47621	CGG	G|0.976;A|0.024	0.024	strong		0.637	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870		A	60696399	G	A	60696399	3	1	24	1	0	0	0	0	1	0	0	0	16060	1116	39	1	847	1	TMEM132A	11	60696399	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1717965	60696399	74310117	361	8578											
TMEM216	51259	hgsc.bcm.edu	37	chr11	61161359	61161359	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcttttgtattggcaggtgTcctgctaccatatccaacag	8	13	10	10	0	0	0	0	0	0	0	2	0	2	0	3	3	3	4	3	3	4	6			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:61161359T>C	ENST00000515837.2	+	3	1085	c.140T>C	c.(139-141)gTc>gCc	p.V47A	TMEM216_ENST00000334888.5_Missense_Mutation_p.V47A|TMEM216_ENST00000398979.3_5'UTR			Q9P0N5	TM216_HUMAN	transmembrane protein 216	47					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)				endometrium(1)|large_intestine(2)|lung(1)|prostate(2)	6						TTGGCAGGTGTCCTGCTACCA	0.433																																					p.V47A		Atlas-SNP	.											.	TMEM216	14	.	0			c.T140C						PASS	.						84	93	90					11																	61161359		1968	4156	6124	SO:0001583	missense	51259	exon3			CAGGTGTCCTGCT		CCDS53640.1	11q13.1	2014-09-17			ENSG00000187049	ENSG00000187049			25018	protein-coding gene	gene with protein product		613277	"cerebello-oculo-renal syndrome 2", "Meckel syndrome, type 2"	CORS2, MKS2		11042152, 20036350, 20512146	Standard	NM_016499		Approved	MGC13379, HSPC244, JBTS2	uc021qkf.1	Q9P0N5		ENST00000515837.2:c.140T>C	11.37:g.61161359T>C	ENSP00000440638:p.Val47Ala	200	0	0		231	91	0.393939	NM_001173990	A8MZ23|B7Z8N1	Missense_Mutation	SNP	ENST00000515837.2	37	CCDS53640.1	.	.	.	.	.	.	.	.	.	.	T	7.289	0.610705	0.14066	.	.	ENSG00000187049	ENST00000515837;ENST00000334888	D;D	0.88124	-2.34;-2.34	5.95	5.95	0.96441	.	.	.	.	.	T	0.77212	0.4097	N	0.14661	0.345	0.28495	N	0.914285	B	0.11235	0.004	B	0.12837	0.008	T	0.63229	-0.6684	9	0.15499	T	0.54	.	13.9469	0.64091	0.0:0.0:0.0:1.0	.	40	Q9P0N5	TM216_HUMAN	A	47	ENSP00000440638:V47A;ENSP00000334844:V47A	ENSP00000334844:V47A	V	+	2	0	TMEM216	60917935	0.988000	0.35896	0.929000	0.37066	0.003000	0.03518	3.612000	0.54142	2.279000	0.76181	0.533000	0.62120	GTC	.	.	none		0.433	TMEM216-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398430.1	NM_016499		C	61161359	T	C	61161359	3	2	24	1	0	0	0	0	1	0	0	0	16154	1667	58	3	150	3	TMEM216	11	61161359	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	464960	61161359	73845157	362	8579											
MAP3K11	4296	hgsc.bcm.edu	37	chr11	65373249	65373249	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccattgagtgctgggggtGtggaaggagatcctaagggg	9	8	18	6	0	0	2	0	1	0	1	1	4	1	3	2	6	1	1	2	6	2	2	rs145297254	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:65373249G>T	ENST00000530153.1	-	8	1564	c.1043C>A	c.(1042-1044)aCa>aAa	p.T348K	MAP3K11_ENST00000532507.1_Missense_Mutation_p.T21K|MAP3K11_ENST00000534432.1_5'UTR|MAP3K11_ENST00000309100.3_Missense_Mutation_p.T605K					mitogen-activated protein kinase kinase kinase 11											breast(3)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(14)|skin(1)	24						TGCTGGGGGTGTGGAAGGAGA	0.602																																					p.T605K		Atlas-SNP	.											.	MAP3K11	67	.	0			c.C1814A						PASS	.	G	LYS/THR	0,4402		0,0,2201	58	51	54		1814	4.1	1	11	dbSNP_134	54	6,8588	5.0+/-18.6	0,6,4291	yes	missense	MAP3K11	NM_002419.3	78	0,6,6492	TT,TG,GG		0.0698,0.0,0.0462	probably-damaging	605/848	65373249	6,12990	2201	4297	6498	SO:0001583	missense	4296	exon8			GGGGGTGTGGAAG		CCDS8107.1	11q13.1-q13.3	2011-06-09			ENSG00000173327	ENSG00000173327	2.7.10.1	"Mitogen-activated protein kinase cascade / Kinase kinase kinases"	6850	protein-coding gene	gene with protein product		600050		MLK3, PTK1		9267807, 8183572	Standard	NM_002419		Approved	SPRK, MEKK11	uc001oew.3	Q16584	OTTHUMG00000166529	ENST00000530153.1:c.1043C>A	11.37:g.65373249G>T	ENSP00000433886:p.Thr348Lys	81	0	0		75	41	0.546667	NM_002419		Missense_Mutation	SNP	ENST00000530153.1	37		.	.	.	.	.	.	.	.	.	.	G	20.3	3.969099	0.74131	0.0	6.98E-4	ENSG00000173327	ENST00000309100;ENST00000532507;ENST00000530153	T;T	0.73681	-0.67;-0.77	5.04	4.12	0.48240	.	0.292498	0.28312	N	0.015805	T	0.65228	0.2671	L	0.29908	0.895	0.35129	D	0.767737	P;D	0.54207	0.911;0.965	P;P	0.48704	0.587;0.456	T	0.67616	-0.5625	10	0.19147	T	0.46	.	9.1853	0.37168	0.0976:0.0:0.9024:0.0	.	112;605	B3KQY4;Q16584	.;M3K11_HUMAN	K	605;21;348	ENSP00000309597:T605K;ENSP00000433886:T348K	ENSP00000309597:T605K	T	-	2	0	MAP3K11	65129825	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	1.629000	0.37071	1.354000	0.45846	0.655000	0.94253	ACA	G|0.999;T|0.001	0.001	strong		0.602	MAP3K11-004	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000390233.2			T	65373249	G	T	65373249	3	4	24	1	0	0	0	0	1	0	0	0	9254	1377	48	4	741	4	MAP3K11	11	65373249	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	4211890	65373249	69633267	363	8580											
RIN1	9610	hgsc.bcm.edu	37	chr11	66099992	66099992	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtctcaggccactccgcccGgcggtagacgaggtagccag	7	5	15	14	4	1	1	1	0	1	1	3	2	2	1	4	5	1	2	4	5	2	2	rs139103405	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:66099992G>A	ENST00000311320.4	-	10	2233	c.2107C>T	c.(2107-2109)Cgg>Tgg	p.R703W	RP11-867G23.12_ENST00000526655.1_RNA|RIN1_ENST00000530056.1_Missense_Mutation_p.R537W|RIN1_ENST00000524804.1_5'Flank|RIN1_ENST00000424433.2_Intron	NM_004292.2	NP_004283.2	Q13671	RIN1_HUMAN	Ras and Rab interactor 1	703	Ras and 14-3-3 protein binding region.|Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				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						CACTCCGCCCGGCGGTAGACG	0.672																																					p.R703W		Atlas-SNP	.											.	RIN1	64	.	0			c.C2107T						PASS	.	G	TRP/ARG	0,4400		0,0,2200	73	84	80		2107	4	1	11	dbSNP_134	80	4,8586	3.7+/-12.6	0,4,4291	no	missense	RIN1	NM_004292.2	101	0,4,6491	AA,AG,GG		0.0466,0.0,0.0308	probably-damaging	703/784	66099992	4,12986	2200	4295	6495	SO:0001583	missense	9610	exon10			CCGCCCGGCGGTA	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.2107C>T	11.37:g.66099992G>A	ENSP00000310406:p.Arg703Trp	79	0	0		106	50	0.471698	NM_004292	O15010|Q00427|Q96CC8	Missense_Mutation	SNP	ENST00000311320.4	37	CCDS31614.1	.	.	.	.	.	.	.	.	.	.	G	17.69	3.451461	0.63290	0.0	4.66E-4	ENSG00000174791	ENST00000311320;ENST00000530056	T;T	0.19394	2.15;2.15	4.93	4.0	0.46444	Ras-association (3);	0.682458	0.13161	N	0.409069	T	0.39009	0.1062	M	0.61703	1.905	0.80722	D	1	D;D;D	0.76494	0.996;0.999;0.99	P;P;P	0.60609	0.849;0.877;0.571	T	0.12967	-1.0527	10	0.87932	D	0	-13.1701	10.7254	0.46066	0.0:0.0:0.7956:0.2044	.	537;334;703	E9PNR2;B4DW96;Q13671	.;.;RIN1_HUMAN	W	703;537	ENSP00000310406:R703W;ENSP00000432798:R537W	ENSP00000310406:R703W	R	-	1	2	RIN1	65856568	0.999000	0.42202	0.998000	0.56505	0.382000	0.30200	3.479000	0.53165	1.166000	0.42689	0.462000	0.41574	CGG	G|0.999;A|0.001	0.001	strong		0.672	RIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392980.2	NM_004292		A	66099992	G	A	66099992	3	1	24	1	0	0	0	0	1	0	0	0	13386	1115	39	1	248	1	RIN1	11	66099992	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	726743	66099992	68906524	364	8581											
SHANK2	22941	hgsc.bcm.edu	37	chr11	70331716	70331716	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgagcgcgtcttgataaagtGcattgcttttgtgaatgatg	9	14	12	6	3	1	3	0	3	1	0	1	4	1	3	0	0	3	2	0	0	3	5			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:70331716G>C	ENST00000423696.2	-	15	3581	c.3545C>G	c.(3544-3546)gCa>gGa	p.A1182G	SHANK2_ENST00000449833.2_Missense_Mutation_p.A966G|SHANK2_ENST00000338508.4_Missense_Mutation_p.A1562G|SHANK2_ENST00000409161.1_Missense_Mutation_p.A965G			Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	1182					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)			TTGATAAAGTGCATTGCTTTT	0.552																																					p.A973G		Atlas-SNP	.											.	SHANK2	340	.	0			c.C2918G						PASS	.						147	145	145					11																	70331716		2200	4294	6494	SO:0001583	missense	22941	exon10			TAAAGTGCATTGC	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.3545C>G	11.37:g.70331716G>C	ENSP00000394536:p.Ala1182Gly	147	0	0		153	76	0.496732	NM_133266	C0SPG8|C0SPG9|Q3Y8G9|Q52LK2|Q9UKP1	Missense_Mutation	SNP	ENST00000423696.2	37		.	.	.	.	.	.	.	.	.	.	G	11.04	1.520786	0.27211	.	.	ENSG00000162105	ENST00000449833;ENST00000409161;ENST00000424924;ENST00000338508;ENST00000423696;ENST00000433693;ENST00000294018	T;T;T;T;T;T	0.19669	2.13;2.13;2.13;2.13;2.13;2.13	5.42	4.51	0.55191	.	0.353602	0.31872	N	0.006936	T	0.20333	0.0489	L	0.32530	0.975	0.80722	D	1	B;P;P	0.43287	0.437;0.802;0.573	B;B;B	0.43536	0.137;0.423;0.267	T	0.01561	-1.1324	10	0.37606	T	0.19	.	14.1457	0.65349	0.0721:0.0:0.9279:0.0	.	1182;1561;966	Q9UPX8;Q9UPX8-3;Q9UPX8-4	SHAN2_HUMAN;.;.	G	966;965;840;1562;1182;1200;1185	ENSP00000399423:A966G;ENSP00000386491:A965G;ENSP00000402944:A840G;ENSP00000345193:A1562G;ENSP00000394536:A1182G;ENSP00000294018:A1185G	ENSP00000294018:A1185G	A	-	2	0	SHANK2	70009364	1.000000	0.71417	0.013000	0.15412	0.999000	0.98932	6.103000	0.71492	1.294000	0.44707	0.655000	0.94253	GCA	.	.	none		0.552	SHANK2-203	KNOWN	basic	protein_coding	protein_coding		NM_012309		C	70331716	G	C	70331716	3	2	24	1	0	0	0	0	1	0	0	0	14280	1319	46	4	875	4	SHANK2	11	70331716	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	4231724	70331716	64674800	365	8582											
POLD3	10714	hgsc.bcm.edu	37	chr11	74347275	74347275	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaaacaaaagaaaacgaaaaCgcgtactaaaatctaaaact	25	5	4	7	3	1	1	0	0	1	1	1	2	1	1	0	0	5	1	0	0	13	3	rs572105600		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:74347275C>T	ENST00000263681.2	+	11	1282	c.1153C>T	c.(1153-1155)Cgc>Tgc	p.R385C	POLD3_ENST00000527458.1_Missense_Mutation_p.R346C|POLD3_ENST00000532497.1_Missense_Mutation_p.R279C	NM_006591.2	NP_006582.1	Q15054	DPOD3_HUMAN	polymerase (DNA-directed), delta 3, accessory subunit	385					base-excision repair (GO:0006284)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|mismatch repair (GO:0006298)|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)	delta DNA polymerase complex (GO:0043625)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)	p.R385G(2)		breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|stomach(1)	18	Breast(11;3.21e-06)					AAAACGAAAACGCGTACTAAA	0.358																																					p.R385C		Atlas-SNP	.											POLD3_ENST00000263681,NS,carcinoma,0,2	POLD3	87	2	2	Substitution - Missense(2)	endometrium(2)	c.C1153T						PASS	.						83	80	81					11																	74347275		2200	4293	6493	SO:0001583	missense	10714	exon11			CGAAAACGCGTAC	D26018	CCDS8233.1	11q14	2014-06-13			ENSG00000077514	ENSG00000077514		"DNA polymerases"	20932	protein-coding gene	gene with protein product	"DNA polymerase delta subunit p66", "Pol delta C subunit (p66)", "protein phosphatase 1, regulatory subunit 128"	611415				10219083	Standard	NM_006591		Approved	P66, KIAA0039, P68, PPP1R128	uc001ovf.2	Q15054	OTTHUMG00000165621	ENST00000263681.2:c.1153C>T	11.37:g.74347275C>T	ENSP00000263681:p.Arg385Cys	151	0	0		163	60	0.368098	NM_006591	B7ZAI6|Q32MZ9|Q32N00	Missense_Mutation	SNP	ENST00000263681.2	37	CCDS8233.1	.	.	.	.	.	.	.	.	.	.	C	18.46	3.629880	0.67015	.	.	ENSG00000077514	ENST00000263681;ENST00000527458;ENST00000532497	.	.	.	5.7	4.71	0.59529	.	0.000000	0.85682	D	0.000000	T	0.78272	0.4257	M	0.76328	2.33	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.80627	-0.1298	9	0.87932	D	0	-18.0768	14.9973	0.71443	0.1522:0.8478:0.0:0.0	.	385	Q15054	DPOD3_HUMAN	C	385;346;279	.	ENSP00000263681:R385C	R	+	1	0	POLD3	74024923	0.997000	0.39634	0.943000	0.38184	0.845000	0.48019	1.348000	0.33987	2.696000	0.92011	0.561000	0.74099	CGC	.	.	none		0.358	POLD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385376.1	NM_006591		T	74347275	C	T	74347275	3	4	24	1	0	0	0	0	1	0	0	0	12201	536	19	1	1195	1	POLD3	11	74347275	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	4015559	74347275	60659241	366	8583											
B3GNT6	192134	hgsc.bcm.edu	37	chr11	76751608	76751608	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccttcggcgtgcagcttgcCtggcgcacagcagtcctcct	4	9	11	17	3	0	0	0	0	0	0	3	0	2	0	4	2	4	4	4	2	0	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:76751608C>T	ENST00000533140.1	+	2	1151	c.1013C>T	c.(1012-1014)cCt>cTt	p.P338L	B3GNT6_ENST00000421061.1_Missense_Mutation_p.P216L|B3GNT6_ENST00000354301.5_Missense_Mutation_p.P337L			O43505	B3GN1_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6 (core 3 synthase)	357					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						TGCAGCTTGCCTGGCGCACAG	0.667																																					p.P337L		Atlas-SNP	.											.	B3GNT6	27	.	0			c.C1010T						PASS	.						12	12	12					11																	76751608		2111	4199	6310	SO:0001583	missense	192134	exon5			GCTTGCCTGGCGC	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.1013C>T	11.37:g.76751608C>T	ENSP00000435352:p.Pro338Leu	11	0	0		17	8	0.470588	NM_138706	Q4TTN0	Missense_Mutation	SNP	ENST00000533140.1	37	CCDS53681.1	.	.	.	.	.	.	.	.	.	.	C	18.27	3.586243	0.66105	.	.	ENSG00000198488	ENST00000533140;ENST00000354301;ENST00000421061	T;T;T	0.60672	1.5;0.17;2.66	2.9	2.9	0.33743	.	0.066129	0.64402	U	0.000007	T	0.76248	0.3961	M	0.86502	2.82	0.52501	D	0.999958	D	0.89917	1.0	D	0.97110	1.0	T	0.79522	-0.1769	10	0.51188	T	0.08	.	12.0142	0.53305	0.0:1.0:0.0:0.0	.	337	Q6ZMB0	B3GN6_HUMAN	L	338;337;216	ENSP00000435352:P338L;ENSP00000346256:P337L;ENSP00000403463:P216L	ENSP00000346256:P337L	P	+	2	0	B3GNT6	76429256	0.000000	0.05858	0.920000	0.36463	0.642000	0.38348	0.234000	0.17930	1.908000	0.55244	0.462000	0.41574	CCT	.	.	none		0.667	B3GNT6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000382740.2	NM_138706		T	76751608	C	T	76751608	3	4	24	1	0	0	0	0	1	0	0	0	1261	681	24	2	1015	2	B3GNT6	11	76751608	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	2404333	76751608	58254908	367	8584											
FAM181B	220382	hgsc.bcm.edu	37	chr11	82444668	82444668	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	catcgtcctcgaaacagcagCccttgtccagggctccgaag	9	7	10	15	3	0	0	0	0	0	0	5	2	3	0	4	1	3	2	4	1	2	1	rs144429777	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:82444668C>G	ENST00000329203.3	-	1	238	c.104G>C	c.(103-105)gGc>gCc	p.G35A		NM_175885.3	NP_787081.2	A6NEQ2	F181B_HUMAN	family with sequence similarity 181, member B	35										large_intestine(1)|lung(2)|prostate(1)	4						GAAACAGCAGCCCTTGTCCAG	0.721													C|||	17	0.00339457	0.0	0.0014	5008	,	,		7441	0.0		0.008	False		,,,				2504	0.0082				p.G35A		Atlas-SNP	.											.	FAM181B	14	.	0			c.G104C						PASS	.	C	ALA/GLY	3,4381		0,3,2189	11	13	12		104	4	1	11	dbSNP_134	12	28,8548		0,28,4260	yes	missense	FAM181B	NM_175885.3	60	0,31,6449	GG,GC,CC		0.3265,0.0684,0.2392	possibly-damaging	35/427	82444668	31,12929	2192	4288	6480	SO:0001583	missense	220382	exon1			CAGCAGCCCTTGT	AK095054, BC039262	CCDS31648.1	11q14.1	2011-11-30			ENSG00000182103	ENSG00000182103			28512	protein-coding gene	gene with protein product						12477932	Standard	NM_175885		Approved	LOC220382, MGC33846	uc001ozp.3	A6NEQ2	OTTHUMG00000166869	ENST00000329203.3:c.104G>C	11.37:g.82444668C>G	ENSP00000365295:p.Gly35Ala	21	0	0		27	21	0.777778	NM_175885	B2RWP1	Missense_Mutation	SNP	ENST00000329203.3	37	CCDS31648.1	.	.	.	.	.	.	.	.	.	.	C	11.54	1.668634	0.29604	6.84E-4	0.003265	ENSG00000182103	ENST00000329203	T	0.36340	1.26	4.04	4.04	0.47022	.	0.636557	0.14564	U	0.311877	T	0.47358	0.1441	L	0.44542	1.39	0.25758	N	0.984974	D	0.89917	1.0	D	0.66602	0.945	T	0.22173	-1.0224	9	.	.	.	.	10.1105	0.42559	0.0:0.9066:0.0:0.0934	.	35	A6NEQ2	F181B_HUMAN	A	35	ENSP00000365295:G35A	.	G	-	2	0	FAM181B	82122316	1.000000	0.71417	1.000000	0.80357	0.007000	0.05969	2.111000	0.41883	2.073000	0.62155	0.455000	0.32223	GGC	C|0.997;G|0.003	0.003	strong		0.721	FAM181B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391626.1	NM_175885		G	82444668	C	G	82444668	3	3	24	1	0	0	0	0	1	0	0	0	5514	739	26	4	1180	4	FAM181B	11	82444668	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	5693060	82444668	52561848	368	8585											
MMP27	64066	hgsc.bcm.edu	37	chr11	102575442	102575442	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttgtcatctatgagactcCtattcttgctttgaacaaga	10	17	6	8	0	3	3	1	2	2	2	4	4	4	3	1	0	2	1	1	0	4	7	rs553456217		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:102575442C>T	ENST00000260229.4	-	2	258	c.167G>A	c.(166-168)aGg>aAg	p.R56K		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	56					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)	TATGAGACTCCTATTCTTGCT	0.383																																					p.R56K		Atlas-SNP	.											.	MMP27	84	.	0			c.G167A						PASS	.						74	72	73					11																	102575442		2203	4299	6502	SO:0001583	missense	64066	exon2			AGACTCCTATTCT	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.167G>A	11.37:g.102575442C>T	ENSP00000260229:p.Arg56Lys	80	0	0		91	38	0.417582	NM_022122	Q6UWK6	Missense_Mutation	SNP	ENST00000260229.4	37	CCDS8319.1	.	.	.	.	.	.	.	.	.	.	C	1.324	-0.598646	0.03744	.	.	ENSG00000137675	ENST00000260229	T	0.36340	1.26	5.55	1.43	0.22495	Peptidoglycan binding-like (2);Metallopeptidase, catalytic domain (1);	0.764123	0.12270	N	0.483911	T	0.13628	0.0330	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.29518	-1.0009	10	0.10111	T	0.7	.	2.5257	0.04690	0.1265:0.4691:0.1116:0.2928	.	56	Q9H306	MMP27_HUMAN	K	56	ENSP00000260229:R56K	ENSP00000260229:R56K	R	-	2	0	MMP27	102080652	0.000000	0.05858	0.610000	0.28997	0.014000	0.08584	-0.364000	0.07583	0.473000	0.27368	0.591000	0.81541	AGG	.	.	none		0.383	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122		T	102575442	C	T	102575442	3	4	24	1	0	0	0	0	1	0	0	0	9673	681	24	2	1410	2	MMP27	11	102575442	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	20130774	102575442	32431074	369	8586											
ATM	472	hgsc.bcm.edu	37	chr11	108141988	108141988	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttaccacagcaatgtgtgtTctttgtatcgtcgtgaccaa	9	15	8	9	2	1	1	0	1	1	0	3	1	1	1	2	0	2	3	2	0	4	5	rs139552233	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:108141988T>C	ENST00000452508.2	+	21	3121	c.2932T>C	c.(2932-2934)Tct>Cct	p.S978P	ATM_ENST00000278616.4_Missense_Mutation_p.S978P			Q13315	ATM_HUMAN	ATM serine/threonine kinase	978					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.S978P(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)	CAATGTGTGTTCTTTGTATCG	0.313			"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)			T|||	3	0.000599042	0.0	0.0	5008	,	,		16164	0.0		0.001	False		,,,				2504	0.002				p.S978P		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	ATM_ENST00000278616,colon,carcinoma,-2,5	ATM	1657	5	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.T2932C						scavenged	.	T	PRO/SER	0,4402		0,0,2201	90	88	89		2932	5.5	1	11	dbSNP_134	89	4,8592	3.7+/-12.6	0,4,4294	yes	missense	ATM	NM_000051.3	74	0,4,6495	CC,CT,TT		0.0465,0.0,0.0308	probably-damaging	978/3057	108141988	4,12994	2201	4298	6499	SO:0001583	missense	472	exon20	Familial Cancer Database	AT, Louis-Bar syndrome	GTGTGTTCTTTGT	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.2932T>C	11.37:g.108141988T>C	ENSP00000388058:p.Ser978Pro	79	1	0.0126582		75	35	0.466667	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	24.8	4.565967	0.86439	0.0	4.65E-4	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.74106	-0.81;-0.81;-0.81	5.5	5.5	0.81552	Armadillo-type fold (1);	0.102849	0.64402	D	0.000001	D	0.85388	0.5685	M	0.70275	2.135	0.45567	D	0.998516	D	0.89917	1.0	D	0.87578	0.998	D	0.86822	0.2005	10	0.66056	D	0.02	.	15.8922	0.79309	0.0:0.0:0.0:1.0	.	978	Q13315	ATM_HUMAN	P	978	ENSP00000435747:S978P;ENSP00000278616:S978P;ENSP00000388058:S978P	ENSP00000278616:S978P	S	+	1	0	ATM	107647198	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.434000	0.73408	2.203000	0.70933	0.459000	0.35465	TCT	T|1.000;C|0.000	0.000	strong		0.313	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		C	108141988	T	C	108141988	3	2	24	1	0	0	0	0	1	0	0	0	1109	1783	62	3	3006	3	ATM	11	108141988	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	5566546	108141988	26864528	370	8587											
PPP2R1B	5519	hgsc.bcm.edu	37	chr11	111608216	111608216	+	IGR	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgggtcttgggaagtggtTcttgtcagcccgagggacac	6	11	16	8	1	3	0	1	0	2	0	3	3	3	2	1	4	1	1	1	4	1	3	rs61756429	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:111608216T>A	ENST00000527614.1	-	0	5587				PPP2R1B_ENST00000426998.2_Missense_Mutation_p.N559Y|PPP2R1B_ENST00000311129.5_Missense_Mutation_p.N623Y|PPP2R1B_ENST00000530787.1_5'Flank	NM_001177562.1|NM_002716.4	NP_001171033.1|NP_002707.3	P30154	2AAB_HUMAN	protein phosphatase 2, regulatory subunit A, beta						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)		GGGAAGTGGTTCTTGTCAGCC	0.597													T|||	10	0.00199681	0.0	0.0043	5008	,	,		20031	0.0		0.007	False		,,,				2504	0.0				p.N623Y		Atlas-SNP	.											.	PPP2R1B	44	.	0			c.A1867T						PASS	.	T	TYR/ASN,TYR/ASN	13,4389	21.2+/-45.6	0,13,2188	155	128	137		1867,1675	4.1	1	11	dbSNP_129	137	86,8508	48.9+/-108.6	0,86,4211	yes	missense,missense	PPP2R1B	NM_181699.2,NM_181700.1	143,143	0,99,6399	AA,AT,TT		1.0007,0.2953,0.7618	possibly-damaging,possibly-damaging	623/668,559/604	111608216	99,12897	2201	4297	6498	SO:0001628	intergenic_variant	5519	exon15			AGTGGTTCTTGTC	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		11.37:g.111608216T>A		85	0	0		85	36	0.423529	NM_181699	A8MY67|B0YJ69|B4DGQ6|B4DK91|B4DWW5|F8W8G1|O75620|Q8NHV8	Missense_Mutation	SNP	ENST00000527614.1	37	CCDS8349.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	T	10.82	1.458179	0.26161	0.002953	0.010007	ENSG00000137713	ENST00000311129;ENST00000426998	.	.	.	5.25	4.13	0.48395	.	0.617749	0.15812	N	0.243438	T	0.27933	0.0688	N	0.08118	0	0.80722	D	1	P;D	0.54207	0.94;0.965	P;P	0.51135	0.459;0.66	T	0.18493	-1.0335	9	0.87932	D	0	-10.7806	7.9175	0.29827	0.0:0.0914:0.0:0.9086	rs61756429	559;623	B4DWW5;P30154-2	.;.	Y	623;559	.	ENSP00000311344:N623Y	N	-	1	0	PPP2R1B	111113426	1.000000	0.71417	0.991000	0.47740	0.214000	0.24535	1.866000	0.39489	1.132000	0.42129	0.496000	0.49642	AAC	T|0.992;A|0.008	0.008	strong		0.597	PPP2R1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391298.1	NM_002716		A	111608216	T	A	111608216	1	1	24	0	1	0	0	0	0	0	0	0	12395	1783	62	5		5	PPP2R1B	11	111608216	IGR	SNP	T	TCGA-G8-6326-01A-11D-2210-10	3466228	111608216	23398300	371	8588											
DSCAML1	57453	hgsc.bcm.edu	37	chr11	117309603	117309603	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atccagacccctcctcacctCggatggagctgcccccattg	7	8	8	18	1	1	1	1	0	0	1	4	3	3	3	7	2	2	1	7	2	0	1			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:117309603C>T	ENST00000321322.6	-	24	4422	c.4421G>A	c.(4420-4422)cGa>cAa	p.R1474Q	DSCAML1_ENST00000527706.1_Missense_Mutation_p.R1204Q	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1414	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		CTCCTCACCTCGGATGGAGCT	0.607																																					p.R1474Q		Atlas-SNP	.											.	DSCAML1	286	.	0			c.G4421A						PASS	.						44	42	43					11																	117309603		2201	4296	6497	SO:0001583	missense	57453	exon24			TCACCTCGGATGG		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.4421G>A	11.37:g.117309603C>T	ENSP00000315465:p.Arg1474Gln	68	0	0		39	21	0.538462	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	37	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	C	32	5.182083	0.94885	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.56611	0.45;0.45	4.8	4.8	0.61643	Fibronectin, type III (4);Immunoglobulin-like fold (1);	.	.	.	.	T	0.57975	0.2090	N	0.14661	0.345	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.63435	-0.6638	9	0.48119	T	0.1	.	18.0562	0.89365	0.0:1.0:0.0:0.0	.	1414	Q8TD84	DSCL1_HUMAN	Q	1204;1474;1181	ENSP00000434335:R1204Q;ENSP00000315465:R1474Q	ENSP00000315465:R1474Q	R	-	2	0	DSCAML1	116814813	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	7.635000	0.83286	2.503000	0.84419	0.561000	0.74099	CGA	.	.	none		0.607	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693		T	117309603	C	T	117309603	3	4	24	1	0	0	0	0	1	0	0	0	4771	884	31	1	1960	1	DSCAML1	11	117309603	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	5701387	117309603	17696913	372	8589											
HYOU1	10525	hgsc.bcm.edu	37	chr11	118925935	118925935	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acagtctgcctctgtgggtcGaaagtcagctcgtgctccgg	6	10	13	12	3	3	0	1	0	2	0	6	1	4	0	2	2	3	2	2	2	1	0	rs511134	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:118925935G>A	ENST00000404233.3	-	5	505	c.381C>T	c.(379-381)ttC>ttT	p.F127F	HYOU1_ENST00000525859.1_Silent_p.F127F|HYOU1_ENST00000543287.1_Silent_p.F40F|HYOU1_ENST00000529972.1_Silent_p.F127F	NM_001130991.1|NM_006389.3	NP_001124463.1|NP_006380.1	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1	127					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)		TCTGTGGGTCGAAAGTCAGCT	0.582													G|||	232	0.0463259	0.1104	0.0216	5008	,	,		20549	0.0089		0.0089	False		,,,				2504	0.0542				p.F127F		Atlas-SNP	.											.	HYOU1	88	.	0			c.C381T						PASS	.	G	,	367,4033	188.8+/-215.1	20,327,1853	118	113	114		381,381	-1.2	0.6	11	dbSNP_83	114	104,8486	56.8+/-118.0	2,100,4193	no	coding-synonymous,coding-synonymous	HYOU1	NM_001130991.1,NM_006389.3	,	22,427,6046	AA,AG,GG		1.2107,8.3409,3.6259	,	127/1000,127/1000	118925935	471,12519	2200	4295	6495	SO:0001819	synonymous_variant	10525	exon5			TGGGTCGAAAGTC	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.381C>T	11.37:g.118925935G>A		126	0	0		121	63	0.520661	NM_006389	A8C1Z0|B7Z909|Q2I204|Q53H25	Silent	SNP	ENST00000404233.3	37	CCDS8408.1																																																																																			G|0.962;A|0.038	0.038	strong		0.582	HYOU1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389353.1	NM_006389		A	118925935	G	A	118925935	2	1	24	1	0	0	0	0	0	0	0	1	7479	1049	37	1		1	HYOU1	11	118925935	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1616332	118925935	16080581	373	8590											
ZNF202	7753	hgsc.bcm.edu	37	chr11	123599897	123599897	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gagctcctctctgcaggaagGtctgggtcctcgggcactgg	5	9	15	12	1	2	0	0	0	2	0	6	2	4	1	2	5	2	3	2	5	1	0	rs11825443	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:123599897G>A	ENST00000529691.1	-	4	858	c.639C>T	c.(637-639)gaC>gaT	p.D213D	ZNF202_ENST00000336139.4_Silent_p.D213D|ZNF202_ENST00000530393.1_Silent_p.D213D			O95125	ZN202_HUMAN	zinc finger protein 202	213					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)		CTGCAGGAAGGTCTGGGTCCT	0.502													G|||	130	0.0259585	0.0953	0.0058	5008	,	,		19804	0.0		0.0	False		,,,				2504	0.0				p.D213D		Atlas-SNP	.											.	ZNF202	72	.	0			c.C639T						PASS	.	G		351,4053	181.5+/-209.5	12,327,1863	72	65	67		639	0.8	0.9	11	dbSNP_120	67	0,8598		0,0,4299	no	coding-synonymous	ZNF202	NM_003455.2		12,327,6162	AA,AG,GG		0.0,7.97,2.6996		213/649	123599897	351,12651	2202	4299	6501	SO:0001819	synonymous_variant	7753	exon6			AGGAAGGTCTGGG	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.639C>T	11.37:g.123599897G>A		40	0	0		58	21	0.362069	NM_003455	B0LPH9|Q4JG21|Q9H1B9|Q9NSM4	Silent	SNP	ENST00000529691.1	37	CCDS8443.1																																																																																			G|0.965;A|0.035	0.035	strong		0.502	ZNF202-003	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387419.1	NM_003455		A	123599897	G	A	123599897	2	1	24	1	0	0	0	0	0	0	0	1	17778	1252	44	2		2	ZNF202	11	123599897	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	4673962	123599897	11406619	374	8591											
OR10G9	219870	hgsc.bcm.edu	37	chr11	123893757	123893757	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtgacagcgttcatcctcaCgggccttccccatgccccag	6	8	9	18	3	2	1	2	1	0	0	4	1	4	1	6	1	2	1	6	1	0	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:123893757C>T	ENST00000375024.1	+	1	38	c.38C>T	c.(37-39)aCg>aTg	p.T13M		NM_001001953.1	NP_001001953.1	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G, member 9	13						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)		TTCATCCTCACGGGCCTTCCC	0.562																																					p.T13M		Atlas-SNP	.											OR10G9,NS,carcinoma,0,2	OR10G9	80	2	0			c.C38T						scavenged	.						175	170	172					11																	123893757		2201	4299	6500	SO:0001583	missense	219870	exon1			TCCTCACGGGCCT	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.38C>T	11.37:g.123893757C>T	ENSP00000364164:p.Thr13Met	308	0	0		387	29	0.0749354	NM_001001953		Missense_Mutation	SNP	ENST00000375024.1	37	CCDS31703.1	.	.	.	.	.	.	.	.	.	.	C	7.277	0.608309	0.14002	.	.	ENSG00000236981	ENST00000375024	T	0.00421	7.46	3.33	-4.34	0.03666	.	1.118960	0.06817	N	0.791372	T	0.00178	0.0005	N	0.04260	-0.245	0.09310	N	0.999992	B	0.06786	0.001	B	0.04013	0.001	T	0.29640	-1.0005	10	0.40728	T	0.16	.	9.7201	0.40297	0.0:0.2623:0.0:0.7377	.	13	Q8NGN4	O10G9_HUMAN	M	13	ENSP00000364164:T13M	ENSP00000364164:T13M	T	+	2	0	OR10G9	123398967	0.000000	0.05858	0.149000	0.22428	0.069000	0.16628	-0.761000	0.04751	-1.009000	0.03400	-0.766000	0.03442	ACG	.	.	none		0.562	OR10G9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387269.1	NM_001001953		T	123893757	C	T	123893757	3	4	24	1	0	0	0	0	1	0	0	0	10913	536	19	1	40	1	OR10G9	11	123893757	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	293860	123893757	11112759	375	8592											
ROBO4	54538	hgsc.bcm.edu	37	chr11	124764176	124764176	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acttgcacgcagtaggagccTggcatatgggtggcgatttc	8	10	14	9	2	0	0	0	0	0	0	1	2	0	1	1	4	2	4	1	4	2	4	rs11820142	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:124764176T>C	ENST00000306534.3	-	8	1724	c.1239A>G	c.(1237-1239)ccA>ccG	p.P413P	ROBO4_ENST00000526899.1_5'Flank|ROBO4_ENST00000533054.1_Silent_p.P268P	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	413	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)			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)		AGTAGGAGCCTGGCATATGGG	0.597													T|||	125	0.0249601	0.0893	0.0086	5008	,	,		3618	0.0		0.001	False		,,,				2504	0.0				p.P413P		Atlas-SNP	.											.	ROBO4	130	.	0			c.A1239G						PASS	.	T		344,4058	179.4+/-207.9	9,326,1866	111	87	95		1239	1.1	1	11	dbSNP_120	95	2,8596	1.2+/-3.3	0,2,4297	no	coding-synonymous	ROBO4	NM_019055.5		9,328,6163	CC,CT,TT		0.0233,7.8146,2.6615		413/1008	124764176	346,12654	2201	4299	6500	SO:0001819	synonymous_variant	54538	exon8			GGAGCCTGGCATA	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.1239A>G	11.37:g.124764176T>C		100	0	0		110	55	0.5	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Silent	SNP	ENST00000306534.3	37	CCDS8455.1																																																																																			T|0.971;C|0.029	0.029	strong		0.597	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055		C	124764176	T	C	124764176	2	2	24	1	0	0	0	0	0	0	0	1	13531	1567	55	3		3	ROBO4	11	124764176	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	870419	124764176	10242340	376	8593											
SLC37A2	219855	hgsc.bcm.edu	37	chr11	124951719	124951719	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctgctctatcagggagagcGgccttgagactgtggccaaa	9	8	13	11	1	2	2	1	1	1	2	2	4	2	2	3	3	2	1	3	3	2	2	rs34485243	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:124951719G>A	ENST00000403796.2	+	9	1103	c.802G>A	c.(802-804)Ggc>Agc	p.G268S	SLC37A2_ENST00000407458.1_Missense_Mutation_p.G268S|SLC37A2_ENST00000298280.5_Missense_Mutation_p.G268S|SLC37A2_ENST00000308074.4_Missense_Mutation_p.G268S	NM_001145290.1	NP_001138762.1	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 2	268			G -> S (in dbSNP:rs34485243).		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)		CAGGGAGAGCGGCCTTGAGAC	0.592													G|||	170	0.0339457	0.1248	0.0058	5008	,	,		18150	0.0		0.001	False		,,,				2504	0.0				p.G268S	Melanoma(11;373 620 21213 26083 47768)	Atlas-SNP	.											.	SLC37A2	105	.	0			c.G802A						PASS	.	G	SER/GLY,SER/GLY	396,4006	198.7+/-222.5	15,366,1820	68	65	66		802,802	-8	0	11	dbSNP_126	66	2,8596	2.2+/-6.3	0,2,4297	yes	missense,missense	SLC37A2	NM_001145290.1,NM_198277.2	56,56	15,368,6117	AA,AG,GG		0.0233,8.9959,3.0615	benign,benign	268/502,268/506	124951719	398,12602	2201	4299	6500	SO:0001583	missense	219855	exon9			GAGAGCGGCCTTG	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.802G>A	11.37:g.124951719G>A	ENSP00000384407:p.Gly268Ser	73	0	0		76	27	0.355263	NM_001145290	A8K2P9|Q6P599|Q7Z7P8|Q8TEM2	Missense_Mutation	SNP	ENST00000403796.2	37	CCDS44757.1	42	0.019230769230769232	39	0.07926829268292683	3	0.008287292817679558	0	0.0	0	0.0	G	1.561	-0.536711	0.04082	0.089959	2.33E-4	ENSG00000134955	ENST00000403796;ENST00000407458;ENST00000298280;ENST00000308074	T;T;T;T	0.31769	1.48;1.48;1.93;1.48	4.86	-7.96	0.01144	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.505550	0.03203	N	0.175066	T	0.00328	0.0010	N	0.01473	-0.845	0.09310	N	1	B;B	0.10296	0.003;0.003	B;B	0.10450	0.005;0.003	T	0.15065	-1.0450	10	0.08599	T	0.76	-3.6249	6.3702	0.21477	0.2968:0.1007:0.5033:0.0992	rs34485243	268;268	Q8TED4-2;Q8TED4	.;SPX2_HUMAN	S	268	ENSP00000384407:G268S;ENSP00000385126:G268S;ENSP00000298280:G268S;ENSP00000311833:G268S	ENSP00000298280:G268S	G	+	1	0	SLC37A2	124456929	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.394000	0.20834	-1.389000	0.02090	-0.880000	0.02959	GGC	G|0.965;A|0.035	0.035	strong		0.592	SLC37A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386837.1	XM_166184		A	124951719	G	A	124951719	3	1	24	1	0	0	0	0	1	0	0	0	14613	1116	39	1	836	1	SLC37A2	11	124951719	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	187543	124951719	10054797	377	8594											
KIRREL3	84623	hgsc.bcm.edu	37	chr11	126294661	126294661	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tccaggaaggagctgctgtcGctgagggagcctctctggaa	8	8	15	10	1	1	1	0	1	1	0	4	5	2	5	2	4	3	3	2	4	2	0	rs34844660	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:126294661G>A	ENST00000525144.2	-	17	2400	c.2151C>T	c.(2149-2151)agC>agT	p.S717S	KIRREL3_ENST00000529097.2_Silent_p.S705S|KIRREL3_ENST00000416561.2_Silent_p.S184S	NM_032531.3	NP_115920.1	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 (Drosophila)	717	Ser-rich.				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)		AGCTGCTGTCGCTGAGGGAGC	0.627													G|||	69	0.013778	0.0514	0.0014	5008	,	,		19048	0.0		0.0	False		,,,				2504	0.0				p.S717S		Atlas-SNP	.											.	KIRREL3	183	.	0			c.C2151T						PASS	.	G		148,4198		0,148,2025	74	82	79		2151	4	1	11	dbSNP_126	79	0,8562		0,0,4281	no	coding-synonymous	KIRREL3	NM_032531.3		0,148,6306	AA,AG,GG		0.0,3.4054,1.1466		717/779	126294661	148,12760	2173	4281	6454	SO:0001819	synonymous_variant	84623	exon17			GCTGTCGCTGAGG	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.2151C>T	11.37:g.126294661G>A		112	0	0		111	51	0.459459	NM_032531	Q3MIJ7|Q6UWJ9|Q6UWL5|Q96JG0	Silent	SNP	ENST00000525144.2	37	CCDS53723.1																																																																																			G|0.992;A|0.008	0.008	strong		0.627	KIRREL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386479.2	NM_032531		A	126294661	G	A	126294661	2	1	24	1	0	0	0	0	0	0	0	1	8335	1078	38	1		1	KIRREL3	11	126294661	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1342942	126294661	8711855	378	8595											
GLB1L2	89944	hgsc.bcm.edu	37	chr11	134234269	134234269	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacacgagctgcagctactgAccacctttctcttcaacgtc	9	10	6	16	2	2	1	1	1	1	0	4	2	2	1	2	0	5	3	2	0	2	3	rs114723326	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:134234269A>G	ENST00000535456.2	+	8	969	c.781A>G	c.(781-783)Acc>Gcc	p.T261A	GLB1L2_ENST00000389881.3_Missense_Mutation_p.T261A|GLB1L2_ENST00000529077.1_3'UTR|GLB1L2_ENST00000339772.7_Missense_Mutation_p.T261A	NM_138342.3	NP_612351.2	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2	261					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	beta-galactosidase activity (GO:0004565)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41	all_hematologic(175;0.127)	all_cancers(12;2.85e-18)|all_epithelial(12;1.21e-12)|all_lung(97;0.000276)|Lung NSC(97;0.000518)|Breast(109;0.00122)|Medulloblastoma(222;0.0399)|all_neural(223;0.0412)|Esophageal squamous(93;0.0844)		Epithelial(10;1.37e-11)|all cancers(11;2.2e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000885)|Lung(977;0.223)		GCAGCTACTGACCACCTTTCT	0.557													A|||	117	0.0233626	0.0817	0.0086	5008	,	,		19623	0.0		0.003	False		,,,				2504	0.0				p.T261A		Atlas-SNP	.											.	GLB1L2	79	.	0			c.A781G						PASS	.	A	ALA/THR	254,4148	148.8+/-183.1	9,236,1956	286	251	263		781	4	0	11	dbSNP_132	263	6,8588	5.0+/-18.6	0,6,4291	yes	missense	GLB1L2	NM_138342.3	58	9,242,6247	GG,GA,AA		0.0698,5.7701,2.0006	benign	261/637	134234269	260,12736	2201	4297	6498	SO:0001583	missense	89944	exon8			CTACTGACCACCT		CCDS31724.1	11q25	2008-01-29			ENSG00000149328	ENSG00000149328			25129	protein-coding gene	gene with protein product						12975309	Standard	NM_138342		Approved		uc001qhp.3	Q8IW92	OTTHUMG00000167179	ENST00000535456.2:c.781A>G	11.37:g.134234269A>G	ENSP00000444628:p.Thr261Ala	100	0	0		106	46	0.433962	NM_138342	A6NCE6|Q6UX60|Q8NC62|Q8NCB3|Q8NCJ1|Q96HP3	Missense_Mutation	SNP	ENST00000535456.2	37	CCDS31724.1	40|40	0.018315018315018316|0.018315018315018316	38|38	0.07723577235772358|0.07723577235772358	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	A|A	5.513|5.513	0.279580|0.279580	0.10458|0.10458	0.057701|0.057701	6.98E-4|6.98E-4	ENSG00000149328|ENSG00000149328	ENST00000525089;ENST00000533324|ENST00000339772;ENST00000535456;ENST00000389881	.|D;D;D	.|0.97752	.|-4.52;-4.52;-4.52	3.97|3.97	3.97|3.97	0.46021|0.46021	.|Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	.|0.599178	.|0.17894	.|N	.|0.158423	T|T	0.41789|0.41789	0.1174|0.1174	N|N	0.01649|0.01649	-0.78|-0.78	0.09310|0.09310	N|N	1|1	.|B	.|0.13145	.|0.007	.|B	.|0.15052	.|0.012	T|T	0.67035|0.67035	-0.5772|-0.5772	5|10	.|0.12430	.|T	.|0.62	-7.5496|-7.5496	11.2062|11.2062	0.48771|0.48771	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|261	.|Q8IW92	.|GLBL2_HUMAN	G|A	199;88|261	.|ENSP00000344659:T261A;ENSP00000444628:T261A;ENSP00000374531:T261A	.|ENSP00000344659:T261A	D|T	+|+	2|1	0|0	GLB1L2|GLB1L2	133739479|133739479	0.002000|0.002000	0.14202|0.14202	0.022000|0.022000	0.16811|0.16811	0.050000|0.050000	0.14768|0.14768	1.637000|1.637000	0.37155|0.37155	2.026000|2.026000	0.59711|0.59711	0.533000|0.533000	0.62120|0.62120	GAC|ACC	A|0.981;G|0.019	0.019	strong		0.557	GLB1L2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393629.2	NM_138342		G	134234269	A	G	134234269	3	3	24	1	0	0	0	0	1	0	0	0	6437	275	10	3	811	3	GLB1L2	11	134234269	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	7939608	134234269	772247	379	8596											
GLB1L2	89944	hgsc.bcm.edu	37	chr11	134239760	134239760	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtacatgaagcttcgagaCttcttcggctccatctcagg	10	11	9	11	2	2	2	1	1	2	1	6	3	3	2	1	2	2	3	1	2	3	4	rs34063963	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr11:134239760C>T	ENST00000535456.2	+	11	1277	c.1089C>T	c.(1087-1089)gaC>gaT	p.D363D	GLB1L2_ENST00000389881.3_Silent_p.D363D|GLB1L2_ENST00000529077.1_3'UTR|GLB1L2_ENST00000339772.7_Silent_p.D363D	NM_138342.3	NP_612351.2	Q8IW92	GLBL2_HUMAN	galactosidase, beta 1-like 2	363					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	beta-galactosidase activity (GO:0004565)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	41	all_hematologic(175;0.127)	all_cancers(12;2.85e-18)|all_epithelial(12;1.21e-12)|all_lung(97;0.000276)|Lung NSC(97;0.000518)|Breast(109;0.00122)|Medulloblastoma(222;0.0399)|all_neural(223;0.0412)|Esophageal squamous(93;0.0844)		Epithelial(10;1.37e-11)|all cancers(11;2.2e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000885)|Lung(977;0.223)		AGCTTCGAGACTTCTTCGGCT	0.537													C|||	155	0.0309505	0.1112	0.0072	5008	,	,		20784	0.0		0.003	False		,,,				2504	0.0				p.D363D		Atlas-SNP	.											.	GLB1L2	79	.	0			c.C1089T						PASS	.	C		315,4087	171.6+/-201.8	8,299,1894	155	137	143		1089	-11.3	0	11	dbSNP_126	143	7,8587	5.7+/-21.5	0,7,4290	no	coding-synonymous	GLB1L2	NM_138342.3		8,306,6184	TT,TC,CC		0.0815,7.1558,2.4777		363/637	134239760	322,12674	2201	4297	6498	SO:0001819	synonymous_variant	89944	exon11			TCGAGACTTCTTC		CCDS31724.1	11q25	2008-01-29			ENSG00000149328	ENSG00000149328			25129	protein-coding gene	gene with protein product						12975309	Standard	NM_138342		Approved		uc001qhp.3	Q8IW92	OTTHUMG00000167179	ENST00000535456.2:c.1089C>T	11.37:g.134239760C>T		113	0	0		89	39	0.438202	NM_138342	A6NCE6|Q6UX60|Q8NC62|Q8NCB3|Q8NCJ1|Q96HP3	Silent	SNP	ENST00000535456.2	37	CCDS31724.1	63	0.028846153846153848	61	0.12398373983739837	2	0.0055248618784530384	0	0.0	0	0.0	C	4.109	0.018381	0.07959	0.071558	8.15E-4	ENSG00000149328	ENST00000525089;ENST00000533324	.	.	.	5.66	-11.3	0.00108	.	.	.	.	.	T	0.00210	0.0006	.	.	.	0.22918	N	0.998562	.	.	.	.	.	.	T	0.03576	-1.1023	4	.	.	.	-4.4127	1.5619	0.02596	0.3994:0.1015:0.2886:0.2106	rs34063963	.	.	.	F	302;191	.	.	L	+	1	0	GLB1L2	133744970	0.000000	0.05858	0.000000	0.03702	0.655000	0.38815	-4.333000	0.00251	-4.016000	0.00081	-0.181000	0.13052	CTT	C|0.976;T|0.024	0.024	strong		0.537	GLB1L2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393629.2	NM_138342		T	134239760	C	T	134239760	2	4	24	1	0	0	0	0	0	0	0	1	6437	564	20	2		2	GLB1L2	11	134239760	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	5491	134239760	766756	380	8597											
TULP3	7289	hgsc.bcm.edu	37	chr12	3047365	3047365	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaggcccccgtctggaacaGtgacactcagtcctatgtcc	9	8	9	15	1	2	1	1	1	1	0	4	2	4	2	4	2	1	0	4	2	3	1	rs34246393	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:3047365G>C	ENST00000448120.2	+	10	1160	c.1109G>C	c.(1108-1110)aGt>aCt	p.S370T	TULP3_ENST00000397132.2_Missense_Mutation_p.S370T	NM_003324.4	NP_003315.2	O75386	TULP3_HUMAN	tubby like protein 3	370					anterior/posterior pattern specification (GO:0009952)|bone development (GO:0060348)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|central nervous system neuron differentiation (GO:0021953)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic neurocranium morphogenesis (GO:0048702)|G-protein coupled receptor signaling pathway (GO:0007186)|ganglion development (GO:0061548)|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 smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cilium (GO:0005929)|extracellular region (GO:0005576)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	enzyme binding (GO:0019899)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)			endometrium(1)|large_intestine(4)|lung(13)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			GTCTGGAACAGTGACACTCAG	0.507													g|||	2	0.000399361	0.0008	0.0	5008	,	,		19047	0.0		0.001	False		,,,				2504	0.0				p.S370T		Atlas-SNP	.											.	TULP3	45	.	0			c.G1109C						PASS	.		THR/SER,THR/SER	4,4402	8.1+/-20.4	0,4,2199	127	118	121		1109,1109	2.8	0.2	12	dbSNP_126	121	24,8576	17.3+/-56.4	0,24,4276	yes	missense,missense	TULP3	NM_001160408.1,NM_003324.4	58,58	0,28,6475	CC,CG,GG		0.2791,0.0908,0.2153	benign,benign	370/502,370/443	3047365	28,12978	2203	4300	6503	SO:0001583	missense	7289	exon10			GGAACAGTGACAC	AF045583	CCDS8519.1, CCDS53737.1	12p13	2014-02-21			ENSG00000078246	ENSG00000078246		"Intraflagellar transport homologs"	12425	protein-coding gene	gene with protein product		604730				9828123	Standard	NM_003324		Approved	TUBL3	uc001qlj.2	O75386	OTTHUMG00000168152	ENST00000448120.2:c.1109G>C	12.37:g.3047365G>C	ENSP00000410051:p.Ser370Thr	121	0	0		118	62	0.525424	NM_003324	B3KNB7|B7Z6A2|D3DUQ4|F8WBZ9|Q8N5B0	Missense_Mutation	SNP	ENST00000448120.2	37	CCDS8519.1	2|2	9.157509157509158E-4|9.157509157509158E-4	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	g|g	13.39|13.39	2.224334|2.224334	0.39300|0.39300	9.08E-4|9.08E-4	0.002791|0.002791	ENSG00000078246|ENSG00000078246	ENST00000541678;ENST00000538704|ENST00000228245;ENST00000544943;ENST00000542730;ENST00000448120;ENST00000397132	.|D;D;D	.|0.85088	.|-1.94;-1.94;-1.94	5.2|5.2	2.83|2.83	0.33086|0.33086	.|Tubby, C-terminal (4);	.|0.196879	.|0.52532	.|D	.|0.000064	T|T	0.72843|0.72843	0.3511|0.3511	N|N	0.19112|0.19112	0.55|0.55	0.22918|0.22918	N|N	0.998569|0.998569	.|B;B;P	.|0.44946	.|0.126;0.249;0.846	.|B;B;B	.|0.41135	.|0.247;0.348;0.333	T|T	0.65911|0.65911	-0.6053|-0.6053	5|10	.|0.87932	.|D	.|0	-2.0951|-2.0951	6.7817|6.7817	0.23650|0.23650	0.766:0.1528:0.0812:0.0|0.766:0.1528:0.0812:0.0	rs34246393|rs34246393	.|194;370;370	.|B7Z1E7;O75386;F8WBZ9	.|.;TULP3_HUMAN;.	H|T	46;35|370;97;194;370;370	.|ENSP00000442631:S97T;ENSP00000410051:S370T;ENSP00000380321:S370T	.|ENSP00000228245:S370T	Q|S	+|+	3|2	2|0	TULP3|TULP3	2917626|2917626	1.000000|1.000000	0.71417|0.71417	0.175000|0.175000	0.22980|0.22980	0.619000|0.619000	0.37552|0.37552	7.521000|7.521000	0.81832|0.81832	0.302000|0.302000	0.22762|0.22762	-1.075000|-1.075000	0.02238|0.02238	CAG|AGT	G|0.998;C|0.002	0.002	strong		0.507	TULP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398468.1	NM_003324		C	3047365	G	C	3047365	3	2	24	1	0	0	0	0	1	0	0	0	16790	1029	36	4	1147	4	TULP3	12	3047365	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10		3047365	130804530	381	8598											
VWF	7450	hgsc.bcm.edu	37	chr12	6172138	6172138	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accttcaccagcagcctcccGcggccatcccagtccatctg	7	7	7	20	2	2	0	1	0	1	0	5	0	5	0	7	1	2	1	7	1	0	1	rs377198574		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:6172138G>A	ENST00000261405.5	-	13	1769	c.1515C>T	c.(1513-1515)cgC>cgT	p.R505R		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	505	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				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)	GCAGCCTCCCGCGGCCATCCC	0.632											OREG0021618	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R505R		Atlas-SNP	.											.	VWF	338	.	0			c.C1515T						PASS	.	G		0,4406		0,0,2203	49	40	43		1515	-10.4	0.2	12		43	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	VWF	NM_000552.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		505/2814	6172138	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	7450	exon13			CCTCCCGCGGCCA		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.1515C>T	12.37:g.6172138G>A		48	0	0	632	31	18	0.580645	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																			.	.	weak		0.632	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		A	6172138	G	A	6172138	2	1	24	1	0	0	0	0	0	0	0	1	17261	1074	38	1		1	VWF	12	6172138	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	3124773	6172138	127679757	382	8599											
FAM90A1	55138	hgsc.bcm.edu	37	chr12	8377348	8377348	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggggagcccttggcccaacTggggccctccgctgcttctg	3	8	15	15	1	1	0	0	0	1	0	2	1	2	1	4	5	3	2	4	5	1	2	rs199649765		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:8377348T>C	ENST00000538603.1	-	4	639	c.81A>G	c.(79-81)ccA>ccG	p.P27P	FAM90A1_ENST00000307435.6_Silent_p.P27P	NM_018088.3	NP_060558.3	Q86YD7	F90A1_HUMAN	family with sequence similarity 90, member A1	27							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)		TTGGCCCAACTGGGGCCCTCC	0.642																																					p.P27P		Atlas-SNP	.											FAM90A1,NS,neuroblastoma,0,1	FAM90A1	68	1	0			c.A81G						scavenged	.						12	16	15					12																	8377348		2192	4271	6463	SO:0001819	synonymous_variant	55138	exon4			CCCAACTGGGGCC	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.81A>G	12.37:g.8377348T>C		12	0	0		41	13	0.317073	NM_018088	D3DUU9|Q9NVZ6	Silent	SNP	ENST00000538603.1	37	CCDS31738.1																																																																																			.	.	weak		0.642	FAM90A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400468.1	NM_018088		C	8377348	T	C	8377348	2	2	24	1	0	0	0	0	0	0	0	1	5658	1567	55	3		3	FAM90A1	12	8377348	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	2205210	8377348	125474547	383	8600											
FAM90A1	55138	hgsc.bcm.edu	37	chr12	8377415	8377415	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgccccaggtttggggtcaCgacgtgccatcatcttcgtc	5	12	11	13	3	3	0	2	0	1	0	5	1	3	0	3	3	2	1	3	3	0	3	rs200454993		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:8377415C>T	ENST00000538603.1	-	4	572	c.14G>A	c.(13-15)cGt>cAt	p.R5H	FAM90A1_ENST00000307435.6_Missense_Mutation_p.R5H	NM_018088.3	NP_060558.3	Q86YD7	F90A1_HUMAN	family with sequence similarity 90, member A1	5							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.R5H(1)		endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	25				Kidney(36;0.0866)		TTTGGGGTCACGACGTGCCAT	0.577													.|||	28	0.00559105	0.0045	0.0072	5008	,	,		14884	0.005		0.008	False		,,,				2504	0.0041				p.R5H		Atlas-SNP	.											FAM90A1,NS,carcinoma,0,2	FAM90A1	68	2	1	Substitution - Missense(1)	stomach(1)	c.G14A						scavenged	.						47	53	51					12																	8377415		2203	4300	6503	SO:0001583	missense	55138	exon4			GGGTCACGACGTG	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.14G>A	12.37:g.8377415C>T	ENSP00000445418:p.Arg5His	20	0	0		41	7	0.170732	NM_018088	D3DUU9|Q9NVZ6	Missense_Mutation	SNP	ENST00000538603.1	37	CCDS31738.1	.	.	.	.	.	.	.	.	.	.	.	5.040	0.193071	0.09599	.	.	ENSG00000171847	ENST00000307435;ENST00000538603;ENST00000442295	T;T	0.14022	2.54;2.54	0.408	-0.719	0.11201	.	.	.	.	.	T	0.05593	0.0147	N	0.11427	0.14	0.09310	N	1	B	0.15719	0.014	B	0.14023	0.01	T	0.44065	-0.9352	8	0.17832	T	0.49	1.8103	.	.	.	.	5	Q86YD7	F90A1_HUMAN	H	5	ENSP00000307798:R5H;ENSP00000445418:R5H	ENSP00000307798:R5H	R	-	2	0	FAM90A1	8268682	0.006000	0.16342	0.000000	0.03702	0.014000	0.08584	0.250000	0.18235	-0.410000	0.07542	0.196000	0.17591	CGT	.	.	weak		0.577	FAM90A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400468.1	NM_018088		T	8377415	C	T	8377415	3	4	24	1	0	0	0	0	1	0	0	0	5658	536	19	1	1396	1	FAM90A1	12	8377415	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	67	8377415	125474480	384	8601											
ATF7IP	55729	hgsc.bcm.edu	37	chr12	14577524	14577524	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccatttctggtgattgtgcCgctgatgatatagcctctag	7	14	10	10	1	2	3	0	3	2	0	2	3	2	3	3	1	2	1	3	1	3	5	rs146972131		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:14577524C>T	ENST00000540793.1	+	1	830	c.675C>T	c.(673-675)gcC>gcT	p.A225A	ATF7IP_ENST00000261168.4_Silent_p.A225A|ATF7IP_ENST00000536444.1_Silent_p.A225A|ATF7IP_ENST00000544627.1_Silent_p.A233A|ATF7IP_ENST00000543189.1_Silent_p.A225A|ATF7IP_ENST00000541654.1_3'UTR			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	225					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						GTGATTGTGCCGCTGATGATA	0.517																																					p.A225A		Atlas-SNP	.											.	ATF7IP	136	.	0			c.C675T						PASS	.	C		0,4406		0,0,2203	127	115	119		675	-0.9	0	12	dbSNP_134	119	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ATF7IP	NM_018179.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		225/1271	14577524	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	55729	exon2			TTGTGCCGCTGAT	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.675C>T	12.37:g.14577524C>T		270	1	0.0037037		280	135	0.482143	NM_018179	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Silent	SNP	ENST00000540793.1	37	CCDS8663.1																																																																																			C|1.000;T|0.000	0.000	weak		0.517	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179		T	14577524	C	T	14577524	2	4	24	1	0	0	0	0	0	0	0	1	1087	639	23	1		1	ATF7IP	12	14577524	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	6200109	14577524	119274371	385	8602											
C12orf69	440087	hgsc.bcm.edu	37	chr12	14959006	14959006	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttatatttttctgaggctgaTttgaactccaccagatgctt	9	17	7	8	0	1	4	0	3	1	1	2	4	2	4	2	1	2	2	2	1	3	6			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:14959006T>G	ENST00000316048.2	-	2	681	c.609A>C	c.(607-609)aaA>aaC	p.K203N	C12orf60_ENST00000330828.2_Intron|WBP11_ENST00000261167.2_5'Flank|C12orf60_ENST00000527783.1_Intron	NM_001013698.2	NP_001013720.2	A2RU48	SMCO3_HUMAN	single-pass membrane protein with coiled-coil domains 3	203						integral component of membrane (GO:0016021)											CTGAGGCTGATTTGAACTCCA	0.403																																					p.K203N		Atlas-SNP	.											.	.	.	.	0			c.A609C						PASS	.						135	132	133					12																	14959006		1900	4122	6022	SO:0001583	missense	0	exon2			GGCTGATTTGAAC		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.609A>C	12.37:g.14959006T>G	ENSP00000381895:p.Lys203Asn	237	0	0		243	104	0.427984	NM_001013698	Q8NAI5	Missense_Mutation	SNP	ENST00000316048.2	37	CCDS41759.1	.	.	.	.	.	.	.	.	.	.	T	14.83	2.652321	0.47362	.	.	ENSG00000179256	ENST00000316048	T	0.16743	2.32	4.38	-0.586	0.11694	.	0.000000	0.41712	U	0.000829	T	0.10465	0.0256	L	0.27053	0.805	0.25005	N	0.991445	B	0.23185	0.081	B	0.25884	0.064	T	0.21042	-1.0257	10	0.72032	D	0.01	-3.6815	7.1498	0.25604	0.0:0.4745:0.0:0.5255	.	203	A2RU48	CL069_HUMAN	N	203	ENSP00000381895:K203N	ENSP00000381895:K203N	K	-	3	2	C12orf69	14850273	0.960000	0.32886	0.981000	0.43875	0.772000	0.43724	0.877000	0.28106	-0.010000	0.14271	-1.017000	0.02453	AAA	.	.	none		0.403	SMCO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394738.1	NM_001013698		G	14959006	T	G	14959006	3	3	24	1	0	0	0	0	1	0	0	0	1713	1490	52	5	72	5	C12orf69	12	14959006	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	381482	14959006	118892889	386	8603											
ERP27	121506	hgsc.bcm.edu	37	chr12	15068620	15068620	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccaccagaataaagagaaTctgcagttggggaagtttga	14	9	12	6	0	1	3	0	1	1	2	2	5	2	4	2	2	1	3	2	2	5	3			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:15068620T>A	ENST00000266397.2	-	6	1150	c.577A>T	c.(577-579)Att>Ttt	p.I193F	ERP27_ENST00000544881.1_5'UTR|ERP27_ENST00000540097.1_Splice_Site_p.I92F	NM_152321.2	NP_689534.1	Q96DN0	ERP27_HUMAN	endoplasmic reticulum protein 27	193						endoplasmic reticulum (GO:0005783)				breast(2)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(3)|prostate(2)|skin(1)	19						ATAAAGAGAATCTGCAGTTGG	0.388																																					p.I193F		Atlas-SNP	.											.	ERP27	37	.	0			c.A577T						PASS	.						52	52	52					12																	15068620		2203	4300	6503	SO:0001630	splice_region_variant	121506	exon6			AGAGAATCTGCAG	AK056677	CCDS8670.1, CCDS73450.1	12p12.3	2011-10-19	2009-02-23	2007-03-26	ENSG00000139055	ENSG00000139055		"Protein disulfide isomerases"	26495	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 8"	610642	"chromosome 12 open reading frame 46", "endoplasmic reticulum protein 27 kDa"	C12orf46		12975309, 16940051	Standard	XM_005253303		Approved	FLJ32115, ERp27, PDIA8	uc001rco.3	Q96DN0	OTTHUMG00000168741	ENST00000266397.2:c.577-1A>T	12.37:g.15068620T>A		110	0	0		95	45	0.473684	NM_152321		Missense_Mutation	SNP	ENST00000266397.2	37	CCDS8670.1	.	.	.	.	.	.	.	.	.	.	T	11.57	1.679429	0.29783	.	.	ENSG00000139055	ENST00000266397;ENST00000540097	T;T	0.33654	1.4;1.4	4.79	1.17	0.20885	Thioredoxin-like fold (1);	0.393229	0.28109	N	0.016563	T	0.26268	0.0641	L	0.46741	1.465	0.42936	D	0.99433	B	0.22983	0.078	B	0.18871	0.023	T	0.05402	-1.0887	10	0.41790	T	0.15	-22.2204	6.2103	0.20626	0.0:0.3251:0.0:0.6749	.	193	Q96DN0	ERP27_HUMAN	F	193;92	ENSP00000266397:I193F;ENSP00000440573:I92F	ENSP00000266397:I193F	I	-	1	0	ERP27	14959887	0.999000	0.42202	0.998000	0.56505	0.833000	0.47200	0.155000	0.16362	0.200000	0.20447	-0.290000	0.09829	ATT	.	.	none		0.388	ERP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400868.1	NM_152321	Missense_Mutation	A	15068620	T	A	15068620	5	1	24	1	0	0	0	0	0	0	1	0	5243	1449	50	5	252	5	ERP27	12	15068620	Splice_Site	SNP	T	TCGA-G8-6326-01A-11D-2210-10	109614	15068620	118783275	387	8604											
RERG	85004	hgsc.bcm.edu	37	chr12	15262273	15262273	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtgctaacctgcctggagTggtccaagtcagctttgttt	6	14	11	10	0	1	0	1	0	0	0	2	1	2	1	3	2	4	3	3	2	2	3			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:15262273T>A	ENST00000256953.2	-	5	707	c.371A>T	c.(370-372)cAc>cTc	p.H124L	RERG_ENST00000536465.1_Missense_Mutation_p.H124L|RERG_ENST00000538313.1_Missense_Mutation_p.H124L|RERG_ENST00000546331.1_Missense_Mutation_p.H105L	NM_032918.2	NP_116307.1	Q96A58	RERG_HUMAN	RAS-like, estrogen-regulated, growth inhibitor	124					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						CTGCCTGGAGTGGTCCAAGTC	0.473																																					p.H124L		Atlas-SNP	.											.	RERG	30	.	0			c.A371T						PASS	.						236	211	219					12																	15262273		2203	4300	6503	SO:0001583	missense	85004	exon5			CTGGAGTGGTCCA	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.371A>T	12.37:g.15262273T>A	ENSP00000256953:p.His124Leu	236	0	0		219	99	0.452055	NM_032918	B2R9R0|B4DI02	Missense_Mutation	SNP	ENST00000256953.2	37	CCDS8673.1	.	.	.	.	.	.	.	.	.	.	T	19.26	3.792870	0.70452	.	.	ENSG00000134533	ENST00000256953;ENST00000538313;ENST00000536465;ENST00000546331	T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32	5.33	5.33	0.75918	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.74898	0.3777	L	0.45744	1.44	0.80722	D	1	B;B	0.26400	0.148;0.012	B;B	0.20577	0.03;0.018	T	0.72679	-0.4220	10	0.44086	T	0.13	.	14.4198	0.67175	0.0:0.0:0.0:1.0	.	105;124	B4DI02;Q96A58	.;RERG_HUMAN	L	124;124;124;105	ENSP00000256953:H124L;ENSP00000441505:H124L;ENSP00000438280:H124L;ENSP00000444485:H105L	ENSP00000256953:H124L	H	-	2	0	RERG	15153540	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.992000	0.88273	2.145000	0.66743	0.533000	0.62120	CAC	.	.	none		0.473	RERG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400882.1	NM_032918		A	15262273	T	A	15262273	3	1	24	1	0	0	0	0	1	0	0	0	13247	1696	59	5	232	5	RERG	12	15262273	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	193653	15262273	118589622	388	8605											
PIK3C2G	5288	hgsc.bcm.edu	37	chr12	18719972	18719972	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catggaacagatattaaatgTatcacatgaagttacaaacg	18	10	7	6	1	1	2	1	1	0	1	1	3	1	3	0	1	3	2	0	1	8	4	rs12099555	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:18719972T>G	ENST00000266497.5	+	27	3907	c.3869T>G	c.(3868-3870)gTa>gGa	p.V1290G	PIK3C2G_ENST00000433979.1_Missense_Mutation_p.V1290G|PIK3C2G_ENST00000538779.1_Missense_Mutation_p.V1331G			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	1290	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.		V -> G (in dbSNP:rs12099555).		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)				ATATTAAATGTATCACATGAA	0.289													G|||	438	0.0874601	0.2943	0.036	5008	,	,		16621	0.0		0.0229	False		,,,				2504	0.001				p.V1290G		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.T3869G						PASS	.	G	GLY/VAL	924,2712		118,688,1012	76	74	75		3869	4.2	0.7	12	dbSNP_120	75	143,7987		4,135,3926	yes	missense	PIK3C2G	NM_004570.4	109	122,823,4938	GG,GT,TT		1.7589,25.4125,9.0685	benign	1290/1446	18719972	1067,10699	1818	4065	5883	SO:0001583	missense	5288	exon28			TAAATGTATCACA	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.3869T>G	12.37:g.18719972T>G	ENSP00000266497:p.Val1290Gly	124	0	0		117	55	0.470085	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	37	CCDS44839.1	164	0.07509157509157509	135	0.27439024390243905	12	0.03314917127071823	0	0.0	17	0.022427440633245383	G	0.026	-1.369431	0.01225	0.254125	0.017589	ENSG00000139144	ENST00000433979;ENST00000266497;ENST00000538779	T;T;T	0.39056	1.1;1.1;1.1	4.18	4.18	0.49190	Phox homologous domain (5);	0.274240	0.29424	N	0.012196	T	0.00012	0.0000	N	0.01048	-1.04	0.32557	P	0.531612	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.25257	-1.0137	9	0.10111	T	0.7	-12.3348	11.8575	0.52446	0.0:0.0:0.8243:0.1756	rs12099555;rs60425948;rs12099555	1330;1331;1290	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	G	1290;1290;1331	ENSP00000404845:V1290G;ENSP00000266497:V1290G;ENSP00000445381:V1331G	ENSP00000266497:V1290G	V	+	2	0	PIK3C2G	18611239	1.000000	0.71417	0.661000	0.29709	0.096000	0.18686	2.898000	0.48672	1.370000	0.46153	-0.121000	0.15023	GTA	T|0.912;G|0.088	0.088	strong		0.289	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570		G	18719972	T	G	18719972	3	3	24	1	0	0	0	0	1	0	0	0	11920	1638	57	5	3975	5	PIK3C2G	12	18719972	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	3457699	18719972	115131923	389	8606											
LST-3TM12	338821	hgsc.bcm.edu	37	chr12	21174496	21174496	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gttatcactcaatagaacacCgtctgagataatagaaagag	17	9	8	7	1	3	4	2	1	1	4	3	5	3	4	1	0	1	1	1	0	7	4	rs12824121	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:21174496C>T	ENST00000421593.2	+	3	320	c.320C>T	c.(319-321)cCg>cTg	p.P107L	SLCO1B7_ENST00000554957.1_Missense_Mutation_p.P154L|LST3_ENST00000381541.3_Missense_Mutation_p.P154L|LST3_ENST00000540229.1_Intron|SLCO1B3_ENST00000553473.1_Intron	NM_001009562.4	NP_001009562.3	G3V0H7	SO1B7_HUMAN	solute carrier organic anion transporter family, member 1B7 (non-functional)	107						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						AATAGAACACCGTCTGAGATA	0.254													C|||	21	0.00419329	0.0008	0.0029	5008	,	,		15614	0.0		0.0179	False		,,,				2504	0.0				p.P107L		Atlas-SNP	.											.	SLCO1B7	85	.	0			c.C320T						PASS	.	C	LEU/PRO	14,3786		0,14,1886	38	34	35		320	2.8	0	12	dbSNP_121	35	139,8183		1,137,4023	yes	missense	SLCO1B7	NM_001009562.4	98	1,151,5909	TT,TC,CC		1.6703,0.3684,1.2622		107/641	21174496	153,11969	1900	4161	6061	SO:0001583	missense	338821	exon3			GAACACCGTCTGA	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	ENST00000421593.2:c.320C>T	12.37:g.21174496C>T	ENSP00000394168:p.Pro107Leu	119	0	0		105	46	0.438095	NM_001009562	Q71QF0	Missense_Mutation	SNP	ENST00000421593.2	37	CCDS44843.1	19	0.0086996336996337	0	0.0	1	0.0027624309392265192	0	0.0	18	0.023746701846965697	.	7.606	0.673791	0.14841	0.003684	0.016703	ENSG00000257046;ENSG00000205754;ENSG00000205754	ENST00000381541;ENST00000554957;ENST00000421593	T;T;T	0.37915	1.17;1.17;1.17	2.79	2.79	0.32731	.	1.095650	0.07077	U	0.836307	T	0.17152	0.0412	L	0.39147	1.195	0.09310	N	1	B;B	0.10296	0.002;0.003	B;B	0.13407	0.007;0.009	T	0.12941	-1.0528	10	0.37606	T	0.19	.	9.1237	0.36801	0.0:1.0:0.0:0.0	rs12824121;rs52800356;rs12824121	107;154	G3V0H7;F5H094	.;.	L	154;154;107	ENSP00000370952:P154L;ENSP00000452013:P154L;ENSP00000394168:P107L	ENSP00000370952:P154L	P	+	2	0	SLCO1B7;RP11-545J16.1	21065763	0.003000	0.15002	0.005000	0.12908	0.124000	0.20399	1.055000	0.30467	1.531000	0.49152	0.205000	0.17691	CCG	C|0.990;T|0.010	0.010	strong		0.254	SLCO1B7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402066.1	NM_001009562		T	21174496	C	T	21174496	3	4	24	1	0	0	0	0	1	0	0	0	9075	652	23	1	330	1	LST-3TM12	12	21174496	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	2454524	21174496	112677399	390	8607											
SLCO1B1	10599	hgsc.bcm.edu	37	chr12	21377717	21377717	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acaacgtgtataaagtggtcCaccaacaactgtggcacacg	14	7	9	11	2	0	0	0	0	0	0	1	0	1	0	2	2	3	2	2	2	6	2	rs143812591		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:21377717C>G	ENST00000256958.2	+	14	1905	c.1809C>G	c.(1807-1809)tcC>tcG	p.S603S		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	603					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)	TAAAGTGGTCCACCAACAACT	0.358																																					p.S603S		Atlas-SNP	.											.	SLCO1B1	151	.	0			c.C1809G						PASS	.	C		0,4406		0,0,2203	148	143	145		1809	-3.8	0	12	dbSNP_134	145	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SLCO1B1	NM_006446.4		0,2,6501	GG,GC,CC		0.0233,0.0,0.0154		603/692	21377717	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	10599	exon14			GTGGTCCACCAAC		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.1809C>G	12.37:g.21377717C>G		82	0	0		83	42	0.506024	NM_006446	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Silent	SNP	ENST00000256958.2	37	CCDS8685.1																																																																																			C|1.000;G|0.000	0.000	weak		0.358	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446		G	21377717	C	G	21377717	2	3	24	1	0	0	0	0	0	0	0	1	14738	581	21	4		4	SLCO1B1	12	21377717	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	203221	21377717	112474178	391	8608											
C12orf35	55196	hgsc.bcm.edu	37	chr12	32137901	32137901	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacgtccactaaaaacaaaaAcagcttttttgccaaataaa	19	9	3	10	1	0	0	0	0	0	0	1	0	1	0	2	0	4	1	2	0	8	5	rs3759296	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:32137901A>C	ENST00000312561.4	+	4	4426	c.4012A>C	c.(4012-4014)Aca>Cca	p.T1338P	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	1338			T -> A (in dbSNP:rs3759296).					p.T1338A(1)									AAAAACAAAAACAGCTTTTTT	0.348																																					p.T1338P		Atlas-SNP	.											C12orf35,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	stomach(1)	c.A4012C						PASS	.						86	90	88					12																	32137901		2203	4300	6503	SO:0001583	missense	55196	exon4			ACAAAAACAGCTT	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.4012A>C	12.37:g.32137901A>C	ENSP00000310338:p.Thr1338Pro	129	0	0		150	74	0.493333	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	37	CCDS8725.2	.	.	.	.	.	.	.	.	.	.	A	10.15	1.271497	0.23221	.	.	ENSG00000174718	ENST00000312561	T	0.12465	2.68	5.3	-8.75	0.00834	.	2.186560	0.01601	N	0.022031	T	0.06280	0.0162	N	0.14661	0.345	0.80722	P	0.0	B	0.24882	0.113	B	0.23275	0.045	T	0.21690	-1.0238	8	.	.	.	.	5.0984	0.14747	0.216:0.2115:0.4686:0.1039	.	1338	Q9HCM1	CL035_HUMAN	P	1338	ENSP00000310338:T1338P	.	T	+	1	0	C12orf35	32029168	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.164000	0.01275	-1.463000	0.01904	0.460000	0.39030	ACA	A|0.986;G|0.014	.	alt		0.348	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169		C	32137901	A	C	32137901	3	2	24	1	0	0	0	0	1	0	0	0	1684	43	2	5	4014	5	C12orf35	12	32137901	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	10760184	32137901	101713994	392	8609											
CPNE8	144402	hgsc.bcm.edu	37	chr12	39299249	39299249	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgtcctcacctgcaggacaCggacacctccacccgcgtgg	7	5	11	18	4	1	0	1	0	0	0	3	2	3	2	5	3	1	1	5	3	0	0			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:39299249C>T	ENST00000331366.5	-	1	184	c.88G>A	c.(88-90)Gtg>Atg	p.V30M	RP11-396F22.1_ENST00000551152.1_RNA|CPNE8_ENST00000360449.3_Intron	NM_153634.2	NP_705898.1	Q86YQ8	CPNE8_HUMAN	copine VIII	30	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.					extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(1)|large_intestine(6)|lung(6)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	21	Esophageal squamous(101;0.187)	Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157)				CTGCAGGACACGGACACCTCC	0.647																																					p.V30M		Atlas-SNP	.											.	CPNE8	66	.	0			c.G88A						PASS	.						62	50	54					12																	39299249		2195	4284	6479	SO:0001583	missense	144402	exon1			AGGACACGGACAC	AY177785	CCDS8733.1	12q12	2008-02-05				ENSG00000139117			23498	protein-coding gene	gene with protein product						12670487	Standard	NM_153634		Approved		uc001rls.1	Q86YQ8	OTTHUMG00000169396	ENST00000331366.5:c.88G>A	12.37:g.39299249C>T	ENSP00000329748:p.Val30Met	66	0	0		63	27	0.428571	NM_153634	Q2TB41|Q86VY2	Missense_Mutation	SNP	ENST00000331366.5	37	CCDS8733.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.377756	0.82682	.	.	ENSG00000139117	ENST00000331366	T	0.55234	0.53	4.53	4.53	0.55603	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.102804	0.38959	N	0.001514	T	0.67126	0.2860	M	0.76938	2.355	0.80722	D	1	P	0.50710	0.938	P	0.54856	0.762	T	0.72798	-0.4184	10	0.72032	D	0.01	-11.5212	15.0267	0.71674	0.0:1.0:0.0:0.0	.	30	Q86YQ8	CPNE8_HUMAN	M	30	ENSP00000329748:V30M	ENSP00000329748:V30M	V	-	1	0	CPNE8	37585516	0.990000	0.36364	0.966000	0.40874	0.994000	0.84299	3.827000	0.55745	2.448000	0.82819	0.563000	0.77884	GTG	.	.	none		0.647	CPNE8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403856.1	NM_153634		T	39299249	C	T	39299249	3	4	24	1	0	0	0	0	1	0	0	0	3820	536	19	1	1686	1	CPNE8	12	39299249	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	7161348	39299249	94552646	393	8610											
SFRS2IP	9169	hgsc.bcm.edu	37	chr12	46321158	46321158	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atctatggtatcttttgggcTttcagatggttgagaaacag	10	15	11	5	0	3	2	1	1	2	2	3	3	3	2	0	3	1	3	0	3	3	6			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:46321158T>G	ENST00000369367.3	-	11	2559	c.2326A>C	c.(2326-2328)Agc>Cgc	p.S776R	SCAF11_ENST00000550629.1_5'Flank|SCAF11_ENST00000465950.1_Missense_Mutation_p.S461R|SCAF11_ENST00000419565.2_Missense_Mutation_p.S776R|SCAF11_ENST00000549162.1_Missense_Mutation_p.S584R	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	776					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)	p.S776G(1)		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						TCTTTTGGGCTTTCAGATGGT	0.383																																					p.S776R		Atlas-SNP	.											SCAF11,NS,carcinoma,0,1	SCAF11	145	1	1	Substitution - Missense(1)	kidney(1)	c.A2326C						PASS	.						177	174	175					12																	46321158		2203	4300	6503	SO:0001583	missense	9169	exon11			TTGGGCTTTCAGA	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.2326A>C	12.37:g.46321158T>G	ENSP00000358374:p.Ser776Arg	117	0	0		125	64	0.512	NM_004719	A6NEU9|A6NLW5|Q8IW59	Missense_Mutation	SNP	ENST00000369367.3	37	CCDS8748.2	.	.	.	.	.	.	.	.	.	.	T	9.433	1.085940	0.20390	.	.	ENSG00000139218	ENST00000465950;ENST00000369367;ENST00000549162;ENST00000419565;ENST00000547018	T;T;T;T;T	0.49139	1.45;2.18;1.45;2.18;0.79	5.93	2.17	0.27698	.	0.432900	0.26146	N	0.026061	T	0.35653	0.0939	L	0.59436	1.845	0.09310	N	1	P;P	0.45078	0.85;0.498	B;B	0.37304	0.246;0.125	T	0.21415	-1.0246	10	0.34782	T	0.22	0.8665	5.4177	0.16384	0.1281:0.1381:0.0:0.7337	.	584;776	F8VXG7;Q99590	.;SCAFB_HUMAN	R	461;776;584;776;716	ENSP00000449812:S461R;ENSP00000358374:S776R;ENSP00000448864:S584R;ENSP00000413036:S776R;ENSP00000446746:S716R	ENSP00000358374:S776R	S	-	1	0	SCAF11	44607425	0.169000	0.23002	0.127000	0.21898	0.023000	0.10783	0.397000	0.20883	0.121000	0.18284	0.533000	0.62120	AGC	.	.	none		0.383	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719		G	46321158	T	G	46321158	3	3	24	1	0	0	0	0	1	0	0	0	14192	1609	56	5	2085	5	SFRS2IP	12	46321158	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	7021909	46321158	87530737	394	8611											
METTL7A	25840	hgsc.bcm.edu	37	chr12	51319238	51319238	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggctgatggctctgtggaTgtggtggtctgcaccctggt	3	13	17	8	0	2	1	0	1	2	0	2	2	2	2	1	6	1	3	1	6	0	0			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:51319238T>C	ENST00000548553.1	+	2	1398	c.417T>C	c.(415-417)gaT>gaC	p.D139D	METTL7A_ENST00000332160.4_Silent_p.D139D			Q9H8H3	MET7A_HUMAN	methyltransferase like 7A	139						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lipid particle (GO:0005811)|membrane (GO:0016020)	methyltransferase activity (GO:0008168)			endometrium(1)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)	10						GCTCTGTGGATGTGGTGGTCT	0.567																																					p.D139D		Atlas-SNP	.											.	METTL7A	19	.	0			c.T417C						PASS	.						74	65	68					12																	51319238		2203	4300	6503	SO:0001819	synonymous_variant	25840	exon1			TGTGGATGTGGTG		CCDS8804.1	12q13.12	2013-06-20			ENSG00000185432	ENSG00000185432			24550	protein-coding gene	gene with protein product						12975309	Standard	XM_006719332		Approved	DKFZP586A0522	uc001rxb.3	Q9H8H3	OTTHUMG00000169484	ENST00000548553.1:c.417T>C	12.37:g.51319238T>C		103	0	0		96	50	0.520833	NM_014033	Q9H7R3|Q9UHZ7|Q9Y422	Silent	SNP	ENST00000548553.1	37	CCDS8804.1																																																																																			.	.	none		0.567	METTL7A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404294.2	NM_014033		C	51319238	T	C	51319238	2	2	24	1	0	0	0	0	0	0	0	1	9514	1461	51	3		3	METTL7A	12	51319238	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	4998080	51319238	82532657	395	8612											
SCN8A	6334	hgsc.bcm.edu	37	chr12	52162823	52162823	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgcaggcccactttaagcagCgtgaggctgatgaggtgaag	10	8	15	8	1	0	4	0	4	0	0	0	4	0	4	1	3	3	3	1	3	2	2	rs117217073	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:52162823C>T	ENST00000354534.6	+	17	3254	c.3076C>T	c.(3076-3078)Cgt>Tgt	p.R1026C	SCN8A_ENST00000545061.1_Missense_Mutation_p.R1026C	NM_001177984.2|NM_014191.3	NP_001171455.1|NP_055006.1	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha subunit	1026					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)	CTTTAAGCAGCGTGAGGCTGA	0.512													C|||	24	0.00479233	0.0	0.0086	5008	,	,		22384	0.0		0.0169	False		,,,				2504	0.001				p.R1026C		Atlas-SNP	.											.	SCN8A	331	.	0			c.C3076T						PASS	.	C	CYS/ARG,CYS/ARG	8,4130		0,8,2061	73	75	74		3076,3076	4.6	1	12	dbSNP_132	74	131,8311		0,131,4090	yes	missense,missense	SCN8A	NM_001177984.1,NM_014191.2	180,180	0,139,6151	TT,TC,CC		1.5518,0.1933,1.1049	probably-damaging,probably-damaging	1026/1940,1026/1981	52162823	139,12441	2069	4221	6290	SO:0001583	missense	6334	exon17			AAGCAGCGTGAGG	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.3076C>T	12.37:g.52162823C>T	ENSP00000346534:p.Arg1026Cys	91	0	0		110	45	0.409091	NM_014191	B9VWG8|O95788|Q9NYX2|Q9UPB2	Missense_Mutation	SNP	ENST00000354534.6	37	CCDS44891.1	16	0.007326007326007326	0	0.0	2	0.0055248618784530384	0	0.0	14	0.018469656992084433	C	16.02	3.004177	0.54254	0.001933	0.015518	ENSG00000196876	ENST00000354534;ENST00000545061;ENST00000355133;ENST00000357961	D;D;D	0.84298	-1.83;-1.83;-1.83	4.55	4.55	0.56014	Sodium ion transport-associated (1);	0.110372	0.64402	D	0.000020	T	0.80944	0.4721	L	0.49778	1.585	0.48040	D	0.999573	D;D	0.89917	1.0;0.997	D;P	0.65987	0.94;0.849	D	0.84692	0.0723	10	0.87932	D	0	.	10.947	0.47306	0.3118:0.6882:0.0:0.0	.	1026;1026	F8VWM7;Q9UQD0	.;SCN8A_HUMAN	C	1026;1026;1026;939	ENSP00000346534:R1026C;ENSP00000440360:R1026C;ENSP00000347255:R1026C	ENSP00000346534:R1026C	R	+	1	0	SCN8A	50449090	0.999000	0.42202	1.000000	0.80357	0.704000	0.40688	1.398000	0.34554	2.816000	0.96949	0.563000	0.77884	CGT	C|0.991;T|0.009	0.009	strong		0.512	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404372.3	NM_014191		T	52162823	C	T	52162823	3	4	24	1	0	0	0	0	1	0	0	0	13939	768	27	1	3138	1	SCN8A	12	52162823	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	843585	52162823	81689072	396	8613											
KRT82	3888	hgsc.bcm.edu	37	chr12	52788814	52788814	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctagcgtcatgctggatttcCgcccgctcccacagctcagt	6	10	9	16	3	2	0	2	0	0	0	4	1	4	1	3	1	3	3	3	1	1	2	rs61730587	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:52788814C>T	ENST00000257974.2	-	9	1564	c.1487G>A	c.(1486-1488)cGg>cAg	p.R496Q	RP3-416H24.4_ENST00000547174.1_RNA	NM_033033.3	NP_149022.3	Q9NSB4	KRT82_HUMAN	keratin 82	496	Tail.					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)		GCTGGATTTCCGCCCGCTCCC	0.642													c|||	21	0.00419329	0.0023	0.0072	5008	,	,		16513	0.0		0.0089	False		,,,				2504	0.0041				p.R496Q		Atlas-SNP	.											KRT82,NS,carcinoma,-1,1	KRT82	45	1	0			c.G1487A						scavenged	.	T	GLN/ARG	14,4392	21.2+/-45.6	0,14,2189	48	48	48		1487	-0.4	0	12	dbSNP_129	48	113,8487	58.7+/-120.3	1,111,4188	yes	missense	KRT82	NM_033033.3	43	1,125,6377	TT,TC,CC		1.314,0.3177,0.9765	benign	496/514	52788814	127,12879	2203	4300	6503	SO:0001583	missense	3888	exon9			GATTTCCGCCCGC	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.1487G>A	12.37:g.52788814C>T	ENSP00000257974:p.Arg496Gln	138	1	0.00724638		125	65	0.52	NM_033033		Missense_Mutation	SNP	ENST00000257974.2	37	CCDS8826.1	11	0.005036630036630037	0	0.0	4	0.011049723756906077	0	0.0	7	0.009234828496042216	c	11.54	1.670563	0.29693	0.003177	0.01314	ENSG00000161850	ENST00000257974	D	0.82255	-1.59	4.59	-0.424	0.12321	.	0.753921	0.10873	N	0.624709	T	0.52933	0.1765	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.04013	0.001	T	0.39800	-0.9596	10	0.25106	T	0.35	.	4.4613	0.11668	0.1481:0.4148:0.0:0.4371	rs61730587	496	Q9NSB4	KRT82_HUMAN	Q	496	ENSP00000257974:R496Q	ENSP00000257974:R496Q	R	-	2	0	KRT82	51075081	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.155000	0.16362	-0.326000	0.08564	-0.215000	0.12644	CGG	C|0.991;T|0.009	0.009	strong		0.642	KRT82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405189.1	NM_033033		T	52788814	C	T	52788814	3	4	24	1	0	0	0	0	1	0	0	0	8505	652	23	1	58	1	KRT82	12	52788814	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	625991	52788814	81063081	397	8614											
KRT72	140807	hgsc.bcm.edu	37	chr12	52992743	52992743	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccgaatccagcctcacccCgtccccagacagcatctcca	9	6	5	21	2	2	1	1	0	1	1	6	2	5	1	8	0	2	1	8	0	1	0	rs142970524	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:52992743C>T	ENST00000537672.2	-	2	590	c.580G>A	c.(580-582)Ggg>Agg	p.G194R	KRT72_ENST00000398066.3_Missense_Mutation_p.G6R|KRT72_ENST00000354310.4_Missense_Mutation_p.G194R|KRT72_ENST00000293745.2_Missense_Mutation_p.G194R|RP11-641A6.2_ENST00000551089.1_RNA	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	194	Coil 1B.|Rod.					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)		AGCCTCACCCCGTCCCCAGAC	0.547																																					p.G194R		Atlas-SNP	.											.	KRT72	70	.	0			c.G580A						PASS	.	T	ARG/GLY,ARG/GLY,ARG/GLY	0,4406		0,0,2203	194	177	183		580,580,580	-4.3	1	12	dbSNP_134	183	10,8590	818.8+/-406.8	0,10,4290	yes	missense,missense,missense	KRT72	NM_001146225.1,NM_001146226.1,NM_080747.2	125,125,125	0,10,6493	TT,TC,CC		0.1163,0.0,0.0769	benign,benign,benign	194/512,194/470,194/512	52992743	10,12996	2203	4300	6503	SO:0001583	missense	140807	exon2			TCACCCCGTCCCC	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.580G>A	12.37:g.52992743C>T	ENSP00000441160:p.Gly194Arg	193	0	0		215	110	0.511628	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Missense_Mutation	SNP	ENST00000537672.2	37	CCDS8833.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	3.962|3.962	-0.010160|-0.010160	0.07727|0.07727	0.0|0.0	0.001163|0.001163	ENSG00000170486|ENSG00000170486	ENST00000537672;ENST00000293745;ENST00000354310;ENST00000398066|ENST00000549979	D;D;D;D|.	0.86432|.	-2.12;-2.12;-2.12;-2.12|.	5.25|5.25	-4.29|-4.29	0.03721|0.03721	Filament (1);|.	0.000000|.	0.47852|.	N|.	0.000214|.	T|T	0.08846|0.08846	0.0219|0.0219	N|N	0.00191|0.00191	-1.88|-1.88	0.19575|0.19575	N|N	0.999963|0.999963	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.04013|.	0.0;0.001|.	T|T	0.42396|0.42396	-0.9454|-0.9454	10|5	0.02654|.	T|.	1|.	.|.	16.5611|16.5611	0.84566|0.84566	0.0:0.0582:0.6555:0.2862|0.0:0.0582:0.6555:0.2862	.|.	194;194|.	B4DEI8;Q14CN4|.	.;K2C72_HUMAN|.	R|Q	194;194;194;6|190	ENSP00000441160:G194R;ENSP00000293745:G194R;ENSP00000346269:G194R;ENSP00000446151:G6R|.	ENSP00000293745:G194R|.	G|R	-|-	1|2	0|0	KRT72|KRT72	51279010|51279010	0.000000|0.000000	0.05858|0.05858	0.951000|0.951000	0.38953|0.38953	0.767000|0.767000	0.43475|0.43475	-0.184000|-0.184000	0.09698|0.09698	-0.750000|-0.750000	0.04740|0.04740	-0.361000|-0.361000	0.07541|0.07541	GGG|CGG	C|0.999;T|0.001	0.001	strong		0.547	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747		T	52992743	C	T	52992743	3	4	24	1	0	0	0	0	1	0	0	0	8494	652	23	1	987	1	KRT72	12	52992743	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	203929	52992743	80859152	398	8615											
SLC39A5	283375	hgsc.bcm.edu	37	chr12	56630444	56630444	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctgggcaccaaggccacaGtcatgggcaccagggtggca	9	5	14	13	0	1	0	1	0	0	0	2	0	2	0	4	5	0	3	4	5	1	0	rs74812296	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:56630444G>C	ENST00000266980.4	+	8	1414	c.1121G>C	c.(1120-1122)aGt>aCt	p.S374T	SLC39A5_ENST00000454355.2_Missense_Mutation_p.S374T|ANKRD52_ENST00000548241.1_5'Flank|SLC39A5_ENST00000419232.1_3'UTR	NM_001135195.1	NP_001128667.1	Q6ZMH5	S39A5_HUMAN	solute carrier family 39 (zinc transporter), member 5	374					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						CAAGGCCACAGTCATGGGCAC	0.627													G|||	34	0.00678914	0.0015	0.0187	5008	,	,		20254	0.0		0.0179	False		,,,				2504	0.001				p.S374T		Atlas-SNP	.											.	SLC39A5	52	.	0			c.G1121C						PASS	.	G	THR/SER,THR/SER	12,4394	16.8+/-37.8	0,12,2191	109	96	101		1121,1121	5	1	12	dbSNP_131	101	168,8432	78.6+/-141.3	1,166,4133	yes	missense,missense	SLC39A5	NM_001135195.1,NM_173596.2	58,58	1,178,6324	CC,CG,GG		1.9535,0.2724,1.384	probably-damaging,probably-damaging	374/541,374/541	56630444	180,12826	2203	4300	6503	SO:0001583	missense	283375	exon10			GCCACAGTCATGG		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.1121G>C	12.37:g.56630444G>C	ENSP00000266980:p.Ser374Thr	79	0	0		93	43	0.462366	NM_173596	B2R808|Q8N6Y3	Missense_Mutation	SNP	ENST00000266980.4	37	CCDS8912.2	22	0.010073260073260074	0	0.0	6	0.016574585635359115	0	0.0	16	0.021108179419525065	G	18.19	3.569542	0.65765	0.002724	0.019535	ENSG00000139540	ENST00000454355;ENST00000266980	T;T	0.51071	0.72;0.72	4.96	4.96	0.65561	.	0.188002	0.37393	N	0.002110	T	0.43122	0.1233	M	0.62088	1.915	0.38031	D	0.935152	D	0.69078	0.997	P	0.62885	0.908	T	0.50575	-0.8812	10	0.21540	T	0.41	-0.8511	12.2396	0.54534	0.0:0.2787:0.7213:0.0	.	374	Q6ZMH5	S39A5_HUMAN	T	374	ENSP00000405360:S374T;ENSP00000266980:S374T	ENSP00000266980:S374T	S	+	2	0	SLC39A5	54916711	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	3.606000	0.54095	2.746000	0.94184	0.655000	0.94253	AGT	G|0.987;C|0.013	0.013	strong		0.627	SLC39A5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346834.1	NM_173596		C	56630444	G	C	56630444	3	2	24	1	0	0	0	0	1	0	0	0	14636	1029	36	4	1147	4	SLC39A5	12	56630444	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	3637701	56630444	77221451	399	8616											
ANKRD52	283373	hgsc.bcm.edu	37	chr12	56638455	56638455	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccacagcagcggtctgcccGttctcagccgccgtcatgag	6	7	11	17	4	3	1	2	1	2	0	4	1	3	1	4	1	4	2	4	1	0	1	rs201117129	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:56638455G>A	ENST00000267116.7	-	24	2824	c.2703C>T	c.(2701-2703)aaC>aaT	p.N901N	ANKRD52_ENST00000548241.1_5'UTR	NM_173595.3	NP_775866.2	Q8NB46	ANR52_HUMAN	ankyrin repeat domain 52	901										endometrium(9)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)|skin(1)	29						CGGTCTGCCCGTTCTCAGCCG	0.647													G|||	3	0.000599042	0.0	0.0	5008	,	,		17818	0.0		0.003	False		,,,				2504	0.0				p.N901N		Atlas-SNP	.											.	ANKRD52	81	.	0			c.C2703T						PASS	.	G		1,4327		0,1,2163	43	47	45		2703	-4.6	0.9	12		45	36,8510		1,34,4238	no	coding-synonymous	ANKRD52	NM_173595.3		1,35,6401	AA,AG,GG		0.4212,0.0231,0.2874		901/1077	56638455	37,12837	2164	4273	6437	SO:0001819	synonymous_variant	283373	exon24			CTGCCCGTTCTCA	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.2703C>T	12.37:g.56638455G>A		189	0	0		180	112	0.622222	NM_173595	A6NE79|B1Q2K2	Silent	SNP	ENST00000267116.7	37	CCDS44920.1																																																																																			G|0.998;A|0.002	0.002	strong		0.647	ANKRD52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408539.1	NM_173595		A	56638455	G	A	56638455	2	1	24	1	0	0	0	0	0	0	0	1	678	1136	40	1		1	ANKRD52	12	56638455	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	8011	56638455	77213440	400	8617											
LRP1	4035	hgsc.bcm.edu	37	chr12	57594552	57594552	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acaaaccctgccttcatctgCgatggcgacaatgactgcca	11	8	8	14	2	2	1	1	1	1	0	2	3	2	1	3	1	4	0	3	1	2	1	rs139916336	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:57594552C>T	ENST00000243077.3	+	64	10645	c.10179C>T	c.(10177-10179)tgC>tgT	p.C3393C		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	3393	LDL-receptor class A 22. {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)	CCTTCATCTGCGATGGCGACA	0.617													C|||	14	0.00279553	0.0	0.0072	5008	,	,		12339	0.0		0.008	False		,,,				2504	0.001				p.C3393C		Atlas-SNP	.											.	LRP1	428	.	0			c.C10179T						PASS	.	C		10,4396	16.8+/-37.8	0,10,2193	91	78	83		10179	0.9	1	12	dbSNP_134	83	73,8527	43.6+/-101.6	0,73,4227	no	coding-synonymous	LRP1	NM_002332.2		0,83,6420	TT,TC,CC		0.8488,0.227,0.6382		3393/4545	57594552	83,12923	2203	4300	6503	SO:0001819	synonymous_variant	4035	exon64			CATCTGCGATGGC	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.10179C>T	12.37:g.57594552C>T		165	0	0		183	90	0.491803	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			C|0.995;T|0.005	0.005	strong		0.617	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		T	57594552	C	T	57594552	2	4	24	1	0	0	0	0	0	0	0	1	8960	776	27	1		1	LRP1	12	57594552	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	956097	57594552	76257343	401	8618											
SHMT2	6472	hgsc.bcm.edu	37	chr12	57624701	57624701	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gacaggccaggagagcctgtCggacagtgatcctgagatgt	10	7	15	9	1	0	3	0	2	0	2	2	7	1	4	3	3	1	0	3	3	0	0	rs73338162	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:57624701C>T	ENST00000328923.3	+	2	601	c.149C>T	c.(148-150)tCg>tTg	p.S50L	SHMT2_ENST00000557487.1_Missense_Mutation_p.S50L|SHMT2_ENST00000393827.4_5'UTR|SHMT2_ENST00000449049.3_Missense_Mutation_p.S29L|SHMT2_ENST00000414700.3_Missense_Mutation_p.S29L|SHMT2_ENST00000554600.1_3'UTR|SHMT2_ENST00000553474.1_Missense_Mutation_p.S29L|Y_RNA_ENST00000365197.1_RNA	NM_001166356.1|NM_005412.5	NP_001159828.1|NP_005403.2	P34897	GLYM_HUMAN	serine hydroxymethyltransferase 2 (mitochondrial)	50					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)	GAGAGCCTGTCGGACAGTGAT	0.622													C|||	118	0.0235623	0.0756	0.0144	5008	,	,		18639	0.0		0.008	False		,,,				2504	0.0				p.S50L	Esophageal Squamous(150;1369 2416 49071 49364)	Atlas-SNP	.											.	SHMT2	40	.	0			c.C149T						PASS	.	C	LEU/SER,LEU/SER,LEU/SER,LEU/SER,LEU/SER	343,4063	179.4+/-207.9	9,325,1869	101	84	90		149,86,86,86,149	3.9	0.5	12	dbSNP_130	90	72,8528	43.1+/-100.9	0,72,4228	yes	missense,missense,missense,missense,missense	SHMT2	NM_001166356.1,NM_001166357.1,NM_001166358.1,NM_001166359.1,NM_005412.5	145,145,145,145,145	9,397,6097	TT,TC,CC		0.8372,7.7848,3.1908	benign,benign,benign,benign,benign	50/495,29/484,29/484,29/484,50/505	57624701	415,12591	2203	4300	6503	SO:0001583	missense	6472	exon2			GCCTGTCGGACAG	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.149C>T	12.37:g.57624701C>T	ENSP00000333667:p.Ser50Leu	225	1	0.00444444		241	108	0.448133	NM_005412	B7Z9F1|E7EQ19|E7EU43|O00740|Q8N1A5	Missense_Mutation	SNP	ENST00000328923.3	37	CCDS8934.1	52	0.023809523809523808	41	0.08333333333333333	5	0.013812154696132596	0	0.0	6	0.0079155672823219	C	16.72	3.201341	0.58234	0.077848	0.008372	ENSG00000182199	ENST00000328923;ENST00000557487;ENST00000556689;ENST00000414700;ENST00000557703;ENST00000553529;ENST00000554310;ENST00000557427;ENST00000553474;ENST00000555773;ENST00000554975;ENST00000449049;ENST00000556737	T;T;T;T;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;0.91;0.91;0.91;0.91	4.81	3.92	0.45320	Pyridoxal phosphate-dependent transferase, major domain (1);	0.198794	0.43579	D	0.000549	T	0.01940	0.0061	L	0.37630	1.12	0.80722	D	1	B;B	0.24092	0.06;0.097	B;B	0.26202	0.067;0.052	T	0.01739	-1.1284	10	0.37606	T	0.19	-8.0204	12.6117	0.56554	0.0:0.9176:0.0:0.0824	.	50;50	Q8N1A5;P34897	.;GLYM_HUMAN	L	50;50;50;29;29;29;29;29;29;29;29;29;29	ENSP00000333667:S50L;ENSP00000452315:S50L;ENSP00000452035:S50L;ENSP00000406881:S29L;ENSP00000450452:S29L;ENSP00000452161:S29L;ENSP00000450893:S29L;ENSP00000452045:S29L;ENSP00000452419:S29L;ENSP00000451968:S29L;ENSP00000452404:S29L;ENSP00000413770:S29L;ENSP00000451495:S29L	ENSP00000333667:S50L	S	+	2	0	SHMT2	55910968	0.961000	0.32948	0.531000	0.27976	0.967000	0.64934	2.233000	0.43027	1.399000	0.46721	-0.137000	0.14449	TCG	C|0.970;T|0.030	0.030	strong		0.622	SHMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412525.2	NM_005412		T	57624701	C	T	57624701	3	4	24	1	0	0	0	0	1	0	0	0	14301	893	31	1	155	1	SHMT2	12	57624701	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	30149	57624701	76227194	402	8619											
ARHGAP9	64333	hgsc.bcm.edu	37	chr12	57867907	57867907	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agaaaaagcttcagggctccGgtgaccacatgaatgtcatc	13	8	10	10	1	2	3	2	2	0	1	4	3	3	3	2	2	1	2	2	2	3	1	rs61754174	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:57867907G>A	ENST00000356411.2	-	16	2031	c.1893C>T	c.(1891-1893)acC>acT	p.T631T	ARHGAP9_ENST00000550288.1_Silent_p.T691T|ARHGAP9_ENST00000550454.1_5'Flank|ARHGAP9_ENST00000393797.2_Silent_p.T702T|ARHGAP9_ENST00000424809.2_Silent_p.T612T|ARHGAP9_ENST00000430041.2_Silent_p.T428T|ARHGAP9_ENST00000393791.3_Silent_p.T612T			Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9	631	Lipid binding.|Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				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)			TCAGGGCTCCGGTGACCACAT	0.557													G|||	23	0.00459265	0.0	0.0115	5008	,	,		15812	0.0		0.0139	False		,,,				2504	0.001				p.T612T		Atlas-SNP	.											.	ARHGAP9	79	.	0			c.C1836T						PASS	.	G	,,	9,4397	15.5+/-35.6	0,9,2194	45	48	47		1284,1836,1836	-4.7	1	12	dbSNP_129	47	72,8528	42.6+/-100.3	0,72,4228	no	coding-synonymous,coding-synonymous,coding-synonymous	ARHGAP9	NM_001080156.1,NM_001080157.1,NM_032496.2	,,	0,81,6422	AA,AG,GG		0.8372,0.2043,0.6228	,,	428/548,612/641,612/732	57867907	81,12925	2203	4300	6503	SO:0001819	synonymous_variant	64333	exon15			GGCTCCGGTGACC	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.1893C>T	12.37:g.57867907G>A		74	0	0		56	23	0.410714	NM_001080157	B4DVI3|E9PDX9|Q8NAF3|Q8TCJ3|Q8WYR0|Q96EZ2|Q96S74	Silent	SNP	ENST00000356411.2	37																																																																																				G|0.994;A|0.006	0.006	strong		0.557	ARHGAP9-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_032496		A	57867907	G	A	57867907	2	1	24	1	0	0	0	0	0	0	0	1	889	1103	39	1		1	ARHGAP9	12	57867907	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	243206	57867907	75983988	403	8620											
MON2	23041	hgsc.bcm.edu	37	chr12	62965212	62965212	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tttgaagtattcctgcccttCtgaaagcacatggaaactag	12	12	8	9	0	1	2	0	2	1	0	2	3	2	3	2	1	3	2	2	1	5	5			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:62965212C>T	ENST00000393632.2	+	30	4755	c.4364C>T	c.(4363-4365)tCt>tTt	p.S1455F	MON2_ENST00000280379.6_Missense_Mutation_p.S1456F|MON2_ENST00000393629.2_Missense_Mutation_p.S1449F|MON2_ENST00000393630.3_Missense_Mutation_p.S1456F|MON2_ENST00000546600.1_Missense_Mutation_p.S1455F|MON2_ENST00000552738.1_Missense_Mutation_p.S1426F	NM_015026.2	NP_055841.2	Q7Z3U7	MON2_HUMAN	MON2 homolog (S. cerevisiae)	1455					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)		TCCTGCCCTTCTGAAAGCACA	0.383																																					p.S1455F		Atlas-SNP	.											.	MON2	160	.	0			c.C4364T						PASS	.						129	135	133					12																	62965212		2203	4300	6503	SO:0001583	missense	23041	exon30			GCCCTTCTGAAAG		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.4364C>T	12.37:g.62965212C>T	ENSP00000377252:p.Ser1455Phe	113	0	0		100	4	0.04	NM_015026	A5D8U7|A7E2Y0|B9EGP5|F8VWA6|F8W1Z6|Q86TA2|Q8N3I5|Q8NAI0|Q8NHE2|Q9UPW1	Missense_Mutation	SNP	ENST00000393632.2	37	CCDS31849.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.607945	0.87258	.	.	ENSG00000061987	ENST00000393632;ENST00000393630;ENST00000280379;ENST00000546600;ENST00000552738;ENST00000393629	T;T;T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09;-0.09;-0.09	5.49	4.6	0.57074	.	0.000000	0.85682	D	0.000000	T	0.73289	0.3568	L	0.58810	1.83	0.80722	D	1	D;D;D;D;D	0.71674	0.997;0.994;0.996;0.984;0.998	P;D;D;P;D	0.65773	0.868;0.938;0.938;0.809;0.938	T	0.73294	-0.4028	9	.	.	.	-15.3521	14.0268	0.64590	0.0:0.9272:0.0:0.0728	.	1449;1426;1455;324;1455	B9EGP5;F8VWA6;F8W1Z6;Q7Z3U7-3;Q7Z3U7-4	.;.;.;.;.	F	1455;1456;1456;1455;1426;1449	ENSP00000377252:S1455F;ENSP00000377250:S1456F;ENSP00000280379:S1456F;ENSP00000447407:S1455F;ENSP00000449215:S1426F;ENSP00000377249:S1449F	.	S	+	2	0	MON2	61251479	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.814000	0.86154	1.316000	0.45131	0.650000	0.86243	TCT	.	.	none		0.383	MON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406767.3	NM_015026		T	62965212	C	T	62965212	3	4	24	1	0	0	0	0	1	0	0	0	9709	913	32	2	4482	2	MON2	12	62965212	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	5097305	62965212	70886683	404	8621											
NUP107	57122	hgsc.bcm.edu	37	chr12	69090684	69090684	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatcttgtggaagagtatgaAaacatctgtggtagtcaggt	12	12	13	4	0	3	2	1	1	2	1	3	4	3	3	0	3	1	2	0	3	5	3	rs35054844	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:69090684A>G	ENST00000229179.4	+	6	866	c.534A>G	c.(532-534)gaA>gaG	p.E178E	NUP107_ENST00000378905.2_Silent_p.E27E|NUP107_ENST00000539906.1_Silent_p.E149E	NM_020401.2	NP_065134.1	P57740	NU107_HUMAN	nucleoporin 107kDa	178					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 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)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|structural constituent of nuclear pore (GO:0017056)		NUP107/LGR5(2)	breast(3)|endometrium(4)|kidney(4)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(2)	39	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)			AAGAGTATGAAAACATCTGTG	0.353													A|||	154	0.0307508	0.0507	0.0403	5008	,	,		19586	0.001		0.0229	False		,,,				2504	0.0358				p.E178E		Atlas-SNP	.											NUP107,NS,carcinoma,+2,1	NUP107	88	1	0			c.A534G						PASS	.	A		178,4228	116.3+/-154.2	3,172,2028	115	106	109		534	1.9	1	12	dbSNP_126	109	194,8406	85.3+/-147.7	3,188,4109	no	coding-synonymous	NUP107	NM_020401.2		6,360,6137	GG,GA,AA		2.2558,4.0399,2.8602		178/926	69090684	372,12634	2203	4300	6503	SO:0001819	synonymous_variant	57122	exon6			GTATGAAAACATC	AK055629	CCDS8985.1	12q14	2004-03-19			ENSG00000111581	ENSG00000111581			29914	protein-coding gene	gene with protein product		607617				12552102, 12705868	Standard	XM_005269037		Approved	NUP84	uc001suf.3	P57740	OTTHUMG00000169265	ENST00000229179.4:c.534A>G	12.37:g.69090684A>G		65	0	0		82	45	0.548781	NM_020401	B4DZ67|Q6PJE1	Silent	SNP	ENST00000229179.4	37	CCDS8985.1																																																																																			A|0.975;G|0.025	0.025	strong		0.353	NUP107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403195.1	NM_020401		G	69090684	A	G	69090684	2	3	24	1	0	0	0	0	0	0	0	1	10762	11	1	3		3	NUP107	12	69090684	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	6125472	69090684	64761211	405	8622											
EPYC	1833	hgsc.bcm.edu	37	chr12	91363909	91363909	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtacagatgatggagatcaTacatgtcctgtaaacattcc	13	11	9	8	0	1	3	1	1	0	2	3	4	3	3	2	2	3	2	2	2	4	4			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:91363909T>C	ENST00000261172.3	-	6	802	c.710A>G	c.(709-711)tAt>tGt	p.Y237C		NM_004950.4	NP_004941.2	Q99645	EPYC_HUMAN	epiphycan	237					female pregnancy (GO:0007565)	proteinaceous extracellular matrix (GO:0005578)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(8)|skin(2)	18						ATGGAGATCATACATGTCCTG	0.408																																					p.Y237C		Atlas-SNP	.											.	EPYC	35	.	0			c.A710G						PASS	.						175	176	175					12																	91363909		2203	4300	6503	SO:0001583	missense	1833	exon6			AGATCATACATGT	AF031658	CCDS31870.1	12q21	2010-03-19	2006-11-21	2006-11-21	ENSG00000083782	ENSG00000083782		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	3053	protein-coding gene	gene with protein product	"epiphycan proteoglycan"	601657	"dermatan sulphate proteoglycan 3", "dermatan sulfate proteoglycan 3"	DSPG3		8975717	Standard	NM_004950		Approved	Pg-Lb, SLRR3B	uc001tbk.3	Q99645	OTTHUMG00000170072	ENST00000261172.3:c.710A>G	12.37:g.91363909T>C	ENSP00000261172:p.Tyr237Cys	85	0	0		91	47	0.516484	NM_004950	A8K3M7|Q8NEJ5	Missense_Mutation	SNP	ENST00000261172.3	37	CCDS31870.1	.	.	.	.	.	.	.	.	.	.	T	12.84	2.059179	0.36373	.	.	ENSG00000083782	ENST00000261172	T	0.02395	4.31	5.33	5.33	0.75918	.	0.379586	0.30556	N	0.009374	T	0.02012	0.0063	N	0.08118	0	0.29020	N	0.886362	P	0.44521	0.837	B	0.38562	0.276	T	0.42310	-0.9459	10	0.56958	D	0.05	.	11.9016	0.52687	0.0:0.0:0.1455:0.8545	.	237	Q99645	EPYC_HUMAN	C	237	ENSP00000261172:Y237C	ENSP00000261172:Y237C	Y	-	2	0	EPYC	89888040	0.977000	0.34250	1.000000	0.80357	0.979000	0.70002	1.131000	0.31406	2.016000	0.59253	0.383000	0.25322	TAT	.	.	none		0.408	EPYC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407146.2	NM_004950		C	91363909	T	C	91363909	3	2	24	1	0	0	0	0	1	0	0	0	5203	1406	49	3	266	3	EPYC	12	91363909	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	22273225	91363909	42487986	406	8623											
ANKS1B	56899	hgsc.bcm.edu	37	chr12	99139552	99139552	+	Intron	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ttcatacttggtattaatgcCcctcttggcttcttggcccg	5	16	8	12	1	3	0	1	0	2	0	3	0	3	0	3	3	2	2	3	3	3	8			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:99139552C>T	ENST00000547776.2	-	25	3672				ANKS1B_ENST00000547446.1_Missense_Mutation_p.G384S|ANKS1B_ENST00000341752.7_Intron|ANKS1B_ENST00000549025.2_Missense_Mutation_p.G347S|ANKS1B_ENST00000333732.7_Missense_Mutation_p.G279S|ANKS1B_ENST00000550693.2_Missense_Mutation_p.G440S|ANKS1B_ENST00000546568.1_Missense_Mutation_p.G416S|ANKS1B_ENST00000547010.1_Intron|ANKS1B_ENST00000332712.7_Missense_Mutation_p.G440S|ANKS1B_ENST00000549558.2_Intron|ANKS1B_ENST00000329257.7_Intron|ANKS1B_ENST00000549493.2_Missense_Mutation_p.G500S	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B							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)		GTATTAATGCCCCTCTTGGCT	0.537																																					p.G500S		Atlas-SNP	.											.	ANKS1B	180	.	0			c.G1498A						PASS	.						107	113	111					12																	99139552		1930	4139	6069	SO:0001627	intron_variant	56899	exon13			TAATGCCCCTCTT	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.3672+5580G>A	12.37:g.99139552C>T		106	0	0		82	38	0.463415	NM_181670	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Missense_Mutation	SNP	ENST00000547776.2	37	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	C	8.874	0.949903	0.18431	.	.	ENSG00000185046	ENST00000550693;ENST00000549025;ENST00000549493;ENST00000547446;ENST00000333732;ENST00000546568;ENST00000332712;ENST00000407362	T;T;T;T;T;T;T	0.68903	0.01;0.57;0.0;-0.36;-0.04;0.07;0.33	4.66	3.76	0.43208	.	.	.	.	.	T	0.57548	0.2061	N	0.04508	-0.205	0.34764	D	0.733028	B;D;D;D;D;B;B;D;B	0.89917	0.019;1.0;1.0;1.0;1.0;0.14;0.027;1.0;0.077	B;D;D;D;D;B;B;D;B	0.85130	0.016;0.997;0.994;0.997;0.994;0.076;0.042;0.997;0.09	T	0.57837	-0.7742	9	0.02654	T	1	.	12.6737	0.56882	0.0:0.9195:0.0:0.0805	.	384;279;280;440;389;464;416;500;347	F8VPM3;F8VR14;B7Z9I9;Q7Z6G8-5;B1VKB5;F8VQW6;Q7Z6G8-2;Q7Z6G8-3;F8VZR9	.;.;.;.;.;.;.;.;.	S	440;347;500;384;279;416;440;340	ENSP00000447999:G440S;ENSP00000447312:G347S;ENSP00000448203:G500S;ENSP00000450015:G384S;ENSP00000331256:G279S;ENSP00000448205:G416S;ENSP00000332683:G440S	ENSP00000332683:G440S	G	-	1	0	ANKS1B	97663683	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.436000	0.59948	1.060000	0.40578	0.549000	0.68633	GGC	.	.	none		0.537	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140		T	99139552	C	T	99139552	1	4	24	0	1	0	0	0	0	0	0	0	689	623	22	2		2	ANKS1B	12	99139552	Intron	SNP	C	TCGA-G8-6326-01A-11D-2210-10	7775643	99139552	34712343	407	8624											
NUP37	79023	hgsc.bcm.edu	37	chr12	102494849	102494849	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagatctgaagtaaataaTctaattttcatatcagcagc	16	13	6	6	0	4	3	2	2	2	1	4	3	4	3	0	0	2	2	0	0	7	6	rs17438178	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:102494849T>C	ENST00000552283.1	-	4	454	c.315A>G	c.(313-315)agA>agG	p.R105R	NUP37_ENST00000543021.1_5'UTR|NUP37_ENST00000251074.1_Silent_p.R105R			Q8NFH4	NUP37_HUMAN	nucleoporin 37kDa	105					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						AAGTAAATAATCTAATTTTCA	0.308													T|||	110	0.0219649	0.0401	0.0058	5008	,	,		16106	0.0		0.0308	False		,,,				2504	0.0225				p.R105R		Atlas-SNP	.											.	NUP37	26	.	0			c.A315G						PASS	.	T		130,4262		4,122,2070	29	31	31		315	0.3	1	12	dbSNP_123	31	211,8361		2,207,4077	no	coding-synonymous	NUP37	NM_024057.2		6,329,6147	CC,CT,TT		2.4615,2.9599,2.6304		105/327	102494849	341,12623	2196	4286	6482	SO:0001819	synonymous_variant	79023	exon3			AAATAATCTAATT	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.315A>G	12.37:g.102494849T>C		163	0	0		144	62	0.430556	NM_024057	Q9H644	Silent	SNP	ENST00000552283.1	37	CCDS9089.1																																																																																			T|0.976;C|0.024	0.024	strong		0.308	NUP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409330.1	NM_024057		C	102494849	T	C	102494849	2	2	24	1	0	0	0	0	0	0	0	1	10773	1432	50	3		3	NUP37	12	102494849	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	3355297	102494849	31357046	408	8625											
C12orf48	55010	hgsc.bcm.edu	37	chr12	102547741	102547741	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accaacaagtaaatacaaccGtgataatgaaaaggtactga	20	7	7	7	1	0	3	0	3	0	0	0	3	0	3	2	1	4	2	2	1	10	4	rs114546604	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:102547741G>A	ENST00000358383.5	+	4	527	c.482G>A	c.(481-483)cGt>cAt	p.R161H	PARPBP_ENST00000541394.1_Missense_Mutation_p.R238H|PARPBP_ENST00000392911.2_Missense_Mutation_p.R80H|PARPBP_ENST00000378128.3_Missense_Mutation_p.R161H|PARPBP_ENST00000543784.1_Intron|PARPBP_ENST00000535811.1_Intron|PARPBP_ENST00000327680.2_Missense_Mutation_p.R80H			Q9NWS1	PARI_HUMAN	PARP1 binding protein	161					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						AAATACAACCGTGATAATGAA	0.353													A|||	153	0.0305511	0.0998	0.0058	5008	,	,		18353	0.0		0.006	False		,,,				2504	0.0112				p.R161H		Atlas-SNP	.											.	PARPBP	40	.	0			c.G482A						PASS	.	A	HIS/ARG	282,4124	800.4+/-415.6	15,252,1936	105	93	97		482	2.8	0.1	12	dbSNP_132	97	21,8577	817.4+/-406.9	0,21,4278	yes	missense	C12orf48	NM_017915.3	29	15,273,6214	AA,AG,GG		0.2442,6.4004,2.3301	benign	161/580	102547741	303,12701	2203	4299	6502	SO:0001583	missense	55010	exon4			ACAACCGTGATAA	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.482G>A	12.37:g.102547741G>A	ENSP00000351153:p.Arg161His	55	0	0		60	27	0.45	NM_017915	B4E0Y0|Q05C00|Q499L8|Q4FZA0|Q4KMW7|Q6NSC6|Q6PJA1|Q86W36	Missense_Mutation	SNP	ENST00000358383.5	37	CCDS9090.2	53	0.024267399267399268	48	0.0975609756097561	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	A	2.534	-0.307796	0.05458	0.064004	0.002442	ENSG00000185480	ENST00000378128;ENST00000327680;ENST00000541394;ENST00000358383;ENST00000392911;ENST00000417507;ENST00000412715	T;T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97;0.97	5.46	2.79	0.32731	.	0.713371	0.14523	N	0.314304	T	0.00412	0.0013	N	0.08118	0	0.09310	N	1	B;B;P;B;B;B	0.35527	0.0;0.0;0.507;0.018;0.0;0.0	B;B;B;B;B;B	0.14023	0.0;0.0;0.01;0.002;0.0;0.0	T	0.07947	-1.0746	10	0.27785	T	0.31	2.3812	5.7553	0.18170	0.7054:0.0:0.1593:0.1353	.	238;161;161;161;161;80	B4DZ31;Q9NWS1-6;Q9NWS1-7;Q9NWS1-3;Q9NWS1;Q9NWS1-2	.;.;.;.;PR1BP_HUMAN;.	H	161;80;238;161;80;128;128	ENSP00000367368:R161H;ENSP00000332915:R80H;ENSP00000440850:R238H;ENSP00000351153:R161H;ENSP00000376643:R80H;ENSP00000411313:R128H;ENSP00000393867:R128H	ENSP00000332915:R80H	R	+	2	0	C12orf48	101071871	0.919000	0.31177	0.084000	0.20598	0.049000	0.14656	1.172000	0.31908	0.371000	0.24564	-0.361000	0.07541	CGT	G|0.976;A|0.024	0.024	strong		0.353	PARPBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397030.2	NM_017915		A	102547741	G	A	102547741	3	1	24	1	0	0	0	0	1	0	0	0	1694	1145	40	1	245	1	C12orf48	12	102547741	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	52892	102547741	31304154	409	8626											
C12orf48	55010	hgsc.bcm.edu	37	chr12	102558369	102558369	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aacatgctgctcgagagaaaCaaatgtctatctttttggta	13	13	8	7	1	2	1	0	0	2	1	3	3	2	1	0	1	4	3	0	1	5	4	rs75438625	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:102558369C>A	ENST00000358383.5	+	5	694	c.649C>A	c.(649-651)Caa>Aaa	p.Q217K	PARPBP_ENST00000541394.1_Missense_Mutation_p.Q294K|PARPBP_ENST00000392911.2_Missense_Mutation_p.Q136K|PARPBP_ENST00000378128.3_Missense_Mutation_p.Q217K|PARPBP_ENST00000543784.1_Missense_Mutation_p.Q103K|PARPBP_ENST00000535811.1_Intron|PARPBP_ENST00000327680.2_Missense_Mutation_p.Q136K			Q9NWS1	PARI_HUMAN	PARP1 binding protein	217					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						TCGAGAGAAACAAATGTCTAT	0.383													C|||	163	0.0325479	0.1082	0.0058	5008	,	,		17316	0.0		0.005	False		,,,				2504	0.0112				p.Q217K		Atlas-SNP	.											.	PARPBP	40	.	0			c.C649A						PASS	.	C	LYS/GLN	318,4088	170.1+/-200.6	16,286,1901	143	152	149		649	4.9	1	12	dbSNP_131	149	21,8579	15.3+/-51.7	0,21,4279	yes	missense	C12orf48	NM_017915.3	53	16,307,6180	AA,AC,CC		0.2442,7.2174,2.6065	benign	217/580	102558369	339,12667	2203	4300	6503	SO:0001583	missense	55010	exon5			GAGAAACAAATGT	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.649C>A	12.37:g.102558369C>A	ENSP00000351153:p.Gln217Lys	81	0	0		90	30	0.333333	NM_017915	B4E0Y0|Q05C00|Q499L8|Q4FZA0|Q4KMW7|Q6NSC6|Q6PJA1|Q86W36	Missense_Mutation	SNP	ENST00000358383.5	37	CCDS9090.2	57	0.0260989010989011	52	0.10569105691056911	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	4.014	-0.000060	0.07819	0.072174	0.002442	ENSG00000185480	ENST00000378128;ENST00000327680;ENST00000541394;ENST00000543784;ENST00000358383;ENST00000392911;ENST00000417507;ENST00000412715	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	5.81	4.91	0.64330	.	0.653601	0.17239	N	0.181630	T	0.00440	0.0014	N	0.13043	0.29	0.26065	N	0.981294	B;B;B;B;B;B	0.16802	0.019;0.01;0.001;0.002;0.005;0.004	B;B;B;B;B;B	0.13407	0.009;0.006;0.003;0.003;0.004;0.006	T	0.05146	-1.0903	10	0.05721	T	0.95	0.0463	13.9017	0.63809	0.3925:0.6075:0.0:0.0	.	103;294;217;217;217;136	B4DT40;B4DZ31;Q9NWS1-6;Q9NWS1-7;Q9NWS1;Q9NWS1-2	.;.;.;.;PR1BP_HUMAN;.	K	217;136;294;103;217;136;184;184	ENSP00000367368:Q217K;ENSP00000332915:Q136K;ENSP00000440850:Q294K;ENSP00000444576:Q103K;ENSP00000351153:Q217K;ENSP00000376643:Q136K;ENSP00000411313:Q184K;ENSP00000393867:Q184K	ENSP00000332915:Q136K	Q	+	1	0	C12orf48	101082499	0.994000	0.37717	0.996000	0.52242	0.976000	0.68499	1.035000	0.30216	1.433000	0.47394	0.460000	0.39030	CAA	C|0.974;A|0.026	0.026	strong		0.383	PARPBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397030.2	NM_017915		A	102558369	C	A	102558369	3	1	24	1	0	0	0	0	1	0	0	0	1694	479	17	4	416	4	C12orf48	12	102558369	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	10628	102558369	31293526	410	8627											
STAB2	55576	hgsc.bcm.edu	37	chr12	104048446	104048446	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttgacagagccatggacaaGttagaacccacatttgagag	14	8	10	9	0	0	4	0	2	0	3	0	6	0	5	2	1	2	1	2	1	3	3	rs149524008	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:104048446G>T	ENST00000388887.2	+	13	1725	c.1521G>T	c.(1519-1521)aaG>aaT	p.K507N	RP11-341G23.2_ENST00000551905.1_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						CCATGGACAAGTTAGAACCCA	0.443													G|||	22	0.00439297	0.0008	0.0029	5008	,	,		21467	0.0		0.0159	False		,,,				2504	0.0031				p.K507N		Atlas-SNP	.											.	STAB2	370	.	0			c.G1521T						PASS	.	G	ASN/LYS	6,4400	14.3+/-33.2	0,6,2197	103	93	96		1521	0.5	0	12	dbSNP_134	96	85,8515	48.9+/-108.6	2,81,4217	yes	missense	STAB2	NM_017564.9	94	2,87,6414	TT,TG,GG		0.9884,0.1362,0.6997	benign	507/2552	104048446	91,12915	2203	4300	6503	SO:0001583	missense	55576	exon13			GGACAAGTTAGAA	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.1521G>T	12.37:g.104048446G>T	ENSP00000373539:p.Lys507Asn	85	0	0		76	41	0.539474	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	37	CCDS31888.1	15	0.006868131868131868	0	0.0	1	0.0027624309392265192	0	0.0	14	0.018469656992084433	G	1.712	-0.498842	0.04291	0.001362	0.009884	ENSG00000136011	ENST00000388887	T	0.63580	-0.05	5.8	0.469	0.16741	FAS1 domain (2);	0.583558	0.18587	N	0.136838	T	0.25494	0.0620	N	0.22421	0.69	0.09310	N	1	B	0.09022	0.002	B	0.11329	0.006	T	0.11421	-1.0588	10	0.24483	T	0.36	.	7.5112	0.27575	0.0643:0.4925:0.2505:0.1927	.	507	Q8WWQ8	STAB2_HUMAN	N	507	ENSP00000373539:K507N	ENSP00000373539:K507N	K	+	3	2	STAB2	102572576	0.991000	0.36638	0.000000	0.03702	0.002000	0.02628	0.356000	0.20181	-0.171000	0.10797	-0.257000	0.10917	AAG	G|0.992;T|0.008	0.008	strong		0.443	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			T	104048446	G	T	104048446	3	4	24	1	0	0	0	0	1	0	0	0	15253	1020	36	4	1571	4	STAB2	12	104048446	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1490077	104048446	29803449	411	8628											
KIAA1033	23325	hgsc.bcm.edu	37	chr12	105550565	105550565	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcattgtagcagcaatgcCattaggtatggatgcaaaca	13	11	9	8	0	1	0	1	0	0	0	1	1	1	1	1	2	5	5	1	2	5	5	rs35149056	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:105550565C>T	ENST00000332180.5	+	27	2907	c.2820C>T	c.(2818-2820)gcC>gcT	p.A940A		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						GCAGCAATGCCATTAGGTATG	0.308													C|||	217	0.0433307	0.0166	0.0692	5008	,	,		14135	0.001		0.0795	False		,,,				2504	0.0675				p.A940A		Atlas-SNP	.											.	KIAA1033	83	.	0			c.C2820T						PASS	.	C		82,3618		1,80,1769	208	186	193		2820	4.9	1	12	dbSNP_126	193	613,7575		27,559,3508	no	coding-synonymous	KIAA1033	NM_015275.1		28,639,5277	TT,TC,CC		7.4866,2.2162,5.8462		940/1174	105550565	695,11193	1850	4094	5944	SO:0001819	synonymous_variant	23325	exon27			CAATGCCATTAGG	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.2820C>T	12.37:g.105550565C>T		102	0	0		96	39	0.40625	NM_015275		Silent	SNP	ENST00000332180.5	37	CCDS41826.1																																																																																			C|0.946;T|0.054	0.054	strong		0.308	KIAA1033-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406138.4	NM_015275		T	105550565	C	T	105550565	2	4	24	1	0	0	0	0	0	0	0	1	8215	581	21	2		2	KIAA1033	12	105550565	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1502119	105550565	28301330	412	8629											
FICD	11153	hgsc.bcm.edu	37	chr12	108912621	108912621	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aatcaggcacatcctggagaCccgctacgccgtgcccggga	9	5	12	15	4	1	1	1	0	0	1	2	3	2	2	4	3	2	2	4	3	2	1	rs146316463		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:108912621C>A	ENST00000552695.1	+	3	981	c.746C>A	c.(745-747)aCc>aAc	p.T249N	FICD_ENST00000361549.2_3'UTR	NM_007076.2	NP_009007.2	Q9BVA6	FICD_HUMAN	FIC domain containing	249					negative regulation of Rho GTPase activity (GO:0034259)|protein adenylylation (GO:0018117)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|protein adenylyltransferase activity (GO:0070733)			NS(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(1)|prostate(1)|upper_aerodigestive_tract(2)	15						ATCCTGGAGACCCGCTACGCC	0.582													C|||	1	0.000199681	0.0	0.0	5008	,	,		22220	0.0		0.001	False		,,,				2504	0.0				p.T249N		Atlas-SNP	.											.	FICD	35	.	0			c.C746A						PASS	.	C	ASN/THR	0,4406		0,0,2203	108	81	90		746	6.1	1	12	dbSNP_134	90	3,8597	3.7+/-12.6	0,3,4297	yes	missense	FICD	NM_007076.2	65	0,3,6500	AA,AC,CC		0.0349,0.0,0.0231	possibly-damaging	249/459	108912621	3,13003	2203	4300	6503	SO:0001583	missense	11153	exon3			TGGAGACCCGCTA	AF049611	CCDS9116.1	12q24.1	2007-12-05				ENSG00000198855			18416	protein-coding gene	gene with protein product	"huntingtin interacting protein 13", "fic S-phase protein cell division homolog (E. coli)"					9700202	Standard	NM_007076		Approved	HYPE, HIP13	uc001tmx.1	Q9BVA6		ENST00000552695.1:c.746C>A	12.37:g.108912621C>A	ENSP00000446479:p.Thr249Asn	106	0	0		134	76	0.567164	NM_007076	O75406	Missense_Mutation	SNP	ENST00000552695.1	37	CCDS9116.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	23.8	4.461591	0.84317	0.0	3.49E-4	ENSG00000198855	ENST00000552695	.	.	.	6.07	6.07	0.98685	Filamentation induced by cAMP/death on curing-related (1);	0.000000	0.85682	D	0.000000	T	0.58221	0.2107	L	0.31926	0.97	0.80722	D	1	D	0.56035	0.974	P	0.51701	0.677	T	0.46610	-0.9179	9	0.11485	T	0.65	-9.4005	20.6439	0.99570	0.0:1.0:0.0:0.0	.	249	Q9BVA6	FICD_HUMAN	N	249	.	ENSP00000446479:T249N	T	+	2	0	FICD	107436751	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.818000	0.86416	2.884000	0.98904	0.655000	0.94253	ACC	C|0.999;A|0.001	0.001	strong		0.582	FICD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404842.1	NM_007076		A	108912621	C	A	108912621	3	1	24	1	0	0	0	0	1	0	0	0	5895	507	18	4	752	4	FICD	12	108912621	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	3362056	108912621	24939274	413	8630											
MYO1H	283446	hgsc.bcm.edu	37	chr12	109826535	109826535	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgtctgcacatggaaggggcGctgactgcccgggacaaggt	8	6	16	11	3	1	1	0	1	1	0	1	3	1	3	1	5	2	2	1	5	2	0	rs61742038	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:109826535G>A	ENST00000431443.2	+	1	12	c.12G>A	c.(10-12)gcG>gcA	p.A4A	MYO1H_ENST00000310903.5_Silent_p.A4A	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	4						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						TGGAAGGGGCGCTGACTGCCC	0.502													G|||	341	0.0680911	0.2474	0.0187	5008	,	,		18985	0.0		0.001	False		,,,				2504	0.0				p.A4A		Atlas-SNP	.											.	MYO1H	98	.	0			c.G12A						PASS	.	G		777,3405		61,655,1375	144	156	152		12	-2.6	0.8	12	dbSNP_129	152	12,8460		0,12,4224	no	coding-synonymous	MYO1H	NM_001101421.3		61,667,5599	AA,AG,GG		0.1416,18.5796,6.2352		4/1023	109826535	789,11865	2091	4236	6327	SO:0001819	synonymous_variant	283446	exon1			AGGGGCGCTGACT		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.12G>A	12.37:g.109826535G>A		132	0	0		172	85	0.494186	NM_001101421	F5H3C6	Silent	SNP	ENST00000431443.2	37																																																																																				G|0.947;A|0.053	0.053	strong		0.502	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597		A	109826535	G	A	109826535	2	1	24	1	0	0	0	0	0	0	0	1	10084	1074	38	1		1	MYO1H	12	109826535	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	913914	109826535	24025360	414	8631											
MYO1H	283446	hgsc.bcm.edu	37	chr12	109838954	109838954	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atagagaagtcccgagttgtCtaccaaaacgaaggcgagcg	14	6	12	9	4	1	1	0	0	1	1	2	5	2	1	2	1	3	1	2	1	6	3	rs138935511	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:109838954C>T	ENST00000431443.2	+	5	579	c.579C>T	c.(577-579)gtC>gtT	p.V193V	MYO1H_ENST00000310903.5_Silent_p.V193V	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	193	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						CCCGAGTTGTCTACCAAAACG	0.512													C|||	5	0.000998403	0.0038	0.0	5008	,	,		17341	0.0		0.0	False		,,,				2504	0.0				p.V193V		Atlas-SNP	.											.	MYO1H	98	.	0			c.C579T						PASS	.	C		3,4061		0,3,2029	69	72	71		579	2.5	1	12	dbSNP_134	71	1,8387		0,1,4193	no	coding-synonymous	MYO1H	NM_001101421.3		0,4,6222	TT,TC,CC		0.0119,0.0738,0.0321		193/1023	109838954	4,12448	2032	4194	6226	SO:0001819	synonymous_variant	283446	exon5			AGTTGTCTACCAA		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.579C>T	12.37:g.109838954C>T		89	0	0		95	45	0.473684	NM_001101421	F5H3C6	Silent	SNP	ENST00000431443.2	37																																																																																				C|0.999;T|0.001	0.001	strong		0.512	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597		T	109838954	C	T	109838954	2	4	24	1	0	0	0	0	0	0	0	1	10084	900	32	2		2	MYO1H	12	109838954	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	12419	109838954	24012941	415	8632											
CIT	11113	hgsc.bcm.edu	37	chr12	120260706	120260706	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttcagtctctctttctggccGcacaacaagctttgaatcag	9	13	7	12	1	5	1	2	1	3	0	6	1	5	1	1	1	2	2	1	1	3	3	rs145804827		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:120260706G>A	ENST00000261833.7	-	9	1081	c.1029C>T	c.(1027-1029)tgC>tgT	p.C343C	CIT_ENST00000392521.2_Silent_p.C343C	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	343	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)		CTTTCTGGCCGCACAACAAGC	0.388													A|||	1	0.000199681	0.0	0.0	5008	,	,		17060	0.0		0.001	False		,,,				2504	0.0				p.C343C		Atlas-SNP	.											.	CIT	535	.	0			c.C1029T						PASS	.	A	,	1,4405	826.1+/-416.6	0,1,2202	100	94	96		1029,1029	4.6	1	12	dbSNP_134	96	8,8592	818.9+/-406.8	0,8,4292	no	coding-synonymous,coding-synonymous	CIT	NM_001206999.1,NM_007174.2	,	0,9,6494	AA,AG,GG		0.093,0.0227,0.0692	,	343/2070,343/2028	120260706	9,12997	2203	4300	6503	SO:0001819	synonymous_variant	11113	exon9			CTGGCCGCACAAC	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.1029C>T	12.37:g.120260706G>A		146	0	0		139	64	0.460432	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Silent	SNP	ENST00000261833.7	37	CCDS9192.1																																																																																			G|0.999;A|0.001	0.001	strong		0.388	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174		A	120260706	G	A	120260706	2	1	24	1	0	0	0	0	0	0	0	1	3440	1079	38	1		1	CIT	12	120260706	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	10421752	120260706	13591189	416	8633											
HNF1A	6927	hgsc.bcm.edu	37	chr12	121416622	121416622	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gagctcctggcggccctgctCgagtcagggctgagcaaaga	8	6	15	12	2	1	2	1	1	0	1	3	4	2	2	2	3	3	4	2	3	1	0	rs1169289	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:121416622C>G	ENST00000257555.6	+	1	277	c.51C>G	c.(49-51)ctC>ctG	p.L17L	HNF1A_ENST00000544413.1_Silent_p.L17L|HNF1A-AS1_ENST00000537361.1_RNA|HNF1A_ENST00000402929.1_Silent_p.L17L|HNF1A_ENST00000400024.2_Silent_p.L17L|HNF1A-AS1_ENST00000535301.1_RNA|HNF1A_ENST00000543427.1_Intron|HNF1A_ENST00000538626.1_Silent_p.L17L|HNF1A-AS1_ENST00000433033.2_RNA|HNF1A_ENST00000541395.1_Silent_p.L17L			P20823	HNF1A_HUMAN	HNF1 homeobox A	17	Dimerization.				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)					CGGCCCTGCTCGAGTCAGGGC	0.687									Hepatic Adenoma, Familial Clustering of				C|||	2146	0.428514	0.3169	0.438	5008	,	,		11818	0.3819		0.4692	False		,,,				2504	0.5787				p.L17L		Atlas-SNP	.											HNF1A,NS,carcinoma,0,1	HNF1A	302	1	1	Unknown(1)	endometrium(1)	c.C51G						PASS	.	C		1508,2894		278,952,971	24	29	27		51	-3.7	0.9	12	dbSNP_87	27	3915,4673		915,2085,1294	no	coding-synonymous	HNF1A	NM_000545.5		1193,3037,2265	GG,GC,CC		45.5869,34.2572,41.7475		17/632	121416622	5423,7567	2201	4294	6495	SO:0001819	synonymous_variant	6927	exon1	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CCTGCTCGAGTCA	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.51C>G	12.37:g.121416622C>G		169	0	0		144	63	0.4375	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Silent	SNP	ENST00000257555.6	37	CCDS9209.1																																																																																			G|0.405;C|0.595	0.405	strong		0.687	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		G	121416622	C	G	121416622	2	3	24	1	0	0	0	0	0	0	0	1	7260	871	31	4		4	HNF1A	12	121416622	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1155916	121416622	12435273	417	8634											
SNRNP35	11066	hgsc.bcm.edu	37	chr12	123950408	123950408	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaggagcgtgccgtgatcaaAgcttaccgagatgctgatgg	10	8	15	8	3	1	3	1	2	0	1	1	6	1	4	2	2	5	2	2	2	2	1	rs28728202	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:123950408A>G	ENST00000526639.2	+	2	900	c.321A>G	c.(319-321)aaA>aaG	p.K107K	SNRNP35_ENST00000527158.2_Intron|SNRNP35_ENST00000412157.2_Silent_p.K112K|SNRNP35_ENST00000350887.5_Silent_p.K107K	NM_022717.3	NP_073208.1	Q16560	U1SBP_HUMAN	small nuclear ribonucleoprotein 35kDa (U11/U12)	107	RRM. {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)			NS(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	8						CCGTGATCAAAGCTTACCGAG	0.532													A|||	8	0.00159744	0.0	0.0043	5008	,	,		18826	0.0		0.005	False		,,,				2504	0.0				p.K112K		Atlas-SNP	.											.	SNRNP35	28	.	0			c.A336G						PASS	.	A	,	6,4400	11.4+/-27.6	0,6,2197	107	105	106		321,336	-1.8	0.2	12	dbSNP_125	106	65,8535	38.8+/-94.9	0,65,4235	no	coding-synonymous,coding-synonymous	SNRNP35	NM_022717.2,NM_180699.2	,	0,71,6432	GG,GA,AA		0.7558,0.1362,0.5459	,	107/247,112/252	123950408	71,12935	2203	4300	6503	SO:0001819	synonymous_variant	11066	exon2			GATCAAAGCTTAC	BC054034	CCDS9249.1, CCDS45005.1	12q24.31	2013-02-12				ENSG00000184209		"RNA binding motif (RRM) containing"	30852	protein-coding gene	gene with protein product	"U1 snRNP binding protein homolog"					10520751, 8889548	Standard	XM_005253545		Approved	U1SNRNPBP	uc001ufb.1	Q16560		ENST00000526639.2:c.321A>G	12.37:g.123950408A>G		37	0	0		43	20	0.465116	NM_180699	A8K262|Q5XKN9	Silent	SNP	ENST00000526639.2	37	CCDS9249.1																																																																																			A|0.995;G|0.005	0.005	strong		0.532	SNRNP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395197.2	NM_007020		G	123950408	A	G	123950408	2	3	24	1	0	0	0	0	0	0	0	1	14870	69	3	3		3	SNRNP35	12	123950408	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	2533786	123950408	9901487	418	8635											
DDX55	57696	hgsc.bcm.edu	37	chr12	124102305	124102305	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaccctgtgttctcacagTgccttcgtgcatcgctgcgg	4	12	10	15	3	1	0	1	0	1	0	5	0	2	0	3	1	3	3	3	1	0	2	rs147152712	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:124102305T>A	ENST00000238146.4	+	11	1100	c.1050T>A	c.(1048-1050)agT>agA	p.S350R	DDX55_ENST00000541259.1_Intron|DDX55_ENST00000538744.1_Splice_Site_p.S319R|SNORA9_ENST00000384170.1_RNA|DDX55_ENST00000421670.3_5'Flank	NM_020936.1	NP_065987.1	Q8NHQ9	DDX55_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55	350	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.					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)		GTTCTCACAGTGCCTTCGTGC	0.582																																					p.S350R		Atlas-SNP	.											.	DDX55	51	.	0			c.T1050A						PASS	.	T	ARG/SER	1,4405	2.1+/-5.4	0,1,2202	90	79	83		1050	-6.2	0.9	12	dbSNP_134	83	9,8591	7.1+/-27.0	0,9,4291	yes	missense-near-splice	DDX55	NM_020936.1	110	0,10,6493	AA,AT,TT		0.1047,0.0227,0.0769	probably-damaging	350/601	124102305	10,12996	2203	4300	6503	SO:0001630	splice_region_variant	57696	exon11			TCACAGTGCCTTC	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.1050-1T>A	12.37:g.124102305T>A		104	0	0		125	63	0.504	NM_020936	Q658L6|Q8IYH0|Q9HCH7	Missense_Mutation	SNP	ENST00000238146.4	37	CCDS9251.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.469762	0.84533	2.27E-4	0.001047	ENSG00000111364	ENST00000238146;ENST00000538744	T;D	0.92699	-0.93;-3.09	5.98	-6.16	0.02098	Helicase, C-terminal (3);	0.084790	0.85682	D	0.000000	D	0.90899	0.7140	L	0.33293	1	0.80722	D	1	P;D	0.58970	0.603;0.984	P;D	0.66847	0.516;0.947	D	0.88317	0.2960	9	.	.	.	.	15.8924	0.79309	0.0:0.5049:0.0:0.4951	.	350;350	B4DVE4;Q8NHQ9	.;DDX55_HUMAN	R	350;319	ENSP00000238146:S350R;ENSP00000443114:S319R	.	S	+	3	2	DDX55	122668258	0.229000	0.23729	0.920000	0.36463	0.971000	0.66376	-0.470000	0.06639	-0.950000	0.03659	-0.274000	0.10170	AGT	T|0.999;A|0.001	0.001	strong		0.582	DDX55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400616.2		Missense_Mutation	A	124102305	T	A	124102305	5	1	24	1	0	0	0	0	0	0	1	0	4375	1710	59	5	1092	5	DDX55	12	124102305	Splice_Site	SNP	T	TCGA-G8-6326-01A-11D-2210-10	151897	124102305	9749590	419	8636											
TCTN2	79867	hgsc.bcm.edu	37	chr12	124171538	124171538	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tttctgtgtgtgcagtccccCcttgccaacacacccttcct	5	13	6	17	0	1	0	0	0	1	0	3	0	3	0	6	0	3	1	6	0	1	3	rs149430216	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:124171538C>G	ENST00000303372.5	+	6	848	c.720C>G	c.(718-720)ccC>ccG	p.P240P	TCTN2_ENST00000426174.2_Silent_p.P239P	NM_001143850.2|NM_024809.4	NP_001137322.1|NP_079085.2	Q96GX1	TECT2_HUMAN	tectonic family member 2	240					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)		TGCAGTCCCCCCTTGCCAACA	0.572													C|||	3	0.000599042	0.0	0.0014	5008	,	,		18850	0.0		0.002	False		,,,				2504	0.0				p.P240P		Atlas-SNP	.											.	TCTN2	50	.	0			c.C720G						PASS	.	C	,	5,4401	9.9+/-24.2	0,5,2198	308	279	289		717,720	-4.8	0	12	dbSNP_134	289	55,8545	33.8+/-87.4	0,55,4245	no	coding-synonymous,coding-synonymous	TCTN2	NM_001143850.1,NM_024809.3	,	0,60,6443	GG,GC,CC		0.6395,0.1135,0.4613	,	239/697,240/698	124171538	60,12946	2203	4300	6503	SO:0001819	synonymous_variant	79867	exon6			GTCCCCCCTTGCC	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.720C>G	12.37:g.124171538C>G		223	0	0		209	98	0.4689	NM_024809	A8K7Y8|B3KPW5|Q9H966	Silent	SNP	ENST00000303372.5	37	CCDS9253.1																																																																																			C|0.996;G|0.004	0.004	strong		0.572	TCTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400652.1	NM_024809		G	124171538	C	G	124171538	2	3	24	1	0	0	0	0	0	0	0	1	15738	610	22	4		4	TCTN2	12	124171538	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	69233	124171538	9680357	420	8637											
TCTN2	79867	hgsc.bcm.edu	37	chr12	124172643	124172643	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagtatatgtggatactgaCgcaaaagactttgcagactt	14	11	10	6	1	0	3	0	1	0	2	0	5	0	4	0	1	2	3	0	1	6	5	rs144567556	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:124172643C>T	ENST00000303372.5	+	7	938	c.810C>T	c.(808-810)gaC>gaT	p.D270D	TCTN2_ENST00000426174.2_Silent_p.D269D	NM_001143850.2|NM_024809.4	NP_001137322.1|NP_079085.2	Q96GX1	TECT2_HUMAN	tectonic family member 2	270					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)		TGGATACTGACGCAAAAGACT	0.368													c|||	8	0.00159744	0.0	0.0043	5008	,	,		20396	0.0		0.005	False		,,,				2504	0.0				p.D270D		Atlas-SNP	.											.	TCTN2	50	.	0			c.C810T						PASS	.		,	6,4400	11.4+/-27.6	0,6,2197	133	137	136		807,810	-11.2	0	12	dbSNP_134	136	64,8536	38.3+/-94.2	0,64,4236	no	coding-synonymous,coding-synonymous	TCTN2	NM_001143850.1,NM_024809.3	,	0,70,6433	TT,TC,CC		0.7442,0.1362,0.5382	,	269/697,270/698	124172643	70,12936	2203	4300	6503	SO:0001819	synonymous_variant	79867	exon7			TACTGACGCAAAA	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.810C>T	12.37:g.124172643C>T		113	0	0		121	43	0.355372	NM_024809	A8K7Y8|B3KPW5|Q9H966	Silent	SNP	ENST00000303372.5	37	CCDS9253.1																																																																																			C|0.994;T|0.006	0.006	strong		0.368	TCTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400652.1	NM_024809		T	124172643	C	T	124172643	2	4	24	1	0	0	0	0	0	0	0	1	15738	535	19	1		1	TCTN2	12	124172643	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1105	124172643	9679252	421	8638											
TMEM132D	121256	hgsc.bcm.edu	37	chr12	130387850	130387850	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatgagtaccggcgaccagTggtgccacagcgtccccatc	8	7	12	14	3	0	2	0	2	0	0	2	3	1	2	5	2	3	1	5	2	1	1	rs142888394	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:130387850T>A	ENST00000422113.2	-	1	361	c.35A>T	c.(34-36)cAc>cTc	p.H12L		NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	12					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)		CGGCGACCAGTGGTGCCACAG	0.672													T|||	27	0.00539137	0.0008	0.0043	5008	,	,		12817	0.001		0.0099	False		,,,				2504	0.0123				p.H12L		Atlas-SNP	.											.	TMEM132D	299	.	0			c.A35T						PASS	.	T	LEU/HIS	8,4268		0,8,2130	30	29	29		35	-4.3	0.3	12	dbSNP_134	29	70,8242		1,68,4087	yes	missense	TMEM132D	NM_133448.2	99	1,76,6217	AA,AT,TT		0.8422,0.1871,0.6196	benign	12/1100	130387850	78,12510	2138	4156	6294	SO:0001583	missense	121256	exon1			GACCAGTGGTGCC	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.35A>T	12.37:g.130387850T>A	ENSP00000408581:p.His12Leu	166	0	0		180	95	0.527778	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	37	CCDS9266.1	10	0.004578754578754579	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	T	4.656	0.122035	0.08931	0.001871	0.008422	ENSG00000151952	ENST00000422113	T	0.03553	3.89	5.2	-4.27	0.03744	.	0.452778	0.19129	N	0.121962	T	0.00637	0.0021	N	0.01352	-0.895	0.09310	N	0.999993	B	0.02656	0.0	B	0.04013	0.001	T	0.41016	-0.9532	9	.	.	.	-15.177	0.934	0.01340	0.4633:0.173:0.1254:0.2384	.	12	Q14C87	T132D_HUMAN	L	12	ENSP00000408581:H12L	.	H	-	2	0	TMEM132D	128953803	0.070000	0.21116	0.312000	0.25196	0.737000	0.42083	0.050000	0.14120	-0.792000	0.04480	0.482000	0.46254	CAC	T|0.996;A|0.004	0.004	strong		0.672	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		A	130387850	T	A	130387850	3	1	24	1	0	0	0	0	1	0	0	0	16062	1696	59	5	3300	5	TMEM132D	12	130387850	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	6215207	130387850	3464045	422	8639											
FZD10	11211	hgsc.bcm.edu	37	chr12	130648576	130648576	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcagcctgggccatcccggcGgtgaagaccatcctgatcct	7	7	12	15	2	0	3	0	2	0	1	3	3	3	3	6	3	1	1	6	3	1	0			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr12:130648576G>T	ENST00000229030.4	+	1	1573	c.1089G>T	c.(1087-1089)gcG>gcT	p.A363A	FZD10-AS1_ENST00000505807.2_RNA|FZD10_ENST00000539839.1_Missense_Mutation_p.G331C			Q9ULW2	FZD10_HUMAN	frizzled class receptor 10	363					brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|gonad development (GO:0008406)|negative regulation of Rho GTPase activity (GO:0034259)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of actin cytoskeleton organization (GO:0032956)|vasculature development (GO:0001944)	cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|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)	p.A363A(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|pancreas(1)|prostate(3)|urinary_tract(1)	35	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.3e-06)|Epithelial(86;1.66e-05)|all cancers(50;5.18e-05)		CCATCCCGGCGGTGAAGACCA	0.667																																					p.A363A		Atlas-SNP	.											FZD10,NS,carcinoma,0,1	FZD10	95	1	1	Substitution - coding silent(1)	prostate(1)	c.G1089T						PASS	.						55	52	53					12																	130648576		2203	4300	6503	SO:0001819	synonymous_variant	11211	exon1			CCCGGCGGTGAAG	AB027464	CCDS9267.1	12q24.33	2014-01-29	2014-01-29			ENSG00000111432		"GPCR / Class F : Frizzled receptors", "CD molecules"	4039	protein-coding gene	gene with protein product		606147	"frizzled (Drosophila) homolog 10", "frizzled homolog 10 (Drosophila)", "frizzled 10, seven transmembrane spanning receptor", "frizzled family receptor 10"			10448064	Standard	NM_007197		Approved	CD350	uc001uii.3	Q9ULW2		ENST00000229030.4:c.1089G>T	12.37:g.130648576G>T		78	0	0		103	55	0.533981	NM_007197		Silent	SNP	ENST00000229030.4	37	CCDS9267.1	.	.	.	.	.	.	.	.	.	.	G	9.518	1.107438	0.20714	.	.	ENSG00000111432	ENST00000539839	.	.	.	5.1	-2.97	0.05530	.	.	.	.	.	T	0.69214	0.3086	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.73575	-0.3939	5	0.87932	D	0	.	12.6005	0.56494	0.0:0.2627:0.5494:0.1879	.	.	.	.	C	331	.	ENSP00000438460:G331C	G	+	1	0	FZD10	129214529	0.004000	0.15560	0.985000	0.45067	0.997000	0.91878	-1.256000	0.02869	-0.391000	0.07763	0.561000	0.74099	GGT	.	.	none		0.667	FZD10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	130648576	G	T	130648576	2	4	24	1	0	0	0	0	0	0	0	1	6137	1103	39	4		4	FZD10	12	130648576	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	260726	130648576	3203319	423	8640											
C1QTNF9B	387911	hgsc.bcm.edu	37	chr13	24465537	24465537	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cctgcagccacatctcatccCcgagcttcagctgcaggaca	9	7	8	17	1	2	0	2	0	1	0	4	2	3	1	4	1	5	4	4	1	0	1	rs140860568	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:24465537C>T	ENST00000382140.2	-	5	953	c.893G>A	c.(892-894)gGg>gAg	p.G298E	C1QTNF9B-AS1_ENST00000435039.2_RNA|C1QTNF9B-AS1_ENST00000417034.1_RNA|C1QTNF9B_ENST00000382145.1_3'UTR|MIPEP_ENST00000469167.1_5'Flank|C1QTNF9B_ENST00000382137.3_Missense_Mutation_p.G298E|MIPEP_ENST00000382172.3_5'Flank|C1QTNF9B_ENST00000556521.1_5'UTR|C1QTNF9B-AS1_ENST00000382133.4_RNA			B2RNN3	C1T9B_HUMAN	C1q and tumor necrosis factor related protein 9B	298	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.					collagen trimer (GO:0005581)|extracellular vesicular exosome (GO:0070062)				breast(1)|central_nervous_system(1)|large_intestine(3)|lung(1)	6						CATCTCATCCCCGAGCTTCAG	0.512													C|||	50	0.00998403	0.0023	0.0187	5008	,	,		16761	0.0		0.0308	False		,,,				2504	0.0031				p.G298E		Atlas-SNP	.											.	C1QTNF9B	27	.	0			c.G893A						PASS	.	C	GLU/GLY,,	34,4310		6,22,2144	92	91	91		893,,	3.1	1	13	dbSNP_134	91	276,8220		29,218,4001	no	missense,utr-5,utr-5	C1QTNF9B,C1QTNF9B-AS1	NM_001007537.1,NM_001014442.2,NM_001135816.1	98,,	35,240,6145	TT,TC,CC		3.2486,0.7827,2.4143	probably-damaging,,	298/334,,	24465537	310,12530	2172	4248	6420	SO:0001583	missense	387911	exon3			TCATCCCCGAGCT	BC110413	CCDS31947.1	13q12.12	2011-05-08			ENSG00000205863	ENSG00000205863			34072	protein-coding gene	gene with protein product		614148				17544811	Standard	NM_001007537		Approved	CTRP9B	uc010tcv.1	B2RNN3	OTTHUMG00000016570	ENST00000382140.2:c.893G>A	13.37:g.24465537C>T	ENSP00000371575:p.Gly298Glu	102	0	0		213	99	0.464789	NM_001007537	A2A3T6|B9EH31|Q0VGC5|Q5VX65|Q5VX66|Q8IUU4	Missense_Mutation	SNP	ENST00000382140.2	37	CCDS31947.1	31	0.014194139194139194	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	20	0.026385224274406333	c	17.20	3.329762	0.60743	0.007827	0.032486	ENSG00000205863	ENST00000382137;ENST00000382140	D;D	0.82255	-1.59;-1.59	3.96	3.08	0.35506	Tumour necrosis factor-like (2);Complement C1q protein (4);	0.100850	0.64402	D	0.000002	T	0.80401	0.4616	M	0.82716	2.605	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85108	0.0961	10	0.49607	T	0.09	.	13.6179	0.62120	0.0:0.8431:0.1569:0.0	.	298	B2RNN3	C1T9B_HUMAN	E	298	ENSP00000371572:G298E;ENSP00000371575:G298E	ENSP00000371572:G298E	G	-	2	0	C1QTNF9B	23363537	1.000000	0.71417	0.954000	0.39281	0.593000	0.36681	5.940000	0.70187	0.762000	0.33152	0.456000	0.33151	GGG	C|0.980;T|0.020	0.020	strong		0.512	C1QTNF9B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044162.3	NM_001007537		T	24465537	C	T	24465537	3	4	24	1	0	0	0	0	1	0	0	0	1973	623	22	2	111	2	C1QTNF9B	13	24465537	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10		24465537	90704341	424	8641											
ATP12A	479	hgsc.bcm.edu	37	chr13	25272807	25272807	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttcccagctctccatccaCgagatggatgacccccacgg	8	7	8	18	2	1	2	0	1	1	1	4	4	3	3	6	2	1	1	6	2	0	1	rs148844496	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:25272807C>T	ENST00000381946.3	+	12	1691	c.1524C>T	c.(1522-1524)caC>caT	p.H508H	ATP12A_ENST00000218548.6_Silent_p.H514H			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	508					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)		TCTCCATCCACGAGATGGATG	0.517																																					p.H514H	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.C1542T						PASS	.	C	,	0,4406		0,0,2203	56	50	52		1542,1524	-2.1	0	13	dbSNP_134	52	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous,coding-synonymous	ATP12A	NM_001185085.1,NM_001676.5	,	0,6,6497	TT,TC,CC		0.0698,0.0,0.0461	,	514/1046,508/1040	25272807	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	479	exon12			CATCCACGAGATG	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.1524C>T	13.37:g.25272807C>T		33	0	0		43	22	0.511628	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Silent	SNP	ENST00000381946.3	37	CCDS31948.1																																																																																			C|0.999;T|0.001	0.001	strong		0.517	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		T	25272807	C	T	25272807	2	4	24	1	0	0	0	0	0	0	0	1	1122	535	19	1		1	ATP12A	13	25272807	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	807270	25272807	89897071	425	8642											
MTMR6	9107	hgsc.bcm.edu	37	chr13	25831928	25831928	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgatatggcgaagccatccCgagctctccaaaccggagta	11	8	10	12	3	1	1	0	1	1	0	3	4	2	2	4	2	3	2	4	2	4	3	rs186466011	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:25831928C>T	ENST00000381801.5	-	8	1676	c.915G>A	c.(913-915)tcG>tcA	p.S305S	MTMR6_ENST00000482345.1_5'Flank|MTMR6_ENST00000540661.1_Silent_p.S305S	NM_004685.3	NP_004676.3	Q9Y217	MTMR6_HUMAN	myotubularin related protein 6	305	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)		GAAGCCATCCCGAGCTCTCCA	0.383													C|||	2	0.000399361	0.0	0.0014	5008	,	,		16484	0.0		0.001	False		,,,				2504	0.0				p.S305S		Atlas-SNP	.											.	MTMR6	75	.	0			c.G915A						PASS	.	C		0,4406		0,0,2203	70	75	74		915	-5.6	0.3	13		74	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MTMR6	NM_004685.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		305/622	25831928	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9107	exon8			CCATCCCGAGCTC	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.915G>A	13.37:g.25831928C>T		56	0	0		42	23	0.547619	NM_004685	B2RBB5|B3KSB4|Q5JRG6|Q86TB7|Q86YH4|Q96P80	Silent	SNP	ENST00000381801.5	37	CCDS9313.1																																																																																			C|1.000;T|0.000	0.000	strong		0.383	MTMR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044225.1	NM_004685		T	25831928	C	T	25831928	2	4	24	1	0	0	0	0	0	0	0	1	9956	639	23	1		1	MTMR6	13	25831928	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	559121	25831928	89337950	426	8643											
FLT3	2322	hgsc.bcm.edu	37	chr13	28624294	28624294	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcacagcaccttatgtccGtcccaaataattcatgaagc	12	10	7	12	1	1	1	1	1	0	0	3	1	3	1	3	1	2	2	3	1	4	3	rs1933437	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:28624294G>A	ENST00000241453.7	-	6	761	c.680C>T	c.(679-681)aCg>aTg	p.T227M	FLT3_ENST00000380982.4_Missense_Mutation_p.T227M|FLT3_ENST00000537084.1_Missense_Mutation_p.T227M	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	227			T -> M (in dbSNP:rs1933437). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:8394751, ECO:0000269|Ref.4}.		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)	CCTTATGTCCGTCCCAAATAA	0.398			"Mis, O"		"AML, ALL"								G|||	2798	0.558706	0.2844	0.6066	5008	,	,		21258	0.7688		0.5805	False		,,,				2504	0.6564				p.T227M		Atlas-SNP	.		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	.	FLT3	15525	.	0			c.C680T						PASS	.	G	MET/THR	1513,2893	481.0+/-359.0	264,985,954	162	136	145		680	3.8	0.6	13	dbSNP_92	145	5288,3312	646.4+/-400.3	1636,2016,648	yes	missense	FLT3	NM_004119.2	81	1900,3001,1602	AA,AG,GG		38.5116,34.3395,47.7087	probably-damaging	227/994	28624294	6801,6205	2203	4300	6503	SO:0001583	missense	2322	exon6			ATGTCCGTCCCAA	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.680C>T	13.37:g.28624294G>A	ENSP00000241453:p.Thr227Met	199	1	0.00502513		160	160	1	NM_004119	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Missense_Mutation	SNP	ENST00000241453.7	37	CCDS31953.1	1241	0.5682234432234432	150	0.3048780487804878	220	0.6077348066298343	431	0.7534965034965035	440	0.5804749340369393	G	12.45	1.941805	0.34283	0.343395	0.614884	ENSG00000122025	ENST00000241453;ENST00000380982;ENST00000537084	T;T;T	0.79749	-1.23;-1.3;-1.03	5.63	3.85	0.44370	.	0.166014	0.42821	D	0.000648	T	0.00012	0.0000	L	0.29908	0.895	0.32868	P	0.491131	D;D	0.76494	0.999;0.999	P;P	0.60789	0.879;0.743	T	0.48547	-0.9026	9	0.41790	T	0.15	.	11.1573	0.48495	0.0:0.1387:0.7168:0.1445	rs1933437;rs52828701;rs57444997;rs1933437	227;227	P36888-2;P36888	.;FLT3_HUMAN	M	227	ENSP00000241453:T227M;ENSP00000370369:T227M;ENSP00000438139:T227M	ENSP00000241453:T227M	T	-	2	0	FLT3	27522294	1.000000	0.71417	0.599000	0.28851	0.006000	0.05464	3.696000	0.54757	0.687000	0.31509	-0.311000	0.09066	ACG	G|0.465;A|0.535	0.535	strong		0.398	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2			A	28624294	G	A	28624294	3	1	24	1	0	0	0	0	1	0	0	0	5950	1145	40	1	2377	1	FLT3	13	28624294	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	2792366	28624294	86545584	427	8644											
USPL1	10208	hgsc.bcm.edu	37	chr13	31231778	31231778	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaaagactaatgaccaacacGctctcagtaatgagaaacca	19	6	6	10	1	1	3	1	2	1	2	2	4	1	3	2	0	2	2	2	0	6	2	rs17609459	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:31231778G>C	ENST00000255304.4	+	9	1906	c.1564G>C	c.(1564-1566)Gct>Cct	p.A522P		NM_005800.4	NP_005791.3	Q5W0Q7	USPL1_HUMAN	ubiquitin specific peptidase like 1	522			A -> P (in dbSNP:rs17609459).		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)		TGACCAACACGCTCTCAGTAA	0.403													G|||	62	0.0123802	0.0204	0.013	5008	,	,		20603	0.0		0.0199	False		,,,				2504	0.0061				p.A522P	Ovarian(60;318 1180 1554 28110 31601)	Atlas-SNP	.											.	USPL1	82	.	0			c.G1564C						PASS	.	G	PRO/ALA	101,4305	80.4+/-118.8	1,99,2103	135	131	133		1564	3.1	0	13	dbSNP_123	133	172,8428	79.5+/-142.1	4,164,4132	yes	missense	USPL1	NM_005800.4	27	5,263,6235	CC,CG,GG		2.0,2.2923,2.099	benign	522/1093	31231778	273,12733	2203	4300	6503	SO:0001583	missense	10208	exon9			CAACACGCTCTCA	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.1564G>C	13.37:g.31231778G>C	ENSP00000255304:p.Ala522Pro	97	0	0		78	34	0.435897	NM_005800	Q14109|Q6AI45|Q8IY30|Q8IYE8	Missense_Mutation	SNP	ENST00000255304.4	37	CCDS9336.1	36	0.016483516483516484	13	0.026422764227642278	7	0.019337016574585635	0	0.0	16	0.021108179419525065	G	13.09	2.132849	0.37630	0.022923	0.02	ENSG00000132952	ENST00000255304	T	0.08102	3.13	5.79	3.06	0.35304	.	0.937697	0.09093	N	0.849598	T	0.03053	0.0090	L	0.54323	1.7	0.09310	N	1	B	0.24186	0.099	B	0.23852	0.049	T	0.40924	-0.9537	10	0.22109	T	0.4	-4.288	9.692	0.40134	0.0:0.1844:0.3512:0.4644	rs17609459;rs52830887;rs56453321;rs17609459	522	Q5W0Q7	USPL1_HUMAN	P	522	ENSP00000255304:A522P	ENSP00000255304:A522P	A	+	1	0	USPL1	30129778	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.189000	0.09629	0.341000	0.23771	-0.169000	0.13324	GCT	C|0.020;G|0.980	0.020	strong		0.403	USPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044369.1	NM_005800		C	31231778	G	C	31231778	3	2	24	1	0	0	0	0	1	0	0	0	17107	1087	38	4	1594	4	USPL1	13	31231778	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	2607484	31231778	83938100	428	8645											
POSTN	10631	hgsc.bcm.edu	37	chr13	38156538	38156538	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gactctgagctgtttgcctcCgatggtttccagtatttgcc	5	15	10	11	1	1	1	0	1	1	0	3	3	3	1	4	1	3	4	4	1	1	4	rs117103342	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:38156538C>T	ENST00000379747.4	-	10	1474	c.1357G>A	c.(1357-1359)Gga>Aga	p.G453R	POSTN_ENST00000379749.4_Missense_Mutation_p.G453R|POSTN_ENST00000541179.1_Missense_Mutation_p.G453R|POSTN_ENST00000541481.1_Missense_Mutation_p.G453R|POSTN_ENST00000379743.4_Missense_Mutation_p.G453R|POSTN_ENST00000379742.4_Missense_Mutation_p.G453R	NM_006475.2	NP_006466.2	Q15063	POSTN_HUMAN	periostin, osteoblast specific factor	453	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)		TGTTTGCCTCCGATGGTTTCC	0.373													C|||	17	0.00339457	0.0	0.0101	5008	,	,		17409	0.0		0.0089	False		,,,				2504	0.001				p.G453R		Atlas-SNP	.											.	POSTN	161	.	0			c.G1357A						PASS	.	C	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	4,4402	9.9+/-24.2	0,4,2199	155	149	151		1357,1357,1357,1357	6.1	1	13	dbSNP_132	151	77,8523	45.8+/-104.6	1,75,4224	yes	missense,missense,missense,missense	POSTN	NM_001135934.1,NM_001135935.1,NM_001135936.1,NM_006475.2	125,125,125,125	1,79,6423	TT,TC,CC		0.8953,0.0908,0.6228	probably-damaging,probably-damaging,probably-damaging,probably-damaging	453/780,453/782,453/752,453/837	38156538	81,12925	2203	4300	6503	SO:0001583	missense	10631	exon10			TGCCTCCGATGGT	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.1357G>A	13.37:g.38156538C>T	ENSP00000369071:p.Gly453Arg	92	0	0		117	56	0.478632	NM_006475	B1ALD8|C0IMJ1|C0IMJ2|C0IMJ4|D2KRH7|F5H628|Q15064|Q29XZ0|Q3KPJ5|Q5VSY5|Q8IZF9	Missense_Mutation	SNP	ENST00000379747.4	37	CCDS9364.1	11	0.005036630036630037	0	0.0	5	0.013812154696132596	0	0.0	6	0.0079155672823219	C	23.8	4.459234	0.84317	9.08E-4	0.008953	ENSG00000133110	ENST00000541179;ENST00000379749;ENST00000379747;ENST00000379743;ENST00000379742;ENST00000541481	T;T;T;T;T;T	0.72615	-0.67;-0.67;-0.67;-0.67;-0.67;-0.67	6.07	6.07	0.98685	FAS1 domain (5);	0.154285	0.56097	D	0.000022	T	0.79215	0.4408	M	0.61703	1.905	0.47476	D	0.999438	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;0.999;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;0.995;1.0;0.999;0.951;0.995	T	0.78788	-0.2067	10	0.42905	T	0.14	-22.8572	20.6593	0.99626	0.0:1.0:0.0:0.0	.	453;453;453;453;453;453;453	C0IMJ4;F5H628;B1ALD8;Q15063-3;Q15063-4;Q15063-2;Q15063	.;.;.;.;.;.;POSTN_HUMAN	R	453	ENSP00000437959:G453R;ENSP00000369073:G453R;ENSP00000369071:G453R;ENSP00000369067:G453R;ENSP00000369066:G453R;ENSP00000437953:G453R	ENSP00000369066:G453R	G	-	1	0	POSTN	37054538	1.000000	0.71417	1.000000	0.80357	0.823000	0.46562	5.590000	0.67530	2.885000	0.99019	0.655000	0.94253	GGA	C|0.994;T|0.006	0.006	strong		0.373	POSTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044566.2	NM_006475		T	38156538	C	T	38156538	3	4	24	1	0	0	0	0	1	0	0	0	12268	661	23	1	1209	1	POSTN	13	38156538	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	6924760	38156538	77013340	429	8646											
TRPC4	7223	hgsc.bcm.edu	37	chr13	38237564	38237564	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagacttacgttgaaaatgcAttattctgcttttcacatct	11	17	5	8	1	3	2	1	1	2	1	3	2	3	2	0	0	3	3	0	0	5	7	rs75514550	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:38237564A>G	ENST00000379705.3	-	6	2534	c.1677T>C	c.(1675-1677)aaT>aaC	p.N559N	TRPC4_ENST00000379679.1_Silent_p.N386N|TRPC4_ENST00000338947.5_Silent_p.N386N|TRPC4_ENST00000379673.2_Silent_p.N559N|TRPC4_ENST00000358477.2_Silent_p.N559N|TRPC4_ENST00000355779.2_Silent_p.N559N|TRPC4_ENST00000447043.1_Silent_p.N559N|TRPC4_ENST00000494529.1_Intron|TRPC4_ENST00000426868.2_Intron|TRPC4_ENST00000379681.3_Silent_p.N559N			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	559					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)		TTGAAAATGCATTATTCTGCT	0.348													A|||	34	0.00678914	0.0008	0.0187	5008	,	,		19000	0.0		0.0179	False		,,,				2504	0.002				p.N559N		Atlas-SNP	.											.	TRPC4	389	.	0			c.T1677C						PASS	.	A	,,,,,	11,4395	20.2+/-43.8	0,11,2192	79	74	75		1677,1677,1677,1158,1677,1677	2.2	1	13	dbSNP_132	75	165,8435	77.8+/-140.4	2,161,4137	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRPC4	NM_001135955.1,NM_001135956.1,NM_001135957.1,NM_001135958.1,NM_003306.1,NM_016179.2	,,,,,	2,172,6329	GG,GA,AA		1.9186,0.2497,1.3532	,,,,,	559/894,559/829,559/837,386/805,559/983,559/978	38237564	176,12830	2203	4300	6503	SO:0001819	synonymous_variant	7223	exon6			AAATGCATTATTC	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.1677T>C	13.37:g.38237564A>G		168	0	0		148	91	0.614865	NM_003306	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Silent	SNP	ENST00000379705.3	37	CCDS9365.1																																																																																			A|0.988;G|0.012	0.012	strong		0.348	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306		G	38237564	A	G	38237564	2	3	24	1	0	0	0	0	0	0	0	1	16595	214	8	3		3	TRPC4	13	38237564	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	81026	38237564	76932314	430	8647											
KBTBD6	89890	hgsc.bcm.edu	37	chr13	41705110	41705110	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgcaggcttcctgaaagtcaTtgcgcttcagagaaacgcac	11	8	10	12	3	2	2	2	1	0	1	3	3	3	2	1	1	2	4	1	1	2	3	rs200203929		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:41705110T>C	ENST00000379485.1	-	1	1772	c.1538A>G	c.(1537-1539)aAt>aGt	p.N513S	KBTBD6_ENST00000499385.2_Missense_Mutation_p.N447S	NM_152903.4	NP_690867.3	Q86V97	KBTB6_HUMAN	kelch repeat and BTB (POZ) domain containing 6	513										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)		CTGAAAGTCATTGCGCTTCAG	0.448																																					p.N513S		Atlas-SNP	.											.	KBTBD6	83	.	0			c.A1538G						PASS	.						87	84	85					13																	41705110		2203	4300	6503	SO:0001583	missense	89890	exon1			AAGTCATTGCGCT	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.1538A>G	13.37:g.41705110T>C	ENSP00000368799:p.Asn513Ser	117	0	0		107	52	0.485981	NM_152903	Q5T6Y8|Q8N8L0|Q8NDM5|Q96MP6	Missense_Mutation	SNP	ENST00000379485.1	37	CCDS9376.1	.	.	.	.	.	.	.	.	.	.	t	0.006	-2.062628	0.00386	.	.	ENSG00000165572	ENST00000379485;ENST00000499385	T;T	0.64618	-0.11;-0.11	3.8	1.68	0.24146	Kelch-type beta propeller (1);	0.396703	0.27349	N	0.019776	T	0.25457	0.0619	N	0.01168	-0.975	0.23023	N	0.998416	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.20505	-1.0273	10	0.15066	T	0.55	.	5.5596	0.17135	0.0:0.6244:0.0:0.3756	.	447;513	F5GZN7;Q86V97	.;KBTB6_HUMAN	S	513;447	ENSP00000368799:N513S;ENSP00000444326:N447S	ENSP00000368799:N513S	N	-	2	0	KBTBD6	40603110	0.993000	0.37304	0.379000	0.26080	0.527000	0.34593	0.732000	0.26072	0.208000	0.20626	-0.464000	0.05259	AAT	T|0.999;C|0.001	0.001	weak		0.448	KBTBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044657.1	NM_152903		C	41705110	T	C	41705110	3	2	24	1	0	0	0	0	1	0	0	0	8006	1493	52	3	490	3	KBTBD6	13	41705110	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	3467546	41705110	73464768	431	8648											
AKAP11	11215	hgsc.bcm.edu	37	chr13	42875258	42875258	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaagtgcccttctcccataTcatatttcatctactgcatg	9	14	6	12	0	4	0	2	0	2	0	5	1	4	1	2	1	3	1	2	1	4	5	rs61741710	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:42875258T>C	ENST00000025301.2	+	8	2551	c.2376T>C	c.(2374-2376)taT>taC	p.Y792Y		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	792					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)		TTCTCCCATATCATATTTCAT	0.418													T|||	55	0.0109824	0.003	0.0029	5008	,	,		19247	0.001		0.0099	False		,,,				2504	0.0389				p.Y792Y		Atlas-SNP	.											.	AKAP11	146	.	0			c.T2376C						PASS	.	T		19,4387	26.2+/-53.5	0,19,2184	145	129	135		2376	0.9	0.3	13	dbSNP_129	135	84,8516	48.5+/-108.0	0,84,4216	no	coding-synonymous	AKAP11	NM_016248.3		0,103,6400	CC,CT,TT		0.9767,0.4312,0.7919		792/1902	42875258	103,12903	2203	4300	6503	SO:0001819	synonymous_variant	11215	exon8			CCCATATCATATT	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.2376T>C	13.37:g.42875258T>C		106	0	0		117	58	0.495726	NM_016248	O75124|Q9NUK7	Silent	SNP	ENST00000025301.2	37	CCDS9383.1																																																																																			T|0.992;C|0.008	0.008	strong		0.418	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248		C	42875258	T	C	42875258	2	2	24	1	0	0	0	0	0	0	0	1	447	1442	50	3		3	AKAP11	13	42875258	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	1170148	42875258	72294620	432	8649											
AKAP11	11215	hgsc.bcm.edu	37	chr13	42875683	42875683	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgcagtgaagctagtagcaAtaaggacatgtttgctgacc	13	10	11	7	0	0	2	0	2	0	0	0	3	0	3	1	1	4	6	1	1	5	4	rs41288309	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:42875683A>G	ENST00000025301.2	+	8	2976	c.2801A>G	c.(2800-2802)aAt>aGt	p.N934S		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	934					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)		GCTAGTAGCAATAAGGACATG	0.358													A|||	50	0.00998403	0.0	0.0014	5008	,	,		19449	0.001		0.0099	False		,,,				2504	0.0389				p.N934S		Atlas-SNP	.											.	AKAP11	146	.	0			c.A2801G						PASS	.	A	SER/ASN	5,4401	8.1+/-20.4	0,5,2198	65	67	67		2801	-2.7	0	13	dbSNP_127	67	84,8516	48.1+/-107.5	0,84,4216	yes	missense	AKAP11	NM_016248.3	46	0,89,6414	GG,GA,AA		0.9767,0.1135,0.6843	benign	934/1902	42875683	89,12917	2203	4300	6503	SO:0001583	missense	11215	exon8			GTAGCAATAAGGA	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.2801A>G	13.37:g.42875683A>G	ENSP00000025301:p.Asn934Ser	83	0	0		96	51	0.53125	NM_016248	O75124|Q9NUK7	Missense_Mutation	SNP	ENST00000025301.2	37	CCDS9383.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	A	2.918	-0.223797	0.06061	0.001135	0.009767	ENSG00000023516	ENST00000025301	T	0.12774	2.65	6.03	-2.7	0.06004	.	1.233830	0.05477	N	0.554106	T	0.04272	0.0118	N	0.04880	-0.145	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.42292	-0.9460	10	0.13108	T	0.6	.	10.713	0.45995	0.4485:0.1412:0.4102:0.0	rs41288309;rs61756565	934	Q9UKA4	AKA11_HUMAN	S	934	ENSP00000025301:N934S	ENSP00000025301:N934S	N	+	2	0	AKAP11	41773683	0.000000	0.05858	0.039000	0.18376	0.069000	0.16628	-0.237000	0.08990	-0.478000	0.06823	-0.250000	0.11733	AAT	A|0.993;G|0.007	0.007	strong		0.358	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248		G	42875683	A	G	42875683	3	3	24	1	0	0	0	0	1	0	0	0	447	101	4	3	2823	3	AKAP11	13	42875683	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	425	42875683	72294195	433	8650											
COG3	83548	hgsc.bcm.edu	37	chr13	46099171	46099171	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agtatactctctcacagcagCcttgggcacaaccaggtatt	11	10	8	12	0	2	0	1	0	1	0	3	0	2	0	2	2	4	4	2	2	4	5	rs144497765		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:46099171C>T	ENST00000349995.5	+	20	2327	c.2215C>T	c.(2215-2217)Cct>Tct	p.P739S		NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	739					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)		CTCACAGCAGCCTTGGGCACA	0.388													C|||	1	0.000199681	0.0	0.0	5008	,	,		18679	0.0		0.001	False		,,,				2504	0.0				p.P739S	Ovarian(150;1048 1859 18083 21577 42700)	Atlas-SNP	.											.	COG3	52	.	0			c.C2215T						PASS	.	C	SER/PRO	2,4404	4.2+/-10.8	0,2,2201	93	87	89		2215	5.2	1	13	dbSNP_134	89	9,8591	7.1+/-27.0	0,9,4291	yes	missense	COG3	NM_031431.3	74	0,11,6492	TT,TC,CC		0.1047,0.0454,0.0846	benign	739/829	46099171	11,12995	2203	4300	6503	SO:0001583	missense	83548	exon20			CAGCAGCCTTGGG	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.2215C>T	13.37:g.46099171C>T	ENSP00000258654:p.Pro739Ser	114	0	0		128	66	0.515625	NM_031431	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Missense_Mutation	SNP	ENST00000349995.5	37	CCDS9398.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	15.16	2.750401	0.49257	4.54E-4	0.001047	ENSG00000136152	ENST00000349995	T	0.54071	0.59	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.62720	0.2451	M	0.64997	1.995	0.80722	D	1	B;D	0.60575	0.264;0.988	B;P	0.54815	0.074;0.761	T	0.58352	-0.7651	10	0.20046	T	0.44	-11.7744	17.7148	0.88333	0.0:1.0:0.0:0.0	.	576;739	B4E2F3;Q96JB2	.;COG3_HUMAN	S	739	ENSP00000258654:P739S	ENSP00000258654:P739S	P	+	1	0	COG3	44997172	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.666000	0.83877	2.426000	0.82243	0.655000	0.94253	CCT	C|0.999;T|0.001	0.001	strong		0.388	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2			T	46099171	C	T	46099171	3	4	24	1	0	0	0	0	1	0	0	0	3661	739	26	2	2293	2	COG3	13	46099171	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	3223488	46099171	69070707	434	8651											
UGGT2	55757	hgsc.bcm.edu	37	chr13	96506633	96506633	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttttccagaaacgatatcCatccatttccctgcggctat	9	14	6	12	2	0	1	0	0	0	1	4	2	4	1	4	1	2	2	4	1	3	5	rs145358686	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr13:96506633C>T	ENST00000376747.3	-	35	4175	c.4105G>A	c.(4105-4107)Gga>Aga	p.G1369R		NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	1369	Glucosyltransferase.				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						AAACGATATCCATCCATTTCC	0.388													C|||	10	0.00199681	0.0008	0.0029	5008	,	,		17239	0.0		0.006	False		,,,				2504	0.001				p.G1369R		Atlas-SNP	.											.	UGGT2	127	.	0			c.G4105A						PASS	.	C	ARG/GLY	3,4403	6.2+/-15.9	0,3,2200	111	106	108		4105	5.4	1	13	dbSNP_134	108	38,8562	25.7+/-73.6	0,38,4262	yes	missense	UGGT2	NM_020121.3	125	0,41,6462	TT,TC,CC		0.4419,0.0681,0.3152	probably-damaging	1369/1517	96506633	41,12965	2203	4300	6503	SO:0001583	missense	55757	exon35			GATATCCATCCAT	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.4105G>A	13.37:g.96506633C>T	ENSP00000365938:p.Gly1369Arg	175	0	0		156	78	0.5	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	37	CCDS9480.1	6	0.0027472527472527475	1	0.0020325203252032522	0	0.0	0	0.0	5	0.006596306068601583	C	31	5.075920	0.94000	6.81E-4	0.004419	ENSG00000102595	ENST00000376747	T	0.42513	0.97	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.70159	0.3192	H	0.95294	3.65	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82500	-0.0426	10	0.87932	D	0	-18.4057	19.0987	0.93265	0.0:1.0:0.0:0.0	.	1369	Q9NYU1	UGGG2_HUMAN	R	1369	ENSP00000365938:G1369R	ENSP00000365938:G1369R	G	-	1	0	UGGT2	95304634	1.000000	0.71417	0.998000	0.56505	0.956000	0.61745	7.487000	0.81328	2.512000	0.84698	0.591000	0.81541	GGA	C|0.997;T|0.003	0.003	strong		0.388	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121		T	96506633	C	T	96506633	3	4	24	1	0	0	0	0	1	0	0	0	16957	603	21	2	465	2	UGGT2	13	96506633	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	50407462	96506633	18663245	435	8652											
PARP2	10038	hgsc.bcm.edu	37	chr14	20822331	20822331	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcgggtacaggagttaataAagttgatctgtaatgttcag	12	14	11	4	1	2	1	1	1	1	0	3	2	2	2	0	2	1	5	0	2	5	7			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:20822331A>C	ENST00000250416.5	+	8	754	c.727A>C	c.(727-729)Aag>Cag	p.K243Q	PARP2_ENST00000429687.3_Missense_Mutation_p.K230Q|PARP2_ENST00000527915.1_Missense_Mutation_p.K243Q	NM_001042618.1|NM_005484.3	NP_001036083.1|NP_005475.2	Q9UGN5	PARP2_HUMAN	poly (ADP-ribose) polymerase 2	243	PARP alpha-helical. {ECO:0000255|PROSITE- ProRule:PRU00398}.				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)		GGAGTTAATAAAGTTGATCTG	0.388								Poly(ADP-ribose) polymerase (PARP) enzymes that bind to DNA																													p.K243Q		Atlas-SNP	.											PARP2_ENST00000250416,NS,carcinoma,0,2	PARP2	92	2	0			c.A727C						PASS	.						130	125	127					14																	20822331		1866	4111	5977	SO:0001583	missense	10038	exon8			TTAATAAAGTTGA	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.727A>C	14.37:g.20822331A>C	ENSP00000250416:p.Lys243Gln	132	0	0		161	70	0.434783	NM_005484	Q8TEU4|Q9NUV2|Q9UMR4|Q9Y6C8	Missense_Mutation	SNP	ENST00000250416.5	37	CCDS41910.1	.	.	.	.	.	.	.	.	.	.	A	9.194	1.026692	0.19512	.	.	ENSG00000129484	ENST00000429687;ENST00000250416;ENST00000527915	T;T;T	0.15718	2.4;2.4;2.4	4.97	1.27	0.21489	Poly(ADP-ribose) polymerase, regulatory domain (4);	0.333967	0.32548	N	0.005946	T	0.09818	0.0241	N	0.25890	0.77	0.33351	D	0.571125	B;B	0.09022	0.0;0.002	B;B	0.04013	0.001;0.001	T	0.08493	-1.0719	10	0.41790	T	0.15	-3.5913	5.4142	0.16363	0.3821:0.4338:0.184:0.0	.	230;243	Q9UGN5-2;Q9UGN5	.;PARP2_HUMAN	Q	230;243;243	ENSP00000392972:K230Q;ENSP00000250416:K243Q;ENSP00000432283:K243Q	ENSP00000250416:K243Q	K	+	1	0	PARP2	19892171	0.812000	0.29077	0.992000	0.48379	0.704000	0.40688	0.898000	0.28404	0.424000	0.26061	0.477000	0.44152	AAG	.	.	none		0.388	PARP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000387847.2			C	20822331	A	C	20822331	3	2	24	1	0	0	0	0	1	0	0	0	11470	15	1	5	757	5	PARP2	14	20822331	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10		20822331	86527209	436	8653											
ANG	283	hgsc.bcm.edu	37	chr14	21161931	21161931	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcaaagacatcaacacatttAttcatggcaacaagcgcagc	16	7	7	11	1	2	1	2	0	0	1	2	1	2	1	0	1	4	3	0	1	5	3	rs121909541		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:21161931A>G	ENST00000336811.6	+	2	808	c.208A>G	c.(208-210)Att>Gtt	p.I70V	RP11-903H12.3_ENST00000554286.1_RNA|RNASE4_ENST00000555597.1_Intron|ANG_ENST00000554073.1_Intron|RNASE4_ENST00000397995.2_Intron|AL163636.6_ENST00000553909.1_Intron|RNASE4_ENST00000304704.4_Intron|ANG_ENST00000397990.4_Missense_Mutation_p.I70V|RNASE4_ENST00000555835.1_Intron	NM_001145.4	NP_001136.1	P03950	ANGI_HUMAN	angiogenin, ribonuclease, RNase A family, 5	70			I -> V (in some ALS9 patients; pathogenicity uncertain; reduced ribonucleolytic activity; moderate reduction of thermal stability). {ECO:0000269|PubMed:16501576, ECO:0000269|PubMed:18087731}.		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)		CAACACATTTATTCATGGCAA	0.478													A|||	1	0.000199681	0.0	0.0	5008	,	,		21764	0.0		0.001	False		,,,				2504	0.0				p.I70V		Atlas-SNP	.											.	ANG	8	.	0			c.A208G	GRCh37	CM060832	ANG	M	rs121909541	PASS	.	A	VAL/ILE,VAL/ILE,,	2,4404	4.2+/-10.8	0,2,2201	118	100	106	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	208,208,,	-3.4	0.8	14	dbSNP_133	106	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense,intron,intron	ANG,RNASE4	NM_001097577.2,NM_001145.4,NM_002937.3,NM_194431.1	29,29,,	0,7,6496	GG,GA,AA		0.0581,0.0454,0.0538	benign,benign,,	70/148,70/148,,	21161931	7,12999	2203	4300	6503	SO:0001583	missense	283	exon2			ACATTTATTCATG		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.208A>G	14.37:g.21161931A>G	ENSP00000336762:p.Ile70Val	172	0	0		163	85	0.521472	NM_001097577	Q05CV1|Q53X86|Q6P5T2|Q8WXE7	Missense_Mutation	SNP	ENST00000336811.6	37	CCDS9554.1	.	.	.	.	.	.	.	.	.	.	A	1.031	-0.681810	0.03353	4.54E-4	5.81E-4	ENSG00000214274	ENST00000336811;ENST00000397990	D;D	0.95788	-3.81;-3.81	4.73	-3.36	0.04913	Ribonuclease A, domain (4);	0.109560	0.31392	N	0.007721	D	0.88347	0.6412	N	0.25332	0.735	0.58432	A	0.999999	B	0.29508	0.246	B	0.30646	0.118	T	0.78914	-0.2016	9	0.15066	T	0.55	.	11.1811	0.48629	0.3918:0.0:0.6082:0.0	.	70	P03950	ANGI_HUMAN	V	70	ENSP00000336762:I70V;ENSP00000381077:I70V	ENSP00000336762:I70V	I	+	1	0	ANG	20231771	0.994000	0.37717	0.846000	0.33378	0.093000	0.18481	0.112000	0.15479	-0.882000	0.03987	-1.231000	0.01572	ATT	A|0.999;G|0.001	0.001	strong		0.478	ANG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073731.3	NM_001097577		G	21161931	A	G	21161931	3	3	24	1	0	0	0	0	1	0	0	0	607	449	16	3	210	3	ANG	14	21161931	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	339600	21161931	86187609	437	8654											
RNASE1	6035	hgsc.bcm.edu	37	chr14	21269811	21269811	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actggcacatatgggctcccTtcacaggccacaatgatgtg	10	9	10	12	0	1	1	1	1	0	0	2	1	2	1	2	3	0	2	2	3	2	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:21269811T>A	ENST00000397967.4	-	2	923	c.417A>T	c.(415-417)gaA>gaT	p.E139D	RNASE1_ENST00000555698.1_Missense_Mutation_p.E99D|RNASE1_ENST00000340900.3_Missense_Mutation_p.E139D|RNASE1_ENST00000397970.4_Missense_Mutation_p.E139D|RNASE1_ENST00000412779.2_Missense_Mutation_p.E139D	NM_002933.4	NP_002924.1	P07998	RNAS1_HUMAN	ribonuclease, RNase A family, 1 (pancreatic)	139					RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	extracellular vesicular exosome (GO:0070062)	nucleic acid binding (GO:0003676)|pancreatic ribonuclease activity (GO:0004522)			central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(1)	5	all_cancers(95;0.00671)	all_lung(585;0.235)	Epithelial(56;9.21e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0126)	Guanidine(DB00536)|L-Aspartic Acid(DB00128)	ATGGGCTCCCTTCACAGGCCA	0.567																																					p.E139D		Atlas-SNP	.											.	RNASE1	14	.	0			c.A417T						PASS	.						151	132	138					14																	21269811		2203	4300	6503	SO:0001583	missense	6035	exon3			GCTCCCTTCACAG	BC005324	CCDS9559.1	14q11.2	2014-03-13			ENSG00000129538	ENSG00000129538	3.1.27.5	"Ribonucleases, RNase A"	10044	protein-coding gene	gene with protein product		180440		RNS1		8588814	Standard	NM_002933		Approved		uc001vyi.3	P07998	OTTHUMG00000029603	ENST00000397967.4:c.417A>T	14.37:g.21269811T>A	ENSP00000381057:p.Glu139Asp	213	0	0		194	105	0.541237	NM_198235	B2R589|D3DS06|Q16830|Q16869|Q1KHR2|Q6ICS5|Q9UCB4|Q9UCB5	Missense_Mutation	SNP	ENST00000397967.4	37	CCDS9559.1	.	.	.	.	.	.	.	.	.	.	T	12.24	1.877944	0.33162	.	.	ENSG00000129538	ENST00000397967;ENST00000340900;ENST00000412779;ENST00000555698;ENST00000397970	T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88	5.21	1.28	0.21552	Ribonuclease A, domain (4);	0.527449	0.18611	N	0.136179	T	0.31888	0.0811	L	0.50333	1.59	0.30340	N	0.785825	B	0.02656	0.0	B	0.04013	0.001	T	0.21586	-1.0241	10	0.51188	T	0.08	-29.0622	5.056	0.14533	0.0:0.4831:0.3303:0.1866	.	139	P07998	RNAS1_HUMAN	D	139;139;139;99;139	ENSP00000381057:E139D;ENSP00000344193:E139D;ENSP00000399493:E139D;ENSP00000451058:E99D;ENSP00000381060:E139D	ENSP00000344193:E139D	E	-	3	2	RNASE1	20339651	0.268000	0.24133	0.971000	0.41717	0.601000	0.36947	-0.503000	0.06383	0.056000	0.16144	-0.248000	0.11899	GAA	.	.	none		0.567	RNASE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073791.3			A	21269811	T	A	21269811	3	1	24	1	0	0	0	0	1	0	0	0	13414	1606	56	5	57	5	RNASE1	14	21269811	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	107880	21269811	86079729	438	8655											
RNASE3	6037	hgsc.bcm.edu	37	chr14	21359987	21359987	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	agcacatcagtctgaaccccCctcgatgcaccattgcaatg	11	8	7	15	1	2	1	1	1	1	0	3	2	2	1	4	0	4	3	4	0	2	1	rs202232277		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:21359987C>G	ENST00000304639.3	+	2	200	c.142C>G	c.(142-144)Cct>Gct	p.P48A		NM_002935.2	NP_002926.2	P12724	ECP_HUMAN	ribonuclease, RNase A family, 3	48	Required for nearly all of the bactericidal activity; partially involved in LPS-binding and bacterial membrane depolarization.				antibacterial humoral response (GO:0019731)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	endonuclease activity (GO:0004519)|nucleic acid binding (GO:0003676)|ribonuclease activity (GO:0004540)			endometrium(1)|large_intestine(1)|lung(6)|ovary(1)	9	all_cancers(95;0.00453)		OV - Ovarian serous cystadenocarcinoma(11;6.3e-09)|Epithelial(56;1.42e-07)|all cancers(55;5.48e-07)	GBM - Glioblastoma multiforme(265;0.0187)	Pranlukast(DB01411)	TCTGAACCCCCCTCGATGCAC	0.478																																					p.P48A		Atlas-SNP	.											.	RNASE3	24	.	0			c.C142G						PASS	.	C	ALA/PRO	0,4382		0,0,2191	111	117	115		142	-4	0	14		115	1,8599	1.2+/-3.3	0,1,4299	yes	missense	RNASE3	NM_002935.2	27	0,1,6490	GG,GC,CC		0.0116,0.0,0.0077	benign	48/161	21359987	1,12981	2191	4300	6491	SO:0001583	missense	6037	exon2			AACCCCCCTCGAT	X55990	CCDS9560.1	14q11.2	2014-03-13	2010-05-07		ENSG00000169397	ENSG00000169397	3.1.27.-	"Ribonucleases, RNase A"	10046	protein-coding gene	gene with protein product	"eosinophil cationic protein"	131398		RNS3		1577491	Standard	NM_002935		Approved	ECP	uc001vyj.3	P12724	OTTHUMG00000029604	ENST00000304639.3:c.142C>G	14.37:g.21359987C>G	ENSP00000302324:p.Pro48Ala	147	0	0		132	64	0.484848	NM_002935	Q4VBC1|Q8WTP7|Q8WZ62|Q9GZN9	Missense_Mutation	SNP	ENST00000304639.3	37	CCDS9560.1	.	.	.	.	.	.	.	.	.	.	c	0.010	-1.759799	0.00657	0.0	1.16E-4	ENSG00000169397	ENST00000304639	T	0.72051	-0.62	2.56	-3.95	0.04118	Ribonuclease A, domain (4);	1.415800	0.04852	U	0.442561	T	0.55401	0.1918	L	0.53249	1.67	0.09310	N	1	B	0.22983	0.078	B	0.17433	0.018	T	0.30621	-0.9972	10	0.09590	T	0.72	.	1.8936	0.03253	0.4903:0.2296:0.1619:0.1183	.	48	P12724	ECP_HUMAN	A	48	ENSP00000302324:P48A	ENSP00000302324:P48A	P	+	1	0	RNASE3	20429827	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.611000	0.00110	-0.998000	0.03446	-0.415000	0.06103	CCT	C|0.999;G|0.001	0.001	weak		0.478	RNASE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073795.2	NM_002935		G	21359987	C	G	21359987	3	3	24	1	0	0	0	0	1	0	0	0	13420	623	22	4	144	4	RNASE3	14	21359987	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	90176	21359987	85989553	439	8656											
OR10G3	26533	hgsc.bcm.edu	37	chr14	22038276	22038276	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accaccccaatgtctacaaaCgtcaccagctcgttgactgt	11	9	6	15	2	2	1	1	1	1	0	3	1	2	1	4	0	3	2	4	0	3	2	rs28436899	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:22038276C>T	ENST00000303532.1	-	1	599	c.600G>A	c.(598-600)acG>acA	p.T200T		NM_001005465.1	NP_001005465.1	Q8NGC4	O10G3_HUMAN	olfactory receptor, family 10, subfamily G, 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)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)	15	all_cancers(95;0.000987)			GBM - Glioblastoma multiforme(265;0.0139)		TGTCTACAAACGTCACCAGCT	0.522													c|||	115	0.0229633	0.0794	0.013	5008	,	,		19542	0.0		0.0	False		,,,				2504	0.001				p.T200T		Atlas-SNP	.											.	OR10G3	40	.	0			c.G600A						PASS	.	T		261,4145	148.8+/-183.1	5,251,1947	196	188	191		600	-0.4	1	14	dbSNP_125	191	10,8590	7.1+/-27.0	0,10,4290	no	coding-synonymous	OR10G3	NM_001005465.1		5,261,6237	TT,TC,CC		0.1163,5.9237,2.0837		200/314	22038276	271,12735	2203	4300	6503	SO:0001819	synonymous_variant	26533	exon1			TACAAACGTCACC		CCDS32046.1	14q11.2	2013-09-24			ENSG00000169208	ENSG00000169208		"GPCR / Class A : Olfactory receptors"	8171	protein-coding gene	gene with protein product						8188290	Standard	NM_001005465		Approved		uc010tmb.2	Q8NGC4	OTTHUMG00000168886	ENST00000303532.1:c.600G>A	14.37:g.22038276C>T		243	1	0.00411523		239	132	0.552301	NM_001005465	Q6IET7|Q96R77	Silent	SNP	ENST00000303532.1	37	CCDS32046.1																																																																																			C|0.978;T|0.022	0.022	strong		0.522	OR10G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401521.1			T	22038276	C	T	22038276	2	4	24	1	0	0	0	0	0	0	0	1	10909	523	19	1		1	OR10G3	14	22038276	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	678289	22038276	85311264	440	8657											
HOMEZ	57594	hgsc.bcm.edu	37	chr14	23744844	23744844	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttcctcctcctcctcctcCtcttcctcatcatcttctgg	2	17	2	20	0	6	0	2	0	4	0	13	0	13	0	7	1	0	0	7	1	0	3			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:23744844C>T	ENST00000357460.5	-	2	1757	c.1593G>A	c.(1591-1593)gaG>gaA	p.E531E	HOMEZ_ENST00000561013.1_Silent_p.E533E|HOMEZ_ENST00000431326.2_Silent_p.E533E	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	531	Glu-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|lung(7)	12	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00643)		cctcctcctcctcttcctcat	0.493																																					p.E531E		Atlas-SNP	.											.	HOMEZ	80	.	0			c.G1593A						PASS	.						37	36	36					14																	23744844		2196	4286	6482	SO:0001819	synonymous_variant	57594	exon2			CTCCTCCTCTTCC	AB037864	CCDS45085.1	14q11.2	2011-06-20	2007-02-15	2007-02-15		ENSG00000215271		"Homeoboxes / ZF class"	20164	protein-coding gene	gene with protein product		608119	"KIAA1443"	KIAA1443		12925734	Standard	NM_020834		Approved		uc001wja.2	Q8IX15		ENST00000357460.5:c.1593G>A	14.37:g.23744844C>T		107	0	0		117	7	0.0598291	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	Silent	SNP	ENST00000357460.5	37	CCDS45085.1																																																																																			.	.	none		0.493	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834		T	23744844	C	T	23744844	2	4	24	1	0	0	0	0	0	0	0	1	7290	680	24	2		2	HOMEZ	14	23744844	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1706568	23744844	83604696	441	8658											
PCK2	5106	hgsc.bcm.edu	37	chr14	24572908	24572908	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggctttggggagaatgctcGggtgctagactggatctgcc	7	10	16	8	1	1	2	0	0	1	2	2	4	1	3	1	5	3	3	1	5	2	2	rs149521304		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:24572908G>A	ENST00000216780.4	+	10	1926	c.1658G>A	c.(1657-1659)cGg>cAg	p.R553Q	PCK2_ENST00000558096.1_Missense_Mutation_p.R387Q|PCK2_ENST00000545054.2_Missense_Mutation_p.R419Q|PCK2_ENST00000559250.1_Intron|NRL_ENST00000561028.1_Intron|PCK2_ENST00000561286.1_Missense_Mutation_p.R419Q	NM_004563.2	NP_004554.2	Q16822	PCKGM_HUMAN	phosphoenolpyruvate carboxykinase 2 (mitochondrial)	553					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)		GAGAATGCTCGGGTGCTAGAC	0.642																																					p.R553Q		Atlas-SNP	.											.	PCK2	66	.	0			c.G1658A						PASS	.	G	GLN/ARG	0,4406		0,0,2203	68	74	72		1658	5.6	1	14	dbSNP_134	72	1,8599	1.2+/-3.3	0,1,4299	no	missense	PCK2	NM_004563.2	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	553/641	24572908	1,13005	2203	4300	6503	SO:0001583	missense	5106	exon10			ATGCTCGGGTGCT	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.1658G>A	14.37:g.24572908G>A	ENSP00000216780:p.Arg553Gln	146	0	0		156	71	0.455128	NM_004563	O43253|Q86U01|Q9BV62	Missense_Mutation	SNP	ENST00000216780.4	37	CCDS9609.1	.	.	.	.	.	.	.	.	.	.	G	36	5.616065	0.96649	0.0	1.16E-4	ENSG00000100889	ENST00000216780;ENST00000545054	T;T	0.07688	3.17;3.17	5.57	5.57	0.84162	Phosphoenolpyruvate carboxykinase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.45135	0.1327	H	0.97158	3.95	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.62196	-0.6905	10	0.87932	D	0	-9.3642	17.4188	0.87508	0.0:0.0:1.0:0.0	.	419;553	B4DW73;Q16822	.;PCKGM_HUMAN	Q	553;419	ENSP00000216780:R553Q;ENSP00000441826:R419Q	ENSP00000216780:R553Q	R	+	2	0	PCK2	23642748	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	9.869000	0.99810	2.793000	0.96121	0.655000	0.94253	CGG	G|1.000;A|0.000	0.000	weak		0.642	PCK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071900.3	NM_001018073		A	24572908	G	A	24572908	3	1	24	1	0	0	0	0	1	0	0	0	11591	1116	39	1	1788	1	PCK2	14	24572908	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	828064	24572908	82776632	442	8659											
CTAGE5	4253	hgsc.bcm.edu	37	chr14	39818076	39818076	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caagaggcccattcttgagaAgaggacctcctttcccccca	10	8	8	15	0	1	3	0	1	1	3	3	5	3	4	6	2	0	0	6	2	2	3	rs61742363	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:39818076A>G	ENST00000280083.3	+	23	2457	c.2143A>G	c.(2143-2145)Aga>Gga	p.R715G	RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.R1250G|CTAGE5_ENST00000556148.1_Missense_Mutation_p.R640G|CTAGE5_ENST00000396165.4_Missense_Mutation_p.R686G|CTAGE5_ENST00000396158.2_Missense_Mutation_p.R720G|CTAGE5_ENST00000553352.1_Missense_Mutation_p.R686G|CTAGE5_ENST00000348007.3_Missense_Mutation_p.R672G|RP11-407N17.3_ENST00000603904.1_Missense_Mutation_p.R686G|CTAGE5_ENST00000341502.5_Missense_Mutation_p.R715G|CTAGE5_ENST00000341749.3_Missense_Mutation_p.R703G|CTAGE5_ENST00000557038.1_Missense_Mutation_p.R635G|CTAGE5_ENST00000553383.1_3'UTR			O15320	CTGE5_HUMAN	CTAGE family, member 5	715	Pro-rich.				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)		ATTCTTGAGAAGAGGACCTCC	0.532													A|||	27	0.00539137	0.0	0.0173	5008	,	,		14299	0.0		0.0149	False		,,,				2504	0.0				p.R720G		Atlas-SNP	.											.	CTAGE5	75	.	0			c.A2158G						PASS	.	A	GLY/ARG,GLY/ARG,GLY/ARG,GLY/ARG	16,4390	22.3+/-47.3	0,16,2187	125	130	129		2143,2107,2014,2056	3.1	1	14	dbSNP_129	129	156,8444	73.5+/-136.2	0,156,4144	yes	missense,missense,missense,missense	CTAGE5	NM_005930.3,NM_203354.2,NM_203355.2,NM_203356.2	125,125,125,125	0,172,6331	GG,GA,AA		1.814,0.3631,1.3225	probably-damaging,probably-damaging,probably-damaging,probably-damaging	715/805,703/793,672/762,686/776	39818076	172,12834	2203	4300	6503	SO:0001583	missense	4253	exon23			TTGAGAAGAGGAC	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.2143A>G	14.37:g.39818076A>G	ENSP00000280083:p.Arg715Gly	197	0	0		169	98	0.579882	NM_001247989	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Missense_Mutation	SNP	ENST00000280083.3	37	CCDS9674.1	22	0.010073260073260074	0	0.0	8	0.022099447513812154	0	0.0	14	0.018469656992084433	A	14.78	2.638501	0.47153	0.003631	0.01814	ENSG00000258941;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527	ENST00000553728;ENST00000341749;ENST00000557038;ENST00000396165;ENST00000341502;ENST00000396158;ENST00000280083;ENST00000556148;ENST00000348007;ENST00000553352	T;T;T;T;T;T;T;T;T;T	0.16324	2.35;2.4;2.37;2.36;2.91;2.63;2.64;2.36;3.17;2.36	5.64	3.12	0.35913	.	0.000000	0.37623	N	0.002009	T	0.12178	0.0296	M	0.83312	2.635	0.29744	N	0.83689	B;B;B;B;B	0.28713	0.22;0.181;0.22;0.181;0.22	B;B;B;B;B	0.29267	0.1;0.074;0.1;0.074;0.1	T	0.06588	-1.0818	9	.	.	.	.	11.6343	0.51194	0.6083:0.3917:0.0:0.0	rs61742363	720;672;715;643;703	O15320-5;O15320-2;O15320;O15320-7;G3XAC5	.;.;CTGE5_HUMAN;.;.	G	1250;703;635;686;715;720;715;640;672;686	ENSP00000452252:R1250G;ENSP00000343897:R703G;ENSP00000450869:R635G;ENSP00000379468:R686G;ENSP00000339286:R715G;ENSP00000379462:R720G;ENSP00000280083:R715G;ENSP00000452562:R640G;ENSP00000343912:R672G;ENSP00000450449:R686G	.	R	+	1	2	CTAGE5;RP11-407N17.3	38887827	1.000000	0.71417	0.992000	0.48379	0.895000	0.52256	0.816000	0.27267	0.940000	0.37473	0.533000	0.62120	AGA	A|0.988;G|0.012	0.012	strong		0.532	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930		G	39818076	A	G	39818076	3	3	24	1	0	0	0	0	1	0	0	0	3996	64	3	3	2264	3	CTAGE5	14	39818076	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	15245168	39818076	67531464	443	8660											
KLHL28	54813	hgsc.bcm.edu	37	chr14	45403616	45403616	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgaattttcatgttttctgaTagtgacgccaggacgcacat	10	14	9	8	2	2	3	1	3	1	0	2	4	2	4	1	1	0	2	1	1	2	5	rs35728857	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:45403616T>C	ENST00000396128.4	-	3	1164	c.1045A>G	c.(1045-1047)Atc>Gtc	p.I349V	KLHL28_ENST00000355081.2_Missense_Mutation_p.I363V	NM_017658.3	NP_060128.2	Q9NXS3	KLH28_HUMAN	kelch-like family member 28	349			I -> V (in dbSNP:rs35728857).							breast(2)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						TGTTTTCTGATAGTGACGCCA	0.388													T|||	6	0.00119808	0.0	0.0029	5008	,	,		19647	0.0		0.003	False		,,,				2504	0.001				p.I349V		Atlas-SNP	.											.	KLHL28	53	.	0			c.A1045G						PASS	.	T	VAL/ILE	6,4400	11.4+/-27.6	0,6,2197	116	108	111		1045	-1.1	1	14	dbSNP_126	111	36,8564	25.1+/-72.6	0,36,4264	yes	missense	KLHL28	NM_017658.3	29	0,42,6461	CC,CT,TT		0.4186,0.1362,0.3229	benign	349/572	45403616	42,12964	2203	4300	6503	SO:0001583	missense	54813	exon3			TTCTGATAGTGAC	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.1045A>G	14.37:g.45403616T>C	ENSP00000379434:p.Ile349Val	155	0	0		140	65	0.464286	NM_017658	Q0VAL5	Missense_Mutation	SNP	ENST00000396128.4	37	CCDS9680.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	T	10.34	1.322698	0.23994	0.001362	0.004186	ENSG00000179454	ENST00000396128;ENST00000355081	T;T	0.77229	-1.08;-1.08	5.38	-1.07	0.09968	Kelch-type beta propeller (1);	0.305531	0.37136	N	0.002234	T	0.48040	0.1478	N	0.12746	0.255	0.23515	N	0.997516	B	0.06786	0.001	B	0.14023	0.01	T	0.15407	-1.0438	10	0.14252	T	0.57	.	0.81	0.01091	0.3527:0.0965:0.2311:0.3196	rs35728857	349	Q9NXS3	KLH28_HUMAN	V	349;363	ENSP00000379434:I349V;ENSP00000347193:I363V	ENSP00000347193:I363V	I	-	1	0	KLHL28	44473366	1.000000	0.71417	0.992000	0.48379	0.986000	0.74619	1.815000	0.38981	0.060000	0.16281	0.455000	0.32223	ATC	T|0.997;C|0.003	0.003	strong		0.388	KLHL28-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276790.3			C	45403616	T	C	45403616	3	2	24	1	0	0	0	0	1	0	0	0	8391	1406	49	3	682	3	KLHL28	14	45403616	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	5585540	45403616	61945924	444	8661											
FANCM	57697	hgsc.bcm.edu	37	chr14	45665434	45665434	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctgttccaagtcaagaccAcatttagctgggacacatac	12	10	7	12	0	1	1	1	0	0	1	3	2	3	2	3	1	2	2	3	1	4	4			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:45665434A>G	ENST00000267430.5	+	21	5485	c.5400A>G	c.(5398-5400)ccA>ccG	p.P1800P	FANCM_ENST00000542564.2_Silent_p.P1774P	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1800	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						AGTCAAGACCACATTTAGCTG	0.433								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.P1800P		Atlas-SNP	.											.	FANCM	225	.	0			c.A5400G						PASS	.						137	134	135					14																	45665434		2203	4300	6503	SO:0001819	synonymous_variant	57697	exon21	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AAGACCACATTTA	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.5400A>G	14.37:g.45665434A>G		131	0	0		140	74	0.528571	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Silent	SNP	ENST00000267430.5	37	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	A	6.666	0.491392	0.12702	.	.	ENSG00000187790	ENST00000554809	.	.	.	5.39	1.43	0.22495	.	.	.	.	.	T	0.26195	0.0639	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.24119	-1.0169	4	.	.	.	.	5.1811	0.15160	0.6463:0.0:0.0786:0.2751	.	.	.	.	A	768	.	.	T	+	1	0	FANCM	44735184	0.000000	0.05858	0.040000	0.18447	0.278000	0.26855	0.476000	0.22180	-0.008000	0.14320	0.460000	0.39030	ACA	.	.	none		0.433	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128		G	45665434	A	G	45665434	2	3	24	1	0	0	0	0	0	0	0	1	5679	146	6	3		3	FANCM	14	45665434	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	261818	45665434	61684106	445	8662											
SYNE2	23224	hgsc.bcm.edu	37	chr14	64580061	64580061	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctttggatttctcttagggCaccacacctcctattgaggc	7	14	8	12	0	2	1	0	1	2	0	4	2	3	2	3	3	0	1	3	3	2	5	rs114604397	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:64580061C>T	ENST00000344113.4	+	66	12824	c.12612C>T	c.(12610-12612)ggC>ggT	p.G4204G	SYNE2_ENST00000358025.3_Silent_p.G4204G|SYNE2_ENST00000555002.1_Silent_p.G838G|SYNE2_ENST00000357395.3_Silent_p.G589G|SYNE2_ENST00000394768.2_Silent_p.G589G|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000554584.1_Silent_p.G4219G	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	4204					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)		TCTCTTAGGGCACCACACCTC	0.522													C|||	30	0.00599042	0.0219	0.0014	5008	,	,		18493	0.0		0.0	False		,,,				2504	0.0				p.G4204G		Atlas-SNP	.											.	SYNE2	577	.	0			c.C12612T						PASS	.	C	,	75,4331	67.0+/-104.6	1,73,2129	54	55	55		12612,12612	2.3	1	14	dbSNP_132	55	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SYNE2	NM_015180.4,NM_182914.2	,	1,73,6429	TT,TC,CC		0.0,1.7022,0.5767	,	4204/6886,4204/6908	64580061	75,12931	2203	4300	6503	SO:0001819	synonymous_variant	23224	exon66			TTAGGGCACCACA	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.12612C>T	14.37:g.64580061C>T		58	0	0		54	20	0.37037	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																			C|0.993;T|0.007	0.007	strong		0.522	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		T	64580061	C	T	64580061	2	4	24	1	0	0	0	0	0	0	0	1	15461	697	25	2		2	SYNE2	14	64580061	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	18914627	64580061	42769479	446	8663											
ABCD4	5826	hgsc.bcm.edu	37	chr14	74759066	74759066	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	catgtccagaagcgtctcccGaagctgcccaattctgaaca	11	8	8	14	2	2	2	0	1	2	1	4	3	3	2	3	0	4	1	3	0	4	1	rs147795328	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:74759066G>A	ENST00000356924.4	-	11	1185	c.1042C>T	c.(1042-1044)Cgg>Tgg	p.R348W	AC005519.4_ENST00000554532.2_RNA|ABCD4_ENST00000557554.1_Intron|ABCD4_ENST00000298816.7_Missense_Mutation_p.R244W	NM_005050.3	NP_005041.1	O14678	ABCD4_HUMAN	ATP-binding cassette, sub-family D (ALD), member 4	348					cobalamin metabolic process (GO:0009235)|transmembrane transport (GO:0055085)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			cervix(2)|endometrium(3)|kidney(3)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00153)		AGCGTCTCCCGAAGCTGCCCA	0.562													G|||	17	0.00339457	0.0008	0.0014	5008	,	,		21281	0.001		0.001	False		,,,				2504	0.0133				p.R348W		Atlas-SNP	.											.	ABCD4	54	.	0			c.C1042T						PASS	.	G	TRP/ARG	0,4406		0,0,2203	56	53	54		1042	4.2	1	14	dbSNP_134	54	3,8597	3.0+/-9.4	0,3,4297	yes	missense	ABCD4	NM_005050.3	101	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	benign	348/607	74759066	3,13003	2203	4300	6503	SO:0001583	missense	5826	exon11			TCTCCCGAAGCTG	AF009746	CCDS9828.1	14q24	2012-03-14			ENSG00000119688	ENSG00000119688		"ATP binding cassette transporters / subfamily D"	68	protein-coding gene	gene with protein product		603214		PXMP1L		9266848, 9302272	Standard	NR_003256		Approved	PMP69, P70R, EST352188	uc001xpr.2	O14678	OTTHUMG00000171207	ENST00000356924.4:c.1042C>T	14.37:g.74759066G>A	ENSP00000349396:p.Arg348Trp	61	0	0		69	34	0.492754	NM_005050	A8K5L7|Q6IAQ0|Q96E75	Missense_Mutation	SNP	ENST00000356924.4	37	CCDS9828.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	12.58	1.981289	0.34942	0.0	3.49E-4	ENSG00000119688	ENST00000356924;ENST00000298816;ENST00000537629	D;D	0.94457	-3.43;-3.12	5.1	4.2	0.49525	ABC transporter, transmembrane domain, type 1 (1);	0.326291	0.37437	N	0.002086	D	0.91068	0.7189	L	0.34521	1.04	0.28094	N	0.931705	P;B;P;B	0.44241	0.829;0.004;0.738;0.012	B;B;B;B	0.42798	0.398;0.007;0.394;0.007	D	0.86008	0.1499	10	0.38643	T	0.18	.	14.4627	0.67462	0.0:0.1467:0.8533:0.0	.	244;244;348;348	F8W7M4;B7Z4V6;A8K5L7;O14678	.;.;.;ABCD4_HUMAN	W	348;244;85	ENSP00000349396:R348W;ENSP00000298816:R244W	ENSP00000298816:R244W	R	-	1	2	ABCD4	73828819	1.000000	0.71417	0.998000	0.56505	0.580000	0.36256	2.853000	0.48317	1.487000	0.48415	0.655000	0.94253	CGG	G|0.999;A|0.001	0.001	strong		0.562	ABCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314382.1	NM_005050		A	74759066	G	A	74759066	3	1	24	1	0	0	0	0	1	0	0	0	63	1057	37	1	814	1	ABCD4	14	74759066	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	10179005	74759066	32590474	447	8664											
TTLL5	23093	hgsc.bcm.edu	37	chr14	76259376	76259376	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggttacagctgaacttcagcGgctagctgagaagcaggcag	11	7	14	9	1	1	2	1	2	0	1	1	3	1	2	0	3	6	6	0	3	4	3			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:76259376G>A	ENST00000298832.9	+	27	3309	c.3104G>A	c.(3103-3105)cGg>cAg	p.R1035Q	TTLL5_ENST00000556893.1_Missense_Mutation_p.R586Q|TTLL5_ENST00000557636.1_Missense_Mutation_p.R1050Q|TTLL5_ENST00000554510.1_Missense_Mutation_p.R544Q	NM_015072.4	NP_055887.3	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	1035					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)		GAACTTCAGCGGCTAGCTGAG	0.473																																					p.R1035Q		Atlas-SNP	.											.	TTLL5	102	.	0			c.G3104A						PASS	.						101	91	94					14																	76259376		2203	4300	6503	SO:0001583	missense	23093	exon27			TTCAGCGGCTAGC	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.3104G>A	14.37:g.76259376G>A	ENSP00000298832:p.Arg1035Gln	118	0	0		124	64	0.516129	NM_015072	B9EGH8|B9EGH9|Q9BUB0|Q9H0G4|Q9H7W2|Q9P1V5|Q9UPZ4	Missense_Mutation	SNP	ENST00000298832.9	37	CCDS32124.1	.	.	.	.	.	.	.	.	.	.	G	15.49	2.848322	0.51164	.	.	ENSG00000119685	ENST00000418433;ENST00000286653;ENST00000557636;ENST00000298832;ENST00000393826;ENST00000556893;ENST00000554510	T;T;T;T	0.27104	3.83;3.91;1.69;1.7	5.41	5.41	0.78517	.	0.711361	0.13654	N	0.372060	T	0.34658	0.0905	N	0.19112	0.55	0.29768	N	0.835037	P;D;P;P	0.76494	0.698;0.999;0.917;0.572	B;D;B;B	0.79784	0.098;0.993;0.202;0.045	T	0.13656	-1.0501	10	0.38643	T	0.18	.	11.7839	0.52030	0.0831:0.0:0.9169:0.0	.	1050;109;586;1035	G3V2J9;F8W7N3;Q6EMB2-2;Q6EMB2	.;.;.;TTLL5_HUMAN	Q	722;109;1050;1035;586;586;544	ENSP00000450713:R1050Q;ENSP00000298832:R1035Q;ENSP00000452524:R586Q;ENSP00000451946:R544Q	ENSP00000286653:R109Q	R	+	2	0	TTLL5	75329129	1.000000	0.71417	0.999000	0.59377	0.894000	0.52154	3.531000	0.53546	2.538000	0.85594	0.563000	0.77884	CGG	.	.	none		0.473	TTLL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414453.1	NM_015072		A	76259376	G	A	76259376	3	1	24	1	0	0	0	0	1	0	0	0	16745	1116	39	1	3206	1	TTLL5	14	76259376	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1500310	76259376	31090164	448	8665											
SNW1	22938	hgsc.bcm.edu	37	chr14	78205189	78205189	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctgcggcgaccttctgtgaTacagatttttctaaggctac	8	13	10	10	2	2	2	0	1	2	1	2	3	2	2	1	2	3	2	1	2	3	6	rs147154490		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:78205189T>C	ENST00000261531.7	-	5	527	c.465A>G	c.(463-465)gtA>gtG	p.V155V	SNW1_ENST00000555761.1_Silent_p.V155V|SLIRP_ENST00000557431.1_Intron|SNW1_ENST00000554775.1_5'UTR	NM_012245.2	NP_036377.1	Q13573	SNW1_HUMAN	SNW domain containing 1	155					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)		CCTTCTGTGATACAGATTTTT	0.403													T|||	1	0.000199681	0.0	0.0	5008	,	,		18116	0.0		0.001	False		,,,				2504	0.0				p.V155V		Atlas-SNP	.											.	SNW1	44	.	0			c.A465G						PASS	.	T		0,4406		0,0,2203	90	93	92		465	-2.5	1	14	dbSNP_134	92	20,8580	14.6+/-50.1	0,20,4280	no	coding-synonymous	SNW1	NM_012245.2		0,20,6483	CC,CT,TT		0.2326,0.0,0.1538		155/537	78205189	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	22938	exon5			CTGTGATACAGAT	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.465A>G	14.37:g.78205189T>C		140	0	0		168	70	0.416667	NM_012245	A8K8A9|Q13483|Q32N03|Q5D0D6	Silent	SNP	ENST00000261531.7	37	CCDS9867.1																																																																																			T|0.999;C|0.001	0.001	strong		0.403	SNW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413912.1	NM_012245		C	78205189	T	C	78205189	2	2	24	1	0	0	0	0	0	0	0	1	14894	1393	49	3		3	SNW1	14	78205189	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	1945813	78205189	29144351	449	8666											
ZC3H14	79882	hgsc.bcm.edu	37	chr14	89042232	89042232	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aacaagaatctgattttgaaGgctatatctgaagctcaaga	16	11	8	6	0	3	5	1	3	2	2	3	5	3	5	0	1	2	2	0	1	8	4	rs147484262		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:89042232G>A	ENST00000251038.5	+	8	1296	c.1071G>A	c.(1069-1071)aaG>aaA	p.K357K	ZC3H14_ENST00000393514.5_Silent_p.K357K|ZC3H14_ENST00000557605.1_3'UTR|ZC3H14_ENST00000557607.1_Silent_p.K202K|ZC3H14_ENST00000555755.1_Silent_p.K357K|ZC3H14_ENST00000336693.4_Silent_p.K323K|ZC3H14_ENST00000359301.3_Silent_p.K323K|ZC3H14_ENST00000302216.8_Silent_p.K357K|ZC3H14_ENST00000556945.1_Silent_p.K357K	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	357						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						TGATTTTGAAGGCTATATCTG	0.299													G|||	1	0.000199681	0.0	0.0	5008	,	,		18726	0.0		0.001	False		,,,				2504	0.0				p.K357K		Atlas-SNP	.											.	ZC3H14	71	.	0			c.G1071A						PASS	.	G	,,,,	0,4406		0,0,2203	99	102	101		1071,1071,1071,1071,969	3.7	1	14	dbSNP_134	101	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZC3H14	NM_001160103.1,NM_001160104.1,NM_024824.4,NM_207660.3,NM_207661.2	,,,,	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	,,,,	357/736,357/731,357/737,357/580,323/572	89042232	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	79882	exon8			TTTGAAGGCTATA	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.1071G>A	14.37:g.89042232G>A		82	0	0		76	40	0.526316	NM_001160104	A8MY46|B4DXU8|B4DZW7|B4E2H4|G3V5R4|Q6MZU4|Q6PJ32|Q6PUI6|Q6PUI8|Q86TQ5|Q86TW0|Q86TW1|Q8NCT6|Q8NCZ3|Q8TDE2|Q9HAC9|Q9Y5A0	Silent	SNP	ENST00000251038.5	37	CCDS32133.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	8.970	0.972602	0.18736	0.0	4.65E-4	ENSG00000100722	ENST00000556000	.	.	.	5.77	3.71	0.42584	.	.	.	.	.	T	0.47948	0.1473	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42766	-0.9432	4	.	.	.	-19.8172	4.4076	0.11416	0.4411:0.0:0.5589:0.0	.	.	.	.	K	273	.	.	R	+	2	0	ZC3H14	88111985	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.779000	0.47734	1.436000	0.47453	0.655000	0.94253	AGG	G|1.000;A|0.000	0.000	strong		0.299	ZC3H14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410387.1	NM_024824		A	89042232	G	A	89042232	2	1	24	1	0	0	0	0	0	0	0	1	17581	991	35	2		2	ZC3H14	14	89042232	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	10837043	89042232	18307308	450	8667											
LGMN	5641	hgsc.bcm.edu	37	chr14	93172903	93172903	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tagcagctgtgccccgtgagCggggctctctcggacaggag	6	7	16	12	3	1	1	0	1	1	0	3	3	1	3	2	4	4	3	2	4	1	1	rs143184687	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:93172903C>T	ENST00000393218.2	-	13	1453	c.1116G>A	c.(1114-1116)ccG>ccA	p.P372P	LGMN_ENST00000555699.1_Intron|LGMN_ENST00000557434.1_Intron|LGMN_ENST00000334869.4_Silent_p.P372P	NM_001008530.2	NP_001008530.1	Q99538	LGMN_HUMAN	legumain	372					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|innate immune response (GO:0045087)|negative regulation of ERBB signaling pathway (GO:1901185)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of neuron apoptotic process (GO:0043524)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|receptor catabolic process (GO:0032801)|renal system process (GO:0003014)|response to acidic pH (GO:0010447)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|toll-like receptor signaling pathway (GO:0002224)|vitamin D metabolic process (GO:0042359)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(5)|skin(2)	18		all_cancers(154;0.0706)		COAD - Colon adenocarcinoma(157;0.224)		GCCCCGTGAGCGGGGCTCTCT	0.647													C|||	31	0.0061901	0.0008	0.0072	5008	,	,		17490	0.0		0.0229	False		,,,				2504	0.002				p.P372P		Atlas-SNP	.											.	LGMN	28	.	0			c.G1116A						PASS	.	C	,	18,4388	23.3+/-48.9	0,18,2185	45	46	46		1116,1116	-1.2	0	14	dbSNP_134	46	216,8384	92.1+/-154.2	0,216,4084	no	coding-synonymous,coding-synonymous	LGMN	NM_001008530.2,NM_005606.6	,	0,234,6269	TT,TC,CC		2.5116,0.4085,1.7992	,	372/434,372/434	93172903	234,12772	2203	4300	6503	SO:0001819	synonymous_variant	5641	exon12			CGTGAGCGGGGCT	D55696	CCDS9904.1	14q32.12	2011-04-08		2002-01-18	ENSG00000100600	ENSG00000100600			9472	protein-coding gene	gene with protein product		602620	"protease, cysteine, 1 (legumain)"	PRSC1		8893817, 9065484	Standard	NM_001008530		Approved	LGMN1	uc001yaw.3	Q99538		ENST00000393218.2:c.1116G>A	14.37:g.93172903C>T		85	0	0		129	74	0.573643	NM_005606	O00123|Q86TV2|Q86TV3|Q9BTY1	Silent	SNP	ENST00000393218.2	37	CCDS9904.1																																																																																			C|0.984;T|0.016	0.016	strong		0.647	LGMN-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412288.1	NM_005606		T	93172903	C	T	93172903	2	4	24	1	0	0	0	0	0	0	0	1	8764	755	27	1		1	LGMN	14	93172903	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	4130671	93172903	14176637	451	8668											
ASB2	51676	hgsc.bcm.edu	37	chr14	94417531	94417531	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgcggttgcagcggtggtTggtgtctgcattgtgctgca	3	12	17	9	3	1	0	0	0	1	0	1	0	1	0	1	4	5	6	1	4	0	3	rs11555542	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:94417531T>C	ENST00000315988.4	-	4	1038	c.550A>G	c.(550-552)Aac>Gac	p.N184D	ASB2_ENST00000556337.1_Intron|ASB2_ENST00000555019.1_Missense_Mutation_p.N232D|MIR4506_ENST00000584693.1_RNA	NM_016150.4	NP_057234.2	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box containing 2	184					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)		CAGCGGTGGTTGGTGTCTGCA	0.632													T|||	104	0.0207668	0.0023	0.0605	5008	,	,		19972	0.001		0.0567	False		,,,				2504	0.001				p.N232D		Atlas-SNP	.											.	ASB2	71	.	0			c.A694G						PASS	.	T	ASP/ASN,ASP/ASN	50,4356	50.9+/-86.3	0,50,2153	76	63	67		694,550	5.6	1	14	dbSNP_120	67	469,8131	139.0+/-195.8	10,449,3841	yes	missense,missense	ASB2	NM_001202429.1,NM_016150.4	23,23	10,499,5994	CC,CT,TT		5.4535,1.1348,3.9905	possibly-damaging,possibly-damaging	232/636,184/588	94417531	519,12487	2203	4300	6503	SO:0001583	missense	51676	exon6			GGTGGTTGGTGTC	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.550A>G	14.37:g.94417531T>C	ENSP00000320675:p.Asn184Asp	47	0	0		69	32	0.463768	NM_001202429	B2RDP9|B4E166|Q9NSU5|Q9Y567	Missense_Mutation	SNP	ENST00000315988.4	37	CCDS9915.1	67	0.030677655677655676	2	0.0040650406504065045	25	0.06906077348066299	1	0.0017482517482517483	39	0.051451187335092345	T	27.5	4.840814	0.91197	0.011348	0.054535	ENSG00000100628	ENST00000555019;ENST00000434324;ENST00000315988;ENST00000543546;ENST00000555507;ENST00000556062	T;T;T;T	0.73789	-0.5;-0.5;-0.5;-0.78	5.62	5.62	0.85841	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.25044	0.0608	N	0.25201	0.72	0.54753	D	0.999986	P;D;P	0.76494	0.922;0.999;0.922	P;D;P	0.83275	0.841;0.996;0.677	T	0.60742	-0.7203	10	0.30078	T	0.28	-2.7607	15.8384	0.78818	0.0:0.0:0.0:1.0	rs11555542;rs11555542	200;232;184	B3KPZ6;B4E166;Q96Q27	.;.;ASB2_HUMAN	D	232;200;184;130;130;78	ENSP00000451575:N232D;ENSP00000320675:N184D;ENSP00000450940:N130D;ENSP00000451694:N78D	ENSP00000320675:N184D	N	-	1	0	ASB2	93487284	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.258000	0.72487	2.137000	0.66172	0.459000	0.35465	AAC	T|0.964;C|0.036	0.036	strong		0.632	ASB2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412845.1			C	94417531	T	C	94417531	3	2	24	1	0	0	0	0	1	0	0	0	1023	1812	63	3	1233	3	ASB2	14	94417531	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	1244628	94417531	12932009	452	8669											
ATG2B	55102	hgsc.bcm.edu	37	chr14	96829302	96829302	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcttgatggactccgaaaaCggccaaggcatagtgactgc	11	9	11	10	2	1	2	0	2	1	0	2	4	2	3	2	3	2	1	2	3	4	3	rs72706804	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:96829302C>T	ENST00000359933.4	-	1	905	c.12G>A	c.(10-12)ccG>ccA	p.P4P	GSKIP_ENST00000556095.1_5'Flank|GSKIP_ENST00000554182.1_5'Flank|GSKIP_ENST00000555181.1_5'Flank	NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	4					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)		ACTCCGAAAACGGCCAAGGCA	0.672													C|||	38	0.00758786	0.0008	0.013	5008	,	,		15753	0.001		0.0239	False		,,,				2504	0.0031				p.P4P		Atlas-SNP	.											.	ATG2B	169	.	0			c.G12A						PASS	.	C		17,4211		0,17,2097	52	56	54		12	0.9	0.7	14	dbSNP_130	54	195,8315		0,195,4060	no	coding-synonymous	ATG2B	NM_018036.5		0,212,6157	TT,TC,CC		2.2914,0.4021,1.6643		4/2079	96829302	212,12526	2114	4255	6369	SO:0001819	synonymous_variant	55102	exon1			CGAAAACGGCCAA	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.12G>A	14.37:g.96829302C>T		132	0	0		142	63	0.443662	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Silent	SNP	ENST00000359933.4	37	CCDS9944.2																																																																																			C|0.986;T|0.014	0.014	strong		0.672	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		T	96829302	C	T	96829302	2	4	24	1	0	0	0	0	0	0	0	1	1094	523	19	1		1	ATG2B	14	96829302	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	2411771	96829302	10520238	453	8670											
TNFAIP2	7127	hgsc.bcm.edu	37	chr14	103601637	103601637	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcatccggagcatcttggaCgtcagcatgggggcgcagga	8	6	16	11	4	2	0	1	0	1	0	3	3	3	3	1	5	2	4	1	5	0	1	rs2234147	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:103601637C>T	ENST00000560869.1	+	12	2544	c.1905C>T	c.(1903-1905)gaC>gaT	p.D635D	TNFAIP2_ENST00000451723.2_Silent_p.D304D|TNFAIP2_ENST00000333007.1_Silent_p.D635D|TNFAIP2_ENST00000538222.1_Silent_p.D118D			Q03169	TNAP2_HUMAN	tumor necrosis factor, alpha-induced protein 2	635					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|exocytosis (GO:0006887)	exocyst (GO:0000145)|extracellular space (GO:0005615)				NS(1)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	11		Melanoma(154;0.155)	Epithelial(46;0.191)			GCATCTTGGACGTCAGCATGG	0.577													c|||	59	0.0117812	0.0015	0.0159	5008	,	,		19498	0.0		0.0119	False		,,,				2504	0.0348				p.D635D		Atlas-SNP	.											.	TNFAIP2	53	.	0			c.C1905T						PASS	.			19,4387	26.2+/-53.5	0,19,2184	167	172	170		1905	0.2	0.5	14	dbSNP_98	170	87,8513	49.8+/-109.6	0,87,4213	no	coding-synonymous	TNFAIP2	NM_006291.2		0,106,6397	TT,TC,CC		1.0116,0.4312,0.815		635/655	103601637	106,12900	2203	4300	6503	SO:0001819	synonymous_variant	7127	exon11			CTTGGACGTCAGC		CCDS9979.1	14q32	2011-01-31				ENSG00000185215			11895	protein-coding gene	gene with protein product	"exocyst complex component 3-like 3"	603300				1374453	Standard	NM_006291		Approved	B94, EXOC3L3	uc001ymm.1	Q03169		ENST00000560869.1:c.1905C>T	14.37:g.103601637C>T		93	0	0		70	34	0.485714	NM_006291	Q86VI0	Silent	SNP	ENST00000560869.1	37	CCDS9979.1																																																																																			C|0.993;T|0.007	0.007	strong		0.577	TNFAIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415674.1	NM_006291		T	103601637	C	T	103601637	2	4	24	1	0	0	0	0	0	0	0	1	16288	535	19	1		1	TNFAIP2	14	103601637	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	6772335	103601637	3747903	454	8671											
KIF26A	26153	hgsc.bcm.edu	37	chr14	104640098	104640098	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgggcagctgtgaggcggcGgctggcagggccggggaggc	4	4	23	10	3	0	1	0	1	0	0	0	2	0	2	1	9	1	4	1	9	0	0	rs61745565	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:104640098G>A	ENST00000423312.2	+	10	1923	c.1923G>A	c.(1921-1923)gcG>gcA	p.A641A	KIF26A_ENST00000315264.7_Silent_p.A502A	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	641	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				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)		GTGAGGCGGCGGCTGGCAGGG	0.687													G|||	83	0.0165735	0.0015	0.0288	5008	,	,		15832	0.0		0.0388	False		,,,				2504	0.0225				p.A641A		Atlas-SNP	.											.	KIF26A	84	.	0			c.G1923A						PASS	.	G		24,3842		0,24,1909	17	24	22		1923	-2.2	0	14	dbSNP_129	22	289,7937		9,271,3833	no	coding-synonymous	KIF26A	NM_015656.1		9,295,5742	AA,AG,GG		3.5133,0.6208,2.5885		641/1883	104640098	313,11779	1933	4113	6046	SO:0001819	synonymous_variant	26153	exon10			GGCGGCGGCTGGC	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.1923G>A	14.37:g.104640098G>A		23	0	0		64	64	1	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Silent	SNP	ENST00000423312.2	37	CCDS45171.1																																																																																			G|0.981;A|0.019	0.019	strong		0.687	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1			A	104640098	G	A	104640098	2	1	24	1	0	0	0	0	0	0	0	1	8303	1103	39	1		1	KIF26A	14	104640098	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1038461	104640098	2709442	455	8672											
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105412335	105412335	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggcagacaccccgaacgaCggcatcttgaacttgggcat	10	6	13	12	3	1	2	0	1	1	1	1	4	1	2	2	4	2	3	2	4	2	2	rs202104959	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr14:105412335C>T	ENST00000333244.5	-	7	9572	c.9453G>A	c.(9451-9453)ccG>ccA	p.P3151P	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3151						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)		p.P3151P(1)		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)			CCCCGAACGACGGCATCTTGA	0.602																																					p.P3151P		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,0,2	AHNAK2	719	2	1	Substitution - coding silent(1)	endometrium(1)	c.G9453A						scavenged	.						198	138	157					14																	105412335		1921	4005	5926	SO:0001819	synonymous_variant	113146	exon7			GAACGACGGCATC	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.9453G>A	14.37:g.105412335C>T		291	0	0		21	4	0.190476	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			C|0.963;T|0.037	0.037	strong		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		T	105412335	C	T	105412335	2	4	24	1	0	0	0	0	0	0	0	1	415	523	19	1		1	AHNAK2	14	105412335	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	772237	105412335	1937205	456	8673											
GABRG3	2567	hgsc.bcm.edu	37	chr15	27725917	27725917	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctcagaaacaccacagaaatCgtgacaacgtctgcaggtag	15	6	9	11	2	2	3	1	1	1	2	3	3	2	3	1	1	3	2	1	1	4	1	rs77771286	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:27725917C>T	ENST00000333743.6	+	6	950	c.696C>T	c.(694-696)atC>atT	p.I232I	RP11-100M12.3_ENST00000556642.1_RNA|GABRG3_ENST00000555083.1_Silent_p.I232I	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	232					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)	CCACAGAAATCGTGACAACGT	0.443													C|||	13	0.00259585	0.0	0.0029	5008	,	,		15354	0.0		0.008	False		,,,				2504	0.0031				p.I232I	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											.	GABRG3	115	.	0			c.C696T						PASS	.	C		7,3769		0,7,1881	54	54	54		696	-4.5	0.2	15	dbSNP_131	54	84,8170		1,82,4044	no	coding-synonymous	GABRG3	NM_033223.4		1,89,5925	TT,TC,CC		1.0177,0.1854,0.7564		232/468	27725917	91,11939	1888	4127	6015	SO:0001819	synonymous_variant	2567	exon6			AGAAATCGTGACA		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.696C>T	15.37:g.27725917C>T		45	0	0		54	24	0.444444	NM_001270873	G3V594|Q9HD46|Q9NYT2	Silent	SNP	ENST00000333743.6	37	CCDS45195.1																																																																																			C|0.994;T|0.006	0.006	strong		0.443	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2			T	27725917	C	T	27725917	2	4	24	1	0	0	0	0	0	0	0	1	6181	874	31	1		1	GABRG3	15	27725917	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10		27725917	74805475	457	8674											
OCA2	4948	hgsc.bcm.edu	37	chr15	28202804	28202804	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttccccagcagcaggcggcGcacagctgtctcctcgcggc	5	6	12	18	4	1	0	0	0	1	0	4	0	2	0	3	3	3	4	3	3	0	1	rs374415755		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:28202804G>A	ENST00000354638.3	-	16	1869	c.1714C>T	c.(1714-1716)Cgc>Tgc	p.R572C	OCA2_ENST00000382996.2_Missense_Mutation_p.R572C|OCA2_ENST00000353809.5_Missense_Mutation_p.R548C	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II	572					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)			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)		AGCAGGCGGCGCACAGCTGTC	0.662									Oculocutaneous Albinism																												p.R572C		Atlas-SNP	.											OCA2,caecum,carcinoma,0,1	OCA2	173	1	0			c.C1714T						PASS	.	G	CYS/ARG	0,4402		0,0,2201	27	30	29		1714	3.8	0.2	15		29	2,8588		0,2,4293	no	missense	OCA2	NM_000275.2	180	0,2,6494	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	572/839	28202804	2,12990	2201	4295	6496	SO:0001583	missense	4948	exon16	Familial Cancer Database		GGCGGCGCACAGC		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.1714C>T	15.37:g.28202804G>A	ENSP00000346659:p.Arg572Cys	29	0	0		55	27	0.490909	NM_000275	Q15211|Q15212|Q96EN1|Q9UMI5	Missense_Mutation	SNP	ENST00000354638.3	37	CCDS10020.1	.	.	.	.	.	.	.	.	.	.	G	15.27	2.784872	0.49997	0.0	2.33E-4	ENSG00000104044	ENST00000354638;ENST00000353809;ENST00000382996	D;D;D	0.91894	-2.92;-2.74;-2.93	5.8	3.79	0.43588	Divalent ion symporter (1);	0.118953	0.53938	D	0.000046	D	0.93700	0.7987	M	0.64997	1.995	0.51012	D	0.999906	D;D	0.89917	0.998;1.0	P;D	0.74023	0.827;0.982	D	0.92961	0.6389	10	0.87932	D	0	-7.3542	6.2138	0.20644	0.0936:0.0:0.6114:0.295	.	548;572	Q04671-2;Q04671	.;P_HUMAN	C	572;548;572	ENSP00000346659:R572C;ENSP00000261276:R548C;ENSP00000372457:R572C	ENSP00000261276:R548C	R	-	1	0	OCA2	25876399	1.000000	0.71417	0.234000	0.24042	0.118000	0.20060	5.943000	0.70211	1.468000	0.48064	-0.229000	0.12294	CGC	.	.	weak		0.662	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	NM_000275		A	28202804	G	A	28202804	3	1	24	1	0	0	0	0	1	0	0	0	10824	1087	38	1	838	1	OCA2	15	28202804	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	476887	28202804	74328588	458	8675											
APBA2	321	hgsc.bcm.edu	37	chr15	29390715	29390715	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctgagggggatgcccagaCgctgacggaagtggacctct	8	8	15	10	2	2	3	0	2	2	1	2	6	2	6	2	4	1	1	2	4	1	1	rs371370074	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:29390715C>T	ENST00000558402.1	+	10	1873	c.1274C>T	c.(1273-1275)aCg>aTg	p.T425M	APBA2_ENST00000561069.1_Missense_Mutation_p.T425M|APBA2_ENST00000411764.1_Missense_Mutation_p.T413M|APBA2_ENST00000558259.1_Missense_Mutation_p.T425M|APBA2_ENST00000558330.1_Missense_Mutation_p.T413M			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	425	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)		GATGCCCAGACGCTGACGGAA	0.423													C|||	2	0.000399361	0.0	0.0	5008	,	,		19432	0.002		0.0	False		,,,				2504	0.0				p.T425M		Atlas-SNP	.											.	APBA2	132	.	0			c.C1274T						PASS	.	C	MET/THR,MET/THR	0,4406		0,0,2203	110	106	108		1238,1274	4	0.8	15		108	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	APBA2	NM_001130414.1,NM_005503.3	81,81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	413/738,425/750	29390715	1,13005	2203	4300	6503	SO:0001583	missense	321	exon8			CCCAGACGCTGAC	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.1274C>T	15.37:g.29390715C>T	ENSP00000453293:p.Thr425Met	70	0	0		67	27	0.402985	NM_005503	E9PGI4|O60571|Q5XKC0	Missense_Mutation	SNP	ENST00000558402.1	37	CCDS10022.1	.	.	.	.	.	.	.	.	.	.	C	14.19	2.461454	0.43736	0.0	1.16E-4	ENSG00000034053	ENST00000411764;ENST00000219865;ENST00000382938	T	0.55760	0.5	4.93	4.02	0.46733	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.184551	0.45361	N	0.000369	T	0.51550	0.1681	N	0.14661	0.345	0.58432	D	0.999997	P;P;D;P	0.67145	0.637;0.66;0.996;0.462	B;B;P;B	0.61397	0.269;0.389;0.888;0.244	T	0.58457	-0.7633	10	0.87932	D	0	.	12.3957	0.55382	0.0:0.9183:0.0:0.0817	.	413;117;413;425	Q5XKC0;Q6ZVB1;E9PGI4;Q99767	.;.;.;APBA2_HUMAN	M	413;425;117	ENSP00000409312:T413M	ENSP00000219865:T425M	T	+	2	0	APBA2	27178007	1.000000	0.71417	0.776000	0.31678	0.297000	0.27493	4.750000	0.62162	1.177000	0.42855	0.655000	0.94253	ACG	.	.	weak		0.423	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503		T	29390715	C	T	29390715	3	4	24	1	0	0	0	0	1	0	0	0	757	536	19	1	1296	1	APBA2	15	29390715	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1187911	29390715	73140677	459	8676											
ARHGAP11B	89839	hgsc.bcm.edu	37	chr15	30927750	30927750	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgggtattgatggtctctGtgctactccatcactggaag	7	14	12	8	0	2	1	1	1	1	0	4	2	3	2	1	3	2	3	1	3	3	4			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:30927750G>A	ENST00000428041.2	+	6	866	c.721G>A	c.(721-723)Gtg>Atg	p.V241M		NM_001039841.1	NP_001034930.1	Q3KRB8	RHGBB_HUMAN	Rho GTPase activating protein 11B	241	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(2)|kidney(1)|large_intestine(3)|lung(1)|prostate(1)	8		all_lung(180;2.71e-09)|Breast(32;0.00116)		all cancers(64;1.9e-15)|Epithelial(43;3.59e-12)|GBM - Glioblastoma multiforme(186;9e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)|Lung(196;0.153)		GATGGTCTCTGTGCTACTCCA	0.413																																					p.V241M		Atlas-SNP	.											ARHGAP11B,colon,carcinoma,-2,1	ARHGAP11B	14	1	0			c.G721A						PASS	.						150	150	150					15																	30927750		2202	4298	6500	SO:0001583	missense	89839	exon6			GTCTCTGTGCTAC	BC105788	CCDS32185.1	15q13.2	2011-07-13				ENSG00000187951		"Rho GTPase activating proteins"	15782	protein-coding gene	gene with protein product	"GAP (1-8)"		"family with sequence similarity 7, member B1"	FAM7B1		11829490	Standard	NM_001039841		Approved	B'-T	uc001zet.1	Q3KRB8		ENST00000428041.2:c.721G>A	15.37:g.30927750G>A	ENSP00000392760:p.Val241Met	250	0	0		252	97	0.384921	NM_001039841		Missense_Mutation	SNP	ENST00000428041.2	37	CCDS32185.1	.	.	.	.	.	.	.	.	.	.	.	5.293	0.239371	0.10023	.	.	ENSG00000187951	ENST00000428041	T	0.10763	2.84	1.49	1.49	0.22878	Rho GTPase-activating protein domain (1);	.	.	.	.	T	0.04407	0.0121	N	0.14661	0.345	0.18873	N	0.999987	P	0.43857	0.819	B	0.28991	0.097	T	0.35699	-0.9778	9	0.44086	T	0.13	.	6.461	0.21956	0.0:0.0:1.0:0.0	.	241	Q3KRB8	RHGBB_HUMAN	M	241	ENSP00000392760:V241M	ENSP00000392760:V241M	V	+	1	0	ARHGAP11B	28715042	1.000000	0.71417	1.000000	0.80357	0.324000	0.28378	1.574000	0.36482	1.121000	0.41925	0.162000	0.16502	GTG	.	.	none		0.413	ARHGAP11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430729.1	NM_001039841		A	30927750	G	A	30927750	3	1	24	1	0	0	0	0	1	0	0	0	864	1377	48	2	743	2	ARHGAP11B	15	30927750	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1537035	30927750	71603642	460	8677											
MTMR10	54893	hgsc.bcm.edu	37	chr15	31246972	31246972	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagaatgaaattaccattaaCgcatagctgcttcagtttta	15	13	6	7	1	1	2	1	1	0	1	1	2	1	2	1	0	4	4	1	0	7	6	rs142149917	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:31246972C>T	ENST00000435680.1	-	10	1157	c.1060G>A	c.(1060-1062)Gtt>Att	p.V354I	MTMR10_ENST00000563714.1_Missense_Mutation_p.V272I|MTMR10_ENST00000314404.8_Missense_Mutation_p.V106I|RNU6-466P_ENST00000391224.1_RNA|MTMR10_ENST00000425768.1_3'UTR	NM_017762.2	NP_060232.2	Q9NXD2	MTMRA_HUMAN	myotubularin related protein 10	354	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.						phosphatase activity (GO:0016791)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	9		all_lung(180;2.81e-11)		all cancers(64;7.26e-15)|Epithelial(43;7.2e-11)|GBM - Glioblastoma multiforme(186;0.000158)|BRCA - Breast invasive adenocarcinoma(123;0.00426)|Lung(196;0.174)		TTACCATTAACGCATAGCTGC	0.333													C|||	19	0.00379393	0.0	0.0043	5008	,	,		17377	0.0		0.007	False		,,,				2504	0.0092				p.V354I		Atlas-SNP	.											MTMR10_ENST00000435680,NS,carcinoma,0,2	MTMR10	74	2	0			c.G1060A						PASS	.	C	ILE/VAL	7,3651		0,7,1822	83	75	77		1060	4.4	0.9	15	dbSNP_134	77	58,8108		0,58,4025	yes	missense	MTMR10	NM_017762.2	29	0,65,5847	TT,TC,CC		0.7103,0.1914,0.5497	benign	354/778	31246972	65,11759	1829	4083	5912	SO:0001583	missense	54893	exon10			CATTAACGCATAG	AK000320	CCDS45204.1	15q13.3	2011-06-09				ENSG00000166912		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	25999	protein-coding gene	gene with protein product						12495846	Standard	NM_017762		Approved	FLJ20313	uc001zfh.1	Q9NXD2		ENST00000435680.1:c.1060G>A	15.37:g.31246972C>T	ENSP00000402537:p.Val354Ile	76	0	0		113	58	0.513274	NM_017762	Q6P4Q6	Missense_Mutation	SNP	ENST00000435680.1	37	CCDS45204.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	C	13.17	2.158574	0.38119	0.001914	0.007103	ENSG00000166912	ENST00000435680;ENST00000314404;ENST00000340566	D;D	0.89415	-2.51;-2.51	5.32	4.4	0.53042	Myotubularin phosphatase domain (1);	0.121057	0.56097	N	0.000032	T	0.79730	0.4496	M	0.65320	2	0.80722	D	1	B;B;P;P	0.37688	0.256;0.066;0.605;0.522	B;B;B;B	0.21151	0.024;0.017;0.033;0.031	T	0.80266	-0.1454	10	0.33940	T	0.23	.	13.6029	0.62031	0.0:0.9259:0.0:0.0741	.	123;272;272;354	Q0IJ45;Q9NXD2-2;A6NGL9;Q9NXD2	.;.;.;MTMRA_HUMAN	I	354;106;272	ENSP00000402537:V354I;ENSP00000313788:V106I	ENSP00000313788:V106I	V	-	1	0	MTMR10	29034264	0.990000	0.36364	0.863000	0.33907	0.849000	0.48306	2.209000	0.42806	1.249000	0.43950	0.650000	0.86243	GTT	C|0.996;T|0.004	0.004	strong		0.333	MTMR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430747.1	NM_017762		T	31246972	C	T	31246972	3	4	24	1	0	0	0	0	1	0	0	0	9948	536	19	1	1301	1	MTMR10	15	31246972	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	319222	31246972	71284420	461	8678											
FMN1	342184	hgsc.bcm.edu	37	chr15	33359093	33359093	+	Intron	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtggccttcggatcagttgcTttcttctcactcttcactgt	4	17	8	12	1	5	0	3	0	3	0	7	1	5	1	1	2	1	2	1	2	0	5	rs74655292	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:33359093T>C	ENST00000559047.1	-	3	2043				FMN1_ENST00000559150.1_Intron|FMN1_ENST00000561249.1_Intron|FMN1_ENST00000558197.1_Silent_p.K331K|FMN1_ENST00000334528.9_Silent_p.K331K			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)		GATCAGTTGCTTTCTTCTCAC	0.522													T|||	29	0.00579073	0.0008	0.0202	5008	,	,		19662	0.0		0.0089	False		,,,				2504	0.0051				p.K331K		Atlas-SNP	.											.	FMN1	174	.	0			c.A993G						PASS	.	T		8,4060		0,8,2026	62	65	64		993	3.9	0	15	dbSNP_132	64	89,8257		0,89,4084	no	coding-synonymous	FMN1	NM_001103184.2		0,97,6110	CC,CT,TT		1.0664,0.1967,0.7814		331/1197	33359093	97,12317	2034	4173	6207	SO:0001627	intron_variant	342184	exon1			AGTTGCTTTCTTC	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.2044-1818A>G	15.37:g.33359093T>C		206	0	0		228	106	0.464912	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Silent	SNP	ENST00000559047.1	37																																																																																				T|0.992;C|0.008	0.008	strong		0.522	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184		C	33359093	T	C	33359093	1	2	24	0	1	0	0	0	0	0	0	0	5957	1606	56	3		3	FMN1	15	33359093	Intron	SNP	T	TCGA-G8-6326-01A-11D-2210-10	2112121	33359093	69172299	462	8679											
RYR3	6263	hgsc.bcm.edu	37	chr15	33842400	33842400	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatggggccaggctttccgActccggcatctcaccacagg	8	7	12	14	2	1	1	1	0	1	1	4	2	3	1	4	5	0	2	4	5	0	1	rs41279202	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:33842400A>T	ENST00000389232.4	+	10	925	c.855A>T	c.(853-855)cgA>cgT	p.R285R	RYR3_ENST00000415757.3_Silent_p.R285R	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	285	MIR 4. {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)			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)		AGGCTTTCCGACTCCGGCATC	0.483													A|||	68	0.0135783	0.0	0.0187	5008	,	,		17879	0.001		0.0447	False		,,,				2504	0.0092				p.R285R		Atlas-SNP	.											.	RYR3	760	.	0			c.A855T						PASS	.	A		34,4350	34.3+/-65.2	0,34,2158	40	42	41		855	-1.1	1	15	dbSNP_127	41	369,8219	120.2+/-179.5	8,353,3933	no	coding-synonymous	RYR3	NM_001036.3		8,387,6091	TT,TA,AA		4.2967,0.7755,3.1067		285/4871	33842400	403,12569	2192	4294	6486	SO:0001819	synonymous_variant	6263	exon10			TTTCCGACTCCGG		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.855A>T	15.37:g.33842400A>T		66	0	0		103	46	0.446602	NM_001243996	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			A|0.970;T|0.030	0.030	strong		0.483	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	33842400	A	T	33842400	2	4	24	1	0	0	0	0	0	0	0	1	13785	262	10	5		5	RYR3	15	33842400	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	483307	33842400	68688992	463	8680											
ITPKA	3706	hgsc.bcm.edu	37	chr15	41793728	41793728	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagccctttcaagaagcgctAcgcctgggtgcagctggcag	9	7	13	12	2	1	1	1	0	0	1	1	1	1	1	2	2	5	4	2	2	4	2	rs143540732		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:41793728A>G	ENST00000260386.5	+	2	610	c.557A>G	c.(556-558)tAc>tGc	p.Y186C		NM_002220.2	NP_002211.1	P23677	IP3KA_HUMAN	inositol-trisphosphate 3-kinase A	186					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)	p.Y186F(1)		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)		AAGAAGCGCTACGCCTGGGTG	0.637																																					p.Y186C		Atlas-SNP	.											ITPKA,NS,carcinoma,0,1	ITPKA	19	1	1	Substitution - Missense(1)	lung(1)	c.A557G						PASS	.	A	CYS/TYR	1,4403	2.1+/-5.4	0,1,2201	29	25	26		557	4.7	1	15	dbSNP_134	26	4,8596	3.7+/-12.6	0,4,4296	yes	missense	ITPKA	NM_002220.2	194	0,5,6497	GG,GA,AA		0.0465,0.0227,0.0384	probably-damaging	186/462	41793728	5,12999	2202	4300	6502	SO:0001583	missense	3706	exon2			AGCGCTACGCCTG	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.557A>G	15.37:g.41793728A>G	ENSP00000260386:p.Tyr186Cys	70	0	0		83	47	0.566265	NM_002220	Q8TAN3	Missense_Mutation	SNP	ENST00000260386.5	37	CCDS10076.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.207364	0.79240	2.27E-4	4.65E-4	ENSG00000137825	ENST00000425927;ENST00000260386	T	0.50548	0.74	4.71	4.71	0.59529	.	0.226565	0.38837	N	0.001556	T	0.66197	0.2765	M	0.70595	2.14	0.53688	D	0.999977	D	0.89917	1.0	D	0.81914	0.995	T	0.70457	-0.4866	10	0.87932	D	0	-10.9047	12.9023	0.58133	1.0:0.0:0.0:0.0	.	186	P23677	IP3KA_HUMAN	C	81;186	ENSP00000260386:Y186C	ENSP00000260386:Y186C	Y	+	2	0	ITPKA	39581020	0.997000	0.39634	0.996000	0.52242	0.995000	0.86356	3.558000	0.53749	1.972000	0.57404	0.379000	0.24179	TAC	A|1.000;G|0.000	0.000	weak		0.637	ITPKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252695.3	NM_002220		G	41793728	A	G	41793728	3	3	24	1	0	0	0	0	1	0	0	0	7926	391	14	3	563	3	ITPKA	15	41793728	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	7951328	41793728	60737664	464	8681											
TP53BP1	7158	hgsc.bcm.edu	37	chr15	43712823	43712823	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caccagcacccacatctgttCgtctggtggagtctggcact	7	10	10	14	1	3	0	0	0	3	0	4	1	3	1	2	3	1	3	2	3	0	1	rs28903077	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:43712823C>T	ENST00000263801.3	-	21	4598	c.4346G>A	c.(4345-4347)cGa>cAa	p.R1449Q	TP53BP1_ENST00000382044.4_Missense_Mutation_p.R1454Q|TP53BP1_ENST00000450115.2_Missense_Mutation_p.R1454Q|TP53BP1_ENST00000382039.3_Missense_Mutation_p.R1404Q	NM_005657.2	NP_005648.1	Q12888	TP53B_HUMAN	tumor protein p53 binding protein 1	1449					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)		CACATCTGTTCGTCTGGTGGA	0.552								Other conserved DNA damage response genes					C|||	2	0.000399361	0.0	0.0	5008	,	,		18672	0.0		0.002	False		,,,				2504	0.0				p.R1454Q		Atlas-SNP	.											.	TP53BP1	157	.	0			c.G4361A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	0,4402		0,0,2201	66	64	64		4361,4361,4346	5.4	0.4	15	dbSNP_125	64	17,8579	11.9+/-42.8	0,17,4281	yes	missense,missense,missense	TP53BP1	NM_001141979.1,NM_001141980.1,NM_005657.2	43,43,43	0,17,6482	TT,TC,CC		0.1978,0.0,0.1308	probably-damaging,probably-damaging,probably-damaging	1454/1976,1454/1978,1449/1973	43712823	17,12981	2201	4298	6499	SO:0001583	missense	7158	exon21			TCTGTTCGTCTGG	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.4346G>A	15.37:g.43712823C>T	ENSP00000263801:p.Arg1449Gln	86	0	0		89	47	0.52809	NM_001141980	F8VY86|Q2M1Z7|Q4LE46|Q5FWZ3|Q7Z3U4	Missense_Mutation	SNP	ENST00000263801.3	37	CCDS10096.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	18.64	3.666759	0.67814	0.0	0.001978	ENSG00000067369	ENST00000263801;ENST00000382044;ENST00000382039;ENST00000450115	T;T;T;T	0.04194	3.68;3.68;3.73;3.68	5.45	5.45	0.79879	.	0.347316	0.27735	N	0.018061	T	0.11239	0.0274	L	0.29908	0.895	0.09310	N	1	D;D;D;D	0.76494	0.999;0.998;0.999;0.999	D;D;D;D	0.72625	0.978;0.945;0.975;0.975	T	0.33574	-0.9863	10	0.21014	T	0.42	-8.3136	14.178	0.65555	0.159:0.8409:0.0:0.0	rs28903077;rs28903077	1454;1449;1454;1454	B7Z3E7;Q12888;Q12888-2;F8VY86	.;TP53B_HUMAN;.;.	Q	1449;1454;1404;1454	ENSP00000263801:R1449Q;ENSP00000371475:R1454Q;ENSP00000371470:R1404Q;ENSP00000393497:R1454Q	ENSP00000263801:R1449Q	R	-	2	0	TP53BP1	41500115	0.970000	0.33590	0.397000	0.26308	0.982000	0.71751	4.145000	0.58065	2.717000	0.92951	0.585000	0.79938	CGA	C|0.998;T|0.002	0.002	strong		0.552	TP53BP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132897.3			T	43712823	C	T	43712823	3	4	24	1	0	0	0	0	1	0	0	0	16398	884	31	1	1604	1	TP53BP1	15	43712823	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1919095	43712823	58818569	465	8682											
CATSPER2	117155	hgsc.bcm.edu	37	chr15	43928340	43928340	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gactgacttcaggcaccttcCagacgtcctgaagcagtgca	10	8	10	13	1	1	3	1	2	0	1	3	4	3	3	3	1	2	3	3	1	1	2	rs146701338	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:43928340C>G	ENST00000321596.5	-	8	1119	c.920G>C	c.(919-921)tGg>tCg	p.W307S	CATSPER2_ENST00000396879.1_Missense_Mutation_p.W307S|CATSPER2_ENST00000354127.4_Missense_Mutation_p.W307S|STRC_ENST00000541030.1_Intron|CATSPER2_ENST00000381761.1_Missense_Mutation_p.W313S|RNU6-610P_ENST00000384264.1_RNA|CATSPER2_ENST00000355438.2_Missense_Mutation_p.W307S			Q96P56	CTSR2_HUMAN	cation channel, sperm associated 2	307					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|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)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	22		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)		AGGCACCTTCCAGACGTCCTG	0.443													.|||	6	0.00119808	0.0	0.0	5008	,	,		20134	0.0		0.004	False		,,,				2504	0.002				p.W307S		Atlas-SNP	.											.	CATSPER2	49	.	0			c.G920C						PASS	.	C	SER/TRP,SER/TRP	4,4390		0,4,2193	27	27	27		920,920	4.8	1	15	dbSNP_134	27	33,8511		0,33,4239	no	missense,missense	CATSPER2	NM_054020.2,NM_172095.1	177,177	0,37,6432	GG,GC,CC		0.3862,0.091,0.286	probably-damaging,probably-damaging	307/529,307/531	43928340	37,12901	2197	4272	6469	SO:0001583	missense	117155	exon8			ACCTTCCAGACGT	AF411817	CCDS10099.1, CCDS32216.1, CCDS73714.1	15q15.3	2011-07-05			ENSG00000166762	ENSG00000166762		"Voltage-gated ion channels / Cation channels, sperm associated"	18810	protein-coding gene	gene with protein product		607249				11675491, 16382101	Standard	NM_172095		Approved		uc001zsh.3	Q96P56	OTTHUMG00000059902	ENST00000321596.5:c.920G>C	15.37:g.43928340C>G	ENSP00000321463:p.Trp307Ser	394	0	0		459	192	0.418301	NM_054020	Q8NHT9|Q96P54|Q96P55	Missense_Mutation	SNP	ENST00000321596.5	37	CCDS10099.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	8.365	0.834073	0.16820	9.1E-4	0.003862	ENSG00000166762	ENST00000396879;ENST00000299989;ENST00000381761;ENST00000321596;ENST00000354127;ENST00000355438	D;D;D;D;D	0.97161	-4.27;-4.27;-4.27;-4.27;-4.27	4.81	4.81	0.61882	Ion transport (1);	0.472448	0.20479	N	0.091522	D	0.96386	0.8821	L	0.54323	1.7	0.53688	D	0.999972	D;D	0.71674	0.997;0.998	D;D	0.71184	0.953;0.972	D	0.94092	0.7354	10	0.26408	T	0.33	.	13.2328	0.59953	0.0:1.0:0.0:0.0	.	313;307	F8W9H2;Q96P56	.;CTSR2_HUMAN	S	307;307;313;307;307;307	ENSP00000380088:W307S;ENSP00000371180:W313S;ENSP00000321463:W307S;ENSP00000339137:W307S;ENSP00000347613:W307S	ENSP00000299989:W307S	W	-	2	0	CATSPER2	41715632	1.000000	0.71417	1.000000	0.80357	0.096000	0.18686	4.485000	0.60279	2.488000	0.83962	0.655000	0.94253	TGG	C|0.997;G|0.003	0.003	strong		0.443	CATSPER2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000133151.2	NM_054020		G	43928340	C	G	43928340	3	3	24	1	0	0	0	0	1	0	0	0	2690	595	21	4	696	4	CATSPER2	15	43928340	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	215517	43928340	58603052	466	8683											
SLC27A2	11001	hgsc.bcm.edu	37	chr15	50475035	50475035	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atggcgtgcctcaattacaaCatccgcgcgaagtccctgct	9	9	9	14	4	1	0	1	0	0	0	3	1	3	0	3	1	4	1	3	1	4	1			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:50475035C>T	ENST00000267842.5	+	1	643	c.411C>T	c.(409-411)aaC>aaT	p.N137N	SLC27A2_ENST00000380902.4_Silent_p.N137N	NM_003645.3	NP_003636.2	O14975	S27A2_HUMAN	solute carrier family 27 (fatty acid transporter), member 2	137					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid alpha-oxidation (GO:0001561)|fatty acid beta-oxidation (GO:0006635)|long-chain fatty acid import (GO:0044539)|long-chain fatty acid metabolic process (GO:0001676)|methyl-branched fatty acid metabolic process (GO:0097089)|small molecule metabolic process (GO:0044281)|very long-chain fatty acid catabolic process (GO:0042760)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of peroxisomal membrane (GO:0005779)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|fatty acid transporter activity (GO:0015245)|long-chain fatty acid-CoA ligase activity (GO:0004467)|phytanate-CoA ligase activity (GO:0050197)|pristanate-CoA ligase activity (GO:0070251)|receptor binding (GO:0005102)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			NS(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_lung(180;0.00177)		all cancers(107;1.16e-06)|GBM - Glioblastoma multiforme(94;0.000113)		TCAATTACAACATCCGCGCGA	0.657																																					p.N137N		Atlas-SNP	.											.	SLC27A2	50	.	0			c.C411T						PASS	.						99	107	104					15																	50475035		2196	4295	6491	SO:0001819	synonymous_variant	11001	exon1			TTACAACATCCGC	D88308	CCDS10133.1, CCDS53943.1	15q21.2	2013-05-22			ENSG00000140284	ENSG00000140284		"Acyl-CoA synthetase family", "Solute carriers"	10996	protein-coding gene	gene with protein product		603247		FACVL1		9730624	Standard	NM_003645		Approved	FATP2, hFACVL1, VLACS, VLCS, HsT17226, ACSVL1	uc001zxw.3	O14975	OTTHUMG00000131643	ENST00000267842.5:c.411C>T	15.37:g.50475035C>T		45	0	0		44	20	0.454545	NM_003645	A8K2J7|Q53FY6|Q6PF09	Silent	SNP	ENST00000267842.5	37	CCDS10133.1																																																																																			.	.	none		0.657	SLC27A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254539.2	NM_003645		T	50475035	C	T	50475035	2	4	24	1	0	0	0	0	0	0	0	1	14541	477	17	2		2	SLC27A2	15	50475035	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	6546695	50475035	52056357	467	8684											
GNB5	10681	hgsc.bcm.edu	37	chr15	52433397	52433397	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggtgtgcatagcaacagaCttctttttggcagccatgtt	8	15	10	8	0	1	1	0	0	1	1	1	1	1	1	1	2	4	4	1	2	2	6	rs17612637	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:52433397C>T	ENST00000261837.7	-	7	632	c.567G>A	c.(565-567)aaG>aaA	p.K189K	GNB5_ENST00000358784.7_Silent_p.K147K|CTD-2184D3.7_ENST00000557898.1_RNA|GNB5_ENST00000559348.1_5'Flank|GNB5_ENST00000396335.4_Intron|CTD-2184D3.7_ENST00000560613.1_RNA	NM_016194.3	NP_057278.2	O14775	GBB5_HUMAN	guanine nucleotide binding protein (G protein), beta 5	189					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)		TAGCAACAGACTTCTTTTTGG	0.473													C|||	82	0.0163738	0.0008	0.0389	5008	,	,		18151	0.0		0.0368	False		,,,				2504	0.0174				p.K189K		Atlas-SNP	.											.	GNB5	28	.	0			c.G567A						PASS	.	C	,	35,4355	39.2+/-71.8	1,33,2161	166	150	155		441,567	5.3	1	15	dbSNP_123	155	317,8269	112.5+/-172.7	4,309,3980	no	coding-synonymous,coding-synonymous	GNB5	NM_006578.3,NM_016194.3	,	5,342,6141	TT,TC,CC		3.6921,0.7973,2.7127	,	147/354,189/396	52433397	352,12624	2195	4293	6488	SO:0001819	synonymous_variant	10681	exon7			AACAGACTTCTTT	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.567G>A	15.37:g.52433397C>T		116	0	0		121	60	0.495868	NM_016194	B2RBR5|Q9HAU9|Q9UFT3	Silent	SNP	ENST00000261837.7	37	CCDS10149.1																																																																																			C|0.973;G|0.000;T|0.027	0.027	strong		0.473	GNB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254842.1			T	52433397	C	T	52433397	2	4	24	1	0	0	0	0	0	0	0	1	6529	564	20	2		2	GNB5	15	52433397	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1958362	52433397	50097995	468	8685											
GNB5	10681	hgsc.bcm.edu	37	chr15	52446260	52446260	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccagggcctccacccgctcCgccacctggtgcactggaat	6	6	10	19	2	0	0	0	0	0	0	2	1	2	1	7	3	1	2	7	3	1	0	rs35581121	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:52446260C>T	ENST00000261837.7	-	4	317	c.252G>A	c.(250-252)gcG>gcA	p.A84A	GNB5_ENST00000358784.7_Silent_p.A42A|GNB5_ENST00000396335.4_Silent_p.A42A|GNB5_ENST00000560116.1_Silent_p.A42A	NM_016194.3	NP_057278.2	O14775	GBB5_HUMAN	guanine nucleotide binding protein (G protein), beta 5	84					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)		CCACCCGCTCCGCCACCTGGT	0.562													C|||	84	0.0167732	0.0008	0.0389	5008	,	,		18869	0.001		0.0378	False		,,,				2504	0.0174				p.A84A		Atlas-SNP	.											.	GNB5	28	.	0			c.G252A						PASS	.	C	,	36,4354	40.0+/-72.8	1,34,2160	79	67	71		126,252	-11.1	0	15	dbSNP_126	71	317,8269	112.5+/-172.7	4,309,3980	no	coding-synonymous,coding-synonymous	GNB5	NM_006578.3,NM_016194.3	,	5,343,6140	TT,TC,CC		3.6921,0.82,2.7204	,	42/354,84/396	52446260	353,12623	2195	4293	6488	SO:0001819	synonymous_variant	10681	exon4			CCGCTCCGCCACC	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.252G>A	15.37:g.52446260C>T		45	0	0		51	28	0.54902	NM_016194	B2RBR5|Q9HAU9|Q9UFT3	Silent	SNP	ENST00000261837.7	37	CCDS10149.1																																																																																			C|0.973;T|0.027	0.027	strong		0.562	GNB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254842.1			T	52446260	C	T	52446260	2	4	24	1	0	0	0	0	0	0	0	1	6529	639	23	1		1	GNB5	15	52446260	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	12863	52446260	50085132	469	8686											
KIAA1370	56204	hgsc.bcm.edu	37	chr15	52905882	52905882	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attctcacctgggccagcttGtcactacattcatgtttggt	7	15	8	11	0	3	0	3	0	1	0	4	0	3	0	2	2	2	2	2	2	1	5			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:52905882G>A	ENST00000261844.7	-	3	341	c.189C>T	c.(187-189)gaC>gaT	p.D63D	FAM214A_ENST00000546305.2_Silent_p.D70D	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	63																	GGGCCAGCTTGTCACTACATT	0.368																																					p.D63D		Atlas-SNP	.											.	.	.	.	0			c.C189T						PASS	.						125	117	119					15																	52905882		1915	4142	6057	SO:0001819	synonymous_variant	56204	exon3			CAGCTTGTCACTA	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.189C>T	15.37:g.52905882G>A		74	0	0		97	32	0.329897	NM_019600	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Silent	SNP	ENST00000261844.7	37	CCDS45263.1																																																																																			.	.	none		0.368	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600		A	52905882	G	A	52905882	2	1	24	1	0	0	0	0	0	0	0	1	8235	1368	48	2		2	KIAA1370	15	52905882	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	459622	52905882	49625510	470	8687											
MYO1E	4643	hgsc.bcm.edu	37	chr15	59517011	59517011	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtttctgctctgcagaggcGccctcgatgagctggagcaa	7	10	13	11	2	2	2	0	1	2	1	3	4	2	3	1	2	4	5	1	2	1	1	rs373337685		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:59517011G>A	ENST00000288235.4	-	8	1053	c.654C>T	c.(652-654)ggC>ggT	p.G218G	MYO1E_ENST00000558814.1_5'UTR	NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	218	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)		CTGCAGAGGCGCCCTCGATGA	0.537																																					p.G218G		Atlas-SNP	.											.	MYO1E	99	.	0			c.C654T						PASS	.	G		0,4380		0,0,2190	93	73	80		654	-5	1	15		80	3,8577	3.0+/-9.4	0,3,4287	no	coding-synonymous	MYO1E	NM_004998.2		0,3,6477	AA,AG,GG		0.035,0.0,0.0231		218/1109	59517011	3,12957	2190	4290	6480	SO:0001819	synonymous_variant	4643	exon8			AGAGGCGCCCTCG	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.654C>T	15.37:g.59517011G>A		90	0	0		82	38	0.463415	NM_004998	Q14778	Silent	SNP	ENST00000288235.4	37	CCDS32254.1																																																																																			.	.	weak		0.537	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416024.1	NM_004998		A	59517011	G	A	59517011	2	1	24	1	0	0	0	0	0	0	0	1	10081	1074	38	1		1	MYO1E	15	59517011	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	6611129	59517011	43014381	471	8688											
NARG2	79664	hgsc.bcm.edu	37	chr15	60747576	60747576	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttcaatggtagctatatcGtcctttgacagctgcaactt	9	15	8	9	1	1	1	1	1	0	0	3	1	2	1	1	1	4	5	1	1	5	6	rs61753854	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:60747576G>A	ENST00000261520.4	-	7	966	c.732C>T	c.(730-732)gaC>gaT	p.D244D	NARG2_ENST00000561114.1_Silent_p.D244D|NARG2_ENST00000439632.1_Silent_p.D107D	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						TAGCTATATCGTCCTTTGACA	0.328													G|||	16	0.00319489	0.0	0.0014	5008	,	,		18300	0.0		0.002	False		,,,				2504	0.0133				p.D244D		Atlas-SNP	.											NARG2,NS,carcinoma,0,1	NARG2	82	1	0			c.C732T						PASS	.	G	,	2,4402	2.1+/-5.4	0,2,2200	193	175	181		321,732	-2.8	0	15	dbSNP_129	181	19,8581	13.3+/-46.6	0,19,4281	no	coding-synonymous,coding-synonymous	NARG2	NM_001018089.1,NM_024611.4	,	0,21,6481	AA,AG,GG		0.2209,0.0454,0.1615	,	107/846,244/983	60747576	21,12983	2202	4300	6502	SO:0001819	synonymous_variant	79664	exon7			TATATCGTCCTTT																												ENST00000261520.4:c.732C>T	15.37:g.60747576G>A		113	0	0		122	59	0.483607	NM_024611		Silent	SNP	ENST00000261520.4	37	CCDS10176.1																																																																																			G|0.998;A|0.002	0.002	strong		0.328	NARG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256136.1			A	60747576	G	A	60747576	2	1	24	1	0	0	0	0	0	0	0	1	10178	1136	40	1		1	NARG2	15	60747576	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1230565	60747576	41783816	472	8689											
DENND4A	10260	hgsc.bcm.edu	37	chr15	65957717	65957717	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agaatgtacaagggctgtccCggatcctgatgtaacttcat	11	11	10	9	1	1	2	1	1	0	1	3	3	3	3	2	2	2	3	2	2	4	3	rs61751113	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:65957717C>G	ENST00000431932.2	-	29	5401	c.5193G>C	c.(5191-5193)ccG>ccC	p.P1731P	DENND4A_ENST00000443035.3_Silent_p.P1774P	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	1731					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						AGGGCTGTCCCGGATCCTGAT	0.373													C|||	21	0.00419329	0.0008	0.0101	5008	,	,		16939	0.0		0.0089	False		,,,				2504	0.0041				p.P1774P		Atlas-SNP	.											.	DENND4A	217	.	0			c.G5322C						PASS	.	C	,	2,3794		0,2,1896	153	152	152		5322,5193	-6.4	0.9	15	dbSNP_129	152	123,8115		1,121,3997	no	coding-synonymous,coding-synonymous	DENND4A	NM_001144823.1,NM_005848.3	,	1,123,5893	GG,GC,CC		1.4931,0.0527,1.0387	,	1774/1907,1731/1864	65957717	125,11909	1898	4119	6017	SO:0001819	synonymous_variant	10260	exon30			CTGTCCCGGATCC	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.5193G>C	15.37:g.65957717C>G		121	0	0		123	69	0.560976	NM_001144823	E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Silent	SNP	ENST00000431932.2	37	CCDS45285.1																																																																																			C|0.991;G|0.009	0.009	strong		0.373	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1	NM_005848		G	65957717	C	G	65957717	2	3	24	1	0	0	0	0	0	0	0	1	4435	639	23	4		4	DENND4A	15	65957717	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	5210141	65957717	36573675	473	8690											
IQCH	64799	hgsc.bcm.edu	37	chr15	67692566	67692566	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cattttgtgatattccttccTacctaaagtgctacaaatgg	11	15	6	9	0	0	1	0	1	0	0	2	1	2	1	3	1	3	1	3	1	6	8	rs35933176	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:67692566T>C	ENST00000335894.4	+	14	2086	c.2020T>C	c.(2020-2022)Tac>Cac	p.Y674H	IQCH_ENST00000546225.1_Missense_Mutation_p.Y331H|IQCH_ENST00000358767.3_Missense_Mutation_p.Y410H|IQCH_ENST00000360277.4_Missense_Mutation_p.Y335H	NM_001031715.2	NP_001026885	Q86VS3	IQCH_HUMAN	IQ motif containing H	674										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)		TATTCCTTCCTACCTAAAGTG	0.428													T|||	5	0.000998403	0.0	0.0	5008	,	,		19892	0.0		0.005	False		,,,				2504	0.0				p.Y674H		Atlas-SNP	.											.	IQCH	81	.	0			c.T2020C						PASS	.	T	HIS/TYR	0,4402		0,0,2201	143	134	137		2020	2.5	1	15	dbSNP_126	137	41,8557	27.4+/-76.7	0,41,4258	yes	missense	IQCH	NM_001031715.2	83	0,41,6459	CC,CT,TT		0.4769,0.0,0.3154	benign	674/1028	67692566	41,12959	2201	4299	6500	SO:0001583	missense	64799	exon14			CCTTCCTACCTAA	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.2020T>C	15.37:g.67692566T>C	ENSP00000336861:p.Tyr674His	197	0	0		224	107	0.477679	NM_001031715	A8K8W3|C9JPR6|D6RJ88|Q4G0S6|Q8NEH9|Q9BWX2|Q9H9Y1|Q9UF88	Missense_Mutation	SNP	ENST00000335894.4	37	CCDS32273.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	T	2.755	-0.259212	0.05791	0.0	0.004769	ENSG00000103599	ENST00000358767;ENST00000546225;ENST00000335894;ENST00000360277	T;T;T;T	0.38722	1.12;1.13;1.15;1.12	5.43	2.45	0.29901	.	0.106121	0.64402	N	0.000006	T	0.06325	0.0163	N	0.00197	-1.87	0.27379	N	0.955461	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.33929	-0.9849	10	0.07644	T	0.81	-22.218	9.1639	0.37038	0.0:0.734:0.0:0.266	rs35933176	331;335;674	Q86VS3-2;Q86VS3-4;Q86VS3	.;.;IQCH_HUMAN	H	410;331;674;335	ENSP00000351617:Y410H;ENSP00000444118:Y331H;ENSP00000336861:Y674H;ENSP00000353419:Y335H	ENSP00000336861:Y674H	Y	+	1	0	IQCH	65479620	0.957000	0.32711	0.983000	0.44433	0.741000	0.42261	2.152000	0.42272	0.224000	0.20940	-0.250000	0.11733	TAC	T|0.997;C|0.003	0.003	strong		0.428	IQCH-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256969.1	NM_022784		C	67692566	T	C	67692566	3	2	24	1	0	0	0	0	1	0	0	0	7820	1522	53	3	2202	3	IQCH	15	67692566	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	1734849	67692566	34838826	474	8691											
ITGA11	22801	hgsc.bcm.edu	37	chr15	68653946	68653946	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actttggagagctggggccaCggtcttggagaacctgaagt	9	9	15	8	1	1	3	0	1	1	2	1	5	1	3	2	5	2	1	2	5	2	2	rs148886354	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:68653946C>T	ENST00000315757.7	-	5	540	c.454G>A	c.(454-456)Gtg>Atg	p.V152M	ITGA11_ENST00000423218.2_Missense_Mutation_p.V152M|ITGA11_ENST00000562826.1_5'UTR	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	152					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						GCTGGGGCCACGGTCTTGGAG	0.557													C|||	3	0.000599042	0.0	0.0014	5008	,	,		20919	0.001		0.001	False		,,,				2504	0.0				p.V152M		Atlas-SNP	.											.	ITGA11	110	.	0			c.G454A						PASS	.	C	MET/VAL	0,3976		0,0,1988	74	74	74		454	4.7	1	15	dbSNP_134	74	12,8308		0,12,4148	yes	missense	ITGA11	NM_001004439.1	21	0,12,6136	TT,TC,CC		0.1442,0.0,0.0976	probably-damaging	152/1189	68653946	12,12284	1988	4160	6148	SO:0001583	missense	22801	exon5			GGGCCACGGTCTT	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.454G>A	15.37:g.68653946C>T	ENSP00000327290:p.Val152Met	51	0	0		51	29	0.568627	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	37	CCDS45291.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	1	0.0017482517482517483	1	0.0013192612137203166	C	14.81	2.646911	0.47258	0.0	0.001442	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000537153	T;T	0.60040	0.22;0.22	4.66	4.66	0.58398	.	0.063133	0.64402	D	0.000004	T	0.52996	0.1769	M	0.61703	1.905	0.43050	D	0.994657	P;P	0.43607	0.812;0.809	B;B	0.34489	0.163;0.184	T	0.62812	-0.6775	10	0.49607	T	0.09	.	16.915	0.86149	0.0:1.0:0.0:0.0	.	152;152	A8K8T0;Q9UKX5	.;ITA11_HUMAN	M	152	ENSP00000327290:V152M;ENSP00000403392:V152M	ENSP00000327290:V152M	V	-	1	0	ITGA11	66441000	0.998000	0.40836	0.999000	0.59377	0.993000	0.82548	3.185000	0.50934	2.282000	0.76494	0.555000	0.69702	GTG	C|0.999;T|0.001	0.001	strong		0.557	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211		T	68653946	C	T	68653946	3	4	24	1	0	0	0	0	1	0	0	0	7883	536	19	1	3216	1	ITGA11	15	68653946	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	961380	68653946	33877446	475	8692											
LINGO1	84894	hgsc.bcm.edu	37	chr15	77907658	77907658	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtcaggttgcatttctccagCgtcagctgctccaggctgtt	5	13	11	12	1	3	0	2	0	1	0	5	0	4	0	2	2	4	6	2	2	0	3			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:77907658C>T	ENST00000355300.6	-	2	765	c.591G>A	c.(589-591)acG>acA	p.T197T	LINGO1_ENST00000561030.1_Silent_p.T191T	NM_032808.5	NP_116197.4	Q96FE5	LIGO1_HUMAN	leucine rich repeat and Ig domain containing 1	197					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						ATTTCTCCAGCGTCAGCTGCT	0.602																																					p.T197T		Atlas-SNP	.											.	LINGO1	76	.	0			c.G591A						PASS	.						111	119	117					15																	77907658		2175	4274	6449	SO:0001819	synonymous_variant	84894	exon2			CTCCAGCGTCAGC	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.591G>A	15.37:g.77907658C>T		104	0	0		124	62	0.5	NM_032808	D3DW80|Q6NUK3|Q6UXM3|Q6VVG0|Q6VVG1|Q6VVG2|Q8N3K5|Q96K52	Silent	SNP	ENST00000355300.6	37	CCDS45313.1																																																																																			.	.	none		0.602	LINGO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419546.1	NM_032808		T	77907658	C	T	77907658	2	4	24	1	0	0	0	0	0	0	0	1	8823	755	27	1		1	LINGO1	15	77907658	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	9253712	77907658	24623734	476	8693											
ADAMTSL3	57188	hgsc.bcm.edu	37	chr15	84639314	84639314	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cagccaaaggtcggcgcatcCccctcagtgagatgatgtgc	9	7	12	13	2	1	2	1	2	0	1	3	3	2	2	3	2	2	1	3	2	1	0			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:84639314C>T	ENST00000286744.5	+	20	2793	c.2569C>T	c.(2569-2571)Ccc>Tcc	p.P857S	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.P857S|ADAMTSL3_ENST00000567716.1_3'UTR	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	857	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)			TCGGCGCATCCCCCTCAGTGA	0.522																																					p.P857S		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.C2569T						PASS	.						189	166	174					15																	84639314		2203	4300	6503	SO:0001583	missense	57188	exon20			CGCATCCCCCTCA	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.2569C>T	15.37:g.84639314C>T	ENSP00000286744:p.Pro857Ser	97	0	0		102	58	0.568627	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	.	.	.	.	.	.	.	.	.	.	C	11.44	1.640716	0.29157	.	.	ENSG00000156218	ENST00000286744	T	0.51574	0.7	4.39	-0.603	0.11630	.	1.472120	0.04463	N	0.374714	T	0.33702	0.0872	L	0.44542	1.39	0.09310	N	1	B;B	0.13145	0.001;0.007	B;B	0.11329	0.006;0.005	T	0.10613	-1.0622	10	0.08599	T	0.76	.	3.5686	0.07909	0.2274:0.39:0.296:0.0866	.	857;857	P82987-2;P82987	.;ATL3_HUMAN	S	857	ENSP00000286744:P857S	ENSP00000286744:P857S	P	+	1	0	ADAMTSL3	82430318	0.000000	0.05858	0.000000	0.03702	0.244000	0.25665	0.095000	0.15127	0.064000	0.16427	0.650000	0.86243	CCC	.	.	none		0.522	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517		T	84639314	C	T	84639314	3	4	24	1	0	0	0	0	1	0	0	0	276	623	22	2	2643	2	ADAMTSL3	15	84639314	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	6731656	84639314	17892078	477	8694											
AGBL1	123624	hgsc.bcm.edu	37	chr15	86790997	86790997	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgacacagccaacgcctacGtgcagatccgacggggcttg	10	6	12	13	4	0	2	0	1	0	1	1	3	1	2	3	2	4	2	3	2	2	2	rs149477284	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:86790997G>A	ENST00000441037.2	+	6	579	c.484G>A	c.(484-486)Gtg>Atg	p.V162M	AGBL1_ENST00000421325.2_Missense_Mutation_p.V162M	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	162					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						CAACGCCTACGTGCAGATCCG	0.642													G|||	14	0.00279553	0.0	0.0029	5008	,	,		19735	0.0		0.0119	False		,,,				2504	0.0				p.V162M		Atlas-SNP	.											.	AGBL1	151	.	0			c.G484A						PASS	.	G	MET/VAL	12,4312		0,12,2150	37	39	38		484	1.9	0	15	dbSNP_134	38	103,8421		1,101,4160	yes	missense	AGBL1	NM_152336.2	21	1,113,6310	AA,AG,GG		1.2084,0.2775,0.8951	probably-damaging	162/1067	86790997	115,12733	2162	4262	6424	SO:0001583	missense	123624	exon6			GCCTACGTGCAGA	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.484G>A	15.37:g.86790997G>A	ENSP00000413001:p.Val162Met	98	0	0		115	58	0.504348	NM_152336	A1A4X5|A6NJH6|C9JHL5	Missense_Mutation	SNP	ENST00000441037.2	37	CCDS58398.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	G	0.010	-1.782928	0.00634	0.002775	0.012084	ENSG00000166748	ENST00000441037;ENST00000421325	T	0.33865	1.39	5.16	1.86	0.25419	Armadillo-like helical (1);Armadillo-type fold (1);	.	.	.	.	T	0.09730	0.0239	L	0.31207	0.915	0.80722	D	1	P	0.39352	0.669	B	0.20955	0.032	T	0.25082	-1.0142	9	0.05525	T	0.97	-7.5937	5.0261	0.14385	0.4866:0.0:0.5134:0.0	.	162	Q96MI9	CBPC4_HUMAN	M	191;162	ENSP00000397173:V162M	ENSP00000397173:V162M	V	+	1	0	AGBL1	84592001	0.099000	0.21834	0.007000	0.13788	0.085000	0.17905	0.616000	0.24344	0.575000	0.29434	-0.258000	0.10820	GTG	G|0.995;A|0.005	0.005	strong		0.642	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336		A	86790997	G	A	86790997	3	1	24	1	0	0	0	0	1	0	0	0	375	1145	40	1	502	1	AGBL1	15	86790997	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	2151683	86790997	15740395	478	8695											
C15orf58	390637	hgsc.bcm.edu	37	chr15	90784632	90784632	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aacgtcagccccctggagtgGggccacgtgctgctggtgcc	5	7	15	14	2	1	0	1	0	0	0	1	1	1	1	4	4	5	2	4	4	1	0	rs144466387	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:90784632G>T	ENST00000558017.1	+	4	912	c.492G>T	c.(490-492)tgG>tgT	p.W164C	GDPGP1_ENST00000329600.6_Missense_Mutation_p.W164C	NM_001013657.2	NP_001013679.2	Q6ZNW5	GDPP1_HUMAN	GDP-D-glucose phosphorylase 1	164					glucose metabolic process (GO:0006006)	cytoplasm (GO:0005737)	GDP-D-glucose phosphorylase activity (GO:0080048)|guanyl-nucleotide exchange factor activity (GO:0005085)|hydrolase activity (GO:0016787)|nucleotide binding (GO:0000166)|nucleotidyltransferase activity (GO:0016779)										CCCTGGAGTGGGGCCACGTGC	0.652													G|||	2	0.000399361	0.0	0.0014	5008	,	,		16490	0.0		0.001	False		,,,				2504	0.0				p.W164C		Atlas-SNP	.											.	.	.	.	0			c.G492T						PASS	.	G	CYS/TRP	0,4398		0,0,2199	49	53	52		492	3.9	1	15	dbSNP_134	52	13,8583	9.8+/-36.6	0,13,4285	yes	missense	C15orf58	NM_001013657.2	215	0,13,6484	TT,TG,GG		0.1512,0.0,0.1	probably-damaging	164/386	90784632	13,12981	2199	4298	6497	SO:0001583	missense	390637	exon4			GGAGTGGGGCCAC		CCDS32327.1	15q26.1	2012-05-04	2012-05-04	2012-05-04	ENSG00000183208	ENSG00000183208	2.7.7.78		34360	protein-coding gene	gene with protein product			"chromosome 15 open reading frame 58"	C15orf58		21507950	Standard	NM_001013657		Approved		uc002bpc.3	Q6ZNW5		ENST00000558017.1:c.492G>T	15.37:g.90784632G>T	ENSP00000452793:p.Trp164Cys	52	0	0		51	24	0.470588	NM_001013657		Missense_Mutation	SNP	ENST00000558017.1	37	CCDS32327.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	15.09	2.729619	0.48833	0.0	0.001512	ENSG00000183208	ENST00000329600	T	0.22539	1.95	5.85	3.93	0.45458	.	0.291899	0.33591	N	0.004747	T	0.35248	0.0925	M	0.67953	2.075	0.58432	D	0.999999	D	0.64830	0.994	P	0.58391	0.838	T	0.04053	-1.0981	10	0.38643	T	0.18	-6.2663	9.1104	0.36723	0.0:0.2636:0.4647:0.2716	.	164	Q6ZNW5	VTC2_HUMAN	C	164	ENSP00000368405:W164C	ENSP00000368405:W164C	W	+	3	0	C15orf58	88585636	1.000000	0.71417	1.000000	0.80357	0.710000	0.40934	2.143000	0.42187	0.776000	0.33473	-0.165000	0.13383	TGG	G|0.999;T|0.001	0.001	strong		0.652	GDPGP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416973.1	NM_001013657		T	90784632	G	T	90784632	3	4	24	1	0	0	0	0	1	0	0	0	1808	1241	43	4	494	4	C15orf58	15	90784632	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	3993635	90784632	11746760	479	8696											
UNC45A	55898	hgsc.bcm.edu	37	chr15	91496233	91496233	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggagcatgagatgatccgccGggcagccacggagtgcatgt	9	6	16	10	3	0	2	0	2	0	1	1	5	1	4	3	3	3	3	3	3	0	0	rs149872991		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:91496233G>A	ENST00000418476.2	+	18	2418	c.2378G>A	c.(2377-2379)cGg>cAg	p.R793Q	AC068831.6_ENST00000553321.1_RNA|UNC45A_ENST00000394275.2_Missense_Mutation_p.R778Q|RCCD1_ENST00000555155.1_5'Flank|RCCD1_ENST00000556618.1_5'Flank|RCCD1_ENST00000394258.2_5'Flank	NM_018671.3	NP_061141.2	Q9H3U1	UN45A_HUMAN	unc-45 homolog A (C. elegans)	793					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)			ATGATCCGCCGGGCAGCCACG	0.582													g|||	1	0.000199681	0.0	0.0	5008	,	,		22008	0.0		0.001	False		,,,				2504	0.0				p.R793Q		Atlas-SNP	.											.	UNC45A	57	.	0			c.G2378A						PASS	.		GLN/ARG,GLN/ARG	1,4395	2.1+/-5.4	0,1,2197	83	62	69		2333,2378	4.9	1	15	dbSNP_134	69	7,8589	5.7+/-21.5	0,7,4291	yes	missense,missense	UNC45A	NM_001039675.1,NM_018671.3	43,43	0,8,6488	AA,AG,GG		0.0814,0.0227,0.0616	benign,benign	778/930,793/945	91496233	8,12984	2198	4298	6496	SO:0001583	missense	55898	exon18			TCCGCCGGGCAGC		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.2378G>A	15.37:g.91496233G>A	ENSP00000407487:p.Arg793Gln	42	0	0		49	27	0.55102	NM_018671	A8K6F7|Q7L3Y6|Q9H3U8|Q9NSE8|Q9NSE9	Missense_Mutation	SNP	ENST00000418476.2	37	CCDS10367.1	.	.	.	.	.	.	.	.	.	.	g	15.13	2.742516	0.49151	2.27E-4	8.14E-4	ENSG00000140553	ENST00000394275;ENST00000418476	T;T	0.49720	0.77;0.77	4.88	4.88	0.63580	Armadillo-like helical (1);Armadillo-type fold (1);	0.457993	0.23413	N	0.048457	T	0.28830	0.0715	N	0.25992	0.78	0.37116	D	0.900608	P;P	0.48640	0.913;0.913	B;B	0.33799	0.17;0.17	T	0.30909	-0.9962	10	0.40728	T	0.16	-27.8398	10.8602	0.46823	0.0:0.0:0.7065:0.2935	.	793;778	Q9H3U1;A8K6F7	UN45A_HUMAN;.	Q	778;793	ENSP00000377816:R778Q;ENSP00000407487:R793Q	ENSP00000377816:R778Q	R	+	2	0	UNC45A	89297237	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.880000	0.39628	2.549000	0.85964	0.645000	0.84053	CGG	G|1.000;A|0.000	0.000	strong		0.582	UNC45A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280406.2	NM_018671		A	91496233	G	A	91496233	3	1	24	1	0	0	0	0	1	0	0	0	17003	1116	39	1	2448	1	UNC45A	15	91496233	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	711601	91496233	11035159	480	8697											
SLCO3A1	28232	hgsc.bcm.edu	37	chr15	92647684	92647684	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggccatgctctccgaaagAgaatacgagagacccaagcc	14	4	10	13	2	1	2	0	0	1	2	2	6	1	2	4	1	3	1	4	1	4	1	rs72655652	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:92647684A>C	ENST00000318445.6	+	4	1135	c.921A>C	c.(919-921)agA>agC	p.R307S	SLCO3A1_ENST00000424469.2_Missense_Mutation_p.R307S|SLCO3A1_ENST00000555549.1_3'UTR	NM_013272.3	NP_037404.2	Q9UIG8	SO3A1_HUMAN	solute carrier organic anion transporter family, member 3A1	307					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)	TCTCCGAAAGAGAATACGAGA	0.592													A|||	35	0.00698882	0.0008	0.0058	5008	,	,		16771	0.0		0.0139	False		,,,				2504	0.0164				p.R307S		Atlas-SNP	.											.	SLCO3A1	84	.	0			c.A921C						PASS	.	A	SER/ARG,SER/ARG	7,4389	15.5+/-35.6	0,7,2191	81	71	74		921,921	5.3	1	15	dbSNP_130	74	123,8473	64.2+/-126.4	2,119,4177	yes	missense,missense	SLCO3A1	NM_001145044.1,NM_013272.3	110,110	2,126,6368	CC,CA,AA		1.4309,0.1592,1.0006	benign,benign	307/693,307/711	92647684	130,12862	2198	4298	6496	SO:0001583	missense	28232	exon4			CGAAAGAGAATAC	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.921A>C	15.37:g.92647684A>C	ENSP00000320634:p.Arg307Ser	157	0	0		191	96	0.502618	NM_013272	A8K4A7|B3KPY5|B3KUR7|C6G486|Q9BW73|Q9GZV2	Missense_Mutation	SNP	ENST00000318445.6	37	CCDS10371.1	14	0.00641025641025641	0	0.0	3	0.008287292817679558	0	0.0	11	0.014511873350923483	A	10.86	1.469546	0.26423	0.001592	0.014309	ENSG00000176463	ENST00000318445;ENST00000424469;ENST00000556649;ENST00000555549	T;T	0.38722	1.12;1.12	5.31	5.31	0.75309	Major facilitator superfamily domain, general substrate transporter (1);	0.648102	0.16571	N	0.208631	T	0.10680	0.0261	N	0.01640	-0.785	0.46203	D	0.998922	B;B;B	0.10296	0.001;0.003;0.0	B;B;B	0.11329	0.001;0.001;0.006	T	0.13737	-1.0498	10	0.09084	T	0.74	.	8.0237	0.30425	0.8765:0.0:0.1235:0.0	.	249;307;307	Q9UIG8-3;Q9UIG8-2;Q9UIG8	.;.;SO3A1_HUMAN	S	307;307;100;26	ENSP00000320634:R307S;ENSP00000387846:R307S	ENSP00000320634:R307S	R	+	3	2	SLCO3A1	90448688	1.000000	0.71417	0.988000	0.46212	0.864000	0.49448	2.032000	0.41127	1.987000	0.57996	0.533000	0.62120	AGA	A|0.990;C|0.010	0.010	strong		0.592	SLCO3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313529.1	NM_013272		C	92647684	A	C	92647684	3	2	24	1	0	0	0	0	1	0	0	0	14743	301	11	5	935	5	SLCO3A1	15	92647684	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	1151451	92647684	9883708	481	8698											
LRRK1	79705	hgsc.bcm.edu	37	chr15	101593597	101593597	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctcgcgccgctcagcagcctCaacaccgtgctgtccgagaa	8	6	10	17	5	2	1	2	0	0	1	4	2	3	1	4	0	4	3	4	0	2	0	rs41418955	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr15:101593597C>T	ENST00000388948.3	+	26	4385	c.4026C>T	c.(4024-4026)ctC>ctT	p.L1342L	RP11-505E24.2_ENST00000559857.1_RNA|LRRK1_ENST00000284395.5_Silent_p.L1339L	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)			TCAGCAGCCTCAACACCGTGC	0.731													C|||	15	0.00299521	0.0	0.0043	5008	,	,		15960	0.0		0.0109	False		,,,				2504	0.001				p.L1342L		Atlas-SNP	.											.	LRRK1	310	.	0			c.C4026T						PASS	.	C		8,4328		0,8,2160	14	17	16		4026	3	1	15	dbSNP_127	16	75,8439		0,75,4182	no	coding-synonymous	LRRK1	NM_024652.3		0,83,6342	TT,TC,CC		0.8809,0.1845,0.6459		1342/2016	101593597	83,12767	2168	4257	6425	SO:0001819	synonymous_variant	79705	exon26			CAGCCTCAACACC	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.4026C>T	15.37:g.101593597C>T		20	0	0		21	12	0.571429	NM_024652		Silent	SNP	ENST00000388948.3	37	CCDS42086.1																																																																																			C|0.993;T|0.007	0.007	strong		0.731	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		T	101593597	C	T	101593597	2	4	24	1	0	0	0	0	0	0	0	1	9041	813	29	2		2	LRRK1	15	101593597	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	8945913	101593597	937795	482	8699											
DECR2	26063	hgsc.bcm.edu	37	chr16	460976	460976	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	actttcttctgtgcagacgcGatgacgcggcacttggctgt	6	12	12	11	4	2	2	0	1	2	1	2	3	2	2	0	2	1	3	0	2	0	3	rs140561403	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:460976G>A	ENST00000219481.5	+	7	699	c.561G>A	c.(559-561)gcG>gcA	p.A187A	DECR2_ENST00000424398.2_Silent_p.A175A|DECR2_ENST00000461947.1_3'UTR	NM_020664.3	NP_065715.1	Q9NUI1	DECR2_HUMAN	2,4-dienoyl CoA reductase 2, peroxisomal	187					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)				GTGCAGACGCGATGACGCGGC	0.657													G|||	28	0.00559105	0.0008	0.0187	5008	,	,		16609	0.001		0.0119	False		,,,				2504	0.001				p.A187A		Atlas-SNP	.											DECR2,NS,carcinoma,+1,1	DECR2	47	1	0			c.G561A						PASS	.	G		37,4355		0,37,2159	43	41	42		561	-11	0.5	16	dbSNP_134	42	141,8453		1,139,4157	no	coding-synonymous	DECR2	NM_020664.3		1,176,6316	AA,AG,GG		1.6407,0.8424,1.3707		187/293	460976	178,12808	2196	4297	6493	SO:0001819	synonymous_variant	26063	exon7			AGACGCGATGACG	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.561G>A	16.37:g.460976G>A		91	0	0		105	55	0.52381	NM_020664	Q6ZRS7|Q96ET0	Silent	SNP	ENST00000219481.5	37	CCDS10409.1																																																																																			G|0.988;A|0.012	0.012	strong		0.657	DECR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109069.4	NM_020664		A	460976	G	A	460976	2	1	24	1	0	0	0	0	0	0	0	1	4385	1045	37	1		1	DECR2	16	460976	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10		460976	89893777	483	8700											
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1268596	1268596	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gtgcctgcctcggcgccccaCccccgcccgctgcaggaggt	3	5	13	20	4	0	0	0	0	0	0	1	1	0	1	7	3	3	2	7	3	0	0	rs372529098		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1268596C>T	ENST00000348261.5	+	33	6080	c.5832C>T	c.(5830-5832)caC>caT	p.H1944H	CACNA1H_ENST00000358590.4_Silent_p.H1938H|CACNA1H_ENST00000565831.1_Silent_p.H1938H	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1944					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)	CGGCGCCCCACCCCCGCCCGC	0.657																																					p.H1944H		Atlas-SNP	.											.	CACNA1H	317	.	0			c.C5832T						PASS	.	C	,	0,3962		0,0,1981	13	17	16		5814,5832	-2.1	0	16		16	2,8230		0,2,4114	no	coding-synonymous,coding-synonymous	CACNA1H	NM_001005407.1,NM_021098.2	,	0,2,6095	TT,TC,CC		0.0243,0.0,0.0164	,	1938/2348,1944/2354	1268596	2,12192	1981	4116	6097	SO:0001819	synonymous_variant	8912	exon33			GCCCCACCCCCGC	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.5832C>T	16.37:g.1268596C>T		97	0	0		103	45	0.436893	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	37	CCDS45375.1																																																																																			.	.	weak		0.657	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		T	1268596	C	T	1268596	2	4	24	1	0	0	0	0	0	0	0	1	2547	506	18	2		2	CACNA1H	16	1268596	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	807620	1268596	89086157	484	8701											
TPSG1	8912	hgsc.bcm.edu	37	chr16	1272655	1272655	+	IGR	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccacgggggctcctcacctcCctcccgcgtatagccccagc	5	6	9	21	3	1	0	1	0	0	0	4	0	4	0	7	2	2	2	7	2	2	2	rs117769620	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1272655C>T	ENST00000348261.5	+	0	8084				TPSG1_ENST00000234798.4_Missense_Mutation_p.G170R	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)	TCCTCACCTCCCTCCCGCGTA	0.667													c|||	13	0.00259585	0.0	0.0014	5008	,	,		15592	0.0		0.0109	False		,,,				2504	0.001				p.G170R		Atlas-SNP	.											.	TPSG1	19	.	0			c.G508A						PASS	.		ARG/GLY	3,4389	6.2+/-15.9	0,3,2193	70	87	81		508	2.5	0.8	16	dbSNP_132	81	56,8540	32.8+/-85.7	0,56,4242	yes	missense	TPSG1	NM_012467.3	125	0,59,6435	TT,TC,CC		0.6515,0.0683,0.4543	possibly-damaging	170/322	1272655	59,12929	2196	4298	6494	SO:0001628	intergenic_variant	25823	exon4			CACCTCCCTCCCG	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			16.37:g.1272655C>T		130	0	0		110	53	0.481818	NM_012467	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	11	0.005036630036630037	0	0.0	1	0.0027624309392265192	0	0.0	10	0.013192612137203167	c	13.73	2.323926	0.41096	6.83E-4	0.006515	ENSG00000116176	ENST00000234798	D	0.93763	-3.28	3.47	2.48	0.30137	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	D	0.90123	0.6914	L	0.58101	1.795	0.39248	D	0.963972	D	0.52996	0.957	P	0.52031	0.688	D	0.87282	0.2293	9	0.25751	T	0.34	.	9.1608	0.37021	0.0:0.8827:0.0:0.1173	.	170	Q9NRR2	TRYG1_HUMAN	R	170	ENSP00000234798:G170R	ENSP00000234798:G170R	G	-	1	0	TPSG1	1212656	0.119000	0.22226	0.814000	0.32528	0.083000	0.17756	0.758000	0.26447	0.518000	0.28383	0.556000	0.70494	GGA	C|0.995;T|0.005	0.005	strong		0.667	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		T	1272655	C	T	1272655	1	4	24	0	1	0	0	0	0	0	0	0	16441	632	22	2		2	TPSG1	16	1272655	IGR	SNP	C	TCGA-G8-6326-01A-11D-2210-10	4059	1272655	89082098	485	8702											
BAIAP3	8938	hgsc.bcm.edu	37	chr16	1384715	1384715	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgccaggtgacctgcaccTgggcaccgccatcggcttcg	5	6	12	18	4	0	1	0	1	0	0	2	1	0	1	6	3	1	3	6	3	0	1	rs200858324	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1384715T>C	ENST00000324385.5	+	1	211	c.53T>C	c.(52-54)cTg>cCg	p.L18P	BAIAP3_ENST00000397489.1_5'UTR|BAIAP3_ENST00000397488.2_Intron|BAIAP3_ENST00000426824.3_Intron|BAIAP3_ENST00000562208.1_Intron|BAIAP3_ENST00000568887.1_Intron|BAIAP3_ENST00000421665.2_5'Flank	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	18					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)				GACCTGCACCTGGGCACCGCC	0.667													T|||	4	0.000798722	0.0	0.0	5008	,	,		13202	0.0		0.004	False		,,,				2504	0.0				p.L18P		Atlas-SNP	.											.	BAIAP3	88	.	0			c.T53C						PASS	.	T	PRO/LEU,,,	0,4224		0,0,2112	8	9	9		53,,,	-3	0	16		9	6,8358		0,6,4176	yes	missense,intron,intron,intron	BAIAP3	NM_003933.4,NM_001199097.1,NM_001199098.1,NM_001199099.1	98,,,	0,6,6288	CC,CT,TT		0.0717,0.0,0.0477	possibly-damaging,,,	18/1188,,,	1384715	6,12582	2112	4182	6294	SO:0001583	missense	8938	exon1			TGCACCTGGGCAC	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.53T>C	16.37:g.1384715T>C	ENSP00000324510:p.Leu18Pro	138	0	0		192	79	0.411458	NM_003933	A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Missense_Mutation	SNP	ENST00000324385.5	37	CCDS10434.1	.	.	.	.	.	.	.	.	.	.	T	9.024	0.985626	0.18889	0.0	7.17E-4	ENSG00000007516	ENST00000324385	T	0.73258	-0.73	1.48	-2.96	0.05547	.	5.452210	0.01821	U	0.034057	T	0.44767	0.1309	N	0.08118	0	0.09310	N	0.999994	P;P	0.44734	0.842;0.617	B;B	0.32342	0.144;0.065	T	0.49021	-0.8982	10	0.56958	D	0.05	.	6.6146	0.22771	0.0:0.0:0.4668:0.5332	.	18;18	B4DGA2;O94812	.;BAIP3_HUMAN	P	18	ENSP00000324510:L18P	ENSP00000324510:L18P	L	+	2	0	BAIAP3	1324716	0.000000	0.05858	0.000000	0.03702	0.082000	0.17680	-2.273000	0.01164	-1.100000	0.03030	0.172000	0.16884	CTG	.	.	weak		0.667	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3			C	1384715	T	C	1384715	3	2	24	1	0	0	0	0	1	0	0	0	1304	1580	55	3	55	3	BAIAP3	16	1384715	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	112060	1384715	88970038	486	8703											
PTX4	390667	hgsc.bcm.edu	37	chr16	1537510	1537510	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctctgaagcttcagggaggtCgggcccagctcctcaggctg	6	8	14	13	1	3	1	2	1	1	0	5	2	4	2	2	4	2	3	2	4	1	1	rs201970670	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1537510C>T	ENST00000447419.2	-	2	628	c.603G>A	c.(601-603)ccG>ccA	p.P201P	PTX4_ENST00000440447.2_Intron|PTX4_ENST00000293922.1_Silent_p.P196P			Q96A99	PTX4_HUMAN	pentraxin 4, long	201						extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						TCAGGGAGGTCGGGCCCAGCT	0.726													C|||	13	0.00259585	0.0	0.0058	5008	,	,		14445	0.0		0.0089	False		,,,				2504	0.0				p.P196P		Atlas-SNP	.											.	PTX4	46	.	0			c.G588A						PASS	.	C		12,4368		0,12,2178	11	13	13		588	-10.4	0	16		13	113,8431		0,113,4159	no	coding-synonymous	PTX4	NM_001013658.1		0,125,6337	TT,TC,CC		1.3226,0.274,0.9672		196/474	1537510	125,12799	2190	4272	6462	SO:0001819	synonymous_variant	390667	exon2			GGAGGTCGGGCCC		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"chromosome 16 open reading frame 38"	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.603G>A	16.37:g.1537510C>T		66	0	0		53	21	0.396226	NM_001013658		Silent	SNP	ENST00000447419.2	37																																																																																				C|0.997;T|0.003	0.003	strong		0.726	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658		T	1537510	C	T	1537510	2	4	24	1	0	0	0	0	0	0	0	1	12838	871	31	1		1	PTX4	16	1537510	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	152795	1537510	88817243	487	8704											
HAGH	3029	hgsc.bcm.edu	37	chr16	1869940	1869940	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atcttgtgagtcagggccccGatacggtcgtcacccccgta	7	9	11	14	4	3	1	2	1	1	0	4	2	3	1	4	2	1	1	4	2	2	3	rs146440574	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1869940G>A	ENST00000397356.3	-	4	796	c.390C>T	c.(388-390)atC>atT	p.I130I	HAGH_ENST00000566709.1_Silent_p.I82I|HAGH_ENST00000455446.2_Silent_p.I130I|HAGH_ENST00000397353.2_Silent_p.I82I	NM_005326.4	NP_005317.2	Q16775	GLO2_HUMAN	hydroxyacylglutathione hydrolase	130					glutathione biosynthetic process (GO:0006750)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxyacylglutathione hydrolase activity (GO:0004416)|zinc ion binding (GO:0008270)			kidney(2)|lung(1)|ovary(1)|skin(1)	5		Hepatocellular(780;0.00335)			Glutathione(DB00143)	TCAGGGCCCCGATACGGTCGT	0.612													G|||	6	0.00119808	0.003	0.0014	5008	,	,		15540	0.0		0.0	False		,,,				2504	0.001				p.I130I	Pancreas(55;1048 1176 25227 40124 41333)	Atlas-SNP	.											.	HAGH	20	.	0			c.C390T						PASS	.	G	,	19,4379	25.3+/-52.1	0,19,2180	126	99	108		246,390	-10	0.6	16	dbSNP_134	108	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	HAGH	NM_001040427.1,NM_005326.4	,	0,22,6477	AA,AG,GG		0.0349,0.432,0.1693	,	82/261,130/309	1869940	22,12976	2199	4300	6499	SO:0001819	synonymous_variant	3029	exon4			GGCCCCGATACGG	X90999	CCDS32366.1, CCDS10447.2, CCDS66900.1	16p13.3	2012-10-02	2003-11-04		ENSG00000063854	ENSG00000063854	3.1.2.6		4805	protein-coding gene	gene with protein product		138760	"hydroxyacyl glutathione hydrolase"			3025077, 7327557	Standard	NM_001286249		Approved	GLO2, GLXII, HAGH1	uc002cna.3	Q16775	OTTHUMG00000128662	ENST00000397356.3:c.390C>T	16.37:g.1869940G>A		89	0	0		94	50	0.531915	NM_005326	A8K290|B4DP33|B4DRA7|E7EN93	Silent	SNP	ENST00000397356.3	37	CCDS10447.2																																																																																			G|0.999;A|0.001	0.001	strong		0.612	HAGH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250548.2	NM_005326		A	1869940	G	A	1869940	2	1	24	1	0	0	0	0	0	0	0	1	6954	1048	37	1		1	HAGH	16	1869940	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	332430	1869940	88484813	488	8705											
RPL3L	6123	hgsc.bcm.edu	37	chr16	1996720	1996720	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgtgcgggcccctgccgatgCggaagatctgccagaagggg	7	6	17	11	3	1	2	0	0	1	2	1	4	1	3	4	4	4	0	4	4	2	0	rs147512517		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:1996720C>T	ENST00000268661.7	-	7	951	c.857G>A	c.(856-858)cGc>cAc	p.R286H		NM_005061.2	NP_005052.1	Q92901	RL3L_HUMAN	ribosomal protein L3-like	286					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)|ribosome (GO:0005840)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	17						CCTGCCGATGCGGAAGATCTG	0.632																																					p.R286H		Atlas-SNP	.											RPL3L,caecum,carcinoma,-1,1	RPL3L	42	1	0			c.G857A						PASS	.	C	HIS/ARG	2,4394	4.2+/-10.8	0,2,2196	37	36	37		857	3.6	1	16	dbSNP_134	37	0,8598		0,0,4299	no	missense	RPL3L	NM_005061.2	29	0,2,6495	TT,TC,CC		0.0,0.0455,0.0154	probably-damaging	286/408	1996720	2,12992	2198	4299	6497	SO:0001583	missense	6123	exon7			CCGATGCGGAAGA	U65581	CCDS10450.1	16p13.3	2008-02-05			ENSG00000140986	ENSG00000140986		"L ribosomal proteins"	10351	protein-coding gene	gene with protein product						8921388	Standard	NM_005061		Approved		uc002cnh.3	Q92901	OTTHUMG00000128685	ENST00000268661.7:c.857G>A	16.37:g.1996720C>T	ENSP00000268661:p.Arg286His	47	0	0		32	15	0.46875	NM_005061		Missense_Mutation	SNP	ENST00000268661.7	37	CCDS10450.1	.	.	.	.	.	.	.	.	.	.	C	14.64	2.594823	0.46318	4.55E-4	0.0	ENSG00000140986	ENST00000268661	T	0.26067	1.76	4.55	3.59	0.41128	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.117044	0.64402	D	0.000012	T	0.63861	0.2547	H	0.97240	3.965	0.58432	D	0.999997	D	0.89917	1.0	D	0.97110	1.0	T	0.75428	-0.3321	10	0.87932	D	0	-32.639	11.9539	0.52970	0.0:0.9145:0.0:0.0855	.	286	Q92901	RL3L_HUMAN	H	286	ENSP00000268661:R286H	ENSP00000268661:R286H	R	-	2	0	RPL3L	1936721	0.990000	0.36364	0.987000	0.45799	0.039000	0.13416	2.583000	0.46094	1.037000	0.40024	-0.258000	0.10820	CGC	C|1.000;T|0.000	0.000	weak		0.632	RPL3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250582.2	NM_005061		T	1996720	C	T	1996720	3	4	24	1	0	0	0	0	1	0	0	0	13609	768	27	1	382	1	RPL3L	16	1996720	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	126780	1996720	88358033	489	8706											
TBL3	10607	hgsc.bcm.edu	37	chr16	2028220	2028220	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgactgcggcgcgaccagaaAggttggcggccagtcagggt	8	5	17	11	5	1	1	1	0	0	1	1	3	1	1	2	5	1	1	2	5	1	1			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:2028220A>G	ENST00000568546.1	+	20	2261	c.2133A>G	c.(2131-2133)aaA>aaG	p.K711K		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	711					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						GCGACCAGAAAGGTTGGCGGC	0.662																																					p.K711K	Melanoma(118;616 1651 35077 38081 48633)	Atlas-SNP	.											.	TBL3	54	.	0			c.A2133G						PASS	.						43	48	47					16																	2028220		2197	4296	6493	SO:0001630	splice_region_variant	10607	exon20			CCAGAAAGGTTGG	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.2134+1A>G	16.37:g.2028220A>G		90	0	0		108	50	0.462963	NM_006453	Q59GD6|Q8IVB7|Q96A78	Silent	SNP	ENST00000568546.1	37	CCDS10453.1																																																																																			.	.	none		0.662	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453	Silent	G	2028220	A	G	2028220	5	3	24	1	0	0	0	0	0	0	1	0	15658	86	3	3	2211	3	TBL3	16	2028220	Splice_Site	SNP	A	TCGA-G8-6326-01A-11D-2210-10	31500	2028220	88326533	490	8707											
SLC9A3R2	9351	hgsc.bcm.edu	37	chr16	2079665	2079665	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agatgaggagctccgccggcGgcagctgacctgtaccgagg	8	5	16	12	4	0	3	0	2	0	1	1	5	1	4	4	4	3	4	4	4	1	1	rs55864883		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:2079665G>A	ENST00000424542.2	+	2	434	c.296G>A	c.(295-297)cGg>cAg	p.R99Q	SLC9A3R2_ENST00000563587.1_5'UTR|SLC9A3R2_ENST00000432365.2_Missense_Mutation_p.R99Q	NM_001130012.2|NM_004785.5	NP_001123484.1|NP_004776.3	Q15599	NHRF2_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3 regulator 2	99					negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|protein complex assembly (GO:0006461)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatase binding (GO:0019902)|protein C-terminus binding (GO:0008022)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(1)	2						CTCCGCCGGCGGCAGCTGACC	0.682																																					p.R99Q	Ovarian(69;105 1552 17724 23473)	Atlas-SNP	.											.	SLC9A3R2	24	.	0			c.G296A						PASS	.	G	GLN/ARG,GLN/ARG	1,4107		0,1,2053	27	38	34		296,296	3.7	1	16	dbSNP_129	34	8,8288		0,8,4140	no	missense,missense	SLC9A3R2	NM_001130012.1,NM_004785.4	43,43	0,9,6193	AA,AG,GG		0.0964,0.0243,0.0726	possibly-damaging,possibly-damaging	99/338,99/327	2079665	9,12395	2054	4148	6202	SO:0001583	missense	9351	exon2			GCCGGCGGCAGCT	AF004900	CCDS45382.1, CCDS45383.1, CCDS58407.1	16p13.3	2014-09-04	2012-03-22		ENSG00000065054	ENSG00000065054			11076	protein-coding gene	gene with protein product		606553	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 3 regulatory factor 2", "solute carrier family 9 (sodium/hydrogen exchanger), isoform 3 regulator 2", "solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 2"			9054412, 9671706	Standard	NM_001130012		Approved	SIP-1, TKA-1, NHERF-2, E3KARP	uc002coi.3	Q15599	OTTHUMG00000176956	ENST00000424542.2:c.296G>A	16.37:g.2079665G>A	ENSP00000408005:p.Arg99Gln	107	0	0		101	48	0.475248	NM_004785	D3DU84|D3DU85|H3BSV6|O00272|O00556|Q3KQY7	Missense_Mutation	SNP	ENST00000424542.2	37	CCDS45382.1	.	.	.	.	.	.	.	.	.	.	G	15.33	2.801819	0.50315	2.43E-4	9.64E-4	ENSG00000065054	ENST00000424542;ENST00000432365	T;T	0.20463	2.09;2.07	4.8	3.74	0.42951	PDZ/DHR/GLGF (1);	0.398384	0.22670	N	0.057068	T	0.12646	0.0307	N	0.22421	0.69	0.80722	D	1	B;P	0.49862	0.146;0.929	B;B	0.41619	0.012;0.361	T	0.07065	-1.0792	10	0.11794	T	0.64	-7.4822	11.2924	0.49258	0.0:0.0:0.7611:0.2389	rs55864883;rs62617116	99;99	D3DU85;Q15599	.;NHRF2_HUMAN	Q	99	ENSP00000408005:R99Q;ENSP00000402857:R99Q	ENSP00000408005:R99Q	R	+	2	0	SLC9A3R2	2019666	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.942000	0.40243	2.215000	0.71742	0.561000	0.74099	CGG	.	.	weak		0.682	SLC9A3R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434448.1			A	2079665	G	A	2079665	3	1	24	1	0	0	0	0	1	0	0	0	14730	1116	39	1	302	1	SLC9A3R2	16	2079665	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	51445	2079665	88275088	491	8708											
PKD1	5310	hgsc.bcm.edu	37	chr16	2161153	2161153	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccgtcgggcacccccgcaCggtcgtgttggaggagccat	6	6	14	15	5	0	0	0	0	0	0	2	2	0	2	4	4	1	3	4	4	0	1	rs147141131	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:2161153C>T	ENST00000262304.4	-	15	4223	c.4015G>A	c.(4015-4017)Gtg>Atg	p.V1339M	RP11-304L19.4_ENST00000568795.1_RNA|PKD1_ENST00000423118.1_Missense_Mutation_p.V1339M	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1339	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						CACCCCCGCACGGTCGTGTTG	0.682																																					p.V1339M		Atlas-SNP	.											.	PKD1	184	.	0			c.G4015A						PASS	.	C	MET/VAL,MET/VAL	0,4374		0,0,2187	28	31	30		4015,4015	-0.2	0	16	dbSNP_134	30	4,8580	3.7+/-12.6	0,4,4288	no	missense,missense	PKD1	NM_000296.3,NM_001009944.2	21,21	0,4,6475	TT,TC,CC		0.0466,0.0,0.0309	benign,benign	1339/4303,1339/4304	2161153	4,12954	2187	4292	6479	SO:0001583	missense	5310	exon15			CCCGCACGGTCGT	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.4015G>A	16.37:g.2161153C>T	ENSP00000262304:p.Val1339Met	97	0	0		111	61	0.54955	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	.	.	.	.	.	.	.	.	.	.	c	10.06	1.246377	0.22796	0.0	4.66E-4	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.62788	0.0;0.0	5.58	-0.241	0.13043	PKD/Chitinase domain (1);Polycystin cation channel (1);PKD domain (4);	0.716298	0.14231	N	0.332727	T	0.69178	0.3082	M	0.63428	1.95	0.09310	N	1	D;D	0.62365	0.991;0.984	P;P	0.61132	0.884;0.88	T	0.60571	-0.7237	10	0.41790	T	0.15	.	9.8488	0.41043	0.0:0.5988:0.0:0.4012	.	1339;1339	P98161-3;P98161	.;PKD1_HUMAN	M	1339;1339;1020	ENSP00000262304:V1339M;ENSP00000399501:V1339M	ENSP00000262304:V1339M	V	-	1	0	PKD1	2101154	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.106000	0.03319	-0.296000	0.08947	-0.401000	0.06369	GTG	C|0.999;T|0.001	0.001	strong		0.682	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			T	2161153	C	T	2161153	3	4	24	1	0	0	0	0	1	0	0	0	11972	536	19	1	9024	1	PKD1	16	2161153	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	81488	2161153	88193600	492	8709											
ABCA3	21	hgsc.bcm.edu	37	chr16	2327929	2327929	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aactcctccagcgcctcctgTtgcccttcactctgcacctt	5	12	5	19	1	2	0	1	0	1	0	5	0	5	0	6	0	4	2	6	0	1	3	rs540282149	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:2327929T>C	ENST00000301732.5	-	31	5560	c.4860A>G	c.(4858-4860)caA>caG	p.Q1620Q	ABCA3_ENST00000382381.3_Silent_p.Q1562Q	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	1620					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)	GCGCCTCCTGTTGCCCTTCAC	0.672													T|||	2	0.000399361	0.0	0.0	5008	,	,		16834	0.0		0.0	False		,,,				2504	0.002				p.Q1620Q		Atlas-SNP	.											.	ABCA3	176	.	0			c.A4860G						PASS	.						28	29	28					16																	2327929		2198	4300	6498	SO:0001819	synonymous_variant	21	exon31			CTCCTGTTGCCCT	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.4860A>G	16.37:g.2327929T>C		78	0	0		98	44	0.44898	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Silent	SNP	ENST00000301732.5	37	CCDS10466.1																																																																																			.	.	none		0.672	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089		C	2327929	T	C	2327929	2	2	24	1	0	0	0	0	0	0	0	1	33	1722	60	3		3	ABCA3	16	2327929	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	166776	2327929	88026824	493	8710											
KREMEN2	79412	hgsc.bcm.edu	37	chr16	3017836	3017836	+	Frame_Shift_Del	DEL	G	G	-																															gtctgctggctccgggaaaaGggcccccggcgctgggggct																										TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:3017836delG	ENST00000303746.5	+	9	1781	c.1204delG	c.(1204-1206)gggfs	p.G402fs	PKMYT1_ENST00000571102.1_5'Flank|KREMEN2_ENST00000571007.1_Frame_Shift_Del_p.G363fs|KREMEN2_ENST00000575769.1_3'UTR|KREMEN2_ENST00000572045.1_3'UTR|PAQR4_ENST00000576565.1_5'Flank|PAQR4_ENST00000293978.8_5'Flank|KREMEN2_ENST00000319500.6_Frame_Shift_Del_p.K375fs|KREMEN2_ENST00000575885.1_Frame_Shift_Del_p.K336fs|PAQR4_ENST00000318782.8_5'Flank|PAQR4_ENST00000572687.1_5'Flank			Q8NCW0	KREM2_HUMAN	kringle containing transmembrane protein 2	402					Wnt signaling pathway (GO:0016055)	integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(1)|large_intestine(1)	4						TCCGGGAAAAGGGCCCCCGGC	0.706																																					p.K401fs		Pindel,Atlas-Indel	.											.	KREMEN2	13	.	0			c.1203delA						PASS	.						8	8	8					16																	3017836		2028	4033	6061	SO:0001589	frameshift_variant	79412	exon9			.	BC003533	CCDS10483.1, CCDS10484.1, CCDS58412.1, CCDS58413.1	16p13.11	2008-08-04			ENSG00000131650	ENSG00000131650			18797	protein-coding gene	gene with protein product		609899				12050670	Standard	NM_172229		Approved	MGC10791, KRM2	uc002csg.3	Q8NCW0	OTTHUMG00000128976	ENST00000303746.5:c.1204delG	16.37:g.3017836delG	ENSP00000304422:p.Gly402fs	136	0	.		130	41	0.315	NM_172229	B4DXF6|I3L2S2|Q8N2J4|Q8NCW1|Q96GL8|Q9BTP9	Frame_Shift_Del	DEL	ENST00000303746.5	37	CCDS10483.1																																																																																			.	.	none		0.706	KREMEN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250964.2	NM_145347		-	3017836	G	-	3017836	7	5	24	1	0	1	0	1	0	0	0	0	8452	1000	35	0	1238	0	KREMEN2	16	3017836	Frame_Shift_Del	DEL	G	TCGA-G8-6326-01A-11D-2210-10	689907	3017836	87336917	494	8711											
SEC14L5	9717	hgsc.bcm.edu	37	chr16	5046919	5046919	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acttccacctggacaaggccCgggaaatgctgcgccagtcc	9	6	11	15	2	0	0	0	0	0	0	2	2	2	2	5	3	2	1	5	3	2	1	rs199609540	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:5046919C>T	ENST00000251170.7	+	8	1024	c.844C>T	c.(844-846)Cgg>Tgg	p.R282W		NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN	SEC14-like 5 (S. cerevisiae)	282						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						GGACAAGGCCCGGGAAATGCT	0.567													C|||	2	0.000399361	0.0	0.0	5008	,	,		17171	0.001		0.001	False		,,,				2504	0.0				p.R282W		Atlas-SNP	.											SEC14L5,NS,lymphoid_neoplasm,0,1	SEC14L5	79	1	0			c.C844T						scavenged	.	C	TRP/ARG	3,3813		0,3,1905	55	54	54		844	3.5	1	16		54	8,8228		0,8,4110	yes	missense	SEC14L5	NM_014692.1	101	0,11,6015	TT,TC,CC		0.0971,0.0786,0.0913	benign	282/697	5046919	11,12041	1908	4118	6026	SO:0001583	missense	9717	exon8			AAGGCCCGGGAAA	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.844C>T	16.37:g.5046919C>T	ENSP00000251170:p.Arg282Trp	161	1	0.00621118		137	65	0.474453	NM_014692		Missense_Mutation	SNP	ENST00000251170.7	37	CCDS45403.1	.	.	.	.	.	.	.	.	.	.	C	15.06	2.719825	0.48728	7.86E-4	9.71E-4	ENSG00000103184	ENST00000251170	D	0.85556	-2.0	4.51	3.48	0.39840	Phosphatidylinositol transfer protein-like, N-terminal (1);Cellular retinaldehyde-binding/triple function, N-terminal (1);	0.464358	0.19561	N	0.111327	D	0.84853	0.5564	M	0.80616	2.505	0.46654	D	0.999142	B	0.31054	0.306	B	0.30782	0.12	D	0.86408	0.1746	10	0.62326	D	0.03	-6.5997	12.6573	0.56793	0.2671:0.7329:0.0:0.0	.	282	O43304	S14L5_HUMAN	W	282	ENSP00000251170:R282W	ENSP00000251170:R282W	R	+	1	2	SEC14L5	4986920	0.598000	0.26882	1.000000	0.80357	0.994000	0.84299	0.860000	0.27871	2.492000	0.84095	0.491000	0.48974	CGG	C|0.996;T|0.004	0.004	strong		0.567	SEC14L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434379.1			T	5046919	C	T	5046919	3	4	24	1	0	0	0	0	1	0	0	0	14000	643	23	1	870	1	SEC14L5	16	5046919	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	2029083	5046919	85307834	495	8712											
PMM2	5373	hgsc.bcm.edu	37	chr16	8906914	8906914	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atactgtctgcgacatgtggAaaatgacggttataagacca	14	10	10	7	2	1	2	0	1	1	1	1	4	1	3	1	2	2	1	1	2	5	3	rs34258285	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:8906914A>C	ENST00000268261.4	+	7	656	c.590A>C	c.(589-591)gAa>gCa	p.E197A	PMM2_ENST00000537352.1_Missense_Mutation_p.E72A|PMM2_ENST00000569958.1_Missense_Mutation_p.E106A|PMM2_ENST00000566983.1_Missense_Mutation_p.E170A|PMM2_ENST00000539622.1_Missense_Mutation_p.E114A	NM_000303.2	NP_000294.1	O15305	PMM2_HUMAN	phosphomannomutase 2	197			E -> A (in CDG1A; dbSNP:rs34258285). {ECO:0000269|PubMed:11058895, ECO:0000269|PubMed:15844218}.		cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|mannose biosynthetic process (GO:0019307)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)	phosphomannomutase activity (GO:0004615)			breast(3)|cervix(1)|endometrium(2)|large_intestine(1)|ovary(1)|skin(1)	9						CGACATGTGGAAAATGACGGT	0.463													A|||	45	0.00898562	0.0015	0.0216	5008	,	,		21288	0.0		0.0249	False		,,,				2504	0.0031				p.E197A	Esophageal Squamous(154;1308 1842 2827 29799 42829)	Atlas-SNP	.											.	PMM2	25	.	0			c.A590C	GRCh37	CM002843	PMM2	M	rs34258285	PASS	.	A	ALA/GLU	21,4373	28.1+/-56.4	0,21,2176	148	131	137		590	4.9	0.9	16	dbSNP_126	137	219,8381	92.1+/-154.2	6,207,4087	yes	missense	PMM2	NM_000303.2	107	6,228,6263	CC,CA,AA		2.5465,0.4779,1.847	benign	197/247	8906914	240,12754	2197	4300	6497	SO:0001583	missense	5373	exon7			ATGTGGAAAATGA	BC008310	CCDS10536.1	16p13	2012-09-06			ENSG00000140650	ENSG00000140650	5.3.1.8		9115	protein-coding gene	gene with protein product	"phosphomannose isomerase 1"	601785		CDG1		9140401	Standard	NM_000303		Approved	CDGS, CDG1a, PMI, PMI1	uc002czf.4	O15305	OTTHUMG00000129697	ENST00000268261.4:c.590A>C	16.37:g.8906914A>C	ENSP00000268261:p.Glu197Ala	122	0	0		131	56	0.427481	NM_000303	A8K672|B7Z6R0|D3DUF3	Missense_Mutation	SNP	ENST00000268261.4	37	CCDS10536.1	28	0.01282051282051282	0	0.0	10	0.027624309392265192	0	0.0	18	0.023746701846965697	A	9.835	1.189414	0.21954	0.004779	0.025465	ENSG00000140650	ENST00000268261;ENST00000539622;ENST00000537352	D;D;D	0.98474	-4.95;-4.95;-4.95	4.89	4.89	0.63831	HAD-like domain (2);	0.049443	0.85682	D	0.000000	D	0.90113	0.6911	L	0.52364	1.645	0.58432	D	0.999991	B;B;B	0.16603	0.018;0.0;0.002	B;B;B	0.19148	0.021;0.008;0.024	D	0.89308	0.3631	10	0.18710	T	0.47	.	10.2623	0.43434	0.8343:0.1657:0.0:0.0	rs34258285	50;114;197	B7Z922;F5H0W0;O15305	.;.;PMM2_HUMAN	A	197;114;72	ENSP00000268261:E197A;ENSP00000445879:E114A;ENSP00000438359:E72A	ENSP00000268261:E197A	E	+	2	0	PMM2	8814415	0.971000	0.33674	0.909000	0.35828	0.101000	0.19017	2.489000	0.45285	1.839000	0.53478	0.533000	0.62120	GAA	A|0.984;C|0.016	0.016	strong		0.463	PMM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251904.1	NM_000303		C	8906914	A	C	8906914	3	2	24	1	0	0	0	0	1	0	0	0	12146	246	9	5	616	5	PMM2	16	8906914	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	3859995	8906914	81447839	496	8713											
ATF7IP2	80063	hgsc.bcm.edu	37	chr16	10565979	10565981	+	In_Frame_Del	DEL	TGT	TGT	-																															cattttagtaacaatgatgaTgttatgttgatttctgtgga																								rs566280429|rs199605421	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:10565979_10565981delTGT	ENST00000396560.2	+	8	1592_1594	c.1365_1367delTGT	c.(1363-1368)gatgtt>gat	p.V456del	ATF7IP2_ENST00000543967.1_5'UTR|ATF7IP2_ENST00000396559.1_In_Frame_Del_p.V456del|ATF7IP2_ENST00000324570.5_In_Frame_Del_p.V456del|ATF7IP2_ENST00000356427.2_In_Frame_Del_p.V456del	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	456					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				large_intestine(3)	3						ACAATGATGATGTTATGTTGATT	0.296														25	0.00499201	0.0008	0.0086	5008	,	,		16695	0.001		0.0099	False		,,,				2504	0.0072				p.455_456del		Pindel,Atlas-Indel	.											.	ATF7IP2	40	.	0			c.1364_1366del						PASS	.			6,4252		0,6,2123						2.3	1			67	99,8125		1,97,4014	no	coding	ATF7IP2	NM_024997.2		1,103,6137	A1A1,A1R,RR		1.2038,0.1409,0.8412				105,12377				SO:0001651	inframe_deletion	80063	exon9			.	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.1365_1367delTGT	16.37:g.10565979_10565981delTGT	ENSP00000379808:p.Val456del	21	0	.		26	10	0.385	NM_001256160	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	In_Frame_Del	DEL	ENST00000396560.2	37	CCDS10540.1																																																																																			.	.	none		0.296	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997		-	10565981	TGT	-	10565979	7	5	24	1	0	1	0	1	0	0	0	0	1088	1461	51	0	1387	0	ATF7IP2	16	10565979	In_Frame_Del	DEL	TGT	TCGA-G8-6326-01A-11D-2210-10	1659065	10565979	79788774	497	8714											
TEKT5	146279	hgsc.bcm.edu	37	chr16	10788219	10788219	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actccagccgcctcttgaccGtctccaagttctggttctca	6	12	7	16	2	4	1	1	1	4	0	7	1	5	1	5	1	1	2	5	1	1	3	rs141349037	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:10788219G>A	ENST00000283025.2	-	1	583	c.512C>T	c.(511-513)aCg>aTg	p.T171M	RP11-109M19.1_ENST00000576710.1_RNA	NM_144674.1	NP_653275.1	Q96M29	TEKT5_HUMAN	tektin 5	171						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						CCTCTTGACCGTCTCCAAGTT	0.597													G|||	3	0.000599042	0.0	0.0	5008	,	,		18281	0.0		0.002	False		,,,				2504	0.001				p.T171M		Atlas-SNP	.											.	TEKT5	66	.	0			c.C512T						PASS	.	G	MET/THR	1,4393	2.1+/-5.4	0,1,2196	140	152	148		512	-1.3	0	16	dbSNP_134	148	9,8591	7.1+/-27.0	0,9,4291	yes	missense	TEKT5	NM_144674.1	81	0,10,6487	AA,AG,GG		0.1047,0.0228,0.077	possibly-damaging	171/486	10788219	10,12984	2197	4300	6497	SO:0001583	missense	146279	exon1			TTGACCGTCTCCA		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.512C>T	16.37:g.10788219G>A	ENSP00000283025:p.Thr171Met	77	0	0		80	26	0.325	NM_144674	A1L3Z3	Missense_Mutation	SNP	ENST00000283025.2	37	CCDS10542.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	6.721	0.501787	0.12822	2.28E-4	0.001047	ENSG00000153060	ENST00000283025	T	0.02631	4.22	5.63	-1.29	0.09288	.	0.388807	0.24722	N	0.036122	T	0.03305	0.0096	L	0.59436	1.845	0.09310	N	1	B	0.31968	0.349	B	0.38020	0.263	T	0.35992	-0.9766	10	0.52906	T	0.07	-7.5255	1.0994	0.01680	0.2102:0.1177:0.3104:0.3617	.	171	Q96M29	TEKT5_HUMAN	M	171	ENSP00000283025:T171M	ENSP00000283025:T171M	T	-	2	0	TEKT5	10695720	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.881000	0.28173	-0.203000	0.10251	-0.143000	0.13931	ACG	G|0.999;A|0.001	0.001	strong		0.597	TEKT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251963.1	NM_144674		A	10788219	G	A	10788219	3	1	24	1	0	0	0	0	1	0	0	0	15771	1145	40	1	973	1	TEKT5	16	10788219	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	222240	10788219	79566534	498	8715											
TNP2	7142	hgsc.bcm.edu	37	chr16	11362797	11362797	+	Frame_Shift_Del	DEL	T	T	-																															ttttcagcttgccttccaagTtctttctgttcttggggcag																										TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:11362797delT	ENST00000312693.3	-	1	392	c.323delA	c.(322-324)aacfs	p.N108fs	RMI2_ENST00000572173.1_Intron	NM_005425.4	NP_005416.1	Q05952	STP2_HUMAN	transition protein 2 (during histone to protamine replacement)	108					acrosome reaction (GO:0007340)|binding of sperm to zona pellucida (GO:0007339)|cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|penetration of zona pellucida (GO:0007341)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.0?(1)		large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	6						GCCTTCCAAGTTCTTTCTGTT	0.522																																					p.N108fs		Pindel,Atlas-Indel	.											.	TNP2	15	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.324delC						PASS	.						77	77	77					16																	11362797		1957	4150	6107	SO:0001589	frameshift_variant	7142	exon1			.		CCDS45410.1	16p13.13	2008-08-01				ENSG00000178279			11952	protein-coding gene	gene with protein product		190232				1395729, 2250010	Standard	NM_005425		Approved	TP2	uc002das.3	Q05952		ENST00000312693.3:c.323delA	16.37:g.11362797delT	ENSP00000325738:p.Asn108fs	232	0	.		266	47	0.177	NM_005425	Q9NZB0	Frame_Shift_Del	DEL	ENST00000312693.3	37	CCDS45410.1																																																																																			.	.	none		0.522	TNP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417806.1	NM_005425		-	11362797	T	-	11362797	7	5	24	1	0	1	0	1	0	0	0	0	16349	1725	60	0	101	0	TNP2	16	11362797	Frame_Shift_Del	DEL	T	TCGA-G8-6326-01A-11D-2210-10	574578	11362797	78991956	499	8716											
RUNDC2A	92017	hgsc.bcm.edu	37	chr16	12145791	12145791	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggaagatgagcagaactctgGggacgtgtttaaaaagacac	15	7	13	6	1	1	4	0	1	1	3	1	6	1	6	0	3	2	2	0	3	5	2	rs118191509	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:12145791G>C	ENST00000566228.1	+	8	905	c.836G>C	c.(835-837)gGg>gCg	p.G279A	SNX29_ENST00000306030.3_5'Flank|SNX29_ENST00000323433.4_5'Flank	NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	279						extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						CAGAACTCTGGGGACGTGTTT	0.473													G|||	34	0.00678914	0.0008	0.0014	5008	,	,		17949	0.001		0.0229	False		,,,				2504	0.0082				p.G279A		Atlas-SNP	.											.	SNX29	60	.	0			c.G836C						PASS	.	G	ALA/GLY	29,4365	32.6+/-62.9	0,29,2168	73	82	79		836	4.8	0.2	16	dbSNP_132	79	247,8353	96.6+/-158.3	3,241,4056	no	missense	SNX29	NM_032167.3	60	3,270,6224	CC,CG,GG		2.8721,0.66,2.1241	benign	279/376	12145791	276,12718	2197	4300	6497	SO:0001583	missense	92017	exon8			ACTCTGGGGACGT	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.836G>C	16.37:g.12145791G>C	ENSP00000456480:p.Gly279Ala	504	0	0		499	217	0.43487	NM_032167	B5MDW2|Q8N2X2|Q9HA26	Missense_Mutation	SNP	ENST00000566228.1	37	CCDS10553.2	21	0.009615384615384616	0	0.0	0	0.0	0	0.0	21	0.027704485488126648	G	4.332	0.060912	0.08339	0.0066	0.028721	ENSG00000140660	ENST00000268271	.	.	.	5.78	4.82	0.62117	.	0.280809	0.33235	N	0.005122	T	0.24547	0.0595	L	0.29908	0.895	0.80722	D	1	.	.	.	.	.	.	T	0.18147	-1.0346	7	0.07175	T	0.84	-11.8625	14.9466	0.71035	0.0:0.2704:0.7296:0.0	.	.	.	.	A	279	.	ENSP00000268271:G279A	G	+	2	0	RUNDC2A	12053292	1.000000	0.71417	0.231000	0.23993	0.455000	0.32408	3.912000	0.56386	1.447000	0.47661	0.313000	0.20887	GGG	G|0.983;C|0.017	0.017	strong		0.473	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422622.1			C	12145791	G	C	12145791	3	2	24	1	0	0	0	0	1	0	0	0	13758	1232	43	4	866	4	RUNDC2A	16	12145791	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	782994	12145791	78208962	500	8717											
SNX29	92017	hgsc.bcm.edu	37	chr16	12492322	12492322	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgcctggagatttgagtcAaacgtccgaagaccagagtt	11	9	13	8	2	1	4	1	1	0	3	2	6	2	4	3	2	2	1	3	2	2	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:12492322A>T	ENST00000566228.1	+	17	1988	c.1919A>T	c.(1918-1920)cAa>cTa	p.Q640L	SNX29_ENST00000306030.3_Missense_Mutation_p.Q255L|SNX29_ENST00000323433.4_Missense_Mutation_p.Q255L	NM_032167.3	NP_115543.3	Q8TEQ0	SNX29_HUMAN	sorting nexin 29	640						extracellular vesicular exosome (GO:0070062)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	7						GATTTGAGTCAAACGTCCGAA	0.463																																					p.Q640L		Atlas-SNP	.											.	SNX29	60	.	0			c.A1919T						PASS	.						136	132	133					16																	12492322		1866	4116	5982	SO:0001583	missense	92017	exon17			TGAGTCAAACGTC	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.1919A>T	16.37:g.12492322A>T	ENSP00000456480:p.Gln640Leu	145	0	0		180	80	0.444444	NM_032167	B5MDW2|Q8N2X2|Q9HA26	Missense_Mutation	SNP	ENST00000566228.1	37	CCDS10553.2	.	.	.	.	.	.	.	.	.	.	A	20.3	3.973375	0.74246	.	.	ENSG00000048471	ENST00000306030;ENST00000323433	.	.	.	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.49236	0.1545	L	0.40543	1.245	0.31498	N	0.665135	.	.	.	.	.	.	T	0.58470	-0.7631	7	0.44086	T	0.13	-15.7683	13.779	0.63071	1.0:0.0:0.0:0.0	.	.	.	.	L	255	.	ENSP00000306940:Q255L	Q	+	2	0	SNX29	12399823	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	6.483000	0.73617	2.129000	0.65627	0.533000	0.62120	CAA	.	.	none		0.463	SNX29-005	PUTATIVE	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422622.1			T	12492322	A	T	12492322	3	4	24	1	0	0	0	0	1	0	0	0	14913	130	5	5	798	5	SNX29	16	12492322	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	346531	12492322	77862431	501	8718											
RRN3	54700	hgsc.bcm.edu	37	chr16	15166809	15166809	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatcacattcttactcaccaAtttgaaactacagaggtaaa	17	11	4	9	0	3	2	2	1	1	1	3	2	3	2	1	1	3	1	1	1	7	5	rs72774849	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:15166809A>G	ENST00000198767.6	-	12	1209	c.1126T>C	c.(1126-1128)Ttg>Ctg	p.L376L	RRN3_ENST00000429751.2_Silent_p.L346L|RRN3_ENST00000563559.1_Silent_p.L376L|RRN3_ENST00000540462.1_Silent_p.L194L|RRN3_ENST00000327307.7_Silent_p.L343L|PDXDC1_ENST00000535621.2_Intron	NM_018427.3	NP_060897.3	Q9NYV6	RRN3_HUMAN	RRN3 RNA polymerase I transcription factor homolog (S. cerevisiae)	376					cell proliferation (GO:0008283)|cytoplasm organization (GO:0007028)|gene expression (GO:0010467)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902254)|nucleolus organization (GO:0007000)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, initiation (GO:2000142)|ribosome biogenesis (GO:0042254)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(2)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)	20						TTACTCACCAATTTGAAACTA	0.383													.|||	22	0.00439297	0.0008	0.0043	5008	,	,		17623	0.0		0.0159	False		,,,				2504	0.002				p.L376L		Atlas-SNP	.											.	RRN3	36	.	0			c.T1126C						PASS	.	A		8,4386		0,8,2189	107	93	98		1126	-0.7	0.9	16	dbSNP_130	98	154,8446		1,152,4147	no	coding-synonymous	RRN3	NM_018427.3		1,160,6336	GG,GA,AA		1.7907,0.1821,1.2467		376/652	15166809	162,12832	2197	4300	6497	SO:0001819	synonymous_variant	54700	exon12			TCACCAATTTGAA	AF227156	CCDS10559.1, CCDS73833.1	16p13.11	2009-10-26	2006-04-04		ENSG00000085721	ENSG00000085721			30346	protein-coding gene	gene with protein product		605121	"RRN3 RNA polymerase I transcription factor homolog (yeast)"			10758157, 11250903	Standard	XM_005255375		Approved	DKFZp566E104	uc002dde.3	Q9NYV6	OTTHUMG00000129847	ENST00000198767.6:c.1126T>C	16.37:g.15166809A>G		102	0	0		105	51	0.485714	NM_018427	A2RTY9|B4E0J7|B4E3T2|Q3MHU9|Q6IPL4|Q9H4F0	Silent	SNP	ENST00000198767.6	37	CCDS10559.1																																																																																			A|0.987;G|0.013	0.013	strong		0.383	RRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252087.2	NM_018427		G	15166809	A	G	15166809	2	3	24	1	0	0	0	0	0	0	0	1	13699	98	4	3		3	RRN3	16	15166809	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	2674487	15166809	75187944	502	8719											
UMOD	7369	hgsc.bcm.edu	37	chr16	20352532	20352532	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccatccaacatggtgcccacGtagagaaaagcctcagtgga	13	6	10	12	1	1	1	1	0	0	1	2	3	2	2	4	2	3	1	4	2	4	1	rs141800038	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:20352532G>A	ENST00000570689.1	-	7	1604	c.1458C>T	c.(1456-1458)taC>taT	p.Y486Y	UMOD_ENST00000396138.4_Silent_p.Y535Y|UMOD_ENST00000424589.1_Silent_p.Y519Y|UMOD_ENST00000396134.2_Silent_p.Y519Y|UMOD_ENST00000570331.1_5'UTR|UMOD_ENST00000396142.2_Silent_p.Y486Y|UMOD_ENST00000302509.4_Silent_p.Y486Y			P07911	UROM_HUMAN	uromodulin	486	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				cellular defense response (GO:0006968)|chemical homeostasis (GO:0048878)|excretion (GO:0007588)|heterophilic cell-cell adhesion (GO:0007157)|leukocyte cell-cell adhesion (GO:0007159)|metanephric ascending thin limb development (GO:0072218)|metanephric distal convoluted tubule development (GO:0072221)|metanephric thick ascending limb development (GO:0072233)|negative regulation of cell proliferation (GO:0008285)|neutrophil migration (GO:1990266)|regulation of ion homeostasis (GO:2000021)|response to organic substance (GO:0010033)	anchored component of membrane (GO:0031225)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|primary cilium (GO:0072372)|spindle pole (GO:0000922)	calcium ion binding (GO:0005509)|IgG binding (GO:0019864)			endometrium(5)|kidney(1)|large_intestine(7)|lung(20)|ovary(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						TGGTGCCCACGTAGAGAAAAG	0.597													G|||	13	0.00259585	0.0	0.0	5008	,	,		16645	0.0		0.0099	False		,,,				2504	0.0031				p.Y486Y		Atlas-SNP	.											.	UMOD	128	.	0			c.C1458T						PASS	.	G	,	7,4399	12.9+/-30.5	0,7,2196	96	75	82		1458,1458	-4.3	0.9	16	dbSNP_134	82	90,8510	52.3+/-112.8	0,90,4210	no	coding-synonymous,coding-synonymous	UMOD	NM_001008389.1,NM_003361.2	,	0,97,6406	AA,AG,GG		1.0465,0.1589,0.7458	,	486/641,486/641	20352532	97,12909	2203	4300	6503	SO:0001819	synonymous_variant	7369	exon7			GCCCACGTAGAGA	M17778	CCDS10583.1, CCDS61876.1	16p12.3	2008-06-23	2008-06-23		ENSG00000169344	ENSG00000169344			12559	protein-coding gene	gene with protein product	"Tamm-Horsfall glycoprotein", "uromucoid"	191845	"uromodulin (uromucoid, Tamm-Horsfall glycoprotein)"			8382593	Standard	NM_003361		Approved		uc002dha.3	P07911	OTTHUMG00000131488	ENST00000570689.1:c.1458C>T	16.37:g.20352532G>A		73	0	0		66	37	0.560606	NM_003361	B3KP48|B3KRN9|E9PEA4|Q540J6|Q6ZS84|Q8IYG0	Silent	SNP	ENST00000570689.1	37	CCDS10583.1																																																																																			G|0.994;A|0.006	0.006	strong		0.597	UMOD-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436862.1			A	20352532	G	A	20352532	2	1	24	1	0	0	0	0	0	0	0	1	16994	1140	40	1		1	UMOD	16	20352532	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	5185723	20352532	70002221	503	8720											
PALB2	79728	hgsc.bcm.edu	37	chr16	23635348	23635348	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctgatctctctgatttccAaatttcccaaagctacacac	12	12	3	14	0	2	2	0	2	2	0	5	2	4	2	3	0	2	1	3	0	3	3	rs45478192	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:23635348A>C	ENST00000261584.4	-	8	2968	c.2816T>G	c.(2815-2817)tTg>tGg	p.L939W	CTD-2196E14.3_ENST00000561764.1_RNA	NM_024675.3	NP_078951.2	Q86YC2	PALB2_HUMAN	partner and localizer of BRCA2	939	Interaction with RAD51, BRCA2 and POLH.|Required for interaction with POLH and POLH DNA synthesis stimulation.		L -> W (may be associated with breast cancer susceptibility; reduces interaction with BRCA2, RAD51 and XRCC3; decreases double-stranded DNA break- initiated homologous recombination; increases sensitivity to IR; dbSNP:rs45478192). {ECO:0000269|PubMed:21618343}.		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)		TCTGATTTCCAAATTTCCCAA	0.378			"F, N, Mis"			"Wilms tumor, medulloblastoma, AML ,breast"		Involved in tolerance or repair of DNA crosslinks					A|||	4	0.000798722	0.0008	0.0014	5008	,	,		17096	0.0		0.002	False		,,,				2504	0.0				p.L939W		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.T2816G						PASS	.	A	TRP/LEU	0,4394		0,0,2197	101	94	96	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2816	5.8	1	16	dbSNP_127	96	20,8580	15.3+/-51.7	0,20,4280	yes	missense	PALB2	NM_024675.3	61	0,20,6477	CC,CA,AA		0.2326,0.0,0.1539	probably-damaging	939/1187	23635348	20,12974	2197	4300	6497	SO:0001583	missense	79728	exon8			ATTTCCAAATTTC		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.2816T>G	16.37:g.23635348A>C	ENSP00000261584:p.Leu939Trp	110	0	0		119	43	0.361345	NM_024675	A6NIE1|Q8N7Y6|Q8ND31|Q9H6W1	Missense_Mutation	SNP	ENST00000261584.4	37	CCDS32406.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	A	20.9	4.060595	0.76074	0.0	0.002326	ENSG00000083093	ENST00000261584	T	0.28666	1.6	5.81	5.81	0.92471	WD40 repeat-like-containing domain (1);	0.000000	0.64402	D	0.000005	T	0.56171	0.1967	M	0.77103	2.36	0.45914	D	0.998756	D	0.89917	1.0	D	0.97110	1.0	T	0.60994	-0.7152	10	0.87932	D	0	-7.0825	12.557	0.56258	1.0:0.0:0.0:0.0	rs45478192;rs61755167	939	Q86YC2	PALB2_HUMAN	W	939	ENSP00000261584:L939W	ENSP00000261584:L939W	L	-	2	0	PALB2	23542849	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.166000	0.64965	2.230000	0.72887	0.528000	0.53228	TTG	A|0.999;C|0.001	0.001	strong		0.378	PALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435287.2	NM_024675		C	23635348	A	C	23635348	3	2	24	1	0	0	0	0	1	0	0	0	11415	131	5	5	768	5	PALB2	16	23635348	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	3282816	23635348	66719405	504	8721											
KIF22	3835	hgsc.bcm.edu	37	chr16	29816237	29816237	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	atgggcgccaaaaaatactgGatctgctgaacgaaggctca	14	7	11	9	2	2	1	1	1	1	0	2	3	2	2	1	3	3	2	1	3	6	1	rs146561986	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:29816237G>A	ENST00000160827.4	+	12	1820	c.1780G>A	c.(1780-1782)Gat>Aat	p.D594N	AC009133.15_ENST00000566537.1_RNA|MAZ_ENST00000566906.2_5'Flank|MAZ_ENST00000563402.1_5'Flank|KIF22_ENST00000569382.2_Missense_Mutation_p.D540N|MAZ_ENST00000219782.6_5'Flank|KIF22_ENST00000400751.5_Missense_Mutation_p.D526N|MAZ_ENST00000545521.1_5'Flank|MAZ_ENST00000562337.1_5'Flank|KIF22_ENST00000561482.1_Missense_Mutation_p.D526N|MAZ_ENST00000322945.6_5'Flank	NM_001256269.1|NM_007317.2	NP_001243198.1|NP_015556.1	Q14807	KIF22_HUMAN	kinesin family member 22	594					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						AAAAATACTGGATCTGCTGAA	0.617													G|||	5	0.000998403	0.0	0.0029	5008	,	,		19086	0.0		0.002	False		,,,				2504	0.001				p.D594N		Atlas-SNP	.											.	KIF22	29	.	0			c.G1780A						PASS	.	G	ASN/ASP	3,4391	6.2+/-15.9	0,3,2194	44	43	43		1780	1.4	0.4	16	dbSNP_134	43	23,8569	17.3+/-56.4	0,23,4273	yes	missense	KIF22	NM_007317.1	23	0,26,6467	AA,AG,GG		0.2677,0.0683,0.2002	benign	594/666	29816237	26,12960	2197	4296	6493	SO:0001583	missense	3835	exon12			ATACTGGATCTGC	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.1780G>A	16.37:g.29816237G>A	ENSP00000160827:p.Asp594Asn	52	0	0		64	33	0.515625	NM_007317	B2R5M0|B7Z265|O60845|O94814|Q53F58|Q9BT46	Missense_Mutation	SNP	ENST00000160827.4	37	CCDS10653.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	15.07	2.723503	0.48728	6.83E-4	0.002677	ENSG00000079616	ENST00000160827;ENST00000400751	T;T	0.74106	-0.73;-0.81	5.64	1.38	0.22167	.	.	.	.	.	T	0.39911	0.1096	N	0.08118	0	0.80722	D	1	B;B	0.18166	0.002;0.026	B;B	0.18263	0.003;0.021	T	0.15521	-1.0434	9	0.39692	T	0.17	.	2.6855	0.05106	0.1508:0.2728:0.4355:0.1409	.	526;594	B7Z265;Q14807	.;KIF22_HUMAN	N	594;526	ENSP00000160827:D594N;ENSP00000383562:D526N	ENSP00000160827:D594N	D	+	1	0	KIF22	29723738	0.998000	0.40836	0.355000	0.25773	0.967000	0.64934	1.528000	0.35985	0.037000	0.15575	0.561000	0.74099	GAT	G|0.998;A|0.002	0.002	strong		0.617	KIF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215012.2			A	29816237	G	A	29816237	3	1	24	1	0	0	0	0	1	0	0	0	8299	1174	41	2	1826	2	KIF22	16	29816237	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	6180889	29816237	60538516	505	8722											
SEZ6L2	26470	hgsc.bcm.edu	37	chr16	29899021	29899021	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaagtgcaggtgcagccggCgcccctcagctgcttcaatg	8	7	12	14	2	2	0	2	0	0	0	2	0	2	0	3	2	5	4	3	2	2	1	rs117448844	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:29899021C>T	ENST00000308713.5	-	7	1684	c.1157G>A	c.(1156-1158)cGc>cAc	p.R386H	SEZ6L2_ENST00000350527.3_Missense_Mutation_p.R316H|SEZ6L2_ENST00000537485.1_Missense_Mutation_p.R342H|SEZ6L2_ENST00000346932.5_Missense_Mutation_p.R272H|SEZ6L2_ENST00000562159.1_5'Flank	NM_001114099.2|NM_201575.3	NP_001107571.1|NP_963869.2	Q6UXD5	SE6L2_HUMAN	seizure related 6 homolog (mouse)-like 2	386	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)|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						GTGCAGCCGGCGCCCCTCAGC	0.637													C|||	6	0.00119808	0.0	0.0043	5008	,	,		15751	0.0		0.003	False		,,,				2504	0.0				p.R386H		Atlas-SNP	.											SEZ6L2_ENST00000350527,NS,carcinoma,0,2	SEZ6L2	137	2	0			c.G1157A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	4,4390	8.1+/-20.4	0,4,2193	78	72	74		947,815,947,1157	5.7	1	16	dbSNP_132	74	26,8574	19.8+/-62.0	0,26,4274	yes	missense,missense,missense,missense	SEZ6L2	NM_001114099.2,NM_001114100.2,NM_012410.3,NM_201575.3	29,29,29,29	0,30,6467	TT,TC,CC		0.3023,0.091,0.2309	benign,benign,benign,benign	316/841,272/810,316/854,386/911	29899021	30,12964	2197	4300	6497	SO:0001583	missense	26470	exon7			AGCCGGCGCCCCT	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.1157G>A	16.37:g.29899021C>T	ENSP00000312550:p.Arg386His	137	0	0		114	62	0.54386	NM_001243332	B7Z1N0|F5H293|H7BXQ6|Q9BW82|Q9UJ45|Q9UJ46|Q9UJ47	Missense_Mutation	SNP	ENST00000308713.5	37	CCDS10659.1	4	0.0018315018315018315	0	0.0	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	C	21.9	4.221861	0.79464	9.1E-4	0.003023	ENSG00000174938	ENST00000350527;ENST00000308713;ENST00000346932;ENST00000537485	T;T;T;T	0.50001	0.76;0.76;0.76;0.76	5.72	5.72	0.89469	CUB (4);	0.000000	0.56097	D	0.000031	T	0.13798	0.0334	N	0.02296	-0.605	0.35617	D	0.809155	B;B;B;B;B;B	0.24963	0.039;0.07;0.07;0.115;0.07;0.115	B;B;B;B;B;B	0.14023	0.01;0.003;0.002;0.006;0.003;0.006	T	0.30475	-0.9977	10	0.15066	T	0.55	.	8.9111	0.35555	0.0:0.8417:0.0:0.1583	.	342;386;272;316;386;316	F5H293;B7Z5L4;Q9BW82;Q6UXD5-2;Q6UXD5;Q6UXD5-3	.;.;.;.;SE6L2_HUMAN;.	H	316;386;272;342	ENSP00000310206:R316H;ENSP00000312550:R386H;ENSP00000319215:R272H;ENSP00000439412:R342H	ENSP00000312550:R386H	R	-	2	0	SEZ6L2	29806522	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.553000	0.67287	2.720000	0.93068	0.555000	0.69702	CGC	C|0.998;T|0.002	0.002	strong		0.637	SEZ6L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255154.2	NM_012410		T	29899021	C	T	29899021	3	4	24	1	0	0	0	0	1	0	0	0	14159	768	27	1	1662	1	SEZ6L2	16	29899021	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	82784	29899021	60455732	506	8723											
TBX6	6911	hgsc.bcm.edu	37	chr16	30100401	30100401	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caggcggggctctgccttgcCgctgggctcccagcgccggc	2	6	16	17	4	1	0	0	0	1	0	2	0	2	0	4	5	3	3	4	5	0	1	rs56098093	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:30100401C>T	ENST00000395224.2	-	4	543	c.484G>A	c.(484-486)Ggc>Agc	p.G162S	TBX6_ENST00000553607.1_Missense_Mutation_p.G162S|TBX6_ENST00000279386.2_Missense_Mutation_p.G162S	NM_004608.3	NP_004599.2	O95947	TBX6_HUMAN	T-box 6	162			G -> S (in dbSNP:rs56098093).		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						TCTGCCTTGCCGCTGGGCTCC	0.647													C|||	4	0.000798722	0.0	0.0	5008	,	,		13926	0.0		0.004	False		,,,				2504	0.0				p.G162S		Atlas-SNP	.											.	TBX6	29	.	0			c.G484A						PASS	.	C	SER/GLY	5,4389	9.9+/-24.2	0,5,2192	47	52	50		484	5.8	1	16	dbSNP_129	50	52,8546	32.3+/-84.9	0,52,4247	yes	missense	TBX6	NM_004608.3	56	0,57,6439	TT,TC,CC		0.6048,0.1138,0.4387	probably-damaging	162/437	30100401	57,12935	2197	4299	6496	SO:0001583	missense	6911	exon4			CCTTGCCGCTGGG	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.484G>A	16.37:g.30100401C>T	ENSP00000378650:p.Gly162Ser	94	0	0		80	45	0.5625	NM_004608	Q8TAS4|Q9HA44	Missense_Mutation	SNP	ENST00000395224.2	37	CCDS10670.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	36	5.633723	0.96682	0.001138	0.006048	ENSG00000149922	ENST00000395224;ENST00000279386;ENST00000553607	D;D;D	0.91237	-2.81;-2.81;-2.81	5.8	5.8	0.92144	p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.95287	0.8471	M	0.90977	3.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.95019	0.8159	10	0.87932	D	0	.	18.8306	0.92137	0.0:1.0:0.0:0.0	rs56098093	162;162	O95947;Q9HA44	TBX6_HUMAN;.	S	162	ENSP00000378650:G162S;ENSP00000279386:G162S;ENSP00000461223:G162S	ENSP00000279386:G162S	G	-	1	0	TBX6	30007902	0.998000	0.40836	0.997000	0.53966	0.971000	0.66376	4.819000	0.62664	2.747000	0.94245	0.462000	0.41574	GGC	C|0.997;T|0.003	0.003	strong		0.647	TBX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255157.2	NM_004608, NM_080758		T	30100401	C	T	30100401	3	4	24	1	0	0	0	0	1	0	0	0	15677	652	23	1	850	1	TBX6	16	30100401	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	201380	30100401	60254352	507	8724											
MYLPF	1731	hgsc.bcm.edu	37	chr16	30387148	30387148	+	IGR	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctcaccctccaggcacccaAgagggccaagagaaggacag	13	2	11	15	0	1	2	1	0	0	2	2	4	2	3	5	3	0	1	5	3	3	0			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:30387148A>G	ENST00000571393.1	-	0	1589				MYLPF_ENST00000322861.7_Missense_Mutation_p.K4R			Q8WYJ6	SEPT1_HUMAN	septin 1						cell cycle (GO:0007049)|cell division (GO:0051301)	septin complex (GO:0031105)	GTP binding (GO:0005525)			breast(2)|endometrium(1)|large_intestine(3)|lung(15)|ovary(1)|skin(1)|urinary_tract(1)	24			Colorectal(24;0.193)			CAGGCACCCAAGAGGGCCAAG	0.572																																					p.K4R		Atlas-SNP	.											.	MYLPF	12	.	0			c.A11G						PASS	.						46	50	48					16																	30387148		2197	4300	6497	SO:0001628	intergenic_variant	29895	exon2			CACCCAAGAGGGC	AF308288	CCDS10678.1, CCDS10678.2, CCDS10678.3	16p11.2	2013-01-21		2001-09-10	ENSG00000180096	ENSG00000180096	3.1.5.1	"Septins"	2879	protein-coding gene	gene with protein product		612897		DIFF6		8697812	Standard	NM_052838		Approved	PNUTL3	uc002dxy.4	Q8WYJ6	OTTHUMG00000176984		16.37:g.30387148A>G		101	0	0		107	48	0.448598	NM_013292	B4DVE6|Q658T1|Q8NEZ1|Q96EL4|Q9H285	Missense_Mutation	SNP	ENST00000571393.1	37		.	.	.	.	.	.	.	.	.	.	A	11.07	1.529847	0.27387	.	.	ENSG00000180209	ENST00000322861	T	0.75154	-0.91	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.71324	0.3326	N	0.10809	0.05	0.58432	D	0.999999	D	0.58268	0.982	D	0.67548	0.952	T	0.68914	-0.5283	10	0.15499	T	0.54	.	14.7308	0.69379	1.0:0.0:0.0:0.0	.	4	Q96A32	MLRS_HUMAN	R	4	ENSP00000325239:K4R	ENSP00000325239:K4R	K	+	2	0	MYLPF	30294649	1.000000	0.71417	1.000000	0.80357	0.004000	0.04260	8.674000	0.91191	2.120000	0.65058	0.372000	0.22366	AAG	.	.	none		0.572	SEPT1-201	KNOWN	basic	protein_coding	protein_coding		NM_052838		G	30387148	A	G	30387148	1	3	24	0	1	0	0	0	0	0	0	0	10069	72	3	3		3	MYLPF	16	30387148	IGR	SNP	A	TCGA-G8-6326-01A-11D-2210-10	286747	30387148	59967605	508	8725											
ZNF646	9726	hgsc.bcm.edu	37	chr16	31090269	31090269	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaccataggcctggggaggCgacctcagcacagcctttcc	9	6	12	14	1	1	0	1	0	0	0	2	3	2	1	5	4	3	1	5	4	2	2	rs75586809	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:31090269C>T	ENST00000394979.2	+	1	3047	c.2624C>T	c.(2623-2625)gCg>gTg	p.A875V	ZNF646_ENST00000300850.5_Missense_Mutation_p.A875V			O15015	ZN646_HUMAN	zinc finger protein 646	875					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						CCTGGGGAGGCGACCTCAGCA	0.642													C|||	24	0.00479233	0.0008	0.0115	5008	,	,		21323	0.0		0.0139	False		,,,				2504	0.001				p.A875V		Atlas-SNP	.											ZNF646,NS,haematopoietic_neoplasm,0,1	ZNF646	133	1	0			c.C2624T						PASS	.	C	VAL/ALA	20,4374	26.2+/-53.5	0,20,2177	51	54	53		2624	2	0.3	16	dbSNP_131	53	149,8451	71.3+/-133.9	1,147,4152	yes	missense	ZNF646	NM_014699.3	64	1,167,6329	TT,TC,CC		1.7326,0.4552,1.3006	benign	875/1833	31090269	169,12825	2197	4300	6497	SO:0001583	missense	9726	exon2			GGGAGGCGACCTC	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.2624C>T	16.37:g.31090269C>T	ENSP00000378429:p.Ala875Val	73	0	0		92	38	0.413043	NM_014699	Q8IVD8	Missense_Mutation	SNP	ENST00000394979.2	37		14	0.00641025641025641	0	0.0	4	0.011049723756906077	0	0.0	10	0.013192612137203167	C	10.60	1.394311	0.25205	0.004552	0.017326	ENSG00000167395	ENST00000300850;ENST00000394979	T;T	0.09538	2.97;2.99	5.1	2.01	0.26516	.	.	.	.	.	T	0.02533	0.0077	N	0.19112	0.55	0.21762	N	0.999553	B	0.24768	0.111	B	0.17722	0.019	T	0.44757	-0.9307	9	0.09590	T	0.72	-4.0386	7.7886	0.29106	0.0:0.6518:0.0:0.3482	.	875	O15015-2	.	V	875	ENSP00000300850:A875V;ENSP00000378429:A875V	ENSP00000300850:A875V	A	+	2	0	ZNF646	30997770	0.000000	0.05858	0.330000	0.25442	0.849000	0.48306	-1.042000	0.03539	0.163000	0.19507	0.563000	0.77884	GCG	C|0.989;T|0.011	0.011	strong		0.642	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699		T	31090269	C	T	31090269	3	4	24	1	0	0	0	0	1	0	0	0	18077	768	27	1	2626	1	ZNF646	16	31090269	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	703121	31090269	59264484	509	8726											
PRSS53	339105	hgsc.bcm.edu	37	chr16	31096495	31096495	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagggctccgccacaggccaGctgtccctggtgcatcagcc	6	6	12	17	1	1	0	1	0	0	0	3	0	3	0	5	3	3	3	5	3	0	0	rs72785539	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:31096495G>C	ENST00000280606.6	-	7	1123	c.970C>G	c.(970-972)Ctg>Gtg	p.L324V		NM_001039503.2	NP_001034592.1	Q2L4Q9	PRS53_HUMAN	protease, serine, 53	324	Peptidase S1 2. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			large_intestine(1)|lung(3)	4						CCACAGGCCAGCTGTCCCTGG	0.637													G|||	4	0.000798722	0.0	0.0	5008	,	,		19514	0.0		0.004	False		,,,				2504	0.0				p.L324V		Atlas-SNP	.											.	PRSS53	29	.	0			c.C970G						PASS	.	G	VAL/LEU	2,4122		0,2,2060	21	26	25		970	4.6	0.9	16	dbSNP_130	25	24,8378		0,24,4177	yes	missense	PRSS53	NM_001039503.2	32	0,26,6237	CC,CG,GG		0.2856,0.0485,0.2076	possibly-damaging	324/554	31096495	26,12500	2062	4201	6263	SO:0001583	missense	339105	exon7			AGGCCAGCTGTCC		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.970C>G	16.37:g.31096495G>C	ENSP00000280606:p.Leu324Val	217	0	0		240	126	0.525	NM_001039503		Missense_Mutation	SNP	ENST00000280606.6	37	CCDS42153.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	13.86	2.364215	0.41902	4.85E-4	0.002856	ENSG00000151006	ENST00000280606	T	0.30448	1.53	5.75	4.61	0.57282	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.302705	0.17712	U	0.164555	T	0.28466	0.0704	L	0.49699	1.58	0.09310	N	1	P	0.43231	0.801	B	0.41374	0.355	T	0.17501	-1.0367	10	0.42905	T	0.14	.	9.359	0.38184	0.0858:0.0:0.7657:0.1485	.	324	Q2L4Q9	PRS53_HUMAN	V	324	ENSP00000280606:L324V	ENSP00000280606:L324V	L	-	1	2	PRSS53	31003996	0.998000	0.40836	0.950000	0.38849	0.578000	0.36192	3.172000	0.50832	2.720000	0.93068	0.655000	0.94253	CTG	G|0.999;C|0.001	0.001	strong		0.637	PRSS53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108580.4	NM_001081268		C	31096495	G	C	31096495	3	2	24	1	0	0	0	0	1	0	0	0	12644	962	34	4	711	4	PRSS53	16	31096495	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	6226	31096495	59258258	510	8727											
ABCC12	94160	hgsc.bcm.edu	37	chr16	48151202	48151202	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tctccataggggaggttgctCaggtccttctggaggccaca	7	10	13	11	0	3	0	1	0	2	0	5	2	4	2	3	6	1	2	3	6	1	3			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:48151202C>T	ENST00000311303.3	-	12	2100	c.1755G>A	c.(1753-1755)ctG>ctA	p.L585L	ABCC12_ENST00000416054.1_Intron|ABCC12_ENST00000448542.1_Silent_p.L585L	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	585	ABC transporter 1. {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)				GGAGGTTGCTCAGGTCCTTCT	0.582																																					p.L585L		Atlas-SNP	.											.	ABCC12	190	.	0			c.G1755A						PASS	.						82	75	77					16																	48151202		2201	4300	6501	SO:0001819	synonymous_variant	94160	exon12			GTTGCTCAGGTCC	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.1755G>A	16.37:g.48151202C>T		84	0	0		123	59	0.479675	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Silent	SNP	ENST00000311303.3	37	CCDS10730.1																																																																																			.	.	none		0.582	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226		T	48151202	C	T	48151202	2	4	24	1	0	0	0	0	0	0	0	1	52	813	29	2		2	ABCC12	16	48151202	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	17054707	48151202	42203551	511	8728											
CCDC135	84229	hgsc.bcm.edu	37	chr16	57758727	57758727	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcactctgagcagtgcagagTcaaacccccggcccattgtg	9	8	10	14	1	3	2	2	1	1	1	3	2	3	2	3	1	3	2	3	1	1	1	rs115241876	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:57758727T>C	ENST00000360716.3	+	13	1959	c.1738T>C	c.(1738-1740)Tca>Cca	p.S580P	CCDC135_ENST00000336825.8_Missense_Mutation_p.S515P|CCDC135_ENST00000394337.4_Missense_Mutation_p.S580P			Q8IY82	CC135_HUMAN		580					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						CAGTGCAGAGTCAAACCCCCG	0.597													.|||	10	0.00199681	0.0	0.0058	5008	,	,		18147	0.0		0.005	False		,,,				2504	0.001				p.S580P		Atlas-SNP	.											.	CCDC135	97	.	0			c.T1738C						PASS	.	T	PRO/SER	2,4392		0,2,2195	49	43	45		1738	4.1	0.2	16	dbSNP_132	45	39,8559		1,37,4261	yes	missense	CCDC135	NM_032269.5	74	1,39,6456	CC,CT,TT		0.4536,0.0455,0.3156	possibly-damaging	580/875	57758727	41,12951	2197	4299	6496	SO:0001583	missense	84229	exon12			GCAGAGTCAAACC																												ENST00000360716.3:c.1738T>C	16.37:g.57758727T>C	ENSP00000353942:p.Ser580Pro	49	0	0		59	30	0.508475	NM_032269	A8K943|Q8NAA0|Q9H080	Missense_Mutation	SNP	ENST00000360716.3	37	CCDS10787.1	6	0.0027472527472527475	0	0.0	4	0.011049723756906077	0	0.0	2	0.002638522427440633	.	18.06	3.538954	0.65085	4.55E-4	0.004536	ENSG00000159625	ENST00000394337;ENST00000336825;ENST00000360716	T;T;T	0.10382	3.03;2.88;3.03	5.29	4.09	0.47781	.	0.814347	0.11090	N	0.600808	T	0.15609	0.0376	M	0.68317	2.08	0.09310	N	1	D;D	0.58970	0.984;0.966	P;P	0.56088	0.791;0.735	T	0.10132	-1.0643	10	0.37606	T	0.19	-14.6732	6.4912	0.22117	0.1385:0.0:0.2281:0.6334	.	515;580	Q8IY82-2;Q8IY82	.;CC135_HUMAN	P	580;515;580	ENSP00000377869:S580P;ENSP00000338938:S515P;ENSP00000353942:S580P	ENSP00000338938:S515P	S	+	1	0	CCDC135	56316228	0.001000	0.12720	0.236000	0.24074	0.737000	0.42083	0.422000	0.21296	2.004000	0.58718	0.533000	0.62120	TCA	T|0.997;C|0.003	0.003	strong		0.597	CCDC135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433323.2			C	57758727	T	C	57758727	3	2	24	1	0	0	0	0	1	0	0	0	2771	1667	58	3	1780	3	CCDC135	16	57758727	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	9607525	57758727	32596026	512	8729											
CNGB1	1258	hgsc.bcm.edu	37	chr16	58001086	58001086	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcggttctggttccacctcCgcctccatctctggctctgg	2	14	9	16	2	3	0	0	0	3	0	8	0	6	0	5	4	0	3	5	4	0	3	rs61997250	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:58001086C>T	ENST00000251102.8	-	2	165	c.105G>A	c.(103-105)gcG>gcA	p.A35A	CNGB1_ENST00000311183.4_Silent_p.A35A|CNGB1_ENST00000564448.1_Silent_p.A35A	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	35	Glu-rich.				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						GTTCCACCTCCGCCTCCATCT	0.647													C|||	41	0.0081869	0.0023	0.0072	5008	,	,		17304	0.0		0.0258	False		,,,				2504	0.0072				p.A35A	Colon(156;1293 1853 16336 28962 38659)	Atlas-SNP	.											.	CNGB1	105	.	0			c.G105A						PASS	.	C	,	32,3990		0,32,1979	96	101	99		105,105	-8.9	0	16	dbSNP_129	99	242,8090		4,234,3928	no	coding-synonymous,coding-synonymous	CNGB1	NM_001135639.1,NM_001297.4	,	4,266,5907	TT,TC,CC		2.9045,0.7956,2.2179	,	35/300,35/1252	58001086	274,12080	2011	4166	6177	SO:0001819	synonymous_variant	1258	exon2			CACCTCCGCCTCC	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.105G>A	16.37:g.58001086C>T		93	0	0		92	44	0.478261	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Silent	SNP	ENST00000251102.8	37	CCDS42169.1																																																																																			C|0.981;T|0.019	0.019	strong		0.647	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297		T	58001086	C	T	58001086	2	4	24	1	0	0	0	0	0	0	0	1	3602	639	23	1		1	CNGB1	16	58001086	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	242359	58001086	32353667	513	8730											
ELMO3	1874	hgsc.bcm.edu	37	chr16	67234197	67234197	+	IGR	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgctggcctcggacatgatcTttgccagggaggtcatcagc	7	9	13	12	2	3	1	2	1	1	0	4	3	3	3	2	4	2	1	2	4	0	1			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:67234197T>C	ENST00000379378.3	+	0	2096				ELMO3_ENST00000393997.2_Missense_Mutation_p.F169L|MIR328_ENST00000385213.1_RNA|ELMO3_ENST00000571638.1_3'UTR|ELMO3_ENST00000360833.1_Missense_Mutation_p.F152L|ELMO3_ENST00000477898.1_Missense_Mutation_p.F3L	NM_001950.3	NP_001941.2	Q16254	E2F4_HUMAN	E2F transcription factor 4, p107/p130-binding						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)		GGACATGATCTTTGCCAGGGA	0.602																																					p.F169L		Atlas-SNP	.											.	ELMO3	41	.	0			c.T505C						PASS	.						49	52	51					16																	67234197		2067	4182	6249	SO:0001628	intergenic_variant	79767	exon5			ATGATCTTTGCCA	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		16.37:g.67234197T>C		119	0	0		121	5	0.0413223	NM_024712	A6NGR8|B5BU56|Q12991|Q15328	Missense_Mutation	SNP	ENST00000379378.3	37	CCDS32464.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.795457	0.90453	.	.	ENSG00000102890	ENST00000360833;ENST00000393997	T;T	0.43688	0.94;0.94	5.2	5.2	0.72013	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.66056	0.2751	M	0.80616	2.505	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.85130	0.997;0.995;0.99	T	0.71523	-0.4567	10	0.87932	D	0	-9.902	13.9039	0.63821	0.0:0.0:0.0:1.0	.	116;152;169	Q96BJ8;F8W9E7;Q96BJ8-3	ELMO3_HUMAN;.;.	L	152;169	ENSP00000354077:F152L;ENSP00000377566:F169L	ENSP00000354077:F152L	F	+	1	0	ELMO3	65791698	1.000000	0.71417	1.000000	0.80357	0.546000	0.35178	7.179000	0.77665	1.971000	0.57363	0.379000	0.24179	TTT	.	.	none		0.602	E2F4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421565.1	NM_001950		C	67234197	T	C	67234197	1	2	24	0	1	0	0	0	0	0	0	0	5069	1609	56	3		3	ELMO3	16	67234197	IGR	SNP	T	TCGA-G8-6326-01A-11D-2210-10	9233111	67234197	23120556	514	8731											
FTSJD1	55783	hgsc.bcm.edu	37	chr16	71317545	71317545	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaggctgttgataatttctTctctctctctttgaataatg	9	18	7	7	0	4	2	0	2	4	0	6	3	4	2	0	1	0	2	0	1	4	6			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:71317545T>C	ENST00000338099.5	-	3	2615	c.2279A>G	c.(2278-2280)gAa>gGa	p.E760G	CMTR2_ENST00000434935.2_Missense_Mutation_p.E760G			Q8IYT2	CMTR2_HUMAN	cap methyltransferase 2	760					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)										GATAATTTCTTCTCTCTCTCT	0.373																																					p.E760G		Atlas-SNP	.											.	FTSJD1	70	.	0			c.A2279G						PASS	.						37	41	40					16																	71317545		2198	4298	6496	SO:0001583	missense	55783	exon3			ATTTCTTCTCTCT	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.2279A>G	16.37:g.71317545T>C	ENSP00000337512:p.Glu760Gly	172	0	0		166	74	0.445783	NM_018348	B2RCD5|D3DWS1|Q8NE77|Q8NFR5|Q9H8Z4|Q9NUS3|Q9NXF5	Missense_Mutation	SNP	ENST00000338099.5	37	CCDS10898.1	.	.	.	.	.	.	.	.	.	.	T	15.55	2.866136	0.51588	.	.	ENSG00000180917	ENST00000338099;ENST00000434935	T;T	0.15603	2.41;2.41	5.08	5.08	0.68730	.	0.364292	0.26234	N	0.025558	T	0.11537	0.0281	N	0.14661	0.345	0.27675	N	0.946633	B	0.27498	0.18	B	0.25405	0.06	T	0.15867	-1.0422	10	0.66056	D	0.02	-4.0194	13.2858	0.60243	0.0:0.0:0.0:1.0	.	760	Q8IYT2	FTSJ1_HUMAN	G	760	ENSP00000337512:E760G;ENSP00000411148:E760G	ENSP00000337512:E760G	E	-	2	0	FTSJD1	69875046	1.000000	0.71417	0.981000	0.43875	0.796000	0.44982	3.431000	0.52814	2.213000	0.71641	0.477000	0.44152	GAA	.	.	none		0.373	CMTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268984.2	NM_018348		C	71317545	T	C	71317545	3	2	24	1	0	0	0	0	1	0	0	0	6098	1783	62	3	37	3	FTSJD1	16	71317545	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	4083348	71317545	19037208	515	8732											
SLC38A8	146167	hgsc.bcm.edu	37	chr16	84050776	84050776	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagcacgatggggtagacagTtacgatggagacagcaaaaa	16	5	14	6	2	0	2	0	0	0	2	0	6	0	2	0	3	3	4	0	3	4	2	rs142821762		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:84050776T>C	ENST00000299709.3	-	7	921	c.922A>G	c.(922-924)Act>Gct	p.T308A		NM_001080442.1	NP_001073911.1	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8	308					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						GGGTAGACAGTTACGATGGAG	0.537													T|||	1	0.000199681	0.0	0.0	5008	,	,		19595	0.0		0.001	False		,,,				2504	0.0				p.T308A		Atlas-SNP	.											.	SLC38A8	60	.	0			c.A922G						PASS	.	T	ALA/THR	0,4400		0,0,2200	113	88	97		922	4.8	0.2	16	dbSNP_134	97	8,8592	6.4+/-24.3	0,8,4292	yes	missense	SLC38A8	NM_001080442.1	58	0,8,6492	CC,CT,TT		0.093,0.0,0.0615	probably-damaging	308/436	84050776	8,12992	2200	4300	6500	SO:0001583	missense	146167	exon7			AGACAGTTACGAT		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.922A>G	16.37:g.84050776T>C	ENSP00000299709:p.Thr308Ala	56	0	0		77	51	0.662338	NM_001080442		Missense_Mutation	SNP	ENST00000299709.3	37	CCDS32495.1	.	.	.	.	.	.	.	.	.	.	T	19.79	3.893044	0.72524	0.0	9.3E-4	ENSG00000166558	ENST00000299709	T	0.02236	4.38	4.75	4.75	0.60458	.	0.110120	0.64402	D	0.000009	T	0.09642	0.0237	M	0.76838	2.35	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.36696	-0.9737	10	0.06099	T	0.92	-17.5765	13.2419	0.60002	0.0:0.0:0.0:1.0	.	308	A6NNN8	S38A8_HUMAN	A	308	ENSP00000299709:T308A	ENSP00000299709:T308A	T	-	1	0	SLC38A8	82608277	1.000000	0.71417	0.184000	0.23157	0.920000	0.55202	7.230000	0.78097	1.773000	0.52216	0.391000	0.25812	ACT	T|1.000;C|0.000	0.000	strong		0.537	SLC38A8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432623.1	NM_001080442		C	84050776	T	C	84050776	3	2	24	1	0	0	0	0	1	0	0	0	14625	1725	60	3	401	3	SLC38A8	16	84050776	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	12733231	84050776	6303977	516	8733											
CPNE7	27132	hgsc.bcm.edu	37	chr16	89657630	89657630	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatcatctccaaggtggcaCgcgtggcggcggccgaggag	7	5	16	13	5	2	0	1	0	1	0	3	2	2	1	3	6	0	1	3	6	1	0	rs377056293		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:89657630C>G	ENST00000268720.5	+	15	1619	c.1489C>G	c.(1489-1491)Cgc>Ggc	p.R497G	CPNE7_ENST00000319518.8_Missense_Mutation_p.R422G	NM_014427.4	NP_055242.1	Q9UBL6	CPNE7_HUMAN	copine VII	497	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				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)		CAAGGTGGCACGCGTGGCGGC	0.687																																					p.R497G		Atlas-SNP	.											.	CPNE7	56	.	0			c.C1489G						PASS	.						18	20	19					16																	89657630		2183	4285	6468	SO:0001583	missense	27132	exon15			GTGGCACGCGTGG	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.1489C>G	16.37:g.89657630C>G	ENSP00000268720:p.Arg497Gly	70	0	0		73	34	0.465753	NM_014427		Missense_Mutation	SNP	ENST00000268720.5	37	CCDS10980.1	.	.	.	.	.	.	.	.	.	.	C	12.45	1.940346	0.34283	.	.	ENSG00000178773	ENST00000319518;ENST00000268720;ENST00000529800	T;T;T	0.22945	1.93;1.93;1.93	3.9	1.73	0.24493	von Willebrand factor, type A (2);Copine (1);	0.305959	0.32161	N	0.006489	T	0.27697	0.0681	M	0.77313	2.365	0.38493	D	0.948011	P;B	0.36660	0.564;0.049	B;B	0.37304	0.246;0.087	T	0.14392	-1.0474	10	0.59425	D	0.04	0.9483	6.5897	0.22639	0.295:0.6139:0.0:0.0911	.	422;497	Q9UBL6-2;Q9UBL6	.;CPNE7_HUMAN	G	422;497;142	ENSP00000317374:R422G;ENSP00000268720:R497G;ENSP00000435876:R142G	ENSP00000268720:R497G	R	+	1	0	CPNE7	88185131	0.518000	0.26234	0.988000	0.46212	0.873000	0.50193	2.044000	0.41241	0.759000	0.33084	0.556000	0.70494	CGC	.	.	alt		0.687	CPNE7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269929.2			G	89657630	C	G	89657630	3	3	24	1	0	0	0	0	1	0	0	0	3819	536	19	4	1547	4	CPNE7	16	89657630	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	5606854	89657630	697123	517	8734											
DBNDD1	79007	hgsc.bcm.edu	37	chr16	90076445	90076445	+	Intron	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ttgagcaaatattcttccagGtttctcccatgtttatttat	9	19	5	8	0	2	1	0	1	2	0	4	1	3	1	2	1	1	3	2	1	4	9			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr16:90076445G>A	ENST00000002501.6	-	2	163				DBNDD1_ENST00000304733.3_Missense_Mutation_p.T4I|DBNDD1_ENST00000568838.1_Intron|DBNDD1_ENST00000392973.3_5'UTR	NM_001042610.1	NP_001036075.1	Q9H9R9	DBND1_HUMAN	dysbindin (dystrobrevin binding protein 1) domain containing 1							cytoplasm (GO:0005737)				kidney(1)|large_intestine(1)|lung(1)	3		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;0.0275)		ATTCTTCCAGGTTTCTCCCAT	0.473																																					p.T4I		Atlas-SNP	.											.	DBNDD1	9	.	0			c.C11T						PASS	.						91	86	87					16																	90076445		1848	4097	5945	SO:0001627	intron_variant	79007	exon1			TTCCAGGTTTCTC	AK090696	CCDS10991.2, CCDS42223.1, CCDS73931.1	16q24.3	2008-02-05			ENSG00000003249	ENSG00000003249			28455	protein-coding gene	gene with protein product						12477932	Standard	NM_001288708		Approved	MGC3101, FLJ12582	uc002fqe.1	Q9H9R9	OTTHUMG00000138984	ENST00000002501.6:c.32-607C>T	16.37:g.90076445G>A		152	0	0		156	71	0.455128	NM_024043	B4DQS3|Q69YT2|Q9BW25	Missense_Mutation	SNP	ENST00000002501.6	37	CCDS42223.1	.	.	.	.	.	.	.	.	.	.	G	11.39	1.624552	0.28889	.	.	ENSG00000003249	ENST00000304733	T	0.47177	0.85	1.92	0.867	0.19085	.	.	.	.	.	T	0.26557	0.0649	.	.	.	0.09310	N	1	B	0.30889	0.299	B	0.21546	0.035	T	0.12682	-1.0538	7	.	.	.	.	6.0374	0.19716	0.0:0.3279:0.6721:0.0	.	4	Q9H9R9-2	.	I	4	ENSP00000306407:T4I	.	T	-	2	0	DBNDD1	88603946	0.300000	0.24435	0.004000	0.12327	0.007000	0.05969	0.637000	0.24659	0.326000	0.23384	0.591000	0.81541	ACC	.	.	none		0.473	DBNDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272872.1	NM_024043		A	90076445	G	A	90076445	1	1	24	0	1	0	0	0	0	0	0	0	4255	1261	44	2		2	DBNDD1	16	90076445	Intron	SNP	G	TCGA-G8-6326-01A-11D-2210-10	418815	90076445	278308	518	8735											
RPH3AL	9501	hgsc.bcm.edu	37	chr17	96910	96910	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaggggacttacctcttcctCgggcccacgtgtagatgcgg	6	9	14	12	3	1	1	0	0	1	1	3	3	2	2	3	4	2	1	3	4	2	3	rs376959240		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:96910C>T	ENST00000331302.7	-	7	912	c.605G>A	c.(604-606)cGa>cAa	p.R202Q	RPH3AL_ENST00000536489.2_Missense_Mutation_p.R173Q|RPH3AL_ENST00000576001.1_5'UTR|RPH3AL_ENST00000323434.8_Missense_Mutation_p.R173Q	NM_001190411.1|NM_006987.3	NP_001177340.1|NP_008918.1	Q9UNE2	RPH3L_HUMAN	rabphilin 3A-like (without C2 domains)	202					exocytosis (GO:0006887)|glucose homeostasis (GO:0042593)|intracellular protein transport (GO:0006886)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|positive regulation of protein secretion (GO:0050714)|regulation of calcium ion-dependent exocytosis (GO:0017158)|response to drug (GO:0042493)	cytoplasm (GO:0005737)|secretory granule membrane (GO:0030667)	cytoskeletal protein binding (GO:0008092)|metal ion binding (GO:0046872)			NS(2)|breast(1)|kidney(1)|large_intestine(1)|skin(1)	6				UCEC - Uterine corpus endometrioid carcinoma (25;0.023)|all cancers(1;4.96e-06)|Epithelial(1;2.86e-05)|BRCA - Breast invasive adenocarcinoma(1;0.00453)|OV - Ovarian serous cystadenocarcinoma(1;0.0716)|LUAD - Lung adenocarcinoma(1115;0.102)|COAD - Colon adenocarcinoma(4;0.107)		ACCTCTTCCTCGGGCCCACGT	0.632													c|||	1	0.000199681	0.0	0.0	5008	,	,		17004	0.001		0.0	False		,,,				2504	0.0				p.R202Q		Atlas-SNP	.											.	RPH3AL	18	.	0			c.G605A						PASS	.		GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	98	91	93		605,518,518,605	5.1	1	17		93	0,8600		0,0,4300	no	missense,missense,missense,missense	RPH3AL	NM_001190411.1,NM_001190412.1,NM_001190413.1,NM_006987.3	43,43,43,43	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	202/316,173/287,173/287,202/316	96910	1,13005	2203	4300	6503	SO:0001583	missense	9501	exon7			CTTCCTCGGGCCC		CCDS10994.1, CCDS54059.1	17p13.3	2014-07-02			ENSG00000181031	ENSG00000181031		"Synaptotagmins"	10296	protein-coding gene	gene with protein product		604881				10395805	Standard	NM_006987		Approved	Noc2	uc021tmx.1	Q9UNE2	OTTHUMG00000090273	ENST00000331302.7:c.605G>A	17.37:g.96910C>T	ENSP00000328977:p.Arg202Gln	98	0	0		85	39	0.458824	NM_006987	D3DTG7|Q9BSB3	Missense_Mutation	SNP	ENST00000331302.7	37	CCDS10994.1	.	.	.	.	.	.	.	.	.	.	c	18.68	3.676535	0.67928	2.27E-4	0.0	ENSG00000181031	ENST00000323434;ENST00000331302;ENST00000536489	.	.	.	5.06	5.06	0.68205	.	0.114746	0.35235	N	0.003345	T	0.62011	0.2393	M	0.77103	2.36	0.22710	N	0.998827	D;D;D	0.76494	0.981;0.999;0.999	P;D;P	0.64237	0.551;0.923;0.849	T	0.55786	-0.8086	9	0.21540	T	0.41	-5.7361	9.6113	0.39665	0.0:0.9048:0.0:0.0952	.	173;173;202	A8K7D5;Q9UNE2-2;Q9UNE2	.;.;RPH3L_HUMAN	Q	202;173;173	.	ENSP00000319210:R202Q	R	-	2	0	RPH3AL	96910	1.000000	0.71417	1.000000	0.80357	0.315000	0.28087	2.084000	0.41625	2.378000	0.81104	0.544000	0.68410	CGA	.	.	weak		0.632	RPH3AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206597.2	NM_006987		T	96910	C	T	96910	3	4	24	1	0	0	0	0	1	0	0	0	13567	884	31	1	358	1	RPH3AL	17	96910	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10		96910	81098300	519	8736											
MYBBP1A	10514	hgsc.bcm.edu	37	chr17	4452638	4452638	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agctcgcacctggccacctgCtcagtcaaggcctcctccat	7	8	8	18	1	2	0	2	0	0	0	5	0	4	0	6	2	2	3	6	2	1	0			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:4452638C>T	ENST00000254718.4	-	10	1725	c.1419G>A	c.(1417-1419)gaG>gaA	p.E473E	MYBBP1A_ENST00000381556.2_Silent_p.E473E			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	473	Interaction with MYB. {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						TGGCCACCTGCTCAGTCAAGG	0.592																																					p.E473E		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.G1419A						PASS	.						87	59	69					17																	4452638		2203	4300	6503	SO:0001819	synonymous_variant	10514	exon10			CACCTGCTCAGTC	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.1419G>A	17.37:g.4452638C>T		30	0	0		35	19	0.542857	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Silent	SNP	ENST00000254718.4	37	CCDS11046.1																																																																																			.	.	none		0.592	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520		T	4452638	C	T	4452638	2	4	24	1	0	0	0	0	0	0	0	1	10017	796	28	2		2	MYBBP1A	17	4452638	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	4355728	4452638	76742572	520	8737											
MED11	400569	hgsc.bcm.edu	37	chr17	4636385	4636385	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgagggctccagctactcttCgaggaaggactgtcagatgg	9	9	14	9	1	2	2	1	1	1	1	4	5	3	4	1	4	2	2	1	4	2	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:4636385C>T	ENST00000293777.5	+	3	313	c.257C>T	c.(256-258)tCg>tTg	p.S86L	RP11-314A20.5_ENST00000570493.2_RNA|CXCL16_ENST00000576153.1_5'Flank|MED11_ENST00000575284.1_3'UTR	NM_001001683.2	NP_001001683.1	Q9P086	MED11_HUMAN	mediator complex subunit 11	86						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			lung(2)|ovary(2)	4						AGCTACTCTTCGAGGAAGGAC	0.557																																					p.S86L		Atlas-SNP	.											.	MED11	5	.	0			c.C257T						PASS	.						94	80	85					17																	4636385		2203	4300	6503	SO:0001583	missense	400569	exon3			ACTCTTCGAGGAA	AF161414	CCDS32533.1	17p13.2	2007-07-30	2007-07-30			ENSG00000161920			32687	protein-coding gene	gene with protein product		612383	"mediator of RNA polymerase II transcription, subunit 11 homolog (S. cerevisiae)"			15175163, 12584197	Standard	NM_001001683		Approved	HSPC296, MGC88387	uc002fyp.3	Q9P086		ENST00000293777.5:c.257C>T	17.37:g.4636385C>T	ENSP00000293777:p.Ser86Leu	149	0	0		154	64	0.415584	NM_001001683	Q6NS89	Missense_Mutation	SNP	ENST00000293777.5	37	CCDS32533.1	.	.	.	.	.	.	.	.	.	.	C	19.38	3.816690	0.70912	.	.	ENSG00000161920	ENST00000293777	.	.	.	5.74	4.74	0.60224	.	0.163543	0.37669	N	0.001992	T	0.47040	0.1424	L	0.38175	1.15	0.41743	D	0.989629	B	0.34313	0.448	B	0.29440	0.102	T	0.51631	-0.8681	9	0.66056	D	0.02	-22.7906	14.2205	0.65823	0.0:0.8492:0.1508:0.0	.	86	Q9P086	MED11_HUMAN	L	86	.	ENSP00000293777:S86L	S	+	2	0	MED11	4583134	0.999000	0.42202	0.893000	0.35052	0.967000	0.64934	4.595000	0.61048	1.365000	0.46057	0.655000	0.94253	TCG	.	.	none		0.557	MED11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439574.1	NM_001001683		T	4636385	C	T	4636385	3	4	24	1	0	0	0	0	1	0	0	0	9436	893	31	1	267	1	MED11	17	4636385	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	183747	4636385	76558825	521	8738											
DHX33	56919	hgsc.bcm.edu	37	chr17	5347788	5347788	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgtgagccaggcagcggcGgacactctccacgtctcctc	6	7	12	16	3	2	1	0	1	2	0	5	2	2	2	3	3	2	2	3	3	0	0	rs75426953	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:5347788G>A	ENST00000225296.3	-	12	2061	c.1861C>T	c.(1861-1863)Cgc>Tgc	p.R621C	DHX33_ENST00000433302.3_Missense_Mutation_p.R397C	NM_001199699.1|NM_020162.3	NP_001186628.1|NP_064547.2	Q9H6R0	DHX33_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 33	621					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						AGGCAGCGGCGGACACTCTCC	0.607													G|||	35	0.00698882	0.0008	0.0086	5008	,	,		19061	0.001		0.0239	False		,,,				2504	0.0031				p.R621C		Atlas-SNP	.											DHX33,NS,carcinoma,0,1	DHX33	41	1	0			c.C1861T						PASS	.	G	CYS/ARG,CYS/ARG	24,4382	30.8+/-60.4	1,22,2180	74	69	70		1342,1861	4.6	1	17	dbSNP_131	70	203,8397	88.4+/-150.7	2,199,4099	yes	missense,missense	DHX33	NM_001199699.1,NM_020162.3	180,180	3,221,6279	AA,AG,GG		2.3605,0.5447,1.7453	probably-damaging,probably-damaging	448/535,621/708	5347788	227,12779	2203	4300	6503	SO:0001583	missense	56919	exon12			AGCGGCGGACACT	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.1861C>T	17.37:g.5347788G>A	ENSP00000225296:p.Arg621Cys	97	0	0		125	65	0.52	NM_020162	B4DHF9|Q4G149|Q5CZ73|Q9H5M9	Missense_Mutation	SNP	ENST00000225296.3	37	CCDS11072.1	24	0.01098901098901099	1	0.0020325203252032522	5	0.013812154696132596	1	0.0017482517482517483	17	0.022427440633245383	G	25.8	4.678553	0.88542	0.005447	0.023605	ENSG00000005100	ENST00000225296;ENST00000433302	T;T	0.02890	4.12;4.12	4.59	4.59	0.56863	Domain of unknown function DUF1605 (1);	0.000000	0.85682	D	0.000000	T	0.08846	0.0219	M	0.85373	2.75	0.80722	D	1	D;P	0.89917	1.0;0.626	D;B	0.81914	0.995;0.287	T	0.00235	-1.1892	10	0.66056	D	0.02	.	16.9197	0.86161	0.0:0.0:1.0:0.0	.	397;621	Q05BE5;Q9H6R0	.;DHX33_HUMAN	C	621;397	ENSP00000225296:R621C;ENSP00000413779:R397C	ENSP00000225296:R621C	R	-	1	0	DHX33	5288512	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	9.073000	0.93992	2.548000	0.85928	0.561000	0.74099	CGC	A|0.014;C|0.000;G|0.986	0.014	strong		0.607	DHX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219826.2	NM_020162		A	5347788	G	A	5347788	3	1	24	1	0	0	0	0	1	0	0	0	4508	1116	39	1	266	1	DHX33	17	5347788	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	711403	5347788	75847422	522	8739											
MYH10	4628	hgsc.bcm.edu	37	chr17	8416982	8416982	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgagtcacttgtagaagcggCttcacctatgacaaaattaa	14	10	8	9	2	2	2	2	1	0	1	2	3	2	2	1	1	1	2	1	1	6	5			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:8416982C>T	ENST00000269243.4	-	21	2664	c.2526G>A	c.(2524-2526)aaG>aaA	p.K842K	MYH10_ENST00000379980.4_Silent_p.K858K|RNU7-43P_ENST00000516554.1_RNA|MYH10_ENST00000360416.3_Silent_p.K873K|MYH10_ENST00000396239.1_Silent_p.K863K	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	842					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						GTAGAAGCGGCTTCACCTATG	0.443																																					p.K873K		Atlas-SNP	.											.	MYH10	148	.	0			c.G2619A						PASS	.						166	159	161					17																	8416982		2203	4300	6503	SO:0001819	synonymous_variant	4628	exon23			AAGCGGCTTCACC	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.2526G>A	17.37:g.8416982C>T		57	0	0		61	26	0.42623	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	37	CCDS11144.1																																																																																			.	.	none		0.443	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			T	8416982	C	T	8416982	2	4	24	1	0	0	0	0	0	0	0	1	10039	796	28	2		2	MYH10	17	8416982	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	3069194	8416982	72778228	523	8740											
WDR16	146845	hgsc.bcm.edu	37	chr17	9511492	9511492	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgttggtgggctctggagcCggactgctggtcttctgtaa	4	14	15	8	1	3	0	0	0	3	0	3	2	3	2	1	5	2	4	1	5	1	4	rs146548028		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:9511492C>T	ENST00000352665.5	+	7	879	c.810C>T	c.(808-810)gcC>gcT	p.A270A	WDR16_ENST00000299764.5_Silent_p.A280A|WDR16_ENST00000396219.3_Silent_p.A202A	NM_145054.4	NP_659491.4			WD repeat domain 16									p.A270A(1)		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						GCTCTGGAGCCGGACTGCTGG	0.507													c|||	1	0.000199681	0.0	0.0	5008	,	,		14489	0.0		0.001	False		,,,				2504	0.0				p.A270A		Atlas-SNP	.											WDR16,NS,carcinoma,0,1	WDR16	67	1	1	Substitution - coding silent(1)	endometrium(1)	c.C810T						PASS	.		,	1,4405	2.1+/-5.4	0,1,2202	76	76	76		606,810	-10.8	0.7	17	dbSNP_134	76	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	WDR16	NM_001080556.1,NM_145054.4	,	0,4,6499	TT,TC,CC		0.0349,0.0227,0.0308	,	202/553,270/621	9511492	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	146845	exon7			TGGAGCCGGACTG	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.810C>T	17.37:g.9511492C>T		134	0	0		171	90	0.526316	NM_145054		Silent	SNP	ENST00000352665.5	37	CCDS11149.2																																																																																			C|0.999;T|0.001	0.001	strong		0.507	WDR16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316569.2	NM_145054		T	9511492	C	T	9511492	2	4	24	1	0	0	0	0	0	0	0	1	17291	639	23	1		1	WDR16	17	9511492	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1094510	9511492	71683718	524	8741											
MYH13	8735	hgsc.bcm.edu	37	chr17	10261086	10261086	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgtcattcctcacagtcttgGcatttccaaaggcctccagc	8	12	7	14	0	3	0	2	0	1	0	6	0	6	0	4	2	1	1	4	2	1	3			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:10261086G>A	ENST00000418404.3	-	7	867	c.704C>T	c.(703-705)gCc>gTc	p.A235V	MYH13_ENST00000252172.4_Missense_Mutation_p.A235V			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	235	Myosin motor.				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						CACAGTCTTGGCATTTCCAAA	0.453																																					p.A235V		Atlas-SNP	.											.	MYH13	533	.	0			c.C704T						PASS	.						99	107	105					17																	10261086		2180	4296	6476	SO:0001583	missense	8735	exon8			GTCTTGGCATTTC	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.704C>T	17.37:g.10261086G>A	ENSP00000404570:p.Ala235Val	137	0	0		143	62	0.433566	NM_003802	O95252|Q9P0U8	Missense_Mutation	SNP	ENST00000418404.3	37	CCDS45613.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.001634	0.93227	.	.	ENSG00000006788	ENST00000252172	D	0.83914	-1.78	3.94	3.94	0.45596	Myosin head, motor domain (3);	.	.	.	.	D	0.94810	0.8324	H	0.99249	4.485	0.53005	D	0.999965	D	0.67145	0.996	D	0.69142	0.962	D	0.97360	0.9969	9	0.87932	D	0	.	16.5222	0.84320	0.0:0.0:1.0:0.0	.	235	Q9UKX3	MYH13_HUMAN	V	235	ENSP00000252172:A235V	ENSP00000252172:A235V	A	-	2	0	MYH13	10201811	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	9.450000	0.97607	2.200000	0.70718	0.467000	0.42956	GCC	.	.	none		0.453	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	10261086	G	A	10261086	3	1	24	1	0	0	0	0	1	0	0	0	10041	1203	42	2	5248	2	MYH13	17	10261086	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	749594	10261086	70934124	525	8742											
NCOR1	9611	hgsc.bcm.edu	37	chr17	16005030	16005030	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttctgtgtttcctcgagaagTagcattttcaggactgtcct	7	16	9	9	1	2	1	1	0	1	1	5	3	4	2	2	1	1	3	2	1	2	5	rs150909544		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:16005030T>C	ENST00000268712.3	-	20	2481	c.2224A>G	c.(2224-2226)Act>Gct	p.T742A	NCOR1_ENST00000583226.1_5'Flank|RNU6-314P_ENST00000516574.1_RNA|NCOR1_ENST00000395848.1_Missense_Mutation_p.T649A|NCOR1_ENST00000395851.1_Missense_Mutation_p.T758A	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	742					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)		CCTCGAGAAGTAGCATTTTCA	0.483													T|||	1	0.000199681	0.0008	0.0	5008	,	,		21166	0.0		0.0	False		,,,				2504	0.0				p.T758A		Atlas-SNP	.											.	NCOR1	240	.	0			c.A2272G						PASS	.	T	ALA/THR,ALA/THR,ALA/THR	1,4405	2.1+/-5.4	0,1,2202	93	88	90		1945,2272,2224	-10.8	0	17	dbSNP_134	90	0,8600		0,0,4300	no	missense,missense,missense	NCOR1	NM_001190438.1,NM_001190440.1,NM_006311.3	58,58,58	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign,benign,benign	649/915,758/2338,742/2441	16005030	1,13005	2203	4300	6503	SO:0001583	missense	9611	exon19			GAGAAGTAGCATT	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.2224A>G	17.37:g.16005030T>C	ENSP00000268712:p.Thr742Ala	93	0	0		96	41	0.427083	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	37	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	T	7.122	0.578209	0.13686	2.27E-4	0.0	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849;ENST00000395848	T;T;T	0.27402	3.47;1.67;1.67	5.77	-10.8	0.00216	.	0.521213	0.24063	N	0.041899	T	0.08313	0.0207	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;0.0;0.0	T	0.25187	-1.0139	10	0.27082	T	0.32	0.119	4.1227	0.10112	0.1739:0.4619:0.1847:0.1796	.	649;742;758	E9PGV6;O75376;O75376-2	.;NCOR1_HUMAN;.	A	742;758;649;649	ENSP00000268712:T742A;ENSP00000379192:T758A;ENSP00000379189:T649A	ENSP00000268712:T742A	T	-	1	0	NCOR1	15945755	0.008000	0.16893	0.027000	0.17364	0.990000	0.78478	-0.887000	0.04152	-1.821000	0.01213	-0.290000	0.09829	ACT	T|1.000;C|0.000	0.000	weak		0.483	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311		C	16005030	T	C	16005030	3	2	24	1	0	0	0	0	1	0	0	0	10244	1638	57	3	5206	3	NCOR1	17	16005030	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	5743944	16005030	65190180	526	8743											
C17orf76	388341	hgsc.bcm.edu	37	chr17	16347001	16347001	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tcctggcctactgtcccttcCcggacctcctccccactgcc	3	10	6	22	1	0	0	0	0	0	0	5	1	5	1	9	2	2	0	9	2	1	2	rs200702301	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:16347001C>T	ENST00000470794.1	-	4	963	c.936G>A	c.(934-936)cgG>cgA	p.R312R	C17orf76-AS1_ENST00000581718.1_RNA|C17orf76-AS1_ENST00000584926.1_RNA|C17orf76-AS1_ENST00000584141.1_RNA|C17orf76-AS1_ENST00000483140.1_RNA|C17orf76-AS1_ENST00000472367.1_RNA|C17orf76-AS1_ENST00000487066.1_RNA|C17orf76-AS1_ENST00000480811.1_RNA|C17orf76-AS1_ENST00000580770.1_RNA|RP11-138I1.3_ENST00000585048.1_lincRNA|C17orf76-AS1_ENST00000580180.1_RNA|C17orf76-AS1_ENST00000584177.1_RNA|C17orf76-AS1_ENST00000478103.2_RNA|C17orf76-AS1_ENST00000484836.1_RNA|C17orf76-AS1_ENST00000391079.1_RNA|FAM211A_ENST00000409083.3_3'UTR|C17orf76-AS1_ENST00000477249.2_RNA|C17orf76-AS1_ENST00000579473.1_RNA|C17orf76-AS1_ENST00000492250.1_RNA|C17orf76-AS1_ENST00000470491.2_RNA|C17orf76-AS1_ENST00000475947.2_RNA|C17orf76-AS1_ENST00000491009.1_RNA|C17orf76-AS1_ENST00000581913.1_RNA|C17orf76-AS1_ENST00000460249.1_RNA|C17orf76-AS1_ENST00000481027.1_RNA|C17orf76-AS1_ENST00000481898.1_RNA|C17orf76-AS1_ENST00000583400.2_RNA|C17orf76-AS1_ENST00000582911.1_RNA|C17orf76-AS1_ENST00000475953.1_RNA	NM_001113567.2	NP_001107039.1														lung(1)	1						CTGTCCCTTCCCGGACCTCCT	0.667													C|||	3	0.000599042	0.0008	0.0	5008	,	,		17848	0.0		0.002	False		,,,				2504	0.0				p.R312R		Atlas-SNP	.											.	FAM211A	21	.	0			c.G936A						PASS	.						28	33	31					17																	16347001		692	1591	2283	SO:0001819	synonymous_variant	388341	exon4			CCCTTCCCGGACC																												ENST00000470794.1:c.936G>A	17.37:g.16347001C>T		75	0	0		69	34	0.492754	NM_001113567		Silent	SNP	ENST00000470794.1	37	CCDS45620.1																																																																																			C|0.996;T|0.004	0.004	weak		0.667	FAM211A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130463.3			T	16347001	C	T	16347001	2	4	24	1	0	0	0	0	0	0	0	1	1883	610	22	2		2	C17orf76	17	16347001	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	341971	16347001	64848209	527	8744											
ZNF287	57336	hgsc.bcm.edu	37	chr17	16469879	16469879	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccatcctgtctggaaagcaTgttttcctctggggtcttcc	5	14	10	12	0	3	0	0	0	3	0	6	1	6	1	4	3	1	2	4	3	1	3	rs149325980		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:16469879T>C	ENST00000395824.1	-	3	1078	c.461A>G	c.(460-462)cAt>cGt	p.H154R	ZNF287_ENST00000395825.3_Missense_Mutation_p.H154R|ZNF287_ENST00000461555.1_5'Flank			Q9HBT7	ZN287_HUMAN	zinc finger protein 287	147					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)		CTGGAAAGCATGTTTTCCTCT	0.438																																					p.H154R		Atlas-SNP	.											.	ZNF287	60	.	0			c.A461G						PASS	.						170	167	168					17																	16469879		2203	4300	6503	SO:0001583	missense	57336	exon3			AAAGCATGTTTTC	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.461A>G	17.37:g.16469879T>C	ENSP00000379168:p.His154Arg	131	0	0		154	85	0.551948	NM_020653	Q6IAG1	Missense_Mutation	SNP	ENST00000395824.1	37	CCDS11179.2	.	.	.	.	.	.	.	.	.	.	T	5.385	0.256302	0.10185	.	.	ENSG00000141040	ENST00000395825;ENST00000395824	T;T	0.04809	3.55;3.55	4.18	-2.2	0.06994	Transcription regulator SCAN (1);	1.448190	0.04304	N	0.347863	T	0.02533	0.0077	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45556	-0.9253	10	0.15952	T	0.53	.	5.8246	0.18546	0.0:0.189:0.5011:0.3099	.	147	Q9HBT7	ZN287_HUMAN	R	154	ENSP00000379169:H154R;ENSP00000379168:H154R	ENSP00000379168:H154R	H	-	2	0	ZNF287	16410604	0.001000	0.12720	0.026000	0.17262	0.849000	0.48306	-0.217000	0.09253	-0.462000	0.06984	-0.290000	0.09829	CAT	T|1.000;A|0.000	.	alt		0.438	ZNF287-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130504.1			C	16469879	T	C	16469879	3	2	24	1	0	0	0	0	1	0	0	0	17840	1464	51	3	1840	3	ZNF287	17	16469879	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	122878	16469879	64725331	528	8745											
RNF112	7732	hgsc.bcm.edu	37	chr17	19316656	19316656	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagggctgcaggtggggcGccaatggcctcgccaggggc	5	5	19	12	2	0	0	0	0	0	0	1	0	0	0	3	7	2	3	3	7	1	0			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:19316656G>A	ENST00000461366.1	+	5	867	c.652G>A	c.(652-654)Gcc>Acc	p.A218T	RNF112_ENST00000580109.1_3'UTR|CTB-187M2.2_ENST00000579897.1_RNA	NM_007148.4	NP_009079.2	Q9ULX5	RN112_HUMAN	ring finger protein 112	218	GB1/RHD3-type G.					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						CAGGTGGGGCGCCAATGGCCT	0.642																																					p.A218T		Atlas-SNP	.											.	RNF112	37	.	0			c.G652A						PASS	.						20	24	23					17																	19316656		1952	4129	6081	SO:0001583	missense	7732	exon5			TGGGGCGCCAATG	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.652G>A	17.37:g.19316656G>A	ENSP00000454919:p.Ala218Thr	101	0	0		98	49	0.5	NM_007148	O60633|Q7Z5V9	Missense_Mutation	SNP	ENST00000461366.1	37	CCDS58529.1																																																																																			.	.	none		0.642	RNF112-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132549.4	NM_007148		A	19316656	G	A	19316656	3	1	24	1	0	0	0	0	1	0	0	0	13441	1087	38	1	380	1	RNF112	17	19316656	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	2846777	19316656	61878554	529	8746											
RNF112	7732	hgsc.bcm.edu	37	chr17	19319353	19319353	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atggtggctgctggagctgcCgtgggggccacaggggccgc	4	6	20	11	2	0	0	0	0	0	0	0	1	0	1	3	7	3	3	3	7	0	0			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:19319353C>T	ENST00000461366.1	+	14	1976	c.1761C>T	c.(1759-1761)gcC>gcT	p.A587A	AC004448.2_ENST00000437646.1_lincRNA|CTB-187M2.2_ENST00000579897.1_RNA	NM_007148.4	NP_009079.2	Q9ULX5	RN112_HUMAN	ring finger protein 112	587						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						CTGGAGCTGCCGTGGGGGCCA	0.701																																					p.A587A		Atlas-SNP	.											.	RNF112	37	.	0			c.C1761T						PASS	.						3	4	4					17																	19319353		1690	3667	5357	SO:0001819	synonymous_variant	7732	exon14			AGCTGCCGTGGGG	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.1761C>T	17.37:g.19319353C>T		60	0	0		47	26	0.553191	NM_007148	O60633|Q7Z5V9	Silent	SNP	ENST00000461366.1	37	CCDS58529.1																																																																																			.	.	none		0.701	RNF112-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132549.4	NM_007148		T	19319353	C	T	19319353	2	4	24	1	0	0	0	0	0	0	0	1	13441	639	23	1		1	RNF112	17	19319353	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	2697	19319353	61875857	530	8747											
SLC47A2	146802	hgsc.bcm.edu	37	chr17	19607432	19607432	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcttggcctgcacagtatcCgcagcccccagagccatccc	7	6	9	19	2	0	1	0	0	0	1	2	1	2	1	6	1	3	4	6	1	1	2	rs34169093	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:19607432C>T	ENST00000325411.5	-	11	1127	c.1077G>A	c.(1075-1077)gcG>gcA	p.A359A	SLC47A2_ENST00000350657.5_Silent_p.A337A|SLC47A2_ENST00000463318.1_5'UTR	NM_152908.3	NP_690872.2	Q86VL8	S47A2_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 2	359					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)	GCACAGTATCCGCAGCCCCCA	0.617													C|||	311	0.0621006	0.1831	0.0187	5008	,	,		18054	0.0		0.0268	False		,,,				2504	0.0297				p.A359A		Atlas-SNP	.											.	SLC47A2	61	.	0			c.G1077A						PASS	.	C	,	663,3743	278.7+/-274.4	51,561,1591	50	49	50		969,1077	-0.3	0	17	dbSNP_126	50	237,8363	94.7+/-156.6	2,233,4065	no	coding-synonymous,coding-synonymous	SLC47A2	NM_001099646.1,NM_152908.3	,	53,794,5656	TT,TC,CC		2.7558,15.0477,6.9199	,	323/567,359/603	19607432	900,12106	2203	4300	6503	SO:0001819	synonymous_variant	146802	exon11			AGTATCCGCAGCC	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.1077G>A	17.37:g.19607432C>T		59	0	0		43	24	0.55814	NM_152908	A0JBX9|A0P8Z7|Q63HJ9|Q8IV44|Q96NA1	Silent	SNP	ENST00000325411.5	37	CCDS11211.1																																																																																			C|0.935;T|0.065	0.065	strong		0.617	SLC47A2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132242.2	NM_152908		T	19607432	C	T	19607432	2	4	24	1	0	0	0	0	0	0	0	1	14663	639	23	1		1	SLC47A2	17	19607432	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	288079	19607432	61587778	531	8748											
SLC46A1	113235	hgsc.bcm.edu	37	chr17	26731959	26731959	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gcgggagccacatagagctgGacaatggatcggtggtgacg	10	6	17	8	3	0	2	0	1	0	1	1	5	0	5	1	5	2	1	1	5	2	1	rs185900287	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:26731959G>C	ENST00000440501.1	-	2	851	c.756C>G	c.(754-756)gtC>gtG	p.V252V	CTD-2350C19.2_ENST00000580714.1_RNA|CTD-2350C19.1_ENST00000583956.1_RNA|SLC46A1_ENST00000321666.5_Silent_p.V252V|SLC46A1_ENST00000584729.1_5'UTR	NM_080669.4	NP_542400.2	Q96NT5	PCFT_HUMAN	solute carrier family 46 (folate transporter), member 1	252					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)	CATAGAGCTGGACAATGGATC	0.542													G|||	4	0.000798722	0.0	0.0014	5008	,	,		18170	0.0		0.001	False		,,,				2504	0.002				p.V252V		Atlas-SNP	.											.	SLC46A1	17	.	0			c.C756G						PASS	.	G	,	0,3912		0,0,1956	120	126	124		756,756	4.4	0.4	17		124	17,8283		0,17,4133	no	coding-synonymous,coding-synonymous	SLC46A1	NM_001242366.1,NM_080669.4	,	0,17,6089	CC,CG,GG		0.2048,0.0,0.1392	,	252/432,252/460	26731959	17,12195	1956	4150	6106	SO:0001819	synonymous_variant	113235	exon2			GAGCTGGACAATG	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.756C>G	17.37:g.26731959G>C		101	0	0		129	72	0.55814	NM_001242366	Q1HE20|Q86T92|Q8TEG3|Q96FL0	Silent	SNP	ENST00000440501.1	37																																																																																				G|0.999;C|0.001	0.001	strong		0.542	SLC46A1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_080669		C	26731959	G	C	26731959	2	2	24	1	0	0	0	0	0	0	0	1	14659	1161	41	4		4	SLC46A1	17	26731959	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	7124527	26731959	54463251	532	8749											
EFCAB5	374786	hgsc.bcm.edu	37	chr17	28381069	28381069	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attgaagtccctctacaggaAaagaggtcttgggaacaaac	15	8	10	8	0	2	2	0	1	2	1	3	4	3	4	1	3	3	0	1	3	6	3			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:28381069A>G	ENST00000394835.3	+	10	2289	c.2097A>G	c.(2095-2097)gaA>gaG	p.E699E	EFCAB5_ENST00000536908.2_Silent_p.E643E|EFCAB5_ENST00000320856.5_Silent_p.E699E|EFCAB5_ENST00000541045.1_Silent_p.E356E|EFCAB5_ENST00000378738.3_Silent_p.E699E|EFCAB5_ENST00000394832.2_Silent_p.E699E	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	699							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						CTCTACAGGAAAAGAGGTCTT	0.378																																					p.E699E		Atlas-SNP	.											.	EFCAB5	122	.	0			c.A2097G						PASS	.						33	31	32					17																	28381069		1831	4083	5914	SO:0001819	synonymous_variant	374786	exon10			ACAGGAAAAGAGG	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.2097A>G	17.37:g.28381069A>G		180	0	0		222	112	0.504505	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Silent	SNP	ENST00000394835.3	37	CCDS11254.2																																																																																			.	.	none		0.378	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529		G	28381069	A	G	28381069	2	3	24	1	0	0	0	0	0	0	0	1	4940	11	1	3		3	EFCAB5	17	28381069	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	1649110	28381069	52814141	533	8750											
EFCAB5	374786	hgsc.bcm.edu	37	chr17	28407861	28407861	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggaaccagtcccgtaataaGcatgattataatggttcatt	13	13	8	7	1	1	1	1	1	0	0	2	2	2	2	2	2	2	3	2	2	5	6	rs147629201	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:28407861G>A	ENST00000394835.3	+	17	3480	c.3288G>A	c.(3286-3288)aaG>aaA	p.K1096K	EFCAB5_ENST00000320856.5_Silent_p.K972K|EFCAB5_ENST00000394832.2_Intron	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	1096							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						CCCGTAATAAGCATGATTATA	0.448													G|||	50	0.00998403	0.0348	0.0029	5008	,	,		19986	0.0		0.002	False		,,,				2504	0.0				p.K1096K		Atlas-SNP	.											.	EFCAB5	122	.	0			c.G3288A						PASS	.	G		73,3703		0,73,1815	82	78	79		3288	4.1	0.1	17	dbSNP_134	79	10,8210		0,10,4100	no	coding-synonymous	EFCAB5	NM_198529.3		0,83,5915	AA,AG,GG		0.1217,1.9333,0.6919		1096/1504	28407861	83,11913	1888	4110	5998	SO:0001819	synonymous_variant	374786	exon17			TAATAAGCATGAT	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.3288G>A	17.37:g.28407861G>A		125	0	0		138	64	0.463768	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Silent	SNP	ENST00000394835.3	37	CCDS11254.2																																																																																			G|0.990;A|0.010	0.010	strong		0.448	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529		A	28407861	G	A	28407861	2	1	24	1	0	0	0	0	0	0	0	1	4940	962	34	2		2	EFCAB5	17	28407861	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	26792	28407861	52787349	534	8751											
EFCAB5	374786	hgsc.bcm.edu	37	chr17	28417576	28417576	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttttaacatcggccaaaataGgatgttgttgtgtcaagaat	13	14	9	5	1	1	1	1	0	0	1	2	2	1	2	1	2	1	2	1	2	6	5	rs35724168	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:28417576G>C	ENST00000394835.3	+	20	4013	c.3821G>C	c.(3820-3822)aGg>aCg	p.R1274T	RP11-1148O4.2_ENST00000582938.1_RNA|EFCAB5_ENST00000320856.5_Missense_Mutation_p.R1150T|EFCAB5_ENST00000394832.2_Intron	NM_198529.3	NP_940931	A4FU69	EFCB5_HUMAN	EF-hand calcium binding domain 5	1274			R -> T (in dbSNP:rs35724168).				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						GGCCAAAATAGGATGTTGTTG	0.438													G|||	94	0.01877	0.0681	0.0029	5008	,	,		20188	0.0		0.002	False		,,,				2504	0.0				p.R1274T		Atlas-SNP	.											.	EFCAB5	122	.	0			c.G3821C						PASS	.	G	THR/ARG	165,3525		8,149,1688	140	137	138		3821	0	0.1	17	dbSNP_126	138	12,8184		0,12,4086	yes	missense	EFCAB5	NM_198529.3	71	8,161,5774	CC,CG,GG		0.1464,4.4715,1.4891	benign	1274/1504	28417576	177,11709	1845	4098	5943	SO:0001583	missense	374786	exon20			AAAATAGGATGTT	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.3821G>C	17.37:g.28417576G>C	ENSP00000378312:p.Arg1274Thr	114	0	0		86	40	0.465116	NM_198529	B2RPN0|B4DS75|B4DZR5|F5GYL2|Q0VD68|Q6ZRM6|Q8NDG9	Missense_Mutation	SNP	ENST00000394835.3	37	CCDS11254.2	34	0.015567765567765568	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	8.356	0.832049	0.16820	0.044715	0.001464	ENSG00000176927	ENST00000394835;ENST00000320856;ENST00000419434	T;T;T	0.10960	2.82;2.84;2.85	5.35	-0.00624	0.14014	.	0.653292	0.15652	N	0.251330	T	0.00580	0.0019	L	0.40543	1.245	0.09310	N	1	P;P	0.41848	0.763;0.763	B;B	0.36608	0.229;0.21	T	0.26121	-1.0112	10	0.66056	D	0.02	-6.6532	8.972	0.35912	0.523:0.0:0.477:0.0	rs35724168	1150;1274	E7EVS9;A4FU69	.;EFCB5_HUMAN	T	1274;1150;956	ENSP00000378312:R1274T;ENSP00000322003:R1150T;ENSP00000417009:R956T	ENSP00000322003:R1150T	R	+	2	0	EFCAB5	25441702	0.038000	0.19896	0.079000	0.20413	0.150000	0.21749	0.447000	0.21710	0.094000	0.17404	0.655000	0.94253	AGG	G|0.984;C|0.016	0.016	strong		0.438	EFCAB5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256120.4	NM_198529		C	28417576	G	C	28417576	3	2	24	1	0	0	0	0	1	0	0	0	4940	1000	35	4	4066	4	EFCAB5	17	28417576	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	9715	28417576	52777634	535	8752											
ATAD5	79915	hgsc.bcm.edu	37	chr17	29221584	29221584	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatgcattacttttacagcaAtgcttggaagaggatatcag	14	12	9	6	0	1	1	1	0	0	1	1	3	1	3	0	2	5	3	0	2	6	5	rs114345202	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:29221584A>G	ENST00000321990.4	+	22	5678	c.5300A>G	c.(5299-5301)aAt>aGt	p.N1767S	TEFM_ENST00000579183.1_5'Flank	NM_024857.3	NP_079133.3	Q96QE3	ATAD5_HUMAN	ATPase family, AAA domain containing 5	1767					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)				TTTTACAGCAATGCTTGGAAG	0.368													A|||	27	0.00539137	0.0189	0.0029	5008	,	,		18155	0.0		0.0	False		,,,				2504	0.0				p.N1767S		Atlas-SNP	.											.	ATAD5	150	.	0			c.A5300G						PASS	.	A	SER/ASN	64,4342	59.3+/-96.0	0,64,2139	79	77	78		5300	-0.4	0.4	17	dbSNP_132	78	11,8589	8.4+/-32.0	0,11,4289	yes	missense	ATAD5	NM_024857.3	46	0,75,6428	GG,GA,AA		0.1279,1.4526,0.5767	benign	1767/1845	29221584	75,12931	2203	4300	6503	SO:0001583	missense	79915	exon22			ACAGCAATGCTTG		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.5300A>G	17.37:g.29221584A>G	ENSP00000313171:p.Asn1767Ser	44	0	0		42	21	0.5	NM_024857	Q05DH0|Q69YR6|Q9H9I1	Missense_Mutation	SNP	ENST00000321990.4	37	CCDS11260.1	11	0.005036630036630037	9	0.018292682926829267	2	0.0055248618784530384	0	0.0	0	0.0	A	3.076	-0.190144	0.06299	0.014526	0.001279	ENSG00000176208	ENST00000321990	T	0.07800	3.16	5.59	-0.38	0.12490	.	0.706131	0.15070	N	0.282249	T	0.01061	0.0035	N	0.01267	-0.92	0.21256	N	0.999741	B	0.10296	0.003	B	0.08055	0.003	T	0.46062	-0.9218	10	0.21540	T	0.41	.	5.7512	0.18148	0.4172:0.0:0.441:0.1418	.	1767	Q96QE3	ATAD5_HUMAN	S	1767	ENSP00000313171:N1767S	ENSP00000313171:N1767S	N	+	2	0	ATAD5	26245710	0.924000	0.31332	0.415000	0.26534	0.785000	0.44390	0.700000	0.25601	-0.099000	0.12263	-0.334000	0.08254	AAT	A|0.994;G|0.006	0.006	strong		0.368	ATAD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256206.2	NM_024857		G	29221584	A	G	29221584	3	3	24	1	0	0	0	0	1	0	0	0	1076	101	4	3	5386	3	ATAD5	17	29221584	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	804008	29221584	51973626	536	8753											
NF1	4763	hgsc.bcm.edu	37	chr17	29679401	29679401	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgagcctggacatggggcaAccttctcaggccaacactaa	12	7	10	12	0	1	1	1	1	1	0	2	2	1	2	3	4	3	1	3	4	3	2	rs55865524	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:29679401A>G	ENST00000358273.4	+	51	7967	c.7584A>G	c.(7582-7584)caA>caG	p.Q2528Q	NF1_ENST00000417592.2_Intron|NF1_ENST00000356175.3_Silent_p.Q2507Q|NF1_ENST00000444181.2_Silent_p.Q321Q	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	2528					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)		ACATGGGGCAACCTTCTCAGG	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)			G|||	5	0.000998403	0.0023	0.0029	5008	,	,		14500	0.0		0.0	False		,,,				2504	0.0				p.Q2528Q		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.A7584G						PASS	.	G	,	4,4402	825.7+/-416.5	0,4,2199	56	53	54		7521,7584	4.9	1	17	dbSNP_129	54	8,8592	818.9+/-406.8	0,8,4292	no	coding-synonymous,coding-synonymous	NF1	NM_000267.3,NM_001042492.2	,	0,12,6491	GG,GA,AA		0.093,0.0908,0.0923	,	2507/2819,2528/2840	29679401	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	4763	exon51	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	GGGGCAACCTTCT		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.7584A>G	17.37:g.29679401A>G		119	0	0		121	66	0.545455	NM_001042492	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	37	CCDS42292.1																																																																																			A|0.999;G|0.001	0.001	strong		0.413	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267		G	29679401	A	G	29679401	2	3	24	1	0	0	0	0	0	0	0	1	10365	40	2	3		3	NF1	17	29679401	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	457817	29679401	51515809	537	8754											
MYO1D	4642	hgsc.bcm.edu	37	chr17	31048141	31048141	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttctacttggtgccggcagcGttcatcatcaaatatctgtg	8	14	9	10	2	5	0	3	0	2	0	5	0	5	0	1	2	3	2	1	2	3	5	rs375202047		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:31048141G>A	ENST00000318217.5	-	15	2117	c.1813C>T	c.(1813-1815)Cgc>Tgc	p.R605C	MYO1D_ENST00000579584.1_Missense_Mutation_p.R605C|MYO1D_ENST00000394649.4_Missense_Mutation_p.R517C	NM_015194.1	NP_056009.1	O94832	MYO1D_HUMAN	myosin ID	605	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)			TGCCGGCAGCGTTCATCATCA	0.428																																					p.R605C		Atlas-SNP	.											.	MYO1D	93	.	0			c.C1813T						PASS	.	G	CYS/ARG	0,4406		0,0,2203	164	172	169		1813	4.3	1	17		169	1,8599	1.2+/-3.3	0,1,4299	no	missense	MYO1D	NM_015194.1	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	605/1007	31048141	1,13005	2203	4300	6503	SO:0001583	missense	4642	exon15			GGCAGCGTTCATC	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.1813C>T	17.37:g.31048141G>A	ENSP00000324527:p.Arg605Cys	140	0	0		162	84	0.518519	NM_015194	A6H8V3|Q8NHP9	Missense_Mutation	SNP	ENST00000318217.5	37	CCDS32615.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.620942	0.87460	0.0	1.16E-4	ENSG00000176658	ENST00000318217	D	0.87179	-2.22	5.33	4.32	0.51571	Myosin head, motor domain (2);	0.000000	0.33834	U	0.004520	D	0.93294	0.7863	M	0.87900	2.915	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.993	D	0.93324	0.6695	10	0.72032	D	0.01	.	11.2797	0.49186	0.0:0.0:0.7002:0.2998	.	516;605	Q7Z3N6;O94832	.;MYO1D_HUMAN	C	605	ENSP00000324527:R605C	ENSP00000324527:R605C	R	-	1	0	MYO1D	28072254	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	6.347000	0.73004	2.781000	0.95711	0.650000	0.86243	CGC	.	.	weak		0.428	MYO1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447457.1			A	31048141	G	A	31048141	3	1	24	1	0	0	0	0	1	0	0	0	10080	1145	40	1	1239	1	MYO1D	17	31048141	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1368740	31048141	50147069	538	8755											
TMEM99	147184	hgsc.bcm.edu	37	chr17	38991100	38991100	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcgtggttgctcttcaacaActggactggaggctcttggt	6	13	12	10	1	3	0	1	0	2	0	4	2	3	2	0	5	3	3	0	5	2	3	rs199620244		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:38991100A>G	ENST00000301665.3	+	3	636	c.332A>G	c.(331-333)aAc>aGc	p.N111S		NM_001195386.1|NM_001195387.1|NM_145274.3	NP_001182315.1|NP_001182316.1|NP_660317.2	Q8N816	TMM99_HUMAN	transmembrane protein 99	111						integral component of membrane (GO:0016021)				cervix(1)|large_intestine(1)|lung(5)|skin(2)|urinary_tract(1)	10		Breast(137;0.000301)				CTCTTCAACAACTGGACTGGA	0.502																																					p.N111S		Atlas-SNP	.											.	TMEM99	21	.	0			c.A332G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN	0,3846		0,0,1923	141	139	140		332,332,332	-0.5	0	17		140	3,8281		0,3,4139	yes	missense,missense,missense	TMEM99	NM_001195386.1,NM_001195387.1,NM_145274.3	46,46,46	0,3,6062	GG,GA,AA		0.0362,0.0,0.0247	benign,benign,benign	111/259,111/259,111/259	38991100	3,12127	1923	4142	6065	SO:0001583	missense	147184	exon3			TCAACAACTGGAC	AK097454	CCDS42319.1	17q21.2	2008-11-06			ENSG00000167920	ENSG00000167920			28305	protein-coding gene	gene with protein product						12477932	Standard	NM_001195386		Approved	MGC21518	uc021txc.1	Q8N816	OTTHUMG00000133579	ENST00000301665.3:c.332A>G	17.37:g.38991100A>G	ENSP00000301665:p.Asn111Ser	140	0	0		170	76	0.447059	NM_001195386	B4DQ34|Q96BP9	Missense_Mutation	SNP	ENST00000301665.3	37	CCDS42319.1	.	.	.	.	.	.	.	.	.	.	A	2.048	-0.418367	0.04766	0.0	3.62E-4	ENSG00000167920	ENST00000436612;ENST00000301665	T;T	0.27402	1.67;1.67	0.235	-0.47	0.12131	.	.	.	.	.	T	0.13329	0.0323	N	0.08118	0	0.09310	N	1	B	0.19073	0.033	B	0.15870	0.014	T	0.21280	-1.0250	8	0.87932	D	0	.	.	.	.	.	111	Q8N816	TMM99_HUMAN	S	111	ENSP00000390036:N111S;ENSP00000301665:N111S	ENSP00000301665:N111S	N	+	2	0	TMEM99	36244626	0.001000	0.12720	0.002000	0.10522	0.002000	0.02628	-1.620000	0.02046	-0.738000	0.04817	-0.736000	0.03550	AAC	.	.	weak		0.502	TMEM99-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257681.1	NM_145274		G	38991100	A	G	38991100	3	3	24	1	0	0	0	0	1	0	0	0	16241	43	2	3	334	3	TMEM99	17	38991100	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	7942959	38991100	42204110	539	8756											
KRT20	54474	hgsc.bcm.edu	37	chr17	39037000	39037000	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcagcttccactgttagacGtattcctctctcagtctcat	8	15	5	13	1	4	1	3	0	2	1	8	1	6	1	2	0	1	3	2	0	2	4	rs143378689	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39037000G>A	ENST00000167588.3	-	3	537	c.496C>T	c.(496-498)Cgt>Tgt	p.R166C		NM_019010.2	NP_061883.1	P35900	K1C20_HUMAN	keratin 20	166	Coil 1B.|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)				ACTGTTAGACGTATTCCTCTC	0.373													G|||	8	0.00159744	0.0	0.0014	5008	,	,		18332	0.0		0.007	False		,,,				2504	0.0				p.R166C		Atlas-SNP	.											.	KRT20	38	.	0			c.C496T						PASS	.	G	CYS/ARG	6,4400	11.4+/-27.6	0,6,2197	147	136	140		496	0.3	0	17	dbSNP_134	140	34,8566	23.4+/-69.3	0,34,4266	yes	missense	KRT20	NM_019010.2	180	0,40,6463	AA,AG,GG		0.3953,0.1362,0.3076	possibly-damaging	166/425	39037000	40,12966	2203	4300	6503	SO:0001583	missense	54474	exon3			TTAGACGTATTCC	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.496C>T	17.37:g.39037000G>A	ENSP00000167588:p.Arg166Cys	93	0	0		80	38	0.475	NM_019010	B2R6W7	Missense_Mutation	SNP	ENST00000167588.3	37	CCDS11379.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	G	11.51	1.659928	0.29515	0.001362	0.003953	ENSG00000171431	ENST00000167588	D	0.91792	-2.91	5.45	0.338	0.15974	Filament (1);	0.496636	0.16942	N	0.193234	D	0.83529	0.5274	L	0.56199	1.76	0.19300	N	0.999978	B	0.29886	0.26	B	0.24974	0.057	T	0.77332	-0.2627	10	0.62326	D	0.03	.	8.0078	0.30336	0.0704:0.0844:0.6039:0.2414	.	166	P35900	K1C20_HUMAN	C	166	ENSP00000167588:R166C	ENSP00000167588:R166C	R	-	1	0	KRT20	36290526	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.030000	0.13688	0.242000	0.21303	0.591000	0.81541	CGT	G|0.996;A|0.004	0.004	strong		0.373	KRT20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257202.2			A	39037000	G	A	39037000	3	1	24	1	0	0	0	0	1	0	0	0	8467	1145	40	1	802	1	KRT20	17	39037000	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	45900	39037000	42158210	540	8757											
KRTAP1-1	81851	hgsc.bcm.edu	37	chr17	39197173	39197173	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcggcaacaggactgtccAcagtaggatgggcggcagca	10	4	17	10	2	0	0	0	0	0	0	1	2	1	2	1	6	2	4	1	6	2	1	rs144980478	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39197173A>G	ENST00000306271.4	-	1	540	c.477T>C	c.(475-477)tgT>tgC	p.C159C		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	159						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)			AGGACTGTCCACAGTAGGATG	0.617													a|||	10	0.00199681	0.0	0.0029	5008	,	,		17718	0.0		0.008	False		,,,				2504	0.0				p.C159C		Atlas-SNP	.											.	KRTAP1-1	23	.	0			c.T477C						PASS	.	A		5,4099		0,5,2047	31	35	34		477	4.1	1	17	dbSNP_134	34	34,8330		0,34,4148	no	coding-synonymous	KRTAP1-1	NM_030967.2		0,39,6195	GG,GA,AA		0.4065,0.1218,0.3128		159/178	39197173	39,12429	2052	4182	6234	SO:0001819	synonymous_variant	81851	exon1			CTGTCCACAGTAG	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.477T>C	17.37:g.39197173A>G		177	0	0		180	96	0.533333	NM_030967	A6NC32|Q96S60|Q96S67	Silent	SNP	ENST00000306271.4	37	CCDS42324.1																																																																																			A|0.996;G|0.004	0.004	strong		0.617	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967		G	39197173	A	G	39197173	2	3	24	1	0	0	0	0	0	0	0	1	8511	157	6	3		3	KRTAP1-1	17	39197173	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	160173	39197173	41998037	541	8758											
KRTAP4-4	84616	hgsc.bcm.edu	37	chr17	39316851	39316865	+	In_Frame_Del	DEL	GCAGCAGGTGGTCTG	GCAGCAGGTGGTCTG	-																															gggcggcagcaggtggtcctGcagcaggtggtctggcagta																								rs199889274|rs201042607	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	GCAGCAGGTGGTCTG	GCAGCAGGTGGTCTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39316851_39316865delGCAGCAGGTGGTCTG	ENST00000390661.3	-	1	118_132	c.79_93delCAGACCACCTGCTGC	c.(79-93)cagaccacctgctgcdel	p.QTTCC27del		NM_032524.1	NP_115913.1	Q9BYR3	KRA44_HUMAN	keratin associated protein 4-4	27	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)			AGGTGGTCCTGCAGCAGGTGGTCTGGCAGTAGCTG	0.637																																					p.27_32del		Pindel,Atlas-Indel	.											.	KRTAP4-4	21	.	0			c.80_94del						PASS	.			19,4221		3,13,2104						-0.9	0.6			51	51,8203		5,41,4081	no	coding	KRTAP4-4	NM_032524.1		8,54,6185	A1A1,A1R,RR		0.6179,0.4481,0.5603				70,12424				SO:0001651	inframe_deletion	84616	exon1			.	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.79_93delCAGACCACCTGCTGC	17.37:g.39316851_39316865delGCAGCAGGTGGTCTG	ENSP00000375076:p.Gln27_Cys31del	120	0	.		130	24	0.185	NM_032524	Q9BYU7	In_Frame_Del	DEL	ENST00000390661.3	37	CCDS11383.1																																																																																			.	.	none		0.637	KRTAP4-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257291.1			-	39316865	GCAGCAGGTGGTCTG	-	39316851	7	5	24	1	0	1	0	1	0	0	0	0	8562	1311	46	0	411	0	KRTAP4-4	17	39316851	In_Frame_Del	DEL	GCAGCAGGTGGTCTG	TCGA-G8-6326-01A-11D-2210-10	119678	39316851	41878359	542	8759											
KRTAP4-3	85290	hgsc.bcm.edu	37	chr17	39324346	39324347	+	In_Frame_Ins	INS	-	-	TTT																															gtggtctggcagcagctgggINSgcggcagcagctctcctggc																										TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39324346_39324347insTTT	ENST00000391356.2	-	1	77_78	c.78_79insAAA	c.(76-81)cgcccc>cgcAAAccc	p.26_27RP>RKP		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	26					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)			CAGCAGCTGGGGCGGCAGCAGC	0.639																																					p.P27delinsKP		Atlas-Indel	.											KRTAP4-3,NS,carcinoma,+2,1	KRTAP4-3	40	1	0			c.79_80insAAA						PASS	.																																			SO:0001652	inframe_insertion	85290	exon1			.	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.78_79insAAA	17.37:g.39324346_39324347insTTT	ENSP00000375151:p.Arg26_Pro27insLys	203	0	0		196	18	0.0918367	NM_033187		In_Frame_Ins	INS	ENST00000391356.2	37	CCDS42331.1																																																																																			.	.	none		0.639	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1			TTT	39324347	-	TTT	39324346	7	5	24	1	0	1	1	0	0	0	0	0	8561	1232	43	0	512	0	KRTAP4-3	17	39324346	In_Frame_Ins	INS	-	TCGA-G8-6326-01A-11D-2210-10	7495	39324346	41870864	543	8760											
FKBP10	60681	hgsc.bcm.edu	37	chr17	39976713	39976713	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cggcacccagctgttcacctCgtgggtccgggggggggccg	3	6	18	14	4	1	0	1	0	0	0	3	0	2	0	4	6	1	3	4	6	0	1	rs146422412	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:39976713C>T	ENST00000321562.4	+	7	1360	c.1256C>T	c.(1255-1257)tCg>tTg	p.S419L	FKBP10_ENST00000544340.1_Splice_Site_p.S192L	NM_021939.3	NP_068758.3	Q96AY3	FKB10_HUMAN	FK506 binding protein 10, 65 kDa	419	PPIase FKBP-type 4. {ECO:0000255|PROSITE- ProRule:PRU00277}.				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)		CTGTTCACCTCGTGGGTCCGG	0.632													C|||	3	0.000599042	0.0008	0.0	5008	,	,		12871	0.0		0.001	False		,,,				2504	0.001				p.S419L		Atlas-SNP	.											.	FKBP10	57	.	0			c.C1256T						PASS	.	C	LEU/SER	2,4404	4.2+/-10.8	0,2,2201	79	85	83		1256	4.9	1	17	dbSNP_134	83	9,8591	7.1+/-27.0	0,9,4291	yes	missense-near-splice	FKBP10	NM_021939.3	145	0,11,6492	TT,TC,CC		0.1047,0.0454,0.0846	probably-damaging	419/583	39976713	11,12995	2203	4300	6503	SO:0001630	splice_region_variant	60681	exon7			TCACCTCGTGGGT	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.1256+1C>T	17.37:g.39976713C>T		72	0	0		91	43	0.472527	NM_021939	Q7Z3R4|Q9H3N3|Q9H6J3|Q9H6N5|Q9UF89	Missense_Mutation	SNP	ENST00000321562.4	37	CCDS11409.1	2|2	9.157509157509158E-4|9.157509157509158E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	C|C	27.5|27.5	4.836108|4.836108	0.91117|0.91117	4.54E-4|4.54E-4	0.001047|0.001047	ENSG00000141756|ENSG00000141756	ENST00000455106|ENST00000269598;ENST00000321562;ENST00000414352;ENST00000544340	.|T;T	.|0.61980	.|0.06;0.06	4.89|4.89	4.89|4.89	0.63831|0.63831	.|Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain (2);	.|0.000000	.|0.64402	.|D	.|0.000001	D|D	0.86016|0.86016	0.5832|0.5832	H|H	0.96333|0.96333	3.805|3.805	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|0.99;1.0	.|P;D	.|0.91635	.|0.874;0.999	D|D	0.90651|0.90651	0.4582|0.4582	5|10	.|0.72032	.|D	.|0.01	-20.3857|-20.3857	18.0311|18.0311	0.89285|0.89285	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|192;419	.|Q9H6J3;Q96AY3	.|.;FKB10_HUMAN	C|L	223|307;419;419;192	.|ENSP00000317232:S419L;ENSP00000442009:S192L	.|ENSP00000269598:S307L	R|S	+|+	1|2	0|0	FKBP10|FKBP10	37230239|37230239	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.966000|0.966000	0.64601|0.64601	5.928000|5.928000	0.70088|0.70088	2.439000|2.439000	0.82584|0.82584	0.655000|0.655000	0.94253|0.94253	CGC|TCG	C|0.999;T|0.001	0.001	strong		0.632	FKBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257410.2	NM_021939	Missense_Mutation	T	39976713	C	T	39976713	5	4	24	1	0	0	0	0	0	0	1	0	5910	898	31	1	1282	1	FKBP10	17	39976713	Splice_Site	SNP	C	TCGA-G8-6326-01A-11D-2210-10	652367	39976713	41218497	544	8761											
TMEM101	84336	hgsc.bcm.edu	37	chr17	42092267	42092267	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtgtgagcagcaccgaaccCaactgcatgatcagctgcaa	12	6	10	13	2	1	2	1	2	0	0	1	3	1	2	2	0	7	5	2	0	3	0	rs35301047	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:42092267C>T	ENST00000589334.1	-	2	369	c.54G>A	c.(52-54)ttG>ttA	p.L18L	TMEM101_ENST00000587529.1_Silent_p.L18L|TMEM101_ENST00000206380.3_Silent_p.L18L|TMEM101_ENST00000542039.1_Intron			Q96IK0	TM101_HUMAN	transmembrane protein 101	18					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)		GCACCGAACCCAACTGCATGA	0.612													C|||	43	0.00858626	0.025	0.0058	5008	,	,		18733	0.0		0.005	False		,,,				2504	0.001				p.L18L		Atlas-SNP	.											.	TMEM101	18	.	0			c.G54A						PASS	.	C		126,4280	93.9+/-132.6	1,124,2078	102	90	94		54	4.7	1	17	dbSNP_126	94	65,8535	40.3+/-97.0	1,63,4236	no	coding-synonymous	TMEM101	NM_032376.2		2,187,6314	TT,TC,CC		0.7558,2.8597,1.4686		18/258	42092267	191,12815	2203	4300	6503	SO:0001819	synonymous_variant	84336	exon1			CGAACCCAACTGC	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.54G>A	17.37:g.42092267C>T		223	0	0		243	102	0.419753	NM_032376	B2R9N6	Silent	SNP	ENST00000589334.1	37	CCDS11474.1																																																																																			C|0.988;T|0.012	0.012	strong		0.612	TMEM101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457665.1	NM_032376		T	42092267	C	T	42092267	2	4	24	1	0	0	0	0	0	0	0	1	16031	593	21	2		2	TMEM101	17	42092267	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	2115554	42092267	39102943	545	8762											
PLEKHM1	9842	hgsc.bcm.edu	37	chr17	43552812	43552812	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcaaagcccagacagggccaAtggggtgagcgtccactcat	11	5	13	12	1	1	2	1	1	0	1	2	2	2	2	3	3	2	1	3	3	2	0	rs71227520	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:43552812A>G	ENST00000430334.3	-	4	710	c.577T>C	c.(577-579)Ttg>Ctg	p.L193L	PLEKHM1_ENST00000421073.2_Silent_p.L104L	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	193					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)					GACAGGGCCAATGGGGTGAGC	0.552													G|||	378	0.0754792	0.034	0.1412	5008	,	,		21329	0.001		0.1819	False		,,,				2504	0.0521				p.L193L		Atlas-SNP	.											.	PLEKHM1	69	.	0			c.T577C						PASS	.						66	58	60					17																	43552812		2199	4249	6448	SO:0001819	synonymous_variant	9842	exon4			GGGCCAATGGGGT	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.577T>C	17.37:g.43552812A>G		194	0	0		106	105	0.990566	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Silent	SNP	ENST00000430334.3	37	CCDS32671.1																																																																																			A|0.925;G|0.075	0.075	strong		0.552	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798		G	43552812	A	G	43552812	2	3	24	1	0	0	0	0	0	0	0	1	12089	98	4	3		3	PLEKHM1	17	43552812	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	1460545	43552812	37642398	546	8763											
KIAA1267	284058	hgsc.bcm.edu	37	chr17	44248783	44248783	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgataatctactgcttccttGaagtgccggctgttccatgg	7	14	10	10	1	1	2	0	2	1	0	3	2	3	2	3	2	3	3	3	2	3	5	rs142096969	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:44248783G>T	ENST00000262419.6	-	2	1197	c.727C>A	c.(727-729)Caa>Aaa	p.Q243K	KANSL1_ENST00000572904.1_Missense_Mutation_p.Q243K|KANSL1_ENST00000576248.1_5'Flank|KANSL1_ENST00000574590.1_Missense_Mutation_p.Q243K|KANSL1_ENST00000393476.3_5'UTR|KANSL1_ENST00000432791.1_Missense_Mutation_p.Q243K|KANSL1_ENST00000575318.1_Missense_Mutation_p.Q243K	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	243					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.Q243E(2)									CTGCTTCCTTGAAGTGCCGGC	0.438													G|||	4	0.000798722	0.0	0.0043	5008	,	,		25143	0.0		0.001	False		,,,				2504	0.0				p.Q243K		Atlas-SNP	.											KIAA1267,NS,carcinoma,0,1	.	.	1	2	Substitution - Missense(2)	prostate(2)	c.C727A						PASS	.	G	LYS/GLN,LYS/GLN,LYS/GLN	1,4405	2.1+/-5.4	0,1,2202	97	122	114		727,727,727	6	1	17	dbSNP_134	114	21,8579	14.0+/-48.4	0,21,4279	yes	missense,missense,missense	KIAA1267	NM_001193465.1,NM_001193466.1,NM_015443.3	53,53,53	0,22,6481	TT,TG,GG		0.2442,0.0227,0.1692	benign,benign,benign	243/1105,243/1106,243/1106	44248783	22,12984	2203	4300	6503	SO:0001583	missense	284058	exon2			TTCCTTGAAGTGC	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.727C>A	17.37:g.44248783G>T	ENSP00000262419:p.Gln243Lys	331	0	0		354	110	0.310734	NM_001193466	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	37	CCDS11503.1	.	.	.	.	.	.	.	.	.	.	G	11.16	1.556207	0.27827	2.27E-4	0.002442	ENSG00000120071	ENST00000262419;ENST00000432791	T;T	0.12039	2.72;2.72	6.04	6.04	0.98038	.	0.144262	0.47852	D	0.000202	T	0.08980	0.0222	N	0.14661	0.345	0.80722	D	1	B;B	0.24426	0.103;0.07	B;B	0.25140	0.058;0.033	T	0.36016	-0.9765	10	0.17369	T	0.5	-9.4613	13.6782	0.62467	0.0:0.1543:0.8457:0.0	.	243;243	C9JHY2;Q7Z3B3	.;K1267_HUMAN	K	243	ENSP00000262419:Q243K;ENSP00000387393:Q243K	ENSP00000262419:Q243K	Q	-	1	0	KIAA1267	41604560	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.286000	0.43496	2.873000	0.98535	0.561000	0.74099	CAA	G|0.998;T|0.002	0.002	strong		0.438	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1	NM_015443		T	44248783	G	T	44248783	3	4	24	1	0	0	0	0	1	0	0	0	8228	1299	45	4	2646	4	KIAA1267	17	44248783	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	695971	44248783	36946427	547	8764											
OSBPL7	114881	hgsc.bcm.edu	37	chr17	45886796	45886796	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcgctgaccactcaggacAttgtgaatgcaggatgtcac	11	8	11	11	1	2	2	2	2	0	0	2	4	2	4	1	2	2	2	1	2	1	1			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:45886796A>C	ENST00000007414.3	-	19	2120	c.1929T>G	c.(1927-1929)aaT>aaG	p.N643K	OSBPL7_ENST00000392507.3_Missense_Mutation_p.N643K	NM_145798.2	NP_665741.1	Q9BZF2	OSBL7_HUMAN	oxysterol binding protein-like 7	643					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						CACTCAGGACATTGTGAATGC	0.547																																					p.N643K		Atlas-SNP	.											.	OSBPL7	65	.	0			c.T1929G						PASS	.						134	98	110					17																	45886796		2203	4300	6503	SO:0001583	missense	114881	exon19			CAGGACATTGTGA	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.1929T>G	17.37:g.45886796A>C	ENSP00000007414:p.Asn643Lys	76	0	0		86	39	0.453488	NM_145798	D3DTT6|Q6PIV6	Missense_Mutation	SNP	ENST00000007414.3	37	CCDS11515.1	.	.	.	.	.	.	.	.	.	.	A	17.75	3.467556	0.63625	.	.	ENSG00000006025	ENST00000007414;ENST00000392507	T;T	0.44881	0.91;0.91	4.91	3.89	0.44902	.	0.043933	0.85682	D	0.000000	T	0.73450	0.3588	H	0.96460	3.825	0.54753	D	0.999983	D	0.89917	1.0	D	0.87578	0.998	T	0.80894	-0.1178	10	0.87932	D	0	-37.8662	12.0721	0.53622	0.087:0.0:0.913:0.0	.	643	Q9BZF2	OSBL7_HUMAN	K	643	ENSP00000007414:N643K;ENSP00000376295:N643K	ENSP00000007414:N643K	N	-	3	2	OSBPL7	43241795	1.000000	0.71417	1.000000	0.80357	0.825000	0.46686	2.907000	0.48743	1.045000	0.40225	-0.337000	0.08149	AAT	.	.	none		0.547	OSBPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441367.1	NM_017731		C	45886796	A	C	45886796	3	2	24	1	0	0	0	0	1	0	0	0	11291	214	8	5	619	5	OSBPL7	17	45886796	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	1638013	45886796	35308414	548	8765											
ABCC3	8714	hgsc.bcm.edu	37	chr17	48745035	48745035	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagcaggtggagggcatcAggcagggtgagctccagctg	9	6	18	8	0	1	2	1	2	0	0	2	3	2	3	1	5	3	5	1	5	1	0	rs11568601	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:48745035A>C	ENST00000285238.8	+	12	1632	c.1552A>C	c.(1552-1554)Agg>Cgg	p.R518R	ABCC3_ENST00000427699.1_Silent_p.R518R	NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	518	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				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)	GGAGGGCATCAGGCAGGGTGA	0.622													A|||	26	0.00519169	0.0015	0.0058	5008	,	,		22136	0.0		0.0189	False		,,,				2504	0.001				p.R518R		Atlas-SNP	.											.	ABCC3	138	.	0			c.A1552C						PASS	.	A	,	21,4385	28.1+/-56.4	0,21,2182	72	58	63		1552,1552	1.7	1	17	dbSNP_126	63	219,8381	91.1+/-153.3	3,213,4084	no	coding-synonymous,coding-synonymous	ABCC3	NM_001144070.1,NM_003786.3	,	3,234,6266	CC,CA,AA		2.5465,0.4766,1.8453	,	518/573,518/1528	48745035	240,12766	2203	4300	6503	SO:0001819	synonymous_variant	8714	exon12			GGCATCAGGCAGG	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.1552A>C	17.37:g.48745035A>C		71	0	0		54	24	0.444444	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Silent	SNP	ENST00000285238.8	37	CCDS32681.1																																																																																			A|0.984;C|0.016	0.016	strong		0.622	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038		C	48745035	A	C	48745035	2	2	24	1	0	0	0	0	0	0	0	1	54	179	7	5		5	ABCC3	17	48745035	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	2858239	48745035	32450175	549	8766											
ABCC3	8714	hgsc.bcm.edu	37	chr17	48761385	48761385	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccgcatcctggaggcggcaAagggtgaaatccgcattgat	10	8	13	10	3	0	2	0	2	0	0	3	3	3	3	3	4	0	3	3	4	2	1	rs150601692	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:48761385A>G	ENST00000285238.8	+	28	4110	c.4030A>G	c.(4030-4032)Aag>Gag	p.K1344E		NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	1344	ABC transporter 2. {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)	GGAGGCGGCAAAGGGTGAAAT	0.622													A|||	5	0.000998403	0.0	0.0	5008	,	,		20086	0.0		0.0	False		,,,				2504	0.0051				p.K1344E		Atlas-SNP	.											.	ABCC3	138	.	0			c.A4030G						PASS	.	A	GLU/LYS	1,4405	2.1+/-5.4	0,1,2202	54	48	50		4030	2.1	0.1	17	dbSNP_134	50	6,8594	5.0+/-18.6	0,6,4294	yes	missense	ABCC3	NM_003786.3	56	0,7,6496	GG,GA,AA		0.0698,0.0227,0.0538	benign	1344/1528	48761385	7,12999	2203	4300	6503	SO:0001583	missense	8714	exon28			GCGGCAAAGGGTG	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.4030A>G	17.37:g.48761385A>G	ENSP00000285238:p.Lys1344Glu	56	0	0		85	60	0.705882	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Missense_Mutation	SNP	ENST00000285238.8	37	CCDS32681.1	.	.	.	.	.	.	.	.	.	.	A	2.739	-0.262675	0.05754	2.27E-4	6.98E-4	ENSG00000108846	ENST00000285238	D	0.92752	-3.1	5.24	2.06	0.26882	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.385040	0.29473	N	0.012046	T	0.76744	0.4030	N	0.05259	-0.085	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.62258	-0.6892	10	0.02654	T	1	-18.184	7.7134	0.28690	0.2169:0.1322:0.6509:0.0	.	1344	O15438	MRP3_HUMAN	E	1344	ENSP00000285238:K1344E	ENSP00000285238:K1344E	K	+	1	0	ABCC3	46116384	0.002000	0.14202	0.127000	0.21898	0.980000	0.70556	1.360000	0.34125	0.656000	0.30886	-0.242000	0.12053	AAG	A|0.999;G|0.001	0.001	strong		0.622	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038		G	48761385	A	G	48761385	3	3	24	1	0	0	0	0	1	0	0	0	54	15	1	3	4224	3	ABCC3	17	48761385	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	16350	48761385	32433825	550	8767											
WFIKKN2	124857	hgsc.bcm.edu	37	chr17	48917384	48917384	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctgagatcacctgggagaaGcagttggaggatcgggagaa	12	6	16	7	1	1	3	1	1	0	3	2	8	1	5	2	4	1	2	2	4	2	1			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:48917384G>A	ENST00000311378.4	+	2	1263	c.735G>A	c.(733-735)aaG>aaA	p.K245K	RP11-506D12.5_ENST00000572491.2_RNA|WFIKKN2_ENST00000426127.1_Silent_p.K152K	NM_175575.5	NP_783165.1	Q8TEU8	WFKN2_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	245	Ig-like C2-type.				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)			CCTGGGAGAAGCAGTTGGAGG	0.597																																					p.K245K		Atlas-SNP	.											.	WFIKKN2	69	.	0			c.G735A						PASS	.						107	103	104					17																	48917384		2203	4300	6503	SO:0001819	synonymous_variant	124857	exon2			GGAGAAGCAGTTG	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.735G>A	17.37:g.48917384G>A		105	0	0		113	46	0.40708	NM_175575	Q6UXZ9	Silent	SNP	ENST00000311378.4	37	CCDS11575.1																																																																																			.	.	none		0.597	WFIKKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368358.1	NM_175575		A	48917384	G	A	48917384	2	1	24	1	0	0	0	0	0	0	0	1	17374	962	34	2		2	WFIKKN2	17	48917384	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	155999	48917384	32277826	551	8768											
PCTP	58488	hgsc.bcm.edu	37	chr17	53844742	53844742	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctttggtgttctggaggactGctcaccaactctactggcag	7	12	11	11	0	3	0	1	0	2	0	3	2	3	2	1	4	3	3	1	4	2	3	rs112454522	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:53844742G>A	ENST00000268896.5	+	2	313	c.188G>A	c.(187-189)tGc>tAc	p.C63Y	PCTP_ENST00000576183.1_Missense_Mutation_p.C63Y|PCTP_ENST00000325214.6_5'UTR|PCTP_ENST00000573500.1_Missense_Mutation_p.C63Y	NM_021213.3	NP_067036.2	Q9UKL6	PPCT_HUMAN	phosphatidylcholine transfer protein	63	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|phospholipid transport (GO:0015914)	cytosol (GO:0005829)	phosphatidylcholine binding (GO:0031210)|phosphatidylcholine transporter activity (GO:0008525)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)	10			BRCA - Breast invasive adenocarcinoma(1;0.00207)			CTGGAGGACTGCTCACCAACT	0.383													G|||	11	0.00219649	0.0	0.0029	5008	,	,		18999	0.0		0.0089	False		,,,				2504	0.0				p.C63Y		Atlas-SNP	.											.	PCTP	17	.	0			c.G188A						PASS	.	G	,TYR/CYS	7,4399	12.9+/-30.5	0,7,2196	138	125	129		,188	5.6	0.1	17	dbSNP_132	129	84,8516	48.5+/-108.0	1,82,4217	yes	utr-5,missense	PCTP	NM_001102402.2,NM_021213.3	,194	1,89,6413	AA,AG,GG		0.9767,0.1589,0.6997	,probably-damaging	,63/215	53844742	91,12915	2203	4300	6503	SO:0001583	missense	58488	exon2			AGGACTGCTCACC	AK024667	CCDS11588.1, CCDS45741.1	17q21-q24	2011-09-13				ENSG00000141179		"StAR-related lipid transfer (START) domain containing"	8752	protein-coding gene	gene with protein product	"StAR-related lipid transfer (START) domain containing 2"	606055					Standard	NM_021213		Approved	STARD2	uc002iul.4	Q9UKL6		ENST00000268896.5:c.188G>A	17.37:g.53844742G>A	ENSP00000268896:p.Cys63Tyr	112	0	0		97	51	0.525773	NM_021213	Q9BSC9|Q9UIT3|Q9UKW7	Missense_Mutation	SNP	ENST00000268896.5	37	CCDS11588.1	9	0.004120879120879121	0	0.0	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	G	25.3	4.628072	0.87560	0.001589	0.009767	ENSG00000141179	ENST00000268896;ENST00000325214	T	0.42131	0.98	5.64	5.64	0.86602	Lipid-binding START (3);START-like domain (1);	0.111691	0.64402	D	0.000007	T	0.56202	0.1969	M	0.77820	2.39	0.80722	D	1	D;D	0.67145	0.996;0.996	D;D	0.66497	0.944;0.944	T	0.63712	-0.6575	10	0.56958	D	0.05	-12.5478	15.2077	0.73192	0.0:0.0:1.0:0.0	.	63;63	Q549N3;Q9UKL6	.;PPCT_HUMAN	Y	63;42	ENSP00000268896:C63Y	ENSP00000268896:C63Y	C	+	2	0	PCTP	51199741	1.000000	0.71417	0.093000	0.20910	0.500000	0.33767	6.637000	0.74304	2.642000	0.89623	0.650000	0.86243	TGC	G|0.993;A|0.007	0.007	strong		0.383	PCTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439271.2	NM_021213		A	53844742	G	A	53844742	3	1	24	1	0	0	0	0	1	0	0	0	11616	1319	46	2	194	2	PCTP	17	53844742	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	4927358	53844742	27350468	552	8769											
BZRAP1	9256	hgsc.bcm.edu	37	chr17	56386732	56386732	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtcagtctcacaaaaggggtCgggctgggactggtggaggt	8	8	18	7	1	2	0	2	0	1	0	4	2	2	2	0	7	0	1	0	7	2	0	rs61741210	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:56386732C>T	ENST00000343736.4	-	22	4064	c.3901G>A	c.(3901-3903)Gac>Aac	p.D1301N	BZRAP1_ENST00000355701.3_Missense_Mutation_p.D1301N|BZRAP1_ENST00000268893.6_Missense_Mutation_p.D1241N			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1301						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)					CAAAAGGGGTCGGGCTGGGAC	0.577													C|||	78	0.0155751	0.0008	0.013	5008	,	,		18724	0.0		0.0328	False		,,,				2504	0.0358				p.D1301N		Atlas-SNP	.											.	BZRAP1	287	.	0			c.G3901A						PASS	.	C	ASN/ASP,ASN/ASP	25,4379	30.8+/-60.4	0,25,2177	39	39	39		3901,3721	5.6	0.9	17	dbSNP_129	39	223,8377	86.9+/-149.2	3,217,4080	yes	missense,missense	BZRAP1	NM_004758.2,NM_024418.1	23,23	3,242,6257	TT,TC,CC		2.593,0.5677,1.9071	benign,benign	1301/1858,1241/1798	56386732	248,12756	2202	4300	6502	SO:0001583	missense	9256	exon22			AGGGGTCGGGCTG	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.3901G>A	17.37:g.56386732C>T	ENSP00000345824:p.Asp1301Asn	36	0	0		40	17	0.425	NM_004758	O75111|Q8N5W3	Missense_Mutation	SNP	ENST00000343736.4	37	CCDS11605.1	32	0.014652014652014652	0	0.0	4	0.011049723756906077	0	0.0	28	0.036939313984168866	C	14.65	2.599495	0.46318	0.005677	0.02593	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	D;D;D	0.87491	-2.26;-2.26;-2.26	5.59	5.59	0.84812	.	0.222124	0.39146	N	0.001447	T	0.60495	0.2273	L	0.59436	1.845	0.26084	N	0.981058	P;B;B	0.51240	0.943;0.014;0.004	B;B;B	0.40825	0.341;0.012;0.001	T	0.70193	-0.4939	10	0.15952	T	0.53	.	16.3282	0.82996	0.0:1.0:0.0:0.0	rs61741210	1301;1241;1301	B7ZVZ7;O95153-2;O95153	.;.;RIMB1_HUMAN	N	1301;1301;1241	ENSP00000347929:D1301N;ENSP00000345824:D1301N;ENSP00000268893:D1241N	ENSP00000268893:D1241N	D	-	1	0	BZRAP1	53741731	0.081000	0.21417	0.906000	0.35671	0.818000	0.46254	2.225000	0.42954	2.643000	0.89663	0.655000	0.94253	GAC	C|0.982;T|0.018	0.018	strong		0.577	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758		T	56386732	C	T	56386732	3	4	24	1	0	0	0	0	1	0	0	0	1579	884	31	1	1712	1	BZRAP1	17	56386732	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	2541990	56386732	24808478	553	8770											
BZRAP1	9256	hgsc.bcm.edu	37	chr17	56405046	56405046	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tgggcagacaagcctctgctCcttcagggtcagttcccccc	6	9	10	16	0	3	1	2	0	1	1	5	1	5	1	5	2	2	3	5	2	1	2	rs61743284	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:56405046C>T	ENST00000343736.4	-	1	399	c.236G>A	c.(235-237)gGa>gAa	p.G79E	BZRAP1_ENST00000355701.3_Missense_Mutation_p.G79E|BZRAP1-AS1_ENST00000578334.1_RNA|BZRAP1-AS1_ENST00000580633.1_RNA|BZRAP1-AS1_ENST00000580515.1_RNA|BZRAP1_ENST00000268893.6_Missense_Mutation_p.G79E|BZRAP1-AS1_ENST00000579527.1_RNA			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	79						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)					AGCCTCTGCTCCTTCAGGGTC	0.622													C|||	79	0.0157748	0.0015	0.013	5008	,	,		17888	0.0		0.0338	False		,,,				2504	0.0348				p.G79E		Atlas-SNP	.											.	BZRAP1	287	.	0			c.G236A						PASS	.	C	GLU/GLY,GLU/GLY	33,4373	38.4+/-70.7	0,33,2170	59	53	55		236,236	0.9	0	17	dbSNP_129	55	224,8376	92.6+/-154.6	3,218,4079	yes	missense,missense	BZRAP1	NM_004758.2,NM_024418.1	98,98	3,251,6249	TT,TC,CC		2.6047,0.749,1.976	possibly-damaging,possibly-damaging	79/1858,79/1798	56405046	257,12749	2203	4300	6503	SO:0001583	missense	9256	exon1			TCTGCTCCTTCAG	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.236G>A	17.37:g.56405046C>T	ENSP00000345824:p.Gly79Glu	88	0	0		76	37	0.486842	NM_024418	O75111|Q8N5W3	Missense_Mutation	SNP	ENST00000343736.4	37	CCDS11605.1	33	0.01510989010989011	0	0.0	4	0.011049723756906077	0	0.0	29	0.03825857519788918	C	9.261	1.043284	0.19748	0.00749	0.026047	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	T;T;T	0.04917	3.64;3.65;3.53	5.19	0.886	0.19194	.	0.524608	0.17491	N	0.172355	T	0.01092	0.0036	L	0.44542	1.39	0.09310	N	1	B;P;B	0.39480	0.005;0.675;0.001	B;B;B	0.40940	0.006;0.344;0.003	T	0.29761	-1.0001	10	0.07482	T	0.82	.	6.3771	0.21513	0.0:0.6127:0.136:0.2513	.	79;79;79	B7ZVZ7;O95153-2;O95153	.;.;RIMB1_HUMAN	E	79	ENSP00000347929:G79E;ENSP00000345824:G79E;ENSP00000268893:G79E	ENSP00000268893:G79E	G	-	2	0	BZRAP1	53760045	0.807000	0.29009	0.014000	0.15608	0.004000	0.04260	0.719000	0.25881	-0.036000	0.13669	-1.598000	0.00824	GGA	C|0.982;T|0.018	0.018	strong		0.622	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758		T	56405046	C	T	56405046	3	4	24	1	0	0	0	0	1	0	0	0	1579	855	30	2	5461	2	BZRAP1	17	56405046	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	18314	56405046	24790164	554	8771											
SCN4A	6329	hgsc.bcm.edu	37	chr17	62018931	62018931	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gaagcagatgccgatggaggGgttgccgcagtcacccttga	9	7	15	10	2	1	2	1	1	0	1	1	5	1	3	3	3	3	3	3	3	1	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:62018931G>A	ENST00000435607.1	-	24	4787	c.4711C>T	c.(4711-4713)Ccc>Tcc	p.P1571S	SCN4A_ENST00000578147.1_Missense_Mutation_p.P1571S	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1571					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)	CCGATGGAGGGGTTGCCGCAG	0.577																																					p.P1571S		Atlas-SNP	.											.	SCN4A	205	.	0			c.C4711T						PASS	.						46	52	50					17																	62018931		2149	4263	6412	SO:0001583	missense	6329	exon24			TGGAGGGGTTGCC	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.4711C>T	17.37:g.62018931G>A	ENSP00000396320:p.Pro1571Ser	142	0	0		139	62	0.446043	NM_000334	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	37	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	g	17.38	3.376136	0.61735	.	.	ENSG00000007314	ENST00000435607	D	0.98178	-4.77	3.9	3.9	0.45041	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98210	0.9408	L	0.46670	1.46	0.58432	D	0.999998	D	0.89917	1.0	D	0.81914	0.995	D	0.98880	1.0769	10	0.62326	D	0.03	.	15.4266	0.75055	0.0:0.0:1.0:0.0	.	1571	P35499	SCN4A_HUMAN	S	1571	ENSP00000396320:P1571S	ENSP00000396320:P1571S	P	-	1	0	SCN4A	59372663	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	9.601000	0.98297	2.177000	0.69029	0.556000	0.70494	CCC	.	.	none		0.577	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		A	62018931	G	A	62018931	3	1	24	1	0	0	0	0	1	0	0	0	13935	1232	43	2	803	2	SCN4A	17	62018931	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	5613885	62018931	19176279	555	8772											
SCN4A	6329	hgsc.bcm.edu	37	chr17	62036738	62036738	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccaaccctgctggaaatactCgtaggggtccatggcaatca	11	8	10	12	1	1	0	1	0	0	0	3	1	2	1	3	4	3	3	3	4	5	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:62036738C>T	ENST00000435607.1	-	12	1982	c.1906G>A	c.(1906-1908)Gag>Aag	p.E636K	SCN4A_ENST00000578147.1_Missense_Mutation_p.E636K	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	636					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)	TGGAAATACTCGTAGGGGTCC	0.562																																					p.E636K		Atlas-SNP	.											.	SCN4A	205	.	0			c.G1906A						PASS	.						83	85	85					17																	62036738		2063	4230	6293	SO:0001583	missense	6329	exon12			AATACTCGTAGGG	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.1906G>A	17.37:g.62036738C>T	ENSP00000396320:p.Glu636Lys	151	0	0		141	69	0.489362	NM_000334	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	37	CCDS45761.1	.	.	.	.	.	.	.	.	.	.	C	19.35	3.810092	0.70797	.	.	ENSG00000007314	ENST00000435607	D	0.98362	-4.89	4.74	4.74	0.60224	Ion transport (1);	0.119294	0.56097	D	0.000022	D	0.94258	0.8156	N	0.20530	0.585	0.39768	D	0.972125	B	0.30281	0.275	B	0.24541	0.054	D	0.93435	0.6789	10	0.44086	T	0.13	.	12.1023	0.53792	0.1716:0.8284:0.0:0.0	.	636	P35499	SCN4A_HUMAN	K	636	ENSP00000396320:E636K	ENSP00000396320:E636K	E	-	1	0	SCN4A	59390470	0.996000	0.38824	1.000000	0.80357	0.927000	0.56198	3.358000	0.52284	2.481000	0.83766	0.556000	0.70494	GAG	.	.	none		0.562	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		T	62036738	C	T	62036738	3	4	24	1	0	0	0	0	1	0	0	0	13935	893	31	1	3656	1	SCN4A	17	62036738	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	17807	62036738	19158472	556	8773											
ERN1	2081	hgsc.bcm.edu	37	chr17	62132160	62132160	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ttgggacagaaggaaattttCccaactatcaccacgctggt	12	10	9	10	1	1	1	1	0	0	1	2	3	2	3	2	3	1	1	2	3	4	4	rs55653398	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:62132160C>T	ENST00000433197.3	-	14	1796	c.1701G>A	c.(1699-1701)ggG>ggA	p.G567G		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						AGGAAATTTTCCCAACTATCA	0.488													C|||	59	0.0117812	0.0015	0.0072	5008	,	,		21939	0.0		0.0169	False		,,,				2504	0.0358				p.G567G		Atlas-SNP	.											.	ERN1	102	.	0			c.G1701A						PASS	.	C		15,4003		0,15,1994	52	53	53		1701	1.1	0.9	17	dbSNP_129	53	191,8155		4,183,3986	no	coding-synonymous	ERN1	NM_001433.3		4,198,5980	TT,TC,CC		2.2885,0.3733,1.6661		567/978	62132160	206,12158	2009	4173	6182	SO:0001819	synonymous_variant	2081	exon14			AATTTTCCCAACT	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.1701G>A	17.37:g.62132160C>T		57	0	0		41	21	0.512195	NM_001433		Silent	SNP	ENST00000433197.3	37	CCDS45762.1																																																																																			C|0.988;T|0.012	0.012	strong		0.488	ERN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443734.2	NM_001433		T	62132160	C	T	62132160	2	4	24	1	0	0	0	0	0	0	0	1	5239	842	30	2		2	ERN1	17	62132160	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	95422	62132160	19063050	557	8774											
HELZ	9931	hgsc.bcm.edu	37	chr17	65199433	65199433	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaattagagcttatcaacatAccagggactctcctgtgagt	13	11	8	9	0	2	2	1	1	1	1	3	3	2	3	2	1	3	1	2	1	5	3			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:65199433A>G	ENST00000358691.5	-	6	539		c.e6+1		HELZ_ENST00000580168.1_Splice_Site|HELZ_ENST00000580662.1_Splice_Site	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger							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)					TTATCAACATACCAGGGACTC	0.398																																					.		Atlas-SNP	.											.	HELZ	160	.	0			c.372+2T>C						PASS	.						100	99	99					17																	65199433		1898	4122	6020	SO:0001630	splice_region_variant	9931	exon7			CAACATACCAGGG	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.372+1T>C	17.37:g.65199433A>G		76	0	0		87	5	0.0574713	NM_014877	I6L9H4	Splice_Site	SNP	ENST00000358691.5	37	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.255640	0.80135	.	.	ENSG00000198265	ENST00000358691;ENST00000417253	.	.	.	6.06	6.06	0.98353	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8543	0.70323	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	HELZ	62629895	1.000000	0.71417	0.999000	0.59377	0.946000	0.59487	6.429000	0.73387	2.323000	0.78572	0.528000	0.53228	.	.	.	none		0.398	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877	Intron	G	65199433	A	G	65199433	5	3	24	1	0	0	0	0	0	0	1	0	7058	405	14	3	5566	3	HELZ	17	65199433	Splice_Site	SNP	A	TCGA-G8-6326-01A-11D-2210-10	3067273	65199433	15995777	558	8775											
CDC42EP4	23580	hgsc.bcm.edu	37	chr17	71282132	71282132	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcaggggaatgtggacccgCggccccattccgacggggca	7	5	16	13	4	1	0	1	0	0	0	2	3	2	2	4	6	0	1	4	6	1	1	rs375486831		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:71282132C>T	ENST00000335793.3	-	2	902	c.508G>A	c.(508-510)Gcg>Acg	p.A170T	CDC42EP4_ENST00000581014.1_Intron|CDC42EP4_ENST00000439510.2_Missense_Mutation_p.A100T			Q9H3Q1	BORG4_HUMAN	CDC42 effector protein (Rho GTPase binding) 4	170					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)			TGTGGACCCGCGGCCCCATTC	0.662																																					p.A170T		Atlas-SNP	.											CDC42EP4,colon,carcinoma,0,1	CDC42EP4	19	1	0			c.G508A						PASS	.	C	THR/ALA	0,4406		0,0,2203	46	41	43		508	-5.5	0	17		43	1,8599	1.2+/-3.3	0,1,4299	no	missense	CDC42EP4	NM_012121.4	58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	170/357	71282132	1,13005	2203	4300	6503	SO:0001583	missense	23580	exon2			GACCCGCGGCCCC	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.508G>A	17.37:g.71282132C>T	ENSP00000338258:p.Ala170Thr	110	0	0		141	68	0.482269	NM_012121	B3KUS7|O95828|Q96FT3	Missense_Mutation	SNP	ENST00000335793.3	37	CCDS11695.1	.	.	.	.	.	.	.	.	.	.	C	4.875	0.162607	0.09287	0.0	1.16E-4	ENSG00000179604	ENST00000335793;ENST00000439510	T;T	0.34275	1.37;1.37	4.5	-5.48	0.02592	.	1.452830	0.05166	N	0.498676	T	0.20292	0.0488	L	0.28115	0.83	0.09310	N	1	B;B	0.09022	0.002;0.0	B;B	0.01281	0.0;0.0	T	0.23726	-1.0180	10	0.12766	T	0.61	-1.5257	6.8507	0.24012	0.118:0.3419:0.0:0.5401	.	100;170	B3KUS7;Q9H3Q1	.;BORG4_HUMAN	T	170;100	ENSP00000338258:A170T;ENSP00000404270:A100T	ENSP00000338258:A170T	A	-	1	0	CDC42EP4	68793727	0.000000	0.05858	0.000000	0.03702	0.041000	0.13682	-0.321000	0.08018	-1.673000	0.01462	-0.678000	0.03780	GCG	.	.	weak		0.662	CDC42EP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441898.1	NM_012121		T	71282132	C	T	71282132	3	4	24	1	0	0	0	0	1	0	0	0	3080	768	27	1	566	1	CDC42EP4	17	71282132	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	6082699	71282132	9913078	559	8776											
GPR142	350383	hgsc.bcm.edu	37	chr17	72368383	72368383	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accggctacggaggaggggcCggagtgggctgcagccccgg	6	3	20	12	4	0	0	0	0	0	0	0	3	0	3	4	8	3	3	4	8	1	1	rs144235997	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:72368383C>A	ENST00000335666.4	+	4	1081	c.1033C>A	c.(1033-1035)Cgg>Agg	p.R345R		NM_181790.1	NP_861455.1	Q7Z601	GP142_HUMAN	G protein-coupled receptor 142	345						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						GAGGAGGGGCCGGAGTGGGCT	0.632													C|||	15	0.00299521	0.0	0.0086	5008	,	,		19090	0.0		0.008	False		,,,				2504	0.001				p.R345R		Atlas-SNP	.											GPR142,bladder,carcinoma,-2,1	GPR142	74	1	0			c.C1033A						PASS	.	C		2,4404	2.1+/-5.4	0,2,2201	93	75	81		1033	2.6	0	17	dbSNP_134	81	77,8523	44.9+/-103.4	0,77,4223	no	coding-synonymous	GPR142	NM_181790.1		0,79,6424	AA,AC,CC		0.8953,0.0454,0.6074		345/463	72368383	79,12927	2203	4300	6503	SO:0001819	synonymous_variant	350383	exon4			AGGGGCCGGAGTG	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.1033C>A	17.37:g.72368383C>A		183	0	0		145	69	0.475862	NM_181790	A4CYJ8|Q86SL3	Silent	SNP	ENST00000335666.4	37	CCDS11698.1																																																																																			C|0.994;A|0.006	0.006	strong		0.632	GPR142-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442545.1	NM_181790		A	72368383	C	A	72368383	2	1	24	1	0	0	0	0	0	0	0	1	6658	643	23	4		4	GPR142	17	72368383	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1086251	72368383	8826827	560	8777											
GPRC5C	55890	hgsc.bcm.edu	37	chr17	72436949	72436949	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagaacaaggccttttccaTggatgagccggttgcaggtg	9	9	15	8	1	0	2	0	1	0	1	1	4	1	3	3	5	3	2	3	5	2	3			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:72436949T>C	ENST00000392627.1	+	2	2295	c.1169T>C	c.(1168-1170)aTg>aCg	p.M390T	GPRC5C_ENST00000342648.5_Missense_Mutation_p.M30T|GPRC5C_ENST00000392629.2_Missense_Mutation_p.M357T|GPRC5C_ENST00000481232.1_Intron	NM_022036.2	NP_071319.2	Q9NQ84	GPC5C_HUMAN	G protein-coupled receptor, class C, group 5, member C	345					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						GCCTTTTCCATGGATGAGCCG	0.577																																					p.M390T		Atlas-SNP	.											.	GPRC5C	92	.	0			c.T1169C						PASS	.						84	82	83					17																	72436949		2203	4300	6503	SO:0001583	missense	55890	exon2			TTTCCATGGATGA	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.1169T>C	17.37:g.72436949T>C	ENSP00000376403:p.Met390Thr	34	0	0		38	18	0.473684	NM_022036	B5BUN4|Q2NL85|Q9NZG5	Missense_Mutation	SNP	ENST00000392627.1	37	CCDS11699.1	.	.	.	.	.	.	.	.	.	.	T	12.94	2.089028	0.36855	.	.	ENSG00000170412	ENST00000392627;ENST00000342648;ENST00000262616;ENST00000392629;ENST00000392628	T	0.20463	2.07	5.42	5.42	0.78866	.	0.125962	0.85682	D	0.000000	T	0.26340	0.0643	L	0.59436	1.845	0.80722	D	1	B;B;B	0.25772	0.134;0.072;0.118	B;B;B	0.29267	0.075;0.046;0.1	T	0.04621	-1.0938	10	0.87932	D	0	-11.5631	14.6481	0.68774	0.0:0.0:0.0:1.0	.	345;345;357	A8MXZ4;Q9NQ84;Q9NQ84-2	.;GPC5C_HUMAN;.	T	345;390;56;357;345	ENSP00000376405:M357T	ENSP00000262616:M56T	M	+	2	0	GPRC5C	69948544	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	6.106000	0.71511	2.061000	0.61500	0.459000	0.35465	ATG	.	.	none		0.577	GPRC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145094.2			C	72436949	T	C	72436949	3	2	24	1	0	0	0	0	1	0	0	0	6735	1464	51	3	1183	3	GPRC5C	17	72436949	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	68566	72436949	8758261	561	8778											
KIAA0195	9772	hgsc.bcm.edu	37	chr17	73492494	73492494	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	agggcagctcaacagcctgcCctgttccctgacctttcgcc	6	9	9	17	1	1	1	1	1	0	0	3	1	2	1	5	1	4	3	5	1	1	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:73492494C>G	ENST00000314256.7	+	24	3579	c.3185C>G	c.(3184-3186)cCc>cGc	p.P1062R	AC100787.1_ENST00000579379.1_RNA|KIAA0195_ENST00000375248.5_Missense_Mutation_p.P1072R|KIAA0195_ENST00000579208.1_Missense_Mutation_p.P713R	NM_014738.4	NP_055553.3	Q12767	K0195_HUMAN	KIAA0195	1062						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)			AACAGCCTGCCCTGTTCCCTG	0.617																																					p.P1062R		Atlas-SNP	.											.	KIAA0195	102	.	0			c.C3185G						PASS	.						57	54	55					17																	73492494		2203	4300	6503	SO:0001583	missense	9772	exon24			GCCTGCCCTGTTC		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.3185C>G	17.37:g.73492494C>G	ENSP00000313885:p.Pro1062Arg	170	0	0		199	100	0.502513	NM_014738	O75536|Q86XF1	Missense_Mutation	SNP	ENST00000314256.7	37	CCDS32732.1	.	.	.	.	.	.	.	.	.	.	C	14.72	2.620105	0.46736	.	.	ENSG00000177728	ENST00000314256;ENST00000375248	T;T	0.55760	0.5;0.5	5.54	5.54	0.83059	ATPase, P-type,  transmembrane domain (1);	0.253079	0.41500	D	0.000877	T	0.67674	0.2918	M	0.67397	2.05	0.53688	D	0.999973	B;P;P;B	0.39535	0.232;0.573;0.677;0.437	B;B;P;B	0.50970	0.077;0.219;0.655;0.109	T	0.68784	-0.5317	10	0.87932	D	0	-32.2942	19.8311	0.96636	0.0:1.0:0.0:0.0	.	1072;1072;1062;1062	B4DGC6;C9JL75;Q12767-2;Q12767	.;.;.;K0195_HUMAN	R	1062;1072	ENSP00000313885:P1062R;ENSP00000364397:P1072R	ENSP00000313885:P1062R	P	+	2	0	KIAA0195	71004089	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.656000	0.61483	2.768000	0.95171	0.561000	0.74099	CCC	.	.	none		0.617	KIAA0195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447303.1	NM_014738		G	73492494	C	G	73492494	3	3	24	1	0	0	0	0	1	0	0	0	8169	623	22	4	3275	4	KIAA0195	17	73492494	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1055545	73492494	7702716	562	8779											
KIAA0195	9772	hgsc.bcm.edu	37	chr17	73493217	73493217	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttcttgcctggtccagctGccgccactcctgagtaccac	5	11	8	17	1	1	1	0	1	1	0	3	1	3	1	6	1	4	2	6	1	1	3	rs372068615		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:73493217G>A	ENST00000314256.7	+	26	3739	c.3345G>A	c.(3343-3345)ctG>ctA	p.L1115L	AC100787.1_ENST00000579379.1_RNA|KIAA0195_ENST00000375248.5_Silent_p.L1125L|KIAA0195_ENST00000579208.1_Silent_p.L766L	NM_014738.4	NP_055553.3	Q12767	K0195_HUMAN	KIAA0195	1115						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)			TGGTCCAGCTGCCGCCACTCC	0.542																																					p.L1115L		Atlas-SNP	.											.	KIAA0195	102	.	0			c.G3345A						PASS	.	G		1,4405		0,1,2202	164	141	149		3345	2.8	1	17		149	0,8600		0,0,4300	no	coding-synonymous	KIAA0195	NM_014738.4		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		1115/1357	73493217	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9772	exon26			CCAGCTGCCGCCA		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.3345G>A	17.37:g.73493217G>A		138	0	0		144	62	0.430556	NM_014738	O75536|Q86XF1	Silent	SNP	ENST00000314256.7	37	CCDS32732.1																																																																																			.	.	weak		0.542	KIAA0195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447303.1	NM_014738		A	73493217	G	A	73493217	2	1	24	1	0	0	0	0	0	0	0	1	8169	1306	46	2		2	KIAA0195	17	73493217	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	723	73493217	7701993	563	8780											
LLGL2	3993	hgsc.bcm.edu	37	chr17	73569211	73569211	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtcgtcgagccgaggactaCggggagcaccacctggcagt	9	5	15	12	4	0	0	0	0	0	0	2	4	0	2	3	4	3	2	3	4	1	1	rs376055189		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:73569211C>T	ENST00000392550.3	+	20	2694	c.2577C>T	c.(2575-2577)taC>taT	p.Y859Y	LLGL2_ENST00000167462.5_Silent_p.Y859Y|LLGL2_ENST00000577200.1_Silent_p.Y859Y	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	859					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)			CCGAGGACTACGGGGAGCACC	0.662																																					p.Y859Y		Atlas-SNP	.											.	LLGL2	155	.	0			c.C2577T						PASS	.	C	,	1,4405		0,1,2202	59	50	53		2577,2577	-6.2	0.8	17		53	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	LLGL2	NM_001031803.1,NM_004524.2	,	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	,	859/1021,859/1016	73569211	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	3993	exon20			GGACTACGGGGAG	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.2577C>T	17.37:g.73569211C>T		188	0	0		179	81	0.452514	NM_004524	Q14521|Q9BR62	Silent	SNP	ENST00000392550.3	37	CCDS32733.1																																																																																			.	.	weak		0.662	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524		T	73569211	C	T	73569211	2	4	24	1	0	0	0	0	0	0	0	1	8843	547	19	1		1	LLGL2	17	73569211	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	75994	73569211	7625999	564	8781											
FBF1	85302	hgsc.bcm.edu	37	chr17	73914040	73914040	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tgctcgtcacgctgccggatCcccagctcccgctcctggga	4	8	11	18	4	1	0	1	0	0	0	5	2	4	2	5	2	3	4	5	2	0	0	rs376546796		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:73914040C>T	ENST00000586717.1	-	21	2589	c.2316G>A	c.(2314-2316)ggG>ggA	p.G772G	FBF1_ENST00000319129.5_Silent_p.G771G|FBF1_ENST00000389570.4_Silent_p.G772G			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	772					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						GCTGCCGGATCCCCAGCTCCC	0.677																																					p.G771G		Atlas-SNP	.											.	FBF1	48	.	0			c.G2313A						PASS	.	C		1,4061		0,1,2030	28	32	31		2313	-4.2	0.1	17		31	0,8382		0,0,4191	no	coding-synonymous	FBF1	NM_001080542.1		0,1,6221	TT,TC,CC		0.0,0.0246,0.0080		771/1134	73914040	1,12443	2031	4191	6222	SO:0001819	synonymous_variant	85302	exon21			CCGGATCCCCAGC	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.2316G>A	17.37:g.73914040C>T		56	0	0		53	33	0.622642	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000586717.1	37																																																																																				.	.	weak		0.677	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542		T	73914040	C	T	73914040	2	4	24	1	0	0	0	0	0	0	0	1	5703	842	30	2		2	FBF1	17	73914040	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	344829	73914040	7281170	565	8782											
GALR2	8811	hgsc.bcm.edu	37	chr17	74072923	74072923	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccatggacatctgcacctTcgtcttcagctacctgcttc	6	12	7	16	2	3	0	1	0	2	0	5	1	3	1	3	1	4	3	3	1	1	4	rs369779116		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:74072923T>G	ENST00000329003.3	+	2	665	c.575T>G	c.(574-576)tTc>tGc	p.F192C	ZACN_ENST00000334586.5_5'Flank|ZACN_ENST00000392503.2_5'Flank	NM_003857.2	NP_003848.1	O43603	GALR2_HUMAN	galanin receptor 2	192					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						ATCTGCACCTTCGTCTTCAGC	0.692																																					p.F192C		Atlas-SNP	.											.	GALR2	17	.	0			c.T575G						PASS	.	T	CYS/PHE	1,4399		0,1,2199	45	31	36		575	5	1	17		36	0,8596		0,0,4298	no	missense	GALR2	NM_003857.2	205	0,1,6497	GG,GT,TT		0.0,0.0227,0.0077	probably-damaging	192/388	74072923	1,12995	2200	4298	6498	SO:0001583	missense	8811	exon2			GCACCTTCGTCTT	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.575T>G	17.37:g.74072923T>G	ENSP00000329684:p.Phe192Cys	50	0	0		65	29	0.446154	NM_003857	A5JUU4|Q32MN8	Missense_Mutation	SNP	ENST00000329003.3	37	CCDS11739.1	.	.	.	.	.	.	.	.	.	.	T	26.6	4.752255	0.89753	2.27E-4	0.0	ENSG00000182687	ENST00000329003	T	0.72394	-0.65	4.97	4.97	0.65823	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.87657	0.6232	M	0.93720	3.45	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90899	0.4767	10	0.87932	D	0	.	14.3163	0.66452	0.0:0.0:0.0:1.0	.	192	O43603	GALR2_HUMAN	C	192	ENSP00000329684:F192C	ENSP00000329684:F192C	F	+	2	0	GALR2	71584518	1.000000	0.71417	0.978000	0.43139	0.984000	0.73092	7.925000	0.87563	1.871000	0.54225	0.379000	0.24179	TTC	.	.	weak		0.692	GALR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394760.1			G	74072923	T	G	74072923	3	3	24	1	0	0	0	0	1	0	0	0	6236	1783	62	5	581	5	GALR2	17	74072923	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	158883	74072923	7122287	566	8783											
RNF157	114804	hgsc.bcm.edu	37	chr17	74208466	74208466	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaactggtctgttccccagAaagttcagatcgctgttctc	9	12	8	12	1	3	2	1	0	2	2	6	2	4	2	2	1	1	4	2	1	2	3	rs61760884	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:74208466A>G	ENST00000269391.6	-	2	318	c.186T>C	c.(184-186)ttT>ttC	p.F62F	RNF157_ENST00000319945.6_Silent_p.F62F|RNF157_ENST00000592271.1_Silent_p.F62F	NM_052916.2	NP_443148.1	Q96PX1	RN157_HUMAN	ring finger protein 157	62							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)			TGTTCCCCAGAAAGTTCAGAT	0.413													A|||	11	0.00219649	0.0	0.0014	5008	,	,		19125	0.0		0.0099	False		,,,				2504	0.0				p.F62F	GBM(186;507 2120 27388 27773 52994)	Atlas-SNP	.											.	RNF157	66	.	0			c.T186C						PASS	.	A		5,4401	9.9+/-24.2	0,5,2198	123	116	119		186	-2.6	1	17	dbSNP_129	119	51,8549	33.3+/-86.6	0,51,4249	no	coding-synonymous	RNF157	NM_052916.2		0,56,6447	GG,GA,AA		0.593,0.1135,0.4306		62/680	74208466	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	114804	exon2			CCCCAGAAAGTTC	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.186T>C	17.37:g.74208466A>G		140	0	0		192	83	0.432292	NM_052916	Q8NB72|Q96N56	Silent	SNP	ENST00000269391.6	37	CCDS32740.1																																																																																			A|0.996;G|0.004	0.004	strong		0.413	RNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255874.2	XM_290732		G	74208466	A	G	74208466	2	3	24	1	0	0	0	0	0	0	0	1	13469	243	9	3		3	RNF157	17	74208466	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	135543	74208466	6986744	567	8784											
SPHK1	8877	hgsc.bcm.edu	37	chr17	74383648	74383648	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagccccagcagatgccacCgccagaagagcccttatgac	12	4	10	15	1	0	4	0	1	0	3	0	5	0	4	6	0	4	1	6	0	3	1	rs56341546	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:74383648C>T	ENST00000545180.1	+	8	1945	c.1136C>T	c.(1135-1137)cCg>cTg	p.P379L	SPHK1_ENST00000323374.4_Missense_Mutation_p.P465L|SPHK1_ENST00000590959.1_Missense_Mutation_p.P393L|SPHK1_ENST00000592299.1_Missense_Mutation_p.P379L|SPHK1_ENST00000392496.3_Missense_Mutation_p.P379L			Q9NYA1	SPHK1_HUMAN	sphingosine kinase 1	379					'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)	CAGATGCCACCGCCAGAAGAG	0.647													C|||	24	0.00479233	0.0	0.0043	5008	,	,		17320	0.0		0.0119	False		,,,				2504	0.0092				p.P465L	GBM(90;966 1307 27369 33775 44498)	Atlas-SNP	.											.	SPHK1	24	.	0			c.C1394T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	6,4400		0,6,2197	27	30	29		1136,1136,1178,1394	0.9	0	17	dbSNP_129	29	52,8544		0,52,4246	yes	missense,missense,missense,missense	SPHK1	NM_001142601.1,NM_001142602.1,NM_021972.3,NM_182965.2	98,98,98,98	0,58,6443	TT,TC,CC		0.6049,0.1362,0.4461	benign,benign,benign,benign	379/385,379/385,393/399,465/471	74383648	58,12944	2203	4298	6501	SO:0001583	missense	8877	exon6			TGCCACCGCCAGA	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.1136C>T	17.37:g.74383648C>T	ENSP00000440970:p.Pro379Leu	19	0	0		27	15	0.555556	NM_182965	Q8N632|Q96GK1|Q9HD92|Q9NY70|Q9NYL3	Missense_Mutation	SNP	ENST00000545180.1	37	CCDS45785.1	13	0.005952380952380952	0	0.0	4	0.011049723756906077	0	0.0	9	0.011873350923482849	C	12.92	2.081367	0.36758	0.001362	0.006049	ENSG00000176170	ENST00000545180;ENST00000323374;ENST00000392496;ENST00000543830	T;T;T	0.24350	1.96;1.86;1.96	4.64	0.926	0.19430	.	1.925830	0.02640	N	0.105239	T	0.14917	0.0360	L	0.32530	0.975	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.0;0.0	T	0.23904	-1.0175	10	0.54805	T	0.06	0.009	4.5549	0.12131	0.1711:0.5944:0.0:0.2345	rs56341546;rs61751848	465;393;379	Q9NYA1-2;Q96GK1;Q9NYA1	.;.;SPHK1_HUMAN	L	379;465;379;378	ENSP00000440970:P379L;ENSP00000313681:P465L;ENSP00000376285:P379L	ENSP00000313681:P465L	P	+	2	0	SPHK1	71895243	0.000000	0.05858	0.005000	0.12908	0.032000	0.12392	0.093000	0.15086	0.480000	0.27534	0.558000	0.71614	CCG	C|0.994;T|0.006	0.006	strong		0.647	SPHK1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450113.1	NM_182965, NM_021972		T	74383648	C	T	74383648	3	4	24	1	0	0	0	0	1	0	0	0	15061	652	23	1	1458	1	SPHK1	17	74383648	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	175182	74383648	6811562	568	8785											
ENPP7	339221	hgsc.bcm.edu	37	chr17	77710990	77710990	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acgtgtacgagctcatgtgcCggctgctgggcatcgtgccc	5	9	14	13	4	1	0	1	0	0	0	2	1	1	0	2	2	5	5	2	2	1	1	rs139719997	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:77710990C>T	ENST00000328313.5	+	4	1398	c.1177C>T	c.(1177-1179)Cgg>Tgg	p.R393W		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)			GCTCATGTGCCGGCTGCTGGG	0.647													C|||	7	0.00139776	0.0	0.0029	5008	,	,		18712	0.0		0.002	False		,,,				2504	0.0031				p.R393W		Atlas-SNP	.											ENPP7,NS,carcinoma,-2,1	ENPP7	63	1	0			c.C1177T						PASS	.	C	TRP/ARG	3,4403	6.2+/-15.9	0,3,2200	61	51	55		1177	0.8	0.7	17	dbSNP_134	55	30,8570	20.4+/-63.3	0,30,4270	yes	missense	ENPP7	NM_178543.3	101	0,33,6470	TT,TC,CC		0.3488,0.0681,0.2537	possibly-damaging	393/459	77710990	33,12973	2203	4300	6503	SO:0001583	missense	339221	exon4			ATGTGCCGGCTGC	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.1177C>T	17.37:g.77710990C>T	ENSP00000332656:p.Arg393Trp	64	0	0		91	38	0.417582	NM_178543		Missense_Mutation	SNP	ENST00000328313.5	37	CCDS11763.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	13.24	2.177465	0.38413	6.81E-4	0.003488	ENSG00000182156	ENST00000328313	T	0.75589	-0.95	3.07	0.824	0.18818	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.824992	0.10969	N	0.614092	T	0.69088	0.3072	L	0.42245	1.32	0.25279	N	0.989453	D	0.54047	0.964	P	0.48677	0.586	T	0.59043	-0.7528	10	0.72032	D	0.01	-10.5339	5.5668	0.17175	0.3222:0.4528:0.225:0.0	.	393	Q6UWV6	ENPP7_HUMAN	W	393	ENSP00000332656:R393W	ENSP00000332656:R393W	R	+	1	2	ENPP7	75325585	0.000000	0.05858	0.698000	0.30274	0.382000	0.30200	-0.066000	0.11598	0.075000	0.16796	0.561000	0.74099	CGG	C|0.997;T|0.003	0.003	strong		0.647	ENPP7-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437038.1	NM_178543		T	77710990	C	T	77710990	3	4	24	1	0	0	0	0	1	0	0	0	5137	643	23	1	1191	1	ENPP7	17	77710990	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	3327342	77710990	3484220	569	8786											
RPTOR	57521	hgsc.bcm.edu	37	chr17	78936339	78936339	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagatcgtgaaggggctgacGgccctggacatccaccccca	9	5	12	15	2	0	3	0	2	0	1	2	4	1	4	4	4	0	1	4	4	1	0	rs17848671	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:78936339G>A	ENST00000306801.3	+	32	4133	c.3771G>A	c.(3769-3771)acG>acA	p.T1257T	CTD-2561B21.3_ENST00000571591.1_RNA|RPTOR_ENST00000544334.2_Silent_p.T1099T|RPTOR_ENST00000575542.1_3'UTR	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	1257					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						AGGGGCTGACGGCCCTGGACA	0.632													G|||	3	0.000599042	0.0	0.0029	5008	,	,		17401	0.001		0.0	False		,,,				2504	0.0				p.T1257T		Atlas-SNP	.											.	RPTOR	122	.	0			c.G3771A						PASS	.						95	83	87					17																	78936339		2203	4300	6503	SO:0001819	synonymous_variant	57521	exon32			GCTGACGGCCCTG		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.3771G>A	17.37:g.78936339G>A		105	0	0		136	62	0.455882	NM_020761	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Silent	SNP	ENST00000306801.3	37	CCDS11773.1																																																																																			G|0.999;A|0.001	0.001	strong		0.632	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761		A	78936339	G	A	78936339	2	1	24	1	0	0	0	0	0	0	0	1	13680	1103	39	1		1	RPTOR	17	78936339	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1225349	78936339	2258871	570	8787											
CHMP6	79643	hgsc.bcm.edu	37	chr17	78968837	78968837	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agacgggccaagctgctgctCaagaagaagcgataccagga	14	4	13	10	2	1	3	1	0	0	3	1	5	1	4	2	2	5	3	2	2	5	1	rs146625286	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:78968837C>A	ENST00000325167.5	+	3	270	c.192C>A	c.(190-192)ctC>ctA	p.L64L		NM_024591.4	NP_078867.2	Q96FZ7	CHMP6_HUMAN	charged multivesicular body protein 6	64					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)			AGCTGCTGCTCAAGAAGAAGC	0.687													C|||	7	0.00139776	0.0	0.0058	5008	,	,		10104	0.0		0.003	False		,,,				2504	0.0				p.L64L		Atlas-SNP	.											.	CHMP6	16	.	0			c.C192A						PASS	.	C		1,4383		0,1,2191	34	33	34		192	-0.4	1	17	dbSNP_134	34	10,8570		0,10,4280	no	coding-synonymous	CHMP6	NM_024591.4		0,11,6471	AA,AC,CC		0.1166,0.0228,0.0849		64/202	78968837	11,12953	2192	4290	6482	SO:0001819	synonymous_variant	79643	exon3			GCTGCTCAAGAAG	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.192C>A	17.37:g.78968837C>A		161	0	0		173	78	0.450867	NM_024591	A8K7U0|Q53FU4|Q9HAE8	Silent	SNP	ENST00000325167.5	37	CCDS11774.1																																																																																			C|0.999;A|0.001	0.001	strong		0.687	CHMP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438215.1	NM_024591		A	78968837	C	A	78968837	2	1	24	1	0	0	0	0	0	0	0	1	3362	813	29	4		4	CHMP6	17	78968837	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	32498	78968837	2226373	571	8788											
C17orf56	146705	hgsc.bcm.edu	37	chr17	79204447	79204447	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctgggggaggaggtcgctgCtccccagggaggcgatggca	6	5	19	11	2	0	0	0	0	0	0	2	4	1	3	3	7	1	3	3	7	0	0	rs143572077		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:79204447C>T	ENST00000300714.3	-	11	983	c.926G>A	c.(925-927)aGc>aAc	p.S309N	ENTHD2_ENST00000374769.2_Missense_Mutation_p.S225N|AC027601.1_ENST00000575922.1_RNA|AC027601.1_ENST00000569559.1_RNA	NM_144679.2	NP_653280.1	Q96N21	AP4AT_HUMAN	ENTH domain containing 2	309						cytoplasmic vesicle (GO:0031410)											GAGGTCGCTGCTCCCCAGGGA	0.692											OREG0024811	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S309N		Atlas-SNP	.											.	.	.	.	0			c.G926A						PASS	.	C	ASN/SER	0,4406		0,0,2203	23	25	24		926	3.1	0	17	dbSNP_134	24	1,8597		0,1,4298	no	missense	C17orf56	NM_144679.2	46	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	309/526	79204447	1,13003	2203	4299	6502	SO:0001583	missense	146705	exon11			TCGCTGCTCCCCA	AK056090	CCDS11779.1	17q25.3	2012-07-18	2012-07-18	2012-07-18	ENSG00000167302	ENSG00000167302			26458	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 56"	C17orf56			Standard	NM_144679		Approved	FLJ31528	uc002jzu.2	Q96N21	OTTHUMG00000177866	ENST00000300714.3:c.926G>A	17.37:g.79204447C>T	ENSP00000300714:p.Ser309Asn	102	0	0	1189	108	57	0.527778	NM_144679	Q6ZQU0|Q6ZSQ9	Missense_Mutation	SNP	ENST00000300714.3	37	CCDS11779.1	.	.	.	.	.	.	.	.	.	.	C	7.062	0.566626	0.13560	0.0	1.16E-4	ENSG00000167302	ENST00000300714;ENST00000374769	T;T	0.27720	1.65;1.65	5.17	3.13	0.36017	.	1.579650	0.03019	N	0.150445	T	0.24624	0.0597	L	0.29908	0.895	0.09310	N	1	P;P	0.41265	0.454;0.744	B;B	0.35813	0.105;0.211	T	0.24941	-1.0146	10	0.38643	T	0.18	-0.3904	8.4158	0.32670	0.0:0.7609:0.1556:0.0835	.	309;225	Q96N21;Q96N21-2	CQ056_HUMAN;.	N	309;225	ENSP00000300714:S309N;ENSP00000363901:S225N	ENSP00000300714:S309N	S	-	2	0	C17orf56	76819042	0.044000	0.20184	0.004000	0.12327	0.007000	0.05969	1.325000	0.33724	0.544000	0.28883	0.555000	0.69702	AGC	C|1.000;T|0.000	0.000	weak		0.692	ENTHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439315.1	NM_144679		T	79204447	C	T	79204447	3	4	24	1	0	0	0	0	1	0	0	0	1866	797	28	2	659	2	C17orf56	17	79204447	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	235610	79204447	1990763	572	8789											
SLC25A10	1468	hgsc.bcm.edu	37	chr17	79686879	79686879	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggcgttttccactgcgccGtggagacagcgaagctcggg	7	7	16	11	5	0	1	0	0	0	1	2	3	1	1	2	3	3	2	2	3	1	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr17:79686879G>A	ENST00000350690.5	+	10	810	c.724G>A	c.(724-726)Gtg>Atg	p.V242M	SLC25A10_ENST00000571730.1_Missense_Mutation_p.V397M|SLC25A10_ENST00000541223.1_Missense_Mutation_p.V397M|SLC25A10_ENST00000545862.1_Missense_Mutation_p.V199M|SLC25A10_ENST00000331531.5_Missense_Mutation_p.V251M	NM_001270953.1|NM_012140.4	NP_001257882.1|NP_036272.2	Q9UBX3	DIC_HUMAN	solute carrier family 25 (mitochondrial carrier; dicarboxylate transporter), member 10	242					carbohydrate metabolic process (GO:0005975)|cellular nitrogen compound metabolic process (GO:0034641)|dicarboxylic acid transport (GO:0006835)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|ion transport (GO:0006811)|mitochondrial transport (GO:0006839)|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)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	dicarboxylic acid transmembrane transporter activity (GO:0005310)	p.V242L(1)		endometrium(1)|lung(9)|ovary(1)|prostate(1)|skin(2)	14	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0117)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)		Succinic acid(DB00139)	CCACTGCGCCGTGGAGACAGC	0.602																																					p.V251M		Atlas-SNP	.											SLC25A10,NS,carcinoma,0,1	SLC25A10	24	1	1	Substitution - Missense(1)	lung(1)	c.G751A						PASS	.						156	180	172					17																	79686879		2203	4300	6503	SO:0001583	missense	1468	exon10			TGCGCCGTGGAGA		CCDS11786.1, CCDS59301.1, CCDS74176.1	17q25.3	2013-07-15			ENSG00000183048	ENSG00000183048		"Solute carriers"	10980	protein-coding gene	gene with protein product		606794		DIC		9733776, 10072589	Standard	NM_001270953		Approved		uc031rew.1	Q9UBX3	OTTHUMG00000178173	ENST00000350690.5:c.724G>A	17.37:g.79686879G>A	ENSP00000345580:p.Val242Met	128	0	0		157	75	0.477707	NM_001270888	Q542Z3|Q96BA1|Q96IP1	Missense_Mutation	SNP	ENST00000350690.5	37	CCDS11786.1	.	.	.	.	.	.	.	.	.	.	G	10.33	1.320337	0.23994	.	.	ENSG00000183048	ENST00000541223;ENST00000331531;ENST00000350690;ENST00000545862	T;T;T;T	0.79352	-1.26;-1.26;-1.26;-1.26	4.36	-8.72	0.00845	Mitochondrial carrier domain (2);	0.647462	0.14300	N	0.328340	T	0.48696	0.1514	N	0.25286	0.73	0.09310	N	1	B;B;B	0.20988	0.018;0.05;0.025	B;B;B	0.20184	0.028;0.017;0.028	T	0.46373	-0.9196	10	0.14656	T	0.56	-2.2797	1.993	0.03450	0.3866:0.2096:0.2979:0.1059	.	397;251;242	B4DLN1;Q9UBX3-2;Q9UBX3	.;.;DIC_HUMAN	M	397;251;242;199	ENSP00000439565:V397M;ENSP00000328403:V251M;ENSP00000345580:V242M;ENSP00000446242:V199M	ENSP00000328403:V251M	V	+	1	0	SLC25A10	77297284	0.000000	0.05858	0.004000	0.12327	0.372000	0.29890	-1.990000	0.01479	-1.305000	0.02327	0.655000	0.94253	GTG	.	.	none		0.602	SLC25A10-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000440816.1			A	79686879	G	A	79686879	3	1	24	1	0	0	0	0	1	0	0	0	14487	1145	40	1	762	1	SLC25A10	17	79686879	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	482432	79686879	1508331	573	8790											
ZNF519	162655	hgsc.bcm.edu	37	chr18	14124427	14124427	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagggtctaggcatttccActcttctggagagaattcta	9	12	11	9	0	4	1	0	0	4	1	5	3	5	2	1	4	0	2	1	4	3	5	rs16941623	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:14124427A>G	ENST00000590202.1	-	2	204	c.52T>C	c.(52-54)Tgg>Cgg	p.W18R	ZNF519_ENST00000589498.1_Missense_Mutation_p.W18R|ZNF519_ENST00000589203.1_Intron	NM_145287.3	NP_660330.2	Q8TB69	ZN519_HUMAN	zinc finger protein 519	18	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.		W -> R (in dbSNP:rs16941623).		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						AGGCATTTCCACTCTTCTGGA	0.403													A|||	37	0.00738818	0.0272	0.0014	5008	,	,		15557	0.0		0.0	False		,,,				2504	0.0				p.W18R		Atlas-SNP	.											.	ZNF519	53	.	0			c.T52C						PASS	.	A	ARG/TRP	134,4272	97.6+/-136.3	2,130,2071	82	88	86		52		0.3	18	dbSNP_123	86	1,8599		0,1,4299	no	missense	ZNF519	NM_145287.3	101	2,131,6370	GG,GA,AA		0.0116,3.0413,1.038	probably-damaging	18/541	14124427	135,12871	2203	4300	6503	SO:0001583	missense	162655	exon2			ATTTCCACTCTTC	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.52T>C	18.37:g.14124427A>G	ENSP00000464872:p.Trp18Arg	96	0	0		114	61	0.535088	NM_145287		Missense_Mutation	SNP	ENST00000590202.1	37	CCDS32797.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	A	9.431	1.085594	0.20390	0.030413	1.16E-4	ENSG00000175322	ENST00000309305	.	.	.	.	.	.	Krueppel-associated box (4);	.	.	.	.	T	0.40196	0.1107	H	0.98155	4.16	0.09310	N	1	B	0.13594	0.008	B	0.04013	0.001	T	0.59705	-0.7404	6	0.87932	D	0	.	.	.	.	rs16941623;rs52802058;rs60926256;rs16941623	18	Q8TB69	ZN519_HUMAN	R	18	.	ENSP00000307908:W18R	W	-	1	0	ZNF519	14114427	0.444000	0.25649	0.272000	0.24630	0.274000	0.26718	1.863000	0.39459	0.077000	0.16863	0.076000	0.15429	TGG	A|0.988;G|0.012	0.012	strong		0.403	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287		G	14124427	A	G	14124427	3	3	24	1	0	0	0	0	1	0	0	0	17979	159	6	3	1578	3	ZNF519	18	14124427	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10		14124427	63952821	574	8791											
LAMA3	3909	hgsc.bcm.edu	37	chr18	21494509	21494509	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctaaggaggcagttatggatCgggtgaaatttcagaggtac	12	10	14	5	1	1	2	1	1	0	1	2	4	1	4	0	5	1	3	0	5	4	4	rs147463397	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:21494509C>T	ENST00000313654.9	+	57	7706	c.7465C>T	c.(7465-7467)Cgg>Tgg	p.R2489W	LAMA3_ENST00000399516.3_Missense_Mutation_p.R2433W|LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000587184.1_Missense_Mutation_p.R824W|LAMA3_ENST00000269217.6_Missense_Mutation_p.R880W	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2489	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)					AGTTATGGATCGGGTGAAATT	0.488																																					p.R2489W		Atlas-SNP	.											.	LAMA3	397	.	0			c.C7465T						PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	75	70	71		2638,7297,2470,7465	4.4	1	18	dbSNP_134	71	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense	LAMA3	NM_000227.3,NM_001127717.1,NM_001127718.1,NM_198129.1	101,101,101,101	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging,probably-damaging,probably-damaging,probably-damaging	880/1725,2433/3278,824/1669,2489/3334	21494509	3,13003	2203	4300	6503	SO:0001583	missense	3909	exon57			ATGGATCGGGTGA	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.7465C>T	18.37:g.21494509C>T	ENSP00000324532:p.Arg2489Trp	38	0	0		49	27	0.55102	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	37	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	C	16.74	3.206989	0.58343	0.0	3.49E-4	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000269217	T;T;T	0.80566	-1.39;-1.39;-1.39	5.25	4.36	0.52297	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	D	0.88973	0.6583	M	0.73598	2.24	0.49915	D	0.999836	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.992;0.989	D	0.90115	0.4195	9	0.72032	D	0.01	.	15.1212	0.72443	0.1427:0.8573:0.0:0.0	.	824;880;2433;2489	Q6VU69;B0YJ33;Q6VU67;Q16787	.;.;.;LAMA3_HUMAN	W	2489;2433;880	ENSP00000324532:R2489W;ENSP00000382432:R2433W;ENSP00000269217:R880W	ENSP00000269217:R880W	R	+	1	2	LAMA3	19748507	1.000000	0.71417	1.000000	0.80357	0.795000	0.44927	2.974000	0.49272	1.179000	0.42884	0.561000	0.74099	CGG	C|1.000;T|0.000	0.000	strong		0.488	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		T	21494509	C	T	21494509	3	4	24	1	0	0	0	0	1	0	0	0	8616	875	31	1	7866	1	LAMA3	18	21494509	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	7370082	21494509	56582739	575	8792											
DSG3	1830	hgsc.bcm.edu	37	chr18	29055635	29055635	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgcctgtgcggaggaagaCgatggccaggaagcaaatga	12	7	15	7	2	0	2	0	1	0	1	0	6	0	5	2	4	3	1	2	4	3	1	rs117661169	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:29055635C>T	ENST00000257189.4	+	16	2495	c.2412C>T	c.(2410-2412)gaC>gaT	p.D804D		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	804					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)			CGGAGGAAGACGATGGCCAGG	0.418													C|||	92	0.0183706	0.0015	0.0202	5008	,	,		19856	0.0		0.0298	False		,,,				2504	0.047				p.D804D		Atlas-SNP	.											.	DSG3	172	.	0			c.C2412T						PASS	.	C		24,4382	32.6+/-62.9	0,24,2179	120	115	117		2412	-10.6	0	18	dbSNP_132	117	288,8312	107.8+/-168.5	2,284,4014	no	coding-synonymous	DSG3	NM_001944.2		2,308,6193	TT,TC,CC		3.3488,0.5447,2.3989		804/1000	29055635	312,12694	2203	4300	6503	SO:0001819	synonymous_variant	1830	exon16			GGAAGACGATGGC	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.2412C>T	18.37:g.29055635C>T		68	0	0		78	37	0.474359	NM_001944	A8K2V2	Silent	SNP	ENST00000257189.4	37	CCDS11898.1																																																																																			C|0.976;T|0.024	0.024	strong		0.418	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944		T	29055635	C	T	29055635	2	4	24	1	0	0	0	0	0	0	0	1	4780	535	19	1		1	DSG3	18	29055635	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	7561126	29055635	49021613	576	8793											
RNF165	494470	hgsc.bcm.edu	37	chr18	44015315	44015315	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccagcttcgacttcggccaActgcagacacctcagcccag	9	6	8	18	2	1	1	1	0	0	1	3	2	1	1	4	1	4	2	4	1	1	2	rs139779598	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:44015315A>G	ENST00000269439.7	+	3	492	c.441A>G	c.(439-441)caA>caG	p.Q147Q	RNF165_ENST00000543885.1_Intron	NM_152470.2	NP_689683.2	Q6ZSG1	RN165_HUMAN	ring finger protein 165	147							zinc ion binding (GO:0008270)			NS(1)|large_intestine(4)|lung(6)	11				READ - Rectum adenocarcinoma(1;0.0873)		ACTTCGGCCAACTGCAGACAC	0.642													A|||	30	0.00599042	0.0008	0.0159	5008	,	,		17217	0.0		0.0159	False		,,,				2504	0.002				p.Q147Q		Atlas-SNP	.											.	RNF165	34	.	0			c.A441G						PASS	.	A		9,4397	15.5+/-35.6	0,9,2194	63	54	57		441	5.7	1	18	dbSNP_134	57	93,8507	52.3+/-112.8	0,93,4207	no	coding-synonymous	RNF165	NM_152470.2		0,102,6401	GG,GA,AA		1.0814,0.2043,0.7843		147/347	44015315	102,12904	2203	4300	6503	SO:0001819	synonymous_variant	494470	exon3			CGGCCAACTGCAG	BC012190	CCDS32823.1, CCDS58621.1	18q21.1	2014-01-03			ENSG00000141622	ENSG00000141622		"RING-type (C3HC4) zinc fingers"	31696	protein-coding gene	gene with protein product							Standard	NR_046357		Approved	ARKL2, RNF111L2	uc002lcb.1	Q6ZSG1		ENST00000269439.7:c.441A>G	18.37:g.44015315A>G		58	0	0		69	34	0.492754	NM_152470	B3KVD1	Silent	SNP	ENST00000269439.7	37	CCDS32823.1																																																																																			A|0.992;G|0.008	0.008	strong		0.642	RNF165-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445358.1	NM_152470		G	44015315	A	G	44015315	2	3	24	1	0	0	0	0	0	0	0	1	13471	40	2	3		3	RNF165	18	44015315	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	14959680	44015315	34061933	577	8794											
DYM	54808	hgsc.bcm.edu	37	chr18	46623854	46623854	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgacagctcagctccagctTgcagcaaccttgagctaaag	11	8	9	13	0	1	2	1	2	0	0	2	2	2	2	2	0	7	6	2	0	3	3	rs146000214		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:46623854T>C	ENST00000269445.6	-	16	2235	c.1778A>G	c.(1777-1779)cAa>cGa	p.Q593R	DYM_ENST00000442713.2_Missense_Mutation_p.Q403R	NM_017653.3	NP_060123.3	Q7RTS9	DYM_HUMAN	dymeclin	593					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						AGCTCCAGCTTGCAGCAACCT	0.433													T|||	1	0.000199681	0.0	0.0014	5008	,	,		22199	0.0		0.0	False		,,,				2504	0.0				p.Q593R		Atlas-SNP	.											.	DYM	52	.	0			c.A1778G						PASS	.	T	ARG/GLN	0,4406		0,0,2203	86	78	81		1778	5.6	0.4	18	dbSNP_134	81	9,8591	7.1+/-27.0	0,9,4291	yes	missense	DYM	NM_017653.3	43	0,9,6494	CC,CT,TT		0.1047,0.0,0.0692	benign	593/670	46623854	9,12997	2203	4300	6503	SO:0001583	missense	54808	exon16			CCAGCTTGCAGCA	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.1778A>G	18.37:g.46623854T>C	ENSP00000269445:p.Gln593Arg	72	0	0		92	38	0.413043	NM_017653	A8K5I8|B2RCF9|B4DKI7|Q3ZTS8|Q6P2P5|Q8N2M0|Q9BVE9|Q9NPU7	Missense_Mutation	SNP	ENST00000269445.6	37	CCDS11937.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	T	14.50	2.554677	0.45487	0.0	0.001047	ENSG00000141627	ENST00000442713;ENST00000269445	D;D	0.82619	-1.63;-1.63	5.61	5.61	0.85477	.	0.053248	0.85682	D	0.000000	D	0.87478	0.6187	L	0.49640	1.575	0.80722	D	1	P;D	0.59357	0.908;0.985	P;D	0.74023	0.888;0.982	D	0.84012	0.0349	10	0.15952	T	0.53	-13.7508	15.7757	0.78214	0.0:0.0:0.0:1.0	.	403;593	Q7RTS9-2;Q7RTS9	.;DYM_HUMAN	R	403;593	ENSP00000395942:Q403R;ENSP00000269445:Q593R	ENSP00000269445:Q593R	Q	-	2	0	DYM	44877852	1.000000	0.71417	0.351000	0.25721	0.899000	0.52679	7.142000	0.77339	2.254000	0.74563	0.533000	0.62120	CAA	T|0.999;C|0.001	0.001	strong		0.433	DYM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255912.3	NM_017653		C	46623854	T	C	46623854	3	2	24	1	0	0	0	0	1	0	0	0	4842	1812	63	3	239	3	DYM	18	46623854	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	2608539	46623854	31453394	578	8795											
CCDC11	220136	hgsc.bcm.edu	37	chr18	47788544	47788544	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgatggctgcgtcggattcTttctagatggtgctcagctc	5	14	12	10	2	3	2	1	1	2	1	5	3	3	3	0	3	3	3	0	3	1	3	rs112087763	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:47788544T>G	ENST00000398545.4	-	2	232	c.115A>C	c.(115-117)Aga>Cga	p.R39R		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)		CGTCGGATTCTTTCTAGATGG	0.438													T|||	6	0.00119808	0.0	0.0014	5008	,	,		19087	0.0		0.004	False		,,,				2504	0.001				p.R39R		Atlas-SNP	.											.	CCDC11	59	.	0			c.A115C						PASS	.	T		1,3831		0,1,1915	113	108	109		115	4	0.2	18	dbSNP_132	109	24,8220		0,24,4098	no	coding-synonymous	CCDC11	NM_145020.3		0,25,6013	GG,GT,TT		0.2911,0.0261,0.207		39/515	47788544	25,12051	1916	4122	6038	SO:0001819	synonymous_variant	220136	exon2			GGATTCTTTCTAG																												ENST00000398545.4:c.115A>C	18.37:g.47788544T>G		74	0	0		100	52	0.52	NM_145020		Silent	SNP	ENST00000398545.4	37	CCDS11940.2																																																																																			T|0.997;G|0.003	0.003	strong		0.438	CCDC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255922.3			G	47788544	T	G	47788544	2	3	24	1	0	0	0	0	0	0	0	1	2748	1617	56	5		5	CCDC11	18	47788544	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	1164690	47788544	30288704	579	8796											
ALPK2	115701	hgsc.bcm.edu	37	chr18	56204417	56204417	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtcctcagtctccctggtcGcttgaaagcactcattatta	8	14	7	12	1	3	1	2	1	1	0	6	1	4	1	2	1	1	2	2	1	3	3			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:56204417G>A	ENST00000361673.3	-	5	3215	c.3002C>T	c.(3001-3003)gCg>gTg	p.A1001V	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1001						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						CTCCCTGGTCGCTTGAAAGCA	0.488																																					p.A1001V		Atlas-SNP	.											.	ALPK2	487	.	0			c.C3002T						PASS	.						111	96	101					18																	56204417		2203	4299	6502	SO:0001583	missense	115701	exon5			CTGGTCGCTTGAA	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.3002C>T	18.37:g.56204417G>A	ENSP00000354991:p.Ala1001Val	143	0	0		91	43	0.472527	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	.	.	.	.	.	.	.	.	.	.	G	1.106	-0.659520	0.03454	.	.	ENSG00000198796	ENST00000361673	T	0.37752	1.18	5.08	-2.78	0.05859	.	4.754620	0.00550	N	0.000240	T	0.07098	0.0180	N	0.00289	-1.7	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39722	-0.9600	10	0.02654	T	1	-3.639	1.1061	0.01694	0.3981:0.281:0.1835:0.1373	.	1001;1001	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	V	1001	ENSP00000354991:A1001V	ENSP00000354991:A1001V	A	-	2	0	ALPK2	54355397	0.000000	0.05858	0.001000	0.08648	0.019000	0.09904	0.073000	0.14640	-0.244000	0.09639	-0.383000	0.06682	GCG	.	.	none		0.488	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		A	56204417	G	A	56204417	3	1	24	1	0	0	0	0	1	0	0	0	545	1087	38	1	3546	1	ALPK2	18	56204417	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	8415873	56204417	21872831	580	8797											
DSEL	92126	hgsc.bcm.edu	37	chr18	65179657	65179657	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caaagccaccgaatcccagaTaattgaatcttgtcttcagg	13	10	7	11	1	3	2	1	1	2	1	4	3	4	2	3	1	1	0	3	1	4	4	rs12953840	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr18:65179657T>C	ENST00000310045.7	-	2	3692	c.2219A>G	c.(2218-2220)tAt>tGt	p.Y740C	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	730					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)				GAATCCCAGATAATTGAATCT	0.403													T|||	4	0.000798722	0.0008	0.0029	5008	,	,		18544	0.0		0.001	False		,,,				2504	0.0				p.Y740C		Atlas-SNP	.											.	DSEL	196	.	0			c.A2219G						PASS	.	T	CYS/TYR	3,4403	6.2+/-15.9	0,3,2200	52	54	53		2219	5.1	1	18	dbSNP_121	53	30,8570	21.6+/-65.8	1,28,4271	yes	missense	DSEL	NM_032160.2	194	1,31,6471	CC,CT,TT		0.3488,0.0681,0.2537	probably-damaging	740/1223	65179657	33,12973	2203	4300	6503	SO:0001583	missense	92126	exon2			CCCAGATAATTGA	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.2219A>G	18.37:g.65179657T>C	ENSP00000310565:p.Tyr740Cys	99	0	0		102	43	0.421569	NM_032160	Q17RH1|Q6P5Z3	Missense_Mutation	SNP	ENST00000310045.7	37	CCDS11995.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	T	15.14	2.743790	0.49151	6.81E-4	0.003488	ENSG00000171451	ENST00000310045;ENST00000397964	T	0.26373	1.74	5.09	5.09	0.68999	.	0.000000	0.64402	U	0.000002	T	0.44201	0.1282	M	0.70595	2.14	0.45806	D	0.99868	D	0.71674	0.998	P	0.60789	0.879	T	0.44406	-0.9330	10	0.87932	D	0	.	10.1284	0.42663	0.1494:0.0:0.0:0.8506	rs12953840;rs12953840	730	Q8IZU8	DSEL_HUMAN	C	740;730	ENSP00000310565:Y740C	ENSP00000310565:Y740C	Y	-	2	0	DSEL	63330637	1.000000	0.71417	0.986000	0.45419	0.966000	0.64601	5.986000	0.70563	2.060000	0.61445	0.374000	0.22700	TAT	T|0.998;C|0.002	0.002	strong		0.403	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160		C	65179657	T	C	65179657	3	2	24	1	0	0	0	0	1	0	0	0	4777	1406	49	3	1453	3	DSEL	18	65179657	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	8975240	65179657	12897591	581	8798											
RPS15	6209	hgsc.bcm.edu	37	chr19	1440374	1440374	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgatcggccactacctgggCgagttctccatcacctacaa	10	9	8	14	2	2	1	1	1	1	0	4	2	2	1	4	2	2	1	4	2	3	3	rs139332437	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:1440374C>T	ENST00000586686.2	+	4	390	c.351C>T	c.(349-351)ggC>ggT	p.G117G	RPS15_ENST00000589656.2_Silent_p.G113G|RPS15_ENST00000233609.4_Silent_p.G90G|RPS15_ENST00000591032.1_Silent_p.G84G|RPS15_ENST00000591804.2_Silent_p.G84G|RPS15_ENST00000593052.1_Silent_p.G124G|RPS15_ENST00000585665.1_Silent_p.G84G|RPS15_ENST00000586096.2_3'UTR|AC027307.3_ENST00000594262.1_5'Flank			P62841	RS15_HUMAN	ribosomal protein S15	117					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)|osteoblast differentiation (GO:0001649)|ribosomal small subunit biogenesis (GO:0042274)|ribosomal small subunit export from nucleus (GO:0000056)|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)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_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)|STAD - Stomach adenocarcinoma(1328;0.18)		ACTACCTGGGCGAGTTCTCCA	0.632													C|||	5	0.000998403	0.0008	0.0	5008	,	,		15262	0.0		0.004	False		,,,				2504	0.0				p.G117G	Ovarian(170;79 2680 5719 44260)	Atlas-SNP	.											.	RPS15	11	.	0			c.C351T						PASS	.	C		4,4402	8.1+/-20.4	0,4,2199	39	40	40		351	2.3	1	19	dbSNP_134	40	27,8571	18.5+/-59.3	0,27,4272	no	coding-synonymous	RPS15	NM_001018.3		0,31,6471	TT,TC,CC		0.314,0.0908,0.2384		117/146	1440374	31,12973	2203	4299	6502	SO:0001819	synonymous_variant	6209	exon4			CCTGGGCGAGTTC		CCDS12067.1	19p13.3	2012-12-20			ENSG00000115268	ENSG00000115268		"S ribosomal proteins"	10388	protein-coding gene	gene with protein product	"40S ribosomal protein S15", "homolog of rat insulinoma", "insulinoma protein"	180535				2159154	Standard	NM_001018		Approved	RIG, MGC111130, S15	uc002lsp.1	P62841	OTTHUMG00000140099	ENST00000586686.2:c.351C>T	19.37:g.1440374C>T		186	0	0		170	87	0.511765	NM_001018	A5D8V9|P11174|Q3KRA1|Q9UDC2	Silent	SNP	ENST00000586686.2	37	CCDS12067.1																																																																																			C|0.998;T|0.002	0.002	strong		0.632	RPS15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449609.4	NM_001018		T	1440374	C	T	1440374	2	4	24	1	0	0	0	0	0	0	0	1	13640	755	27	1		1	RPS15	19	1440374	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10		1440374	57688609	582	8799											
PCSK4	54760	hgsc.bcm.edu	37	chr19	1487059	1487059	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagagcgtgcccagcccgccGcggccctgggaaaccaggag	9	2	15	15	4	0	1	0	0	0	1	0	3	0	3	5	3	4	0	5	3	2	0			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:1487059G>T	ENST00000300954.5	-	8	922	c.861C>A	c.(859-861)cgC>cgA	p.R287R	PCSK4_ENST00000587784.1_5'Flank|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)		CCAGCCCGCCGCGGCCCTGGG	0.697																																					p.R287R		Atlas-SNP	.											.	PCSK4	44	.	0			c.C861A						PASS	.						28	29	29					19																	1487059		2199	4296	6495	SO:0001819	synonymous_variant	54760	exon8			CCCGCCGCGGCCC	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.861C>A	19.37:g.1487059G>T		17	0	0		21	15	0.714286	NM_017573		Silent	SNP	ENST00000300954.5	37	CCDS12069.2																																																																																			.	.	none		0.697	PCSK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449703.1	NM_017573		T	1487059	G	T	1487059	2	4	24	1	0	0	0	0	0	0	0	1	11611	1074	38	4		4	PCSK4	19	1487059	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	46685	1487059	57641924	583	8800											
DOT1L	84444	hgsc.bcm.edu	37	chr19	2222327	2222327	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcaccatcaccactggtgcGggcagtgccaagcagtcgcc	8	7	11	15	2	2	0	2	0	0	0	3	0	2	0	4	2	3	2	4	2	1	1	rs373960110		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2222327G>A	ENST00000398665.3	+	24	3195	c.3159G>A	c.(3157-3159)gcG>gcA	p.A1053A		NM_032482.2	NP_115871.1	Q8TEK3	DOT1L_HUMAN	DOT1-like histone H3K79 methyltransferase	1053					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)		CCACTGGTGCGGGCAGTGCCA	0.662																																					p.A1053A		Atlas-SNP	.											.	DOT1L	205	.	0			c.G3159A						PASS	.	G		0,4246		0,0,2123	26	32	30		3159	-8.4	0	19		30	1,8471		0,1,4235	no	coding-synonymous	DOT1L	NM_032482.2		0,1,6358	AA,AG,GG		0.0118,0.0,0.0079		1053/1538	2222327	1,12717	2123	4236	6359	SO:0001819	synonymous_variant	84444	exon24			TGGTGCGGGCAGT	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.3159G>A	19.37:g.2222327G>A		127	0	0		132	80	0.606061	NM_032482	O60379|Q96JL1	Silent	SNP	ENST00000398665.3	37	CCDS42460.1	.	.	.	.	.	.	.	.	.	.	G	0.204	-1.042205	0.01997	0.0	1.18E-4	ENSG00000104885	ENST00000440640	.	.	.	4.21	-8.42	0.00957	.	.	.	.	.	T	0.14657	0.0354	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.19257	-1.0311	4	.	.	.	-2.2	0.8379	0.01143	0.3872:0.2217:0.212:0.1791	.	.	.	.	Q	840	.	.	R	+	2	0	DOT1L	2173327	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.688000	0.05150	-1.857000	0.01159	-0.379000	0.06801	CGG	.	.	weak		0.662	DOT1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318066.1	NM_032482		A	2222327	G	A	2222327	2	1	24	1	0	0	0	0	0	0	0	1	4711	1103	39	1		1	DOT1L	19	2222327	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	735268	2222327	56906656	584	8801											
ZNF57	126295	hgsc.bcm.edu	37	chr19	2917178	2917178	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctcacacctacacagtcacGgaagaactgacactgaggag	14	5	9	13	1	2	3	2	2	0	1	2	5	2	5	2	2	2	0	2	2	3	1	rs61742111	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2917178G>A	ENST00000306908.5	+	4	707	c.559G>A	c.(559-561)Gga>Aga	p.G187R	ZNF57_ENST00000523428.1_Missense_Mutation_p.G155R|AC006277.2_ENST00000520090.2_RNA	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	187					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)		ACACAGTCACGGAAGAACTGA	0.498													G|||	131	0.0261581	0.0257	0.0288	5008	,	,		21208	0.001		0.0169	False		,,,				2504	0.0603				p.G187R	NSCLC(150;910 1964 4303 10464 26498)	Atlas-SNP	.											.	ZNF57	57	.	0			c.G559A						PASS	.	G	ARG/GLY	95,4311	77.3+/-115.6	0,95,2108	109	81	90		559	-3.2	0	19	dbSNP_129	90	209,8391	88.9+/-151.2	4,201,4095	yes	missense	ZNF57	NM_173480.2	125	4,296,6203	AA,AG,GG		2.4302,2.1562,2.3374	benign	187/556	2917178	304,12702	2203	4300	6503	SO:0001583	missense	126295	exon4			AGTCACGGAAGAA	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.559G>A	19.37:g.2917178G>A	ENSP00000303696:p.Gly187Arg	108	0	0		107	46	0.429907	NM_173480	Q8N6R9	Missense_Mutation	SNP	ENST00000306908.5	37	CCDS12098.1	41	0.018772893772893772	17	0.034552845528455285	13	0.03591160220994475	1	0.0017482517482517483	10	0.013192612137203167	G	11.69	1.714569	0.30413	0.021562	0.024302	ENSG00000171970	ENST00000306908;ENST00000395204;ENST00000523428	T;T	0.14144	2.53;2.53	1.7	-3.23	0.05109	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00666	0.0022	N	0.00599	-1.345	0.09310	N	1	B	0.17667	0.023	B	0.08055	0.003	T	0.39292	-0.9621	9	0.44086	T	0.13	.	3.5597	0.07877	0.3623:0.3552:0.2825:0.0	rs61742111	187	Q68EA5	ZNF57_HUMAN	R	187;189;155	ENSP00000303696:G187R;ENSP00000430223:G155R	ENSP00000303696:G187R	G	+	1	0	ZNF57	2868178	0.006000	0.16342	0.000000	0.03702	0.004000	0.04260	-0.336000	0.07863	-0.406000	0.07588	0.407000	0.27541	GGA	G|0.973;A|0.027	0.027	strong		0.498	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480		A	2917178	G	A	2917178	3	1	24	1	0	0	0	0	1	0	0	0	18016	1117	39	1	573	1	ZNF57	19	2917178	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	694851	2917178	56211805	585	8802			3	41		3	3	621	N	G_A	9.337408e-05
ZNF57	126295	hgsc.bcm.edu	37	chr19	2917509	2917509	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttacccccaggcttttcaaaGacatgagaagacgcacacgg	13	7	9	12	2	1	3	1	1	0	3	1	4	1	3	2	2	1	2	2	2	3	3	rs61754927	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2917509G>A	ENST00000306908.5	+	4	1038	c.890G>A	c.(889-891)aGa>aAa	p.R297K	ZNF57_ENST00000523428.1_Missense_Mutation_p.R265K|AC006277.2_ENST00000520090.2_RNA	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	297					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)		GCTTTTCAAAGACATGAGAAG	0.488													G|||	130	0.0259585	0.0257	0.0288	5008	,	,		19431	0.0		0.0169	False		,,,				2504	0.0603				p.R297K	NSCLC(150;910 1964 4303 10464 26498)	Atlas-SNP	.											.	ZNF57	57	.	0			c.G890A						PASS	.	G	LYS/ARG	95,4311	76.8+/-115.0	0,95,2108	74	80	78		890	-4.1	0	19	dbSNP_129	78	208,8392	88.1+/-150.5	4,200,4096	yes	missense	ZNF57	NM_173480.2	26	4,295,6204	AA,AG,GG		2.4186,2.1562,2.3297	benign	297/556	2917509	303,12703	2203	4300	6503	SO:0001583	missense	126295	exon4			TTCAAAGACATGA	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.890G>A	19.37:g.2917509G>A	ENSP00000303696:p.Arg297Lys	44	0	0		48	20	0.416667	NM_173480	Q8N6R9	Missense_Mutation	SNP	ENST00000306908.5	37	CCDS12098.1	40	0.018315018315018316	17	0.034552845528455285	13	0.03591160220994475	0	0.0	10	0.013192612137203167	G	2.867	-0.234775	0.05983	0.021562	0.024186	ENSG00000171970	ENST00000306908;ENST00000395204;ENST00000523428	T;T	0.02197	4.4;4.4	2.25	-4.14	0.03892	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00384	0.0012	L	0.31207	0.915	0.09310	N	1	B	0.33171	0.4	B	0.37943	0.261	T	0.41787	-0.9489	9	0.05721	T	0.95	.	0.9159	0.01304	0.2475:0.1759:0.3978:0.1788	rs61754927	297	Q68EA5	ZNF57_HUMAN	K	297;299;265	ENSP00000303696:R297K;ENSP00000430223:R265K	ENSP00000303696:R297K	R	+	2	0	ZNF57	2868509	0.000000	0.05858	0.001000	0.08648	0.558000	0.35554	-7.471000	0.00035	-1.087000	0.03081	0.511000	0.50034	AGA	G|0.974;A|0.026	0.026	strong		0.488	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480		A	2917509	G	A	2917509	3	1	24	1	0	0	0	0	1	0	0	0	18016	942	33	2	904	2	ZNF57	19	2917509	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	331	2917509	56211474	586	8803			3	41		3	3	621	N	G_A	9.337408e-05
ZNF57	126295	hgsc.bcm.edu	37	chr19	2917798	2917798	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acgcaagagcagctctataaAtgtgaacaatgtgggaaggc	15	7	12	7	1	1	2	0	1	1	1	1	3	1	3	0	2	3	3	0	2	7	2	rs61755868	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:2917798A>G	ENST00000306908.5	+	4	1327	c.1179A>G	c.(1177-1179)aaA>aaG	p.K393K	ZNF57_ENST00000523428.1_Silent_p.K361K|AC006277.2_ENST00000520090.2_RNA	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	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)			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)		AGCTCTATAAATGTGAACAAT	0.433													A|||	125	0.0249601	0.0219	0.0288	5008	,	,		22248	0.0		0.0169	False		,,,				2504	0.0603				p.K393K	NSCLC(150;910 1964 4303 10464 26498)	Atlas-SNP	.											.	ZNF57	57	.	0			c.A1179G						PASS	.	A		85,4321	71.4+/-109.4	0,85,2118	92	84	86		1179	-0.5	0	19	dbSNP_129	86	208,8392	88.6+/-150.9	4,200,4096	no	coding-synonymous	ZNF57	NM_173480.2		4,285,6214	GG,GA,AA		2.4186,1.9292,2.2528		393/556	2917798	293,12713	2203	4300	6503	SO:0001819	synonymous_variant	126295	exon4			CTATAAATGTGAA	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.1179A>G	19.37:g.2917798A>G		140	0	0		147	67	0.455782	NM_173480	Q8N6R9	Silent	SNP	ENST00000306908.5	37	CCDS12098.1																																																																																			A|0.975;G|0.025	0.025	strong		0.433	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480		G	2917798	A	G	2917798	2	3	24	1	0	0	0	0	0	0	0	1	18016	98	4	3		3	ZNF57	19	2917798	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	289	2917798	56211185	587	8804			3	41		3	3	621	N	G_A	9.337408e-05
APBA3	9546	hgsc.bcm.edu	37	chr19	3752601	3752601	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gatgctgagggcccccgagcGctcagcaggccccccgtgca	6	4	14	17	3	1	1	1	1	0	0	1	3	1	1	5	2	4	4	5	2	0	0	rs147130540	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:3752601G>A	ENST00000316757.3	-	8	1500	c.1300C>T	c.(1300-1302)Cgc>Tgc	p.R434C	AC005954.3_ENST00000591962.1_RNA|AC005954.4_ENST00000586503.1_RNA	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	434	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)		GCCCCCGAGCGCTCAGCAGGC	0.751													G|||	57	0.0113818	0.0083	0.0288	5008	,	,		13216	0.0		0.0199	False		,,,				2504	0.0061				p.R434C		Atlas-SNP	.											.	APBA3	28	.	0			c.C1300T						PASS	.	G	CYS/ARG	29,4221		0,29,2096	6	9	8		1300	4.2	0.9	19	dbSNP_134	8	160,8140		1,158,3991	yes	missense	APBA3	NM_004886.3	180	1,187,6087	AA,AG,GG		1.9277,0.6824,1.506	probably-damaging	434/576	3752601	189,12361	2125	4150	6275	SO:0001583	missense	9546	exon8			CCGAGCGCTCAGC	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.1300C>T	19.37:g.3752601G>A	ENSP00000315136:p.Arg434Cys	3	0	0		12	9	0.75	NM_004886	O60483|Q9UPZ2	Missense_Mutation	SNP	ENST00000316757.3	37	CCDS12110.1	28	0.01282051282051282	6	0.012195121951219513	8	0.022099447513812154	0	0.0	14	0.018469656992084433	G	14.60	2.583092	0.46006	0.006824	0.019277	ENSG00000011132	ENST00000316757	T	0.29655	1.56	4.21	4.21	0.49690	PDZ/DHR/GLGF (4);	0.000000	0.64402	D	0.000001	T	0.49660	0.1570	H	0.95574	3.69	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.72030	-0.4413	10	0.87932	D	0	.	12.3996	0.55405	0.0:0.0:0.8316:0.1684	.	434	O96018	APBA3_HUMAN	C	434	ENSP00000315136:R434C	ENSP00000315136:R434C	R	-	1	0	APBA3	3703601	1.000000	0.71417	0.911000	0.35937	0.297000	0.27493	1.807000	0.38902	1.894000	0.54839	0.462000	0.41574	CGC	G|0.987;A|0.013	0.013	strong		0.751	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2			A	3752601	G	A	3752601	3	1	24	1	0	0	0	0	1	0	0	0	758	1087	38	1	443	1	APBA3	19	3752601	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	834803	3752601	55376382	588	8805											
APBA3	9546	hgsc.bcm.edu	37	chr19	3760027	3760027	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	caatgtgtaggggacaggggGctccacctggggatgggccc	7	6	18	10	0	0	0	0	0	0	0	1	2	1	2	3	7	0	2	3	7	2	1	rs11556574	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:3760027G>A	ENST00000316757.3	-	2	436	c.236C>T	c.(235-237)gCc>gTc	p.A79V	MRPL54_ENST00000330133.4_5'Flank	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	79					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)		GGGACAGGGGGCTCCACCTGG	0.627													G|||	15	0.00299521	0.0008	0.0	5008	,	,		16690	0.0		0.0129	False		,,,				2504	0.001				p.A79V		Atlas-SNP	.											.	APBA3	28	.	0			c.C236T						PASS	.	G	VAL/ALA	7,4399	12.9+/-30.5	0,7,2196	39	42	41		236	-0.5	0	19	dbSNP_120	41	97,8503	51.9+/-112.3	0,97,4203	yes	missense	APBA3	NM_004886.3	64	0,104,6399	AA,AG,GG		1.1279,0.1589,0.7996	benign	79/576	3760027	104,12902	2203	4300	6503	SO:0001583	missense	9546	exon2			CAGGGGGCTCCAC	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.236C>T	19.37:g.3760027G>A	ENSP00000315136:p.Ala79Val	75	0	0		87	42	0.482759	NM_004886	O60483|Q9UPZ2	Missense_Mutation	SNP	ENST00000316757.3	37	CCDS12110.1	11	0.005036630036630037	1	0.0020325203252032522	0	0.0	0	0.0	10	0.013192612137203167	G	4.003	-0.002070	0.07819	0.001589	0.011279	ENSG00000011132	ENST00000316757	T	0.43688	0.94	4.73	-0.517	0.11947	.	1.883730	0.03191	N	0.173342	T	0.20495	0.0493	N	0.24115	0.695	0.09310	N	1	B	0.13594	0.008	B	0.14578	0.011	T	0.15607	-1.0431	10	0.33940	T	0.23	.	3.9246	0.09257	0.0925:0.2707:0.4794:0.1574	rs11556574	79	O96018	APBA3_HUMAN	V	79	ENSP00000315136:A79V	ENSP00000315136:A79V	A	-	2	0	APBA3	3711027	0.001000	0.12720	0.043000	0.18650	0.078000	0.17371	0.002000	0.13061	0.389000	0.25086	0.561000	0.74099	GCC	G|0.993;A|0.007	0.007	strong		0.627	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2			A	3760027	G	A	3760027	3	1	24	1	0	0	0	0	1	0	0	0	758	1203	42	2	1531	2	APBA3	19	3760027	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	7426	3760027	55368956	589	8806											
CREB3L3	84699	hgsc.bcm.edu	37	chr19	4159722	4159722	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gctgatccggtggacctgtcCccacgatgcaatctcaccgt	7	9	10	15	3	1	1	1	1	1	0	4	3	3	2	5	2	1	2	5	2	1	0	rs144868958	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:4159722C>T	ENST00000078445.2	+	4	666	c.519C>T	c.(517-519)tcC>tcT	p.S173S	CREB3L3_ENST00000602147.1_Silent_p.S173S|CREB3L3_ENST00000602257.1_Silent_p.S173S|CREB3L3_ENST00000595923.1_Silent_p.S172S|CREB3L3_ENST00000252587.3_Intron	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	173					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)		TGGACCTGTCCCCACGATGCA	0.632													C|||	3	0.000599042	0.0	0.0014	5008	,	,		17296	0.0		0.002	False		,,,				2504	0.0				p.S173S		Atlas-SNP	.											.	CREB3L3	53	.	0			c.C519T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	92	84	87		519	-6.4	0	19	dbSNP_134	87	22,8578	16.0+/-53.3	0,22,4278	no	coding-synonymous	CREB3L3	NM_032607.1		0,24,6479	TT,TC,CC		0.2558,0.0454,0.1845		173/462	4159722	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	84699	exon4			CCTGTCCCCACGA		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.519C>T	19.37:g.4159722C>T		41	0	0		66	30	0.454545	NM_001271997	B2R7S6|B7ZL69|M0QYW7|Q6ZMC5|Q96TB9	Silent	SNP	ENST00000078445.2	37	CCDS12121.1																																																																																			C|0.998;T|0.002	0.002	strong		0.632	CREB3L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457922.1	NM_032607		T	4159722	C	T	4159722	2	4	24	1	0	0	0	0	0	0	0	1	3860	610	22	2		2	CREB3L3	19	4159722	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	399695	4159722	54969261	590	8807											
EMR1	2015	hgsc.bcm.edu	37	chr19	6906469	6906469	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcttcaaatgtaaggaagaTgtgatacccgataataagca	16	10	8	7	1	2	2	1	1	1	1	2	4	2	3	1	1	2	2	1	1	6	5	rs78491083	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:6906469T>C	ENST00000312053.4	+	9	1012	c.975T>C	c.(973-975)gaT>gaC	p.D325D	EMR1_ENST00000381407.5_Silent_p.D184D|EMR1_ENST00000450315.3_Silent_p.D148D|EMR1_ENST00000381404.4_Silent_p.D273D|EMR1_ENST00000250572.8_Silent_p.D325D	NM_001974.4	NP_001965.3	Q14246	EMR1_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 1	325	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)					GTAAGGAAGATGTGATACCCG	0.383													T|||	20	0.00399361	0.0008	0.0058	5008	,	,		20677	0.0		0.0109	False		,,,				2504	0.0041				p.D325D		Atlas-SNP	.											EMR1,NS,carcinoma,+1,1	EMR1	153	1	0			c.T975C						PASS	.	T		11,4395	17.9+/-39.9	0,11,2192	143	136	138		975	-0.2	0.2	19	dbSNP_133	138	78,8522	46.3+/-105.2	1,76,4223	no	coding-synonymous	EMR1	NM_001974.3		1,87,6415	CC,CT,TT		0.907,0.2497,0.6843		325/887	6906469	89,12917	2203	4300	6503	SO:0001819	synonymous_variant	2015	exon9			GGAAGATGTGATA	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.975T>C	19.37:g.6906469T>C		254	0	0		259	130	0.50193	NM_001256253	A6NHV2|B7Z486|B7Z489|E7EPX9|E9PD45|H9KV79|Q2I7G5|Q6ZMN0|Q8NGA7	Silent	SNP	ENST00000312053.4	37	CCDS12175.1																																																																																			T|0.994;C|0.006	0.006	strong		0.383	EMR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458485.1			C	6906469	T	C	6906469	2	2	24	1	0	0	0	0	0	0	0	1	5106	1461	51	3		3	EMR1	19	6906469	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	2746747	6906469	52222514	591	8808											
FBN3	84467	hgsc.bcm.edu	37	chr19	8203392	8203392	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcgagtgtagtggccggcgaGgtctccagcacagcggcccc	6	5	16	14	4	1	0	0	0	1	0	2	2	1	0	4	4	2	2	4	4	1	1	rs61729623	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:8203392G>C	ENST00000600128.1	-	9	1336	c.922C>G	c.(922-924)Ctc>Gtc	p.L308V	FBN3_ENST00000270509.2_Missense_Mutation_p.L308V|FBN3_ENST00000601739.1_Missense_Mutation_p.L308V			Q75N90	FBN3_HUMAN	fibrillin 3	308	TB 2.					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						TGGCCGGCGAGGTCTCCAGCA	0.652													g|||	14	0.00279553	0.0015	0.0014	5008	,	,		15853	0.0		0.008	False		,,,				2504	0.0031				p.L308V		Atlas-SNP	.											.	FBN3	300	.	0			c.C922G						PASS	.		VAL/LEU	9,4393		0,9,2192	24	26	25		922	1.7	0	19	dbSNP_129	25	90,8510		0,90,4210	yes	missense	FBN3	NM_032447.3	32	0,99,6402	CC,CG,GG		1.0465,0.2045,0.7614	probably-damaging	308/2810	8203392	99,12903	2201	4300	6501	SO:0001583	missense	84467	exon8			CGGCGAGGTCTCC		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.922C>G	19.37:g.8203392G>C	ENSP00000470498:p.Leu308Val	99	0	0		79	37	0.468354	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	9	0.004120879120879121	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	g	10.79	1.450741	0.26074	0.002045	0.010465	ENSG00000142449	ENST00000270509	D	0.94828	-3.53	4.06	1.72	0.24424	Matrix fibril-associated (3);TGF-beta binding (1);	0.090982	0.45867	N	0.000325	D	0.87826	0.6275	M	0.65498	2.005	0.25192	N	0.990126	P	0.35192	0.489	B	0.30179	0.112	T	0.77624	-0.2518	10	0.20519	T	0.43	.	9.7313	0.40363	0.0:0.1538:0.6867:0.1595	rs61729623	308	Q75N90	FBN3_HUMAN	V	308	ENSP00000270509:L308V	ENSP00000270509:L308V	L	-	1	0	FBN3	8109392	0.994000	0.37717	0.001000	0.08648	0.000000	0.00434	1.255000	0.32909	0.235000	0.21160	-0.313000	0.08912	CTC	G|0.983;C|0.017	0.017	strong		0.652	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		C	8203392	G	C	8203392	3	2	24	1	0	0	0	0	1	0	0	0	5712	1000	35	4	7731	4	FBN3	19	8203392	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1296923	8203392	50925591	592	8809											
ZNF414	84330	hgsc.bcm.edu	37	chr19	8577924	8577924	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagatcacctggaggtgggCgtcgtctgggaggccgcagg	7	6	18	10	3	2	1	1	0	1	1	3	3	2	3	2	6	0	1	2	6	0	0			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:8577924C>T	ENST00000255616.8	-	2	406	c.305G>A	c.(304-306)cGc>cAc	p.R102H	ZNF414_ENST00000393927.4_Missense_Mutation_p.R102H	NM_032370.2	NP_115746.2	Q96IQ9	ZN414_HUMAN	zinc finger protein 414	102					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						TGGAGGTGGGCGTCGTCTGGG	0.617																																					p.R102H		Atlas-SNP	.											.	ZNF414	25	.	0			c.G305A						PASS	.						7	5	6					19																	8577924		1959	3887	5846	SO:0001583	missense	84330	exon2			GGTGGGCGTCGTC	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.305G>A	19.37:g.8577924C>T	ENSP00000255616:p.Arg102His	105	0	0		83	54	0.650602	NM_032370	A8MY94	Missense_Mutation	SNP	ENST00000255616.8	37	CCDS12205.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.302311	0.81136	.	.	ENSG00000133250	ENST00000393927;ENST00000255616	T;T	0.09817	2.94;2.94	4.52	3.4	0.38934	.	0.170242	0.37304	N	0.002141	T	0.23965	0.0580	L	0.61036	1.89	0.29293	N	0.869209	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.991	T	0.02893	-1.1097	10	0.15499	T	0.54	-24.3645	11.0252	0.47741	0.0:0.8107:0.1893:0.0	.	102;102	Q96IQ9;A8MY94	ZN414_HUMAN;.	H	102	ENSP00000377504:R102H;ENSP00000255616:R102H	ENSP00000255616:R102H	R	-	2	0	ZNF414	8483924	0.975000	0.34042	0.995000	0.50966	0.988000	0.76386	0.720000	0.25896	2.219000	0.72066	0.655000	0.94253	CGC	.	.	none		0.617	ZNF414-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000460199.2	NM_032370		T	8577924	C	T	8577924	3	4	24	1	0	0	0	0	1	0	0	0	17906	768	27	1	909	1	ZNF414	19	8577924	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	374532	8577924	50551059	593	8810											
MUC16	94025	hgsc.bcm.edu	37	chr19	9091771	9091771	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgctccctgtcatcaaggagCgggtgggagaagatgaccca	10	7	14	10	1	2	3	2	1	0	2	3	5	3	4	2	3	2	1	2	3	2	0	rs375862521		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9091771C>T	ENST00000397910.4	-	1	247	c.44G>A	c.(43-45)cGc>cAc	p.R15H		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	15	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						CATCAAGGAGCGGGTGGGAGA	0.532																																					p.R15H		Atlas-SNP	.											MUC16_ENST00000397910,NS,carcinoma,0,2	MUC16	4315	2	0			c.G44A						scavenged	.	C	HIS/ARG	1,4003		0,1,2001	76	73	74		44	-2.7	0	19		74	0,8326		0,0,4163	no	missense	MUC16	NM_024690.2	29	0,1,6164	TT,TC,CC		0.0,0.025,0.0081	benign	15/14508	9091771	1,12329	2002	4163	6165	SO:0001583	missense	94025	exon1			AAGGAGCGGGTGG	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.44G>A	19.37:g.9091771C>T	ENSP00000381008:p.Arg15His	153	1	0.00653595		144	62	0.430556	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	c	0.061	-1.224947	0.01530	2.5E-4	0.0	ENSG00000181143	ENST00000397910	T	0.02916	4.11	1.35	-2.7	0.06004	.	.	.	.	.	T	0.01421	0.0046	N	0.08118	0	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.47018	-0.9149	8	0.87932	D	0	.	0.3222	0.00305	0.1936:0.1814:0.2537:0.3713	.	15	B5ME49	.	H	15	ENSP00000381008:R15H	ENSP00000381008:R15H	R	-	2	0	MUC16	8952771	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.995000	0.00317	-2.527000	0.00494	-2.577000	0.00169	CGC	.	.	weak		0.532	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9091771	C	T	9091771	3	4	24	1	0	0	0	0	1	0	0	0	9982	768	27	1	43815	1	MUC16	19	9091771	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	513847	9091771	50037212	594	8811											
OR1M1	125963	hgsc.bcm.edu	37	chr19	9203994	9203994	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaaagccagagcaggagaCgcttctcttttccctgttct	10	11	9	11	1	2	3	0	0	2	3	4	4	3	3	2	1	2	3	2	1	2	4	rs61738474	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:9203994C>T	ENST00000429566.3	+	1	140	c.74C>T	c.(73-75)aCg>aTg	p.T25M		NM_001004456.1	NP_001004456.1	Q8NGA1	OR1M1_HUMAN	olfactory receptor, family 1, subfamily M, 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)	p.T25K(1)		breast(1)|endometrium(4)|large_intestine(3)|lung(17)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						GAGCAGGAGACGCTTCTCTTT	0.522													c|||	58	0.0115815	0.0424	0.0029	5008	,	,		16171	0.0		0.0	False		,,,				2504	0.0				p.T25M		Atlas-SNP	.											OR1M1,NS,carcinoma,0,1	OR1M1	52	1	1	Substitution - Missense(1)	lung(1)	c.C74T						PASS	.	C	MET/THR	169,4237	111.6+/-149.8	6,157,2040	116	98	104		74	2.4	0	19	dbSNP_129	104	2,8598	2.2+/-6.3	0,2,4298	yes	missense	OR1M1	NM_001004456.1	81	6,159,6338	TT,TC,CC		0.0233,3.8357,1.3148	probably-damaging	25/314	9203994	171,12835	2203	4300	6503	SO:0001583	missense	125963	exon1			AGGAGACGCTTCT		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.74C>T	19.37:g.9203994C>T	ENSP00000401966:p.Thr25Met	178	0	0		185	75	0.405405	NM_001004456	B9EHA6|Q6IFJ3|Q96R91	Missense_Mutation	SNP	ENST00000429566.3	37	CCDS32896.1	32	0.014652014652014652	32	0.06504065040650407	0	0.0	0	0.0	0	0.0	c	11.15	1.552933	0.27739	0.038357	2.33E-4	ENSG00000170929	ENST00000305465;ENST00000429566	T	0.00428	7.44	3.49	2.44	0.29823	.	2.059810	0.02106	N	0.054364	T	0.00039	0.0001	N	0.11789	0.175	0.09310	N	1	D	0.54047	0.964	P	0.44477	0.451	T	0.48525	-0.9028	10	0.62326	D	0.03	.	5.4607	0.16615	0.0:0.6579:0.0:0.3421	rs61738474	25	Q8NGA1	OR1M1_HUMAN	M	28;25	ENSP00000401966:T25M	ENSP00000303195:T28M	T	+	2	0	OR1M1	9064994	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-4.203000	0.00275	0.801000	0.34066	0.400000	0.26472	ACG	C|0.987;T|0.013	0.013	strong		0.522	OR1M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448993.1			T	9203994	C	T	9203994	3	4	24	1	0	0	0	0	1	0	0	0	10977	536	19	1	76	1	OR1M1	19	9203994	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	112223	9203994	49924989	595	8812											
ZNF653	115950	hgsc.bcm.edu	37	chr19	11598224	11598224	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	catggcacagggcacctcctCgcccagtccactgccgggga	7	5	12	17	2	0	0	0	0	0	0	3	1	2	1	5	4	1	2	5	4	0	0	rs74552618	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:11598224C>T	ENST00000293771.5	-	4	1190	c.1054G>A	c.(1054-1056)Gag>Aag	p.E352K	CTC-398G3.6_ENST00000585656.1_Intron	NM_138783.3	NP_620138.2	Q96CK0	ZN653_HUMAN	zinc finger protein 653	352					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)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	17						GGCACCTCCTCGCCCAGTCCA	0.652													C|||	29	0.00579073	0.0015	0.0043	5008	,	,		16677	0.001		0.0129	False		,,,				2504	0.0102				p.E352K	Pancreas(83;980 1446 4542 6441 43352)	Atlas-SNP	.											.	ZNF653	48	.	0			c.G1054A						PASS	.	C	LYS/GLU	5,4401	9.9+/-24.2	0,5,2198	63	52	56		1054	4.1	1	19	dbSNP_131	56	120,8480	62.4+/-124.4	1,118,4181	yes	missense	ZNF653	NM_138783.3	56	1,123,6379	TT,TC,CC		1.3953,0.1135,0.9611	benign	352/616	11598224	125,12881	2203	4300	6503	SO:0001583	missense	115950	exon4			CCTCCTCGCCCAG	AY072704	CCDS12261.1	19p13.2	2013-01-08						"Zinc fingers, C2H2-type"	25196	protein-coding gene	gene with protein product		611371				12477932	Standard	NM_138783		Approved	Zip67	uc002mrz.2	Q96CK0		ENST00000293771.5:c.1054G>A	19.37:g.11598224C>T	ENSP00000293771:p.Glu352Lys	39	0	0		40	15	0.375	NM_138783	Q96AS7	Missense_Mutation	SNP	ENST00000293771.5	37	CCDS12261.1	17	0.007783882783882784	1	0.0020325203252032522	2	0.0055248618784530384	1	0.0017482517482517483	13	0.017150395778364115	C	20.3	3.959028	0.74016	0.001135	0.013953	ENSG00000161914	ENST00000293771	T	0.15487	2.42	4.14	4.14	0.48551	.	0.057370	0.64402	D	0.000002	T	0.09774	0.0240	L	0.32530	0.975	0.54753	D	0.999987	D	0.62365	0.991	P	0.47402	0.546	T	0.01819	-1.1267	10	0.87932	D	0	-13.1491	15.5534	0.76170	0.0:1.0:0.0:0.0	.	352	Q96CK0	ZN653_HUMAN	K	352	ENSP00000293771:E352K	ENSP00000293771:E352K	E	-	1	0	ZNF653	11459224	0.994000	0.37717	0.996000	0.52242	0.730000	0.41778	3.644000	0.54381	2.002000	0.58637	0.462000	0.41574	GAG	C|0.991;T|0.009	0.009	strong		0.652	ZNF653-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458836.2	NM_138783		T	11598224	C	T	11598224	3	4	24	1	0	0	0	0	1	0	0	0	18081	893	31	1	817	1	ZNF653	19	11598224	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	2394230	11598224	47530759	596	8813											
ZSWIM4	65249	hgsc.bcm.edu	37	chr19	13919757	13919757	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agctactgtccaatggcggcTactacggggccagccagcag	9	6	13	13	2	0	0	0	0	0	0	1	0	1	0	3	4	6	3	3	4	4	3			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:13919757T>C	ENST00000254323.2	+	4	1009	c.820T>C	c.(820-822)Tac>Cac	p.Y274H	ZSWIM4_ENST00000440752.2_5'UTR	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	274							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)			CAATGGCGGCTACTACGGGGC	0.701																																					p.Y274H		Atlas-SNP	.											.	ZSWIM4	69	.	0			c.T820C						PASS	.						18	18	18					19																	13919757		2184	4276	6460	SO:0001583	missense	65249	exon4			GGCGGCTACTACG	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.820T>C	19.37:g.13919757T>C	ENSP00000254323:p.Tyr274His	96	0	0		77	4	0.0519481	NM_023072		Missense_Mutation	SNP	ENST00000254323.2	37	CCDS32924.1	.	.	.	.	.	.	.	.	.	.	T	14.41	2.527572	0.44969	.	.	ENSG00000132003	ENST00000254323	T	0.41400	1.0	4.07	3.03	0.35002	.	0.129202	0.33895	N	0.004453	T	0.38108	0.1028	M	0.68593	2.085	0.80722	D	1	B	0.02656	0.0	B	0.10450	0.005	T	0.20438	-1.0275	10	0.51188	T	0.08	-0.0495	6.9161	0.24361	0.0:0.1211:0.0:0.8789	.	274	Q9H7M6	ZSWM4_HUMAN	H	274	ENSP00000254323:Y274H	ENSP00000254323:Y274H	Y	+	1	0	ZSWIM4	13780757	1.000000	0.71417	1.000000	0.80357	0.342000	0.28953	4.760000	0.62235	0.456000	0.26937	0.155000	0.16302	TAC	.	.	none		0.701	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457457.1	XM_031342		C	13919757	T	C	13919757	3	2	24	1	0	0	0	0	1	0	0	0	18258	1522	53	3	834	3	ZSWIM4	19	13919757	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	2321533	13919757	45209226	597	8814											
C19orf57	79173	hgsc.bcm.edu	37	chr19	14000196	14000196	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gccccgggctcctggagaggGtcgtctgctatttctctgtg	3	12	14	12	2	2	1	0	0	2	1	5	2	3	1	3	3	1	2	3	3	1	2	rs61732721	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:14000196G>T	ENST00000586783.1	-	5	1472	c.1473C>A	c.(1471-1473)gaC>gaA	p.D491E	C19orf57_ENST00000591586.1_Intron|C19orf57_ENST00000346736.2_Missense_Mutation_p.D491E|C19orf57_ENST00000454313.1_Missense_Mutation_p.D491E			Q0VDD7	CS057_HUMAN	chromosome 19 open reading frame 57	491				D -> E (in Ref. 2; AAI19720). {ECO:0000305}.	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)			CCTGGAGAGGGTCGTCTGCTA	0.617													G|||	11	0.00219649	0.0	0.0029	5008	,	,		17053	0.0		0.008	False		,,,				2504	0.001				p.D491E		Atlas-SNP	.											.	C19orf57	34	.	0			c.C1473A						PASS	.	G	GLU/ASP	7,4399	12.9+/-30.5	0,7,2196	66	72	70		1473	1.3	0	19	dbSNP_129	70	85,8515	48.1+/-107.5	0,85,4215	yes	missense	C19orf57	NM_024323.3	45	0,92,6411	TT,TG,GG		0.9884,0.1589,0.7074	benign	491/638	14000196	92,12914	2203	4300	6503	SO:0001583	missense	79173	exon6			GAGAGGGTCGTCT	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.1473C>A	19.37:g.14000196G>T	ENSP00000465822:p.Asp491Glu	88	0	0		86	39	0.453488	NM_024323	Q13411|Q8N825|Q96D63|Q9BU49	Missense_Mutation	SNP	ENST00000586783.1	37		8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	G	12.21	1.868899	0.32977	0.001589	0.009884	ENSG00000132016	ENST00000454313;ENST00000346736	T;T	0.52057	0.68;0.68	4.73	1.32	0.21799	.	1.305730	0.05407	N	0.541685	T	0.25382	0.0617	N	0.19112	0.55	0.09310	N	1	B;B	0.15473	0.013;0.013	B;B	0.21917	0.025;0.037	T	0.26121	-1.0112	10	0.41790	T	0.15	-2.8432	5.2907	0.15725	0.3744:0.0:0.6256:0.0	.	491;491	Q0VDD7-2;Q0VDD7	.;CS057_HUMAN	E	491	ENSP00000404382:D491E;ENSP00000254336:D491E	ENSP00000254336:D491E	D	-	3	2	C19orf57	13861196	0.007000	0.16637	0.003000	0.11579	0.014000	0.08584	0.845000	0.27668	0.599000	0.29845	0.637000	0.83480	GAC	G|0.996;T|0.004	0.004	strong		0.617	C19orf57-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000457947.1	NM_024323		T	14000196	G	T	14000196	3	4	24	1	0	0	0	0	1	0	0	0	1941	1252	44	4	452	4	C19orf57	19	14000196	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	80439	14000196	45128787	598	8815											
CC2D1A	54862	hgsc.bcm.edu	37	chr19	14024269	14024269	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggcaatgccattgacgaagCggacatcccgccgccagtgg	9	5	14	13	4	0	1	0	1	0	0	1	3	1	2	4	3	2	1	4	3	2	1	rs61740117	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:14024269C>T	ENST00000318003.7	+	6	807	c.566C>T	c.(565-567)gCg>gTg	p.A189V	CC2D1A_ENST00000589606.1_Missense_Mutation_p.A189V	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	189					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)			ATTGACGAAGCGGACATCCCG	0.602													C|||	15	0.00299521	0.0	0.0029	5008	,	,		17181	0.0		0.0119	False		,,,				2504	0.001				p.A189V		Atlas-SNP	.											.	CC2D1A	67	.	0			c.C566T						PASS	.	C	VAL/ALA	7,4065		0,7,2029	35	44	41		566	-10.4	0	19	dbSNP_129	41	100,8246		0,100,4073	yes	missense	CC2D1A	NM_017721.4	64	0,107,6102	TT,TC,CC		1.1982,0.1719,0.8617	benign	189/952	14024269	107,12311	2036	4173	6209	SO:0001583	missense	54862	exon6			ACGAAGCGGACAT	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.566C>T	19.37:g.14024269C>T	ENSP00000313601:p.Ala189Val	87	0	0		107	56	0.523364	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Missense_Mutation	SNP	ENST00000318003.7	37	CCDS42512.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	C	10.62	1.400963	0.25291	0.001719	0.011982	ENSG00000132024	ENST00000318003;ENST00000254346;ENST00000389233	T	0.22539	1.95	5.2	-10.4	0.00318	Domain of unknown function DM14 (1);	0.466636	0.22488	N	0.059413	T	0.07279	0.0184	L	0.46157	1.445	0.24389	N	0.994752	P;P	0.37731	0.489;0.607	B;B	0.32724	0.151;0.143	T	0.01791	-1.1273	10	0.59425	D	0.04	-4.4191	6.3202	0.21213	0.5862:0.255:0.0806:0.0783	rs61740117	189;189	Q6P1N0-2;Q6P1N0	.;C2D1A_HUMAN	V	189;27;164	ENSP00000313601:A189V	ENSP00000254346:A27V	A	+	2	0	CC2D1A	13885269	0.983000	0.35010	0.037000	0.18230	0.014000	0.08584	0.328000	0.19681	-2.793000	0.00355	-1.555000	0.00892	GCG	C|0.995;T|0.005	0.005	strong		0.602	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721		T	14024269	C	T	14024269	3	4	24	1	0	0	0	0	1	0	0	0	2728	768	27	1	588	1	CC2D1A	19	14024269	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	24073	14024269	45104714	599	8816											
PGLYRP2	114770	hgsc.bcm.edu	37	chr19	15580694	15580694	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtgtgggcgcccacccagtGccagccgcgtccctcgtaca	5	6	12	18	5	0	0	0	0	0	0	2	0	1	0	5	1	3	1	5	1	1	1	rs61734899	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:15580694G>A	ENST00000340880.4	-	4	1870	c.1390C>T	c.(1390-1392)Cac>Tac	p.H464Y	PGLYRP2_ENST00000292609.4_Missense_Mutation_p.H464Y	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	464					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						CCCACCCAGTGCCAGCCGCGT	0.716													G|||	124	0.0247604	0.0484	0.0058	5008	,	,		13687	0.006		0.008	False		,,,				2504	0.0429				p.H464Y		Atlas-SNP	.											.	PGLYRP2	116	.	0			c.C1390T						PASS	.	G	TYR/HIS	161,4189		2,157,2016	11	15	14		1390	2.9	1	19	dbSNP_129	14	65,8451		0,65,4193	yes	missense	PGLYRP2	NM_052890.3	83	2,222,6209	AA,AG,GG		0.7633,3.7011,1.7566	benign	464/577	15580694	226,12640	2175	4258	6433	SO:0001583	missense	114770	exon4			CCCAGTGCCAGCC	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.1390C>T	19.37:g.15580694G>A	ENSP00000345968:p.His464Tyr	33	0	0		47	17	0.361702	NM_052890	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Missense_Mutation	SNP	ENST00000340880.4	37	CCDS12330.2	34	0.015567765567765568	21	0.042682926829268296	3	0.008287292817679558	2	0.0034965034965034965	8	0.010554089709762533	G	12.80	2.046263	0.36085	0.037011	0.007633	ENSG00000161031	ENST00000340880;ENST00000292609	T;T	0.17213	2.29;2.29	5.04	2.91	0.33838	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (4);	0.380248	0.27554	N	0.018848	T	0.03564	0.0102	M	0.66378	2.025	0.35512	D	0.80071	B;B	0.09022	0.001;0.002	B;B	0.13407	0.008;0.009	T	0.08249	-1.0731	10	0.35671	T	0.21	-13.9263	4.8686	0.13620	0.1811:0.0:0.6507:0.1682	.	464;464	Q96PD5-2;Q96PD5	.;PGRP2_HUMAN	Y	464	ENSP00000345968:H464Y;ENSP00000292609:H464Y	ENSP00000292609:H464Y	H	-	1	0	PGLYRP2	15441694	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	0.700000	0.25601	0.540000	0.28808	-0.448000	0.05591	CAC	G|0.983;A|0.017	0.017	strong		0.716	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890		A	15580694	G	A	15580694	3	1	24	1	0	0	0	0	1	0	0	0	11803	1319	46	2	348	2	PGLYRP2	19	15580694	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1556425	15580694	43548289	600	8817											
PGLYRP2	114770	hgsc.bcm.edu	37	chr19	15587103	15587103	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagccctgcctccagcccCgccagcagaggctccacagc	7	4	10	20	1	0	1	0	0	0	1	2	1	2	1	7	1	6	3	7	1	0	0	rs35973013	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:15587103C>T	ENST00000340880.4	-	2	858	c.378G>A	c.(376-378)gcG>gcA	p.A126A	PGLYRP2_ENST00000292609.4_Silent_p.A126A	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	126					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						CCTCCAGCCCCGCCAGCAGAG	0.607													C|||	123	0.0245607	0.0477	0.0058	5008	,	,		19723	0.006		0.008	False		,,,				2504	0.0429				p.A126A		Atlas-SNP	.											.	PGLYRP2	116	.	0			c.G378A						PASS	.	C		193,4213	120.4+/-158.0	3,187,2013	100	86	91		378	-10.3	0.1	19	dbSNP_126	91	75,8525	44.0+/-102.2	0,75,4225	no	coding-synonymous	PGLYRP2	NM_052890.3		3,262,6238	TT,TC,CC		0.8721,4.3804,2.0606		126/577	15587103	268,12738	2203	4300	6503	SO:0001819	synonymous_variant	114770	exon2			CAGCCCCGCCAGC	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.378G>A	19.37:g.15587103C>T		146	0	0		155	86	0.554839	NM_052890	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Silent	SNP	ENST00000340880.4	37	CCDS12330.2																																																																																			C|0.981;T|0.019	0.019	strong		0.607	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890		T	15587103	C	T	15587103	2	4	24	1	0	0	0	0	0	0	0	1	11803	639	23	1		1	PGLYRP2	19	15587103	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	6409	15587103	43541880	601	8818											
FAM125A	93343	hgsc.bcm.edu	37	chr19	17534540	17534540	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gcggacagcgtcaaggctggGctctcgggcatccactctgc	6	7	14	14	3	3	0	1	0	2	0	5	1	4	1	1	4	2	3	1	4	1	0	rs147706400	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:17534540G>T	ENST00000317040.7	+	6	1627	c.572G>T	c.(571-573)gGc>gTc	p.G191V	MVB12A_ENST00000543795.1_Missense_Mutation_p.G191V|MVB12A_ENST00000529939.1_Missense_Mutation_p.G191V|MVB12A_ENST00000392702.2_Missense_Mutation_p.G151V|MVB12A_ENST00000528515.1_Missense_Mutation_p.A149S|CTD-2521M24.6_ENST00000593957.1_RNA			Q96EY5	MB12A_HUMAN	multivesicular body subunit 12A	191					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)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ESCRT I complex (GO:0000813)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|vesicle (GO:0031982)	lipid binding (GO:0008289)|ubiquitin binding (GO:0043130)										TCAAGGCTGGGCTCTCGGGCA	0.622													G|||	4	0.000798722	0.0008	0.0014	5008	,	,		15707	0.0		0.001	False		,,,				2504	0.001				p.G191V		Atlas-SNP	.											.	.	.	.	0			c.G572T						PASS	.	G	VAL/GLY	3,4403		0,3,2200	56	56	56		572	5.1	1	19	dbSNP_134	56	7,8593		0,7,4293	yes	missense	FAM125A	NM_138401.2	109	0,10,6493	TT,TG,GG		0.0814,0.0681,0.0769	possibly-damaging	191/274	17534540	10,12996	2203	4300	6503	SO:0001583	missense	93343	exon6			GGCTGGGCTCTCG	BC011840	CCDS12359.1	19p13.11	2013-10-11	2012-12-03	2012-12-03	ENSG00000141971	ENSG00000141971			25153	protein-coding gene	gene with protein product			"family with sequence similarity 125, member A"	FAM125A		18005716, 20654576, 22232651	Standard	NM_138401		Approved	FLJ32495	uc002ngo.1	Q96EY5	OTTHUMG00000166252	ENST00000317040.7:c.572G>T	19.37:g.17534540G>T	ENSP00000324810:p.Gly191Val	86	0	0		65	37	0.569231	NM_138401	Q96I18	Missense_Mutation	SNP	ENST00000317040.7	37	CCDS12359.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	.|.	10.70|10.70	1.424914|1.424914	0.25639|0.25639	6.81E-4|6.81E-4	8.14E-4|8.14E-4	ENSG00000141971|ENSG00000141971	ENST00000528515|ENST00000528911;ENST00000528604;ENST00000317040;ENST00000392702;ENST00000529939;ENST00000543795	.|T;T;T;T;T	.|0.44482	.|0.94;0.96;1.02;0.92;0.96	5.1|5.1	5.1|5.1	0.69264|0.69264	.|.	.|0.319630	.|0.37483	.|N	.|0.002062	T|T	0.36441|0.36441	0.0967|0.0967	L|L	0.44542|0.44542	1.39|1.39	0.58432|0.58432	D|D	0.999998|0.999998	.|P	.|0.37914	.|0.611	.|B	.|0.35114	.|0.196	T|T	0.34601|0.34601	-0.9822|-0.9822	6|10	0.54805|0.66056	T|D	0.06|0.02	-28.1606|-28.1606	14.0584|14.0584	0.64784|0.64784	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|191	.|Q96EY5	.|F125A_HUMAN	S|V	149|99;52;191;151;191;191	.|ENSP00000433280:G99V;ENSP00000324810:G191V;ENSP00000376466:G151V;ENSP00000432526:G191V;ENSP00000444653:G191V	ENSP00000433677:A149S|ENSP00000324810:G191V	A|G	+|+	1|2	0|0	FAM125A|FAM125A	17395540|17395540	0.998000|0.998000	0.40836|0.40836	0.978000|0.978000	0.43139|0.43139	0.183000|0.183000	0.23260|0.23260	4.163000|4.163000	0.58183|0.58183	2.371000|2.371000	0.80710|0.80710	0.558000|0.558000	0.71614|0.71614	GCT|GGC	G|0.999;T|0.001	0.001	strong		0.622	MVB12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388723.2	NM_138401		T	17534540	G	T	17534540	3	4	24	1	0	0	0	0	1	0	0	0	5432	1203	42	4	594	4	FAM125A	19	17534540	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1947437	17534540	41594443	602	8819											
FAM129C	199786	hgsc.bcm.edu	37	chr19	17638144	17638144	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggagccccgggagacgacAgcagcatgggtgggcggcct	8	3	19	11	3	0	1	0	0	0	1	0	5	0	2	3	5	3	2	3	5	0	0	rs200304763	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:17638144A>C	ENST00000335393.4	+	2	226	c.88A>C	c.(88-90)Agc>Cgc	p.S30R	FAM129C_ENST00000300971.2_Missense_Mutation_p.S30R|FAM129C_ENST00000599124.1_5'UTR|FAM129C_ENST00000599164.1_5'UTR|FAM129C_ENST00000352727.3_Missense_Mutation_p.S30R|FAM129C_ENST00000332386.5_Missense_Mutation_p.S30R|FAM129C_ENST00000597887.1_3'UTR|FAM129C_ENST00000449408.2_5'UTR|FAM129C_ENST00000595684.1_Missense_Mutation_p.S30R|FAM129C_ENST00000601861.1_5'UTR|FAM129C_ENST00000600871.1_5'UTR	NM_173544.4	NP_775815	Q86XR2	NIBL2_HUMAN	family with sequence similarity 129, member C	30										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						GGGAGACGACAGCAGCATGGG	0.692													A|||	7	0.00139776	0.0	0.0014	5008	,	,		11745	0.0		0.0	False		,,,				2504	0.0061				p.S30R		Atlas-SNP	.											.	FAM129C	110	.	0			c.A88C						PASS	.	A	ARG/SER,ARG/SER	0,4044		0,0,2022	25	21	23		88,88	-3.7	0	19		23	1,7935		0,1,3967	yes	missense,missense	FAM129C	NM_001098524.1,NM_173544.4	110,110	0,1,5989	CC,CA,AA		0.0126,0.0,0.0083	probably-damaging,probably-damaging	30/652,30/698	17638144	1,11979	2022	3968	5990	SO:0001583	missense	199786	exon2			GACGACAGCAGCA	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.88A>C	19.37:g.17638144A>C	ENSP00000335040:p.Ser30Arg	194	0	0		208	89	0.427885	NM_001098524	B4DNU3|B4DVN7|Q7Z6H6|Q86XR3|Q86XR4|Q8TEQ3	Missense_Mutation	SNP	ENST00000335393.4	37	CCDS12362.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	A	15.73	2.920339	0.52653	0.0	1.26E-4	ENSG00000167483	ENST00000335393;ENST00000332386;ENST00000352727;ENST00000300971	T;T;T;T	0.26810	1.93;2.03;1.71;1.72	3.98	-3.67	0.04476	.	0.829479	0.10133	N	0.711885	T	0.13756	0.0333	L	0.51422	1.61	0.19300	N	0.999979	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.23048	-1.0199	10	0.39692	T	0.17	.	6.6521	0.22967	0.3189:0.1624:0.5187:0.0	.	30;30	Q86XR2;Q86XR2-3	NIBL2_HUMAN;.	R	30	ENSP00000335040:S30R;ENSP00000333447:S30R;ENSP00000341067:S30R;ENSP00000300971:S30R	ENSP00000300971:S30R	S	+	1	0	FAM129C	17499144	0.004000	0.15560	0.001000	0.08648	0.023000	0.10783	-0.012000	0.12699	-0.984000	0.03507	-0.415000	0.06103	AGC	A|0.998;C|0.002	0.002	strong		0.692	FAM129C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464206.1	NM_173544		C	17638144	A	C	17638144	3	2	24	1	0	0	0	0	1	0	0	0	5443	188	7	5	94	5	FAM129C	19	17638144	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	103604	17638144	41490839	603	8820											
KLHL26	55295	hgsc.bcm.edu	37	chr19	18779113	18779113	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagatgcagtctccgcgcacCgccgtgcgctcggatgtgcc	5	7	14	15	6	1	1	0	0	1	1	3	3	1	2	4	1	3	3	4	1	0	0	rs17852385	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:18779113C>T	ENST00000300976.4	+	3	996	c.906C>T	c.(904-906)acC>acT	p.T302T	KLHL26_ENST00000599006.1_Intron	NM_018316.1	NP_060786.1	Q53HC5	KLH26_HUMAN	kelch-like family member 26	302										breast(1)|central_nervous_system(1)|kidney(1)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						CTCCGCGCACCGCCGTGCGCT	0.657													C|||	81	0.0161741	0.003	0.0288	5008	,	,		16478	0.0		0.0477	False		,,,				2504	0.0092				p.T302T		Atlas-SNP	.											.	KLHL26	43	.	0			c.C906T						PASS	.	C		39,4351		0,39,2156	42	44	43		906	-10.1	0	19	dbSNP_123	43	461,8099		12,437,3831	no	coding-synonymous	KLHL26	NM_018316.1		12,476,5987	TT,TC,CC		5.3855,0.8884,3.861		302/616	18779113	500,12450	2195	4280	6475	SO:0001819	synonymous_variant	55295	exon3			GCGCACCGCCGTG		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.906C>T	19.37:g.18779113C>T		30	0	0		37	25	0.675676	NM_018316	Q8TAP0|Q9NUX3	Silent	SNP	ENST00000300976.4	37	CCDS12384.1																																																																																			C|0.969;T|0.031	0.031	strong		0.657	KLHL26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465145.1	NM_018316		T	18779113	C	T	18779113	2	4	24	1	0	0	0	0	0	0	0	1	8390	639	23	1		1	KLHL26	19	18779113	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1140969	18779113	40349870	604	8821											
COMP	1311	hgsc.bcm.edu	37	chr19	18896823	18896823	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caccaggcggcagttgtcccGactgtcagggactccgtcat	7	8	12	14	3	2	0	2	0	0	0	4	2	4	1	3	3	0	2	3	3	0	1			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:18896823G>A	ENST00000222271.2	-	13	1485	c.1441C>T	c.(1441-1443)Cgg>Tgg	p.R481W	COMP_ENST00000542601.2_Missense_Mutation_p.R448W|COMP_ENST00000425807.1_Missense_Mutation_p.R428W	NM_000095.2	NP_000086.2	P49747	COMP_HUMAN	cartilage oligomeric matrix protein	481					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						CAGTTGTCCCGACTGTCAGGG	0.701																																					p.R481W		Atlas-SNP	.											.	COMP	62	.	0			c.C1441T						PASS	.						46	37	40					19																	18896823		2203	4300	6503	SO:0001583	missense	1311	exon13			TGTCCCGACTGTC	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.1441C>T	19.37:g.18896823G>A	ENSP00000222271:p.Arg481Trp	58	0	0		49	22	0.44898	NM_000095	B4DKJ3|O14592|Q16388|Q16389|Q2NL86|Q8N4T2	Missense_Mutation	SNP	ENST00000222271.2	37	CCDS12385.1	.	.	.	.	.	.	.	.	.	.	G	18.61	3.660379	0.67586	.	.	ENSG00000105664	ENST00000542601;ENST00000222271;ENST00000425807;ENST00000454701	D;D;D	0.98362	-4.89;-4.89;-4.89	4.05	2.98	0.34508	.	0.243213	0.29133	U	0.013053	D	0.97901	0.9310	M	0.82716	2.605	0.37365	D	0.911397	P;P	0.47409	0.895;0.799	P;P	0.48114	0.469;0.567	D	0.98175	1.0454	10	0.72032	D	0.01	-29.5678	11.6098	0.51053	0.0:0.0:0.8201:0.1798	.	428;481	B4DKJ3;P49747	.;COMP_HUMAN	W	448;481;428;468	ENSP00000439156:R448W;ENSP00000222271:R481W;ENSP00000403792:R428W	ENSP00000222271:R481W	R	-	1	2	COMP	18757823	0.001000	0.12720	0.993000	0.49108	0.590000	0.36582	1.014000	0.29950	0.670000	0.31165	0.491000	0.48974	CGG	.	.	none		0.701	COMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403457.1	NM_000095		A	18896823	G	A	18896823	3	1	24	1	0	0	0	0	1	0	0	0	3726	1057	37	1	860	1	COMP	19	18896823	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	117710	18896823	40232160	605	8822											
LPAR2	9170	hgsc.bcm.edu	37	chr19	19737992	19737992	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtcagccccagtgccaccacGaccacatccttgggccgcca	8	5	9	19	2	1	0	1	0	0	0	2	1	2	0	8	1	2	0	8	1	0	1	rs150741448	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:19737992G>A	ENST00000542587.1	-	5	1004	c.102C>T	c.(100-102)gtC>gtT	p.V34V	LPAR2_ENST00000586703.1_Silent_p.V34V|LPAR2_ENST00000407877.3_Silent_p.V34V|LPAR2_ENST00000589311.1_5'Flank			Q9HBW0	LPAR2_HUMAN	lysophosphatidic acid receptor 2	34					activation of MAPK activity (GO:0000187)|activation of phospholipase C activity (GO:0007202)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of Rho protein signal transduction (GO:0035025)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|lysophosphatidic acid receptor activity (GO:0070915)			breast(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|urinary_tract(1)	10						GTGCCACCACGACCACATCCT	0.592													G|||	7	0.00139776	0.0	0.0029	5008	,	,		18269	0.0		0.005	False		,,,				2504	0.0				p.V34V		Atlas-SNP	.											.	LPAR2	28	.	0			c.C102T						PASS	.	G		4,4400	6.2+/-15.9	0,4,2198	33	32	33		102	-8.9	0.4	19	dbSNP_134	33	39,8561	24.0+/-70.4	0,39,4261	no	coding-synonymous	LPAR2	NM_004720.5		0,43,6459	AA,AG,GG		0.4535,0.0908,0.3307		34/352	19737992	43,12961	2202	4300	6502	SO:0001819	synonymous_variant	9170	exon2			CACCACGACCACA	AF011466	CCDS12407.1	19p12	2012-08-08	2008-04-11	2008-04-11		ENSG00000064547		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	3168	protein-coding gene	gene with protein product		605110	"endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 4"	EDG4		9525886, 9804623	Standard	NM_004720		Approved	EDG-4, LPA2	uc002nnb.4	Q9HBW0		ENST00000542587.1:c.102C>T	19.37:g.19737992G>A		59	0	0		63	29	0.460317	NM_004720	O00543|O43431	Silent	SNP	ENST00000542587.1	37	CCDS12407.1																																																																																			G|0.997;A|0.003	0.003	strong		0.592	LPAR2-003	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460544.1	NM_004720		A	19737992	G	A	19737992	2	1	24	1	0	0	0	0	0	0	0	1	8914	1045	37	1		1	LPAR2	19	19737992	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	841169	19737992	39390991	606	8823											
ZNF101	94039	hgsc.bcm.edu	37	chr19	19790690	19790690	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcagttgttccagttcccttCacagacatgaaagaactcat	12	12	6	11	0	3	3	3	1	0	2	5	3	5	3	2	0	1	3	2	0	2	4	rs35358946	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:19790690C>T	ENST00000592502.1	+	4	1002	c.892C>T	c.(892-894)Cac>Tac	p.H298Y	ZNF101_ENST00000444249.2_3'UTR|ZNF101_ENST00000415784.2_Missense_Mutation_p.H178Y			Q8IZC7	ZN101_HUMAN	zinc finger protein 101	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)			breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)	17						CAGTTCCCTTCACAGACATGA	0.453													C|||	29	0.00579073	0.0008	0.0115	5008	,	,		19424	0.0		0.007	False		,,,				2504	0.0133				p.H298Y		Atlas-SNP	.											.	ZNF101	43	.	0			c.C892T						PASS	.	C	TYR/HIS	8,4398	12.9+/-30.5	0,8,2195	48	46	47		892	0.2	0	19	dbSNP_126	47	63,8537	38.8+/-94.9	1,61,4238	yes	missense	ZNF101	NM_033204.2	83	1,69,6433	TT,TC,CC		0.7326,0.1816,0.5459	benign	298/437	19790690	71,12935	2203	4300	6503	SO:0001583	missense	94039	exon4			TCCCTTCACAGAC	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.892C>T	19.37:g.19790690C>T	ENSP00000468049:p.His298Tyr	39	0	0		50	23	0.46	NM_033204	C9JU83|Q0VDG9	Missense_Mutation	SNP	ENST00000592502.1	37	CCDS32971.1	11	0.005036630036630037	0	0.0	4	0.011049723756906077	0	0.0	7	0.009234828496042216	C	4.392	0.072382	0.08436	0.001816	0.007326	ENSG00000181896	ENST00000318110;ENST00000415440;ENST00000415784	T;T	0.27557	1.66;1.66	0.235	0.235	0.15431	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07098	0.0180	N	0.04245	-0.25	0.09310	N	0.999997	B	0.33940	0.433	B	0.29663	0.105	T	0.21042	-1.0257	8	.	.	.	.	3.123	0.06397	0.4753:0.5244:1.0E-4:1.0E-4	rs35358946;rs35358946	298	Q8IZC7	ZN101_HUMAN	Y	298;298;178	ENSP00000319716:H298Y;ENSP00000400952:H178Y	.	H	+	1	0	ZNF101	19651690	0.000000	0.05858	0.047000	0.18901	0.047000	0.14425	-0.669000	0.05262	0.308000	0.22923	0.313000	0.20887	CAC	C|0.994;T|0.006	0.006	strong		0.453	ZNF101-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460559.1	NM_033204		T	19790690	C	T	19790690	3	4	24	1	0	0	0	0	1	0	0	0	17729	826	29	2	906	2	ZNF101	19	19790690	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	52698	19790690	39338293	607	8824											
TSHZ3	57616	hgsc.bcm.edu	37	chr19	31768890	31768890	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atggcatgaaagtttgtcttGggcatgggggacgtctggct	7	12	16	6	1	2	1	0	1	2	0	2	2	2	2	0	5	0	4	0	5	1	2	rs138330927	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:31768890G>A	ENST00000240587.4	-	2	2136	c.1809C>T	c.(1807-1809)ccC>ccT	p.P603P		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	603					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)					AGTTTGTCTTGGGCATGGGGG	0.547													G|||	3	0.000599042	0.0	0.0	5008	,	,		17796	0.0		0.003	False		,,,				2504	0.0				p.P603P		Atlas-SNP	.											.	TSHZ3	549	.	0			c.C1809T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	91	99	96		1809	3.1	1	19	dbSNP_134	96	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	TSHZ3	NM_020856.2		0,7,6496	AA,AG,GG		0.0698,0.0227,0.0538		603/1082	31768890	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	57616	exon2			TGTCTTGGGCATG	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.1809C>T	19.37:g.31768890G>A		262	1	0.00381679		244	108	0.442623	NM_020856	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																			G|0.999;A|0.001	0.001	strong		0.547	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		A	31768890	G	A	31768890	2	1	24	1	0	0	0	0	0	0	0	1	16640	1335	47	2		2	TSHZ3	19	31768890	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	11978200	31768890	27360093	608	8825											
NUDT19	390916	hgsc.bcm.edu	37	chr19	33200275	33200275	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatcatcttgttaactgctgAtgggatggtccatcttttac	8	16	9	8	0	3	1	1	1	2	0	4	3	4	2	1	2	3	2	1	2	2	4	rs371226805		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:33200275A>T	ENST00000397061.3	+	2	899	c.899A>T	c.(898-900)gAt>gTt	p.D300V		NM_001105570.1	NP_001099040.1	A8MXV4	NUD19_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 19	300						mitochondrion (GO:0005739)|peroxisome (GO:0005777)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)			endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	8	Esophageal squamous(110;0.137)					TTAACTGCTGATGGGATGGTC	0.473																																					p.D300V		Atlas-SNP	.											.	NUDT19	15	.	0			c.A899T						PASS	.	A	VAL/ASP	0,3924		0,0,1962	145	132	136		899	4.9	1	19		136	3,8289		0,3,4143	no	missense	NUDT19	NM_001105570.1	152	0,3,6105	TT,TA,AA		0.0362,0.0,0.0246	probably-damaging	300/376	33200275	3,12213	1962	4146	6108	SO:0001583	missense	390916	exon2			CTGCTGATGGGAT		CCDS42543.1	19q13.11	2011-11-16			ENSG00000213965	ENSG00000213965		"Nudix motif containing"	32036	protein-coding gene	gene with protein product							Standard	NM_001105570		Approved	RP2	uc010edf.3	A8MXV4		ENST00000397061.3:c.899A>T	19.37:g.33200275A>T	ENSP00000380251:p.Asp300Val	96	0	0		107	55	0.514019	NM_001105570		Missense_Mutation	SNP	ENST00000397061.3	37	CCDS42543.1	.	.	.	.	.	.	.	.	.	.	A	19.01	3.743338	0.69418	0.0	3.62E-4	ENSG00000213965	ENST00000397061	T	0.53206	0.63	4.88	4.88	0.63580	.	0.252366	0.32719	U	0.005722	T	0.67655	0.2916	M	0.80746	2.51	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.72384	-0.4310	10	0.87932	D	0	-10.9605	11.1678	0.48554	1.0:0.0:0.0:0.0	.	300	A8MXV4	NUD19_HUMAN	V	300	ENSP00000380251:D300V	ENSP00000380251:D300V	D	+	2	0	NUDT19	37892115	1.000000	0.71417	0.981000	0.43875	0.072000	0.16883	4.851000	0.62896	1.948000	0.56530	0.482000	0.46254	GAT	.	.	weak		0.473	NUDT19-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000450338.3	XM_372723		T	33200275	A	T	33200275	3	4	24	1	0	0	0	0	1	0	0	0	10745	333	12	5	905	5	NUDT19	19	33200275	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	1431385	33200275	25928708	609	8826											
ZNF570	148268	hgsc.bcm.edu	37	chr19	37976121	37976123	+	In_Frame_Del	DEL	CAC	CAC	-																															caccacccaacccagtcaatCaccaagtcctatagatcctg																										TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	CAC	CAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:37976121_37976123delCAC	ENST00000330173.1	+	5	2126_2128	c.1597_1599delCAC	c.(1597-1599)cacdel	p.H533del	ZNF570_ENST00000388801.3_In_Frame_Del_p.H330del|CTD-2086O20.3_ENST00000591976.1_lincRNA|ZNF570_ENST00000586475.1_In_Frame_Del_p.H589del	NM_144694.1	NP_653295.1	Q96NI8	ZN570_HUMAN	zinc finger protein 570	533					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(6)|lung(12)|ovary(1)|prostate(1)|skin(1)	27			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			cccagtcaatcaccaagtcctat	0.404																																					p.532_533del		Pindel,Atlas-Indel	.											ZNF570,NS,carcinoma,+2,1	ZNF570	58	1	0			c.1596_1598del						PASS	.																																			SO:0001651	inframe_deletion	148268	exon5			.	AK055353	CCDS12504.1, CCDS74355.1	19q13.12	2013-09-20			ENSG00000171827	ENSG00000171827		"Zinc fingers, C2H2-type", "-"	26416	protein-coding gene	gene with protein product							Standard	XM_005258567		Approved	FLJ30791	uc002ogk.1	Q96NI8	OTTHUMG00000048176	ENST00000330173.1:c.1597_1599delCAC	19.37:g.37976121_37976123delCAC	ENSP00000331540:p.His533del	80	0	.		81	25	0.309	NM_144694	A1L472|B4DMP1	In_Frame_Del	DEL	ENST00000330173.1	37	CCDS12504.1																																																																																			.	.	none		0.404	ZNF570-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109600.1	NM_144694		-	37976123	CAC	-	37976121	7	5	24	1	0	1	0	1	0	0	0	0	18017	826	29	0	1611	0	ZNF570	19	37976121	In_Frame_Del	DEL	CAC	TCGA-G8-6326-01A-11D-2210-10	4775846	37976121	21152862	610	8827											
CAPN12	147968	hgsc.bcm.edu	37	chr19	39229075	39229075	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacctgtcgctccaggccccCgtccactccacgcagcccca	6	5	7	23	3	0	0	0	0	0	0	4	0	3	0	8	1	1	2	8	1	0	0	rs201486563	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:39229075C>T	ENST00000328867.4	-	7	1181	c.873G>A	c.(871-873)acG>acA	p.T291T	CAPN12_ENST00000601953.1_Silent_p.T142T|CTD-2540F13.2_ENST00000602255.1_RNA	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	291	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)			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)			TCCAGGCCCCCGTCCACTCCA	0.697													C|||	2	0.000399361	0.0008	0.0014	5008	,	,		14837	0.0		0.0	False		,,,				2504	0.0				p.T291T		Atlas-SNP	.											.	CAPN12	43	.	0			c.G873A						PASS	.	C		1,4399	2.1+/-5.4	0,1,2199	29	32	31		873	-7.4	0.5	19		31	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	CAPN12	NM_144691.3		0,2,6497	TT,TC,CC		0.0116,0.0227,0.0154		291/720	39229075	2,12996	2200	4299	6499	SO:0001819	synonymous_variant	147968	exon7			GGCCCCCGTCCAC	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.873G>A	19.37:g.39229075C>T		41	0	0		41	16	0.390244	NM_144691		Silent	SNP	ENST00000328867.4	37	CCDS12519.1																																																																																			C|1.000;T|0.000	0.000	strong		0.697	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1			T	39229075	C	T	39229075	2	4	24	1	0	0	0	0	0	0	0	1	2627	639	23	1		1	CAPN12	19	39229075	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1252954	39229075	19899908	611	8828											
PAPL	390928	hgsc.bcm.edu	37	chr19	39589191	39589191	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgtcggggcccctgccccTccgcgcccagggcaccttcg	2	5	13	21	5	0	0	0	0	0	0	3	0	1	0	8	3	1	1	8	3	0	1	rs566749338		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:39589191T>A	ENST00000331256.5	+	3	489	c.215T>A	c.(214-216)cTc>cAc	p.L72H	PAPL_ENST00000594229.1_Missense_Mutation_p.L72H	NM_001004318.2	NP_001004318.2	Q6ZNF0	PAPL_HUMAN		72						extracellular region (GO:0005576)	acid phosphatase activity (GO:0003993)|metal ion binding (GO:0046872)										CCCCTGCCCCTCCGCGCCCAG	0.642													t|||	1	0.000199681	0.0	0.0	5008	,	,		13097	0.0		0.001	False		,,,				2504	0.0				p.L72H		Atlas-SNP	.											.	.	.	.	0			c.T215A						PASS	.						35	33	34					19																	39589191		2203	4300	6503	SO:0001583	missense	0	exon3			TGCCCCTCCGCGC																												ENST00000331256.5:c.215T>A	19.37:g.39589191T>A	ENSP00000327557:p.Leu72His	48	0	0		41	25	0.609756	NM_001004318	B2RN68	Missense_Mutation	SNP	ENST00000331256.5	37	CCDS33018.1	.	.	.	.	.	.	.	.	.	.	T	1.006	-0.689462	0.03328	.	.	ENSG00000183760	ENST00000331256	D	0.82711	-1.64	5.2	4.19	0.49359	Purple acid phosphatase-like, N-terminal (1);Purple acid phosphatase, N-terminal (1);	0.743246	0.12988	N	0.422733	T	0.73273	0.3566	L	0.39245	1.2	0.09310	N	1	B	0.12013	0.005	B	0.12156	0.007	T	0.56613	-0.7950	10	0.14252	T	0.57	-12.7226	8.4714	0.32988	0.0:0.0927:0.0:0.9073	.	72	Q6ZNF0	PAPL_HUMAN	H	72	ENSP00000327557:L72H	ENSP00000327557:L72H	L	+	2	0	AC011443.1	44281031	0.001000	0.12720	0.249000	0.24280	0.063000	0.16089	0.986000	0.29590	1.956000	0.56807	0.533000	0.62120	CTC	.	.	none		0.642	PAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463810.1			A	39589191	T	A	39589191	3	1	24	1	0	0	0	0	1	0	0	0	11436	1551	54	5	221	5	PAPL	19	39589191	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	360116	39589191	19539792	612	8829											
PAK4	10298	hgsc.bcm.edu	37	chr19	39663757	39663757	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cccagggaaggcaggcagccGaggccggttcgccggtcaca	8	3	16	14	4	1	0	1	0	0	0	2	2	1	1	4	6	1	3	4	6	1	1	rs56099436	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:39663757G>A	ENST00000593690.1	+	5	831	c.404G>A	c.(403-405)cGa>cAa	p.R135Q	PAK4_ENST00000321944.4_Intron|PAK4_ENST00000599386.1_Intron|PAK4_ENST00000358301.3_Missense_Mutation_p.R135Q|PAK4_ENST00000599470.1_Intron|PAK4_ENST00000435673.2_Missense_Mutation_p.R135Q|PAK4_ENST00000360442.3_Missense_Mutation_p.R135Q	NM_001014831.2	NP_001014831.1	O96013	PAK4_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 4	135	Linker.		R -> Q (in dbSNP:rs56099436). {ECO:0000269|PubMed:17344846}.		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)			GCAGGCAGCCGAGGCCGGTTC	0.736													g|||	34	0.00678914	0.0008	0.0115	5008	,	,		10680	0.0		0.0189	False		,,,				2504	0.0061				p.R135Q		Atlas-SNP	.											.	PAK4	40	.	0			c.G404A						PASS	.		GLN/ARG,GLN/ARG,,,GLN/ARG	13,3671		0,13,1829	3	4	4		404,404,,,404	1.7	0	19	dbSNP_129	4	147,7075		0,147,3464	no	missense,missense,intron,intron,missense	PAK4	NM_001014831.2,NM_001014832.1,NM_001014834.2,NM_001014835.1,NM_005884.3	43,43,,,43	0,160,5293	AA,AG,GG		2.0354,0.3529,1.4671	possibly-damaging,possibly-damaging,,,possibly-damaging	135/592,135/592,,,135/592	39663757	160,10746	1842	3611	5453	SO:0001583	missense	10298	exon3			GCAGCCGAGGCCG	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.404G>A	19.37:g.39663757G>A	ENSP00000469413:p.Arg135Gln	10	0	0		10	8	0.8	NM_001014832	B4DGG6|Q8N4E1|Q8NCH5|Q8NDE3|Q9BU33|Q9ULS8	Missense_Mutation	SNP	ENST00000593690.1	37	CCDS12528.1	25	0.011446886446886446	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	15	0.01978891820580475	G	0.017	-1.510561	0.00984	0.003529	0.020354	ENSG00000130669	ENST00000358301;ENST00000435673;ENST00000360442	T;T;T	0.71103	-0.54;-0.54;-0.54	3.9	1.73	0.24493	.	1.445110	0.04338	N	0.353591	T	0.32734	0.0839	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21075	-1.0256	10	0.12430	T	0.62	.	7.4578	0.27276	0.3592:0.0:0.6408:0.0	rs56099436	135	O96013	PAK4_HUMAN	Q	135	ENSP00000351049:R135Q;ENSP00000392753:R135Q;ENSP00000353625:R135Q	ENSP00000351049:R135Q	R	+	2	0	PAK4	44355597	0.000000	0.05858	0.026000	0.17262	0.011000	0.07611	0.293000	0.19029	-0.014000	0.14175	-1.157000	0.01802	CGA	G|0.989;A|0.011	0.011	strong		0.736	PAK4-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463823.1			A	39663757	G	A	39663757	3	1	24	1	0	0	0	0	1	0	0	0	11412	1058	37	1	410	1	PAK4	19	39663757	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	74566	39663757	19465226	613	8830											
ZNF780B	163131	hgsc.bcm.edu	37	chr19	40540812	40540812	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttgaacaaggtttgagacacGattaaaggacttcccacatt	14	11	8	8	1	0	2	0	2	0	1	1	5	1	3	1	2	1	1	1	2	4	5	rs115484124	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:40540812G>A	ENST00000434248.1	-	5	2019	c.1954C>T	c.(1954-1956)Cgt>Tgt	p.R652C	ZNF780B_ENST00000221355.6_Missense_Mutation_p.R504C	NM_001005851.2	NP_001005851.1	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	652					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)					TTTGAGACACGATTAAAGGAC	0.403													g|||	156	0.0311502	0.0666	0.0101	5008	,	,		22218	0.0069		0.0089	False		,,,				2504	0.046				p.R652C		Atlas-SNP	.											ZNF780B_ENST00000434248,NS,carcinoma,+1,2	ZNF780B	143	2	0			c.C1954T						PASS	.	G	CYS/ARG	266,4134	138.8+/-174.5	5,256,1939	169	182	178		1954	-1.2	0	19	dbSNP_132	178	57,8543	35.9+/-90.5	1,55,4244	no	missense	ZNF780B	NM_001005851.2	180	6,311,6183	AA,AG,GG		0.6628,6.0455,2.4846	benign	652/834	40540812	323,12677	2200	4300	6500	SO:0001583	missense	163131	exon5			AGACACGATTAAA	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.1954C>T	19.37:g.40540812G>A	ENSP00000391641:p.Arg652Cys	113	0	0		118	54	0.457627	NM_001005851	B9EH00	Missense_Mutation	SNP	ENST00000434248.1	37	CCDS46077.1	52	0.023809523809523808	34	0.06910569105691057	6	0.016574585635359115	5	0.008741258741258742	7	0.009234828496042216	g	8.444	0.851485	0.17034	0.060455	0.006628	ENSG00000128000	ENST00000434248;ENST00000221355	T;T	0.16073	2.37;2.37	2.56	-1.21	0.09524	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00695	0.0023	N	0.25957	0.775	0.09310	N	1	B	0.14012	0.009	B	0.06405	0.002	T	0.33214	-0.9877	9	0.33141	T	0.24	.	6.8154	0.23826	0.3924:0.0:0.6076:0.0	.	652	Q9Y6R6	Z780B_HUMAN	C	652;504	ENSP00000391641:R652C;ENSP00000221355:R504C	ENSP00000221355:R504C	R	-	1	0	ZNF780B	45232652	0.000000	0.05858	0.001000	0.08648	0.172000	0.22775	-1.463000	0.02361	-0.088000	0.12506	-0.448000	0.05591	CGT	G|0.979;A|0.021	0.021	strong		0.403	ZNF780B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338466.1	NM_001005851		A	40540812	G	A	40540812	3	1	24	1	0	0	0	0	1	0	0	0	18168	1058	37	1	551	1	ZNF780B	19	40540812	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	877055	40540812	18588171	614	8831											
ZNF780A	284323	hgsc.bcm.edu	37	chr19	40580426	40580426	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttccacattccttacattcaAgatgccttctcacctgtgtg	8	15	5	13	0	2	1	2	0	1	1	5	1	4	1	4	0	2	0	4	0	2	5	rs399405	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:40580426A>G	ENST00000595687.2	-	6	2132	c.1923T>C	c.(1921-1923)tcT>tcC	p.S641S	ZNF780A_ENST00000594395.1_Silent_p.S642S|ZNF780A_ENST00000450241.2_Silent_p.S607S|ZNF780A_ENST00000455521.1_Silent_p.S642S|ZNF780A_ENST00000414720.2_Intron|AC005614.5_ENST00000595508.1_RNA|ZNF780A_ENST00000340963.5_Silent_p.S641S	NM_001010880.2	NP_001010880.2	O75290	Z780A_HUMAN	zinc finger protein 780A	641					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)					CTTACATTCAAGATGCCTTCT	0.418													a|||	547	0.109225	0.3449	0.0403	5008	,	,		22537	0.0069		0.0109	False		,,,				2504	0.046				p.S642S		Atlas-SNP	.											.	ZNF780A	156	.	0			c.T1926C						PASS	.	A	,,,	1370,3036	454.7+/-350.8	220,930,1053	153	148	150		1923,1926,1923,	-2.3	0	19	dbSNP_80	150	68,8532	41.7+/-99.0	1,66,4233	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	ZNF780A	NM_001010880.2,NM_001142577.1,NM_001142578.1,NM_001142579.1	,,,	221,996,5286	GG,GA,AA		0.7907,31.094,11.0564	,,,	641/642,642/643,641/642,	40580426	1438,11568	2203	4300	6503	SO:0001819	synonymous_variant	284323	exon6			CATTCAAGATGCC	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.1923T>C	19.37:g.40580426A>G		190	0	0		199	90	0.452261	NM_001142577	E9PB48|Q6ZN87	Silent	SNP	ENST00000595687.2	37	CCDS33026.2																																																																																			A|0.899;G|0.101	0.101	strong		0.418	ZNF780A-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000470066.1	NM_001010880		G	40580426	A	G	40580426	2	3	24	1	0	0	0	0	0	0	0	1	18167	59	3	3		3	ZNF780A	19	40580426	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	39614	40580426	18548557	615	8832											
CNTD2	79935	hgsc.bcm.edu	37	chr19	40732484	40732484	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gcaaaggagagggcctggggGcccagcgcctaacgataggc	10	3	17	11	2	0	1	0	0	0	1	0	3	0	1	3	5	2	1	3	5	3	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:40732484G>T	ENST00000430325.2	-	1	113	c.65C>A	c.(64-66)gCc>gAc	p.A22D	CNTD2_ENST00000433940.1_Missense_Mutation_p.A22D|CNTD2_ENST00000513948.1_5'Flank	NM_024877.3	NP_079153.2	Q9H8S5	CNTD2_HUMAN	cyclin N-terminal domain containing 2	22					regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)					lung(1)|prostate(1)	2						GGGCCTGGGGGCCCAGCGCCT	0.711																																					p.A22D		Atlas-SNP	.											.	CNTD2	22	.	0			c.C65A						PASS	.						7	10	9					19																	40732484		2153	4229	6382	SO:0001583	missense	79935	exon1			CTGGGGGCCCAGC	AK023327	CCDS12551.1, CCDS12551.2	19q13.2	2014-07-03				ENSG00000105219			25805	protein-coding gene	gene with protein product	"cyclin P"					11237006	Standard	NM_024877		Approved	FLJ13265, CCNP	uc010xvi.2	Q9H8S5		ENST00000430325.2:c.65C>A	19.37:g.40732484G>T	ENSP00000396755:p.Ala22Asp	69	0	0		73	40	0.547945	NM_024877	B4DX65	Missense_Mutation	SNP	ENST00000430325.2	37	CCDS12551.2	.	.	.	.	.	.	.	.	.	.	G	2.608	-0.291537	0.05568	.	.	ENSG00000105219	ENST00000430325;ENST00000433940	T	0.34859	1.34	2.44	-0.257	0.12979	.	3.315080	0.01764	N	0.030742	T	0.22085	0.0532	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.10268	-1.0637	9	0.22706	T	0.39	.	4.6612	0.12643	0.1483:0.0:0.6432:0.2085	.	22	B4DX65	.	D	22	ENSP00000396755:A22D	ENSP00000221818:A22D	A	-	2	0	CNTD2	45424324	0.011000	0.17503	0.000000	0.03702	0.002000	0.02628	0.152000	0.16302	-0.034000	0.13713	-1.134000	0.01955	GCC	.	.	none		0.711	CNTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360785.1	NM_024877		T	40732484	G	T	40732484	3	4	24	1	0	0	0	0	1	0	0	0	3638	1203	42	4	878	4	CNTD2	19	40732484	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	152058	40732484	18396499	616	8833											
ATP5SL	55101	hgsc.bcm.edu	37	chr19	41944270	41944270	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccactgccgcacccaggcgaTggatgcccctgatacgccca	8	5	10	18	3	0	1	0	1	0	0	0	3	0	2	6	2	3	1	6	2	1	1	rs2231939	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:41944270T>C	ENST00000221943.9	-	2	73	c.68A>G	c.(67-69)cAt>cGt	p.H23R	ATP5SL_ENST00000597457.1_Missense_Mutation_p.H23R|ATP5SL_ENST00000590641.2_Missense_Mutation_p.H29R|ATP5SL_ENST00000589970.1_Missense_Mutation_p.H23R|ATP5SL_ENST00000301183.11_Missense_Mutation_p.H29R|ATP5SL_ENST00000417807.3_Missense_Mutation_p.H29R|ATP5SL_ENST00000438807.3_Missense_Mutation_p.H23R|ATP5SL_ENST00000592922.2_Missense_Mutation_p.H23R|ATP5SL_ENST00000595425.1_Missense_Mutation_p.H23R	NM_018035.2	NP_060505.2	Q9NW81	AT5SL_HUMAN	ATP5S-like	23			H -> R (in dbSNP:rs2231939). {ECO:0000269|PubMed:14702039}.			mitochondrion (GO:0005739)				breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(2)|stomach(1)	11						ACCCAGGCGATGGATGCCCCT	0.602													T|||	10	0.00199681	0.0	0.0058	5008	,	,		18463	0.0		0.004	False		,,,				2504	0.002				p.H29R		Atlas-SNP	.											.	ATP5SL	20	.	0			c.A86G						PASS	.	T	ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS	6,4400	11.4+/-27.6	0,6,2197	80	73	76		86,86,68,68,68,68	-1.9	0	19	dbSNP_98	76	95,8505	52.7+/-113.3	0,95,4205	yes	missense,missense,missense,missense,missense,missense	ATP5SL	NM_001167867.1,NM_001167868.1,NM_001167869.1,NM_001167870.1,NM_001167871.1,NM_018035.2	29,29,29,29,29,29	0,101,6402	CC,CT,TT		1.1047,0.1362,0.7766	benign,benign,benign,benign,benign,benign	29/264,29/192,23/186,23/159,23/231,23/258	41944270	101,12905	2203	4300	6503	SO:0001583	missense	55101	exon2			AGGCGATGGATGC	AK001103	CCDS33032.1, CCDS54269.1, CCDS54270.1, CCDS54271.1, CCDS59389.1, CCDS59390.1	19q13.2	2007-12-13				ENSG00000105341			25496	protein-coding gene	gene with protein product						12477932	Standard	NM_001167867		Approved	FLJ10241	uc002oqv.3	Q9NW81		ENST00000221943.9:c.68A>G	19.37:g.41944270T>C	ENSP00000221943:p.His23Arg	96	0	0		109	51	0.46789	NM_001167867	B4DDC0|B4DMZ4|B4DP55|B4DXE8|F5H4W7|K7EMF6|Q96D43	Missense_Mutation	SNP	ENST00000221943.9	37	CCDS33032.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	T	4.961	0.178467	0.09443	0.001362	0.011047	ENSG00000105341	ENST00000221943;ENST00000438807;ENST00000417807;ENST00000301183;ENST00000507129	T;T;T;T	0.21191	3.29;2.07;3.26;2.02	3.28	-1.89	0.07689	.	0.628545	0.14348	N	0.325281	T	0.04998	0.0134	N	0.04705	-0.18	0.09310	N	1	B;B;B;B;B;B	0.09022	0.001;0.001;0.002;0.001;0.001;0.001	B;B;B;B;B;B	0.08055	0.002;0.001;0.001;0.003;0.003;0.003	T	0.40384	-0.9566	10	0.10377	T	0.69	-11.0354	8.2202	0.31537	0.0:0.6733:0.0:0.3267	rs2231939;rs2231939	29;29;23;23;23;29	B4DFT4;B4DDC0;Q9NW81-2;E9PDC6;Q9NW81;F5H4W7	.;.;.;.;AT5SL_HUMAN;.	R	23;23;29;29;99	ENSP00000221943:H23R;ENSP00000397413:H23R;ENSP00000403910:H29R;ENSP00000301183:H29R	ENSP00000221943:H23R	H	-	2	0	ATP5SL	46636110	0.101000	0.21875	0.002000	0.10522	0.018000	0.09664	0.329000	0.19698	-0.358000	0.08162	-0.250000	0.11733	CAT	T|0.996;C|0.004	0.004	strong		0.602	ATP5SL-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460602.1	NM_018035		C	41944270	T	C	41944270	3	2	24	1	0	0	0	0	1	0	0	0	1164	1464	51	3	725	3	ATP5SL	19	41944270	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	1211786	41944270	17184713	617	8834											
PHLDB3	653583	hgsc.bcm.edu	37	chr19	43990438	43990438	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cgtgatggcaggaacagcagGgcctgaggaaccttccgtgc	9	6	15	11	2	0	2	0	2	0	0	1	4	1	4	3	4	4	2	3	4	2	1	rs201337364		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:43990438G>A	ENST00000292140.5	-	13	1825	c.1465C>T	c.(1465-1467)Cct>Tct	p.P489S		NM_198850.3	NP_942147.3	Q6NSJ2	PHLB3_HUMAN	pleckstrin homology-like domain, family B, member 3	489							enzyme binding (GO:0019899)			breast(1)|central_nervous_system(1)|lung(5)	7		Prostate(69;0.0153)				GGAACAGCAGGGCCTGAGGAA	0.582																																					p.P489S		Atlas-SNP	.											.	PHLDB3	30	.	0			c.C1465T						PASS	.	G	SER/PRO	0,4164		0,0,2082	53	68	63		1465	-2.1	0	19		63	4,8378		0,4,4187	yes	missense	PHLDB3	NM_198850.3	74	0,4,6269	AA,AG,GG		0.0477,0.0,0.0319	possibly-damaging	489/641	43990438	4,12542	2082	4191	6273	SO:0001583	missense	653583	exon13			CAGCAGGGCCTGA		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.1465C>T	19.37:g.43990438G>A	ENSP00000292140:p.Pro489Ser	38	0	0		30	15	0.5	NM_198850	Q8N7Z4	Missense_Mutation	SNP	ENST00000292140.5	37	CCDS12621.2	.	.	.	.	.	.	.	.	.	.	G	6.513	0.462872	0.12402	0.0	4.77E-4	ENSG00000176531	ENST00000292140	T	0.45276	0.9	4.29	-2.07	0.07276	.	2.063540	0.02567	N	0.097370	T	0.27419	0.0673	L	0.29908	0.895	0.09310	N	1	B;B	0.14438	0.006;0.01	B;B	0.10450	0.005;0.003	T	0.07616	-1.0763	10	0.17369	T	0.5	.	3.9887	0.09527	0.4359:0.1828:0.3813:0.0	.	193;489	B2RXH3;Q6NSJ2	.;PHLB3_HUMAN	S	489	ENSP00000292140:P489S	ENSP00000292140:P489S	P	-	1	0	PHLDB3	48682278	0.668000	0.27493	0.028000	0.17463	0.253000	0.25986	0.582000	0.23834	-0.045000	0.13468	-0.385000	0.06624	CCT	.	.	weak		0.582	PHLDB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319643.2			A	43990438	G	A	43990438	3	1	24	1	0	0	0	0	1	0	0	0	11862	1232	43	2	473	2	PHLDB3	19	43990438	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	2046168	43990438	15138545	618	8835											
ZNF230	7773	hgsc.bcm.edu	37	chr19	44514422	44514422	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcattctgtgtccttataggCggcaagactattgcggaagc	9	12	11	9	2	2	1	1	0	1	1	3	2	3	2	1	3	2	1	1	3	5	5	rs146185685		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:44514422C>T	ENST00000429154.2	+	5	459	c.231C>T	c.(229-231)ggC>ggT	p.G77G		NM_006300.3	NP_006291.2	Q9UIE0	ZN230_HUMAN	zinc finger protein 230	77					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)				TCCTTATAGGCGGCAAGACTA	0.428													c|||	1	0.000199681	0.0	0.0	5008	,	,		19264	0.0		0.0	False		,,,				2504	0.001				p.G77G	GBM(175;914 2069 22996 47111 52600)	Atlas-SNP	.											.	ZNF230	44	.	0			c.C231T						PASS	.	T		7,4399	12.9+/-30.5	0,7,2196	51	49	50		231	-2.3	0	19	dbSNP_134	50	0,8600		0,0,4300	yes	coding-synonymous-near-splice	ZNF230	NM_006300.3		0,7,6496	TT,TC,CC		0.0,0.1589,0.0538		77/475	44514422	7,12999	2203	4300	6503	SO:0001630	splice_region_variant	7773	exon5			TATAGGCGGCAAG	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.230-1C>T	19.37:g.44514422C>T		95	0	0		84	40	0.47619	NM_006300	O15322|Q504X7|Q86W84|Q9P1U6	Silent	SNP	ENST00000429154.2	37	CCDS33044.1																																																																																			C|1.000;T|0.000	0.000	weak		0.428	ZNF230-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460456.1		Silent	T	44514422	C	T	44514422	5	4	24	1	0	0	0	0	0	0	1	0	17799	782	27	1	245	1	ZNF230	19	44514422	Splice_Site	SNP	C	TCGA-G8-6326-01A-11D-2210-10	523984	44514422	14614561	619	8836											
ZNF222	7673	hgsc.bcm.edu	37	chr19	44536397	44536397	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagctcacgtctgcaaacTcatcaaagagtccacactgg	13	7	8	13	1	4	2	3	0	1	2	5	2	5	2	1	1	3	2	1	1	2	0	rs151037918	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:44536397T>C	ENST00000187879.8	+	4	732	c.570T>C	c.(568-570)acT>acC	p.T190T	ZNF223_ENST00000591793.1_Intron|ZNF222_ENST00000391960.3_Silent_p.T230T	NM_013360.2	NP_037492.2	Q9UK12	ZN222_HUMAN	zinc finger protein 222	190					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)				GTCTGCAAACTCATCAAAGAG	0.428													T|||	12	0.00239617	0.0008	0.0029	5008	,	,		21542	0.0		0.008	False		,,,				2504	0.001				p.T230T		Atlas-SNP	.											.	ZNF222	90	.	0			c.T690C						PASS	.	T	,	9,4397	15.5+/-35.6	0,9,2194	135	138	137		690,570	0.3	0	19	dbSNP_134	137	59,8541	36.9+/-92.0	0,59,4241	no	coding-synonymous,coding-synonymous	ZNF222	NM_001129996.1,NM_013360.2	,	0,68,6435	CC,CT,TT		0.686,0.2043,0.5228	,	230/492,190/452	44536397	68,12938	2203	4300	6503	SO:0001819	synonymous_variant	7673	exon4			GCAAACTCATCAA	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.570T>C	19.37:g.44536397T>C		143	0	0		124	62	0.5	NM_001129996	G5E9B9|Q8N6G7|Q9P1U5	Silent	SNP	ENST00000187879.8	37	CCDS33045.1																																																																																			T|0.996;C|0.004	0.004	strong		0.428	ZNF222-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000460465.2			C	44536397	T	C	44536397	2	2	24	1	0	0	0	0	0	0	0	1	17791	1538	54	3		3	ZNF222	19	44536397	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	21975	44536397	14592586	620	8837											
EXOC3L2	90332	hgsc.bcm.edu	37	chr19	45716364	45716364	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcgcgctagagacggaggcCggggccgaggcagacaggcc	8	2	19	12	5	0	2	0	0	0	2	1	5	0	3	3	6	0	2	3	6	1	1	rs189063316	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:45716364C>T	ENST00000252482.3	-	9	1220	c.1193G>A	c.(1192-1194)cGg>cAg	p.R398Q	EXOC3L2_ENST00000413988.1_Missense_Mutation_p.R398Q|AC006126.3_ENST00000591569.1_Intron			Q2M3D2	EX3L2_HUMAN	exocyst complex component 3-like 2	398					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)		AGACGGAGGCCGGGGCCGAGG	0.687													C|||	43	0.00858626	0.0	0.0043	5008	,	,		13018	0.0		0.0199	False		,,,				2504	0.0204				p.R398Q		Atlas-SNP	.											EXOC3L2,NS,lymphoid_neoplasm,0,1	EXOC3L2	30	1	0			c.G1193A						scavenged	.	C	GLN/ARG	13,4303		0,13,2145	8	10	9		1193	1.3	0.1	19		9	108,8370		1,106,4132	no	missense	EXOC3L2	NM_138568.3	43	1,119,6277	TT,TC,CC		1.2739,0.3012,0.9458	possibly-damaging	398/410	45716364	121,12673	2158	4239	6397	SO:0001583	missense	90332	exon10			GGAGGCCGGGGCC	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.1193G>A	19.37:g.45716364C>T	ENSP00000252482:p.Arg398Gln	26	0	0		29	18	0.62069	NM_138568	Q8N9W2|Q96GV2	Missense_Mutation	SNP	ENST00000252482.3	37	CCDS12657.1	17	0.007783882783882784	0	0.0	3	0.008287292817679558	0	0.0	14	0.018469656992084433	C	15.67	2.903346	0.52333	0.003012	0.012739	ENSG00000130201	ENST00000252482;ENST00000413988	T;T	0.15718	2.4;2.4	3.52	1.26	0.21427	.	0.302293	0.21905	U	0.067396	T	0.03651	0.0104	L	0.27053	0.805	0.09310	N	1	P	0.34629	0.46	B	0.23419	0.046	T	0.24154	-1.0168	10	0.54805	T	0.06	.	4.0747	0.09899	0.0:0.6097:0.249:0.1413	.	398	Q2M3D2	EX3L2_HUMAN	Q	398	ENSP00000252482:R398Q;ENSP00000400713:R398Q	ENSP00000252482:R398Q	R	-	2	0	EXOC3L2	50408204	0.077000	0.21312	0.112000	0.21494	0.386000	0.30323	0.957000	0.29215	0.444000	0.26612	0.305000	0.20034	CGG	C|0.992;T|0.008	0.008	strong		0.687	EXOC3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338073.1	NM_138568		T	45716364	C	T	45716364	3	4	24	1	0	0	0	0	1	0	0	0	5307	652	23	1	40	1	EXOC3L2	19	45716364	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1179967	45716364	13412619	621	8838											
CD3EAP	10849	hgsc.bcm.edu	37	chr19	45911669	45911669	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccctcctggcctgaggcctcGgttctgtgcctttgggggca	2	11	14	14	1	1	1	0	1	1	0	3	1	2	1	5	5	1	2	5	5	0	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:45911669G>A	ENST00000309424.3	+	3	931	c.443G>A	c.(442-444)cGg>cAg	p.R148Q	ERCC1_ENST00000588738.1_5'Flank|ERCC1_ENST00000423698.2_3'UTR|PPP1R13L_ENST00000418234.2_5'Flank|CD3EAP_ENST00000589804.1_Missense_Mutation_p.R150Q|ERCC1_ENST00000300853.3_3'UTR	NM_012099.1	NP_036231.1	O15446	RPA34_HUMAN	CD3e molecule, epsilon associated protein	148					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)		CTGAGGCCTCGGTTCTGTGCC	0.617																																					p.R148Q		Atlas-SNP	.											.	CD3EAP	27	.	0			c.G443A						PASS	.						42	44	43					19																	45911669		2203	4299	6502	SO:0001583	missense	10849	exon3			GGCCTCGGTTCTG	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.443G>A	19.37:g.45911669G>A	ENSP00000310966:p.Arg148Gln	54	0	0		71	30	0.422535	NM_012099	Q32N11|Q7Z5U2|Q9UPF6	Missense_Mutation	SNP	ENST00000309424.3	37	CCDS12661.1	.	.	.	.	.	.	.	.	.	.	G	32	5.145864	0.94603	.	.	ENSG00000117877	ENST00000309424	T	0.54279	0.58	5.27	5.27	0.74061	.	0.000000	0.64402	D	0.000003	T	0.70228	0.3200	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.73275	-0.4034	10	0.87932	D	0	-21.8983	14.3879	0.66958	0.0:0.0:1.0:0.0	.	150;148	O15446-2;O15446	.;RPA34_HUMAN	Q	148	ENSP00000310966:R148Q	ENSP00000310966:R148Q	R	+	2	0	CD3EAP	50603509	0.998000	0.40836	1.000000	0.80357	0.971000	0.66376	5.734000	0.68580	2.463000	0.83235	0.561000	0.74099	CGG	.	.	none		0.617	CD3EAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459538.1	NM_012099		A	45911669	G	A	45911669	3	1	24	1	0	0	0	0	1	0	0	0	3014	1116	39	1	453	1	CD3EAP	19	45911669	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	195305	45911669	13217314	622	8839											
ERCC1	2067	hgsc.bcm.edu	37	chr19	45922389	45922389	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	acaagcaggacccgcaaggcGaagttcttccccaggctctg	10	6	11	14	2	2	0	0	0	2	0	3	2	3	1	3	3	1	4	3	3	3	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:45922389G>C	ENST00000300853.3	-	5	1083	c.492C>G	c.(490-492)ttC>ttG	p.F164L	ERCC1_ENST00000591636.1_Missense_Mutation_p.F164L|ERCC1_ENST00000423698.2_Missense_Mutation_p.F92L|ERCC1_ENST00000340192.7_Missense_Mutation_p.F164L|ERCC1_ENST00000589165.1_Missense_Mutation_p.F164L|ERCC1_ENST00000013807.5_Missense_Mutation_p.F164L	NM_001983.3	NP_001974.1	P07992	ERCC1_HUMAN	excision repair cross-complementation group 1	164					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)		CCCGCAAGGCGAAGTTCTTCC	0.627								Nucleotide excision repair (NER)																													p.F164L		Atlas-SNP	.											.	ERCC1	46	.	0			c.C492G						PASS	.						68	55	59					19																	45922389		2202	4299	6501	SO:0001583	missense	2067	exon5			CAAGGCGAAGTTC		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.492C>G	19.37:g.45922389G>C	ENSP00000300853:p.Phe164Leu	52	0	0		47	27	0.574468	NM_001983	B2RC01|B3KRR0|Q7Z7F5|Q96S40	Missense_Mutation	SNP	ENST00000300853.3	37	CCDS12662.1	.	.	.	.	.	.	.	.	.	.	G	17.89	3.499600	0.64298	.	.	ENSG00000012061	ENST00000300853;ENST00000340192;ENST00000423698;ENST00000013807	T;T;T;T	0.44482	0.94;0.92;0.95;0.92	4.71	1.33	0.21861	Restriction endonuclease, type II-like (1);	0.170692	0.51477	D	0.000090	T	0.47154	0.1430	M	0.74258	2.255	0.48040	D	0.999578	D;D;P;P	0.60575	0.984;0.988;0.898;0.95	P;B;B;B	0.50537	0.643;0.441;0.344;0.426	T	0.47699	-0.9097	10	0.72032	D	0.01	-17.7424	7.097	0.25315	0.3011:0.0:0.6989:0.0	.	164;92;164;164	Q7Z7F5;B3KRR0;Q96S40;P07992	.;.;.;ERCC1_HUMAN	L	164;164;92;164	ENSP00000300853:F164L;ENSP00000345203:F164L;ENSP00000394875:F92L;ENSP00000013807:F164L	ENSP00000013807:F164L	F	-	3	2	ERCC1	50614229	1.000000	0.71417	0.995000	0.50966	0.977000	0.68977	0.770000	0.26618	0.418000	0.25898	0.462000	0.41574	TTC	.	.	none		0.627	ERCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459542.1	NM_001983		C	45922389	G	C	45922389	3	2	24	1	0	0	0	0	1	0	0	0	5214	1049	37	4	554	4	ERCC1	19	45922389	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	10720	45922389	13206594	623	8840											
PTGIR	5739	hgsc.bcm.edu	37	chr19	47126807	47126807	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctctccggtgcgcggccgtgGacccagagagccctggtggc	4	6	16	15	4	1	1	0	0	1	1	2	3	1	2	4	5	2	0	4	5	0	0	rs138619017	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:47126807G>T	ENST00000291294.2	-	2	809	c.676C>A	c.(676-678)Cca>Aca	p.P226T	PTGIR_ENST00000597185.1_Intron|PTGIR_ENST00000598865.1_Missense_Mutation_p.P14T|PTGIR_ENST00000596260.1_Missense_Mutation_p.P226T|PTGIR_ENST00000594275.1_5'UTR	NM_000960.3	NP_000951.1	P43119	PI2R_HUMAN	prostaglandin I2 (prostacyclin) receptor (IP)	226					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of GTPase activity (GO:0043547)|response to lipopolysaccharide (GO:0032496)	cytosol (GO:0005829)|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)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	13		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000327)|all cancers(93;0.000641)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0331)	Dinoprost Tromethamine(DB01160)|Epoprostenol(DB01240)|Iloprost(DB01088)|Treprostinil(DB00374)	CGCGGCCGTGGACCCAGAGAG	0.672													G|||	6	0.00119808	0.0	0.0029	5008	,	,		16491	0.0		0.003	False		,,,				2504	0.001				p.P226T		Atlas-SNP	.											.	PTGIR	31	.	0			c.C676A						PASS	.	G	THR/PRO	0,4362		0,0,2181	14	15	15		676	4.8	0	19	dbSNP_134	15	30,8496		0,30,4233	yes	missense	PTGIR	NM_000960.3	38	0,30,6414	TT,TG,GG		0.3519,0.0,0.2328	benign	226/387	47126807	30,12858	2181	4263	6444	SO:0001583	missense	5739	exon2			GCCGTGGACCCAG		CCDS12686.1	19q13.3	2012-08-08				ENSG00000160013		"GPCR / Class A : Prostanoid receptors"	9602	protein-coding gene	gene with protein product		600022				7759114	Standard	NM_000960		Approved	IP	uc002pex.3	P43119		ENST00000291294.2:c.676C>A	19.37:g.47126807G>T	ENSP00000291294:p.Pro226Thr	51	0	0		65	27	0.415385	NM_000960		Missense_Mutation	SNP	ENST00000291294.2	37	CCDS12686.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	0.270	-0.993357	0.02145	0.0	0.003519	ENSG00000160013	ENST00000291294	T	0.71341	-0.56	4.75	4.75	0.60458	GPCR, rhodopsin-like superfamily (1);	0.212063	0.37669	N	0.001994	T	0.57755	0.2075	L	0.34521	1.04	0.23156	N	0.998204	B	0.06786	0.001	B	0.11329	0.006	T	0.31971	-0.9924	10	0.09590	T	0.72	-14.1054	15.2825	0.73797	0.0:0.0:1.0:0.0	.	226	P43119	PI2R_HUMAN	T	226	ENSP00000291294:P226T	ENSP00000291294:P226T	P	-	1	0	PTGIR	51818647	0.995000	0.38212	0.012000	0.15200	0.002000	0.02628	3.196000	0.51020	2.454000	0.82982	0.563000	0.77884	CCA	G|0.999;T|0.001	0.001	strong		0.672	PTGIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466581.1			T	47126807	G	T	47126807	3	4	24	1	0	0	0	0	1	0	0	0	12764	1174	41	4	492	4	PTGIR	19	47126807	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1204418	47126807	12002176	624	8841											
KPTN	11133	hgsc.bcm.edu	37	chr19	47987230	47987230	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagctccttggccactggcCggattttctgtcggaggtct	4	12	13	12	2	2	0	0	0	2	0	4	2	3	2	3	5	1	2	3	5	0	3	rs142867197	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:47987230C>T	ENST00000338134.3	-	1	295	c.188G>A	c.(187-189)cGg>cAg	p.R63Q	NAPA-AS1_ENST00000593284.1_RNA|NAPA-AS1_ENST00000594367.1_RNA|KPTN_ENST00000595484.1_5'UTR|KPTN_ENST00000536339.1_5'UTR	NM_007059.2	NP_008990.2	Q9Y664	KPTN_HUMAN	kaptin (actin binding protein)	63					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)		GGCCACTGGCCGGATTTTCTG	0.667											OREG0025593	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2	0.000399361	0.0	0.0	5008	,	,		14783	0.0		0.002	False		,,,				2504	0.0				p.R63Q		Atlas-SNP	.											.	KPTN	34	.	0			c.G188A						PASS	.	C	GLN/ARG	1,3881		0,1,1940	42	48	46		188	4.6	1	19	dbSNP_134	46	13,8253		0,13,4120	yes	missense	KPTN	NM_007059.2	43	0,14,6060	TT,TC,CC		0.1573,0.0258,0.1152	possibly-damaging	63/437	47987230	14,12134	1941	4133	6074	SO:0001583	missense	11133	exon1			ACTGGCCGGATTT	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.188G>A	19.37:g.47987230C>T	ENSP00000337850:p.Arg63Gln	25	0	0	951	44	22	0.5	NM_007059	B3KN86|B4DQ76|Q96GT1	Missense_Mutation	SNP	ENST00000338134.3	37	CCDS42583.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	22.0	4.231215	0.79688	2.58E-4	0.001573	ENSG00000118162	ENST00000338134	.	.	.	4.59	4.59	0.56863	.	0.128494	0.50627	D	0.000103	T	0.57388	0.2050	L	0.56396	1.775	0.80722	D	1	B	0.30281	0.275	B	0.23716	0.048	T	0.58053	-0.7704	9	0.33940	T	0.23	-22.8261	16.3101	0.82865	0.0:1.0:0.0:0.0	.	63	Q9Y664	KPTN_HUMAN	Q	63	.	ENSP00000337850:R63Q	R	-	2	0	KPTN	52679042	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.799000	0.75160	2.390000	0.81377	0.313000	0.20887	CGG	C|0.998;T|0.002	0.002	strong		0.667	KPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466672.2			T	47987230	C	T	47987230	3	4	24	1	0	0	0	0	1	0	0	0	8446	652	23	1	1170	1	KPTN	19	47987230	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	860423	47987230	11141753	625	8842											
FAM83E	54854	hgsc.bcm.edu	37	chr19	49107039	49107039	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cctatgaccgagggtttctgGgggggcgcaggtgggagcgg	5	7	21	8	3	1	1	0	1	1	0	1	3	1	2	2	7	1	2	2	7	1	2	rs201027346	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:49107039G>T	ENST00000263266.3	-	4	1077	c.888C>A	c.(886-888)ccC>ccA	p.P296P	SPACA4_ENST00000321762.1_5'Flank	NM_017708.3	NP_060178.2	Q2M2I3	FA83E_HUMAN	family with sequence similarity 83, member E	296										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)		AGGGTTTCTGGGGGGGCGCAG	0.721																																					p.P296P		Atlas-SNP	.											.	FAM83E	34	.	0			c.C888A						PASS	.	G		0,3978		0,0,1989	12	13	13		888	1.2	0	19		13	2,8210		0,2,4104	no	coding-synonymous	FAM83E	NM_017708.3		0,2,6093	TT,TG,GG		0.0244,0.0,0.0164		296/479	49107039	2,12188	1989	4106	6095	SO:0001819	synonymous_variant	54854	exon4			TTTCTGGGGGGGC	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.888C>A	19.37:g.49107039G>T		48	0	0		63	32	0.507937	NM_017708	Q9NXK1	Silent	SNP	ENST00000263266.3	37	CCDS42587.1																																																																																			G|0.999;T|0.001	0.001	weak		0.721	FAM83E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466145.1	NM_017708		T	49107039	G	T	49107039	2	4	24	1	0	0	0	0	0	0	0	1	5645	1219	43	4		4	FAM83E	19	49107039	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1119809	49107039	10021944	626	8843											
CPT1C	126129	hgsc.bcm.edu	37	chr19	50212024	50212024	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctgggctactcaacagaCggccactgcaaggggcaccc	10	4	12	15	1	1	1	1	0	0	1	1	1	1	1	2	4	4	4	2	4	3	1	rs61747405	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:50212024C>T	ENST00000392518.4	+	14	1866	c.1494C>T	c.(1492-1494)gaC>gaT	p.D498D	CPT1C_ENST00000598293.1_Silent_p.D498D|CPT1C_ENST00000354199.5_Silent_p.D498D|CPT1C_ENST00000405931.2_Silent_p.D487D|CPT1C_ENST00000323446.5_Silent_p.D498D	NM_001199752.1	NP_001186681.1	Q8TCG5	CPT1C_HUMAN	carnitine palmitoyltransferase 1C	498					carnitine metabolic process (GO:0009437)|fatty acid beta-oxidation (GO:0006635)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|endoplasmic reticulum membrane (GO:0005789)|mitochondrial outer membrane (GO:0005741)|synapse (GO:0045202)	carnitine O-palmitoyltransferase activity (GO:0004095)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		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;0.0011)|GBM - Glioblastoma multiforme(134;0.00786)		ACTCAACAGACGGCCACTGCA	0.607													c|||	75	0.014976	0.0272	0.0101	5008	,	,		15016	0.001		0.0278	False		,,,				2504	0.0031				p.D498D		Atlas-SNP	.											.	CPT1C	93	.	0			c.C1494T						PASS	.	C	,,,	81,4325	72.5+/-110.5	1,79,2123	121	110	114		1461,1494,1494,1494	-4.4	0.7	19	dbSNP_129	114	206,8394	89.2+/-151.4	3,200,4097	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CPT1C	NM_001136052.2,NM_001199752.1,NM_001199753.1,NM_152359.2	,,,	4,279,6220	TT,TC,CC		2.3953,1.8384,2.2067	,,,	487/793,498/804,498/804,498/804	50212024	287,12719	2203	4300	6503	SO:0001819	synonymous_variant	126129	exon14			AACAGACGGCCAC	AF357970	CCDS12779.1, CCDS46147.1	19q13.33	2014-03-14				ENSG00000169169			18540	protein-coding gene	gene with protein product		608846				12376098, 11001805	Standard	NM_001136052		Approved	FLJ23809, CPTIC, CPT1P	uc010eng.3	Q8TCG5		ENST00000392518.4:c.1494C>T	19.37:g.50212024C>T		91	0	0		108	63	0.583333	NM_001199752	A8K0Z8|Q5K6N5|Q8N6Q9|Q8NDS6|Q8TE84	Silent	SNP	ENST00000392518.4	37	CCDS12779.1																																																																																			C|0.978;T|0.022	0.022	strong		0.607	CPT1C-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465873.1	NM_152359		T	50212024	C	T	50212024	2	4	24	1	0	0	0	0	0	0	0	1	3835	535	19	1		1	CPT1C	19	50212024	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1104985	50212024	8916959	627	8844											
LILRB1	10859	hgsc.bcm.edu	37	chr19	55143395	55143395	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctctcctaggagcctacaTcaaacccaccctctcagccc	9	9	4	19	0	3	0	2	0	2	0	6	1	4	1	5	1	4	0	5	1	3	3	rs370374304		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:55143395T>G	ENST00000396331.1	+	6	725	c.368T>G	c.(367-369)aTc>aGc	p.I123S	LILRB1_ENST00000396327.3_Missense_Mutation_p.I123S|LILRB1_ENST00000324602.7_Missense_Mutation_p.I123S|LILRB1_ENST00000427581.2_Missense_Mutation_p.I159S|LILRB1_ENST00000396321.2_Missense_Mutation_p.I123S|LILRB1_ENST00000418536.2_Missense_Mutation_p.I123S|LILRB1_ENST00000396315.1_Missense_Mutation_p.I123S|AC009892.1_ENST00000578908.1_RNA|LILRB1_ENST00000434867.2_Missense_Mutation_p.I123S|LILRB1_ENST00000396332.4_Missense_Mutation_p.I123S|LILRB1_ENST00000396317.1_Missense_Mutation_p.I123S|LILRB1_ENST00000448689.1_Missense_Mutation_p.I123S	NM_006669.3	NP_006660.3	Q8NHL6	LIRB1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 1	123	Ig-like C2-type 2.				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)		GGAGCCTACATCAAACCCACC	0.587										HNSCC(37;0.09)			N|||	1	0.000199681	0.0008	0.0	5008	,	,		17815	0.0		0.0	False		,,,				2504	0.0				p.I123S		Atlas-SNP	.											.	LILRB1	140	.	0			c.T368G						PASS	.	G	SER/ILE,SER/ILE,SER/ILE,SER/ILE	0,4406		0,0,2203	72	75	74		368,368,368,368	-3	0	19		74	2,8598	818.7+/-406.8	0,2,4298	no	missense,missense,missense,missense	LILRB1	NM_001081637.1,NM_001081638.1,NM_001081639.1,NM_006669.3	142,142,142,142	0,2,6501	GG,GT,TT		0.0233,0.0,0.0154	benign,benign,benign,benign	123/653,123/652,123/652,123/651	55143395	2,13004	2203	4300	6503	SO:0001583	missense	10859	exon5			CCTACATCAAACC	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.368T>G	19.37:g.55143395T>G	ENSP00000379622:p.Ile123Ser	99	0	0		109	46	0.422018	NM_001081637	A2IXV4|A8MXT0|O75024|O75025|Q8NHJ9|Q8NHK0	Missense_Mutation	SNP	ENST00000396331.1	37	CCDS42617.1	.	.	.	.	.	.	.	.	.	.	g	0	-2.736760	0.00088	0.0	2.33E-4	ENSG00000104972	ENST00000396321;ENST00000418536;ENST00000448689;ENST00000396331;ENST00000396327;ENST00000324602;ENST00000434867;ENST00000396332;ENST00000427581;ENST00000396317;ENST00000396315	T;T;T;T;T;T;T;T;T;T;T	0.21191	2.02;2.02;2.02;2.02;2.02;2.02;2.02;2.02;2.02;2.02;2.02	1.57	-2.95	0.05564	Immunoglobulin-like fold (1);	1.339760	0.04742	N	0.422960	T	0.02929	0.0087	N	0.00121	-2.07	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;0.001;0.0;0.0;0.0	T	0.35525	-0.9785	10	0.02654	T	1	.	2.0172	0.03500	0.3909:0.0:0.3453:0.2638	.	123;123;123;123;123	A8MVE2;Q8NHL6-3;A2IXV4;Q8NHL6-2;Q8NHL6	.;.;.;.;LIRB1_HUMAN	S	123;123;123;123;123;123;123;123;159;123;123	ENSP00000379614:I123S;ENSP00000391514:I123S;ENSP00000409968:I123S;ENSP00000379622:I123S;ENSP00000379618:I123S;ENSP00000315997:I123S;ENSP00000405243:I123S;ENSP00000379623:I123S;ENSP00000395004:I159S;ENSP00000379610:I123S;ENSP00000379608:I123S	ENSP00000315997:I123S	I	+	2	0	LILRB1	59835207	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-5.408000	0.00124	-0.614000	0.05687	-3.867000	0.00017	ATC	.	.	weak		0.587	LILRB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000140796.4			G	55143395	T	G	55143395	3	3	24	1	0	0	0	0	1	0	0	0	8799	1435	50	5	382	5	LILRB1	19	55143395	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	4931371	55143395	3985588	628	8845											
LILRB4	11006	hgsc.bcm.edu	37	chr19	55177358	55177358	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcctcctccaacactggCgtcagggaaaacacaggaca	12	6	8	15	1	1	0	1	0	0	0	5	2	5	2	4	3	2	0	4	3	3	0	rs200475774		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:55177358C>T	ENST00000391736.1	+	9	1165	c.850C>T	c.(850-852)Cgt>Tgt	p.R284C	LILRB4_ENST00000270452.2_Missense_Mutation_p.R284C|LILRB4_ENST00000391733.3_Missense_Mutation_p.R284C|LILRB4_ENST00000430952.2_Missense_Mutation_p.R284C|LILRB4_ENST00000391734.3_Missense_Mutation_p.R284C	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	284					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)		ccAACACTGGCGTCAGGGAAA	0.592																																					p.R284C		Atlas-SNP	.											LILRB4,NS,carcinoma,0,2	LILRB4	86	2	0			c.C850T						PASS	.	C	CYS/ARG,CYS/ARG	0,4406		0,0,2203	138	92	108		850,850	-0.5	0	19		108	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	LILRB4	NM_001081438.1,NM_006847.3	180,180	0,4,6499	TT,TC,CC		0.0465,0.0,0.0308	probably-damaging,probably-damaging	284/448,284/449	55177358	4,13002	2203	4300	6503	SO:0001583	missense	11006	exon7			CACTGGCGTCAGG	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.850C>T	19.37:g.55177358C>T	ENSP00000375616:p.Arg284Cys	146	0	0		127	60	0.472441	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Missense_Mutation	SNP	ENST00000391736.1	37	CCDS12902.1	.	.	.	.	.	.	.	.	.	.	C	6.615	0.481950	0.12581	0.0	4.65E-4	ENSG00000186818	ENST00000391736;ENST00000270452;ENST00000430952;ENST00000391734;ENST00000391733;ENST00000434286	T;T;T;T;T;T	0.00490	7.1;7.1;7.1;7.03;7.12;7.03	1.86	-0.498	0.12019	.	.	.	.	.	T	0.00356	0.0011	L	0.43701	1.375	0.09310	N	1	D;D;P;P;B	0.62365	0.991;0.978;0.954;0.875;0.017	B;B;B;P;B	0.44561	0.446;0.265;0.335;0.453;0.002	T	0.50734	-0.8793	9	0.49607	T	0.09	.	2.8633	0.05593	0.0:0.4992:0.3032:0.1976	.	284;283;284;284;284	A8MUE1;C9JST2;Q8NHJ6-3;Q8NHJ6-2;Q8NHJ6	.;.;.;.;LIRB4_HUMAN	C	284;284;284;284;284;283	ENSP00000375616:R284C;ENSP00000270452:R284C;ENSP00000408995:R284C;ENSP00000375614:R284C;ENSP00000375613:R284C;ENSP00000401962:R283C	ENSP00000270452:R284C	R	+	1	0	LILRB4	59869170	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.104000	0.03326	-0.054000	0.13266	0.407000	0.27541	CGT	C|0.999;T|0.001	0.001	weak		0.592	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3			T	55177358	C	T	55177358	3	4	24	1	0	0	0	0	1	0	0	0	8802	768	27	1	876	1	LILRB4	19	55177358	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	33963	55177358	3951625	629	8846											
NLRP4	147945	hgsc.bcm.edu	37	chr19	56369914	56369914	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgttcacacctgagggtgcCgagggcccgactccgcaaac	8	6	12	15	3	1	1	1	1	0	0	2	3	2	1	4	2	2	2	4	2	1	1	rs113444208	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:56369914C>T	ENST00000301295.6	+	3	1577	c.1155C>T	c.(1153-1155)gcC>gcT	p.A385A	NLRP4_ENST00000587891.1_Silent_p.A310A|NLRP4_ENST00000346986.5_Silent_p.A385A	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	385	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)		CTGAGGGTGCCGAGGGCCCGA	0.557													C|||	21	0.00419329	0.0008	0.0	5008	,	,		17743	0.0		0.006	False		,,,				2504	0.0143				p.A385A		Atlas-SNP	.											.	NLRP4	331	.	0			c.C1155T						PASS	.	C		15,4391	23.3+/-48.9	0,15,2188	55	52	53		1155	-7.7	0	19	dbSNP_132	53	50,8550	31.7+/-84.0	0,50,4250	no	coding-synonymous	NLRP4	NM_134444.4		0,65,6438	TT,TC,CC		0.5814,0.3404,0.4998		385/995	56369914	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	147945	exon3			GGGTGCCGAGGGC	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.1155C>T	19.37:g.56369914C>T		53	0	0		73	33	0.452055	NM_134444	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																			C|0.996;T|0.004	0.004	strong		0.557	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444		T	56369914	C	T	56369914	2	4	24	1	0	0	0	0	0	0	0	1	10488	639	23	1		1	NLRP4	19	56369914	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1192556	56369914	2759069	630	8847											
NLRP8	126205	hgsc.bcm.edu	37	chr19	56467167	56467167	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttccaatgcaaggtgtctttCggtaataagaggaaactgct	12	12	10	7	1	1	1	0	0	1	1	3	2	2	2	1	3	3	3	1	3	5	4	rs375534172		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:56467167C>T	ENST00000291971.3	+	3	1814	c.1743C>T	c.(1741-1743)ttC>ttT	p.F581F	NLRP8_ENST00000590542.1_Silent_p.F581F	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	581					neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		AGGTGTCTTTCGGTAATAAGA	0.488																																					p.F581F		Atlas-SNP	.											.	NLRP8	225	.	0			c.C1743T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	49	46	47		1743	-0.4	0	19		47	0,8600		0,0,4300	no	coding-synonymous	NLRP8	NM_176811.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		581/1049	56467167	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	126205	exon3			GTCTTTCGGTAAT	AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"Nucleotide-binding domain and leucine rich repeat containing"	22940	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"	609659	"NACHT, leucine rich repeat and PYD containing 8"	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.1743C>T	19.37:g.56467167C>T		115	0	0		150	58	0.386667	NM_176811	Q7RTR4	Silent	SNP	ENST00000291971.3	37	CCDS12937.1																																																																																			.	.	weak		0.488	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811		T	56467167	C	T	56467167	2	4	24	1	0	0	0	0	0	0	0	1	10492	883	31	1		1	NLRP8	19	56467167	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	97253	56467167	2661816	631	8848											
ZIM2	23619	hgsc.bcm.edu	37	chr19	57286688	57286688	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ctcttgggatgctgactgggGactcgtacatattccaggag	8	11	13	9	1	1	1	0	1	1	0	3	4	2	4	1	4	2	2	1	4	2	4			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:57286688G>A	ENST00000391708.3	-	12	1494	c.952C>T	c.(952-954)Ccc>Tcc	p.P318S	ZIM2_ENST00000599935.1_Missense_Mutation_p.P318S|ZIM2_ENST00000221722.5_Missense_Mutation_p.P318S|ZIM2_ENST00000593711.1_Missense_Mutation_p.P318S|ZIM2_ENST00000601070.1_Missense_Mutation_p.P318S|AC006115.3_ENST00000595954.1_RNA|AC006115.3_ENST00000594400.1_RNA|AC006115.3_ENST00000597946.1_RNA	NM_001146326.1|NM_001146327.1	NP_001139798.1|NP_001139799.1	Q9NZV7	ZIM2_HUMAN	zinc finger, imprinted 2	318					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)		GCTGACTGGGGACTCGTACAT	0.448																																					p.P318S		Atlas-SNP	.											ZIM2,NS,malignant_melanoma,+1,1	ZIM2	511	1	0			c.C952T						PASS	.						136	126	130					19																	57286688		2203	4300	6503	SO:0001583	missense	23619	exon11			ACTGGGGACTCGT	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.952C>T	19.37:g.57286688G>A	ENSP00000375589:p.Pro318Ser	268	0	0		310	149	0.480645	NM_015363	Q2M3K1	Missense_Mutation	SNP	ENST00000391708.3	37	CCDS33123.1	.	.	.	.	.	.	.	.	.	.	G	5.759	0.324523	0.10900	.	.	ENSG00000198300	ENST00000391708;ENST00000221722	T;T	0.05081	3.5;3.5	3.89	-0.711	0.11230	.	.	.	.	.	T	0.02970	0.0088	N	0.08118	0	.	.	.	B	0.23058	0.079	B	0.18263	0.021	T	0.39354	-0.9618	8	0.87932	D	0	.	3.4921	0.07641	0.3462:0.1968:0.4569:0.0	.	318	Q9NZV7	ZIM2_HUMAN	S	318	ENSP00000375589:P318S;ENSP00000221722:P318S	ENSP00000221722:P318S	P	-	1	0	ZIM2	61978500	.	.	0.000000	0.03702	0.211000	0.24417	.	.	-0.024000	0.13941	0.655000	0.94253	CCC	.	.	none		0.448	ZIM2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416094.2			A	57286688	G	A	57286688	3	1	24	1	0	0	0	0	1	0	0	0	17699	1174	41	2	635	2	ZIM2	19	57286688	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	819521	57286688	1842295	632	8849											
ZSCAN18	65982	hgsc.bcm.edu	37	chr19	58598358	58598369	+	In_Frame_Del	DEL	TGGAAAGGACTT	TGGAAAGGACTT	-																															cccaggtgctgagggtcctcTggaaaggacttcagcttctg																								rs368736992	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	TGGAAAGGACTT	TGGAAAGGACTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:58598358_58598369delTGGAAAGGACTT	ENST00000240727.6	-	5	1048_1059	c.649_660delAAGTCCTTTCCA	c.(649-660)aagtcctttccadel	p.KSFP217del	ZSCAN18_ENST00000601144.1_In_Frame_Del_p.KSFP217del|ZSCAN18_ENST00000421612.2_In_Frame_Del_p.KSFP82del|ZSCAN18_ENST00000600404.1_In_Frame_Del_p.KSFP273del	NM_023926.4	NP_076415.3	Q8TBC5	ZSC18_HUMAN	zinc finger and SCAN domain containing 18	217					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)		GAGGGTCCTCTGGAAAGGACTTCAGCTTCTGA	0.637														7	0.00139776	0.0	0.0	5008	,	,		18211	0.0		0.0	False		,,,				2504	0.0072				p.273_277del		Pindel,Atlas-Indel	.											.	ZSCAN18	104	.	0			c.818_829del						PASS	.																																			SO:0001651	inframe_deletion	65982	exon5			.	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.649_660delAAGTCCTTTCCA	19.37:g.58598358_58598369delTGGAAAGGACTT	ENSP00000240727:p.Lys217_Pro220del	77	0	.		44	11	0.25	NM_001145542	B4DG23|E9PBI0|Q9BRK7|Q9H9A0	In_Frame_Del	DEL	ENST00000240727.6	37	CCDS12971.1																																																																																			.	.	weak		0.637	ZSCAN18-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466706.1	NM_023926		-	58598369	TGGAAAGGACTT	-	58598358	7	5	24	1	0	1	0	1	0	0	0	0	18245	1567	55	0	884	0	ZSCAN18	19	58598358	In_Frame_Del	DEL	TGGAAAGGACTT	TCGA-G8-6326-01A-11D-2210-10	1311670	58598358	530625	633	8850											
ZSCAN22	342945	hgsc.bcm.edu	37	chr19	58849789	58849789	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gagaggtctggactatcaggGgagatctggacaaagtctgt	11	9	15	6	0	4	2	1	0	3	2	4	6	4	4	0	5	0	0	0	5	2	1	rs368211476		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:58849789G>A	ENST00000329665.4	+	3	720	c.573G>A	c.(571-573)ggG>ggA	p.G191G		NM_181846.2	NP_862829.1	P10073	ZSC22_HUMAN	zinc finger and SCAN domain containing 22	191					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)		GACTATCAGGGGAGATCTGGA	0.537													G|||	1	0.000199681	0.0	0.0	5008	,	,		20257	0.0		0.0	False		,,,				2504	0.001				p.G191G		Atlas-SNP	.											ZSCAN22,NS,carcinoma,+1,1	ZSCAN22	47	1	0			c.G573A						PASS	.						114	112	112					19																	58849789		2203	4300	6503	SO:0001819	synonymous_variant	342945	exon3			ATCAGGGGAGATC	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.573G>A	19.37:g.58849789G>A		113	0	0		121	59	0.487603	NM_181846	Q15922|Q7Z3L8	Silent	SNP	ENST00000329665.4	37	CCDS12975.1																																																																																			.	.	weak		0.537	ZSCAN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466765.1	NM_181846		A	58849789	G	A	58849789	2	1	24	1	0	0	0	0	0	0	0	1	18249	1219	43	2		2	ZSCAN22	19	58849789	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	251431	58849789	279194	634	8851											
SLC27A5	10998	hgsc.bcm.edu	37	chr19	59009949	59009949	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tcaggggccggaaggactggGcccggttgtccagtacaaac	9	6	15	11	2	1	0	1	0	0	0	2	2	2	2	3	6	2	2	3	6	3	2	rs145618122	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr19:59009949G>C	ENST00000263093.2	-	10	2115	c.2006C>G	c.(2005-2007)gCc>gGc	p.A669G	SLC27A5_ENST00000601355.1_Missense_Mutation_p.A585G|SLC27A5_ENST00000599700.1_5'UTR|SLC27A5_ENST00000594786.1_Missense_Mutation_p.A74G	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	669					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)		GAAGGACTGGGCCCGGTTGTC	0.582													G|||	22	0.00439297	0.0015	0.0043	5008	,	,		18662	0.0		0.008	False		,,,				2504	0.0092				p.A669G		Atlas-SNP	.											.	SLC27A5	58	.	0			c.C2006G						PASS	.	G	GLY/ALA	2,4404	4.2+/-10.8	0,2,2201	124	106	112		2006	2.5	0	19	dbSNP_134	112	78,8522	42.2+/-99.7	0,78,4222	yes	missense	SLC27A5	NM_012254.2	60	0,80,6423	CC,CG,GG		0.907,0.0454,0.6151	benign	669/691	59009949	80,12926	2203	4300	6503	SO:0001583	missense	10998	exon10			GACTGGGCCCGGT	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.2006C>G	19.37:g.59009949G>C	ENSP00000263093:p.Ala669Gly	83	0	0		52	25	0.480769	NM_012254	B3KVP6|B4DPQ1	Missense_Mutation	SNP	ENST00000263093.2	37	CCDS12983.1	11	0.005036630036630037	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	G	7.891	0.732413	0.15507	4.54E-4	0.00907	ENSG00000083807	ENST00000263093	T	0.53423	0.62	4.85	2.51	0.30379	.	0.370857	0.28130	N	0.016500	T	0.22742	0.0549	N	0.25245	0.725	0.09310	N	1	B	0.11235	0.004	B	0.16289	0.015	T	0.12426	-1.0548	10	0.27082	T	0.32	-8.9846	9.675	0.40034	0.0:0.0:0.6228:0.3772	.	669	Q9Y2P5	S27A5_HUMAN	G	669	ENSP00000263093:A669G	ENSP00000263093:A669G	A	-	2	0	SLC27A5	63701761	0.000000	0.05858	0.005000	0.12908	0.392000	0.30506	0.058000	0.14301	1.137000	0.42214	0.655000	0.94253	GCC	G|0.992;C|0.008	0.008	strong		0.582	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254		C	59009949	G	C	59009949	3	2	24	1	0	0	0	0	1	0	0	0	14544	1203	42	4	70	4	SLC27A5	19	59009949	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	160160	59009949	119034	635	8852											
MCM8	84515	hgsc.bcm.edu	37	chr20	5966626	5966626	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gctattgagaaagtacattgGctatgctcggcagtatgtgt	10	13	12	6	1	0	1	0	1	0	1	1	2	0	1	0	2	2	6	0	2	5	6	rs150257637		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:5966626G>T	ENST00000378896.3	+	16	2389	c.2012G>T	c.(2011-2013)gGc>gTc	p.G671V	MCM8_ENST00000378886.2_Missense_Mutation_p.G711V|MCM8_ENST00000265187.4_Missense_Mutation_p.G655V|MCM8_ENST00000378883.1_Missense_Mutation_p.G624V	NM_001281520.1|NM_032485.4|NM_182802.1	NP_001268449.1|NP_115874.3|NP_877954.1	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	671					cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)|G1/S transition of mitotic cell cycle (GO:0000082)|male gamete generation (GO:0048232)|mitotic cell cycle (GO:0000278)	MCM8-MCM9 complex (GO:0097362)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	23						AAGTACATTGGCTATGCTCGG	0.448													G|||	1	0.000199681	0.0	0.0	5008	,	,		18852	0.0		0.001	False		,,,				2504	0.0				p.G671V		Atlas-SNP	.											.	MCM8	125	.	0			c.G2012T						PASS	.	G	VAL/GLY,VAL/GLY	1,4405	2.1+/-5.4	0,1,2202	135	121	126		2012,1964	5.3	1	20	dbSNP_134	126	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	MCM8	NM_032485.4,NM_182802.1	109,109	0,6,6497	TT,TG,GG		0.0581,0.0227,0.0461	possibly-damaging,possibly-damaging	671/841,655/825	5966626	6,13000	2203	4300	6503	SO:0001583	missense	84515	exon16			ACATTGGCTATGC	AJ439063	CCDS13094.1, CCDS13095.1, CCDS63226.1, CCDS63227.1	20p12.3	2007-04-04	2007-04-04	2003-07-09	ENSG00000125885	ENSG00000125885			16147	protein-coding gene	gene with protein product	"REC homolog (Drosophila)"	608187	"chromosome 20 open reading frame 154"	C20orf154		12527764	Standard	NM_032485		Approved	MGC4816, MGC12866, MGC119522, MGC119523, dJ967N21.5, REC	uc002wmi.3	Q9UJA3	OTTHUMG00000031822	ENST00000378896.3:c.2012G>T	20.37:g.5966626G>T	ENSP00000368174:p.Gly671Val	115	0	0		156	70	0.448718	NM_032485	B2RBG7|D3DW08|E7EQU7|Q495R4|Q495R6|Q495R7|Q86US4|Q969I5	Missense_Mutation	SNP	ENST00000378896.3	37	CCDS13094.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	20.9	4.060936	0.76074	2.27E-4	5.81E-4	ENSG00000125885	ENST00000378896;ENST00000378883;ENST00000378886;ENST00000265187	T;T;T;T	0.06068	3.35;3.35;3.35;3.35	5.33	5.33	0.75918	.	0.096141	0.64402	D	0.000001	T	0.10937	0.0267	L	0.39898	1.24	0.80722	D	1	P;P;B;P	0.47191	0.73;0.891;0.431;0.772	B;P;B;B	0.47346	0.219;0.544;0.219;0.326	T	0.12142	-1.0559	10	0.30078	T	0.28	-14.9313	19.4129	0.94683	0.0:0.0:1.0:0.0	.	624;711;655;671	Q9UJA3-2;E7EQU7;Q9UJA3-3;Q9UJA3	.;.;.;MCM8_HUMAN	V	671;624;711;655	ENSP00000368174:G671V;ENSP00000368161:G624V;ENSP00000368164:G711V;ENSP00000265187:G655V	ENSP00000265187:G655V	G	+	2	0	MCM8	5914626	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.648000	0.98483	2.652000	0.90054	0.655000	0.94253	GGC	G|0.999;T|0.001	0.001	strong		0.448	MCM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077900.1	NM_032485		T	5966626	G	T	5966626	3	4	24	1	0	0	0	0	1	0	0	0	9402	1203	42	4	2070	4	MCM8	20	5966626	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10		5966626	57058894	636	8853											
KIF16B	55614	hgsc.bcm.edu	37	chr20	16352344	16352344	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagatgtactgcagccttcaCtaatcacacgatgcaaatcc	13	9	6	13	1	2	1	2	0	0	1	3	2	3	1	2	0	4	3	2	0	3	3	rs75989969	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:16352344C>T	ENST00000354981.2	-	21	3570	c.3413G>A	c.(3412-3414)aGt>aAt	p.S1138N	KIF16B_ENST00000378003.2_Missense_Mutation_p.S364N|KIF16B_ENST00000408042.1_Missense_Mutation_p.S1138N|KIF16B_ENST00000355755.3_Missense_Mutation_p.S1138N	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	1138					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						GCAGCCTTCACTAATCACACG	0.408													c|||	65	0.0129792	0.0454	0.0072	5008	,	,		20897	0.0		0.0	False		,,,				2504	0.0				p.S1138N		Atlas-SNP	.											.	KIF16B	305	.	0			c.G3413A						PASS	.	T	ASN/SER,ASN/SER,ASN/SER	148,4258	103.0+/-141.5	2,144,2057	143	118	126		3260,3413,3413	3.8	0	20	dbSNP_131	126	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense,missense	KIF16B	NM_001199865.1,NM_001199866.1,NM_024704.4	46,46,46	2,148,6353	TT,TC,CC		0.0465,3.3591,1.1687	benign,benign,benign	1087/1267,1138/1393,1138/1318	16352344	152,12854	2203	4300	6503	SO:0001583	missense	55614	exon21			CCTTCACTAATCA	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.3413G>A	20.37:g.16352344C>T	ENSP00000347076:p.Ser1138Asn	123	0	0		155	80	0.516129	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	37	CCDS13122.1	30	0.013736263736263736	25	0.0508130081300813	5	0.013812154696132596	0	0.0	0	0.0	c	10.36	1.329121	0.24167	0.033591	4.65E-4	ENSG00000089177	ENST00000354981;ENST00000355755;ENST00000377997;ENST00000378003;ENST00000408042	T;T;T;T	0.70986	-0.53;-0.52;2.51;-0.47	5.8	3.8	0.43715	.	0.550979	0.21055	N	0.080929	T	0.16085	0.0387	L	0.29908	0.895	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.0	T	0.07028	-1.0794	10	0.18710	T	0.47	.	8.6668	0.34125	0.0:0.6904:0.0:0.3096	.	1138;1138;1138	Q96L93-2;Q96L93-6;Q96L93	.;.;KI16B_HUMAN	N	1138;1138;982;364;1138	ENSP00000347076:S1138N;ENSP00000347995:S1138N;ENSP00000367242:S364N;ENSP00000384164:S1138N	ENSP00000347076:S1138N	S	-	2	0	KIF16B	16300344	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.629000	0.24538	0.743000	0.32719	-1.124000	0.02001	AGT	C|0.989;T|0.011	0.011	strong		0.408	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683		T	16352344	C	T	16352344	3	4	24	1	0	0	0	0	1	0	0	0	8287	565	20	2	564	2	KIF16B	20	16352344	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	10385718	16352344	46673176	637	8854											
RIN2	54453	hgsc.bcm.edu	37	chr20	19915769	19915769	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gacacaattgcctcggagatCggagaactgaaacaggagat	15	6	12	8	2	0	4	0	1	0	3	2	8	0	4	1	3	3	0	1	3	3	1	rs181853315	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:19915769C>T	ENST00000255006.6	+	3	380	c.231C>T	c.(229-231)atC>atT	p.I77I	RIN2_ENST00000440354.2_Silent_p.I28I|RIN2_ENST00000484638.1_3'UTR	NM_001242581.1|NM_018993.3	NP_001229510.1|NP_061866.1	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	28					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						CCTCGGAGATCGGAGAACTGA	0.527													C|||	9	0.00179712	0.0	0.0072	5008	,	,		17587	0.0		0.003	False		,,,				2504	0.001				p.I77I		Atlas-SNP	.											.	RIN2	126	.	0			c.C231T						PASS	.	C	,	7,3941		0,7,1967	70	67	68		231,84	4.8	1	20		68	83,8219		0,83,4068	no	coding-synonymous,coding-synonymous	RIN2	NM_001242581.1,NM_018993.3	,	0,90,6035	TT,TC,CC		0.9998,0.1773,0.7347	,	77/945,28/896	19915769	90,12160	1974	4151	6125	SO:0001819	synonymous_variant	54453	exon3			GGAGATCGGAGAA	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.231C>T	20.37:g.19915769C>T		87	0	0		84	40	0.47619	NM_001242581	Q00425|Q5TFT8|Q9BQL3|Q9H071	Silent	SNP	ENST00000255006.6	37	CCDS56182.1																																																																																			C|0.995;T|0.005	0.005	strong		0.527	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1			T	19915769	C	T	19915769	2	4	24	1	0	0	0	0	0	0	0	1	13387	874	31	1		1	RIN2	20	19915769	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	3563425	19915769	43109751	638	8855											
SSTR4	6754	hgsc.bcm.edu	37	chr20	23016819	23016819	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	attggcctgtgctacctgctCatcgtgggcaagatgcgcgc	6	10	13	12	3	1	1	1	0	0	1	2	1	1	1	2	2	4	3	2	2	2	2	rs141700474	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:23016819C>T	ENST00000255008.3	+	1	763	c.699C>T	c.(697-699)ctC>ctT	p.L233L	RP4-753D10.3_ENST00000440921.1_RNA	NM_001052.2	NP_001043.2	P31391	SSR4_HUMAN	somatostatin receptor 4	233					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)					GCTACCTGCTCATCGTGGGCA	0.657													C|||	34	0.00678914	0.0113	0.0072	5008	,	,		17179	0.0		0.006	False		,,,				2504	0.0082				p.L233L	Esophageal Squamous(15;850 1104 16640)	Atlas-SNP	.											.	SSTR4	83	.	0			c.C699T						PASS	.	C		50,4310		0,50,2130	78	85	83		699	-1.4	0.5	20	dbSNP_134	83	81,8495		0,81,4207	no	coding-synonymous	SSTR4	NM_001052.2		0,131,6337	TT,TC,CC		0.9445,1.1468,1.0127		233/389	23016819	131,12805	2180	4288	6468	SO:0001819	synonymous_variant	6754	exon1			CCTGCTCATCGTG		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.699C>T	20.37:g.23016819C>T		40	0	0		59	24	0.40678	NM_001052	Q17RM1|Q17RM3|Q9UIY1	Silent	SNP	ENST00000255008.3	37	CCDS42856.1																																																																																			C|0.993;T|0.007	0.007	strong		0.657	SSTR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078308.1			T	23016819	C	T	23016819	2	4	24	1	0	0	0	0	0	0	0	1	15215	813	29	2		2	SSTR4	20	23016819	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	3101050	23016819	40008701	639	8856											
TTLL9	164395	hgsc.bcm.edu	37	chr20	30510797	30510798	+	Frame_Shift_Del	DEL	AT	AT	-																															ctctgacgaccagaaagatgAtattcccgtggagaactatg																										TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:30510797_30510798delAT	ENST00000375938.4	+	8	858_859	c.605_606delAT	c.(604-606)gatfs	p.D202fs	TTLL9_ENST00000535842.1_Frame_Shift_Del_p.D202fs|TTLL9_ENST00000375934.4_Frame_Shift_Del_p.D184fs|TTLL9_ENST00000375921.2_Frame_Shift_Del_p.D129fs|TTLL9_ENST00000310998.4_Frame_Shift_Del_p.D152fs|TTLL9_ENST00000375922.4_Frame_Shift_Del_p.D129fs			Q3SXZ7	TTLL9_HUMAN	tubulin tyrosine ligase-like family, member 9	202	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)			CAGAAAGATGATATTCCCGTGG	0.401																																					p.202_202del		Pindel,Atlas-Indel	.											.	TTLL9	95	.	0			c.604_605del						PASS	.																																			SO:0001589	frameshift_variant	164395	exon8			.	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.605_606delAT	20.37:g.30510799_30510800delAT	ENSP00000365105:p.Asp202fs	80	0	.		101	34	0.337	NM_001008409	A6NH06|A6NIS5|B3KSG8|Q3SXZ8|Q5JYS3|Q5JYS4	Frame_Shift_Del	DEL	ENST00000375938.4	37	CCDS42863.1																																																																																			.	.	none		0.401	TTLL9-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001008409		-	30510798	AT	-	30510797	7	5	24	1	0	1	0	1	0	0	0	0	16749	333	12	0	631	0	TTLL9	20	30510797	Frame_Shift_Del	DEL	AT	TCGA-G8-6326-01A-11D-2210-10	7493978	30510797	32514723	640	8857											
C20orf186	149954	hgsc.bcm.edu	37	chr20	31671575	31671575	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcaggccaaggtggcctgcTcggcggaggtggtctccttg	4	8	17	12	3	1	0	0	0	1	0	3	1	1	1	3	7	1	2	3	7	1	1	rs144272671	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:31671575T>G	ENST00000375483.3	+	3	572	c.572T>G	c.(571-573)cTc>cGc	p.L191R		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	191	Gly-rich.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										GGTGGCCTGCTCGGCGGAGGT	0.662													T|||	23	0.00459265	0.0	0.0	5008	,	,		15553	0.001		0.0	False		,,,				2504	0.0225				p.L191R		Atlas-SNP	.											.	.	.	.	0			c.T572G						PASS	.	T	ARG/LEU	0,4400		0,0,2200	26	32	30		572	3.3	1	20	dbSNP_134	30	17,8581		0,17,4282	yes	missense	BPIFB4	NM_182519.2	102	0,17,6482	GG,GT,TT		0.1977,0.0,0.1308	probably-damaging	191/615	31671575	17,12981	2200	4299	6499	SO:0001583	missense	149954	exon3			GCCTGCTCGGCGG	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.572T>G	20.37:g.31671575T>G	ENSP00000364632:p.Leu191Arg	90	0	0		127	74	0.582677	NM_182519	Q5TDX6	Missense_Mutation	SNP	ENST00000375483.3	37	CCDS13213.2	.	.	.	.	.	.	.	.	.	.	T	13.01	2.109728	0.37242	0.0	0.001977	ENSG00000186191	ENST00000375483	T	0.01430	4.9	3.33	3.33	0.38152	.	0.672431	0.13031	N	0.419352	T	0.03695	0.0105	L	0.29908	0.895	0.36259	D	0.854418	D	0.65815	0.995	D	0.72982	0.979	T	0.57039	-0.7879	10	0.62326	D	0.03	-15.6488	8.2721	0.31851	0.0:0.0:0.0:1.0	.	191	P59827	BPIB4_HUMAN	R	191	ENSP00000364632:L191R	ENSP00000364632:L191R	L	+	2	0	BPIFB4	31135236	0.999000	0.42202	0.992000	0.48379	0.309000	0.27889	3.953000	0.56699	1.516000	0.48900	0.334000	0.21626	CTC	T|0.998;G|0.002	0.002	strong		0.662	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519		G	31671575	T	G	31671575	3	3	24	1	0	0	0	0	1	0	0	0	2100	1551	54	5	582	5	C20orf186	20	31671575	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	1160778	31671575	31353945	641	8858											
KIAA1755	85449	hgsc.bcm.edu	37	chr20	36869741	36869741	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtcctggctgaccacctcGtccatcctgaaagccacctc	9	8	7	17	1	0	2	0	2	0	0	5	2	3	2	7	1	1	1	7	1	2	0			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:36869741G>A	ENST00000279024.4	-	3	1063	c.792C>T	c.(790-792)gaC>gaT	p.D264D		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	264										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)				TGACCACCTCGTCCATCCTGA	0.572																																					p.D264D		Atlas-SNP	.											KIAA1755,NS,malignant_melanoma,-2,2	KIAA1755	145	2	0			c.C792T						scavenged	.						138	122	127					20																	36869741		2203	4300	6503	SO:0001819	synonymous_variant	85449	exon3			CACCTCGTCCATC	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.792C>T	20.37:g.36869741G>A		162	1	0.00617284		185	89	0.481081	NM_001029864	Q9C0A8	Silent	SNP	ENST00000279024.4	37	CCDS33467.1																																																																																			.	.	none		0.572	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864		A	36869741	G	A	36869741	2	1	24	1	0	0	0	0	0	0	0	1	8266	1136	40	1		1	KIAA1755	20	36869741	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	5198166	36869741	26155779	642	8859											
CHD6	84181	hgsc.bcm.edu	37	chr20	40049450	40049450	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgcatccacctctccatgTgtttgcagtggcactgacag	8	11	9	13	0	1	1	0	1	1	0	3	1	2	1	3	1	2	4	3	1	0	1	rs140143834	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:40049450T>A	ENST00000373233.3	-	31	6002	c.5825A>T	c.(5824-5826)cAc>cTc	p.H1942L		NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1942					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)				CCTCTCCATGTGTTTGCAGTG	0.478													T|||	13	0.00259585	0.0008	0.0029	5008	,	,		19525	0.0		0.007	False		,,,				2504	0.0031				p.H1942L		Atlas-SNP	.											.	CHD6	312	.	0			c.A5825T						PASS	.	T	LEU/HIS	3,4403	6.2+/-15.9	0,3,2200	138	131	134		5825	3.6	1	20	dbSNP_134	134	59,8541	37.8+/-93.5	0,59,4241	yes	missense	CHD6	NM_032221.3	99	0,62,6441	AA,AT,TT		0.686,0.0681,0.4767	benign	1942/2716	40049450	62,12944	2203	4300	6503	SO:0001583	missense	84181	exon31			TCCATGTGTTTGC	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.5825A>T	20.37:g.40049450T>A	ENSP00000362330:p.His1942Leu	244	0	0		263	136	0.51711	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	37	CCDS13317.1	8	0.003663003663003663	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	T	12.05	1.822032	0.32237	6.81E-4	0.00686	ENSG00000124177	ENST00000373233	D	0.85339	-1.97	5.86	3.56	0.40772	.	0.195101	0.36101	N	0.002783	T	0.72293	0.3442	L	0.51422	1.61	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.67952	-0.5537	10	0.26408	T	0.33	-16.7152	8.1319	0.31033	0.1166:0.0:0.1688:0.7146	.	1942	Q8TD26	CHD6_HUMAN	L	1942	ENSP00000362330:H1942L	ENSP00000362330:H1942L	H	-	2	0	CHD6	39482864	0.810000	0.29049	0.998000	0.56505	0.808000	0.45660	1.583000	0.36579	1.005000	0.39183	0.533000	0.62120	CAC	T|0.995;A|0.005	0.005	strong		0.478	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			A	40049450	T	A	40049450	3	1	24	1	0	0	0	0	1	0	0	0	3331	1696	59	5	2350	5	CHD6	20	40049450	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	3179709	40049450	22976070	643	8860											
CHD6	84181	hgsc.bcm.edu	37	chr20	40079655	40079655	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ccacctcggggttgcaggtgGctagccaatctgcatccttt	6	11	11	13	1	1	0	0	0	1	0	3	0	2	0	4	4	3	4	4	4	2	3	rs41278126	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:40079655G>C	ENST00000373233.3	-	23	3791	c.3614C>G	c.(3613-3615)gCc>gGc	p.A1205G	CHD6_ENST00000309279.7_Missense_Mutation_p.A688G	NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1205					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)				GTTGCAGGTGGCTAGCCAATC	0.532													G|||	59	0.0117812	0.0008	0.0086	5008	,	,		19751	0.0		0.0457	False		,,,				2504	0.0061				p.A1205G		Atlas-SNP	.											.	CHD6	312	.	0			c.C3614G						PASS	.	G	GLY/ALA	46,4360	48.9+/-83.8	1,44,2158	174	139	151		3614	5.8	1	20	dbSNP_127	151	360,8240	121.0+/-180.1	12,336,3952	yes	missense	CHD6	NM_032221.3	60	13,380,6110	CC,CG,GG		4.186,1.044,3.1216	possibly-damaging	1205/2716	40079655	406,12600	2203	4300	6503	SO:0001583	missense	84181	exon23			CAGGTGGCTAGCC	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.3614C>G	20.37:g.40079655G>C	ENSP00000362330:p.Ala1205Gly	181	0	0		215	105	0.488372	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	37	CCDS13317.1	45|45	0.020604395604395604|0.020604395604395604	0|0	0.0|0.0	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	42|42	0.055408970976253295|0.055408970976253295	G|G	16.59|16.59	3.164784|3.164784	0.57476|0.57476	0.01044|0.01044	0.04186|0.04186	ENSG00000124177|ENSG00000124177	ENST00000373233;ENST00000309279|ENST00000440697	D;D|.	0.84800|.	-1.9;-1.9|.	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	0.199876|.	0.35739|.	N|.	0.003018|.	T|T	0.12518|0.12518	0.0304|0.0304	L|L	0.47716|0.47716	1.5|1.5	0.27988|0.27988	N|N	0.935797|0.935797	B|.	0.02656|.	0.0|.	B|.	0.04013|.	0.001|.	T|T	0.08973|0.08973	-1.0696|-1.0696	10|5	0.45353|.	T|.	0.12|.	-9.1677|-9.1677	20.0204|20.0204	0.97499|0.97499	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs41278126;rs61753662|rs41278126;rs61753662	1205|.	Q8TD26|.	CHD6_HUMAN|.	G|A	1205;688|391	ENSP00000362330:A1205G;ENSP00000308684:A688G|.	ENSP00000308684:A688G|.	A|P	-|-	2|1	0|0	CHD6|CHD6	39513069|39513069	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	6.429000|6.429000	0.73387|0.73387	2.729000|2.729000	0.93468|0.93468	0.650000|0.650000	0.86243|0.86243	GCC|CCA	G|0.971;C|0.029	0.029	strong		0.532	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			C	40079655	G	C	40079655	3	2	24	1	0	0	0	0	1	0	0	0	3331	1203	42	4	4593	4	CHD6	20	40079655	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	30205	40079655	22945865	644	8861											
BCAS4	55653	hgsc.bcm.edu	37	chr20	49411689	49411689	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcgagctcgcgctcttcctGacccccgagcctggggccga	4	6	13	18	6	1	1	0	1	1	0	3	4	2	1	5	2	2	2	5	2	0	1	rs117388674	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:49411689G>T	ENST00000358791.5	+	1	259	c.159G>T	c.(157-159)ctG>ctT	p.L53L	BCAS4_ENST00000262591.5_Silent_p.L53L|BCAS4_ENST00000371608.2_Silent_p.L53L|BCAS4_ENST00000485049.1_3'UTR|BCAS4_ENST00000609336.1_Silent_p.L23L	NM_017843.3	NP_060313.3	Q8TDM0	BCAS4_HUMAN	breast carcinoma amplified sequence 4	53						cytoplasm (GO:0005737)				large_intestine(2)|lung(2)|pancreas(1)|upper_aerodigestive_tract(1)	6						CGCTCTTCCTGACCCCCGAGC	0.736													G|||	168	0.0335463	0.0605	0.0101	5008	,	,		9022	0.0169		0.0298	False		,,,				2504	0.0348				p.L53L		Atlas-SNP	.											.	BCAS4	41	.	0			c.G159T						PASS	.	G	,,	67,2413		0,67,1173	1	2	2		159,159,159	1.5	1	20	dbSNP_132	2	106,5142		0,106,2518	no	coding-synonymous,coding-synonymous,coding-synonymous	BCAS4	NM_001010974.1,NM_017843.3,NM_198799.2	,,	0,173,3691	TT,TG,GG		2.0198,2.7016,2.2386	,,	53/159,53/212,53/204	49411689	173,7555	1240	2624	3864	SO:0001819	synonymous_variant	55653	exon1			CTTCCTGACCCCC	AK000502	CCDS13432.2, CCDS33487.1	20q13	2008-07-03			ENSG00000124243	ENSG00000124243			14367	protein-coding gene	gene with protein product		607471				12378525	Standard	NM_001010974		Approved	FLJ20495, CNOL	uc002xvq.3	Q8TDM0	OTTHUMG00000032735	ENST00000358791.5:c.159G>T	20.37:g.49411689G>T		16	0	0		22	12	0.545455	NM_198799	Q5TD52|Q5TD53|Q5TD54|Q5U5K7|Q5XKE8|Q8IXI7|Q8NEZ6|Q8TDL9|Q9NX13|Q9Y511	Silent	SNP	ENST00000358791.5	37	CCDS33487.1	80	0.03663003663003663	34	0.06910569105691057	5	0.013812154696132596	17	0.02972027972027972	24	0.0316622691292876	G	8.976	0.974160	0.18736	0.027016	0.020198	ENSG00000124243	ENST00000445038	.	.	.	4.77	1.51	0.23008	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-21.7382	3.8781	0.09066	0.0999:0.1588:0.5791:0.1622	.	.	.	.	L	28	.	.	X	+	2	2	BCAS4	48845096	1.000000	0.71417	1.000000	0.80357	0.438000	0.31896	0.689000	0.25437	1.004000	0.39156	0.484000	0.47621	TGA	G|0.963;T|0.037	0.037	strong		0.736	BCAS4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079700.1	NM_017843		T	49411689	G	T	49411689	2	4	24	1	0	0	0	0	0	0	0	1	1353	1277	45	4		4	BCAS4	20	49411689	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	9332034	49411689	13613831	645	8862											
RTEL1	51750	hgsc.bcm.edu	37	chr20	62322290	62322290	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	acagcgggcggggagccctgGcgaggagcaggtacagttcc	8	4	18	11	3	0	0	0	0	0	0	1	3	1	2	2	6	4	3	2	6	1	2	rs190887884	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:62322290G>A	ENST00000360203.5	+	27	2871	c.2546G>A	c.(2545-2547)gGc>gAc	p.G849D	RTEL1_ENST00000318100.4_Missense_Mutation_p.G849D|RTEL1_ENST00000370018.3_Missense_Mutation_p.G849D|RTEL1-TNFRSF6B_ENST00000482936.1_Missense_Mutation_p.G849D|RTEL1_ENST00000508582.2_Missense_Mutation_p.G873D|RTEL1_ENST00000370003.1_Missense_Mutation_p.G94D					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)			GGGAGCCCTGGCGAGGAGCAG	0.687													G|||	23	0.00459265	0.0023	0.0058	5008	,	,		15022	0.0		0.0099	False		,,,				2504	0.0061				p.G873D		Atlas-SNP	.											.	RTEL1	114	.	0			c.G2618A						PASS	.	G	ASP/GLY,ASP/GLY	9,4167		0,9,2079	14	15	14		2546,2618	-0.1	0	20		14	113,8185		0,113,4036	yes	missense,missense	RTEL1	NM_016434.3,NM_032957.4	94,94	0,122,6115	AA,AG,GG		1.3618,0.2155,0.978	benign,benign	849/1220,873/1244	62322290	122,12352	2088	4149	6237	SO:0001583	missense	51750	exon27			GCCCTGGCGAGGA	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.2546G>A	20.37:g.62322290G>A	ENSP00000353332:p.Gly849Asp	37	0	0		37	20	0.540541	NM_032957		Missense_Mutation	SNP	ENST00000360203.5	37		13	0.005952380952380952	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	G	11.51	1.659474	0.29515	0.002155	0.013618	ENSG00000258366	ENST00000370018;ENST00000318100;ENST00000508582;ENST00000360203;ENST00000370003	T;T;T;T;T	0.09255	3.0;3.0;3.0;3.0;3.0	4.77	-0.131	0.13494	.	0.888187	0.09800	N	0.754121	T	0.04679	0.0127	L	0.34521	1.04	0.09310	N	1	B;B;B;B	0.34290	0.052;0.447;0.003;0.008	B;B;B;B	0.35413	0.075;0.202;0.017;0.046	T	0.38972	-0.9636	10	0.23302	T	0.38	-13.4816	2.5812	0.04818	0.4374:0.0:0.343:0.2196	.	873;94;849;849	Q9NZ71-7;Q9NZ71-5;Q9NZ71;Q9NZ71-6	.;.;RTEL1_HUMAN;.	D	849;849;873;849;94	ENSP00000359035:G849D;ENSP00000322287:G849D;ENSP00000424307:G873D;ENSP00000353332:G849D;ENSP00000359020:G94D	ENSP00000353332:G849D	G	+	2	0	AL353715.1	61792734	0.001000	0.12720	0.005000	0.12908	0.006000	0.05464	0.096000	0.15147	0.093000	0.17368	-0.217000	0.12591	GGC	G|0.994;A|0.006	0.006	strong		0.687	RTEL1-011	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000289781.1	NM_032957		A	62322290	G	A	62322290	3	1	24	1	0	0	0	0	1	0	0	0	13735	1203	42	2	2648	2	RTEL1	20	62322290	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	12910601	62322290	703230	646	8863											
ZGPAT	84619	hgsc.bcm.edu	37	chr20	62339959	62339959	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggagagcctggagtcggcCttgcagacctaccgtgcgca	8	6	15	12	3	0	2	0	0	0	2	1	5	0	3	4	3	4	2	4	3	1	2	rs148155917		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr20:62339959C>G	ENST00000328969.5	+	2	154	c.27C>G	c.(25-27)gcC>gcG	p.A9A	ZGPAT_ENST00000357119.4_Silent_p.A9A|ARFRP1_ENST00000359715.5_5'Flank|ZGPAT_ENST00000448100.2_Silent_p.A9A|RP4-583P15.15_ENST00000490623.2_5'Flank|ARFRP1_ENST00000440854.1_5'Flank|ZGPAT_ENST00000369967.3_Silent_p.A9A|ARFRP1_ENST00000607873.1_5'Flank|ARFRP1_ENST00000324228.2_5'Flank|ARFRP1_ENST00000609142.1_5'Flank|ZGPAT_ENST00000355969.6_Silent_p.A9A	NM_032527.4	NP_115916.3	Q8N5A5	ZGPAT_HUMAN	zinc finger, CCCH-type with G patch domain	9					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)					TGGAGTCGGCCTTGCAGACCT	0.687																																					p.A9A		Atlas-SNP	.											.	ZGPAT	57	.	0			c.C27G						PASS	.						22	24	24					20																	62339959		2194	4282	6476	SO:0001819	synonymous_variant	84619	exon2			GTCGGCCTTGCAG	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.27C>G	20.37:g.62339959C>G		109	0	0		111	57	0.513514	NM_032527	E1P5K1|Q4VXN9|Q5JWI9|Q5JWJ0|Q8NC55|Q8WUV4|Q96JI0|Q96JU4|Q9H401	Silent	SNP	ENST00000328969.5	37	CCDS13534.1																																																																																			C|1.000;T|0.000	.	alt		0.687	ZGPAT-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080214.1	NM_181484		G	62339959	C	G	62339959	2	3	24	1	0	0	0	0	0	0	0	1	17689	668	24	4		4	ZGPAT	20	62339959	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	17669	62339959	685561	647	8864											
USP25	29761	hgsc.bcm.edu	37	chr21	17172112	17172112	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tggaatttagaagattagttCtgaattacaagcctccatca	14	13	7	7	0	2	3	1	1	1	2	3	4	3	4	2	1	2	1	2	1	7	5	rs145029756	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:17172112C>T	ENST00000285679.6	+	6	961	c.592C>T	c.(592-594)Ctg>Ttg	p.L198L	USP25_ENST00000547201.1_3'UTR|USP25_ENST00000285681.2_Silent_p.L198L|USP25_ENST00000351097.5_Silent_p.L198L|USP25_ENST00000400183.2_Silent_p.L198L	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	198	USP.				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)		AAGATTAGTTCTGAATTACAA	0.289													C|||	2	0.000399361	0.0	0.0	5008	,	,		16107	0.0		0.002	False		,,,				2504	0.0				p.L198L		Atlas-SNP	.											.	USP25	156	.	0			c.C592T						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	90	89	89		592	2.2	1	21	dbSNP_134	89	28,8558	17.9+/-57.8	0,28,4265	no	coding-synonymous	USP25	NM_013396.3		0,31,6465	TT,TC,CC		0.3261,0.0681,0.2386		198/1056	17172112	31,12961	2203	4293	6496	SO:0001819	synonymous_variant	29761	exon6			TTAGTTCTGAATT	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.592C>T	21.37:g.17172112C>T		201	0	0		178	87	0.488764	NM_013396	C0LSZ0|Q6DHZ9|Q9H9W1	Silent	SNP	ENST00000285679.6	37	CCDS33515.1																																																																																			C|0.998;T|0.002	0.002	strong		0.289	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			T	17172112	C	T	17172112	2	4	24	1	0	0	0	0	0	0	0	1	17071	912	32	2		2	USP25	21	17172112	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10		17172112	30957783	648	8865											
USP25	29761	hgsc.bcm.edu	37	chr21	17250244	17250244	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggtggatgaaatggaagaaAaggatatactagctgtagaa	17	9	13	2	0	0	3	0	1	0	2	0	6	0	6	0	4	2	2	0	4	9	4	rs149241751		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:17250244A>C	ENST00000285679.6	+	23	3298	c.2929A>C	c.(2929-2931)Aag>Cag	p.K977Q	USP25_ENST00000285681.2_Missense_Mutation_p.K1009Q|USP25_ENST00000351097.5_Missense_Mutation_p.K372Q|USP25_ENST00000400183.2_Missense_Mutation_p.K1047Q	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	977					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)		AATGGAAGAAAAGGATATACT	0.373													A|||	1	0.000199681	0.0	0.0	5008	,	,		15290	0.0		0.001	False		,,,				2504	0.0				p.K977Q		Atlas-SNP	.											.	USP25	156	.	0			c.A2929C						PASS	.	A	GLN/LYS	1,4405	2.1+/-5.4	0,1,2202	111	113	113		2929	4.5	1	21	dbSNP_134	113	14,8586	10.5+/-38.8	0,14,4286	yes	missense	USP25	NM_013396.3	53	0,15,6488	CC,CA,AA		0.1628,0.0227,0.1153	benign	977/1056	17250244	15,12991	2203	4300	6503	SO:0001583	missense	29761	exon23			GAAGAAAAGGATA	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.2929A>C	21.37:g.17250244A>C	ENSP00000285679:p.Lys977Gln	160	0	0		177	98	0.553672	NM_013396	C0LSZ0|Q6DHZ9|Q9H9W1	Missense_Mutation	SNP	ENST00000285679.6	37	CCDS33515.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	12.67	2.007030	0.35415	2.27E-4	0.001628	ENSG00000155313	ENST00000285681;ENST00000285679;ENST00000351097;ENST00000400183	T;T;T;T	0.29917	1.94;1.95;1.55;1.95	5.67	4.51	0.55191	.	0.131563	0.64402	D	0.000001	T	0.29458	0.0734	L	0.51422	1.61	0.41488	D	0.9882	B;P;B;P	0.50272	0.082;0.862;0.214;0.933	B;B;B;B	0.41917	0.059;0.37;0.127;0.323	T	0.05037	-1.0910	10	0.49607	T	0.09	-20.4276	11.8858	0.52602	0.8691:0.0:0.0:0.1309	.	1047;372;1009;977	Q9UHP3-3;Q96B65;Q9UHP3-1;Q9UHP3	.;.;.;UBP25_HUMAN	Q	1009;977;372;1047	ENSP00000285681:K1009Q;ENSP00000285679:K977Q;ENSP00000299574:K372Q;ENSP00000383044:K1047Q	ENSP00000285679:K977Q	K	+	1	0	USP25	16172115	1.000000	0.71417	0.999000	0.59377	0.173000	0.22820	8.932000	0.92897	0.970000	0.38263	-0.336000	0.08194	AAG	A|0.999;C|0.001	0.001	strong		0.373	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			C	17250244	A	C	17250244	3	2	24	1	0	0	0	0	1	0	0	0	17071	15	1	5	3019	5	USP25	21	17250244	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	78132	17250244	30879651	649	8866											
KRTAP13-4	284827	hgsc.bcm.edu	37	chr21	31803054	31803054	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagaccaatctgtggatctcGcttctatcaattcacctgct	9	13	6	13	1	5	1	2	0	3	1	6	2	5	2	2	1	1	2	2	1	3	3	rs999597	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:31803054G>A	ENST00000334068.2	+	1	483	c.461G>A	c.(460-462)cGc>cAc	p.R154H		NM_181600.1	NP_853631.1	Q3LI77	KR134_HUMAN	keratin associated protein 13-4	154			R -> H (in dbSNP:rs999597).			intermediate filament (GO:0005882)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	15						TGTGGATCTCGCTTCTATCAA	0.433													-|||	62	0.0123802	0.0053	0.0274	5008	,	,		17173	0.002		0.0298	False		,,,				2504	0.0041				p.R154H	NSCLC(196;2401 3038 18004 35753)	Atlas-SNP	.											.	KRTAP13-4	46	.	0			c.G461A						PASS	.		HIS/ARG	30,4376		1,28,2174	92	95	94		461	0.4	0	21	dbSNP_86	94	280,8320		4,272,4024	yes	missense	KRTAP13-4	NM_181600.1	29	5,300,6198	AA,AG,GG		3.2558,0.6809,2.3835	possibly-damaging	154/161	31803054	310,12696	2203	4300	6503	SO:0001583	missense	284827	exon1			GATCTCGCTTCTA	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.461G>A	21.37:g.31803054G>A	ENSP00000334834:p.Arg154His	84	0	0		94	46	0.489362	NM_181600	A2RRL3	Missense_Mutation	SNP	ENST00000334068.2	37	CCDS13592.1	37	0.01694139194139194	3	0.006097560975609756	8	0.022099447513812154	2	0.0034965034965034965	24	0.0316622691292876	-	14.66	2.600639	0.46423	0.006809	0.032558	ENSG00000186971	ENST00000334068	T	0.03152	4.03	4.67	0.445	0.16597	.	0.318065	0.22031	N	0.065594	T	0.01092	0.0036	L	0.40543	1.245	0.09310	N	1	P	0.45011	0.848	B	0.41946	0.371	T	0.41752	-0.9491	10	0.66056	D	0.02	.	5.1511	0.15009	0.2002:0.3157:0.4841:0.0	rs999597;rs52799706;rs999597	154	Q3LI77	KR134_HUMAN	H	154	ENSP00000334834:R154H	ENSP00000334834:R154H	R	+	2	0	KRTAP13-4	30724925	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.844000	0.04345	-0.040000	0.13580	-0.364000	0.07487	CGC	G|0.979;A|0.021	0.021	strong		0.433	KRTAP13-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128222.1			A	31803054	G	A	31803054	3	1	24	1	0	0	0	0	1	0	0	0	8534	1087	38	1	463	1	KRTAP13-4	21	31803054	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	14552810	31803054	16326841	650	8867											
FAM165B	54065	hgsc.bcm.edu	37	chr21	35757787	35757787	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcttgaaggttcttgagcaCgtgcccctgctgctgtatat	6	15	10	10	1	2	2	0	2	2	0	2	2	2	2	2	1	4	5	2	1	3	6	rs61747964	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:35757787C>T	ENST00000399295.2	+	3	394	c.24C>T	c.(22-24)caC>caT	p.H8H	SMIM11_ENST00000481710.1_3'UTR|SMIM11_ENST00000399292.3_Silent_p.H8H|SMIM11_ENST00000399299.1_Intron			P58511	SIM11_HUMAN	small integral membrane protein 11	8						integral component of membrane (GO:0016021)											TTCTTGAGCACGTGCCCCTGC	0.403													C|||	121	0.0241613	0.0408	0.0245	5008	,	,		20251	0.002		0.0129	False		,,,				2504	0.0358				p.H8H		Atlas-SNP	.											.	.	.	.	0			c.C24T						PASS	.	C		200,4206	126.1+/-163.2	2,196,2005	106	89	95		24	0.4	0.8	21	dbSNP_129	95	269,8331	103.8+/-164.8	4,261,4035	no	coding-synonymous	FAM165B	NM_058182.4		6,457,6040	TT,TC,CC		3.1279,4.5393,3.606		8/59	35757787	469,12537	2203	4300	6503	SO:0001819	synonymous_variant	54065	exon3			TGAGCACGTGCCC	BC015596	CCDS33550.1	21q22.12	2012-12-03	2012-12-03	2012-12-03	ENSG00000205670	ENSG00000205670			1293	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 51", "family with sequence similarity 165, member B"	C21orf51, FAM165B			Standard	NM_058182		Approved		uc002ytu.4	P58511	OTTHUMG00000086193	ENST00000399295.2:c.24C>T	21.37:g.35757787C>T		241	0	0		263	135	0.513308	NM_058182		Silent	SNP	ENST00000399295.2	37	CCDS33550.1																																																																																			C|0.971;T|0.029	0.029	strong		0.403	SMIM11-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194078.1	NM_058182		T	35757787	C	T	35757787	2	4	24	1	0	0	0	0	0	0	0	1	5485	535	19	1		1	FAM165B	21	35757787	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	3954733	35757787	12372108	651	8868											
FAM165B	54065	hgsc.bcm.edu	37	chr21	35757915	35757915	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actggaggctgaaaggaagaAgcaatcagagaaaaaagata	21	4	12	4	0	1	4	1	1	0	3	1	7	1	6	0	3	1	2	0	3	8	1	rs34016792	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:35757915A>G	ENST00000399295.2	+	3	522	c.152A>G	c.(151-153)aAg>aGg	p.K51R	SMIM11_ENST00000481710.1_3'UTR|SMIM11_ENST00000399292.3_Missense_Mutation_p.K51R|SMIM11_ENST00000399299.1_Intron			P58511	SIM11_HUMAN	small integral membrane protein 11	51			K -> R (in dbSNP:rs34016792).			integral component of membrane (GO:0016021)											GAAAGGAAGAAGCAATCAGAG	0.433													A|||	81	0.0161741	0.0113	0.0231	5008	,	,		20372	0.002		0.0129	False		,,,				2504	0.0358				p.K51R		Atlas-SNP	.											.	.	.	.	0			c.A152G						PASS	.	A	ARG/LYS	67,4339	61.1+/-98.1	0,67,2136	51	47	49		152	-3.9	0	21	dbSNP_126	49	269,8331	100.1+/-161.6	4,261,4035	yes	missense	FAM165B	NM_058182.4	26	4,328,6171	GG,GA,AA		3.1279,1.5207,2.5834	benign	51/59	35757915	336,12670	2203	4300	6503	SO:0001583	missense	54065	exon3			GGAAGAAGCAATC	BC015596	CCDS33550.1	21q22.12	2012-12-03	2012-12-03	2012-12-03	ENSG00000205670	ENSG00000205670			1293	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 51", "family with sequence similarity 165, member B"	C21orf51, FAM165B			Standard	NM_058182		Approved		uc002ytu.4	P58511	OTTHUMG00000086193	ENST00000399295.2:c.152A>G	21.37:g.35757915A>G	ENSP00000382234:p.Lys51Arg	112	0	0		95	45	0.473684	NM_058182		Missense_Mutation	SNP	ENST00000399295.2	37	CCDS33550.1	26	0.011904761904761904	4	0.008130081300813009	12	0.03314917127071823	1	0.0017482517482517483	9	0.011873350923482849	A	10.26	1.300114	0.23650	0.015207	0.031279	ENSG00000205670	ENST00000399292;ENST00000399295	T;T	0.36520	1.25;1.25	5.64	-3.86	0.04230	.	.	.	.	.	T	0.04679	0.0127	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.23691	-1.0181	8	0.15952	T	0.53	.	2.0315	0.03530	0.3294:0.3538:0.2024:0.1144	rs34016792	51	P58511	F165B_HUMAN	R	51	ENSP00000382231:K51R;ENSP00000382234:K51R	ENSP00000382231:K51R	K	+	2	0	FAM165B	34679785	0.000000	0.05858	0.000000	0.03702	0.143000	0.21401	0.555000	0.23422	-0.979000	0.03529	-0.371000	0.07208	AAG	A|0.979;G|0.021	0.021	strong		0.433	SMIM11-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194078.1	NM_058182		G	35757915	A	G	35757915	3	3	24	1	0	0	0	0	1	0	0	0	5485	72	3	3	158	3	FAM165B	21	35757915	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	128	35757915	12371980	652	8869											
UMODL1	89766	hgsc.bcm.edu	37	chr21	43531085	43531085	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcagccctcggcctagagAacttcaccttgtcacccagt	9	8	8	16	1	2	1	2	0	0	1	3	2	2	1	4	1	3	1	4	1	2	3	rs139776068	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:43531085A>T	ENST00000408910.2	+	11	1753	c.1753A>T	c.(1753-1755)Aac>Tac	p.N585Y	UMODL1_ENST00000400427.1_Missense_Mutation_p.N513Y|C21orf128_ENST00000329015.2_5'Flank|UMODL1_ENST00000400424.2_Missense_Mutation_p.N513Y|UMODL1_ENST00000408989.2_Missense_Mutation_p.N585Y	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	585					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						CGGCCTAGAGAACTTCACCTT	0.662													A|||	27	0.00539137	0.0197	0.0014	5008	,	,		15612	0.0		0.0	False		,,,				2504	0.0				p.N585Y	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.A1753T						PASS	.	A	TYR/ASN,TYR/ASN,TYR/ASN,TYR/ASN	72,4004		0,72,1966	30	38	35		1753,1537,1537,1753	2.6	0.2	21	dbSNP_134	35	0,8368		0,0,4184	yes	missense,missense,missense,missense	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	143,143,143,143	0,72,6150	TT,TA,AA		0.0,1.7664,0.5786	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	585/1319,513/1375,513/1247,585/1447	43531085	72,12372	2038	4184	6222	SO:0001583	missense	89766	exon11			CTAGAGAACTTCA		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.1753A>T	21.37:g.43531085A>T	ENSP00000386147:p.Asn585Tyr	180	0	0		193	94	0.487047	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	A	12.14	1.849160	0.32699	0.017664	0.0	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910	T;T;T;T	0.72167	-0.63;-0.61;-0.63;-0.61	3.83	2.64	0.31445	.	0.534882	0.15278	N	0.270826	T	0.39572	0.1083	N	0.19112	0.55	0.21527	N	0.999656	D;P	0.64830	0.994;0.947	P;P	0.56751	0.805;0.453	T	0.43294	-0.9400	10	0.87932	D	0	-7.3138	3.9168	0.09227	0.6689:0.2198:0.1113:0.0	.	585;585	Q5DID0-2;Q5DID0	.;UROL1_HUMAN	Y	513;513;585;585	ENSP00000383279:N513Y;ENSP00000383276:N513Y;ENSP00000386126:N585Y;ENSP00000386147:N585Y	ENSP00000383276:N513Y	N	+	1	0	UMODL1	42404154	0.482000	0.25948	0.191000	0.23289	0.007000	0.05969	0.802000	0.27069	0.780000	0.33566	0.533000	0.62120	AAC	A|0.992;T|0.008	0.008	strong		0.662	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2			T	43531085	A	T	43531085	3	4	24	1	0	0	0	0	1	0	0	0	16995	246	9	5	1795	5	UMODL1	21	43531085	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	7773170	43531085	4598810	653	8870											
SIK1	150094	hgsc.bcm.edu	37	chr21	44839263	44839263	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagctctggagctcacagtcCatctcggcctggaggacgga	8	7	14	12	2	3	0	1	0	2	0	5	5	4	4	2	5	2	2	2	5	0	0	rs34987632	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:44839263C>T	ENST00000270162.6	-	10	1347	c.1215G>A	c.(1213-1215)atG>atA	p.M405I		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	405					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)	GCTCACAGTCCATCTCGGCCT	0.682													C|||	7	0.00139776	0.0	0.0029	5008	,	,		16988	0.0		0.003	False		,,,				2504	0.002				p.M405I		Atlas-SNP	.											.	SIK1	65	.	0			c.G1215A						PASS	.	C	ILE/MET	8,4394	15.5+/-35.6	0,8,2193	40	42	41		1215	4.3	1	21	dbSNP_126	41	60,8540	36.9+/-92.0	0,60,4240	yes	missense	SIK1	NM_173354.3	10	0,68,6433	TT,TC,CC		0.6977,0.1817,0.523	benign	405/784	44839263	68,12934	2201	4300	6501	SO:0001583	missense	150094	exon10			ACAGTCCATCTCG	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.1215G>A	21.37:g.44839263C>T	ENSP00000270162:p.Met405Ile	130	0	0		144	68	0.472222	NM_173354	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Missense_Mutation	SNP	ENST00000270162.6	37	CCDS33575.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	11.67	1.707255	0.30322	0.001817	0.006977	ENSG00000142178	ENST00000270162	T	0.71222	-0.55	5.16	4.26	0.50523	.	0.469281	0.25310	N	0.031582	T	0.50531	0.1621	L	0.38838	1.175	0.29858	N	0.827879	B	0.06786	0.001	B	0.04013	0.001	T	0.52682	-0.8543	10	0.36615	T	0.2	.	10.2121	0.43147	0.0:0.9064:0.0:0.0936	rs34987632	405	P57059	SIK1_HUMAN	I	405	ENSP00000270162:M405I	ENSP00000270162:M405I	M	-	3	0	SIK1	43663691	1.000000	0.71417	0.970000	0.41538	0.589000	0.36550	2.583000	0.46094	1.140000	0.42260	0.561000	0.74099	ATG	C|0.996;T|0.004	0.004	strong		0.682	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354		T	44839263	C	T	44839263	3	4	24	1	0	0	0	0	1	0	0	0	14332	594	21	2	1156	2	SIK1	21	44839263	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1308178	44839263	3290632	654	8871											
RRP1B	23076	hgsc.bcm.edu	37	chr21	45106786	45106786	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaagaaaggaaataaacttTtagagaaaactaacttggaa	22	8	8	3	0	0	3	0	0	0	3	0	6	0	5	0	2	3	0	0	2	10	5	rs138939671	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:45106786T>G	ENST00000340648.4	+	12	1228	c.1111T>G	c.(1111-1113)Tta>Gta	p.L371V		NM_015056.2	NP_055871.1	Q14684	RRP1B_HUMAN	ribosomal RNA processing 1B	371					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)		AAATAAACTTTTAGAGAAAAC	0.438													T|||	11	0.00219649	0.0008	0.0014	5008	,	,		18271	0.0		0.006	False		,,,				2504	0.0031				p.L371V		Atlas-SNP	.											.	RRP1B	51	.	0			c.T1111G						PASS	.	T	VAL/LEU	6,4400	11.4+/-27.6	0,6,2197	94	97	96		1111	-10.6	0	21	dbSNP_134	96	63,8537	38.8+/-94.9	0,63,4237	yes	missense	RRP1B	NM_015056.2	32	0,69,6434	GG,GT,TT		0.7326,0.1362,0.5305	possibly-damaging	371/759	45106786	69,12937	2203	4300	6503	SO:0001583	missense	23076	exon12			AAACTTTTAGAGA	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.1111T>G	21.37:g.45106786T>G	ENSP00000339145:p.Leu371Val	36	0	0		27	12	0.444444	NM_015056	Q8TBZ4	Missense_Mutation	SNP	ENST00000340648.4	37	CCDS33577.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	T	3.798	-0.042253	0.07452	0.001362	0.007326	ENSG00000160208	ENST00000340648	T	0.01005	5.45	5.3	-10.6	0.00265	.	2.342010	0.01390	N	0.013218	T	0.00815	0.0027	M	0.71581	2.175	0.09310	N	1	B	0.15473	0.013	B	0.12156	0.007	T	0.49214	-0.8963	10	0.87932	D	0	-2.2485	1.3182	0.02111	0.1812:0.2897:0.2753:0.2539	.	371	Q14684	RRP1B_HUMAN	V	371	ENSP00000339145:L371V	ENSP00000339145:L371V	L	+	1	2	RRP1B	43931214	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-3.909000	0.00337	-1.445000	0.01948	-1.275000	0.01399	TTA	T|0.996;G|0.004	0.004	strong		0.438	RRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195651.1	NM_015056		G	45106786	T	G	45106786	3	3	24	1	0	0	0	0	1	0	0	0	13703	1838	64	5	1157	5	RRP1B	21	45106786	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	267523	45106786	3023109	655	8872											
C21orf29	54084	hgsc.bcm.edu	37	chr21	45948342	45948342	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agggctgcctcacctgctaaCacggagacccactcgttgcc	8	7	10	16	2	1	1	1	0	0	1	2	2	1	1	4	2	4	3	4	2	1	2	rs201202780		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:45948342C>T	ENST00000323084.4	-	6	980	c.915G>A	c.(913-915)gtG>gtA	p.V305V	TSPEAR_ENST00000397916.1_Silent_p.V237V	NM_001272037.1|NM_144991.2	NP_001258966.1|NP_659428.2	Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	305					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						CACCTGCTAACACGGAGACCC	0.642																																					p.V305V		Atlas-SNP	.											.	TSPEAR	110	.	0			c.G915A						PASS	.						152	141	144					21																	45948342		2203	4300	6503	SO:0001819	synonymous_variant	54084	exon6			TGCTAACACGGAG	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.915G>A	21.37:g.45948342C>T		56	0	0		74	26	0.351351	NM_144991		Silent	SNP	ENST00000323084.4	37	CCDS13712.1																																																																																			C|0.999;T|0.001	0.001	weak		0.642	TSPEAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098761.1	NM_144991		T	45948342	C	T	45948342	2	4	24	1	0	0	0	0	0	0	0	1	2126	465	17	2		2	C21orf29	21	45948342	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	841556	45948342	2181553	656	8873											
PCNT	5116	hgsc.bcm.edu	37	chr21	47847547	47847547	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcctttaggaagtgcccacCgcgtgccccgattggagagg	7	9	13	12	3	0	1	0	0	0	1	1	4	1	2	5	3	2	0	5	3	2	4	rs150882711	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:47847547C>T	ENST00000359568.5	+	34	7439	c.7332C>T	c.(7330-7332)acC>acT	p.T2444T	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2444					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)					AAGTGCCCACCGCGTGCCCCG	0.557													C|||	2	0.000399361	0.0	0.0	5008	,	,		21792	0.0		0.002	False		,,,				2504	0.0				p.T2444T		Atlas-SNP	.											.	PCNT	283	.	0			c.C7332T						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	68	70	70		7332	-4.9	0	21	dbSNP_134	70	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	PCNT	NM_006031.5		0,11,6492	TT,TC,CC		0.093,0.0681,0.0846		2444/3337	47847547	11,12995	2203	4300	6503	SO:0001819	synonymous_variant	5116	exon34			GCCCACCGCGTGC	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.7332C>T	21.37:g.47847547C>T		71	0	0		48	20	0.416667	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			C|0.999;T|0.001	0.001	strong		0.557	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		T	47847547	C	T	47847547	2	4	24	1	0	0	0	0	0	0	0	1	11599	639	23	1		1	PCNT	21	47847547	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1899205	47847547	282348	657	8874											
PCNT	5116	hgsc.bcm.edu	37	chr21	47856916	47856916	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gttaatgattggacgtcatcCaatgagaaagcagtgatgtc	13	11	11	6	1	1	3	1	3	0	1	3	5	2	4	1	1	1	2	1	1	3	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr21:47856916C>T	ENST00000359568.5	+	40	9128	c.9021C>T	c.(9019-9021)tcC>tcT	p.S3007S	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	3007	Interaction with NEK2.				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)					GGACGTCATCCAATGAGAAAG	0.498																																					p.S3007S		Atlas-SNP	.											.	PCNT	283	.	0			c.C9021T						PASS	.						111	94	100					21																	47856916		2203	4300	6503	SO:0001819	synonymous_variant	5116	exon40			GTCATCCAATGAG	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.9021C>T	21.37:g.47856916C>T		53	0	0		77	4	0.0519481	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			.	.	none		0.498	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		T	47856916	C	T	47856916	2	4	24	1	0	0	0	0	0	0	0	1	11599	581	21	2		2	PCNT	21	47856916	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	9369	47856916	272979	658	8875											
CECR5	27440	hgsc.bcm.edu	37	chr22	17618937	17618937	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caaagcccagccctccttgcGgaagaccagctgcacagcct	10	5	9	17	1	0	1	0	0	0	1	1	2	1	2	5	1	6	2	5	1	2	1	rs35327402	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:17618937G>A	ENST00000336737.4	-	8	1271	c.1246C>T	c.(1246-1248)Cgc>Tgc	p.R416C	CECR5_ENST00000155674.5_Missense_Mutation_p.R386C|CECR5_ENST00000399852.3_Missense_Mutation_p.R216C	NM_033070.2	NP_149061.1	Q9BXW7	CECR5_HUMAN	cat eye syndrome chromosome region, candidate 5	416			R -> C (in dbSNP:rs35327402).			mitochondrion (GO:0005739)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(1)|lung(10)|pancreas(1)|prostate(1)	21		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)				CCCTCCTTGCGGAAGACCAGC	0.632													G|||	15	0.00299521	0.0008	0.0043	5008	,	,		19931	0.0		0.008	False		,,,				2504	0.0031				p.R416C		Atlas-SNP	.											.	CECR5	46	.	0			c.C1246T						PASS	.	G	CYS/ARG,CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	98	85	90		1156,1246	2.2	0.6	22	dbSNP_126	90	32,8568	21.6+/-65.8	0,32,4268	yes	missense,missense	CECR5	NM_017829.5,NM_033070.2	180,180	0,34,6469	AA,AG,GG		0.3721,0.0454,0.2614	benign,benign	386/394,416/424	17618937	34,12972	2203	4300	6503	SO:0001583	missense	27440	exon8			CCTTGCGGAAGAC	AF273270	CCDS13741.1, CCDS33595.1	22q11.2	2008-06-12			ENSG00000069998	ENSG00000069998			1843	protein-coding gene	gene with protein product						11381032	Standard	NM_017829		Approved		uc002zmf.3	Q9BXW7	OTTHUMG00000150071	ENST00000336737.4:c.1246C>T	22.37:g.17618937G>A	ENSP00000337358:p.Arg416Cys	103	0	0		113	64	0.566372	NM_033070	B2RCK5|Q9BXW8|Q9NWA8|Q9NX41	Missense_Mutation	SNP	ENST00000336737.4	37	CCDS33595.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	G	10.55	1.382430	0.24944	4.54E-4	0.003721	ENSG00000069998	ENST00000155674;ENST00000336737;ENST00000399852	T;T;T	0.25250	1.81;1.81;1.81	4.47	2.2	0.27929	HAD-like domain (1);	0.532262	0.21527	N	0.073110	T	0.12475	0.0303	L	0.44542	1.39	0.22112	N	0.999352	B;B;B;B	0.24426	0.103;0.015;0.014;0.023	B;B;B;B	0.18263	0.021;0.008;0.006;0.008	T	0.15321	-1.0441	10	0.59425	D	0.04	-8.9079	3.6609	0.08238	0.0871:0.1262:0.4078:0.3789	rs35327402	386;216;416;280	Q9BXW7-2;A8MYZ9;Q9BXW7;B3KVW8	.;.;CECR5_HUMAN;.	C	386;416;216	ENSP00000155674:R386C;ENSP00000337358:R416C;ENSP00000382745:R216C	ENSP00000155674:R386C	R	-	1	0	CECR5	15998937	0.000000	0.05858	0.641000	0.29422	0.811000	0.45836	-0.486000	0.06513	1.065000	0.40693	0.561000	0.74099	CGC	G|0.996;A|0.004	0.004	strong		0.632	CECR5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316100.1	NM_017829		A	17618937	G	A	17618937	3	1	24	1	0	0	0	0	1	0	0	0	3209	1116	39	1	29	1	CECR5	22	17618937	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10		17618937	33685629	659	8876											
MICAL3	57553	hgsc.bcm.edu	37	chr22	18379640	18379640	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgatggcaaaatccagagaCggcagctgctgctgggtaga	11	8	14	8	1	0	3	0	1	0	2	1	4	1	3	1	3	3	6	1	3	3	2	rs61739477	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:18379640C>T	ENST00000441493.2	-	8	1408	c.1056G>A	c.(1054-1056)ccG>ccA	p.P352P	MICAL3_ENST00000207726.7_Silent_p.P352P|MICAL3_ENST00000383094.3_Silent_p.P352P|MICAL3_ENST00000429452.1_Silent_p.P352P|MICAL3_ENST00000400561.2_Silent_p.P352P|MICAL3_ENST00000444520.1_Silent_p.P352P|MICAL3_ENST00000585038.1_Silent_p.P352P|MICAL3_ENST00000414725.2_Silent_p.P352P	NM_015241.2	NP_056056.2	Q7RTP6	MICA3_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 3	352	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)		AATCCAGAGACGGCAGCTGCT	0.582											OREG0026285	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	56	0.0111821	0.0	0.0029	5008	,	,		19187	0.0248		0.0149	False		,,,				2504	0.0143				p.P352P		Atlas-SNP	.											.	MICAL3	53	.	0			c.G1056A						PASS	.	C	,,	7,3129		0,7,1561	58	56	57		1056,1056,1056	-11.7	0	22	dbSNP_129	57	108,7056		1,106,3475	no	coding-synonymous,coding-synonymous,coding-synonymous	MICAL3	NM_001122731.1,NM_001136004.1,NM_015241.2	,,	1,113,5036	TT,TC,CC		1.5075,0.2232,1.1165	,,	352/967,352/1074,352/2003	18379640	115,10185	1568	3582	5150	SO:0001819	synonymous_variant	57553	exon8			CAGAGACGGCAGC	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.1056G>A	22.37:g.18379640C>T		64	0	0	725	67	34	0.507463	NM_015241	B2RXJ5|E9PEF0|O94909|Q5U4P4|Q6ICK4|Q96DF2|Q9P2I3	Silent	SNP	ENST00000441493.2	37	CCDS46659.1																																																																																			C|0.987;T|0.013	0.013	strong		0.582	MICAL3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447351.1			T	18379640	C	T	18379640	2	4	24	1	0	0	0	0	0	0	0	1	9580	523	19	1		1	MICAL3	22	18379640	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	760703	18379640	32924926	660	8877											
PEX26	55670	hgsc.bcm.edu	37	chr22	18561342	18561342	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcctggcagagtctggccaAccacgccgtggcagaggaac	9	4	15	13	2	1	2	0	0	1	2	1	3	1	3	4	5	2	2	4	5	2	0	rs201884779|rs267608189	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:18561342A>G	ENST00000329627.7	+	2	406	c.200A>G	c.(199-201)aAc>aGc	p.N67S	PEX26_ENST00000399744.3_Missense_Mutation_p.N67S|PEX26_ENST00000428061.2_Missense_Mutation_p.N67S|XXbac-B476C20.9_ENST00000426483.1_RNA|XXbac-B476C20.9_ENST00000607927.1_RNA	NM_017929.5	NP_060399.1	Q7Z412	PEX26_HUMAN	peroxisomal biogenesis factor 26	67					protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome membrane (GO:0045046)	integral component of peroxisomal membrane (GO:0005779)|peroxisome (GO:0005777)	ATPase binding (GO:0051117)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			breast(1)|kidney(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						AGTCTGGCCAACCACGCCGTG	0.677													A|||	3	0.000599042	0.0	0.0	5008	,	,		13652	0.0		0.003	False		,,,				2504	0.0				p.N67S		Atlas-SNP	.											.	PEX26	27	.	0			c.A200G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN	0,4084		0,0,2042	6	7	7		200,200,200	-3.6	0	22		7	13,8139		0,13,4063	no	missense,missense,missense	PEX26	NM_001127649.2,NM_001199319.1,NM_017929.5	46,46,46	0,13,6105	GG,GA,AA		0.1595,0.0,0.1062	benign,benign,benign	67/306,67/257,67/306	18561342	13,12223	2042	4076	6118	SO:0001583	missense	55670	exon1			TGGCCAACCACGC	AB089678	CCDS13750.1, CCDS56221.1	22q11.21	2008-08-26	2008-08-26		ENSG00000215193	ENSG00000215193			22965	protein-coding gene	gene with protein product		608666	"peroxisome biogenesis factor 26"			12717447, 12851857	Standard	NM_017929		Approved	FLJ20695	uc002znp.4	Q7Z412	OTTHUMG00000149970	ENST00000329627.7:c.200A>G	22.37:g.18561342A>G	ENSP00000331106:p.Asn67Ser	31	0	0		26	11	0.423077	NM_001127649	F6UBB5|Q7Z413|Q7Z414|Q7Z415|Q7Z416|Q96B12|Q9NWQ0|Q9NXU0	Missense_Mutation	SNP	ENST00000329627.7	37	CCDS13750.1	.	.	.	.	.	.	.	.	.	.	A	5.785	0.329161	0.10956	0.0	0.001595	ENSG00000215193	ENST00000329627;ENST00000399744;ENST00000428061;ENST00000399746	D;D;D	0.92647	-3.08;-3.08;-3.08	5.21	-3.6	0.04570	.	1.979650	0.02715	U	0.113263	T	0.79975	0.4539	N	0.05199	-0.095	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.001;0.002	T	0.73088	-0.4093	10	0.09843	T	0.71	2.4468	7.7401	0.28837	0.265:0.4559:0.2791:0.0	.	67;67	F6UBB5;Q7Z412	.;PEX26_HUMAN	S	67	ENSP00000331106:N67S;ENSP00000382648:N67S;ENSP00000412441:N67S	ENSP00000331106:N67S	N	+	2	0	PEX26	16941342	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.459000	0.02370	-1.053000	0.03218	-0.435000	0.05868	AAC	A|0.994;G|0.006	0.006	weak		0.677	PEX26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314644.3	NM_017929		G	18561342	A	G	18561342	3	3	24	1	0	0	0	0	1	0	0	0	11755	43	2	3	202	3	PEX26	22	18561342	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	181702	18561342	32743224	661	8878											
CLTCL1	8218	hgsc.bcm.edu	37	chr22	19213091	19213091	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctgtctgatgttagcagaCagcatggcatgcagacactc	10	11	10	10	0	2	3	0	1	2	2	3	3	2	3	0	1	3	5	0	1	1	2	rs367815723		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:19213091C>T	ENST00000263200.10	-	13	2085	c.2013G>A	c.(2011-2013)ctG>ctA	p.L671L	CLTCL1_ENST00000427926.1_Silent_p.L671L|CLTCL1_ENST00000353891.5_Silent_p.L671L	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	671	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)					TGTTAGCAGACAGCATGGCAT	0.532			T	?	ALCL																																p.L671L		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"clathrin, heavy polypeptide-like 1"		L	.	CLTCL1	115	.	0			c.G2013A						PASS	.	C	,	0,4168		0,0,2084	46	47	47		2013,2013	0.6	0.9	22		47	1,8459		0,1,4229	no	coding-synonymous,coding-synonymous	CLTCL1	NM_001835.3,NM_007098.3	,	0,1,6313	TT,TC,CC		0.0118,0.0,0.0079	,	671/1584,671/1641	19213091	1,12627	2084	4230	6314	SO:0001819	synonymous_variant	8218	exon13			AGCAGACAGCATG		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.2013G>A	22.37:g.19213091C>T		74	0	0		68	33	0.485294	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Silent	SNP	ENST00000263200.10	37	CCDS46662.1																																																																																			.	.	weak		0.532	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098		T	19213091	C	T	19213091	2	4	24	1	0	0	0	0	0	0	0	1	3569	465	17	2		2	CLTCL1	22	19213091	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	651749	19213091	32091475	662	8879											
PI4KA	5297	hgsc.bcm.edu	37	chr22	21065652	21065652	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtggatgatatgacccttcTtgtccagcataatgttgccg	8	14	10	9	1	1	2	0	2	1	0	2	3	2	3	3	1	2	2	3	1	2	5			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:21065652T>C	ENST00000572273.1	-	51	5956	c.5726A>G	c.(5725-5727)aAg>aGg	p.K1909R	PI4KA_ENST00000414196.3_Missense_Mutation_p.K719R|PI4KA_ENST00000255882.6_Missense_Mutation_p.K1967R			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	1909	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)			ATGACCCTTCTTGTCCAGCAT	0.597																																					p.K1967R	GBM(136;1332 1831 3115 23601 50806)	Atlas-SNP	.											PI4KA_ENST00000255882,NS,carcinoma,+1,2	PI4KA	313	2	0			c.A5900G						scavenged	.						101	122	115					22																	21065652		2072	4111	6183	SO:0001583	missense	5297	exon51			CCCTTCTTGTCCA	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.5726A>G	22.37:g.21065652T>C	ENSP00000458238:p.Lys1909Arg	375	2	0.00533333		59	26	0.440678	NM_058004	Q7Z625|Q9UPG2	Missense_Mutation	SNP	ENST00000572273.1	37		.	.	.	.	.	.	.	.	.	.	T	16.62	3.174495	0.57692	.	.	ENSG00000241973	ENST00000255882;ENST00000414196;ENST00000399213	T;T	0.81330	-1.48;-1.48	5.04	5.04	0.67666	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.112508	0.64402	D	0.000001	T	0.71854	0.3389	L	0.28274	0.84	0.53005	D	0.999967	B;B	0.18166	0.001;0.026	B;B	0.29176	0.02;0.099	T	0.66204	-0.5982	10	0.21014	T	0.42	-24.001	15.0754	0.72074	0.0:0.0:0.0:1.0	.	300;1909	A8MTF1;P42356	.;PI4KA_HUMAN	R	1909;719;300	ENSP00000402981:K719R;ENSP00000382162:K300R	ENSP00000255882:K1909R	K	-	2	0	PI4KA	19395652	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.560000	0.60802	2.031000	0.59945	0.443000	0.29094	AAG	.	.	none		0.597	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004		C	21065652	T	C	21065652	3	2	24	1	0	0	0	0	1	0	0	0	11882	1609	56	3	428	3	PI4KA	22	21065652	Missense_Mutation	SNP	T	TCGA-G8-6326-01A-11D-2210-10	1852561	21065652	30238914	663	8880											
TOP3B	8940	hgsc.bcm.edu	37	chr22	22323003	22323003	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caaggaaccttggcctgcagCacccagtaggtctctggttt	8	10	11	12	0	1	0	0	0	1	0	2	1	1	1	3	4	3	4	3	4	3	3	rs114760416	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:22323003C>A	ENST00000398793.2	-	7	1160	c.726G>T	c.(724-726)gtG>gtT	p.V242V	TOP3B_ENST00000413067.2_5'UTR|TOP3B_ENST00000357179.5_Silent_p.V242V	NM_003935.3	NP_003926.1	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	242					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)		TGGCCTGCAGCACCCAGTAGG	0.532													C|||	4	0.000798722	0.0	0.0	5008	,	,		19610	0.0		0.004	False		,,,				2504	0.0				p.V242V		Atlas-SNP	.											.	TOP3B	107	.	0			c.G726T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	122	119	120		726	4	1	22	dbSNP_132	120	16,8584	12.6+/-44.7	0,16,4284	no	coding-synonymous	TOP3B	NM_003935.3		0,18,6485	AA,AC,CC		0.186,0.0454,0.1384		242/863	22323003	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	8940	exon7			CTGCAGCACCCAG	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.726G>T	22.37:g.22323003C>A		109	0	0		104	44	0.423077	NM_003935	A0M8Q3|Q9BUP5	Silent	SNP	ENST00000398793.2	37	CCDS13797.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	9.680	1.148957	0.21288	4.54E-4	0.00186	ENSG00000100038	ENST00000457270	.	.	.	5.04	4.01	0.46588	.	.	.	.	.	T	0.48095	0.1481	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49908	-0.8889	4	.	.	.	.	6.9623	0.24603	0.0:0.7019:0.1436:0.1544	.	.	.	.	F	37	.	.	C	-	2	0	TOP3B	20653003	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.312000	0.33574	1.318000	0.45170	0.555000	0.69702	TGC	C|0.998;A|0.002	0.002	strong		0.532	TOP3B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320251.1	NM_003935		A	22323003	C	A	22323003	2	1	24	1	0	0	0	0	0	0	0	1	16383	697	25	4		4	TOP3B	22	22323003	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1257351	22323003	28981563	664	8881											
SEZ6L	23544	hgsc.bcm.edu	37	chr22	26693026	26693026	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccaggacgacggccttgggaCcttccagcttcactaccagg	8	7	11	15	2	1	0	1	0	0	0	2	3	2	2	5	4	2	1	5	4	1	4	rs146559583	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:26693026C>A	ENST00000248933.6	+	4	1237	c.1142C>A	c.(1141-1143)aCc>aAc	p.T381N	SEZ6L_ENST00000404234.3_Missense_Mutation_p.T381N|SEZ6L_ENST00000360929.3_Missense_Mutation_p.T381N|SEZ6L_ENST00000403121.1_Missense_Mutation_p.T154N|SEZ6L_ENST00000402979.1_Missense_Mutation_p.T154N|SEZ6L_ENST00000343706.4_Missense_Mutation_p.T381N|SEZ6L_ENST00000529632.2_Missense_Mutation_p.T381N			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	381	CUB 1. {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						GGCCTTGGGACCTTCCAGCTT	0.542																																					p.T381N		Atlas-SNP	.											.	SEZ6L	174	.	0			c.C1142A						PASS	.	C	ASN/THR,ASN/THR,ASN/THR,ASN/THR,ASN/THR,ASN/THR	0,4406		0,0,2203	41	37	38		1142,1142,1142,1142,1142,1142	1.7	0.9	22	dbSNP_134	38	6,8594	4.3+/-15.6	0,6,4294	yes	missense,missense,missense,missense,missense,missense	SEZ6L	NM_001184773.1,NM_001184774.1,NM_001184775.1,NM_001184776.1,NM_001184777.1,NM_021115.4	65,65,65,65,65,65	0,6,6497	AA,AC,CC		0.0698,0.0,0.0461	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	381/1024,381/1014,381/1012,381/950,381/949,381/1025	26693026	6,13000	2203	4300	6503	SO:0001583	missense	23544	exon4			TTGGGACCTTCCA	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.1142C>A	22.37:g.26693026C>A	ENSP00000248933:p.Thr381Asn	109	0	0		107	48	0.448598	NM_001184777	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	37	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	C	12.94	2.088478	0.36855	0.0	6.98E-4	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706;ENST00000403121;ENST00000402979	T;T;T;T;T;T;T	0.18016	2.24;2.24;2.24;2.24;2.24;2.24;2.24	5.13	1.7	0.24286	CUB (5);	0.214517	0.31071	N	0.008302	T	0.16128	0.0388	L	0.55481	1.735	0.80722	D	1	B;B;B;B;B;B;B	0.23990	0.033;0.075;0.016;0.061;0.095;0.034;0.044	B;B;B;B;B;B;B	0.24848	0.03;0.056;0.016;0.033;0.038;0.022;0.056	T	0.05468	-1.0883	10	0.34782	T	0.22	.	10.0647	0.42297	0.2781:0.5879:0.134:0.0	.	381;381;154;381;381;381;381	B7ZLJ8;B7ZLJ6;B0QYH4;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;.;.;SE6L1_HUMAN	N	381;381;381;381;381;154;154	ENSP00000384772:T381N;ENSP00000437037:T381N;ENSP00000354185:T381N;ENSP00000248933:T381N;ENSP00000342661:T381N;ENSP00000384838:T154N;ENSP00000384733:T154N	ENSP00000248933:T381N	T	+	2	0	SEZ6L	25023026	0.954000	0.32549	0.916000	0.36221	0.995000	0.86356	1.759000	0.38420	0.139000	0.18822	0.561000	0.74099	ACC	C|1.000;A|0.000	0.000	strong		0.542	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3			A	26693026	C	A	26693026	3	1	24	1	0	0	0	0	1	0	0	0	14158	507	18	4	1156	4	SEZ6L	22	26693026	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	4370023	26693026	24611540	665	8882											
MN1	4330	hgsc.bcm.edu	37	chr22	28194962	28194963	+	In_Frame_Ins	INS	-	-	CTGCTG																															tgctgctgctgctgctgctgINSttgcagggactggtggtccg																										TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:28194962_28194963insCTGCTG	ENST00000302326.4	-	1	2523_2524	c.1569_1570insCAGCAG	c.(1567-1572)caacag>caaCAGCAGcag	p.523_524QQ>QQQQ		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	523	Poly-Gln.				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						tgctgctgctgttgcAGGGACT	0.668			T	ETV6	"AML, meningioma"																																p.Q524delinsQQQ		Atlas-Indel	.		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"L, O"	MN1,NS,carcinoma,+2,1	MN1	122	1	0			c.1570_1571insCAGCAG						PASS	.																																			SO:0001652	inframe_insertion	4330	exon1			.	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.1564_1569dupCAGCAG	22.37:g.28194957_28194962dupCTGCTG	ENSP00000304956:p.Gln549_Gln550dup	76	0	0		81	10	0.123457	NM_002430	A9Z1V9	In_Frame_Ins	INS	ENST00000302326.4	37	CCDS42998.1																																																																																			.	.	none		0.668	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430		CTGCTG	28194963	-	CTGCTG	28194962	7	5	24	1	0	1	1	0	0	0	0	0	9682	1386	48	0	2400	0	MN1	22	28194962	In_Frame_Ins	INS	-	TCGA-G8-6326-01A-11D-2210-10	1501936	28194962	23109604	666	8883											
GAS2L1	10634	hgsc.bcm.edu	37	chr22	29704627	29704627	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cacccccagcccccaacgccCctgccgctggggaggacacc	7	2	10	22	2	0	0	0	0	0	0	0	2	0	2	8	3	3	1	8	3	1	0	rs191844093	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:29704627C>T	ENST00000406549.3	+	2	682	c.532C>T	c.(532-534)Cct>Tct	p.P178S	GAS2L1_ENST00000403764.1_Missense_Mutation_p.P178S|GAS2L1_ENST00000407854.1_Missense_Mutation_p.P178S|GAS2L1_ENST00000407647.2_Missense_Mutation_p.P178S|GAS2L1_ENST00000471961.1_Missense_Mutation_p.P178S|GAS2L1_ENST00000360113.2_Missense_Mutation_p.P178S|GAS2L1_ENST00000341313.6_Missense_Mutation_p.P178S	NM_001278730.1	NP_001265659.1	Q99501	GA2L1_HUMAN	growth arrest-specific 2 like 1	178					cell cycle arrest (GO:0007050)|cellular response to starvation (GO:0009267)|cellular response to thyroid hormone stimulus (GO:0097067)|microtubule bundle formation (GO:0001578)|negative regulation of cell growth (GO:0030308)|negative regulation of erythrocyte differentiation (GO:0045647)|negative regulation of gene expression (GO:0010629)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)|thyroid hormone receptor binding (GO:0046966)			endometrium(2)|lung(2)|prostate(1)	5						CCCCAACGCCCCTGCCGCTGG	0.726													C|||	10	0.00199681	0.0008	0.0072	5008	,	,		14057	0.0		0.004	False		,,,				2504	0.0				p.P178S		Atlas-SNP	.											.	GAS2L1	54	.	0			c.C532T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO	1,4357		0,1,2178	10	14	13		532,532,532	3.8	0.1	22		13	45,8529		0,45,4242	yes	missense,missense,missense	GAS2L1	NM_006478.3,NM_152236.1,NM_152237.1	74,74,74	0,46,6420	TT,TC,CC		0.5248,0.0229,0.3557	probably-damaging,probably-damaging,probably-damaging	178/682,178/682,178/338	29704627	46,12886	2179	4287	6466	SO:0001583	missense	10634	exon2			AACGCCCCTGCCG	BC001782	CCDS63438.1, CCDS74840.1	22q12.2	2008-06-11			ENSG00000185340	ENSG00000185340			16955	protein-coding gene	gene with protein product		602128				8975699, 12584248, 1607387	Standard	NM_001278730		Approved	GAR22	uc003afc.1	Q99501	OTTHUMG00000151108	ENST00000406549.3:c.532C>T	22.37:g.29704627C>T	ENSP00000383995:p.Pro178Ser	15	0	0		34	20	0.588235	NM_152237	B5MCR7|Q53EN7|Q92640|Q9BUY9	Missense_Mutation	SNP	ENST00000406549.3	37		8	0.003663003663003663	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	3	0.00395778364116095	C	11.65	1.700485	0.30142	2.29E-4	0.005248	ENSG00000185340	ENST00000407647;ENST00000333679;ENST00000406549;ENST00000360113;ENST00000341313;ENST00000403764;ENST00000471961;ENST00000407854	T;T;T;T;T;T;T	0.49139	0.79;0.87;0.91;0.92;0.79;0.79;0.79	4.85	3.81	0.43845	Calponin homology domain (1);	0.846890	0.10081	N	0.718392	T	0.24198	0.0586	L	0.29908	0.895	0.09310	N	0.999996	P;B;B;B	0.35527	0.507;0.113;0.03;0.03	B;B;B;B	0.28232	0.087;0.04;0.031;0.031	T	0.03259	-1.1055	10	0.08837	T	0.75	-16.2742	12.6928	0.56985	0.0:0.6044:0.3956:0.0	.	178;178;178;178	B5MCR7;E7EQM6;A0A5E8;Q99501	.;.;.;GA2L1_HUMAN	S	178	ENSP00000385554:P178S;ENSP00000383995:P178S;ENSP00000353229:P178S;ENSP00000344012:P178S;ENSP00000385358:P178S;ENSP00000450152:P178S;ENSP00000385023:P178S	ENSP00000332834:P178S	P	+	1	0	GAS2L1	28034627	0.007000	0.16637	0.093000	0.20910	0.064000	0.16182	1.674000	0.37544	1.014000	0.39417	0.491000	0.48974	CCT	C|0.996;T|0.004	0.004	strong		0.726	GAS2L1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000321365.1	NM_006478		T	29704627	C	T	29704627	3	4	24	1	0	0	0	0	1	0	0	0	6254	623	22	2	534	2	GAS2L1	22	29704627	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1509665	29704627	21599939	667	8884											
SLC35E4	339665	hgsc.bcm.edu	37	chr22	31032881	31032881	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accacacctctgttcaccctGgccctgtcggcgctgctgct	4	10	9	18	2	2	0	1	0	1	0	3	0	2	0	4	2	2	4	4	2	0	1	rs8136373	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:31032881G>A	ENST00000343605.4	+	1	1243	c.444G>A	c.(442-444)ctG>ctA	p.L148L	SLC35E4_ENST00000406566.1_Silent_p.L148L|SLC35E4_ENST00000300385.8_Silent_p.L148L	NM_001001479.2	NP_001001479.1	Q6ICL7	S35E4_HUMAN	solute carrier family 35, member E4	148	EamA.|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						TGTTCACCCTGGCCCTGTCGG	0.677													G|||	440	0.0878594	0.2988	0.0303	5008	,	,		14087	0.0		0.0149	False		,,,				2504	0.0092				p.L148L		Atlas-SNP	.											.	SLC35E4	22	.	0			c.G444A						PASS	.	G		1219,3185	391.9+/-328.3	165,889,1148	65	36	46		444	5.2	1	22	dbSNP_116	46	171,8429	72.9+/-135.5	1,169,4130	no	coding-synonymous	SLC35E4	NM_001001479.2		166,1058,5278	AA,AG,GG		1.9884,27.6794,10.689		148/351	31032881	1390,11614	2202	4300	6502	SO:0001819	synonymous_variant	339665	exon1			CACCCTGGCCCTG		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.444G>A	22.37:g.31032881G>A		42	0	0		38	22	0.578947	NM_001001479	Q567P0	Silent	SNP	ENST00000343605.4	37	CCDS13882.1																																																																																			G|0.900;A|0.100	0.100	strong		0.677	SLC35E4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321382.1	XM_290973		A	31032881	G	A	31032881	2	1	24	1	0	0	0	0	0	0	0	1	14602	1335	47	2		2	SLC35E4	22	31032881	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1328254	31032881	20271685	668	8885											
RFPL3	10738	hgsc.bcm.edu	37	chr22	32754286	32754286	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagccccatggggaggatctGctttgctgttgctgttccat	5	13	13	10	0	1	0	0	0	1	0	2	3	2	2	3	3	4	5	3	3	0	3	rs9621426	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:32754286G>A	ENST00000249007.4	+	1	433	c.228G>A	c.(226-228)ctG>ctA	p.L76L	RFPL3_ENST00000382088.3_Silent_p.L47L|RFPL3_ENST00000397468.1_Silent_p.L47L|RFPL3S_ENST00000461833.1_5'Flank	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	76							zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						GGGAGGATCTGCTTTGCTGTT	0.537													a|||	62	0.0123802	0.0015	0.0216	5008	,	,		19556	0.0		0.0378	False		,,,				2504	0.0072				p.L76L		Atlas-SNP	.											.	RFPL3	91	.	0			c.G228A						PASS	.	A	,	20,4386	824.5+/-416.5	0,20,2183	127	119	122		228,141	-0.6	0	22	dbSNP_119	122	264,8336	807.6+/-407.2	4,256,4040	no	coding-synonymous,coding-synonymous	RFPL3	NM_001098535.1,NM_006604.2	,	4,276,6223	AA,AG,GG		3.0698,0.4539,2.1836	,	76/318,47/289	32754286	284,12722	2203	4300	6503	SO:0001819	synonymous_variant	10738	exon1			GGATCTGCTTTGC	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.228G>A	22.37:g.32754286G>A		266	0	0		271	137	0.505535	NM_001098535	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Silent	SNP	ENST00000249007.4	37	CCDS43011.1																																																																																			G|0.979;A|0.021	0.021	strong		0.537	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604		A	32754286	G	A	32754286	2	1	24	1	0	0	0	0	0	0	0	1	13270	1306	46	2		2	RFPL3	22	32754286	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1721405	32754286	18550280	669	8886											
MYH9	4627	hgsc.bcm.edu	37	chr22	36691691	36691691	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gactccaggtcttcctggagTtcagagatctgagattccag	9	11	11	10	0	3	2	1	1	2	2	6	6	6	3	3	2	0	1	3	2	0	3	rs875725	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:36691691T>C	ENST00000216181.5	-	26	3575	c.3345A>G	c.(3343-3345)gaA>gaG	p.E1115E		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1115					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						CTTCCTGGAGTTCAGAGATCT	0.522			T	ALK	ALCL		"Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"		Hereditary Macrothrombocytopenia, MYH9-associated				T|||	128	0.0255591	0.0696	0.0159	5008	,	,		20546	0.0		0.0199	False		,,,				2504	0.0051				p.E1115E		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"myosin, heavy polypeptide 9, non-muscle"	yes	L	.	MYH9	225	.	0			c.A3345G						PASS	.	T		346,4060	177.3+/-206.3	15,316,1872	51	48	49		3345	-1.8	0.9	22	dbSNP_86	49	106,8494	57.9+/-119.4	1,104,4195	no	coding-synonymous	MYH9	NM_002473.4		16,420,6067	CC,CT,TT		1.2326,7.8529,3.4753		1115/1961	36691691	452,12554	2203	4300	6503	SO:0001819	synonymous_variant	4627	exon26	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	CTGGAGTTCAGAG		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.3345A>G	22.37:g.36691691T>C		113	0	0		108	53	0.490741	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Silent	SNP	ENST00000216181.5	37	CCDS13927.1																																																																																			T|0.965;C|0.035	0.035	strong		0.522	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473		C	36691691	T	C	36691691	2	2	24	1	0	0	0	0	0	0	0	1	10051	1722	60	3		3	MYH9	22	36691691	Silent	SNP	T	TCGA-G8-6326-01A-11D-2210-10	3937405	36691691	14612875	670	8887											
KCTD17	79734	hgsc.bcm.edu	37	chr22	37458571	37458571	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcttttttttctagctgttaCaagccagaggcacccggatg	8	14	9	10	1	2	1	0	0	2	1	2	2	2	2	2	2	3	3	2	2	3	6	rs142739650	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:37458571C>T	ENST00000403888.3	+	9	904	c.903C>T	c.(901-903)taC>taT	p.Y301Y	KCTD17_ENST00000402077.3_Silent_p.Y277Y	NM_001282684.1	NP_001269613.1	Q8N5Z5	KCD17_HUMAN	potassium channel tetramerization domain containing 17	301	Pro-rich.				protein homooligomerization (GO:0051260)		identical protein binding (GO:0042802)			NS(1)|breast(1)|endometrium(1)|lung(1)|prostate(1)	5						CTAGCTGTTACAAGCCAGAGG	0.612																																					p.Y277Y		Atlas-SNP	.											.	KCTD17	17	.	0			c.C831T						PASS	.	C		0,4406		0,0,2203	48	48	48		831	3.8	1	22	dbSNP_134	48	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	KCTD17	NM_024681.2		0,7,6496	TT,TC,CC		0.0814,0.0,0.0538		277/298	37458571	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	79734	exon8			CTGTTACAAGCCA	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.903C>T	22.37:g.37458571C>T		71	0	0		80	44	0.55	NM_024681	B0QYA9|B0QYB0|O95517	Silent	SNP	ENST00000403888.3	37																																																																																				C|0.999;T|0.001	0.001	strong		0.612	KCTD17-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000318781.1	NM_024681		T	37458571	C	T	37458571	2	4	24	1	0	0	0	0	0	0	0	1	8113	489	17	2		2	KCTD17	22	37458571	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	766880	37458571	13845995	671	8888											
CDC42EP1	11135	hgsc.bcm.edu	37	chr22	37962583	37962583	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagctccgggagcacccatcGctcaccccgcagcttcctgg	6	6	10	19	3	1	0	1	0	0	0	4	1	3	1	5	2	3	5	5	2	0	1	rs61739954	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:37962583G>A	ENST00000249014.4	+	2	647	c.227G>A	c.(226-228)cGc>cAc	p.R76H		NM_152243.2	NP_689449.1	Q00587	BORG5_HUMAN	CDC42 effector protein (Rho GTPase binding) 1	76					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)					AGCACCCATCGCTCACCCCGC	0.701													G|||	69	0.013778	0.0477	0.0043	5008	,	,		14619	0.0		0.003	False		,,,				2504	0.0				p.R76H		Atlas-SNP	.											CDC42EP1,colon,carcinoma,0,1	CDC42EP1	53	1	0			c.G227A						PASS	.	G	HIS/ARG	235,4171	133.3+/-169.7	4,227,1972	31	31	31		227	4.7	1	22	dbSNP_129	31	33,8565	21.6+/-65.8	0,33,4266	yes	missense	CDC42EP1	NM_152243.2	29	4,260,6238	AA,AG,GG		0.3838,5.3336,2.0609	probably-damaging	76/392	37962583	268,12736	2203	4299	6502	SO:0001583	missense	11135	exon2			CCCATCGCTCACC	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.227G>A	22.37:g.37962583G>A	ENSP00000249014:p.Arg76His	153	0	0		135	59	0.437037	NM_152243	A8K825|Q96GN1	Missense_Mutation	SNP	ENST00000249014.4	37	CCDS13949.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	G	17.07	3.295024	0.60086	0.053336	0.003838	ENSG00000128283	ENST00000249014	T	0.32515	1.45	4.7	4.7	0.59300	.	0.376263	0.27331	N	0.019849	T	0.04092	0.0114	L	0.29908	0.895	0.31658	N	0.64598	D	0.58620	0.983	P	0.46208	0.507	T	0.03545	-1.1026	10	0.42905	T	0.14	-24.6436	8.6301	0.33915	0.0834:0.2361:0.6805:0.0	rs61739954	76	Q00587	BORG5_HUMAN	H	76	ENSP00000249014:R76H	ENSP00000249014:R76H	R	+	2	0	CDC42EP1	36292529	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	1.119000	0.31258	2.429000	0.82318	0.563000	0.77884	CGC	G|0.980;A|0.020	0.020	strong		0.701	CDC42EP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318993.1	NM_152243		A	37962583	G	A	37962583	3	1	24	1	0	0	0	0	1	0	0	0	3077	1087	38	1	229	1	CDC42EP1	22	37962583	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	504012	37962583	13341983	672	8889											
BAIAP2L2	80115	hgsc.bcm.edu	37	chr22	38483174	38483174	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcatgggtgtcatgggggAcatggaggtcatggaggtca	8	10	18	5	0	4	0	4	0	0	0	4	3	4	3	0	7	0	1	0	7	0	1	rs374089121|rs200930717|rs78489217	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:38483174A>T	ENST00000381669.3	-	11	1360	c.1216T>A	c.(1216-1218)Tcc>Acc	p.S406T	CTA-228A9.3_ENST00000609162.1_lincRNA	NM_025045.4	NP_079321.3	Q6UXY1	BI2L2_HUMAN	BAI1-associated protein 2-like 2	406					filopodium assembly (GO:0046847)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|signal transduction (GO:0007165)	cell-cell contact zone (GO:0044291)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	phospholipid binding (GO:0005543)	p.M405_S406insTSM(1)		large_intestine(2)|lung(1)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)	8	Melanoma(58;0.045)					gtcatgggggacatggaggtc	0.657													A|||	84	0.0167732	0.0076	0.0159	5008	,	,		13137	0.001		0.0278	False		,,,				2504	0.0348				p.S406T		Atlas-SNP	.											.	BAIAP2L2	39	.	1	Insertion - In frame(1)	ovary(1)	c.T1216A						PASS	.						32	38	36					22																	38483174		1925	4121	6046	SO:0001583	missense	80115	exon11			TGGGGGACATGGA	BC015619	CCDS43018.1	22q13.1	2005-02-09			ENSG00000128298	ENSG00000128298			26203	protein-coding gene	gene with protein product							Standard	NM_025045		Approved	FLJ22582	uc003auw.3	Q6UXY1	OTTHUMG00000151197	ENST00000381669.3:c.1216T>A	22.37:g.38483174A>T	ENSP00000371085:p.Ser406Thr	76	0	0		79	58	0.734177	NM_025045	B0QYE2|Q96BG7	Missense_Mutation	SNP	ENST00000381669.3	37	CCDS43018.1	254	0.1163003663003663	58	0.11788617886178862	58	0.16022099447513813	32	0.055944055944055944	106	0.13984168865435356	A	0.010	-1.753658	0.00663	.	.	ENSG00000128298	ENST00000381669;ENST00000402500;ENST00000428572	T;T	0.21543	2.0;2.0	0.235	-0.47	0.12131	.	2.310980	0.01612	N	0.022579	T	0.00039	0.0001	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27434	-1.0074	9	0.18276	T	0.48	.	.	.	.	.	406	Q6UXY1	BI2L2_HUMAN	T	406;406;97	ENSP00000371085:S406T;ENSP00000410074:S97T	ENSP00000371085:S406T	S	-	1	0	BAIAP2L2	36813120	0.121000	0.22262	0.001000	0.08648	0.001000	0.01503	0.410000	0.21098	-2.434000	0.00554	-2.582000	0.00168	TCC	A|0.886;T|0.114	0.114	strong		0.657	BAIAP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321727.1	NM_025045		T	38483174	A	T	38483174	3	4	24	1	0	0	0	0	1	0	0	0	1303	275	10	5	389	5	BAIAP2L2	22	38483174	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	520591	38483174	12821392	673	8890											
EP300	2033	hgsc.bcm.edu	37	chr22	41542753	41542753	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttactctagatggccctctAcctgacccaagtatgatccg	9	12	7	13	1	2	3	0	2	2	1	3	3	3	3	4	1	2	1	4	1	5	5	rs61756763	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:41542753A>G	ENST00000263253.7	+	11	3283	c.2064A>G	c.(2062-2064)ctA>ctG	p.L688L		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	688					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						ATGGCCCTCTACCTGACCCAA	0.368			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome				A|||	7	0.00139776	0.0	0.0	5008	,	,		16320	0.0		0.006	False		,,,				2504	0.001				p.L688L		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300	367	.	0			c.A2064G						PASS	.	A		4,4402	8.1+/-20.4	0,4,2199	95	93	93		2064	-11.5	0.3	22	dbSNP_129	93	41,8559	25.1+/-72.6	1,39,4260	no	coding-synonymous	EP300	NM_001429.3		1,43,6459	GG,GA,AA		0.4767,0.0908,0.346		688/2415	41542753	45,12961	2203	4300	6503	SO:0001819	synonymous_variant	2033	exon11	Familial Cancer Database	Broad Thumb-Hallux syndrome	CCCTCTACCTGAC	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.2064A>G	22.37:g.41542753A>G		32	0	0		43	24	0.55814	NM_001429	B1AKC2	Silent	SNP	ENST00000263253.7	37	CCDS14010.1																																																																																			A|0.997;G|0.003	0.003	strong		0.368	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		G	41542753	A	G	41542753	2	3	24	1	0	0	0	0	0	0	0	1	5150	378	14	3		3	EP300	22	41542753	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	3059579	41542753	9761813	674	8891											
SCUBE1	80274	hgsc.bcm.edu	37	chr22	43618695	43618695	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gccgttgcgtttctgcagcgCcttgccctgcggccctggaa	3	10	13	15	4	1	0	0	0	1	0	1	1	1	1	4	2	5	3	4	2	1	3	rs148458324	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:43618695C>A	ENST00000360835.4	-	12	1507	c.1381G>T	c.(1381-1383)Gcg>Tcg	p.A461S		NM_173050.3	NP_766638.2	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	461					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)				TTCTGCAGCGCCTTGCCCTGC	0.657													C|||	13	0.00259585	0.0	0.0072	5008	,	,		18680	0.0		0.008	False		,,,				2504	0.0				p.A461S		Atlas-SNP	.											.	SCUBE1	105	.	0			c.G1381T						PASS	.	C	SER/ALA	6,4392	9.9+/-24.2	0,6,2193	52	40	44		1381	-1.2	0	22	dbSNP_134	44	96,8502	51.9+/-112.3	2,92,4205	yes	missense	SCUBE1	NM_173050.3	99	2,98,6398	AA,AC,CC		1.1165,0.1364,0.7849	benign	461/989	43618695	102,12894	2199	4299	6498	SO:0001583	missense	80274	exon12			GCAGCGCCTTGCC		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.1381G>T	22.37:g.43618695C>A	ENSP00000354080:p.Ala461Ser	71	0	0		82	49	0.597561	NM_173050	Q5R336	Missense_Mutation	SNP	ENST00000360835.4	37	CCDS14048.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	C	0.029	-1.348806	0.01266	0.001364	0.011165	ENSG00000159307	ENST00000360835	D	0.84873	-1.91	5.16	-1.2	0.09554	.	0.847688	0.11048	N	0.605376	T	0.49949	0.1587	N	0.02391	-0.57	0.54753	D	0.999981	B	0.02656	0.0	B	0.04013	0.001	T	0.48692	-0.9013	10	0.07030	T	0.85	.	6.1713	0.20418	0.2337:0.4632:0.0:0.3031	.	461	Q8IWY4	SCUB1_HUMAN	S	461	ENSP00000354080:A461S	ENSP00000354080:A461S	A	-	1	0	SCUBE1	41948639	0.001000	0.12720	0.034000	0.17996	0.045000	0.14185	-0.867000	0.04241	-0.138000	0.11434	-0.302000	0.09304	GCG	C|0.994;A|0.006	0.006	strong		0.657	SCUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319582.3	NM_173050		A	43618695	C	A	43618695	3	1	24	1	0	0	0	0	1	0	0	0	13959	739	26	4	1629	4	SCUBE1	22	43618695	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	2075942	43618695	7685871	675	8892											
ARHGAP8	23779	hgsc.bcm.edu	37	chr22	45258343	45258343	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggaggcacctggggagcaCggcctggcaccatgggaaca	9	3	16	13	2	0	0	0	0	0	0	0	3	0	3	4	7	2	3	4	7	1	0	rs41278889	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chr22:45258343C>T	ENST00000389774.2	+	13	1404	c.1263C>T	c.(1261-1263)caC>caT	p.H421H	ARHGAP8_ENST00000356099.6_Silent_p.H390H|ARHGAP8_ENST00000517296.3_Silent_p.H600H|ARHGAP8_ENST00000336963.4_3'UTR|PRR5-ARHGAP8_ENST00000361473.5_Silent_p.H521H|PRR5-ARHGAP8_ENST00000352766.7_Silent_p.H600H|ARHGAP8_ENST00000389773.5_Silent_p.H512H	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	421					positive regulation of ERK1 and ERK2 cascade (GO:0070374)|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)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(9)|prostate(1)|skin(7)	29		all_neural(38;0.00409)|Ovarian(80;0.00976)|Glioma(61;0.0649)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0204)		CTGGGGAGCACGGCCTGGCAC	0.612													C|||	33	0.00658946	0.0212	0.0014	5008	,	,		17491	0.001		0.003	False		,,,				2504	0.0				p.H512H		Atlas-SNP	.											.	PRR5-ARHGAP8	53	.	0			c.C1536T						PASS	.	C	,,,	52,4354	53.6+/-89.4	1,50,2152	50	49	49		1263,,1536,1170	-6.1	0	22	dbSNP_127	49	21,8579	15.3+/-51.7	0,21,4279	no	coding-synonymous,utr-3,coding-synonymous,coding-synonymous	ARHGAP8,PRR5-ARHGAP8	NM_001017526.1,NM_001198726.1,NM_181334.4,NM_181335.2	,,,	1,71,6431	TT,TC,CC		0.2442,1.1802,0.5613	,,,	421/465,,512/556,390/434	45258343	73,12933	2203	4300	6503	SO:0001819	synonymous_variant	553158	exon15			GGAGCACGGCCTG	AF177331	CCDS14060.2, CCDS33664.1, CCDS56233.1	22q13.3	2010-05-11			ENSG00000241484	ENSG00000241484		"Rho GTPase activating proteins"	677	protein-coding gene	gene with protein product		609405				10591208	Standard	NM_001198726		Approved	FLJ20185, BPGAP1		P85298	OTTHUMG00000030234	ENST00000389774.2:c.1263C>T	22.37:g.45258343C>T		82	0	0		67	31	0.462687	NM_181334	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Silent	SNP	ENST00000389774.2	37	CCDS33664.1	10	0.004578754578754579	6	0.012195121951219513	1	0.0027624309392265192	1	0.0017482517482517483	2	0.002638522427440633	C	2.018	-0.425336	0.04701	0.011802	0.002442	ENSG00000248405	ENST00000515632	.	.	.	3.04	-6.08	0.02151	.	.	.	.	.	T	0.10937	0.0267	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.23762	-1.0179	4	.	.	.	.	0.5	0.00578	0.2906:0.2175:0.2876:0.2043	rs41278889	.	.	.	M	461	.	.	T	+	2	0	PRR5-ARHGAP8	43637007	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.542000	0.06091	-1.256000	0.02478	-0.964000	0.02622	ACG	C|0.995;T|0.005	0.005	strong		0.612	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701		T	45258343	C	T	45258343	2	4	24	1	0	0	0	0	0	0	0	1	888	535	19	1		1	ARHGAP8	22	45258343	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	1639648	45258343	6046223	676	8893											
PLCXD1	55344	hgsc.bcm.edu	37	chrX	200939	200939	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	actggatgtcggcactgtgtCcccggctctgggatgtgccc	4	10	14	13	2	1	0	0	0	1	0	3	2	2	2	3	4	1	2	3	4	0	0			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:200939C>T	ENST00000381657.2	+	2	599	c.85C>T	c.(85-87)Ccc>Tcc	p.P29S	PLCXD1_ENST00000399012.1_Missense_Mutation_p.P29S|PLCXD1_ENST00000484611.2_3'UTR|PLCXD1_ENST00000381663.3_Missense_Mutation_p.P29S	NM_018390.3	NP_060860.1	Q9NUJ7	PLCX1_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 1	29					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)				GGCACTGTGTCCCCGGCTCTG	0.652													c|||	7	0.00139776	0.0008	0.0058	5008	,	,		15888	0.0		0.002	False		,,,				2504	0.0				p.P29S		Atlas-SNP	.											.	PLCXD1	18	.	0			c.C85T						PASS	.		SER/PRO	7,4399		0,7,2196	131	118	123		85	2	0.4	X	dbSNP_134	123	74,8518		0,74,4222	no	missense	PLCXD1	NM_018390.3	74	0,81,6418	TT,TC,CC		0.8613,0.1589,0.6232	benign	29/324	200939	81,12917	2203	4296	6499	SO:0001583	missense	55344	exon2			CTGTGTCCCCGGC	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.85C>T	X.37:g.200939C>T	ENSP00000371073:p.Pro29Ser	376	1	0.00265957		343	169	0.492711	NM_018390	A2BH51|A2BH52	Missense_Mutation	SNP	ENST00000381657.2	37	CCDS14103.1	5	0.0022893772893772895	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	.	0.110	-1.139616	0.01728	0.001589	0.008613	ENSG00000182378	ENST00000399012;ENST00000430923;ENST00000445062;ENST00000381657;ENST00000429181;ENST00000381663;ENST00000443019;ENST00000415337;ENST00000447472;ENST00000448477	.	.	.	1.98	1.98	0.26296	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	0.820267	0.11258	U	0.582867	T	0.10208	0.0250	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.27262	-1.0079	8	0.05721	T	0.95	.	7.6567	0.28379	0.0:1.0:0.0:0.0	.	29	Q9NUJ7	PLCX1_HUMAN	S	29	.	ENSP00000371073:P29S	P	+	1	0	PLCXD1	140939	0.000000	0.05858	0.388000	0.26195	0.309000	0.27889	-0.301000	0.08232	0.793000	0.33875	0.449000	0.29647	CCC	C|0.995;T|0.005	0.005	strong		0.652	PLCXD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058879.2	NM_018390		T	200939	C	T	200939	3	4	24	1	0	0	0	0	1	0	0	0	12050	855	30	2	87	2	PLCXD1	23	200939	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10		200939	155069621	677	8894											
SLC25A6	293	hgsc.bcm.edu	37	chrX	1510877	1510877	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctccggccaagaagtctttgGcgaaggagatggcctgttcc	8	9	13	11	2	1	2	0	0	1	2	3	4	3	2	4	4	0	1	4	4	3	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:1510877G>C	ENST00000381401.5	-	1	740	c.26C>G	c.(25-27)gCc>gGc	p.A9G	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	9					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)	GAAGTCTTTGGCGAAGGAGAT	0.692																																					p.A9G		Atlas-SNP	.											.	SLC25A6	27	.	0			c.C26G						PASS	.						36	37	36					X																	1510877		2202	4295	6497	SO:0001583	missense	293	exon1			TCTTTGGCGAAGG	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.26C>G	X.37:g.1510877G>C	ENSP00000370808:p.Ala9Gly	81	0	0		63	28	0.444444	NM_001636	Q96C49	Missense_Mutation	SNP	ENST00000381401.5	37	CCDS14114.1	.	.	.	.	.	.	.	.	.	.	g	8.851	0.944558	0.18356	.	.	ENSG00000169100	ENST00000381401;ENST00000447786	T	0.79454	-1.27	1.54	1.54	0.23209	Mitochondrial carrier domain (2);	0.000000	0.41500	U	0.000862	T	0.69575	0.3126	L	0.52364	1.645	0.09310	N	1	B	0.09022	0.002	B	0.21708	0.036	T	0.61068	-0.7137	10	0.40728	T	0.16	.	10.0455	0.42184	0.0:0.0:1.0:0.0	.	9	P12236	ADT3_HUMAN	G	9	ENSP00000370808:A9G	ENSP00000370808:A9G	A	-	2	0	SLC25A6	1470877	0.997000	0.39634	0.724000	0.30704	0.047000	0.14425	1.204000	0.32296	0.807000	0.34208	0.281000	0.19383	GCC	.	.	none		0.692	SLC25A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055596.1	NM_001636		C	1510877	G	C	1510877	3	2	24	1	0	0	0	0	1	0	0	0	14528	1203	42	4	886	4	SLC25A6	23	1510877	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1309938	1510877	153759683	678	8895											
KAL1	3730	hgsc.bcm.edu	37	chrX	8538659	8538659	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggctcctcggggagatcccAaactatagtgacggtcacac	10	7	11	13	3	1	2	1	1	0	1	4	3	3	2	2	4	1	1	2	4	3	2			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:8538659A>C	ENST00000262648.3	-	7	1092	c.943T>G	c.(943-945)Tgg>Ggg	p.W315G		NM_000216.2	NP_000207.2	P23352	KALM_HUMAN	Kallmann syndrome 1 sequence	315	Fibronectin type-III 2. {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						GGGAGATCCCAAACTATAGTG	0.542																																					p.W315G		Atlas-SNP	.											.	KAL1	78	.	0			c.T943G						PASS	.						81	60	67					X																	8538659		2203	4300	6503	SO:0001583	missense	3730	exon7			GATCCCAAACTAT		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.943T>G	X.37:g.8538659A>C	ENSP00000262648:p.Trp315Gly	166	0	0		218	9	0.0412844	NM_000216	B2RPF8	Missense_Mutation	SNP	ENST00000262648.3	37	CCDS14130.1	.	.	.	.	.	.	.	.	.	.	A	12.48	1.950679	0.34377	.	.	ENSG00000011201	ENST00000262648	D	0.86297	-2.1	4.11	4.11	0.48088	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.125962	0.64402	D	0.000019	D	0.92034	0.7476	M	0.73962	2.25	0.80722	D	1	D	0.71674	0.998	D	0.69824	0.966	D	0.92526	0.6029	10	0.87932	D	0	-9.6393	11.7793	0.52003	1.0:0.0:0.0:0.0	.	315	P23352	KALM_HUMAN	G	315	ENSP00000262648:W315G	ENSP00000262648:W315G	W	-	1	0	KAL1	8498659	1.000000	0.71417	0.464000	0.27143	0.040000	0.13550	7.362000	0.79507	1.356000	0.45884	0.352000	0.21897	TGG	.	.	none		0.542	KAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055692.1	NM_000216		C	8538659	A	C	8538659	3	2	24	1	0	0	0	0	1	0	0	0	7983	130	5	5	1131	5	KAL1	23	8538659	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	7027782	8538659	146731901	679	8896											
SHROOM4	57477	hgsc.bcm.edu	37	chrX	50350751	50350751	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcctcctcctcctcctcctGttgcttctgctgctgctgtt	0	17	6	18	0	1	0	0	0	1	0	7	0	7	0	6	0	4	6	6	0	0	3	rs201290098		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:50350751G>C	ENST00000289292.7	-	6	3674	c.3391C>G	c.(3391-3393)Cag>Gag	p.Q1131E	SHROOM4_ENST00000460112.3_Missense_Mutation_p.Q1015E|SHROOM4_ENST00000376020.2_Missense_Mutation_p.Q1131E			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1131	Gln-rich.			KQQ -> QQQQKQQE (in Ref. 1; BAA86516 and 3; AAI51241). {ECO:0000305}.	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)					tcctcctcctgttgcttctgc	0.582																																					p.Q1131E		Atlas-SNP	.											.	SHROOM4	171	.	0			c.C3391G						PASS	.						15	14	15					X																	50350751		2199	4294	6493	SO:0001583	missense	57477	exon6			CCTCCTGTTGCTT	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.3391C>G	X.37:g.50350751G>C	ENSP00000289292:p.Gln1131Glu	66	0	0		52	6	0.115385	NM_020717	A7E2X9|D6RFW0|Q96LA0	Missense_Mutation	SNP	ENST00000289292.7	37	CCDS35277.1	.	.	.	.	.	.	.	.	.	.	G	0.015	-1.554911	0.00918	.	.	ENSG00000158352	ENST00000289292;ENST00000376020;ENST00000460112	T;T;T	0.06449	3.3;3.3;3.3	4.89	-0.0454	0.13851	.	1.383290	0.04423	N	0.367895	T	0.03827	0.0108	N	0.24115	0.695	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.36456	-0.9747	10	0.02654	T	1	.	4.0399	0.09746	0.093:0.4322:0.3193:0.1556	.	1131	Q9ULL8	SHRM4_HUMAN	E	1131;1131;1015	ENSP00000289292:Q1131E;ENSP00000365188:Q1131E;ENSP00000421450:Q1015E	ENSP00000289292:Q1131E	Q	-	1	0	SHROOM4	50367491	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	0.374000	0.20501	-0.047000	0.13423	-0.434000	0.05882	CAG	.	.	weak		0.582	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717		C	50350751	G	C	50350751	3	2	24	1	0	0	0	0	1	0	0	0	14311	1386	48	4	1106	4	SHROOM4	23	50350751	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	41812092	50350751	104919809	680	8897											
KDM5C	8242	hgsc.bcm.edu	37	chrX	53223819	53223819	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atagaggttgtagaggaggcCgtgctcgatgatgccagtgg	9	9	17	6	2	0	3	0	1	0	2	1	5	0	4	2	4	2	3	2	4	2	3	rs76525703	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:53223819C>T	ENST00000375401.3	-	23	4072	c.3540G>A	c.(3538-3540)acG>acA	p.T1180T	KDM5C_ENST00000404049.3_Silent_p.T1179T|KDM5C_ENST00000375379.3_Silent_p.T1180T|KDM5C_ENST00000452825.3_Silent_p.T1113T|KDM5C_ENST00000375383.3_Silent_p.T1139T	NM_001282622.1|NM_004187.3	NP_001269551.1|NP_004178.2	P41229	KDM5C_HUMAN	lysine (K)-specific demethylase 5C	1180					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						TAGAGGAGGCCGTGCTCGATG	0.612			"N, F, S"		clear cell renal carcinoma								c|||	18	0.00476821	0.0136	0.0	3775	,	,		14232	0.0		0.0	False		,,,				2504	0.0				p.T1180T		Atlas-SNP	.		Rec	yes		X	Xp11.22-p11.21	8242	lysine (K)-specific demethylase 5C (JARID1C)		E	.	KDM5C	385	.	0			c.G3540A						PASS	.	C	,	37,3798		0,28,9,1604,562	221	158	179		3339,3540	-4.5	0	X	dbSNP_131	179	1,6727		0,0,1,2428,1871	no	coding-synonymous,coding-synonymous	KDM5C	NM_001146702.1,NM_004187.3	,	0,28,10,4032,2433	TT,TC,T,CC,C		0.0149,0.9648,0.3597	,	1113/1380,1180/1561	53223819	38,10525	2203	4300	6503	SO:0001819	synonymous_variant	8242	exon23			GGAGGCCGTGCTC	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.3540G>A	X.37:g.53223819C>T		245	1	0.00408163		279	278	0.996416	NM_004187	B0QZ44|B4E3I2|F5H3T1|Q5JUX3|Q5JUX4|Q5JUX5|Q7Z5S5	Silent	SNP	ENST00000375401.3	37	CCDS14351.1																																																																																			C|0.996;T|0.004	0.004	strong		0.612	KDM5C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056737.2	NM_004187		T	53223819	C	T	53223819	2	4	24	1	0	0	0	0	0	0	0	1	8144	639	23	1		1	KDM5C	23	53223819	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	2873068	53223819	102046741	681	8898											
KDM5C	8242	hgsc.bcm.edu	37	chrX	53230909	53230909	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcggtagtgctcaatgcaCtggcgcccagcaggcaactg	8	6	14	13	3	1	0	1	0	0	0	1	0	1	0	1	4	4	5	1	4	3	1	rs74850270	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:53230909C>T	ENST00000375401.3	-	14	2416	c.1884G>A	c.(1882-1884)caG>caA	p.Q628Q	KDM5C_ENST00000404049.3_Silent_p.Q627Q|KDM5C_ENST00000465402.1_5'UTR|KDM5C_ENST00000375379.3_Silent_p.Q628Q|KDM5C_ENST00000452825.3_Silent_p.Q561Q|KDM5C_ENST00000375383.3_Silent_p.Q587Q	NM_001282622.1|NM_004187.3	NP_001269551.1|NP_004178.2	P41229	KDM5C_HUMAN	lysine (K)-specific demethylase 5C	628	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				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						GCTCAATGCACTGGCGCCCAG	0.592			"N, F, S"		clear cell renal carcinoma								C|||	35	0.00927152	0.025	0.0029	3775	,	,		13930	0.0		0.0	False		,,,				2504	0.0				p.Q628Q		Atlas-SNP	.		Rec	yes		X	Xp11.22-p11.21	8242	lysine (K)-specific demethylase 5C (JARID1C)		E	.	KDM5C	385	.	0			c.G1884A						PASS	.	C	,	119,3716		1,96,21,1535,550	47	42	44		1683,1884	-0.3	1	X	dbSNP_131	44	1,6727		0,0,1,2428,1871	no	coding-synonymous,coding-synonymous	KDM5C	NM_001146702.1,NM_004187.3	,	1,96,22,3963,2421	TT,TC,T,CC,C		0.0149,3.103,1.136	,	561/1380,628/1561	53230909	120,10443	2203	4300	6503	SO:0001819	synonymous_variant	8242	exon14			AATGCACTGGCGC	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.1884G>A	X.37:g.53230909C>T		90	0	0		110	110	1	NM_004187	B0QZ44|B4E3I2|F5H3T1|Q5JUX3|Q5JUX4|Q5JUX5|Q7Z5S5	Silent	SNP	ENST00000375401.3	37	CCDS14351.1																																																																																			C|0.988;T|0.012	0.012	strong		0.592	KDM5C-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056737.2	NM_004187		T	53230909	C	T	53230909	2	4	24	1	0	0	0	0	0	0	0	1	8144	564	20	2		2	KDM5C	23	53230909	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	7090	53230909	102039651	682	8899											
IQSEC2	23096	hgsc.bcm.edu	37	chrX	53263764	53263764	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggcaggactgtacaggggCagtggggatgtgggctggtg	6	7	23	5	0	0	0	0	0	0	0	0	2	0	2	0	9	1	4	0	9	1	1	rs184087864		TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:53263764C>T	ENST00000375368.5	-	14	4274	c.4074G>A	c.(4072-4074)ctG>ctA	p.L1358L	IQSEC2_ENST00000396435.3_Silent_p.L1368L|IQSEC2_ENST00000375365.2_3'UTR			Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2	1358	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						TGTACAGGGGCAGTGGGGATG	0.672													c|||	294	0.0778808	0.2133	0.0173	3775	,	,		4478	0.0		0.0	False		,,,				2504	0.0				p.L1368L		Atlas-SNP	.											.	IQSEC2	195	.	0			c.G4104A						PASS	.						10	11	10					X																	53263764		689	1580	2269	SO:0001819	synonymous_variant	23096	exon15			CAGGGGCAGTGGG	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.4074G>A	X.37:g.53263764C>T		80	0	0		103	96	0.932039	NM_001111125	B3KT97|C7SDG1|O60275|Q5JUX1	Silent	SNP	ENST00000375368.5	37																																																																																				C|0.937;T|0.063	0.063	strong		0.672	IQSEC2-201	KNOWN	basic	protein_coding	protein_coding		XM_291345		T	53263764	C	T	53263764	2	4	24	1	0	0	0	0	0	0	0	1	7827	697	25	2		2	IQSEC2	23	53263764	Silent	SNP	C	TCGA-G8-6326-01A-11D-2210-10	32855	53263764	102006796	683	8900											
MTMR8	55613	hgsc.bcm.edu	37	chrX	63488670	63488670	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	catccccagagatatttatgGccctaaggctgcccacaatc	11	9	7	14	0	0	1	0	0	0	1	2	2	1	1	4	2	1	1	4	2	4	4			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:63488670G>T	ENST00000374852.3	-	14	1929	c.1862C>A	c.(1861-1863)gCc>gAc	p.A621D	MTMR8_ENST00000453546.1_Intron	NM_017677.3	NP_060147.2	Q96EF0	MTMR8_HUMAN	myotubularin related protein 8	621						nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)	p.0?(2)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|skin(3)	37						GATATTTATGGCCCTAAGGCT	0.527																																					p.A621D		Atlas-SNP	.											.	MTMR8	178	.	2	Whole gene deletion(2)	ovary(1)|large_intestine(1)	c.C1862A						PASS	.						83	65	71					X																	63488670		2203	4300	6503	SO:0001583	missense	55613	exon14			TTTATGGCCCTAA	AK000133	CCDS14379.1	Xq11.2-q12	2013-01-11			ENSG00000102043	ENSG00000102043		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	16825	protein-coding gene	gene with protein product						11275328	Standard	NM_017677		Approved	FLJ20126	uc004dvs.3	Q96EF0	OTTHUMG00000021707	ENST00000374852.3:c.1862C>A	X.37:g.63488670G>T	ENSP00000363985:p.Ala621Asp	71	0	0		75	75	1	NM_017677	Q5JT99|Q9NXP6	Missense_Mutation	SNP	ENST00000374852.3	37	CCDS14379.1	.	.	.	.	.	.	.	.	.	.	G	12.94	2.088488	0.36855	.	.	ENSG00000102043	ENST00000374852;ENST00000247400	D	0.95272	-3.66	2.51	2.51	0.30379	.	0.460045	0.16633	U	0.205952	D	0.85969	0.5821	N	0.08118	0	0.09310	N	1	P	0.41232	0.743	B	0.40602	0.334	T	0.80162	-0.1497	10	0.87932	D	0	.	6.6727	0.23078	0.0:0.2931:0.7069:0.0	.	621	Q96EF0	MTMR8_HUMAN	D	621;507	ENSP00000363985:A621D	ENSP00000247400:A507D	A	-	2	0	MTMR8	63405395	0.859000	0.29813	0.004000	0.12327	0.057000	0.15508	1.348000	0.33987	1.541000	0.49316	0.436000	0.28706	GCC	.	.	none		0.527	MTMR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056949.2	NM_017677		T	63488670	G	T	63488670	3	4	24	1	0	0	0	0	1	0	0	0	9958	1203	42	4	256	4	MTMR8	23	63488670	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	10224906	63488670	91781890	684	8901											
VSIG4	11326	hgsc.bcm.edu	37	chrX	65242157	65242157	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcataatccagaggaactGtgtccagcaggcgggcgtag	11	7	13	10	2	1	1	1	0	0	1	3	2	3	2	2	3	2	2	2	3	3	2	rs41307375	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:65242157G>A	ENST00000374737.4	-	8	1256	c.1148C>T	c.(1147-1149)aCa>aTa	p.T383I	VSIG4_ENST00000455586.2_3'UTR|VSIG4_ENST00000412866.2_Missense_Mutation_p.T289I	NM_001257403.1|NM_007268.2	NP_001244332.1|NP_009199.1	Q9Y279	VSIG4_HUMAN	V-set and immunoglobulin domain containing 4	383					complement activation, alternative pathway (GO:0006957)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of T cell proliferation (GO:0042130)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CAGAGGAACTGTGTCCAGCAG	0.507													G|||	14	0.00370861	0.0	0.0058	3775	,	,		15026	0.0		0.007	False		,,,				2504	0.0031				p.T383I		Atlas-SNP	.											.	VSIG4	54	.	0			c.C1148T						PASS	.	G	ILE/THR,,,ILE/THR	5,3830		0,4,1,1628,570	81	68	73		866,,,1148	2.7	0	X	dbSNP_127	73	55,6673		0,35,20,2393,1852	yes	missense,utr-3,utr-3,missense	VSIG4	NM_001100431.1,NM_001184830.1,NM_001184831.1,NM_007268.2	89,,,89	0,39,21,4021,2422	AA,AG,A,GG,G		0.8175,0.1304,0.568	probably-damaging,,,probably-damaging	289/306,,,383/400	65242157	60,10503	2203	4300	6503	SO:0001583	missense	11326	exon8			GGAACTGTGTCCA	AJ132502	CCDS14383.1, CCDS48132.1, CCDS55435.1	Xq12-q13.3	2013-01-29			ENSG00000155659	ENSG00000155659		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17032	protein-coding gene	gene with protein product		300353				10899594, 11004523, 17016555, 17016562	Standard	NM_007268		Approved	Z39IG	uc004dwh.2	Q9Y279	OTTHUMG00000021727	ENST00000374737.4:c.1148C>T	X.37:g.65242157G>A	ENSP00000363869:p.Thr383Ile	132	0	0		139	138	0.992806	NM_007268	Q6UXI4	Missense_Mutation	SNP	ENST00000374737.4	37	CCDS14383.1	10	0.006027727546714889	0	0.0	4	0.011049723756906077	0	0.0	4	0.005305039787798408	G	6.391	0.440248	0.12104	0.001304	0.008175	ENSG00000155659	ENST00000374737;ENST00000412866	T;T	0.29142	1.58;2.06	4.55	2.69	0.31865	.	0.562854	0.14925	N	0.290449	T	0.23532	0.0569	L	0.57536	1.79	0.09310	N	0.999995	P;B	0.35908	0.527;0.232	B;B	0.37989	0.262;0.082	T	0.13045	-1.0524	10	0.72032	D	0.01	-2.997	8.7467	0.34591	0.0:0.0:0.5888:0.4112	rs41307375	289;383	Q9Y279-3;Q9Y279	.;VSIG4_HUMAN	I	383;289	ENSP00000363869:T383I;ENSP00000394143:T289I	ENSP00000363869:T383I	T	-	2	0	VSIG4	65158882	0.010000	0.17322	0.007000	0.13788	0.011000	0.07611	0.952000	0.29149	0.423000	0.26033	0.513000	0.50165	ACA	G|0.994;A|0.006	0.006	strong		0.507	VSIG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056986.1	NM_007268		A	65242157	G	A	65242157	3	1	24	1	0	0	0	0	1	0	0	0	17240	1377	48	2	55	2	VSIG4	23	65242157	Missense_Mutation	SNP	G	TCGA-G8-6326-01A-11D-2210-10	1753487	65242157	90028403	685	8902											
VSIG4	11326	hgsc.bcm.edu	37	chrX	65253454	65253454	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gagggatacatctcctggaaCcttgtggctcacatgcaggc	9	9	12	11	0	2	0	1	0	1	0	3	3	2	2	2	4	3	2	2	4	2	2	rs41306131	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:65253454C>A	ENST00000374737.4	-	2	382	c.274G>T	c.(274-276)Gtt>Ttt	p.V92F	VSIG4_ENST00000455586.2_Missense_Mutation_p.V92F|VSIG4_ENST00000412866.2_Missense_Mutation_p.V92F	NM_001257403.1|NM_007268.2	NP_001244332.1|NP_009199.1	Q9Y279	VSIG4_HUMAN	V-set and immunoglobulin domain containing 4	92	Ig-like 1.				complement activation, alternative pathway (GO:0006957)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of T cell proliferation (GO:0042130)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TCTCCTGGAACCTTGTGGCTC	0.547													C|||	14	0.00370861	0.0	0.0058	3775	,	,		14684	0.0		0.007	False		,,,				2504	0.0031				p.V92F		Atlas-SNP	.											.	VSIG4	54	.	0			c.G274T						PASS	.	C	PHE/VAL,PHE/VAL,PHE/VAL,PHE/VAL	5,3830		0,4,1,1628,570	136	115	122		274,274,274,274	-0.5	0.1	X	dbSNP_127	122	55,6673		0,35,20,2393,1852	yes	missense,missense,missense,missense	VSIG4	NM_001100431.1,NM_001184830.1,NM_001184831.1,NM_007268.2	50,50,50,50	0,39,21,4021,2422	AA,AC,A,CC,C		0.8175,0.1304,0.568	probably-damaging,probably-damaging,probably-damaging,probably-damaging	92/306,92/322,92/228,92/400	65253454	60,10503	2203	4300	6503	SO:0001583	missense	11326	exon2			CTGGAACCTTGTG	AJ132502	CCDS14383.1, CCDS48132.1, CCDS55435.1	Xq12-q13.3	2013-01-29			ENSG00000155659	ENSG00000155659		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	17032	protein-coding gene	gene with protein product		300353				10899594, 11004523, 17016555, 17016562	Standard	NM_007268		Approved	Z39IG	uc004dwh.2	Q9Y279	OTTHUMG00000021727	ENST00000374737.4:c.274G>T	X.37:g.65253454C>A	ENSP00000363869:p.Val92Phe	139	1	0.00719424		135	134	0.992593	NM_001100431	Q6UXI4	Missense_Mutation	SNP	ENST00000374737.4	37	CCDS14383.1	10|10	0.006027727546714889|0.006027727546714889	0|0	0.0|0.0	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	4|4	0.005305039787798408|0.005305039787798408	C|C	9.614|9.614	1.131982|1.131982	0.21041|0.21041	0.001304|0.001304	0.008175|0.008175	ENSG00000155659|ENSG00000155659	ENST00000427538|ENST00000374737;ENST00000455586;ENST00000412866	.|T;T;T	.|0.04156	.|3.69;3.69;3.69	4.93|4.93	-0.487|-0.487	0.12060|0.12060	.|Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|0.656229	.|0.14136	.|N	.|0.339047	T|T	0.08358|0.08358	0.0208|0.0208	L|L	0.57536|0.57536	1.79|1.79	0.09310|0.09310	N|N	1|1	.|P;D;D;P;D	.|0.65815	.|0.825;0.994;0.995;0.889;0.995	.|P;P;D;P;D	.|0.69307	.|0.597;0.884;0.963;0.543;0.929	T|T	0.11275|0.11275	-1.0594|-1.0594	5|10	.|0.56958	.|D	.|0.05	-3.6037|-3.6037	4.5823|4.5823	0.12264|0.12264	0.0:0.4461:0.2494:0.3045|0.0:0.4461:0.2494:0.3045	rs41306131|rs41306131	.|92;92;82;92;92	.|C9J1L3;Q9Y279-2;C9JH67;Q9Y279-3;Q9Y279	.|.;.;.;.;VSIG4_HUMAN	V|F	18|92	.|ENSP00000363869:V92F;ENSP00000411581:V92F;ENSP00000394143:V92F	.|ENSP00000363869:V92F	G|V	-|-	2|1	0|0	VSIG4|VSIG4	65170179|65170179	0.000000|0.000000	0.05858|0.05858	0.076000|0.076000	0.20297|0.20297	0.004000|0.004000	0.04260|0.04260	-1.190000|-1.190000	0.03058|0.03058	0.038000|0.038000	0.15604|0.15604	-0.198000|-0.198000	0.12761|0.12761	GGT|GTT	C|0.994;A|0.006	0.006	strong		0.547	VSIG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056986.1	NM_007268		A	65253454	C	A	65253454	3	1	24	1	0	0	0	0	1	0	0	0	17240	507	18	4	957	4	VSIG4	23	65253454	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	11297	65253454	90017106	686	8903											
POF1B	79983	hgsc.bcm.edu	37	chrX	84563194	84563194	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	taaatgtggacagcactagtCggagtgacttatcagacata	14	10	10	7	1	1	2	1	1	0	1	2	4	1	4	0	2	1	1	0	2	5	4	rs75398746	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:84563194C>T	ENST00000262753.4	-	10	1131	c.986G>A	c.(985-987)cGa>cAa	p.R329Q	POF1B_ENST00000373145.3_Missense_Mutation_p.R329Q	NM_024921.3	NP_079197.3	Q8WVV4	POF1B_HUMAN	premature ovarian failure, 1B	329			R -> Q (in POF2B; disrupts binding to nonmuscle actin filaments; abolishes tight junction localization; altered ciliogenesis and cystogenesis; dbSNP:rs75398746). {ECO:0000269|PubMed:15459172, ECO:0000269|PubMed:16773570}.			tight junction (GO:0005923)				central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|liver(2)|lung(17)|ovary(1)|prostate(1)	35						CAGCACTAGTCGGAGTGACTT	0.343													C|||	11	0.00291391	0.0045	0.0058	3775	,	,		11719	0.0		0.001	False		,,,				2504	0.0				p.R329Q		Atlas-SNP	.											.	POF1B	77	.	0			c.G986A	GRCh37	CM066591	POF1B	M	rs75398746	PASS	.	C	GLN/ARG	26,3809		0,23,3,1609,568	93	80	84	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	986	5	0.7	X	dbSNP_131	84	17,6711		0,12,5,2416,1867	yes	missense	POF1B	NM_024921.3	43	0,35,8,4025,2435	TT,TC,T,CC,C		0.2527,0.678,0.4071	probably-damaging	329/590	84563194	43,10520	2203	4300	6503	SO:0001583	missense	79983	exon10			ACTAGTCGGAGTG	BC017500	CCDS14452.1	Xq21.2	2008-02-05			ENSG00000124429	ENSG00000124429			13711	protein-coding gene	gene with protein product		300603				11299520	Standard	NM_024921		Approved	POF, FLJ22792	uc004eer.2	Q8WVV4	OTTHUMG00000021934	ENST00000262753.4:c.986G>A	X.37:g.84563194C>T	ENSP00000262753:p.Arg329Gln	158	0	0		139	139	1	NM_024921	A8K2U5|Q5H9E9|Q5H9F0|Q8NG12|Q9H5Y2|Q9H738|Q9H744	Missense_Mutation	SNP	ENST00000262753.4	37	CCDS14452.1	6	0.003616636528028933	1	0.0020408163265306124	3	0.008333333333333333	0	0.0	0	0.0	C	16.37	3.102992	0.56183	0.00678	0.002527	ENSG00000124429	ENST00000262753;ENST00000373145	T;T	0.16073	2.37;2.37	5.86	5.0	0.66597	.	0.101855	0.64402	N	0.000003	T	0.12347	0.0300	L	0.58101	1.795	0.29902	A	0.175686	B;B	0.32968	0.392;0.392	B;B	0.19946	0.027;0.027	T	0.16424	-1.0403	9	0.72032	D	0.01	-4.9537	12.8282	0.57731	0.0:0.9187:0.0:0.0813	.	329;329	Q8WVV4-1;Q8WVV4	.;POF1B_HUMAN	Q	329	ENSP00000262753:R329Q;ENSP00000362238:R329Q	ENSP00000262753:R329Q	R	-	2	0	POF1B	84449850	0.934000	0.31675	0.671000	0.29857	0.941000	0.58515	2.969000	0.49232	1.236000	0.43740	0.600000	0.82982	CGA	C|0.996;T|0.004	0.004	strong		0.343	POF1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057391.2	NM_024921		T	84563194	C	T	84563194	3	4	24	1	0	0	0	0	1	0	0	0	12191	884	31	1	815	1	POF1B	23	84563194	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	19309740	84563194	70707366	687	8904											
NRK	203447	hgsc.bcm.edu	37	chrX	105193709	105193709	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatccttgaaatgtggaaagAcataccatcttctataggta	14	12	8	7	0	2	2	0	1	2	1	3	4	3	3	2	2	1	1	2	2	6	6			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:105193709A>G	ENST00000243300.9	+	27	4799	c.4496A>G	c.(4495-4497)gAc>gGc	p.D1499G	NRK_ENST00000540278.1_Missense_Mutation_p.D80G|NRK_ENST00000428173.2_Missense_Mutation_p.D1500G	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	1499	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						ATGTGGAAAGACATACCATCT	0.383										HNSCC(51;0.14)																											p.D1499G		Atlas-SNP	.											.	NRK	321	.	0			c.A4496G						PASS	.						70	59	62					X																	105193709		1868	4085	5953	SO:0001583	missense	203447	exon27			GGAAAGACATACC	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.4496A>G	X.37:g.105193709A>G	ENSP00000434830:p.Asp1499Gly	100	1	0.01		110	110	1	NM_198465	Q32ND6|Q5H9K2|Q6ZMP2	Missense_Mutation	SNP	ENST00000243300.9	37		.	.	.	.	.	.	.	.	.	.	A	18.18	3.567047	0.65651	.	.	ENSG00000123572	ENST00000243300;ENST00000428173;ENST00000540278	T;T;T	0.03982	3.74;3.74;3.74	5.96	5.96	0.96718	Citron-like (2);	0.000000	0.47093	D	0.000252	T	0.10895	0.0266	L	0.36672	1.1	0.39530	D	0.968642	P;P	0.49447	0.674;0.924	P;P	0.55785	0.457;0.784	T	0.02505	-1.1149	10	0.87932	D	0	.	12.9799	0.58557	1.0:0.0:0.0:0.0	.	80;1499	B7Z1I7;Q7Z2Y5	.;NRK_HUMAN	G	1499;1500;80	ENSP00000434830:D1499G;ENSP00000438378:D1500G;ENSP00000438148:D80G	ENSP00000434830:D1499G	D	+	2	0	NRK	105080365	1.000000	0.71417	0.998000	0.56505	0.958000	0.62258	6.778000	0.75043	2.002000	0.58637	0.486000	0.48141	GAC	.	.	none		0.383	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465		G	105193709	A	G	105193709	3	3	24	1	0	0	0	0	1	0	0	0	10664	275	10	3	4602	3	NRK	23	105193709	Missense_Mutation	SNP	A	TCGA-G8-6326-01A-11D-2210-10	20630515	105193709	50076851	688	8905											
SMARCA1	6594	hgsc.bcm.edu	37	chrX	128582381	128582381	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aatttccatattttctttctCaatcaatgaaatcagagtgt	13	17	4	7	0	4	2	3	1	2	1	6	2	5	2	1	0	0	0	1	0	5	5			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:128582381C>T	ENST00000371122.4	-	24	3199	c.3070G>A	c.(3070-3072)Gag>Aag	p.E1024K	SMARCA1_ENST00000371123.1_Missense_Mutation_p.E1012K|SMARCA1_ENST00000371121.3_Missense_Mutation_p.E1012K	NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	1024					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						TTTTCTTTCTCAATCAATGAA	0.323																																					p.E1024K		Atlas-SNP	.											.	SMARCA1	126	.	0			c.G3070A						PASS	.						125	117	120					X																	128582381		2203	4298	6501	SO:0001583	missense	6594	exon24			CTTTCTCAATCAA	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.3070G>A	X.37:g.128582381C>T	ENSP00000360163:p.Glu1024Lys	112	0	0		120	7	0.0583333	NM_003069	Q5JV41|Q5JV42	Missense_Mutation	SNP	ENST00000371122.4	37	CCDS14612.1	.	.	.	.	.	.	.	.	.	.	C	18.53	3.645013	0.67358	.	.	ENSG00000102038	ENST00000371121;ENST00000371123;ENST00000371122;ENST00000450039	D;D;D;D	0.91792	-2.91;-2.91;-2.9;-2.89	5.87	5.87	0.94306	SLIDE (1);Homeodomain-like (1);	0.000000	0.64402	D	0.000009	D	0.96436	0.8837	M	0.84773	2.715	0.80722	D	1	D;D;D;D	0.76494	0.992;0.999;0.99;0.992	D;D;D;D	0.79784	0.979;0.993;0.964;0.979	D	0.95323	0.8422	10	0.35671	T	0.21	-17.3926	19.3889	0.94570	0.0:1.0:0.0:0.0	.	1003;1024;1012;1024	E9PCY3;B7ZLQ5;P28370-2;P28370	.;.;.;SMCA1_HUMAN	K	1012;1012;1024;1003	ENSP00000360162:E1012K;ENSP00000360164:E1012K;ENSP00000360163:E1024K;ENSP00000404275:E1003K	ENSP00000360162:E1012K	E	-	1	0	SMARCA1	128410062	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.177000	0.71961	2.618000	0.88619	0.600000	0.82982	GAG	.	.	none		0.323	SMARCA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058206.1	NM_003069		T	128582381	C	T	128582381	3	4	24	1	0	0	0	0	1	0	0	0	14783	835	29	2	98	2	SMARCA1	23	128582381	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	23388672	128582381	26688179	689	8906											
FRMD7	90167	hgsc.bcm.edu	37	chrX	131212944	131212944	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctcagatgcgtgcactccAttcacattttggtagtagcc	8	12	10	11	1	2	1	2	0	0	1	3	1	3	1	2	2	3	4	2	2	2	5	rs7051368	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:131212944A>G	ENST00000298542.4	-	12	1276	c.1101T>C	c.(1099-1101)aaT>aaC	p.N367N	FRMD7_ENST00000464296.1_Silent_p.N352N|FRMD7_ENST00000370879.1_Silent_p.N247N	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	367					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)					cGTGCACTCCATTCACATTTT	0.483													A|||	179	0.0474172	0.0628	0.0231	3775	,	,		13883	0.0		0.0726	False		,,,				2504	0.0072				p.N367N		Atlas-SNP	.											.	FRMD7	69	.	0			c.T1101C						PASS	.	A		379,3456		11,295,62,1326,509	174	160	165		1101	-0.6	0.9	X	dbSNP_116	165	659,6069		23,440,173,1965,1699	no	coding-synonymous	FRMD7	NM_194277.2		34,735,235,3291,2208	GG,GA,G,AA,A		9.7949,9.8827,9.8268		367/715	131212944	1038,9525	2203	4300	6503	SO:0001819	synonymous_variant	90167	exon12			CACTCCATTCACA	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.1101T>C	X.37:g.131212944A>G		41	0	0		42	42	1	NM_194277	C0LLJ3|Q5JX99	Silent	SNP	ENST00000298542.4	37	CCDS35397.1																																																																																			A|0.911;G|0.089	0.089	strong		0.483	FRMD7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355031.1	NM_194277		G	131212944	A	G	131212944	2	3	24	1	0	0	0	0	0	0	0	1	6063	214	8	3		3	FRMD7	23	131212944	Silent	SNP	A	TCGA-G8-6326-01A-11D-2210-10	2630563	131212944	24057616	690	8907											
MAGEC1	9947	hgsc.bcm.edu	37	chrX	140993737	140993737	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgagtattttccagagttccCctgagagtactcaaagtcct	10	13	8	10	0	1	3	1	2	0	2	4	4	4	3	4	0	1	3	4	0	3	5			TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:140993737C>T	ENST00000285879.4	+	4	833	c.547C>T	c.(547-549)Cct>Tct	p.P183S	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	183										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)					CCAGAGTTCCCCTGAGAGTAC	0.493										HNSCC(15;0.026)																											p.P183S		Atlas-SNP	.											.	MAGEC1	317	.	0			c.C547T						PASS	.						80	91	87					X																	140993737		2203	4298	6501	SO:0001583	missense	9947	exon4			AGTTCCCCTGAGA	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.547C>T	X.37:g.140993737C>T	ENSP00000285879:p.Pro183Ser	266	0	0		230	13	0.0565217	NM_005462	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	.	.	.	.	.	.	.	.	.	.	c	6.525	0.465191	0.12402	.	.	ENSG00000155495	ENST00000285879	T	0.03301	3.98	.	.	.	.	.	.	.	.	T	0.01976	0.0062	N	0.08118	0	0.09310	N	0.999996	B	0.17038	0.02	B	0.09377	0.004	T	0.45086	-0.9285	8	0.87932	D	0	.	3.8388	0.08905	0.0:0.6604:0.0:0.3396	.	183	O60732	MAGC1_HUMAN	S	183	ENSP00000285879:P183S	ENSP00000285879:P183S	P	+	1	0	MAGEC1	140821403	0.149000	0.22717	0.039000	0.18376	0.039000	0.13416	1.804000	0.38873	0.054000	0.16065	0.054000	0.15206	CCT	.	.	none		0.493	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462		T	140993737	C	T	140993737	3	4	24	1	0	0	0	0	1	0	0	0	9189	623	22	2	553	2	MAGEC1	23	140993737	Missense_Mutation	SNP	C	TCGA-G8-6326-01A-11D-2210-10	9780793	140993737	14276823	691	8908											
AFF2	2334	hgsc.bcm.edu	37	chrX	148035200	148035200	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcggagagcagctctgagtcGgattcagacactgaaagtag	12	8	13	8	2	2	4	1	2	1	2	4	6	2	5	0	2	2	3	0	2	2	2	rs12011040	byFrequency	TCGA-G8-6326-01A-11D-2210-10	TCGA-G8-6326-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	6ae5496e-cf5b-4e6d-8bb1-a2c0cb904077	7b21bfff-b5f1-4796-b0bc-d4c529ebcbfd	g.chrX:148035200G>A	ENST00000370460.2	+	10	1967	c.1488G>A	c.(1486-1488)tcG>tcA	p.S496S	AFF2_ENST00000286437.5_Silent_p.S137S|AFF2_ENST00000370457.5_Silent_p.S463S|AFF2_ENST00000342251.3_Silent_p.S463S	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	496					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)					GCTCTGAGTCGGATTCAGACA	0.587													A|||	536	0.141987	0.3381	0.0476	3775	,	,		11768	0.003		0.0388	False		,,,				2504	0.0143				p.S496S		Atlas-SNP	.											.	AFF2	679	.	0			c.G1488A						PASS	.	A	,,,,,	1531,2304		268,774,221,590,350	126	118	121		1389,1458,1383,1371,411,1488	-10	0	X	dbSNP_120	121	287,6441		3,196,85,2229,1787	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AFF2	NM_001169122.1,NM_001169123.1,NM_001169124.1,NM_001169125.1,NM_001170628.1,NM_002025.3	,,,,,	271,970,306,2819,2137	AA,AG,A,GG,G		4.2658,39.9218,17.211	,,,,,	463/1277,486/1302,461/1277,457/1273,137/953,496/1312	148035200	1818,8745	2203	4300	6503	SO:0001819	synonymous_variant	2334	exon10			TGAGTCGGATTCA	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.1488G>A	X.37:g.148035200G>A		183	0	0		171	170	0.994152	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Silent	SNP	ENST00000370460.2	37	CCDS14684.1																																																																																			0|0.003;A|0.180	0.180	strong		0.587	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025		A	148035200	G	A	148035200	2	1	24	1	0	0	0	0	0	0	0	1	357	1103	39	1		1	AFF2	23	148035200	Silent	SNP	G	TCGA-G8-6326-01A-11D-2210-10	7041463	148035200	7235360	692	8909											
PLEKHN1	84069	hgsc.bcm.edu	37	chr1	906122	906122	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcgaggggtcccgagagcaCgccttccagatcacaggtgt	8	7	13	13	3	1	2	1	0	0	2	4	4	3	2	3	3	1	1	3	3	0	1	rs41285812	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:906122C>T	ENST00000379409.2	+	5	498	c.468C>T	c.(466-468)caC>caT	p.H156H	PLEKHN1_ENST00000379407.3_Silent_p.H156H|PLEKHN1_ENST00000379410.3_Silent_p.H156H			Q494U1	PKHN1_HUMAN	pleckstrin homology domain containing, family N member 1	156	PH 1.									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)		CCCGAGAGCACGCCTTCCAGA	0.662													C|||	9	0.00179712	0.0023	0.0	5008	,	,		15705	0.0		0.005	False		,,,				2504	0.001				p.H156H		Atlas-SNP	.											.	PLEKHN1	49	.	0			c.C468T						PASS	.	C	,	7,4399	12.9+/-30.5	1,5,2197	50	59	56		468,468	-3.5	0.9	1	dbSNP_127	56	68,8532	40.8+/-97.7	0,68,4232	no	coding-synonymous,coding-synonymous	PLEKHN1	NM_001160184.1,NM_032129.2	,	1,73,6429	TT,TC,CC		0.7907,0.1589,0.5767	,	156/577,156/612	906122	75,12931	2203	4300	6503	SO:0001819	synonymous_variant	84069	exon5			AGAGCACGCCTTC	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.468C>T	1.37:g.906122C>T		118	1	0.00847458		106	99	0.933962	NM_001160184	Q494U2|Q5SV98|Q9H0M7	Silent	SNP	ENST00000379409.2	37																																																																																				C|0.995;T|0.005	0.005	strong		0.662	PLEKHN1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000473256.1	NM_032129		T	906122	C	T	906122	2	4	25	1	0	0	0	0	0	0	0	1	12092	535	19	1		1	PLEKHN1	1	906122	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10		906122	248344499	1	8910											
AGRN	375790	hgsc.bcm.edu	37	chr1	978800	978800	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaggccacggcctgtaccctCgggcgggagatccaggtggc	6	5	17	13	3	0	1	0	0	0	1	2	3	1	1	4	6	1	1	4	6	1	1	rs375687903		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:978800C>T	ENST00000379370.2	+	8	1616	c.1566C>T	c.(1564-1566)ctC>ctT	p.L522L		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	522	Kazal-like 5. {ECO:0000255|PROSITE- ProRule:PRU00798}.				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)		CCTGTACCCTCGGGCGGGAGA	0.682																																					p.L522L		Atlas-SNP	.											.	AGRN	110	.	0			c.C1566T						PASS	.	C		0,4374		0,0,2187	35	35	35		1566	-7.6	0.1	1		35	2,8588		0,2,4293	no	coding-synonymous	AGRN	NM_198576.3		0,2,6480	TT,TC,CC		0.0233,0.0,0.0154		522/2046	978800	2,12962	2187	4295	6482	SO:0001819	synonymous_variant	375790	exon8			TACCCTCGGGCGG	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.1566C>T	1.37:g.978800C>T		43	0	0		80	4	0.05	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Silent	SNP	ENST00000379370.2	37	CCDS30551.1																																																																																			.	.	none		0.682	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576		T	978800	C	T	978800	2	4	25	1	0	0	0	0	0	0	0	1	397	871	31	1		1	AGRN	1	978800	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	72678	978800	248271821	2	8911											
SCNN1D	6339	hgsc.bcm.edu	37	chr1	1222622	1222622	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgggaggacagccacgggaGccaggacggccacttcgtcc	9	4	15	13	3	0	0	0	0	0	0	2	4	1	4	4	5	2	0	4	5	0	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1222622G>A	ENST00000338555.2	+	6	1905	c.761G>A	c.(760-762)aGc>aAc	p.S254N	SCNN1D_ENST00000400928.3_Missense_Mutation_p.S254N|SCNN1D_ENST00000379116.5_Missense_Mutation_p.S418N|SCNN1D_ENST00000325425.8_Missense_Mutation_p.S320N			P51172	SCNND_HUMAN	sodium channel, non-voltage-gated 1, delta subunit	254					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)	AGCCACGGGAGCCAGGACGGC	0.677																																					p.S418N		Atlas-SNP	.											.	SCNN1D	60	.	0			c.G1253A						PASS	.						22	20	21					1																	1222622		2169	4249	6418	SO:0001583	missense	6339	exon9			ACGGGAGCCAGGA	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.761G>A	1.37:g.1222622G>A	ENSP00000339504:p.Ser254Asn	77	0	0		79	75	0.949367	NM_001130413	A9Z1X6|B1PS44|Q08AQ3|Q09HT0|Q5T7L3|Q8NA24	Missense_Mutation	SNP	ENST00000338555.2	37		.	.	.	.	.	.	.	.	.	.	G	8.390	0.839506	0.16891	.	.	ENSG00000162572	ENST00000379110;ENST00000379116;ENST00000338555;ENST00000325425;ENST00000400928;ENST00000379099	T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04	4.4	-0.589	0.11683	.	8.235220	0.00166	N	0.000001	T	0.53286	0.1787	L	0.51422	1.61	0.09310	N	1	B;B	0.32968	0.392;0.003	B;B	0.33960	0.173;0.001	T	0.26360	-1.0105	10	0.27785	T	0.31	.	2.8715	0.05618	0.2348:0.1198:0.5233:0.1222	.	254;418	P51172;A6NNF7	SCNND_HUMAN;.	N	285;418;254;320;254;45	ENSP00000368411:S418N;ENSP00000339504:S254N;ENSP00000321594:S320N;ENSP00000383717:S254N	ENSP00000321594:S320N	S	+	2	0	SCNN1D	1212485	0.000000	0.05858	0.001000	0.08648	0.030000	0.12068	-0.212000	0.09319	0.280000	0.22209	0.313000	0.20887	AGC	.	.	none		0.677	SCNN1D-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000005802.2	NM_002978		A	1222622	G	A	1222622	3	1	25	1	0	0	0	0	1	0	0	0	13944	971	34	2	981	2	SCNN1D	1	1222622	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	243822	1222622	248027999	3	8912											
ATAD3B	83858	hgsc.bcm.edu	37	chr1	1431048	1431048	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacctcatggagcctggccAcggacccctcctacccctgc	6	7	8	20	1	2	0	2	0	0	0	3	2	3	2	8	3	3	0	8	3	1	1	rs201429000		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1431048A>G	ENST00000308647.7	+	16	1914	c.1798A>G	c.(1798-1800)Acg>Gcg	p.T600A		NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	600						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)		GAGCCTGGCCACGGACCCCTC	0.672																																					p.T600A		Atlas-SNP	.											ATAD3B,NS,neuroblastoma,0,1	ATAD3B	68	1	0			c.A1798G						scavenged	.																																			SO:0001583	missense	83858	exon16			CTGGCCACGGACC	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.1798A>G	1.37:g.1431048A>G	ENSP00000311766:p.Thr600Ala	119	2	0.0168067		147	9	0.0612245	NM_031921	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Missense_Mutation	SNP	ENST00000308647.7	37	CCDS30.1	.	.	.	.	.	.	.	.	.	.	g	0.005	-2.129716	0.00338	.	.	ENSG00000160072	ENST00000378737;ENST00000308647	D	0.93189	-3.18	1.2	-1.67	0.08238	.	0.186138	0.20546	N	0.090207	T	0.78220	0.4249	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	0.65792	-0.6082	10	0.12766	T	0.61	.	2.0444	0.03557	0.4037:0.0:0.3428:0.2535	.	554;600	Q5T9A4-3;Q5T9A4	.;ATD3B_HUMAN	A	434;600	ENSP00000311766:T600A	ENSP00000311766:T600A	T	+	1	0	ATAD3B	1420911	0.007000	0.16637	0.000000	0.03702	0.003000	0.03518	0.259000	0.18405	-1.264000	0.02452	-1.032000	0.02404	ACG	.	.	weak		0.672	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921		G	1431048	A	G	1431048	3	3	25	1	0	0	0	0	1	0	0	0	1074	159	6	3	1860	3	ATAD3B	1	1431048	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	208426	1431048	247819573	4	8913											
ATAD3A	55210	hgsc.bcm.edu	37	chr1	1458150	1458150	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggctgacgctgctggctgtTggggtctactcagccaagaa	7	9	15	10	1	2	2	1	1	1	1	2	2	2	2	1	4	3	5	1	4	3	2	rs1135025	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1458150T>C	ENST00000378755.5	+	8	1015	c.921T>C	c.(919-921)gtT>gtC	p.V307V	ATAD3A_ENST00000378756.3_Silent_p.V259V|ATAD3A_ENST00000536055.1_Silent_p.V180V	NM_018188.3	NP_060658.3	Q9NVI7	ATD3A_HUMAN	ATPase family, AAA domain containing 3A	307					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)		TGCTGGCTGTTGGGGTCTACT	0.677													N|||	134	0.0267572	0.0507	0.0504	5008	,	,		14272	0.0109		0.0109	False		,,,				2504	0.0102				p.V307V		Atlas-SNP	.											.	ATAD3A	35	.	0			c.T921C						PASS	.	C	,,	39,4357	795.2+/-415.3	2,35,2161	40	52	48		777,540,921	-9.5	0	1	dbSNP_86	48	67,8533	811.9+/-407.1	0,67,4233	no	coding-synonymous,coding-synonymous,coding-synonymous	ATAD3A	NM_001170535.1,NM_001170536.1,NM_018188.3	,,	2,102,6394	CC,CT,TT		0.7791,0.8872,0.8156	,,	259/587,180/508,307/635	1458150	106,12890	2198	4300	6498	SO:0001819	synonymous_variant	55210	exon8			GGCTGTTGGGGTC	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.921T>C	1.37:g.1458150T>C		255	1	0.00392157		384	346	0.901042	NM_018188	B3KPB3|D2K8Q1|G3V1I6|Q5SV23|Q8N275|Q96A50	Silent	SNP	ENST00000378755.5	37	CCDS31.1	44	0.020146520146520148	13	0.026422764227642278	15	0.04143646408839779	7	0.012237762237762238	9	0.011873350923482849	c	2.002	-0.429111	0.04701	0.008872	0.007791	ENSG00000197785	ENST00000339113	.	.	.	4.92	-9.49	0.00587	.	.	.	.	.	T	0.18718	0.0449	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58255	-0.7668	4	.	.	.	.	10.7083	0.45969	0.0:0.127:0.3056:0.5674	rs1135025	.	.	.	R	245	.	.	W	+	1	0	ATAD3A	1448013	0.908000	0.30866	0.008000	0.14137	0.071000	0.16799	-0.105000	0.10907	-2.425000	0.00561	-0.768000	0.03414	TGG	T|0.991;C|0.009	0.009	strong		0.677	ATAD3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000001365.1	NM_018188		C	1458150	T	C	1458150	2	2	25	1	0	0	0	0	0	0	0	1	1073	1799	63	3		3	ATAD3A	1	1458150	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	27102	1458150	247792471	5	8914											
PRKCZ	5590	hgsc.bcm.edu	37	chr1	2105427	2105427	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcatcaccgacaacccggaCatgaacacagaggactacct	15	5	7	14	2	2	2	2	1	0	1	2	5	2	4	3	2	3	0	3	2	3	1	rs142352833	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:2105427C>T	ENST00000400921.2	+	11	1511	c.828C>T	c.(826-828)gaC>gaT	p.D276D	PRKCZ_ENST00000479263.1_3'UTR|PRKCZ_ENST00000400920.1_Silent_p.D276D	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)	ACAACCCGGACATGAACACAG	0.597											OREG0013007	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D459D		Atlas-SNP	.											.	PRKCZ	84	.	0			c.C1377T						PASS	.	C	,,,	0,4406	2.1+/-5.4	0,0,2203	136	116	122		828,828,1065,1377	3	1	1	dbSNP_134	122	15,8585	11.2+/-40.8	0,15,4285	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRKCZ	NM_001033581.1,NM_001033582.1,NM_001242874.1,NM_002744.4	,,,	0,15,6488	TT,TC,CC		0.1744,0.0,0.1153	,,,	276/410,276/410,355/489,459/593	2105427	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	5590	exon14			CCCGGACATGAAC	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.828C>T	1.37:g.2105427C>T		134	0	0	601	98	89	0.908163	NM_002744	A8K4N0|A8MU64|B7Z2J7|E9PCW2|Q15207|Q5SYT5|Q969S4	Silent	SNP	ENST00000400921.2	37	CCDS41229.1																																																																																			C|0.999;T|0.001	0.001	strong		0.597	PRKCZ-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000098533.3	NM_002744		T	2105427	C	T	2105427	2	4	25	1	0	0	0	0	0	0	0	1	12529	477	17	2		2	PRKCZ	1	2105427	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	647277	2105427	247145194	6	8915											
PLCH2	9651	hgsc.bcm.edu	37	chr1	2436256	2436256	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	agcctgggcctcccgggaggGacacggcgggtgtcggggcc	4	4	20	13	4	0	0	0	0	0	0	2	2	1	2	4	7	1	0	4	7	0	0	rs138038983	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:2436256G>A	ENST00000419816.2	+	22	4129	c.3855G>A	c.(3853-3855)ggG>ggA	p.G1285G	PLCH2_ENST00000449969.1_3'UTR|PLCH2_ENST00000378486.3_Silent_p.G1285G|PLCH2_ENST00000378488.3_Silent_p.G1249G			O75038	PLCH2_HUMAN	phospholipase C, eta 2	1285					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)		TCCCGGGAGGGACACGGCGGG	0.662													G|||	53	0.0105831	0.0008	0.0245	5008	,	,		15355	0.0		0.0298	False		,,,				2504	0.0051				p.G1285G		Atlas-SNP	.											.	PLCH2	131	.	0			c.G3855A						PASS	.	G		21,3963		0,21,1971	13	16	15		3855	-0.4	0	1	dbSNP_134	15	235,8037		3,229,3904	no	coding-synonymous	PLCH2	NM_014638.2		3,250,5875	AA,AG,GG		2.8409,0.5271,2.0888		1285/1417	2436256	256,12000	1992	4136	6128	SO:0001819	synonymous_variant	9651	exon22			GGGAGGGACACGG	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.3855G>A	1.37:g.2436256G>A		78	0	0		110	6	0.0545455	NM_014638	A2VCM3|B9DI80|Q3LUA8|Q86XJ2|Q86XU1|Q86YU7|Q8TEH5|Q8WUS6	Silent	SNP	ENST00000419816.2	37		30	0.013736263736263736	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	20	0.026385224274406333	G	0.060	-1.225743	0.01530	0.005271	0.028409	ENSG00000149527	ENST00000419816	.	.	.	4.32	-0.385	0.12470	.	2.338380	0.02026	N	0.048201	T	0.09468	0.0233	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.23904	-1.0175	6	0.42905	T	0.14	.	1.6475	0.02764	0.1628:0.1426:0.4036:0.291	.	.	.	.	E	580	.	ENSP00000389803:G580E	G	+	2	0	PLCH2	2426116	0.000000	0.05858	0.001000	0.08648	0.030000	0.12068	-0.414000	0.07114	0.781000	0.33589	0.491000	0.48974	GGA	G|0.983;A|0.017	0.017	strong		0.662	PLCH2-009	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467514.1	NM_014638		A	2436256	G	A	2436256	2	1	25	1	0	0	0	0	0	0	0	1	12047	1161	41	2		2	PLCH2	1	2436256	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	330829	2436256	246814365	7	8916											
TNFRSF14	8764	hgsc.bcm.edu	37	chr1	2493168	2493168	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagcagctcccactgggtatGgtggtttctctcagggagcc	6	10	13	12	0	2	0	1	0	1	0	4	1	3	1	2	4	3	4	2	4	1	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:2493168G>A	ENST00000355716.4	+	6	907	c.608G>A	c.(607-609)tGg>tAg	p.W203*		NM_003820.2	NP_003811.2	Q92956	TNR14_HUMAN	tumor necrosis factor receptor superfamily, member 14	203					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)		CACTGGGTATGGTGGTTTCTC	0.607			"Mis, N, F"		follicular lymphoma																																p.W203X		Atlas-SNP	.		Rec	yes		1	1p36.32	8764	"tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)"		L	.	TNFRSF14	89	.	0			c.G608A						PASS	.						91	83	86					1																	2493168		2203	4300	6503	SO:0001587	stop_gained	8764	exon6			GGGTATGGTGGTT	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.608G>A	1.37:g.2493168G>A	ENSP00000347948:p.Trp203*	67	0	0		72	47	0.652778	NM_003820	B3KW30|B9DI89|Q6IB95|Q8N634|Q8WXR1|Q96J31|Q9UM65	Nonsense_Mutation	SNP	ENST00000355716.4	37	CCDS44046.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.243726	0.58995	.	.	ENSG00000157873	ENST00000434817;ENST00000435221;ENST00000451778;ENST00000355716	.	.	.	1.34	1.34	0.21922	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	-4.8029	6.0814	0.19942	0.0:0.0:1.0:0.0	.	.	.	.	X	203	.	ENSP00000347948:W203X	W	+	2	0	TNFRSF14	2481250	0.000000	0.05858	0.005000	0.12908	0.025000	0.11179	-0.033000	0.12246	1.091000	0.41335	0.205000	0.17691	TGG	.	.	none		0.607	TNFRSF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002088.1			A	2493168	G	A	2493168	4	1	25	1	0	0	0	0	0	1	0	0	16304	1357	47	2	630	2	TNFRSF14	1	2493168	Nonsense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	56912	2493168	246757453	8	8917											
PRDM16	63976	hgsc.bcm.edu	37	chr1	3329037	3329037	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggccgagccaaagtcaccccGggacgccctcaaggtgggcg	8	3	15	15	4	2	0	2	0	0	0	2	2	2	1	5	4	1	0	5	4	2	0			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:3329037G>A	ENST00000270722.5	+	9	2325	c.2276G>A	c.(2275-2277)cGg>cAg	p.R759Q	PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000442529.2_Missense_Mutation_p.R759Q|PRDM16_ENST00000511072.1_Missense_Mutation_p.R760Q|PRDM16_ENST00000378391.2_Missense_Mutation_p.R759Q|PRDM16_ENST00000514189.1_Missense_Mutation_p.R760Q|PRDM16_ENST00000378398.3_Missense_Mutation_p.R760Q|PRDM16_ENST00000441472.2_Missense_Mutation_p.R759Q			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	759	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)		AAGTCACCCCGGGACGCCCTC	0.652			T	EVI1	"MDS, AML"																																p.R759Q		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	PRDM16,NS,lymphoid_neoplasm,+1,1	PRDM16	147	1	0			c.G2276A						PASS	.						53	61	58					1																	3329037		2015	4158	6173	SO:0001583	missense	63976	exon9			CACCCCGGGACGC	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.2276G>A	1.37:g.3329037G>A	ENSP00000270722:p.Arg759Gln	70	0	0		85	77	0.905882	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Missense_Mutation	SNP	ENST00000270722.5	37	CCDS41236.2	.	.	.	.	.	.	.	.	.	.	G	14.09	2.433145	0.43224	.	.	ENSG00000142611	ENST00000511072;ENST00000378398;ENST00000441472;ENST00000442529;ENST00000378391;ENST00000514189;ENST00000270722;ENST00000512462;ENST00000408992;ENST00000509860	T;T;T;T;T;T;T;T;T	0.05649	3.41;3.44;3.46;3.44;3.43;3.44;3.46;3.41;3.41	4.41	4.41	0.53225	.	0.000000	0.46758	U	0.000280	T	0.19208	0.0461	M	0.67953	2.075	0.51012	D	0.999903	D;D;D;D	0.76494	0.999;0.998;0.999;0.997	P;P;P;P	0.62184	0.75;0.821;0.899;0.667	T	0.10382	-1.0632	10	0.16420	T	0.52	.	17.3359	0.87281	0.0:0.0:1.0:0.0	.	759;759;759;759	Q9HAZ2;Q9HAZ2-2;F8WEV3;D3YTA5	PRD16_HUMAN;.;.;.	Q	760;760;759;759;759;760;759;575;575;568	ENSP00000426975:R760Q;ENSP00000367651:R760Q;ENSP00000407968:R759Q;ENSP00000405253:R759Q;ENSP00000367643:R759Q;ENSP00000421400:R760Q;ENSP00000270722:R759Q;ENSP00000422504:R575Q;ENSP00000425796:R568Q	ENSP00000270722:R759Q	R	+	2	0	PRDM16	3318897	1.000000	0.71417	1.000000	0.80357	0.557000	0.35523	4.285000	0.58989	2.169000	0.68431	0.453000	0.30009	CGG	.	.	none		0.652	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114		A	3329037	G	A	3329037	3	1	25	1	0	0	0	0	1	0	0	0	12469	1116	39	1	2310	1	PRDM16	1	3329037	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	835869	3329037	245921584	9	8918											
GPR153	387509	hgsc.bcm.edu	37	chr1	6314758	6314758	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaagtcggggcgctgccgccGcagctgcaccacggagtagg	7	4	17	13	5	0	0	0	0	0	0	1	2	0	1	3	4	3	5	3	4	2	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:6314758G>A	ENST00000377893.2	-	2	467	c.208C>T	c.(208-210)Cgg>Tgg	p.R70W		NM_207370.2	NP_997253.2	Q6NV75	GP153_HUMAN	G protein-coupled receptor 153	70						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|liver(1)|lung(7)|skin(1)	14	Ovarian(185;0.0634)	all_cancers(23;8.07e-33)|all_epithelial(116;4.45e-18)|all_lung(118;1.09e-06)|all_neural(13;3.68e-06)|Lung NSC(185;1.52e-05)|all_hematologic(16;2.39e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00475)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;1.91e-37)|GBM - Glioblastoma multiforme(13;4.87e-29)|OV - Ovarian serous cystadenocarcinoma(86;3.03e-19)|Colorectal(212;1.33e-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(365;0.00109)|STAD - Stomach adenocarcinoma(132;0.00313)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.246)		CGCTGCCGCCGCAGCTGCACC	0.607																																					p.R70W		Atlas-SNP	.											.	GPR153	44	.	0			c.C208T						PASS	.						119	107	111					1																	6314758		2203	4300	6503	SO:0001583	missense	387509	exon2			GCCGCCGCAGCTG	AY255529	CCDS64.1	1p36.31	2012-08-21			ENSG00000158292	ENSG00000158292		"GPCR / Class A : Orphans"	23618	protein-coding gene	gene with protein product		614269				12679517	Standard	NM_207370		Approved	PGR1	uc001amp.2	Q6NV75	OTTHUMG00000001272	ENST00000377893.2:c.208C>T	1.37:g.6314758G>A	ENSP00000367125:p.Arg70Trp	115	0	0		115	9	0.0782609	NM_207370	Q5TGR5|Q6AHW8|Q86SP8	Missense_Mutation	SNP	ENST00000377893.2	37	CCDS64.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.546288	0.86022	.	.	ENSG00000158292	ENST00000377893	T	0.37584	1.19	5.42	5.42	0.78866	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.48447	0.1500	L	0.32530	0.975	0.58432	D	0.99999	D	0.89917	1.0	D	0.97110	1.0	T	0.48625	-0.9019	10	0.87932	D	0	-53.1149	12.8394	0.57793	0.0:0.0:0.8368:0.1632	.	70	Q6NV75	GP153_HUMAN	W	70	ENSP00000367125:R70W	ENSP00000367125:R70W	R	-	1	2	GPR153	6237345	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.795000	0.85887	2.534000	0.85438	0.557000	0.71058	CGG	.	.	none		0.607	GPR153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003717.2			A	6314758	G	A	6314758	3	1	25	1	0	0	0	0	1	0	0	0	6667	1086	38	1	1641	1	GPR153	1	6314758	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2985721	6314758	242935863	10	8919											
ESPN	83715	hgsc.bcm.edu	37	chr1	6500762	6500762	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gcacttcgcggcgagccgcgGccacaccaaggtgctcagct	7	5	13	16	5	1	0	1	0	0	0	2	1	1	0	3	3	3	3	3	3	1	1	rs200602012		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:6500762G>A	ENST00000377828.1	+	4	920	c.752G>A	c.(751-753)gGc>gAc	p.G251D	RP1-202O8.2_ENST00000419034.1_RNA	NM_031475.2	NP_113663.2	B1AK53	ESPN_HUMAN	espin	251					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)		GCGAGCCGCGGCCACACCAAG	0.726																																					p.G251D		Atlas-SNP	.											.	ESPN	32	.	0			c.G752A						PASS	.						5	6	5					1																	6500762		1942	3927	5869	SO:0001583	missense	83715	exon4			GCCGCGGCCACAC	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.752G>A	1.37:g.6500762G>A	ENSP00000367059:p.Gly251Asp	7	0	0		16	11	0.6875	NM_031475	Q6XYB2|Q9H0A2|Q9Y329	Missense_Mutation	SNP	ENST00000377828.1	37	CCDS70.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.650081	0.87958	.	.	ENSG00000187017	ENST00000377828;ENST00000418286	T;T	0.72394	-0.65;0.89	3.84	3.84	0.44239	Ankyrin repeat-containing domain (5);	0.233607	0.34959	N	0.003544	T	0.81772	0.4893	M	0.80982	2.52	0.80722	D	1	D	0.65815	0.995	D	0.63283	0.913	D	0.83857	0.0266	10	0.54805	T	0.06	-5.9744	12.6418	0.56714	0.0:0.0:1.0:0.0	.	251	B1AK53	ESPN_HUMAN	D	251;36	ENSP00000367059:G251D;ENSP00000401793:G36D	ENSP00000367059:G251D	G	+	2	0	ESPN	6423349	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.972000	0.93424	1.989000	0.58080	0.430000	0.28490	GGC	G|0.991;A|0.010	0.010	weak		0.726	ESPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001887.3	NM_031475		A	6500762	G	A	6500762	3	1	25	1	0	0	0	0	1	0	0	0	5256	1203	42	2	766	2	ESPN	1	6500762	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	186004	6500762	242749859	11	8920											
LZIC	84328	hgsc.bcm.edu	37	chr1	9992024	9992024	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caagaaggcctcatcatctgCagtcagctaaacaaaatgaa	17	7	7	10	0	4	2	3	1	1	1	4	2	4	2	1	1	3	2	1	1	7	1	rs146375448	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:9992024C>G	ENST00000377223.1	-	7	686	c.439G>C	c.(439-441)Gca>Cca	p.A147P	LZIC_ENST00000400903.2_Missense_Mutation_p.A147P|LZIC_ENST00000541052.1_Missense_Mutation_p.A168P|LZIC_ENST00000377213.1_Missense_Mutation_p.A147P	NM_032368.3	NP_115744.2	Q8WZA0	LZIC_HUMAN	leucine zipper and CTNNBIP1 domain containing	147					response to ionizing radiation (GO:0010212)					breast(1)|endometrium(2)|large_intestine(2)|lung(1)|skin(1)	7		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;5.29e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;0.000242)|BRCA - Breast invasive adenocarcinoma(304;0.000299)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|STAD - Stomach adenocarcinoma(132;0.00842)|READ - Rectum adenocarcinoma(331;0.0419)		TCATCATCTGCAGTCAGCTAA	0.453													C|||	5	0.000998403	0.0008	0.0014	5008	,	,		16195	0.0		0.003	False		,,,				2504	0.0				p.A147P		Atlas-SNP	.											LZIC,NS,carcinoma,+1,1	LZIC	11	1	0			c.G439C						PASS	.	C	PRO/ALA	1,4405	2.1+/-5.4	0,1,2202	83	75	78		439	3.4	1	1	dbSNP_134	78	12,8588	9.1+/-34.3	0,12,4288	yes	missense	LZIC	NM_032368.3	27	0,13,6490	GG,GC,CC		0.1395,0.0227,0.1	benign	147/191	9992024	13,12993	2203	4300	6503	SO:0001583	missense	84328	exon6			CATCTGCAGTCAG	AB060688	CCDS107.1	1p36.22	2008-02-05			ENSG00000162441	ENSG00000162441			17497	protein-coding gene	gene with protein product		610458				11712074	Standard	NM_032368		Approved	MGC15436	uc001aqm.3	Q8WZA0	OTTHUMG00000001804	ENST00000377223.1:c.439G>C	1.37:g.9992024C>G	ENSP00000366430:p.Ala147Pro	68	0	0		104	7	0.0673077	NM_032368	B2R6F0|B4E2N0|Q96IU1	Missense_Mutation	SNP	ENST00000377223.1	37	CCDS107.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	4.176	0.031261	0.08101	2.27E-4	0.001395	ENSG00000162441	ENST00000377223;ENST00000400903;ENST00000541052;ENST00000377213	T;T;T;T	0.42513	0.98;0.98;0.97;0.98	5.42	3.44	0.39384	.	0.625117	0.18198	N	0.148607	T	0.12817	0.0311	N	0.00642	-1.3	0.23336	N	0.997886	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.17623	-1.0363	9	.	.	.	-3.6864	10.6507	0.45647	0.1167:0.6093:0.274:0.0	.	168;147	B4E2N0;Q8WZA0	.;LZIC_HUMAN	P	147;147;168;147	ENSP00000366430:A147P;ENSP00000383695:A147P;ENSP00000437432:A168P;ENSP00000366418:A147P	.	A	-	1	0	LZIC	9914611	0.366000	0.25014	1.000000	0.80357	0.994000	0.84299	0.170000	0.16663	2.700000	0.92200	0.650000	0.86243	GCA	C|0.999;G|0.001	0.001	strong		0.453	LZIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005037.1	NM_032368		G	9992024	C	G	9992024	3	3	25	1	0	0	0	0	1	0	0	0	9144	710	25	4	141	4	LZIC	1	9992024	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	3491262	9992024	239258597	12	8921											
CLCNKA	1187	hgsc.bcm.edu	37	chr1	16349137	16349137	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggagttggtggggctgcGtgagggcttctcaggggacc	5	8	21	7	1	1	1	1	1	1	0	2	4	1	4	1	8	1	3	1	8	0	2	rs9442189	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:16349137G>A	ENST00000331433.4	+	2	42	c.23G>A	c.(22-24)cGt>cAt	p.R8H	CLCNKA_ENST00000420078.1_Missense_Mutation_p.R8H|CLCNKA_ENST00000375692.1_Missense_Mutation_p.R8H|CLCNKA_ENST00000464764.1_3'UTR|CLCNKA_ENST00000439316.2_Missense_Mutation_p.R8H			P51800	CLCKA_HUMAN	chloride channel, voltage-sensitive Ka	8			R -> H (in dbSNP:rs9442189).		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)	GTGGGGCTGCGTGAGGGCTTC	0.667													G|||	61	0.0121805	0.0	0.0058	5008	,	,		17257	0.001		0.0278	False		,,,				2504	0.0286				p.R8H		Atlas-SNP	.											.	CLCNKA	56	.	0			c.G23A						PASS	.	G	HIS/ARG,HIS/ARG	12,4378		1,10,2184	48	42	44		23,23	2.2	0.6	1	dbSNP_119	44	182,8400		2,178,4111	yes	missense,missense	CLCNKA	NM_001042704.1,NM_004070.3	29,29	3,188,6295	AA,AG,GG		2.1207,0.2733,1.4955	benign,benign	8/687,8/688	16349137	194,12778	2195	4291	6486	SO:0001583	missense	1187	exon2			GGCTGCGTGAGGG		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.23G>A	1.37:g.16349137G>A	ENSP00000332771:p.Arg8His	95	0	0		128	7	0.0546875	NM_004070	B4DPD3|E7EPH6|Q5T5P8|Q5T5Q4|Q7Z6D1|Q86VT1	Missense_Mutation	SNP	ENST00000331433.4	37	CCDS167.1	21	0.009615384615384616	0	0.0	2	0.0055248618784530384	0	0.0	19	0.025065963060686015	G	10.27	1.304871	0.23736	0.002733	0.021207	ENSG00000186510	ENST00000375692;ENST00000420078;ENST00000439316;ENST00000331433	D;D;D;D	0.86562	-1.93;-1.93;-2.14;-1.93	4.12	2.15	0.27550	.	0.835714	0.10474	U	0.670447	T	0.68595	0.3018	M	0.75447	2.3	0.23138	N	0.998237	B;B;B	0.29671	0.254;0.254;0.254	B;B;B	0.25614	0.062;0.062;0.062	T	0.69221	-0.5202	10	0.62326	D	0.03	.	6.152	0.20316	0.2539:0.0:0.7461:0.0	rs9442189;rs9442189	8;8;8	E7EPH6;Q5T5Q4;P51800	.;.;CLCKA_HUMAN	H	8	ENSP00000364844:R8H;ENSP00000410353:R8H;ENSP00000414445:R8H;ENSP00000332771:R8H	ENSP00000332771:R8H	R	+	2	0	CLCNKA	16221724	0.001000	0.12720	0.588000	0.28705	0.445000	0.32107	-0.259000	0.08721	0.337000	0.23665	-0.657000	0.03884	CGT	G|0.989;A|0.011	0.011	strong		0.667	CLCNKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026326.1			A	16349137	G	A	16349137	3	1	25	1	0	0	0	0	1	0	0	0	3471	1145	40	1	25	1	CLCNKA	1	16349137	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	6357113	16349137	232901484	13	8922											
PADI2	11240	hgsc.bcm.edu	37	chr1	17405814	17405814	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggtatgtcttgccgttcaCggtcactgggggactgacct	5	11	14	11	3	3	1	2	1	1	0	3	2	3	2	2	4	1	2	2	4	1	3	rs148233687	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:17405814C>T	ENST00000375486.4	-	11	1318	c.1255G>A	c.(1255-1257)Gtg>Atg	p.V419M	PADI2_ENST00000444885.2_Missense_Mutation_p.V303M|PADI2_ENST00000375481.1_Missense_Mutation_p.V419M|PADI2_ENST00000466151.1_5'UTR	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	419					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)	TTGCCGTTCACGGTCACTGGG	0.597													C|||	5	0.000998403	0.0	0.0043	5008	,	,		15043	0.0		0.002	False		,,,				2504	0.0				p.V419M		Atlas-SNP	.											.	PADI2	72	.	0			c.G1255A						PASS	.	C	MET/VAL	2,4404	4.2+/-10.8	0,2,2201	65	65	65		1255	5	1	1	dbSNP_134	65	16,8584	11.9+/-42.8	0,16,4284	yes	missense	PADI2	NM_007365.2	21	0,18,6485	TT,TC,CC		0.186,0.0454,0.1384	probably-damaging	419/666	17405814	18,12988	2203	4300	6503	SO:0001583	missense	11240	exon11			CGTTCACGGTCAC	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.1255G>A	1.37:g.17405814C>T	ENSP00000364635:p.Val419Met	65	0	0		57	48	0.842105	NM_007365	Q96DA7|Q9UPN2	Missense_Mutation	SNP	ENST00000375486.4	37	CCDS177.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	C	28.5	4.926678	0.92319	4.54E-4	0.00186	ENSG00000117115	ENST00000375486;ENST00000444885;ENST00000375481	T;T;T	0.30182	1.54;1.54;1.54	4.97	4.97	0.65823	Protein-arginine deiminase, C-terminal (1);	0.244684	0.41500	D	0.000874	T	0.52773	0.1755	M	0.85197	2.74	0.51233	D	0.999919	D;D	0.89917	1.0;0.998	D;D	0.83275	0.996;0.938	T	0.62676	-0.6804	10	0.56958	D	0.05	-20.6685	17.3265	0.87249	0.0:1.0:0.0:0.0	.	303;419	B4DIU3;Q9Y2J8	.;PADI2_HUMAN	M	419;303;419	ENSP00000364635:V419M;ENSP00000405894:V303M;ENSP00000364630:V419M	ENSP00000364630:V419M	V	-	1	0	PADI2	17278401	1.000000	0.71417	0.994000	0.49952	0.998000	0.95712	7.127000	0.77210	2.758000	0.94735	0.561000	0.74099	GTG	C|0.999;T|0.001	0.001	strong		0.597	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1			T	17405814	C	T	17405814	3	4	25	1	0	0	0	0	1	0	0	0	11387	536	19	1	766	1	PADI2	1	17405814	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1056677	17405814	231844807	14	8923											
PLA2G5	5322	hgsc.bcm.edu	37	chr1	20417066	20417066	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtgtccttttgcagagcccGggcccttctgccatgtgaac	5	11	12	13	1	1	2	0	1	1	1	2	2	2	2	4	2	4	1	4	2	1	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:20417066G>A	ENST00000375108.3	+	5	566	c.298G>A	c.(298-300)Ggg>Agg	p.G100R	PLA2G5_ENST00000486277.1_3'UTR	NM_000929.2	NP_000920.1	P39877	PA2G5_HUMAN	phospholipase A2, group V	100					arachidonic acid secretion (GO:0050482)|glycerophospholipid biosynthetic process (GO:0046474)|leukotriene biosynthetic process (GO:0019370)|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)|platelet activating factor biosynthetic process (GO:0006663)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|small molecule metabolic process (GO:0044281)	cell surface (GO:0009986)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|heparin binding (GO:0008201)			NS(1)|large_intestine(1)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	14		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000249)|Lung NSC(340;0.000287)|Breast(348;0.000812)|Ovarian(437;0.00328)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.22e-05)|BRCA - Breast invasive adenocarcinoma(304;8.15e-05)|Kidney(64;0.000184)|GBM - Glioblastoma multiforme(114;0.00089)|KIRC - Kidney renal clear cell carcinoma(64;0.0027)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0652)		TGCAGAGCCCGGGCCCTTCTG	0.557																																					p.G100R		Atlas-SNP	.											.	PLA2G5	21	.	0			c.G298A						PASS	.						145	127	133					1																	20417066		2203	4300	6503	SO:0001583	missense	5322	exon5			GAGCCCGGGCCCT	U03090	CCDS202.1	1p36-p34	2008-09-19			ENSG00000127472	ENSG00000127472	3.1.1.4		9038	protein-coding gene	gene with protein product		601192				8838795, 8300559	Standard	NM_000929		Approved		uc001bcy.3	P39877	OTTHUMG00000002698	ENST00000375108.3:c.298G>A	1.37:g.20417066G>A	ENSP00000364249:p.Gly100Arg	134	0	0		174	65	0.373563	NM_000929	Q8N435	Missense_Mutation	SNP	ENST00000375108.3	37	CCDS202.1	.	.	.	.	.	.	.	.	.	.	G	17.88	3.498320	0.64186	.	.	ENSG00000127472	ENST00000375108	T	0.26223	1.75	5.77	5.77	0.91146	Phospholipase A2 (3);	0.847373	0.10252	N	0.697050	T	0.46639	0.1403	L	0.48642	1.525	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.71656	0.974;0.939	T	0.39251	-0.9623	10	0.51188	T	0.08	-16.3128	15.4945	0.75637	0.0:0.0:1.0:0.0	.	100;73	P39877;B3KUQ4	PA2G5_HUMAN;.	R	100	ENSP00000364249:G100R	ENSP00000364249:G100R	G	+	1	0	PLA2G5	20289653	0.484000	0.25964	0.010000	0.14722	0.004000	0.04260	3.297000	0.51810	2.720000	0.93068	0.557000	0.71058	GGG	.	.	none		0.557	PLA2G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007668.1	NM_000929		A	20417066	G	A	20417066	3	1	25	1	0	0	0	0	1	0	0	0	12016	1116	39	1	312	1	PLA2G5	1	20417066	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	3011252	20417066	228833555	15	8924											
UBXN11	91544	hgsc.bcm.edu	37	chr1	26608849	26608849	+	Missense_Mutation	SNP	T	T	A																															gccgggaccgggaccgggacTggggccgggaccgggaccgg																								rs199707978		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:26608849T>A	ENST00000374222.1	-	16	1968	c.1504A>T	c.(1504-1506)Agt>Tgt	p.S502C	UBXN11_ENST00000357089.4_Missense_Mutation_p.S469C|UBXN11_ENST00000314675.7_Missense_Mutation_p.S382C|UBXN11_ENST00000374223.1_Missense_Mutation_p.S259C|UBXN11_ENST00000374221.3_Missense_Mutation_p.S502C|UBXN11_ENST00000374217.2_Missense_Mutation_p.S469C			Q5T124	UBX11_HUMAN	UBX domain protein 11	502	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						ggaccgggactggggccggga	0.731																																					p.S502C		Atlas-SNP	.											.	UBXN11	54	.	1	Deletion - In frame(1)	ovary(1)	c.A1504T						PASS	.						19	22	21					1																	26608849		1706	3905	5611	SO:0001583	missense	91544	exon16			CGGGACTGGGGCC	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.1504A>T	1.37:g.26608849T>A	ENSP00000363339:p.Ser502Cys	25	0	0		40	16	0.4	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Missense_Mutation	SNP	ENST00000374222.1	37	CCDS41288.1	.	.	.	.	.	.	.	.	.	.	-	8.284	0.816212	0.16607	.	.	ENSG00000158062	ENST00000314675;ENST00000374223;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217	T;T;T;T;T;T	0.19105	2.17;2.18;2.44;2.43;2.43;2.44	.	.	.	.	.	.	.	.	T	0.10594	0.0259	N	0.08118	0	0.09310	N	0.999993	.	.	.	.	.	.	T	0.30446	-0.9978	5	0.66056	D	0.02	.	.	.	.	.	469;382;502	Q5T124-2;Q5T124-3;Q5T124	.;.;UBX11_HUMAN	C	382;259;469;502;502;469	ENSP00000324721:S382C;ENSP00000363340:S259C;ENSP00000349601:S469C;ENSP00000363338:S502C;ENSP00000363339:S502C;ENSP00000363334:S469C	ENSP00000324721:S382C	S	-	1	0	UBXN11	26481436	0.000000	0.05858	0.168000	0.22838	0.175000	0.22909	-0.694000	0.05115	0.000000	0.14550	0.000000	0.15137	AGT	.	.	weak		0.731	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345		A	26608849	T	A	26608849	3	1	25	1	0	0	0	0	1	0	0	0	16928	1580	55	5	62	5	UBXN11	1	26608849	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	6191783	26608849	222641772	16	8925	110	3									
UBXN11	91544	hgsc.bcm.edu	37	chr1	26608853	26608853	+	Silent	SNP	G	G	A																															ggaccgggaccgggactgggGccgggaccgggaccgggact																										TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:26608853G>A	ENST00000374222.1	-	16	1964	c.1500C>T	c.(1498-1500)ggC>ggT	p.G500G	UBXN11_ENST00000357089.4_Silent_p.G467G|UBXN11_ENST00000314675.7_Silent_p.G380G|UBXN11_ENST00000374223.1_Silent_p.G257G|UBXN11_ENST00000374221.3_Silent_p.G500G|UBXN11_ENST00000374217.2_Silent_p.G467G			Q5T124	UBX11_HUMAN	UBX domain protein 11	500	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						cgggactggggccgggaccgg	0.731																																					p.G500G		Atlas-SNP	.											.	UBXN11	54	.	1	Deletion - In frame(1)	ovary(1)	c.C1500T						PASS	.						20	23	22					1																	26608853		1694	3910	5604	SO:0001819	synonymous_variant	91544	exon16			ACTGGGGCCGGGA	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.1500C>T	1.37:g.26608853G>A		24	0	0		38	15	0.394737	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Silent	SNP	ENST00000374222.1	37	CCDS41288.1																																																																																			.	.	none		0.731	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345		A	26608853	G	A	26608853	2	1	25	1	0	0	0	0	0	0	0	1	16928	1190	42	2		2	UBXN11	1	26608853	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	4	26608853	222641768	17	8926	110	3									
UBXN11	91544	hgsc.bcm.edu	37	chr1	26608855	26608855	+	Missense_Mutation	SNP	C	C	T																															accgggaccgggactggggcCgggaccgggaccgggactgg																								rs201756933		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:26608855C>T	ENST00000374222.1	-	16	1962	c.1498G>A	c.(1498-1500)Ggc>Agc	p.G500S	UBXN11_ENST00000357089.4_Missense_Mutation_p.G467S|UBXN11_ENST00000314675.7_Missense_Mutation_p.G380S|UBXN11_ENST00000374223.1_Missense_Mutation_p.G257S|UBXN11_ENST00000374221.3_Missense_Mutation_p.G500S|UBXN11_ENST00000374217.2_Missense_Mutation_p.G467S			Q5T124	UBX11_HUMAN	UBX domain protein 11	500	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						ggactggggccgggaccggga	0.731																																					p.G500S		Atlas-SNP	.											.	UBXN11	54	.	1	Deletion - In frame(1)	ovary(1)	c.G1498A						PASS	.						20	24	23					1																	26608855		1677	3891	5568	SO:0001583	missense	91544	exon16			TGGGGCCGGGACC	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.1498G>A	1.37:g.26608855C>T	ENSP00000363339:p.Gly500Ser	26	0	0		40	15	0.375	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Missense_Mutation	SNP	ENST00000374222.1	37	CCDS41288.1	.	.	.	.	.	.	.	.	.	.	-	0.087	-1.172989	0.01646	.	.	ENSG00000158062	ENST00000314675;ENST00000374223;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217	T;T;T;T;T;T	0.18174	2.23;2.24;2.54;2.51;2.51;2.54	.	.	.	.	.	.	.	.	T	0.07143	0.0181	N	0.08118	0	0.18873	N	0.999989	.	.	.	.	.	.	T	0.37979	-0.9682	6	0.28530	T	0.3	.	4.1991	0.10457	0.0:0.6625:0.0:0.3375	.	467;462;380;500	Q5T124-2;Q5T124-4;Q5T124-3;Q5T124	.;.;.;UBX11_HUMAN	S	380;257;467;500;500;467	ENSP00000324721:G380S;ENSP00000363340:G257S;ENSP00000349601:G467S;ENSP00000363338:G500S;ENSP00000363339:G500S;ENSP00000363334:G467S	ENSP00000324721:G380S	G	-	1	0	UBXN11	26481442	0.000000	0.05858	0.163000	0.22734	0.170000	0.22686	-0.959000	0.03853	-0.000000	0.14550	0.000000	0.15137	GGC	.	.	weak		0.731	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345		T	26608855	C	T	26608855	3	4	25	1	0	0	0	0	1	0	0	0	16928	652	23	1	68	1	UBXN11	1	26608855	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2	26608855	222641766	18	8927	110	3									
SDC3	9672	hgsc.bcm.edu	37	chr1	31349642	31349642	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	agtgggagaggcagaagcctCcgtacgccagtggtccttat	9	8	14	10	2	0	2	0	0	0	2	2	3	2	2	4	3	2	2	4	3	3	2	rs41269521	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:31349642C>T	ENST00000339394.6	-	3	801	c.627G>A	c.(625-627)cgG>cgA	p.R209R	SDC3_ENST00000336798.7_Silent_p.R151R|SDC3_ENST00000471567.1_5'UTR	NM_014654.3	NP_055469.3	O75056	SDC3_HUMAN	syndecan 3	209	Ser/Thr-rich (mucin-like).				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)		GCAGAAGCCTCCGTACGCCAG	0.682													C|||	75	0.014976	0.0015	0.0331	5008	,	,		13855	0.0		0.0427	False		,,,				2504	0.0072				p.R209R		Atlas-SNP	.											.	SDC3	45	.	0			c.G627A						PASS	.	C		35,4371	37.6+/-69.7	0,35,2168	26	29	28		627	1.8	0.8	1	dbSNP_127	28	343,8255	115.5+/-175.4	10,323,3966	no	coding-synonymous	SDC3	NM_014654.3		10,358,6134	TT,TC,CC		3.9893,0.7944,2.9068		209/443	31349642	378,12626	2203	4299	6502	SO:0001819	synonymous_variant	9672	exon3			AAGCCTCCGTACG	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.627G>A	1.37:g.31349642C>T		55	0	0		82	9	0.109756	NM_014654	Q5T1Z6|Q5T1Z7|Q96CT3|Q96PR8	Silent	SNP	ENST00000339394.6	37	CCDS30661.1																																																																																			C|0.972;G|0.000;T|0.028	0.028	strong		0.682	SDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102017.1	NM_014654		T	31349642	C	T	31349642	2	4	25	1	0	0	0	0	0	0	0	1	13968	842	30	2		2	SDC3	1	31349642	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	4740787	31349642	217900979	19	8928											
CCDC28B	79140	hgsc.bcm.edu	37	chr1	32669645	32669645	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tctggccggctgcaggccttCggtgagtcctgggggctggt	2	10	18	11	2	1	1	0	1	1	0	3	1	2	1	3	7	1	3	3	7	0	1	rs41263993	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:32669645C>T	ENST00000373602.5	+	3	677	c.330C>T	c.(328-330)ttC>ttT	p.F110F	IQCC_ENST00000291358.6_5'Flank|CCDC28B_ENST00000483009.1_3'UTR|CCDC28B_ENST00000421922.2_Splice_Site_p.F110F|RP4-622L5.7_ENST00000373604.4_RNA|IQCC_ENST00000537469.1_5'Flank|RP4-622L5.7_ENST00000421616.1_RNA	NM_024296.3	NP_077272.2	Q9BUN5	CC28B_HUMAN	coiled-coil domain containing 28B	110					cilium assembly (GO:0042384)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				large_intestine(4)|lung(3)|ovary(1)|upper_aerodigestive_tract(2)	10		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				TGCAGGCCTTCGGTGAGTCCT	0.607													C|||	28	0.00559105	0.0015	0.0115	5008	,	,		18193	0.0		0.0139	False		,,,				2504	0.0041				p.F110F		Atlas-SNP	.											.	CCDC28B	21	.	0			c.C330T	GRCh37	CS066273	CCDC28B	S	rs41263993	PASS	.	C		7,4399	12.9+/-30.5	0,7,2196	45	46	46		330	-9.5	0.7	1	dbSNP_127	46	169,8431	78.1+/-140.7	4,161,4135	yes	coding-synonymous-near-splice	CCDC28B	NM_024296.3		4,168,6331	TT,TC,CC		1.9651,0.1589,1.3532		110/201	32669645	176,12830	2203	4300	6503	SO:0001630	splice_region_variant	79140	exon3			GGCCTTCGGTGAG	BC022848	CCDS354.2, CCDS72749.1	1p36.11-p34.2	2008-02-05			ENSG00000160050	ENSG00000160050			28163	protein-coding gene	gene with protein product		610162				16327777	Standard	XM_006710892		Approved	MGC1203, RP4-622L5.5	uc001bul.1	Q9BUN5	OTTHUMG00000005738	ENST00000373602.5:c.331+1C>T	1.37:g.32669645C>T		56	0	0		49	5	0.102041	NM_024296	A8K789|Q8TBV8	Silent	SNP	ENST00000373602.5	37	CCDS354.2																																																																																			C|0.987;T|0.013	0.013	strong		0.607	CCDC28B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015723.4	NM_024296	Silent	T	32669645	C	T	32669645	5	4	25	1	0	0	0	0	0	0	1	0	2805	898	31	1	336	1	CCDC28B	1	32669645	Splice_Site	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1320003	32669645	216580976	20	8929											
PHC2	1912	hgsc.bcm.edu	37	chr1	33820515	33820515	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gttgaggggtgtggggcacgCcctcgggatgtccattctga	5	10	17	9	2	1	2	0	2	1	0	3	3	2	3	2	5	0	2	2	5	0	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:33820515C>G	ENST00000257118.5	-	7	1369	c.1316G>C	c.(1315-1317)gGc>gCc	p.G439A	PHC2_ENST00000373422.3_Missense_Mutation_p.G44A|PHC2_ENST00000431992.1_Missense_Mutation_p.G410A|PHC2_ENST00000419414.2_Missense_Mutation_p.G439A|PHC2_ENST00000373416.1_5'UTR|RP11-415J8.5_ENST00000432703.1_RNA	NM_198040.2	NP_932157.1	Q8IXK0	PHC2_HUMAN	polyhomeotic homolog 2 (Drosophila)	439					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)				GTGGGGCACGCCCTCGGGATG	0.607																																					p.G439A		Atlas-SNP	.											.	PHC2	78	.	0			c.G1316C						PASS	.						75	70	72					1																	33820515		2203	4300	6503	SO:0001583	missense	1912	exon7			GGCACGCCCTCGG	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.1316G>C	1.37:g.33820515C>G	ENSP00000257118:p.Gly439Ala	72	0	0		98	93	0.94898	NM_198040	A1L4Q1|A8KA40|D3DPR2|Q2TAL3|Q5T0C1|Q6NUJ6|Q6ZQR1|Q8N306|Q8TAG8|Q96BL4|Q9Y4Y7	Missense_Mutation	SNP	ENST00000257118.5	37	CCDS378.1	.	.	.	.	.	.	.	.	.	.	C	0.732	-0.779508	0.02929	.	.	ENSG00000134686	ENST00000431992;ENST00000257118;ENST00000373422;ENST00000419414	T;T;T;T	0.39997	2.06;1.68;1.05;2.1	5.86	2.88	0.33553	.	0.800952	0.11105	N	0.599163	T	0.29684	0.0741	L	0.56769	1.78	0.54753	D	0.999989	P;P;P	0.40050	0.7;0.7;0.7	B;B;B	0.36092	0.217;0.217;0.217	T	0.36335	-0.9752	10	0.02654	T	1	-2.4586	4.4467	0.11600	0.1605:0.6014:0.1549:0.0832	.	439;410;439	A8KA40;B7ZLY0;Q8IXK0	.;.;PHC2_HUMAN	A	410;439;44;439	ENSP00000389436:G410A;ENSP00000257118:G439A;ENSP00000362521:G44A;ENSP00000391440:G439A	ENSP00000257118:G439A	G	-	2	0	PHC2	33593102	0.989000	0.36119	0.212000	0.23672	0.034000	0.12701	1.042000	0.30303	0.339000	0.23719	0.591000	0.81541	GGC	.	.	none		0.607	PHC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000011895.1	NM_198040		G	33820515	C	G	33820515	3	3	25	1	0	0	0	0	1	0	0	0	11826	739	26	4	1292	4	PHC2	1	33820515	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1150870	33820515	215430106	21	8930											
CLSPN	63967	hgsc.bcm.edu	37	chr1	36202125	36202125	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccaaatatttgaagatgcttCgcgtcaatcctgaagtgcta	12	12	8	9	2	1	3	1	2	0	1	3	3	2	3	2	0	2	2	2	0	6	4	rs115320551		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:36202125C>T	ENST00000318121.3	-	25	4049	c.3992G>A	c.(3991-3993)cGa>cAa	p.R1331Q	CLSPN_ENST00000466308.1_5'UTR|RP11-435D7.3_ENST00000373226.2_RNA|CLSPN_ENST00000251195.5_Intron|CLSPN_ENST00000373220.3_Missense_Mutation_p.R1267Q|CLSPN_ENST00000520551.1_Missense_Mutation_p.R1278Q	NM_022111.3	NP_071394.2	Q9HAW4	CLSPN_HUMAN	claspin	1331					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)	p.R1331Q(1)		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)				GAAGATGCTTCGCGTCAATCC	0.423													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18800	0.0		0.0	False		,,,				2504	0.0				p.R1331Q		Atlas-SNP	.											CLSPN,colon,carcinoma,-1,4	CLSPN	248	4	1	Substitution - Missense(1)	ovary(1)	c.G3992A						PASS	.						150	141	144					1																	36202125		2203	4300	6503	SO:0001583	missense	63967	exon25			ATGCTTCGCGTCA	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.3992G>A	1.37:g.36202125C>T	ENSP00000312995:p.Arg1331Gln	133	0	0		144	132	0.916667	NM_022111	A6NFL4|Q1RMC6|Q2KHM3|Q5VYG0|Q6P6H5|Q8IWI1	Missense_Mutation	SNP	ENST00000318121.3	37	CCDS396.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	13.64	2.298942	0.40694	.	.	ENSG00000092853	ENST00000318121;ENST00000373220;ENST00000520551	T;T;T	0.27557	1.66;1.71;1.72	5.29	-1.26	0.09376	.	0.312008	0.29046	N	0.013319	T	0.14960	0.0361	N	0.12746	0.255	0.24776	N	0.992842	B;B	0.25007	0.116;0.068	B;B	0.15052	0.012;0.012	T	0.13176	-1.0519	10	0.32370	T	0.25	0.0185	13.1085	0.59261	0.0:0.8736:0.0:0.1264	.	1267;1331	Q9HAW4-2;Q9HAW4	.;CLSPN_HUMAN	Q	1331;1267;1278	ENSP00000312995:R1331Q;ENSP00000362317:R1267Q;ENSP00000428848:R1278Q	ENSP00000312995:R1331Q	R	-	2	0	CLSPN	35974712	0.998000	0.40836	0.974000	0.42286	0.967000	0.64934	0.428000	0.21395	-0.357000	0.08175	-0.290000	0.09829	CGA	C|0.999;T|0.001	0.001	strong		0.423	CLSPN-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377857.1	NM_022111		T	36202125	C	T	36202125	3	4	25	1	0	0	0	0	1	0	0	0	3562	884	31	1	31	1	CLSPN	1	36202125	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2381610	36202125	213048496	22	8931											
COL8A2	1296	hgsc.bcm.edu	37	chr1	36563509	36563509	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agagtccggtcaaatttcacGggcatgcccgaggcggggaa	10	6	15	10	4	2	1	2	0	0	1	3	3	3	2	2	5	1	1	2	5	2	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:36563509G>A	ENST00000397799.1	-	4	1997	c.1773C>T	c.(1771-1773)ccC>ccT	p.P591P	COL8A2_ENST00000481785.1_Silent_p.P526P|COL8A2_ENST00000303143.4_Silent_p.P591P			P25067	CO8A2_HUMAN	collagen, type VIII, alpha 2	591	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.|Nonhelical region (NC1).				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)				CAAATTTCACGGGCATGCCCG	0.632																																					p.P591P		Atlas-SNP	.											.	COL8A2	41	.	0			c.C1773T						PASS	.						39	36	37					1																	36563509		2202	4300	6502	SO:0001819	synonymous_variant	1296	exon2			TTTCACGGGCATG	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.1773C>T	1.37:g.36563509G>A		46	0	0		69	67	0.971014	NM_005202	Q5JV31|Q8TEJ5	Silent	SNP	ENST00000397799.1	37	CCDS403.1																																																																																			.	.	none		0.632	COL8A2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313674.1	NM_005202		A	36563509	G	A	36563509	2	1	25	1	0	0	0	0	0	0	0	1	3708	1103	39	1		1	COL8A2	1	36563509	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	361384	36563509	212687112	23	8932											
MANEAL	149175	hgsc.bcm.edu	37	chr1	38265653	38265653	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggtcaatggcaagtactaTgagacggccctgcaggcggc	10	6	15	10	2	1	1	1	1	0	1	1	2	1	1	1	5	2	3	1	5	4	2	rs41267339	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:38265653T>C	ENST00000373045.6	+	4	1533	c.1152T>C	c.(1150-1152)taT>taC	p.Y384Y	MANEAL_ENST00000329006.5_Silent_p.Y162Y|MANEAL_ENST00000397631.3_3'UTR|MANEAL_ENST00000525897.1_Silent_p.Y190Y|RP11-109P14.9_ENST00000433474.1_RNA	NM_001113482.1	NP_001106954.1	Q5VSG8	MANEL_HUMAN	mannosidase, endo-alpha-like	384						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(1)|liver(1)|lung(1)|prostate(3)	7	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				GCAAGTACTATGAGACGGCCC	0.567													T|||	28	0.00559105	0.0	0.0115	5008	,	,		19471	0.0		0.0189	False		,,,				2504	0.001				p.Y384Y		Atlas-SNP	.											.	MANEAL	43	.	0			c.T1152C						PASS	.	T	,,	30,4376	35.2+/-66.4	0,30,2173	79	86	83		,1152,486	-0.6	1	1	dbSNP_127	83	232,8368	94.5+/-156.4	3,226,4071	no	utr-3,coding-synonymous,coding-synonymous	MANEAL	NM_001031740.2,NM_001113482.1,NM_152496.2	,,	3,256,6244	CC,CT,TT		2.6977,0.6809,2.0145	,,	,384/458,162/236	38265653	262,12744	2203	4300	6503	SO:0001819	synonymous_variant	149175	exon4			GTACTATGAGACG	AK055996	CCDS426.1, CCDS44110.1, CCDS44111.1	1p34.3	2008-02-05			ENSG00000185090	ENSG00000185090			26452	protein-coding gene	gene with protein product							Standard	NM_152496		Approved	FLJ31434	uc001cby.2	Q5VSG8	OTTHUMG00000004317	ENST00000373045.6:c.1152T>C	1.37:g.38265653T>C		128	1	0.0078125		125	118	0.944	NM_001113482	Q6DD86|Q6P497|Q8N5P8|Q96G55|Q96N42	Silent	SNP	ENST00000373045.6	37	CCDS44110.1																																																																																			T|0.982;C|0.018	0.018	strong		0.567	MANEAL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012469.2	NM_152496		C	38265653	T	C	38265653	2	2	25	1	0	0	0	0	0	0	0	1	9231	1471	51	3		3	MANEAL	1	38265653	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	1702144	38265653	210984968	24	8933											
MACF1	23499	hgsc.bcm.edu	37	chr1	39549942	39549942	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcggtcatgtcggagtgagCggtcttgtcggagtgagcga	7	9	18	7	5	2	2	1	2	1	0	4	5	2	4	0	4	3	0	0	4	0	1	rs369843705		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:39549942C>T	ENST00000372915.3	+	1	139	c.52C>T	c.(52-54)Cgg>Tgg	p.R18W	MACF1_ENST00000317713.7_Missense_Mutation_p.R18W|MACF1_ENST00000484793.1_Missense_Mutation_p.R18W|MACF1_ENST00000361689.2_Missense_Mutation_p.R18W|MACF1_ENST00000545844.1_Missense_Mutation_p.R18W|MACF1_ENST00000539005.1_Missense_Mutation_p.R18W|MACF1_ENST00000602421.1_Missense_Mutation_p.R18W|MACF1_ENST00000567887.1_Missense_Mutation_p.R18W			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	18	Actin-binding.				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)			TCGGAGTGAGCGGTCTTGTCG	0.642													C|||	1	0.000199681	0.0	0.0014	5008	,	,		16833	0.0		0.0	False		,,,				2504	0.0				p.R18W		Atlas-SNP	.											MACF1_ENST00000361689,caecum,carcinoma,-1,1	MACF1	909	1	0			c.C52T						PASS	.	C	TRP/ARG	0,4406		0,0,2203	68	61	64		52	0.7	1	1		64	1,8599	1.2+/-3.3	0,1,4299	no	missense	MACF1	NM_012090.4	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		18/5431	39549942	1,13005	2203	4300	6503	SO:0001583	missense	23499	exon3			AGTGAGCGGTCTT	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.52C>T	1.37:g.39549942C>T	ENSP00000362006:p.Arg18Trp	76	0	0		80	74	0.925	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	C	16.64	3.178377	0.57692	0.0	1.16E-4	ENSG00000127603	ENST00000484793;ENST00000545844;ENST00000372915;ENST00000361689;ENST00000404645;ENST00000317713;ENST00000539005	T;T;T;T;T	0.66099	-0.15;-0.13;-0.15;-0.19;0.0	5.35	0.69	0.18039	.	.	.	.	.	T	0.58466	0.2124	N	0.08118	0	0.80722	D	1	D	0.89917	1.0	D	0.70227	0.968	T	0.63598	-0.6601	9	0.62326	D	0.03	.	12.8938	0.58087	0.6321:0.3679:0.0:0.0	.	18	F8W8Q1	.	W	18;18;18;18;34;18;18	ENSP00000439537:R18W;ENSP00000362006:R18W;ENSP00000354573:R18W;ENSP00000313438:R18W;ENSP00000444364:R18W	ENSP00000313438:R18W	R	+	1	2	MACF1	39322529	0.998000	0.40836	0.998000	0.56505	0.963000	0.63663	0.510000	0.22723	0.559000	0.29153	0.655000	0.94253	CGG	.	.	none		0.642	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		T	39549942	C	T	39549942	3	4	25	1	0	0	0	0	1	0	0	0	9153	759	27	1	54	1	MACF1	1	39549942	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1284289	39549942	209700679	25	8934											
KCNQ4	9132	hgsc.bcm.edu	37	chr1	41289831	41289831	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggggcctacggcccctggAggtgcggcgggcgccggtac	3	5	20	13	5	0	0	0	0	0	0	0	1	0	1	4	8	3	1	4	8	2	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:41289831A>G	ENST00000347132.5	+	9	1275	c.1193A>G	c.(1192-1194)gAg>gGg	p.E398G	KCNQ4_ENST00000506017.1_3'UTR|KCNQ4_ENST00000509682.2_Intron	NM_004700.3|NM_172163.2	NP_004691.2|NP_751895.1	P56696	KCNQ4_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 4	398					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)	CGGCCCCTGGAGGTGCGGCGG	0.706																																					p.E398G		Atlas-SNP	.											.	KCNQ4	58	.	0			c.A1193G						PASS	.						6	7	7					1																	41289831		2093	4057	6150	SO:0001583	missense	9132	exon9			CCCTGGAGGTGCG	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.1193A>G	1.37:g.41289831A>G	ENSP00000262916:p.Glu398Gly	45	0	0		44	39	0.886364	NM_004700	O96025	Missense_Mutation	SNP	ENST00000347132.5	37	CCDS456.1	.	.	.	.	.	.	.	.	.	.	A	14.89	2.669119	0.47677	.	.	ENSG00000117013	ENST00000347132	D	0.98947	-5.26	5.74	5.74	0.90152	.	0.381642	0.26255	N	0.025436	D	0.96281	0.8787	N	0.08118	0	0.80722	D	1	D	0.58268	0.982	P	0.53006	0.715	D	0.95540	0.8611	10	0.30078	T	0.28	-19.2463	12.4719	0.55792	1.0:0.0:0.0:0.0	.	398	P56696	KCNQ4_HUMAN	G	398	ENSP00000262916:E398G	ENSP00000262916:E398G	E	+	2	0	KCNQ4	41062418	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.349000	0.59385	2.201000	0.70794	0.477000	0.44152	GAG	.	.	none		0.706	KCNQ4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000020812.1	NM_004700		G	41289831	A	G	41289831	3	3	25	1	0	0	0	0	1	0	0	0	8094	304	11	3	1227	3	KCNQ4	1	41289831	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	1739889	41289831	207960790	26	8935											
SLFNL1	200172	hgsc.bcm.edu	37	chr1	41482917	41482917	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttccgtacctgcctgcaccActcctggatggcgctggcag	5	9	11	16	2	0	0	0	0	0	0	2	1	2	1	5	3	3	4	5	3	1	2	rs147062455	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:41482917A>G	ENST00000359345.1	-	3	3666	c.1090T>C	c.(1090-1092)Tgg>Cgg	p.W364R	SLFNL1_ENST00000372613.2_Intron|SLFNL1_ENST00000302946.8_Missense_Mutation_p.W364R|SLFNL1_ENST00000439569.2_Missense_Mutation_p.W364R|SLFNL1_ENST00000372611.1_Missense_Mutation_p.W305R|SLFNL1_ENST00000397197.2_Intron	NM_144990.3	NP_659427.3	Q499Z3	SLNL1_HUMAN	schlafen-like 1	364							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)				TGCCTGCACCACTCCTGGATG	0.682													A|||	10	0.00199681	0.0	0.0072	5008	,	,		17107	0.0		0.005	False		,,,				2504	0.0				p.W364R		Atlas-SNP	.											.	SLFNL1	37	.	0			c.T1090C						PASS	.	A	ARG/TRP,ARG/TRP	2,4388		0,2,2193	23	23	23		1090,1090	5.6	1	1	dbSNP_134	23	14,8572		0,14,4279	no	missense,missense	SLFNL1	NM_001168247.1,NM_144990.3	101,101	0,16,6472	GG,GA,AA		0.1631,0.0456,0.1233	probably-damaging,probably-damaging	364/408,364/408	41482917	16,12960	2195	4293	6488	SO:0001583	missense	200172	exon5			TGCACCACTCCTG	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.1090T>C	1.37:g.41482917A>G	ENSP00000352299:p.Trp364Arg	44	0	0		51	48	0.941176	NM_001168247	A8K8D1|Q49AG8|Q5VW72|Q5VW74|Q8N7V7|Q8TCH6|Q8WVZ8	Missense_Mutation	SNP	ENST00000359345.1	37	CCDS460.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	A	20.3	3.971902	0.74246	4.56E-4	0.001631	ENSG00000171790	ENST00000302946;ENST00000372611;ENST00000359345;ENST00000439569	T;T;T;T	0.37915	1.17;1.42;1.17;1.17	5.57	5.57	0.84162	.	0.000000	0.47852	D	0.000220	T	0.39118	0.1066	L	0.34521	1.04	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.71656	0.974;0.915	T	0.43147	-0.9409	10	0.72032	D	0.01	-16.654	12.1224	0.53900	1.0:0.0:0.0:0.0	.	305;364	Q499Z3-2;Q499Z3	.;SLNL1_HUMAN	R	364;305;364;364	ENSP00000304401:W364R;ENSP00000361694:W305R;ENSP00000352299:W364R;ENSP00000398938:W364R	ENSP00000304401:W364R	W	-	1	0	SLFNL1	41255504	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.980000	0.70516	2.117000	0.64856	0.459000	0.35465	TGG	A|0.998;G|0.002	0.002	strong		0.682	SLFNL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015650.1	NM_144990		G	41482917	A	G	41482917	3	3	25	1	0	0	0	0	1	0	0	0	14753	159	6	3	141	3	SLFNL1	1	41482917	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	193086	41482917	207767704	27	8936											
LEPRE1	64175	hgsc.bcm.edu	37	chr1	43228049	43228049	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cctccttcactccagacatgGtttggtaatagtctaggttc	8	14	8	11	0	2	1	1	0	1	1	5	1	4	1	3	3	0	3	3	3	3	6			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:43228049G>A	ENST00000296388.5	-	2	614	c.563C>T	c.(562-564)aCc>aTc	p.T188I	LEPRE1_ENST00000397054.3_Missense_Mutation_p.T188I|LEPRE1_ENST00000236040.4_Missense_Mutation_p.T188I			Q32P28	P3H1_HUMAN	leucine proline-enriched proteoglycan (leprecan) 1	188					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)	TCCAGACATGGTTTGGTAATA	0.428																																					p.T188I		Atlas-SNP	.											.	LEPRE1	130	.	0			c.C563T						PASS	.						168	159	162					1																	43228049		2203	4300	6503	SO:0001583	missense	64175	exon2			GACATGGTTTGGT	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.563C>T	1.37:g.43228049G>A	ENSP00000296388:p.Thr188Ile	102	0	0		117	51	0.435897	NM_001146289	Q7KZR4|Q96BR8|Q96SK8|Q96SL5|Q96SN3|Q9H6K3|Q9HC86|Q9HC87	Missense_Mutation	SNP	ENST00000296388.5	37	CCDS472.2	.	.	.	.	.	.	.	.	.	.	G	14.28	2.489214	0.44249	.	.	ENSG00000117385	ENST00000397054;ENST00000236040;ENST00000296388;ENST00000540027	T;T;T	0.32988	1.43;1.43;1.43	5.82	4.88	0.63580	Tetratricopeptide-like helical (1);	0.083955	0.85682	D	0.000000	T	0.21962	0.0529	L	0.40543	1.245	0.29400	N	0.862025	P;P;B;P	0.45283	0.855;0.708;0.391;0.544	B;B;B;B	0.37480	0.251;0.251;0.116;0.162	T	0.17077	-1.0381	10	0.45353	T	0.12	-25.5115	7.968	0.30111	0.0835:0.1631:0.7534:0.0	.	188;188;53;188	Q32P28-2;Q32P28-3;B4DNM8;Q32P28	.;.;.;P3H1_HUMAN	I	188;188;188;53	ENSP00000380245:T188I;ENSP00000236040:T188I;ENSP00000296388:T188I	ENSP00000236040:T188I	T	-	2	0	LEPRE1	43000636	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.101000	0.41787	1.400000	0.46741	0.563000	0.77884	ACC	.	.	none		0.428	LEPRE1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019790.2	NM_022356		A	43228049	G	A	43228049	3	1	25	1	0	0	0	0	1	0	0	0	8738	1261	44	2	1722	2	LEPRE1	1	43228049	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1745132	43228049	206022572	28	8937											
WDR65	149465	hgsc.bcm.edu	37	chr1	43675539	43675539	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgaagtaccctctgcctctGcagaaggaattcaatgagta	13	10	9	9	0	3	3	1	2	2	1	3	4	3	4	2	1	3	3	2	1	6	3	rs148341430	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:43675539G>A	ENST00000372492.4	+	11	2205	c.1881G>A	c.(1879-1881)ctG>ctA	p.L627L	WDR65_ENST00000528956.1_Silent_p.L627L	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		627										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)				CTCTGCCTCTGCAGAAGGAAT	0.572													g|||	2	0.000399361	0.0	0.0014	5008	,	,		18599	0.0		0.001	False		,,,				2504	0.0				p.L627L		Atlas-SNP	.											.	WDR65	76	.	0			c.G1881A						PASS	.	G	,,	0,4406		0,0,2203	176	149	158		1881,1881,1881	1.7	1	1	dbSNP_134	158	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	WDR65	NM_001167965.1,NM_001167966.1,NM_152498.3	,,	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	,,	627/699,627/699,627/699	43675539	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	149465	exon11			GCCTCTGCAGAAG																												ENST00000372492.4:c.1881G>A	1.37:g.43675539G>A		117	0	0		117	58	0.495726	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Silent	SNP	ENST00000372492.4	37																																																																																				G|0.999;A|0.001	0.001	strong		0.572	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1			A	43675539	G	A	43675539	2	1	25	1	0	0	0	0	0	0	0	1	17331	1306	46	2		2	WDR65	1	43675539	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	447490	43675539	205575082	29	8938											
HYI	81888	hgsc.bcm.edu	37	chr1	43917888	43917888	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tttctcacctgagccaaaacCccagctgcatgcctcaggtt	9	10	7	15	0	2	1	2	1	1	0	3	1	2	1	5	1	5	3	5	1	2	2	rs41270373	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:43917888C>G	ENST00000372425.4	-	3	609	c.414G>C	c.(412-414)ggG>ggC	p.G138G	HYI_ENST00000372426.1_Silent_p.G90G|HYI_ENST00000583037.1_Silent_p.G65G|HYI_ENST00000486909.1_Silent_p.G138G|HYI-AS1_ENST00000444386.1_RNA|SZT2_ENST00000372442.1_3'UTR|SZT2_ENST00000562955.1_3'UTR|HYI_ENST00000372432.1_Silent_p.G138G|HYI_ENST00000372434.1_Silent_p.G163G			Q5T013	HYI_HUMAN	hydroxypyruvate isomerase (putative)	138							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)				GAGCCAAAACCCCAGCTGCAT	0.572													C|||	49	0.00978435	0.0	0.0231	5008	,	,		22722	0.0		0.0308	False		,,,				2504	0.002				p.G163G		Atlas-SNP	.											.	HYI	23	.	0			c.G489C						PASS	.	C	,,	26,4380	31.7+/-61.6	1,24,2178	174	153	160		414,,414	-1	1	1	dbSNP_127	160	243,8357	95.0+/-156.8	3,237,4060	no	coding-synonymous,utr-3,coding-synonymous	SZT2,HYI	NM_001190880.2,NM_015284.3,NM_031207.5	,,	4,261,6238	GG,GC,CC		2.8256,0.5901,2.0683	,,	138/278,,138/248	43917888	269,12737	2203	4300	6503	SO:0001819	synonymous_variant	81888	exon4			CAAAACCCCAGCT		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	ENST00000372425.4:c.414G>C	1.37:g.43917888C>G		87	0	0		94	51	0.542553	NM_001243526	D3DPX4|D3DPX5|Q5Q9A2|Q7Z778|Q96S83|Q9BZR3|Q9BZR4	Silent	SNP	ENST00000372425.4	37	CCDS53309.1	33	0.01510989010989011	0	0.0	9	0.024861878453038673	0	0.0	24	0.0316622691292876	C	8.031	0.761814	0.15914	0.005901	0.028256	ENSG00000178922	ENST00000470662;ENST00000487366	T;T	0.40476	1.03;1.03	5.38	-1.03	0.10102	.	0.308735	0.38111	N	0.001809	T	0.11879	0.0289	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.02654	-1.1128	7	0.18710	T	0.47	.	6.2682	0.20939	0.1866:0.2033:0.5363:0.0739	rs41270373	.	.	.	A	57;62	ENSP00000428803:G57A;ENSP00000428501:G62A	ENSP00000428803:G57A	G	-	2	0	HYI	43690475	0.752000	0.28338	0.967000	0.41034	0.766000	0.43426	0.384000	0.20668	0.028000	0.15324	0.462000	0.41574	GGG	C|0.981;G|0.019	0.019	strong		0.572	HYI-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031207		G	43917888	C	G	43917888	2	3	25	1	0	0	0	0	0	0	0	1	7477	610	22	4		4	HYI	1	43917888	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	242349	43917888	205332733	30	8939											
SPATA6	54558	hgsc.bcm.edu	37	chr1	48825355	48825355	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caaggtcctcgctgaatgccGgggcttactacacgaccttg	8	9	11	13	3	0	1	0	1	0	0	2	2	1	1	3	3	3	2	3	3	4	3	rs1338314	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:48825355G>A	ENST00000371847.3	-	10	1161	c.997C>T	c.(997-999)Cgg>Tgg	p.R333W	SPATA6_ENST00000371843.3_Missense_Mutation_p.R333W|SPATA6_ENST00000396199.3_Missense_Mutation_p.R261W	NM_019073.2	NP_061946.1	Q9NWH7	SPAT6_HUMAN	spermatogenesis associated 6	333			R -> W (in dbSNP:rs1338314).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	21						GCTGAATGCCGGGGCTTACTA	0.458													G|||	70	0.0139776	0.0008	0.0331	5008	,	,		14053	0.0		0.0408	False		,,,				2504	0.0051				p.R333W		Atlas-SNP	.											.	SPATA6	45	.	0			c.C997T						PASS	.	G	TRP/ARG	53,4353	52.3+/-87.9	0,53,2150	102	97	99		997	4.1	1	1	dbSNP_88	99	307,8293	109.8+/-170.3	4,299,3997	yes	missense	SPATA6	NM_019073.2	101	4,352,6147	AA,AG,GG		3.5698,1.2029,2.768	possibly-damaging	333/489	48825355	360,12646	2203	4300	6503	SO:0001583	missense	54558	exon10			AATGCCGGGGCTT	AK000869	CCDS551.1, CCDS65535.1, CCDS72787.1	1p32.3	2012-03-15			ENSG00000132122	ENSG00000132122			18309	protein-coding gene	gene with protein product	"spermatogenesis-related factor-1"	613947					Standard	XM_005270948		Approved	SRF1, FLJ10007, SRF-1	uc001crr.2	Q9NWH7	OTTHUMG00000007794	ENST00000371847.3:c.997C>T	1.37:g.48825355G>A	ENSP00000360913:p.Arg333Trp	74	0	0		54	27	0.5	NM_019073	Q5T3N7|Q8WUE6	Missense_Mutation	SNP	ENST00000371847.3	37	CCDS551.1	38	0.0173992673992674	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	25	0.032981530343007916	G	10.35	1.324952	0.24080	0.012029	0.035698	ENSG00000132122	ENST00000371847;ENST00000371843;ENST00000396199;ENST00000371841	T;T;T;T	0.46063	2.71;2.71;2.71;0.88	4.99	4.05	0.47172	.	1.098750	0.06782	N	0.785446	T	0.06462	0.0166	N	0.08118	0	0.19945	N	0.999948	P;P;P	0.44281	0.61;0.831;0.831	B;B;B	0.39152	0.292;0.219;0.219	T	0.06092	-1.0846	10	0.51188	T	0.08	.	8.7171	0.34419	0.0803:0.2907:0.6291:0.0	rs1338314;rs17429088;rs52805877;rs59077352;rs1338314	261;333;333	B4DX17;Q9NWH7-2;Q9NWH7	.;.;SPAT6_HUMAN	W	333;333;261;174	ENSP00000360913:R333W;ENSP00000360909:R333W;ENSP00000379502:R261W;ENSP00000360907:R174W	ENSP00000360907:R174W	R	-	1	2	SPATA6	48597942	0.971000	0.33674	1.000000	0.80357	0.015000	0.08874	1.086000	0.30853	1.278000	0.44430	0.655000	0.94253	CGG	G|0.975;A|0.025	0.025	strong		0.458	SPATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021347.1	NM_019073		A	48825355	G	A	48825355	3	1	25	1	0	0	0	0	1	0	0	0	15028	1115	39	1	485	1	SPATA6	1	48825355	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	4907467	48825355	200425266	31	8940											
ZFYVE9	9372	hgsc.bcm.edu	37	chr1	52803595	52803595	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgggtggatgatgacaagaaCgttagcaaggggtaaatgca	14	8	15	4	1	0	3	0	2	0	1	0	4	0	4	0	4	3	4	0	4	6	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:52803595C>T	ENST00000371591.1	+	15	3953	c.3822C>T	c.(3820-3822)aaC>aaT	p.N1274N	ZFYVE9_ENST00000287727.3_Silent_p.N1274N|ZFYVE9_ENST00000357206.2_Silent_p.N1215N	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	1274					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						ATGACAAGAACGTTAGCAAGG	0.502																																					p.N1274N		Atlas-SNP	.											.	ZFYVE9	131	.	0			c.C3822T						PASS	.						83	61	69					1																	52803595		2203	4300	6503	SO:0001819	synonymous_variant	9372	exon16			CAAGAACGTTAGC	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.3822C>T	1.37:g.52803595C>T		145	0	0		128	73	0.570312	NM_004799	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Silent	SNP	ENST00000371591.1	37	CCDS563.1																																																																																			.	.	none		0.502	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324		T	52803595	C	T	52803595	2	4	25	1	0	0	0	0	0	0	0	1	17686	535	19	1		1	ZFYVE9	1	52803595	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	3978240	52803595	196447026	32	8941											
C8B	732	hgsc.bcm.edu	37	chr1	57409459	57409459	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcaccaccaattttaaaatCatttttggcacaggcatgga	13	11	8	9	0	1	0	1	0	0	0	1	1	1	1	2	4	0	3	2	4	3	4	rs139498867	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:57409459C>A	ENST00000371237.4	-	8	1210	c.1144G>T	c.(1144-1146)Gat>Tat	p.D382Y	C8B_ENST00000543257.1_Missense_Mutation_p.D330Y|C8B_ENST00000535057.1_Missense_Mutation_p.D320Y	NM_000066.2	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide	382	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						ATTTTAAAATCATTTTTGGCA	0.403													C|||	14	0.00279553	0.0	0.0058	5008	,	,		21667	0.0		0.0099	False		,,,				2504	0.0				p.D382Y		Atlas-SNP	.											.	C8B	107	.	0			c.G1144T						PASS	.	C	TYR/ASP	4,4402	8.1+/-20.4	0,4,2199	187	166	173		1144	3.7	0	1	dbSNP_134	173	73,8527	44.5+/-102.8	0,73,4227	yes	missense	C8B	NM_000066.2	160	0,77,6426	AA,AC,CC		0.8488,0.0908,0.592	possibly-damaging	382/592	57409459	77,12929	2203	4300	6503	SO:0001583	missense	732	exon8			TAAAATCATTTTT	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.1144G>T	1.37:g.57409459C>A	ENSP00000360281:p.Asp382Tyr	159	0	0		173	74	0.427746	NM_000066	A1L4K7	Missense_Mutation	SNP	ENST00000371237.4	37	CCDS30730.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	C	26.5	4.741358	0.89573	9.08E-4	0.008488	ENSG00000021852	ENST00000371237;ENST00000543257;ENST00000535057	D;D;D	0.84146	-1.81;-1.81;-1.81	4.59	3.66	0.41972	Membrane attack complex component/perforin (MACPF) domain (3);	0.458353	0.25651	N	0.029202	D	0.83977	0.5371	L	0.51422	1.61	0.29294	N	0.869162	P;D;D	0.61080	0.874;0.974;0.989	P;P;P	0.58331	0.568;0.66;0.837	T	0.81992	-0.0678	10	0.72032	D	0.01	-3.603	12.8556	0.57884	0.0:0.9173:0.0:0.0827	.	330;320;382	F5H7G1;F5GY80;P07358	.;.;CO8B_HUMAN	Y	382;330;320	ENSP00000360281:D382Y;ENSP00000442548:D330Y;ENSP00000440113:D320Y	ENSP00000360281:D382Y	D	-	1	0	C8B	57182047	0.013000	0.17824	0.013000	0.15412	0.915000	0.54546	2.152000	0.42272	1.507000	0.48752	0.655000	0.94253	GAT	C|0.994;A|0.006	0.006	strong		0.403	C8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022886.2			A	57409459	C	A	57409459	3	1	25	1	0	0	0	0	1	0	0	0	2419	826	29	4	651	4	C8B	1	57409459	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	4605864	57409459	191841162	33	8942											
CACHD1	57685	hgsc.bcm.edu	37	chr1	65142686	65142686	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcaggtgcagtcagaggctGgaaagtgggtaagcagaatc	13	6	16	6	0	1	2	1	0	0	2	2	3	1	3	0	4	3	5	0	4	3	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:65142686G>A	ENST00000371073.2	+	22	3084	c.3084G>A	c.(3082-3084)ctG>ctA	p.L1028L	CACHD1_ENST00000495994.1_3'UTR|CACHD1_ENST00000290039.5_Silent_p.L977L			Q5VU97	CAHD1_HUMAN	cache domain containing 1	1028					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						GTCAGAGGCTGGAAAGTGGGT	0.453																																					p.L977L		Atlas-SNP	.											.	CACHD1	125	.	0			c.G2931A						PASS	.						74	69	71					1																	65142686		2203	4300	6503	SO:0001819	synonymous_variant	57685	exon22			GAGGCTGGAAAGT	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.3084G>A	1.37:g.65142686G>A		161	0	0		169	67	0.39645	NM_020925	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Silent	SNP	ENST00000371073.2	37																																																																																				.	.	none		0.453	CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925		A	65142686	G	A	65142686	2	1	25	1	0	0	0	0	0	0	0	1	2539	1335	47	2		2	CACHD1	1	65142686	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	7733227	65142686	184107935	34	8943											
ASB17	127247	hgsc.bcm.edu	37	chr1	76387795	76387795	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgactgaaatgacagaaagCactctggaacatagtaccaa	17	8	8	8	0	1	4	0	3	1	1	1	5	1	5	1	1	3	2	1	1	6	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:76387795C>T	ENST00000284142.6	-	2	790	c.651G>A	c.(649-651)gtG>gtA	p.V217V		NM_080868.2	NP_543144.1	Q8WXJ9	ASB17_HUMAN	ankyrin repeat and SOCS box containing 17	217					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						TGACAGAAAGCACTCTGGAAC	0.353																																					p.V217V		Atlas-SNP	.											.	ASB17	53	.	0			c.G651A						PASS	.						80	68	72					1																	76387795		2203	4300	6503	SO:0001819	synonymous_variant	127247	exon2			AGAAAGCACTCTG	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.651G>A	1.37:g.76387795C>T		105	0	0		104	48	0.461538	NM_080868	B1APB8|Q8N0X5	Silent	SNP	ENST00000284142.6	37	CCDS671.1																																																																																			.	.	none		0.353	ASB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026982.1	NM_080868		T	76387795	C	T	76387795	2	4	25	1	0	0	0	0	0	0	0	1	1021	697	25	2		2	ASB17	1	76387795	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	11245109	76387795	172862826	35	8944											
RBMXL1	494115	hgsc.bcm.edu	37	chr1	89449037	89449037	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	atctcttaggagaaggacccCcacttcttggtggtggtcct	7	12	11	11	0	2	1	0	0	2	1	4	3	3	2	3	5	0	0	3	5	2	3	rs200081893		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:89449037C>A	ENST00000321792.5	-	2	900	c.473G>T	c.(472-474)gGg>gTg	p.G158V	CCBL2_ENST00000260508.4_Intron|RBMXL1_ENST00000413769.1_5'UTR|CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000446900.2_Intron|CCBL2_ENST00000370485.2_Intron|RBMXL1_ENST00000399794.2_Missense_Mutation_p.G158V	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	158					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										AGAAGGACCCCCACTTCTTGG	0.493																																					p.G158V		Atlas-SNP	.											.	.	.	.	0			c.G473T						PASS	.						146	153	151					1																	89449037		2203	4300	6503	SO:0001583	missense	494115	exon3			GGACCCCCACTTC	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.473G>T	1.37:g.89449037C>A	ENSP00000318415:p.Gly158Val	473	0	0		486	23	0.0473251	NM_001162536		Missense_Mutation	SNP	ENST00000321792.5	37	CCDS716.1	.	.	.	.	.	.	.	.	.	.	C	15.99	2.995423	0.54147	.	.	ENSG00000213516	ENST00000321792;ENST00000399794	T;T	0.78924	-1.22;-1.22	1.76	0.711	0.18162	.	0.000000	0.85682	U	0.000000	T	0.57888	0.2084	M	0.72894	2.215	0.80722	D	1	B	0.23316	0.083	B	0.19391	0.025	T	0.55483	-0.8134	10	0.51188	T	0.08	-9.2612	6.8205	0.23855	0.2788:0.7212:0.0:0.0	.	158	Q96E39	RBMXL_HUMAN	V	158	ENSP00000318415:G158V;ENSP00000446099:G158V	ENSP00000318415:G158V	G	-	2	0	RBMXL1	89221625	0.997000	0.39634	0.791000	0.31998	0.903000	0.53119	2.436000	0.44819	0.049000	0.15920	0.306000	0.20318	GGG	C|0.997;A|0.003	0.003	weak		0.493	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610		A	89449037	C	A	89449037	3	1	25	1	0	0	0	0	1	0	0	0	13168	623	22	4	703	4	RBMXL1	1	89449037	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	13061242	89449037	159801584	36	8945											
ZNF326	284695	hgsc.bcm.edu	37	chr1	90484253	90484253	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ttgttttctaggagtgtatgGtgaataaattcaagaaaaca	15	14	9	3	0	2	2	1	1	1	1	2	3	2	3	0	2	1	2	0	2	8	7			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:90484253G>A	ENST00000340281.4	+	9	1227	c.1084G>A	c.(1084-1086)Gtg>Atg	p.V362M	ZNF326_ENST00000370447.3_Missense_Mutation_p.V273M|ZNF326_ENST00000455342.2_Missense_Mutation_p.V156M	NM_182976.2	NP_892021.1	Q5BKZ1	ZN326_HUMAN	zinc finger protein 326	362					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)		GGAGTGTATGGTGAATAAATT	0.289																																					p.V362M		Atlas-SNP	.											.	ZNF326	60	.	0			c.G1084A						PASS	.						52	57	55					1																	90484253		2198	4280	6478	SO:0001583	missense	284695	exon9			TGTATGGTGAATA	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.1084G>A	1.37:g.90484253G>A	ENSP00000340796:p.Val362Met	131	0	0		148	66	0.445946	NM_182976	A8MYX1|B4DLN0|B4E179|Q5VW93|Q5VW94|Q5VW96|Q5VW97|Q6NSA2|Q7Z638|Q7Z6C2	Missense_Mutation	SNP	ENST00000340281.4	37	CCDS727.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.094288	0.76870	.	.	ENSG00000162664	ENST00000394590;ENST00000340281;ENST00000370447;ENST00000455342	T;T;T	0.17528	2.27;2.27;2.27	5.56	5.56	0.83823	.	0.066635	0.64402	D	0.000018	T	0.32496	0.0831	M	0.62723	1.935	0.50313	D	0.999865	D;D	0.63046	0.992;0.992	D;P	0.66847	0.947;0.9	T	0.02457	-1.1156	10	0.62326	D	0.03	-10.1859	19.1298	0.93400	0.0:0.0:1.0:0.0	.	362;362	A8MYX1;Q5BKZ1	.;ZN326_HUMAN	M	362;362;273;156	ENSP00000340796:V362M;ENSP00000359476:V273M;ENSP00000403470:V156M	ENSP00000340796:V362M	V	+	1	0	ZNF326	90256841	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.778000	0.75043	2.620000	0.88729	0.650000	0.86243	GTG	.	.	none		0.289	ZNF326-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029428.2	NM_181781		A	90484253	G	A	90484253	3	1	25	1	0	0	0	0	1	0	0	0	17861	1261	44	2	1122	2	ZNF326	1	90484253	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1035216	90484253	158766368	37	8946											
HFM1	164045	hgsc.bcm.edu	37	chr1	91809036	91809036	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctttattaagtccagggaTgataaatcattcagattctt	13	16	6	6	0	4	2	2	1	2	1	5	3	5	3	1	1	0	0	1	1	4	7	rs148872247	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:91809036T>C	ENST00000370425.3	-	20	2384	c.2286A>G	c.(2284-2286)tcA>tcG	p.S762S	HFM1_ENST00000462405.1_5'UTR|HFM1_ENST00000294696.5_5'UTR|HFM1_ENST00000370424.3_Silent_p.S441S	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	762					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)		AGTCCAGGGATGATAAATCAT	0.249													T|||	34	0.00678914	0.0	0.0	5008	,	,		13475	0.0		0.0	False		,,,				2504	0.0348				p.S762S		Atlas-SNP	.											.	HFM1	188	.	0			c.A2286G						PASS	.	T		1,4379		0,1,2189	27	27	27		2286	4.2	1	1	dbSNP_134	27	1,8511		0,1,4255	no	coding-synonymous	HFM1	NM_001017975.3		0,2,6444	CC,CT,TT		0.0117,0.0228,0.0155		762/1436	91809036	2,12890	2190	4256	6446	SO:0001819	synonymous_variant	164045	exon20			CAGGGATGATAAA	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.2286A>G	1.37:g.91809036T>C		211	0	0		246	113	0.45935	NM_001017975	B1B0B6|Q8N9Q0	Silent	SNP	ENST00000370425.3	37	CCDS30769.2	.	.	.	.	.	.	.	.	.	.	T	9.635	1.137319	0.21123	2.28E-4	1.17E-4	ENSG00000162669	ENST00000430465	.	.	.	5.35	4.18	0.49190	.	.	.	.	.	T	0.43787	0.1263	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45571	-0.9252	4	.	.	.	.	6.5979	0.22685	0.217:0.082:0.0:0.7009	.	.	.	.	R	18	.	.	H	-	2	0	HFM1	91581624	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.354000	0.34056	2.015000	0.59207	0.377000	0.23210	CAT	T|0.999;C|0.001	0.001	strong		0.249	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		C	91809036	T	C	91809036	2	2	25	1	0	0	0	0	0	0	0	1	7092	1451	51	3		3	HFM1	1	91809036	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	1324783	91809036	157441585	38	8947											
HFM1	164045	hgsc.bcm.edu	37	chr1	91816313	91816313	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accataatgagatggattttTcaaggctctgatataaagca	15	12	8	6	0	2	2	1	2	1	1	2	4	2	3	1	2	1	2	1	2	5	5			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:91816313T>C	ENST00000370425.3	-	18	2286	c.2188A>G	c.(2188-2190)Aaa>Gaa	p.K730E	HFM1_ENST00000462405.1_Intron|HFM1_ENST00000294696.5_5'UTR|HFM1_ENST00000370424.3_Missense_Mutation_p.K409E	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	730					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)		GATGGATTTTTCAAGGCTCTG	0.343																																					p.K730E		Atlas-SNP	.											.	HFM1	188	.	0			c.A2188G						PASS	.						119	107	111					1																	91816313		1834	4085	5919	SO:0001583	missense	164045	exon18			GATTTTTCAAGGC	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.2188A>G	1.37:g.91816313T>C	ENSP00000359454:p.Lys730Glu	65	0	0		108	53	0.490741	NM_001017975	B1B0B6|Q8N9Q0	Missense_Mutation	SNP	ENST00000370425.3	37	CCDS30769.2	.	.	.	.	.	.	.	.	.	.	T	23.5	4.421719	0.83559	.	.	ENSG00000162669	ENST00000370425;ENST00000370424;ENST00000370421	T;T	0.68181	0.03;-0.31	5.36	5.36	0.76844	.	0.000000	0.47852	U	0.000204	T	0.80433	0.4622	M	0.88031	2.925	0.80722	D	1	D;D	0.64830	0.994;0.986	D;P	0.65874	0.939;0.904	D	0.83812	0.0242	10	0.54805	T	0.06	.	15.6548	0.77124	0.0:0.0:0.0:1.0	.	409;730	A6NGI5;A2PYH4	.;HFM1_HUMAN	E	730;409;414	ENSP00000359454:K730E;ENSP00000359453:K409E	ENSP00000359450:K414E	K	-	1	0	HFM1	91588901	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.939000	0.87685	2.162000	0.67917	0.377000	0.23210	AAA	.	.	none		0.343	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975		C	91816313	T	C	91816313	3	2	25	1	0	0	0	0	1	0	0	0	7092	1792	62	3	2207	3	HFM1	1	91816313	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	7277	91816313	157434308	39	8948											
AMY2A	279	hgsc.bcm.edu	37	chr1	104166590	104166590	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	atgactgggtctgtgaacatCgatggcgccaaataaggtga	12	9	13	7	2	1	3	0	3	1	0	2	4	1	3	1	3	1	0	1	3	3	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:104166590C>G	ENST00000414303.2	+	8	1268	c.1204C>G	c.(1204-1206)Cga>Gga	p.R402G	AMY2A_ENST00000497748.1_3'UTR	NM_000699.2	NP_000690.1	P04746	AMYP_HUMAN	amylase, alpha 2A (pancreatic)	402					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)	p.R402*(1)		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)	CTGTGAACATCGATGGCGCCA	0.343																																					p.R402G		Atlas-SNP	.											AMY2A,colon,carcinoma,0,1	AMY2A	36	1	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1204G						scavenged	.						9	9	9					1																	104166590		1665	3373	5038	SO:0001583	missense	279	exon8			GAACATCGATGGC	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.1204C>G	1.37:g.104166590C>G	ENSP00000397582:p.Arg402Gly	468	0	0		492	93	0.189024	NM_000699	B9EJG1|Q9UBH3	Missense_Mutation	SNP	ENST00000414303.2	37	CCDS783.1	.	.	.	.	.	.	.	.	.	.	-	13.88	2.369406	0.42003	.	.	ENSG00000243480	ENST00000414303;ENST00000393932	.	.	.	2.94	1.99	0.26369	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	0.81384	0.4811	H	0.96239	3.79	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.83784	0.0227	9	0.87932	D	0	.	9.5171	0.39113	0.3781:0.6219:0.0:0.0	.	402	P04746	AMYP_HUMAN	G	402	.	ENSP00000377509:R402G	R	+	1	2	AMY2A	103968113	0.999000	0.42202	0.992000	0.48379	0.892000	0.51952	1.860000	0.39428	0.540000	0.28808	0.305000	0.20034	CGA	.	.	weak		0.343	AMY2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030315.1	NM_000699		G	104166590	C	G	104166590	3	3	25	1	0	0	0	0	1	0	0	0	594	876	31	4	1234	4	AMY2A	1	104166590	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	12350277	104166590	145084031	40	8949											
SLC16A4	9122	hgsc.bcm.edu	37	chr1	110924316	110924316	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaaagaaaaggaatacttgTggcccagctgctgatcagat	15	8	10	8	0	1	3	1	1	0	2	1	4	1	4	1	2	3	2	1	2	5	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:110924316T>C	ENST00000369779.4	-	4	571	c.322A>G	c.(322-324)Aca>Gca	p.T108A	SLC16A4_ENST00000497687.1_Intron|LAMTOR5-AS1_ENST00000590413.1_RNA|SLC16A4_ENST00000369781.4_Missense_Mutation_p.T108A|SLC16A4_ENST00000472422.2_Intron|SLC16A4_ENST00000437429.2_Intron|SLC16A4_ENST00000541986.1_Missense_Mutation_p.T46A	NM_001201547.1|NM_004696.2	NP_001188476.1|NP_004687.1	O15374	MOT5_HUMAN	solute carrier family 16, member 4	108					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)	GGAATACTTGTGGCCCAGCTG	0.458																																					p.T108A		Atlas-SNP	.											.	SLC16A4	47	.	0			c.A322G						PASS	.						102	94	96					1																	110924316		2203	4300	6503	SO:0001583	missense	9122	exon4			TACTTGTGGCCCA	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.322A>G	1.37:g.110924316T>C	ENSP00000358794:p.Thr108Ala	259	0	0		228	110	0.482456	NM_004696	A8K3V5|B2R9C9|B4DJ67|B4DPX7|E7EPY8|G3V175|Q5T612|Q8WU09	Missense_Mutation	SNP	ENST00000369779.4	37	CCDS823.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.129800	0.77549	.	.	ENSG00000168679	ENST00000369779;ENST00000369781;ENST00000541986	T;T;T	0.55760	0.5;0.5;0.5	4.86	3.73	0.42828	Major facilitator superfamily domain, general substrate transporter (1);	0.253587	0.45867	N	0.000340	T	0.61602	0.2360	M	0.87971	2.92	0.80722	D	1	D;D;P;D	0.65815	0.995;0.994;0.947;0.992	D;D;P;D	0.68621	0.91;0.959;0.823;0.91	T	0.63633	-0.6593	10	0.30854	T	0.27	.	9.0678	0.36473	0.0:0.0848:0.0:0.9152	.	46;108;108;108	B4DJ67;Q53FH9;Q8WU09;O15374	.;.;.;MOT5_HUMAN	A	108;108;46	ENSP00000358794:T108A;ENSP00000358796:T108A;ENSP00000446087:T46A	ENSP00000358794:T108A	T	-	1	0	SLC16A4	110725839	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	5.203000	0.65174	0.994000	0.38892	0.533000	0.62120	ACA	.	.	none		0.458	SLC16A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000031115.3	NM_004696		C	110924316	T	C	110924316	3	2	25	1	0	0	0	0	1	0	0	0	14425	1696	59	3	1165	3	SLC16A4	1	110924316	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	6757726	110924316	138326305	41	8950											
NOTCH2	4853	hgsc.bcm.edu	37	chr1	120458161	120458161	+	Nonsense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtgttcgctcagcagcatttGaggaagcataactgtgctgt	9	12	12	8	1	1	1	1	1	0	0	2	2	1	2	0	1	5	6	0	1	2	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:120458161G>C	ENST00000256646.2	-	34	7403	c.7184C>G	c.(7183-7185)tCa>tGa	p.S2395*		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	2395					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)		AGCAGCATTTGAGGAAGCATA	0.567			"N, F, Mis"		"marginal zone lymphoma, DLBCL"				Alagille Syndrome																												p.S2395X		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.C7184G						PASS	.						123	108	113					1																	120458161		2203	4300	6503	SO:0001587	stop_gained	4853	exon34	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	GCATTTGAGGAAG	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.7184C>G	1.37:g.120458161G>C	ENSP00000256646:p.Ser2395*	104	0	0		125	51	0.408	NM_024408	Q5T3X7|Q99734|Q9H240	Nonsense_Mutation	SNP	ENST00000256646.2	37	CCDS908.1	.	.	.	.	.	.	.	.	.	.	G	48	14.309534	0.99789	.	.	ENSG00000134250	ENST00000256646	.	.	.	5.35	5.35	0.76521	.	0.000000	0.30879	U	0.008688	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	16.2129	0.82178	0.0:0.0:1.0:0.0	.	.	.	.	X	2395	.	ENSP00000256646:S2395X	S	-	2	0	NOTCH2	120259684	1.000000	0.71417	0.953000	0.39169	0.975000	0.68041	9.145000	0.94634	2.506000	0.84524	0.591000	0.81541	TCA	.	.	none		0.567	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408		C	120458161	G	C	120458161	4	2	25	1	0	0	0	0	0	1	0	0	10557	1294	45	4	235	4	NOTCH2	1	120458161	Nonsense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	9533845	120458161	128792460	42	8951											
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144922252	144922252	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccattgtgtcattttgacCttcaattacctggtacaact	9	16	6	10	0	2	1	2	1	0	0	2	1	2	1	3	1	4	1	3	1	4	6	rs147451175	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:144922252C>G	ENST00000369354.3	-	8	1105	c.916G>C	c.(916-918)Ggt>Cgt	p.G306R	PDE4DIP_ENST00000530740.1_Missense_Mutation_p.G443R|PDE4DIP_ENST00000529945.1_Missense_Mutation_p.G469R|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.G306R|PDE4DIP_ENST00000369351.3_Missense_Mutation_p.G306R|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.G372R|PDE4DIP_ENST00000479408.2_Missense_Mutation_p.G93R|PDE4DIP_ENST00000369349.3_Missense_Mutation_p.G306R|PDE4DIP_ENST00000313431.9_Missense_Mutation_p.G469R|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.G443R			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	306					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)		TCATTTTGACCTTCAATTACC	0.398			T	PDGFRB	MPD								C|||	19	0.00379393	0.0	0.0072	5008	,	,		45130	0.0		0.0089	False		,,,				2504	0.0051				p.G469R		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.G1405C						PASS	.	C	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	3,4403	6.2+/-15.9	0,3,2200	163	141	148		1405,916,1114,916,916	3.1	1	1	dbSNP_134	148	52,8548	29.6+/-80.5	0,52,4248	yes	missense,missense,missense,missense,missense	PDE4DIP	NM_001002811.1,NM_001002812.1,NM_001198832.1,NM_001198834.2,NM_014644.4	125,125,125,125,125	0,55,6448	GG,GC,CC		0.6047,0.0681,0.4229	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	469/1133,306/970,372/2241,306/2363,306/2347	144922252	55,12951	2203	4300	6503	SO:0001583	missense	9659	exon4			TTTGACCTTCAAT	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.916G>C	1.37:g.144922252C>G	ENSP00000358360:p.Gly306Arg	132	0	0		144	26	0.180556	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	37	CCDS30824.1	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	C	19.82	3.898738	0.72639	6.81E-4	0.006047	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000369353;ENST00000530740;ENST00000369359;ENST00000369351;ENST00000369349;ENST00000313431;ENST00000529945;ENST00000479408	T;T;T;T;T;T;T;T;T;T	0.12774	4.6;4.69;4.69;4.7;4.69;3.72;3.72;2.67;2.67;2.65	5.92	3.07	0.35406	.	.	.	.	.	T	0.18964	0.0455	M	0.67953	2.075	0.80722	D	1	D;D;D;D;D	0.71674	0.997;0.985;0.997;0.998;0.994	D;P;D;D;D	0.71870	0.931;0.859;0.954;0.975;0.929	T	0.00931	-1.1510	9	0.48119	T	0.1	.	9.4783	0.38884	0.0:0.7702:0.0:0.2298	.	469;306;469;372;306	E9PL24;Q5VU43-7;Q5VU43-2;Q5VU43-3;Q5VU43	.;.;.;.;MYOME_HUMAN	R	372;306;306;469;443;443;306;306;469;469;93	ENSP00000327209:G372R;ENSP00000358360:G306R;ENSP00000358363:G306R;ENSP00000435654:G443R;ENSP00000358366:G443R;ENSP00000358357:G306R;ENSP00000358355:G306R;ENSP00000316434:G469R;ENSP00000433392:G469R;ENSP00000436791:G93R	ENSP00000327209:G372R	G	-	1	0	PDE4DIP	143633609	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	1.718000	0.38001	0.411000	0.25702	0.650000	0.86243	GGT	C|0.996;G|0.004	0.004	strong		0.398	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		G	144922252	C	G	144922252	3	3	25	1	0	0	0	0	1	0	0	0	11652	681	24	4	6282	4	PDE4DIP	1	144922252	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	24464091	144922252	104328369	43	8952											
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	145015976	145015976	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctccagatctgtgactgcaCtggagggcctcgatctttag	7	12	11	11	1	3	2	0	1	3	1	5	4	3	3	2	2	1	1	2	2	1	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:145015976C>T	ENST00000530740.1	-	3	363	c.325G>A	c.(325-327)Gtg>Atg	p.V109M	RP11-326G21.1_ENST00000610119.1_RNA|PDE4DIP_ENST00000493130.2_Missense_Mutation_p.V38M|PDE4DIP_ENST00000478649.2_Missense_Mutation_p.V38M|PDE4DIP_ENST00000369348.3_Missense_Mutation_p.V109M|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.V38M|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.V109M			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	0				I -> M (in Ref. 1; BAB17759/BAB17760/ BAB17761/BAB17762 and 6; AAH25406/ AAI10295). {ECO:0000305}.	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)		TGTGACTGCACTGGAGGGCCT	0.423			T	PDGFRB	MPD																																p.V109M		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.G325A						PASS	.																																			SO:0001583	missense	9659	exon3			ACTGCACTGGAGG	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.325G>A	1.37:g.145015976C>T	ENSP00000435654:p.Val109Met	174	0	0		214	30	0.140187	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	37		.	.	.	.	.	.	.	.	.	.	C	9.285	1.049170	0.19827	.	.	ENSG00000178104	ENST00000313382;ENST00000530740;ENST00000369359;ENST00000532801;ENST00000530078;ENST00000369348;ENST00000531369;ENST00000493130;ENST00000478649	T;T;T;T;T;T	0.49139	4.55;4.67;4.67;0.79;2.96;1.88	5.26	-0.476	0.12100	.	.	.	.	.	T	0.09905	0.0243	N	0.14661	0.345	0.09310	N	1	B;B;B	0.18863	0.007;0.004;0.031	B;B;B	0.14023	0.003;0.002;0.01	T	0.29610	-1.0006	9	0.36615	T	0.2	.	4.6702	0.12685	0.1441:0.2711:0.4924:0.0925	.	38;109;38	Q5VU43-3;E9PJ64;E9PQH9	.;.;.	M	38;109;109;38;38;109;39;38;38	ENSP00000327209:V38M;ENSP00000435654:V109M;ENSP00000358366:V109M;ENSP00000436751:V38M;ENSP00000358354:V109M;ENSP00000435616:V39M	ENSP00000327209:V38M	V	-	1	0	PDE4DIP	143727333	0.000000	0.05858	0.002000	0.10522	0.350000	0.29205	0.037000	0.13840	0.046000	0.15833	0.655000	0.94253	GTG	.	.	none		0.423	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000384663.2	NM_022359		T	145015976	C	T	145015976	3	4	25	1	0	0	0	0	1	0	0	0	11652	565	20	2	8479	2	PDE4DIP	1	145015976	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	93724	145015976	104234645	44	8953											
NUDT17	200035	hgsc.bcm.edu	37	chr1	145586672	145586679	+	Frame_Shift_Del	DEL	TTTTACAC	TTTTACAC	-																															tgggtccaggtaagctgcacTtttacacggtgggggtgttc																								rs201063949|rs199513201|rs199927874|rs150364859	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TTTTACAC	TTTTACAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:145586672_145586679delTTTTACAC	ENST00000334513.5	-	8	908_915	c.897_904delGTGTAAAA	c.(895-906)ccgtgtaaaagtfs	p.CKS300fs	NUDT17_ENST00000444015.2_5'Flank	NM_001012758.2	NP_001012776.1	P0C025	NUD17_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 17	300							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)					TAAGCTGCACTTTTACACGGTGGGGGTG	0.534																																					p.300_302del		Pindel	.											.	NUDT17	25	.	0			c.898_905del						PASS	.																																			SO:0001589	frameshift_variant	200035	exon8			.	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.897_904delGTGTAAAA	1.37:g.145586672_145586679delTTTTACAC	ENSP00000334437:p.Cys300fs	137	0	.		133	27	0.203	NM_001012758		Frame_Shift_Del	DEL	ENST00000334513.5	37	CCDS30830.1																																																																																			-|0.017;TTTTA|0.983	0.017	alt		0.534	NUDT17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038541.3	XM_496395		-	145586679	TTTTACAC	-	145586672	7	5	25	1	0	1	0	1	0	0	0	0	10743	1609	56	0	86	0	NUDT17	1	145586672	Frame_Shift_Del	DEL	TTTTACAC	TCGA-G8-6906-01A-11D-2210-10	570696	145586672	103663949	45	8954											
OTUD7B	56957	hgsc.bcm.edu	37	chr1	149916118	149916118	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaaggtggcatatggtggtaGgcccccgacacatggacccc	9	6	14	12	1	0	0	0	0	0	0	0	3	0	1	4	6	0	2	4	6	3	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:149916118G>C	ENST00000369135.4	-	12	2464	c.2170C>G	c.(2170-2172)Cta>Gta	p.L724V		NM_020205.2	NP_064590.2	Q6GQQ9	OTU7B_HUMAN	OTU deubiquitinase 7B	724					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)			TATGGTGGTAGGCCCCCGACA	0.652																																					p.L724V		Atlas-SNP	.											.	OTUD7B	76	.	0			c.C2170G						PASS	.						28	32	31					1																	149916118		1961	4133	6094	SO:0001583	missense	56957	exon12			GTGGTAGGCCCCC	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.2170C>G	1.37:g.149916118G>C	ENSP00000358131:p.Leu724Val	38	0	0		65	34	0.523077	NM_020205	B7Z643|D3DUZ8|Q5SZ60|Q8WWA7|Q9NQ53|Q9UFF4	Missense_Mutation	SNP	ENST00000369135.4	37	CCDS41389.1	.	.	.	.	.	.	.	.	.	.	G	11.68	1.710511	0.30322	.	.	ENSG00000163113	ENST00000369135;ENST00000543330	T	0.35789	1.29	4.37	3.44	0.39384	.	0.146689	0.45606	D	0.000347	T	0.13756	0.0333	L	0.50333	1.59	0.41982	D	0.990803	P	0.44241	0.829	B	0.33254	0.16	T	0.03157	-1.1066	9	.	.	.	-23.4143	10.4837	0.44708	0.098:0.0:0.902:0.0	.	724	Q6GQQ9	OTU7B_HUMAN	V	724	ENSP00000358131:L724V	.	L	-	1	2	OTUD7B	148182742	0.998000	0.40836	0.903000	0.35520	0.767000	0.43475	3.982000	0.56909	1.027000	0.39758	0.455000	0.32223	CTA	.	.	none		0.652	OTUD7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034146.3	NM_020205		C	149916118	G	C	149916118	3	2	25	1	0	0	0	0	1	0	0	0	11328	991	35	4	365	4	OTUD7B	1	149916118	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	4329446	149916118	99334503	46	8955											
RPRD2	23248	hgsc.bcm.edu	37	chr1	150445058	150445058	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tccagagagagccagtggggCcatcatctgccccacctgtc	8	7	11	15	0	2	2	1	0	1	2	4	3	3	2	6	2	2	0	6	2	0	0	rs201108869		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:150445058C>T	ENST00000369068.4	+	11	3638	c.3634C>T	c.(3634-3636)Cca>Tca	p.P1212S	RPRD2_ENST00000401000.4_Missense_Mutation_p.P1186S|RPRD2_ENST00000492220.1_3'UTR	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2	1212	Pro-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						GCCAGTGGGGCCATCATCTGC	0.537																																					p.P1212S		Atlas-SNP	.											.	RPRD2	189	.	0			c.C3634T						PASS	.	C	SER/PRO	0,3984		0,0,1992	84	87	86		3634	4.6	1	1		86	2,8300		0,2,4149	yes	missense	RPRD2	NM_015203.3	74	0,2,6141	TT,TC,CC		0.0241,0.0,0.0163	probably-damaging	1212/1462	150445058	2,12284	1992	4151	6143	SO:0001583	missense	23248	exon11			GTGGGGCCATCAT	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.3634C>T	1.37:g.150445058C>T	ENSP00000358064:p.Pro1212Ser	127	0	0		132	76	0.575758	NM_015203	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	Missense_Mutation	SNP	ENST00000369068.4	37	CCDS44216.1	.	.	.	.	.	.	.	.	.	.	C	15.88	2.965007	0.53507	0.0	2.41E-4	ENSG00000163125	ENST00000401000;ENST00000369068	T;T	0.61510	0.1;0.12	4.59	4.59	0.56863	.	0.161530	0.43416	D	0.000574	T	0.57548	0.2061	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.992;0.996	T	0.65537	-0.6144	10	0.72032	D	0.01	-7.9501	17.1925	0.86883	0.0:1.0:0.0:0.0	.	1212;1186	Q5VT52;Q5VT52-3	RPRD2_HUMAN;.	S	1186;1212	ENSP00000383785:P1186S;ENSP00000358064:P1212S	ENSP00000358064:P1212S	P	+	1	0	RPRD2	148711682	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.389000	0.52516	2.363000	0.80096	0.563000	0.77884	CCA	.	.	weak		0.537	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203		T	150445058	C	T	150445058	3	4	25	1	0	0	0	0	1	0	0	0	13632	739	26	2	3676	2	RPRD2	1	150445058	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	528940	150445058	98805563	47	8956											
CRNN	49860	hgsc.bcm.edu	37	chr1	152383373	152383373	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtccctgtgtggtcttcaTccagcagacgcaggacctca	8	9	10	14	1	3	1	2	0	1	1	5	2	5	2	3	2	1	2	3	2	0	1	rs571572587	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152383373T>A	ENST00000271835.3	-	3	247	c.185A>T	c.(184-186)gAt>gTt	p.D62V	RP1-91G5.3_ENST00000411804.1_RNA	NM_016190.2	NP_057274.1	Q9UBG3	CRNN_HUMAN	cornulin	62	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.				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)			GTGGTCTTCATCCAGCAGACG	0.537													T|||	4	0.000798722	0.0	0.0	5008	,	,		18928	0.0		0.0	False		,,,				2504	0.0041				p.D62V		Atlas-SNP	.											.	CRNN	78	.	0			c.A185T						PASS	.						45	47	47					1																	152383373		2196	4287	6483	SO:0001583	missense	49860	exon3			TCTTCATCCAGCA	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.185A>T	1.37:g.152383373T>A	ENSP00000271835:p.Asp62Val	60	0	0		88	44	0.5	NM_016190	B2RE60|Q8N613	Missense_Mutation	SNP	ENST00000271835.3	37	CCDS1010.1	.	.	.	.	.	.	.	.	.	.	T	17.17	3.321521	0.60634	.	.	ENSG00000143536	ENST00000271835;ENST00000451038	T	0.55234	0.53	4.73	4.73	0.59995	EF-hand-like domain (1);	0.000000	0.48286	D	0.000186	T	0.77458	0.4133	H	0.97940	4.11	0.58432	D	0.999995	D	0.89917	1.0	D	0.85130	0.997	D	0.84507	0.0620	10	0.87932	D	0	.	10.5413	0.45035	0.0:0.0:0.0:1.0	.	62	Q9UBG3	CRNN_HUMAN	V	62	ENSP00000271835:D62V	ENSP00000271835:D62V	D	-	2	0	CRNN	150649997	1.000000	0.71417	1.000000	0.80357	0.669000	0.39330	3.886000	0.56190	1.983000	0.57843	0.254000	0.18369	GAT	.	.	none		0.537	CRNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034503.1	NM_016190		A	152383373	T	A	152383373	3	1	25	1	0	0	0	0	1	0	0	0	3894	1435	50	5	1306	5	CRNN	1	152383373	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	1938315	152383373	96867248	48	8957											
NPR1	4881	hgsc.bcm.edu	37	chr1	153662423	153662423	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gaatccgccaccggccccagGagcagctgcgcttgcgcatt	7	6	12	16	4	0	0	0	0	0	0	1	2	1	1	5	2	4	4	5	2	1	2	rs35479618	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:153662423G>A	ENST00000368680.3	+	19	3371	c.2899G>A	c.(2899-2901)Gag>Aag	p.E967K		NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1	967	Guanylate cyclase. {ECO:0000255|PROSITE- ProRule:PRU00099}.		E -> K (in dbSNP:rs35479618). {ECO:0000269|PubMed:17344846}.		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)	CCGGCCCCAGGAGCAGCTGCG	0.662													G|||	17	0.00339457	0.0	0.0014	5008	,	,		14197	0.0		0.0139	False		,,,				2504	0.002				p.E967K	Pancreas(141;1349 1870 15144 15830 40702)	Atlas-SNP	.											.	NPR1	104	.	0			c.G2899A						PASS	.	G	LYS/GLU	11,4311		0,11,2150	15	16	15		2899	2.9	1	1	dbSNP_126	15	105,8313		1,103,4105	yes	missense	NPR1	NM_000906.3	56	1,114,6255	AA,AG,GG		1.2473,0.2545,0.9105	possibly-damaging	967/1062	153662423	116,12624	2161	4209	6370	SO:0001583	missense	4881	exon19			CCCCAGGAGCAGC	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.2899G>A	1.37:g.153662423G>A	ENSP00000357669:p.Glu967Lys	79	0	0		85	33	0.388235	NM_000906	B0ZBF0|Q5SR08|Q6P4Q3	Missense_Mutation	SNP	ENST00000368680.3	37	CCDS1051.1	10	0.004578754578754579	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	G	15.02	2.709779	0.48517	0.002545	0.012473	ENSG00000169418	ENST00000368680;ENST00000428723;ENST00000368677	D	0.81739	-1.53	2.87	2.87	0.33458	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.294578	0.26324	N	0.025023	T	0.55178	0.1904	L	0.34521	1.04	0.38332	D	0.943827	B;P	0.35628	0.201;0.513	B;B	0.36922	0.236;0.134	T	0.58358	-0.7650	10	0.37606	T	0.19	.	5.8634	0.18760	0.1433:0.0:0.8567:0.0	rs35479618;rs61758573	446;967	B7Z4Y7;P16066	.;ANPRA_HUMAN	K	967;446;148	ENSP00000357669:E967K	ENSP00000357666:E148K	E	+	1	0	NPR1	151929047	0.886000	0.30341	1.000000	0.80357	0.912000	0.54170	1.368000	0.34216	1.907000	0.55213	0.462000	0.41574	GAG	G|0.993;A|0.007	0.007	strong		0.662	NPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090034.1	NM_000906		A	153662423	G	A	153662423	3	1	25	1	0	0	0	0	1	0	0	0	10603	1175	41	2	2973	2	NPR1	1	153662423	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1279050	153662423	95588198	49	8958											
INTS3	65123	hgsc.bcm.edu	37	chr1	153737498	153737498	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccgagctatatcagaagcaGcccaagattggctaccacct	12	8	8	13	1	1	2	1	0	0	2	2	3	2	2	4	1	4	3	4	1	5	4			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:153737498G>T	ENST00000318967.2	+	20	2617	c.2049G>T	c.(2047-2049)caG>caT	p.Q683H	INTS3_ENST00000476843.1_3'UTR|INTS3_ENST00000512605.1_Missense_Mutation_p.Q477H|INTS3_ENST00000456435.1_Missense_Mutation_p.Q477H|INTS3_ENST00000435409.2_Missense_Mutation_p.Q683H	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	684					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)			ATCAGAAGCAGCCCAAGATTG	0.532																																					p.Q683H		Atlas-SNP	.											.	INTS3	83	.	0			c.G2049T						PASS	.						233	222	226					1																	153737498		2203	4300	6503	SO:0001583	missense	65123	exon20			GAAGCAGCCCAAG	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.2049G>T	1.37:g.153737498G>T	ENSP00000318641:p.Gln683His	86	0	0		105	31	0.295238	NM_023015	A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Missense_Mutation	SNP	ENST00000318967.2	37	CCDS1052.1	.	.	.	.	.	.	.	.	.	.	G	15.62	2.887087	0.52014	.	.	ENSG00000143624	ENST00000318967;ENST00000456435;ENST00000435409;ENST00000512605	.	.	.	4.91	1.99	0.26369	.	0.000000	0.85682	D	0.000000	T	0.57770	0.2076	M	0.64404	1.975	0.42968	D	0.994425	D;D;D	0.64830	0.994;0.98;0.988	D;D;D	0.78314	0.991;0.948;0.977	T	0.59925	-0.7362	9	0.62326	D	0.03	.	7.1424	0.25564	0.2806:0.0:0.7194:0.0	.	477;684;683	Q68E01-3;Q68E01;Q68E01-2	.;INT3_HUMAN;.	H	683;477;683;477	.	ENSP00000318641:Q683H	Q	+	3	2	INTS3	152004122	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.298000	0.43602	0.258000	0.21686	0.563000	0.77884	CAG	.	.	none		0.532	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015		T	153737498	G	T	153737498	3	4	25	1	0	0	0	0	1	0	0	0	7788	962	34	4	2127	4	INTS3	1	153737498	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	75075	153737498	95513123	50	8959											
TMEM79	84283	hgsc.bcm.edu	37	chr1	156255560	156255560	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgaggcagtggtgaggccGcctggctgttcctgtggggg	3	9	20	9	1	0	2	0	2	0	0	1	2	1	2	3	6	0	4	3	6	0	1	rs140033065	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:156255560G>A	ENST00000405535.2	+	2	714	c.543G>A	c.(541-543)ccG>ccA	p.P181P	SMG5_ENST00000361813.5_5'Flank|TMEM79_ENST00000295694.5_Silent_p.P181P|TMEM79_ENST00000495881.1_3'UTR|TMEM79_ENST00000357501.2_Intron|SMG5_ENST00000368267.5_5'Flank	NM_032323.2	NP_115699.1	Q9BSE2	TMM79_HUMAN	transmembrane protein 79	181					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)					TGGTGAGGCCGCCTGGCTGTT	0.682													G|||	5	0.000998403	0.0	0.0	5008	,	,		12551	0.0		0.004	False		,,,				2504	0.001				p.P181P		Atlas-SNP	.											.	TMEM79	43	.	0			c.G543A						PASS	.	G		5,4395		0,5,2195	39	45	43		543	-11.3	0	1	dbSNP_134	43	29,8569		1,27,4271	no	coding-synonymous	TMEM79	NM_032323.2		1,32,6466	AA,AG,GG		0.3373,0.1136,0.2616		181/395	156255560	34,12964	2200	4299	6499	SO:0001819	synonymous_variant	84283	exon2			GAGGCCGCCTGGC	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.543G>A	1.37:g.156255560G>A		81	0	0		70	39	0.557143	NM_032323	B2RE22|D3DVB8	Silent	SNP	ENST00000405535.2	37	CCDS1138.1																																																																																			G|0.997;A|0.003	0.003	strong		0.682	TMEM79-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052101.1	NM_032323		A	156255560	G	A	156255560	2	1	25	1	0	0	0	0	0	0	0	1	16218	1074	38	1		1	TMEM79	1	156255560	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2518062	156255560	92995061	51	8960											
CD1D	912	hgsc.bcm.edu	37	chr1	158151892	158151892	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctcaaataacttcttccaTgtagcatttcaaggaaaaga	15	11	6	9	0	3	1	2	0	1	1	4	2	4	2	2	1	2	2	2	1	6	5	rs140563679	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:158151892T>C	ENST00000368171.3	+	4	898	c.399T>C	c.(397-399)caT>caC	p.H133H		NM_001766.3	NP_001757.1	P15813	CD1D_HUMAN	CD1d molecule	133					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)					ACTTCTTCCATGTAGCATTTC	0.498													T|||	3	0.000599042	0.0	0.0	5008	,	,		19718	0.0		0.003	False		,,,				2504	0.0				p.H133H		Atlas-SNP	.											.	CD1D	60	.	0			c.T399C						PASS	.	T		0,4406		0,0,2203	130	143	138		399	-9.5	0	1	dbSNP_134	138	17,8583	12.6+/-44.7	0,17,4283	no	coding-synonymous	CD1D	NM_001766.3		0,17,6486	CC,CT,TT		0.1977,0.0,0.1307		133/336	158151892	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	912	exon4			CTTCCATGTAGCA	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.399T>C	1.37:g.158151892T>C		201	0	0		218	107	0.490826	NM_001766	D3DVD5|Q5W0J3|Q9UMM3|Q9Y5M4	Silent	SNP	ENST00000368171.3	37	CCDS1173.1																																																																																			T|0.999;C|0.001	0.001	strong		0.498	CD1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058340.1	NM_001766		C	158151892	T	C	158151892	2	2	25	1	0	0	0	0	0	0	0	1	2979	1461	51	3		3	CD1D	1	158151892	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	1896332	158151892	91098729	52	8961											
ARHGAP30	257106	hgsc.bcm.edu	37	chr1	161021121	161021122	+	In_Frame_Ins	INS	-	-	GGCCAG																															acctggggggccagggccaaINSggccagggccagggccaggg																								rs201733366		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:161021121_161021122insGGCCAG	ENST00000368013.3	-	10	1722_1723	c.1402_1403insCTGGCC	c.(1402-1404)ctt>cCTGGCCtt	p.467_468insPG	ARHGAP30_ENST00000368015.1_In_Frame_Ins_p.290_291insPG|ARHGAP30_ENST00000368016.3_In_Frame_Ins_p.467_468insPG	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	467					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)			gccagggccaaggccagggcca	0.619																																					p.L468delinsPGL		Atlas-Indel	.											.	ARHGAP30	105	.	0			c.1403_1404insCTGGCC						PASS	.																																			SO:0001652	inframe_insertion	257106	exon10			.	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.1397_1402dupCTGGCC	1.37:g.161021122_161021127dupGGCCAG	ENSP00000356992:p.Pro466_Gly467dup	41	0	0		50	16	0.32	NM_181720	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	In_Frame_Ins	INS	ENST00000368013.3	37	CCDS30918.1																																																																																			.	.	none		0.619	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720		GGCCAG	161021122	-	GGCCAG	161021121	7	5	25	1	0	1	1	0	0	0	0	0	879	72	3	0	1914	0	ARHGAP30	1	161021121	In_Frame_Ins	INS	-	TCGA-G8-6906-01A-11D-2210-10	2869229	161021121	88229500	53	8962											
POU2F1	5451	hgsc.bcm.edu	37	chr1	167358837	167358837	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccaacagccagcaaccccaAcacgcacaatagcagcaacc	16	2	5	18	1	0	0	0	0	0	0	1	0	1	0	5	0	8	4	5	0	6	1	rs142378150	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:167358837A>G	ENST00000541643.3	+	10	919	c.757A>G	c.(757-759)Aca>Gca	p.T253A	POU2F1_ENST00000367862.5_Missense_Mutation_p.T265A|POU2F1_ENST00000452019.1_3'UTR|POU2F1_ENST00000367865.1_3'UTR|POU2F1_ENST00000367866.2_Missense_Mutation_p.T276A|POU2F1_ENST00000429375.2_Missense_Mutation_p.T213A|POU2F1_ENST00000420254.3_Missense_Mutation_p.T253A			P14859	PO2F1_HUMAN	POU class 2 homeobox 1	253					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						AGCAACCCCAACACGCACAAT	0.458													A|||	2	0.000399361	0.0	0.0	5008	,	,		20298	0.0		0.002	False		,,,				2504	0.0				p.T276A		Atlas-SNP	.											.	POU2F1	120	.	0			c.A826G						PASS	.	A	ALA/THR,ALA/THR,ALA/THR	6,4400	11.4+/-27.6	0,6,2197	131	136	134		793,637,826	5.8	1	1	dbSNP_134	134	35,8565	25.1+/-72.6	0,35,4265	yes	missense,missense,missense	POU2F1	NM_001198783.1,NM_001198786.1,NM_002697.3	58,58,58	0,41,6462	GG,GA,AA		0.407,0.1362,0.3152	probably-damaging,probably-damaging,probably-damaging	265/756,213/704,276/767	167358837	41,12965	2203	4300	6503	SO:0001583	missense	5451	exon9			ACCCCAACACGCA	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.757A>G	1.37:g.167358837A>G	ENSP00000441285:p.Thr253Ala	115	0	0		153	72	0.470588	NM_002697	B1AL91|B1AL93|B4E029|J3KP77|Q5TBT7|Q6PK46|Q8NEU9|Q9BPV1	Missense_Mutation	SNP	ENST00000541643.3	37		.	.	.	.	.	.	.	.	.	.	A	19.63	3.863521	0.71949	0.001362	0.00407	ENSG00000143190	ENST00000367866;ENST00000429375;ENST00000367865;ENST00000420254;ENST00000541643;ENST00000367862;ENST00000443275	T;D;T;T;T;T;T	0.86097	-1.09;-2.07;-1.09;-1.09;-1.09;-1.09;-1.09	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.88250	0.6386	L	0.54323	1.7	0.80722	D	1	D;D;D;D;D	0.61697	0.984;0.971;0.99;0.99;0.984	D;P;D;D;D	0.73380	0.935;0.79;0.971;0.98;0.935	D	0.87855	0.2660	10	0.41790	T	0.15	.	16.1747	0.81844	1.0:0.0:0.0:0.0	.	213;253;265;251;253	B4E029;P14859-4;P14859-2;P14859-3;P14859	.;.;.;.;PO2F1_HUMAN	A	276;213;251;253;253;265;161	ENSP00000356840:T276A;ENSP00000401217:T213A;ENSP00000356839:T251A;ENSP00000414660:T253A;ENSP00000441285:T253A;ENSP00000356836:T265A;ENSP00000415993:T161A	ENSP00000356836:T265A	T	+	1	0	POU2F1	165625461	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.923000	0.92808	2.225000	0.72522	0.455000	0.32223	ACA	A|0.997;G|0.003	0.003	strong		0.458	POU2F1-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_002697		G	167358837	A	G	167358837	3	3	25	1	0	0	0	0	1	0	0	0	12280	43	2	3	787	3	POU2F1	1	167358837	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	6337716	167358837	81891784	54	8963											
C1orf129	80133	hgsc.bcm.edu	37	chr1	170952652	170952652	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttctacccaaggagtttcaaCaagacgaaagtaaaatagct	17	9	7	8	1	2	1	1	0	1	1	2	3	2	2	1	1	3	3	1	1	8	5	rs112394419	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:170952652C>A	ENST00000367758.3	+	9	805	c.706C>A	c.(706-708)Caa>Aaa	p.Q236K	MROH9_ENST00000367759.4_Missense_Mutation_p.Q236K	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	236																	GGAGTTTCAACAAGACGAAAG	0.358													C|||	14	0.00279553	0.0008	0.0014	5008	,	,		16447	0.0		0.0099	False		,,,				2504	0.002				p.Q236K		Atlas-SNP	.											.	.	.	.	0			c.C706A						PASS	.	C	LYS/GLN,LYS/GLN	8,3616		0,8,1804	80	73	76		706,706	-5.2	0	1	dbSNP_132	76	71,8085		0,71,4007	yes	missense,missense	C1orf129	NM_001163629.1,NM_025063.2	53,53	0,79,5811	AA,AC,CC		0.8705,0.2208,0.6706	benign,benign	236/862,236/574	170952652	79,11701	1812	4078	5890	SO:0001583	missense	80133	exon9			TTTCAACAAGACG	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.706C>A	1.37:g.170952652C>A	ENSP00000356732:p.Gln236Lys	27	0	0		36	16	0.444444	NM_025063	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Missense_Mutation	SNP	ENST00000367758.3	37	CCDS41436.1	7	0.003205128205128205	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	C	0.018	-1.467182	0.01053	0.002208	0.008705	ENSG00000117501	ENST00000367759;ENST00000367758	T;T	0.31769	4.08;1.48	3.86	-5.21	0.02815	.	2.159800	0.02223	N	0.064196	T	0.05227	0.0139	L	0.34521	1.04	0.09310	N	1	B;B	0.13594	0.008;0.008	B;B	0.11329	0.006;0.006	T	0.10337	-1.0634	10	0.02654	T	1	6.0798	7.38	0.26849	0.4342:0.1874:0.3784:0.0	.	236;236	F5GWX6;Q5TGP6	.;CA129_HUMAN	K	236	ENSP00000356733:Q236K;ENSP00000356732:Q236K	ENSP00000356732:Q236K	Q	+	1	0	C1orf129	169219276	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.168000	0.09925	-0.676000	0.05238	-0.499000	0.04595	CAA	C|0.996;A|0.004	0.004	strong		0.358	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063		A	170952652	C	A	170952652	3	1	25	1	0	0	0	0	1	0	0	0	1998	479	17	4	736	4	C1orf129	1	170952652	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	3593815	170952652	78297969	55	8964											
TPR	7175	hgsc.bcm.edu	37	chr1	186330768	186330768	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acttaccttcaccagcttctTtcaaaagtttgtgtagttcc	9	16	5	11	0	3	0	2	0	1	0	4	0	4	0	3	0	2	4	3	0	4	7	rs201760745		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:186330768T>C	ENST00000367478.4	-	9	1240	c.944A>G	c.(943-945)aAa>aGa	p.K315R	TPR_ENST00000474852.1_5'UTR	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	315					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)		ACCAGCTTCTTTCAAAAGTTT	0.343			T	NTRK1	papillary thyroid								T|||	1	0.000199681	0.0	0.0	5008	,	,		16594	0.0		0.001	False		,,,				2504	0.0				p.K315R		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.A944G						PASS	.	T	ARG/LYS	0,3662		0,0,1831	128	119	122		944	5.5	1	1		122	2,8168		0,2,4083	yes	missense	TPR	NM_003292.2	26	0,2,5914	CC,CT,TT		0.0245,0.0,0.0169	probably-damaging	315/2364	186330768	2,11830	1831	4085	5916	SO:0001583	missense	7175	exon9			GCTTCTTTCAAAA	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.944A>G	1.37:g.186330768T>C	ENSP00000356448:p.Lys315Arg	239	0	0		202	97	0.480198	NM_003292	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	37	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.567818	0.86439	0.0	2.45E-4	ENSG00000047410	ENST00000367478	T	0.24723	1.84	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.46658	0.1404	L	0.60455	1.87	0.42919	D	0.994283	D;D	0.69078	0.976;0.997	P;D	0.75020	0.693;0.985	T	0.39333	-0.9619	10	0.45353	T	0.12	.	14.7725	0.69691	0.0:0.0:0.0:1.0	.	315;315	Q15624;P12270	.;TPR_HUMAN	R	315	ENSP00000356448:K315R	ENSP00000356448:K315R	K	-	2	0	TPR	184597391	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.877000	0.69675	2.076000	0.62316	0.533000	0.62120	AAA	.	.	weak		0.343	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		C	186330768	T	C	186330768	3	2	25	1	0	0	0	0	1	0	0	0	16431	1841	64	3	6319	3	TPR	1	186330768	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	15378116	186330768	62919853	56	8965											
PLA2G4A	5321	hgsc.bcm.edu	37	chr1	186946869	186946869	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggagaaagattgcccaaccAtcatccactttgttctggcc	10	11	8	12	0	2	2	1	0	1	2	3	3	3	2	4	2	2	1	4	2	2	3	rs28395831	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:186946869A>G	ENST00000367466.3	+	16	2061	c.1909A>G	c.(1909-1911)Atc>Gtc	p.I637V	PLA2G4A_ENST00000442353.2_Missense_Mutation_p.I577V	NM_024420.2	NP_077734	P47712	PA24A_HUMAN	phospholipase A2, group IVA (cytosolic, calcium-dependent)	637	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.		I -> V (in dbSNP:rs28395831).		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)	TTGCCCAACCATCATCCACTT	0.418													A|||	33	0.00658946	0.0015	0.0014	5008	,	,		19824	0.0		0.0189	False		,,,				2504	0.0112				p.I637V		Atlas-SNP	.											.	PLA2G4A	125	.	0			c.A1909G						PASS	.	A	VAL/ILE	6,4400	11.4+/-27.6	0,6,2197	121	112	115		1909	3.7	0.6	1	dbSNP_126	115	94,8506	53.6+/-114.3	0,94,4206	yes	missense	PLA2G4A	NM_024420.2	29	0,100,6403	GG,GA,AA		1.093,0.1362,0.7689	benign	637/750	186946869	100,12906	2203	4300	6503	SO:0001583	missense	5321	exon16			CCAACCATCATCC	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.1909A>G	1.37:g.186946869A>G	ENSP00000356436:p.Ile637Val	248	0	0		219	97	0.442922	NM_024420	B1AKG4|Q29R80	Missense_Mutation	SNP	ENST00000367466.3	37	CCDS1372.1	15	0.006868131868131868	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	13	0.017150395778364115	A	7.587	0.670036	0.14776	0.001362	0.01093	ENSG00000116711	ENST00000367466;ENST00000442353	T;T	0.03124	4.04;4.04	5.98	3.68	0.42216	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.250277	0.47093	N	0.000250	T	0.00784	0.0026	N	0.03177	-0.4	0.36550	D	0.871822	B;B	0.11235	0.004;0.003	B;B	0.21708	0.036;0.026	T	0.42849	-0.9427	10	0.02654	T	1	-15.1412	8.1494	0.31132	0.7827:0.0:0.2173:0.0	rs28395831;rs45544833	577;637	E7EU42;P47712	.;PA24A_HUMAN	V	637;577	ENSP00000356436:I637V;ENSP00000406892:I577V	ENSP00000356436:I637V	I	+	1	0	PLA2G4A	185213492	0.996000	0.38824	0.615000	0.29064	0.985000	0.73830	3.247000	0.51422	0.516000	0.28340	0.533000	0.62120	ATC	A|0.992;G|0.008	0.008	strong		0.418	PLA2G4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086236.1	NM_024420		G	186946869	A	G	186946869	3	3	25	1	0	0	0	0	1	0	0	0	12010	217	8	3	1967	3	PLA2G4A	1	186946869	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	616101	186946869	62303752	57	8966											
ELF3	1999	hgsc.bcm.edu	37	chr1	201981774	201981774	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cctcctcttcccagaccaggGcagcccctttgcccaggagc	6	7	9	19	0	1	1	0	0	1	1	3	2	3	2	7	2	3	1	7	2	0	2	rs55729978	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:201981774G>A	ENST00000359651.3	+	4	3677	c.485G>A	c.(484-486)gGc>gAc	p.G162D	RP11-510N19.5_ENST00000504773.1_RNA|ELF3_ENST00000367283.3_Missense_Mutation_p.G162D|ELF3_ENST00000367284.5_Missense_Mutation_p.G162D|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						CCAGACCAGGGCAGCCCCTTT	0.642													G|||	364	0.0726837	0.2421	0.0159	5008	,	,		14680	0.0		0.0229	False		,,,				2504	0.0102				p.G162D		Atlas-SNP	.											ELF3_ENST00000359651,NS,carcinoma,0,2	ELF3	92	2	0			c.G485A						PASS	.	G	ASP/GLY,ASP/GLY	690,3716		51,588,1564	28	34	32		485,485	3.3	1	1	dbSNP_129	32	147,8451		1,145,4153	yes	missense,missense	ELF3	NM_001114309.1,NM_004433.4	94,94	52,733,5717	AA,AG,GG		1.7097,15.6605,6.4365	benign,benign	162/372,162/372	201981774	837,12167	2203	4299	6502	SO:0001583	missense	1999	exon5			ACCAGGGCAGCCC	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.485G>A	1.37:g.201981774G>A	ENSP00000352673:p.Gly162Asp	71	0	0		96	40	0.416667	NM_001114309		Missense_Mutation	SNP	ENST00000359651.3	37	CCDS1419.1	157	0.07188644688644688	129	0.2621951219512195	9	0.024861878453038673	0	0.0	19	0.025065963060686015	G	10.76	1.441663	0.25900	0.156605	0.017097	ENSG00000163435	ENST00000359651;ENST00000367284;ENST00000367283;ENST00000310044;ENST00000446188	T;T;T;T	0.56103	2.47;2.47;2.47;0.48	5.2	3.29	0.37713	.	0.821186	0.11026	N	0.607832	T	0.00012	0.0000	L	0.37561	1.115	0.27380	P	0.9554544	B	0.10296	0.003	B	0.09377	0.004	T	0.09796	-1.0658	9	0.37606	T	0.19	.	7.8653	0.29533	0.0862:0.164:0.7499:0.0	rs55729978	162	P78545	ELF3_HUMAN	D	162;162;162;162;160	ENSP00000352673:G162D;ENSP00000356253:G162D;ENSP00000356252:G162D;ENSP00000405162:G160D	ENSP00000311348:G162D	G	+	2	0	ELF3	200248397	0.174000	0.23070	0.988000	0.46212	0.681000	0.39784	0.316000	0.19469	1.168000	0.42723	0.655000	0.94253	GGC	G|0.938;A|0.062	0.062	strong		0.642	ELF3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087360.1	NM_004433		A	201981774	G	A	201981774	3	1	25	1	0	0	0	0	1	0	0	0	5057	1203	42	2	499	2	ELF3	1	201981774	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	15034905	201981774	47268847	58	8967											
PPFIA4	8497	hgsc.bcm.edu	37	chr1	203044777	203044777	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgcgggagcaccacggtcgcGgcggcatgctcagcgcttcc	5	5	15	16	7	1	0	1	0	0	0	3	1	2	1	2	4	3	4	2	4	0	1	rs12130501	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:203044777G>A	ENST00000447715.2	+	34	3841	c.3400G>A	c.(3400-3402)Ggc>Agc	p.G1134S	PPFIA4_ENST00000599966.1_Missense_Mutation_p.G641S|PPFIA4_ENST00000414050.2_Missense_Mutation_p.G863S|PPFIA4_ENST00000367240.2_Missense_Mutation_p.G1135S|PPFIA4_ENST00000272198.6_Missense_Mutation_p.G650S|PPFIA4_ENST00000295706.4_Missense_Mutation_p.G641S			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	1134				G -> A (in Ref. 5; AAC26102). {ECO:0000305}.	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						CCACGGTCGCGGCGGCATGCT	0.716													g|||	32	0.00638978	0.0	0.0115	5008	,	,		11140	0.0		0.0189	False		,,,				2504	0.0051				p.G650S		Atlas-SNP	.											PPFIA4_ENST00000272198,colon,carcinoma,-1,2	PPFIA4	139	2	0			c.G1948A						PASS	.		SER/GLY	15,3733		0,15,1859	11	14	13		1948	-0.2	0	1	dbSNP_120	13	228,7910		2,224,3843	no	missense	PPFIA4	NM_015053.1	56	2,239,5702	AA,AG,GG		2.8017,0.4002,2.0444	benign	650/702	203044777	243,11643	1874	4069	5943	SO:0001583	missense	8497	exon16			GGTCGCGGCGGCA	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.3400G>A	1.37:g.203044777G>A	ENSP00000402576:p.Gly1134Ser	14	0	0		11	6	0.545455	NM_015053	A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Missense_Mutation	SNP	ENST00000447715.2	37		16	0.007326007326007326	0	0.0	5	0.013812154696132596	0	0.0	11	0.014511873350923483	g	12.32	1.901775	0.33535	0.004002	0.028017	ENSG00000143847	ENST00000367240;ENST00000447715;ENST00000295706;ENST00000414050;ENST00000272198	T;T;T;T;T	0.21734	2.32;2.0;1.99;2.0;1.99	4.58	-0.158	0.13383	.	1.035160	0.07805	U	0.957214	T	0.03564	0.0102	N	0.17474	0.49	0.09310	N	1	B;B;B;B;B	0.17038	0.0;0.0;0.005;0.02;0.012	B;B;B;B;B	0.16722	0.0;0.0;0.002;0.016;0.007	T	0.34875	-0.9811	10	0.32370	T	0.25	-0.3686	4.4121	0.11438	0.4118:0.2651:0.3231:0.0	rs12130501	863;1134;336;641;650	B4DIS5;B1N949;B3KN22;O75335-2;O75335	.;.;.;.;LIPA4_HUMAN	S	1135;1134;641;863;650	ENSP00000356209:G1135S;ENSP00000402576:G1134S;ENSP00000295706:G641S;ENSP00000400379:G863S;ENSP00000272198:G650S	ENSP00000272198:G650S	G	+	1	0	PPFIA4	201311400	0.948000	0.32251	0.014000	0.15608	0.413000	0.31143	1.380000	0.34351	-0.369000	0.08028	0.298000	0.19748	GGC	G|0.992;A|0.008	0.008	strong		0.716	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000462949.1	NM_015053		A	203044777	G	A	203044777	3	1	25	1	0	0	0	0	1	0	0	0	12321	1116	39	1	2010	1	PPFIA4	1	203044777	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1063003	203044777	46205844	59	8968											
CR1L	1379	hgsc.bcm.edu	37	chr1	207870916	207870916	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acaaggacaacttttcacccGggcaggaagtgttctacagc	12	8	10	11	1	2	0	1	0	1	0	2	2	2	2	1	3	3	2	1	3	4	4	rs201832831	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:207870916G>A	ENST00000508064.2	+	6	991	c.931G>A	c.(931-933)Ggg>Agg	p.G311R	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)		p.G319W(1)|p.G311W(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						CTTTTCACCCGGGCAGGAAGT	0.557													g|||	5	0.000998403	0.0	0.0	5008	,	,		18305	0.004		0.0	False		,,,				2504	0.001				p.G311R		Atlas-SNP	.											.	CR1L	97	.	2	Substitution - Missense(2)	lung(2)	c.G931A						PASS	.	G	ARG/GLY	1,3789		0,1,1894	151	149	149		931	1.5	0	1		149	1,8223		0,1,4111	no	missense	CR1L	NM_175710.1	125	0,2,6005	AA,AG,GG		0.0122,0.0264,0.0166	probably-damaging	311/570	207870916	2,12012	1895	4112	6007	SO:0001583	missense	1379	exon6			TCACCCGGGCAGG	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.931G>A	1.37:g.207870916G>A	ENSP00000421736:p.Gly311Arg	394	0	0		480	231	0.48125	NM_175710	Q32MC9|Q8NEU7	Missense_Mutation	SNP	ENST00000508064.2	37	CCDS44310.1	3	0.0013736263736263737	0	0.0	0	0.0	3	0.005244755244755245	0	0.0	.	12.71	2.018389	0.35606	2.64E-4	1.22E-4	ENSG00000197721	ENST00000444269;ENST00000508064	T	0.71698	-0.59	2.53	1.55	0.23275	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.75295	0.3830	M	0.81614	2.55	0.09310	N	0.999996	D	0.89917	1.0	D	0.68353	0.957	T	0.64702	-0.6345	9	0.87932	D	0	.	5.7056	0.17907	0.1679:0.0:0.8321:0.0	.	311	Q2VPA4	CR1L_HUMAN	R	311	ENSP00000421736:G311R	ENSP00000434864:G255R	G	+	1	0	CR1L	205937539	0.009000	0.17119	0.001000	0.08648	0.005000	0.04900	0.673000	0.25203	0.354000	0.24105	0.298000	0.19748	GGG	G|0.999;A|0.001	0.001	strong		0.557	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735		A	207870916	G	A	207870916	3	1	25	1	0	0	0	0	1	0	0	0	3843	1116	39	1	953	1	CR1L	1	207870916	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	4826139	207870916	41379705	60	8969											
SERTAD4	56256	hgsc.bcm.edu	37	chr1	210415626	210415626	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggaaaaagtccttacggaaaAaggaggcttcaccaccaagt	16	6	10	9	1	1	0	1	0	0	0	2	3	2	3	3	4	1	1	3	4	6	2	rs559261349		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:210415626A>C	ENST00000367012.3	+	4	1245	c.1015A>C	c.(1015-1017)Aag>Cag	p.K339Q		NM_019605.3	NP_062551.1	Q9NUC0	SRTD4_HUMAN	SERTA domain containing 4	339						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)		CTTACGGAAAAAGGAGGCTTC	0.388													A|||	1	0.000199681	0.0	0.0	5008	,	,		20269	0.0		0.001	False		,,,				2504	0.0				p.K339Q		Atlas-SNP	.											.	SERTAD4	53	.	0			c.A1015C						PASS	.						54	55	54					1																	210415626		2202	4300	6502	SO:0001583	missense	56256	exon4			CGGAAAAAGGAGG	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.1015A>C	1.37:g.210415626A>C	ENSP00000355979:p.Lys339Gln	66	0	0		90	34	0.377778	NM_019605	B2RD32	Missense_Mutation	SNP	ENST00000367012.3	37	CCDS1494.1	.	.	.	.	.	.	.	.	.	.	A	17.59	3.427383	0.62733	.	.	ENSG00000082497	ENST00000367012	.	.	.	5.84	5.84	0.93424	.	0.000000	0.64402	D	0.000001	T	0.56077	0.1961	L	0.29908	0.895	0.34642	D	0.720729	D	0.60160	0.987	P	0.54544	0.755	T	0.69094	-0.5236	9	0.72032	D	0.01	-2.7444	16.2108	0.82158	1.0:0.0:0.0:0.0	.	339	Q9NUC0	SRTD4_HUMAN	Q	339	.	ENSP00000355979:K339Q	K	+	1	0	SERTAD4	208482249	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	6.336000	0.72954	2.232000	0.73038	0.533000	0.62120	AAG	.	.	none		0.388	SERTAD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088577.1	NM_019605		C	210415626	A	C	210415626	3	2	25	1	0	0	0	0	1	0	0	0	14138	15	1	5	1025	5	SERTAD4	1	210415626	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	2544710	210415626	38834995	61	8970											
RPS6KC1	26750	hgsc.bcm.edu	37	chr1	213414948	213414948	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agaagctgcagcaatgggacCtactaagtttacacaaacta	16	8	8	9	0	0	1	0	0	0	1	0	2	0	2	1	1	6	4	1	1	7	5			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:213414948C>T	ENST00000366960.3	+	11	2279	c.2129C>T	c.(2128-2130)cCt>cTt	p.P710L	RPS6KC1_ENST00000366959.3_Missense_Mutation_p.P698L|RPS6KC1_ENST00000543470.1_Missense_Mutation_p.P498L|RPS6KC1_ENST00000490299.1_3'UTR|RPS6KC1_ENST00000543354.1_Missense_Mutation_p.P413L	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1	710					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)		GCAATGGGACCTACTAAGTTT	0.398																																					p.P710L		Atlas-SNP	.											.	RPS6KC1	114	.	0			c.C2129T						PASS	.						65	68	67					1																	213414948		2203	4300	6503	SO:0001583	missense	26750	exon11			TGGGACCTACTAA	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.2129C>T	1.37:g.213414948C>T	ENSP00000355927:p.Pro710Leu	100	0	0		93	4	0.0430108	NM_012424	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Missense_Mutation	SNP	ENST00000366960.3	37	CCDS1513.1	.	.	.	.	.	.	.	.	.	.	C	9.247	1.039788	0.19669	.	.	ENSG00000136643	ENST00000543470;ENST00000366960;ENST00000366959;ENST00000543354	T;T;T;T	0.39997	1.46;1.49;1.5;1.05	5.44	4.52	0.55395	.	0.244148	0.42821	D	0.000641	T	0.31606	0.0802	L	0.38838	1.175	0.38907	D	0.957457	B;B;B	0.21753	0.06;0.016;0.016	B;B;B	0.20955	0.032;0.01;0.01	T	0.23013	-1.0200	10	0.56958	D	0.05	-40.1504	8.6494	0.34025	0.1519:0.7721:0.0:0.076	.	498;710;698	F5H7T0;Q96S38;B1APS8	.;KS6C1_HUMAN;.	L	498;710;698;413	ENSP00000442306:P498L;ENSP00000355927:P710L;ENSP00000355926:P698L;ENSP00000439282:P413L	ENSP00000355926:P698L	P	+	2	0	RPS6KC1	211481571	0.936000	0.31750	0.931000	0.37212	0.967000	0.64934	1.929000	0.40114	2.541000	0.85698	0.650000	0.86243	CCT	.	.	none		0.398	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3	NM_012424		T	213414948	C	T	213414948	3	4	25	1	0	0	0	0	1	0	0	0	13673	681	24	2	2171	2	RPS6KC1	1	213414948	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2999322	213414948	35835673	62	8971											
USH2A	7399	hgsc.bcm.edu	37	chr1	216363590	216363590	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctaaagtttgtcctgctccCgaagcactggtcacacaacc	10	9	8	14	1	1	0	1	0	0	0	3	1	3	0	3	1	3	4	3	1	4	2	rs56013136	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:216363590C>T	ENST00000307340.3	-	20	4757	c.4371G>A	c.(4369-4371)tcG>tcA	p.S1457S	USH2A_ENST00000366942.3_Silent_p.S1457S|USH2A_ENST00000366943.2_Silent_p.S1457S	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1457	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)		GTCCTGCTCCCGAAGCACTGG	0.368										HNSCC(13;0.011)			C|||	28	0.00559105	0.0015	0.0072	5008	,	,		17343	0.0		0.0199	False		,,,				2504	0.001				p.S1457S		Atlas-SNP	.											.	USH2A	1168	.	0			c.G4371A						PASS	.	C	,	25,4381	31.7+/-61.6	0,25,2178	101	98	99	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4371,4371	-10.4	0	1	dbSNP_129	99	180,8420	81.2+/-143.8	2,176,4122	no	coding-synonymous,coding-synonymous	USH2A	NM_007123.5,NM_206933.2	,	2,201,6300	TT,TC,CC		2.093,0.5674,1.5762	,	1457/1547,1457/5203	216363590	205,12801	2203	4300	6503	SO:0001819	synonymous_variant	7399	exon20			TGCTCCCGAAGCA	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.4371G>A	1.37:g.216363590C>T		115	0	0		86	42	0.488372	NM_007123	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	CCDS31025.1																																																																																			C|0.987;T|0.013	0.013	strong		0.368	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216363590	C	T	216363590	2	4	25	1	0	0	0	0	0	0	0	1	17051	639	23	1		1	USH2A	1	216363590	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2948642	216363590	32887031	63	8972											
CAPN2	824	hgsc.bcm.edu	37	chr1	223949900	223949900	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccttccagttcgacatcagcGaggatgacattgatgatgga	11	10	11	9	2	1	3	1	3	0	0	3	7	2	5	2	2	1	1	2	2	0	3	rs145816861		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:223949900G>A	ENST00000295006.5	+	14	1888	c.1579G>A	c.(1579-1581)Gag>Aag	p.E527K	CAPN2_ENST00000474026.1_3'UTR|CAPN2_ENST00000433674.2_Missense_Mutation_p.E449K	NM_001748.4	NP_001739	P17655	CAN2_HUMAN	calpain 2, (m/II) large subunit	527	Linker.				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)		CGACATCAGCGAGGATGACAT	0.517																																					p.E527K		Atlas-SNP	.											.	CAPN2	69	.	0			c.G1579A						PASS	.	G	LYS/GLU,LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	174	128	143		1345,1579	4.7	0.9	1	dbSNP_134	143	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	CAPN2	NM_001146068.1,NM_001748.4	56,56	0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231	probably-damaging,probably-damaging	449/623,527/701	223949900	3,13003	2203	4300	6503	SO:0001583	missense	824	exon14			ATCAGCGAGGATG	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.1579G>A	1.37:g.223949900G>A	ENSP00000295006:p.Glu527Lys	64	0	0		83	36	0.433735	NM_001748	A6NDG7|B7ZA96|E7ES58|Q16738|Q6PJT3|Q8WU26|Q9HBB1	Missense_Mutation	SNP	ENST00000295006.5	37	CCDS31035.1	.	.	.	.	.	.	.	.	.	.	G	13.78	2.339343	0.41398	2.27E-4	2.33E-4	ENSG00000162909	ENST00000433674;ENST00000295006;ENST00000366869	T;T	0.30714	1.52;1.52	5.63	4.71	0.59529	.	0.442904	0.27284	N	0.020073	T	0.30448	0.0765	L	0.57536	1.79	0.80722	D	1	B;B;B	0.28128	0.003;0.201;0.036	B;B;B	0.20184	0.005;0.028;0.007	T	0.04946	-1.0916	10	0.33141	T	0.24	.	14.7507	0.69522	0.0:0.0:0.8544:0.1456	.	449;110;527	B7ZA96;B3KUH9;P17655	.;.;CAN2_HUMAN	K	449;527;556	ENSP00000413158:E449K;ENSP00000295006:E527K	ENSP00000295006:E527K	E	+	1	0	CAPN2	222016523	1.000000	0.71417	0.853000	0.33588	0.071000	0.16799	9.176000	0.94839	1.364000	0.46038	0.655000	0.94253	GAG	G|1.000;A|0.000	0.000	weak		0.517	CAPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090973.1	NM_001748		A	223949900	G	A	223949900	3	1	25	1	0	0	0	0	1	0	0	0	2629	1059	37	1	1640	1	CAPN2	1	223949900	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	7586310	223949900	25300721	64	8973											
LBR	3930	hgsc.bcm.edu	37	chr1	225603029	225603029	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcaataagaggcgttccttcTacaaccttaaaagaaaaaaa	19	9	5	8	1	2	2	1	0	1	2	3	2	3	2	2	1	2	1	2	1	9	5	rs61749339	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:225603029T>C	ENST00000338179.2	-	7	968	c.843A>G	c.(841-843)gtA>gtG	p.V281V	LBR_ENST00000487054.1_5'Flank|LBR_ENST00000272163.4_Silent_p.V281V	NM_194442.2	NP_919424.1	Q14739	LBR_HUMAN	lamin B receptor	281					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)		GCGTTCCTTCTACAACCTTAA	0.269													T|||	28	0.00559105	0.0	0.0058	5008	,	,		18270	0.0		0.0169	False		,,,				2504	0.0072				p.V281V		Atlas-SNP	.											.	LBR	54	.	0			c.A843G						PASS	.	T	,	10,4374		0,10,2182	32	32	32		843,843	0.4	1	1	dbSNP_129	32	138,8426		1,136,4145	no	coding-synonymous,coding-synonymous	LBR	NM_002296.3,NM_194442.2	,	1,146,6327	CC,CT,TT		1.6114,0.2281,1.143	,	281/616,281/616	225603029	148,12800	2192	4282	6474	SO:0001819	synonymous_variant	3930	exon7			TCCTTCTACAACC	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.843A>G	1.37:g.225603029T>C		131	0	0		177	82	0.463277	NM_194442	B2R5P3|Q14740|Q53GU7|Q59FE6	Silent	SNP	ENST00000338179.2	37	CCDS1545.1																																																																																			T|0.991;C|0.009	0.009	strong		0.269	LBR-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091398.1	NM_002296		C	225603029	T	C	225603029	2	2	25	1	0	0	0	0	0	0	0	1	8661	1509	53	3		3	LBR	1	225603029	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	1653129	225603029	23647592	65	8974											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228437757	228437757	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	acgctgagctgcgaggtggcCcaggcccagacagaggtgac	9	4	16	12	2	0	4	0	2	0	2	0	5	0	4	2	4	2	2	2	4	0	0			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228437757C>A	ENST00000422127.1	+	14	4169	c.4125C>A	c.(4123-4125)gcC>gcA	p.A1375A	OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Silent_p.A1375A|OBSCN_ENST00000570156.2_Silent_p.A1467A	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1375	Ig-like 14.				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)				GCGAGGTGGCCCAGGCCCAGA	0.642																																					p.A1467A		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C4401A						PASS	.						69	72	71					1																	228437757		2065	4189	6254	SO:0001819	synonymous_variant	84033	exon15			GGTGGCCCAGGCC	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.4125C>A	1.37:g.228437757C>A		290	1	0.00344828		258	95	0.368217	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			.	.	none		0.642	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228437757	C	A	228437757	2	1	25	1	0	0	0	0	0	0	0	1	10821	610	22	4		4	OBSCN	1	228437757	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2834728	228437757	20812864	66	8975											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228557755	228557755	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcccacctcagcgaagacGccaaagacttcatcaaggct	12	6	8	15	2	3	2	3	0	0	2	3	3	3	2	3	1	2	1	3	1	3	1	rs145597580	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228557755G>A	ENST00000422127.1	+	91	20124	c.20080G>A	c.(20080-20082)Gcc>Acc	p.A6694T	OBSCN_ENST00000366707.4_Missense_Mutation_p.A4328T|OBSCN_ENST00000570156.2_Missense_Mutation_p.A7651T	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	6694	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)				CAGCGAAGACGCCAAAGACTT	0.667													G|||	12	0.00239617	0.0	0.0014	5008	,	,		19459	0.0		0.004	False		,,,				2504	0.0072				p.A7651T		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G22951A						PASS	.	G	THR/ALA	0,3934		0,0,1967	59	62	61		20080	4.7	0.8	1	dbSNP_134	61	10,8296		0,10,4143	yes	missense	OBSCN	NM_001098623.1	58	0,10,6110	AA,AG,GG		0.1204,0.0,0.0817	probably-damaging	6694/7969	228557755	10,12230	1967	4153	6120	SO:0001583	missense	84033	exon102			GAAGACGCCAAAG	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.20080G>A	1.37:g.228557755G>A	ENSP00000409493:p.Ala6694Thr	80	0	0		74	45	0.608108	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	37	CCDS58065.1	5|5	0.0022893772893772895|0.0022893772893772895	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	4|4	0.005277044854881266|0.005277044854881266	G|G	16.97|16.97	3.269577|3.269577	0.59540|0.59540	0.0|0.0	0.001204|0.001204	ENSG00000154358|ENSG00000154358	ENST00000422127;ENST00000366707|ENST00000441106	T;T|.	0.68025|.	-0.3;-0.3|.	4.72|4.72	4.72|4.72	0.59763|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);|.	.|.	.|.	.|.	.|.	T|T	0.73281|0.73281	0.3567|0.3567	M|M	0.85710|0.85710	2.77|2.77	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	D|.	0.64410|.	0.925|.	T|T	0.79752|0.79752	-0.1671|-0.1671	9|5	0.87932|.	D|.	0|.	.|.	16.025|16.025	0.80536|0.80536	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	6694|.	Q5VST9|.	OBSCN_HUMAN|.	T|H	6694;4328|1310	ENSP00000409493:A6694T;ENSP00000355668:A4328T|.	ENSP00000355668:A4328T|.	A|R	+|+	1|2	0|0	OBSCN|OBSCN	226624378|226624378	1.000000|1.000000	0.71417|0.71417	0.819000|0.819000	0.32651|0.32651	0.185000|0.185000	0.23345|0.23345	6.988000|6.988000	0.76212|0.76212	2.459000|2.459000	0.83118|0.83118	0.455000|0.455000	0.32223|0.32223	GCC|CGC	G|0.998;A|0.002	0.002	strong		0.667	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228557755	G	A	228557755	3	1	25	1	0	0	0	0	1	0	0	0	10821	1087	38	1	21648	1	OBSCN	1	228557755	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	119998	228557755	20692866	67	8976											
TRIM17	51127	hgsc.bcm.edu	37	chr1	228602459	228602459	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ttctggcagaaaagcttgagGggctcgtggtgctcctggca	7	10	15	9	1	1	2	0	1	1	1	3	2	2	2	1	5	2	5	1	5	2	2	rs142505325	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228602459G>A	ENST00000366697.2	-	1	1271	c.315C>T	c.(313-315)ccC>ccT	p.P105P	TRIM17_ENST00000366698.2_Silent_p.P105P|TRIM17_ENST00000295033.3_Silent_p.P105P|TRIM17_ENST00000456946.2_Silent_p.P105P			Q9Y577	TRI17_HUMAN	tripartite motif containing 17	105					protein autoubiquitination (GO:0051865)	intracellular (GO:0005622)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)	10		Prostate(94;0.0724)				AAAGCTTGAGGGGCTCGTGGT	0.657													G|||	12	0.00239617	0.0	0.0014	5008	,	,		17247	0.0		0.004	False		,,,				2504	0.0072				p.P105P		Atlas-SNP	.											.	TRIM17	66	.	0			c.C315T						PASS	.	G	,,	0,4406		0,0,2203	77	84	82		315,315,315	0.3	1	1	dbSNP_134	82	10,8590	6.4+/-24.3	0,10,4290	no	coding-synonymous,coding-synonymous,coding-synonymous	TRIM17	NM_001024940.2,NM_001134855.1,NM_016102.3	,,	0,10,6493	AA,AG,GG		0.1163,0.0,0.0769	,,	105/478,105/344,105/478	228602459	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	51127	exon2			CTTGAGGGGCTCG	AF156271	CCDS1571.1, CCDS44327.1	1q42	2013-01-09	2011-01-25	2001-11-30	ENSG00000162931	ENSG00000162931		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	13430	protein-coding gene	gene with protein product	"ring finger protein 16", "RING finger protein terf", "testis RING finger protein"	606123	"tripartite motif-containing 17"	RNF16		9792805, 10894938	Standard	NM_016102		Approved	terf, RBCC	uc001hsv.3	Q9Y577	OTTHUMG00000039974	ENST00000366697.2:c.315C>T	1.37:g.228602459G>A		115	0	0		122	56	0.459016	NM_001024940	B4DVJ2|Q5VST8	Silent	SNP	ENST00000366697.2	37	CCDS1571.1																																																																																			G|0.999;A|0.001	0.001	strong		0.657	TRIM17-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096439.2	NM_016102		A	228602459	G	A	228602459	2	1	25	1	0	0	0	0	0	0	0	1	16508	1219	43	2		2	TRIM17	1	228602459	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	44704	228602459	20648162	68	8977											
SMYD3	64754	hgsc.bcm.edu	37	chr1	246078851	246078851	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccttgtcctgggtttggcaaCggaaacagtcacattcaaag	11	10	10	10	1	2	0	2	0	0	0	3	1	3	1	2	3	2	2	2	3	3	3	rs61762672	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:246078851C>T	ENST00000388985.4	-	8	793	c.794G>A	c.(793-795)cGt>cAt	p.R265H	SMYD3_ENST00000490107.1_Missense_Mutation_p.R206H|SMYD3_ENST00000366517.1_5'UTR|SMYD3_ENST00000541742.1_Missense_Mutation_p.R206H			Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3	265					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)		GGTTTGGCAACGGAAACAGTC	0.488													C|||	5	0.000998403	0.0	0.0029	5008	,	,		17129	0.0		0.003	False		,,,				2504	0.0				p.R265H		Atlas-SNP	.											.	SMYD3	77	.	0			c.G794A						PASS	.	C	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	145	120	128		794,617	5	0.2	1	dbSNP_129	128	12,8588	8.4+/-32.0	0,12,4288	yes	missense,missense	SMYD3	NM_001167740.1,NM_022743.2	29,29	0,13,6490	TT,TC,CC		0.1395,0.0227,0.1	probably-damaging,probably-damaging	265/429,206/370	246078851	13,12993	2203	4300	6503	SO:0001583	missense	64754	exon8			TGGCAACGGAAAC	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.794G>A	1.37:g.246078851C>T	ENSP00000373637:p.Arg265His	83	0	0		103	43	0.417476	NM_001167740	A8K0P0|B1AN38|Q86TL8|Q8N5Z6|Q96AI5	Missense_Mutation	SNP	ENST00000388985.4	37	CCDS53486.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	16.78	3.217791	0.58560	2.27E-4	0.001395	ENSG00000185420	ENST00000541742;ENST00000490107;ENST00000544586;ENST00000388985;ENST00000391836	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	5.97	5.03	0.67393	.	0.287715	0.33438	N	0.004906	T	0.31765	0.0807	L	0.28400	0.85	0.20489	N	0.999892	D;D	0.89917	1.0;1.0	P;D	0.69142	0.865;0.962	T	0.09796	-1.0658	10	0.37606	T	0.19	-18.4741	12.7104	0.57086	0.1631:0.8369:0.0:0.0	rs61762672	265;76	Q9H7B4;B3KN46	SMYD3_HUMAN;.	H	206;206;95;265;76	ENSP00000444184:R206H;ENSP00000419184:R206H;ENSP00000373637:R265H;ENSP00000375712:R76H	ENSP00000373637:R265H	R	-	2	0	SMYD3	244145474	0.032000	0.19561	0.156000	0.22583	0.785000	0.44390	0.472000	0.22116	2.836000	0.97738	0.655000	0.94253	CGT	C|0.999;T|0.001	0.001	strong		0.488	SMYD3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022743		T	246078851	C	T	246078851	3	4	25	1	0	0	0	0	1	0	0	0	14838	536	19	1	512	1	SMYD3	1	246078851	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	17476392	246078851	3171770	69	8978											
TTC15	51112	hgsc.bcm.edu	37	chr2	3392021	3392021	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agccccagcctcagcacgttCttcggagacacggccgccag	8	5	11	17	4	2	1	1	0	1	1	3	2	2	1	5	2	3	2	5	2	0	2	rs140551015	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:3392021C>T	ENST00000324266.5	+	2	822	c.627C>T	c.(625-627)ttC>ttT	p.F209F	TRAPPC12_ENST00000382110.2_Silent_p.F209F	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	209					vesicle-mediated transport (GO:0016192)												TCAGCACGTTCTTCGGAGACA	0.672													C|||	12	0.00239617	0.0008	0.0014	5008	,	,		7296	0.0		0.0099	False		,,,				2504	0.0				p.F209F		Atlas-SNP	.											.	.	.	.	0			c.C627T						PASS	.	C		16,4390	19.1+/-41.9	0,16,2187	32	39	37		627	-2.8	0.6	2	dbSNP_134	37	122,8478	57.2+/-118.5	0,122,4178	no	coding-synonymous	TTC15	NM_016030.5		0,138,6365	TT,TC,CC		1.4186,0.3631,1.061		209/736	3392021	138,12868	2203	4300	6503	SO:0001819	synonymous_variant	51112	exon2			CACGTTCTTCGGA	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.627C>T	2.37:g.3392021C>T		11	0	0		58	24	0.413793	NM_016030	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Silent	SNP	ENST00000324266.5	37	CCDS1652.1																																																																																			C|0.991;T|0.009	0.009	strong		0.672	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030		T	3392021	C	T	3392021	2	4	25	1	0	0	0	0	0	0	0	1	16697	912	32	2		2	TTC15	2	3392021	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10		3392021	239807352	70	8979											
ASXL2	55252	hgsc.bcm.edu	37	chr2	25991689	25991689	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gttggaggagatggatatgcTtggcctgcattgctgctgct	6	13	15	7	0	0	1	0	0	0	1	0	4	0	3	1	4	5	6	1	4	1	4	rs147191545	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:25991689T>C	ENST00000435504.4	-	7	846	c.553A>G	c.(553-555)Agc>Ggc	p.S185G	ASXL2_ENST00000336112.4_Missense_Mutation_p.S157G|ASXL2_ENST00000272341.4_5'UTR|ASXL2_ENST00000404843.1_5'UTR|ASXL2_ENST00000497092.1_5'UTR			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	185	Ser-rich.				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)					ATGGATATGCTTGGCCTGCAT	0.438													T|||	3	0.000599042	0.0	0.0	5008	,	,		13298	0.0		0.003	False		,,,				2504	0.0				p.S185G		Atlas-SNP	.											.	ASXL2	217	.	0			c.A553G						PASS	.	T	GLY/SER	1,4041		0,1,2020	170	173	172		553	3.7	0.8	2	dbSNP_134	172	29,8385		0,29,4178	yes	missense	ASXL2	NM_018263.4	56	0,30,6198	CC,CT,TT		0.3447,0.0247,0.2408	probably-damaging	185/1436	25991689	30,12426	2021	4207	6228	SO:0001583	missense	55252	exon6			ATATGCTTGGCCT			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.553A>G	2.37:g.25991689T>C	ENSP00000391447:p.Ser185Gly	137	0	0		121	52	0.429752	NM_018263	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Missense_Mutation	SNP	ENST00000435504.4	37		3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	5.976	0.364036	0.11296	2.47E-4	0.003447	ENSG00000143970	ENST00000435504;ENST00000336112	T;T	0.16897	2.31;2.31	6.03	3.67	0.42095	.	0.312422	0.39544	N	0.001327	T	0.07908	0.0198	N	0.04508	-0.205	0.80722	D	1	B	0.12013	0.005	B	0.12156	0.007	T	0.16217	-1.0410	10	0.87932	D	0	-5.0436	7.3591	0.26735	0.0:0.2424:0.0:0.7576	.	185	Q76L83	ASXL2_HUMAN	G	185;157	ENSP00000391447:S185G;ENSP00000337250:S157G	ENSP00000337250:S157G	S	-	1	0	ASXL2	25845193	0.966000	0.33281	0.772000	0.31596	0.755000	0.42902	1.653000	0.37323	0.530000	0.28619	0.533000	0.62120	AGC	T|0.998;C|0.002	0.002	strong		0.438	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263		C	25991689	T	C	25991689	3	2	25	1	0	0	0	0	1	0	0	0	1067	1609	56	3	3782	3	ASXL2	2	25991689	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	22599668	25991689	217207684	71	8980											
CAD	790	hgsc.bcm.edu	37	chr2	27447310	27447310	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gttctgatcctgggctcaggGggcctctccattggccaagc	5	10	13	13	0	3	1	1	1	2	0	5	1	4	1	4	4	1	2	4	4	1	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:27447310G>A	ENST00000403525.1	+	9	1350	c.1206G>A	c.(1204-1206)ggG>ggA	p.G402G	CAD_ENST00000264705.4_Silent_p.G402G			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)					TGGGCTCAGGGGGCCTCTCCA	0.597																																					p.G402G		Atlas-SNP	.											CAD,NS,carcinoma,+2,1	CAD	199	1	0			c.G1206A						PASS	.						67	72	70					2																	27447310		2203	4300	6503	SO:0001819	synonymous_variant	790	exon9			CTCAGGGGGCCTC	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.1206G>A	2.37:g.27447310G>A		88	0	0		90	40	0.444444	NM_004341	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Silent	SNP	ENST00000403525.1	37																																																																																				.	.	none		0.597	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1			A	27447310	G	A	27447310	2	1	25	1	0	0	0	0	0	0	0	1	2567	1219	43	2		2	CAD	2	27447310	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1455621	27447310	215752063	72	8981											
C2orf71	388939	hgsc.bcm.edu	37	chr2	29293837	29293837	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcttgtttccttgtgctcCtgagaaggggacattggggg	5	14	14	8	0	1	1	0	1	1	1	4	3	3	2	2	4	1	2	2	4	1	4	rs183536545	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:29293837C>T	ENST00000331664.5	-	1	3290	c.3291G>A	c.(3289-3291)caG>caA	p.Q1097Q		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	1097					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						CCTTGTGCTCCTGAGAAGGGG	0.562													C|||	24	0.00479233	0.0008	0.0115	5008	,	,		12777	0.0		0.0119	False		,,,				2504	0.0031				p.Q1097Q		Atlas-SNP	.											.	C2orf71	146	.	0			c.G3291A						PASS	.	C		13,3861		0,13,1924	62	69	66		3291	2.7	0	2		66	114,8170		0,114,4028	no	coding-synonymous	C2orf71	NM_001029883.1		0,127,5952	TT,TC,CC		1.3761,0.3356,1.0446		1097/1289	29293837	127,12031	1937	4142	6079	SO:0001819	synonymous_variant	388939	exon1			GTGCTCCTGAGAA		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.3291G>A	2.37:g.29293837C>T		117	0	0		114	48	0.421053	NM_001029883		Silent	SNP	ENST00000331664.5	37	CCDS42669.1																																																																																			C|0.990;T|0.010	0.010	strong		0.562	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883		T	29293837	C	T	29293837	2	4	25	1	0	0	0	0	0	0	0	1	2193	680	24	2		2	C2orf71	2	29293837	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1846527	29293837	213905536	73	8982											
C2orf71	388939	hgsc.bcm.edu	37	chr2	29295476	29295476	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacagggacaaacttgatcCtttcgctgattgactccttc	9	12	8	12	1	0	3	0	3	0	0	4	4	2	4	2	1	1	2	2	1	1	4			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:29295476C>T	ENST00000331664.5	-	1	1651	c.1652G>A	c.(1651-1653)aGg>aAg	p.R551K		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	551					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						AAACTTGATCCTTTCGCTGAT	0.592																																					p.R551K		Atlas-SNP	.											.	C2orf71	146	.	0			c.G1652A						PASS	.						48	51	50					2																	29295476		2016	4170	6186	SO:0001583	missense	388939	exon1			TTGATCCTTTCGC		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.1652G>A	2.37:g.29295476C>T	ENSP00000332809:p.Arg551Lys	115	0	0		103	52	0.504854	NM_001029883		Missense_Mutation	SNP	ENST00000331664.5	37	CCDS42669.1	.	.	.	.	.	.	.	.	.	.	C	10.57	1.386668	0.25031	.	.	ENSG00000179270	ENST00000331664	T	0.20738	2.05	5.17	2.4	0.29515	.	0.258207	0.38111	N	0.001807	T	0.10035	0.0246	N	0.25647	0.755	0.27894	N	0.939233	B	0.32040	0.353	B	0.25884	0.064	T	0.25606	-1.0127	10	0.12766	T	0.61	-19.7104	5.7968	0.18392	0.0:0.4904:0.0:0.5096	.	551	A6NGG8	CB071_HUMAN	K	551	ENSP00000332809:R551K	ENSP00000332809:R551K	R	-	2	0	C2orf71	29148980	1.000000	0.71417	0.999000	0.59377	0.868000	0.49771	2.616000	0.46376	0.593000	0.29745	0.561000	0.74099	AGG	.	.	none		0.592	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883		T	29295476	C	T	29295476	3	4	25	1	0	0	0	0	1	0	0	0	2193	681	24	2	2222	2	C2orf71	2	29295476	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1639	29295476	213903897	74	8983											
ALK	238	hgsc.bcm.edu	37	chr2	29416615	29416615	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcagccttgccagaggaggtGgtaggcagaggtggtggggc	7	6	21	7	0	0	2	0	0	0	2	0	3	0	3	2	8	2	3	2	8	1	2	rs56132472	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:29416615G>A	ENST00000389048.3	-	29	5244	c.4338C>T	c.(4336-4338)acC>acT	p.T1446T	ALK_ENST00000431873.1_Silent_p.T276T	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1446					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)	CAGAGGAGGTGGTAGGCAGAG	0.617			"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				G|||	296	0.0591054	0.0779	0.0648	5008	,	,		15538	0.001		0.1233	False		,,,				2504	0.0235				p.T1446T		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	.	ALK	533	.	0			c.C4338T						PASS	.			375,4031	187.8+/-214.3	15,345,1843	76	80	78		4338	1.4	0	2	dbSNP_129	78	968,7632	210.7+/-251.5	48,872,3380	no	coding-synonymous	ALK	NM_004304.4		63,1217,5223	AA,AG,GG		11.2558,8.5111,10.326		1446/1621	29416615	1343,11663	2203	4300	6503	SO:0001819	synonymous_variant	238	exon29	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	GGAGGTGGTAGGC	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.4338C>T	2.37:g.29416615G>A		133	0	0		86	40	0.465116	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			G|0.903;A|0.097	0.097	strong		0.617	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		A	29416615	G	A	29416615	2	1	25	1	0	0	0	0	0	0	0	1	525	1335	47	2		2	ALK	2	29416615	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	121139	29416615	213782758	75	8984											
ALK	238	hgsc.bcm.edu	37	chr2	29449819	29449819	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acgccatcctcagccagcacCgtcccgtggtcacagaagca	10	5	9	17	3	2	1	2	0	0	1	4	1	4	1	5	1	3	2	5	1	1	0	rs2293563	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:29449819C>T	ENST00000389048.3	-	18	3942	c.3036G>A	c.(3034-3036)acG>acA	p.T1012T	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1012			T -> M (in dbSNP:rs35073634). {ECO:0000269|PubMed:17344846}.		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)	p.T1012T(1)	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)	CAGCCAGCACCGTCCCGTGGT	0.542			"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				C|||	851	0.169928	0.2277	0.147	5008	,	,		21422	0.119		0.1928	False		,,,				2504	0.137				p.T1012T		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	ALK,NS,carcinoma,0,1	ALK	533	1	1	Substitution - coding silent(1)	stomach(1)	c.G3036A						PASS	.	C		974,3432	366.4+/-317.8	105,764,1334	202	180	187		3036	-10.8	0.1	2	dbSNP_100	187	1492,7108	283.2+/-296.0	137,1218,2945	no	coding-synonymous	ALK	NM_004304.4		242,1982,4279	TT,TC,CC		17.3488,22.1062,18.9605		1012/1621	29449819	2466,10540	2203	4300	6503	SO:0001819	synonymous_variant	238	exon18	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	CAGCACCGTCCCG	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.3036G>A	2.37:g.29449819C>T		135	0	0		109	109	1	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			C|0.816;T|0.184	0.184	strong		0.542	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		T	29449819	C	T	29449819	2	4	25	1	0	0	0	0	0	0	0	1	525	639	23	1		1	ALK	2	29449819	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	33204	29449819	213749554	76	8985											
NLRC4	58484	hgsc.bcm.edu	37	chr2	32463365	32463365	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcttcttcaggtttttcaggCcttcagctgaaaaatgatag	10	15	8	8	0	5	2	3	2	2	0	5	2	5	2	1	2	1	2	1	2	3	6	rs149451729	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:32463365C>A	ENST00000404025.2	-	7	2845	c.2357G>T	c.(2356-2358)gGc>gTc	p.G786V	NLRC4_ENST00000342905.6_Missense_Mutation_p.G121V|NLRC4_ENST00000402280.1_Missense_Mutation_p.G786V|NLRC4_ENST00000360906.5_Missense_Mutation_p.G786V			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	786					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)					GTTTTTCAGGCCTTCAGCTGA	0.358													C|||	3	0.000599042	0.0	0.0043	5008	,	,		19325	0.0		0.0	False		,,,				2504	0.0				p.G786V		Atlas-SNP	.											.	NLRC4	165	.	0			c.G2357T						PASS	.	C	VAL/GLY,VAL/GLY,VAL/GLY	4,4402	8.1+/-20.4	0,4,2199	94	93	94		2357,2357,2357	2.8	0	2	dbSNP_134	94	39,8561	25.7+/-73.6	0,39,4261	yes	missense,missense,missense	NLRC4	NM_001199138.1,NM_001199139.1,NM_021209.4	109,109,109	0,43,6460	AA,AC,CC		0.4535,0.0908,0.3306	probably-damaging,probably-damaging,probably-damaging	786/1025,786/1025,786/1025	32463365	43,12963	2203	4300	6503	SO:0001583	missense	58484	exon6			TTCAGGCCTTCAG	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.2357G>T	2.37:g.32463365C>A	ENSP00000385090:p.Gly786Val	102	0	0		83	37	0.445783	NM_001199138	A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	Missense_Mutation	SNP	ENST00000404025.2	37	CCDS33174.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	C	7.093	0.572525	0.13623	9.08E-4	0.004535	ENSG00000091106	ENST00000360906;ENST00000402280;ENST00000342905;ENST00000404025	T;T;T;T	0.53423	0.62;0.62;0.62;0.62	4.63	2.78	0.32641	.	0.000000	0.41294	D	0.000913	T	0.42787	0.1218	L	0.56769	1.78	0.36099	D	0.843987	D;D	0.62365	0.98;0.991	P;P	0.58013	0.693;0.831	T	0.56080	-0.8038	9	0.16420	T	0.52	-8.9282	6.4653	0.21977	0.0:0.7173:0.1834:0.0993	.	121;786	Q9NPP4-2;Q9NPP4	.;NLRC4_HUMAN	V	786;786;121;786	ENSP00000354159:G786V;ENSP00000385428:G786V;ENSP00000339666:G121V;ENSP00000385090:G786V	ENSP00000339666:G121V	G	-	2	0	NLRC4	32316869	0.035000	0.19736	0.016000	0.15963	0.041000	0.13682	0.929000	0.28844	0.663000	0.31027	-0.150000	0.13652	GGC	C|0.997;A|0.003	0.003	strong		0.358	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325222.2	NM_021209		A	32463365	C	A	32463365	3	1	25	1	0	0	0	0	1	0	0	0	10478	739	26	4	733	4	NLRC4	2	32463365	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	3013546	32463365	210736008	77	8986											
HEATR5B	54497	hgsc.bcm.edu	37	chr2	37289177	37289177	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagttcgtaaaagatcttcaGcaatactaactaccatctgc	14	11	5	11	1	3	1	1	0	2	1	4	1	3	1	1	0	5	3	1	0	6	6			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:37289177G>T	ENST00000233099.5	-	11	1696	c.1601C>A	c.(1600-1602)gCt>gAt	p.A534D	HEATR5B_ENST00000354531.2_Missense_Mutation_p.A534D	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	534						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)				AAGATCTTCAGCAATACTAAC	0.348																																					p.A534D		Atlas-SNP	.											.	HEATR5B	185	.	0			c.C1601A						PASS	.						96	99	98					2																	37289177		2203	4300	6503	SO:0001583	missense	54497	exon11			TCTTCAGCAATAC	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.1601C>A	2.37:g.37289177G>T	ENSP00000233099:p.Ala534Asp	52	0	0		40	11	0.275	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Missense_Mutation	SNP	ENST00000233099.5	37	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	G	32	5.127527	0.94473	.	.	ENSG00000008869	ENST00000233099;ENST00000354531;ENST00000424416	T;T	0.08458	3.09;3.09	5.7	5.7	0.88788	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.40767	0.1130	M	0.91300	3.195	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.49082	-0.8976	10	0.87932	D	0	-21.1412	19.8411	0.96685	0.0:0.0:1.0:0.0	.	534	Q9P2D3	HTR5B_HUMAN	D	534	ENSP00000233099:A534D;ENSP00000346531:A534D	ENSP00000233099:A534D	A	-	2	0	HEATR5B	37142681	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.624000	0.98398	2.683000	0.91414	0.655000	0.94253	GCT	.	.	none		0.348	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024		T	37289177	G	T	37289177	3	4	25	1	0	0	0	0	1	0	0	0	7041	971	34	4	4718	4	HEATR5B	2	37289177	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	4825812	37289177	205910196	78	8987											
CEBPZ	10153	hgsc.bcm.edu	37	chr2	37441091	37441091	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgtttctctttaacagcaaCttttttataatacctataat	12	20	2	7	0	1	0	0	0	1	0	2	0	1	0	1	0	4	2	1	0	7	11			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:37441091C>A	ENST00000234170.5	-	10	2606	c.2461G>T	c.(2461-2463)Gtt>Ttt	p.V821F	RP11-423P10.2_ENST00000606229.1_RNA|AC007390.5_ENST00000438935.2_Intron	NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	821					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)				TTAACAGCAACTTTTTTATAA	0.299																																					p.V821F		Atlas-SNP	.											.	CEBPZ	68	.	0			c.G2461T						PASS	.						132	128	130					2																	37441091		2201	4299	6500	SO:0001583	missense	10153	exon10			CAGCAACTTTTTT	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.2461G>T	2.37:g.37441091C>A	ENSP00000234170:p.Val821Phe	121	0	0		76	32	0.421053	NM_005760	Q8NE75	Missense_Mutation	SNP	ENST00000234170.5	37	CCDS1787.1	.	.	.	.	.	.	.	.	.	.	C	6.869	0.529703	0.13127	.	.	ENSG00000115816	ENST00000234170;ENST00000545744	T	0.14640	2.49	5.41	3.53	0.40419	Armadillo-type fold (1);	0.871941	0.10183	N	0.705591	T	0.13713	0.0332	L	0.47716	1.5	0.29558	N	0.850814	B	0.09022	0.002	B	0.08055	0.003	T	0.15925	-1.0420	10	0.87932	D	0	.	7.0108	0.24861	0.5827:0.3154:0.0:0.1019	.	821	Q03701	CEBPZ_HUMAN	F	821	ENSP00000234170:V821F	ENSP00000234170:V821F	V	-	1	0	CEBPZ	37294595	0.982000	0.34865	1.000000	0.80357	0.994000	0.84299	1.441000	0.35035	0.577000	0.29470	-0.181000	0.13052	GTT	.	.	none		0.299	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760		A	37441091	C	A	37441091	3	1	25	1	0	0	0	0	1	0	0	0	3206	565	20	4	731	4	CEBPZ	2	37441091	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	151914	37441091	205758282	79	8988											
ATL2	64225	hgsc.bcm.edu	37	chr2	38537579	38537579	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctgaagctcttcatgttgaTtttgttttacctgagggcgg	6	17	11	7	1	3	3	1	3	2	0	3	3	3	3	1	2	2	3	1	2	2	6	rs34873284	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:38537579T>C	ENST00000378954.4	-	8	816	c.815A>G	c.(814-816)aAt>aGt	p.N272S	ATL2_ENST00000402054.1_Missense_Mutation_p.N101S|ATL2_ENST00000419554.2_Missense_Mutation_p.N272S|ATL2_ENST00000546051.1_Missense_Mutation_p.N101S|ATL2_ENST00000539122.1_Missense_Mutation_p.N101S|ATL2_ENST00000332337.4_Missense_Mutation_p.N254S|ATL2_ENST00000406122.1_Missense_Mutation_p.N101S|ATL2_ENST00000452935.2_Missense_Mutation_p.N254S	NM_001135673.1|NM_022374.2	NP_001129145.1|NP_071769.2	Q8NHH9	ATLA2_HUMAN	atlastin GTPase 2	272	GB1/RHD3-type G.		N -> S (in dbSNP:rs34873284).		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						TTCATGTTGATTTTGTTTTAC	0.383													T|||	72	0.014377	0.0045	0.0216	5008	,	,		17843	0.0		0.0398	False		,,,				2504	0.0112				p.N272S		Atlas-SNP	.											.	ATL2	49	.	0			c.A815G						PASS	.	T	SER/ASN,SER/ASN	48,4358	48.9+/-83.8	1,46,2156	133	118	123		815,815	5.1	1	2	dbSNP_126	123	420,8180	130.8+/-188.7	10,400,3890	yes	missense,missense	ATL2	NM_001135673.1,NM_022374.2	46,46	11,446,6046	CC,CT,TT		4.8837,1.0894,3.5983	benign,benign	272/584,272/580	38537579	468,12538	2203	4300	6503	SO:0001583	missense	64225	exon8			TGTTGATTTTGTT		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.815A>G	2.37:g.38537579T>C	ENSP00000368237:p.Asn272Ser	93	0	0		105	43	0.409524	NM_001135673	B7Z1X2|B7Z7X8|Q4ZG30|Q7Z630|Q8NHH8|Q9H5M7	Missense_Mutation	SNP	ENST00000378954.4	37	CCDS46260.1	40|40	0.018315018315018316|0.018315018315018316	4|4	0.008130081300813009|0.008130081300813009	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	31|31	0.040897097625329816|0.040897097625329816	T|T	15.82|15.82	2.945674|2.945674	0.53079|0.53079	0.010894|0.010894	0.048837|0.048837	ENSG00000119787|ENSG00000119787	ENST00000443098|ENST00000378954;ENST00000406122;ENST00000402054;ENST00000539122;ENST00000332337;ENST00000419554;ENST00000452935;ENST00000546051;ENST00000449130	.|T;T;T;T;T;T;T;T;T	.|0.74421	.|-0.84;-0.84;-0.84;-0.84;-0.84;-0.84;-0.84;-0.84;-0.84	5.11|5.11	5.11|5.11	0.69529|0.69529	.|Guanylate-binding protein, N-terminal (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.28764|0.28764	0.0713|0.0713	L|L	0.47078|0.47078	1.49|1.49	0.80722|0.80722	D|D	1|1	.|B;B;B;B;B	.|0.17268	.|0.021;0.001;0.003;0.005;0.001	.|B;B;B;B;B	.|0.11329	.|0.006;0.001;0.001;0.002;0.002	T|T	0.53542|0.53542	-0.8424|-0.8424	5|10	.|0.44086	.|T	.|0.13	-21.5939|-21.5939	14.0983|14.0983	0.65037|0.65037	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs34873284;rs61754250|rs34873284;rs61754250	.|101;254;254;272;272	.|B5MCN0;B7Z7X8;Q8NHH9-4;Q8NHH9-2;Q8NHH9	.|.;.;.;.;ATLA2_HUMAN	V|S	191|272;101;101;101;254;272;254;101;90	.|ENSP00000368237:N272S;ENSP00000385446:N101S;ENSP00000384062:N101S;ENSP00000446192:N101S;ENSP00000333393:N254S;ENSP00000415336:N272S;ENSP00000390743:N254S;ENSP00000438938:N101S;ENSP00000409811:N90S	.|ENSP00000333393:N254S	I|N	-|-	1|2	0|0	ATL2|ATL2	38391083|38391083	1.000000|1.000000	0.71417|0.71417	0.973000|0.973000	0.42090|0.42090	0.982000|0.982000	0.71751|0.71751	6.134000|6.134000	0.71689|0.71689	1.917000|1.917000	0.55516|0.55516	0.455000|0.455000	0.32223|0.32223	ATC|AAT	T|0.967;C|0.033	0.033	strong		0.383	ATL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219886.2	NM_022374		C	38537579	T	C	38537579	3	2	25	1	0	0	0	0	1	0	0	0	1107	1493	52	3	1072	3	ATL2	2	38537579	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	1096488	38537579	204661794	80	8989											
ABCG8	64241	hgsc.bcm.edu	37	chr2	44078913	44078913	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gagaccttggccttcattgcCcagatgcggctgcccagaac	8	8	11	14	1	1	3	1	0	0	3	1	4	1	3	4	2	4	1	4	2	1	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:44078913C>A	ENST00000272286.2	+	4	603	c.513C>A	c.(511-513)gcC>gcA	p.A171A		NM_022437.2	NP_071882.1	Q9H221	ABCG8_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 8	171	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)|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)	CCTTCATTGCCCAGATGCGGC	0.612																																					p.A171A		Atlas-SNP	.											.	ABCG8	98	.	0			c.C513A						PASS	.						113	116	115					2																	44078913		2203	4300	6503	SO:0001819	synonymous_variant	64241	exon4			CATTGCCCAGATG	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.513C>A	2.37:g.44078913C>A		104	0	0		105	38	0.361905	NM_022437	Q53QN8	Silent	SNP	ENST00000272286.2	37	CCDS1815.1																																																																																			.	.	none		0.612	ABCG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250671.1	NM_022437		A	44078913	C	A	44078913	2	1	25	1	0	0	0	0	0	0	0	1	72	610	22	4		4	ABCG8	2	44078913	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	5541334	44078913	199120460	81	8990											
MSH2	4436	hgsc.bcm.edu	37	chr2	47637439	47637439	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tccaatcttgaggctctcctCatccagattggaccaaagga	11	10	8	12	0	3	2	1	1	2	1	6	4	5	4	4	3	0	1	4	3	2	2	rs1800151	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:47637439C>T	ENST00000233146.2	+	3	796	c.573C>T	c.(571-573)ctC>ctT	p.L191L	MSH2_ENST00000406134.1_Silent_p.L191L|MSH2_ENST00000543555.1_Silent_p.L125L	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	191					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)			AGGCTCTCCTCATCCAGATTG	0.463			"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				C|||	97	0.019369	0.0696	0.0072	5008	,	,		15087	0.0		0.0	False		,,,				2504	0.0				p.L191L		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.C573T						PASS	.	C		254,4152	146.9+/-181.5	4,246,1953	182	176	178	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	573	1.6	1	2	dbSNP_89	178	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	MSH2	NM_000251.1		4,250,6249	TT,TC,CC		0.0465,5.7649,1.9837		191/935	47637439	258,12748	2203	4300	6503	SO:0001819	synonymous_variant	4436	exon3	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	TCTCCTCATCCAG	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.573C>T	2.37:g.47637439C>T		79	0	0		98	49	0.5	NM_000251	B4E2Z2|O75488	Silent	SNP	ENST00000233146.2	37	CCDS1834.1																																																																																			C|0.977;T|0.023	0.023	strong		0.463	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3			T	47637439	C	T	47637439	2	4	25	1	0	0	0	0	0	0	0	1	9879	813	29	2		2	MSH2	2	47637439	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	3558526	47637439	195561934	82	8991											
MSH6	2956	hgsc.bcm.edu	37	chr2	48027375	48027375	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttttctgaatggaacaaaTggttctactgaaggaaccct	13	13	8	7	0	2	2	0	2	2	0	2	4	2	4	1	3	3	1	1	3	6	4	rs2020913	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:48027375T>C	ENST00000234420.5	+	4	2405	c.2253T>C	c.(2251-2253)aaT>aaC	p.N751N	MSH6_ENST00000538136.1_Silent_p.N449N|MSH6_ENST00000540021.1_Silent_p.N621N|FBXO11_ENST00000405808.1_Intron	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	751					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)			ATGGAACAAATGGTTCTACTG	0.443			"Mis, N, F, S"		colorectal	"colorectal, endometrial, ovarian"		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				T|||	120	0.0239617	0.0885	0.0043	5008	,	,		20418	0.0		0.0	False		,,,				2504	0.0				p.N751N		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.T2253C						PASS	.	T		266,4140	150.3+/-184.3	8,250,1945	135	132	133	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2253	-0.9	1	2	dbSNP_98	133	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MSH6	NM_000179.2		8,251,6244	CC,CT,TT		0.0116,6.0372,2.0529		751/1361	48027375	267,12739	2203	4300	6503	SO:0001819	synonymous_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	AACAAATGGTTCT	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.2253T>C	2.37:g.48027375T>C		108	0	0		101	47	0.465347	NM_000179	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Silent	SNP	ENST00000234420.5	37	CCDS1836.1																																																																																			T|0.980;C|0.020	0.020	strong		0.443	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179		C	48027375	T	C	48027375	2	2	25	1	0	0	0	0	0	0	0	1	9883	1461	51	3		3	MSH6	2	48027375	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	389936	48027375	195171998	83	8992											
RTN4	57142	hgsc.bcm.edu	37	chr2	55253973	55253973	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatctgcaaaacattttttaTccactttactttccaagttg	11	18	3	9	0	1	0	0	0	1	0	3	0	3	0	2	0	3	2	2	0	6	8			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:55253973T>G	ENST00000337526.6	-	3	1505	c.1262A>C	c.(1261-1263)gAt>gCt	p.D421A	RTN4_ENST00000357732.4_Intron|RTN4_ENST00000405240.1_Missense_Mutation_p.D215A|RTN4_ENST00000394611.2_Missense_Mutation_p.D215A|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000404909.1_Missense_Mutation_p.D215A|RTN4_ENST00000357376.3_Missense_Mutation_p.D215A|RTN4_ENST00000354474.6_Missense_Mutation_p.D189A|RTN4_ENST00000317610.7_Intron	NM_020532.4	NP_065393.1	Q9NQC3	RTN4_HUMAN	reticulon 4	421					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						ACATTTTTTATCCACTTTACT	0.383																																					p.D421A		Atlas-SNP	.											.	RTN4	189	.	0			c.A1262C						PASS	.						236	233	234					2																	55253973		2202	4300	6502	SO:0001583	missense	57142	exon3			TTTTTATCCACTT	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.1262A>C	2.37:g.55253973T>G	ENSP00000337838:p.Asp421Ala	232	0	0		227	120	0.528634	NM_020532	O94962|Q7L7Q5|Q7L7Q6|Q7L7Q8|Q8IUA4|Q96B16|Q9BXG5|Q9H212|Q9H3I3|Q9UQ42|Q9Y293|Q9Y2Y7|Q9Y5U6	Missense_Mutation	SNP	ENST00000337526.6	37	CCDS42684.1	.	.	.	.	.	.	.	.	.	.	t	10.97	1.500459	0.26861	.	.	ENSG00000115310	ENST00000405240;ENST00000357376;ENST00000337526;ENST00000394611;ENST00000404909;ENST00000354474	T;T;T;T;T;T	0.27557	1.66;1.66;2.34;1.66;1.66;1.72	6.06	0.962	0.19643	.	0.933951	0.09057	N	0.854885	T	0.33876	0.0878	M	0.66939	2.045	0.33241	D	0.557225	P	0.48294	0.908	P	0.44422	0.449	T	0.48139	-0.9061	10	0.87932	D	0	-1.8717	6.2376	0.20772	0.0:0.1944:0.148:0.6577	.	421	Q9NQC3	RTN4_HUMAN	A	215;215;421;215;215;189	ENSP00000384471:D215A;ENSP00000349944:D215A;ENSP00000337838:D421A;ENSP00000378109:D215A;ENSP00000385650:D215A;ENSP00000346465:D189A	ENSP00000337838:D421A	D	-	2	0	RTN4	55107477	0.005000	0.15991	0.153000	0.22517	0.300000	0.27592	0.122000	0.15687	-0.072000	0.12864	-0.266000	0.10368	GAT	.	.	none		0.383	RTN4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251484.1			G	55253973	T	G	55253973	3	3	25	1	0	0	0	0	1	0	0	0	13743	1435	50	5	2382	5	RTN4	2	55253973	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	7226598	55253973	187945400	84	8993											
PEX13	5194	hgsc.bcm.edu	37	chr2	61258816	61258816	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcttccacccagtagatttGttcagcaagctgaagaaagc	13	10	8	10	0	2	3	1	1	1	2	3	3	3	3	2	0	3	4	2	0	4	4	rs147707348	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:61258816G>A	ENST00000295030.5	+	2	393	c.355G>A	c.(355-357)Gtt>Att	p.V119I	PEX13_ENST00000472678.1_3'UTR	NM_002618.3	NP_002609.1	Q92968	PEX13_HUMAN	peroxisomal biogenesis factor 13	119					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)			CAGTAGATTTGTTCAGCAAGC	0.433													G|||	2	0.000399361	0.0	0.0	5008	,	,		20269	0.0		0.002	False		,,,				2504	0.0				p.V119I		Atlas-SNP	.											.	PEX13	27	.	0			c.G355A						PASS	.	G	ILE/VAL	2,4404	4.2+/-10.8	0,2,2201	139	133	135		355	5.8	1	2	dbSNP_134	135	22,8578	16.0+/-53.3	0,22,4278	yes	missense	PEX13	NM_002618.3	29	0,24,6479	AA,AG,GG		0.2558,0.0454,0.1845	possibly-damaging	119/404	61258816	24,12982	2203	4300	6503	SO:0001583	missense	5194	exon2			AGATTTGTTCAGC	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.355G>A	2.37:g.61258816G>A	ENSP00000295030:p.Val119Ile	157	0	0		132	70	0.530303	NM_002618	B2RCS1	Missense_Mutation	SNP	ENST00000295030.5	37	CCDS1866.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	18.70	3.679588	0.68042	4.54E-4	0.002558	ENSG00000162928	ENST00000295030	T	0.77098	-1.07	5.85	5.85	0.93711	Peroxin 13, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.77432	0.4129	L	0.31420	0.93	0.80722	D	1	P	0.45240	0.854	P	0.49361	0.608	T	0.75525	-0.3287	10	0.38643	T	0.18	-24.2526	20.1649	0.98147	0.0:0.0:1.0:0.0	.	119	Q92968	PEX13_HUMAN	I	119	ENSP00000295030:V119I	ENSP00000295030:V119I	V	+	1	0	PEX13	61112320	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.588000	0.98232	2.753000	0.94483	0.655000	0.94253	GTT	G|0.998;A|0.002	0.002	strong		0.433	PEX13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251581.3	NM_002618		A	61258816	G	A	61258816	3	1	25	1	0	0	0	0	1	0	0	0	11750	1377	48	2	361	2	PEX13	2	61258816	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	6004843	61258816	181940557	85	8994											
CEP68	23177	hgsc.bcm.edu	37	chr2	65299330	65299330	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaggccactgccctgccatTttctgggcccagagagccaa	9	7	11	14	0	1	2	0	0	1	2	1	3	1	2	5	2	3	0	5	2	1	2	rs141499084	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:65299330T>A	ENST00000377990.2	+	3	1303	c.1100T>A	c.(1099-1101)tTt>tAt	p.F367Y	CEP68_ENST00000537589.1_5'UTR|CEP68_ENST00000497039.1_3'UTR|CEP68_ENST00000260569.4_Missense_Mutation_p.F367Y|RAB1A_ENST00000494188.1_Intron|CEP68_ENST00000546106.1_Missense_Mutation_p.F367Y	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	367					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						GCCCTGCCATTTTCTGGGCCC	0.567													T|||	21	0.00419329	0.0	0.0086	5008	,	,		18965	0.0		0.0139	False		,,,				2504	0.001				p.F367Y		Atlas-SNP	.											.	CEP68	69	.	0			c.T1100A						PASS	.	T	TYR/PHE	16,4390	22.3+/-47.3	0,16,2187	90	95	93		1100	2.9	0.1	2	dbSNP_134	93	169,8431	76.9+/-139.5	0,169,4131	yes	missense	CEP68	NM_015147.2	22	0,185,6318	AA,AT,TT		1.9651,0.3631,1.4224	possibly-damaging	367/758	65299330	185,12821	2203	4300	6503	SO:0001583	missense	23177	exon3			TGCCATTTTCTGG	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.1100T>A	2.37:g.65299330T>A	ENSP00000367229:p.Phe367Tyr	97	0	0		77	39	0.506494	NM_015147	B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	Missense_Mutation	SNP	ENST00000377990.2	37	CCDS1880.2	17	0.007783882783882784	0	0.0	6	0.016574585635359115	0	0.0	11	0.014511873350923483	T	23.4	4.415682	0.83449	0.003631	0.019651	ENSG00000011523	ENST00000377990;ENST00000546106;ENST00000260569;ENST00000545501	T;T;T	0.16196	2.37;2.36;2.37	5.66	2.91	0.33838	.	0.460130	0.22130	N	0.064202	T	0.16854	0.0405	M	0.63428	1.95	0.09310	N	1	D;D;D;P;D	0.71674	0.995;0.987;0.983;0.933;0.998	P;P;P;P;P	0.62649	0.836;0.775;0.67;0.597;0.905	T	0.01863	-1.1258	10	0.62326	D	0.03	-11.404	6.9502	0.24540	0.0:0.0893:0.1532:0.7575	.	355;367;367;367;367	F5H3N9;F5H2Y2;Q76N32;Q76N32-2;Q05C09	.;.;CEP68_HUMAN;.;.	Y	367;367;367;355	ENSP00000367229:F367Y;ENSP00000438306:F367Y;ENSP00000260569:F367Y	ENSP00000260569:F367Y	F	+	2	0	CEP68	65152834	0.001000	0.12720	0.112000	0.21494	0.810000	0.45777	0.594000	0.24014	0.951000	0.37770	0.402000	0.26972	TTT	T|0.987;A|0.013	0.013	strong		0.567	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2	NM_015147		A	65299330	T	A	65299330	3	1	25	1	0	0	0	0	1	0	0	0	3260	1841	64	5	1106	5	CEP68	2	65299330	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	4040514	65299330	177900043	86	8995											
APLF	200558	hgsc.bcm.edu	37	chr2	68805143	68805143	+	Frame_Shift_Del	DEL	A	A	-																															aagaagcaaaaaggtttatgAaaagaaaatagtaactaact																								rs149897324	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:68805143delA	ENST00000303795.4	+	10	1696	c.1525delA	c.(1525-1527)aaafs	p.K509fs	APLF_ENST00000471727.1_Intron	NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	509					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of DNA ligation (GO:0051106)|regulation of isotype switching (GO:0045191)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|endodeoxyribonuclease activity (GO:0004520)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	25						AAGGTTTATGAAAAGAAAATA	0.358													AAAA|AAAA|AAA|deletion	23	0.00459265	0.0008	0.0058	5008	,	,		20808	0.0		0.0119	False		,,,				2504	0.0061				p.M508fs		Pindel,Atlas-Indel	.											.	APLF	69	.	0			c.1524delG						PASS	.			15,4251		0,15,2118	68	74	72			2.8	1	2	dbSNP_134	73	121,8127		3,115,4006	no	frameshift	APLF	NM_173545.2		3,130,6124	A1A1,A1R,RR		1.467,0.3516,1.0868			68805143	136,12378	2203	4299	6502	SO:0001589	frameshift_variant	200558	exon10			.	BC030711	CCDS1888.1	2p14	2014-02-20	2008-10-01	2008-10-01	ENSG00000169621	ENSG00000169621			28724	protein-coding gene	gene with protein product	"XRCC1-interacting protein 1", "zinc finger, CX5CX6HX5H motif containing 1"	611035	"chromosome 2 open reading frame 13"	C2orf13		18474613, 18077224, 17353262	Standard	NM_173545		Approved	MGC47799, Xip1, ZCCHH1	uc002sep.3	Q8IW19	OTTHUMG00000129566	ENST00000303795.4:c.1525delA	2.37:g.68805143delA	ENSP00000307004:p.Lys509fs	58	0	.		64	26	0.406	NM_173545	A8K476|Q53P47|Q53PB9|Q53QU0	Frame_Shift_Del	DEL	ENST00000303795.4	37	CCDS1888.1																																																																																			A|0.991;-|0.009	0.009	strong		0.358	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545		-	68805143	A	-	68805143	7	5	25	1	0	1	0	1	0	0	0	0	776	247	9	0	1563	0	APLF	2	68805143	Frame_Shift_Del	DEL	A	TCGA-G8-6906-01A-11D-2210-10	3505813	68805143	174394230	87	8996											
MRPL19	9801	hgsc.bcm.edu	37	chr2	75879359	75879359	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atatgttagaaaggagaaaaGtactccacattccagagttc	16	10	8	7	0	0	3	0	0	0	3	3	4	2	3	2	1	1	3	2	1	6	5	rs41382847	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:75879359G>A	ENST00000393909.2	+	3	338	c.313G>A	c.(313-315)Gta>Ata	p.V105I	MRPL19_ENST00000409374.1_Missense_Mutation_p.V105I|MRPL19_ENST00000358788.6_Missense_Mutation_p.V105I	NM_014763.3	NP_055578.2	P49406	RM19_HUMAN	mitochondrial ribosomal protein L19	105					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						AAGGAGAAAAGTACTCCACAT	0.343													G|||	35	0.00698882	0.0008	0.0115	5008	,	,		15222	0.0		0.0149	False		,,,				2504	0.0112				p.V105I		Atlas-SNP	.											.	MRPL19	21	.	0			c.G313A						PASS	.	G	ILE/VAL	3,3617		0,3,1807	73	71	72		313	-0.5	1	2	dbSNP_127	72	74,8042		1,72,3985	yes	missense	MRPL19	NM_014763.3	29	1,75,5792	AA,AG,GG		0.9118,0.0829,0.6561	benign	105/293	75879359	77,11659	1810	4058	5868	SO:0001583	missense	9801	exon3			AGAAAAGTACTCC	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.313G>A	2.37:g.75879359G>A	ENSP00000377486:p.Val105Ile	371	0	0		349	177	0.507163	NM_014763	Q53TX9|Q96Q52	Missense_Mutation	SNP	ENST00000393909.2	37	CCDS1960.2	14	0.00641025641025641	0	0.0	5	0.013812154696132596	0	0.0	9	0.011873350923482849	G	12.24	1.877138	0.33162	8.29E-4	0.009118	ENSG00000115364	ENST00000393909;ENST00000409374	.	.	.	4.85	-0.463	0.12164	Translation protein SH3-like (1);	0.350899	0.32736	N	0.005705	T	0.50222	0.1603	M	0.69185	2.1	0.80722	D	1	B	0.20887	0.049	B	0.32022	0.139	T	0.48603	-0.9021	9	0.33940	T	0.23	-6.8784	10.7534	0.46221	0.3156:0.0:0.6844:0.0	rs41382847	105	P49406	RM19_HUMAN	I	105	.	ENSP00000377486:V105I	V	+	1	0	MRPL19	75732867	1.000000	0.71417	0.976000	0.42696	0.971000	0.66376	2.018000	0.40991	-0.205000	0.10219	-0.145000	0.13849	GTA	G|0.992;A|0.008	0.008	strong		0.343	MRPL19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252256.1	NM_014763		A	75879359	G	A	75879359	3	1	25	1	0	0	0	0	1	0	0	0	9793	1029	36	2	323	2	MRPL19	2	75879359	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	7074216	75879359	167320014	88	8997											
ACOXL	55289	hgsc.bcm.edu	37	chr2	111551725	111551725	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acgcgagagggatccagaccGaagccacctttgacctctct	10	7	10	14	3	1	3	0	1	1	2	3	6	2	4	5	1	1	0	5	1	1	1	rs150003283	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:111551725G>A	ENST00000389811.4	+	5	543	c.319G>A	c.(319-321)Gaa>Aaa	p.E107K	ACOXL_ENST00000439055.1_Missense_Mutation_p.E107K|ACOXL_ENST00000340561.4_Missense_Mutation_p.E107K			Q9NUZ1	ACOXL_HUMAN	acyl-CoA oxidase-like	107					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						GATCCAGACCGAAGCCACCTT	0.537													G|||	43	0.00858626	0.0	0.0043	5008	,	,		19322	0.001		0.007	False		,,,				2504	0.0327				p.E107K		Atlas-SNP	.											ACOXL_ENST00000439055,colon,carcinoma,0,2	ACOXL	93	2	0			c.G319A						PASS	.	G	LYS/GLU	1,3935		0,1,1967	88	96	94		319	3.5	0.1	2	dbSNP_134	94	37,8249		0,37,4106	yes	missense	ACOXL	NM_001142807.1	56	0,38,6073	AA,AG,GG		0.4465,0.0254,0.3109	probably-damaging	107/581	111551725	38,12184	1968	4143	6111	SO:0001583	missense	55289	exon5			CAGACCGAAGCCA		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.319G>A	2.37:g.111551725G>A	ENSP00000374461:p.Glu107Lys	100	0	0		109	57	0.522936	NM_001142807	A2RRB7|B7WPB3|B7WPP7|E9PB20|Q53R27|Q53R31|Q53SC6|Q8TCE7	Missense_Mutation	SNP	ENST00000389811.4	37		11	0.005036630036630037	0	0.0	3	0.008287292817679558	1	0.0017482517482517483	7	0.009234828496042216	G	22.8	4.335963	0.81801	2.54E-4	0.004465	ENSG00000153093	ENST00000389811;ENST00000439055;ENST00000340561	D;D;D	0.94862	-3.54;-3.54;-3.54	5.33	3.53	0.40419	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA oxidase/dehydrogenase, central domain (2);	0.269326	0.27787	N	0.017858	D	0.87529	0.6200	N	0.04162	-0.26	0.33945	D	0.643766	D;D;D	0.71674	0.998;0.997;0.963	P;P;P	0.58130	0.833;0.742;0.49	D	0.90091	0.4177	10	0.59425	D	0.04	-7.9556	9.0146	0.36161	0.0824:0.1491:0.7686:0.0	.	107;107;107	E9PB20;Q9NUZ1-2;Q9NUZ1	.;.;ACOXL_HUMAN	K	107	ENSP00000374461:E107K;ENSP00000407761:E107K;ENSP00000343717:E107K	ENSP00000343717:E107K	E	+	1	0	ACOXL	111268196	0.988000	0.35896	0.122000	0.21767	0.936000	0.57629	2.001000	0.40825	0.615000	0.30124	0.655000	0.94253	GAA	G|0.995;A|0.005	0.005	strong		0.537	ACOXL-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000254024.2	NM_018308		A	111551725	G	A	111551725	3	1	25	1	0	0	0	0	1	0	0	0	161	1059	37	1	333	1	ACOXL	2	111551725	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	35672366	111551725	131647648	89	8998											
RGPD5	727851	hgsc.bcm.edu	37	chr2	113127773	113127773	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctcatccagaagaacgggaAggattttcttcctcatcttt	10	13	8	10	1	4	2	2	0	2	2	6	4	6	4	2	2	1	1	2	2	3	4	rs186330915	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:113127773A>G	ENST00000302558.3	-	23	5471	c.5280T>C	c.(5278-5280)ccT>ccC	p.P1760P	RGPD8_ENST00000409750.1_Silent_p.P1620P	NM_001164463.1	NP_001157935.1	O14715	RGPD8_HUMAN	RANBP2-like and GRIP domain containing 8	1760				P -> A (in Ref. 3; CAI56757). {ECO:0000305}.	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						AAGAACGGGAAGGATTTTCTT	0.308													.|||	8	0.00159744	0.0	0.0029	5008	,	,		13164	0.0		0.0	False		,,,				2504	0.0061				p.P1760P		Atlas-SNP	.											RGPD8_ENST00000302558,NS,carcinoma,-2,18	RGPD8	81	18	0			c.T5280C						PASS	.	A		2,1372		0,2,685	231	167	186		5280	0.7	0.9	2		186	4,3110		0,4,1553	no	coding-synonymous	RGPD8	NM_001164463.1		0,6,2238	GG,GA,AA		0.1285,0.1456,0.1337		1760/1766	113127773	6,4482	687	1557	2244	SO:0001819	synonymous_variant	727851	exon23			ACGGGAAGGATTT	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.5280T>C	2.37:g.113127773A>G		621	0	0		568	264	0.464789	NM_001164463	Q5CZA8	Silent	SNP	ENST00000302558.3	37	CCDS46394.1																																																																																			A|0.999;G|0.001	0.001	strong		0.308	RGPD8-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375951.1	XM_001722279		G	113127773	A	G	113127773	2	3	25	1	0	0	0	0	0	0	0	1	13304	59	3	3		3	RGPD5	2	113127773	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	1576048	113127773	130071600	90	8999											
SMPD4	80097	hgsc.bcm.edu	37	chr2	130939163	130939163	+	5'Flank	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccattccgccacggcgccGaaagtcgtcatcaagctgcg	8	6	11	16	7	2	0	2	0	0	0	4	1	3	0	4	1	2	1	4	1	2	1	rs146359515	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:130939163G>T	ENST00000281871.6	+	0	0				MZT2B_ENST00000409255.1_5'Flank|SMPD4_ENST00000431183.2_Missense_Mutation_p.F4L|SMPD4_ENST00000409031.1_Missense_Mutation_p.F4L|SMPD4_ENST00000452225.2_5'UTR|SMPD4_ENST00000426662.2_5'UTR|SMPD4_ENST00000339679.7_5'UTR|SMPD4_ENST00000443958.2_5'UTR|AC018804.1_ENST00000578074.1_RNA|SMPD4_ENST00000453750.1_Missense_Mutation_p.F4L|SMPD4_ENST00000473720.1_5'UTR|SMPD4_ENST00000351288.6_Missense_Mutation_p.F4L	NM_025029.3	NP_079305.2	Q6NZ67	MZT2B_HUMAN	mitotic spindle organizing protein 2B							centrosome (GO:0005813)|gamma-tubulin ring complex (GO:0008274)|spindle (GO:0005819)				lung(1)	1						CCACGGCGCCGAAAGTCGTCA	0.677													.|||	18	0.00359425	0.0	0.0086	5008	,	,		12025	0.0		0.0119	False		,,,				2504	0.0				p.F4L		Atlas-SNP	.											.	SMPD4	67	.	0			c.C12A						PASS	.	G	LEU/PHE,LEU/PHE,LEU/PHE	7,3753		0,7,1873	8	11	10		12,12,12	0.2	1	2	dbSNP_134	10	85,8099		0,85,4007	no	missense,missense,missense	SMPD4	NM_001171083.2,NM_017751.4,NM_017951.4	22,22,22	0,92,5880	TT,TG,GG		1.0386,0.1862,0.7703	benign,benign,benign	4/765,4/838,4/867	130939163	92,11852	1880	4092	5972	SO:0001631	upstream_gene_variant	55627	exon1			GGCGCCGAAAGTC	BC066296	CCDS2157.1	2q21.1	2013-10-11	2010-07-22	2010-07-22	ENSG00000152082	ENSG00000152082			25886	protein-coding gene	gene with protein product	"mitotic-spindle organizing protein associated with a ring of gamma-tubulin 2B"	613450	"family with sequence similarity 128, member B"	FAM128B		20360068	Standard	NM_025029		Approved	FLJ14346, MOZART2B	uc002tqu.3	Q6NZ67	OTTHUMG00000131625		2.37:g.130939163G>T	Exception_encountered	48	0	0		69	33	0.478261	NM_017751	Q96CG4	Missense_Mutation	SNP	ENST00000281871.6	37	CCDS2157.1	7	0.003205128205128205	0	0.0	3	0.008287292817679558	0	0.0	4	0.005277044854881266	N	8.707	0.911139	0.17833	0.001862	0.010386	ENSG00000136699	ENST00000351288;ENST00000409031;ENST00000431183;ENST00000453750	.	.	.	3.38	0.175	0.15045	.	.	.	.	.	T	0.21550	0.0519	N	0.19112	0.55	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	0.05683	-1.0870	7	.	.	.	.	3.9534	0.09379	0.1266:0.0:0.4426:0.4308	.	4;4;4	E7ESA2;B4DM23;B1PBA3	.;.;.	L	4	.	.	F	-	3	2	SMPD4	130655633	0.722000	0.28017	0.965000	0.40720	0.152000	0.21847	-0.022000	0.12480	-0.086000	0.12550	0.455000	0.32223	TTC	G|0.996;T|0.004	0.004	strong		0.677	MZT2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254518.1	NM_025029		T	130939163	G	T	130939163	1	4	25	0	1	0	0	0	0	0	0	0	14822	1049	37	4		4	SMPD4	2	130939163	5'Flank	SNP	G	TCGA-G8-6906-01A-11D-2210-10	17811390	130939163	112260210	91	9000											
CCDC74A	90557	hgsc.bcm.edu	37	chr2	132290912	132290912	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccccgaagaacaactttgccGagaggcagaagaggctgcag	13	4	13	11	2	0	4	0	0	0	4	0	6	0	4	3	2	4	3	3	2	4	1	rs140033985	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:132290912G>A	ENST00000295171.6	+	8	1216	c.1078G>A	c.(1078-1080)Gag>Aag	p.E360K	CCDC74A_ENST00000409856.3_Missense_Mutation_p.E294K|CCDC74A_ENST00000467992.2_3'UTR	NM_001258304.1|NM_001258305.1|NM_138770.2	NP_001245233.1|NP_001245234.1|NP_620125.1	Q96AQ1	CC74A_HUMAN	coiled-coil domain containing 74A	360										endometrium(4)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						CAACTTTGCCGAGAGGCAGAA	0.632													g|||	28	0.00559105	0.0	0.0058	5008	,	,		18487	0.0		0.0179	False		,,,				2504	0.0061				p.E360K		Atlas-SNP	.											.	CCDC74A	44	.	0			c.G1078A						PASS	.	G	LYS/GLU	11,4395		0,11,2192	44	42	43		1078	3.1	0.8	2	dbSNP_134	43	139,8455		2,135,4160	no	missense	CCDC74A	NM_138770.1	56	2,146,6352	AA,AG,GG		1.6174,0.2497,1.1538	probably-damaging	360/379	132290912	150,12850	2203	4297	6500	SO:0001583	missense	90557	exon8			TTTGCCGAGAGGC		CCDS2167.1, CCDS58732.1, CCDS74578.1	2q21.1	2008-02-05		2006-02-16	ENSG00000163040	ENSG00000163040			25197	protein-coding gene	gene with protein product						12477932	Standard	NM_138770		Approved	FLJ40345	uc002ttb.4	Q96AQ1	OTTHUMG00000131667	ENST00000295171.6:c.1078G>A	2.37:g.132290912G>A	ENSP00000295171:p.Glu360Lys	272	1	0.00367647		255	118	0.462745	NM_138770	Q6P4I5	Missense_Mutation	SNP	ENST00000295171.6	37	CCDS2167.1	16	0.007326007326007326	0	0.0	3	0.008287292817679558	0	0.0	13	0.017150395778364115	.	15.00	2.701859	0.48307	0.002497	0.016174	ENSG00000163040	ENST00000295171;ENST00000409856	T;T	0.36878	1.23;1.23	3.07	3.07	0.35406	.	0.000000	0.33235	U	0.005125	T	0.36248	0.0960	M	0.69823	2.125	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.76071	0.987;0.925	T	0.46775	-0.9167	10	0.72032	D	0.01	.	6.44	0.21845	0.1445:0.0:0.8555:0.0	.	294;360	Q96AQ1-2;Q96AQ1	.;CC74A_HUMAN	K	360;294	ENSP00000295171:E360K;ENSP00000387009:E294K	ENSP00000295171:E360K	E	+	1	0	CCDC74A	132007382	1.000000	0.71417	0.764000	0.31436	0.199000	0.23934	4.182000	0.58310	1.436000	0.47453	0.430000	0.28490	GAG	G|0.991;A|0.009	0.009	strong		0.632	CCDC74A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254570.2	NM_138770		A	132290912	G	A	132290912	3	1	25	1	0	0	0	0	1	0	0	0	2849	1059	37	1	1108	1	CCDC74A	2	132290912	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1351749	132290912	110908461	92	9001											
ZEB2	9839	hgsc.bcm.edu	37	chr2	145157593	145157593	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggttctgttttaattttaagTaagcctgtctgttcagacat	9	18	8	6	0	3	1	1	0	2	1	3	1	3	1	1	1	1	4	1	1	3	7	rs146673563	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:145157593T>C	ENST00000558170.2	-	8	2345	c.1161A>G	c.(1159-1161)ttA>ttG	p.L387L	ZEB2_ENST00000303660.4_Silent_p.L387L|ZEB2_ENST00000539609.3_Silent_p.L363L|ZEB2_ENST00000409487.3_Silent_p.L387L	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN	zinc finger E-box binding homeobox 2	387					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)		TAATTTTAAGTAAGCCTGTCT	0.383													T|||	4	0.000798722	0.0	0.0029	5008	,	,		20112	0.0		0.002	False		,,,				2504	0.0				p.L387L	Melanoma(33;1235 1264 5755 16332)	Atlas-SNP	.											ZEB2,NS,carcinoma,0,1	ZEB2	218	1	0			c.A1161G						PASS	.	T	,	0,4406		0,0,2203	101	103	102		1089,1161	1.8	1	2	dbSNP_134	102	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous,coding-synonymous	ZEB2	NM_001171653.1,NM_014795.3	,	0,13,6490	CC,CT,TT		0.1512,0.0,0.1	,	363/1191,387/1215	145157593	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	9839	exon8			TTTAAGTAAGCCT	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.1161A>G	2.37:g.145157593T>C		105	0	0		101	48	0.475248	NM_014795	A0JP09|B7Z2P2|F5H814|Q9UED1	Silent	SNP	ENST00000558170.2	37	CCDS2186.1																																																																																			T|0.999;C|0.001	0.001	strong		0.383	ZEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254778.5	NM_014795		C	145157593	T	C	145157593	2	2	25	1	0	0	0	0	0	0	0	1	17639	1635	57	3		3	ZEB2	2	145157593	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	12866681	145157593	98041780	93	9002											
GALNT13	114805	hgsc.bcm.edu	37	chr2	155102403	155102403	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgggtcagacatgacttaTgggggttttaactggaaact	10	12	13	6	0	1	2	1	1	0	1	1	3	1	3	0	4	2	2	0	4	3	3	rs375635744		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:155102403T>C	ENST00000392825.3	+	7	1332	c.765T>C	c.(763-765)taT>taC	p.Y255Y	GALNT13_ENST00000409237.1_Silent_p.Y255Y	NM_052917.2	NP_443149.2	Q8IUC8	GLT13_HUMAN	polypeptide N-acetylgalactosaminyltransferase 13	255					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						ACATGACTTATGGGGGTTTTA	0.413																																					p.Y255Y		Atlas-SNP	.											.	GALNT13	170	.	0			c.T765C						PASS	.	T		0,4406		0,0,2203	109	108	108		765	0.3	1	2		108	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	GALNT13	NM_052917.2		0,2,6501	CC,CT,TT		0.0233,0.0,0.0154		255/557	155102403	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	114805	exon7			GACTTATGGGGGT	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.765T>C	2.37:g.155102403T>C		77	0	0		48	23	0.479167	NM_052917	Q08ER7|Q68VI8|Q6ZWG1|Q96PX0|Q9UIE5	Silent	SNP	ENST00000392825.3	37	CCDS2199.1																																																																																			.	.	weak		0.413	GALNT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254870.2	NM_052917		C	155102403	T	C	155102403	2	2	25	1	0	0	0	0	0	0	0	1	6219	1471	51	3		3	GALNT13	2	155102403	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	9944810	155102403	88096970	94	9003											
NR4A2	4929	hgsc.bcm.edu	37	chr2	157184995	157184995	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cggcgacgcttgtccactggGcagtttttatttgctaaaca	8	13	10	10	3	0	0	0	0	0	0	1	1	1	0	1	2	2	4	1	2	3	6	rs201103933	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:157184995G>A	ENST00000339562.4	-	4	1277	c.915C>T	c.(913-915)tgC>tgT	p.C305C	NR4A2_ENST00000429376.1_Silent_p.C242C|NR4A2_ENST00000426264.1_Silent_p.C242C|NR4A2_ENST00000539077.1_Silent_p.C316C|NR4A2_ENST00000409108.2_Silent_p.C305C|NR4A2_ENST00000409572.1_Silent_p.C305C	NM_006186.3	NP_006177.1	P43354	NR4A2_HUMAN	nuclear receptor subfamily 4, group A, member 2	305					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						TGTCCACTGGGCAGTTTTTAT	0.453													G|||	2	0.000399361	0.0	0.0	5008	,	,		18722	0.0		0.0	False		,,,				2504	0.002				p.C305C		Atlas-SNP	.											.	NR4A2	82	.	0			c.C915T						PASS	.						91	87	88					2																	157184995		2203	4300	6503	SO:0001819	synonymous_variant	4929	exon4			CACTGGGCAGTTT	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.915C>T	2.37:g.157184995G>A		207	0	0		215	102	0.474419	NM_006186	Q16311|Q53RZ2|Q6NXU0	Silent	SNP	ENST00000339562.4	37	CCDS2201.1	.	.	.	.	.	.	.	.	.	.	G	3.579	-0.085989	0.07097	.	.	ENSG00000153234	ENST00000406048	.	.	.	6.07	5.2	0.72013	.	.	.	.	.	T	0.63248	0.2495	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62153	-0.6914	4	.	.	.	.	11.2859	0.49222	0.138:0.0:0.862:0.0	.	.	.	.	S	87	.	.	P	-	1	0	NR4A2	156893241	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.696000	0.37773	1.584000	0.49913	0.655000	0.94253	CCC	G|0.999;A|0.001	0.001	weak		0.453	NR4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254909.2			A	157184995	G	A	157184995	2	1	25	1	0	0	0	0	0	0	0	1	10642	1195	42	2		2	NR4A2	2	157184995	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2082592	157184995	86014378	95	9004											
COBLL1	22837	hgsc.bcm.edu	37	chr2	165551000	165551000	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaaagttttcaaagtcttcaGattttgtgtggatacctgac	12	15	8	6	0	3	2	2	1	1	1	3	3	3	3	1	1	1	1	1	1	4	6			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:165551000G>A	ENST00000392717.2	-	13	3134	c.3130C>T	c.(3130-3132)Ctg>Ttg	p.L1044L	COBLL1_ENST00000194871.6_Silent_p.L1073L|COBLL1_ENST00000342193.4_Silent_p.L1006L|COBLL1_ENST00000375458.2_Silent_p.L968L|COBLL1_ENST00000409184.3_Silent_p.L1006L			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	1044						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						AAAGTCTTCAGATTTTGTGTG	0.473																																					p.L1006L		Atlas-SNP	.											.	COBLL1	122	.	0			c.C3016T						PASS	.						107	106	106					2																	165551000		2203	4300	6503	SO:0001819	synonymous_variant	22837	exon12			TCTTCAGATTTTG	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.3130C>T	2.37:g.165551000G>A		137	0	0		147	65	0.442177	NM_014900	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Silent	SNP	ENST00000392717.2	37																																																																																				.	.	none		0.473	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900		A	165551000	G	A	165551000	2	1	25	1	0	0	0	0	0	0	0	1	3656	933	33	2		2	COBLL1	2	165551000	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	8366005	165551000	77648373	96	9005											
GALNT3	2591	hgsc.bcm.edu	37	chr2	166621413	166621413	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatctacactagcatcatcCaccaaaatgatttccttcag	13	11	3	14	0	3	1	2	1	1	0	5	1	5	1	4	0	2	1	4	0	4	4	rs13423840	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:166621413C>T	ENST00000392701.3	-	3	1444	c.669G>A	c.(667-669)gtG>gtA	p.V223V	GALNT3_ENST00000409882.1_5'Flank	NM_004482.3	NP_004473.2	Q14435	GALT3_HUMAN	polypeptide N-acetylgalactosaminyltransferase 3	223	Catalytic subdomain A.				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						TAGCATCATCCACCAAAATGA	0.393													t|||	50	0.00998403	0.034	0.0072	5008	,	,		17855	0.0		0.0	False		,,,				2504	0.0				p.V223V		Atlas-SNP	.											.	GALNT3	65	.	0			c.G669A						PASS	.	T		126,4280	92.0+/-130.7	1,124,2078	177	165	169		669	2.8	1	2	dbSNP_121	169	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GALNT3	NM_004482.3		1,125,6377	TT,TC,CC		0.0116,2.8597,0.9765		223/634	166621413	127,12879	2203	4300	6503	SO:0001819	synonymous_variant	2591	exon3			ATCATCCACCAAA		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.669G>A	2.37:g.166621413C>T		232	1	0.00431034		269	117	0.434944	NM_004482	Q53TG9|Q7Z476	Silent	SNP	ENST00000392701.3	37	CCDS2226.1																																																																																			C|0.987;T|0.013	0.013	strong		0.393	GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255205.2	NM_004482		T	166621413	C	T	166621413	2	4	25	1	0	0	0	0	0	0	0	1	6222	581	21	2		2	GALNT3	2	166621413	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1070413	166621413	76577960	97	9006											
SCN9A	6335	hgsc.bcm.edu	37	chr2	167128972	167128972	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcattcatattttccaaatcGgattccccaggtgcaattgg	10	13	8	10	1	1	0	1	0	0	0	4	1	3	1	3	3	1	2	3	3	3	6			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:167128972G>A	ENST00000409435.1	-	16	3287	c.3288C>T	c.(3286-3288)tcC>tcT	p.S1096S	AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Silent_p.S1097S|SCN9A_ENST00000409672.1_Silent_p.S1085S|SCN9A_ENST00000375387.4_Silent_p.S1097S			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	1096					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)	p.S1085S(1)		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)	TTTCCAAATCGGATTCCCCAG	0.413																																					p.S1085S		Atlas-SNP	.											SCN9A,colon,carcinoma,0,1	SCN9A	296	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C3255T						PASS	.						71	65	67					2																	167128972		1897	4121	6018	SO:0001819	synonymous_variant	6335	exon17			CAAATCGGATTCC	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.3288C>T	2.37:g.167128972G>A		180	0	0		150	78	0.52	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Silent	SNP	ENST00000409435.1	37	CCDS46441.1																																																																																			.	.	none		0.413	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		A	167128972	G	A	167128972	2	1	25	1	0	0	0	0	0	0	0	1	13940	1103	39	1		1	SCN9A	2	167128972	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	507559	167128972	76070401	98	9007											
XIRP2	129446	hgsc.bcm.edu	37	chr2	168104679	168104679	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttctaatgaaaacaaatacTtccacaggcttaaaaatggc	17	11	5	8	0	1	1	0	1	1	0	2	1	2	1	1	2	2	1	1	2	8	5			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:168104679T>G	ENST00000409195.1	+	9	6866	c.6777T>G	c.(6775-6777)acT>acG	p.T2259T	XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000295237.9_Silent_p.T2259T|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Silent_p.T2037T	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2084					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						AAACAAATACTTCCACAGGCT	0.388																																					p.T2259T		Atlas-SNP	.											.	XIRP2	914	.	0			c.T6777G						PASS	.						68	64	65					2																	168104679		1834	4085	5919	SO:0001819	synonymous_variant	129446	exon9			AAATACTTCCACA	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.6777T>G	2.37:g.168104679T>G		196	0	0		176	60	0.340909	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	37	CCDS42769.1																																																																																			.	.	none		0.388	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		G	168104679	T	G	168104679	2	3	25	1	0	0	0	0	0	0	0	1	17445	1596	56	5		5	XIRP2	2	168104679	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	975707	168104679	75094694	99	9008											
LASS6	253782	hgsc.bcm.edu	37	chr2	169312974	169312974	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaagatggcagggatcttaGcctggttctggaacgagagg	10	8	16	7	1	2	2	0	0	2	2	2	5	2	4	1	5	2	3	1	5	3	2	rs4496303	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:169312974G>A	ENST00000305747.6	+	1	603	c.16G>A	c.(16-18)Gcc>Acc	p.A6T	CERS6_ENST00000392687.4_Missense_Mutation_p.A6T	NM_203463.2	NP_982288.1	Q6ZMG9	CERS6_HUMAN	ceramide synthase 6	6					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)										AGGGATCTTAGCCTGGTTCTG	0.657													G|||	39	0.00778754	0.0061	0.0101	5008	,	,		8564	0.0		0.0209	False		,,,				2504	0.0031				p.A6T		Atlas-SNP	.											.	.	.	.	0			c.G16A						PASS	.	G	THR/ALA	35,4371	40.0+/-72.8	2,31,2170	162	130	141		16	4.3	1	2	dbSNP_111	141	101,8499	56.4+/-117.6	0,101,4199	yes	missense	CERS6	NM_203463.1	58	2,132,6369	AA,AG,GG		1.1744,0.7944,1.0457	benign	6/385	169312974	136,12870	2203	4300	6503	SO:0001583	missense	253782	exon1			ATCTTAGCCTGGT	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.16G>A	2.37:g.169312974G>A	ENSP00000306579:p.Ala6Thr	55	0	0		82	36	0.439024	NM_001256126	Q32M63|Q8N617	Missense_Mutation	SNP	ENST00000305747.6	37	CCDS2228.1	24	0.01098901098901099	4	0.008130081300813009	4	0.011049723756906077	0	0.0	16	0.021108179419525065	G	21.6	4.173118	0.78452	0.007944	0.011744	ENSG00000172292	ENST00000305747;ENST00000392687	T;T	0.21734	1.99;1.99	5.22	4.34	0.51931	.	0.105238	0.64402	N	0.000004	T	0.08358	0.0208	L	0.40543	1.245	0.58432	D	0.999999	B;B	0.32203	0.209;0.36	B;B	0.28465	0.045;0.09	T	0.04165	-1.0972	10	0.22706	T	0.39	-18.0462	13.4206	0.60996	0.0755:0.0:0.9245:0.0	.	6;6	Q32M63;Q6ZMG9	.;CERS6_HUMAN	T	6	ENSP00000306579:A6T;ENSP00000376453:A6T	ENSP00000306579:A6T	A	+	1	0	CERS6	169021220	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	9.346000	0.97056	1.188000	0.43014	0.467000	0.42956	GCC	A|0.008;G|0.990;T|0.002	0.008	strong		0.657	CERS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255235.2	NM_203463		A	169312974	G	A	169312974	3	1	25	1	0	0	0	0	1	0	0	0	8652	971	34	2	18	2	LASS6	2	169312974	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1208295	169312974	73886399	100	9009											
AGPS	8540	hgsc.bcm.edu	37	chr2	178364363	178364363	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagtttaaaggatttgacccAaatcagctaagtgtagccac	14	11	8	8	0	1	1	1	1	0	0	1	2	1	2	2	1	2	3	2	1	6	6	rs148418568	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:178364363A>C	ENST00000264167.4	+	14	1526	c.1380A>C	c.(1378-1380)ccA>ccC	p.P460P	AGPS_ENST00000409888.1_Intron	NM_003659.3	NP_003650.1	O00116	ADAS_HUMAN	alkylglycerone phosphate synthase	460					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)			GATTTGACCCAAATCAGCTAA	0.308													A|||	2	0.000399361	0.0	0.0029	5008	,	,		14276	0.0		0.0	False		,,,				2504	0.0				p.P460P		Atlas-SNP	.											.	AGPS	56	.	0			c.A1380C						PASS	.	A		0,4406		0,0,2203	94	90	91		1380	1.5	1	2	dbSNP_134	91	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	AGPS	NM_003659.3		0,1,6502	CC,CA,AA		0.0116,0.0,0.0077		460/659	178364363	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8540	exon14			TGACCCAAATCAG	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.1380A>C	2.37:g.178364363A>C		32	0	0		23	6	0.26087	NM_003659	A5D8U9|Q2TU35	Silent	SNP	ENST00000264167.4	37	CCDS2275.1																																																																																			A|1.000;C|0.000	0.000	strong		0.308	AGPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255730.2			C	178364363	A	C	178364363	2	2	25	1	0	0	0	0	0	0	0	1	394	117	5	5		5	AGPS	2	178364363	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	9051389	178364363	64835010	101	9010											
FAM171B	165215	hgsc.bcm.edu	37	chr2	187615953	187615953	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggtcaatggctctattcaaGtttctcttcctcttctacgt	7	17	6	11	1	6	0	2	0	4	0	8	0	7	0	1	2	1	2	1	2	4	6	rs201119796		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:187615953G>A	ENST00000304698.5	+	5	1020	c.817G>A	c.(817-819)Gtt>Att	p.V273I		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	273						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)	p.V273F(1)		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						CTCTATTCAAGTTTCTCTTCC	0.363																																					p.V273I		Atlas-SNP	.											FAM171B,rectum,carcinoma,-1,2	FAM171B	146	2	1	Substitution - Missense(1)	breast(1)	c.G817A						PASS	.						108	115	113					2																	187615953		2203	4300	6503	SO:0001583	missense	165215	exon5			ATTCAAGTTTCTC	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.817G>A	2.37:g.187615953G>A	ENSP00000304108:p.Val273Ile	83	0	0		77	29	0.376623	NM_177454	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Missense_Mutation	SNP	ENST00000304698.5	37	CCDS33347.1	.	.	.	.	.	.	.	.	.	.	A	7.399	0.632436	0.14322	.	.	ENSG00000144369	ENST00000304698;ENST00000272804	T	0.38401	1.14	5.53	-4.51	0.03483	.	0.550372	0.20261	N	0.095865	T	0.10208	0.0250	N	0.02202	-0.64	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.28554	-1.0040	10	0.05436	T	0.98	-0.8584	11.0846	0.48080	0.5502:0.0853:0.3645:0.0	.	273;274	Q6P995;A8K122	F171B_HUMAN;.	I	273	ENSP00000304108:V273I	ENSP00000272804:V273I	V	+	1	0	FAM171B	187324198	0.694000	0.27738	0.178000	0.23040	0.632000	0.37999	0.201000	0.17276	-1.197000	0.02673	-1.372000	0.01188	GTT	G|0.999;A|0.001	0.001	weak		0.363	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454		A	187615953	G	A	187615953	3	1	25	1	0	0	0	0	1	0	0	0	5496	1029	36	2	835	2	FAM171B	2	187615953	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	9251590	187615953	55583420	102	9011											
CALCRL	10203	hgsc.bcm.edu	37	chr2	188245439	188245439	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgaaagtaatcagggcagAgctgcattgattcagttcct	11	11	10	9	0	2	3	2	2	0	1	3	3	3	3	2	1	2	5	2	1	2	4	rs61739909		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:188245439A>G	ENST00000409998.1	-	7	1041	c.260T>C	c.(259-261)cTc>cCc	p.L87P	AC007319.1_ENST00000412276.1_RNA|CALCRL_ENST00000392370.3_Missense_Mutation_p.L87P|CALCRL_ENST00000410068.1_Missense_Mutation_p.L87P|AC007319.1_ENST00000453517.1_RNA			Q16602	CALRL_HUMAN	calcitonin receptor-like	87					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|angiogenesis (GO:0001525)|calcium ion transport (GO:0006816)|cAMP biosynthetic process (GO:0006171)|cellular response to sucrose stimulus (GO:0071329)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|heart development (GO:0007507)|negative regulation of inflammatory response (GO:0050728)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|regulation of muscle contraction (GO:0006937)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	adrenomedullin receptor activity (GO:0001605)|calcitonin gene-related polypeptide receptor activity (GO:0001635)|calcitonin receptor activity (GO:0004948)|G-protein coupled receptor activity (GO:0004930)|protein transporter activity (GO:0008565)			endometrium(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227)			ATCAGGGCAGAGCTGCATTGA	0.408													A|||	1	0.000199681	0.0	0.0	5008	,	,		13904	0.0		0.001	False		,,,				2504	0.0				p.L87P		Atlas-SNP	.											.	CALCRL	73	.	0			c.T260C						PASS	.	A	PRO/LEU	0,4406		0,0,2203	68	66	67		260	0	1	2	dbSNP_129	67	21,8579	14.6+/-50.1	1,19,4280	yes	missense	CALCRL	NM_005795.4	98	1,19,6483	GG,GA,AA		0.2442,0.0,0.1615	benign	87/462	188245439	21,12985	2203	4300	6503	SO:0001583	missense	10203	exon5			GGGCAGAGCTGCA	U17473	CCDS2293.1	2q21.1-q21.3	2012-08-10			ENSG00000064989	ENSG00000064989		"GPCR / Class B : Calcitonin receptors"	16709	protein-coding gene	gene with protein product		114190				7818539, 8626685	Standard	NM_005795		Approved	CGRPR, CRLR	uc010frt.4	Q16602	OTTHUMG00000132636	ENST00000409998.1:c.260T>C	2.37:g.188245439A>G	ENSP00000386972:p.Leu87Pro	192	0	0		174	96	0.551724	NM_001271751	A8K6G5|A8KAD3|Q53S02|Q53TS5	Missense_Mutation	SNP	ENST00000409998.1	37	CCDS2293.1	.	.	.	.	.	.	.	.	.	.	A	13.48	2.249542	0.39797	0.0	0.002442	ENSG00000064989	ENST00000392370;ENST00000409998;ENST00000410068	T;T;T	0.46063	0.88;0.88;0.88	5.42	-0.0292	0.13919	GPCR, family 2, secretin-like, conserved site (1);GPCR, family 2, extracellular hormone receptor domain (3);	0.519591	0.18887	N	0.128407	T	0.15522	0.0374	N	0.04335	-0.225	0.47949	D	0.999551	B	0.31519	0.327	B	0.37267	0.245	T	0.25537	-1.0129	10	0.02654	T	1	.	4.3429	0.11119	0.518:0.1646:0.0:0.3174	.	87	Q16602	CALRL_HUMAN	P	87	ENSP00000376177:L87P;ENSP00000386972:L87P;ENSP00000387190:L87P	ENSP00000376177:L87P	L	-	2	0	CALCRL	187953684	0.998000	0.40836	0.996000	0.52242	0.996000	0.88848	0.409000	0.21082	-0.162000	0.10964	0.528000	0.53228	CTC	A|0.999;G|0.001	0.001	strong		0.408	CALCRL-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334648.1	NM_005795		G	188245439	A	G	188245439	3	3	25	1	0	0	0	0	1	0	0	0	2582	304	11	3	1165	3	CALCRL	2	188245439	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	629486	188245439	54953934	103	9012											
DIRC1	116093	hgsc.bcm.edu	37	chr2	189599497	189599497	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccaatgttgcagcagcagAagaacaattttgagcattct	13	11	8	9	0	1	3	0	1	1	2	2	3	2	3	1	0	5	5	1	0	4	4	rs72902678	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:189599497A>C	ENST00000308100.4	-	2	421	c.151T>G	c.(151-153)Tct>Gct	p.S51A	AC079613.1_ENST00000431708.1_RNA	NM_052952.2	NP_443184.1	Q969H9	DIRC1_HUMAN	disrupted in renal carcinoma 1	51			S -> A (in dbSNP:rs72902678). {ECO:0000269|PubMed:11587072}.							large_intestine(1)|lung(6)	7			OV - Ovarian serous cystadenocarcinoma(117;0.00842)|Epithelial(96;0.102)			GCAGCAGCAGAAGAACAATTT	0.438													C|||	46	0.0091853	0.0015	0.0043	5008	,	,		19145	0.0		0.0258	False		,,,				2504	0.0153				p.S51A		Atlas-SNP	.											.	DIRC1	13	.	0			c.T151G						PASS	.	C	ALA/SER	20,4386	824.4+/-416.5	0,20,2183	163	153	156		151	-1	0	2	dbSNP_130	156	197,8403	810.5+/-407.1	4,189,4107	yes	missense	DIRC1	NM_052952.2	99	4,209,6290	CC,CA,AA		2.2907,0.4539,1.6685	benign	51/105	189599497	217,12789	2203	4300	6503	SO:0001583	missense	116093	exon2			CAGCAGAAGAACA	AY039011	CCDS2296.1	2q33	2008-05-22			ENSG00000174325	ENSG00000174325			15760	protein-coding gene	gene with protein product		606423				11587072	Standard	NM_052952		Approved		uc002uqi.1	Q969H9	OTTHUMG00000132646	ENST00000308100.4:c.151T>G	2.37:g.189599497A>C	ENSP00000307860:p.Ser51Ala	209	0	0		166	87	0.524096	NM_052952	Q08AK1	Missense_Mutation	SNP	ENST00000308100.4	37	CCDS2296.1	26	0.011904761904761904	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	24	0.0316622691292876	C	3.267	-0.149923	0.06585	0.004539	0.022907	ENSG00000174325	ENST00000308100	T	0.34667	1.35	3.32	-0.974	0.10293	.	.	.	.	.	T	0.05181	0.0138	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16808	-1.0390	9	0.87932	D	0	.	2.3607	0.04307	0.1301:0.428:0.2831:0.1587	.	51	Q969H9	DIRC1_HUMAN	A	51	ENSP00000307860:S51A	ENSP00000307860:S51A	S	-	1	0	DIRC1	189307742	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.093000	0.03362	-0.472000	0.06881	-2.196000	0.00310	TCT	A|0.985;C|0.015	0.015	strong		0.438	DIRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255897.2	NM_052952		C	189599497	A	C	189599497	3	2	25	1	0	0	0	0	1	0	0	0	4535	246	9	5	167	5	DIRC1	2	189599497	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	1354058	189599497	53599876	104	9013											
DNAH7	56171	hgsc.bcm.edu	37	chr2	196825256	196825256	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttcatgtctaaaaaagaggaGactgtggagtcatctgatgg	13	11	12	5	0	4	3	2	1	2	2	4	5	4	4	0	3	0	0	0	3	3	2	rs115124743	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:196825256G>C	ENST00000312428.6	-	18	2719	c.2619C>G	c.(2617-2619)gtC>gtG	p.V873V		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	873	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						AAAAAGAGGAGACTGTGGAGT	0.448													G|||	94	0.01877	0.0045	0.0389	5008	,	,		19851	0.0		0.0507	False		,,,				2504	0.0102				p.V873V		Atlas-SNP	.											.	DNAH7	512	.	0			c.C2619G						PASS	.	G		30,3736		0,30,1853	105	103	104		2619	2.4	0.8	2	dbSNP_132	104	347,7895		8,331,3782	no	coding-synonymous	DNAH7	NM_018897.2		8,361,5635	CC,CG,GG		4.2101,0.7966,3.1396		873/4025	196825256	377,11631	1883	4121	6004	SO:0001819	synonymous_variant	56171	exon18			AGAGGAGACTGTG	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.2619C>G	2.37:g.196825256G>C		161	0	0		163	74	0.453988	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	37	CCDS42794.1																																																																																			G|0.969;C|0.031	0.031	strong		0.448	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		C	196825256	G	C	196825256	2	2	25	1	0	0	0	0	0	0	0	1	4608	929	33	4		4	DNAH7	2	196825256	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	7225759	196825256	46374117	105	9014											
FAM126B	285172	hgsc.bcm.edu	37	chr2	201846180	201846180	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctccctcagtgccaaccccaAtgctggtacttgcttgactg	7	11	8	15	0	1	1	1	1	0	0	2	1	2	1	4	1	5	3	4	1	3	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:201846180A>G	ENST00000418596.3	-	12	1593	c.1406T>C	c.(1405-1407)aTt>aCt	p.I469T	AC005037.3_ENST00000413848.1_RNA|AC005037.3_ENST00000332935.6_RNA	NM_173822.3	NP_776183.1	Q8IXS8	F126B_HUMAN	family with sequence similarity 126, member B	469						intracellular (GO:0005622)				endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16						GCCAACCCCAATGCTGGTACT	0.463																																					p.I469T		Atlas-SNP	.											FAM126B,NS,carcinoma,-1,1	FAM126B	34	1	0			c.T1406C						PASS	.						107	83	91					2																	201846180		2203	4300	6503	SO:0001583	missense	285172	exon12			ACCCCAATGCTGG	BC039295	CCDS2335.1	2q33.1	2008-10-02			ENSG00000155744	ENSG00000155744			28593	protein-coding gene	gene with protein product						12477932	Standard	NM_173822		Approved	MGC39518, HYCC2	uc002uws.4	Q8IXS8	OTTHUMG00000132823	ENST00000418596.3:c.1406T>C	2.37:g.201846180A>G	ENSP00000393667:p.Ile469Thr	127	0	0		132	63	0.477273	NM_173822	B2RCG7|Q4ZG87|Q53TX6	Missense_Mutation	SNP	ENST00000418596.3	37	CCDS2335.1	.	.	.	.	.	.	.	.	.	.	A	1.870	-0.460559	0.04508	.	.	ENSG00000155744	ENST00000418596	T	0.76578	-1.03	5.72	5.72	0.89469	.	0.413650	0.27773	N	0.017905	T	0.63331	0.2502	N	0.22421	0.69	0.29765	N	0.835254	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.54662	-0.8260	10	0.16896	T	0.51	-6.7283	11.9287	0.52835	0.8549:0.1451:0.0:0.0	.	275;469	B3KUG1;Q8IXS8	.;F126B_HUMAN	T	469	ENSP00000393667:I469T	ENSP00000393667:I469T	I	-	2	0	FAM126B	201554425	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.848000	0.48278	2.177000	0.69029	0.533000	0.62120	ATT	.	.	none		0.463	FAM126B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256285.3	NM_173822		G	201846180	A	G	201846180	3	3	25	1	0	0	0	0	1	0	0	0	5435	101	4	3	190	3	FAM126B	2	201846180	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	5020924	201846180	41353193	106	9015											
NOP58	51602	hgsc.bcm.edu	37	chr2	203157538	203157538	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tatcgaacccagctctatgaAtatctacaaaatcgaatgat	16	11	5	9	2	2	2	0	2	2	0	4	4	2	2	1	0	3	1	1	0	9	4	rs16839032	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:203157538A>G	ENST00000264279.5	+	9	1045	c.819A>G	c.(817-819)gaA>gaG	p.E273E	SNORD11_ENST00000459124.1_RNA|SNORD11B_ENST00000607707.1_RNA	NM_015934.3	NP_057018.1	Q9Y2X3	NOP58_HUMAN	NOP58 ribonucleoprotein	273					cell growth (GO:0016049)|rRNA processing (GO:0006364)|snRNP protein import into nucleus (GO:0006608)	box C/D snoRNP complex (GO:0031428)|Cajal body (GO:0015030)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)	p.E273E(1)		breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|lung(4)|prostate(2)	16						AGCTCTATGAATATCTACAAA	0.368													A|||	31	0.0061901	0.0	0.0187	5008	,	,		18977	0.0		0.0159	False		,,,				2504	0.002				p.E273E		Atlas-SNP	.											NOP58,NS,carcinoma,0,1	NOP58	41	1	1	Substitution - coding silent(1)	prostate(1)	c.A819G						PASS	.	A		12,4394	19.1+/-41.9	0,12,2191	159	160	160		819	0.3	1	2	dbSNP_123	160	133,8467	67.0+/-129.4	3,127,4170	no	coding-synonymous	NOP58	NM_015934.3		3,139,6361	GG,GA,AA		1.5465,0.2724,1.1149		273/530	203157538	145,12861	2203	4300	6503	SO:0001819	synonymous_variant	51602	exon9			CTATGAATATCTA		CCDS2353.1	2q33.1	2012-12-10	2012-12-10		ENSG00000055044	ENSG00000055044			29926	protein-coding gene	gene with protein product			"NOP58 ribonucleoprotein homolog (yeast)"			10606270, 10925205	Standard	NM_015934		Approved	NOP5, HSPC120	uc002uzb.3	Q9Y2X3	OTTHUMG00000132840	ENST00000264279.5:c.819A>G	2.37:g.203157538A>G		117	0	0		119	62	0.521008	NM_015934	Q53SA4|Q6PK08|Q9P036|Q9UFN3	Silent	SNP	ENST00000264279.5	37	CCDS2353.1																																																																																			A|0.989;G|0.011	0.011	strong		0.368	NOP58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256313.2	NM_015934		G	203157538	A	G	203157538	2	3	25	1	0	0	0	0	0	0	0	1	10549	98	4	3		3	NOP58	2	203157538	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	1311358	203157538	40041835	107	9016											
ACADL	33	hgsc.bcm.edu	37	chr2	211068100	211068100	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagcttttctttgtttaacAtagttcctggtttcttcaaa	10	19	5	7	0	3	0	1	0	2	0	4	0	4	0	1	1	2	4	1	1	4	9	rs148069105	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:211068100A>G	ENST00000233710.3	-	8	1166	c.939T>C	c.(937-939)taT>taC	p.Y313Y	AC006994.2_ENST00000412065.1_RNA	NM_001608.3	NP_001599.1	P28330	ACADL_HUMAN	acyl-CoA dehydrogenase, long chain	313					carnitine catabolic process (GO:0042413)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid catabolic process (GO:0044242)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|long-chain fatty acid catabolic process (GO:0042758)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of fatty acid oxidation (GO:0046322)|oxidation-reduction process (GO:0055114)|protein homotetramerization (GO:0051289)|regulation of cholesterol metabolic process (GO:0090181)|small molecule metabolic process (GO:0044281)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|palmitoyl-CoA oxidase activity (GO:0016401)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	14		Renal(323;0.202)		Epithelial(149;0.00631)|Lung(261;0.0438)|LUSC - Lung squamous cell carcinoma(261;0.0466)|all cancers(144;0.0621)		TTTGTTTAACATAGTTCCTGG	0.343																																					p.Y313Y		Atlas-SNP	.											.	ACADL	38	.	0			c.T939C						PASS	.	A		1,4405	2.1+/-5.4	0,1,2202	113	98	103		939	-5.7	0.9	2	dbSNP_134	103	12,8586	9.1+/-34.3	0,12,4287	no	coding-synonymous	ACADL	NM_001608.3		0,13,6489	GG,GA,AA		0.1396,0.0227,0.1		313/431	211068100	13,12991	2203	4299	6502	SO:0001819	synonymous_variant	33	exon8			TTTAACATAGTTC	M74096	CCDS2389.1	2q34	2012-07-13	2010-04-30		ENSG00000115361	ENSG00000115361	1.3.99.13		88	protein-coding gene	gene with protein product		609576	"acyl-Coenzyme A dehydrogenase, long chain"			1774065	Standard	NM_001608		Approved	LCAD, ACAD4	uc002vdz.4	P28330	OTTHUMG00000132989	ENST00000233710.3:c.939T>C	2.37:g.211068100A>G		64	0	0		80	30	0.375	NM_001608	B2R8T3|Q8IUN8	Silent	SNP	ENST00000233710.3	37	CCDS2389.1																																																																																			A|0.999;G|0.001	0.001	strong		0.343	ACADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256561.2	NM_001608		G	211068100	A	G	211068100	2	3	25	1	0	0	0	0	0	0	0	1	112	224	8	3		3	ACADL	2	211068100	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	7910562	211068100	32131273	108	9017											
ACADL	33	hgsc.bcm.edu	37	chr2	211085491	211085491	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttaattttttagcagaaggaGtttctagacgttcttcccct	9	17	7	8	1	2	2	0	0	2	2	3	3	3	3	2	1	1	3	2	1	4	8	rs61731470	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:211085491G>A	ENST00000233710.3	-	2	340	c.113C>T	c.(112-114)aCt>aTt	p.T38I	AC006994.2_ENST00000412065.1_RNA	NM_001608.3	NP_001599.1	P28330	ACADL_HUMAN	acyl-CoA dehydrogenase, long chain	38					carnitine catabolic process (GO:0042413)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid catabolic process (GO:0044242)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|long-chain fatty acid catabolic process (GO:0042758)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of fatty acid oxidation (GO:0046322)|oxidation-reduction process (GO:0055114)|protein homotetramerization (GO:0051289)|regulation of cholesterol metabolic process (GO:0090181)|small molecule metabolic process (GO:0044281)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|palmitoyl-CoA oxidase activity (GO:0016401)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	14		Renal(323;0.202)		Epithelial(149;0.00631)|Lung(261;0.0438)|LUSC - Lung squamous cell carcinoma(261;0.0466)|all cancers(144;0.0621)		AGCAGAAGGAGTTTCTAGACG	0.333													G|||	78	0.0155751	0.0015	0.0274	5008	,	,		18116	0.001		0.0358	False		,,,				2504	0.0204				p.T38I		Atlas-SNP	.											.	ACADL	38	.	0			c.C113T						PASS	.	G	ILE/THR	25,4381	29.0+/-57.7	0,25,2178	60	59	60		113	1.5	0.3	2	dbSNP_129	60	310,8290	108.0+/-168.7	2,306,3992	yes	missense	ACADL	NM_001608.3	89	2,331,6170	AA,AG,GG		3.6047,0.5674,2.5757	benign	38/431	211085491	335,12671	2203	4300	6503	SO:0001583	missense	33	exon2			GAAGGAGTTTCTA	M74096	CCDS2389.1	2q34	2012-07-13	2010-04-30		ENSG00000115361	ENSG00000115361	1.3.99.13		88	protein-coding gene	gene with protein product		609576	"acyl-Coenzyme A dehydrogenase, long chain"			1774065	Standard	NM_001608		Approved	LCAD, ACAD4	uc002vdz.4	P28330	OTTHUMG00000132989	ENST00000233710.3:c.113C>T	2.37:g.211085491G>A	ENSP00000233710:p.Thr38Ile	44	0	0		39	25	0.641026	NM_001608	B2R8T3|Q8IUN8	Missense_Mutation	SNP	ENST00000233710.3	37	CCDS2389.1	39	0.017857142857142856	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	27	0.03562005277044855	G	12.72	2.022726	0.35701	0.005674	0.036047	ENSG00000115361	ENST00000233710	D	0.97553	-4.43	5.69	1.46	0.22682	.	0.233058	0.42294	D	0.000738	T	0.76147	0.3947	N	0.08118	0	0.34426	D	0.697969	B	0.15141	0.012	B	0.12156	0.007	T	0.81678	-0.0824	10	0.48119	T	0.1	.	13.294	0.60286	0.0639:0.3386:0.5975:0.0	rs61731470	38	P28330	ACADL_HUMAN	I	38	ENSP00000233710:T38I	ENSP00000233710:T38I	T	-	2	0	ACADL	210793736	0.999000	0.42202	0.338000	0.25549	0.833000	0.47200	1.967000	0.40491	0.319000	0.23209	-0.126000	0.14955	ACT	G|0.976;A|0.024	0.024	strong		0.333	ACADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256561.2	NM_001608		A	211085491	G	A	211085491	3	1	25	1	0	0	0	0	1	0	0	0	112	1029	36	2	1219	2	ACADL	2	211085491	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	17391	211085491	32113882	109	9018											
PNKD	25953	hgsc.bcm.edu	37	chr2	219206738	219206738	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagatgtggtcagcgtgggaCggcttcagatccgggccctg	7	8	16	10	3	2	2	2	0	0	2	3	3	3	3	2	4	1	1	2	4	1	1	rs34745867	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:219206738C>A	ENST00000273077.4	+	7	703	c.652C>A	c.(652-654)Cgg>Agg	p.R218R	PNKD_ENST00000258362.3_Silent_p.R194R|PNKD_ENST00000436005.2_Silent_p.R158R|AC021016.8_ENST00000411433.1_RNA	NM_015488.4	NP_056303.3	Q8N490	PNKD_HUMAN	paroxysmal nonkinesigenic dyskinesia	218					glutathione biosynthetic process (GO:0006750)|neuromuscular process controlling posture (GO:0050884)|regulation of dopamine metabolic process (GO:0042053)|regulation of synaptic transmission, dopaminergic (GO:0032225)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	hydroxyacylglutathione hydrolase activity (GO:0004416)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)	10		Renal(207;0.0474)		Epithelial(149;7.33e-07)|all cancers(144;0.000133)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CAGCGTGGGACGGCTTCAGAT	0.597													C|||	28	0.00559105	0.0023	0.0101	5008	,	,		19253	0.0		0.0169	False		,,,				2504	0.001				p.R218R		Atlas-SNP	.											.	PNKD	58	.	0			c.C652A						PASS	.	C	,	18,4388	25.3+/-52.1	0,18,2185	132	109	117		652,580	2.7	1	2	dbSNP_126	117	222,8378	93.1+/-155.1	4,214,4082	no	coding-synonymous,coding-synonymous	PNKD	NM_015488.4,NM_022572.4	,	4,232,6267	AA,AC,CC		2.5814,0.4085,1.8453	,	218/386,194/362	219206738	240,12766	2203	4300	6503	SO:0001819	synonymous_variant	25953	exon7			GTGGGACGGCTTC		CCDS2411.1, CCDS2413.1, CCDS42816.1	2q35	2011-01-21	2007-07-12		ENSG00000127838	ENSG00000127838			9153	protein-coding gene	gene with protein product	"myofibrillogenesis regulator 1"	609023	"paroxysmal nonkinesiogenic dyskinesia"			8659518	Standard	NM_015488		Approved	DYT8, PDC, DKFZp564N1362, FPD1, MR-1, BRP17, FKSG19, TAHCCP2, KIAA1184, KIPP1184, MGC31943, PKND1	uc002vhn.3	Q8N490	OTTHUMG00000133110	ENST00000273077.4:c.652C>A	2.37:g.219206738C>A		127	0	0		102	47	0.460784	NM_015488	A8K1F2|Q96A48|Q9BU26|Q9NSX4|Q9ULN6|Q9Y4T1	Silent	SNP	ENST00000273077.4	37	CCDS2411.1																																																																																			C|0.982;A|0.018	0.018	strong		0.597	PNKD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256775.2			A	219206738	C	A	219206738	2	1	25	1	0	0	0	0	0	0	0	1	12155	527	19	4		4	PNKD	2	219206738	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	8121247	219206738	23992635	110	9019											
CDK5R2	8941	hgsc.bcm.edu	37	chr2	219824731	219824731	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccgtccgtgctcatctcggcGctcacctggaagcgcctggt	4	9	12	16	5	3	0	2	0	1	0	5	1	4	1	4	3	2	2	4	3	1	0	rs78141300	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:219824731G>C	ENST00000302625.4	+	1	355	c.189G>C	c.(187-189)gcG>gcC	p.A63A	AC097468.7_ENST00000429343.1_RNA	NM_003936.4	NP_003927.1	Q13319	CD5R2_HUMAN	cyclin-dependent kinase 5, regulatory subunit 2 (p39)	63					cerebellum development (GO:0021549)|hippocampus development (GO:0021766)|layer formation in cerebral cortex (GO:0021819)|neuron migration (GO:0001764)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|superior olivary nucleus maturation (GO:0021722)	cyclin-dependent protein kinase 5 holoenzyme complex (GO:0016533)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	cyclin-dependent protein kinase 5 activator activity (GO:0016534)|lipid binding (GO:0008289)			central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(1)|ovary(1)	8		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)		TCATCTCGGCGCTCACCTGGA	0.716													G|||	163	0.0325479	0.0061	0.0375	5008	,	,		7620	0.0179		0.0398	False		,,,				2504	0.0726				p.A63A		Atlas-SNP	.											.	CDK5R2	17	.	0			c.G189C						PASS	.	G		22,4302		2,18,2142	10	14	13		189	2.5	1	2	dbSNP_131	13	213,8313		1,211,4051	no	coding-synonymous	CDK5R2	NM_003936.3		3,229,6193	CC,CG,GG		2.4982,0.5088,1.8288		63/368	219824731	235,12615	2162	4263	6425	SO:0001819	synonymous_variant	8941	exon1			CTCGGCGCTCACC	U34051	CCDS2427.1	2q35	2008-05-22			ENSG00000171450	ENSG00000171450			1776	protein-coding gene	gene with protein product	"neuronal CDK5 activator isoform"	603764				7592934	Standard	NM_003936		Approved	p39nck5ai, P39, NCK5AI	uc002vjf.4	Q13319	OTTHUMG00000133083	ENST00000302625.4:c.189G>C	2.37:g.219824731G>C		3	0	0		23	13	0.565217	NM_003936	Q4ZFW6	Silent	SNP	ENST00000302625.4	37	CCDS2427.1																																																																																			G|0.972;C|0.028	0.028	strong		0.716	CDK5R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256728.1	NM_003936		C	219824731	G	C	219824731	2	2	25	1	0	0	0	0	0	0	0	1	3146	1074	38	4		4	CDK5R2	2	219824731	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	617993	219824731	23374642	111	9020											
CCDC108	255101	hgsc.bcm.edu	37	chr2	219900300	219900300	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctttccaatgcagctcctcAgccacctcaatgccccagat	9	9	5	18	0	2	1	2	0	0	1	4	1	4	1	7	0	4	2	7	0	2	1	rs77746575	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:219900300A>C	ENST00000341552.5	-	5	527	c.444T>G	c.(442-444)gcT>gcG	p.A148A	CCDC108_ENST00000409865.3_Silent_p.A137A|CCDC108_ENST00000410037.1_Silent_p.A83A|CCDC108_ENST00000441968.1_Silent_p.A148A|CCDC108_ENST00000295729.2_Silent_p.A83A|CCDC108_ENST00000453220.1_Silent_p.A148A|CCDC108_ENST00000324264.6_Silent_p.A83A	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	148						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)		GCAGCTCCTCAGCCACCTCAA	0.517													A|||	2	0.000399361	0.0	0.0	5008	,	,		18210	0.0		0.002	False		,,,				2504	0.0				p.A148A		Atlas-SNP	.											CCDC108_ENST00000295729,colon,carcinoma,-2,2	CCDC108	208	2	0			c.T444G						PASS	.	A	,	0,4406		0,0,2203	167	151	156		249,444	-10.8	0	2	dbSNP_132	156	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	CCDC108	NM_152389.2,NM_194302.2	,	0,5,6498	CC,CA,AA		0.0581,0.0,0.0384	,	83/165,148/1926	219900300	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	255101	exon5			CTCCTCAGCCACC	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.444T>G	2.37:g.219900300A>C		277	1	0.00361011		310	150	0.483871	NM_194302	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Silent	SNP	ENST00000341552.5	37	CCDS2430.2																																																																																			A|0.999;C|0.001	0.001	strong		0.517	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302		C	219900300	A	C	219900300	2	2	25	1	0	0	0	0	0	0	0	1	2745	175	7	5		5	CCDC108	2	219900300	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	75569	219900300	23299073	112	9021											
STK16	8576	hgsc.bcm.edu	37	chr2	220113145	220113145	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggctcctccctccacaggcAttcttcagcattgcggcagc	6	9	10	16	1	2	0	1	0	1	0	5	0	5	0	3	3	3	4	3	3	0	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:220113145A>G	ENST00000409638.3	+	8	954	c.782A>G	c.(781-783)cAt>cGt	p.H261R	GLB1L_ENST00000392089.2_5'Flank|STK16_ENST00000396738.2_Missense_Mutation_p.H261R|GLB1L_ENST00000295759.7_5'Flank|TUBA4A_ENST00000498660.1_5'Flank|STK16_ENST00000409743.1_Missense_Mutation_p.H229R|STK16_ENST00000409516.3_Missense_Mutation_p.H143R|STK16_ENST00000409260.1_Missense_Mutation_p.H306R	NM_001008910.2	NP_001008910.1	O75716	STK16_HUMAN	serine/threonine kinase 16	261	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to transforming growth factor beta stimulus (GO:0071560)|protein autophosphorylation (GO:0046777)	Golgi-associated vesicle (GO:0005798)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			skin(1)	1		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)		CTCCACAGGCATTCTTCAGCA	0.567																																					p.H261R	Pancreas(34;887 922 17165 36961 39622)	Atlas-SNP	.											.	STK16	22	.	0			c.A782G						PASS	.						128	135	133					2																	220113145		2088	4216	6304	SO:0001583	missense	8576	exon8			ACAGGCATTCTTC	AF060798	CCDS42822.1	2q35	2010-04-16			ENSG00000115661	ENSG00000115661			11394	protein-coding gene	gene with protein product		604719				9712705	Standard	NM_001008910		Approved	PKL12, MPSK	uc002vko.2	O75716	OTTHUMG00000154520	ENST00000409638.3:c.782A>G	2.37:g.220113145A>G	ENSP00000386928:p.His261Arg	107	0	0		91	42	0.461538	NM_001008910	A8K9H9|Q5U0F8|Q96KI2|Q9BUH4|Q9UEN3|Q9UP78	Missense_Mutation	SNP	ENST00000409638.3	37	CCDS42822.1	.	.	.	.	.	.	.	.	.	.	A	14.44	2.534997	0.45073	.	.	ENSG00000115661	ENST00000409638;ENST00000396738;ENST00000409516;ENST00000409260;ENST00000409743	T;T;T;T;T	0.73363	2.13;2.13;-0.74;-0.74;2.13	4.98	4.98	0.66077	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.301734	0.37530	N	0.002044	T	0.64405	0.2595	L	0.27944	0.81	0.48288	D	0.999628	B;B;B	0.33022	0.394;0.084;0.084	B;B;B	0.33042	0.072;0.157;0.026	T	0.68629	-0.5358	10	0.72032	D	0.01	-3.1791	14.8415	0.70230	1.0:0.0:0.0:0.0	.	143;306;261	B4DPS1;B8ZZN3;O75716	.;.;STK16_HUMAN	R	261;261;143;306;229	ENSP00000386928:H261R;ENSP00000379964:H261R;ENSP00000386309:H143R;ENSP00000387156:H306R;ENSP00000386553:H229R	ENSP00000379964:H261R	H	+	2	0	STK16	219821389	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.637000	0.74304	2.098000	0.63641	0.459000	0.35465	CAT	.	.	none		0.567	STK16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335679.1			G	220113145	A	G	220113145	3	3	25	1	0	0	0	0	1	0	0	0	15304	217	8	3	808	3	STK16	2	220113145	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	212845	220113145	23086228	113	9022											
ACSL3	2181	hgsc.bcm.edu	37	chr2	223799388	223799388	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tgaggtacttaaagtgctttCcgaagctgctatttcaggtg	9	14	11	7	1	1	1	1	1	0	0	2	2	2	1	1	2	4	4	1	2	5	5			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:223799388C>T	ENST00000357430.3	+	16	2519	c.1988C>T	c.(1987-1989)tCc>tTc	p.S663F	ACSL3_ENST00000392066.3_Missense_Mutation_p.S663F|AC013476.1_ENST00000582868.1_RNA	NM_004457.3	NP_004448.2	O95573	ACSL3_HUMAN	acyl-CoA synthetase long-chain family member 3	663					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)	AAAGTGCTTTCCGAAGCTGCT	0.398			T	ETV1	prostate																																p.S663F		Atlas-SNP	.		Dom	yes		2	2q36	2181	acyl-CoA synthetase long-chain family member 3		E	.	ACSL3	107	.	0			c.C1988T						PASS	.						123	111	115					2																	223799388		2203	4300	6503	SO:0001583	missense	2181	exon15			TGCTTTCCGAAGC	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.1988C>T	2.37:g.223799388C>T	ENSP00000350012:p.Ser663Phe	113	0	0		101	44	0.435644	NM_203372	Q60I92|Q8IUM9	Missense_Mutation	SNP	ENST00000357430.3	37	CCDS2455.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.26|19.26	3.793730|3.793730	0.70452|0.70452	.|.	.|.	ENSG00000123983|ENSG00000123983	ENST00000407441|ENST00000357430;ENST00000392066	.|T;T	.|0.11277	.|2.79;2.79	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	.|0.106594	.|0.64402	.|D	.|0.000004	T|T	0.15825|0.15825	0.0381|0.0381	L|L	0.43152|0.43152	1.355|1.355	0.58432|0.58432	D|D	0.999991|0.999991	.|B	.|0.27625	.|0.183	.|B	.|0.33392	.|0.163	T|T	0.02539|0.02539	-1.1144|-1.1144	5|10	.|0.56958	.|D	.|0.05	-17.9388|-17.9388	20.0411|20.0411	0.97590|0.97590	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|663	.|O95573	.|ACSL3_HUMAN	S|F	164|663	.|ENSP00000350012:S663F;ENSP00000375918:S663F	.|ENSP00000350012:S663F	P|S	+|+	1|2	0|0	ACSL3|ACSL3	223507632|223507632	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	3.908000|3.908000	0.56355|0.56355	2.739000|2.739000	0.93911|0.93911	0.655000|0.655000	0.94253|0.94253	CCG|TCC	.	.	none		0.398	ACSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256862.2	NM_004457		T	223799388	C	T	223799388	3	4	25	1	0	0	0	0	1	0	0	0	178	855	30	2	2038	2	ACSL3	2	223799388	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	3686243	223799388	19399985	114	9023											
AP1S3	130340	hgsc.bcm.edu	37	chr2	224642579	224642579	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcgactgaagagcaatatgAaatgtatctagaacaaagga	18	8	10	5	1	1	4	0	2	1	2	2	6	1	5	0	1	2	2	0	1	8	3	rs116107386	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:224642579A>C	ENST00000446015.2	-	2	44	c.11T>G	c.(10-12)tTc>tGc	p.F4C	AP1S3_ENST00000396653.2_Missense_Mutation_p.F4C|AP1S3_ENST00000443700.1_Missense_Mutation_p.F4C|AP1S3_ENST00000423110.1_Missense_Mutation_p.F4C|AP1S3_ENST00000409375.1_Missense_Mutation_p.F4C|AP1S3_ENST00000396654.2_Missense_Mutation_p.F4C			Q96PC3	AP1S3_HUMAN	adaptor-related protein complex 1, sigma 3 subunit	4					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)	coated pit (GO:0005905)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|membrane coat (GO:0030117)|trans-Golgi network membrane (GO:0032588)	protein transporter activity (GO:0008565)			NS(1)|breast(1)|lung(2)	4		Renal(207;0.0112)|Lung NSC(271;0.0186)|all_lung(227;0.0272)		Epithelial(121;7.6e-10)|all cancers(144;3.62e-07)|Lung(261;0.0086)|LUSC - Lung squamous cell carcinoma(224;0.00902)		GAGCAATATGAAATGTATCTA	0.408													A|||	15	0.00299521	0.0015	0.0029	5008	,	,		16772	0.0		0.0099	False		,,,				2504	0.001				p.F4C		Atlas-SNP	.											.	AP1S3	10	.	0			c.T11G						PASS	.	A	CYS/PHE	10,3754		0,10,1872	60	55	56		11	5.8	1	2	dbSNP_132	56	105,8127		0,105,4011	yes	missense	AP1S3	NM_001039569.1	205	0,115,5883	CC,CA,AA		1.2755,0.2657,0.9587	probably-damaging	4/155	224642579	115,11881	1882	4116	5998	SO:0001583	missense	130340	exon2			AATATGAAATGTA	AF393369	CCDS42827.1	2q36.3	2008-02-05			ENSG00000152056	ENSG00000152056			18971	protein-coding gene	gene with protein product		615781					Standard	NR_110905		Approved		uc002vnn.3	Q96PC3	OTTHUMG00000133165	ENST00000446015.2:c.11T>G	2.37:g.224642579A>C	ENSP00000388738:p.Phe4Cys	67	0	0		73	31	0.424658	NM_001039569	B4DQZ1|Q8WTY1|Q96DD1	Missense_Mutation	SNP	ENST00000446015.2	37		11	0.005036630036630037	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	A	22.0	4.226842	0.79576	0.002657	0.012755	ENSG00000152056	ENST00000443700;ENST00000396654;ENST00000396653;ENST00000446015;ENST00000409375;ENST00000423110	.	.	.	5.81	5.81	0.92471	Longin-like (1);AP complex, mu/sigma subunit (1);	0.000000	0.85682	D	0.000000	D	0.82747	0.5104	M	0.93594	3.435	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.996;0.997	D	0.88388	0.3006	9	0.87932	D	0	.	16.1652	0.81750	1.0:0.0:0.0:0.0	.	4;4	Q96PC3;Q96PC3-4	AP1S3_HUMAN;.	C	4	.	ENSP00000333888:F4C	F	-	2	0	AP1S3	224350823	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	8.940000	0.92958	2.230000	0.72887	0.528000	0.53228	TTC	A|0.993;C|0.007	0.007	strong		0.408	AP1S3-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000383293.1			C	224642579	A	C	224642579	3	2	25	1	0	0	0	0	1	0	0	0	738	246	9	5	469	5	AP1S3	2	224642579	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	843191	224642579	18556794	115	9024											
COL4A4	1286	hgsc.bcm.edu	37	chr2	227920747	227920747	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggaccatgtgccccaggcCgtcctgggagtccggggagg	5	5	19	12	2	0	0	0	0	0	0	2	3	2	3	6	7	1	0	6	7	0	0	rs150979437	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:227920747C>T	ENST00000396625.3	-	30	2837	c.2630G>A	c.(2629-2631)cGg>cAg	p.R877Q	COL4A4_ENST00000329662.7_Missense_Mutation_p.R877Q	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	877	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)		TGCCCCAGGCCGTCCTGGGAG	0.627													C|||	26	0.00519169	0.0	0.0	5008	,	,		15399	0.0258		0.0	False		,,,				2504	0.0				p.R877Q		Atlas-SNP	.											.	COL4A4	215	.	0			c.G2630A						PASS	.	C	GLN/ARG	4,3654		0,4,1825	36	39	39		2630	-1.9	0	2	dbSNP_134	39	27,8121		0,27,4047	no	missense	COL4A4	NM_000092.4	43	0,31,5872	TT,TC,CC		0.3314,0.1093,0.2626	benign	877/1691	227920747	31,11775	1829	4074	5903	SO:0001583	missense	1286	exon30			CCAGGCCGTCCTG		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.2630G>A	2.37:g.227920747C>T	ENSP00000379866:p.Arg877Gln	95	0	0		108	57	0.527778	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Missense_Mutation	SNP	ENST00000396625.3	37	CCDS42828.1	224	0.10256410256410256	71	0.1443089430894309	23	0.06353591160220995	44	0.07692307692307693	86	0.11345646437994723	C	3.151	-0.174203	0.06421	0.001093	0.003314	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.93307	-3.2;-3.2	5.63	-1.9	0.07665	.	.	.	.	.	T	0.02533	0.0077	N	0.16743	0.435	0.09310	N	1	B	0.13145	0.007	B	0.09377	0.004	T	0.40701	-0.9549	9	0.13470	T	0.59	.	2.2257	0.03983	0.2432:0.4338:0.1032:0.2199	.	877	P53420	CO4A4_HUMAN	Q	877	ENSP00000379866:R877Q;ENSP00000328553:R877Q	ENSP00000328553:R877Q	R	-	2	0	COL4A4	227628991	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.006000	0.13152	-0.756000	0.04703	-0.271000	0.10264	CGG	C|0.930;T|0.070	0.070	strong		0.627	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092		T	227920747	C	T	227920747	3	4	25	1	0	0	0	0	1	0	0	0	3695	652	23	1	2518	1	COL4A4	2	227920747	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	3278168	227920747	15278626	116	9025											
TM4SF20	79853	hgsc.bcm.edu	37	chr2	228228462	228228462	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acacaatttgacttcttcgcTtagagactccacacagacag	13	10	6	12	1	1	3	0	1	1	2	3	4	2	3	1	0	0	1	1	0	2	4	rs137891000	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:228228462T>G	ENST00000304568.3	-	4	705	c.668A>C	c.(667-669)aAg>aCg	p.K223T		NM_024795.3	NP_079071.2	Q53R12	T4S20_HUMAN	transmembrane 4 L six family member 20	223						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(2)|large_intestine(1)|lung(4)|stomach(2)	10		Renal(207;0.025)|all_lung(227;0.123)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;3.8e-11)|all cancers(144;2.57e-08)|Lung(261;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0115)		ACTTCTTCGCTTAGAGACTCC	0.373													T|||	27	0.00539137	0.0008	0.0072	5008	,	,		19702	0.0		0.006	False		,,,				2504	0.0153				p.K223T		Atlas-SNP	.											.	TM4SF20	24	.	0			c.A668C						PASS	.	T	THR/LYS	5,4401	9.9+/-24.2	0,5,2198	104	107	106		668	2	0	2	dbSNP_134	106	41,8559	27.9+/-77.7	0,41,4259	yes	missense	TM4SF20	NM_024795.3	78	0,46,6457	GG,GT,TT		0.4767,0.1135,0.3537	possibly-damaging	223/230	228228462	46,12960	2203	4300	6503	SO:0001583	missense	79853	exon4			CTTCGCTTAGAGA	AK026453	CCDS2466.1	2q36.3	2008-02-05			ENSG00000168955	ENSG00000168955			26230	protein-coding gene	gene with protein product		615404				12975309	Standard	NM_024795		Approved	FLJ22800, TCCE518	uc002vpb.2	Q53R12	OTTHUMG00000133187	ENST00000304568.3:c.668A>C	2.37:g.228228462T>G	ENSP00000303028:p.Lys223Thr	70	0	0		84	42	0.5	NM_024795	B2RP42|Q5U609|Q6UWS1|Q9H5X9	Missense_Mutation	SNP	ENST00000304568.3	37	CCDS2466.1	9	0.004120879120879121	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	3	0.00395778364116095	T	16.53	3.150382	0.57151	0.001135	0.004767	ENSG00000168955	ENST00000304568	T	0.30448	1.53	5.62	1.98	0.26296	.	0.601254	0.17265	N	0.180637	T	0.33177	0.0854	M	0.72118	2.19	0.09310	N	1	P	0.52577	0.954	P	0.57057	0.812	T	0.19484	-1.0304	10	0.20519	T	0.43	-6.6529	7.0811	0.25231	0.0:0.2599:0.0:0.7401	.	223	Q53R12	T4S20_HUMAN	T	223	ENSP00000303028:K223T	ENSP00000303028:K223T	K	-	2	0	TM4SF20	227936706	0.000000	0.05858	0.004000	0.12327	0.576000	0.36127	-0.112000	0.10791	0.109000	0.17891	0.533000	0.62120	AAG	T|0.995;G|0.005	0.005	strong		0.373	TM4SF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256896.2	NM_024795		G	228228462	T	G	228228462	3	3	25	1	0	0	0	0	1	0	0	0	15984	1609	56	5	25	5	TM4SF20	2	228228462	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	307715	228228462	14970911	117	9026											
SP100	6672	hgsc.bcm.edu	37	chr2	231379967	231379967	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttatgaaagagaaatgaaaaCctatatccctcctaaagggg	17	9	8	7	0	0	3	0	2	0	1	2	4	2	3	3	2	1	0	3	2	9	4			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:231379967C>T	ENST00000264052.5	+	25	2607	c.2252C>T	c.(2251-2253)aCc>aTc	p.T751I	SP100_ENST00000340126.4_Intron	NM_003113.3	NP_003104.2	P23497	SP100_HUMAN	SP100 nuclear antigen	751					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)		GAAATGAAAACCTATATCCCT	0.428																																					p.T751I		Atlas-SNP	.											.	SP100	167	.	0			c.C2252T						PASS	.						53	57	55					2																	231379967		2201	4297	6498	SO:0001583	missense	6672	exon25			TGAAAACCTATAT	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.2252C>T	2.37:g.231379967C>T	ENSP00000264052:p.Thr751Ile	81	0	0		78	36	0.461538	NM_003113	B4DDX5|B8ZZD8|E7EUA7|E9PH61|F8WFE2|O75450|Q13343|Q8TE34|Q96F70|Q96T24|Q96T95|Q9NP33|Q9UE32	Missense_Mutation	SNP	ENST00000264052.5	37	CCDS2477.1	.	.	.	.	.	.	.	.	.	.	C	7.765	0.706193	0.15239	.	.	ENSG00000067066	ENST00000264052	T	0.17854	2.25	0.158	0.158	0.14942	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	.	.	.	.	T	0.18635	0.0447	M	0.66297	2.02	0.80722	D	1	B	0.34313	0.448	B	0.38156	0.266	T	0.05402	-1.0887	9	0.54805	T	0.06	.	6.0348	0.19702	0.0:0.9995:0.0:5.0E-4	.	751	P23497	SP100_HUMAN	I	751	ENSP00000264052:T751I	ENSP00000264052:T751I	T	+	2	0	SP100	231088211	0.593000	0.26840	0.022000	0.16811	0.022000	0.10575	-0.367000	0.07553	0.202000	0.20498	0.205000	0.17691	ACC	.	.	none		0.428	SP100-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256914.2	NM_003113		T	231379967	C	T	231379967	3	4	25	1	0	0	0	0	1	0	0	0	14975	507	18	2	2350	2	SP100	2	231379967	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	3151505	231379967	11819406	118	9027											
IL17RC	84818	hgsc.bcm.edu	37	chr3	9962634	9962634	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agggggctcgaagtctggaaCagcatcccgagctgctgggg	8	6	17	10	2	1	0	0	0	1	0	3	3	2	1	1	5	4	4	1	5	2	0			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:9962634C>T	ENST00000295981.3	+	7	1034	c.816C>T	c.(814-816)aaC>aaT	p.N272N	IL17RC_ENST00000498214.1_Intron|IL17RC_ENST00000403601.3_Silent_p.N201N|IL17RC_ENST00000413608.1_Silent_p.N201N|RNU6-882P_ENST00000391025.1_RNA|IL17RC_ENST00000383812.4_Intron|IL17RC_ENST00000455057.1_Intron|IL17RC_ENST00000416074.2_Intron	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	272					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						AAGTCTGGAACAGCATCCCGA	0.612																																					p.N272N		Atlas-SNP	.											.	IL17RC	55	.	0			c.C816T						PASS	.						27	30	29					3																	9962634		2203	4300	6503	SO:0001819	synonymous_variant	84818	exon7			CTGGAACAGCATC	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.816C>T	3.37:g.9962634C>T		317	0	0		332	176	0.53012	NM_153461	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	Silent	SNP	ENST00000295981.3	37	CCDS2590.1																																																																																			.	.	none		0.612	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732		T	9962634	C	T	9962634	2	4	25	1	0	0	0	0	0	0	0	1	7650	477	17	2		2	IL17RC	3	9962634	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10		9962634	188059796	119	9028											
IL17RC	84818	hgsc.bcm.edu	37	chr3	9965582	9965582	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagccctgccctggctcaacGtgtcagcagatggtgacaac	9	7	11	14	1	2	2	2	1	0	1	2	2	2	2	2	2	5	2	2	2	2	0	rs75692599	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:9965582G>A	ENST00000295981.3	+	8	1071	c.853G>A	c.(853-855)Gtg>Atg	p.V285M	IL17RC_ENST00000498214.1_3'UTR|IL17RC_ENST00000403601.3_Missense_Mutation_p.V214M|IL17RC_ENST00000413608.1_Missense_Mutation_p.V214M|IL17RC_ENST00000383812.4_Missense_Mutation_p.V199M|IL17RC_ENST00000455057.1_Missense_Mutation_p.V199M|IL17RC_ENST00000416074.2_Missense_Mutation_p.V70M	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	285					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						CTGGCTCAACGTGTCAGCAGA	0.567													G|||	24	0.00479233	0.003	0.0058	5008	,	,		19241	0.0		0.0159	False		,,,				2504	0.0				p.V285M		Atlas-SNP	.											.	IL17RC	55	.	0			c.G853A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	10,4396	16.8+/-37.8	0,10,2193	83	76	78		640,640,595,595,640,853	2.2	0.1	3	dbSNP_131	78	202,8398	87.9+/-150.2	5,192,4103	yes	missense,missense,missense,missense,missense,missense	IL17RC	NM_001203263.1,NM_001203264.1,NM_001203265.1,NM_032732.5,NM_153460.3,NM_153461.3	21,21,21,21,21,21	5,202,6296	AA,AG,GG		2.3488,0.227,1.63	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	214/708,214/691,199/689,199/706,214/721,285/792	9965582	212,12794	2203	4300	6503	SO:0001583	missense	84818	exon8			CTCAACGTGTCAG	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.853G>A	3.37:g.9965582G>A	ENSP00000295981:p.Val285Met	117	0	0		125	54	0.432	NM_153461	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	Missense_Mutation	SNP	ENST00000295981.3	37	CCDS2590.1	15	0.006868131868131868	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	11	0.014511873350923483	G	8.788	0.929765	0.18131	0.00227	0.023488	ENSG00000163702	ENST00000383812;ENST00000438091;ENST00000295981;ENST00000436503;ENST00000403601;ENST00000416074;ENST00000455057;ENST00000413608	T;T;T;T;T;T;T;T	0.20069	2.1;2.1;2.1;2.1;2.1;2.1;2.1;2.1	5.47	2.2	0.27929	.	0.636179	0.13137	N	0.410970	T	0.17577	0.0422	M	0.64997	1.995	0.09310	N	1	D;D;P;P;D;D;D;D;D	0.76494	0.981;0.999;0.943;0.943;0.994;0.99;0.966;0.997;0.997	B;P;B;B;P;P;B;P;P	0.57283	0.428;0.817;0.246;0.246;0.557;0.557;0.428;0.654;0.704	T	0.06625	-1.0816	10	0.62326	D	0.03	-8.7325	4.2685	0.10775	0.0961:0.1562:0.5875:0.1602	.	199;70;199;214;214;214;199;285;214	Q8NAC3-4;F5H4Z2;E9PHG1;A8BWD5;E9PHJ6;A8BWC9;Q8NAC3-3;Q8NAC3;Q8NAC3-2	.;.;.;.;.;.;.;I17RC_HUMAN;.	M	199;174;285;189;214;70;199;214	ENSP00000373323:V199M;ENSP00000414609:V174M;ENSP00000295981:V285M;ENSP00000401128:V189M;ENSP00000384969:V214M;ENSP00000395315:V70M;ENSP00000407894:V199M;ENSP00000396064:V214M	ENSP00000295981:V285M	V	+	1	0	IL17RC	9940582	0.951000	0.32395	0.104000	0.21259	0.258000	0.26162	1.493000	0.35605	0.687000	0.31509	0.638000	0.83543	GTG	G|0.988;A|0.012	0.012	strong		0.567	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732		A	9965582	G	A	9965582	3	1	25	1	0	0	0	0	1	0	0	0	7650	1145	40	1	883	1	IL17RC	3	9965582	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2948	9965582	188056848	120	9029											
C3orf20	84077	hgsc.bcm.edu	37	chr3	14769980	14769980	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaatatcccaccaaaaaggaGgaggaagaatttgttcggtt	15	9	11	6	1	0	1	0	0	0	1	2	5	1	4	2	4	0	2	2	4	6	4			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:14769980G>A	ENST00000253697.3	+	12	2177	c.1725G>A	c.(1723-1725)gaG>gaA	p.E575E	C3orf20_ENST00000435614.1_Silent_p.E453E|C3orf20_ENST00000412910.1_Silent_p.E453E	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	575	Poly-Glu.					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						CCAAAAAGGAGGAGGAAGAAT	0.473																																					p.E575E		Atlas-SNP	.											.	C3orf20	109	.	0			c.G1725A						PASS	.						81	82	82					3																	14769980		2203	4300	6503	SO:0001819	synonymous_variant	84077	exon12			AAAGGAGGAGGAA	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.1725G>A	3.37:g.14769980G>A		165	0	0		150	49	0.326667	NM_032137	Q7L0U6|Q8NCP2|Q9H0I7	Silent	SNP	ENST00000253697.3	37	CCDS33706.1																																																																																			.	.	none		0.473	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137		A	14769980	G	A	14769980	2	1	25	1	0	0	0	0	0	0	0	1	2215	991	35	2		2	C3orf20	3	14769980	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	4804398	14769980	183252450	121	9030											
GADL1	339896	hgsc.bcm.edu	37	chr3	30819751	30819751	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaccaaaagcaaatattggCatattcaggctgagaattag	16	10	9	6	0	1	1	1	1	0	1	1	2	1	1	1	2	2	4	1	2	8	6	rs143542109	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:30819751C>T	ENST00000282538.5	-	14	1462	c.1312G>A	c.(1312-1314)Gcc>Acc	p.A438T	GADL1_ENST00000498387.1_5'UTR	NM_207359.2	NP_997242.2	Q6ZQY3	GADL1_HUMAN	glutamate decarboxylase-like 1	438					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						CAAATATTGGCATATTCAGGC	0.328													C|||	10	0.00199681	0.0	0.0058	5008	,	,		18837	0.0		0.003	False		,,,				2504	0.0031				p.A438T		Atlas-SNP	.											.	GADL1	91	.	0			c.G1312A						PASS	.	C	THR/ALA	7,4399	9.9+/-24.2	0,7,2196	64	69	67		1312	3.9	1	3	dbSNP_134	67	57,8543	35.3+/-89.8	1,55,4244	yes	missense	GADL1	NM_207359.2	58	1,62,6440	TT,TC,CC		0.6628,0.1589,0.4921	benign	438/522	30819751	64,12942	2203	4300	6503	SO:0001583	missense	339896	exon14			TATTGGCATATTC	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.1312G>A	3.37:g.30819751C>T	ENSP00000282538:p.Ala438Thr	235	0	0		259	117	0.451737	NM_207359		Missense_Mutation	SNP	ENST00000282538.5	37	CCDS2649.2	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	6.061	0.379542	0.11466	0.001589	0.006628	ENSG00000144644	ENST00000282538	T	0.37752	1.18	6.02	3.86	0.44501	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.241129	0.41938	N	0.000786	T	0.08179	0.0204	N	0.01742	-0.745	0.80722	D	1	B	0.02656	0.0	B	0.09377	0.004	T	0.17289	-1.0374	10	0.02654	T	1	-3.3176	9.603	0.39617	0.0:0.7967:0.0:0.2033	.	438	Q6ZQY3	GADL1_HUMAN	T	438	ENSP00000282538:A438T	ENSP00000282538:A438T	A	-	1	0	GADL1	30794755	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.300000	0.51834	1.213000	0.43380	0.655000	0.94253	GCC	C|0.995;T|0.005	0.005	strong		0.328	GADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253106.2	NM_207359		T	30819751	C	T	30819751	3	4	25	1	0	0	0	0	1	0	0	0	6193	710	25	2	261	2	GADL1	3	30819751	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	16049771	30819751	167202679	122	9031											
MLH1	4292	hgsc.bcm.edu	37	chr3	37053568	37053568	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtggacaatattcgctccAtctttggaaatgctgttagt	9	14	9	9	2	1	0	0	0	1	0	3	2	2	2	2	2	1	3	2	2	4	4	rs1799977	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:37053568A>G	ENST00000231790.2	+	8	871	c.655A>G	c.(655-657)Atc>Gtc	p.I219V	MLH1_ENST00000458205.2_5'UTR|MLH1_ENST00000455445.2_5'UTR|MLH1_ENST00000536378.1_5'UTR|MLH1_ENST00000539477.1_5'UTR|MLH1_ENST00000435176.1_Missense_Mutation_p.I121V	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	219			I -> V (common polymorphism; found in 37% of alleles; dbSNP:rs1799977). {ECO:0000269|PubMed:10375096, ECO:0000269|PubMed:10777691, ECO:0000269|PubMed:11754112, ECO:0000269|PubMed:12115348, ECO:0000269|PubMed:12200596, ECO:0000269|PubMed:12362047, ECO:0000269|PubMed:9032648, ECO:0000269|PubMed:9067757, ECO:0000269|PubMed:9087566, ECO:0000269|PubMed:9218993, ECO:0000269|PubMed:9833759, ECO:0000269|Ref.5}.		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.I219V(1)|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						TATTCGCTCCATCTTTGGAAA	0.368		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				A|||	649	0.129593	0.0386	0.1686	5008	,	,		18149	0.0258		0.325	False		,,,				2504	0.1309				p.I219V		Atlas-SNP	.	yes	Rec	yes	"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	3	3p21.3	4292	E.coli MutL homolog gene		"E, O"	MLH1,NS,carcinoma,0,1	MLH1	226	1	2	Substitution - Missense(1)|Whole gene deletion(1)	ovary(1)|prostate(1)	c.A655G	GRCh37	CM970958	MLH1	M	rs1799977	PASS	.	A	VAL/ILE,VAL/ILE,,	406,4000	199.4+/-223.0	27,352,1824	145	129	135	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	655,361,,	4.6	1	3	dbSNP_89	135	2754,5846	438.0+/-358.8	442,1870,1988	yes	missense,missense,utr-5,utr-5	MLH1	NM_000249.3,NM_001167617.1,NM_001167618.1,NM_001167619.1	29,29,,	469,2222,3812	GG,GA,AA		32.0233,9.2147,24.2965	benign,benign,,	219/757,121/659,,	37053568	3160,9846	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	CGCTCCATCTTTG	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.655A>G	3.37:g.37053568A>G	ENSP00000231790:p.Ile219Val	118	0	0		101	44	0.435644	NM_000249	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	37	CCDS2663.1	374	0.17124542124542125	28	0.056910569105691054	72	0.19889502762430938	16	0.027972027972027972	258	0.3403693931398417	A	14.01	2.408011	0.42715	0.092147	0.320233	ENSG00000076242	ENST00000231790;ENST00000436867;ENST00000537937;ENST00000383761;ENST00000435176	D;D	0.83591	-1.74;-1.74	5.76	4.61	0.57282	Ribosomal protein S5 domain 2-type fold (1);DNA mismatch repair protein, N-terminal (1);ATPase-like, ATP-binding domain (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);DNA mismatch repair protein, C-terminal (1);	0.113678	0.64402	D	0.000010	T	0.00012	0.0000	N	0.25992	0.78	0.09310	P	1.0	B;B;B	0.16603	0.018;0.018;0.018	B;B;B	0.26864	0.028;0.074;0.06	T	0.07424	-1.0773	9	0.12430	T	0.62	-17.9526	7.4844	0.27423	0.7886:0.0:0.2114:0.0	rs1799977;rs2229023;rs11541861;rs17809298;rs52803721;rs56722302;rs1799977	121;219;219	E9PCU2;Q53GX1;P40692	.;.;MLH1_HUMAN	V	219;185;185;83;121	ENSP00000231790:I219V;ENSP00000402564:I121V	ENSP00000231790:I219V	I	+	1	0	MLH1	37028572	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.446000	0.44908	2.209000	0.71365	0.533000	0.62120	ATC	A|0.799;G|0.201	0.201	strong		0.368	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249		G	37053568	A	G	37053568	3	3	25	1	0	0	0	0	1	0	0	0	9626	217	8	3	685	3	MLH1	3	37053568	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	6233817	37053568	160968862	123	9032											
GOLGA4	2803	hgsc.bcm.edu	37	chr3	37368600	37368600	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaagaaaaaatcagtgttttAcaaagaaacttaactgaaaa	22	9	6	4	0	1	3	1	1	0	2	1	4	1	3	0	0	3	1	0	0	10	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:37368600A>T	ENST00000361924.2	+	14	5597	c.5223A>T	c.(5221-5223)ttA>ttT	p.L1741F	GOLGA4_ENST00000356847.4_Missense_Mutation_p.L1763F|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1741	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						TCAGTGTTTTACAAAGAAACT	0.388																																					p.L1763F		Atlas-SNP	.											.	GOLGA4	173	.	0			c.A5289T						PASS	.						103	109	107					3																	37368600		2203	4299	6502	SO:0001583	missense	2803	exon15			TGTTTTACAAAGA	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.5223A>T	3.37:g.37368600A>T	ENSP00000354486:p.Leu1741Phe	146	0	0		126	50	0.396825	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	37	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	A	15.09	2.729120	0.48833	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000437131	T;T;T	0.34472	1.36;1.36;1.37	4.39	-3.04	0.05412	.	0.000000	0.27636	N	0.018486	T	0.48642	0.1511	M	0.76002	2.32	0.18873	N	0.999985	D;D;D;D	0.89917	0.96;0.96;0.96;1.0	P;P;P;D	0.85130	0.731;0.684;0.684;0.997	T	0.35919	-0.9769	10	0.48119	T	0.1	.	5.1769	0.15139	0.4641:0.0:0.3958:0.1401	.	1741;1741;1763;1741	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	F	1741;1763;1612	ENSP00000354486:L1741F;ENSP00000349305:L1763F;ENSP00000405842:L1612F	ENSP00000349305:L1763F	L	+	3	2	GOLGA4	37343604	0.979000	0.34478	0.002000	0.10522	0.888000	0.51559	0.310000	0.19356	-0.410000	0.07542	-0.379000	0.06801	TTA	.	.	none		0.388	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		T	37368600	A	T	37368600	3	4	25	1	0	0	0	0	1	0	0	0	6563	388	14	5	5347	5	GOLGA4	3	37368600	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	315032	37368600	160653830	124	9033											
MYRIP	25924	hgsc.bcm.edu	37	chr3	40231810	40231810	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagttggccagcagggagacCtcggacagcagcgagccgga	10	3	16	12	3	0	1	0	0	0	1	1	5	0	3	3	4	4	3	3	4	0	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:40231810C>T	ENST00000302541.6	+	10	1863	c.1521C>T	c.(1519-1521)acC>acT	p.T507T	MYRIP_ENST00000539167.1_Silent_p.T320T|MYRIP_ENST00000444716.1_Silent_p.T507T|MYRIP_ENST00000396217.3_Silent_p.T418T|MYRIP_ENST00000425621.1_Silent_p.T507T|MYRIP_ENST00000459828.1_3'UTR	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	507	Actin-binding.|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)		GCAGGGAGACCTCGGACAGCA	0.642																																					p.T507T		Atlas-SNP	.											.	MYRIP	98	.	0			c.C1521T						PASS	.						60	67	65					3																	40231810		2203	4300	6503	SO:0001819	synonymous_variant	25924	exon10			GGAGACCTCGGAC	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.1521C>T	3.37:g.40231810C>T		146	0	0		186	86	0.462366	NM_015460	B3KWM3|B3KWW4|B7Z2H1|B7Z9V3|G3XAI8|Q32M41|Q32M42|Q569F7|Q8IUF5|Q9Y3V4	Silent	SNP	ENST00000302541.6	37	CCDS2689.1																																																																																			.	.	none		0.642	MYRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254181.2	NM_015460		T	40231810	C	T	40231810	2	4	25	1	0	0	0	0	0	0	0	1	10109	668	24	2		2	MYRIP	3	40231810	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2863210	40231810	157790620	125	9034											
ULK4	54986	hgsc.bcm.edu	37	chr3	41877410	41877410	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gttggtaaaaggcactgtttTaatttgctgttcctgaagtt	9	17	10	5	0	0	1	0	1	0	0	1	1	1	1	1	2	1	7	1	2	4	7	rs192218045	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:41877410T>G	ENST00000301831.4	-	18	2172	c.1710A>C	c.(1708-1710)ttA>ttC	p.L570F		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	570				AIVLLTELIRENFRNSKLKQCLLPTLGE -> TTSSIGIGI LNCLVQHSTPVPRQCLVYV (in Ref. 3; AAH14794). {ECO:0000305}.	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)		GGCACTGTTTTAATTTGCTGT	0.363													T|||	5	0.000998403	0.0008	0.0014	5008	,	,		14639	0.0		0.003	False		,,,				2504	0.0				p.L570F		Atlas-SNP	.											.	ULK4	150	.	0			c.A1710C						PASS	.	T	PHE/LEU	2,3672		0,2,1835	136	136	136		1710	1.3	1	3		136	29,8139		0,29,4055	yes	missense	ULK4	NM_017886.2	22	0,31,5890	GG,GT,TT		0.355,0.0544,0.2618	probably-damaging	570/1276	41877410	31,11811	1837	4084	5921	SO:0001583	missense	54986	exon18			CTGTTTTAATTTG	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.1710A>C	3.37:g.41877410T>G	ENSP00000301831:p.Leu570Phe	215	0	0		255	118	0.462745	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	4	0.0018315018315018315	1	0.0020325203252032522	0	0.0	0	0.0	3	0.00395778364116095	T	19.99	3.928909	0.73327	5.44E-4	0.00355	ENSG00000168038	ENST00000301831	T	0.67171	-0.25	5.37	1.28	0.21552	Armadillo-like helical (1);Armadillo-type fold (2);	0.091392	0.45361	U	0.000380	T	0.71762	0.3378	L	0.57536	1.79	0.80722	D	1	D;D	0.65815	0.991;0.995	P;P	0.61800	0.894;0.894	T	0.70063	-0.4975	10	0.62326	D	0.03	.	8.263	0.31797	0.0:0.4472:0.0:0.5528	.	570;570	B4E2M4;Q96C45	.;ULK4_HUMAN	F	570	ENSP00000301831:L570F	ENSP00000301831:L570F	L	-	3	2	ULK4	41852414	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.467000	0.22035	0.316000	0.23135	0.528000	0.53228	TTA	T|0.997;G|0.003	0.003	strong		0.363	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989		G	41877410	T	G	41877410	3	3	25	1	0	0	0	0	1	0	0	0	16993	1751	61	5	2197	5	ULK4	3	41877410	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	1645600	41877410	156145020	126	9035											
NKTR	4820	hgsc.bcm.edu	37	chr3	42662976	42662976	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttttatcaatggcaaatcgAgggaaacataccaatggttc	14	11	8	8	1	1	0	1	0	0	0	3	2	1	1	1	3	2	2	1	3	6	4	rs35419602	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:42662976A>C	ENST00000232978.8	+	6	530	c.342A>C	c.(340-342)cgA>cgC	p.R114R	RP4-613B23.1_ENST00000438017.1_RNA|RP4-613B23.1_ENST00000445452.1_RNA	NM_005385.3	NP_005376.2	P30414	NKTR_HUMAN	natural killer cell triggering receptor	114	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				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)		TGGCAAATCGAGGGAAACATA	0.358													A|||	35	0.00698882	0.0083	0.0072	5008	,	,		15576	0.0		0.0179	False		,,,				2504	0.001				p.R114R		Atlas-SNP	.											.	NKTR	116	.	0			c.A342C						PASS	.	A		32,4374	39.2+/-71.8	0,32,2171	76	73	74		342	-1.8	1	3	dbSNP_126	74	128,8470	65.6+/-127.9	1,126,4172	no	coding-synonymous	NKTR	NM_005385.3		1,158,6343	CC,CA,AA		1.4887,0.7263,1.2304		114/1463	42662976	160,12844	2203	4299	6502	SO:0001819	synonymous_variant	4820	exon6			AAATCGAGGGAAA		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.342A>C	3.37:g.42662976A>C		109	0	0		79	30	0.379747	NM_005385		Silent	SNP	ENST00000232978.8	37	CCDS2702.1																																																																																			A|0.988;C|0.012	0.012	strong		0.358	NKTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256642.2	NM_005385		C	42662976	A	C	42662976	2	2	25	1	0	0	0	0	0	0	0	1	10457	291	11	5		5	NKTR	3	42662976	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	785566	42662976	155359454	127	9036											
C3orf39	84892	hgsc.bcm.edu	37	chr3	43121743	43121743	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttctctggcatcatgttcCgccaggctacatactggagg	7	12	11	11	1	2	0	1	0	1	0	4	1	3	1	2	4	2	4	2	4	2	4	rs199612856	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:43121743C>T	ENST00000344697.2	-	2	1526	c.1181G>A	c.(1180-1182)cGg>cAg	p.R394Q	POMGNT2_ENST00000441964.1_Missense_Mutation_p.R394Q	NM_032806.5	NP_116195.2	Q8NAT1	PMGT2_HUMAN	protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)	394					protein O-linked glycosylation (GO:0006493)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein O-GlcNAc transferase activity (GO:0097363)										CATCATGTTCCGCCAGGCTAC	0.587													C|||	5	0.000998403	0.0	0.0	5008	,	,		22992	0.002		0.0	False		,,,				2504	0.0031				p.R394Q		Atlas-SNP	.											.	.	.	.	0			c.G1181A						PASS	.						80	71	74					3																	43121743		2203	4300	6503	SO:0001583	missense	84892	exon2			ATGTTCCGCCAGG	AK092147	CCDS2709.1	3p22.1	2014-07-15	2013-08-22	2013-08-22	ENSG00000144647	ENSG00000144647			25902	protein-coding gene	gene with protein product		614828	"chromosome 3 open reading frame 39", "glycosyltransferase-like domain containing 2"	C3orf39, GTDC2		12477932	Standard	NM_032806		Approved	FLJ14566, AGO61	uc003cmr.2	Q8NAT1	OTTHUMG00000133038	ENST00000344697.2:c.1181G>A	3.37:g.43121743C>T	ENSP00000344125:p.Arg394Gln	184	0	0		185	92	0.497297	NM_032806	B3KWC3|Q96SY3	Missense_Mutation	SNP	ENST00000344697.2	37	CCDS2709.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	11.87	1.767376	0.31320	.	.	ENSG00000144647	ENST00000441964;ENST00000344697	T;T	0.77229	-1.08;-1.08	5.53	1.22	0.21188	.	0.363726	0.31233	N	0.008011	T	0.57946	0.2088	N	0.17278	0.47	0.37391	D	0.912468	B	0.09022	0.002	B	0.10450	0.005	T	0.48127	-0.9062	10	0.30078	T	0.28	-25.7255	7.9623	0.30079	0.0:0.4895:0.0:0.5105	.	394	Q8NAT1	AGO61_HUMAN	Q	394	ENSP00000408992:R394Q;ENSP00000344125:R394Q	ENSP00000344125:R394Q	R	-	2	0	C3orf39	43096747	0.970000	0.33590	0.988000	0.46212	0.986000	0.74619	0.528000	0.23002	0.318000	0.23185	0.650000	0.86243	CGG	C|1.000;T|0.000	0.000	strong		0.587	POMGNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256643.1	NM_032806		T	43121743	C	T	43121743	3	4	25	1	0	0	0	0	1	0	0	0	2231	652	23	1	565	1	C3orf39	3	43121743	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	458767	43121743	154900687	128	9037											
LTF	4057	hgsc.bcm.edu	37	chr3	46490456	46490456	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacttgcgcagctcctgctcGcccaccgcacaccacacgac	8	5	7	21	4	0	0	0	0	0	0	2	1	1	0	4	0	3	4	4	0	0	1	rs61737000	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:46490456G>A	ENST00000231751.4	-	9	1405	c.1110C>T	c.(1108-1110)ggC>ggT	p.G370G	LTF_ENST00000426532.2_Silent_p.G326G|LTF_ENST00000417439.1_Silent_p.G370G	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	370	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)		GCTCCTGCTCGCCCACCGCAC	0.667													G|||	300	0.0599042	0.2057	0.0187	5008	,	,		15791	0.001		0.003	False		,,,				2504	0.0112				p.G370G		Atlas-SNP	.											.	LTF	98	.	0			c.C1110T						PASS	.	G	,	837,3569	321.5+/-297.2	71,695,1437	42	37	39		978,1110	3	0.6	3	dbSNP_129	39	49,8543	30.1+/-81.4	0,49,4247	no	coding-synonymous,coding-synonymous	LTF	NM_001199149.1,NM_002343.3	,	71,744,5684	AA,AG,GG		0.5703,18.9968,6.8164	,	326/667,370/711	46490456	886,12112	2203	4296	6499	SO:0001819	synonymous_variant	4057	exon9			CTGCTCGCCCACC		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.1110C>T	3.37:g.46490456G>A		136	0	0		106	54	0.509434	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Silent	SNP	ENST00000231751.4	37	CCDS33747.1																																																																																			G|0.929;A|0.071	0.071	strong		0.667	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343		A	46490456	G	A	46490456	2	1	25	1	0	0	0	0	0	0	0	1	9088	1074	38	1		1	LTF	3	46490456	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	3368713	46490456	151531974	129	9038											
USP19	10869	hgsc.bcm.edu	37	chr3	49146612	49146612	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctccagctcctgccaaatccGggaagcctagggtatgtgga	9	8	12	12	1	0	0	0	0	0	0	3	2	3	2	5	3	3	2	5	3	4	2	rs79965514		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:49146612G>A	ENST00000398888.2	-	26	4054	c.3736C>T	c.(3736-3738)Cgg>Tgg	p.R1246W	USP19_ENST00000453664.1_Intron|USP19_ENST00000398896.1_Intron|USP19_ENST00000417901.1_Intron|USP19_ENST00000398892.3_Missense_Mutation_p.R1286W|USP19_ENST00000434032.2_Missense_Mutation_p.R1347W|USP19_ENST00000398898.2_Intron	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	1246					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)		TGCCAAATCCGGGAAGCCTAG	0.682													G|||	1	0.000199681	0.0	0.0	5008	,	,		17126	0.001		0.0	False		,,,				2504	0.0				p.R1347W		Atlas-SNP	.											.	USP19	158	.	0			c.C4039T						PASS	.						7	9	8					3																	49146612		1839	3927	5766	SO:0001583	missense	10869	exon27			AAATCCGGGAAGC	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.3736C>T	3.37:g.49146612G>A	ENSP00000381863:p.Arg1246Trp	124	0	0		103	30	0.291262	NM_001199160	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Missense_Mutation	SNP	ENST00000398888.2	37	CCDS43090.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	19.42	3.823416	0.71143	.	.	ENSG00000172046	ENST00000398892;ENST00000398888;ENST00000434032	T;T;T	0.20463	2.07;2.17;2.17	5.3	4.43	0.53597	.	0.730358	0.12840	N	0.434921	T	0.16557	0.0398	N	0.19112	0.55	0.41423	D	0.987818	B;B;B	0.11235	0.004;0.004;0.001	B;B;B	0.08055	0.002;0.003;0.0	T	0.04078	-1.0979	10	0.59425	D	0.04	-2.2965	13.9763	0.64275	0.0724:0.0:0.9276:0.0	.	1347;1246;1286	E9PEG8;O94966;B5MEG5	.;UBP19_HUMAN;.	W	1286;1246;1347	ENSP00000381867:R1286W;ENSP00000381863:R1246W;ENSP00000401197:R1347W	ENSP00000381863:R1246W	R	-	1	2	USP19	49121616	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.009000	0.88606	1.473000	0.48159	0.655000	0.94253	CGG	G|0.999;A|0.001	0.001	strong		0.682	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677		A	49146612	G	A	49146612	3	1	25	1	0	0	0	0	1	0	0	0	17065	1115	39	1	224	1	USP19	3	49146612	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2656156	49146612	148875818	130	9039											
LAMB2	3913	hgsc.bcm.edu	37	chr3	49159152	49159152	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcacgaccctgggcactgcCtgccgtttcttctgctgtag	4	11	12	14	2	2	0	0	0	2	0	2	1	2	0	3	2	3	5	3	2	1	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:49159152C>A	ENST00000418109.1	-	31	5229	c.5065G>T	c.(5065-5067)Ggc>Tgc	p.G1689C	USP19_ENST00000453664.1_5'Flank|USP19_ENST00000398888.2_5'Flank|USP19_ENST00000488993.1_5'Flank|LAMB2_ENST00000305544.4_Missense_Mutation_p.G1689C|USP19_ENST00000417901.1_5'Flank|USP19_ENST00000398892.3_5'Flank|USP19_ENST00000434032.2_5'Flank|USP19_ENST00000398898.2_5'Flank	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	1689	Domain I.				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)		TGGGCACTGCCTGCCGTTTCT	0.597																																					p.G1689C		Atlas-SNP	.											.	LAMB2	156	.	0			c.G5065T						PASS	.						71	74	73					3																	49159152		2203	4300	6503	SO:0001583	missense	3913	exon30			CACTGCCTGCCGT		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.5065G>T	3.37:g.49159152C>A	ENSP00000388325:p.Gly1689Cys	77	0	0		103	36	0.349515	NM_002292	Q16321	Missense_Mutation	SNP	ENST00000418109.1	37	CCDS2789.1	.	.	.	.	.	.	.	.	.	.	C	17.39	3.378244	0.61735	.	.	ENSG00000172037	ENST00000418109;ENST00000305544	T;T	0.34859	1.34;1.34	5.79	1.37	0.22104	.	0.448886	0.23889	N	0.043563	T	0.36413	0.0966	L	0.40543	1.245	0.37970	D	0.93324	D	0.69078	0.997	P	0.55667	0.781	T	0.29305	-1.0016	10	0.59425	D	0.04	.	5.0677	0.14591	0.0:0.4547:0.1499:0.3954	.	1689	P55268	LAMB2_HUMAN	C	1689	ENSP00000388325:G1689C;ENSP00000307156:G1689C	ENSP00000307156:G1689C	G	-	1	0	LAMB2	49134156	0.288000	0.24324	0.990000	0.47175	0.978000	0.69477	0.697000	0.25556	0.342000	0.23796	0.655000	0.94253	GGC	.	.	none		0.597	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		A	49159152	C	A	49159152	3	1	25	1	0	0	0	0	1	0	0	0	8620	681	24	4	343	4	LAMB2	3	49159152	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	12540	49159152	148863278	131	9040											
LAMB2	3913	hgsc.bcm.edu	37	chr3	49161004	49161004	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcattgaagttctcatcttgCacatctgtcaggtctgcctc	7	14	8	12	0	5	1	2	1	4	0	7	1	5	1	1	1	2	3	1	1	1	3	rs34967349	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:49161004C>A	ENST00000418109.1	-	26	4022	c.3858G>T	c.(3856-3858)gtG>gtT	p.V1286V	USP19_ENST00000453664.1_5'Flank|USP19_ENST00000398888.2_5'Flank|LAMB2_ENST00000464891.1_5'Flank|USP19_ENST00000488993.1_5'Flank|LAMB2_ENST00000305544.4_Silent_p.V1286V|USP19_ENST00000417901.1_5'Flank|USP19_ENST00000398892.3_5'Flank|USP19_ENST00000434032.2_5'Flank	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	1286	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)		TCTCATCTTGCACATCTGTCA	0.537													C|||	12	0.00239617	0.0	0.0058	5008	,	,		24506	0.0		0.008	False		,,,				2504	0.0				p.V1286V		Atlas-SNP	.											.	LAMB2	156	.	0			c.G3858T						PASS	.	C		7,4399	14.3+/-33.2	0,7,2196	133	122	126		3858	0.8	1	3	dbSNP_126	126	50,8550	32.8+/-85.7	0,50,4250	no	coding-synonymous	LAMB2	NM_002292.3		0,57,6446	AA,AC,CC		0.5814,0.1589,0.4383		1286/1799	49161004	57,12949	2203	4300	6503	SO:0001819	synonymous_variant	3913	exon25			ATCTTGCACATCT		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.3858G>T	3.37:g.49161004C>A		134	0	0		143	70	0.48951	NM_002292	Q16321	Silent	SNP	ENST00000418109.1	37	CCDS2789.1																																																																																			C|0.996;A|0.004	0.004	strong		0.537	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		A	49161004	C	A	49161004	2	1	25	1	0	0	0	0	0	0	0	1	8620	697	25	4		4	LAMB2	3	49161004	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1852	49161004	148861426	132	9041											
LAMB2	3913	hgsc.bcm.edu	37	chr3	49166460	49166460	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggaggccccacacctgccctCgggtgtcctcagcctcccaa	6	6	10	19	1	1	0	1	0	0	0	4	1	3	1	7	3	2	0	7	3	1	0	rs61729152	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:49166460C>T	ENST00000418109.1	-	14	1888	c.1724G>A	c.(1723-1725)cGa>cAa	p.R575Q	LAMB2_ENST00000305544.4_Missense_Mutation_p.R575Q	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	575	Laminin IV type B. {ECO:0000255|PROSITE- ProRule:PRU00462}.				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)		CACCTGCCCTCGGGTGTCCTC	0.622													C|||	32	0.00638978	0.0	0.013	5008	,	,		18383	0.0		0.0209	False		,,,				2504	0.002				p.R575Q		Atlas-SNP	.											LAMB2,NS,carcinoma,-1,1	LAMB2	156	1	0			c.G1724A						scavenged	.	C	GLN/ARG	17,4389	26.2+/-53.5	0,17,2186	52	55	54		1724	-1.9	0	3	dbSNP_129	54	139,8461	63.5+/-125.6	2,135,4163	yes	missense	LAMB2	NM_002292.3	43	2,152,6349	TT,TC,CC		1.6163,0.3858,1.1994	benign	575/1799	49166460	156,12850	2203	4300	6503	SO:0001583	missense	3913	exon13			TGCCCTCGGGTGT		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.1724G>A	3.37:g.49166460C>T	ENSP00000388325:p.Arg575Gln	33	1	0.030303		34	14	0.411765	NM_002292	Q16321	Missense_Mutation	SNP	ENST00000418109.1	37	CCDS2789.1	22	0.010073260073260074	0	0.0	7	0.019337016574585635	0	0.0	15	0.01978891820580475	C	3.211	-0.161592	0.06502	0.003858	0.016163	ENSG00000172037	ENST00000418109;ENST00000305544	T;T	0.34275	1.37;1.37	5.18	-1.88	0.07713	Laminin IV (1);	0.609454	0.16134	N	0.228066	T	0.07052	0.0179	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.29027	-1.0025	10	0.10377	T	0.69	.	9.9192	0.41453	0.0:0.5495:0.0:0.4505	.	575	P55268	LAMB2_HUMAN	Q	575	ENSP00000388325:R575Q;ENSP00000307156:R575Q	ENSP00000307156:R575Q	R	-	2	0	LAMB2	49141464	0.000000	0.05858	0.014000	0.15608	0.012000	0.07955	-1.165000	0.03132	-0.448000	0.07128	-0.423000	0.05987	CGA	C|0.991;T|0.009	0.009	strong		0.622	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292		T	49166460	C	T	49166460	3	4	25	1	0	0	0	0	1	0	0	0	8620	884	31	1	3752	1	LAMB2	3	49166460	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	5456	49166460	148855970	133	9042											
AMT	275	hgsc.bcm.edu	37	chr3	49459683	49459683	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccaggtggaagtcatagaGcggtgtcctgcggagcacct	8	7	16	10	2	1	1	1	0	0	1	2	3	2	3	3	5	3	1	3	5	2	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:49459683G>A	ENST00000273588.3	-	2	414	c.112C>T	c.(112-114)Ctc>Ttc	p.L38F	AMT_ENST00000458307.2_Missense_Mutation_p.L38F|AMT_ENST00000538581.1_Intron|AMT_ENST00000395338.2_Missense_Mutation_p.L38F|NICN1-AS1_ENST00000424915.1_RNA|AMT_ENST00000546031.1_Intron|NICN1_ENST00000422593.1_5'Flank|AMT_ENST00000476226.1_5'UTR	NM_000481.3	NP_000472.2	P48728	GCST_HUMAN	aminomethyltransferase	38					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|transaminase activity (GO:0008483)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)	Tetrahydrofolic acid(DB00116)	AAGTCATAGAGCGGTGTCCTG	0.657																																					p.L38F		Atlas-SNP	.											.	AMT	22	.	0			c.C112T						PASS	.						101	105	103					3																	49459683		2203	4300	6503	SO:0001583	missense	275	exon2			CATAGAGCGGTGT	D13811	CCDS2797.1, CCDS54583.1, CCDS54584.1, CCDS54585.1	3p21.2-p21.1	2014-09-17	2006-05-22		ENSG00000145020	ENSG00000145020	2.1.2.10		473	protein-coding gene	gene with protein product	"glycine cleavage system protein T"	238310	"aminomethyltransferase (glycine cleavage system protein T)"			1993704, 8188235	Standard	NM_000481		Approved	GCST, NKH	uc003cww.3	P48728	OTTHUMG00000156847	ENST00000273588.3:c.112C>T	3.37:g.49459683G>A	ENSP00000273588:p.Leu38Phe	111	0	0		95	23	0.242105	NM_001164712	A8K3I5|B4DE61|B4DJQ0|E9PBG1|Q96IG6	Missense_Mutation	SNP	ENST00000273588.3	37	CCDS2797.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.53|15.53	2.861431|2.861431	0.51482|0.51482	.|.	.|.	ENSG00000145020|ENSG00000145020	ENST00000427987|ENST00000395338;ENST00000458307;ENST00000273588	.|D;D;D	.|0.86097	.|-2.07;-2.07;-2.07	5.22|5.22	4.33|4.33	0.51752|0.51752	.|.	.|0.148983	.|0.46145	.|D	.|0.000309	D|D	0.90089|0.90089	0.6904|0.6904	L|L	0.56769|0.56769	1.78|1.78	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	0.90373|0.90373	0.4382|0.4382	5|10	.|0.59425	.|D	.|0.04	-14.4114|-14.4114	13.1666|13.1666	0.59575|0.59575	0.0:0.0:0.8386:0.1614|0.0:0.0:0.8386:0.1614	.|.	.|38;38;38	.|B4DJQ0;E9PBG1;P48728	.|.;.;GCST_HUMAN	V|F	35|38	.|ENSP00000378747:L38F;ENSP00000415619:L38F;ENSP00000273588:L38F	.|ENSP00000273588:L38F	A|L	-|-	2|1	0|0	AMT|AMT	49434687|49434687	1.000000|1.000000	0.71417|0.71417	0.034000|0.034000	0.17996|0.17996	0.003000|0.003000	0.03518|0.03518	9.009000|9.009000	0.93606|0.93606	1.299000|1.299000	0.44798|0.44798	-0.181000|-0.181000	0.13052|0.13052	GCT|CTC	.	.	none		0.657	AMT-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346216.2	NM_000481		A	49459683	G	A	49459683	3	1	25	1	0	0	0	0	1	0	0	0	589	971	34	2	1159	2	AMT	3	49459683	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	293223	49459683	148562747	134	9043											
GNAI2	2771	hgsc.bcm.edu	37	chr3	50294456	50294458	+	In_Frame_Del	DEL	AAG	AAG	-																															ccatcatcctcttcctcaacAagaaggacctgtttgaggag																										TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:50294456_50294458delAAG	ENST00000313601.6	+	7	1195_1197	c.811_813delAAG	c.(811-813)aagdel	p.K272del	GNAI2_ENST00000266027.5_In_Frame_Del_p.K256del|GNAI2_ENST00000491100.1_3'UTR|GNAI2_ENST00000440628.1_In_Frame_Del_p.K220del|GNAI2_ENST00000536647.1_In_Frame_Del_p.K191del|GNAI2_ENST00000422163.1_In_Frame_Del_p.K256del|GNAI2_ENST00000451956.1_In_Frame_Del_p.K235del	NM_002070.2	NP_002061.1	P04899	GNAI2_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 2	272					activation of MAPKK activity (GO:0000186)|adenosine receptor signaling pathway (GO:0001973)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of synaptic transmission (GO:0050805)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|regulation of calcium ion transport (GO:0051924)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|membrane (GO:0016020)|membrane raft (GO:0045121)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	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)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|liver(2)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(193;0.000288)|KIRC - Kidney renal clear cell carcinoma(197;0.00571)|Kidney(197;0.00651)		CTTCCTCAACAAGAAGGACCTGT	0.517											OREG0015582	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.270_271del		Atlas-Indel	.											.	GNAI2	42	.	0			c.810_812del						PASS	.																																			SO:0001651	inframe_deletion	2771	exon7			.	X04828	CCDS2813.1, CCDS54587.1, CCDS63642.1, CCDS63644.1	3p21.31	2010-08-27			ENSG00000114353	ENSG00000114353			4385	protein-coding gene	gene with protein product	"GTP-binding regulatory protein Gi alpha-2 chain"	139360		GNAI2B		3100330, 1733849	Standard	NM_001166425		Approved	GIP	uc003cyq.1	P04899	OTTHUMG00000156940	ENST00000313601.6:c.811_813delAAG	3.37:g.50294459_50294461delAAG	ENSP00000312999:p.Lys272del	160	0	0	968	174	18	0.103448	NM_002070	B3KTZ0|B4DYA0|B4E2X5|Q6B6N3|Q8IZ71	In_Frame_Del	DEL	ENST00000313601.6	37	CCDS2813.1																																																																																			.	.	none		0.517	GNAI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346688.1	NM_002070		-	50294458	AAG	-	50294456	7	5	25	1	0	1	0	1	0	0	0	0	6513	131	5	0	848	0	GNAI2	3	50294456	In_Frame_Del	DEL	AAG	TCGA-G8-6906-01A-11D-2210-10	834773	50294456	147727974	135	9044											
NAT6	24142	hgsc.bcm.edu	37	chr3	50334568	50334568	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gcttcaagtgtggggtggggGcttagcagcatcaggcagag	8	8	18	7	0	2	1	2	0	0	1	2	1	2	1	0	5	2	5	0	5	2	2	rs199554290		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:50334568G>A	ENST00000443842.1	-	2	1134	c.327C>T	c.(325-327)agC>agT	p.S109S	NAT6_ENST00000354862.4_Silent_p.S131S|HYAL3_ENST00000359051.3_Intron|NAT6_ENST00000417393.1_Silent_p.S109S|HYAL3_ENST00000450982.1_Intron|HYAL3_ENST00000513170.1_Intron|HYAL3_ENST00000415204.1_Intron|HYAL3_ENST00000336307.1_Intron|NAT6_ENST00000443094.2_Silent_p.S109S			Q93015	NAT6_HUMAN	N-acetyltransferase 6 (GCN5-related)	109	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)		TGGGGTGGGGGCTTAGCAGCA	0.647																																					p.S131S		Atlas-SNP	.											.	NAT6	14	.	0			c.C393T						PASS	.	G	,,,,,,,	3,4157		0,3,2077	20	25	23		327,327,,,,,,393	1.6	0.9	3		23	20,8362		0,20,4171	no	coding-synonymous,coding-synonymous,intron,intron,intron,intron,intron,coding-synonymous	HYAL3,NAT6	NM_001200016.1,NM_001200018.1,NM_001200029.1,NM_001200030.1,NM_001200031.1,NM_001200032.1,NM_003549.3,NM_012191.3	,,,,,,,	0,23,6248	AA,AG,GG		0.2386,0.0721,0.1834	,,,,,,,	109/287,109/287,,,,,,131/309	50334568	23,12519	2080	4191	6271	SO:0001819	synonymous_variant	24142	exon2			GTGGGGGCTTAGC	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.327C>T	3.37:g.50334568G>A		91	0	0		113	66	0.584071	NM_012191	Q93014	Silent	SNP	ENST00000443842.1	37	CCDS56258.1																																																																																			G|0.997;A|0.003	0.003	weak		0.647	NAT6-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346681.1	NM_012191		A	50334568	G	A	50334568	2	1	25	1	0	0	0	0	0	0	0	1	10187	1194	42	2		2	NAT6	3	50334568	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	40112	50334568	147687862	136	9045											
NAT6	24142	hgsc.bcm.edu	37	chr3	50334592	50334592	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	agcagcatcaggcagaggggGaaggcatctgaggactggcc	11	4	17	9	0	2	2	1	1	1	1	2	4	2	4	1	6	2	4	1	6	1	0	rs374560438		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:50334592G>A	ENST00000443842.1	-	2	1110	c.303C>T	c.(301-303)ttC>ttT	p.F101F	NAT6_ENST00000354862.4_Silent_p.F123F|HYAL3_ENST00000359051.3_Intron|NAT6_ENST00000417393.1_Silent_p.F101F|HYAL3_ENST00000450982.1_Intron|HYAL3_ENST00000513170.1_Intron|HYAL3_ENST00000415204.1_Intron|HYAL3_ENST00000336307.1_Intron|NAT6_ENST00000443094.2_Silent_p.F101F			Q93015	NAT6_HUMAN	N-acetyltransferase 6 (GCN5-related)	101	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)		GGCAGAGGGGGAAGGCATCTG	0.652																																					p.F123F		Atlas-SNP	.											.	NAT6	14	.	0			c.C369T						PASS	.	G	,,,,,,,	2,4212		0,2,2105	27	34	32		303,303,,,,,,369	4.6	1	3		32	17,8403		0,17,4193	no	coding-synonymous,coding-synonymous,intron,intron,intron,intron,intron,coding-synonymous	HYAL3,NAT6	NM_001200016.1,NM_001200018.1,NM_001200029.1,NM_001200030.1,NM_001200031.1,NM_001200032.1,NM_003549.3,NM_012191.3	,,,,,,,	0,19,6298	AA,AG,GG		0.2019,0.0475,0.1504	,,,,,,,	101/287,101/287,,,,,,123/309	50334592	19,12615	2107	4210	6317	SO:0001819	synonymous_variant	24142	exon2			GAGGGGGAAGGCA	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.303C>T	3.37:g.50334592G>A		112	0	0		131	74	0.564885	NM_012191	Q93014	Silent	SNP	ENST00000443842.1	37	CCDS56258.1																																																																																			.	.	weak		0.652	NAT6-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346681.1	NM_012191		A	50334592	G	A	50334592	2	1	25	1	0	0	0	0	0	0	0	1	10187	1165	41	2		2	NAT6	3	50334592	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	24	50334592	147687838	137	9046											
RFT1	91869	hgsc.bcm.edu	37	chr3	53159970	53159970	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctttgacaggaagcgaagaAtaaatgcattcaagacaaag	18	7	9	7	1	1	3	1	1	0	2	1	5	1	4	1	1	2	1	1	1	7	3	rs146354877	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:53159970A>G	ENST00000296292.3	-	2	165	c.104T>C	c.(103-105)aTt>aCt	p.I35T	RFT1_ENST00000394738.3_Missense_Mutation_p.I35T	NM_052859.3	NP_443091.1	Q96AA3	RFT1_HUMAN	RFT1 homolog (S. cerevisiae)	35					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)		GAAGCGAAGAATAAATGCATT	0.413																																					p.I35T		Atlas-SNP	.											.	RFT1	34	.	0			c.T104C						PASS	.	A	THR/ILE	1,4405	2.1+/-5.4	0,1,2202	114	92	99		104	3.7	1	3	dbSNP_134	99	0,8600		0,0,4300	yes	missense	RFT1	NM_052859.3	89	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	benign	35/542	53159970	1,13005	2203	4300	6503	SO:0001583	missense	91869	exon2			CGAAGAATAAATG	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.104T>C	3.37:g.53159970A>G	ENSP00000296292:p.Ile35Thr	143	0	0		92	35	0.380435	NM_052859	Q96J03	Missense_Mutation	SNP	ENST00000296292.3	37	CCDS2869.1	.	.	.	.	.	.	.	.	.	.	A	12.89	2.073820	0.36566	2.27E-4	0.0	ENSG00000163933	ENST00000296292;ENST00000394738;ENST00000467048	D;D;D	0.86497	-2.13;-2.13;-2.13	6.02	3.71	0.42584	.	0.103749	0.64402	D	0.000005	T	0.73799	0.3633	N	0.16790	0.44	0.33518	D	0.591968	B;B	0.17465	0.022;0.003	B;B	0.17433	0.018;0.01	T	0.72178	-0.4369	10	0.35671	T	0.21	.	6.0431	0.19746	0.7465:0.0:0.2535:0.0	.	35;35	B5MDE0;Q96AA3	.;RFT1_HUMAN	T	35	ENSP00000296292:I35T;ENSP00000378223:I35T;ENSP00000420325:I35T	ENSP00000296292:I35T	I	-	2	0	RFT1	53135010	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	4.784000	0.62411	2.304000	0.77564	0.528000	0.53228	ATT	A|0.999;G|0.001	0.001	strong		0.413	RFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157136.2	NM_052859		G	53159970	A	G	53159970	3	3	25	1	0	0	0	0	1	0	0	0	13272	101	4	3	1569	3	RFT1	3	53159970	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	2825378	53159970	144862460	138	9047											
ERC2	26059	hgsc.bcm.edu	37	chr3	55922561	55922561	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtctggtcttctccagtgcaTtcatcagttcctctatctga	6	16	7	12	0	7	1	2	1	5	0	9	1	8	1	2	1	1	2	2	1	1	4	rs61745935	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:55922561T>G	ENST00000288221.6	-	14	2675	c.2420A>C	c.(2419-2421)aAt>aCt	p.N807T		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	807						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)		CTCCAGTGCATTCATCAGTTC	0.502													T|||	2	0.000399361	0.0	0.0	5008	,	,		18713	0.0		0.002	False		,,,				2504	0.0				p.N805T		Atlas-SNP	.											ERC2_ENST00000288221,NS,carcinoma,+1,2	ERC2	221	2	0			c.A2414C						PASS	.	T	THR/ASN	2,4176		0,2,2087	220	226	224		2420	4.8	0.9	3	dbSNP_129	224	18,8410		0,18,4196	yes	missense	ERC2	NM_015576.1	65	0,20,6283	GG,GT,TT		0.2136,0.0479,0.1587	benign	807/958	55922561	20,12586	2089	4214	6303	SO:0001583	missense	26059	exon13			AGTGCATTCATCA	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.2420A>C	3.37:g.55922561T>G	ENSP00000288221:p.Asn807Thr	213	0	0		226	117	0.517699	NM_015576	Q2T9F6|Q86TK4	Missense_Mutation	SNP	ENST00000288221.6	37	CCDS46851.1	2|2	9.157509157509158E-4|9.157509157509158E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	T|T	3.251|3.251	-0.153272|-0.153272	0.06585|0.06585	4.79E-4|4.79E-4	0.002136|0.002136	ENSG00000187672|ENSG00000187672	ENST00000492584|ENST00000288221	.|T	.|0.42131	.|0.98	5.93|5.93	4.76|4.76	0.60689|0.60689	.|.	.|0.171337	.|0.51477	.|N	.|0.000089	T|T	0.30198|0.30198	0.0757|0.0757	L|L	0.34521|0.34521	1.04|1.04	0.35402|0.35402	D|D	0.791684|0.791684	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.28073|0.28073	-1.0055|-1.0055	5|10	.|0.14252	.|T	.|0.57	-14.0227|-14.0227	12.0725|12.0725	0.53624|0.53624	0.0:0.0:0.2732:0.7268|0.0:0.0:0.2732:0.7268	.|.	.|807	.|O15083	.|ERC2_HUMAN	L|T	454|807	.|ENSP00000288221:N807T	.|ENSP00000288221:N807T	M|N	-|-	1|2	0|0	ERC2|ERC2	55897601|55897601	0.378000|0.378000	0.25114|0.25114	0.875000|0.875000	0.34327|0.34327	0.574000|0.574000	0.36063|0.36063	0.622000|0.622000	0.24433|0.24433	1.037000|1.037000	0.40024|0.40024	-0.316000|-0.316000	0.08728|0.08728	ATG|AAT	T|0.999;G|0.001	0.001	strong		0.502	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576		G	55922561	T	G	55922561	3	3	25	1	0	0	0	0	1	0	0	0	5213	1493	52	5	469	5	ERC2	3	55922561	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	2762591	55922561	142099869	139	9048											
ACOX2	8309	hgsc.bcm.edu	37	chr3	58517520	58517520	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgggcctggaccagggcAtgggtggctgaccgtcccac	6	6	16	13	1	0	1	0	1	0	0	1	2	1	2	4	5	1	3	4	5	0	0	rs57216393	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:58517520A>G	ENST00000302819.5	-	6	894	c.603T>C	c.(601-603)caT>caC	p.H201H	ACOX2_ENST00000459701.2_Silent_p.H201H	NM_003500.3	NP_003491.1	Q99424	ACOX2_HUMAN	acyl-CoA oxidase 2, branched chain	201					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)		GGACCAGGGCATGGGTGGCTG	0.627													G|||	355	0.0708866	0.2262	0.0375	5008	,	,		18088	0.0		0.0189	False		,,,				2504	0.0112				p.H201H		Atlas-SNP	.											.	ACOX2	53	.	0			c.T603C						PASS	.	G		884,3522	741.6+/-411.3	92,700,1411	59	53	55		603	-9.4	0.1	3	dbSNP_129	55	184,8416	810.9+/-407.1	3,178,4119	no	coding-synonymous	ACOX2	NM_003500.3		95,878,5530	GG,GA,AA		2.1395,20.0635,8.2116		201/682	58517520	1068,11938	2203	4300	6503	SO:0001819	synonymous_variant	8309	exon6			CAGGGCATGGGTG	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.603T>C	3.37:g.58517520A>G		57	0	0		53	28	0.528302	NM_003500	A6NF16|B2R8U5	Silent	SNP	ENST00000302819.5	37	CCDS33775.1																																																																																			A|0.923;G|0.077	0.077	strong		0.627	ACOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353541.1			G	58517520	A	G	58517520	2	3	25	1	0	0	0	0	0	0	0	1	159	214	8	3		3	ACOX2	3	58517520	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	2594959	58517520	139504910	140	9049											
ADAMTS9	56999	hgsc.bcm.edu	37	chr3	64606840	64606840	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaatgtgtccaggctggggCagccgatcgcatctttgatc	7	11	13	10	2	1	1	0	1	1	0	4	2	2	1	2	3	1	4	2	3	1	2	rs149253049	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:64606840C>A	ENST00000498707.1	-	19	3105	c.2763G>T	c.(2761-2763)ctG>ctT	p.L921L	ADAMTS9_ENST00000295903.4_Silent_p.L893L	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	921	TSP type-1 2. {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)		CAGGCTGGGGCAGCCGATCGC	0.463													C|||	5	0.000998403	0.0023	0.0014	5008	,	,		16289	0.0		0.001	False		,,,				2504	0.0				p.L921L		Atlas-SNP	.											.	ADAMTS9	206	.	0			c.G2763T						PASS	.	C		7,4399	14.3+/-33.2	0,7,2196	70	71	71		2763	3	1	3	dbSNP_134	71	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	ADAMTS9	NM_182920.1		0,10,6493	AA,AC,CC		0.0349,0.1589,0.0769		921/1936	64606840	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	56999	exon19			CTGGGGCAGCCGA	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.2763G>T	3.37:g.64606840C>A		170	0	0		208	98	0.471154	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Silent	SNP	ENST00000498707.1	37	CCDS2903.1																																																																																			A|0.001;C|0.999;G|0.000	0.001	strong		0.463	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1			A	64606840	C	A	64606840	2	1	25	1	0	0	0	0	0	0	0	1	273	697	25	4		4	ADAMTS9	3	64606840	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	6089320	64606840	133415590	141	9050											
LRIG1	26018	hgsc.bcm.edu	37	chr3	66432717	66432717	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cattgctctcaatgtgcccaTtggcctgagggccaccctcg	6	10	10	15	1	1	1	1	1	1	0	3	1	1	1	4	2	2	1	4	2	1	2	rs148946048	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:66432717T>C	ENST00000273261.3	-	16	3121	c.2597A>G	c.(2596-2598)aAt>aGt	p.N866S	LRIG1_ENST00000496559.2_5'UTR|LRIG1_ENST00000383703.3_Missense_Mutation_p.N843S|SLC25A26_ENST00000536651.1_Intron	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	866					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)		AATGTGCCCATTGGCCTGAGG	0.567													T|||	36	0.0071885	0.0265	0.0014	5008	,	,		20726	0.0		0.0	False		,,,				2504	0.0				p.N866S		Atlas-SNP	.											.	LRIG1	138	.	0			c.A2597G						PASS	.	T	SER/ASN	72,4334	67.0+/-104.6	1,70,2132	143	144	143		2597	1.6	0.9	3	dbSNP_134	143	3,8597	3.0+/-9.4	0,3,4297	yes	missense	LRIG1	NM_015541.2	46	1,73,6429	CC,CT,TT		0.0349,1.6341,0.5767	benign	866/1094	66432717	75,12931	2203	4300	6503	SO:0001583	missense	26018	exon16			TGCCCATTGGCCT	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.2597A>G	3.37:g.66432717T>C	ENSP00000273261:p.Asn866Ser	113	0	0		100	55	0.55	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Missense_Mutation	SNP	ENST00000273261.3	37	CCDS33783.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	T	12.51	1.960779	0.34565	0.016341	3.49E-4	ENSG00000144749	ENST00000273261;ENST00000383703;ENST00000383702	T;T	0.67171	-0.14;-0.25	5.5	1.56	0.23342	.	0.106092	0.64402	N	0.000008	T	0.36331	0.0963	L	0.45581	1.43	0.33964	D	0.645981	B;B;B	0.15141	0.009;0.001;0.012	B;B;B	0.17979	0.02;0.005;0.005	T	0.46190	-0.9209	10	0.34782	T	0.22	.	5.3801	0.16186	0.0:0.2128:0.1362:0.651	.	843;866;866	Q96JA1-2;Q5XWD3;Q96JA1	.;.;LRIG1_HUMAN	S	866;843;769	ENSP00000273261:N866S;ENSP00000373208:N843S	ENSP00000273261:N866S	N	-	2	0	LRIG1	66515407	0.940000	0.31905	0.906000	0.35671	0.814000	0.46013	0.909000	0.28558	0.373000	0.24621	-0.264000	0.10439	AAT	T|0.995;C|0.005	0.005	strong		0.567	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541		C	66432717	T	C	66432717	3	2	25	1	0	0	0	0	1	0	0	0	8953	1493	52	3	700	3	LRIG1	3	66432717	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	1825877	66432717	131589713	142	9051											
EPHA3	2042	hgsc.bcm.edu	37	chr3	89448530	89448530	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	acaaatgttaccatcagtagCctcaagcctgacactatata	15	10	5	11	0	2	1	2	1	0	0	2	1	2	1	3	0	3	2	3	0	7	5	rs144696297	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:89448530C>A	ENST00000336596.2	+	7	1719	c.1494C>A	c.(1492-1494)agC>agA	p.S498R	EPHA3_ENST00000494014.1_Missense_Mutation_p.S498R|EPHA3_ENST00000452448.2_Missense_Mutation_p.S498R	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	498	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		CCATCAGTAGCCTCAAGCCTG	0.423										TSP Lung(6;0.00050)			C|||	2	0.000399361	0.0	0.0	5008	,	,		15456	0.0		0.002	False		,,,				2504	0.0				p.S498R		Atlas-SNP	.											.	EPHA3	501	.	0			c.C1494A						PASS	.						93	90	91					3																	89448530		2203	4300	6503	SO:0001583	missense	2042	exon7			CAGTAGCCTCAAG	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.1494C>A	3.37:g.89448530C>A	ENSP00000337451:p.Ser498Arg	103	0	0		101	55	0.544554	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	17.56	3.420551	0.62622	.	.	ENSG00000044524	ENST00000336596;ENST00000452448;ENST00000494014	T;T;T	0.57595	0.39;0.39;0.39	5.35	5.35	0.76521	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.045473	0.85682	D	0.000000	T	0.38612	0.1047	N	0.20845	0.615	0.41304	D	0.987066	B;B	0.32101	0.106;0.356	B;B	0.37422	0.249;0.212	T	0.25984	-1.0116	9	.	.	.	.	10.524	0.44936	0.0:0.7909:0.1352:0.0739	.	498;498	P29320;P29320-2	EPHA3_HUMAN;.	R	498	ENSP00000337451:S498R;ENSP00000399926:S498R;ENSP00000419190:S498R	.	S	+	3	2	EPHA3	89531220	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	0.799000	0.27028	2.505000	0.84491	0.563000	0.77884	AGC	C|0.999;A|0.001	0.001	strong		0.423	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		A	89448530	C	A	89448530	3	1	25	1	0	0	0	0	1	0	0	0	5170	738	26	4	1520	4	EPHA3	3	89448530	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	23015813	89448530	108573900	143	9052											
CEP97	79598	hgsc.bcm.edu	37	chr3	101477214	101477214	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aaagatgtgcgttacgaaatCcggctacgcagaatgcaaga	15	7	11	8	4	0	3	0	0	0	3	1	4	1	3	1	1	4	4	1	1	6	2	rs368609945		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:101477214C>A	ENST00000341893.3	+	9	2516	c.1764C>A	c.(1762-1764)atC>atA	p.I588I	CEP97_ENST00000327230.4_Silent_p.I588I|CEP97_ENST00000494050.1_Silent_p.I529I			Q8IW35	CEP97_HUMAN	centrosomal protein 97kDa	588	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						GTTACGAAATCCGGCTACGCA	0.463													C|||	1	0.000199681	0.0	0.0	5008	,	,		21512	0.0		0.0	False		,,,				2504	0.001				p.I588I		Atlas-SNP	.											.	CEP97	122	.	0			c.C1764A						PASS	.	C		0,4406		0,0,2203	62	66	65		1764	-0.3	1	3		65	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CEP97	NM_024548.2		0,1,6502	AA,AC,CC		0.0116,0.0,0.0077		588/866	101477214	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	79598	exon9			CGAAATCCGGCTA	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.1764C>A	3.37:g.101477214C>A		54	0	0		65	21	0.323077	NM_024548	B5MDY8|Q8NA71|Q9H5T9	Silent	SNP	ENST00000341893.3	37	CCDS2944.1																																																																																			.	.	weak		0.463	CEP97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353597.2	NM_024548		A	101477214	C	A	101477214	2	1	25	1	0	0	0	0	0	0	0	1	3265	845	30	4		4	CEP97	3	101477214	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	12028684	101477214	96545216	144	9053											
FAM55C	91775	hgsc.bcm.edu	37	chr3	101540552	101540552	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatcgaagcccaaagaccgtGgtggtcatccggacggccaa	11	5	13	12	4	1	1	1	0	0	1	3	4	2	2	4	4	1	0	4	4	3	0			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:101540552G>T	ENST00000491511.2	+	8	2390	c.1434G>T	c.(1432-1434)gtG>gtT	p.V478V	NXPE3_ENST00000273347.5_Silent_p.V478V|NXPE3_ENST00000477909.1_Silent_p.V478V|NXPE3_ENST00000422132.1_Silent_p.V478V|RP11-49I4.3_ENST00000490324.2_RNA	NM_001134456.1	NP_001127928.1	Q969Y0	NXPE3_HUMAN	neurexophilin and PC-esterase domain family, member 3	478						extracellular region (GO:0005576)											CAAAGACCGTGGTGGTCATCC	0.582																																					p.V478V		Atlas-SNP	.											.	.	.	.	0			c.G1434T						PASS	.						96	98	97					3																	101540552		2203	4300	6503	SO:0001819	synonymous_variant	91775	exon8			GACCGTGGTGGTC	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.1434G>T	3.37:g.101540552G>T		139	0	0		124	63	0.508065	NM_145037	A8K0X4|D3DN53|Q7Z2S8	Silent	SNP	ENST00000491511.2	37	CCDS2945.1																																																																																			.	.	none		0.582	NXPE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353711.2	NM_145037		T	101540552	G	T	101540552	2	4	25	1	0	0	0	0	0	0	0	1	5594	1335	47	4		4	FAM55C	3	101540552	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	63338	101540552	96481878	145	9054											
BBX	56987	hgsc.bcm.edu	37	chr3	107491892	107491892	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttatgatcattgaggatcccGcagcattaaacaagccagaa	15	9	8	9	1	1	3	1	2	0	1	2	4	2	4	2	1	3	2	2	1	5	3	rs138961599	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:107491892G>A	ENST00000325805.8	+	11	1611	c.1324G>A	c.(1324-1326)Gca>Aca	p.A442T	BBX_ENST00000406780.1_Missense_Mutation_p.A442T|BBX_ENST00000415149.2_Missense_Mutation_p.A442T|BBX_ENST00000402543.1_Missense_Mutation_p.A442T|BBX_ENST00000416476.2_Intron			Q8WY36	BBX_HUMAN	bobby sox homolog (Drosophila)	442					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)			TGAGGATCCCGCAGCATTAAA	0.358													G|||	9	0.00179712	0.0	0.0014	5008	,	,		18346	0.0		0.006	False		,,,				2504	0.002				p.A442T		Atlas-SNP	.											.	BBX	156	.	0			c.G1324A						PASS	.	G	THR/ALA,THR/ALA	9,4397	15.5+/-35.6	0,9,2194	67	73	71		1324,1324	0.5	1	3	dbSNP_134	71	84,8516	47.6+/-106.9	2,80,4218	yes	missense,missense	BBX	NM_001142568.1,NM_020235.5	58,58	2,89,6412	AA,AG,GG		0.9767,0.2043,0.7151	benign,benign	442/942,442/912	107491892	93,12913	2203	4300	6503	SO:0001583	missense	56987	exon11			GATCCCGCAGCAT	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.1324G>A	3.37:g.107491892G>A	ENSP00000319974:p.Ala442Thr	86	0	0		112	58	0.517857	NM_001142568	A2RRM7|Q2TAJ1|Q7L3J8|Q7LBY8|Q8NDB0|Q8WY35|Q9H0J6	Missense_Mutation	SNP	ENST00000325805.8	37	CCDS46881.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	G	0.656	-0.807550	0.02819	0.002043	0.009767	ENSG00000114439	ENST00000415149;ENST00000325767;ENST00000402543;ENST00000325805;ENST00000402163;ENST00000406780	D;D;D;D;D	0.98192	-4.39;-4.38;-4.39;-4.78;-4.39	6.07	0.455	0.16649	.	0.817289	0.11680	N	0.539909	D	0.84584	0.5504	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	0.82059	-0.0645	10	0.02654	T	1	-1.6382	0.4743	0.00537	0.3839:0.1217:0.2416:0.2529	.	442;442;442	C9JA69;Q8WY36;Q8WY36-2	.;BBX_HUMAN;.	T	442;293;442;442;442;442	ENSP00000408358:A442T;ENSP00000385317:A442T;ENSP00000319974:A442T;ENSP00000385518:A442T;ENSP00000385530:A442T	ENSP00000319742:A293T	A	+	1	0	BBX	108974582	0.002000	0.14202	0.974000	0.42286	0.699000	0.40488	0.163000	0.16520	0.528000	0.28580	-0.438000	0.05819	GCA	G|0.993;A|0.007	0.007	strong		0.358	BBX-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317820.1	NM_020235		A	107491892	G	A	107491892	3	1	25	1	0	0	0	0	1	0	0	0	1343	1087	38	1	1354	1	BBX	3	107491892	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	5951340	107491892	90530538	146	9055											
BOC	91653	hgsc.bcm.edu	37	chr3	112989763	112989763	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acccaggaagtgaaaacctcCggctccagcgacaggctacg	12	4	11	14	3	0	1	0	1	0	0	2	3	2	2	4	3	3	2	4	3	4	1	rs9819129	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:112989763C>T	ENST00000495514.1	+	6	1343	c.639C>T	c.(637-639)tcC>tcT	p.S213S	BOC_ENST00000355385.3_Silent_p.S213S|BOC_ENST00000273395.4_Silent_p.S213S			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	213	Ig-like C2-type 2.				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)			TGAAAACCTCCGGCTCCAGCG	0.607													C|||	113	0.0225639	0.0484	0.0173	5008	,	,		20556	0.0		0.0258	False		,,,				2504	0.0112				p.S213S		Atlas-SNP	.											.	BOC	139	.	0			c.C639T						PASS	.	C		167,4239	110.4+/-148.6	2,163,2038	126	126	126		639	-11.6	0.5	3	dbSNP_119	126	209,8391	89.7+/-151.9	2,205,4093	no	coding-synonymous	BOC	NM_033254.2		4,368,6131	TT,TC,CC		2.4302,3.7903,2.891		213/1115	112989763	376,12630	2203	4300	6503	SO:0001819	synonymous_variant	91653	exon6			AACCTCCGGCTCC	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.639C>T	3.37:g.112989763C>T		82	0	0		65	21	0.323077	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Silent	SNP	ENST00000495514.1	37	CCDS2971.1																																																																																			C|0.974;T|0.026	0.026	strong		0.607	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254		T	112989763	C	T	112989763	2	4	25	1	0	0	0	0	0	0	0	1	1481	639	23	1		1	BOC	3	112989763	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	5497871	112989763	85032667	147	9056											
CCDC52	152185	hgsc.bcm.edu	37	chr3	113175984	113175984	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actttagaagaagacttaccGtcctgaagaggagagaattt	15	10	10	6	1	0	6	0	1	0	5	1	8	1	7	2	1	1	0	2	1	6	4	rs146846950	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:113175984G>A	ENST00000295872.4	-	13	1915	c.1656C>T	c.(1654-1656)gaC>gaT	p.D552D		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	552					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						AAGACTTACCGTCCTGAAGAG	0.353													g|||	46	0.0091853	0.0008	0.0014	5008	,	,		19525	0.0		0.0119	False		,,,				2504	0.0327				p.D552D		Atlas-SNP	.											SPICE1_ENST00000295872,NS,carcinoma,0,2	SPICE1	130	2	0			c.C1656T						PASS	.	A		3,4403	6.2+/-15.9	0,3,2200	55	55	55		1656	-11.3	0.8	3	dbSNP_134	55	46,8554	30.7+/-82.3	0,46,4254	yes	coding-synonymous-near-splice	SPICE1	NM_144718.3		0,49,6454	AA,AG,GG		0.5349,0.0681,0.3767		552/856	113175984	49,12957	2203	4300	6503	SO:0001630	splice_region_variant	152185	exon13			CTTACCGTCCTGA	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.1657+1C>T	3.37:g.113175984G>A		46	0	0		45	24	0.533333	NM_144718	D3DN72|Q8WUX6	Silent	SNP	ENST00000295872.4	37	CCDS2973.1																																																																																			G|0.995;A|0.005	0.005	strong		0.353	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718	Silent	A	113175984	G	A	113175984	5	1	25	1	0	0	0	0	0	0	1	0	2824	1159	40	1	935	1	CCDC52	3	113175984	Splice_Site	SNP	G	TCGA-G8-6906-01A-11D-2210-10	186221	113175984	84846446	148	9057											
GPR156	165829	hgsc.bcm.edu	37	chr3	119886101	119886101	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gactcagtatcaaaatagctGtgttgagaagacagggaggc	14	8	13	6	0	2	2	2	1	0	2	2	5	2	3	0	2	1	3	0	2	5	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:119886101G>A	ENST00000464295.1	-	10	2668	c.2223C>T	c.(2221-2223)caC>caT	p.H741H	GPR156_ENST00000315843.3_Silent_p.H741H|GPR156_ENST00000461057.1_Silent_p.H737H			Q8NFN8	GP156_HUMAN	G protein-coupled receptor 156	741						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)		CAAAATAGCTGTGTTGAGAAG	0.567																																					p.H741H		Atlas-SNP	.											.	GPR156	85	.	0			c.C2223T						PASS	.						58	65	63					3																	119886101		2203	4300	6503	SO:0001819	synonymous_variant	165829	exon9			ATAGCTGTGTTGA	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.2223C>T	3.37:g.119886101G>A		81	0	0		95	46	0.484211	NM_153002	B7ZL66|E9PFZ4|Q14CM1|Q86SN6	Silent	SNP	ENST00000464295.1	37	CCDS2997.1																																																																																			.	.	none		0.567	GPR156-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355139.1	NM_153002		A	119886101	G	A	119886101	2	1	25	1	0	0	0	0	0	0	0	1	6669	1368	48	2		2	GPR156	3	119886101	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	6710117	119886101	78136329	149	9058											
KALRN	8997	hgsc.bcm.edu	37	chr3	124044859	124044859	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aacatcaaccgcatcatgtcCgtggcttcccgcctctctga	8	10	7	16	3	3	1	2	1	1	0	6	1	5	1	4	1	2	2	4	1	2	1	rs16835275	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:124044859C>T	ENST00000240874.3	+	7	1276	c.1119C>T	c.(1117-1119)tcC>tcT	p.S373S	KALRN_ENST00000360013.3_Silent_p.S373S|KALRN_ENST00000460856.1_Silent_p.S373S	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	373					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						GCATCATGTCCGTGGCTTCCC	0.547													C|||	29	0.00579073	0.0061	0.0058	5008	,	,		16950	0.0099		0.005	False		,,,				2504	0.002				p.S373S		Atlas-SNP	.											KALRN_ENST00000360013,NS,malignant_melanoma,+1,2	KALRN	556	2	0			c.C1119T						PASS	.	C	,	27,4379	32.6+/-62.9	0,27,2176	102	93	97		1119,1119	-9.3	0	3	dbSNP_123	97	73,8525	42.2+/-99.7	1,71,4227	no	coding-synonymous,coding-synonymous	KALRN	NM_001024660.3,NM_003947.4	,	1,98,6403	TT,TC,CC		0.849,0.6128,0.769	,	373/2987,373/1664	124044859	100,12904	2203	4299	6502	SO:0001819	synonymous_variant	8997	exon7			CATGTCCGTGGCT	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.1119C>T	3.37:g.124044859C>T		134	0	0		191	86	0.450262	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	37	CCDS3027.1	16	0.007326007326007326	1	0.0020325203252032522	5	0.013812154696132596	7	0.012237762237762238	3	0.00395778364116095	C	6.705	0.498764	0.12762	0.006128	0.00849	ENSG00000160145	ENST00000354186	.	.	.	4.64	-9.28	0.00656	.	.	.	.	.	T	0.49830	0.1580	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.74463	-0.3657	4	.	.	.	.	12.8333	0.57759	0.0:0.4623:0.2765:0.2612	rs16835275;rs16835275	.	.	.	L	351	.	.	P	+	2	0	KALRN	125527549	0.000000	0.05858	0.012000	0.15200	0.920000	0.55202	-5.264000	0.00136	-4.734000	0.00034	-1.876000	0.00548	CCG	C|0.992;T|0.008	0.008	strong		0.547	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		T	124044859	C	T	124044859	2	4	25	1	0	0	0	0	0	0	0	1	7984	639	23	1		1	KALRN	3	124044859	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	4158758	124044859	73977571	150	9059											
HEG1	57493	hgsc.bcm.edu	37	chr3	124746237	124746237	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacagtccattcttctgacAgccccatcgccctctctgtt	6	12	6	17	1	3	1	0	1	3	0	6	1	4	1	4	0	1	2	4	0	0	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:124746237A>T	ENST00000311127.4	-	3	792	c.725T>A	c.(724-726)cTg>cAg	p.L242Q		NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	242					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						TTCTTCTGACAGCCCCATCGC	0.547																																					p.L242Q		Atlas-SNP	.											.	HEG1	109	.	0			c.T725A						PASS	.						66	67	66					3																	124746237		1989	4156	6145	SO:0001583	missense	57493	exon3			TCTGACAGCCCCA	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.725T>A	3.37:g.124746237A>T	ENSP00000311502:p.Leu242Gln	199	0	0		213	106	0.497653	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Missense_Mutation	SNP	ENST00000311127.4	37	CCDS46898.1	.	.	.	.	.	.	.	.	.	.	A	18.45	3.626598	0.66901	.	.	ENSG00000173706	ENST00000311127	T	0.42513	0.97	4.69	3.54	0.40534	.	.	.	.	.	T	0.53334	0.1790	L	0.60455	1.87	0.26084	N	0.981056	D;D	0.67145	0.996;0.994	D;D	0.69479	0.964;0.922	T	0.37267	-0.9713	9	0.27785	T	0.31	.	6.9296	0.24434	0.8966:0.0:0.1034:0.0	.	242;242	Q9ULI3-2;Q9ULI3	.;HEG1_HUMAN	Q	242	ENSP00000311502:L242Q	ENSP00000311502:L242Q	L	-	2	0	HEG1	126228927	0.000000	0.05858	0.750000	0.31169	0.261000	0.26267	0.557000	0.23454	0.931000	0.37242	0.528000	0.53228	CTG	.	.	none		0.547	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386		T	124746237	A	T	124746237	3	4	25	1	0	0	0	0	1	0	0	0	7053	188	7	5	3480	5	HEG1	3	124746237	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	701378	124746237	73276193	151	9060											
SLC12A8	84561	hgsc.bcm.edu	37	chr3	124829057	124829057	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcccagacaggcaagtgcAgggatcactttctcctgggc	8	9	12	12	0	2	1	1	0	1	1	4	2	3	2	2	3	1	2	2	3	1	1	rs11714448	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:124829057A>G	ENST00000393469.4	-	8	1084	c.1035T>C	c.(1033-1035)ccT>ccC	p.P345P	SLC12A8_ENST00000465475.1_5'UTR|SLC12A8_ENST00000430155.2_Silent_p.P146P|SLC12A8_ENST00000423114.2_Silent_p.P374P|SLC12A8_ENST00000469902.1_Silent_p.P345P|SLC12A8_ENST00000314584.7_Silent_p.P98P	NM_001195483.1	NP_001182412	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8	345					potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			endometrium(2)|kidney(2)|lung(12)	16						AGGCAAGTGCAGGGATCACTT	0.493													A|||	56	0.0111821	0.0015	0.0173	5008	,	,		19172	0.0		0.0219	False		,,,				2504	0.0204				p.P345P		Atlas-SNP	.											.	SLC12A8	81	.	0			c.T1035C						PASS	.	A	,	20,3788		0,20,1884	89	90	89		1035,1035	-6.4	0.9	3	dbSNP_120	89	255,7991		3,249,3871	no	coding-synonymous,coding-synonymous	SLC12A8	NM_001195483.1,NM_024628.5	,	3,269,5755	GG,GA,AA		3.0924,0.5252,2.2814	,	345/715,345/715	124829057	275,11779	1904	4123	6027	SO:0001819	synonymous_variant	84561	exon9			AAGTGCAGGGATC		CCDS43143.1	3q21.2	2013-07-18	2013-07-18		ENSG00000221955	ENSG00000221955		"Solute carriers"	15595	protein-coding gene	gene with protein product	"solute carrier family 12 (sodium/potassium/chloride transporters), member 8", "cation-chloride cotransporter 9"	611316				11863360	Standard	NM_024628		Approved	CCC9	uc003ehv.4	A0AV02	OTTHUMG00000159483	ENST00000393469.4:c.1035T>C	3.37:g.124829057A>G		67	0	0		72	24	0.333333	NM_024628	C9JJJ2|Q68D04|Q6I9Z2|Q6P4C0|Q7Z3A6|Q86WK0|Q8NFX9|Q8WUI3|Q96RF9|Q9H5P9	Silent	SNP	ENST00000393469.4	37	CCDS43143.1																																																																																			A|0.986;G|0.013	0.013	strong		0.493	SLC12A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355711.4	NM_024628		G	124829057	A	G	124829057	2	3	25	1	0	0	0	0	0	0	0	1	14404	175	7	3		3	SLC12A8	3	124829057	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	82820	124829057	73193373	152	9061											
PODXL2	50512	hgsc.bcm.edu	37	chr3	127379635	127379635	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caccccaactacagtgactcCgggggaccaggactccacca	11	4	9	17	1	0	1	0	1	0	0	2	3	2	3	6	3	2	0	6	3	2	1	rs34691761	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:127379635C>T	ENST00000342480.6	+	3	803	c.764C>T	c.(763-765)cCg>cTg	p.P255L		NM_015720.2	NP_056535.1	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2	255					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						ACAGTGACTCCGGGGGACCAG	0.627													C|||	13	0.00259585	0.0	0.0058	5008	,	,		18265	0.0		0.0089	False		,,,				2504	0.0				p.P255L		Atlas-SNP	.											.	PODXL2	53	.	0			c.C764T						PASS	.	C	LEU/PRO	3,4403	6.2+/-15.9	0,3,2200	35	39	37		764	-0.9	0	3	dbSNP_126	37	47,8553	30.1+/-81.4	1,45,4254	yes	missense	PODXL2	NM_015720.2	98	1,48,6454	TT,TC,CC		0.5465,0.0681,0.3844	benign	255/606	127379635	50,12956	2203	4300	6503	SO:0001583	missense	50512	exon3			TGACTCCGGGGGA	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.764C>T	3.37:g.127379635C>T	ENSP00000345359:p.Pro255Leu	127	0	0		123	49	0.398374	NM_015720	Q6UVY4|Q8WUV6	Missense_Mutation	SNP	ENST00000342480.6	37	CCDS3044.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	0	-2.607312	0.00121	6.81E-4	0.005465	ENSG00000114631	ENST00000342480;ENST00000302192	T	0.20738	2.05	4.67	-0.937	0.10415	.	1.475550	0.04280	N	0.343618	T	0.07863	0.0197	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31806	-0.9930	10	0.20519	T	0.43	0.0338	9.3502	0.38133	0.0:0.4699:0.0:0.5301	rs34691761	255	Q9NZ53	PDXL2_HUMAN	L	255	ENSP00000345359:P255L	ENSP00000304498:P255L	P	+	2	0	PODXL2	128862325	0.000000	0.05858	0.001000	0.08648	0.025000	0.11179	-0.299000	0.08254	-0.341000	0.08376	-0.573000	0.04149	CCG	C|0.995;T|0.005	0.005	strong		0.627	PODXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356638.1	NM_015720		T	127379635	C	T	127379635	3	4	25	1	0	0	0	0	1	0	0	0	12190	652	23	1	774	1	PODXL2	3	127379635	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2550578	127379635	70642795	153	9062											
DNAJB8	165721	hgsc.bcm.edu	37	chr3	128181964	128181964	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagcttgaacttcttctccGcctcctccttattgtcaggg	5	14	7	15	1	3	1	1	1	2	0	6	1	5	1	5	1	2	1	5	1	2	5	rs142768827		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:128181964G>A	ENST00000469083.1	-	2	2682	c.125C>T	c.(124-126)gCg>gTg	p.A42V	DNAJB8_ENST00000319153.3_Missense_Mutation_p.A42V|DNAJB8-AS1_ENST00000471626.1_RNA			Q8NHS0	DNJB8_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 8	42	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)		CTTCTTCTCCGCCTCCTCCTT	0.592																																					p.A42V		Atlas-SNP	.											.	DNAJB8	34	.	0			c.C125T						PASS	.	G	VAL/ALA	0,4406		0,0,2203	162	160	161		125	4.4	0.8	3	dbSNP_134	161	1,8599	1.2+/-3.3	0,1,4299	no	missense	DNAJB8	NM_153330.2	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	42/233	128181964	1,13005	2203	4300	6503	SO:0001583	missense	165721	exon3			TTCTCCGCCTCCT		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.125C>T	3.37:g.128181964G>A	ENSP00000417418:p.Ala42Val	185	0	0		203	75	0.369458	NM_153330	B3KWV7	Missense_Mutation	SNP	ENST00000469083.1	37	CCDS3048.1	.	.	.	.	.	.	.	.	.	.	G	15.83	2.949383	0.53186	0.0	1.16E-4	ENSG00000179407	ENST00000469083;ENST00000319153	T;T	0.39056	1.1;1.1	4.42	4.42	0.53409	Heat shock protein DnaJ, N-terminal (5);	0.000000	0.85682	D	0.000000	T	0.68540	0.3012	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.76391	-0.2976	10	0.87932	D	0	.	17.0136	0.86413	0.0:0.0:1.0:0.0	.	42	Q8NHS0	DNJB8_HUMAN	V	42	ENSP00000417418:A42V;ENSP00000316053:A42V	ENSP00000316053:A42V	A	-	2	0	DNAJB8	129664654	1.000000	0.71417	0.844000	0.33320	0.003000	0.03518	7.784000	0.85713	2.003000	0.58678	0.561000	0.74099	GCG	G|1.000;A|0.000	0.000	weak		0.592	DNAJB8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356933.1	NM_153330		A	128181964	G	A	128181964	3	1	25	1	0	0	0	0	1	0	0	0	4628	1087	38	1	577	1	DNAJB8	3	128181964	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	802329	128181964	69840466	154	9063											
COPG	22820	hgsc.bcm.edu	37	chr3	128971751	128971751	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cggatgtgctacttgaccatCaaggagatgtcttgcattgc	9	12	11	9	1	2	2	1	1	1	1	2	4	2	3	1	2	4	2	1	2	2	4	rs73202214	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:128971751C>T	ENST00000314797.6	+	5	380	c.276C>T	c.(274-276)atC>atT	p.I92I		NM_016128.3	NP_057212.1	Q9Y678	COPG1_HUMAN	coatomer protein complex, subunit gamma 1	92					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)										ACTTGACCATCAAGGAGATGT	0.542													C|||	4	0.000798722	0.0	0.0043	5008	,	,		21362	0.0		0.001	False		,,,				2504	0.0				p.I92I		Atlas-SNP	.											.	.	.	.	0			c.C276T						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	186	160	169		276	5.1	1	3	dbSNP_130	169	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	COPG	NM_016128.3		0,17,6486	TT,TC,CC		0.1628,0.0681,0.1307		92/875	128971751	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	22820	exon5			GACCATCAAGGAG	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.276C>T	3.37:g.128971751C>T		120	0	0		127	66	0.519685	NM_016128	A8K6M8|B3KMF6|Q54AC4	Silent	SNP	ENST00000314797.6	37	CCDS33851.1																																																																																			C|0.998;T|0.002	0.002	strong		0.542	COPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355456.1	NM_016128		T	128971751	C	T	128971751	2	4	25	1	0	0	0	0	0	0	0	1	3733	816	29	2		2	COPG	3	128971751	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	789787	128971751	69050679	155	9064											
IFT122	55764	hgsc.bcm.edu	37	chr3	129237966	129237966	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ccaggctcccagattctgcgGctagtggagaccaaggactc	9	7	12	13	1	1	2	0	0	1	2	3	4	2	3	3	4	1	2	3	4	2	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:129237966G>A	ENST00000348417.2	+	28	3485	c.3408G>A	c.(3406-3408)cgG>cgA	p.R1136R	IFT122_ENST00000349441.2_Silent_p.R1026R|IFT122_ENST00000296266.3_Silent_p.R1187R|IFT122_ENST00000440957.2_Silent_p.R927R|IFT122_ENST00000347300.2_Silent_p.R1077R|IFT122_ENST00000507564.1_Silent_p.R1129R|IFT122_ENST00000504021.1_Silent_p.R1013R|IFT122_ENST00000431818.2_Silent_p.R986R	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	1136					camera-type eye morphogenesis (GO:0048593)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|establishment of protein localization to organelle (GO:0072594)|intraciliary anterograde transport (GO:0035720)|intraciliary retrograde transport (GO:0035721)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|protein localization to cilium (GO:0061512)|signal transduction downstream of smoothened (GO:0007227)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)				breast(3)|cervix(1)|endometrium(9)|large_intestine(10)|lung(21)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						AGATTCTGCGGCTAGTGGAGA	0.577																																					p.R1187R		Atlas-SNP	.											.	IFT122	117	.	0			c.G3561A						PASS	.						120	121	121					3																	129237966		2203	4300	6503	SO:0001819	synonymous_variant	55764	exon29			TCTGCGGCTAGTG	AF244930	CCDS3059.1, CCDS3060.1, CCDS3061.1, CCDS3062.1, CCDS63770.1, CCDS63772.1, CCDS63773.1	3q21	2014-07-03	2014-07-03	2005-11-02	ENSG00000163913	ENSG00000163913		"WD repeat domain containing", "Intraflagellar transport homologs"	13556	protein-coding gene	gene with protein product		606045	"WD repeat domain 10", "intraflagellar transport 122 homolog (Chlamydomonas)"	WDR10		11242542	Standard	NM_052985		Approved	WDR140, WDR10p, SPG	uc003emm.3	Q9HBG6	OTTHUMG00000159516	ENST00000348417.2:c.3408G>A	3.37:g.129237966G>A		81	0	0		100	42	0.42	NM_052985	B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Silent	SNP	ENST00000348417.2	37	CCDS3061.1																																																																																			.	.	none		0.577	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1	NM_018262		A	129237966	G	A	129237966	2	1	25	1	0	0	0	0	0	0	0	1	7564	1190	42	2		2	IFT122	3	129237966	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	266215	129237966	68784464	156	9065											
PLXND1	23129	hgsc.bcm.edu	37	chr3	129303236	129303236	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cagcgtgcttaccctggttgGgggggaagggcggaaactgg	7	7	19	8	2	0	0	0	0	0	0	0	2	0	2	1	7	4	2	1	7	3	2	rs201334507	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:129303236G>C	ENST00000324093.4	-	6	2199	c.2021C>G	c.(2020-2022)cCc>cGc	p.P674R	PLXND1_ENST00000393239.1_Missense_Mutation_p.P674R	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	674					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						ACCCTGGTTGGGGGGGAAGGG	0.637													G|||	2	0.000399361	0.0008	0.0	5008	,	,		19988	0.001		0.0	False		,,,				2504	0.0				p.P674R	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.C2021G						PASS	.	G	ARG/PRO	0,4406		0,0,2203	53	53	53		2021	2.9	0	3		53	3,8597	3.0+/-9.4	0,3,4297	yes	missense	PLXND1	NM_015103.2	103	0,3,6500	CC,CG,GG		0.0349,0.0,0.0231	benign	674/1926	129303236	3,13003	2203	4300	6503	SO:0001583	missense	23129	exon6			TGGTTGGGGGGGA	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.2021C>G	3.37:g.129303236G>C	ENSP00000317128:p.Pro674Arg	93	0	0		70	40	0.571429	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	37	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	G	1.556	-0.538035	0.04082	0.0	3.49E-4	ENSG00000004399	ENST00000324093;ENST00000393239	T;T	0.34275	1.42;1.37	4.77	2.94	0.34122	.	0.473004	0.19301	N	0.117635	T	0.33644	0.0870	M	0.65975	2.015	0.09310	N	1	B	0.21688	0.059	B	0.26310	0.068	T	0.31530	-0.9940	10	0.12103	T	0.63	.	10.1176	0.42601	0.0:0.1326:0.593:0.2744	.	674	Q9Y4D7	PLXD1_HUMAN	R	674	ENSP00000317128:P674R;ENSP00000376931:P674R	ENSP00000317128:P674R	P	-	2	0	PLXND1	130785926	0.013000	0.17824	0.002000	0.10522	0.049000	0.14656	1.150000	0.31639	0.528000	0.28580	-0.218000	0.12543	CCC	.	.	weak		0.637	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103		C	129303236	G	C	129303236	3	2	25	1	0	0	0	0	1	0	0	0	12136	1232	43	4	3880	4	PLXND1	3	129303236	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	65270	129303236	68719194	157	9066											
NEK11	79858	hgsc.bcm.edu	37	chr3	130947466	130947466	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaggaggaagaagaaatagcGttagaaagaccagagaaaga	21	3	14	3	1	0	6	0	0	0	6	0	10	0	8	1	2	1	1	1	2	7	2	rs138864243	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:130947466G>A	ENST00000510769.1	+	11	1432	c.1179G>A	c.(1177-1179)gcG>gcA	p.A393A	NEK11_ENST00000412440.2_Silent_p.A314A|NEK11_ENST00000429253.2_Silent_p.A498A|NEK11_ENST00000508196.1_Silent_p.A498A|NEK11_ENST00000383366.4_Silent_p.A498A|NEK11_ENST00000510688.1_Silent_p.A498A					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						AAGAAATAGCGTTAGAAAGAC	0.453													G|||	5	0.000998403	0.0023	0.0014	5008	,	,		19611	0.0		0.001	False		,,,				2504	0.0				p.A498A		Atlas-SNP	.											.	NEK11	76	.	0			c.G1494A						PASS	.	G	,	6,4400	11.4+/-27.6	0,6,2197	117	109	112		1494,1494	1.6	0	3	dbSNP_134	112	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous,coding-synonymous	NEK11	NM_001146003.1,NM_024800.4	,	0,16,6487	AA,AG,GG		0.1163,0.1362,0.123	,	498/600,498/646	130947466	16,12990	2203	4300	6503	SO:0001819	synonymous_variant	79858	exon15			AATAGCGTTAGAA	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.1179G>A	3.37:g.130947466G>A		51	0	0		42	21	0.5	NM_024800		Silent	SNP	ENST00000510769.1	37																																																																																				G|0.998;A|0.002	0.002	strong		0.453	NEK11-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000356757.1	NM_024800		A	130947466	G	A	130947466	2	1	25	1	0	0	0	0	0	0	0	1	10332	1132	40	1		1	NEK11	3	130947466	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1644230	130947466	67074964	158	9067											
DNAJC13	23317	hgsc.bcm.edu	37	chr3	132166302	132166302	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagcacagaacagaacttctTacagaagcattggtaagaag	17	7	10	7	0	1	4	0	0	1	4	1	5	1	4	0	1	5	3	0	1	6	4	rs116489157	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:132166302T>G	ENST00000260818.6	+	4	530	c.282T>G	c.(280-282)ctT>ctG	p.L94L	DNAJC13_ENST00000486798.1_3'UTR	NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	94					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						CAGAACTTCTTACAGAAGCAT	0.318													T|||	22	0.00439297	0.0008	0.0058	5008	,	,		14614	0.0		0.0129	False		,,,				2504	0.0041				p.L94L		Atlas-SNP	.											.	DNAJC13	253	.	0			c.T282G						PASS	.	T		10,4396	16.8+/-37.8	0,10,2193	34	37	36		282	2.1	1	3	dbSNP_132	36	158,8432	71.6+/-134.2	2,154,4139	no	coding-synonymous	DNAJC13	NM_015268.3		2,164,6332	GG,GT,TT		1.8393,0.227,1.2927		94/2244	132166302	168,12828	2203	4295	6498	SO:0001819	synonymous_variant	23317	exon4			ACTTCTTACAGAA	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.282T>G	3.37:g.132166302T>G		130	0	0		137	76	0.554745	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Silent	SNP	ENST00000260818.6	37	CCDS33857.1																																																																																			T|0.990;G|0.010	0.010	strong		0.318	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268		G	132166302	T	G	132166302	2	3	25	1	0	0	0	0	0	0	0	1	4634	1741	61	5		5	DNAJC13	3	132166302	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	1218836	132166302	65856128	159	9068											
ACAD11	84129	hgsc.bcm.edu	37	chr3	132337477	132337477	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gttttcaattaatgtagtaaCctggtgcttggcagttaaag	11	15	10	5	0	1	0	1	0	0	0	1	0	1	0	1	2	2	6	1	2	6	7	rs41272317	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:132337477C>A	ENST00000264990.6	-	11	2386		c.e11+1		ACAD11_ENST00000545291.1_Intron|ACAD11_ENST00000481970.2_Missense_Mutation_p.G472V|ACAD11_ENST00000355458.3_Splice_Site	NM_032169.4	NP_115545	Q709F0	ACD11_HUMAN	acyl-CoA dehydrogenase family, member 11						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.?(1)		breast(2)|endometrium(6)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	36						AATGTAGTAACCTGGTGCTTG	0.338													C|||	212	0.0423323	0.0333	0.0029	5008	,	,		15862	0.0704		0.0159	False		,,,				2504	0.0808				.		Atlas-SNP	.											ACAD11,NS,carcinoma,0,1	ACAD11	78	1	1	Unknown(1)	stomach(1)	c.1414+1G>T						scavenged	.	C		114,4292	76.2+/-114.5	1,112,2090	65	66	66			5.5	1	3	dbSNP_127	66	133,8465	63.9+/-126.0	1,131,4167	yes	splice-5	ACAD11	NM_032169.4		2,243,6257	AA,AC,CC		1.5469,2.5874,1.8994			132337477	247,12757	2203	4299	6502	SO:0001630	splice_region_variant	84129	exon12			TAGTAACCTGGTG	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.1414+1G>T	3.37:g.132337477C>A		136	2	0.0147059		153	66	0.431373	NM_032169	Q08AF0|Q658N9|Q658Y2|Q6ZND2|Q8WUT6|Q9H9R3	Splice_Site	SNP	ENST00000264990.6	37	CCDS3074.1	78|78	0.03571428571428571|0.03571428571428571	22|22	0.044715447154471545|0.044715447154471545	2|2	0.0055248618784530384|0.0055248618784530384	42|42	0.07342657342657342|0.07342657342657342	12|12	0.0158311345646438|0.0158311345646438	C|C	18.10|18.10	3.548345|3.548345	0.65311|0.65311	0.025874|0.025874	0.015469|0.015469	ENSG00000240303|ENSG00000240303	ENST00000355458;ENST00000264990|ENST00000481970	.|T	.|0.22134	.|1.97	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	.|.	.|.	.|.	.|.	.|T	.|0.06872	.|0.0175	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.91635	.|0.999	.|T	.|0.03473	.|-1.1033	.|8	.|0.87932	.|D	.|0	.|.	19.3995|19.3995	0.94621|0.94621	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs41272317|rs41272317	.|472	.|D6RDI8	.|.	.|V	-1|472	.|ENSP00000420907:G472V	.|ENSP00000420907:G472V	.|G	-|-	.|2	.|0	ACAD11|ACAD11	133820167|133820167	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.712000|0.712000	0.41017|0.41017	7.426000|7.426000	0.80270|0.80270	2.754000|2.754000	0.94517|0.94517	0.650000|0.650000	0.86243|0.86243	.|GGT	A|0.027;C|0.973;T|0.000	0.027	strong		0.338	ACAD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357279.2	NM_032169	Intron	A	132337477	C	A	132337477	5	1	25	1	0	0	0	0	0	0	1	0	109	521	18	4	967	4	ACAD11	3	132337477	Splice_Site	SNP	C	TCGA-G8-6906-01A-11D-2210-10	171175	132337477	65684953	160	9069											
FAIM	55179	hgsc.bcm.edu	37	chr3	138347988	138347988	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atggtgcaatggtaaaaaatTggagacagcggtaagttgac	15	9	13	4	1	0	2	0	1	0	1	0	3	0	2	0	4	2	4	0	4	5	4	rs13043	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:138347988T>C	ENST00000393035.2	+	4	489	c.380T>C	c.(379-381)tTg>tCg	p.L127S	FAIM_ENST00000360570.3_Missense_Mutation_p.L149S|FAIM_ENST00000464668.1_Missense_Mutation_p.L127S|FAIM_ENST00000393034.2_Missense_Mutation_p.L127S|FAIM_ENST00000338446.4_Missense_Mutation_p.L161S	NM_001033032.1	NP_001028204.1	Q9NVQ4	FAIM1_HUMAN	Fas apoptotic inhibitory molecule	127			L -> S (in dbSNP:rs13043). {ECO:0000269|PubMed:12107411}.		apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)	cytoplasm (GO:0005737)				kidney(1)|upper_aerodigestive_tract(1)	2						GGTAAAAAATTGGAGACAGCG	0.313													T|||	893	0.178315	0.6256	0.0735	5008	,	,		17281	0.0		0.0139	False		,,,				2504	0.001				p.L161S		Atlas-SNP	.											.	FAIM	27	.	0			c.T482C						PASS	.	T	SER/LEU,SER/LEU,SER/LEU,SER/LEU	2378,2028	610.6+/-391.6	646,1086,471	134	150	144		482,446,380,380	4.9	0.9	3	dbSNP_52	144	131,8469	65.3+/-127.6	1,129,4170	yes	missense,missense,missense,missense	FAIM	NM_001033030.1,NM_001033031.1,NM_001033032.1,NM_018147.3	145,145,145,145	647,1215,4641	CC,CT,TT		1.5233,46.0281,19.2911	benign,benign,benign,benign	161/214,149/202,127/180,127/180	138347988	2509,10497	2203	4300	6503	SO:0001583	missense	55179	exon5			AAAAATTGGAGAC	AK001444	CCDS3103.1, CCDS33864.1, CCDS33865.1	3q23	2008-07-18			ENSG00000158234	ENSG00000158234			18703	protein-coding gene	gene with protein product						10075978	Standard	NM_018147		Approved	FLJ10582, FAIM1	uc003esq.3	Q9NVQ4	OTTHUMG00000159885	ENST00000393035.2:c.380T>C	3.37:g.138347988T>C	ENSP00000376755:p.Leu127Ser	95	0	0		149	77	0.516779	NM_001033030	Q6IAN2	Missense_Mutation	SNP	ENST00000393035.2	37	CCDS3103.1	338	0.15476190476190477	301	0.6117886178861789	26	0.0718232044198895	0	0.0	11	0.014511873350923483	T	15.38	2.816084	0.50527	0.539719	0.015233	ENSG00000158234	ENST00000338446;ENST00000360570;ENST00000393035;ENST00000393034;ENST00000464668;ENST00000479848	T;T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59;1.59	4.94	4.94	0.65067	.	0.123452	0.64402	D	0.000001	T	0.00012	0.0000	L	0.29908	0.895	0.32280	P	0.567723	B;B;B;P	0.36647	0.008;0.007;0.023;0.563	B;B;B;P	0.45610	0.043;0.019;0.069;0.487	T	0.42565	-0.9444	9	0.52906	T	0.07	-9.8443	12.8554	0.57882	0.0:0.0:0.0:1.0	rs13043;rs640979;rs1136174;rs1672960;rs3199418;rs11556767;rs16848257;rs52837206;rs56519713;rs57680134;rs13043	127;149;161;127	Q9NVQ4;Q9NVQ4-3;Q9NVQ4-2;C9JDZ2	FAIM1_HUMAN;.;.;.	S	161;149;127;127;127;127	ENSP00000342805:L161S;ENSP00000353775:L149S;ENSP00000376755:L127S;ENSP00000376754:L127S;ENSP00000417642:L127S;ENSP00000420543:L127S	ENSP00000342805:L161S	L	+	2	0	FAIM	139830678	1.000000	0.71417	0.921000	0.36526	0.937000	0.57800	7.513000	0.81739	2.195000	0.70347	0.533000	0.62120	TTG	T|0.810;C|0.190	0.190	strong		0.313	FAIM-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357979.1	NM_001033032		C	138347988	T	C	138347988	3	2	25	1	0	0	0	0	1	0	0	0	5380	1821	63	3	544	3	FAIM	3	138347988	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	6010511	138347988	59674442	161	9070											
CPB1	1360	hgsc.bcm.edu	37	chr3	148575250	148575250	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtttcttttgcagaatgccCtggctaaagctactgtgaaa	10	14	9	8	0	1	2	0	1	1	1	1	2	1	2	1	1	4	4	1	1	5	5			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:148575250C>T	ENST00000491148.1	+	11	1322	c.988C>T	c.(988-990)Ctg>Ttg	p.L330L	RP11-680B3.2_ENST00000488190.1_RNA|CPB1_ENST00000282957.4_Silent_p.L330L|CPB1_ENST00000498639.1_3'UTR			P15086	CBPB1_HUMAN	carboxypeptidase B1 (tissue)	330						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)			GCAGAATGCCCTGGCTAAAGC	0.423																																					p.L330L		Atlas-SNP	.											.	CPB1	74	.	0			c.C988T						PASS	.						111	102	105					3																	148575250		2203	4300	6503	SO:0001819	synonymous_variant	1360	exon10			AATGCCCTGGCTA	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.988C>T	3.37:g.148575250C>T		130	0	0		126	56	0.444444	NM_001871	O60834|Q53XJ0|Q96BQ8	Silent	SNP	ENST00000491148.1	37	CCDS33874.1																																																																																			.	.	none		0.423	CPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355928.1	NM_001871		T	148575250	C	T	148575250	2	4	25	1	0	0	0	0	0	0	0	1	3798	680	24	2		2	CPB1	3	148575250	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	10227262	148575250	49447180	162	9071											
SUCNR1	56670	hgsc.bcm.edu	37	chr3	151599267	151599267	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgatgaatcaactgagacaCaacttcaaatcccttacatc	15	10	4	12	0	2	3	2	3	0	1	4	4	3	3	1	0	3	0	1	0	5	2	rs139804843		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:151599267C>T	ENST00000362032.5	+	3	1041	c.936C>T	c.(934-936)caC>caT	p.H312H	RP11-454C18.2_ENST00000475855.1_RNA|RP11-454C18.2_ENST00000483843.2_RNA	NM_033050.4	NP_149039.2	Q9BXA5	SUCR1_HUMAN	succinate receptor 1	312						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)	AACTGAGACACAACTTCAAAT	0.433																																					p.H312H		Atlas-SNP	.											.	SUCNR1	31	.	0			c.C936T						PASS	.	C		0,4406		0,0,2203	93	94	93		936	-7.4	0	3	dbSNP_134	93	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SUCNR1	NM_033050.4		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		312/335	151599267	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	56670	exon3			GAGACACAACTTC	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.936C>T	3.37:g.151599267C>T		101	0	0		103	49	0.475728	NM_033050	A8K305|Q8TDQ8	Silent	SNP	ENST00000362032.5	37	CCDS3162.1																																																																																			C|1.000;T|0.000	0.000	weak		0.433	SUCNR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357897.2	NM_033050		T	151599267	C	T	151599267	2	4	25	1	0	0	0	0	0	0	0	1	15381	477	17	2		2	SUCNR1	3	151599267	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	3024017	151599267	46423163	163	9072											
IGF2BP2	10644	hgsc.bcm.edu	37	chr3	185542653	185542653	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggacttcagcaggacctgTcccgccaggggcagcttcct	6	7	12	16	2	1	0	1	0	0	0	3	2	3	2	5	4	2	3	5	4	0	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:185542653T>A	ENST00000382199.2	-	1	191	c.96A>T	c.(94-96)ggA>ggT	p.G32G	IGF2BP2_ENST00000457616.2_Silent_p.G32G|IGF2BP2_ENST00000346192.3_Silent_p.G32G	NM_006548.4	NP_006539.3	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding protein 2	32	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)	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)			GCAGGACCTGTCCCGCCAGGG	0.657																																					p.G32G		Atlas-SNP	.											.	IGF2BP2	69	.	0			c.A96T						PASS	.						24	25	25					3																	185542653		2197	4294	6491	SO:0001819	synonymous_variant	10644	exon1			GACCTGTCCCGCC	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.96A>T	3.37:g.185542653T>A		132	0	0		187	81	0.433155	NM_001007225	A0A4Z0|B3FTN2|B3FTN3|B3FTN4	Silent	SNP	ENST00000382199.2	37	CCDS3273.2																																																																																			.	.	none		0.657	IGF2BP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157087.2	NM_006548		A	185542653	T	A	185542653	2	1	25	1	0	0	0	0	0	0	0	1	7583	1654	58	5		5	IGF2BP2	3	185542653	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	33943386	185542653	12479777	164	9073											
RTP2	344892	hgsc.bcm.edu	37	chr3	187419764	187419764	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctctcacctgcctgaggcGtgctgctccaggtactgctt	5	11	10	15	1	1	1	1	1	1	0	3	1	2	1	4	2	5	4	4	2	1	2	rs150707467		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:187419764G>A	ENST00000358241.1	-	1	581	c.153C>T	c.(151-153)caC>caT	p.H51H	RP11-211G3.3_ENST00000437407.1_5'Flank|RP11-211G3.3_ENST00000449623.1_5'Flank	NM_001004312.2	NP_001004312.2	Q5QGT7	RTP2_HUMAN	receptor (chemosensory) transporter protein 2	51					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)		TGCCTGAGGCGTGCTGCTCCA	0.627																																					p.H51H		Atlas-SNP	.											RTP2,right_upper_lobe,carcinoma,-2,1	RTP2	38	1	0			c.C153T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	98	102	100		153	-6	0.9	3	dbSNP_134	100	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	RTP2	NM_001004312.2		0,9,6494	AA,AG,GG		0.093,0.0227,0.0692		51/226	187419764	9,12997	2203	4300	6503	SO:0001819	synonymous_variant	344892	exon1			TGAGGCGTGCTGC	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.153C>T	3.37:g.187419764G>A		124	0	0		124	65	0.524194	NM_001004312	Q6NVH4	Silent	SNP	ENST00000358241.1	37	CCDS33911.1																																																																																			G|1.000;A|0.000	0.000	weak		0.627	RTP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344259.1	NM_001004312		A	187419764	G	A	187419764	2	1	25	1	0	0	0	0	0	0	0	1	13749	1136	40	1		1	RTP2	3	187419764	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1877111	187419764	10602666	165	9074											
LPP	4026	hgsc.bcm.edu	37	chr3	188478055	188478055	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtggaaaagaaagcatactgCgagccctgctacattgtaag	14	8	11	8	1	0	1	0	0	0	1	0	3	0	2	1	1	6	3	1	1	6	4	rs6771786	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:188478055C>T	ENST00000312675.4	+	8	1641	c.1395C>T	c.(1393-1395)tgC>tgT	p.C465C	LPP_ENST00000543006.1_Silent_p.C465C	NM_001167672.1|NM_005578.3	NP_001161144.1|NP_005569.1	Q93052	LPP_HUMAN	LIM domain containing preferred translocation partner in lipoma	465	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)		HMGA2/LPP(161)	NS(1)|breast(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		AAGCATACTGCGAGCCCTGCT	0.458			T	"HMGA2, MLL, C12orf9"	"lipoma, leukemia"								C|||	15	0.00299521	0.0	0.0029	5008	,	,		19555	0.001		0.0099	False		,,,				2504	0.002				p.C465C		Atlas-SNP	.		Dom	yes		3	3q28	4026	LIM domain containing preferred translocation partner in lipoma		"L, M"	.	LPP	72	.	0			c.C1395T						PASS	.	C	,,	6,4400	11.4+/-27.6	0,6,2197	140	131	134		1395,954,1395	-5.8	0.8	3	dbSNP_116	134	80,8520	47.2+/-106.3	1,78,4221	no	coding-synonymous,coding-synonymous,coding-synonymous	LPP	NM_001167671.1,NM_001167672.1,NM_005578.3	,,	1,84,6418	TT,TC,CC		0.9302,0.1362,0.6612	,,	465/613,318/466,465/613	188478055	86,12920	2203	4300	6503	SO:0001819	synonymous_variant	4026	exon8			ATACTGCGAGCCC	AL833171	CCDS3291.1	3q27-q28	2004-03-02	2002-01-14		ENSG00000145012	ENSG00000145012			6679	protein-coding gene	gene with protein product		600700	"LIM domain-containing preferred translocation partner in lipoma"			8812423	Standard	XM_005247453		Approved		uc003frs.2	Q93052	OTTHUMG00000156387	ENST00000312675.4:c.1395C>T	3.37:g.188478055C>T		167	0	0		185	88	0.475676	NM_005578	A1L4L6|D3DNV6|Q8NFX5	Silent	SNP	ENST00000312675.4	37	CCDS3291.1																																																																																			C|0.994;T|0.006	0.006	strong		0.458	LPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344030.1	NM_005578		T	188478055	C	T	188478055	2	4	25	1	0	0	0	0	0	0	0	1	8932	776	27	1		1	LPP	3	188478055	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1058291	188478055	9544375	166	9075											
ATP13A3	79572	hgsc.bcm.edu	37	chr3	194157937	194157937	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tccaaaacgttttgaaaatcGacaggaactttttaaaagaa	18	11	6	6	2	0	2	0	1	0	1	2	4	1	3	1	1	2	1	1	1	8	5	rs369809078		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:194157937G>A	ENST00000439040.1	-	20	2798	c.2007C>T	c.(2005-2007)gtC>gtT	p.V669V	ATP13A3_ENST00000256031.4_Silent_p.V669V			Q9H7F0	AT133_HUMAN	ATPase type 13A3	669						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)		TTTGAAAATCGACAGGAACTT	0.348																																					p.V669V		Atlas-SNP	.											.	ATP13A3	94	.	0			c.C2007T						PASS	.	G		0,3612		0,0,1806	98	93	94		2007	-1.1	0.8	3		94	1,8175		0,1,4087	no	coding-synonymous	ATP13A3	NM_024524.3		0,1,5893	AA,AG,GG		0.0122,0.0,0.0085		669/1227	194157937	1,11787	1806	4088	5894	SO:0001819	synonymous_variant	79572	exon19			AAAATCGACAGGA	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.2007C>T	3.37:g.194157937G>A		95	0	0		83	41	0.493976	NM_024524	Q8NC11|Q96KS1	Silent	SNP	ENST00000439040.1	37	CCDS43187.1																																																																																			.	.	weak		0.348	ATP13A3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342799.2	NM_024524		A	194157937	G	A	194157937	2	1	25	1	0	0	0	0	0	0	0	1	1125	1045	37	1		1	ATP13A3	3	194157937	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	5679882	194157937	3864493	167	9076											
C3orf21	152002	hgsc.bcm.edu	37	chr3	194790782	194790782	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gaagcccggcagcccctcggGgggcgggcccccaacccggg	5	1	17	18	4	0	0	0	0	0	0	1	1	0	0	6	6	3	1	6	6	2	0			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:194790782G>A	ENST00000310380.6	-	4	952	c.844C>T	c.(844-846)Ccc>Tcc	p.P282S	XXYLT1_ENST00000429994.1_Missense_Mutation_p.P136S|XXYLT1_ENST00000460582.1_5'UTR|XXYLT1_ENST00000437101.1_Missense_Mutation_p.P79S|XXYLT1_ENST00000355729.4_Missense_Mutation_p.P79S|XXYLT1_ENST00000356740.5_Missense_Mutation_p.P76S	NM_152531.4	NP_689744.3	Q8NBI6	XXLT1_HUMAN	xyloside xylosyltransferase 1	282						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring pentosyl groups (GO:0016763)										AGCCCCTCGGGGGGCGGGCCC	0.672																																					p.P282S		Atlas-SNP	.											C3orf21,bladder,carcinoma,+2,1	.	.	1	0			c.C844T						scavenged	.						22	27	26					3																	194790782		1802	3994	5796	SO:0001583	missense	152002	exon4			CCTCGGGGGGCGG	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.844C>T	3.37:g.194790782G>A	ENSP00000309640:p.Pro282Ser	5	0	0		14	2	0.142857	NM_152531	D3DNW5|Q8NAL3|Q8WV03|Q96ME0	Missense_Mutation	SNP	ENST00000310380.6	37	CCDS43188.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.232940	0.79688	.	.	ENSG00000173950	ENST00000310380;ENST00000437101;ENST00000355729;ENST00000429994;ENST00000356740	T;T;T;T;T	0.21932	1.98;1.98;1.98;1.98;1.98	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.50051	0.1593	M	0.81497	2.545	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.97110	1.0;0.976;0.975	T	0.32134	-0.9918	10	0.24483	T	0.36	-21.2021	19.2443	0.93896	0.0:0.0:1.0:0.0	.	282;79;76	Q8NBI6;Q8NBI6-2;Q8NBI6-3	XXLT1_HUMAN;.;.	S	282;79;79;136;76	ENSP00000309640:P282S;ENSP00000409865:P79S;ENSP00000347967:P79S;ENSP00000399422:P136S;ENSP00000349179:P76S	ENSP00000309640:P282S	P	-	1	0	C3orf21	196272071	1.000000	0.71417	0.712000	0.30502	0.863000	0.49368	7.752000	0.85141	2.797000	0.96272	0.563000	0.77884	CCC	.	.	none		0.672	XXYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342290.1	NM_152531		A	194790782	G	A	194790782	3	1	25	1	0	0	0	0	1	0	0	0	2216	1232	43	2	341	2	C3orf21	3	194790782	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	632845	194790782	3231648	168	9077											
FBXO45	200933	hgsc.bcm.edu	37	chr3	196295974	196295974	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gggggccgggggccggctgcCcagccgggtgctggagttgg	2	5	23	11	3	0	0	0	0	0	0	0	1	0	1	4	8	3	3	4	8	0	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:196295974C>T	ENST00000311630.6	+	1	416	c.119C>T	c.(118-120)cCc>cTc	p.P40L	WDR53_ENST00000433160.1_5'Flank|FBXO45_ENST00000440469.1_Intron|WDR53_ENST00000332629.5_5'Flank|WDR53_ENST00000429115.1_5'Flank	NM_001105573.1	NP_001099043.1	P0C2W1	FBSP1_HUMAN	F-box protein 45	40	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)		ggccggcTGCCCAGCCGGGTG	0.771																																					p.P40L		Atlas-SNP	.											.	FBXO45	18	.	0			c.C119T						PASS	.						2	3	3					3																	196295974		1415	3033	4448	SO:0001583	missense	200933	exon1			GGCTGCCCAGCCG	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.119C>T	3.37:g.196295974C>T	ENSP00000310332:p.Pro40Leu	19	0	0		55	27	0.490909	NM_001105573	A6NF90|D3DXB5	Missense_Mutation	SNP	ENST00000311630.6	37	CCDS46985.1	.	.	.	.	.	.	.	.	.	.	c	23.0	4.361705	0.82353	.	.	ENSG00000174013	ENST00000311630	D	0.99709	-6.48	4.78	4.78	0.61160	F-box domain, cyclin-like (2);F-box domain, Skp2-like (1);	0.124714	0.56097	N	0.000035	D	0.99760	0.9903	M	0.92833	3.35	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	D	0.97050	0.9763	10	0.87932	D	0	.	16.7012	0.85349	0.0:1.0:0.0:0.0	.	40	P0C2W1	FBSP1_HUMAN	L	40	ENSP00000310332:P40L	ENSP00000310332:P40L	P	+	2	0	FBXO45	197780371	1.000000	0.71417	1.000000	0.80357	0.627000	0.37826	4.709000	0.61867	2.214000	0.71695	0.531000	0.56144	CCC	.	.	none		0.771	FBXO45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340687.2			T	196295974	C	T	196295974	3	4	25	1	0	0	0	0	1	0	0	0	5762	623	22	2	121	2	FBXO45	3	196295974	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1505192	196295974	1726456	169	9078											
PIGZ	80235	hgsc.bcm.edu	37	chr3	196675397	196675397	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcgaggccccaccagcagcGcatagccgctcaccaggcca	9	3	11	18	3	1	0	1	0	0	0	2	1	1	0	6	2	3	3	6	2	1	1	rs144088027	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:196675397G>A	ENST00000412723.1	-	3	517	c.371C>T	c.(370-372)gCg>gTg	p.A124V	PIGZ_ENST00000443835.1_Intron	NM_025163.2	NP_079439.2	Q86VD9	PIGZ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Z	124					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)		CACCAGCAGCGCATAGCCGCT	0.682													g|||	12	0.00239617	0.0023	0.0	5008	,	,		14442	0.0		0.007	False		,,,				2504	0.002				p.A124V		Atlas-SNP	.											.	PIGZ	34	.	0			c.C371T						PASS	.		VAL/ALA	5,4389		0,5,2192	21	19	20		371	-10.5	0	3	dbSNP_134	20	30,8560		0,30,4265	yes	missense	PIGZ	NM_025163.2	64	0,35,6457	AA,AG,GG		0.3492,0.1138,0.2696	benign	124/580	196675397	35,12949	2197	4295	6492	SO:0001583	missense	80235	exon3			AGCAGCGCATAGC	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.371C>T	3.37:g.196675397G>A	ENSP00000413405:p.Ala124Val	47	0	0		75	44	0.586667	NM_025163	Q9H9G6	Missense_Mutation	SNP	ENST00000412723.1	37	CCDS3324.1	9	0.004120879120879121	2	0.0040650406504065045	0	0.0	0	0.0	7	0.009234828496042216	g	1.154	-0.645692	0.03531	0.001138	0.003492	ENSG00000119227	ENST00000412723	T	0.11495	2.77	5.25	-10.5	0.00291	.	2.309490	0.01740	N	0.029334	T	0.03608	0.0103	N	0.11341	0.13	0.18873	N	0.999989	B	0.09022	0.002	B	0.06405	0.002	T	0.28996	-1.0026	10	0.08381	T	0.77	3.9812	15.9089	0.79456	0.0966:0.0:0.8226:0.0808	.	124	Q86VD9	PIGZ_HUMAN	V	124	ENSP00000413405:A124V	ENSP00000413405:A124V	A	-	2	0	PIGZ	198159794	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	-0.517000	0.06275	-3.012000	0.00272	-1.122000	0.02009	GCG	G|0.997;A|0.003	0.003	strong		0.682	PIGZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340486.2	NM_025163		A	196675397	G	A	196675397	3	1	25	1	0	0	0	0	1	0	0	0	11914	1087	38	1	1372	1	PIGZ	3	196675397	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	379423	196675397	1347033	170	9079											
LETM1	3954	hgsc.bcm.edu	37	chr4	1824020	1824020	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttggggagcagctaccacaCgttcgggctcaaaatccttc	9	10	10	12	2	1	0	1	0	0	0	4	1	2	1	2	3	3	4	2	3	3	4	rs28681468	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1824020C>T	ENST00000302787.2	-	10	1792	c.1496G>A	c.(1495-1497)cGt>cAt	p.R499H		NM_012318.2	NP_036450.1	O95202	LETM1_HUMAN	leucine zipper-EF-hand containing transmembrane protein 1	499					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)			AGCTACCACACGTTCGGGCTC	0.592													c|||	59	0.0117812	0.0091	0.0173	5008	,	,		18177	0.0		0.0268	False		,,,				2504	0.0082				p.R499H		Atlas-SNP	.											.	LETM1	48	.	0			c.G1496A						PASS	.	C	HIS/ARG	52,4354	50.9+/-86.3	0,52,2151	59	53	55		1496	-0.7	0	4	dbSNP_125	55	266,8334	102.3+/-163.5	3,260,4037	yes	missense	LETM1	NM_012318.2	29	3,312,6188	TT,TC,CC		3.093,1.1802,2.445	benign	499/740	1824020	318,12688	2203	4300	6503	SO:0001583	missense	3954	exon10			ACCACACGTTCGG	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.1496G>A	4.37:g.1824020C>T	ENSP00000305653:p.Arg499His	129	0	0		110	53	0.481818	NM_012318	B4DED2|Q9UF65	Missense_Mutation	SNP	ENST00000302787.2	37	CCDS3355.1	24	0.01098901098901099	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	17	0.022427440633245383	C	11.17	1.560042	0.27827	0.011802	0.03093	ENSG00000168924	ENST00000302787	.	.	.	4.65	-0.707	0.11245	.	0.970810	0.08436	N	0.946208	T	0.05456	0.0144	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18745	-1.0327	9	0.45353	T	0.12	-2.8575	3.2806	0.06913	0.6202:0.1675:0.0962:0.1161	rs28681468;rs28681468	499	O95202	LETM1_HUMAN	H	499	.	ENSP00000305653:R499H	R	-	2	0	LETM1	1793818	0.001000	0.12720	0.002000	0.10522	0.002000	0.02628	0.573000	0.23699	-0.059000	0.13154	0.456000	0.33151	CGT	C|0.980;T|0.020	0.020	strong		0.592	LETM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241634.1			T	1824020	C	T	1824020	3	4	25	1	0	0	0	0	1	0	0	0	8743	536	19	1	743	1	LETM1	4	1824020	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10		1824020	189330256	171	9080											
LRPAP1	4043	hgsc.bcm.edu	37	chr4	3520701	3520701	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tccagttcttcgccggagaaTttcccagaggtcttcgccta	7	12	9	13	3	2	2	0	0	2	2	6	3	4	2	4	2	0	1	4	2	2	5			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:3520701T>C	ENST00000500728.2	-	4	635	c.489A>G	c.(487-489)aaA>aaG	p.K163K	LRPAP1_ENST00000296325.5_5'UTR	NM_002337.3	NP_002328.1	P30533	AMRP_HUMAN	low density lipoprotein receptor-related protein associated protein 1	163					extracellular negative regulation of signal transduction (GO:1900116)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of protein binding (GO:0032091)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|protein folding (GO:0006457)|receptor-mediated endocytosis (GO:0006898)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|rough endoplasmic reticulum lumen (GO:0048237)|vesicle (GO:0031982)	asialoglycoprotein receptor activity (GO:0004873)|heparin binding (GO:0008201)|low-density lipoprotein particle receptor binding (GO:0050750)|receptor antagonist activity (GO:0048019)|unfolded protein binding (GO:0051082)|very-low-density lipoprotein particle receptor binding (GO:0070326)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(2)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.165)		CGCCGGAGAATTTCCCAGAGG	0.597																																					p.K163K		Atlas-SNP	.											.	LRPAP1	29	.	0			c.A489G						PASS	.						49	53	51					4																	3520701		2203	4300	6503	SO:0001819	synonymous_variant	4043	exon4			GGAGAATTTCCCA		CCDS3371.1	4p16.3	2008-05-02	2003-03-17		ENSG00000163956	ENSG00000163956			6701	protein-coding gene	gene with protein product		104225	"low density lipoprotein-related protein-associated protein 1 (alpha-2-macroglobulin receptor-associated protein 1)"	A2MRAP		1712782	Standard	NM_002337		Approved	HBP44	uc003ghh.4	P30533	OTTHUMG00000090299	ENST00000500728.2:c.489A>G	4.37:g.3520701T>C		97	0	0		84	43	0.511905	NM_002337	D3DVR9|Q2M310|Q53HQ3|Q53HS6	Silent	SNP	ENST00000500728.2	37	CCDS3371.1																																																																																			.	.	none		0.597	LRPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206659.4			C	3520701	T	C	3520701	2	2	25	1	0	0	0	0	0	0	0	1	8973	1490	52	3		3	LRPAP1	4	3520701	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	1696681	3520701	187633575	172	9081											
LRPAP1	4043	hgsc.bcm.edu	37	chr4	3534042	3534042	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tcttctcccgcgagtacttgCcgccgtggctcgcagcgggc	3	9	13	16	6	2	0	0	0	2	0	4	1	2	0	3	2	3	3	3	2	1	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:3534042C>A	ENST00000500728.2	-	1	244	c.98G>T	c.(97-99)gGc>gTc	p.G33V	LRPAP1_ENST00000296325.5_5'Flank	NM_002337.3	NP_002328.1	P30533	AMRP_HUMAN	low density lipoprotein receptor-related protein associated protein 1	33					extracellular negative regulation of signal transduction (GO:1900116)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of protein binding (GO:0032091)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|protein folding (GO:0006457)|receptor-mediated endocytosis (GO:0006898)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|rough endoplasmic reticulum lumen (GO:0048237)|vesicle (GO:0031982)	asialoglycoprotein receptor activity (GO:0004873)|heparin binding (GO:0008201)|low-density lipoprotein particle receptor binding (GO:0050750)|receptor antagonist activity (GO:0048019)|unfolded protein binding (GO:0051082)|very-low-density lipoprotein particle receptor binding (GO:0070326)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(2)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.165)		CGAGTACTTGCCGCCGTGGCT	0.672																																					p.G33V		Atlas-SNP	.											.	LRPAP1	29	.	0			c.G98T						PASS	.						20	20	20					4																	3534042		2170	4270	6440	SO:0001583	missense	4043	exon1			TACTTGCCGCCGT		CCDS3371.1	4p16.3	2008-05-02	2003-03-17		ENSG00000163956	ENSG00000163956			6701	protein-coding gene	gene with protein product		104225	"low density lipoprotein-related protein-associated protein 1 (alpha-2-macroglobulin receptor-associated protein 1)"	A2MRAP		1712782	Standard	NM_002337		Approved	HBP44	uc003ghh.4	P30533	OTTHUMG00000090299	ENST00000500728.2:c.98G>T	4.37:g.3534042C>A	ENSP00000421922:p.Gly33Val	65	0	0		130	60	0.461538	NM_002337	D3DVR9|Q2M310|Q53HQ3|Q53HS6	Missense_Mutation	SNP	ENST00000500728.2	37	CCDS3371.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.740844	0.89573	.	.	ENSG00000163956	ENST00000500728	T	0.46451	0.87	3.8	3.8	0.43715	Alpha-2-macroglobulin receptor-associated protein, domain 1 (1);	0.120269	0.56097	D	0.000032	T	0.58395	0.2119	M	0.68317	2.08	0.80722	D	1	D	0.76494	0.999	D	0.71414	0.973	T	0.60459	-0.7259	10	0.52906	T	0.07	-30.362	11.0418	0.47835	0.0:1.0:0.0:0.0	.	33	P30533	AMRP_HUMAN	V	33	ENSP00000421922:G33V	ENSP00000421922:G33V	G	-	2	0	LRPAP1	3503840	0.998000	0.40836	1.000000	0.80357	0.924000	0.55760	4.856000	0.62932	1.937000	0.56155	0.591000	0.81541	GGC	.	.	none		0.672	LRPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206659.4			A	3534042	C	A	3534042	3	1	25	1	0	0	0	0	1	0	0	0	8973	739	26	4	1007	4	LRPAP1	4	3534042	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	13341	3534042	187620234	173	9082											
ADRA2C	152	hgsc.bcm.edu	37	chr4	3769573	3769573	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tctgccgcgaggcctgccagGtgcccggcccgctcttcaag	4	7	13	17	4	3	0	1	0	2	0	3	1	3	0	5	3	3	1	5	3	1	1	rs370580020		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:3769573G>C	ENST00000330055.5	+	1	1449	c.1240G>C	c.(1240-1242)Gtg>Ctg	p.V414L	ADRA2C_ENST00000509482.1_Intron	NM_000683.3	NP_000674.2	P18825	ADA2C_HUMAN	adrenoceptor alpha 2C	414					activation of MAPK activity by adrenergic receptor signaling pathway (GO:0071883)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|energy reserve metabolic process (GO:0006112)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of norepinephrine secretion (GO:0010700)|negative regulation of uterine smooth muscle contraction (GO:0070473)|platelet activation (GO:0030168)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of vasoconstriction (GO:0045907)|regulation of insulin secretion (GO:0050796)|regulation of sensory perception of pain (GO:0051930)|small molecule metabolic process (GO:0044281)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|alpha2-adrenergic receptor activity (GO:0004938)|epinephrine binding (GO:0051379)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)	8				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)	Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bethanidine(DB00217)|Brimonidine(DB00484)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Desipramine(DB01151)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Fenoldopam(DB00800)|Iloperidone(DB04946)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Tizanidine(DB00697)|Tolazoline(DB00797)|Xylometazoline(DB06694)|Yohimbine(DB01392)|Ziprasidone(DB00246)	GGCCTGCCAGGTGCCCGGCCC	0.592																																					p.V414L	Esophageal Squamous(12;454 628 4517 14479)	Atlas-SNP	.											.	ADRA2C	24	.	0			c.G1240C						PASS	.						34	40	38					4																	3769573		2195	4299	6494	SO:0001583	missense	152	exon1			TGCCAGGTGCCCG	AY455666	CCDS47004.1	4p16.3	2013-10-22	2012-05-09		ENSG00000184160	ENSG00000184160		"GPCR / Class A : Adrenoceptors : alpha"	283	protein-coding gene	gene with protein product		104250	"adrenergic, alpha-2C-, receptor"	ADRA2L2, ADRA2RL2		1849485	Standard	NM_000683		Approved	ADRARL2	uc003ghm.3	P18825	OTTHUMG00000159830	ENST00000330055.5:c.1240G>C	4.37:g.3769573G>C	ENSP00000386069:p.Val414Leu	72	0	0		77	35	0.454545	NM_000683	P35369|Q9HB49	Missense_Mutation	SNP	ENST00000330055.5	37	CCDS47004.1	.	.	.	.	.	.	.	.	.	.	G	15.87	2.960398	0.53400	.	.	ENSG00000184160	ENST00000330055	T	0.72394	-0.65	3.66	1.85	0.25348	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.60830	0.2299	L	0.39692	1.235	0.24721	N	0.993141	P	0.38551	0.636	B	0.40602	0.334	T	0.47548	-0.9109	9	0.33940	T	0.23	.	8.0626	0.30642	0.0:0.2357:0.6079:0.1563	.	414	P18825	ADA2C_HUMAN	L	414	ENSP00000386069:V414L	ENSP00000386069:V414L	V	+	1	0	ADRA2C	3739371	0.246000	0.23909	0.999000	0.59377	0.985000	0.73830	0.541000	0.23207	0.202000	0.20498	0.603000	0.83216	GTG	.	.	alt		0.592	ADRA2C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357607.1	NM_000683		C	3769573	G	C	3769573	3	2	25	1	0	0	0	0	1	0	0	0	339	1261	44	4	1242	4	ADRA2C	4	3769573	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	235531	3769573	187384703	174	9083											
MSX1	4487	hgsc.bcm.edu	37	chr4	4864582	4864582	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgcgcggagttctccagctcGctcagcctcactgagacgca	7	7	11	16	5	3	1	2	1	1	1	5	3	3	2	2	1	2	4	2	1	0	1	rs369820958		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:4864582G>T	ENST00000382723.4	+	2	858	c.624G>T	c.(622-624)tcG>tcT	p.S208S	MSX1_ENST00000468421.1_3'UTR	NM_002448.3	NP_002439.2	P28360	MSX1_HUMAN	msh homeobox 1	208					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)		TCTCCAGCTCGCTCAGCCTCA	0.632																																					p.S208S		Atlas-SNP	.											MSX1,NS,carcinoma,+1,1	MSX1	19	1	0			c.G624T						PASS	.	G		0,4406		0,0,2203	40	42	41		624	0.7	1	4		41	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MSX1	NM_002448.3		0,1,6502	TT,TG,GG		0.0116,0.0,0.0077		208/304	4864582	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	4487	exon2			CAGCTCGCTCAGC	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.624G>T	4.37:g.4864582G>T		100	0	0		119	70	0.588235	NM_002448	A0SZU5|A8K3M1|Q96NY4	Silent	SNP	ENST00000382723.4	37	CCDS3378.2																																																																																			.	.	weak		0.632	MSX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206700.3			T	4864582	G	T	4864582	2	4	25	1	0	0	0	0	0	0	0	1	9904	1074	38	4		4	MSX1	4	4864582	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1095009	4864582	186289694	175	9084											
CRMP1	1400	hgsc.bcm.edu	37	chr4	5837708	5837708	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagatgaccacgtcggcatcCgagcccacggcaatccgccc	9	4	10	18	5	0	2	0	1	0	1	3	3	2	2	5	2	1	2	5	2	1	0			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:5837708C>T	ENST00000397890.2	-	11	1429	c.1215G>A	c.(1213-1215)tcG>tcA	p.S405S	CRMP1_ENST00000324989.7_Silent_p.S519S|CRMP1_ENST00000511535.1_5'UTR|CRMP1_ENST00000512574.1_Silent_p.S403S	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	405					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)	p.S519S(1)		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)		CGTCGGCATCCGAGCCCACGG	0.522																																					p.S519S		Atlas-SNP	.											CRMP1,NS,carcinoma,-1,2	CRMP1	118	2	1	Substitution - coding silent(1)	stomach(1)	c.G1557A						PASS	.						149	135	140					4																	5837708		2203	4300	6503	SO:0001819	synonymous_variant	1400	exon11			GGCATCCGAGCCC	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.1215G>A	4.37:g.5837708C>T		175	0	0		183	77	0.420765	NM_001014809	A0EJG6|Q13024|Q4W5F1|Q96TC8	Silent	SNP	ENST00000397890.2	37	CCDS43207.1																																																																																			.	.	none		0.522	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313		T	5837708	C	T	5837708	2	4	25	1	0	0	0	0	0	0	0	1	3892	639	23	1		1	CRMP1	4	5837708	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	973126	5837708	185316568	176	9085											
TBC1D14	57533	hgsc.bcm.edu	37	chr4	7006636	7006636	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cccttagcacaggaggctctGaagtggagaacgaaggtaga	13	6	14	8	1	1	3	0	1	1	2	1	6	1	4	1	4	2	3	1	4	5	2	rs11731231	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:7006636G>C	ENST00000409757.4	+	8	1460	c.1336G>C	c.(1336-1338)Gaa>Caa	p.E446Q	TBC1D14_ENST00000446947.2_Missense_Mutation_p.E59Q|TBC1D14_ENST00000451522.2_Missense_Mutation_p.E166Q|TBC1D14_ENST00000448507.1_Missense_Mutation_p.E446Q|TBC1D14_ENST00000410031.1_Missense_Mutation_p.E218Q	NM_020773.2	NP_065824.2	Q9P2M4	TBC14_HUMAN	TBC1 domain family, member 14	446	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.		E -> Q (in dbSNP:rs11731231).		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						AGGAGGCTCTGAAGTGGAGAA	0.458													G|||	8	0.00159744	0.0	0.0	5008	,	,		16696	0.0		0.006	False		,,,				2504	0.002				p.E446Q		Atlas-SNP	.											.	TBC1D14	110	.	0			c.G1336C						PASS	.	G	GLN/GLU,GLN/GLU,GLN/GLU	4,4402	8.1+/-20.4	0,4,2199	108	110	109		1336,496,1336	5.3	0	4	dbSNP_120	109	45,8555	29.6+/-80.5	0,45,4255	yes	missense,missense,missense	TBC1D14	NM_001113361.1,NM_001113363.1,NM_020773.2	29,29,29	0,49,6454	CC,CG,GG		0.5233,0.0908,0.3767	benign,benign,benign	446/694,166/414,446/694	7006636	49,12957	2203	4300	6503	SO:0001583	missense	57533	exon8			GGCTCTGAAGTGG	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.1336G>C	4.37:g.7006636G>C	ENSP00000386921:p.Glu446Gln	62	0	0		57	27	0.473684	NM_001113361	B9A6L5|D3DVT4|E9PAZ6|Q8IW15|Q8NDK3	Missense_Mutation	SNP	ENST00000409757.4	37	CCDS3394.2	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	17.41	3.381565	0.61845	9.08E-4	0.005233	ENSG00000132405	ENST00000448507;ENST00000409757;ENST00000410031;ENST00000451522;ENST00000439515;ENST00000446947	T;T;T;T;T;T	0.33216	3.46;3.46;3.43;3.44;1.42;3.0	5.27	5.27	0.74061	Rab-GAP/TBC domain (4);	0.405543	0.28718	N	0.014366	T	0.33323	0.0859	M	0.63843	1.955	0.80722	D	1	B;B;B	0.22211	0.059;0.003;0.066	B;B;B	0.36092	0.097;0.009;0.217	T	0.23583	-1.0184	10	0.49607	T	0.09	-2.7179	18.059	0.89371	0.0:0.0:1.0:0.0	rs11731231;rs52800326;rs11731231	59;166;446	F5GXK4;Q9P2M4-2;Q9P2M4	.;.;TBC14_HUMAN	Q	446;446;218;166;65;59	ENSP00000404041:E446Q;ENSP00000386921:E446Q;ENSP00000386343:E218Q;ENSP00000388886:E166Q;ENSP00000389082:E65Q;ENSP00000405875:E59Q	ENSP00000386921:E446Q	E	+	1	0	TBC1D14	7057537	0.408000	0.25360	0.029000	0.17559	0.574000	0.36063	3.009000	0.49552	2.722000	0.93159	0.655000	0.94253	GAA	G|0.997;C|0.003	0.003	strong		0.458	TBC1D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206981.3	NM_020773		C	7006636	G	C	7006636	3	2	25	1	0	0	0	0	1	0	0	0	15618	1291	45	4	1369	4	TBC1D14	4	7006636	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1168928	7006636	184147640	177	9086											
DCAF4L1	285429	hgsc.bcm.edu	37	chr4	41984782	41984782	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgcccctgcatgtgcacgagGaagagggaatcgtggtggca	9	7	16	9	2	0	1	0	0	0	1	1	4	0	3	2	4	3	3	2	4	2	0	rs369307123		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:41984782G>A	ENST00000333141.5	+	1	1070	c.973G>A	c.(973-975)Gaa>Aaa	p.E325K		NM_001029955.3	NP_001025126.2	Q3SXM0	DC4L1_HUMAN	DDB1 and CUL4 associated factor 4-like 1	325										breast(1)|endometrium(5)|kidney(6)|large_intestine(11)|lung(12)|prostate(1)|skin(1)	37						TGTGCACGAGGAAGAGGGAAT	0.562																																					p.E325K		Atlas-SNP	.											.	DCAF4L1	70	.	0			c.G973A						PASS	.	G	LYS/GLU	0,4406		0,0,2203	125	92	103		973	-0.3	0.7	4		103	1,8599	1.2+/-3.3	0,1,4299	no	missense	DCAF4L1	NM_001029955.3	56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	325/397	41984782	1,13005	2203	4300	6503	SO:0001583	missense	285429	exon1			CACGAGGAAGAGG	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.973G>A	4.37:g.41984782G>A	ENSP00000327796:p.Glu325Lys	156	0	0		205	86	0.419512	NM_001029955	B3KVI3|Q3ZCW8|Q499Y5|Q9UFI0	Missense_Mutation	SNP	ENST00000333141.5	37	CCDS33978.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.245448	0.59103	0.0	1.16E-4	ENSG00000182308	ENST00000333141	T	0.70045	-0.45	0.97	-0.348	0.12613	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.285662	0.40064	N	0.001186	T	0.63165	0.2488	L	0.60455	1.87	0.31255	N	0.693609	P	0.46578	0.88	P	0.50270	0.636	T	0.62388	-0.6865	10	0.34782	T	0.22	.	5.6253	0.17478	0.0:0.0:0.6821:0.3179	.	325	Q3SXM0	DC4L1_HUMAN	K	325	ENSP00000327796:E325K	ENSP00000327796:E325K	E	+	1	0	DCAF4L1	41679539	1.000000	0.71417	0.729000	0.30791	0.811000	0.45836	1.846000	0.39289	-0.124000	0.11724	0.313000	0.20887	GAA	.	.	weak		0.562	DCAF4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360958.1	NM_001029955		A	41984782	G	A	41984782	3	1	25	1	0	0	0	0	1	0	0	0	4273	1175	41	2	975	2	DCAF4L1	4	41984782	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	34978146	41984782	149169494	178	9087											
FIP1L1	81608	hgsc.bcm.edu	37	chr4	54324914	54324914	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaacgacatagagaaagaCgacacagggagaaagaggaa	22	1	13	5	2	0	5	0	0	0	5	0	10	0	6	0	2	1	0	0	2	6	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:54324914C>T	ENST00000337488.6	+	17	1788	c.1594C>T	c.(1594-1596)Cga>Tga	p.R532*	FIP1L1_ENST00000358575.5_Nonsense_Mutation_p.R526*|FIP1L1_ENST00000306932.6_Nonsense_Mutation_p.R458*|FIP1L1_ENST00000507166.1_Intron	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1	532	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)			TAGAGAAAGACGACACAGGGA	0.393			T	PDGFRA	idiopathic hypereosinophilic syndrome																																p.R532X		Atlas-SNP	.		Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	.	FIP1L1	60	.	0			c.C1594T						PASS	.						98	110	106					4																	54324914		2203	4300	6503	SO:0001587	stop_gained	81608	exon17			GAAAGACGACACA	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.1594C>T	4.37:g.54324914C>T	ENSP00000336752:p.Arg532*	194	0	0		213	92	0.431925	NM_030917	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Nonsense_Mutation	SNP	ENST00000337488.6	37	CCDS3491.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.044750	0.93685	.	.	ENSG00000145216	ENST00000337488;ENST00000358575;ENST00000306932;ENST00000504094	.	.	.	4.93	4.02	0.46733	.	0.000000	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.7173	10.9749	0.47461	0.3547:0.6453:0.0:0.0	.	.	.	.	X	532;526;458;192	.	ENSP00000302993:R458X	R	+	1	2	FIP1L1	54019671	1.000000	0.71417	0.953000	0.39169	0.010000	0.07245	1.951000	0.40333	2.706000	0.92434	0.591000	0.81541	CGA	.	.	none		0.393	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250602.1	NM_030917		T	54324914	C	T	54324914	4	4	25	1	0	0	0	0	0	1	0	0	5904	528	19	1	1691	1	FIP1L1	4	54324914	Nonsense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	12340132	54324914	136829362	179	9088											
DCK	1633	hgsc.bcm.edu	37	chr4	71888240	71888240	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agctcaaagatgcagagaaaCctgtattattttttgaacga	15	12	8	6	1	1	3	1	1	0	2	1	5	1	3	1	0	4	3	1	0	5	5	rs67437265	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:71888240C>T	ENST00000286648.5	+	3	761	c.364C>T	c.(364-366)Cct>Tct	p.P122S	DCK_ENST00000504730.1_Missense_Mutation_p.P122S|DCK_ENST00000504952.1_Missense_Mutation_p.P122S	NM_000788.2	NP_000779.1	P27707	DCK_HUMAN	deoxycytidine kinase	122				P -> S (in Ref. 4; AAV38744/AAV38745). {ECO:0000305}.	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)	TGCAGAGAAACCTGTATTATT	0.388													C|||	165	0.0329473	0.0635	0.0216	5008	,	,		18820	0.0387		0.0099	False		,,,				2504	0.0174				p.P122S		Atlas-SNP	.											.	DCK	23	.	0			c.C364T	GRCh37	CM076146	DCK	M	rs67437265	PASS	.	C	SER/PRO	209,4197	128.6+/-165.4	7,195,2001	110	111	111		364	5.8	1	4	dbSNP_130	111	87,8513	48.9+/-108.6	0,87,4213	yes	missense	DCK	NM_000788.2	74	7,282,6214	TT,TC,CC		1.0116,4.7435,2.2759	benign	122/261	71888240	296,12710	2203	4300	6503	SO:0001583	missense	1633	exon3			GAGAAACCTGTAT	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.364C>T	4.37:g.71888240C>T	ENSP00000286648:p.Pro122Ser	44	0	0		29	14	0.482759	NM_000788	B2R8V6|Q5TZY7|Q6FI11	Missense_Mutation	SNP	ENST00000286648.5	37	CCDS3548.1	73	0.033424908424908424	29	0.05894308943089431	9	0.024861878453038673	25	0.043706293706293704	10	0.013192612137203167	C	31	5.089919	0.94149	0.047435	0.010116	ENSG00000156136	ENST00000286648;ENST00000504730;ENST00000504952	D;D;D	0.97811	-4.55;-4.55;-4.55	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	D	0.89989	0.6875	L	0.57536	1.79	0.09310	P	0.999999999887503	D	0.89917	1.0	D	0.81914	0.995	D	0.86615	0.1875	8	.	.	.	.	20.1162	0.97934	0.0:1.0:0.0:0.0	.	122	P27707	DCK_HUMAN	S	122	ENSP00000286648:P122S;ENSP00000425578:P122S;ENSP00000421508:P122S	.	P	+	1	0	DCK	72107104	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.625000	0.83145	2.757000	0.94681	0.563000	0.77884	CCT	C|0.975;T|0.025	0.025	strong		0.388	DCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252159.2			T	71888240	C	T	71888240	3	4	25	1	0	0	0	0	1	0	0	0	4292	507	18	2	374	2	DCK	4	71888240	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	17563326	71888240	119266036	180	9089											
ART3	419	hgsc.bcm.edu	37	chr4	77003484	77003484	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	catattcagccaaacctcagGctgctaatgaccagctcact	12	9	6	14	0	3	1	3	1	0	0	3	1	3	1	3	1	4	3	3	1	3	3	rs142545952	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:77003484G>A	ENST00000355810.4	+	3	696	c.577G>A	c.(577-579)Gct>Act	p.A193T	ART3_ENST00000513494.1_3'UTR|ART3_ENST00000341029.5_Missense_Mutation_p.A193T|ART3_ENST00000349321.3_Missense_Mutation_p.A193T	NM_001130016.2	NP_001123488.1	Q13508	NAR3_HUMAN	ADP-ribosyltransferase 3	193					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)	p.A193T(1)		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)			CAAACCTCAGGCTGCTAATGA	0.403																																					p.A193T		Atlas-SNP	.											ART3,NS,carcinoma,0,1	ART3	34	1	1	Substitution - Missense(1)	lung(1)	c.G577A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	0,4406		0,0,2203	46	43	44		577,577,577	1	0	4	dbSNP_134	44	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense,missense	ART3	NM_001130016.1,NM_001130017.1,NM_001179.4	58,58,58	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	benign,benign,benign	193/390,193/368,193/379	77003484	4,13002	2203	4300	6503	SO:0001583	missense	419	exon3			CCTCAGGCTGCTA	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.577G>A	4.37:g.77003484G>A	ENSP00000348064:p.Ala193Thr	77	0	0		96	40	0.416667	NM_001130017	Q53XW3|Q6FHT7|Q8WVJ7|Q93069|Q96HL1	Missense_Mutation	SNP	ENST00000355810.4	37	CCDS47079.1	.	.	.	.	.	.	.	.	.	.	G	3.557	-0.090400	0.07053	0.0	4.65E-4	ENSG00000156219	ENST00000341029;ENST00000513122;ENST00000355810;ENST00000349321	T;T;T;T	0.14766	2.48;2.48;2.48;2.48	6.04	1.03	0.20045	.	0.443020	0.25575	N	0.029735	T	0.10121	0.0248	L	0.46157	1.445	0.09310	N	1	B;B;P;B;B;B	0.34977	0.007;0.003;0.478;0.015;0.023;0.254	B;B;B;B;B;B	0.31390	0.019;0.007;0.129;0.038;0.016;0.098	T	0.21518	-1.0243	9	.	.	.	-6.6012	7.7094	0.28669	0.2965:0.1213:0.5823:0.0	.	163;193;193;193;193;193	D6RBN3;E7ESB3;B4DHX3;Q13508;Q13508-3;Q13508-2	.;.;.;NAR3_HUMAN;.;.	T	193	ENSP00000343843:A193T;ENSP00000422287:A193T;ENSP00000348064:A193T;ENSP00000304313:A193T	.	A	+	1	0	ART3	77222508	0.002000	0.14202	0.000000	0.03702	0.015000	0.08874	0.959000	0.29240	0.154000	0.19237	-0.251000	0.11542	GCT	G|1.000;A|0.000	0.000	strong		0.403	ART3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252416.2	NM_001179		A	77003484	G	A	77003484	3	1	25	1	0	0	0	0	1	0	0	0	998	1203	42	2	583	2	ART3	4	77003484	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	5115244	77003484	114150792	181	9090											
HPSE	10855	hgsc.bcm.edu	37	chr4	84222208	84222208	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaccgcaagtacttggtgacAttatggaggtttatggcata	12	12	11	6	1	0	1	0	1	0	0	0	2	0	2	1	4	2	4	1	4	6	6	rs11031	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:84222208A>G	ENST00000405413.2	-	12	1513	c.1377T>C	c.(1375-1377)aaT>aaC	p.N459N	HPSE_ENST00000512196.1_Silent_p.N385N|HPSE_ENST00000513463.1_Silent_p.N401N|HPSE_ENST00000311412.5_Silent_p.N459N	NM_006665.5	NP_006656.2	Q9Y251	HPSE_HUMAN	heparanase	459					carbohydrate metabolic process (GO:0005975)|cell-matrix adhesion (GO:0007160)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|positive regulation of blood coagulation (GO:0030194)|positive regulation of hair follicle development (GO:0051798)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation vascular endothelial growth factor production (GO:0010575)|proteoglycan metabolic process (GO:0006029)|regulation of hair follicle development (GO:0051797)|small molecule metabolic process (GO:0044281)|vascular wound healing (GO:0061042)	extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)	beta-glucuronidase activity (GO:0004566)|heparanase activity (GO:0030305)|protein dimerization activity (GO:0046983)|syndecan binding (GO:0045545)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	20		Hepatocellular(203;0.114)		COAD - Colon adenocarcinoma(81;0.141)	Dalteparin(DB06779)|Heparin(DB01109)	ACTTGGTGACATTATGGAGGT	0.353													A|||	426	0.0850639	0.3064	0.0259	5008	,	,		18825	0.0		0.003	False		,,,				2504	0.0				p.N459N		Atlas-SNP	.											.	HPSE	55	.	0			c.T1377C						PASS	.	A	,,,	1123,3283	402.2+/-332.3	156,811,1236	119	126	123		1377,1155,1203,1377	-3.8	1	4	dbSNP_52	123	18,8582	11.9+/-42.8	0,18,4282	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HPSE	NM_001098540.2,NM_001166498.2,NM_001199830.1,NM_006665.5	,,,	156,829,5518	GG,GA,AA		0.2093,25.488,8.7729	,,,	459/544,385/470,401/486,459/544	84222208	1141,11865	2203	4300	6503	SO:0001819	synonymous_variant	10855	exon11			GGTGACATTATGG	AF144325	CCDS3602.1, CCDS54774.1, CCDS56337.1	4q21.3	2008-02-05			ENSG00000173083	ENSG00000173083			5164	protein-coding gene	gene with protein product		604724				10395325, 10395326	Standard	NM_006665		Approved	HPA, HSE1, HPSE1	uc003hoj.4	Q9Y251	OTTHUMG00000130425	ENST00000405413.2:c.1377T>C	4.37:g.84222208A>G		143	0	0		94	47	0.5	NM_001098540	A9JIG7|C7F7I3|C7F7I4|E9PCA9|E9PGR1|Q53GE5|Q9UL39	Silent	SNP	ENST00000405413.2	37	CCDS3602.1																																																																																			A|0.911;G|0.089	0.089	strong		0.353	HPSE-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252812.2	NM_006665		G	84222208	A	G	84222208	2	3	25	1	0	0	0	0	0	0	0	1	7353	214	8	3		3	HPSE	4	84222208	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	7218724	84222208	106932068	182	9091											
DSPP	1834	hgsc.bcm.edu	37	chr4	88537115	88537115	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtgacagcagcgatagcagcGacagcagcgacagcagcgat	13	3	14	11	4	0	1	0	1	0	0	0	5	0	1	0	0	8	4	0	0	1	1	rs201186956	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:88537115G>A	ENST00000282478.7	+	4	3334	c.3301G>A	c.(3301-3303)Gac>Aac	p.D1101N	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.D1101N			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1101	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)		cgatagcagcgacagcagcga	0.542													G|||	7	0.00139776	0.0038	0.0	5008	,	,		12523	0.001		0.0	False		,,,				2504	0.001				p.D1101N		Atlas-SNP	.											.	DSPP	174	.	0			c.G3301A						PASS	.																																			SO:0001583	missense	1834	exon5			AGCAGCGACAGCA	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.3301G>A	4.37:g.88537115G>A	ENSP00000282478:p.Asp1101Asn	25	0	0		12	5	0.416667	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	g	5.679	0.309927	0.10733	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.90004	-2.6;-2.6	1.51	0.638	0.17742	.	.	.	.	.	T	0.78698	0.4324	L	0.34521	1.04	0.09310	N	0.999993	B	0.14438	0.01	B	0.04013	0.001	T	0.60383	-0.7274	9	0.19147	T	0.46	.	4.1914	0.10422	0.2248:0.0:0.7752:0.0	.	1101	Q9NZW4	DSPP_HUMAN	N	1101	ENSP00000382213:D1101N;ENSP00000282478:D1101N	ENSP00000282478:D1101N	D	+	1	0	DSPP	88756139	0.671000	0.27521	0.311000	0.25182	0.002000	0.02628	0.881000	0.28173	0.216000	0.20781	-0.791000	0.03333	GAC	.	.	weak		0.542	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208		A	88537115	G	A	88537115	3	1	25	1	0	0	0	0	1	0	0	0	4784	1058	37	1	3315	1	DSPP	4	88537115	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	4314907	88537115	102617161	183	9092											
MMRN1	22915	hgsc.bcm.edu	37	chr4	90857518	90857518	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagagatcaggctcttcaacTgcaagtattaaattccagat	14	11	8	8	0	3	2	2	0	1	2	4	4	4	2	1	1	2	3	1	1	5	4	rs200343754	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:90857518T>A	ENST00000394980.1	+	7	3006	c.2687T>A	c.(2686-2688)cTg>cAg	p.L896Q	MMRN1_ENST00000394981.1_Intron|MMRN1_ENST00000264790.2_Missense_Mutation_p.L896Q|MMRN1_ENST00000508372.1_Missense_Mutation_p.L638Q			Q13201	MMRN1_HUMAN	multimerin 1	896					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)		GCTCTTCAACTGCAAGTATTA	0.348													T|||	3	0.000599042	0.0	0.0	5008	,	,		19216	0.0		0.001	False		,,,				2504	0.002				p.L896Q		Atlas-SNP	.											.	MMRN1	174	.	0			c.T2687A						PASS	.	T	GLN/LEU	0,4402		0,0,2201	60	63	62		2687	4.1	1	4		62	2,8594	2.2+/-6.3	0,2,4296	no	missense	MMRN1	NM_007351.2	113	0,2,6497	AA,AT,TT		0.0233,0.0,0.0154	benign	896/1229	90857518	2,12996	2201	4298	6499	SO:0001583	missense	22915	exon6			TTCAACTGCAAGT	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.2687T>A	4.37:g.90857518T>A	ENSP00000378431:p.Leu896Gln	116	0	0		111	52	0.468468	NM_007351	Q4W5L1|Q6P3T8|Q6ZUL9	Missense_Mutation	SNP	ENST00000394980.1	37	CCDS3635.1	.	.	.	.	.	.	.	.	.	.	T	14.79	2.640952	0.47153	0.0	2.33E-4	ENSG00000138722	ENST00000394980;ENST00000264790;ENST00000508372	T;T;T	0.68624	-0.03;-0.03;-0.34	5.3	4.1	0.47936	.	0.211787	0.33290	N	0.005070	T	0.54631	0.1870	L	0.44542	1.39	0.80722	D	1	B	0.33857	0.429	B	0.27170	0.077	T	0.57423	-0.7814	10	0.72032	D	0.01	.	10.1863	0.43000	0.2658:0.0:0.0:0.7342	.	896	Q13201	MMRN1_HUMAN	Q	896;896;638	ENSP00000378431:L896Q;ENSP00000264790:L896Q;ENSP00000426461:L638Q	ENSP00000264790:L896Q	L	+	2	0	MMRN1	91076541	0.093000	0.21703	1.000000	0.80357	0.828000	0.46876	1.331000	0.33793	1.082000	0.41137	0.533000	0.62120	CTG	T|0.999;A|0.001	0.001	weak		0.348	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351		A	90857518	T	A	90857518	3	1	25	1	0	0	0	0	1	0	0	0	9679	1580	55	5	2709	5	MMRN1	4	90857518	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	2320403	90857518	100296758	184	9093											
GRID2	2895	hgsc.bcm.edu	37	chr4	94137954	94137954	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggaaggttaacgattattcgGcagacatttccagttcccca	11	11	9	10	2	0	1	0	0	0	1	3	3	2	2	3	3	1	3	3	3	3	5	rs75225211	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:94137954G>A	ENST00000282020.4	+	6	1113	c.855G>A	c.(853-855)cgG>cgA	p.R285R	GRID2_ENST00000510992.1_Silent_p.R190R|GRID2_ENST00000505687.1_3'UTR	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	285					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)		CGATTATTCGGCAGACATTTC	0.408													G|||	20	0.00399361	0.0008	0.0014	5008	,	,		16944	0.0		0.0179	False		,,,				2504	0.0				p.R285R		Atlas-SNP	.											GRID2,NS,malignant_melanoma,+2,1	GRID2	233	1	0			c.G855A						PASS	.	G		12,4394	19.1+/-41.9	0,12,2191	157	150	152		855	-2.1	1	4	dbSNP_131	152	105,8495	57.2+/-118.5	0,105,4195	no	coding-synonymous	GRID2	NM_001510.2		0,117,6386	AA,AG,GG		1.2209,0.2724,0.8996		285/1008	94137954	117,12889	2203	4300	6503	SO:0001819	synonymous_variant	2895	exon6			TATTCGGCAGACA	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.855G>A	4.37:g.94137954G>A		112	0	0		96	48	0.5	NM_001510	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Silent	SNP	ENST00000282020.4	37	CCDS3637.1																																																																																			G|0.990;A|0.010	0.010	strong		0.408	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2			A	94137954	G	A	94137954	2	1	25	1	0	0	0	0	0	0	0	1	6781	1190	42	2		2	GRID2	4	94137954	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	3280436	94137954	97016322	185	9094											
UNC5C	8633	hgsc.bcm.edu	37	chr4	96127798	96127798	+	Missense_Mutation	SNP	G	G	T																															cctcccactgtccctgtgctGcctggttcttgagcagtatt																								rs141976218	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:96127798G>T	ENST00000453304.1	-	11	2231	c.1883C>A	c.(1882-1884)gCa>gAa	p.A628E		NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	628	ZU5. {ECO:0000255|PROSITE- ProRule:PRU00485}.				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)		TCCCTGTGCTGCCTGGTTCTT	0.537													G|||	3	0.000599042	0.0	0.0014	5008	,	,		15925	0.0		0.002	False		,,,				2504	0.0				p.A628E		Atlas-SNP	.											.	UNC5C	141	.	0			c.C1883A						PASS	.	G	GLU/ALA	1,4405	2.1+/-5.4	0,1,2202	106	94	98		1883	3.5	0.8	4	dbSNP_134	98	19,8581	10.5+/-38.8	0,19,4281	yes	missense	UNC5C	NM_003728.3	107	0,20,6483	TT,TG,GG		0.2209,0.0227,0.1538	benign	628/932	96127798	20,12986	2203	4300	6503	SO:0001583	missense	8633	exon11			TGTGCTGCCTGGT	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.1883C>A	4.37:g.96127798G>T	ENSP00000406022:p.Ala628Glu	119	0	0		117	50	0.42735	NM_003728	Q8IUT0	Missense_Mutation	SNP	ENST00000453304.1	37	CCDS3643.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	10.51	1.369746	0.24771	2.27E-4	0.002209	ENSG00000182168	ENST00000453304;ENST00000331502;ENST00000513796	T;T	0.40476	1.03;1.03	5.28	3.45	0.39498	ZU5 (3);	0.761342	0.12964	N	0.424732	T	0.28433	0.0703	N	0.19112	0.55	0.28023	N	0.934452	B;B	0.17852	0.004;0.024	B;B	0.19391	0.01;0.025	T	0.19844	-1.0293	10	0.34782	T	0.22	.	9.8179	0.40865	0.0805:0.1393:0.7802:0.0	.	628;628	A8K385;O95185	.;UNC5C_HUMAN	E	628;587;647	ENSP00000406022:A628E;ENSP00000426924:A647E	ENSP00000328673:A587E	A	-	2	0	UNC5C	96346821	0.714000	0.27936	0.807000	0.32361	0.801000	0.45260	3.981000	0.56902	0.633000	0.30452	-0.300000	0.09419	GCA	G|0.998;T|0.002	0.002	strong		0.537	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728		T	96127798	G	T	96127798	3	4	25	1	0	0	0	0	1	0	0	0	17008	1319	46	4	936	4	UNC5C	4	96127798	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1989844	96127798	95026478	186	9095	111	2									
UNC5C	8633	hgsc.bcm.edu	37	chr4	96127799	96127799	+	Missense_Mutation	SNP	C	C	T																															ctcccactgtccctgtgctgCctggttcttgagcagtattt																								rs146123204	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:96127799C>T	ENST00000453304.1	-	11	2230	c.1882G>A	c.(1882-1884)Gca>Aca	p.A628T		NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	628	ZU5. {ECO:0000255|PROSITE- ProRule:PRU00485}.				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)		CCCTGTGCTGCCTGGTTCTTG	0.537													C|||	3	0.000599042	0.0	0.0014	5008	,	,		15911	0.0		0.002	False		,,,				2504	0.0				p.A628T		Atlas-SNP	.											.	UNC5C	141	.	0			c.G1882A						PASS	.	C	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	106	94	98		1882	-2.4	0.8	4	dbSNP_134	98	17,8583	10.5+/-38.8	0,17,4283	yes	missense	UNC5C	NM_003728.3	58	0,18,6485	TT,TC,CC		0.1977,0.0227,0.1384	benign	628/932	96127799	18,12988	2203	4300	6503	SO:0001583	missense	8633	exon11			GTGCTGCCTGGTT	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.1882G>A	4.37:g.96127799C>T	ENSP00000406022:p.Ala628Thr	119	0	0		118	51	0.432203	NM_003728	Q8IUT0	Missense_Mutation	SNP	ENST00000453304.1	37	CCDS3643.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	7.398	0.632177	0.14322	2.27E-4	0.001977	ENSG00000182168	ENST00000453304;ENST00000331502;ENST00000513796	T;T	0.41400	1.0;1.0	5.28	-2.41	0.06562	ZU5 (3);	0.761342	0.12964	N	0.424732	T	0.13628	0.0330	N	0.02225	-0.63	0.35230	D	0.776799	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.38779	-0.9645	10	0.09338	T	0.73	.	8.1752	0.31278	0.1126:0.2927:0.0:0.5947	.	628;628	A8K385;O95185	.;UNC5C_HUMAN	T	628;587;647	ENSP00000406022:A628T;ENSP00000426924:A647T	ENSP00000328673:A587T	A	-	1	0	UNC5C	96346822	0.002000	0.14202	0.791000	0.31998	0.797000	0.45037	-0.626000	0.05527	-0.391000	0.07763	-0.251000	0.11542	GCA	C|0.998;T|0.002	0.002	strong		0.537	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728		T	96127799	C	T	96127799	3	4	25	1	0	0	0	0	1	0	0	0	17008	739	26	2	937	2	UNC5C	4	96127799	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1	96127799	95026477	187	9096	111	2									
PPA2	27068	hgsc.bcm.edu	37	chr4	106345379	106345379	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actttgaggcttcaggatcaTtcgcattgatagcaattaat	12	14	8	7	1	2	2	2	2	0	0	3	3	2	3	0	2	1	3	0	2	3	6			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:106345379T>C	ENST00000341695.5	-	7	659	c.629A>G	c.(628-630)aAt>aGt	p.N210S	PPA2_ENST00000310267.7_Missense_Mutation_p.N131S|PPA2_ENST00000380004.2_Missense_Mutation_p.N192S|PPA2_ENST00000432483.2_Missense_Mutation_p.N108S|PPA2_ENST00000357415.4_Missense_Mutation_p.N225S|PPA2_ENST00000509426.1_5'UTR|PPA2_ENST00000354147.3_Intron|PPA2_ENST00000348706.5_Missense_Mutation_p.N181S	NM_176869.2	NP_789845.1	Q9H2U2	IPYR2_HUMAN	pyrophosphatase (inorganic) 2	210					diphosphate metabolic process (GO:0071344)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|pancreas(1)	11		Myeloproliferative disorder(5;0.0255)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.03e-07)		TTCAGGATCATTCGCATTGAT	0.348																																					p.N210S		Atlas-SNP	.											.	PPA2	23	.	0			c.A629G						PASS	.						136	134	134					4																	106345379		2203	4300	6503	SO:0001583	missense	27068	exon7			GGATCATTCGCAT		CCDS3667.1, CCDS3668.2, CCDS3669.2, CCDS34043.1	4q25	2005-10-07			ENSG00000138777	ENSG00000138777			28883	protein-coding gene	gene with protein product		609988				11042152	Standard	NM_176869		Approved	FLJ20459	uc003hxl.3	Q9H2U2	OTTHUMG00000128781	ENST00000341695.5:c.629A>G	4.37:g.106345379T>C	ENSP00000343885:p.Asn210Ser	43	0	0		75	31	0.413333	NM_176869	B4DLP7|F8WDN9|I6L9B6|Q4W5E9|Q6PG51|Q8TBW0|Q96E55|Q9H0T0|Q9NX37|Q9P033|Q9ULX0	Missense_Mutation	SNP	ENST00000341695.5	37	CCDS3667.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.95|14.95	2.687529|2.687529	0.48097|0.48097	.|.	.|.	ENSG00000138777|ENSG00000138777	ENST00000508518|ENST00000341695;ENST00000348706;ENST00000432483;ENST00000357415;ENST00000380004;ENST00000510015;ENST00000310267	.|T;T;T;T;T;T;T	.|0.43688	.|0.94;0.94;0.94;0.94;0.94;0.94;0.94	5.4|5.4	4.14|4.14	0.48551|0.48551	.|.	.|0.202955	.|0.50627	.|D	.|0.000102	T|T	0.39708|0.39708	0.1088|0.1088	L|L	0.53671|0.53671	1.685|1.685	0.38017|0.38017	D|D	0.934732|0.934732	.|B;B;B;B;B	.|0.31680	.|0.009;0.335;0.182;0.181;0.023	.|B;B;B;B;B	.|0.34991	.|0.01;0.109;0.193;0.079;0.073	T|T	0.49214|0.49214	-0.8963|-0.8963	5|10	.|0.52906	.|T	.|0.07	-2.6133|-2.6133	11.196|11.196	0.48713|0.48713	0.0:0.0:0.1536:0.8464|0.0:0.0:0.1536:0.8464	.|.	.|131;108;181;192;210	.|B4DFH3;F8WDN9;Q9H2U2-3;E2QRM6;Q9H2U2	.|.;.;.;.;IPYR2_HUMAN	V|S	189|210;181;108;225;192;137;131	.|ENSP00000343885:N210S;ENSP00000313061:N181S;ENSP00000389957:N108S;ENSP00000349996:N225S;ENSP00000369340:N192S;ENSP00000423363:N137S;ENSP00000311150:N131S	.|ENSP00000311150:N131S	M|N	-|-	1|2	0|0	PPA2|PPA2	106564828|106564828	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.794000|0.794000	0.44872|0.44872	5.215000|5.215000	0.65241|0.65241	2.045000|2.045000	0.60652|0.60652	0.459000|0.459000	0.35465|0.35465	ATG|AAT	.	.	none		0.348	PPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250704.4	NM_176869		C	106345379	T	C	106345379	3	2	25	1	0	0	0	0	1	0	0	0	12296	1493	52	3	399	3	PPA2	4	106345379	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	10217580	106345379	84808897	188	9097											
MAML3	55534	hgsc.bcm.edu	37	chr4	140640527	140640527	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctgcatccactcgtcccctgGcccgcctttgatgatggagt	5	11	10	15	2	0	2	0	2	0	0	3	3	2	3	5	2	1	1	5	2	0	1	rs61743025	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:140640527G>A	ENST00000509479.2	-	5	4223	c.3367C>T	c.(3367-3369)Cca>Tca	p.P1123S	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)					TCGTCCCCTGGCCCGCCTTTG	0.537													G|||	4	0.000798722	0.0	0.0014	5008	,	,		18196	0.0		0.003	False		,,,				2504	0.0				p.P1119S		Atlas-SNP	.											.	MAML3	192	.	0			c.C3355T						PASS	.	G	,,SER/PRO	1,4041		0,1,2020	47	52	50		,,3367	5	0.8	4	dbSNP_129	50	25,8321		0,25,4148	yes	intron,intron,missense	MGST2,MAML3	NM_001204366.1,NM_001204367.1,NM_018717.4	,,74	0,26,6168	AA,AG,GG		0.2995,0.0247,0.2099	,,probably-damaging	,,1123/1139	140640527	26,12362	2021	4173	6194	SO:0001583	missense	55534	exon6			CCCCTGGCCCGCC	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.3367C>T	4.37:g.140640527G>A	ENSP00000421180:p.Pro1123Ser	68	0	0		94	41	0.43617	NM_018717		Missense_Mutation	SNP	ENST00000509479.2	37	CCDS54805.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	14.26	2.483745	0.44147	2.47E-4	0.002995	ENSG00000196782	ENST00000509479;ENST00000538400	T	0.24151	1.87	4.99	4.99	0.66335	.	0.000000	0.64402	D	0.000003	T	0.50565	0.1623	M	0.76838	2.35	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.47849	-0.9085	10	0.10377	T	0.69	.	18.623	0.91327	0.0:0.0:1.0:0.0	.	1123;1119	E7EVW8;Q96JK9	.;MAML3_HUMAN	S	1123;430	ENSP00000421180:P1123S	ENSP00000421180:P1123S	P	-	1	0	MAML3	140859977	1.000000	0.71417	0.778000	0.31720	0.978000	0.69477	4.784000	0.62411	2.461000	0.83175	0.591000	0.81541	CCA	G|0.999;A|0.001	0.001	strong		0.537	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2			A	140640527	G	A	140640527	3	1	25	1	0	0	0	0	1	0	0	0	9216	1203	42	2	53	2	MAML3	4	140640527	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	34295148	140640527	50513749	189	9098											
LSM6	11157	hgsc.bcm.edu	37	chr4	147110790	147110790	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagtgttgtacatcagtacAcagaagagacggatgtgaag	14	9	12	6	1	2	3	2	1	0	2	2	5	2	4	0	1	2	3	0	1	4	3	rs41280529	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:147110790A>T	ENST00000502781.1	+	4	944	c.225A>T	c.(223-225)acA>acT	p.T75T	LSM6_ENST00000296581.5_Silent_p.T75T			P62312	LSM6_HUMAN	LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae)	75					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|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)|rRNA processing (GO:0006364)|tRNA processing (GO:0008033)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)					all_hematologic(180;0.151)					ACATCAGTACACAGAAGAGAC	0.299													A|||	23	0.00459265	0.0015	0.0043	5008	,	,		18321	0.0		0.0179	False		,,,				2504	0.0				p.T75T	Ovarian(181;1591 2748 12147 31551)	Atlas-SNP	.											.	LSM6	5	.	0			c.A225T						PASS	.	A		9,4397	12.9+/-30.5	0,9,2194	68	75	72		225	-1	1	4	dbSNP_127	72	115,8483	61.7+/-123.6	0,115,4184	no	coding-synonymous	LSM6	NM_007080.2		0,124,6378	TT,TA,AA		1.3375,0.2043,0.9536		75/81	147110790	124,12880	2203	4299	6502	SO:0001819	synonymous_variant	11157	exon4			CAGTACACAGAAG	AF182292	CCDS3767.1	4q31.21	2008-02-05				ENSG00000164167			17017	protein-coding gene	gene with protein product		607286				10369684, 10523320	Standard	NM_007080		Approved	YDR378C	uc003ikq.4	P62312		ENST00000502781.1:c.225A>T	4.37:g.147110790A>T		118	0	0		119	49	0.411765	NM_007080	Q4W5J5|Q9Y4Y8	Silent	SNP	ENST00000502781.1	37	CCDS3767.1																																																																																			A|0.991;T|0.009	0.009	strong		0.299	LSM6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364929.1			T	147110790	A	T	147110790	2	4	25	1	0	0	0	0	0	0	0	1	9069	146	6	5		5	LSM6	4	147110790	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	6470263	147110790	44043486	190	9099											
PRMT10	90826	hgsc.bcm.edu	37	chr4	148560193	148560193	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctggcttgcttaaaggtataCagggcaatgaggataggtcc	11	10	13	7	0	0	1	0	1	0	0	1	2	1	2	1	5	2	4	1	5	6	5	rs11557361	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:148560193C>T	ENST00000322396.6	-	11	2482	c.2240G>A	c.(2239-2241)tGt>tAt	p.C747Y	PRMT10_ENST00000541232.1_Missense_Mutation_p.C634Y|TMEM184C_ENST00000508208.1_Intron	NM_138364.2	NP_612373.2	Q6P2P2	ANM9_HUMAN		747	SAM-dependent MTase PRMT-type 2. {ECO:0000255|PROSITE-ProRule:PRU01015}.		C -> Y (in dbSNP:rs11557361).			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						TAAAGGTATACAGGGCAATGA	0.368													C|||	41	0.0081869	0.0	0.0101	5008	,	,		16840	0.0		0.0338	False		,,,				2504	0.0				p.C747Y		Atlas-SNP	.											.	PRMT10	68	.	0			c.G2240A						PASS	.	C	TYR/CYS	21,4385	26.2+/-53.5	0,21,2182	98	99	98		2240	5.2	0.7	4	dbSNP_120	98	245,8355	97.7+/-159.3	1,243,4056	yes	missense	PRMT10	NM_138364.2	194	1,264,6238	TT,TC,CC		2.8488,0.4766,2.0452	probably-damaging	747/846	148560193	266,12740	2203	4300	6503	SO:0001583	missense	90826	exon11			GGTATACAGGGCA																												ENST00000322396.6:c.2240G>A	4.37:g.148560193C>T	ENSP00000314396:p.Cys747Tyr	104	0	0		103	47	0.456311	NM_138364	A8KA39|B3KU92|Q6ZR58|Q8N383|Q9BT55|Q9NT98	Missense_Mutation	SNP	ENST00000322396.6	37	CCDS3771.1	31	0.014194139194139194	0	0.0	2	0.0055248618784530384	0	0.0	29	0.03825857519788918	C	8.851	0.944484	0.18356	0.004766	0.028488	ENSG00000164169	ENST00000322396;ENST00000541232	T;T	0.33438	1.41;1.41	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.06645	0.0170	L	0.54323	1.7	0.58432	D	0.999996	P	0.51653	0.947	B	0.42282	0.382	T	0.08330	-1.0727	10	0.02654	T	1	-33.0667	13.1858	0.59680	0.0:0.9234:0.0:0.0766	rs11557361;rs52794661;rs11557361	747	Q6P2P2	ANM10_HUMAN	Y	747;634	ENSP00000314396:C747Y;ENSP00000439508:C634Y	ENSP00000314396:C747Y	C	-	2	0	PRMT10	148779643	1.000000	0.71417	0.665000	0.29768	0.998000	0.95712	5.321000	0.65846	2.428000	0.82296	0.650000	0.86243	TGT	C|0.981;T|0.019	0.019	strong		0.368	PRMT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364650.1			T	148560193	C	T	148560193	3	4	25	1	0	0	0	0	1	0	0	0	12548	478	17	2	305	2	PRMT10	4	148560193	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1449403	148560193	42594083	191	9100											
ETFDH	2110	hgsc.bcm.edu	37	chr4	159627845	159627845	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgagtatccaaaacccgaTggacagatcagttttgacct	13	11	8	9	1	1	3	1	2	0	1	2	5	2	4	3	1	1	2	3	1	3	4	rs77484245	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:159627845T>C	ENST00000511912.1	+	12	1865	c.1533T>C	c.(1531-1533)gaT>gaC	p.D511D	ETFDH_ENST00000307738.5_Silent_p.D464D	NM_001281738.1|NM_004453.2	NP_001268667.1|NP_004444.2	Q16134	ETFD_HUMAN	electron-transferring-flavoprotein dehydrogenase	511					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)		CAAAACCCGATGGACAGATCA	0.433													T|||	10	0.00199681	0.0	0.0	5008	,	,		16740	0.0		0.0099	False		,,,				2504	0.0				p.D511D		Atlas-SNP	.											.	ETFDH	57	.	0			c.T1533C						PASS	.	T		3,4403	6.2+/-15.9	0,3,2200	203	192	196		1533	-1	0.9	4	dbSNP_132	196	54,8546	33.8+/-87.4	0,54,4246	no	coding-synonymous	ETFDH	NM_004453.2		0,57,6446	CC,CT,TT		0.6279,0.0681,0.4383		511/618	159627845	57,12949	2203	4300	6503	SO:0001819	synonymous_variant	2110	exon12			ACCCGATGGACAG	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.1533T>C	4.37:g.159627845T>C		91	0	0		91	38	0.417582	NM_004453	B4E3R9|J3KND9|Q7Z347	Silent	SNP	ENST00000511912.1	37	CCDS3800.1																																																																																			T|0.996;C|0.004	0.004	strong		0.433	ETFDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365718.2			C	159627845	T	C	159627845	2	2	25	1	0	0	0	0	0	0	0	1	5273	1461	51	3		3	ETFDH	4	159627845	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	11067652	159627845	31526431	192	9101											
NEK1	4750	hgsc.bcm.edu	37	chr4	170506525	170506525	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagagagaaacttttcaatgCgtttggctataaaacctttc	13	13	8	7	1	1	2	1	0	0	2	2	4	1	2	1	1	3	2	1	1	5	6	rs200161705	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:170506525C>T	ENST00000439128.2	-	9	1422	c.782G>A	c.(781-783)cGc>cAc	p.R261H	NEK1_ENST00000510533.1_Missense_Mutation_p.R261H|NEK1_ENST00000512193.1_Missense_Mutation_p.R261H|NEK1_ENST00000511633.1_Missense_Mutation_p.R261H|NEK1_ENST00000507142.1_Missense_Mutation_p.R261H	NM_012224.2	NP_036356.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	261					cellular response to DNA damage stimulus (GO:0006974)|cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.R261L(2)		NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|stomach(1)	45		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		CTTTTCAATGCGTTTGGCTAT	0.388													C|||	4	0.000798722	0.0	0.0029	5008	,	,		18346	0.0		0.001	False		,,,				2504	0.001				p.R261H		Atlas-SNP	.											NEK1_ENST00000507142,NS,carcinoma,0,2	NEK1	203	2	2	Substitution - Missense(2)	breast(2)	c.G782A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	3,3653		0,3,1825	72	68	69		782,782,782,782,782	5.8	1	4		69	31,8137		0,31,4053	yes	missense,missense,missense,missense,missense	NEK1	NM_001199397.1,NM_001199398.1,NM_001199399.1,NM_001199400.1,NM_012224.2	29,29,29,29,29	0,34,5878	TT,TC,CC		0.3795,0.0821,0.2876	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	261/1287,261/1243,261/1190,261/1215,261/1259	170506525	34,11790	1828	4084	5912	SO:0001583	missense	4750	exon10			TCAATGCGTTTGG	AB067488	CCDS47162.1, CCDS56348.1, CCDS56349.1, CCDS56350.1, CCDS56351.1	4q32.3	2012-11-15	2012-11-15		ENSG00000137601	ENSG00000137601			7744	protein-coding gene	gene with protein product		604588	"NIMA (never in mitosis gene a)-related kinase 1"			1382974, 8274451	Standard	NM_012224		Approved	NY-REN-55, KIAA1901	uc003isd.2	Q96PY6	OTTHUMG00000160963	ENST00000439128.2:c.782G>A	4.37:g.170506525C>T	ENSP00000408020:p.Arg261His	172	0	0		133	63	0.473684	NM_001199399	G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	Missense_Mutation	SNP	ENST00000439128.2	37	CCDS47162.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	C	33	5.219726	0.95139	8.21E-4	0.003795	ENSG00000137601	ENST00000439128;ENST00000511633;ENST00000510533;ENST00000507142;ENST00000512193	T;T;T;T;T	0.24350	1.86;1.86;1.86;1.86;1.86	5.82	5.82	0.92795	Protein kinase-like domain (1);	0.000000	0.64402	D	0.000004	T	0.42471	0.1204	M	0.62016	1.91	0.80722	D	1	D;D;D;D;D;D	0.89917	0.972;1.0;1.0;1.0;1.0;1.0	P;D;D;D;D;D	0.97110	0.55;0.999;1.0;1.0;0.997;0.999	T	0.11108	-1.0601	10	0.30078	T	0.28	.	20.0909	0.97817	0.0:1.0:0.0:0.0	.	261;261;261;261;261;261	Q96PY6-5;Q96PY6-4;G5E9Z3;Q96PY6-3;Q96PY6-2;Q96PY6	.;.;.;.;.;NEK1_HUMAN	H	261	ENSP00000408020:R261H;ENSP00000423332:R261H;ENSP00000427653:R261H;ENSP00000424757:R261H;ENSP00000424938:R261H	ENSP00000408020:R261H	R	-	2	0	NEK1	170743100	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.709000	0.84645	2.756000	0.94617	0.591000	0.81541	CGC	C|0.999;T|0.001	0.001	strong		0.388	NEK1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363157.3			T	170506525	C	T	170506525	3	4	25	1	0	0	0	0	1	0	0	0	10330	768	27	1	3098	1	NEK1	4	170506525	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	10878680	170506525	20647751	193	9102											
GALNTL6	442117	hgsc.bcm.edu	37	chr4	172735851	172735851	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagcacctggtgaagtcagcGgagcccggggagcagcaggt	10	4	17	10	2	1	1	1	1	0	0	1	3	1	3	2	5	5	3	2	5	2	0	rs111570068	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:172735851G>A	ENST00000506823.1	+	2	777	c.120G>A	c.(118-120)gcG>gcA	p.A40A	GALNTL6_ENST00000511251.1_Silent_p.A40A	NM_001034845.2	NP_001030017.2	Q49A17	GLTL6_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 6	40					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)	p.A40A(1)		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						TGAAGTCAGCGGAGCCCGGGG	0.537													G|||	52	0.0103834	0.0174	0.0086	5008	,	,		17897	0.0129		0.007	False		,,,				2504	0.0031				p.A40A		Atlas-SNP	.											GALNTL6,NS,carcinoma,0,1	GALNTL6	102	1	1	Substitution - coding silent(1)	pancreas(1)	c.G120A						PASS	.	G		69,4337	61.7+/-98.7	0,69,2134	79	77	78		120	-10.2	0	4	dbSNP_132	78	24,8576	17.3+/-56.4	0,24,4276	no	coding-synonymous	GALNTL6	NM_001034845.2		0,93,6410	AA,AG,GG		0.2791,1.566,0.7151		40/602	172735851	93,12913	2203	4300	6503	SO:0001819	synonymous_variant	442117	exon2			GTCAGCGGAGCCC		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.120G>A	4.37:g.172735851G>A		93	0	0		94	42	0.446809	NM_001034845	Q2L4S6	Silent	SNP	ENST00000506823.1	37	CCDS34104.1																																																																																			G|0.991;A|0.009	0.009	strong		0.537	GALNTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362395.1	NM_001034845		A	172735851	G	A	172735851	2	1	25	1	0	0	0	0	0	0	0	1	6233	1103	39	1		1	GALNTL6	4	172735851	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2229326	172735851	18418425	194	9103											
WDR17	116966	hgsc.bcm.edu	37	chr4	177089839	177089839	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	acaggaatttggcagctgatCttcttctgatgattcctgat	9	15	9	8	0	3	4	0	4	3	0	4	5	4	5	1	2	1	2	1	2	1	4	rs375753370|rs140459637	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:177089839C>G	ENST00000280190.4	+	25	3280	c.3124C>G	c.(3124-3126)Ctt>Gtt	p.L1042V	WDR17_ENST00000508596.1_Missense_Mutation_p.L1003V|WDR17_ENST00000393643.2_Missense_Mutation_p.L1018V|WDR17_ENST00000507824.2_Missense_Mutation_p.L1017V			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	1042										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)		GGCAGCTGATCTTCTTCTGAT	0.348													C|||	16	0.00319489	0.0	0.0029	5008	,	,		17511	0.0		0.0129	False		,,,				2504	0.001				p.L1042V		Atlas-SNP	.											.	WDR17	198	.	0			c.C3124G						PASS	.	C	VAL/LEU,VAL/LEU	4,4402	8.1+/-20.4	0,4,2199	140	134	136		3124,3007	5.1	1	4	dbSNP_134	136	50,8550	33.3+/-86.6	0,50,4250	yes	missense,missense	WDR17	NM_170710.4,NM_181265.3	32,32	0,54,6449	GG,GC,CC		0.5814,0.0908,0.4152	possibly-damaging,possibly-damaging	1042/1323,1003/1284	177089839	54,12952	2203	4300	6503	SO:0001583	missense	116966	exon25			GCTGATCTTCTTC	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.3124C>G	4.37:g.177089839C>G	ENSP00000280190:p.Leu1042Val	150	0	0		131	51	0.389313	NM_170710	E7EQX0|Q0QD35	Missense_Mutation	SNP	ENST00000280190.4	37	CCDS3825.1	10|10	0.004578754578754579|0.004578754578754579	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	9|9	0.011873350923482849|0.011873350923482849	C|C	12.08|12.08	1.831352|1.831352	0.32329|0.32329	9.08E-4|9.08E-4	0.005814|0.005814	ENSG00000150627|ENSG00000150627	ENST00000508596;ENST00000393643;ENST00000280190;ENST00000507824|ENST00000443118	T;T;T|.	0.61392|.	0.31;0.18;0.11|.	5.1|5.1	5.1|5.1	0.69264|0.69264	.|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.68302|0.68302	0.2986|0.2986	M|M	0.68317|0.68317	2.08|2.08	0.53688|0.53688	D|D	0.999974|0.999974	D;D;D|.	0.76494|.	0.97;0.999;0.999|.	P;D;D|.	0.77557|.	0.591;0.99;0.99|.	T|T	0.70857|0.70857	-0.4758|-0.4758	10|5	0.56958|.	D|.	0.05|.	-22.4333|-22.4333	18.6954|18.6954	0.91599|0.91599	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1018;1003;1042|.	E7EP77;E7EQX0;Q8IZU2|.	.;.;WDR17_HUMAN|.	V|C	1003;1018;1042;1018|276	ENSP00000422763:L1003V;ENSP00000377258:L1018V;ENSP00000280190:L1042V|.	ENSP00000280190:L1042V|.	L|S	+|+	1|2	0|0	WDR17|WDR17	177326833|177326833	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.055000|0.055000	0.15305|0.15305	4.228000|4.228000	0.58619|0.58619	2.647000|2.647000	0.89833|0.89833	0.591000|0.591000	0.81541|0.81541	CTT|TCT	C|0.995;G|0.005	0.005	strong		0.348	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2			G	177089839	C	G	177089839	3	3	25	1	0	0	0	0	1	0	0	0	17292	913	32	4	3218	4	WDR17	4	177089839	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	4353988	177089839	14064437	195	9104											
CCDC111	201973	hgsc.bcm.edu	37	chr4	185578337	185578337	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aactgaagcaaattgaagaaCgagcatctcattatgagagg	17	8	10	6	1	1	4	1	3	1	2	2	6	1	4	0	1	4	2	0	1	6	2	rs145651098		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:185578337C>T	ENST00000314970.6	+	3	476	c.43C>T	c.(43-45)Cga>Tga	p.R15*	PRIMPOL_ENST00000512834.1_Nonsense_Mutation_p.R15*|PRIMPOL_ENST00000503752.1_Nonsense_Mutation_p.R15*|PRIMPOL_ENST00000515774.1_Intron	NM_152683.2	NP_689896	Q96LW4	PRIPO_HUMAN	primase and polymerase (DNA-directed)	15					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)										AATTGAAGAACGAGCATCTCA	0.398																																					p.R15X		Atlas-SNP	.											.	CCDC111	43	.	0			c.C43T						PASS	.	C	stop/ARG	1,4405	2.1+/-5.4	0,1,2202	118	109	112		43	5.6	0.9	4	dbSNP_134	112	0,8600		0,0,4300	no	stop-gained	CCDC111	NM_152683.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		15/561	185578337	1,13005	2203	4300	6503	SO:0001587	stop_gained	201973	exon3			GAAGAACGAGCAT	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.43C>T	4.37:g.185578337C>T	ENSP00000313816:p.Arg15*	67	0	0		63	31	0.492063	NM_152683	D3DP55|D6RDM1|Q5HYJ9	Nonsense_Mutation	SNP	ENST00000314970.6	37	CCDS3837.1	.	.	.	.	.	.	.	.	.	.	C	37	6.625279	0.97714	2.27E-4	0.0	ENSG00000164306	ENST00000314970;ENST00000503752;ENST00000512834	.	.	.	5.64	5.64	0.86602	.	0.353602	0.27362	N	0.019716	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07990	T	0.79	-2.1277	19.7127	0.96102	0.0:1.0:0.0:0.0	.	.	.	.	X	15	.	ENSP00000313816:R15X	R	+	1	2	CCDC111	185815331	0.999000	0.42202	0.894000	0.35097	0.999000	0.98932	3.362000	0.52314	2.652000	0.90054	0.655000	0.94253	CGA	C|1.000;T|0.000	0.000	weak		0.398	PRIMPOL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360827.1	NM_152683		T	185578337	C	T	185578337	4	4	25	1	0	0	0	0	0	1	0	0	2750	528	19	1	45	1	CCDC111	4	185578337	Nonsense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	8488498	185578337	5575939	196	9105											
SNX25	83891	hgsc.bcm.edu	37	chr4	186283092	186283092	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaaagacaaatccgggacaCagtcagctggattttcagtg	14	9	10	8	1	2	1	2	0	0	1	3	3	3	3	1	2	1	1	1	2	3	3	rs34120554	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:186283092C>T	ENST00000504273.1	+	17	2468	c.2174C>T	c.(2173-2175)aCa>aTa	p.T725I	SNX25_ENST00000512853.1_3'UTR|SNX25_ENST00000264694.8_Missense_Mutation_p.T725I			Q9H3E2	SNX25_HUMAN	sorting nexin 25	725			T -> I (in dbSNP:rs34120554).		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)		ATCCGGGACACAGTCAGCTGG	0.383													C|||	17	0.00339457	0.0008	0.0058	5008	,	,		15815	0.0		0.0099	False		,,,				2504	0.002				p.T725I		Atlas-SNP	.											.	SNX25	100	.	0			c.C2174T						PASS	.	C	ILE/THR	9,4397	16.8+/-37.8	0,9,2194	83	86	85		2174	4.3	1	4	dbSNP_126	85	105,8495	57.2+/-118.5	0,105,4195	yes	missense	SNX25	NM_031953.2	89	0,114,6389	TT,TC,CC		1.2209,0.2043,0.8765	probably-damaging	725/841	186283092	114,12892	2203	4300	6503	SO:0001583	missense	83891	exon17			GGGACACAGTCAG	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.2174C>T	4.37:g.186283092C>T	ENSP00000426255:p.Thr725Ile	47	0	0		30	13	0.433333	NM_031953	Q3ZT30|Q8N6K3	Missense_Mutation	SNP	ENST00000504273.1	37	CCDS34116.1	11	0.005036630036630037	0	0.0	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	C	21.1	4.091462	0.76756	0.002043	0.012209	ENSG00000109762	ENST00000504273;ENST00000264694;ENST00000264693	T;T	0.30714	1.52;1.52	5.15	4.3	0.51218	Sorting nexin, C-terminal (1);	0.053228	0.85682	D	0.000000	T	0.35335	0.0928	L	0.41573	1.285	0.50313	D	0.99986	D;P;D	0.89917	0.999;0.728;1.0	D;B;D	0.91635	0.995;0.299;0.999	T	0.09818	-1.0657	10	0.21540	T	0.41	-3.1783	13.6912	0.62547	0.0:0.9249:0.0:0.0751	rs34120554	441;258;725	Q8N6K3;Q9H5Q8;Q9H3E2	.;.;SNX25_HUMAN	I	725;725;258	ENSP00000426255:T725I;ENSP00000264694:T725I	ENSP00000264693:T258I	T	+	2	0	SNX25	186520086	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.732000	0.68563	1.300000	0.44818	0.542000	0.68232	ACA	C|0.993;T|0.007	0.007	strong		0.383	SNX25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360756.1	NM_031953		T	186283092	C	T	186283092	3	4	25	1	0	0	0	0	1	0	0	0	14911	478	17	2	2236	2	SNX25	4	186283092	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	704755	186283092	4871184	197	9106											
F11	2160	hgsc.bcm.edu	37	chr4	187195373	187195373	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagaaagatgcacggatgaCgtccactgccactttttcac	12	9	8	12	2	1	3	1	1	0	2	2	4	2	4	2	1	2	1	2	1	2	2	rs5973	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:187195373C>T	ENST00000403665.2	+	5	781	c.429C>T	c.(427-429)gaC>gaT	p.D143D	F11_ENST00000264692.4_Intron|F11_ENST00000492972.2_Silent_p.D143D	NM_000128.3	NP_000119.1	P03951	FA11_HUMAN	coagulation factor XI	143	Apple 2. {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)	GCACGGATGACGTCCACTGCC	0.483													C|||	315	0.0628994	0.1853	0.0418	5008	,	,		18531	0.0		0.0358	False		,,,				2504	0.0051				p.D143D		Atlas-SNP	.											.	F11	65	.	0			c.C429T						PASS	.	C		647,3759	277.2+/-273.6	51,545,1607	171	139	150		429	-1.3	0	4	dbSNP_52	150	249,8351	98.4+/-159.9	5,239,4056	no	coding-synonymous	F11	NM_000128.3		56,784,5663	TT,TC,CC		2.8953,14.6845,6.8891		143/626	187195373	896,12110	2203	4300	6503	SO:0001819	synonymous_variant	2160	exon5			GGATGACGTCCAC	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.429C>T	4.37:g.187195373C>T		169	0	0		198	94	0.474747	NM_000128	D3DP64|Q4W5C2|Q9Y495	Silent	SNP	ENST00000403665.2	37	CCDS3847.1																																																																																			C|0.938;T|0.062	0.062	strong		0.483	F11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317519.4			T	187195373	C	T	187195373	2	4	25	1	0	0	0	0	0	0	0	1	5339	535	19	1		1	F11	4	187195373	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	912281	187195373	3958903	198	9107											
FAT1	2195	hgsc.bcm.edu	37	chr4	187509931	187509931	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctctcgacagcgggcgcctCgaagtgtctttgataccctg	6	10	12	13	4	2	1	0	1	2	0	4	3	2	1	2	1	2	1	2	1	2	2	rs192609167	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:187509931C>T	ENST00000441802.2	-	27	13791	c.13582G>A	c.(13582-13584)Gag>Aag	p.E4528K		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	4528					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						GCGGGCGCCTCGAAGTGTCTT	0.562										HNSCC(5;0.00058)			C|||	3	0.000599042	0.0	0.0014	5008	,	,		17560	0.0		0.002	False		,,,				2504	0.0				p.E4528K	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.G13582A						PASS	.	C	LYS/GLU	5,4159		0,5,2077	60	70	67		13582	5.4	0	4		67	67,8369		0,67,4151	yes	missense	FAT1	NM_005245.3	56	0,72,6228	TT,TC,CC		0.7942,0.1201,0.5714	benign	4528/4589	187509931	72,12528	2082	4218	6300	SO:0001583	missense	2195	exon27			GCGCCTCGAAGTG	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.13582G>A	4.37:g.187509931C>T	ENSP00000406229:p.Glu4528Lys	108	0	0		110	49	0.445455	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	3|3	0.0013736263736263737|0.0013736263736263737	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	C|C	13.46|13.46	2.243967|2.243967	0.39697|0.39697	0.001201|0.001201	0.007942|0.007942	ENSG00000083857|ENSG00000083857	ENST00000441802;ENST00000260147|ENST00000512772	T|.	0.38077|.	1.16|.	5.37|5.37	5.37|5.37	0.77165|0.77165	.|.	0.411428|.	0.30311|.	N|.	0.009906|.	T|T	0.67420|0.67420	0.2891|0.2891	M|M	0.62723|0.62723	1.935|1.935	0.58432|0.58432	D|D	0.999994|0.999994	P|.	0.42337|.	0.776|.	B|.	0.26770|.	0.073|.	T|T	0.68232|0.68232	-0.5463|-0.5463	10|5	0.21014|.	T|.	0.42|.	.|.	19.3098|19.3098	0.94182|0.94182	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	4528|.	Q14517|.	FAT1_HUMAN|.	K|Q	4528;4530|307	ENSP00000406229:E4528K|.	ENSP00000260147:E4530K|.	E|R	-|-	1|2	0|0	FAT1|FAT1	187746925|187746925	1.000000|1.000000	0.71417|0.71417	0.043000|0.043000	0.18650|0.18650	0.008000|0.008000	0.06430|0.06430	7.309000|7.309000	0.78937|0.78937	2.800000|2.800000	0.96347|0.96347	0.455000|0.455000	0.32223|0.32223	GAG|CGA	C|0.999;T|0.001	0.001	strong		0.562	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		T	187509931	C	T	187509931	3	4	25	1	0	0	0	0	1	0	0	0	5697	893	31	1	188	1	FAT1	4	187509931	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	314558	187509931	3644345	199	9108											
UGT3A1	133688	hgsc.bcm.edu	37	chr5	35965611	35965611	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacaactctgctttcagtagAagatgagacaaaactggcct	14	9	8	10	0	2	3	1	1	1	3	2	4	2	3	1	1	3	2	1	1	5	2	rs61733467	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:35965611A>G	ENST00000274278.3	-	4	1077	c.720T>C	c.(718-720)ctT>ctC	p.L240L	UGT3A1_ENST00000507113.1_Silent_p.L206L|UGT3A1_ENST00000513233.1_Intron|UGT3A1_ENST00000333811.4_Silent_p.L186L|UGT3A1_ENST00000503189.1_Silent_p.L240L	NM_152404.3	NP_689617.3	Q6NUS8	UD3A1_HUMAN	UDP glycosyltransferase 3 family, polypeptide A1	240						integral component of membrane (GO:0016021)|UDP-N-acetylglucosamine transferase complex (GO:0043541)	glucuronosyltransferase activity (GO:0015020)|UDP-glycosyltransferase activity (GO:0008194)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|skin(4)	46	all_lung(31;0.000197)		Epithelial(62;0.107)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CTTTCAGTAGAAGATGAGACA	0.448													A|||	56	0.0111821	0.0393	0.0058	5008	,	,		20825	0.0		0.0	False		,,,				2504	0.0				p.L240L		Atlas-SNP	.											.	UGT3A1	95	.	0			c.T720C						PASS	.	A	,	155,4251	104.3+/-142.8	2,151,2050	116	120	118		558,720	1.8	0.9	5	dbSNP_129	118	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	UGT3A1	NM_001171873.1,NM_152404.3	,	2,152,6349	GG,GA,AA		0.0116,3.5179,1.1994	,	186/253,240/524	35965611	156,12850	2203	4300	6503	SO:0001819	synonymous_variant	133688	exon4			CAGTAGAAGATGA		CCDS3913.1, CCDS54841.1	5p13.2	2014-05-20			ENSG00000145626	ENSG00000145626		"UDP glucuronosyltransferases"	26625	protein-coding gene	gene with protein product							Standard	NM_152404		Approved	FLJ34658	uc003jjv.2	Q6NUS8	OTTHUMG00000131107	ENST00000274278.3:c.720T>C	5.37:g.35965611A>G		237	0	0		223	114	0.511211	NM_152404	G5E961|Q8IYS9|Q8NAW4|Q96DM6	Silent	SNP	ENST00000274278.3	37	CCDS3913.1																																																																																			A|0.988;G|0.012	0.012	strong		0.448	UGT3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253770.2	NM_152404		G	35965611	A	G	35965611	2	3	25	1	0	0	0	0	0	0	0	1	16978	233	9	3		3	UGT3A1	5	35965611	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10		35965611	144949649	200	9109											
EGFLAM	133584	hgsc.bcm.edu	37	chr5	38409147	38409147	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgctctactgtggggagaaCgaacacgggaggggggattt	9	8	17	7	2	1	1	0	0	1	1	1	5	1	3	0	6	4	1	0	6	3	2	rs16903964	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:38409147C>T	ENST00000354891.3	+	10	1636	c.1290C>T	c.(1288-1290)aaC>aaT	p.N430N	EGFLAM_ENST00000397202.2_Intron|EGFLAM_ENST00000322350.5_Silent_p.N430N|EGFLAM_ENST00000336740.6_Silent_p.N196N	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	430	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)					GTGGGGAGAACGAACACGGGA	0.502													C|||	235	0.0469249	0.1717	0.0101	5008	,	,		15939	0.001		0.0	False		,,,				2504	0.0				p.N430N	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											.	EGFLAM	302	.	0			c.C1290T						PASS	.	C	,,	599,3807		33,533,1637	83	80	81		1290,1290,588	-9.4	0	5	dbSNP_123	81	12,8588		0,12,4288	no	coding-synonymous,coding-synonymous,coding-synonymous	EGFLAM	NM_001205301.1,NM_152403.3,NM_182798.2	,,	33,545,5925	TT,TC,CC		0.1395,13.5951,4.6978	,,	430/1018,430/1010,196/776	38409147	611,12395	2203	4300	6503	SO:0001819	synonymous_variant	133584	exon10			GGAGAACGAACAC	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.1290C>T	5.37:g.38409147C>T		105	0	0		105	53	0.504762	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Silent	SNP	ENST00000354891.3	37	CCDS56363.1																																																																																			C|0.949;T|0.051	0.051	strong		0.502	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403		T	38409147	C	T	38409147	2	4	25	1	0	0	0	0	0	0	0	1	4968	535	19	1		1	EGFLAM	5	38409147	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2443536	38409147	142506113	201	9110											
FYB	2533	hgsc.bcm.edu	37	chr5	39124367	39124367	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ttacttacccaattgtttagGaggagcagggaaactacaaa	15	10	9	7	0	0	0	0	0	0	0	0	3	0	3	1	3	5	2	1	3	7	6			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:39124367G>A	ENST00000351578.6	-	12	2111	c.1921C>T	c.(1921-1923)Cct>Tct	p.P641S	FYB_ENST00000505428.1_Missense_Mutation_p.P687S|FYB_ENST00000512982.1_Missense_Mutation_p.P687S|FYB_ENST00000540520.1_Missense_Mutation_p.P697S|FYB_ENST00000515010.1_Missense_Mutation_p.P641S	NM_199335.3	NP_955367.1	O15117	FYB_HUMAN	FYN binding protein	641					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)			AATTGTTTAGGAGGAGCAGGG	0.353																																					p.P697S		Atlas-SNP	.											.	FYB	354	.	0			c.C2089T						PASS	.						93	84	86					5																	39124367		1850	4103	5953	SO:0001583	missense	2533	exon13			GTTTAGGAGGAGC	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.1921C>T	5.37:g.39124367G>A	ENSP00000316460:p.Pro641Ser	332	1	0.00301205		302	149	0.493377	NM_001243093	A8K2Y8|B4DLN2|E9PBV9|O00359|Q9NZI9	Missense_Mutation	SNP	ENST00000351578.6	37	CCDS47200.1	.	.	.	.	.	.	.	.	.	.	G	11.87	1.766616	0.31228	.	.	ENSG00000082074	ENST00000351578;ENST00000515010;ENST00000512982;ENST00000505428;ENST00000540520;ENST00000542542	T;T;T;T;T	0.23950	1.88;1.88;2.01;2.01;2.01	5.52	4.64	0.57946	.	0.316489	0.33419	N	0.004937	T	0.19208	0.0461	L	0.43701	1.375	0.26889	N	0.967371	B;P	0.43094	0.376;0.799	B;B	0.35931	0.186;0.214	T	0.10706	-1.0618	10	0.22706	T	0.39	-1.5143	12.0613	0.53564	0.0:0.1728:0.8272:0.0	.	697;641	B4DLN2;O15117	.;FYB_HUMAN	S	641;641;687;687;697;687	ENSP00000316460:P641S;ENSP00000426346:P641S;ENSP00000425845:P687S;ENSP00000427114:P687S;ENSP00000442840:P697S	ENSP00000316460:P641S	P	-	1	0	FYB	39160124	1.000000	0.71417	1.000000	0.80357	0.683000	0.39861	1.917000	0.39996	1.532000	0.49169	0.650000	0.86243	CCT	.	.	none		0.353	FYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367098.1	NM_001465		A	39124367	G	A	39124367	3	1	25	1	0	0	0	0	1	0	0	0	6132	1174	41	2	458	2	FYB	5	39124367	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	715220	39124367	141790893	202	9111											
C6	729	hgsc.bcm.edu	37	chr5	41161898	41161898	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tctcccatgccaaagctgctCcatattcactccttccacct	8	12	3	18	0	2	0	1	0	1	0	6	0	5	0	6	0	3	2	6	0	2	3	rs142896559	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:41161898C>T	ENST00000263413.3	-	10	1619	c.1355G>A	c.(1354-1356)gGa>gAa	p.G452E	C6_ENST00000337836.5_Missense_Mutation_p.G452E|C6_ENST00000475349.1_5'UTR	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	452	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)				CAAAGCTGCTCCATATTCACT	0.423													C|||	11	0.00219649	0.0008	0.0014	5008	,	,		18136	0.0		0.004	False		,,,				2504	0.0051				p.G452E		Atlas-SNP	.											.	C6	197	.	0			c.G1355A						PASS	.	C	GLU/GLY,GLU/GLY	5,4401	9.9+/-24.2	0,5,2198	127	124	125		1355,1355	4.5	0.4	5	dbSNP_134	125	54,8546	34.3+/-88.2	0,54,4246	yes	missense,missense	C6	NM_000065.2,NM_001115131.1	98,98	0,59,6444	TT,TC,CC		0.6279,0.1135,0.4536	benign,benign	452/935,452/935	41161898	59,12947	2203	4300	6503	SO:0001583	missense	729	exon10			GCTGCTCCATATT	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.1355G>A	5.37:g.41161898C>T	ENSP00000263413:p.Gly452Glu	131	0	0		137	74	0.540146	NM_001115131		Missense_Mutation	SNP	ENST00000263413.3	37	CCDS3936.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	16.72	3.202704	0.58234	0.001135	0.006279	ENSG00000039537	ENST00000337836;ENST00000263413	D;D	0.83335	-1.71;-1.71	5.35	4.48	0.54585	Membrane attack complex component/perforin (MACPF) domain (3);	0.311897	0.38778	N	0.001563	T	0.70090	0.3184	L	0.29908	0.895	0.30383	N	0.78175	B	0.09022	0.002	B	0.06405	0.002	T	0.72811	-0.4180	10	0.72032	D	0.01	-7.7633	16.7694	0.85533	0.0:0.1292:0.8708:0.0	.	452	P13671	CO6_HUMAN	E	452	ENSP00000338861:G452E;ENSP00000263413:G452E	ENSP00000263413:G452E	G	-	2	0	C6	41197655	0.998000	0.40836	0.415000	0.26534	0.970000	0.65996	5.677000	0.68142	1.638000	0.50547	-0.128000	0.14901	GGA	C|0.996;T|0.004	0.004	strong		0.423	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1			T	41161898	C	T	41161898	3	4	25	1	0	0	0	0	1	0	0	0	2317	855	30	2	1485	2	C6	5	41161898	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2037531	41161898	139753362	203	9112											
IL31RA	133396	hgsc.bcm.edu	37	chr5	55147405	55147405	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacctcagctgggaatgtgcAtcaggcaactcaagtttttc	10	11	9	11	0	3	0	3	0	0	0	4	1	3	1	1	2	3	4	1	2	3	2	rs75528518		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:55147405A>C	ENST00000447346.2	+	1	72	c.7A>C	c.(7-9)Atc>Ctc	p.I3L	IL31RA_ENST00000297015.3_5'Flank|IL31RA_ENST00000359040.5_Missense_Mutation_p.I3L|IL31RA_ENST00000354961.4_5'Flank|IL31RA_ENST00000396836.2_Missense_Mutation_p.I3L|IL31RA_ENST00000396834.1_5'UTR|IL31RA_ENST00000490985.1_5'Flank	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)				gggaatgtgcatcaggcaact	0.438																																					p.I3L		Atlas-SNP	.											.	IL31RA	84	.	0			c.A7C						PASS	.						133	138	136					5																	55147405		2024	4184	6208	SO:0001583	missense	133396	exon1			ATGTGCATCAGGC	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.7A>C	5.37:g.55147405A>C	ENSP00000415900:p.Ile3Leu	133	0	0		160	69	0.43125	NM_001242637	A6NIF8|Q2TBA1|Q6EBC3|Q6EBC4|Q6EBC5|Q6EBC6|Q6UWL8|Q8WYJ0	Missense_Mutation	SNP	ENST00000447346.2	37	CCDS3970.2	.	.	.	.	.	.	.	.	.	.	.	4.977	0.181530	0.09495	.	.	ENSG00000164509	ENST00000396836;ENST00000447346;ENST00000359040	T;T;T	0.37915	1.33;1.2;1.17	2.33	-2.34	0.06704	.	1.884850	0.02918	N	0.137637	T	0.25865	0.0630	.	.	.	0.09310	N	1	B;B;B	0.19583	0.037;0.037;0.037	B;B;B	0.24541	0.036;0.054;0.054	T	0.28713	-1.0035	9	0.87932	D	0	.	2.59	0.04840	0.4946:0.0:0.1516:0.3539	.	3;3;3	Q8NI17-5;Q8NI17-2;Q8NI17-8	.;.;.	L	3	ENSP00000380048:I3L;ENSP00000415900:I3L;ENSP00000351935:I3L	ENSP00000351935:I3L	I	+	1	0	IL31RA	55183162	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-0.332000	0.07904	-0.487000	0.06735	-0.415000	0.06103	ATC	.	.	alt		0.438	IL31RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214148.1	NM_139017		C	55147405	A	C	55147405	3	2	25	1	0	0	0	0	1	0	0	0	7700	217	8	5	9	5	IL31RA	5	55147405	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	13985507	55147405	125767855	204	9113											
IL6ST	3572	hgsc.bcm.edu	37	chr5	55272085	55272085	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aataaacaaggcttgcactaGccaagtctgcaacgtcaaca	16	7	7	11	1	2	0	1	0	1	0	2	0	2	0	1	1	6	3	1	1	8	3	rs1063560	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:55272085G>C	ENST00000381298.2	-	3	334	c.22C>G	c.(22-24)Cta>Gta	p.L8V	IL6ST_ENST00000577363.1_5'UTR|IL6ST_ENST00000336909.5_Missense_Mutation_p.L8V|IL6ST_ENST00000381287.4_Missense_Mutation_p.L8V|IL6ST_ENST00000522633.2_Missense_Mutation_p.L8V|IL6ST_ENST00000381286.3_Missense_Mutation_p.L8V|IL6ST_ENST00000502326.3_Missense_Mutation_p.L8V|IL6ST_ENST00000381293.2_Missense_Mutation_p.L8V|IL6ST_ENST00000396816.1_Missense_Mutation_p.L8V|IL6ST_ENST00000536319.1_Missense_Mutation_p.L8V|IL6ST_ENST00000381294.3_Missense_Mutation_p.L8V	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	8			L -> V (in dbSNP:rs1063560). {ECO:0000269|PubMed:10880057, ECO:0000269|PubMed:2261637}.		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)				GCTTGCACTAGCCAAGTCTGC	0.323			O		hepatocellular ca								g|||	42	0.00838658	0.0015	0.0	5008	,	,		12985	0.001		0.0129	False		,,,				2504	0.0266				p.L8V		Atlas-SNP	.		Dom	yes		5	5q11	3572	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"		E	.	IL6ST	75	.	0			c.C22G						PASS	.	A	VAL/LEU,VAL/LEU,VAL/LEU	5,4401	9.9+/-24.2	0,5,2198	70	64	66		22,22,22	-1.1	0	5	dbSNP_86	66	99,8501	54.4+/-115.2	1,97,4202	yes	missense,missense,missense	IL6ST	NM_001190981.1,NM_002184.3,NM_175767.2	32,32,32	1,102,6400	CC,CG,GG		1.1512,0.1135,0.7996	benign,benign,benign	8/858,8/919,8/330	55272085	104,12902	2203	4300	6503	SO:0001583	missense	3572	exon3			GCACTAGCCAAGT	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.22C>G	5.37:g.55272085G>C	ENSP00000370698:p.Leu8Val	163	0	0		180	82	0.455556	NM_175767	A0N0L4|Q5FC04|Q9UQ41	Missense_Mutation	SNP	ENST00000381298.2	37	CCDS3971.1	12	0.005494505494505495	1	0.0020325203252032522	0	0.0	0	0.0	11	0.014511873350923483	g	0.001	-3.108750	0.00033	0.001135	0.011512	ENSG00000134352	ENST00000381298;ENST00000336909;ENST00000381294;ENST00000381287;ENST00000536319;ENST00000381293;ENST00000381286;ENST00000522633;ENST00000542298	T;T;T;T;T;T;T;T	0.61980	1.52;1.52;1.27;1.49;1.49;1.88;0.06;1.49	4.85	-1.07	0.09968	.	0.996520	0.08132	N	0.993050	T	0.35451	0.0932	L	0.40543	1.245	0.09310	N	1	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.0	T	0.17289	-1.0374	10	0.20519	T	0.43	.	0.7244	0.00946	0.2881:0.1764:0.3444:0.1911	rs1063560;rs3204590;rs52794902;rs1063560	8;8;8;8	Q5FC05;Q5FC04;P40189-2;P40189	.;.;.;IL6RB_HUMAN	V	8	ENSP00000370698:L8V;ENSP00000338799:L8V;ENSP00000370694:L8V;ENSP00000370687:L8V;ENSP00000444456:L8V;ENSP00000370693:L8V;ENSP00000370686:L8V;ENSP00000435399:L8V	ENSP00000338799:L8V	L	-	1	2	IL6ST	55307842	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-0.516000	0.06282	-0.573000	0.05998	-3.277000	0.00047	CTA	G|0.989;C|0.011	0.011	strong		0.323	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184		C	55272085	G	C	55272085	3	2	25	1	0	0	0	0	1	0	0	0	7712	962	34	4	2794	4	IL6ST	5	55272085	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	124680	55272085	125643175	205	9114											
HTR1A	3350	hgsc.bcm.edu	37	chr5	63257310	63257310	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gacaccatgaggtcggtgacCgccaaagagccaataagata	15	5	11	10	2	0	4	0	2	0	2	1	5	0	4	4	2	1	0	4	2	4	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:63257310C>T	ENST00000323865.3	-	1	470	c.237G>A	c.(235-237)gcG>gcA	p.A79A	RP11-158J3.2_ENST00000502882.1_RNA	NM_000524.3	NP_000515.2	P08908	5HT1A_HUMAN	5-hydroxytryptamine (serotonin) receptor 1A, G protein-coupled	79					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)	p.A79A(1)		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)	GGTCGGTGACCGCCAAAGAGC	0.597																																					p.A79A		Atlas-SNP	.											HTR1A,colon,carcinoma,-1,2	HTR1A	128	2	1	Substitution - coding silent(1)	lung(1)	c.G237A						PASS	.						43	49	47					5																	63257310		2203	4300	6503	SO:0001819	synonymous_variant	3350	exon1			GGTGACCGCCAAA	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.237G>A	5.37:g.63257310C>T		125	0	0		155	62	0.4	NM_000524	Q6LAE7	Silent	SNP	ENST00000323865.3	37	CCDS34168.1																																																																																			.	.	none		0.597	HTR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368397.1	NM_000524		T	63257310	C	T	63257310	2	4	25	1	0	0	0	0	0	0	0	1	7445	639	23	1		1	HTR1A	5	63257310	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	7985225	63257310	117657950	206	9115											
ERAP2	64167	hgsc.bcm.edu	37	chr5	96231056	96231056	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taatgctacatatccagagcTgcaatttgtaagttcacaat	14	13	6	8	0	1	1	1	0	0	1	2	1	2	1	1	0	4	5	1	0	6	6	rs34261036	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:96231056T>G	ENST00000437043.3	+	7	1943	c.1232T>G	c.(1231-1233)cTg>cGg	p.L411R	ERAP2_ENST00000379904.4_Missense_Mutation_p.L366R|CTD-2260A17.2_ENST00000501338.1_Intron|ERAP2_ENST00000515095.1_3'UTR	NM_001130140.1|NM_022350.3	NP_001123612.1|NP_071745.1	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	411			L -> R (in dbSNP:rs34261036).		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)		TATCCAGAGCTGCAATTTGTA	0.343													T|||	13	0.00259585	0.0015	0.0	5008	,	,		17876	0.0		0.002	False		,,,				2504	0.0092				p.L411R		Atlas-SNP	.											.	ERAP2	77	.	0			c.T1232G						PASS	.	T	ARG/LEU,ARG/LEU	4,4402	8.1+/-20.4	0,4,2199	136	133	134		1232,1232	4.7	0.7	5	dbSNP_126	134	41,8559	27.4+/-76.7	0,41,4259	yes	missense,missense	ERAP2	NM_001130140.1,NM_022350.3	102,102	0,45,6458	GG,GT,TT		0.4767,0.0908,0.346	probably-damaging,probably-damaging	411/961,411/961	96231056	45,12961	2203	4300	6503	SO:0001583	missense	64167	exon7			CAGAGCTGCAATT	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.1232T>G	5.37:g.96231056T>G	ENSP00000400376:p.Leu411Arg	75	0	0		91	40	0.43956	NM_001130140	Q7Z5K1|Q8TD32|Q8WVJ4|Q9HBX2	Missense_Mutation	SNP	ENST00000437043.3	37	CCDS4086.1	5	0.0022893772893772895	2	0.0040650406504065045	0	0.0	0	0.0	3	0.00395778364116095	T	18.69	3.677983	0.68042	9.08E-4	0.004767	ENSG00000164308	ENST00000437043;ENST00000510373;ENST00000513084;ENST00000379904	T;T;T;T	0.02763	4.17;4.17;4.17;4.17	4.74	4.74	0.60224	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.50627	D	0.000108	T	0.16557	0.0398	M	0.84683	2.71	0.80722	D	1	D;P	0.57571	0.98;0.915	D;D	0.72982	0.964;0.979	T	0.00380	-1.1776	10	0.87932	D	0	.	13.5065	0.61486	0.0:0.0:0.0:1.0	rs34261036	366;411	Q6P179-3;Q6P179	.;ERAP2_HUMAN	R	411;411;411;366	ENSP00000400376:L411R;ENSP00000421175:L411R;ENSP00000421849:L411R;ENSP00000369235:L366R	ENSP00000369235:L366R	L	+	2	0	ERAP2	96256812	0.989000	0.36119	0.697000	0.30258	0.966000	0.64601	5.502000	0.66956	1.904000	0.55121	0.460000	0.39030	CTG	T|0.997;G|0.003	0.003	strong		0.343	ERAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250623.2	NM_022350		G	96231056	T	G	96231056	3	3	25	1	0	0	0	0	1	0	0	0	5206	1580	55	5	1254	5	ERAP2	5	96231056	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	32973746	96231056	84684204	207	9116											
DCP2	167227	hgsc.bcm.edu	37	chr5	112349109	112349109	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tgtaatggacattgcaagttCcccttttcatccagagcctt	9	14	7	11	0	1	1	1	0	0	1	3	2	3	2	4	1	2	3	4	1	2	6	rs149633478	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:112349109C>T	ENST00000389063.2	+	11	1389	c.1191C>T	c.(1189-1191)ttC>ttT	p.F397F	DCP2_ENST00000515408.1_Silent_p.F362F|DCP2_ENST00000543319.1_Silent_p.F186F	NM_152624.5	NP_689837	Q8IU60	DCP2_HUMAN	decapping mRNA 2	397					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)		ATTGCAAGTTCCCCTTTTCAT	0.418													C|||	9	0.00179712	0.0008	0.0	5008	,	,		19749	0.0		0.001	False		,,,				2504	0.0072				p.F397F		Atlas-SNP	.											.	DCP2	34	.	0			c.C1191T						PASS	.	C	,	0,4404		0,0,2202	233	204	214		1086,1191	2.8	1	5	dbSNP_134	214	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	DCP2	NM_001242377.1,NM_152624.5	,	0,3,6499	TT,TC,CC		0.0349,0.0,0.0231	,	362/386,397/421	112349109	3,13001	2202	4300	6502	SO:0001819	synonymous_variant	167227	exon11			CAAGTTCCCCTTT	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.1191C>T	5.37:g.112349109C>T		84	0	0		81	36	0.444444	NM_152624	C9J778|Q6P2D4|Q7Z5W5|Q8NBG5	Silent	SNP	ENST00000389063.2	37	CCDS34210.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	c	9.005	0.981066	0.18812	0.0	3.49E-4	ENSG00000172795	ENST00000513585	.	.	.	5.83	2.76	0.32466	.	.	.	.	.	T	0.54598	0.1868	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43523	-0.9386	4	.	.	.	.	6.4401	0.21845	0.0:0.6123:0.1279:0.2598	.	.	.	.	S	379	.	.	P	+	1	0	DCP2	112377008	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	0.796000	0.26986	0.242000	0.21303	0.552000	0.68991	CCC	C|0.999;T|0.001	0.001	strong		0.418	DCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370765.3	NM_152624		T	112349109	C	T	112349109	2	4	25	1	0	0	0	0	0	0	0	1	4302	854	30	2		2	DCP2	5	112349109	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	16118053	112349109	68566151	208	9117											
C5orf48	389320	hgsc.bcm.edu	37	chr5	125968301	125968301	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atgatcccaagacgttatgtCatgccttggaaagaaaacat	15	10	8	8	1	1	3	1	1	0	2	2	4	2	4	2	1	2	1	2	1	5	2	rs6887295	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:125968301C>T	ENST00000357147.3	+	2	163	c.150C>T	c.(148-150)gtC>gtT	p.V50V		NM_207408.1	NP_997291.1	Q6ZNM6	TEX43_HUMAN		50										large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	7						GACGTTATGTCATGCCTTGGA	0.368													T|||	676	0.134984	0.4818	0.0375	5008	,	,		21723	0.001		0.0	False		,,,				2504	0.0123				p.V50V		Atlas-SNP	.											.	C5orf48	21	.	0			c.C150T						PASS	.	T		1693,2713	652.3+/-399.4	334,1025,844	109	104	105		150	-6.3	0.1	5	dbSNP_116	105	12,8588	818.7+/-406.8	0,12,4288	no	coding-synonymous	C5orf48	NM_207408.1		334,1037,5132	TT,TC,CC		0.1395,38.4249,13.1093		50/135	125968301	1705,11301	2203	4300	6503	SO:0001819	synonymous_variant	389320	exon2			TTATGTCATGCCT																												ENST00000357147.3:c.150C>T	5.37:g.125968301C>T		89	0	0		78	43	0.551282	NM_207408		Silent	SNP	ENST00000357147.3	37	CCDS4139.1																																																																																			C|0.870;T|0.130	0.130	strong		0.368	C5orf48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250923.1			T	125968301	C	T	125968301	2	4	25	1	0	0	0	0	0	0	0	1	2308	813	29	2		2	C5orf48	5	125968301	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	13619192	125968301	54946959	209	9118											
MEGF10	84466	hgsc.bcm.edu	37	chr5	126746147	126746147	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagacctgccagtgtgtcaaCggagggaagtgttaccacgt	10	8	14	9	2	1	1	1	0	0	1	1	4	1	3	3	2	3	1	3	2	3	1	rs35550094	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:126746147C>T	ENST00000274473.6	+	10	1251	c.984C>T	c.(982-984)aaC>aaT	p.N328N	MEGF10_ENST00000508365.1_Silent_p.N328N|MEGF10_ENST00000418761.2_Silent_p.N328N|MEGF10_ENST00000503335.2_Silent_p.N328N	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10	328	EGF-like 6. {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)		AGTGTGTCAACGGAGGGAAGT	0.587													T|||	82	0.0163738	0.0582	0.0072	5008	,	,		20739	0.0		0.0	False		,,,				2504	0.0				p.N328N		Atlas-SNP	.											.	MEGF10	152	.	0			c.C984T						PASS	.	T		194,4212	808.7+/-415.9	4,186,2013	123	103	110		984	-0.9	0.9	5	dbSNP_126	110	20,8580	818.4+/-406.9	0,20,4280	no	coding-synonymous	MEGF10	NM_032446.2		4,206,6293	TT,TC,CC		0.2326,4.4031,1.6454		328/1141	126746147	214,12792	2203	4300	6503	SO:0001819	synonymous_variant	84466	exon10			TGTCAACGGAGGG	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.984C>T	5.37:g.126746147C>T		132	0	0		145	68	0.468966	NM_032446	Q68DE5|Q8WUL3	Silent	SNP	ENST00000274473.6	37	CCDS4142.1																																																																																			C|0.983;T|0.017	0.017	strong		0.587	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446		T	126746147	C	T	126746147	2	4	25	1	0	0	0	0	0	0	0	1	9469	535	19	1		1	MEGF10	5	126746147	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	777846	126746147	54169113	210	9119											
FBN2	2201	hgsc.bcm.edu	37	chr5	127595153	127595153	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aagtctgtgaagggttaataGagctgaatctgcagcctcat	12	11	11	7	0	3	3	1	2	2	1	3	3	3	3	1	1	3	3	1	1	5	2	rs34383505	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:127595153G>C	ENST00000508053.1	-	71	9707	c.8733C>G	c.(8731-8733)ctC>ctG	p.L2911L	FBN2_ENST00000262464.4_Silent_p.L2911L			P35556	FBN2_HUMAN	fibrillin 2	2911					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)		AGGGTTAATAGAGCTGAATCT	0.458													G|||	138	0.0275559	0.0998	0.0086	5008	,	,		15857	0.0		0.0	False		,,,				2504	0.0				p.L2911L		Atlas-SNP	.											.	FBN2	858	.	0			c.C8733G						PASS	.	G		323,4083	171.9+/-202.1	11,301,1891	96	95	95		8733	3.7	1	5	dbSNP_126	95	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	FBN2	NM_001999.3		11,303,6189	CC,CG,GG		0.0233,7.3309,2.4988		2911/2913	127595153	325,12681	2203	4300	6503	SO:0001819	synonymous_variant	2201	exon65			TTAATAGAGCTGA	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.8733C>G	5.37:g.127595153G>C		197	0	0		220	111	0.504545	NM_001999	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	37	CCDS34222.1																																																																																			G|0.973;C|0.027	0.027	strong		0.458	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		C	127595153	G	C	127595153	2	2	25	1	0	0	0	0	0	0	0	1	5711	929	33	4		4	FBN2	5	127595153	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	849006	127595153	53320107	211	9120											
ADAMTS19	171019	hgsc.bcm.edu	37	chr5	129001247	129001247	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agaagaatcaaagttgtggaGgaaaagccggcacatagcta	17	6	12	6	1	1	2	1	0	0	2	1	4	1	4	1	3	2	3	1	3	7	3	rs77945368	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:129001247G>A	ENST00000274487.4	+	16	2608	c.2463G>A	c.(2461-2463)gaG>gaA	p.E821E	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	821	Spacer.					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)		AAGTTGTGGAGGAAAAGCCGG	0.428													G|||	18	0.00359425	0.0136	0.0	5008	,	,		13404	0.0		0.0	False		,,,				2504	0.0				p.E821E		Atlas-SNP	.											ADAMTS19,NS,carcinoma,0,1	ADAMTS19	216	1	0			c.G2463A						PASS	.	G		79,4327	68.1+/-105.8	0,79,2124	119	107	111		2463	0.8	1	5	dbSNP_132	111	0,8600		0,0,4300	no	coding-synonymous	ADAMTS19	NM_133638.3		0,79,6424	AA,AG,GG		0.0,1.793,0.6074		821/1208	129001247	79,12927	2203	4300	6503	SO:0001819	synonymous_variant	171019	exon16			TGTGGAGGAAAAG	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.2463G>A	5.37:g.129001247G>A		83	0	0		62	25	0.403226	NM_133638		Silent	SNP	ENST00000274487.4	37	CCDS4146.1																																																																																			G|0.993;A|0.007	0.007	strong		0.428	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		A	129001247	G	A	129001247	2	1	25	1	0	0	0	0	0	0	0	1	264	991	35	2		2	ADAMTS19	5	129001247	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1406094	129001247	51914013	212	9121											
RAD50	10111	hgsc.bcm.edu	37	chr5	131924538	131924538	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaacttgtgagagagagacAagaaggggaagcaaaaactg	19	4	13	5	0	0	4	0	1	0	3	0	7	0	5	0	2	3	1	0	2	6	1	rs200017020	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:131924538A>G	ENST00000265335.6	+	8	1598	c.1211A>G	c.(1210-1212)cAa>cGa	p.Q404R	RAD50_ENST00000378823.3_Missense_Mutation_p.Q265R			Q92878	RAD50_HUMAN	RAD50 homolog (S. cerevisiae)	404					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)			AGAGAGAGACAAGAAGGGGAA	0.358								Homologous recombination					A|||	2	0.000399361	0.0	0.0	5008	,	,		16369	0.002		0.0	False		,,,				2504	0.0				p.Q404R		Atlas-SNP	.											.	RAD50	246	.	0			c.A1211G						PASS	.						77	77	77					5																	131924538		2203	4300	6503	SO:0001583	missense	10111	exon8			AGAGACAAGAAGG	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.1211A>G	5.37:g.131924538A>G	ENSP00000265335:p.Gln404Arg	182	0	0		174	95	0.545977	NM_005732	B9EGF5|O43254|Q6GMT7|Q6P5X3|Q9UP86	Missense_Mutation	SNP	ENST00000265335.6	37	CCDS34233.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	A	9.857	1.195145	0.22037	.	.	ENSG00000113522	ENST00000378823;ENST00000265335;ENST00000453394	T;T;T	0.09073	3.51;3.02;3.02	5.97	4.8	0.61643	.	0.173879	0.52532	D	0.000075	T	0.09992	0.0245	L	0.57536	1.79	0.33889	D	0.637111	B	0.30511	0.282	B	0.26517	0.07	T	0.10132	-1.0643	10	0.32370	T	0.25	-11.145	11.8328	0.52305	0.8688:0.0:0.0:0.1312	.	404	Q92878	RAD50_HUMAN	R	265;404;404	ENSP00000368100:Q265R;ENSP00000265335:Q404R;ENSP00000400049:Q404R	ENSP00000265335:Q404R	Q	+	2	0	RAD50	131952437	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	3.243000	0.51392	1.062000	0.40625	-0.333000	0.08304	CAA	A|1.000;G|0.000	0.000	strong		0.358	RAD50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132566.5	NM_005732		G	131924538	A	G	131924538	3	3	25	1	0	0	0	0	1	0	0	0	12999	130	5	3	1241	3	RAD50	5	131924538	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	2923291	131924538	48990722	213	9122											
KLHL3	26249	hgsc.bcm.edu	37	chr5	136975604	136975604	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgatcccaccggtcctcctcGaaatcatagcactccacact	10	9	5	17	2	1	1	1	1	0	0	6	2	5	1	5	1	1	1	5	1	2	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:136975604G>A	ENST00000309755.4	-	9	1409	c.966C>T	c.(964-966)ttC>ttT	p.F322F	KLHL3_ENST00000541417.1_Intron|KLHL3_ENST00000506873.1_5'UTR|KLHL3_ENST00000508657.1_Silent_p.F290F|KLHL3_ENST00000506491.1_Silent_p.F240F	NM_017415.2	NP_059111.2	Q9UH77	KLHL3_HUMAN	kelch-like family member 3	322			F -> C (in PHA2D). {ECO:0000269|PubMed:22266938}.		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)		GGTCCTCCTCGAAATCATAGC	0.577																																					p.F322F		Atlas-SNP	.											.	KLHL3	54	.	0			c.C966T						PASS	.						104	90	95					5																	136975604		2203	4300	6503	SO:0001819	synonymous_variant	26249	exon9			CTCCTCGAAATCA	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.966C>T	5.37:g.136975604G>A		150	0	0		139	58	0.417266	NM_017415	B2RBK7|Q9UH75|Q9UH76|Q9ULU0|Q9Y6V6	Silent	SNP	ENST00000309755.4	37	CCDS4192.1																																																																																			.	.	none		0.577	KLHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251220.2			A	136975604	G	A	136975604	2	1	25	1	0	0	0	0	0	0	0	1	8392	1049	37	1		1	KLHL3	5	136975604	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	5051066	136975604	43939656	214	9123											
ANKHD1	54882	hgsc.bcm.edu	37	chr5	139838786	139838786	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagacagaagaaactcaagaAactgctcttactttggcttg	14	10	8	9	0	2	4	1	0	1	4	2	4	2	4	0	1	4	2	0	1	5	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:139838786A>C	ENST00000360839.2	+	9	1672	c.1518A>C	c.(1516-1518)gaA>gaC	p.E506D	ANKHD1_ENST00000297183.6_Missense_Mutation_p.E506D|ANKHD1_ENST00000394722.3_Missense_Mutation_p.E495D|ANKHD1-EIF4EBP3_ENST00000532219.1_Missense_Mutation_p.E506D|ANKHD1_ENST00000394723.3_Missense_Mutation_p.E506D	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	506						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)			AAACTCAAGAAACTGCTCTTA	0.363																																					p.E506D		Atlas-SNP	.											ANKHD1-EIF4EBP3,rectum,carcinoma,+2,2	ANKHD1	233	2	0			c.A1518C						PASS	.						75	77	76					5																	139838786		2203	4300	6503	SO:0001583	missense	54882	exon9			TCAAGAAACTGCT	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.1518A>C	5.37:g.139838786A>C	ENSP00000354085:p.Glu506Asp	188	0	0		150	70	0.466667	NM_024668	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Missense_Mutation	SNP	ENST00000360839.2	37	CCDS4225.1	.	.	.	.	.	.	.	.	.	.	A	19.90	3.912101	0.72983	.	.	ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996	ENST00000360839;ENST00000422011;ENST00000297183;ENST00000253810;ENST00000310356;ENST00000421134;ENST00000394723;ENST00000394722;ENST00000532219	T;T;T;T;T;T	0.64618	-0.11;-0.11;2.39;2.39;2.39;-0.11	5.51	5.51	0.81932	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.61565	0.2357	N	0.11927	0.2	0.58432	D	0.999997	D;D;D;D;D	0.89917	0.999;0.997;0.992;0.971;1.0	D;D;D;P;D	0.80764	0.98;0.992;0.989;0.77;0.994	T	0.66826	-0.5825	10	0.62326	D	0.03	.	9.8994	0.41338	0.879:0.0:0.121:0.0	.	506;506;506;495;506	Q8IWZ3-5;Q8IWZ2;Q8IWZ3;Q8IWZ3-3;Q8IWZ3-2	.;.;ANKH1_HUMAN;.;.	D	506;520;506;506;21;506;506;495;506	ENSP00000354085:E506D;ENSP00000297183:E506D;ENSP00000394489:E506D;ENSP00000378212:E506D;ENSP00000378211:E495D;ENSP00000432016:E506D	ENSP00000432016:E506D	E	+	3	2	ANKHD1-EIF4EBP3;ANKHD1	139818970	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.935000	0.56560	2.105000	0.64084	0.454000	0.30748	GAA	.	.	none		0.363	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747		C	139838786	A	C	139838786	3	2	25	1	0	0	0	0	1	0	0	0	628	11	1	5	1552	5	ANKHD1	5	139838786	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	2863182	139838786	41076474	215	9124											
PCDHA8	56140	hgsc.bcm.edu	37	chr5	140222316	140222316	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgaaggagaacaacccgccGggctgccacatcttcacggt	10	6	12	13	3	2	2	1	1	1	1	2	3	2	2	3	3	3	1	3	3	3	1	rs202126810		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140222316G>A	ENST00000531613.1	+	1	1410	c.1410G>A	c.(1408-1410)ccG>ccA	p.P470P	PCDHA8_ENST00000378123.3_Silent_p.P470P|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	470	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(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)			ACAACCCGCCGGGCTGCCACA	0.672																																					p.P470P		Atlas-SNP	.											PCDHA8_ENST00000531613,rectum,carcinoma,0,2	PCDHA8	366	2	0			c.G1410A						PASS	.						38	43	41					5																	140222316		2193	4252	6445	SO:0001819	synonymous_variant	56140	exon1			CCCGCCGGGCTGC	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.1410G>A	5.37:g.140222316G>A		242	0	0		304	152	0.5	NM_031856	B9EGT7|O75281	Silent	SNP	ENST00000531613.1	37	CCDS54919.1																																																																																			G|0.999;T|0.001	.	alt		0.672	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911		A	140222316	G	A	140222316	2	1	25	1	0	0	0	0	0	0	0	1	11539	1103	39	1		1	PCDHA8	5	140222316	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	383530	140222316	40692944	216	9125											
PCDHB2	56133	hgsc.bcm.edu	37	chr5	140475665	140475665	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccgtcaccgacttcgggacaCccaggctgaaaaccgagcac	11	4	10	16	4	1	1	1	1	0	0	2	4	1	2	4	2	2	2	4	2	2	1	rs116177548	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140475665C>A	ENST00000194155.4	+	1	1439	c.1291C>A	c.(1291-1293)Ccc>Acc	p.P431T		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	431	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(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)			CTTCGGGACACCCAGGCTGAA	0.557													C|||	48	0.00958466	0.0	0.0043	5008	,	,		19536	0.001		0.003	False		,,,				2504	0.0419				p.P431T		Atlas-SNP	.											PCDHB2,NS,carcinoma,-2,1	PCDHB2	163	1	0			c.C1291A						PASS	.	C	THR/PRO	2,4404	4.2+/-10.8	0,2,2201	138	127	131		1291	5.1	0.9	5	dbSNP_132	131	48,8552	31.2+/-83.2	0,48,4252	yes	missense	PCDHB2	NM_018936.2	38	0,50,6453	AA,AC,CC		0.5581,0.0454,0.3844	probably-damaging	431/799	140475665	50,12956	2203	4300	6503	SO:0001583	missense	56133	exon1			GGGACACCCAGGC	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.1291C>A	5.37:g.140475665C>A	ENSP00000194155:p.Pro431Thr	153	0	0		239	113	0.472803	NM_018936	Q4KMU1	Missense_Mutation	SNP	ENST00000194155.4	37	CCDS4244.1	5	0.0022893772893772895	0	0.0	3	0.008287292817679558	0	0.0	2	0.002638522427440633	C	13.48	2.249833	0.39797	4.54E-4	0.005581	ENSG00000112852	ENST00000194155	T	0.56275	0.47	5.11	5.11	0.69529	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.77631	0.4159	H	0.98133	4.155	0.45284	D	0.998288	D	0.89917	1.0	D	0.91635	0.999	D	0.86973	0.2099	9	0.87932	D	0	.	14.5945	0.68395	0.1465:0.8535:0.0:0.0	.	431	Q9Y5E7	PCDB2_HUMAN	T	431	ENSP00000194155:P431T	ENSP00000194155:P431T	P	+	1	0	PCDHB2	140455849	0.889000	0.30405	0.880000	0.34516	0.050000	0.14768	2.396000	0.44468	2.542000	0.85734	0.650000	0.86243	CCC	C|0.996;A|0.004	0.004	strong		0.557	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936		A	140475665	C	A	140475665	3	1	25	1	0	0	0	0	1	0	0	0	11551	507	18	4	1293	4	PCDHB2	5	140475665	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	253349	140475665	40439595	217	9126											
PCDHB4	56131	hgsc.bcm.edu	37	chr5	140502433	140502433	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atggcttattccaagcatcaGatgaaattaaacaaactttc	16	12	5	8	0	1	2	1	1	0	1	3	2	2	2	1	1	3	2	1	1	6	4	rs149340599	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140502433G>C	ENST00000194152.1	+	1	853	c.853G>C	c.(853-855)Gat>Cat	p.D285H	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	285	Cadherin 3. {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)			CCAAGCATCAGATGAAATTAA	0.348													G|||	48	0.00958466	0.0	0.0043	5008	,	,		20653	0.001		0.003	False		,,,				2504	0.0419				p.D285H		Atlas-SNP	.											.	PCDHB4	177	.	0			c.G853C						PASS	.	G	HIS/ASP	2,4398	4.2+/-10.8	0,2,2198	92	107	102		853	4.4	1	5	dbSNP_134	102	46,8554	29.6+/-80.5	0,46,4254	yes	missense	PCDHB4	NM_018938.2	81	0,48,6452	CC,CG,GG		0.5349,0.0455,0.3692	possibly-damaging	285/796	140502433	48,12952	2200	4300	6500	SO:0001583	missense	56131	exon1			GCATCAGATGAAA	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.853G>C	5.37:g.140502433G>C	ENSP00000194152:p.Asp285His	112	0	0		115	53	0.46087	NM_018938	Q4V761	Missense_Mutation	SNP	ENST00000194152.1	37	CCDS4246.1	5	0.0022893772893772895	0	0.0	3	0.008287292817679558	0	0.0	2	0.002638522427440633	G	15.05	2.718902	0.48622	4.55E-4	0.005349	ENSG00000081818	ENST00000194152	T	0.66099	-0.19	4.41	4.41	0.53225	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.66257	0.2771	L	0.45285	1.41	0.43448	D	0.995638	P	0.37370	0.592	P	0.57620	0.824	T	0.72107	-0.4390	9	0.56958	D	0.05	.	17.5536	0.87884	0.0:0.0:1.0:0.0	.	285	Q9Y5E5	PCDB4_HUMAN	H	285	ENSP00000194152:D285H	ENSP00000194152:D285H	D	+	1	0	PCDHB4	140482617	0.015000	0.18098	0.996000	0.52242	0.671000	0.39405	1.433000	0.34947	2.449000	0.82847	0.650000	0.86243	GAT	G|0.996;C|0.004	0.004	strong		0.348	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938		C	140502433	G	C	140502433	3	2	25	1	0	0	0	0	1	0	0	0	11553	942	33	4	855	4	PCDHB4	5	140502433	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	26768	140502433	40412827	218	9127											
PCDHB10	56126	hgsc.bcm.edu	37	chr5	140573956	140573956	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	accagctgctcaaggccacgGagcccgggctgttcggtgtg	6	7	15	13	3	1	0	1	0	0	0	2	1	1	1	3	4	3	4	3	4	1	1	rs554525456	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140573956G>A	ENST00000239446.4	+	1	2015	c.1831G>A	c.(1831-1833)Gag>Aag	p.E611K		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	611	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(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)			CAAGGCCACGGAGCCCGGGCT	0.706													G|||	11	0.00219649	0.0	0.0014	5008	,	,		15886	0.0		0.005	False		,,,				2504	0.0051				p.E611K		Atlas-SNP	.											.	PCDHB10	177	.	0			c.G1831A						PASS	.						6	8	7					5																	140573956		1542	3066	4608	SO:0001583	missense	56126	exon1			GCCACGGAGCCCG	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.1831G>A	5.37:g.140573956G>A	ENSP00000239446:p.Glu611Lys	5	0	0		19	13	0.684211	NM_018930	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	37	CCDS4252.1	.	.	.	.	.	.	.	.	.	.	g	19.21	3.783989	0.70222	.	.	ENSG00000120324	ENST00000239446	T	0.53857	0.6	3.34	3.34	0.38264	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.72244	0.3436	M	0.79475	2.455	0.32066	N	0.595055	D	0.89917	1.0	D	0.79108	0.992	T	0.78425	-0.2209	9	0.87932	D	0	.	14.8686	0.70437	0.0:0.0:1.0:0.0	.	611	Q9UN67	PCDBA_HUMAN	K	611	ENSP00000239446:E611K	ENSP00000239446:E611K	E	+	1	0	PCDHB10	140554140	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	5.119000	0.64679	1.884000	0.54569	0.479000	0.44913	GAG	.	.	none		0.706	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930		A	140573956	G	A	140573956	3	1	25	1	0	0	0	0	1	0	0	0	11544	1175	41	2	1833	2	PCDHB10	5	140573956	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	71523	140573956	40341304	219	9128											
PCDHB12	56124	hgsc.bcm.edu	37	chr5	140590641	140590641	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caggaggagcagggcggcccCggtcggtcgctgctcggtgc	4	5	19	13	5	0	0	0	0	0	0	3	2	0	2	2	7	3	3	2	7	0	0	rs150562956	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140590641C>G	ENST00000239450.2	+	1	2351	c.2162C>G	c.(2161-2163)cCg>cGg	p.P721R	PCDHB12_ENST00000541609.1_Missense_Mutation_p.P384R|PCDHB13_ENST00000341948.4_5'Flank	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	721					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)			AGGGCGGCCCCGGTCGGTCGC	0.657													C|||	36	0.0071885	0.0	0.0014	5008	,	,		14069	0.001		0.005	False		,,,				2504	0.0297				p.P721R		Atlas-SNP	.											PCDHB12,colon,carcinoma,0,1	PCDHB12	179	1	0			c.C2162G						PASS	.	C	ARG/PRO	2,4404		0,2,2201	70	79	76		2162	1.7	0	5	dbSNP_134	76	47,8553		0,47,4253	no	missense	PCDHB12	NM_018932.3	103	0,49,6454	GG,GC,CC		0.5465,0.0454,0.3767	benign	721/796	140590641	49,12957	2203	4300	6503	SO:0001583	missense	56124	exon1			CGGCCCCGGTCGG	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.2162C>G	5.37:g.140590641C>G	ENSP00000239450:p.Pro721Arg	53	0	0		90	46	0.511111	NM_018932	B4DDU1	Missense_Mutation	SNP	ENST00000239450.2	37	CCDS4254.1	.	.	.	.	.	.	.	.	.	.	C	8.354	0.831566	0.16820	4.54E-4	0.005465	ENSG00000120328	ENST00000541609;ENST00000239450;ENST00000507840	T;T	0.52295	0.67;0.85	3.67	1.7	0.24286	.	.	.	.	.	T	0.27384	0.0672	L	0.38838	1.175	0.09310	N	1	B	0.21821	0.061	B	0.21360	0.034	T	0.18745	-1.0327	9	0.38643	T	0.18	.	7.7474	0.28877	0.2725:0.3123:0.4152:0.0	.	721	Q9Y5F1	PCDBC_HUMAN	R	384;721;341	ENSP00000440199:P384R;ENSP00000239450:P721R	ENSP00000239450:P721R	P	+	2	0	PCDHB12	140570825	0.006000	0.16342	0.002000	0.10522	0.053000	0.15095	0.784000	0.26816	0.128000	0.18479	0.479000	0.44913	CCG	C|0.998;G|0.002;T|0.000	0.002	strong		0.657	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932		G	140590641	C	G	140590641	3	3	25	1	0	0	0	0	1	0	0	0	11546	652	23	4	2164	4	PCDHB12	5	140590641	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	16685	140590641	40324619	220	9129											
FCHSD1	89848	hgsc.bcm.edu	37	chr5	141021108	141021108	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caggatccggggctttagccGgcgggggaggtggtggacgc	5	6	21	9	4	0	0	0	0	0	0	1	3	1	3	2	9	1	1	2	9	1	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:141021108G>A	ENST00000435817.2	-	20	2080	c.2030C>T	c.(2029-2031)cCg>cTg	p.P677L	FCHSD1_ENST00000522126.1_3'UTR|FCHSD1_ENST00000522783.1_3'UTR|FCHSD1_ENST00000523856.1_5'UTR	NM_033449.2	NP_258260.1	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	677	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)			GGCTTTAGCCGGCGGGGGAGG	0.587																																					p.P677L		Atlas-SNP	.											.	FCHSD1	51	.	0			c.C2030T						PASS	.						37	45	42					5																	141021108		1941	4133	6074	SO:0001583	missense	89848	exon20			TTAGCCGGCGGGG	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.2030C>T	5.37:g.141021108G>A	ENSP00000399259:p.Pro677Leu	90	0	0		112	62	0.553571	NM_033449	Q6UX75|Q86Y77|Q9NXX8	Missense_Mutation	SNP	ENST00000435817.2	37	CCDS47295.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.401255	0.62288	.	.	ENSG00000197948	ENST00000435817	T	0.28454	1.61	5.25	5.25	0.73442	.	0.143676	0.48286	D	0.000182	T	0.44787	0.1310	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	0.31475	-0.9942	10	0.72032	D	0.01	-9.0948	14.5305	0.67923	0.0:0.0:1.0:0.0	.	357;677	Q86WN1-2;Q86WN1	.;FCSD1_HUMAN	L	677	ENSP00000399259:P677L	ENSP00000399259:P677L	P	-	2	0	FCHSD1	141001292	0.998000	0.40836	0.831000	0.32960	0.910000	0.53928	4.883000	0.63128	2.885000	0.99019	0.655000	0.94253	CCG	.	.	none		0.587	FCHSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375282.2	NM_033449		A	141021108	G	A	141021108	3	1	25	1	0	0	0	0	1	0	0	0	5797	1116	39	1	46	1	FCHSD1	5	141021108	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	430467	141021108	39894152	221	9130											
PLAC8L1	153770	hgsc.bcm.edu	37	chr5	145464130	145464130	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagccagtcttcacacagTgtgccctagggcaagaccag	10	6	11	14	0	2	1	1	0	1	1	2	1	2	1	4	1	2	1	4	1	2	2	rs1859897	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:145464130T>C	ENST00000311450.4	-	4	456	c.399A>G	c.(397-399)acA>acG	p.T133T		NM_001029869.1	NP_001025040.1	A1L4L8	PL8L1_HUMAN	PLAC8-like 1	133										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)			CTTCACACAGTGTGCCCTAGG	0.527													T|||	178	0.0355431	0.1218	0.0216	5008	,	,		17606	0.0		0.002	False		,,,				2504	0.0				p.T133T		Atlas-SNP	.											.	PLAC8L1	17	.	0			c.A399G						PASS	.	T		480,3926	226.5+/-242.0	28,424,1751	95	93	93		399	-10.1	0	5	dbSNP_92	93	16,8584	11.9+/-42.8	0,16,4284	no	coding-synonymous	PLAC8L1	NM_001029869.1		28,440,6035	CC,CT,TT		0.186,10.8942,3.8136		133/178	145464130	496,12510	2203	4300	6503	SO:0001819	synonymous_variant	153770	exon4			ACACAGTGTGCCC		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.399A>G	5.37:g.145464130T>C		64	0	0		70	42	0.6	NM_001029869		Silent	SNP	ENST00000311450.4	37	CCDS34264.1																																																																																			T|0.967;C|0.033	0.033	strong		0.527	PLAC8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373290.1	XM_087761		C	145464130	T	C	145464130	2	2	25	1	0	0	0	0	0	0	0	1	12025	1683	59	3		3	PLAC8L1	5	145464130	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	4443022	145464130	35451130	222	9131											
POU4F3	5459	hgsc.bcm.edu	37	chr5	145719368	145719368	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctggagcacatctcgcccacGctgagtgtgagcggcctggg	6	7	15	13	3	1	2	0	2	1	0	2	3	1	3	2	3	2	2	2	3	0	0	rs113137300	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:145719368G>A	ENST00000230732.4	+	2	467	c.378G>A	c.(376-378)acG>acA	p.T126T	CTC-359M8.1_ENST00000515598.1_RNA	NM_002700.2	NP_002691.1	Q15319	PO4F3_HUMAN	POU class 4 homeobox 3	126					auditory receptor cell differentiation (GO:0042491)|axon extension (GO:0048675)|inner ear morphogenesis (GO:0042472)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retinal ganglion cell axon guidance (GO:0031290)|sensory perception of sound (GO:0007605)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	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)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCTCGCCCACGCTGAGTGTGA	0.687													G|||	14	0.00279553	0.0091	0.0029	5008	,	,		13001	0.0		0.0	False		,,,				2504	0.0				p.T126T		Atlas-SNP	.											.	POU4F3	47	.	0			c.G378A						PASS	.	G		34,4372	39.2+/-71.8	0,34,2169	76	71	73		378	1.8	1	5	dbSNP_132	73	0,8598		0,0,4299	no	coding-synonymous	POU4F3	NM_002700.2		0,34,6468	AA,AG,GG		0.0,0.7717,0.2615		126/339	145719368	34,12970	2203	4299	6502	SO:0001819	synonymous_variant	5459	exon2			GCCCACGCTGAGT	U10060	CCDS4281.1	5q32	2011-06-20	2007-07-13		ENSG00000091010	ENSG00000091010		"Homeoboxes / POU class"	9220	protein-coding gene	gene with protein product		602460	"POU domain class 4, transcription factor 3"	DFNA15		9506947	Standard	NM_002700		Approved	BRN3C	uc003loa.2	Q15319	OTTHUMG00000129684	ENST00000230732.4:c.378G>A	5.37:g.145719368G>A		44	0	0		59	29	0.491525	NM_002700	O60557|Q2M3F8	Silent	SNP	ENST00000230732.4	37	CCDS4281.1																																																																																			G|0.997;A|0.003	0.003	strong		0.687	POU4F3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251887.2	NM_002700		A	145719368	G	A	145719368	2	1	25	1	0	0	0	0	0	0	0	1	12289	1074	38	1		1	POU4F3	5	145719368	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	255238	145719368	35195892	223	9132											
ABLIM3	22885	hgsc.bcm.edu	37	chr5	148596547	148596547	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agggaagcactaccacccaaCctgtgccaggtgtgtacgct	10	7	11	13	1	0	0	0	0	0	0	0	1	0	1	4	2	5	3	4	2	4	2	rs116226381	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:148596547C>T	ENST00000506113.1	+	7	1177	c.695C>T	c.(694-696)aCc>aTc	p.T232I	RP11-331K21.1_ENST00000522685.1_RNA|RP11-331K21.1_ENST00000512647.2_RNA|AC012613.2_ENST00000523176.1_RNA|ABLIM3_ENST00000326685.7_Missense_Mutation_p.T232I|ABLIM3_ENST00000508983.1_Missense_Mutation_p.T232I|ABLIM3_ENST00000504238.1_Missense_Mutation_p.T232I|ABLIM3_ENST00000356541.3_Missense_Mutation_p.T232I|ABLIM3_ENST00000309868.7_Missense_Mutation_p.T232I			O94929	ABLM3_HUMAN	actin binding LIM protein family, member 3	232	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|cilium assembly (GO:0042384)|lamellipodium assembly (GO:0030032)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TACCACCCAACCTGTGCCAGG	0.522													C|||	10	0.00199681	0.0008	0.0	5008	,	,		21664	0.0		0.005	False		,,,				2504	0.0041				p.T232I		Atlas-SNP	.											.	ABLIM3	91	.	0			c.C695T						PASS	.	C	ILE/THR	2,4404	4.2+/-10.8	0,2,2201	94	81	85		695	2.6	1	5	dbSNP_132	85	46,8554	30.1+/-81.4	0,46,4254	yes	missense	ABLIM3	NM_014945.2	89	0,48,6455	TT,TC,CC		0.5349,0.0454,0.3691	benign	232/684	148596547	48,12958	2203	4300	6503	SO:0001583	missense	22885	exon8			ACCCAACCTGTGC	AB020650	CCDS4294.1	5q33.1	2008-02-05			ENSG00000173210	ENSG00000173210			29132	protein-coding gene	gene with protein product		611305					Standard	XM_005268392		Approved	KIAA0843	uc003lpy.2	O94929	OTTHUMG00000129932	ENST00000506113.1:c.695C>T	5.37:g.148596547C>T	ENSP00000425394:p.Thr232Ile	106	0	0		79	39	0.493671	NM_014945	A8K121|Q19VH3|Q658S1|Q68CI5|Q9BV32	Missense_Mutation	SNP	ENST00000506113.1	37	CCDS4294.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	15.76	2.928929	0.52759	4.54E-4	0.005349	ENSG00000173210	ENST00000326685;ENST00000356541;ENST00000309868;ENST00000506113;ENST00000504238;ENST00000508983	D;D;D;D;D;D	0.87491	-2.26;-2.26;-2.26;-2.26;-2.26;-2.26	5.49	2.56	0.30785	Zinc finger, LIM-type (5);	0.416904	0.28192	N	0.016242	T	0.81851	0.4910	M	0.77820	2.39	0.28363	N	0.920359	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.13407	0.001;0.001;0.009	T	0.79105	-0.1940	10	0.72032	D	0.01	.	10.4399	0.44460	0.0:0.6783:0.2521:0.0696	.	232;232;232	O94929-3;O94929-2;O94929	.;.;ABLM3_HUMAN	I	232	ENSP00000315841:T232I;ENSP00000348938:T232I;ENSP00000310309:T232I;ENSP00000425394:T232I;ENSP00000421183:T232I;ENSP00000420855:T232I	ENSP00000310309:T232I	T	+	2	0	ABLIM3	148576740	0.957000	0.32711	0.991000	0.47740	0.991000	0.79684	3.543000	0.53633	0.790000	0.33803	0.655000	0.94253	ACC	C|0.997;T|0.003	0.003	strong		0.522	ABLIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373435.1	NM_014945		T	148596547	C	T	148596547	3	4	25	1	0	0	0	0	1	0	0	0	96	507	18	2	721	2	ABLIM3	5	148596547	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2877179	148596547	32318713	224	9133											
PPARGC1B	133522	hgsc.bcm.edu	37	chr5	149216095	149216095	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctgttcctttggagaccatGactactgccaggtgctccga	7	11	10	13	1	0	2	0	1	0	1	2	4	2	2	5	2	3	2	5	2	1	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:149216095G>A	ENST00000309241.5	+	8	2109	c.2077G>A	c.(2077-2079)Gac>Aac	p.D693N	PPARGC1B_ENST00000403750.1_Missense_Mutation_p.D629N|PPARGC1B_ENST00000360453.4_Missense_Mutation_p.D654N|PPARGC1B_ENST00000394320.3_Missense_Mutation_p.D693N	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	693					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)			TGGAGACCATGACTACTGCCA	0.632																																					p.D693N		Atlas-SNP	.											.	PPARGC1B	74	.	0			c.G2077A						PASS	.						53	56	55					5																	149216095		2203	4300	6503	SO:0001583	missense	133522	exon8			GACCATGACTACT	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.2077G>A	5.37:g.149216095G>A	ENSP00000312649:p.Asp693Asn	97	0	0		63	34	0.539683	NM_133263	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Missense_Mutation	SNP	ENST00000309241.5	37	CCDS4298.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.737115	0.89482	.	.	ENSG00000155846	ENST00000360453;ENST00000394320;ENST00000309241;ENST00000403750	T;T;T;T	0.50813	0.77;0.73;0.81;0.75	4.47	4.47	0.54385	.	0.282850	0.37623	N	0.002014	T	0.66436	0.2789	M	0.81341	2.54	0.50632	D	0.99988	D;P;D;P;D	0.60575	0.976;0.948;0.976;0.93;0.988	P;P;P;P;P	0.57101	0.799;0.558;0.799;0.634;0.813	T	0.74300	-0.3710	10	0.87932	D	0	-13.9513	17.5766	0.87952	0.0:0.0:1.0:0.0	.	672;672;654;693;693	Q86YN6-2;Q86YN6-4;Q86YN6-5;Q86YN6;Q86YN6-3	.;.;.;PRGC2_HUMAN;.	N	654;693;693;629	ENSP00000353638:D654N;ENSP00000377855:D693N;ENSP00000312649:D693N;ENSP00000384403:D629N	ENSP00000312649:D693N	D	+	1	0	PPARGC1B	149196288	1.000000	0.71417	0.986000	0.45419	0.993000	0.82548	8.449000	0.90337	2.212000	0.71576	0.456000	0.33151	GAC	.	.	none		0.632	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263		A	149216095	G	A	149216095	3	1	25	1	0	0	0	0	1	0	0	0	12310	1290	45	2	2114	2	PPARGC1B	5	149216095	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	619548	149216095	31699165	225	9134											
SGCD	6444	hgsc.bcm.edu	37	chr5	155935708	155935708	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cgccaaagaaatccagtcccGaccagtaagtttctgctgag	12	8	9	12	2	1	2	0	1	1	1	3	3	3	2	4	0	1	3	4	0	3	2	rs45559835	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:155935708G>A	ENST00000435422.3	+	3	774	c.287G>A	c.(286-288)cGa>cAa	p.R96Q	SGCD_ENST00000337851.4_Missense_Mutation_p.R97Q|SGCD_ENST00000447401.1_Missense_Mutation_p.R97Q|SGCD_ENST00000517913.1_Missense_Mutation_p.R97Q	NM_001128209.1	NP_001121681.1	Q92629	SGCD_HUMAN	sarcoglycan, delta (35kDa dystrophin-associated glycoprotein)	96			R -> Q (in dbSNP:rs1801194). {ECO:0000269|PubMed:8842738}.		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)			ATCCAGTCCCGACCAGTAAGT	0.438													G|||	95	0.0189696	0.003	0.0317	5008	,	,		17897	0.0		0.0517	False		,,,				2504	0.0174				p.R97Q		Atlas-SNP	.											SGCD,NS,carcinoma,+1,1	SGCD	52	1	0			c.G290A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	44,3666		0,44,1811	76	69	71		290,287,290	5.5	1	5	dbSNP_127	71	527,7677		14,499,3589	yes	missense,missense,missense	SGCD	NM_000337.5,NM_001128209.1,NM_172244.2	43,43,43	14,543,5400	AA,AG,GG		6.4237,1.186,4.7927	benign,benign,benign	97/291,96/290,97/257	155935708	571,11343	1855	4102	5957	SO:0001583	missense	6444	exon4			AGTCCCGACCAGT	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.287G>A	5.37:g.155935708G>A	ENSP00000403003:p.Arg96Gln	60	0	0		61	26	0.42623	NM_000337	A8K9S9|Q53XA5|Q99644	Missense_Mutation	SNP	ENST00000435422.3	37	CCDS47327.1	49	0.022435897435897436	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	34	0.044854881266490766	G	26.3	4.727809	0.89390	0.01186	0.064237	ENSG00000170624	ENST00000517913;ENST00000435422;ENST00000337851;ENST00000447401	D;D;D;D	0.95656	-3.77;-3.77;-3.77;-3.77	5.49	5.49	0.81192	.	0.127312	0.53938	D	0.000051	T	0.71685	0.3369	M	0.78049	2.395	0.43559	D	0.99587	P;P;D	0.56287	0.826;0.792;0.975	B;B;B	0.39738	0.105;0.063;0.308	T	0.80774	-0.1232	10	0.27082	T	0.32	-2.0249	12.2832	0.54776	0.0783:0.0:0.9217:0.0	rs45559835;rs61742485	96;97;97	Q92629;Q92629-2;Q92629-3	SGCD_HUMAN;.;.	Q	97;96;97;97	ENSP00000429378:R97Q;ENSP00000403003:R96Q;ENSP00000338343:R97Q;ENSP00000408324:R97Q	ENSP00000338343:R97Q	R	+	2	0	SGCD	155868286	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.094000	0.57721	2.732000	0.93576	0.585000	0.79938	CGA	G|0.972;A|0.028	0.028	strong		0.438	SGCD-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000373469.3			A	155935708	G	A	155935708	3	1	25	1	0	0	0	0	1	0	0	0	14216	1058	37	1	300	1	SGCD	5	155935708	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	6719613	155935708	24979552	226	9135											
ODZ2	57451	hgsc.bcm.edu	37	chr5	167689162	167689162	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccagcatccgagagaaagcaGgtcactggtttgccaccacc	11	6	10	14	1	1	1	1	0	0	1	2	3	2	1	5	2	3	3	5	2	1	1	rs370473451		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:167689162G>A	ENST00000518659.1	+	29	7711	c.7672G>A	c.(7672-7674)Ggt>Agt	p.G2558S	TENM2_ENST00000519204.1_Missense_Mutation_p.G2437S|TENM2_ENST00000545108.1_Missense_Mutation_p.G2557S|TENM2_ENST00000403607.2_Missense_Mutation_p.G2382S|TENM2_ENST00000520394.1_Missense_Mutation_p.G2319S	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	2558					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)										AGAGAAAGCAGGTCACTGGTT	0.547																																					p.G2549S		Atlas-SNP	.											.	.	.	.	0			c.G7645A						PASS	.	G	SER/GLY	0,4040		0,0,2020	34	35	35		7645	5.4	1	5		35	1,8379		0,1,4189	no	missense	ODZ2	NM_001122679.1	56	0,1,6209	AA,AG,GG		0.0119,0.0,0.0081	probably-damaging	2549/2766	167689162	1,12419	2020	4190	6210	SO:0001583	missense	57451	exon29			AAAGCAGGTCACT	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.7672G>A	5.37:g.167689162G>A	ENSP00000429430:p.Gly2558Ser	117	0	0		125	59	0.472	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	37		.	.	.	.	.	.	.	.	.	.	G	18.78	3.697687	0.68386	0.0	1.19E-4	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.88896	-1.97;-1.96;-2.07;-2.43;-2.44	5.42	5.42	0.78866	.	0.102393	0.64402	D	0.000002	D	0.90397	0.6994	N	0.24115	0.695	0.58432	D	0.999992	D;D;D	0.89917	0.999;0.991;1.0	D;P;D	0.83275	0.974;0.842;0.996	D	0.87772	0.2606	10	0.21540	T	0.41	.	19.5868	0.95493	0.0:0.0:1.0:0.0	.	2557;2558;2319	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	S	2558;2557;2437;2319;2382	ENSP00000429430:G2558S;ENSP00000438635:G2557S;ENSP00000428964:G2437S;ENSP00000427874:G2319S;ENSP00000384905:G2382S	ENSP00000384905:G2382S	G	+	1	0	ODZ2	167621740	1.000000	0.71417	0.977000	0.42913	0.886000	0.51366	9.809000	0.99208	2.694000	0.91930	0.655000	0.94253	GGT	.	.	weak		0.547	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		A	167689162	G	A	167689162	3	1	25	1	0	0	0	0	1	0	0	0	10844	1000	35	2	7759	2	ODZ2	5	167689162	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	11753454	167689162	13226098	227	9136											
NSD1	64324	hgsc.bcm.edu	37	chr5	176721879	176721879	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggggcatatgccgagagctGttgagaaaggctgtgtgtca	9	10	16	6	1	1	2	1	1	0	2	1	4	1	2	1	3	2	4	1	3	2	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:176721879G>A	ENST00000439151.2	+	23	7555	c.7510G>A	c.(7510-7512)Gtt>Att	p.V2504I	NSD1_ENST00000354179.4_Missense_Mutation_p.V2235I|NSD1_ENST00000347982.4_Missense_Mutation_p.V2235I|NSD1_ENST00000361032.4_Missense_Mutation_p.V2401I	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2504					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)		GCCGAGAGCTGTTGAGAAAGG	0.542			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.V2504I		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.G7510A						PASS	.						125	121	123					5																	176721879		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	AGAGCTGTTGAGA	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.7510G>A	5.37:g.176721879G>A	ENSP00000395929:p.Val2504Ile	34	0	0		42	17	0.404762	NM_022455	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	37	CCDS4412.1	.	.	.	.	.	.	.	.	.	.	G	4.395	0.072998	0.08485	.	.	ENSG00000165671	ENST00000354179;ENST00000439151;ENST00000347982;ENST00000361032	D;D;D;D	0.93366	-3.11;-3.11;-3.11;-3.21	4.33	-0.92	0.10475	.	1.377650	0.04932	N	0.457076	D	0.84415	0.5467	N	0.14661	0.345	0.09310	N	1	B;B	0.23249	0.082;0.008	B;B	0.18561	0.022;0.006	T	0.71461	-0.4586	10	0.42905	T	0.14	.	2.489	0.04606	0.2231:0.3057:0.3602:0.111	.	2235;2504	Q96L73-2;Q96L73	.;NSD1_HUMAN	I	2235;2504;2235;2401	ENSP00000346111:V2235I;ENSP00000395929:V2504I;ENSP00000343209:V2235I;ENSP00000354310:V2401I	ENSP00000343209:V2235I	V	+	1	0	NSD1	176654485	0.000000	0.05858	0.008000	0.14137	0.469000	0.32828	-0.079000	0.11357	-0.438000	0.07232	0.462000	0.41574	GTT	.	.	none		0.542	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		A	176721879	G	A	176721879	3	1	25	1	0	0	0	0	1	0	0	0	10678	1377	48	2	7596	2	NSD1	5	176721879	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	9032717	176721879	4193381	228	9137											
DDX41	51428	hgsc.bcm.edu	37	chr5	176943352	176943352	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacgttggactgagggcctaGcgggatgtcgtcctcatctc	6	10	14	11	3	2	1	1	1	1	0	5	4	3	3	2	3	1	1	2	3	1	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:176943352G>C	ENST00000507955.1	-	3	758	c.235C>G	c.(235-237)Cta>Gta	p.L79V	DDX41_ENST00000506965.1_5'UTR	NM_016222.2	NP_057306.2	Q9UJV9	DDX41_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 41	79					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)			TGAGGGCCTAGCGGGATGTCG	0.607																																					p.L79V		Atlas-SNP	.											.	DDX41	49	.	0			c.C235G						PASS	.						133	126	128					5																	176943352		2203	4300	6503	SO:0001583	missense	51428	exon3			GGCCTAGCGGGAT	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.235C>G	5.37:g.176943352G>C	ENSP00000422753:p.Leu79Val	131	0	0		126	59	0.468254	NM_016222	B2RDC8|Q96BK6|Q96K05|Q9NT96|Q9NW04	Missense_Mutation	SNP	ENST00000507955.1	37	CCDS4427.1	.	.	.	.	.	.	.	.	.	.	G	9.895	1.205196	0.22205	.	.	ENSG00000183258	ENST00000330503;ENST00000507955	T;T	0.26810	1.71;1.72	5.38	2.1	0.27182	.	0.377447	0.23291	N	0.049795	T	0.17408	0.0418	L	0.34521	1.04	0.31726	N	0.637673	B	0.14805	0.011	B	0.11329	0.006	T	0.12656	-1.0539	10	0.30078	T	0.28	-7.6704	9.3594	0.38186	0.3981:0.0:0.6019:0.0	.	79	Q9UJV9	DDX41_HUMAN	V	97;79	ENSP00000330349:L97V;ENSP00000422753:L79V	ENSP00000330349:L97V	L	-	1	2	DDX41	176875958	0.121000	0.22262	0.561000	0.28357	0.816000	0.46133	0.337000	0.19841	0.620000	0.30215	0.491000	0.48974	CTA	.	.	none		0.607	DDX41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253432.2	NM_016222		C	176943352	G	C	176943352	3	2	25	1	0	0	0	0	1	0	0	0	4363	962	34	4	1693	4	DDX41	5	176943352	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	221473	176943352	3971908	229	9138											
MAK	4117	hgsc.bcm.edu	37	chr6	10775600	10775600	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agcaagttctgccccaacggGtcccagtgacttggggaata	10	8	12	11	1	1	1	0	1	1	0	2	2	2	2	3	3	3	2	3	3	4	3	rs567083	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:10775600G>A	ENST00000313243.2	-	12	1940	c.1558C>T	c.(1558-1560)Ccc>Tcc	p.P520S	MAK_ENST00000538030.1_3'UTR|MAK_ENST00000354489.2_Missense_Mutation_p.P520S|MAK_ENST00000474039.1_Missense_Mutation_p.P520S|SYCP2L_ENST00000543878.1_Intron|RP11-637O19.3_ENST00000480294.1_Intron			P20794	MAK_HUMAN	male germ cell-associated kinase	520			P -> S (in dbSNP:rs567083). {ECO:0000269|PubMed:17344846}.		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)				GCCCCAACGGGTCCCAGTGAC	0.453													G|||	99	0.0197684	0.0015	0.0908	5008	,	,		20809	0.0		0.0209	False		,,,				2504	0.0133				p.P520S		Atlas-SNP	.											.	MAK	47	.	0			c.C1558T						PASS	.	G	SER/PRO,SER/PRO	19,4387	26.2+/-53.5	0,19,2184	200	199	199		1558,1558	3.4	0.9	6	dbSNP_83	199	179,8421	81.8+/-144.4	2,175,4123	yes	missense,missense	MAK	NM_001242385.1,NM_005906.4	74,74	2,194,6307	AA,AG,GG		2.0814,0.4312,1.5224	benign,benign	520/584,520/624	10775600	198,12808	2203	4300	6503	SO:0001583	missense	4117	exon12			CAACGGGTCCCAG		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.1558C>T	6.37:g.10775600G>A	ENSP00000313021:p.Pro520Ser	165	0	0		196	98	0.5	NM_005906	F1T0K6|G1FL29|Q547D0|Q9NUH7	Missense_Mutation	SNP	ENST00000313243.2	37	CCDS4516.1	43	0.019688644688644688	1	0.0020325203252032522	27	0.07458563535911603	0	0.0	15	0.01978891820580475	G	2.302	-0.359970	0.05103	0.004312	0.020814	ENSG00000111837	ENST00000313243;ENST00000354489	T;T	0.71461	-0.57;-0.57	6.17	3.36	0.38483	.	0.165506	0.53938	N	0.000048	T	0.27098	0.0664	N	0.20685	0.6	0.48571	D	0.999672	B	0.09022	0.002	B	0.09377	0.004	T	0.17137	-1.0379	10	0.08381	T	0.77	.	6.315	0.21186	0.1638:0.1538:0.6825:0.0	rs567083;rs1627871;rs17640406;rs52803991;rs567083	520	P20794	MAK_HUMAN	S	520	ENSP00000313021:P520S;ENSP00000346484:P520S	ENSP00000313021:P520S	P	-	1	0	MAK	10883586	0.831000	0.29352	0.918000	0.36340	0.161000	0.22273	0.171000	0.16685	0.884000	0.36064	0.655000	0.94253	CCC	A|0.017;C|0.006	0.017	strong		0.453	MAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039841.1	NM_005906		A	10775600	G	A	10775600	3	1	25	1	0	0	0	0	1	0	0	0	9206	1261	44	2	325	2	MAK	6	10775600	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10		10775600	160339467	230	9139											
TDP2	51567	hgsc.bcm.edu	37	chr6	24667074	24667074	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctccctcccgccctccaggCaactccccaactccatcttc	6	8	3	24	1	1	0	0	0	1	0	7	0	6	0	8	1	2	1	8	1	2	1	rs61760186	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:24667074C>A	ENST00000378198.4	-	1	187	c.17G>T	c.(16-18)tGc>tTc	p.C6F	TDP2_ENST00000545995.1_Missense_Mutation_p.C36F|ACOT13_ENST00000230048.4_5'Flank|TDP2_ENST00000341060.3_5'Flank|ACOT13_ENST00000537591.1_5'Flank			O95551	TYDP2_HUMAN	tyrosyl-DNA phosphodiesterase 2	6					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						GCCCTCCAGGCAACTCCCCAA	0.657								Direct reversal of damage					C|||	11	0.00219649	0.003	0.0029	5008	,	,		14407	0.0		0.005	False		,,,				2504	0.0				p.C6F		Atlas-SNP	.											.	TDP2	29	.	0			c.G17T						PASS	.	C	PHE/CYS	11,4395	17.9+/-39.9	0,11,2192	92	107	102		17	0.6	0	6	dbSNP_129	102	28,8572	20.4+/-63.3	1,26,4273	yes	missense	TDP2	NM_016614.2	205	1,37,6465	AA,AC,CC		0.3256,0.2497,0.2999	probably-damaging	6/363	24667074	39,12967	2203	4300	6503	SO:0001583	missense	51567	exon1			TCCAGGCAACTCC	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.17G>T	6.37:g.24667074C>A	ENSP00000367440:p.Cys6Phe	43	0	0		48	29	0.604167	NM_016614	B4DKL8|B4DQ95|Q2TBE2|Q5JYM0|Q7Z6U5|Q9NUK5|Q9NYY9	Missense_Mutation	SNP	ENST00000378198.4	37	CCDS4557.1	9	0.004120879120879121	3	0.006097560975609756	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	C	11.65	1.701925	0.30232	0.002497	0.003256	ENSG00000111802	ENST00000378198;ENST00000545995;ENST00000545780	T;T	0.25085	1.93;1.82	4.51	0.603	0.17541	.	2.748860	0.00807	N	0.001479	T	0.05547	0.0146	N	0.22421	0.69	0.09310	N	1	B;B	0.28783	0.222;0.122	B;B	0.25759	0.063;0.025	T	0.22906	-1.0203	10	0.40728	T	0.16	-12.8014	3.1399	0.06452	0.1875:0.4951:0.0:0.3174	rs61760186	36;6	O95551-2;O95551	.;TYDP2_HUMAN	F	6;36;6	ENSP00000367440:C6F;ENSP00000437637:C36F	ENSP00000367440:C6F	C	-	2	0	TDP2	24775053	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.717000	0.04986	0.218000	0.20820	-0.127000	0.14921	TGC	C|0.997;A|0.003	0.003	strong		0.657	TDP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000040012.1			A	24667074	C	A	24667074	3	1	25	1	0	0	0	0	1	0	0	0	15744	710	25	4	1099	4	TDP2	6	24667074	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	13891474	24667074	146447993	231	9140											
SLC17A1	6568	hgsc.bcm.edu	37	chr6	25820126	25820126	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	attccctggatatctgggctCcaattatacatagggttcta	10	14	8	9	0	2	0	0	0	2	0	4	1	4	1	2	3	1	2	2	3	6	7	rs149708935		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:25820126C>A	ENST00000244527.4	-	4	340	c.225G>T	c.(223-225)tgG>tgT	p.W75C	SLC17A1_ENST00000476801.1_Missense_Mutation_p.W75C|SLC17A1_ENST00000468082.1_Missense_Mutation_p.W75C|SLC17A1_ENST00000427328.1_Missense_Mutation_p.W75C	NM_005074.3	NP_005065.2	Q14916	NPT1_HUMAN	solute carrier family 17 (organic anion transporter), member 1	75					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						TATCTGGGCTCCAATTATACA	0.408													C|||	1	0.000199681	0.0	0.0	5008	,	,		19051	0.0		0.001	False		,,,				2504	0.0				p.W75C		Atlas-SNP	.											.	SLC17A1	71	.	0			c.G225T						PASS	.	C	CYS/TRP	1,4403	2.1+/-5.4	0,1,2201	63	68	66		225	4.3	1	6	dbSNP_134	66	9,8591	7.1+/-27.0	0,9,4291	yes	missense	SLC17A1	NM_005074.3	215	0,10,6492	AA,AC,CC		0.1047,0.0227,0.0769	probably-damaging	75/468	25820126	10,12994	2202	4300	6502	SO:0001583	missense	6568	exon4			TGGGCTCCAATTA		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.225G>T	6.37:g.25820126C>A	ENSP00000244527:p.Trp75Cys	53	0	0		68	27	0.397059	NM_005074	A8K418|O60761|Q13783|Q3MIP5|Q5MJP8|Q5TB83|Q96KL8	Missense_Mutation	SNP	ENST00000244527.4	37	CCDS4565.1	.	.	.	.	.	.	.	.	.	.	C	12.63	1.994860	0.35226	2.27E-4	0.001047	ENSG00000124568	ENST00000244527;ENST00000427328;ENST00000476801;ENST00000468082	T;T;T;T	0.59083	0.29;0.29;0.29;0.29	4.33	4.33	0.51752	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.43110	D	0.000602	T	0.77350	0.4117	M	0.93241	3.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.82697	-0.0329	10	0.87932	D	0	.	12.53	0.56109	0.0:1.0:0.0:0.0	.	75;75	Q14916-2;Q14916	.;NPT1_HUMAN	C	75	ENSP00000244527:W75C;ENSP00000410549:W75C;ENSP00000420614:W75C;ENSP00000420546:W75C	ENSP00000244527:W75C	W	-	3	0	SLC17A1	25928105	1.000000	0.71417	1.000000	0.80357	0.280000	0.26924	4.467000	0.60155	2.423000	0.82170	0.650000	0.86243	TGG	C|1.000;A|0.000	0.000	weak		0.408	SLC17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043647.2			A	25820126	C	A	25820126	3	1	25	1	0	0	0	0	1	0	0	0	14431	856	30	4	1214	4	SLC17A1	6	25820126	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1153052	25820126	145294941	232	9141											
HIST1H4B	8366	hgsc.bcm.edu	37	chr6	26027286	26027286	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcacggcgtcccggatcacGttctccagaaacaccttgag	9	8	10	14	4	3	2	2	1	1	1	5	3	4	3	3	2	1	1	3	2	1	2	rs115249469	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26027286G>A	ENST00000377364.3	-	1	194	c.195C>T	c.(193-195)aaC>aaT	p.N65N		NM_003544.2	NP_003535.1	P62805	H4_HUMAN	histone cluster 1, H4b	65					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						CCCGGATCACGTTCTCCAGAA	0.567											OREG0017238	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	13	0.00259585	0.0008	0.0	5008	,	,		14349	0.0		0.005	False		,,,				2504	0.0072				p.N65N		Atlas-SNP	.											.	HIST1H4B	27	.	0			c.C195T						PASS	.	G		5,4401	9.9+/-24.2	0,5,2198	103	87	92		195	0.9	1	6	dbSNP_132	92	31,8569	21.6+/-65.8	0,31,4269	no	coding-synonymous	HIST1H4B	NM_003544.2		0,36,6467	AA,AG,GG		0.3605,0.1135,0.2768		65/104	26027286	36,12970	2203	4300	6503	SO:0001819	synonymous_variant	8366	exon1			GATCACGTTCTCC	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.195C>T	6.37:g.26027286G>A		87	0	0	783	116	66	0.568965	NM_003544	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Silent	SNP	ENST00000377364.3	37	CCDS4572.1																																																																																			G|0.998;A|0.002	0.002	strong		0.567	HIST1H4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040079.2	NM_003544		A	26027286	G	A	26027286	2	1	25	1	0	0	0	0	0	0	0	1	7175	1136	40	1		1	HIST1H4B	6	26027286	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	207160	26027286	145087781	233	9142											
HIST1H4D	8360	hgsc.bcm.edu	37	chr6	26189010	26189010	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agctcagccgccgaagccatAaagagtgcgtccctggcgct	9	6	12	14	4	1	1	1	0	0	1	2	2	2	1	4	1	4	2	4	1	3	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26189010A>C	ENST00000340756.2	-	1	294	c.295T>G	c.(295-297)Tat>Gat	p.Y99D		NM_003539.3	NP_003530.1	P62805	H4_HUMAN	histone cluster 1, H4d	99					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)				CCGAAGCCATAAAGAGTGCGT	0.552																																					p.Y99D		Atlas-SNP	.											HIST1H4D,colon,carcinoma,0,1	HIST1H4D	28	1	0			c.T295G						PASS	.						119	102	108					6																	26189010		2203	4300	6503	SO:0001583	missense	8360	exon1			AGCCATAAAGAGT	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.295T>G	6.37:g.26189010A>C	ENSP00000343282:p.Tyr99Asp	163	0	0		152	71	0.467105	NM_003539	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000340756.2	37	CCDS4589.1	.	.	.	.	.	.	.	.	.	.	.	17.92	3.506691	0.64410	.	.	ENSG00000188987	ENST00000340756	.	.	.	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.68961	0.3058	.	.	.	0.46499	D	0.999071	.	.	.	.	.	.	T	0.74708	-0.3574	6	0.87932	D	0	.	14.4576	0.67428	1.0:0.0:0.0:0.0	.	.	.	.	D	99	.	ENSP00000343282:Y99D	Y	-	1	0	HIST1H4D	26296989	1.000000	0.71417	0.740000	0.30986	0.041000	0.13682	8.784000	0.91818	2.017000	0.59298	0.528000	0.53228	TAT	.	.	none		0.552	HIST1H4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040085.1	NM_003539		C	26189010	A	C	26189010	3	2	25	1	0	0	0	0	1	0	0	0	7177	362	13	5	20	5	HIST1H4D	6	26189010	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	161724	26189010	144926057	234	9143											
BTN2A1	11120	hgsc.bcm.edu	37	chr6	26458871	26458871	+	Missense_Mutation	SNP	T	T	C																															tgctctgggtgctcatggaaTcagctgctgccctgcacttc																								rs146399224	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26458871T>C	ENST00000312541.5	+	2	255	c.7T>C	c.(7-9)Tca>Cca	p.S3P	BTN2A1_ENST00000541522.1_Intron|BTN2A1_ENST00000429381.1_Missense_Mutation_p.S3P|BTN2A1_ENST00000469185.1_Missense_Mutation_p.S3P	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	3					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						GCTCATGGAATCAGCTGCTGC	0.617													T|||	2	0.000399361	0.0	0.0	5008	,	,		15890	0.0		0.002	False		,,,				2504	0.0				p.S3P		Atlas-SNP	.											.	BTN2A1	118	.	0			c.T7C						PASS	.						233	171	192					6																	26458871		2203	4300	6503	SO:0001583	missense	11120	exon2			ATGGAATCAGCTG	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.7T>C	6.37:g.26458871T>C	ENSP00000312158:p.Ser3Pro	101	0	0		111	6	0.0540541	NM_001197234	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Missense_Mutation	SNP	ENST00000312541.5	37	CCDS4613.1	.	.	.	.	.	.	.	.	.	.	T	0.016	-1.519967	0.00967	.	.	ENSG00000112763	ENST00000312541;ENST00000429381;ENST00000265424;ENST00000469185	T;T;T	0.76448	-0.46;-1.02;-1.01	3.03	0.0692	0.14373	.	0.876207	0.09516	N	0.791659	T	0.24392	0.0591	N	0.01668	-0.77	0.09310	N	0.999992	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18053	-1.0349	10	0.42905	T	0.14	.	3.2421	0.06784	0.0:0.505:0.2251:0.2699	.	3;3	Q96AV7;Q7KYR7	.;BT2A1_HUMAN	P	3	ENSP00000312158:S3P;ENSP00000416945:S3P;ENSP00000419043:S3P	ENSP00000265424:S3P	S	+	1	0	BTN2A1	26566850	0.150000	0.22732	0.014000	0.15608	0.022000	0.10575	0.087000	0.14958	-0.002000	0.14469	-0.354000	0.07668	TCA	T|0.999;C|0.001	0.001	weak		0.617	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049		C	26458871	T	C	26458871	3	2	25	1	0	0	0	0	1	0	0	0	1562	1435	50	3	9	3	BTN2A1	6	26458871	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	269861	26458871	144656196	235	9144	112	2									
BTN2A1	11120	hgsc.bcm.edu	37	chr6	26458872	26458872	+	Missense_Mutation	SNP	C	C	T																															gctctgggtgctcatggaatCagctgctgccctgcacttct																										TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26458872C>T	ENST00000312541.5	+	2	256	c.8C>T	c.(7-9)tCa>tTa	p.S3L	BTN2A1_ENST00000541522.1_Intron|BTN2A1_ENST00000429381.1_Missense_Mutation_p.S3L|BTN2A1_ENST00000469185.1_Missense_Mutation_p.S3L	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	3					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						CTCATGGAATCAGCTGCTGCC	0.622																																					p.S3L		Atlas-SNP	.											.	BTN2A1	118	.	0			c.C8T						PASS	.						232	171	191					6																	26458872		2203	4300	6503	SO:0001583	missense	11120	exon2			TGGAATCAGCTGC	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.8C>T	6.37:g.26458872C>T	ENSP00000312158:p.Ser3Leu	103	0	0		111	6	0.0540541	NM_001197234	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Missense_Mutation	SNP	ENST00000312541.5	37	CCDS4613.1	.	.	.	.	.	.	.	.	.	.	C	11.00	1.510906	0.27036	.	.	ENSG00000112763	ENST00000312541;ENST00000429381;ENST00000265424;ENST00000469185	T;T;T	0.77098	-0.48;-1.07;-1.06	3.03	0.102	0.14522	.	0.876207	0.09516	N	0.791659	T	0.41581	0.1165	L	0.27053	0.805	0.09310	N	0.999998	B;B	0.12013	0.005;0.005	B;B	0.11329	0.004;0.006	T	0.31806	-0.9930	10	0.44086	T	0.13	.	5.0586	0.14546	0.0:0.4487:0.4235:0.1277	.	3;3	Q96AV7;Q7KYR7	.;BT2A1_HUMAN	L	3	ENSP00000312158:S3L;ENSP00000416945:S3L;ENSP00000419043:S3L	ENSP00000265424:S3L	S	+	2	0	BTN2A1	26566851	0.020000	0.18652	0.003000	0.11579	0.023000	0.10783	0.059000	0.14322	-0.006000	0.14370	0.484000	0.47621	TCA	.	.	none		0.622	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049		T	26458872	C	T	26458872	3	4	25	1	0	0	0	0	1	0	0	0	1562	838	29	2	10	2	BTN2A1	6	26458872	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1	26458872	144656195	236	9145	112	2									
HIST1H1B	3009	hgsc.bcm.edu	37	chr6	27835055	27835055	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caccaagctcttgaggcccaGcttaatgcggctgttattct	8	12	9	12	1	2	1	0	1	2	0	2	1	2	1	2	2	3	4	2	2	3	4	rs116008322	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:27835055G>A	ENST00000331442.3	-	1	304	c.253C>T	c.(253-255)Ctg>Ttg	p.L85L		NM_005322.2	NP_005313.1	P16401	H15_HUMAN	histone cluster 1, H1b	85	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				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						TTGAGGCCCAGCTTAATGCGG	0.577													G|||	45	0.00898562	0.0038	0.0101	5008	,	,		16701	0.004		0.0278	False		,,,				2504	0.001				p.L85L		Atlas-SNP	.											.	HIST1H1B	54	.	0			c.C253T						PASS	.	G		40,4366	43.8+/-77.6	0,40,2163	124	135	131		253	3.7	1	6	dbSNP_132	131	238,8362	96.6+/-158.3	4,230,4066	no	coding-synonymous	HIST1H1B	NM_005322.2		4,270,6229	AA,AG,GG		2.7674,0.9079,2.1375		85/227	27835055	278,12728	2203	4300	6503	SO:0001819	synonymous_variant	3009	exon1			GGCCCAGCTTAAT	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.253C>T	6.37:g.27835055G>A		152	0	0		157	82	0.522293	NM_005322	Q14529|Q3MJ42	Silent	SNP	ENST00000331442.3	37	CCDS4635.1																																																																																			G|0.982;A|0.018	0.018	strong		0.577	HIST1H1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043371.1	NM_005322		A	27835055	G	A	27835055	2	1	25	1	0	0	0	0	0	0	0	1	7132	962	34	2		2	HIST1H1B	6	27835055	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1376183	27835055	143280012	237	9146											
OR2H1	26716	hgsc.bcm.edu	37	chr6	29429766	29429766	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggacctctgctttaccacaAgttgtgtcccccagatgctg	7	12	9	13	0	1	1	0	0	1	1	2	2	2	2	4	1	3	3	4	1	2	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29429766A>G	ENST00000377136.1	+	4	685	c.220A>G	c.(220-222)Agt>Ggt	p.S74G	OR2H1_ENST00000442615.1_Missense_Mutation_p.S74G|OR2H1_ENST00000377132.1_Missense_Mutation_p.S74G|OR2H1_ENST00000396792.2_Missense_Mutation_p.S74G|OR2H1_ENST00000473369.1_Splice_Site|OR2H1_ENST00000377133.1_Missense_Mutation_p.S74G			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, 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)			large_intestine(5)|lung(12)	17						CTTTACCACAAGTTGTGTCCC	0.537																																					p.S74G		Atlas-SNP	.											.	OR2H1	38	.	0			c.A220G						PASS	.						108	107	107					6																	29429766		1511	2709	4220	SO:0001583	missense	26716	exon3			ACCACAAGTTGTG	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.220A>G	6.37:g.29429766A>G	ENSP00000366340:p.Ser74Gly	206	0	0		203	93	0.458128	NM_030883	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Missense_Mutation	SNP	ENST00000377136.1	37	CCDS4660.1	.	.	.	.	.	.	.	.	.	.	A	0.142	-1.100996	0.01843	.	.	ENSG00000204688	ENST00000377136;ENST00000377133;ENST00000442615;ENST00000377132;ENST00000396792	T;T;T;T;T	0.01933	4.55;4.55;4.55;4.55;4.55	2.92	2.92	0.33932	GPCR, rhodopsin-like superfamily (1);	0.149339	0.31257	N	0.007964	T	0.02012	0.0063	M	0.90977	3.165	0.09310	N	1	P	0.47962	0.903	B	0.39876	0.312	T	0.31752	-0.9932	10	0.56958	D	0.05	.	6.2425	0.20800	0.8763:0.0:0.1237:0.0	.	74	Q9GZK4	OR2H1_HUMAN	G	74	ENSP00000366340:S74G;ENSP00000366337:S74G;ENSP00000393254:S74G;ENSP00000366336:S74G;ENSP00000380010:S74G	ENSP00000366336:S74G	S	+	1	0	OR2H1	29537745	0.000000	0.05858	0.013000	0.15412	0.048000	0.14542	-0.288000	0.08377	1.582000	0.49881	0.491000	0.48974	AGT	.	.	none		0.537	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3			G	29429766	A	G	29429766	3	3	25	1	0	0	0	0	1	0	0	0	11010	72	3	3	222	3	OR2H1	6	29429766	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	1594711	29429766	141685301	238	9147											
HLA-F	3134	hgsc.bcm.edu	37	chr6	29693019	29693019	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtggtggtgcctcctggagaGgaacagagatacacatgcca	11	7	14	9	0	0	2	0	0	0	2	1	5	1	3	3	4	4	0	3	4	2	1	rs201844059		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29693019G>A	ENST00000376861.1	+	5	1206	c.822G>A	c.(820-822)gaG>gaA	p.E274E	HLA-F_ENST00000334668.4_Silent_p.E274E|HLA-F_ENST00000434407.2_Intron|HLA-F_ENST00000440587.2_Silent_p.E156E|HLA-F_ENST00000259951.7_Silent_p.E274E			P30511	HLAF_HUMAN	major histocompatibility complex, class I, F	274	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)|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)	early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|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)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)			cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8						CTCCTGGAGAGGAACAGAGAT	0.612													.|||	1	0.000199681	0.0	0.0014	5008	,	,		18491	0.0		0.0	False		,,,				2504	0.0				p.E274E		Atlas-SNP	.											.	HLA-F	41	.	0			c.G822A						PASS	.	G	,,	2,4404		0,2,2201	53	47	49		,822,822	-0.1	0.9	6		49	8,8592		0,8,4292	no	intron,coding-synonymous,coding-synonymous	HLA-F	NM_001098478.1,NM_001098479.1,NM_018950.2	,,	0,10,6493	AA,AG,GG		0.093,0.0454,0.0769	,,	,274/443,274/347	29693019	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	3134	exon4			TGGAGAGGAACAG	AY253269	CCDS43437.1, CCDS43438.1, CCDS43439.1	6p21.3	2013-01-11			ENSG00000204642	ENSG00000204642		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4963	protein-coding gene	gene with protein product		143110				1688605	Standard	NM_018950		Approved		uc003nno.4	P30511	OTTHUMG00000031156	ENST00000376861.1:c.822G>A	6.37:g.29693019G>A		191	0	0		156	60	0.384615	NM_001098479	Q5JQI8|Q5JQJ1|Q5SPT5|Q860R0|Q8MGQ1|Q8WLP5|Q95HC0|Q9TP68	Silent	SNP	ENST00000376861.1	37	CCDS43438.1	.	.	.	.	.	.	.	.	.	.	.	0.413	-0.912347	0.02415	4.54E-4	9.3E-4	ENSG00000204642	ENST00000429294	.	.	.	1.92	-0.104	0.13605	.	.	.	.	.	T	0.28466	0.0704	.	.	.	0.39086	D	0.961008	.	.	.	.	.	.	T	0.15464	-1.0436	4	.	.	.	.	4.3592	0.11194	0.3972:0.0:0.6028:0.0	.	.	.	.	K	153	.	.	R	+	2	0	HLA-F	29800998	0.000000	0.05858	0.855000	0.33649	0.268000	0.26511	-0.944000	0.03913	-0.248000	0.09583	-0.436000	0.05848	AGG	G|0.999;A|0.001	0.001	weak		0.612	HLA-F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195083.1	NM_018950		A	29693019	G	A	29693019	2	1	25	1	0	0	0	0	0	0	0	1	7220	991	35	2		2	HLA-F	6	29693019	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	263253	29693019	141422048	239	9148											
DDR1	780	hgsc.bcm.edu	37	chr6	30860313	30860313	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttcagcgaaatctccttcAtctctggtaagccctggagt	8	13	8	12	1	5	0	2	0	3	0	7	2	5	1	2	2	2	1	2	2	2	3	rs143367160	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:30860313A>T	ENST00000324771.8	+	10	1641	c.1093A>T	c.(1093-1095)Atc>Ttc	p.I365F	DDR1_ENST00000454612.2_Missense_Mutation_p.I365F|DDR1_ENST00000452441.1_Missense_Mutation_p.I365F|MIR4640_ENST00000581824.1_RNA|DDR1_ENST00000513240.1_Missense_Mutation_p.I365F|DDR1_ENST00000361741.4_Missense_Mutation_p.I96F|DDR1_ENST00000376575.3_Missense_Mutation_p.I365F|DDR1_ENST00000418800.2_Missense_Mutation_p.I365F|DDR1_ENST00000446312.1_3'UTR|DDR1_ENST00000376569.3_Missense_Mutation_p.I365F|DDR1_ENST00000508312.1_Missense_Mutation_p.I383F|DDR1_ENST00000376568.3_Missense_Mutation_p.I365F|DDR1_ENST00000376567.2_Missense_Mutation_p.I365F|DDR1_ENST00000376570.4_Missense_Mutation_p.I365F			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	365	DS-like domain.				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)	AATCTCCTTCATCTCTGGTAA	0.547													A|||	13	0.00259585	0.0	0.0086	5008	,	,		16593	0.0		0.003	False		,,,				2504	0.0041				p.I383F		Atlas-SNP	.											.	DDR1	213	.	0			c.A1147T						PASS	.	A	PHE/ILE,PHE/ILE,PHE/ILE,PHE/ILE,PHE/ILE,PHE/ILE	2,4404	4.2+/-10.8	0,2,2201	63	69	67		1093,1093,1147,1093,1093,1093	3.1	1	6	dbSNP_134	67	50,8550	31.2+/-83.2	0,50,4250	yes	missense,missense,missense,missense,missense,missense	DDR1	NM_001202521.1,NM_001202522.1,NM_001202523.1,NM_001954.4,NM_013993.2,NM_013994.2	21,21,21,21,21,21	0,52,6451	TT,TA,AA		0.5814,0.0454,0.3998	benign,benign,benign,benign,benign,benign	365/509,365/768,383/895,365/877,365/914,365/920	30860313	52,12954	2203	4300	6503	SO:0001583	missense	780	exon8			TCCTTCATCTCTG	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.1093A>T	6.37:g.30860313A>T	ENSP00000318217:p.Ile365Phe	42	0	0		63	23	0.365079	NM_001202523	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Missense_Mutation	SNP	ENST00000324771.8	37	CCDS34385.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	A	13.80	2.344152	0.41498	4.54E-4	0.005814	ENSG00000204580	ENST00000324771;ENST00000418800;ENST00000454612;ENST00000376569;ENST00000376575;ENST00000376570;ENST00000376568;ENST00000452441;ENST00000508312;ENST00000376567;ENST00000513240;ENST00000417521;ENST00000361741;ENST00000451954	T;T;T;T;T;T;T;T;T;T;T;T;T	0.21734	1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99	4.23	3.12	0.35913	.	0.077437	0.51477	D	0.000083	T	0.08313	0.0207	L	0.43923	1.385	0.41933	D	0.990575	B;P;B;B	0.48230	0.045;0.907;0.004;0.005	B;B;B;B	0.44224	0.021;0.444;0.038;0.007	T	0.09885	-1.0654	9	.	.	.	.	4.0728	0.09891	0.5736:0.2983:0.1282:0.0	.	383;161;365;365	B7Z2K0;A2ABM8;Q08345-5;Q08345	.;.;.;DDR1_HUMAN	F	365;365;365;365;365;365;365;365;383;365;365;161;96;48	ENSP00000318217:I365F;ENSP00000407699:I365F;ENSP00000406091:I365F;ENSP00000365753:I365F;ENSP00000365759:I365F;ENSP00000365754:I365F;ENSP00000365752:I365F;ENSP00000405039:I365F;ENSP00000422442:I383F;ENSP00000365751:I365F;ENSP00000427552:I365F;ENSP00000398682:I161F;ENSP00000354844:I96F	.	I	+	1	0	DDR1	30968292	0.967000	0.33354	1.000000	0.80357	0.979000	0.70002	2.245000	0.43133	1.559000	0.49555	0.379000	0.24179	ATC	A|0.997;T|0.003	0.003	strong		0.547	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994		T	30860313	A	T	30860313	3	4	25	1	0	0	0	0	1	0	0	0	4338	217	8	5	1119	5	DDR1	6	30860313	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	1167294	30860313	140254754	240	9149											
HLA-C	3107	hgsc.bcm.edu	37	chr6	31239622	31239622	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gggccgggacacggcggtgtCgaaatacctcatggagtggg	8	6	18	9	4	1	0	1	0	0	0	2	3	1	2	2	6	1	0	2	6	2	1	rs9264668	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31239622C>G	ENST00000376228.5	-	2	111	c.97G>C	c.(97-99)Gac>Cac	p.D33H	HLA-C_ENST00000383329.3_Missense_Mutation_p.D33H	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	33	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)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						ACGGCGGTGTCGAAATACCTC	0.726													a|||	20	0.00399361	0.0113	0.0	5008	,	,		11654	0.001		0.003	False		,,,				2504	0.001				p.D33H		Atlas-SNP	.											HLA-C_ENST00000383329,NS,neuroblastoma,0,2	HLA-C	92	2	0			c.G97C						scavenged	.						16	17	17					6																	31239622		1477	2676	4153	SO:0001583	missense	3107	exon2			CGGTGTCGAAATA	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4933	protein-coding gene	gene with protein product		142840	"psoriasis susceptibility 1"	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.97G>C	6.37:g.31239622C>G	ENSP00000365402:p.Asp33His	25	0	0		58	11	0.189655	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	0.003|0.003	-2.468672|-2.468672	0.00169|0.00169	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|.	0.00009|.	9.5;9.5|.	2.16|2.16	-4.32|-4.32	0.03688|0.03688	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);|.	10.311600|.	0.00879|.	N|.	0.002109|.	T|T	0.03390|0.03390	0.0098|0.0098	L|L	0.31578|0.31578	0.945|0.945	0.09310|0.09310	N|N	1|1	P;P;P;P|.	0.51351|.	0.944;0.822;0.822;0.888|.	P;P;P;D|.	0.68483|.	0.904;0.904;0.829;0.958|.	T|T	0.58504|0.58504	-0.7625|-0.7625	10|5	0.42905|.	T|.	0.14|.	.|.	0.4543|0.4543	0.00506|0.00506	0.2454:0.267:0.2544:0.2332|0.2454:0.267:0.2544:0.2332	.|.	33;33;33;33|.	A2AEA4;A6H578;A2AEA2;P10321|.	.;.;.;1C07_HUMAN|.	H|P	33;33;33;70|32	ENSP00000365402:D33H;ENSP00000372819:D33H|.	ENSP00000365402:D33H|.	D|R	-|-	1|2	0|0	HLA-C|HLA-C	31347601|31347601	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-13.217000|-13.217000	0.00001|0.00001	-7.736000|-7.736000	0.00000|0.00000	-4.008000|-4.008000	0.00013|0.00013	GAC|CGA	A|0.575;C|0.423;G|0.002	0.002	strong		0.726	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117		G	31239622	C	G	31239622	3	3	25	1	0	0	0	0	1	0	0	0	7206	884	31	4	1031	4	HLA-C	6	31239622	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	379309	31239622	139875445	241	9150											
C6orf26	401251	hgsc.bcm.edu	37	chr6	31731301	31731301	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccatctgagggaggcacagcGacagcagctgcatctagggg	10	5	15	11	1	2	1	0	1	2	0	2	3	2	2	1	4	4	4	1	4	1	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31731301G>A	ENST00000425424.1	+	2	283	c.224G>A	c.(223-225)cGa>cAa	p.R75Q	MSH5-SAPCD1_ENST00000493662.2_3'UTR|SAPCD1-AS1_ENST00000419679.1_RNA|VWA7_ENST00000467576.1_5'Flank|SAPCD1_ENST00000415669.2_Missense_Mutation_p.R75Q|MSH5_ENST00000534153.4_3'UTR			Q5SSQ6	SAPC1_HUMAN	suppressor APC domain containing 1	75																	GAGGCACAGCGACAGCAGCTG	0.607																																					p.R75Q		Atlas-SNP	.											.	.	.	.	0			c.G224A						PASS	.						76	78	77					6																	31731301		1509	2708	4217	SO:0001583	missense	401251	exon2			CACAGCGACAGCA		CCDS34411.1	6p21	2011-12-13	2011-12-13	2011-12-13	ENSG00000228727	ENSG00000228727			13938	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 26"	C6orf26			Standard	NM_001039651		Approved	NG23		Q5SSQ6	OTTHUMG00000031131	ENST00000425424.1:c.224G>A	6.37:g.31731301G>A	ENSP00000413372:p.Arg75Gln	54	0	0		76	38	0.5	NM_001039651	A2ABF2|A2ABS9|Q9Y335	Missense_Mutation	SNP	ENST00000425424.1	37		.	.	.	.	.	.	.	.	.	.	G	1.914	-0.450071	0.04572	.	.	ENSG00000228727	ENST00000433778;ENST00000415669;ENST00000425424	T;T	0.79845	-1.31;-1.31	5.01	-3.43	0.04810	.	.	.	.	.	T	0.44519	0.1297	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.36480	-0.9746	8	0.18710	T	0.47	-5.3272	12.7855	0.57502	0.2885:0.0:0.7115:0.0	.	75	Q5SSQ6-2	.	Q	75	ENSP00000411948:R75Q;ENSP00000413372:R75Q	ENSP00000411948:R75Q	R	+	2	0	C6orf26	31839280	0.000000	0.05858	0.330000	0.25442	0.801000	0.45260	-0.272000	0.08560	-0.674000	0.05253	-1.004000	0.02495	CGA	.	.	none		0.607	SAPCD1-203	KNOWN	basic	protein_coding	protein_coding		NM_001039651		A	31731301	G	A	31731301	3	1	25	1	0	0	0	0	1	0	0	0	2363	1058	37	1	230	1	C6orf26	6	31731301	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	491679	31731301	139383766	242	9151											
FKBP5	2289	hgsc.bcm.edu	37	chr6	35544942	35544942	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccttggctgactcaaactcGttcatgagcagctgggcttc	7	11	10	13	1	2	2	2	2	0	0	4	2	2	2	1	2	3	5	1	2	1	3	rs34866878	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:35544942G>A	ENST00000539068.1	-	10	1297	c.1095C>T	c.(1093-1095)aaC>aaT	p.N365N	FKBP5_ENST00000357266.4_Silent_p.N365N|FKBP5_ENST00000536438.1_Silent_p.N365N|FKBP5_ENST00000540787.1_Silent_p.N186N	NM_001145776.1	NP_001139248.1	Q13451	FKBP5_HUMAN	FK506 binding protein 5	365					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						ACTCAAACTCGTTCATGAGCA	0.483													G|||	334	0.0666933	0.2239	0.0245	5008	,	,		18453	0.001		0.0179	False		,,,				2504	0.002				p.N365N		Atlas-SNP	.											.	FKBP5	64	.	0			c.C1095T						PASS	.	G	,,	815,3591	326.1+/-299.4	68,679,1456	161	154	156		1095,1095,1095	-3.6	0.8	6	dbSNP_126	156	225,8375	92.8+/-154.8	5,215,4080	no	coding-synonymous,coding-synonymous,coding-synonymous	FKBP5	NM_001145775.1,NM_001145776.1,NM_004117.3	,,	73,894,5536	AA,AG,GG		2.6163,18.4975,7.9963	,,	365/458,365/458,365/458	35544942	1040,11966	2203	4300	6503	SO:0001819	synonymous_variant	2289	exon11			AAACTCGTTCATG	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.1095C>T	6.37:g.35544942G>A		160	0	0		168	90	0.535714	NM_001145775	F5H7R1|Q59EB8|Q5TGM6	Silent	SNP	ENST00000539068.1	37	CCDS4808.1																																																																																			G|0.928;A|0.072	0.072	strong		0.483	FKBP5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040309.2			A	35544942	G	A	35544942	2	1	25	1	0	0	0	0	0	0	0	1	5919	1136	40	1		1	FKBP5	6	35544942	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	3813641	35544942	135570125	243	9152											
PI16	221476	hgsc.bcm.edu	37	chr6	36926952	36926952	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggagctggccgccttcgccaAggcctacgcacggcagtgcg	6	5	15	15	5	0	0	0	0	0	0	1	1	0	1	4	4	3	3	4	4	2	2	rs113848006	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:36926952A>G	ENST00000373674.3	+	2	531	c.203A>G	c.(202-204)aAg>aGg	p.K68R		NM_001199159.1|NM_153370.2	NP_001186088.1|NP_699201.2	Q6UXB8	PI16_HUMAN	peptidase inhibitor 16	68	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						GCCTTCGCCAAGGCCTACGCA	0.652													A|||	80	0.0159744	0.0477	0.0072	5008	,	,		17606	0.0		0.0119	False		,,,				2504	0.0				p.K68R		Atlas-SNP	.											.	PI16	50	.	0			c.A203G						PASS	.	A	ARG/LYS,ARG/LYS	163,4237		2,159,2039	23	19	21		203,203	4.1	1	6	dbSNP_132	21	55,8541		0,55,4243	yes	missense,missense	PI16	NM_001199159.1,NM_153370.2	26,26	2,214,6282	GG,GA,AA		0.6398,3.7045,1.6774	probably-damaging,probably-damaging	68/464,68/464	36926952	218,12778	2200	4298	6498	SO:0001583	missense	221476	exon3			TCGCCAAGGCCTA		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.203A>G	6.37:g.36926952A>G	ENSP00000362778:p.Lys68Arg	96	0	0		107	54	0.504673	NM_001199159	Q6ZVG9|Q8IYL8|Q8NBK0|Q8TCB8	Missense_Mutation	SNP	ENST00000373674.3	37	CCDS34440.1	38	0.0173992673992674	28	0.056910569105691054	3	0.008287292817679558	0	0.0	7	0.009234828496042216	A	23.5	4.418054	0.83449	0.037045	0.006398	ENSG00000164530	ENST00000536757;ENST00000373674	T	0.07800	3.16	5.29	4.09	0.47781	CAP domain (3);	0.128596	0.52532	D	0.000078	T	0.05914	0.0154	N	0.20685	0.6	0.31202	N	0.699673	D;P	0.57257	0.979;0.892	P;P	0.60609	0.877;0.57	T	0.18871	-1.0323	10	0.45353	T	0.12	.	11.8387	0.52342	0.8531:0.1469:0.0:0.0	.	68;68	Q6UXB8;Q6UXB8-2	PI16_HUMAN;.	R	68	ENSP00000362778:K68R	ENSP00000362778:K68R	K	+	2	0	PI16	37034930	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	3.619000	0.54196	0.809000	0.34255	0.418000	0.28097	AAG	A|0.982;G|0.018	0.018	strong		0.652	PI16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040380.1	NM_153370		G	36926952	A	G	36926952	3	3	25	1	0	0	0	0	1	0	0	0	11878	72	3	3	209	3	PI16	6	36926952	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	1382010	36926952	134188115	244	9153											
LRFN2	57497	hgsc.bcm.edu	37	chr6	40360492	40360492	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgtgcatggactggcactgCgggtagtcagccttggtgaa	7	10	15	9	1	1	1	1	1	0	0	1	2	1	2	1	4	3	3	1	4	2	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:40360492C>T	ENST00000338305.6	-	3	2102	c.1560G>A	c.(1558-1560)ccG>ccA	p.P520P		NM_020737.1	NP_065788.1	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III domain containing 2	520						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)					ACTGGCACTGCGGGTAGTCAG	0.602																																					p.P520P		Atlas-SNP	.											.	LRFN2	133	.	0			c.G1560A						PASS	.						78	55	63					6																	40360492		2203	4300	6503	SO:0001819	synonymous_variant	57497	exon3			GCACTGCGGGTAG	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.1560G>A	6.37:g.40360492C>T		106	0	0		119	67	0.563025	NM_020737	A5PKU3|Q5SYP9	Silent	SNP	ENST00000338305.6	37	CCDS34443.1																																																																																			.	.	none		0.602	LRFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040488.1	XM_166372		T	40360492	C	T	40360492	2	4	25	1	0	0	0	0	0	0	0	1	8947	755	27	1		1	LRFN2	6	40360492	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	3433540	40360492	130754575	245	9154											
PGC	5225	hgsc.bcm.edu	37	chr6	41704716	41704716	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggacaggtaggtgggctcGactcccacggtgcagtagcc	8	6	16	11	2	0	0	0	0	0	0	2	3	1	1	2	5	2	4	2	5	2	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:41704716G>T	ENST00000373025.3	-	9	1103	c.1041C>A	c.(1039-1041)gtC>gtA	p.V347V	TFEB_ENST00000358871.2_5'Flank|TFEB_ENST00000230323.4_5'Flank|TFEB_ENST00000373033.1_5'Flank|TFEB_ENST00000403298.4_5'Flank|TFEB_ENST00000420312.1_5'Flank|RP11-298J23.5_ENST00000438967.1_RNA	NM_002630.3	NP_002621.1	P20142	PEPC_HUMAN	progastricsin (pepsinogen C)	347					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)			AGGTGGGCTCGACTCCCACGG	0.572																																					p.V347V		Atlas-SNP	.											.	PGC	56	.	0			c.C1041A						PASS	.						69	64	66					6																	41704716		2203	4300	6503	SO:0001819	synonymous_variant	5225	exon9			GGGCTCGACTCCC		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.1041C>A	6.37:g.41704716G>T		118	0	0		104	53	0.509615	NM_002630	B4DVZ3|Q5T3D7|Q5T3D8	Silent	SNP	ENST00000373025.3	37	CCDS4859.1																																																																																			.	.	none		0.572	PGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040521.2			T	41704716	G	T	41704716	2	4	25	1	0	0	0	0	0	0	0	1	11794	1045	37	4		4	PGC	6	41704716	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1344224	41704716	129410351	246	9155											
BYSL	705	hgsc.bcm.edu	37	chr6	41895153	41895153	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gatcagatgacgaggacgagGagtggcccaccctggagaag	12	4	16	9	2	1	3	1	1	0	2	1	9	1	5	2	4	0	0	2	4	1	0			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:41895153G>A	ENST00000230340.4	+	2	685	c.310G>A	c.(310-312)Gag>Aag	p.E104K		NM_004053.3	NP_004044.3	Q13895	BYST_HUMAN	bystin-like	104					cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|female pregnancy (GO:0007565)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|trophectodermal cell differentiation (GO:0001829)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(5)|skin(1)	8	Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000473)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CGAGGACGAGGAGTGGCCCAC	0.542																																					p.E104K		Atlas-SNP	.											.	BYSL	17	.	0			c.G310A						PASS	.						127	115	119					6																	41895153		2203	4300	6503	SO:0001583	missense	705	exon2			GACGAGGAGTGGC	L36720	CCDS34450.1	6p21.1	2008-08-29			ENSG00000112578	ENSG00000112578			1157	protein-coding gene	gene with protein product		603871				9925933, 17381424	Standard	NM_004053		Approved		uc003orl.3	Q13895	OTTHUMG00000014687	ENST00000230340.4:c.310G>A	6.37:g.41895153G>A	ENSP00000230340:p.Glu104Lys	144	0	0		135	52	0.385185	NM_004053	Q6P5W4|Q86W44|Q96IP8	Missense_Mutation	SNP	ENST00000230340.4	37	CCDS34450.1	.	.	.	.	.	.	.	.	.	.	G	34	5.317664	0.95682	.	.	ENSG00000112578	ENST00000230340	T	0.21734	1.99	5.37	4.5	0.54988	.	0.049967	0.85682	D	0.000000	T	0.12732	0.0309	M	0.74647	2.275	0.80722	D	1	B	0.12013	0.005	B	0.09377	0.004	T	0.04522	-1.0945	10	0.24483	T	0.36	-14.342	13.8124	0.63270	0.0747:0.0:0.9253:0.0	.	104	Q13895	BYST_HUMAN	K	104	ENSP00000230340:E104K	ENSP00000230340:E104K	E	+	1	0	BYSL	42003131	1.000000	0.71417	0.998000	0.56505	0.966000	0.64601	9.177000	0.94849	1.267000	0.44247	0.643000	0.83706	GAG	.	.	none		0.542	BYSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040535.2			A	41895153	G	A	41895153	3	1	25	1	0	0	0	0	1	0	0	0	1578	1175	41	2	316	2	BYSL	6	41895153	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	190437	41895153	129219914	247	9156											
KIAA0240	23506	hgsc.bcm.edu	37	chr6	42832683	42832683	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gacaaagtgggcttagtgcaGtaccagagcacgtctgaaga	13	7	13	8	1	1	3	0	1	1	2	1	4	1	3	1	1	3	4	1	1	4	2	rs10456519	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:42832683G>A	ENST00000314073.5	+	13	2915	c.2739G>A	c.(2737-2739)caG>caA	p.Q913Q	GLTSCR1L_ENST00000394168.1_Silent_p.Q913Q			Q6AI39	GSC1L_HUMAN	GLTSCR1-like	913																	GCTTAGTGCAGTACCAGAGCA	0.517													G|||	36	0.0071885	0.0053	0.0101	5008	,	,		19729	0.001		0.0129	False		,,,				2504	0.0082				p.Q913Q		Atlas-SNP	.											.	.	.	.	0			c.G2739A						PASS	.	G		30,4376	36.8+/-68.6	0,30,2173	51	50	50		2739	-3	0.1	6	dbSNP_119	50	96,8504	52.7+/-113.3	3,90,4207	no	coding-synonymous	KIAA0240	NM_015349.1		3,120,6380	AA,AG,GG		1.1163,0.6809,0.9688		913/1080	42832683	126,12880	2203	4300	6503	SO:0001819	synonymous_variant	23506	exon12			AGTGCAGTACCAG	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.2739G>A	6.37:g.42832683G>A		40	0	0		59	28	0.474576	NM_015349	A1L3W2|Q5TFZ3|Q92514	Silent	SNP	ENST00000314073.5	37	CCDS34451.1																																																																																			G|0.989;A|0.011	0.011	strong		0.517	GLTSCR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040562.3	NM_015349		A	42832683	G	A	42832683	2	1	25	1	0	0	0	0	0	0	0	1	8173	1020	36	2		2	KIAA0240	6	42832683	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	937530	42832683	128282384	248	9157											
PTCRA	171558	hgsc.bcm.edu	37	chr6	42893254	42893254	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggtgacacccctccgggtcGgaagcccgggagcccagtat	7	5	15	14	3	0	1	0	1	0	0	2	3	1	3	5	4	2	1	5	4	2	1	rs146531157	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:42893254G>A	ENST00000304672.1	+	4	761	c.680G>A	c.(679-681)cGg>cAg	p.R227Q	PTCRA_ENST00000446507.1_Missense_Mutation_p.R120Q|PTCRA_ENST00000441198.1_Missense_Mutation_p.R202Q	NM_001243168.1|NM_138296.2	NP_001230097.1|NP_612153.2	Q6ISU1	PTCRA_HUMAN	pre T-cell antigen receptor alpha	227					negative regulation of thymocyte apoptotic process (GO:0070244)	integral component of membrane (GO:0016021)				large_intestine(2)|lung(4)|ovary(2)	8	Colorectal(47;0.196)		all cancers(41;0.000731)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|OV - Ovarian serous cystadenocarcinoma(102;0.0218)|Kidney(15;0.0388)			CCTCCGGGTCGGAAGCCCGGG	0.682													G|||	6	0.00119808	0.0	0.0014	5008	,	,		14322	0.0		0.005	False		,,,				2504	0.0				p.R242Q		Atlas-SNP	.											.	PTCRA	24	.	0			c.G725A						PASS	.	G	GLN/ARG	1,4387		0,1,2193	15	14	14		680	-6.3	0	6	dbSNP_134	14	41,8511		0,41,4235	yes	missense	PTCRA	NM_138296.2	43	0,42,6428	AA,AG,GG		0.4794,0.0228,0.3246	benign	227/282	42893254	42,12898	2194	4276	6470	SO:0001583	missense	171558	exon4			CGGGTCGGAAGCC	AF084941	CCDS4874.1, CCDS59019.1, CCDS59020.1, CCDS75457.1	6p21.3	2008-02-05			ENSG00000171611	ENSG00000171611			21290	protein-coding gene	gene with protein product		606817				8618853, 9842925	Standard	NM_138296		Approved	PTA, PT-ALPHA	uc021yzp.1	Q6ISU1	OTTHUMG00000014709	ENST00000304672.1:c.680G>A	6.37:g.42893254G>A	ENSP00000304447:p.Arg227Gln	52	0	0		45	25	0.555556	NM_001243168	Q5TFZ7	Missense_Mutation	SNP	ENST00000304672.1	37	CCDS4874.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	7.257	0.604442	0.14002	2.28E-4	0.004794	ENSG00000171611	ENST00000304672;ENST00000441198;ENST00000446507;ENST00000418903	T;T;T	0.55234	1.21;1.18;0.53	3.14	-6.28	0.02020	.	1.969100	0.03135	N	0.165837	T	0.10423	0.0255	N	0.14661	0.345	0.09310	N	1	B;B;B	0.15930	0.015;0.006;0.002	B;B;B	0.08055	0.003;0.003;0.003	T	0.03315	-1.1049	10	0.59425	D	0.04	.	1.8301	0.03128	0.3078:0.3482:0.2246:0.1194	.	120;202;227	Q6ISU1-2;Q6ISU1-3;Q6ISU1	.;.;PTCRA_HUMAN	Q	227;202;120;73	ENSP00000304447:R227Q;ENSP00000409550:R202Q;ENSP00000392288:R120Q	ENSP00000304447:R227Q	R	+	2	0	PTCRA	43001232	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.350000	0.01092	-2.666000	0.00416	-0.175000	0.13238	CGG	G|0.999;A|0.001	0.001	strong		0.682	PTCRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040565.2	NM_138296		A	42893254	G	A	42893254	3	1	25	1	0	0	0	0	1	0	0	0	12747	1116	39	1	694	1	PTCRA	6	42893254	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	60571	42893254	128221813	249	9158											
C6orf108	23113	hgsc.bcm.edu	37	chr6	43193877	43193877	+	IGR	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggctgtgtcacttctgccacGaccactgggaggaaagatga	10	8	13	10	1	2	2	1	1	1	1	2	5	2	4	2	3	1	1	2	3	1	1	rs7832	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:43193877G>A	ENST00000252050.4	+	0	7780				DNPH1_ENST00000230431.6_Silent_p.V90V|RP3-330M21.5_ENST00000500590.1_RNA|DNPH1_ENST00000393987.2_Silent_p.V90V	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9						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						CTTCTGCCACGACCACTGGGA	0.592													G|||	208	0.0415335	0.0023	0.0908	5008	,	,		21379	0.003		0.0706	False		,,,				2504	0.0695				p.V90V		Atlas-SNP	.											C6orf108_ENST00000393987,NS,carcinoma,0,2	.	.	2	0			c.C270T						PASS	.	G	,	85,4303		1,83,2110	30	24	26		270,270	-9.2	0	6	dbSNP_52	26	882,7688		43,796,3446	no	coding-synonymous,coding-synonymous	C6orf108	NM_006443.2,NM_199184.1	,	44,879,5556	AA,AG,GG		10.2917,1.9371,7.4626	,	90/175,90/149	43193877	967,11991	2194	4285	6479	SO:0001628	intergenic_variant	10591	exon3			TGCCACGACCACT	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		6.37:g.43193877G>A		34	0	0		31	16	0.516129	NM_006443	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	37	CCDS4890.1																																																																																			G|0.942;A|0.058	0.058	strong		0.592	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		A	43193877	G	A	43193877	1	1	25	0	1	0	0	0	0	0	0	0	2322	1045	37	1		1	C6orf108	6	43193877	IGR	SNP	G	TCGA-G8-6906-01A-11D-2210-10	300623	43193877	127921190	250	9159											
CD2AP	23607	hgsc.bcm.edu	37	chr6	47563608	47563608	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaatcttagatgaaaaatcaAcactggaacagaaaccttct	19	9	5	8	0	3	3	1	1	2	2	3	4	3	4	1	1	3	0	1	1	7	2	rs138727736	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:47563608A>G	ENST00000359314.5	+	12	1576	c.1120A>G	c.(1120-1122)Aca>Gca	p.T374A		NM_012120.2	NP_036252.1	Q9Y5K6	CD2AP_HUMAN	CD2-associated protein	374	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)			TGAAAAATCAACACTGGAACA	0.353													A|||	23	0.00459265	0.0	0.0115	5008	,	,		14171	0.001		0.003	False		,,,				2504	0.0112				p.T374A		Atlas-SNP	.											.	CD2AP	43	.	0			c.A1120G	GRCh37	CM090139	CD2AP	M	rs138727736	PASS	.	A	ALA/THR	2,4404	4.2+/-10.8	0,2,2201	149	169	162		1120	-5.2	0	6	dbSNP_134	162	46,8554	28.5+/-78.6	0,46,4254	yes	missense	CD2AP	NM_012120.2	58	0,48,6455	GG,GA,AA		0.5349,0.0454,0.3691	benign	374/640	47563608	48,12958	2203	4300	6503	SO:0001583	missense	23607	exon12			AAATCAACACTGG	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.1120A>G	6.37:g.47563608A>G	ENSP00000352264:p.Thr374Ala	24	0	0		29	16	0.551724	NM_012120	A6NL34|Q5VYA3|Q9UG97	Missense_Mutation	SNP	ENST00000359314.5	37	CCDS34472.1	8	0.003663003663003663	0	0.0	6	0.016574585635359115	0	0.0	2	0.002638522427440633	A	3.633	-0.075108	0.07184	4.54E-4	0.005349	ENSG00000198087	ENST00000359314	T	0.22945	1.93	5.57	-5.18	0.02840	.	5.281300	0.00481	N	0.000133	T	0.01627	0.0052	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21690	-1.0238	10	0.07644	T	0.81	4.6781	2.2995	0.04159	0.4573:0.1057:0.271:0.166	.	374	Q9Y5K6	CD2AP_HUMAN	A	374	ENSP00000352264:T374A	ENSP00000352264:T374A	T	+	1	0	CD2AP	47671567	0.000000	0.05858	0.011000	0.14972	0.933000	0.57130	-1.282000	0.02799	-0.673000	0.05259	-0.467000	0.05162	ACA	A|0.995;G|0.005	0.005	strong		0.353	CD2AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040817.2			G	47563608	A	G	47563608	3	3	25	1	0	0	0	0	1	0	0	0	2996	43	2	3	1166	3	CD2AP	6	47563608	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	4369731	47563608	123551459	251	9160											
TFAP2D	83741	hgsc.bcm.edu	37	chr6	50682935	50682935	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	ctcctctcctttaacttactCcaccaccggcaccgagtttg	7	12	5	17	2	1	0	0	0	1	0	4	1	3	0	6	1	2	2	6	1	2	4			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:50682935C>G	ENST00000008391.3	+	2	374	c.146C>G	c.(145-147)tCc>tGc	p.S49C		NM_172238.3	NP_758438.2			transcription factor AP-2 delta (activating enhancer binding protein 2 delta)											NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(26)|ovary(6)|pancreas(1)|prostate(5)|stomach(1)	60	Lung NSC(77;0.0334)					TTAACTTACTCCACCACCGGC	0.547																																					p.S49C		Atlas-SNP	.											.	TFAP2D	144	.	0			c.C146G						PASS	.						245	195	212					6																	50682935		2203	4300	6503	SO:0001583	missense	83741	exon2			CTTACTCCACCAC	AY028376	CCDS4933.1	6p12.3	2008-02-05	2004-10-26	2004-10-27		ENSG00000008197			15581	protein-coding gene	gene with protein product		610161	"transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)-like 1"	TFAP2BL1		11733187	Standard	NM_172238		Approved		uc003paf.3	Q7Z6R9		ENST00000008391.3:c.146C>G	6.37:g.50682935C>G	ENSP00000008391:p.Ser49Cys	196	0	0		206	10	0.0485437	NM_172238		Missense_Mutation	SNP	ENST00000008391.3	37	CCDS4933.1	.	.	.	.	.	.	.	.	.	.	C	14.00	2.404207	0.42613	.	.	ENSG00000008197	ENST00000008391	D	0.97505	-4.41	5.07	5.07	0.68467	.	0.127543	0.53938	D	0.000045	D	0.91112	0.7202	N	0.08118	0	0.54753	D	0.999988	B	0.28713	0.22	B	0.33846	0.171	D	0.90227	0.4276	10	0.87932	D	0	0.3288	18.8076	0.92045	0.0:1.0:0.0:0.0	.	49	Q7Z6R9	AP2D_HUMAN	C	49	ENSP00000008391:S49C	ENSP00000008391:S49C	S	+	2	0	TFAP2D	50790894	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.763000	0.68818	2.498000	0.84270	0.655000	0.94253	TCC	.	.	none		0.547	TFAP2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040881.1	NM_172238		G	50682935	C	G	50682935	3	3	25	1	0	0	0	0	1	0	0	0	15805	855	30	4	152	4	TFAP2D	6	50682935	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	3119327	50682935	120432132	252	9161											
PKHD1	5314	hgsc.bcm.edu	37	chr6	51613012	51613012	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagttgtcaagtccactttcCttatagagatgaaggccatg	11	12	9	9	0	1	2	1	1	0	1	3	3	3	2	3	1	0	1	3	1	4	4	rs143737660		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:51613012C>T	ENST00000371117.3	-	58	9677	c.9402G>A	c.(9400-9402)aaG>aaA	p.K3134K	PKHD1_ENST00000340994.4_Silent_p.K3134K	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3134					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)					GTCCACTTTCCTTATAGAGAT	0.463													C|||	1	0.000199681	0.0	0.0	5008	,	,		21874	0.0		0.0	False		,,,				2504	0.001				p.K3134K		Atlas-SNP	.											.	PKHD1	927	.	0			c.G9402A						PASS	.	C	,	0,4406		0,0,2203	201	209	206		9402,9402	3	0.1	6	dbSNP_134	206	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	PKHD1	NM_138694.3,NM_170724.2	,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,	3134/4075,3134/3397	51613012	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	5314	exon58			ACTTTCCTTATAG	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.9402G>A	6.37:g.51613012C>T		108	0	0		91	43	0.472527	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			C|0.999;T|0.001	0.001	strong		0.463	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		T	51613012	C	T	51613012	2	4	25	1	0	0	0	0	0	0	0	1	11980	680	24	2		2	PKHD1	6	51613012	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	930077	51613012	119502055	253	9162											
GSTA3	2940	hgsc.bcm.edu	37	chr6	52767193	52767193	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggttgtatttgctggcaaTgtagttgagaatggctctgg	8	14	15	4	0	1	1	0	1	1	1	1	3	1	1	0	4	1	7	0	4	4	5			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:52767193T>C	ENST00000211122.3	-	4	288	c.223A>G	c.(223-225)Att>Gtt	p.I75V	GSTA3_ENST00000370968.1_Missense_Mutation_p.I25V	NM_000847.4	NP_000838.3	Q16772	GSTA3_HUMAN	glutathione S-transferase alpha 3	75	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)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(2)	10	Lung NSC(77;0.0912)				Glutathione(DB00143)	TTGCTGGCAATGTAGTTGAGA	0.423																																					p.I75V		Atlas-SNP	.											.	GSTA3	21	.	0			c.A223G						PASS	.						199	193	195					6																	52767193		2203	4300	6503	SO:0001583	missense	2940	exon4			TGGCAATGTAGTT	AF020919	CCDS4947.1	6p12.2	2012-06-21	2008-11-26		ENSG00000174156	ENSG00000174156	2.5.1.18	"Glutathione S-transferases / Soluble"	4628	protein-coding gene	gene with protein product		605449	"glutathione S-transferase A3"			8307579, 9480897	Standard	NM_000847		Approved		uc003pbb.3	Q16772	OTTHUMG00000014865	ENST00000211122.3:c.223A>G	6.37:g.52767193T>C	ENSP00000211122:p.Ile75Val	148	0	0		202	84	0.415842	NM_000847	O43468|Q068V6|Q8WWA8|Q9H415	Missense_Mutation	SNP	ENST00000211122.3	37	CCDS4947.1	.	.	.	.	.	.	.	.	.	.	T	12.40	1.925899	0.34002	.	.	ENSG00000174156	ENST00000370968;ENST00000211122;ENST00000431899	T;T;T	0.15487	2.42;2.42;2.42	4.16	1.75	0.24633	Glutathione S-transferase, N-terminal (2);Thioredoxin-like fold (2);	0.055329	0.64402	D	0.000001	T	0.05868	0.0153	L	0.43646	1.37	0.36011	D	0.838043	B	0.18461	0.028	B	0.24006	0.05	T	0.11891	-1.0569	10	0.46703	T	0.11	.	8.092	0.30805	0.0:0.1721:0.0:0.8279	.	75	Q16772	GSTA3_HUMAN	V	25;75;25	ENSP00000360007:I25V;ENSP00000211122:I75V;ENSP00000399142:I25V	ENSP00000211122:I75V	I	-	1	0	GSTA3	52875152	1.000000	0.71417	0.949000	0.38748	0.738000	0.42128	2.245000	0.43133	0.263000	0.21812	0.533000	0.62120	ATT	.	.	none		0.423	GSTA3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040933.1			C	52767193	T	C	52767193	3	2	25	1	0	0	0	0	1	0	0	0	6841	1464	51	3	461	3	GSTA3	6	52767193	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	1154181	52767193	118347874	254	9163											
DST	667	hgsc.bcm.edu	37	chr6	56505175	56505175	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcaggcgggaagtcatcccTgatgacaggccagaagtcat	11	7	13	10	1	3	3	3	2	0	1	4	4	4	4	2	3	0	0	2	3	2	0	rs113432929	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:56505175T>A	ENST00000361203.3	-	14	1630	c.1623A>T	c.(1621-1623)tcA>tcT	p.S541S	DST_ENST00000518935.1_Silent_p.S215S|DST_ENST00000370788.2_Silent_p.S541S|DST_ENST00000370754.5_Silent_p.S719S|DST_ENST00000446842.2_Silent_p.S215S|DST_ENST00000244364.6_Silent_p.S215S|DST_ENST00000370765.6_Silent_p.S215S|DST_ENST00000312431.6_Silent_p.S541S|DST_ENST00000421834.2_Silent_p.S541S|DST_ENST00000370769.4_Silent_p.S541S			Q03001	DYST_HUMAN	dystonin	541					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)			AAGTCATCCCTGATGACAGGC	0.483													T|||	11	0.00219649	0.0	0.0	5008	,	,		18999	0.0		0.005	False		,,,				2504	0.0061				p.S215S		Atlas-SNP	.											.	DST	1427	.	0			c.A645T						PASS	.	T	,	4,4402	8.1+/-20.4	0,4,2199	139	141	141		645,645	-4.8	0.6	6	dbSNP_132	141	36,8564	25.1+/-72.6	0,36,4264	yes	coding-synonymous,coding-synonymous	DST	NM_001723.5,NM_015548.4	,	0,40,6463	AA,AT,TT		0.4186,0.0908,0.3076	,	215/2650,215/5172	56505175	40,12966	2203	4300	6503	SO:0001819	synonymous_variant	667	exon4			CATCCCTGATGAC	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.1623A>T	6.37:g.56505175T>A		168	0	0		156	69	0.442308	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	37																																																																																				T|0.997;A|0.003	0.003	strong		0.483	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		A	56505175	T	A	56505175	2	1	25	1	0	0	0	0	0	0	0	1	4785	1567	55	5		5	DST	6	56505175	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	3737982	56505175	114609892	255	9164											
KHDRBS2	202559	hgsc.bcm.edu	37	chr6	62390920	62390920	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccctctggctgacctttgcGgtggtgccttcaagctagag	5	11	12	13	1	2	2	1	1	1	1	2	2	2	2	4	3	3	2	4	3	2	3	rs61753606	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:62390920G>A	ENST00000281156.4	-	9	1276	c.998C>T	c.(997-999)cCg>cTg	p.P333L	RP1-240B8.3_ENST00000511849.2_RNA	NM_152688.2	NP_689901.2	Q5VWX1	KHDR2_HUMAN	KH domain containing, RNA binding, signal transduction associated 2	333					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)		TGACCTTTGCGGTGGTGCCTT	0.478													G|||	29	0.00579073	0.003	0.0086	5008	,	,		16587	0.0		0.0139	False		,,,				2504	0.0051				p.P333L		Atlas-SNP	.											KHDRBS2,NS,carcinoma,+1,2	KHDRBS2	103	2	0			c.C998T						PASS	.	G	LEU/PRO	13,4393	21.2+/-45.6	0,13,2190	186	130	149		998	5.1	0.8	6	dbSNP_129	149	141,8459	70.0+/-132.6	1,139,4160	no	missense	KHDRBS2	NM_152688.2	98	1,152,6350	AA,AG,GG		1.6395,0.2951,1.1841	benign	333/350	62390920	154,12852	2203	4300	6503	SO:0001583	missense	202559	exon9			CTTTGCGGTGGTG	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.998C>T	6.37:g.62390920G>A	ENSP00000281156:p.Pro333Leu	157	0	0		88	69	0.784091	NM_152688	A8K7M8|Q8N4I4|Q8TCZ4	Missense_Mutation	SNP	ENST00000281156.4	37	CCDS4963.1	15	0.006868131868131868	4	0.008130081300813009	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	G	10.68	1.419456	0.25552	0.002951	0.016395	ENSG00000112232	ENST00000281156	T	0.44083	0.93	5.13	5.13	0.70059	.	0.316534	0.34411	N	0.003988	T	0.14960	0.0361	N	0.15975	0.35	0.43959	D	0.996637	B	0.19817	0.039	B	0.11329	0.006	T	0.05241	-1.0897	10	0.56958	D	0.05	.	12.3163	0.54958	0.0783:0.0:0.9217:0.0	rs61753606	333	Q5VWX1	KHDR2_HUMAN	L	333	ENSP00000281156:P333L	ENSP00000281156:P333L	P	-	2	0	KHDRBS2	62448879	1.000000	0.71417	0.847000	0.33407	0.169000	0.22640	4.271000	0.58902	2.541000	0.85698	0.650000	0.86243	CCG	G|0.987;A|0.013	0.013	strong		0.478	KHDRBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041066.2	NM_152688		A	62390920	G	A	62390920	3	1	25	1	0	0	0	0	1	0	0	0	8156	1116	39	1	55	1	KHDRBS2	6	62390920	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	5885745	62390920	108724147	256	9165											
EYS	346007	hgsc.bcm.edu	37	chr6	65622420	65622420	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tttgcgtctaccaaagctaaGcatgttgagttgtttctgca	9	15	9	8	1	2	1	0	1	2	0	2	1	2	1	1	0	5	6	1	0	3	6	rs183814213		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:65622420G>A	ENST00000370621.3	-	16	3124	c.2598C>T	c.(2596-2598)tgC>tgT	p.C866C	EYS_ENST00000370616.2_Silent_p.C866C|EYS_ENST00000503581.1_Silent_p.C866C			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	866	EGF-like 12. {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						CCAAAGCTAAGCATGTTGAGT	0.353													G|||	1	0.000199681	0.0	0.0014	5008	,	,		17718	0.0		0.0	False		,,,				2504	0.0				p.C866C		Atlas-SNP	.											.	EYS	527	.	0			c.C2598T						PASS	.	G		0,1384		0,0,692	156	129	137		2598	2.6	0	6		137	1,3181		0,1,1590	no	coding-synonymous	EYS	NM_001142800.1		0,1,2282	AA,AG,GG		0.0314,0.0,0.0219		866/3145	65622420	1,4565	692	1591	2283	SO:0001819	synonymous_variant	346007	exon16			AGCTAAGCATGTT		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.2598C>T	6.37:g.65622420G>A		291	0	0		167	19	0.113772	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Silent	SNP	ENST00000370621.3	37																																																																																				G|1.000;A|0.000	0.000	strong		0.353	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050		A	65622420	G	A	65622420	2	1	25	1	0	0	0	0	0	0	0	1	5334	963	34	2		2	EYS	6	65622420	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	3231500	65622420	105492647	257	9166											
TMEM30A	55754	hgsc.bcm.edu	37	chr6	75965985	75965985	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcaagatcatccgttttcGtccatcaaaataatgtacag	13	12	6	10	2	3	1	3	0	0	1	6	1	5	1	2	0	1	3	2	0	5	4			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:75965985G>A	ENST00000230461.6	-	7	1248	c.919C>T	c.(919-921)Cga>Tga	p.R307*	TMEM30A_ENST00000475111.2_Nonsense_Mutation_p.R271*|TMEM30A_ENST00000370050.5_Nonsense_Mutation_p.R188*	NM_018247.3	NP_060717.1	Q9NV96	CC50A_HUMAN	transmembrane protein 30A	307					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						ATCCGTTTTCGTCCATCAAAA	0.378																																					p.R307X		Atlas-SNP	.											TMEM30A,NS,carcinoma,+1,3	TMEM30A	40	3	0			c.C919T						PASS	.						105	101	102					6																	75965985		2203	4300	6503	SO:0001587	stop_gained	55754	exon7			GTTTTCGTCCATC	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.919C>T	6.37:g.75965985G>A	ENSP00000230461:p.Arg307*	83	0	0		55	41	0.745455	NM_018247	A8K9V8|E1P539|Q658Z3|Q96H09|Q9NSL9	Nonsense_Mutation	SNP	ENST00000230461.6	37	CCDS4983.1	.	.	.	.	.	.	.	.	.	.	G	39	7.619958	0.98393	.	.	ENSG00000112697	ENST00000230461;ENST00000545449;ENST00000370050;ENST00000475111	.	.	.	5.88	5.88	0.94601	.	0.055311	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	.	13.6255	0.62161	0.0:0.0:0.7294:0.2706	.	.	.	.	X	307;291;188;271	.	ENSP00000230461:R307X	R	-	1	2	TMEM30A	76022705	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.821000	0.55700	2.780000	0.95670	0.655000	0.94253	CGA	.	.	none		0.378	TMEM30A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041248.2	NM_018247		A	75965985	G	A	75965985	4	1	25	1	0	0	0	0	0	1	0	0	16168	1153	40	1	170	1	TMEM30A	6	75965985	Nonsense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	10343565	75965985	95149082	258	9167											
EPB41L2	2037	hgsc.bcm.edu	37	chr6	131186718	131186718	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgttgacacggactcagaTgtgatggtttgtgcggtcag	7	13	15	6	2	2	3	2	2	0	1	2	4	2	4	0	3	1	3	0	3	0	3	rs149001048		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:131186718T>A	ENST00000337057.3	-	17	2968	c.2787A>T	c.(2785-2787)acA>acT	p.T929T	EPB41L2_ENST00000525271.1_Intron|EPB41L2_ENST00000527659.1_Silent_p.T735T|EPB41L2_ENST00000529208.1_Silent_p.T859T|EPB41L2_ENST00000368128.2_Silent_p.T929T|EPB41L2_ENST00000530757.1_Intron|EPB41L2_ENST00000527411.1_Silent_p.T859T|EPB41L2_ENST00000392427.3_Intron|EPB41L2_ENST00000524581.1_Silent_p.T307T|EPB41L2_ENST00000531410.1_Silent_p.T50T|EPB41L2_ENST00000528282.1_Silent_p.T671T|EPB41L2_ENST00000445890.2_Silent_p.T671T|EPB41L2_ENST00000530481.1_Silent_p.T776T|EPB41L2_ENST00000525193.1_Silent_p.T630T	NM_001431.3	NP_001422.1	O43491	E41L2_HUMAN	erythrocyte membrane protein band 4.1-like 2	929	C-terminal (CTD).				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)		CGGACTCAGATGTGATGGTTT	0.458													T|||	1	0.000199681	0.0	0.0	5008	,	,		5461	0.0		0.001	False		,,,				2504	0.0				p.T929T		Atlas-SNP	.											.	EPB41L2	96	.	0			c.A2787T						PASS	.						357	260	293					6																	131186718		2203	4300	6503	SO:0001819	synonymous_variant	2037	exon17			CTCAGATGTGATG	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.2787A>T	6.37:g.131186718T>A		247	0	0		154	19	0.123377	NM_001431	B4DHI8|E9PPD9|Q5T4F0|Q68DV2	Silent	SNP	ENST00000337057.3	37	CCDS5141.1																																																																																			T|1.000;A|0.000	0.000	strong		0.458	EPB41L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042204.3			A	131186718	T	A	131186718	2	1	25	1	0	0	0	0	0	0	0	1	5155	1451	51	5		5	EPB41L2	6	131186718	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	55220733	131186718	39928349	259	9168											
MYB	4602	hgsc.bcm.edu	37	chr6	135518402	135518402	+	Intron	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctccttcatatttgctgacGtcagcagttcaactcccaag	9	12	7	13	1	3	1	3	1	0	0	5	1	5	1	2	0	3	4	2	0	3	4	rs547508696		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:135518402G>A	ENST00000367814.4	+	9	1389				MYB-AS1_ENST00000455534.1_RNA|MYB_ENST00000533624.1_Intron|MYB_ENST00000534121.1_Missense_Mutation_p.V487I|MYB_ENST00000527615.1_Intron|MYB_ENST00000534044.1_Intron|MYB_ENST00000531845.1_Intron|MYB_ENST00000528774.1_Missense_Mutation_p.V500I|MYB_ENST00000341911.5_Missense_Mutation_p.V503I|MYB_ENST00000316528.8_Intron|MYB_ENST00000525369.1_Intron|MYB_ENST00000442647.2_Intron	NM_001161659.1|NM_005375.2	NP_001155131.1|NP_005366.2	P10242	MYB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog						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)		ATTTGCTGACGTCAGCAGTTC	0.507			T	NFIB	adenoid cystic carcinoma								G|||	1	0.000199681	0.0	0.0	5008	,	,		20039	0.001		0.0	False		,,,				2504	0.0				p.V503I		Atlas-SNP	.		Dom	yes		6	6q22-23	4602	v-myb myeloblastosis viral oncogene homolog		E	.	MYB	137	.	0			c.G1507A						PASS	.						77	72	73					6																	135518402		1568	3582	5150	SO:0001627	intron_variant	4602	exon10			GCTGACGTCAGCA		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.1203+1262G>A	6.37:g.135518402G>A		105	0	0		72	70	0.972222	NM_001130173	E9PI07|E9PLZ5|E9PNA4|E9PNL6|E9PRS2|P78391|P78392|P78525|P78526|Q14023|Q14024|Q708E4|Q708E7|Q9UE83	Missense_Mutation	SNP	ENST00000367814.4	37	CCDS5174.1	.	.	.	.	.	.	.	.	.	.	G	11.15	1.553390	0.27739	.	.	ENSG00000118513	ENST00000341911;ENST00000528774;ENST00000534121	T;T;T	0.11277	2.79;2.79;2.8	5.78	2.96	0.34315	.	0.514050	0.19050	N	0.124064	T	0.01976	0.0062	N	0.22421	0.69	0.80722	D	1	B;B;B	0.15719	0.004;0.005;0.014	B;B;B	0.11329	0.002;0.002;0.006	T	0.40683	-0.9550	10	0.17369	T	0.5	-0.0596	6.0033	0.19533	0.2267:0.1344:0.6389:0.0	.	500;487;503	E9PNL6;E9PNA4;P10242-4	.;.;.	I	503;500;487	ENSP00000339992:V503I;ENSP00000434723:V500I;ENSP00000432851:V487I	ENSP00000339992:V503I	V	+	1	0	MYB	135560095	0.999000	0.42202	0.999000	0.59377	0.999000	0.98932	0.652000	0.24888	0.337000	0.23665	0.655000	0.94253	GTC	.	.	none		0.507	MYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042347.4			A	135518402	G	A	135518402	1	1	25	0	1	0	0	0	0	0	0	0	10016	1145	40	1		1	MYB	6	135518402	Intron	SNP	G	TCGA-G8-6906-01A-11D-2210-10	4331684	135518402	35596665	260	9169											
UST	10090	hgsc.bcm.edu	37	chr6	149395197	149395197	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actggaaaccgaggagccaaTcgacgatgaagaacaggatg	16	4	13	8	3	0	2	0	1	0	1	1	8	0	5	2	3	3	0	2	3	4	0			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:149395197T>A	ENST00000367463.4	+	8	1269	c.1166T>A	c.(1165-1167)aTc>aAc	p.I389N	UST_ENST00000466695.1_3'UTR	NM_005715.2	NP_005706.1	Q9Y2C2	UST_HUMAN	uronyl-2-sulfotransferase	389					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)		GAGGAGCCAATCGACGATGAA	0.483																																					p.I389N		Atlas-SNP	.											UST,right_upper_lobe,carcinoma,0,2	UST	42	2	0			c.T1166A						PASS	.						95	95	95					6																	149395197		2203	4300	6503	SO:0001583	missense	10090	exon8			AGCCAATCGACGA	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.1166T>A	6.37:g.149395197T>A	ENSP00000356433:p.Ile389Asn	126	0	0		86	14	0.162791	NM_005715	B2RCX6	Missense_Mutation	SNP	ENST00000367463.4	37	CCDS5213.1	.	.	.	.	.	.	.	.	.	.	T	15.45	2.835824	0.50951	.	.	ENSG00000111962	ENST00000367463	T	0.53857	0.6	5.3	5.3	0.74995	.	0.184757	0.48767	D	0.000180	T	0.18467	0.0443	N	0.14661	0.345	0.40188	D	0.977379	P	0.35982	0.531	B	0.27796	0.083	T	0.20974	-1.0259	10	0.72032	D	0.01	-6.0612	10.7296	0.46089	0.0:0.0747:0.0:0.9252	.	389	Q9Y2C2	UST_HUMAN	N	389	ENSP00000356433:I389N	ENSP00000356433:I389N	I	+	2	0	UST	149436890	0.272000	0.24172	0.034000	0.17996	0.910000	0.53928	2.116000	0.41930	2.127000	0.65507	0.460000	0.39030	ATC	.	.	none		0.483	UST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043363.1	NM_005715		A	149395197	T	A	149395197	3	1	25	1	0	0	0	0	1	0	0	0	17108	1435	50	5	1196	5	UST	6	149395197	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	13876795	149395197	21719870	261	9170											
RBM16	22828	hgsc.bcm.edu	37	chr6	155152262	155152262	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	accagatttcttctggtgaaAacaccagatcaggtaaataa	16	10	7	8	0	3	3	1	1	2	2	3	3	3	3	2	2	1	1	2	2	5	4			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:155152262A>G	ENST00000367178.3	+	19	2923	c.2347A>G	c.(2347-2349)Aac>Gac	p.N783D	TIAM2_ENST00000461783.3_5'Flank|SCAF8_ENST00000367186.4_Missense_Mutation_p.N849D|SCAF8_ENST00000417268.1_Missense_Mutation_p.N783D	NM_014892.3	NP_055707.3	Q9UPN6	SCAF8_HUMAN	SR-related CTD-associated factor 8	783	Pro-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase core enzyme binding (GO:0043175)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(15)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	46						TTCTGGTGAAAACACCAGATC	0.383																																					p.N783D		Atlas-SNP	.											.	SCAF8	122	.	0			c.A2347G						PASS	.						28	27	28					6																	155152262		2203	4300	6503	SO:0001583	missense	22828	exon19			GGTGAAAACACCA	AB029039	CCDS5247.1, CCDS69226.1, CCDS75541.1	6q25.1-q25.3	2013-02-12	2011-01-10	2011-01-10	ENSG00000213079	ENSG00000213079		"RNA binding motif (RRM) containing"	20959	protein-coding gene	gene with protein product			"RNA binding motif protein 16"	RBM16		10470851	Standard	NM_001286189		Approved	KIAA1116	uc003qpz.3	Q9UPN6	OTTHUMG00000015877	ENST00000367178.3:c.2347A>G	6.37:g.155152262A>G	ENSP00000356146:p.Asn783Asp	25	0	0		21	20	0.952381	NM_014892	B7Z888|Q5TBU6|Q6NSK3|Q9BQN8|Q9BX43	Missense_Mutation	SNP	ENST00000367178.3	37	CCDS5247.1	.	.	.	.	.	.	.	.	.	.	A	15.09	2.731115	0.48939	.	.	ENSG00000213079	ENST00000367178;ENST00000417268;ENST00000367186	T;T;T	0.47528	0.87;0.87;0.84	5.32	4.08	0.47627	.	0.189894	0.24940	U	0.034400	T	0.20047	0.0482	L	0.44542	1.39	0.29468	N	0.857268	B;B;P;P	0.37864	0.094;0.094;0.61;0.61	B;B;B;B	0.35510	0.016;0.016;0.204;0.145	T	0.04579	-1.0941	10	0.26408	T	0.33	.	10.1615	0.42855	0.8517:0.0:0.0:0.1483	.	828;849;861;783	B7Z876;B7Z888;B7Z3A4;Q9UPN6	.;.;.;SCAF8_HUMAN	D	783;783;849	ENSP00000356146:N783D;ENSP00000413098:N783D;ENSP00000356154:N849D	ENSP00000356146:N783D	N	+	1	0	SCAF8	155193954	0.999000	0.42202	1.000000	0.80357	0.992000	0.81027	3.825000	0.55730	2.136000	0.66102	0.533000	0.62120	AAC	.	.	none		0.383	SCAF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042798.1	NM_014892		G	155152262	A	G	155152262	3	3	25	1	0	0	0	0	1	0	0	0	13133	14	1	3	2421	3	RBM16	6	155152262	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	5757065	155152262	15962805	262	9171											
PLG	5340	hgsc.bcm.edu	37	chr6	161159619	161159619	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgatatccccagagtgggtgTtgactgctgcccactgcttg	6	12	12	11	0	0	3	0	2	0	1	1	3	1	3	3	1	3	3	3	1	1	3	rs4252195	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:161159619T>C	ENST00000308192.9	+	15	1915	c.1852T>C	c.(1852-1854)Ttg>Ctg	p.L618L		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	618	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				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)	AGAGTGGGTGTTGACTGCTGC	0.413													T|||	3	0.000599042	0.0	0.0014	5008	,	,		21373	0.0		0.002	False		,,,				2504	0.0				p.L618L		Atlas-SNP	.											.	PLG	150	.	0			c.T1852C						PASS	.	T		9,4397		0,9,2194	150	139	143		1852	-4.5	1	6	dbSNP_111	143	55,8545		0,55,4245	no	coding-synonymous	PLG	NM_000301.3		0,64,6439	CC,CT,TT		0.6395,0.2043,0.4921		618/811	161159619	64,12942	2203	4300	6503	SO:0001819	synonymous_variant	5340	exon15			TGGGTGTTGACTG	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.1852T>C	6.37:g.161159619T>C		175	0	0		93	81	0.870968	NM_000301	Q15146|Q5TEH4|Q6PA00	Silent	SNP	ENST00000308192.9	37	CCDS5279.1																																																																																			T|0.996;C|0.004	0.004	strong		0.413	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301		C	161159619	T	C	161159619	2	2	25	1	0	0	0	0	0	0	0	1	12095	1722	60	3		3	PLG	6	161159619	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	6007357	161159619	9955448	263	9172											
TTLL2	83887	hgsc.bcm.edu	37	chr6	167754360	167754360	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	catggttgtaaatggacgctCagcagatttttttcctacct	9	15	8	9	1	1	1	1	0	0	1	2	2	2	2	2	2	2	4	2	2	3	6	rs77767783	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:167754360C>T	ENST00000239587.5	+	3	1060	c.972C>T	c.(970-972)ctC>ctT	p.L324L		NM_031949.4	NP_114155.4	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	324	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				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)		AATGGACGCTCAGCAGATTTT	0.438													C|||	9	0.00179712	0.0	0.0043	5008	,	,		20069	0.0		0.006	False		,,,				2504	0.0				p.L324L		Atlas-SNP	.											.	TTLL2	82	.	0			c.C972T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	159	168	165		972	0.3	0.5	6	dbSNP_132	165	28,8572	19.8+/-62.0	0,28,4272	no	coding-synonymous	TTLL2	NM_031949.4		0,29,6474	TT,TC,CC		0.3256,0.0227,0.223		324/593	167754360	29,12977	2203	4300	6503	SO:0001819	synonymous_variant	83887	exon3			GACGCTCAGCAGA	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.972C>T	6.37:g.167754360C>T		174	0	0		90	80	0.888889	NM_031949	B2RB11|B3KS77|Q7Z6R8|Q86X22	Silent	SNP	ENST00000239587.5	37	CCDS5301.1																																																																																			C|0.998;T|0.002	0.002	strong		0.438	TTLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043127.3	NM_031949		T	167754360	C	T	167754360	2	4	25	1	0	0	0	0	0	0	0	1	16742	813	29	2		2	TTLL2	6	167754360	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	6594741	167754360	3360707	264	9173											
KIAA0415	9907	hgsc.bcm.edu	37	chr7	4821300	4821300	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	cgccatcctgcgagagatgtCcccctctgacagcctcagcc	7	7	9	18	2	2	2	1	1	1	1	4	4	4	2	6	0	3	0	6	0	0	0	rs11549839	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4821300C>G	ENST00000348624.4	+	3	375	c.281C>G	c.(280-282)tCc>tGc	p.S94C	AP5Z1_ENST00000401897.1_Missense_Mutation_p.S94C	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	94			S -> C (in dbSNP:rs11549839).		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)											CGAGAGATGTCCCCCTCTGAC	0.662													C|||	63	0.0125799	0.0015	0.0187	5008	,	,		18244	0.0		0.0249	False		,,,				2504	0.0235				p.S94C		Atlas-SNP	.											.	.	.	.	0			c.C281G						PASS	.	C	CYS/SER	12,4262		0,12,2125	25	30	28		281	5.1	0.6	7	dbSNP_120	28	208,8290		5,198,4046	yes	missense	KIAA0415	NM_014855.2	112	5,210,6171	GG,GC,CC		2.4476,0.2808,1.7225	benign	94/808	4821300	220,12552	2137	4249	6386	SO:0001583	missense	9907	exon3			AGATGTCCCCCTC	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.281C>G	7.37:g.4821300C>G	ENSP00000297562:p.Ser94Cys	130	0	0		126	70	0.555556	NM_014855	Q8N3X2|Q96H80	Missense_Mutation	SNP	ENST00000348624.4	37	CCDS47528.1	33	0.01510989010989011	2	0.0040650406504065045	12	0.03314917127071823	0	0.0	19	0.025065963060686015	C	12.67	2.008321	0.35415	0.002808	0.024476	ENSG00000242802	ENST00000348624;ENST00000401897	T;T	0.64085	-0.08;0.67	5.08	5.08	0.68730	.	0.645959	0.15127	N	0.279052	T	0.38585	0.1046	M	0.65975	2.015	0.18873	N	0.999984	B	0.22080	0.064	B	0.21917	0.037	T	0.46665	-0.9175	10	0.41790	T	0.15	.	15.7732	0.78187	0.0:1.0:0.0:0.0	rs11549839;rs11549839	94	O43299	K0415_HUMAN	C	94	ENSP00000297562:S94C;ENSP00000384980:S94C	ENSP00000297562:S94C	S	+	2	0	KIAA0415	4787826	0.990000	0.36364	0.650000	0.29550	0.856000	0.48823	3.089000	0.50183	2.640000	0.89533	0.655000	0.94253	TCC	C|0.987;G|0.013	0.013	strong		0.662	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1			G	4821300	C	G	4821300	3	3	25	1	0	0	0	0	1	0	0	0	8184	855	30	4	291	4	KIAA0415	7	4821300	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10		4821300	154317363	265	9174											
KIAA0415	9907	hgsc.bcm.edu	37	chr7	4821352	4821352	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacacgcagaacagccggcaGctgagcctggtggcctccgt	8	5	13	15	3	0	2	0	1	0	1	1	2	1	2	4	3	4	3	4	3	1	0	rs11549840	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4821352G>C	ENST00000348624.4	+	3	427	c.333G>C	c.(331-333)caG>caC	p.Q111H	AP5Z1_ENST00000401897.1_Missense_Mutation_p.Q111H	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	111					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)											ACAGCCGGCAGCTGAGCCTGG	0.662													G|||	63	0.0125799	0.0015	0.0187	5008	,	,		17920	0.0		0.0249	False		,,,				2504	0.0235				p.Q111H		Atlas-SNP	.											.	.	.	.	0			c.G333C						PASS	.	G	HIS/GLN	13,4247		0,13,2117	21	26	24		333	2.1	0.8	7	dbSNP_120	24	205,8303		4,197,4053	yes	missense	KIAA0415	NM_014855.2	24	4,210,6170	CC,CG,GG		2.4095,0.3052,1.7074	possibly-damaging	111/808	4821352	218,12550	2130	4254	6384	SO:0001583	missense	9907	exon3			CCGGCAGCTGAGC	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.333G>C	7.37:g.4821352G>C	ENSP00000297562:p.Gln111His	122	0	0		114	57	0.5	NM_014855	Q8N3X2|Q96H80	Missense_Mutation	SNP	ENST00000348624.4	37	CCDS47528.1	33	0.01510989010989011	2	0.0040650406504065045	12	0.03314917127071823	0	0.0	19	0.025065963060686015	G	10.63	1.404230	0.25378	0.003052	0.024095	ENSG00000242802	ENST00000348624;ENST00000401897	T;T	0.44482	0.92;0.92	5.08	2.13	0.27403	.	0.485095	0.20242	N	0.096270	T	0.13970	0.0338	M	0.63428	1.95	0.24747	N	0.993007	B	0.23316	0.083	B	0.20184	0.028	T	0.12941	-1.0528	10	0.27785	T	0.31	.	5.8299	0.18574	0.1763:0.2946:0.5291:0.0	rs11549840	111	O43299	K0415_HUMAN	H	111	ENSP00000297562:Q111H;ENSP00000384980:Q111H	ENSP00000297562:Q111H	Q	+	3	2	KIAA0415	4787878	0.601000	0.26907	0.815000	0.32552	0.847000	0.48162	-0.102000	0.10956	0.256000	0.21614	0.655000	0.94253	CAG	G|0.986;C|0.014	0.014	strong		0.662	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1			C	4821352	G	C	4821352	3	2	25	1	0	0	0	0	1	0	0	0	8184	962	34	4	343	4	KIAA0415	7	4821352	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	52	4821352	154317311	266	9175											
KIAA0415	9907	hgsc.bcm.edu	37	chr7	4827859	4827859	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagctgcctggaggccttccGggacccgcagttccagggtc	5	7	14	15	2	0	0	0	0	0	0	3	2	2	2	5	4	2	3	5	4	0	2	rs77890266	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4827859G>A	ENST00000348624.4	+	12	1623	c.1529G>A	c.(1528-1530)cGg>cAg	p.R510Q	AP5Z1_ENST00000401897.1_Missense_Mutation_p.R510Q|MIR4656_ENST00000579503.1_RNA	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	510					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)											GAGGCCTTCCGGGACCCGCAG	0.687													G|||	62	0.0123802	0.0015	0.0187	5008	,	,		16573	0.0		0.0239	False		,,,				2504	0.0235				p.R510Q		Atlas-SNP	.											.	.	.	.	0			c.G1529A						PASS	.	G	GLN/ARG	12,3796		0,12,1892	10	13	12		1529	2.6	0.2	7	dbSNP_131	12	197,8015		5,187,3914	yes	missense	KIAA0415	NM_014855.2	43	5,199,5806	AA,AG,GG		2.3989,0.3151,1.7388	benign	510/808	4827859	209,11811	1904	4106	6010	SO:0001583	missense	9907	exon12			CCTTCCGGGACCC	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.1529G>A	7.37:g.4827859G>A	ENSP00000297562:p.Arg510Gln	136	0	0		154	68	0.441558	NM_014855	Q8N3X2|Q96H80	Missense_Mutation	SNP	ENST00000348624.4	37	CCDS47528.1	32	0.014652014652014652	2	0.0040650406504065045	12	0.03314917127071823	0	0.0	18	0.023746701846965697	G	13.91	2.377627	0.42105	0.003151	0.023989	ENSG00000242802	ENST00000348624;ENST00000401897	T;T	0.44881	0.91;0.91	4.48	2.62	0.31277	.	0.079729	0.52532	N	0.000077	T	0.10121	0.0248	L	0.45228	1.405	0.38035	D	0.93527	P	0.37864	0.61	B	0.25405	0.06	T	0.04103	-1.0977	10	0.36615	T	0.2	.	8.8683	0.35300	0.1868:0.0:0.8132:0.0	.	510	O43299	K0415_HUMAN	Q	510	ENSP00000297562:R510Q;ENSP00000384980:R510Q	ENSP00000297562:R510Q	R	+	2	0	KIAA0415	4794385	0.959000	0.32827	0.180000	0.23079	0.851000	0.48451	1.465000	0.35299	0.310000	0.22990	0.478000	0.44815	CGG	G|0.986;A|0.014	0.014	strong		0.687	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1			A	4827859	G	A	4827859	3	1	25	1	0	0	0	0	1	0	0	0	8184	1116	39	1	1575	1	KIAA0415	7	4827859	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	6507	4827859	154310804	267	9176											
KIAA0415	9907	hgsc.bcm.edu	37	chr7	4830971	4830971	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgcccctggccctgcgcacGgtcagccggctggtggagag	4	6	16	15	3	1	1	1	0	0	1	1	2	1	1	4	5	3	2	4	5	0	0	rs77393809	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4830971G>T	ENST00000348624.4	+	17	2473	c.2379G>T	c.(2377-2379)acG>acT	p.T793T	AP5Z1_ENST00000490487.1_3'UTR|MIR4656_ENST00000579503.1_RNA	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	793					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)											CCCTGCGCACGGTCAGCCGGC	0.677													G|||	62	0.0123802	0.0015	0.0187	5008	,	,		17357	0.0		0.0239	False		,,,				2504	0.0235				p.T793T		Atlas-SNP	.											.	.	.	.	0			c.G2379T						PASS	.	G		12,4080		0,12,2034	15	20	18		2379	-9.4	0	7	dbSNP_133	18	204,8148		4,196,3976	no	coding-synonymous	KIAA0415	NM_014855.2		4,208,6010	TT,TG,GG		2.4425,0.2933,1.7358		793/808	4830971	216,12228	2046	4176	6222	SO:0001819	synonymous_variant	9907	exon17			GCGCACGGTCAGC	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.2379G>T	7.37:g.4830971G>T		109	0	0		137	73	0.532847	NM_014855	Q8N3X2|Q96H80	Silent	SNP	ENST00000348624.4	37	CCDS47528.1																																																																																			G|0.985;T|0.015	0.015	strong		0.677	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1			T	4830971	G	T	4830971	2	4	25	1	0	0	0	0	0	0	0	1	8184	1103	39	4		4	KIAA0415	7	4830971	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	3112	4830971	154307692	268	9177											
RADIL	55698	hgsc.bcm.edu	37	chr7	4841614	4841614	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggtgcccgtcaaggaccaCgtggtgcataccctagggag	9	6	14	12	2	1	0	1	0	0	0	1	2	1	2	3	4	3	1	3	4	3	2	rs117943885	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4841614C>T	ENST00000399583.3	-	12	2699	c.2512G>A	c.(2512-2514)Gtg>Atg	p.V838M	RADIL_ENST00000536091.1_3'UTR|RADIL_ENST00000538469.1_Missense_Mutation_p.V598M	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	838					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)		TCAAGGACCACGTGGTGCATA	0.677													C|||	64	0.0127796	0.0015	0.0187	5008	,	,		13575	0.0		0.0249	False		,,,				2504	0.0245				p.V838M		Atlas-SNP	.											.	RADIL	110	.	0			c.G2512A						PASS	.	C	MET/VAL	10,3304		0,10,1647	5	6	6		2512	-3.5	0	7	dbSNP_132	6	139,6811		3,133,3339	yes	missense	RADIL	NM_018059.4	21	3,143,4986	TT,TC,CC		2.0,0.3018,1.4517	benign	838/1076	4841614	149,10115	1657	3475	5132	SO:0001583	missense	55698	exon12			GGACCACGTGGTG	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.2512G>A	7.37:g.4841614C>T	ENSP00000382492:p.Val838Met	66	0	0		78	33	0.423077	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	34	0.015567765567765568	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	19	0.025065963060686015	C	8.995	0.978733	0.18812	0.003018	0.02	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000544486;ENST00000538469	T;T	0.07114	3.29;3.22	4.15	-3.5	0.04710	.	0.941613	0.08946	N	0.870830	T	0.00815	0.0027	N	0.08118	0	0.09310	N	1	B;B	0.16396	0.017;0.004	B;B	0.06405	0.002;0.0	T	0.41645	-0.9497	10	0.51188	T	0.08	-1.412	5.9949	0.19489	0.0:0.1746:0.2538:0.5716	.	838;146	Q96JH8;Q75LH2	RADIL_HUMAN;.	M	838;809;572;598	ENSP00000382492:V838M;ENSP00000442966:V598M	ENSP00000320946:V809M	V	-	1	0	RADIL	4808140	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.693000	0.05121	-1.147000	0.02851	-1.340000	0.01251	GTG	C|0.984;T|0.016	0.016	strong		0.677	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059		T	4841614	C	T	4841614	3	4	25	1	0	0	0	0	1	0	0	0	13012	536	19	1	731	1	RADIL	7	4841614	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	10643	4841614	154297049	269	9178											
RADIL	55698	hgsc.bcm.edu	37	chr7	4843307	4843307	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agatgctgtcgtccaggcagTtggcttccaagtccacctgg	7	10	12	12	1	0	1	0	0	0	1	4	1	3	1	4	3	1	4	4	3	1	2	rs187128776	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4843307T>C	ENST00000399583.3	-	11	2556	c.2369A>G	c.(2368-2370)aAc>aGc	p.N790S	RADIL_ENST00000536091.1_3'UTR|RADIL_ENST00000538469.1_Missense_Mutation_p.N550S	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	790					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)		p.N790S(1)		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)		GTCCAGGCAGTTGGCTTCCAA	0.647													T|||	63	0.0125799	0.0015	0.0187	5008	,	,		11788	0.0		0.0239	False		,,,				2504	0.0245				p.N790S		Atlas-SNP	.											RADIL,brain,glioma,0,1	RADIL	110	1	1	Substitution - Missense(1)	central_nervous_system(1)	c.A2369G						PASS	.						19	26	24					7																	4843307		1977	4092	6069	SO:0001583	missense	55698	exon11			AGGCAGTTGGCTT	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.2369A>G	7.37:g.4843307T>C	ENSP00000382492:p.Asn790Ser	97	0	0		72	27	0.375	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	33	0.01510989010989011	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	18	0.023746701846965697	T	0.543	-0.852823	0.02630	.	.	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000544486;ENST00000538469	T;T	0.06449	3.37;3.3	4.27	3.12	0.35913	.	0.502188	0.20854	N	0.084468	T	0.00695	0.0023	N	0.08118	0	0.19300	N	0.999978	B;B	0.09022	0.0;0.002	B;B	0.01281	0.0;0.0	T	0.46925	-0.9156	10	0.23302	T	0.38	-15.6944	6.6406	0.22906	0.0:0.187:0.0:0.813	.	790;98	Q96JH8;Q75LH2	RADIL_HUMAN;.	S	790;761;524;550	ENSP00000382492:N790S;ENSP00000442966:N550S	ENSP00000320946:N761S	N	-	2	0	RADIL	4809833	0.936000	0.31750	0.004000	0.12327	0.026000	0.11368	3.515000	0.53429	0.692000	0.31613	0.459000	0.35465	AAC	T|0.985;C|0.015	0.015	strong		0.647	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059		C	4843307	T	C	4843307	3	2	25	1	0	0	0	0	1	0	0	0	13012	1725	60	3	878	3	RADIL	7	4843307	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	1693	4843307	154295356	270	9179											
RADIL	55698	hgsc.bcm.edu	37	chr7	4874729	4874729	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcctccccgcggcctggcCgctgtccgggagcggttgcc	2	6	15	18	5	0	0	0	0	0	0	2	1	2	1	7	4	3	2	7	4	0	1	rs144507770	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4874729C>G	ENST00000399583.3	-	4	1112	c.925G>C	c.(925-927)Ggc>Cgc	p.G309R	RADIL_ENST00000536091.1_Missense_Mutation_p.G309R|RADIL_ENST00000538469.1_Missense_Mutation_p.G69R	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	309					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)		GCGGCCTGGCCGCTGTCCGGG	0.711													C|||	60	0.0119808	0.0015	0.0173	5008	,	,		10553	0.0		0.0249	False		,,,				2504	0.0215				p.G309R		Atlas-SNP	.											.	RADIL	110	.	0			c.G925C						PASS	.	C	ARG/GLY	8,3996		0,8,1994	9	13	12		925	-1.8	0	7	dbSNP_134	12	168,8110		4,160,3975	yes	missense	RADIL	NM_018059.4	125	4,168,5969	GG,GC,CC		2.0295,0.1998,1.433	possibly-damaging	309/1076	4874729	176,12106	2002	4139	6141	SO:0001583	missense	55698	exon4			CCTGGCCGCTGTC	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.925G>C	7.37:g.4874729C>G	ENSP00000382492:p.Gly309Arg	27	0	0		41	21	0.512195	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	29	0.013278388278388278	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	18	0.023746701846965697	-	4.272	0.049630	0.08243	0.001998	0.020295	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000536091;ENST00000538469	T;T;T	0.06068	3.35;3.35;3.35	4.3	-1.83	0.07833	Forkhead-associated (FHA) domain (1);SMAD/FHA domain (1);	1.742530	0.03218	N	0.177080	T	0.02193	0.0068	L	0.40543	1.245	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.39643	-0.9604	10	0.18710	T	0.47	-0.7787	0.4916	0.00565	0.1804:0.2431:0.2692:0.3073	.	309	Q96JH8	RADIL_HUMAN	R	309;280;309;69	ENSP00000382492:G309R;ENSP00000442533:G309R;ENSP00000442966:G69R	ENSP00000320946:G280R	G	-	1	0	RADIL	4841255	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.164000	0.16542	-0.261000	0.09405	-0.759000	0.03464	GGC	C|0.987;G|0.013	0.013	strong		0.711	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059		G	4874729	C	G	4874729	3	3	25	1	0	0	0	0	1	0	0	0	13012	652	23	4	2350	4	RADIL	7	4874729	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	31422	4874729	154263934	271	9180											
RADIL	55698	hgsc.bcm.edu	37	chr7	4876064	4876064	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	taccgcatggcgtcggggccGggctcctcggggccctgggc	2	6	18	15	5	0	0	0	0	0	0	3	0	1	0	4	7	1	2	4	7	1	1	rs150209652	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4876064G>A	ENST00000399583.3	-	3	895	c.708C>T	c.(706-708)ccC>ccT	p.P236P	RADIL_ENST00000536091.1_Silent_p.P236P|RADIL_ENST00000538469.1_5'UTR	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	236					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)		CGTCGGGGCCGGGCTCCTCGG	0.706													G|||	60	0.0119808	0.0015	0.0173	5008	,	,		12929	0.0		0.0249	False		,,,				2504	0.0215				p.P236P		Atlas-SNP	.											.	RADIL	110	.	0			c.C708T						PASS	.	G		15,4077		0,15,2031	12	19	17		708	-9.7	0	7	dbSNP_134	17	196,8144		5,186,3979	no	coding-synonymous	RADIL	NM_018059.4		5,201,6010	AA,AG,GG		2.3501,0.3666,1.6972		236/1076	4876064	211,12221	2046	4170	6216	SO:0001819	synonymous_variant	55698	exon3			GGGGCCGGGCTCC	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.708C>T	7.37:g.4876064G>A		34	0	0		55	34	0.618182	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Silent	SNP	ENST00000399583.3	37	CCDS43544.1																																																																																			G|0.987;A|0.013	0.013	strong		0.706	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059		A	4876064	G	A	4876064	2	1	25	1	0	0	0	0	0	0	0	1	13012	1103	39	1		1	RADIL	7	4876064	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1335	4876064	154262599	272	9181											
RADIL	55698	hgsc.bcm.edu	37	chr7	4876100	4876100	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgggcggcagcgggcagggcGttcactgggctcaggctggt	4	7	20	10	3	2	0	2	0	0	0	2	0	2	0	0	7	1	5	0	7	0	1	rs138811640	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4876100G>A	ENST00000399583.3	-	3	859	c.672C>T	c.(670-672)aaC>aaT	p.N224N	RADIL_ENST00000536091.1_Silent_p.N224N|RADIL_ENST00000538469.1_De_novo_Start_OutOfFrame	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	224					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)		p.N224N(1)		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)		CGGGCAGGGCGTTCACTGGGC	0.721													G|||	60	0.0119808	0.0015	0.0173	5008	,	,		12942	0.0		0.0249	False		,,,				2504	0.0215				p.N224N		Atlas-SNP	.											RADIL,brain,glioma,0,2	RADIL	110	2	1	Substitution - coding silent(1)	lung(1)	c.C672T						PASS	.	G		16,4162		0,16,2073	11	18	16		672	0.3	0.1	7	dbSNP_134	16	205,8153		6,193,3980	no	coding-synonymous	RADIL	NM_018059.4		6,209,6053	AA,AG,GG		2.4527,0.383,1.7629		224/1076	4876100	221,12315	2089	4179	6268	SO:0001819	synonymous_variant	55698	exon3			CAGGGCGTTCACT	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.672C>T	7.37:g.4876100G>A		8	0	0		19	17	0.894737	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Silent	SNP	ENST00000399583.3	37	CCDS43544.1																																																																																			G|0.987;A|0.013	0.013	strong		0.721	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059		A	4876100	G	A	4876100	2	1	25	1	0	0	0	0	0	0	0	1	13012	1136	40	1		1	RADIL	7	4876100	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	36	4876100	154262563	273	9182											
WIPI2	26100	hgsc.bcm.edu	37	chr7	5257639	5257639	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	actaaacttgccacggcttcGgagaaggtgagtctgctttt	9	12	11	9	2	1	2	0	1	1	1	2	3	1	2	1	3	3	2	1	3	3	5	rs147063855	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:5257639G>A	ENST00000288828.4	+	7	895	c.663G>A	c.(661-663)tcG>tcA	p.S221S	WIPI2_ENST00000404704.3_Silent_p.S221S|WIPI2_ENST00000382384.2_Silent_p.S203S|WIPI2_ENST00000401525.3_Silent_p.S203S|WIPI2_ENST00000484262.1_Silent_p.S162S	NM_001033518.1|NM_001278299.1|NM_015610.3	NP_001028690.1|NP_001265228.1|NP_056425.1	Q9Y4P8	WIPI2_HUMAN	WD repeat domain, phosphoinositide interacting 2	221					autophagic vacuole assembly (GO:0000045)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|pre-autophagosomal structure (GO:0000407)|pre-autophagosomal structure membrane (GO:0034045)|protein complex (GO:0043234)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)	16		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0925)|OV - Ovarian serous cystadenocarcinoma(56;2.59e-14)		CCACGGCTTCGGAGAAGGTGA	0.537																																					p.S221S		Atlas-SNP	.											WIPI2,NS,carcinoma,+1,1	WIPI2	41	1	0			c.G663A						PASS	.	G	,,,,	0,4406		0,0,2203	125	116	119		663,609,486,663,609	-11.6	0.1	7	dbSNP_134	119	15,8585	11.2+/-40.8	0,15,4285	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WIPI2	NM_001033518.1,NM_001033519.1,NM_001033520.1,NM_015610.3,NM_016003.3	,,,,	0,15,6488	AA,AG,GG		0.1744,0.0,0.1153	,,,,	221/444,203/426,162/385,221/455,203/437	5257639	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	26100	exon7			GGCTTCGGAGAAG		CCDS5339.1, CCDS34593.1, CCDS47531.1, CCDS47532.1, CCDS47533.1	7p22.1	2014-02-12			ENSG00000157954	ENSG00000157954		"WD repeat domain containing"	32225	protein-coding gene	gene with protein product		609225				15602573	Standard	NM_001278299		Approved	Atg21, CGI-50, FLJ12979, FLJ14217, FLJ42984, DKFZP434J154, DKFZp686P02188, ATG18B	uc003snv.3	Q9Y4P8	OTTHUMG00000121179	ENST00000288828.4:c.663G>A	7.37:g.5257639G>A		130	0	0		171	84	0.491228	NM_015610	B3KNC2|Q5MNZ8|Q6FI96|Q75L50|Q96IE4|Q9Y364	Silent	SNP	ENST00000288828.4	37	CCDS5339.1																																																																																			G|0.999;A|0.001	0.001	strong		0.537	WIPI2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000241669.2	NM_015610		A	5257639	G	A	5257639	2	1	25	1	0	0	0	0	0	0	0	1	17386	1103	39	1		1	WIPI2	7	5257639	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	381539	5257639	153881024	274	9183											
PHF14	9678	hgsc.bcm.edu	37	chr7	11091329	11091330	+	Frame_Shift_Ins	INS	-	-	A																															atggaaccaaacgatcaaggINSaggcagattaaggaaccagt																										TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:11091329_11091330insA	ENST00000403050.3	+	14	2855_2856	c.2403_2404insA	c.(2404-2406)aggfs	p.R802fs	PHF14_ENST00000445996.2_Frame_Shift_Ins_p.R517fs	NM_014660.3	NP_055475.2	O94880	PHF14_HUMAN	PHD finger protein 14	802					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)		AACGATCAAGGAGGCAGATTAA	0.446																																					p.R801fs		Atlas-Indel	.											.	PHF14	90	.	0			c.2403_2404insA						PASS	.																																			SO:0001589	frameshift_variant	9678	exon14			.	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.2404dupA	7.37:g.11091330_11091330dupA	ENSP00000385795:p.Arg802fs	82	0	0		76	16	0.210526	NM_014660	A7MCZ3|B4DI82	Frame_Shift_Ins	INS	ENST00000403050.3	37	CCDS47542.1																																																																																			.	.	none		0.446	PHF14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318212.1	NM_014660		A	11091330	-	A	11091329	7	5	25	1	0	1	1	0	0	0	0	0	11834	1165	41	0	2457	0	PHF14	7	11091329	Frame_Shift_Ins	INS	-	TCGA-G8-6906-01A-11D-2210-10	5833690	11091329	148047334	275	9184											
PKD1L1	168507	hgsc.bcm.edu	37	chr7	47925520	47925520	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtcacgggtgaaggttccCgtgagaatggtgtggtcgtt	6	11	18	6	3	1	2	1	2	0	1	3	3	2	2	1	5	0	2	1	5	2	2	rs141646493	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:47925520C>T	ENST00000289672.2	-	18	3019	c.2969G>A	c.(2968-2970)cGg>cAg	p.R990Q		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	990	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						TGAAGGTTCCCGTGAGAATGG	0.587													c|||	9	0.00179712	0.0023	0.0029	5008	,	,		15149	0.0		0.004	False		,,,				2504	0.0				p.R990Q		Atlas-SNP	.											PKD1L1,colon,carcinoma,-1,1	PKD1L1	328	1	0			c.G2969A						scavenged	.	T	GLN/ARG	14,4392	22.3+/-47.3	0,14,2189	94	86	89		2969	-8.7	0	7	dbSNP_134	89	62,8538	39.8+/-96.3	1,60,4239	yes	missense	PKD1L1	NM_138295.3	43	1,74,6428	TT,TC,CC		0.7209,0.3177,0.5843	possibly-damaging	990/2850	47925520	76,12930	2203	4300	6503	SO:0001583	missense	168507	exon18			GGTTCCCGTGAGA	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.2969G>A	7.37:g.47925520C>T	ENSP00000289672:p.Arg990Gln	145	2	0.0137931		194	98	0.505155	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	5	0.0022893772893772895	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	c	5.043	0.193531	0.09599	0.003177	0.007209	ENSG00000158683	ENST00000289672	T	0.19938	2.11	4.97	-8.7	0.00851	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	165.707000	0.00166	N	0.000000	T	0.04588	0.0125	N	0.08118	0	0.09310	N	1	B	0.28605	0.217	B	0.14578	0.011	T	0.18366	-1.0339	10	0.19590	T	0.45	0.4961	1.9019	0.03269	0.1463:0.1646:0.3674:0.3217	.	990	Q8TDX9	PK1L1_HUMAN	Q	990	ENSP00000289672:R990Q	ENSP00000289672:R990Q	R	-	2	0	PKD1L1	47892045	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.006000	0.01459	-2.302000	0.00657	-0.835000	0.03068	CGG	C|0.995;T|0.005	0.005	strong		0.587	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295		T	47925520	C	T	47925520	3	4	25	1	0	0	0	0	1	0	0	0	11973	652	23	1	5740	1	PKD1L1	7	47925520	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	36834191	47925520	111213143	276	9185											
ABCA13	154664	hgsc.bcm.edu	37	chr7	48312084	48312084	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgaaccacaaaaacaagaaGttgataaaattttgactcac	19	9	5	8	0	1	4	1	3	0	1	1	4	1	4	1	0	2	1	1	0	7	4	rs78575608	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:48312084G>C	ENST00000435803.1	+	17	2845	c.2821G>C	c.(2821-2823)Gtt>Ctt	p.V941L		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	941					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						AAAACAAGAAGTTGATAAAAT	0.368													G|||	126	0.0251597	0.003	0.0202	5008	,	,		17420	0.0		0.0557	False		,,,				2504	0.0532				p.V941L		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G2821C						PASS	.	G	LEU/VAL	45,3611		0,45,1783	58	56	56		2821	-6.4	0	7	dbSNP_131	56	532,7648		14,504,3572	yes	missense	ABCA13	NM_152701.3	32	14,549,5355	CC,CG,GG		6.5037,1.2309,4.875	benign	941/5059	48312084	577,11259	1828	4090	5918	SO:0001583	missense	154664	exon17			CAAGAAGTTGATA	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.2821G>C	7.37:g.48312084G>C	ENSP00000411096:p.Val941Leu	214	0	0		200	85	0.425	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	47	0.02152014652014652	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	37	0.048812664907651716	G	4.662	0.123148	0.08931	0.012309	0.065037	ENSG00000179869	ENST00000435803	D	0.82984	-1.67	5.81	-6.43	0.01926	.	1.110050	0.06993	N	0.821921	T	0.09202	0.0227	N	0.16368	0.405	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.45775	-0.9238	10	0.05525	T	0.97	.	1.2609	0.02001	0.3788:0.2867:0.186:0.1485	.	941	Q86UQ4	ABCAD_HUMAN	L	941	ENSP00000411096:V941L	ENSP00000411096:V941L	V	+	1	0	ABCA13	48282630	0.000000	0.05858	0.000000	0.03702	0.986000	0.74619	-1.314000	0.02715	-0.919000	0.03803	0.655000	0.94253	GTT	G|0.974;C|0.026	0.026	strong		0.368	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		C	48312084	G	C	48312084	3	2	25	1	0	0	0	0	1	0	0	0	31	1029	36	4	2716	4	ABCA13	7	48312084	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	386564	48312084	110826579	277	9186											
ABCA13	154664	hgsc.bcm.edu	37	chr7	48318242	48318242	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	attagttggtgctatttcaaGagcaagtgaagaaagtcacg	14	11	11	5	1	2	3	2	1	0	2	2	3	2	3	0	1	2	3	0	1	6	4	rs79834369	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:48318242G>A	ENST00000435803.1	+	18	7475	c.7451G>A	c.(7450-7452)aGa>aAa	p.R2484K		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	2484					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						GCTATTTCAAGAGCAAGTGAA	0.393													G|||	10	0.00199681	0.0	0.0	5008	,	,		18633	0.0		0.0099	False		,,,				2504	0.0				p.R2484K		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G7451A						PASS	.	G	LYS/ARG	10,3654		0,10,1822	149	150	150		7451	0	0	7	dbSNP_132	150	73,8097		0,73,4012	yes	missense	ABCA13	NM_152701.3	26	0,83,5834	AA,AG,GG		0.8935,0.2729,0.7014	benign	2484/5059	48318242	83,11751	1832	4085	5917	SO:0001583	missense	154664	exon18			TTTCAAGAGCAAG	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.7451G>A	7.37:g.48318242G>A	ENSP00000411096:p.Arg2484Lys	108	0	0		100	54	0.54	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	9	0.004120879120879121	0	0.0	0	0.0	0	0.0	9	0.011873350923482849	G	9.467	1.094712	0.20471	0.002729	0.008935	ENSG00000179869	ENST00000435803	T	0.56611	0.45	4.11	-0.0121	0.13989	.	0.877287	0.09429	N	0.803261	T	0.24431	0.0592	N	0.24115	0.695	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.16158	-1.0412	10	0.27082	T	0.32	.	3.6594	0.08233	0.3281:0.191:0.4809:0.0	.	2484	Q86UQ4	ABCAD_HUMAN	K	2484	ENSP00000411096:R2484K	ENSP00000411096:R2484K	R	+	2	0	ABCA13	48288788	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	0.015000	0.13355	0.085000	0.17107	0.655000	0.94253	AGA	G|0.996;A|0.004	0.004	strong		0.393	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		A	48318242	G	A	48318242	3	1	25	1	0	0	0	0	1	0	0	0	31	942	33	2	7350	2	ABCA13	7	48318242	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	6158	48318242	110820421	278	9187											
EGFR	1956	hgsc.bcm.edu	37	chr7	55229255	55229255	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgctggggcccggagcccaGggactgcgtctcttgccgga	4	7	16	14	3	1	0	0	0	1	0	2	3	1	3	3	5	4	1	3	5	0	1	rs2227983	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:55229255G>A	ENST00000275493.2	+	13	1739	c.1562G>A	c.(1561-1563)aGg>aAg	p.R521K	EGFR_ENST00000454757.2_Missense_Mutation_p.R468K|EGFR_ENST00000455089.1_Missense_Mutation_p.R476K|EGFR_ENST00000442591.1_Missense_Mutation_p.R521K|EGFR_ENST00000342916.3_Missense_Mutation_p.R521K|EGFR_ENST00000344576.2_Missense_Mutation_p.R521K	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	521			R -> K (in dbSNP:rs2227983). {ECO:0000269|PubMed:17344846, ECO:0000269|Ref.7}.		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)	CCGGAGCCCAGGGACTGCGTC	0.617		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			G|||	1463	0.292133	0.0643	0.33	5008	,	,		17432	0.5238		0.2763	False		,,,				2504	0.3507				p.R521K		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.G1562A	GRCh37	CM942312	EGFR	M	rs2227983	PASS	.	G	LYS/ARG,LYS/ARG,LYS/ARG	391,4015	196.0+/-220.5	12,367,1824	111	114	113		1562,1562,1562	-5.8	0	7	dbSNP_98	113	2245,6355	380.6+/-339.7	317,1611,2372	yes	missense,missense,missense	EGFR	NM_005228.3,NM_201282.1,NM_201284.1	26,26,26	329,1978,4196	AA,AG,GG		26.1047,8.8743,20.2676	benign,benign,benign	521/1211,521/629,521/706	55229255	2636,10370	2203	4300	6503	SO:0001583	missense	1956	exon13	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	AGCCCAGGGACTG		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.1562G>A	7.37:g.55229255G>A	ENSP00000275493:p.Arg521Lys	69	0	0		65	65	1	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	CCDS5514.1	652	0.29853479853479853	29	0.05894308943089431	108	0.2983425414364641	302	0.527972027972028	213	0.28100263852242746	G	1.353	-0.590998	0.03799	0.088743	0.261047	ENSG00000146648	ENST00000455089;ENST00000342916;ENST00000395504;ENST00000344576;ENST00000275493;ENST00000442591;ENST00000454757;ENST00000533450	T;T;T;T;T;T	0.28069	1.63;1.63;1.63;1.63;1.63;1.63	6.07	-5.79	0.02354	Growth factor, receptor (1);	1.067450	0.06989	N	0.821201	T	0.00012	0.0000	N	0.16368	0.405	0.80722	P	0.0	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	0.48043	-0.9069	9	0.10377	T	0.69	.	2.4933	0.04615	0.5094:0.1722:0.17:0.1484	rs2227983;rs3752650;rs11543848;rs12234746;rs17336807;rs11543848	476;521;521;521	Q504U8;P00533;P00533-3;P00533-4	.;EGFR_HUMAN;.;.	K	476;521;391;521;521;521;468;315	ENSP00000415559:R476K;ENSP00000342376:R521K;ENSP00000345973:R521K;ENSP00000275493:R521K;ENSP00000410031:R521K;ENSP00000395243:R468K	ENSP00000275493:R521K	R	+	2	0	EGFR	55196749	0.000000	0.05858	0.000000	0.03702	0.265000	0.26407	-0.793000	0.04589	-1.106000	0.03008	-0.165000	0.13383	AGG	A|0.243;C|0.000;G|0.757;T|0.000	0.243	strong		0.617	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		A	55229255	G	A	55229255	3	1	25	1	0	0	0	0	1	0	0	0	4969	1000	35	2	1623	2	EGFR	7	55229255	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	6911013	55229255	103909408	279	9188											
EGFR	1956	hgsc.bcm.edu	37	chr7	55238874	55238874	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcacttcctacagatgcacTgggccaggtcttgaaggctg	8	11	11	11	0	2	2	1	1	1	1	3	2	3	2	2	3	2	2	2	3	2	4	rs2227984	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:55238874T>A	ENST00000275493.2	+	16	2064	c.1887T>A	c.(1885-1887)acT>acA	p.T629T	EGFR_ENST00000454757.2_Silent_p.T576T|EGFR_ENST00000455089.1_Silent_p.T584T|EGFR_ENST00000442591.1_Silent_p.T629T	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	629					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)	ACAGATGCACTGGGCCAGGTC	0.398		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			T|||	1955	0.390375	0.2678	0.3977	5008	,	,		21298	0.5347		0.3559	False		,,,				2504	0.4376				p.T629T		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.T1887A						PASS	.	T		1213,3193	422.3+/-339.7	168,877,1158	135	120	125		1887	-5.9	0	7	dbSNP_123	125	2981,5619	461.9+/-365.5	537,1907,1856	no	coding-synonymous	EGFR	NM_005228.3		705,2784,3014	AA,AT,TT		34.6628,27.5306,32.2467		629/1211	55238874	4194,8812	2203	4300	6503	SO:0001819	synonymous_variant	1956	exon16	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	ATGCACTGGGCCA		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.1887T>A	7.37:g.55238874T>A		65	0	0		54	54	1	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																			T|0.645;A|0.355	0.355	strong		0.398	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		A	55238874	T	A	55238874	2	1	25	1	0	0	0	0	0	0	0	1	4969	1567	55	5		5	EGFR	7	55238874	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	9619	55238874	103899789	280	9189											
EGFR	1956	hgsc.bcm.edu	37	chr7	55259450	55259450	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccgtcgcttggtgcaccgCgacctggcagccaggaacgt	7	6	14	14	5	0	0	0	0	0	0	1	3	0	1	4	3	3	3	4	3	1	1	rs2229066	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:55259450C>T	ENST00000275493.2	+	21	2685	c.2508C>T	c.(2506-2508)cgC>cgT	p.R836R	EGFR-AS1_ENST00000442411.1_RNA|EGFR_ENST00000454757.2_Silent_p.R783R|EGFR_ENST00000455089.1_Silent_p.R791R|EGFR_ENST00000442591.1_Intron	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	836	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.R836R(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)	TGGTGCACCGCGACCTGGCAG	0.542		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			C|||	27	0.00539137	0.0008	0.0058	5008	,	,		20375	0.0		0.0169	False		,,,				2504	0.0051				p.R836R		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,0,8	EGFR	20426	8	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C2508T						scavenged	.	C		25,4381	31.7+/-61.6	0,25,2178	112	97	102		2508	-11.6	0	7	dbSNP_123	102	196,8404	86.9+/-149.2	3,190,4107	no	coding-synonymous	EGFR	NM_005228.3		3,215,6285	TT,TC,CC		2.2791,0.5674,1.6992		836/1211	55259450	221,12785	2203	4300	6503	SO:0001819	synonymous_variant	1956	exon21	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	GCACCGCGACCTG		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.2508C>T	7.37:g.55259450C>T		20	0	0		19	3	0.157895	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																			C|0.986;T|0.014	0.014	strong		0.542	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		T	55259450	C	T	55259450	2	4	25	1	0	0	0	0	0	0	0	1	4969	755	27	1		1	EGFR	7	55259450	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	20576	55259450	103879213	281	9190											
ZNF713	349075	hgsc.bcm.edu	37	chr7	56007498	56007498	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaatgtggtttctgtggcaaAgccttcagtcagaggacaca	11	10	12	8	0	3	1	2	0	1	1	3	3	3	2	1	3	1	2	1	3	2	2	rs112798657	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:56007498A>G	ENST00000429591.2	+	4	1130	c.1092A>G	c.(1090-1092)aaA>aaG	p.K364K	MRPS17_ENST00000426595.1_Intron	NM_182633.1	NP_872439.1	Q8N859	ZN713_HUMAN	zinc finger protein 713	364					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)			TCTGTGGCAAAGCCTTCAGTC	0.423													A|||	6	0.00119808	0.0	0.0029	5008	,	,		18360	0.0		0.002	False		,,,				2504	0.002				p.K364K		Atlas-SNP	.											.	ZNF713	47	.	0			c.A1092G						PASS	.	A		2,4404	4.2+/-10.8	0,2,2201	65	66	66		1092	0.8	1	7	dbSNP_132	66	20,8580	14.0+/-48.4	0,20,4280	no	coding-synonymous	ZNF713	NM_182633.1		0,22,6481	GG,GA,AA		0.2326,0.0454,0.1692		364/431	56007498	22,12984	2203	4300	6503	SO:0001819	synonymous_variant	349075	exon4			TGGCAAAGCCTTC	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.1092A>G	7.37:g.56007498A>G		63	0	0		72	41	0.569444	NM_182633		Silent	SNP	ENST00000429591.2	37	CCDS34639.1																																																																																			A|0.998;G|0.002	0.002	strong		0.423	ZNF713-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343297.1	NM_182633		G	56007498	A	G	56007498	2	3	25	1	0	0	0	0	0	0	0	1	18132	69	3	3		3	ZNF713	7	56007498	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	748048	56007498	103131165	282	9191											
DTX2	113878	hgsc.bcm.edu	37	chr7	76112299	76112299	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccaggcctttgcaccgtacaAcaaaccctcactctccgggg	9	7	8	17	2	2	0	1	0	1	0	3	0	2	0	5	3	4	2	5	3	3	2	rs145151450	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:76112299A>G	ENST00000324432.5	+	5	1253	c.743A>G	c.(742-744)aAc>aGc	p.N248S	DTX2_ENST00000446600.1_Missense_Mutation_p.N157S|DTX2_ENST00000413936.2_Missense_Mutation_p.N248S|DTX2_ENST00000307569.8_Missense_Mutation_p.N248S|DTX2_ENST00000446820.2_Missense_Mutation_p.N248S|DTX2_ENST00000430490.2_Missense_Mutation_p.N248S	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	248					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						GCACCGTACAACAAACCCTCA	0.672													.|||	11	0.00219649	0.0	0.0029	5008	,	,		18951	0.001		0.008	False		,,,				2504	0.0				p.N248S		Atlas-SNP	.											.	DTX2	64	.	0			c.A743G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN,SER/ASN	3,4403		0,3,2200	151	159	157		743,743,743,743	1.4	1	7	dbSNP_134	157	46,8554		0,46,4254	yes	missense,missense,missense,missense	DTX2	NM_001102594.1,NM_001102595.1,NM_001102596.1,NM_020892.2	46,46,46,46	0,49,6454	GG,GA,AA		0.5349,0.0681,0.3767	benign,benign,benign,benign	248/623,248/623,248/576,248/623	76112299	49,12957	2203	4300	6503	SO:0001583	missense	113878	exon2			CGTACAACAAACC		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.743A>G	7.37:g.76112299A>G	ENSP00000322885:p.Asn248Ser	329	1	0.00303951		266	116	0.43609	NM_001102596	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Missense_Mutation	SNP	ENST00000324432.5	37	CCDS5587.1	4	0.0018315018315018315	0	0.0	0	0.0	2	0.0034965034965034965	2	0.002638522427440633	.	0.016	-1.528964	0.00951	6.81E-4	0.005349	ENSG00000091073	ENST00000324432;ENST00000307569;ENST00000541989;ENST00000446600;ENST00000413936;ENST00000430490;ENST00000446820	T;T;T;T;T;T	0.10668	2.85;2.86;2.85;2.85;2.85;2.86	5.18	1.39	0.22231	.	0.598456	0.18389	N	0.142736	T	0.02688	0.0081	N	0.08118	0	0.24585	N	0.993856	B;B;B	0.11235	0.004;0.001;0.0	B;B;B	0.12837	0.006;0.008;0.002	T	0.45716	-0.9242	10	0.08381	T	0.77	-14.9182	6.4167	0.21719	0.5953:0.1273:0.2774:0.0	.	157;248;248	F5GX89;Q86UW9-2;Q86UW9	.;.;DTX2_HUMAN	S	248;248;157;157;248;248;248	ENSP00000322885:N248S;ENSP00000305242:N248S;ENSP00000397648:N157S;ENSP00000390218:N248S;ENSP00000411986:N248S;ENSP00000392545:N248S	ENSP00000305242:N248S	N	+	2	0	AC005522.1	75950235	0.994000	0.37717	0.993000	0.49108	0.282000	0.26991	0.532000	0.23067	0.005000	0.14708	-1.447000	0.01057	AAC	A|0.997;G|0.003	0.003	strong		0.672	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2			G	76112299	A	G	76112299	3	3	25	1	0	0	0	0	1	0	0	0	4796	43	2	3	749	3	DTX2	7	76112299	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	20104801	76112299	83026364	283	9192											
PCLO	27445	hgsc.bcm.edu	37	chr7	82785304	82785304	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtccttgctgcttaggaatcGgcttgggtggctgttgttgt	3	16	15	7	1	0	0	0	0	0	0	2	1	1	1	1	4	2	6	1	4	2	5	rs61738783	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:82785304G>A	ENST00000333891.9	-	2	990	c.653C>T	c.(652-654)cCg>cTg	p.P218L	PCLO_ENST00000423517.2_Missense_Mutation_p.P218L	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						CTTAGGAATCGGCTTGGGTGG	0.443													G|||	27	0.00539137	0.0	0.0043	5008	,	,		18249	0.0		0.0169	False		,,,				2504	0.0072				p.P218L		Atlas-SNP	.											Q9Y6V0-3,NS,carcinoma,+1,5	PCLO	1506	5	0			c.C653T						PASS	.	G	LEU/PRO,LEU/PRO	11,3805		0,11,1897	83	88	86		653,653	4.6	0	7	dbSNP_129	86	141,8103		0,141,3981	yes	missense,missense	PCLO	NM_033026.5,NM_014510.2	98,98	0,152,5878	AA,AG,GG		1.7103,0.2883,1.2604	benign,benign	218/5143,218/4936	82785304	152,11908	1908	4122	6030	SO:0001583	missense	27445	exon2			GGAATCGGCTTGG	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.653C>T	7.37:g.82785304G>A	ENSP00000334319:p.Pro218Leu	235	1	0.00425532		238	134	0.563025	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	19	0.0086996336996337	0	0.0	3	0.008287292817679558	0	0.0	16	0.021108179419525065	G	4.810	0.150680	0.09185	0.002883	0.017103	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.16196	2.36;2.37	5.48	4.59	0.56863	.	.	.	.	.	T	0.06645	0.0170	N	0.22421	0.69	0.24930	N	0.991927	B;B	0.16396	0.017;0.017	B;B	0.08055	0.003;0.003	T	0.15464	-1.0436	9	0.87932	D	0	.	12.7097	0.57082	0.1393:0.0:0.8607:0.0	.	218;218	Q9Y6V0-5;Q9Y6V0-6	.;.	L	218	ENSP00000334319:P218L;ENSP00000388393:P218L	ENSP00000334319:P218L	P	-	2	0	PCLO	82623240	0.613000	0.27009	0.002000	0.10522	0.071000	0.16799	4.026000	0.57232	1.301000	0.44836	0.655000	0.94253	CCG	G|0.989;A|0.011	0.011	strong		0.443	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		A	82785304	G	A	82785304	3	1	25	1	0	0	0	0	1	0	0	0	11592	1116	39	1	14888	1	PCLO	7	82785304	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	6673005	82785304	76353359	284	9193											
ANKIB1	54467	hgsc.bcm.edu	37	chr7	92027064	92027064	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agaaggcggcagcagcagccGcaggcctggcacatccgtgg	9	3	16	13	3	0	1	0	0	0	1	1	1	1	1	3	5	3	5	3	5	1	0	rs200132000		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:92027064G>T	ENST00000265742.3	+	19	2799	c.2423G>T	c.(2422-2424)cGc>cTc	p.R808L		NM_019004.1	NP_061877.1	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	808							zinc ion binding (GO:0008270)	p.R808L(1)		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)			AGCAGCAGCCGCAGGCCTGGC	0.473																																					p.R808L		Atlas-SNP	.											ANKIB1,NS,carcinoma,0,1	ANKIB1	92	1	1	Substitution - Missense(1)	lung(1)	c.G2423T						PASS	.						153	164	161					7																	92027064		1949	4164	6113	SO:0001583	missense	54467	exon19			GCAGCCGCAGGCC	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.2423G>T	7.37:g.92027064G>T	ENSP00000265742:p.Arg808Leu	59	0	0		63	33	0.52381	NM_019004	Q6GMS4|Q6P3S9|Q9NTD7|Q9NW49	Missense_Mutation	SNP	ENST00000265742.3	37	CCDS47639.1	.	.	.	.	.	.	.	.	.	.	G	16.98	3.271294	0.59649	.	.	ENSG00000001629	ENST00000265742	T	0.10763	2.84	5.87	3.91	0.45181	.	0.335987	0.35615	N	0.003097	T	0.11367	0.0277	L	0.29908	0.895	0.46823	D	0.999216	P;P	0.35551	0.509;0.465	B;B	0.40165	0.321;0.069	T	0.07028	-1.0794	10	0.87932	D	0	.	12.8561	0.57886	0.1408:0.0:0.8592:0.0	.	160;808	Q4VBX8;Q9P2G1	.;AKIB1_HUMAN	L	808	ENSP00000265742:R808L	ENSP00000265742:R808L	R	+	2	0	ANKIB1	91865000	1.000000	0.71417	0.999000	0.59377	0.817000	0.46193	1.255000	0.32909	0.816000	0.34421	0.655000	0.94253	CGC	.	.	alt		0.473	ANKIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342018.1			T	92027064	G	T	92027064	3	4	25	1	0	0	0	0	1	0	0	0	630	1087	38	4	2493	4	ANKIB1	7	92027064	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	9241760	92027064	67111599	285	9194											
SAMD9	54809	hgsc.bcm.edu	37	chr7	92730687	92730687	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gtgggcctccaatggaaaatCccaggtaaaaagacaccttc	14	7	9	11	0	0	1	0	0	0	1	3	2	2	2	4	3	0	1	4	3	6	2	rs148724199	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:92730687C>T	ENST00000379958.2	-	3	4993	c.4724G>A	c.(4723-4725)gGa>gAa	p.G1575E		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	1575						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)			AATGGAAAATCCCAGGTAAAA	0.368																																					p.G1575E		Atlas-SNP	.											.	SAMD9	239	.	0			c.G4724A						PASS	.	C	GLU/GLY,GLU/GLY	1,4405	2.1+/-5.4	0,1,2202	126	133	131		4724,4724	4.4	1	7	dbSNP_134	131	7,8591	5.7+/-21.5	0,7,4292	yes	missense,missense	SAMD9	NM_001193307.1,NM_017654.3	98,98	0,8,6494	TT,TC,CC		0.0814,0.0227,0.0615	probably-damaging,probably-damaging	1575/1590,1575/1590	92730687	8,12996	2203	4299	6502	SO:0001583	missense	54809	exon2			GAAAATCCCAGGT	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.4724G>A	7.37:g.92730687C>T	ENSP00000369292:p.Gly1575Glu	66	0	0		64	28	0.4375	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	37	CCDS34680.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.106178	0.77096	2.27E-4	8.14E-4	ENSG00000205413	ENST00000379958	T	0.77750	-1.12	4.44	4.44	0.53790	.	0.000000	0.64402	U	0.000003	D	0.86176	0.5870	M	0.62723	1.935	0.51482	D	0.999924	D	0.89917	1.0	D	0.91635	0.999	D	0.87750	0.2591	10	0.87932	D	0	.	16.1321	0.81446	0.0:1.0:0.0:0.0	.	1575	Q5K651	SAMD9_HUMAN	E	1575	ENSP00000369292:G1575E	ENSP00000369292:G1575E	G	-	2	0	SAMD9	92568623	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.170000	0.77587	2.478000	0.83669	0.609000	0.83330	GGA	C|0.999;T|0.001	0.001	strong		0.368	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		T	92730687	C	T	92730687	3	4	25	1	0	0	0	0	1	0	0	0	13841	855	30	2	49	2	SAMD9	7	92730687	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	703623	92730687	66407976	286	9195											
PON1	5444	hgsc.bcm.edu	37	chr7	94940880	94940880	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttcaccaccaggaggtacAtggcattatctgagaggaga	12	8	13	8	0	2	2	1	1	1	2	2	5	2	3	2	5	1	3	2	5	2	3	rs144390653	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:94940880A>C	ENST00000222381.3	-	5	611	c.380T>G	c.(379-381)aTg>aGg	p.M127R	PON1_ENST00000542556.1_Missense_Mutation_p.M127R	NM_000446.5	NP_000437.3	P27169	PON1_HUMAN	paraoxonase 1	127					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)	p.M127R(1)		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)	CAGGAGGTACATGGCATTATC	0.403													A|||	13	0.00259585	0.0	0.0072	5008	,	,		18834	0.0		0.002	False		,,,				2504	0.0061				p.M127R	GBM(119;715 1622 17358 22490 33240)	Atlas-SNP	.											PON1,NS,carcinoma,0,1	PON1	55	1	1	Substitution - Missense(1)	pancreas(1)	c.T380G						PASS	.	A	ARG/MET	1,4405	2.1+/-5.4	0,1,2202	115	108	111		380	4.9	0.6	7	dbSNP_134	111	12,8588	8.4+/-32.0	0,12,4288	yes	missense	PON1	NM_000446.5	91	0,13,6490	CC,CA,AA		0.1395,0.0227,0.1	benign	127/356	94940880	13,12993	2203	4300	6503	SO:0001583	missense	5444	exon5			AGGTACATGGCAT	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.380T>G	7.37:g.94940880A>C	ENSP00000222381:p.Met127Arg	81	0	0		52	29	0.557692	NM_000446	B2RA40|Q16052|Q6B0J6|Q9UCB1	Missense_Mutation	SNP	ENST00000222381.3	37	CCDS5638.1	7	0.003205128205128205	0	0.0	5	0.013812154696132596	0	0.0	2	0.002638522427440633	A	10.59	1.391561	0.25118	2.27E-4	0.001395	ENSG00000005421	ENST00000222381;ENST00000542556	T;T	0.39406	1.08;1.08	4.88	4.88	0.63580	Six-bladed beta-propeller, TolB-like (1);	0.186666	0.47093	D	0.000258	T	0.20536	0.0494	N	0.08118	0	0.33135	D	0.543587	B;B	0.18741	0.03;0.005	B;B	0.25614	0.062;0.017	T	0.36065	-0.9763	10	0.87932	D	0	-9.4635	14.9578	0.71131	1.0:0.0:0.0:0.0	.	127;127	F5H4W9;P27169	.;PON1_HUMAN	R	127	ENSP00000222381:M127R;ENSP00000444854:M127R	ENSP00000222381:M127R	M	-	2	0	PON1	94778816	0.997000	0.39634	0.588000	0.28705	0.083000	0.17756	8.294000	0.89934	2.187000	0.69744	0.533000	0.62120	ATG	A|0.998;C|0.002	0.002	strong		0.403	PON1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000332865.2	NM_000446		C	94940880	A	C	94940880	3	2	25	1	0	0	0	0	1	0	0	0	12257	217	8	5	707	5	PON1	7	94940880	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	2210193	94940880	64197783	287	9196											
TRRAP	8295	hgsc.bcm.edu	37	chr7	98592335	98592335	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgaagaagttggtgagcacGtttggggtgggcctggagaa	9	9	19	4	1	0	4	0	2	0	2	0	5	0	4	1	5	1	3	1	5	3	2	rs56282945		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:98592335G>A	ENST00000359863.4	+	66	10340	c.10131G>A	c.(10129-10131)acG>acA	p.T3377T	TRRAP_ENST00000446306.3_Silent_p.T3366T|TRRAP_ENST00000355540.3_Silent_p.T3348T	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	3377					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)			TGGTGAGCACGTTTGGGGTGG	0.567													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18543	0.0		0.0	False		,,,				2504	0.0				p.T3377T		Atlas-SNP	.											.	TRRAP	863	.	0			c.G10131A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	187	180	182		10044	-9.6	0.1	7	dbSNP_129	182	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TRRAP	NM_003496.3		0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231		3348/3831	98592335	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	8295	exon66			GAGCACGTTTGGG	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.10131G>A	7.37:g.98592335G>A		152	0	0		171	76	0.444444	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Silent	SNP	ENST00000359863.4	37	CCDS59066.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	8.130	0.782960	0.16189	2.27E-4	2.33E-4	ENSG00000196367	ENST00000456197	.	.	.	5.29	-9.63	0.00544	.	.	.	.	.	T	0.35248	0.0925	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42582	-0.9443	4	.	.	.	.	3.8434	0.08925	0.5236:0.2218:0.107:0.1476	rs56282945	.	.	.	H	3106	.	.	R	+	2	0	TRRAP	98430271	0.000000	0.05858	0.094000	0.20943	0.949000	0.60115	-2.691000	0.00830	-1.767000	0.01300	-0.502000	0.04539	CGT	G|1.000;A|0.000	0.000	strong		0.567	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496		A	98592335	G	A	98592335	2	1	25	1	0	0	0	0	0	0	0	1	16616	1132	40	1		1	TRRAP	7	98592335	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	3651455	98592335	60546328	288	9197											
PTCD1	26024	hgsc.bcm.edu	37	chr7	99022873	99022873	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggtggcttcagggccactgCggtgagggctgctgtgtggc	4	9	19	9	1	1	1	1	1	0	0	1	1	1	1	1	6	2	3	1	6	0	1	rs147045279	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:99022873C>T	ENST00000292478.4	-	6	1532	c.1282G>A	c.(1282-1284)Gca>Aca	p.A428T	ATP5J2-PTCD1_ENST00000413834.1_Missense_Mutation_p.A477T|PTCD1_ENST00000555673.1_Missense_Mutation_p.A477T	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	428					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)			AGGGCCACTGCGGTGAGGGCT	0.662													G|||	11	0.00219649	0.0	0.0	5008	,	,		17554	0.0		0.001	False		,,,				2504	0.0102				p.A477T		Atlas-SNP	.											.	.	.	.	0			c.G1429A						PASS	.	G	THR/ALA,THR/ALA	2,4404		0,2,2201	96	96	96		1429,1282	2.8	0	7	dbSNP_134	96	13,8587		0,13,4287	yes	missense,missense	PTCD1,ATP5J2-PTCD1	NM_001198879.1,NM_015545.3	58,58	0,15,6488	TT,TC,CC		0.1512,0.0454,0.1153	benign,benign	477/750,428/701	99022873	15,12991	2203	4300	6503	SO:0001583	missense	100526740	exon7			CCACTGCGGTGAG	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.1282G>A	7.37:g.99022873C>T	ENSP00000292478:p.Ala428Thr	78	0	0		92	51	0.554348	NM_001198879	Q3ZB78|Q66K60|Q9UDV2	Missense_Mutation	SNP	ENST00000292478.4	37	CCDS34691.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	9.484	1.098951	0.20552	4.54E-4	0.001512	ENSG00000106246;ENSG00000106246;ENSG00000106246;ENSG00000248919	ENST00000292478;ENST00000438524;ENST00000555673;ENST00000413834	T;T;T	0.64803	-0.12;-0.09;-0.09	5.66	2.75	0.32379	.	0.719311	0.14379	N	0.323285	T	0.38719	0.1051	N	0.14661	0.345	0.09310	N	1	B;B	0.21753	0.06;0.036	B;B	0.18263	0.021;0.005	T	0.20806	-1.0264	10	0.15952	T	0.53	-2.2895	6.6526	0.22971	0.3204:0.1307:0.5489:0.0	.	477;428	G3V325;O75127	.;PTCD1_HUMAN	T	428;210;477;477	ENSP00000292478:A428T;ENSP00000450995:A477T;ENSP00000400168:A477T	ENSP00000400168:A477T	A	-	1	0	ATP5J2-PTCD1;PTCD1	98860809	0.005000	0.15991	0.015000	0.15790	0.007000	0.05969	0.090000	0.15025	0.275000	0.22094	-0.216000	0.12614	GCA	C|1.000;T|0.000	0.000	strong		0.662	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1	NM_015545		T	99022873	C	T	99022873	3	4	25	1	0	0	0	0	1	0	0	0	12739	768	27	1	832	1	PTCD1	7	99022873	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	430538	99022873	60115790	289	9198											
PTCD1	26024	hgsc.bcm.edu	37	chr7	99032559	99032559	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaactgggctgcggatttgcGgaatagtctccgggaggagt	8	9	17	7	3	1	0	0	0	1	0	2	5	1	4	1	5	3	1	1	5	3	2	rs150504114	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:99032559G>A	ENST00000292478.4	-	2	557	c.307C>T	c.(307-309)Cgc>Tgc	p.R103C	ATP5J2-PTCD1_ENST00000413834.1_Missense_Mutation_p.R152C|ATP5J2-PTCD1_ENST00000437572.1_5'Flank|PTCD1_ENST00000485746.1_5'UTR|PTCD1_ENST00000555673.1_Missense_Mutation_p.R152C	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	103					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)			GCGGATTTGCGGAATAGTCTC	0.577													G|||	36	0.0071885	0.0	0.0259	5008	,	,		19143	0.0		0.0089	False		,,,				2504	0.0092				p.R152C		Atlas-SNP	.											.	.	.	.	0			c.C454T						PASS	.	G	CYS/ARG,CYS/ARG	15,4391	22.3+/-47.3	0,15,2188	127	136	133		454,307	6	0.9	7	dbSNP_134	133	121,8479	63.5+/-125.6	1,119,4180	yes	missense,missense	PTCD1,ATP5J2-PTCD1	NM_001198879.1,NM_015545.3	180,180	1,134,6368	AA,AG,GG		1.407,0.3404,1.0457	probably-damaging,probably-damaging	152/750,103/701	99032559	136,12870	2203	4300	6503	SO:0001583	missense	100526740	exon3			ATTTGCGGAATAG	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.307C>T	7.37:g.99032559G>A	ENSP00000292478:p.Arg103Cys	144	0	0		137	76	0.554745	NM_001198879	Q3ZB78|Q66K60|Q9UDV2	Missense_Mutation	SNP	ENST00000292478.4	37	CCDS34691.1	15	0.006868131868131868	0	0.0	13	0.03591160220994475	0	0.0	2	0.002638522427440633	G	16.59	3.166435	0.57476	0.003404	0.01407	ENSG00000106246;ENSG00000106246;ENSG00000106246;ENSG00000106246;ENSG00000106246;ENSG00000248919	ENST00000292478;ENST00000555673;ENST00000430982;ENST00000430029;ENST00000419981;ENST00000413834	T;T;D;D;D;T	0.85556	-0.23;-0.21;-2.0;-1.99;-1.87;-0.21	5.97	5.97	0.96955	.	0.496389	0.23896	N	0.043488	T	0.70824	0.3268	M	0.63843	1.955	0.31971	N	0.607147	D;D	0.71674	0.998;0.996	P;P	0.55667	0.781;0.564	D	0.83520	0.0085	10	0.62326	D	0.03	-2.9079	15.1788	0.72938	0.0:0.0:0.859:0.1409	.	152;103	G3V325;O75127	.;PTCD1_HUMAN	C	103;152;103;103;103;152	ENSP00000292478:R103C;ENSP00000450995:R152C;ENSP00000390530:R103C;ENSP00000408059:R103C;ENSP00000401600:R103C;ENSP00000400168:R152C	ENSP00000400168:R152C	R	-	1	0	ATP5J2-PTCD1;PTCD1	98870495	1.000000	0.71417	0.924000	0.36721	0.089000	0.18198	5.560000	0.67332	2.837000	0.97791	0.655000	0.94253	CGC	G|0.991;A|0.009	0.009	strong		0.577	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1	NM_015545		A	99032559	G	A	99032559	3	1	25	1	0	0	0	0	1	0	0	0	12739	1116	39	1	1823	1	PTCD1	7	99032559	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	9686	99032559	60106104	290	9199											
CYP3A5	1577	hgsc.bcm.edu	37	chr7	99273810	99273811	+	Frame_Shift_Ins	INS	-	-	C																															ttcccagtctcttaaaaagtINSccatgtgtacgggtcccata																								rs200579169|rs28383469	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:99273810_99273811insC	ENST00000222982.4	-	2	191_192	c.92_93insG	c.(91-93)ggafs	p.G31fs	CYP3A5_ENST00000439761.1_Frame_Shift_Ins_p.G31fs|CYP3A5_ENST00000480723.1_5'UTR|CYP3A5_ENST00000343703.5_Frame_Shift_Ins_p.G21fs|CYP3A5_ENST00000339843.2_3'UTR	NM_000777.3	NP_000768.1	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 5	31					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)	TCTTAAAAAGTCCATGTGTACG	0.46													CC|CC|CCC|insertion	17	0.00339457	0.0	0.0014	5008	,	,		20943	0.0		0.0119	False		,,,				2504	0.0041				p.G31fs		Pindel,Atlas-Indel	.											.	CYP3A5	46	.	0			c.93_94insG	GRCh37	CI067571	CYP3A5	I		PASS	.		,	6,4258		0,6,2126					,	-4.4	0		dbSNP_125	108	77,8175		0,77,4049	no	frameshift,frameshift	CYP3A5	NM_001190484.1,NM_000777.3	,	0,83,6175	A1A1,A1R,RR		0.9331,0.1407,0.6632	,	,		83,12433				SO:0001589	frameshift_variant	1577	exon2			.	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.93dupG	7.37:g.99273812_99273812dupC	ENSP00000222982:p.Gly31fs	92	0	.		127	38	0.299	NM_001190484	A4D289|B7Z5I7|Q53WY8|Q75MV0|Q9HB56	Frame_Shift_Ins	INS	ENST00000222982.4	37	CCDS5672.1																																																																																			-|0.994;C|0.006	0.006	strong		0.46	CYP3A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345469.1			C	99273811	-	C	99273810	7	5	25	1	0	1	1	0	0	0	0	0	4182	1654	58	0	1463	0	CYP3A5	7	99273810	Frame_Shift_Ins	INS	-	TCGA-G8-6906-01A-11D-2210-10	241251	99273810	59864853	291	9200	113	2									
CYP3A5	1577	hgsc.bcm.edu	37	chr7	99273815	99273815	+	Missense_Mutation	SNP	G	G	A																															cagtctcttaaaaagtccatGtgtacgggtcccatatctac																								rs28383468	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:99273815G>A	ENST00000222982.4	-	2	187	c.88C>T	c.(88-90)Cat>Tat	p.H30Y	CYP3A5_ENST00000439761.1_Missense_Mutation_p.H30Y|CYP3A5_ENST00000480723.1_5'UTR|CYP3A5_ENST00000343703.5_Missense_Mutation_p.H20Y|CYP3A5_ENST00000339843.2_3'UTR	NM_000777.3	NP_000768.1	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 5	30			H -> Y (in dbSNP:rs28383468). {ECO:0000269|PubMed:15469410}.		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)	AAAAGTCCATGTGTACGGGTC	0.463													G|||	17	0.00339457	0.0	0.0014	5008	,	,		20808	0.0		0.0119	False		,,,				2504	0.0041				p.H30Y		Atlas-SNP	.											.	CYP3A5	46	.	0			c.C88T						PASS	.	G	TYR/HIS,TYR/HIS	6,4400	11.4+/-27.6	0,6,2197	110	100	104		88,88	1.9	0	7	dbSNP_125	104	82,8518	48.1+/-107.5	0,82,4218	yes	missense,missense	CYP3A5	NM_000777.3,NM_001190484.1	83,83	0,88,6415	AA,AG,GG		0.9535,0.1362,0.6766	,	30/503,30/141	99273815	88,12918	2203	4300	6503	SO:0001583	missense	1577	exon2			GTCCATGTGTACG	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.88C>T	7.37:g.99273815G>A	ENSP00000222982:p.His30Tyr	88	0	0		124	50	0.403226	NM_001190484	A4D289|B7Z5I7|Q53WY8|Q75MV0|Q9HB56	Missense_Mutation	SNP	ENST00000222982.4	37	CCDS5672.1	13	0.005952380952380952	0	0.0	4	0.011049723756906077	0	0.0	9	0.011873350923482849	G	0.239	-1.015455	0.02078	0.001362	0.009535	ENSG00000106258	ENST00000222982;ENST00000343703;ENST00000439761	T;T;T	0.08896	3.04;3.04;3.04	3.78	1.87	0.25490	.	0.279306	0.35320	N	0.003281	T	0.04048	0.0113	L	0.34521	1.04	0.09310	N	0.999998	B;B;B	0.14012	0.002;0.009;0.004	B;B;B	0.21151	0.021;0.033;0.012	T	0.42068	-0.9473	10	0.19147	T	0.46	.	8.2763	0.31874	0.2274:0.0:0.7726:0.0	rs28383468;rs59353336	20;30;30	F5H4S0;B7Z5I7;P20815	.;.;CP3A5_HUMAN	Y	30;20;30	ENSP00000222982:H30Y;ENSP00000342969:H20Y;ENSP00000401269:H30Y	ENSP00000222982:H30Y	H	-	1	0	CYP3A5	99111751	0.350000	0.24878	0.003000	0.11579	0.009000	0.06853	1.409000	0.34680	0.209000	0.20645	-1.644000	0.00765	CAT	G|0.994;A|0.006	0.006	strong		0.463	CYP3A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345469.1			A	99273815	G	A	99273815	3	1	25	1	0	0	0	0	1	0	0	0	4182	1377	48	2	1468	2	CYP3A5	7	99273815	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	5	99273815	59864848	292	9201	113	2									
OR2AE1	81392	hgsc.bcm.edu	37	chr7	99474438	99474438	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcaggatgattgtggagacAtgcatcagatccatgaggga	12	10	13	6	0	2	4	2	2	0	2	3	7	3	6	1	3	1	1	1	3	0	2	rs139077767	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:99474438A>G	ENST00000316368.2	-	1	242	c.219T>C	c.(217-219)caT>caC	p.H73H		NM_001005276.1	NP_001005276.1	Q8NHA4	O2AE1_HUMAN	olfactory receptor, family 2, subfamily AE, member 1	73						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(2)|lung(3)|prostate(2)	11	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					TTGTGGAGACATGCATCAGAT	0.488													A|||	19	0.00379393	0.0008	0.0029	5008	,	,		23330	0.001		0.007	False		,,,				2504	0.0082				p.H73H		Atlas-SNP	.											.	OR2AE1	32	.	0			c.T219C						PASS	.	A		9,4397	15.5+/-35.6	0,9,2194	113	96	102		219	-7.2	0	7	dbSNP_134	102	68,8532	42.2+/-99.7	0,68,4232	no	coding-synonymous	OR2AE1	NM_001005276.1		0,77,6426	GG,GA,AA		0.7907,0.2043,0.592		73/324	99474438	77,12929	2203	4300	6503	SO:0001819	synonymous_variant	81392	exon1			GGAGACATGCATC	AC011904	CCDS34696.1	7q22.1	2014-02-19	2002-02-28		ENSG00000244623	ENSG00000244623		"GPCR / Class A : Olfactory receptors"	15087	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily AE, member 2"	OR2AE2			Standard	NM_001005276		Approved		uc003usc.1	Q8NHA4	OTTHUMG00000156650	ENST00000316368.2:c.219T>C	7.37:g.99474438A>G		100	0	0		107	49	0.457944	NM_001005276	B2RPD2	Silent	SNP	ENST00000316368.2	37	CCDS34696.1																																																																																			A|0.994;G|0.006	0.006	strong		0.488	OR2AE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345053.1			G	99474438	A	G	99474438	2	3	25	1	0	0	0	0	0	0	0	1	10992	214	8	3		3	OR2AE1	7	99474438	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	200623	99474438	59664225	293	9202											
ZCWPW1	55063	hgsc.bcm.edu	37	chr7	99998750	99998750	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	catgagttgctccaggtccaGgtcactggaggcttcgtcct	6	11	12	12	1	1	1	1	1	0	0	5	2	4	2	3	4	1	3	3	4	0	2	rs145308367	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:99998750G>A	ENST00000398027.2	-	18	2081	c.1834C>T	c.(1834-1836)Ctg>Ttg	p.L612L	ZCWPW1_ENST00000360951.4_3'UTR|ZCWPW1_ENST00000490721.1_Silent_p.L441L|ZCWPW1_ENST00000324725.6_Silent_p.L441L	NM_017984.4	NP_060454.3	Q9H0M4	ZCPW1_HUMAN	zinc finger, CW type with PWWP domain 1	612							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)					TCCAGGTCCAGGTCACTGGAG	0.637													g|||	12	0.00239617	0.0	0.0043	5008	,	,		16848	0.0		0.006	False		,,,				2504	0.0031				p.L612L		Atlas-SNP	.											.	ZCWPW1	41	.	0			c.C1834T						PASS	.	G		4,4012		0,4,2004	49	51	51		1834	4.1	1	7	dbSNP_134	51	76,8316		1,74,4121	no	coding-synonymous	ZCWPW1	NM_017984.3		1,78,6125	AA,AG,GG		0.9056,0.0996,0.6447		612/649	99998750	80,12328	2008	4196	6204	SO:0001819	synonymous_variant	55063	exon18			GGTCCAGGTCACT	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.1834C>T	7.37:g.99998750G>A		82	0	0		111	49	0.441441	NM_017984	A8MVF5|B4DUQ2|Q8NA98|Q9BUD0|Q9NWF7	Silent	SNP	ENST00000398027.2	37	CCDS43623.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	G	10.34	1.323458	0.24080	9.96E-4	0.009056	ENSG00000233389	ENST00000449355	.	.	.	5.04	4.12	0.48240	.	.	.	.	.	T	0.50274	0.1606	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52939	-0.8508	4	.	.	.	-5.4653	8.2412	0.31660	0.1153:0.0:0.8847:0.0	.	.	.	.	K	7	.	.	R	+	2	0	AC005071.3	99836686	0.998000	0.40836	1.000000	0.80357	0.228000	0.25075	0.143000	0.16115	1.416000	0.47057	0.655000	0.94253	AGG	G|0.994;A|0.006	0.006	strong		0.637	ZCWPW1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356083.1	NM_017984		A	99998750	G	A	99998750	2	1	25	1	0	0	0	0	0	0	0	1	17612	991	35	2		2	ZCWPW1	7	99998750	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	524312	99998750	59139913	294	9203											
PCOLCE	5118	hgsc.bcm.edu	37	chr7	100205365	100205365	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tggaggactggacctgccttCtccacccactggtgcctccc	5	9	10	17	0	1	0	0	0	1	0	3	3	2	3	6	4	2	0	6	4	0	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:100205365C>T	ENST00000223061.5	+	8	1398	c.1118C>T	c.(1117-1119)tCt>tTt	p.S373F		NM_002593.3	NP_002584.2	Q15113	PCOC1_HUMAN	procollagen C-endopeptidase enhancer	373	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				multicellular organismal development (GO:0007275)|positive regulation of peptidase activity (GO:0010952)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|peptidase activator activity (GO:0016504)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	23	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					GACCTGCCTTCTCCACCCACT	0.552																																					p.S373F		Atlas-SNP	.											.	PCOLCE	37	.	0			c.C1118T						PASS	.						154	146	149					7																	100205365		2203	4300	6503	SO:0001583	missense	5118	exon8			TGCCTTCTCCACC	L33799	CCDS5700.1	7q22	2008-07-18			ENSG00000106333	ENSG00000106333			8738	protein-coding gene	gene with protein product	"procollagen, type 1, COOH-terminal proteinase enhancer", "procollagen C-proteinase enhancer 1"	600270				8824813, 9799793	Standard	NM_002593		Approved	PCPE, PCPE1	uc003uvo.3	Q15113	OTTHUMG00000156675	ENST00000223061.5:c.1118C>T	7.37:g.100205365C>T	ENSP00000223061:p.Ser373Phe	140	0	0		145	61	0.42069	NM_002593	B2R9E1|O14550	Missense_Mutation	SNP	ENST00000223061.5	37	CCDS5700.1	.	.	.	.	.	.	.	.	.	.	C	14.38	2.518752	0.44763	.	.	ENSG00000106333	ENST00000223061	T	0.23552	1.9	4.42	3.5	0.40072	Tissue inhibitor of metalloproteinases-like, OB-fold (1);Netrin domain (1);Netrin module, non-TIMP type (2);	0.587059	0.17803	N	0.161488	T	0.38348	0.1037	L	0.44542	1.39	0.09310	N	1	D	0.65815	0.995	D	0.68943	0.961	T	0.07597	-1.0764	10	0.54805	T	0.06	-6.1274	9.2378	0.37477	0.2159:0.7841:0.0:0.0	.	373	Q15113	PCOC1_HUMAN	F	373	ENSP00000223061:S373F	ENSP00000223061:S373F	S	+	2	0	PCOLCE	100043301	0.082000	0.21442	0.994000	0.49952	0.730000	0.41778	1.614000	0.36911	1.017000	0.39495	0.462000	0.41574	TCT	.	.	none		0.552	PCOLCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345285.1	NM_002593		T	100205365	C	T	100205365	3	4	25	1	0	0	0	0	1	0	0	0	11603	913	32	2	1148	2	PCOLCE	7	100205365	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	206615	100205365	58933298	295	9204											
GNB2	2783	hgsc.bcm.edu	37	chr7	100276355	100276355	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gacaaccgcgtgagctgcctCggggtcaccgacgatggcat	8	6	14	13	5	1	1	1	1	0	0	2	4	1	1	3	3	3	2	3	3	1	0	rs17850902	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:100276355C>T	ENST00000303210.4	+	10	1436	c.954C>T	c.(952-954)ctC>ctT	p.L318L	GNB2_ENST00000427895.1_Silent_p.L218L|GNB2_ENST00000419828.1_Silent_p.L218L|GNB2_ENST00000436220.1_Silent_p.L274L|GNB2_ENST00000393926.1_Silent_p.L318L|GNB2_ENST00000424361.1_Silent_p.L274L|GNB2_ENST00000393924.1_Silent_p.L318L	NM_005273.3	NP_005264.2	P62879	GBB2_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 2	318					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)				TGAGCTGCCTCGGGGTCACCG	0.652													C|||	17	0.00339457	0.0008	0.0029	5008	,	,		16180	0.001		0.005	False		,,,				2504	0.0082				p.L318L		Atlas-SNP	.											.	GNB2	29	.	0			c.C954T						PASS	.	C		7,4399		0,7,2196	60	63	62		954	-6	0.9	7	dbSNP_123	62	76,8524		0,76,4224	no	coding-synonymous	GNB2	NM_005273.3		0,83,6420	TT,TC,CC		0.8837,0.1589,0.6382		318/341	100276355	83,12923	2203	4300	6503	SO:0001819	synonymous_variant	2783	exon10			CTGCCTCGGGGTC	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.954C>T	7.37:g.100276355C>T		145	0	0		147	83	0.564626	NM_005273	B3KPU1|P11016|P54312	Silent	SNP	ENST00000303210.4	37	CCDS5703.1																																																																																			C|0.995;T|0.005	0.005	strong		0.652	GNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268391.2	NM_005273		T	100276355	C	T	100276355	2	4	25	1	0	0	0	0	0	0	0	1	6525	871	31	1		1	GNB2	7	100276355	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	70990	100276355	58862308	296	9205											
EPHB4	2050	hgsc.bcm.edu	37	chr7	100403131	100403131	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagtcctcacccgccattCtcccgggccacgattttgag	6	10	9	16	3	2	1	1	1	1	0	4	2	3	1	5	1	1	1	5	1	0	3	rs35638378	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:100403131C>A	ENST00000358173.3	-	15	3138	c.2670G>T	c.(2668-2670)gaG>gaT	p.E890D	EPHB4_ENST00000360620.3_Missense_Mutation_p.E890D	NM_004444.4	NP_004435.3	P54760	EPHB4_HUMAN	EPH receptor B4	890	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		E -> D (in dbSNP:rs35638378). {ECO:0000269|PubMed:17344846}.		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)					ACCCGCCATTCTCCCGGGCCA	0.652													C|||	13	0.00259585	0.0	0.0043	5008	,	,		15943	0.0		0.006	False		,,,				2504	0.0041				p.E890D	GBM(200;2113 3072 25865 52728)	Atlas-SNP	.											.	EPHB4	106	.	0			c.G2670T						PASS	.	C	ASP/GLU	7,4399	14.3+/-33.2	0,7,2196	53	60	58		2670	2.3	1	7	dbSNP_126	58	80,8520	44.9+/-103.4	1,78,4221	yes	missense	EPHB4	NM_004444.4	45	1,85,6417	AA,AC,CC		0.9302,0.1589,0.6689	benign	890/988	100403131	87,12919	2203	4300	6503	SO:0001583	missense	2050	exon15			GCCATTCTCCCGG	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.2670G>T	7.37:g.100403131C>A	ENSP00000350896:p.Glu890Asp	79	0	0		100	46	0.46	NM_004444	B5A970|B5A971|B5A972|Q7Z635|Q9BTA5|Q9BXP0	Missense_Mutation	SNP	ENST00000358173.3	37	CCDS5706.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	9.167	1.020236	0.19433	0.001589	0.009302	ENSG00000196411	ENST00000360620;ENST00000358173	T;T	0.76316	-1.01;-0.79	5.28	2.33	0.28932	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.120844	0.36972	N	0.002303	T	0.41488	0.1161	N	0.05031	-0.125	0.28430	N	0.917311	B;B	0.09022	0.002;0.001	B;B	0.12156	0.007;0.002	T	0.23261	-1.0193	10	0.13470	T	0.59	.	4.4028	0.11395	0.0:0.5648:0.1653:0.2699	rs35638378	890;890	Q96L35;P54760	.;EPHB4_HUMAN	D	890	ENSP00000353833:E890D;ENSP00000350896:E890D	ENSP00000350896:E890D	E	-	3	2	EPHB4	100241067	0.733000	0.28132	1.000000	0.80357	0.923000	0.55619	0.224000	0.17738	0.625000	0.30304	-0.258000	0.10820	GAG	C|0.993;A|0.007	0.007	strong		0.652	EPHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347222.1	NM_004444		A	100403131	C	A	100403131	3	1	25	1	0	0	0	0	1	0	0	0	5179	912	32	4	305	4	EPHB4	7	100403131	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	126776	100403131	58735532	297	9206											
SLC12A9	56996	hgsc.bcm.edu	37	chr7	100464053	100464053	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggagggccgggtgggccggaGggtggggatgctgagggccc	4	4	25	8	2	0	1	0	1	0	0	0	4	0	4	3	9	1	1	3	9	0	0	rs199582669	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:100464053G>A	ENST00000354161.3	+	14	2696	c.2571G>A	c.(2569-2571)gaG>gaA	p.E857E	TRIP6_ENST00000200457.4_5'Flank	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9	857				E -> K (in Ref. 3; BAB40456). {ECO:0000305}.	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)					GTGGGCCGGAGGGTGGGGATG	0.736													G|||	19	0.00379393	0.0	0.0058	5008	,	,		9921	0.001		0.0089	False		,,,				2504	0.0051				p.E857E		Atlas-SNP	.											.	SLC12A9	81	.	0			c.G2571A						PASS	.	G		7,4113		0,7,2053	11	12	12		2571	-0.8	0	7		12	77,7943		0,77,3933	no	coding-synonymous	SLC12A9	NM_020246.2		0,84,5986	AA,AG,GG		0.9601,0.1699,0.6919		857/915	100464053	84,12056	2060	4010	6070	SO:0001819	synonymous_variant	56996	exon14			GCCGGAGGGTGGG	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.2571G>A	7.37:g.100464053G>A		16	0	0		18	8	0.444444	NM_020246	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Silent	SNP	ENST00000354161.3	37	CCDS5707.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	1	0.0017482517482517483	6	0.0079155672823219	G	2.646	-0.283100	0.05642	0.001699	0.009601	ENSG00000146828	ENST00000539308	.	.	.	4.7	-0.816	0.10839	.	.	.	.	.	T	0.50086	0.1595	.	.	.	0.40595	D	0.981521	.	.	.	.	.	.	T	0.57195	-0.7853	5	0.87932	D	0	.	5.1517	0.15013	0.2797:0.2866:0.4337:0.0	.	.	.	.	R	483	.	ENSP00000442859:G483R	G	+	1	0	SLC12A9	100301989	0.977000	0.34250	0.023000	0.16930	0.499000	0.33736	0.261000	0.18442	-0.044000	0.13491	0.555000	0.69702	GGG	G|0.995;A|0.005	0.005	strong		0.736	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246		A	100464053	G	A	100464053	2	1	25	1	0	0	0	0	0	0	0	1	14405	991	35	2		2	SLC12A9	7	100464053	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	60922	100464053	58674610	298	9207											
MUC17	140453	hgsc.bcm.edu	37	chr7	100686291	100686291	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgctgaagtcactaccatacGtatttcaattaccagtgaaa	14	12	6	9	1	2	2	2	2	0	0	2	2	2	2	2	0	4	2	2	0	7	5			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:100686291G>A	ENST00000306151.4	+	3	11658	c.11594G>A	c.(11593-11595)cGt>cAt	p.R3865H		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3865					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)					ACTACCATACGTATTTCAATT	0.488																																					p.R3865H		Atlas-SNP	.											MUC17,NS,carcinoma,+1,1	MUC17	804	1	0			c.G11594A						PASS	.						143	130	135					7																	100686291		2203	4300	6503	SO:0001583	missense	140453	exon3			CCATACGTATTTC	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.11594G>A	7.37:g.100686291G>A	ENSP00000302716:p.Arg3865His	99	0	0		101	55	0.544554	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	g	3.518	-0.098385	0.07010	.	.	ENSG00000169876	ENST00000306151	T	0.02140	4.43	0.558	-1.12	0.09808	.	.	.	.	.	T	0.02571	0.0078	N	0.08118	0	0.09310	N	1	D	0.76494	0.999	D	0.65443	0.935	T	0.40001	-0.9586	8	0.38643	T	0.18	.	.	.	.	.	3865	Q685J3	MUC17_HUMAN	H	3865	ENSP00000302716:R3865H	ENSP00000302716:R3865H	R	+	2	0	MUC17	100473011	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-1.161000	0.03144	-1.475000	0.01876	-1.089000	0.02181	CGT	.	.	none		0.488	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100686291	G	A	100686291	3	1	25	1	0	0	0	0	1	0	0	0	9983	1145	40	1	11604	1	MUC17	7	100686291	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	222238	100686291	58452372	299	9208											
MET	4233	hgsc.bcm.edu	37	chr7	116339315	116339315	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagaatgtcattctacatgaGcatcacattttccttggtgc	10	14	7	10	0	3	2	2	1	1	1	4	2	4	2	1	1	3	1	1	1	2	5			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:116339315G>A	ENST00000318493.6	+	2	364	c.177G>A	c.(175-177)gaG>gaA	p.E59E	MET_ENST00000397752.3_Silent_p.E59E|MET_ENST00000436117.2_Silent_p.E59E			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)			TTCTACATGAGCATCACATTT	0.443			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.E59E		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.G177A						PASS	.						104	101	102					7																	116339315		1947	4135	6082	SO:0001819	synonymous_variant	4233	exon2	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	ACATGAGCATCAC	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.177G>A	7.37:g.116339315G>A		139	0	0		129	58	0.449612	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			.	.	none		0.443	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			A	116339315	G	A	116339315	2	1	25	1	0	0	0	0	0	0	0	1	9494	962	34	2		2	MET	7	116339315	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	15653024	116339315	42799348	300	9209											
MET	4233	hgsc.bcm.edu	37	chr7	116397572	116397572	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatggccacgggacaacacaAtacagtacattctcctatgt	14	9	7	11	1	1	0	0	0	1	0	2	1	1	1	2	2	3	1	2	2	6	4	rs13223756	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:116397572A>G	ENST00000318493.6	+	7	2131	c.1944A>G	c.(1942-1944)caA>caG	p.Q648Q	MET_ENST00000397752.3_Silent_p.Q648Q|MET_ENST00000436117.2_Silent_p.Q648Q			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0	Arg/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)			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)			GGACAACACAATACAGTACAT	0.318			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				A|||	941	0.187899	0.1089	0.1254	5008	,	,		17860	0.2728		0.2048	False		,,,				2504	0.2342				p.Q648Q		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.A1944G						PASS	.	A	,	486,3224		27,432,1396	93	92	92		1944,1944	-6.5	0	7	dbSNP_121	92	1521,6665		129,1263,2701	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	156,1695,4097	GG,GA,AA		18.5805,13.0997,16.8712	,	648/1391,648/1409	116397572	2007,9889	1855	4093	5948	SO:0001819	synonymous_variant	4233	exon7	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	AACACAATACAGT	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.1944A>G	7.37:g.116397572A>G		74	0	0		72	39	0.541667	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			A|0.817;G|0.183	0.183	strong		0.318	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			G	116397572	A	G	116397572	2	3	25	1	0	0	0	0	0	0	0	1	9494	98	4	3		3	MET	7	116397572	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	58257	116397572	42741091	301	9210											
CFTR	1080	hgsc.bcm.edu	37	chr7	117144306	117144307	+	Splice_Site	INS	-	-	C																															tcctcctctctttattttagINSctggaccagaccaattttga																										TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:117144306_117144307insC	ENST00000003084.6	+	2	185_186		c.e2-1		CFTR_ENST00000454343.1_Splice_Site	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)						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)	CTTTATTTTAGCTGGACCAGAC	0.381									Cystic Fibrosis																												.		Pindel,Atlas-Indel	.											.	CFTR	171	.	0			c.54-1->C						PASS	.																																			SO:0001630	splice_region_variant	1080	exon2	Familial Cancer Database	CF	.	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.54-1->C	7.37:g.117144307_117144307dupC		88	0	.		87	20	0.23	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Splice_Site	INS	ENST00000003084.6	37	CCDS5773.1																																																																																			.	.	none		0.381	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492	Intron	C	117144307	-	C	117144306	8	5	25	1	0	1	1	0	0	0	1	0	3296	985	34	0	59	0	CFTR	7	117144306	Splice_Site	INS	-	TCGA-G8-6906-01A-11D-2210-10	746734	117144306	41994357	302	9211											
C7orf58	79974	hgsc.bcm.edu	37	chr7	120876835	120876835	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatttcttctgactacattgAagccattttacagtctgaac	11	16	5	9	0	3	3	0	3	3	0	3	3	3	3	1	0	4	0	1	0	5	7	rs35793694	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:120876835A>G	ENST00000310396.5	+	17	2590	c.2123A>G	c.(2122-2124)gAa>gGa	p.E708G	CPED1_ENST00000450913.2_Missense_Mutation_p.E708G|CPED1_ENST00000423795.1_Missense_Mutation_p.E488G	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	708			E -> G (in dbSNP:rs35793694). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.			endoplasmic reticulum (GO:0005783)											GACTACATTGAAGCCATTTTA	0.348													A|||	182	0.0363419	0.0325	0.0403	5008	,	,		15919	0.0		0.0805	False		,,,				2504	0.0307				p.E708G		Atlas-SNP	.											.	.	.	.	0			c.A2123G						PASS	.	A	GLY/GLU,GLY/GLU	200,4206	124.5+/-161.8	3,194,2006	98	97	97		2123,2123	4.8	1	7	dbSNP_126	97	684,7916	169.4+/-220.8	30,624,3646	yes	missense,missense	C7orf58	NM_001105533.1,NM_024913.4	98,98	33,818,5652	GG,GA,AA		7.9535,4.5393,6.7969	benign,benign	708/784,708/1027	120876835	884,12122	2203	4300	6503	SO:0001583	missense	79974	exon16			ACATTGAAGCCAT		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.2123A>G	7.37:g.120876835A>G	ENSP00000309772:p.Glu708Gly	93	0	0		89	48	0.539326	NM_001105533	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Missense_Mutation	SNP	ENST00000310396.5	37	CCDS34739.1	105	0.04807692307692308	21	0.042682926829268296	16	0.04419889502762431	0	0.0	68	0.08970976253298153	A	20.3	3.965228	0.74131	0.045393	0.079535	ENSG00000106034	ENST00000310396;ENST00000450913;ENST00000423795	T;T;T	0.25085	2.15;1.82;1.83	5.86	4.75	0.60458	.	0.200573	0.43416	D	0.000573	T	0.00637	0.0021	L	0.40543	1.245	0.80722	D	1	P;P;B	0.38078	0.617;0.617;0.329	B;B;B	0.30855	0.121;0.121;0.077	T	0.03112	-1.1071	10	0.46703	T	0.11	.	10.2136	0.43156	0.6934:0.3066:0.0:0.0	rs35793694	488;708;708	G5E9U2;A4D0V7-2;A4D0V7	.;.;CG058_HUMAN	G	708;708;488	ENSP00000309772:E708G;ENSP00000406122:E708G;ENSP00000415573:E488G	ENSP00000309772:E708G	E	+	2	0	C7orf58	120664071	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.980000	0.40618	2.238000	0.73509	0.477000	0.44152	GAA	A|0.939;G|0.061	0.061	strong		0.348	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913		G	120876835	A	G	120876835	3	3	25	1	0	0	0	0	1	0	0	0	2407	246	9	3	2185	3	C7orf58	7	120876835	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	3732529	120876835	38261828	303	9212											
IQUB	154865	hgsc.bcm.edu	37	chr7	123152157	123152157	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	tcttggtgatataacctcttCcatgagttgttcattgtctg	7	18	8	8	0	4	2	1	2	3	0	5	2	5	2	2	1	1	2	2	1	2	7			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:123152157C>G	ENST00000466202.1	-	2	814	c.238G>C	c.(238-240)Gaa>Caa	p.E80Q	IQUB_ENST00000488987.1_Intron|IQUB_ENST00000324698.6_Missense_Mutation_p.E80Q|IQUB_ENST00000434450.1_Missense_Mutation_p.E80Q	NM_001282855.1	NP_001269784.1	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	80					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						ATAACCTCTTCCATGAGTTGT	0.408																																					p.E80Q		Atlas-SNP	.											.	IQUB	117	.	0			c.G238C						PASS	.						245	205	218					7																	123152157		2203	4300	6503	SO:0001583	missense	154865	exon2			CCTCTTCCATGAG	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.238G>C	7.37:g.123152157C>G	ENSP00000417769:p.Glu80Gln	299	0	0		293	139	0.474403	NM_178827	A4D0X0|Q49AL6|Q4G189|Q5BJD9|Q6NUH6|Q8N9Y2	Missense_Mutation	SNP	ENST00000466202.1	37	CCDS5787.1	.	.	.	.	.	.	.	.	.	.	C	11.50	1.656291	0.29425	.	.	ENSG00000164675	ENST00000466202;ENST00000324698;ENST00000434450	T;T;T	0.48201	1.84;1.84;0.82	5.1	2.24	0.28232	.	0.791632	0.10762	N	0.637086	T	0.40546	0.1121	L	0.29908	0.895	0.09310	N	1	B;P;P	0.48016	0.244;0.904;0.718	B;P;B	0.48227	0.084;0.571;0.203	T	0.17198	-1.0377	10	0.45353	T	0.12	.	6.4052	0.21660	0.1487:0.6816:0.0:0.1697	.	80;80;80	A1A4Z1;Q8NA54-2;Q8NA54	.;.;IQUB_HUMAN	Q	80	ENSP00000417769:E80Q;ENSP00000324882:E80Q;ENSP00000388498:E80Q	ENSP00000324882:E80Q	E	-	1	0	IQUB	122939393	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	0.554000	0.23407	0.404000	0.25506	-0.813000	0.03139	GAA	.	.	none		0.408	IQUB-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348529.1	NM_178827		G	123152157	C	G	123152157	3	3	25	1	0	0	0	0	1	0	0	0	7829	864	30	4	2185	4	IQUB	7	123152157	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2275322	123152157	35986506	304	9213											
FAM40B	57464	hgsc.bcm.edu	37	chr7	129093179	129093179	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcctggagctactccacaTggaaattgagtgagaagcct	11	10	10	10	0	0	2	0	2	0	1	2	5	2	4	3	2	3	1	3	2	3	3	rs201255678		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:129093179T>C	ENST00000249344.2	+	5	561	c.521T>C	c.(520-522)aTg>aCg	p.M174T	STRIP2_ENST00000435494.2_Missense_Mutation_p.M174T	NM_020704.2	NP_065755.1	Q9ULQ0	STRP2_HUMAN	striatin interacting protein 2	174					cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)											CTACTCCACATGGAAATTGAG	0.512													T|||	1	0.000199681	0.0	0.0014	5008	,	,		20828	0.0		0.0	False		,,,				2504	0.0				p.M174T		Atlas-SNP	.											.	.	.	.	0			c.T521C						PASS	.						142	114	124					7																	129093179		2203	4300	6503	SO:0001583	missense	57464	exon5			TCCACATGGAAAT	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.521T>C	7.37:g.129093179T>C	ENSP00000249344:p.Met174Thr	77	0	0		110	46	0.418182	NM_020704	Q8WUZ4	Missense_Mutation	SNP	ENST00000249344.2	37	CCDS34752.1	.	.	.	.	.	.	.	.	.	.	T	14.21	2.467920	0.43839	.	.	ENSG00000128578	ENST00000249344;ENST00000435494	T;T	0.47177	0.86;0.85	5.68	5.68	0.88126	.	0.041546	0.85682	D	0.000000	T	0.56202	0.1969	M	0.62723	1.935	0.80722	D	1	B;P	0.46395	0.071;0.877	B;P	0.53861	0.062;0.736	T	0.51772	-0.8663	10	0.13108	T	0.6	-20.1919	13.8875	0.63717	0.0:0.0:0.0:1.0	.	174;174	Q9ULQ0;Q9ULQ0-2	FA40B_HUMAN;.	T	174	ENSP00000249344:M174T;ENSP00000392393:M174T	ENSP00000249344:M174T	M	+	2	0	FAM40B	128880415	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.651000	0.83577	2.179000	0.69175	0.459000	0.35465	ATG	T|0.999;C|0.001	0.001	weak		0.512	STRIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349418.1	NM_001134336		C	129093179	T	C	129093179	3	2	25	1	0	0	0	0	1	0	0	0	5569	1464	51	3	539	3	FAM40B	7	129093179	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	5941022	129093179	30045484	305	9214											
ZC3HC1	51530	hgsc.bcm.edu	37	chr7	129663533	129663533	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agagtcccagctccgagttcGagagacaatgggaccagggc	11	5	14	11	2	0	2	0	0	0	2	3	6	2	3	3	2	1	2	3	2	1	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:129663533G>A	ENST00000358303.4	-	8	1135	c.1051C>T	c.(1051-1053)Cga>Tga	p.R351*	RP11-306G20.1_ENST00000587038.1_RNA|ZC3HC1_ENST00000311873.5_Nonsense_Mutation_p.R330*|ZC3HC1_ENST00000360708.5_Intron|ZC3HC1_ENST00000481503.1_Nonsense_Mutation_p.R308*|RP11-306G20.1_ENST00000480018.1_RNA	NM_016478.3	NP_057562.3	Q86WB0	NIPA_HUMAN	zinc finger, C3HC-type containing 1	351					mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein ubiquitination (GO:0016567)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(6)|large_intestine(10)|lung(2)|prostate(1)|urinary_tract(1)	22	Melanoma(18;0.0435)					CTCCGAGTTCGAGAGACAATG	0.512																																					p.R351X	Melanoma(115;540 1606 16325 28853 48167)	Atlas-SNP	.											ZC3HC1,NS,carcinoma,0,1	ZC3HC1	45	1	0			c.C1051T						PASS	.						67	62	64					7																	129663533		2203	4300	6503	SO:0001587	stop_gained	51530	exon8			GAGTTCGAGAGAC	AF151050	CCDS34753.1, CCDS64767.1, CCDS75659.1	7q32.2	2013-01-17			ENSG00000091732	ENSG00000091732		"Zinc fingers, C3HC-type"	29913	protein-coding gene	gene with protein product	"nuclear interaction partner of ALK"					11042152	Standard	XM_005250403		Approved	NIPA	uc003vpi.3	Q86WB0	OTTHUMG00000157648	ENST00000358303.4:c.1051C>T	7.37:g.129663533G>A	ENSP00000351052:p.Arg351*	63	0	0		74	27	0.364865	NM_016478	A6NH66|Q75MF3|Q75MF4|Q8N330|Q96F75|Q9HA34|Q9NVX4|Q9P0R0	Nonsense_Mutation	SNP	ENST00000358303.4	37	CCDS34753.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.305782	0.81247	.	.	ENSG00000091732	ENST00000358303;ENST00000311873;ENST00000481503	.	.	.	5.49	3.59	0.41128	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.802	12.559	0.56271	0.0:0.0:0.5483:0.4517	.	.	.	.	X	351;330;308	.	ENSP00000309301:R330X	R	-	1	2	ZC3HC1	129450769	0.997000	0.39634	0.999000	0.59377	0.984000	0.73092	2.978000	0.49305	1.297000	0.44761	0.563000	0.77884	CGA	.	.	none		0.512	ZC3HC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349316.1	NM_016478		A	129663533	G	A	129663533	4	1	25	1	0	0	0	0	0	1	0	0	17592	1066	37	1	469	1	ZC3HC1	7	129663533	Nonsense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	570354	129663533	29475130	306	9215											
PLXNA4	91584	hgsc.bcm.edu	37	chr7	131864652	131864652	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggcaatgtacaccatccccGgggagtactccatgccaccg	9	6	11	15	2	0	0	0	0	0	0	2	1	2	1	6	3	3	3	6	3	3	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:131864652G>A	ENST00000359827.3	-	20	4630	c.3668C>T	c.(3667-3669)cCg>cTg	p.P1223L	PLXNA4_ENST00000321063.4_Missense_Mutation_p.P1223L			Q9HCM2	PLXA4_HUMAN	plexin A4	1223	IPT/TIG 4.				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						CACCATCCCCGGGGAGTACTC	0.652																																					p.P1223L		Atlas-SNP	.											.	PLXNA4	873	.	0			c.C3668T						PASS	.						15	18	17					7																	131864652		2134	4237	6371	SO:0001583	missense	91584	exon20			ATCCCCGGGGAGT	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.3668C>T	7.37:g.131864652G>A	ENSP00000352882:p.Pro1223Leu	64	0	0		66	21	0.318182	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	G	14.48	2.549153	0.45383	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.57752	0.38;0.38	4.92	4.92	0.64577	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.097949	0.64402	D	0.000001	T	0.65133	0.2662	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.58132	-0.7690	10	0.06625	T	0.88	.	18.3041	0.90175	0.0:0.0:1.0:0.0	.	1223	Q9HCM2	PLXA4_HUMAN	L	1223	ENSP00000323194:P1223L;ENSP00000352882:P1223L	ENSP00000323194:P1223L	P	-	2	0	PLXNA4	131515192	1.000000	0.71417	0.986000	0.45419	0.951000	0.60555	9.623000	0.98386	2.582000	0.87167	0.484000	0.47621	CCG	.	.	none		0.652	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		A	131864652	G	A	131864652	3	1	25	1	0	0	0	0	1	0	0	0	12131	1116	39	1	2068	1	PLXNA4	7	131864652	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2201119	131864652	27274011	307	9216											
DGKI	9162	hgsc.bcm.edu	37	chr7	137263068	137263068	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgttgaatttctctggatttGcttctgtgaaagaggaaaag	11	15	11	4	0	2	3	0	2	2	1	3	5	2	5	0	2	1	2	0	2	4	4			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:137263068G>T	ENST00000288490.5	-	16	1646	c.1646C>A	c.(1645-1647)gCa>gAa	p.A549E	DGKI_ENST00000446122.1_Missense_Mutation_p.A549E|DGKI_ENST00000424189.2_Missense_Mutation_p.A549E|DGKI_ENST00000453654.2_Missense_Mutation_p.A249E	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	549					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						CTCTGGATTTGCTTCTGTGAA	0.373																																					p.A549E		Atlas-SNP	.											DGKI_ENST00000288490,NS,carcinoma,-1,2	DGKI	335	2	0			c.C1646A						PASS	.						67	68	67					7																	137263068		2202	4299	6501	SO:0001583	missense	9162	exon16			GGATTTGCTTCTG	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.1646C>A	7.37:g.137263068G>T	ENSP00000288490:p.Ala549Glu	120	0	0		115	49	0.426087	NM_004717	A4D1Q9|Q9NZ49	Missense_Mutation	SNP	ENST00000288490.5	37	CCDS5845.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.920853	0.92249	.	.	ENSG00000157680	ENST00000453654;ENST00000540376;ENST00000424189;ENST00000288490;ENST00000446122	T;T;T	0.27890	1.64;1.64;1.64	5.15	5.15	0.70609	Diacylglycerol kinase, accessory domain (2);	0.000000	0.85682	D	0.000000	T	0.45256	0.1333	L	0.28694	0.88	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.81914	0.987;0.995	T	0.31998	-0.9923	10	0.42905	T	0.14	.	18.6041	0.91261	0.0:0.0:1.0:0.0	.	249;549	E9PFX6;O75912	.;DGKI_HUMAN	E	249;497;549;549;549	ENSP00000392161:A249E;ENSP00000288490:A549E;ENSP00000399131:A549E	ENSP00000288490:A549E	A	-	2	0	DGKI	136913608	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.610000	0.98337	2.573000	0.86826	0.462000	0.41574	GCA	.	.	none		0.373	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717		T	137263068	G	T	137263068	3	4	25	1	0	0	0	0	1	0	0	0	4473	1319	46	4	1627	4	DGKI	7	137263068	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	5398416	137263068	21875595	308	9217											
BRAF	673	hgsc.bcm.edu	37	chr7	140477811	140477811	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgagtactcctacttcattTttgaaggcttgtaactgctg	8	16	8	9	0	1	2	1	2	0	0	2	2	2	2	1	1	4	4	1	1	4	7	rs397507476		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:140477811T>A	ENST00000288602.6	-	12	1557	c.1497A>T	c.(1495-1497)aaA>aaT	p.K499N		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	499	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		K -> E (in CFC1). {ECO:0000269|PubMed:16439621, ECO:0000269|PubMed:16474404, ECO:0000269|PubMed:18042262}.|K -> N (in CFC1). {ECO:0000269|PubMed:18042262, ECO:0000269|PubMed:19206169}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|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 stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	CTACTTCATTTTTGAAGGCTT	0.393		61	"Mis, T, O"	"AKAP9, KIAA1549"	"melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												p.K499N	Colon(40;35 892 2973 5743 27438)	Atlas-SNP	.		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	.	BRAF	36346	.	0			c.A1497T	GRCh37	CM080110	BRAF	M		PASS	.						108	97	101					7																	140477811		2203	4300	6503	SO:0001583	missense	673	exon12	Familial Cancer Database	CFC, CFCS	TTCATTTTTGAAG	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1497A>T	7.37:g.140477811T>A	ENSP00000288602:p.Lys499Asn	54	0	0		70	26	0.371429	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.5|23.5	4.427562|4.427562	0.83667|0.83667	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000496384|ENST00000288602	D|D	0.81739|0.82619	-1.53|-1.63	4.96|4.96	4.96|4.96	0.65561|0.65561	.|Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	D|D	0.82742|0.82742	0.5103|0.5103	L|L	0.35793|0.35793	1.09|1.09	0.80722|0.80722	D|D	1|1	.|P	.|0.51653	.|0.947	.|P	.|0.52031	.|0.688	D|D	0.85140|0.85140	0.0980|0.0980	8|10	0.87932|0.87932	D|D	0|0	.|.	14.3436|14.3436	0.66643|0.66643	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|499	.|P15056	.|BRAF_HUMAN	I|N	107|499	ENSP00000419060:K107I|ENSP00000288602:K499N	ENSP00000419060:K107I|ENSP00000288602:K499N	K|K	-|-	2|3	0|2	BRAF|BRAF	140124280|140124280	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.114000|3.114000	0.50383|0.50383	1.853000|1.853000	0.53794|0.53794	0.472000|0.472000	0.43445|0.43445	AAA|AAA	.	.	none		0.393	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		A	140477811	T	A	140477811	3	1	25	1	0	0	0	0	1	0	0	0	1498	1838	64	5	831	5	BRAF	7	140477811	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	3214743	140477811	18660852	309	9218											
MGAM	8972	hgsc.bcm.edu	37	chr7	141708306	141708329	+	Splice_Site	DEL	CCCCAGATCCTGGGACAACTGGTA	CCCCAGATCCTGGGACAACTGGTA	-																															tatgtttgcttttggtatagCcccagatcctgggacaactg																								rs199885071	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CCCCAGATCCTGGGACAACTGGTA	CCCCAGATCCTGGGACAACTGGTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:141708306_141708329delCCCCAGATCCTGGGACAACTGGTA	ENST00000549489.2	+	3	223_246	c.128_151delCCCCAGATCCTGGGACAACTGGTA	c.(127-153)gccccagatcctgggacaactggtacc>gcc	p.PDPGTTGT60del	MGAM_ENST00000475668.2_Splice_Site_p.PDPGTTGT60del	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	60	Ser/Thr-rich.				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)	TTTGGTATAGCCCCAGATCCTGGGACAACTGGTACCCCAGATCC	0.469																																					p.43_50del		Atlas-Indel	.											.	MGAM	767	.	0			c.128_150del						PASS	.			10,3480		0,10,1735						0.4	0			57	7,7801		1,5,3898	no	coding-near-splice	MGAM	NM_004668.2		1,15,5633	A1A1,A1R,RR		0.0897,0.2865,0.1505				17,11281				SO:0001630	splice_region_variant	8972	exon3			.	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.128-1CCCCAGATCCTGGGACAACTGGTA>-	7.37:g.141708306_141708329delCCCCAGATCCTGGGACAACTGGTA		154	0	0		135	40	0.296296	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Frame_Shift_Del	DEL	ENST00000549489.2	37	CCDS47727.1																																																																																			.	.	none		0.469	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		In_Frame_Del	-	141708329	CCCCAGATCCTGGGACAACTGGTA	-	141708306	8	5	25	1	0	1	0	1	0	0	1	0	9550	753	26	0	134	0	MGAM	7	141708306	Splice_Site	DEL	CCCCAGATCCTGGGACAACTGGTA	TCGA-G8-6906-01A-11D-2210-10	1230495	141708306	17430357	310	9219											
MGAM	8972	hgsc.bcm.edu	37	chr7	141752154	141752154	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catacacagtggaatggagcAtaaagataagggatgaagaa	19	6	12	4	0	0	3	0	1	0	2	0	6	0	6	0	3	2	1	0	3	7	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:141752154A>T	ENST00000549489.2	+	25	2961	c.2866A>T	c.(2866-2868)Ata>Tta	p.I956L	MGAM_ENST00000475668.2_Missense_Mutation_p.I956L	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	956	P-type 2. {ECO:0000255|PROSITE- ProRule:PRU00779}.				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)	GGAATGGAGCATAAAGATAAG	0.428																																					p.I956L		Atlas-SNP	.											.	MGAM	767	.	0			c.A2866T						PASS	.						72	64	67					7																	141752154		1893	4125	6018	SO:0001583	missense	8972	exon25			TGGAGCATAAAGA	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.2866A>T	7.37:g.141752154A>T	ENSP00000447378:p.Ile956Leu	52	0	0		52	30	0.576923	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	37	CCDS47727.1	.	.	.	.	.	.	.	.	.	.	A	4.008	-0.001239	0.07819	.	.	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	D	0.88431	-2.38	4.64	-9.28	0.00656	P-type trefoil (2);	5.617280	0.00166	N	0.000008	T	0.66636	0.2809	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.64676	-0.6351	10	0.11485	T	0.65	.	1.9557	0.03375	0.2744:0.3783:0.0822:0.2652	.	956	O43451	MGA_HUMAN	L	956;956;833	ENSP00000447378:I956L	ENSP00000316431:I833L	I	+	1	0	MGAM	141398623	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.999000	0.01467	-1.559000	0.01688	-0.661000	0.03856	ATA	.	.	none		0.428	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			T	141752154	A	T	141752154	3	4	25	1	0	0	0	0	1	0	0	0	9550	217	8	5	2960	5	MGAM	7	141752154	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	43848	141752154	17386509	311	9220											
C7orf33	202865	hgsc.bcm.edu	37	chr7	148288135	148288135	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgccggattgaccttcgcCtgagtgggagggcagtcgct	5	8	17	11	4	0	2	0	2	0	0	2	4	0	4	3	4	0	2	3	4	0	2	rs111320068	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:148288135C>T	ENST00000307003.2	+	1	479	c.118C>T	c.(118-120)Ctg>Ttg	p.L40L		NM_145304.2	NP_660347.1	Q8WU49	CG033_HUMAN	chromosome 7 open reading frame 33	40										central_nervous_system(1)|large_intestine(4)|lung(7)|prostate(2)	14	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			TGACCTTCGCCTGAGTGGGAG	0.552													C|||	131	0.0261581	0.0015	0.0908	5008	,	,		17766	0.001		0.0249	False		,,,				2504	0.0409				p.L40L		Atlas-SNP	.											.	C7orf33	28	.	0			c.C118T						PASS	.	C		39,4367	43.1+/-76.7	1,37,2165	91	76	81		118	1.9	0	7	dbSNP_132	81	296,8304	108.4+/-169.1	4,288,4008	no	coding-synonymous	C7orf33	NM_145304.2		5,325,6173	TT,TC,CC		3.4419,0.8852,2.5757		40/178	148288135	335,12671	2203	4300	6503	SO:0001819	synonymous_variant	202865	exon1			CTTCGCCTGAGTG	BC021251	CCDS5890.1	7q36.1	2011-11-24			ENSG00000170279	ENSG00000170279			21724	protein-coding gene	gene with protein product							Standard	NM_145304		Approved		uc003wew.3	Q8WU49	OTTHUMG00000152756	ENST00000307003.2:c.118C>T	7.37:g.148288135C>T		89	0	0		116	57	0.491379	NM_145304		Silent	SNP	ENST00000307003.2	37	CCDS5890.1																																																																																			C|0.974;T|0.026	0.026	strong		0.552	C7orf33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327684.1	NM_145304		T	148288135	C	T	148288135	2	4	25	1	0	0	0	0	0	0	0	1	2390	680	24	2		2	C7orf33	7	148288135	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	6535981	148288135	10850528	312	9221											
SSPO	23145	hgsc.bcm.edu	37	chr7	149479935	149479935	+	RNA	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	catcagaccccctgttccagGagctgtgctggtcaatgggc	7	9	12	13	0	2	1	2	0	0	1	3	2	3	2	3	3	2	3	3	3	1	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:149479935G>A	ENST00000378016.2	+	0	1901							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)			CCTGTTCCAGGAGCTGTGCTG	0.612																																					p.G634E		Atlas-SNP	.											.	.	.	.	0			c.G1901A						PASS	.						36	40	39					7																	149479935		2080	4195	6275			23145	exon15			TTCCAGGAGCTGT	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.149479935G>A		118	0	0		108	38	0.351852	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				.	.	none		0.612	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				A	149479935	G	A	149479935	1	1	25	0	1	0	0	0	0	0	0	0	15204	1188	41	2		2	SSPO	7	149479935	RNA	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1191800	149479935	9658728	313	9222											
MLL3	58508	hgsc.bcm.edu	37	chr7	151962289	151962289	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cactgcacagtttgcatcttCcttcgctataattaacagtg	10	14	6	11	1	1	0	0	0	1	0	3	0	2	0	1	0	3	4	1	0	3	6			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:151962289C>T	ENST00000262189.6	-	8	1236	c.1018G>A	c.(1018-1020)Gaa>Aaa	p.E340K	KMT2C_ENST00000355193.2_Missense_Mutation_p.E340K	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	340					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)										TTTGCATCTTCCTTCGCTATA	0.363																																					p.E340K		Atlas-SNP	.											MLL3_ENST00000355193,NS,carcinoma,+2,2	MLL3	1564	2	0			c.G1018A						scavenged	.						80	74	76					7																	151962289		2203	4299	6502	SO:0001583	missense	58508	exon8			CATCTTCCTTCGC	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.1018G>A	7.37:g.151962289C>T	ENSP00000262189:p.Glu340Lys	177	0	0		172	11	0.0639535	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	14.11	2.437062	0.43224	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.98947	-5.26;-5.26	4.65	4.65	0.58169	Zinc finger, RING/FYVE/PHD-type (1);Protein kinase C-like, phorbol ester/diacylglycerol binding (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.42821	U	0.000650	D	0.97688	0.9242	N	0.25890	0.77	0.80722	D	1	D	0.60575	0.988	P	0.54759	0.76	D	0.98897	1.0775	10	0.62326	D	0.03	.	17.9157	0.88950	0.0:1.0:0.0:0.0	.	340	Q8NEZ4	MLL3_HUMAN	K	340	ENSP00000262189:E340K;ENSP00000347325:E340K	ENSP00000262189:E340K	E	-	1	0	MLL3	151593222	1.000000	0.71417	1.000000	0.80357	0.009000	0.06853	7.772000	0.85439	2.271000	0.75665	0.557000	0.71058	GAA	.	.	none		0.363	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			T	151962289	C	T	151962289	3	4	25	1	0	0	0	0	1	0	0	0	9631	864	30	2	13925	2	MLL3	7	151962289	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2482354	151962289	7176374	314	9223											
MNX1	3110	hgsc.bcm.edu	37	chr7	156802363	156802363	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agggtactcacagttgaagtCgggcatcttaggcaggatca	11	9	13	8	1	3	1	2	1	1	0	4	2	3	2	0	4	1	4	0	4	3	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:156802363C>T	ENST00000252971.6	-	1	982	c.682G>A	c.(682-684)Gac>Aac	p.D228N	MNX1-AS1_ENST00000480284.1_RNA|MNX1_ENST00000543409.1_5'Flank|MNX1-AS2_ENST00000429228.1_RNA|MNX1_ENST00000469500.1_5'Flank	NM_005515.3	NP_005506.3	P50219	MNX1_HUMAN	motor neuron and pancreas homeobox 1	228					anatomical structure morphogenesis (GO:0009653)|diaphragm development (GO:0060539)|dorsal/ventral neural tube patterning (GO:0021904)|endocrine pancreas development (GO:0031018)|humoral immune response (GO:0006959)|motor neuron axon guidance (GO:0008045)|nerve development (GO:0021675)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spinal cord motor neuron cell fate specification (GO:0021520)|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(1)|lung(4)|skin(1)	7	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CAGTTGAAGTCGGGCATCTTA	0.716																																					p.D228N		Atlas-SNP	.											.	MNX1	17	.	0			c.G682A						PASS	.						11	12	12					7																	156802363		2137	4195	6332	SO:0001583	missense	3110	exon1			TGAAGTCGGGCAT	AF107457	CCDS34788.1, CCDS55187.1	7q36	2012-03-09	2007-08-09	2007-08-09	ENSG00000130675	ENSG00000130675		"Homeoboxes / ANTP class : HOXL subclass"	4979	protein-coding gene	gene with protein product		142994	"homeo box HB9", "homeobox HB9"	HLXB9		9843207	Standard	NM_001165255		Approved	HB9, HOXHB9, SCRA1	uc003wmz.4	P50219	OTTHUMG00000157181	ENST00000252971.6:c.682G>A	7.37:g.156802363C>T	ENSP00000252971:p.Asp228Asn	15	0	0		43	22	0.511628	NM_005515	F5H401|Q9Y648	Missense_Mutation	SNP	ENST00000252971.6	37	CCDS34788.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.603729	0.87157	.	.	ENSG00000130675	ENST00000252971;ENST00000542972	D	0.95656	-3.77	3.12	2.21	0.28008	Homeodomain-like (1);	0.000000	0.40222	U	0.001156	D	0.96034	0.8708	M	0.65498	2.005	0.80722	D	1	D	0.71674	0.998	P	0.59115	0.852	D	0.95038	0.8175	10	0.66056	D	0.02	-25.9529	11.1823	0.48636	0.0:0.8115:0.1885:0.0	.	228	P50219	MNX1_HUMAN	N	228;58	ENSP00000252971:D228N	ENSP00000252971:D228N	D	-	1	0	MNX1	156495124	1.000000	0.71417	0.996000	0.52242	0.993000	0.82548	4.845000	0.62853	0.536000	0.28733	0.549000	0.68633	GAC	.	.	none		0.716	MNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347796.3			T	156802363	C	T	156802363	3	4	25	1	0	0	0	0	1	0	0	0	9688	884	31	1	594	1	MNX1	7	156802363	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	4840074	156802363	2336300	315	9224											
PTPRN2	5799	hgsc.bcm.edu	37	chr7	157369324	157369324	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcggaagtccaggagggAccttgaggaggaagggactc	10	5	17	9	1	0	1	0	1	0	0	2	7	1	7	3	6	1	0	3	6	2	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:157369324A>G	ENST00000389418.4	-	19	2773	c.2764T>C	c.(2764-2766)Tcc>Ccc	p.S922P	PTPRN2_ENST00000389413.3_Missense_Mutation_p.S893P|PTPRN2_ENST00000389416.4_Missense_Mutation_p.S905P|PTPRN2_ENST00000409483.1_Missense_Mutation_p.S884P|PTPRN2_ENST00000404321.2_Missense_Mutation_p.S945P|MIR153-2_ENST00000385225.1_RNA	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	922	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				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)		TCCAGGAGGGACCTTGAGGAG	0.647																																					p.S922P		Atlas-SNP	.											.	PTPRN2	243	.	0			c.T2764C						PASS	.						62	49	54					7																	157369324		2203	4300	6503	SO:0001583	missense	5799	exon19			GGAGGGACCTTGA	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.2764T>C	7.37:g.157369324A>G	ENSP00000374069:p.Ser922Pro	45	0	0		57	20	0.350877	NM_002847	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	.	.	.	.	.	.	.	.	.	.	A	8.190	0.795727	0.16327	.	.	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	D;D;D;D;D	0.84298	-1.83;-1.83;-1.83;-1.83;-1.83	5.44	1.67	0.24075	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.066743	0.64402	D	0.000012	T	0.57814	0.2079	N	0.02266	-0.62	0.80722	D	1	B;B;B;B;B	0.29301	0.203;0.241;0.203;0.208;0.241	B;B;B;B;B	0.30495	0.071;0.116;0.071;0.044;0.116	T	0.55224	-0.8174	10	0.02654	T	1	.	5.9778	0.19391	0.7094:0.1376:0.153:0.0	.	945;884;893;905;922	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	P	884;893;905;922;945	ENSP00000387114:S884P;ENSP00000374064:S893P;ENSP00000374067:S905P;ENSP00000374069:S922P;ENSP00000385464:S945P	ENSP00000374064:S893P	S	-	1	0	PTPRN2	157062085	1.000000	0.71417	0.100000	0.21137	0.015000	0.08874	2.455000	0.44988	0.041000	0.15688	0.528000	0.53228	TCC	.	.	none		0.647	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1			G	157369324	A	G	157369324	3	3	25	1	0	0	0	0	1	0	0	0	12823	275	10	3	303	3	PTPRN2	7	157369324	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	566961	157369324	1769339	316	9225											
ZNF596	169270	hgsc.bcm.edu	37	chr8	194695	194695	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagggcacgtccaccatcagCacaatggtaagctttatgga	13	8	10	10	1	1	0	1	0	0	0	2	1	2	1	2	3	2	4	2	3	4	3	rs148383942	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:194695C>A	ENST00000398612.1	+	5	683	c.300C>A	c.(298-300)agC>agA	p.S100R	ZNF596_ENST00000308811.4_Missense_Mutation_p.S100R|ZNF596_ENST00000320552.2_Intron	NM_001042415.1|NM_001042416.1	NP_001035880.1|NP_001035881.1	Q8TC21	ZN596_HUMAN	zinc finger protein 596	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)			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)		CCACCATCAGCACAATGGTAA	0.358													.|||	10	0.00199681	0.0008	0.0014	5008	,	,		19470	0.0		0.002	False		,,,				2504	0.0061				p.S100R		Atlas-SNP	.											.	ZNF596	34	.	0			c.C300A						PASS	.	C	ARG/SER,ARG/SER,ARG/SER	0,4406		0,0,2203	120	101	108		300,300,300	-3.2	0	8	dbSNP_134	108	20,8580		0,20,4280	yes	missense,missense,missense	ZNF596	NM_001042415.1,NM_001042416.1,NM_173539.2	110,110,110	0,20,6483	AA,AC,CC		0.2326,0.0,0.1538	benign,benign,benign	100/505,100/505,100/505	194695	20,12986	2203	4300	6503	SO:0001583	missense	169270	exon5			CATCAGCACAATG	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.300C>A	8.37:g.194695C>A	ENSP00000381613:p.Ser100Arg	212	1	0.00471698		219	117	0.534247	NM_173539	B2R8P4|O95015|Q8N9X0	Missense_Mutation	SNP	ENST00000398612.1	37	CCDS5951.2	6	0.0027472527472527475	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	.	6.943	0.543844	0.13312	0.0	0.002326	ENSG00000172748	ENST00000521145;ENST00000308811;ENST00000522866;ENST00000398612	T;T;T	0.13778	2.56;3.47;3.47	2.91	-3.16	0.05217	.	.	.	.	.	T	0.02342	0.0072	N	0.03194	-0.395	0.09310	N	1	B	0.21381	0.055	B	0.12837	0.008	T	0.40757	-0.9546	9	0.10111	T	0.7	.	1.2469	0.01974	0.2252:0.2777:0.3413:0.1559	.	100	Q8TC21	ZN596_HUMAN	R	100	ENSP00000429671:S100R;ENSP00000310033:S100R;ENSP00000381613:S100R	ENSP00000310033:S100R	S	+	3	2	ZNF596	184695	0.000000	0.05858	0.000000	0.03702	0.242000	0.25591	-1.119000	0.03276	-0.755000	0.04709	0.591000	0.81541	AGC	C|0.997;A|0.003	0.003	strong		0.358	ZNF596-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195858.4	NM_173539		A	194695	C	A	194695	3	1	25	1	0	0	0	0	1	0	0	0	18041	709	25	4	314	4	ZNF596	8	194695	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10		194695	146169327	317	9226											
PDGFRL	5157	hgsc.bcm.edu	37	chr8	17447018	17447018	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agaacaagcgtccaaaagaaCcaggagagaatagaatcaaa	22	3	9	7	1	1	4	1	0	0	4	2	6	2	5	2	1	3	0	2	1	9	1	rs374832042		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:17447018C>A	ENST00000541323.1	+	3	542	c.97C>A	c.(97-99)Cca>Aca	p.P33T	PDGFRL_ENST00000251630.6_Missense_Mutation_p.P33T|PDGFRL_ENST00000398074.3_Missense_Mutation_p.P33T	NM_006207.2	NP_006198.1	Q15198	PGFRL_HUMAN	platelet-derived growth factor receptor-like	33					G-protein coupled receptor signaling pathway (GO:0007186)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)	extracellular region (GO:0005576)	platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)	9				Colorectal(111;0.0752)		TCCAAAAGAACCAGGAGAGAA	0.433																																					p.P33T		Atlas-SNP	.											.	PDGFRL	27	.	0			c.C97A						PASS	.	C	THR/PRO	0,4406		0,0,2203	146	148	147		97	4.5	0.9	8		147	1,8599	1.2+/-3.3	0,1,4299	no	missense	PDGFRL	NM_006207.2	38	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	benign	33/376	17447018	1,13005	2203	4300	6503	SO:0001583	missense	5157	exon3			AAAGAACCAGGAG	D37965	CCDS6003.1	8p22-p21.3	2013-01-29			ENSG00000104213	ENSG00000104213		"Immunoglobulin superfamily / I-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	8805	protein-coding gene	gene with protein product		604584					Standard	NM_006207		Approved	PRLTS	uc003wxr.3	Q15198	OTTHUMG00000130818	ENST00000541323.1:c.97C>A	8.37:g.17447018C>A	ENSP00000444211:p.Pro33Thr	37	0	0		31	21	0.677419	NM_006207	A8K085|Q6FH04	Missense_Mutation	SNP	ENST00000541323.1	37	CCDS6003.1	.	.	.	.	.	.	.	.	.	.	C	11.77	1.737518	0.30774	0.0	1.16E-4	ENSG00000104213	ENST00000251630;ENST00000541323;ENST00000398074	T;T;T	0.32272	1.46;1.46;1.46	4.52	4.52	0.55395	.	0.256475	0.39146	N	0.001451	T	0.32102	0.0818	L	0.56769	1.78	0.32797	N	0.500418	B	0.27559	0.181	B	0.26969	0.075	T	0.37174	-0.9717	10	0.22706	T	0.39	-18.4186	17.8077	0.88606	0.0:1.0:0.0:0.0	.	33	Q15198	PGFRL_HUMAN	T	33	ENSP00000251630:P33T;ENSP00000444211:P33T;ENSP00000381149:P33T	ENSP00000251630:P33T	P	+	1	0	PDGFRL	17491278	0.996000	0.38824	0.943000	0.38184	0.677000	0.39632	2.992000	0.49417	2.503000	0.84419	0.591000	0.81541	CCA	.	.	weak		0.433	PDGFRL-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253366.3	NM_006207		A	17447018	C	A	17447018	3	1	25	1	0	0	0	0	1	0	0	0	11672	507	18	4	103	4	PDGFRL	8	17447018	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	17252323	17447018	128917004	318	9227											
MTUS1	57509	hgsc.bcm.edu	37	chr8	17513484	17513484	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gattctctcgttctgtttttTcagcctggtgctgctggacg	3	17	11	10	2	3	0	1	0	2	0	5	2	3	1	1	2	3	4	1	2	0	5	rs61733708	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:17513484T>C	ENST00000262102.6	-	9	3220	c.2996A>G	c.(2995-2997)gAa>gGa	p.E999G	MTUS1_ENST00000381861.3_Missense_Mutation_p.E246G|MTUS1_ENST00000381869.3_Missense_Mutation_p.E945G|MTUS1_ENST00000297488.6_Missense_Mutation_p.E165G|MTUS1_ENST00000518713.1_5'UTR|MTUS1_ENST00000400046.1_Missense_Mutation_p.E71G|MTUS1_ENST00000544260.1_Missense_Mutation_p.E144G|MTUS1_ENST00000519263.1_Missense_Mutation_p.E945G	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	999				E -> G (in Ref. 5; CAH56128). {ECO:0000305}.	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)		TTCTGTTTTTTCAGCCTGGTG	0.418													T|||	15	0.00299521	0.0	0.0029	5008	,	,		19675	0.0		0.0129	False		,,,				2504	0.0				p.E999G		Atlas-SNP	.											.	MTUS1	144	.	0			c.A2996G						PASS	.	T	GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU	8,3748		0,8,1870	190	173	178		2996,2834,737,431,494	5.1	0.1	8	dbSNP_129	178	76,8168		1,74,4047	yes	missense,missense,missense,missense,missense	MTUS1	NM_001001924.2,NM_001001925.2,NM_001001931.2,NM_001166393.1,NM_020749.4	98,98,98,98,98	1,82,5917	CC,CT,TT		0.9219,0.213,0.7	benign,benign,benign,benign,benign	999/1271,945/1217,246/518,144/416,165/437	17513484	84,11916	1878	4122	6000	SO:0001583	missense	57509	exon9			GTTTTTTCAGCCT	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.2996A>G	8.37:g.17513484T>C	ENSP00000262102:p.Glu999Gly	245	0	0		209	110	0.526316	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	12	0.005494505494505495	0	0.0	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	T	18.28	3.589263	0.66105	0.00213	0.009219	ENSG00000129422	ENST00000381869;ENST00000544260;ENST00000400046;ENST00000297488;ENST00000381861;ENST00000262102;ENST00000519263	T;T;T;T;T;T;T	0.39056	1.1;1.1;1.6;1.1;1.1;1.1;1.1	5.13	5.13	0.70059	.	0.199759	0.51477	D	0.000098	T	0.45337	0.1337	M	0.79258	2.445	0.80722	D	1	P;P;B;B	0.40970	0.734;0.734;0.411;0.246	B;P;B;B	0.44946	0.302;0.465;0.281;0.157	T	0.58504	-0.7625	10	0.87932	D	0	-18.4737	15.2621	0.73631	0.0:0.0:0.0:1.0	rs61733708	945;999;246;165	Q9ULD2-2;Q9ULD2;Q9ULD2-6;Q9ULD2-3	.;MTUS1_HUMAN;.;.	G	945;144;71;165;246;999;945	ENSP00000371293:E945G;ENSP00000445738:E144G;ENSP00000382921:E71G;ENSP00000297488:E165G;ENSP00000371285:E246G;ENSP00000262102:E999G;ENSP00000430167:E945G	ENSP00000262102:E999G	E	-	2	0	MTUS1	17557764	1.000000	0.71417	0.086000	0.20670	0.802000	0.45316	7.411000	0.80078	2.079000	0.62486	0.482000	0.46254	GAA	T|0.992;C|0.008	0.008	strong		0.418	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		C	17513484	T	C	17513484	3	2	25	1	0	0	0	0	1	0	0	0	9974	1783	62	3	844	3	MTUS1	8	17513484	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	66466	17513484	128850538	319	9228											
LGI3	203190	hgsc.bcm.edu	37	chr8	22006123	22006123	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgactccactgatagatgacGggtgcctgggagctgctgga	8	8	15	10	2	0	3	0	2	0	1	1	6	1	5	2	3	3	2	2	3	1	1	rs201271501	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22006123G>A	ENST00000306317.2	-	8	1486	c.1197C>T	c.(1195-1197)ccC>ccT	p.P399P	LGI3_ENST00000424267.2_Silent_p.P375P	NM_139278.2	NP_644807.1	Q8N145	LGI3_HUMAN	leucine-rich repeat LGI family, member 3	399					exocytosis (GO:0006887)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|extracellular region (GO:0005576)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	catalytic activity (GO:0003824)			endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	17				Colorectal(74;0.00189)|COAD - Colon adenocarcinoma(73;0.0612)|READ - Rectum adenocarcinoma(644;0.0999)		GATAGATGACGGGTGCCTGGG	0.632													g|||	3	0.000599042	0.0	0.0	5008	,	,		16962	0.003		0.0	False		,,,				2504	0.0				p.P399P		Atlas-SNP	.											.	LGI3	44	.	0			c.C1197T						PASS	.	A		1,4405	2.1+/-5.4	0,1,2202	76	62	67		1197	-10.3	0	8		67	0,8600		0,0,4300	no	coding-synonymous	LGI3	NM_139278.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		399/549	22006123	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	203190	exon8			GATGACGGGTGCC	AJ487518	CCDS6025.1	8p21.2	2008-07-28			ENSG00000168481	ENSG00000168481			18711	protein-coding gene	gene with protein product		608302				12023020, 18628660	Standard	NM_139278		Approved		uc003xav.3	Q8N145	OTTHUMG00000131599	ENST00000306317.2:c.1197C>T	8.37:g.22006123G>A		55	0	0		68	34	0.5	NM_139278	A5PLP2|Q86TL4|Q8N296	Silent	SNP	ENST00000306317.2	37	CCDS6025.1																																																																																			G|1.000;A|0.000	0.000	strong		0.632	LGI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254482.1			A	22006123	G	A	22006123	2	1	25	1	0	0	0	0	0	0	0	1	8762	1103	39	1		1	LGI3	8	22006123	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	4492639	22006123	124357899	320	9229											
PDLIM2	64236	hgsc.bcm.edu	37	chr8	22442908	22442908	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctcaggccgccctggaagccGacaggtgaggctccctgggg	6	5	16	14	2	1	1	1	1	0	0	2	3	2	2	4	6	1	1	4	6	1	0	rs11989168	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22442908G>A	ENST00000397760.4	+	6	936	c.536G>A	c.(535-537)cGa>cAa	p.R179Q	PDLIM2_ENST00000409417.1_Missense_Mutation_p.R179Q|PDLIM2_ENST00000448520.1_3'UTR|PDLIM2_ENST00000409141.1_Missense_Mutation_p.R179Q|PDLIM2_ENST00000397761.2_Missense_Mutation_p.R179Q|PDLIM2_ENST00000339162.7_Missense_Mutation_p.R179Q|PDLIM2_ENST00000308354.7_Missense_Mutation_p.R429Q|PDLIM2_ENST00000265810.4_Missense_Mutation_p.R179Q			Q96JY6	PDLI2_HUMAN	PDZ and LIM domain 2 (mystique)	179						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)		CCTGGAAGCCGACAGGTGAGG	0.667													G|||	25	0.00499201	0.0144	0.0072	5008	,	,		11606	0.0		0.001	False		,,,				2504	0.0				p.R429Q		Atlas-SNP	.											PDLIM2_ENST00000308354,colon,carcinoma,+1,2	PDLIM2	42	2	0			c.G1286A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	57,4345		0,57,2144	26	20	22		1286,536,536	-2.1	0.1	8	dbSNP_120	22	4,8590		0,4,4293	yes	missense,missense,missense	PDLIM2	NM_021630.5,NM_176871.3,NM_198042.3	43,43,43	0,61,6437	AA,AG,GG		0.0465,1.2949,0.4694	benign,benign,benign	429/603,179/367,179/279	22442908	61,12935	2201	4297	6498	SO:0001583	missense	64236	exon6			GAAGCCGACAGGT	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.536G>A	8.37:g.22442908G>A	ENSP00000380867:p.Arg179Gln	77	0	0		98	46	0.469388	NM_021630	D3DSR5|J3KNH4|Q7Z584|Q86WM8|Q8WZ29|Q9H4L9|Q9H7I2	Missense_Mutation	SNP	ENST00000397760.4	37		15	0.006868131868131868	10	0.02032520325203252	3	0.008287292817679558	0	0.0	2	0.002638522427440633	G	8.308	0.821380	0.16678	0.012949	4.65E-4	ENSG00000120913	ENST00000456545;ENST00000308354;ENST00000452226;ENST00000397760;ENST00000339162;ENST00000397761;ENST00000429812;ENST00000409141;ENST00000265810;ENST00000409417	T;T;T;T;T;T;T;T;T;T	0.25749	2.06;3.57;2.65;2.65;2.64;2.65;1.78;2.64;2.74;2.65	4.75	-2.07	0.07276	.	0.808770	0.10844	N	0.627938	T	0.01730	0.0055	N	0.00162	-1.95	0.09310	N	1	B;B;B;B	0.23490	0.005;0.086;0.007;0.052	B;B;B;B	0.15052	0.003;0.012;0.002;0.007	T	0.39623	-0.9605	10	0.11485	T	0.65	-0.0402	4.6558	0.12617	0.477:0.0:0.3754:0.1476	rs11989168	179;179;179;179	Q96JY6-3;Q96JY6-4;Q96JY6;C9JS55	.;.;PDLI2_HUMAN;.	Q	179;429;179;179;179;179;179;179;179;179	ENSP00000401992:R179Q;ENSP00000312634:R429Q;ENSP00000394376:R179Q;ENSP00000380867:R179Q;ENSP00000342035:R179Q;ENSP00000380868:R179Q;ENSP00000407643:R179Q;ENSP00000386868:R179Q;ENSP00000265810:R179Q;ENSP00000387084:R179Q	ENSP00000265810:R179Q	R	+	2	0	PDLIM2	22498853	0.000000	0.05858	0.068000	0.19968	0.166000	0.22503	-0.518000	0.06267	-0.292000	0.08999	-0.448000	0.05591	CGA	G|0.993;A|0.007	0.007	strong		0.667	PDLIM2-202	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000334167.1			A	22442908	G	A	22442908	3	1	25	1	0	0	0	0	1	0	0	0	11689	1058	37	1	554	1	PDLIM2	8	22442908	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	436785	22442908	123921114	321	9230											
PEBP4	157310	hgsc.bcm.edu	37	chr8	22570904	22570904	+	Silent	SNP	C	C	T																															tagcaggcagctatctccgcCtggtttttgtgcttgggctc																								rs386723487|rs61732772	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22570904C>T	ENST00000256404.6	-	7	754	c.663G>A	c.(661-663)caG>caA	p.Q221Q	RP11-459E5.1_ENST00000523627.1_RNA	NM_144962.2	NP_659399.2	Q96S96	PEBP4_HUMAN	phosphatidylethanolamine-binding protein 4	221						extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)				breast(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|stomach(2)	10		Prostate(55;0.0453)|Breast(100;0.103)		Colorectal(74;0.0434)|COAD - Colon adenocarcinoma(73;0.124)		CTATCTCCGCCTGGTTTTTGT	0.587													C|||	55	0.0109824	0.0098	0.0072	5008	,	,		16308	0.004		0.0199	False		,,,				2504	0.0133				p.Q221Q		Atlas-SNP	.											.	PEBP4	23	.	0			c.G663A						PASS	.						71	78	76					8																	22570904		1953	4153	6106	SO:0001819	synonymous_variant	157310	exon7			CTCCGCCTGGTTT	BC020779	CCDS43724.1	8p21.3	2009-08-13			ENSG00000134020	ENSG00000134020			28319	protein-coding gene	gene with protein product	"cousin-of-RKIP 1 protein"	612473				15302887, 16865237	Standard	NM_144962		Approved	MGC22776, CORK1, hPEBP4	uc003xcn.1	Q96S96	OTTHUMG00000163749	ENST00000256404.6:c.663G>A	8.37:g.22570904C>T		129	0	0		108	58	0.537037	NM_144962	Q5EVA1|Q8WW74	Silent	SNP	ENST00000256404.6	37	CCDS43724.1																																																																																			C|0.986;T|0.014	0.014	strong		0.587	PEBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375141.2	NM_144962		T	22570904	C	T	22570904	2	4	25	1	0	0	0	0	0	0	0	1	11723	680	24	2		2	PEBP4	8	22570904	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	127996	22570904	123793118	322	9231	114	2									
PEBP4	157310	hgsc.bcm.edu	37	chr8	22570905	22570905	+	Missense_Mutation	SNP	T	T	G																															agcaggcagctatctccgccTggtttttgtgcttgggctcg																								rs386723487|rs79936857	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22570905T>G	ENST00000256404.6	-	7	753	c.662A>C	c.(661-663)cAg>cCg	p.Q221P	RP11-459E5.1_ENST00000523627.1_RNA	NM_144962.2	NP_659399.2	Q96S96	PEBP4_HUMAN	phosphatidylethanolamine-binding protein 4	221						extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)				breast(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|stomach(2)	10		Prostate(55;0.0453)|Breast(100;0.103)		Colorectal(74;0.0434)|COAD - Colon adenocarcinoma(73;0.124)		TATCTCCGCCTGGTTTTTGTG	0.592													T|||	374	0.0746805	0.2428	0.0231	5008	,	,		16389	0.004		0.0199	False		,,,				2504	0.0133				p.Q221P		Atlas-SNP	.											.	PEBP4	23	.	0			c.A662C						PASS	.						72	79	77					8																	22570905		1953	4151	6104	SO:0001583	missense	157310	exon7			TCCGCCTGGTTTT	BC020779	CCDS43724.1	8p21.3	2009-08-13			ENSG00000134020	ENSG00000134020			28319	protein-coding gene	gene with protein product	"cousin-of-RKIP 1 protein"	612473				15302887, 16865237	Standard	NM_144962		Approved	MGC22776, CORK1, hPEBP4	uc003xcn.1	Q96S96	OTTHUMG00000163749	ENST00000256404.6:c.662A>C	8.37:g.22570905T>G	ENSP00000256404:p.Gln221Pro	131	0	0		108	59	0.546296	NM_144962	Q5EVA1|Q8WW74	Missense_Mutation	SNP	ENST00000256404.6	37	CCDS43724.1	114	0.0521978021978022	96	0.1951219512195122	6	0.016574585635359115	5	0.008741258741258742	7	0.009234828496042216	T	11.07	1.531292	0.27387	.	.	ENSG00000134020	ENST00000256404	T	0.33438	1.41	5.01	-1.92	0.07618	.	47.664200	0.00166	N	0.000000	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	D	0.65815	0.995	P	0.56278	0.795	T	0.02539	-1.1144	9	0.59425	D	0.04	8.4188	4.2246	0.10574	0.1617:0.3762:0.0:0.4621	.	221	Q96S96	PEBP4_HUMAN	P	221	ENSP00000256404:Q221P	ENSP00000256404:Q221P	Q	-	2	0	PEBP4	22626850	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-0.839000	0.04368	-0.336000	0.08438	0.459000	0.35465	CAG	T|0.962;G|0.038	0.038	strong		0.592	PEBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375141.2	NM_144962		G	22570905	T	G	22570905	3	3	25	1	0	0	0	0	1	0	0	0	11723	1580	55	5	25	5	PEBP4	8	22570905	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	1	22570905	123793117	323	9232	114	2									
TNFRSF10C	8794	hgsc.bcm.edu	37	chr8	22960654	22960654	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	catggcccggatccccaagaCcctaaagttcgtcgtcgtca	9	8	9	15	4	1	1	1	0	0	1	5	2	2	2	4	2	0	1	4	2	3	2	rs10107826|rs374790272	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22960654C>T	ENST00000356864.3	+	1	552	c.20C>T	c.(19-21)aCc>aTc	p.T7I	TNFRSF10C_ENST00000520607.1_Intron|TNFRSF10C_ENST00000540813.1_5'UTR|TNFRSF10C_ENST00000397703.2_Missense_Mutation_p.T47I	NM_003841.3	NP_003832	O14798	TR10C_HUMAN	tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain	7					apoptotic process (GO:0006915)|signal transduction (GO:0007165)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(6)|lung(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	15		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		ATCCCCAAGACCCTAAAGTTC	0.711													C|||	208	0.0415335	0.149	0.0101	5008	,	,		14783	0.0		0.004	False		,,,				2504	0.0				p.T7I		Atlas-SNP	.											.	TNFRSF10C	30	.	0			c.C20T						PASS	.	C	ILE/THR	443,3961	170.9+/-201.2	25,393,1784	79	59	66		20	0.6	0	8	dbSNP_119	66	12,8584	5.7+/-21.5	0,12,4286	yes	missense	TNFRSF10C	NM_003841.3	89	25,405,6070	TT,TC,CC		0.1396,10.059,3.5	probably-damaging	7/260	22960654	455,12545	2202	4298	6500	SO:0001583	missense	8794	exon1			CCAAGACCCTAAA	AF012536	CCDS6037.1	8p22-p21	2006-02-22			ENSG00000173535	ENSG00000173535		"Tumor necrosis factor receptor superfamily", "CD molecules"	11906	protein-coding gene	gene with protein product		603613				9314565, 9325248	Standard	NM_003841		Approved	DcR1, TRAILR3, LIT, TRID, CD263	uc003xcy.3	O14798	OTTHUMG00000097844	ENST00000356864.3:c.20C>T	8.37:g.22960654C>T	ENSP00000349324:p.Thr7Ile	47	0	0		76	44	0.578947	NM_003841	O14755|Q08AS6|Q6FH98|Q6UXM5	Missense_Mutation	SNP	ENST00000356864.3	37	CCDS6037.1	56	0.02564102564102564	50	0.1016260162601626	4	0.011049723756906077	0	0.0	2	0.002638522427440633	C	4.995	0.184796	0.09495	0.10059	0.001396	ENSG00000173535	ENST00000397703;ENST00000356864;ENST00000544885	T	0.62364	0.03	1.76	0.639	0.17747	.	2.630870	0.02547	U	0.095275	T	0.01627	0.0052	N	0.19112	0.55	0.52099	P	5.100000000002325E-5	B	0.21225	0.053	B	0.06405	0.002	T	0.08186	-1.0734	9	0.52906	T	0.07	.	4.4054	0.11407	0.0:0.717:0.0:0.283	rs10107826;rs10107826	7	O14798	TR10C_HUMAN	I	47;7;7	ENSP00000349324:T7I	ENSP00000349324:T7I	T	+	2	0	TNFRSF10C	23016599	0.000000	0.05858	0.001000	0.08648	0.053000	0.15095	-0.737000	0.04877	-0.010000	0.14271	0.205000	0.17691	ACC	C|0.958;T|0.042	0.042	strong		0.711	TNFRSF10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215134.3			T	22960654	C	T	22960654	3	4	25	1	0	0	0	0	1	0	0	0	16297	507	18	2	22	2	TNFRSF10C	8	22960654	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	389749	22960654	123403368	324	9233											
TNFRSF10C	8794	hgsc.bcm.edu	37	chr8	22974405	22974405	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	agctgctgaagagacaatgaCcaccagcccggggactcctg	11	5	12	13	1	0	3	0	2	0	1	1	5	1	4	4	2	3	2	4	2	2	0	rs61736406	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22974405C>T	ENST00000356864.3	+	5	1173	c.641C>T	c.(640-642)aCc>aTc	p.T214I	TNFRSF10C_ENST00000540813.1_Missense_Mutation_p.T112I	NM_003841.3	NP_003832	O14798	TR10C_HUMAN	tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain	214					apoptotic process (GO:0006915)|signal transduction (GO:0007165)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)	p.T214N(7)		endometrium(1)|large_intestine(6)|lung(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	15		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		GAGACAATGACCACCAGCCCG	0.612																																					p.T214I		Atlas-SNP	.											TNFRSF10C,NS,carcinoma,0,5	TNFRSF10C	30	5	7	Substitution - Missense(7)	prostate(4)|large_intestine(3)	c.C641T						PASS	.						63	71	68					8																	22974405		2203	4298	6501	SO:0001583	missense	8794	exon5			CAATGACCACCAG	AF012536	CCDS6037.1	8p22-p21	2006-02-22			ENSG00000173535	ENSG00000173535		"Tumor necrosis factor receptor superfamily", "CD molecules"	11906	protein-coding gene	gene with protein product		603613				9314565, 9325248	Standard	NM_003841		Approved	DcR1, TRAILR3, LIT, TRID, CD263	uc003xcy.3	O14798	OTTHUMG00000097844	ENST00000356864.3:c.641C>T	8.37:g.22974405C>T	ENSP00000349324:p.Thr214Ile	126	0	0		152	35	0.230263	NM_003841	O14755|Q08AS6|Q6FH98|Q6UXM5	Missense_Mutation	SNP	ENST00000356864.3	37	CCDS6037.1	32	0.014652014652014652	27	0.054878048780487805	3	0.008287292817679558	0	0.0	2	0.002638522427440633	c	0.284	-0.984715	0.02180	.	.	ENSG00000173535	ENST00000356864;ENST00000540813;ENST00000544885	T;T	0.62498	0.02;0.38	.	.	.	.	7739.210000	0.00166	U	0.000000	T	0.06872	0.0175	N	0.03608	-0.345	0.09310	N	1	B	0.22909	0.077	B	0.06405	0.002	T	0.19031	-1.0318	9	0.62326	D	0.03	.	5.2848	0.15696	0.3272:0.6728:0.0:0.0	.	214	O14798	TR10C_HUMAN	I	214;112;214	ENSP00000349324:T214I;ENSP00000437612:T112I	ENSP00000349324:T214I	T	+	2	0	TNFRSF10C	23030350	0.033000	0.19621	0.001000	0.08648	0.141000	0.21300	0.550000	0.23345	-2.089000	0.00860	-2.399000	0.00225	ACC	A|0.000;C|0.990;T|0.009	0.009	strong		0.612	TNFRSF10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215134.3			T	22974405	C	T	22974405	3	4	25	1	0	0	0	0	1	0	0	0	16297	507	18	2	659	2	TNFRSF10C	8	22974405	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	13751	22974405	123389617	325	9234											
GNRH1	2796	hgsc.bcm.edu	37	chr8	25279148	25279148	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgcgtggtgcattcgaagcGttgggtttctgccagttgac	5	13	15	8	3	1	1	0	1	1	0	2	2	1	1	1	2	4	4	1	2	1	4	rs574867408		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:25279148G>A	ENST00000276414.4	-	2	1501	c.178C>T	c.(178-180)Cgc>Tgc	p.R60C	GNRH1_ENST00000421054.2_Missense_Mutation_p.R60C	NM_000825.3	NP_000816.4	P01148	GON1_HUMAN	gonadotropin-releasing hormone 1 (luteinizing-releasing hormone)	60					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)		CATTCGAAGCGTTGGGTTTCT	0.448													G|||	1	0.000199681	0.0	0.0014	5008	,	,		14545	0.0		0.0	False		,,,				2504	0.0				p.R64C		Atlas-SNP	.											.	GNRH1	8	.	0			c.C190T						PASS	.						102	110	107					8																	25279148		2033	4193	6226	SO:0001583	missense	2796	exon2			CGAAGCGTTGGGT	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.178C>T	8.37:g.25279148G>A	ENSP00000276414:p.Arg60Cys	195	0	0		150	67	0.446667	NM_000825	A0AVP0	Missense_Mutation	SNP	ENST00000276414.4	37	CCDS43725.1	.	.	.	.	.	.	.	.	.	.	G	5.063	0.197253	0.09599	.	.	ENSG00000147437	ENST00000421054;ENST00000276414	T;T	0.47528	0.84;0.84	4.91	2.09	0.27110	.	1.839800	0.02297	N	0.070879	T	0.38214	0.1032	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.25047	-1.0143	9	0.46703	T	0.11	0.5379	7.6257	0.28210	0.0774:0.0:0.5127:0.4099	.	60	P01148	GON1_HUMAN	C	60	ENSP00000391280:R60C;ENSP00000276414:R60C	ENSP00000276414:R60C	R	-	1	0	GNRH1	25335065	0.003000	0.15002	0.000000	0.03702	0.003000	0.03518	1.075000	0.30716	0.250000	0.21479	0.561000	0.74099	CGC	.	.	none		0.448	GNRH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375982.1	NM_001083111		A	25279148	G	A	25279148	3	1	25	1	0	0	0	0	1	0	0	0	6555	1145	40	1	108	1	GNRH1	8	25279148	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2304743	25279148	121084874	326	9235											
CHRNA2	1135	hgsc.bcm.edu	37	chr8	27327369	27327369	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgcccagcggttgtagcccCggaagaggtgtttgaagagc	8	7	16	10	3	0	3	0	1	0	2	0	4	0	4	3	3	3	3	3	3	3	3	rs548268816		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:27327369C>T	ENST00000520933.2	-	2	356	c.203G>A	c.(202-204)cGg>cAg	p.R68Q	CHRNA2_ENST00000240132.2_Missense_Mutation_p.R68Q|CHRNA2_ENST00000407991.1_Missense_Mutation_p.R68Q			Q15822	ACHA2_HUMAN	cholinergic receptor, nicotinic, alpha 2 (neuronal)	68					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)	p.R68Q(1)		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)	GTTGTAGCCCCGGAAGAGGTG	0.632																																					p.R68Q		Atlas-SNP	.											CHRNA2,caecum,carcinoma,-1,2	CHRNA2	48	2	1	Substitution - Missense(1)	endometrium(1)	c.G203A						PASS	.						87	86	86					8																	27327369		2203	4300	6503	SO:0001583	missense	1135	exon3			TAGCCCCGGAAGA	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.203G>A	8.37:g.27327369C>T	ENSP00000429616:p.Arg68Gln	79	0	0		92	43	0.467391	NM_000742	A8KAX3|B4DK19|J3KMY9|Q9HAQ3	Missense_Mutation	SNP	ENST00000520933.2	37	CCDS6059.1	.	.	.	.	.	.	.	.	.	.	C	13.44	2.237311	0.39498	.	.	ENSG00000120903	ENST00000407991;ENST00000520933;ENST00000240132;ENST00000524096;ENST00000518712	T;T;T;T;T	0.62105	0.05;0.05;0.05;0.05;0.05	4.77	3.89	0.44902	Neurotransmitter-gated ion-channel ligand-binding (3);	0.410909	0.25143	N	0.032809	T	0.47488	0.1448	L	0.33753	1.03	0.09310	N	1	B;B	0.33073	0.396;0.396	B;B	0.33568	0.166;0.166	T	0.41251	-0.9519	10	0.45353	T	0.12	.	6.9775	0.24683	0.0:0.7318:0.1747:0.0935	.	68;68	B4DK19;Q15822	.;ACHA2_HUMAN	Q	68	ENSP00000385026:R68Q;ENSP00000429616:R68Q;ENSP00000240132:R68Q;ENSP00000430422:R68Q;ENSP00000430856:R68Q	ENSP00000240132:R68Q	R	-	2	0	CHRNA2	27383286	0.000000	0.05858	0.789000	0.31954	0.875000	0.50365	0.006000	0.13152	1.380000	0.46344	0.561000	0.74099	CGG	.	.	none		0.632	CHRNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376125.4			T	27327369	C	T	27327369	3	4	25	1	0	0	0	0	1	0	0	0	3385	652	23	1	1406	1	CHRNA2	8	27327369	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2048221	27327369	119036653	327	9236											
DUSP4	1846	hgsc.bcm.edu	37	chr8	29197685	29197685	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgtggcactggggggaaccGggggtgggatggctgccagg	5	6	22	8	1	0	0	0	0	0	0	0	2	0	2	2	9	2	2	2	9	1	0	rs371579846		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:29197685G>A	ENST00000240100.2	-	2	898	c.509C>T	c.(508-510)cCg>cTg	p.P170L	DUSP4_ENST00000240101.2_Missense_Mutation_p.P79L	NM_001394.6	NP_001385.1	Q13115	DUS4_HUMAN	dual specificity phosphatase 4	170					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)		GGGGGGAACCGGGGGTGGGAT	0.602											OREG0018686	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P170L		Atlas-SNP	.											.	DUSP4	58	.	0			c.C509T						PASS	.	G	LEU/PRO,LEU/PRO	2,4404		0,2,2201	17	22	21		509,236	4.1	0	8		21	0,8600		0,0,4300	no	missense,missense	DUSP4	NM_001394.6,NM_057158.3	98,98	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	possibly-damaging,possibly-damaging	170/395,79/304	29197685	2,13004	2203	4300	6503	SO:0001583	missense	1846	exon2			GGAACCGGGGGTG	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.509C>T	8.37:g.29197685G>A	ENSP00000240100:p.Pro170Leu	47	0	0	807	52	20	0.384615	NM_001394	B2RBU5|D3DSU4|G5E930|Q13524	Missense_Mutation	SNP	ENST00000240100.2	37	CCDS6072.1	.	.	.	.	.	.	.	.	.	.	G	13.44	2.237221	0.39498	4.54E-4	0.0	ENSG00000120875	ENST00000240100;ENST00000240101	T;T	0.03413	4.17;3.94	5.01	4.13	0.48395	Rhodanese-like (1);	0.585786	0.16408	N	0.215753	T	0.03739	0.0106	L	0.42245	1.32	0.58432	D	0.999995	P;P	0.35774	0.458;0.519	B;B	0.24974	0.017;0.057	T	0.48433	-0.9036	10	0.59425	D	0.04	.	9.9081	0.41388	0.0962:0.0:0.9038:0.0	.	170;79	Q13115;G5E930	DUS4_HUMAN;.	L	170;79	ENSP00000240100:P170L;ENSP00000240101:P79L	ENSP00000240100:P170L	P	-	2	0	DUSP4	29253604	1.000000	0.71417	0.019000	0.16419	0.332000	0.28634	5.751000	0.68720	1.427000	0.47276	0.650000	0.86243	CCG	.	.	weak		0.602	DUSP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257249.1	NM_001394		A	29197685	G	A	29197685	3	1	25	1	0	0	0	0	1	0	0	0	4829	1116	39	1	687	1	DUSP4	8	29197685	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1870316	29197685	117166337	328	9237											
NRG1	3084	hgsc.bcm.edu	37	chr8	32611970	32611970	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtggtcggcatcatgtgtGtggtggcctactgcaaaacc	7	12	13	9	1	1	0	1	0	0	0	2	0	1	0	2	4	3	2	2	4	3	2	rs74942016	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:32611970G>T	ENST00000405005.3	+	8	781	c.781G>T	c.(781-783)Gtg>Ttg	p.V261L	NRG1_ENST00000519301.1_Missense_Mutation_p.V211L|NRG1_ENST00000341377.5_3'UTR|NRG1_ENST00000287842.3_Missense_Mutation_p.V258L|NRG1_ENST00000523079.1_Missense_Mutation_p.V258L|NRG1_ENST00000521670.1_Missense_Mutation_p.V261L|NRG1_ENST00000539990.1_Missense_Mutation_p.V104L|NRG1_ENST00000287845.5_Missense_Mutation_p.V232L|NRG1_ENST00000356819.4_Missense_Mutation_p.V266L|NRG1_ENST00000338921.4_Missense_Mutation_p.V269L			Q02297	NRG1_HUMAN	neuregulin 1	261				V -> L (in Ref. 10; ABQ53540). {ECO:0000305}.	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)		CATCATGTGTGTGGTGGCCTA	0.527													G|||	72	0.014377	0.0008	0.0259	5008	,	,		17487	0.0		0.0467	False		,,,				2504	0.0061				p.V266L		Atlas-SNP	.											.	NRG1	260	.	0			c.G796T	GRCh37	CM066934	NRG1	M	rs74942016	PASS	.	G	LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL	47,4359	48.9+/-83.8	0,47,2156	226	165	186		682,319,733,631,772,772,796,772,781,781	5.6	1	8	dbSNP_131	186	405,8195	127.5+/-185.8	12,381,3907	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	NRG1	NM_001159995.1,NM_001159996.1,NM_001159999.1,NM_001160001.1,NM_001160004.1,NM_001160008.1,NM_013956.3,NM_013957.3,NM_013960.3,NM_013964.3	32,32,32,32,32,32,32,32,32,32	12,428,6063	TT,TG,GG		4.7093,1.0667,3.4753	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	228/608,107/309,245/625,211/591,258/460,258/421,266/646,258/638,261/463,261/641	32611970	452,12554	2203	4300	6503	SO:0001583	missense	3084	exon9			ATGTGTGTGGTGG	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.781G>T	8.37:g.32611970G>T	ENSP00000384620:p.Val261Leu	146	0	0		168	76	0.452381	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	37	CCDS6085.1	40	0.018315018315018316	0	0.0	9	0.024861878453038673	0	0.0	31	0.040897097625329816	G	35	5.558867	0.96514	0.010667	0.047093	ENSG00000157168	ENST00000518104;ENST00000519301;ENST00000523534;ENST00000523079;ENST00000338921;ENST00000356819;ENST00000287840;ENST00000287845;ENST00000287842;ENST00000405005;ENST00000521670;ENST00000522402;ENST00000519240;ENST00000539990	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.61040	0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;2.63;0.14	5.62	5.62	0.85841	Neuregulin 1-related, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.40932	0.1137	M	0.73962	2.25	0.80722	D	1	D;D;D;D;D;D;P;D;P;D;D	0.71674	0.979;0.998;0.995;0.979;0.983;0.995;0.599;0.962;0.946;0.979;0.994	D;D;D;P;D;D;B;P;P;P;D	0.85130	0.986;0.997;0.972;0.879;0.926;0.972;0.283;0.879;0.893;0.879;0.914	T	0.67722	-0.5597	10	0.72032	D	0.01	-36.9375	19.6569	0.95845	0.0:0.0:1.0:0.0	.	104;107;258;232;266;257;269;258;261;266;261	B7Z1E3;B7Z1D7;E9PHH4;F8W9E3;Q7RTW4;B0FYA9;Q02297-2;Q02297-7;Q02297;Q02297-6;Q02297-3	.;.;.;.;.;.;.;.;NRG1_HUMAN;.;.	L	228;211;334;258;269;266;261;232;258;261;261;107;104;104	ENSP00000430053:V228L;ENSP00000429582:V211L;ENSP00000429067:V334L;ENSP00000430120:V258L;ENSP00000343395:V269L;ENSP00000349275:V266L;ENSP00000287840:V261L;ENSP00000287845:V232L;ENSP00000287842:V258L;ENSP00000384620:V261L;ENSP00000428828:V261L;ENSP00000430862:V107L;ENSP00000428411:V104L;ENSP00000439276:V104L	ENSP00000287840:V261L	V	+	1	0	NRG1	32731512	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.639000	0.89480	0.650000	0.86243	GTG	G|0.968;T|0.032	0.032	strong		0.527	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1			T	32611970	G	T	32611970	3	4	25	1	0	0	0	0	1	0	0	0	10656	1377	48	4	2407	4	NRG1	8	32611970	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	3414285	32611970	113752052	329	9238											
BAG4	9530	hgsc.bcm.edu	37	chr8	38034402	38034402	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gatcccatgtcggccctgagGcgctcgggctacggccccag	5	6	14	16	4	0	1	0	1	0	0	3	2	1	1	4	4	1	2	4	4	1	1	rs61731143	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:38034402G>A	ENST00000287322.4	+	1	286	c.15G>A	c.(13-15)agG>agA	p.R5R	LSM1_ENST00000311351.4_5'Flank|LSM1_ENST00000520755.1_5'Flank|BAG4_ENST00000521282.1_Intron|BAG4_ENST00000432471.2_Silent_p.R5R|LSM1_ENST00000522515.1_5'Flank	NM_004874.3	NP_004865.1	O95429	BAG4_HUMAN	BCL2-associated athanogene 4	5					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)				CGGCCCTGAGGCGCTCGGGCT	0.701													G|||	16	0.00319489	0.0	0.0144	5008	,	,		12933	0.0		0.006	False		,,,				2504	0.0				p.R5R		Atlas-SNP	.											.	BAG4	32	.	0			c.G15A						PASS	.	G	,	3,4047		0,3,2022	12	10	11		15,15	3.6	1	8	dbSNP_129	11	56,7836		0,56,3890	no	coding-synonymous,coding-synonymous	BAG4	NM_001204878.1,NM_004874.3	,	0,59,5912	AA,AG,GG		0.7096,0.0741,0.4941	,	5/422,5/458	38034402	59,11883	2025	3946	5971	SO:0001819	synonymous_variant	9530	exon1			CCTGAGGCGCTCG	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.15G>A	8.37:g.38034402G>A		39	0	0		72	36	0.5	NM_001204878	B4E217|O95818	Silent	SNP	ENST00000287322.4	37	CCDS6104.1																																																																																			G|0.995;A|0.005	0.005	strong		0.701	BAG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377038.2	NM_004874		A	38034402	G	A	38034402	2	1	25	1	0	0	0	0	0	0	0	1	1289	1194	42	2		2	BAG4	8	38034402	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	5422432	38034402	108329620	330	9239											
LETM2	137994	hgsc.bcm.edu	37	chr8	38250202	38250202	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggatcctagtcagccaggcAatacagtacttcacccagga	12	7	9	13	1	2	0	2	0	0	0	3	2	3	2	3	3	3	2	3	3	4	4			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:38250202A>G	ENST00000379957.4	+	3	317	c.190A>G	c.(190-192)Aat>Gat	p.N64D	LETM2_ENST00000297720.5_Missense_Mutation_p.N17D|LETM2_ENST00000519476.2_Missense_Mutation_p.N64D|LETM2_ENST00000524874.1_Missense_Mutation_p.N64D|LETM2_ENST00000523983.2_Missense_Mutation_p.N17D	NM_001199659.1	NP_001186588.1	Q2VYF4	LETM2_HUMAN	leucine zipper-EF-hand containing transmembrane protein 2	64						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				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)			TCAGCCAGGCAATACAGTACT	0.453																																					p.N17D		Atlas-SNP	.											.	LETM2	57	.	0			c.A49G						PASS	.						86	89	88					8																	38250202		2203	4300	6503	SO:0001583	missense	137994	exon3			CCAGGCAATACAG	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.190A>G	8.37:g.38250202A>G	ENSP00000369291:p.Asn64Asp	79	0	0		71	37	0.521127	NM_001199659	A6NMG3|Q8NCR2|Q96LL1	Missense_Mutation	SNP	ENST00000379957.4	37		.	.	.	.	.	.	.	.	.	.	A	6.285	0.420678	0.11928	.	.	ENSG00000165046	ENST00000527334;ENST00000519476;ENST00000297720;ENST00000524874;ENST00000379957;ENST00000523983;ENST00000526356	.	.	.	5.75	1.81	0.25067	.	1.355500	0.04352	N	0.355909	T	0.30386	0.0763	L	0.56769	1.78	0.09310	N	0.999997	B;B;P	0.34462	0.201;0.094;0.454	B;B;B	0.30401	0.016;0.016;0.115	T	0.14504	-1.0470	9	0.18276	T	0.48	.	2.9332	0.05805	0.3552:0.4136:0.098:0.1332	.	64;64;64	Q2VYF4;E9PMA4;A8K1M9	LETM2_HUMAN;.;.	D	64;64;17;64;64;17;64	.	ENSP00000297720:N17D	N	+	1	0	LETM2	38369359	0.000000	0.05858	0.020000	0.16555	0.053000	0.15095	-0.173000	0.09854	0.059000	0.16252	0.533000	0.62120	AAT	.	.	none		0.453	LETM2-013	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000381816.1	NM_144652		G	38250202	A	G	38250202	3	3	25	1	0	0	0	0	1	0	0	0	8744	130	5	3	51	3	LETM2	8	38250202	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	215800	38250202	108113820	331	9240											
ADAM18	8749	hgsc.bcm.edu	37	chr8	39468070	39468070	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatttctccagtttgaaaatAtcagttatggaattgaacca	14	14	7	6	0	2	2	1	2	1	0	3	4	2	3	2	1	1	2	2	1	6	5	rs139114737	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:39468070A>C	ENST00000265707.5	+	6	412	c.367A>C	c.(367-369)Atc>Ctc	p.I123L	ADAM18_ENST00000541111.1_Intron|ADAM18_ENST00000379866.1_Missense_Mutation_p.I123L|ADAM18_ENST00000520772.1_Missense_Mutation_p.I123L	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	123					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)			GTTTGAAAATATCAGTTATGG	0.289													a|||	22	0.00439297	0.0106	0.0072	5008	,	,		16258	0.0		0.003	False		,,,				2504	0.0				p.I123L		Atlas-SNP	.											.	ADAM18	169	.	0			c.A367C						PASS	.	G	LEU/ILE,LEU/ILE	31,4357	33.5+/-64.1	0,31,2163	37	38	38		367,367	-3.8	0.5	8	dbSNP_134	38	11,8575	8.4+/-32.0	0,11,4282	yes	missense,missense	ADAM18	NM_001190956.1,NM_014237.2	5,5	0,42,6445	CC,CA,AA		0.1281,0.7065,0.3237	benign,benign	123/183,123/740	39468070	42,12932	2194	4293	6487	SO:0001583	missense	8749	exon6			GAAAATATCAGTT	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.367A>C	8.37:g.39468070A>C	ENSP00000265707:p.Ile123Leu	208	0	0		225	93	0.413333	NM_001190956	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	37	CCDS6113.1	10	0.004578754578754579	6	0.012195121951219513	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	a	8.502	0.864400	0.17250	0.007065	0.001281	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000520772;ENST00000522198	T;T;T	0.05513	3.43;3.43;3.43	5.25	-3.75	0.04372	Peptidase M12B, propeptide (1);	0.750320	0.11876	N	0.521007	T	0.04272	0.0118	L	0.40543	1.245	0.29468	N	0.857287	B;B;B	0.26845	0.133;0.161;0.056	B;B;B	0.39152	0.192;0.292;0.042	T	0.45818	-0.9235	10	0.22109	T	0.4	.	6.7801	0.23640	0.5203:0.0:0.3672:0.1125	.	123;123;123	Q9Y3Q7-2;Q9Y3Q7;Q6IRW9	.;ADA18_HUMAN;.	L	123;123;123;79	ENSP00000265707:I123L;ENSP00000369195:I123L;ENSP00000429908:I123L	ENSP00000265707:I123L	I	+	1	0	ADAM18	39587227	0.275000	0.24201	0.488000	0.27440	0.089000	0.18198	-0.094000	0.11094	-0.734000	0.04843	-2.260000	0.00280	ATC	A|0.997;C|0.003	0.003	strong		0.289	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237		C	39468070	A	C	39468070	3	2	25	1	0	0	0	0	1	0	0	0	239	449	16	5	389	5	ADAM18	8	39468070	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	1217868	39468070	106895952	332	9241											
ADAM2	2515	hgsc.bcm.edu	37	chr8	39695677	39695677	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	catccgcagcccgccgagccCgctgagcagaaacaagacgc	11	2	11	17	5	0	3	0	1	0	2	1	4	1	3	4	0	4	3	4	0	2	0	rs34800519	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:39695677C>A	ENST00000265708.4	-	1	131	c.28G>T	c.(28-30)Ggg>Tgg	p.G10W	ADAM2_ENST00000379853.2_Missense_Mutation_p.G10W|ADAM2_ENST00000523181.1_5'UTR|ADAM2_ENST00000521880.1_Missense_Mutation_p.G10W|ADAM2_ENST00000347580.4_Missense_Mutation_p.G10W	NM_001464.3	NP_001455.3	Q99965	ADAM2_HUMAN	ADAM metallopeptidase domain 2	10			G -> W (in dbSNP:rs34800519).		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)		CCGCCGAGCCCGCTGAGCAGA	0.572													C|||	132	0.0263578	0.0923	0.0101	5008	,	,		16527	0.0		0.003	False		,,,				2504	0.0				p.G10W		Atlas-SNP	.											ADAM2,NS,carcinoma,+1,1	ADAM2	124	1	0			c.G28T						PASS	.	C	TRP/GLY	299,4107	164.4+/-196.0	19,261,1923	80	80	80		28	3.3	0.3	8	dbSNP_126	80	16,8584	11.9+/-42.8	0,16,4284	yes	missense	ADAM2	NM_001464.3	184	19,277,6207	AA,AC,CC		0.186,6.7862,2.422	probably-damaging	10/736	39695677	315,12691	2203	4300	6503	SO:0001583	missense	2515	exon1			CGAGCCCGCTGAG	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.28G>T	8.37:g.39695677C>A	ENSP00000265708:p.Gly10Trp	113	0	0		124	49	0.395161	NM_001464	P78326|Q9UQQ8	Missense_Mutation	SNP	ENST00000265708.4	37	CCDS34884.1	54	0.024725274725274724	47	0.09552845528455285	4	0.011049723756906077	0	0.0	3	0.00395778364116095	C	15.16	2.751827	0.49362	0.067862	0.00186	ENSG00000104755	ENST00000347580;ENST00000379853;ENST00000265708;ENST00000521880	T;T;T;T	0.02258	5.01;4.37;5.24;5.21	3.26	3.26	0.37387	.	.	.	.	.	T	0.00300	0.0009	M	0.80982	2.52	0.19300	N	0.999973	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.98;0.999;0.991;0.971	T	0.04053	-1.0981	8	.	.	.	.	10.2854	0.43564	0.0:1.0:0.0:0.0	rs34800519	10;10;10;10	B4DWY7;Q6P2G0;Q99965-2;Q99965	.;.;.;ADAM2_HUMAN	W	10	ENSP00000343854:G10W;ENSP00000369182:G10W;ENSP00000265708:G10W;ENSP00000429352:G10W	.	G	-	1	0	ADAM2	39814834	0.048000	0.20356	0.275000	0.24674	0.128000	0.20619	1.104000	0.31074	2.114000	0.64651	0.460000	0.39030	GGG	C|0.977;A|0.023	0.023	strong		0.572	ADAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376926.1	NM_001464		A	39695677	C	A	39695677	3	1	25	1	0	0	0	0	1	0	0	0	241	652	23	4	2259	4	ADAM2	8	39695677	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	227607	39695677	106668345	333	9242											
PXDNL	137902	hgsc.bcm.edu	37	chr8	52321966	52321966	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cagcgccgcgccccacgtggGctgctgcaggttgttgcacg	4	7	15	15	5	0	0	0	0	0	0	0	0	0	0	3	2	4	6	3	2	0	2	rs201280324	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:52321966G>A	ENST00000356297.4	-	17	2318	c.2218C>T	c.(2218-2220)Ccc>Tcc	p.P740S	PXDNL_ENST00000543296.1_Missense_Mutation_p.P740S	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	740					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)				CCCCACGTGGGCTGCTGCAGG	0.701													G|||	7	0.00139776	0.0	0.0014	5008	,	,		8293	0.0		0.005	False		,,,				2504	0.001				p.P740S		Atlas-SNP	.											PXDNL_ENST00000356297,NS,carcinoma,+2,1	PXDNL	414	1	0			c.C2218T						scavenged	.	G	SER/PRO	8,4010		0,8,2001	17	19	18		2218	1.8	0	8		18	58,8254		0,58,4098	yes	missense	PXDNL	NM_144651.4	74	0,66,6099	AA,AG,GG		0.6978,0.1991,0.5353	probably-damaging	740/1464	52321966	66,12264	2009	4156	6165	SO:0001583	missense	137902	exon17			ACGTGGGCTGCTG		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.2218C>T	8.37:g.52321966G>A	ENSP00000348645:p.Pro740Ser	28	0	0		34	14	0.411765	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	G	16.46	3.130556	0.56828	0.001991	0.006978	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.78246	-1.16;-1.16	3.71	1.79	0.24919	.	.	.	.	.	T	0.79736	0.4497	M	0.76727	2.345	0.36838	D	0.887265	D	0.65815	0.995	D	0.70016	0.967	T	0.81002	-0.1130	9	0.72032	D	0.01	.	5.8018	0.18417	0.1109:0.0:0.6977:0.1914	.	740	A1KZ92	PXDNL_HUMAN	S	740	ENSP00000348645:P740S;ENSP00000444865:P740S	ENSP00000348645:P740S	P	-	1	0	PXDNL	52484519	1.000000	0.71417	0.042000	0.18584	0.667000	0.39255	8.437000	0.90302	0.153000	0.19213	0.555000	0.69702	CCC	G|0.998;A|0.002	0.002	strong		0.701	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		A	52321966	G	A	52321966	3	1	25	1	0	0	0	0	1	0	0	0	12863	1203	42	2	2201	2	PXDNL	8	52321966	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	12626289	52321966	94042056	334	9243											
NPBWR1	2831	hgsc.bcm.edu	37	chr8	53853160	53853160	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accctgctgtgccggctgcaTgccatgcggctggacagcca	6	7	13	15	2	0	0	0	0	0	0	0	1	0	1	4	3	6	4	4	3	0	0	rs75387626	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:53853160T>C	ENST00000331251.3	+	1	2170	c.693T>C	c.(691-693)caT>caC	p.H231H		NM_005285.3	NP_005276.2	P48145	NPBW1_HUMAN	neuropeptides B/W receptor 1	231					G-protein coupled receptor signaling pathway (GO:0007186)|opioid receptor signaling pathway (GO:0038003)|regulation of metabolic process (GO:0019222)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|opioid receptor activity (GO:0004985)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)	17		Lung NSC(129;0.0222)|all_epithelial(80;0.0301)|all_lung(136;0.0431)				GCCGGCTGCATGCCATGCGGC	0.667													T|||	170	0.0339457	0.0023	0.0245	5008	,	,		16708	0.0079		0.0527	False		,,,				2504	0.091				p.H231H		Atlas-SNP	.											.	NPBWR1	38	.	0			c.T693C						PASS	.	T		28,4360		0,28,2166	30	17	21		693	-2.3	1	8	dbSNP_132	21	291,8255		5,281,3987	no	coding-synonymous	NPBWR1	NM_005285.3		5,309,6153	CC,CT,TT		3.4051,0.6381,2.4664		231/329	53853160	319,12615	2194	4273	6467	SO:0001819	synonymous_variant	2831	exon1			GCTGCATGCCATG	BC033145	CCDS6151.1	8p22-q21.13	2012-08-08	2006-02-15	2006-02-15		ENSG00000183729		"GPCR / Class A : Neuropeptide receptors : W/B"	4522	protein-coding gene	gene with protein product		600730	"G protein-coupled receptor 7"	GPR7		7590751, 12401809	Standard	NM_005285		Approved		uc011ldu.2	P48145		ENST00000331251.3:c.693T>C	8.37:g.53853160T>C		68	0	0		62	29	0.467742	NM_005285	Q6NTC7	Silent	SNP	ENST00000331251.3	37	CCDS6151.1																																																																																			T|0.975;C|0.025	0.025	strong		0.667	NPBWR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378047.1	NM_005285		C	53853160	T	C	53853160	2	2	25	1	0	0	0	0	0	0	0	1	10577	1461	51	3		3	NPBWR1	8	53853160	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	1531194	53853160	92510862	335	9244											
UBXN2B	137886	hgsc.bcm.edu	37	chr8	59358556	59358556	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcttattgatgattcagtGccaacaacaaaaattcaaat	16	13	5	7	0	3	2	2	2	1	0	3	2	3	2	1	0	3	1	1	0	6	5			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:59358556G>A	ENST00000399598.2	+	7	884	c.762G>A	c.(760-762)gtG>gtA	p.V254V		NM_001077619.1	NP_001071087.1	Q14CS0	UBX2B_HUMAN	UBX domain protein 2B	254	UBX. {ECO:0000255|PROSITE- ProRule:PRU00215}.					endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	13						ATGATTCAGTGCCAACAACAA	0.373																																					p.V254V		Atlas-SNP	.											.	UBXN2B	36	.	0			c.G762A						PASS	.						139	122	128					8																	59358556		1863	4092	5955	SO:0001819	synonymous_variant	137886	exon7			TTCAGTGCCAACA	AK054658	CCDS43741.1	8q12.1	2008-08-08			ENSG00000215114	ENSG00000215114		"UBX domain containing"	27035	protein-coding gene	gene with protein product		610686				8619474, 9110174	Standard	NM_001077619		Approved	p37	uc003xtl.3	Q14CS0	OTTHUMG00000164300	ENST00000399598.2:c.762G>A	8.37:g.59358556G>A		78	0	0		62	30	0.483871	NM_001077619	B3KWZ3	Silent	SNP	ENST00000399598.2	37	CCDS43741.1																																																																																			.	.	none		0.373	UBXN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378184.1	NM_001077619		A	59358556	G	A	59358556	2	1	25	1	0	0	0	0	0	0	0	1	16930	1306	46	2		2	UBXN2B	8	59358556	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	5505396	59358556	87005466	336	9245											
KCNB2	9312	hgsc.bcm.edu	37	chr8	73849768	73849768	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggaaaatagaggcagtgcAccacagaccccgcccagcac	15	2	10	14	1	0	2	0	0	0	2	0	3	0	3	4	2	2	3	4	2	4	1	rs142525254	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:73849768A>C	ENST00000523207.1	+	3	2766	c.2178A>C	c.(2176-2178)gcA>gcC	p.A726A		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	726					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)	GAGGCAGTGCACCACAGACCC	0.522													A|||	49	0.00978435	0.0083	0.0058	5008	,	,		17236	0.0		0.0139	False		,,,				2504	0.0204				p.A726A		Atlas-SNP	.											.	KCNB2	228	.	0			c.A2178C						PASS	.	A		43,4363	45.3+/-79.5	0,43,2160	94	99	98		2178	-10.1	0.2	8	dbSNP_134	98	132,8468	66.0+/-128.3	0,132,4168	no	coding-synonymous	KCNB2	NM_004770.2		0,175,6328	CC,CA,AA		1.5349,0.9759,1.3455		726/912	73849768	175,12831	2203	4300	6503	SO:0001819	synonymous_variant	9312	exon3			CAGTGCACCACAG	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.2178A>C	8.37:g.73849768A>C		63	0	0		56	23	0.410714	NM_004770	Q7Z7D0|Q9BXD3	Silent	SNP	ENST00000523207.1	37	CCDS6209.1																																																																																			A|0.989;C|0.011	0.011	strong		0.522	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770		C	73849768	A	C	73849768	2	2	25	1	0	0	0	0	0	0	0	1	8022	146	6	5		5	KCNB2	8	73849768	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	14491212	73849768	72514254	337	9246											
RAD54B	25788	hgsc.bcm.edu	37	chr8	95399378	95399378	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttatcacaagttgagctacAttccttttcctattcaaaat	12	17	3	9	0	2	1	2	1	0	0	4	1	4	1	2	0	2	2	2	0	6	9			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:95399378A>G	ENST00000336148.5	-	11	1943	c.1819T>C	c.(1819-1821)Tgt>Cgt	p.C607R		NM_012415.3	NP_036547.1	Q9Y620	RA54B_HUMAN	RAD54 homolog B (S. cerevisiae)	607					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)			GTTGAGCTACATTCCTTTTCC	0.348								Direct reversal of damage;Homologous recombination																													p.C607R		Atlas-SNP	.											.	RAD54B	88	.	0			c.T1819C						PASS	.						101	94	97					8																	95399378		2203	4300	6503	SO:0001583	missense	25788	exon11			AGCTACATTCCTT	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.1819T>C	8.37:g.95399378A>G	ENSP00000336606:p.Cys607Arg	190	0	0		180	81	0.45	NM_012415	F6WBS8	Missense_Mutation	SNP	ENST00000336148.5	37	CCDS6262.1	.	.	.	.	.	.	.	.	.	.	A	7.240	0.601139	0.13939	.	.	ENSG00000197275	ENST00000336148;ENST00000546218	D	0.88586	-2.4	5.28	-0.253	0.12996	.	1.072940	0.06949	N	0.814172	T	0.81550	0.4846	L	0.60455	1.87	0.21416	N	0.999695	B	0.33413	0.411	B	0.25506	0.061	T	0.63462	-0.6632	10	0.14656	T	0.56	-24.2196	3.5354	0.07792	0.5686:0.0:0.1549:0.2765	.	607	Q9Y620	RA54B_HUMAN	R	607;279	ENSP00000336606:C607R	ENSP00000336606:C607R	C	-	1	0	RAD54B	95468554	0.224000	0.23674	0.348000	0.25681	0.965000	0.64279	0.519000	0.22862	0.025000	0.15241	0.477000	0.44152	TGT	.	.	none		0.348	RAD54B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257806.3	NM_012415		G	95399378	A	G	95399378	3	3	25	1	0	0	0	0	1	0	0	0	13007	217	8	3	933	3	RAD54B	8	95399378	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	21549610	95399378	50964644	338	9247											
VPS13B	157680	hgsc.bcm.edu	37	chr8	100443885	100443885	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatgcagtgaagcatctcaCactacaggtaaaataaaagt	18	8	8	7	0	1	1	1	1	1	0	2	2	1	1	0	1	3	3	0	1	7	3	rs61753722	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:100443885C>T	ENST00000358544.2	+	22	3314	c.3203C>T	c.(3202-3204)aCa>aTa	p.T1068I	VPS13B_ENST00000395996.1_Missense_Mutation_p.T1068I|VPS13B_ENST00000357162.2_Missense_Mutation_p.T1068I	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	1068					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)			AAGCATCTCACACTACAGGTA	0.308													C|||	55	0.0109824	0.0	0.013	5008	,	,		15552	0.0		0.006	False		,,,				2504	0.0409				p.T1068I	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.C3203T						PASS	.	C	ILE/THR,ILE/THR	5,4401	8.1+/-20.4	0,5,2198	59	64	62		3203,3203	4.4	1	8	dbSNP_129	62	89,8511	49.4+/-109.1	1,87,4212	yes	missense,missense	VPS13B	NM_017890.3,NM_152564.3	89,89	1,92,6410	TT,TC,CC		1.0349,0.1135,0.7227	probably-damaging,probably-damaging	1068/4023,1068/3998	100443885	94,12912	2203	4300	6503	SO:0001583	missense	157680	exon22			ATCTCACACTACA	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.3203C>T	8.37:g.100443885C>T	ENSP00000351346:p.Thr1068Ile	17	0	0		19	7	0.368421	NM_152564	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	9	0.004120879120879121	0	0.0	5	0.013812154696132596	0	0.0	4	0.005277044854881266	C	11.46	1.645534	0.29246	0.001135	0.010349	ENSG00000132549	ENST00000357162;ENST00000358544;ENST00000395996	T;T;T	0.46819	0.86;0.86;0.86	4.41	4.41	0.53225	.	0.119576	0.52532	D	0.000061	T	0.45054	0.1323	N	0.24115	0.695	0.53688	D	0.999974	D;D;D;B	0.71674	0.986;0.986;0.998;0.291	P;P;D;B	0.80764	0.558;0.675;0.994;0.143	T	0.42137	-0.9469	10	0.16420	T	0.52	.	17.3622	0.87354	0.0:1.0:0.0:0.0	rs61753722	1067;1068;1068;1068	Q7Z7G8-6;Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3	.;.;VP13B_HUMAN;.	I	1068	ENSP00000349685:T1068I;ENSP00000351346:T1068I;ENSP00000379318:T1068I	ENSP00000349685:T1068I	T	+	2	0	VPS13B	100513061	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.920000	0.75799	2.154000	0.67381	0.555000	0.69702	ACA	C|0.994;T|0.006	0.006	strong		0.308	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		T	100443885	C	T	100443885	3	4	25	1	0	0	0	0	1	0	0	0	17205	478	17	2	3408	2	VPS13B	8	100443885	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	5044507	100443885	45920137	339	9248											
KCNV1	27012	hgsc.bcm.edu	37	chr8	110986480	110986480	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagagcacgaagcggctgccGcccacgttgaccgtgaagca	10	4	14	13	5	0	3	0	2	0	1	0	5	0	3	3	1	4	4	3	1	2	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:110986480G>A	ENST00000524391.1	-	2	1170	c.138C>T	c.(136-138)ggC>ggT	p.G46G	RP11-696P8.2_ENST00000530667.1_RNA|KCNV1_ENST00000297404.1_Silent_p.G46G			Q6PIU1	KCNV1_HUMAN	potassium channel, subfamily V, member 1	46					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|ion channel inhibitor activity (GO:0008200)|potassium channel regulator activity (GO:0015459)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(20)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;5.35e-13)			AGCGGCTGCCGCCCACGTTGA	0.692																																					p.G46G		Atlas-SNP	.											.	KCNV1	101	.	0			c.C138T						PASS	.						8	7	8					8																	110986480		2140	4178	6318	SO:0001819	synonymous_variant	27012	exon1			GCTGCCGCCCACG	AF167082	CCDS6314.1	8q23.2	2011-07-05				ENSG00000164794		"Potassium channels", "Voltage-gated ion channels / Potassium channels"	18861	protein-coding gene	gene with protein product		608164				8670833, 16382104	Standard	NM_014379		Approved	Kv8.1	uc003ynr.4	Q6PIU1		ENST00000524391.1:c.138C>T	8.37:g.110986480G>A		8	0	0		14	7	0.5	NM_014379	Q9UHJ4	Silent	SNP	ENST00000524391.1	37	CCDS6314.1																																																																																			.	.	none		0.692	KCNV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385525.1	NM_014379		A	110986480	G	A	110986480	2	1	25	1	0	0	0	0	0	0	0	1	8103	1074	38	1		1	KCNV1	8	110986480	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	10542595	110986480	35377542	340	9249											
COL14A1	7373	hgsc.bcm.edu	37	chr8	121222046	121222046	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtacgacgtgactgagaacaGcatgcgagtcaaatgggatg	13	7	14	7	3	1	2	1	2	0	1	1	6	1	3	0	1	4	2	0	1	3	1	rs61753752	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:121222046G>A	ENST00000297848.3	+	12	1643	c.1373G>A	c.(1372-1374)aGc>aAc	p.S458N	COL14A1_ENST00000309791.4_Missense_Mutation_p.S458N|COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000537875.1_Missense_Mutation_p.S458N|COL14A1_ENST00000247781.3_Missense_Mutation_p.S363N	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)			ACTGAGAACAGCATGCGAGTC	0.468													G|||	5	0.000998403	0.0	0.0029	5008	,	,		14372	0.0		0.003	False		,,,				2504	0.0				p.S458N		Atlas-SNP	.											COL14A1,NS,carcinoma,-1,1	COL14A1	292	1	0			c.G1373A						PASS	.	G	ASN/SER	2,4404	2.1+/-5.4	0,2,2201	119	111	114		1373	5.3	1	8	dbSNP_129	114	26,8574	18.5+/-59.3	0,26,4274	yes	missense	COL14A1	NM_021110.1	46	0,28,6475	AA,AG,GG		0.3023,0.0454,0.2153	probably-damaging	458/1797	121222046	28,12978	2203	4300	6503	SO:0001583	missense	7373	exon12			AGAACAGCATGCG		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.1373G>A	8.37:g.121222046G>A	ENSP00000297848:p.Ser458Asn	93	0	0		114	56	0.491228	NM_021110		Missense_Mutation	SNP	ENST00000297848.3	37	CCDS34938.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	17.53	3.412148	0.62511	4.54E-4	0.003023	ENSG00000187955	ENST00000537875;ENST00000309791;ENST00000297848;ENST00000247781;ENST00000434620	T;T;T;T;T	0.62639	0.01;0.01;0.01;0.01;0.01	5.31	5.31	0.75309	Fibronectin, type III (4);	0.148564	0.64402	D	0.000013	T	0.79616	0.4476	M	0.84156	2.68	0.48135	D	0.999599	D;D	0.67145	0.996;0.99	P;P	0.60173	0.857;0.87	T	0.82534	-0.0409	10	0.87932	D	0	.	19.1802	0.93620	0.0:0.0:1.0:0.0	rs61753752	458;458	Q05707-2;Q05707	.;COEA1_HUMAN	N	458;458;458;363;271	ENSP00000443974:S458N;ENSP00000311809:S458N;ENSP00000297848:S458N;ENSP00000247781:S363N;ENSP00000409461:S271N	ENSP00000247781:S363N	S	+	2	0	COL14A1	121291227	1.000000	0.71417	0.960000	0.40013	0.256000	0.26092	4.592000	0.61027	2.748000	0.94277	0.650000	0.86243	AGC	G|0.998;A|0.002	0.002	strong		0.468	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		A	121222046	G	A	121222046	3	1	25	1	0	0	0	0	1	0	0	0	3673	971	34	2	1415	2	COL14A1	8	121222046	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	10235566	121222046	25141976	341	9250											
COL14A1	7373	hgsc.bcm.edu	37	chr8	121357700	121357700	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tccaagggcctcctggggagCctgggaggccaggctcacct	6	6	15	14	0	1	0	1	0	0	0	3	2	3	2	6	6	1	1	6	6	1	0	rs137867605		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:121357700C>G	ENST00000297848.3	+	45	5245	c.4975C>G	c.(4975-4977)Cct>Gct	p.P1659A	COL14A1_ENST00000309791.4_Missense_Mutation_p.P1659A|COL14A1_ENST00000247781.3_Missense_Mutation_p.P1564A	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)			TCCTGGGGAGCCTGGGAGGCC	0.637													C|||	1	0.000199681	0.0	0.0	5008	,	,		16125	0.0		0.001	False		,,,				2504	0.0				p.P1659A		Atlas-SNP	.											.	COL14A1	292	.	0			c.C4975G						PASS	.	C	ALA/PRO	1,4405	2.1+/-5.4	0,1,2202	57	56	56		4975	5.8	1	8	dbSNP_134	56	10,8590	7.7+/-29.5	0,10,4290	yes	missense	COL14A1	NM_021110.1	27	0,11,6492	GG,GC,CC		0.1163,0.0227,0.0846	probably-damaging	1659/1797	121357700	11,12995	2203	4300	6503	SO:0001583	missense	7373	exon45			GGGGAGCCTGGGA		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.4975C>G	8.37:g.121357700C>G	ENSP00000297848:p.Pro1659Ala	99	0	0		124	73	0.58871	NM_021110		Missense_Mutation	SNP	ENST00000297848.3	37	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.712324	0.89112	2.27E-4	0.001163	ENSG00000187955	ENST00000309791;ENST00000297848;ENST00000247781;ENST00000440844	D;D;D;D	0.93906	-3.3;-3.3;-3.3;-3.31	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	D	0.95962	0.8685	M	0.62016	1.91	0.80722	D	1	D	0.61697	0.99	D	0.77004	0.989	D	0.94953	0.8101	10	0.39692	T	0.17	.	17.7738	0.88501	0.0:1.0:0.0:0.0	.	1659	Q05707	COEA1_HUMAN	A	1659;1659;1564;6	ENSP00000311809:P1659A;ENSP00000297848:P1659A;ENSP00000247781:P1564A;ENSP00000403640:P6A	ENSP00000247781:P1564A	P	+	1	0	COL14A1	121426881	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.773000	0.55333	2.736000	0.93811	0.555000	0.69702	CCT	C|0.999;G|0.001	0.001	strong		0.637	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		G	121357700	C	G	121357700	3	3	25	1	0	0	0	0	1	0	0	0	3673	739	26	4	5149	4	COL14A1	8	121357700	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	135654	121357700	25006322	342	9251											
ZHX2	22882	hgsc.bcm.edu	37	chr8	123964819	123964819	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cccagttggcccccacaaagGtgacgcagcccatcctccag	9	5	9	18	1	0	1	0	1	0	0	2	1	2	1	6	2	1	2	6	2	1	1	rs9649951	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:123964819G>A	ENST00000314393.4	+	3	1904	c.1069G>A	c.(1069-1071)Gtg>Atg	p.V357M		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	357	Required for homodimerization.|Required for interaction with NFYA.|Required for nuclear localization.|Required for repressor activity.		V -> M (in dbSNP:rs9649951).		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)			CCCCACAAAGGTGACGCAGCC	0.617													G|||	50	0.00998403	0.0015	0.0144	5008	,	,		17314	0.001		0.0258	False		,,,				2504	0.0112				p.V357M	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											.	ZHX2	106	.	0			c.G1069A						PASS	.	G	MET/VAL	41,4365	45.3+/-79.5	0,41,2162	77	64	69		1069	1.4	0.4	8	dbSNP_119	69	373,8227	123.1+/-182.0	6,361,3933	yes	missense	ZHX2	NM_014943.3	21	6,402,6095	AA,AG,GG		4.3372,0.9305,3.1831	benign	357/838	123964819	414,12592	2203	4300	6503	SO:0001583	missense	22882	exon3			ACAAAGGTGACGC	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.1069G>A	8.37:g.123964819G>A	ENSP00000314709:p.Val357Met	121	0	0		130	56	0.430769	NM_014943		Missense_Mutation	SNP	ENST00000314393.4	37	CCDS6336.1	29	0.013278388278388278	1	0.0020325203252032522	10	0.027624309392265192	1	0.0017482517482517483	17	0.022427440633245383	G	6.657	0.489767	0.12702	0.009305	0.043372	ENSG00000178764	ENST00000314393	T	0.17370	2.28	5.62	1.42	0.22433	.	0.551628	0.20995	N	0.081968	T	0.02119	0.0066	N	0.22421	0.69	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.24404	-1.0161	10	0.40728	T	0.16	-6.6533	8.5687	0.33556	0.636:0.0:0.364:0.0	rs9649951;rs9649951	357	Q9Y6X8	ZHX2_HUMAN	M	357	ENSP00000314709:V357M	ENSP00000314709:V357M	V	+	1	0	ZHX2	124034000	1.000000	0.71417	0.392000	0.26245	0.782000	0.44232	1.466000	0.35310	0.008000	0.14787	-0.361000	0.07541	GTG	G|0.974;A|0.026	0.026	strong		0.617	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943		A	123964819	G	A	123964819	3	1	25	1	0	0	0	0	1	0	0	0	17691	1261	44	2	1071	2	ZHX2	8	123964819	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2607119	123964819	22399203	343	9252											
KCNQ3	3786	hgsc.bcm.edu	37	chr8	133153451	133153451	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctctttattgtttaagccaaCaggctttggttctttagaag	9	17	8	7	0	2	1	0	0	2	1	2	1	2	1	1	2	2	3	1	2	5	9			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:133153451C>T	ENST00000388996.4	-	10	1810	c.1390G>A	c.(1390-1392)Gtt>Att	p.V464I	KCNQ3_ENST00000519445.1_Missense_Mutation_p.V464I|KCNQ3_ENST00000521134.1_Missense_Mutation_p.V344I	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	464					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)	TTTAAGCCAACAGGCTTTGGT	0.448																																					p.V464I		Atlas-SNP	.											.	KCNQ3	164	.	0			c.G1390A						PASS	.						135	140	138					8																	133153451		2203	4300	6503	SO:0001583	missense	3786	exon10			AGCCAACAGGCTT	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.1390G>A	8.37:g.133153451C>T	ENSP00000373648:p.Val464Ile	97	0	0		124	41	0.330645	NM_004519	A2VCT8|B4DJY4|E7EQ89	Missense_Mutation	SNP	ENST00000388996.4	37	CCDS34943.1	.	.	.	.	.	.	.	.	.	.	C	18.21	3.573918	0.65765	.	.	ENSG00000184156	ENST00000388996;ENST00000521134;ENST00000519445;ENST00000542679;ENST00000423790	D;D;D	0.99594	-6.25;-6.25;-6.25	5.63	5.63	0.86233	Potassium channel, voltage dependent, KCNQ, C-terminal (1);	0.189166	0.45606	D	0.000344	D	0.97102	0.9053	N	0.03608	-0.345	0.32328	N	0.561483	P;P	0.42123	0.771;0.771	B;B	0.39971	0.315;0.315	D	0.98773	1.0729	10	0.41790	T	0.15	-9.8868	13.6375	0.62230	0.1545:0.8455:0.0:0.0	.	464;464	E7ET42;O43525	.;KCNQ3_HUMAN	I	464;344;464;453;343	ENSP00000373648:V464I;ENSP00000429799:V344I;ENSP00000428790:V464I	ENSP00000373648:V464I	V	-	1	0	KCNQ3	133222633	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.046000	0.49846	2.652000	0.90054	0.655000	0.94253	GTT	.	.	none		0.448	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519		T	133153451	C	T	133153451	3	4	25	1	0	0	0	0	1	0	0	0	8093	478	17	2	1252	2	KCNQ3	8	133153451	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	9188632	133153451	13210571	344	9253											
TG	7038	hgsc.bcm.edu	37	chr8	134145885	134145885	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctggtccaagtacatctcGtctctgaagacatctgcagg	9	12	9	11	1	4	2	0	1	4	1	7	2	5	2	1	2	2	2	1	2	3	2	rs111563366		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:134145885G>A	ENST00000220616.4	+	47	8209	c.8169G>A	c.(8167-8169)tcG>tcA	p.S2723S	TG_ENST00000519543.1_Silent_p.S856S|TG_ENST00000542445.1_Silent_p.S1093S|TG_ENST00000377869.1_Silent_p.S2666S	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2723					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)		AGTACATCTCGTCTCTGAAGA	0.562																																					p.S2723S		Atlas-SNP	.											.	TG	416	.	0			c.G8169A						PASS	.	G		1,4405	4.2+/-10.8	0,1,2202	55	51	53		8169	-1.1	0.2	8	dbSNP_132	53	0,8600		0,0,4300	no	coding-synonymous	TG	NM_003235.4		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		2723/2769	134145885	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	7038	exon47			CATCTCGTCTCTG	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.8169G>A	8.37:g.134145885G>A		122	0	0		152	52	0.342105	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	G	0.026	-1.372534	0.01214	2.27E-4	0.0	ENSG00000042832	ENST00000519178	.	.	.	4.84	-1.12	0.09808	.	.	.	.	.	T	0.23171	0.0560	.	.	.	0.20403	N	0.999907	.	.	.	.	.	.	T	0.28554	-1.0040	4	.	.	.	.	4.4635	0.11678	0.3929:0.0:0.4574:0.1498	.	.	.	.	I	1179	.	.	V	+	1	0	TG	134215067	0.002000	0.14202	0.191000	0.23289	0.059000	0.15707	0.558000	0.23469	-0.078000	0.12730	-1.332000	0.01269	GTC	G|0.500;A|0.500	0.500	weak		0.562	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		A	134145885	G	A	134145885	2	1	25	1	0	0	0	0	0	0	0	1	15828	1132	40	1		1	TG	8	134145885	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	992434	134145885	12218137	345	9254											
ARC	23237	hgsc.bcm.edu	37	chr8	143694520	143694520	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctccgcctcatcctccacCgggaggtgggggccggccgg	3	6	16	16	4	2	0	1	0	1	0	5	1	4	1	7	6	0	0	7	6	0	0	rs371075422		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:143694520C>T	ENST00000356613.2	-	1	2313	c.1113G>A	c.(1111-1113)ccG>ccA	p.P371P	ARC_ENST00000581404.1_5'Flank	NM_015193.4	NP_056008.1	O60936	NOL3_HUMAN	activity-regulated cytoskeleton-associated protein	122					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)				CATCCTCCACCGGGAGGTGGG	0.726																																					p.P371P		Atlas-SNP	.											ARC,colon,carcinoma,-2,1	ARC	34	1	0			c.G1113A						PASS	.	C		0,4302		0,0,2151	8	11	10		1113	-2.4	0	8		10	1,8483		0,1,4241	no	coding-synonymous	ARC	NM_015193.3		0,1,6392	TT,TC,CC		0.0118,0.0,0.0078		371/397	143694520	1,12785	2151	4242	6393	SO:0001819	synonymous_variant	23237	exon1			CTCCACCGGGAGG	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.1113G>A	8.37:g.143694520C>T		32	0	0		53	23	0.433962	NM_015193	B4DFL0|O60937	Silent	SNP	ENST00000356613.2	37	CCDS34950.1																																																																																			.	.	weak		0.726	ARC-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259274.2			T	143694520	C	T	143694520	2	4	25	1	0	0	0	0	0	0	0	1	841	639	23	1		1	ARC	8	143694520	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	9548635	143694520	2669502	346	9255											
TOP1MT	116447	hgsc.bcm.edu	37	chr8	144399993	144399993	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcagctcctggaggtgcttGttcaggctggtcgtctgggg	4	12	16	9	1	3	0	2	0	1	0	5	1	4	1	1	6	2	4	1	6	0	2	rs146827342	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:144399993G>A	ENST00000329245.4	-	10	1264	c.1230C>T	c.(1228-1230)aaC>aaT	p.N410N	TOP1MT_ENST00000523676.1_Silent_p.N312N|TOP1MT_ENST00000519148.1_Silent_p.N312N|AC087793.1_ENST00000585120.1_RNA|TOP1MT_ENST00000521193.1_Silent_p.N312N	NM_052963.2	NP_443195.1	Q969P6	TOP1M_HUMAN	topoisomerase (DNA) I, mitochondrial	410		Interaction with DNA. {ECO:0000250}.			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)	GGAGGTGCTTGTTCAGGCTGG	0.617													G|||	5	0.000998403	0.0	0.0014	5008	,	,		16371	0.0		0.004	False		,,,				2504	0.0				p.N410N		Atlas-SNP	.											.	TOP1MT	63	.	0			c.C1230T						PASS	.	G		6,4400	12.9+/-30.5	0,6,2197	65	60	62		1230	1.9	0.4	8	dbSNP_134	62	27,8573	19.2+/-60.6	0,27,4273	no	coding-synonymous	TOP1MT	NM_052963.1		0,33,6470	AA,AG,GG		0.314,0.1362,0.2537		410/602	144399993	33,12973	2203	4300	6503	SO:0001819	synonymous_variant	116447	exon10			GTGCTTGTTCAGG	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.1230C>T	8.37:g.144399993G>A		83	0	0		98	43	0.438776	NM_052963	B7ZAR5|E7ES89|Q86ST4|Q86V82	Silent	SNP	ENST00000329245.4	37	CCDS6400.1																																																																																			G|0.997;A|0.003	0.003	strong		0.617	TOP1MT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381247.3	NM_052963		A	144399993	G	A	144399993	2	1	25	1	0	0	0	0	0	0	0	1	16379	1368	48	2		2	TOP1MT	8	144399993	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	705473	144399993	1964029	347	9256											
MAPK15	225689	hgsc.bcm.edu	37	chr8	144804000	144804000	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggccaaccaggccctgatcCggggtgactggaaccggggc	7	5	16	13	2	0	2	0	2	0	0	1	3	1	3	5	7	2	0	5	7	2	0	rs536928468		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:144804000C>T	ENST00000338033.4	+	13	1527	c.1408C>T	c.(1408-1410)Cgg>Tgg	p.R470W	RP11-429J17.5_ENST00000527908.1_RNA	NM_139021.2	NP_620590.2	Q8TD08	MK15_HUMAN	mitogen-activated protein kinase 15	470					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)			GGCCCTGATCCGGGGTGACTG	0.687													c|||	1	0.000199681	0.0008	0.0	5008	,	,		13081	0.0		0.0	False		,,,				2504	0.0				p.R470W		Atlas-SNP	.											.	MAPK15	32	.	0			c.C1408T						PASS	.						30	39	36					8																	144804000		1960	4118	6078	SO:0001583	missense	225689	exon13			CTGATCCGGGGTG	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.1408C>T	8.37:g.144804000C>T	ENSP00000337691:p.Arg470Trp	75	0	0		69	22	0.318841	NM_139021	Q2TCF9|Q8N362	Missense_Mutation	SNP	ENST00000338033.4	37	CCDS6409.2	.	.	.	.	.	.	.	.	.	.	c	12.80	2.045324	0.36085	.	.	ENSG00000181085	ENST00000338033	T	0.81330	-1.48	3.23	2.31	0.28768	.	0.000000	0.85682	U	0.000000	T	0.81884	0.4917	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.80761	-0.1238	10	0.87932	D	0	-20.9811	9.0646	0.36455	0.2217:0.7783:0.0:0.0	.	470	Q8TD08	MK15_HUMAN	W	470	ENSP00000337691:R470W	ENSP00000337691:R470W	R	+	1	2	MAPK15	144875988	0.017000	0.18338	0.486000	0.27416	0.049000	0.14656	1.449000	0.35123	0.519000	0.28406	0.306000	0.20318	CGG	.	.	none		0.687	MAPK15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000300348.1	NM_139021		T	144804000	C	T	144804000	3	4	25	1	0	0	0	0	1	0	0	0	9286	643	23	1	1458	1	MAPK15	8	144804000	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	404007	144804000	1560022	348	9257											
SCRIB	23513	hgsc.bcm.edu	37	chr8	144895018	144895018	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggcagcctccgcagcaggttCtgggacagcagcaggtcagt	8	6	15	12	1	2	0	1	0	1	0	3	1	3	1	2	4	4	6	2	4	0	1	rs75171224	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:144895018C>T	ENST00000320476.3	-	8	762	c.756G>A	c.(754-756)caG>caA	p.Q252Q	MIR937_ENST00000401271.1_RNA|SCRIB_ENST00000377533.3_Silent_p.Q171Q|SCRIB_ENST00000356994.2_Silent_p.Q252Q	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	252	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)			GCAGCAGGTTCTGGGACAGCA	0.706													C|||	24	0.00479233	0.0008	0.0072	5008	,	,		14449	0.0		0.0169	False		,,,				2504	0.001				p.Q252Q	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.G756A						PASS	.	C	,	8,4398	14.3+/-33.2	0,8,2195	35	35	35		756,756	4.2	1	8	dbSNP_131	35	140,8456	64.6+/-126.8	1,138,4159	no	coding-synonymous,coding-synonymous	SCRIB	NM_015356.3,NM_182706.3	,	1,146,6354	TT,TC,CC		1.6287,0.1816,1.1383	,	252/1631,252/1656	144895018	148,12854	2203	4298	6501	SO:0001819	synonymous_variant	23513	exon8			CAGGTTCTGGGAC	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.756G>A	8.37:g.144895018C>T		32	0	0		57	40	0.701754	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Silent	SNP	ENST00000320476.3	37	CCDS6411.1																																																																																			C|0.991;T|0.009	0.009	strong		0.706	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356		T	144895018	C	T	144895018	2	4	25	1	0	0	0	0	0	0	0	1	13952	912	32	2		2	SCRIB	8	144895018	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	91018	144895018	1469004	349	9258											
EPPK1	83481	hgsc.bcm.edu	37	chr8	144944225	144944225	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcctggtcaacatagccaCgctgaatggccactggcatg	9	9	10	13	1	2	1	1	1	1	0	3	1	2	1	3	3	2	2	3	3	3	1	rs118079568	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:144944225C>T	ENST00000525985.1	-	2	3268	c.3197G>A	c.(3196-3198)cGt>cAt	p.R1066H				P58107	EPIPL_HUMAN	epiplakin 1	1066						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)			AACATAGCCACGCTGAATGGC	0.642													C|||	26	0.00519169	0.0008	0.0144	5008	,	,		18612	0.001		0.0139	False		,,,				2504	0.0				p.R1066H		Atlas-SNP	.											.	EPPK1	199	.	0			c.G3197A						PASS	.	C	HIS/ARG	10,4230		1,8,2111	36	40	39		3197	3.6	0.9	8	dbSNP_132	39	145,8341		1,143,4099	yes	missense	EPPK1	NM_031308.1	29	2,151,6210	TT,TC,CC		1.7087,0.2358,1.218	probably-damaging	1066/2420	144944225	155,12571	2120	4243	6363	SO:0001583	missense	83481	exon1			TAGCCACGCTGAA	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.3197G>A	8.37:g.144944225C>T	ENSP00000436337:p.Arg1066His	154	0	0		167	90	0.538922	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		22	0.010073260073260074	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	15	0.01978891820580475	C	17.80	3.478453	0.63849	0.002358	0.017087	ENSG00000227184	ENST00000525985	T	0.79247	-1.25	4.54	3.64	0.41730	.	.	.	.	.	T	0.79227	0.4410	M	0.79693	2.465	0.28124	N	0.930474	D	0.89917	1.0	D	0.72338	0.977	T	0.75428	-0.3321	9	0.66056	D	0.02	.	11.5171	0.50529	0.1804:0.8195:0.0:0.0	.	1066	E9PPU0	.	H	1066	ENSP00000436337:R1066H	ENSP00000436337:R1066H	R	-	2	0	EPPK1	145016213	0.117000	0.22190	0.871000	0.34182	0.301000	0.27625	0.709000	0.25734	1.067000	0.40740	0.563000	0.77884	CGT	C|0.990;T|0.010	0.010	strong		0.642	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		T	144944225	C	T	144944225	3	4	25	1	0	0	0	0	1	0	0	0	5192	536	19	1	4069	1	EPPK1	8	144944225	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	49207	144944225	1419797	350	9259											
SPATC1	375686	hgsc.bcm.edu	37	chr8	145095328	145095328	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggccccactgggccccagTccccagcttgcgtggtaccc	5	6	12	18	1	0	0	0	0	0	0	1	1	1	0	7	3	3	2	7	3	1	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:145095328T>A	ENST00000377470.3	+	2	832	c.730T>A	c.(730-732)Tcc>Acc	p.S244T	SPATC1_ENST00000447830.2_Missense_Mutation_p.S244T	NM_198572.2	NP_940974.2	Q76KD6	SPERI_HUMAN	spermatogenesis and centriole associated 1	244						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)			TGGGCCCCAGTCCCCAGCTTG	0.677																																					p.S244T		Atlas-SNP	.											.	SPATC1	77	.	0			c.T730A						PASS	.						14	16	16					8																	145095328		2198	4293	6491	SO:0001583	missense	375686	exon2			CCCCAGTCCCCAG	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.730T>A	8.37:g.145095328T>A	ENSP00000366690:p.Ser244Thr	69	0	0		90	53	0.588889	NM_001134374	B4DWW9|Q5U5I8|Q7Z6L7	Missense_Mutation	SNP	ENST00000377470.3	37	CCDS6413.2	.	.	.	.	.	.	.	.	.	.	T	5.096	0.203364	0.09704	.	.	ENSG00000186583	ENST00000377470;ENST00000447830	T	0.44083	0.93	3.69	-3.7	0.04437	.	1.671390	0.03864	N	0.274514	T	0.23094	0.0558	L	0.36672	1.1	0.09310	N	1	B;B	0.14012	0.009;0.003	B;B	0.16289	0.015;0.006	T	0.16541	-1.0399	10	0.02654	T	1	-2.9873	0.8322	0.01132	0.172:0.1768:0.344:0.3072	.	244;244	B4DWW9;Q76KD6	.;SPERI_HUMAN	T	244	ENSP00000366690:S244T	ENSP00000366690:S244T	S	+	1	0	SPATC1	145167316	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-1.964000	0.01512	-0.526000	0.06383	0.260000	0.18958	TCC	.	.	none		0.677	SPATC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346926.1	NM_198572		A	145095328	T	A	145095328	3	1	25	1	0	0	0	0	1	0	0	0	15032	1667	58	5	736	5	SPATC1	8	145095328	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	151103	145095328	1268694	351	9260											
OPLAH	26873	hgsc.bcm.edu	37	chr8	145108191	145108191	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaccagctggatgcccttcTggttggctgccacctgggca	5	9	12	15	0	1	0	0	0	1	0	1	1	1	1	5	4	3	4	5	4	0	2	rs200702041	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:145108191T>C	ENST00000426825.1	-	20	2873	c.2792A>G	c.(2791-2793)cAg>cGg	p.Q931R	CTD-3065J16.6_ENST00000528912.1_RNA|CTD-3065J16.6_ENST00000561181.1_RNA|OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	931					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)			GATGCCCTTCTGGTTGGCTGC	0.657													T|||	2	0.000399361	0.0	0.0	5008	,	,		19625	0.0		0.002	False		,,,				2504	0.0				p.Q931R		Atlas-SNP	.											.	OPLAH	78	.	0			c.A2792G						PASS	.	T	ARG/GLN	2,4156		0,2,2077	50	56	54		2792	4.6	1	8		54	46,8358		0,46,4156	yes	missense	OPLAH	NM_017570.3	43	0,48,6233	CC,CT,TT		0.5474,0.0481,0.3821	benign	931/1289	145108191	48,12514	2079	4202	6281	SO:0001583	missense	26873	exon20			CCCTTCTGGTTGG	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.2792A>G	8.37:g.145108191T>C	ENSP00000475943:p.Gln931Arg	124	0	0		152	63	0.414474	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Missense_Mutation	SNP	ENST00000426825.1	37		.	.	.	.	.	.	.	.	.	.	T	15.78	2.934711	0.52866	4.81E-4	0.005474	ENSG00000178814	ENST00000426825	.	.	.	4.56	4.56	0.56223	.	0.000000	0.85682	D	0.000000	T	0.40815	0.1132	.	.	.	0.42144	D	0.991525	B	0.21225	0.053	B	0.25759	0.063	T	0.57039	-0.7879	7	0.42905	T	0.14	.	11.8502	0.52407	0.0:0.0:0.0:1.0	.	931	O14841	OPLA_HUMAN	R	931	.	ENSP00000412071:Q931R	Q	-	2	0	OPLAH	145180179	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.215000	0.42862	1.681000	0.50988	0.368000	0.22195	CAG	T|0.996;C|0.004	0.004	weak		0.657	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570		C	145108191	T	C	145108191	3	2	25	1	0	0	0	0	1	0	0	0	10885	1580	55	3	1108	3	OPLAH	8	145108191	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	12863	145108191	1255831	352	9261											
RECQL4	113655	hgsc.bcm.edu	37	chr8	145737123	145737123	+	IGR	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	acttctcctctggcctcaggGacaggaactggcggatgtcg	7	9	13	12	2	3	0	1	0	2	0	5	3	3	3	2	5	1	0	2	5	1	1	rs35346077	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:145737123G>A	ENST00000301327.4	+	0	1548				RECQL4_ENST00000428558.2_Missense_Mutation_p.S1148F|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)			TGGCCTCAGGGACAGGAACTG	0.662													G|||	4	0.000798722	0.0	0.0	5008	,	,		18429	0.0		0.002	False		,,,				2504	0.002				p.S1148F		Atlas-SNP	.											.	RECQL4	75	.	0			c.C3443T						PASS	.	G	PHE/SER	1,4329		0,1,2164	66	79	75		3444	5	1	8	dbSNP_126	75	13,8505		0,13,4246	no	missense	RECQL4	NM_004260.3	155	0,14,6410	AA,AG,GG		0.1526,0.0231,0.109	possibly-damaging	1148/1209	145737123	14,12834	2165	4259	6424	SO:0001628	intergenic_variant	9401	exon21			CTCAGGGACAGGA		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		8.37:g.145737123G>A		57	0	0		79	50	0.632911	NM_004260		Missense_Mutation	SNP	ENST00000301327.4	37	CCDS6431.1																																																																																			G|0.995;A|0.005	0.005	weak		0.662	MFSD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382478.2	NM_138431		A	145737123	G	A	145737123	1	1	25	0	1	0	0	0	0	0	0	0	13217	1174	41	2		2	RECQL4	8	145737123	IGR	SNP	G	TCGA-G8-6906-01A-11D-2210-10	628932	145737123	626899	353	9262											
VLDLR	7436	hgsc.bcm.edu	37	chr9	2644799	2644799	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcaaagacctagttataggcTacgagtgtgactgtgcagct	11	10	12	8	1	0	2	0	1	0	1	0	3	0	2	1	1	3	5	1	1	5	4	rs142885301	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:2644799T>C	ENST00000382100.3	+	8	1488	c.1132T>C	c.(1132-1134)Tac>Cac	p.Y378H	VLDLR_ENST00000382099.2_Missense_Mutation_p.Y378H	NM_003383.3	NP_003374.3	P98155	VLDLR_HUMAN	very low density lipoprotein receptor	378	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)		AGTTATAGGCTACGAGTGTGA	0.413																																					p.Y378H		Atlas-SNP	.											.	VLDLR	68	.	0			c.T1132C						PASS	.	T	HIS/TYR,HIS/TYR	1,4405	2.1+/-5.4	0,1,2202	95	95	95		1132,1132	5.8	1	9	dbSNP_134	95	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	VLDLR	NM_001018056.1,NM_003383.3	83,83	0,2,6501	CC,CT,TT		0.0116,0.0227,0.0154	possibly-damaging,possibly-damaging	378/846,378/874	2644799	2,13004	2203	4300	6503	SO:0001583	missense	7436	exon8			ATAGGCTACGAGT		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.1132T>C	9.37:g.2644799T>C	ENSP00000371532:p.Tyr378His	109	0	0		131	70	0.534351	NM_003383	B2RMZ7|D3DRH6|Q5VVF6	Missense_Mutation	SNP	ENST00000382100.3	37	CCDS6446.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.797534	0.90538	2.27E-4	1.16E-4	ENSG00000147852	ENST00000382100;ENST00000382099;ENST00000382092	D;D	0.96913	-4.17;-4.17	5.83	5.83	0.93111	Growth factor, receptor (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.48286	D	0.000194	D	0.97046	0.9035	L	0.52573	1.65	0.53688	D	0.999971	D;D;D	0.57257	0.979;0.964;0.964	D;P;P	0.65874	0.939;0.87;0.87	D	0.96766	0.9565	10	0.39692	T	0.17	.	16.1968	0.82036	0.0:0.0:0.0:1.0	.	378;378;378	P98155-2;Q5VVF5;P98155	.;.;VLDLR_HUMAN	H	378;378;257	ENSP00000371532:Y378H;ENSP00000371531:Y378H	ENSP00000371524:Y257H	Y	+	1	0	VLDLR	2634799	1.000000	0.71417	0.967000	0.41034	0.975000	0.68041	5.983000	0.70540	2.225000	0.72522	0.533000	0.62120	TAC	T|0.999;C|0.001	0.001	strong		0.413	VLDLR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051519.2	NM_003383		C	2644799	T	C	2644799	3	2	25	1	0	0	0	0	1	0	0	0	17189	1522	53	3	1162	3	VLDLR	9	2644799	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10		2644799	138568632	354	9263											
CDC37L1	55664	hgsc.bcm.edu	37	chr9	4679847	4679847	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaggaagagagtgacttcgAcgtgttccccagttctcccc	8	10	11	12	2	1	3	0	2	1	1	4	6	2	4	4	1	0	2	4	1	1	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:4679847A>C	ENST00000381854.3	+	1	282	c.80A>C	c.(79-81)gAc>gCc	p.D27A	RP11-6J24.6_ENST00000607997.1_lincRNA|CDC37L1_ENST00000381858.1_Missense_Mutation_p.D27A|CDC37L1_ENST00000479095.1_3'UTR	NM_017913.2	NP_060383.2	Q7L3B6	CD37L_HUMAN	cell division cycle 37-like 1	27	Self-association.					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)		AGTGACTTCGACGTGTTCCCC	0.697											OREG0019085	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D27A		Atlas-SNP	.											.	CDC37L1	19	.	0			c.A80C						PASS	.						43	49	47					9																	4679847		2202	4299	6501	SO:0001583	missense	55664	exon1			ACTTCGACGTGTT	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.80A>C	9.37:g.4679847A>C	ENSP00000371278:p.Asp27Ala	78	0	0	620	105	38	0.361905	NM_017913	B1AL70|Q9NWS3|Q9NX16	Missense_Mutation	SNP	ENST00000381854.3	37	CCDS6454.1	.	.	.	.	.	.	.	.	.	.	A	12.29	1.894709	0.33442	.	.	ENSG00000106993	ENST00000381858;ENST00000381854	T;T	0.44083	0.93;0.93	5.09	5.09	0.68999	.	0.233816	0.37053	N	0.002269	T	0.46908	0.1417	N	0.19112	0.55	0.32054	N	0.596549	D	0.63880	0.993	D	0.70227	0.968	T	0.57300	-0.7835	10	0.72032	D	0.01	-13.2073	11.1808	0.48627	1.0:0.0:0.0:0.0	.	27	Q7L3B6	CD37L_HUMAN	A	27	ENSP00000371282:D27A;ENSP00000371278:D27A	ENSP00000371278:D27A	D	+	2	0	CDC37L1	4669847	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	3.755000	0.55197	2.139000	0.66308	0.455000	0.32223	GAC	.	.	none		0.697	CDC37L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051564.1	NM_017913		C	4679847	A	C	4679847	3	2	25	1	0	0	0	0	1	0	0	0	3071	275	10	5	82	5	CDC37L1	9	4679847	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	2035048	4679847	136533584	355	9264											
JAK2	3717	hgsc.bcm.edu	37	chr9	5050706	5050706	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcggcatgattttgtgcaCggatggataaaagtacctgt	10	12	13	6	2	0	1	0	1	0	0	0	3	0	3	1	4	2	3	1	4	3	4	rs2230722	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:5050706C>T	ENST00000381652.3	+	6	983	c.489C>T	c.(487-489)caC>caT	p.H163H	JAK2_ENST00000539801.1_Silent_p.H163H|JAK2_ENST00000544510.1_Silent_p.H14H	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	163	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)	ATTTTGTGCACGGATGGATAA	0.343		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial				T|||	1794	0.358227	0.4887	0.3905	5008	,	,		15245	0.2708		0.3002	False		,,,				2504	0.3088				p.H163H		Atlas-SNP	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	35466	.	0			c.C489T						PASS	.	T		2047,2359	609.9+/-391.4	488,1071,644	110	123	118		489	-0.9	0.9	9	dbSNP_119	118	2589,6011	689.4+/-404.4	366,1857,2077	no	coding-synonymous	JAK2	NM_004972.3		854,2928,2721	TT,TC,CC		30.1047,46.4594,35.6451		163/1133	5050706	4636,8370	2203	4300	6503	SO:0001819	synonymous_variant	3717	exon6	Familial Cancer Database		TGTGCACGGATGG		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.489C>T	9.37:g.5050706C>T		75	0	0		83	82	0.987952	NM_004972	O14636|O75297	Silent	SNP	ENST00000381652.3	37	CCDS6457.1																																																																																			C|0.647;T|0.353	0.353	strong		0.343	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			T	5050706	C	T	5050706	2	4	25	1	0	0	0	0	0	0	0	1	7947	535	19	1		1	JAK2	9	5050706	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	370859	5050706	136162725	356	9265											
ERMP1	79956	hgsc.bcm.edu	37	chr9	5787439	5787439	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaaattggcacctgcacttcTatccagaactgccatgcaga	12	9	8	12	0	1	2	0	0	1	2	2	3	2	2	3	1	4	3	3	1	3	3	rs148237651		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:5787439T>C	ENST00000339450.5	-	14	2630	c.2541A>G	c.(2539-2541)atA>atG	p.I847M	ERMP1_ENST00000543230.1_3'UTR|ERMP1_ENST00000381506.3_3'UTR|ERMP1_ENST00000214893.5_5'UTR	NM_024896.2	NP_079172.2	Q7Z2K6	ERMP1_HUMAN	endoplasmic reticulum metallopeptidase 1	847						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)		CCTGCACTTCTATCCAGAACT	0.473																																					p.I847M		Atlas-SNP	.											.	ERMP1	63	.	0			c.A2541G						PASS	.	T	MET/ILE	0,4406		0,0,2203	110	108	108		2541	-3.8	1	9	dbSNP_134	108	3,8597	3.0+/-9.4	0,3,4297	yes	missense	ERMP1	NM_024896.2	10	0,3,6500	CC,CT,TT		0.0349,0.0,0.0231	probably-damaging	847/905	5787439	3,13003	2203	4300	6503	SO:0001583	missense	79956	exon14			CACTTCTATCCAG	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.2541A>G	9.37:g.5787439T>C	ENSP00000340427:p.Ile847Met	51	0	0		56	27	0.482143	NM_024896	B2RNA4|B3KSB1|Q8N5T5|Q9H5M1	Missense_Mutation	SNP	ENST00000339450.5	37	CCDS34983.1	.	.	.	.	.	.	.	.	.	.	T	11.10	1.538188	0.27475	0.0	3.49E-4	ENSG00000099219	ENST00000339450	T	0.53206	0.63	5.77	-3.81	0.04294	.	0.089070	0.85682	D	0.000000	T	0.50939	0.1645	L	0.55990	1.75	0.80722	D	1	D	0.71674	0.998	D	0.66602	0.945	T	0.51092	-0.8749	10	0.33940	T	0.23	-20.1147	7.7681	0.28991	0.3034:0.0:0.3774:0.3192	.	847	Q7Z2K6	ERMP1_HUMAN	M	847	ENSP00000340427:I847M	ENSP00000340427:I847M	I	-	3	3	ERMP1	5777439	0.996000	0.38824	0.989000	0.46669	0.032000	0.12392	0.236000	0.17967	-0.521000	0.06426	-0.472000	0.04984	ATA	T|1.000;C|0.000	0.000	weak		0.473	ERMP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354877.1	NM_024896		C	5787439	T	C	5787439	3	2	25	1	0	0	0	0	1	0	0	0	5238	1512	53	3	181	3	ERMP1	9	5787439	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	736733	5787439	135425992	357	9266											
MPDZ	8777	hgsc.bcm.edu	37	chr9	13183486	13183486	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caagaactgccatgaagagaTaaaatagaggcttgagtaga	18	7	11	5	0	0	6	0	2	0	4	0	7	0	6	1	1	2	2	1	1	7	4	rs34704118	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:13183486T>C	ENST00000319217.7	-	19	2827	c.2580A>G	c.(2578-2580)ttA>ttG	p.L860L	MPDZ_ENST00000536827.1_Silent_p.L860L|MPDZ_ENST00000381015.4_Silent_p.L860L|MPDZ_ENST00000381022.2_Silent_p.L860L|MPDZ_ENST00000447879.1_Silent_p.L860L|MPDZ_ENST00000546205.1_Silent_p.L860L|MPDZ_ENST00000541718.1_Silent_p.L860L	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	860					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)		CATGAAGAGATAAAATAGAGG	0.408													T|||	7	0.00139776	0.0	0.0072	5008	,	,		18769	0.0		0.001	False		,,,				2504	0.001				p.L860L		Atlas-SNP	.											MPDZ_ENST00000541718,colon,carcinoma,-2,2	MPDZ	324	2	0			c.A2580G						PASS	.	T		4,3782		0,4,1889	93	91	92		2580	0.8	0.8	9	dbSNP_126	92	55,8201		0,55,4073	no	coding-synonymous	MPDZ	NM_003829.3		0,59,5962	CC,CT,TT		0.6662,0.1057,0.49		860/2042	13183486	59,11983	1893	4128	6021	SO:0001819	synonymous_variant	8777	exon19			AAGAGATAAAATA	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.2580A>G	9.37:g.13183486T>C		109	0	0		91	41	0.450549	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Silent	SNP	ENST00000319217.7	37																																																																																				T|0.997;C|0.003	0.003	strong		0.408	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829		C	13183486	T	C	13183486	2	2	25	1	0	0	0	0	0	0	0	1	9731	1403	49	3		3	MPDZ	9	13183486	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	7396047	13183486	128029945	358	9267											
SNAPC3	6619	hgsc.bcm.edu	37	chr9	15459821	15459821	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaggcaacaaactgggggAattccttgcttatccttatg	12	11	10	8	0	0	1	0	0	0	1	2	2	2	2	2	3	3	2	2	3	6	4	rs3087653	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:15459821A>C	ENST00000380821.3	+	9	1369	c.1193A>C	c.(1192-1194)gAa>gCa	p.E398A		NM_001039697.1	NP_001034786.1	Q92966	SNPC3_HUMAN	small nuclear RNA activating complex, polypeptide 3, 50kDa	398			E -> A (in dbSNP:rs3087653).		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)		AAACTGGGGGAATTCCTTGCT	0.413													A|||	193	0.0385383	0.0416	0.0231	5008	,	,		16799	0.0		0.0596	False		,,,				2504	0.0634				p.E398A		Atlas-SNP	.											.	SNAPC3	28	.	0			c.A1193C						PASS	.	A	ALA/GLU	145,4261	101.2+/-139.8	0,145,2058	134	122	126		1193	5.9	1	9	dbSNP_102	126	425,8175	131.8+/-189.6	13,399,3888	yes	missense	SNAPC3	NM_001039697.1	107	13,544,5946	CC,CA,AA		4.9419,3.291,4.3826	probably-damaging	398/412	15459821	570,12436	2203	4300	6503	SO:0001583	missense	6619	exon9			TGGGGGAATTCCT	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.1193A>C	9.37:g.15459821A>C	ENSP00000370200:p.Glu398Ala	95	0	0		134	72	0.537313	NM_001039697	D3DRI8|Q2VPI6|Q5T285	Missense_Mutation	SNP	ENST00000380821.3	37	CCDS6478.1	78	0.03571428571428571	26	0.052845528455284556	11	0.03038674033149171	0	0.0	41	0.05408970976253298	A	31	5.081553	0.94050	0.03291	0.049419	ENSG00000164975	ENST00000380821	T	0.44083	0.93	5.86	5.86	0.93980	.	0.138414	0.64402	D	0.000005	T	0.17450	0.0419	M	0.65498	2.005	0.80722	D	1	D	0.57571	0.98	P	0.53224	0.721	T	0.31447	-0.9943	10	0.56958	D	0.05	-42.6534	16.5602	0.84551	1.0:0.0:0.0:0.0	rs3087653;rs3198208;rs52828246;rs3087653	398	Q92966	SNPC3_HUMAN	A	398	ENSP00000370200:E398A	ENSP00000370200:E398A	E	+	2	0	SNAPC3	15449821	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.283000	0.78640	2.367000	0.80283	0.528000	0.53228	GAA	A|0.956;C|0.044	0.044	strong		0.413	SNAPC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051763.2	NM_001039697		C	15459821	A	C	15459821	3	2	25	1	0	0	0	0	1	0	0	0	14851	246	9	5	1227	5	SNAPC3	9	15459821	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	2276335	15459821	125753610	359	9268											
C9orf93	203238	hgsc.bcm.edu	37	chr9	15874585	15874585	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagtaggaatgacttcacccTacagctacccaaactgcacc	14	7	6	14	0	1	1	1	1	0	0	1	2	1	2	3	1	5	3	3	1	6	4	rs149814894	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:15874585T>G	ENST00000380701.3	+	24	3852	c.3524T>G	c.(3523-3525)cTa>cGa	p.L1175R	CCDC171_ENST00000486641.2_3'UTR|CCDC171_ENST00000297641.3_Missense_Mutation_p.L1175R	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	1175																	GACTTCACCCTACAGCTACCC	0.493													T|||	34	0.00678914	0.0	0.0058	5008	,	,		17965	0.0		0.0109	False		,,,				2504	0.0194				p.L1175R		Atlas-SNP	.											C9orf93_ENST00000380689,NS,lymphoid_neoplasm,0,2	.	.	2	0			c.T3524G						PASS	.	T	ARG/LEU	5,4401	9.9+/-24.2	0,5,2198	139	125	130		3524	5.7	1	9	dbSNP_134	130	61,8539	37.8+/-93.5	0,61,4239	yes	missense	C9orf93	NM_173550.2	102	0,66,6437	GG,GT,TT		0.7093,0.1135,0.5075	probably-damaging	1175/1327	15874585	66,12940	2203	4300	6503	SO:0001583	missense	203238	exon24			TCACCCTACAGCT	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.3524T>G	9.37:g.15874585T>G	ENSP00000370077:p.Leu1175Arg	175	0	0		196	92	0.469388	NM_173550	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Missense_Mutation	SNP	ENST00000380701.3	37	CCDS6481.1	11|11	0.005036630036630037|0.005036630036630037	0|0	0.0|0.0	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	8|8	0.010554089709762533|0.010554089709762533	T|T	18.34|18.34	3.602189|3.602189	0.66445|0.66445	0.001135|0.001135	0.007093|0.007093	ENSG00000164989|ENSG00000164989	ENST00000297641;ENST00000380689;ENST00000380701;ENST00000359391|ENST00000449575;ENST00000432954	T;T|.	0.19938|.	2.14;2.11|.	5.74|5.74	5.74|5.74	0.90152|0.90152	.|.	0.000000|.	0.64402|.	D|.	0.000020|.	T|T	0.46889|0.46889	0.1416|0.1416	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;1.0;1.0|.	D;D;D|.	0.91635|.	0.999;0.998;0.999|.	T|T	0.48031|0.48031	-0.9070|-0.9070	10|5	0.45353|.	T|.	0.12|.	-5.9924|-5.9924	16.1053|16.1053	0.81216|0.81216	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1183;442;1175|.	B7ZM22;A6NK04;Q6TFL3|.	.;.;CI093_HUMAN|.	R|D	1175;442;1175;29|415;229	ENSP00000297641:L1175R;ENSP00000370077:L1175R|.	ENSP00000297641:L1175R|.	L|Y	+|+	2|1	0|0	C9orf93|C9orf93	15864585|15864585	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	5.172000|5.172000	0.65003|0.65003	2.205000|2.205000	0.71048|0.71048	0.524000|0.524000	0.50904|0.50904	CTA|TAC	T|0.993;G|0.007	0.007	strong		0.493	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550		G	15874585	T	G	15874585	3	3	25	1	0	0	0	0	1	0	0	0	2508	1522	53	5	3614	5	C9orf93	9	15874585	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	414764	15874585	125338846	360	9269											
BNC2	54796	hgsc.bcm.edu	37	chr9	16419519	16419519	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cgagccccatggggtgctggGcaccatatatcttcaccaaa	10	8	10	13	1	2	0	1	0	1	0	2	1	2	0	4	3	2	2	4	3	3	3	rs117452684	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:16419519G>A	ENST00000380672.4	-	7	2825	c.2768C>T	c.(2767-2769)gCc>gTc	p.A923V	BNC2_ENST00000545497.1_Missense_Mutation_p.A828V|BNC2_ENST00000380667.2_Missense_Mutation_p.A856V	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)		GGGGTGCTGGGCACCATATAT	0.572													G|||	45	0.00898562	0.0008	0.0086	5008	,	,		16876	0.0		0.0288	False		,,,				2504	0.0092				p.A923V		Atlas-SNP	.											.	BNC2	166	.	0			c.C2768T						PASS	.	G	VAL/ALA	30,4376	36.0+/-67.5	0,30,2173	83	87	86		2768	5.5	1	9	dbSNP_132	86	293,8307	107.0+/-167.8	3,287,4010	yes	missense	BNC2	NM_017637.5	64	3,317,6183	AA,AG,GG		3.407,0.6809,2.4835	benign	923/1100	16419519	323,12683	2203	4300	6503	SO:0001583	missense	54796	exon7			TGCTGGGCACCAT	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.2768C>T	9.37:g.16419519G>A	ENSP00000370047:p.Ala923Val	116	0	0		89	46	0.516854	NM_017637		Missense_Mutation	SNP	ENST00000380672.4	37	CCDS6482.2	26	0.011904761904761904	0	0.0	3	0.008287292817679558	0	0.0	23	0.030343007915567283	G	13.60	2.286262	0.40494	0.006809	0.03407	ENSG00000173068	ENST00000380672;ENST00000380667;ENST00000545497	T;T;T	0.31510	1.49;1.5;1.5	5.5	5.5	0.81552	.	0.166180	0.51477	D	0.000083	T	0.07954	0.0199	N	0.22421	0.69	0.80722	D	1	P;P;B	0.41673	0.578;0.759;0.18	B;B;B	0.39027	0.158;0.288;0.051	T	0.01844	-1.1262	10	0.27082	T	0.32	-9.5452	14.94	0.70986	0.0:0.1426:0.8574:0.0	.	828;923;688	F5H586;Q6ZN30;D3DRJ1	.;BNC2_HUMAN;.	V	923;856;828	ENSP00000370047:A923V;ENSP00000370042:A856V;ENSP00000444640:A828V	ENSP00000370042:A856V	A	-	2	0	BNC2	16409519	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.336000	0.52113	2.586000	0.87340	0.591000	0.81541	GCC	G|0.979;A|0.021	0.021	strong		0.572	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637		A	16419519	G	A	16419519	3	1	25	1	0	0	0	0	1	0	0	0	1475	1203	42	2	535	2	BNC2	9	16419519	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	544934	16419519	124793912	361	9270											
LRRC19	64922	hgsc.bcm.edu	37	chr9	26998122	26998122	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaagtatgtctgtagaactcTtgtgtctgtaccattaagag	12	14	9	6	0	3	2	0	0	3	2	3	2	3	2	1	0	2	3	1	0	6	5			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:26998122T>G	ENST00000380055.5	-	3	309	c.199A>C	c.(199-201)Aga>Cga	p.R67R	IFT74_ENST00000433700.1_Intron|LRRC19_ENST00000482770.1_5'Flank|IFT74_ENST00000380062.5_Intron|IFT74_ENST00000429045.2_Intron|IFT74_ENST00000443698.1_Intron	NM_022901.2	NP_075052.1	Q9H756	LRC19_HUMAN	leucine rich repeat containing 19	67						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)		TGTAGAACTCTTGTGTCTGTA	0.328																																					p.R67R		Atlas-SNP	.											.	LRRC19	24	.	0			c.A199C						PASS	.						73	81	78					9																	26998122		2203	4296	6499	SO:0001819	synonymous_variant	64922	exon3			GAACTCTTGTGTC	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.199A>C	9.37:g.26998122T>G		95	0	0		80	38	0.475	NM_022901	A0AV00|B9EG91	Silent	SNP	ENST00000380055.5	37	CCDS6518.1																																																																																			.	.	none		0.328	LRRC19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051961.2	NM_022901		G	26998122	T	G	26998122	2	3	25	1	0	0	0	0	0	0	0	1	8984	1617	56	5		5	LRRC19	9	26998122	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	10578603	26998122	114215309	362	9271											
NPR2	4882	hgsc.bcm.edu	37	chr9	35806500	35806500	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctatctggaggaaaaacgCaaggctgaagctctgctcta	12	8	11	10	1	3	1	0	1	3	0	3	3	3	3	1	3	3	4	1	3	6	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:35806500C>T	ENST00000342694.2	+	16	2739	c.2484C>T	c.(2482-2484)cgC>cgT	p.R828R		NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2	828					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)	AGGAAAAACGCAAGGCTGAAG	0.512																																					p.R828R		Atlas-SNP	.											.	NPR2	162	.	0			c.C2484T						PASS	.						119	106	110					9																	35806500		2203	4300	6503	SO:0001819	synonymous_variant	4882	exon16			AAAACGCAAGGCT	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.2484C>T	9.37:g.35806500C>T		99	0	0		102	54	0.529412	NM_003995	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Silent	SNP	ENST00000342694.2	37	CCDS6590.1	.	.	.	.	.	.	.	.	.	.	C	6.453	0.451797	0.12283	.	.	ENSG00000159899	ENST00000421267	.	.	.	6.17	5.26	0.73747	.	.	.	.	.	T	0.72787	0.3504	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72561	-0.4256	4	.	.	.	.	16.1789	0.81887	0.0:0.8665:0.1335:0.0	.	.	.	.	V	175	.	.	A	+	2	0	NPR2	35796500	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.000000	0.29770	1.587000	0.49959	0.655000	0.94253	GCA	.	.	none		0.512	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1			T	35806500	C	T	35806500	2	4	25	1	0	0	0	0	0	0	0	1	10604	697	25	2		2	NPR2	9	35806500	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	8808378	35806500	105406931	363	9272											
HRCT1	646962	hgsc.bcm.edu	37	chr9	35906583	35906583	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgccacacccctcaccaccTccaccaccaccaccaccccc	9	2	1	29	1	1	0	1	0	0	0	2	0	2	0	13	0	0	0	13	0	0	0	rs112821450|rs143611048|rs79156963	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:35906583T>A	ENST00000354323.2	+	1	395	c.299T>A	c.(298-300)cTc>cAc	p.L100H	LINC00961_ENST00000443779.1_lincRNA	NM_001039792.1	NP_001034881.1	Q6UXD1	HRCT1_HUMAN	histidine rich carboxyl terminus 1	100	His-rich.					integral component of membrane (GO:0016021)		p.L100H(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(1)	4						cctcaccacctccaccaccac	0.667																																					p.L100H		Atlas-SNP	.											HRCT1,NS,malignant_melanoma,0,1	HRCT1	14	1	1	Substitution - Missense(1)	NS(1)	c.T299A						scavenged	.						13	10	11					9																	35906583		1961	3863	5824	SO:0001583	missense	646962	exon1			ACCACCTCCACCA		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.299T>A	9.37:g.35906583T>A	ENSP00000346283:p.Leu100His	20	0	0		34	3	0.0882353	NM_001039792	B7ZBJ1	Missense_Mutation	SNP	ENST00000354323.2	37	CCDS35012.1	.	.	.	.	.	.	.	.	.	.	T	9.866	1.197686	0.22037	.	.	ENSG00000196196	ENST00000354323	.	.	.	3.43	-0.386	0.12466	.	.	.	.	.	T	0.09730	0.0239	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.25117	-1.0141	8	0.87932	D	0	-5.7925	0.5802	0.00711	0.4571:0.1878:0.1238:0.2312	.	100	Q6UXD1	HRCT1_HUMAN	H	100	.	ENSP00000346283:L100H	L	+	2	0	HRCT1	35896583	0.000000	0.05858	0.107000	0.21349	0.466000	0.32739	-0.309000	0.08145	-0.078000	0.12730	-0.376000	0.06991	CTC	T|0.500;A|0.500	0.500	weak		0.667	HRCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334099.1	NM_001039792		A	35906583	T	A	35906583	3	1	25	1	0	0	0	0	1	0	0	0	7362	1551	54	5	301	5	HRCT1	9	35906583	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	100083	35906583	105306848	364	9273											
RECK	8434	hgsc.bcm.edu	37	chr9	36107981	36107981	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgcttgtacaggttgcaaaCtgggagaagcttctgatttc	9	14	11	7	0	1	2	0	1	1	1	2	3	1	2	0	2	5	5	0	2	3	6	rs148296262	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:36107981C>G	ENST00000377966.3	+	14	2151	c.1585C>G	c.(1585-1587)Ctg>Gtg	p.L529V		NM_021111.2	NP_066934.1	O95980	RECK_HUMAN	reversion-inducing-cysteine-rich protein with kazal motifs	529					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)			AGGTTGCAAACTGGGAGAAGC	0.383													C|||	2	0.000399361	0.0	0.0	5008	,	,		17308	0.0		0.002	False		,,,				2504	0.0				p.L529V		Atlas-SNP	.											.	RECK	73	.	0			c.C1585G						PASS	.	C	VAL/LEU	6,4400	9.9+/-24.2	0,6,2197	92	84	87		1585	0.6	1	9	dbSNP_134	87	22,8578	16.0+/-53.3	0,22,4278	yes	missense	RECK	NM_021111.2	32	0,28,6475	GG,GC,CC		0.2558,0.1362,0.2153	possibly-damaging	529/972	36107981	28,12978	2203	4300	6503	SO:0001583	missense	8434	exon14			TGCAAACTGGGAG	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.1585C>G	9.37:g.36107981C>G	ENSP00000367202:p.Leu529Val	97	0	0		92	45	0.48913	NM_021111	B2RNS1|Q5W0K6|Q8WX37	Missense_Mutation	SNP	ENST00000377966.3	37	CCDS6597.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	16.95	3.264660	0.59431	0.001362	0.002558	ENSG00000122707	ENST00000377966	T	0.56941	0.43	5.45	0.56	0.17279	.	0.000000	0.64402	D	0.000002	T	0.41282	0.1152	L	0.53561	1.675	0.39944	D	0.974446	P;P	0.48407	0.91;0.91	B;B	0.39217	0.294;0.294	T	0.34950	-0.9808	10	0.52906	T	0.07	-9.0488	8.2357	0.31625	0.0:0.3492:0.0:0.6508	.	529;529	A8K9D8;O95980	.;RECK_HUMAN	V	529	ENSP00000367202:L529V	ENSP00000367202:L529V	L	+	1	2	RECK	36097981	0.999000	0.42202	1.000000	0.80357	0.989000	0.77384	0.655000	0.24933	0.125000	0.18397	-0.302000	0.09304	CTG	C|0.997;G|0.003	0.003	strong		0.383	RECK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052409.1			G	36107981	C	G	36107981	3	3	25	1	0	0	0	0	1	0	0	0	13215	564	20	4	1639	4	RECK	9	36107981	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	201398	36107981	105105450	365	9274											
POLR1E	64425	hgsc.bcm.edu	37	chr9	37498215	37498215	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagctcatagggtagttaagCggaaaagtaagtctatgata	15	10	12	4	1	2	1	1	1	1	0	2	3	2	2	0	2	2	4	0	2	8	6			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:37498215C>T	ENST00000377798.4	+	9	993	c.880C>T	c.(880-882)Cgg>Tgg	p.R294W	POLR1E_ENST00000442009.2_Missense_Mutation_p.R224W|POLR1E_ENST00000377792.3_Missense_Mutation_p.R356W	NM_022490.1	NP_071935.1	O15160	RPAC1_HUMAN	polymerase (RNA) I polypeptide E, 53kDa	0					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)			autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|skin(1)|stomach(1)	12				GBM - Glioblastoma multiforme(29;0.00851)|Lung(182;0.229)		GGTAGTTAAGCGGAAAAGTAA	0.388																																					p.R294W	Ovarian(116;843 1620 18506 32459 34463)	Atlas-SNP	.											.	POLR1E	28	.	0			c.C880T						PASS	.						96	93	94					9																	37498215		2203	4300	6503	SO:0001583	missense	64425	exon9			GTTAAGCGGAAAA	AK091294	CCDS6611.1	9p13.1	2013-01-21	2006-03-09	2006-03-09	ENSG00000137054	ENSG00000137054		"RNA polymerase subunits"	17631	protein-coding gene	gene with protein product	"RNA polymerase I associated factor 53"		"polymerase (RNA) I associated factor 1"	PRAF1		8641287	Standard	XM_005251547		Approved	FLJ13390, PAF53, FLJ13970	uc003zzy.1	Q9GZS1	OTTHUMG00000019920	ENST00000377798.4:c.880C>T	9.37:g.37498215C>T	ENSP00000367029:p.Arg294Trp	110	0	0		97	46	0.474227	NM_022490	O75395|Q5JTE3	Missense_Mutation	SNP	ENST00000377798.4	37	CCDS6611.1	.	.	.	.	.	.	.	.	.	.	C	15.27	2.783965	0.49891	.	.	ENSG00000137054	ENST00000377798;ENST00000442009;ENST00000377792	T;T;T	0.24723	1.84;1.84;1.84	5.76	3.78	0.43462	.	0.538678	0.19258	N	0.118753	T	0.43612	0.1255	L	0.59436	1.845	0.35039	D	0.75957	D;D;D	0.89917	1.0;1.0;0.999	D;D;P	0.69479	0.939;0.964;0.862	T	0.56619	-0.7949	10	0.56958	D	0.05	-12.8494	11.1968	0.48717	0.1376:0.7205:0.1419:0.0	.	224;356;294	E7EX70;Q9GZS1;Q9GZS1-2	.;RPA49_HUMAN;.	W	294;224;356	ENSP00000367029:R294W;ENSP00000399887:R224W;ENSP00000367023:R356W	ENSP00000367023:R356W	R	+	1	2	POLR1E	37488215	1.000000	0.71417	1.000000	0.80357	0.155000	0.21991	2.300000	0.43620	1.534000	0.49203	0.655000	0.94253	CGG	.	.	none		0.388	POLR1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052464.1	NM_022490		T	37498215	C	T	37498215	3	4	25	1	0	0	0	0	1	0	0	0	12222	759	27	1	914	1	POLR1E	9	37498215	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1390234	37498215	103715216	366	9275											
CNTNAP3	79937	hgsc.bcm.edu	37	chr9	39149904	39149904	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gctttgtcaccaatggtgatGagccttaggcagccctgaaa	10	10	11	10	0	1	3	1	3	0	0	1	3	1	3	3	2	2	2	3	2	3	2	rs200999166	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:39149904G>A	ENST00000297668.6	-	10	1621	c.1548C>T	c.(1546-1548)ctC>ctT	p.L516L	CNTNAP3_ENST00000323947.7_Intron|CNTNAP3_ENST00000377656.2_Silent_p.L516L|CNTNAP3_ENST00000358144.2_Silent_p.L428L|CNTNAP3_ENST00000377659.1_Silent_p.L516L	NM_033655.3	NP_387504.2	Q9BZ76	CNTP3_HUMAN	contactin associated protein-like 3	516	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell recognition (GO:0008037)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	24				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		CAATGGTGATGAGCCTTAGGC	0.532													.|||	3	0.000599042	0.0	0.0014	5008	,	,		14869	0.0		0.002	False		,,,				2504	0.0				p.L516L		Atlas-SNP	.											.	CNTNAP3	82	.	0			c.C1548T						PASS	.	G		0,4292		0,0,2146	10	11	11		1548	1.2	1	9		11	6,8376		0,6,4185	no	coding-synonymous	CNTNAP3	NM_033655.3		0,6,6331	AA,AG,GG		0.0716,0.0,0.0473		516/1289	39149904	6,12668	2146	4191	6337	SO:0001819	synonymous_variant	79937	exon10			GGTGATGAGCCTT	AF333769	CCDS6616.1	9q12	2008-02-05			ENSG00000106714	ENSG00000106714			13834	protein-coding gene	gene with protein product	"cell recognition molecule CASPR3 (FLJ14195, KIAA1714)"	610517				12093160	Standard	NM_033655		Approved	CASPR3, KIAA1714, FLJ14195, CNTNAP3A	uc004abi.3	Q9BZ76	OTTHUMG00000019954	ENST00000297668.6:c.1548C>T	9.37:g.39149904G>A		816	0	0		1008	254	0.251984	NM_033655	B1AMA0|Q9C0E9	Silent	SNP	ENST00000297668.6	37	CCDS6616.1																																																																																			G|0.999;A|0.001	0.001	weak		0.532	CNTNAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052511.1	NM_033655		A	39149904	G	A	39149904	2	1	25	1	0	0	0	0	0	0	0	1	3650	1277	45	2		2	CNTNAP3	9	39149904	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1651689	39149904	102063527	367	9276											
FLJ46321	389763	hgsc.bcm.edu	37	chr9	84605344	84605344	+	Nonsense_Mutation	SNP	G	G	A																															ctattcaggtttcccagactGgaaaagtttccagagagaag																										TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:84605344G>A	ENST00000344803.2	+	3	292	c.245G>A	c.(244-246)tGg>tAg	p.W82*		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	82					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TTCCCAGACTGGAAAAGTTTC	0.433																																					p.W82X		Atlas-SNP	.											.	.	.	.	0			c.G245A						PASS	.						83	77	79					9																	84605344		1855	4089	5944	SO:0001587	stop_gained	389763	exon3			CAGACTGGAAAAG		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.245G>A	9.37:g.84605344G>A	ENSP00000341988:p.Trp82*	137	0	0		138	59	0.427536	NM_001001670		Nonsense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	G	12.07	1.828944	0.32329	.	.	ENSG00000214929	ENST00000344803	.	.	.	2.82	-3.37	0.04898	.	1.436640	0.04947	N	0.459585	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	10.638	4.091	0.09970	0.3449:0.3377:0.3174:0.0	.	.	.	.	X	82	.	ENSP00000341988:W82X	W	+	2	0	FAM75D1	83795164	0.039000	0.19947	0.000000	0.03702	0.000000	0.00434	0.316000	0.19469	-0.774000	0.04590	-0.902000	0.02854	TGG	.	.	none		0.433	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		A	84605344	G	A	84605344	4	1	25	1	0	0	0	0	0	1	0	0	5940	1357	47	2	255	2	FLJ46321	9	84605344	Nonsense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	45455440	84605344	56608087	368	9277	115	2									
FLJ46321	389763	hgsc.bcm.edu	37	chr9	84605350	84605350	+	Missense_Mutation	SNP	G	G	C																															aggtttcccagactggaaaaGtttccagagagaagaggaag																								rs367877053		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:84605350G>C	ENST00000344803.2	+	3	298	c.251G>C	c.(250-252)aGt>aCt	p.S84T		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	84					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GACTGGAAAAGTTTCCAGAGA	0.433																																					p.S84T		Atlas-SNP	.											.	.	.	.	0			c.G251C						PASS	.	G	THR/SER	0,3710		0,0,1855	85	79	81		251	-5.6	0	9		81	1,8179		0,1,4089	no	missense	FAM75D1	NM_001001670.2	58	0,1,5944	CC,CG,GG		0.0122,0.0,0.0084	benign	84/1577	84605350	1,11889	1855	4090	5945	SO:0001583	missense	389763	exon3			GGAAAAGTTTCCA		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.251G>C	9.37:g.84605350G>C	ENSP00000341988:p.Ser84Thr	142	0	0		145	70	0.482759	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	G	0.010	-1.766413	0.00651	0.0	1.22E-4	ENSG00000214929	ENST00000344803	T	0.05081	3.5	2.82	-5.63	0.02474	.	16.493900	0.00166	N	0.000000	T	0.02304	0.0071	N	0.02916	-0.46	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.35574	-0.9783	10	0.18276	T	0.48	18.5219	1.232	0.01945	0.1706:0.3724:0.205:0.252	.	84	Q6ZQQ2	F75D1_HUMAN	T	84	ENSP00000341988:S84T	ENSP00000341988:S84T	S	+	2	0	FAM75D1	83795170	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.865000	0.01649	-4.130000	0.00071	-1.316000	0.01300	AGT	.	.	weak		0.433	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		C	84605350	G	C	84605350	3	2	25	1	0	0	0	0	1	0	0	0	5940	1029	36	4	261	4	FLJ46321	9	84605350	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	6	84605350	56608081	369	9278	115	2									
COL15A1	1306	hgsc.bcm.edu	37	chr9	101804366	101804366	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgacactggtttacctggcTttccaggactaaaaggagaa	12	10	11	8	0	0	2	0	1	0	1	1	4	1	3	2	4	1	2	2	4	4	4	rs35901514	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:101804366T>C	ENST00000375001.3	+	24	2974	c.2551T>C	c.(2551-2553)Ttt>Ctt	p.F851L		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	851	Collagen-like 3.|Triple-helical region 4 (COL4).				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)				TTTACCTGGCTTTCCAGGACT	0.423													T|||	16	0.00319489	0.0015	0.0058	5008	,	,		17702	0.0		0.008	False		,,,				2504	0.002				p.F851L		Atlas-SNP	.											.	COL15A1	211	.	0			c.T2551C						PASS	.	T	LEU/PHE	11,4395	17.9+/-39.9	0,11,2192	95	103	100		2551	5.9	1	9	dbSNP_126	100	108,8492	57.2+/-118.5	0,108,4192	yes	missense	COL15A1	NM_001855.3	22	0,119,6384	CC,CT,TT		1.2558,0.2497,0.915	probably-damaging	851/1389	101804366	119,12887	2203	4300	6503	SO:0001583	missense	1306	exon24			CCTGGCTTTCCAG	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.2551T>C	9.37:g.101804366T>C	ENSP00000364140:p.Phe851Leu	49	0	0		50	18	0.36	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	37	CCDS35081.1	11	0.005036630036630037	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	T	19.54	3.846980	0.71603	0.002497	0.012558	ENSG00000204291	ENST00000375001	D	0.93133	-3.17	5.92	5.92	0.95590	.	0.251977	0.40818	N	0.001007	D	0.88815	0.6539	N	0.10760	0.04	0.40583	D	0.981411	D	0.69078	0.997	D	0.77004	0.989	D	0.88409	0.3020	10	0.20046	T	0.44	-12.7642	12.7552	0.57331	0.0:0.0:0.0:1.0	rs35901514	851	P39059	COFA1_HUMAN	L	851	ENSP00000364140:F851L	ENSP00000364140:F851L	F	+	1	0	COL15A1	100844187	0.997000	0.39634	1.000000	0.80357	0.986000	0.74619	2.145000	0.42207	2.270000	0.75569	0.459000	0.35465	TTT	T|0.993;C|0.007	0.007	strong		0.423	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855		C	101804366	T	C	101804366	3	2	25	1	0	0	0	0	1	0	0	0	3674	1609	56	3	2645	3	COL15A1	9	101804366	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	17199016	101804366	39409065	370	9279											
LPPR1	54886	hgsc.bcm.edu	37	chr9	103947810	103947810	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaacactcaacgaagttatTccatcatcccgtgttttata	13	13	4	11	2	2	0	2	0	0	0	4	1	4	0	2	0	2	2	2	0	6	5	rs41296085	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:103947810T>G	ENST00000374874.3	+	2	473	c.34T>G	c.(34-36)Tcc>Gcc	p.S12A	LPPR1_ENST00000395056.2_Missense_Mutation_p.S12A|LPPR1_ENST00000494890.1_3'UTR	NM_207299.1	NP_997182.1	Q8TBJ4	LPPR1_HUMAN		12					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)										ACGAAGTTATTCCATCATCCC	0.338													T|||	42	0.00838658	0.0	0.0144	5008	,	,		16008	0.0		0.0169	False		,,,				2504	0.0153				p.S12A		Atlas-SNP	.											.	.	.	.	0			c.T34G						PASS	.	T	ALA/SER,ALA/SER	17,4389	24.3+/-50.5	0,17,2186	221	202	208		34,34	5.9	1	9	dbSNP_127	208	133,8467	67.3+/-129.8	1,131,4168	yes	missense,missense	LPPR1	NM_017753.2,NM_207299.1	99,99	1,148,6354	GG,GT,TT		1.5465,0.3858,1.1533	benign,benign	12/326,12/326	103947810	150,12856	2203	4300	6503	SO:0001583	missense	0	exon2			AGTTATTCCATCA																												ENST00000374874.3:c.34T>G	9.37:g.103947810T>G	ENSP00000364008:p.Ser12Ala	214	1	0.0046729		207	99	0.478261	NM_207299	Q5VX23|Q9NXE2	Missense_Mutation	SNP	ENST00000374874.3	37	CCDS6751.1	20	0.009157509157509158	0	0.0	6	0.016574585635359115	0	0.0	14	0.018469656992084433	T	15.22	2.768539	0.49680	0.003858	0.015465	ENSG00000148123	ENST00000374874;ENST00000456287;ENST00000374871;ENST00000395056	T;T;T	0.38077	1.16;1.16;1.16	5.93	5.93	0.95920	.	0.431258	0.25774	N	0.028386	T	0.23094	0.0558	M	0.65498	2.005	0.34363	D	0.691192	B	0.02656	0.0	B	0.08055	0.003	T	0.40384	-0.9566	10	0.34782	T	0.22	-32.2815	14.3318	0.66561	0.0:0.0:0.0:1.0	rs41296085;rs61755095	12	Q8TBJ4	LPPR1_HUMAN	A	12	ENSP00000364008:S12A;ENSP00000410223:S12A;ENSP00000378496:S12A	ENSP00000364005:S12A	S	+	1	0	RP11-35N6.1	102987631	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.743000	0.62110	2.271000	0.75665	0.533000	0.62120	TCC	T|0.990;G|0.010	0.010	strong		0.338	LPPR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053425.1			G	103947810	T	G	103947810	3	3	25	1	0	0	0	0	1	0	0	0	8933	1783	62	5	36	5	LPPR1	9	103947810	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	2143444	103947810	37265621	371	9280											
ZNF189	7743	hgsc.bcm.edu	37	chr9	104170227	104170227	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccagatgttttgaacagagaTaaggatgaggagccaactgt	14	9	12	6	0	0	4	0	2	0	2	0	7	0	6	2	2	3	1	2	2	3	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:104170227T>G	ENST00000339664.2	+	3	306	c.177T>G	c.(175-177)gaT>gaG	p.D59E	ZNF189_ENST00000374861.3_Missense_Mutation_p.D45E|ZNF189_ENST00000259395.4_Missense_Mutation_p.D17E	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	59	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)				TGAACAGAGATAAGGATGAGG	0.358																																					p.D59E		Atlas-SNP	.											.	ZNF189	79	.	0			c.T177G						PASS	.						51	54	53					9																	104170227		2202	4300	6502	SO:0001583	missense	7743	exon3			CAGAGATAAGGAT	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.177T>G	9.37:g.104170227T>G	ENSP00000342019:p.Asp59Glu	57	0	0		78	40	0.512821	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Missense_Mutation	SNP	ENST00000339664.2	37	CCDS6754.1	.	.	.	.	.	.	.	.	.	.	T	0.024	-1.384786	0.01194	.	.	ENSG00000136870	ENST00000374861;ENST00000339664;ENST00000259395	T;T;T	0.05081	5.68;5.68;3.5	4.79	4.79	0.61399	Krueppel-associated box (3);	0.402704	0.21477	N	0.073890	T	0.03695	0.0105	N	0.11870	0.19	0.24556	N	0.993991	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.10450	0.0;0.0;0.005	T	0.38415	-0.9662	10	0.06365	T	0.9	.	12.9471	0.58379	0.0:0.0:0.0:1.0	.	44;45;59	B7ZLK9;Q5T7D8;O75820	.;.;ZN189_HUMAN	E	45;59;17	ENSP00000363995:D45E;ENSP00000342019:D59E;ENSP00000259395:D17E	ENSP00000259395:D17E	D	+	3	2	ZNF189	103210048	.	.	1.000000	0.80357	0.966000	0.64601	.	.	2.371000	0.80710	0.533000	0.62120	GAT	.	.	none		0.358	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452		G	104170227	T	G	104170227	3	3	25	1	0	0	0	0	1	0	0	0	17769	1403	49	5	187	5	ZNF189	9	104170227	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	222417	104170227	37043204	372	9281											
TMEM38B	55151	hgsc.bcm.edu	37	chr9	108536246	108536246	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcagccgttttcatcatGtgagaagaaaagtgaagcaa	15	8	11	7	1	2	3	2	2	0	2	2	4	2	3	1	0	3	4	1	0	5	2	rs35232724	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:108536246G>C	ENST00000374692.3	+	6	878	c.761G>C	c.(760-762)tGt>tCt	p.C254S	TMEM38B_ENST00000374688.1_Missense_Mutation_p.C200S	NM_018112.1	NP_060582.1	Q9NVV0	TM38B_HUMAN	transmembrane protein 38B	254			C -> S (in dbSNP:rs35232724).			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						TTTTCATCATGTGAGAAGAAA	0.418													G|||	142	0.0283546	0.0968	0.0101	5008	,	,		16874	0.0		0.005	False		,,,				2504	0.002				p.C254S		Atlas-SNP	.											.	TMEM38B	31	.	0			c.G761C						PASS	.	G	SER/CYS	488,3918	227.8+/-242.9	29,430,1744	105	101	103		761	1.3	0	9	dbSNP_126	103	80,8520	46.3+/-105.2	0,80,4220	yes	missense	TMEM38B	NM_018112.1	112	29,510,5964	CC,CG,GG		0.9302,11.0758,4.3672	benign	254/292	108536246	568,12438	2203	4300	6503	SO:0001583	missense	55151	exon6			CATCATGTGAGAA	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.761G>C	9.37:g.108536246G>C	ENSP00000363824:p.Cys254Ser	79	0	0		65	37	0.569231	NM_018112	Q5JR63|Q5SVN5|Q5SVN6|Q5VTE2|Q6IA97	Missense_Mutation	SNP	ENST00000374692.3	37	CCDS6768.1	62	0.028388278388278388	54	0.10975609756097561	3	0.008287292817679558	0	0.0	5	0.006596306068601583	G	0.255	-1.003554	0.02128	0.110758	0.009302	ENSG00000095209	ENST00000374692;ENST00000374688	T;T	0.39056	1.1;1.1	4.25	1.3	0.21679	.	0.987695	0.08274	N	0.970939	T	0.00356	0.0011	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.12502	-1.0545	10	0.07990	T	0.79	-3.46	7.6203	0.28181	0.0:0.3465:0.4746:0.1789	rs35232724	254	Q9NVV0	TM38B_HUMAN	S	254;200	ENSP00000363824:C254S;ENSP00000363820:C200S	ENSP00000363820:C200S	C	+	2	0	TMEM38B	107576067	0.178000	0.23122	0.014000	0.15608	0.185000	0.23345	0.189000	0.17037	0.289000	0.22422	-0.234000	0.12200	TGT	G|0.960;C|0.040	0.040	strong		0.418	TMEM38B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053517.1	NM_018112		C	108536246	G	C	108536246	3	2	25	1	0	0	0	0	1	0	0	0	16175	1377	48	4	783	4	TMEM38B	9	108536246	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	4366019	108536246	32677185	373	9282											
ASTN2	23245	hgsc.bcm.edu	37	chr9	119448979	119448979	+	Intron	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tttgggttcccgggtaccttCagtctgcagggacaggggct	5	11	15	10	1	2	0	1	0	1	0	3	1	3	1	2	5	2	4	2	5	1	4	rs10983304	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:119448979C>T	ENST00000313400.4	-	17	2907				ASTN2_ENST00000341734.4_Intron|ASTN2_ENST00000358637.4_Intron|ASTN2_ENST00000288520.5_Missense_Mutation_p.E36K|ASTN2_ENST00000361477.3_Intron|TRIM32_ENST00000450136.1_5'Flank|ASTN2_ENST00000373996.3_Intron|TRIM32_ENST00000373983.2_5'Flank|ASTN2_ENST00000361209.2_Intron			O75129	ASTN2_HUMAN	astrotactin 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						CGGGTACCTTCAGTCTGCAGG	0.542													C|||	60	0.0119808	0.0015	0.013	5008	,	,		19721	0.0		0.0288	False		,,,				2504	0.0204				p.E36K		Atlas-SNP	.											.	ASTN2	307	.	0			c.G106A						PASS	.																																			SO:0001627	intron_variant	23245	exon1			TACCTTCAGTCTG	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.2807-34907G>A	9.37:g.119448979C>T		55	0	0		47	22	0.468085	NM_198186	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Missense_Mutation	SNP	ENST00000313400.4	37		33	0.01510989010989011	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	26	0.03430079155672823	C	13.53	2.264293	0.39995	.	.	ENSG00000148219	ENST00000288520	T	0.13307	2.6	3.9	0.998	0.19857	.	.	.	.	.	T	0.02012	0.0063	.	.	.	0.09310	N	0.999992	B	0.02656	0.0	B	0.01281	0.0	T	0.41770	-0.9490	7	.	.	.	.	4.1278	0.10134	0.0:0.5889:0.1934:0.2177	rs10983304;rs52793392;rs10983304	36	O75129-4	.	K	36	ENSP00000288520:E36K	.	E	-	1	0	ASTN2	118488800	0.041000	0.20044	0.006000	0.13384	0.020000	0.10135	0.363000	0.20301	0.224000	0.20940	0.555000	0.69702	GAA	C|0.979;T|0.021	0.021	strong		0.542	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010		T	119448979	C	T	119448979	1	4	25	0	1	0	0	0	0	0	0	0	1065	835	29	2		2	ASTN2	9	119448979	Intron	SNP	C	TCGA-G8-6906-01A-11D-2210-10	10912733	119448979	21764452	374	9283											
DBC1	1620	hgsc.bcm.edu	37	chr9	121929932	121929932	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagggcatgttccagccctcCgaatggctcccgctaaaggg	9	7	12	13	2	0	0	0	0	0	0	3	1	3	0	4	3	1	4	4	3	4	2	rs147029533	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:121929932C>T	ENST00000265922.3	-	8	2177	c.1716G>A	c.(1714-1716)tcG>tcA	p.S572S	BRINP1_ENST00000482797.1_Intron	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	572					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)											TCCAGCCCTCCGAATGGCTCC	0.557													C|||	10	0.00199681	0.0	0.0043	5008	,	,		19432	0.0		0.007	False		,,,				2504	0.0				p.S572S		Atlas-SNP	.											DBC1,NS,carcinoma,-2,1	DBC1	194	1	0			c.G1716A						PASS	.	C		5,4401		0,5,2198	43	44	44		1716	-11.3	0.3	9	dbSNP_134	44	70,8524		1,68,4228	no	coding-synonymous	DBC1	NM_014618.2		1,73,6426	TT,TC,CC		0.8145,0.1135,0.5769		572/762	121929932	75,12925	2203	4297	6500	SO:0001819	synonymous_variant	1620	exon8			GCCCTCCGAATGG	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.1716G>A	9.37:g.121929932C>T		87	0	0		86	41	0.476744	NM_014618	Q6IPV6|Q6P1A0|Q8WU22	Silent	SNP	ENST00000265922.3	37	CCDS6822.1																																																																																			C|0.994;T|0.006	0.006	strong		0.557	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618		T	121929932	C	T	121929932	2	4	25	1	0	0	0	0	0	0	0	1	4249	639	23	1		1	DBC1	9	121929932	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2480953	121929932	19283499	375	9284											
FAM129B	64855	hgsc.bcm.edu	37	chr9	130270782	130270782	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ttccccagctcctggtgcagGagggtctcgaacgtatacac	8	9	11	13	2	1	0	0	0	1	0	4	2	3	1	3	3	4	3	3	3	3	3	rs11545937	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:130270782G>A	ENST00000373312.3	-	11	1566	c.1353C>T	c.(1351-1353)ctC>ctT	p.L451L	FAM129B_ENST00000373314.3_Silent_p.L438L|FAM129B_ENST00000468379.1_Intron	NM_022833.2	NP_073744.2	Q96TA1	NIBL1_HUMAN	family with sequence similarity 129, member B	451					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						CCTGGTGCAGGAGGGTCTCGA	0.652													G|||	118	0.0235623	0.0045	0.0389	5008	,	,		17611	0.0		0.0596	False		,,,				2504	0.0256				p.L451L		Atlas-SNP	.											.	FAM129B	84	.	0			c.C1353T						PASS	.	G	,	56,4350	55.5+/-91.7	0,56,2147	137	133	135		1314,1353	-1.5	1	9	dbSNP_120	135	570,8030	153.9+/-208.2	20,530,3750	no	coding-synonymous,coding-synonymous	FAM129B	NM_001035534.1,NM_022833.2	,	20,586,5897	AA,AG,GG		6.6279,1.271,4.8132	,	438/734,451/747	130270782	626,12380	2203	4300	6503	SO:0001819	synonymous_variant	64855	exon11			GTGCAGGAGGGTC	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.1353C>T	9.37:g.130270782G>A		28	0	0		37	12	0.324324	NM_022833	Q4LE55|Q5VVW6|Q5VVW7|Q9BUS2|Q9NT35	Silent	SNP	ENST00000373312.3	37	CCDS35145.1																																																																																			G|0.957;C|0.000;A|0.043	0.043	strong		0.652	FAM129B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054196.1	NM_022833		A	130270782	G	A	130270782	2	1	25	1	0	0	0	0	0	0	0	1	5442	1161	41	2		2	FAM129B	9	130270782	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	8340850	130270782	10942649	376	9285											
FPGS	2356	hgsc.bcm.edu	37	chr9	130566678	130566678	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatggaactgtacctggcaCggagtgggctgcaggtaagg	9	7	16	9	1	0	0	0	0	0	0	0	2	0	2	2	6	3	5	2	6	3	2	rs41306702	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:130566678C>T	ENST00000373247.2	+	2	303	c.253C>T	c.(253-255)Cgg>Tgg	p.R85W	FPGS_ENST00000373245.1_Missense_Mutation_p.R85W|FPGS_ENST00000373225.3_Missense_Mutation_p.R35W|FPGS_ENST00000460181.1_3'UTR|FPGS_ENST00000393706.2_Missense_Mutation_p.R85W	NM_004957.4	NP_004948.4	Q05932	FOLC_HUMAN	folylpolyglutamate synthase	85					brain development (GO:0007420)|folic acid metabolic process (GO:0046655)|liver development (GO:0001889)|nucleobase-containing compound metabolic process (GO:0006139)|one-carbon metabolic process (GO:0006730)|organ regeneration (GO:0031100)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|tetrahydrofolylpolyglutamate synthase activity (GO:0004326)			endometrium(2)|kidney(1)|lung(3)|ovary(1)	7					Methotrexate(DB00563)|Pralatrexate(DB06813)|Raltitrexed(DB00293)	GTACCTGGCACGGAGTGGGCT	0.607													C|||	7	0.00139776	0.0008	0.0	5008	,	,		19694	0.0		0.006	False		,,,				2504	0.0				p.R85W		Atlas-SNP	.											.	FPGS	30	.	0			c.C253T						PASS	.	C	TRP/ARG,TRP/ARG	2,4404	4.2+/-10.8	0,2,2201	116	98	104		103,253	4.2	1	9	dbSNP_127	104	30,8570	21.0+/-64.5	0,30,4270	yes	missense,missense	FPGS	NM_001018078.1,NM_004957.4	101,101	0,32,6471	TT,TC,CC		0.3488,0.0454,0.246	probably-damaging,probably-damaging	35/538,85/588	130566678	32,12974	2203	4300	6503	SO:0001583	missense	2356	exon2			CTGGCACGGAGTG		CCDS35148.1, CCDS35149.1, CCDS75905.1	9q34.11	2013-09-19			ENSG00000136877	ENSG00000136877	6.3.2.17		3824	protein-coding gene	gene with protein product		136510					Standard	NM_004957		Approved		uc004bsg.1	Q05932	OTTHUMG00000020716	ENST00000373247.2:c.253C>T	9.37:g.130566678C>T	ENSP00000362344:p.Arg85Trp	96	0	0		93	54	0.580645	NM_004957	B3KPW4|B7Z2Z3|F5H0K6|Q5JU19|Q5JU22|Q6P2P6	Missense_Mutation	SNP	ENST00000373247.2	37	CCDS35148.1	7	0.003205128205128205	1	0.0020325203252032522	0	0.0	0	0.0	6	0.0079155672823219	C	18.11	3.550644	0.65311	4.54E-4	0.003488	ENSG00000136877	ENST00000373247;ENST00000373245;ENST00000393706;ENST00000373228;ENST00000373225;ENST00000431857;ENST00000423577	T;T;T;T;T	0.38722	2.53;1.12;2.57;1.12;2.15	5.17	4.25	0.50352	Mur ligase, central (2);	0.062573	0.64402	D	0.000005	T	0.64427	0.2597	H	0.94964	3.605	0.58432	D	0.999994	D;D	0.89917	1.0;1.0	D;D	0.80764	0.992;0.994	T	0.75414	-0.3326	10	0.87932	D	0	-1.3396	10.6558	0.45673	0.3481:0.6519:0.0:0.0	rs41306702	85;85	Q05932-4;Q05932	.;FOLC_HUMAN	W	85;85;85;85;35;35;35	ENSP00000362344:R85W;ENSP00000362342:R85W;ENSP00000377309:R85W;ENSP00000362325:R85W;ENSP00000362322:R35W	ENSP00000362322:R35W	R	+	1	2	FPGS	129606499	1.000000	0.71417	1.000000	0.80357	0.588000	0.36517	1.130000	0.31393	1.124000	0.41980	0.563000	0.77884	CGG	C|0.997;T|0.003	0.003	strong		0.607	FPGS-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054251.1			T	130566678	C	T	130566678	3	4	25	1	0	0	0	0	1	0	0	0	6044	527	19	1	259	1	FPGS	9	130566678	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	295896	130566678	10646753	377	9286											
FPGS	2356	hgsc.bcm.edu	37	chr9	130569258	130569258	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	agctgtcccggcagctctccCcacctggtgcaggttcggga	5	8	13	15	2	1	0	0	0	1	0	4	1	2	1	4	4	3	5	4	4	0	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:130569258C>T	ENST00000373247.2	+	5	443	c.393C>T	c.(391-393)ccC>ccT	p.P131P	FPGS_ENST00000373245.1_Silent_p.P131P|FPGS_ENST00000373225.3_Silent_p.P81P|FPGS_ENST00000460181.1_Intron|FPGS_ENST00000393706.2_Silent_p.P131P	NM_004957.4	NP_004948.4	Q05932	FOLC_HUMAN	folylpolyglutamate synthase	131					brain development (GO:0007420)|folic acid metabolic process (GO:0046655)|liver development (GO:0001889)|nucleobase-containing compound metabolic process (GO:0006139)|one-carbon metabolic process (GO:0006730)|organ regeneration (GO:0031100)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|tetrahydrofolylpolyglutamate synthase activity (GO:0004326)			endometrium(2)|kidney(1)|lung(3)|ovary(1)	7					Methotrexate(DB00563)|Pralatrexate(DB06813)|Raltitrexed(DB00293)	GCAGCTCTCCCCACCTGGTGC	0.652																																					p.P131P		Atlas-SNP	.											.	FPGS	30	.	0			c.C393T						PASS	.						58	59	59					9																	130569258		2203	4300	6503	SO:0001819	synonymous_variant	2356	exon5			CTCTCCCCACCTG		CCDS35148.1, CCDS35149.1, CCDS75905.1	9q34.11	2013-09-19			ENSG00000136877	ENSG00000136877	6.3.2.17		3824	protein-coding gene	gene with protein product		136510					Standard	NM_004957		Approved		uc004bsg.1	Q05932	OTTHUMG00000020716	ENST00000373247.2:c.393C>T	9.37:g.130569258C>T		69	0	0		84	42	0.5	NM_004957	B3KPW4|B7Z2Z3|F5H0K6|Q5JU19|Q5JU22|Q6P2P6	Silent	SNP	ENST00000373247.2	37	CCDS35148.1																																																																																			.	.	none		0.652	FPGS-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054251.1			T	130569258	C	T	130569258	2	4	25	1	0	0	0	0	0	0	0	1	6044	610	22	2		2	FPGS	9	130569258	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2580	130569258	10644173	378	9287											
ODF2	4957	hgsc.bcm.edu	37	chr9	131245130	131245130	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgcaagacaaggacaaggaGgtggaagagctccttcagga	14	5	14	8	0	1	2	1	0	0	2	2	6	2	6	1	5	2	2	1	5	4	1	rs139481144	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:131245130G>A	ENST00000434106.3	+	10	1314	c.951G>A	c.(949-951)gaG>gaA	p.E317E	ODF2_ENST00000546203.1_Silent_p.E298E|ODF2_ENST00000372791.3_Silent_p.E298E|ODF2_ENST00000393527.3_Silent_p.E293E|ODF2_ENST00000448249.3_Silent_p.E236E|ODF2_ENST00000444119.2_Silent_p.E293E|ODF2_ENST00000372807.5_Silent_p.E312E|ODF2_ENST00000372814.3_Silent_p.E361E|ODF2_ENST00000535026.1_3'UTR|ODF2_ENST00000604420.1_Silent_p.E317E|ODF2_ENST00000351030.3_Silent_p.E312E|ODF2_ENST00000393533.2_Silent_p.E317E	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	317					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						AGGACAAGGAGGTGGAAGAGC	0.537													G|||	3	0.000599042	0.0	0.0014	5008	,	,		16148	0.0		0.002	False		,,,				2504	0.0				p.E381E		Atlas-SNP	.											.	ODF2	227	.	0			c.G1143A						PASS	.	G	,,,,,,,,,,	0,4406		0,0,2203	97	100	99		936,951,708,879,1083,951,1143,951,894,1026,894	1.1	1	9	dbSNP_134	99	21,8579	14.0+/-48.4	0,21,4279	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ODF2	NM_001242352.1,NM_001242353.1,NM_001242354.1,NM_002540.4,NM_153432.1,NM_153433.1,NM_153435.1,NM_153436.1,NM_153437.2,NM_153439.1,NM_153440.1	,,,,,,,,,,	0,21,6482	AA,AG,GG		0.2442,0.0,0.1615	,,,,,,,,,,	312/825,317/830,236/577,293/806,361/702,317/830,381/894,317/658,298/639,342/654,298/639	131245130	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	4957	exon10			CAAGGAGGTGGAA	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.951G>A	9.37:g.131245130G>A		57	0	0		82	41	0.5	NM_153435	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Silent	SNP	ENST00000434106.3	37	CCDS56588.1																																																																																			G|0.999;A|0.001	0.001	strong		0.537	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3			A	131245130	G	A	131245130	2	1	25	1	0	0	0	0	0	0	0	1	10836	991	35	2		2	ODF2	9	131245130	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	675872	131245130	9968301	379	9288											
ODF2	4957	hgsc.bcm.edu	37	chr9	131262512	131262512	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctgactagctctcccatccGctcccgatctcctcctgcct	4	11	5	21	2	2	1	0	1	2	0	7	2	5	1	7	0	2	2	7	0	1	1	rs142129915	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:131262512G>A	ENST00000434106.3	+	21	2831	c.2468G>A	c.(2467-2469)cGc>cAc	p.R823H	ODF2_ENST00000393527.3_Missense_Mutation_p.R799H|ODF2_ENST00000444119.2_Missense_Mutation_p.R799H|ODF2_ENST00000372807.5_Missense_Mutation_p.R818H|ODF2_ENST00000604420.1_Missense_Mutation_p.R823H|ODF2_ENST00000351030.3_Missense_Mutation_p.R818H	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	823					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						TCTCCCATCCGCTCCCGATCT	0.557													G|||	13	0.00259585	0.0	0.0014	5008	,	,		17126	0.001		0.005	False		,,,				2504	0.0061				p.R887H		Atlas-SNP	.											ODF2,NS,carcinoma,+1,1	ODF2	227	1	0			c.G2660A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	12,4394	19.1+/-41.9	0,12,2191	181	152	162		2453,2468,2396,2468,2660	5.5	1	9	dbSNP_134	162	66,8534	40.3+/-97.0	1,64,4235	yes	missense,missense,missense,missense,missense	ODF2	NM_001242352.1,NM_001242353.1,NM_002540.4,NM_153433.1,NM_153435.1	29,29,29,29,29	1,76,6426	AA,AG,GG		0.7674,0.2724,0.5997	benign,benign,benign,benign,benign	818/825,823/830,799/806,823/830,887/894	131262512	78,12928	2203	4300	6503	SO:0001583	missense	4957	exon21			CCATCCGCTCCCG	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.2468G>A	9.37:g.131262512G>A	ENSP00000403453:p.Arg823His	105	0	0		111	58	0.522523	NM_153435	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Missense_Mutation	SNP	ENST00000434106.3	37	CCDS56588.1	5	0.0022893772893772895	0	0.0	0	0.0	1	0.0017482517482517483	4	0.005277044854881266	G	18.25	3.581992	0.65992	0.002724	0.007674	ENSG00000136811	ENST00000351030;ENST00000372796;ENST00000303890	T;T;T	0.28666	1.64;1.6;1.65	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.15609	0.0376	L	0.32530	0.975	0.80722	D	1	P;B;B;B	0.44690	0.841;0.231;0.054;0.016	B;B;B;B	0.34536	0.185;0.04;0.018;0.002	T	0.02138	-1.1207	10	0.45353	T	0.12	-4.1319	13.6785	0.62469	0.0762:0.0:0.9238:0.0	.	818;168;823;799	Q5BJF6-4;Q6PJQ8;Q5BJF6;Q5BJF6-3	.;.;ODFP2_HUMAN;.	H	818;823;799	ENSP00000342581:R818H;ENSP00000361882:R823H;ENSP00000307781:R799H	ENSP00000307781:R799H	R	+	2	0	ODF2	130302333	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	3.562000	0.53777	2.581000	0.87130	0.561000	0.74099	CGC	G|0.996;A|0.004	0.004	strong		0.557	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3			A	131262512	G	A	131262512	3	1	25	1	0	0	0	0	1	0	0	0	10836	1087	38	1	2664	1	ODF2	9	131262512	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	17382	131262512	9950919	380	9289											
RALGDS	5900	hgsc.bcm.edu	37	chr9	135982493	135982493	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctggccacctcgatccagtgCtccaccaccctggccctgtc	5	8	8	20	1	0	0	0	0	0	0	4	1	2	0	7	2	1	1	7	2	0	0	rs45487303	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:135982493C>T	ENST00000372050.3	-	7	1413	c.1392G>A	c.(1390-1392)gaG>gaA	p.E464E	RALGDS_ENST00000542690.1_Silent_p.E535E|RALGDS_ENST00000372062.3_Silent_p.E435E|RALGDS_ENST00000393157.3_Silent_p.E463E|RALGDS_ENST00000372047.3_Silent_p.E452E|RALGDS_ENST00000393160.3_Silent_p.E409E|RALGDS_ENST00000469972.1_5'UTR	NM_006266.2	NP_006257.1	Q12967	GNDS_HUMAN	ral guanine nucleotide dissociation stimulator	464	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)		CGATCCAGTGCTCCACCACCC	0.617			T	CIITA	"PMBL, Hodgkin Lymphona, "								C|||	50	0.00998403	0.0	0.0144	5008	,	,		18802	0.0		0.0288	False		,,,				2504	0.0112				p.E464E	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.G1392A						PASS	.	C	,	20,4386	27.2+/-55.0	0,20,2183	80	74	76		1227,1392	0.1	1	9	dbSNP_127	76	158,8442	73.5+/-136.2	0,158,4142	no	coding-synonymous,coding-synonymous	RALGDS	NM_001042368.1,NM_006266.2	,	0,178,6325	TT,TC,CC		1.8372,0.4539,1.3686	,	409/860,464/915	135982493	178,12828	2203	4300	6503	SO:0001819	synonymous_variant	5900	exon7			CCAGTGCTCCACC	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.1392G>A	9.37:g.135982493C>T		151	0	0		132	132	1	NM_006266	B7Z753|E7ER93|E7ERZ0|Q5T7V4|Q6KH11|Q6PCE1|Q6ZSD5|Q9HAX7|Q9HAY1|Q9HCT1|Q9P2N8	Silent	SNP	ENST00000372050.3	37	CCDS6959.1																																																																																			C|0.985;T|0.015	0.015	strong		0.617	RALGDS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054837.1	NM_006266		T	135982493	C	T	135982493	2	4	25	1	0	0	0	0	0	0	0	1	13031	796	28	2		2	RALGDS	9	135982493	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	4719981	135982493	5230938	381	9290											
GBGT1	26301	hgsc.bcm.edu	37	chr9	136029138	136029138	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccgccaggcagccatgatGccattggccttgtccgccag	6	8	11	16	2	0	1	0	1	0	0	2	1	2	1	7	2	2	1	7	2	0	2	rs35902535	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:136029138G>A	ENST00000372040.3	-	7	1181	c.870C>T	c.(868-870)ggC>ggT	p.G290G	RALGDS_ENST00000542690.1_Intron|GBGT1_ENST00000540636.1_Silent_p.G273G|GBGT1_ENST00000372043.3_Missense_Mutation_p.A284V|GBGT1_ENST00000472281.1_5'UTR	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	290					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)		CAGCCATGATGCCATTGGCCT	0.587													G|||	210	0.0419329	0.0333	0.0403	5008	,	,		17659	0.002		0.0795	False		,,,				2504	0.0573				p.G290G		Atlas-SNP	.											.	GBGT1	25	.	0			c.C870T						PASS	.	G		200,4206	124.9+/-162.1	8,184,2011	121	113	116		870	2.3	1	9	dbSNP_126	116	618,7982	160.3+/-213.4	16,586,3698	no	coding-synonymous	GBGT1	NM_021996.4		24,770,5709	AA,AG,GG		7.186,4.5393,6.2894		290/348	136029138	818,12188	2203	4300	6503	SO:0001819	synonymous_variant	26301	exon7			CATGATGCCATTG	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.870C>T	9.37:g.136029138G>A		102	0	0		100	52	0.52	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Silent	SNP	ENST00000372040.3	37	CCDS6960.1	105	0.04807692307692308	21	0.042682926829268296	15	0.04143646408839779	2	0.0034965034965034965	67	0.08839050131926121	G	12.72	2.022220	0.35701	0.045393	0.07186	ENSG00000148288	ENST00000372043	T	0.23348	1.91	5.38	2.31	0.28768	.	.	.	.	.	T	0.01287	0.0042	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.00460	-1.1726	6	0.87932	D	0	-15.1162	5.0909	0.14708	0.2677:0.3054:0.4269:0.0	rs35902535;rs62638711	.	.	.	V	284	ENSP00000361113:A284V	ENSP00000361113:A284V	A	-	2	0	GBGT1	135018959	0.629000	0.27146	0.992000	0.48379	0.929000	0.56500	0.761000	0.26489	0.542000	0.28846	0.561000	0.74099	GCA	G|0.944;A|0.056	0.056	strong		0.587	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996		A	136029138	G	A	136029138	2	1	25	1	0	0	0	0	0	0	0	1	6280	1306	46	2		2	GBGT1	9	136029138	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	46645	136029138	5184293	382	9291											
GBGT1	26301	hgsc.bcm.edu	37	chr9	136029645	136029645	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaggactggatgaaatgagtGtacctagtgatgatcacccg	13	9	12	7	1	1	4	1	4	0	0	1	6	1	6	2	2	1	1	2	2	4	2	rs35898523	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:136029645G>T	ENST00000372040.3	-	7	674	c.363C>A	c.(361-363)taC>taA	p.Y121*	RALGDS_ENST00000542690.1_Intron|GBGT1_ENST00000540636.1_Nonsense_Mutation_p.Y104*|GBGT1_ENST00000372043.3_Intron|GBGT1_ENST00000472281.1_5'UTR|GBGT1_ENST00000372038.3_Missense_Mutation_p.H134N	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	121					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)		TGAAATGAGTGTACCTAGTGA	0.587													G|||	215	0.0429313	0.034	0.0418	5008	,	,		18455	0.002		0.0815	False		,,,				2504	0.0583				p.Y121X		Atlas-SNP	.											GBGT1,NS,carcinoma,-2,1	GBGT1	25	1	0			c.C363A						PASS	.	G	stop/TYR	199,4207	121.7+/-159.2	8,183,2012	39	40	39		363	1.5	0.9	9	dbSNP_126	39	629,7971	155.7+/-209.7	18,593,3689	yes	stop-gained	GBGT1	NM_021996.4		26,776,5701	TT,TG,GG		7.314,4.5166,6.3663		121/348	136029645	828,12178	2203	4300	6503	SO:0001587	stop_gained	26301	exon7			ATGAGTGTACCTA	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.363C>A	9.37:g.136029645G>T	ENSP00000361110:p.Tyr121*	20	0	0		28	13	0.464286	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Nonsense_Mutation	SNP	ENST00000372040.3	37	CCDS6960.1	108|108	0.04945054945054945|0.04945054945054945	23|23	0.046747967479674794|0.046747967479674794	16|16	0.04419889502762431|0.04419889502762431	2|2	0.0034965034965034965|0.0034965034965034965	67|67	0.08839050131926121|0.08839050131926121	G|G	17.35|17.35	3.367115|3.367115	0.61513|0.61513	0.045166|0.045166	0.07314|0.07314	ENSG00000148288|ENSG00000148288	ENST00000372038|ENST00000372040;ENST00000540636	T|.	0.36157|.	1.27|.	5.38|5.38	1.47|1.47	0.22746|0.22746	.|.	.|0.137701	.|0.50627	.|D	.|0.000106	T|.	0.01156|.	0.0038|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.02358|.	-1.1171|.	6|.	0.05833|0.07813	T|T	0.94|0.8	-15.2709|-15.2709	6.0904|6.0904	0.19991|0.19991	0.2143:0.0:0.6535:0.1322|0.2143:0.0:0.6535:0.1322	rs35898523;rs62638704|rs35898523;rs62638704	.|.	.|.	.|.	N|X	134|121;104	ENSP00000361108:H134N|.	ENSP00000361108:H134N|ENSP00000361110:Y121X	H|Y	-|-	1|3	0|2	GBGT1|GBGT1	135019466|135019466	0.883000|0.883000	0.30277|0.30277	0.900000|0.900000	0.35374|0.35374	0.243000|0.243000	0.25628|0.25628	0.687000|0.687000	0.25407|0.25407	0.008000|0.008000	0.14787|0.14787	0.491000|0.491000	0.48974|0.48974	CAC|TAC	G|0.941;T|0.059	0.059	strong		0.587	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996		T	136029645	G	T	136029645	4	4	25	1	0	0	0	0	0	1	0	0	6280	1372	48	4	684	4	GBGT1	9	136029645	Nonsense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	507	136029645	5183786	383	9292											
SLC2A6	11182	hgsc.bcm.edu	37	chr9	136341407	136341407	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgccatgagctggggtgTggcccccagagccccacgaa	8	5	13	15	1	0	2	0	1	0	1	0	3	0	2	5	3	3	1	5	3	1	0	rs147872568	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:136341407T>C	ENST00000371899.4	-	4	591	c.514A>G	c.(514-516)Aca>Gca	p.T172A	SLC2A6_ENST00000485978.1_5'UTR|SLC2A6_ENST00000371897.4_Missense_Mutation_p.T172A	NM_017585.3	NP_060055.2	Q9UGQ3	GTR6_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 6	172					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)		AGCTGGGGTGTGGCCCCCAGA	0.627													T|||	2	0.000399361	0.0	0.0	5008	,	,		16727	0.0		0.0	False		,,,				2504	0.002				p.T172A		Atlas-SNP	.											.	SLC2A6	31	.	0			c.A514G						PASS	.	T	ALA/THR,ALA/THR	0,4404		0,0,2202	85	66	72		514,514	5	1	9	dbSNP_134	72	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	SLC2A6	NM_001145099.1,NM_017585.3	58,58	0,3,6499	CC,CT,TT		0.0349,0.0,0.0231	benign,benign	172/446,172/508	136341407	3,13001	2202	4300	6502	SO:0001583	missense	11182	exon4			GGGGTGTGGCCCC	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.514A>G	9.37:g.136341407T>C	ENSP00000360966:p.Thr172Ala	50	0	0		69	30	0.434783	NM_017585	A6NNU6|Q5SXD7|Q8NCC2	Missense_Mutation	SNP	ENST00000371899.4	37	CCDS6975.1	.	.	.	.	.	.	.	.	.	.	T	12.05	1.820748	0.32145	0.0	3.49E-4	ENSG00000160326	ENST00000371897;ENST00000371899;ENST00000432868;ENST00000414172	T;T;T	0.58506	0.33;0.33;0.33	4.98	4.98	0.66077	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.098719	0.64402	D	0.000002	T	0.39489	0.1080	N	0.17723	0.515	0.32320	N	0.562593	B;B;P;P	0.42556	0.012;0.024;0.783;0.679	B;B;B;B	0.40636	0.05;0.089;0.287;0.335	T	0.48703	-0.9012	10	0.22706	T	0.39	.	8.2846	0.31922	0.2861:0.0:0.0:0.7139	.	172;172;172;172	B4DH85;F2Z2F6;Q9UGQ3-2;Q9UGQ3	.;.;.;GTR6_HUMAN	A	172;172;172;99	ENSP00000360964:T172A;ENSP00000360966:T172A;ENSP00000405124:T172A	ENSP00000360964:T172A	T	-	1	0	SLC2A6	135331228	1.000000	0.71417	0.999000	0.59377	0.930000	0.56654	6.118000	0.71583	1.853000	0.53794	0.533000	0.62120	ACA	T|1.000;C|0.000	0.000	strong		0.627	SLC2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054909.1	NM_017585		C	136341407	T	C	136341407	3	2	25	1	0	0	0	0	1	0	0	0	14564	1696	59	3	1037	3	SLC2A6	9	136341407	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	311762	136341407	4872024	384	9293											
SEC16A	9919	hgsc.bcm.edu	37	chr9	139371700	139371700	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgtcaatgcaccagaaaacGgactggcatgtgctctgggc	10	8	13	10	1	2	1	1	0	1	1	2	2	2	2	1	3	3	3	1	3	3	0	rs371074782		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:139371700G>A	ENST00000313050.7	-	1	441	c.368C>T	c.(367-369)cCg>cTg	p.P123L	SEC16A_ENST00000290037.6_5'Flank|SEC16A_ENST00000431893.2_5'Flank|SEC16A_ENST00000371706.3_5'Flank	NM_014866.1	NP_055681.1	O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	0					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)		ACCAGAAAACGGACTGGCATG	0.577																																					p.P123L		Atlas-SNP	.											.	SEC16A	249	.	0			c.C368T						PASS	.	G	LEU/PRO	0,4068		0,0,2034	82	86	85		368	-7.8	0	9		85	1,8361		0,1,4180	no	missense	SEC16A	NM_014866.1	98	0,1,6214	AA,AG,GG		0.012,0.0,0.0080	benign	123/2358	139371700	1,12429	2034	4181	6215	SO:0001583	missense	9919	exon3			GAAAACGGACTGG	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	ENST00000313050.7:c.368C>T	9.37:g.139371700G>A	ENSP00000325827:p.Pro123Leu	140	0	0		118	10	0.0847458	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Missense_Mutation	SNP	ENST00000313050.7	37	CCDS55351.1	.	.	.	.	.	.	.	.	.	.	G	8.006	0.756537	0.15846	0.0	1.2E-4	ENSG00000148396	ENST00000313050	T	0.21031	2.03	5.02	-7.76	0.01232	.	.	.	.	.	T	0.06645	0.0170	N	0.04508	-0.205	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.38090	-0.9677	8	.	.	.	.	6.51	0.22216	0.607:0.0887:0.2148:0.0895	.	123	F1T0I1	.	L	123	ENSP00000325827:P123L	.	P	-	2	0	SEC16A	138491521	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.064000	0.14437	-1.641000	0.01523	-0.794000	0.03295	CCG	.	.	weak		0.577	SEC16A-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_088459		A	139371700	G	A	139371700	3	1	25	1	0	0	0	0	1	0	0	0	14001	1116	39	1	6825	1	SEC16A	9	139371700	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	3030293	139371700	1841731	385	9294											
NOTCH1	4851	hgsc.bcm.edu	37	chr9	139391636	139391636	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagcaggcagcccttgccGtcctgggacttcttcctccg	4	10	10	17	2	1	0	0	0	1	0	5	1	5	1	6	2	3	2	6	2	0	3	rs2229974	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:139391636G>A	ENST00000277541.6	-	34	6630	c.6555C>T	c.(6553-6555)gaC>gaT	p.D2185D		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	2185					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.K2182fs*61(1)|p.S2163_T2283del(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)		AGCCCTTGCCGTCCTGGGACT	0.662			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)			G|||	3481	0.695088	0.6278	0.6542	5008	,	,		16337	0.9494		0.5775	False		,,,				2504	0.6738				p.D2185D		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	.	NOTCH1	1980	.	2	Deletion - Frameshift(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(2)	c.C6555T						PASS	.	G		2777,1589		891,995,297	47	54	52		6555	-0.8	1	9	dbSNP_98	52	4726,3816		1319,2088,864	no	coding-synonymous	NOTCH1	NM_017617.3		2210,3083,1161	AA,AG,GG		44.6734,36.3949,41.8733		2185/2556	139391636	7503,5405	2183	4271	6454	SO:0001819	synonymous_variant	4851	exon34			CTTGCCGTCCTGG	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.6555C>T	9.37:g.139391636G>A		115	0	0		107	107	1	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			G|0.341;A|0.659	0.659	strong		0.662	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		A	139391636	G	A	139391636	2	1	25	1	0	0	0	0	0	0	0	1	10556	1136	40	1		1	NOTCH1	9	139391636	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	19936	139391636	1821795	386	9295											
NOTCH1	4851	hgsc.bcm.edu	37	chr9	139399213	139399213	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggccttcacctggcccagcaGggcgtcaggtgcggcccagc	5	5	15	16	2	2	0	2	0	0	0	2	0	2	0	4	5	3	1	4	5	0	1	rs568700183	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:139399213G>A	ENST00000277541.6	-	26	5005	c.4930C>T	c.(4930-4932)Ctg>Ttg	p.L1644L		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	1644					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.A1641fs*2(2)|p.E1637_Q1648del(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)		TGGCCCAGCAGGGCGTCAGGT	0.711			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)			G|||	2	0.000399361	0.0	0.0	5008	,	,		14356	0.0		0.002	False		,,,				2504	0.0				p.L1644L		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	NOTCH1,NS,lymphoid_neoplasm,+2,1	NOTCH1	1980	1	3	Deletion - Frameshift(2)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(3)	c.C4930T						PASS	.						6	7	7					9																	139399213		1882	3984	5866	SO:0001819	synonymous_variant	4851	exon26			CCAGCAGGGCGTC	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.4930C>T	9.37:g.139399213G>A		25	0	0		20	10	0.5	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			.	.	none		0.711	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		A	139399213	G	A	139399213	2	1	25	1	0	0	0	0	0	0	0	1	10556	991	35	2		2	NOTCH1	9	139399213	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	7577	139399213	1814218	387	9296											
PNPLA7	375775	hgsc.bcm.edu	37	chr9	140444627	140444628	+	Frame_Shift_Ins	INS	-	-	T																															cgagttacatacctgtgggcINStgtcatctttctcttcctcc																								rs372921391|rs372038516	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:140444627_140444628insT	ENST00000277531.4	-	1	208_209	c.22_23insA	c.(22-24)agcfs	p.S8fs	PNPLA7_ENST00000406427.1_Frame_Shift_Ins_p.S8fs|MRPL41_ENST00000371443.5_5'Flank	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	8					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)		TACCTGTGGGCTGTCATCTTTC	0.559													C|T|TT|complex_insertion	13	0.00259585	0.0	0.0043	5008	,	,		18178	0.0		0.0099	False		,,,				2504	0.0				p.S8fs		Pindel,Atlas-Indel	.											.	PNPLA7	124	.	0			c.23_24insA						PASS	.		,	12,4252		0,12,2120					,	0.2	0			114	100,8154		0,100,4027	no	frameshift,frameshift	PNPLA7	NM_152286.3,NM_001098537.1	,	0,112,6147	A1A1,A1R,RR		1.2115,0.2814,0.8947	,	,		112,12406				SO:0001589	frameshift_variant	375775	exon1			.	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.23dupA	9.37:g.140444628_140444628dupT	ENSP00000277531:p.Ser8fs	49	0	.		67	22	0.328	NM_001098537	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Frame_Shift_Ins	INS	ENST00000277531.4	37	CCDS7045.1																																																																																			.	.	weak		0.559	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286		T	140444628	-	T	140444627	7	5	25	1	0	1	1	0	0	0	0	0	12179	797	28	0	4145	0	PNPLA7	9	140444627	Frame_Shift_Ins	INS	-	TCGA-G8-6906-01A-11D-2210-10	1045414	140444627	768804	388	9297											
C10orf18	54906	hgsc.bcm.edu	37	chr10	5790738	5790738	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcctttgatacttctgtttGtggaatagccacagagcacg	10	13	9	9	1	1	2	0	1	1	1	2	3	2	3	2	1	3	2	2	1	3	5	rs183849963	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:5790738G>A	ENST00000328090.5	+	15	5979	c.5354G>A	c.(5353-5355)tGt>tAt	p.C1785Y		NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	1785																	ACTTCTGTTTGTGGAATAGCC	0.498													G|||	5	0.000998403	0.0	0.0029	5008	,	,		20410	0.0		0.003	False		,,,				2504	0.0				p.C1785Y		Atlas-SNP	.											.	.	.	.	0			c.G5354A						PASS	.	G	TYR/CYS	2,3712		0,2,1855	82	79	80		5354	3	0.1	10		80	26,8222		1,24,4099	yes	missense	FAM208B	NM_017782.4	194	1,26,5954	AA,AG,GG		0.3152,0.0539,0.2341	probably-damaging	1785/2431	5790738	28,11934	1857	4124	5981	SO:0001583	missense	54906	exon15			CTGTTTGTGGAAT	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.5354G>A	10.37:g.5790738G>A	ENSP00000328426:p.Cys1785Tyr	91	0	0		106	41	0.386792	NM_017782	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Missense_Mutation	SNP	ENST00000328090.5	37	CCDS41485.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	3.608	-0.080146	0.07141	5.39E-4	0.003152	ENSG00000108021	ENST00000328090;ENST00000442808	T	0.05258	3.47	5.82	2.98	0.34508	.	0.369488	0.27000	N	0.021434	T	0.04272	0.0118	L	0.29908	0.895	0.09310	N	1	B	0.19583	0.037	B	0.20184	0.028	T	0.45920	-0.9228	10	0.14252	T	0.57	.	5.9626	0.19308	0.1676:0.1569:0.6754:0.0	.	1785	Q5VWN6	F208B_HUMAN	Y	1785;980	ENSP00000328426:C1785Y	ENSP00000328426:C1785Y	C	+	2	0	C10orf18	5830744	0.330000	0.24705	0.086000	0.20670	0.005000	0.04900	0.357000	0.20199	0.383000	0.24910	-0.302000	0.09304	TGT	G|0.999;A|0.001	0.001	strong		0.498	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782		A	5790738	G	A	5790738	3	1	25	1	0	0	0	0	1	0	0	0	1598	1377	48	2	5400	2	C10orf18	10	5790738	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10		5790738	129744009	389	9298											
TAF3	83860	hgsc.bcm.edu	37	chr10	8007260	8007260	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttaaaatcaaagaatttgAagatgttgatcccaaagtga	17	12	8	4	0	1	5	1	3	0	2	2	5	2	5	1	0	0	2	1	0	6	4			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:8007260A>C	ENST00000344293.5	+	3	1993	c.1787A>C	c.(1786-1788)gAa>gCa	p.E596A		NM_031923.3	NP_114129.1	Q5VWG9	TAF3_HUMAN	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140kDa	596	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						AAAGAATTTGAAGATGTTGAT	0.373																																					p.E596A		Atlas-SNP	.											.	TAF3	93	.	0			c.A1787C						PASS	.						78	77	77					10																	8007260		1819	4076	5895	SO:0001583	missense	83860	exon3			AATTTGAAGATGT	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.1787A>C	10.37:g.8007260A>C	ENSP00000340271:p.Glu596Ala	84	0	0		74	41	0.554054	NM_031923	Q05DA0|Q6GMS5|Q6P6B5|Q86VY6|Q9BQS9|Q9UFI8	Missense_Mutation	SNP	ENST00000344293.5	37	CCDS41487.1	.	.	.	.	.	.	.	.	.	.	A	7.734	0.699927	0.15106	.	.	ENSG00000165632	ENST00000344293	T	0.20332	2.08	5.82	5.82	0.92795	.	0.540850	0.18799	N	0.130845	T	0.29158	0.0725	M	0.73962	2.25	0.38863	D	0.956539	B	0.17038	0.02	B	0.15870	0.014	T	0.05903	-1.0857	10	0.39692	T	0.17	-14.8166	15.8582	0.79000	1.0:0.0:0.0:0.0	.	596	Q5VWG9	TAF3_HUMAN	A	596	ENSP00000340271:E596A	ENSP00000340271:E596A	E	+	2	0	TAF3	8047266	0.999000	0.42202	0.941000	0.38009	0.097000	0.18754	3.650000	0.54424	2.232000	0.73038	0.528000	0.53228	GAA	.	.	none		0.373	TAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046725.1	NM_031923		C	8007260	A	C	8007260	3	2	25	1	0	0	0	0	1	0	0	0	15540	246	9	5	1797	5	TAF3	10	8007260	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	2216522	8007260	127527487	390	9299											
OPTN	10133	hgsc.bcm.edu	37	chr10	13168025	13168025	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cattgaaaacaattgaggaaCtaacaagaaaagaggtattc	20	8	8	5	0	0	4	0	2	0	2	1	5	0	5	0	2	3	1	0	2	9	5			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:13168025C>A	ENST00000378748.3	+	12	1590	c.1228C>A	c.(1228-1230)Cta>Ata	p.L410I	OPTN_ENST00000263036.5_Missense_Mutation_p.L410I|OPTN_ENST00000378752.3_Missense_Mutation_p.L404I|OPTN_ENST00000378764.2_Missense_Mutation_p.L404I|OPTN_ENST00000378757.2_Missense_Mutation_p.L410I|OPTN_ENST00000378747.3_Missense_Mutation_p.L410I	NM_001008211.1|NM_001008213.1	NP_001008212|NP_001008214	Q96CV9	OPTN_HUMAN	optineurin	410					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						AATTGAGGAACTAACAAGAAA	0.294																																					p.L410I		Atlas-SNP	.											.	OPTN	57	.	0			c.C1228A						PASS	.						75	74	74					10																	13168025		2203	4298	6501	SO:0001583	missense	10133	exon11			GAGGAACTAACAA	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.1228C>A	10.37:g.13168025C>A	ENSP00000368022:p.Leu410Ile	79	0	0		64	26	0.40625	NM_001008212	B3KP00|D3DRS4|D3DRS8|Q5T672|Q5T673|Q5T674|Q5T675|Q7LDL9|Q8N562|Q9UET9|Q9UEV4|Q9Y218	Missense_Mutation	SNP	ENST00000378748.3	37	CCDS7094.1	.	.	.	.	.	.	.	.	.	.	C	13.12	2.141179	0.37825	.	.	ENSG00000123240	ENST00000263036;ENST00000378764;ENST00000378757;ENST00000378752;ENST00000378748;ENST00000378747	D;D;D;D;D;D	0.87809	-2.28;-2.3;-2.28;-2.3;-2.28;-2.28	5.57	4.67	0.58626	.	0.427472	0.25981	N	0.027066	D	0.87896	0.6293	L	0.59436	1.845	0.27698	N	0.945886	P;P	0.46457	0.878;0.807	P;P	0.52481	0.7;0.504	T	0.81267	-0.1010	10	0.40728	T	0.16	-2.6754	8.8732	0.35330	0.0:0.83:0.0:0.17	.	404;410	Q96CV9-2;Q96CV9	.;OPTN_HUMAN	I	410;404;410;404;410;410	ENSP00000263036:L410I;ENSP00000368040:L404I;ENSP00000368032:L410I;ENSP00000368027:L404I;ENSP00000368022:L410I;ENSP00000368021:L410I	ENSP00000263036:L410I	L	+	1	2	OPTN	13208031	1.000000	0.71417	0.730000	0.30809	0.374000	0.29953	1.614000	0.36911	1.490000	0.48466	0.650000	0.86243	CTA	.	.	none		0.294	OPTN-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046834.1	NM_021980		A	13168025	C	A	13168025	3	1	25	1	0	0	0	0	1	0	0	0	10898	564	20	4	1262	4	OPTN	10	13168025	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	5160765	13168025	122366722	391	9300											
PRPF18	8559	hgsc.bcm.edu	37	chr10	13642257	13642257	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatatagatacagccaaaagAggaggaccagaaaccattaa	21	5	8	7	0	0	3	0	0	0	3	0	5	0	5	3	2	3	0	3	2	8	4	rs142307573	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:13642257A>G	ENST00000378572.3	+	3	318	c.158A>G	c.(157-159)gAg>gGg	p.E53G		NM_003675.3	NP_003666.1	Q99633	PRP18_HUMAN	pre-mRNA processing factor 18	53					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	potassium channel inhibitor activity (GO:0019870)			central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(5)|prostate(1)	17						CAGCCAAAAGAGGAGGACCAG	0.333													A|||	11	0.00219649	0.0	0.0043	5008	,	,		18338	0.0		0.008	False		,,,				2504	0.0				p.E53G		Atlas-SNP	.											.	PRPF18	32	.	0			c.A158G						PASS	.	A	GLY/GLU	0,4406		0,0,2203	93	93	93		158	5.8	1	10	dbSNP_134	93	26,8574	15.3+/-51.7	0,26,4274	yes	missense	PRPF18	NM_003675.3	98	0,26,6477	GG,GA,AA		0.3023,0.0,0.1999	benign	53/343	13642257	26,12980	2203	4300	6503	SO:0001583	missense	8559	exon3			CAAAAGAGGAGGA	U51990	CCDS7100.1	10p12.33	2013-06-10	2013-06-10		ENSG00000165630	ENSG00000165630			17351	protein-coding gene	gene with protein product		604993	"PRP18 pre-mRNA processing factor 18 homolog (yeast)", "PRP18 pre-mRNA processing factor 18 homolog (S. cerevisiae)"			9000057	Standard	XM_005252634		Approved	hPrp18	uc001imp.3	Q99633	OTTHUMG00000017702	ENST00000378572.3:c.158A>G	10.37:g.13642257A>G	ENSP00000367835:p.Glu53Gly	65	0	0		53	22	0.415094	NM_003675	Q5T9P9|Q9BUI9	Missense_Mutation	SNP	ENST00000378572.3	37	CCDS7100.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	A	15.59	2.878789	0.51801	0.0	0.003023	ENSG00000165630	ENST00000378572;ENST00000417658;ENST00000320054;ENST00000378544	.	.	.	5.76	5.76	0.90799	.	0.242726	0.48286	D	0.000184	T	0.42245	0.1194	L	0.31207	0.915	0.52501	D	0.999951	B	0.02656	0.0	B	0.04013	0.001	T	0.37709	-0.9694	9	0.23302	T	0.38	-18.2333	14.9492	0.71057	1.0:0.0:0.0:0.0	.	53	Q99633	PRP18_HUMAN	G	53;47;38;47	.	ENSP00000367824:E38G	E	+	2	0	PRPF18	13682263	1.000000	0.71417	0.995000	0.50966	0.978000	0.69477	5.371000	0.66150	2.323000	0.78572	0.528000	0.53228	GAG	A|0.998;G|0.002	0.002	strong		0.333	PRPF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046879.1			G	13642257	A	G	13642257	3	3	25	1	0	0	0	0	1	0	0	0	12575	304	11	3	168	3	PRPF18	10	13642257	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	474232	13642257	121892490	392	9301											
CUBN	8029	hgsc.bcm.edu	37	chr10	16877110	16877110	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggggggctgtgagagtaacgGtgcaatccttgtcattgtcg	7	11	16	7	2	1	1	1	1	0	1	3	2	2	1	1	4	2	3	1	4	2	3	rs1801230	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:16877110G>A	ENST00000377833.4	-	64	10330	c.10265C>T	c.(10264-10266)aCc>aTc	p.T3422I		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	3422	CUB 26. {ECO:0000255|PROSITE- ProRule:PRU00059}.		T -> I (in dbSNP:rs1801230). {ECO:0000269|PubMed:10080186}.		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)	GAGAGTAACGGTGCAATCCTT	0.458													G|||	41	0.0081869	0.0038	0.0144	5008	,	,		17717	0.0		0.0229	False		,,,				2504	0.0031				p.T3422I		Atlas-SNP	.											.	CUBN	515	.	0			c.C10265T						PASS	.	G	ILE/THR	29,4377	35.2+/-66.4	0,29,2174	178	151	160		10265	3.9	0.7	10	dbSNP_89	160	248,8352	98.6+/-160.1	4,240,4056	yes	missense	CUBN	NM_001081.3	89	4,269,6230	AA,AG,GG		2.8837,0.6582,2.1298	benign	3422/3624	16877110	277,12729	2203	4300	6503	SO:0001583	missense	8029	exon64			GTAACGGTGCAAT	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.10265C>T	10.37:g.16877110G>A	ENSP00000367064:p.Thr3422Ile	112	0	0		138	55	0.398551	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	30	0.013736263736263736	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	20	0.026385224274406333	G	14.17	2.455908	0.43634	0.006582	0.028837	ENSG00000107611	ENST00000377833;ENST00000545090	T	0.35421	1.31	4.84	3.94	0.45596	CUB (5);	0.538075	0.15554	N	0.256250	T	0.13243	0.0321	L	0.33753	1.03	0.80722	D	1	P	0.40000	0.698	B	0.42798	0.398	T	0.01596	-1.1316	10	0.38643	T	0.18	.	13.2177	0.59869	0.0768:0.0:0.9232:0.0	rs1801230;rs52825510	3422	O60494	CUBN_HUMAN	I	3422;263	ENSP00000367064:T3422I	ENSP00000367064:T3422I	T	-	2	0	CUBN	16917116	0.983000	0.35010	0.712000	0.30502	0.003000	0.03518	1.834000	0.39171	1.262000	0.44165	-0.258000	0.10820	ACC	G|0.982;A|0.018	0.018	strong		0.458	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		A	16877110	G	A	16877110	3	1	25	1	0	0	0	0	1	0	0	0	4053	1261	44	2	622	2	CUBN	10	16877110	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	3234853	16877110	118657637	393	9302											
PDSS1	23590	hgsc.bcm.edu	37	chr10	27035396	27035396	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaaattgtactcacaagagaTaaatgacaactctttctgtt	15	13	6	7	0	3	2	1	1	2	1	3	4	3	2	0	0	2	2	0	0	6	5			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:27035396T>A	ENST00000376215.5	+	12	1295	c.1242T>A	c.(1240-1242)gaT>gaA	p.D414E	PDSS1_ENST00000470978.1_3'UTR|PDSS1_ENST00000376203.5_3'UTR	NM_014317.3	NP_055132.2	Q5T2R2	DPS1_HUMAN	prenyl (decaprenyl) diphosphate synthase, subunit 1	414					isoprenoid biosynthetic process (GO:0008299)|protein heterotetramerization (GO:0051290)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrial matrix (GO:0005759)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|trans-hexaprenyltranstransferase activity (GO:0000010)|trans-octaprenyltranstransferase activity (GO:0050347)			autonomic_ganglia(1)|endometrium(1)|kidney(7)|large_intestine(6)|lung(5)|prostate(1)	21						TCACAAGAGATAAATGACAAC	0.403																																					p.D414E		Atlas-SNP	.											.	PDSS1	36	.	0			c.T1242A						PASS	.						91	79	83					10																	27035396		2203	4300	6503	SO:0001583	missense	23590	exon12			AAGAGATAAATGA	AF118395	CCDS31168.1	10p12.2	2006-04-12	2006-02-14	2006-02-14	ENSG00000148459	ENSG00000148459			17759	protein-coding gene	gene with protein product	"coenzyme Q1 homolog (yeast)"	607429	"trans-prenyltransferase"	TPRT		10972372	Standard	NM_014317		Approved	TPT, COQ1	uc001isv.3	Q5T2R2	OTTHUMG00000017844	ENST00000376215.5:c.1242T>A	10.37:g.27035396T>A	ENSP00000365388:p.Asp414Glu	82	0	0		74	31	0.418919	NM_014317	Q53F75|Q6P473|Q86WQ8|Q9Y2W5	Missense_Mutation	SNP	ENST00000376215.5	37	CCDS31168.1	.	.	.	.	.	.	.	.	.	.	T	3.921	-0.018056	0.07681	.	.	ENSG00000148459	ENST00000376215;ENST00000396343	T	0.62941	-0.01	5.54	-3.27	0.05048	Terpenoid synthase (2);	0.093864	0.64402	N	0.000001	T	0.39682	0.1087	L	0.52905	1.665	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.40478	-0.9561	10	0.02654	T	1	-16.2141	2.2506	0.04042	0.1373:0.2408:0.4191:0.2028	.	152;414	B4DJY1;Q5T2R2	.;DPS1_HUMAN	E	414;375	ENSP00000365388:D414E	ENSP00000365388:D414E	D	+	3	2	PDSS1	27075402	0.994000	0.37717	0.997000	0.53966	0.680000	0.39746	0.372000	0.20467	-0.207000	0.10187	-0.257000	0.10917	GAT	.	.	none		0.403	PDSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047276.1			A	27035396	T	A	27035396	3	1	25	1	0	0	0	0	1	0	0	0	11702	1403	49	5	1288	5	PDSS1	10	27035396	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	10158286	27035396	108499351	394	9303											
ZNF25	219749	hgsc.bcm.edu	37	chr10	38241220	38241220	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgagaaaaggacttcccacaTtccttgcatgcatagggctt	11	11	9	10	0	0	1	0	1	0	1	2	3	2	2	2	2	2	3	2	2	3	5	rs146555827	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:38241220T>C	ENST00000302609.7	-	6	1418	c.1206A>G	c.(1204-1206)gaA>gaG	p.E402E	AL117337.1_ENST00000582458.1_RNA|ZNF25_ENST00000374633.1_5'UTR	NM_145011.2	NP_659448.1	P17030	ZNF25_HUMAN	zinc finger protein 25	402					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)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_neural(218;0.0218)|Breast(68;0.0389)|Ovarian(717;0.0443)|Renal(717;0.157)				ACTTCCCACATTCCTTGCATG	0.433																																					p.E402E		Atlas-SNP	.											.	ZNF25	66	.	0			c.A1206G						PASS	.	T		1,4405	2.1+/-5.4	0,1,2202	92	90	90		1206	-4.1	0.7	10	dbSNP_134	90	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous	ZNF25	NM_145011.2		0,10,6493	CC,CT,TT		0.1047,0.0227,0.0769		402/457	38241220	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	219749	exon6			CCCACATTCCTTG	AK056452	CCDS7195.1	10p11.2	2013-01-08	2006-05-10		ENSG00000175395	ENSG00000175395		"Zinc fingers, C2H2-type", "-"	13043	protein-coding gene	gene with protein product		194528	"zinc finger protein 25 (KOX 19)"			1639412, 8464732	Standard	NM_145011		Approved	KOX19, FLJ31890, Zfp9	uc001ize.1	P17030	OTTHUMG00000019344	ENST00000302609.7:c.1206A>G	10.37:g.38241220T>C		78	0	0		92	51	0.554348	NM_145011	A9Z1X5|Q8IYE3|Q8NDD6|Q96MU2	Silent	SNP	ENST00000302609.7	37	CCDS7195.1																																																																																			T|0.999;C|0.001	0.001	strong		0.433	ZNF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051214.1	NM_145011, NM_006966		C	38241220	T	C	38241220	2	2	25	1	0	0	0	0	0	0	0	1	17809	1490	52	3		3	ZNF25	10	38241220	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	11205824	38241220	97293527	395	9304											
ZNF33A	7581	hgsc.bcm.edu	37	chr10	38345455	38345455	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagagtattcacactgtggAgaaagccctgatgacatcct	12	10	9	10	0	2	4	2	2	0	2	3	5	3	4	2	1	1	1	2	1	2	2	rs12242343	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:38345455A>G	ENST00000458705.2	+	5	2558	c.2400A>G	c.(2398-2400)ggA>ggG	p.G800G	ZNF33A_ENST00000469037.2_Intron|ZNF33A_ENST00000432900.2_Silent_p.G807G|ZNF33A_ENST00000307441.9_Silent_p.G800G|ZNF33A_ENST00000374618.3_Silent_p.G801G			Q06730	ZN33A_HUMAN	zinc finger protein 33A	800					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						CACACTGTGGAGAAAGCCCTG	0.388													A|||	140	0.0279553	0.0915	0.013	5008	,	,		18836	0.0		0.0099	False		,,,				2504	0.0				p.G801G		Atlas-SNP	.											.	ZNF33A	103	.	0			c.A2403G						PASS	.	A	,	359,4047	175.9+/-205.1	19,321,1863	61	59	60		2403,2400	1.9	0.1	10	dbSNP_120	60	53,8547	32.3+/-84.9	0,53,4247	no	coding-synonymous,coding-synonymous	ZNF33A	NM_006954.1,NM_006974.2	,	19,374,6110	GG,GA,AA		0.6163,8.148,3.1678	,	801/812,800/811	38345455	412,12594	2203	4300	6503	SO:0001819	synonymous_variant	7581	exon5			CTGTGGAGAAAGC	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.2400A>G	10.37:g.38345455A>G		84	0	0		71	40	0.56338	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Silent	SNP	ENST00000458705.2	37	CCDS31182.1																																																																																			A|0.968;G|0.032	0.032	strong		0.388	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974		G	38345455	A	G	38345455	2	3	25	1	0	0	0	0	0	0	0	1	17869	291	11	3		3	ZNF33A	10	38345455	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	104235	38345455	97189292	396	9305											
TMEM72	643236	hgsc.bcm.edu	37	chr10	45430153	45430153	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tacttccttctgagcaagcgGaagaagaggaaagctgcccc	12	7	11	11	1	1	3	0	1	1	2	2	5	2	5	3	2	5	2	3	2	5	3	rs17157262	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:45430153G>A	ENST00000544540.1	+	4	529	c.45G>A	c.(43-45)cgG>cgA	p.R15R	TMEM72-AS1_ENST00000450287.2_RNA|RP11-285G1.9_ENST00000425541.2_lincRNA			A0PK05	TMM72_HUMAN	transmembrane protein 72	133						integral component of membrane (GO:0016021)				breast(2)|kidney(1)|large_intestine(2)|lung(10)	15						TGAGCAAGCGGAAGAAGAGGA	0.602													G|||	57	0.0113818	0.0386	0.0086	5008	,	,		17472	0.0		0.0	False		,,,				2504	0.0				p.R133R		Atlas-SNP	.											.	TMEM72	25	.	0			c.G399A						PASS	.	G		91,3045		1,89,1478	77	81	80		399	-3.8	0.9	10	dbSNP_123	80	2,7162		0,2,3580	no	coding-synonymous	TMEM72	NM_001123376.1		1,91,5058	AA,AG,GG		0.0279,2.9018,0.9029		133/276	45430153	93,10207	1568	3582	5150	SO:0001819	synonymous_variant	643236	exon5			CAAGCGGAAGAAG	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.45G>A	10.37:g.45430153G>A		67	0	0		80	38	0.475	NM_001123376	A1L181|Q5T740	Silent	SNP	ENST00000544540.1	37																																																																																				G|0.990;A|0.010	0.010	strong		0.602	TMEM72-201	KNOWN	basic	protein_coding	protein_coding		NM_001123376		A	45430153	G	A	45430153	2	1	25	1	0	0	0	0	0	0	0	1	16216	1161	41	2		2	TMEM72	10	45430153	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	7084698	45430153	90104594	397	9306											
C10orf10	11067	hgsc.bcm.edu	37	chr10	45473432	45473432	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatctcctccgtggtctccCgaattgtgggcagatgggcc	5	10	13	13	2	2	1	0	0	2	1	5	2	3	1	4	3	0	2	4	3	1	1	rs149255069	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:45473432C>T	ENST00000298295.3	-	2	264	c.47G>A	c.(46-48)cGg>cAg	p.R16Q	C10orf10_ENST00000496638.1_Intron|RASSF4_ENST00000340258.5_Intron|RASSF4_ENST00000334940.6_Intron|RASSF4_ENST00000374417.2_Intron|RASSF4_ENST00000472561.1_Intron	NM_007021.3	NP_008952.1	Q9NTK1	DEPP_HUMAN	chromosome 10 open reading frame 10	16						mitochondrion (GO:0005739)				lung(1)	1						CGTGGTCTCCCGAATTGTGGG	0.607													C|||	5	0.000998403	0.0038	0.0	5008	,	,		16956	0.0		0.0	False		,,,				2504	0.0				p.R16Q		Atlas-SNP	.											.	C10orf10	6	.	0			c.G47A						PASS	.	C	GLN/ARG,	11,4393		0,11,2191	44	50	48		47,	2.7	1	10	dbSNP_134	48	0,8596		0,0,4298	yes	missense,intron	C10orf10,RASSF4	NM_007021.3,NM_032023.3	43,	0,11,6489	TT,TC,CC		0.0,0.2498,0.0846	benign,	16/213,	45473432	11,12989	2202	4298	6500	SO:0001583	missense	11067	exon2			GTCTCCCGAATTG	AB022718	CCDS7210.1	10q11.21	2014-07-31			ENSG00000165507	ENSG00000165507			23355	protein-coding gene	gene with protein product	"decidual protein induced by progesterone", "fasting induced", "fat-specific expressed gene"	611309				24530860, 19937567, 16123073	Standard	NM_007021		Approved	DEPP, FIG, Fseg	uc001jbr.4	Q9NTK1	OTTHUMG00000018063	ENST00000298295.3:c.47G>A	10.37:g.45473432C>T	ENSP00000298295:p.Arg16Gln	101	0	0		91	36	0.395604	NM_007021	B2R6A1|O94997|Q5T735|Q76MX8	Missense_Mutation	SNP	ENST00000298295.3	37	CCDS7210.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.249917	0.80024	0.002498	0.0	ENSG00000165507	ENST00000298295;ENST00000432283;ENST00000448778	T;T	0.51574	0.73;0.7	5.63	2.73	0.32206	.	0.512064	0.16368	N	0.217438	T	0.22627	0.0546	N	0.12746	0.255	0.28270	N	0.924451	B	0.32800	0.385	B	0.21546	0.035	T	0.10064	-1.0646	10	0.37606	T	0.19	-18.3777	5.2281	0.15406	0.1628:0.6657:0.0:0.1715	.	16	Q9NTK1	DEPP_HUMAN	Q	16	ENSP00000298295:R16Q;ENSP00000414494:R16Q	ENSP00000298295:R16Q	R	-	2	0	C10orf10	44793438	0.989000	0.36119	0.982000	0.44146	0.994000	0.84299	0.343000	0.19944	0.302000	0.22762	0.561000	0.74099	CGG	C|0.999;T|0.001	0.001	strong		0.607	C10orf10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047758.1	NM_007021		T	45473432	C	T	45473432	3	4	25	1	0	0	0	0	1	0	0	0	1582	652	23	1	595	1	C10orf10	10	45473432	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	43279	45473432	90061315	398	9307											
RASSF4	83937	hgsc.bcm.edu	37	chr10	45488738	45488738	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttccaagccctgcgtctgacGatgctgcagcgcctggagca	7	8	12	14	3	1	1	0	1	1	0	2	3	2	2	3	1	6	3	3	1	1	1	rs145503557	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:45488738G>A	ENST00000340258.5	+	11	1040	c.927G>A	c.(925-927)acG>acA	p.T309T	RASSF4_ENST00000334940.6_Silent_p.T318T|RASSF4_ENST00000374417.2_3'UTR|RASSF4_ENST00000472561.1_3'UTR	NM_032023.3	NP_114412.2	Q8WYP3	RIN2_HUMAN	Ras association (RalGDS/AF-6) domain family member 4	0	Poly-Pro.				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						TGCGTCTGACGATGCTGCAGC	0.627													G|||	5	0.000998403	0.0038	0.0	5008	,	,		19979	0.0		0.0	False		,,,				2504	0.0				p.T309T		Atlas-SNP	.											.	RASSF4	33	.	0			c.G927A						PASS	.	G		11,4395	19.1+/-41.9	0,11,2192	67	51	56		927	-8.1	1	10	dbSNP_134	56	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RASSF4	NM_032023.3		0,12,6491	AA,AG,GG		0.0116,0.2497,0.0923		309/322	45488738	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	83937	exon11			TCTGACGATGCTG	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.927G>A	10.37:g.45488738G>A		31	0	0		20	11	0.55	NM_032023	Q00425|Q5TFT8|Q9BQL3|Q9H071	Silent	SNP	ENST00000340258.5	37	CCDS7208.1																																																																																			G|0.999;A|0.001	0.001	strong		0.627	RASSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047745.2	NM_032023		A	45488738	G	A	45488738	2	1	25	1	0	0	0	0	0	0	0	1	13103	1045	37	1		1	RASSF4	10	45488738	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	15306	45488738	90046009	399	9308											
OR13A1	79290	hgsc.bcm.edu	37	chr10	45799451	45799451	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gggtggcagatggctgcgtaCcggtcataggccatgaccgt	7	8	16	10	3	1	2	1	1	0	1	1	2	1	2	3	5	2	3	3	5	2	2	rs17157674	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:45799451C>T	ENST00000553795.1	-	4	728	c.420G>A	c.(418-420)cgG>cgA	p.R140R	OR13A1_ENST00000536058.1_Silent_p.R140R|OR13A1_ENST00000374401.2_Silent_p.R140R	NM_001004297.2	NP_001004297.2	Q8NGR1	O13A1_HUMAN	olfactory receptor, family 13, subfamily A, 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(1)|kidney(1)|large_intestine(5)|lung(9)|skin(2)|urinary_tract(1)	19						TGGCTGCGTACCGGTCATAGG	0.617													C|||	38	0.00758786	0.0265	0.0043	5008	,	,		19585	0.0		0.0	False		,,,				2504	0.0				p.R140R		Atlas-SNP	.											.	OR13A1	49	.	0			c.G420A						PASS	.	C		83,4323	69.2+/-107.0	1,81,2121	35	28	30		420	-6.5	0.1	10	dbSNP_123	30	0,8600		0,0,4300	no	coding-synonymous	OR13A1	NM_001004297.2		1,81,6421	TT,TC,CC		0.0,1.8838,0.6382		140/329	45799451	83,12923	2203	4300	6503	SO:0001819	synonymous_variant	79290	exon4			TGCGTACCGGTCA	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.420G>A	10.37:g.45799451C>T		59	0	0		81	37	0.45679	NM_001004297	Q2M3M4|Q5VV57|Q6IFH5|Q6ZMN6	Silent	SNP	ENST00000553795.1	37	CCDS31188.1																																																																																			C|0.992;T|0.008	0.008	strong		0.617	OR13A1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047779.2	NM_001004297		T	45799451	C	T	45799451	2	4	25	1	0	0	0	0	0	0	0	1	10942	494	18	2		2	OR13A1	10	45799451	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	310713	45799451	89735296	400	9309											
GPRIN2	9721	hgsc.bcm.edu	37	chr10	46998904	46998904	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agctccagccgccccgagccGggtccctgggcacccctgag	5	4	13	19	3	0	1	0	1	0	0	2	2	2	1	8	2	3	2	8	2	0	0	rs140651048		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:46998904G>A	ENST00000374317.1	+	3	297	c.24G>A	c.(22-24)ccG>ccA	p.P8P	GPRIN2_ENST00000374314.4_Silent_p.P8P	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	8										breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						GCCCCGAGCCGGGTCCCTGGG	0.642													G|||	1	0.000199681	0.0	0.0	5008	,	,		31822	0.001		0.0	False		,,,				2504	0.0				p.P8P		Atlas-SNP	.											.	GPRIN2	94	.	0			c.G24A						PASS	.	G		1,4371		0,1,2185	51	71	64		24	-10.7	0	10	dbSNP_134	64	0,8544		0,0,4272	no	coding-synonymous	GPRIN2	NM_014696.3		0,1,6457	AA,AG,GG		0.0,0.0229,0.0077		8/459	46998904	1,12915	2186	4272	6458	SO:0001819	synonymous_variant	9721	exon3			CGAGCCGGGTCCC	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.24G>A	10.37:g.46998904G>A		239	0	0		140	32	0.228571	NM_014696	Q5SVF0	Silent	SNP	ENST00000374317.1	37	CCDS31192.1																																																																																			G|0.999;A|0.001	0.001	strong		0.642	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696		A	46998904	G	A	46998904	2	1	25	1	0	0	0	0	0	0	0	1	6739	1103	39	1		1	GPRIN2	10	46998904	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1199453	46998904	88535843	401	9310											
ARHGAP22	58504	hgsc.bcm.edu	37	chr10	49658842	49658842	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctccagggatgagccgccccCcttcgggcttcccgataggg	5	7	13	16	3	0	1	0	1	0	0	3	3	2	2	6	3	1	1	6	3	1	3	rs34940331	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:49658842C>G	ENST00000249601.4	-	9	1626	c.1330G>C	c.(1330-1332)Ggg>Cgg	p.G444R	ARHGAP22_ENST00000417247.2_Missense_Mutation_p.G354R|ARHGAP22_ENST00000417912.2_Missense_Mutation_p.G460R|ARHGAP22_ENST00000374172.1_Missense_Mutation_p.G335R|ARHGAP22_ENST00000477708.2_Missense_Mutation_p.G277R|ARHGAP22_ENST00000374170.1_Missense_Mutation_p.G285R|ARHGAP22_ENST00000435790.2_Missense_Mutation_p.G450R	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	444	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						GAGCCGCCCCCCTTCGGGCTT	0.701													C|||	29	0.00579073	0.0	0.0115	5008	,	,		14381	0.0		0.0169	False		,,,				2504	0.0041				p.G460R		Atlas-SNP	.											.	ARHGAP22	94	.	0			c.G1378C						PASS	.	C	ARG/GLY	18,4346		0,18,2164	16	16	16		1330	1.9	0.1	10	dbSNP_126	16	120,8452		0,120,4166	yes	missense	ARHGAP22	NM_021226.2	125	0,138,6330	GG,GC,CC		1.3999,0.4125,1.0668	benign	444/699	49658842	138,12798	2182	4286	6468	SO:0001583	missense	58504	exon9			CGCCCCCCTTCGG	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.1330G>C	10.37:g.49658842C>G	ENSP00000249601:p.Gly444Arg	84	0	0		90	39	0.433333	NM_001256024	A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Missense_Mutation	SNP	ENST00000249601.4	37	CCDS7227.1	16	0.007326007326007326	0	0.0	4	0.011049723756906077	0	0.0	12	0.0158311345646438	C	1.420	-0.573198	0.03882	0.004125	0.013999	ENSG00000128805	ENST00000249601;ENST00000374172;ENST00000374170;ENST00000477708;ENST00000417247;ENST00000435790;ENST00000417912	T;T;T;T;T;T;T	0.25250	2.93;2.6;1.81;2.22;2.59;2.89;2.93	4.94	1.9	0.25705	.	1.698030	0.02544	N	0.094901	T	0.10852	0.0265	L	0.36672	1.1	0.09310	N	1	B;B;B;B;B;B	0.17038	0.001;0.0;0.0;0.0;0.0;0.02	B;B;B;B;B;B	0.13407	0.002;0.001;0.001;0.001;0.002;0.009	T	0.16689	-1.0394	10	0.15952	T	0.53	.	7.5489	0.27783	0.2549:0.3359:0.4092:0.0	rs34940331	450;444;460;444;354;277	B4DED8;A6NDI7;Q7Z5H3-2;Q7Z5H3;Q7Z5H3-3;D6R9V6	.;.;.;RHG22_HUMAN;.;.	R	444;335;285;277;354;450;460	ENSP00000249601:G444R;ENSP00000363287:G335R;ENSP00000363285:G285R;ENSP00000422868:G277R;ENSP00000410054:G354R;ENSP00000416701:G450R;ENSP00000412461:G460R	ENSP00000249601:G444R	G	-	1	0	ARHGAP22	49328848	0.001000	0.12720	0.081000	0.20488	0.304000	0.27724	-0.001000	0.12947	1.074000	0.40909	-0.226000	0.12346	GGG	C|0.991;G|0.009	0.009	strong		0.701	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226		G	49658842	C	G	49658842	3	3	25	1	0	0	0	0	1	0	0	0	872	623	22	4	774	4	ARHGAP22	10	49658842	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2659938	49658842	85875905	402	9311											
ERCC6	2074	hgsc.bcm.edu	37	chr10	50678544	50678544	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgggtctttctcttttgtaAgaaagacctaacttttcatc	9	17	6	9	0	3	2	1	0	2	2	5	2	3	2	1	1	1	1	1	1	3	7			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:50678544A>C	ENST00000355832.5	-	18	3540	c.3462T>G	c.(3460-3462)tcT>tcG	p.S1154S	ERCC6_ENST00000542458.1_Silent_p.S524S|RP11-123B3.2_ENST00000423283.1_RNA|ERCC6_ENST00000465653.1_5'Flank	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	1154					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						CTCTTTTGTAAGAAAGACCTA	0.358								Direct reversal of damage;Nucleotide excision repair (NER)																													p.A1154A		Atlas-SNP	.											ERCC6,NS,haematopoietic_neoplasm,-1,1	ERCC6	162	1	0			c.C3462G						scavenged	.						75	74	74					10																	50678544		2203	4300	6503	SO:0001819	synonymous_variant	2074	exon18			TTTGTAAGAAAGA	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.3462T>G	10.37:g.50678544A>C		142	1	0.00704225		156	58	0.371795	NM_000124	D3DX94|Q5W0L9	Silent	SNP	ENST00000355832.5	37	CCDS7229.1																																																																																			.	.	none		0.358	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124		C	50678544	A	C	50678544	2	2	25	1	0	0	0	0	0	0	0	1	5219	59	3	5		5	ERCC6	10	50678544	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	1019702	50678544	84856203	403	9312											
ZWINT	11130	hgsc.bcm.edu	37	chr10	58118569	58118569	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgctcccgaacttacctcTgcagcttgtcccgctcctgt	5	12	7	17	2	1	0	0	0	1	0	4	1	4	0	4	0	5	4	4	0	2	2	rs370677108		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:58118569T>C	ENST00000373944.3	-	6	658	c.620A>G	c.(619-621)cAg>cGg	p.Q207R	ZWINT_ENST00000318387.2_Missense_Mutation_p.Q87R|ZWINT_ENST00000395405.1_Missense_Mutation_p.Q207R|ZWINT_ENST00000361148.6_Intron|ZWINT_ENST00000460654.1_5'UTR			O95229	ZWINT_HUMAN	ZW10 interacting kinetochore protein	207					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						AACTTACCTCTGCAGCTTGTC	0.522																																					p.Q207R		Atlas-SNP	.											.	ZWINT	39	.	0			c.A620G						PASS	.	T	ARG/GLN,ARG/GLN,	0,4406		0,0,2203	136	130	132		620,620,	4.5	1	10		132	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,intron	ZWINT	NM_007057.3,NM_032997.2,NM_001005413.1	43,43,	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	probably-damaging,probably-damaging,	207/278,207/278,	58118569	1,13005	2203	4300	6503	SO:0001583	missense	11130	exon6			TACCTCTGCAGCT	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.620A>G	10.37:g.58118569T>C	ENSP00000363055:p.Gln207Arg	278	0	0		243	117	0.481481	NM_007057	A6NNV6|Q0D2I3|Q9BWD0	Missense_Mutation	SNP	ENST00000373944.3	37	CCDS7249.1	.	.	.	.	.	.	.	.	.	.	T	11.24	1.581660	0.28180	0.0	1.16E-4	ENSG00000122952	ENST00000373944;ENST00000395405;ENST00000318387	T;T;T	0.50548	0.74;0.74;0.74	4.48	4.48	0.54585	.	0.154517	0.30911	N	0.008632	T	0.59622	0.2207	M	0.62723	1.935	0.29902	N	0.824315	D	0.63046	0.992	P	0.60541	0.876	T	0.61446	-0.7061	10	0.87932	D	0	.	10.4401	0.44460	0.0:0.0:0.0:1.0	.	207	O95229	ZWINT_HUMAN	R	207;207;87	ENSP00000363055:Q207R;ENSP00000378801:Q207R;ENSP00000322850:Q87R	ENSP00000322850:Q87R	Q	-	2	0	ZWINT	57788575	0.992000	0.36948	1.000000	0.80357	0.070000	0.16714	1.076000	0.30729	2.237000	0.73441	0.533000	0.62120	CAG	.	.	none		0.522	ZWINT-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048132.1			C	58118569	T	C	58118569	3	2	25	1	0	0	0	0	1	0	0	0	18264	1580	55	3	225	3	ZWINT	10	58118569	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	7440025	58118569	77416178	404	9313											
ANK3	288	hgsc.bcm.edu	37	chr10	61832131	61832131	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttgctaaatctgaggttatAtgacatgccaagtctttagc	11	14	9	7	0	2	2	0	2	2	0	2	2	2	2	1	1	3	3	1	1	6	6	rs11815168	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:61832131A>G	ENST00000280772.2	-	37	8699	c.8508T>C	c.(8506-8508)caT>caC	p.H2836H	ANK3_ENST00000373827.2_Intron|ANK3_ENST00000355288.2_Intron|ANK3_ENST00000503366.1_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	2836					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						CTGAGGTTATATGACATGCCA	0.408													A|||	12	0.00239617	0.0	0.0014	5008	,	,		18183	0.0		0.007	False		,,,				2504	0.0041				p.H2836H		Atlas-SNP	.											.	ANK3	703	.	0			c.T8508C						PASS	.	A	,,,	12,4394	17.9+/-39.9	0,12,2191	102	102	102		,,,8508	0.7	1	10	dbSNP_120	102	55,8545	33.8+/-87.4	0,55,4245	no	intron,intron,intron,coding-synonymous	ANK3	NM_001149.3,NM_001204403.1,NM_001204404.1,NM_020987.3	,,,	0,67,6436	GG,GA,AA		0.6395,0.2724,0.5151	,,,	,,,2836/4378	61832131	67,12939	2203	4300	6503	SO:0001819	synonymous_variant	288	exon37			GGTTATATGACAT	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.8508T>C	10.37:g.61832131A>G		121	0	0		116	67	0.577586	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	37	CCDS7258.1																																																																																			A|0.995;G|0.005	0.005	strong		0.408	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987		G	61832131	A	G	61832131	2	3	25	1	0	0	0	0	0	0	0	1	622	446	16	3		3	ANK3	10	61832131	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	3713562	61832131	73702616	405	9314											
ATOH7	220202	hgsc.bcm.edu	37	chr10	69991099	69991099	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgcggccgaagtgctcacaGtggagacccacccagtcccg	8	5	12	16	4	1	1	1	0	0	1	3	3	2	1	4	2	1	1	4	2	1	0	rs201955526		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:69991099G>A	ENST00000373673.3	-	1	772	c.336C>T	c.(334-336)caC>caT	p.H112H	RP11-153K11.3_ENST00000444086.1_lincRNA	NM_145178.3	NP_660161.1	Q8N100	ATOH7_HUMAN	atonal homolog 7 (Drosophila)	112					cell differentiation (GO:0030154)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|neural retina development (GO:0003407)|optic nerve development (GO:0021554)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)										AGTGCTCACAGTGGAGACCCA	0.672																																					p.H112H		Atlas-SNP	.											.	ATOH7	4	.	0			c.C336T						PASS	.	G		0,4406		0,0,2203	33	34	34		336	4.1	1	10		34	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ATOH7	NM_145178.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		112/153	69991099	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	220202	exon1			CTCACAGTGGAGA	AF418922	CCDS7276.1	10q22.2	2013-05-21			ENSG00000179774	ENSG00000179774		"Basic helix-loop-helix proteins"	13907	protein-coding gene	gene with protein product		609875				11889557	Standard	NM_145178		Approved	Math5, bHLHa13	uc001jnq.3	Q8N100	OTTHUMG00000018346	ENST00000373673.3:c.336C>T	10.37:g.69991099G>A		44	0	0		74	41	0.554054	NM_145178		Silent	SNP	ENST00000373673.3	37	CCDS7276.1																																																																																			G|0.999;A|0.001	0.001	weak		0.672	ATOH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048312.1			A	69991099	G	A	69991099	2	1	25	1	0	0	0	0	0	0	0	1	1113	1020	36	2		2	ATOH7	10	69991099	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	8158968	69991099	65543648	406	9315											
ADAMTS14	140766	hgsc.bcm.edu	37	chr10	72520417	72520417	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctctggatacaagctccccAgggacccagcatccctttgc	8	8	9	16	0	1	0	0	0	1	0	3	2	3	2	4	2	4	3	4	2	2	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:72520417A>G	ENST00000373207.1	+	22	3480	c.3480A>G	c.(3478-3480)ccA>ccG	p.P1160P	ADAMTS14_ENST00000373208.1_Silent_p.P1163P	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	1160	Pro-rich.				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						CAAGCTCCCCAGGGACCCAGC	0.632																																					p.P1163P		Atlas-SNP	.											ADAMTS14,rectum,carcinoma,+2,2	ADAMTS14	148	2	0			c.A3489G						PASS	.						61	60	60					10																	72520417		2203	4300	6503	SO:0001819	synonymous_variant	140766	exon22			CTCCCCAGGGACC	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.3480A>G	10.37:g.72520417A>G		70	0	0		75	38	0.506667	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Silent	SNP	ENST00000373207.1	37	CCDS7306.1																																																																																			.	.	none		0.632	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722		G	72520417	A	G	72520417	2	3	25	1	0	0	0	0	0	0	0	1	259	175	7	3		3	ADAMTS14	10	72520417	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	2529318	72520417	63014330	407	9316											
ANAPC16	119504	hgsc.bcm.edu	37	chr10	73992862	73992862	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctgctgggattcaccccCtcttcaggttgatactgcct	6	12	9	14	0	3	1	2	1	1	0	3	2	3	2	3	2	4	3	3	2	1	4	rs9275	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:73992862C>G	ENST00000299381.4	+	4	439	c.321C>G	c.(319-321)ccC>ccG	p.P107P	ANAPC16_ENST00000470481.2_3'UTR	NM_001242546.1|NM_001242547.1|NM_001242548.1|NM_173473.3	NP_001229475.1|NP_001229476.1|NP_001229477.1|NP_775744.1	Q96DE5	APC16_HUMAN	anaphase promoting complex subunit 16	107					mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	anaphase-promoting complex (GO:0005680)|cytoplasm (GO:0005737)				large_intestine(1)|ovary(1)	2						GATTCACCCCCTCTTCAGGTT	0.542													C|||	364	0.0726837	0.2595	0.0274	5008	,	,		14954	0.0		0.002	False		,,,				2504	0.0				p.P107P		Atlas-SNP	.											.	ANAPC16	10	.	0			c.C321G						PASS	.	C	,,,	919,3487	344.1+/-307.9	90,739,1374	66	64	65		321,321,246,321	-0.3	1	10	dbSNP_52	65	13,8587	9.1+/-34.3	0,13,4287	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ANAPC16	NM_001242546.1,NM_001242547.1,NM_001242548.1,NM_173473.3	,,,	90,752,5661	GG,GC,CC		0.1512,20.8579,7.1659	,,,	107/111,107/111,82/86,107/111	73992862	932,12074	2203	4300	6503	SO:0001819	synonymous_variant	119504	exon5			CACCCCCTCTTCA	BC009530	CCDS7314.1, CCDS73147.1	10q22.2	2011-08-12	2010-04-06	2010-04-06	ENSG00000166295	ENSG00000166295		"Anaphase promoting complex subunits"	26976	protein-coding gene	gene with protein product	"centromere protein 27"	613427	"chromosome 10 open reading frame 104"	C10orf104		14702039, 20360068	Standard	NM_001242546		Approved	bA570G20.3, FLJ33728, APC16, CENP-27	uc021psp.1	Q96DE5	OTTHUMG00000018433	ENST00000299381.4:c.321C>G	10.37:g.73992862C>G		39	0	0		40	24	0.6	NM_001242546		Silent	SNP	ENST00000299381.4	37	CCDS7314.1																																																																																			G|0.064;C|0.936	0.064	strong		0.542	ANAPC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048565.2	NM_173473		G	73992862	C	G	73992862	2	3	25	1	0	0	0	0	0	0	0	1	602	668	24	4		4	ANAPC16	10	73992862	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1472445	73992862	61541885	408	9317											
DNAJC9	23234	hgsc.bcm.edu	37	chr10	75006932	75006932	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccgaacacttcctcgcaaaGgtccagcagccccatgccgg	9	5	10	17	3	0	0	0	0	0	0	3	1	2	0	6	2	4	2	6	2	2	1	rs201308148	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:75006932G>T	ENST00000372950.4	-	1	1688	c.16C>A	c.(16-18)Ctt>Att	p.L6I	MRPS16_ENST00000479005.1_5'Flank|DNAJC9-AS1_ENST00000440197.2_RNA|DNAJC9-AS1_ENST00000513954.1_RNA|MRPS16_ENST00000416782.2_3'UTR	NM_015190.3	NP_056005.1	Q8WXX5	DNJC9_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 9	6					social behavior (GO:0035176)	nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|stomach(1)	6	Prostate(51;0.0119)					TCCTCGCAAAGGTCCAGCAGC	0.672													G|||	3	0.000599042	0.0	0.0043	5008	,	,		14564	0.0		0.0	False		,,,				2504	0.0				p.L6I		Atlas-SNP	.											.	DNAJC9	19	.	0			c.C16A						PASS	.	G	ILE/LEU	1,4373		0,1,2186	10	12	11		16	5	1	10		11	3,8543		0,3,4270	no	missense	DNAJC9	NM_015190.3	5	0,4,6456	TT,TG,GG		0.0351,0.0229,0.031	possibly-damaging	6/261	75006932	4,12916	2187	4273	6460	SO:0001583	missense	23234	exon1			CGCAAAGGTCCAG	AF327347	CCDS7322.1	10q22.3	2011-09-02			ENSG00000213551	ENSG00000213551		"Heat shock proteins / DNAJ (HSP40)"	19123	protein-coding gene	gene with protein product		611206					Standard	NM_015190		Approved	JDD1, SB73	uc001jtr.3	Q8WXX5	OTTHUMG00000018461	ENST00000372950.4:c.16C>A	10.37:g.75006932G>T	ENSP00000362041:p.Leu6Ile	42	0	0		61	27	0.442623	NM_015190	B2RMW6	Missense_Mutation	SNP	ENST00000372950.4	37	CCDS7322.1	.	.	.	.	.	.	.	.	.	.	g	20.4	3.980759	0.74474	2.29E-4	3.51E-4	ENSG00000213551	ENST00000372950	T	0.19250	2.16	5.93	5.02	0.67125	Heat shock protein DnaJ, N-terminal (1);	0.546225	0.18936	N	0.127072	T	0.18087	0.0434	L	0.39898	1.24	0.80722	D	1	B	0.25955	0.138	B	0.24541	0.054	T	0.03608	-1.1020	10	0.33141	T	0.24	-12.0946	11.1756	0.48596	0.0844:0.0:0.9156:0.0	.	6	Q8WXX5	DNJC9_HUMAN	I	6	ENSP00000362041:L6I	ENSP00000362041:L6I	L	-	1	0	DNAJC9	74676938	0.996000	0.38824	1.000000	0.80357	0.989000	0.77384	2.876000	0.48498	1.518000	0.48934	0.586000	0.80456	CTT	.	.	weak		0.672	DNAJC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048643.1	NM_015190		T	75006932	G	T	75006932	3	4	25	1	0	0	0	0	1	0	0	0	4658	1000	35	4	786	4	DNAJC9	10	75006932	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1014070	75006932	60527815	409	9318											
TTC18	118491	hgsc.bcm.edu	37	chr10	75037999	75037999	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tttggcttatacttggatccCaagtttgtgtagtcaaaatg	10	16	9	6	0	1	0	1	0	0	0	2	1	2	1	1	2	1	3	1	2	6	6	rs12256262	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:75037999C>A	ENST00000310715.3	-	21	2666	c.2546G>T	c.(2545-2547)tGg>tTg	p.W849L	TTC18_ENST00000394865.1_Missense_Mutation_p.W849L|TTC18_ENST00000401621.2_Missense_Mutation_p.W849L|TTC18_ENST00000493787.1_Intron|TTC18_ENST00000340329.3_Intron|DNAJC9-AS1_ENST00000440197.2_RNA|RNU6-833P_ENST00000363486.1_RNA|TTC18_ENST00000355577.3_Missense_Mutation_p.W318L	NM_145170.3	NP_660153.3	Q5T0N1	TTC18_HUMAN		849			W -> L (in dbSNP:rs12256262).			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)					ACTTGGATCCCAAGTTTGTGT	0.378													C|||	121	0.0241613	0.0847	0.013	5008	,	,		18710	0.0		0.0	False		,,,				2504	0.0				p.W849L		Atlas-SNP	.											.	TTC18	106	.	0			c.G2546T						PASS	.	C	LEU/TRP	294,4112	161.4+/-193.6	9,276,1918	184	180	181		2546	0.2	0.7	10	dbSNP_120	181	20,8580	14.6+/-50.1	0,20,4280	yes	missense	TTC18	NM_145170.3	61	9,296,6198	AA,AC,CC		0.2326,6.6727,2.4143	benign	849/1122	75037999	314,12692	2203	4300	6503	SO:0001583	missense	118491	exon21			GGATCCCAAGTTT																												ENST00000310715.3:c.2546G>T	10.37:g.75037999C>A	ENSP00000310829:p.Trp849Leu	224	1	0.00446429		251	120	0.478088	NM_145170	C9JIZ9|Q5T0M4|Q5T0M9|Q5T0N0|Q69YH9|Q8IYZ8|Q8N7D5|Q8NI30|Q8NI31	Missense_Mutation	SNP	ENST00000310715.3	37	CCDS7324.3	49	0.022435897435897436	36	0.07317073170731707	6	0.016574585635359115	2	0.0034965034965034965	5	0.006596306068601583	C	2.654	-0.281206	0.05642	0.066727	0.002326	ENSG00000156042	ENST00000310715;ENST00000401621;ENST00000355577;ENST00000433268;ENST00000394865	T;T;T;T	0.28666	2.03;2.03;1.6;1.63	4.56	0.152	0.14893	.	0.762705	0.11325	N	0.575616	T	0.00695	0.0023	N	0.03115	-0.41	0.25123	N	0.990622	B	0.02656	0.0	B	0.01281	0.0	T	0.31308	-0.9948	10	0.11485	T	0.65	-0.0236	3.4795	0.07597	0.4634:0.1102:0.0:0.4264	rs12256262;rs52797721;rs57681861;rs12256262	849	Q5T0N1	TTC18_HUMAN	L	849;849;849;256;849	ENSP00000310829:W849L;ENSP00000384479:W849L;ENSP00000409527:W256L;ENSP00000378334:W849L	ENSP00000310829:W849L	W	-	2	0	TTC18	74708005	0.691000	0.27709	0.746000	0.31095	0.029000	0.11900	0.181000	0.16880	-0.081000	0.12662	-0.312000	0.09012	TGG	C|0.973;A|0.027	0.027	strong		0.378	TTC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				A	75037999	C	A	75037999	3	1	25	1	0	0	0	0	1	0	0	0	16700	595	21	4	851	4	TTC18	10	75037999	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	31067	75037999	60496748	410	9319											
SEC24C	9632	hgsc.bcm.edu	37	chr10	75523634	75523634	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaatgcaagtccccgatacAtccgatgtacatcctataat	13	10	7	11	2	0	0	0	0	0	0	3	3	3	1	4	1	3	2	4	1	6	4	rs35528438	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:75523634A>G	ENST00000339365.2	+	9	1282	c.1120A>G	c.(1120-1122)Atc>Gtc	p.I374V	SEC24C_ENST00000345254.4_Missense_Mutation_p.I374V|SEC24C_ENST00000546025.1_Intron|SEC24C_ENST00000411652.2_Missense_Mutation_p.I255V|SEC24C_ENST00000535742.1_Intron|SEC24C_ENST00000540668.1_Intron	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C	374					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)					TCCCCGATACATCCGATGTAC	0.542													A|||	40	0.00798722	0.0008	0.0202	5008	,	,		15779	0.0		0.0219	False		,,,				2504	0.0031				p.I374V		Atlas-SNP	.											.	SEC24C	86	.	0			c.A1120G						PASS	.	A	VAL/ILE,VAL/ILE	24,4382	29.0+/-57.7	0,24,2179	84	71	75		1120,1120	5.8	1	10	dbSNP_126	75	219,8381	91.9+/-153.9	4,211,4085	yes	missense,missense	SEC24C	NM_004922.3,NM_198597.2	29,29	4,235,6264	GG,GA,AA		2.5465,0.5447,1.8684	benign,benign	374/1095,374/1095	75523634	243,12763	2203	4300	6503	SO:0001583	missense	9632	exon8			CGATACATCCGAT	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.1120A>G	10.37:g.75523634A>G	ENSP00000343405:p.Ile374Val	143	0	0		158	76	0.481013	NM_198597	B4DZT4|Q8WV25	Missense_Mutation	SNP	ENST00000339365.2	37	CCDS7332.1	25	0.011446886446886446	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	17	0.022427440633245383	A	15.89	2.965859	0.53507	0.005447	0.025465	ENSG00000176986	ENST00000345254;ENST00000339365;ENST00000411652	T;T;T	0.20200	2.09;2.09;2.09	5.77	5.77	0.91146	.	0.093915	0.64402	D	0.000001	T	0.08670	0.0215	L	0.52266	1.64	0.80722	D	1	B;B;B	0.31209	0.189;0.313;0.209	B;B;B	0.36378	0.064;0.223;0.111	T	0.03384	-1.1042	10	0.14656	T	0.56	-14.7248	16.1024	0.81184	1.0:0.0:0.0:0.0	rs35528438	255;374;374	E7EP00;G5EA31;P53992	.;.;SC24C_HUMAN	V	374;374;255	ENSP00000321845:I374V;ENSP00000343405:I374V;ENSP00000402913:I255V	ENSP00000343405:I374V	I	+	1	0	SEC24C	75193640	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.393000	0.59665	2.200000	0.70718	0.459000	0.35465	ATC	A|0.983;G|0.017	0.017	strong		0.542	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1			G	75523634	A	G	75523634	3	3	25	1	0	0	0	0	1	0	0	0	14011	217	8	3	1146	3	SEC24C	10	75523634	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	485635	75523634	60011113	411	9320											
KIAA0913	23053	hgsc.bcm.edu	37	chr10	75552298	75552298	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgagcccccagatacttaTgaagaagatggtggtgtgta	11	10	12	8	0	0	5	0	2	0	3	0	5	0	5	3	2	2	1	3	2	5	3	rs200674189	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:75552298T>C	ENST00000605216.1	+	10	2218	c.2001T>C	c.(1999-2001)taT>taC	p.Y667Y	ZSWIM8_ENST00000398706.2_Silent_p.Y667Y|ZSWIM8_ENST00000603114.1_Intron|ZSWIM8_ENST00000604524.1_Silent_p.Y667Y|ZSWIM8_ENST00000604729.1_Silent_p.Y667Y|ZSWIM8_ENST00000431225.1_3'UTR	NM_001242487.1	NP_001229416.1	A7E2V4	ZSWM8_HUMAN	zinc finger, SWIM-type containing 8	667							zinc ion binding (GO:0008270)										CAGATACTTATGAAGAAGATG	0.622													T|||	7	0.00139776	0.003	0.0043	5008	,	,		16349	0.0		0.0	False		,,,				2504	0.0				p.Y667Y		Atlas-SNP	.											.	.	.	.	0			c.T2001C						PASS	.	T	,,	2,3828		0,2,1913	46	49	48		2001,2001,2001	1.6	1	10		48	5,8241		0,5,4118	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA0913	NM_001242487.1,NM_001242488.1,NM_015037.3	,,	0,7,6031	CC,CT,TT		0.0606,0.0522,0.058	,,	667/1838,667/1893,667/1843	75552298	7,12069	1915	4123	6038	SO:0001819	synonymous_variant	23053	exon10			TACTTATGAAGAA	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.2001T>C	10.37:g.75552298T>C		144	0	0		141	63	0.446809	NM_001242488	B2RP37|O94987|Q17RS8|Q2TAB8|Q6P439|Q8IW81|Q8NB34|Q9H8F3	Silent	SNP	ENST00000605216.1	37		4|4	0.0018315018315018315|0.0018315018315018315	3|3	0.006097560975609756|0.006097560975609756	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	T|T	4.874|4.874	0.162425|0.162425	0.09287|0.09287	5.22E-4|5.22E-4	6.06E-4|6.06E-4	ENSG00000214655|ENSG00000214655	ENST00000431225|ENST00000433366	.|.	.|.	.|.	5.4|5.4	1.63|1.63	0.23807|0.23807	.|.	.|.	.|.	.|.	.|.	T|.	0.49389|.	0.1554|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.44620|.	-0.9316|.	4|.	.|.	.|.	.|.	-4.1973|-4.1973	9.2674|9.2674	0.37650|0.37650	0.0:0.2171:0.0:0.7829|0.0:0.2171:0.0:0.7829	.|.	.|.	.|.	.|.	T|R	164|390	.|.	.|.	M|X	+|+	2|1	0|0	KIAA0913|KIAA0913	75222304|75222304	0.236000|0.236000	0.23804|0.23804	1.000000|1.000000	0.80357|0.80357	0.977000|0.977000	0.68977|0.68977	-0.663000|-0.663000	0.05299|0.05299	0.112000|0.112000	0.17975|0.17975	-0.256000|-0.256000	0.11100|0.11100	ATG|TGA	T|0.997;C|0.003	0.003	strong		0.622	ZSWIM8-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000468545.1	NM_001242487		C	75552298	T	C	75552298	2	2	25	1	0	0	0	0	0	0	0	1	8209	1471	51	3		3	KIAA0913	10	75552298	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	28664	75552298	59982449	412	9321											
POLR3A	11128	hgsc.bcm.edu	37	chr10	79744042	79744042	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catccttgtctagctgtgctGtgataattggagtgctgttg	6	16	12	7	0	1	1	0	1	1	0	2	2	2	2	1	1	3	4	1	1	2	5			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:79744042G>T	ENST00000372371.3	-	25	3394	c.3257C>A	c.(3256-3258)aCa>aAa	p.T1086K		NM_007055.3	NP_008986.2	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide A, 155kDa	1086					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)			TAGCTGTGCTGTGATAATTGG	0.458																																					p.T1086K		Atlas-SNP	.											.	POLR3A	104	.	0			c.C3257A						PASS	.						111	97	102					10																	79744042		2203	4300	6503	SO:0001583	missense	11128	exon25			TGTGCTGTGATAA	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.3257C>A	10.37:g.79744042G>T	ENSP00000361446:p.Thr1086Lys	70	0	0		77	34	0.441558	NM_007055	Q8IW34|Q8TCW5	Missense_Mutation	SNP	ENST00000372371.3	37	CCDS7354.1	.	.	.	.	.	.	.	.	.	.	G	18.88	3.717429	0.68844	.	.	ENSG00000148606	ENST00000372371;ENST00000540842	T	0.77489	-1.1	5.62	5.62	0.85841	RNA polymerase Rpb1, domain 5 (1);	0.051059	0.85682	D	0.000000	D	0.87951	0.6307	M	0.80508	2.5	0.80722	D	1	P	0.48998	0.918	P	0.60345	0.873	D	0.87312	0.2312	9	.	.	.	-17.2577	19.6607	0.95868	0.0:0.0:1.0:0.0	.	1086	O14802	RPC1_HUMAN	K	1086;1065	ENSP00000361446:T1086K	.	T	-	2	0	POLR3A	79414048	1.000000	0.71417	0.970000	0.41538	0.983000	0.72400	7.320000	0.79064	2.660000	0.90430	0.650000	0.86243	ACA	.	.	none		0.458	POLR3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048923.1	NM_007055		T	79744042	G	T	79744042	3	4	25	1	0	0	0	0	1	0	0	0	12237	1377	48	4	943	4	POLR3A	10	79744042	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	4191744	79744042	55790705	413	9322											
DYDC1	143241	hgsc.bcm.edu	37	chr10	82098881	82098881	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtagaatatcttcattcctaActagattttccatattcatt	12	18	3	8	0	3	2	2	0	1	2	5	2	5	2	2	0	1	1	2	0	6	11	rs35605779	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:82098881A>T	ENST00000372204.3	-	6	535	c.371T>A	c.(370-372)gTt>gAt	p.V124D	DYDC1_ENST00000372202.1_Missense_Mutation_p.V124D|DYDC1_ENST00000421924.2_Missense_Mutation_p.V124D	NM_138812.3	NP_620167.1	Q8WWB3	DYDC1_HUMAN	DPY30 domain containing 1	124										kidney(1)|large_intestine(3)|skin(1)	5			Colorectal(32;0.229)			TTCATTCCTAACTAGATTTTC	0.254													A|||	10	0.00199681	0.0	0.0014	5008	,	,		13230	0.0		0.008	False		,,,				2504	0.001				p.V124D		Atlas-SNP	.											.	DYDC1	15	.	0			c.T371A						PASS	.	A	ASP/VAL	9,4361		0,9,2176	59	53	55		371	-3.6	0	10	dbSNP_126	55	106,8454		0,106,4174	yes	missense	DYDC1	NM_138812.2	152	0,115,6350	TT,TA,AA		1.2383,0.2059,0.8894	benign	124/178	82098881	115,12815	2185	4280	6465	SO:0001583	missense	143241	exon5			TTCCTAACTAGAT	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.371T>A	10.37:g.82098881A>T	ENSP00000361278:p.Val124Asp	111	0	0		112	51	0.455357	NM_001269053	A8K927|Q5QP03|Q5QP04|Q6WNP4|Q6ZU87	Missense_Mutation	SNP	ENST00000372204.3	37	CCDS7366.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	A	3.197	-0.164454	0.06502	0.002059	0.012383	ENSG00000170788	ENST00000372204;ENST00000372202;ENST00000421924;ENST00000454362	.	.	.	4.56	-3.64	0.04515	.	2.257240	0.01811	N	0.033424	T	0.12646	0.0307	N	0.08118	0	0.09310	N	1	B;B	0.24092	0.097;0.057	B;B	0.18871	0.023;0.014	T	0.10405	-1.0631	9	0.30078	T	0.28	5.9472	5.9793	0.19399	0.3843:0.4372:0.1785:0.0	rs35605779	124;124	A8K927;Q8WWB3	.;DYDC1_HUMAN	D	124	.	ENSP00000361276:V124D	V	-	2	0	DYDC1	82088861	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.099000	0.15210	-0.644000	0.05465	-1.276000	0.01395	GTT	A|0.994;T|0.006	0.006	strong		0.254	DYDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049059.1	NM_138812		T	82098881	A	T	82098881	3	4	25	1	0	0	0	0	1	0	0	0	4840	43	2	5	174	5	DYDC1	10	82098881	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	2354839	82098881	53435866	414	9323											
GRID1	2894	hgsc.bcm.edu	37	chr10	88126071	88126071	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcctccagccgcgcttacCgatgtggatgatggagtcgg	6	8	15	12	5	0	1	0	1	0	0	2	4	1	3	4	4	2	1	4	4	1	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:88126071C>T	ENST00000327946.7	-	1	164	c.79G>A	c.(79-81)Ggt>Agt	p.G27S		NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	27					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						CCGCGCTTACCGATGTGGATG	0.716										Multiple Myeloma(13;0.14)																											p.G27S		Atlas-SNP	.											.	GRID1	204	.	0			c.G79A						PASS	.						9	9	9					10																	88126071		2110	4138	6248	SO:0001630	splice_region_variant	2894	exon1			GCTTACCGATGTG	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.79+1G>A	10.37:g.88126071C>T		3	0	0		20	13	0.65	NM_017551	B3KXD5|B7Z7L0|Q8IXT3	Missense_Mutation	SNP	ENST00000327946.7	37	CCDS31236.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.491269	0.64074	.	.	ENSG00000182771	ENST00000327946	D	0.95588	-3.75	2.24	2.24	0.28232	.	0.288147	0.21374	U	0.075581	D	0.94198	0.8138	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.65684	0.937	D	0.91741	0.5404	9	.	.	.	.	9.8853	0.41257	0.0:1.0:0.0:0.0	.	27	Q9ULK0	GRID1_HUMAN	S	27	ENSP00000330148:G27S	.	G	-	1	0	GRID1	88116051	1.000000	0.71417	0.972000	0.41901	0.495000	0.33615	6.014000	0.70784	1.228000	0.43614	0.305000	0.20034	GGT	.	.	none		0.716	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613	Missense_Mutation	T	88126071	C	T	88126071	5	4	25	1	0	0	0	0	0	0	1	0	6780	666	23	1	3014	1	GRID1	10	88126071	Splice_Site	SNP	C	TCGA-G8-6906-01A-11D-2210-10	6027190	88126071	47408676	415	9324											
KIF11	3832	hgsc.bcm.edu	37	chr10	94369247	94369247	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaaggacaactgcagctactCtgatgaatgcatactctagg	14	9	9	9	0	2	2	0	2	2	0	2	3	2	3	0	2	6	3	0	2	6	3	rs145656661		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:94369247C>T	ENST00000260731.3	+	6	769	c.679C>T	c.(679-681)Ctg>Ttg	p.L227L		NM_004523.3	NP_004514.2	P52732	KIF11_HUMAN	kinesin family member 11	227	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						TGCAGCTACTCTGATGAATGC	0.378																																					p.L227L	Colon(47;212 1003 2764 4062 8431)	Atlas-SNP	.											.	KIF11	58	.	0			c.C679T						PASS	.	C		0,4406		0,0,2203	201	222	215		679	-4.9	0	10	dbSNP_134	215	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	KIF11	NM_004523.3		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		227/1057	94369247	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	3832	exon6			GCTACTCTGATGA	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.679C>T	10.37:g.94369247C>T		49	0	0		54	20	0.37037	NM_004523	A0AV49|B2RMV3|Q15716|Q5VWX0	Silent	SNP	ENST00000260731.3	37	CCDS7422.1																																																																																			C|1.000;T|0.000	0.000	weak		0.378	KIF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049401.1	NM_004523		T	94369247	C	T	94369247	2	4	25	1	0	0	0	0	0	0	0	1	8281	912	32	2		2	KIF11	10	94369247	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	6243176	94369247	41165500	416	9325											
PIK3AP1	118788	hgsc.bcm.edu	37	chr10	98369563	98369563	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggggccactctcatagacTccaaactccacttttgcagg	9	10	8	14	0	1	1	1	0	1	1	4	1	3	1	3	3	2	1	3	3	2	3	rs141067860	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:98369563T>C	ENST00000339364.5	-	14	2195	c.2076A>G	c.(2074-2076)ggA>ggG	p.G692G	PIK3AP1_ENST00000371110.2_Silent_p.G514G|PIK3AP1_ENST00000371109.3_Silent_p.G291G	NM_152309.2	NP_689522.2	Q6ZUJ8	BCAP_HUMAN	phosphoinositide-3-kinase adaptor protein 1	692					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)		TCTCATAGACTCCAAACTCCA	0.532													T|||	4	0.000798722	0.0	0.0029	5008	,	,		6366	0.0		0.002	False		,,,				2504	0.0				p.G692G		Atlas-SNP	.											.	PIK3AP1	111	.	0			c.A2076G						PASS	.	T		3,4403	6.2+/-15.9	0,3,2200	236	242	240		2076	-2.2	1	10	dbSNP_134	240	12,8588	9.1+/-34.3	0,12,4288	no	coding-synonymous	PIK3AP1	NM_152309.2		0,15,6488	CC,CT,TT		0.1395,0.0681,0.1153		692/806	98369563	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	118788	exon14			ATAGACTCCAAAC	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.2076A>G	10.37:g.98369563T>C		119	0	0		144	59	0.409722	NM_152309	Q5TB56|Q5VXJ9|Q8N6J6|Q8NAC8	Silent	SNP	ENST00000339364.5	37	CCDS31259.1																																																																																			T|0.999;C|0.001	0.001	strong		0.532	PIK3AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049619.2	NM_152309		C	98369563	T	C	98369563	2	2	25	1	0	0	0	0	0	0	0	1	11917	1538	54	3		3	PIK3AP1	10	98369563	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	4000316	98369563	37165184	417	9326											
RRP12	23223	hgsc.bcm.edu	37	chr10	99118716	99118716	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaccttggccttgtattcaGccccaggcatagccttcttg	6	14	8	13	0	2	0	1	0	1	0	2	0	2	0	5	2	3	2	5	2	3	8	rs143870774	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:99118716G>T	ENST00000370992.4	-	32	3803	c.3692C>A	c.(3691-3693)gCt>gAt	p.A1231D	RRP12_ENST00000414986.1_Missense_Mutation_p.A1170D|RRP12_ENST00000536831.1_Missense_Mutation_p.A949D|RRP12_ENST00000315563.6_Missense_Mutation_p.A1131D|RRP12_ENST00000479481.1_5'UTR	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	1231						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)		CTTGTATTCAGCCCCAGGCAT	0.612																																					p.A1231D		Atlas-SNP	.											.	RRP12	97	.	0			c.C3692A						PASS	.						91	65	74					10																	99118716		2203	4300	6503	SO:0001583	missense	23223	exon32			TATTCAGCCCCAG		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.3692C>A	10.37:g.99118716G>T	ENSP00000360031:p.Ala1231Asp	44	0	0		45	27	0.6	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Missense_Mutation	SNP	ENST00000370992.4	37	CCDS7457.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.730886	0.48939	.	.	ENSG00000052749	ENST00000370992;ENST00000315563;ENST00000414986;ENST00000536831	T;T;T;T	0.29917	1.55;1.55;1.55;1.55	5.58	5.58	0.84498	.	0.228748	0.45126	D	0.000387	T	0.34454	0.0898	L	0.43923	1.385	0.48762	D	0.999708	P;P;D;P	0.53745	0.937;0.935;0.962;0.937	B;P;P;B	0.51833	0.276;0.681;0.528;0.218	T	0.02498	-1.1150	10	0.12103	T	0.63	-6.7512	13.8164	0.63295	0.0733:0.0:0.9267:0.0	.	1170;1131;949;1231	E9PCK7;Q5JTH9-2;F5H456;Q5JTH9	.;.;.;RRP12_HUMAN	D	1231;1131;1170;949	ENSP00000360031:A1231D;ENSP00000324315:A1131D;ENSP00000414863:A1170D;ENSP00000446184:A949D	ENSP00000324315:A1131D	A	-	2	0	RRP12	99108706	0.963000	0.33076	0.875000	0.34327	0.341000	0.28922	3.020000	0.49643	2.635000	0.89317	0.561000	0.74099	GCT	G|0.998;A|0.002	.	alt		0.612	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179		T	99118716	G	T	99118716	3	4	25	1	0	0	0	0	1	0	0	0	13701	971	34	4	213	4	RRP12	10	99118716	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	749153	99118716	36416031	418	9327											
RRP12	23223	hgsc.bcm.edu	37	chr10	99126513	99126513	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcacctgtcacctttgccCtgggcgggctcctcctcctc	2	12	8	19	1	2	0	2	0	1	0	7	0	5	0	6	2	1	1	6	2	0	1	rs45527941	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:99126513C>T	ENST00000370992.4	-	27	3312	c.3201G>A	c.(3199-3201)caG>caA	p.Q1067Q	RRP12_ENST00000414986.1_Silent_p.Q1006Q|RRP12_ENST00000536831.1_Silent_p.Q785Q|RRP12_ENST00000315563.6_Silent_p.Q967Q|RRP12_ENST00000479481.1_5'UTR	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	1067	Glu-rich.					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)		CACCTTTGCCCTGGGCGGGct	0.672													C|||	128	0.0255591	0.0038	0.0548	5008	,	,		15272	0.0		0.0716	False		,,,				2504	0.0133				p.Q1067Q		Atlas-SNP	.											.	RRP12	97	.	0			c.G3201A						PASS	.	C	,	58,4348	56.2+/-92.4	0,58,2145	70	82	78		3018,3201	4.8	1	10	dbSNP_127	78	501,8099	143.6+/-199.6	17,467,3816	no	coding-synonymous,coding-synonymous	RRP12	NM_001145114.1,NM_015179.3	,	17,525,5961	TT,TC,CC		5.8256,1.3164,4.298	,	1006/1237,1067/1298	99126513	559,12447	2203	4300	6503	SO:0001819	synonymous_variant	23223	exon27			TTTGCCCTGGGCG		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.3201G>A	10.37:g.99126513C>T		38	0	0		62	36	0.580645	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																			C|0.962;T|0.038	0.038	strong		0.672	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179		T	99126513	C	T	99126513	2	4	25	1	0	0	0	0	0	0	0	1	13701	680	24	2		2	RRP12	10	99126513	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	7797	99126513	36408234	419	9328											
RRP12	23223	hgsc.bcm.edu	37	chr10	99130282	99130282	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgcaaaagcgttcttccgTgcgcccaccgacacctcctt	8	9	8	16	4	1	0	0	0	1	0	3	1	3	0	5	0	3	2	5	0	2	3	rs11189170	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:99130282T>G	ENST00000370992.4	-	23	2730	c.2619A>C	c.(2617-2619)gcA>gcC	p.A873A	RRP12_ENST00000414986.1_Silent_p.A812A|RRP12_ENST00000536831.1_Silent_p.A591A|RRP12_ENST00000315563.6_Silent_p.A773A|RRP12_ENST00000479481.1_5'UTR	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	873						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)		CGTTCTTCCGTGCGCCCACCG	0.607													T|||	201	0.0401358	0.059	0.0548	5008	,	,		19934	0.0		0.0716	False		,,,				2504	0.0133				p.A873A		Atlas-SNP	.											RRP12,NS,carcinoma,-2,1	RRP12	97	1	0			c.A2619C						scavenged	.	T	,	254,4152	147.3+/-181.8	9,236,1958	118	90	99		2436,2619	-9.4	0.4	10	dbSNP_120	99	503,8097	144.7+/-200.5	17,469,3814	no	coding-synonymous,coding-synonymous	RRP12	NM_001145114.1,NM_015179.3	,	26,705,5772	GG,GT,TT		5.8488,5.7649,5.8204	,	812/1237,873/1298	99130282	757,12249	2203	4300	6503	SO:0001819	synonymous_variant	23223	exon23			CTTCCGTGCGCCC		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.2619A>C	10.37:g.99130282T>G		109	2	0.0183486		110	57	0.518182	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																			T|0.952;G|0.048	0.048	strong		0.607	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179		G	99130282	T	G	99130282	2	3	25	1	0	0	0	0	0	0	0	1	13701	1683	59	5		5	RRP12	10	99130282	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	3769	99130282	36404465	420	9329											
RRP12	23223	hgsc.bcm.edu	37	chr10	99150237	99150237	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggtacacctgaagggtcacGgggtagccccaggcctccag	8	6	14	13	1	1	1	1	1	0	0	2	1	2	1	5	5	2	2	5	5	3	2	rs41300219	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:99150237G>A	ENST00000370992.4	-	6	807	c.696C>T	c.(694-696)ccC>ccT	p.P232P	RRP12_ENST00000414986.1_Silent_p.P171P|RRP12_ENST00000536831.1_Silent_p.P38P|RRP12_ENST00000315563.6_Intron	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	232						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)		GAAGGGTCACGGGGTAGCCCC	0.612													G|||	201	0.0401358	0.0598	0.0533	5008	,	,		19526	0.0		0.0716	False		,,,				2504	0.0133				p.P232P		Atlas-SNP	.											.	RRP12	97	.	0			c.C696T						PASS	.	G	,	254,4152	148.0+/-182.4	9,236,1958	58	56	57		513,696	-11	0	10	dbSNP_127	57	501,8099	144.5+/-200.4	17,467,3816	no	coding-synonymous,coding-synonymous	RRP12	NM_001145114.1,NM_015179.3	,	26,703,5774	AA,AG,GG		5.8256,5.7649,5.805	,	171/1237,232/1298	99150237	755,12251	2203	4300	6503	SO:0001819	synonymous_variant	23223	exon6			GGTCACGGGGTAG		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.696C>T	10.37:g.99150237G>A		42	0	0		48	19	0.395833	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																			G|0.949;A|0.051	0.051	strong		0.612	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179		A	99150237	G	A	99150237	2	1	25	1	0	0	0	0	0	0	0	1	13701	1103	39	1		1	RRP12	10	99150237	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	19955	99150237	36384510	421	9330											
PGAM1	5223	hgsc.bcm.edu	37	chr10	99190185	99190185	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acctcagtgcagaagagagcGatccggaccctctggacagt	11	6	12	12	2	2	2	1	0	1	2	3	6	3	4	3	2	2	1	3	2	1	0			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:99190185G>A	ENST00000334828.5	+	2	337	c.189G>A	c.(187-189)gcG>gcA	p.A63A	PGAM1_ENST00000467867.1_3'UTR	NM_002629.2	NP_002620.1	P18669	PGAM1_HUMAN	phosphoglycerate mutase 1 (brain)	63					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|regulation of glycolytic process (GO:0006110)|regulation of pentose-phosphate shunt (GO:0043456)|respiratory burst (GO:0045730)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	bisphosphoglycerate 2-phosphatase activity (GO:0004083)|bisphosphoglycerate mutase activity (GO:0004082)|phosphoglycerate mutase activity (GO:0004619)|protein kinase binding (GO:0019901)			endometrium(1)|kidney(1)|large_intestine(3)|lung(1)	6		Colorectal(252;0.162)		Epithelial(162;8.36e-10)|all cancers(201;5.62e-08)		AGAAGAGAGCGATCCGGACCC	0.522																																					p.A63A		Atlas-SNP	.											PGAM1,caecum,carcinoma,+1,1	PGAM1	11	1	0			c.G189A						PASS	.						101	105	104					10																	99190185		2203	4297	6500	SO:0001819	synonymous_variant	5223	exon2			GAGAGCGATCCGG	BC010038	CCDS7458.1	10q25.3	2012-10-02			ENSG00000171314	ENSG00000171314	5.4.2.1		8888	protein-coding gene	gene with protein product	"Phosphoglycerate mutase A, nonmuscle form"	172250		PGAMA		2846553	Standard	NM_002629		Approved	PGAM-B	uc001knh.3	P18669	OTTHUMG00000018846	ENST00000334828.5:c.189G>A	10.37:g.99190185G>A		82	0	0		81	41	0.506173	NM_002629	Q9BWC0	Silent	SNP	ENST00000334828.5	37	CCDS7458.1																																																																																			.	.	none		0.522	PGAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049652.1	NM_002629		A	99190185	G	A	99190185	2	1	25	1	0	0	0	0	0	0	0	1	11782	1045	37	1		1	PGAM1	10	99190185	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	39948	99190185	36344562	422	9331											
TLX1NB	100038246	hgsc.bcm.edu	37	chr10	102849370	102849370	+	Frame_Shift_Del	DEL	T	T	-																															ggattctggatttctccagcTgaggtgacctgggcaccaga																								rs200664029	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:102849370delT	ENST00000445873.1	-	3	1569	c.293delA	c.(292-294)cagfs	p.Q98fs	TLX1NB_ENST00000425505.1_5'Flank	NM_001085398.1	NP_001078867.1	P0CAT3	TLXNB_HUMAN	TLX1 neighbor	98																	TTTCTCCAGCTGAGGTGACCT	0.572													T|T|-|deletion	7	0.00139776	0.0008	0.0014	5008	,	,		15955	0.0		0.005	False		,,,				2504	0.0				p.Q98fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.294delG						PASS	.			8,3620		0,8,1806	33	33	33			1.1	0	10		33	75,7807		1,73,3867	no	frameshift	TLX1NB	NM_001085398.1		1,81,5673	A1A1,A1R,RR		0.9515,0.2205,0.7211			102849370	83,11427	1881	4116	5997	SO:0001589	frameshift_variant	100038246	exon3			.	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.293delA	10.37:g.102849370delT	ENSP00000475001:p.Gln98fs	94	0	.		97	33	0.34	NM_001085398		Frame_Shift_Del	DEL	ENST00000445873.1	37																																																																																				T|0.996;-|0.004	0.004	strong		0.572	TLX1NB-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000049925.2	NM_001085398		-	102849370	T	-	102849370	7	5	25	1	0	1	0	1	0	0	0	0	15975	1580	55	0	79	0	TLX1NB	10	102849370	Frame_Shift_Del	DEL	T	TCGA-G8-6906-01A-11D-2210-10	3659185	102849370	32685377	423	9332											
SLK	9748	hgsc.bcm.edu	37	chr10	105762933	105762933	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tactgaccaaaaggctttagGaagtgaagttcaggatgctt	13	11	11	6	0	1	2	1	2	0	0	1	4	1	4	1	3	2	3	1	3	6	5	rs7071400	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:105762933G>A	ENST00000369755.3	+	9	2542	c.1997G>A	c.(1996-1998)gGa>gAa	p.G666E	SLK_ENST00000335753.4_Missense_Mutation_p.G666E	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	666			G -> E (in dbSNP:rs7071400).		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)		AAGGCTTTAGGAAGTGAAGTT	0.393													G|||	84	0.0167732	0.059	0.0086	5008	,	,		19341	0.0		0.0	False		,,,				2504	0.0				p.G666E	NSCLC(111;540 1651 1927 4474 17706)	Atlas-SNP	.											.	SLK	107	.	0			c.G1997A						PASS	.	G	GLU/GLY	206,4200	127.4+/-164.3	5,196,2002	126	114	118		1997	-0.6	0	10	dbSNP_116	118	3,8597	3.0+/-9.4	0,3,4297	yes	missense	SLK	NM_014720.2	98	5,199,6299	AA,AG,GG		0.0349,4.6754,1.607	benign	666/1236	105762933	209,12797	2203	4300	6503	SO:0001583	missense	9748	exon9			CTTTAGGAAGTGA		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.1997G>A	10.37:g.105762933G>A	ENSP00000358770:p.Gly666Glu	94	0	0		101	44	0.435644	NM_014720	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	Missense_Mutation	SNP	ENST00000369755.3	37	CCDS7553.1	29	0.013278388278388278	24	0.04878048780487805	5	0.013812154696132596	0	0.0	0	0.0	G	0.021	-1.419805	0.01136	0.046754	3.49E-4	ENSG00000065613	ENST00000335753;ENST00000369755	T;T	0.66995	-0.24;-0.24	5.6	-0.619	0.11572	Protein kinase-like domain (1);	0.516601	0.20063	N	0.100027	T	0.09247	0.0228	N	0.17082	0.46	0.09310	N	1	B;B	0.12630	0.006;0.003	B;B	0.12156	0.005;0.007	T	0.05386	-1.0888	10	0.15499	T	0.54	.	6.5662	0.22513	0.3317:0.0:0.4868:0.1815	rs7071400;rs52824513;rs56426845;rs7071400	666;666	Q9H2G2-2;Q9H2G2	.;SLK_HUMAN	E	666	ENSP00000336824:G666E;ENSP00000358770:G666E	ENSP00000336824:G666E	G	+	2	0	SLK	105752923	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.468000	0.06656	-0.380000	0.07894	-1.471000	0.01009	GGA	G|0.982;A|0.018	0.018	strong		0.393	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720		A	105762933	G	A	105762933	3	1	25	1	0	0	0	0	1	0	0	0	14763	1174	41	2	2031	2	SLK	10	105762933	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2913563	105762933	29771814	424	9333											
COL17A1	1308	hgsc.bcm.edu	37	chr10	105836066	105836066	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgggactgataccttcataCgcatggcgggtaacgtgagt	9	10	14	8	3	1	2	1	2	0	0	1	3	1	3	1	3	3	2	1	3	3	4	rs61731085	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:105836066C>T	ENST00000353479.5	-	5	614	c.324G>A	c.(322-324)gcG>gcA	p.A108A	COL17A1_ENST00000369733.3_Silent_p.A108A|COL17A1_ENST00000393211.3_Silent_p.A108A	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	108	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)		TACCTTCATACGCATGGCGGG	0.502													C|||	69	0.013778	0.0492	0.0043	5008	,	,		20980	0.0		0.001	False		,,,				2504	0.0				p.A108A		Atlas-SNP	.											.	COL17A1	149	.	0			c.G324A						PASS	.	C		198,4208	124.1+/-161.4	4,190,2009	203	202	202		324	-11.2	0	10	dbSNP_129	202	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	COL17A1	NM_000494.3		4,196,6303	TT,TC,CC		0.0698,4.4939,1.5685		108/1498	105836066	204,12802	2203	4300	6503	SO:0001819	synonymous_variant	1308	exon5			TTCATACGCATGG	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.324G>A	10.37:g.105836066C>T		132	0	0		142	70	0.492958	NM_000494	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Silent	SNP	ENST00000353479.5	37	CCDS7554.1																																																																																			C|0.988;T|0.012	0.012	strong		0.502	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494		T	105836066	C	T	105836066	2	4	25	1	0	0	0	0	0	0	0	1	3676	523	19	1		1	COL17A1	10	105836066	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	73133	105836066	29698681	425	9334											
SORCS3	22986	hgsc.bcm.edu	37	chr10	106974224	106974224	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cggcggattgtgtccaacaaCtgcacagatgggctaaggga	11	7	14	9	2	0	1	0	0	0	1	1	3	1	3	1	4	3	2	1	4	3	2	rs200098588	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:106974224C>A	ENST00000369701.3	+	18	2627	c.2400C>A	c.(2398-2400)aaC>aaA	p.N800K	SORCS3_ENST00000369699.4_Missense_Mutation_p.N86K	NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	800					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)		TGTCCAACAACTGCACAGATG	0.522													c|||	5	0.000998403	0.0038	0.0	5008	,	,		18731	0.0		0.0	False		,,,				2504	0.0				p.N800K	NSCLC(116;1497 1690 7108 13108 14106)	Atlas-SNP	.											.	SORCS3	282	.	0			c.C2400A						PASS	.		LYS/ASN	20,4386	26.2+/-53.5	0,20,2183	124	104	111		2400	5	1	10		111	0,8600		0,0,4300	yes	missense	SORCS3	NM_014978.1	94	0,20,6483	AA,AC,CC		0.0,0.4539,0.1538	possibly-damaging	800/1223	106974224	20,12986	2203	4300	6503	SO:0001583	missense	22986	exon18			CAACAACTGCACA	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.2400C>A	10.37:g.106974224C>A	ENSP00000358715:p.Asn800Lys	112	0	0		123	62	0.504065	NM_014978	Q5VXF9|Q9NQJ2	Missense_Mutation	SNP	ENST00000369701.3	37	CCDS7558.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	c	13.79	2.343489	0.41498	0.004539	0.0	ENSG00000156395	ENST00000369701;ENST00000369699	T;T	0.68025	-0.3;-0.3	5.89	4.98	0.66077	VPS10 (1);PKD domain (1);	0.151901	0.56097	N	0.000021	T	0.74921	0.3780	L	0.41573	1.285	0.54753	D	0.999989	D	0.76494	0.999	D	0.70935	0.971	T	0.74000	-0.3805	9	.	.	.	.	17.0953	0.86633	0.0:0.8732:0.1268:0.0	.	800	Q9UPU3	SORC3_HUMAN	K	800;86	ENSP00000358715:N800K;ENSP00000358713:N86K	.	N	+	3	2	SORCS3	106964214	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.828000	0.55753	1.482000	0.48325	0.558000	0.71614	AAC	C|1.000;A|0.000	0.000	strong		0.522	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978		A	106974224	C	A	106974224	3	1	25	1	0	0	0	0	1	0	0	0	14947	564	20	4	2470	4	SORCS3	10	106974224	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1138158	106974224	28560523	426	9335											
INPP5F	79892	hgsc.bcm.edu	37	chr10	121587116	121587116	+	IGR	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tctctccctttgccaagattCgaagttccatggtccaggtt	7	14	8	12	1	1	1	0	0	1	1	6	2	4	1	4	2	1	2	4	2	2	4			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:121587116C>T	ENST00000360003.3	-	0	4113				INPP5F_ENST00000361976.2_Nonsense_Mutation_p.R1075*|INPP5F_ENST00000369080.3_Nonsense_Mutation_p.R465*	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						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.R1075*(1)		breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(2)|skin(2)	21						TGCCAAGATTCGAAGTTCCAT	0.483																																					p.R1075X		Atlas-SNP	.											INPP5F,NS,carcinoma,0,1	INPP5F	112	1	1	Substitution - Nonsense(1)	endometrium(1)	c.C3223T						PASS	.						97	97	97					10																	121587116		2203	4300	6503	SO:0001628	intergenic_variant	22876	exon20			AAGATTCGAAGTT	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		10.37:g.121587116C>T		134	0	0		116	58	0.5	NM_014937	B3KSP7|Q6IA56|Q9BVT9|Q9H916	Nonsense_Mutation	SNP	ENST00000360003.3	37	CCDS7617.1	.	.	.	.	.	.	.	.	.	.	C	41	8.746755	0.98937	.	.	ENSG00000198825	ENST00000361976;ENST00000369080	.	.	.	6.02	3.07	0.35406	.	0.182665	0.46758	D	0.000275	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.7045	10.5033	0.44819	0.2383:0.6993:0.0:0.0624	.	.	.	.	X	1075;465	.	ENSP00000354519:R1075X	R	+	1	2	INPP5F	121577106	0.999000	0.42202	0.956000	0.39512	0.996000	0.88848	2.619000	0.46401	0.873000	0.35799	0.655000	0.94253	CGA	.	.	none		0.483	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834		T	121587116	C	T	121587116	1	4	25	0	1	0	0	0	0	0	0	0	7767	876	31	1		1	INPP5F	10	121587116	IGR	SNP	C	TCGA-G8-6906-01A-11D-2210-10	14612892	121587116	13947631	427	9336											
FGFR2	2263	hgsc.bcm.edu	37	chr10	123239112	123239112	+	3'UTR	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcctactggtccacagccaGtacgcacggcaggtgagagg	9	6	14	12	2	0	1	0	1	0	1	2	2	2	1	3	4	3	3	3	4	2	2	rs1047057	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:123239112G>A	ENST00000358487.5	-	0	2997				FGFR2_ENST00000357555.5_Silent_p.L703L|FGFR2_ENST00000369060.4_3'UTR|FGFR2_ENST00000478859.1_3'UTR|FGFR2_ENST00000369061.4_3'UTR|FGFR2_ENST00000356226.4_3'UTR	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2						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)	p.L703L(1)		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)	TCCACAGCCAGTACGCACGGC	0.483		5	Mis		"gastric. NSCLC, endometrial"		"Crouzon, Pfeiffer, and Apert syndromes"		Saethre-Chotzen syndrome;Apert syndrome				G|||	2075	0.414337	0.0938	0.6873	5008	,	,		15689	0.3512		0.5099	False		,,,				2504	0.6207				p.L703L		Atlas-SNP	.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	FGFR2_ENST00000357555,NS,carcinoma,0,1	FGFR2	758	1	1	Substitution - coding silent(1)	stomach(1)	c.C2107T						PASS	.	G	,,,,,,	237,1147		19,199,474	86	84	85		,,2107,,,,	4.5	0.9	10	dbSNP_86	85	1747,1435		500,747,344	no	utr-3,utr-3,coding-synonymous,utr-3,utr-3,utr-3,utr-3	FGFR2	NM_000141.4,NM_001144914.1,NM_001144915.1,NM_001144916.1,NM_001144917.1,NM_001144918.1,NM_022970.3	,,,,,,	519,946,818	AA,AG,GG		45.0974,17.1243,43.4516	,,,,,,	,,703/708,,,,	123239112	1984,2582	692	1591	2283	SO:0001624	3_prime_UTR_variant	2263	exon17	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	CAGCCAGTACGCA	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.*259C>T	10.37:g.123239112G>A		84	0	0		102	100	0.980392	NM_001144915	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	Silent	SNP	ENST00000358487.5	37	CCDS31298.1																																																																																			G|0.609;A|0.391	0.391	strong		0.483	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141		A	123239112	G	A	123239112	1	1	25	0	1	0	0	0	0	0	0	0	5874	1020	36	2		2	FGFR2	10	123239112	3'UTR	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1651996	123239112	12295635	428	9337											
ATE1	11101	hgsc.bcm.edu	37	chr10	123670575	123670575	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctctttgatgtcatcactGagtgttttaagatcacactg	9	16	7	9	0	4	3	3	2	1	1	5	3	4	3	0	0	0	1	0	0	1	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:123670575G>T	ENST00000224652.6	-	5	514	c.429C>A	c.(427-429)ctC>ctA	p.L143L	ATE1_ENST00000535655.1_5'UTR|ATE1_ENST00000369040.3_Silent_p.L47L|ATE1_ENST00000543447.1_Silent_p.L28L|ATE1_ENST00000540606.1_Silent_p.L136L|ATE1_ENST00000369043.3_Silent_p.L143L	NM_001001976.1	NP_001001976.1	O95260	ATE1_HUMAN	arginyltransferase 1	143					protein arginylation (GO:0016598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	arginyltransferase activity (GO:0004057)	p.L143L(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		all_neural(114;0.061)|Lung NSC(174;0.095)|all_lung(145;0.124)|Breast(234;0.212)				TGTCATCACTGAGTGTTTTAA	0.378																																					p.L143L		Atlas-SNP	.											ATE1,mouth,carcinoma,0,1	ATE1	67	1	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C429A						PASS	.						136	139	138					10																	123670575		2203	4300	6503	SO:0001819	synonymous_variant	11101	exon5			ATCACTGAGTGTT	AF079098	CCDS31299.1, CCDS31300.1, CCDS73211.1, CCDS73212.1, CCDS73213.1	10q26	2013-05-08			ENSG00000107669	ENSG00000107669	2.3.2.8		782	protein-coding gene	gene with protein product		607103				16002466, 16943202	Standard	XM_005269458		Approved		uc001lfq.3	O95260	OTTHUMG00000019178	ENST00000224652.6:c.429C>A	10.37:g.123670575G>T		197	0	0		188	104	0.553191	NM_001001976	O95261|Q5SQQ3|Q8WW04	Silent	SNP	ENST00000224652.6	37	CCDS31300.1	.	.	.	.	.	.	.	.	.	.	G	0.199	-1.046145	0.01997	.	.	ENSG00000107669	ENST00000423243	.	.	.	5.78	-2.6	0.06190	.	.	.	.	.	T	0.18173	0.0436	.	.	.	0.28353	N	0.920826	.	.	.	.	.	.	T	0.27400	-1.0075	4	.	.	.	-12.2001	0.864	0.01199	0.242:0.2723:0.2842:0.2015	.	.	.	.	K	140	.	.	Q	-	1	0	ATE1	123660565	0.003000	0.15002	0.000000	0.03702	0.179000	0.23085	-0.111000	0.10807	-0.488000	0.06726	-0.253000	0.11424	CAG	.	.	none		0.378	ATE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001001976		T	123670575	G	T	123670575	2	4	25	1	0	0	0	0	0	0	0	1	1078	1277	45	4		4	ATE1	10	123670575	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	431463	123670575	11864172	429	9338											
DMBT1	1755	hgsc.bcm.edu	37	chr10	124330421	124330421	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	tgcaggttctccatttccctCggagtcgaccctggagtcaa	7	11	10	13	2	2	0	1	0	1	0	6	3	3	2	3	3	1	2	3	3	1	2	rs75209396	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:124330421C>G	ENST00000338354.3	+	4	261	c.155C>G	c.(154-156)tCg>tGg	p.S52W	DMBT1_ENST00000344338.3_Missense_Mutation_p.S52W|DMBT1_ENST00000330163.4_Missense_Mutation_p.S52W|DMBT1_ENST00000368956.2_Missense_Mutation_p.S52W|DMBT1_ENST00000359586.6_Missense_Mutation_p.S52W|DMBT1_ENST00000368909.3_Missense_Mutation_p.S52W|DMBT1_ENST00000368955.3_Missense_Mutation_p.S52W			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	52			S -> W (in dbSNP:rs75209396). {ECO:0000269|PubMed:12185598, ECO:0000269|PubMed:12353266}.		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)				CCATTTCCCTCGGAGTCGACC	0.537													c|||	329	0.0656949	0.23	0.0231	5008	,	,		22102	0.001		0.007	False		,,,				2504	0.001				p.S52W	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.C155G						PASS	.	C	TRP/SER,TRP/SER,TRP/SER	658,3106		51,556,1275	168	167	167		155,155,155	1	0	10	dbSNP_132	167	51,8185		0,51,4067	yes	missense,missense,missense	DMBT1	NM_004406.2,NM_007329.2,NM_017579.2	177,177,177	51,607,5342	GG,GC,CC		0.6192,17.4814,5.9083	probably-damaging,probably-damaging,probably-damaging	52/1786,52/2414,52/2404	124330421	709,11291	1882	4118	6000	SO:0001583	missense	1755	exon4			TTCCCTCGGAGTC		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.155C>G	10.37:g.124330421C>G	ENSP00000342210:p.Ser52Trp	188	0	0		185	81	0.437838	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	37		130	0.05952380952380952	118	0.23983739837398374	9	0.024861878453038673	0	0.0	3	0.00395778364116095	C	10.71	1.426167	0.25726	0.174814	0.006192	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956;ENST00000359586	T;T;T;T;T;T;T	0.26223	1.85;1.84;1.78;1.85;1.84;1.78;1.75	1.9	0.968	0.19680	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D;P;P;P;D	0.76494	0.997;0.572;0.922;0.529;0.999	D;B;B;B;P	0.65443	0.935;0.152;0.206;0.202;0.902	T	0.24476	-1.0159	8	0.66056	D	0.02	.	4.3987	0.11376	0.0:0.7908:0.0:0.2092	.	52;52;52;52;52	F8WEF7;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;DMBT1_HUMAN	W	52	ENSP00000342210:S52W;ENSP00000343175:S52W;ENSP00000327747:S52W;ENSP00000357905:S52W;ENSP00000357951:S52W;ENSP00000357952:S52W;ENSP00000352593:S52W	ENSP00000331522:S52W	S	+	2	0	DMBT1	124320411	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.122000	0.15687	0.337000	0.23665	0.205000	0.17691	TCG	C|0.950;G|0.050	0.050	strong		0.537	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		G	124330421	C	G	124330421	3	3	25	1	0	0	0	0	1	0	0	0	4579	893	31	4	169	4	DMBT1	10	124330421	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	659846	124330421	11204326	430	9339											
C10orf120	399814	hgsc.bcm.edu	37	chr10	124457480	124457480	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgatttgcgatcatttccAtggtatgttaaacatttttt	11	19	6	5	1	1	1	1	1	0	0	2	2	2	1	1	1	2	2	1	1	4	7			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:124457480A>G	ENST00000329446.4	-	3	808	c.777T>C	c.(775-777)caT>caC	p.H259H		NM_001010912.1	NP_001010912.1	Q5SQS8	CJ120_HUMAN	chromosome 10 open reading frame 120	259										endometrium(1)|kidney(1)|large_intestine(6)|lung(9)|skin(2)|stomach(1)|urinary_tract(1)	21		all_neural(114;0.169)|Glioma(114;0.222)				GATCATTTCCATGGTATGTTA	0.388																																					p.H259H		Atlas-SNP	.											.	C10orf120	55	.	0			c.T777C						PASS	.						140	136	137					10																	124457480		2203	4300	6503	SO:0001819	synonymous_variant	399814	exon3			ATTTCCATGGTAT		CCDS31302.1	10q26.13	2012-06-12			ENSG00000183559	ENSG00000183559			25707	protein-coding gene	gene with protein product							Standard	NM_001010912		Approved	bA318C4.1	uc001lgn.3	Q5SQS8	OTTHUMG00000019187	ENST00000329446.4:c.777T>C	10.37:g.124457480A>G		132	0	0		124	55	0.443548	NM_001010912	B2RU17	Silent	SNP	ENST00000329446.4	37	CCDS31302.1																																																																																			.	.	none		0.388	C10orf120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050803.1	NM_001010912		G	124457480	A	G	124457480	2	3	25	1	0	0	0	0	0	0	0	1	1592	214	8	3		3	C10orf120	10	124457480	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	127059	124457480	11077267	431	9340											
FAM53B	9679	hgsc.bcm.edu	37	chr10	126370638	126370638	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tagcgctggacgctgcccccGctgtagcagcgtctcttttc	4	11	11	15	4	1	0	0	0	1	0	3	1	1	1	2	1	4	5	2	1	2	4	rs148943049		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:126370638G>A	ENST00000337318.3	-	4	655	c.444C>T	c.(442-444)agC>agT	p.S148S	FAM53B_ENST00000392754.3_Silent_p.S148S|RP11-12J10.3_ENST00000494792.1_3'UTR|FAM53B_ENST00000280780.6_Silent_p.S148S	NM_014661.3	NP_055476.3	Q14153	FA53B_HUMAN	family with sequence similarity 53, member B	148										cervix(1)|lung(5)|ovary(2)|pancreas(1)	9		all_lung(145;0.0191)|Lung NSC(174;0.0301)|Colorectal(57;0.106)|all_neural(114;0.117)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.15)		CGCTGCCCCCGCTGTAGCAGC	0.612													G|||	1	0.000199681	0.0	0.0	5008	,	,		19147	0.0		0.0	False		,,,				2504	0.001				p.S148S		Atlas-SNP	.											.	FAM53B	22	.	0			c.C444T						PASS	.	G		0,4406		0,0,2203	28	29	28		444	-8.4	0.2	10	dbSNP_134	28	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous	FAM53B	NM_014661.3		0,9,6494	AA,AG,GG		0.1047,0.0,0.0692		148/423	126370638	9,12997	2203	4300	6503	SO:0001819	synonymous_variant	9679	exon4			GCCCCCGCTGTAG	D50930	CCDS7641.1	10q26.13	2004-11-24	2004-11-24	2004-11-24	ENSG00000189319	ENSG00000189319			28968	protein-coding gene	gene with protein product			"KIAA0140"	KIAA0140		8590280	Standard	NM_014661		Approved	bA12J10.2	uc001lhv.1	Q14153	OTTHUMG00000019215	ENST00000337318.3:c.444C>T	10.37:g.126370638G>A		90	0	0		61	29	0.47541	NM_014661	D3DRF1|Q5VUW1|Q5VUW2|Q8N5S6	Silent	SNP	ENST00000337318.3	37	CCDS7641.1																																																																																			G|0.999;A|0.001	0.001	strong		0.612	FAM53B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050879.1	NM_014661		A	126370638	G	A	126370638	2	1	25	1	0	0	0	0	0	0	0	1	5588	1078	38	1		1	FAM53B	10	126370638	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1913158	126370638	9164109	432	9341											
CLRN3	119467	hgsc.bcm.edu	37	chr10	129690990	129690990	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tagagcaaattacaatgaagGacccaaggctggtgaaaaag	18	6	11	6	0	0	3	0	2	0	1	0	4	0	4	1	3	2	2	1	3	8	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:129690990G>T	ENST00000368671.3	-	1	221	c.59C>A	c.(58-60)tCc>tAc	p.S20Y		NM_152311.3	NP_689524.1	Q8NCR9	CLRN3_HUMAN	clarin 3	20						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	6		all_epithelial(44;0.00168)|all_lung(145;0.0586)|Lung NSC(174;0.0765)|all_neural(114;0.201)|Glioma(114;0.222)|Colorectal(57;0.235)				TACAATGAAGGACCCAAGGCT	0.383																																					p.S20Y		Atlas-SNP	.											.	CLRN3	27	.	0			c.C59A						PASS	.						114	102	106					10																	129690990		2203	4300	6503	SO:0001583	missense	119467	exon1			ATGAAGGACCCAA	BC029478	CCDS7656.1	10q26.2	2006-11-24	2006-11-23	2006-11-23	ENSG00000180745	ENSG00000180745			20795	protein-coding gene	gene with protein product			"transmembrane protein 12"	TMEM12		12145752, 12080385	Standard	NM_152311		Approved	MGC32871, USH3AL1	uc001lka.1	Q8NCR9	OTTHUMG00000019253	ENST00000368671.3:c.59C>A	10.37:g.129690990G>T	ENSP00000357660:p.Ser20Tyr	63	0	0		46	20	0.434783	NM_152311	Q6MZX8	Missense_Mutation	SNP	ENST00000368671.3	37	CCDS7656.1	.	.	.	.	.	.	.	.	.	.	G	17.06	3.291288	0.59976	.	.	ENSG00000180745	ENST00000368671	T	0.71103	-0.54	5.52	5.52	0.82312	.	0.222808	0.38837	N	0.001554	T	0.81631	0.4863	M	0.62723	1.935	0.19945	N	0.999946	D	0.65815	0.995	D	0.66716	0.946	T	0.74615	-0.3606	10	0.66056	D	0.02	-14.6668	16.4802	0.84156	0.0:0.0:1.0:0.0	.	20	Q8NCR9	CLRN3_HUMAN	Y	20	ENSP00000357660:S20Y	ENSP00000357660:S20Y	S	-	2	0	CLRN3	129580980	0.324000	0.24652	0.009000	0.14445	0.104000	0.19210	4.040000	0.57333	2.880000	0.98712	0.655000	0.94253	TCC	.	.	none		0.383	CLRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050987.1	NM_152311		T	129690990	G	T	129690990	3	4	25	1	0	0	0	0	1	0	0	0	3561	1174	41	4	633	4	CLRN3	10	129690990	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	3320352	129690990	5843757	433	9342											
VENTX	27287	hgsc.bcm.edu	37	chr10	135053784	135053784	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggccccggggcctgtgtgctAtgccacagacgggggatgca	6	6	17	12	2	0	1	0	0	0	1	0	2	0	2	4	5	3	2	4	5	1	1	rs148086757	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:135053784A>G	ENST00000325980.9	+	3	1262	c.751A>G	c.(751-753)Atg>Gtg	p.M251V		NM_014468.3	NP_055283.1	O95231	VENTX_HUMAN	VENT homeobox	251					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)		CCTGTGTGCTATGCCACAGAC	0.667													a|||	28	0.00559105	0.0	0.013	5008	,	,		9132	0.001		0.008	False		,,,				2504	0.0102				p.M251V		Atlas-SNP	.											.	VENTX	24	.	0			c.A751G						PASS	.	A	VAL/MET	1,4105		0,1,2052	15	17	17		751	0.9	0	10	dbSNP_134	17	32,8112		0,32,4040	yes	missense	VENTX	NM_014468.2	21	0,33,6092	GG,GA,AA		0.3929,0.0244,0.2694	benign	251/259	135053784	33,12217	2053	4072	6125	SO:0001583	missense	27287	exon3			TGTGCTATGCCAC	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.751A>G	10.37:g.135053784A>G	ENSP00000357556:p.Met251Val	19	0	0		41	15	0.365854	NM_014468	Q32MZ3	Missense_Mutation	SNP	ENST00000325980.9	37	CCDS7675.1	11	0.005036630036630037	0	0.0	5	0.013812154696132596	0	0.0	6	0.0079155672823219	a	7.807	0.714805	0.15306	2.44E-4	0.003929	ENSG00000151650	ENST00000325980	D	0.89939	-2.59	2.96	0.867	0.19085	.	0.369811	0.17386	U	0.176135	T	0.68540	0.3012	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.63152	-0.6701	10	0.62326	D	0.03	.	7.6583	0.28388	0.4764:0.5236:0.0:0.0	.	251	O95231	VENTX_HUMAN	V	251	ENSP00000357556:M251V	ENSP00000357556:M251V	M	+	1	0	VENTX	134903774	0.000000	0.05858	0.002000	0.10522	0.013000	0.08279	-0.801000	0.04550	0.052000	0.16007	-0.447000	0.05616	ATG	A|0.995;G|0.005	0.005	strong		0.667	VENTX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051116.4	NM_014468		G	135053784	A	G	135053784	3	3	25	1	0	0	0	0	1	0	0	0	17168	449	16	3	761	3	VENTX	10	135053784	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	5362794	135053784	480963	434	9343											
BET1L	60626	hgsc.bcm.edu	37	chr11	205398	205398	+	5'Flank	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcttccggttgtcttgtccGgaccttgccattgtggaaaa	7	13	11	10	2	1	0	0	0	1	0	3	2	3	2	4	3	2	2	4	3	2	5	rs190584141	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:205398G>A	ENST00000526104.1	+	0	0				BET1L_ENST00000410108.1_Intron|BET1L_ENST00000382762.3_Silent_p.S80S|BET1L_ENST00000486280.1_Silent_p.S57S|BET1L_ENST00000325147.9_3'UTR|RP11-304M2.5_ENST00000526963.1_RNA|BET1L_ENST00000332865.6_3'UTR|BET1L_ENST00000529614.2_Silent_p.S61S			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)		TGTCTTGTCCGGACCTTGCCA	0.537													G|||	4	0.000798722	0.0	0.0	5008	,	,		21271	0.0		0.004	False		,,,				2504	0.0				p.S80S		Atlas-SNP	.											.	BET1L	7	.	0			c.C240T						PASS	.	G	,	5,4401	9.9+/-24.2	0,5,2198	84	88	87		240,	-4.5	1	11		87	15,8585	11.2+/-40.8	0,15,4285	no	coding-synonymous,utr-3	BET1L	NM_001098787.1,NM_016526.4	,	0,20,6483	AA,AG,GG		0.1744,0.1135,0.1538	,	80/112,	205398	20,12986	2203	4300	6503	SO:0001631	upstream_gene_variant	51272	exon4			TTGTCCGGACCTT	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		11.37:g.205398G>A	Exception_encountered	118	0	0		161	90	0.559006	NM_001098787	Q0P508|Q2T9J1|Q7Z352|Q96EZ1|Q96SZ2|Q9H064|Q9H5H3|Q9H9E7	Silent	SNP	ENST00000526104.1	37																																																																																				G|0.998;A|0.002	0.002	strong		0.537	RIC8A-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000384761.1	NM_021932		A	205398	G	A	205398	1	1	25	0	1	0	0	0	0	0	0	0	1409	1103	39	1		1	BET1L	11	205398	5'Flank	SNP	G	TCGA-G8-6906-01A-11D-2210-10		205398	134801118	435	9344											
HRAS	3265	hgsc.bcm.edu	37	chr11	534242	534242	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggtcgtattcgtccacaaaAtggttctggatcagctggat	9	12	12	8	2	2	0	1	0	1	0	5	2	3	2	1	4	1	3	1	4	3	3	rs12628	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:534242A>G	ENST00000451590.1	-	2	268	c.81T>C	c.(79-81)caT>caC	p.H27H	HRAS_ENST00000397596.2_Silent_p.H27H|HRAS_ENST00000311189.7_Silent_p.H27H|HRAS_ENST00000397594.1_Silent_p.H27H|HRAS_ENST00000417302.1_Silent_p.H27H|HRAS_ENST00000468682.2_5'UTR	NM_001130442.1|NM_005343.2	NP_001123914.1|NP_005334.1	P01112	RASH_HUMAN	Harvey rat sarcoma viral oncogene homolog	27					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular senescence (GO:0090398)|chemotaxis (GO:0006935)|endocytosis (GO:0006897)|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)|intrinsic apoptotic signaling pathway (GO:0097193)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Rho GTPase activity (GO:0034259)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|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 DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of wound healing (GO:0090303)|protein heterooligomerization (GO:0051291)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein C-terminus binding (GO:0008022)	p.H27H(26)		adrenal_gland(1)|bone(3)|breast(7)|cervix(23)|endometrium(4)|haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|oesophagus(2)|penis(2)|pituitary(10)|prostate(31)|salivary_gland(24)|skin(184)|soft_tissue(38)|stomach(14)|testis(5)|thymus(1)|thyroid(173)|upper_aerodigestive_tract(122)|urinary_tract(225)	901		all_cancers(49;4.37e-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;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)		CGTCCACAAAATGGTTCTGGA	0.642		6	Mis		"infrequent sarcomas, rare other types"	"rhadomyosarcoma, ganglioneuroblastoma, bladder"			Costello syndrome	HNSCC(11;0.0054)			G|||	1488	0.297125	0.3729	0.3646	5008	,	,		18347	0.1726		0.3121	False		,,,				2504	0.2597				p.H27H		Atlas-SNP	.	yes	Dom	yes	Costello syndrome	11	11p15.5	3265	v-Ha-ras Harvey rat sarcoma viral oncogene homolog		"E, L, M"	HRAS,arm,benign_melanocytic_nevus,0,26	HRAS	1232	26	26	Substitution - coding silent(26)	urinary_tract(25)|skin(1)	c.T81C	GRCh37	CM035804	HRAS	M	rs12628	PASS	.	G	,,	1652,2754	653.2+/-399.5	309,1034,860	135	123	127	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	81,81,81	1	1	11	dbSNP_52	127	2959,5641	665.8+/-402.3	510,1939,1851	no	coding-synonymous,coding-synonymous,coding-synonymous	HRAS	NM_001130442.1,NM_005343.2,NM_176795.3	,,	819,2973,2711	GG,GA,AA		34.407,37.4943,35.4529	,,	27/190,27/190,27/171	534242	4611,8395	2203	4300	6503	SO:0001819	synonymous_variant	3265	exon2	Familial Cancer Database	incl.: Facio-Cutaneous-Skeletal syndrome	CACAAAATGGTTC	AJ437024	CCDS7698.1, CCDS7699.1	11p15.5	2014-09-17	2013-07-08		ENSG00000174775	ENSG00000174775			5173	protein-coding gene	gene with protein product		190020	"v-Ha-ras Harvey rat sarcoma viral oncogene homolog"	HRAS1			Standard	NM_176795		Approved		uc010qvx.2	P01112	OTTHUMG00000131919	ENST00000451590.1:c.81T>C	11.37:g.534242A>G		69	0	0		87	40	0.45977	NM_001130442	B5BUA0|Q14080|Q6FHV9|Q9BR65|Q9UCE2	Silent	SNP	ENST00000451590.1	37	CCDS7698.1																																																																																			A|0.663;G|0.337	0.337	strong		0.642	HRAS-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259403.2	NM_176795		G	534242	A	G	534242	2	3	25	1	0	0	0	0	0	0	0	1	7357	98	4	3		3	HRAS	11	534242	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	328844	534242	134472274	436	9345											
SLC25A22	79751	hgsc.bcm.edu	37	chr11	794790	794790	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcacatgctcgtgtacacGcgctggccgttctgctggtt	5	12	11	13	4	2	0	1	0	1	0	3	0	2	0	1	2	3	6	1	2	1	3	rs146402942	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:794790G>A	ENST00000320230.5	-	3	613	c.132C>T	c.(130-132)cgC>cgT	p.R44R	SLC25A22_ENST00000531214.1_Silent_p.R44R	NM_001191061.1|NM_024698.5	NP_001177990.1|NP_078974.1	Q9H936	GHC1_HUMAN	solute carrier family 25 (mitochondrial carrier: glutamate), member 22	44					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)		TCGTGTACACGCGCTGGCCGT	0.667																																					p.R44R	Colon(93;848 1468 3270 23355 49636)	Atlas-SNP	.											.	SLC25A22	19	.	0			c.C132T						PASS	.	G	,,	0,4396		0,0,2198	39	37	37		132,132,132	2.3	1	11	dbSNP_134	37	13,8579		0,13,4283	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC25A22	NM_001191060.1,NM_001191061.1,NM_024698.5	,,	0,13,6481	AA,AG,GG		0.1513,0.0,0.1001	,,	44/324,44/324,44/324	794790	13,12975	2198	4296	6494	SO:0001819	synonymous_variant	79751	exon3			GTACACGCGCTGG	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.132C>T	11.37:g.794790G>A		140	0	0		148	73	0.493243	NM_001191061	A8K366|C9J1H6|E9PJD3|E9PKB2|E9PL68|E9PN26|E9PNQ3|E9PP01|E9PR97|Q8TBU8	Silent	SNP	ENST00000320230.5	37	CCDS7715.1																																																																																			G|0.999;A|0.001	0.001	strong		0.667	SLC25A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257107.2			A	794790	G	A	794790	2	1	25	1	0	0	0	0	0	0	0	1	14500	1074	38	1		1	SLC25A22	11	794790	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	260548	794790	134211726	437	9346											
MUC6	4588	hgsc.bcm.edu	37	chr11	1016630	1016630	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	attggtggggctgtgtgggtGgaccctgtggccttgagcgt	3	12	19	7	1	0	1	0	1	0	0	0	2	0	2	2	6	1	1	2	6	0	2	rs369775657		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1016630G>A	ENST00000421673.2	-	31	6221	c.6171C>T	c.(6169-6171)tcC>tcT	p.S2057S		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	2057	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)		CTGTGTGGGTGGACCCTGTGG	0.562																																					p.S2057S		Atlas-SNP	.											.	MUC6	408	.	0			c.C6171T						PASS	.	G		32,4354	2.1+/-5.4	0,32,2161	389	386	387		6171	-2.5	0	11		387	18,8558	1.2+/-3.3	0,18,4270	no	coding-synonymous	MUC6	NM_005961.2		0,50,6431	AA,AG,GG		0.2099,0.7296,0.3857		2057/2440	1016630	50,12912	2193	4288	6481	SO:0001819	synonymous_variant	4588	exon31			GTGGGTGGACCCT	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.6171C>T	11.37:g.1016630G>A		429	0	0		446	27	0.0605381	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			.	.	weak		0.562	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		A	1016630	G	A	1016630	2	1	25	1	0	0	0	0	0	0	0	1	9989	1335	47	2		2	MUC6	11	1016630	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	221840	1016630	133989886	438	9347											
MUC6	4588	hgsc.bcm.edu	37	chr11	1017522	1017522	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtagaagttgaggtgactTcaggatggtgtgtggaggaa	10	11	18	2	0	1	3	1	2	0	1	1	6	1	6	0	6	0	2	0	6	3	3	rs199592093		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1017522T>G	ENST00000421673.2	-	31	5329	c.5279A>C	c.(5278-5280)gAa>gCa	p.E1760A		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1760	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)		TGAGGTGACTTCAGGATGGTG	0.567																																					p.E1760A		Atlas-SNP	.											.	MUC6	408	.	0			c.A5279C						PASS	.						751	715	727					11																	1017522		2200	4294	6494	SO:0001583	missense	4588	exon31			GTGACTTCAGGAT	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.5279A>C	11.37:g.1017522T>G	ENSP00000406861:p.Glu1760Ala	479	0	0		596	32	0.0536913	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	-	0.655	-0.808100	0.02819	.	.	ENSG00000184956	ENST00000421673	T	0.20332	2.08	0.235	0.235	0.15431	.	.	.	.	.	T	0.25195	0.0612	L	0.38175	1.15	0.09310	N	1	D	0.67145	0.996	D	0.70227	0.968	T	0.11966	-1.0566	8	0.05833	T	0.94	.	.	.	.	.	1760	Q6W4X9	MUC6_HUMAN	A	1760	ENSP00000406861:E1760A	ENSP00000406861:E1760A	E	-	2	0	MUC6	1007522	0.000000	0.05858	0.002000	0.10522	0.045000	0.14185	-3.356000	0.00499	0.263000	0.21812	0.260000	0.18958	GAA	.	.	weak		0.567	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		G	1017522	T	G	1017522	3	3	25	1	0	0	0	0	1	0	0	0	9989	1783	62	5	2052	5	MUC6	11	1017522	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	892	1017522	133988994	439	9348											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1251357	1251357	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgacctgcatggtgactgcaGctacgttctgtccaaggtct	7	11	11	12	2	2	1	0	1	2	0	3	2	3	1	2	2	4	4	2	2	2	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1251357G>C	ENST00000529681.1	+	11	1401	c.1343G>C	c.(1342-1344)aGc>aCc	p.S448T	MUC5B_ENST00000447027.1_Missense_Mutation_p.S451T	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	448	VWFD 2. {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)		GGTGACTGCAGCTACGTTCTG	0.637																																					p.S448T		Atlas-SNP	.											.	MUC5B	473	.	0			c.G1343C						PASS	.						112	115	114					11																	1251357		1991	4140	6131	SO:0001583	missense	727897	exon11			ACTGCAGCTACGT	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.1343G>C	11.37:g.1251357G>C	ENSP00000436812:p.Ser448Thr	66	0	0		71	34	0.478873	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	G	3.587	-0.084422	0.07097	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.59638	0.25;0.25	4.26	2.37	0.29283	von Willebrand factor, type D domain (3);VWC out (1);	.	.	.	.	T	0.44286	0.1286	N	0.21617	0.685	0.25405	N	0.988402	B;P;P	0.39094	0.051;0.659;0.659	B;B;B	0.42882	0.049;0.401;0.401	T	0.35375	-0.9791	9	0.87932	D	0	.	4.8917	0.13730	0.2846:0.2117:0.5037:0.0	.	448;1107;451	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	T	448;451;449;484	ENSP00000436812:S448T;ENSP00000415793:S451T	ENSP00000343037:S449T	S	+	2	0	MUC5B	1207933	0.001000	0.12720	1.000000	0.80357	0.111000	0.19643	-0.241000	0.08940	0.270000	0.21984	0.313000	0.20887	AGC	.	.	none		0.637	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		C	1251357	G	C	1251357	3	2	25	1	0	0	0	0	1	0	0	0	9988	971	34	4	1394	4	MUC5B	11	1251357	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	233835	1251357	133755159	440	9349											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1258184	1258184	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgcggcctgtgcgggaacttCgacgacaatgccatcaatga	10	8	12	11	4	1	1	1	1	0	0	2	4	1	2	2	2	4	0	2	2	3	1	rs55703838	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1258184C>T	ENST00000529681.1	+	25	3145	c.3087C>T	c.(3085-3087)ttC>ttT	p.F1029F	MUC5B_ENST00000447027.1_Silent_p.F1032F	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1029	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)		GCGGGAACTTCGACGACAATG	0.672													c|||	25	0.00499201	0.0008	0.0058	5008	,	,		17982	0.0		0.0139	False		,,,				2504	0.0061				p.F1029F		Atlas-SNP	.											.	MUC5B	473	.	0			c.C3087T						PASS	.	C		11,4265		0,11,2127	26	34	32		3087	-4.5	0.8	11	dbSNP_129	32	107,8349		0,107,4121	no	coding-synonymous	MUC5B	NM_002458.2		0,118,6248	TT,TC,CC		1.2654,0.2572,0.9268		1029/5763	1258184	118,12614	2138	4228	6366	SO:0001819	synonymous_variant	727897	exon25			GAACTTCGACGAC	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.3087C>T	11.37:g.1258184C>T		48	0	0		44	21	0.477273	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			C|0.993;T|0.007	0.007	strong		0.672	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		T	1258184	C	T	1258184	2	4	25	1	0	0	0	0	0	0	0	1	9988	883	31	1		1	MUC5B	11	1258184	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	6827	1258184	133748332	441	9350											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1264795	1264795	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgggcaccacccacatcacaGagccttccacggtgacttcc	9	7	8	17	1	1	2	1	1	0	1	3	2	3	2	5	2	1	1	5	2	0	2	rs200138247	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1264795G>C	ENST00000529681.1	+	31	6743	c.6685G>C	c.(6685-6687)Gag>Cag	p.E2229Q	MUC5B_ENST00000447027.1_Missense_Mutation_p.E2232Q|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2229	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)		CCACATCACAGAGCCTTCCAC	0.652													g|||	19	0.00379393	0.0008	0.0058	5008	,	,		13832	0.0		0.0119	False		,,,				2504	0.002				p.E2229Q		Atlas-SNP	.											.	MUC5B	473	.	0			c.G6685C						PASS	.	G	GLN/GLU	5,4165		0,5,2080	95	120	112		6685	-1.5	0	11		112	55,8297		0,55,4121	no	missense	MUC5B	NM_002458.2	29	0,60,6201	CC,CG,GG		0.6585,0.1199,0.4792	possibly-damaging	2229/5763	1264795	60,12462	2085	4176	6261	SO:0001583	missense	727897	exon31			ATCACAGAGCCTT	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.6685G>C	11.37:g.1264795G>C	ENSP00000436812:p.Glu2229Gln	347	0	0		322	117	0.363354	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	g	4.475	0.088061	0.08583	0.001199	0.006585	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.21031	2.03;2.21	1.87	-1.45	0.08828	.	.	.	.	.	T	0.06280	0.0162	L	0.36672	1.1	0.09310	N	1	P;P	0.47604	0.813;0.898	B;B	0.28784	0.053;0.094	T	0.24512	-1.0158	9	0.87932	D	0	.	0.5061	0.00588	0.4066:0.1743:0.2245:0.1945	.	2867;2232	A7Y9J9;E9PBJ0	.;.	Q	2229;2232;2230;2244	ENSP00000436812:E2229Q;ENSP00000415793:E2232Q	ENSP00000343037:E2230Q	E	+	1	0	MUC5B	1221371	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.475000	0.06599	-0.394000	0.07727	0.305000	0.20034	GAG	.	.	weak		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		C	1264795	G	C	1264795	3	2	25	1	0	0	0	0	1	0	0	0	9988	943	33	4	6816	4	MUC5B	11	1264795	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	6611	1264795	133741721	442	9351											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1264941	1264941	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accaccccgggccacaccacGgccacctccaggaccacagc	10	1	8	22	2	0	0	0	0	0	0	1	1	1	1	9	3	1	0	9	3	0	0	rs200834421	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1264941G>A	ENST00000529681.1	+	31	6889	c.6831G>A	c.(6829-6831)acG>acA	p.T2277T	MUC5B_ENST00000447027.1_Silent_p.T2280T|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2277	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)		GCCACACCACGGCCACCTCCA	0.682													g|||	24	0.00479233	0.0008	0.0058	5008	,	,		15879	0.0		0.0129	False		,,,				2504	0.0061				p.T2277T		Atlas-SNP	.											MUC5B,NS,carcinoma,+1,2	MUC5B	473	2	0			c.G6831A						PASS	.	G		9,4263		0,9,2127	98	136	123		6831	-6	0	11		123	100,8354		0,100,4127	no	coding-synonymous	MUC5B	NM_002458.2		0,109,6254	AA,AG,GG		1.1829,0.2107,0.8565		2277/5763	1264941	109,12617	2136	4227	6363	SO:0001819	synonymous_variant	727897	exon31			CACCACGGCCACC	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.6831G>A	11.37:g.1264941G>A		537	0	0		607	179	0.294893	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			G|0.988;A|0.012	0.012	strong		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1264941	G	A	1264941	2	1	25	1	0	0	0	0	0	0	0	1	9988	1103	39	1		1	MUC5B	11	1264941	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	146	1264941	133741575	443	9352											
KRTAP5-4	387267	hgsc.bcm.edu	37	chr11	1643255	1643255	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccccacagccagagccacaGcccccacagccggagccaca	11	0	8	22	1	0	1	0	0	0	1	0	2	0	2	8	1	5	0	8	1	0	0			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1643255G>A	ENST00000399682.1	-	1	113	c.69C>T	c.(67-69)ggC>ggT	p.G23G		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0						keratin filament (GO:0045095)		p.G23G(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)		cagagccacagcccccacagc	0.687																																					p.G23G		Atlas-SNP	.											KRTAP5-4,NS,carcinoma,0,1	KRTAP5-4	78	1	1	Substitution - coding silent(1)	kidney(1)	c.C69T						scavenged	.						4	8	7					11																	1643255		646	1526	2172	SO:0001819	synonymous_variant	387267	exon1			GCCACAGCCCCCA	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.69C>T	11.37:g.1643255G>A		89	1	0.011236		154	8	0.0519481	NM_001012709		Silent	SNP	ENST00000399682.1	37																																																																																				.	.	none		0.687	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709		A	1643255	G	A	1643255	2	1	25	1	0	0	0	0	0	0	0	1	8572	958	34	2		2	KRTAP5-4	11	1643255	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	378314	1643255	133363261	444	9353											
TRPM5	29850	hgsc.bcm.edu	37	chr11	2436201	2436201	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcccacaggaacaggtccCgccaggggttctcgctcttc	6	7	12	16	3	2	0	0	0	2	0	5	1	3	1	3	5	1	2	3	5	1	2	rs202052284		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:2436201C>T	ENST00000155858.6	-	10	1564	c.1556G>A	c.(1555-1557)cGg>cAg	p.R519Q	TRPM5_ENST00000528453.1_Missense_Mutation_p.R519Q|TRPM5_ENST00000533060.1_Missense_Mutation_p.R519Q|TRPM5_ENST00000452833.1_Missense_Mutation_p.R521Q	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)		GAACAGGTCCCGCCAGGGGTT	0.711																																					p.R519Q	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.G1556A						PASS	.	C	GLN/ARG	1,4355		0,1,2177	23	29	27		1556	3.7	1	11		27	2,8566		0,2,4282	yes	missense	TRPM5	NM_014555.3	43	0,3,6459	TT,TC,CC		0.0233,0.023,0.0232	probably-damaging	519/1166	2436201	3,12921	2178	4284	6462	SO:0001583	missense	29850	exon10			AGGTCCCGCCAGG	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.1556G>A	11.37:g.2436201C>T	ENSP00000155858:p.Arg519Gln	13	0	0		20	16	0.8	NM_014555		Missense_Mutation	SNP	ENST00000155858.6	37	CCDS31340.1	.	.	.	.	.	.	.	.	.	.	C	19.41	3.822268	0.71028	2.3E-4	2.33E-4	ENSG00000070985	ENST00000533881;ENST00000155858;ENST00000452833;ENST00000533060;ENST00000528453;ENST00000437542	D;D;D;D;D	0.84944	-1.92;-1.92;-1.92;-1.92;-1.92	3.68	3.68	0.42216	.	0.000000	0.85682	D	0.000000	D	0.87309	0.6145	L	0.46885	1.475	0.47214	D	0.999352	D;D;D	0.89917	1.0;1.0;0.993	D;D;P	0.65443	0.935;0.935;0.837	D	0.86502	0.1804	10	0.48119	T	0.1	-29.7753	9.9877	0.41852	0.2027:0.7973:0.0:0.0	.	519;521;519	E9PRW0;Q9NZQ8-2;Q9NZQ8	.;.;TRPM5_HUMAN	Q	513;519;521;519;519;519	ENSP00000434383:R513Q;ENSP00000155858:R519Q;ENSP00000387965:R521Q;ENSP00000434121:R519Q;ENSP00000436809:R519Q	ENSP00000155858:R519Q	R	-	2	0	TRPM5	2392777	0.861000	0.29849	0.957000	0.39632	0.939000	0.58152	3.421000	0.52742	2.069000	0.61940	0.491000	0.48974	CGG	C|0.998;T|0.002	0.002	weak		0.711	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555		T	2436201	C	T	2436201	3	4	25	1	0	0	0	0	1	0	0	0	16604	652	23	1	2001	1	TRPM5	11	2436201	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	792946	2436201	132570315	445	9354											
KCNQ1	3784	hgsc.bcm.edu	37	chr11	2869086	2869086	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagcacccccggcagcggCggcccccccagagagggcgg	6	0	17	18	4	0	1	0	0	0	1	0	2	0	1	5	6	2	3	5	6	0	0	rs144610043|rs397508102		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:2869086C>T	ENST00000155840.5	+	16	1992	c.1884C>T	c.(1882-1884)ggC>ggT	p.G628G	KCNQ1-AS1_ENST00000440887.2_RNA|KCNQ1_ENST00000335475.5_Silent_p.G501G|KCNQ1_ENST00000526095.1_3'UTR	NM_000218.2	NP_000209.2	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 1	628				LHGGSTPGSGGPPREGGAHITQPCGS -> MQQGGPTCNSR SQVVASNE (in Ref. 4; AAM94040). {ECO:0000305}.	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)	CCGGCAGCGGCGGCCCCCCCA	0.701																																					p.G628G		Atlas-SNP	.											.	KCNQ1	60	.	0			c.C1884T						PASS	.						10	10	10					11																	2869086		2141	4219	6360	SO:0001819	synonymous_variant	3784	exon16			CAGCGGCGGCCCC	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.1884C>T	11.37:g.2869086C>T		31	0	0		66	36	0.545455	NM_000218	O00347|O60607|O94787|Q14D14|Q7Z6G9|Q92960|Q9UMN8|Q9UMN9	Silent	SNP	ENST00000155840.5	37	CCDS7736.1																																																																																			.	.	none		0.701	KCNQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027382.2	NM_000218		T	2869086	C	T	2869086	2	4	25	1	0	0	0	0	0	0	0	1	8091	755	27	1		1	KCNQ1	11	2869086	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	432885	2869086	132137430	446	9355											
SLC22A18	5002	hgsc.bcm.edu	37	chr11	2929502	2929502	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcctggattccattgccttcGgctacctgcaaaccaccttc	7	11	7	16	1	0	0	0	0	0	0	3	1	1	1	6	2	4	2	6	2	2	5	rs143044180	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:2929502G>T	ENST00000380574.1	+	3	615	c.184G>T	c.(184-186)Ggc>Tgc	p.G62C	SLC22A18_ENST00000312221.5_Missense_Mutation_p.G62C|SLC22A18_ENST00000347936.2_Missense_Mutation_p.G62C|SLC22A18_ENST00000449793.2_Missense_Mutation_p.G62C			Q96BI1	S22AI_HUMAN	solute carrier family 22, member 18	62					drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|excretion (GO:0007588)|organic cation transport (GO:0015695)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|symporter activity (GO:0015293)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	8		all_epithelial(84;0.000124)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)|all_lung(207;0.198)		BRCA - Breast invasive adenocarcinoma(625;0.00256)|LUSC - Lung squamous cell carcinoma(625;0.192)		CATTGCCTTCGGCTACCTGCA	0.617													G|||	5	0.000998403	0.0	0.0029	5008	,	,		15811	0.0		0.002	False		,,,				2504	0.001				p.G62C		Atlas-SNP	.											SLC22A18,NS,carcinoma,0,1	SLC22A18	20	1	0			c.G184T						PASS	.	G	CYS/GLY,CYS/GLY	2,4402	4.2+/-10.8	0,2,2200	86	82	84		184,184	3.3	0.9	11	dbSNP_134	84	33,8565	22.8+/-68.1	0,33,4266	yes	missense,missense	SLC22A18	NM_002555.5,NM_183233.2	159,159	0,35,6466	TT,TG,GG		0.3838,0.0454,0.2692	probably-damaging,probably-damaging	62/425,62/425	2929502	35,12967	2202	4299	6501	SO:0001583	missense	5002	exon3			GCCTTCGGCTACC	AF028738	CCDS7740.1	11p15.5	2013-05-22	2008-01-11	2004-01-21	ENSG00000110628	ENSG00000110628		"Solute carriers"	10964	protein-coding gene	gene with protein product		602631	"solute carrier family 22 (organic cation transporter), member 1-like"	ORCTL2, BWSCR1A, IMPT1, SLC22A1L		9499412, 9520460	Standard	NM_183233		Approved	BWR1A, TSSC5, ITM	uc001lwx.3	Q96BI1	OTTHUMG00000010037	ENST00000380574.1:c.184G>T	11.37:g.2929502G>T	ENSP00000369948:p.Gly62Cys	92	0	0		81	45	0.555556	NM_002555	O14906|O43562|O60485|O60680|Q7LDS5|Q7LGF7	Missense_Mutation	SNP	ENST00000380574.1	37	CCDS7740.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	13.97	2.395838	0.42512	4.54E-4	0.003838	ENSG00000110628	ENST00000347936;ENST00000312221;ENST00000449793;ENST00000380574;ENST00000485423	T;T;T;T;D	0.86097	-0.21;-0.21;-0.21;-0.21;-2.07	4.27	3.34	0.38264	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.64402	D	0.000001	D	0.90861	0.7129	M	0.83953	2.67	0.58432	D	0.99999	D;D	0.89917	1.0;1.0	D;D	0.97110	0.986;1.0	D	0.90662	0.4591	10	0.87932	D	0	-1.8758	7.3817	0.26859	0.1199:0.0:0.8801:0.0	.	62;62	E9PRM7;Q96BI1	.;S22AI_HUMAN	C	62	ENSP00000307859:G62C;ENSP00000311139:G62C;ENSP00000392072:G62C;ENSP00000369948:G62C;ENSP00000433019:G62C	ENSP00000311139:G62C	G	+	1	0	SLC22A18	2886078	1.000000	0.71417	0.933000	0.37362	0.037000	0.13140	2.882000	0.48546	2.105000	0.64084	0.491000	0.48974	GGC	G|0.998;T|0.002	0.002	strong		0.617	SLC22A18-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027770.1	NM_183233		T	2929502	G	T	2929502	3	4	25	1	0	0	0	0	1	0	0	0	14464	1116	39	4	190	4	SLC22A18	11	2929502	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	60416	2929502	132077014	447	9356											
OR52E6	390078	hgsc.bcm.edu	37	chr11	5862416	5862416	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agagccacaggtgttgagagCtttgagtcgagcttcccagg	9	9	14	9	1	0	3	0	2	0	2	2	5	1	3	2	2	3	3	2	2	0	3	rs61735020	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5862416C>T	ENST00000329322.5	-	1	711	c.712G>A	c.(712-714)Gct>Act	p.A238T	OR52E6_ENST00000379946.2_Missense_Mutation_p.A242T|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													C|||	43	0.00858626	0.0008	0.013	5008	,	,		19247	0.0		0.0308	False		,,,				2504	0.002				p.A238T		Atlas-SNP	.											.	OR52E6	70	.	0			c.G712A						PASS	.	C	THR/ALA	30,4364	31.7+/-61.6	0,30,2167	64	65	65		712	3.2	0.5	11	dbSNP_129	65	271,8317	102.3+/-163.5	5,261,4028	yes	missense	OR52E6	NM_001005167.1	58	5,291,6195	TT,TC,CC		3.1556,0.6827,2.3186	probably-damaging	238/314	5862416	301,12681	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>A	11.37:g.5862416C>T	ENSP00000328878:p.Ala238Thr	125	0	0		123	60	0.487805	NM_001005167	Q6IFF8	Missense_Mutation	SNP	ENST00000329322.5	37	CCDS53597.1	31	0.014194139194139194	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	27	0.03562005277044855	C	15.10	2.732139	0.48939	0.006827	0.031556	ENSG00000205409	ENST00000329322;ENST00000379946	T;T	0.00357	7.89;7.89	3.23	3.23	0.37069	GPCR, rhodopsin-like superfamily (1);	0.110508	0.40144	N	0.001174	T	0.00144	0.0004	M	0.67397	2.05	0.40032	D	0.975546	D	0.53462	0.96	P	0.54924	0.764	D	0.84518	0.0626	10	0.51188	T	0.08	.	13.1659	0.59571	0.0:1.0:0.0:0.0	rs61735020	238	Q96RD3	O52E6_HUMAN	T	238;242	ENSP00000328878:A238T;ENSP00000369279:A242T	ENSP00000328878:A238T	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	0.016	strong		0.443	OR52E6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401144.1	NM_001005167		T	5862416	C	T	5862416	3	4	25	1	0	0	0	0	1	0	0	0	11126	797	28	2	231	2	OR52E6	11	5862416	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2932914	5862416	129144100	448	9357											
SMPD1	6609	hgsc.bcm.edu	37	chr11	6413108	6413108	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggctgggcccagccggcccTtttgatatggtgtactggac	5	10	15	11	1	0	1	0	1	0	0	0	2	0	2	3	5	2	2	3	5	2	4	rs61876771	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6413108T>C	ENST00000342245.4	+	2	981	c.813T>C	c.(811-813)ccT>ccC	p.P271P	SMPD1_ENST00000533196.1_Intron|SMPD1_ENST00000299397.3_Silent_p.P271P|SMPD1_ENST00000356761.2_Silent_p.P271P|SMPD1_ENST00000527275.1_Silent_p.P270P	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	269					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)	CAGCCGGCCCTTTTGATATGG	0.622													T|||	13	0.00259585	0.0008	0.0029	5008	,	,		12884	0.0		0.0099	False		,,,				2504	0.0				p.P271P		Atlas-SNP	.											.	SMPD1	108	.	0			c.T813C						PASS	.	T	,	3,4399	6.2+/-15.9	0,3,2198	85	102	96		813,810	-1.8	1	11	dbSNP_129	96	55,8537	30.1+/-81.4	0,55,4241	no	coding-synonymous,coding-synonymous	SMPD1	NM_000543.4,NM_001007593.2	,	0,58,6439	CC,CT,TT		0.6401,0.0682,0.4464	,	271/632,270/631	6413108	58,12936	2201	4296	6497	SO:0001819	synonymous_variant	6609	exon2			CGGCCCTTTTGAT	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.813T>C	11.37:g.6413108T>C		68	0	0		71	43	0.605634	NM_000543	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	Silent	SNP	ENST00000342245.4	37	CCDS44531.1	11	0.005036630036630037	0	0.0	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	T	10.10	1.258006	0.22965	6.82E-4	0.006401	ENSG00000166311	ENST00000526280	.	.	.	5.02	-1.8	0.07907	.	.	.	.	.	T	0.39784	0.1091	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.32561	-0.9902	4	.	.	.	-21.0652	4.6701	0.12685	0.0:0.3147:0.3048:0.3805	rs61876771	.	.	.	P	1	.	.	L	+	2	0	SMPD1	6369684	0.796000	0.28864	0.992000	0.48379	0.966000	0.64601	-0.140000	0.10342	-0.243000	0.09653	0.459000	0.35465	CTT	A|0.000;C|0.006;T|0.993	0.006	strong		0.622	SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543		C	6413108	T	C	6413108	2	2	25	1	0	0	0	0	0	0	0	1	14819	1596	56	3		3	SMPD1	11	6413108	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	550692	6413108	128593408	449	9358											
DNHD1	144132	hgsc.bcm.edu	37	chr11	6592951	6592951	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acatgcggagtgggacccaaTagctggagccttgcaggaca	11	6	14	10	1	0	0	0	0	0	0	0	4	0	4	2	4	4	2	2	4	2	2	rs11604362	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6592951T>C	ENST00000527990.2	+	41	13997	c.13997T>C	c.(13996-13998)aTa>aCa	p.I4666T	DNHD1_ENST00000254579.6_Missense_Mutation_p.I4666T			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	4666			I -> T (in dbSNP:rs11604362).		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)		TGGGACCCAATAGCTGGAGCC	0.632													T|||	10	0.00199681	0.0	0.0058	5008	,	,		17689	0.0		0.006	False		,,,				2504	0.0				p.I4666T		Atlas-SNP	.											.	DNHD1	198	.	0			c.T13997C						PASS	.	T	THR/ILE	10,4218		0,10,2104	38	49	45		13997	-0.8	0	11	dbSNP_120	45	65,8389		0,65,4162	yes	missense	DNHD1	NM_144666.2	89	0,75,6266	CC,CT,TT		0.7689,0.2365,0.5914	benign	4666/4754	6592951	75,12607	2114	4227	6341	SO:0001583	missense	144132	exon43			ACCCAATAGCTGG	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.13997T>C	11.37:g.6592951T>C	ENSP00000436180:p.Ile4666Thr	94	0	0		127	75	0.590551	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	11	0.005036630036630037	2	0.0040650406504065045	3	0.008287292817679558	2	0.0034965034965034965	4	0.005277044854881266	T	0.823	-0.748044	0.03065	0.002365	0.007689	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000530197	T;T	0.07444	3.19;3.19	4.75	-0.827	0.10802	Dynein heavy chain (1);	1.500610	0.03937	N	0.286257	T	0.01489	0.0048	N	0.00538	-1.39	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	0.40001	-0.9586	10	0.14252	T	0.57	0.038	3.778	0.08668	0.3386:0.1861:0.0:0.4753	rs11604362;rs11604362	3754;719;4666	B0I1S4;Q9NSW8;Q96M86	.;.;DNHD1_HUMAN	T	4666;4666;934	ENSP00000254579:I4666T;ENSP00000436180:I4666T	ENSP00000254579:I4666T	I	+	2	0	DNHD1	6549527	0.000000	0.05858	0.003000	0.11579	0.389000	0.30415	-0.299000	0.08254	0.009000	0.14813	-0.274000	0.10170	ATA	T|0.994;C|0.006	0.006	strong		0.632	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		C	6592951	T	C	6592951	3	2	25	1	0	0	0	0	1	0	0	0	4670	1406	49	3	14168	3	DNHD1	11	6592951	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	179843	6592951	128413565	450	9359											
DCHS1	8642	hgsc.bcm.edu	37	chr11	6647596	6647596	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtctagcccctctgctgagCgaactgtgatggcacctggg	7	9	13	12	1	2	2	0	2	2	0	2	3	2	2	3	2	4	2	3	2	2	1	rs142577975		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6647596C>T	ENST00000299441.3	-	16	6791	c.6380G>A	c.(6379-6381)cGc>cAc	p.R2127H		NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	2127	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)		CTCTGCTGAGCGAACTGTGAT	0.587													c|||	1	0.000199681	0.0	0.0	5008	,	,		20274	0.0		0.001	False		,,,				2504	0.0				p.R2127H		Atlas-SNP	.											.	DCHS1	277	.	0			c.G6380A						PASS	.	T	HIS/ARG	0,4402		0,0,2201	58	57	57		6380	-1.9	0.2	11	dbSNP_134	57	1,8591	1.2+/-3.3	0,1,4295	yes	missense	DCHS1	NM_003737.2	29	0,1,6496	TT,TC,CC		0.0116,0.0,0.0077	benign	2127/3299	6647596	1,12993	2201	4296	6497	SO:0001583	missense	8642	exon16			GCTGAGCGAACTG	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.6380G>A	11.37:g.6647596C>T	ENSP00000299441:p.Arg2127His	50	0	0		67	40	0.597015	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	37	CCDS7771.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	c	10.48	1.362070	0.24684	0.0	1.16E-4	ENSG00000166341	ENST00000299441	T	0.53206	0.63	4.92	-1.87	0.07737	Cadherin (4);Cadherin-like (1);	1.016160	0.07896	N	0.971952	T	0.35307	0.0927	L	0.41824	1.3	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.35500	-0.9786	10	0.52906	T	0.07	.	6.5512	0.22436	0.0:0.2635:0.1437:0.5928	.	2127	Q96JQ0	PCD16_HUMAN	H	2127	ENSP00000299441:R2127H	ENSP00000299441:R2127H	R	-	2	0	DCHS1	6604172	0.115000	0.22152	0.189000	0.23252	0.888000	0.51559	0.617000	0.24359	-0.190000	0.10465	-0.224000	0.12420	CGC	C|1.000;T|0.000	0.000	strong		0.587	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737		T	6647596	C	T	6647596	3	4	25	1	0	0	0	0	1	0	0	0	4289	768	27	1	3540	1	DCHS1	11	6647596	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	54645	6647596	128358920	451	9360											
ZNF215	7762	hgsc.bcm.edu	37	chr11	6977109	6977109	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttacactgaggaggaagatTttgaatgtagtgaaaataag	16	12	11	2	0	0	4	0	3	0	1	0	6	0	6	0	2	1	1	0	2	7	6	rs149189074	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6977109T>C	ENST00000278319.5	+	7	1489	c.901T>C	c.(901-903)Ttt>Ctt	p.F301L	ZNF215_ENST00000527171.1_3'UTR|ZNF215_ENST00000414517.2_Missense_Mutation_p.F301L|ZNF215_ENST00000529903.1_Intron	NM_013250.2	NP_037382.2	Q9UL58	ZN215_HUMAN	zinc finger protein 215	301					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)		GGAGGAAGATTTTGAATGTAG	0.353													T|||	12	0.00239617	0.0	0.0014	5008	,	,		18696	0.0		0.0099	False		,,,				2504	0.001				p.F301L		Atlas-SNP	.											.	ZNF215	72	.	0			c.T901C						PASS	.	T	LEU/PHE	4,4398	8.1+/-20.4	0,4,2197	72	83	79		901	3.1	0	11	dbSNP_134	79	56,8530	31.7+/-84.0	0,56,4237	yes	missense	ZNF215	NM_013250.2	22	0,60,6434	CC,CT,TT		0.6522,0.0909,0.462	possibly-damaging	301/518	6977109	60,12928	2201	4293	6494	SO:0001583	missense	7762	exon7			GAAGATTTTGAAT	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.901T>C	11.37:g.6977109T>C	ENSP00000278319:p.Phe301Leu	74	0	0		108	51	0.472222	NM_013250	Q96C84	Missense_Mutation	SNP	ENST00000278319.5	37	CCDS7775.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	T	10.32	1.318071	0.23994	9.09E-4	0.006522	ENSG00000149054	ENST00000278319;ENST00000414517	T;T	0.04809	3.55;3.55	4.27	3.11	0.35812	.	0.516746	0.16372	N	0.217295	T	0.02047	0.0064	N	0.14661	0.345	0.21675	N	0.999599	B	0.22346	0.068	B	0.15484	0.013	T	0.45056	-0.9287	10	0.30854	T	0.27	-2.7081	8.4029	0.32597	0.1755:0.0:0.0:0.8245	.	301	Q9UL58	ZN215_HUMAN	L	301	ENSP00000278319:F301L;ENSP00000393202:F301L	ENSP00000278319:F301L	F	+	1	0	ZNF215	6933685	0.001000	0.12720	0.001000	0.08648	0.011000	0.07611	0.972000	0.29409	0.757000	0.33036	0.533000	0.62120	TTT	T|0.996;C|0.004	0.004	strong		0.353	ZNF215-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384550.1			C	6977109	T	C	6977109	3	2	25	1	0	0	0	0	1	0	0	0	17786	1841	64	3	919	3	ZNF215	11	6977109	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	329513	6977109	128029407	452	9361											
NLRP14	338323	hgsc.bcm.edu	37	chr11	7064560	7064560	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gccaagtcgctgccaaaggaAtatggactatgacttacgtg	12	9	11	9	2	0	1	0	1	0	0	1	3	0	3	2	2	2	1	2	2	6	3	rs200574634		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:7064560A>T	ENST00000299481.4	+	4	1649	c.1303A>T	c.(1303-1305)Ata>Tta	p.I435L		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	435	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)		TGCCAAAGGAATATGGACTAT	0.428													A|||	1	0.000199681	0.0	0.0	5008	,	,		20937	0.0		0.001	False		,,,				2504	0.0				p.I435L		Atlas-SNP	.											.	NLRP14	187	.	0			c.A1303T						PASS	.						128	131	130					11																	7064560		2201	4296	6497	SO:0001583	missense	338323	exon4			AAAGGAATATGGA	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.1303A>T	11.37:g.7064560A>T	ENSP00000299481:p.Ile435Leu	171	0	0		136	73	0.536765	NM_176822	Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	37	CCDS7776.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	5.302	0.241082	0.10077	.	.	ENSG00000158077	ENST00000299481	T	0.74421	-0.84	4.48	-0.234	0.13074	.	0.513668	0.17972	N	0.155815	T	0.49389	0.1554	N	0.12637	0.245	0.23542	N	0.997459	B	0.22800	0.075	B	0.21151	0.033	T	0.30736	-0.9968	10	0.17369	T	0.5	.	7.7052	0.28646	0.5723:0.0:0.4277:0.0	.	435	Q86W24	NAL14_HUMAN	L	435	ENSP00000299481:I435L	ENSP00000299481:I435L	I	+	1	0	NLRP14	7021136	0.888000	0.30383	0.733000	0.30861	0.937000	0.57800	0.803000	0.27083	-0.106000	0.12110	-0.256000	0.11100	ATA	A|1.000;T|0.000	0.000	strong		0.428	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822		T	7064560	A	T	7064560	3	4	25	1	0	0	0	0	1	0	0	0	10485	101	4	5	1313	5	NLRP14	11	7064560	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	87451	7064560	127941956	453	9362											
MICAL2	9645	hgsc.bcm.edu	37	chr11	12248590	12248590	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agattcttggcgcaaaaactAtggagaaaatgctgacctca	15	9	9	8	1	2	3	1	1	1	2	2	4	2	3	1	2	2	2	1	2	5	3	rs35228638	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:12248590A>G	ENST00000256194.4	+	15	2195	c.1907A>G	c.(1906-1908)tAt>tGt	p.Y636C	MICAL2_ENST00000527546.1_Missense_Mutation_p.Y636C|MICAL2_ENST00000537344.1_Missense_Mutation_p.Y636C|MICAL2_ENST00000379612.3_Missense_Mutation_p.Y636C|MICAL2_ENST00000342902.5_Missense_Mutation_p.Y636C	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	636					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)		CGCAAAAACTATGGAGAAAAT	0.453													A|||	12	0.00239617	0.0	0.0014	5008	,	,		21389	0.0		0.0109	False		,,,				2504	0.0				p.Y636C		Atlas-SNP	.											.	MICAL2	114	.	0			c.A1907G						PASS	.	A	CYS/TYR	13,4389	19.1+/-41.9	0,13,2188	111	101	104		1907	3.8	1	11	dbSNP_126	104	97,8491	54.0+/-114.7	2,93,4199	yes	missense	MICAL2	NM_014632.2	194	2,106,6387	GG,GA,AA		1.1295,0.2953,0.8468	benign	636/1125	12248590	110,12880	2201	4294	6495	SO:0001583	missense	9645	exon15			AAAACTATGGAGA	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.1907A>G	11.37:g.12248590A>G	ENSP00000256194:p.Tyr636Cys	130	0	0		124	51	0.41129	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Missense_Mutation	SNP	ENST00000256194.4	37	CCDS7809.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	A	7.192	0.591637	0.13812	0.002953	0.011295	ENSG00000133816	ENST00000537344;ENST00000544073;ENST00000256194;ENST00000527546;ENST00000342902;ENST00000379612	T;T;T;T;T	0.60920	0.15;0.15;0.15;0.15;0.24	4.88	3.75	0.43078	.	0.567421	0.17466	N	0.173256	T	0.40222	0.1108	L	0.44542	1.39	0.31618	N	0.650676	B;B;B;B;B;B	0.10296	0.003;0.001;0.001;0.0;0.001;0.0	B;B;B;B;B;B	0.04013	0.001;0.001;0.001;0.0;0.001;0.001	T	0.50457	-0.8826	10	0.46703	T	0.11	.	10.4565	0.44553	0.9224:0.0:0.0776:0.0	rs35228638	169;636;636;636;636;636	B4DYS3;G3XAC8;B7Z849;Q5KTR3;Q5KTR4;O94851	.;.;.;.;.;MICA2_HUMAN	C	636;169;636;636;636;636	ENSP00000441689:Y636C;ENSP00000256194:Y636C;ENSP00000433965:Y636C;ENSP00000344894:Y636C;ENSP00000368932:Y636C	ENSP00000256194:Y636C	Y	+	2	0	MICAL2	12205166	1.000000	0.71417	0.977000	0.42913	0.336000	0.28762	4.903000	0.63272	0.881000	0.35993	0.533000	0.62120	TAT	A|0.992;G|0.008	0.008	strong		0.453	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632		G	12248590	A	G	12248590	3	3	25	1	0	0	0	0	1	0	0	0	9579	449	16	3	1957	3	MICAL2	11	12248590	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	5184030	12248590	122757926	454	9363											
MICAL2	9645	hgsc.bcm.edu	37	chr11	12281414	12281414	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagttcttgcgcagtggccGccattggcaccctggaaggc	8	8	13	12	2	1	0	0	0	1	0	1	1	1	1	3	4	1	3	3	4	2	3	rs148517207		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:12281414G>A	ENST00000256194.4	+	26	3592	c.3304G>A	c.(3304-3306)Gcc>Acc	p.A1102T	MICAL2_ENST00000527546.1_Missense_Mutation_p.A912T|MICAL2_ENST00000537344.1_Missense_Mutation_p.A912T|MICAL2_ENST00000379612.3_Missense_Mutation_p.A876T|RP11-265D17.2_ENST00000527288.1_RNA|MICAL2_ENST00000342902.5_Missense_Mutation_p.A1081T	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	1102					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)		CGCAGTGGCCGCCATTGGCAC	0.597																																					p.A1102T		Atlas-SNP	.											.	MICAL2	114	.	0			c.G3304A						PASS	.	G	THR/ALA	1,4401	2.1+/-5.4	0,1,2200	43	43	43		3304	3.7	0.4	11	dbSNP_134	43	0,8588		0,0,4294	no	missense	MICAL2	NM_014632.2	58	0,1,6494	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	1102/1125	12281414	1,12989	2201	4294	6495	SO:0001583	missense	9645	exon26			GTGGCCGCCATTG	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.3304G>A	11.37:g.12281414G>A	ENSP00000256194:p.Ala1102Thr	108	0	0		141	53	0.375887	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Missense_Mutation	SNP	ENST00000256194.4	37	CCDS7809.1	.	.	.	.	.	.	.	.	.	.	G	6.866	0.529211	0.13127	2.27E-4	0.0	ENSG00000133816	ENST00000537344;ENST00000544073;ENST00000256194;ENST00000527546;ENST00000342902;ENST00000379612	T;T;T;T;T	0.61040	0.14;0.15;0.14;0.15;0.15	5.56	3.68	0.42216	.	0.230508	0.30940	N	0.008579	T	0.40570	0.1122	N	0.24115	0.695	0.09310	N	1	B;D;B;B;B;D	0.67145	0.224;0.972;0.007;0.209;0.007;0.996	B;B;B;B;B;P	0.44518	0.016;0.367;0.003;0.015;0.003;0.452	T	0.22208	-1.0223	10	0.15499	T	0.54	.	9.8179	0.40865	0.2194:0.0:0.7806:0.0	.	445;1081;912;855;876;1102	B4DYS3;G3XAC8;B7Z849;Q5KTR3;Q5KTR4;O94851	.;.;.;.;.;MICA2_HUMAN	T	912;445;1102;912;1081;876	ENSP00000441689:A912T;ENSP00000256194:A1102T;ENSP00000433965:A912T;ENSP00000344894:A1081T;ENSP00000368932:A876T	ENSP00000256194:A1102T	A	+	1	0	MICAL2	12237990	0.987000	0.35691	0.433000	0.26760	0.023000	0.10783	2.954000	0.49113	1.333000	0.45449	0.591000	0.81541	GCC	G|1.000;A|0.000	0.000	weak		0.597	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632		A	12281414	G	A	12281414	3	1	25	1	0	0	0	0	1	0	0	0	9579	1087	38	1	3398	1	MICAL2	11	12281414	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	32824	12281414	122725102	455	9364											
MICALCL	84953	hgsc.bcm.edu	37	chr11	12313845	12313845	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	atggttcctccccgcctcagGtgagtgtccctgagggtcct	4	11	12	14	1	1	2	1	2	0	0	5	2	5	2	6	3	0	1	6	3	0	1	rs200949393		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:12313845G>A	ENST00000256186.2	+	2	420		c.e2+1			NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like						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)		CCCGCCTCAGGTGAGTGTCCC	0.527																																					.		Atlas-SNP	.											.	MICALCL	59	.	0			c.129+1G>A						PASS	.	G		2,3888		0,2,1943	107	106	106			5.4	1	11		106	1,8273		0,1,4136	yes	splice-5	MICALCL	NM_032867.2		0,3,6079	AA,AG,GG		0.0121,0.0514,0.0247			12313845	3,12161	1945	4137	6082	SO:0001630	splice_region_variant	84953	exon2			CCTCAGGTGAGTG	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.129+1G>A	11.37:g.12313845G>A		87	0	0		100	52	0.52	NM_032867	Q7RTP7|Q96JU6	Splice_Site	SNP	ENST00000256186.2	37	CCDS41620.1	.	.	.	.	.	.	.	.	.	.	G	13.36	2.212670	0.39102	5.14E-4	1.21E-4	ENSG00000133808	ENST00000256186	.	.	.	5.39	5.39	0.77823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0104	0.71545	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MICALCL	12270421	1.000000	0.71417	1.000000	0.80357	0.329000	0.28539	4.368000	0.59505	2.671000	0.90904	0.591000	0.81541	.	.	.	weak		0.527	MICALCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386164.1	NM_032867	Intron	A	12313845	G	A	12313845	5	1	25	1	0	0	0	0	0	0	1	0	9581	1275	44	2	132	2	MICALCL	11	12313845	Splice_Site	SNP	G	TCGA-G8-6906-01A-11D-2210-10	32431	12313845	122692671	456	9365											
TMEM86A	144110	hgsc.bcm.edu	37	chr11	18723210	18723210	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gacaggtctggtgatggcagCgctgtcgggcctgtgctatg	5	10	17	9	2	1	1	0	1	1	0	2	2	1	1	1	4	2	3	1	4	1	1	rs144559255	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:18723210C>T	ENST00000280734.2	+	3	473	c.377C>T	c.(376-378)gCg>gTg	p.A126V	TMEM86A_ENST00000527002.1_3'UTR	NM_153347.1	NP_699178.1	Q8N2M4	TM86A_HUMAN	transmembrane protein 86A	126						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|skin(2)	11						GTGATGGCAGCGCTGTCGGGC	0.602													C|||	46	0.0091853	0.0	0.0173	5008	,	,		17494	0.0		0.0249	False		,,,				2504	0.0092				p.A126V		Atlas-SNP	.											TMEM86A,caecum,carcinoma,-1,1	TMEM86A	29	1	0			c.C377T						PASS	.	C	VAL/ALA	23,4375	29.0+/-57.7	0,23,2176	97	85	89		377	2.6	1	11	dbSNP_134	89	155,8431	75.1+/-137.7	1,153,4139	yes	missense	TMEM86A	NM_153347.1	64	1,176,6315	TT,TC,CC		1.8053,0.523,1.3709	benign	126/241	18723210	178,12806	2199	4293	6492	SO:0001583	missense	144110	exon3			TGGCAGCGCTGTC	BC035692	CCDS7844.1	11p15.1	2005-10-28				ENSG00000151117			26890	protein-coding gene	gene with protein product							Standard	NM_153347		Approved	FLJ90119	uc001moz.1	Q8N2M4		ENST00000280734.2:c.377C>T	11.37:g.18723210C>T	ENSP00000280734:p.Ala126Val	131	0	0		112	52	0.464286	NM_153347	Q96AJ0	Missense_Mutation	SNP	ENST00000280734.2	37	CCDS7844.1	22	0.010073260073260074	0	0.0	6	0.016574585635359115	0	0.0	16	0.021108179419525065	C	0.322	-0.961477	0.02249	0.00523	0.018053	ENSG00000151117	ENST00000535380;ENST00000280734	T	0.20069	2.1	5.03	2.64	0.31445	.	0.537430	0.19759	N	0.106710	T	0.02848	0.0085	N	0.02403	-0.565	0.19300	N	0.999975	B	0.02656	0.0	B	0.04013	0.001	T	0.39482	-0.9612	10	0.06891	T	0.86	-2.3684	8.0781	0.30729	0.0:0.0707:0.1359:0.7934	.	126	Q8N2M4	TM86A_HUMAN	V	126	ENSP00000280734:A126V	ENSP00000280734:A126V	A	+	2	0	TMEM86A	18679786	0.054000	0.20591	0.984000	0.44739	0.608000	0.37181	2.275000	0.43399	0.477000	0.27464	-1.402000	0.01139	GCG	C|0.987;T|0.013	0.013	strong		0.602	TMEM86A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387812.1	NM_153347		T	18723210	C	T	18723210	3	4	25	1	0	0	0	0	1	0	0	0	16223	768	27	1	387	1	TMEM86A	11	18723210	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	6409365	18723210	116283306	457	9366											
MRGPRX1	259249	hgsc.bcm.edu	37	chr11	18956210	18956210	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	caactgcgtttcctgtcagcCcgacaagggaaacgatgcac	11	7	10	13	3	1	0	1	0	0	0	2	3	2	1	2	1	5	2	2	1	3	1	rs139433266		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:18956210C>G	ENST00000302797.3	-	1	346	c.122G>C	c.(121-123)gGg>gCg	p.G41A	RP11-583F24.8_ENST00000528646.1_RNA|MRGPRX1_ENST00000526914.1_5'UTR	NM_147199.3	NP_671732.3	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	41					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						TCCTGTCAGCCCGACAAGGGA	0.562																																					p.G41A		Atlas-SNP	.											MRGPRX1,NS,carcinoma,-1,1	MRGPRX1	84	1	0			c.G122C						PASS	.	C	ALA/GLY	1,4387		0,1,2193	187	176	180		122	0.3	0	11	dbSNP_134	180	1,8571		0,1,4285	no	missense	MRGPRX1	NM_147199.3	60	0,2,6478	GG,GC,CC		0.0117,0.0228,0.0154	possibly-damaging	41/323	18956210	2,12958	2194	4286	6480	SO:0001583	missense	259249	exon1			GTCAGCCCGACAA		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.122G>C	11.37:g.18956210C>G	ENSP00000305766:p.Gly41Ala	112	0	0		127	73	0.574803	NM_147199	Q4V9L2|Q8TDD8|Q8TDD9	Missense_Mutation	SNP	ENST00000302797.3	37	CCDS7846.1	.	.	.	.	.	.	.	.	.	.	.	11.92	1.781660	0.31502	2.28E-4	1.17E-4	ENSG00000170255	ENST00000302797	T	0.18016	2.24	2.43	0.304	0.15796	.	0.000000	0.64402	D	0.000005	T	0.19765	0.0475	L	0.52905	1.665	0.09310	N	1	P	0.39003	0.654	P	0.47162	0.54	T	0.09100	-1.0690	10	0.66056	D	0.02	.	4.8899	0.13722	0.2076:0.6607:0.0:0.1317	.	41	Q96LB2	MRGX1_HUMAN	A	41	ENSP00000305766:G41A	ENSP00000305766:G41A	G	-	2	0	MRGPRX1	18912786	0.950000	0.32346	0.000000	0.03702	0.004000	0.04260	2.750000	0.47500	0.075000	0.16796	0.491000	0.48974	GGG	C|1.000;G|0.000	0.000	weak		0.562	MRGPRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369913.1	NM_147199		G	18956210	C	G	18956210	3	3	25	1	0	0	0	0	1	0	0	0	9775	623	22	4	850	4	MRGPRX1	11	18956210	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	233000	18956210	116050306	458	9367											
CCDC34	91057	hgsc.bcm.edu	37	chr11	27379026	27379026	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acacctcccatggtgtcaggCggctttctggtaagcgcacc	7	9	11	14	2	2	0	1	0	1	0	3	0	3	0	3	4	1	3	3	4	1	2	rs138159804		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:27379026C>T	ENST00000328697.6	-	2	1095	c.422G>A	c.(421-423)cGc>cAc	p.R141H	CCDC34_ENST00000317945.6_Missense_Mutation_p.R141H	NM_030771.1	NP_110398.1	Q96HJ3	CCD34_HUMAN	coiled-coil domain containing 34	141										endometrium(2)|large_intestine(4)|lung(1)|prostate(1)|urinary_tract(1)	9						TGGTGTCAGGCGGCTTTCTGG	0.428																																					p.R141H		Atlas-SNP	.											.	CCDC34	48	.	0			c.G422A						PASS	.	C	HIS/ARG,HIS/ARG	0,4404		0,0,2202	150	139	143		422,422	1.2	0.1	11	dbSNP_134	143	3,8595	3.0+/-9.4	0,3,4296	yes	missense,missense	CCDC34	NM_030771.1,NM_080654.2	29,29	0,3,6498	TT,TC,CC		0.0349,0.0,0.0231	benign,benign	141/374,141/230	27379026	3,12999	2202	4299	6501	SO:0001583	missense	91057	exon2			GTCAGGCGGCTTT	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.422G>A	11.37:g.27379026C>T	ENSP00000330240:p.Arg141His	187	0	0		151	72	0.476821	NM_030771	B2R8G2|Q8IX69|Q9H2A6|Q9Y599	Missense_Mutation	SNP	ENST00000328697.6	37	CCDS31448.1	.	.	.	.	.	.	.	.	.	.	C	12.06	1.825829	0.32237	0.0	3.49E-4	ENSG00000109881	ENST00000328697;ENST00000317945	T;T	0.22743	1.94;1.94	5.39	1.21	0.21127	.	0.954155	0.08803	N	0.891475	T	0.11367	0.0277	N	0.14661	0.345	0.09310	N	1	B;B	0.11235	0.004;0.001	B;B	0.04013	0.001;0.001	T	0.32322	-0.9911	10	0.38643	T	0.18	7.2849	4.8599	0.13579	0.0:0.4435:0.2345:0.322	.	141;141	Q96HJ3-2;Q96HJ3	.;CCD34_HUMAN	H	141	ENSP00000330240:R141H;ENSP00000321563:R141H	ENSP00000321563:R141H	R	-	2	0	CCDC34	27335602	0.026000	0.19158	0.117000	0.21633	0.190000	0.23558	0.086000	0.14935	0.361000	0.24292	-0.812000	0.03155	CGC	C|1.000;T|0.000	0.000	weak		0.428	CCDC34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388396.2	NM_030771		T	27379026	C	T	27379026	3	4	25	1	0	0	0	0	1	0	0	0	2809	768	27	1	803	1	CCDC34	11	27379026	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	8422816	27379026	107627490	459	9368											
GYLTL1B	120071	hgsc.bcm.edu	37	chr11	45948962	45948962	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctcagcagttcctgcatttCgtcgaggcctcaccagtgct	6	11	10	14	2	2	0	2	0	0	0	5	1	3	0	3	1	3	5	3	1	0	2	rs138897549		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:45948962C>T	ENST00000531526.1	+	11	1533	c.1422C>T	c.(1420-1422)ttC>ttT	p.F474F	GYLTL1B_ENST00000401752.1_Silent_p.F474F|GYLTL1B_ENST00000389968.3_Silent_p.F201F|GYLTL1B_ENST00000325468.5_Silent_p.F474F|GYLTL1B_ENST00000529052.1_Silent_p.F443F|GYLTL1B_ENST00000536139.1_Silent_p.F443F	NM_152312.3	NP_689525.3	Q8N3Y3	LARG2_HUMAN	glycosyltransferase-like 1B	474				HF -> IS (in Ref. 5; AAG23791). {ECO:0000305}.	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)		TCCTGCATTTCGTCGAGGCCT	0.617													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20898	0.0		0.0	False		,,,				2504	0.0				p.F474F		Atlas-SNP	.											.	GYLTL1B	45	.	0			c.C1422T						PASS	.	C		0,4406		0,0,2203	89	74	79		1422	-1.3	0.7	11	dbSNP_134	79	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	GYLTL1B	NM_152312.3		0,1,6501	TT,TC,CC		0.0116,0.0,0.0077		474/722	45948962	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	120071	exon11			GCATTTCGTCGAG		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.1422C>T	11.37:g.45948962C>T		84	0	0		83	32	0.385542	NM_152312	A6NN75|Q8N8Y6|Q8NAK3|Q8WY62	Silent	SNP	ENST00000531526.1	37	CCDS31473.1																																																																																			C|1.000;T|0.000	0.000	strong		0.617	GYLTL1B-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392572.1	NM_152312		T	45948962	C	T	45948962	2	4	25	1	0	0	0	0	0	0	0	1	6916	883	31	1		1	GYLTL1B	11	45948962	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	18569936	45948962	89057554	460	9369											
AMBRA1	55626	hgsc.bcm.edu	37	chr11	46431914	46431914	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtactcaacaccagagtttaAggccctaaaaatcagttggg	14	9	9	9	0	2	1	2	0	0	1	2	1	2	1	2	2	2	3	2	2	6	5			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:46431914A>C	ENST00000458649.2	-	16	3539	c.3121T>G	c.(3121-3123)Tta>Gta	p.L1041V	AMBRA1_ENST00000528950.1_Missense_Mutation_p.L1012V|AMBRA1_ENST00000298834.3_Missense_Mutation_p.L981V|AMBRA1_ENST00000314845.3_Missense_Mutation_p.L951V|AMBRA1_ENST00000534300.1_Missense_Mutation_p.L981V|AMBRA1_ENST00000426438.1_Missense_Mutation_p.L1012V|AMBRA1_ENST00000533727.1_Missense_Mutation_p.L922V			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	1041					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)		CCAGAGTTTAAGGCCCTAAAA	0.507																																					p.L1044V		Atlas-SNP	.											.	AMBRA1	201	.	0			c.T3130G						PASS	.						91	81	84					11																	46431914		2201	4299	6500	SO:0001583	missense	55626	exon18			AGTTTAAGGCCCT	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.3121T>G	11.37:g.46431914A>C	ENSP00000415327:p.Leu1041Val	56	0	0		87	34	0.390805	NM_001267782	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Missense_Mutation	SNP	ENST00000458649.2	37		.	.	.	.	.	.	.	.	.	.	A	18.00	3.526152	0.64860	.	.	ENSG00000110497	ENST00000314845;ENST00000533727;ENST00000534300;ENST00000426438;ENST00000298834;ENST00000458649;ENST00000528950	T;T;T;T;T;T;T	0.71222	-0.37;-0.55;-0.14;-0.27;-0.14;-0.24;-0.27	5.86	5.86	0.93980	.	0.249598	0.35436	N	0.003219	T	0.54415	0.1857	N	0.12182	0.205	0.41696	D	0.989373	B;B;B;B;P;B	0.34639	0.012;0.116;0.106;0.25;0.461;0.116	B;B;B;B;B;B	0.32393	0.006;0.103;0.042;0.103;0.145;0.103	T	0.62300	-0.6883	10	0.87932	D	0	.	14.8261	0.70113	1.0:0.0:0.0:0.0	.	1041;1012;981;922;1044;951	Q9C0C7;Q9C0C7-3;Q9C0C7-2;G3V193;Q9C0C7-5;Q9C0C7-4	AMRA1_HUMAN;.;.;.;.;.	V	951;922;981;1012;981;1041;1012	ENSP00000318313:L951V;ENSP00000433372:L922V;ENSP00000431926:L981V;ENSP00000410899:L1012V;ENSP00000298834:L981V;ENSP00000415327:L1041V;ENSP00000433945:L1012V	ENSP00000298834:L981V	L	-	1	2	AMBRA1	46388490	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.398000	0.59697	2.240000	0.73641	0.533000	0.62120	TTA	.	.	none		0.507	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749		C	46431914	A	C	46431914	3	2	25	1	0	0	0	0	1	0	0	0	565	69	3	5	787	5	AMBRA1	11	46431914	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	482952	46431914	88574602	461	9370											
PTPRJ	5795	hgsc.bcm.edu	37	chr11	48157625	48157625	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttgacatccacgtggtctaCgtcaccaccacggagatgtg	9	10	10	12	3	2	2	1	1	1	1	3	3	3	2	3	2	1	0	3	2	1	2	rs148782546	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:48157625C>T	ENST00000418331.2	+	9	2002	c.1650C>T	c.(1648-1650)taC>taT	p.Y550Y		NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	550	Fibronectin type-III 6. {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						ACGTGGTCTACGTCACCACCA	0.512													C|||	12	0.00239617	0.0	0.0	5008	,	,		21414	0.0		0.0119	False		,,,				2504	0.0				p.Y550Y		Atlas-SNP	.											PTPRJ_ENST00000418331,caecum,carcinoma,0,2	PTPRJ	225	2	0			c.C1650T						PASS	.	C		3,4399	6.2+/-15.9	0,3,2198	184	160	168		1650	-11.2	0	11	dbSNP_134	168	3,8593	3.0+/-9.4	0,3,4295	no	coding-synonymous	PTPRJ	NM_002843.3		0,6,6493	TT,TC,CC		0.0349,0.0682,0.0462		550/1338	48157625	6,12992	2201	4298	6499	SO:0001819	synonymous_variant	5795	exon9			GGTCTACGTCACC	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.1650C>T	11.37:g.48157625C>T		212	0	0		246	127	0.51626	NM_002843	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Silent	SNP	ENST00000418331.2	37	CCDS7945.1																																																																																			C|0.998;T|0.002	0.002	strong		0.512	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1			T	48157625	C	T	48157625	2	4	25	1	0	0	0	0	0	0	0	1	12819	547	19	1		1	PTPRJ	11	48157625	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1725711	48157625	86848891	462	9371											
OR5AK2	390181	hgsc.bcm.edu	37	chr11	56757056	56757056	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ttcctacatctacatcatggCcaccatcctgaaaatgtctt	11	13	4	13	0	3	1	1	1	2	0	5	1	5	1	4	1	2	0	4	1	4	4			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:56757056C>T	ENST00000326855.2	+	1	710	c.668C>T	c.(667-669)gCc>gTc	p.A223V		NM_001005323.1	NP_001005323.1	Q8NH90	O5AK2_HUMAN	olfactory receptor, family 5, subfamily AK, member 2	223						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(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21						TACATCATGGCCACCATCCTG	0.433																																					p.A223V		Atlas-SNP	.											.	OR5AK2	45	.	0			c.C668T						PASS	.						175	160	165					11																	56757056		2201	4296	6497	SO:0001583	missense	390181	exon1			TCATGGCCACCAT	AB065496	CCDS31538.1	11q11	2012-08-09			ENSG00000181273	ENSG00000181273		"GPCR / Class A : Olfactory receptors"	15251	protein-coding gene	gene with protein product							Standard	NM_001005323		Approved		uc010rjp.2	Q8NH90	OTTHUMG00000167019	ENST00000326855.2:c.668C>T	11.37:g.56757056C>T	ENSP00000322784:p.Ala223Val	290	0	0		313	118	0.376997	NM_001005323	B2RNZ9	Missense_Mutation	SNP	ENST00000326855.2	37	CCDS31538.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.735318	0.00681	.	.	ENSG00000181273	ENST00000326855	T	0.36157	1.27	3.97	2.05	0.26809	GPCR, rhodopsin-like superfamily (1);	0.590959	0.13870	N	0.357078	T	0.16811	0.0404	N	0.12853	0.265	0.09310	N	1	B	0.15719	0.014	B	0.24006	0.05	T	0.25779	-1.0122	10	0.19147	T	0.46	-0.0979	2.6585	0.05019	0.1802:0.5133:0.1997:0.1068	.	223	Q8NH90	O5AK2_HUMAN	V	223	ENSP00000322784:A223V	ENSP00000322784:A223V	A	+	2	0	OR5AK2	56513632	0.000000	0.05858	0.001000	0.08648	0.044000	0.14063	-0.408000	0.07169	0.435000	0.26365	0.400000	0.26472	GCC	.	.	none		0.433	OR5AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392446.1	NM_001005323		T	56757056	C	T	56757056	3	4	25	1	0	0	0	0	1	0	0	0	11151	739	26	2	670	2	OR5AK2	11	56757056	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	8599431	56757056	78249460	463	9372											
TNKS1BP1	85456	hgsc.bcm.edu	37	chr11	57069375	57069375	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcggctctgaggttcctccActacctcttcatctgaagat	7	12	9	13	1	4	3	1	2	3	1	6	3	6	3	3	3	1	2	3	3	2	3	rs34069781	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57069375A>G	ENST00000532437.1	-	8	5188	c.4877T>C	c.(4876-4878)gTg>gCg	p.V1626A	TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.V1626A			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1626	Arg/Glu/Lys-rich (charged).				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)				AGGTTCCTCCACTACCTCTTC	0.612													A|||	101	0.0201677	0.0023	0.0389	5008	,	,		17084	0.002		0.0447	False		,,,				2504	0.0245				p.V1626A		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.T4877C						PASS	.	A	ALA/VAL	46,4356	46.7+/-81.2	0,46,2155	78	72	74		4877	1.2	0.1	11	dbSNP_126	74	402,8190	128.3+/-186.6	8,386,3902	yes	missense	TNKS1BP1	NM_033396.2	64	8,432,6057	GG,GA,AA		4.6788,1.045,3.4477	benign	1626/1730	57069375	448,12546	2201	4296	6497	SO:0001583	missense	85456	exon9			TCCTCCACTACCT	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.4877T>C	11.37:g.57069375A>G	ENSP00000437271:p.Val1626Ala	55	0	0		60	18	0.3	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	37	CCDS7951.1	56	0.02564102564102564	2	0.0040650406504065045	14	0.03867403314917127	2	0.0034965034965034965	38	0.05013192612137203	A	1.725	-0.495729	0.04291	0.01045	0.046788	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.29917	1.55;1.55	4.94	1.18	0.20946	.	0.844445	0.10282	N	0.693393	T	0.03053	0.0090	L	0.35723	1.085	0.09310	N	1	B;B	0.15930	0.015;0.0	B;B	0.16722	0.016;0.002	T	0.26744	-1.0094	10	0.20519	T	0.43	-7.5445	4.0079	0.09610	0.595:0.0:0.2591:0.1459	rs34069781	1626;208	Q9C0C2;Q86TK2	TB182_HUMAN;.	A	1626	ENSP00000350990:V1626A;ENSP00000437271:V1626A	ENSP00000350990:V1626A	V	-	2	0	TNKS1BP1	56825951	0.003000	0.15002	0.065000	0.19835	0.987000	0.75469	0.402000	0.20965	0.226000	0.20979	0.459000	0.35465	GTG	A|0.968;G|0.032;T|0.000	0.032	strong		0.612	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396		G	57069375	A	G	57069375	3	3	25	1	0	0	0	0	1	0	0	0	16335	159	6	3	324	3	TNKS1BP1	11	57069375	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	312319	57069375	77937141	464	9373			1	42		8	8	11674	N	T_G_C_A	4.843729e-08
TNKS1BP1	85456	hgsc.bcm.edu	37	chr11	57069568	57069568	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtagagtcctggaacaggTgtgcatccgagtctgctgcc	7	10	13	11	1	1	1	0	0	1	1	3	3	3	2	3	2	4	3	3	2	2	1	rs35272228	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57069568T>C	ENST00000532437.1	-	7	5125	c.4814A>G	c.(4813-4815)cAc>cGc	p.H1605R	TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.H1605R			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1605	Arg/Glu/Lys-rich (charged).				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)				CTGGAACAGGTGTGCATCCGA	0.597													C|||	101	0.0201677	0.0023	0.0389	5008	,	,		18503	0.002		0.0447	False		,,,				2504	0.0245				p.H1605R		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.A4814G						PASS	.	C	ARG/HIS	46,4356	822.0+/-416.4	0,46,2155	118	117	117		4814	4.3	0.7	11	dbSNP_126	117	402,8190	800.9+/-407.4	8,386,3902	yes	missense	TNKS1BP1	NM_033396.2	29	8,432,6057	CC,CT,TT		4.6788,1.045,3.4477	benign	1605/1730	57069568	448,12546	2201	4296	6497	SO:0001583	missense	85456	exon8			AACAGGTGTGCAT	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.4814A>G	11.37:g.57069568T>C	ENSP00000437271:p.His1605Arg	55	0	0		58	23	0.396552	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	37	CCDS7951.1	56	0.02564102564102564	2	0.0040650406504065045	14	0.03867403314917127	2	0.0034965034965034965	38	0.05013192612137203	C	2.177	-0.388487	0.04932	0.01045	0.046788	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.27402	1.67;1.67	5.22	4.31	0.51392	.	0.082812	0.51477	N	0.000091	T	0.00936	0.0031	N	0.00289	-1.7	0.09310	N	0.999997	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33701	-0.9858	10	0.05959	T	0.93	-9.0253	9.3555	0.38164	0.0:0.8307:0.0:0.1693	rs35272228	1605;187	Q9C0C2;Q86TK2	TB182_HUMAN;.	R	1605	ENSP00000350990:H1605R;ENSP00000437271:H1605R	ENSP00000350990:H1605R	H	-	2	0	TNKS1BP1	56826144	0.228000	0.23718	0.705000	0.30386	0.649000	0.38597	0.896000	0.28377	0.608000	0.30000	-0.974000	0.02594	CAC	T|0.969;C|0.031	0.031	strong		0.597	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396		C	57069568	T	C	57069568	3	2	25	1	0	0	0	0	1	0	0	0	16335	1696	59	3	391	3	TNKS1BP1	11	57069568	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	193	57069568	77936948	465	9374			1	42		8	8	11674	N	T_G_C_A	4.843729e-08
TNKS1BP1	85456	hgsc.bcm.edu	37	chr11	57070089	57070089	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctggcctcaccatcaggctgCggcctccaggagggtggaga	7	6	15	13	1	2	1	2	0	0	1	3	3	3	2	4	6	1	1	4	6	0	0	rs34498883	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57070089C>T	ENST00000532437.1	-	6	4838	c.4527G>A	c.(4525-4527)ccG>ccA	p.P1509P	TNKS1BP1_ENST00000358252.3_Silent_p.P1509P			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1509	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)				CATCAGGCTGCGGCCTCCAGG	0.677													G|||	102	0.0203674	0.0023	0.0389	5008	,	,		15780	0.002		0.0457	False		,,,				2504	0.0245				p.P1509P		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.G4527A						PASS	.	G		46,4356		0,46,2155	26	26	26		4527	-4.9	0.9	11	dbSNP_126	26	401,8191		8,385,3903	no	coding-synonymous	TNKS1BP1	NM_033396.2		8,431,6058	TT,TC,CC		4.6671,1.045,3.44		1509/1730	57070089	447,12547	2201	4296	6497	SO:0001819	synonymous_variant	85456	exon7			AGGCTGCGGCCTC	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.4527G>A	11.37:g.57070089C>T		57	0	0		59	24	0.40678	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Silent	SNP	ENST00000532437.1	37	CCDS7951.1																																																																																			C|0.969;T|0.031	0.031	strong		0.677	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396		T	57070089	C	T	57070089	2	4	25	1	0	0	0	0	0	0	0	1	16335	755	27	1		1	TNKS1BP1	11	57070089	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	521	57070089	77936427	466	9375			1	42		8	8	11674	N	T_G_C_A	4.843729e-08
TNKS1BP1	85456	hgsc.bcm.edu	37	chr11	57070170	57070170	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccccggctccttcctcctcCaacaggcccccaaggcccga	6	5	8	22	2	0	0	0	0	0	0	4	1	4	0	9	3	1	1	9	3	2	1	rs34905018	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57070170C>T	ENST00000532437.1	-	6	4757	c.4446G>A	c.(4444-4446)ttG>ttA	p.L1482L	TNKS1BP1_ENST00000358252.3_Silent_p.L1482L			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1482	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)				CTTCCTCCTCCAACAGGCCCC	0.706													c|||	47	0.00938498	0.0015	0.0288	5008	,	,		13982	0.0		0.0229	False		,,,				2504	0.002				p.L1482L		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.G4446A						PASS	.			23,4377		0,23,2177	14	15	14		4446	-2.7	0	11	dbSNP_126	14	196,8390		2,192,4099	no	coding-synonymous	TNKS1BP1	NM_033396.2		2,215,6276	TT,TC,CC		2.2828,0.5227,1.6864		1482/1730	57070170	219,12767	2200	4293	6493	SO:0001819	synonymous_variant	85456	exon7			CTCCTCCAACAGG	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.4446G>A	11.37:g.57070170C>T		39	0	0		52	29	0.557692	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Silent	SNP	ENST00000532437.1	37	CCDS7951.1																																																																																			C|0.987;T|0.013	0.013	strong		0.706	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396		T	57070170	C	T	57070170	2	4	25	1	0	0	0	0	0	0	0	1	16335	593	21	2		2	TNKS1BP1	11	57070170	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	81	57070170	77936346	467	9376			1	42		8	8	11674	N	T_G_C_A	4.843729e-08
TNKS1BP1	85456	hgsc.bcm.edu	37	chr11	57076080	57076080	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctgggcactggctcacccCgcccaccccatgctccctgg	4	7	9	21	1	2	0	1	0	1	0	3	0	3	0	6	3	1	3	6	3	0	0			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57076080C>T	ENST00000532437.1	-	5	4416	c.4105G>A	c.(4105-4107)Ggg>Agg	p.G1369R	TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.G1369R|TNKS1BP1_ENST00000530920.1_5'Flank			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1369	Acidic.				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)				TGGCTCACCCCGCCCACCCCA	0.667																																					p.G1369R		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.G4105A						PASS	.						59	69	65					11																	57076080		2201	4296	6497	SO:0001583	missense	85456	exon6			TCACCCCGCCCAC	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.4105G>A	11.37:g.57076080C>T	ENSP00000437271:p.Gly1369Arg	45	0	0		64	26	0.40625	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	37	CCDS7951.1	.	.	.	.	.	.	.	.	.	.	C	8.708	0.911309	0.17833	.	.	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.28666	1.6;1.6	4.78	1.35	0.21983	.	1.049680	0.07553	N	0.915820	T	0.12944	0.0314	N	0.03608	-0.345	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.31916	-0.9926	10	0.20046	T	0.44	-1.079	6.365	0.21449	0.0:0.4339:0.4537:0.1124	.	1369	Q9C0C2	TB182_HUMAN	R	1369	ENSP00000350990:G1369R;ENSP00000437271:G1369R	ENSP00000350990:G1369R	G	-	1	0	TNKS1BP1	56832656	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	0.405000	0.21015	0.512000	0.28257	0.462000	0.41574	GGG	.	.	none		0.667	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396		T	57076080	C	T	57076080	3	4	25	1	0	0	0	0	1	0	0	0	16335	652	23	1	1108	1	TNKS1BP1	11	57076080	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	5910	57076080	77930436	468	9377			1	42		8	8	11674	N	T_G_C_A	4.843729e-08
TNKS1BP1	85456	hgsc.bcm.edu	37	chr11	57076895	57076895	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctaaatgctgcctctcgcTgggggccaacactgaggcta	8	8	13	12	1	1	1	0	1	1	0	2	1	1	1	2	4	3	4	2	4	4	2	rs35950335	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57076895T>C	ENST00000532437.1	-	5	3601	c.3290A>G	c.(3289-3291)cAg>cGg	p.Q1097R	TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.Q1097R|TNKS1BP1_ENST00000530920.1_5'Flank			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1097	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)				TGCCTCTCGCTGGGGGCCAAC	0.617													C|||	101	0.0201677	0.0023	0.0389	5008	,	,		19520	0.002		0.0447	False		,,,				2504	0.0245				p.Q1097R		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.A3290G						PASS	.	C	ARG/GLN	46,4356	821.9+/-416.4	0,46,2155	76	66	69		3290	2.6	0.1	11	dbSNP_126	69	402,8190	800.7+/-407.4	8,386,3902	yes	missense	TNKS1BP1	NM_033396.2	43	8,432,6057	CC,CT,TT		4.6788,1.045,3.4477	benign	1097/1730	57076895	448,12546	2201	4296	6497	SO:0001583	missense	85456	exon6			TCTCGCTGGGGGC	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.3290A>G	11.37:g.57076895T>C	ENSP00000437271:p.Gln1097Arg	75	0	0		60	34	0.566667	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	37	CCDS7951.1	56	0.02564102564102564	2	0.0040650406504065045	14	0.03867403314917127	2	0.0034965034965034965	38	0.05013192612137203	C	0.621	-0.821246	0.02755	0.01045	0.046788	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.31769	1.48;1.48	5.05	2.58	0.30949	.	0.438549	0.19467	N	0.113554	T	0.03220	0.0094	L	0.29908	0.895	0.09310	N	1	B	0.24576	0.106	B	0.29353	0.101	T	0.16512	-1.0400	10	0.25751	T	0.34	-6.1023	7.9512	0.30017	0.0:0.1873:0.0:0.8127	rs35950335	1097	Q9C0C2	TB182_HUMAN	R	1097	ENSP00000350990:Q1097R;ENSP00000437271:Q1097R	ENSP00000350990:Q1097R	Q	-	2	0	TNKS1BP1	56833471	0.125000	0.22332	0.082000	0.20525	0.005000	0.04900	0.530000	0.23036	0.270000	0.21984	-1.694000	0.00725	CAG	T|0.968;C|0.032	0.032	strong		0.617	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396		C	57076895	T	C	57076895	3	2	25	1	0	0	0	0	1	0	0	0	16335	1580	55	3	1923	3	TNKS1BP1	11	57076895	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	815	57076895	77929621	469	9378			1	42		8	8	11674	N	T_G_C_A	4.843729e-08
TNKS1BP1	85456	hgsc.bcm.edu	37	chr11	57080352	57080352	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgcctccctggtagccagggGgagaggggactcctgtccag	6	7	16	12	0	0	1	0	0	0	1	3	3	3	2	5	5	2	1	5	5	1	1	rs12801000	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57080352G>A	ENST00000532437.1	-	4	2121	c.1810C>T	c.(1810-1812)Ccc>Tcc	p.P604S	TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.P604S|TNKS1BP1_ENST00000530920.1_5'Flank			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	604	Acidic.|Pro-rich.			P -> S (in Ref. 1; AAM15531). {ECO:0000305}.	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)				GTAGCCAGGGGGAGAGGGGAC	0.637													G|||	101	0.0201677	0.0023	0.0389	5008	,	,		18898	0.002		0.0447	False		,,,				2504	0.0245				p.P604S		Atlas-SNP	.											TNKS1BP1,caecum,carcinoma,+1,1	TNKS1BP1	148	1	0			c.C1810T						PASS	.	G	SER/PRO	46,4356	46.0+/-80.4	0,46,2155	53	59	57		1810	1.9	0	11	dbSNP_121	57	399,8193	125.5+/-184.1	8,383,3905	yes	missense	TNKS1BP1	NM_033396.2	74	8,429,6060	AA,AG,GG		4.6439,1.045,3.4247	benign	604/1730	57080352	445,12549	2201	4296	6497	SO:0001583	missense	85456	exon5			CCAGGGGGAGAGG	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.1810C>T	11.37:g.57080352G>A	ENSP00000437271:p.Pro604Ser	112	0	0		136	56	0.411765	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	37	CCDS7951.1	56	0.02564102564102564	2	0.0040650406504065045	14	0.03867403314917127	2	0.0034965034965034965	38	0.05013192612137203	G	12.00	1.805475	0.31961	0.01045	0.046439	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.34275	1.37;1.37	3.89	1.9	0.25705	.	0.255524	0.20503	U	0.091051	T	0.03915	0.0110	L	0.27053	0.805	0.09310	N	1	P	0.36909	0.573	B	0.37780	0.258	T	0.04678	-1.0934	10	0.62326	D	0.03	-0.7947	7.0645	0.25143	0.0:0.1818:0.6143:0.2039	rs12801000	604	Q9C0C2	TB182_HUMAN	S	604	ENSP00000350990:P604S;ENSP00000437271:P604S	ENSP00000350990:P604S	P	-	1	0	TNKS1BP1	56836928	0.002000	0.14202	0.002000	0.10522	0.834000	0.47266	0.618000	0.24373	0.271000	0.22005	0.462000	0.41574	CCC	G|0.968;A|0.032	0.032	strong		0.637	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396		A	57080352	G	A	57080352	3	1	25	1	0	0	0	0	1	0	0	0	16335	1232	43	2	3407	2	TNKS1BP1	11	57080352	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	3457	57080352	77926164	470	9379			1	42		8	8	11674	N	T_G_C_A	4.843729e-08
TNKS1BP1	85456	hgsc.bcm.edu	37	chr11	57081048	57081048	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atggggctccaagacctcagGgggtgggctgctgggtctgg	5	8	19	9	0	2	1	1	0	1	1	3	1	3	1	2	7	1	3	2	7	1	0	rs79638626	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57081048G>C	ENST00000532437.1	-	4	1425	c.1114C>G	c.(1114-1116)Cct>Gct	p.P372A	TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.P372A|TNKS1BP1_ENST00000530920.1_5'Flank			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	372	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)	p.P372A(1)		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)				AAGACCTCAGGGGGTGGGCTG	0.701													G|||	108	0.0215655	0.0023	0.0418	5008	,	,		13311	0.002		0.0487	False		,,,				2504	0.0256				p.P372A		Atlas-SNP	.											TNKS1BP1,NS,haematopoietic_neoplasm,0,1	TNKS1BP1	148	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C1114G						PASS	.	G	ALA/PRO	48,4254		1,46,2104	7	10	9		1114	-6	0	11	dbSNP_132	9	403,8029		9,385,3822	yes	missense	TNKS1BP1	NM_033396.2	27	10,431,5926	CC,CG,GG		4.7794,1.1158,3.5417	benign	372/1730	57081048	451,12283	2151	4216	6367	SO:0001583	missense	85456	exon5			CCTCAGGGGGTGG	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.1114C>G	11.37:g.57081048G>C	ENSP00000437271:p.Pro372Ala	40	0	0		44	23	0.522727	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	37	CCDS7951.1	63	0.028846153846153848	2	0.0040650406504065045	16	0.04419889502762431	2	0.0034965034965034965	43	0.05672823218997362	G	8.473	0.857895	0.17178	0.011158	0.047794	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.29397	1.57;1.57	4.18	-6.04	0.02178	.	.	.	.	.	T	0.00906	0.0030	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.28170	-1.0052	9	0.08381	T	0.77	0.8305	1.441	0.02354	0.1918:0.3296:0.267:0.2116	.	372	Q9C0C2	TB182_HUMAN	A	372	ENSP00000350990:P372A;ENSP00000437271:P372A	ENSP00000350990:P372A	P	-	1	0	TNKS1BP1	56837624	0.001000	0.12720	0.000000	0.03702	0.644000	0.38419	-0.111000	0.10807	-1.098000	0.03038	0.462000	0.41574	CCT	G|0.970;C|0.030	0.030	strong		0.701	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396		C	57081048	G	C	57081048	3	2	25	1	0	0	0	0	1	0	0	0	16335	1232	43	4	4103	4	TNKS1BP1	11	57081048	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	696	57081048	77925468	471	9380			1	42		8	8	11674	N	T_G_C_A	4.843729e-08
SSRP1	6749	hgsc.bcm.edu	37	chr11	57099661	57099661	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggcactgtgatcttgcggttTaccagtgctttcatgacccg	6	13	11	11	2	2	2	1	2	1	0	2	2	2	2	2	2	3	3	2	2	1	4	rs2230648	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57099661T>C	ENST00000278412.2	-	8	1232	c.966A>G	c.(964-966)gtA>gtG	p.V322V		NM_003146.2	NP_003137.1	Q08945	SSRP1_HUMAN	structure specific recognition protein 1	322					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						TCTTGCGGTTTACCAGTGCTT	0.542													C|||	110	0.0219649	0.0136	0.0389	5008	,	,		22838	0.001		0.0388	False		,,,				2504	0.0256				p.V322V	Colon(89;1000 1340 6884 23013 41819)	Atlas-SNP	.											.	SSRP1	75	.	0			c.A966G						PASS	.	C		104,4298	816.5+/-416.3	1,102,2098	113	91	98		966	0.6	1	11	dbSNP_98	98	391,8201	801.2+/-407.4	8,375,3913	no	coding-synonymous	SSRP1	NM_003146.2		9,477,6011	CC,CT,TT		4.5507,2.3626,3.8095		322/710	57099661	495,12499	2201	4296	6497	SO:0001819	synonymous_variant	6749	exon8			GCGGTTTACCAGT	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.966A>G	11.37:g.57099661T>C		73	0	0		48	19	0.395833	NM_003146	Q5BJG8	Silent	SNP	ENST00000278412.2	37	CCDS7952.1																																																																																			T|0.967;C|0.033;A|0.000	0.033	strong		0.542	SSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392460.1	NM_003146		C	57099661	T	C	57099661	2	2	25	1	0	0	0	0	0	0	0	1	15209	1741	61	3		3	SSRP1	11	57099661	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	18613	57099661	77906855	472	9381											
P2RX3	5024	hgsc.bcm.edu	37	chr11	57114109	57114109	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagggctccggactctacGccaacagagtcatggatgtg	10	8	13	10	2	2	2	1	1	1	1	3	4	3	4	2	3	2	1	2	3	3	1	rs34572680	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57114109G>A	ENST00000263314.2	+	2	245	c.211G>A	c.(211-213)Gcc>Acc	p.A71T		NM_002559.3	NP_002550.2	P56373	P2RX3_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 3	71					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						CGGACTCTACGCCAACAGAGT	0.567													G|||	96	0.0191693	0.003	0.0375	5008	,	,		21427	0.004		0.0368	False		,,,				2504	0.0256				p.A71T		Atlas-SNP	.											.	P2RX3	55	.	0			c.G211A						PASS	.	G	THR/ALA	50,4352	50.2+/-85.5	0,50,2151	136	95	109		211	4.7	1	11	dbSNP_126	109	371,8221	123.1+/-182.0	8,355,3933	yes	missense	P2RX3	NM_002559.3	58	8,405,6084	AA,AG,GG		4.318,1.1358,3.24	possibly-damaging	71/398	57114109	421,12573	2201	4296	6497	SO:0001583	missense	5024	exon2			CTCTACGCCAACA	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.211G>A	11.37:g.57114109G>A	ENSP00000263314:p.Ala71Thr	92	0	0		83	39	0.46988	NM_002559	Q6DK37|Q9UQB6	Missense_Mutation	SNP	ENST00000263314.2	37	CCDS7953.1	48	0.02197802197802198	2	0.0040650406504065045	12	0.03314917127071823	4	0.006993006993006993	30	0.0395778364116095	G	13.93	2.384147	0.42308	0.011358	0.04318	ENSG00000109991	ENST00000439993;ENST00000263314	T	0.04156	3.69	4.66	4.66	0.58398	.	0.243784	0.41605	D	0.000844	T	0.00580	0.0019	N	0.04508	-0.205	0.29540	N	0.852188	P	0.45212	0.853	B	0.38106	0.265	T	0.34054	-0.9844	10	0.56958	D	0.05	-25.3858	8.6535	0.34049	0.1014:0.0:0.8986:0.0	rs34572680;rs58315342	71	P56373	P2RX3_HUMAN	T	71	ENSP00000263314:A71T	ENSP00000263314:A71T	A	+	1	0	P2RX3	56870685	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	3.662000	0.54510	2.408000	0.81797	0.561000	0.74099	GCC	G|0.971;A|0.029	0.029	strong		0.567	P2RX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392465.1	NM_002559		A	57114109	G	A	57114109	3	1	25	1	0	0	0	0	1	0	0	0	11350	1087	38	1	217	1	P2RX3	11	57114109	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	14448	57114109	77892407	473	9382											
OR5B21	219968	hgsc.bcm.edu	37	chr11	58275303	58275303	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aactgagctgcacatccatcGtaggagatggccttgtcccc	9	9	10	13	1	0	2	0	1	0	1	3	3	2	2	4	2	3	3	4	2	2	2	rs146345059	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:58275303G>A	ENST00000360374.2	-	1	275	c.276C>T	c.(274-276)taC>taT	p.Y92Y		NM_001005218.1	NP_001005218.1	A6NL26	OR5BL_HUMAN	olfactory receptor, family 5, subfamily B, member 21	92						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)				CACATCCATCGTAGGAGATGG	0.532													G|||	4	0.000798722	0.0	0.0058	5008	,	,		21630	0.0		0.0	False		,,,				2504	0.0				p.Y92Y		Atlas-SNP	.											OR5B21,rectum,NS,0,1	OR5B21	59	1	0			c.C276T						scavenged	.	G		0,4402		0,0,2201	122	96	105		276	2.2	0.5	11	dbSNP_134	105	8,8582	6.4+/-24.3	0,8,4287	no	coding-synonymous	OR5B21	NM_001005218.1		0,8,6488	AA,AG,GG		0.0931,0.0,0.0616		92/310	58275303	8,12984	2201	4295	6496	SO:0001819	synonymous_variant	219968	exon1			TCCATCGTAGGAG		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.276C>T	11.37:g.58275303G>A		134	1	0.00746269		118	54	0.457627	NM_001005218		Silent	SNP	ENST00000360374.2	37	CCDS31552.1																																																																																			G|0.999;A|0.001	0.001	strong		0.532	OR5B21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394891.1	NM_001005218		A	58275303	G	A	58275303	2	1	25	1	0	0	0	0	0	0	0	1	11160	1140	40	1		1	OR5B21	11	58275303	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1161194	58275303	76731213	474	9383											
MS4A6A	64231	hgsc.bcm.edu	37	chr11	59945789	59945789	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tagagagccagagatgataaActaagataaaagagaaaatg	22	6	10	3	0	0	5	0	1	0	4	0	8	0	5	1	0	2	0	1	0	8	4			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:59945789A>G	ENST00000530839.1	-	5	775	c.283T>C	c.(283-285)Ttt>Ctt	p.F95L	MS4A6A_ENST00000412309.2_Splice_Site_p.F123L|MS4A6A_ENST00000529054.1_Splice_Site_p.F123L|MS4A6A_ENST00000426738.2_Splice_Site_p.F50L|MS4A6A_ENST00000420732.2_Splice_Site_p.F95L|MS4A6A_ENST00000533023.1_Intron|MS4A6A_ENST00000528851.1_Splice_Site_p.F95L|MS4A6A_ENST00000529906.1_5'UTR|MS4A6A_ENST00000323961.3_Splice_Site_p.F95L	NM_152852.2	NP_690591.1	Q9H2W1	M4A6A_HUMAN	membrane-spanning 4-domains, subfamily A, member 6A	95						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						GAGATGATAAACTAAGATAAA	0.393																																					p.F123L		Atlas-SNP	.											.	MS4A6A	85	.	0			c.T367C						PASS	.						113	110	111					11																	59945789		2201	4295	6496	SO:0001630	splice_region_variant	64231	exon5			TGATAAACTAAGA	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.283-1T>C	11.37:g.59945789A>G		98	0	0		130	60	0.461538	NM_001247999	A8K755|F8W9K1|Q7Z4E8|Q8TBV7|Q8TEZ4|Q8TEZ5|Q96PG6|Q9H2L1|Q9H2N3|Q9H3V1|Q9HC76	Missense_Mutation	SNP	ENST00000530839.1	37	CCDS7981.1	.	.	.	.	.	.	.	.	.	.	A	19.17	3.775052	0.70107	.	.	ENSG00000110077	ENST00000323961;ENST00000528851;ENST00000420732;ENST00000530839;ENST00000529054;ENST00000426738;ENST00000412309	T;T;T;T;T;T;T	0.03242	4.0;4.0;4.0;4.0;4.0;4.0;4.0	4.73	3.6	0.41247	.	0.201048	0.42821	D	0.000645	T	0.12305	0.0299	M	0.81682	2.555	0.34555	D	0.711745	D;D;D;D;P	0.55385	0.971;0.964;0.971;0.971;0.703	P;P;P;P;B	0.57548	0.716;0.728;0.823;0.823;0.342	T	0.08351	-1.0726	10	0.66056	D	0.02	.	6.9541	0.24562	0.8964:0.0:0.1036:0.0	.	50;123;123;95;95	E7EMT7;F8W9K1;E9PSA9;Q9H2W1;Q9H2W1-3	.;.;.;M4A6A_HUMAN;.	L	95;95;95;95;123;50;123	ENSP00000315878:F95L;ENSP00000431901:F95L;ENSP00000392921:F95L;ENSP00000436979:F95L;ENSP00000435844:F123L;ENSP00000392770:F50L;ENSP00000403212:F123L	ENSP00000315878:F95L	F	-	1	0	MS4A6A	59702365	1.000000	0.71417	0.772000	0.31596	0.009000	0.06853	2.298000	0.43602	0.942000	0.37525	0.533000	0.62120	TTT	.	.	none		0.393	MS4A6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393848.1		Missense_Mutation	G	59945789	A	G	59945789	5	3	25	1	0	0	0	0	0	0	1	0	9873	57	2	3	506	3	MS4A6A	11	59945789	Splice_Site	SNP	A	TCGA-G8-6906-01A-11D-2210-10	1670486	59945789	75060727	475	9384											
TAF6L	10629	hgsc.bcm.edu	37	chr11	62543326	62543326	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggctcatggcggagagcaCgggcctggagctgagcgatg	7	5	18	11	4	1	2	1	1	0	1	1	5	1	3	2	5	3	3	2	5	0	0	rs76769410	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:62543326C>T	ENST00000294168.3	+	2	272	c.71C>T	c.(70-72)aCg>aTg	p.T24M	TMEM223_ENST00000527073.1_Intron	NM_006473.3	NP_006464.1	Q9Y6J9	TAF6L_HUMAN	TAF6-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa	24					chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|histone H3 acetylation (GO:0043966)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	histone deacetylase complex (GO:0000118)|STAGA complex (GO:0030914)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			endometrium(2)|large_intestine(5)|lung(4)|ovary(3)|prostate(1)|skin(1)	16						GCGGAGAGCACGGGCCTGGAG	0.637													C|||	13	0.00259585	0.0015	0.0014	5008	,	,		18124	0.0		0.008	False		,,,				2504	0.002				p.T24M		Atlas-SNP	.											.	TAF6L	39	.	0			c.C71T						PASS	.	C	MET/THR	9,4393	16.8+/-37.8	0,9,2192	69	68	68		71	3.9	1	11	dbSNP_131	68	78,8520	45.4+/-104.0	2,74,4223	yes	missense	TAF6L	NM_006473.3	81	2,83,6415	TT,TC,CC		0.9072,0.2045,0.6692	possibly-damaging	24/623	62543326	87,12913	2201	4299	6500	SO:0001583	missense	10629	exon2			AGAGCACGGGCCT	BC008785	CCDS8035.1	11q12.3	2008-02-01	2002-08-29		ENSG00000162227	ENSG00000162227			17305	protein-coding gene	gene with protein product		602946	"TAF6-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65 kD"			9674425	Standard	NM_006473		Approved	PAF65A	uc001nvc.3	Q9Y6J9	OTTHUMG00000167610	ENST00000294168.3:c.71C>T	11.37:g.62543326C>T	ENSP00000294168:p.Thr24Met	53	0	0		57	33	0.578947	NM_006473	B2RAT0|Q96HA6	Missense_Mutation	SNP	ENST00000294168.3	37	CCDS8035.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	12.19	1.864603	0.32977	0.002045	0.009072	ENSG00000162227	ENST00000294168;ENST00000526261;ENST00000529509	T;T;T	0.42131	0.98;0.98;0.98	4.78	3.86	0.44501	Histone-fold (2);TATA box binding protein associated factor (TAF) (2);	0.211038	0.39615	N	0.001303	T	0.15478	0.0373	N	0.11427	0.14	0.80722	D	1	B;B	0.22146	0.013;0.065	B;B	0.17098	0.006;0.017	T	0.04522	-1.0945	10	0.37606	T	0.19	1.1681	7.4374	0.27164	0.0:0.8078:0.0:0.1922	.	24;24	B4DVM4;Q9Y6J9	.;TAF6L_HUMAN	M	24	ENSP00000294168:T24M;ENSP00000435116:T24M;ENSP00000434662:T24M	ENSP00000294168:T24M	T	+	2	0	TAF6L	62299902	0.996000	0.38824	0.963000	0.40424	0.968000	0.65278	3.349000	0.52217	1.364000	0.46038	0.561000	0.74099	ACG	C|0.995;T|0.005	0.005	strong		0.637	TAF6L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395352.1	NM_006473		T	62543326	C	T	62543326	3	4	25	1	0	0	0	0	1	0	0	0	15546	536	19	1	73	1	TAF6L	11	62543326	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2597537	62543326	72463190	476	9385											
SLC22A20	823	hgsc.bcm.edu	37	chr11	64981818	64981818	+	IGR	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggatctggtgtgtgaggccCgcactctccgagacctggcg	5	8	16	12	3	2	2	0	1	2	1	3	4	2	3	3	4	0	1	3	4	0	0			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:64981818C>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)		GTGTGAGGCCCGCACTCTCCG	0.662																																					p.R135C		Atlas-SNP	.											.	SLC22A20	36	.	0			c.C403T						PASS	.						35	39	38					11																	64981818		2065	4197	6262	SO:0001628	intergenic_variant	440044	exon2			GAGGCCCGCACTC	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		11.37:g.64981818C>T		62	0	0		72	45	0.625	NM_001004326	Q2TTR0|Q6DHV4	Missense_Mutation	SNP	ENST00000527323.1	37	CCDS44644.1																																																																																			.	.	none		0.662	CAPN1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385325.1			T	64981818	C	T	64981818	1	4	25	0	1	0	0	0	0	0	0	0	14466	652	23	1		1	SLC22A20	11	64981818	IGR	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2438492	64981818	70024698	477	9386											
C11orf24	53838	hgsc.bcm.edu	37	chr11	68029738	68029738	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagggggtacagggcttgccGcggtgtcactgggcatgtgc	5	9	18	9	2	1	0	1	0	0	0	1	0	1	0	1	5	3	3	1	5	2	3	rs143548724	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:68029738G>A	ENST00000304271.6	-	4	1127	c.725C>T	c.(724-726)gCg>gTg	p.A242V	C11orf24_ENST00000533310.1_Intron|C11orf24_ENST00000530166.1_5'Flank	NM_022338.3	NP_071733.1	Q96F05	CK024_HUMAN	chromosome 11 open reading frame 24	242	Pro-rich.					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						AGGGCTTGCCGCGGTGTCACT	0.562													G|||	12	0.00239617	0.0	0.0043	5008	,	,		17040	0.0		0.005	False		,,,				2504	0.0041				p.A242V	NSCLC(21;855 905 4198 36694)	Atlas-SNP	.											.	C11orf24	35	.	0			c.C725T						PASS	.	G	VAL/ALA	1,4399	4.2+/-10.8	0,1,2199	110	108	108		725	2.7	0	11	dbSNP_134	108	41,8547	26.3+/-74.7	1,39,4254	yes	missense	C11orf24	NM_022338.3	64	1,40,6453	AA,AG,GG		0.4774,0.0227,0.3234	benign	242/450	68029738	42,12946	2200	4294	6494	SO:0001583	missense	53838	exon4			CTTGCCGCGGTGT	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.725C>T	11.37:g.68029738G>A	ENSP00000307264:p.Ala242Val	452	0	0		475	238	0.501053	NM_022338	Q9H2K4	Missense_Mutation	SNP	ENST00000304271.6	37	CCDS8180.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	12.16	1.854439	0.32791	2.27E-4	0.004774	ENSG00000171067	ENST00000304271	T	0.30448	1.53	4.61	2.73	0.32206	.	1.566200	0.04540	N	0.387933	T	0.20251	0.0487	N	0.14661	0.345	0.21984	N	0.999436	B	0.29862	0.259	B	0.22880	0.042	T	0.26503	-1.0101	10	0.33940	T	0.23	0.7561	9.9733	0.41768	0.1699:0.0:0.8301:0.0	.	242	Q96F05	CK024_HUMAN	V	242	ENSP00000307264:A242V	ENSP00000307264:A242V	A	-	2	0	C11orf24	67786314	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.126000	0.15769	0.487000	0.27698	-0.459000	0.05422	GCG	G|0.998;A|0.002	0.002	strong		0.562	C11orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394750.1	NM_022338		A	68029738	G	A	68029738	3	1	25	1	0	0	0	0	1	0	0	0	1637	1087	38	1	628	1	C11orf24	11	68029738	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	3047920	68029738	66976778	478	9387											
DHCR7	1717	hgsc.bcm.edu	37	chr11	71152459	71152459	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgaggagccaggcttgcaggCcattgatctgatacttgttc	8	12	12	9	0	1	3	0	3	1	0	2	4	1	4	2	3	3	3	2	3	1	5			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:71152459C>T	ENST00000355527.3	-	6	716	c.440G>A	c.(439-441)gGc>gAc	p.G147D	DHCR7_ENST00000407721.2_Missense_Mutation_p.G147D	NM_001163817.1|NM_001360.2	NP_001157289.1|NP_001351.2	Q9UBM7	DHCR7_HUMAN	7-dehydrocholesterol reductase	147			G -> D (in SLOS). {ECO:0000269|PubMed:10677299}.		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						GGCTTGCAGGCCATTGATCTG	0.547									Smith-Lemli-Opitz syndrome																												p.G147D		Atlas-SNP	.											DHCR7_ENST00000355527,NS,haematopoietic_neoplasm,-1,2	DHCR7	98	2	0			c.G440A	GRCh37	CM000680	DHCR7	M		PASS	.						135	105	115					11																	71152459		2200	4294	6494	SO:0001583	missense	1717	exon6	Familial Cancer Database	SLOS type I & II	TGCAGGCCATTGA	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.440G>A	11.37:g.71152459C>T	ENSP00000347717:p.Gly147Asp	155	0	0		142	68	0.478873	NM_001163817	B2R6Z2|O60492|O60717	Missense_Mutation	SNP	ENST00000355527.3	37	CCDS8200.1	.	.	.	.	.	.	.	.	.	.	C	16.46	3.128197	0.56721	.	.	ENSG00000172893	ENST00000407721;ENST00000355527;ENST00000524694;ENST00000527316;ENST00000526780	D;D;D;D	0.99523	-4.85;-4.85;-4.85;-6.08	4.14	4.14	0.48551	.	0.000000	0.85682	D	0.000000	D	0.99625	0.9863	H	0.94306	3.52	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97590	1.0116	10	0.87932	D	0	-30.5655	14.271	0.66152	0.0:1.0:0.0:0.0	.	147	Q9UBM7	DHCR7_HUMAN	D	147;147;159;115;147	ENSP00000384739:G147D;ENSP00000347717:G147D;ENSP00000435047:G115D;ENSP00000435668:G147D	ENSP00000347717:G147D	G	-	2	0	DHCR7	70830107	1.000000	0.71417	0.838000	0.33150	0.133000	0.20885	6.765000	0.74965	2.035000	0.60131	0.313000	0.20887	GGC	.	.	none		0.547	DHCR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394243.1	NM_001360		T	71152459	C	T	71152459	3	4	25	1	0	0	0	0	1	0	0	0	4479	739	26	2	1003	2	DHCR7	11	71152459	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	3122721	71152459	63854057	479	9388											
NUMA1	4926	hgsc.bcm.edu	37	chr11	71725281	71725281	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttagccagctgttccttcaGttgcttcacggtttgccgaa	6	14	9	12	2	2	0	2	0	0	0	3	1	3	0	3	1	4	5	3	1	2	6	rs200298289		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:71725281G>A	ENST00000393695.3	-	15	3599	c.3268C>T	c.(3268-3270)Ctg>Ttg	p.L1090L	NUMA1_ENST00000351960.6_Intron|NUMA1_ENST00000358965.6_Silent_p.L1090L|RP11-849H4.4_ENST00000502284.1_RNA	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						TGTTCCTTCAGTTGCTTCACG	0.562			T	RARA	APL																																p.L1090L		Atlas-SNP	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1	142	.	0			c.C3268T						PASS	.						127	139	135					11																	71725281		2200	4293	6493	SO:0001819	synonymous_variant	4926	exon15			CCTTCAGTTGCTT	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.3268C>T	11.37:g.71725281G>A		167	0	0		209	104	0.497608	NM_006185		Silent	SNP	ENST00000393695.3	37	CCDS31633.1																																																																																			A|0.001;G|0.999	0.001	weak		0.562	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1			A	71725281	G	A	71725281	2	1	25	1	0	0	0	0	0	0	0	1	10759	1020	36	2		2	NUMA1	11	71725281	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	572822	71725281	63281235	480	9389											
PLEKHB1	58473	hgsc.bcm.edu	37	chr11	73371842	73371842	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gactactacgaggtggtgccCcccaatgcacacgaggccac	10	5	11	15	2	0	0	0	0	0	0	0	3	0	0	4	3	4	1	4	3	3	2	rs147173613	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:73371842C>G	ENST00000354190.5	+	7	971	c.540C>G	c.(538-540)ccC>ccG	p.P180P	PLEKHB1_ENST00000227214.6_Silent_p.P126P|PLEKHB1_ENST00000543085.1_Silent_p.P75P|PLEKHB1_ENST00000398494.4_Silent_p.P161P|PLEKHB1_ENST00000398492.4_Silent_p.P145P|PLEKHB1_ENST00000535129.1_Silent_p.P126P	NM_021200.2	NP_067023.1	Q9UF11	PKHB1_HUMAN	pleckstrin homology domain containing, family B (evectins) member 1	180					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						AGGTGGTGCCCCCCAATGCAC	0.637											OREG0021217	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	24	0.00479233	0.0008	0.013	5008	,	,		17175	0.001		0.0129	False		,,,				2504	0.0				p.P180P		Atlas-SNP	.											.	PLEKHB1	16	.	0			c.C540G						PASS	.	C	,,,,	12,4134		0,12,2061	55	63	60		435,483,378,378,540	-6.7	0.3	11	dbSNP_134	60	121,8227		2,117,4055	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEKHB1	NM_001130033.1,NM_001130034.1,NM_001130035.1,NM_001130036.1,NM_021200.2	,,,,	2,129,6116	GG,GC,CC		1.4494,0.2894,1.0645	,,,,	145/209,161/225,126/190,126/190,180/244	73371842	133,12361	2073	4174	6247	SO:0001819	synonymous_variant	58473	exon7			GGTGCCCCCCAAT	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.540C>G	11.37:g.73371842C>G		69	0	0	1144	103	48	0.466019	NM_021200	A8K0Q5|B2RBP1|B7Z716|Q9UBF5|Q9UI37|Q9UI44	Silent	SNP	ENST00000354190.5	37	CCDS44672.1																																																																																			C|0.993;G|0.007	0.007	strong		0.637	PLEKHB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397593.1			G	73371842	C	G	73371842	2	3	25	1	0	0	0	0	0	0	0	1	12073	610	22	4		4	PLEKHB1	11	73371842	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1646561	73371842	61634674	481	9390											
MYO7A	4647	hgsc.bcm.edu	37	chr11	76883797	76883797	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgtccgtccccccagggcGccgagaccaggaagcgctcg	6	3	14	18	6	0	1	0	0	0	1	3	3	2	2	7	2	1	1	7	2	1	0			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:76883797G>A	ENST00000409709.3	+	16	2073	c.1801G>A	c.(1801-1803)Gcc>Acc	p.A601T	MYO7A_ENST00000409619.2_Missense_Mutation_p.A590T|MYO7A_ENST00000409893.1_Missense_Mutation_p.A601T|MYO7A_ENST00000458637.2_Missense_Mutation_p.A601T	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	601	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						CCCCCAGGGCGCCGAGACCAG	0.692																																					p.A601T		Atlas-SNP	.											.	MYO7A	164	.	0			c.G1801A						PASS	.						12	15	14					11																	76883797		1977	4041	6018	SO:0001583	missense	4647	exon16			CAGGGCGCCGAGA	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.1801G>A	11.37:g.76883797G>A	ENSP00000386331:p.Ala601Thr	105	0	0		88	45	0.511364	NM_001127179	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	37	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	G	14.98	2.697112	0.48202	.	.	ENSG00000137474	ENST00000409709;ENST00000409893;ENST00000458637;ENST00000409619;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000343419	D;D;D;D	0.87412	-2.25;-2.25;-2.25;-2.25	4.77	3.84	0.44239	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	T	0.80654	0.4664	L	0.37466	1.105	0.46849	D	0.999226	B;B;B	0.28291	0.206;0.085;0.123	B;B;B	0.26416	0.037;0.022;0.069	T	0.74910	-0.3503	10	0.19590	T	0.45	.	15.0945	0.72223	0.0:0.1428:0.8572:0.0	.	601;601;601	B9A012;F8VUN5;Q13402	.;.;MYO7A_HUMAN	T	601;601;601;590;600;600;477;600	ENSP00000386331:A601T;ENSP00000386689:A601T;ENSP00000392185:A601T;ENSP00000386635:A590T	ENSP00000345075:A477T	A	+	1	0	MYO7A	76561445	0.993000	0.37304	0.994000	0.49952	0.906000	0.53458	5.244000	0.65400	1.107000	0.41642	0.549000	0.68633	GCC	.	.	none		0.692	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		A	76883797	G	A	76883797	3	1	25	1	0	0	0	0	1	0	0	0	10091	1087	38	1	1859	1	MYO7A	11	76883797	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	3511955	76883797	58122719	482	9391											
MYO7A	4647	hgsc.bcm.edu	37	chr11	76924066	76924066	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agtatggggtcagcctcatcGatcccaaaacgaaggtgagc	12	7	12	10	2	2	1	2	1	0	0	4	3	3	1	2	3	3	1	2	3	4	1	rs1132036	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:76924066G>A	ENST00000409709.3	+	47	6696	c.6424G>A	c.(6424-6426)Gat>Aat	p.D2142N	MYO7A_ENST00000605744.1_3'UTR|MYO7A_ENST00000409619.2_Missense_Mutation_p.D2093N|MYO7A_ENST00000458637.2_Missense_Mutation_p.D2102N	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	2142	FERM 2. {ECO:0000255|PROSITE- ProRule:PRU00084}.		D -> N (in dbSNP:rs1132036).		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						CAGCCTCATCGATCCCAAAAC	0.532													G|||	151	0.0301518	0.1089	0.0086	5008	,	,		20348	0.0		0.001	False		,,,				2504	0.0				p.D2142N		Atlas-SNP	.											MYO7A,rectum,carcinoma,0,1	MYO7A	164	1	0			c.G6424A						scavenged	.	G	ASN/ASP,ASN/ASP	312,3634		18,276,1679	61	55	57	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6424,6304	3.8	0.9	11	dbSNP_86	57	2,8300		0,2,4149	yes	missense,missense	MYO7A	NM_000260.3,NM_001127180.1	23,23	18,278,5828	AA,AG,GG		0.0241,7.9067,2.5637	benign,benign	2142/2216,2102/2176	76924066	314,11934	1973	4151	6124	SO:0001583	missense	4647	exon47			CTCATCGATCCCA	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.6424G>A	11.37:g.76924066G>A	ENSP00000386331:p.Asp2142Asn	86	1	0.0116279		67	23	0.343284	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	37	CCDS53683.1	57	0.0260989010989011	52	0.10569105691056911	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	13.65	2.300715	0.40694	0.079067	2.41E-4	ENSG00000137474	ENST00000409709;ENST00000458637;ENST00000409619;ENST00000545136;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000458169	T;T;T;T	0.80123	-1.34;-1.34;-1.34;-1.34	4.74	3.83	0.44106	FERM domain (1);Pleckstrin homology-type (1);	0.201491	0.49916	D	0.000122	T	0.02649	0.0080	N	0.20328	0.56	0.58432	D	0.999998	B;B	0.31485	0.068;0.325	B;B	0.20384	0.014;0.029	T	0.05146	-1.0903	10	0.24483	T	0.36	.	13.242	0.60002	0.0776:0.0:0.9224:0.0	rs1132036;rs3192425;rs7117511;rs11546951;rs17417614;rs52822228;rs1132036	2102;2142	F8VUN5;Q13402	.;MYO7A_HUMAN	N	2142;2102;2093;1315;2141;2111;2018;1284	ENSP00000386331:D2142N;ENSP00000392185:D2102N;ENSP00000386635:D2093N;ENSP00000417017:D1284N	ENSP00000345075:D2018N	D	+	1	0	MYO7A	76601714	1.000000	0.71417	0.932000	0.37286	0.858000	0.48976	5.057000	0.64294	1.117000	0.41842	0.585000	0.79938	GAT	G|0.966;A|0.034	0.034	strong		0.532	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		A	76924066	G	A	76924066	3	1	25	1	0	0	0	0	1	0	0	0	10091	1058	37	1	6640	1	MYO7A	11	76924066	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	40269	76924066	58082450	483	9392											
AQP11	282679	hgsc.bcm.edu	37	chr11	77301385	77301385	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggggcatgtcccccgagacGggtgcggtgaggctattggc	5	7	19	10	3	0	2	0	1	0	1	1	3	1	2	2	6	1	2	2	6	1	2	rs145642525	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:77301385G>A	ENST00000313578.3	+	1	706	c.348G>A	c.(346-348)acG>acA	p.T116T	AQP11_ENST00000528638.1_Intron	NM_173039.2	NP_766627.1	Q8NBQ7	AQP11_HUMAN	aquaporin 11	116					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)			CCCCCGAGACGGGTGCGGTGA	0.612													G|||	6	0.00119808	0.0015	0.0014	5008	,	,		19669	0.0		0.003	False		,,,				2504	0.0				p.T116T		Atlas-SNP	.											.	AQP11	14	.	0			c.G348A						PASS	.	G		1,4399	2.1+/-5.4	0,1,2199	88	70	76		348	0.2	0	11	dbSNP_134	76	12,8572	9.1+/-34.3	0,12,4280	no	coding-synonymous	AQP11	NM_173039.2		0,13,6479	AA,AG,GG		0.1398,0.0227,0.1001		116/272	77301385	13,12971	2200	4292	6492	SO:0001819	synonymous_variant	282679	exon1			CGAGACGGGTGCG	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.348G>A	11.37:g.77301385G>A		85	0	0		113	51	0.451327	NM_173039		Silent	SNP	ENST00000313578.3	37	CCDS8251.1																																																																																			G|0.998;A|0.002	0.002	strong		0.612	AQP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382582.1	NM_173039		A	77301385	G	A	77301385	2	1	25	1	0	0	0	0	0	0	0	1	823	1103	39	1		1	AQP11	11	77301385	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	377319	77301385	57705131	484	9393											
ODZ4	26011	hgsc.bcm.edu	37	chr11	78565314	78565314	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	cccctctaggctccgcgcctCctgggttaggagcctcctgc	3	9	11	18	2	1	0	0	0	1	0	4	1	4	1	7	3	2	2	7	3	2	2	rs17137261	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:78565314C>G	ENST00000278550.7	-	12	1978	c.1516G>C	c.(1516-1518)Gag>Cag	p.E506Q		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	506			E -> Q (in dbSNP:rs17137261).		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)										CTCCGCGCCTCCTGGGTTAGG	0.587													C|||	155	0.0309505	0.0068	0.0504	5008	,	,		16854	0.0317		0.0487	False		,,,				2504	0.0307				p.E506Q		Atlas-SNP	.											.	.	.	.	0			c.G1516C						PASS	.	C	GLN/GLU	17,1367		0,17,675	12	14	14		1516	5.1	1	11	dbSNP_123	14	117,3065		5,107,1479	yes	missense	ODZ4	NM_001098816.2	29	5,124,2154	GG,GC,CC		3.6769,1.2283,2.9347	possibly-damaging	506/2770	78565314	134,4432	692	1591	2283	SO:0001583	missense	26011	exon12			GCGCCTCCTGGGT	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.1516G>C	11.37:g.78565314C>G	ENSP00000278550:p.Glu506Gln	30	0	0		15	9	0.6	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	37	CCDS44688.1	79	0.036172161172161175	4	0.008130081300813009	21	0.058011049723756904	17	0.02972027972027972	37	0.048812664907651716	C	20.2	3.954131	0.73902	0.012283	0.036769	ENSG00000149256	ENST00000278550	T	0.21932	1.98	5.07	5.07	0.68467	.	0.174787	0.49305	D	0.000153	T	0.01592	0.0051	L	0.34521	1.04	0.53005	D	0.999968	P	0.39391	0.671	B	0.29785	0.107	T	0.08973	-1.0696	9	.	.	.	.	18.6486	0.91421	0.0:1.0:0.0:0.0	rs17137261	506	Q6N022	TEN4_HUMAN	Q	506	ENSP00000278550:E506Q	.	E	-	1	0	ODZ4	78242962	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	7.651000	0.83577	2.631000	0.89168	0.561000	0.74099	GAG	C|0.969;G|0.031	0.031	strong		0.587	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			G	78565314	C	G	78565314	3	3	25	1	0	0	0	0	1	0	0	0	10846	864	30	4	6885	4	ODZ4	11	78565314	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1263929	78565314	56441202	485	9394											
MED17	9440	hgsc.bcm.edu	37	chr11	93529674	93529674	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggaggaccacctttatgtcCtagagcataatttgcatcta	11	12	8	10	1	1	1	0	0	1	1	2	3	2	3	3	2	2	2	3	2	4	6			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:93529674C>T	ENST00000251871.3	+	7	1398	c.1111C>T	c.(1111-1113)Cta>Tta	p.L371L	snoU13_ENST00000459243.1_RNA|MED17_ENST00000533367.1_3'UTR	NM_004268.4	NP_004259.3	Q9NVC6	MED17_HUMAN	mediator complex subunit 17	371			L -> P (in MCPHSBA). {ECO:0000269|PubMed:20950787}.		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)				CCTTTATGTCCTAGAGCATAA	0.403																																					p.L371L		Atlas-SNP	.											.	MED17	37	.	0			c.C1111T						PASS	.						157	151	153					11																	93529674		2201	4298	6499	SO:0001819	synonymous_variant	9440	exon7			TATGTCCTAGAGC	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.1111C>T	11.37:g.93529674C>T		55	0	0		83	4	0.0481928	NM_004268	B3KN07|Q9HA81|Q9UNP7|Q9Y2W0|Q9Y660	Silent	SNP	ENST00000251871.3	37	CCDS8295.1																																																																																			.	.	none		0.403	MED17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394800.2	NM_004268		T	93529674	C	T	93529674	2	4	25	1	0	0	0	0	0	0	0	1	9444	680	24	2		2	MED17	11	93529674	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	14964360	93529674	41476842	486	9395											
MAML2	84441	hgsc.bcm.edu	37	chr11	95826485	95826485	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagtctttcgcaggggtgctTggctcataggcaaggtccct	6	12	13	10	1	2	0	1	0	1	0	4	0	3	0	1	5	1	4	1	5	3	4	rs61749253	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:95826485T>C	ENST00000524717.1	-	2	1994	c.710A>G	c.(709-711)cAa>cGa	p.Q237R		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	237					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)				CAGGGGTGCTTGGCTCATAGG	0.478			T	"MECT1, CRTC3"	salivary gland mucoepidermoid								T|||	27	0.00539137	0.0015	0.0043	5008	,	,		19485	0.0		0.0209	False		,,,				2504	0.001				p.Q237R		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2	94	.	0			c.A710G						PASS	.	T	ARG/GLN	12,3878		0,12,1933	122	118	119		710	5.4	0.7	11	dbSNP_129	119	166,8120		2,162,3979	yes	missense	MAML2	NM_032427.1	43	2,174,5912	CC,CT,TT		2.0034,0.3085,1.4619	probably-damaging	237/1157	95826485	178,11998	1945	4143	6088	SO:0001583	missense	84441	exon2			GGTGCTTGGCTCA	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.710A>G	11.37:g.95826485T>C	ENSP00000434552:p.Gln237Arg	307	0	0		286	171	0.597902	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Missense_Mutation	SNP	ENST00000524717.1	37	CCDS44714.1	17	0.007783882783882784	0	0.0	2	0.0055248618784530384	0	0.0	15	0.01978891820580475	T	8.969	0.972374	0.18736	0.003085	0.020034	ENSG00000184384	ENST00000524717;ENST00000440572	T;T	0.47869	0.83;0.83	5.42	5.42	0.78866	.	0.109437	0.42682	D	0.000666	T	0.33847	0.0877	L	0.54323	1.7	0.31335	N	0.684305	D	0.58268	0.982	P	0.52554	0.702	T	0.49283	-0.8956	10	0.17832	T	0.49	-9.134	10.6675	0.45739	0.1428:0.0:0.0:0.8572	rs61749253	237	Q8IZL2	MAML2_HUMAN	R	237	ENSP00000434552:Q237R;ENSP00000412394:Q237R	ENSP00000412394:Q237R	Q	-	2	0	MAML2	95466133	1.000000	0.71417	0.692000	0.30179	0.890000	0.51754	4.231000	0.58639	2.050000	0.60909	0.374000	0.22700	CAA	T|0.990;C|0.010	0.010	strong		0.478	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			C	95826485	T	C	95826485	3	2	25	1	0	0	0	0	1	0	0	0	9215	1812	63	3	2776	3	MAML2	11	95826485	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	2296811	95826485	39180031	487	9396											
CUL5	8065	hgsc.bcm.edu	37	chr11	107965639	107965639	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaactggaggacttgataccGgaagtagaagaattctacaa	16	8	11	6	1	1	3	0	1	1	2	1	7	1	6	1	3	3	1	1	3	8	5	rs146843253	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:107965639G>A	ENST00000393094.2	+	15	2284	c.1668G>A	c.(1666-1668)ccG>ccA	p.P556P		NM_003478.3	NP_003469.2	Q93034	CUL5_HUMAN	cullin 5	556					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)		ACTTGATACCGGAAGTAGAAG	0.353													G|||	5	0.000998403	0.0038	0.0	5008	,	,		16265	0.0		0.0	False		,,,				2504	0.0				p.P556P		Atlas-SNP	.											.	CUL5	71	.	0			c.G1668A						PASS	.	G		4,4398	8.1+/-20.4	0,4,2197	58	63	61		1668	0.6	1	11	dbSNP_134	61	0,8596		0,0,4298	no	coding-synonymous	CUL5	NM_003478.3		0,4,6495	AA,AG,GG		0.0,0.0909,0.0308		556/781	107965639	4,12994	2201	4298	6499	SO:0001819	synonymous_variant	8065	exon15			GATACCGGAAGTA	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.1668G>A	11.37:g.107965639G>A		72	0	0		92	53	0.576087	NM_003478	A8K960|O14766|Q9BZC6	Silent	SNP	ENST00000393094.2	37	CCDS31668.1																																																																																			G|1.000;A|0.000	0.000	strong		0.353	CUL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389429.1			A	107965639	G	A	107965639	2	1	25	1	0	0	0	0	0	0	0	1	4061	1103	39	1		1	CUL5	11	107965639	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	12139154	107965639	27040877	488	9397											
ATM	472	hgsc.bcm.edu	37	chr11	108163487	108163487	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	attgttggtacacttataccCcttgtgtatgagcaggtgga	9	14	11	7	0	0	1	0	1	0	0	0	2	0	2	2	3	3	4	2	3	4	7	rs1800889	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:108163487C>T	ENST00000452508.2	+	31	4767	c.4578C>T	c.(4576-4578)ccC>ccT	p.P1526P	ATM_ENST00000278616.4_Silent_p.P1526P			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1526					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)	CACTTATACCCCTTGTGTATG	0.358			"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)			C|||	77	0.0153754	0.003	0.0288	5008	,	,		18654	0.0		0.0398	False		,,,				2504	0.0133				p.P1526P		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	.	ATM	1657	.	0			c.C4578T						PASS	.	C		43,4359	44.6+/-78.6	0,43,2158	197	173	181		4578	-0.5	0.9	11	dbSNP_89	181	438,8158	133.0+/-190.5	21,396,3881	no	coding-synonymous	ATM	NM_000051.3		21,439,6039	TT,TC,CC		5.0954,0.9768,3.7006		1526/3057	108163487	481,12517	2201	4298	6499	SO:0001819	synonymous_variant	472	exon30	Familial Cancer Database	AT, Louis-Bar syndrome	TATACCCCTTGTG	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.4578C>T	11.37:g.108163487C>T		164	0	0		147	67	0.455782	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Silent	SNP	ENST00000452508.2	37	CCDS31669.1																																																																																			C|0.972;T|0.028	0.028	strong		0.358	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		T	108163487	C	T	108163487	2	4	25	1	0	0	0	0	0	0	0	1	1109	610	22	2		2	ATM	11	108163487	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	197848	108163487	26843029	489	9398											
ZNF259	8882	hgsc.bcm.edu	37	chr11	116652892	116652892	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acctggtccatcttctggctAaactcctgtagtctctccgt	6	14	7	14	1	3	0	0	0	3	0	7	0	6	0	4	2	1	2	4	2	3	3	rs11550892	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:116652892A>T	ENST00000227322.3	-	12	1220	c.1161T>A	c.(1159-1161)ttT>ttA	p.F387L		NM_003904.3	NP_003895.1	O75312	ZPR1_HUMAN		387					apoptotic process involved in development (GO:1902742)|axon development (GO:0061564)|Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA endoreduplication (GO:0042023)|inner cell mass cell proliferation (GO:0001833)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of motor neuron apoptotic process (GO:2000672)|positive regulation of gene expression (GO:0010628)|positive regulation of growth (GO:0045927)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of RNA splicing (GO:0033120)|positive regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071931)|pre-mRNA catabolic process (GO:1990261)|regulation of myelination (GO:0031641)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)|spinal cord development (GO:0021510)|trophectodermal cell proliferation (GO:0001834)	axon (GO:0030424)|Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perikaryon (GO:0043204)|SMN complex (GO:0032797)	translation initiation factor binding (GO:0031369)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	9	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;5.61e-06)|all cancers(92;0.000139)|OV - Ovarian serous cystadenocarcinoma(223;0.153)		TCTTCTGGCTAAACTCCTGTA	0.478													A|||	3	0.000599042	0.0	0.0014	5008	,	,		17633	0.0		0.002	False		,,,				2504	0.0				p.F387L		Atlas-SNP	.											.	ZNF259	27	.	0			c.T1161A						PASS	.	A	LEU/PHE	4,4398	8.1+/-20.4	0,4,2197	114	93	100		1161	1.1	1	11	dbSNP_120	100	69,8523	41.7+/-99.0	0,69,4227	yes	missense	ZNF259	NM_003904.3	22	0,73,6424	TT,TA,AA		0.8031,0.0909,0.5618	probably-damaging	387/460	116652892	73,12921	2201	4296	6497	SO:0001583	missense	8882	exon12			CTGGCTAAACTCC																												ENST00000227322.3:c.1161T>A	11.37:g.116652892A>T	ENSP00000227322:p.Phe387Leu	115	0	0		99	47	0.474747	NM_003904	Q2TAA0	Missense_Mutation	SNP	ENST00000227322.3	37	CCDS8375.1	5|5	0.0022893772893772895|0.0022893772893772895	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	4|4	0.005277044854881266|0.005277044854881266	A|A	24.5|24.5	4.534777|4.534777	0.85812|0.85812	9.09E-4|9.09E-4	0.008031|0.008031	ENSG00000109917|ENSG00000109917	ENST00000227322|ENST00000429220	T|.	0.45276|.	0.9|.	6.02|6.02	1.12|1.12	0.20585|0.20585	Zinc finger, ZPR1-type (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.63046|.	0.2478|.	M|M	0.79011|0.79011	2.435|2.435	0.80722|0.80722	D|D	1|1	D|.	0.56035|.	0.974|.	P|.	0.61201|.	0.885|.	T|.	0.64193|.	-0.6465|.	10|.	0.62326|.	D|.	0.03|.	-11.3214|-11.3214	10.2019|10.2019	0.43089|0.43089	0.63:0.0:0.37:0.0|0.63:0.0:0.37:0.0	rs11550892;rs35417469|rs11550892;rs35417469	387|.	O75312|.	ZPR1_HUMAN|.	L|K	387|314	ENSP00000227322:F387L|.	ENSP00000227322:F387L|.	F|X	-|-	3|1	2|0	ZNF259|ZNF259	116158102|116158102	0.888000|0.888000	0.30383|0.30383	0.998000|0.998000	0.56505|0.56505	0.935000|0.935000	0.57460|0.57460	0.349000|0.349000	0.20055|0.20055	-0.047000|-0.047000	0.13423|0.13423	0.533000|0.533000	0.62120|0.62120	TTT|TAG	A|0.996;T|0.004	0.004	strong		0.478	ZNF259-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106283.2			T	116652892	A	T	116652892	3	4	25	1	0	0	0	0	1	0	0	0	17816	359	13	5	230	5	ZNF259	11	116652892	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	8489405	116652892	18353624	490	9399											
UBE4A	9354	hgsc.bcm.edu	37	chr11	118242324	118242324	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctctgctgatcgagatgcAggagagaggcacattttttg	9	12	12	8	1	1	3	0	1	1	2	3	6	1	4	0	2	2	3	0	2	0	3	rs145949976	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:118242324A>G	ENST00000431736.2	+	5	576	c.504A>G	c.(502-504)gcA>gcG	p.A168A	UBE4A_ENST00000252108.3_Silent_p.A168A					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)		ATCGAGATGCAGGAGAGAGGC	0.433													A|||	6	0.00119808	0.0038	0.0014	5008	,	,		16924	0.0		0.0	False		,,,				2504	0.0				p.A168A		Atlas-SNP	.											.	UBE4A	97	.	0			c.A504G						PASS	.	A	,	11,4389	17.9+/-39.9	0,11,2189	138	128	131		504,504	0.3	1	11	dbSNP_134	131	1,8591	1.2+/-3.3	0,1,4295	no	coding-synonymous,coding-synonymous	UBE4A	NM_001204077.1,NM_004788.3	,	0,12,6484	GG,GA,AA		0.0116,0.25,0.0924	,	168/1067,168/1074	118242324	12,12980	2200	4296	6496	SO:0001819	synonymous_variant	9354	exon5			AGATGCAGGAGAG	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.504A>G	11.37:g.118242324A>G		79	0	0		80	48	0.6	NM_004788		Silent	SNP	ENST00000431736.2	37	CCDS8396.1																																																																																			A|0.999;G|0.001	0.001	strong		0.433	UBE4A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398143.1	NM_004788		G	118242324	A	G	118242324	2	3	25	1	0	0	0	0	0	0	0	1	16897	175	7	3		3	UBE4A	11	118242324	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	1589432	118242324	16764192	491	9400											
H2AFX	3014	hgsc.bcm.edu	37	chr11	118965688	118965688	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccctcttagtactcctgggaGgcctgggtggccttcttgcc	3	12	12	14	0	2	0	0	0	2	0	3	1	3	1	5	4	2	1	5	4	2	4	rs1064180	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:118965688G>A	ENST00000530167.1	-	1	489	c.417C>T	c.(415-417)gcC>gcT	p.A139A		NM_002105.2	NP_002096.1	P16104	H2AX_HUMAN	H2A histone family, member X	139					cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|meiotic nuclear division (GO:0007126)|nucleosome assembly (GO:0006334)|positive regulation of DNA repair (GO:0045739)|response to ionizing radiation (GO:0010212)|spermatogenesis (GO:0007283)	condensed nuclear chromosome (GO:0000794)|extracellular vesicular exosome (GO:0070062)|male germ cell nucleus (GO:0001673)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|replication fork (GO:0005657)|site of double-strand break (GO:0035861)|XY body (GO:0001741)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone binding (GO:0042393)			lung(3)	3	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.47e-05)		ACTCCTGGGAGGCCTGGGTGG	0.701								Chromatin Structure			OREG0021395	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	g|||	4	0.000798722	0.0	0.0	5008	,	,		10753	0.0		0.0	False		,,,				2504	0.0041				p.A139A		Atlas-SNP	.											.	H2AFX	8	.	0			c.C417T						PASS	.						17	21	20					11																	118965688		2196	4287	6483	SO:0001819	synonymous_variant	3014	exon1			CTGGGAGGCCTGG	X14850	CCDS8410.1	11q23.3	2011-01-27						"Histones / Replication-independent"	4739	protein-coding gene	gene with protein product		601772		H2AX		8076949	Standard	NM_002105		Approved		uc001pvg.3	P16104		ENST00000530167.1:c.417C>T	11.37:g.118965688G>A		9	0	0	1492	25	12	0.48	NM_002105	Q4ZGJ7|Q6IAS5	Silent	SNP	ENST00000530167.1	37	CCDS8410.1																																																																																			G|0.999;A|0.001	0.001	weak		0.701	H2AFX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388330.2	NM_002105		A	118965688	G	A	118965688	2	1	25	1	0	0	0	0	0	0	0	1	6937	987	35	2		2	H2AFX	11	118965688	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	723364	118965688	16040828	492	9401											
ABCG4	64137	hgsc.bcm.edu	37	chr11	119025270	119025270	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagctgagtgagaagcaggaGgtgaagaaggagctggtgag	14	5	19	3	0	0	5	0	4	0	2	0	8	0	7	0	4	3	3	0	4	4	0	rs200058802	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:119025270G>A	ENST00000449422.2	+	5	713	c.525G>A	c.(523-525)gaG>gaA	p.E175E	ABCG4_ENST00000531739.1_Silent_p.E175E|ABCG4_ENST00000307417.3_Silent_p.E175E	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	175	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)		AGAAGCAGGAGGTGAAGAAGG	0.592													G|||	4	0.000798722	0.0	0.0	5008	,	,		18764	0.0		0.0	False		,,,				2504	0.0041				p.E175E		Atlas-SNP	.											.	ABCG4	77	.	0			c.G525A						PASS	.	G	,	0,4400		0,0,2200	62	60	61		525,525	1.2	1	11		61	2,8588	2.2+/-6.3	0,2,4293	no	coding-synonymous,coding-synonymous	ABCG4	NM_001142505.1,NM_022169.4	,	0,2,6493	AA,AG,GG		0.0233,0.0,0.0154	,	175/647,175/647	119025270	2,12988	2200	4295	6495	SO:0001819	synonymous_variant	64137	exon5			GCAGGAGGTGAAG	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.525G>A	11.37:g.119025270G>A		66	0	0		52	20	0.384615	NM_022169	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Silent	SNP	ENST00000449422.2	37	CCDS8415.1																																																																																			G|0.999;A|0.001	0.001	weak		0.592	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169		A	119025270	G	A	119025270	2	1	25	1	0	0	0	0	0	0	0	1	70	991	35	2		2	ABCG4	11	119025270	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	59582	119025270	15981246	493	9402											
TECTA	7007	hgsc.bcm.edu	37	chr11	121030874	121030874	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacaagtgaatgttccatttAtaactggtttggcaaccaaa	14	12	7	8	0	0	1	0	1	0	0	1	1	1	1	2	2	2	3	2	2	6	5	rs147354818		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:121030874A>G	ENST00000392793.1	+	15	4991	c.4720A>G	c.(4720-4722)Ata>Gta	p.I1574V	TECTA_ENST00000264037.2_Missense_Mutation_p.I1574V			O75443	TECTA_HUMAN	tectorin alpha	1574	VWFD 4. {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)		TGTTCCATTTATAACTGGTTT	0.413													A|||	1	0.000199681	0.0	0.0014	5008	,	,		23199	0.0		0.0	False		,,,				2504	0.0				p.I1574V		Atlas-SNP	.											.	TECTA	329	.	0			c.A4720G						PASS	.	A	VAL/ILE	0,4406		0,0,2203	88	91	90		4720	1.2	1	11	dbSNP_134	90	14,8584	10.5+/-38.8	0,14,4285	yes	missense	TECTA	NM_005422.2	29	0,14,6488	GG,GA,AA		0.1628,0.0,0.1077	benign	1574/2156	121030874	14,12990	2203	4299	6502	SO:0001583	missense	7007	exon14			CCATTTATAACTG	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.4720A>G	11.37:g.121030874A>G	ENSP00000376543:p.Ile1574Val	97	0	0		124	65	0.524194	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	37	CCDS8434.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	A	1.012	-0.687529	0.03328	0.0	0.001628	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.58652	0.32;0.32	4.87	1.2	0.21068	von Willebrand factor, type D domain (3);	0.304381	0.32273	N	0.006326	T	0.23766	0.0575	N	0.02802	-0.49	0.27653	N	0.947345	B	0.06786	0.001	B	0.08055	0.003	T	0.31613	-0.9937	10	0.02654	T	1	.	8.3001	0.32008	0.4982:0.0:0.5018:0.0	.	1574	O75443	TECTA_HUMAN	V	1574	ENSP00000376543:I1574V;ENSP00000264037:I1574V	ENSP00000264037:I1574V	I	+	1	0	TECTA	120536084	0.926000	0.31397	0.991000	0.47740	0.997000	0.91878	1.014000	0.29950	0.033000	0.15463	0.533000	0.62120	ATA	A|0.999;G|0.001	0.001	strong		0.413	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		G	121030874	A	G	121030874	3	3	25	1	0	0	0	0	1	0	0	0	15762	449	16	3	4774	3	TECTA	11	121030874	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	2005604	121030874	13975642	494	9403											
OR8B4	283162	hgsc.bcm.edu	37	chr11	124294127	124294127	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtatcaaagcgtaagagatgAcgatgcttatgctggatagc	13	10	12	6	2	1	2	1	1	0	1	1	5	1	3	0	1	4	4	0	1	5	4	rs370187249		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:124294127A>G	ENST00000356130.3	-	1	662	c.641T>C	c.(640-642)gTc>gCc	p.V214A		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	214						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)		GTAAGAGATGACGATGCTTAT	0.483																																					p.V214A		Atlas-SNP	.											OR8B4,NS,carcinoma,-1,1	OR8B4	60	1	0			c.T641C						PASS	.	A	ALA/VAL	0,4402		0,0,2201	89	75	80		641	1.8	0.4	11		80	1,8597		0,1,4298	no	missense	OR8B4	NM_001005196.1	64	0,1,6499	GG,GA,AA		0.0116,0.0,0.0077	benign	214/310	124294127	1,12999	2201	4299	6500	SO:0001583	missense	283162	exon1			GAGATGACGATGC	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.641T>C	11.37:g.124294127A>G	ENSP00000348449:p.Val214Ala	99	0	0		88	46	0.522727	NM_001005196	B2RNF8|Q6IFQ7	Missense_Mutation	SNP	ENST00000356130.3	37	CCDS31710.1	.	.	.	.	.	.	.	.	.	.	a	5.431	0.264595	0.10294	0.0	1.16E-4	ENSG00000198657	ENST00000356130	T	0.00272	8.36	4.14	1.8	0.24995	GPCR, rhodopsin-like superfamily (1);	0.367346	0.23494	N	0.047561	T	0.00178	0.0005	L	0.33792	1.035	0.09310	N	1	B	0.16603	0.018	B	0.22601	0.04	T	0.40213	-0.9575	10	0.87932	D	0	.	6.2461	0.20818	0.7765:0.0:0.0809:0.1426	.	214	Q96RC9	OR8B4_HUMAN	A	214	ENSP00000348449:V214A	ENSP00000348449:V214A	V	-	2	0	OR8B4	123799337	0.019000	0.18553	0.397000	0.26308	0.088000	0.18126	2.931000	0.48932	0.389000	0.25086	0.533000	0.62120	GTC	.	.	weak		0.483	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196		G	124294127	A	G	124294127	3	3	25	1	0	0	0	0	1	0	0	0	11238	275	10	3	290	3	OR8B4	11	124294127	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	3263253	124294127	10712389	495	9404											
DCPS	28960	hgsc.bcm.edu	37	chr11	126215285	126215285	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gatgaagggagaccatctgcGagtatacctgcactacctgc	11	8	11	11	1	1	2	0	1	1	1	1	5	1	2	3	1	5	2	3	1	4	3	rs140377449	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:126215285G>A	ENST00000263579.4	+	6	1120	c.791G>A	c.(790-792)cGa>cAa	p.R264Q	DCPS_ENST00000530860.1_3'UTR	NM_014026.3	NP_054745.1	Q96C86	DCPS_HUMAN	decapping enzyme, scavenger	264					cellular response to menadione (GO:0036245)|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 cis splicing, via spliceosome (GO:0045292)|mRNA metabolic process (GO:0016071)|negative regulation of programmed cell death (GO:0043069)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	m7G(5')pppN diphosphatase activity (GO:0050072)|RNA 7-methylguanosine cap binding (GO:0000340)			endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00949)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.08)		GACCATCTGCGAGTATACCTG	0.667													G|||	2	0.000399361	0.0	0.0	5008	,	,		18562	0.0		0.0	False		,,,				2504	0.002				p.R264Q		Atlas-SNP	.											.	DCPS	33	.	0			c.G791A						PASS	.	G	GLN/ARG	0,4402		0,0,2201	205	133	157		791	5.2	0.2	11	dbSNP_134	157	11,8585	8.4+/-32.0	0,11,4287	yes	missense	DCPS	NM_014026.3	43	0,11,6488	AA,AG,GG		0.128,0.0,0.0846	probably-damaging	264/338	126215285	11,12987	2201	4298	6499	SO:0001583	missense	28960	exon6			ATCTGCGAGTATA	AF077201	CCDS8473.1	11q24	2008-02-05			ENSG00000110063	ENSG00000110063			29812	protein-coding gene	gene with protein product		610534				12198172, 14523240	Standard	NM_014026		Approved	HSPC015, HINT-5, HSL1	uc001qdp.3	Q96C86	OTTHUMG00000165829	ENST00000263579.4:c.791G>A	11.37:g.126215285G>A	ENSP00000263579:p.Arg264Gln	56	0	0		54	23	0.425926	NM_014026	Q8NHL8|Q9Y2S5	Missense_Mutation	SNP	ENST00000263579.4	37	CCDS8473.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.344847	0.82022	0.0	0.00128	ENSG00000110063	ENST00000263579	D	0.96200	-3.94	5.16	5.16	0.70880	Histidine triad, conserved site (1);Histidine triad-like motif (1);	0.000000	0.85682	D	0.000000	D	0.98385	0.9463	M	0.93375	3.41	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.99364	1.0918	10	0.66056	D	0.02	-12.5139	18.7289	0.91726	0.0:0.0:1.0:0.0	.	264	Q96C86	DCPS_HUMAN	Q	264	ENSP00000263579:R264Q	ENSP00000263579:R264Q	R	+	2	0	DCPS	125720495	1.000000	0.71417	0.226000	0.23910	0.260000	0.26232	9.476000	0.97823	2.421000	0.82119	0.555000	0.69702	CGA	G|0.999;A|0.001	0.001	strong		0.667	DCPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386455.1	NM_014026		A	126215285	G	A	126215285	3	1	25	1	0	0	0	0	1	0	0	0	4303	1058	37	1	813	1	DCPS	11	126215285	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1921158	126215285	8791231	496	9405											
IGSF9B	22997	hgsc.bcm.edu	37	chr11	133801990	133801990	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaacctgcaggggacggccGtccttgttccacttgaccac	7	9	10	15	2	1	1	1	1	0	0	3	2	3	2	5	3	2	2	5	3	1	3	rs375960322		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:133801990G>A	ENST00000321016.8	-	8	1316	c.1086C>T	c.(1084-1086)gaC>gaT	p.D362D	IGSF9B_ENST00000533871.2_Silent_p.D362D			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	362	Ig-like 4.				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)		GGGGACGGCCGTCCTTGTTCC	0.607																																					p.D362D		Atlas-SNP	.											.	IGSF9B	290	.	0			c.C1086T						PASS	.			0,4278		0,0,2139	70	86	81		1086	-8.2	0.8	11		81	1,8453		0,1,4226	no	coding-synonymous	IGSF9B	NM_014987.1		0,1,6365	AA,AG,GG		0.0118,0.0,0.0079		362/1350	133801990	1,12731	2139	4227	6366	SO:0001819	synonymous_variant	22997	exon8			ACGGCCGTCCTTG	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.1086C>T	11.37:g.133801990G>A		143	0	0		155	84	0.541936	NM_014987	G5EA26	Silent	SNP	ENST00000321016.8	37																																																																																				.	.	weak		0.607	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502		A	133801990	G	A	133801990	2	1	25	1	0	0	0	0	0	0	0	1	7615	1136	40	1		1	IGSF9B	11	133801990	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	7586705	133801990	1204526	497	9406											
EFCAB4B	84766	hgsc.bcm.edu	37	chr12	3805977	3805977	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgaagcccttgccttcagcAtcacaggtctgaaagaactc	12	9	8	12	0	3	3	2	2	1	1	4	3	3	3	2	1	4	1	2	1	3	2	rs144314920	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:3805977A>C	ENST00000252322.1	-	4	657	c.189T>G	c.(187-189)gaT>gaG	p.D63E	EFCAB4B_ENST00000440314.2_Missense_Mutation_p.D63E|EFCAB4B_ENST00000444507.1_Missense_Mutation_p.D63E	NM_032680.3	NP_116069.1	Q9BSW2	EFC4B_HUMAN		63	EF-hand 1. {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)			TGCCTTCAGCATCACAGGTCT	0.567													A|||	2	0.000399361	0.0	0.0014	5008	,	,		20268	0.0		0.001	False		,,,				2504	0.0				p.D63E		Atlas-SNP	.											.	EFCAB4B	100	.	0			c.T189G						PASS	.	A	GLU/ASP,GLU/ASP	0,4406		0,0,2203	133	96	108		189,189	-4.5	0	12	dbSNP_134	108	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	EFCAB4B	NM_001144958.1,NM_032680.3	45,45	0,5,6498	CC,CA,AA		0.0581,0.0,0.0384	probably-damaging,probably-damaging	63/732,63/396	3805977	5,13001	2203	4300	6503	SO:0001583	missense	84766	exon4			TTCAGCATCACAG																												ENST00000252322.1:c.189T>G	12.37:g.3805977A>C	ENSP00000252322:p.Asp63Glu	66	0	0		85	42	0.494118	NM_001144958	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000252322.1	37	CCDS8522.1	.	.	.	.	.	.	.	.	.	.	A	18.58	3.653645	0.67472	0.0	5.81E-4	ENSG00000130038	ENST00000440314;ENST00000444507;ENST00000252322	T;D;T	0.95821	-0.03;-3.82;-0.03	5.57	-4.47	0.03525	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.97430	0.9159	M	0.89904	3.07	0.21553	N	0.999645	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	1.0;0.996;0.991	D	0.94659	0.7846	10	0.87932	D	0	-24.417	15.1484	0.72677	0.2367:0.0:0.7633:0.0	.	63;63;63	D7UEQ6;Q9BSW2-2;Q9BSW2	.;.;EFC4B_HUMAN	E	63	ENSP00000409382:D63E;ENSP00000412496:D63E;ENSP00000252322:D63E	ENSP00000252322:D63E	D	-	3	2	EFCAB4B	3676238	0.001000	0.12720	0.009000	0.14445	0.854000	0.48673	-0.320000	0.08028	-0.748000	0.04753	-0.263000	0.10527	GAT	A|1.000;C|0.000	0.000	strong		0.567	EFCAB4B-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398673.1			C	3805977	A	C	3805977	3	2	25	1	0	0	0	0	1	0	0	0	4939	214	8	5	2266	5	EFCAB4B	12	3805977	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10		3805977	130045918	498	9407											
NCAPD2	9918	hgsc.bcm.edu	37	chr12	6634817	6634817	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctgtgggagcgggccacCgagaaggtcgcctgctgtcc	5	7	16	13	3	0	1	0	0	0	1	2	3	1	2	4	3	3	2	4	3	1	0	rs71579347	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:6634817C>T	ENST00000315579.5	+	18	3082	c.2283C>T	c.(2281-2283)acC>acT	p.T761T	NCAPD2_ENST00000542492.1_3'UTR|NCAPD2_ENST00000545962.1_Silent_p.T716T	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	761					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						AGCGGGCCACCGAGAAGGTCG	0.547													C|||	8	0.00159744	0.0	0.0	5008	,	,		18865	0.0		0.0	False		,,,				2504	0.0082				p.T761T		Atlas-SNP	.											.	NCAPD2	99	.	0			c.C2283T						PASS	.	C		0,4406		0,0,2203	78	70	73		2283	-11.7	0	12	dbSNP_130	73	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	NCAPD2	NM_014865.3		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		761/1402	6634817	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	9918	exon18			GGCCACCGAGAAG	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.2283C>T	12.37:g.6634817C>T		116	0	0		87	51	0.586207	NM_014865	D3DUR4|Q8N6U3	Silent	SNP	ENST00000315579.5	37	CCDS8548.1																																																																																			C|0.999;T|0.001	0.001	strong		0.547	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865		T	6634817	C	T	6634817	2	4	25	1	0	0	0	0	0	0	0	1	10214	639	23	1		1	NCAPD2	12	6634817	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2828840	6634817	127217078	499	9408											
APOBEC1	339	hgsc.bcm.edu	37	chr12	7805154	7805154	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gatcactagagtcacaccagGgtgccgactcagaaactctc	12	7	9	13	1	4	2	3	0	1	2	5	4	4	2	2	1	2	0	2	1	2	1	rs61753204	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:7805154G>A	ENST00000229304.4	-	3	342	c.322C>T	c.(322-324)Cct>Tct	p.P108S		NM_001644.3	NP_001635.2	P41238	ABEC1_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	108					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						GTCACACCAGGGTGCCGACTC	0.498													G|||	45	0.00898562	0.0015	0.0072	5008	,	,		-128	0.002		0.0139	False		,,,				2504	0.0225				p.P108S	Pancreas(135;929 1826 4531 10527 41012)	Atlas-SNP	.											.	APOBEC1	43	.	0			c.C322T						PASS	.	G	SER/PRO	14,4392	21.2+/-45.6	1,12,2190	65	64	64		322	3.2	0.2	12	dbSNP_129	64	129,8471	66.7+/-129.0	1,127,4172	yes	missense	APOBEC1	NM_001644.3	74	2,139,6362	AA,AG,GG		1.5,0.3177,1.0995	probably-damaging	108/237	7805154	143,12863	2203	4300	6503	SO:0001583	missense	339	exon3			CACCAGGGTGCCG	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.322C>T	12.37:g.7805154G>A	ENSP00000229304:p.Pro108Ser	86	0	0		80	44	0.55	NM_001644	Q9UE64|Q9UM71	Missense_Mutation	SNP	ENST00000229304.4	37	CCDS8579.1	15	0.006868131868131868	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	G	10.29	1.309349	0.23821	0.003177	0.015	ENSG00000111701	ENST00000229304	T	0.64991	-0.13	4.12	3.23	0.37069	APOBEC-like, N-terminal (1);	0.000000	0.56097	D	0.000039	T	0.66934	0.2840	M	0.73319	2.225	0.26925	N	0.966593	D	0.89917	1.0	D	0.81914	0.995	T	0.60880	-0.7175	10	0.54805	T	0.06	-14.1848	7.9106	0.29789	0.1139:0.0:0.8861:0.0	rs61753204	108	P41238	ABEC1_HUMAN	S	108	ENSP00000229304:P108S	ENSP00000229304:P108S	P	-	1	0	APOBEC1	7696421	0.975000	0.34042	0.171000	0.22900	0.014000	0.08584	2.996000	0.49449	1.105000	0.41606	0.462000	0.41574	CCT	G|0.989;A|0.011	0.011	strong		0.498	APOBEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280523.1	NM_001644		A	7805154	G	A	7805154	3	1	25	1	0	0	0	0	1	0	0	0	787	1232	43	2	400	2	APOBEC1	12	7805154	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1170337	7805154	126046741	500	9409											
GRIN2B	2904	hgsc.bcm.edu	37	chr12	13724742	13724742	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggaagcagttcttaccctgTtttcagggagagcaatgcat	10	12	11	8	0	2	1	1	0	1	1	2	3	2	2	1	2	4	5	1	2	3	4			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:13724742T>C	ENST00000609686.1	-	10	2376	c.2167A>G	c.(2167-2169)Aca>Gca	p.T723A		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	723					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)	TCTTACCCTGTTTTCAGGGAG	0.418																																					p.T723A		Atlas-SNP	.											.	GRIN2B	303	.	0			c.A2167G						PASS	.						235	206	216					12																	13724742		2203	4300	6503	SO:0001583	missense	2904	exon10			ACCCTGTTTTCAG		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.2167A>G	12.37:g.13724742T>C	ENSP00000477455:p.Thr723Ala	144	0	0		163	7	0.0429448	NM_000834	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Missense_Mutation	SNP	ENST00000609686.1	37	CCDS8662.1	.	.	.	.	.	.	.	.	.	.	T	14.21	2.466424	0.43839	.	.	ENSG00000150086	ENST00000279593	T	0.49720	0.77	5.66	5.66	0.87406	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.107478	0.64402	D	0.000004	T	0.40619	0.1124	L	0.33189	0.99	0.58432	D	0.999996	B	0.06786	0.001	B	0.18561	0.022	T	0.16012	-1.0417	10	0.40728	T	0.16	.	16.1922	0.82000	0.0:0.0:0.0:1.0	.	723	Q13224	NMDE2_HUMAN	A	723	ENSP00000279593:T723A	ENSP00000279593:T723A	T	-	1	0	GRIN2B	13616009	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.074000	0.57577	2.280000	0.76307	0.533000	0.62120	ACA	.	.	none		0.418	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2			C	13724742	T	C	13724742	3	2	25	1	0	0	0	0	1	0	0	0	6789	1725	60	3	2303	3	GRIN2B	12	13724742	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	5919588	13724742	120127153	501	9410											
HIST4H4	121504	hgsc.bcm.edu	37	chr12	14923988	14923988	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttggcgcctcccttacccaGccccttgccacctttacctc	4	11	5	21	1	0	0	0	0	0	0	2	0	1	0	8	1	4	0	8	1	2	5			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:14923988G>T	ENST00000539745.1	-	1	77	c.31C>A	c.(31-33)Ctg>Atg	p.L11M	HIST4H4_ENST00000541592.1_5'Flank	NM_175054.2	NP_778224.1	P62805	H4_HUMAN	histone cluster 4, H4	11					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)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)	6						CCCTTACCCAGCCCCTTGCCA	0.617																																					p.L11M		Atlas-SNP	.											.	HIST4H4	13	.	0			c.C31A						PASS	.						46	52	50					12																	14923988		2203	4300	6503	SO:0001583	missense	121504	exon1			TACCCAGCCCCTT	AY128653	CCDS8665.1	12p12.3	2011-01-27	2006-10-11			ENSG00000197837		"Histones / Replication-dependent"	20510	protein-coding gene	gene with protein product		615069	"histone 4, H4"			12408966	Standard	NM_175054		Approved	MGC24116	uc001rcf.4	P62805		ENST00000539745.1:c.31C>A	12.37:g.14923988G>T	ENSP00000443017:p.Leu11Met	69	0	0		75	38	0.506667	NM_175054	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000539745.1	37	CCDS8665.1	.	.	.	.	.	.	.	.	.	.	G	11.51	1.660167	0.29515	.	.	ENSG00000197837	ENST00000539745	.	.	.	4.07	4.07	0.47477	.	0.000000	0.43260	U	0.000587	T	0.64080	0.2566	.	.	.	0.51482	D	0.999927	.	.	.	.	.	.	T	0.67409	-0.5678	6	0.87932	D	0	.	7.8764	0.29597	0.1106:0.0:0.8894:0.0	.	.	.	.	M	11	.	ENSP00000350767:L11M	L	-	1	2	HIST4H4	14815255	1.000000	0.71417	0.737000	0.30932	0.392000	0.30506	3.606000	0.54095	2.275000	0.75901	0.650000	0.86243	CTG	.	.	none		0.617	HIST4H4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400844.1	NM_175054		T	14923988	G	T	14923988	3	4	25	1	0	0	0	0	1	0	0	0	7194	962	34	4	284	4	HIST4H4	12	14923988	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1199246	14923988	118927907	502	9411											
SLCO1C1	53919	hgsc.bcm.edu	37	chr12	20854303	20854303	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttgccaaagcattggcagaaGgctatctgaagagcaccatc	13	8	10	10	0	1	3	0	1	1	2	2	3	1	3	2	2	3	4	2	2	4	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:20854303G>T	ENST00000266509.2	+	3	549	c.181G>T	c.(181-183)Ggc>Tgc	p.G61C	SLCO1C1_ENST00000545604.1_Missense_Mutation_p.G61C|SLCO1C1_ENST00000545102.1_Intron|SLCO1C1_ENST00000540354.1_Missense_Mutation_p.G61C|SLCO1C1_ENST00000381552.1_Missense_Mutation_p.G61C	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	61					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)	ATTGGCAGAAGGCTATCTGAA	0.418																																					p.G61C		Atlas-SNP	.											.	SLCO1C1	216	.	0			c.G181T						PASS	.						272	207	229					12																	20854303		2203	4300	6503	SO:0001583	missense	53919	exon3			GCAGAAGGCTATC	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.181G>T	12.37:g.20854303G>T	ENSP00000266509:p.Gly61Cys	179	0	0		179	74	0.413408	NM_017435	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Missense_Mutation	SNP	ENST00000266509.2	37	CCDS8683.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.981799	0.74474	.	.	ENSG00000139155	ENST00000545604;ENST00000540354;ENST00000266509;ENST00000381552	T;T;T;T	0.60299	0.2;0.2;0.2;0.2	5.09	5.09	0.68999	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.046510	0.85682	D	0.000000	T	0.70996	0.3288	M	0.80183	2.485	0.41867	D	0.990257	D;D;D	0.62365	0.973;0.98;0.991	P;P;D	0.64506	0.852;0.852;0.926	T	0.74435	-0.3666	10	0.66056	D	0.02	.	6.0855	0.19964	0.2193:0.0:0.7807:0.0	.	61;61;61	B7Z3Q3;Q5JPA4;Q9NYB5	.;.;SO1C1_HUMAN	C	61	ENSP00000444149:G61C;ENSP00000438665:G61C;ENSP00000266509:G61C;ENSP00000370964:G61C	ENSP00000266509:G61C	G	+	1	0	SLCO1C1	20745570	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.764000	0.62264	2.652000	0.90054	0.655000	0.94253	GGC	.	.	none		0.418	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435		T	20854303	G	T	20854303	3	4	25	1	0	0	0	0	1	0	0	0	14740	1000	35	4	187	4	SLCO1C1	12	20854303	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	5930315	20854303	112997592	503	9412											
KRAS	3845	hgsc.bcm.edu	37	chr12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aggcactcttgcctacgccaCcagctccaactaccacaagt	11	7	6	17	1	1	0	0	0	1	0	2	0	2	0	5	1	5	2	5	1	4	3	rs121913529		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000311936.3_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000556131.1_Missense_Mutation_p.G12V	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.G12V	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,0,25136	KRAS	30930	25136	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.G35T						PASS	.						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>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val	165	0	0		211	89	0.421801	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	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	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	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	.	.	weak		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25398284	C	A	25398284	3	1	25	1	0	0	0	0	1	0	0	0	8447	507	18	4	671	4	KRAS	12	25398284	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	4543981	25398284	108453611	504	9413											
DENND5B	160518	hgsc.bcm.edu	37	chr12	31600503	31600503	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaagtgctgcatttctgataTatagatgtccgcaaggtggg	11	12	12	6	1	1	2	0	1	1	1	2	2	2	2	1	2	2	3	1	2	5	4	rs34129725	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:31600503T>C	ENST00000389082.5	-	6	2094	c.1830A>G	c.(1828-1830)atA>atG	p.I610M	DENND5B_ENST00000306833.6_Missense_Mutation_p.I645M|DENND5B_ENST00000354285.4_Missense_Mutation_p.I632M|snoU13_ENST00000458765.1_RNA|DENND5B_ENST00000536562.1_Missense_Mutation_p.I645M	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	610					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						ATTTCTGATATATAGATGTCC	0.398													T|||	8	0.00159744	0.0	0.0	5008	,	,		18530	0.0		0.005	False		,,,				2504	0.0031				p.I610M		Atlas-SNP	.											.	DENND5B	114	.	0			c.A1830G						PASS	.	T	MET/ILE	13,3669		0,13,1828	60	57	58		1830	-4.4	1	12	dbSNP_126	58	86,8100		1,84,4008	yes	missense	DENND5B	NM_144973.3	10	1,97,5836	CC,CT,TT		1.0506,0.3531,0.8342	benign	610/1275	31600503	99,11769	1841	4093	5934	SO:0001583	missense	160518	exon6			CTGATATATAGAT	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.1830A>G	12.37:g.31600503T>C	ENSP00000373734:p.Ile610Met	109	0	0		152	69	0.453947	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Missense_Mutation	SNP	ENST00000389082.5	37	CCDS44857.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	T	8.110	0.778637	0.16120	0.003531	0.010506	ENSG00000170456	ENST00000389082;ENST00000306833;ENST00000536562;ENST00000354285	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.05	-4.42	0.03579	.	0.231333	0.35903	N	0.002910	T	0.09379	0.0231	N	0.03115	-0.41	0.24313	N	0.99507	B;B;B	0.13145	0.007;0.001;0.003	B;B;B	0.16289	0.015;0.004;0.009	T	0.06303	-1.0834	10	0.40728	T	0.16	-11.2663	3.3897	0.07285	0.3423:0.0629:0.3752:0.2196	rs34129725	632;610;645	Q6ZUT9-4;Q6ZUT9;G3V1S3	.;DEN5B_HUMAN;.	M	610;645;645;632	ENSP00000373734:I610M;ENSP00000306482:I645M;ENSP00000444889:I645M;ENSP00000346238:I632M	ENSP00000306482:I645M	I	-	3	3	DENND5B	31491770	0.000000	0.05858	0.988000	0.46212	0.994000	0.84299	-2.825000	0.00747	-0.495000	0.06659	0.460000	0.39030	ATA	T|0.995;C|0.005	0.005	strong		0.398	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973		C	31600503	T	C	31600503	3	2	25	1	0	0	0	0	1	0	0	0	4439	1396	49	3	2058	3	DENND5B	12	31600503	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	6202219	31600503	102251392	505	9414											
PUS7L	83448	hgsc.bcm.edu	37	chr12	44130330	44130330	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgcgtgaacatagaatatgcGcatggaatggggtaaagaga	15	8	14	4	2	0	3	0	1	0	2	0	5	0	4	0	3	3	2	0	3	7	3	rs116948464	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:44130330G>A	ENST00000416848.2	-	7	2067	c.1579C>T	c.(1579-1581)Cgc>Tgc	p.R527C	PUS7L_ENST00000431332.3_Missense_Mutation_p.R214C|PUS7L_ENST00000344862.5_Missense_Mutation_p.R527C|PUS7L_ENST00000551923.1_Missense_Mutation_p.R527C	NM_001098615.1|NM_001271826.1	NP_001092085.1|NP_001258755.1	Q9H0K6	PUS7L_HUMAN	pseudouridylate synthase 7 homolog (S. cerevisiae)-like	527	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)		TAGAATATGCGCATGGAATGG	0.458													G|||	9	0.00179712	0.0008	0.0	5008	,	,		20268	0.001		0.006	False		,,,				2504	0.001				p.R527C		Atlas-SNP	.											PUS7L,NS,carcinoma,+1,1	PUS7L	73	1	0			c.C1579T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	179	145	157		1579,1579,1579	5	1	12	dbSNP_132	157	53,8547	33.3+/-86.6	1,51,4248	yes	missense,missense,missense	PUS7L	NM_001098614.1,NM_001098615.1,NM_031292.3	180,180,180	1,53,6449	AA,AG,GG		0.6163,0.0454,0.4229	probably-damaging,probably-damaging,probably-damaging	527/702,527/702,527/702	44130330	55,12951	2203	4300	6503	SO:0001583	missense	83448	exon7			ATATGCGCATGGA	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.1579C>T	12.37:g.44130330G>A	ENSP00000415899:p.Arg527Cys	142	0	0		168	74	0.440476	NM_001098614	B3KUJ1|Q05CU0|Q6AHZ3|Q6NUP2	Missense_Mutation	SNP	ENST00000416848.2	37	CCDS8743.1	7	0.003205128205128205	0	0.0	0	0.0	1	0.0017482517482517483	6	0.0079155672823219	G	22.0	4.231553	0.79688	4.54E-4	0.006163	ENSG00000129317	ENST00000416848;ENST00000344862;ENST00000551923;ENST00000431332	T;T;T;T	0.50548	0.74;0.74;0.74;0.74	5.02	5.02	0.67125	Pseudouridine synthase, catalytic domain (1);Pseudouridine synthase, TruD, insertion domain (1);	0.000000	0.85682	D	0.000000	T	0.72684	0.3491	H	0.94658	3.565	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.83148	-0.0105	10	0.87932	D	0	-10.4718	19.2216	0.93799	0.0:0.0:1.0:0.0	.	527	Q9H0K6	PUS7L_HUMAN	C	527;527;527;214	ENSP00000415899:R527C;ENSP00000343081:R527C;ENSP00000447706:R527C;ENSP00000398497:R214C	ENSP00000343081:R527C	R	-	1	0	PUS7L	42416597	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.921000	0.70028	2.723000	0.93209	0.591000	0.81541	CGC	G|0.996;A|0.004	0.004	strong		0.458	PUS7L-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403931.1	NM_031292		A	44130330	G	A	44130330	3	1	25	1	0	0	0	0	1	0	0	0	12849	1087	38	1	538	1	PUS7L	12	44130330	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	12529827	44130330	89721565	506	9415											
MLL2	8085	hgsc.bcm.edu	37	chr12	49422949	49422950	+	Frame_Shift_Ins	INS	-	-	CA																															aaacgaggggcctcctccccINScaagatgctctcaggggatg																								rs376628232		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:49422949_49422950insCA	ENST00000301067.7	-	44	14144_14145	c.14145_14146insTG	c.(14143-14148)ttggggfs	p.G4716fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	4716					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)										GCCTCCTCCCCCAAGATGCTCT	0.589																																					p.G4716fs		Pindel,Atlas-Indel	.											.	MLL2	1173	.	0			c.14146_14147insTG						PASS	.																																			SO:0001589	frameshift_variant	8085	exon44			.	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.14144_14145dupTG	12.37:g.49422950_49422951dupCA	ENSP00000301067:p.Gly4716fs	71	0	.		94	29	0.309	NM_003482	O14687	Frame_Shift_Ins	INS	ENST00000301067.7	37	CCDS44873.1																																																																																			.	.	none		0.589	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			CA	49422950	-	CA	49422949	7	5	25	1	0	1	1	0	0	0	0	0	9630	623	22	0	2511	0	MLL2	12	49422949	Frame_Shift_Ins	INS	-	TCGA-G8-6906-01A-11D-2210-10	5292619	49422949	84428946	507	9416											
MLL2	8085	hgsc.bcm.edu	37	chr12	49444214	49444214	+	Frame_Shift_Del	DEL	A	A	-																															ccctatgggactcaacggggAgggaacggacagtggtaggg																										TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:49444214delA	ENST00000301067.7	-	11	3156	c.3157delT	c.(3157-3159)tccfs	p.S1053fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1053	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)										CTCAACGGGGAGGGAACGGAC	0.572																																					p.S1053fs		Pindel,Atlas-Indel	.											.	MLL2	1173	.	0			c.3158delC						PASS	.						49	55	53					12																	49444214		2068	4208	6276	SO:0001589	frameshift_variant	8085	exon11			.	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.3157delT	12.37:g.49444214delA	ENSP00000301067:p.Ser1053fs	214	0	.		193	47	0.244	NM_003482	O14687	Frame_Shift_Del	DEL	ENST00000301067.7	37	CCDS44873.1																																																																																			.	.	none		0.572	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			-	49444214	A	-	49444214	7	5	25	1	0	1	0	1	0	0	0	0	9630	304	11	0	13632	0	MLL2	12	49444214	Frame_Shift_Del	DEL	A	TCGA-G8-6906-01A-11D-2210-10	21265	49444214	84407681	508	9417											
SLC11A2	4891	hgsc.bcm.edu	37	chr12	51390685	51390685	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctgttcaatctgtggagtgCgacagcctgaacaggatggt	9	10	13	9	1	2	1	1	1	1	0	2	4	2	3	2	3	3	1	2	3	2	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:51390685C>T	ENST00000262051.7	-	9	833	c.746G>A	c.(745-747)cGc>cAc	p.R249H	SLC11A2_ENST00000262052.5_Missense_Mutation_p.R249H|SLC11A2_ENST00000541174.2_Missense_Mutation_p.R249H|SLC11A2_ENST00000547688.1_Missense_Mutation_p.R278H|SLC11A2_ENST00000547198.1_Missense_Mutation_p.R249H|SLC11A2_ENST00000394904.3_Missense_Mutation_p.R278H|SLC11A2_ENST00000545993.2_Missense_Mutation_p.R245H|SLC11A2_ENST00000546743.1_Missense_Mutation_p.R170H	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	249					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						CTGTGGAGTGCGACAGCCTGA	0.498																																					p.R278H		Atlas-SNP	.											SLC11A2,caecum,carcinoma,0,1	SLC11A2	51	1	0			c.G833A						PASS	.						233	148	177					12																	51390685		2203	4300	6503	SO:0001583	missense	4891	exon9			GGAGTGCGACAGC	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.746G>A	12.37:g.51390685C>T	ENSP00000262051:p.Arg249His	132	0	0		148	63	0.425676	NM_001174125	B3KT08|B4DK84|F5H741|O43288|O60932|O94801|Q498Z5|Q8IUD7|Q96J35	Missense_Mutation	SNP	ENST00000262051.7	37	CCDS53792.1	.	.	.	.	.	.	.	.	.	.	C	13.21	2.170540	0.38315	.	.	ENSG00000110911	ENST00000262051;ENST00000547198;ENST00000262052;ENST00000394904;ENST00000547688;ENST00000541174;ENST00000545993;ENST00000546743	T;T;T;T;T;T;T;T	0.30714	1.93;1.93;1.93;1.93;1.93;1.93;1.93;1.52	5.79	-5.03	0.02973	.	1.323470	0.04699	N	0.415517	T	0.18964	0.0455	N	0.19112	0.55	0.09310	N	1	B;B;B;B;B;B	0.06786	0.0;0.001;0.001;0.0;0.0;0.0	B;B;B;B;B;B	0.10450	0.003;0.003;0.005;0.003;0.003;0.003	T	0.34453	-0.9828	10	0.48119	T	0.1	8.703	8.5091	0.33206	0.0:0.402:0.0991:0.4989	.	212;245;278;249;98;249	B7Z9M2;F5H741;P49281-3;P49281-2;B3KY44;P49281	.;.;.;.;.;NRAM2_HUMAN	H	249;249;249;278;278;249;245;170	ENSP00000262051:R249H;ENSP00000446769:R249H;ENSP00000262052:R249H;ENSP00000378364:R278H;ENSP00000449200:R278H;ENSP00000444542:R249H;ENSP00000442810:R245H;ENSP00000446914:R170H	ENSP00000262051:R249H	R	-	2	0	SLC11A2	49676952	0.000000	0.05858	0.001000	0.08648	0.493000	0.33554	0.566000	0.23593	-0.836000	0.04229	-0.140000	0.14226	CGC	.	.	none		0.498	SLC11A2-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404383.1			T	51390685	C	T	51390685	3	4	25	1	0	0	0	0	1	0	0	0	14396	768	27	1	1053	1	SLC11A2	12	51390685	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1946471	51390685	82461210	509	9418											
SCN8A	6334	hgsc.bcm.edu	37	chr12	52200499	52200499	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggaacccctcagtgggcatCttcttctttgtaagctacat	8	13	9	11	0	4	0	1	0	3	0	4	1	4	1	2	2	3	3	2	2	3	5	rs370268493		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52200499C>A	ENST00000354534.6	+	27	5407	c.5229C>A	c.(5227-5229)atC>atA	p.I1743I	SCN8A_ENST00000545061.1_Silent_p.I1702I|RP11-923I11.3_ENST00000565518.1_lincRNA	NM_001177984.2|NM_014191.3	NP_001171455.1|NP_055006.1	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha subunit	1743					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)	CAGTGGGCATCTTCTTCTTTG	0.498																																					p.I1743I		Atlas-SNP	.											.	SCN8A	331	.	0			c.C5229A						PASS	.	C	,	1,4343		0,1,2171	81	89	87		5106,5229	5.3	1	12		87	3,8567		0,3,4282	no	coding-synonymous,coding-synonymous	SCN8A	NM_001177984.1,NM_014191.2	,	0,4,6453	AA,AC,CC		0.035,0.023,0.031	,	1702/1940,1743/1981	52200499	4,12910	2172	4285	6457	SO:0001819	synonymous_variant	6334	exon27			GGGCATCTTCTTC	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.5229C>A	12.37:g.52200499C>A		177	0	0		163	96	0.588957	NM_014191	B9VWG8|O95788|Q9NYX2|Q9UPB2	Silent	SNP	ENST00000354534.6	37	CCDS44891.1																																																																																			.	.	weak		0.498	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404372.3	NM_014191		A	52200499	C	A	52200499	2	1	25	1	0	0	0	0	0	0	0	1	13939	903	32	4		4	SCN8A	12	52200499	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	809814	52200499	81651396	510	9419											
KRT80	144501	hgsc.bcm.edu	37	chr12	52579315	52579315	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagatggctgagtcctggccCtgcaggaagctccagcgtgt	8	8	14	11	1	0	2	0	1	0	1	2	3	2	3	3	3	3	3	3	3	2	0	rs151324530	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52579315C>T	ENST00000394815.2	-	2	454	c.357G>A	c.(355-357)caG>caA	p.Q119Q	KRT80_ENST00000313234.5_Silent_p.Q119Q	NM_182507.2	NP_872313.2	Q6KB66	K2C80_HUMAN	keratin 80	119	Linker 1.|Rod.					cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(2)|large_intestine(2)|lung(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.108)		AGTCCTGGCCCTGCAGGAAGC	0.632													C|||	3	0.000599042	0.0	0.0	5008	,	,		17710	0.0		0.003	False		,,,				2504	0.0				p.Q119Q	GBM(178;2309 2916 15678 35873)	Atlas-SNP	.											.	KRT80	68	.	0			c.G357A						PASS	.	C	,	3,4403	8.1+/-20.4	0,3,2200	46	45	45		357,357	4.2	1	12	dbSNP_134	45	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous,coding-synonymous	KRT80	NM_001081492.1,NM_182507.2	,	0,12,6491	TT,TC,CC		0.1047,0.0681,0.0923	,	119/423,119/453	52579315	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	144501	exon2			CTGGCCCTGCAGG	BX537567	CCDS8821.2, CCDS41784.1	12q13.13	2013-01-16			ENSG00000167767	ENSG00000167767		"-", "Intermediate filaments type II, keratins (basic)"	27056	protein-coding gene	gene with protein product		611161				16831889	Standard	NM_001081492		Approved	KB20	uc001rzx.3	Q6KB66	OTTHUMG00000150193	ENST00000394815.2:c.357G>A	12.37:g.52579315C>T		33	0	0		33	19	0.575758	NM_182507	Q6P1A5|Q7Z3Q0	Silent	SNP	ENST00000394815.2	37	CCDS8821.2																																																																																			C|0.999;T|0.001	0.001	strong		0.632	KRT80-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316757.1	NM_182507		T	52579315	C	T	52579315	2	4	25	1	0	0	0	0	0	0	0	1	8503	680	24	2		2	KRT80	12	52579315	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	378816	52579315	81272580	511	9420											
HOXC6	3223	hgsc.bcm.edu	37	chr12	54422479	54422479	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	actcccttttattcgccacaGgagaatgtcgtgttcagttc	8	14	8	11	2	1	1	1	0	0	1	5	2	2	1	2	1	0	2	2	1	2	5	rs145731630	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:54422479G>A	ENST00000243108.4	+	1	338	c.174G>A	c.(172-174)caG>caA	p.Q58Q	HOXC4_ENST00000303406.4_Intron|HOXC6_ENST00000394331.3_5'UTR|RP11-834C11.14_ENST00000512206.1_RNA|RP11-834C11.12_ENST00000513209.1_Intron	NM_004503.3	NP_004494.1	P09630	HXC6_HUMAN	homeobox C6	58					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						ATTCGCCACAGGAGAATGTCG	0.512													G|||	6	0.00119808	0.0	0.0	5008	,	,		17413	0.0		0.002	False		,,,				2504	0.0041				p.Q58Q		Atlas-SNP	.											.	HOXC6	30	.	0			c.G174A						PASS	.	G	,,	7,4399	12.9+/-30.5	0,7,2196	87	81	83		174,,	2.5	1	12	dbSNP_134	83	46,8554	30.1+/-81.4	0,46,4254	no	coding-synonymous,intron,utr-5	HOXC4,HOXC6	NM_004503.3,NM_014620.4,NM_153693.3	,,	0,53,6450	AA,AG,GG		0.5349,0.1589,0.4075	,,	58/236,,	54422479	53,12953	2203	4300	6503	SO:0001819	synonymous_variant	3223	exon1			GCCACAGGAGAAT		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.174G>A	12.37:g.54422479G>A		97	0	0		112	58	0.517857	NM_004503	B2RBV2|Q6DK09	Silent	SNP	ENST00000243108.4	37	CCDS8871.1																																																																																			G|0.997;A|0.003	0.003	strong		0.512	HOXC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358943.2			A	54422479	G	A	54422479	2	1	25	1	0	0	0	0	0	0	0	1	7324	991	35	2		2	HOXC6	12	54422479	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1843164	54422479	79429416	512	9421											
CS	1431	hgsc.bcm.edu	37	chr12	56669799	56669799	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctgtggatggtgaggtacaGgcgcgtgagctcagtgaact	8	9	16	8	2	1	3	1	3	0	0	1	4	1	4	1	4	3	2	1	4	2	1	rs61738833	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:56669799G>A	ENST00000351328.3	-	7	959	c.769C>T	c.(769-771)Ctg>Ttg	p.L257L	CS_ENST00000548567.1_Silent_p.L191L|CS_ENST00000542324.2_Silent_p.L244L	NM_004077.2	NP_004068.2	O75390	CISY_HUMAN	citrate synthase	257					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)		GTGAGGTACAGGCGCGTGAGC	0.478													G|||	28	0.00559105	0.0008	0.0101	5008	,	,		20736	0.0		0.0189	False		,,,				2504	0.001				p.L257L		Atlas-SNP	.											.	CS	44	.	0			c.C769T						PASS	.	G		11,4395	19.1+/-41.9	0,11,2192	136	117	123		769	1.7	1	12	dbSNP_129	123	120,8480	62.4+/-124.4	2,116,4182	no	coding-synonymous	CS	NM_004077.2		2,127,6374	AA,AG,GG		1.3953,0.2497,1.0072		257/467	56669799	131,12875	2203	4300	6503	SO:0001819	synonymous_variant	1431	exon7			GGTACAGGCGCGT		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.769C>T	12.37:g.56669799G>A		163	0	0		215	104	0.483721	NM_004077	Q71UT9|Q7KZH0|Q96FZ8|Q9BWN8	Silent	SNP	ENST00000351328.3	37	CCDS8913.1																																																																																			G|0.991;A|0.009	0.009	strong		0.478	CS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408588.2	NM_004077		A	56669799	G	A	56669799	2	1	25	1	0	0	0	0	0	0	0	1	3926	991	35	2		2	CS	12	56669799	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2247320	56669799	77182096	513	9422											
LRP1	4035	hgsc.bcm.edu	37	chr12	57571249	57571249	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggatgccagcctgccccgCattgaggcagcctccatgag	7	7	13	14	1	0	2	0	2	0	0	1	3	1	3	6	2	4	2	6	2	0	1	rs2228187	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:57571249C>T	ENST00000243077.3	+	26	4702	c.4236C>T	c.(4234-4236)cgC>cgT	p.R1412R		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	1412					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)	GCCTGCCCCGCATTGAGGCAG	0.677													C|||	18	0.00359425	0.0008	0.0101	5008	,	,		15185	0.0		0.007	False		,,,				2504	0.0031				p.R1412R		Atlas-SNP	.											.	LRP1	428	.	0			c.C4236T						PASS	.	C		1,4405		0,1,2202	36	39	38		4236	-7.2	0.8	12	dbSNP_98	38	73,8527	41.7+/-99.0	0,73,4227	no	coding-synonymous	LRP1	NM_002332.2		0,74,6429	TT,TC,CC		0.8488,0.0227,0.569		1412/4545	57571249	74,12932	2203	4300	6503	SO:0001819	synonymous_variant	4035	exon26			GCCCCGCATTGAG	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.4236C>T	12.37:g.57571249C>T		149	0	0		175	94	0.537143	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			C|0.994;T|0.006	0.006	strong		0.677	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		T	57571249	C	T	57571249	2	4	25	1	0	0	0	0	0	0	0	1	8960	697	25	2		2	LRP1	12	57571249	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	901450	57571249	76280646	514	9423											
INHBE	83729	hgsc.bcm.edu	37	chr12	57850304	57850319	+	Frame_Shift_Del	DEL	TGCGACCCCCTTATGT	TGCGACCCCCTTATGT	-																															aggacccccacctgtgagccTgcgacccccttatgttgcag																								rs536111730		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TGCGACCCCCTTATGT	TGCGACCCCCTTATGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:57850304_57850319delTGCGACCCCCTTATGT	ENST00000266646.2	+	2	942_957	c.726_741delTGCGACCCCCTTATGT	c.(724-741)cctgcgacccccttatgtfs	p.PATPLC242fs	INHBE_ENST00000551553.1_3'UTR	NM_031479.3	NP_113667.1	P58166	INHBE_HUMAN	inhibin, beta E	242					growth (GO:0040007)	extracellular region (GO:0005576)				breast(2)|central_nervous_system(1)|large_intestine(2)|lung(7)|prostate(1)|skin(2)	15						CCTGTGAGCCTGCGACCCCCTTATGTTGCAGGCGAG	0.611											OREG0021944	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.242_247del	GBM(191;1808 2166 15720 36624 50371)	Pindel,Atlas-Indel	.											.	INHBE	38	.	0			c.725_740del						PASS	.																																			SO:0001589	frameshift_variant	83729	exon2			.		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.726_741delTGCGACCCCCTTATGT	12.37:g.57850304_57850319delTGCGACCCCCTTATGT	ENSP00000266646:p.Pro242fs	105	0	.	1026	73	20	0.274	NM_031479		Frame_Shift_Del	DEL	ENST00000266646.2	37	CCDS8939.1																																																																																			.	.	none		0.611	INHBE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406773.1	NM_031479		-	57850319	TGCGACCCCCTTATGT	-	57850304	7	5	25	1	0	1	0	1	0	0	0	0	7753	1567	55	0	732	0	INHBE	12	57850304	Frame_Shift_Del	DEL	TGCGACCCCCTTATGT	TCGA-G8-6906-01A-11D-2210-10	279055	57850304	76001591	515	9424											
C12orf64	283310	hgsc.bcm.edu	37	chr12	80665473	80665473	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtatttcgactgcaggtttcCtgaccctgaattaccagctg	8	13	9	11	1	0	2	0	2	0	0	2	3	1	2	3	1	3	4	3	1	3	4	rs183159689	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:80665473C>T	ENST00000547103.1	+	23	2543	c.2537C>T	c.(2536-2538)cCt>cTt	p.P846L	OTOGL_ENST00000458043.2_Missense_Mutation_p.P846L			Q3ZCN5	OTOGL_HUMAN	otogelin-like	846					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						TGCAGGTTTCCTGACCCTGAA	0.458													C|||	3	0.000599042	0.0	0.0	5008	,	,		17643	0.0		0.003	False		,,,				2504	0.0				p.P846L		Atlas-SNP	.											.	OTOGL	235	.	0			c.C2537T						PASS	.	C	LEU/PRO	4,3910		0,4,1953	97	100	99		2537	5.1	1	12		99	3,8259		0,3,4128	yes	missense	OTOGL	NM_173591.3	98	0,7,6081	TT,TC,CC		0.0363,0.1022,0.0575		846/2345	80665473	7,12169	1957	4131	6088	SO:0001583	missense	283310	exon23			GGTTTCCTGACCC	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.2537C>T	12.37:g.80665473C>T	ENSP00000447211:p.Pro846Leu	133	0	0		156	74	0.474359	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	37		4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	15.16	2.751832	0.49362	0.001022	3.63E-4	ENSG00000165899	ENST00000547103;ENST00000458043	T;T	0.16324	2.35;2.35	5.14	5.14	0.70334	.	.	.	.	.	T	0.22475	0.0542	L	0.59912	1.85	0.58432	D	0.999999	.	.	.	.	.	.	T	0.00420	-1.1750	7	0.29301	T	0.29	.	14.6719	0.68951	0.1459:0.8541:0.0:0.0	.	.	.	.	L	846	ENSP00000447211:P846L;ENSP00000400895:P846L	ENSP00000400895:P846L	P	+	2	0	OTOGL	79189604	0.962000	0.33011	1.000000	0.80357	0.977000	0.68977	1.923000	0.40055	2.551000	0.86045	0.655000	0.94253	CCT	C|0.998;T|0.002	0.002	strong		0.458	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591		T	80665473	C	T	80665473	3	4	25	1	0	0	0	0	1	0	0	0	1709	681	24	2	2627	2	C12orf64	12	80665473	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	22815169	80665473	53186422	516	9425											
C12orf64	283310	hgsc.bcm.edu	37	chr12	80764360	80764360	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgatttttaggtagggagtaCctggcactacaattgcacca	11	12	10	8	0	0	1	0	1	0	0	0	2	0	2	2	3	3	4	2	3	5	7	rs146572555	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:80764360C>T	ENST00000547103.1	+	55	6569	c.6563C>T	c.(6562-6564)aCc>aTc	p.T2188I	OTOGL_ENST00000458043.2_Missense_Mutation_p.T2200I|OTOGL_ENST00000546620.1_Missense_Mutation_p.T219I			Q3ZCN5	OTOGL_HUMAN	otogelin-like	2188					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						GTAGGGAGTACCTGGCACTAC	0.308													C|||	14	0.00279553	0.0068	0.0029	5008	,	,		13968	0.0		0.003	False		,,,				2504	0.0				p.T2200I		Atlas-SNP	.											.	OTOGL	235	.	0			c.C6599T						PASS	.	C	ILE/THR	12,4394	17.9+/-39.9	0,12,2191	132	129	130		6599	0.1	0	12	dbSNP_134	130	4,8596	3.7+/-12.6	0,4,4296	yes	missense	OTOGL	NM_173591.3	89	0,16,6487	TT,TC,CC		0.0465,0.2724,0.123	benign	2200/2345	80764360	16,12990	2203	4300	6503	SO:0001583	missense	283310	exon55			GGAGTACCTGGCA	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.6563C>T	12.37:g.80764360C>T	ENSP00000447211:p.Thr2188Ile	67	0	0		47	29	0.617021	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	37		15|15	0.006868131868131868|0.006868131868131868	9|9	0.018292682926829267|0.018292682926829267	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	C|C	6.727|6.727	0.502843|0.502843	0.12822|0.12822	0.002724|0.002724	4.65E-4|4.65E-4	ENSG00000165899|ENSG00000165899	ENST00000298820|ENST00000547103;ENST00000458043;ENST00000546620;ENST00000550182	.|T;T;T;T	.|0.46063	.|2.23;2.23;2.13;0.88	5.44|5.44	0.118|0.118	0.14667|0.14667	.|.	.|0.315004	.|0.30869	.|N	.|0.008710	T|T	0.21801|0.21801	0.0525|0.0525	M|M	0.62723|0.62723	1.935|1.935	0.09310|0.09310	N|N	1|1	.|B	.|0.14012	.|0.009	.|B	.|0.16289	.|0.015	T|T	0.30357|0.30357	-0.9981|-0.9981	5|10	.|0.72032	.|D	.|0.01	.|.	9.8313|9.8313	0.40944|0.40944	0.0:0.6306:0.0:0.3694|0.0:0.6306:0.0:0.3694	.|.	.|565	.|Q3ZCN5	.|OTOGL_HUMAN	S|I	608|2188;2200;219;217	.|ENSP00000447211:T2188I;ENSP00000400895:T2200I;ENSP00000449094:T219I;ENSP00000449641:T217I	.|ENSP00000400895:T2200I	P|T	+|+	1|2	0|0	OTOGL|OTOGL	79288491|79288491	0.990000|0.990000	0.36364|0.36364	0.019000|0.019000	0.16419|0.16419	0.184000|0.184000	0.23303|0.23303	2.773000|2.773000	0.47686|0.47686	-0.268000|-0.268000	0.09312|0.09312	-0.229000|-0.229000	0.12294|0.12294	CCT|ACC	C|0.997;T|0.003	0.003	strong		0.308	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591		T	80764360	C	T	80764360	3	4	25	1	0	0	0	0	1	0	0	0	1709	507	18	2	6817	2	C12orf64	12	80764360	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	98887	80764360	53087535	517	9426											
ACSS3	79611	hgsc.bcm.edu	37	chr12	81627215	81627215	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggatgatgtaataaatgttGcaggtcacagaatttctgca	13	13	10	5	0	2	2	1	1	1	1	2	3	2	3	0	2	2	4	0	2	4	4	rs145641313	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:81627215G>T	ENST00000548058.1	+	13	2594	c.1684G>T	c.(1684-1686)Gca>Tca	p.A562S	ACSS3_ENST00000548324.1_Missense_Mutation_p.A244S|ACSS3_ENST00000261206.3_Missense_Mutation_p.A561S			Q9H6R3	ACSS3_HUMAN	acyl-CoA synthetase short-chain family member 3	562						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						AATAAATGTTGCAGGTCACAG	0.393													G|||	2	0.000399361	0.0015	0.0	5008	,	,		18493	0.0		0.0	False		,,,				2504	0.0				p.A562S		Atlas-SNP	.											.	ACSS3	118	.	0			c.G1684T						PASS	.	G	SER/ALA	3,4403	6.2+/-15.9	0,3,2200	227	221	223		1684	5.8	1	12	dbSNP_134	223	0,8600		0,0,4300	yes	missense	ACSS3	NM_024560.2	99	0,3,6500	TT,TG,GG		0.0,0.0681,0.0231	possibly-damaging	562/687	81627215	3,13003	2203	4300	6503	SO:0001583	missense	79611	exon13			AATGTTGCAGGTC		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.1684G>T	12.37:g.81627215G>T	ENSP00000449535:p.Ala562Ser	144	0	0		154	63	0.409091	NM_024560	Q8NC66	Missense_Mutation	SNP	ENST00000548058.1	37	CCDS9022.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	32	5.163767	0.94727	6.81E-4	0.0	ENSG00000111058	ENST00000548058;ENST00000261206;ENST00000548324	T;T;T	0.46451	2.94;2.94;0.87	5.84	5.84	0.93424	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.53706	0.1813	N	0.26130	0.795	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.44667	-0.9313	10	0.30854	T	0.27	-15.5203	19.7715	0.96367	0.0:0.0:1.0:0.0	.	244;562	Q9H6R3-2;Q9H6R3	.;ACSS3_HUMAN	S	562;561;244	ENSP00000449535:A562S;ENSP00000261206:A561S;ENSP00000448965:A244S	ENSP00000261206:A561S	A	+	1	0	ACSS3	80151346	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.315000	0.78998	2.777000	0.95525	0.650000	0.86243	GCA	G|0.999;T|0.001	0.001	strong		0.393	ACSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407794.1	NM_024560		T	81627215	G	T	81627215	3	4	25	1	0	0	0	0	1	0	0	0	190	1319	46	4	1734	4	ACSS3	12	81627215	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	862855	81627215	52224680	518	9427											
KITLG	4254	hgsc.bcm.edu	37	chr12	88900891	88900891	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcccagtgtaggctggagtCtccagggggatttttggcct	5	12	15	9	0	1	0	0	0	1	0	2	2	1	2	3	5	1	2	3	5	1	3	rs41283112	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:88900891C>A	ENST00000228280.5	-	7	810	c.628G>T	c.(628-630)Gac>Tac	p.D210Y	KITLG_ENST00000357116.4_5'UTR|KITLG_ENST00000347404.5_Missense_Mutation_p.D182Y|KITLG_ENST00000378535.4_5'UTR	NM_000899.4	NP_000890.1	P21583	SCF_HUMAN	KIT ligand	210			D -> Y (in dbSNP:rs41283112).		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						AGGCTGGAGTCTCCAGGGGGA	0.418									Testicular Cancer, Familial Clustering of				C|||	20	0.00399361	0.0	0.0101	5008	,	,		14689	0.0		0.0099	False		,,,				2504	0.0031				p.D210Y		Atlas-SNP	.											.	KITLG	26	.	0			c.G628T						PASS	.	C	TYR/ASP,TYR/ASP	15,4391	24.3+/-50.5	0,15,2188	63	67	65		628,544	2.8	0	12	dbSNP_127	65	138,8462	68.7+/-131.2	0,138,4162	yes	missense,missense	KITLG	NM_000899.4,NM_003994.5	160,160	0,153,6350	AA,AC,CC		1.6047,0.3404,1.1764	probably-damaging,probably-damaging	210/274,182/246	88900891	153,12853	2203	4300	6503	SO:0001583	missense	4254	exon7	Familial Cancer Database		TGGAGTCTCCAGG	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.628G>T	12.37:g.88900891C>A	ENSP00000228280:p.Asp210Tyr	46	0	0		29	14	0.482759	NM_000899	A0AV09|A8K2Q4|B7ZLM4|Q16487|Q68DZ2|Q7M4N8|Q9UQK7	Missense_Mutation	SNP	ENST00000228280.5	37	CCDS31868.1	11|11	0.005036630036630037|0.005036630036630037	0|0	0.0|0.0	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	8|8	0.010554089709762533|0.010554089709762533	C|C	17.16|17.16	3.317419|3.317419	0.60524|0.60524	0.003404|0.003404	0.016047|0.016047	ENSG00000049130|ENSG00000049130	ENST00000378535;ENST00000228280;ENST00000347404|ENST00000537835	T;T|.	0.67523|.	-0.27;-0.27|.	5.68|5.68	2.84|2.84	0.33178|0.33178	.|.	0.350727|.	0.32819|.	N|.	0.005616|.	T|T	0.25419|0.25419	0.0618|0.0618	L|L	0.54323|0.54323	1.7|1.7	0.26217|0.26217	N|N	0.979217|0.979217	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.72982|.	0.964;0.979|.	T|T	0.34875|0.34875	-0.9811|-0.9811	10|6	0.59425|0.87932	D|D	0.04|0	-2.0558|-2.0558	3.7484|3.7484	0.08556|0.08556	0.0:0.5316:0.1938:0.2746|0.0:0.5316:0.1938:0.2746	rs41283112;rs61754238|rs41283112;rs61754238	182;210|.	P21583-2;P21583|.	.;SCF_HUMAN|.	Y|D	175;210;182|13	ENSP00000228280:D210Y;ENSP00000054216:D182Y|.	ENSP00000228280:D210Y|ENSP00000438889:E13D	D|E	-|-	1|3	0|2	KITLG|KITLG	87425022|87425022	0.712000|0.712000	0.27916|0.27916	0.041000|0.041000	0.18516|0.18516	0.359000|0.359000	0.29487|0.29487	1.040000|1.040000	0.30278|0.30278	0.735000|0.735000	0.32537|0.32537	0.655000|0.655000	0.94253|0.94253	GAC|GAG	C|0.991;A|0.009	0.009	strong		0.418	KITLG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406424.2	NM_003994		A	88900891	C	A	88900891	3	1	25	1	0	0	0	0	1	0	0	0	8339	913	32	4	205	4	KITLG	12	88900891	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	7273676	88900891	44951004	519	9428											
POC1B	282809	hgsc.bcm.edu	37	chr12	89865394	89865394	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gttaggaaaattgttaccttGgtaatgctgtagtaatttgt	11	17	10	3	0	0	0	0	0	0	0	0	1	0	1	1	2	2	6	1	2	7	8	rs145981936		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:89865394G>C	ENST00000313546.3	-	6	801	c.673C>G	c.(673-675)Caa>Gaa	p.Q225E	POC1B_ENST00000378528.2_Intron|POC1B_ENST00000549504.1_Intron|POC1B_ENST00000549035.1_Missense_Mutation_p.Q183E|POC1B_ENST00000393179.4_Missense_Mutation_p.Q95E|POC1B_ENST00000541909.1_Missense_Mutation_p.Q95E	NM_172240.2	NP_758440.1	Q8TC44	POC1B_HUMAN	POC1 centriolar protein B	225					cell proliferation (GO:0008283)|cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|spindle pole (GO:0000922)				endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	14						TTGTTACCTTGGTAATGCTGT	0.413													G|||	1	0.000199681	0.0	0.0	5008	,	,		17728	0.0		0.001	False		,,,				2504	0.0				p.Q225E		Atlas-SNP	.											.	POC1B	41	.	0			c.C673G						PASS	.	G	GLU/GLN,GLU/GLN	0,4406		0,0,2203	147	137	140		547,673	6	1	12	dbSNP_134	140	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	POC1B	NM_001199777.1,NM_172240.2	29,29	0,5,6498	CC,CG,GG		0.0581,0.0,0.0384	,	183/437,225/479	89865394	5,13001	2203	4300	6503	SO:0001583	missense	282809	exon6			TACCTTGGTAATG	AL832918	CCDS31869.1, CCDS55859.1	12q21.33	2014-05-02	2013-08-21	2010-03-26	ENSG00000139323	ENSG00000139323		"WD repeat domain containing"	30836	protein-coding gene	gene with protein product		614784	"WD repeat domain 51B", "POC1 centriolar protein homolog B (Chlamydomonas)"	WDR51B		19109428	Standard	NM_172240		Approved	TUWD12, FLJ14923		Q8TC44	OTTHUMG00000169944	ENST00000313546.3:c.673C>G	12.37:g.89865394G>C	ENSP00000323302:p.Gln225Glu	96	0	0		101	34	0.336634	NM_172240	G3V1X0	Missense_Mutation	SNP	ENST00000313546.3	37	CCDS31869.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.471636	0.43942	0.0	5.81E-4	ENSG00000139323	ENST00000393179;ENST00000313546;ENST00000549035;ENST00000541909	T;T;T;T	0.59224	0.28;0.28;0.28;0.28	6.02	6.02	0.97574	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.155036	0.64402	D	0.000014	T	0.40719	0.1128	N	0.10972	0.075	0.80722	D	1	B	0.31655	0.334	B	0.35182	0.197	T	0.31308	-0.9948	10	0.13853	T	0.58	.	16.1501	0.81611	0.0:0.0:0.8588:0.1412	.	225	Q8TC44	POC1B_HUMAN	E	95;225;183;95	ENSP00000376877:Q95E;ENSP00000323302:Q225E;ENSP00000447916:Q183E;ENSP00000440301:Q95E	ENSP00000323302:Q225E	Q	-	1	0	POC1B	88389525	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.072000	0.64389	2.857000	0.98124	0.650000	0.86243	CAA	G|0.999;C|0.001	0.001	strong		0.413	POC1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406637.1	NM_172240		C	89865394	G	C	89865394	3	2	25	1	0	0	0	0	1	0	0	0	12185	1357	47	4	791	4	POC1B	12	89865394	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	964503	89865394	43986501	520	9429											
GALNT4	8693	hgsc.bcm.edu	37	chr12	89917349	89917349	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acttccattcctgtgtcataCgttccaaggtactgaaaata	12	13	6	10	1	1	1	1	1	0	0	4	1	4	1	3	1	2	2	3	1	6	6	rs200228838	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:89917349C>T	ENST00000529983.2	-	1	1234	c.978G>A	c.(976-978)acG>acA	p.T326T	POC1B-GALNT4_ENST00000547474.1_3'UTR|POC1B_ENST00000549504.1_Intron|POC1B_ENST00000549035.1_Intron|RP11-734K2.4_ENST00000605233.1_RNA|POC1B_ENST00000393179.4_Intron|GALNT4_ENST00000413530.1_Silent_p.T154T|POC1B_ENST00000313546.3_Intron|POC1B-GALNT4_ENST00000548729.1_Silent_p.T323T|POC1B_ENST00000541909.1_Intron	NM_003774.4	NP_003765.2	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	326	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)	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						CTGTGTCATACGTTCCAAGGT	0.493													C|||	2	0.000399361	0.0	0.0	5008	,	,		19273	0.0		0.002	False		,,,				2504	0.0				p.T326T		Atlas-SNP	.											.	GALNT4	38	.	0			c.G978A						PASS	.	C	,,,,	0,4026		0,0,2013	182	183	182		,969,462,978,	-11.7	0	12		182	15,8367		0,15,4176	no	intron,coding-synonymous,coding-synonymous,coding-synonymous,intron	GALNT4,POC1B,POC1B-GALNT4	NM_001199777.1,NM_001199781.1,NM_001199782.1,NM_003774.4,NM_172240.2	,,,,	0,15,6189	TT,TC,CC		0.179,0.0,0.1209	,,,,	,323/576,154/407,326/579,	89917349	15,12393	2013	4191	6204	SO:0001819	synonymous_variant	8693	exon1			GTCATACGTTCCA	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.978G>A	12.37:g.89917349C>T		275	0	0		290	141	0.486207	NM_003774	B2R775|B4DMX6|O00208	Silent	SNP	ENST00000529983.2	37	CCDS53817.1																																																																																			C|0.996;T|0.004	0.004	strong		0.493	GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388973.2	NM_003774		T	89917349	C	T	89917349	2	4	25	1	0	0	0	0	0	0	0	1	6223	523	19	1		1	GALNT4	12	89917349	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	51955	89917349	43934546	521	9430											
BTG1	694	hgsc.bcm.edu	37	chr12	92539246	92539246	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttggtgcggagaaacttggaGatgaaggacacggcggcggc	10	6	18	7	4	0	3	0	1	0	2	0	6	0	4	0	7	2	0	0	7	2	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:92539246G>A	ENST00000256015.3	-	1	427	c.66C>T	c.(64-66)atC>atT	p.I22I	C12orf79_ENST00000546975.1_5'Flank|C12orf79_ENST00000549802.1_5'Flank|C12orf79_ENST00000551563.2_5'Flank|RP11-796E2.4_ENST00000499685.2_RNA|RP11-796E2.4_ENST00000501008.2_RNA	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	22					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)			haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				GAAACTTGGAGATGAAGGACA	0.701			T	MYC	BCLL																																p.I22I		Atlas-SNP	.		Dom	yes		12	12q22	694	"B-cell translocation gene 1, anti-proliferative"		L	.	BTG1	30	.	0			c.C66T						PASS	.						44	48	47					12																	92539246		2203	4300	6503	SO:0001819	synonymous_variant	694	exon1			CTTGGAGATGAAG		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.66C>T	12.37:g.92539246G>A		110	0	0		164	8	0.0487805	NM_001731	P31607	Silent	SNP	ENST00000256015.3	37	CCDS9043.1																																																																																			.	.	none		0.701	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1			A	92539246	G	A	92539246	2	1	25	1	0	0	0	0	0	0	0	1	1555	932	33	2		2	BTG1	12	92539246	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2621897	92539246	41312649	522	9431											
IKBIP	121457	hgsc.bcm.edu	37	chr12	99007411	99007411	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcatctttaatatccttaatCtcagcttggactattgttaa	11	18	4	8	0	3	0	2	0	2	0	5	1	4	1	1	1	1	2	1	1	5	8	rs201283576	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:99007411C>T	ENST00000342502.2	-	3	1416	c.1005G>A	c.(1003-1005)gaG>gaA	p.E335E	IKBIP_ENST00000420861.1_Silent_p.E229E|IKBIP_ENST00000393042.3_3'UTR	NM_201612.2	NP_963906.1	Q70UQ0	IKIP_HUMAN	IKBKB interacting protein	335					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						TATCCTTAATCTCAGCTTGGA	0.308																																					p.E335E		Atlas-SNP	.											.	IKBIP	46	.	0			c.G1005A						PASS	.						52	58	56					12																	99007411		2199	4297	6496	SO:0001819	synonymous_variant	121457	exon3			CTTAATCTCAGCT	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.1005G>A	12.37:g.99007411C>T		45	0	0		47	15	0.319149	NM_201612	Q6ZWH4|Q70UP9|Q86V91|Q96ND2	Silent	SNP	ENST00000342502.2	37	CCDS9067.1																																																																																			C|0.999;A|0.001	.	alt		0.308	IKBIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000408003.2	NM_153687		T	99007411	C	T	99007411	2	4	25	1	0	0	0	0	0	0	0	1	7618	912	32	2		2	IKBIP	12	99007411	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	6468165	99007411	34844484	523	9432											
GAS2L3	283431	hgsc.bcm.edu	37	chr12	101017839	101017839	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtaaaaacacttcttcacCagctttaccaagaactgcac	15	9	5	12	0	2	1	1	0	1	1	2	1	2	1	2	1	5	3	2	1	6	5	rs148236676	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:101017839C>T	ENST00000539410.1	+	9	1642	c.1256C>T	c.(1255-1257)cCa>cTa	p.P419L	GAS2L3_ENST00000547754.1_Missense_Mutation_p.P419L|GAS2L3_ENST00000266754.5_Missense_Mutation_p.P419L|GAS2L3_ENST00000537247.1_Missense_Mutation_p.P315L			Q86XJ1	GA2L3_HUMAN	growth arrest-specific 2 like 3	419					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						ACTTCTTCACCAGCTTTACCA	0.423													C|||	17	0.00339457	0.0008	0.0115	5008	,	,		19471	0.0		0.006	False		,,,				2504	0.002				p.P419L		Atlas-SNP	.											.	GAS2L3	76	.	0			c.C1256T						PASS	.	C	LEU/PRO	7,4399	12.9+/-30.5	0,7,2196	91	93	92		1256	4.1	0	12	dbSNP_134	92	61,8539	37.8+/-93.5	0,61,4239	yes	missense	GAS2L3	NM_174942.1	98	0,68,6435	TT,TC,CC		0.7093,0.1589,0.5228	benign	419/695	101017839	68,12938	2203	4300	6503	SO:0001583	missense	283431	exon10			CTTCACCAGCTTT	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.1256C>T	12.37:g.101017839C>T	ENSP00000439672:p.Pro419Leu	102	0	0		102	44	0.431373	NM_174942	B2RCN2	Missense_Mutation	SNP	ENST00000539410.1	37	CCDS9079.1	8	0.003663003663003663	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	C	4.648	0.120536	0.08881	0.001589	0.007093	ENSG00000139354	ENST00000266754;ENST00000547754;ENST00000537247;ENST00000539410	T;T;T;T	0.25085	1.86;1.86;1.82;1.86	4.95	4.06	0.47325	.	0.368200	0.25089	N	0.033227	T	0.16041	0.0386	L	0.43152	1.355	0.28581	N	0.910137	B	0.09022	0.002	B	0.08055	0.003	T	0.11966	-1.0566	10	0.62326	D	0.03	-3.2328	10.2064	0.43116	0.0:0.7873:0.1365:0.0761	.	419	Q86XJ1	GA2L3_HUMAN	L	419;419;315;419	ENSP00000266754:P419L;ENSP00000448955:P419L;ENSP00000442406:P315L;ENSP00000439672:P419L	ENSP00000266754:P419L	P	+	2	0	GAS2L3	99541970	0.005000	0.15991	0.008000	0.14137	0.047000	0.14425	2.030000	0.41108	1.080000	0.41073	0.603000	0.83216	CCA	C|0.995;T|0.005	0.005	strong		0.423	GAS2L3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409143.1	NM_174942		T	101017839	C	T	101017839	3	4	25	1	0	0	0	0	1	0	0	0	6256	594	21	2	1286	2	GAS2L3	12	101017839	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2010428	101017839	32834056	524	9433											
UTP20	27340	hgsc.bcm.edu	37	chr12	101761753	101761753	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctgggctccatggatgtgaAggtaagcatcggtttgcact	8	11	13	9	1	0	1	0	1	0	0	2	2	1	2	2	4	2	5	2	4	2	2	rs117476305	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:101761753A>G	ENST00000261637.4	+	48	6557	c.6383A>G	c.(6382-6384)aAg>aGg	p.K2128R		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	2128					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						ATGGATGTGAAGGTAAGCATC	0.433													A|||	15	0.00299521	0.0	0.0043	5008	,	,		19984	0.0		0.0099	False		,,,				2504	0.002				p.K2128R		Atlas-SNP	.											.	UTP20	222	.	0			c.A6383G						PASS	.	A	ARG/LYS	3,4403	6.2+/-15.9	0,3,2200	240	211	221		6383	4.4	1	12	dbSNP_132	221	99,8501	54.4+/-115.2	0,99,4201	yes	missense-near-splice	UTP20	NM_014503.2	26	0,102,6401	GG,GA,AA		1.1512,0.0681,0.7843	possibly-damaging	2128/2786	101761753	102,12904	2203	4300	6503	SO:0001630	splice_region_variant	27340	exon48			ATGTGAAGGTAAG	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.6384+1A>G	12.37:g.101761753A>G		136	0	0		125	58	0.464	NM_014503	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	37	CCDS9081.1	11	0.005036630036630037	0	0.0	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	A	14.07	2.424265	0.43020	6.81E-4	0.011512	ENSG00000120800	ENST00000261637	T	0.65364	-0.15	5.59	4.44	0.53790	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.43322	0.1242	L	0.52126	1.63	0.58432	D	0.999997	P	0.40431	0.717	B	0.35039	0.194	T	0.38866	-0.9641	10	0.25751	T	0.34	-13.9985	11.5039	0.50454	0.9298:0.0:0.0702:0.0	.	2128	O75691	UTP20_HUMAN	R	2128	ENSP00000261637:K2128R	ENSP00000261637:K2128R	K	+	2	0	UTP20	100285884	1.000000	0.71417	1.000000	0.80357	0.225000	0.24961	5.758000	0.68776	0.942000	0.37525	0.528000	0.53228	AAG	A|0.991;G|0.009	0.009	strong		0.433	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	Missense_Mutation	G	101761753	A	G	101761753	5	3	25	1	0	0	0	0	0	0	1	0	17114	86	3	3	6573	3	UTP20	12	101761753	Splice_Site	SNP	A	TCGA-G8-6906-01A-11D-2210-10	743914	101761753	32090142	525	9434											
IFT81	28981	hgsc.bcm.edu	37	chr12	110600841	110600841	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gaaatcagacccgtgaatttGatggtactgaagttttaaag	14	12	10	5	1	1	4	1	3	0	1	1	5	1	4	1	1	1	2	1	1	6	4			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:110600841G>C	ENST00000242591.5	+	11	1665	c.1159G>C	c.(1159-1161)Gat>Cat	p.D387H	IFT81_ENST00000361948.4_Missense_Mutation_p.D387H|IFT81_ENST00000552912.1_Missense_Mutation_p.D387H|IFT81_ENST00000549009.1_3'UTR	NM_014055.3	NP_054774.2	Q8WYA0	IFT81_HUMAN	intraflagellar transport 81	387					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						CCGTGAATTTGATGGTACTGA	0.413																																					p.D387H		Atlas-SNP	.											.	IFT81	86	.	0			c.G1159C						PASS	.						131	124	126					12																	110600841		2203	4300	6503	SO:0001583	missense	28981	exon11			GAATTTGATGGTA	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.1159G>C	12.37:g.110600841G>C	ENSP00000242591:p.Asp387His	77	0	0		74	29	0.391892	NM_014055	Q2YDY1|Q8NB51|Q9BSV2|Q9UNY8	Missense_Mutation	SNP	ENST00000242591.5	37	CCDS41831.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.756569	0.49362	.	.	ENSG00000122970	ENST00000361948;ENST00000552912;ENST00000242591;ENST00000546374	T	0.30714	1.52	5.42	5.42	0.78866	.	0.356693	0.31601	N	0.007377	T	0.32010	0.0815	L	0.50333	1.59	0.80722	D	1	B;P	0.46220	0.343;0.874	B;B	0.44224	0.398;0.444	T	0.03773	-1.1005	10	0.45353	T	0.12	-5.4288	11.8083	0.52169	0.0804:0.0:0.9196:0.0	.	387;387	Q8WYA0;Q8WYA0-3	IFT81_HUMAN;.	H	387;387;387;357	ENSP00000355372:D387H	ENSP00000242591:D387H	D	+	1	0	IFT81	109085224	1.000000	0.71417	0.621000	0.29145	0.917000	0.54804	6.328000	0.72915	2.553000	0.86117	0.655000	0.94253	GAT	.	.	none		0.413	IFT81-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403529.1	NM_014055		C	110600841	G	C	110600841	3	2	25	1	0	0	0	0	1	0	0	0	7574	1290	45	4	1197	4	IFT81	12	110600841	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	8839088	110600841	23251054	526	9435											
ATP2A2	488	hgsc.bcm.edu	37	chr12	110765378	110765378	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ggtacaaacattgctgctggGaaagctatgggagtggtggt	10	10	16	5	0	0	0	0	0	0	0	0	2	0	2	0	5	5	4	0	5	4	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:110765378G>A	ENST00000539276.2	+	8	760	c.651G>A	c.(649-651)ggG>ggA	p.G217G	ATP2A2_ENST00000395494.2_Silent_p.G190G|ATP2A2_ENST00000308664.6_Silent_p.G217G			P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	217					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						TTGCTGCTGGGAAAGCTATGG	0.483																																					p.G217G		Atlas-SNP	.											.	ATP2A2	78	.	0			c.G651A						PASS	.						186	186	186					12																	110765378		2203	4300	6503	SO:0001819	synonymous_variant	488	exon8			TGCTGGGAAAGCT		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.651G>A	12.37:g.110765378G>A		134	0	0		127	45	0.354331	NM_001681	A6NDN7|B4DF05|P16614|Q86VJ2	Silent	SNP	ENST00000539276.2	37	CCDS9144.1	.	.	.	.	.	.	.	.	.	.	G	9.772	1.172980	0.21704	.	.	ENSG00000174437	ENST00000548169	.	.	.	5.38	-0.366	0.12545	.	.	.	.	.	T	0.43233	0.1238	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.22173	-1.0224	4	.	.	.	.	3.2414	0.06782	0.2326:0.4733:0.1189:0.1752	.	.	.	.	K	108	.	.	E	+	1	0	ATP2A2	109249761	0.385000	0.25172	0.994000	0.49952	0.998000	0.95712	-0.274000	0.08537	-0.198000	0.10333	0.585000	0.79938	GAA	.	.	none		0.483	ATP2A2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403539.1	NM_001681		A	110765378	G	A	110765378	2	1	25	1	0	0	0	0	0	0	0	1	1137	1161	41	2		2	ATP2A2	12	110765378	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	164537	110765378	23086517	527	9436											
CCDC63	160762	hgsc.bcm.edu	37	chr12	111342460	111342460	+	Frame_Shift_Del	DEL	G	G	-																															ggcgcatcctggaagtggaaGgggcagaggctgagatcccg																										TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:111342460delG	ENST00000308208.5	+	11	1653	c.1411delG	c.(1411-1413)gggfs	p.G471fs	CCDC63_ENST00000552694.1_Frame_Shift_Del_p.G392fs|CCDC63_ENST00000545036.1_Frame_Shift_Del_p.G431fs	NM_152591.1	NP_689804.1	Q8NA47	CCD63_HUMAN	coiled-coil domain containing 63	471										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						GGAAGTGGAAGGGGCAGAGGC	0.572																																					p.E470fs		Pindel,Atlas-Indel	.											.	CCDC63	89	.	0			c.1410delA						PASS	.			1,4263		0,1,2131	82	78	79			-5	0	12		79	6,8248		0,6,4121	no	frameshift	CCDC63	NM_152591.1		0,7,6252	A1A1,A1R,RR		0.0727,0.0235,0.0559			111342460	7,12511	2203	4300	6503	SO:0001589	frameshift_variant	160762	exon11			.	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.1411delG	12.37:g.111342460delG	ENSP00000312399:p.Gly471fs	107	0	.		164	52	0.317	NM_152591	B4DY03|Q0P603|Q6P2E1	Frame_Shift_Del	DEL	ENST00000308208.5	37	CCDS9151.1																																																																																			.	.	none		0.572	CCDC63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404673.2	NM_152591		-	111342460	G	-	111342460	7	5	25	1	0	1	0	1	0	0	0	0	2836	1000	35	0	1449	0	CCDC63	12	111342460	Frame_Shift_Del	DEL	G	TCGA-G8-6906-01A-11D-2210-10	577082	111342460	22509435	528	9437											
C12orf51	283450	hgsc.bcm.edu	37	chr12	112600883	112600883	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggggcgatcttcatggggtaCgggggcacatgggcagtgtc	6	8	19	8	2	2	0	1	0	1	0	3	1	2	0	0	7	1	3	0	7	1	2	rs183882784	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:112600883C>T	ENST00000430131.2	-	74	12962	c.11817G>A	c.(11815-11817)ccG>ccA	p.P3939P	HECTD4_ENST00000549141.1_5'Flank|HECTD4_ENST00000550722.1_Silent_p.P4215P|HECTD4_ENST00000377560.5_Silent_p.P4189P			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3939	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)										TCATGGGGTACGGGGGCACAT	0.602													C|||	14	0.00279553	0.0008	0.0014	5008	,	,		16711	0.001		0.006	False		,,,				2504	0.0051				p.P4227P		Atlas-SNP	.											.	.	.	.	0			c.G12681A						PASS	.	C		6,4042		0,6,2018	89	98	95		12567	-11.6	0.1	12		95	63,8265		0,63,4101	no	coding-synonymous	C12orf51	NM_001109662.2		0,69,6119	TT,TC,CC		0.7565,0.1482,0.5575		4189/4247	112600883	69,12307	2024	4164	6188	SO:0001819	synonymous_variant	283450	exon75			GGGGTACGGGGGC	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.11817G>A	12.37:g.112600883C>T		164	0	0		178	86	0.483146	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	37																																																																																				C|0.995;T|0.005	0.005	strong		0.602	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		T	112600883	C	T	112600883	2	4	25	1	0	0	0	0	0	0	0	1	1698	523	19	1		1	C12orf51	12	112600883	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1258423	112600883	21251012	529	9438											
OAS3	4940	hgsc.bcm.edu	37	chr12	113400593	113400593	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catggcccaaggcttccggaCggtgctggggctcgtgcaac	6	7	15	13	3	0	0	0	0	0	0	2	1	1	1	2	6	3	4	2	6	2	1	rs200778728		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:113400593C>T	ENST00000228928.7	+	9	2149	c.1970C>T	c.(1969-1971)aCg>aTg	p.T657M	RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	657	OAS domain 2.				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						GGCTTCCGGACGGTGCTGGGG	0.597																																					p.T657M		Atlas-SNP	.											OAS3,NS,carcinoma,-1,1	OAS3	63	1	0			c.C1970T						PASS	.	C	MET/THR	1,4099		0,1,2049	119	128	125		1970	3.2	0	12		125	2,8408		0,2,4203	yes	missense	OAS3	NM_006187.2	81	0,3,6252	TT,TC,CC		0.0238,0.0244,0.024	probably-damaging	657/1088	113400593	3,12507	2050	4205	6255	SO:0001583	missense	4940	exon9			TCCGGACGGTGCT	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.1970C>T	12.37:g.113400593C>T	ENSP00000228928:p.Thr657Met	111	0	0		119	57	0.478992	NM_006187	Q2HJ14|Q9H3P5	Missense_Mutation	SNP	ENST00000228928.7	37	CCDS44981.1	.	.	.	.	.	.	.	.	.	.	C	14.24	2.476130	0.44044	2.44E-4	2.38E-4	ENSG00000111331	ENST00000228928;ENST00000323881	T	0.59224	0.28	4.1	3.19	0.36642	-oligoadenylate synthetase 1, domain 2/C-terminal (2);-5&apos (2);2&apos (2);	.	.	.	.	T	0.76271	0.3964	M	0.87900	2.915	0.18873	N	0.999981	D	0.89917	1.0	D	0.77557	0.99	T	0.64415	-0.6413	9	0.87932	D	0	.	8.9438	0.35747	0.2222:0.7778:0.0:0.0	.	657	Q9Y6K5	OAS3_HUMAN	M	657;656	ENSP00000228928:T657M	ENSP00000228928:T657M	T	+	2	0	OAS3	111884976	0.568000	0.26635	0.002000	0.10522	0.012000	0.07955	2.416000	0.44644	0.917000	0.36895	0.655000	0.94253	ACG	.	.	weak		0.597	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1			T	113400593	C	T	113400593	3	4	25	1	0	0	0	0	1	0	0	0	10810	536	19	1	2004	1	OAS3	12	113400593	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	799710	113400593	20451302	530	9439											
FBXW8	26259	hgsc.bcm.edu	37	chr12	117402583	117402583	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctggaatcagaggacgaggaGgatgagcctggaatgcagcc	12	5	16	8	1	1	2	1	1	0	1	1	8	1	7	2	5	3	1	2	5	2	0	rs141777878	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:117402583G>C	ENST00000309909.5	+	5	841	c.759G>C	c.(757-759)gaG>gaC	p.E253D	FBXW8_ENST00000455858.2_Missense_Mutation_p.E187D			Q8N3Y1	FBXW8_HUMAN	F-box and WD repeat domain containing 8	253					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)		AGGACGAGGAGGATGAGCCTG	0.532													G|||	4	0.000798722	0.0015	0.0014	5008	,	,		18740	0.0		0.0	False		,,,				2504	0.001				p.E253D		Atlas-SNP	.											.	FBXW8	53	.	0			c.G759C						PASS	.	G	ASP/GLU,ASP/GLU	4,4402	8.1+/-20.4	0,4,2199	183	159	167		561,759	4.3	1	12	dbSNP_134	167	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	FBXW8	NM_012174.1,NM_153348.2	45,45	0,9,6494	CC,CG,GG		0.0581,0.0908,0.0692	possibly-damaging,possibly-damaging	187/533,253/599	117402583	9,12997	2203	4300	6503	SO:0001583	missense	26259	exon5			CGAGGAGGATGAG	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.759G>C	12.37:g.117402583G>C	ENSP00000310686:p.Glu253Asp	93	0	0		83	47	0.566265	NM_153348	Q9UK95	Missense_Mutation	SNP	ENST00000309909.5	37	CCDS9182.1	3	0.0013736263736263737	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	G	15.67	2.901463	0.52227	9.08E-4	5.81E-4	ENSG00000174989	ENST00000309909;ENST00000455858;ENST00000505227	T;T	0.09163	3.02;3.01	5.28	4.33	0.51752	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.195075	0.45126	D	0.000397	T	0.09818	0.0241	L	0.48642	1.525	0.28382	N	0.919506	P;P	0.49559	0.925;0.774	B;B	0.40285	0.325;0.236	T	0.18808	-1.0325	10	0.13108	T	0.6	-32.349	13.4249	0.61020	0.0:0.0:0.7974:0.2026	.	253;187	Q8N3Y1;Q8N3Y1-2	FBXW8_HUMAN;.	D	253;187;187	ENSP00000310686:E253D;ENSP00000389144:E187D	ENSP00000310686:E253D	E	+	3	2	FBXW8	115886966	0.999000	0.42202	1.000000	0.80357	0.924000	0.55760	0.860000	0.27871	2.906000	0.99361	0.655000	0.94253	GAG	G|0.999;C|0.001	0.001	strong		0.532	FBXW8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403561.1	NM_012174		C	117402583	G	C	117402583	3	2	25	1	0	0	0	0	1	0	0	0	5778	991	35	4	777	4	FBXW8	12	117402583	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	4001990	117402583	16449312	531	9440											
TESC	54997	hgsc.bcm.edu	37	chr12	117486947	117486947	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctcatcagccaggccactggGtcccttgcgcaggttcctac	6	9	10	16	1	2	0	2	0	0	0	4	0	4	0	4	3	3	2	4	3	1	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:117486947G>T	ENST00000335209.7	-	4	412	c.226C>A	c.(226-228)Ccc>Acc	p.P76T	TESC_ENST00000541210.1_Missense_Mutation_p.P49T|TESC_ENST00000392545.4_Missense_Mutation_p.P129T|TESC_ENST00000535198.1_5'UTR			Q96BS2	CHP3_HUMAN	tescalcin	76					cell differentiation (GO:0030154)|cellular response to retinoic acid (GO:0071300)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell proliferation (GO:0008285)|positive regulation of gene expression (GO:0010628)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of sodium:proton antiporter activity (GO:0032417)|positive regulation of transcription, DNA-templated (GO:0045893)|protein maturation (GO:0051604)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of cell adhesion mediated by integrin (GO:0033628)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|phosphatase inhibitor activity (GO:0019212)|protein homodimerization activity (GO:0042803)|protein kinase inhibitor activity (GO:0004860)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	6	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0297)		AGGCCACTGGGTCCCTTGCGC	0.537																																					p.P76T		Atlas-SNP	.											.	TESC	16	.	0			c.C226A						PASS	.						131	119	123					12																	117486947		2203	4300	6503	SO:0001583	missense	54997	exon4			CACTGGGTCCCTT	AF443207	CCDS9183.2, CCDS9183.3, CCDS53835.1	12q24.22	2013-01-10			ENSG00000088992	ENSG00000088992		"EF-hand domain containing"	26065	protein-coding gene	gene with protein product	"calcineurin-like EF hand protein 3"	611585				11145610, 11696366, 12809501, 14661968	Standard	NM_017899		Approved	TSC, FLJ20607, CHP3	uc001twh.3	Q96BS2	OTTHUMG00000144168	ENST00000335209.7:c.226C>A	12.37:g.117486947G>T	ENSP00000334785:p.Pro76Thr	66	0	0		73	31	0.424658	NM_017899	F5H1Y5|Q9NWT9	Missense_Mutation	SNP	ENST00000335209.7	37	CCDS9183.3	.	.	.	.	.	.	.	.	.	.	G	7.196	0.592551	0.13875	.	.	ENSG00000088992	ENST00000335209;ENST00000392545;ENST00000541210	T;T;T	0.39997	1.05;1.05;1.13	5.92	0.671	0.17929	EF-hand-like domain (1);	0.691593	0.14781	N	0.298762	T	0.18635	0.0447	N	0.13043	0.29	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.22243	-1.0222	10	0.14252	T	0.57	-11.9903	2.8483	0.05550	0.3475:0.109:0.4322:0.1112	.	76	Q96BS2	TESC_HUMAN	T	76;129;49	ENSP00000334785:P76T;ENSP00000376328:P129T;ENSP00000445689:P49T	ENSP00000334785:P76T	P	-	1	0	TESC	115971330	0.000000	0.05858	0.478000	0.27316	0.638000	0.38207	-0.280000	0.08468	-0.381000	0.07882	-1.164000	0.01763	CCC	.	.	none		0.537	TESC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291363.2	NM_017899		T	117486947	G	T	117486947	3	4	25	1	0	0	0	0	1	0	0	0	15781	1261	44	4	438	4	TESC	12	117486947	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	84364	117486947	16364948	532	9441											
HSPB8	26353	hgsc.bcm.edu	37	chr12	119617350	119617350	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggccccactgccaccgccaGgtttggggtgcctgccgagg	4	6	16	15	2	0	0	0	0	0	0	0	1	0	0	7	5	3	1	7	5	0	1	rs55826713		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:119617350G>T	ENST00000281938.2	+	1	904	c.233G>T	c.(232-234)aGg>aTg	p.R78M	RP11-64B16.4_ENST00000535921.1_RNA	NM_014365.2	NP_055180.1	Q9UJY1	HSPB8_HUMAN	heat shock 22kDa protein 8	78			R -> M (in dbSNP:rs55826713). {ECO:0000269|PubMed:17344846}.		cell death (GO:0008219)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(9)|skin(1)	14	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GCCACCGCCAGGTTTGGGGTG	0.672													G|||	1	0.000199681	0.0	0.0	5008	,	,		14955	0.0		0.001	False		,,,				2504	0.0				p.R78M		Atlas-SNP	.											.	HSPB8	45	.	0			c.G233T						PASS	.	G	MET/ARG	0,4404		0,0,2202	26	31	30		233	4.4	0.9	12	dbSNP_129	30	8,8592	6.4+/-24.3	0,8,4292	no	missense	HSPB8	NM_014365.2	91	0,8,6494	TT,TG,GG		0.093,0.0,0.0615	benign	78/197	119617350	8,12996	2202	4300	6502	SO:0001583	missense	26353	exon1			CCGCCAGGTTTGG	AF191017	CCDS9189.1	12q24.23	2014-09-17	2004-04-23					"Heat shock proteins / HSPB"	30171	protein-coding gene	gene with protein product		608014	"heat shock 27kDa protein 8"			10833516, 11085516	Standard	NM_014365		Approved	H11, E2IG1, HSP22, HspB8	uc001txb.3	Q9UJY1		ENST00000281938.2:c.233G>T	12.37:g.119617350G>T	ENSP00000281938:p.Arg78Met	25	0	0		42	22	0.52381	NM_014365	B2R6A6|Q6FIH3|Q9UKS3	Missense_Mutation	SNP	ENST00000281938.2	37	CCDS9189.1	.	.	.	.	.	.	.	.	.	.	G	14.24	2.476262	0.44044	0.0	9.3E-4	ENSG00000152137	ENST00000281938	D	0.87650	-2.28	4.42	4.42	0.53409	HSP20-like chaperone (1);	0.414383	0.24285	N	0.039876	D	0.83968	0.5369	L	0.53249	1.67	0.47183	D	0.999349	P	0.44578	0.838	B	0.41691	0.364	D	0.83545	0.0098	9	.	.	.	.	12.7024	0.57041	0.0823:0.0:0.9177:0.0	rs55826713	78	Q9UJY1	HSPB8_HUMAN	M	78	ENSP00000281938:R78M	.	R	+	2	0	HSPB8	118101733	1.000000	0.71417	0.938000	0.37757	0.256000	0.26092	5.565000	0.67365	2.294000	0.77228	0.563000	0.77884	AGG	G|0.999;T|0.001	0.001	strong		0.672	HSPB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401647.1	NM_014365		T	119617350	G	T	119617350	3	4	25	1	0	0	0	0	1	0	0	0	7432	1000	35	4	235	4	HSPB8	12	119617350	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2130403	119617350	14234545	533	9442											
RPLP0	6175	hgsc.bcm.edu	37	chr12	120636498	120636498	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgttcagcagcgtggcttcGctggctcccactttgtctcc	4	13	10	14	2	2	0	1	0	1	0	5	0	3	0	2	2	2	5	2	2	0	3	rs138718343		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:120636498G>A	ENST00000551150.1	-	5	825	c.510C>T	c.(508-510)agC>agT	p.S170S	RPLP0_ENST00000228306.4_Silent_p.S170S|PXN-AS1_ENST00000538804.1_RNA|RPLP0_ENST00000392514.4_Silent_p.S170S|RPLP0_ENST00000313104.5_Intron|RPLP0_ENST00000546989.1_Intron|PXN-AS1_ENST00000535200.1_RNA|PXN-AS1_ENST00000542314.1_RNA|PXN-AS1_ENST00000539446.1_RNA|RPLP0_ENST00000550296.1_5'Flank|PXN-AS1_ENST00000542265.1_RNA|RPLP0_ENST00000552292.1_5'Flank			P05388	RLA0_HUMAN	ribosomal protein, large, P0	170					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)					GCGTGGCTTCGCTGGCTCCCA	0.527																																					p.S170S		Atlas-SNP	.											.	RPLP0	27	.	0			c.C510T						PASS	.	G	,	0,4406		0,0,2203	72	69	70		510,510	-0.5	1	12	dbSNP_134	70	3,8593	3.0+/-9.4	0,3,4295	no	coding-synonymous,coding-synonymous	RPLP0	NM_001002.3,NM_053275.3	,	0,3,6498	AA,AG,GG		0.0349,0.0,0.0231	,	170/318,170/318	120636498	3,12999	2203	4298	6501	SO:0001819	synonymous_variant	6175	exon6			GGCTTCGCTGGCT	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.510C>T	12.37:g.120636498G>A		153	0	0		201	86	0.427861	NM_053275	Q3B7A4|Q9BVK4	Silent	SNP	ENST00000551150.1	37	CCDS9193.1																																																																																			G|1.000;A|0.000	0.000	weak		0.527	RPLP0-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403448.3	NM_053275		A	120636498	G	A	120636498	2	1	25	1	0	0	0	0	0	0	0	1	13619	1078	38	1		1	RPLP0	12	120636498	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1019148	120636498	13215397	534	9443											
HNF1A	6927	hgsc.bcm.edu	37	chr12	121435342	121435342	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggcagcagcctgaccaccCtgcagcccgtccagttctcc	6	7	10	18	1	1	1	0	1	1	0	3	1	2	1	6	1	4	4	6	1	0	1	rs544842497|rs2259820	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:121435342C>T	ENST00000257555.6	+	7	1601	c.1375C>T	c.(1375-1377)Ctg>Ttg	p.L459L	HNF1A_ENST00000400024.2_Silent_p.L459L|HNF1A_ENST00000402929.1_3'UTR|HNF1A_ENST00000538626.1_Silent_p.L41L|RP11-216P16.2_ENST00000606238.1_RNA|HNF1A_ENST00000544413.1_Silent_p.L459L|HNF1A_ENST00000541395.1_Silent_p.L459L			P20823	HNF1A_HUMAN	HNF1 homeobox A	459					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)					CCTGACCACCCTGCAGCCCGT	0.667									Hepatic Adenoma, Familial Clustering of				c|||	1586	0.316693	0.1089	0.3501	5008	,	,		17758	0.4732		0.3161	False		,,,				2504	0.4131				p.L459L		Atlas-SNP	.											.	HNF1A	302	.	0			c.C1375T						PASS	.	C		529,3877	232.0+/-245.7	41,447,1715	33	35	34		1375	4.6	1	12	dbSNP_100	34	2675,5923	412.6+/-350.9	434,1807,2058	no	coding-synonymous	HNF1A	NM_000545.5		475,2254,3773	TT,TC,CC		31.1119,12.0064,24.6386		459/632	121435342	3204,9800	2203	4299	6502	SO:0001819	synonymous_variant	6927	exon7	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	ACCACCCTGCAGC	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.1375C>T	12.37:g.121435342C>T		116	0	0		103	45	0.436893	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Silent	SNP	ENST00000257555.6	37	CCDS9209.1																																																																																			C|0.718;T|0.282	0.282	strong		0.667	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		T	121435342	C	T	121435342	2	4	25	1	0	0	0	0	0	0	0	1	7260	680	24	2		2	HNF1A	12	121435342	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	798844	121435342	12416553	535	9444											
HNF1A	6927	hgsc.bcm.edu	37	chr12	121435427	121435427	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagagccatgtgacccagaGccccttcatggccaccatgg	9	6	11	15	0	1	3	1	1	0	2	1	3	1	3	6	2	2	1	6	2	0	1	rs2464196	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:121435427G>A	ENST00000257555.6	+	7	1686	c.1460G>A	c.(1459-1461)aGc>aAc	p.S487N	HNF1A_ENST00000400024.2_Missense_Mutation_p.S487N|HNF1A_ENST00000402929.1_3'UTR|HNF1A_ENST00000538626.1_Missense_Mutation_p.S69N|RP11-216P16.2_ENST00000606238.1_RNA|HNF1A_ENST00000544413.1_Missense_Mutation_p.S487N|HNF1A_ENST00000541395.1_Missense_Mutation_p.S487N			P20823	HNF1A_HUMAN	HNF1 homeobox A	487			S -> N (in dbSNP:rs2464196). {ECO:0000269|PubMed:9112026, ECO:0000269|PubMed:9133564, ECO:0000269|PubMed:9287055, ECO:0000269|PubMed:9604876, ECO:0000269|PubMed:9621514, ECO:0000269|Ref.6}.		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)					GTGACCCAGAGCCCCTTCATG	0.637									Hepatic Adenoma, Familial Clustering of				g|||	1591	0.317692	0.112	0.3501	5008	,	,		18114	0.4732		0.3161	False		,,,				2504	0.4141				p.S487N		Atlas-SNP	.											.	HNF1A	302	.	0			c.G1460A	GRCh37	CM067474	HNF1A	M	rs2464196	PASS	.	G	ASN/SER	541,3865	230.4+/-244.6	42,457,1704	29	28	29		1460	3.5	1	12	dbSNP_100	29	2676,5924	411.0+/-350.3	431,1814,2055	yes	missense	HNF1A	NM_000545.5	46	473,2271,3759	AA,AG,GG		31.1163,12.2787,24.7347	possibly-damaging	487/632	121435427	3217,9789	2203	4300	6503	SO:0001583	missense	6927	exon7	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CCCAGAGCCCCTT	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.1460G>A	12.37:g.121435427G>A	ENSP00000257555:p.Ser487Asn	148	0	0		133	62	0.466165	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Missense_Mutation	SNP	ENST00000257555.6	37	CCDS9209.1	715	0.3273809523809524	54	0.10975609756097561	132	0.36464088397790057	296	0.5174825174825175	233	0.3073878627968338	G	12.39	1.924644	0.34002	0.122787	0.311163	ENSG00000135100	ENST00000257555;ENST00000535125;ENST00000537424;ENST00000543027;ENST00000541395;ENST00000340577;ENST00000544413	D;D;D	0.97455	-4.39;-4.39;-4.39	4.49	3.53	0.40419	Hepatocyte nuclear factor 1, beta isoform, C-terminal (1);	0.068781	0.64402	N	0.000014	T	0.00012	0.0000	L	0.40543	1.245	0.09310	P	0.99999999123403	B;B;B	0.24576	0.0;0.014;0.106	B;B;B	0.32533	0.005;0.085;0.147	T	0.04153	-1.0973	9	0.42905	T	0.14	-9.2011	10.4952	0.44772	0.104:0.0:0.896:0.0	rs2464196;rs2708085;rs16950667;rs17847503;rs56962510;rs2464196	487;487;487	F5H0K0;P20823;E7EUQ4	.;HNF1A_HUMAN;.	N	487;379;487;308;487;487;487	ENSP00000257555:S487N;ENSP00000443112:S487N;ENSP00000438804:S487N	ENSP00000257555:S487N	S	+	2	0	HNF1A	119919810	0.950000	0.32346	0.992000	0.48379	0.944000	0.59088	1.527000	0.35975	0.976000	0.38417	0.655000	0.94253	AGC	G|0.725;A|0.275	0.275	strong		0.637	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		A	121435427	G	A	121435427	3	1	25	1	0	0	0	0	1	0	0	0	7260	971	34	2	1486	2	HNF1A	12	121435427	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	85	121435427	12416468	536	9445											
KNTC1	9735	hgsc.bcm.edu	37	chr12	123032478	123032478	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttaggcaaggaattacaaatCtcaaattaatagctctgaca	17	11	6	7	0	2	1	1	1	2	0	3	2	2	2	0	2	2	2	0	2	8	4	rs61751321	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:123032478C>T	ENST00000333479.7	+	12	1126	c.949C>T	c.(949-951)Ctc>Ttc	p.L317F	KNTC1_ENST00000450485.2_Missense_Mutation_p.L280F	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	317					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)		AATTACAAATCTCAAATTAAT	0.259													C|||	5	0.000998403	0.0	0.0	5008	,	,		15154	0.0		0.001	False		,,,				2504	0.0041				p.L317F		Atlas-SNP	.											.	KNTC1	182	.	0			c.C949T						PASS	.	C	PHE/LEU	1,3563		0,1,1781	43	40	41		949	5.3	1	12	dbSNP_129	41	27,8073		0,27,4023	yes	missense	KNTC1	NM_014708.4	22	0,28,5804	TT,TC,CC		0.3333,0.0281,0.2401	possibly-damaging	317/2210	123032478	28,11636	1782	4050	5832	SO:0001583	missense	9735	exon12			ACAAATCTCAAAT		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.949C>T	12.37:g.123032478C>T	ENSP00000328236:p.Leu317Phe	43	0	0		40	14	0.35	NM_014708	A7E2C4|B3KSG2	Missense_Mutation	SNP	ENST00000333479.7	37	CCDS45002.1	.	.	.	.	.	.	.	.	.	.	C	12.64	2.000039	0.35320	2.81E-4	0.003333	ENSG00000184445	ENST00000450485;ENST00000333479	T;T	0.17054	2.3;2.3	5.35	5.35	0.76521	.	0.201753	0.44483	D	0.000444	T	0.32285	0.0824	L	0.56769	1.78	0.80722	D	1	D;D	0.63880	0.983;0.993	P;P	0.59288	0.799;0.855	T	0.00722	-1.1594	10	0.46703	T	0.11	-12.1835	12.9217	0.58237	0.0:0.8244:0.1756:0.0	rs61751321	280;317	E7ES84;P50748	.;KNTC1_HUMAN	F	280;317	ENSP00000397992:L280F;ENSP00000328236:L317F	ENSP00000328236:L317F	L	+	1	0	KNTC1	121598431	1.000000	0.71417	1.000000	0.80357	0.577000	0.36160	3.241000	0.51376	2.668000	0.90789	0.573000	0.79308	CTC	C|0.991;T|0.008	0.008	strong		0.259	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2			T	123032478	C	T	123032478	3	4	25	1	0	0	0	0	1	0	0	0	8437	913	32	2	991	2	KNTC1	12	123032478	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1597051	123032478	10819417	537	9446											
DNAH10	196385	hgsc.bcm.edu	37	chr12	124366300	124366300	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggccacgccctgctggtcggGgtagggggctcagggaagca	6	5	19	11	2	1	0	1	0	0	0	2	1	1	1	2	7	2	4	2	7	2	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:124366300G>T	ENST00000409039.3	+	50	8434	c.8409G>T	c.(8407-8409)ggG>ggT	p.G2803G		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2803	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(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)		TGCTGGTCGGGGTAGGGGGCT	0.582																																					p.G2803G		Atlas-SNP	.											.	DNAH10	888	.	0			c.G8409T						PASS	.						17	20	19					12																	124366300		1775	3736	5511	SO:0001819	synonymous_variant	196385	exon50			GGTCGGGGTAGGG	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.8409G>T	12.37:g.124366300G>T		101	0	0		92	43	0.467391	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																			.	.	none		0.582	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124366300	G	T	124366300	2	4	25	1	0	0	0	0	0	0	0	1	4600	1219	43	4		4	DNAH10	12	124366300	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1333822	124366300	9485595	538	9447											
NCOR2	9612	hgsc.bcm.edu	37	chr12	124886979	124886979	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttccttgtcgttctccacCtccggcttctcctcctcctt	1	17	4	19	2	3	0	0	0	3	0	10	0	7	0	7	1	0	2	7	1	0	5	rs202047482	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:124886979C>T	ENST00000405201.1	-	14	1611	c.1611G>A	c.(1609-1611)gaG>gaA	p.E537E	NCOR2_ENST00000404121.2_Silent_p.E107E|NCOR2_ENST00000397355.1_Silent_p.E537E|NCOR2_ENST00000356219.3_Silent_p.E537E|NCOR2_ENST00000404621.1_Silent_p.E536E|NCOR2_ENST00000429285.2_Silent_p.E536E			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	537					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)		CGTTCTCCACCTCCGGcttct	0.637													C|||	2	0.000399361	0.0	0.0014	5008	,	,		15261	0.0		0.001	False		,,,				2504	0.0				p.E537E		Atlas-SNP	.											.	NCOR2	475	.	0			c.G1611A						PASS	.	C	,,	0,4292		0,0,2146	97	119	112		1608,1608,1611	-7.6	0.1	12		112	6,8488		0,6,4241	no	coding-synonymous,coding-synonymous,coding-synonymous	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	,,	0,6,6387	TT,TC,CC		0.0706,0.0,0.0469	,,	536/2459,536/2505,537/2515	124886979	6,12780	2146	4247	6393	SO:0001819	synonymous_variant	9612	exon16			CTCCACCTCCGGC	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.1611G>A	12.37:g.124886979C>T		101	0	0		122	70	0.57377	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	37	CCDS41858.2																																																																																			C|0.999;T|0.001	0.001	weak		0.637	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		T	124886979	C	T	124886979	2	4	25	1	0	0	0	0	0	0	0	1	10245	680	24	2		2	NCOR2	12	124886979	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	520679	124886979	8964916	539	9448											
TMEM132D	121256	hgsc.bcm.edu	37	chr12	130184947	130184947	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgggcttttagtttccagtTaagagaaaatttgttggtga	10	16	12	3	0	0	2	0	1	0	1	1	3	1	2	1	2	0	4	1	2	4	6			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:130184947T>A	ENST00000422113.2	-	2	702	c.376A>T	c.(376-378)Aac>Tac	p.N126Y	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	126					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)		AGTTTCCAGTTAAGAGAAAAT	0.517																																					p.N126Y		Atlas-SNP	.											.	TMEM132D	299	.	0			c.A376T						PASS	.						56	56	56					12																	130184947		2203	4300	6503	SO:0001583	missense	121256	exon2			TCCAGTTAAGAGA	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.376A>T	12.37:g.130184947T>A	ENSP00000408581:p.Asn126Tyr	82	0	0		88	34	0.386364	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	37	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	T	17.73	3.462540	0.63513	.	.	ENSG00000151952	ENST00000422113	T	0.13307	2.6	5.33	5.33	0.75918	.	0.082670	0.48767	D	0.000166	T	0.38878	0.1057	M	0.79123	2.44	0.44754	D	0.997754	D	0.89917	1.0	D	0.78314	0.991	T	0.21075	-1.0256	9	.	.	.	-44.5477	15.3082	0.74011	0.0:0.0:0.0:1.0	.	126	Q14C87	T132D_HUMAN	Y	126	ENSP00000408581:N126Y	.	N	-	1	0	TMEM132D	128750900	1.000000	0.71417	0.881000	0.34555	0.437000	0.31866	4.073000	0.57570	2.001000	0.58596	0.454000	0.30748	AAC	.	.	none		0.517	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		A	130184947	T	A	130184947	3	1	25	1	0	0	0	0	1	0	0	0	16062	1754	61	5	2955	5	TMEM132D	12	130184947	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	5297968	130184947	3666948	540	9449											
GPR133	283383	hgsc.bcm.edu	37	chr12	131471699	131471699	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagggcctgaaagtctacGtcaacgggaccctgagcacc	11	5	13	12	2	2	2	1	2	1	0	2	4	2	4	3	3	3	1	3	3	3	1	rs61732860	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:131471699G>A	ENST00000261654.5	+	6	1109	c.550G>A	c.(550-552)Gtc>Atc	p.V184I	GPR133_ENST00000535015.1_Missense_Mutation_p.V216I|RP11-76C10.5_ENST00000542980.1_lincRNA	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	184					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.V184I(1)		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)		GAAAGTCTACGTCAACGGGAC	0.517													G|||	44	0.00878594	0.0008	0.0202	5008	,	,		20919	0.0		0.0209	False		,,,				2504	0.0082				p.V184I		Atlas-SNP	.											GPR133,NS,carcinoma,0,1	GPR133	136	1	1	Substitution - Missense(1)	prostate(1)	c.G550A						PASS	.	G	ILE/VAL	15,4391	22.3+/-47.3	0,15,2188	115	107	110		550	3.7	1	12	dbSNP_129	110	173,8427	79.5+/-142.1	3,167,4130	yes	missense	GPR133	NM_198827.3	29	3,182,6318	AA,AG,GG		2.0116,0.3404,1.4455	possibly-damaging	184/875	131471699	188,12818	2203	4300	6503	SO:0001583	missense	283383	exon6			GTCTACGTCAACG	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.550G>A	12.37:g.131471699G>A	ENSP00000261654:p.Val184Ile	133	0	0		129	63	0.488372	NM_198827	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Missense_Mutation	SNP	ENST00000261654.5	37	CCDS9272.1	23	0.010531135531135532	0	0.0	7	0.019337016574585635	0	0.0	16	0.021108179419525065	G	9.840	1.190859	0.21954	0.003404	0.020116	ENSG00000111452	ENST00000261654;ENST00000542091;ENST00000535015	T;T;T	0.74526	-0.85;-0.85;-0.85	4.55	3.67	0.42095	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.146844	0.46442	N	0.000283	T	0.43478	0.1249	L	0.28014	0.82	0.80722	D	1	B;B	0.28512	0.003;0.214	B;B	0.24006	0.01;0.05	T	0.48917	-0.8992	10	0.33141	T	0.24	.	11.9058	0.52711	0.0852:0.0:0.9148:0.0	rs61732860	216;184	B7ZLF7;Q6QNK2	.;GP133_HUMAN	I	184;124;216	ENSP00000261654:V184I;ENSP00000442501:V124I;ENSP00000444425:V216I	ENSP00000261654:V184I	V	+	1	0	GPR133	130037652	0.991000	0.36638	0.999000	0.59377	0.690000	0.40134	2.351000	0.44071	0.912000	0.36772	-0.126000	0.14955	GTC	G|0.985;A|0.015	0.015	strong		0.517	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827		A	131471699	G	A	131471699	3	1	25	1	0	0	0	0	1	0	0	0	6651	1145	40	1	572	1	GPR133	12	131471699	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1286752	131471699	2380196	541	9450											
MTUS2	23281	hgsc.bcm.edu	37	chr13	29675049	29675049	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggagctccagcgtctcctcAgtctccagcacccagtccgg	6	7	10	18	3	3	0	1	0	2	0	7	1	5	1	5	2	3	2	5	2	0	0	rs140464903	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:29675049A>T	ENST00000431530.3	+	3	2674	c.2616A>T	c.(2614-2616)tcA>tcT	p.S872S		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	862	Localization to the growing distal tip of microtubules.|Mediates interaction with MAPRE1.|Sufficient for interaction with KIF2C.					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						GCGTCTCCTCAGTCTCCAGCA	0.632													A|||	114	0.0227636	0.0053	0.0259	5008	,	,		12307	0.002		0.0596	False		,,,				2504	0.0276				p.S872S		Atlas-SNP	.											MTUS2_ENST00000431530,NS,carcinoma,0,1	MTUS2	279	1	0			c.A2616T						PASS	.	A		41,4015		1,39,1988	8	9	9		2616	-10.5	0	13	dbSNP_134	9	361,8001		4,353,3824	no	coding-synonymous	MTUS2	NM_001033602.2		5,392,5812	TT,TA,AA		4.3171,1.0108,3.2372		872/1380	29675049	402,12016	2028	4181	6209	SO:0001819	synonymous_variant	23281	exon3			CTCCTCAGTCTCC	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.2616A>T	13.37:g.29675049A>T		72	0	0		87	40	0.45977	NM_001033602	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Silent	SNP	ENST00000431530.3	37	CCDS45022.1																																																																																			A|0.965;T|0.035	0.035	strong		0.632	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270		T	29675049	A	T	29675049	2	4	25	1	0	0	0	0	0	0	0	1	9975	175	7	5		5	MTUS2	13	29675049	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10		29675049	85494829	542	9451											
RXFP2	122042	hgsc.bcm.edu	37	chr13	32367214	32367214	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aagcaaagggtattctcttgGaattttcctaggtaaattat	13	15	8	5	0	1	0	0	0	1	0	3	1	2	1	1	3	1	3	1	3	8	8			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:32367214G>A	ENST00000298386.2	+	16	1846	c.1775G>A	c.(1774-1776)gGa>gAa	p.G592E	RXFP2_ENST00000380314.1_Missense_Mutation_p.G568E	NM_130806.3	NP_570718.1	Q8WXD0	RXFP2_HUMAN	relaxin/insulin-like family peptide receptor 2	592					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oocyte maturation (GO:0001556)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	peptide hormone binding (GO:0017046)|protein-hormone receptor activity (GO:0016500)			cervix(1)|endometrium(2)|large_intestine(15)|lung(13)|prostate(1)|stomach(1)	33		Lung SC(185;0.0262)		all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535)		TATTCTCTTGGAATTTTCCTA	0.294																																					p.G592E		Atlas-SNP	.											RXFP2,colon,carcinoma,0,1	RXFP2	95	1	0			c.G1775A						scavenged	.						30	34	33					13																	32367214		2188	4292	6480	SO:0001583	missense	122042	exon16			CTCTTGGAATTTT	AF403384	CCDS9342.1, CCDS53862.1	13q12.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000133105	ENSG00000133105		"GPCR / Class A : Relaxin family peptide receptors"	17318	protein-coding gene	gene with protein product		606655	"leucine-rich repeat-containing G protein-coupled receptor 8"	LGR8		12217959, 12970298, 15956688, 16507880	Standard	NM_130806		Approved	GREAT, GPR106, INSL3R, RXFPR2	uc001utt.3	Q8WXD0	OTTHUMG00000016690	ENST00000298386.2:c.1775G>A	13.37:g.32367214G>A	ENSP00000298386:p.Gly592Glu	50	0	0		68	3	0.0441176	NM_130806	B1ALE9|Q3KU23	Missense_Mutation	SNP	ENST00000298386.2	37	CCDS9342.1	.	.	.	.	.	.	.	.	.	.	G	18.67	3.673744	0.67928	.	.	ENSG00000133105	ENST00000380314;ENST00000298386	T;T	0.37235	1.21;1.21	5.73	4.88	0.63580	GPCR, rhodopsin-like superfamily (1);	0.102880	0.64402	D	0.000003	T	0.55401	0.1918	M	0.70275	2.135	0.80722	D	1	D;D	0.67145	0.996;0.996	D;D	0.65684	0.937;0.937	T	0.53920	-0.8370	10	0.28530	T	0.3	.	13.8607	0.63559	0.0:0.0:0.8462:0.1538	.	568;592	Q3KU23;Q8WXD0	.;RXFP2_HUMAN	E	568;592	ENSP00000369670:G568E;ENSP00000298386:G592E	ENSP00000298386:G592E	G	+	2	0	RXFP2	31265214	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	2.997000	0.49457	1.412000	0.46977	0.655000	0.94253	GGA	.	.	none		0.294	RXFP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044399.1	NM_130806		A	32367214	G	A	32367214	3	1	25	1	0	0	0	0	1	0	0	0	13775	1174	41	2	1837	2	RXFP2	13	32367214	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2692165	32367214	82802664	543	9452											
FRY	10129	hgsc.bcm.edu	37	chr13	32768428	32768428	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	agccatagcaactgtgtgtgGaagcaggtacgaatttttat	12	12	11	6	1	0	0	0	0	0	0	0	2	0	1	1	2	5	3	1	2	6	5	rs41292163	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:32768428G>A	ENST00000380250.3	+	29	4236	c.3740G>A	c.(3739-3741)gGa>gAa	p.G1247E		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1247						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)		ACTGTGTGTGGAAGCAGGTAC	0.413													G|||	6	0.00119808	0.0	0.0014	5008	,	,		19625	0.0		0.005	False		,,,				2504	0.0				p.G1247E		Atlas-SNP	.											.	FRY	312	.	0			c.G3740A						PASS	.	G	GLU/GLY	7,3831		0,7,1912	97	92	93		3740	5.2	1	13	dbSNP_127	93	45,8251		0,45,4103	yes	missense	FRY	NM_023037.2	98	0,52,6015	AA,AG,GG		0.5424,0.1824,0.4285	benign	1247/3014	32768428	52,12082	1919	4148	6067	SO:0001583	missense	10129	exon29			TGTGTGGAAGCAG	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.3740G>A	13.37:g.32768428G>A	ENSP00000369600:p.Gly1247Glu	93	0	0		106	58	0.54717	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	21.1	4.104845	0.77096	0.001824	0.005424	ENSG00000073910	ENST00000380250;ENST00000380257	T	0.65549	-0.16	5.2	5.2	0.72013	.	0.112550	0.64402	D	0.000008	T	0.53206	0.1782	L	0.50333	1.59	0.80722	D	1	P	0.41848	0.763	P	0.46208	0.507	T	0.56341	-0.7995	10	0.05436	T	0.98	.	19.0865	0.93204	0.0:0.0:1.0:0.0	rs41292163	1247	Q5TBA9	FRY_HUMAN	E	1247;86	ENSP00000369600:G1247E	ENSP00000369600:G1247E	G	+	2	0	FRY	31666428	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	7.659000	0.83766	2.567000	0.86603	0.563000	0.77884	GGA	G|0.996;A|0.004	0.004	strong		0.413	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037		A	32768428	G	A	32768428	3	1	25	1	0	0	0	0	1	0	0	0	6071	1174	41	2	3854	2	FRY	13	32768428	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	401214	32768428	82401450	544	9453											
BRCA2	675	hgsc.bcm.edu	37	chr13	32914126	32914126	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaagtaattaaggaaaacaaCgagaataaatcaaaaatttg	24	8	6	3	1	1	1	1	0	0	1	1	3	1	2	0	1	2	1	0	1	11	4	rs80358784		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:32914126C>G	ENST00000380152.3	+	11	5867	c.5634C>G	c.(5632-5634)aaC>aaG	p.N1878K	BRCA2_ENST00000544455.1_Missense_Mutation_p.N1878K			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1878					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)		AGGAAAACAACGAGAATAAAT	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.N1878K	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.C5634G						PASS	.						44	43	43					13																	32914126		2203	4300	6503	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)	AAACAACGAGAAT	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.5634C>G	13.37:g.32914126C>G	ENSP00000369497:p.Asn1878Lys	81	0	0		61	27	0.442623	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	C	4.413	0.076344	0.08485	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.68181	-0.31;-0.31	5.71	-5.99	0.02213	.	0.505217	0.19599	N	0.110421	T	0.29588	0.0738	N	0.08118	0	0.09310	N	1	B	0.15930	0.015	B	0.14578	0.011	T	0.32903	-0.9889	10	0.12766	T	0.61	.	0.9378	0.01348	0.3907:0.1216:0.2013:0.2864	.	1878	P51587	BRCA2_HUMAN	K	1878	ENSP00000369497:N1878K;ENSP00000439902:N1878K	ENSP00000369497:N1878K	N	+	3	2	BRCA2	31812126	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.132000	0.10467	-1.353000	0.02191	-0.295000	0.09555	AAC	C|0.999;T|0.001	.	weak		0.323	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		G	32914126	C	G	32914126	3	3	25	1	0	0	0	0	1	0	0	0	1501	535	19	4	5672	4	BRCA2	13	32914126	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	145698	32914126	82255752	545	9454											
BRCA2	675	hgsc.bcm.edu	37	chr13	32968840	32968840	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctaggacttgcccctttcGtctatttgtcagacgaatgt	7	16	8	10	2	3	1	1	0	2	1	4	3	3	2	2	1	1	0	2	1	3	6	rs80359194		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:32968840G>A	ENST00000380152.3	+	25	9504	c.9271G>A	c.(9271-9273)Gtc>Atc	p.V3091I	BRCA2_ENST00000544455.1_Missense_Mutation_p.V3091I			P51587	BRCA2_HUMAN	breast cancer 2, early onset	3091					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)		TGCCCCTTTCGTCTATTTGTC	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.V3091I	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.G9271A						PASS	.						60	60	60					13																	32968840		2203	4300	6503	SO:0001583	missense	675	exon25	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)	CCTTTCGTCTATT	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.9271G>A	13.37:g.32968840G>A	ENSP00000369497:p.Val3091Ile	73	0	0		67	40	0.597015	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	G	7.433	0.639093	0.14386	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	D;D	0.85702	-2.02;-2.02	5.9	4.16	0.48862	Nucleic acid-binding, OB-fold-like (1);BRCA2, oligonucleotide/oligosaccharide-binding 3 (1);	0.182235	0.48767	N	0.000170	D	0.84529	0.5492	M	0.70903	2.155	0.34869	D	0.74338	B	0.24043	0.096	B	0.26202	0.067	T	0.83263	-0.0047	10	0.52906	T	0.07	.	13.938	0.64036	0.1334:0.0:0.8666:0.0	.	3091	P51587	BRCA2_HUMAN	I	3091	ENSP00000369497:V3091I;ENSP00000439902:V3091I	ENSP00000369497:V3091I	V	+	1	0	BRCA2	31866840	1.000000	0.71417	0.998000	0.56505	0.025000	0.11179	2.306000	0.43673	0.409000	0.25649	-1.119000	0.02030	GTC	.	.	weak		0.323	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		A	32968840	G	A	32968840	3	1	25	1	0	0	0	0	1	0	0	0	1501	1145	40	1	9365	1	BRCA2	13	32968840	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	54714	32968840	82201038	546	9455											
CSNK1A1L	122011	hgsc.bcm.edu	37	chr13	37679120	37679120	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcgaggctgggtcccagaaGgtccatgactagcacattgt	9	10	12	10	1	0	2	0	1	0	1	3	3	2	2	2	3	1	2	2	3	2	3	rs139953443	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:37679120G>C	ENST00000379800.3	-	1	683	c.274C>G	c.(274-276)Ctt>Gtt	p.L92V		NM_145203.5	NP_660204.2	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like	92	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)		GGTCCCAGAAGGTCCATGACT	0.458													G|||	8	0.00159744	0.0053	0.0	5008	,	,		20187	0.0		0.001	False		,,,				2504	0.0				p.L92V		Atlas-SNP	.											.	CSNK1A1L	69	.	0			c.C274G						PASS	.	G	VAL/LEU	19,4387	26.2+/-53.5	0,19,2184	116	108	111		274	1	0.9	13	dbSNP_134	111	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CSNK1A1L	NM_145203.5	32	0,21,6482	CC,CG,GG		0.0233,0.4312,0.1615	possibly-damaging	92/338	37679120	21,12985	2203	4300	6503	SO:0001583	missense	122011	exon1			CCAGAAGGTCCAT	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.274C>G	13.37:g.37679120G>C	ENSP00000369126:p.Leu92Val	134	0	0		127	65	0.511811	NM_145203	Q5T2N2	Missense_Mutation	SNP	ENST00000379800.3	37	CCDS9363.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	16.63	3.176449	0.57692	0.004312	2.33E-4	ENSG00000180138	ENST00000379800	T	0.23348	1.91	1.01	1.01	0.19927	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	0.54727	0.1876	H	0.96996	3.92	0.44447	D	0.99737	D	0.63880	0.993	P	0.60173	0.87	T	0.63422	-0.6641	10	0.87932	D	0	.	7.8591	0.29499	0.0:0.0:1.0:0.0	.	92	Q8N752	KC1AL_HUMAN	V	92	ENSP00000369126:L92V	ENSP00000369126:L92V	L	-	1	0	CSNK1A1L	36577120	1.000000	0.71417	0.926000	0.36857	0.971000	0.66376	2.973000	0.49264	0.825000	0.34637	0.561000	0.74099	CTT	G|0.998;C|0.002	0.002	strong		0.458	CSNK1A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044563.1	NM_145203		C	37679120	G	C	37679120	3	2	25	1	0	0	0	0	1	0	0	0	3953	1000	35	4	743	4	CSNK1A1L	13	37679120	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	4710280	37679120	77490758	547	9456											
TRPC4	7223	hgsc.bcm.edu	37	chr13	38211046	38211046	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctccttcaagtatcacaaTcttgtggtcacgtaatcttc	9	15	5	12	1	5	0	3	0	2	0	8	0	7	0	2	1	0	2	2	1	4	5	rs731860	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:38211046T>C	ENST00000379705.3	-	11	3785	c.2928A>G	c.(2926-2928)agA>agG	p.R976R	TRPC4_ENST00000379673.2_Silent_p.R827R|TRPC4_ENST00000355779.2_Silent_p.R835R|TRPC4_ENST00000379681.3_Silent_p.R981R|TRPC4_ENST00000447043.1_Silent_p.R835R|TRPC4_ENST00000338947.5_Silent_p.R803R|TRPC4_ENST00000426868.2_3'UTR|TRPC4_ENST00000358477.2_Silent_p.R892R|TRPC4_ENST00000379679.1_Silent_p.R803R			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	976	Binds to ITPR1, ITPR2 and ITPR3.|PDZ-binding domain.				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)		AGTATCACAATCTTGTGGTCA	0.403													T|||	154	0.0307508	0.1112	0.0086	5008	,	,		19821	0.0		0.001	False		,,,				2504	0.0				p.R981R		Atlas-SNP	.											.	TRPC4	389	.	0			c.A2943G						PASS	.	T	,,,,,	428,3978	208.5+/-229.5	24,380,1799	118	111	114		2676,2481,2505,2409,2943,2928	-1.3	0.2	13	dbSNP_86	114	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRPC4	NM_001135955.1,NM_001135956.1,NM_001135957.1,NM_001135958.1,NM_003306.1,NM_016179.2	,,,,,	24,387,6092	CC,CT,TT		0.0814,9.714,3.3446	,,,,,	892/894,827/829,835/837,803/805,981/983,976/978	38211046	435,12571	2203	4300	6503	SO:0001819	synonymous_variant	7223	exon11			TCACAATCTTGTG	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.2928A>G	13.37:g.38211046T>C		118	0	0		127	59	0.464567	NM_003306	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Silent	SNP	ENST00000379705.3	37	CCDS9365.1																																																																																			T|0.959;C|0.041	0.041	strong		0.403	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306		C	38211046	T	C	38211046	2	2	25	1	0	0	0	0	0	0	0	1	16595	1432	50	3		3	TRPC4	13	38211046	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	531926	38211046	76958832	548	9457											
FREM2	341640	hgsc.bcm.edu	37	chr13	39261784	39261784	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggtgttgcaggtgcagccCggggaccgctgcgcggtttc	3	9	17	12	4	0	0	0	0	0	0	1	1	0	1	2	5	4	5	2	5	0	2	rs8002488	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:39261784C>A	ENST00000280481.7	+	1	519	c.303C>A	c.(301-303)ccC>ccA	p.P101P		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	101					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)		AGGTGCAGCCCGGGGACCGCT	0.677													C|||	289	0.0577077	0.2073	0.0216	5008	,	,		14748	0.0		0.0	False		,,,				2504	0.0				p.P101P		Atlas-SNP	.											.	FREM2	385	.	0			c.C303A						PASS	.	C		759,3645		77,605,1520	16	17	17		303	-5.8	0.9	13	dbSNP_116	17	11,8585		0,11,4287	no	coding-synonymous	FREM2	NM_207361.4		77,616,5807	AA,AC,CC		0.128,17.2343,5.9231		101/3170	39261784	770,12230	2202	4298	6500	SO:0001819	synonymous_variant	341640	exon1			GCAGCCCGGGGAC	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.303C>A	13.37:g.39261784C>A		36	0	0		66	38	0.575758	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																			C|0.944;A|0.056	0.056	strong		0.677	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		A	39261784	C	A	39261784	2	1	25	1	0	0	0	0	0	0	0	1	6053	639	23	4		4	FREM2	13	39261784	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1050738	39261784	75908094	549	9458											
FREM2	341640	hgsc.bcm.edu	37	chr13	39263772	39263772	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgggtaccttggtcttgaCtgacaacccctcagtcgtgg	7	11	11	12	1	2	2	1	2	1	0	3	2	2	2	3	3	2	1	3	3	2	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:39263772C>T	ENST00000280481.7	+	1	2507	c.2291C>T	c.(2290-2292)aCt>aTt	p.T764I		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	764					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)		TTGGTCTTGACTGACAACCCC	0.532																																					p.T764I		Atlas-SNP	.											.	FREM2	385	.	0			c.C2291T						PASS	.						84	89	87					13																	39263772		2203	4300	6503	SO:0001583	missense	341640	exon1			TCTTGACTGACAA	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.2291C>T	13.37:g.39263772C>T	ENSP00000280481:p.Thr764Ile	132	0	0		99	50	0.50505	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	C	14.36	2.512067	0.44660	.	.	ENSG00000150893	ENST00000280481	T	0.42131	0.98	5.8	4.95	0.65309	.	0.222181	0.45606	D	0.000354	T	0.44767	0.1309	M	0.69523	2.12	0.53688	D	0.999972	P	0.42161	0.772	B	0.40864	0.342	T	0.48080	-0.9066	10	0.54805	T	0.06	.	11.9366	0.52876	0.1368:0.7317:0.1316:0.0	.	764	Q5SZK8	FREM2_HUMAN	I	764	ENSP00000280481:T764I	ENSP00000280481:T764I	T	+	2	0	FREM2	38161772	0.998000	0.40836	0.895000	0.35142	0.761000	0.43186	3.899000	0.56288	1.437000	0.47472	0.655000	0.94253	ACT	.	.	none		0.532	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39263772	C	T	39263772	3	4	25	1	0	0	0	0	1	0	0	0	6053	565	20	2	2293	2	FREM2	13	39263772	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1988	39263772	75906106	550	9459											
FREM2	341640	hgsc.bcm.edu	37	chr13	39452993	39452993	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agctcagccagagacacaagCgaccagttttggaaatgtcc	13	7	10	11	1	1	1	1	0	0	1	2	4	2	2	3	1	3	2	3	1	2	2	rs7996253	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:39452993C>T	ENST00000280481.7	+	23	9101	c.8885C>T	c.(8884-8886)gCg>gTg	p.A2962V		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2962			A -> V (in dbSNP:rs7996253).		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)		GAGACACAAGCGACCAGTTTT	0.438													C|||	113	0.0225639	0.0817	0.0058	5008	,	,		18911	0.0		0.001	False		,,,				2504	0.0				p.A2962V		Atlas-SNP	.											.	FREM2	385	.	0			c.C8885T						PASS	.	C	VAL/ALA	291,4115	158.5+/-191.2	6,279,1918	152	139	144		8885	2.8	1	13	dbSNP_116	144	0,8600		0,0,4300	yes	missense	FREM2	NM_207361.4	64	6,279,6218	TT,TC,CC		0.0,6.6046,2.2374	benign	2962/3170	39452993	291,12715	2203	4300	6503	SO:0001583	missense	341640	exon23			CACAAGCGACCAG	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.8885C>T	13.37:g.39452993C>T	ENSP00000280481:p.Ala2962Val	158	0	0		155	66	0.425806	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	39	0.017857142857142856	35	0.07113821138211382	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	C	15.76	2.927535	0.52759	0.066046	0.0	ENSG00000150893	ENST00000280481	T	0.63580	-0.05	5.71	2.83	0.33086	.	0.227351	0.44902	N	0.000401	T	0.07954	0.0199	M	0.69823	2.125	0.58432	D	0.999992	P	0.43750	0.816	B	0.37198	0.243	T	0.04333	-1.0959	10	0.26408	T	0.33	.	9.1802	0.37136	0.2607:0.6709:0.0:0.0683	rs7996253;rs52813429;rs7996253	2962	Q5SZK8	FREM2_HUMAN	V	2962	ENSP00000280481:A2962V	ENSP00000280481:A2962V	A	+	2	0	FREM2	38350993	0.994000	0.37717	0.999000	0.59377	0.713000	0.41058	3.132000	0.50523	0.723000	0.32274	0.563000	0.77884	GCG	C|0.978;T|0.022	0.022	strong		0.438	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39452993	C	T	39452993	3	4	25	1	0	0	0	0	1	0	0	0	6053	768	27	1	8975	1	FREM2	13	39452993	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	189221	39452993	75716885	551	9460											
WBP4	11193	hgsc.bcm.edu	37	chr13	41639377	41639377	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gctgcaatggaggcagctgcCctgaaagcataccaagagga	13	5	13	10	0	0	2	0	1	0	1	0	4	0	4	2	3	5	5	2	3	4	1	rs61740513	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:41639377C>T	ENST00000379487.3	+	4	616	c.216C>T	c.(214-216)gcC>gcT	p.A72A	WBP4_ENST00000542082.1_Silent_p.A51A	NM_007187.3	NP_009118.1	O75554	WBP4_HUMAN	WW domain binding protein 4	72					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)		AGGCAGCTGCCCTGAAAGCAT	0.368													C|||	126	0.0251597	0.0908	0.0072	5008	,	,		14418	0.0		0.001	False		,,,				2504	0.0				p.A72A		Atlas-SNP	.											.	WBP4	40	.	0			c.C216T						PASS	.	C		411,3995	201.5+/-224.5	14,383,1806	64	69	67		216	2.8	1	13	dbSNP_129	67	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	WBP4	NM_007187.3		14,385,6104	TT,TC,CC		0.0233,9.3282,3.1755		72/377	41639377	413,12593	2203	4300	6503	SO:0001819	synonymous_variant	11193	exon4			AGCTGCCCTGAAA	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.216C>T	13.37:g.41639377C>T		54	0	0		71	39	0.549296	NM_007187	B7Z4M2|Q32P29	Silent	SNP	ENST00000379487.3	37	CCDS9375.1																																																																																			C|0.967;T|0.033	0.033	strong		0.368	WBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044655.2	NM_007187		T	41639377	C	T	41639377	2	4	25	1	0	0	0	0	0	0	0	1	17276	610	22	2		2	WBP4	13	41639377	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2186384	41639377	73530501	552	9461											
AKAP11	11215	hgsc.bcm.edu	37	chr13	42876103	42876103	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcattcacatactttctcatCtacagcacttacctgtgtag	10	15	4	12	0	4	0	3	0	2	0	5	0	4	0	1	0	4	2	1	0	4	6	rs61756566	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:42876103C>T	ENST00000025301.2	+	8	3396	c.3221C>T	c.(3220-3222)tCt>tTt	p.S1074F		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	1074					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)	p.S1074F(1)		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)		ACTTTCTCATCTACAGCACTT	0.398													C|||	113	0.0225639	0.0136	0.0	5008	,	,		22265	0.0813		0.004	False		,,,				2504	0.0092				p.S1074F		Atlas-SNP	.											AKAP11,NS,carcinoma,0,1	AKAP11	146	1	1	Substitution - Missense(1)	stomach(1)	c.C3221T						PASS	.	C	PHE/SER	51,4355	51.6+/-87.1	1,49,2153	159	151	153		3221	5.8	0.4	13	dbSNP_129	153	3,8597	3.0+/-9.4	0,3,4297	yes	missense	AKAP11	NM_016248.3	155	1,52,6450	TT,TC,CC		0.0349,1.1575,0.4152	possibly-damaging	1074/1902	42876103	54,12952	2203	4300	6503	SO:0001583	missense	11215	exon8			TCTCATCTACAGC	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.3221C>T	13.37:g.42876103C>T	ENSP00000025301:p.Ser1074Phe	86	0	0		78	40	0.512821	NM_016248	O75124|Q9NUK7	Missense_Mutation	SNP	ENST00000025301.2	37	CCDS9383.1	54	0.024725274725274724	7	0.014227642276422764	0	0.0	43	0.07517482517482517	4	0.005277044854881266	C	13.10	2.136954	0.37728	0.011575	3.49E-4	ENSG00000023516	ENST00000025301	T	0.18502	2.21	5.8	5.8	0.92144	.	0.527839	0.19579	N	0.110907	T	0.02727	0.0082	M	0.67953	2.075	0.43054	D	0.994668	D	0.64830	0.994	P	0.60473	0.875	T	0.00020	-1.2350	10	0.62326	D	0.03	.	20.0706	0.97721	0.0:1.0:0.0:0.0	rs61756566	1074	Q9UKA4	AKA11_HUMAN	F	1074	ENSP00000025301:S1074F	ENSP00000025301:S1074F	S	+	2	0	AKAP11	41774103	0.269000	0.24143	0.389000	0.26208	0.087000	0.18053	3.666000	0.54540	2.744000	0.94065	0.655000	0.94253	TCT	C|0.988;T|0.012	0.012	strong		0.398	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248		T	42876103	C	T	42876103	3	4	25	1	0	0	0	0	1	0	0	0	447	913	32	2	3243	2	AKAP11	13	42876103	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1236726	42876103	72293775	553	9462											
ENOX1	55068	hgsc.bcm.edu	37	chr13	43987003	43987003	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcagccatcatctgaggaagCtcctggggaagctgggtgat	9	8	15	9	0	2	2	1	2	1	0	3	4	3	4	2	4	3	3	2	4	2	0	rs7338624	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:43987003C>G	ENST00000261488.6	-	4	625	c.48G>C	c.(46-48)gaG>gaC	p.E16D	ENOX1_ENST00000412891.1_Missense_Mutation_p.E16D	NM_001242863.1|NM_017993.3	NP_001229792.1|NP_060463.2	Q8TC92	ENOX1_HUMAN	ecto-NOX disulfide-thiol exchanger 1	16			E -> D (in dbSNP:rs7338624). {ECO:0000269|PubMed:19055324}.		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)		TCTGAGGAAGCTCCTGGGGAA	0.498													C|||	242	0.0483227	0.1778	0.0101	5008	,	,		16486	0.0		0.0	False		,,,				2504	0.0				p.E16D		Atlas-SNP	.											.	ENOX1	158	.	0			c.G48C						PASS	.	C	ASP/GLU,ASP/GLU,ASP/GLU	677,3729	286.3+/-278.7	49,579,1575	125	111	116		48,48,48	2.9	0.9	13	dbSNP_116	116	9,8591	5.7+/-21.5	0,9,4291	yes	missense,missense,missense	ENOX1	NM_001127615.1,NM_001242863.1,NM_017993.3	45,45,45	49,588,5866	GG,GC,CC		0.1047,15.3654,5.2745	benign,benign,benign	16/644,16/644,16/644	43987003	686,12320	2203	4300	6503	SO:0001583	missense	55068	exon4			AGGAAGCTCCTGG	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.48G>C	13.37:g.43987003C>G	ENSP00000261488:p.Glu16Asp	80	0	0		69	21	0.304348	NM_017993	A4GU15|A6NMH9|B7Z5K1|Q2TU81|Q5VT11|Q9NWE0	Missense_Mutation	SNP	ENST00000261488.6	37	CCDS9389.1	78	0.03571428571428571	74	0.15040650406504066	4	0.011049723756906077	0	0.0	0	0.0	C	11.61	1.690096	0.29962	0.153654	0.001047	ENSG00000120658	ENST00000261488;ENST00000412891	T;T	0.44083	0.93;0.93	5.91	2.88	0.33553	.	0.688144	0.14119	N	0.340181	T	0.00109	0.0003	N	0.08118	0	0.09310	P	0.99999166027	B	0.02656	0.0	B	0.01281	0.0	T	0.18241	-1.0343	9	0.19590	T	0.45	-0.328	2.7291	0.05222	0.2036:0.4159:0.0:0.3805	rs7338624;rs52798713;rs7338624	16	Q8TC92	ENOX1_HUMAN	D	16	ENSP00000261488:E16D;ENSP00000415054:E16D	ENSP00000261488:E16D	E	-	3	2	ENOX1	42885003	0.996000	0.38824	0.871000	0.34182	0.975000	0.68041	1.058000	0.30504	0.842000	0.35045	0.655000	0.94253	GAG	C|0.955;G|0.045	0.045	strong		0.498	ENOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044717.2	NM_017993		G	43987003	C	G	43987003	3	3	25	1	0	0	0	0	1	0	0	0	5128	796	28	4	1939	4	ENOX1	13	43987003	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1110900	43987003	71182875	554	9463											
CKAP2	26586	hgsc.bcm.edu	37	chr13	53039547	53039547	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ttattgaaccaatcacaagtCctattgaaaatattattgca	16	14	4	7	0	1	2	1	2	0	0	2	2	2	2	2	0	2	1	2	0	9	7	rs143514154	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:53039547C>T	ENST00000378037.5	+	6	1516	c.1426C>T	c.(1426-1428)Cct>Tct	p.P476S	CKAP2_ENST00000378034.3_Missense_Mutation_p.P475S|CKAP2_ENST00000258607.5_Missense_Mutation_p.P475S|CKAP2_ENST00000490903.1_Missense_Mutation_p.P427S	NM_001098525.1|NM_018204.3	NP_001091995.1|NP_060674.3			cytoskeleton associated protein 2											breast(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(3)|skin(1)|urinary_tract(1)	20		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;2.6e-08)		AATCACAAGTCCTATTGAAAA	0.338													c|||	17	0.00339457	0.0	0.0101	5008	,	,		16813	0.0		0.0099	False		,,,				2504	0.0				p.P476S		Atlas-SNP	.											.	CKAP2	51	.	0			c.C1426T						PASS	.	C	SER/PRO,SER/PRO	12,4394		0,12,2191	86	91	89		1426,1423	2.9	1	13	dbSNP_134	89	88,8504		0,88,4208	yes	missense,missense	CKAP2	NM_001098525.1,NM_018204.3	74,74	0,100,6399	TT,TC,CC		1.0242,0.2724,0.7693	probably-damaging,probably-damaging	476/684,475/683	53039547	100,12898	2203	4296	6499	SO:0001583	missense	26586	exon6			ACAAGTCCTATTG	AF177227	CCDS9435.1, CCDS41893.1, CCDS66557.1, CCDS73578.1	13q14	2014-03-21			ENSG00000136108	ENSG00000136108			1990	protein-coding gene	gene with protein product		611569				9771967	Standard	XM_005266343		Approved	LB1, FLJ10749, se20-10, TMAP	uc001vgv.2	Q8WWK9	OTTHUMG00000016967	ENST00000378037.5:c.1426C>T	13.37:g.53039547C>T	ENSP00000367276:p.Pro476Ser	222	0	0		182	78	0.428571	NM_001098525		Missense_Mutation	SNP	ENST00000378037.5	37	CCDS41893.1	11	0.005036630036630037	0	0.0	6	0.016574585635359115	0	0.0	5	0.006596306068601583	.	14.37	2.516023	0.44763	0.002724	0.010242	ENSG00000136108	ENST00000398044;ENST00000258607;ENST00000378034;ENST00000378037;ENST00000490903	T;T;T;T	0.22134	1.97;1.97;1.97;1.97	5.63	2.94	0.34122	.	0.512341	0.20916	N	0.083379	T	0.11922	0.0290	M	0.82056	2.57	0.36976	D	0.894063	P;P;P;P	0.40211	0.513;0.513;0.513;0.707	B;B;B;B	0.38655	0.147;0.147;0.147;0.278	T	0.08086	-1.0739	10	0.56958	D	0.05	-1.6008	3.444	0.07474	0.1396:0.5775:0.135:0.148	.	427;476;475;476	E9PD90;Q8WWK9;B2RMQ4;A8MYU4	.;CKAP2_HUMAN;.;.	S	476;475;475;476;427	ENSP00000258607:P475S;ENSP00000367273:P475S;ENSP00000367276:P476S;ENSP00000417830:P427S	ENSP00000258607:P475S	P	+	1	0	CKAP2	51937548	0.976000	0.34144	1.000000	0.80357	0.993000	0.82548	0.547000	0.23299	0.390000	0.25115	0.655000	0.94253	CCT	C|0.994;T|0.006	0.006	strong		0.338	CKAP2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355010.2			T	53039547	C	T	53039547	3	4	25	1	0	0	0	0	1	0	0	0	3444	855	30	2	1448	2	CKAP2	13	53039547	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	9052544	53039547	62130331	555	9464											
PCDH17	27253	hgsc.bcm.edu	37	chr13	58207711	58207711	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacggtcaagctcatcgaccGcaacgacaatgcgccgtcca	11	5	9	16	6	2	0	2	0	0	0	4	2	3	0	3	1	3	2	3	1	3	0	rs41292834	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:58207711G>T	ENST00000377918.3	+	1	1057	c.1031G>T	c.(1030-1032)cGc>cTc	p.R344L		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	344	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)		CTCATCGACCGCAACGACAAT	0.647													G|||	24	0.00479233	0.0015	0.0043	5008	,	,		13628	0.0		0.0169	False		,,,				2504	0.002				p.R344L	Melanoma(72;952 1291 1619 12849 33676)	Atlas-SNP	.											.	PCDH17	304	.	0			c.G1031T						PASS	.	G	LEU/ARG	9,4397	15.5+/-35.6	0,9,2194	75	72	73		1031	5.6	1	13	dbSNP_127	73	97,8503	54.4+/-115.2	0,97,4203	yes	missense	PCDH17	NM_001040429.2	102	0,106,6397	TT,TG,GG		1.1279,0.2043,0.815	benign	344/1160	58207711	106,12900	2203	4300	6503	SO:0001583	missense	27253	exon1			TCGACCGCAACGA	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.1031G>T	13.37:g.58207711G>T	ENSP00000367151:p.Arg344Leu	22	0	0		31	21	0.677419	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Missense_Mutation	SNP	ENST00000377918.3	37	CCDS31986.1	14	0.00641025641025641	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	12	0.0158311345646438	G	11.47	1.647374	0.29246	0.002043	0.011279	ENSG00000118946	ENST00000377918	T	0.59638	0.25	5.57	5.57	0.84162	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.043754	0.85682	D	0.000000	T	0.15825	0.0381	N	0.02011	-0.69	0.46149	D	0.998891	B;B	0.19935	0.016;0.04	B;B	0.17098	0.017;0.012	T	0.18777	-1.0326	9	.	.	.	.	12.8315	0.57748	0.0746:0.0:0.9254:0.0	rs41292834	344;344	O14917-2;O14917	.;PCD17_HUMAN	L	344	ENSP00000367151:R344L	.	R	+	2	0	PCDH17	57105712	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.511000	0.53400	2.640000	0.89533	0.650000	0.86243	CGC	G|0.993;T|0.007	0.007	strong		0.647	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		T	58207711	G	T	58207711	3	4	25	1	0	0	0	0	1	0	0	0	11521	1087	38	4	1033	4	PCDH17	13	58207711	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	5168164	58207711	56962167	556	9465											
TBC1D4	9882	hgsc.bcm.edu	37	chr13	75861001	75861001	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagcaacaggtcacaattgActagagcatccgcgggcagc	12	6	11	12	2	2	2	2	1	0	1	3	2	3	2	1	2	4	3	1	2	3	2	rs557337	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:75861001A>G	ENST00000377636.3	-	21	4170	c.3824T>C	c.(3823-3825)gTc>gCc	p.V1275A	TBC1D4_ENST00000425511.1_Missense_Mutation_p.V439A|TBC1D4_ENST00000377625.2_Missense_Mutation_p.V1212A|TBC1D4_ENST00000431480.2_Missense_Mutation_p.V1267A	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	1275			V -> A (in dbSNP:rs557337). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:19077034, ECO:0000269|PubMed:9628581}.		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)		GTCACAATTGACTAGAGCATC	0.463													G|||	873	0.174321	0.556	0.0778	5008	,	,		16760	0.0		0.0666	False		,,,				2504	0.0174				p.V1275A		Atlas-SNP	.											.	TBC1D4	142	.	0			c.T3824C						PASS	.	G	ALA/VAL	1770,2058		428,914,572	104	107	106		3824	3.9	0	13	dbSNP_83	106	484,7778		13,458,3660	yes	missense	TBC1D4	NM_014832.2	64	441,1372,4232	GG,GA,AA		5.8581,46.2382,18.6435	benign	1275/1299	75861001	2254,9836	1914	4131	6045	SO:0001583	missense	9882	exon21			CAATTGACTAGAG	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.3824T>C	13.37:g.75861001A>G	ENSP00000366863:p.Val1275Ala	307	0	0		305	163	0.534426	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Missense_Mutation	SNP	ENST00000377636.3	37	CCDS41901.1	333	0.15247252747252749	256	0.5203252032520326	32	0.08839779005524862	0	0.0	45	0.059366754617414245	G	0.218	-1.030972	0.02029	0.462382	0.058581	ENSG00000136111	ENST00000377636;ENST00000431480;ENST00000377625;ENST00000425511	T;T;T;T	0.03358	4.23;4.23;4.23;3.96	5.63	3.87	0.44632	.	0.297360	0.28841	N	0.013979	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	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	0.38329	-0.9666	9	0.02654	T	1	-5.6523	10.4567	0.44555	0.2148:0.0:0.7852:0.0	rs557337;rs52811417;rs60191388;rs557337	439;1212;1267;1275	O60343-4;O60343-2;O60343-3;O60343	.;.;.;TBCD4_HUMAN	A	1275;1267;1212;439	ENSP00000366863:V1275A;ENSP00000395986:V1267A;ENSP00000366852:V1212A;ENSP00000390654:V439A	ENSP00000366852:V1212A	V	-	2	0	TBC1D4	74759002	1.000000	0.71417	0.008000	0.14137	0.004000	0.04260	4.134000	0.57990	0.847000	0.35167	-0.119000	0.15052	GTC	A|0.827;G|0.173	0.173	strong		0.463	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832		G	75861001	A	G	75861001	3	3	25	1	0	0	0	0	1	0	0	0	15637	275	10	3	76	3	TBC1D4	13	75861001	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	17653290	75861001	39308877	557	9466											
LMO7	4008	hgsc.bcm.edu	37	chr13	76370887	76370887	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggacaagcactgacgaaggTaagtaaactacatctgtgtg	15	8	11	7	1	1	1	0	1	1	0	1	3	1	2	0	2	3	3	0	2	6	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:76370887T>C	ENST00000321797.8	+	4	484		c.e4+2		RP11-29G8.3_ENST00000563635.1_RNA|LMO7_ENST00000357063.3_Splice_Site|LMO7_ENST00000377534.3_Splice_Site|LMO7_ENST00000341547.4_Splice_Site|LMO7_ENST00000465261.2_Splice_Site|LMO7_ENST00000526202.1_Splice_Site			Q8WWI1	LMO7_HUMAN	LIM domain 7						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)		CTGACGAAGGTAAGTAAACTA	0.398																																					.		Atlas-SNP	.											.	LMO7	334	.	0			c.618+2T>C						PASS	.						112	99	103					13																	76370887		2203	4300	6503	SO:0001630	splice_region_variant	4008	exon7			CGAAGGTAAGTAA	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.-238+2T>C	13.37:g.76370887T>C		60	0	0		100	26	0.26	NM_005358	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Splice_Site	SNP	ENST00000321797.8	37		.	.	.	.	.	.	.	.	.	.	T	9.699	1.153939	0.21371	.	.	ENSG00000136153	ENST00000341547;ENST00000357063;ENST00000377534;ENST00000377499;ENST00000526202	.	.	.	5.11	3.89	0.44902	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.397	0.49847	0.1357:0.0:0.0:0.8643	.	.	.	.	.	-1	.	.	.	+	.	.	LMO7	75268888	1.000000	0.71417	1.000000	0.80357	0.040000	0.13550	7.075000	0.76798	0.844000	0.35094	0.459000	0.35465	.	.	.	none		0.398	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358	Intron	C	76370887	T	C	76370887	5	2	25	1	0	0	0	0	0	0	1	0	8864	1652	57	3	646	3	LMO7	13	76370887	Splice_Site	SNP	T	TCGA-G8-6906-01A-11D-2210-10	509886	76370887	38798991	558	9467											
SLC15A1	6564	hgsc.bcm.edu	37	chr13	99340578	99340578	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aattaggttgacattgtggcGgaatctctgttgagcttatt	9	16	11	5	1	1	2	0	2	1	0	2	3	1	3	0	3	1	3	0	3	4	6			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:99340578G>A	ENST00000376503.5	-	20	1662	c.1607C>T	c.(1606-1608)cCg>cTg	p.P536L		NM_005073.3	NP_005064.1	P46059	S15A1_HUMAN	solute carrier family 15 (oligopeptide transporter), member 1	536					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)	ACATTGTGGCGGAATCTCTGT	0.308																																					p.P536L		Atlas-SNP	.											.	SLC15A1	92	.	0			c.C1607T						PASS	.						78	78	78					13																	99340578		2203	4300	6503	SO:0001583	missense	6564	exon20			TGTGGCGGAATCT	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.1607C>T	13.37:g.99340578G>A	ENSP00000365686:p.Pro536Leu	107	0	0		97	38	0.391753	NM_005073	Q5VW82	Missense_Mutation	SNP	ENST00000376503.5	37	CCDS9489.1	.	.	.	.	.	.	.	.	.	.	G	6.435	0.448320	0.12223	.	.	ENSG00000088386	ENST00000376503	T	0.01963	4.53	5.09	1.21	0.21127	Major facilitator superfamily domain, general substrate transporter (1);	1.449500	0.03719	N	0.251497	T	0.01695	0.0054	N	0.14661	0.345	0.09310	N	1	B	0.25486	0.127	B	0.20384	0.029	T	0.44832	-0.9302	10	0.23891	T	0.37	-9.85	3.6908	0.08346	0.3572:0.1832:0.4596:0.0	.	536	P46059	S15A1_HUMAN	L	536	ENSP00000365686:P536L	ENSP00000365686:P536L	P	-	2	0	SLC15A1	98138579	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.380000	0.20602	0.674000	0.31244	-0.768000	0.03414	CCG	.	.	none		0.308	SLC15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045560.3	NM_005073		A	99340578	G	A	99340578	3	1	25	1	0	0	0	0	1	0	0	0	14413	1116	39	1	535	1	SLC15A1	13	99340578	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	22969691	99340578	15829300	559	9468											
MYO16	23026	hgsc.bcm.edu	37	chr13	109613929	109613929	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctagcagcaatattgcacCttggagacattcggtttact	10	14	8	9	1	1	1	0	0	1	1	2	2	1	1	1	2	4	4	1	2	4	8			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:109613929C>T	ENST00000357550.2	+	17	2055	c.2014C>T	c.(2014-2016)Ctt>Ttt	p.L672F	MYO16_ENST00000356711.2_Missense_Mutation_p.L672F|MYO16_ENST00000251041.5_Missense_Mutation_p.L672F|MYO16_ENST00000457511.2_Missense_Mutation_p.L184F	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)			AATATTGCACCTTGGAGACAT	0.453																																					p.L694F		Atlas-SNP	.											.	MYO16	285	.	0			c.C2080T						PASS	.						191	153	166					13																	109613929		2203	4300	6503	SO:0001583	missense	23026	exon18			TTGCACCTTGGAG		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.2014C>T	13.37:g.109613929C>T	ENSP00000350160:p.Leu672Phe	137	0	0		99	4	0.040404	NM_001198950		Missense_Mutation	SNP	ENST00000357550.2	37	CCDS32008.1	.	.	.	.	.	.	.	.	.	.	C	11.79	1.743813	0.30865	.	.	ENSG00000041515	ENST00000356711;ENST00000397258;ENST00000357550;ENST00000251041;ENST00000375857;ENST00000457511	D;D;D;D	0.97959	-4.63;-4.63;-4.63;-4.63	5.07	-8.68	0.00859	Myosin head, motor domain (2);	0.760287	0.10614	U	0.654105	D	0.96253	0.8778	M	0.74389	2.26	0.23913	N	0.996482	P;P;P	0.46987	0.888;0.888;0.733	P;P;B	0.46885	0.474;0.53;0.375	D	0.93439	0.6792	9	.	.	.	.	11.4832	0.50337	0.2328:0.5853:0.182:0.0	.	184;672;672	F8W883;Q9Y6X6-2;Q9Y6X6	.;.;MYO16_HUMAN	F	672;672;672;672;460;184	ENSP00000349145:L672F;ENSP00000350160:L672F;ENSP00000251041:L672F;ENSP00000401633:L184F	.	L	+	1	0	MYO16	108411930	0.881000	0.30235	0.010000	0.14722	0.052000	0.14988	-0.121000	0.10643	-1.924000	0.01064	-1.513000	0.00942	CTT	.	.	none		0.453	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011		T	109613929	C	T	109613929	3	4	25	1	0	0	0	0	1	0	0	0	10073	681	24	2	2080	2	MYO16	13	109613929	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	10273351	109613929	5555949	560	9469											
CUL4A	8451	hgsc.bcm.edu	37	chr13	113882307	113882307	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tacagactcactagatagtgTtttatttttaaagaagatta	15	16	6	4	0	1	4	1	0	0	4	1	4	1	4	0	0	1	1	0	0	8	9	rs113697945	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:113882307T>C	ENST00000375440.4	+	4	470	c.386T>C	c.(385-387)gTt>gCt	p.V129A	CUL4A_ENST00000451881.1_Missense_Mutation_p.V29A|CUL4A_ENST00000375441.3_Missense_Mutation_p.V29A|CUL4A_ENST00000463426.1_3'UTR|CUL4A_ENST00000326335.4_Missense_Mutation_p.V29A	NM_001008895.1	NP_001008895.1	Q13619	CUL4A_HUMAN	cullin 4A	129					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)			CTAGATAGTGTTTTATTTTTA	0.363													T|||	10	0.00199681	0.0	0.0014	5008	,	,		20658	0.0		0.008	False		,,,				2504	0.001				p.V129A		Atlas-SNP	.											.	CUL4A	50	.	0			c.T386C						PASS	.	T	ALA/VAL,ALA/VAL	9,4397	16.8+/-37.8	0,9,2194	73	73	73		386,86	5.1	0.7	13	dbSNP_132	73	78,8522	45.4+/-104.0	1,76,4223	yes	missense,missense	CUL4A	NM_001008895.1,NM_003589.2	64,64	1,85,6417	CC,CT,TT		0.907,0.2043,0.6689	benign,benign	129/760,29/660	113882307	87,12919	2203	4300	6503	SO:0001583	missense	8451	exon4			ATAGTGTTTTATT	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.386T>C	13.37:g.113882307T>C	ENSP00000364589:p.Val129Ala	46	0	0		50	37	0.74	NM_001008895	A2A2W2|O75834|Q589T6|Q5TC62|Q6UP08|Q9UP17	Missense_Mutation	SNP	ENST00000375440.4	37	CCDS41908.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	T	11.40	1.626934	0.28978	0.002043	0.00907	ENSG00000139842	ENST00000375441;ENST00000451881;ENST00000326335;ENST00000375440	T;T;T;T	0.76709	-1.04;-1.04;-1.04;-1.04	5.12	5.12	0.69794	Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);	0.413435	0.24245	N	0.040226	T	0.70430	0.3223	M	0.71581	2.175	0.47862	D	0.999532	B	0.09022	0.002	B	0.25506	0.061	T	0.69881	-0.5025	10	0.16420	T	0.52	-22.1362	15.2361	0.73432	0.0:0.0:0.0:1.0	.	129	Q13619	CUL4A_HUMAN	A	29;29;29;129	ENSP00000364590:V29A;ENSP00000389118:V29A;ENSP00000322132:V29A;ENSP00000364589:V129A	ENSP00000322132:V29A	V	+	2	0	CUL4A	112930308	1.000000	0.71417	0.667000	0.29798	0.042000	0.13812	7.791000	0.85805	2.058000	0.61347	0.528000	0.53228	GTT	T|0.995;C|0.005	0.005	strong		0.363	CUL4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045888.3	NM_003589		C	113882307	T	C	113882307	3	2	25	1	0	0	0	0	1	0	0	0	4059	1725	60	3	400	3	CUL4A	13	113882307	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	4268378	113882307	1287571	561	9470											
MYH6	4624	hgsc.bcm.edu	37	chr14	23852443	23852443	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctgaactcaccgcctcctcGgcctggcgcttgtaggcctt	4	11	10	16	3	2	1	1	1	1	0	4	1	3	1	5	3	1	2	5	3	2	3	rs200662317	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:23852443G>A	ENST00000356287.3	-	36	5681	c.5652C>T	c.(5650-5652)gcC>gcT	p.A1884A	MYH6_ENST00000405093.3_Silent_p.A1884A			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	1884					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)		CCGCCTCCTCGGCCTGGCGCT	0.532													G|||	2	0.000399361	0.0	0.0	5008	,	,		12269	0.002		0.0	False		,,,				2504	0.0				p.A1884A		Atlas-SNP	.											.	MYH6	274	.	0			c.C5652T						PASS	.	G		0,4406		0,0,2203	84	74	78		5652	-7.8	0.9	14		78	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	MYH6	NM_002471.3		0,5,6498	AA,AG,GG		0.0581,0.0,0.0384		1884/1940	23852443	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	4624	exon37			CTCCTCGGCCTGG	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.5652C>T	14.37:g.23852443G>A		113	0	0		97	47	0.484536	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Silent	SNP	ENST00000356287.3	37	CCDS9600.1																																																																																			G|0.997;A|0.003	0.003	strong		0.532	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			A	23852443	G	A	23852443	2	1	25	1	0	0	0	0	0	0	0	1	10047	1103	39	1		1	MYH6	14	23852443	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10		23852443	83497097	562	9471											
RNF31	55072	hgsc.bcm.edu	37	chr14	24620710	24620710	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gcaggtgcaggagctccagtCtctaggctttgggcctgagg	6	9	16	10	0	1	1	0	1	1	0	3	2	2	2	2	5	2	4	2	5	1	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:24620710C>G	ENST00000324103.6	+	10	2074	c.1754C>G	c.(1753-1755)tCt>tGt	p.S585C	RNF31_ENST00000382687.3_Missense_Mutation_p.S434C|RNF31_ENST00000559275.1_Missense_Mutation_p.S434C|RP11-468E2.4_ENST00000558468.1_Missense_Mutation_p.S60C	NM_017999.4	NP_060469.4	Q96EP0	RNF31_HUMAN	ring finger protein 31	585	Interaction with RBCK1.|UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				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)		GAGCTCCAGTCTCTAGGCTTT	0.587																																					p.S585C		Atlas-SNP	.											RNF31,NS,carcinoma,0,1	RNF31	95	1	0			c.C1754G						PASS	.						53	55	55					14																	24620710		2021	4210	6231	SO:0001583	missense	55072	exon10			TCCAGTCTCTAGG	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.1754C>G	14.37:g.24620710C>G	ENSP00000315112:p.Ser585Cys	88	0	0		81	37	0.45679	NM_017999	A0A962|Q86VI2|Q8TEI0|Q96GB4|Q96NF1|Q9H5F1|Q9NWD2	Missense_Mutation	SNP	ENST00000324103.6	37	CCDS41931.1	.	.	.	.	.	.	.	.	.	.	C	9.929	1.214179	0.22289	.	.	ENSG00000092098	ENST00000324103;ENST00000382687	T;T	0.47869	0.83;0.83	5.42	3.47	0.39725	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (1);UBA-like (1);	0.583409	0.18022	N	0.154194	T	0.37461	0.1004	N	0.19112	0.55	0.09310	N	1	D;P;D	0.54964	0.969;0.947;0.969	P;B;P	0.49683	0.619;0.36;0.563	T	0.14364	-1.0475	10	0.72032	D	0.01	-7.8769	6.4608	0.21956	0.0:0.6637:0.1566:0.1797	.	344;585;434	B3KV71;Q96EP0;Q96EP0-3	.;RNF31_HUMAN;.	C	585;434	ENSP00000315112:S585C;ENSP00000372134:S434C	ENSP00000315112:S585C	S	+	2	0	RNF31	23690550	0.059000	0.20769	0.991000	0.47740	0.196000	0.23810	1.449000	0.35123	1.523000	0.49018	0.655000	0.94253	TCT	.	.	none		0.587	RNF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071921.3	NM_017999		G	24620710	C	G	24620710	3	3	25	1	0	0	0	0	1	0	0	0	13502	913	32	4	1792	4	RNF31	14	24620710	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	768267	24620710	82728830	563	9472											
RNF31	55072	hgsc.bcm.edu	37	chr14	24620821	24620821	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgcctagagcccttccgccAgcgcctctgggacagtggcc	6	6	12	17	3	1	1	0	0	1	1	2	2	2	2	6	2	2	0	6	2	1	2	rs149481717	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:24620821A>T	ENST00000324103.6	+	10	2185	c.1865A>T	c.(1864-1866)cAg>cTg	p.Q622L	RNF31_ENST00000382687.3_Missense_Mutation_p.Q471L|RNF31_ENST00000559275.1_Missense_Mutation_p.Q471L|RP11-468E2.4_ENST00000558468.1_Missense_Mutation_p.Q97L	NM_017999.4	NP_060469.4	Q96EP0	RNF31_HUMAN	ring finger protein 31	622					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)		CCCTTCCGCCAGCGCCTCTGG	0.652													A|||	9	0.00179712	0.0	0.0029	5008	,	,		18657	0.0		0.005	False		,,,				2504	0.002				p.Q622L		Atlas-SNP	.											.	RNF31	95	.	0			c.A1865T						PASS	.	A	LEU/GLN	6,3962		0,6,1978	34	37	36		1865	5.4	1	14	dbSNP_134	36	41,8285		0,41,4122	yes	missense	RNF31	NM_017999.4	113	0,47,6100	TT,TA,AA		0.4924,0.1512,0.3823	possibly-damaging	622/1073	24620821	47,12247	1984	4163	6147	SO:0001583	missense	55072	exon10			TCCGCCAGCGCCT	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.1865A>T	14.37:g.24620821A>T	ENSP00000315112:p.Gln622Leu	47	0	0		42	23	0.547619	NM_017999	A0A962|Q86VI2|Q8TEI0|Q96GB4|Q96NF1|Q9H5F1|Q9NWD2	Missense_Mutation	SNP	ENST00000324103.6	37	CCDS41931.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	A	14.27	2.485749	0.44147	0.001512	0.004924	ENSG00000092098	ENST00000324103;ENST00000382687	T;T	0.47869	0.83;0.83	5.42	5.42	0.78866	.	0.068650	0.64402	D	0.000016	T	0.34395	0.0896	L	0.56769	1.78	0.46028	D	0.998828	B;B;B	0.33171	0.301;0.278;0.4	B;B;B	0.30855	0.08;0.039;0.121	T	0.42292	-0.9460	10	0.66056	D	0.02	-11.1548	9.8917	0.41294	0.8475:0.0:0.0:0.1524	.	381;622;471	B3KV71;Q96EP0;Q96EP0-3	.;RNF31_HUMAN;.	L	622;471	ENSP00000315112:Q622L;ENSP00000372134:Q471L	ENSP00000315112:Q622L	Q	+	2	0	RNF31	23690661	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	4.311000	0.59147	2.274000	0.75844	0.533000	0.62120	CAG	A|0.998;T|0.002	0.002	strong		0.652	RNF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071921.3	NM_017999		T	24620821	A	T	24620821	3	4	25	1	0	0	0	0	1	0	0	0	13502	188	7	5	1903	5	RNF31	14	24620821	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	111	24620821	82728719	564	9473											
HEATR5A	25938	hgsc.bcm.edu	37	chr14	31856407	31856407	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttttctccaagaagaccacCtatagtagttcgaagaataa	15	11	6	9	1	1	3	0	0	1	3	3	4	1	3	3	0	0	2	3	0	8	7	rs73259359	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:31856407C>T	ENST00000389961.3	-	7	1089	c.1090G>A	c.(1090-1092)Ggt>Agt	p.G364S	HEATR5A_ENST00000543095.2_Missense_Mutation_p.G370S|HEATR5A_ENST00000404677.3_Missense_Mutation_p.G370S|HEATR5A_ENST00000439727.1_Missense_Mutation_p.G77S|HEATR5A_ENST00000439348.1_Missense_Mutation_p.G364S			Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	364										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)		AGAAGACCACCTATAGTAGTT	0.468													C|||	145	0.0289537	0.0968	0.0187	5008	,	,		16103	0.0		0.003	False		,,,				2504	0.001				p.G370S		Atlas-SNP	.											.	HEATR5A	181	.	0			c.G1108A						PASS	.	C	SER/GLY	239,3561		9,221,1670	126	119	121		1108	4.7	1	14	dbSNP_130	121	15,8239		0,15,4112	yes	missense	HEATR5A	NM_015473.3	56	9,236,5782	TT,TC,CC		0.1817,6.2895,2.1072	probably-damaging	370/2047	31856407	254,11800	1900	4127	6027	SO:0001583	missense	25938	exon8			GACCACCTATAGT	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.1090G>A	14.37:g.31856407C>T	ENSP00000374611:p.Gly364Ser	156	0	0		178	91	0.511236	NM_015473	Q68DD8|Q6P3S5|Q6P5R9|Q9H8D7|Q9NXB7|Q9P2N0|Q9UFQ3	Missense_Mutation	SNP	ENST00000389961.3	37		60|60	0.027472527472527472|0.027472527472527472	53|53	0.10772357723577236|0.10772357723577236	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	C|C	29.3|29.3	4.991400|4.991400	0.93106|0.93106	0.062895|0.062895	0.001817|0.001817	ENSG00000129493|ENSG00000129493	ENST00000389961;ENST00000439348;ENST00000439727;ENST00000543095;ENST00000404677|ENST00000550366	T;T;T;T;T|.	0.07567|.	3.18;3.18;3.18;3.18;3.18|.	5.53|5.53	4.65|4.65	0.58169|0.58169	.|.	0.124234|.	0.53938|.	D|.	0.000055|.	T|T	0.04907|0.04907	0.0132|0.0132	M|M	0.77313|0.77313	2.365|2.365	0.09310|0.09310	P|P	0.9999999539453|0.9999999539453	D|.	0.58970|.	0.984|.	P|.	0.59643|.	0.861|.	T|T	0.51911|0.51911	-0.8645|-0.8645	9|4	0.72032|.	D|.	0.01|.	.|.	14.2073|14.2073	0.65741|0.65741	0.0:0.9281:0.0:0.0719|0.0:0.9281:0.0:0.0719	.|.	370|.	B5MC49|.	.|.	S|K	364;364;77;370;370|28	ENSP00000374611:G364S;ENSP00000405407:G364S;ENSP00000408681:G77S;ENSP00000437968:G370S;ENSP00000384646:G370S|.	ENSP00000374611:G364S|.	G|R	-|-	1|2	0|0	HEATR5A|HEATR5A	30926158|30926158	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.901000|0.901000	0.52897|0.52897	7.632000|7.632000	0.83247|0.83247	1.339000|1.339000	0.45563|0.45563	0.491000|0.491000	0.48974|0.48974	GGT|AGG	C|0.977;T|0.023	0.023	strong		0.468	HEATR5A-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015473		T	31856407	C	T	31856407	3	4	25	1	0	0	0	0	1	0	0	0	7040	681	24	2	5148	2	HEATR5A	14	31856407	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	7235586	31856407	75493133	565	9474											
PRPF39	55015	hgsc.bcm.edu	37	chr14	45564675	45564675	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaacagaagcaaatttccCtccagaatatgaaaaatttt	19	10	5	7	0	0	4	0	1	0	3	2	4	2	4	2	0	2	1	2	0	7	4			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:45564675C>T	ENST00000355765.6	+	2	403	c.233C>T	c.(232-234)cCt>cTt	p.P78L		NM_017922.3	NP_060392.3	Q86UA1	PRP39_HUMAN	pre-mRNA processing factor 39	78					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(4)|lung(3)|ovary(1)	12						GCAAATTTCCCTCCAGAATAT	0.398																																					p.P78L		Atlas-SNP	.											.	PRPF39	46	.	0			c.C233T						PASS	.						40	40	40					14																	45564675		1996	4194	6190	SO:0001583	missense	55015	exon2			ATTTCCCTCCAGA	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.233C>T	14.37:g.45564675C>T	ENSP00000348010:p.Pro78Leu	84	0	0		94	4	0.0425532	NM_017922	Q08AL1|Q08AL2|Q9NUU5	Missense_Mutation	SNP	ENST00000355765.6	37	CCDS9682.2	.	.	.	.	.	.	.	.	.	.	C	18.84	3.710181	0.68730	.	.	ENSG00000185246	ENST00000355765;ENST00000553605	T	0.50548	0.74	5.72	5.72	0.89469	.	.	.	.	.	T	0.49064	0.1535	N	0.22421	0.69	0.80722	D	1	P	0.47962	0.903	P	0.53266	0.722	T	0.28427	-1.0044	9	0.23891	T	0.37	-12.9614	19.4498	0.94862	0.0:1.0:0.0:0.0	.	78	Q86UA1	PRP39_HUMAN	L	78	ENSP00000348010:P78L	ENSP00000348010:P78L	P	+	2	0	PRPF39	44634425	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.130000	0.77235	2.702000	0.92279	0.591000	0.81541	CCT	.	.	none		0.398	PRPF39-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319683.2			T	45564675	C	T	45564675	3	4	25	1	0	0	0	0	1	0	0	0	12581	681	24	2	235	2	PRPF39	14	45564675	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	13708268	45564675	61784865	566	9475											
SOS2	6655	hgsc.bcm.edu	37	chr14	50585109	50585109	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	caaaggcagtctgtacaatgGggggtgcgaaagctcccgtt	10	8	14	9	2	1	0	0	0	1	0	2	1	2	0	1	4	3	4	1	4	4	2	rs140995728	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:50585109G>A	ENST00000216373.5	-	23	4226	c.3952C>T	c.(3952-3954)Cca>Tca	p.P1318S	VCPKMT_ENST00000395860.2_5'Flank|VCPKMT_ENST00000395859.2_5'Flank|SOS2_ENST00000543680.1_Missense_Mutation_p.P1285S	NM_006939.2	NP_008870.2	Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	1318					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)					CTGTACAATGGGGGGTGCGAA	0.463													G|||	4	0.000798722	0.0	0.0014	5008	,	,		17130	0.0		0.003	False		,,,				2504	0.0				p.P1318S		Atlas-SNP	.											.	SOS2	195	.	0			c.C3952T						PASS	.	G	SER/PRO	2,4404	4.2+/-10.8	0,2,2201	74	72	72		3952	5.4	0.8	14	dbSNP_134	72	11,8589	8.4+/-32.0	0,11,4289	yes	missense	SOS2	NM_006939.2	74	0,13,6490	AA,AG,GG		0.1279,0.0454,0.1	benign	1318/1333	50585109	13,12993	2203	4300	6503	SO:0001583	missense	6655	exon23			ACAATGGGGGGTG	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.3952C>T	14.37:g.50585109G>A	ENSP00000216373:p.Pro1318Ser	206	0	0		165	73	0.442424	NM_006939	B7ZKT6|D3DSB4|Q15503|Q17RN1	Missense_Mutation	SNP	ENST00000216373.5	37	CCDS9697.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	3.971	-0.008341	0.07727	4.54E-4	0.001279	ENSG00000100485	ENST00000216373;ENST00000543680	T;T	0.78003	-1.14;-1.01	5.37	5.37	0.77165	.	0.056414	0.64402	D	0.000001	T	0.81293	0.4792	L	0.33485	1.01	0.58432	D	0.999999	D;D	0.63880	0.993;0.993	D;D	0.70227	0.968;0.968	T	0.75099	-0.3437	10	0.10636	T	0.68	.	19.1021	0.93277	0.0:0.0:1.0:0.0	.	1285;1318	B7ZKT6;Q07890	.;SOS2_HUMAN	S	1318;1285	ENSP00000216373:P1318S;ENSP00000445328:P1285S	ENSP00000216373:P1318S	P	-	1	0	SOS2	49654859	1.000000	0.71417	0.829000	0.32907	0.982000	0.71751	3.088000	0.50175	2.490000	0.84030	0.563000	0.77884	CCA	G|0.999;A|0.001	0.001	strong		0.463	SOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276878.2			A	50585109	G	A	50585109	3	1	25	1	0	0	0	0	1	0	0	0	14952	1232	43	2	50	2	SOS2	14	50585109	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	5020434	50585109	56764431	567	9476											
NID2	22795	hgsc.bcm.edu	37	chr14	52508842	52508842	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcgaggctgaagccgttCtcagagccaggtttttctaa	8	11	11	11	2	2	2	1	1	2	1	3	3	2	2	3	2	3	3	3	2	2	4	rs61747585	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:52508842C>A	ENST00000216286.5	-	7	1805	c.1806G>T	c.(1804-1806)gaG>gaT	p.E602D	NID2_ENST00000541773.1_Missense_Mutation_p.E549D	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	602	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)					TGAAGCCGTTCTCAGAGCCAG	0.577													c|||	161	0.0321486	0.062	0.0303	5008	,	,		19175	0.0		0.0517	False		,,,				2504	0.0061				p.E602D		Atlas-SNP	.											NID2,NS,carcinoma,-2,1	NID2	201	1	0			c.G1806T						scavenged	.	C	ASP/GLU	249,4157	142.3+/-177.5	9,231,1963	75	83	80		1806	4.1	0.8	14	dbSNP_129	80	371,8229	121.7+/-180.7	4,363,3933	yes	missense	NID2	NM_007361.3	45	13,594,5896	AA,AC,CC		4.314,5.6514,4.767	probably-damaging	602/1376	52508842	620,12386	2203	4300	6503	SO:0001583	missense	22795	exon7			GCCGTTCTCAGAG	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.1806G>T	14.37:g.52508842C>A	ENSP00000216286:p.Glu602Asp	85	1	0.0117647		77	35	0.454545	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	37	CCDS9706.1	88	0.040293040293040296	33	0.06707317073170732	13	0.03591160220994475	0	0.0	42	0.055408970976253295	C	13.76	2.334393	0.41297	0.056514	0.04314	ENSG00000087303	ENST00000216286;ENST00000316204;ENST00000541773;ENST00000395707	T;T	0.31247	1.5;1.5	5.93	4.11	0.48088	G2 nidogen/fibulin G2F (3);Green fluorescent protein-like (1);	0.473992	0.25319	N	0.031528	T	0.03095	0.0091	M	0.68952	2.095	0.29539	N	0.85222	P;P;P;P	0.48998	0.542;0.799;0.918;0.741	B;B;P;P	0.49140	0.348;0.158;0.601;0.491	T	0.03103	-1.1072	10	0.25751	T	0.34	.	6.2035	0.20590	0.0:0.6512:0.1381:0.2107	.	196;549;604;602	E7EPP3;Q14112-2;Q5CZI2;Q14112	.;.;.;NID2_HUMAN	D	602;196;549;604	ENSP00000216286:E602D;ENSP00000443730:E549D	ENSP00000216286:E602D	E	-	3	2	NID2	51578592	0.990000	0.36364	0.769000	0.31535	0.920000	0.55202	0.896000	0.28377	0.853000	0.35312	0.655000	0.94253	GAG	C|0.953;A|0.047	0.047	strong		0.577	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			A	52508842	C	A	52508842	3	1	25	1	0	0	0	0	1	0	0	0	10424	912	32	4	2385	4	NID2	14	52508842	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1923733	52508842	54840698	568	9477											
SAMD4A	23034	hgsc.bcm.edu	37	chr14	55227152	55227152	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gcagctgcgatggggagctgGccgtcgcccccctgccagag	5	5	16	15	3	0	1	0	0	0	1	1	3	0	2	5	3	4	3	5	3	0	0	rs149416017	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:55227152G>T	ENST00000554335.1	+	7	2113	c.1450G>T	c.(1450-1452)Gcc>Tcc	p.A484S	SAMD4A_ENST00000392067.3_Missense_Mutation_p.A484S|SAMD4A_ENST00000357634.3_Missense_Mutation_p.A483S|SAMD4A_ENST00000555192.1_Missense_Mutation_p.A75S|SAMD4A_ENST00000251091.5_Missense_Mutation_p.A396S			Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4A	484					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						TGGGGAGCTGGCCGTCGCCCC	0.682													G|||	40	0.00798722	0.0023	0.0159	5008	,	,		13068	0.0		0.0249	False		,,,				2504	0.001				p.A484S		Atlas-SNP	.											.	SAMD4A	68	.	0			c.G1450T						PASS	.	G	SER/ALA,SER/ALA,SER/ALA	21,3909		0,21,1944	4	6	5		1183,223,1447	5.2	1	14	dbSNP_134	5	153,7591		3,147,3722	no	missense,missense,missense	SAMD4A	NM_001161576.2,NM_001161577.1,NM_015589.5	99,99,99	3,168,5666	TT,TG,GG		1.9757,0.5344,1.4905	benign,benign,benign	395/630,75/346,483/718	55227152	174,11500	1965	3872	5837	SO:0001583	missense	23034	exon6			GAGCTGGCCGTCG	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.1450G>T	14.37:g.55227152G>T	ENSP00000452535:p.Ala484Ser	0	0	.		6	4	0.666667	NM_015589	A8MPZ5|Q0VA96|Q6PEW4	Missense_Mutation	SNP	ENST00000554335.1	37	CCDS32084.2	29	0.013278388278388278	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	20	0.026385224274406333	G	15.72	2.917871	0.52546	0.005344	0.019757	ENSG00000020577	ENST00000554335;ENST00000392067;ENST00000305831;ENST00000251091;ENST00000357634;ENST00000555192	.	.	.	5.22	5.22	0.72569	.	0.112512	0.64402	D	0.000017	T	0.20251	0.0487	N	0.12182	0.205	0.34882	D	0.744671	B;B;B	0.16802	0.019;0.011;0.003	B;B;B	0.23574	0.047;0.037;0.002	T	0.34650	-0.9820	9	0.28530	T	0.3	-24.0747	18.9689	0.92707	0.0:0.0:1.0:0.0	.	75;396;484	G3V2R1;Q9UPU9-3;Q9UPU9	.;.;SMAG1_HUMAN	S	484;484;396;395;483;75	.	ENSP00000251091:A113S	A	+	1	0	SAMD4A	54296902	1.000000	0.71417	0.999000	0.59377	0.774000	0.43823	5.707000	0.68370	2.711000	0.92665	0.609000	0.83330	GCC	G|0.987;T|0.013	0.013	strong		0.682	SAMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411186.1	NM_015589		T	55227152	G	T	55227152	3	4	25	1	0	0	0	0	1	0	0	0	13836	1203	42	4	1469	4	SAMD4A	14	55227152	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2718310	55227152	52122388	569	9478											
KTN1	3895	hgsc.bcm.edu	37	chr14	56105908	56105908	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atttttctttcttagacctcCgcttcagttctagcagaaga	9	16	6	10	1	4	3	1	0	3	3	5	3	5	3	2	0	1	3	2	0	3	7	rs80214241	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:56105908C>T	ENST00000395314.3	+	13	1859	c.1791C>T	c.(1789-1791)tcC>tcT	p.S597S	KTN1_ENST00000395309.3_Silent_p.S597S|KTN1_ENST00000416613.1_Silent_p.S597S|KTN1_ENST00000413890.2_Silent_p.S597S|KTN1_ENST00000395311.1_Silent_p.S597S|KTN1_ENST00000395308.1_Silent_p.S597S|KTN1_ENST00000438792.2_Silent_p.S597S	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	597					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						CTTAGACCTCCGCTTCAGTTC	0.313			T	RET	papillary thryoid								C|||	73	0.0145767	0.0219	0.0014	5008	,	,		17209	0.003		0.002	False		,,,				2504	0.0389				p.S597S		Atlas-SNP	.		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	KTN1	147	.	0			c.C1791T						PASS	.	C	,,,	73,4331	65.8+/-103.3	2,69,2131	91	90	90		1791,1791,1791,1791	-6.3	0.9	14	dbSNP_132	90	31,8567	22.2+/-67.0	0,31,4268	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KTN1	NM_001079521.1,NM_001079522.1,NM_004986.2,NM_182926.2	,,,	2,100,6399	TT,TC,CC		0.3605,1.6576,0.7999	,,,	597/1358,597/1307,597/1301,597/1358	56105908	104,12898	2202	4299	6501	SO:0001819	synonymous_variant	3895	exon13			GACCTCCGCTTCA		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.1791C>T	14.37:g.56105908C>T		184	0	0		174	78	0.448276	NM_004986	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Silent	SNP	ENST00000395314.3	37	CCDS41957.1																																																																																			C|0.991;T|0.009	0.009	strong		0.313	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2			T	56105908	C	T	56105908	2	4	25	1	0	0	0	0	0	0	0	1	8594	639	23	1		1	KTN1	14	56105908	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	878756	56105908	51243632	570	9479											
KIAA0586	9786	hgsc.bcm.edu	37	chr14	58899157	58899157	+	Frame_Shift_Del	DEL	G	G	-																															gggacagaaagatgctctaaGaacagttttaaagcaaaagt																								rs534542684	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:58899157delG	ENST00000556134.1	+	5	621	c.347delG	c.(346-348)agafs	p.R116fs	KIAA0586_ENST00000423743.3_Frame_Shift_Del_p.R46fs|KIAA0586_ENST00000261244.5_Frame_Shift_Del_p.R131fs|KIAA0586_ENST00000354386.6_Frame_Shift_Del_p.R143fs	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	Q9BVV6	TALD3_HUMAN	KIAA0586	116					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						GATGCTCTAAGAACAGTTTTA	0.279													G|G|-|deletion	12	0.00239617	0.0	0.0058	5008	,	,		15268	0.0		0.007	False		,,,				2504	0.001				p.R143fs		Pindel,Atlas-Indel	.											.	KIAA0586	180	.	0			c.427delA						PASS	.			3,3511		0,3,1754	44	43	43			5.2	1	14		43	25,7757		0,25,3866	no	frameshift	KIAA0586	NM_014749.3		0,28,5620	A1A1,A1R,RR		0.3213,0.0854,0.2479			58899157	28,11268	1814	4055	5869	SO:0001589	frameshift_variant	9786	exon5			.	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.347delG	14.37:g.58899157delG	ENSP00000452351:p.Arg116fs	154	0	.		171	61	0.357	NM_001244189	B4DZB6|E7EWM8|J3KQH9|O60328|Q6NYC6|Q6UV20	Frame_Shift_Del	DEL	ENST00000556134.1	37	CCDS58321.1																																																																																			.	.	none		0.279	KIAA0586-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411887.1	NM_014749		-	58899157	G	-	58899157	7	5	25	1	0	1	0	1	0	0	0	0	8195	942	33	0	406	0	KIAA0586	14	58899157	Frame_Shift_Del	DEL	G	TCGA-G8-6906-01A-11D-2210-10	2793249	58899157	48450383	571	9480											
PLEKHH1	57475	hgsc.bcm.edu	37	chr14	68022572	68022572	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tggagcagaggctgctggagGcagagcagagagcagagaac	13	3	18	7	0	0	4	0	0	0	4	0	8	0	6	0	4	5	6	0	4	1	0	rs200379117		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:68022572G>A	ENST00000329153.5	+	3	289	c.157G>A	c.(157-159)Gca>Aca	p.A53T		NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	53						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)		GCTGCTGGAGGCAGAGCAGAG	0.607																																					p.A53T		Atlas-SNP	.											.	PLEKHH1	118	.	0			c.G157A						PASS	.						35	41	39					14																	68022572		2129	4263	6392	SO:0001583	missense	57475	exon3			CTGGAGGCAGAGC	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.157G>A	14.37:g.68022572G>A	ENSP00000330278:p.Ala53Thr	256	1	0.00390625		263	120	0.456274	NM_020715	A6H8X6|Q6PJL4|Q6ZWC7	Missense_Mutation	SNP	ENST00000329153.5	37	CCDS45128.1	.	.	.	.	.	.	.	.	.	.	G	31	5.099177	0.94197	.	.	ENSG00000054690	ENST00000329153	T	0.39229	1.09	4.44	4.44	0.53790	.	0.000000	0.85682	D	0.000000	T	0.64427	0.2597	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.67237	-0.5721	10	0.52906	T	0.07	.	14.4383	0.67298	0.0:0.0:1.0:0.0	.	53	Q9ULM0	PKHH1_HUMAN	T	53	ENSP00000330278:A53T	ENSP00000330278:A53T	A	+	1	0	PLEKHH1	67092325	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	5.665000	0.68052	2.476000	0.83614	0.655000	0.94253	GCA	.	.	weak		0.607	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054		A	68022572	G	A	68022572	3	1	25	1	0	0	0	0	1	0	0	0	12085	1203	42	2	163	2	PLEKHH1	14	68022572	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	9123415	68022572	39326968	572	9481											
ZFYVE26	23503	hgsc.bcm.edu	37	chr14	68229051	68229051	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaacttctcccgtgcagcagTgaggttcccggctttgaggc	6	10	13	12	2	1	2	0	2	1	0	3	3	2	2	2	3	3	4	2	3	1	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:68229051T>C	ENST00000347230.4	-	34	6376	c.6238A>G	c.(6238-6240)Act>Gct	p.T2080A	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.T2080A|ZFYVE26_ENST00000557306.1_5'Flank	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	2080					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)		CGTGCAGCAGTGAGGTTCCCG	0.562																																					p.T2080A		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.A6238G						PASS	.						93	76	82					14																	68229051		2203	4300	6503	SO:0001583	missense	23503	exon34			CAGCAGTGAGGTT	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.6238A>G	14.37:g.68229051T>C	ENSP00000251119:p.Thr2080Ala	89	0	0		105	45	0.428571	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	37	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	T	3.183	-0.167539	0.06461	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.26518	1.88;1.73	5.55	0.543	0.17179	.	0.468395	0.22794	N	0.055575	T	0.06872	0.0175	N	0.02011	-0.69	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.001	T	0.36335	-0.9752	10	0.11182	T	0.66	-0.8863	4.9027	0.13782	0.0:0.23:0.2765:0.4935	.	2080;2080	G3V2D8;Q68DK2	.;ZFY26_HUMAN	A	2080;2059;2080	ENSP00000251119:T2080A;ENSP00000450603:T2080A	ENSP00000251119:T2080A	T	-	1	0	ZFYVE26	67298804	0.979000	0.34478	0.895000	0.35142	0.474000	0.32979	0.238000	0.18004	0.071000	0.16664	-0.313000	0.08912	ACT	.	.	none		0.562	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346		C	68229051	T	C	68229051	3	2	25	1	0	0	0	0	1	0	0	0	17683	1696	59	3	1417	3	ZFYVE26	14	68229051	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	206479	68229051	39120489	573	9482											
MAP3K9	4293	hgsc.bcm.edu	37	chr14	71267772	71267772	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccaataatctcttccaaggtGagctccgcaaaatcaatttc	13	11	5	12	1	2	1	1	1	1	0	6	1	4	1	3	1	1	2	3	1	6	3	rs147891121	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:71267772G>A	ENST00000554752.2	-	2	431	c.432C>T	c.(430-432)ctC>ctT	p.L144L	MAP3K9_ENST00000381250.4_Silent_p.L144L|MAP3K9_ENST00000555993.2_Silent_p.L144L	NM_001284230.1	NP_001271159.1	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase 9	144	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)		CTTCCAAGGTGAGCTCCGCAA	0.438																																					p.L144L	GBM(114;411 1587 13539 28235 50070)	Atlas-SNP	.											.	MAP3K9	109	.	0			c.C432T						PASS	.	G		0,4406		0,0,2203	57	58	58		432	-2	1	14	dbSNP_134	58	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	MAP3K9	NM_033141.2		0,4,6499	AA,AG,GG		0.0465,0.0,0.0308		144/1119	71267772	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	4293	exon2			CAAGGTGAGCTCC	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.432C>T	14.37:g.71267772G>A		68	0	0		75	35	0.466667	NM_033141	A3KN85|Q0D2G7|Q6EH31|Q9H2N5	Silent	SNP	ENST00000554752.2	37																																																																																				G|1.000;A|0.000	0.000	strong		0.438	MAP3K9-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412550.2			A	71267772	G	A	71267772	2	1	25	1	0	0	0	0	0	0	0	1	9266	1277	45	2		2	MAP3K9	14	71267772	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	3038721	71267772	36081768	574	9483											
C14orf156	81892	hgsc.bcm.edu	37	chr14	78182188	78182188	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaaggacttcggaatgcacTacaacaggaaaatcatatta	18	8	8	7	1	1	1	1	0	0	1	2	4	1	4	0	3	3	1	0	3	8	4	rs199752740		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:78182188T>A	ENST00000557342.1	+	3	271	c.230T>A	c.(229-231)cTa>cAa	p.L77Q	SLIRP_ENST00000238688.5_Missense_Mutation_p.L77Q|SLIRP_ENST00000557623.1_Missense_Mutation_p.L77Q|SLIRP_ENST00000557431.1_Missense_Mutation_p.L77Q	NM_001267864.1|NM_031210.5	NP_001254793.1|NP_112487.1	Q9GZT3	SLIRP_HUMAN	SRA stem-loop interacting RNA binding protein	77	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				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						CGGAATGCACTACAACAGGAA	0.328																																					p.L77Q		Atlas-SNP	.											.	SLIRP	6	.	0			c.T230A						PASS	.	T	GLN/LEU	0,4398		0,0,2199	75	89	84		230	5.8	1	14		84	2,8594	1.2+/-3.3	0,2,4296	no	missense	SLIRP	NM_031210.4	113	0,2,6495	AA,AT,TT		0.0233,0.0,0.0154	probably-damaging	77/110	78182188	2,12992	2199	4298	6497	SO:0001583	missense	81892	exon3			ATGCACTACAACA	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.230T>A	14.37:g.78182188T>A	ENSP00000450909:p.Leu77Gln	238	0	0		222	102	0.459459	NM_001267864	J3KMY7	Missense_Mutation	SNP	ENST00000557342.1	37	CCDS9866.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.2|20.2	3.956115|3.956115	0.73902|0.73902	0.0|0.0	2.33E-4|2.33E-4	ENSG00000119705|ENSG00000119705	ENST00000557342;ENST00000238688;ENST00000557623;ENST00000557431|ENST00000556831;ENST00000553981	T;T;T;T|.	0.21734|.	1.99;1.99;1.99;1.99|.	5.77|5.77	5.77|5.77	0.91146|0.91146	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);|.	0.162010|.	0.41396|.	D|.	0.000897|.	T|T	0.77631|0.77631	0.4159|0.4159	M|M	0.79693|0.79693	2.465|2.465	0.44247|0.44247	D|D	0.997098|0.997098	D|.	0.89917|.	1.0|.	D|.	0.80764|.	0.994|.	T|T	0.78669|0.78669	-0.2114|-0.2114	10|5	0.87932|.	D|.	0|.	-5.4684|-5.4684	16.3818|16.3818	0.83467|0.83467	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	77|.	Q9GZT3|.	SLIRP_HUMAN|.	Q|N	77|75;50	ENSP00000450909:L77Q;ENSP00000238688:L77Q;ENSP00000452057:L77Q;ENSP00000450849:L77Q|.	ENSP00000238688:L77Q|.	L|Y	+|+	2|1	0|0	SLIRP|SLIRP	77251941|77251941	0.839000|0.839000	0.29477|0.29477	0.998000|0.998000	0.56505|0.56505	0.946000|0.946000	0.59487|0.59487	6.378000|6.378000	0.73150|0.73150	2.330000|2.330000	0.79161|0.79161	0.528000|0.528000	0.53228|0.53228	CTA|TAC	T|0.999;A|0.001	0.001	weak		0.328	SLIRP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000413901.1	NM_031210		A	78182188	T	A	78182188	3	1	25	1	0	0	0	0	1	0	0	0	1756	1522	53	5	240	5	C14orf156	14	78182188	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	6914416	78182188	29167352	575	9484											
FLRT2	23768	hgsc.bcm.edu	37	chr14	86089032	86089032	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccctctctattccaaaccctAgcagaagctacacgcctcca	11	8	4	18	1	1	1	0	0	1	1	4	1	3	1	5	0	4	2	5	0	5	4	rs137990800	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:86089032A>G	ENST00000330753.4	+	2	1941	c.1174A>G	c.(1174-1176)Agc>Ggc	p.S392G	FLRT2_ENST00000554746.1_Missense_Mutation_p.S392G	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	392					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)		TCCAAACCCTAGCAGAAGCTA	0.572													A|||	2	0.000399361	0.0	0.0014	5008	,	,		16226	0.0		0.001	False		,,,				2504	0.0				p.S392G		Atlas-SNP	.											.	FLRT2	168	.	0			c.A1174G						PASS	.	A	GLY/SER	0,4406		0,0,2203	78	81	80		1174	2.6	0.1	14	dbSNP_134	80	11,8589	8.4+/-32.0	0,11,4289	yes	missense	FLRT2	NM_013231.4	56	0,11,6492	GG,GA,AA		0.1279,0.0,0.0846	benign	392/661	86089032	11,12995	2203	4300	6503	SO:0001583	missense	23768	exon2			AACCCTAGCAGAA	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.1174A>G	14.37:g.86089032A>G	ENSP00000332879:p.Ser392Gly	79	0	0		81	42	0.518519	NM_013231	A0AV84|B7ZLP3	Missense_Mutation	SNP	ENST00000330753.4	37	CCDS9877.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	0.009	-1.812472	0.00600	0.0	0.001279	ENSG00000185070	ENST00000330753;ENST00000554746;ENST00000535800	T;T	0.56941	0.43;0.43	6.17	2.57	0.30868	.	0.309770	0.41001	N	0.000969	T	0.28234	0.0697	N	0.08118	0	0.28921	N	0.892133	B	0.02656	0.0	B	0.01281	0.0	T	0.15723	-1.0427	10	0.20046	T	0.44	-12.0086	9.8404	0.40996	0.8088:0.0:0.1912:0.0	.	392	O43155	FLRT2_HUMAN	G	392;392;45	ENSP00000332879:S392G;ENSP00000451050:S392G	ENSP00000332879:S392G	S	+	1	0	FLRT2	85158785	0.870000	0.30015	0.060000	0.19600	0.021000	0.10359	1.891000	0.39738	0.207000	0.20607	0.533000	0.62120	AGC	A|0.999;G|0.001	0.001	strong		0.572	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1			G	86089032	A	G	86089032	3	3	25	1	0	0	0	0	1	0	0	0	5947	420	15	3	1176	3	FLRT2	14	86089032	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	7906844	86089032	21260508	576	9485											
TTC8	123016	hgsc.bcm.edu	37	chr14	89319359	89319359	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acagaacattctcagtacaaGgactggtggtggaaagtaca	15	8	11	7	0	1	1	1	0	1	1	2	3	1	3	0	4	3	2	0	4	5	3	rs141304350	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:89319359G>A	ENST00000345383.5	+	7	723	c.639G>A	c.(637-639)aaG>aaA	p.K213K	TTC8_ENST00000358622.5_Silent_p.K25K|TTC8_ENST00000346301.4_Silent_p.K183K|TTC8_ENST00000380656.2_Silent_p.K223K|TTC8_ENST00000338104.6_Silent_p.K239K|TTC8_ENST00000354441.6_Intron|TTC8_ENST00000536576.1_5'UTR	NM_198309.2	NP_938051.1	Q8TAM2	TTC8_HUMAN	tetratricopeptide repeat domain 8	249					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						CTCAGTACAAGGACTGGTGGT	0.378													G|||	5	0.000998403	0.0	0.0029	5008	,	,		16565	0.0		0.001	False		,,,				2504	0.002				p.K223K		Atlas-SNP	.											.	TTC8	42	.	0			c.G669A						PASS	.	G	,,	1,4405	2.1+/-5.4	0,1,2202	91	80	84		669,639,549	5.3	1	14	dbSNP_134	84	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	TTC8	NM_144596.2,NM_198309.2,NM_198310.2	,,	0,6,6497	AA,AG,GG		0.0581,0.0227,0.0461	,,	223/516,213/506,183/476	89319359	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	123016	exon8			GTACAAGGACTGG	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.639G>A	14.37:g.89319359G>A		139	0	0		151	73	0.483444	NM_144596	A6NFG2|B3KWA5|Q67B97|Q86SY0|Q86TV9|Q86U26|Q8NDH9|Q96DG8	Silent	SNP	ENST00000345383.5	37	CCDS9885.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	9.139	1.013312	0.19277	2.27E-4	5.81E-4	ENSG00000165533	ENST00000554686	.	.	.	5.32	5.32	0.75619	.	.	.	.	.	T	0.60907	0.2305	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58317	-0.7657	4	.	.	.	-26.5066	9.7161	0.40276	0.1556:0.0:0.8444:0.0	.	.	.	.	K	173	.	.	R	+	2	0	TTC8	88389112	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.332000	0.65911	2.660000	0.90430	0.655000	0.94253	AGG	G|1.000;A|0.000	0.000	strong		0.378	TTC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410861.1	NM_144596		A	89319359	G	A	89319359	2	1	25	1	0	0	0	0	0	0	0	1	16729	991	35	2		2	TTC8	14	89319359	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	3230327	89319359	18030181	577	9486											
KCNK13	56659	hgsc.bcm.edu	37	chr14	90651079	90651079	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtgatgccaggcagcgtccGgaaccgctgcaacatctcca	9	6	12	14	3	1	1	0	1	1	0	3	2	2	2	4	3	5	3	4	3	2	0	rs150186575	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:90651079G>A	ENST00000282146.4	+	2	1400	c.959G>A	c.(958-960)cGg>cAg	p.R320Q		NM_022054.2	NP_071337.2	Q9HB14	KCNKD_HUMAN	potassium channel, subfamily K, member 13	320					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)				GGCAGCGTCCGGAACCGCTGC	0.597																																					p.R320Q		Atlas-SNP	.											.	KCNK13	76	.	0			c.G959A						PASS	.						65	69	68					14																	90651079		2203	4300	6503	SO:0001583	missense	56659	exon2			GCGTCCGGAACCG	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.959G>A	14.37:g.90651079G>A	ENSP00000282146:p.Arg320Gln	129	0	0		141	74	0.524823	NM_022054	B5TJL8|Q96E79	Missense_Mutation	SNP	ENST00000282146.4	37	CCDS9889.1	.	.	.	.	.	.	.	.	.	.	G	8.030	0.761526	0.15914	.	.	ENSG00000152315	ENST00000282146	T	0.12255	2.7	5.28	-0.111	0.13576	.	2.504590	0.01759	N	0.030439	T	0.11879	0.0289	L	0.36672	1.1	0.46981	D	0.999276	B	0.06786	0.001	B	0.09377	0.004	T	0.46219	-0.9207	10	0.07813	T	0.8	.	10.1408	0.42734	0.3118:0.0:0.6882:0.0	.	320	Q9HB14	KCNKD_HUMAN	Q	320	ENSP00000282146:R320Q	ENSP00000282146:R320Q	R	+	2	0	KCNK13	89720832	0.952000	0.32445	0.001000	0.08648	0.007000	0.05969	4.029000	0.57253	-0.355000	0.08199	0.655000	0.94253	CGG	G|0.999;T|0.001	.	alt		0.597	KCNK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411251.1	NM_022054		A	90651079	G	A	90651079	3	1	25	1	0	0	0	0	1	0	0	0	8070	1116	39	1	965	1	KCNK13	14	90651079	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1331720	90651079	16698461	578	9487											
TRIP11	9321	hgsc.bcm.edu	37	chr14	92460176	92460176	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	taatgatatcacttttccttCcagattttctgcgtttttct	7	21	4	9	1	3	2	1	1	2	1	5	2	5	2	2	0	1	1	2	0	2	9	rs137974620	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:92460176C>G	ENST00000267622.4	-	15	5510	c.5137G>C	c.(5137-5139)Gaa>Caa	p.E1713Q		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	1713					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)		ACTTTTCCTTCCAGATTTTCT	0.328			T	PDGFRB	AML								C|||	4	0.000798722	0.0	0.0	5008	,	,		18129	0.0		0.004	False		,,,				2504	0.0				p.E1713Q	Ovarian(84;609 1888 9852 42686)	Atlas-SNP	.		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	.	TRIP11	184	.	0			c.G5137C						PASS	.	C	GLN/GLU	3,4401	6.2+/-15.9	0,3,2199	141	128	133		5137	4.5	1	14	dbSNP_134	133	29,8567	21.0+/-64.5	0,29,4269	yes	missense	TRIP11	NM_004239.3	29	0,32,6468	GG,GC,CC		0.3374,0.0681,0.2462	probably-damaging	1713/1980	92460176	32,12968	2202	4298	6500	SO:0001583	missense	9321	exon15			TTCCTTCCAGATT	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.5137G>C	14.37:g.92460176C>G	ENSP00000267622:p.Glu1713Gln	136	0	0		158	86	0.544304	NM_004239	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	37	CCDS9899.1	4|4	0.0018315018315018315|0.0018315018315018315	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	4|4	0.005277044854881266|0.005277044854881266	C|C	17.47|17.47	3.397608|3.397608	0.62177|0.62177	6.81E-4|6.81E-4	0.003374|0.003374	ENSG00000100815|ENSG00000100815	ENST00000267622;ENST00000542257|ENST00000554357	T|.	0.04862|.	3.54|.	5.41|5.41	4.51|4.51	0.55191|0.55191	.|.	0.050641|.	0.85682|.	N|.	0.000000|.	T|T	0.66228|0.66228	0.2768|0.2768	M|M	0.70275|0.70275	2.135|2.135	0.44899|0.44899	D|D	0.99791|0.99791	D;D|.	0.58970|.	0.976;0.984|.	P;P|.	0.62435|.	0.799;0.902|.	T|T	0.70749|0.70749	-0.4787|-0.4787	10|5	0.42905|.	T|.	0.14|.	.|.	15.1012|15.1012	0.72279|0.72279	0.0:0.8575:0.1425:0.0|0.0:0.8575:0.1425:0.0	.|.	1449;1713|.	F5H1Z0;Q15643|.	.;TRIPB_HUMAN|.	Q|A	1713;1449|1428	ENSP00000267622:E1713Q|.	ENSP00000267622:E1713Q|.	E|G	-|-	1|2	0|0	TRIP11|TRIP11	91529929|91529929	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	3.187000|3.187000	0.50950|0.50950	1.363000|1.363000	0.46019|0.46019	0.655000|0.655000	0.94253|0.94253	GAA|GGA	C|0.998;G|0.002	0.002	strong		0.328	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1			G	92460176	C	G	92460176	3	3	25	1	0	0	0	0	1	0	0	0	16570	864	30	4	830	4	TRIP11	14	92460176	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1809097	92460176	14889364	579	9488											
RIN3	79890	hgsc.bcm.edu	37	chr14	93118790	93118790	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccccccaggaaaaaacggAtctctcgacaactggcctcg	11	5	9	16	4	1	0	0	0	1	0	4	3	1	2	4	3	2	0	4	3	4	0	rs139248637	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:93118790A>C	ENST00000216487.7	+	6	1555	c.1396A>C	c.(1396-1398)Atc>Ctc	p.I466L	RIN3_ENST00000418924.2_3'UTR	NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	466	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)				GAAAAAACGGATCTCTCGACA	0.627													A|||	15	0.00299521	0.0	0.0014	5008	,	,		16397	0.0		0.007	False		,,,				2504	0.0072				p.I466L		Atlas-SNP	.											.	RIN3	81	.	0			c.A1396C						PASS	.	A	LEU/ILE	0,4406		0,0,2203	94	118	110		1396	-3.2	0.7	14	dbSNP_134	110	32,8568	22.2+/-67.0	0,32,4268	yes	missense	RIN3	NM_024832.3	5	0,32,6471	CC,CA,AA		0.3721,0.0,0.246	benign	466/986	93118790	32,12974	2203	4300	6503	SO:0001583	missense	79890	exon6			AAACGGATCTCTC	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.1396A>C	14.37:g.93118790A>C	ENSP00000216487:p.Ile466Leu	85	0	0		83	34	0.409639	NM_024832	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Missense_Mutation	SNP	ENST00000216487.7	37	CCDS32144.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	A	6.565	0.472587	0.12461	0.0	0.003721	ENSG00000100599	ENST00000216487;ENST00000428147	T	0.05199	3.48	4.22	-3.16	0.05217	.	1.726180	0.03309	N	0.190221	T	0.03263	0.0095	L	0.38531	1.155	0.22591	N	0.99896	P;B;B;B	0.42518	0.782;0.0;0.001;0.001	B;B;B;B	0.41813	0.367;0.001;0.001;0.001	T	0.35126	-0.9801	10	0.02654	T	1	-7.5443	4.3078	0.10956	0.1825:0.2771:0.438:0.1024	.	466;512;391;466	Q8TB24-4;Q86U22;Q6ZRC2;Q8TB24	.;.;.;RIN3_HUMAN	L	466;390	ENSP00000216487:I466L	ENSP00000216487:I466L	I	+	1	0	RIN3	92188543	0.047000	0.20315	0.692000	0.30179	0.814000	0.46013	-0.512000	0.06313	-1.044000	0.03254	0.260000	0.18958	ATC	A|0.998;C|0.002	0.002	strong		0.627	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1			C	93118790	A	C	93118790	3	2	25	1	0	0	0	0	1	0	0	0	13388	333	12	5	1418	5	RIN3	14	93118790	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	658614	93118790	14230750	580	9489											
C15orf2	23742	hgsc.bcm.edu	37	chr15	24923129	24923129	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctatgcataccactcctccTtccaaggctgtcatcttgca	8	12	6	15	0	2	0	1	0	1	0	5	0	5	0	4	1	3	4	4	1	3	4			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:24923129T>C	ENST00000329468.2	+	1	2589	c.2115T>C	c.(2113-2115)ccT>ccC	p.P705P		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	705					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											CCACTCCTCCTTCCAAGGCTG	0.507																																					p.P705P		Atlas-SNP	.											.	.	.	.	0			c.T2115C						PASS	.						176	163	168					15																	24923129		2203	4300	6503	SO:0001819	synonymous_variant	23742	exon1			TCCTCCTTCCAAG	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.2115T>C	15.37:g.24923129T>C		280	0	0		271	110	0.405904	NM_018958		Silent	SNP	ENST00000329468.2	37	CCDS10015.1																																																																																			.	.	none		0.507	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958		C	24923129	T	C	24923129	2	2	25	1	0	0	0	0	0	0	0	1	1786	1596	56	3		3	C15orf2	15	24923129	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10		24923129	77608263	581	9490											
HERC2	8924	hgsc.bcm.edu	37	chr15	28420676	28420676	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acctgccccgagtccgtgacCgccaggcagtgcagggcccc	6	4	13	18	3	0	1	0	1	0	0	1	2	1	1	8	2	2	2	8	2	0	0	rs139728053	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:28420676C>T	ENST00000261609.7	-	64	9921	c.9813G>A	c.(9811-9813)gcG>gcA	p.A3271A		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)		AGTCCGTGACCGCCAGGCAGT	0.662													C|||	5	0.000998403	0.0	0.0	5008	,	,		16999	0.005		0.0	False		,,,				2504	0.0				p.A3271A		Atlas-SNP	.											.	HERC2	501	.	0			c.G9813A						PASS	.	C		0,4406		0,0,2203	38	30	33		9813	-7.9	0.9	15	dbSNP_134	33	1,8587		0,1,4293	no	coding-synonymous	HERC2	NM_004667.4		0,1,6496	TT,TC,CC		0.0116,0.0,0.0077		3271/4835	28420676	1,12993	2203	4294	6497	SO:0001819	synonymous_variant	8924	exon64			CGTGACCGCCAGG	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.9813G>A	15.37:g.28420676C>T		73	0	0		91	49	0.538462	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			C|1.000;T|0.000	0.000	weak		0.662	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		T	28420676	C	T	28420676	2	4	25	1	0	0	0	0	0	0	0	1	7067	639	23	1		1	HERC2	15	28420676	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	3497547	28420676	74110716	582	9491											
HERC2	8924	hgsc.bcm.edu	37	chr15	28459092	28459092	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccacttcagggttctcggaGtcggggaagtagtcctctaa	8	10	12	11	2	3	0	1	0	2	0	6	2	4	2	2	4	0	2	2	4	3	4	rs187225254		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:28459092G>A	ENST00000261609.7	-	42	6690	c.6582C>T	c.(6580-6582)gaC>gaT	p.D2194D		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)		GGTTCTCGGAGTCGGGGAAGT	0.587																																					p.D2194D		Atlas-SNP	.											.	HERC2	501	.	0			c.C6582T						PASS	.						35	32	33					15																	28459092		2203	4298	6501	SO:0001819	synonymous_variant	8924	exon42			CTCGGAGTCGGGG	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.6582C>T	15.37:g.28459092G>A		219	0	0		194	12	0.0618557	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			G|0.993;A|0.007	0.007	strong		0.587	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		A	28459092	G	A	28459092	2	1	25	1	0	0	0	0	0	0	0	1	7067	1020	36	2		2	HERC2	15	28459092	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	38416	28459092	74072300	583	9492											
HERC2	8924	hgsc.bcm.edu	37	chr15	28459325	28459325	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagtcagggagtgcagcgtgCgcagcagtgccaccacctcc	8	5	14	14	2	1	0	1	0	0	0	2	2	2	1	4	1	5	3	4	1	0	0			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:28459325C>T	ENST00000261609.7	-	41	6560	c.6452G>A	c.(6451-6453)cGc>cAc	p.R2151H		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2									p.R2151H(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)		GTGCAGCGTGCGCAGCAGTGC	0.637																																					p.R2151H		Atlas-SNP	.											HERC2,NS,carcinoma,0,2	HERC2	501	2	2	Substitution - Missense(2)	prostate(2)	c.G6452A						scavenged	.						60	56	57					15																	28459325		2203	4300	6503	SO:0001583	missense	8924	exon41			AGCGTGCGCAGCA	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.6452G>A	15.37:g.28459325C>T	ENSP00000261609:p.Arg2151His	90	1	0.0111111		104	5	0.0480769	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	37	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	C	18.08	3.544886	0.65198	.	.	ENSG00000128731	ENST00000261609	T	0.61392	0.11	4.75	4.75	0.60458	.	0.057517	0.64402	D	0.000004	T	0.77485	0.4137	M	0.81942	2.565	0.80722	D	1	D	0.71674	0.998	D	0.72075	0.976	T	0.81212	-0.1035	10	0.72032	D	0.01	.	17.9388	0.89021	0.0:1.0:0.0:0.0	.	2151	O95714	HERC2_HUMAN	H	2151	ENSP00000261609:R2151H	ENSP00000261609:R2151H	R	-	2	0	HERC2	26132920	1.000000	0.71417	0.415000	0.26534	0.134000	0.20937	7.305000	0.78891	2.461000	0.83175	0.484000	0.47621	CGC	.	.	none		0.637	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		T	28459325	C	T	28459325	3	4	25	1	0	0	0	0	1	0	0	0	7067	768	27	1	8264	1	HERC2	15	28459325	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	233	28459325	74072067	584	9493											
C15orf55	256646	hgsc.bcm.edu	37	chr15	34649336	34649336	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggaagcagaggaagaggatGaggaactctccaactttgct	14	7	13	7	0	1	3	0	1	1	2	2	7	1	7	1	4	4	2	1	4	4	1	rs149177074	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:34649336G>A	ENST00000333756.4	+	7	3198	c.3043G>A	c.(3043-3045)Gag>Aag	p.E1015K	NUTM1_ENST00000537011.1_Missense_Mutation_p.E1043K|NUTM1_ENST00000438749.3_Missense_Mutation_p.E1033K	NM_175741.1	NP_786883	Q86Y26	NUTM1_HUMAN	NUT midline carcinoma, family member 1	1015						cytoplasm (GO:0005737)|nucleus (GO:0005634)											GGAAGAGGATGAGGAACTCTC	0.498													G|||	8	0.00159744	0.0	0.0029	5008	,	,		20984	0.0		0.006	False		,,,				2504	0.0				p.E1015K		Atlas-SNP	.											C15orf55_ENST00000333756,NS,lymphoid_neoplasm,0,1	C15orf55	110	1	0			c.G3043A						PASS	.	G	LYS/GLU	4,4398	9.9+/-24.2	0,4,2197	76	61	66		3043	4.3	1	15	dbSNP_134	66	31,8565	22.8+/-68.1	0,31,4267	yes	missense	C15orf55	NM_175741.1	56	0,35,6464	AA,AG,GG		0.3606,0.0909,0.2693	benign	1015/1133	34649336	35,12963	2201	4298	6499	SO:0001583	missense	256646	exon7			GAGGATGAGGAAC	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.3043G>A	15.37:g.34649336G>A	ENSP00000329448:p.Glu1015Lys	56	0	0		55	26	0.472727	NM_175741	B4DZ00|B7Z7Y4|E7EVE8|F5H4I6|Q86YS8|Q8N7F2|Q9NTB3	Missense_Mutation	SNP	ENST00000333756.4	37	CCDS32190.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	G	15.74	2.923315	0.52653	9.09E-4	0.003606	ENSG00000184507	ENST00000537011;ENST00000438749;ENST00000333756	T;T;T	0.13307	2.62;2.6;2.61	5.2	4.28	0.50868	.	0.557345	0.16563	N	0.208980	T	0.11324	0.0276	L	0.61387	1.9	0.33479	D	0.58722	B;B;B	0.29085	0.232;0.154;0.192	B;B;B	0.27076	0.059;0.076;0.031	T	0.10222	-1.0639	10	0.66056	D	0.02	.	9.6167	0.39696	0.0944:0.0:0.9056:0.0	.	1033;1043;1015	E7EVE8;F5H4I6;Q86Y26	.;.;NUT_HUMAN	K	1043;1033;1015	ENSP00000444896:E1043K;ENSP00000407031:E1033K;ENSP00000329448:E1015K	ENSP00000329448:E1015K	E	+	1	0	C15orf55	32436628	0.965000	0.33210	0.991000	0.47740	0.842000	0.47809	1.928000	0.40104	1.422000	0.47177	0.655000	0.94253	GAG	G|0.998;A|0.002	0.002	strong		0.498	NUTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418026.1	NM_175741		A	34649336	G	A	34649336	3	1	25	1	0	0	0	0	1	0	0	0	1805	1291	45	2	3069	2	C15orf55	15	34649336	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	6190011	34649336	67882056	585	9494											
TYRO3	7301	hgsc.bcm.edu	37	chr15	41862356	41862356	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggaaagagacgcggtttgggTaaggggatggggatgtggag	10	7	22	2	2	0	1	0	0	0	1	0	6	0	5	0	8	0	2	0	8	2	2	rs149022093		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:41862356T>C	ENST00000263798.3	+	10	1606		c.e10+2		TYRO3_ENST00000559066.1_Splice_Site	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase						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)		GCGGTTTGGGTAAGGGGATGG	0.567																																					.		Atlas-SNP	.											TYRO3_ENST00000263798,NS,carcinoma,0,2	TYRO3	169	2	0			c.1382+2T>C						PASS	.						76	75	75					15																	41862356		2203	4300	6503	SO:0001630	splice_region_variant	7301	exon10			TTTGGGTAAGGGG	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.1382+2T>C	15.37:g.41862356T>C		110	0	0		119	8	0.0672269	NM_006293	O14953|Q86VR3	Splice_Site	SNP	ENST00000263798.3	37	CCDS10080.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.181954	0.78677	.	.	ENSG00000092445	ENST00000540218;ENST00000263798	.	.	.	5.26	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3401	0.74290	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	TYRO3	39649648	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	6.789000	0.75110	2.208000	0.71279	0.533000	0.62120	.	.	.	weak		0.567	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2		Intron	C	41862356	T	C	41862356	5	2	25	1	0	0	0	0	0	0	1	0	16829	1652	57	3	1422	3	TYRO3	15	41862356	Splice_Site	SNP	T	TCGA-G8-6906-01A-11D-2210-10	7213020	41862356	60669036	586	9495											
UBR1	197131	hgsc.bcm.edu	37	chr15	43299467	43299467	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagcaattctagagtagtcActgactgctggggtgctacc	11	10	11	9	0	2	2	1	1	1	1	2	2	2	2	1	2	4	4	1	2	5	4	rs141543407	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:43299467A>C	ENST00000290650.4	-	30	3303	c.3225T>G	c.(3223-3225)agT>agG	p.S1075R	UBR1_ENST00000382177.2_3'UTR|UBR1_ENST00000568782.1_5'UTR	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	1075					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)		TAGAGTAGTCACTGACTGCTG	0.423																																					p.S1075R		Atlas-SNP	.											.	UBR1	124	.	0			c.T3225G						PASS	.	A	ARG/SER	0,4406		0,0,2203	62	56	58		3225	5	1	15	dbSNP_134	58	1,8597	1.2+/-3.3	0,1,4298	no	missense	UBR1	NM_174916.2	110	0,1,6501	CC,CA,AA		0.0116,0.0,0.0077	benign	1075/1750	43299467	1,13003	2203	4299	6502	SO:0001583	missense	197131	exon30			GTAGTCACTGACT		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.3225T>G	15.37:g.43299467A>C	ENSP00000290650:p.Ser1075Arg	83	0	0		69	37	0.536232	NM_174916	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	37	CCDS10091.1	.	.	.	.	.	.	.	.	.	.	A	12.24	1.879865	0.33162	0.0	1.16E-4	ENSG00000159459	ENST00000290650	T	0.50277	0.75	4.99	4.99	0.66335	.	0.403021	0.31507	N	0.007537	T	0.28532	0.0706	L	0.32530	0.975	0.80722	D	1	B	0.31125	0.309	B	0.19391	0.025	T	0.10086	-1.0645	10	0.13853	T	0.58	0.1735	6.762	0.23546	0.7868:0.0:0.0763:0.1369	.	1075	Q8IWV7	UBR1_HUMAN	R	1075	ENSP00000290650:S1075R	ENSP00000290650:S1075R	S	-	3	2	UBR1	41086759	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.608000	0.46308	2.096000	0.63516	0.533000	0.62120	AGT	A|0.999;C|0.001	0.001	strong		0.423	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916		C	43299467	A	C	43299467	3	2	25	1	0	0	0	0	1	0	0	0	16916	156	6	5	2096	5	UBR1	15	43299467	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	1437111	43299467	59231925	587	9496											
DUOX2	50506	hgsc.bcm.edu	37	chr15	45398797	45398797	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tttgtagcttcttgtgttctCggccccggaaataggccacc	6	13	10	12	2	2	0	0	0	2	0	3	1	2	1	4	3	1	3	4	3	3	6	rs373620034		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:45398797C>T	ENST00000603300.1	-	16	2076	c.1874G>A	c.(1873-1875)cGa>cAa	p.R625Q	DUOX2_ENST00000389039.6_Missense_Mutation_p.R625Q	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	625					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)		CTTGTGTTCTCGGCCCCGGAA	0.557																																					p.R625Q		Atlas-SNP	.											DUOX2,NS,carcinoma,-1,1	DUOX2	137	1	0			c.G1874A						PASS	.	C	GLN/ARG	0,4396		0,0,2198	154	150	151		1874	-1	1	15		151	1,8595	1.2+/-3.3	0,1,4297	no	missense	DUOX2	NM_014080.4	43	0,1,6495	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	625/1549	45398797	1,12991	2198	4298	6496	SO:0001583	missense	50506	exon16			TGTTCTCGGCCCC	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.1874G>A	15.37:g.45398797C>T	ENSP00000475084:p.Arg625Gln	158	0	0		154	72	0.467532	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Missense_Mutation	SNP	ENST00000603300.1	37	CCDS10117.1	.	.	.	.	.	.	.	.	.	.	C	13.84	2.357373	0.41801	0.0	1.16E-4	ENSG00000140279	ENST00000389039	.	.	.	5.42	-1.02	0.10135	.	0.584816	0.18081	N	0.152290	T	0.49287	0.1548	M	0.72894	2.215	0.40470	D	0.980336	B;B	0.31931	0.188;0.347	B;B	0.24701	0.023;0.055	T	0.44467	-0.9326	9	0.42905	T	0.14	-3.1592	9.9682	0.41738	0.0:0.6012:0.0:0.3988	.	625;187	Q9NRD8;Q59GU9	DUOX2_HUMAN;.	Q	625	.	ENSP00000373691:R625Q	R	-	2	0	DUOX2	43186089	0.024000	0.19004	0.990000	0.47175	0.648000	0.38561	-0.235000	0.09016	-0.185000	0.10550	0.455000	0.32223	CGA	.	.	weak		0.557	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080		T	45398797	C	T	45398797	3	4	25	1	0	0	0	0	1	0	0	0	4803	884	31	1	2848	1	DUOX2	15	45398797	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2099330	45398797	57132595	588	9497											
SEMA6D	80031	hgsc.bcm.edu	37	chr15	48056050	48056050	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctatccgttgggcaggctGtgtattcccgcgtggcccgc	3	12	13	13	4	1	0	0	0	1	0	3	0	3	0	3	3	0	4	3	3	2	5	rs151039709	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:48056050G>A	ENST00000316364.5	+	10	1190	c.751G>A	c.(751-753)Gtg>Atg	p.V251M	SEMA6D_ENST00000355997.3_Missense_Mutation_p.V251M|SEMA6D_ENST00000537942.1_Missense_Mutation_p.V251M|SEMA6D_ENST00000558014.1_Missense_Mutation_p.V251M|SEMA6D_ENST00000389433.2_Missense_Mutation_p.V251M|SEMA6D_ENST00000389428.3_Missense_Mutation_p.V251M|SEMA6D_ENST00000558816.1_Missense_Mutation_p.V251M|SEMA6D_ENST00000354744.4_Missense_Mutation_p.V251M|SEMA6D_ENST00000389425.3_Missense_Mutation_p.V251M|SEMA6D_ENST00000358066.4_Missense_Mutation_p.V251M|SEMA6D_ENST00000536845.2_Missense_Mutation_p.V251M|SEMA6D_ENST00000389432.2_Missense_Mutation_p.V251M	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	251	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)		TGGGCAGGCTGTGTATTCCCG	0.473																																					p.V251M		Atlas-SNP	.											.	SEMA6D	322	.	0			c.G751A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	2,4394	4.2+/-10.8	0,2,2196	132	131	131		751,751,751,751,751,751,751	4.9	0.9	15	dbSNP_134	131	1,8593	1.2+/-3.3	0,1,4296	yes	missense,missense,missense,missense,missense,missense,missense	SEMA6D	NM_001198999.1,NM_020858.1,NM_024966.2,NM_153616.1,NM_153617.1,NM_153618.1,NM_153619.1	21,21,21,21,21,21,21	0,3,6492	AA,AG,GG		0.0116,0.0455,0.0231	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	251/1012,251/1012,251/477,251/999,251/1018,251/1074,251/598	48056050	3,12987	2198	4297	6495	SO:0001583	missense	80031	exon10			CAGGCTGTGTATT	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.751G>A	15.37:g.48056050G>A	ENSP00000324857:p.Val251Met	133	0	0		131	62	0.473282	NM_153617	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Missense_Mutation	SNP	ENST00000316364.5	37	CCDS32225.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.513526	0.85389	4.55E-4	1.16E-4	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428;ENST00000355997;ENST00000389425	T;T;T;T;T;T;T;T;T;T	0.12672	2.66;2.66;2.66;2.66;2.66;2.66;2.66;2.66;2.66;2.66	5.87	4.93	0.64822	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.105633	0.64402	D	0.000005	T	0.37489	0.1005	M	0.71581	2.175	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;1.0;0.98;1.0	D;D;D;P;D	0.71870	0.975;0.952;0.975;0.821;0.975	T	0.25641	-1.0126	10	0.66056	D	0.02	.	16.8154	0.85733	0.0:0.1288:0.8712:0.0	.	251;251;251;251;251	Q8NFY4-3;A6NM95;Q8NFY4-4;Q8NFY4;Q8NFY4-2	.;.;.;SEM6D_HUMAN;.	M	251	ENSP00000442040:V251M;ENSP00000446152:V251M;ENSP00000324857:V251M;ENSP00000374084:V251M;ENSP00000374083:V251M;ENSP00000346786:V251M;ENSP00000350770:V251M;ENSP00000374079:V251M;ENSP00000348276:V251M;ENSP00000374076:V251M	ENSP00000324857:V251M	V	+	1	0	SEMA6D	45843342	1.000000	0.71417	0.918000	0.36340	0.881000	0.50899	6.757000	0.74924	1.452000	0.47756	0.655000	0.94253	GTG	G|1.000;A|0.000	0.000	strong		0.473	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		A	48056050	G	A	48056050	3	1	25	1	0	0	0	0	1	0	0	0	14057	1377	48	2	785	2	SEMA6D	15	48056050	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2657253	48056050	54475342	589	9498											
ATP8B4	79895	hgsc.bcm.edu	37	chr15	50212572	50212572	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatccaggtctctgtatgcGatggccaaggtccgaaggcc	8	9	12	12	2	2	0	1	0	1	0	5	2	4	0	4	4	1	1	4	4	3	1	rs72733094	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:50212572G>T	ENST00000284509.6	-	18	1935	c.1794C>A	c.(1792-1794)atC>atA	p.I598I	ATP8B4_ENST00000559829.1_Silent_p.I598I	NM_024837.2	NP_079113.2	Q8TF62	AT8B4_HUMAN	ATPase, class I, type 8B, member 4	598						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)		CTCTGTATGCGATGGCCAAGG	0.458													G|||	7	0.00139776	0.0	0.0	5008	,	,		20424	0.0		0.007	False		,,,				2504	0.0				p.I598I		Atlas-SNP	.											.	ATP8B4	173	.	0			c.C1794A						PASS	.	G		6,4386	9.9+/-24.2	0,6,2190	84	76	79		1794	-11.3	0	15	dbSNP_130	79	85,8505	48.5+/-108.0	0,85,4210	no	coding-synonymous	ATP8B4	NM_024837.2		0,91,6400	TT,TG,GG		0.9895,0.1366,0.701		598/1193	50212572	91,12891	2196	4295	6491	SO:0001819	synonymous_variant	79895	exon18			GTATGCGATGGCC	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.1794C>A	15.37:g.50212572G>T		199	1	0.00502513		174	92	0.528736	NM_024837	Q9H727	Silent	SNP	ENST00000284509.6	37	CCDS32238.1																																																																																			G|0.994;T|0.006	0.006	strong		0.458	ATP8B4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418100.1	NM_024837		T	50212572	G	T	50212572	2	4	25	1	0	0	0	0	0	0	0	1	1197	1048	37	4		4	ATP8B4	15	50212572	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2156522	50212572	52318820	590	9499											
UNC13C	440279	hgsc.bcm.edu	37	chr15	54838957	54838957	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaatctgtgagaaaacagtcCtaaagcgagttttaaaagag	18	9	9	5	1	1	2	0	1	1	2	2	4	2	2	1	0	2	1	1	0	7	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:54838957C>A	ENST00000260323.11	+	26	5734	c.5734C>A	c.(5734-5736)Cta>Ata	p.L1912I	UNC13C_ENST00000537900.1_Missense_Mutation_p.L1910I|UNC13C_ENST00000545554.1_Missense_Mutation_p.L1912I	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1912	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)		GAAAACAGTCCTAAAGCGAGT	0.294																																					p.L1912I		Atlas-SNP	.											.	UNC13C	674	.	0			c.C5734A						PASS	.						37	32	33					15																	54838957		1748	4012	5760	SO:0001583	missense	440279	exon25			ACAGTCCTAAAGC	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.5734C>A	15.37:g.54838957C>A	ENSP00000260323:p.Leu1912Ile	112	0	0		133	54	0.406015	NM_001080534	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	37	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	C	14.35	2.509347	0.44660	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	D;D;D	0.81996	-1.56;-1.56;-1.56	5.59	4.68	0.58851	Mammalian uncoordinated homology 13, domain 2 (1);Mammalian uncoordinated homology 13, subgroup, domain 2 (1);	0.000000	0.64402	D	0.000002	D	0.90830	0.7120	M	0.87682	2.9	0.42046	D	0.991092	D	0.76494	0.999	D	0.87578	0.998	D	0.91027	0.4861	10	0.54805	T	0.06	.	9.6213	0.39723	0.0:0.8427:0.0:0.1573	.	1912	Q8NB66	UN13C_HUMAN	I	1912;1912;1910	ENSP00000260323:L1912I;ENSP00000438156:L1912I;ENSP00000442569:L1910I	ENSP00000260323:L1912I	L	+	1	2	UNC13C	52626249	0.999000	0.42202	0.571000	0.28486	0.201000	0.24016	2.469000	0.45110	1.364000	0.46038	0.561000	0.74099	CTA	.	.	none		0.294	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		A	54838957	C	A	54838957	3	1	25	1	0	0	0	0	1	0	0	0	17001	680	24	4	5832	4	UNC13C	15	54838957	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	4626385	54838957	47692435	591	9500											
FAM63B	54629	hgsc.bcm.edu	37	chr15	59064214	59064214	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggtccctgaggaggaggaggGcgcggcggtgttgcccgggg	4	5	23	9	4	0	1	0	1	0	0	1	4	1	4	2	9	1	1	2	9	0	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:59064214G>A	ENST00000559228.1	+	1	702	c.620G>A	c.(619-621)gGc>gAc	p.G207D	RP11-30K9.6_ENST00000500929.2_lincRNA|FAM63B_ENST00000450403.2_Missense_Mutation_p.G207D			Q8NBR6	FA63B_HUMAN	family with sequence similarity 63, member B	207										central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	15						GAGGAGGAGGGCGCGGCGGTG	0.622																																					p.G207D		Atlas-SNP	.											.	FAM63B	33	.	0			c.G620A						PASS	.						31	35	34					15																	59064214		1929	4117	6046	SO:0001583	missense	54629	exon1			AGGAGGGCGCGGC	AK075319	CCDS42046.1, CCDS45268.1	15q21.3	2005-08-09							26954	protein-coding gene	gene with protein product						10574461	Standard	NM_001040450		Approved	KIAA1164	uc002afj.3	Q8NBR6		ENST00000559228.1:c.620G>A	15.37:g.59064214G>A	ENSP00000452885:p.Gly207Asp	79	0	0		82	36	0.439024	NM_001040450	B2RTT8|Q9ULQ6	Missense_Mutation	SNP	ENST00000559228.1	37	CCDS42046.1	.	.	.	.	.	.	.	.	.	.	G	14.67	2.603459	0.46423	.	.	ENSG00000128923	ENST00000316848;ENST00000450403	T	0.51574	0.7	3.92	2.95	0.34219	.	0.870346	0.10083	N	0.718159	T	0.36331	0.0963	N	0.22421	0.69	0.41810	D	0.989967	P;P	0.41131	0.483;0.739	B;B	0.43082	0.084;0.407	T	0.06789	-1.0807	10	0.12430	T	0.62	-14.985	12.3052	0.54898	0.0:0.2553:0.7447:0.0	.	207;207	Q8NBR6;Q8NBR6-2	FA63B_HUMAN;.	D	207	ENSP00000393231:G207D	ENSP00000326194:G207D	G	+	2	0	FAM63B	56851506	0.985000	0.35326	0.961000	0.40146	0.496000	0.33645	0.082000	0.14847	2.024000	0.59613	0.543000	0.68304	GGC	.	.	none		0.622	FAM63B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416230.1	NM_019092		A	59064214	G	A	59064214	3	1	25	1	0	0	0	0	1	0	0	0	5605	1203	42	2	622	2	FAM63B	15	59064214	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	4225257	59064214	43467178	592	9501											
MYO1E	4643	hgsc.bcm.edu	37	chr15	59500970	59500970	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atctgaagtttctggagcagCgtctgatctgccccctcacc	7	11	9	14	1	5	2	1	2	4	0	5	3	5	3	3	1	3	2	3	1	1	1	rs117265950	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:59500970C>T	ENST00000288235.4	-	14	1839	c.1440G>A	c.(1438-1440)acG>acA	p.T480T		NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	480	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)		TCTGGAGCAGCGTCTGATCTG	0.532													c|||	47	0.00938498	0.0015	0.0086	5008	,	,		19011	0.0		0.0149	False		,,,				2504	0.0245				p.T480T		Atlas-SNP	.											.	MYO1E	99	.	0			c.G1440A						PASS	.	T		10,4372	16.8+/-37.8	0,10,2181	176	148	157		1440	-10.7	0.2	15	dbSNP_132	157	116,8464	61.0+/-122.8	2,112,4176	no	coding-synonymous	MYO1E	NM_004998.2		2,122,6357	TT,TC,CC		1.352,0.2282,0.9721		480/1109	59500970	126,12836	2191	4290	6481	SO:0001819	synonymous_variant	4643	exon14			GAGCAGCGTCTGA	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.1440G>A	15.37:g.59500970C>T		152	0	0		158	63	0.398734	NM_004998	Q14778	Silent	SNP	ENST00000288235.4	37	CCDS32254.1																																																																																			C|0.991;T|0.009	0.009	strong		0.532	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416024.1	NM_004998		T	59500970	C	T	59500970	2	4	25	1	0	0	0	0	0	0	0	1	10081	755	27	1		1	MYO1E	15	59500970	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	436756	59500970	43030422	593	9502											
HERC1	8925	hgsc.bcm.edu	37	chr15	63967170	63967170	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttggtgctctgtttgcccAtgtcttcatgaacgccagtg	5	15	11	10	1	3	1	1	1	2	0	3	1	3	1	2	1	3	3	2	1	1	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:63967170A>G	ENST00000443617.2	-	38	7304	c.7217T>C	c.(7216-7218)aTg>aCg	p.M2406T	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	2406					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						CTGTTTGCCCATGTCTTCATG	0.502																																					p.M2406T		Atlas-SNP	.											.	HERC1	624	.	0			c.T7217C						PASS	.						152	144	146					15																	63967170		2042	4201	6243	SO:0001583	missense	8925	exon38			TTGCCCATGTCTT	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.7217T>C	15.37:g.63967170A>G	ENSP00000390158:p.Met2406Thr	275	0	0		243	106	0.436214	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	37	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	A	7.518	0.656022	0.14580	.	.	ENSG00000103657	ENST00000443617	T	0.22743	1.94	5.51	4.39	0.52855	.	0.515835	0.20490	N	0.091313	T	0.09379	0.0231	N	0.08118	0	0.19575	N	0.999966	B	0.02656	0.0	B	0.01281	0.0	T	0.35699	-0.9778	10	0.13470	T	0.59	.	7.9035	0.29748	0.7169:0.0:0.2831:0.0	.	2406	Q15751	HERC1_HUMAN	T	2406	ENSP00000390158:M2406T	ENSP00000390158:M2406T	M	-	2	0	HERC1	61754223	0.091000	0.21658	1.000000	0.80357	0.964000	0.63967	0.681000	0.25320	0.931000	0.37242	0.528000	0.53228	ATG	.	.	none		0.502	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922		G	63967170	A	G	63967170	3	3	25	1	0	0	0	0	1	0	0	0	7066	217	8	3	7532	3	HERC1	15	63967170	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	4466200	63967170	38564222	594	9503											
RPL4	6124	hgsc.bcm.edu	37	chr15	66791920	66791920	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggcttcttgcctgcaaccGccgccttctcatctgatttg	5	13	8	15	2	3	1	1	1	3	0	4	1	3	1	4	1	3	2	4	1	1	4			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:66791920G>A	ENST00000307961.6	-	10	1201	c.1109C>T	c.(1108-1110)gCg>gTg	p.A370V	MIR4512_ENST00000583257.1_RNA|SNAPC5_ENST00000566658.1_5'Flank|SNAPC5_ENST00000307979.7_5'Flank|SNAPC5_ENST00000395589.2_5'Flank|SNORD18C_ENST00000362704.1_RNA|SNORD18B_ENST00000365659.1_RNA|SNAPC5_ENST00000563480.2_5'Flank|SNAPC5_ENST00000316634.5_5'Flank|RPL4_ENST00000568588.1_Missense_Mutation_p.A276V	NM_000968.3	NP_000959.2	P36578	RL4_HUMAN	ribosomal protein L4	370	Lys-rich.				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						GCCTGCAACCGCCGCCTTCTC	0.512																																					p.A370V		Atlas-SNP	.											.	RPL4	29	.	0			c.C1109T						PASS	.						37	40	39					15																	66791920		2198	4295	6493	SO:0001583	missense	6124	exon10			GCAACCGCCGCCT	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.1109C>T	15.37:g.66791920G>A	ENSP00000311430:p.Ala370Val	122	0	0		89	33	0.370787	NM_000968	A8K502|P39029|Q4VBR0|Q969Z9	Missense_Mutation	SNP	ENST00000307961.6	37	CCDS10218.1	.	.	.	.	.	.	.	.	.	.	G	8.795	0.931551	0.18131	.	.	ENSG00000174444	ENST00000307961;ENST00000432669	.	.	.	5.76	-3.16	0.05217	.	.	.	.	.	T	0.13072	0.0317	N	0.08118	0	0.09310	N	1	B	0.17465	0.022	B	0.04013	0.001	T	0.22138	-1.0225	8	0.27082	T	0.32	.	0.968	0.01410	0.2269:0.1496:0.3465:0.2771	.	370	P36578	RL4_HUMAN	V	370	.	ENSP00000311430:A370V	A	-	2	0	RPL4	64578974	0.000000	0.05858	0.003000	0.11579	0.207000	0.24258	-0.538000	0.06120	-0.170000	0.10816	-0.785000	0.03343	GCG	.	.	none		0.512	RPL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256903.2	NM_000968		A	66791920	G	A	66791920	3	1	25	1	0	0	0	0	1	0	0	0	13610	1087	38	1	178	1	RPL4	15	66791920	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2824750	66791920	35739472	595	9504											
ITGA11	22801	hgsc.bcm.edu	37	chr15	68643659	68643659	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	atcaccttctccaggtctggGctgtcgtgggactccccatc	5	11	10	15	1	3	0	1	0	2	0	7	1	4	1	4	3	0	1	4	3	0	1	rs61729770	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:68643659G>A	ENST00000315757.7	-	8	917	c.831C>T	c.(829-831)agC>agT	p.S277S	ITGA11_ENST00000423218.2_Silent_p.S277S|ITGA11_ENST00000562826.1_5'UTR	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	277	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				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						CCAGGTCTGGGCTGTCGTGGG	0.567													G|||	13	0.00259585	0.0	0.0043	5008	,	,		20370	0.0		0.0099	False		,,,				2504	0.0				p.S277S		Atlas-SNP	.											.	ITGA11	110	.	0			c.C831T						PASS	.	G		9,4145		0,9,2068	122	130	127		831	4.5	1	15	dbSNP_129	127	78,8372		0,78,4147	no	coding-synonymous	ITGA11	NM_001004439.1		0,87,6215	AA,AG,GG		0.9231,0.2167,0.6903		277/1189	68643659	87,12517	2077	4225	6302	SO:0001819	synonymous_variant	22801	exon8			GTCTGGGCTGTCG	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.831C>T	15.37:g.68643659G>A		146	0	0		152	72	0.473684	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Silent	SNP	ENST00000315757.7	37	CCDS45291.1																																																																																			G|0.995;A|0.005	0.005	strong		0.567	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211		A	68643659	G	A	68643659	2	1	25	1	0	0	0	0	0	0	0	1	7883	1194	42	2		2	ITGA11	15	68643659	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1851739	68643659	33887733	596	9505											
TLE3	7090	hgsc.bcm.edu	37	chr15	70347482	70347482	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacctgtgtagacgtgcctcGtggggttgctgatggtcacg	5	11	15	10	3	1	2	1	1	0	1	2	2	1	2	2	3	2	3	2	3	1	2	rs200508723	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:70347482G>A	ENST00000558939.1	-	15	2870	c.1493C>T	c.(1492-1494)aCg>aTg	p.T498M	TLE3_ENST00000440567.3_Missense_Mutation_p.T488M|TLE3_ENST00000558379.1_Missense_Mutation_p.T493M|TLE3_ENST00000442299.2_Missense_Mutation_p.T490M|TLE3_ENST00000451782.2_Missense_Mutation_p.T495M|TLE3_ENST00000560589.1_Missense_Mutation_p.T442M|TLE3_ENST00000557997.1_Missense_Mutation_p.T490M|TLE3_ENST00000559929.1_Missense_Mutation_p.T508M|TLE3_ENST00000559191.1_Missense_Mutation_p.T79M|TLE3_ENST00000560939.1_Missense_Mutation_p.T500M|TLE3_ENST00000539550.1_Missense_Mutation_p.T425M|TLE3_ENST00000557907.1_Missense_Mutation_p.T490M|TLE3_ENST00000559048.1_Missense_Mutation_p.T498M|TLE3_ENST00000558201.1_Missense_Mutation_p.T504M|TLE3_ENST00000317509.8_Missense_Mutation_p.T486M	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	498				T -> S (in Ref. 1; AAA61194). {ECO:0000305}.	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						GACGTGCCTCGTGGGGTTGCT	0.657													G|||	2	0.000399361	0.0	0.0	5008	,	,		18004	0.0		0.002	False		,,,				2504	0.0				p.T498M		Atlas-SNP	.											.	TLE3	104	.	0			c.C1493T						PASS	.	G	MET/THR,MET/THR,MET/THR	4,4394	6.2+/-15.9	0,4,2195	66	70	69		1484,1493,1457	4.5	1	15		69	32,8564	22.2+/-67.0	0,32,4266	yes	missense,missense,missense	TLE3	NM_001105192.1,NM_005078.2,NM_020908.1	81,81,81	0,36,6461	AA,AG,GG		0.3723,0.091,0.2771	probably-damaging,probably-damaging,probably-damaging	495/770,498/773,486/761	70347482	36,12958	2199	4298	6497	SO:0001583	missense	7090	exon15			TGCCTCGTGGGGT	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.1493C>T	15.37:g.70347482G>A	ENSP00000452871:p.Thr498Met	94	0	0		109	56	0.513761	NM_005078	B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Missense_Mutation	SNP	ENST00000558939.1	37	CCDS45293.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.436998	0.83885	9.1E-4	0.003723	ENSG00000140332	ENST00000442299;ENST00000451782;ENST00000317509;ENST00000440567;ENST00000539550;ENST00000542329	T;T;T;T	0.11604	2.76;2.76;2.76;2.76	4.54	4.54	0.55810	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	0.33673	0.0871	M	0.76170	2.325	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	0.80764	0.978;0.987;0.935;0.987;0.989;0.994;0.985;0.965	T	0.12372	-1.0550	10	0.87932	D	0	-9.2287	16.2284	0.82315	0.0:0.0:1.0:0.0	.	488;495;490;493;486;498;498;425	F8W964;E9PD64;Q04726-3;Q6PI57;Q04726-2;Q04726;Q04726-4;F5H7D6	.;.;.;.;.;TLE3_HUMAN;.;.	M	490;495;498;488;425;165	ENSP00000390007:T490M;ENSP00000394717:T495M;ENSP00000415057:T488M;ENSP00000442594:T425M	ENSP00000319233:T498M	T	-	2	0	TLE3	68134536	1.000000	0.71417	0.968000	0.41197	0.975000	0.68041	9.530000	0.98051	2.352000	0.79861	0.462000	0.41574	ACG	G|0.999;A|0.001	0.001	weak		0.657	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416913.1	NM_005078		A	70347482	G	A	70347482	3	1	25	1	0	0	0	0	1	0	0	0	15955	1145	40	1	849	1	TLE3	15	70347482	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1703823	70347482	32183910	597	9506											
CD276	80381	hgsc.bcm.edu	37	chr15	73995247	73995247	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggcaggatgggcagggtgtgCccctgactggcaacgtgacc	7	6	17	11	1	0	2	0	2	0	0	0	3	0	3	3	5	2	3	3	5	1	0	rs142744437	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:73995247C>T	ENST00000318443.5	+	4	855	c.553C>T	c.(553-555)Ccc>Tcc	p.P185S	CD276_ENST00000318424.5_Intron|CD276_ENST00000537340.2_Missense_Mutation_p.P39S|CD276_ENST00000564751.1_Intron|CD276_ENST00000561213.1_Missense_Mutation_p.P185S	NM_001024736.1	NP_001019907.1	Q5ZPR3	CD276_HUMAN	CD276 molecule	185	Ig-like C2-type 1.				cell proliferation (GO:0008283)|immune response (GO:0006955)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of bone mineralization (GO:0030501)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			endometrium(3)|lung(5)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	13						GCAGGGTGTGCCCCTGACTGG	0.622													C|||	3	0.000599042	0.0	0.0	5008	,	,		19371	0.0		0.003	False		,,,				2504	0.0				p.P185S		Atlas-SNP	.											.	CD276	29	.	0			c.C553T						PASS	.	C	SER/PRO,	1,4395	2.1+/-5.4	0,1,2197	89	76	80		553,	-0.7	0	15	dbSNP_134	80	13,8577	9.1+/-34.3	0,13,4282	no	missense,intron	CD276	NM_001024736.1,NM_025240.2	74,	0,14,6479	TT,TC,CC		0.1513,0.0227,0.1078	possibly-damaging,	185/535,	73995247	14,12972	2198	4295	6493	SO:0001583	missense	80381	exon4			GGTGTGCCCCTGA	AF302102	CCDS10251.1, CCDS32288.1	15q23-q24	2013-01-11	2006-03-28		ENSG00000103855	ENSG00000103855		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing"	19137	protein-coding gene	gene with protein product		605715	"CD276 antigen"			11224528, 12055244	Standard	XM_005254699		Approved	B7-H3, B7H3, B7RP-2	uc002avv.1	Q5ZPR3	OTTHUMG00000137585	ENST00000318443.5:c.553C>T	15.37:g.73995247C>T	ENSP00000320084:p.Pro185Ser	204	0	0		228	120	0.526316	NM_001024736	Q6P5Y4|Q6UXI2|Q8NBI8|Q8NC34|Q8NCB6|Q9BXR1	Missense_Mutation	SNP	ENST00000318443.5	37	CCDS32288.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	0.107	-1.143273	0.01728	2.27E-4	0.001513	ENSG00000103855	ENST00000318443;ENST00000379823;ENST00000537340	T;T	0.76448	-1.02;-1.02	3.14	-0.671	0.11381	Immunoglobulin subtype 2 (1);CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.55561	0.1928	N	0.12502	0.225	0.09310	N	0.999994	B;B;B	0.16396	0.017;0.017;0.013	B;B;B	0.20184	0.028;0.028;0.017	T	0.39482	-0.9612	9	0.21540	T	0.41	.	6.3988	0.21626	0.3327:0.2617:0.4056:0.0	.	131;185;185	B4DK26;Q5ZPR3;Q5ZPR3-4	.;CD276_HUMAN;.	S	185;185;39	ENSP00000320084:P185S;ENSP00000441087:P39S	ENSP00000320084:P185S	P	+	1	0	CD276	71782300	0.021000	0.18746	0.011000	0.14972	0.203000	0.24098	1.959000	0.40412	0.103000	0.17682	0.313000	0.20887	CCC	C|0.999;T|0.001	0.001	strong		0.622	CD276-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268979.1	NM_025240		T	73995247	C	T	73995247	3	4	25	1	0	0	0	0	1	0	0	0	2994	739	26	2	563	2	CD276	15	73995247	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	3647765	73995247	28536145	598	9507											
NEIL1	79661	hgsc.bcm.edu	37	chr15	75641682	75641682	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggagtaccagcagttcaggTagggccagcaccaggtgtga	11	6	15	9	0	1	1	1	1	0	0	1	2	1	2	3	4	3	5	3	4	2	3	rs5745908	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:75641682T>C	ENST00000564784.1	+	3	1063		c.e3+2		NEIL1_ENST00000355059.4_Splice_Site|NEIL1_ENST00000569035.1_Splice_Site|NEIL1_ENST00000567959.1_Intron			Q96FI4	NEIL1_HUMAN	nei endonuclease VIII-like 1 (E. coli)						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						GCAGTTCAGGTAGGGCCAGCA	0.632								Base excision repair (BER), DNA glycosylases					T|||	14	0.00279553	0.0	0.0072	5008	,	,		14728	0.0		0.008	False		,,,				2504	0.001				.		Atlas-SNP	.											.	NEIL1	36	.	0			c.434+2T>C						PASS	.	T		7,4251		0,7,2122	18	20	20			5.4	1	15	dbSNP_114	20	105,8207		1,103,4052	yes	splice-5	NEIL1	NM_024608.2		1,110,6174	CC,CT,TT		1.2632,0.1644,0.891			75641682	112,12458	2129	4156	6285	SO:0001630	splice_region_variant	79661	exon2			TTCAGGTAGGGCC	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.434+2T>C	15.37:g.75641682T>C		23	0	0		31	15	0.483871	NM_024608	D3DW75|Q6ZRA7|Q86XW7|Q9H6C3	Splice_Site	SNP	ENST00000564784.1	37	CCDS10278.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	T	20.9	4.072179	0.76415	0.001644	0.012632	ENSG00000140398	ENST00000355059;ENST00000336572	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5906	0.68362	0.0:0.0:0.0:1.0	rs5745908;rs5745908	.	.	.	.	-1	.	.	.	+	.	.	NEIL1	73428735	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	7.327000	0.79147	2.042000	0.60477	0.459000	0.35465	.	T|0.993;C|0.007	0.007	strong		0.632	NEIL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419885.1	NM_024608	Intron	C	75641682	T	C	75641682	5	2	25	1	0	0	0	0	0	0	1	0	10327	1652	57	3	438	3	NEIL1	15	75641682	Splice_Site	SNP	T	TCGA-G8-6906-01A-11D-2210-10	1646435	75641682	26889710	599	9508											
CSPG4	1464	hgsc.bcm.edu	37	chr15	75980159	75980159	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctcttcctgaggtcctcctGggtgaagcggtagatgggcc	5	10	14	12	1	1	3	0	2	1	1	4	3	4	3	5	4	1	1	5	4	2	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:75980159G>T	ENST00000308508.5	-	3	3339	c.3247C>A	c.(3247-3249)Cag>Aag	p.Q1083K		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	1083	Gly/Ser-rich (glycosaminoglycan attachment domain).|Interaction with COL5A1. {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						AGGTCCTCCTGGGTGAAGCGG	0.637																																					p.Q1083K		Atlas-SNP	.											.	CSPG4	175	.	0			c.C3247A						PASS	.						67	64	65					15																	75980159		2197	4292	6489	SO:0001583	missense	1464	exon3			CCTCCTGGGTGAA	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.3247C>A	15.37:g.75980159G>T	ENSP00000312506:p.Gln1083Lys	123	0	0		184	92	0.5	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	25.0	4.590308	0.86851	.	.	ENSG00000173546	ENST00000308508	T	0.52754	0.65	5.07	5.07	0.68467	.	0.000000	0.64402	D	0.000006	T	0.69815	0.3153	M	0.78456	2.415	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	T	0.72246	-0.4349	10	0.49607	T	0.09	.	17.4549	0.87604	0.0:0.0:1.0:0.0	.	1083	Q6UVK1	CSPG4_HUMAN	K	1083	ENSP00000312506:Q1083K	ENSP00000312506:Q1083K	Q	-	1	0	CSPG4	73767214	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	9.869000	0.99810	2.356000	0.79943	0.555000	0.69702	CAG	.	.	none		0.637	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		T	75980159	G	T	75980159	3	4	25	1	0	0	0	0	1	0	0	0	3962	1357	47	4	3753	4	CSPG4	15	75980159	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	338477	75980159	26551233	600	9509											
CIB2	10518	hgsc.bcm.edu	37	chr15	78398139	78398139	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcagcaaagcccagcttgcCgtcaccgtccaagtcagcct	9	7	9	16	2	3	0	3	0	0	0	4	0	4	0	5	0	5	2	5	0	2	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:78398139C>T	ENST00000258930.3	-	5	812	c.484G>A	c.(484-486)Ggc>Agc	p.G162S	CIB2_ENST00000539011.1_Missense_Mutation_p.G119S|CIB2_ENST00000557846.1_Missense_Mutation_p.G113S|CIB2_ENST00000560618.1_Missense_Mutation_p.G119S	NM_006383.2	NP_006374.1	O75838	CIB2_HUMAN	calcium and integrin binding family member 2	162	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				calcium ion homeostasis (GO:0055074)|photoreceptor cell maintenance (GO:0045494)	blood microparticle (GO:0072562)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|photoreceptor inner segment (GO:0001917)|sarcolemma (GO:0042383)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	11						CCCAGCTTGCCGTCACCGTCC	0.617																																					p.G162S		Atlas-SNP	.											.	CIB2	24	.	0			c.G484A						PASS	.						183	150	161					15																	78398139		2196	4293	6489	SO:0001583	missense	10518	exon5			GCTTGCCGTCACC	BC047381	CCDS10296.1, CCDS61722.1, CCDS61723.1	15q24	2013-01-10			ENSG00000136425	ENSG00000136425		"EF-hand domain containing"	24579	protein-coding gene	gene with protein product		605564	"deafness, autosomal recessive 48", "Usher syndrome 1J (autosomal recessive)"	DFNB48, USH1J		9931475, 23023331	Standard	NM_006383		Approved	KIP2	uc002bdb.2	O75838	OTTHUMG00000143731	ENST00000258930.3:c.484G>A	15.37:g.78398139C>T	ENSP00000258930:p.Gly162Ser	66	0	0		63	27	0.428571	NM_006383	B4DDF0|H0YM71|Q05BT6	Missense_Mutation	SNP	ENST00000258930.3	37	CCDS10296.1	.	.	.	.	.	.	.	.	.	.	C	17.71	3.457318	0.63401	.	.	ENSG00000136425	ENST00000258930;ENST00000539011	D;D	0.83591	-1.74;-1.74	5.59	5.59	0.84812	EF-hand-like domain (1);	0.239373	0.43110	D	0.000604	D	0.90556	0.7040	M	0.90977	3.165	0.53688	D	0.999973	D;P	0.65815	0.995;0.657	P;B	0.51516	0.672;0.147	D	0.92297	0.5846	10	0.62326	D	0.03	-22.6145	18.5768	0.91158	0.0:1.0:0.0:0.0	.	162;162	B4DDF0;O75838	.;CIB2_HUMAN	S	162;119	ENSP00000258930:G162S;ENSP00000442459:G119S	ENSP00000258930:G162S	G	-	1	0	CIB2	76185194	0.992000	0.36948	0.956000	0.39512	0.792000	0.44763	2.522000	0.45572	2.641000	0.89580	0.591000	0.81541	GGC	.	.	none		0.617	CIB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289798.1	NM_006383		T	78398139	C	T	78398139	3	4	25	1	0	0	0	0	1	0	0	0	3423	652	23	1	87	1	CIB2	15	78398139	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2417980	78398139	24133253	601	9510											
ADAMTS7	11173	hgsc.bcm.edu	37	chr15	79065483	79065483	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcaggtggagccgttgccGtggcacacaccacagcggtc	7	6	15	13	3	0	0	0	0	0	0	1	1	0	1	3	5	3	3	3	5	0	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:79065483G>A	ENST00000388820.4	-	14	2283	c.2073C>T	c.(2071-2073)caC>caT	p.H691H	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	691	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						AGCCGTTGCCGTGGCACACAC	0.652																																					p.H691H		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.C2073T						PASS	.						10	10	10					15																	79065483		2113	4023	6136	SO:0001819	synonymous_variant	11173	exon14			GTTGCCGTGGCAC	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.2073C>T	15.37:g.79065483G>A		610	0	0		709	69	0.0973202	NM_014272	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	37	CCDS32303.1																																																																																			.	.	none		0.652	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272		A	79065483	G	A	79065483	2	1	25	1	0	0	0	0	0	0	0	1	271	1136	40	1		1	ADAMTS7	15	79065483	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	667344	79065483	23465909	602	9511											
MESDC1	59274	hgsc.bcm.edu	37	chr15	81294774	81294774	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gctgacctgctgctgctgtcGagcgaggcgcggcccgtgct	3	8	16	14	5	0	1	0	1	0	0	1	3	0	1	2	2	5	5	2	2	0	0	rs11541231	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:81294774G>C	ENST00000267984.2	+	1	1480	c.162G>C	c.(160-162)tcG>tcC	p.S54S		NM_022566.2	NP_072088.1	Q9H1K6	MESD1_HUMAN	mesoderm development candidate 1	54										endometrium(1)|lung(2)	3						TGCTGCTGTCGAGCGAGGCGC	0.701													G|||	137	0.0273562	0.003	0.0951	5008	,	,		9514	0.0		0.0457	False		,,,				2504	0.0215				p.S54S		Atlas-SNP	.											.	MESDC1	7	.	0			c.G162C						PASS	.	G		48,3752		2,44,1854	11	9	10		162	-8.7	0.9	15	dbSNP_120	10	281,7351		5,271,3540	no	coding-synonymous	MESDC1	NM_022566.2		7,315,5394	CC,CG,GG		3.6819,1.2632,2.8779		54/363	81294774	329,11103	1900	3816	5716	SO:0001819	synonymous_variant	59274	exon1			GCTGTCGAGCGAG	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.162G>C	15.37:g.81294774G>C		5	0	0		12	10	0.833333	NM_022566		Silent	SNP	ENST00000267984.2	37	CCDS10316.1																																																																																			G|0.972;C|0.028	0.028	strong		0.701	MESDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291390.1	NM_022566		C	81294774	G	C	81294774	2	2	25	1	0	0	0	0	0	0	0	1	9489	1045	37	4		4	MESDC1	15	81294774	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2229291	81294774	21236618	603	9512											
ADAMTSL3	57188	hgsc.bcm.edu	37	chr15	84611805	84611805	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gtgccaggacagactgtcctCcacatttagctgtgggagac	9	9	12	11	0	0	2	0	0	0	2	2	4	2	3	3	2	2	1	3	2	1	2	rs61752778	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:84611805C>T	ENST00000286744.5	+	19	2685	c.2461C>T	c.(2461-2463)Cca>Tca	p.P821S	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.P821S	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	821	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)			AGACTGTCCTCCACATTTAGC	0.493													C|||	66	0.0131789	0.0008	0.0101	5008	,	,		21353	0.0		0.0288	False		,,,				2504	0.0297				p.P821S		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.C2461T						PASS	.	C	SER/PRO	11,4395	17.9+/-39.9	0,11,2192	66	58	60		2461	5.1	0.5	15	dbSNP_129	60	160,8440	75.7+/-138.4	1,158,4141	yes	missense	ADAMTSL3	NM_207517.2	74	1,169,6333	TT,TC,CC		1.8605,0.2497,1.3148	probably-damaging	821/1692	84611805	171,12835	2203	4300	6503	SO:0001583	missense	57188	exon19			TGTCCTCCACATT	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.2461C>T	15.37:g.84611805C>T	ENSP00000286744:p.Pro821Ser	91	0	0		65	33	0.507692	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	28	0.01282051282051282	0	0.0	4	0.011049723756906077	0	0.0	24	0.0316622691292876	C	14.08	2.428426	0.43122	0.002497	0.018605	ENSG00000156218	ENST00000286744	T	0.60797	0.16	5.08	5.08	0.68730	.	0.450530	0.16546	N	0.209689	T	0.47857	0.1468	L	0.53671	1.685	0.54753	D	0.999986	P;D	0.89917	0.754;1.0	P;D	0.85130	0.45;0.997	T	0.57242	-0.7845	10	0.11794	T	0.64	.	18.0594	0.89372	0.0:1.0:0.0:0.0	rs61752778	821;821	P82987-2;P82987	.;ATL3_HUMAN	S	821	ENSP00000286744:P821S	ENSP00000286744:P821S	P	+	1	0	ADAMTSL3	82402809	0.994000	0.37717	0.490000	0.27465	0.988000	0.76386	4.535000	0.60629	2.358000	0.79984	0.655000	0.94253	CCA	C|0.988;T|0.012	0.012	strong		0.493	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517		T	84611805	C	T	84611805	3	4	25	1	0	0	0	0	1	0	0	0	276	855	30	2	2531	2	ADAMTSL3	15	84611805	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	3317031	84611805	17919587	604	9513											
ALPK3	57538	hgsc.bcm.edu	37	chr15	85400564	85400564	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcctgagccaggaggtaccCacgatgccttctcttcctgg	6	9	12	14	1	1	1	0	1	1	0	3	3	2	2	5	4	3	1	5	4	1	3	rs114957070	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:85400564C>T	ENST00000258888.5	+	6	3368	c.3201C>T	c.(3199-3201)ccC>ccT	p.P1067P		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1067					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)			AGGAGGTACCCACGATGCCTT	0.647													C|||	9	0.00179712	0.0	0.0	5008	,	,		19517	0.0		0.0089	False		,,,				2504	0.0				p.P1067P		Atlas-SNP	.											.	ALPK3	289	.	0			c.C3201T						PASS	.	C		7,4399	12.9+/-30.5	0,7,2196	69	54	59		3201	0.4	0	15	dbSNP_132	59	53,8545	34.3+/-88.2	0,53,4246	no	coding-synonymous	ALPK3	NM_020778.4		0,60,6442	TT,TC,CC		0.6164,0.1589,0.4614		1067/1908	85400564	60,12944	2203	4299	6502	SO:0001819	synonymous_variant	57538	exon6			GGTACCCACGATG	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.3201C>T	15.37:g.85400564C>T		54	0	0		65	42	0.646154	NM_020778	Q9P2L6	Silent	SNP	ENST00000258888.5	37	CCDS10333.1																																																																																			C|0.996;T|0.004	0.004	strong		0.647	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778		T	85400564	C	T	85400564	2	4	25	1	0	0	0	0	0	0	0	1	546	581	21	2		2	ALPK3	15	85400564	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	788759	85400564	17130828	605	9514											
HAPLN3	145864	hgsc.bcm.edu	37	chr15	89422353	89422353	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcatcctgcagccagcccGcgttgcaccagtccaggccc	6	6	11	18	2	0	0	0	0	0	0	2	0	2	0	6	2	4	4	6	2	0	1	rs569695538	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:89422353G>A	ENST00000359595.3	-	4	855	c.641C>T	c.(640-642)gCg>gTg	p.A214V	HAPLN3_ENST00000562889.1_Missense_Mutation_p.A276V	NM_178232.2	NP_839946.1	Q96S86	HPLN3_HUMAN	hyaluronan and proteoglycan link protein 3	214	Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323, ECO:0000305}.				cell adhesion (GO:0007155)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	17	Lung NSC(78;0.0392)|all_lung(78;0.077)				Hyaluronan(DB08818)	CAGCCAGCCCGCGTTGCACCA	0.701											OREG0023445	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2	0.000399361	0.0	0.0	5008	,	,		15072	0.001		0.0	False		,,,				2504	0.001				p.A214V		Atlas-SNP	.											.	HAPLN3	43	.	0			c.C641T						PASS	.						29	33	32					15																	89422353		2199	4299	6498	SO:0001583	missense	145864	exon4			CAGCCCGCGTTGC	AY262759	CCDS10346.1	15q26.1	2013-01-11			ENSG00000140511	ENSG00000140511		"Immunoglobulin superfamily / V-set domain containing"	21446	protein-coding gene	gene with protein product			"extracellular link domain containing, 1"	EXLD1		12663660	Standard	NM_178232		Approved	HsT19883	uc002bnc.3	Q96S86	OTTHUMG00000148680	ENST00000359595.3:c.641C>T	15.37:g.89422353G>A	ENSP00000352606:p.Ala214Val	23	0	0	1267	54	26	0.481481	NM_178232	A8K7P0	Missense_Mutation	SNP	ENST00000359595.3	37	CCDS10346.1	.	.	.	.	.	.	.	.	.	.	G	14.09	2.432313	0.43122	.	.	ENSG00000140511	ENST00000359595	T	0.13778	2.56	4.36	3.44	0.39384	C-type lectin fold (1);Link (5);C-type lectin-like (1);	0.054620	0.64402	D	0.000001	T	0.33000	0.0848	M	0.79123	2.44	0.54753	D	0.999987	D;D	0.65815	0.995;0.995	P;P	0.62184	0.899;0.899	T	0.09530	-1.0670	10	0.72032	D	0.01	-15.2009	11.1418	0.48406	0.0927:0.0:0.9073:0.0	.	214;214	A8K7T8;Q96S86	.;HPLN3_HUMAN	V	214	ENSP00000352606:A214V	ENSP00000352606:A214V	A	-	2	0	HAPLN3	87223357	1.000000	0.71417	0.066000	0.19879	0.986000	0.74619	9.207000	0.95064	0.940000	0.37473	0.655000	0.94253	GCG	.	.	none		0.701	HAPLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309070.1	NM_178232		A	89422353	G	A	89422353	3	1	25	1	0	0	0	0	1	0	0	0	6965	1087	38	1	449	1	HAPLN3	15	89422353	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	4021789	89422353	13109039	606	9515											
FURIN	5045	hgsc.bcm.edu	37	chr15	91419548	91419548	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcggtccctgtcgcctcacCgcccgcggcacagccggctg	4	5	13	19	6	1	0	1	0	0	0	3	0	2	0	5	3	2	2	5	3	0	0	rs148110342	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:91419548C>T	ENST00000268171.3	+	3	520	c.241C>T	c.(241-243)Cgc>Tgc	p.R81C		NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	81					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)			GTCGCCTCACCGCCCGCGGCA	0.647													C|||	10	0.00199681	0.0	0.0101	5008	,	,		14336	0.0		0.002	False		,,,				2504	0.001				p.R81C		Atlas-SNP	.											FURIN,NS,carcinoma,-1,1	FURIN	85	1	0			c.C241T						PASS	.	C	CYS/ARG	1,4395	2.1+/-5.4	0,1,2197	62	69	66		241	3.7	1	15	dbSNP_134	66	29,8567	19.8+/-62.0	0,29,4269	yes	missense	FURIN	NM_002569.2	180	0,30,6466	TT,TC,CC		0.3374,0.0227,0.2309	probably-damaging	81/795	91419548	30,12962	2198	4298	6496	SO:0001583	missense	5045	exon3			CCTCACCGCCCGC	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.241C>T	15.37:g.91419548C>T	ENSP00000268171:p.Arg81Cys	78	0	0		83	37	0.445783	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Missense_Mutation	SNP	ENST00000268171.3	37	CCDS10364.1	4	0.0018315018315018315	0	0.0	4	0.011049723756906077	0	0.0	0	0.0	C	16.37	3.103601	0.56291	2.27E-4	0.003374	ENSG00000140564	ENST00000268171	T	0.32515	1.45	4.58	3.67	0.42095	Proteinase inhibitor, propeptide (1);	0.447962	0.23209	N	0.050699	T	0.35653	0.0939	M	0.85945	2.785	0.52501	D	0.999957	D	0.61080	0.989	P	0.48677	0.586	T	0.43750	-0.9372	10	0.39692	T	0.17	-17.545	11.108	0.48214	0.0:0.9142:0.0:0.0858	.	81	P09958	FURIN_HUMAN	C	81	ENSP00000268171:R81C	ENSP00000268171:R81C	R	+	1	0	FURIN	89220552	0.624000	0.27102	0.998000	0.56505	0.701000	0.40568	1.792000	0.38754	1.170000	0.42753	-0.266000	0.10368	CGC	C|0.998;T|0.002	0.002	strong		0.647	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569		T	91419548	C	T	91419548	3	4	25	1	0	0	0	0	1	0	0	0	6107	652	23	1	247	1	FURIN	15	91419548	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1997195	91419548	11111844	607	9516											
LRRC28	123355	hgsc.bcm.edu	37	chr15	99892589	99892589	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tccagatttaggtcgatctcGagaactacagtatgtatacg	12	12	9	8	3	1	2	0	0	1	2	4	4	2	2	1	1	3	2	1	1	6	6	rs139516247		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:99892589G>A	ENST00000301981.3	+	7	848	c.608G>A	c.(607-609)cGa>cAa	p.R203Q	LRRC28_ENST00000447360.2_Missense_Mutation_p.R203Q|LRRC28_ENST00000442993.2_3'UTR|LRRC28_ENST00000558879.1_Intron|LRRC28_ENST00000331450.5_Intron|LRRC28_ENST00000422500.2_Missense_Mutation_p.R134Q	NM_144598.2	NP_653199.2	Q86X40	LRC28_HUMAN	leucine rich repeat containing 28	203										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)			GGTCGATCTCGAGAACTACAG	0.353																																					p.R203Q		Atlas-SNP	.											LRRC28,NS,malignant_melanoma,+1,1	LRRC28	38	1	0			c.G608A						PASS	.	G	GLN/ARG	0,4394		0,0,2197	166	157	160		608	5.5	1	15	dbSNP_134	160	1,8593	1.2+/-3.3	0,1,4296	no	missense	LRRC28	NM_144598.2	43	0,1,6493	AA,AG,GG		0.0116,0.0,0.0077	benign	203/368	99892589	1,12987	2197	4297	6494	SO:0001583	missense	123355	exon7			GATCTCGAGAACT	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.608G>A	15.37:g.99892589G>A	ENSP00000304923:p.Arg203Gln	39	0	0		33	16	0.484848	NM_144598	A8KA22|Q6UY49|Q6ZSS6	Missense_Mutation	SNP	ENST00000301981.3	37	CCDS10380.1	.	.	.	.	.	.	.	.	.	.	G	17.23	3.336020	0.60853	0.0	1.16E-4	ENSG00000168904	ENST00000301981;ENST00000447360;ENST00000422500	T;T;T	0.31247	2.23;2.23;1.5	5.52	5.52	0.82312	.	0.131334	0.49916	D	0.000129	T	0.51856	0.1699	M	0.62723	1.935	0.80722	D	1	D;D;B	0.76494	0.999;0.999;0.046	D;D;B	0.77557	0.984;0.99;0.003	T	0.35500	-0.9786	10	0.15499	T	0.54	.	18.4386	0.90656	0.0:0.0:1.0:0.0	.	134;203;203	B4DHL3;Q86X40-2;Q86X40	.;.;LRC28_HUMAN	Q	203;203;134	ENSP00000304923:R203Q;ENSP00000404520:R203Q;ENSP00000398606:R134Q	ENSP00000304923:R203Q	R	+	2	0	LRRC28	97710112	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.864000	0.62990	2.597000	0.87782	0.655000	0.94253	CGA	G|1.000;A|0.000	0.000	weak		0.353	LRRC28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313546.1	NM_144598		A	99892589	G	A	99892589	3	1	25	1	0	0	0	0	1	0	0	0	8991	1058	37	1	630	1	LRRC28	15	99892589	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	8473041	99892589	2638803	608	9517											
ALDH1A3	220	hgsc.bcm.edu	37	chr15	101432798	101432798	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgtattagaaccctcagataCtttgcagggtgggcagacaa	12	10	11	8	0	1	3	1	0	0	3	1	3	1	3	1	2	3	3	1	2	5	4			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:101432798C>G	ENST00000329841.5	+	4	961	c.429C>G	c.(427-429)taC>taG	p.Y143*	ALDH1A3_ENST00000346623.6_Intron|RP11-66B24.4_ENST00000560351.1_RNA	NM_000693.2	NP_000684.2	P47895	AL1A3_HUMAN	aldehyde dehydrogenase 1 family, member A3	143					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)	CCCTCAGATACTTTGCAGGGT	0.478																																					p.Y143X		Atlas-SNP	.											.	ALDH1A3	61	.	0			c.C429G						PASS	.						131	131	131					15																	101432798		2203	4300	6503	SO:0001587	stop_gained	220	exon4			CAGATACTTTGCA	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.429C>G	15.37:g.101432798C>G	ENSP00000332256:p.Tyr143*	136	0	0		127	70	0.551181	NM_000693	Q6NT64	Nonsense_Mutation	SNP	ENST00000329841.5	37	CCDS10389.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.702411	0.88924	.	.	ENSG00000184254	ENST00000329841	.	.	.	5.52	2.11	0.27256	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.2979	0.43635	0.0:0.7892:0.0:0.2108	.	.	.	.	X	143	.	ENSP00000332256:Y143X	Y	+	3	2	ALDH1A3	99250321	0.827000	0.29292	0.998000	0.56505	0.980000	0.70556	-0.072000	0.11486	0.120000	0.18254	0.555000	0.69702	TAC	.	.	none		0.478	ALDH1A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313620.2			G	101432798	C	G	101432798	4	3	25	1	0	0	0	0	0	1	0	0	492	576	20	4	443	4	ALDH1A3	15	101432798	Nonsense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1540209	101432798	1098594	609	9518											
SSTR5	6755	hgsc.bcm.edu	37	chr16	1129441	1129441	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acctgcaacgccagctggccGgagcccgtggggctgtgggg	5	5	18	13	3	0	0	0	0	0	0	0	1	0	1	4	6	4	3	4	6	1	0	rs34608001	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1129441G>A	ENST00000293897.4	+	1	661	c.573G>A	c.(571-573)ccG>ccA	p.P191P	SSTR5_ENST00000562758.1_Silent_p.P191P|SSTR5_ENST00000397547.2_Silent_p.P191P|SSTR5-AS1_ENST00000569832.1_RNA	NM_001053.3	NP_001044.1	P35346	SSR5_HUMAN	somatostatin receptor 5	191					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)	CCAGCTGGCCGGAGCCCGTGG	0.687													G|||	59	0.0117812	0.0008	0.0231	5008	,	,		13403	0.0		0.0298	False		,,,				2504	0.0123				p.P191P		Atlas-SNP	.											.	SSTR5	36	.	0			c.G573A						PASS	.	G	,	19,4333		1,17,2158	23	27	26		573,573	-9.5	0.7	16	dbSNP_126	26	215,8347		2,211,4068	no	coding-synonymous,coding-synonymous	SSTR5	NM_001053.3,NM_001172560.1	,	3,228,6226	AA,AG,GG		2.5111,0.4366,1.812	,	191/365,191/365	1129441	234,12680	2176	4281	6457	SO:0001819	synonymous_variant	6755	exon2			CTGGCCGGAGCCC	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.573G>A	16.37:g.1129441G>A		33	0	0		70	37	0.528571	NM_001172560	P34988|Q541E0|Q9UJI5	Silent	SNP	ENST00000293897.4	37	CCDS10429.1																																																																																			G|0.983;A|0.017	0.017	strong		0.687	SSTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420836.1			A	1129441	G	A	1129441	2	1	25	1	0	0	0	0	0	0	0	1	15216	1103	39	1		1	SSTR5	16	1129441	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10		1129441	89225312	610	9519											
C1QTNF8	390664	hgsc.bcm.edu	37	chr16	1143605	1143605	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gtcgcgctggaacatgcgcaCccagacggcgtcgcccgccg	6	4	14	17	8	0	1	0	0	0	1	2	2	0	2	3	2	2	2	3	2	1	0	rs116934818	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1143605C>A	ENST00000328449.5	-	4	928	c.655G>T	c.(655-657)Gtg>Ttg	p.V219L		NM_207419.3	NP_997302.2	P60827	C1QT8_HUMAN	C1q and tumor necrosis factor related protein 8	219	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)				AACATGCGCACCCAGACGGCG	0.716													C|||	54	0.0107827	0.0008	0.0187	5008	,	,		8643	0.0		0.0298	False		,,,				2504	0.0102				p.V219L		Atlas-SNP	.											.	C1QTNF8	15	.	0			c.G655T						PASS	.	C	LEU/VAL	17,4307		1,15,2146	12	13	13		655	3.2	1	16	dbSNP_132	13	170,8368		1,168,4100	yes	missense	C1QTNF8	NM_207419.3	32	2,183,6246	AA,AC,CC		1.9911,0.3932,1.4539	possibly-damaging	219/253	1143605	187,12675	2162	4269	6431	SO:0001583	missense	390664	exon4			TGCGCACCCAGAC	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.655G>T	16.37:g.1143605C>A	ENSP00000330426:p.Val219Leu	13	0	0		36	15	0.416667	NM_207419	B7U178	Missense_Mutation	SNP	ENST00000328449.5	37	CCDS32358.1	32	0.014652014652014652	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	22	0.029023746701846966	C	12.81	2.050482	0.36181	0.003932	0.019911	ENSG00000184471	ENST00000328449	D	0.82711	-1.64	3.24	3.24	0.37175	Tumour necrosis factor-like (2);Complement C1q protein (3);	0.000000	0.46442	D	0.000298	T	0.53190	0.1781	L	0.52759	1.655	0.36281	D	0.855751	P	0.43231	0.801	P	0.45610	0.487	T	0.71265	-0.4644	10	0.02654	T	1	.	5.9986	0.19507	0.0:0.6915:0.1956:0.1129	.	219	P60827	C1QT8_HUMAN	L	219	ENSP00000330426:V219L	ENSP00000330426:V219L	V	-	1	0	C1QTNF8	1083606	1.000000	0.71417	0.979000	0.43373	0.865000	0.49528	1.250000	0.32850	1.654000	0.50703	0.557000	0.71058	GTG	C|0.987;A|0.013	0.013	strong		0.716	C1QTNF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396120.1	XM_372606		A	1143605	C	A	1143605	3	1	25	1	0	0	0	0	1	0	0	0	1971	507	18	4	107	4	C1QTNF8	16	1143605	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	14164	1143605	89211148	611	9520											
PKD1	5310	hgsc.bcm.edu	37	chr16	2161087	2161087	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctgttcacgcggctggacaGcaccagcgccagggggaacg	8	4	15	14	4	1	0	1	0	0	0	1	2	1	2	3	4	3	3	3	4	1	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:2161087G>C	ENST00000262304.4	-	15	4289	c.4081C>G	c.(4081-4083)Ctg>Gtg	p.L1361V	RP11-304L19.4_ENST00000568795.1_RNA|PKD1_ENST00000423118.1_Missense_Mutation_p.L1361V	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1361	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						CGGCTGGACAGCACCAGCGCC	0.652																																					p.L1361V		Atlas-SNP	.											.	PKD1	184	.	0			c.C4081G						PASS	.						35	37	37					16																	2161087		2193	4295	6488	SO:0001583	missense	5310	exon15			TGGACAGCACCAG	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.4081C>G	16.37:g.2161087G>C	ENSP00000262304:p.Leu1361Val	66	0	0		122	64	0.52459	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	.	.	.	.	.	.	.	.	.	.	g	4.600	0.111428	0.08831	.	.	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.45276	0.9;0.9	5.58	2.51	0.30379	PKD/Chitinase domain (1);Polycystin cation channel (1);PKD domain (4);	0.236328	0.35349	N	0.003270	T	0.37128	0.0992	L	0.59436	1.845	0.21915	N	0.999479	P;P	0.40638	0.702;0.725	B;P	0.47786	0.421;0.557	T	0.16719	-1.0393	10	0.09084	T	0.74	.	2.4934	0.04615	0.2134:0.125:0.5333:0.1283	.	1361;1361	P98161-3;P98161	.;PKD1_HUMAN	V	1361;1361;1042	ENSP00000262304:L1361V;ENSP00000399501:L1361V	ENSP00000262304:L1361V	L	-	1	2	PKD1	2101088	0.548000	0.26473	0.582000	0.28627	0.017000	0.09413	0.802000	0.27069	0.705000	0.31890	0.450000	0.29827	CTG	.	.	none		0.652	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			C	2161087	G	C	2161087	3	2	25	1	0	0	0	0	1	0	0	0	11972	962	34	4	8958	4	PKD1	16	2161087	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1017482	2161087	88193666	612	9521											
CLUAP1	23059	hgsc.bcm.edu	37	chr16	3554799	3554799	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtacacccaattttggactTgtatctgaagtgcttctctg	8	15	8	10	1	2	1	0	1	2	0	3	2	2	2	1	1	2	3	1	1	4	6	rs34672214	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3554799T>C	ENST00000576634.1	+	2	246	c.102T>C	c.(100-102)ctT>ctC	p.L34L	CLUAP1_ENST00000417763.2_5'UTR|CLUAP1_ENST00000341633.5_Silent_p.L34L|LA16c-306E5.3_ENST00000574423.2_RNA|CLUAP1_ENST00000571025.1_Silent_p.L34L	NM_015041.2	NP_055856.1	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1	34					cilium assembly (GO:0042384)	centrosome (GO:0005813)|cilium (GO:0005929)|intracellular membrane-bounded organelle (GO:0043231)|intraciliary transport particle B (GO:0030992)|nucleus (GO:0005634)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(2)	16						ATTTTGGACTTGTATCTGAAG	0.383													T|||	283	0.0565096	0.115	0.0331	5008	,	,		19316	0.0556		0.0159	False		,,,				2504	0.0368				p.L34L		Atlas-SNP	.											.	CLUAP1	32	.	0			c.T102C						PASS	.	T		427,3967	207.5+/-228.8	19,389,1789	111	109	110		102	3.1	1	16	dbSNP_126	110	138,8462	69.0+/-131.5	0,138,4162	no	coding-synonymous	CLUAP1	NM_015041.1		19,527,5951	CC,CT,TT		1.6047,9.7178,4.3482		34/414	3554799	565,12429	2197	4300	6497	SO:0001819	synonymous_variant	23059	exon2			TGGACTTGTATCT	BC017070	CCDS32381.1, CCDS45398.1	16p13.3	2014-07-18				ENSG00000103351		"Intraflagellar transport homologs"	19009	protein-coding gene	gene with protein product	"flagellar associated protein 22, qilin-like protein, homolog (Chlamydomonas)", "cilia and flagella associated protein 22"					15480429, 9734811, 19253336	Standard	NM_015041		Approved	FLJ13297, KIAA0643, FAP22, CFAP22	uc002cvk.2	Q96AJ1		ENST00000576634.1:c.102T>C	16.37:g.3554799T>C		218	0	0		203	91	0.448276	NM_015041	O75138|Q65ZA3|Q9H8R4|Q9H8T1	Silent	SNP	ENST00000576634.1	37	CCDS32381.1																																																																																			T|0.955;C|0.045	0.045	strong		0.383	CLUAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437883.2	NM_024793		C	3554799	T	C	3554799	2	2	25	1	0	0	0	0	0	0	0	1	3571	1799	63	3		3	CLUAP1	16	3554799	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	1393712	3554799	86799954	613	9522											
BTBD12	84464	hgsc.bcm.edu	37	chr16	3656645	3656645	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggtttggagggacttggcActgctgttgtcaaacaggaa	9	10	16	6	0	1	0	1	0	0	0	1	3	1	3	0	6	2	4	0	6	2	3	rs147826749	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3656645A>G	ENST00000294008.3	-	3	1230	c.590T>C	c.(589-591)gTg>gCg	p.V197A		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	197	Interaction with SLX4IP, ERCC4 and MSH2.		V -> A (in dbSNP:rs147826749). {ECO:0000269|PubMed:22911665}.		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						GGGACTTGGCACTGCTGTTGT	0.527								Direct reversal of damage					A|||	2	0.000399361	0.0	0.0029	5008	,	,		19478	0.0		0.0	False		,,,				2504	0.0				p.V197A		Atlas-SNP	.											.	SLX4	173	.	0			c.T590C						PASS	.	A	ALA/VAL	1,4393	2.1+/-5.4	0,1,2196	167	166	167		590	-3.5	0	16	dbSNP_134	167	26,8574	18.5+/-59.3	0,26,4274	yes	missense	SLX4	NM_032444.2	64	0,27,6470	GG,GA,AA		0.3023,0.0228,0.2078	benign	197/1835	3656645	27,12967	2197	4300	6497	SO:0001583	missense	84464	exon3			CTTGGCACTGCTG	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.590T>C	16.37:g.3656645A>G	ENSP00000294008:p.Val197Ala	197	0	0		186	90	0.483871	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	A	10.77	1.443209	0.25987	2.28E-4	0.003023	ENSG00000188827	ENST00000294008	T	0.01369	4.97	5.03	-3.52	0.04682	.	2.372270	0.01586	N	0.021329	T	0.00815	0.0027	N	0.17474	0.49	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.48068	-0.9067	10	0.18276	T	0.48	.	6.9022	0.24288	0.4116:0.1398:0.4486:0.0	.	197	Q8IY92	SLX4_HUMAN	A	197	ENSP00000294008:V197A	ENSP00000294008:V197A	V	-	2	0	SLX4	3596646	0.000000	0.05858	0.002000	0.10522	0.452000	0.32318	-0.831000	0.04405	-0.925000	0.03775	-0.441000	0.05720	GTG	A|0.997;G|0.003	0.003	strong		0.527	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444		G	3656645	A	G	3656645	3	3	25	1	0	0	0	0	1	0	0	0	1542	159	6	3	4966	3	BTBD12	16	3656645	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	101846	3656645	86698108	614	9523											
CREBBP	1387	hgsc.bcm.edu	37	chr16	3788618	3788618	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcatggtaaacggctgtgcGgaggcaacgtggccggaaga	10	6	16	9	4	1	1	1	0	0	1	1	3	1	3	1	6	3	3	1	6	4	1	rs398124146		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3788618G>A	ENST00000262367.5	-	26	5145	c.4336C>T	c.(4336-4338)Cgc>Tgc	p.R1446C	CREBBP_ENST00000382070.3_Missense_Mutation_p.R1408C	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1446	Acetyl-CoA binding. {ECO:0000250|UniProtKB:Q09472}.|CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.|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)	p.R1446C(6)|p.R1446G(1)		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)		ACGGCTGTGCGGAGGCAACGT	0.413			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.R1446C		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	CREBBP,rectum,carcinoma,0,21	CREBBP	546	21	7	Substitution - Missense(7)	haematopoietic_and_lymphoid_tissue(4)|urinary_tract(1)|lung(1)|central_nervous_system(1)	c.C4336T						PASS	.						75	68	71					16																	3788618		2197	4300	6497	SO:0001583	missense	1387	exon26			CTGTGCGGAGGCA	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.4336C>T	16.37:g.3788618G>A	ENSP00000262367:p.Arg1446Cys	54	0	0		53	22	0.415094	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	g	17.20	3.329498	0.60743	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.94330	-3.4;-3.4	5.28	4.29	0.51040	.	0.000000	0.64402	D	0.000004	D	0.97739	0.9258	H	0.96080	3.765	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98988	1.0807	10	0.87932	D	0	-29.6499	15.2916	0.73870	0.0:0.0:0.8588:0.1412	.	1476;1446	Q4LE28;Q92793	.;CBP_HUMAN	C	1446;1476;1408;35	ENSP00000262367:R1446C;ENSP00000371502:R1408C	ENSP00000262367:R1446C	R	-	1	0	CREBBP	3728619	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.937000	0.63513	1.303000	0.44873	0.561000	0.74099	CGC	.	.	none		0.413	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		A	3788618	G	A	3788618	3	1	25	1	0	0	0	0	1	0	0	0	3863	1116	39	1	3016	1	CREBBP	16	3788618	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	131973	3788618	86566135	615	9524											
GSPT1	2935	hgsc.bcm.edu	37	chr16	11969985	11969985	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caggtatgaatatgcagcacCgcattatagcctgggcagat	12	9	11	9	1	0	2	0	1	0	1	0	2	0	2	2	2	3	5	2	2	5	4	rs369462446		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:11969985C>T	ENST00000563468.1	-	11	1262	c.1236G>A	c.(1234-1236)gcG>gcA	p.A412A	GSPT1_ENST00000434724.2_Silent_p.A550A|GSPT1_ENST00000439887.2_Silent_p.A549A|RP11-166B2.8_ENST00000574364.1_RNA|GSPT1_ENST00000420576.2_Silent_p.A412A			P15170	ERF3A_HUMAN	G1 to S phase transition 1	412					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						TATGCAGCACCGCATTATAGC	0.333																																					p.A550A		Atlas-SNP	.											.	GSPT1	71	.	0			c.G1650A						PASS	.	C	,,	2,4392		0,2,2195	180	182	182		1647,1236,1650	3	1	16		182	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	GSPT1	NM_001130006.1,NM_001130007.1,NM_002094.3	,,	0,2,6495	TT,TC,CC		0.0,0.0455,0.0154	,,	549/637,412/500,550/638	11969985	2,12992	2197	4300	6497	SO:0001819	synonymous_variant	2935	exon13			CAGCACCGCATTA	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.1236G>A	16.37:g.11969985C>T		121	0	0		122	56	0.459016	NM_002094	J3KQG6|Q96GF2	Silent	SNP	ENST00000563468.1	37	CCDS45414.1																																																																																			.	.	weak		0.333	GSPT1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421513.1	NM_002094		T	11969985	C	T	11969985	2	4	25	1	0	0	0	0	0	0	0	1	6835	639	23	1		1	GSPT1	16	11969985	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	8181367	11969985	78384768	616	9525											
ABCC6	368	hgsc.bcm.edu	37	chr16	16263662	16263662	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaagagtgcgtagaggcagaGgggggtgcccacggcacgca	10	3	19	9	3	0	3	0	0	0	3	0	4	0	3	1	5	2	4	1	5	2	1	rs74315152|rs61340537	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:16263662G>T	ENST00000205557.7	-	22	2865	c.2836C>A	c.(2836-2838)Ctc>Atc	p.L946I		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	946			L -> I (in dbSNP:rs61340537). {ECO:0000269|PubMed:16086317, ECO:0000269|PubMed:19339160}.		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)	TAGAGGCAGAGGGGGGTGCCC	0.662													G|||	54	0.0107827	0.0008	0.0202	5008	,	,		16733	0.0		0.0219	False		,,,				2504	0.0174				p.L946I		Atlas-SNP	.											.	ABCC6	110	.	0			c.C2836A	GRCh37	CM034642	ABCC6	M	rs61340537	PASS	.	G	ILE/LEU	20,4332		0,20,2156	20	17	18	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2836	-1.1	0	16	dbSNP_129	18	131,8445		0,131,4157	yes	missense	ABCC6	NM_001171.5	5	0,151,6313	TT,TG,GG		1.5275,0.4596,1.168	benign	946/1504	16263662	151,12777	2176	4288	6464	SO:0001583	missense	368	exon22			GGCAGAGGGGGGT	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.2836C>A	16.37:g.16263662G>T	ENSP00000205557:p.Leu946Ile	113	0	0		100	41	0.41	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	CCDS10568.1	27	0.012362637362637362	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	19	0.025065963060686015	G	0.010	-1.770641	0.00645	0.004596	0.015275	ENSG00000091262	ENST00000205557	D	0.95103	-3.61	5.0	-1.06	0.10002	ABC transporter, transmembrane domain, type 1 (1);	1.097620	0.07160	N	0.850486	T	0.72946	0.3524	N	0.25957	0.775	0.31769	N	0.632287	B	0.26363	0.147	B	0.24541	0.054	T	0.74583	-0.3617	10	0.20046	T	0.44	.	3.4997	0.07668	0.0871:0.3098:0.3635:0.2396	rs61340537	946	O95255	MRP6_HUMAN	I	946	ENSP00000205557:L946I	ENSP00000205557:L946I	L	-	1	0	ABCC6	16171163	0.001000	0.12720	0.015000	0.15790	0.057000	0.15508	-0.218000	0.09240	0.121000	0.18284	-0.904000	0.02843	CTC	G|0.989;T|0.011	0.011	strong		0.662	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2			T	16263662	G	T	16263662	3	4	25	1	0	0	0	0	1	0	0	0	57	1000	35	4	1715	4	ABCC6	16	16263662	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	4293677	16263662	74091091	617	9526											
XYLT1	64131	hgsc.bcm.edu	37	chr16	17353090	17353090	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cgtggctgctgttggctgcgGctctgtccccgggaggcagc	2	9	17	13	3	1	0	0	0	1	0	2	1	2	1	2	5	3	6	2	5	0	1	rs113276942	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:17353090G>C	ENST00000261381.6	-	3	752	c.668C>G	c.(667-669)gCc>gGc	p.A223G		NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	223					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						GTTGGCTGCGGCTCTGTCCCC	0.592													G|||	265	0.0529153	0.1914	0.0173	5008	,	,		17039	0.0		0.0	False		,,,				2504	0.0				p.A223G		Atlas-SNP	.											XYLT1,NS,carcinoma,+1,1	XYLT1	147	1	0			c.C668G						PASS	.	G	GLY/ALA	697,3697	288.1+/-279.7	67,563,1567	106	117	113		668	4.5	0	16	dbSNP_132	113	19,8581	11.2+/-40.8	0,19,4281	yes	missense	XYLT1	NM_022166.3	60	67,582,5848	CC,CG,GG		0.2209,15.8625,5.5102	benign	223/960	17353090	716,12278	2197	4300	6497	SO:0001583	missense	64131	exon3			GCTGCGGCTCTGT	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.668C>G	16.37:g.17353090G>C	ENSP00000261381:p.Ala223Gly	169	0	0		144	78	0.541667	NM_022166	Q9H1B6	Missense_Mutation	SNP	ENST00000261381.6	37	CCDS10569.1	89	0.04075091575091575	81	0.16463414634146342	8	0.022099447513812154	0	0.0	0	0.0	G	9.870	1.198774	0.22121	0.158625	0.002209	ENSG00000103489	ENST00000261381	T	0.04809	3.55	5.43	4.47	0.54385	.	0.429861	0.27500	N	0.019098	T	0.00039	0.0001	L	0.44542	1.39	0.09310	N	1	B	0.32245	0.361	B	0.19148	0.024	T	0.49021	-0.8982	10	0.31617	T	0.26	-19.7884	11.4244	0.50001	0.1501:0.0:0.8499:0.0	.	223	Q86Y38	XYLT1_HUMAN	G	223	ENSP00000261381:A223G	ENSP00000261381:A223G	A	-	2	0	XYLT1	17260591	0.015000	0.18098	0.011000	0.14972	0.446000	0.32137	1.886000	0.39688	1.296000	0.44742	0.655000	0.94253	GCC	G|0.950;C|0.050	0.050	strong		0.592	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166		C	17353090	G	C	17353090	3	2	25	1	0	0	0	0	1	0	0	0	17478	1203	42	4	2251	4	XYLT1	16	17353090	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1089428	17353090	73001663	618	9527											
SMG1	23049	hgsc.bcm.edu	37	chr16	18882775	18882775	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acttcttcattaaaacagctGcttccaaagcccaagtcatt	13	12	4	12	0	3	0	2	0	1	0	4	0	4	0	2	0	4	2	2	0	4	5			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:18882775G>A	ENST00000446231.2	-	16	2625	c.2213C>T	c.(2212-2214)gCa>gTa	p.A738V	SMG1_ENST00000389467.3_Missense_Mutation_p.A738V|snoU13_ENST00000459248.1_RNA			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	738	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						TAAAACAGCTGCTTCCAAAGC	0.348																																					p.A738V		Atlas-SNP	.											.	SMG1	401	.	0			c.C2213T						PASS	.						59	54	55					16																	18882775		1816	4081	5897	SO:0001583	missense	23049	exon16			ACAGCTGCTTCCA	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.2213C>T	16.37:g.18882775G>A	ENSP00000402515:p.Ala738Val	282	0	0		295	118	0.4	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	37	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	A	10.24	1.295768	0.23564	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.64803	-0.12;-0.12	5.21	5.21	0.72293	Armadillo-type fold (1);	0.096968	0.41823	N	0.000802	T	0.27663	0.0680	N	0.00926	-1.1	0.24424	N	0.99461	B	0.02656	0.0	B	0.01281	0.0	T	0.23261	-1.0193	10	0.05436	T	0.98	.	11.34	0.49527	0.9281:0.0:0.0719:0.0	.	738	Q96Q15	SMG1_HUMAN	V	738	ENSP00000402515:A738V;ENSP00000374118:A738V	ENSP00000374118:A738V	A	-	2	0	SMG1	18790276	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.236000	0.78154	0.925000	0.37094	-0.381000	0.06696	GCA	.	.	none		0.348	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092		A	18882775	G	A	18882775	3	1	25	1	0	0	0	0	1	0	0	0	14810	1319	46	2	8964	2	SMG1	16	18882775	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1529685	18882775	71471978	619	9528											
USP31	57478	hgsc.bcm.edu	37	chr16	23079408	23079408	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccgtgcagaggtttgcatgcTagaagataacttttttgagg	10	13	12	6	1	0	4	0	1	0	3	0	4	0	4	1	2	4	4	1	2	3	6	rs114976439	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:23079408T>C	ENST00000219689.7	-	16	4017	c.4018A>G	c.(4018-4020)Agc>Ggc	p.S1340G	USP31_ENST00000567975.1_Missense_Mutation_p.S633G	NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	0					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)		GTTTGCATGCTAGAAGATAAC	0.448													T|||	4	0.000798722	0.0	0.0029	5008	,	,		19237	0.0		0.002	False		,,,				2504	0.0				p.S1340G		Atlas-SNP	.											.	USP31	122	.	0			c.A4018G						PASS	.	T	GLY/SER	2,4392	4.2+/-10.8	0,2,2195	66	70	69		4018	4.6	1	16	dbSNP_132	69	30,8570	19.8+/-62.0	0,30,4270	yes	missense	USP31	NM_020718.3	56	0,32,6465	CC,CT,TT		0.3488,0.0455,0.2463	possibly-damaging	1340/1353	23079408	32,12962	2197	4300	6497	SO:0001583	missense	57478	exon16			GCATGCTAGAAGA	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.4018A>G	16.37:g.23079408T>C	ENSP00000219689:p.Ser1340Gly	99	0	0		106	44	0.415094	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000219689.7	37	CCDS10607.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	T	17.73	3.460859	0.63513	4.55E-4	0.003488	ENSG00000103404	ENST00000219689	T	0.13420	2.59	5.68	4.6	0.57074	.	0.381647	0.25164	N	0.032643	T	0.15912	0.0383	L	0.60455	1.87	0.48135	D	0.999591	B;B	0.19583	0.012;0.037	B;B	0.19148	0.006;0.024	T	0.01966	-1.1238	10	0.72032	D	0.01	-9.5109	10.6397	0.45586	0.0:0.0746:0.0:0.9253	.	1340;633	Q70CQ4;B3KS48	UBP31_HUMAN;.	G	1340	ENSP00000219689:S1340G	ENSP00000219689:S1340G	S	-	1	0	USP31	22986909	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.848000	0.55903	0.989000	0.38761	0.533000	0.62120	AGC	T|0.997;C|0.003	0.003	strong		0.448	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718		C	23079408	T	C	23079408	3	2	25	1	0	0	0	0	1	0	0	0	17077	1522	53	3	44	3	USP31	16	23079408	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	4196633	23079408	67275345	620	9529											
PLK1	5347	hgsc.bcm.edu	37	chr16	23701313	23701313	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagctggccagccggctcCgctacgcccgcactatggtg	6	6	14	15	4	0	0	0	0	0	0	1	1	1	1	4	4	3	4	4	4	2	2	rs34359215		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:23701313C>T	ENST00000300093.4	+	10	1852	c.1741C>T	c.(1741-1743)Cgc>Tgc	p.R581C	CTD-2196E14.5_ENST00000566143.1_RNA	NM_005030.3	NP_005021.2	P53350	PLK1_HUMAN	polo-like kinase 1	581	POLO box 2. {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)		CAGCCGGCTCCGCTACGCCCG	0.652																																					p.R581C	Colon(12;240 564 27038 33155)	Atlas-SNP	.											.	PLK1	67	.	0			c.C1741T						PASS	.						64	59	61					16																	23701313		2197	4300	6497	SO:0001583	missense	5347	exon10			CGGCTCCGCTACG		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.1741C>T	16.37:g.23701313C>T	ENSP00000300093:p.Arg581Cys	51	0	0		50	18	0.36	NM_005030	Q15153|Q99746	Missense_Mutation	SNP	ENST00000300093.4	37	CCDS10616.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.832085	0.91036	.	.	ENSG00000166851	ENST00000300093;ENST00000425844	T	0.12672	2.66	5.13	5.13	0.70059	POLO box duplicated domain (2);	0.000000	0.85682	D	0.000000	T	0.42810	0.1219	M	0.87682	2.9	0.80722	D	1	D	0.89917	1.0	D	0.69654	0.965	T	0.50448	-0.8827	10	0.87932	D	0	-25.8067	16.0722	0.80943	0.0:1.0:0.0:0.0	rs34359215	581	P53350	PLK1_HUMAN	C	581;484	ENSP00000300093:R581C	ENSP00000300093:R581C	R	+	1	0	PLK1	23608814	1.000000	0.71417	0.994000	0.49952	0.978000	0.69477	5.740000	0.68629	2.372000	0.80975	0.555000	0.69702	CGC	.	.	weak		0.652	PLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214057.2	NM_005030		T	23701313	C	T	23701313	3	4	25	1	0	0	0	0	1	0	0	0	12103	652	23	1	1779	1	PLK1	16	23701313	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	621905	23701313	66653440	621	9530											
ZKSCAN2	342357	hgsc.bcm.edu	37	chr16	25255503	25255503	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctacagccccatacaatttGctcttccgatgacaggcttg	9	11	8	13	1	1	1	0	1	1	0	2	2	2	1	3	1	4	3	3	1	3	5	rs116889865		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:25255503G>C	ENST00000328086.7	-	6	2387	c.1584C>G	c.(1582-1584)agC>agG	p.S528R		NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	528					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)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	36				GBM - Glioblastoma multiforme(48;0.0378)		CATACAATTTGCTCTTCCGAT	0.507													G|||	1	0.000199681	0.0	0.0	5008	,	,		18493	0.0		0.001	False		,,,				2504	0.0				p.S528R		Atlas-SNP	.											.	ZKSCAN2	90	.	0			c.C1584G						PASS	.	G	ARG/SER	3,4391	6.2+/-15.9	0,3,2194	68	68	68		1584	4.5	1	16	dbSNP_133	68	7,8593	6.4+/-24.3	0,7,4293	yes	missense	ZKSCAN2	NM_001012981.4	110	0,10,6487	CC,CG,GG		0.0814,0.0683,0.077	probably-damaging	528/968	25255503	10,12984	2197	4300	6497	SO:0001583	missense	342357	exon6			CAATTTGCTCTTC	AK026852	CCDS32410.1	16p12.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000155592		"Zinc fingers, C2H2-type", "-", "-", "-"	25677	protein-coding gene	gene with protein product			"zinc finger protein 694"	ZNF694			Standard	NM_001012981		Approved	FLJ23199, ZSCAN34	uc002dod.4	Q63HK3		ENST00000328086.7:c.1584C>G	16.37:g.25255503G>C	ENSP00000331626:p.Ser528Arg	89	0	0		94	41	0.43617	NM_001012981	A1L3B4|Q6ZN77	Missense_Mutation	SNP	ENST00000328086.7	37	CCDS32410.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	18.80	3.700874	0.68501	6.83E-4	8.14E-4	ENSG00000155592	ENST00000328086;ENST00000536768	T	0.41400	1.0	5.48	4.53	0.55603	SANT domain, DNA binding (1);	0.000000	0.85682	D	0.000000	T	0.55689	0.1936	L	0.52011	1.625	0.37889	D	0.930635	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.998	T	0.60596	-0.7232	10	0.51188	T	0.08	-19.0721	10.586	0.45284	0.0889:0.0:0.9111:0.0	.	324;528	B4DYF0;Q63HK3	.;ZKSC2_HUMAN	R	528	ENSP00000331626:S528R	ENSP00000331626:S528R	S	-	3	2	ZKSCAN2	25163004	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.061000	0.30542	1.457000	0.47850	0.655000	0.94253	AGC	G|0.999;C|0.001	0.001	strong		0.507	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981		C	25255503	G	C	25255503	3	2	25	1	0	0	0	0	1	0	0	0	17702	1310	46	4	1327	4	ZKSCAN2	16	25255503	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1554190	25255503	65099250	622	9531											
DOC2A	8448	hgsc.bcm.edu	37	chr16	30017536	30017536	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggacagagccccggccgcagGgggcagctcactggtcaggg	7	3	18	13	2	2	1	2	0	0	1	2	2	2	2	3	6	2	3	3	6	0	0	rs202062683	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:30017536G>C	ENST00000350119.4	-	11	1364	c.1174C>G	c.(1174-1176)Cct>Gct	p.P392A	DOC2A_ENST00000564944.1_Missense_Mutation_p.P392A|DOC2A_ENST00000564979.1_Missense_Mutation_p.P392A	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	392	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						CCGGCCGCAGGGGGCAGCTCA	0.692													G|||	12	0.00239617	0.0023	0.0029	5008	,	,		15719	0.0		0.006	False		,,,				2504	0.001				p.P392A		Atlas-SNP	.											.	DOC2A	40	.	0			c.C1174G						PASS	.	G	ALA/PRO	3,4359		0,3,2178	9	9	9		1174	1.9	0.3	16		9	73,8487		0,73,4207	no	missense	DOC2A	NM_003586.2	27	0,76,6385	CC,CG,GG		0.8528,0.0688,0.5881	possibly-damaging	392/401	30017536	76,12846	2181	4280	6461	SO:0001583	missense	8448	exon11			CCGCAGGGGGCAG	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.1174C>G	16.37:g.30017536G>C	ENSP00000340017:p.Pro392Ala	72	0	0		90	50	0.555556	NM_003586	B4DEJ2|H3BNH6|Q6P4G4|Q7Z5G0|Q8IVX0	Missense_Mutation	SNP	ENST00000350119.4	37	CCDS10666.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.413386	0.00191	6.88E-4	0.008528	ENSG00000149927	ENST00000350119	T	0.61040	0.14	5.09	1.85	0.25348	.	0.263699	0.27048	N	0.021185	T	0.31765	0.0807	L	0.44542	1.39	0.25635	N	0.986269	P	0.35745	0.518	B	0.30316	0.114	T	0.34153	-0.9840	10	0.02654	T	1	.	12.9913	0.58620	0.0:0.4802:0.5198:0.0	.	392	Q14183	DOC2A_HUMAN	A	392	ENSP00000340017:P392A	ENSP00000340017:P392A	P	-	1	0	DOC2A	29925037	0.913000	0.31002	0.274000	0.24659	0.075000	0.17131	-0.678000	0.05209	0.214000	0.20742	0.491000	0.48974	CCT	.	.	weak		0.692	DOC2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255148.2	NM_003586		C	30017536	G	C	30017536	3	2	25	1	0	0	0	0	1	0	0	0	4685	1232	43	4	32	4	DOC2A	16	30017536	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	4762033	30017536	60337217	623	9532											
CD2BP2	10421	hgsc.bcm.edu	37	chr16	30364805	30364805	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctagggtctgacaccccaaaCccttcagacgcatagccaac	12	6	7	16	1	2	2	1	1	1	1	2	2	2	2	4	1	3	1	4	1	4	3	rs13330462	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:30364805C>T	ENST00000305596.3	-	5	867	c.692G>A	c.(691-693)gGt>gAt	p.G231D	CD2BP2_ENST00000569466.1_Missense_Mutation_p.G231D|RP11-347C12.10_ENST00000563252.1_lincRNA	NM_006110.2	NP_006101.1	O95400	CD2B2_HUMAN	CD2 (cytoplasmic tail) binding protein 2	231			G -> D (in dbSNP:rs13330462).		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						ACACCCCAAACCCTTCAGACG	0.632													c|||	517	0.103235	0.3359	0.0432	5008	,	,		16256	0.001		0.0119	False		,,,				2504	0.0307				p.G231D		Atlas-SNP	.											.	CD2BP2	30	.	0			c.G692A						PASS	.	C	ASP/GLY	1197,3197	418.5+/-338.3	163,871,1163	65	64	65		692	3.4	1	16	dbSNP_121	65	119,8481	61.7+/-123.6	1,117,4182	yes	missense	CD2BP2	NM_006110.2	94	164,988,5345	TT,TC,CC		1.3837,27.2417,10.1278	benign	231/342	30364805	1316,11678	2197	4300	6497	SO:0001583	missense	10421	exon5			CCCAAACCCTTCA	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.692G>A	16.37:g.30364805C>T	ENSP00000304903:p.Gly231Asp	57	0	0		56	30	0.535714	NM_006110	B2RDX2|Q9ULP2	Missense_Mutation	SNP	ENST00000305596.3	37	CCDS10675.1	184	0.08424908424908426	154	0.3130081300813008	20	0.055248618784530384	1	0.0017482517482517483	9	0.011873350923482849	c	10.63	1.405572	0.25378	0.272417	0.013837	ENSG00000169217	ENST00000305596	T	0.28666	1.6	5.51	3.4	0.38934	.	0.446171	0.27631	N	0.018511	T	0.00012	0.0000	L	0.27053	0.805	0.31159	P	0.704604	B	0.27559	0.181	B	0.18561	0.022	T	0.39961	-0.9588	9	0.13108	T	0.6	-0.0537	14.0925	0.65000	0.0:0.6336:0.3664:0.0	rs13330462;rs13330462	231	O95400	CD2B2_HUMAN	D	231	ENSP00000304903:G231D	ENSP00000304903:G231D	G	-	2	0	CD2BP2	30272306	0.332000	0.24722	0.977000	0.42913	0.887000	0.51463	0.830000	0.27462	1.314000	0.45095	0.643000	0.83706	GGT	C|0.892;T|0.108	0.108	strong		0.632	CD2BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255528.1	NM_006110		T	30364805	C	T	30364805	3	4	25	1	0	0	0	0	1	0	0	0	2997	507	18	2	345	2	CD2BP2	16	30364805	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	347269	30364805	59989948	624	9533											
RNF40	9810	hgsc.bcm.edu	37	chr16	30780861	30780861	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cgagccttgcagggcagcctCgggggtgtggagaaggagct	7	6	19	9	2	0	1	0	0	0	1	1	4	0	2	2	5	4	3	2	5	1	1	rs142343572	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:30780861C>T	ENST00000324685.6	+	17	2961	c.2526C>T	c.(2524-2526)ctC>ctT	p.L842L	RNF40_ENST00000567365.1_3'UTR|RNF40_ENST00000402121.3_Silent_p.L534L|RNF40_ENST00000357890.5_Silent_p.L742L|RNF40_ENST00000563683.1_Silent_p.L802L	NM_001207033.1|NM_014771.3	NP_001193962.1|NP_055586	O75150	BRE1B_HUMAN	ring finger protein 40, E3 ubiquitin protein ligase	842					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)			AGGGCAGCCTCGGGGGTGTGG	0.647													c|||	2	0.000399361	0.0	0.0014	5008	,	,		19891	0.0		0.001	False		,,,				2504	0.0				p.L842L		Atlas-SNP	.											.	RNF40	83	.	0			c.C2526T						PASS	.		,,	2,4392	4.2+/-10.8	0,2,2195	28	26	27		2526,2226,2526	-12.1	0	16	dbSNP_134	27	7,8591	4.3+/-15.6	0,7,4292	no	coding-synonymous,coding-synonymous,coding-synonymous	RNF40	NM_001207033.1,NM_001207034.1,NM_014771.3	,,	0,9,6487	TT,TC,CC		0.0814,0.0455,0.0693	,,	842/1001,742/902,842/1002	30780861	9,12983	2197	4299	6496	SO:0001819	synonymous_variant	9810	exon17			CAGCCTCGGGGGT	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.2526C>T	16.37:g.30780861C>T		71	0	0		58	25	0.431034	NM_014771	Q6AHZ6|Q6N005|Q7L3T6|Q8N615|Q96T18|Q9BSV9|Q9HC82	Silent	SNP	ENST00000324685.6	37	CCDS10691.1																																																																																			C|0.997;T|0.003	0.003	strong		0.647	RNF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255524.2	NM_014771		T	30780861	C	T	30780861	2	4	25	1	0	0	0	0	0	0	0	1	13508	871	31	1		1	RNF40	16	30780861	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	416056	30780861	59573892	625	9534											
PRSS53	339105	hgsc.bcm.edu	37	chr16	31095999	31095999	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctaggccccaggagggtcacGggcactgtctggagggagct	7	6	17	11	1	2	0	1	0	1	0	2	3	2	3	2	6	1	2	2	6	1	1	rs138417092	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:31095999G>A	ENST00000280606.6	-	9	1458	c.1305C>T	c.(1303-1305)ccC>ccT	p.P435P		NM_001039503.2	NP_001034592.1	Q2L4Q9	PRS53_HUMAN	protease, serine, 53	435	Peptidase S1 2. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			large_intestine(1)|lung(3)	4						GGAGGGTCACGGGCACTGTCT	0.667													G|||	43	0.00858626	0.0008	0.0187	5008	,	,		17066	0.0		0.0268	False		,,,				2504	0.002				p.P435P		Atlas-SNP	.											PRSS53,NS,haematopoietic_neoplasm,0,1	PRSS53	29	1	0			c.C1305T						scavenged	.	G		9,4091		0,9,2041	15	19	18		1305	0.3	1	16	dbSNP_134	18	95,8309		0,95,4107	no	coding-synonymous	PRSS53	NM_001039503.2		0,104,6148	AA,AG,GG		1.1304,0.2195,0.8317		435/554	31095999	104,12400	2050	4202	6252	SO:0001819	synonymous_variant	339105	exon9			GGTCACGGGCACT		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.1305C>T	16.37:g.31095999G>A		177	1	0.00564972		177	65	0.367232	NM_001039503		Silent	SNP	ENST00000280606.6	37	CCDS42153.1																																																																																			G|0.988;A|0.012	0.012	strong		0.667	PRSS53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108580.4	NM_001081268		A	31095999	G	A	31095999	2	1	25	1	0	0	0	0	0	0	0	1	12644	1103	39	1		1	PRSS53	16	31095999	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	315138	31095999	59258754	626	9535											
VKORC1	79001	hgsc.bcm.edu	37	chr16	31106015	31106015	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cccgtcaggcaaagagcgagCcgcacccagccagggctccc	9	2	12	18	3	1	1	1	0	0	1	2	2	2	1	5	2	3	3	5	2	1	0	rs55894764	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:31106015C>T	ENST00000394975.2	-	1	263	c.36G>A	c.(34-36)cgG>cgA	p.R12R	VKORC1_ENST00000394971.3_5'Flank|VKORC1_ENST00000498155.1_Intron|RP11-196G11.1_ENST00000529564.1_Silent_p.R12R|VKORC1_ENST00000354895.4_Silent_p.R12R|VKORC1_ENST00000319788.7_Silent_p.R12R|VKORC1_ENST00000300851.6_Silent_p.R12R	NM_024006.4	NP_076869.1	Q9BQB6	VKOR1_HUMAN	vitamin K epoxide reductase complex, subunit 1	12					blood coagulation (GO:0007596)|bone development (GO:0060348)|cellular protein metabolic process (GO:0044267)|drug metabolic process (GO:0017144)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)|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)			lung(3)|urinary_tract(1)	4					Acenocoumarol(DB01418)|Dicoumarol(DB00266)|Menadione(DB00170)|Phenindione(DB00498)|Phenprocoumon(DB00946)|Warfarin(DB00682)	AAAGAGCGAGCCGCACCCAGC	0.721													C|||	43	0.00858626	0.0008	0.0187	5008	,	,		13567	0.0		0.0268	False		,,,				2504	0.002				p.R12R		Atlas-SNP	.											.	VKORC1	9	.	0			c.G36A						PASS	.	C	,	12,4280		0,12,2134	13	13	13		36,36	2.5	1	16	dbSNP_129	13	92,8316		0,92,4112	no	coding-synonymous,coding-synonymous	VKORC1	NM_024006.4,NM_206824.1	,	0,104,6246	TT,TC,CC		1.0942,0.2796,0.8189	,	12/164,12/93	31106015	104,12596	2146	4204	6350	SO:0001819	synonymous_variant	79001	exon1			AGCGAGCCGCACC		CCDS10703.1, CCDS10704.1	16p11.2	2008-02-05	2004-07-23		ENSG00000167397	ENSG00000167397			23663	protein-coding gene	gene with protein product		608547	"vitamin K dependent clotting factors deficiency 2"	VKCFD2			Standard	NM_024006		Approved		uc002eas.3	Q9BQB6	OTTHUMG00000047408	ENST00000394975.2:c.36G>A	16.37:g.31106015C>T		18	0	0		47	27	0.574468	NM_024006	A6NIQ6|B2R4Z6|Q6UX90|Q7Z2R4	Silent	SNP	ENST00000394975.2	37	CCDS10703.1																																																																																			C|0.990;T|0.010	0.010	strong		0.721	VKORC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108582.1	NM_024006		T	31106015	C	T	31106015	2	4	25	1	0	0	0	0	0	0	0	1	17187	726	26	2		2	VKORC1	16	31106015	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	10016	31106015	59248738	627	9536											
ARMC5	79798	hgsc.bcm.edu	37	chr16	31471283	31471283	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgtacggaaggggcgtgccgGaccgaagtgcgcagactcgg	8	5	18	10	6	0	1	0	0	0	1	1	4	0	3	2	5	3	2	2	5	3	1	rs201280100	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:31471283G>A	ENST00000563544.1	+	2	984	c.438G>A	c.(436-438)cgG>cgA	p.R146R	ARMC5_ENST00000538189.1_Silent_p.R178R|RP11-452L6.5_ENST00000564629.1_RNA|ARMC5_ENST00000412665.2_5'UTR|ARMC5_ENST00000457010.2_Silent_p.R146R|ARMC5_ENST00000408912.3_Silent_p.R241R|ARMC5_ENST00000268314.4_Silent_p.R146R			Q96C12	ARMC5_HUMAN	armadillo repeat containing 5	146										central_nervous_system(1)|endometrium(4)|large_intestine(3)|liver(2)|lung(12)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						GGGCGTGCCGGACCGAAGTGC	0.602													G|||	19	0.00379393	0.0	0.0043	5008	,	,		14517	0.0		0.0159	False		,,,				2504	0.0				p.R146R		Atlas-SNP	.											.	ARMC5	94	.	0			c.G438A						PASS	.	G	,	8,4040		0,8,2016	52	55	54		438,438	2.5	1	16		54	80,8282		1,78,4102	no	coding-synonymous,coding-synonymous	ARMC5	NM_001105247.1,NM_024742.2	,	1,86,6118	AA,AG,GG		0.9567,0.1976,0.7091	,	146/936,146/726	31471283	88,12322	2024	4181	6205	SO:0001819	synonymous_variant	79798	exon1			GTGCCGGACCGAA	AY217348	CCDS42155.1, CCDS45472.1, CCDS73874.1	16p11	2013-02-14			ENSG00000140691	ENSG00000140691		"Armadillo repeat containing"	25781	protein-coding gene	gene with protein product		615549					Standard	NM_024742		Approved	FLJ13063	uc002ecc.3	Q96C12	OTTHUMG00000176618	ENST00000563544.1:c.438G>A	16.37:g.31471283G>A		24	0	0		21	12	0.571429	NM_024742	Q86WM9|Q9H7P8|Q9H925	Silent	SNP	ENST00000563544.1	37	CCDS45472.1																																																																																			G|0.993;A|0.007	0.007	strong		0.602	ARMC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432847.1	NM_024742		A	31471283	G	A	31471283	2	1	25	1	0	0	0	0	0	0	0	1	954	1161	41	2		2	ARMC5	16	31471283	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	365268	31471283	58883470	628	9537											
PHKB	5257	hgsc.bcm.edu	37	chr16	47533770	47533770	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atccaggacagcctatactgCgctgctggggcctgggcttt	6	10	13	12	1	0	0	0	0	0	0	1	1	1	1	3	4	4	3	3	4	2	3	rs139431568	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:47533770C>T	ENST00000323584.5	+	3	294	c.270C>T	c.(268-270)tgC>tgT	p.C90C	PHKB_ENST00000299167.8_Silent_p.C90C|PHKB_ENST00000567402.1_3'UTR|PHKB_ENST00000566044.1_Silent_p.C83C|PHKB_ENST00000455779.1_Silent_p.C83C	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	90					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.C90C(2)|p.C83C(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)				GCCTATACTGCGCTGCTGGGG	0.507													C|||	3	0.000599042	0.0	0.0014	5008	,	,		19579	0.0		0.002	False		,,,				2504	0.0				p.C90C		Atlas-SNP	.											PHKB_ENST00000323584,colon,carcinoma,0,3	PHKB	298	3	3	Substitution - coding silent(3)	large_intestine(3)	c.C270T						PASS	.	C	,	0,4402		0,0,2201	137	124	128		270,249	0.2	1	16	dbSNP_134	128	12,8588	8.4+/-32.0	0,12,4288	no	coding-synonymous,coding-synonymous	PHKB	NM_000293.2,NM_001031835.2	,	0,12,6489	TT,TC,CC		0.1395,0.0,0.0923	,	90/1094,83/1087	47533770	12,12990	2201	4300	6501	SO:0001819	synonymous_variant	5257	exon3			ATACTGCGCTGCT		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.270C>T	16.37:g.47533770C>T		163	0	0		135	55	0.407407	NM_000293	Q8N4T5	Silent	SNP	ENST00000323584.5	37	CCDS10729.1																																																																																			C|0.999;T|0.001	0.001	strong		0.507	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1			T	47533770	C	T	47533770	2	4	25	1	0	0	0	0	0	0	0	1	11854	776	27	1		1	PHKB	16	47533770	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	16062487	47533770	42820983	629	9538											
ABCC12	94160	hgsc.bcm.edu	37	chr16	48139232	48139232	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acacatggtcctgttgccctGgggcccacaggtcatctttg	6	11	11	13	0	2	0	1	0	1	0	3	0	3	0	3	4	1	1	3	4	0	2	rs151150316	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:48139232G>A	ENST00000311303.3	-	19	2836	c.2491C>T	c.(2491-2493)Cag>Tag	p.Q831*	ABCC12_ENST00000416054.1_3'UTR|ABCC12_ENST00000448542.1_Nonsense_Mutation_p.Q828*	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	831	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)				CTGTTGCCCTGGGGCCCACAG	0.517													G|||	3	0.000599042	0.0008	0.0	5008	,	,		20402	0.0		0.002	False		,,,				2504	0.0				p.Q831X		Atlas-SNP	.											.	ABCC12	190	.	0			c.C2491T						PASS	.	G	stop/GLN	5,4397	8.1+/-20.4	0,5,2196	61	49	53		2491	3.2	0	16	dbSNP_134	53	37,8563	22.8+/-68.1	0,37,4263	yes	stop-gained	ABCC12	NM_033226.2		0,42,6459	AA,AG,GG		0.4302,0.1136,0.323		831/1360	48139232	42,12960	2201	4300	6501	SO:0001587	stop_gained	94160	exon19			TGCCCTGGGGCCC	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.2491C>T	16.37:g.48139232G>A	ENSP00000311030:p.Gln831*	42	0	0		39	25	0.641026	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Nonsense_Mutation	SNP	ENST00000311303.3	37	CCDS10730.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	35	5.497679	0.96355	0.001136	0.004302	ENSG00000140798	ENST00000311303;ENST00000448542;ENST00000449939	.	.	.	5.21	3.23	0.37069	.	1.089020	0.06851	N	0.797314	.	.	.	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	9.3552	0.38161	0.1553:0.0:0.8447:0.0	.	.	.	.	X	831;828;749	.	ENSP00000311030:Q831X	Q	-	1	0	ABCC12	46696733	0.001000	0.12720	0.009000	0.14445	0.127000	0.20565	0.706000	0.25690	2.405000	0.81733	0.655000	0.94253	CAG	G|0.998;A|0.002	0.002	strong		0.517	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226		A	48139232	G	A	48139232	4	1	25	1	0	0	0	0	0	1	0	0	52	1357	47	2	1632	2	ABCC12	16	48139232	Nonsense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	605462	48139232	42215521	630	9539											
N4BP1	9683	hgsc.bcm.edu	37	chr16	48595110	48595110	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcagggtctgtgttacaaaTgtagttctggtttgaacccc	8	15	10	8	0	3	1	1	1	2	0	3	1	3	1	2	2	2	4	2	2	4	5	rs371090316		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:48595110T>C	ENST00000262384.3	-	2	1680	c.1444A>G	c.(1444-1446)Att>Gtt	p.I482V	RP11-44I10.3_ENST00000563994.1_RNA	NM_153029.3	NP_694574.3	O75113	N4BP1_HUMAN	NEDD4 binding protein 1	482					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)				GTGTTACAAATGTAGTTCTGG	0.413																																					p.I482V		Atlas-SNP	.											.	N4BP1	121	.	0			c.A1444G						PASS	.	T	VAL/ILE	1,3799		0,1,1899	139	141	141		1444	-12.2	0	16		141	0,8216		0,0,4108	no	missense	N4BP1	NM_153029.3	29	0,1,6007	CC,CT,TT		0.0,0.0263,0.0083	benign	482/897	48595110	1,12015	1900	4108	6008	SO:0001583	missense	9683	exon2			TACAAATGTAGTT	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.1444A>G	16.37:g.48595110T>C	ENSP00000262384:p.Ile482Val	145	0	0		118	64	0.542373	NM_153029	A7MD49|Q2YDX1	Missense_Mutation	SNP	ENST00000262384.3	37	CCDS45479.1	.	.	.	.	.	.	.	.	.	.	T	0.004	-2.369847	0.00209	2.63E-4	0.0	ENSG00000102921	ENST00000262384	T	0.39787	1.06	6.08	-12.2	0.00006	.	2.515080	0.01180	N	0.007078	T	0.17492	0.0420	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.10823	-1.0613	10	0.25751	T	0.34	5.5903	9.9679	0.41736	0.061:0.0984:0.1832:0.6574	.	482	O75113	N4BP1_HUMAN	V	482	ENSP00000262384:I482V	ENSP00000262384:I482V	I	-	1	0	N4BP1	47152611	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.256000	0.02869	-3.027000	0.00267	-1.021000	0.02439	ATT	.	.	weak		0.413	N4BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429920.1	NM_014664		C	48595110	T	C	48595110	3	2	25	1	0	0	0	0	1	0	0	0	10118	1464	51	3	1270	3	N4BP1	16	48595110	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	455878	48595110	41759643	631	9540											
SALL1	6299	hgsc.bcm.edu	37	chr16	51172786	51172786	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcagaactggggatgtggcaGaggaagacagaggcccagac	13	3	17	8	0	0	5	0	0	0	5	0	7	0	7	1	5	1	2	1	5	2	0			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:51172786G>A	ENST00000251020.4	-	2	3380	c.3347C>T	c.(3346-3348)tCt>tTt	p.S1116F	SALL1_ENST00000541611.1_Intron|SALL1_ENST00000440970.1_Missense_Mutation_p.S1019F|SALL1_ENST00000566102.1_Intron	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	1116					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)			GGATGTGGCAGAGGAAGACAG	0.567																																					p.S1116F	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.C3347T						PASS	.						91	76	81					16																	51172786		2198	4300	6498	SO:0001583	missense	6299	exon2			GTGGCAGAGGAAG	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.3347C>T	16.37:g.51172786G>A	ENSP00000251020:p.Ser1116Phe	119	0	0		114	46	0.403509	NM_002968	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	37	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.576037	0.86645	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.07800	3.16;3.17	5.42	5.42	0.78866	.	0.104526	0.64402	D	0.000003	T	0.07683	0.0193	N	0.14661	0.345	0.58432	D	0.999999	P	0.44478	0.836	B	0.40329	0.326	T	0.26430	-1.0103	10	0.59425	D	0.04	.	19.2277	0.93824	0.0:0.0:1.0:0.0	.	1116	Q9NSC2	SALL1_HUMAN	F	1116;1019;1080	ENSP00000251020:S1116F;ENSP00000407914:S1019F	ENSP00000251020:S1116F	S	-	2	0	SALL1	49730287	1.000000	0.71417	0.994000	0.49952	0.970000	0.65996	7.866000	0.87056	2.529000	0.85273	0.563000	0.77884	TCT	.	.	none		0.567	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		A	51172786	G	A	51172786	3	1	25	1	0	0	0	0	1	0	0	0	13825	942	33	2	635	2	SALL1	16	51172786	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2577676	51172786	39181967	632	9541											
KIFC3	3801	hgsc.bcm.edu	37	chr16	57794643	57794643	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	acccaaggtcctcacctgtaCcaccatgagggtcttgctgt	8	10	9	14	0	2	1	1	1	1	0	3	1	3	1	5	2	2	2	5	2	2	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:57794643C>T	ENST00000379655.4	-	16	2484	c.2227G>A	c.(2227-2229)Gta>Ata	p.V743I	KIFC3_ENST00000421376.2_Missense_Mutation_p.V604I|KIFC3_ENST00000562903.1_Missense_Mutation_p.V604I|KIFC3_ENST00000543930.1_Missense_Mutation_p.V601I|KIFC3_ENST00000445690.2_Missense_Mutation_p.V743I|KIFC3_ENST00000541240.1_Missense_Mutation_p.V765I|KIFC3_ENST00000539578.1_Missense_Mutation_p.V685I|KIFC3_ENST00000465878.2_Missense_Mutation_p.V604I|KIFC3_ENST00000540079.2_Missense_Mutation_p.V641I	NM_005550.3	NP_005541.3	Q9BVG8	KIFC3_HUMAN	kinesin family member C3	743	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)				CTCACCTGTACCACCATGAGG	0.622																																					p.V743I		Atlas-SNP	.											.	KIFC3	55	.	0			c.G2227A						PASS	.						49	52	51					16																	57794643		2198	4299	6497	SO:0001583	missense	3801	exon16			CCTGTACCACCAT	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.2227G>A	16.37:g.57794643C>T	ENSP00000368976:p.Val743Ile	87	0	0		87	4	0.045977	NM_001130100	A8K6S2|B7Z484|O75299|Q49A29|Q49AQ0|Q59G19|Q8IUT3|Q96HW6	Missense_Mutation	SNP	ENST00000379655.4	37	CCDS10789.2	.	.	.	.	.	.	.	.	.	.	C	17.13	3.311199	0.60414	.	.	ENSG00000140859	ENST00000379655;ENST00000445690;ENST00000421376;ENST00000541240;ENST00000540079;ENST00000543930;ENST00000539578	T;T;T;T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07;-1.07;-1.07;-1.07	4.99	4.99	0.66335	Kinesin, motor domain (3);	0.061337	0.64402	D	0.000004	D	0.83321	0.5229	M	0.69823	2.125	0.54753	D	0.999987	P;P;P;P;P;P	0.42692	0.571;0.747;0.787;0.554;0.571;0.52	B;B;P;B;B;B	0.52386	0.428;0.411;0.697;0.377;0.312;0.346	D	0.85208	0.1019	10	0.72032	D	0.01	.	13.0651	0.59028	0.0:0.8385:0.1614:0.0	.	765;685;601;641;743;604	B7Z484;F5H4I9;B7Z896;F5H3M2;Q9BVG8;A8K6S2	.;.;.;.;KIFC3_HUMAN;.	I	743;743;604;765;641;601;685	ENSP00000368976:V743I;ENSP00000401696:V743I;ENSP00000396399:V604I;ENSP00000442008:V765I;ENSP00000438805:V641I;ENSP00000444012:V601I;ENSP00000444884:V685I	ENSP00000368976:V743I	V	-	1	0	KIFC3	56352144	1.000000	0.71417	1.000000	0.80357	0.463000	0.32649	4.881000	0.63114	2.341000	0.79615	0.205000	0.17691	GTA	.	.	none		0.622	KIFC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257329.2	NM_005550		T	57794643	C	T	57794643	3	4	25	1	0	0	0	0	1	0	0	0	8323	507	18	2	299	2	KIFC3	16	57794643	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	6621857	57794643	32560110	633	9542											
CSNK2A2	1459	hgsc.bcm.edu	37	chr16	58201631	58201631	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtcccttgaagtaccttgaGgctacacgaacattgtactc	10	11	9	11	1	0	2	0	2	0	0	2	3	1	2	2	2	4	3	2	2	5	6	rs55748630	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:58201631G>A	ENST00000262506.3	-	7	765	c.582C>T	c.(580-582)gcC>gcT	p.A194A	CSNK2A2_ENST00000566813.1_5'UTR	NM_001896.2	NP_001887.1	P19784	CSK22_HUMAN	casein kinase 2, alpha prime polypeptide	194	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|mitotic cell cycle (GO:0000278)|mitotic spindle checkpoint (GO:0071174)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)	1						AGTACCTTGAGGCTACACGAA	0.438													G|||	4	0.000798722	0.0	0.0	5008	,	,		18027	0.001		0.003	False		,,,				2504	0.0				p.A194A	Melanoma(54;119 1219 18349 35700 39738)	Atlas-SNP	.											.	CSNK2A2	25	.	0			c.C582T						PASS	.	G		2,4394	4.2+/-10.8	0,2,2196	110	98	102		582	0.9	1	16	dbSNP_129	102	51,8549	32.8+/-85.7	0,51,4249	no	coding-synonymous	CSNK2A2	NM_001896.2		0,53,6445	AA,AG,GG		0.593,0.0455,0.4078		194/351	58201631	53,12943	2198	4300	6498	SO:0001819	synonymous_variant	1459	exon7			CCTTGAGGCTACA	M55268	CCDS10794.1	16q21	2013-01-17			ENSG00000070770	ENSG00000070770			2459	protein-coding gene	gene with protein product		115442				2174700, 1766873	Standard	NM_001896		Approved	CSNK2A1	uc002enc.3	P19784	OTTHUMG00000133488	ENST00000262506.3:c.582C>T	16.37:g.58201631G>A		88	0	0		89	43	0.483146	NM_001896		Silent	SNP	ENST00000262506.3	37	CCDS10794.1																																																																																			G|0.997;A|0.003	0.003	strong		0.438	CSNK2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257386.2	NM_001896		A	58201631	G	A	58201631	2	1	25	1	0	0	0	0	0	0	0	1	3960	987	35	2		2	CSNK2A2	16	58201631	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	406988	58201631	32153122	634	9543											
SETD6	79918	hgsc.bcm.edu	37	chr16	58550386	58550386	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtgggtgtccctgcaggccaGaggaggagcgccggtgcctg	5	6	19	11	2	0	1	0	0	0	1	1	3	1	3	4	5	3	1	4	5	0	0	rs147467868	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:58550386G>A	ENST00000219315.4	+	4	531	c.481G>A	c.(481-483)Gag>Aag	p.E161K	SETD6_ENST00000418480.1_3'UTR|SETD6_ENST00000310682.2_Missense_Mutation_p.E137K|SETD6_ENST00000394266.4_Intron			Q8TBK2	SETD6_HUMAN	SET domain containing 6	161	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				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						CTGCAGGCCAGAGGAGGAGCG	0.617													G|||	3	0.000599042	0.0	0.0014	5008	,	,		14632	0.0		0.002	False		,,,				2504	0.0				p.E161K		Atlas-SNP	.											.	SETD6	27	.	0			c.G481A						PASS	.	G	LYS/GLU,LYS/GLU	0,4396		0,0,2198	78	92	87		481,409	3.4	1	16	dbSNP_134	87	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	SETD6	NM_001160305.1,NM_024860.2	56,56	0,5,6493	AA,AG,GG		0.0581,0.0,0.0385	benign,benign	161/474,137/450	58550386	5,12991	2198	4300	6498	SO:0001583	missense	79918	exon4			AGGCCAGAGGAGG	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.481G>A	16.37:g.58550386G>A	ENSP00000219315:p.Glu161Lys	53	0	0		70	30	0.428571	NM_001160305	A8K380|B5ME38|Q9H787	Missense_Mutation	SNP	ENST00000219315.4	37	CCDS54013.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	15.38	2.815025	0.50527	0.0	5.81E-4	ENSG00000103037	ENST00000310682;ENST00000219315	T;T	0.15603	2.41;2.41	5.37	3.37	0.38596	SET domain (2);	0.113840	0.64402	D	0.000016	T	0.13628	0.0330	L	0.49455	1.56	0.49483	D	0.999793	B;B;B	0.30914	0.14;0.3;0.004	B;B;B	0.22152	0.018;0.038;0.006	T	0.06698	-1.0812	10	0.33940	T	0.23	-20.8516	8.6244	0.33881	0.0812:0.2933:0.6254:0.0	.	137;161;137	E9PC53;Q8TBK2;Q8TBK2-2	.;SETD6_HUMAN;.	K	137;161	ENSP00000310082:E137K;ENSP00000219315:E161K	ENSP00000219315:E161K	E	+	1	0	SETD6	57107887	0.999000	0.42202	0.956000	0.39512	0.884000	0.51177	2.924000	0.48876	1.215000	0.43411	0.313000	0.20887	GAG	G|0.999;A|0.001	0.001	strong		0.617	SETD6-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317274.2	NM_024860		A	58550386	G	A	58550386	3	1	25	1	0	0	0	0	1	0	0	0	14150	943	33	2	495	2	SETD6	16	58550386	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	348755	58550386	31804367	635	9544											
CDH8	1006	hgsc.bcm.edu	37	chr16	61935330	61935330	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtcccagctccatcacctgaTaggatatacttgattttttt	9	16	6	10	0	1	2	1	2	0	0	3	3	3	3	3	1	2	1	3	1	3	7	rs368241476		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:61935330T>C	ENST00000577390.1	-	3	1254	c.300A>G	c.(298-300)ctA>ctG	p.L100L	CDH8_ENST00000577730.1_Silent_p.L100L|CDH8_ENST00000584337.1_Silent_p.L100L|CDH8_ENST00000299345.6_Silent_p.L100L	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	100	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)|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)		CATCACCTGATAGGATATACT	0.388																																					p.L100L		Atlas-SNP	.											.	CDH8	273	.	0			c.A300G						PASS	.	T		0,4406		0,0,2203	93	89	90		300	-3	1	16		90	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CDH8	NM_001796.4		0,1,6502	CC,CT,TT		0.0116,0.0,0.0077		100/800	61935330	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1006	exon3			ACCTGATAGGATA	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.300A>G	16.37:g.61935330T>C		117	0	0		109	44	0.40367	NM_001796	B3KWC1|Q14DC6|Q9ULB2	Silent	SNP	ENST00000577390.1	37	CCDS10802.1																																																																																			.	.	weak		0.388	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		C	61935330	T	C	61935330	2	2	25	1	0	0	0	0	0	0	0	1	3118	1393	49	3		3	CDH8	16	61935330	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	3384944	61935330	28419423	636	9545											
C16orf70	80262	hgsc.bcm.edu	37	chr16	67166731	67166731	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccccaacagtgtacaactccGctgagcagctcttccatctc	9	9	6	17	1	2	1	0	1	2	0	5	1	4	1	4	0	5	4	4	0	3	2	rs34017457	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67166731G>A	ENST00000219139.3	+	6	555	c.367G>A	c.(367-369)Gct>Act	p.A123T	C16orf70_ENST00000569683.1_3'UTR|C16orf70_ENST00000569600.1_Missense_Mutation_p.A123T	NM_025187.3	NP_079463.2	Q9BSU1	CP070_HUMAN	chromosome 16 open reading frame 70	123										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)		GTACAACTCCGCTGAGCAGCT	0.483													G|||	14	0.00279553	0.0	0.0014	5008	,	,		23042	0.0		0.0119	False		,,,				2504	0.001				p.A123T		Atlas-SNP	.											.	C16orf70	38	.	0			c.G367A						PASS	.	G	THR/ALA	12,4388	17.9+/-39.9	0,12,2188	129	119	122		367	4.1	1	16	dbSNP_126	122	81,8519	47.6+/-106.9	1,79,4220	yes	missense	C16orf70	NM_025187.3	58	1,91,6408	AA,AG,GG		0.9419,0.2727,0.7154	possibly-damaging	123/423	67166731	93,12907	2200	4300	6500	SO:0001583	missense	80262	exon6			AACTCCGCTGAGC	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	ENST00000219139.3:c.367G>A	16.37:g.67166731G>A	ENSP00000219139:p.Ala123Thr	190	0	0		134	60	0.447761	NM_025187	Q9HA86	Missense_Mutation	SNP	ENST00000219139.3	37	CCDS10828.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	G	15.47	2.842233	0.51057	0.002727	0.009419	ENSG00000125149	ENST00000219139	.	.	.	6.05	4.08	0.47627	.	0.051952	0.85682	N	0.000000	T	0.42877	0.1222	L	0.52759	1.655	0.58432	D	0.999998	B;D	0.56521	0.295;0.976	B;P	0.49451	0.089;0.611	T	0.35201	-0.9798	9	0.17832	T	0.49	-11.1355	11.3429	0.49543	0.1492:0.0:0.8508:0.0	rs34017457	198;123	Q9BSU1-2;Q9BSU1	.;CP070_HUMAN	T	123	.	ENSP00000219139:A123T	A	+	1	0	C16orf70	65724232	1.000000	0.71417	0.963000	0.40424	0.990000	0.78478	6.526000	0.73799	0.871000	0.35750	-0.142000	0.14014	GCT	G|0.994;A|0.006	0.006	strong		0.483	C16orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268829.2	NM_025187		A	67166731	G	A	67166731	3	1	25	1	0	0	0	0	1	0	0	0	1831	1087	38	1	389	1	C16orf70	16	67166731	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	5231401	67166731	23188022	637	9546											
EXOC3L	283849	hgsc.bcm.edu	37	chr16	67222676	67222676	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gcctgcagttgcttgtgctgGgcaacccgctcccgtagggg	4	9	15	13	2	0	0	0	0	0	0	1	0	1	0	3	3	4	7	3	3	2	3	rs13334403	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67222676G>A	ENST00000314586.6	-	4	615	c.375C>T	c.(373-375)gcC>gcT	p.A125A	EXOC3L1_ENST00000562887.1_Intron	NM_178516.3	NP_848611.2	Q86VI1	EX3L1_HUMAN	exocyst complex component 3-like 1	125	Mediates interaction with EXOC2, EXOC4 and EXOC5. {ECO:0000250}.				exocytosis (GO:0006887)|peptide hormone secretion (GO:0030072)	exocyst (GO:0000145)|secretory granule (GO:0030141)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	21						GCTTGTGCTGGGCAACCCGCT	0.662													G|||	405	0.0808706	0.2519	0.0187	5008	,	,		17923	0.0109		0.0268	False		,,,				2504	0.0215				p.A125A		Atlas-SNP	.											LOC283849,NS,carcinoma,-1,2	EXOC3L1	52	2	0			c.C375T						PASS	.	G		890,3506	332.5+/-302.5	96,698,1404	44	46	45		375	-1.6	0.1	16	dbSNP_121	45	273,8327	102.3+/-163.5	8,257,4035	no	coding-synonymous	EXOC3L1	NM_178516.3		104,955,5439	AA,AG,GG		3.1744,20.2457,8.9489		125/747	67222676	1163,11833	2198	4300	6498	SO:0001819	synonymous_variant	283849	exon4			GTGCTGGGCAACC	AK092858	CCDS10832.1	16q22.1	2011-01-31	2011-01-31	2011-01-31	ENSG00000179044	ENSG00000179044			27540	protein-coding gene	gene with protein product		614117	"exocyst complex component 3-like"	EXOC3L		12477932	Standard	NM_178516		Approved	FLJ35539, FLJ35587	uc002erx.1	Q86VI1	OTTHUMG00000137508	ENST00000314586.6:c.375C>T	16.37:g.67222676G>A		124	0	0		141	72	0.510638	NM_178516	A8K7I9|Q8NAD2|Q8TEN2	Silent	SNP	ENST00000314586.6	37	CCDS10832.1																																																																																			G|0.920;A|0.080	0.080	strong		0.662	EXOC3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268827.2	NM_178516		A	67222676	G	A	67222676	2	1	25	1	0	0	0	0	0	0	0	1	5306	1219	43	2		2	EXOC3L	16	67222676	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	55945	67222676	23132077	638	9547											
LRRC29	26231	hgsc.bcm.edu	37	chr16	67241930	67241930	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggccacagcaaccaagcCgttgtctgtgagttctggca	8	9	11	13	1	2	1	0	1	2	0	2	1	2	1	4	2	3	4	4	2	2	2	rs34595673	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67241930C>T	ENST00000409037.1	-	3	1245	c.349G>A	c.(349-351)Ggc>Agc	p.G117S	LRRC29_ENST00000393992.1_Missense_Mutation_p.G117S|LRRC29_ENST00000409509.1_Missense_Mutation_p.G117S|LRRC29_ENST00000462169.1_5'Flank|LRRC29_ENST00000341546.3_Missense_Mutation_p.G117S			Q8WV35	LRC29_HUMAN	leucine rich repeat containing 29	117			G -> S (in dbSNP:rs34595673).							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)		GCAACCAAGCCGTTGTCTGTG	0.612													C|||	455	0.0908546	0.2844	0.0288	5008	,	,		19362	0.0099		0.0278	False		,,,				2504	0.0215				p.G117S		Atlas-SNP	.											.	LRRC29	13	.	0			c.G349A						PASS	.	C	SER/GLY,SER/GLY	1023,3373		129,765,1304	22	20	21		349,349	5.6	0.5	16	dbSNP_126	21	273,8327		8,257,4035	yes	missense,missense	LRRC29	NM_001004055.1,NM_012163.2	56,56	137,1022,5339	TT,TC,CC		3.1744,23.2712,9.9723	possibly-damaging,possibly-damaging	117/224,117/224	67241930	1296,11700	2198	4300	6498	SO:0001583	missense	26231	exon5			CCAAGCCGTTGTC	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.349G>A	16.37:g.67241930C>T	ENSP00000387318:p.Gly117Ser	90	0	0		111	54	0.486486	NM_001004055	B2RE92|Q9UKA0	Missense_Mutation	SNP	ENST00000409037.1	37	CCDS32465.1	157	0.07188644688644688	124	0.25203252032520324	10	0.027624309392265192	4	0.006993006993006993	19	0.025065963060686015	C	19.59	3.855436	0.71719	0.232712	0.031744	ENSG00000125122	ENST00000409509;ENST00000393992;ENST00000409037;ENST00000341546;ENST00000433915;ENST00000424285	T;T;T;T;T;T	0.01172	5.23;5.23;5.23;5.23;5.23;5.23	5.57	5.57	0.84162	.	0.603229	0.17346	N	0.177597	T	0.00012	0.0000	L	0.55103	1.725	0.47584	P	5.309999999999482E-4	P	0.37824	0.609	B	0.21546	0.035	T	0.62751	-0.6788	9	0.35671	T	0.21	.	15.0432	0.71807	0.0:1.0:0.0:0.0	rs34595673	117	Q8WV35	LRC29_HUMAN	S	117;117;117;117;69;117	ENSP00000386622:G117S;ENSP00000377561:G117S;ENSP00000387318:G117S;ENSP00000344364:G117S;ENSP00000413129:G69S;ENSP00000409459:G117S	ENSP00000344364:G117S	G	-	1	0	LRRC29	65799431	0.968000	0.33430	0.482000	0.27366	0.824000	0.46624	2.258000	0.43249	2.617000	0.88574	0.655000	0.94253	GGC	C|0.909;T|0.091	0.091	strong		0.612	LRRC29-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335073.1	NM_012163		T	67241930	C	T	67241930	3	4	25	1	0	0	0	0	1	0	0	0	8992	652	23	1	330	1	LRRC29	16	67241930	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	19254	67241930	23112823	639	9548											
KCTD19	146212	hgsc.bcm.edu	37	chr16	67327642	67327642	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctgggctgggaagcagcctCgcttcccaaggggagctgca	7	6	16	12	1	0	0	0	0	0	0	2	2	1	2	2	4	4	6	2	4	2	1	rs145649592	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67327642C>T	ENST00000304372.5	-	12	2078	c.2023G>A	c.(2023-2025)Gag>Aag	p.E675K		NM_001100915.1	NP_001094385.1	Q17RG1	KCD19_HUMAN	potassium channel tetramerization domain containing 19	675					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)		GAAGCAGCCTCGCTTCCCAAG	0.617													C|||	14	0.00279553	0.0	0.0029	5008	,	,		17949	0.0		0.006	False		,,,				2504	0.0061				p.E675K		Atlas-SNP	.											.	KCTD19	82	.	0			c.G2023A						PASS	.	C	LYS/GLU	2,4160		0,2,2079	76	86	83		2023	4.9	0.9	16	dbSNP_134	83	43,8353		0,43,4155	yes	missense	KCTD19	NM_001100915.1	56	0,45,6234	TT,TC,CC		0.5121,0.0481,0.3583	probably-damaging	675/927	67327642	45,12513	2081	4198	6279	SO:0001583	missense	146212	exon12			CAGCCTCGCTTCC	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.2023G>A	16.37:g.67327642C>T	ENSP00000305702:p.Glu675Lys	96	0	0		70	30	0.428571	NM_001100915	B4DZ49|Q8N804	Missense_Mutation	SNP	ENST00000304372.5	37	CCDS42179.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	C	13.27	2.187741	0.38609	4.81E-4	0.005121	ENSG00000168676	ENST00000304372	T	0.58940	0.3	5.86	4.92	0.64577	.	0.101032	0.43747	D	0.000539	T	0.37945	0.1022	N	0.24115	0.695	0.27940	N	0.937539	D	0.67145	0.996	P	0.48063	0.565	T	0.31052	-0.9957	10	0.32370	T	0.25	-21.685	9.3289	0.38010	0.0:0.8369:0.0:0.1631	.	675	Q17RG1	KCD19_HUMAN	K	675	ENSP00000305702:E675K	ENSP00000305702:E675K	E	-	1	0	KCTD19	65885143	0.747000	0.28283	0.940000	0.37924	0.914000	0.54420	1.272000	0.33109	1.493000	0.48517	-0.244000	0.11960	GAG	C|0.997;T|0.003	0.003	strong		0.617	KCTD19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422061.1	XM_085367		T	67327642	C	T	67327642	3	4	25	1	0	0	0	0	1	0	0	0	8115	893	31	1	777	1	KCTD19	16	67327642	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	85712	67327642	23027111	640	9549											
ZDHHC1	29800	hgsc.bcm.edu	37	chr16	67434917	67434917	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgacatgtgcgtgctggcttCggttgaagatgggcaggggc	6	10	18	7	2	0	3	0	2	0	1	1	3	0	3	0	5	2	4	0	5	1	2	rs34229857	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67434917C>T	ENST00000348579.2	-	4	712	c.371G>A	c.(370-372)cGa>cAa	p.R124Q		NM_013304.2	NP_037436.1	Q8WTX9	ZDHC1_HUMAN	zinc finger, DHHC-type containing 1	124			R -> Q (in dbSNP:rs34229857).		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)		GTGCTGGCTTCGGTTGAAGAT	0.602													C|||	51	0.0101837	0.0	0.0014	5008	,	,		20071	0.0089		0.0249	False		,,,				2504	0.0164				p.R124Q		Atlas-SNP	.											.	ZDHHC1	28	.	0			c.G371A						PASS	.	C	GLN/ARG	22,4374	28.1+/-56.4	0,22,2176	131	113	119		371	5.1	1	16	dbSNP_126	119	229,8371	93.5+/-155.5	5,219,4076	yes	missense	ZDHHC1	NM_013304.2	43	5,241,6252	TT,TC,CC		2.6628,0.5005,1.9314	probably-damaging	124/486	67434917	251,12745	2198	4300	6498	SO:0001583	missense	29800	exon4			TGGCTTCGGTTGA	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.371G>A	16.37:g.67434917C>T	ENSP00000340299:p.Arg124Gln	120	0	0		164	89	0.542683	NM_013304	O15461	Missense_Mutation	SNP	ENST00000348579.2	37	CCDS10836.1	20	0.009157509157509158	0	0.0	1	0.0027624309392265192	3	0.005244755244755245	16	0.021108179419525065	C	26.2	4.710737	0.89112	0.005005	0.026628	ENSG00000159714	ENST00000348579	T	0.37411	1.2	6.06	5.1	0.69264	.	0.081104	0.53938	D	0.000060	T	0.26011	0.0634	L	0.55834	1.745	0.51482	D	0.999921	D	0.89917	1.0	D	0.75484	0.986	T	0.21484	-1.0244	10	0.23302	T	0.38	.	9.8809	0.41233	0.0:0.7878:0.1405:0.0716	rs34229857	124	Q8WTX9	ZDHC1_HUMAN	Q	124	ENSP00000340299:R124Q	ENSP00000340299:R124Q	R	-	2	0	ZDHHC1	65992418	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.674000	0.61612	1.557000	0.49525	0.655000	0.94253	CGA	C|0.983;T|0.017	0.017	strong		0.602	ZDHHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268845.1	NM_013304		T	67434917	C	T	67434917	3	4	25	1	0	0	0	0	1	0	0	0	17615	884	31	1	1118	1	ZDHHC1	16	67434917	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	107275	67434917	22919836	641	9550											
AGRP	181	hgsc.bcm.edu	37	chr16	67516605	67516605	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagcagaaggcattgaagaaGcggcagtagcacgtggcaca	14	5	14	8	2	0	3	0	1	0	2	0	3	0	3	0	3	3	6	0	3	5	3	rs34730014	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67516605G>C	ENST00000290953.2	-	4	632	c.333C>G	c.(331-333)cgC>cgG	p.R111R	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	111	Agouti. {ECO:0000255|PROSITE- ProRule:PRU00494}.|Interaction with melanocortin receptors.				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)		CATTGAAGAAGCGGCAGTAGC	0.637													G|||	4	0.000798722	0.0	0.0014	5008	,	,		19478	0.0		0.003	False		,,,				2504	0.0				p.R111R		Atlas-SNP	.											.	AGRP	8	.	0			c.C333G						PASS	.	G		6,4390	9.9+/-24.2	0,6,2192	106	99	101		333	0.6	1	16	dbSNP_126	101	44,8556	29.0+/-79.6	0,44,4256	no	coding-synonymous	AGRP	NM_001138.1		0,50,6448	CC,CG,GG		0.5116,0.1365,0.3847		111/133	67516605	50,12946	2198	4300	6498	SO:0001819	synonymous_variant	181	exon4			GAAGAAGCGGCAG	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.333C>G	16.37:g.67516605G>C		138	0	0		147	63	0.428571	NM_001138	O15459|Q2TBD9	Silent	SNP	ENST00000290953.2	37	CCDS10839.1																																																																																			G|0.997;C|0.003	0.003	strong		0.637	AGRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268828.1			C	67516605	G	C	67516605	2	2	25	1	0	0	0	0	0	0	0	1	398	958	34	4		4	AGRP	16	67516605	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	81688	67516605	22838148	642	9551											
ESRP2	80004	hgsc.bcm.edu	37	chr16	68269820	68269820	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gtctcgtccgagcccaggtcCcgtcccagcgcacccgccgt	4	6	11	20	6	1	0	0	0	1	0	5	1	4	0	6	1	2	1	6	1	0	0	rs150603076	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:68269820C>T	ENST00000565858.1	-	1	215	c.129G>A	c.(127-129)cgG>cgA	p.R43R	ESRP2_ENST00000473183.2_Silent_p.R43R|RP11-96D1.6_ENST00000564147.1_RNA	NM_024939.2	NP_079215.2	Q9H6T0	ESRP2_HUMAN	epithelial splicing regulatory protein 2	43					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						AGCCCAGGTCCCGTCCCAGCG	0.711													C|||	15	0.00299521	0.0	0.0029	5008	,	,		7867	0.0		0.007	False		,,,				2504	0.0061				p.R43R		Atlas-SNP	.											.	ESRP2	118	.	0			c.G129A						PASS	.	C		3,4377		0,3,2187	18	14	15		129	-6.1	0.7	16	dbSNP_134	15	38,8532		0,38,4247	no	coding-synonymous	ESRP2	NM_024939.2		0,41,6434	TT,TC,CC		0.4434,0.0685,0.3166		43/718	68269820	41,12909	2190	4285	6475	SO:0001819	synonymous_variant	80004	exon1			CAGGTCCCGTCCC	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.129G>A	16.37:g.68269820C>T		24	0	0		34	18	0.529412	NM_024939	Q8N6H8|Q8WZ15|Q9H6I4	Silent	SNP	ENST00000565858.1	37																																																																																				C|0.997;T|0.003	0.003	strong		0.711	ESRP2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000433083.1	NM_024939		T	68269820	C	T	68269820	2	4	25	1	0	0	0	0	0	0	0	1	5261	610	22	2		2	ESRP2	16	68269820	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	753215	68269820	22084933	643	9552											
PRMT7	54496	hgsc.bcm.edu	37	chr16	68390697	68390697	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcctggagcctgcagacccCgaggtagtgcctgcgcaccg	6	6	13	16	3	0	1	0	0	0	1	1	3	1	2	6	2	4	3	6	2	1	1	rs61733486	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:68390697C>T	ENST00000339507.5	+	18	2735	c.1905C>T	c.(1903-1905)ccC>ccT	p.P635P	PRMT7_ENST00000441236.1_Silent_p.P585P|PRMT7_ENST00000348497.4_Silent_p.P487P|PRMT7_ENST00000449359.3_Silent_p.P585P			Q9NVM4	ANM7_HUMAN	protein arginine methyltransferase 7	635	SAM-dependent MTase PRMT-type 2. {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)		CTGCAGACCCCGAGGTAGTGC	0.687													c|||	226	0.0451278	0.0688	0.0533	5008	,	,		16243	0.0		0.0477	False		,,,				2504	0.0511				p.P635P		Atlas-SNP	.											.	PRMT7	51	.	0			c.C1905T						PASS	.		,	302,4088		13,276,1906	20	20	20		1755,1905	3.8	0.2	16	dbSNP_129	20	492,8106		12,468,3819	no	coding-synonymous,coding-synonymous	PRMT7	NM_001184824.1,NM_019023.2	,	25,744,5725	TT,TC,CC		5.7223,6.8793,6.1133	,	585/643,635/693	68390697	794,12194	2195	4299	6494	SO:0001819	synonymous_variant	54496	exon18			AGACCCCGAGGTA	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.1905C>T	16.37:g.68390697C>T		116	0	0		128	52	0.40625	NM_019023	B3KPR0|B3KUG9|B4E379|Q96PV5|Q9H9L0	Silent	SNP	ENST00000339507.5	37	CCDS10866.1																																																																																			C|0.941;T|0.059	0.059	strong		0.687	PRMT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268892.3	NM_019023		T	68390697	C	T	68390697	2	4	25	1	0	0	0	0	0	0	0	1	12553	639	23	1		1	PRMT7	16	68390697	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	120877	68390697	21964056	644	9553											
DHODH	1723	hgsc.bcm.edu	37	chr16	72055078	72055078	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagacctcagtggacgccgcGgaggactacgcagaaggggt	11	4	16	10	4	1	2	1	0	0	2	1	5	1	5	2	5	1	1	2	5	3	1	rs148523165	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:72055078G>A	ENST00000219240.4	+	5	594	c.573G>A	c.(571-573)gcG>gcA	p.A191A	DHODH_ENST00000572887.1_Silent_p.A191A|DHODH_ENST00000573922.1_Intron	NM_001361.4	NP_001352.2	Q02127	PYRD_HUMAN	dihydroorotate dehydrogenase (quinone)	191					'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)	TGGACGCCGCGGAGGACTACG	0.642													G|||	17	0.00339457	0.0008	0.0	5008	,	,		16661	0.0		0.0099	False		,,,				2504	0.0061				p.A191A		Atlas-SNP	.											.	DHODH	33	.	0			c.G573A						PASS	.	G		13,4125		0,13,2056	33	44	40		573	-5.8	0	16	dbSNP_134	40	105,8249		0,105,4072	no	coding-synonymous	DHODH	NM_001361.4		0,118,6128	AA,AG,GG		1.2569,0.3142,0.9446		191/396	72055078	118,12374	2069	4177	6246	SO:0001819	synonymous_variant	1723	exon5			CGCCGCGGAGGAC		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.573G>A	16.37:g.72055078G>A		68	0	0		82	45	0.548781	NM_001361	A8K8C8|Q6P176	Silent	SNP	ENST00000219240.4	37	CCDS42192.1																																																																																			G|0.996;A|0.004	0.004	strong		0.642	DHODH-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001361		A	72055078	G	A	72055078	2	1	25	1	0	0	0	0	0	0	0	1	4486	1103	39	1		1	DHODH	16	72055078	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	3664381	72055078	18299675	645	9554											
ADAMTS18	170692	hgsc.bcm.edu	37	chr16	77327042	77327042	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtccaagcacacagccctcCtgcagctcaggtctggggag	8	6	12	15	1	2	0	1	0	1	0	4	1	4	1	3	3	4	3	3	3	1	0	rs61754842	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:77327042C>T	ENST00000282849.5	-	20	3538	c.3120G>A	c.(3118-3120)caG>caA	p.Q1040Q	RP11-538I12.3_ENST00000561672.1_RNA	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	1040	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						CACAGCCCTCCTGCAGCTCAG	0.607													C|||	10	0.00199681	0.0008	0.0014	5008	,	,		15978	0.0		0.005	False		,,,				2504	0.0031				p.Q1040Q		Atlas-SNP	.											ADAMTS18,breast,lymphoid_neoplasm,-2,1	ADAMTS18	270	1	0			c.G3120A						PASS	.	C		8,4388	14.3+/-33.2	0,8,2190	86	81	82		3120	3	1	16	dbSNP_129	82	65,8535	40.8+/-97.7	1,63,4236	no	coding-synonymous	ADAMTS18	NM_199355.2		1,71,6426	TT,TC,CC		0.7558,0.182,0.5617		1040/1222	77327042	73,12923	2198	4300	6498	SO:0001819	synonymous_variant	170692	exon20			GCCCTCCTGCAGC	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.3120G>A	16.37:g.77327042C>T		59	0	0		61	39	0.639344	NM_199355	Q6P4R5|Q6ZWJ9	Silent	SNP	ENST00000282849.5	37	CCDS10926.1																																																																																			C|0.995;T|0.005	0.005	strong		0.607	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1			T	77327042	C	T	77327042	2	4	25	1	0	0	0	0	0	0	0	1	263	680	24	2		2	ADAMTS18	16	77327042	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	5271964	77327042	13027711	646	9555											
NECAB2	54550	hgsc.bcm.edu	37	chr16	84030848	84030848	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttcgacctgcagcagcgcCtgtcagatgaagatggcacc	9	7	13	12	2	1	3	1	1	0	2	2	4	1	3	3	2	3	4	3	2	1	1	rs7193267	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84030848C>T	ENST00000305202.4	+	9	840	c.823C>T	c.(823-825)Ctg>Ttg	p.L275L	NECAB2_ENST00000565691.1_Silent_p.L192L|NECAB2_ENST00000567703.1_3'UTR	NM_019065.2	NP_061938.2	Q7Z6G3	NECA2_HUMAN	N-terminal EF-hand calcium binding protein 2	275						cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	19						GCAGCAGCGCCTGTCAGATGA	0.607													C|||	17	0.00339457	0.0015	0.0072	5008	,	,		16661	0.0		0.0099	False		,,,				2504	0.0				p.L275L		Atlas-SNP	.											.	NECAB2	36	.	0			c.C823T						PASS	.	C		14,4386	21.2+/-45.6	0,14,2186	188	136	154		823	4.5	0.9	16	dbSNP_116	154	99,8501	54.4+/-115.2	1,97,4202	no	coding-synonymous	NECAB2	NM_019065.2		1,111,6388	TT,TC,CC		1.1512,0.3182,0.8692		275/387	84030848	113,12887	2200	4300	6500	SO:0001819	synonymous_variant	54550	exon9			CAGCGCCTGTCAG	AY299331	CCDS10940.1	16q23.3-q24.1	2013-01-10	2007-12-06	2007-12-06	ENSG00000103154	ENSG00000103154		"N-terminal EF-hand calcium binding proteins", "EF-hand domain containing"	23746	protein-coding gene	gene with protein product			"EF-hand calcium binding protein 2"	EFCBP2		12044471	Standard	NM_019065		Approved		uc002fhd.3	Q7Z6G3	OTTHUMG00000137636	ENST00000305202.4:c.823C>T	16.37:g.84030848C>T		108	0	0		133	64	0.481203	NM_019065	A2RRG3|O75547|Q6ZSK0	Silent	SNP	ENST00000305202.4	37	CCDS10940.1																																																																																			C|0.992;T|0.008	0.008	strong		0.607	NECAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269077.2	NM_019065		T	84030848	C	T	84030848	2	4	25	1	0	0	0	0	0	0	0	1	10314	680	24	2		2	NECAB2	16	84030848	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	6703806	84030848	6323905	647	9556											
IRF8	3394	hgsc.bcm.edu	37	chr16	85954879	85954879	+	Frame_Shift_Del	DEL	C	C	-																															ttcagagaaaaccaacagatCaccgtctaagtgcgtcgctt																										TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:85954879delC	ENST00000268638.5	+	9	1694	c.1272delC	c.(1270-1272)atcfs	p.I424fs	IRF8_ENST00000562492.1_Frame_Shift_Del_p.I220fs	NM_002163.2	NP_002154.1	Q02556	IRF8_HUMAN	interferon regulatory factor 8	424					cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	24		Prostate(104;0.0771)				ACCAACAGATCACCGTCTAAG	0.557																																					p.I424fs		Atlas-Indel	.											IRF8,NS,lymphoid_neoplasm,0,1	IRF8	65	1	0			c.1271delT						PASS	.						71	77	75					16																	85954879		2198	4300	6498	SO:0001589	frameshift_variant	3394	exon9			.	M91196	CCDS10956.1	16q24.1	2014-09-17	2004-11-12	2004-11-12	ENSG00000140968	ENSG00000140968			5358	protein-coding gene	gene with protein product		601565	"interferon consensus sequence binding protein 1"	ICSBP1		1460054, 11997525	Standard	NM_002163		Approved	IRF-8, ICSBP	uc002fjh.3	Q02556	OTTHUMG00000137648	ENST00000268638.5:c.1272delC	16.37:g.85954879delC	ENSP00000268638:p.Ile424fs	39	0	0		36	10	0.277778	NM_002163	A0AV82	Frame_Shift_Del	DEL	ENST00000268638.5	37	CCDS10956.1																																																																																			.	.	none		0.557	IRF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269100.2	NM_002163		-	85954879	C	-	85954879	7	5	25	1	0	1	0	1	0	0	0	0	7845	816	29	0	1302	0	IRF8	16	85954879	Frame_Shift_Del	DEL	C	TCGA-G8-6906-01A-11D-2210-10	1924031	85954879	4399874	648	9557	116	2									
IRF8	3394	hgsc.bcm.edu	37	chr16	85954881	85954886	+	Stop_Codon_Del	DEL	CCGTCT	CCGTCT	-																															cagagaaaaccaacagatcaCcgtctaagtgcgtcgcttgg																								rs147057451|rs146135491	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CCGTCT	CCGTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:85954881_85954886delCCGTCT	ENST00000268638.5	+	0	1696_1701				IRF8_ENST00000562492.1_Stop_Codon_Del	NM_002163.2	NP_002154.1	Q02556	IRF8_HUMAN	interferon regulatory factor 8						cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	24		Prostate(104;0.0771)				CAACAGATCACCGTCTAAGTGCGTCG	0.558																																					p.425_426del		Atlas-Indel	.											.	IRF8	65	.	0			c.1273_1278del						PASS	.																																			SO:0001567	stop_retained_variant	3394	exon9			.	M91196	CCDS10956.1	16q24.1	2014-09-17	2004-11-12	2004-11-12	ENSG00000140968	ENSG00000140968			5358	protein-coding gene	gene with protein product		601565	"interferon consensus sequence binding protein 1"	ICSBP1		1460054, 11997525	Standard	NM_002163		Approved	IRF-8, ICSBP	uc002fjh.3	Q02556	OTTHUMG00000137648	Exception_encountered	16.37:g.85954881_85954886delCCGTCT	ENSP00000268638:p.*427Tyrext*22	38	0	0		38	10	0.263158	NM_002163	A0AV82	In_Frame_Del	DEL	ENST00000268638.5	37	CCDS10956.1																																																																																			.	.	none		0.558	IRF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269100.2	NM_002163		-	85954886	CCGTCT	-	85954881	7	5	25	1	0	1	0	1	0	0	0	0	7845	507	18	0	1304	0	IRF8	16	85954881	Stop_Codon_Del	DEL	CCGTCT	TCGA-G8-6906-01A-11D-2210-10	2	85954881	4399872	649	9558	116	2									
JPH3	57338	hgsc.bcm.edu	37	chr16	87678302	87678302	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaggctgaggccgagctggCggtcatcgaggacgacatcg	8	5	17	11	6	1	1	1	1	0	0	3	6	1	2	1	5	1	2	1	5	0	0	rs144403955	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:87678302C>T	ENST00000284262.2	+	2	1063	c.821C>T	c.(820-822)gCg>gTg	p.A274V		NM_020655.2	NP_065706.2	Q8WXH2	JPH3_HUMAN	junctophilin 3	274					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)		GCCGAGCTGGCGGTCATCGAG	0.667													C|||	4	0.000798722	0.0	0.0014	5008	,	,		12745	0.001		0.001	False		,,,				2504	0.001				p.A274V		Atlas-SNP	.											.	JPH3	95	.	0			c.C821T						PASS	.	C	VAL/ALA	0,4396		0,0,2198	75	68	70		821	4.9	0.9	16	dbSNP_134	70	15,8585	11.9+/-42.8	0,15,4285	yes	missense	JPH3	NM_020655.2	64	0,15,6483	TT,TC,CC		0.1744,0.0,0.1154	benign	274/749	87678302	15,12981	2198	4300	6498	SO:0001583	missense	57338	exon2			AGCTGGCGGTCAT	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.821C>T	16.37:g.87678302C>T	ENSP00000284262:p.Ala274Val	46	0	0		60	34	0.566667	NM_020655	D3DUN2|Q8N471|Q9HDC3|Q9HDC4	Missense_Mutation	SNP	ENST00000284262.2	37	CCDS10962.1	3	0.0013736263736263737	0	0.0	0	0.0	1	0.0017482517482517483	2	0.002638522427440633	C	13.94	2.387189	0.42308	0.0	0.001744	ENSG00000154118	ENST00000537256;ENST00000284262	T	0.46819	0.86	4.91	4.91	0.64330	.	0.252030	0.40144	N	0.001172	T	0.28466	0.0704	N	0.08118	0	0.38661	D	0.952087	B	0.06786	0.001	B	0.09377	0.004	T	0.13926	-1.0491	10	0.13470	T	0.59	.	17.1059	0.86663	0.0:1.0:0.0:0.0	.	274	Q8WXH2	JPH3_HUMAN	V	137;274	ENSP00000284262:A274V	ENSP00000284262:A274V	A	+	2	0	JPH3	86235803	0.998000	0.40836	0.884000	0.34674	0.875000	0.50365	3.934000	0.56553	2.286000	0.76751	0.561000	0.74099	GCG	C|0.998;T|0.002	0.002	strong		0.667	JPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269108.2			T	87678302	C	T	87678302	3	4	25	1	0	0	0	0	1	0	0	0	7971	768	27	1	827	1	JPH3	16	87678302	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1723421	87678302	2676451	650	9559											
BANP	54971	hgsc.bcm.edu	37	chr16	88071611	88071611	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atccatcacgtggggcaggaCggtcaggtgagtgtcccagt	8	8	15	10	2	2	1	2	1	0	0	4	2	4	2	2	5	0	1	2	5	0	0	rs149196674	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:88071611C>T	ENST00000393207.1	+	11	1493	c.1272C>T	c.(1270-1272)gaC>gaT	p.D424D	BANP_ENST00000355163.5_Silent_p.D402D|BANP_ENST00000479780.2_Silent_p.D393D|BANP_ENST00000286122.7_Silent_p.D424D|BANP_ENST00000538234.1_Silent_p.D435D|BANP_ENST00000355022.4_Silent_p.D396D|BANP_ENST00000393208.2_Silent_p.D396D	NM_001173543.1	NP_001167014.1	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein	424	Gln-rich.				cell cycle (GO:0007049)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of protein catabolic process (GO:0042177)|protein localization to nucleus (GO:0034504)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.00551)		TGGGGCAGGACGGTCAGGTGA	0.612													c|||	2	0.000399361	0.0015	0.0	5008	,	,		11861	0.0		0.0	False		,,,				2504	0.0				p.D435D		Atlas-SNP	.											.	BANP	67	.	0			c.C1305T						PASS	.	C	,,,,,,	4,4392	8.1+/-20.4	0,4,2194	118	99	106		1296,1206,1179,1305,1272,1188,1188	-6.3	0.7	16	dbSNP_134	106	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BANP	NM_001173539.1,NM_001173540.1,NM_001173541.1,NM_001173542.1,NM_001173543.1,NM_017869.3,NM_079837.2	,,,,,,	0,4,6494	TT,TC,CC		0.0,0.091,0.0308	,,,,,,	432/506,402/498,393/467,435/509,424/520,396/470,396/492	88071611	4,12992	2198	4300	6498	SO:0001819	synonymous_variant	54971	exon11			GCAGGACGGTCAG	AK094158	CCDS10966.2, CCDS42215.1, CCDS54052.1, CCDS54053.1, CCDS54054.1	16q24	2012-11-22			ENSG00000172530	ENSG00000172530		"BEN domain containing"	13450	protein-coding gene	gene with protein product	"BEN domain containing 1"	611564				10940556, 10950932	Standard	NM_017869		Approved	SMARBP1, SMAR1, FLJ20538, DKFZp761H172, FLJ10177, BEND1	uc010vow.2	Q8N9N5	OTTHUMG00000137678	ENST00000393207.1:c.1272C>T	16.37:g.88071611C>T		151	0	0		130	69	0.530769	NM_001173542	A8MU25|A8MX25|B2RCF7|B4DNJ9|F5GZM0|Q96GJ7|Q9NWY1	Silent	SNP	ENST00000393207.1	37	CCDS54054.1																																																																																			C|0.999;T|0.001	0.001	strong		0.612	BANP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269166.1	NM_017869		T	88071611	C	T	88071611	2	4	25	1	0	0	0	0	0	0	0	1	1310	535	19	1		1	BANP	16	88071611	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	393309	88071611	2283142	651	9560											
C16orf55	124045	hgsc.bcm.edu	37	chr16	89724755	89724755	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caggcaggcagacagggagtCggagaagcctgtggacagcc	11	3	17	10	1	0	2	0	0	0	2	1	5	0	4	2	5	2	2	2	5	1	0	rs13329897	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:89724755C>T	ENST00000301031.4	+	2	134	c.134C>T	c.(133-135)tCg>tTg	p.S45L	SPATA33_ENST00000579310.1_Missense_Mutation_p.S46L|SPATA33_ENST00000568929.1_Missense_Mutation_p.S15L|CHMP1A_ENST00000547614.1_5'Flank|CHMP1A_ENST00000535997.2_5'Flank|CHMP1A_ENST00000550102.1_5'Flank|CHMP1A_ENST00000397901.3_5'Flank|CHMP1A_ENST00000253475.5_5'Flank	NM_001271908.1|NM_153025.1	NP_001258837.1|NP_694570.1	Q96N06	SPT33_HUMAN	spermatogenesis associated 33	45			S -> L (in dbSNP:rs13329897).			cytoplasm (GO:0005737)|nucleus (GO:0005634)											GACAGGGAGTCGGAGAAGCCT	0.612													C|||	37	0.00738818	0.0	0.013	5008	,	,		13663	0.0		0.0249	False		,,,				2504	0.0031				p.S46L		Atlas-SNP	.											.	C16orf55	6	.	0			c.C137T						PASS	.		LEU/SER	24,4370	29.9+/-59.1	0,24,2173	34	38	37		134	-1.5	0	16	dbSNP_121	37	174,8426	79.5+/-142.1	2,170,4128	yes	missense	C16orf55	NM_153025.1	145	2,194,6301	TT,TC,CC		2.0233,0.5462,1.5238	possibly-damaging	45/140	89724755	198,12796	2197	4300	6497	SO:0001583	missense	124045	exon2			GGGAGTCGGAGAA	AK056168	CCDS10983.1, CCDS62012.1, CCDS73929.1	16q24.3	2013-07-16	2013-07-05	2013-07-05	ENSG00000167523	ENSG00000167523			26463	protein-coding gene	gene with protein product		615409	"chromosome 16 open reading frame 55"	C16orf55		23844118	Standard	NM_153025		Approved	FLJ31606	uc010vpk.2	Q96N06	OTTHUMG00000138048	ENST00000301031.4:c.134C>T	16.37:g.89724755C>T	ENSP00000301031:p.Ser45Leu	62	0	0		84	35	0.416667	NM_001271910	A8WFL2|B4DZN8	Missense_Mutation	SNP	ENST00000301031.4	37	CCDS10983.1	23	0.010531135531135532	0	0.0	6	0.016574585635359115	0	0.0	17	0.022427440633245383	C	6.839	0.524082	0.13066	0.005462	0.020233	ENSG00000167523	ENST00000301031;ENST00000457689	T	0.40225	1.04	1.95	-1.52	0.08637	.	.	.	.	.	T	0.11665	0.0284	L	0.27053	0.805	0.09310	N	1	B;B;B	0.22851	0.004;0.076;0.008	B;B;B	0.08055	0.001;0.003;0.001	T	0.12426	-1.0548	9	0.36615	T	0.2	.	2.8748	0.05628	0.0:0.4326:0.2424:0.325	rs13329897;rs52799200;rs13329897	46;59;45	B4DZN8;Q86XC3;Q96N06	.;.;CP055_HUMAN	L	45;46	ENSP00000301031:S45L	ENSP00000301031:S45L	S	+	2	0	C16orf55	88252256	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.868000	0.04236	-0.356000	0.08187	-2.290000	0.00267	TCG	C|0.987;T|0.013	0.013	strong		0.612	SPATA33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269924.2	NM_153025		T	89724755	C	T	89724755	3	4	25	1	0	0	0	0	1	0	0	0	1822	893	31	1	140	1	C16orf55	16	89724755	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1653144	89724755	629998	652	9561											
ABR	29	hgsc.bcm.edu	37	chr17	1028676	1028676	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctcctcattcccctctccgtCgtactcgtccgtcccgtagc	3	12	6	20	5	2	0	1	0	1	0	9	0	6	0	6	0	2	2	6	0	2	3	rs117732533	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:1028676C>T	ENST00000302538.5	-	2	234	c.88G>A	c.(88-90)Gac>Aac	p.D30N	ABR_ENST00000574437.1_5'UTR|ABR_ENST00000544583.2_5'UTR	NM_001282149.1|NM_021962.3	NP_001269078.1|NP_068781.2	Q12979	ABR_HUMAN	active BCR-related	30					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)		CCCTCTCCGTCGTACTCGTCC	0.627													C|||	21	0.00419329	0.0	0.0058	5008	,	,		12183	0.0		0.0169	False		,,,				2504	0.0				p.D30N	Esophageal Squamous(197;2016 2115 4129 29033 46447)	Atlas-SNP	.											.	ABR	119	.	0			c.G88A						PASS	.	C	,ASN/ASP	8,4398	14.3+/-33.2	0,8,2195	112	103	106		,88	5.5	1	17	dbSNP_132	106	90,8510	51.5+/-111.7	1,88,4211	yes	utr-5,missense	ABR	NM_001159746.1,NM_021962.2	,23	1,96,6406	TT,TC,CC		1.0465,0.1816,0.7535	,benign	,30/860	1028676	98,12908	2203	4300	6503	SO:0001583	missense	29	exon2			CTCCGTCGTACTC	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.88G>A	17.37:g.1028676C>T	ENSP00000303909:p.Asp30Asn	56	0	0		71	38	0.535211	NM_021962	B3KW89|B7Z6H7|D3DTH3|D3DTH4|F5H3S2|F5H8B3|Q13693|Q13694	Missense_Mutation	SNP	ENST00000302538.5	37	CCDS10999.1	15	0.006868131868131868	0	0.0	2	0.0055248618784530384	0	0.0	13	0.017150395778364115	C	16.51	3.142274	0.57044	0.001816	0.010465	ENSG00000159842	ENST00000302538	T	0.21361	2.01	5.46	5.46	0.80206	.	0.182095	0.48286	D	0.000187	T	0.08133	0.0203	L	0.40543	1.245	0.80722	D	1	P	0.36438	0.553	B	0.25291	0.059	T	0.05241	-1.0897	10	0.23302	T	0.38	.	16.8188	0.85740	0.0:1.0:0.0:0.0	.	30	Q12979	ABR_HUMAN	N	30	ENSP00000303909:D30N	ENSP00000303909:D30N	D	-	1	0	ABR	975426	1.000000	0.71417	1.000000	0.80357	0.613000	0.37349	5.071000	0.64382	2.567000	0.86603	0.561000	0.74099	GAC	C|0.992;T|0.008	0.008	strong		0.627	ABR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206675.4			T	1028676	C	T	1028676	3	4	25	1	0	0	0	0	1	0	0	0	99	884	31	1	2718	1	ABR	17	1028676	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10		1028676	80166534	653	9562											
MYBBP1A	10514	hgsc.bcm.edu	37	chr17	4451570	4451570	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccctgggtctggcccggtGcctgcttgaactgcgtgctg	3	10	14	14	2	1	1	0	1	1	0	1	1	1	1	3	3	5	2	3	3	1	1	rs142700966	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:4451570G>A	ENST00000254718.4	-	12	1898	c.1592C>T	c.(1591-1593)gCa>gTa	p.A531V	MYBBP1A_ENST00000381556.2_Missense_Mutation_p.A531V			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	531	Interaction with MYB. {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						CTGGCCCGGTGCCTGCTTGAA	0.632													G|||	4	0.000798722	0.0	0.0	5008	,	,		17643	0.0		0.004	False		,,,				2504	0.0				p.A531V		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.C1592T						PASS	.						66	65	65					17																	4451570		2203	4300	6503	SO:0001583	missense	10514	exon12			CCCGGTGCCTGCT	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.1592C>T	17.37:g.4451570G>A	ENSP00000254718:p.Ala531Val	62	0	0		65	34	0.523077	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Missense_Mutation	SNP	ENST00000254718.4	37	CCDS11046.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	3.338	-0.135261	0.06711	.	.	ENSG00000132382	ENST00000381556;ENST00000254718	T;T	0.50813	0.73;0.73	5.48	-0.24	0.13047	Armadillo-type fold (1);	0.643159	0.16655	N	0.205055	T	0.21186	0.0510	L	0.35414	1.06	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.12156	0.007;0.004	T	0.11155	-1.0599	10	0.22706	T	0.39	-5.7941	4.1307	0.10148	0.4189:0.1728:0.4083:0.0	.	531;531	Q9BQG0;Q9BQG0-2	MBB1A_HUMAN;.	V	531	ENSP00000370968:A531V;ENSP00000254718:A531V	ENSP00000254718:A531V	A	-	2	0	MYBBP1A	4398319	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.430000	0.21428	0.040000	0.15660	0.655000	0.94253	GCA	G|0.998;A|0.002	0.002	strong		0.632	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520		A	4451570	G	A	4451570	3	1	25	1	0	0	0	0	1	0	0	0	10017	1319	46	2	2494	2	MYBBP1A	17	4451570	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	3422894	4451570	76743640	654	9563											
PLD2	5338	hgsc.bcm.edu	37	chr17	4720522	4720522	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggccaatcagctccccttcAcacttccaggagggcagtgc	8	7	10	16	1	2	0	2	0	0	0	4	1	4	1	4	3	2	2	4	3	1	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:4720522A>T	ENST00000263088.6	+	17	1914	c.1783A>T	c.(1783-1785)Aca>Tca	p.T595S	PLD2_ENST00000572940.1_Missense_Mutation_p.T595S	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2	595	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)	GCTCCCCTTCACACTTCCAGG	0.602																																					p.T595S		Atlas-SNP	.											.	PLD2	138	.	0			c.A1783T						PASS	.						225	193	204					17																	4720522		2203	4300	6503	SO:0001583	missense	5338	exon17			CCCTTCACACTTC	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.1783A>T	17.37:g.4720522A>T	ENSP00000263088:p.Thr595Ser	129	0	0		187	79	0.42246	NM_001243108	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Missense_Mutation	SNP	ENST00000263088.6	37	CCDS11057.1	.	.	.	.	.	.	.	.	.	.	A	2.773	-0.255213	0.05829	.	.	ENSG00000129219	ENST00000263088	T	0.05447	3.44	4.48	2.18	0.27775	.	0.430330	0.25572	N	0.029760	T	0.03053	0.0090	N	0.13327	0.33	0.27520	N	0.951422	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.11329	0.001;0.006;0.002	T	0.40232	-0.9574	10	0.21540	T	0.41	0.6258	3.2221	0.06719	0.6276:0.0:0.1983:0.1741	.	452;595;595	B7Z905;O14939-2;O14939	.;.;PLD2_HUMAN	S	595	ENSP00000263088:T595S	ENSP00000263088:T595S	T	+	1	0	PLD2	4667488	0.016000	0.18221	0.659000	0.29680	0.288000	0.27193	0.396000	0.20867	0.747000	0.32809	0.454000	0.30748	ACA	.	.	none		0.602	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663		T	4720522	A	T	4720522	3	4	25	1	0	0	0	0	1	0	0	0	12055	159	6	5	1845	5	PLD2	17	4720522	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	268952	4720522	76474688	655	9564											
ZNF232	7775	hgsc.bcm.edu	37	chr17	5012935	5012935	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagtctcctggtagcggagAtgcctgaagcgttggcggaa	8	8	17	8	3	1	2	0	1	1	1	2	5	1	4	2	5	3	2	2	5	3	2	rs200108859		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:5012935A>C	ENST00000250076.3	-	3	906	c.252T>G	c.(250-252)caT>caG	p.H84Q	ZNF232_ENST00000416429.2_Missense_Mutation_p.H57Q|ZNF232_ENST00000575898.1_Missense_Mutation_p.H84Q|ZNF232_ENST00000575538.1_Intron|AC012146.7_ENST00000413077.1_RNA|AC012146.7_ENST00000571138.1_RNA	NM_014519.2	NP_055334.2	Q9UNY5	ZN232_HUMAN	zinc finger protein 232	57	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)			kidney(1)|large_intestine(2)|liver(1)|lung(4)|ovary(1)|prostate(2)	11						GGTAGCGGAGATGCCTGAAGC	0.557																																					p.H84Q		Atlas-SNP	.											.	ZNF232	42	.	0			c.T252G						PASS	.	A	GLN/HIS	0,4406		0,0,2203	154	125	135		252	-6.3	0.8	17		135	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ZNF232	NM_014519.2	24	0,1,6502	CC,CA,AA		0.0116,0.0,0.0077	benign	84/445	5012935	1,13005	2203	4300	6503	SO:0001583	missense	7775	exon3			GCGGAGATGCCTG	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.252T>G	17.37:g.5012935A>C	ENSP00000250076:p.His84Gln	186	0	0		184	86	0.467391	NM_014519		Missense_Mutation	SNP	ENST00000250076.3	37	CCDS11068.1	.	.	.	.	.	.	.	.	.	.	A	0.344	-0.948705	0.02304	0.0	1.16E-4	ENSG00000167840	ENST00000250076;ENST00000416429	T;T	0.03772	3.81;3.81	3.15	-6.3	0.02007	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.277051	0.19503	N	0.112683	T	0.00998	0.0033	N	0.01096	-1.015	0.23581	N	0.997361	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.11329	0.006;0.001;0.0;0.0	T	0.25433	-1.0132	10	0.02654	T	1	.	5.1735	0.15122	0.419:0.432:0.0:0.1491	.	84;57;57;57	B4DNA7;B4DP49;Q9UNY5;Q9UNY5-2	.;.;ZN232_HUMAN;.	Q	84;57	ENSP00000250076:H84Q;ENSP00000416430:H57Q	ENSP00000250076:H84Q	H	-	3	2	ZNF232	4953659	0.000000	0.05858	0.841000	0.33234	0.923000	0.55619	-1.797000	0.01749	-1.716000	0.01387	-0.472000	0.04984	CAT	.	.	weak		0.557	ZNF232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216915.1	NM_014519		C	5012935	A	C	5012935	3	2	25	1	0	0	0	0	1	0	0	0	17800	330	12	5	1094	5	ZNF232	17	5012935	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	292413	5012935	76182275	656	9565											
USP6	9098	hgsc.bcm.edu	37	chr17	5039138	5039138	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agggacctgagccacatcacCgccttgttcctcctttatct	7	12	7	15	1	2	1	1	1	1	0	4	2	4	2	6	1	1	1	6	1	1	4	rs3213878	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:5039138C>T	ENST00000574788.1	+	17	2809	c.579C>T	c.(577-579)acC>acT	p.T193T	USP6_ENST00000304328.5_5'UTR|USP6_ENST00000332776.4_Silent_p.T193T|USP6_ENST00000250066.6_Silent_p.T193T			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	193	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				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						GCCACATCACCGCCTTGTTCC	0.607			T	"COL1A1, CDH11, ZNF9, OMD"	aneurysmal bone cysts								C|||	490	0.0978435	0.1853	0.0375	5008	,	,		20475	0.0774		0.1143	False		,,,				2504	0.0266				p.T193T		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	.	USP6	213	.	0			c.C579T						PASS	.	C		682,3724	287.2+/-279.2	60,562,1581	126	110	115		579	-1.7	0.2	17	dbSNP_106	115	949,7651	208.0+/-249.6	52,845,3403	no	coding-synonymous	USP6	NM_004505.2		112,1407,4984	TT,TC,CC		11.0349,15.4789,12.5404		193/1407	5039138	1631,11375	2203	4300	6503	SO:0001819	synonymous_variant	9098	exon9			CATCACCGCCTTG	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.579C>T	17.37:g.5039138C>T		12	0	0		14	7	0.5	NM_004505	Q15634|Q86WP6|Q8IWT4	Silent	SNP	ENST00000574788.1	37	CCDS11069.2																																																																																			C|0.883;T|0.117	0.117	strong		0.607	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505		T	5039138	C	T	5039138	2	4	25	1	0	0	0	0	0	0	0	1	17101	639	23	1		1	USP6	17	5039138	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	26203	5039138	76156072	657	9566											
NLRP1	22861	hgsc.bcm.edu	37	chr17	5442790	5442790	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccctcacagagcagtcgcaCgccaacgtcatccaggttgt	9	7	9	16	3	2	1	2	0	0	1	4	1	3	1	4	1	2	3	4	1	1	1	rs61754791	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:5442790C>T	ENST00000572272.1	-	7	2814	c.2815G>A	c.(2815-2817)Gtg>Atg	p.V939M	NLRP1_ENST00000269280.4_Missense_Mutation_p.V939M|NLRP1_ENST00000577119.1_Missense_Mutation_p.V939M|NLRP1_ENST00000262467.5_Missense_Mutation_p.V939M|NLRP1_ENST00000354411.3_Missense_Mutation_p.V939M|NLRP1_ENST00000571307.1_5'UTR|NLRP1_ENST00000345221.3_Missense_Mutation_p.V939M			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	939					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)				AGCAGTCGCACGCCAACGTCA	0.622													C|||	58	0.0115815	0.0318	0.0058	5008	,	,		18777	0.0		0.0109	False		,,,				2504	0.001				p.V939M		Atlas-SNP	.											.	NLRP1	358	.	0			c.G2815A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	105,4301	82.9+/-121.4	3,99,2101	79	62	67		2815,2815,2815,2815,2815	0.5	0	17	dbSNP_129	67	134,8466	67.7+/-130.1	2,130,4168	yes	missense,missense,missense,missense,missense	NLRP1	NM_001033053.2,NM_014922.4,NM_033004.3,NM_033006.3,NM_033007.3	21,21,21,21,21	5,229,6269	TT,TC,CC		1.5581,2.3831,1.8376	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	939/1376,939/1430,939/1474,939/1444,939/1400	5442790	239,12767	2203	4300	6503	SO:0001583	missense	22861	exon7			GTCGCACGCCAAC	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.2815G>A	17.37:g.5442790C>T	ENSP00000460475:p.Val939Met	51	0	0		67	25	0.373134	NM_033007	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	37	CCDS42246.1	26	0.011904761904761904	14	0.028455284552845527	3	0.008287292817679558	0	0.0	9	0.011873350923482849	C	14.12	2.440438	0.43326	0.023831	0.015581	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000354411;ENST00000345221;ENST00000537069	T;T;T;T;T	0.14766	2.48;2.48;2.48;2.48;2.48	3.7	0.477	0.16784	.	0.224064	0.22878	N	0.054551	T	0.10680	0.0261	M	0.74546	2.27	0.09310	N	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;0.997;1.0	D;D;D;D;P;D	0.91635	0.912;0.999;0.997;0.982;0.896;0.982	T	0.03641	-1.1017	10	0.87932	D	0	.	2.8517	0.05560	0.2212:0.5366:0.0:0.2423	rs61754791	205;939;939;939;939;939	F5H042;Q9C000-3;Q9C000-4;Q9C000;Q9C000-2;E9PE50	.;.;.;NALP1_HUMAN;.;.	M	939;939;939;939;939;205	ENSP00000442029:V939M;ENSP00000262467:V939M;ENSP00000269280:V939M;ENSP00000346390:V939M;ENSP00000324366:V939M	ENSP00000262467:V939M	V	-	1	0	NLRP1	5383514	0.000000	0.05858	0.004000	0.12327	0.009000	0.06853	0.004000	0.13106	0.155000	0.19261	0.650000	0.86243	GTG	A|0.000;C|0.986;T|0.014	0.014	strong		0.622	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004		T	5442790	C	T	5442790	3	4	25	1	0	0	0	0	1	0	0	0	10480	536	19	1	1725	1	NLRP1	17	5442790	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	403652	5442790	75752420	658	9567											
CHD3	1107	hgsc.bcm.edu	37	chr17	7807904	7807904	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcaagcgggttcgcaagcaaGttaactacaatgatgctgct	12	9	11	9	2	0	1	0	1	0	0	1	1	0	1	0	1	6	7	0	1	6	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:7807904G>A	ENST00000330494.7	+	25	4189	c.4039G>A	c.(4039-4041)Gtt>Att	p.V1347I	SCARNA21_ENST00000517026.1_RNA|CHD3_ENST00000358181.4_Missense_Mutation_p.V1347I|CHD3_ENST00000380358.4_Missense_Mutation_p.V1406I	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	1347					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)				TCGCAAGCAAGTTAACTACAA	0.547																																					p.V1406I		Atlas-SNP	.											.	CHD3	169	.	0			c.G4216A						PASS	.						98	82	87					17																	7807904		2203	4300	6503	SO:0001583	missense	1107	exon25			AAGCAAGTTAACT	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.4039G>A	17.37:g.7807904G>A	ENSP00000332628:p.Val1347Ile	95	0	0		102	55	0.539216	NM_001005271	D3DTQ9|E9PG89|Q9Y4I0	Missense_Mutation	SNP	ENST00000330494.7	37	CCDS32554.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.177879	0.78564	.	.	ENSG00000170004	ENST00000380358;ENST00000358181;ENST00000330494	D;D;D	0.91631	-2.88;-2.81;-2.82	4.9	4.9	0.64082	Domain of unknown function DUF1087 (1);	0.000000	0.41712	D	0.000823	D	0.95284	0.8470	M	0.64404	1.975	0.80722	D	1	D;D;D	0.69078	0.99;0.992;0.997	D;D;D	0.79108	0.98;0.989;0.992	D	0.95219	0.8332	10	0.54805	T	0.06	-19.8382	18.2591	0.90028	0.0:0.0:1.0:0.0	.	1347;1347;1406	Q12873-2;Q12873;E9PG89	.;CHD3_HUMAN;.	I	1406;1347;1347	ENSP00000369716:V1406I;ENSP00000350907:V1347I;ENSP00000332628:V1347I	ENSP00000332628:V1347I	V	+	1	0	CHD3	7748629	1.000000	0.71417	0.869000	0.34112	0.998000	0.95712	9.263000	0.95617	2.539000	0.85634	0.561000	0.74099	GTT	.	.	none		0.547	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273		A	7807904	G	A	7807904	3	1	25	1	0	0	0	0	1	0	0	0	3328	1029	36	2	4418	2	CHD3	17	7807904	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2365114	7807904	73387306	659	9568											
MYH10	4628	hgsc.bcm.edu	37	chr17	8455419	8455419	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taaaagatatgaaaagtacgTtcatcttttgcttgacgaac	15	13	7	6	2	2	3	1	2	1	1	2	4	2	3	0	0	3	3	0	0	7	7			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:8455419T>C	ENST00000269243.4	-	8	972	c.834A>G	c.(832-834)gaA>gaG	p.E278E	MYH10_ENST00000360416.3_Silent_p.E288E|MYH10_ENST00000396239.1_Silent_p.E278E|MYH10_ENST00000379980.4_Silent_p.E294E	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	278	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						GAAAAGTACGTTCATCTTTTG	0.308																																					p.E288E		Atlas-SNP	.											.	MYH10	148	.	0			c.A864G						PASS	.						48	49	49					17																	8455419		2203	4300	6503	SO:0001819	synonymous_variant	4628	exon9			AGTACGTTCATCT	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.834A>G	17.37:g.8455419T>C		107	0	0		131	6	0.0458015	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	37	CCDS11144.1																																																																																			.	.	none		0.308	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			C	8455419	T	C	8455419	2	2	25	1	0	0	0	0	0	0	0	1	10039	1722	60	3		3	MYH10	17	8455419	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	647515	8455419	72739791	660	9569											
PIK3R6	146850	hgsc.bcm.edu	37	chr17	8733110	8733110	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgctcttggacaaggtcacCtgcagaaaggagcaggctgt	10	7	13	11	1	2	1	1	0	1	1	2	3	2	3	2	4	2	4	2	4	2	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:8733110C>T	ENST00000434064.2	-	9	802		c.e9-1		PIK3R6_ENST00000311434.9_Splice_Site			Q5UE93	PI3R6_HUMAN	phosphoinositide-3-kinase, regulatory subunit 6						angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|G-protein coupled receptor signaling pathway (GO:0007186)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of MAP kinase activity (GO:0043406)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)										ACAAGGTCACCTGCAGAAAGG	0.632																																					.		Atlas-SNP	.											.	.	.	.	0			c.803-1G>A						PASS	.						51	61	58					17																	8733110		1949	3988	5937	SO:0001630	splice_region_variant	146850	exon11			GGTCACCTGCAGA	AK091819	CCDS73985.1	17p13.1	2013-01-31	2008-02-04	2008-02-04	ENSG00000174083	ENSG00000276231			27101	protein-coding gene	gene with protein product		611462	"chromosome 17 open reading frame 38"	C17orf38		16476736	Standard	NM_001010855		Approved	FLJ34500, HsT41028, p87PIKAP	uc002glq.1	Q5UE93	OTTHUMG00000132861	ENST00000434064.2:c.1463-1G>A	17.37:g.8733110C>T		44	0	0		35	12	0.342857	NM_001010855	Q658R3	Splice_Site	SNP	ENST00000434064.2	37																																																																																				.	.	none		0.632	PIK3R6-002	KNOWN	sequence_error|basic	processed_transcript	protein_coding	OTTHUMT00000400327.2	NM_001010855	Intron	T	8733110	C	T	8733110	5	4	25	1	0	0	0	0	0	0	1	0	11932	695	24	2	1505	2	PIK3R6	17	8733110	Splice_Site	SNP	C	TCGA-G8-6906-01A-11D-2210-10	277691	8733110	72462100	661	9570											
MYO1D	4642	hgsc.bcm.edu	37	chr17	30980871	30980871	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgccttaccttacggacgTgacaggaaaagaggacattc	12	9	10	10	2	0	2	0	1	0	1	1	5	0	5	2	3	3	0	2	3	4	4	rs138039699	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:30980871T>A	ENST00000318217.5	-	19	2889	c.2585A>T	c.(2584-2586)cAc>cTc	p.H862L	RP11-220C2.1_ENST00000582272.1_RNA|MYO1D_ENST00000579584.1_Missense_Mutation_p.H862L|MYO1D_ENST00000394649.4_Missense_Mutation_p.H774L	NM_015194.1	NP_056009.1	O94832	MYO1D_HUMAN	myosin ID	862	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)			CTTACGGACGTGACAGGAAAA	0.408													T|||	5	0.000998403	0.0	0.0	5008	,	,		22025	0.0		0.003	False		,,,				2504	0.002				p.H862L		Atlas-SNP	.											.	MYO1D	93	.	0			c.A2585T						PASS	.	T	LEU/HIS	2,4404	4.2+/-10.8	0,2,2201	135	109	118		2585	5.9	1	17	dbSNP_134	118	28,8572	20.4+/-63.3	0,28,4272	yes	missense	MYO1D	NM_015194.1	99	0,30,6473	AA,AT,TT		0.3256,0.0454,0.2307	benign	862/1007	30980871	30,12976	2203	4300	6503	SO:0001583	missense	4642	exon19			CGGACGTGACAGG	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.2585A>T	17.37:g.30980871T>A	ENSP00000324527:p.His862Leu	58	0	0		45	22	0.488889	NM_015194	A6H8V3|Q8NHP9	Missense_Mutation	SNP	ENST00000318217.5	37	CCDS32615.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	16.55	3.153297	0.57259	4.54E-4	0.003256	ENSG00000176658	ENST00000318217;ENST00000394649	T	0.35421	1.31	5.89	5.89	0.94794	Myosin tail 2 (1);	0.000000	0.40554	U	0.001063	T	0.41026	0.1141	M	0.65498	2.005	0.80722	D	1	P;B	0.35033	0.481;0.292	B;B	0.40982	0.345;0.186	T	0.21415	-1.0246	10	0.12103	T	0.63	.	14.2432	0.65971	0.0:0.0:0.0:1.0	.	773;862	Q7Z3N6;O94832	.;MYO1D_HUMAN	L	862;54	ENSP00000324527:H862L	ENSP00000324527:H862L	H	-	2	0	MYO1D	28004984	1.000000	0.71417	0.994000	0.49952	0.931000	0.56810	7.278000	0.78587	2.251000	0.74343	0.482000	0.46254	CAC	T|0.998;A|0.002	0.002	strong		0.408	MYO1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447457.1			A	30980871	T	A	30980871	3	1	25	1	0	0	0	0	1	0	0	0	10080	1696	59	5	451	5	MYO1D	17	30980871	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	22247761	30980871	50214339	662	9571											
SLFN13	146857	hgsc.bcm.edu	37	chr17	33767943	33767943	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgtctgccacataggtcaCtatttgctccaaagtaaagt	11	12	9	9	0	2	0	1	0	1	0	3	0	3	0	2	2	2	2	2	2	5	4	rs138317636	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:33767943C>T	ENST00000285013.6	-	6	2640	c.2365G>A	c.(2365-2367)Gtg>Atg	p.V789M	SLFN13_ENST00000534689.1_Missense_Mutation_p.V471M|SLFN13_ENST00000360502.2_Missense_Mutation_p.V471M|SLFN13_ENST00000533791.1_Missense_Mutation_p.V789M|SLFN13_ENST00000526861.1_Missense_Mutation_p.V789M|SLFN13_ENST00000542635.1_Missense_Mutation_p.V789M	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	789						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)		ACATAGGTCACTATTTGCTCC	0.458																																					p.V789M		Atlas-SNP	.											.	SLFN13	79	.	0			c.G2365A						PASS	.	C	MET/VAL	0,4406		0,0,2203	78	76	77		2365	2.2	0	17	dbSNP_134	77	3,8597	3.0+/-9.4	0,3,4297	yes	missense	SLFN13	NM_144682.5	21	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	benign	789/898	33767943	3,13003	2203	4300	6503	SO:0001583	missense	146857	exon6			AGGTCACTATTTG	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.2365G>A	17.37:g.33767943C>T	ENSP00000285013:p.Val789Met	76	0	0		82	40	0.487805	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Missense_Mutation	SNP	ENST00000285013.6	37	CCDS32620.1	.	.	.	.	.	.	.	.	.	.	c	8.383	0.838010	0.16891	0.0	3.49E-4	ENSG00000154760	ENST00000285013;ENST00000360502;ENST00000526861;ENST00000542635;ENST00000534689	D;D;D;D;D	0.83419	-1.72;-1.72;-1.72;-1.72;-1.72	3.26	2.22	0.28083	.	0.899723	0.09181	N	0.837387	T	0.78972	0.4368	L	0.53780	1.695	0.09310	N	1	P;B	0.36222	0.544;0.2	B;B	0.36989	0.238;0.037	T	0.65973	-0.6038	10	0.44086	T	0.13	.	8.2184	0.31526	0.0:0.7525:0.2475:0.0	.	471;789	Q68D06-2;Q68D06	.;SLN13_HUMAN	M	789;471;789;789;471	ENSP00000285013:V789M;ENSP00000353692:V471M;ENSP00000434439:V789M;ENSP00000444016:V789M;ENSP00000435442:V471M	ENSP00000285013:V789M	V	-	1	0	SLFN13	30792056	0.000000	0.05858	0.001000	0.08648	0.062000	0.15995	0.425000	0.21346	0.637000	0.30526	0.400000	0.26472	GTG	C|1.000;T|0.000	0.000	strong		0.458	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682		T	33767943	C	T	33767943	3	4	25	1	0	0	0	0	1	0	0	0	14751	565	20	2	332	2	SLFN13	17	33767943	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2787072	33767943	47427267	663	9572											
SLFN12L	100506736	hgsc.bcm.edu	37	chr17	33801989	33801990	+	Frame_Shift_Ins	INS	-	-	AAAA																															caaacaaacaaacaaaaacgINSaaacaaacaaacaaacaaaa																								rs532206571		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:33801989_33801990insAAAA	ENST00000260908.7	-	4	1836_1837	c.1719_1720insTTTT	c.(1717-1722)tttcgtfs	p.R574fs	SLFN12L_ENST00000449046.1_Frame_Shift_Ins_p.R605fs|SLFN12L_ENST00000361112.4_Frame_Shift_Ins_p.R603fs	NM_001195790.1	NP_001182719.1	Q6IEE8	SN12L_HUMAN	schlafen family member 12-like	574						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)			breast(1)|endometrium(4)|kidney(5)|large_intestine(2)|lung(3)|ovary(1)	16						aaacaaaaacgaaacaaacaaa	0.381																																					p.R574fs		Pindel,Atlas-Indel	.											.	SLFN12L	140	.	0			c.1720_1721insTTTT						PASS	.																																			SO:0001589	frameshift_variant	100506736	exon4			.	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.1719_1720insTTTT	17.37:g.33801989_33801990insAAAA	ENSP00000437635:p.Arg574fs	86	0	.		61	25	0.41	NM_001195790	F5H6G3	Frame_Shift_Ins	INS	ENST00000260908.7	37	CCDS56026.1																																																																																			.	.	none		0.381	SLFN12L-004	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395748.2	XM_496206		AAAA	33801990	-	AAAA	33801989	7	5	25	1	0	1	1	0	0	0	0	0	14750	1058	37	0	50	0	SLFN12L	17	33801989	Frame_Shift_Ins	INS	-	TCGA-G8-6906-01A-11D-2210-10	34046	33801989	47393221	664	9573											
KRT26	353288	hgsc.bcm.edu	37	chr17	38927462	38927462	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcattttgtagaacaatgctGgcattgcagatggtcgcaga	11	12	11	7	1	1	3	1	0	0	3	2	3	1	3	0	2	3	5	0	2	3	4	rs113285472	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:38927462G>A	ENST00000335552.4	-	2	516	c.468C>T	c.(466-468)gcC>gcT	p.A156A		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)				GAACAATGCTGGCATTGCAGA	0.348													G|||	6	0.00119808	0.0	0.0014	5008	,	,		15657	0.0		0.005	False		,,,				2504	0.0				p.A156A		Atlas-SNP	.											.	KRT26	49	.	0			c.C468T						PASS	.	G		7,4399	11.4+/-27.6	0,7,2196	43	43	43		468	5.3	1	17	dbSNP_132	43	41,8559	25.7+/-73.6	0,41,4259	no	coding-synonymous	KRT26	NM_181539.4		0,48,6455	AA,AG,GG		0.4767,0.1589,0.3691		156/469	38927462	48,12958	2203	4300	6503	SO:0001819	synonymous_variant	353288	exon2			AATGCTGGCATTG	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.468C>T	17.37:g.38927462G>A		118	0	0		128	66	0.515625	NM_181539		Silent	SNP	ENST00000335552.4	37	CCDS11374.1																																																																																			G|0.997;A|0.003	0.003	strong		0.348	KRT26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257215.1	NM_181539		A	38927462	G	A	38927462	2	1	25	1	0	0	0	0	0	0	0	1	8472	1335	47	2		2	KRT26	17	38927462	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	5125473	38927462	42267748	665	9574											
KRT33B	3884	hgsc.bcm.edu	37	chr17	39521058	39521058	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcgctctccagcaggctcCggtatgtgttgatctcacac	6	11	9	15	2	2	1	1	1	2	0	6	1	3	1	3	2	1	5	3	2	1	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39521058C>G	ENST00000251646.3	-	6	1119	c.1070G>C	c.(1069-1071)cGg>cCg	p.R357P		NM_002279.4	NP_002270.1	Q14525	KT33B_HUMAN	keratin 33B	357	Coil 2.|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)				CAGCAGGCTCCGGTATGTGTT	0.597																																					p.R357P		Atlas-SNP	.											KRT33B,NS,carcinoma,-1,1	KRT33B	46	1	0			c.G1070C						PASS	.						74	83	80					17																	39521058		2191	4300	6491	SO:0001583	missense	3884	exon6			AGGCTCCGGTATG	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.1070G>C	17.37:g.39521058C>G	ENSP00000251646:p.Arg357Pro	118	0	0		115	57	0.495652	NM_002279	O76010	Missense_Mutation	SNP	ENST00000251646.3	37	CCDS11389.1	.	.	.	.	.	.	.	.	.	.	c	14.69	2.609786	0.46527	.	.	ENSG00000131738	ENST00000251646	D	0.94793	-3.52	4.72	2.74	0.32292	Filament (1);Intermediate filament protein, conserved site (1);	0.000000	0.64402	D	0.000012	D	0.98197	0.9404	H	0.99454	4.575	0.31011	N	0.71926	D	0.64830	0.994	D	0.77557	0.99	D	0.94737	0.7915	10	0.87932	D	0	.	8.178	0.31294	0.0:0.7468:0.0:0.2532	.	357	Q14525	KT33B_HUMAN	P	357	ENSP00000251646:R357P	ENSP00000251646:R357P	R	-	2	0	KRT33B	36774584	0.992000	0.36948	1.000000	0.80357	0.118000	0.20060	2.344000	0.44010	1.341000	0.45600	0.555000	0.69702	CGG	.	.	none		0.597	KRT33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257292.1	NM_002279		G	39521058	C	G	39521058	3	3	25	1	0	0	0	0	1	0	0	0	8479	652	23	4	152	4	KRT33B	17	39521058	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	593596	39521058	41674152	666	9575											
KRT9	3857	hgsc.bcm.edu	37	chr17	39724810	39724810	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caactcctggacaccgtgccGgagctgggtcacctccttgg	6	8	12	15	2	1	0	1	0	0	0	3	2	3	2	5	4	3	1	5	4	1	1	rs116216460	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39724810G>A	ENST00000246662.4	-	5	1185	c.1120C>T	c.(1120-1122)Cgg>Tgg	p.R374W	KRT9_ENST00000588431.1_Missense_Mutation_p.R141W	NM_000226.3	NP_000217.2	P35527	K1C9_HUMAN	keratin 9	374	Coil 2.|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)				ACACCGTGCCGGAGCTGGGTC	0.547																																					p.R374W		Atlas-SNP	.											.	KRT9	78	.	0			c.C1120T						PASS	.	G	TRP/ARG	2,4404	4.2+/-10.8	0,2,2201	287	271	277		1120	0.6	0.1	17	dbSNP_132	277	17,8583	12.6+/-44.7	0,17,4283	yes	missense	KRT9	NM_000226.3	101	0,19,6484	AA,AG,GG		0.1977,0.0454,0.1461	probably-damaging	374/624	39724810	19,12987	2203	4300	6503	SO:0001583	missense	3857	exon5			CGTGCCGGAGCTG		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.1120C>T	17.37:g.39724810G>A	ENSP00000246662:p.Arg374Trp	114	0	0		124	68	0.548387	NM_000226	O00109|Q0IJ47|Q14665	Missense_Mutation	SNP	ENST00000246662.4	37	CCDS32654.1	.	.	.	.	.	.	.	.	.	.	G	18.04	3.535278	0.64972	4.54E-4	0.001977	ENSG00000171403	ENST00000246662	D	0.92149	-2.98	5.15	0.585	0.17428	Filament (1);	0.304329	0.18190	N	0.148859	D	0.91202	0.7228	M	0.92649	3.33	0.09310	N	1	B	0.30236	0.274	B	0.26094	0.066	D	0.85544	0.1217	10	0.87932	D	0	.	4.1908	0.10419	0.2528:0.0:0.4257:0.3215	.	374	P35527	K1C9_HUMAN	W	374	ENSP00000246662:R374W	ENSP00000246662:R374W	R	-	1	2	KRT9	36978336	0.000000	0.05858	0.061000	0.19648	0.351000	0.29236	0.349000	0.20055	0.133000	0.18654	-0.224000	0.12420	CGG	G|0.998;A|0.002	0.002	strong		0.547	KRT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257707.1	NM_000226		A	39724810	G	A	39724810	3	1	25	1	0	0	0	0	1	0	0	0	8510	1115	39	1	763	1	KRT9	17	39724810	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	203752	39724810	41470400	667	9576											
KAT2A	2648	hgsc.bcm.edu	37	chr17	40266533	40266533	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ccaggaacgctctccacaggGatctgcctcacgccctcctt	7	8	8	18	2	3	0	1	0	2	0	5	2	4	2	5	2	2	1	5	2	1	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:40266533G>A	ENST00000225916.5	-	14	2162	c.2109C>T	c.(2107-2109)atC>atT	p.I703I	DHX58_ENST00000251642.3_5'Flank	NM_021078.2	NP_066564.2	Q92830	KAT2A_HUMAN	K(lysine) acetyltransferase 2A	703					cell proliferation (GO:0008283)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|histone H3-K14 acetylation (GO:0044154)|in utero embryonic development (GO:0001701)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|positive regulation of gluconeogenesis (GO:0045722)|regulation of protein stability (GO:0031647)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|somitogenesis (GO:0001756)|telencephalon development (GO:0021537)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|extracellular space (GO:0005615)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	chromatin binding (GO:0003682)|H3 histone acetyltransferase activity (GO:0010484)|histone acetyltransferase activity (GO:0004402)|histone acetyltransferase activity (H4-K12 specific) (GO:0043997)|histone deacetylase binding (GO:0042826)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						TCTCCACAGGGATCTGCCTCA	0.577																																					p.I703I		Atlas-SNP	.											.	KAT2A	54	.	0			c.C2109T						PASS	.						168	159	162					17																	40266533		2203	4300	6503	SO:0001819	synonymous_variant	2648	exon14			CACAGGGATCTGC	AF029777	CCDS11417.1	17q12-q21	2011-07-01	2008-07-04	2008-07-04	ENSG00000108773	ENSG00000108773		"Chromatin-modifying enzymes / K-acetyltransferases"	4201	protein-coding gene	gene with protein product		602301	"GCN5 general control of amino-acid synthesis 5-like 2 (yeast)"	GCN5L2		8552087	Standard	NM_021078		Approved	GCN5, PCAF-b	uc002hyx.2	Q92830	OTTHUMG00000133504	ENST00000225916.5:c.2109C>T	17.37:g.40266533G>A		85	0	0		95	57	0.6	NM_021078	Q8N1A2|Q9UCW1	Silent	SNP	ENST00000225916.5	37	CCDS11417.1																																																																																			.	.	none		0.577	KAT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257458.1	NM_021078		A	40266533	G	A	40266533	2	1	25	1	0	0	0	0	0	0	0	1	7990	1164	41	2		2	KAT2A	17	40266533	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	541723	40266533	40928677	668	9577											
KCNH4	23415	hgsc.bcm.edu	37	chr17	40312349	40312349	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggagggtctggggtccaagcGgagcctgctgggtggcctgg	4	7	21	9	1	1	0	0	0	1	0	2	2	2	2	3	8	3	1	3	8	1	0	rs138917401	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:40312349G>A	ENST00000264661.3	-	16	3095	c.2763C>T	c.(2761-2763)tcC>tcT	p.S921S	KCNH4_ENST00000607371.1_Silent_p.S921S	NM_012285.2	NP_036417.1	Q9UQ05	KCNH4_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 4	921					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)		GGGTCCAAGCGGAGCCTGCTG	0.647													G|||	11	0.00219649	0.0008	0.0043	5008	,	,		16423	0.0		0.004	False		,,,				2504	0.0031				p.S921S	NSCLC(117;707 1703 2300 21308 31858)	Atlas-SNP	.											.	KCNH4	105	.	0			c.C2763T						PASS	.	G		7,4399	12.9+/-30.5	0,7,2196	53	48	49		2763	-9.9	0	17	dbSNP_134	49	60,8540	36.9+/-92.0	1,58,4241	no	coding-synonymous	KCNH4	NM_012285.2		1,65,6437	AA,AG,GG		0.6977,0.1589,0.5151		921/1018	40312349	67,12939	2203	4300	6503	SO:0001819	synonymous_variant	23415	exon16			CCAAGCGGAGCCT	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.2763C>T	17.37:g.40312349G>A		122	0	0		110	50	0.454545	NM_012285		Silent	SNP	ENST00000264661.3	37	CCDS11420.1																																																																																			G|0.996;A|0.004	0.004	strong		0.647	KCNH4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449791.2	NM_012285		A	40312349	G	A	40312349	2	1	25	1	0	0	0	0	0	0	0	1	8043	1103	39	1		1	KCNH4	17	40312349	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	45816	40312349	40882861	669	9578											
SLC4A1	6521	hgsc.bcm.edu	37	chr17	42328846	42328846	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttgaacagaagcaagatgcGgtcaaagagctggatgccgc	13	6	13	9	2	1	4	1	1	0	3	1	5	1	5	1	2	5	2	1	2	4	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:42328846G>A	ENST00000262418.6	-	18	2577	c.2422C>T	c.(2422-2424)Cgc>Tgc	p.R808C	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)	808	Membrane (anion exchange).		R -> C (in SPH4; Jablonec). {ECO:0000269|PubMed:7530501}.|R -> H (in SPH4; Nara). {ECO:0000269|PubMed:10745622}.		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)		AGCAAGATGCGGTCAAAGAGC	0.587																																					p.R808C		Atlas-SNP	.											SLC4A1,NS,carcinoma,+1,2	SLC4A1	104	2	0			c.C2422T	GRCh37	CM951172	SLC4A1	M		PASS	.						130	116	121					17																	42328846		2203	4300	6503	SO:0001583	missense	6521	exon18			AGATGCGGTCAAA		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.2422C>T	17.37:g.42328846G>A	ENSP00000262418:p.Arg808Cys	133	0	0		138	47	0.34058	NM_000342	G4V2I6|P78487|Q1ZZ45|Q4KKW9|Q4VB84|Q9UCY7|Q9UDJ1	Missense_Mutation	SNP	ENST00000262418.6	37	CCDS11481.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.454721	0.84209	.	.	ENSG00000004939	ENST00000262418	D	0.86694	-2.16	5.22	5.22	0.72569	Bicarbonate transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.96200	0.8761	H	0.97564	4.03	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97607	1.0127	10	0.87932	D	0	.	18.7637	0.91864	0.0:0.0:1.0:0.0	.	808	P02730	B3AT_HUMAN	C	808	ENSP00000262418:R808C	ENSP00000262418:R808C	R	-	1	0	SLC4A1	39684372	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.507000	0.81676	2.579000	0.87056	0.561000	0.74099	CGC	.	.	none		0.587	SLC4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346194.1	NM_000342		A	42328846	G	A	42328846	3	1	25	1	0	0	0	0	1	0	0	0	14665	1116	39	1	325	1	SLC4A1	17	42328846	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2016497	42328846	38866364	670	9579											
GPATCH8	23131	hgsc.bcm.edu	37	chr17	42475670	42475670	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacagggcctggctgactgcTgctatccagggactccaggg	7	7	14	13	0	0	1	0	1	0	0	2	2	2	2	3	4	2	3	3	4	1	1	rs760339	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:42475670T>C	ENST00000591680.1	-	8	3805	c.3775A>G	c.(3775-3777)Agc>Ggc	p.S1259G	GPATCH8_ENST00000434000.1_Missense_Mutation_p.S1181G	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	1259			S -> G (in dbSNP:rs760339). {ECO:0000269|PubMed:10477733}.				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)		GGCTGACTGCTGCTATCCAGG	0.582													T|||	21	0.00419329	0.0	0.0043	5008	,	,		18567	0.0		0.003	False		,,,				2504	0.0153				p.S1259G		Atlas-SNP	.											.	GPATCH8	114	.	0			c.A3775G						PASS	.	T	GLY/SER	0,4406		0,0,2203	126	124	125		3775	-1.1	0.8	17	dbSNP_86	125	32,8568	22.2+/-67.0	0,32,4268	yes	missense	GPATCH8	NM_001002909.2	56	0,32,6471	CC,CT,TT		0.3721,0.0,0.246	benign	1259/1503	42475670	32,12974	2203	4300	6503	SO:0001583	missense	23131	exon8			GACTGCTGCTATC	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.3775A>G	17.37:g.42475670T>C	ENSP00000467556:p.Ser1259Gly	49	0	0		47	24	0.510638	NM_001002909	B9EGP9|O60300|Q8TB99	Missense_Mutation	SNP	ENST00000591680.1	37	CCDS32666.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	T	0.003	-2.450966	0.00175	0.0	0.003721	ENSG00000186566	ENST00000335500;ENST00000434000	T	0.11169	2.8	4.76	-1.12	0.09808	.	0.595775	0.18361	N	0.143579	T	0.02012	0.0063	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45131	-0.9282	10	0.06365	T	0.9	-4.6956	9.4564	0.38758	0.0:0.6109:0.0:0.3891	rs760339;rs760339	1259	Q9UKJ3	GPTC8_HUMAN	G	1259;1181	ENSP00000395016:S1181G	ENSP00000335486:S1259G	S	-	1	0	GPATCH8	39831196	0.060000	0.20803	0.835000	0.33067	0.534000	0.34807	0.338000	0.19858	-0.063000	0.13065	-0.479000	0.04858	AGC	T|0.997;C|0.003	0.003	strong		0.582	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457797.1	NM_001002909		C	42475670	T	C	42475670	3	2	25	1	0	0	0	0	1	0	0	0	6602	1580	55	3	737	3	GPATCH8	17	42475670	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	146824	42475670	38719540	671	9580											
ZNF652	22834	hgsc.bcm.edu	37	chr17	47394516	47394516	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagaggcagctctcctggttCtcctttgtgtaacgctgact	6	13	10	12	1	2	2	0	1	2	1	4	2	2	2	2	2	2	5	2	2	1	3	rs368716483		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:47394516C>T	ENST00000362063.2	-	2	890	c.572G>A	c.(571-573)aGa>aAa	p.R191K	ZNF652_ENST00000430262.2_Missense_Mutation_p.R191K	NM_014897.2	NP_055712.1	Q9Y2D9	ZN652_HUMAN	zinc finger protein 652	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)			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)			TCTCCTGGTTCTCCTTTGTGT	0.483																																					p.R191K		Atlas-SNP	.											.	ZNF652	54	.	0			c.G572A						PASS	.	C	LYS/ARG,LYS/ARG	0,4406		0,0,2203	91	95	93		572,572	5.2	1	17		93	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ZNF652	NM_001145365.1,NM_014897.2	26,26	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	191/607,191/607	47394516	1,13005	2203	4300	6503	SO:0001583	missense	22834	exon2			CTGGTTCTCCTTT	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.572G>A	17.37:g.47394516C>T	ENSP00000354686:p.Arg191Lys	162	0	0		188	93	0.494681	NM_001145365	A4QPD9|Q5H9Q0	Missense_Mutation	SNP	ENST00000362063.2	37	CCDS32677.1	.	.	.	.	.	.	.	.	.	.	C	14.71	2.616802	0.46736	0.0	1.16E-4	ENSG00000198740	ENST00000362063;ENST00000430262	T;T	0.07444	3.19;3.19	5.22	5.22	0.72569	.	0.213072	0.50627	D	0.000118	T	0.05777	0.0151	N	0.14661	0.345	0.42015	D	0.990951	B	0.20261	0.043	B	0.22601	0.04	T	0.13872	-1.0493	10	0.02654	T	1	-12.121	18.5632	0.91108	0.0:1.0:0.0:0.0	.	191	Q9Y2D9	ZN652_HUMAN	K	191	ENSP00000354686:R191K;ENSP00000416305:R191K	ENSP00000354686:R191K	R	-	2	0	ZNF652	44749515	1.000000	0.71417	0.969000	0.41365	0.980000	0.70556	3.567000	0.53813	2.715000	0.92844	0.655000	0.94253	AGA	.	.	weak		0.483	ZNF652-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364524.1	NM_014897		T	47394516	C	T	47394516	3	4	25	1	0	0	0	0	1	0	0	0	18080	913	32	2	1268	2	ZNF652	17	47394516	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	4918846	47394516	33800694	672	9581											
ITGA3	3675	hgsc.bcm.edu	37	chr17	48151296	48151296	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagatattgctgtgggagcTccgtttgaaggcttgggcaa	8	11	15	7	1	0	2	0	1	0	1	1	3	1	3	1	3	2	6	1	3	3	4	rs117783166	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:48151296T>C	ENST00000320031.8	+	8	1503	c.1173T>C	c.(1171-1173)gcT>gcC	p.A391A	ITGA3_ENST00000544892.1_Silent_p.A166A|ITGA3_ENST00000007722.7_Silent_p.A391A	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)	391					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						CTGTGGGAGCTCCGTTTGAAG	0.557													T|||	10	0.00199681	0.0	0.0014	5008	,	,		17926	0.0		0.0089	False		,,,				2504	0.0				p.A391A		Atlas-SNP	.											.	ITGA3	128	.	0			c.T1173C						PASS	.	T	,	1,4405	2.1+/-5.4	0,1,2202	120	115	117		1173,1173	-3.8	0.9	17	dbSNP_133	117	44,8556	29.0+/-79.6	0,44,4256	no	coding-synonymous,coding-synonymous	ITGA3	NM_002204.2,NM_005501.2	,	0,45,6458	CC,CT,TT		0.5116,0.0227,0.346	,	391/1052,391/1067	48151296	45,12961	2203	4300	6503	SO:0001819	synonymous_variant	3675	exon8			GGGAGCTCCGTTT	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.1173T>C	17.37:g.48151296T>C		78	0	0		62	20	0.322581	NM_005501	A7E246|B7ZM80|B9EGQ1|D3DTX4|D3DTX5	Silent	SNP	ENST00000320031.8	37	CCDS11558.1																																																																																			T|0.997;C|0.003	0.003	strong		0.557	ITGA3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000366298.1	NM_005501		C	48151296	T	C	48151296	2	2	25	1	0	0	0	0	0	0	0	1	7886	1538	54	3		3	ITGA3	17	48151296	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	756780	48151296	33043914	673	9582											
WFIKKN2	124857	hgsc.bcm.edu	37	chr17	48918275	48918275	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcatggccatgctgcgcccCgatagctttgtgggcgcatc	5	9	14	13	3	0	0	0	0	0	0	1	1	0	0	3	3	3	4	3	3	1	2	rs139049586	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:48918275C>T	ENST00000311378.4	+	2	2154	c.1626C>T	c.(1624-1626)ccC>ccT	p.P542P	RP11-506D12.5_ENST00000572491.2_RNA|WFIKKN2_ENST00000426127.1_Silent_p.P449P	NM_175575.5	NP_783165.1	Q8TEU8	WFKN2_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	542	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				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)			TGCTGCGCCCCGATAGCTTTG	0.622													C|||	12	0.00239617	0.0008	0.0115	5008	,	,		16132	0.0		0.002	False		,,,				2504	0.001				p.P542P		Atlas-SNP	.											WFIKKN2,colon,carcinoma,0,1	WFIKKN2	69	1	0			c.C1626T						scavenged	.	C		3,4403	2.1+/-5.4	0,3,2200	50	42	45		1626	-10.2	0.2	17	dbSNP_134	45	42,8558	27.4+/-76.7	0,42,4258	no	coding-synonymous	WFIKKN2	NM_175575.5		0,45,6458	TT,TC,CC		0.4884,0.0681,0.346		542/577	48918275	45,12961	2203	4300	6503	SO:0001819	synonymous_variant	124857	exon2			GCGCCCCGATAGC	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.1626C>T	17.37:g.48918275C>T		139	1	0.00719424		116	56	0.482759	NM_175575	Q6UXZ9	Silent	SNP	ENST00000311378.4	37	CCDS11575.1																																																																																			C|0.997;T|0.003	0.003	strong		0.622	WFIKKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368358.1	NM_175575		T	48918275	C	T	48918275	2	4	25	1	0	0	0	0	0	0	0	1	17374	639	23	1		1	WFIKKN2	17	48918275	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	766979	48918275	32276935	674	9583											
FTSJ3	11325	hgsc.bcm.edu	37	chr17	61898928	61898928	+	IGR	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgctgccgtcccttccgccGgttctcaaataacagctggg	6	10	10	15	3	1	0	1	0	1	0	4	0	3	0	4	2	4	3	4	2	2	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:61898928G>A	ENST00000578681.1	+	0	4337				FTSJ3_ENST00000427159.2_Missense_Mutation_p.R558W	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						CCCTTCCGCCGGTTCTCAAAT	0.567																																					p.R558W		Atlas-SNP	.											FTSJ3,NS,carcinoma,0,1	FTSJ3	63	1	0			c.C1672T						PASS	.						56	59	58					17																	61898928		2203	4300	6503	SO:0001628	intergenic_variant	117246	exon16			TCCGCCGGTTCTC	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			17.37:g.61898928G>A		55	0	0		41	26	0.634146	NM_017647	A6NML1|A8KA43|O75619|Q68G51|Q96BK1|Q96HR7|Q9Y3V8	Missense_Mutation	SNP	ENST00000578681.1	37	CCDS32704.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.994511	0.74703	.	.	ENSG00000108592	ENST00000427159	T	0.34275	1.37	5.17	5.17	0.71159	.	0.410282	0.25651	N	0.029207	T	0.37652	0.1011	N	0.22421	0.69	0.39415	D	0.966828	D	0.69078	0.997	P	0.53490	0.727	T	0.29941	-0.9995	10	0.72032	D	0.01	-4.4553	14.0344	0.64636	0.0:0.0:1.0:0.0	.	558	Q8IY81	RRMJ3_HUMAN	W	558	ENSP00000396673:R558W	ENSP00000396673:R558W	R	-	1	2	FTSJ3	59252660	0.045000	0.20229	0.773000	0.31616	0.045000	0.14185	2.138000	0.42140	2.688000	0.91661	0.563000	0.77884	CGG	.	.	none		0.567	DDX42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444368.1	NM_007372		A	61898928	G	A	61898928	1	1	25	0	1	0	0	0	0	0	0	0	6097	1115	39	1		1	FTSJ3	17	61898928	IGR	SNP	G	TCGA-G8-6906-01A-11D-2210-10	12980653	61898928	19296282	675	9584											
SMURF2	64750	hgsc.bcm.edu	37	chr17	62587204	62587204	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttaaattccacacttacctActatctgtcctctaactgta	11	16	2	12	0	2	0	0	0	2	0	4	0	4	0	3	0	3	1	3	0	7	8			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:62587204A>G	ENST00000262435.9	-	5	585	c.398T>C	c.(397-399)gTa>gCa	p.V133A	SMURF2_ENST00000578200.1_Intron	NM_022739.3	NP_073576.1	Q9HAU4	SMUF2_HUMAN	SMAD specific E3 ubiquitin protein ligase 2	133					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)			ACACTTACCTACTATCTGTCC	0.318																																					p.V133A		Atlas-SNP	.											.	SMURF2	63	.	0			c.T398C						PASS	.						130	116	121					17																	62587204		2203	4299	6502	SO:0001583	missense	64750	exon5			TTACCTACTATCT	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.398T>C	17.37:g.62587204A>G	ENSP00000262435:p.Val133Ala	120	0	0		101	5	0.049505	NM_022739	Q52LL1|Q9H260	Missense_Mutation	SNP	ENST00000262435.9	37	CCDS32707.1	.	.	.	.	.	.	.	.	.	.	A	15.64	2.892338	0.52121	.	.	ENSG00000108854	ENST00000262435	T	0.67171	-0.25	5.41	5.41	0.78517	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.78477	0.4289	M	0.68593	2.085	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.74509	-0.3642	10	0.14656	T	0.56	.	15.7378	0.77859	1.0:0.0:0.0:0.0	.	133	Q9HAU4	SMUF2_HUMAN	A	133	ENSP00000262435:V133A	ENSP00000262435:V133A	V	-	2	0	SMURF2	60017666	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.971000	0.93419	2.184000	0.69523	0.477000	0.44152	GTA	.	.	none		0.318	SMURF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445227.1	NM_022739		G	62587204	A	G	62587204	3	3	25	1	0	0	0	0	1	0	0	0	14835	391	14	3	1908	3	SMURF2	17	62587204	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	688276	62587204	18608006	676	9585											
HELZ	9931	hgsc.bcm.edu	37	chr17	65103373	65103373	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caatagcatgttgatgattcTgtatttgtacaaaagggttc	12	15	9	5	0	1	2	0	2	1	0	2	2	1	2	0	1	2	5	0	1	6	7			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:65103373T>C	ENST00000358691.5	-	31	5319	c.5153A>G	c.(5152-5154)cAg>cGg	p.Q1718R	HELZ_ENST00000580168.1_Missense_Mutation_p.Q1719R	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	1718						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)					TTGATGATTCTGTATTTGTAC	0.453																																					p.Q1718R		Atlas-SNP	.											.	HELZ	160	.	0			c.A5153G						PASS	.						185	192	190					17																	65103373		1974	4156	6130	SO:0001583	missense	9931	exon31			TGATTCTGTATTT	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.5153A>G	17.37:g.65103373T>C	ENSP00000351524:p.Gln1718Arg	306	0	0		315	147	0.466667	NM_014877	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	37	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	T	12.03	1.815470	0.32145	.	.	ENSG00000198265	ENST00000358691	D	0.88201	-2.35	5.31	4.2	0.49525	.	0.067201	0.64402	D	0.000013	T	0.80909	0.4714	L	0.29908	0.895	0.44048	D	0.996786	P;P	0.37466	0.596;0.596	B;B	0.29785	0.107;0.107	T	0.79995	-0.1568	10	0.87932	D	0	-4.8142	12.192	0.54277	0.0:0.0:0.1429:0.8571	.	1719;1718	B7ZLW2;P42694	.;HELZ_HUMAN	R	1718	ENSP00000351524:Q1718R	ENSP00000351524:Q1718R	Q	-	2	0	HELZ	62533835	1.000000	0.71417	0.982000	0.44146	0.993000	0.82548	2.537000	0.45702	0.827000	0.34685	0.472000	0.43445	CAG	.	.	none		0.453	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877		C	65103373	T	C	65103373	3	2	25	1	0	0	0	0	1	0	0	0	7058	1580	55	3	687	3	HELZ	17	65103373	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	2516169	65103373	16091837	677	9586											
KCNJ16	3773	hgsc.bcm.edu	37	chr17	68128417	68128417	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tatgtggttgacatcttcacCactcttgtggacaccaagtg	9	13	9	10	0	3	1	1	1	2	0	3	2	3	2	2	2	0	1	2	2	2	4	rs34408089	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:68128417C>T	ENST00000589377.1	+	2	352	c.189C>T	c.(187-189)acC>acT	p.T63T	KCNJ16_ENST00000392671.1_Silent_p.T63T|KCNJ16_ENST00000392670.1_Silent_p.T63T|KCNJ16_ENST00000585558.1_Silent_p.T98T|KCNJ16_ENST00000586462.1_Silent_p.T102T|KCNJ16_ENST00000283936.1_Silent_p.T63T	NM_001270422.1	NP_001257351.1	Q9NPI9	KCJ16_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 16	63					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)			breast(3)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	32	Breast(10;2.96e-09)					ACATCTTCACCACTCTTGTGG	0.413													C|||	84	0.0167732	0.0159	0.0115	5008	,	,		21473	0.0		0.0288	False		,,,				2504	0.0266				p.T63T		Atlas-SNP	.											.	KCNJ16	72	.	0			c.C189T						PASS	.	C	,,	73,4333	65.3+/-102.7	1,71,2131	283	249	261		189,189,189	3.1	1	17	dbSNP_126	261	220,8380	92.6+/-154.6	2,216,4082	no	coding-synonymous,coding-synonymous,coding-synonymous	KCNJ16	NM_018658.1,NM_170741.1,NM_170742.1	,,	3,287,6213	TT,TC,CC		2.5581,1.6568,2.2528	,,	63/419,63/419,63/419	68128417	293,12713	2203	4300	6503	SO:0001819	synonymous_variant	3773	exon6			CTTCACCACTCTT	AF153815	CCDS11687.1, CCDS74141.1	17q24.3	2011-07-05				ENSG00000153822		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6262	protein-coding gene	gene with protein product		605722				11240146, 16382105	Standard	NM_018658		Approved	Kir5.1, BIR9	uc002jio.4	Q9NPI9		ENST00000589377.1:c.189C>T	17.37:g.68128417C>T		149	0	0		137	69	0.50365	NM_001270422		Silent	SNP	ENST00000589377.1	37	CCDS11687.1																																																																																			C|0.976;T|0.024	0.024	strong		0.413	KCNJ16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450880.1	NM_018658		T	68128417	C	T	68128417	2	4	25	1	0	0	0	0	0	0	0	1	8059	581	21	2		2	KCNJ16	17	68128417	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	3025044	68128417	13066793	678	9587											
OTOP3	347741	hgsc.bcm.edu	37	chr17	72943184	72943184	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acacggtcaagaaccctaccCgcagcctggatgtggtgctg	9	7	12	13	2	1	1	1	0	0	1	1	2	1	2	3	3	4	2	3	3	3	1	rs142183564	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:72943184C>T	ENST00000328801.4	+	6	1234	c.1234C>T	c.(1234-1236)Cgc>Tgc	p.R412C		NM_178233.1	NP_839947.1	Q7RTS5	OTOP3_HUMAN	otopetrin 3	412						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)					GAACCCTACCCGCAGCCTGGA	0.622																																					p.R412C		Atlas-SNP	.											.	OTOP3	64	.	0			c.C1234T						PASS	.	C	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	94	92	93		1234	4.5	1	17	dbSNP_134	93	4,8596	3.7+/-12.6	0,4,4296	yes	missense	OTOP3	NM_178233.1	180	0,5,6498	TT,TC,CC		0.0465,0.0227,0.0384	probably-damaging	412/597	72943184	5,13001	2203	4300	6503	SO:0001583	missense	347741	exon6			CCTACCCGCAGCC	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.1234C>T	17.37:g.72943184C>T	ENSP00000328090:p.Arg412Cys	66	0	0		83	42	0.506024	NM_178233		Missense_Mutation	SNP	ENST00000328801.4	37	CCDS11709.1	.	.	.	.	.	.	.	.	.	.	C	17.93	3.508979	0.64410	2.27E-4	4.65E-4	ENSG00000182938	ENST00000328801	T	0.22743	1.94	4.54	4.54	0.55810	.	0.000000	0.64402	D	0.000001	T	0.52208	0.1720	M	0.86028	2.79	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.62793	-0.6779	10	0.87932	D	0	-16.6297	17.2793	0.87124	0.0:1.0:0.0:0.0	.	412	Q7RTS5	OTOP3_HUMAN	C	412	ENSP00000328090:R412C	ENSP00000328090:R412C	R	+	1	0	OTOP3	70454779	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	4.414000	0.59802	2.073000	0.62155	0.462000	0.41574	CGC	C|0.999;T|0.001	0.001	strong		0.622	OTOP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445308.1	NM_178233		T	72943184	C	T	72943184	3	4	25	1	0	0	0	0	1	0	0	0	11316	652	23	1	1256	1	OTOP3	17	72943184	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	4814767	72943184	8252026	679	9588											
KCTD2	23510	hgsc.bcm.edu	37	chr17	73058249	73058249	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atcttcctataactacggcaAtgaggatcaggcagaattcc	13	10	8	10	1	2	2	1	1	1	1	4	3	4	3	2	3	2	2	2	3	5	5	rs61750318	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:73058249A>G	ENST00000322444.6	+	5	677	c.671A>G	c.(670-672)aAt>aGt	p.N224S	KCTD2_ENST00000581589.1_Missense_Mutation_p.N25S	NM_015353.1	NP_056168.1	Q14681	KCTD2_HUMAN	potassium channel tetramerization domain containing 2	224					protein homooligomerization (GO:0051260)		protein complex binding (GO:0032403)			kidney(1)|lung(2)	3	all_lung(278;0.226)					AACTACGGCAATGAGGATCAG	0.438													A|||	4	0.000798722	0.0	0.0014	5008	,	,		20398	0.001		0.002	False		,,,				2504	0.0				p.N224S		Atlas-SNP	.											.	KCTD2	15	.	0			c.A671G						PASS	.	A	SER/ASN	1,4405	2.1+/-5.4	0,1,2202	147	130	135		671	4.5	1	17	dbSNP_129	135	3,8597	3.0+/-9.4	0,3,4297	yes	missense	KCTD2	NM_015353.1	46	0,4,6499	GG,GA,AA		0.0349,0.0227,0.0308	benign	224/264	73058249	4,13002	2203	4300	6503	SO:0001583	missense	23510	exon5			ACGGCAATGAGGA	BC033329	CCDS32728.1	17q25.2	2013-06-20	2013-06-20			ENSG00000180901			21294	protein-coding gene	gene with protein product		613422	"potassium channel tetramerisation domain containing 2"			12620391	Standard	XR_248405		Approved	KIAA0176	uc002jmp.3	Q14681		ENST00000322444.6:c.671A>G	17.37:g.73058249A>G	ENSP00000312814:p.Asn224Ser	195	0	0		239	95	0.39749	NM_015353		Missense_Mutation	SNP	ENST00000322444.6	37	CCDS32728.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	A	12.24	1.879309	0.33162	2.27E-4	3.49E-4	ENSG00000180901	ENST00000322444;ENST00000375286	T	0.75821	-0.97	5.55	4.48	0.54585	.	0.045672	0.85682	D	0.000000	T	0.55130	0.1901	N	0.16743	0.435	0.52501	D	0.999952	B	0.10296	0.003	B	0.06405	0.002	T	0.50311	-0.8843	10	0.14656	T	0.56	-8.6415	10.8859	0.46965	0.9267:0.0:0.0733:0.0	rs61750318	224	Q14681	KCTD2_HUMAN	S	224;206	ENSP00000312814:N224S	ENSP00000312814:N224S	N	+	2	0	KCTD2	70569844	1.000000	0.71417	0.994000	0.49952	0.986000	0.74619	6.366000	0.73095	2.110000	0.64415	0.460000	0.39030	AAT	A|0.999;G|0.001	0.001	strong		0.438	KCTD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445538.1			G	73058249	A	G	73058249	3	3	25	1	0	0	0	0	1	0	0	0	8116	101	4	3	689	3	KCTD2	17	73058249	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	115065	73058249	8136961	680	9589											
ITGB4	3691	hgsc.bcm.edu	37	chr17	73729660	73729660	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacaagccgtgctccggccGtggggagtgccagtgcgggc	5	5	19	12	4	0	0	0	0	0	0	1	2	1	2	4	5	4	1	4	5	1	0	rs61735297	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:73729660G>A	ENST00000200181.3	+	13	1731	c.1544G>A	c.(1543-1545)cGt>cAt	p.R515H	ITGB4_ENST00000584558.1_3'UTR|ITGB4_ENST00000450894.3_Missense_Mutation_p.R515H|ITGB4_ENST00000579662.1_Missense_Mutation_p.R515H|ITGB4_ENST00000339591.3_Missense_Mutation_p.R515H|ITGB4_ENST00000449880.2_Missense_Mutation_p.R515H	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	515	Cysteine-rich tandem repeats.				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)			TGCTCCGGCCGTGGGGAGTGC	0.647													G|||	27	0.00539137	0.0008	0.0115	5008	,	,		13114	0.001		0.0129	False		,,,				2504	0.0041				p.R515H		Atlas-SNP	.											ITGB4,caecum,carcinoma,0,1	ITGB4	165	1	0			c.G1544A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG	15,4391	22.3+/-47.3	0,15,2188	69	59	62		1544,1544,1544	-0.9	0	17	dbSNP_129	62	163,8437	76.6+/-139.3	0,163,4137	yes	missense,missense,missense	ITGB4	NM_000213.3,NM_001005619.1,NM_001005731.1	29,29,29	0,178,6325	AA,AG,GG		1.8953,0.3404,1.3686	benign,benign,benign	515/1823,515/1806,515/1753	73729660	178,12828	2203	4300	6503	SO:0001583	missense	3691	exon13			CCGGCCGTGGGGA		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.1544G>A	17.37:g.73729660G>A	ENSP00000200181:p.Arg515His	36	0	0		53	23	0.433962	NM_001005731	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Missense_Mutation	SNP	ENST00000200181.3	37	CCDS11727.1	16	0.007326007326007326	1	0.0020325203252032522	7	0.019337016574585635	1	0.0017482517482517483	7	0.009234828496042216	G	9.385	1.074039	0.20147	0.003404	0.018953	ENSG00000132470	ENST00000450894;ENST00000200181;ENST00000339591;ENST00000449880	D;D;D	0.97688	-4.49;-4.49;-4.49	4.78	-0.858	0.10689	.	0.072851	0.53938	N	0.000050	D	0.88764	0.6525	L	0.38531	1.155	0.42452	D	0.992753	B;B;B;B;B	0.31485	0.303;0.325;0.015;0.031;0.031	B;B;B;B;B	0.26770	0.058;0.073;0.021;0.016;0.009	T	0.82532	-0.0410	10	0.45353	T	0.12	.	9.7846	0.40668	0.4551:0.0:0.5449:0.0	rs61735297	475;515;515;515;515	B4E3N0;P16144-5;P16144-3;A0AVL6;P16144	.;.;.;.;ITB4_HUMAN	H	431;515;515;515	ENSP00000200181:R515H;ENSP00000344079:R515H;ENSP00000400217:R515H	ENSP00000200181:R515H	R	+	2	0	ITGB4	71241255	0.974000	0.33945	0.025000	0.17156	0.421000	0.31385	2.990000	0.49401	-0.424000	0.07382	-0.263000	0.10527	CGT	G|0.988;A|0.012	0.012	strong		0.647	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			A	73729660	G	A	73729660	3	1	25	1	0	0	0	0	1	0	0	0	7906	1145	40	1	1590	1	ITGB4	17	73729660	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	671411	73729660	7465550	681	9590											
EVPL	2125	hgsc.bcm.edu	37	chr17	74006317	74006317	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgccacttccaggtctgccTgcaggccagcccgccgcttg	4	8	11	18	2	1	0	0	0	1	0	2	0	2	0	6	2	4	2	6	2	0	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:74006317T>C	ENST00000301607.3	-	22	3222	c.2969A>G	c.(2968-2970)cAg>cGg	p.Q990R	EVPL_ENST00000586740.1_Missense_Mutation_p.Q1012R	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	990	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						CAGGTCTGCCTGCAGGCCAGC	0.637																																					p.Q990R		Atlas-SNP	.											.	EVPL	155	.	0			c.A2969G						PASS	.						39	43	42					17																	74006317		2203	4300	6503	SO:0001583	missense	2125	exon22			TCTGCCTGCAGGC	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.2969A>G	17.37:g.74006317T>C	ENSP00000301607:p.Gln990Arg	105	0	0		101	54	0.534653	NM_001988	A0AUV5	Missense_Mutation	SNP	ENST00000301607.3	37	CCDS11737.1	.	.	.	.	.	.	.	.	.	.	T	12.10	1.836978	0.32421	.	.	ENSG00000167880	ENST00000301607	T	0.66815	-0.23	4.72	3.63	0.41609	.	0.198103	0.44285	D	0.000466	T	0.56877	0.2015	L	0.53780	1.695	0.33077	D	0.536119	B;B	0.16396	0.017;0.013	B;B	0.16289	0.015;0.005	T	0.64728	-0.6339	10	0.66056	D	0.02	-42.4684	5.9853	0.19430	0.1469:0.081:0.0:0.772	.	1012;990	B7ZLH8;Q92817	.;EVPL_HUMAN	R	990	ENSP00000301607:Q990R	ENSP00000301607:Q990R	Q	-	2	0	EVPL	71517912	1.000000	0.71417	1.000000	0.80357	0.713000	0.41058	5.028000	0.64115	1.887000	0.54652	0.402000	0.26972	CAG	.	.	none		0.637	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988		C	74006317	T	C	74006317	3	2	25	1	0	0	0	0	1	0	0	0	5294	1580	55	3	3136	3	EVPL	17	74006317	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	276657	74006317	7188893	682	9591											
DNAH17	8632	hgsc.bcm.edu	37	chr17	76567708	76567708	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgaggttcagcagccgagtGtcccagaactcgaactccac	10	8	10	13	2	1	2	1	1	0	1	4	4	3	2	3	1	4	2	3	1	2	2	rs555197985	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:76567708G>A	ENST00000585328.1	-	4	820	c.696C>T	c.(694-696)gaC>gaT	p.D232D	DNAH17_ENST00000389840.5_Silent_p.D232D	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	232	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)			GCAGCCGAGTGTCCCAGAACT	0.642													G|||	2	0.000399361	0.0008	0.0014	5008	,	,		17482	0.0		0.0	False		,,,				2504	0.0				p.D232D		Atlas-SNP	.											.	DNAH17	347	.	0			c.C696T						PASS	.						60	66	64					17																	76567708		2030	4179	6209	SO:0001819	synonymous_variant	8632	exon4			CCGAGTGTCCCAG	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.696C>T	17.37:g.76567708G>A		111	0	0		143	73	0.51049	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				.	.	none		0.642	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		A	76567708	G	A	76567708	2	1	25	1	0	0	0	0	0	0	0	1	4603	1368	48	2		2	DNAH17	17	76567708	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2561391	76567708	4627502	683	9592											
LGALS3BP	3959	hgsc.bcm.edu	37	chr17	76970803	76970803	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacaccagcgtctctctcgtGcctgcagttgctcttcagcc	5	11	8	17	2	4	0	1	0	3	0	6	0	4	0	3	0	5	3	3	0	0	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:76970803G>A	ENST00000262776.3	-	4	651	c.343C>T	c.(343-345)Cac>Tac	p.H115Y	LGALS3BP_ENST00000585407.1_Missense_Mutation_p.H115Y|LGALS3BP_ENST00000591778.1_Missense_Mutation_p.H115Y	NM_005567.3	NP_005558.1	Q08380	LG3BP_HUMAN	lectin, galactoside-binding, soluble, 3 binding protein	115	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				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)			TCTCTCTCGTGCCTGCAGTTG	0.677																																					p.H115Y	GBM(89;1105 1755 18102 21513)	Atlas-SNP	.											.	LGALS3BP	47	.	0			c.C343T						PASS	.						76	56	63					17																	76970803		2203	4300	6503	SO:0001583	missense	3959	exon4			TCTCGTGCCTGCA	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.343C>T	17.37:g.76970803G>A	ENSP00000262776:p.His115Tyr	126	0	0		117	46	0.393162	NM_005567	Q7M4S0|Q9UCH8|Q9UCH9|Q9UCI0	Missense_Mutation	SNP	ENST00000262776.3	37	CCDS11759.1	.	.	.	.	.	.	.	.	.	.	G	15.15	2.748237	0.49257	.	.	ENSG00000108679	ENST00000262776;ENST00000536190	T	0.34072	1.38	3.22	3.22	0.36961	Speract/scavenger receptor (3);Speract/scavenger receptor-related (2);	0.000000	0.35615	N	0.003090	T	0.67420	0.2891	H	0.95114	3.625	0.41107	D	0.985716	D	0.89917	1.0	D	0.91635	0.999	T	0.75961	-0.3133	10	0.87932	D	0	-44.0802	10.1799	0.42961	0.0:0.0:1.0:0.0	.	115	Q08380	LG3BP_HUMAN	Y	115;103	ENSP00000262776:H115Y	ENSP00000262776:H115Y	H	-	1	0	LGALS3BP	74482398	1.000000	0.71417	0.034000	0.17996	0.284000	0.27059	8.854000	0.92228	2.091000	0.63221	0.313000	0.20887	CAC	.	.	none		0.677	LGALS3BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437785.3	NM_005567		A	76970803	G	A	76970803	3	1	25	1	0	0	0	0	1	0	0	0	8753	1319	46	2	1426	2	LGALS3BP	17	76970803	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	403095	76970803	4224407	684	9593											
HGS	9146	hgsc.bcm.edu	37	chr17	79658569	79658569	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcatcgagaaggaggtgcgCgtgtgtgagccctgctacga	8	7	17	9	4	0	2	0	1	0	1	1	5	0	3	1	3	4	2	1	3	2	1	rs148002494	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79658569C>T	ENST00000329138.4	+	8	765	c.630C>T	c.(628-630)cgC>cgT	p.R210R		NM_004712.4	NP_004703.1	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine kinase substrate	210					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)			AGGAGGTGCGCGTGTGTGAGC	0.592																																					p.R210R		Atlas-SNP	.											.	HGS	54	.	0			c.C630T						PASS	.	C		0,4406		0,0,2203	141	120	127		630	-3.2	1	17	dbSNP_134	127	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	HGS	NM_004712.4		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		210/778	79658569	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	9146	exon8			GGTGCGCGTGTGT	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.630C>T	17.37:g.79658569C>T		110	0	0		120	58	0.483333	NM_004712	Q9NR36	Silent	SNP	ENST00000329138.4	37	CCDS11784.1																																																																																			C|0.999;T|0.001	0.001	strong		0.592	HGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440541.1	NM_004712		T	79658569	C	T	79658569	2	4	25	1	0	0	0	0	0	0	0	1	7096	755	27	1		1	HGS	17	79658569	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2687766	79658569	1536641	685	9594											
ASPSCR1	79058	hgsc.bcm.edu	37	chr17	79941511	79941511	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaagctggagatggtgccCgcttcccggagccgtgaggg	6	6	17	12	3	0	2	0	1	0	1	1	4	1	3	4	4	3	2	4	4	1	1	rs11539917	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79941511C>T	ENST00000306739.4	+	3	337	c.240C>T	c.(238-240)ccC>ccT	p.P80P	ASPSCR1_ENST00000581647.1_Silent_p.P80P|ASPSCR1_ENST00000306729.7_Silent_p.P80P|ASPSCR1_ENST00000580534.1_Silent_p.P3P	NM_024083.3	NP_076988.1	Q9BZE9	ASPC1_HUMAN	alveolar soft part sarcoma chromosome region, candidate 1	80					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)			AGATGGTGCCCGCTTCCCGGA	0.622			T	TFE3	alveolar soft part sarcoma								C|||	63	0.0125799	0.0015	0.0231	5008	,	,		12243	0.0		0.0209	False		,,,				2504	0.0245				p.P80P		Atlas-SNP	.		Dom	yes		17	17q25	79058	"alveolar soft part sarcoma chromosome region, candidate 1"		M	ASPSCR1_ENST00000306729,colon,carcinoma,0,1	ASPSCR1	27	1	0			c.C240T						PASS	.	C		22,4384	29.0+/-57.7	0,22,2181	80	63	69		240	-8	0	17	dbSNP_120	69	162,8438	76.3+/-139.0	2,158,4140	no	coding-synonymous	ASPSCR1	NM_024083.2		2,180,6321	TT,TC,CC		1.8837,0.4993,1.4147		80/554	79941511	184,12822	2203	4300	6503	SO:0001819	synonymous_variant	79058	exon3			GGTGCCCGCTTCC	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.240C>T	17.37:g.79941511C>T		55	0	0		56	31	0.553571	NM_001251888	A8K3K9|Q7Z6N7|Q8WV59|Q96LS5|Q96M40	Silent	SNP	ENST00000306739.4	37	CCDS11796.1																																																																																			C|0.988;T|0.012	0.012	strong		0.622	ASPSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441972.1	NM_024083		T	79941511	C	T	79941511	2	4	25	1	0	0	0	0	0	0	0	1	1059	639	23	1		1	ASPSCR1	17	79941511	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	282942	79941511	1253699	686	9595											
FOXK2	3607	hgsc.bcm.edu	37	chr17	80543901	80543901	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcgacctcccagccacccgtCgtgcagacggttcacgtcgt	6	8	10	17	6	1	1	1	0	0	1	5	2	2	1	4	1	2	2	4	1	0	1	rs61737960	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:80543901C>T	ENST00000335255.5	+	7	1575	c.1401C>T	c.(1399-1401)gtC>gtT	p.V467V	RP13-638C3.3_ENST00000575085.1_RNA	NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	467					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)			AGCCACCCGTCGTGCAGACGG	0.627													C|||	58	0.0115815	0.0121	0.0202	5008	,	,		16342	0.0		0.0179	False		,,,				2504	0.0102				p.V467V		Atlas-SNP	.											.	FOXK2	46	.	0			c.C1401T						PASS	.	C		30,4370	37.6+/-69.7	0,30,2170	66	53	58		1401	-10.6	0	17	dbSNP_129	58	173,8413	79.2+/-141.9	2,169,4122	no	coding-synonymous	FOXK2	NM_004514.3		2,199,6292	TT,TC,CC		2.0149,0.6818,1.5632		467/661	80543901	203,12783	2200	4293	6493	SO:0001819	synonymous_variant	3607	exon7			ACCCGTCGTGCAG	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.1401C>T	17.37:g.80543901C>T		85	0	0		98	48	0.489796	NM_004514	A6NEP5|Q13622|Q13623|Q13624	Silent	SNP	ENST00000335255.5	37	CCDS11813.1																																																																																			C|0.986;T|0.014	0.014	strong		0.627	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430		T	80543901	C	T	80543901	2	4	25	1	0	0	0	0	0	0	0	1	6023	871	31	1		1	FOXK2	17	80543901	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	602390	80543901	651309	687	9596											
FOXK2	3607	hgsc.bcm.edu	37	chr17	80545021	80545021	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagacggcacagaccaccccGgtccagacggtgaccatagt	11	4	11	15	3	0	4	0	1	0	3	1	4	1	4	5	3	0	1	5	3	1	1	rs139592674		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:80545021G>A	ENST00000335255.5	+	8	1833	c.1659G>A	c.(1657-1659)ccG>ccA	p.P553P	RP13-638C3.3_ENST00000575085.1_RNA	NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	553					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)			AGACCACCCCGGTCCAGACGG	0.532																																					p.P553P		Atlas-SNP	.											.	FOXK2	46	.	0			c.G1659A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	100	83	89		1659	-4.4	0.7	17	dbSNP_134	89	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FOXK2	NM_004514.3		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		553/661	80545021	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	3607	exon8			CACCCCGGTCCAG	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.1659G>A	17.37:g.80545021G>A		126	0	0		125	69	0.552	NM_004514	A6NEP5|Q13622|Q13623|Q13624	Silent	SNP	ENST00000335255.5	37	CCDS11813.1																																																																																			G|1.000;A|0.000	0.000	weak		0.532	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430		A	80545021	G	A	80545021	2	1	25	1	0	0	0	0	0	0	0	1	6023	1103	39	1		1	FOXK2	17	80545021	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1120	80545021	650189	688	9597											
WDR45L	56270	hgsc.bcm.edu	37	chr17	80573888	80573888	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaatttgtagtagctgccGtctgcacaaattgctgggat	10	12	12	7	1	1	0	0	0	1	0	1	2	1	2	1	2	4	5	1	2	4	4	rs147083174	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:80573888G>A	ENST00000392325.4	-	10	1136	c.942C>T	c.(940-942)gaC>gaT	p.D314D	WDR45B_ENST00000571835.1_5'Flank	NM_019613.3	NP_062559.2	Q5MNZ6	WIPI3_HUMAN	WD repeat domain 45B	314																	AGTAGCTGCCGTCTGCACAAA	0.498													G|||	19	0.00379393	0.003	0.0072	5008	,	,		18962	0.0		0.0089	False		,,,				2504	0.001				p.D314D		Atlas-SNP	.											.	.	.	.	0			c.C942T						PASS	.	G		8,4398	12.9+/-30.5	0,8,2195	119	100	107		942	-2.3	0.9	17	dbSNP_134	107	74,8526	44.0+/-102.2	0,74,4226	yes	coding-synonymous	WDR45L	NM_019613.3		0,82,6421	AA,AG,GG		0.8605,0.1816,0.6305		314/345	80573888	82,12924	2203	4300	6503	SO:0001819	synonymous_variant	56270	exon10			GCTGCCGTCTGCA	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.942C>T	17.37:g.80573888G>A		23	0	0		53	24	0.45283	NM_019613	O95328|Q2MCP6|Q6IBN2	Silent	SNP	ENST00000392325.4	37	CCDS11815.2																																																																																			G|0.995;A|0.005	0.005	strong		0.498	WDR45B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316536.1	NM_019613		A	80573888	G	A	80573888	2	1	25	1	0	0	0	0	0	0	0	1	17313	1136	40	1		1	WDR45L	17	80573888	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	28867	80573888	621322	689	9598											
FN3KRP	79672	hgsc.bcm.edu	37	chr17	80676896	80676896	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccccaggcggcgggagcgtgCtggtgatggagcacatggac	7	5	18	11	3	0	1	0	1	0	0	0	4	0	4	2	6	3	2	2	6	0	0			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:80676896C>T	ENST00000269373.6	+	2	329	c.256C>T	c.(256-258)Ctg>Ttg	p.L86L	RP11-388C12.1_ENST00000574471.1_lincRNA|FN3KRP_ENST00000535965.1_Silent_p.L36L	NM_024619.3	NP_078895.2	Q9HA64	KT3K_HUMAN	fructosamine 3 kinase related protein	86							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)			CGGGAGCGTGCTGGTGATGGA	0.547																																					p.L86L		Atlas-SNP	.											.	FN3KRP	31	.	0			c.C256T						PASS	.						105	103	104					17																	80676896		2203	4300	6503	SO:0001819	synonymous_variant	79672	exon2			AGCGTGCTGGTGA	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.256C>T	17.37:g.80676896C>T		94	0	0		109	59	0.541284	NM_024619	Q969F4|Q9H0U7	Silent	SNP	ENST00000269373.6	37	CCDS11817.1																																																																																			.	.	none		0.547	FN3KRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439219.1	NM_024619		T	80676896	C	T	80676896	2	4	25	1	0	0	0	0	0	0	0	1	5972	796	28	2		2	FN3KRP	17	80676896	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	103008	80676896	518314	690	9599											
METTL4	64863	hgsc.bcm.edu	37	chr18	2554915	2554915	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aattctgacaaactgcaggcGtcaagtggtaaagtaatggg	14	9	12	6	1	2	1	1	1	1	0	2	1	2	1	0	3	2	3	0	3	6	3	rs61749937	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:2554915G>A	ENST00000574538.1	-	4	1357	c.582C>T	c.(580-582)gaC>gaT	p.D194D	METTL4_ENST00000319888.6_Silent_p.D194D|snoU109_ENST00000459316.1_RNA	NM_022840.3	NP_073751.3	Q8N3J2	METL4_HUMAN	methyltransferase like 4	194					nucleobase-containing compound metabolic process (GO:0006139)		methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	17						AACTGCAGGCGTCAAGTGGTA	0.393													G|||	75	0.014976	0.0318	0.0086	5008	,	,		20011	0.0		0.0239	False		,,,				2504	0.0031				p.D194D		Atlas-SNP	.											.	METTL4	40	.	0			c.C582T						PASS	.	G		124,4282	91.6+/-130.3	4,116,2083	120	113	115		582	2	0.5	18	dbSNP_129	115	95,8505	54.0+/-114.7	1,93,4206	no	coding-synonymous	METTL4	NM_022840.3		5,209,6289	AA,AG,GG		1.1047,2.8143,1.6838		194/473	2554915	219,12787	2203	4300	6503	SO:0001819	synonymous_variant	64863	exon4			GCAGGCGTCAAGT		CCDS11826.1	18p11.31	2008-02-05			ENSG00000101574	ENSG00000101574			24726	protein-coding gene	gene with protein product						12477932	Standard	NM_022840		Approved	FLJ23017, HsT661	uc002klh.4	Q8N3J2	OTTHUMG00000131482	ENST00000574538.1:c.582C>T	18.37:g.2554915G>A		201	0	0		172	71	0.412791	NM_022840	B2RNA1|Q2TAA7|Q9H5U9	Silent	SNP	ENST00000574538.1	37	CCDS11826.1																																																																																			G|0.984;A|0.016	0.016	strong		0.393	METTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254326.3	NM_022840		A	2554915	G	A	2554915	2	1	25	1	0	0	0	0	0	0	0	1	9511	1136	40	1		1	METTL4	18	2554915	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10		2554915	75522333	691	9600											
LAMA1	284217	hgsc.bcm.edu	37	chr18	6978233	6978233	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcagaagctggtgtgtctctCgtaatgtggtgttgaccctg	6	13	14	8	1	1	2	0	1	1	1	3	2	1	2	1	2	1	4	1	2	2	2	rs145781920	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:6978233C>T	ENST00000389658.3	-	43	6245	c.6152G>A	c.(6151-6153)cGa>cAa	p.R2051Q		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2051	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)				GTGTGTCTCTCGTAATGTGGT	0.602													C|||	2	0.000399361	0.0	0.0	5008	,	,		17990	0.0		0.002	False		,,,				2504	0.0				p.R2051Q		Atlas-SNP	.											.	LAMA1	458	.	0			c.G6152A						PASS	.	C	GLN/ARG	0,4406		0,0,2203	231	199	210		6152	-10.1	0	18	dbSNP_134	210	10,8590	7.1+/-27.0	0,10,4290	yes	missense	LAMA1	NM_005559.3	43	0,10,6493	TT,TC,CC		0.1163,0.0,0.0769	benign	2051/3076	6978233	10,12996	2203	4300	6503	SO:0001583	missense	284217	exon43			GTCTCTCGTAATG	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.6152G>A	18.37:g.6978233C>T	ENSP00000374309:p.Arg2051Gln	179	0	0		174	85	0.488506	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	6.111	0.388642	0.11581	0.0	0.001163	ENSG00000101680	ENST00000389658	T	0.40756	1.02	5.64	-10.1	0.00402	Laminin II (1);	0.727738	0.12726	N	0.444249	T	0.14184	0.0343	N	0.03253	-0.375	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.35649	-0.9780	10	0.10902	T	0.67	.	14.4677	0.67494	0.0841:0.5919:0.0:0.324	.	2051	P25391	LAMA1_HUMAN	Q	2051	ENSP00000374309:R2051Q	ENSP00000374309:R2051Q	R	-	2	0	LAMA1	6968233	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.580000	0.02121	-1.900000	0.01097	-1.874000	0.00550	CGA	C|0.999;T|0.001	0.001	strong		0.602	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		T	6978233	C	T	6978233	3	4	25	1	0	0	0	0	1	0	0	0	8614	884	31	1	3159	1	LAMA1	18	6978233	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	4423318	6978233	71099015	692	9601											
TXNDC2	84203	hgsc.bcm.edu	37	chr18	9886275	9886275	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agaaacaagtgaaggtgatgCtaatggtaagtaggggagga	16	7	16	2	0	0	3	0	2	0	1	0	5	0	5	0	5	2	3	0	5	6	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:9886275C>T	ENST00000306084.6	+	1	303	c.104C>T	c.(103-105)gCt>gTt	p.A35V	TXNDC2_ENST00000357775.5_Intron|TXNDC2_ENST00000536353.2_Intron|TXNDC2_ENST00000426718.3_3'UTR	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	35					cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)|multicellular organismal development (GO:0007275)|oxidation-reduction process (GO:0055114)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)	nutrient reservoir activity (GO:0045735)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(7)|urinary_tract(1)	31						GAAGGTGATGCTAATGGTAAG	0.468																																					p.A35V		Atlas-SNP	.											.	TXNDC2	168	.	0			c.C104T						PASS	.						75	75	75					18																	9886275		1940	4140	6080	SO:0001583	missense	84203	exon1			GTGATGCTAATGG	AF080095	CCDS11846.1, CCDS42414.1	18p11.31-p11.2	2009-03-11	2009-03-11	2007-08-16	ENSG00000168454	ENSG00000168454			16470	protein-coding gene	gene with protein product	"sperm-specific thioredoxin 1"					11230166, 11399755	Standard	NM_001098529		Approved	SPTRX1	uc002koi.4	Q86VQ3	OTTHUMG00000131602	ENST00000306084.6:c.104C>T	18.37:g.9886275C>T	ENSP00000304908:p.Ala35Val	94	0	0		72	34	0.472222	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Missense_Mutation	SNP	ENST00000306084.6	37	CCDS42414.1	.	.	.	.	.	.	.	.	.	.	C	9.184	1.024442	0.19433	.	.	ENSG00000168454	ENST00000306084;ENST00000426718	T	0.05199	3.48	3.92	1.03	0.20045	.	.	.	.	.	T	0.03739	0.0106	L	0.27053	0.805	0.09310	N	1	B	0.26809	0.16	B	0.23275	0.045	T	0.44982	-0.9292	8	.	.	.	1.9805	2.2617	0.04068	0.1932:0.4906:0.2043:0.1119	.	35	Q86VQ3	TXND2_HUMAN	V	35	ENSP00000304908:A35V	.	A	+	2	0	TXNDC2	9876275	0.000000	0.05858	0.004000	0.12327	0.067000	0.16453	-0.468000	0.06656	0.206000	0.20587	0.563000	0.77884	GCT	.	.	none		0.468	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1			T	9886275	C	T	9886275	3	4	25	1	0	0	0	0	1	0	0	0	16812	797	28	2	106	2	TXNDC2	18	9886275	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2908042	9886275	68190973	693	9602											
ASXL3	80816	hgsc.bcm.edu	37	chr18	31323500	31323500	+	Frame_Shift_Del	DEL	C	C	-																															aaaatagcagtgtgcccatgCtttttaataaaaattctgtc																										TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:31323500delC	ENST00000269197.5	+	12	3688	c.3688delC	c.(3688-3690)cttfs	p.L1230fs		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	1230	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						TGTGCCCATGCTTTTTAATAA	0.368																																					p.M1229fs		Atlas-Indel	.											ASXL3_ENST00000269197,NS,carcinoma,+2,2	ASXL3	405	2	0			c.3687delG						PASS	.						82	74	76					18																	31323500		1835	4083	5918	SO:0001589	frameshift_variant	80816	exon12			.	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.3688delC	18.37:g.31323500delC	ENSP00000269197:p.Leu1230fs	78	0	0		68	33	0.485294	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Frame_Shift_Del	DEL	ENST00000269197.5	37	CCDS45847.1																																																																																			.	.	none		0.368	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			-	31323500	C	-	31323500	7	5	25	1	0	1	0	1	0	0	0	0	1068	797	28	0	3734	0	ASXL3	18	31323500	Frame_Shift_Del	DEL	C	TCGA-G8-6906-01A-11D-2210-10	21437225	31323500	46753748	694	9603	117	2									
ASXL3	80816	hgsc.bcm.edu	37	chr18	31323501	31323501	+	Frame_Shift_Del	DEL	T	T	-																															aaatagcagtgtgcccatgcTttttaataaaaattctgtcc																										TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:31323501delT	ENST00000269197.5	+	12	3689	c.3689delT	c.(3688-3690)cttfs	p.L1230fs		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	1230	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						GTGCCCATGCTTTTTAATAAA	0.373																																					p.L1230fs		Pindel	.											.	ASXL3	405	.	0			c.3688delC						PASS	.						81	73	76					18																	31323501		1834	4083	5917	SO:0001589	frameshift_variant	80816	exon12			.	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.3689delT	18.37:g.31323501delT	ENSP00000269197:p.Leu1230fs	76	0	.		68	25	0.368	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Frame_Shift_Del	DEL	ENST00000269197.5	37	CCDS45847.1																																																																																			.	.	none		0.373	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			-	31323501	T	-	31323501	7	5	25	1	0	1	0	1	0	0	0	0	1068	1609	56	0	3735	0	ASXL3	18	31323501	Frame_Shift_Del	DEL	T	TCGA-G8-6906-01A-11D-2210-10	1	31323501	46753747	695	9604	117	2									
ZNF397OS	100101467	hgsc.bcm.edu	37	chr18	32833766	32833766	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggcttctctccagtgtggAttctccgatgcctgatgagc	7	12	11	11	1	2	2	0	2	2	0	5	4	3	3	3	2	2	1	3	2	1	2	rs61731888	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:32833766A>C	ENST00000420878.3	-	5	1588	c.1133T>G	c.(1132-1134)aTc>aGc	p.I378S	ZNF397_ENST00000261333.6_Intron|ZNF397_ENST00000355632.4_Intron|ZNF397_ENST00000592264.1_Intron|ZNF397_ENST00000589420.1_Intron|ZSCAN30_ENST00000333206.5_Missense_Mutation_p.I378S	NM_001166012.1	NP_001159484.1	Q86W11	ZSC30_HUMAN	zinc finger and SCAN domain containing 30	378					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						TCCAGTGTGGATTCTCCGATG	0.453													A|||	114	0.0227636	0.0522	0.0202	5008	,	,		20229	0.001		0.0209	False		,,,				2504	0.0092				p.I378S		Atlas-SNP	.											.	ZSCAN30	34	.	0			c.T1133G						PASS	.	A	SER/ILE,SER/ILE,	147,2989		5,137,1426	96	90	92		1133,1133,	2.4	1	18	dbSNP_129	92	153,7011		2,149,3431	yes	missense,missense,intron	ZNF397,ZSCAN30	NM_001112734.2,NM_001166012.1,NM_032347.2	142,142,	7,286,4857	CC,CA,AA		2.1357,4.6875,2.9126	probably-damaging,probably-damaging,	378/495,378/495,	32833766	300,10000	1568	3582	5150	SO:0001583	missense	100101467	exon5			GTGTGGATTCTCC	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.1133T>G	18.37:g.32833766A>C	ENSP00000392371:p.Ile378Ser	79	0	0		80	42	0.525	NM_001166012	B4E0N0|Q6ZNB3|Q96PN3	Missense_Mutation	SNP	ENST00000420878.3	37	CCDS42427.1	63	0.028846153846153848	34	0.06910569105691057	12	0.03314917127071823	1	0.0017482517482517483	16	0.021108179419525065	A	17.36	3.370099	0.61624	0.046875	0.021357	ENSG00000186814	ENST00000420878;ENST00000333206;ENST00000360932	T;T	0.06933	3.24;3.24	4.7	2.37	0.29283	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.217388	0.23491	N	0.047605	T	0.00815	0.0027	N	0.20685	0.6	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.19095	-1.0316	10	0.59425	D	0.04	.	5.4094	0.16341	0.6984:0.0:0.3016:0.0	rs61731888	378	Q86W11	ZSC30_HUMAN	S	378;378;313	ENSP00000392371:I378S;ENSP00000329738:I378S	ENSP00000329738:I378S	I	-	2	0	ZSCAN30	31087764	0.024000	0.19004	1.000000	0.80357	0.996000	0.88848	0.796000	0.26986	0.933000	0.37291	0.533000	0.62120	ATC	A|0.975;C|0.025	0.025	strong		0.453	ZSCAN30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442510.1	NM_001112734		C	32833766	A	C	32833766	3	2	25	1	0	0	0	0	1	0	0	0	17899	333	12	5	355	5	ZNF397OS	18	32833766	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	1510265	32833766	45243482	696	9605											
INO80C	125476	hgsc.bcm.edu	37	chr18	33048617	33048617	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcctcagggccaggtagccGgtgacgacgtcagagggcag	8	6	16	11	3	2	2	2	1	0	1	3	3	3	2	3	4	1	2	3	4	1	2	rs34130630	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:33048617G>A	ENST00000334598.7	-	5	653	c.537C>T	c.(535-537)acC>acT	p.T179T	RP11-322E11.5_ENST00000591141.1_lincRNA|INO80C_ENST00000590757.1_Silent_p.T82T|INO80C_ENST00000592173.1_Intron|INO80C_ENST00000586489.1_Silent_p.T124T|INO80C_ENST00000441607.2_Silent_p.T215T|RP11-322E11.6_ENST00000589258.1_Intron	NM_194281.3	NP_919257.2	Q6PI98	IN80C_HUMAN	INO80 complex subunit C	179					chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)				central_nervous_system(1)|endometrium(1)|lung(3)|prostate(2)|skin(1)	8						CCAGGTAGCCGGTGACGACGT	0.542													G|||	64	0.0127796	0.0461	0.0043	5008	,	,		15661	0.0		0.0	False		,,,				2504	0.0				p.T215T		Atlas-SNP	.											.	INO80C	18	.	0			c.C645T						PASS	.	G	,	174,4232	115.0+/-153.0	6,162,2035	136	138	137		645,537	-10.5	1	18	dbSNP_126	137	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	INO80C	NM_001098817.1,NM_194281.3	,	6,167,6330	AA,AG,GG		0.0581,3.9492,1.3763	,	215/229,179/193	33048617	179,12827	2203	4300	6503	SO:0001819	synonymous_variant	125476	exon7			GTAGCCGGTGACG		CCDS11914.1, CCDS45853.1	18q12.2	2011-07-06	2008-08-07	2008-08-07	ENSG00000153391	ENSG00000153391		"INO80 complex subunits"	26994	protein-coding gene	gene with protein product	"IES6 homolog (S. cerevisiae)"		"chromosome 18 open reading frame 37"	C18orf37		16230350	Standard	NM_001098817		Approved	FLJ38183, hIes6, IES6	uc010dmt.3	Q6PI98	OTTHUMG00000132564	ENST00000334598.7:c.537C>T	18.37:g.33048617G>A		80	0	0		65	38	0.584615	NM_001098817	B4DUI4|E9PCS7|Q86WR1|Q8N994	Silent	SNP	ENST00000334598.7	37	CCDS11914.1																																																																																			G|0.986;A|0.014	0.014	strong		0.542	INO80C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255768.1	NM_194281		A	33048617	G	A	33048617	2	1	25	1	0	0	0	0	0	0	0	1	7757	1103	39	1		1	INO80C	18	33048617	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	214851	33048617	45028631	697	9606											
MOCOS	55034	hgsc.bcm.edu	37	chr18	33828916	33828916	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atagaggtgcctcttgaggaAaatagtgaacggactcagat	14	9	12	6	1	2	4	1	2	1	2	2	6	2	6	1	3	2	0	1	3	5	3	rs55701019	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:33828916A>G	ENST00000261326.5	+	10	2013	c.1992A>G	c.(1990-1992)gaA>gaG	p.E664E		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						CTCTTGAGGAAAATAGTGAAC	0.408													A|||	34	0.00678914	0.0219	0.0058	5008	,	,		20756	0.0		0.001	False		,,,				2504	0.0				p.E664E		Atlas-SNP	.											.	MOCOS	84	.	0			c.A1992G						PASS	.	A		63,4343	59.3+/-96.0	0,63,2140	98	94	95		1992	-1.8	0.1	18	dbSNP_129	95	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	MOCOS	NM_017947.2		0,65,6438	GG,GA,AA		0.0233,1.4299,0.4998		664/889	33828916	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	55034	exon10			TGAGGAAAATAGT	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.1992A>G	18.37:g.33828916A>G		56	0	0		59	29	0.491525	NM_017947		Silent	SNP	ENST00000261326.5	37	CCDS11919.1																																																																																			A|0.995;G|0.005	0.005	strong		0.408	MOCOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255801.1			G	33828916	A	G	33828916	2	3	25	1	0	0	0	0	0	0	0	1	9698	11	1	3		3	MOCOS	18	33828916	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	780299	33828916	44248332	698	9607											
SETBP1	26040	hgsc.bcm.edu	37	chr18	42530295	42530295	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagcccccagaaccacctacGgtgggcagcaagaaaaagtc	14	3	11	13	1	0	2	0	0	0	2	1	3	0	2	4	2	4	2	4	2	5	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:42530295G>A	ENST00000282030.5	+	4	1286	c.990G>A	c.(988-990)acG>acA	p.T330T		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	330						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)		AACCACCTACGGTGGGCAGCA	0.527									Schinzel-Giedion syndrome																												p.T330T		Atlas-SNP	.											.	SETBP1	577	.	0			c.G990A						PASS	.						68	74	72					18																	42530295		2202	4300	6502	SO:0001819	synonymous_variant	26040	exon4	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	ACCTACGGTGGGC	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.990G>A	18.37:g.42530295G>A		59	0	0		60	35	0.583333	NM_015559	A6H8W5|Q6P6C3|Q9UEF3	Silent	SNP	ENST00000282030.5	37	CCDS11923.2																																																																																			.	.	none		0.527	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110		A	42530295	G	A	42530295	2	1	25	1	0	0	0	0	0	0	0	1	14144	1103	39	1		1	SETBP1	18	42530295	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	8701379	42530295	35546953	699	9608											
CXXC1	30827	hgsc.bcm.edu	37	chr18	47813157	47813157	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcagatgcagtagatgggCgcattctccccattctcgga	8	9	12	12	3	2	2	0	0	2	2	4	3	2	3	2	3	1	4	2	3	1	3	rs375253589		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:47813157C>A	ENST00000285106.6	-	2	789	c.75G>T	c.(73-75)gcG>gcT	p.A25A	CXXC1_ENST00000589940.1_Silent_p.A25A|CXXC1_ENST00000412036.2_Silent_p.A25A|CXXC1_ENST00000587396.1_5'UTR	NM_001101654.1|NM_014593.3	NP_001095124.1|NP_055408.2	Q9P0U4	CXXC1_HUMAN	CXXC finger protein 1	25					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)|histone H3-K4 methylation (GO:0051568)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	24						AGTAGATGGGCGCATTCTCCC	0.612																																					p.A25A		Atlas-SNP	.											.	CXXC1	50	.	0			c.G75T						PASS	.	C	,	0,4406		0,0,2203	115	91	99		75,75	-4.2	1	18		99	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	CXXC1	NM_001101654.1,NM_014593.3	,	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	,	25/661,25/657	47813157	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	30827	exon2			GATGGGCGCATTC	BC014940	CCDS11945.1, CCDS45866.1	18q12	2014-02-20	2014-02-20		ENSG00000154832	ENSG00000154832		"Zinc fingers, PHD-type"	24343	protein-coding gene	gene with protein product	"CpG binding protein", "DNA-binding protein with PHD finger and CXXC domain", "zinc finger, CpG binding-type containing 1"	609150	"CXXC finger 1 (PHD domain)"			10799292, 10688657	Standard	NM_014593		Approved	HsT2645, PCCX1, hCGBP, PHF18, CGBP, SPP1, CFP1, ZCGPC1	uc002ler.4	Q9P0U4	OTTHUMG00000132670	ENST00000285106.6:c.75G>T	18.37:g.47813157C>A		114	0	0		138	62	0.449275	NM_001101654	B2RC03|Q8N2W4|Q96BC8|Q9P2V7	Silent	SNP	ENST00000285106.6	37	CCDS11945.1																																																																																			.	.	weak		0.612	CXXC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255927.2	NM_014593		A	47813157	C	A	47813157	2	1	25	1	0	0	0	0	0	0	0	1	4099	755	27	4		4	CXXC1	18	47813157	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	5282862	47813157	30264091	700	9609											
LMAN1	3998	hgsc.bcm.edu	37	chr18	57026450	57026450	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	agcggccgaactctggcccgGagacccctttgcctggatcc	6	7	12	16	3	1	1	0	0	1	1	2	4	2	2	6	4	3	0	6	4	1	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:57026450G>C	ENST00000251047.5	-	1	744	c.27C>G	c.(25-27)ctC>ctG	p.L9L	RP11-27G24.1_ENST00000591331.1_lincRNA	NM_005570.3	NP_005561.1	P49257	LMAN1_HUMAN	lectin, mannose-binding, 1	9					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)	CTCTGGCCCGGAGACCCCTTT	0.701																																					p.L9L		Atlas-SNP	.											.	LMAN1	57	.	0			c.C27G						PASS	.						41	49	46					18																	57026450		2203	4300	6503	SO:0001819	synonymous_variant	3998	exon1			GGCCCGGAGACCC	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.27C>G	18.37:g.57026450G>C		80	0	0		115	51	0.443478	NM_005570	Q12895|Q8N5I7|Q9UQG1|Q9UQG2|Q9UQG3|Q9UQG4|Q9UQG5|Q9UQG6|Q9UQG7|Q9UQG8|Q9UQG9|Q9UQH0|Q9UQH1|Q9UQH2	Silent	SNP	ENST00000251047.5	37	CCDS11974.1																																																																																			.	.	none		0.701	LMAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256129.2	NM_005570		C	57026450	G	C	57026450	2	2	25	1	0	0	0	0	0	0	0	1	8845	1161	41	4		4	LMAN1	18	57026450	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	9213293	57026450	21050798	701	9610											
BCL2	596	hgsc.bcm.edu	37	chr18	60985833	60985833	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcgtagcccctctgcgacaGcttataatggatgtacttca	9	12	8	12	2	2	0	1	0	1	0	3	2	2	1	2	1	4	3	2	1	4	5			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:60985833G>A	ENST00000398117.1	-	1	1528	c.67C>T	c.(67-69)Ctg>Ttg	p.L23L	BCL2_ENST00000333681.4_Silent_p.L23L|BCL2_ENST00000444484.1_Silent_p.L23L|BCL2_ENST00000589955.1_Silent_p.L23L	NM_000633.2	NP_000624.2	P10415	BCL2_HUMAN	B-cell CLL/lymphoma 2	23					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)	CTCTGCGACAGCTTATAATGG	0.652			T	IGH@	"NHL, CLL"																																p.L23L		Atlas-SNP	.		Dom	yes		18	18q21.3	596	B-cell CLL/lymphoma 2		L	.	BCL2	272	.	0			c.C67T						PASS	.						68	76	73					18																	60985833		1972	4119	6091	SO:0001819	synonymous_variant	596	exon2			GCGACAGCTTATA	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.67C>T	18.37:g.60985833G>A		28	0	0		33	17	0.515152	NM_000633	C9JHD5|P10416|Q13842|Q16197	Silent	SNP	ENST00000398117.1	37	CCDS11981.1																																																																																			.	.	none		0.652	BCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256199.1	NM_000633, NM_000657		A	60985833	G	A	60985833	2	1	25	1	0	0	0	0	0	0	0	1	1365	962	34	2		2	BCL2	18	60985833	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	3959383	60985833	17091415	702	9611											
ZNF407	55628	hgsc.bcm.edu	37	chr18	72346701	72346701	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacgcaggagacggtggaggTgttgtcccccacagacacct	10	6	13	12	2	0	2	0	0	0	2	1	4	1	3	3	4	1	2	3	4	1	1	rs146635665	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:72346701T>C	ENST00000299687.5	+	1	3726	c.3726T>C	c.(3724-3726)ggT>ggC	p.G1242G	ZNF407_ENST00000582337.1_Silent_p.G1242G|ZNF407_ENST00000577538.1_Silent_p.G1242G|ZNF407_ENST00000309902.6_Silent_p.G1242G	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	1242					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)		ACGGTGGAGGTGTTGTCCCCC	0.537													T|||	15	0.00299521	0.0	0.0058	5008	,	,		17029	0.0		0.007	False		,,,				2504	0.0041				p.G1242G		Atlas-SNP	.											.	ZNF407	231	.	0			c.T3726C						PASS	.	T	,,	5,4097		0,5,2046	53	61	58		3726,3726,3726	-6.3	0	18	dbSNP_134	58	48,8320		0,48,4136	yes	coding-synonymous,coding-synonymous,coding-synonymous	ZNF407	NM_001146189.1,NM_001146190.1,NM_017757.2	,,	0,53,6182	CC,CT,TT		0.5736,0.1219,0.425	,,	1242/1816,1242/1661,1242/2249	72346701	53,12417	2051	4184	6235	SO:0001819	synonymous_variant	55628	exon1			TGGAGGTGTTGTC	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.3726T>C	18.37:g.72346701T>C		72	0	0		58	27	0.465517	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Silent	SNP	ENST00000299687.5	37	CCDS45885.1																																																																																			T|0.997;C|0.003	0.003	strong		0.537	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757		C	72346701	T	C	72346701	2	2	25	1	0	0	0	0	0	0	0	1	17902	1683	59	3		3	ZNF407	18	72346701	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	11360868	72346701	5730547	703	9612											
ZNF516	9658	hgsc.bcm.edu	37	chr18	74154296	74154296	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggctcagctcgggcttgcCgttctccacgcaggcctcgc	3	8	14	16	4	2	0	1	0	1	0	5	0	2	0	3	4	2	5	3	4	0	2	rs12961584		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:74154296C>T	ENST00000443185.2	-	3	1032	c.715G>A	c.(715-717)Ggc>Agc	p.G239S	ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	239			G -> S (in dbSNP:rs12961584).		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)		TCGGGCTTGCCGTTCTCCACG	0.692													C|||	1	0.000199681	0.0	0.0	5008	,	,		15391	0.0		0.001	False		,,,				2504	0.0				p.G239S		Atlas-SNP	.											.	ZNF516	102	.	0			c.G715A						PASS	.	C	SER/GLY	2,4128		0,2,2063	12	14	14		715	3.5	1	18	dbSNP_121	14	33,8345		0,33,4156	no	missense	ZNF516	NM_014643.3	56	0,35,6219	TT,TC,CC		0.3939,0.0484,0.2798	probably-damaging	239/1164	74154296	35,12473	2065	4189	6254	SO:0001583	missense	9658	exon3			GCTTGCCGTTCTC	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.715G>A	18.37:g.74154296C>T	ENSP00000394757:p.Gly239Ser	22	0	0		39	26	0.666667	NM_014643		Missense_Mutation	SNP	ENST00000443185.2	37		.	.	.	.	.	.	.	.	.	.	C	16.18	3.050132	0.55218	4.84E-4	0.003939	ENSG00000101493	ENST00000443185	T	0.11063	2.81	4.39	3.5	0.40072	.	0.497156	0.19611	N	0.110146	T	0.16854	0.0405	.	.	.	0.30781	N	0.741935	D	0.69078	0.997	P	0.53760	0.734	T	0.04509	-1.0946	9	0.22109	T	0.4	-22.5334	12.8858	0.58042	0.3101:0.6899:0.0:0.0	rs12961584	239	Q92618	ZN516_HUMAN	S	239	ENSP00000394757:G239S	ENSP00000394757:G239S	G	-	1	0	ZNF516	72283284	0.628000	0.27138	0.994000	0.49952	0.971000	0.66376	1.269000	0.33074	1.187000	0.43000	0.557000	0.71058	GGC	C|0.667;T|0.333	0.333	strong		0.692	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643		T	74154296	C	T	74154296	3	4	25	1	0	0	0	0	1	0	0	0	17975	652	23	1	2797	1	ZNF516	18	74154296	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1807595	74154296	3922952	704	9613											
ZNF236	7776	hgsc.bcm.edu	37	chr18	74672703	74672703	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagtgcgctgcaggtgcacAtgaagaagcacacgggggag	12	4	17	8	2	0	3	0	1	0	2	0	4	0	4	0	3	4	4	0	3	2	0	rs183845634		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:74672703A>G	ENST00000253159.8	+	30	5503	c.5305A>G	c.(5305-5307)Atg>Gtg	p.M1769V	ZNF236_ENST00000320610.9_Missense_Mutation_p.M1771V	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	1769					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)		GCAGGTGCACATGAAGAAGCA	0.552													A|||	1	0.000199681	0.0	0.0	5008	,	,		19924	0.0		0.001	False		,,,				2504	0.0				p.M1769V		Atlas-SNP	.											.	ZNF236	325	.	0			c.A5305G						PASS	.	A	VAL/MET	0,4100		0,0,2050	88	95	92		5305	1.8	1	18		92	5,8409		0,5,4202	yes	missense	ZNF236	NM_007345.3	21	0,5,6252	GG,GA,AA		0.0594,0.0,0.04	benign	1769/1846	74672703	5,12509	2050	4207	6257	SO:0001583	missense	7776	exon30			GTGCACATGAAGA	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.5305A>G	18.37:g.74672703A>G	ENSP00000253159:p.Met1769Val	44	0	0		68	31	0.455882	NM_007345	B2RTX9|Q9UL37	Missense_Mutation	SNP	ENST00000253159.8	37	CCDS42447.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	11.72	1.724148	0.30593	0.0	5.94E-4	ENSG00000130856	ENST00000253159	T	0.10573	2.86	5.61	1.76	0.24704	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	0.07773	0.0195	L	0.37750	1.13	0.28794	N	0.899167	B	0.24186	0.099	B	0.28465	0.09	T	0.27971	-1.0058	10	0.27785	T	0.31	.	4.7999	0.13292	0.6934:0.1236:0.065:0.118	.	1769	Q9UL36	ZN236_HUMAN	V	1769	ENSP00000253159:M1769V	ENSP00000253159:M1769V	M	+	1	0	ZNF236	72801691	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.024000	0.57218	0.058000	0.16222	0.533000	0.62120	ATG	A|0.999;G|0.001	0.001	strong		0.552	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1			G	74672703	A	G	74672703	3	3	25	1	0	0	0	0	1	0	0	0	17804	217	8	3	5423	3	ZNF236	18	74672703	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	518407	74672703	3404545	705	9614											
NFATC1	4772	hgsc.bcm.edu	37	chr18	77170505	77170505	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caaccttcagacctccacacCgggcatcatcccgccggcgg	8	5	9	19	4	2	1	2	0	0	1	4	1	4	1	6	3	1	1	6	3	1	1	rs143045693	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:77170505C>T	ENST00000427363.2	+	2	230	c.230C>T	c.(229-231)cCg>cTg	p.P77L	NFATC1_ENST00000586434.1_Missense_Mutation_p.P64L|NFATC1_ENST00000592223.1_Missense_Mutation_p.P64L|NFATC1_ENST00000397790.2_Intron|NFATC1_ENST00000587635.1_Missense_Mutation_p.P77L|NFATC1_ENST00000591814.1_Missense_Mutation_p.P77L|NFATC1_ENST00000329101.4_Missense_Mutation_p.P64L|NFATC1_ENST00000542384.1_Missense_Mutation_p.P77L|NFATC1_ENST00000545796.1_Intron|NFATC1_ENST00000253506.5_Missense_Mutation_p.P77L|NFATC1_ENST00000318065.5_Missense_Mutation_p.P64L			O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1	77					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)	ACCTCCACACCGGGCATCATC	0.692													C|||	2	0.000399361	0.0	0.0	5008	,	,		13489	0.0		0.002	False		,,,				2504	0.0				p.P77L	GBM(151;1210 2593 28719 45011)	Atlas-SNP	.											.	NFATC1	105	.	0			c.C230T						PASS	.	C	LEU/PRO,LEU/PRO,,LEU/PRO,LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	50	56	54		230,191,,191,230	4.4	0	18	dbSNP_134	54	3,8595	3.0+/-9.4	0,3,4296	yes	missense,missense,intron,missense,missense	NFATC1	NM_006162.3,NM_172387.1,NM_172388.1,NM_172389.1,NM_172390.1	98,98,,98,98	0,4,6498	TT,TC,CC		0.0349,0.0227,0.0308	benign,benign,,benign,benign	77/826,64/931,,64/813,77/717	77170505	4,13000	2203	4299	6502	SO:0001583	missense	4772	exon2			CCACACCGGGCAT	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.230C>T	18.37:g.77170505C>T	ENSP00000389377:p.Pro77Leu	49	0	0		81	44	0.54321	NM_172390	B5B2M4|B5B2M5|B5B2M6|B5B2M7|B5B2M8|B5B2M9|B5B2N1|Q12865|Q15793|Q2M1S3	Missense_Mutation	SNP	ENST00000427363.2	37		0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	22.8	4.334065	0.81801	2.27E-4	3.49E-4	ENSG00000131196	ENST00000318065;ENST00000253506;ENST00000542384;ENST00000329101;ENST00000427363;ENST00000397794	T;T;T	0.39229	1.09;1.09;1.09	4.39	4.39	0.52855	.	0.400014	0.28146	N	0.016430	T	0.46386	0.1390	M	0.61703	1.905	0.80722	D	1	P;P;P;D;D;P;P	0.55605	0.904;0.904;0.946;0.972;0.972;0.773;0.946	B;B;B;B;B;B;B	0.43916	0.344;0.23;0.344;0.436;0.436;0.121;0.436	T	0.57894	-0.7732	10	0.87932	D	0	-17.9221	17.1373	0.86743	0.0:1.0:0.0:0.0	.	64;64;77;77;77;64;77	B5B2M7;B5B2N1;B5B2M6;O95644;B5B2M4;B5B2M5;Q2M1S3	.;.;.;NFAC1_HUMAN;.;.;.	L	77;77;77;64;64;41	ENSP00000253506:P77L;ENSP00000442435:P77L;ENSP00000327850:P64L	ENSP00000253506:P77L	P	+	2	0	NFATC1	75271493	0.997000	0.39634	0.025000	0.17156	0.028000	0.11728	6.807000	0.75201	2.267000	0.75376	0.561000	0.74099	CCG	C|1.000;T|0.000	0.000	strong		0.692	NFATC1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000450507.1	NM_172390		T	77170505	C	T	77170505	3	4	25	1	0	0	0	0	1	0	0	0	10370	652	23	1	328	1	NFATC1	18	77170505	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2497802	77170505	906743	706	9615											
POLRMT	5442	hgsc.bcm.edu	37	chr19	621148	621148	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agcggctcccgcttcttcaaCcccgtgagattgaccaggtg	7	9	11	14	3	2	2	1	2	1	1	3	3	3	2	4	2	2	2	4	2	1	3	rs143192895	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:621148C>T	ENST00000588649.2	-	10	2634	c.2550G>A	c.(2548-2550)ggG>ggA	p.G850G	LLNLR-299G3.1_ENST00000607288.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	850	Mediates interaction with TEFM.				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)		GCTTCTTCAACCCCGTGAGAT	0.687													C|||	15	0.00299521	0.0	0.0014	5008	,	,		5814	0.0		0.007	False		,,,				2504	0.0072				p.G850G		Atlas-SNP	.											.	POLRMT	91	.	0			c.G2550A						PASS	.	C		7,4399		0,7,2196	28	33	32		2550	-5.4	0.6	19	dbSNP_134	32	35,8555		1,33,4261	no	coding-synonymous	POLRMT	NM_005035.3		1,40,6457	TT,TC,CC		0.4075,0.1589,0.3232		850/1231	621148	42,12954	2203	4295	6498	SO:0001819	synonymous_variant	5442	exon10			CTTCAACCCCGTG		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.2550G>A	19.37:g.621148C>T		74	0	0		86	26	0.302326	NM_005035	O60370	Silent	SNP	ENST00000588649.2	37	CCDS12036.1																																																																																			C|0.997;T|0.003	0.003	strong		0.687	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035		T	621148	C	T	621148	2	4	25	1	0	0	0	0	0	0	0	1	12247	494	18	2		2	POLRMT	19	621148	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10		621148	58507835	707	9616											
AZU1	566	hgsc.bcm.edu	37	chr19	831865	831865	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gttctcaacaacccgggaccGgggccagcctaggggggcct	7	5	15	14	2	1	0	1	0	1	0	2	1	1	1	5	6	3	1	5	6	3	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:831865G>A	ENST00000233997.2	+	5	765	c.744G>A	c.(742-744)ccG>ccA	p.P248P		NM_001700.3	NP_001691.1	P20160	CAP7_HUMAN	azurocidin 1	248			Missing (in 50% of the molecules).		cellular extravasation (GO:0045123)|defense response to Gram-negative bacterium (GO:0050829)|glial cell migration (GO:0008347)|induction of positive chemotaxis (GO:0050930)|inflammatory response (GO:0006954)|macrophage chemotaxis (GO:0048246)|microglial cell activation (GO:0001774)|monocyte activation (GO:0042117)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell adhesion (GO:0045785)|positive regulation of fractalkine biosynthetic process (GO:0050754)|positive regulation of interleukin-1 beta biosynthetic process (GO:0050725)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of phagocytosis (GO:0050766)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of vascular permeability (GO:0043114)	azurophil granule (GO:0042582)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)|toxic substance binding (GO:0015643)			NS(1)|endometrium(1)|kidney(1)|lung(4)|pancreas(1)|upper_aerodigestive_tract(2)	10		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)		ACCCGGGACCGGGGCCAGCCT	0.711																																					p.P248P		Atlas-SNP	.											.	AZU1	31	.	0			c.G744A						PASS	.						27	33	31					19																	831865		2189	4270	6459	SO:0001819	synonymous_variant	566	exon5			GGGACCGGGGCCA	X58794	CCDS12044.1	19p13.3	2012-03-30	2008-08-01		ENSG00000172232	ENSG00000172232			913	protein-coding gene	gene with protein product	"cationic antimicrobial protein 37", "heparin-binding protein", "neutrophil azurocidin"	162815				1919011	Standard	NM_001700		Approved	AZU, CAP37, AZAMP, HBP, NAZC, HUMAZUR	uc002lpz.1	P20160		ENST00000233997.2:c.744G>A	19.37:g.831865G>A		41	0	0		67	30	0.447761	NM_001700	P80014|Q52LG4|Q9UCM1|Q9UCT5	Silent	SNP	ENST00000233997.2	37	CCDS12044.1																																																																																			.	.	none		0.711	AZU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457472.2	NM_001700		A	831865	G	A	831865	2	1	25	1	0	0	0	0	0	0	0	1	1243	1103	39	1		1	AZU1	19	831865	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	210717	831865	58297118	708	9617											
ABCA7	10347	hgsc.bcm.edu	37	chr19	1054267	1054267	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagggctgggcactgacccGccagcagctccaggccctgc	7	4	13	17	1	0	1	0	1	0	0	1	1	1	1	4	3	3	4	4	3	0	0	rs534172941		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:1054267G>A	ENST00000263094.6	+	27	3884	c.3653G>A	c.(3652-3654)cGc>cAc	p.R1218H	ABCA7_ENST00000433129.1_Missense_Mutation_p.R1218H|ABCA7_ENST00000435683.2_Missense_Mutation_p.R1080H	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1218					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)		GCACTGACCCGCCAGCAGCTC	0.697													G|||	1	0.000199681	0.0	0.0	5008	,	,		14782	0.0		0.0	False		,,,				2504	0.001				p.R1218H		Atlas-SNP	.											.	ABCA7	174	.	0			c.G3653A						PASS	.						12	16	15					19																	1054267		2185	4270	6455	SO:0001583	missense	10347	exon27			TGACCCGCCAGCA	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.3653G>A	19.37:g.1054267G>A	ENSP00000263094:p.Arg1218His	26	0	0		25	13	0.52	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	g	11.52	1.664688	0.29604	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.86865	-2.18;-2.18	3.54	-5.43	0.02632	.	.	.	.	.	T	0.74068	0.3668	L	0.42529	1.33	0.09310	N	1	B;B	0.24426	0.103;0.007	B;B	0.23852	0.049;0.004	T	0.59958	-0.7356	9	0.17369	T	0.5	.	0.5118	0.00597	0.3927:0.134:0.2029:0.2704	.	1080;1218	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	H	1218	ENSP00000263094:R1218H;ENSP00000414062:R1218H	ENSP00000263094:R1218H	R	+	2	0	ABCA7	1005267	0.000000	0.05858	0.002000	0.10522	0.778000	0.44026	-1.209000	0.03002	-1.417000	0.02017	-0.649000	0.03915	CGC	.	.	none		0.697	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		A	1054267	G	A	1054267	3	1	25	1	0	0	0	0	1	0	0	0	37	1087	38	1	3755	1	ABCA7	19	1054267	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	222402	1054267	58074716	709	9618											
STK11	6794	hgsc.bcm.edu	37	chr19	1207176	1207176	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aagaagaagttgcgaaggatCcccaacggggaggccaacgt	14	4	14	9	3	0	2	0	0	0	2	1	5	1	4	3	4	3	1	3	4	6	1	rs56354945	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:1207176C>A	ENST00000326873.7	+	1	1437	c.264C>A	c.(262-264)atC>atA	p.I88I	STK11_ENST00000585748.1_Intron	NM_000455.4	NP_000446.1	Q15831	STK11_HUMAN	serine/threonine kinase 11	88	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|Sufficient for interaction with SIRT1.				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)		TGCGAAGGATCCCCAACGGGG	0.597		14	"D, Mis, N, F, S"		"NSCLC, pancreatic"	"jejunal harmartoma, ovarian, testicular, pancreatic"			Peutz-Jeghers syndrome	TSP Lung(3;<1E-08)			C|||	119	0.023762	0.0832	0.0086	5008	,	,		18552	0.0		0.003	False		,,,				2504	0.0				p.I88I		Atlas-SNP	.	yes	Rec	yes	Peutz-Jeghers syndrome	19	19p13.3	6794	serine/threonine kinase 11 gene (LKB1)		"E, M, O"	STK11,brain,glioma,0,2	STK11	410	2	23	Whole gene deletion(20)|Unknown(2)|Deletion - Frameshift(1)	cervix(15)|lung(3)|skin(1)|oesophagus(1)|ovary(1)|kidney(1)|pancreas(1)	c.C264A						PASS	.	C		255,3773		6,243,1765	29	32	31		264	3.9	1	19	dbSNP_129	31	2,8300		0,2,4149	no	coding-synonymous	STK11	NM_000455.4		6,245,5914	AA,AC,CC		0.0241,6.3307,2.0843		88/434	1207176	257,12073	2014	4151	6165	SO:0001819	synonymous_variant	6794	exon1	Familial Cancer Database	PJS, Hamartous Intestinal Polyposis	AAGGATCCCCAAC	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.264C>A	19.37:g.1207176C>A		132	0	0		133	69	0.518797	NM_000455	B2RBX7|E7EW76	Silent	SNP	ENST00000326873.7	37	CCDS45896.1																																																																																			C|0.980;A|0.020	0.020	strong		0.597	STK11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449839.3	NM_000455		A	1207176	C	A	1207176	2	1	25	1	0	0	0	0	0	0	0	1	15302	845	30	4		4	STK11	19	1207176	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	152909	1207176	57921807	710	9619											
HDGFRP2	84717	hgsc.bcm.edu	37	chr19	4498017	4498019	+	In_Frame_Del	DEL	AGA	AGA	-																															ctcgatggacaggaaggtagAgaagaagaaaggtgaggcct																										TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4498017_4498019delAGA	ENST00000301284.4	+	11	1455_1457	c.1391_1393delAGA	c.(1390-1395)gagaag>gag	p.K467del	HDGFRP2_ENST00000586684.1_In_Frame_Del_p.K467del	NM_001001520.1|NM_032631.2	NP_001001520|NP_116020.1	Q7Z4V5	HDGR2_HUMAN		467					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										AGGAAGGTAGAGAAGAAGAAAGG	0.66																																					p.464_464del		Pindel,Atlas-Indel	.											.	.	.	.	0			c.1390_1392del						PASS	.																																			SO:0001651	inframe_deletion	0	exon11			.																												ENST00000301284.4:c.1391_1393delAGA	19.37:g.4498023_4498025delAGA	ENSP00000301284:p.Lys467del	78	0	.		79	32	0.405	NM_032631	I3L080|K7EQZ6|Q96GI5|Q9BW08	In_Frame_Del	DEL	ENST00000301284.4	37	CCDS42472.1																																																																																			.	.	none		0.66	HDGFRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458642.1			-	4498019	AGA	-	4498017	7	5	25	1	0	1	0	1	0	0	0	0	7029	304	11	0	1433	0	HDGFRP2	19	4498017	In_Frame_Del	DEL	AGA	TCGA-G8-6906-01A-11D-2210-10	3290841	4498017	54630966	711	9620											
PRR22	163154	hgsc.bcm.edu	37	chr19	5783713	5783713	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggggggtgggggtggcagcGgggccgggccttcctctagg	2	7	23	9	2	1	0	0	0	1	0	2	0	2	0	3	10	1	1	3	10	1	2	rs141874203	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:5783713G>A	ENST00000419421.2	-	3	649	c.545C>T	c.(544-546)cCg>cTg	p.P182L		NM_001134316.1	NP_001127788.1	Q8IZ63	PRR22_HUMAN	proline rich 22	182	Pro-rich.									endometrium(2)|large_intestine(1)|prostate(1)|urinary_tract(1)	5						GGGTGGCAGCGGGGCCGGGCC	0.716													G|||	51	0.0101837	0.0	0.0202	5008	,	,		8447	0.0		0.0258	False		,,,				2504	0.0112				p.P182L		Atlas-SNP	.											PRR22_ENST00000419421,NS,carcinoma,+1,2	PRR22	25	2	0			c.C545T						PASS	.	G	LEU/PRO	23,3621		0,23,1799	3	5	4		545	2.6	0	19	dbSNP_134	4	224,7348		0,224,3562	no	missense	PRR22	NM_001134316.1	98	0,247,5361	AA,AG,GG		2.9583,0.6312,2.2022	possibly-damaging	182/423	5783713	247,10969	1822	3786	5608	SO:0001583	missense	163154	exon3			GGCAGCGGGGCCG	BC023278	CCDS45933.1	19p13.3	2012-12-20			ENSG00000212123	ENSG00000212123			28354	protein-coding gene	gene with protein product						12477932	Standard	NM_001134316		Approved	MGC24975	uc010xiv.1	Q8IZ63	OTTHUMG00000180553	ENST00000419421.2:c.545C>T	19.37:g.5783713G>A	ENSP00000407653:p.Pro182Leu	25	0	0		36	21	0.583333	NM_001134316	E9PB31	Missense_Mutation	SNP	ENST00000419421.2	37	CCDS45933.1	35	0.016025641025641024	0	0.0	8	0.022099447513812154	1	0.0017482517482517483	26	0.03430079155672823	G	13.85	2.360615	0.41801	0.006312	0.029583	ENSG00000212123	ENST00000419421	T	0.20200	2.09	2.58	2.58	0.30949	.	.	.	.	.	T	0.04588	0.0125	L	0.32530	0.975	0.09310	N	1	P;P	0.42161	0.772;0.772	B;B	0.34779	0.189;0.189	T	0.10800	-1.0614	9	0.62326	D	0.03	.	8.7627	0.34685	0.0:0.0:1.0:0.0	.	182;180	E9PB31;Q8IZ63	.;PRR22_HUMAN	L	182	ENSP00000407653:P182L	ENSP00000407653:P182L	P	-	2	0	PRR22	5734713	0.123000	0.22298	0.002000	0.10522	0.003000	0.03518	2.157000	0.42320	1.759000	0.51996	0.491000	0.48974	CCG	G|0.984;A|0.016	0.016	strong		0.716	PRR22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368523.1	NM_153359		A	5783713	G	A	5783713	3	1	25	1	0	0	0	0	1	0	0	0	12605	1116	39	1	727	1	PRR22	19	5783713	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1285696	5783713	53345270	712	9621											
CAPS	8498	hgsc.bcm.edu	37	chr19	5914470	5914470	+	IGR	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgggcacagtgcctgtcccGcggggcctcgggcatccagg	4	5	16	16	4	0	0	0	0	0	0	3	0	2	0	5	5	1	2	5	5	0	0	rs143117009	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:5914470G>A	ENST00000340578.6	-	0	3233				AC104532.4_ENST00000591109.1_RNA|CAPS_ENST00000588776.1_Missense_Mutation_p.R104H|AC104532.2_ENST00000588891.1_3'UTR|CAPS_ENST00000222125.5_Missense_Mutation_p.R18H|CAPS_ENST00000452990.2_Missense_Mutation_p.R18H	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						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						TGCCTGTCCCGCGGGGCCTCG	0.672													G|||	17	0.00339457	0.0	0.0029	5008	,	,		15870	0.0		0.0129	False		,,,				2504	0.002				p.R18H		Atlas-SNP	.											.	CAPS	14	.	0			c.G53A						PASS	.	G	HIS/ARG,HIS/ARG	12,4394	19.1+/-41.9	0,12,2191	43	47	45		53,53	5	1	19	dbSNP_134	45	130,8470	64.6+/-126.8	1,128,4171	yes	missense,missense	CAPS	NM_004058.3,NM_080590.2	29,29	1,140,6362	AA,AG,GG		1.5116,0.2724,1.0918	probably-damaging,probably-damaging	18/190,18/163	5914470	142,12864	2203	4300	6503	SO:0001628	intergenic_variant	828	exon2			TGTCCCGCGGGGC	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			19.37:g.5914470G>A		112	0	0		104	52	0.5	NM_080590	B2RAT8|O60405|O75759|O75760|Q9BT47|Q9UG74	Missense_Mutation	SNP	ENST00000340578.6	37	CCDS42478.1	13	0.005952380952380952	0	0.0	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	G	25.1	4.602108	0.87055	0.002724	0.015116	ENSG00000105519	ENST00000394521;ENST00000222125;ENST00000452990	T;T	0.57273	0.41;0.79	4.98	4.98	0.66077	.	0.000000	0.64402	D	0.000017	T	0.46288	0.1385	M	0.80332	2.49	0.20403	N	0.999902	D;P	0.65815	0.995;0.877	P;B	0.47402	0.546;0.097	T	0.58578	-0.7612	10	0.59425	D	0.04	-10.7081	15.7308	0.77804	0.0:0.0:1.0:0.0	.	151;18	Q8NF12;Q13938	.;CAYP1_HUMAN	H	151;18;18	ENSP00000222125:R18H;ENSP00000403263:R18H	ENSP00000222125:R18H	R	+	2	0	CAPS	5865470	0.867000	0.29959	0.990000	0.47175	0.760000	0.43138	5.362000	0.66098	2.307000	0.77673	0.561000	0.74099	CGC	G|0.988;A|0.012	0.012	strong		0.672	RANBP3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452304.1	NM_007322		A	5914470	G	A	5914470	1	1	25	0	1	0	0	0	0	0	0	0	2639	1087	38	1		1	CAPS	19	5914470	IGR	SNP	G	TCGA-G8-6906-01A-11D-2210-10	130757	5914470	53214513	713	9622											
DENND1C	79958	hgsc.bcm.edu	37	chr19	6468907	6468907	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttgctgcaggcggtctgagcGgctggggagggctggggccc	3	7	21	10	2	1	1	0	1	1	0	1	2	1	2	1	8	3	4	1	8	0	1	rs35001260	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:6468907G>A	ENST00000381480.2	-	20	1577	c.1465C>T	c.(1465-1467)Cgc>Tgc	p.R489C	DENND1C_ENST00000543576.1_Missense_Mutation_p.R445C	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	489			R -> C (in dbSNP:rs35001260).		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						CGGTCTGAGCGGCTGGGGAGG	0.607													G|||	50	0.00998403	0.0015	0.0058	5008	,	,		13199	0.0		0.0229	False		,,,				2504	0.0215				p.R489C		Atlas-SNP	.											.	DENND1C	93	.	0			c.C1465T						PASS	.	G	CYS/ARG	10,3842		0,10,1916	25	29	28		1465	4.7	1	19	dbSNP_126	28	170,8058		3,164,3947	yes	missense	DENND1C	NM_024898.2	180	3,174,5863	AA,AG,GG		2.0661,0.2596,1.4901	probably-damaging	489/802	6468907	180,11900	1926	4114	6040	SO:0001583	missense	79958	exon20			CTGAGCGGCTGGG	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.1465C>T	19.37:g.6468907G>A	ENSP00000370889:p.Arg489Cys	40	0	0		60	28	0.466667	NM_024898	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Missense_Mutation	SNP	ENST00000381480.2	37	CCDS45938.1	20	0.009157509157509158	0	0.0	1	0.0027624309392265192	0	0.0	19	0.025065963060686015	G	16.60	3.168788	0.57584	0.002596	0.020661	ENSG00000205744	ENST00000381480;ENST00000543576	T;T	0.11821	2.91;2.74	4.69	4.69	0.59074	.	0.327353	0.28815	N	0.014059	T	0.09598	0.0236	L	0.53249	1.67	0.47123	D	0.999325	D	0.89917	1.0	P	0.56278	0.795	T	0.00171	-1.1959	10	0.62326	D	0.03	-15.0887	13.1025	0.59228	0.0:0.0:1.0:0.0	rs35001260;rs35001260	489	Q8IV53	DEN1C_HUMAN	C	489;445	ENSP00000370889:R489C;ENSP00000437805:R445C	ENSP00000370889:R489C	R	-	1	0	DENND1C	6419907	1.000000	0.71417	1.000000	0.80357	0.062000	0.15995	2.749000	0.47492	2.167000	0.68274	0.491000	0.48974	CGC	G|0.983;A|0.017	0.017	strong		0.607	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898		A	6468907	G	A	6468907	3	1	25	1	0	0	0	0	1	0	0	0	4430	1116	39	1	956	1	DENND1C	19	6468907	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	554437	6468907	52660076	714	9623											
ARHGEF18	23370	hgsc.bcm.edu	37	chr19	7505146	7505146	+	Missense_Mutation	SNP	A	A	C																															cctgtctgtgctgcggccgcAgtcggagcggggcttccgcg																								rs200643326		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:7505146A>C	ENST00000359920.6	+	1	573	c.320A>C	c.(319-321)cAg>cCg	p.Q107P	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	107					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)				CTGCGGCCGCAGTCGGAGCGG	0.602													A|||	1	0.000199681	0.0	0.0	5008	,	,		13226	0.0		0.0	False		,,,				2504	0.001				p.Q107P		Atlas-SNP	.											.	ARHGEF18	129	.	0			c.A320C						PASS	.						27	34	32					19																	7505146		692	1591	2283	SO:0001583	missense	23370	exon1			GGCCGCAGTCGGA	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.320A>C	19.37:g.7505146A>C	ENSP00000352995:p.Gln107Pro	74	0	0		118	53	0.449153	NM_001130955	A8MV62|B5ME81|O60274|Q6DD92	Missense_Mutation	SNP	ENST00000359920.6	37	CCDS45946.1	.	.	.	.	.	.	.	.	.	.	A	12.64	1.999042	0.35226	.	.	ENSG00000104880	ENST00000359920	T	0.32988	1.43	5.23	1.88	0.25563	.	0.187822	0.25607	U	0.029507	T	0.17023	0.0409	N	0.24115	0.695	0.09310	N	0.999999	P	0.44521	0.837	B	0.37451	0.25	T	0.10382	-1.0632	10	0.62326	D	0.03	-7.5996	7.6096	0.28122	0.7026:0.0:0.2974:0.0	.	107	Q6ZSZ5	ARHGI_HUMAN	P	107	ENSP00000352995:Q107P	ENSP00000352995:Q107P	Q	+	2	0	ARHGEF18	7411146	0.023000	0.18921	0.031000	0.17742	0.874000	0.50279	0.774000	0.26675	0.330000	0.23485	0.459000	0.35465	CAG	A|0.999;C|0.001	0.001	weak		0.602	ARHGEF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436340.1	NM_015318		C	7505146	A	C	7505146	3	2	25	1	0	0	0	0	1	0	0	0	901	188	7	5	322	5	ARHGEF18	19	7505146	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	1036239	7505146	51623837	715	9624	118	2									
ARHGEF18	23370	hgsc.bcm.edu	37	chr19	7505147	7505147	+	Missense_Mutation	SNP	G	G	T																															ctgtctgtgctgcggccgcaGtcggagcggggcttccgcgc																								rs201598844		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:7505147G>T	ENST00000359920.6	+	1	574	c.321G>T	c.(319-321)caG>caT	p.Q107H	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	107					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)				TGCGGCCGCAGTCGGAGCGGG	0.602													G|||	1	0.000199681	0.0	0.0	5008	,	,		13103	0.0		0.0	False		,,,				2504	0.001				p.Q107H		Atlas-SNP	.											.	ARHGEF18	129	.	0			c.G321T						PASS	.						27	35	33					19																	7505147		692	1591	2283	SO:0001583	missense	23370	exon1			GCCGCAGTCGGAG	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.321G>T	19.37:g.7505147G>T	ENSP00000352995:p.Gln107His	74	0	0		116	52	0.448276	NM_001130955	A8MV62|B5ME81|O60274|Q6DD92	Missense_Mutation	SNP	ENST00000359920.6	37	CCDS45946.1	.	.	.	.	.	.	.	.	.	.	G	7.449	0.642374	0.14451	.	.	ENSG00000104880	ENST00000359920	T	0.30182	1.54	5.23	4.17	0.49024	.	0.187822	0.25607	U	0.029507	T	0.15565	0.0375	N	0.11560	0.145	0.09310	N	0.999997	B	0.10296	0.003	B	0.08055	0.003	T	0.13791	-1.0496	10	0.16896	T	0.51	-7.5996	11.9999	0.53224	0.0:0.0:0.7921:0.2079	.	107	Q6ZSZ5	ARHGI_HUMAN	H	107	ENSP00000352995:Q107H	ENSP00000352995:Q107H	Q	+	3	2	ARHGEF18	7411147	0.006000	0.16342	0.034000	0.17996	0.874000	0.50279	0.359000	0.20233	2.442000	0.82660	0.561000	0.74099	CAG	G|0.999;T|0.001	0.001	weak		0.602	ARHGEF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436340.1	NM_015318		T	7505147	G	T	7505147	3	4	25	1	0	0	0	0	1	0	0	0	901	1020	36	4	323	4	ARHGEF18	19	7505147	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1	7505147	51623836	716	9625	118	2									
MUC16	94025	hgsc.bcm.edu	37	chr19	9070873	9070873	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatggatgttctgctagaggAgatttctgttctggaggcct	7	14	14	6	0	3	2	0	0	3	2	3	6	3	4	1	4	1	3	1	4	1	4	rs79202331	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9070873A>G	ENST00000397910.4	-	3	16776	c.16573T>C	c.(16573-16575)Tcc>Ccc	p.S5525P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5527	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						CTGCTAGAGGAGATTTCTGTT	0.507													A|||	24	0.00479233	0.0015	0.0043	5008	,	,		20120	0.0		0.0149	False		,,,				2504	0.0041				p.S5525P		Atlas-SNP	.											.	MUC16	4315	.	0			c.T16573C						PASS	.		PRO/SER	3,3913		0,3,1955	157	142	147		16573	0.9	0	19	dbSNP_131	147	59,8275		0,59,4108	yes	missense	MUC16	NM_024690.2	74	0,62,6063	GG,GA,AA		0.7079,0.0766,0.5061	benign	5525/14508	9070873	62,12188	1958	4167	6125	SO:0001583	missense	94025	exon3			TAGAGGAGATTTC	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.16573T>C	19.37:g.9070873A>G	ENSP00000381008:p.Ser5525Pro	236	1	0.00423729		248	115	0.46371	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	14	0.00641025641025641	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	9	0.011873350923482849	a	3.455	-0.111140	0.06881	7.66E-4	0.007079	ENSG00000181143	ENST00000397910	T	0.02709	4.19	1.89	0.851	0.18989	.	.	.	.	.	T	0.01730	0.0055	L	0.32530	0.975	.	.	.	B	0.06786	0.001	B	0.04013	0.001	T	0.33471	-0.9867	8	0.87932	D	0	.	3.8711	0.09036	0.8048:0.0:0.1952:0.0	.	5525	B5ME49	.	P	5525	ENSP00000381008:S5525P	ENSP00000381008:S5525P	S	-	1	0	MUC16	8931873	0.005000	0.15991	0.001000	0.08648	0.086000	0.17979	0.206000	0.17375	0.192000	0.20272	-0.933000	0.02702	TCC	A|0.993;G|0.007	0.007	strong		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9070873	A	G	9070873	3	3	25	1	0	0	0	0	1	0	0	0	9982	304	11	3	27278	3	MUC16	19	9070873	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	1565726	9070873	50058110	717	9626											
RDH8	50700	hgsc.bcm.edu	37	chr19	10124257	10124257	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gcagtgcaactggcccatgaCcccaagaagcgctaccaggg	11	4	12	14	1	0	2	0	1	0	1	0	2	0	2	4	2	4	3	4	2	4	1	rs150712129	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10124257C>T	ENST00000171214.1	+	1	333	c.84C>T	c.(82-84)gaC>gaT	p.D28D	RDH8_ENST00000591589.1_Silent_p.D48D	NM_015725.2	NP_056540.2	Q9NYR8	RDH8_HUMAN	retinol dehydrogenase 8 (all-trans)	28					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)	TGGCCCATGACCCCAAGAAGC	0.612																																					p.D48D		Atlas-SNP	.											.	RDH8	51	.	0			c.C144T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	83	76	78		84	1.5	0.9	19	dbSNP_134	78	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RDH8	NM_015725.2		0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154		28/312	10124257	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	50700	exon1			CCATGACCCCAAG	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.84C>T	19.37:g.10124257C>T		28	0	0		37	16	0.432432	NM_015725	Q9H838	Silent	SNP	ENST00000171214.1	37																																																																																				C|1.000;T|0.000	0.000	strong		0.612	RDH8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				T	10124257	C	T	10124257	2	4	25	1	0	0	0	0	0	0	0	1	13211	506	18	2		2	RDH8	19	10124257	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1053384	10124257	49004726	718	9627											
PPAN	56342	hgsc.bcm.edu	37	chr19	10221227	10221227	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagaagctgcggctgaaggCgcagaggcaggcccagcagg	11	2	18	10	2	0	3	0	1	0	2	0	4	0	3	1	5	3	5	1	5	3	0	rs139737427		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10221227C>T	ENST00000253107.7	+	10	1074	c.968C>T	c.(967-969)gCg>gTg	p.A323V	P2RY11_ENST00000321826.4_5'Flank|SNORD105_ENST00000386910.1_RNA|SNORD105B_ENST00000458770.1_RNA|PPAN-P2RY11_ENST00000393796.4_Missense_Mutation_p.A323V|PPAN-P2RY11_ENST00000428358.1_Missense_Mutation_p.A323V|PPAN_ENST00000556468.1_Missense_Mutation_p.A323V|PPAN_ENST00000393793.1_Missense_Mutation_p.A270V	NM_020230.5	NP_064615.3	Q9NQ55	SSF1_HUMAN	peter pan homolog (Drosophila)	323					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)			CGGCTGAAGGCGCAGAGGCAG	0.667													C|||	1	0.000199681	0.0	0.0	5008	,	,		15026	0.0		0.001	False		,,,				2504	0.0				p.A323V		Atlas-SNP	.											.	PPAN	43	.	0			c.C968T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA	1,4399		0,1,2199	14	17	16		968,968,968	3.8	0.4	19	dbSNP_134	16	18,8574		0,18,4278	yes	missense,missense,missense	PPAN,PPAN-P2RY11	NM_001040664.2,NM_001198690.1,NM_020230.5	64,64,64	0,19,6477	TT,TC,CC		0.2095,0.0227,0.1462	possibly-damaging,possibly-damaging,possibly-damaging	323/795,323/521,323/474	10221227	19,12973	2200	4296	6496	SO:0001583	missense	56342	exon10			TGAAGGCGCAGAG	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.968C>T	19.37:g.10221227C>T	ENSP00000253107:p.Ala323Val	89	0	0		82	43	0.52439	NM_020230	C9J3F9|Q9BW97|Q9H170	Missense_Mutation	SNP	ENST00000253107.7	37	CCDS12225.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	C|C	12.64|12.64	1.999423|1.999423	0.35320|0.35320	2.27E-4|2.27E-4	0.002095|0.002095	ENSG00000243207;ENSG00000243207;ENSG00000130810;ENSG00000130810;ENSG00000130810;ENSG00000130810|ENSG00000130810	ENST00000428358;ENST00000393796;ENST00000253107;ENST00000556468;ENST00000342696;ENST00000393793|ENST00000444703	T;T;T;T;T|.	0.63255|.	1.39;-0.03;1.42;-0.03;1.44|.	4.78|4.78	3.75|3.75	0.43078|0.43078	.|.	.|.	.|.	.|.	.|.	T|T	0.49677|0.49677	0.1571|0.1571	L|L	0.61036|0.61036	1.89|1.89	0.29207|0.29207	N|N	0.874799|0.874799	P;P;P|.	0.50710|.	0.931;0.87;0.938|.	B;B;B|.	0.33960|.	0.173;0.101;0.146|.	T|T	0.47971|0.47971	-0.9075|-0.9075	9|5	0.51188|.	T|.	0.08|.	-14.6112|-14.6112	7.0518|7.0518	0.25077|0.25077	0.1706:0.7394:0.0:0.09|0.1706:0.7394:0.0:0.09	.|.	323;323;323|.	C9J3F9;C9JW41;Q9NQ55|.	.;.;SSF1_HUMAN|.	V|C	323;323;323;323;323;270|83	ENSP00000411918:A323V;ENSP00000377385:A323V;ENSP00000253107:A323V;ENSP00000450710:A323V;ENSP00000377382:A270V|.	ENSP00000253107:A323V|.	A|R	+|+	2|1	0|0	PPAN;PPAN-P2RY11|PPAN	10082227|10082227	0.950000|0.950000	0.32346|0.32346	0.433000|0.433000	0.26760|0.26760	0.029000|0.029000	0.11900|0.11900	2.089000|2.089000	0.41672|0.41672	1.008000|1.008000	0.39264|0.39264	0.561000|0.561000	0.74099|0.74099	GCG|CGC	C|0.999;T|0.001	0.001	strong		0.667	PPAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316658.1	NM_020230		T	10221227	C	T	10221227	3	4	25	1	0	0	0	0	1	0	0	0	12297	768	27	1	1006	1	PPAN	19	10221227	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	96970	10221227	48907756	719	9628											
MRPL4	51073	hgsc.bcm.edu	37	chr19	10370310	10370310	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggcctaaatgtgcacagcAtgctcaagcaccagacgctg	12	6	10	13	1	1	1	1	0	0	1	1	1	1	1	2	1	4	5	2	1	3	1	rs77884668	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10370310A>G	ENST00000253099.6	+	9	1044	c.757A>G	c.(757-759)Atg>Gtg	p.M253V	MRPL4_ENST00000393733.2_3'UTR|CTD-2369P2.4_ENST00000587088.1_RNA|CTD-2369P2.5_ENST00000592893.1_RNA|MRPL4_ENST00000307422.5_Missense_Mutation_p.M253V	NM_015956.2|NM_146388.1	NP_057040.2|NP_666500.1	Q9BYD3	RM04_HUMAN	mitochondrial ribosomal protein L4	253					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	11		Renal(1328;0.0112)	OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;1.99e-06)|all cancers(31;4.81e-06)	Lung(535;0.00705)		TGTGCACAGCATGCTCAAGCA	0.677													A|||	73	0.0145767	0.0537	0.0029	5008	,	,		6135	0.0		0.0	False		,,,				2504	0.0				p.M253V		Atlas-SNP	.											.	MRPL4	22	.	0			c.A757G						PASS	.	A	VAL/MET,VAL/MET,	184,4222	109.5+/-147.8	2,180,2021	38	29	32		757,757,	2.9	1	19	dbSNP_131	32	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,utr-3	MRPL4	NM_015956.2,NM_146387.1,NM_146388.1	21,21,	2,181,6320	GG,GA,AA		0.0116,4.1761,1.4224	possibly-damaging,possibly-damaging,	253/312,253/312,	10370310	185,12821	2203	4300	6503	SO:0001583	missense	51073	exon10			CACAGCATGCTCA	AB049635	CCDS12230.1, CCDS42499.1	19p13.2	2012-11-14			ENSG00000105364	ENSG00000105364		"Mitochondrial ribosomal proteins / large subunits"	14276	protein-coding gene	gene with protein product		611823					Standard	NM_015956		Approved	CGI-28	uc002mnn.3	Q9BYD3	OTTHUMG00000180400	ENST00000253099.6:c.757A>G	19.37:g.10370310A>G	ENSP00000253099:p.Met253Val	71	0	0		74	40	0.540541	NM_146387	A6NNV7|Q9BW07|Q9H4N2|Q9Y317	Missense_Mutation	SNP	ENST00000253099.6	37	CCDS12230.1	31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	a	14.63	2.592614	0.46214	0.041761	1.16E-4	ENSG00000105364	ENST00000253099;ENST00000307422	.	.	.	5.1	2.89	0.33648	Ribosomal protein L4 domain (2);	0.224207	0.50627	D	0.000113	T	0.12860	0.0312	L	0.32530	0.975	0.39810	D	0.972685	P	0.37955	0.612	P	0.51055	0.657	T	0.20338	-1.0278	9	0.44086	T	0.13	-21.9678	10.159	0.42840	0.678:0.322:0.0:0.0	.	253	Q9BYD3	RM04_HUMAN	V	253	.	ENSP00000253099:M253V	M	+	1	0	MRPL4	10231310	1.000000	0.71417	1.000000	0.80357	0.649000	0.38597	1.695000	0.37763	0.232000	0.21100	0.449000	0.29647	ATG	A|0.984;G|0.016	0.016	strong		0.677	MRPL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451197.1			G	10370310	A	G	10370310	3	3	25	1	0	0	0	0	1	0	0	0	9812	217	8	3	844	3	MRPL4	19	10370310	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	149083	10370310	48758673	720	9629											
TYK2	7297	hgsc.bcm.edu	37	chr19	10472452	10472452	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccctgcccactcaccagggcGatgtcatggtgactagggtc	7	8	12	14	1	2	1	2	1	0	0	3	2	2	1	3	3	1	0	3	3	1	1	rs12720355	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10472452G>A	ENST00000525621.1	-	13	2434	c.1953C>T	c.(1951-1953)atC>atT	p.I651I	TYK2_ENST00000529370.1_Silent_p.I651I|TYK2_ENST00000264818.6_Silent_p.I651I|TYK2_ENST00000524462.1_Silent_p.I466I	NM_003331.4	NP_003322.3	P29597	TYK2_HUMAN	tyrosine kinase 2	651	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)			TCACCAGGGCGATGTCATGGT	0.652													g|||	25	0.00499201	0.0008	0.0058	5008	,	,		15733	0.0		0.0139	False		,,,				2504	0.0061				p.I651I		Atlas-SNP	.											.	TYK2	126	.	0			c.C1953T						PASS	.	G		13,4393	20.2+/-43.8	0,13,2190	83	81	82		1953	-3.9	0.4	19	dbSNP_121	82	132,8468	66.7+/-129.0	1,130,4169	no	coding-synonymous	TYK2	NM_003331.4		1,143,6359	AA,AG,GG		1.5349,0.2951,1.1149		651/1188	10472452	145,12861	2203	4300	6503	SO:0001819	synonymous_variant	7297	exon13			CAGGGCGATGTCA		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.1953C>T	19.37:g.10472452G>A		69	0	0		68	34	0.5	NM_003331	Q6QB10|Q96CH0	Silent	SNP	ENST00000525621.1	37	CCDS12236.1																																																																																			G|0.992;A|0.008	0.008	strong		0.652	TYK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389443.1			A	10472452	G	A	10472452	2	1	25	1	0	0	0	0	0	0	0	1	16825	1048	37	1		1	TYK2	19	10472452	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	102142	10472452	48656531	721	9630											
S1PR5	53637	hgsc.bcm.edu	37	chr19	10624863	10624863	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caggtgcgcgccgggcacgcCacgtcgagcaacagcagcag	9	2	15	15	6	0	0	0	0	0	0	1	1	0	0	2	2	5	4	2	2	1	0	rs75861469	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10624863C>T	ENST00000439028.3	-	2	950	c.825G>A	c.(823-825)gtG>gtA	p.V275V	S1PR5_ENST00000333430.4_Silent_p.V275V	NM_001166215.1	NP_001159687.1	Q9H228	S1PR5_HUMAN	sphingosine-1-phosphate receptor 5	275					regulation of neuron differentiation (GO:0045664)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sphingosine-1-phosphate receptor activity (GO:0038036)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	12					Fingolimod(DB08868)	CCGGGCACGCCACGTCGAGCA	0.652													C|||	96	0.0191693	0.0711	0.0029	5008	,	,		15206	0.0		0.0	False		,,,				2504	0.0				p.V275V		Atlas-SNP	.											.	S1PR5	33	.	0			c.G825A						PASS	.	C	,	236,4150	125.7+/-162.9	9,218,1966	31	29	29		825,825	1.2	1	19	dbSNP_132	29	3,8593	1.2+/-3.3	0,3,4295	no	coding-synonymous,coding-synonymous	S1PR5	NM_001166215.1,NM_030760.4	,	9,221,6261	TT,TC,CC		0.0349,5.3808,1.841	,	275/399,275/399	10624863	239,12743	2193	4298	6491	SO:0001819	synonymous_variant	53637	exon2			GCACGCCACGTCG	AK074661	CCDS12240.1	19p13.2	2012-08-08	2008-04-30	2008-04-30		ENSG00000180739		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"	14299	protein-coding gene	gene with protein product		605146	"endothelial differentiation, sphingolipid G-protein-coupled receptor, 8"	EDG8		10799507	Standard	NM_030760		Approved	Edg-8	uc002mou.2	Q9H228		ENST00000439028.3:c.825G>A	19.37:g.10624863C>T		46	0	0		56	31	0.553571	NM_030760	Q6NW11	Silent	SNP	ENST00000439028.3	37	CCDS12240.1	35	0.016025641025641024	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	9.558	1.117787	0.20877	0.053808	3.49E-4	ENSG00000180739	ENST00000359134	.	.	.	5.15	1.24	0.21308	.	.	.	.	.	T	0.05456	0.0144	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.09228	-1.0684	5	0.41790	T	0.15	.	1.7012	0.02873	0.1474:0.4422:0.1546:0.2558	.	.	.	.	S	244	.	ENSP00000352045:G244S	G	-	1	0	S1PR5	10485863	0.002000	0.14202	1.000000	0.80357	0.816000	0.46133	-0.292000	0.08332	0.541000	0.28827	0.491000	0.48974	GGC	C|0.981;T|0.019	0.019	strong		0.652	S1PR5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452015.1	NM_030760		T	10624863	C	T	10624863	2	4	25	1	0	0	0	0	0	0	0	1	13812	581	21	2		2	S1PR5	19	10624863	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	152411	10624863	48504120	722	9631											
YIPF2	78992	hgsc.bcm.edu	37	chr19	11036415	11036415	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacaaagttgtggccaggcCggggcagcagtgagcctttg	8	7	16	10	1	0	1	0	1	0	0	0	1	0	1	3	4	2	4	3	4	1	2	rs148361413	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:11036415C>T	ENST00000586748.1	-	5	486	c.314G>A	c.(313-315)cGg>cAg	p.R105Q	YIPF2_ENST00000590329.1_Missense_Mutation_p.R105Q|YIPF2_ENST00000253031.2_Missense_Mutation_p.R105Q|C19orf52_ENST00000270502.6_5'Flank			Q9BWQ6	YIPF2_HUMAN	Yip1 domain family, member 2	105						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)				cervix(1)|endometrium(1)|lung(3)|ovary(2)	7						GTGGCCAGGCCGGGGCAGCAG	0.577																																					p.R105Q		Atlas-SNP	.											.	YIPF2	13	.	0			c.G314A						PASS	.	C	GLN/ARG	0,4404		0,0,2202	90	74	80		314	2.5	1	19	dbSNP_134	80	1,8599	1.2+/-3.3	0,1,4299	no	missense	YIPF2	NM_024029.3	43	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	105/317	11036415	1,13003	2202	4300	6502	SO:0001583	missense	78992	exon5			CCAGGCCGGGGCA	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.314G>A	19.37:g.11036415C>T	ENSP00000466055:p.Arg105Gln	58	0	0		83	49	0.590361	NM_024029		Missense_Mutation	SNP	ENST00000586748.1	37	CCDS12251.1	.	.	.	.	.	.	.	.	.	.	C	13.29	2.191861	0.38707	0.0	1.16E-4	ENSG00000130733	ENST00000253031	.	.	.	4.71	2.46	0.29980	Yip1 domain (1);	0.599360	0.15816	N	0.243259	T	0.24160	0.0585	L	0.27053	0.805	0.09310	N	1	B	0.23591	0.088	B	0.14023	0.01	T	0.11060	-1.0603	9	0.27785	T	0.31	-12.2256	4.8429	0.13500	0.4337:0.4455:0.0:0.1208	.	105	Q9BWQ6	YIPF2_HUMAN	Q	105	.	ENSP00000253031:R105Q	R	-	2	0	YIPF2	10897415	0.003000	0.15002	0.998000	0.56505	0.981000	0.71138	2.003000	0.40844	0.930000	0.37217	0.542000	0.68232	CGG	C|1.000;T|0.000	0.000	strong		0.577	YIPF2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453045.1	NM_024029		T	11036415	C	T	11036415	3	4	25	1	0	0	0	0	1	0	0	0	17493	652	23	1	656	1	YIPF2	19	11036415	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	411552	11036415	48092568	723	9632											
TSPAN16	26526	hgsc.bcm.edu	37	chr19	11407019	11407019	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttccttgaagaaactgttaTctttactcaatggcttcgtg	9	16	7	9	1	2	2	1	1	1	1	4	2	3	2	1	1	2	2	1	1	5	6			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:11407019T>C	ENST00000316737.1	+	1	196	c.46T>C	c.(46-48)Tct>Cct	p.S16P	TSPAN16_ENST00000592955.1_Missense_Mutation_p.S16P|TSPAN16_ENST00000590327.1_Missense_Mutation_p.S16P	NM_012466.2	NP_036598.1	Q9UKR8	TSN16_HUMAN	tetraspanin 16	16						integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	12						GAAACTGTTATCTTTACTCAA	0.463																																					p.S16P		Atlas-SNP	.											.	TSPAN16	22	.	0			c.T46C						PASS	.						122	114	117					19																	11407019		2203	4300	6503	SO:0001583	missense	26526	exon1			CTGTTATCTTTAC	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.46T>C	19.37:g.11407019T>C	ENSP00000319486:p.Ser16Pro	126	0	0		121	57	0.471074	NM_012466	K7EN22|K7EPD8|Q8N6J7	Missense_Mutation	SNP	ENST00000316737.1	37	CCDS12256.1	.	.	.	.	.	.	.	.	.	.	T	14.76	2.630464	0.46944	.	.	ENSG00000130167	ENST00000316737;ENST00000337994	T;T	0.79554	-1.28;-1.28	3.78	-0.82	0.10826	.	2.367380	0.02315	N	0.072502	T	0.65260	0.2674	N	0.12182	0.205	0.09310	N	1	B	0.15719	0.014	B	0.18263	0.021	T	0.54410	-0.8298	10	0.66056	D	0.02	-0.0342	3.9199	0.09239	0.0:0.3253:0.192:0.4827	.	16	Q9UKR8	TSN16_HUMAN	P	16	ENSP00000319486:S16P;ENSP00000338759:S16P	ENSP00000319486:S16P	S	+	1	0	TSPAN16	11268019	0.000000	0.05858	0.000000	0.03702	0.298000	0.27526	0.403000	0.20982	-0.257000	0.09459	-0.379000	0.06801	TCT	.	.	none		0.463	TSPAN16-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000453204.1	NM_012466		C	11407019	T	C	11407019	3	2	25	1	0	0	0	0	1	0	0	0	16655	1435	50	3	48	3	TSPAN16	19	11407019	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	370604	11407019	47721964	724	9633											
RAB3D	9545	hgsc.bcm.edu	37	chr19	11436221	11436221	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctcgaagacctgcttcacAttgatgttctccttggcact	7	13	8	13	2	2	2	1	1	1	1	4	3	2	2	2	1	1	4	2	1	1	4	rs12981706	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:11436221A>G	ENST00000222120.3	-	5	773	c.513T>C	c.(511-513)aaT>aaC	p.N171N	CTC-510F12.4_ENST00000586356.1_RNA|TSPAN16_ENST00000316737.1_Intron|RAB3D_ENST00000589655.1_Silent_p.N171N|CTC-510F12.6_ENST00000586051.1_RNA	NM_004283.3	NP_004274.1	O95716	RAB3D_HUMAN	RAB3D, member RAS oncogene family	171					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						CCTGCTTCACATTGATGTTCT	0.557													A|||	286	0.0571086	0.1762	0.0187	5008	,	,		14659	0.0		0.0318	False		,,,				2504	0.0082				p.N171N		Atlas-SNP	.											.	RAB3D	24	.	0			c.T513C						PASS	.	A	,	617,3789	268.6+/-268.5	43,531,1629	146	132	136		513,	-6.2	1	19	dbSNP_121	136	293,8307	108.0+/-168.7	3,287,4010	no	coding-synonymous,intron	RAB3D,TSPAN16	NM_004283.3,NM_012466.2	,	46,818,5639	GG,GA,AA		3.407,14.0036,6.9968	,	171/220,	11436221	910,12096	2203	4300	6503	SO:0001819	synonymous_variant	9545	exon5			CTTCACATTGATG	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.513T>C	19.37:g.11436221A>G		32	0	0		35	16	0.457143	NM_004283		Silent	SNP	ENST00000222120.3	37	CCDS12257.1																																																																																			A|0.939;G|0.061;T|0.000	0.061	strong		0.557	RAB3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453211.1	NM_004283		G	11436221	A	G	11436221	2	3	25	1	0	0	0	0	0	0	0	1	12949	214	8	3		3	RAB3D	19	11436221	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	29202	11436221	47692762	725	9634											
C19orf39	126074	hgsc.bcm.edu	37	chr19	11486514	11486514	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagtgctggctgcagccagAtgcaccaggtccaggagagc	9	5	14	13	0	0	2	0	0	0	2	1	3	1	2	4	3	5	4	4	3	0	0	rs317926	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:11486514A>G	ENST00000312423.2	+	2	571	c.512A>G	c.(511-513)gAt>gGt	p.D171G	CTD-2342J14.6_ENST00000590399.1_RNA	NM_175871.3	NP_787067.2	Q6NVH7	SWAP1_HUMAN	SWIM-type zinc finger 7 associated protein 1	171			D -> G (in dbSNP:rs317926).		ATP catabolic process (GO:0006200)|double-strand break repair via homologous recombination (GO:0000724)|protein stabilization (GO:0050821)	nucleus (GO:0005634)|Shu complex (GO:0097196)	ATPase activity (GO:0016887)|single-stranded DNA binding (GO:0003697)										CTGCAGCCAGATGCACCAGGT	0.642													A|||	69	0.013778	0.0507	0.0029	5008	,	,		16689	0.0		0.0	False		,,,				2504	0.0				p.D171G		Atlas-SNP	.											C19orf39,NS,carcinoma,0,1	.	.	1	0			c.A512G						PASS	.	A	GLY/ASP	196,4210	117.5+/-155.4	3,190,2010	42	40	41		512	0.5	0	19	dbSNP_79	41	3,8597	3.0+/-9.4	0,3,4297	no	missense	C19orf39	NM_175871.3	94	3,193,6307	GG,GA,AA		0.0349,4.4485,1.5301	possibly-damaging	171/230	11486514	199,12807	2203	4300	6503	SO:0001583	missense	126074	exon2			AGCCAGATGCACC	AK092438	CCDS12259.1	19p13.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000173928	ENSG00000173928			26638	protein-coding gene	gene with protein product	"zinc finger, SWIM-type containing 7 associated protein 1", "SWS1-associated protein 1"	614536	"chromosome 19 open reading frame 39"	C19orf39		21965664	Standard	NM_175871		Approved	FLJ35119, ZSWIM7AP1, SWS1AP1	uc002mrg.1	Q6NVH7		ENST00000312423.2:c.512A>G	19.37:g.11486514A>G	ENSP00000310008:p.Asp171Gly	49	0	0		60	26	0.433333	NM_175871	Q8NAM1	Missense_Mutation	SNP	ENST00000312423.2	37	CCDS12259.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	A	9.198	1.027667	0.19512	0.044485	3.49E-4	ENSG00000173928	ENST00000312423	T	0.48522	0.81	5.15	0.528	0.17089	.	1.321610	0.04957	N	0.461333	T	0.13072	0.0317	L	0.60455	1.87	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.16778	-1.0391	10	0.48119	T	0.1	1.0742	1.487	0.02449	0.5539:0.1458:0.16:0.1402	rs317926;rs318715;rs317926	171	Q6NVH7	CS039_HUMAN	G	171	ENSP00000310008:D171G	ENSP00000310008:D171G	D	+	2	0	C19orf39	11347514	0.000000	0.05858	0.000000	0.03702	0.315000	0.28087	0.288000	0.18939	-0.287000	0.09064	0.533000	0.62120	GAT	A|0.984;G|0.016	0.016	strong		0.642	SWSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458789.1	NM_175871		G	11486514	A	G	11486514	3	3	25	1	0	0	0	0	1	0	0	0	1924	333	12	3	518	3	C19orf39	19	11486514	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	50293	11486514	47642469	726	9635											
ZNF491	126069	hgsc.bcm.edu	37	chr19	11916914	11916914	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggagaaatcttcatgggatAttcatcctttaataggaaca	14	13	8	6	0	3	1	2	0	1	1	4	4	4	3	1	3	1	0	1	3	5	6	rs141870350	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:11916914A>G	ENST00000323169.5	+	3	477	c.146A>G	c.(145-147)tAt>tGt	p.Y49C	ZNF491_ENST00000492230.1_Intron	NM_152356.3	NP_689569.2	Q8N8L2	ZN491_HUMAN	zinc finger protein 491	49					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						TTCATGGGATATTCATCCTTT	0.383													A|||	3	0.000599042	0.0	0.0014	5008	,	,		18120	0.0		0.002	False		,,,				2504	0.0				p.Y49C		Atlas-SNP	.											.	ZNF491	61	.	0			c.A146G						PASS	.	A	CYS/TYR	6,4400	9.9+/-24.2	0,6,2197	72	76	75		146	1	0	19	dbSNP_134	75	66,8534	41.2+/-98.3	1,64,4235	yes	missense	ZNF491	NM_152356.3	194	1,70,6432	GG,GA,AA		0.7674,0.1362,0.5536	benign	49/438	11916914	72,12934	2203	4300	6503	SO:0001583	missense	126069	exon3			TGGGATATTCATC	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.146A>G	19.37:g.11916914A>G	ENSP00000313443:p.Tyr49Cys	78	0	0		76	38	0.5	NM_152356	Q3MJ35|Q8NAT8	Missense_Mutation	SNP	ENST00000323169.5	37	CCDS12267.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	a	9.874	1.199678	0.22121	0.001362	0.007674	ENSG00000177599	ENST00000323169;ENST00000455048;ENST00000450087	T;T	0.15256	2.44;2.44	1.01	1.01	0.19927	Zinc finger, C2H2 (1);	.	.	.	.	T	0.05273	0.0140	N	0.12831	0.26	0.09310	N	1	B	0.28900	0.227	B	0.19148	0.024	T	0.30851	-0.9964	9	0.37606	T	0.19	.	5.9285	0.19126	1.0:0.0:0.0:0.0	.	49	Q8N8L2	ZN491_HUMAN	C	49	ENSP00000313443:Y49C;ENSP00000392176:Y49C	ENSP00000313443:Y49C	Y	+	2	0	ZNF491	11777914	0.000000	0.05858	0.007000	0.13788	0.007000	0.05969	-1.435000	0.02423	0.710000	0.31997	0.413000	0.27773	TAT	A|0.997;G|0.003	0.003	strong		0.383	ZNF491-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344518.1	NM_152356		G	11916914	A	G	11916914	3	3	25	1	0	0	0	0	1	0	0	0	17957	449	16	3	148	3	ZNF491	19	11916914	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	430400	11916914	47212069	727	9636											
ZNF700	90592	hgsc.bcm.edu	37	chr19	12060627	12060627	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaccctatgagtgtaagcaAtgtgggaaagccttcagttg	13	10	11	7	0	1	1	1	1	0	0	1	2	1	2	2	1	3	3	2	1	5	4	rs78201704	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12060627A>G	ENST00000254321.5	+	4	1931	c.1788A>G	c.(1786-1788)caA>caG	p.Q596Q	CTD-2006C1.12_ENST00000586394.1_RNA|ZNF763_ENST00000538752.1_Intron|ZNF763_ENST00000591944.1_Intron|ZNF700_ENST00000482090.1_Silent_p.Q578Q|ZNF763_ENST00000590798.1_Intron	NM_001271848.1|NM_144566.1	NP_001258777.1|NP_653167.1	Q9H0M5	ZN700_HUMAN	zinc finger protein 700	596					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.Q596Q(1)	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						AGTGTAAGCAATGTGGGAAAG	0.473													a|||	75	0.014976	0.0492	0.0058	5008	,	,		23157	0.0		0.006	False		,,,				2504	0.0				p.Q599Q		Atlas-SNP	.											ZNF700,NS,carcinoma,0,1	ZNF700	81	1	1	Substitution - coding silent(1)	pancreas(1)	c.A1797G						PASS	.	A		254,4152	145.4+/-180.2	8,238,1957	105	103	104		1788	-1	0	19	dbSNP_131	104	30,8570	21.0+/-64.5	0,30,4270	no	coding-synonymous	ZNF700	NM_144566.1		8,268,6227	GG,GA,AA		0.3488,5.7649,2.1836		596/743	12060627	284,12722	2203	4300	6503	SO:0001819	synonymous_variant	90592	exon4			TAAGCAATGTGGG	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.1788A>G	19.37:g.12060627A>G		34	0	0		39	21	0.538462	NM_001271848	B9EGU4	Silent	SNP	ENST00000254321.5	37	CCDS32915.1																																																																																			A|0.979;G|0.021	0.021	strong		0.473	ZNF700-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344126.2	NM_144566		G	12060627	A	G	12060627	2	3	25	1	0	0	0	0	0	0	0	1	18119	98	4	3		3	ZNF700	19	12060627	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	143713	12060627	47068356	728	9637											
ZNF844	284391	hgsc.bcm.edu	37	chr19	12187316	12187317	+	Frame_Shift_Del	DEL	CA	CA	-																															gaaagccttcagatctgcctCacaccttcaaatgcatggaa																								rs201088213|rs61471402	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12187316_12187317delCA	ENST00000439326.3	+	4	1556_1557	c.1381_1382delCA	c.(1381-1383)cacfs	p.H461fs	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	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)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						AGATCTGCCTCACACCTTCAAA	0.431														57	0.0113818	0.0371	0.0029	5008	,	,		24663	0.0		0.006	False		,,,				2504	0.0				p.460_461del		Atlas-Indel	.											.	ZNF844	69	.	0			c.1380_1381del						PASS	.			196,4068		7,182,1943						-5	0		dbSNP_129	63	24,8228		1,22,4103	no	frameshift	ZNF844	NM_001136501.1		8,204,6046	A1A1,A1R,RR		0.2908,4.5966,1.7578				220,12296				SO:0001589	frameshift_variant	284391	exon4			.	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.1381_1382delCA	19.37:g.12187318_12187319delCA	ENSP00000392024:p.His461fs	52	0	0		38	14	0.368421	NM_001136501	Q5JPI8	Frame_Shift_Del	DEL	ENST00000439326.3	37	CCDS45985.1																																																																																			CA|0.987;-|0.013	0.013	strong		0.431	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2			-	12187317	CA	-	12187316	7	5	25	1	0	1	0	1	0	0	0	0	18205	826	29	0	1395	0	ZNF844	19	12187316	Frame_Shift_Del	DEL	CA	TCGA-G8-6906-01A-11D-2210-10	126689	12187316	46941667	729	9638											
ZNF844	284391	hgsc.bcm.edu	37	chr19	12187907	12187907	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagtttgcctggttcctttcGtagacataaaagggctcaca	10	12	9	10	1	1	1	1	0	0	1	3	1	2	1	2	2	1	4	2	2	3	5	rs55703333	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12187907G>A	ENST00000439326.3	+	4	2147	c.1972G>A	c.(1972-1974)Gta>Ata	p.V658I	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	658			V -> I (in dbSNP:rs55703333).		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						GGTTCCTTTCGTAGACATAAA	0.403													.|||	76	0.0151757	0.0378	0.0086	5008	,	,		22386	0.001		0.0179	False		,,,				2504	0.001				p.V658I		Atlas-SNP	.											.	ZNF844	69	.	0			c.G1972A						PASS	.	G	ILE/VAL	71,1313		4,63,625	47	51	50		1972	-5.8	0	19	dbSNP_129	50	50,3132		2,46,1543	yes	missense	ZNF844	NM_001136501.1	29	6,109,2168	AA,AG,GG		1.5713,5.1301,2.65	benign	658/667	12187907	121,4445	692	1591	2283	SO:0001583	missense	284391	exon4			CCTTTCGTAGACA	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.1972G>A	19.37:g.12187907G>A	ENSP00000392024:p.Val658Ile	43	0	0		64	28	0.4375	NM_001136501	Q5JPI8	Missense_Mutation	SNP	ENST00000439326.3	37	CCDS45985.1	43	0.019688644688644688	23	0.046747967479674794	4	0.011049723756906077	1	0.0017482517482517483	15	0.01978891820580475	G	9.085	1.000237	0.19121	0.051301	0.015713	ENSG00000223547	ENST00000439326	T	0.05996	3.36	2.92	-5.83	0.02325	.	.	.	.	.	T	0.00356	0.0011	N	0.08118	0	0.09310	N	1	P	0.40476	0.718	B	0.21917	0.037	T	0.41233	-0.9520	9	0.87932	D	0	.	4.1975	0.10450	0.1349:0.1113:0.5622:0.1917	rs55703333	658	Q08AG5	ZN844_HUMAN	I	658	ENSP00000392024:V658I	ENSP00000392024:V658I	V	+	1	0	ZNF844	12048907	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-4.792000	0.00185	-1.709000	0.01399	-0.300000	0.09419	GTA	G|0.980;A|0.020	0.020	strong		0.403	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2			A	12187907	G	A	12187907	3	1	25	1	0	0	0	0	1	0	0	0	18205	1145	40	1	1986	1	ZNF844	19	12187907	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	591	12187907	46941076	730	9639											
ZNF442	79973	hgsc.bcm.edu	37	chr19	12463856	12463856	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacatctctgtacagactctTctgtgatggacccagcaaag	11	10	8	12	0	3	2	0	1	3	1	4	3	3	3	1	1	2	2	1	1	2	2	rs73921445	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12463856T>C	ENST00000242804.4	-	4	733	c.151A>G	c.(151-153)Aag>Gag	p.K51E	ZNF442_ENST00000438182.1_Intron	NM_030824.2	NP_110451.1	Q9H7R0	ZN442_HUMAN	zinc finger protein 442	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(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	31						TACAGACTCTTCTGTGATGGA	0.438													T|||	63	0.0125799	0.0378	0.0058	5008	,	,		19281	0.0		0.008	False		,,,				2504	0.001				p.K51E		Atlas-SNP	.											.	ZNF442	102	.	0			c.A151G						PASS	.	T	GLU/LYS	139,4267	98.9+/-137.6	3,133,2067	142	139	140		151	1	0.1	19	dbSNP_130	140	33,8567	22.2+/-67.0	0,33,4267	yes	missense	ZNF442	NM_030824.2	56	3,166,6334	CC,CT,TT		0.3837,3.1548,1.3225	probably-damaging	51/628	12463856	172,12834	2203	4300	6503	SO:0001583	missense	79973	exon4			GACTCTTCTGTGA	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.151A>G	19.37:g.12463856T>C	ENSP00000242804:p.Lys51Glu	71	0	0		87	38	0.436782	NM_030824	B4DJ48	Missense_Mutation	SNP	ENST00000242804.4	37	CCDS12271.1	25	0.011446886446886446	15	0.03048780487804878	3	0.008287292817679558	0	0.0	7	0.009234828496042216	T	16.79	3.219430	0.58560	0.031548	0.003837	ENSG00000198342	ENST00000242804	T	0.02863	4.13	1.03	1.03	0.20045	Krueppel-associated box (4);	.	.	.	.	T	0.06462	0.0166	H	0.95850	3.73	0.36021	D	0.838739	D	0.89917	1.0	D	0.87578	0.998	T	0.03202	-1.1061	9	0.87932	D	0	.	6.2028	0.20585	0.0:0.0:0.0:1.0	.	51	Q9H7R0	ZN442_HUMAN	E	51	ENSP00000242804:K51E	ENSP00000242804:K51E	K	-	1	0	ZNF442	12324856	0.683000	0.27633	0.066000	0.19879	0.547000	0.35210	1.198000	0.32223	0.710000	0.31997	0.260000	0.18958	AAG	T|0.986;C|0.014	0.014	strong		0.438	ZNF442-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344109.1	NM_030824		C	12463856	T	C	12463856	3	2	25	1	0	0	0	0	1	0	0	0	17930	1792	62	3	1744	3	ZNF442	19	12463856	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	275949	12463856	46665127	731	9640											
RTBDN	83546	hgsc.bcm.edu	37	chr19	12936693	12936693	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	acgggctccaggagcagccaCcggtagggcgtggcccagag	8	3	17	13	3	0	1	0	0	0	1	1	2	1	2	4	5	2	3	4	5	1	1	rs148952767	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12936693C>T	ENST00000458671.2	-	6	669	c.517G>A	c.(517-519)Gtg>Atg	p.V173M	RTBDN_ENST00000592204.1_Missense_Mutation_p.V183M|RTBDN_ENST00000589272.1_3'UTR|RTBDN_ENST00000393233.2_3'UTR|RTBDN_ENST00000322912.5_Missense_Mutation_p.V205M|CTD-2265O21.3_ENST00000588469.1_RNA	NM_001080997.2	NP_001074466.1	Q9BSG5	RTBDN_HUMAN	retbindin	173						extracellular region (GO:0005576)				kidney(1)|large_intestine(5)|liver(1)|lung(4)|prostate(1)	12						GGAGCAGCCACCGGTAGGGCG	0.647											OREG0025275	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	19	0.00379393	0.0	0.0086	5008	,	,		13754	0.0		0.0109	False		,,,				2504	0.002				p.V205M		Atlas-SNP	.											.	RTBDN	26	.	0			c.G613A						PASS	.	C	MET/VAL,MET/VAL	4,4396		0,4,2196	29	26	27		517,613	1.9	0	19	dbSNP_134	27	77,8513		0,77,4218	yes	missense,missense	RTBDN	NM_001080997.1,NM_031429.1	21,21	0,81,6414	TT,TC,CC		0.8964,0.0909,0.6236	probably-damaging,probably-damaging	173/230,205/262	12936693	81,12909	2200	4295	6495	SO:0001583	missense	83546	exon7			CAGCCACCGGTAG	AY028917	CCDS12283.1, CCDS45994.1, CCDS59355.1, CCDS59356.1	19p13	2006-03-22				ENSG00000132026			30310	protein-coding gene	gene with protein product		609553				12107411	Standard	NM_001080997		Approved	FLJ36353	uc002mvj.4	Q9BSG5		ENST00000458671.2:c.517G>A	19.37:g.12936693C>T	ENSP00000416375:p.Val173Met	84	0	0	683	127	59	0.464567	NM_031429	F1T0I8|Q9BWT5	Missense_Mutation	SNP	ENST00000458671.2	37	CCDS45994.1	13	0.005952380952380952	0	0.0	3	0.008287292817679558	0	0.0	10	0.013192612137203167	C	16.73	3.204950	0.58234	9.09E-4	0.008964	ENSG00000132026	ENST00000322912;ENST00000458671	T;T	0.79033	-1.23;-1.23	4.36	1.89	0.25635	Folate receptor-like (1);	0.581337	0.14332	N	0.326316	T	0.79673	0.4486	M	0.70595	2.14	0.19300	N	0.999978	D;D	0.89917	1.0;1.0	D;D	0.74674	0.973;0.984	T	0.68949	-0.5274	10	0.72032	D	0.01	-26.9761	5.851	0.18694	0.0:0.7037:0.0:0.2963	.	205;173	Q9BSG5-2;Q9BSG5	.;RTBDN_HUMAN	M	205;173	ENSP00000326253:V205M;ENSP00000416375:V173M	ENSP00000326253:V205M	V	-	1	0	RTBDN	12797693	0.043000	0.20138	0.045000	0.18777	0.048000	0.14542	0.110000	0.15437	0.404000	0.25506	0.591000	0.81541	GTG	C|0.993;T|0.007	0.007	strong		0.647	RTBDN-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000451513.1	NM_031429		T	12936693	C	T	12936693	3	4	25	1	0	0	0	0	1	0	0	0	13732	507	18	2	176	2	RTBDN	19	12936693	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	472837	12936693	46192290	732	9641											
PKN1	5585	hgsc.bcm.edu	37	chr19	14580197	14580197	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggcggcagtgaccagtgcggGacaccccttcctggtgaacc	7	6	14	14	2	0	2	0	2	0	0	1	3	1	3	5	4	2	1	5	4	1	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:14580197G>T	ENST00000242783.6	+	16	2186	c.2021G>T	c.(2020-2022)gGa>gTa	p.G674V	PKN1_ENST00000342216.4_Missense_Mutation_p.G680V	NM_002741.3	NP_002732.3	Q16512	PKN1_HUMAN	protein kinase N1	674	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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						ACCAGTGCGGGACACCCCTTC	0.602																																					p.G680V	NSCLC(185;2539 2965 10733 52867)	Atlas-SNP	.											.	PKN1	99	.	0			c.G2039T						PASS	.						106	120	116					19																	14580197		2123	4227	6350	SO:0001583	missense	5585	exon16			GTGCGGGACACCC	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.2021G>T	19.37:g.14580197G>T	ENSP00000242783:p.Gly674Val	150	0	0		142	82	0.577465	NM_213560	A8K7W5|B2R9R4|B3KVN3|Q15143|Q504U4|Q8IUV5|Q9UD44	Missense_Mutation	SNP	ENST00000242783.6	37	CCDS42513.1	.	.	.	.	.	.	.	.	.	.	G	4.532	0.098772	0.08681	.	.	ENSG00000123143	ENST00000242783;ENST00000342216	T;T	0.25912	1.77;1.77	3.45	3.45	0.39498	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.356188	0.26407	U	0.024542	T	0.20170	0.0485	L	0.39514	1.22	0.28256	N	0.925049	B;B	0.26744	0.131;0.158	B;B	0.26310	0.04;0.068	T	0.13522	-1.0506	10	0.56958	D	0.05	-18.5356	8.9541	0.35807	0.0:0.2289:0.7711:0.0	.	680;674	Q16512-2;Q16512	.;PKN1_HUMAN	V	674;680	ENSP00000242783:G674V;ENSP00000343325:G680V	ENSP00000242783:G674V	G	+	2	0	PKN1	14441197	0.001000	0.12720	0.885000	0.34714	0.129000	0.20672	1.374000	0.34283	1.926000	0.55796	0.491000	0.48974	GGA	.	.	none		0.602	PKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095510.1	NM_002741, NM_213560		T	14580197	G	T	14580197	3	4	25	1	0	0	0	0	1	0	0	0	11988	1174	41	4	2126	4	PKN1	19	14580197	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1643504	14580197	44548786	733	9642											
ZNF333	84449	hgsc.bcm.edu	37	chr19	14829345	14829345	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcaagaatgtgggcaagcCttcaaatattcctcgaatct	12	12	8	9	1	3	1	2	0	1	1	5	2	4	1	2	1	1	1	2	1	6	3	rs147332855	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:14829345C>T	ENST00000292530.6	+	12	1297	c.1206C>T	c.(1204-1206)gcC>gcT	p.A402A	ZNF333_ENST00000536363.1_Silent_p.A293A|ZNF333_ENST00000540689.2_Intron	NM_032433.2	NP_115809.1	Q96JL9	ZN333_HUMAN	zinc finger protein 333	402					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)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|prostate(1)	21						GTGGGCAAGCCTTCAAATATT	0.443													C|||	5	0.000998403	0.0	0.0043	5008	,	,		20841	0.0		0.001	False		,,,				2504	0.001				p.A402A	NSCLC(60;75 1281 16985 25154 29885)	Atlas-SNP	.											.	ZNF333	76	.	0			c.C1206T						PASS	.	C		0,4406		0,0,2203	58	56	57		1206	1.1	0.9	19	dbSNP_134	57	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous	ZNF333	NM_032433.2		0,13,6490	TT,TC,CC		0.1512,0.0,0.1		402/666	14829345	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	84449	exon12			GCAAGCCTTCAAA		CCDS12316.1, CCDS74298.1	19p13	2013-01-08				ENSG00000160961		"Zinc fingers, C2H2-type", "-"	15624	protein-coding gene	gene with protein product		611811				12151103	Standard	XM_005260098		Approved	KIAA1806	uc002mzn.3	Q96JL9		ENST00000292530.6:c.1206C>T	19.37:g.14829345C>T		78	0	0		81	43	0.530864	NM_032433	Q6P2E6|Q86WS6|Q8TDL0	Silent	SNP	ENST00000292530.6	37	CCDS12316.1																																																																																			C|0.999;T|0.001	0.001	strong		0.443	ZNF333-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466496.1	NM_032433		T	14829345	C	T	14829345	2	4	25	1	0	0	0	0	0	0	0	1	17865	668	24	2		2	ZNF333	19	14829345	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	249148	14829345	44299638	734	9643											
OR7A5	26659	hgsc.bcm.edu	37	chr19	14938190	14938190	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttattcctcagactatagatAaaggggttcagcatgggggt	11	12	12	6	0	2	2	2	0	0	2	3	2	3	2	1	4	1	2	1	4	5	6	rs2240561	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:14938190A>G	ENST00000322301.3	-	2	951	c.864T>C	c.(862-864)ttT>ttC	p.F288F	OR7A5_ENST00000594432.1_Silent_p.F288F|OR7A5_ENST00000601611.1_Intron			Q15622	OR7A5_HUMAN	olfactory receptor, family 7, subfamily A, member 5	288					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						GACTATAGATAAAGGGGTTCA	0.473																																					p.F288F		Atlas-SNP	.											.	OR7A5	43	.	0			c.T864C						PASS	.						73	71	71					19																	14938190		2203	4300	6503	SO:0001819	synonymous_variant	26659	exon1			ATAGATAAAGGGG	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.864T>C	19.37:g.14938190A>G		69	0	0		115	9	0.0782609	NM_017506	B2R682|Q6IFP1|Q96R96	Silent	SNP	ENST00000322301.3	37	CCDS12318.1																																																																																			A|0.999;G|0.001	0.001	strong		0.473	OR7A5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466518.1	NM_017506		G	14938190	A	G	14938190	2	3	25	1	0	0	0	0	0	0	0	1	11225	359	13	3		3	OR7A5	19	14938190	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	108845	14938190	44190793	735	9644											
CPAMD8	27151	hgsc.bcm.edu	37	chr19	17062905	17062905	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtcttcagcagggagggctcGgcgatgcctaagccctgaga	8	7	15	11	2	2	1	1	1	1	1	3	4	2	2	2	3	3	2	2	3	1	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:17062905G>A	ENST00000443236.1	-	20	2554	c.2523C>T	c.(2521-2523)gcC>gcT	p.A841A		NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	794						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						GGGAGGGCTCGGCGATGCCTA	0.617																																					p.A841A		Atlas-SNP	.											.	CPAMD8	192	.	0			c.C2523T						PASS	.						27	30	29					19																	17062905		2015	4149	6164	SO:0001819	synonymous_variant	27151	exon20			GGGCTCGGCGATG	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.2523C>T	19.37:g.17062905G>A		63	0	0		57	31	0.54386	NM_015692	Q8NC09|Q9ULD7	Silent	SNP	ENST00000443236.1	37	CCDS42519.1	.	.	.	.	.	.	.	.	.	.	G	12.31	1.899355	0.33535	.	.	ENSG00000160111	ENST00000443236	.	.	.	3.14	-6.29	0.02013	.	.	.	.	.	T	0.35278	0.0926	.	.	.	0.50467	D	0.999877	.	.	.	.	.	.	T	0.37619	-0.9698	4	.	.	.	.	1.5938	0.02659	0.4277:0.1287:0.2994:0.1442	.	.	.	.	L	852	.	.	P	-	2	0	CPAMD8	16923905	0.005000	0.15991	0.000000	0.03702	0.825000	0.46686	-0.070000	0.11523	-1.304000	0.02329	0.491000	0.48974	CCG	.	.	none		0.617	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692		A	17062905	G	A	17062905	2	1	25	1	0	0	0	0	0	0	0	1	3797	1103	39	1		1	CPAMD8	19	17062905	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2124715	17062905	42066078	736	9645											
USHBP1	83878	hgsc.bcm.edu	37	chr19	17367354	17367354	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgggccagcctgggtccccaGaatggcctgcaccatggctt	6	8	13	14	0	0	1	0	0	0	1	1	1	1	1	6	4	2	2	6	4	1	1	rs141680124	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:17367354G>A	ENST00000252597.3	-	9	1569	c.1396C>T	c.(1396-1398)Ctg>Ttg	p.L466L	USHBP1_ENST00000431146.2_Silent_p.L402L|AC010646.3_ENST00000594059.1_5'Flank	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						TGGGTCCCCAGAATGGCCTGC	0.612													G|||	21	0.00419329	0.0	0.013	5008	,	,		18612	0.0		0.007	False		,,,				2504	0.0051				p.L466L		Atlas-SNP	.											.	USHBP1	85	.	0			c.C1396T						PASS	.	G		11,4395	19.1+/-41.9	0,11,2192	74	77	76		1396	3.8	1	19	dbSNP_134	76	96,8504	51.9+/-112.3	0,96,4204	no	coding-synonymous	USHBP1	NM_031941.3		0,107,6396	AA,AG,GG		1.1163,0.2497,0.8227		466/704	17367354	107,12899	2203	4300	6503	SO:0001819	synonymous_variant	83878	exon9			TCCCCAGAATGGC	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.1396C>T	19.37:g.17367354G>A		70	0	0		79	40	0.506329	NM_031941		Silent	SNP	ENST00000252597.3	37	CCDS12353.1																																																																																			G|0.992;A|0.008	0.008	strong		0.612	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941		A	17367354	G	A	17367354	2	1	25	1	0	0	0	0	0	0	0	1	17052	933	33	2		2	USHBP1	19	17367354	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	304449	17367354	41761629	737	9646											
CILP2	148113	hgsc.bcm.edu	37	chr19	19653231	19653231	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggaccacatcctcctgggcTcggtggtcaccccatctggg	5	8	12	16	2	2	0	1	0	1	0	5	1	4	1	5	5	0	1	5	5	0	0	rs186322474		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:19653231T>A	ENST00000291495.5	+	5	725	c.640T>A	c.(640-642)Tcg>Acg	p.S214T	CILP2_ENST00000588333.2_3'UTR|CILP2_ENST00000586018.1_Missense_Mutation_p.S220T	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	214						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						CCTCCTGGGCTCGGTGGTCAC	0.627																																					p.S214T		Atlas-SNP	.											.	CILP2	84	.	0			c.T640A						PASS	.	T	THR/SER	0,4406		0,0,2203	34	31	32		640	1.5	0.1	19		32	2,8598	2.2+/-6.3	0,2,4298	no	missense	CILP2	NM_153221.2	58	0,2,6501	AA,AT,TT		0.0233,0.0,0.0154	benign	214/1157	19653231	2,13004	2203	4300	6503	SO:0001583	missense	148113	exon5			CTGGGCTCGGTGG	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.640T>A	19.37:g.19653231T>A	ENSP00000291495:p.Ser214Thr	56	0	0		62	33	0.532258	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Missense_Mutation	SNP	ENST00000291495.5	37	CCDS12405.1	.	.	.	.	.	.	.	.	.	.	T	1.434	-0.569499	0.03910	0.0	2.33E-4	ENSG00000160161	ENST00000291495	T	0.39229	1.09	5.23	1.46	0.22682	Carboxypeptidase-like, regulatory domain (1);Carboxypeptidase, regulatory domain (1);	0.617705	0.16243	N	0.223061	T	0.17577	0.0422	N	0.13235	0.315	0.09310	N	1	B;B	0.14012	0.009;0.009	B;B	0.18871	0.023;0.014	T	0.18871	-1.0323	10	0.10902	T	0.67	-14.2755	0.421	0.00456	0.4059:0.1494:0.1428:0.3019	.	214;214	B2RAJ0;Q8IUL8	.;CILP2_HUMAN	T	214	ENSP00000291495:S214T	ENSP00000291495:S214T	S	+	1	0	CILP2	19514231	0.001000	0.12720	0.086000	0.20670	0.209000	0.24338	0.967000	0.29344	-0.119000	0.11830	0.454000	0.30748	TCG	T|0.999;A|0.001	0.001	weak		0.627	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221		A	19653231	T	A	19653231	3	1	25	1	0	0	0	0	1	0	0	0	3432	1551	54	5	658	5	CILP2	19	19653231	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	2285877	19653231	39475752	738	9647											
ZNF98	148198	hgsc.bcm.edu	37	chr19	22585674	22585674	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggtgatcaggtctggcttaGaggcagcaatacctgtttta	10	12	12	7	0	2	2	1	1	1	1	2	2	2	2	1	4	2	4	1	4	4	4			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:22585674G>A	ENST00000357774.5	-	3	291	c.170C>T	c.(169-171)tCt>tTt	p.S57F	ZNF98_ENST00000601553.1_Missense_Mutation_p.S57F	NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	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)	p.S57Y(2)		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)				GTCTGGCTTAGAGGCAGCAAT	0.393																																					p.S57F		Atlas-SNP	.											ZNF98_ENST00000357774,NS,carcinoma,0,2	ZNF98	230	2	2	Substitution - Missense(2)	prostate(2)	c.C170T						PASS	.																																			SO:0001583	missense	148198	exon3			GGCTTAGAGGCAG		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.170C>T	19.37:g.22585674G>A	ENSP00000350418:p.Ser57Phe	43	0	0		51	23	0.45098	NM_001098626		Missense_Mutation	SNP	ENST00000357774.5	37	CCDS46031.1	.	.	.	.	.	.	.	.	.	.	.	13.75	2.330284	0.41297	.	.	ENSG00000197360	ENST00000357774	T	0.00848	5.62	0.476	0.476	0.16779	Krueppel-associated box (3);	.	.	.	.	T	0.01029	0.0034	L	0.35793	1.09	0.22389	N	0.999141	P	0.37525	0.598	B	0.37888	0.26	T	0.50923	-0.8770	8	0.45353	T	0.12	.	.	.	.	.	57	A6NK75	ZNF98_HUMAN	F	57	ENSP00000350418:S57F	ENSP00000350418:S57F	S	-	2	0	ZNF98	22377514	0.164000	0.22935	0.816000	0.32577	0.950000	0.60333	0.418000	0.21230	0.532000	0.28657	0.298000	0.19748	TCT	.	.	none		0.393	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626		A	22585674	G	A	22585674	3	1	25	1	0	0	0	0	1	0	0	0	18218	942	33	2	1556	2	ZNF98	19	22585674	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2932443	22585674	36543309	739	9648											
PLEKHF1	79156	hgsc.bcm.edu	37	chr19	30165157	30165157	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggcggcaactgagggccacGggccgcccgcccagcacgga	7	1	16	17	6	0	1	0	1	0	0	0	2	0	2	4	5	2	2	4	5	1	0			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:30165157G>T	ENST00000436066.3	+	2	877	c.411G>T	c.(409-411)acG>acT	p.T137T	PLEKHF1_ENST00000592810.1_Silent_p.T137T	NM_024310.4	NP_077286.3	Q96S99	PKHF1_HUMAN	pleckstrin homology domain containing, family F (with FYVE domain) member 1	137					apoptotic process (GO:0006915)|endosome organization (GO:0007032)|positive regulation of autophagy (GO:0010508)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|protein localization to plasma membrane (GO:0072659)|vesicle organization (GO:0016050)	endosome membrane (GO:0010008)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			breast(1)|lung(3)|ovary(1)|prostate(1)	6	Ovarian(5;0.000567)|Breast(6;0.0602)|Esophageal squamous(110;0.239)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|STAD - Stomach adenocarcinoma(5;1.7e-06)|Lung(7;0.0623)|LUAD - Lung adenocarcinoma(5;0.0989)|BRCA - Breast invasive adenocarcinoma(6;0.225)			TGAGGGCCACGGGCCGCCCGC	0.682																																					p.T137T		Atlas-SNP	.											.	PLEKHF1	16	.	0			c.G411T						PASS	.						23	26	25					19																	30165157		2200	4296	6496	SO:0001819	synonymous_variant	79156	exon2			GGCCACGGGCCGC	AF434818	CCDS12417.1	19q11	2013-01-10				ENSG00000166289		"Zinc fingers, FYVE domain containing", "Pleckstrin homology (PH) domain containing"	20764	protein-coding gene	gene with protein product		615200					Standard	NM_024310		Approved	APPD, MGC4090, PHAFIN1, ZFYVE15	uc002nsh.4	Q96S99		ENST00000436066.3:c.411G>T	19.37:g.30165157G>T		10	0	0		15	7	0.466667	NM_024310	Q96K11|Q9BUB9	Silent	SNP	ENST00000436066.3	37	CCDS12417.1																																																																																			.	.	none		0.682	PLEKHF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459323.1	NM_024310		T	30165157	G	T	30165157	2	4	25	1	0	0	0	0	0	0	0	1	12075	1103	39	4		4	PLEKHF1	19	30165157	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	7579483	30165157	28963826	740	9649											
RHPN2	85415	hgsc.bcm.edu	37	chr19	33482821	33482821	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccttcttctgcagtgaagcGgatgcttcgaggaggcgtcc	6	10	13	12	3	2	1	0	1	2	0	4	4	3	3	2	3	3	2	2	3	1	3	rs79314177	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:33482821G>A	ENST00000254260.3	-	13	1587	c.1552C>T	c.(1552-1554)Cgc>Tgc	p.R518C	RHPN2_ENST00000588683.1_5'Flank|RHPN2_ENST00000400226.4_Missense_Mutation_p.R367C	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	518	PDZ.				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)					GCAGTGAAGCGGATGCTTCGA	0.547													G|||	208	0.0415335	0.0	0.0288	5008	,	,		16695	0.0169		0.0368	False		,,,				2504	0.137				p.R518C		Atlas-SNP	.											.	RHPN2	107	.	0			c.C1552T						PASS	.	G	CYS/ARG	19,4387	26.2+/-53.5	0,19,2184	69	62	64		1552	3.1	0.6	19	dbSNP_131	64	294,8306	107.6+/-168.3	1,292,4007	no	missense	RHPN2	NM_033103.4	180	1,311,6191	AA,AG,GG		3.4186,0.4312,2.4066	benign	518/687	33482821	313,12693	2203	4300	6503	SO:0001583	missense	85415	exon13			TGAAGCGGATGCT	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.1552C>T	19.37:g.33482821G>A	ENSP00000254260:p.Arg518Cys	173	0	0		204	113	0.553922	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	47	0.02152014652014652	0	0.0	16	0.04419889502762431	10	0.017482517482517484	21	0.027704485488126648	G	12.86	2.063219	0.36373	0.004312	0.034186	ENSG00000131941	ENST00000254260;ENST00000544458;ENST00000400226	T;T	0.30981	1.51;1.51	5.22	3.08	0.35506	PDZ/DHR/GLGF (1);	0.573078	0.19174	N	0.120873	T	0.05823	0.0152	L	0.41492	1.28	0.43761	D	0.996271	B	0.12013	0.005	B	0.08055	0.003	T	0.02805	-1.1108	10	0.33141	T	0.24	-5.1732	10.146	0.42764	0.1578:0.0:0.8422:0.0	.	518	Q8IUC4	RHPN2_HUMAN	C	518;248;367	ENSP00000254260:R518C;ENSP00000402244:R367C	ENSP00000254260:R518C	R	-	1	0	RHPN2	38174661	0.988000	0.35896	0.591000	0.28745	0.766000	0.43426	2.061000	0.41403	0.726000	0.32339	-0.119000	0.15052	CGC	G|0.974;A|0.026	0.026	strong		0.547	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103		A	33482821	G	A	33482821	3	1	25	1	0	0	0	0	1	0	0	0	13366	1116	39	1	520	1	RHPN2	19	33482821	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	3317664	33482821	25646162	741	9650											
CD22	933	hgsc.bcm.edu	37	chr19	35832468	35832468	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgctgggtgaacaactccaTaggacagacagcgtccaagg	12	6	12	11	1	0	2	0	1	0	1	2	3	2	3	2	3	4	1	2	3	4	1	rs369129095		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:35832468T>C	ENST00000085219.5	+	8	1796	c.1730T>C	c.(1729-1731)aTa>aCa	p.I577T	CD22_ENST00000536635.2_Missense_Mutation_p.I489T|CD22_ENST00000544992.2_Missense_Mutation_p.I577T|CD22_ENST00000270311.6_Missense_Mutation_p.I457T|CD22_ENST00000341773.6_Missense_Mutation_p.I400T|CD22_ENST00000419549.2_Missense_Mutation_p.I405T|CD22_ENST00000594250.1_Missense_Mutation_p.I400T	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule	577	Ig-like C2-type 5.				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)			AACAACTCCATAGGACAGACA	0.557																																					p.I577T	Ovarian(42;1009 1133 23674 26041)	Atlas-SNP	.											.	CD22	129	.	0			c.T1730C						PASS	.	T	THR/ILE,THR/ILE,THR/ILE,THR/ILE	0,4406		0,0,2203	73	72	72		1466,1730,1199,1730	3.5	0	19		72	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	CD22	NM_001185099.1,NM_001185100.1,NM_001185101.1,NM_001771.3	89,89,89,89	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	489/760,577/752,400/671,577/848	35832468	1,13005	2203	4300	6503	SO:0001583	missense	933	exon8			ACTCCATAGGACA	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.1730T>C	19.37:g.35832468T>C	ENSP00000085219:p.Ile577Thr	43	0	0		40	23	0.575	NM_001185100	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	Missense_Mutation	SNP	ENST00000085219.5	37	CCDS12457.1	.	.	.	.	.	.	.	.	.	.	T	14.05	2.420287	0.42918	0.0	1.16E-4	ENSG00000012124	ENST00000085219;ENST00000536635;ENST00000341773;ENST00000544992;ENST00000270311;ENST00000419549	T;T;T;T;T;T	0.11604	2.76;2.76;2.76;2.76;2.76;2.76	5.73	3.54	0.40534	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.679676	0.13703	N	0.368667	T	0.18882	0.0453	L	0.56124	1.755	0.09310	N	1	P;P;D;B;D	0.54964	0.931;0.9;0.969;0.223;0.96	P;P;P;B;P	0.59357	0.765;0.653;0.856;0.129;0.755	T	0.11397	-1.0589	10	0.22706	T	0.39	.	5.5235	0.16945	0.0:0.0879:0.1731:0.739	.	405;577;489;577;400	Q32M46;F5GYU4;F5H7U3;P20273;P20273-2	.;.;.;CD22_HUMAN;.	T	577;489;400;577;457;405	ENSP00000085219:I577T;ENSP00000442279:I489T;ENSP00000339349:I400T;ENSP00000441237:I577T;ENSP00000270311:I457T;ENSP00000403822:I405T	ENSP00000085219:I577T	I	+	2	0	CD22	40524308	0.002000	0.14202	0.013000	0.15412	0.133000	0.20885	1.081000	0.30791	1.001000	0.39076	-0.411000	0.06167	ATA	.	.	weak		0.557	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466099.1	NM_001771		C	35832468	T	C	35832468	3	2	25	1	0	0	0	0	1	0	0	0	2987	1406	49	3	1756	3	CD22	19	35832468	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	2349647	35832468	23296515	742	9651											
ZNF570	148268	hgsc.bcm.edu	37	chr19	37975379	37975379	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgtaggaaagccttcagtcaGaatgcacacctagttcaaca	14	9	8	10	0	3	1	3	0	0	1	3	2	3	2	2	1	3	3	2	1	5	4			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:37975379G>A	ENST00000330173.1	+	5	1384	c.855G>A	c.(853-855)caG>caA	p.Q285Q	ZNF570_ENST00000388801.3_Silent_p.Q82Q|ZNF570_ENST00000586475.1_Silent_p.Q341Q	NM_144694.1	NP_653295.1	Q96NI8	ZN570_HUMAN	zinc finger protein 570	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)			endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(1)	27			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CCTTCAGTCAGAATGCACACC	0.423																																					p.Q285Q		Atlas-SNP	.											.	ZNF570	58	.	0			c.G855A						PASS	.						72	69	70					19																	37975379		2203	4300	6503	SO:0001819	synonymous_variant	148268	exon5			CAGTCAGAATGCA	AK055353	CCDS12504.1, CCDS74355.1	19q13.12	2013-09-20			ENSG00000171827	ENSG00000171827		"Zinc fingers, C2H2-type", "-"	26416	protein-coding gene	gene with protein product							Standard	XM_005258567		Approved	FLJ30791	uc002ogk.1	Q96NI8	OTTHUMG00000048176	ENST00000330173.1:c.855G>A	19.37:g.37975379G>A		35	0	0		39	16	0.410256	NM_144694	A1L472|B4DMP1	Silent	SNP	ENST00000330173.1	37	CCDS12504.1																																																																																			.	.	none		0.423	ZNF570-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109600.1	NM_144694		A	37975379	G	A	37975379	2	1	25	1	0	0	0	0	0	0	0	1	18017	933	33	2		2	ZNF570	19	37975379	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	2142911	37975379	21153604	743	9652											
ZNF781	163115	hgsc.bcm.edu	37	chr19	38160742	38160742	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctttgatgtcgaataagaTgtgcactccgcctaaacgtc	10	13	8	10	3	1	2	0	1	1	1	4	3	2	2	2	0	2	1	2	0	4	4	rs149500211	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:38160742T>C	ENST00000590008.1	-	5	1160	c.308A>G	c.(307-309)cAt>cGt	p.H103R	ZNF781_ENST00000593040.1_5'Flank|ZFP30_ENST00000586732.1_Intron|ZNF781_ENST00000358582.4_Missense_Mutation_p.H103R			Q8N8C0	ZN781_HUMAN	zinc finger protein 781	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)			NS(1)|breast(2)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24						TCGAATAAGATGTGCACTCCG	0.368																																					p.H103R		Atlas-SNP	.											.	ZNF781	66	.	0			c.A308G						PASS	.	T	ARG/HIS	3,4403	6.2+/-15.9	0,3,2200	122	119	120		308	1.2	0	19	dbSNP_134	120	7,8593	7.1+/-27.0	0,7,4293	yes	missense	ZNF781	NM_152605.3	29	0,10,6493	CC,CT,TT		0.0814,0.0681,0.0769	possibly-damaging	103/328	38160742	10,12996	2203	4300	6503	SO:0001583	missense	163115	exon4			ATAAGATGTGCAC	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.308A>G	19.37:g.38160742T>C	ENSP00000466370:p.His103Arg	46	0	0		44	29	0.659091	NM_152605	Q2VPJ8	Missense_Mutation	SNP	ENST00000590008.1	37	CCDS12507.1	.	.	.	.	.	.	.	.	.	.	T	5.903	0.350770	0.11182	6.81E-4	8.14E-4	ENSG00000196381	ENST00000358582;ENST00000545586	T	0.18174	2.23	2.23	1.16	0.20824	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13030	0.0316	N	0.25789	0.76	0.09310	N	1	B	0.29862	0.259	B	0.37601	0.254	T	0.37314	-0.9711	9	0.35671	T	0.21	.	6.1414	0.20261	0.0:0.1428:0.0:0.8572	.	103	Q8N8C0	ZN781_HUMAN	R	103	ENSP00000351391:H103R	ENSP00000351391:H103R	H	-	2	0	ZNF781	42852582	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.032000	0.12266	0.114000	0.18032	-0.410000	0.06199	CAT	T|0.999;C|0.001	0.001	strong		0.368	ZNF781-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000459495.2	NM_152605		C	38160742	T	C	38160742	3	2	25	1	0	0	0	0	1	0	0	0	18169	1464	51	3	679	3	ZNF781	19	38160742	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	185363	38160742	20968241	744	9653											
MAP4K1	11184	hgsc.bcm.edu	37	chr19	39101772	39101772	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aagttgtggaaggcagccgaCcttgggaagaagaagccagg	13	5	16	7	1	0	2	0	0	0	2	0	5	0	4	3	4	2	2	3	4	5	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:39101772C>T	ENST00000591517.1	-	11	757	c.729G>A	c.(727-729)tgG>tgA	p.W243*	MAP4K1_ENST00000396857.2_Splice_Site_p.W243*|MAP4K1_ENST00000586296.1_Splice_Site_p.W243*|MAP4K1_ENST00000423454.2_Intron|MAP4K1_ENST00000589002.1_Intron|MAP4K1_ENST00000589130.1_Splice_Site_p.W239*	NM_007181.4	NP_009112.1	Q92918	M4K1_HUMAN	mitogen-activated protein kinase kinase kinase kinase 1	243	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)			AGGCAGCCGACCTTGGGAAGA	0.577																																					p.W243X		Atlas-SNP	.											.	MAP4K1	165	.	0			c.G729A						PASS	.						99	110	106					19																	39101772		1982	4153	6135	SO:0001630	splice_region_variant	11184	exon11			AGCCGACCTTGGG	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.729-1G>A	19.37:g.39101772C>T		117	0	0		164	65	0.396341	NM_007181		Nonsense_Mutation	SNP	ENST00000591517.1	37	CCDS59385.1	.	.	.	.	.	.	.	.	.	.	C	37	6.181791	0.97352	.	.	ENSG00000104814	ENST00000396857;ENST00000221409	.	.	.	4.21	4.21	0.49690	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.4865	0.75571	0.0:1.0:0.0:0.0	.	.	.	.	X	243	.	ENSP00000221409:W243X	W	-	3	0	MAP4K1	43793612	1.000000	0.71417	0.999000	0.59377	0.823000	0.46562	7.190000	0.77755	2.175000	0.68902	0.555000	0.69702	TGG	.	.	none		0.577	MAP4K1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000453390.1	NM_001042600	Nonsense_Mutation	T	39101772	C	T	39101772	5	4	25	1	0	0	0	0	0	0	1	0	9268	521	18	2	1922	2	MAP4K1	19	39101772	Splice_Site	SNP	C	TCGA-G8-6906-01A-11D-2210-10	941030	39101772	20027211	745	9654											
LGALS14	56891	hgsc.bcm.edu	37	chr19	40195183	40195183	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agaacaatgtcatcactaccCgtgagttgaaaagtcacagc	15	8	8	10	1	3	3	3	2	0	1	3	3	3	3	1	0	3	1	1	0	5	2	rs117106744	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:40195183C>T	ENST00000392052.3	+	1	238	c.15C>T	c.(13-15)ccC>ccT	p.P5P	LGALS14_ENST00000360675.3_5'UTR	NM_020129.2	NP_064514.1	Q8TCE9	PPL13_HUMAN	lectin, galactoside-binding, soluble, 14	5				SLPV -> ITPG (in Ref. 1; AAP97241). {ECO:0000305}.	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)			CATCACTACCCGTGAGTTGAA	0.423													C|||	7	0.00139776	0.0	0.0014	5008	,	,		22816	0.0		0.006	False		,,,				2504	0.0				p.P5P		Atlas-SNP	.											.	LGALS14	38	.	0			c.C15T						PASS	.	C	,	14,4336		0,14,2161	62	63	63		15,	-1.8	0	19	dbSNP_132	63	73,8495		0,73,4211	yes	coding-synonymous-near-splice,utr-5	LGALS14	NM_020129.2,NM_203471.1	,	0,87,6372	TT,TC,CC		0.852,0.3218,0.6735	,	5/140,	40195183	87,12831	2175	4284	6459	SO:0001630	splice_region_variant	56891	exon1			ACTACCCGTGAGT	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.15+1C>T	19.37:g.40195183C>T		199	0	0		214	103	0.481308	NM_020129	A8MPV8|B2R530|C5HZ19|Q7Z4X8|Q96KD4|Q96KD5|Q96KD6|Q9NR03	Silent	SNP	ENST00000392052.3	37	CCDS46073.1																																																																																			C|0.996;T|0.004	0.004	strong		0.423	LGALS14-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465222.1	NM_020129	Silent	T	40195183	C	T	40195183	5	4	25	1	0	0	0	0	0	0	1	0	8750	666	23	1	17	1	LGALS14	19	40195183	Splice_Site	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1093411	40195183	18933800	746	9655											
PSMC4	5704	hgsc.bcm.edu	37	chr19	40478362	40478362	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaaaaaggaatttctccaTgcccaggaggaggtgaagcg	13	7	13	8	1	1	2	0	2	1	0	2	5	1	5	2	4	2	0	2	4	4	1	rs35555615	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:40478362T>C	ENST00000157812.2	+	3	420	c.222T>C	c.(220-222)caT>caC	p.H74H	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	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)|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)					AATTTCTCCATGCCCAGGAGG	0.517													T|||	93	0.0185703	0.0008	0.0115	5008	,	,		16447	0.0		0.0249	False		,,,				2504	0.0603				p.H74H	Colon(105;1478 1543 4034 6132 38638)	Atlas-SNP	.											.	PSMC4	48	.	0			c.T222C						PASS	.	T	,	35,4371	40.0+/-72.8	0,35,2168	77	77	77		222,	-5.6	0.9	19	dbSNP_126	77	297,8303	108.6+/-169.2	10,277,4013	no	coding-synonymous,intron	PSMC4	NM_006503.2,NM_153001.1	,	10,312,6181	CC,CT,TT		3.4535,0.7944,2.5527	,	74/419,	40478362	332,12674	2203	4300	6503	SO:0001819	synonymous_variant	5704	exon3			TCTCCATGCCCAG	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.222T>C	19.37:g.40478362T>C		43	0	0		45	15	0.333333	NM_006503	Q96FV5|Q9UBM3|Q9UEX3	Silent	SNP	ENST00000157812.2	37	CCDS12547.1																																																																																			T|0.976;C|0.024	0.024	strong		0.517	PSMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462485.1	NM_006503		C	40478362	T	C	40478362	2	2	25	1	0	0	0	0	0	0	0	1	12701	1461	51	3		3	PSMC4	19	40478362	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	283179	40478362	18650621	747	9656											
AXL	558	hgsc.bcm.edu	37	chr19	41745608	41745608	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttctcacagggcaagcacAgccagtccaccagctgggta	10	7	10	14	0	2	0	1	0	2	0	4	0	3	0	3	2	3	4	3	2	2	2	rs199928489		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:41745608A>C	ENST00000301178.4	+	10	1485	c.1295A>C	c.(1294-1296)cAg>cCg	p.Q432P	AXL_ENST00000593513.1_Missense_Mutation_p.Q164P|AXL_ENST00000359092.3_Intron	NM_001278599.1|NM_021913.3	NP_001265528.1|NP_068713	P30530	UFO_HUMAN	AXL receptor tyrosine kinase	432					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						GGGCAAGCACAGCCAGTCCAC	0.572													a|||	1	0.000199681	0.0	0.0	5008	,	,		21079	0.0		0.001	False		,,,				2504	0.0				p.Q432P		Atlas-SNP	.											.	AXL	126	.	0			c.A1295C						PASS	.		,PRO/GLN	1,4405		0,1,2202	287	234	252		,1295	3.2	1	19		252	1,8599		0,1,4299	no	intron,missense	AXL	NM_001699.4,NM_021913.3	,76	0,2,6501	CC,CA,AA		0.0116,0.0227,0.0154	,possibly-damaging	,432/895	41745608	2,13004	2203	4300	6503	SO:0001583	missense	558	exon10			AAGCACAGCCAGT	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.1295A>C	19.37:g.41745608A>C	ENSP00000301178:p.Gln432Pro	109	0	0		130	67	0.515385	NM_021913	Q8N5L2|Q9UD27	Missense_Mutation	SNP	ENST00000301178.4	37	CCDS12575.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	N	8.956	0.969405	0.18659	2.27E-4	1.16E-4	ENSG00000167601	ENST00000301178	T	0.75260	-0.92	4.29	3.25	0.37280	.	0.612388	0.15184	N	0.275979	T	0.47002	0.1422	N	0.08118	0	0.80722	D	1	B	0.31931	0.347	B	0.23018	0.043	T	0.29610	-1.0006	10	0.29301	T	0.29	-5.3294	4.8946	0.13744	0.6168:0.1953:0.0:0.1879	.	432	P30530	UFO_HUMAN	P	432	ENSP00000301178:Q432P	ENSP00000301178:Q432P	Q	+	2	0	AXL	46437448	1.000000	0.71417	0.997000	0.53966	0.847000	0.48162	1.875000	0.39578	0.686000	0.31488	0.307000	0.20424	CAG	A|1.000;C|0.000	0.000	strong		0.572	AXL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463323.2			C	41745608	A	C	41745608	3	2	25	1	0	0	0	0	1	0	0	0	1238	188	7	5	1333	5	AXL	19	41745608	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	1267246	41745608	17383375	748	9657											
HNRNPUL1	11100	hgsc.bcm.edu	37	chr19	41811706	41811706	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcggttacaacccggccccCtataccccaccgccaccccc	7	4	7	23	3	0	0	0	0	0	0	0	0	0	0	9	3	3	1	9	3	4	3	rs372346124		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:41811706C>T	ENST00000392006.3	+	14	2561	c.2388C>T	c.(2386-2388)ccC>ccT	p.P796P	HNRNPUL1_ENST00000593587.1_Silent_p.P696P|HNRNPUL1_ENST00000263367.3_Silent_p.P707P|HNRNPUL1_ENST00000602130.1_Intron|HNRNPUL1_ENST00000595018.1_Silent_p.P696P|HNRNPUL1_ENST00000378215.4_Silent_p.P692P|HNRNPUL1_ENST00000352456.3_Silent_p.P706P	NM_007040.3	NP_008971.2	Q9BUJ2	HNRL1_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 1	796	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						ACCCGGCCCCCTATACCCCAC	0.627																																					p.P796P		Atlas-SNP	.											.	HNRNPUL1	73	.	0			c.C2388T						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	57	57	57		2388,2088	-2.8	1	19		57	1,8599	2.2+/-6.3	0,1,4299	no	coding-synonymous,coding-synonymous	HNRNPUL1	NM_007040.3,NM_144732.2	,	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	,	796/857,696/757	41811706	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	11100	exon14			GGCCCCCTATACC	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.2388C>T	19.37:g.41811706C>T		91	0	0		128	62	0.484375	NM_007040	B3KMW7|O76022|Q6ZSZ0|Q7L8P4|Q8N6Z4|Q96G37|Q9HAL3|Q9UG75	Silent	SNP	ENST00000392006.3	37	CCDS12576.1																																																																																			.	.	weak		0.627	HNRNPUL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463406.1	NM_144732, NM_007040		T	41811706	C	T	41811706	2	4	25	1	0	0	0	0	0	0	0	1	7283	668	24	2		2	HNRNPUL1	19	41811706	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	66098	41811706	17317277	749	9658											
BCKDHA	593	hgsc.bcm.edu	37	chr19	41920030	41920030	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccgccgccctggacaacaCggacctggtgtttggccagt	6	8	13	14	3	0	0	0	0	0	0	0	2	0	2	5	4	2	1	5	4	1	1	rs34442879	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:41920030C>T	ENST00000269980.2	+	4	820	c.452C>T	c.(451-453)aCg>aTg	p.T151M	BCKDHA_ENST00000595085.1_Missense_Mutation_p.T185M|BCKDHA_ENST00000457836.2_Missense_Mutation_p.T129M|CTC-435M10.3_ENST00000540732.1_Missense_Mutation_p.T185M	NM_000709.3|NM_001164783.1	NP_000700.1|NP_001158255.1	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha polypeptide	151			T -> M (in dbSNP:rs34442879).		branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity (GO:0003863)|alpha-ketoacid dehydrogenase activity (GO:0003826)|carboxy-lyase activity (GO:0016831)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	10						CTGGACAACACGGACCTGGTG	0.602													C|||	21	0.00419329	0.0	0.0058	5008	,	,		18861	0.001		0.0139	False		,,,				2504	0.002				p.T151M		Atlas-SNP	.											.	BCKDHA	36	.	0			c.C452T	GRCh37	CM021497	BCKDHA	M	rs34442879	PASS	.	C	MET/THR,MET/THR	7,4399	14.3+/-33.2	0,7,2196	73	57	63		452,452	4.7	0.9	19	dbSNP_126	63	91,8509	50.6+/-110.7	2,87,4211	yes	missense,missense	BCKDHA	NM_000709.3,NM_001164783.1	81,81	2,94,6407	TT,TC,CC		1.0581,0.1589,0.7535	possibly-damaging,possibly-damaging	151/446,151/445	41920030	98,12908	2203	4300	6503	SO:0001583	missense	593	exon4			ACAACACGGACCT	J04474	CCDS12581.1	19q13.1-q13.2	2008-07-09	2005-11-29		ENSG00000248098	ENSG00000248098			986	protein-coding gene	gene with protein product	"maple syrup urine disease"	608348	"branched chain keto acid dehydrogenase E1, alpha polypeptide (maple syrup urine disease)", "2-oxoisovalerate dehydrogenase (lipoamide)"	OVD1A			Standard	NM_000709		Approved	MSU	uc002oqq.3	P12694	OTTHUMG00000168128	ENST00000269980.2:c.452C>T	19.37:g.41920030C>T	ENSP00000269980:p.Thr151Met	86	0	0		107	60	0.560748	NM_000709	B4DP47|E7EW46|Q16034|Q16472	Missense_Mutation	SNP	ENST00000269980.2	37	CCDS12581.1	12|12	0.005494505494505495|0.005494505494505495	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	11|11	0.014511873350923483|0.014511873350923483	C|C	20.7|20.7	4.042043|4.042043	0.75732|0.75732	0.001589|0.001589	0.010581|0.010581	ENSG00000248098|ENSG00000255730;ENSG00000248098;ENSG00000248098;ENSG00000248098;ENSG00000248098	ENST00000541315|ENST00000540732;ENST00000269980;ENST00000542943;ENST00000457836;ENST00000378196	.|D;D;D;D	.|0.96011	.|-3.88;-3.88;-3.88;-3.88	4.66|4.66	4.66|4.66	0.58398|0.58398	.|Dehydrogenase, E1 component (1);	.|0.167160	.|0.51477	.|D	.|0.000089	D|D	0.94961|0.94961	0.8370|0.8370	L|L	0.57536|0.57536	1.79|1.79	0.40759|0.40759	D|D	0.98298|0.98298	.|D;D;D;P	.|0.54964	.|0.969;0.962;0.963;0.953	.|P;P;P;P	.|0.56788	.|0.806;0.622;0.622;0.488	D|D	0.94832|0.94832	0.7997|0.7997	5|10	.|0.62326	.|D	.|0.03	-23.707|-23.707	16.8305|16.8305	0.85943|0.85943	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs34442879|rs34442879	.|129;151;151;185	.|B4DP47;Q59EI3;P12694;F5H5P2	.|.;.;ODBA_HUMAN;.	W|M	87|185;151;122;129;151	.|ENSP00000443246:T185M;ENSP00000269980:T151M;ENSP00000440345:T122M;ENSP00000416000:T129M	.|ENSP00000269980:T151M	R|T	+|+	1|2	2|0	BCKDHA|BCKDHA;CTC-435M10.3	46611870|46611870	0.488000|0.488000	0.25996|0.25996	0.874000|0.874000	0.34290|0.34290	0.931000|0.931000	0.56810|0.56810	1.755000|1.755000	0.38379|0.38379	2.578000|2.578000	0.87016|0.87016	0.563000|0.563000	0.77884|0.77884	CGG|ACG	C|0.993;T|0.007	0.007	strong		0.602	BCKDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398313.3	NM_000709		T	41920030	C	T	41920030	3	4	25	1	0	0	0	0	1	0	0	0	1359	536	19	1	466	1	BCKDHA	19	41920030	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	108324	41920030	17208953	750	9659											
POU2F2	5452	hgsc.bcm.edu	37	chr19	42600030	42600030	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcgaagcgggaaatggtcgTctggctgaagtcgttgccgt	7	10	15	9	5	1	1	0	1	1	0	4	3	1	2	1	3	2	2	1	3	3	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:42600030T>C	ENST00000526816.2	-	9	730	c.715A>G	c.(715-717)Acg>Gcg	p.T239A	POU2F2_ENST00000529067.1_Missense_Mutation_p.T223A|POU2F2_ENST00000342301.4_Missense_Mutation_p.T239A|POU2F2_ENST00000560558.1_Missense_Mutation_p.T184A|POU2F2_ENST00000529952.1_Missense_Mutation_p.T239A|POU2F2_ENST00000389341.5_Missense_Mutation_p.T223A|POU2F2_ENST00000533720.1_Missense_Mutation_p.T223A|POU2F2_ENST00000560398.1_Missense_Mutation_p.T245A			P09086	PO2F2_HUMAN	POU class 2 homeobox 2	239	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				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)	GAAATGGTCGTCTGGCTGAAG	0.627																																					p.T239A		Atlas-SNP	.											POU2F2_ENST00000292077,NS,lymphoid_neoplasm,0,8	POU2F2	106	8	0			c.A715G						PASS	.						119	118	118					19																	42600030		2203	4300	6503	SO:0001583	missense	5452	exon9			TGGTCGTCTGGCT		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.715A>G	19.37:g.42600030T>C	ENSP00000431603:p.Thr239Ala	30	0	0		79	31	0.392405	NM_001207025	Q16648|Q7M4M8|Q9BRS4	Missense_Mutation	SNP	ENST00000526816.2	37	CCDS56095.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.957613	0.73902	.	.	ENSG00000028277	ENST00000389341;ENST00000342301;ENST00000292077;ENST00000533720;ENST00000526816;ENST00000529067;ENST00000529952	D;D;D;D;D	0.85861	-2.04;-2.04;-2.04;-2.04;-2.04	4.38	2.18	0.27775	POU-specific (4);Lambda repressor-like, DNA-binding (2);POU (1);	0.247967	0.39834	N	0.001250	D	0.91492	0.7314	M	0.88310	2.945	0.52501	D	0.999956	D;P;B	0.76494	0.999;0.953;0.262	D;D;B	0.79784	0.993;0.938;0.37	D	0.89325	0.3643	10	0.87932	D	0	.	6.8485	0.24003	0.15:0.0:0.1568:0.6932	.	223;239;223	P09086-4;P09086;P09086-3	.;PO2F2_HUMAN;.	A	223;239;239;223;238;223;239	ENSP00000373992:T223A;ENSP00000339369:T239A;ENSP00000437221:T223A;ENSP00000437224:T223A;ENSP00000436988:T239A	ENSP00000292077:T239A	T	-	1	0	POU2F2	47291870	1.000000	0.71417	0.972000	0.41901	0.994000	0.84299	7.819000	0.86621	0.269000	0.21961	0.454000	0.30748	ACG	.	.	none		0.627	POU2F2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387329.3			C	42600030	T	C	42600030	3	2	25	1	0	0	0	0	1	0	0	0	12281	1667	58	3	748	3	POU2F2	19	42600030	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	680000	42600030	16528953	751	9660											
GIPR	2696	hgsc.bcm.edu	37	chr19	46177997	46177997	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgttcacgtctttcatgctGcgagctgcggccattctcag	5	13	10	13	3	4	0	3	0	2	0	5	1	4	0	1	1	4	3	1	1	0	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:46177997G>T	ENST00000590918.1	+	7	645	c.546G>T	c.(544-546)ctG>ctT	p.L182L	MIR642A_ENST00000385039.1_RNA|GIPR_ENST00000263281.3_Silent_p.L182L|GIPR_ENST00000304207.8_Silent_p.L146L	NM_000164.2	NP_000155.1	P48546	GIPR_HUMAN	gastric inhibitory polypeptide receptor	182					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)		CTTTCATGCTGCGAGCTGCGG	0.597																																					p.L182L		Atlas-SNP	.											.	GIPR	36	.	0			c.G546T						PASS	.						76	67	70					19																	46177997		2203	4300	6503	SO:0001819	synonymous_variant	2696	exon7			CATGCTGCGAGCT		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.546G>T	19.37:g.46177997G>T		89	0	0		96	48	0.5	NM_000164	B7WP14|B7ZKQ0|Q14401|Q16400|Q52M04|Q9UPI1	Silent	SNP	ENST00000590918.1	37	CCDS12671.1																																																																																			.	.	none		0.597	GIPR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459640.1			T	46177997	G	T	46177997	2	4	25	1	0	0	0	0	0	0	0	1	6403	1306	46	4		4	GIPR	19	46177997	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	3577967	46177997	12950986	752	9661											
PNMAL1	55228	hgsc.bcm.edu	37	chr19	46974077	46974077	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agattcacaccttcaccaacCtcaatgagggcagctttaac	13	9	6	13	0	3	2	3	1	0	1	3	2	3	2	3	1	3	2	3	1	3	4			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:46974077C>T	ENST00000313683.10	-	2	521	c.216G>A	c.(214-216)gaG>gaA	p.E72E	PNMAL1_ENST00000602246.1_Splice_Site_p.E72E|PNMAL1_ENST00000438932.2_Silent_p.E72E	NM_001103149.1|NM_018215.3	NP_001096619.1|NP_060685.2	Q86V59	PNML1_HUMAN	paraneoplastic Ma antigen family-like 1	72										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)		cttcaccaacctcaatgaggg	0.547																																					p.E72E		Atlas-SNP	.											.	PNMAL1	87	.	0			c.G216A						PASS	.						65	52	56					19																	46974077		2203	4300	6503	SO:0001819	synonymous_variant	55228	exon2			ACCAACCTCAATG	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.216G>A	19.37:g.46974077C>T		66	0	0		77	31	0.402597	NM_018215	A8K2F3|Q5U638|Q8N3H4|Q9NVE8	Silent	SNP	ENST00000313683.10	37	CCDS33059.1																																																																																			.	.	none		0.547	PNMAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403929.1	NM_018215		T	46974077	C	T	46974077	2	4	25	1	0	0	0	0	0	0	0	1	12166	680	24	2		2	PNMAL1	19	46974077	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	796080	46974077	12154906	753	9662											
GLTSCR2	29997	hgsc.bcm.edu	37	chr19	48248907	48248907	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ggctgcggcccacttcggtgGacccagcgctgaggcggcgg	4	5	18	14	5	0	1	0	1	0	0	1	2	0	2	2	7	2	2	2	7	0	1	rs78530808	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48248907G>C	ENST00000246802.5	+	1	129	c.91G>C	c.(91-93)Gac>Cac	p.D31H	GLTSCR2_ENST00000598681.1_3'UTR	NM_015710.4	NP_056525.2	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	31						intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	15		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)		CACTTCGGTGGACCCAGCGCT	0.657													G|||	79	0.0157748	0.0053	0.0029	5008	,	,		9702	0.0069		0.0149	False		,,,				2504	0.0491				p.D31H	Colon(58;613 1041 9473 10089 15241)	Atlas-SNP	.											.	GLTSCR2	45	.	0			c.G91C						PASS	.	G	HIS/ASP	45,4361	48.2+/-83.0	0,45,2158	49	58	55		91	4.6	1	19	dbSNP_131	55	151,8449	70.7+/-133.2	0,151,4149	yes	missense	GLTSCR2	NM_015710.4	81	0,196,6307	CC,CG,GG		1.7558,1.0213,1.507	probably-damaging	31/479	48248907	196,12810	2203	4300	6503	SO:0001583	missense	29997	exon1			TCGGTGGACCCAG	AF182076	CCDS12705.1	19q13.3	2014-01-20				ENSG00000105373			4333	protein-coding gene	gene with protein product		605691				10708517, 16971513, 17657248	Standard	NM_015710		Approved	PICT-1	uc002phm.2	Q9NZM5		ENST00000246802.5:c.91G>C	19.37:g.48248907G>C	ENSP00000246802:p.Asp31His	98	0	0		147	81	0.55102	NM_015710	Q9BTC6|Q9HAX6|Q9NPP1|Q9NPR4|Q9UFI2	Missense_Mutation	SNP	ENST00000246802.5	37	CCDS12705.1	20	0.009157509157509158	6	0.012195121951219513	1	0.0027624309392265192	2	0.0034965034965034965	11	0.014511873350923483	G	23.9	4.465428	0.84425	0.010213	0.017558	ENSG00000105373	ENST00000246802;ENST00000325566;ENST00000446535	T	0.34472	1.36	4.55	4.55	0.56014	.	0.276137	0.34133	N	0.004227	T	0.29945	0.0749	L	0.34521	1.04	0.52501	D	0.999954	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.65573	0.936;0.936;0.936	T	0.34625	-0.9821	10	0.87932	D	0	-24.6863	13.1558	0.59516	0.0:0.0:1.0:0.0	.	31;31;29	Q53YP0;Q9NZM5;Q96CS0	.;GSCR2_HUMAN;.	H	31	ENSP00000246802:D31H	ENSP00000246802:D31H	D	+	1	0	GLTSCR2	52940719	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	4.935000	0.63498	2.227000	0.72691	0.655000	0.94253	GAC	G|0.987;C|0.013	0.013	strong		0.657	GLTSCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464870.1	NM_015710		C	48248907	G	C	48248907	3	2	25	1	0	0	0	0	1	0	0	0	6483	1174	41	4	93	4	GLTSCR2	19	48248907	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1274830	48248907	10880076	754	9663											
GLTSCR2	29997	hgsc.bcm.edu	37	chr19	48254799	48254799	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccctggacaggccgttggtTggccaggatgagtttttcct	5	12	13	11	1	0	1	0	1	0	0	1	3	1	3	5	5	0	3	5	5	0	4	rs11538669	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48254799T>C	ENST00000246802.5	+	5	659	c.621T>C	c.(619-621)gtT>gtC	p.V207V	GLTSCR2_ENST00000598681.1_3'UTR	NM_015710.4	NP_056525.2	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	207				SDNPLDRPLVGQDEFFLE -> LNNPDKPVVWPGCLFPG (in Ref. 3; AAG30413). {ECO:0000305}.		intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	15		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)		GGCCGTTGGTTGGCCAGGATG	0.607													T|||	77	0.0153754	0.0053	0.0029	5008	,	,		18264	0.0069		0.0149	False		,,,				2504	0.047				p.V207V	Colon(58;613 1041 9473 10089 15241)	Atlas-SNP	.											.	GLTSCR2	45	.	0			c.T621C						PASS	.	T		46,4360	48.9+/-83.8	0,46,2157	84	76	79		621	-7	0	19	dbSNP_120	79	151,8449	73.2+/-135.9	0,151,4149	no	coding-synonymous	GLTSCR2	NM_015710.4		0,197,6306	CC,CT,TT		1.7558,1.044,1.5147		207/479	48254799	197,12809	2203	4300	6503	SO:0001819	synonymous_variant	29997	exon5			GTTGGTTGGCCAG	AF182076	CCDS12705.1	19q13.3	2014-01-20				ENSG00000105373			4333	protein-coding gene	gene with protein product		605691				10708517, 16971513, 17657248	Standard	NM_015710		Approved	PICT-1	uc002phm.2	Q9NZM5		ENST00000246802.5:c.621T>C	19.37:g.48254799T>C		74	0	0		81	39	0.481481	NM_015710	Q9BTC6|Q9HAX6|Q9NPP1|Q9NPR4|Q9UFI2	Silent	SNP	ENST00000246802.5	37	CCDS12705.1																																																																																			T|0.987;C|0.013	0.013	strong		0.607	GLTSCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464870.1	NM_015710		C	48254799	T	C	48254799	2	2	25	1	0	0	0	0	0	0	0	1	6483	1799	63	3		3	GLTSCR2	19	48254799	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	5892	48254799	10874184	755	9664											
GLTSCR2	29997	hgsc.bcm.edu	37	chr19	48259787	48259787	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccctctctgtcctgtagccCgagggcaacatccttcgaga	7	10	9	15	2	1	1	0	0	1	1	6	3	4	1	4	1	2	2	4	1	2	2	rs11538664	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48259787C>T	ENST00000246802.5	+	11	1337	c.1299C>T	c.(1297-1299)ccC>ccT	p.P433P	CTD-2571L23.6_ENST00000602048.1_RNA|GLTSCR2_ENST00000598681.1_3'UTR|SNORD23_ENST00000408876.1_RNA	NM_015710.4	NP_056525.2	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	433				PEGNILRDRFKSFQRRNMIEPRERAKFKRKYKVKLVEKRAF REIQ -> VLTVSCRGAPCPVMTPSLLPVPPRGYGRHHGCP WAGPVGPMPRG (in Ref. 5). {ECO:0000305}.		intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	15		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)		TCCTGTAGCCCGAGGGCAACA	0.642													C|||	80	0.0159744	0.0053	0.0043	5008	,	,		17005	0.0069		0.0149	False		,,,				2504	0.0491				p.P433P	Colon(58;613 1041 9473 10089 15241)	Atlas-SNP	.											.	GLTSCR2	45	.	0			c.C1299T						PASS	.	C		49,4357	49.6+/-84.7	0,49,2154	32	34	33		1299	-7.4	0.9	19	dbSNP_120	33	168,8432	77.2+/-139.8	0,168,4132	no	coding-synonymous	GLTSCR2	NM_015710.4		0,217,6286	TT,TC,CC		1.9535,1.1121,1.6685		433/479	48259787	217,12789	2203	4300	6503	SO:0001819	synonymous_variant	29997	exon11			GTAGCCCGAGGGC	AF182076	CCDS12705.1	19q13.3	2014-01-20				ENSG00000105373			4333	protein-coding gene	gene with protein product		605691				10708517, 16971513, 17657248	Standard	NM_015710		Approved	PICT-1	uc002phm.2	Q9NZM5		ENST00000246802.5:c.1299C>T	19.37:g.48259787C>T		40	0	0		48	21	0.4375	NM_015710	Q9BTC6|Q9HAX6|Q9NPP1|Q9NPR4|Q9UFI2	Silent	SNP	ENST00000246802.5	37	CCDS12705.1																																																																																			C|0.984;T|0.016	0.016	strong		0.642	GLTSCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464870.1	NM_015710		T	48259787	C	T	48259787	2	4	25	1	0	0	0	0	0	0	0	1	6483	639	23	1		1	GLTSCR2	19	48259787	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	4988	48259787	10869196	756	9665											
GRIN2D	2906	hgsc.bcm.edu	37	chr19	48908452	48908452	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggctgtttgcagtgcgctcGgctggctggcgggatgacct	3	10	18	10	3	0	1	0	1	0	0	1	2	0	2	1	5	2	6	1	5	0	1	rs369747884		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48908452G>A	ENST00000263269.3	+	3	1015	c.927G>A	c.(925-927)tcG>tcA	p.S309S		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	309					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)	CAGTGCGCTCGGCTGGCTGGC	0.716													G|||	1	0.000199681	0.0	0.0014	5008	,	,		14132	0.0		0.0	False		,,,				2504	0.0				p.S309S		Atlas-SNP	.											.	GRIN2D	76	.	0			c.G927A						PASS	.	G		0,4306		0,0,2153	10	13	12		927	-8.9	0.8	19		12	2,8414		0,2,4206	no	coding-synonymous	GRIN2D	NM_000836.2		0,2,6359	AA,AG,GG		0.0238,0.0,0.0157		309/1337	48908452	2,12720	2153	4208	6361	SO:0001819	synonymous_variant	2906	exon3			GCGCTCGGCTGGC	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.927G>A	19.37:g.48908452G>A		8	0	0		21	13	0.619048	NM_000836		Silent	SNP	ENST00000263269.3	37	CCDS12719.1																																																																																			.	.	weak		0.716	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1			A	48908452	G	A	48908452	2	1	25	1	0	0	0	0	0	0	0	1	6791	1103	39	1		1	GRIN2D	19	48908452	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	648665	48908452	10220531	757	9666											
PLEKHA4	57664	hgsc.bcm.edu	37	chr19	49340661	49340661	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cccagggggtgggacctcctCcacgcccactccctcggcga	5	5	12	19	3	0	0	0	0	0	0	4	2	3	1	6	4	0	0	6	4	0	0	rs35965411	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:49340661C>A	ENST00000263265.6	-	20	2780	c.2225G>T	c.(2224-2226)gGa>gTa	p.G742V	PLEKHA4_ENST00000355496.5_3'UTR|HSD17B14_ENST00000263278.4_5'Flank|HSD17B14_ENST00000599157.1_5'Flank	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	742			G -> V (in dbSNP:rs35965411).			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)		GGGACCTCCTCCACGCCCACT	0.706													.|||	489	0.0976438	0.2716	0.0375	5008	,	,		11132	0.001		0.0159	False		,,,				2504	0.089				p.G742V		Atlas-SNP	.											.	PLEKHA4	70	.	0			c.G2225T						PASS	.		,VAL/GLY	832,3560		77,678,1441	24	28	26		,2225	4.2	0.1	19	dbSNP_126	26	92,8490		0,92,4199	yes	utr-3,missense	PLEKHA4	NM_001161354.1,NM_020904.2	,109	77,770,5640	AA,AC,CC		1.072,18.9435,7.1219	,possibly-damaging	,742/780	49340661	924,12050	2196	4291	6487	SO:0001583	missense	57664	exon20			CCTCCTCCACGCC	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.2225G>T	19.37:g.49340661C>A	ENSP00000263265:p.Gly742Val	98	0	0		79	39	0.493671	NM_020904	Q8N4M8|Q8N658	Missense_Mutation	SNP	ENST00000263265.6	37	CCDS12737.1	149	0.06822344322344322	120	0.24390243902439024	17	0.04696132596685083	0	0.0	12	0.0158311345646438	c	15.22	2.769097	0.49680	0.189435	0.01072	ENSG00000105559	ENST00000263265	T	0.10477	2.87	4.22	4.22	0.49857	.	0.000000	0.38381	N	0.001702	T	0.00012	0.0000	N	0.24115	0.695	0.19575	P	0.9999659469	P	0.41313	0.745	B	0.37346	0.247	T	0.44667	-0.9313	9	0.87932	D	0	.	12.3514	0.55151	0.0:1.0:0.0:0.0	rs35965411;rs61755450	742	Q9H4M7	PKHA4_HUMAN	V	742	ENSP00000263265:G742V	ENSP00000263265:G742V	G	-	2	0	PLEKHA4	54032473	0.000000	0.05858	0.056000	0.19401	0.173000	0.22820	-0.053000	0.11846	2.385000	0.81259	0.450000	0.29827	GGA	C|0.932;A|0.068	0.068	strong		0.706	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466216.1			A	49340661	C	A	49340661	3	1	25	1	0	0	0	0	1	0	0	0	12067	855	30	4	118	4	PLEKHA4	19	49340661	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	432209	49340661	9788322	758	9667											
PLEKHA4	57664	hgsc.bcm.edu	37	chr19	49340746	49340746	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggaggggtctcctggcgcgTggggtccgaaggaggcagcg	5	5	22	9	4	1	0	0	0	1	0	3	3	2	2	2	8	1	1	2	8	1	0	rs34460869	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:49340746T>C	ENST00000263265.6	-	20	2695	c.2140A>G	c.(2140-2142)Acg>Gcg	p.T714A	PLEKHA4_ENST00000355496.5_3'UTR|HSD17B14_ENST00000263278.4_5'Flank|HSD17B14_ENST00000599157.1_5'Flank	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	714			T -> A (in dbSNP:rs34460869).			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)		TCCTGGCGCGTGGGGTCCGAA	0.652													.|||	489	0.0976438	0.2716	0.0375	5008	,	,		12165	0.001		0.0159	False		,,,				2504	0.089				p.T714A		Atlas-SNP	.											.	PLEKHA4	70	.	0			c.A2140G						PASS	.		,ALA/THR	867,3535		87,693,1421	31	38	36		,2140	1.5	0	19	dbSNP_126	36	94,8506		0,94,4206	yes	utr-3,missense	PLEKHA4	NM_001161354.1,NM_020904.2	,58	87,787,5627	CC,CT,TT		1.093,19.6956,7.3912	,benign	,714/780	49340746	961,12041	2201	4300	6501	SO:0001583	missense	57664	exon20			GGCGCGTGGGGTC	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.2140A>G	19.37:g.49340746T>C	ENSP00000263265:p.Thr714Ala	146	0	0		143	76	0.531469	NM_020904	Q8N4M8|Q8N658	Missense_Mutation	SNP	ENST00000263265.6	37	CCDS12737.1	149	0.06822344322344322	120	0.24390243902439024	17	0.04696132596685083	0	0.0	12	0.0158311345646438	t	12.76	2.033282	0.35893	0.196956	0.01093	ENSG00000105559	ENST00000263265	T	0.08634	3.07	3.76	1.51	0.23008	.	1.395420	0.04808	N	0.434704	T	0.00012	0.0000	N	0.24115	0.695	0.58432	P	4.000000000004E-6	B	0.26002	0.139	B	0.19391	0.025	T	0.47983	-0.9074	9	0.20519	T	0.43	.	8.0169	0.30387	0.0:0.0:0.4338:0.5662	rs34460869	714	Q9H4M7	PKHA4_HUMAN	A	714	ENSP00000263265:T714A	ENSP00000263265:T714A	T	-	1	0	PLEKHA4	54032558	0.001000	0.12720	0.001000	0.08648	0.315000	0.28087	0.381000	0.20619	0.142000	0.18901	0.249000	0.18162	ACG	T|0.929;C|0.071	0.071	strong		0.652	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466216.1			C	49340746	T	C	49340746	3	2	25	1	0	0	0	0	1	0	0	0	12067	1696	59	3	203	3	PLEKHA4	19	49340746	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	85	49340746	9788237	759	9668											
SIGLEC7	27036	hgsc.bcm.edu	37	chr19	51650520	51650520	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcggcaaggccagcagcggaCgtgggagacataggcatgaa	12	4	16	9	3	0	2	0	1	0	1	1	4	0	3	1	5	2	3	1	5	3	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:51650520C>T	ENST00000317643.6	+	6	1236	c.1167C>T	c.(1165-1167)gaC>gaT	p.D389D	SIGLEC7_ENST00000305628.7_Silent_p.D296D|SIGLEC7_ENST00000600577.1_Intron	NM_014385.2	NP_055200.1	Q9Y286	SIGL7_HUMAN	sialic acid binding Ig-like lectin 7	389					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)		CAGCAGCGGACGTGGGAGACA	0.577																																					p.D389D		Atlas-SNP	.											.	SIGLEC7	74	.	0			c.C1167T						PASS	.						124	99	107					19																	51650520		2203	4300	6503	SO:0001819	synonymous_variant	27036	exon6			AGCGGACGTGGGA	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.1167C>T	19.37:g.51650520C>T		134	0	0		154	79	0.512987	NM_014385	Q9NZQ1|Q9UJ86|Q9UJ87|Q9Y502	Silent	SNP	ENST00000317643.6	37	CCDS12826.1																																																																																			.	.	none		0.577	SIGLEC7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464226.2	NM_016543		T	51650520	C	T	51650520	2	4	25	1	0	0	0	0	0	0	0	1	14328	535	19	1		1	SIGLEC7	19	51650520	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2309774	51650520	7478463	760	9669											
SIGLEC10	89790	hgsc.bcm.edu	37	chr19	51919231	51919231	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtagcgccctgaatccccAgccttcaccccgggcagctc	6	7	10	18	2	1	1	1	1	0	0	3	1	2	1	6	1	3	3	6	1	2	2	rs112584540	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:51919231A>G	ENST00000339313.5	-	5	1061	c.945T>C	c.(943-945)gcT>gcC	p.A315A	SIGLEC10_ENST00000439889.2_Silent_p.A257A|SIGLEC10_ENST00000525998.1_Intron|SIGLEC10_ENST00000436984.2_Silent_p.A267A|SIGLEC10_ENST00000442846.3_Intron|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000353836.5_Silent_p.A315A|SIGLEC10_ENST00000432469.2_Silent_p.A232A|SIGLEC10_ENST00000441969.3_Silent_p.A257A|SIGLEC10_ENST00000356298.5_Silent_p.A315A|CTD-2616J11.2_ENST00000526996.1_RNA|CTD-2616J11.3_ENST00000532473.1_RNA			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	315	Ig-like C2-type 2.				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)		CTGAATCCCCAGCCTTCACCC	0.677													a|||	19	0.00379393	0.0015	0.0058	5008	,	,		18136	0.0		0.0089	False		,,,				2504	0.0041				p.A315A		Atlas-SNP	.											.	SIGLEC10	112	.	0			c.T945C						PASS	.						41	46	45					19																	51919231		2203	4300	6503	SO:0001819	synonymous_variant	89790	exon5			ATCCCCAGCCTTC	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.945T>C	19.37:g.51919231A>G		199	0	0		120	41	0.341667	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Silent	SNP	ENST00000339313.5	37	CCDS12832.1																																																																																			A|0.994;G|0.006	0.006	strong		0.677	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130		G	51919231	A	G	51919231	2	3	25	1	0	0	0	0	0	0	0	1	14321	175	7	3		3	SIGLEC10	19	51919231	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	268711	51919231	7209752	761	9670											
SIGLEC10	89790	hgsc.bcm.edu	37	chr19	51919244	51919244	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aatccccagccttcaccccgGgcagctccagccccaggggt	7	5	10	19	1	1	0	1	0	0	0	3	0	3	0	8	3	3	2	8	3	1	1	rs200798488	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:51919244G>C	ENST00000339313.5	-	5	1048	c.932C>G	c.(931-933)cCc>cGc	p.P311R	SIGLEC10_ENST00000439889.2_Missense_Mutation_p.P253R|SIGLEC10_ENST00000525998.1_Intron|SIGLEC10_ENST00000436984.2_Missense_Mutation_p.P263R|SIGLEC10_ENST00000442846.3_Intron|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000353836.5_Missense_Mutation_p.P311R|SIGLEC10_ENST00000432469.2_Missense_Mutation_p.P228R|SIGLEC10_ENST00000441969.3_Missense_Mutation_p.P253R|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.P311R|CTD-2616J11.2_ENST00000526996.1_RNA|CTD-2616J11.3_ENST00000532473.1_RNA			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	311	Ig-like C2-type 2.				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)		CTTCACCCCGGGCAGCTCCAG	0.667																																					p.P311R		Atlas-SNP	.											.	SIGLEC10	112	.	0			c.C932G						PASS	.						33	38	37					19																	51919244		2203	4300	6503	SO:0001583	missense	89790	exon5			ACCCCGGGCAGCT	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.932C>G	19.37:g.51919244G>C	ENSP00000345243:p.Pro311Arg	176	0	0		108	39	0.361111	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	37	CCDS12832.1	.	.	.	.	.	.	.	.	.	.	.	5.587	0.293054	0.10567	.	.	ENSG00000142512	ENST00000353836;ENST00000432469;ENST00000356298;ENST00000441969;ENST00000439889;ENST00000436984;ENST00000339313;ENST00000529627	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	4.37	1.01	0.19927	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.141960	0.32868	N	0.005554	T	0.54631	0.1870	L	0.45051	1.395	0.23834	N	0.996719	B;P;P;B;B;B	0.41848	0.383;0.763;0.72;0.332;0.332;0.395	P;P;P;B;B;B	0.48571	0.464;0.582;0.447;0.333;0.333;0.208	T	0.44892	-0.9298	10	0.44086	T	0.13	.	3.6772	0.08297	0.2098:0.0:0.5964:0.1939	.	263;311;311;253;253;311	C9JM10;B7ZL04;Q96LC7-2;Q96LC7-6;Q96LC7-3;Q96LC7	.;.;.;.;.;SIG10_HUMAN	R	311;228;311;253;253;263;311;125	ENSP00000342389:P311R;ENSP00000396742:P228R;ENSP00000348646:P311R;ENSP00000408387:P253R;ENSP00000389132:P253R;ENSP00000414324:P263R;ENSP00000345243:P311R;ENSP00000435281:P125R	ENSP00000345243:P311R	P	-	2	0	SIGLEC10	56611056	0.544000	0.26441	0.193000	0.23327	0.071000	0.16799	0.847000	0.27696	0.130000	0.18549	0.313000	0.20887	CCC	G|0.993;C|0.007	0.007	strong		0.667	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130		C	51919244	G	C	51919244	3	2	25	1	0	0	0	0	1	0	0	0	14321	1232	43	4	1189	4	SIGLEC10	19	51919244	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	13	51919244	7209739	762	9671											
KIR3DL1	3811	hgsc.bcm.edu	37	chr19	55329851	55329851	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgtgactcttcggtgtcactAtcgtcataggtttaacaatt	9	15	8	9	3	3	1	2	1	1	0	5	1	3	1	0	2	1	1	0	2	4	6	rs145262243	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55329851A>G	ENST00000391728.4	+	3	185	c.152A>G	c.(151-153)tAt>tGt	p.Y51C	KIR3DL1_ENST00000538269.1_Missense_Mutation_p.Y51C|KIR3DL1_ENST00000326542.7_Missense_Mutation_p.Y51C|KIR3DL1_ENST00000541392.1_Missense_Mutation_p.Y51C|KIR3DL1_ENST00000402254.2_Missense_Mutation_p.Y51C|KIR3DL1_ENST00000358178.4_Intron	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	51	Ig-like C2-type 1.				immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		CGGTGTCACTATCGTCATAGG	0.517													a|||	25	0.00499201	0.0	0.0144	5008	,	,		13050	0.0		0.008	False		,,,				2504	0.0072				p.Y51C		Atlas-SNP	.											.	KIR3DL1	174	.	0			c.A152G						PASS	.	A	CYS/TYR	6,4344		0,6,2169	101	102	101		152	-2.5	0	19	dbSNP_134	101	100,8154		20,60,4047	no	missense	KIR3DL1	NM_013289.2	194	20,66,6216	GG,GA,AA		1.2115,0.1379,0.841		51/445	55329851	106,12498	2175	4127	6302	SO:0001583	missense	3811	exon3			GTCACTATCGTCA	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"Killer cell immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.152A>G	19.37:g.55329851A>G	ENSP00000375608:p.Tyr51Cys	26	0	0		35	20	0.571429	NM_013289	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000391728.4	37	CCDS42621.1	9	0.004120879120879121	0	0.0	6	0.016574585635359115	0	0.0	3	0.00395778364116095	A	9.452	1.090889	0.20471	0.001379	0.012115	ENSG00000167633	ENST00000402254;ENST00000538269;ENST00000541392;ENST00000355608;ENST00000391728;ENST00000326542	T;T;T;T;T	0.12361	2.69;2.69;2.69;2.69;2.69	1.25	-2.51	0.06365	Immunoglobulin subtype (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.14743	0.0356	M	0.75447	2.3	0.09310	N	1	D;B	0.89917	1.0;0.022	D;B	0.91635	0.999;0.034	T	0.11591	-1.0581	9	0.66056	D	0.02	.	2.0319	0.03531	0.3118:0.4675:0.0:0.2207	.	51;51	F6QF33;P43629	.;KI3L1_HUMAN	C	51;51;51;29;51;51	ENSP00000384528:Y51C;ENSP00000443350:Y51C;ENSP00000442355:Y51C;ENSP00000375608:Y51C;ENSP00000326868:Y51C	ENSP00000326868:Y51C	Y	+	2	0	KIR3DL1	60021663	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.542000	0.06091	-0.292000	0.08999	-1.429000	0.01096	TAT	A|0.992;G|0.008	0.008	strong		0.517	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289		G	55329851	A	G	55329851	3	3	25	1	0	0	0	0	1	0	0	0	8329	449	16	3	162	3	KIR3DL1	19	55329851	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	3410607	55329851	3799132	763	9672											
KIR3DL2	3812	hgsc.bcm.edu	37	chr19	55367311	55367311	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagatgcttcggctctttccGtgccctgccctgcgtgtggt	2	13	12	14	3	1	1	0	0	1	1	3	1	2	1	3	2	4	2	3	2	0	2	rs113800142	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55367311G>A	ENST00000326321.3	+	5	926	c.893G>A	c.(892-894)cGt>cAt	p.R298H	KIR3DL1_ENST00000402254.2_Intron|KIR3DL2_ENST00000270442.5_Missense_Mutation_p.R298H	NM_006737.3	NP_006728.2	P43630	KI3L2_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 2	298	Ig-like C2-type 3.				cellular defense response (GO:0006968)|regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	23				GBM - Glioblastoma multiforme(193;0.0192)		GGCTCTTTCCGTGCCCTGCCC	0.567													.|||	348	0.0694888	0.0794	0.0591	5008	,	,		10257	0.0397		0.0636	False		,,,				2504	0.1002				p.R298H		Atlas-SNP	.											KIR3DL2,NS,carcinoma,0,1	KIR3DL2	55	1	0			c.G893A						scavenged	.	G	HIS/ARG	173,3101		9,155,1473	5	6	6		893	-2	0	19	dbSNP_132	6	521,6479		39,443,3018	no	missense	KIR3DL2	NM_006737.3	29	48,598,4491	AA,AG,GG		7.4429,5.2841,6.7549	benign	298/456	55367311	694,9580	1637	3500	5137	SO:0001583	missense	3812	exon5			CTTTCCGTGCCCT	L41270	CCDS12906.1, CCDS58677.1	19q13.4	2014-05-22			ENSG00000240403	ENSG00000240403		"Killer cell immunoglobulin-like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6339	protein-coding gene	gene with protein product		604947				7716543, 8662091	Standard	NM_006737		Approved	cl-5, nkat4, nkat4a, nkat4b, CD158K	uc002qho.4	P43630	OTTHUMG00000065935	ENST00000326321.3:c.893G>A	19.37:g.55367311G>A	ENSP00000325525:p.Arg298His	78	0	0		69	31	0.449275	NM_001242867	Q13238|Q14947|Q14948|Q92684|Q95366|Q95367|Q95368	Missense_Mutation	SNP	ENST00000326321.3	37	CCDS12906.1	.	.	.	.	.	.	.	.	.	.	g	0.311	-0.967828	0.02232	0.052841	0.074429	ENSG00000240403	ENST00000326321;ENST00000270442	T;T	0.00768	5.72;5.72	0.993	-1.99	0.07457	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00073	0.0002	L	0.43701	1.375	0.09310	N	1	B;B;B	0.15930	0.015;0.011;0.013	B;B;B	0.06405	0.002;0.001;0.0	T	0.44544	-0.9321	9	0.52906	T	0.07	.	2.9371	0.05818	0.3559:0.2417:0.4024:0.0	.	298;298;103	Q95366;P43630;B5MCJ6	.;KI3L2_HUMAN;.	H	298	ENSP00000325525:R298H;ENSP00000270442:R298H	ENSP00000270442:R298H	R	+	2	0	KIR3DL2	60059123	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-4.304000	0.00256	-1.364000	0.02161	-1.254000	0.01491	CGT	G|0.910;A|0.091	0.091	strong		0.567	KIR3DL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000141241.1			A	55367311	G	A	55367311	3	1	25	1	0	0	0	0	1	0	0	0	8330	1145	40	1	911	1	KIR3DL2	19	55367311	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	37460	55367311	3761672	764	9673											
SAPS1	22870	hgsc.bcm.edu	37	chr19	55752662	55752662	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgtgcgtcagggctgcatcaTtggcgctcagggcactggcc	5	8	15	13	3	3	0	3	0	0	0	3	0	3	0	1	4	2	4	1	4	0	1	rs200841391	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55752662T>C	ENST00000412770.2	-	9	1672	c.1106A>G	c.(1105-1107)aAt>aGt	p.N369S	PPP6R1_ENST00000587283.1_Missense_Mutation_p.N369S	NM_014931.3	NP_055746.3	Q9UPN7	PP6R1_HUMAN	protein phosphatase 6, regulatory subunit 1	369	Interaction with PPP6C.				regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)	protein phosphatase binding (GO:0019903)			breast(1)	1						GGCTGCATCATTGGCGCTCAG	0.687													T|||	6	0.00119808	0.0015	0.0029	5008	,	,		11133	0.0		0.002	False		,,,				2504	0.0				p.N369S		Atlas-SNP	.											.	PPP6R1	63	.	0			c.A1106G						PASS	.	T	SER/ASN	2,4224		0,2,2111	25	30	29		1106	2.8	0.8	19		29	9,8481		0,9,4236	yes	missense	PPP6R1	NM_014931.3	46	0,11,6347	CC,CT,TT		0.106,0.0473,0.0865	benign	369/882	55752662	11,12705	2113	4245	6358	SO:0001583	missense	22870	exon9			GCATCATTGGCGC	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.1106A>G	19.37:g.55752662T>C	ENSP00000414202:p.Asn369Ser	126	0	0		128	61	0.476562	NM_014931	Q2M2H3|Q504V2|Q6NVJ6|Q9BU97	Missense_Mutation	SNP	ENST00000412770.2	37	CCDS46186.1	3	0.0013736263736263737	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	17.04	3.286210	0.59867	4.73E-4	0.00106	ENSG00000105063	ENST00000412770	T	0.66815	-0.23	4.98	2.81	0.32909	.	0.000000	0.64402	D	0.000017	T	0.63628	0.2527	M	0.62723	1.935	0.34351	D	0.689847	P	0.45986	0.87	P	0.48334	0.574	T	0.65529	-0.6146	10	0.19590	T	0.45	-21.6412	6.5383	0.22367	0.1379:0.0786:0.0:0.7835	.	369	Q9UPN7	PP6R1_HUMAN	S	369	ENSP00000414202:N369S	ENSP00000414202:N369S	N	-	2	0	PPP6R1	60444474	0.533000	0.26354	0.751000	0.31187	0.782000	0.44232	0.629000	0.24538	0.296000	0.22592	0.379000	0.24179	AAT	T|0.998;C|0.002	0.002	strong		0.687	PPP6R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452663.1	NM_014931		C	55752662	T	C	55752662	3	2	25	1	0	0	0	0	1	0	0	0	13851	1493	52	3	1603	3	SAPS1	19	55752662	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	385351	55752662	3376321	765	9674											
BRSK1	84446	hgsc.bcm.edu	37	chr19	55817694	55817694	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggccagtggcggcccctcCgtcttccaaaagcccgtccg	7	6	11	17	4	1	0	0	0	1	0	4	0	4	0	7	3	1	0	7	3	3	1	rs200320831		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55817694C>T	ENST00000309383.1	+	17	2242	c.1965C>T	c.(1963-1965)tcC>tcT	p.S655S	BRSK1_ENST00000590333.1_Silent_p.S671S|BRSK1_ENST00000326848.7_Silent_p.S350S	NM_032430.1	NP_115806.1	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1	655					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)	p.S655S(2)		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)		GCGGCCCCTCCGTCTTCCAAA	0.637																																					p.S655S		Atlas-SNP	.											BRSK1_ENST00000309383,NS,carcinoma,0,2	BRSK1	192	2	2	Substitution - coding silent(2)	endometrium(2)	c.C1965T						PASS	.						59	58	58					19																	55817694		2203	4300	6503	SO:0001819	synonymous_variant	84446	exon17			CCCCTCCGTCTTC	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.1965C>T	19.37:g.55817694C>T		56	0	0		71	35	0.492958	NM_032430	F1DG44|Q5J5B5|Q8NDD0|Q8NDR4|Q8TDC2|Q96AV4|Q96JL4	Silent	SNP	ENST00000309383.1	37	CCDS12921.1																																																																																			C|0.999;T|0.001	0.001	weak		0.637	BRSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452787.1	NM_032430		T	55817694	C	T	55817694	2	4	25	1	0	0	0	0	0	0	0	1	1525	639	23	1		1	BRSK1	19	55817694	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	65032	55817694	3311289	766	9675											
DUXA	503835	hgsc.bcm.edu	37	chr19	57669827	57669827	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgtaggtggtacgacaccGtctggcttctctacctaggg	6	11	13	11	2	2	0	0	0	2	0	3	1	2	0	2	4	2	4	2	4	4	5	rs140589597	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:57669827G>A	ENST00000554048.2	-	4	306	c.307C>T	c.(307-309)Cgg>Tgg	p.R103W		NM_001012729.1	NP_001012747.1	A6NLW8	DUXA_HUMAN	double homeobox A	103					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	17		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;0.0123)		GTACGACACCGTCTGGCTTCT	0.468																																					p.R103W		Atlas-SNP	.											DUXA,NS,carcinoma,+1,3	DUXA	46	3	0			c.C307T						PASS	.	G	TRP/ARG	0,4406		0,0,2203	64	64	64		307	2.8	0.1	19	dbSNP_134	64	6,8594	4.3+/-15.6	0,6,4294	yes	missense	DUXA	NM_001012729.1	101	0,6,6497	AA,AG,GG		0.0698,0.0,0.0461	probably-damaging	103/205	57669827	6,13000	2203	4300	6503	SO:0001583	missense	503835	exon4			GACACCGTCTGGC		CCDS33126.1	19q13.43	2012-10-04			ENSG00000258873	ENSG00000258873		"Homeoboxes / PRD class"	32179	protein-coding gene	gene with protein product		611168					Standard	NM_001012729		Approved		uc002qoa.1	A6NLW8	OTTHUMG00000170714	ENST00000554048.2:c.307C>T	19.37:g.57669827G>A	ENSP00000452398:p.Arg103Trp	100	0	0		80	37	0.4625	NM_001012729		Missense_Mutation	SNP	ENST00000554048.2	37	CCDS33126.1	.	.	.	.	.	.	.	.	.	.	G	14.63	2.593578	0.46214	0.0	6.98E-4	ENSG00000258873	ENST00000554048	D	0.96940	-4.18	2.85	2.85	0.33270	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.281548	0.19295	N	0.117793	D	0.98213	0.9409	M	0.93507	3.425	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92627	0.6113	10	0.87932	D	0	-12.0051	9.41	0.38485	0.0:0.0:1.0:0.0	.	103	A6NLW8	DUXA_HUMAN	W	103	ENSP00000452398:R103W	ENSP00000365415:R103W	R	-	1	2	DUXA	62361639	0.030000	0.19436	0.064000	0.19789	0.033000	0.12548	0.925000	0.28791	1.900000	0.55004	0.655000	0.94253	CGG	G|0.999;A|0.001	0.001	strong		0.468	DUXA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410075.3	NM_001012729		A	57669827	G	A	57669827	3	1	25	1	0	0	0	0	1	0	0	0	4836	1144	40	1	319	1	DUXA	19	57669827	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1852133	57669827	1459156	767	9676											
ZNF154	7710	hgsc.bcm.edu	37	chr19	58213743	58213743	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aaaggacttcccacactctcGacattcataaggcttttctc	11	12	5	13	1	3	0	1	0	2	0	6	2	4	1	1	2	0	1	1	2	2	5	rs74939505	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58213743G>A	ENST00000512439.2	-	3	770	c.574C>T	c.(574-576)Cga>Tga	p.R192*	AC003006.7_ENST00000594684.1_Intron|ZNF154_ENST00000426889.1_Nonsense_Mutation_p.R192*|ZNF551_ENST00000596085.1_Intron|AC003006.7_ENST00000599221.1_Intron			Q13106	ZN154_HUMAN	zinc finger protein 154	192					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)		CCACACTCTCGACATTCATAA	0.428													G|||	26	0.00519169	0.0008	0.0029	5008	,	,		23939	0.001		0.0179	False		,,,				2504	0.0041				p.R192X		Atlas-SNP	.											.	ZNF154	34	.	0			c.C574T						PASS	.	G	stop/ARG	9,4345	12.9+/-30.5	0,9,2168	129	128	128		574	-2.7	0	19	dbSNP_132	128	114,8456	59.5+/-121.1	0,114,4171	yes	stop-gained	ZNF154	NM_001085384.1		0,123,6339	AA,AG,GG		1.3302,0.2067,0.9517		192/438	58213743	123,12801	2177	4285	6462	SO:0001587	stop_gained	7710	exon3			ACTCTCGACATTC	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.574C>T	19.37:g.58213743G>A	ENSP00000421258:p.Arg192*	169	0	0		207	101	0.487923	NM_001085384	A7MCY3|Q8IVG7|Q8NAR0	Nonsense_Mutation	SNP	ENST00000512439.2	37	CCDS42639.1	16	0.007326007326007326	0	0.0	2	0.0055248618784530384	0	0.0	14	0.018469656992084433	G	14.30	2.495078	0.44352	0.002067	0.013302	ENSG00000179909	ENST00000512439;ENST00000426889	.	.	.	2.82	-2.67	0.06059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	.	2.8458	0.05542	0.2637:0.2107:0.4239:0.1018	.	.	.	.	X	192	.	ENSP00000442370:R192X	R	-	1	2	ZNF154	62905555	0.000000	0.05858	0.001000	0.08648	0.112000	0.19704	-8.748000	0.00017	-0.786000	0.04516	-1.268000	0.01426	CGA	G|0.993;A|0.007	0.007	strong		0.428	ZNF154-002	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277102.2			A	58213743	G	A	58213743	4	1	25	1	0	0	0	0	0	1	0	0	17750	1066	37	1	743	1	ZNF154	19	58213743	Nonsense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	543916	58213743	915240	768	9677											
ZNF587	84914	hgsc.bcm.edu	37	chr19	58371212	58371212	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aattatttggcaataagcacAgcgtgactatacatcagagg	15	10	9	7	1	1	2	1	1	0	1	1	2	1	2	0	2	3	2	0	2	6	5			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58371212A>T	ENST00000339656.5	+	3	1614	c.1432A>T	c.(1432-1434)Agc>Tgc	p.S478C	ZNF587_ENST00000423137.1_Missense_Mutation_p.S477C|ZNF587_ENST00000419854.1_Missense_Mutation_p.S435C|ZNF814_ENST00000597652.1_5'Flank|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597832.1_Intron	NM_001204817.1|NM_032828.3	NP_001191746.1|NP_116217.1	Q96SQ5	ZN587_HUMAN	zinc finger protein 587	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)			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)		CAATAAGCACAGCGTGACTAT	0.423																																					p.S478C	Pancreas(59;641 1233 1885 20055 50741)	Atlas-SNP	.											.	ZNF587	53	.	0			c.A1432T						PASS	.						156	149	152					19																	58371212		2203	4300	6503	SO:0001583	missense	84914	exon3			AAGCACAGCGTGA	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.1432A>T	19.37:g.58371212A>T	ENSP00000345479:p.Ser478Cys	199	0	0		250	17	0.068	NM_032828	A0AV72|G3V0H5|Q6ZMK8	Missense_Mutation	SNP	ENST00000339656.5	37	CCDS12964.1	.	.	.	.	.	.	.	.	.	.	.	7.068	0.567735	0.13560	.	.	ENSG00000198466	ENST00000376209;ENST00000423137;ENST00000339656;ENST00000540851;ENST00000419854	T;T;T	0.08008	3.14;3.14;3.14	0.882	-0.521	0.11931	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08980	0.0222	M	0.64630	1.985	0.24750	N	0.992985	B;B	0.27140	0.169;0.025	B;B	0.29598	0.104;0.033	T	0.20773	-1.0265	8	0.38643	T	0.18	.	4.8451	0.13510	0.7267:0.0:0.0:0.2733	.	477;478	G3V0H5;Q96SQ5	.;ZN587_HUMAN	C	435;477;478;478;435	ENSP00000393865:S477C;ENSP00000345479:S478C;ENSP00000406999:S435C	ENSP00000345479:S478C	S	+	1	0	ZNF587	63063024	0.000000	0.05858	0.000000	0.03702	0.344000	0.29017	-2.794000	0.00765	-0.256000	0.09473	0.164000	0.16699	AGC	.	.	none		0.423	ZNF587-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337594.2	NM_032828		T	58371212	A	T	58371212	3	4	25	1	0	0	0	0	1	0	0	0	18035	188	7	5	1442	5	ZNF587	19	58371212	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	157469	58371212	757771	769	9678											
ZSCAN1	284312	hgsc.bcm.edu	37	chr19	58549395	58549395	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagctctggacgctgtgccGccagtggctgaggcccgagg	5	6	16	14	3	1	1	0	1	1	0	1	3	1	2	4	4	2	3	4	4	0	0	rs369859464		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58549395G>A	ENST00000282326.1	+	3	438	c.191G>A	c.(190-192)cGc>cAc	p.R64H	ZSCAN1_ENST00000601162.1_Missense_Mutation_p.R64H|ZSCAN1_ENST00000391700.1_Missense_Mutation_p.R64H	NM_182572.3	NP_872378.3	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	64	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)|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)		ACGCTGTGCCGCCAGTGGCTG	0.706																																					p.R64H		Atlas-SNP	.											.	ZSCAN1	102	.	0			c.G191A						PASS	.	G	HIS/ARG	0,4342		0,0,2171	15	15	15		191	-0.6	0.4	19		15	1,8511		0,1,4255	no	missense	ZSCAN1	NM_182572.3	29	0,1,6426	AA,AG,GG		0.0117,0.0,0.0078	possibly-damaging	64/409	58549395	1,12853	2171	4256	6427	SO:0001583	missense	284312	exon3			TGTGCCGCCAGTG	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.191G>A	19.37:g.58549395G>A	ENSP00000282326:p.Arg64His	12	0	0		24	12	0.5	NM_182572	Q3B798|Q6WLH8|Q86WS8	Missense_Mutation	SNP	ENST00000282326.1	37	CCDS12969.1	.	.	.	.	.	.	.	.	.	.	G	11.77	1.737403	0.30774	0.0	1.17E-4	ENSG00000152467	ENST00000391700;ENST00000282326	T;T	0.05786	3.39;3.39	2.09	-0.628	0.11537	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	.	.	.	.	T	0.03348	0.0097	N	0.25245	0.725	0.23126	N	0.998253	P;P	0.41102	0.738;0.584	B;B	0.36134	0.218;0.054	T	0.39187	-0.9626	9	0.35671	T	0.21	.	2.1585	0.03819	0.2018:0.0:0.4923:0.3059	.	64;64	Q8NBB4;Q8NBB4-2	ZSCA1_HUMAN;.	H	64	ENSP00000375581:R64H;ENSP00000282326:R64H	ENSP00000282326:R64H	R	+	2	0	ZSCAN1	63241207	0.000000	0.05858	0.395000	0.26283	0.143000	0.21401	0.248000	0.18198	0.216000	0.20781	0.407000	0.27541	CGC	.	.	weak		0.706	ZSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466427.1	NM_182572		A	58549395	G	A	58549395	3	1	25	1	0	0	0	0	1	0	0	0	18241	1087	38	1	193	1	ZSCAN1	19	58549395	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	178183	58549395	579588	770	9679											
TGM6	343641	hgsc.bcm.edu	37	chr20	2377204	2377204	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agacaggagtacgtgctcagCgacagcggcatcatcttccg	10	7	12	12	4	3	1	2	0	1	1	4	3	4	2	1	2	4	3	1	2	1	2	rs16984872	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:2377204C>T	ENST00000202625.2	+	4	538	c.477C>T	c.(475-477)agC>agT	p.S159S	TGM6_ENST00000477505.1_Intron|TGM6_ENST00000381423.1_Silent_p.S159S	NM_198994.2	NP_945345.2	O95932	TGM3L_HUMAN	transglutaminase 6	159					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)	ACGTGCTCAGCGACAGCGGCA	0.612													C|||	193	0.0385383	0.1225	0.0259	5008	,	,		19129	0.0		0.0099	False		,,,				2504	0.0031				p.S159S		Atlas-SNP	.											TGM6,NS,carcinoma,0,1	TGM6	126	1	0			c.C477T						PASS	.	C		447,3959	215.8+/-234.7	28,391,1784	96	85	89		477	-5.3	0.9	20	dbSNP_123	89	87,8513	49.4+/-109.1	0,87,4213	no	coding-synonymous	TGM6	NM_198994.2		28,478,5997	TT,TC,CC		1.0116,10.1453,4.1058		159/707	2377204	534,12472	2203	4300	6503	SO:0001819	synonymous_variant	343641	exon4			GCTCAGCGACAGC	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.477C>T	20.37:g.2377204C>T		217	0	0		250	115	0.46	NM_198994	Q5JXU4|Q5JXU5|Q719M2|Q719M3|Q9Y4U8	Silent	SNP	ENST00000202625.2	37	CCDS13025.1																																																																																			C|0.960;T|0.040	0.040	strong		0.612	TGM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077581.2	NM_198994		T	2377204	C	T	2377204	2	4	25	1	0	0	0	0	0	0	0	1	15849	767	27	1		1	TGM6	20	2377204	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10		2377204	60648316	771	9680											
SLC4A11	83959	hgsc.bcm.edu	37	chr20	3208967	3208967	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttcatgtagggcagggagctCatgccgaaggcacacagcag	11	6	14	10	1	2	0	2	0	0	0	2	2	2	1	1	3	3	5	1	3	2	2	rs34224785	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:3208967C>T	ENST00000380056.3	-	18	2591	c.2544G>A	c.(2542-2544)atG>atA	p.M848I	SLC4A11_ENST00000539553.2_Missense_Mutation_p.M832I|SLC4A11_ENST00000380059.3_Missense_Mutation_p.M875I|SLC4A11_ENST00000488544.1_5'Flank	NM_032034.3	NP_114423.1	Q8NBS3	S4A11_HUMAN	solute carrier family 4, sodium borate transporter, member 11	848	Membrane (bicarbonate transporter).		M -> I (in dbSNP:rs34224785).		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						GCAGGGAGCTCATGCCGAAGG	0.617													C|||	57	0.0113818	0.0386	0.0058	5008	,	,		13939	0.0		0.002	False		,,,				2504	0.0				p.M875I	NSCLC(190;922 2139 10266 10292 38692)	Atlas-SNP	.											.	SLC4A11	188	.	0			c.G2625A						PASS	.	C	ILE/MET,ILE/MET,ILE/MET	120,4286	90.2+/-128.9	2,116,2085	106	94	98		2496,2625,2544	4.4	1	20	dbSNP_126	98	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	SLC4A11	NM_001174089.1,NM_001174090.1,NM_032034.3	10,10,10	2,117,6384	TT,TC,CC		0.0116,2.7236,0.9303	probably-damaging,probably-damaging,probably-damaging	832/876,875/919,848/892	3208967	121,12885	2203	4300	6503	SO:0001583	missense	83959	exon19			GGAGCTCATGCCG	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.2544G>A	20.37:g.3208967C>T	ENSP00000369396:p.Met848Ile	170	0	0		156	64	0.410256	NM_001174090	B4DKC8|B4DKX9|G3V1M3|Q2TB62|Q2TB63|Q9BXF4|Q9NTW9	Missense_Mutation	SNP	ENST00000380056.3	37	CCDS13052.1	30	0.013736263736263736	23	0.046747967479674794	5	0.013812154696132596	0	0.0	2	0.002638522427440633	C	14.38	2.517442	0.44763	0.027236	1.16E-4	ENSG00000088836	ENST00000380059;ENST00000380056;ENST00000539553	T;T;T	0.79454	-1.27;-1.27;-1.26	5.37	4.41	0.53225	.	0.000000	0.85682	D	0.000000	T	0.42585	0.1209	M	0.81682	2.555	0.58432	D	0.999999	B;B;B	0.29766	0.122;0.256;0.043	B;B;B	0.31614	0.133;0.063;0.035	T	0.65372	-0.6184	10	0.24483	T	0.36	.	15.9593	0.79914	0.0:0.8646:0.1354:0.0	rs34224785	832;875;848	G3V1M3;B4DKC8;Q8NBS3	.;.;S4A11_HUMAN	I	875;848;832	ENSP00000369399:M875I;ENSP00000369396:M848I;ENSP00000441370:M832I	ENSP00000369396:M848I	M	-	3	0	SLC4A11	3156967	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	3.253000	0.51469	1.239000	0.43787	0.455000	0.32223	ATG	C|0.988;T|0.012	0.012	strong		0.617	SLC4A11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077728.1			T	3208967	C	T	3208967	3	4	25	1	0	0	0	0	1	0	0	0	14667	826	29	2	139	2	SLC4A11	20	3208967	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	831763	3208967	59816553	772	9681											
C20orf194	25943	hgsc.bcm.edu	37	chr20	3356878	3356878	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tctccaatgtgccacataagGtaagagatagcgaaagttta	15	10	9	7	1	1	1	0	0	1	1	2	3	1	1	2	1	2	2	2	1	6	5			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:3356878G>A	ENST00000252032.9	-	4	422	c.355C>T	c.(355-357)Cct>Tct	p.P119S		NM_001009984.2	NP_001009984.1	Q5TEA3	CT194_HUMAN	chromosome 20 open reading frame 194	119										NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	39						GCCACATAAGGTAAGAGATAG	0.368																																					p.P119S		Atlas-SNP	.											.	C20orf194	83	.	0			c.C355T						PASS	.						148	134	138					20																	3356878		1869	4112	5981	SO:0001583	missense	25943	exon4			CATAAGGTAAGAG	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.355C>T	20.37:g.3356878G>A	ENSP00000252032:p.Pro119Ser	154	0	0		197	90	0.456853	NM_001009984	Q66K86|Q6P2R9|Q9UFX9	Missense_Mutation	SNP	ENST00000252032.9	37	CCDS42851.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.822991	0.90873	.	.	ENSG00000088854	ENST00000252032	T	0.27890	1.64	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.59432	0.2193	M	0.78801	2.425	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.62421	-0.6858	10	0.87932	D	0	.	18.4941	0.90858	0.0:0.0:1.0:0.0	.	119	Q5TEA3	CT194_HUMAN	S	119	ENSP00000252032:P119S	ENSP00000252032:P119S	P	-	1	0	C20orf194	3304878	1.000000	0.71417	0.981000	0.43875	0.981000	0.71138	7.298000	0.78815	2.740000	0.93945	0.561000	0.74099	CCT	.	.	none		0.368	C20orf194-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077734.1	NM_001009984		A	3356878	G	A	3356878	3	1	25	1	0	0	0	0	1	0	0	0	2101	1261	44	2	3314	2	C20orf194	20	3356878	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	147911	3356878	59668642	773	9682											
CENPB	1059	hgsc.bcm.edu	37	chr20	3766885	3766885	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cggatctgctggaaccaggcGatgagcaagccctcgagctt	9	7	13	12	3	1	1	0	1	1	0	2	5	1	3	2	3	5	3	2	3	2	1	rs140023764	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:3766885G>A	ENST00000379751.4	-	1	452	c.246C>T	c.(244-246)atC>atT	p.I82I	CDC25B_ENST00000379598.5_5'Flank|CDC25B_ENST00000344256.6_5'Flank	NM_001810.5	NP_001801.1	P07199	CENPB_HUMAN	centromere protein B, 80kDa	82	HTH CENPB-type. {ECO:0000255|PROSITE- ProRule:PRU00583}.				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						GGAACCAGGCGATGAGCAAGC	0.657													g|||	16	0.00319489	0.0121	0.0	5008	,	,		8145	0.0		0.0	False		,,,				2504	0.0				p.I82I		Atlas-SNP	.											.	CENPB	24	.	0			c.C246T						PASS	.	G		28,4378	33.5+/-64.1	0,28,2175	67	66	67		246	-0.4	1	20	dbSNP_134	67	4,8596	4.3+/-15.6	0,4,4296	no	coding-synonymous	CENPB	NM_001810.5		0,32,6471	AA,AG,GG		0.0465,0.6355,0.246		82/600	3766885	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	1059	exon1			CCAGGCGATGAGC	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.246C>T	20.37:g.3766885G>A		29	0	0		35	16	0.457143	NM_001810	Q96EI4	Silent	SNP	ENST00000379751.4	37	CCDS13064.1																																																																																			G|0.997;A|0.003	0.003	strong		0.657	CENPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077772.2	NM_001810		A	3766885	G	A	3766885	2	1	25	1	0	0	0	0	0	0	0	1	3229	1048	37	1		1	CENPB	20	3766885	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	410007	3766885	59258635	774	9683											
ADRA1D	146	hgsc.bcm.edu	37	chr20	4228779	4228779	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcgcgcgaccacgtacacgcGgcagtacatgaccacgatga	11	4	12	14	7	0	2	0	2	0	0	0	4	0	2	2	1	2	3	2	1	2	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:4228779G>T	ENST00000379453.4	-	1	942	c.826C>A	c.(826-828)Cgc>Agc	p.R276S		NM_000678.3	NP_000669.1	P25100	ADA1D_HUMAN	adrenoceptor alpha 1D	276					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)	ACGTACACGCGGCAGTACATG	0.672																																					p.R276S		Atlas-SNP	.											.	ADRA1D	36	.	0			c.C826A						PASS	.						25	19	21					20																	4228779		2179	4285	6464	SO:0001583	missense	146	exon1			ACACGCGGCAGTA	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.826C>A	20.37:g.4228779G>T	ENSP00000368766:p.Arg276Ser	32	0	0		29	16	0.551724	NM_000678	Q9NPY0	Missense_Mutation	SNP	ENST00000379453.4	37	CCDS13079.1	.	.	.	.	.	.	.	.	.	.	g	18.67	3.673764	0.67928	.	.	ENSG00000171873	ENST00000379453	T	0.38560	1.13	4.25	4.25	0.50352	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.67813	0.2933	M	0.91140	3.18	0.47862	D	0.999538	D	0.76494	0.999	D	0.80764	0.994	T	0.73895	-0.3838	10	0.87932	D	0	.	9.4862	0.38931	0.0:0.0:0.7892:0.2108	.	276	P25100	ADA1D_HUMAN	S	276	ENSP00000368766:R276S	ENSP00000368766:R276S	R	-	1	0	ADRA1D	4176779	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.525000	0.45598	2.208000	0.71279	0.552000	0.68991	CGC	.	.	none		0.672	ADRA1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077812.2	NM_000678		T	4228779	G	T	4228779	3	4	25	1	0	0	0	0	1	0	0	0	336	1116	39	4	900	4	ADRA1D	20	4228779	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	461894	4228779	58796741	775	9684											
SLC23A2	9962	hgsc.bcm.edu	37	chr20	4855309	4855309	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggaaatttaacatttctggcGtattgagaaaacagtaatac	16	12	8	5	1	1	1	0	1	1	1	1	3	1	2	0	2	3	2	0	2	7	7	rs41282100	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:4855309G>A	ENST00000379333.1	-	10	1250	c.858C>T	c.(856-858)taC>taT	p.Y286Y	SLC23A2_ENST00000468355.1_5'UTR|SLC23A2_ENST00000338244.1_Silent_p.Y286Y|SLC23A2_ENST00000424750.2_Silent_p.Y172Y	NM_203327.1	NP_976072.1	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 2	286					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						CATTTCTGGCGTATTGAGAAA	0.368													A|||	32	0.00638978	0.0129	0.0101	5008	,	,		20889	0.0		0.008	False		,,,				2504	0.0				p.Y286Y		Atlas-SNP	.											.	SLC23A2	62	.	0			c.C858T						PASS	.	A	,	55,4351	821.2+/-416.4	0,55,2148	119	122	121		858,858	3.7	1	20	dbSNP_127	121	107,8493	814.5+/-407.0	1,105,4194	no	coding-synonymous,coding-synonymous	SLC23A2	NM_005116.5,NM_203327.1	,	1,160,6342	AA,AG,GG		1.2442,1.2483,1.2456	,	286/651,286/651	4855309	162,12844	2203	4300	6503	SO:0001819	synonymous_variant	9962	exon10			TCTGGCGTATTGA	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.858C>T	20.37:g.4855309G>A		58	0	0		80	36	0.45	NM_203327	B4DJZ1|Q8WWR4|Q92512|Q96D54|Q9UNU1|Q9UP85	Silent	SNP	ENST00000379333.1	37	CCDS13085.1	11	0.005036630036630037	3	0.006097560975609756	5	0.013812154696132596	0	0.0	3	0.00395778364116095	A	0.141	-1.102585	0.01828	0.012483	0.012442	ENSG00000089057	ENST00000423430	.	.	.	5.9	3.67	0.42095	.	.	.	.	.	T	0.50000	0.1590	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44772	-0.9306	4	.	.	.	-10.7793	8.3011	0.32014	0.7051:0.0:0.2949:0.0	rs41282100	.	.	.	C	43	.	.	R	-	1	0	SLC23A2	4803309	1.000000	0.71417	0.982000	0.44146	0.006000	0.05464	2.001000	0.40825	0.161000	0.19458	-0.982000	0.02568	CGC	G|0.990;A|0.010	0.010	strong		0.368	SLC23A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077832.1			A	4855309	G	A	4855309	2	1	25	1	0	0	0	0	0	0	0	1	14478	1140	40	1		1	SLC23A2	20	4855309	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	626530	4855309	58170211	776	9685											
C20orf30	29058	hgsc.bcm.edu	37	chr20	5086918	5086918	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aacagcacagtggcaagtgcGatggccttataagggatctt	12	9	12	8	1	1	0	0	0	1	0	1	2	1	1	1	3	3	2	1	3	4	3	rs147693982	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:5086918G>A	ENST00000379286.2	-	4	558	c.138C>T	c.(136-138)atC>atT	p.I46I	TMEM230_ENST00000202834.7_Silent_p.I46I|TMEM230_ENST00000379277.2_Silent_p.I46I|TMEM230_ENST00000492419.1_5'UTR|TMEM230_ENST00000379283.2_Silent_p.I46I|TMEM230_ENST00000379279.2_Silent_p.I46I|TMEM230_ENST00000342308.5_Silent_p.I109I	NM_001009924.1	NP_001009924.1	Q96A57	TM230_HUMAN	transmembrane protein 230	46						integral component of membrane (GO:0016021)											TGGCAAGTGCGATGGCCTTAT	0.443													G|||	21	0.00419329	0.0	0.0058	5008	,	,		15312	0.0		0.0169	False		,,,				2504	0.0				p.I109I		Atlas-SNP	.											.	.	.	.	0			c.C327T						PASS	.	G	,,,	26,4380	32.6+/-62.9	0,26,2177	63	62	62		327,138,138,138	-5.4	0.7	20	dbSNP_134	62	156,8444	74.5+/-137.1	2,152,4146	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	C20orf30	NM_001009923.1,NM_001009924.1,NM_001009925.1,NM_014145.4	,,,	2,178,6323	AA,AG,GG		1.814,0.5901,1.3994	,,,	109/184,46/121,46/121,46/121	5086918	182,12824	2203	4300	6503	SO:0001819	synonymous_variant	29058	exon4			AAGTGCGATGGCC	AF161392	CCDS13086.1, CCDS33438.1	20p13	2012-03-16	2012-03-16	2012-03-16	ENSG00000089063	ENSG00000089063			15876	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 30"	C20orf30			Standard	XM_005260713		Approved	HSPC274	uc002wlk.3	Q96A57	OTTHUMG00000031796	ENST00000379286.2:c.138C>T	20.37:g.5086918G>A		93	0	0		94	53	0.56383	NM_001009923	B2RDM8|D3DVZ9|Q0VGC8|Q5TDS5|Q96ES2|Q9P0A7	Silent	SNP	ENST00000379286.2	37	CCDS13086.1																																																																																			G|0.990;A|0.010	0.010	strong		0.443	TMEM230-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077846.1			A	5086918	G	A	5086918	2	1	25	1	0	0	0	0	0	0	0	1	2112	1048	37	1		1	C20orf30	20	5086918	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	231609	5086918	57938602	777	9686											
TRMT6	51605	hgsc.bcm.edu	37	chr20	5924828	5924828	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttttttttcttctttttaatAtatttatcttgggcaaattc	8	25	3	5	0	3	0	0	0	3	0	4	0	3	0	0	1	0	1	0	1	5	14	rs35861347	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:5924828A>G	ENST00000203001.2	-	4	568	c.438T>C	c.(436-438)taT>taC	p.Y146Y	TRMT6_ENST00000453074.2_5'UTR|TRMT6_ENST00000473131.1_5'UTR	NM_015939.3	NP_057023.2	Q9UJA5	TRM6_HUMAN	tRNA methyltransferase 6 homolog (S. cerevisiae)	146					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						TCTTTTTAATATATTTATCTT	0.239													A|||	284	0.0567093	0.1127	0.098	5008	,	,		12906	0.001		0.0199	False		,,,				2504	0.047				p.Y146Y		Atlas-SNP	.											.	TRMT6	28	.	0			c.T438C						PASS	.	A		424,3858		22,380,1739	16	17	17		438	3.3	1	20	dbSNP_126	17	178,8304		2,174,4065	no	coding-synonymous	TRMT6	NM_015939.3		24,554,5804	GG,GA,AA		2.0986,9.9019,4.7164		146/498	5924828	602,12162	2141	4241	6382	SO:0001819	synonymous_variant	51605	exon4			TTTAATATATTTA	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.438T>C	20.37:g.5924828A>G		53	0	0		71	33	0.464789	NM_015939	B4DUV6|Q76P92|Q9BQV5|Q9ULR7|Q9Y2Z8	Silent	SNP	ENST00000203001.2	37	CCDS13093.1																																																																																			A|0.958;G|0.042	0.042	strong		0.239	TRMT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077889.2			G	5924828	A	G	5924828	2	3	25	1	0	0	0	0	0	0	0	1	16583	456	16	3		3	TRMT6	20	5924828	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	837910	5924828	57100692	778	9687											
MCM8	84515	hgsc.bcm.edu	37	chr20	5935303	5935303	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagattcaagcatttgaaaaAtttttcacaaggcatattga	17	13	6	5	0	2	3	2	2	0	1	2	3	2	3	0	1	1	2	0	1	6	6	rs6117014	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:5935303A>C	ENST00000378896.3	+	4	680	c.303A>C	c.(301-303)aaA>aaC	p.K101N	MCM8_ENST00000265187.4_Missense_Mutation_p.K101N|MCM8_ENST00000378886.2_Missense_Mutation_p.K101N|MCM8_ENST00000378883.1_Missense_Mutation_p.K101N	NM_001281520.1|NM_032485.4|NM_182802.1	NP_001268449.1|NP_115874.3|NP_877954.1	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	101			K -> N (in dbSNP:rs6117014).		cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)|G1/S transition of mitotic cell cycle (GO:0000082)|male gamete generation (GO:0048232)|mitotic cell cycle (GO:0000278)	MCM8-MCM9 complex (GO:0097362)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	23						CATTTGAAAAATTTTTCACAA	0.373													A|||	351	0.0700879	0.1626	0.1009	5008	,	,		19997	0.001		0.0199	False		,,,				2504	0.046				p.K101N		Atlas-SNP	.											.	MCM8	125	.	0			c.A303C						PASS	.	A	ASN/LYS,ASN/LYS	652,3750	276.0+/-272.9	51,550,1600	101	97	98		303,303	-10.4	0.5	20	dbSNP_114	98	183,8417	83.1+/-145.7	2,179,4119	yes	missense,missense	MCM8	NM_032485.4,NM_182802.1	94,94	53,729,5719	CC,CA,AA		2.1279,14.8114,6.4221	benign,benign	101/841,101/825	5935303	835,12167	2201	4300	6501	SO:0001583	missense	84515	exon4			TGAAAAATTTTTC	AJ439063	CCDS13094.1, CCDS13095.1, CCDS63226.1, CCDS63227.1	20p12.3	2007-04-04	2007-04-04	2003-07-09	ENSG00000125885	ENSG00000125885			16147	protein-coding gene	gene with protein product	"REC homolog (Drosophila)"	608187	"chromosome 20 open reading frame 154"	C20orf154		12527764	Standard	NM_032485		Approved	MGC4816, MGC12866, MGC119522, MGC119523, dJ967N21.5, REC	uc002wmi.3	Q9UJA3	OTTHUMG00000031822	ENST00000378896.3:c.303A>C	20.37:g.5935303A>C	ENSP00000368174:p.Lys101Asn	87	0	0		100	36	0.36	NM_032485	B2RBG7|D3DW08|E7EQU7|Q495R4|Q495R6|Q495R7|Q86US4|Q969I5	Missense_Mutation	SNP	ENST00000378896.3	37	CCDS13094.1	145	0.06639194139194139	92	0.18699186991869918	29	0.08011049723756906	2	0.0034965034965034965	22	0.029023746701846966	A	11.02	1.515159	0.27123	0.148114	0.021279	ENSG00000125885	ENST00000378896;ENST00000378883;ENST00000399350;ENST00000378886;ENST00000265187	T;T;T;T	0.04119	3.7;3.7;3.7;3.7	5.37	-10.4	0.00318	Nucleic acid-binding, OB-fold-like (1);	0.302307	0.39475	N	0.001357	T	0.00012	0.0000	L	0.29908	0.895	0.27511	P	0.9516967	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.001;0.002;0.001	T	0.38265	-0.9669	9	0.11485	T	0.65	-1.2423	2.7834	0.05367	0.2356:0.137:0.3949:0.2325	rs6117014;rs52802444;rs6117014	101;101;101;101	Q9UJA3-2;E7EQU7;Q9UJA3-3;Q9UJA3	.;.;.;MCM8_HUMAN	N	101	ENSP00000368174:K101N;ENSP00000368161:K101N;ENSP00000368164:K101N;ENSP00000265187:K101N	ENSP00000265187:K101N	K	+	3	2	MCM8	5883303	0.041000	0.20044	0.522000	0.27862	0.993000	0.82548	-1.262000	0.02852	-1.754000	0.01321	-0.250000	0.11733	AAA	A|0.936;C|0.064	0.064	strong		0.373	MCM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077900.1	NM_032485		C	5935303	A	C	5935303	3	2	25	1	0	0	0	0	1	0	0	0	9402	98	4	5	313	5	MCM8	20	5935303	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	10475	5935303	57090217	779	9688											
MCM8	84515	hgsc.bcm.edu	37	chr20	5974265	5974265	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atttatttctgctctcaacaAcgttgctgaaagaacttata	13	15	5	8	1	2	2	1	1	2	1	3	2	2	2	0	0	5	3	0	0	7	6	rs16991638	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:5974265A>G	ENST00000378896.3	+	18	2731	c.2354A>G	c.(2353-2355)aAc>aGc	p.N785S	MCM8_ENST00000265187.4_Missense_Mutation_p.N769S|MCM8_ENST00000378886.2_Missense_Mutation_p.N825S|MCM8_ENST00000378883.1_Missense_Mutation_p.N738S	NM_001281520.1|NM_032485.4|NM_182802.1	NP_001268449.1|NP_115874.3|NP_877954.1	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	785			N -> S (in dbSNP:rs16991638).		cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)|G1/S transition of mitotic cell cycle (GO:0000082)|male gamete generation (GO:0048232)|mitotic cell cycle (GO:0000278)	MCM8-MCM9 complex (GO:0097362)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	23						GCTCTCAACAACGTTGCTGAA	0.358													A|||	378	0.0754792	0.1853	0.1009	5008	,	,		18096	0.001		0.0199	False		,,,				2504	0.0429				p.N785S		Atlas-SNP	.											.	MCM8	125	.	0			c.A2354G						PASS	.	A	SER/ASN,SER/ASN	703,3703	283.4+/-277.1	58,587,1558	57	62	61		2354,2306	0.4	1	20	dbSNP_123	61	181,8419	82.3+/-144.9	2,177,4121	yes	missense,missense	MCM8	NM_032485.4,NM_182802.1	46,46	60,764,5679	GG,GA,AA		2.1047,15.9555,6.7969	benign,benign	785/841,769/825	5974265	884,12122	2203	4300	6503	SO:0001583	missense	84515	exon18			TCAACAACGTTGC	AJ439063	CCDS13094.1, CCDS13095.1, CCDS63226.1, CCDS63227.1	20p12.3	2007-04-04	2007-04-04	2003-07-09	ENSG00000125885	ENSG00000125885			16147	protein-coding gene	gene with protein product	"REC homolog (Drosophila)"	608187	"chromosome 20 open reading frame 154"	C20orf154		12527764	Standard	NM_032485		Approved	MGC4816, MGC12866, MGC119522, MGC119523, dJ967N21.5, REC	uc002wmi.3	Q9UJA3	OTTHUMG00000031822	ENST00000378896.3:c.2354A>G	20.37:g.5974265A>G	ENSP00000368174:p.Asn785Ser	44	0	0		52	20	0.384615	NM_032485	B2RBG7|D3DW08|E7EQU7|Q495R4|Q495R6|Q495R7|Q86US4|Q969I5	Missense_Mutation	SNP	ENST00000378896.3	37	CCDS13094.1	128	0.05860805860805861	86	0.17479674796747968	26	0.0718232044198895	1	0.0017482517482517483	15	0.01978891820580475	A	9.100	1.003892	0.19199	0.159555	0.021047	ENSG00000125885	ENST00000378896;ENST00000378883;ENST00000378886;ENST00000265187	T;T;T;T	0.02812	4.25;4.15;4.23;4.25	5.82	0.411	0.16392	.	0.769958	0.13000	N	0.421768	T	0.00012	0.0000	N	0.01576	-0.805	0.54753	P	1.3000000000040757E-5	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	0.45056	-0.9287	9	0.17832	T	0.49	-3.3433	6.6121	0.22757	0.2319:0.3374:0.4307:0.0	rs16991638;rs56419414;rs16991638	738;825;769;785	Q9UJA3-2;E7EQU7;Q9UJA3-3;Q9UJA3	.;.;.;MCM8_HUMAN	S	785;738;825;769	ENSP00000368174:N785S;ENSP00000368161:N738S;ENSP00000368164:N825S;ENSP00000265187:N769S	ENSP00000265187:N769S	N	+	2	0	MCM8	5922265	0.001000	0.12720	0.997000	0.53966	0.995000	0.86356	-0.073000	0.11468	0.055000	0.16094	0.533000	0.62120	AAC	A|0.934;G|0.066	0.066	strong		0.358	MCM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077900.1	NM_032485		G	5974265	A	G	5974265	3	3	25	1	0	0	0	0	1	0	0	0	9402	43	2	3	2420	3	MCM8	20	5974265	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	38962	5974265	57051255	780	9689											
ISM1	140862	hgsc.bcm.edu	37	chr20	13251325	13251325	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atttccccagatcctttctcCttgatctaccaaactttcca	9	15	2	15	0	2	2	0	1	2	1	6	2	5	2	6	0	2	0	6	0	2	5	rs76665689	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:13251325C>T	ENST00000262487.4	+	2	319	c.313C>T	c.(313-315)Ctt>Ttt	p.L105F	TASP1_ENST00000539805.1_Intron	NM_080826.1	NP_543016.1	B1AKI9	ISM1_HUMAN	isthmin 1, angiogenesis inhibitor	105						extracellular region (GO:0005576)				NS(1)|autonomic_ganglia(1)|endometrium(1)|large_intestine(8)|lung(5)|urinary_tract(1)	17						ATCCTTTCTCCTTGATCTACC	0.488													C|||	21	0.00419329	0.0045	0.0101	5008	,	,		20403	0.0		0.008	False		,,,				2504	0.0				p.L105F		Atlas-SNP	.											.	ISM1	41	.	0			c.C313T						PASS	.	C	PHE/LEU	21,3715		0,21,1847	94	87	89		313	3.5	1	20	dbSNP_131	89	7,8223		0,7,4108	yes	missense	ISM1	NM_080826.1	22	0,28,5955	TT,TC,CC		0.0851,0.5621,0.234	possibly-damaging	105/465	13251325	28,11938	1868	4115	5983	SO:0001583	missense	140862	exon2			TTTCTCCTTGATC	AL133463	CCDS46579.1	20p12.1	2013-05-15	2013-05-15	2008-12-23	ENSG00000101230	ENSG00000101230			16213	protein-coding gene	gene with protein product		615793	"chromosome 20 open reading frame 82", "isthmin 1 homolog (zebrafish)"	C20orf82			Standard	NM_080826		Approved	bA149I18.1	uc010gce.1	B1AKI9		ENST00000262487.4:c.313C>T	20.37:g.13251325C>T	ENSP00000262487:p.Leu105Phe	90	0	0		93	47	0.505376	NM_080826	Q8WVH9	Missense_Mutation	SNP	ENST00000262487.4	37	CCDS46579.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	16.02	3.005070	0.54254	0.005621	8.51E-4	ENSG00000101230	ENST00000262487;ENST00000447521	T;T	0.66638	-0.22;-0.07	5.71	3.45	0.39498	.	0.000000	0.85682	D	0.000000	T	0.54175	0.1842	L	0.57536	1.79	0.80722	D	1	B	0.06786	0.001	B	0.09377	0.004	T	0.61559	-0.7038	10	0.52906	T	0.07	3.7228	13.6816	0.62489	0.0:0.8541:0.0:0.1459	.	105	B1AKI9	ISM1_HUMAN	F	105;59	ENSP00000262487:L105F;ENSP00000409938:L59F	ENSP00000262487:L105F	L	+	1	0	ISM1	13199325	0.996000	0.38824	1.000000	0.80357	0.988000	0.76386	2.360000	0.44151	1.417000	0.47077	0.591000	0.81541	CTT	C|0.997;T|0.003	0.003	strong		0.488	ISM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078039.2			T	13251325	C	T	13251325	3	4	25	1	0	0	0	0	1	0	0	0	7869	681	24	2	319	2	ISM1	20	13251325	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	7277060	13251325	49774195	781	9690											
RRBP1	6238	hgsc.bcm.edu	37	chr20	17602571	17602571	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtctgcgcctcaatcagacAgagctgcttctccgattcct	7	11	9	14	2	4	2	2	0	2	2	6	3	5	2	3	1	3	2	3	1	1	2	rs2229886	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:17602571A>G	ENST00000377813.1	-	14	3472	c.3169T>C	c.(3169-3171)Tgt>Cgt	p.C1057R	RRBP1_ENST00000360807.4_Missense_Mutation_p.C624R|RRBP1_ENST00000377807.2_Missense_Mutation_p.C624R|RRBP1_ENST00000246043.4_Missense_Mutation_p.C1057R|RRBP1_ENST00000470422.1_5'UTR|RRBP1_ENST00000455029.2_Missense_Mutation_p.C398R			Q9P2E9	RRBP1_HUMAN	ribosome binding protein 1	1057					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						TCAATCAGACAGAGCTGCTTC	0.617													A|||	99	0.0197684	0.0008	0.0303	5008	,	,		15560	0.001		0.0477	False		,,,				2504	0.0286				p.C624R		Atlas-SNP	.											.	RRBP1	157	.	0			c.T1870C						PASS	.	A	ARG/CYS,ARG/CYS	52,4354	50.2+/-85.5	2,48,2153	63	70	68		1870,1870	-0.2	0	20	dbSNP_98	68	479,8121	139.5+/-196.2	5,469,3826	yes	missense,missense	RRBP1	NM_001042576.1,NM_004587.2	180,180	7,517,5979	GG,GA,AA		5.5698,1.1802,4.0827	benign,benign	624/978,624/978	17602571	531,12475	2203	4300	6503	SO:0001583	missense	6238	exon14			TCAGACAGAGCTG	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.3169T>C	20.37:g.17602571A>G	ENSP00000367044:p.Cys1057Arg	44	0	0		63	36	0.571429	NM_004587	A2A2S6|A6NCN6|O75300|O75301|Q5W165|Q96SB2|Q9BWP1|Q9H476	Missense_Mutation	SNP	ENST00000377813.1	37		51	0.023351648351648352	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	38	0.05013192612137203	A	0.010	-1.795706	0.00617	0.011802	0.055698	ENSG00000125844	ENST00000360807;ENST00000377813;ENST00000377807;ENST00000246043;ENST00000455029	T;T;T;T;T	0.32515	1.45;1.45;1.45;1.45;1.45	4.98	-0.19	0.13256	.	2.041510	0.02459	N	0.086394	T	0.00998	0.0033	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	0.14420	-1.0473	10	0.17832	T	0.49	2.3478	3.1217	0.06393	0.0856:0.1954:0.3645:0.3545	rs2229886;rs34246888	581;624	A1A5C4;Q9P2E9-3	.;.	R	624;1057;624;1057;398	ENSP00000354045:C624R;ENSP00000367044:C1057R;ENSP00000367038:C624R;ENSP00000246043:C1057R;ENSP00000401206:C398R	ENSP00000246043:C1057R	C	-	1	0	RRBP1	17550571	0.000000	0.05858	0.009000	0.14445	0.003000	0.03518	-0.055000	0.11807	0.106000	0.17784	-0.232000	0.12228	TGT	A|0.964;G|0.036	0.036	strong		0.617	RRBP1-002	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000078125.1	NM_001042576		G	17602571	A	G	17602571	3	3	25	1	0	0	0	0	1	0	0	0	13693	188	7	3	1111	3	RRBP1	20	17602571	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	4351246	17602571	45422949	782	9691											
RALGAPA2	57186	hgsc.bcm.edu	37	chr20	20565512	20565512	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catttcccggaacttactctTctgtctttccctacattttc	6	18	3	14	1	3	0	0	0	3	0	6	1	5	1	2	1	3	0	2	1	3	7			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:20565512T>A	ENST00000202677.7	-	19	2534	c.2527A>T	c.(2527-2529)Aag>Tag	p.K843*		NM_020343.3	NP_065076.2	Q2PPJ7	RGPA2_HUMAN	Ral GTPase activating protein, alpha subunit 2 (catalytic)	843					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						AACTTACTCTTCTGTCTTTCC	0.358																																					p.K843X		Atlas-SNP	.											.	RALGAPA2	274	.	0			c.A2527T						PASS	.						155	153	154					20																	20565512		1833	4097	5930	SO:0001587	stop_gained	57186	exon19			TACTCTTCTGTCT	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.2527A>T	20.37:g.20565512T>A	ENSP00000202677:p.Lys843*	64	0	0		75	36	0.48	NM_020343	Q4VXU6|Q5JUA3|Q5JUA4|Q5T9K3|Q96CX9|Q9BQT7|Q9H9D9|Q9ULE8	Nonsense_Mutation	SNP	ENST00000202677.7	37	CCDS46584.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	38|38	7.167061|7.167061	0.98107|0.98107	.|.	.|.	ENSG00000188559|ENSG00000188559	ENST00000202677|ENST00000430436	.|.	.|.	.|.	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	0.301070|.	0.35291|.	N|.	0.003317|.	.|T	.|0.64811	.|0.2632	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.71130	.|-0.4682	.|3	0.02654|.	T|.	1|.	.|.	13.4407|13.4407	0.61112|0.61112	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	X|S	843|659	.|.	ENSP00000202677:K843X|.	K|R	-|-	1|3	0|2	RALGAPA2|RALGAPA2	20513512|20513512	1.000000|1.000000	0.71417|0.71417	0.965000|0.965000	0.40720|0.40720	0.124000|0.124000	0.20399|0.20399	4.597000|4.597000	0.61062|0.61062	2.217000|2.217000	0.71921|0.71921	0.482000|0.482000	0.46254|0.46254	AAG|AGA	.	.	none		0.358	RALGAPA2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471941.1	NM_020343		A	20565512	T	A	20565512	4	1	25	1	0	0	0	0	0	1	0	0	13029	1792	62	5	3178	5	RALGAPA2	20	20565512	Nonsense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	2962941	20565512	42460008	783	9692											
BPIL3	128859	hgsc.bcm.edu	37	chr20	31619515	31619515	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tggcacgcgagctgaccctgGggcactgctgcggttgggca	5	7	17	12	3	0	1	0	1	0	0	0	2	0	1	1	5	3	6	1	5	0	1	rs41293138	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:31619515G>A	ENST00000349552.1	+	1	62	c.62G>A	c.(61-63)gGg>gAg	p.G21E		NM_174897.2	NP_777557.1	Q8NFQ5	BPIB6_HUMAN	BPI fold containing family B, member 6	21						extracellular region (GO:0005576)	lipid binding (GO:0008289)										GCTGACCCTGGGGCACTGCTG	0.662													G|||	10	0.00199681	0.0008	0.0014	5008	,	,		17401	0.0		0.008	False		,,,				2504	0.0				p.G21E		Atlas-SNP	.											.	.	.	.	0			c.G62A						PASS	.	G	GLU/GLY	9,4397	15.5+/-35.6	0,9,2194	43	33	37		62	4.8	1	20	dbSNP_127	37	62,8538	36.4+/-91.3	1,60,4239	yes	missense	BPIFB6	NM_174897.2	98	1,69,6433	AA,AG,GG		0.7209,0.2043,0.5459	possibly-damaging	21/454	31619515	71,12935	2203	4300	6503	SO:0001583	missense	128859	exon1			ACCCTGGGGCACT	AF465767	CCDS13211.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000167104	ENSG00000167104		"BPI fold containing"	16504	protein-coding gene	gene with protein product		614110	"bactericidal/permeability-increasing protein-like 3"	BPIL3		12185532, 21787333	Standard	NM_174897		Approved	LPLUNC6	uc010zuc.2	Q8NFQ5	OTTHUMG00000032238	ENST00000349552.1:c.62G>A	20.37:g.31619515G>A	ENSP00000344929:p.Gly21Glu	138	0	0		165	50	0.30303	NM_174897		Missense_Mutation	SNP	ENST00000349552.1	37	CCDS13211.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	G	17.66	3.445168	0.63178	0.002043	0.007209	ENSG00000167104	ENST00000349552	T	0.02498	4.27	4.85	4.85	0.62838	.	0.117103	0.38111	N	0.001818	T	0.06325	0.0163	L	0.57536	1.79	0.38042	D	0.935492	D	0.62365	0.991	P	0.56823	0.807	T	0.03587	-1.1022	10	0.59425	D	0.04	.	13.4708	0.61281	0.0:0.0:1.0:0.0	rs41293138	21	Q8NFQ5	BPIB6_HUMAN	E	21	ENSP00000344929:G21E	ENSP00000344929:G21E	G	+	2	0	BPIFB6	31083176	1.000000	0.71417	0.981000	0.43875	0.451000	0.32288	4.825000	0.62708	2.240000	0.73641	0.561000	0.74099	GGG	G|0.995;A|0.005	0.005	strong		0.662	BPIFB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078658.2	NM_174897		A	31619515	G	A	31619515	3	1	25	1	0	0	0	0	1	0	0	0	1495	1232	43	2	64	2	BPIL3	20	31619515	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	11054003	31619515	31406005	784	9693											
TRPC4AP	26133	hgsc.bcm.edu	37	chr20	33665969	33665969	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tccctctccgtcaaaaaagtCtcagtgaactgtgagtcaaa	13	10	7	11	1	4	2	3	2	2	0	7	2	5	2	2	0	1	0	2	0	5	0	rs139800499	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:33665969C>T	ENST00000252015.2	-	2	266	c.177G>A	c.(175-177)gaG>gaA	p.E59E	TRPC4AP_ENST00000451813.2_Silent_p.E59E|TRPC4AP_ENST00000432634.2_Silent_p.E59E			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein	59	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)			TCAAAAAAGTCTCAGTGAACT	0.458													C|||	6	0.00119808	0.0008	0.0014	5008	,	,		17571	0.0		0.004	False		,,,				2504	0.0				p.E59E		Atlas-SNP	.											.	TRPC4AP	64	.	0			c.G177A						PASS	.	C	,	12,4394	19.1+/-41.9	0,12,2191	99	90	93		177,177	0.4	1	20	dbSNP_134	93	65,8535	39.3+/-95.6	0,65,4235	no	coding-synonymous,coding-synonymous	TRPC4AP	NM_015638.2,NM_199368.1	,	0,77,6426	TT,TC,CC		0.7558,0.2724,0.592	,	59/798,59/790	33665969	77,12929	2203	4300	6503	SO:0001819	synonymous_variant	26133	exon2			AAAAGTCTCAGTG	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.177G>A	20.37:g.33665969C>T		83	0	0		77	32	0.415584	NM_199368	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Silent	SNP	ENST00000252015.2	37	CCDS13246.1																																																																																			C|0.995;T|0.005	0.005	strong		0.458	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638		T	33665969	C	T	33665969	2	4	25	1	0	0	0	0	0	0	0	1	16596	912	32	2		2	TRPC4AP	20	33665969	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2046454	33665969	29359551	785	9694											
KIAA0406	9675	hgsc.bcm.edu	37	chr20	36642101	36642101	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaagggcactgtcactcaCagcttgtagtcgtgtctgca	8	11	11	11	1	3	1	2	1	1	0	4	1	3	1	0	1	2	4	0	1	2	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:36642101C>T	ENST00000373448.2	-	3	356	c.118G>A	c.(118-120)Gtg>Atg	p.V40M	TTI1_ENST00000373447.3_Missense_Mutation_p.V40M|TTI1_ENST00000449821.1_Missense_Mutation_p.V40M|TTI1_ENST00000487362.1_Splice_Site	NM_014657.1	NP_055472.1	O43156	TTI1_HUMAN	TELO2 interacting protein 1	40					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						CTGTCACTCACAGCTTGTAGT	0.517																																					p.V40M		Atlas-SNP	.											.	TTI1	104	.	0			c.G118A						PASS	.						143	117	126					20																	36642101		2203	4300	6503	SO:0001583	missense	9675	exon3			CACTCACAGCTTG	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.118G>A	20.37:g.36642101C>T	ENSP00000362547:p.Val40Met	106	0	0		102	47	0.460784	NM_014657	D6W4K3|Q5JX67|Q96A38|Q9BR47|Q9H4K0	Missense_Mutation	SNP	ENST00000373448.2	37	CCDS13300.1	.	.	.	.	.	.	.	.	.	.	C	15.02	2.710534	0.48517	.	.	ENSG00000101407	ENST00000373448;ENST00000373447;ENST00000449821	T;T;T	0.68181	-0.31;-0.31;-0.31	5.33	3.35	0.38373	Armadillo-type fold (1);	0.247212	0.40908	D	0.000983	T	0.69522	0.3120	M	0.62723	1.935	0.40385	D	0.979489	P	0.46512	0.879	P	0.51385	0.668	T	0.69624	-0.5095	10	0.36615	T	0.2	-9.5996	10.6162	0.45451	0.0:0.8401:0.0:0.1599	.	40	O43156	TTI1_HUMAN	M	40	ENSP00000362547:V40M;ENSP00000362546:V40M;ENSP00000407270:V40M	ENSP00000362546:V40M	V	-	1	0	TTI1	36075515	0.976000	0.34144	0.815000	0.32552	0.871000	0.50021	2.440000	0.44855	1.457000	0.47850	0.655000	0.94253	GTG	.	.	none		0.517	TTI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079138.2	NM_014657		T	36642101	C	T	36642101	3	4	25	1	0	0	0	0	1	0	0	0	8182	478	17	2	3179	2	KIAA0406	20	36642101	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2976132	36642101	26383419	786	9695											
KIAA1755	85449	hgsc.bcm.edu	37	chr20	36842086	36842086	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccccaggactgacccttgaGgtcttgtccagcctgagctg	6	10	11	14	0	1	3	0	3	1	0	3	4	3	4	5	2	2	1	5	2	0	2	rs112401596	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:36842086G>A	ENST00000279024.4	-	14	3232	c.2961C>T	c.(2959-2961)acC>acT	p.T987T		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	987										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)				TGACCCTTGAGGTCTTGTCCA	0.642													G|||	31	0.0061901	0.003	0.0058	5008	,	,		17289	0.0		0.0169	False		,,,				2504	0.0061				p.T987T		Atlas-SNP	.											.	KIAA1755	145	.	0			c.C2961T						PASS	.	G		19,4387		0,19,2184	21	19	20		2961	-0.3	0	20	dbSNP_132	20	179,8421		2,175,4123	no	coding-synonymous	KIAA1755	NM_001029864.1		2,194,6307	AA,AG,GG		2.0814,0.4312,1.5224		987/1201	36842086	198,12808	2203	4300	6503	SO:0001819	synonymous_variant	85449	exon14			CCTTGAGGTCTTG	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.2961C>T	20.37:g.36842086G>A		73	0	0		82	39	0.47561	NM_001029864	Q9C0A8	Silent	SNP	ENST00000279024.4	37	CCDS33467.1																																																																																			G|0.986;A|0.014	0.014	strong		0.642	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864		A	36842086	G	A	36842086	2	1	25	1	0	0	0	0	0	0	0	1	8266	987	35	2		2	KIAA1755	20	36842086	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	199985	36842086	26183434	787	9696											
RALGAPB	57148	hgsc.bcm.edu	37	chr20	37198582	37198582	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ctcagggtcgccctgttcctCcccttggacctgagacaaga	7	9	10	15	1	1	2	1	1	0	2	4	4	3	3	5	2	0	1	5	2	1	2	rs142678293	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:37198582C>T	ENST00000262879.6	+	27	4290	c.4006C>T	c.(4006-4008)Ccc>Tcc	p.P1336S	RALGAPB_ENST00000397038.1_Missense_Mutation_p.P1115S|RALGAPB_ENST00000397040.1_Missense_Mutation_p.P1336S|RALGAPB_ENST00000397042.3_Missense_Mutation_p.P1333S			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	1336	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				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						CCCTGTTCCTCCCCTTGGACC	0.453													C|||	7	0.00139776	0.0015	0.0014	5008	,	,		18979	0.0		0.004	False		,,,				2504	0.0				p.P1336S		Atlas-SNP	.											.	RALGAPB	134	.	0			c.C4006T						PASS	.	C	SER/PRO	5,4401	9.9+/-24.2	0,5,2198	102	87	92		4006	5.6	1	20	dbSNP_134	92	68,8532	41.2+/-98.3	1,66,4233	yes	missense	RALGAPB	NM_020336.2	74	1,71,6431	TT,TC,CC		0.7907,0.1135,0.5613	possibly-damaging	1336/1495	37198582	73,12933	2203	4300	6503	SO:0001583	missense	57148	exon27			GTTCCTCCCCTTG	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.4006C>T	20.37:g.37198582C>T	ENSP00000262879:p.Pro1336Ser	149	0	0		138	66	0.478261	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Missense_Mutation	SNP	ENST00000262879.6	37	CCDS13305.1	3	0.0013736263736263737	1	0.0020325203252032522	0	0.0	0	0.0	2	0.002638522427440633	C	16.06	3.015096	0.54468	0.001135	0.007907	ENSG00000170471	ENST00000262879;ENST00000397042;ENST00000397038;ENST00000397040;ENST00000438490	D;D;D;D;D	0.93604	-3.25;-3.25;-3.25;-3.25;-3.25	5.64	5.64	0.86602	Rap/ran-GAP (1);	0.052081	0.85682	D	0.000000	D	0.87904	0.6295	L	0.28400	0.85	0.80722	D	1	P;P	0.44139	0.827;0.827	B;B	0.44044	0.439;0.439	D	0.87073	0.2161	10	0.22109	T	0.4	.	19.7154	0.96115	0.0:1.0:0.0:0.0	.	1333;1336	A2A2E9;Q86X10	.;RLGPB_HUMAN	S	1336;1333;1115;1336;1165	ENSP00000262879:P1336S;ENSP00000380235:P1333S;ENSP00000380231:P1115S;ENSP00000380233:P1336S;ENSP00000416646:P1165S	ENSP00000262879:P1336S	P	+	1	0	RALGAPB	36631996	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.601000	0.82783	2.664000	0.90586	0.655000	0.94253	CCC	C|0.995;T|0.005	0.005	strong		0.453	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336		T	37198582	C	T	37198582	3	4	25	1	0	0	0	0	1	0	0	0	13030	855	30	2	4108	2	RALGAPB	20	37198582	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	356496	37198582	25826938	788	9697											
HNF4A	3172	hgsc.bcm.edu	37	chr20	43048368	43048368	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaacccttccaggcaatgaCtacattgtccctcggcactg	9	9	7	16	1	0	1	0	1	0	0	3	1	2	1	4	2	2	2	4	2	3	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:43048368C>T	ENST00000316099.4	+	7	833	c.744C>T	c.(742-744)gaC>gaT	p.D248D	HNF4A_ENST00000443598.2_Silent_p.D248D|HNF4A_ENST00000609795.1_Silent_p.D226D|HNF4A_ENST00000457232.1_Silent_p.D226D|HNF4A_ENST00000316673.4_Silent_p.D226D|HNF4A_ENST00000415691.2_Silent_p.D248D	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	248					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)			CAGGCAATGACTACATTGTCC	0.582																																					p.D248D	Colon(79;2 1269 8820 14841 52347)	Atlas-SNP	.											.	HNF4A	150	.	0			c.C744T						PASS	.						89	79	83					20																	43048368		2203	4300	6503	SO:0001819	synonymous_variant	3172	exon7			CAATGACTACATT	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.744C>T	20.37:g.43048368C>T		58	0	0		54	24	0.444444	NM_178849	A5JW41|B2RPP8|O00659|O00723|Q14540|Q5QPB8|Q6B4V5|Q6B4V6|Q6B4V7|Q92653|Q92654|Q92655|Q99864|Q9NQH0	Silent	SNP	ENST00000316099.4	37	CCDS13330.1																																																																																			.	.	none		0.582	HNF4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079363.3			T	43048368	C	T	43048368	2	4	25	1	0	0	0	0	0	0	0	1	7262	564	20	2		2	HNF4A	20	43048368	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	5849786	43048368	19977152	789	9698											
SDC4	6385	hgsc.bcm.edu	37	chr20	43964514	43964514	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtagggctccggagaagtatCggccttctaggaggtcctgg	7	9	16	9	2	1	1	0	0	1	1	4	3	3	2	3	6	0	3	3	6	4	4			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:43964514C>T	ENST00000372733.3	-	2	146	c.107G>A	c.(106-108)cGa>cAa	p.R36Q	SDC4_ENST00000537976.1_Intron	NM_002999.3	NP_002990.2	P31431	SDC4_HUMAN	syndecan 4	36					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)				GGAGAAGTATCGGCCTTCTAG	0.552			T	ROS1	NSCLC																																p.R36Q		Atlas-SNP	.		Dom	yes		20	20q12	6385	syndecan 4		E	.	SDC4	16	.	0			c.G107A						PASS	.						70	65	66					20																	43964514		2203	4300	6503	SO:0001583	missense	6385	exon2			AAGTATCGGCCTT	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.107G>A	20.37:g.43964514C>T	ENSP00000361818:p.Arg36Gln	27	0	0		52	24	0.461538	NM_002999	O00773|Q16833|Q53FN9|Q6FGN3	Missense_Mutation	SNP	ENST00000372733.3	37	CCDS13350.1	.	.	.	.	.	.	.	.	.	.	C	12.90	2.075721	0.36662	.	.	ENSG00000124145	ENST00000372733	T	0.30182	1.54	4.79	1.8	0.24995	.	0.602744	0.16677	N	0.204118	T	0.16685	0.0401	N	0.25426	0.745	0.27144	N	0.961575	B	0.16802	0.019	B	0.08055	0.003	T	0.30794	-0.9966	10	0.11485	T	0.65	-0.7809	7.1145	0.25409	0.0:0.7099:0.0:0.2901	.	36	P31431	SDC4_HUMAN	Q	36	ENSP00000361818:R36Q	ENSP00000361818:R36Q	R	-	2	0	SDC4	43397928	0.000000	0.05858	0.901000	0.35422	0.714000	0.41099	-1.122000	0.03267	0.201000	0.20466	0.561000	0.74099	CGA	.	.	none		0.552	SDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080515.1	NM_002999		T	43964514	C	T	43964514	3	4	25	1	0	0	0	0	1	0	0	0	13969	884	31	1	505	1	SDC4	20	43964514	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	916146	43964514	19061006	790	9699											
ELMO2	63916	hgsc.bcm.edu	37	chr20	45003211	45003211	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggtggactttagccaagtaCagcatgttgtccaaggccag	10	10	12	9	0	0	0	0	0	0	0	1	1	1	1	3	3	3	3	3	3	4	4	rs8124302	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:45003211C>T	ENST00000290246.6	-	14	1328	c.1134G>A	c.(1132-1134)ctG>ctA	p.L378L	ELMO2_ENST00000372176.1_Silent_p.L290L|ELMO2_ENST00000439931.2_Silent_p.L390L|ELMO2_ENST00000454865.2_Silent_p.L110L|ELMO2_ENST00000488853.1_5'UTR|ELMO2_ENST00000396391.1_Silent_p.L378L|ELMO2_ENST00000445496.2_Silent_p.L195L|ELMO2_ENST00000352077.2_Silent_p.L376L	NM_133171.3	NP_573403.1	Q96JJ3	ELMO2_HUMAN	engulfment and cell motility 2	378	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)				TAGCCAAGTACAGCATGTTGT	0.517													C|||	5	0.000998403	0.0	0.0	5008	,	,		21226	0.0		0.004	False		,,,				2504	0.001				p.L378L		Atlas-SNP	.											.	ELMO2	51	.	0			c.G1134A						PASS	.	C	,	5,4401	9.9+/-24.2	0,5,2198	120	99	106		1134,1134	0.4	1	20	dbSNP_116	106	27,8573	19.2+/-60.6	0,27,4273	no	coding-synonymous,coding-synonymous	ELMO2	NM_133171.3,NM_182764.1	,	0,32,6471	TT,TC,CC		0.314,0.1135,0.246	,	378/721,378/721	45003211	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	63916	exon13			CAAGTACAGCATG	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.1134G>A	20.37:g.45003211C>T		106	0	0		120	60	0.5	NM_182764	E1P5T3|Q5JVZ6|Q7Z5G9|Q96CJ2|Q96ME5|Q96PA9|Q9H938|Q9H9L5|Q9HAH0|Q9NQQ6	Silent	SNP	ENST00000290246.6	37	CCDS13398.1																																																																																			C|0.997;T|0.003	0.003	strong		0.517	ELMO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080466.1	NM_022086		T	45003211	C	T	45003211	2	4	25	1	0	0	0	0	0	0	0	1	5068	465	17	2		2	ELMO2	20	45003211	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1038697	45003211	18022309	791	9700											
PARD6B	84612	hgsc.bcm.edu	37	chr20	49366879	49366879	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtcattaacacagatagagCtaagctttgagtctggacag	14	10	10	7	0	2	3	1	1	1	2	2	4	2	4	0	1	3	2	0	1	3	4	rs41283606	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:49366879C>T	ENST00000371610.2	+	3	1216	c.973C>T	c.(973-975)Cta>Tta	p.L325L	PARD6B_ENST00000396039.1_Intron	NM_032521.2	NP_115910.1	Q9BYG5	PAR6B_HUMAN	par-6 family cell polarity regulator beta	325					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						ACAGATAGAGCTAAGCTTTGA	0.433													C|||	6	0.00119808	0.0	0.0	5008	,	,		20869	0.0		0.006	False		,,,				2504	0.0				p.L325L		Atlas-SNP	.											.	PARD6B	31	.	0			c.C973T						PASS	.	C		14,4392	20.2+/-43.8	0,14,2189	109	102	104		973	4.8	0.5	20	dbSNP_127	104	56,8544	35.9+/-90.5	1,54,4245	no	coding-synonymous	PARD6B	NM_032521.2		1,68,6434	TT,TC,CC		0.6512,0.3177,0.5382		325/373	49366879	70,12936	2203	4300	6503	SO:0001819	synonymous_variant	84612	exon3			ATAGAGCTAAGCT	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.973C>T	20.37:g.49366879C>T		165	0	0		194	98	0.505155	NM_032521	A2A2A7|Q9Y510	Silent	SNP	ENST00000371610.2	37	CCDS33485.1																																																																																			C|0.996;T|0.004	0.004	strong		0.433	PARD6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079697.2	NM_032521		T	49366879	C	T	49366879	2	4	25	1	0	0	0	0	0	0	0	1	11455	796	28	2		2	PARD6B	20	49366879	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	4363668	49366879	13658641	792	9701											
C20orf108	116151	hgsc.bcm.edu	37	chr20	54940148	54940148	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgatttgtacacaggacccCagccaggccacggggacaac	11	5	11	14	1	0	1	0	1	0	0	0	3	0	3	4	4	3	1	4	4	2	2	rs148836702	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:54940148C>T	ENST00000371384.3	+	2	283	c.192C>T	c.(190-192)ccC>ccT	p.P64P		NM_080821.2	NP_543011.2	Q96KR6	F210B_HUMAN	family with sequence similarity 210, member B	64						integral component of membrane (GO:0016021)											CACAGGACCCCAGCCAGGCCA	0.498													C|||	7	0.00139776	0.0	0.0	5008	,	,		19155	0.001		0.005	False		,,,				2504	0.001				p.P64P		Atlas-SNP	.											.	.	.	.	0			c.C192T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	47	43	45		192	3.2	0.4	20	dbSNP_134	45	22,8578	15.3+/-51.7	0,22,4278	no	coding-synonymous	C20orf108	NM_080821.2		0,23,6480	TT,TC,CC		0.2558,0.0227,0.1768		64/193	54940148	23,12983	2203	4300	6503	SO:0001819	synonymous_variant	116151	exon2			GGACCCCAGCCAG	AL121914	CCDS13450.1	20q13.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000124098	ENSG00000124098			16102	protein-coding gene	gene with protein product	"hypothetical protein LOC116151"		"chromosome 20 open reading frame 108"	C20orf108		11780052	Standard	NM_080821		Approved	dJ1167H4.1, DKFZP434A1114	uc002xxc.3	Q96KR6	OTTHUMG00000032793	ENST00000371384.3:c.192C>T	20.37:g.54940148C>T		82	0	0		80	38	0.475	NM_080821	B2RBQ9|E1P5Y7|Q8WVN2|Q9BYL6|Q9H418	Silent	SNP	ENST00000371384.3	37	CCDS13450.1																																																																																			C|0.998;T|0.002	0.002	strong		0.498	FAM210B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079800.2	NM_080821		T	54940148	C	T	54940148	2	4	25	1	0	0	0	0	0	0	0	1	2080	581	21	2		2	C20orf108	20	54940148	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	5573269	54940148	8085372	793	9702											
C20orf107	388799	hgsc.bcm.edu	37	chr20	55108589	55108589	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agcaaatggctctggcttttGtttgctgttgtgccgtttgt	4	18	12	7	1	1	0	0	0	1	0	1	0	1	0	1	2	3	7	1	2	1	5	rs386815439		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:55108589G>T	ENST00000371325.1	+	1	288	c.192G>T	c.(190-192)ttG>ttT	p.L64F		NM_001013646.2	NP_001013668.2	Q5JX69	F209B_HUMAN	family with sequence similarity 209, member B	64						integral component of membrane (GO:0016021)|nucleus (GO:0005634)											TCTGGCTTTTGTTTGCTGTTG	0.483																																					p.L64F		Atlas-SNP	.											.	.	.	.	0			c.G192T						PASS	.						168	146	153					20																	55108589		2203	4300	6503	SO:0001583	missense	388799	exon1			GCTTTTGTTTGCT	AL109806	CCDS33494.1	20q13.31	2011-11-24	2011-11-24	2011-11-24	ENSG00000213714	ENSG00000213714			16101	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 107"	C20orf107			Standard	NM_001013646		Approved	dJ1153D9.4	uc002xxz.4	Q5JX69	OTTHUMG00000032800	ENST00000371325.1:c.192G>T	20.37:g.55108589G>T	ENSP00000360376:p.Leu64Phe	203	0	0		260	19	0.0730769	NM_001013646	Q3KRB5	Missense_Mutation	SNP	ENST00000371325.1	37	CCDS33494.1	.	.	.	.	.	.	.	.	.	.	G	0.325	-0.959853	0.02267	.	.	ENSG00000213714	ENST00000371325	T	0.08896	3.04	2.8	-3.7	0.04437	.	1.580090	0.04046	N	0.303922	T	0.04137	0.0115	N	0.17474	0.49	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.38090	-0.9677	10	0.07990	T	0.79	0.1847	4.0099	0.09618	0.0:0.2385:0.3799:0.3817	.	64	Q5JX69	CT107_HUMAN	F	64	ENSP00000360376:L64F	ENSP00000360376:L64F	L	+	3	2	C20orf107	54541996	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-1.684000	0.01932	-1.037000	0.03283	-0.782000	0.03352	TTG	.	.	none		0.483	FAM209B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079816.1			T	55108589	G	T	55108589	3	4	25	1	0	0	0	0	1	0	0	0	2079	1368	48	4	194	4	C20orf107	20	55108589	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	168441	55108589	7916931	794	9703											
GNAS	2778	hgsc.bcm.edu	37	chr20	57429163	57429163	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctctgggtcccaggcgccatCggcagcccatcccaagaggc	7	5	12	17	2	1	1	0	0	1	1	4	1	3	1	4	4	1	1	4	4	1	0			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:57429163C>T	ENST00000306120.3	+	1	653	c.653C>T	c.(652-654)tCg>tTg	p.S218L	GNAS_ENST00000371102.4_Silent_p.I281I|GNAS_ENST00000371075.3_Intron|GNAS_ENST00000371100.4_Silent_p.I281I|GNAS_ENST00000313949.7_Intron|GNAS_ENST00000371099.2_Silent_p.I281I|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000371098.2_Intron			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)			CAGGCGCCATCGGCAGCCCAT	0.687			Mis		pituitary adenoma		"McCune-Albright syndrome; pseudohypoparathyroidism, type IA"			TSP Lung(22;0.16)																											p.S219L	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.C656T						PASS	.						14	15	15					20																	57429163		1811	3992	5803	SO:0001583	missense	2778	exon1			CGCCATCGGCAGC	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.653C>T	20.37:g.57429163C>T	ENSP00000302237:p.Ser218Leu	53	0	0		63	22	0.349206	NM_001077490	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	ENST00000306120.3	37		.	.	.	.	.	.	.	.	.	.	C	2.592	-0.295042	0.05532	.	.	ENSG00000087460	ENST00000306120	.	.	.	4.03	0.906	0.19314	.	.	.	.	.	T	0.23611	0.0571	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.23833	-1.0177	5	0.27082	T	0.32	.	3.761	0.08604	0.0:0.5632:0.2068:0.23	.	.	.	.	L	218	.	ENSP00000302237:S218L	S	+	2	0	GNAS	56862558	0.000000	0.05858	0.008000	0.14137	0.415000	0.31203	0.170000	0.16663	0.235000	0.21160	0.561000	0.74099	TCG	.	.	none		0.687	GNAS-050	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000267987.1	NM_000516		T	57429163	C	T	57429163	3	4	25	1	0	0	0	0	1	0	0	0	6518	893	31	1	1587	1	GNAS	20	57429163	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	2320574	57429163	5596357	795	9704											
LAMA5	3911	hgsc.bcm.edu	37	chr20	60885978	60885978	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttgtgccagcggccaggccGggagcgctggcggctctggg	3	6	19	13	4	1	0	0	0	1	0	1	1	1	1	3	6	3	2	3	6	0	1	rs201094237	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:60885978G>T	ENST00000252999.3	-	74	10327	c.10261C>A	c.(10261-10263)Cgg>Agg	p.R3421R	LAMA5_ENST00000492698.1_5'Flank	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	3421	Laminin G-like 4. {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)			CGGCCAGGCCGGGAGCGCTGG	0.697													.|||	3	0.000599042	0.0	0.0	5008	,	,		12759	0.0		0.001	False		,,,				2504	0.002				p.R3421R		Atlas-SNP	.											.	LAMA5	268	.	0			c.C10261A						PASS	.			0,4154		0,0,2077	12	16	14		10261	0.8	0	20		14	4,8320		0,4,4158	no	coding-synonymous	LAMA5	NM_005560.3		0,4,6235	TT,TG,GG		0.0481,0.0,0.0321		3421/3696	60885978	4,12474	2077	4162	6239	SO:0001819	synonymous_variant	3911	exon74			CAGGCCGGGAGCG	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.10261C>A	20.37:g.60885978G>T		11	0	0		42	30	0.714286	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			.	.	weak		0.697	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		T	60885978	G	T	60885978	2	4	25	1	0	0	0	0	0	0	0	1	8618	1115	39	4		4	LAMA5	20	60885978	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	3456815	60885978	2139542	796	9705											
TPTE	7179	hgsc.bcm.edu	37	chr21	10920086	10920086	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttaaaaagaaaacttacctGagaaggagtttttactccct	15	13	6	7	0	0	2	0	1	0	2	1	4	1	3	2	1	3	1	2	1	8	6			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:10920086G>T	ENST00000361285.4	-	19	1497	c.1168C>A	c.(1168-1170)Cag>Aag	p.Q390K	TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000298232.7_Missense_Mutation_p.Q372K|TPTE_ENST00000342420.5_Missense_Mutation_p.Q352K	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	390	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)	p.Q390K(1)|p.Q372K(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)		AAACTTACCTGAGAAGGAGTT	0.378																																					p.Q390K		Atlas-SNP	.											TPTE_ENST00000361285,NS,carcinoma,0,3	TPTE	513	3	2	Substitution - Missense(2)	lung(2)	c.C1168A						PASS	.						70	70	70					21																	10920086		2202	4300	6502	SO:0001583	missense	7179	exon19			TTACCTGAGAAGG	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.1168C>A	21.37:g.10920086G>T	ENSP00000355208:p.Gln390Lys	99	0	0		127	30	0.23622	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	37	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	.	12.26	1.885014	0.33255	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420	D;D;D	0.99488	-6.0;-6.0;-6.0	2.32	2.32	0.28847	Phosphatase tensin type (1);	0.000000	0.85682	D	0.000000	D	0.99629	0.9864	H	0.97962	4.115	0.46798	D	0.999209	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.996;0.996;0.999	D	0.98186	1.0460	10	0.87932	D	0	-18.4997	8.1818	0.31315	0.0:0.0:1.0:0.0	.	352;372;390	P56180-3;P56180-2;P56180	.;.;TPTE_HUMAN	K	372;390;352	ENSP00000298232:Q372K;ENSP00000355208:Q390K;ENSP00000344441:Q352K	ENSP00000298232:Q372K	Q	-	1	0	TPTE	9941957	1.000000	0.71417	0.997000	0.53966	0.311000	0.27955	5.387000	0.66243	1.313000	0.45069	0.184000	0.17185	CAG	.	.	none		0.378	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1			T	10920086	G	T	10920086	3	4	25	1	0	0	0	0	1	0	0	0	16445	1299	45	4	511	4	TPTE	21	10920086	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10		10920086	37209809	797	9706											
BAGE2	85319	hgsc.bcm.edu	37	chr21	11049616	11049616	+	RNA	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cactgcacagtttgcatcttCcttcgctataattaacagta	11	14	5	11	1	1	0	0	0	1	0	3	0	2	0	1	0	3	5	1	0	4	7			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:11049616C>T	ENST00000470054.1	-	0	492							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)		TTTGCATCTTCCTTCGCTATA	0.368																																					p.R95R		Atlas-SNP	.											.	.	.	.	0			c.G285A						PASS	.						135	96	108					21																	11049616		692	1591	2283			85318	exon4			CATCTTCCTTCGC	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		21.37:g.11049616C>T		430	0	0		388	27	0.0695876	NM_182481	A8K925|Q08ER0	Silent	SNP	ENST00000470054.1	37																																																																																				.	.	none		0.368	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482		T	11049616	C	T	11049616	1	4	25	0	1	0	0	0	0	0	0	0	1292	854	30	2		2	BAGE2	21	11049616	RNA	SNP	C	TCGA-G8-6906-01A-11D-2210-10	129530	11049616	37080279	798	9707											
ADAMTS5	11096	hgsc.bcm.edu	37	chr21	28315841	28315841	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttcacagaatttggaatcGtcatgggagaggccaagtaa	13	10	11	7	1	3	2	2	0	1	2	4	4	3	3	1	3	0	1	1	3	4	3	rs61088614	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:28315841G>A	ENST00000284987.5	-	3	1384	c.1263C>T	c.(1261-1263)gaC>gaT	p.D421D		NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	421	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				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						ATTTGGAATCGTCATGGGAGA	0.418													G|||	251	0.0501198	0.1755	0.0144	5008	,	,		20735	0.0		0.006	False		,,,				2504	0.0031				p.D421D	Esophageal Squamous(53;683 1080 10100 14424 45938)	Atlas-SNP	.											.	ADAMTS5	184	.	0			c.C1263T						PASS	.	G		601,3805	262.8+/-265.1	44,513,1646	75	70	72		1263	-10.1	0.1	21	dbSNP_129	72	28,8572	19.8+/-62.0	0,28,4272	no	coding-synonymous	ADAMTS5	NM_007038.3		44,541,5918	AA,AG,GG		0.3256,13.6405,4.8362		421/931	28315841	629,12377	2203	4300	6503	SO:0001819	synonymous_variant	11096	exon3			GGAATCGTCATGG	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.1263C>T	21.37:g.28315841G>A		100	0	0		114	55	0.482456	NM_007038	Q52LV4|Q9UKP2	Silent	SNP	ENST00000284987.5	37	CCDS13579.1																																																																																			G|0.957;A|0.043	0.043	strong		0.418	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1			A	28315841	G	A	28315841	2	1	25	1	0	0	0	0	0	0	0	1	269	1136	40	1		1	ADAMTS5	21	28315841	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	17266225	28315841	19814054	799	9708											
CCT8	10694	hgsc.bcm.edu	37	chr21	30437344	30437344	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtacactgctatttttgcaTctttgacagatgttacatca	11	16	6	8	0	2	2	1	1	1	1	2	2	2	2	0	0	4	4	0	0	3	6			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:30437344T>C	ENST00000286788.4	-	7	913	c.707A>G	c.(706-708)gAt>gGt	p.D236G	CCT8_ENST00000470450.1_5'UTR|CCT8_ENST00000542732.1_Missense_Mutation_p.D217G|CCT8_ENST00000540844.1_Missense_Mutation_p.D163G	NM_006585.2	NP_006576.2	P50990	TCPQ_HUMAN	chaperonin containing TCP1, subunit 8 (theta)	236					'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						TATTTTTGCATCTTTGACAGA	0.378																																					p.D236G		Atlas-SNP	.											.	CCT8	38	.	0			c.A707G						PASS	.						193	175	181					21																	30437344		2203	4300	6503	SO:0001583	missense	10694	exon7			TTTGCATCTTTGA	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.707A>G	21.37:g.30437344T>C	ENSP00000286788:p.Asp236Gly	85	0	0		94	4	0.0425532	NM_006585	A6NN54|B4DEM7|B4DQH4|Q4VBP8	Missense_Mutation	SNP	ENST00000286788.4	37	CCDS33528.1	.	.	.	.	.	.	.	.	.	.	T	18.24	3.580704	0.65992	.	.	ENSG00000156261	ENST00000389159;ENST00000286788;ENST00000542732;ENST00000540844	T;T;T	0.67865	-0.29;-0.29;-0.29	5.25	5.25	0.73442	.	0.043440	0.85682	D	0.000000	T	0.58694	0.2140	L	0.38649	1.16	0.80722	D	1	B;B;B;B;B	0.32653	0.018;0.006;0.018;0.014;0.379	B;B;B;B;B	0.33339	0.043;0.007;0.027;0.016;0.162	T	0.59794	-0.7387	10	0.42905	T	0.14	-23.8735	15.6084	0.76692	0.0:0.0:0.0:1.0	.	163;217;236;235;236	B4DQH4;B4DEM7;Q53HU0;G5E9B2;P50990	.;.;.;.;TCPQ_HUMAN	G	235;236;217;163	ENSP00000286788:D236G;ENSP00000444984:D217G;ENSP00000442730:D163G	ENSP00000286788:D236G	D	-	2	0	CCT8	29359215	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.728000	0.68531	2.326000	0.78906	0.533000	0.62120	GAT	.	.	none		0.378	CCT8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171822.1			C	30437344	T	C	30437344	3	2	25	1	0	0	0	0	1	0	0	0	2962	1435	50	3	975	3	CCT8	21	30437344	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	2121503	30437344	17692551	800	9709											
AGPAT3	56894	hgsc.bcm.edu	37	chr21	45389034	45389034	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctaagaaggagctgctctaCgtgcccctcatcggctggac	8	8	12	13	2	2	1	1	0	1	1	3	3	2	3	2	3	4	4	2	3	3	2	rs61737069	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:45389034C>T	ENST00000398063.2	+	4	876	c.384C>T	c.(382-384)taC>taT	p.Y128Y	AGPAT3_ENST00000398061.1_Silent_p.Y128Y|AGPAT3_ENST00000479117.1_3'UTR|AGPAT3_ENST00000291572.8_Silent_p.Y128Y|AGPAT3_ENST00000398058.1_Silent_p.Y128Y|AGPAT3_ENST00000546158.1_Silent_p.Y128Y|AGPAT3_ENST00000327505.2_Silent_p.Y128Y	NM_001037553.1	NP_001032642.1	Q9NRZ7	PLCC_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 3	128					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)		AGCTGCTCTACGTGCCCCTCA	0.632													C|||	42	0.00838658	0.0023	0.0072	5008	,	,		19868	0.0		0.0179	False		,,,				2504	0.0164				p.Y128Y	Pancreas(60;623 1650 5574 52796)	Atlas-SNP	.											.	AGPAT3	37	.	0			c.C384T						PASS	.	C	,	18,4388	25.3+/-52.1	0,18,2185	130	105	113		384,384	0.4	1	21	dbSNP_129	113	171,8429	78.9+/-141.6	1,169,4130	no	coding-synonymous,coding-synonymous	AGPAT3	NM_001037553.1,NM_020132.4	,	1,187,6315	TT,TC,CC		1.9884,0.4085,1.4532	,	128/377,128/377	45389034	189,12817	2203	4300	6503	SO:0001819	synonymous_variant	56894	exon4			GCTCTACGTGCCC	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.384C>T	21.37:g.45389034C>T		145	0	0		167	93	0.556886	NM_001037553	D3DSL2|Q3ZCU2|Q6UWP6|Q6ZUC6|Q8N3Q7|Q9NRZ6	Silent	SNP	ENST00000398063.2	37	CCDS13703.1																																																																																			C|0.986;T|0.014	0.014	strong		0.632	AGPAT3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195722.1	NM_020132		T	45389034	C	T	45389034	2	4	25	1	0	0	0	0	0	0	0	1	388	547	19	1		1	AGPAT3	21	45389034	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	14951690	45389034	2740861	801	9710											
DNMT3L	29947	hgsc.bcm.edu	37	chr21	45675997	45675997	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacccggactggctgtctcCtccacacaggcacggtttcg	6	8	11	16	3	1	0	0	0	1	0	4	1	2	1	3	4	0	4	3	4	0	1	rs142917827		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:45675997C>T	ENST00000418993.1	-	7	1040	c.557G>A	c.(556-558)aGg>aAg	p.R186K	DNMT3L_ENST00000270172.3_Missense_Mutation_p.R186K	NM_175867.2	NP_787063.1	Q9UJW3	DNM3L_HUMAN	DNA (cytosine-5-)-methyltransferase 3-like	186					chorionic trophoblast cell differentiation (GO:0060718)|DNA methylation (GO:0006306)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|placenta development (GO:0001890)|positive regulation of catalytic activity (GO:0043085)|regulation of gene expression by genetic imprinting (GO:0006349)|spermatogenesis (GO:0007283)	condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(3)	11				Colorectal(79;0.0165)|READ - Rectum adenocarcinoma(84;0.0781)		TGGCTGTCTCCTCCACACAGG	0.478													C|||	1	0.000199681	0.0	0.0	5008	,	,		13853	0.0		0.001	False		,,,				2504	0.0				p.R186K		Atlas-SNP	.											.	DNMT3L	33	.	0			c.G557A						PASS	.	C	LYS/ARG,LYS/ARG	1,4405	2.1+/-5.4	0,1,2202	108	108	108		557,557	1.1	0.3	21	dbSNP_134	108	17,8583	12.6+/-44.7	0,17,4283	yes	missense,missense	DNMT3L	NM_013369.2,NM_175867.1	26,26	0,18,6485	TT,TC,CC		0.1977,0.0227,0.1384	benign,benign	186/388,186/387	45675997	18,12988	2203	4300	6503	SO:0001583	missense	29947	exon7			TGTCTCCTCCACA	AF194032	CCDS13705.1	21q22.3	2008-07-31			ENSG00000142182	ENSG00000142182			2980	protein-coding gene	gene with protein product	"cytosine-5-methyltransferase 3-like protein", "human cytosine-5-methyltransferase 3-like protein"	606588				10857753	Standard	NM_013369		Approved	MGC1090	uc002zeh.2	Q9UJW3	OTTHUMG00000086914	ENST00000418993.1:c.557G>A	21.37:g.45675997C>T	ENSP00000412862:p.Arg186Lys	139	0	0		183	98	0.535519	NM_013369	E9PB42|Q9BUJ4	Missense_Mutation	SNP	ENST00000418993.1	37	CCDS46650.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	0.006	-2.100319	0.00360	2.27E-4	0.001977	ENSG00000142182	ENST00000270172;ENST00000418993;ENST00000431166	T;T;T	0.73258	-0.73;-0.73;-0.73	3.44	1.07	0.20283	.	0.493499	0.20721	N	0.086902	T	0.29620	0.0739	N	0.01091	-1.02	0.24720	N	0.993155	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36648	-0.9739	10	0.02654	T	1	-19.7411	4.7202	0.12915	0.0:0.3025:0.0:0.6975	.	186;186	Q9UJW3-2;Q9UJW3	.;DNM3L_HUMAN	K	186;186;171	ENSP00000270172:R186K;ENSP00000412862:R186K;ENSP00000400242:R171K	ENSP00000270172:R186K	R	-	2	0	DNMT3L	44500425	0.992000	0.36948	0.271000	0.24616	0.065000	0.16274	2.203000	0.42752	0.118000	0.18165	-0.379000	0.06801	AGG	C|0.999;T|0.001	0.001	strong		0.478	DNMT3L-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000195820.1	NM_013369		T	45675997	C	T	45675997	3	4	25	1	0	0	0	0	1	0	0	0	4680	681	24	2	630	2	DNMT3L	21	45675997	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	286963	45675997	2453898	802	9711											
TRPM2	7226	hgsc.bcm.edu	37	chr21	45826486	45826486	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtcctgcagatgaaggacGtcttcttcttcctcttcctg	5	15	8	13	1	4	2	0	1	4	1	7	3	7	3	3	1	1	1	3	1	1	4	rs56379273	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:45826486G>A	ENST00000397928.1	+	19	3245	c.2800G>A	c.(2800-2802)Gtc>Atc	p.V934I	TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000397932.2_Missense_Mutation_p.V934I|TRPM2_ENST00000300482.5_Missense_Mutation_p.V934I|TRPM2_ENST00000300481.9_Missense_Mutation_p.V914I	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	934					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						GATGAAGGACGTCTTCTTCTT	0.627													g|||	30	0.00599042	0.0015	0.0086	5008	,	,		16988	0.0		0.0199	False		,,,				2504	0.002				p.V934I		Atlas-SNP	.											.	TRPM2	196	.	0			c.G2800A						PASS	.	G	ILE/VAL	12,4372	21.2+/-45.6	0,12,2180	41	39	40		2800	3.2	1	21	dbSNP_129	40	133,8439	66.7+/-129.0	0,133,4153	yes	missense	TRPM2	NM_003307.3	29	0,145,6333	AA,AG,GG		1.5516,0.2737,1.1192	possibly-damaging	934/1504	45826486	145,12811	2192	4286	6478	SO:0001583	missense	7226	exon19			AAGGACGTCTTCT	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.2800G>A	21.37:g.45826486G>A	ENSP00000381023:p.Val934Ile	16	0	0		29	14	0.482759	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	37	CCDS13710.1	19	0.0086996336996337	0	0.0	4	0.011049723756906077	0	0.0	15	0.01978891820580475	g	12.27	1.888364	0.33348	0.002737	0.015516	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932	T;T;T;T	0.74209	-0.82;-0.82;-0.82;-0.82	4.12	3.23	0.37069	Ion transport (1);	0.453240	0.21370	N	0.075647	T	0.49558	0.1564	L	0.41632	1.29	0.37070	D	0.898505	B;B;B	0.24043	0.096;0.056;0.056	B;B;B	0.19391	0.025;0.025;0.025	T	0.63382	-0.6650	10	0.62326	D	0.03	-29.5505	12.4046	0.55432	0.0842:0.0:0.9158:0.0	rs56379273	934;720;934	E9PGK7;Q5KTC1;O94759	.;.;TRPM2_HUMAN	I	934;934;914;934	ENSP00000300482:V934I;ENSP00000381023:V934I;ENSP00000300481:V914I;ENSP00000381026:V934I	ENSP00000300481:V914I	V	+	1	0	TRPM2	44650914	0.998000	0.40836	1.000000	0.80357	0.981000	0.71138	2.350000	0.44063	0.861000	0.35504	0.536000	0.68110	GTC	G|0.988;A|0.012	0.012	strong		0.627	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307		A	45826486	G	A	45826486	3	1	25	1	0	0	0	0	1	0	0	0	16601	1145	40	1	2874	1	TRPM2	21	45826486	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	150489	45826486	2303409	803	9712											
KRTAP10-10	353333	hgsc.bcm.edu	37	chr21	46057634	46057634	+	Silent	SNP	T	T	C																															tgctgtgtgcctgtctgctgTgtgcccgtctgctgcgtgcc																								rs61029972	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46057634T>C	ENST00000380095.1	+	1	362	c.300T>C	c.(298-300)tgT>tgC	p.C100C	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	100	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						ctgtctgctgtgtgcccgtct	0.632													C|||	539	0.107628	0.2383	0.0591	5008	,	,		18755	0.0109		0.0557	False		,,,				2504	0.1186				p.C100C		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.T300C						PASS	.						126	121	123					21																	46057634		2203	4298	6501	SO:0001819	synonymous_variant	353333	exon1			CTGCTGTGTGCCC	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.300T>C	21.37:g.46057634T>C		142	0	0		145	84	0.57931	NM_181688		Silent	SNP	ENST00000380095.1	37	CCDS33585.1																																																																																			C|1.000;|0.000	1.000	weak		0.632	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688		C	46057634	T	C	46057634	2	2	25	1	0	0	0	0	0	0	0	1	8515	1702	59	3		3	KRTAP10-10	21	46057634	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	231148	46057634	2072261	804	9713	119	2									
KRTAP10-10	353333	hgsc.bcm.edu	37	chr21	46057635	46057635	+	Missense_Mutation	SNP	G	G	A																															gctgtgtgcctgtctgctgtGtgcccgtctgctgcgtgccc																								rs114397261	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46057635G>A	ENST00000380095.1	+	1	363	c.301G>A	c.(301-303)Gtg>Atg	p.V101M	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	101	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						tgtctgctgtgtgcccgtctg	0.632													A|||	306	0.0611022	0.2118	0.0173	5008	,	,		18765	0.002		0.001	False		,,,				2504	0.0112				p.V101M		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.G301A						PASS	.	A	,MET/VAL	438,3968		76,286,1841	130	123	125		,301	-1.7	0	21	dbSNP_132	125	2,8594		0,2,4296	no	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,21	76,288,6137	AA,AG,GG		0.0233,9.941,3.3841	,possibly-damaging	,101/252	46057635	440,12562	2203	4298	6501	SO:0001583	missense	353333	exon1			TGCTGTGTGCCCG	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.301G>A	21.37:g.46057635G>A	ENSP00000369438:p.Val101Met	142	0	0		145	85	0.586207	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	.	.	.	.	.	.	.	.	.	.	a	1.285	-0.609223	0.03690	0.09941	2.33E-4	ENSG00000221859	ENST00000380095	T	0.01430	4.9	2.86	-1.68	0.08212	.	.	.	.	.	T	0.00073	0.0002	L	0.36672	1.1	0.09310	N	1	B	0.26195	0.144	B	0.34452	0.183	T	0.44128	-0.9348	9	0.44086	T	0.13	.	9.7593	0.40522	0.4446:0.0:0.5554:0.0	.	101	P60014	KR10A_HUMAN	M	101	ENSP00000369438:V101M	ENSP00000369438:V101M	V	+	1	0	KRTAP10-10	44882063	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-0.140000	0.10342	-1.728000	0.01366	-2.786000	0.00116	GTG	G|0.928;A|0.072	0.072	strong		0.632	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688		A	46057635	G	A	46057635	3	1	25	1	0	0	0	0	1	0	0	0	8515	1377	48	2	303	2	KRTAP10-10	21	46057635	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1	46057635	2072260	805	9714	119	2									
KRTAP10-10	353333	hgsc.bcm.edu	37	chr21	46057666	46057666	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgcgtgcccgtctgtaacaAgcctgtgtgcttcgtgccta	5	12	11	13	3	1	0	0	0	1	0	2	0	1	0	3	0	6	2	3	0	3	3	rs116100696	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46057666A>T	ENST00000380095.1	+	1	394	c.332A>T	c.(331-333)aAg>aTg	p.K111M	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	111	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						gtctgtaacaagcctgtgtgc	0.632													A|||	91	0.0181709	0.0651	0.0072	5008	,	,		20883	0.0		0.0	False		,,,				2504	0.0				p.K111M		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.A332T						PASS	.	A	,MET/LYS	231,4175	136.5+/-172.5	10,211,1982	222	189	200		,332	-6.2	0	21	dbSNP_132	200	0,8600		0,0,4300	yes	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,95	10,211,6282	TT,TA,AA		0.0,5.2429,1.7761	,benign	,111/252	46057666	231,12775	2203	4300	6503	SO:0001583	missense	353333	exon1			GTAACAAGCCTGT	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.332A>T	21.37:g.46057666A>T	ENSP00000369438:p.Lys111Met	140	0	0		150	90	0.6	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	35	0.016025641025641024	32	0.06504065040650407	3	0.008287292817679558	0	0.0	0	0.0	a	6.984	0.551656	0.13374	0.052429	0.0	ENSG00000221859	ENST00000380095	T	0.01438	4.89	3.13	-6.25	0.02039	.	.	.	.	.	T	0.00241	0.0007	M	0.84846	2.72	0.09310	N	1	P	0.47302	0.893	P	0.46543	0.52	T	0.00529	-1.1687	9	0.52906	T	0.07	.	0.1928	0.00136	0.2301:0.2328:0.1914:0.3458	.	111	P60014	KR10A_HUMAN	M	111	ENSP00000369438:K111M	ENSP00000369438:K111M	K	+	2	0	KRTAP10-10	44882094	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.719000	0.04974	-2.037000	0.00920	-0.711000	0.03637	AAG	A|0.982;T|0.018	0.018	strong		0.632	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688		T	46057666	A	T	46057666	3	4	25	1	0	0	0	0	1	0	0	0	8515	72	3	5	334	5	KRTAP10-10	21	46057666	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	31	46057666	2072229	806	9715											
POFUT2	23275	hgsc.bcm.edu	37	chr21	46707778	46707778	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaggaagacgaagctgagTgtcgccatggccccgggcgg	9	4	17	11	4	0	2	0	1	0	1	1	4	0	3	3	4	2	2	3	4	2	0			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46707778T>C	ENST00000349485.5	-	1	35	c.9A>G	c.(7-9)acA>acG	p.T3T	BX322557.10_ENST00000454115.2_RNA|POFUT2_ENST00000331343.7_Silent_p.T3T	NM_133635.4	NP_598368.2	Q9Y2G5	OFUT2_HUMAN	protein O-fucosyltransferase 2	3					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)		CGAAGCTGAGTGTCGCCATGG	0.706																																					p.T3T		Atlas-SNP	.											.	POFUT2	77	.	0			c.A9G						PASS	.						5	6	6					21																	46707778		2017	3977	5994	SO:0001819	synonymous_variant	23275	exon1			GCTGAGTGTCGCC	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.9A>G	21.37:g.46707778T>C		11	0	0		20	12	0.6	NM_015227	Q6PJV1|Q7Z4N0|Q8WWU6|Q9BQS4|Q9BQS5|Q9UFY3	Silent	SNP	ENST00000349485.5	37	CCDS13719.1																																																																																			.	.	none		0.706	POFUT2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192573.2	NM_015227		C	46707778	T	C	46707778	2	2	25	1	0	0	0	0	0	0	0	1	12193	1683	59	3		3	POFUT2	21	46707778	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	650112	46707778	1422117	807	9716											
COL18A1	80781	hgsc.bcm.edu	37	chr21	46875586	46875586	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cagctaccacgatccctgagCcccaggggcccctgcctgtg	6	6	11	18	1	0	1	0	1	0	0	1	2	1	1	7	2	4	1	7	2	1	1	rs61749002	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46875586C>G	ENST00000359759.4	+	1	163	c.142C>G	c.(142-144)Ccc>Gcc	p.P48A	COL18A1_ENST00000400337.2_Intron|COL18A1_ENST00000355480.5_Missense_Mutation_p.P48A			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	48					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)		GATCCCTGAGCCCCAGGGGCC	0.637													C|||	99	0.0197684	0.0688	0.0115	5008	,	,		16000	0.0		0.0	False		,,,				2504	0.0				p.P48A		Atlas-SNP	.											.	COL18A1	129	.	0			c.C142G						PASS	.	C	,ALA/PRO	243,3931		6,231,1850	52	69	63		,142	0.2	0	21	dbSNP_129	63	1,8439		0,1,4219	yes	intron,missense	COL18A1	NM_130445.2,NM_030582.3	,27	6,232,6069	GG,GC,CC		0.0118,5.8218,1.9344	,benign	,48/1520	46875586	244,12370	2087	4220	6307	SO:0001583	missense	80781	exon1			CCTGAGCCCCAGG		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.142C>G	21.37:g.46875586C>G	ENSP00000352798:p.Pro48Ala	111	0	0		145	66	0.455172	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	37		54	0.024725274725274724	48	0.0975609756097561	4	0.011049723756906077	2	0.0034965034965034965	0	0.0	C	8.524	0.869347	0.17322	0.058218	1.18E-4	ENSG00000182871	ENST00000355480;ENST00000359759;ENST00000539645	T;T	0.59906	0.23;0.23	3.33	0.153	0.14897	Domain of unknown function DUF959, collagen XVIII, N-terminal (1);	1.487630	0.05437	N	0.546948	T	0.01627	0.0052	L	0.34521	1.04	0.09310	N	1	B;B	0.14438	0.01;0.002	B;B	0.17098	0.017;0.003	T	0.15407	-1.0438	10	0.87932	D	0	.	6.156	0.20338	0.0:0.5294:0.3598:0.1108	rs61749002	48;48	P39060;P39060-1	COIA1_HUMAN;.	A	48	ENSP00000347665:P48A;ENSP00000352798:P48A	ENSP00000347665:P48A	P	+	1	0	COL18A1	45700014	0.000000	0.05858	0.049000	0.19019	0.056000	0.15407	-0.676000	0.05221	-0.110000	0.12022	0.436000	0.28706	CCC	C|0.976;G|0.024	0.024	strong		0.637	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			G	46875586	C	G	46875586	3	3	25	1	0	0	0	0	1	0	0	0	3677	739	26	4	258	4	COL18A1	21	46875586	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	167808	46875586	1254309	808	9717											
COL18A1	80781	hgsc.bcm.edu	37	chr21	46875683	46875683	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcgacagcccctggcagccCtgagccaccctcagagctgc	8	4	11	18	1	1	2	1	1	0	1	1	3	1	2	5	1	6	2	5	1	0	0	rs61739237	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46875683C>G	ENST00000359759.4	+	1	260	c.239C>G	c.(238-240)cCt>cGt	p.P80R	COL18A1_ENST00000400337.2_Intron|COL18A1_ENST00000355480.5_Missense_Mutation_p.P80R			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	80					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)		CCTGGCAGCCCTGAGCCACCC	0.677													C|||	99	0.0197684	0.0688	0.0115	5008	,	,		16653	0.0		0.0	False		,,,				2504	0.0				p.P80R		Atlas-SNP	.											.	COL18A1	129	.	0			c.C239G						PASS	.	C	,ARG/PRO	249,3887		6,237,1825	45	58	54		,239	1.3	0	21	dbSNP_129	54	1,8375		0,1,4187	yes	intron,missense	COL18A1	NM_130445.2,NM_030582.3	,103	6,238,6012	GG,GC,CC		0.0119,6.0203,1.9981	,benign	,80/1520	46875683	250,12262	2068	4188	6256	SO:0001583	missense	80781	exon1			GCAGCCCTGAGCC		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.239C>G	21.37:g.46875683C>G	ENSP00000352798:p.Pro80Arg	107	0	0		114	47	0.412281	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	37		54	0.024725274725274724	50	0.1016260162601626	4	0.011049723756906077	0	0.0	0	0.0	C	7.818	0.717135	0.15372	0.060203	1.19E-4	ENSG00000182871	ENST00000355480;ENST00000359759;ENST00000539645	T;T	0.32515	1.45;1.45	3.31	1.34	0.21922	Domain of unknown function DUF959, collagen XVIII, N-terminal (1);	2.030890	0.02888	N	0.133800	T	0.00845	0.0028	L	0.42245	1.32	0.09310	N	1	B;B	0.14805	0.011;0.009	B;B	0.17433	0.018;0.011	T	0.27123	-1.0083	10	0.72032	D	0.01	.	10.5387	0.45020	0.0:0.6186:0.3814:0.0	rs61739237	80;80	P39060;P39060-1	COIA1_HUMAN;.	R	80	ENSP00000347665:P80R;ENSP00000352798:P80R	ENSP00000347665:P80R	P	+	2	0	COL18A1	45700111	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.377000	0.20552	0.174000	0.19809	0.491000	0.48974	CCT	C|0.976;G|0.024	0.024	strong		0.677	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			G	46875683	C	G	46875683	3	3	25	1	0	0	0	0	1	0	0	0	3677	681	24	4	355	4	COL18A1	21	46875683	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	97	46875683	1254212	809	9718											
COL18A1	80781	hgsc.bcm.edu	37	chr21	46895427	46895427	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagcgggctcggggacgcccGggagcttctcagggaggaga	7	4	19	11	4	1	1	1	0	1	1	3	5	1	4	1	6	2	2	1	6	0	1	rs62000965	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46895427G>T	ENST00000359759.4	+	4	2042	c.2021G>T	c.(2020-2022)cGg>cTg	p.R674L	COL18A1_ENST00000400337.2_Missense_Mutation_p.R259L|COL18A1_ENST00000355480.5_Missense_Mutation_p.R439L			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	674	Nonhelical region 1 (NC1).				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)		GGGGACGCCCGGGAGCTTCTC	0.692													G|||	96	0.0191693	0.0666	0.0115	5008	,	,		14324	0.0		0.0	False		,,,				2504	0.0				p.R439L		Atlas-SNP	.											.	COL18A1	129	.	0			c.G1316T						PASS	.	G	LEU/ARG,LEU/ARG	231,3473		6,219,1627	13	16	15		776,1316	-4.6	0	21	dbSNP_129	15	1,8171		0,1,4085	no	missense,missense	COL18A1	NM_130445.2,NM_030582.3	102,102	6,220,5712	TT,TG,GG		0.0122,6.2365,1.9535	benign,benign	259/1340,439/1520	46895427	232,11644	1852	4086	5938	SO:0001583	missense	80781	exon4			ACGCCCGGGAGCT		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.2021G>T	21.37:g.46895427G>T	ENSP00000352798:p.Arg674Leu	141	0	0		148	65	0.439189	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	37		53	0.024267399267399268	48	0.0975609756097561	5	0.013812154696132596	0	0.0	0	0.0	G	9.059	0.994091	0.19043	0.062365	1.22E-4	ENSG00000182871	ENST00000400337;ENST00000400347;ENST00000355480;ENST00000359759;ENST00000539645	D;D;D	0.90563	-2.66;-2.69;-2.57	2.98	-4.62	0.03370	.	1.760170	0.02944	N	0.140855	T	0.11452	0.0279	N	0.24115	0.695	0.09310	N	1	B;B;B	0.29716	0.166;0.255;0.255	B;B;B	0.25614	0.028;0.062;0.045	T	0.57528	-0.7796	10	0.25751	T	0.34	.	5.8286	0.18568	0.6231:0.1574:0.2195:0.0	rs62000965	674;439;259	P39060;P39060-1;P39060-2	COIA1_HUMAN;.;.	L	259;259;439;674;674	ENSP00000383191:R259L;ENSP00000347665:R439L;ENSP00000352798:R674L	ENSP00000347665:R439L	R	+	2	0	COL18A1	45719855	0.000000	0.05858	0.000000	0.03702	0.056000	0.15407	-2.199000	0.01238	-1.208000	0.02634	0.196000	0.17591	CGG	G|0.976;T|0.024	0.024	strong		0.692	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1			T	46895427	G	T	46895427	3	4	25	1	0	0	0	0	1	0	0	0	3677	1116	39	4	2149	4	COL18A1	21	46895427	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	19744	46895427	1234468	810	9719											
COL6A1	1291	hgsc.bcm.edu	37	chr21	47422174	47422174	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atggcgggcggcaccttcacGggggaggccctgcagtacac	7	5	16	13	3	1	0	1	0	0	0	1	1	1	1	2	6	2	3	2	6	1	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47422174G>A	ENST00000361866.3	+	32	2223	c.2109G>A	c.(2107-2109)acG>acA	p.T703T	COL6A1_ENST00000498614.1_3'UTR	NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	703	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)		GCACCTTCACGGGGGAGGCCC	0.697																																					p.T703T		Atlas-SNP	.											.	COL6A1	101	.	0			c.G2109A						PASS	.						12	12	12					21																	47422174		2176	4278	6454	SO:0001819	synonymous_variant	1291	exon32			CTTCACGGGGGAG	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.2109G>A	21.37:g.47422174G>A		36	0	0		40	20	0.5	NM_001848	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Silent	SNP	ENST00000361866.3	37	CCDS13727.1																																																																																			.	.	none		0.697	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848		A	47422174	G	A	47422174	2	1	25	1	0	0	0	0	0	0	0	1	3701	1103	39	1		1	COL6A1	21	47422174	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	526747	47422174	707721	811	9720											
COL6A2	1292	hgsc.bcm.edu	37	chr21	47552449	47552449	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggcttcttcgaccgcttcAtccgctggatctgctagcgc	4	11	10	16	5	3	0	1	0	2	0	5	2	4	1	3	2	2	4	3	2	1	4	rs11910483	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47552449A>C	ENST00000300527.4	+	28	3147	c.3043A>C	c.(3043-3045)Atc>Ctc	p.I1015L		NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	1015	Nonhelical region.		I -> L (in dbSNP:rs11910483).		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)		CGACCGCTTCATCCGCTGGAT	0.697													A|||	106	0.0211661	0.0756	0.0072	5008	,	,		13410	0.0		0.001	False		,,,				2504	0.0				p.I1015L		Atlas-SNP	.											.	COL6A2	351	.	0			c.A3043C						PASS	.	A	LEU/ILE	281,4115		10,261,1927	38	32	34		3043	4.4	1	21	dbSNP_120	34	4,8592		0,4,4294	yes	missense	COL6A2	NM_001849.3	5	10,265,6221	CC,CA,AA		0.0465,6.3922,2.1937	possibly-damaging	1015/1020	47552449	285,12707	2198	4298	6496	SO:0001583	missense	1292	exon28			CGCTTCATCCGCT	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.3043A>C	21.37:g.47552449A>C	ENSP00000300527:p.Ile1015Leu	24	0	0		65	29	0.446154	NM_001849	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Missense_Mutation	SNP	ENST00000300527.4	37	CCDS13728.1	40	0.018315018315018316	37	0.07520325203252033	3	0.008287292817679558	0	0.0	0	0.0	A	11.98	1.799818	0.31869	0.063922	4.65E-4	ENSG00000142173	ENST00000300527	T	0.77098	-1.07	4.4	4.4	0.53042	.	0.115804	0.56097	D	0.000028	T	0.16557	0.0398	L	0.53249	1.67	0.80722	D	1	P	0.44690	0.841	P	0.45449	0.481	T	0.49835	-0.8897	10	0.32370	T	0.25	-18.2856	13.6411	0.62251	1.0:0.0:0.0:0.0	rs11910483	1015	P12110	CO6A2_HUMAN	L	1015	ENSP00000300527:I1015L	ENSP00000300527:I1015L	I	+	1	0	COL6A2	46376877	1.000000	0.71417	1.000000	0.80357	0.661000	0.39034	2.891000	0.48617	1.628000	0.50416	0.247000	0.18012	ATC	A|0.975;C|0.025	0.025	strong		0.697	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1			C	47552449	A	C	47552449	3	2	25	1	0	0	0	0	1	0	0	0	3702	217	8	5	3479	5	COL6A2	21	47552449	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	130275	47552449	577446	812	9721											
C21orf56	84221	hgsc.bcm.edu	37	chr21	47588427	47588427	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggactgaggaaggccttgaaGggtgcctgggagggggctgc	7	6	21	7	0	0	2	0	2	0	0	0	5	0	5	2	7	2	1	2	7	2	1	rs74486947	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47588427G>A	ENST00000291672.5	-	3	1400	c.339C>T	c.(337-339)ccC>ccT	p.P113P	SPATC1L_ENST00000330205.6_5'UTR	NM_001142854.1	NP_001136326.1	Q9H0A9	SPC1L_HUMAN	spermatogenesis and centriole associated 1-like	113			P -> L (in dbSNP:rs884134).														AGGCCTTGAAGGGTGCCTGGG	0.652													G|||	278	0.0555112	0.1982	0.0202	5008	,	,		15628	0.0		0.002	False		,,,				2504	0.0				p.P113P		Atlas-SNP	.											.	.	.	.	0			c.C339T						PASS	.	G	,	227,1157		18,191,483	41	43	42		339,	1.4	0.9	21	dbSNP_132	42	6,3176		0,6,1585	no	coding-synonymous,utr-5	C21orf56	NM_001142854.1,NM_032261.4	,	18,197,2068	AA,AG,GG		0.1886,16.4017,5.1029	,	113/341,	47588427	233,4333	692	1591	2283	SO:0001819	synonymous_variant	84221	exon3			CTTGAAGGGTGCC	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.339C>T	21.37:g.47588427G>A		52	0	0		90	42	0.466667	NM_001142854	B4E323|Q52LS9|Q6FIH5|Q6P0L3|Q9NSE5	Silent	SNP	ENST00000291672.5	37	CCDS46653.1																																																																																			G|0.966;A|0.034	0.034	strong		0.652	SPATC1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376654.1	NM_032261		A	47588427	G	A	47588427	2	1	25	1	0	0	0	0	0	0	0	1	2129	987	35	2		2	C21orf56	21	47588427	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	35978	47588427	541468	813	9722											
LSS	4047	hgsc.bcm.edu	37	chr21	47635686	47635686	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccagccagtcaatgctggCgaagtcctccacatagagct	10	7	10	14	2	1	1	1	0	0	1	3	2	3	1	4	1	3	2	4	1	3	1	rs143692945	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47635686C>T	ENST00000397728.3	-	8	883	c.805G>A	c.(805-807)Gcc>Acc	p.A269T	LSS_ENST00000464357.1_5'UTR|LSS_ENST00000356396.4_Missense_Mutation_p.A269T|LSS_ENST00000522411.1_Missense_Mutation_p.A258T|LSS_ENST00000457828.2_Missense_Mutation_p.A189T	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	269					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)					TCAATGCTGGCGAAGTCCTCC	0.652													C|||	19	0.00379393	0.0136	0.0014	5008	,	,		15065	0.0		0.0	False		,,,				2504	0.0				p.A269T	Pancreas(114;955 2313 34923 50507)	Atlas-SNP	.											.	LSS	50	.	0			c.G805A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA	40,4366	43.1+/-76.7	0,40,2163	28	33	31		805,772,565,805	0.9	0.2	21	dbSNP_134	31	1,8597		0,1,4298	yes	missense,missense,missense,missense	LSS	NM_001001438.2,NM_001145436.1,NM_001145437.1,NM_002340.5	58,58,58,58	0,41,6461	TT,TC,CC		0.0116,0.9079,0.3153	benign,benign,benign,benign	269/733,258/722,189/653,269/733	47635686	41,12963	2203	4299	6502	SO:0001583	missense	4047	exon8			TGCTGGCGAAGTC	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.805G>A	21.37:g.47635686C>T	ENSP00000380837:p.Ala269Thr	87	0	0		118	64	0.542373	NM_001001438	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Missense_Mutation	SNP	ENST00000397728.3	37	CCDS13733.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	7.049	0.564068	0.13498	0.009079	1.16E-4	ENSG00000160285	ENST00000356396;ENST00000457828;ENST00000397728;ENST00000522411	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	5.32	0.867	0.19085	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.573488	0.18205	N	0.148380	T	0.11410	0.0278	L	0.35542	1.07	0.20873	N	0.999835	B;B	0.31153	0.31;0.206	B;B	0.18561	0.022;0.01	T	0.12268	-1.0554	10	0.28530	T	0.3	.	5.0794	0.14649	0.3294:0.4293:0.0:0.2412	.	258;269	E9PEI9;P48449	.;ERG7_HUMAN	T	269;189;269;258	ENSP00000348762:A269T;ENSP00000409191:A189T;ENSP00000380837:A269T;ENSP00000429133:A258T	ENSP00000348762:A269T	A	-	1	0	LSS	46460114	0.011000	0.17503	0.155000	0.22561	0.080000	0.17528	0.200000	0.17257	0.226000	0.20979	-0.258000	0.10820	GCC	C|0.997;T|0.003	0.003	strong		0.652	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2			T	47635686	C	T	47635686	3	4	25	1	0	0	0	0	1	0	0	0	9074	768	27	1	1453	1	LSS	21	47635686	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	47259	47635686	494209	814	9723											
MCM3AP	8888	hgsc.bcm.edu	37	chr21	47695220	47695220	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagtcctcgctttgtccagAtcggttctcttcacccgagc	7	12	8	14	3	2	1	1	0	1	1	7	2	4	1	3	1	1	2	3	1	1	3	rs2839190	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47695220A>G	ENST00000397708.1	-	7	2132	c.1878T>C	c.(1876-1878)gaT>gaC	p.D626D	MCM3AP_ENST00000291688.1_Silent_p.D626D			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	626					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)					CTTTGTCCAGATCGGTTCTCT	0.473													A|||	700	0.139776	0.4251	0.0591	5008	,	,		19284	0.004		0.0129	False		,,,				2504	0.0818				p.D626D		Atlas-SNP	.											.	MCM3AP	146	.	0			c.T1878C						PASS	.	A		1581,2825	492.9+/-362.5	271,1039,893	97	76	83		1878	-3.5	0.6	21	dbSNP_100	83	114,8486	59.5+/-121.1	1,112,4187	yes	coding-synonymous	MCM3AP	NM_003906.3		272,1151,5080	GG,GA,AA		1.3256,35.8829,13.0324		626/1981	47695220	1695,11311	2203	4300	6503	SO:0001819	synonymous_variant	8888	exon6			GTCCAGATCGGTT	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.1878T>C	21.37:g.47695220A>G		65	0	0		88	42	0.477273	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Silent	SNP	ENST00000397708.1	37	CCDS13734.1																																																																																			A|0.864;G|0.136	0.136	strong		0.473	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906		G	47695220	A	G	47695220	2	3	25	1	0	0	0	0	0	0	0	1	9397	330	12	3		3	MCM3AP	21	47695220	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	59534	47695220	434675	815	9724											
C21orf58	54058	hgsc.bcm.edu	37	chr21	47734777	47734777	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctgggcccgagagagctcGtccaggaggtgttgttcctg	5	9	16	11	2	0	1	0	0	0	1	3	4	2	2	4	3	1	3	4	3	0	2	rs56036022	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47734777G>A	ENST00000291691.7	-	5	1598	c.462C>T	c.(460-462)gaC>gaT	p.D154D	C21orf58_ENST00000397683.1_Silent_p.D48D|C21orf58_ENST00000397679.1_Silent_p.D48D|C21orf58_ENST00000397682.3_Silent_p.D48D|C21orf58_ENST00000397680.1_Silent_p.D48D	NM_058180.3	NP_478060.2	P58505	CU058_HUMAN	chromosome 21 open reading frame 58	154										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(1)|pancreas(1)	9	Breast(49;0.112)			Colorectal(79;0.239)		GAGAGAGCTCGTCCAGGAGGT	0.701													G|||	174	0.0347444	0.1248	0.0101	5008	,	,		14424	0.0		0.002	False		,,,				2504	0.0				p.D154D		Atlas-SNP	.											.	C21orf58	25	.	0			c.C462T						PASS	.	G		383,3735		17,349,1693	9	11	10		462	-9.5	0.2	21	dbSNP_129	10	8,8092		0,8,4042	no	coding-synonymous	C21orf58	NM_058180.3		17,357,5735	AA,AG,GG		0.0988,9.3006,3.2002		154/323	47734777	391,11827	2059	4050	6109	SO:0001819	synonymous_variant	54058	exon5			GAGCTCGTCCAGG		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.462C>T	21.37:g.47734777G>A		74	0	0		91	40	0.43956	NM_058180	B3KPI1	Silent	SNP	ENST00000291691.7	37	CCDS13735.1																																																																																			G|0.975;A|0.025	0.025	strong		0.701	C21orf58-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207283.1	NM_058180		A	47734777	G	A	47734777	2	1	25	1	0	0	0	0	0	0	0	1	2131	1136	40	1		1	C21orf58	21	47734777	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	39557	47734777	395118	816	9725											
PCNT	5116	hgsc.bcm.edu	37	chr21	47850107	47850107	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaagagcgaacagctgtcccGgtccctctgcgaggtgcagc	8	6	14	13	3	1	1	0	0	1	1	3	4	3	1	2	2	6	2	2	2	2	0	rs8131693	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47850107G>A	ENST00000359568.5	+	36	7981	c.7874G>A	c.(7873-7875)cGg>cAg	p.R2625Q	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2625			R -> Q (in dbSNP:rs8131693).		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)					CAGCTGTCCCGGTCCCTCTGC	0.622													G|||	319	0.0636981	0.2269	0.0245	5008	,	,		17998	0.0		0.002	False		,,,				2504	0.0				p.R2625Q		Atlas-SNP	.											.	PCNT	283	.	0			c.G7874A						PASS	.	G	GLN/ARG	879,3527	340.2+/-306.1	96,687,1420	67	65	66		7874	0.3	0	21	dbSNP_116	66	14,8586	8.4+/-32.0	0,14,4286	yes	missense	PCNT	NM_006031.5	43	96,701,5706	AA,AG,GG		0.1628,19.9501,6.8661	benign	2625/3337	47850107	893,12113	2203	4300	6503	SO:0001583	missense	5116	exon36			TGTCCCGGTCCCT	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.7874G>A	21.37:g.47850107G>A	ENSP00000352572:p.Arg2625Gln	93	0	0		111	55	0.495495	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	95	0.043498168498168496	88	0.17886178861788618	7	0.019337016574585635	0	0.0	0	0.0	G	6.228	0.410216	0.11812	0.199501	0.001628	ENSG00000160299	ENST00000359568	T	0.01359	4.98	4.31	0.32	0.15878	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.17852	0.002;0.024	B;B	0.06405	0.002;0.001	T	0.43114	-0.9411	8	0.36615	T	0.2	.	5.7279	0.18022	0.5019:0.3993:0.0988:0.0	rs8131693;rs8131693	2507;2625	O95613-2;O95613	.;PCNT_HUMAN	Q	2625	ENSP00000352572:R2625Q	ENSP00000352572:R2625Q	R	+	2	0	PCNT	46674535	0.038000	0.19896	0.003000	0.11579	0.002000	0.02628	1.973000	0.40550	-0.055000	0.13244	-0.391000	0.06502	CGG	G|0.933;A|0.067	0.067	strong		0.622	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		A	47850107	G	A	47850107	3	1	25	1	0	0	0	0	1	0	0	0	11599	1116	39	1	8016	1	PCNT	21	47850107	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	115330	47850107	279788	817	9726											
CCT8L2	150160	hgsc.bcm.edu	37	chr22	17072411	17072411	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aaccctctggcacttgcctgGcctctggggagggagcagac	7	7	14	13	0	2	1	0	0	2	1	2	3	2	3	3	5	3	2	3	5	1	1	rs41277596	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:17072411G>T	ENST00000359963.3	-	1	1289	c.1030C>A	c.(1030-1032)Cca>Aca	p.P344T		NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2	344					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)				CACTTGCCTGGCCTCTGGGGA	0.547													g|||	17	0.00339457	0.0	0.0072	5008	,	,		19488	0.0		0.0109	False		,,,				2504	0.001				p.P344T		Atlas-SNP	.											.	CCT8L2	150	.	0			c.C1030A						PASS	.	G	THR/PRO	3,4403	6.2+/-15.9	0,3,2200	101	100	100		1030	0.7	0.7	22	dbSNP_127	100	69,8531	41.2+/-98.3	0,69,4231	no	missense	CCT8L2	NM_014406.4	38	0,72,6431	TT,TG,GG		0.8023,0.0681,0.5536	probably-damaging	344/558	17072411	72,12934	2203	4300	6503	SO:0001583	missense	150160	exon1			TGCCTGGCCTCTG	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	ENST00000359963.3:c.1030C>A	22.37:g.17072411G>T	ENSP00000353048:p.Pro344Thr	95	0	0		95	52	0.547368	NM_014406	A4QPH3|Q9UJS3	Missense_Mutation	SNP	ENST00000359963.3	37	CCDS13738.1	15	0.006868131868131868	0	0.0	5	0.013812154696132596	0	0.0	10	0.013192612137203167	g	1.736	-0.492944	0.04322	6.81E-4	0.008023	ENSG00000198445	ENST00000359963	T	0.77877	-1.13	1.98	0.711	0.18162	.	0.201946	0.24693	U	0.036363	T	0.61726	0.2370	L	0.41236	1.265	0.24066	N	0.99599	B	0.34255	0.445	B	0.41723	0.365	T	0.60367	-0.7277	10	0.72032	D	0.01	-14.4681	5.6792	0.17765	0.0:0.347:0.653:0.0	rs41277596	344	Q96SF2	TCPQM_HUMAN	T	344	ENSP00000353048:P344T	ENSP00000353048:P344T	P	-	1	0	CCT8L2	15452411	0.005000	0.15991	0.710000	0.30468	0.079000	0.17450	0.660000	0.25009	1.115000	0.41800	0.379000	0.24179	CCA	G|0.994;T|0.006	0.006	strong		0.547	CCT8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280580.1			T	17072411	G	T	17072411	3	4	25	1	0	0	0	0	1	0	0	0	2963	1203	42	4	647	4	CCT8L2	22	17072411	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10		17072411	34232155	818	9727											
TUBA8	51807	hgsc.bcm.edu	37	chr22	18613739	18613739	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgcctcgaccacaagttcGacctcatgtacgccaagcgg	9	6	9	17	5	1	0	1	0	0	0	3	2	1	0	5	1	2	2	5	1	3	2	rs146821364		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:18613739G>T	ENST00000330423.3	+	5	1259	c.1186G>T	c.(1186-1188)Gac>Tac	p.D396Y	TUBA8_ENST00000316027.6_Missense_Mutation_p.D330Y	NM_018943.2	NP_061816.1	Q9NY65	TBA8_HUMAN	tubulin, alpha 8	396					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						CCACAAGTTCGACCTCATGTA	0.622																																					p.D396Y		Atlas-SNP	.											TUBA8,NS,carcinoma,0,1	TUBA8	36	1	0			c.G1186T						PASS	.	G	TYR/ASP,TYR/ASP	1,4405		0,1,2202	63	58	60		988,1186	5.2	1	22	dbSNP_134	60	0,8600		0,0,4300	no	missense,missense	TUBA8	NM_001193414.1,NM_018943.2	160,160	0,1,6502	TT,TG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	330/384,396/450	18613739	1,13005	2203	4300	6503	SO:0001583	missense	51807	exon5			AAGTTCGACCTCA	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.1186G>T	22.37:g.18613739G>T	ENSP00000333326:p.Asp396Tyr	130	0	0		143	61	0.426573	NM_018943	B2RCX2|B3KPW9|B4DWG3|Q2M3N4	Missense_Mutation	SNP	ENST00000330423.3	37	CCDS13751.1	.	.	.	.	.	.	.	.	.	.	.	18.66	3.671959	0.67928	2.27E-4	0.0	ENSG00000183785	ENST00000316027;ENST00000330423;ENST00000416740	D;D;D	0.86097	-2.07;-2.07;-2.07	5.19	5.19	0.71726	Tubulin, C-terminal (1);Tubulin/FtsZ, C-terminal (1);	0.097032	0.64402	D	0.000002	D	0.95089	0.8409	H	0.96489	3.83	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.991;0.989;1.0	D	0.96490	0.9363	10	0.87932	D	0	.	18.0766	0.89428	0.0:0.0:1.0:0.0	.	330;420;396	B3KPW9;C9J2C0;Q9NY65	.;.;TBA8_HUMAN	Y	330;396;420	ENSP00000318575:D330Y;ENSP00000333326:D396Y;ENSP00000412646:D420Y	ENSP00000318575:D330Y	D	+	1	0	TUBA8	16993739	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	9.835000	0.99442	2.569000	0.86673	0.655000	0.94253	GAC	G|1.000;T|0.000	0.000	weak		0.622	TUBA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316232.3	NM_018943		T	18613739	G	T	18613739	3	4	25	1	0	0	0	0	1	0	0	0	16765	1058	37	4	1204	4	TUBA8	22	18613739	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1541328	18613739	32690827	819	9728											
CLTCL1	8218	hgsc.bcm.edu	37	chr22	19263266	19263266	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gacctgtgcctgctcaccaaCtttctctcggatacatatga	9	12	7	13	1	2	1	1	1	1	0	4	3	2	2	3	1	4	1	3	1	3	3	rs34869740	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:19263266C>A	ENST00000263200.10	-	2	202	c.130G>T	c.(130-132)Gtt>Ttt	p.V44F	CLTCL1_ENST00000353891.5_Missense_Mutation_p.V44F|CLTCL1_ENST00000427926.1_Missense_Mutation_p.V44F	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	44	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)					TGCTCACCAACTTTCTCTCGG	0.468			T	?	ALCL								C|||	45	0.00898562	0.0	0.0058	5008	,	,		17693	0.001		0.004	False		,,,				2504	0.0368				p.V44F		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"clathrin, heavy polypeptide-like 1"		L	.	CLTCL1	115	.	0			c.G130T						PASS	.	C	PHE/VAL,PHE/VAL	2,3930		0,2,1964	64	64	64		130,130	1.9	0	22	dbSNP_126	64	71,8235		0,71,4082	yes	missense,missense	CLTCL1	NM_001835.3,NM_007098.3	50,50	0,73,6046	AA,AC,CC		0.8548,0.0509,0.5965	possibly-damaging,possibly-damaging	44/1584,44/1641	19263266	73,12165	1966	4153	6119	SO:0001583	missense	8218	exon2			CACCAACTTTCTC		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.130G>T	22.37:g.19263266C>A	ENSP00000445677:p.Val44Phe	124	0	0		128	58	0.453125	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	37	CCDS46662.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	14.65	2.600102	0.46423	5.09E-4	0.008548	ENSG00000070371	ENST00000353891;ENST00000263200;ENST00000427926;ENST00000449918	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	4.07	1.93	0.25924	Clathrin, heavy chain, propeller, N-terminal (1);Clathrin, heavy chain, linker/propeller domain (1);	0.078972	0.50627	D	0.000108	T	0.53642	0.1809	M	0.87827	2.91	0.45914	D	0.998752	B;D	0.54047	0.177;0.964	B;D	0.64321	0.325;0.924	T	0.59053	-0.7526	10	0.56958	D	0.05	-6.7814	8.2311	0.31599	0.1561:0.7604:0.0:0.0836	rs34869740	44;44	P53675-2;P53675	.;CLH2_HUMAN	F	44	ENSP00000439662:V44F;ENSP00000445677:V44F;ENSP00000441158:V44F;ENSP00000443264:V44F	ENSP00000445677:V44F	V	-	1	0	CLTCL1	17643266	1.000000	0.71417	0.009000	0.14445	0.231000	0.25187	3.255000	0.51484	0.367000	0.24454	-0.142000	0.14014	GTT	C|0.994;A|0.006	0.006	strong		0.468	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098		A	19263266	C	A	19263266	3	1	25	1	0	0	0	0	1	0	0	0	3569	565	20	4	4916	4	CLTCL1	22	19263266	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	649527	19263266	32041300	820	9729											
MRPL40	64976	hgsc.bcm.edu	37	chr22	19423257	19423257	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagcagcaagagcgtaagatGgagagggacaccatcagggc	15	3	15	8	1	1	3	1	0	0	3	1	5	1	4	1	3	3	3	1	3	3	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:19423257G>A	ENST00000333130.3	+	4	1046	c.393G>A	c.(391-393)atG>atA	p.M131I	MRPL40_ENST00000443660.1_3'UTR|HIRA_ENST00000546308.1_Intron|HIRA_ENST00000541063.1_Intron	NM_003776.2	NP_003767.2	Q9NQ50	RM40_HUMAN	mitochondrial ribosomal protein L40	131					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)					AGCGTAAGATGGAGAGGGACA	0.567																																					p.M131I		Atlas-SNP	.											.	MRPL40	13	.	0			c.G393A						PASS	.						145	147	146					22																	19423257		2203	4300	6503	SO:0001583	missense	64976	exon4			TAAGATGGAGAGG	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.393G>A	22.37:g.19423257G>A	ENSP00000333401:p.Met131Ile	118	0	0		120	5	0.0416667	NM_003776	B3KVZ7|O95134	Missense_Mutation	SNP	ENST00000333130.3	37	CCDS13760.1	.	.	.	.	.	.	.	.	.	.	G	8.714	0.912730	0.17907	.	.	ENSG00000185608	ENST00000333130	T	0.43294	0.95	5.22	-0.486	0.12064	.	0.620008	0.17767	N	0.162711	T	0.28433	0.0703	L	0.56769	1.78	0.35764	D	0.820406	B	0.14012	0.009	B	0.17098	0.017	T	0.11941	-1.0567	10	0.17832	T	0.49	-1.0103	1.306	0.02088	0.445:0.1498:0.2525:0.1527	.	131	Q9NQ50	RM40_HUMAN	I	131	ENSP00000333401:M131I	ENSP00000333401:M131I	M	+	3	0	MRPL40	17803257	0.988000	0.35896	0.439000	0.26833	0.259000	0.26198	0.659000	0.24994	0.366000	0.24427	-0.251000	0.11542	ATG	.	.	none		0.567	MRPL40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316491.2	NM_003776		A	19423257	G	A	19423257	3	1	25	1	0	0	0	0	1	0	0	0	9813	1348	47	2	407	2	MRPL40	22	19423257	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	159991	19423257	31881309	821	9730											
CYTSA	23384	hgsc.bcm.edu	37	chr22	24718408	24718408	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgaagatgtaaaaagtgggcGctatatggaattagagcaac	16	9	12	4	1	0	3	0	1	0	2	0	4	0	4	0	2	2	3	0	2	9	4	rs55723436	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:24718408G>A	ENST00000314328.9	+	5	1745	c.1460G>A	c.(1459-1461)cGc>cAc	p.R487H	SPECC1L_ENST00000541492.1_Missense_Mutation_p.R487H|SPECC1L_ENST00000437398.1_Missense_Mutation_p.R487H|SPECC1L_ENST00000416735.1_Intron|SPECC1L-ADORA2A_ENST00000358654.2_Missense_Mutation_p.R487H	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	487					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						AAAAGTGGGCGCTATATGGAA	0.423													G|||	18	0.00359425	0.0008	0.0058	5008	,	,		22148	0.0		0.0099	False		,,,				2504	0.0031				p.R487H		Atlas-SNP	.											.	SPECC1L	85	.	0			c.G1460A						PASS	.	G	HIS/ARG,HIS/ARG	9,4397	16.8+/-37.8	0,9,2194	88	89	89		1460,1460	5.4	1	22	dbSNP_129	89	80,8520	45.8+/-104.6	0,80,4220	yes	missense,missense	SPECC1L	NM_001145468.1,NM_015330.2	29,29	0,89,6414	AA,AG,GG		0.9302,0.2043,0.6843	probably-damaging,probably-damaging	487/1118,487/1118	24718408	89,12917	2203	4300	6503	SO:0001583	missense	23384	exon4			GTGGGCGCTATAT	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.1460G>A	22.37:g.24718408G>A	ENSP00000325785:p.Arg487His	105	0	0		91	42	0.461538	NM_001145468	B7Z758|F5H1H6|O15081	Missense_Mutation	SNP	ENST00000314328.9	37	CCDS33619.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	G	27.1	4.796160	0.90453	0.002043	0.009302	ENSG00000100014	ENST00000398280;ENST00000437398;ENST00000421374;ENST00000314328;ENST00000541492	T;T;T;T	0.08370	3.1;3.1;3.1;3.1	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.17280	0.0415	L	0.45581	1.43	0.80722	D	1	D;D	0.89917	1.0;0.999	D;P	0.70716	0.97;0.893	T	0.00085	-1.2098	10	0.56958	D	0.05	-15.9709	18.1791	0.89771	0.0:0.0:1.0:0.0	rs55723436	487;487	F5H1H6;Q69YQ0	.;CYTSA_HUMAN	H	515;487;487;487;487	ENSP00000393363:R487H;ENSP00000405671:R487H;ENSP00000325785:R487H;ENSP00000439633:R487H	ENSP00000325785:R487H	R	+	2	0	SPECC1L	23048408	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	9.647000	0.98478	2.550000	0.86006	0.591000	0.81541	CGC	G|0.993;A|0.007	0.007	strong		0.423	SPECC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319986.2	NM_015330		A	24718408	G	A	24718408	3	1	25	1	0	0	0	0	1	0	0	0	4211	1087	38	1	1470	1	CYTSA	22	24718408	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	5295151	24718408	26586158	822	9731											
MYO18B	84700	hgsc.bcm.edu	37	chr22	26422651	26422651	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cggagtacaaatacatccccGctgtcgagggaaaagctgcc	12	6	11	12	3	0	0	0	0	0	0	2	3	1	2	3	2	4	3	3	2	5	2	rs199593757	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:26422651G>A	ENST00000407587.2	+	43	6883	c.6714G>A	c.(6712-6714)ccG>ccA	p.P2238P	MYO18B_ENST00000335473.7_Silent_p.P2237P|MYO18B_ENST00000536101.1_Silent_p.P2237P			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2237						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						ATACATCCCCGCTGTCGAGGG	0.597													G|||	13	0.00259585	0.0	0.0014	5008	,	,		18385	0.0		0.001	False		,,,				2504	0.0112				p.P2237P		Atlas-SNP	.											.	MYO18B	322	.	0			c.G6711A						PASS	.	G		2,3830		0,2,1914	25	27	26		6711	-4.2	0	22		26	25,8189		0,25,4082	no	coding-synonymous	MYO18B	NM_032608.5		0,27,5996	AA,AG,GG		0.3044,0.0522,0.2241		2237/2568	26422651	27,12019	1916	4107	6023	SO:0001819	synonymous_variant	84700	exon43			ATCCCCGCTGTCG	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.6714G>A	22.37:g.26422651G>A		66	0	0		86	48	0.55814	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37		.	.	.	.	.	.	.	.	.	.	G	11.64	1.698433	0.30142	5.22E-4	0.003044	ENSG00000133454	ENST00000543971	.	.	.	4.94	-4.2	0.03823	.	.	.	.	.	T	0.32793	0.0841	.	.	.	0.31759	N	0.633626	.	.	.	.	.	.	T	0.42032	-0.9475	4	.	.	.	.	5.7129	0.17945	0.2701:0.3964:0.3335:0.0	.	.	.	.	H	187	.	.	R	+	2	0	MYO18B	24752651	0.000000	0.05858	0.003000	0.11579	0.699000	0.40488	-2.672000	0.00843	-1.013000	0.03383	0.491000	0.48974	CGC	G|0.993;A|0.007	0.007	strong		0.597	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		A	26422651	G	A	26422651	2	1	25	1	0	0	0	0	0	0	0	1	10075	1074	38	1		1	MYO18B	22	26422651	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1704243	26422651	24881915	823	9732											
MYO18B	84700	hgsc.bcm.edu	37	chr22	26423124	26423124	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gtcctctgtggacgatgcggGctgtccagaccttggaaagg	7	9	15	10	2	1	1	0	0	1	1	3	4	3	3	3	4	1	1	3	4	1	1	rs6004901	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:26423124G>C	ENST00000407587.2	+	43	7356	c.7187G>C	c.(7186-7188)gGc>gCc	p.G2396A	MYO18B_ENST00000335473.7_Missense_Mutation_p.G2395A|MYO18B_ENST00000536101.1_Missense_Mutation_p.G2395A			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2395						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						GACGATGCGGGCTGTCCAGAC	0.592													G|||	488	0.0974441	0.2663	0.0476	5008	,	,		15885	0.004		0.0348	False		,,,				2504	0.0654				p.G2395A		Atlas-SNP	.											.	MYO18B	322	.	0			c.G7184C						PASS	.	G	ALA/GLY	855,3101		95,665,1218	66	72	70		7184	-1.6	0	22	dbSNP_114	70	253,8029		6,241,3894	yes	missense	MYO18B	NM_032608.5	60	101,906,5112	CC,CG,GG		3.0548,21.6127,9.0538	benign	2395/2568	26423124	1108,11130	1978	4141	6119	SO:0001583	missense	84700	exon43			ATGCGGGCTGTCC	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.7187G>C	22.37:g.26423124G>C	ENSP00000386096:p.Gly2396Ala	76	0	0		87	37	0.425287	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		166|166	0.076007326007326|0.076007326007326	119|119	0.241869918699187|0.241869918699187	22|22	0.06077348066298342|0.06077348066298342	4|4	0.006993006993006993|0.006993006993006993	21|21	0.027704485488126648|0.027704485488126648	G|G	0.007|0.007	-1.985354|-1.985354	0.00443|0.00443	0.216127|0.216127	0.030548|0.030548	ENSG00000133454|ENSG00000133454	ENST00000543971|ENST00000536101;ENST00000335473;ENST00000407587	.|D;D;D	.|0.86956	.|-2.17;-2.17;-2.19	5.12|5.12	-1.6|-1.6	0.08426|0.08426	.|.	.|0.491877	.|0.18417	.|N	.|0.141867	T|T	0.00073|0.00073	0.0002|0.0002	L|L	0.45581|0.45581	1.43|1.43	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B;B;B	.|0.06786	.|0.001;0.001;0.001;0.001;0.001	.|B;B;B;B;B	.|0.08055	.|0.003;0.001;0.001;0.003;0.003	T|T	0.02877|0.02877	-1.1099|-1.1099	4|9	.|0.19147	.|T	.|0.46	.|.	1.509|1.509	0.02492|0.02492	0.1649:0.2383:0.3545:0.2424|0.1649:0.2383:0.3545:0.2424	rs6004901;rs52824215;rs6004901|rs6004901;rs52824215;rs6004901	.|1908;2397;2395;2396;2395	.|Q8IUG5-2;B0QYF5;Q8IUG5;F5GXR6;F5GYU7	.|.;.;MY18B_HUMAN;.;.	P|A	345|2395;2395;2396	.|ENSP00000441229:G2395A;ENSP00000334563:G2395A;ENSP00000386096:G2396A	.|ENSP00000334563:G2395A	A|G	+|+	1|2	0|0	MYO18B|MYO18B	24753124|24753124	0.003000|0.003000	0.15002|0.15002	0.011000|0.011000	0.14972|0.14972	0.130000|0.130000	0.20726|0.20726	0.135000|0.135000	0.15952|0.15952	0.154000|0.154000	0.19237|0.19237	-0.264000|-0.264000	0.10439|0.10439	GCT|GGC	G|0.912;C|0.088	0.088	strong		0.592	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		C	26423124	G	C	26423124	3	2	25	1	0	0	0	0	1	0	0	0	10075	1203	42	4	7350	4	MYO18B	22	26423124	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	473	26423124	24881442	824	9733											
MYO18B	84700	hgsc.bcm.edu	37	chr22	26423477	26423477	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgactcgtcctcatcctccGgctccatcgtgtccttcaaa	6	12	6	17	3	2	1	2	1	0	0	9	1	7	1	5	1	0	1	5	1	1	1	rs7284177	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:26423477G>A	ENST00000407587.2	+	43	7709	c.7540G>A	c.(7540-7542)Ggc>Agc	p.G2514S	MYO18B_ENST00000335473.7_Missense_Mutation_p.G2513S|MYO18B_ENST00000536101.1_Missense_Mutation_p.G2513S			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2513	Poly-Ser.					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						CTCATCCTCCGGCTCCATCGT	0.587													A|||	352	0.0702875	0.2005	0.0259	5008	,	,		18932	0.004		0.0179	False		,,,				2504	0.0481				p.G2513S		Atlas-SNP	.											.	MYO18B	322	.	0			c.G7537A						PASS	.	A	SER/GLY	695,3407		58,579,1414	53	55	55		7537	1.8	1	22	dbSNP_116	55	146,8242		1,144,4049	yes	missense	MYO18B	NM_032608.5	56	59,723,5463	AA,AG,GG		1.7406,16.943,6.7334	benign	2513/2568	26423477	841,11649	2051	4194	6245	SO:0001583	missense	84700	exon43			TCCTCCGGCTCCA	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.7540G>A	22.37:g.26423477G>A	ENSP00000386096:p.Gly2514Ser	60	0	0		49	19	0.387755	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		123	0.05631868131868132	92	0.18699186991869918	13	0.03591160220994475	4	0.006993006993006993	14	0.018469656992084433	A	4.656	0.121893	0.08931	0.16943	0.017406	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.85088	-1.92;-1.92;-1.94	5.17	1.8	0.24995	.	0.170297	0.37437	N	0.002083	T	0.00109	0.0003	N	0.00729	-1.24	0.54753	P	1.0999999999983245E-5	B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.001	B;B;B;B;B	0.06405	0.002;0.001;0.001;0.002;0.002	T	0.12426	-1.0548	9	0.02654	T	1	.	4.0444	0.09766	0.4128:0.0:0.4136:0.1736	rs7284177;rs52837742;rs59696890;rs7284177	2026;2515;2513;2514;2513	Q8IUG5-2;B0QYF5;Q8IUG5;F5GXR6;F5GYU7	.;.;MY18B_HUMAN;.;.	S	2513;2513;2514	ENSP00000441229:G2513S;ENSP00000334563:G2513S;ENSP00000386096:G2514S	ENSP00000334563:G2513S	G	+	1	0	MYO18B	24753477	0.459000	0.25768	0.958000	0.39756	0.893000	0.52053	0.694000	0.25512	-0.007000	0.14345	-0.361000	0.07541	GGC	G|0.931;A|0.069	0.069	strong		0.587	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		A	26423477	G	A	26423477	3	1	25	1	0	0	0	0	1	0	0	0	10075	1116	39	1	7703	1	MYO18B	22	26423477	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	353	26423477	24881089	825	9734											
SEZ6L	23544	hgsc.bcm.edu	37	chr22	26692953	26692953	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	accagacactcctggtggagGggcaggtaatccgaagcccc	10	5	13	13	1	0	1	0	0	0	1	2	3	2	2	5	5	1	2	5	5	2	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:26692953G>A	ENST00000248933.6	+	4	1164	c.1069G>A	c.(1069-1071)Ggg>Agg	p.G357R	SEZ6L_ENST00000402979.1_Missense_Mutation_p.G130R|SEZ6L_ENST00000360929.3_Missense_Mutation_p.G357R|SEZ6L_ENST00000403121.1_Missense_Mutation_p.G130R|SEZ6L_ENST00000404234.3_Missense_Mutation_p.G357R|SEZ6L_ENST00000529632.2_Missense_Mutation_p.G357R|SEZ6L_ENST00000343706.4_Missense_Mutation_p.G357R			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	357	CUB 1. {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						CCTGGTGGAGGGGCAGGTAAT	0.622																																					p.G357R		Atlas-SNP	.											.	SEZ6L	174	.	0			c.G1069A						PASS	.						60	47	52					22																	26692953		2203	4300	6503	SO:0001583	missense	23544	exon4			GTGGAGGGGCAGG	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.1069G>A	22.37:g.26692953G>A	ENSP00000248933:p.Gly357Arg	104	0	0		100	4	0.04	NM_001184777	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	37	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	G	31	5.087781	0.94100	.	.	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706;ENST00000403121;ENST00000402979	T;T;T;T;T;T;T	0.59772	0.24;0.24;0.24;0.24;0.24;0.24;0.24	5.26	5.26	0.73747	CUB (5);	0.000000	0.56097	D	0.000037	T	0.78162	0.4240	M	0.79926	2.475	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	T	0.81420	-0.0941	10	0.87932	D	0	.	17.8539	0.88756	0.0:0.0:1.0:0.0	.	357;357;130;357;357;357;357	B7ZLJ8;B7ZLJ6;B0QYH4;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;.;.;SE6L1_HUMAN	R	357;357;357;357;357;130;130	ENSP00000384772:G357R;ENSP00000437037:G357R;ENSP00000354185:G357R;ENSP00000248933:G357R;ENSP00000342661:G357R;ENSP00000384838:G130R;ENSP00000384733:G130R	ENSP00000248933:G357R	G	+	1	0	SEZ6L	25022953	1.000000	0.71417	0.997000	0.53966	0.870000	0.49936	9.244000	0.95423	2.446000	0.82766	0.655000	0.94253	GGG	.	.	none		0.622	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3			A	26692953	G	A	26692953	3	1	25	1	0	0	0	0	1	0	0	0	14158	1232	43	2	1083	2	SEZ6L	22	26692953	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	269476	26692953	24611613	826	9735											
APOBEC3G	60489	hgsc.bcm.edu	37	chr22	39482557	39482557	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggctggggccaaaatttcaAtaatgacatacagtggtgag	14	9	12	6	0	1	2	1	2	0	0	1	2	1	2	1	4	1	1	1	4	5	3	rs139265278		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:39482557A>G	ENST00000407997.3	+	6	1366	c.1009A>G	c.(1009-1011)Ata>Gta	p.I337V	APOBEC3G_ENST00000452957.2_Missense_Mutation_p.I337V	NM_021822.3	NP_068594.1	Q9HC16	ABC3G_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3G	337					base conversion or substitution editing (GO:0016553)|cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|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 genome replication (GO:0045071)|negative regulation of viral process (GO:0048525)|positive regulation of defense response to virus by host (GO:0002230)|viral process (GO:0016032)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|ribonucleoprotein complex (GO:0030529)	cytidine deaminase activity (GO:0004126)|deoxycytidine deaminase activity (GO:0047844)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			central_nervous_system(1)|large_intestine(4)|lung(5)|skin(1)|stomach(1)	12	Melanoma(58;0.04)					CAAAATTTCAATAATGACATA	0.572																																					p.I337V		Atlas-SNP	.											.	APOBEC3G	69	.	0			c.A1009G						PASS	.		VAL/ILE	0,4406		0,0,2203	85	95	91		1009	1.5	0	22	dbSNP_134	91	2,8598		0,2,4298	no	missense	APOBEC3G	NM_021822.3	29	0,2,6501	GG,GA,AA		0.0233,0.0,0.0154	benign	337/385	39482557	2,13004	2203	4300	6503	SO:0001583	missense	60489	exon6			ATTTCAATAATGA	AF182420	CCDS13984.1	22q13.1-q13.2	2008-05-15			ENSG00000239713	ENSG00000239713		"Apolipoprotein B mRNA editing enzymes"	17357	protein-coding gene	gene with protein product		607113				11863358	Standard	NM_021822		Approved	CEM15, MDS019, dJ494G10.1, FLJ12740, bK150C2.7		Q9HC16	OTTHUMG00000151081	ENST00000407997.3:c.1009A>G	22.37:g.39482557A>G	ENSP00000385057:p.Ile337Val	96	0	0		72	37	0.513889	NM_021822	B2RDR9|Q45F02|Q5TF77|Q7Z2N1|Q7Z2N4|Q9H9H8	Missense_Mutation	SNP	ENST00000407997.3	37	CCDS13984.1	.	.	.	.	.	.	.	.	.	.	.	3.799	-0.042054	0.07452	0.0	2.33E-4	ENSG00000239713	ENST00000452957;ENST00000407997	T;T	0.64438	-0.1;-0.1	1.51	1.51	0.23008	APOBEC-like, C-terminal (1);Cytidine deaminase-like (1);	.	.	.	.	T	0.43765	0.1262	L	0.38175	1.15	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.19778	-1.0295	9	0.18276	T	0.48	.	3.2677	0.06870	0.7742:0.0:0.2258:0.0	.	337	Q9HC16	ABC3G_HUMAN	V	337	ENSP00000413376:I337V;ENSP00000385057:I337V	ENSP00000385057:I337V	I	+	1	0	APOBEC3G	37812503	0.070000	0.21116	0.024000	0.17045	0.002000	0.02628	0.249000	0.18216	0.946000	0.37632	0.373000	0.22412	ATA	A|1.000;G|0.000	0.000	weak		0.572	APOBEC3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321219.1	NM_021822		G	39482557	A	G	39482557	3	3	25	1	0	0	0	0	1	0	0	0	794	101	4	3	1031	3	APOBEC3G	22	39482557	Missense_Mutation	SNP	A	TCGA-G8-6906-01A-11D-2210-10	12789604	39482557	11822009	827	9736											
ATF4	468	hgsc.bcm.edu	37	chr22	39917787	39917787	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgttttgcagaggatgcctTctccgggacagattggatgt	8	13	13	7	1	1	2	0	0	1	2	2	5	1	5	2	3	2	2	2	3	0	4	rs141575018		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:39917787T>G	ENST00000337304.2	+	2	1118	c.236T>G	c.(235-237)tTc>tGc	p.F79C	ATF4_ENST00000396680.1_Missense_Mutation_p.F79C|ATF4_ENST00000404241.2_Missense_Mutation_p.F79C	NM_001675.2	NP_001666.2	P18848	ATF4_HUMAN	activating transcription factor 4	79					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)	GAGGATGCCTTCTCCGGGACA	0.502																																					p.F79C		Atlas-SNP	.											.	ATF4	27	.	0			c.T236G						PASS	.	T	CYS/PHE,CYS/PHE	0,4406		0,0,2203	100	103	102		236,236	4.7	1	22	dbSNP_134	102	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	ATF4	NM_001675.2,NM_182810.1	205,205	0,4,6499	GG,GT,TT		0.0465,0.0,0.0308	probably-damaging,probably-damaging	79/352,79/352	39917787	4,13002	2203	4300	6503	SO:0001583	missense	468	exon2			ATGCCTTCTCCGG	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.236T>G	22.37:g.39917787T>G	ENSP00000336790:p.Phe79Cys	76	0	0		61	30	0.491803	NM_001675	Q9UH31	Missense_Mutation	SNP	ENST00000337304.2	37	CCDS13996.1	.	.	.	.	.	.	.	.	.	.	T	19.58	3.853455	0.71719	0.0	4.65E-4	ENSG00000128272	ENST00000404241;ENST00000337304;ENST00000396680	T;T;T	0.49432	0.78;0.78;0.78	4.74	4.74	0.60224	.	0.052105	0.85682	D	0.000000	T	0.68869	0.3048	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.74144	-0.3760	10	0.87932	D	0	-24.7248	14.269	0.66140	0.0:0.0:0.0:1.0	.	79	P18848	ATF4_HUMAN	C	79	ENSP00000384587:F79C;ENSP00000336790:F79C;ENSP00000379912:F79C	ENSP00000336790:F79C	F	+	2	0	ATF4	38247733	1.000000	0.71417	0.998000	0.56505	0.902000	0.53008	7.654000	0.83653	1.770000	0.52166	0.459000	0.35465	TTC	T|1.000;G|0.000	0.000	weak		0.502	ATF4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321305.1	NM_001675		G	39917787	T	G	39917787	3	3	25	1	0	0	0	0	1	0	0	0	1082	1783	62	5	242	5	ATF4	22	39917787	Missense_Mutation	SNP	T	TCGA-G8-6906-01A-11D-2210-10	435230	39917787	11386779	828	9737											
TEF	7008	hgsc.bcm.edu	37	chr22	41790179	41790179	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtggatgtgaacttcaatccGgaccccgccgacctggtgct	7	9	12	13	3	1	1	1	1	0	0	2	4	2	3	5	3	2	1	5	3	2	1	rs17365991	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:41790179G>A	ENST00000266304.4	+	3	671	c.555G>A	c.(553-555)ccG>ccA	p.P185P	TEF_ENST00000406644.3_Silent_p.P155P	NM_003216.3	NP_003207.1	Q10587	TEF_HUMAN	thyrotrophic embryonic factor	185	Pro-rich (proline/acidic region (PAR)).				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)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)	6						ACTTCAATCCGGACCCCGCCG	0.567													G|||	90	0.0179712	0.003	0.0288	5008	,	,		16633	0.003		0.0507	False		,,,				2504	0.0123				p.P185P		Atlas-SNP	.											.	TEF	21	.	0			c.G555A						PASS	.	G	,	44,4362	46.7+/-81.2	0,44,2159	86	89	88		465,555	-6.4	0.9	22	dbSNP_123	88	447,8153	135.1+/-192.4	8,431,3861	no	coding-synonymous,coding-synonymous	TEF	NM_001145398.1,NM_003216.2	,	8,475,6020	AA,AG,GG		5.1977,0.9986,3.7752	,	155/274,185/304	41790179	491,12515	2203	4300	6503	SO:0001819	synonymous_variant	7008	exon3			CAATCCGGACCCC		CCDS14014.1, CCDS46716.1	22q13.2	2013-01-10			ENSG00000167074	ENSG00000167074		"basic leucine zipper proteins"	11722	protein-coding gene	gene with protein product		188595				7835883, 15665112	Standard	NM_001145398		Approved	KIAA1655	uc003azy.4	Q10587	OTTHUMG00000150968	ENST00000266304.4:c.555G>A	22.37:g.41790179G>A		55	0	0		71	23	0.323944	NM_003216	B0QYS8|B2RC22|Q15729|Q7Z3J7|Q8IU94|Q96TG4	Silent	SNP	ENST00000266304.4	37	CCDS14014.1	57	0.0260989010989011	2	0.0040650406504065045	10	0.027624309392265192	3	0.005244755244755245	42	0.055408970976253295	G	9.184	1.024330	0.19433	0.009986	0.051977	ENSG00000167074	ENST00000413942	.	.	.	5.78	-6.36	0.01969	.	.	.	.	.	T	0.04724	0.0128	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31861	-0.9928	4	.	.	.	-14.0578	1.4557	0.02384	0.2829:0.3399:0.1884:0.1888	rs17365991;rs59727856;rs17365991	.	.	.	Q	151	.	.	R	+	2	0	TEF	40120125	0.000000	0.05858	0.903000	0.35520	0.978000	0.69477	-2.554000	0.00926	-1.214000	0.02614	-1.259000	0.01468	CGG	G|0.970;A|0.030	0.030	strong		0.567	TEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320692.1	NM_003216		A	41790179	G	A	41790179	2	1	25	1	0	0	0	0	0	0	0	1	15765	1103	39	1		1	TEF	22	41790179	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	1872392	41790179	9514387	829	9738											
POLDIP3	84271	hgsc.bcm.edu	37	chr22	43010821	43010821	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcaccgtcctttcgccgccgCcccgcgcttcctgatgagtt	3	11	9	18	6	1	2	1	2	0	0	4	2	3	2	7	0	0	2	7	0	0	3	rs61744232	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:43010821C>T	ENST00000252115.5	-	1	147	c.43G>A	c.(43-45)Gcg>Acg	p.A15T	POLDIP3_ENST00000348657.2_Missense_Mutation_p.A15T|POLDIP3_ENST00000339677.6_Missense_Mutation_p.A15T|RNU12_ENST00000362512.1_lincRNA	NM_032311.3	NP_115687.2	Q9BY77	PDIP3_HUMAN	polymerase (DNA-directed), delta interacting protein 3	15					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						TTCGCCGCCGCCCCGCGCTTC	0.672													C|||	19	0.00379393	0.0	0.0115	5008	,	,		12867	0.0		0.0089	False		,,,				2504	0.002				p.A15T	Ovarian(52;967 1128 5875 19997 42537)	Atlas-SNP	.											.	POLDIP3	58	.	0			c.G43A						PASS	.	C	THR/ALA,THR/ALA	13,4393	20.2+/-43.8	0,13,2190	45	50	48		43,43	-1.5	0	22	dbSNP_129	48	93,8507	51.9+/-112.3	1,91,4208	yes	missense,missense	POLDIP3	NM_032311.3,NM_178136.1	58,58	1,104,6398	TT,TC,CC		1.0814,0.2951,0.815	benign,benign	15/422,15/393	43010821	106,12900	2203	4300	6503	SO:0001583	missense	84271	exon1			CCGCCGCCCCGCG		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.43G>A	22.37:g.43010821C>T	ENSP00000252115:p.Ala15Thr	52	0	0		99	41	0.414141	NM_178136	A8K6F8|A8K6V9|Q009A7|Q5H972|Q6PGN6|Q7Z6Z0|Q9NSP5|Q9NSP6	Missense_Mutation	SNP	ENST00000252115.5	37	CCDS14038.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	C	3.855	-0.030975	0.07543	0.002951	0.010814	ENSG00000100227	ENST00000348657;ENST00000252115;ENST00000415122;ENST00000339677;ENST00000452567	.	.	.	4.4	-1.47	0.08772	.	0.803483	0.11757	N	0.532429	T	0.08891	0.0220	N	0.04508	-0.205	0.09310	N	0.999995	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.08055	0.001;0.003;0.001;0.0	T	0.29882	-0.9997	9	0.13470	T	0.59	-16.8684	4.6712	0.12691	0.1382:0.4646:0.0:0.3972	.	15;15;15;15	B4E0L0;Q6R954;Q9BY77-2;Q9BY77	.;.;.;PDIP3_HUMAN	T	15	.	ENSP00000252115:A15T	A	-	1	0	POLDIP3	41340765	0.001000	0.12720	0.000000	0.03702	0.689000	0.40095	0.621000	0.24418	-0.251000	0.09542	-0.259000	0.10710	GCG	C|0.995;T|0.005	0.005	strong		0.672	POLDIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320433.1	NM_032311		T	43010821	C	T	43010821	3	4	25	1	0	0	0	0	1	0	0	0	12204	739	26	2	1258	2	POLDIP3	22	43010821	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1220642	43010821	8293745	830	9739											
TRMU	55687	hgsc.bcm.edu	37	chr22	46733831	46733831	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acgtaaaggagtattggaatGatgtgttcaggtgagtgcgg	11	11	16	3	2	1	2	1	2	0	0	1	4	1	4	0	4	1	3	0	4	4	4	rs55952751	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:46733831G>A	ENST00000290846.4	+	2	578	c.238G>A	c.(238-240)Gat>Aat	p.D80N	TRMU_ENST00000424260.2_Missense_Mutation_p.D45N|TRMU_ENST00000381019.3_Missense_Mutation_p.D80N	NM_018006.4	NP_060476.2	O75648	MTU1_HUMAN	tRNA 5-methylaminomethyl-2-thiouridylate methyltransferase	80					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)		GTATTGGAATGATGTGTTCAG	0.502													G|||	5	0.000998403	0.0	0.0	5008	,	,		23073	0.0		0.005	False		,,,				2504	0.0				p.D80N		Atlas-SNP	.											.	TRMU	23	.	0			c.G238A						PASS	.	G	ASN/ASP	0,4406	2.1+/-5.4	0,0,2203	188	159	169		238	2.5	0.1	22	dbSNP_129	169	9,8591	7.1+/-27.0	0,9,4291	yes	missense	TRMU	NM_018006.4	23	0,9,6494	AA,AG,GG		0.1047,0.0,0.0692	possibly-damaging	80/422	46733831	9,12997	2203	4300	6503	SO:0001583	missense	55687	exon2			TGGAATGATGTGT	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.238G>A	22.37:g.46733831G>A	ENSP00000290846:p.Asp80Asn	124	0	0		92	32	0.347826	NM_018006	A8K3U7|Q05C99|Q5W9C8|Q66K31|Q6ICC3|Q9NWC1	Missense_Mutation	SNP	ENST00000290846.4	37	CCDS14075.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	9.359	1.067422	0.20067	0.0	0.001047	ENSG00000100416	ENST00000290846;ENST00000381019;ENST00000424260	T;T;T	0.72282	-0.64;-0.64;-0.64	4.8	2.45	0.29901	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.550552	0.19343	N	0.116585	T	0.36276	0.0961	N	0.12527	0.23	0.33732	D	0.618343	P;B;B	0.39920	0.695;0.435;0.005	B;B;B	0.34452	0.183;0.085;0.019	T	0.55366	-0.8152	10	0.02654	T	1	-12.8828	14.316	0.66452	0.0:0.2562:0.7438:0.0	rs55952751	80;80;80	B4DHM1;O75648-2;O75648	.;.;MTU1_HUMAN	N	80;80;45	ENSP00000290846:D80N;ENSP00000370407:D80N;ENSP00000406038:D45N	ENSP00000290846:D80N	D	+	1	0	TRMU	45112495	1.000000	0.71417	0.071000	0.20095	0.176000	0.22953	3.992000	0.56980	2.197000	0.70478	0.557000	0.71058	GAT	G|0.999;A|0.001	0.001	strong		0.502	TRMU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318042.2	NM_018006		A	46733831	G	A	46733831	3	1	25	1	0	0	0	0	1	0	0	0	16586	1290	45	2	244	2	TRMU	22	46733831	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	3723010	46733831	4570735	831	9740											
MLC1	23209	hgsc.bcm.edu	37	chr22	50512732	50512732	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcaatgatccccccgaggacGgcagagatgcctgcgattac	10	6	12	13	3	0	2	0	1	0	1	1	6	1	3	4	2	3	2	4	2	2	1	rs138153307		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50512732G>A	ENST00000311597.5	-	8	1233	c.627C>T	c.(625-627)gcC>gcT	p.A209A	MLC1_ENST00000535444.1_Silent_p.A130A|MLC1_ENST00000395876.2_Silent_p.A209A|MLC1_ENST00000538737.1_Silent_p.A175A|MLC1_ENST00000450140.2_Silent_p.A157A|MLC1_ENST00000431262.2_Silent_p.A179A|MLC1_ENST00000483836.1_5'Flank	NM_015166.3	NP_055981.1	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with subcortical cysts 1	209					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)		CCCCGAGGACGGCAGAGATGC	0.572													G|||	1	0.000199681	0.0	0.0	5008	,	,		16208	0.0		0.001	False		,,,				2504	0.0				p.A209A		Atlas-SNP	.											.	MLC1	48	.	0			c.C627T						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	108	76	87		627,627	-10.2	0.1	22	dbSNP_134	87	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous,coding-synonymous	MLC1	NM_015166.3,NM_139202.2	,	0,15,6488	AA,AG,GG		0.1628,0.0227,0.1153	,	209/378,209/378	50512732	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	23209	exon8			GAGGACGGCAGAG	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.627C>T	22.37:g.50512732G>A		82	0	0		66	32	0.484848	NM_015166	B3KW61|B7Z659|Q5JZ83|Q8TAG4|Q96RP5|Q9UGY8	Silent	SNP	ENST00000311597.5	37	CCDS14083.1																																																																																			G|0.999;A|0.001	0.001	strong		0.572	MLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316979.2	NM_015166		A	50512732	G	A	50512732	2	1	25	1	0	0	0	0	0	0	0	1	9621	1103	39	1		1	MLC1	22	50512732	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	3778901	50512732	791834	832	9741											
FAM116B	414918	hgsc.bcm.edu	37	chr22	50755782	50755782	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgcctgaagtacacgtagccGaagtagtgtgccggctccct	8	9	12	12	3	0	1	0	1	0	0	1	2	1	1	4	1	4	4	4	1	5	3	rs145811594	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50755782G>A	ENST00000413817.3	-	5	464	c.393C>T	c.(391-393)ttC>ttT	p.F131F	XX-C283C717.1_ENST00000453835.1_RNA	NM_001001794.3	NP_001001794.3	Q8NEG7	DEN6B_HUMAN	DENN/MADD domain containing 6B	131					positive regulation of Rab GTPase activity (GO:0032851)	endosome (GO:0005768)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)										ACACGTAGCCGAAGTAGTGTG	0.637													G|||	28	0.00559105	0.0	0.0043	5008	,	,		12216	0.0		0.0129	False		,,,				2504	0.0123				p.F131F		Atlas-SNP	.											FAM116B,colon,carcinoma,0,1	.	.	1	0			c.C393T						scavenged	.	G		4,4192		0,4,2094	54	62	60		393	-9.6	0.6	22	dbSNP_134	60	63,8363		1,61,4151	no	coding-synonymous	FAM116B	NM_001001794.3		1,65,6245	AA,AG,GG		0.7477,0.0953,0.5308		131/586	50755782	67,12555	2098	4213	6311	SO:0001819	synonymous_variant	414918	exon5			GTAGCCGAAGTAG	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.393C>T	22.37:g.50755782G>A		87	1	0.0114943		82	41	0.5	NM_001001794	A6X8I5	Silent	SNP	ENST00000413817.3	37	CCDS46732.1	11	0.005036630036630037	0	0.0	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	G	1.803	-0.476686	0.04414	9.53E-4	0.007477	ENSG00000205593	ENST00000433760	.	.	.	4.8	-9.6	0.00553	.	.	.	.	.	T	0.41696	0.1170	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60712	-0.7209	4	.	.	.	-6.8758	10.8518	0.46775	0.3823:0.1029:0.5148:0.0	.	.	.	.	L	103	.	.	S	-	2	0	FAM116B	49098354	0.005000	0.15991	0.579000	0.28588	0.026000	0.11368	-0.863000	0.04259	-2.344000	0.00622	-1.855000	0.00564	TCG	G|0.992;A|0.008	0.008	strong		0.637	DENND6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316845.3	NM_001001794		A	50755782	G	A	50755782	2	1	25	1	0	0	0	0	0	0	0	1	5413	1049	37	1		1	FAM116B	22	50755782	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	243050	50755782	548784	833	9742											
SBF1	6305	hgsc.bcm.edu	37	chr22	50885658	50885658	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaagttgtaaacgcgacgCgttgtcttcacctggggaag	10	9	13	9	4	2	1	1	0	1	1	2	3	2	2	1	2	1	3	1	2	4	4	rs371139013		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50885658C>T	ENST00000390679.3	-	40	5701	c.5517G>A	c.(5515-5517)acG>acA	p.T1839T	SBF1_ENST00000380817.3_Silent_p.T1865T|SBF1_ENST00000348911.6_Silent_p.T1840T			O95248	MTMR5_HUMAN	SET binding factor 1	1839	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)		AAACGCGACGCGTTGTCTTCA	0.667													C|||	1	0.000199681	0.0	0.0	5008	,	,		12737	0.0		0.0	False		,,,				2504	0.001				p.T1865T		Atlas-SNP	.											.	SBF1	211	.	0			c.G5595A						PASS	.	C		0,4186		0,0,2093	47	57	53		5595	-0.8	1	22		53	2,8400		0,2,4199	no	coding-synonymous	SBF1	NM_002972.2		0,2,6292	TT,TC,CC		0.0238,0.0,0.0159		1865/1894	50885658	2,12586	2093	4201	6294	SO:0001819	synonymous_variant	6305	exon41			GCGACGCGTTGTC	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.5517G>A	22.37:g.50885658C>T		135	0	0		178	80	0.449438	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Silent	SNP	ENST00000390679.3	37		.	.	.	.	.	.	.	.	.	.	C	7.644	0.681479	0.14907	0.0	2.38E-4	ENSG00000100241	ENST00000418590	.	.	.	3.51	-0.837	0.10766	.	.	.	.	.	T	0.39886	0.1095	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.23976	-1.0173	4	.	.	.	.	1.2292	0.01940	0.1426:0.3402:0.2736:0.2437	.	.	.	.	T	387	.	.	A	-	1	0	SBF1	49232524	0.061000	0.20836	0.996000	0.52242	0.814000	0.46013	-0.957000	0.03861	-0.171000	0.10797	0.462000	0.41574	GCG	.	.	weak		0.667	SBF1-201	KNOWN	basic	protein_coding	protein_coding				T	50885658	C	T	50885658	2	4	25	1	0	0	0	0	0	0	0	1	13873	755	27	1		1	SBF1	22	50885658	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	129876	50885658	418908	834	9743											
ARSE	415	hgsc.bcm.edu	37	chrX	2852957	2852957	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacggtctccagatgttgccCagcctgtccagctgcagagg	7	8	12	14	1	1	2	0	0	1	2	3	2	2	2	4	2	4	3	4	2	0	1			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:2852957C>G	ENST00000381134.3	-	11	1752	c.1686G>C	c.(1684-1686)ctG>ctC	p.L562L	ARSE_ENST00000540563.1_Silent_p.L517L|ARSE_ENST00000545496.1_Silent_p.L587L	NM_000047.2	NP_000038.2	P51690	ARSE_HUMAN	arylsulfatase E (chondrodysplasia punctata 1)	562					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)				AGATGTTGCCCAGCCTGTCCA	0.592																																					p.L562L		Atlas-SNP	.											.	ARSE	43	.	0			c.G1686C						PASS	.						43	32	36					X																	2852957		2203	4296	6499	SO:0001819	synonymous_variant	415	exon11			GTTGCCCAGCCTG	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.1686G>C	X.37:g.2852957C>G		138	0	0		144	143	0.993056	NM_000047	Q53FT2|Q53FU8	Silent	SNP	ENST00000381134.3	37	CCDS14122.1																																																																																			.	.	none		0.592	ARSE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055643.1	NM_000047		G	2852957	C	G	2852957	2	3	25	1	0	0	0	0	0	0	0	1	990	581	21	4		4	ARSE	23	2852957	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10		2852957	152417603	835	9744											
MAP3K15	389840	hgsc.bcm.edu	37	chrX	19387318	19387318	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttcagtctcacaggtaggCtcaaagtgggctcggagctc	8	9	12	12	1	3	0	3	0	1	0	6	1	3	1	1	4	1	4	1	4	2	2			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:19387318C>A	ENST00000338883.4	-	25	3419	c.3420G>T	c.(3418-3420)gaG>gaT	p.E1140D	MAP3K15_ENST00000469203.2_Missense_Mutation_p.E972D|MAP3K15_ENST00000518578.1_5'UTR|MAP3K15_ENST00000359173.3_Missense_Mutation_p.E575D	NM_001001671.3	NP_001001671.3	Q6ZN16	M3K15_HUMAN	mitogen-activated protein kinase kinase kinase 15	1140							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)					CACAGGTAGGCTCAAAGTGGG	0.602																																					p.E1140D		Atlas-SNP	.											.	MAP3K15	108	.	0			c.G3420T						PASS	.						71	64	66					X																	19387318		2203	4300	6503	SO:0001583	missense	389840	exon25			GGTAGGCTCAAAG	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.3420G>T	X.37:g.19387318C>A	ENSP00000345629:p.Glu1140Asp	24	0	0		36	36	1	NM_001001671	A2AI49|A2AI50|A6NJ61|Q5JPR4|Q6ZMV3	Missense_Mutation	SNP	ENST00000338883.4	37		.	.	.	.	.	.	.	.	.	.	C	11.19	1.564365	0.27915	.	.	ENSG00000180815	ENST00000338883;ENST00000359173;ENST00000469203	T;T;T	0.73047	-0.67;-0.71;-0.67	5.34	3.51	0.40186	.	0.104397	0.64402	N	0.000005	T	0.64294	0.2585	M	0.63428	1.95	0.25693	N	0.985669	P;D	0.56521	0.68;0.976	B;P	0.45913	0.431;0.497	T	0.58544	-0.7618	10	0.37606	T	0.19	.	2.7745	0.05344	0.1497:0.5478:0.1421:0.1604	.	615;1140	Q6ZN16-3;Q6ZN16	.;M3K15_HUMAN	D	1140;575;972	ENSP00000345629:E1140D;ENSP00000352093:E575D;ENSP00000428356:E972D	ENSP00000345629:E1140D	E	-	3	2	MAP3K15	19297239	0.032000	0.19561	0.063000	0.19743	0.727000	0.41649	-0.364000	0.07583	0.430000	0.26230	0.506000	0.49869	GAG	.	.	none		0.602	MAP3K15-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001001671		A	19387318	C	A	19387318	3	1	25	1	0	0	0	0	1	0	0	0	9258	796	28	4	541	4	MAP3K15	23	19387318	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	16534361	19387318	135883242	836	9745											
MAGEB3	4114	hgsc.bcm.edu	37	chrX	30254064	30254064	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcctcggggtcagaagagtaCgctccatgcacgtgagaaac	11	6	13	11	3	1	3	1	1	0	3	3	4	2	3	2	2	3	3	2	2	3	1	rs201131077		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:30254064C>T	ENST00000361644.2	+	5	760	c.23C>T	c.(22-24)aCg>aTg	p.T8M		NM_002365.4	NP_002356.2	O15480	MAGB3_HUMAN	melanoma antigen family B, 3	8										NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	25						CAGAAGAGTACGCTCCATGCA	0.542																																					p.T8M		Atlas-SNP	.											.	MAGEB3	54	.	0			c.C23T						PASS	.	A	MET/THR	0,3833		0,0,1631,571	61	51	55		23	-1.8	0	X		55	1,6727		0,1,2427,1872	yes	missense	MAGEB3	NM_002365.4	81	0,1,4058,2443	TT,TC,CC,C		0.0149,0.0,0.0095	possibly-damaging	8/347	30254064	1,10560	2202	4300	6502	SO:0001583	missense	4114	exon5			AGAGTACGCTCCA	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.23C>T	X.37:g.30254064C>T	ENSP00000355198:p.Thr8Met	122	1	0.00819672		130	129	0.992308	NM_002365	A0AVE4|B3KQ52|O75861	Missense_Mutation	SNP	ENST00000361644.2	37	CCDS14220.1	.	.	.	.	.	.	.	.	.	.	c	13.20	2.166490	0.38217	0.0	1.49E-4	ENSG00000198798	ENST00000378986;ENST00000361644	T;T	0.04360	3.64;3.64	3.77	-1.77	0.07982	Melanoma associated antigen, MAGE, N-terminal (1);	11.449600	0.01612	U	0.022560	T	0.07052	0.0179	N	0.22421	0.69	0.09310	N	1	D	0.54397	0.966	P	0.51701	0.677	T	0.22591	-1.0212	10	0.87932	D	0	.	5.614	0.17420	0.5656:0.3294:0.1051:0.0	.	8	O15480	MAGB3_HUMAN	M	8	ENSP00000368271:T8M;ENSP00000355198:T8M	ENSP00000355198:T8M	T	+	2	0	MAGEB3	30163985	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.113000	0.15499	-0.461000	0.06993	-1.548000	0.00902	ACG	.	.	weak		0.542	MAGEB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056158.2	NM_002365		T	30254064	C	T	30254064	3	4	25	1	0	0	0	0	1	0	0	0	9186	536	19	1	25	1	MAGEB3	23	30254064	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	10866746	30254064	125016496	837	9746											
CASK	8573	hgsc.bcm.edu	37	chrX	41604809	41604809	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcactgtacacaaaaccagcGtcagctcgctttacgatttc	11	11	6	13	3	2	0	2	0	0	0	4	1	2	0	1	0	5	3	1	0	4	4			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:41604809G>A	ENST00000378163.1	-	4	798	c.324C>T	c.(322-324)gaC>gaT	p.D108D	CASK_ENST00000378154.1_Silent_p.D108D|CASK_ENST00000442742.2_Silent_p.D108D|CASK_ENST00000318588.9_Silent_p.D108D|CASK_ENST00000378166.4_Silent_p.D108D|CASK_ENST00000378158.1_Silent_p.D108D|CASK_ENST00000421587.2_Silent_p.D108D|CASK_ENST00000361962.4_Silent_p.D108D			O14936	CSKP_HUMAN	calcium/calmodulin-dependent serine protein kinase (MAGUK family)	108	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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						CAAAACCAGCGTCAGCTCGCT	0.358																																					p.D108D	NSCLC(42;104 1086 3090 27189 35040)	Atlas-SNP	.											.	CASK	93	.	0			c.C324T						PASS	.						89	74	79					X																	41604809		2203	4300	6503	SO:0001819	synonymous_variant	8573	exon4			ACCAGCGTCAGCT	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.324C>T	X.37:g.41604809G>A		70	0	0		127	126	0.992126	NM_001126054	A6NES1|B7ZKY0|O43215|Q17RI4|Q59HA0|Q5VT16|Q5VT17|Q5VT18|Q5VT19|Q66T42|Q9BYH6|Q9NYB2|Q9NYB3	Silent	SNP	ENST00000378163.1	37																																																																																				.	.	none		0.358	CASK-007	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000056285.1	NM_003688		A	41604809	G	A	41604809	2	1	25	1	0	0	0	0	0	0	0	1	2667	1136	40	1		1	CASK	23	41604809	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	11350745	41604809	113665751	838	9747											
OTUD5	55593	hgsc.bcm.edu	37	chrX	48783183	48783183	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcccgcaaccactgcaggtaGgattcccgagccacctgctc	8	7	9	17	2	0	0	0	0	0	0	3	2	2	1	5	2	4	4	5	2	2	2	rs141488277	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:48783183G>C	ENST00000156084.4	-	6	1278	c.1218C>G	c.(1216-1218)tcC>tcG	p.S406S	OTUD5_ENST00000428668.2_Silent_p.S184S|OTUD5_ENST00000484499.1_5'Flank|OTUD5_ENST00000396743.3_Silent_p.S401S|OTUD5_ENST00000376488.3_Silent_p.S401S	NM_017602.3	NP_060072.1	Q96G74	OTUD5_HUMAN	OTU deubiquitinase 5	406					innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|response to lipopolysaccharide (GO:0032496)	cytosol (GO:0005829)	ubiquitin-specific protease activity (GO:0004843)			endometrium(2)|large_intestine(3)|lung(6)|pancreas(2)	13						ACTGCAGGTAGGATTCCCGAG	0.572													G|||	5	0.0013245	0.0	0.0014	3775	,	,		13554	0.0		0.001	False		,,,				2504	0.0031				p.S406S		Atlas-SNP	.											.	OTUD5	66	.	0			c.C1218G						PASS	.	G	,,,	0,3835		0,0,0,1632,571	102	75	85		1203,1203,552,1218	2.4	1	X	dbSNP_134	85	31,6697		0,22,9,2406,1863	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OTUD5	NM_001136157.1,NM_001136158.1,NM_001136159.1,NM_017602.3	,,,	0,22,9,4038,2434	CC,CG,C,GG,G		0.4608,0.0,0.2935	,,,	401/567,401/567,184/350,406/572	48783183	31,10532	2203	4300	6503	SO:0001819	synonymous_variant	55593	exon6			CAGGTAGGATTCC		CCDS14313.1, CCDS48104.1, CCDS48105.1	Xp11.23	2014-06-09	2014-02-24		ENSG00000068308	ENSG00000068308		"OTU domain containing"	25402	protein-coding gene	gene with protein product		300713	"OTU domain containing 5"			24143256	Standard	NM_001136157		Approved	DKFZp761A052, DUBA	uc004dlu.3	Q96G74	OTTHUMG00000024130	ENST00000156084.4:c.1218C>G	X.37:g.48783183G>C		39	0	0		30	30	1	NM_017602	B4DGG7|G5E9D7|Q4KMN9|Q8N6T5|Q9H650|Q9H9U0|Q9NT65	Silent	SNP	ENST00000156084.4	37	CCDS14313.1																																																																																			G|0.998;C|0.002	0.002	strong		0.572	OTUD5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000060799.1	NM_017602		C	48783183	G	C	48783183	2	2	25	1	0	0	0	0	0	0	0	1	11324	987	35	4		4	OTUD5	23	48783183	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	7178374	48783183	106487377	839	9748											
SYP	6855	hgsc.bcm.edu	37	chrX	49047924	49047924	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggagaaggaggtgggtgcAccctgcgggccgtagccttg	6	8	18	9	2	0	1	0	0	0	1	0	3	0	2	3	5	3	2	3	5	2	3			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:49047924A>G	ENST00000263233.4	-	6	984	c.912T>C	c.(910-912)ggT>ggC	p.G304G	SYP_ENST00000479808.1_Silent_p.G304G|SYP_ENST00000538567.1_Silent_p.G186G	NM_003179.2	NP_003170.1	P08247	SYPH_HUMAN	synaptophysin	304	Repeats, Gly-rich.				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)				AGGTGGGTGCACCCTGCGGGC	0.647																																					p.G304G		Atlas-SNP	.											.	SYP	71	.	0			c.T912C						PASS	.						20	19	19					X																	49047924		2203	4296	6499	SO:0001819	synonymous_variant	6855	exon6			GGGTGCACCCTGC	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.912T>C	X.37:g.49047924A>G		28	0	0		31	30	0.967742	NM_003179	B2R7L6|B7Z359|Q6P2F7	Silent	SNP	ENST00000263233.4	37	CCDS14321.1	.	.	.	.	.	.	.	.	.	.	A	11.63	1.694606	0.30052	.	.	ENSG00000102003	ENST00000472598	.	.	.	5.5	0.389	0.16269	.	.	.	.	.	T	0.40040	0.1101	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.32929	-0.9888	4	.	.	.	-9.7988	0.3716	0.00380	0.2718:0.3005:0.1615:0.2662	.	.	.	.	A	194	.	.	V	-	2	0	SYP	48934868	0.083000	0.21467	1.000000	0.80357	0.997000	0.91878	-0.907000	0.04067	0.693000	0.31634	0.486000	0.48141	GTG	.	.	none		0.647	SYP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083625.2	NM_003179		G	49047924	A	G	49047924	2	3	25	1	0	0	0	0	0	0	0	1	15476	146	6	3		3	SYP	23	49047924	Silent	SNP	A	TCGA-G8-6906-01A-11D-2210-10	264741	49047924	106222636	840	9749											
ALAS2	212	hgsc.bcm.edu	37	chrX	55039959	55039959	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgagggctgtggtggggggaGggtgccaagcgcaggagctc	6	6	22	7	1	0	1	0	1	0	0	1	3	0	3	1	7	3	3	1	7	1	0	rs150055592	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:55039959G>T	ENST00000330807.5	-	10	1697	c.1560C>A	c.(1558-1560)ccC>ccA	p.P520P	ALAS2_ENST00000498636.1_Intron|ALAS2_ENST00000335854.4_Silent_p.P483P|ALAS2_ENST00000396198.3_Silent_p.P507P	NM_000032.4	NP_000023.2	P22557	HEM0_HUMAN	aminolevulinate, delta-, synthase 2	520			P -> L (in dbSNP:rs201062903). {ECO:0000269|PubMed:21309041}.		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)	GGTGGGGGGAGGGTGCCAAGC	0.577													G|||	10	0.00264901	0.0	0.0029	3775	,	,		12458	0.0		0.008	False		,,,				2504	0.0				p.P520P		Atlas-SNP	.											.	ALAS2	163	.	0			c.C1560A						PASS	.	G	,,	1,3834		0,1,0,1631,571	62	51	55		1560,1449,1521	1.4	1	X	dbSNP_134	55	42,6686		0,25,17,2403,1855	no	coding-synonymous,coding-synonymous,coding-synonymous	ALAS2	NM_000032.4,NM_001037967.3,NM_001037968.3	,,	0,26,17,4034,2426	TT,TG,T,GG,G		0.6243,0.0261,0.4071	,,	520/588,483/551,507/575	55039959	43,10520	2203	4300	6503	SO:0001819	synonymous_variant	212	exon10			GGGGGAGGGTGCC		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.1560C>A	X.37:g.55039959G>T		65	0	0		66	64	0.969697	NM_000032	A8K3F0|A8K6C4|Q13735|Q5JZF5|Q8N6H3	Silent	SNP	ENST00000330807.5	37	CCDS14366.1																																																																																			G|0.997;T|0.003	0.003	strong		0.577	ALAS2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056843.3	NM_000032		T	55039959	G	T	55039959	2	4	25	1	0	0	0	0	0	0	0	1	485	987	35	4		4	ALAS2	23	55039959	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	5992035	55039959	100230601	841	9750											
FAM104B	90736	hgsc.bcm.edu	37	chrX	55172630	55172630	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atacccctcatgcaagaactGgggaaagtttgcatcgggtt	11	10	11	9	1	1	1	1	0	0	1	2	2	1	2	2	3	4	4	2	3	4	3	rs113263757		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:55172630G>A	ENST00000358460.4	-	3	388	c.235C>T	c.(235-237)Cag>Tag	p.Q79*	FAM104B_ENST00000477847.2_Nonsense_Mutation_p.Q76*|FAM104B_ENST00000332132.4_Nonsense_Mutation_p.Q80*|FAM104B_ENST00000472571.2_3'UTR|FAM104B_ENST00000425133.2_Nonsense_Mutation_p.Q80*|FAM104B_ENST00000489298.1_Nonsense_Mutation_p.Q78*|FAM104B_ENST00000478918.1_5'Flank			Q5XKR9	F104B_HUMAN	family with sequence similarity 104, member B	79										endometrium(3)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	8						TGCAAGAACTGGGGAAAGTTT	0.493																																					p.Q80X		Atlas-SNP	.											.	FAM104B	28	.	0			c.C238T						PASS	.						127	104	112					X																	55172630		2203	4300	6503	SO:0001587	stop_gained	90736	exon3			AGAACTGGGGAAA	BC000919	CCDS35305.1, CCDS35305.2, CCDS55422.1, CCDS55423.1, CCDS55424.1, CCDS55425.1, CCDS55426.1	Xp11.22	2008-02-05	2006-05-16	2006-05-16	ENSG00000182518	ENSG00000182518			25085	protein-coding gene	gene with protein product			"chromosome X open reading frame 44"	CXorf44		12477932	Standard	NM_138362		Approved	FLJ20434	uc004dug.2	Q5XKR9	OTTHUMG00000021646	ENST00000358460.4:c.235C>T	X.37:g.55172630G>A	ENSP00000364101:p.Gln79*	33	0	0		46	4	0.0869565	NM_001166699	A6NEH1|B4DSV6|D6R9S5|D6RDJ5|E9PH40|Q8WVU5|Q9BRA1	Nonsense_Mutation	SNP	ENST00000358460.4	37	CCDS35305.2	.	.	.	.	.	.	.	.	.	.	g	11.17	1.559418	0.27827	.	.	ENSG00000182518	ENST00000358460;ENST00000332132;ENST00000425133;ENST00000477847;ENST00000489298	.	.	.	1.6	1.6	0.23607	.	0.325359	0.21941	U	0.066869	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-0.2487	6.0913	0.19995	0.0:0.0:1.0:0.0	.	.	.	.	X	79;80;80;76;78	.	ENSP00000333394:Q80X	Q	-	1	0	FAM104B	55189355	0.905000	0.30787	0.015000	0.15790	0.033000	0.12548	1.600000	0.36762	1.084000	0.41184	0.436000	0.28706	CAG	.	.	weak		0.493	FAM104B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056851.1	NM_138362		A	55172630	G	A	55172630	4	1	25	1	0	0	0	0	0	1	0	0	5391	1357	47	2	217	2	FAM104B	23	55172630	Nonsense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	132671	55172630	100097930	842	9751											
PJA1	64219	hgsc.bcm.edu	37	chrX	68382422	68382422	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctcccttctctccctctcCgagctgtcaccttttgtagc	3	15	6	17	1	3	0	1	0	2	0	7	1	5	0	4	0	3	3	4	0	1	4	rs149179614	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:68382422C>T	ENST00000361478.1	-	2	1037	c.660G>A	c.(658-660)tcG>tcA	p.S220S	PJA1_ENST00000374584.3_Intron|PJA1_ENST00000374583.1_Silent_p.S220S|PJA1_ENST00000477231.1_5'UTR|PJA1_ENST00000374571.4_Silent_p.S165S	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	220					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						TCTCCCTCTCCGAGCTGTCAC	0.532													c|||	6	0.0015894	0.0	0.0	3775	,	,		14255	0.0		0.0	False		,,,				2504	0.0061				p.S220S		Atlas-SNP	.											.	PJA1	106	.	0			c.G660A						PASS	.		,,	1,3834		0,1,0,1631,571	47	38	41		495,,660	1	0	X	dbSNP_134	41	4,6724		0,3,1,2425,1871	no	coding-synonymous,intron,coding-synonymous	PJA1	NM_001032396.2,NM_022368.4,NM_145119.3	,,	0,4,1,4056,2442	TT,TC,T,CC,C		0.0595,0.0261,0.0473	,,	165/589,,220/644	68382422	5,10558	2203	4300	6503	SO:0001819	synonymous_variant	64219	exon2			CCTCTCCGAGCTG	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.660G>A	X.37:g.68382422C>T		89	0	0		92	91	0.98913	NM_145119	A2A322|Q5JUT8|Q5JUT9|Q8NG28|Q9HAC1	Silent	SNP	ENST00000361478.1	37	CCDS14393.1																																																																																			C|0.999;T|0.001	0.001	strong		0.532	PJA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057031.2	NM_145119		T	68382422	C	T	68382422	2	4	25	1	0	0	0	0	0	0	0	1	11970	639	23	1		1	PJA1	23	68382422	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	13209792	68382422	86888138	843	9752											
CXorf26	51260	hgsc.bcm.edu	37	chrX	75394784	75394784	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	catgctgaagtctattacaaGgtgagttgtctttcttcatc	9	16	8	8	0	4	2	1	2	3	0	5	2	4	2	0	1	2	2	0	1	4	5			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:75394784G>T	ENST00000373358.3	+	3	359	c.156G>T	c.(154-156)aaG>aaT	p.K52N	PBDC1_ENST00000373357.3_Splice_Site_p.K52N	NM_016500.3	NP_057584.2	Q9BVG4	PBDC1_HUMAN	polysaccharide biosynthesis domain containing 1	52																	TCTATTACAAGGTGAGTTGTC	0.398																																					p.K52N		Atlas-SNP	.											.	.	.	.	0			c.G156T						PASS	.						131	106	114					X																	75394784		2203	4300	6503	SO:0001630	splice_region_variant	51260	exon3			TTACAAGGTGAGT	BC001220	CCDS14432.1, CCDS75995.1	Xq13.2	2012-11-28	2012-11-28	2012-11-28	ENSG00000102390	ENSG00000102390			28790	protein-coding gene	gene with protein product			"chromosome X open reading frame 26"	CXorf26		11042152	Standard	NM_016500		Approved	MGC874	uc004ecl.1	Q9BVG4	OTTHUMG00000021876	ENST00000373358.3:c.156+1G>T	X.37:g.75394784G>T		97	0	0		99	99	1	NM_016500		Missense_Mutation	SNP	ENST00000373358.3	37	CCDS14432.1	.	.	.	.	.	.	.	.	.	.	G	8.506	0.865350	0.17250	.	.	ENSG00000102390	ENST00000373358;ENST00000373357	.	.	.	4.8	1.69	0.24217	Yst0336-like domain (1);	0.044941	0.85682	D	0.000000	T	0.14570	0.0352	N	0.02111	-0.68	0.37122	D	0.900873	B	0.21520	0.057	B	0.23275	0.045	T	0.04242	-1.0966	9	0.15066	T	0.55	-21.0255	0.5888	0.00724	0.2492:0.1861:0.3716:0.1931	.	52	Q9BVG4	CX026_HUMAN	N	52	.	ENSP00000362455:K52N	K	+	3	2	CXorf26	75311186	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	0.813000	0.27225	0.469000	0.27268	0.600000	0.82982	AAG	.	.	none		0.398	PBDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057294.1	NM_016500	Missense_Mutation	T	75394784	G	T	75394784	5	4	25	1	0	0	0	0	0	0	1	0	4106	1014	35	4	166	4	CXorf26	23	75394784	Splice_Site	SNP	G	TCGA-G8-6906-01A-11D-2210-10	7012362	75394784	79875776	844	9753											
TAF7L	54457	hgsc.bcm.edu	37	chrX	100547804	100547804	+	Missense_Mutation	SNP	G	G	C																															cttcctggaagttttctgggGcctgggcagcagcctgggcg																										TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:100547804G>C	ENST00000372907.3	-	1	241	c.230C>G	c.(229-231)gCc>gGc	p.A77G	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	77					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						GTTTTCTGGGGCCTGGGCAGC	0.557																																					p.A77G	Ovarian(104;431 1530 3210 15406 18594)	Atlas-SNP	.											.	TAF7L	64	.	0			c.C230G						PASS	.						69	70	70					X																	100547804		2203	4300	6503	SO:0001583	missense	54457	exon1			TCTGGGGCCTGGG	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.230C>G	X.37:g.100547804G>C	ENSP00000361998:p.Ala77Gly	52	0	0		47	45	0.957447	NM_024885	Q5H9L6|Q86XI4|Q9BXU5|Q9H5R0	Missense_Mutation	SNP	ENST00000372907.3	37	CCDS35347.1	.	.	.	.	.	.	.	.	.	.	G	8.991	0.977721	0.18812	.	.	ENSG00000102387	ENST00000372907	T	0.15834	2.39	3.06	2.19	0.27852	.	2.099320	0.02710	N	0.112725	T	0.12305	0.0299	L	0.27053	0.805	0.09310	N	0.999996	B	0.33694	0.421	B	0.24006	0.05	T	0.24476	-1.0159	10	0.72032	D	0.01	-1.4147	5.2676	0.15607	0.165:0.0:0.8349:0.0	.	77	Q5H9L4	TAF7L_HUMAN	G	77	ENSP00000361998:A77G	ENSP00000361998:A77G	A	-	2	0	TAF7L	100434460	0.006000	0.16342	0.001000	0.08648	0.009000	0.06853	1.723000	0.38053	0.681000	0.31386	0.600000	0.82982	GCC	.	.	none		0.557	TAF7L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057526.2			C	100547804	G	C	100547804	3	2	25	1	0	0	0	0	1	0	0	0	15548	1203	42	4	1210	4	TAF7L	23	100547804	Missense_Mutation	SNP	G	TCGA-G8-6906-01A-11D-2210-10	25153020	100547804	54722756	845	9754	120	3									
TAF7L	54457	hgsc.bcm.edu	37	chrX	100547805	100547805	+	Missense_Mutation	SNP	C	C	T																															ttcctggaagttttctggggCctgggcagcagcctgggcgc																										TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:100547805C>T	ENST00000372907.3	-	1	240	c.229G>A	c.(229-231)Gcc>Acc	p.A77T	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	77					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						TTTTCTGGGGCCTGGGCAGCA	0.557																																					p.A77T	Ovarian(104;431 1530 3210 15406 18594)	Atlas-SNP	.											.	TAF7L	64	.	0			c.G229A						PASS	.						70	70	70					X																	100547805		2203	4300	6503	SO:0001583	missense	54457	exon1			CTGGGGCCTGGGC	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.229G>A	X.37:g.100547805C>T	ENSP00000361998:p.Ala77Thr	52	0	0		46	44	0.956522	NM_024885	Q5H9L6|Q86XI4|Q9BXU5|Q9H5R0	Missense_Mutation	SNP	ENST00000372907.3	37	CCDS35347.1	.	.	.	.	.	.	.	.	.	.	C	9.433	1.086161	0.20390	.	.	ENSG00000102387	ENST00000372907	T	0.14391	2.51	3.17	-6.35	0.01975	.	2.099320	0.02710	N	0.112725	T	0.10380	0.0254	L	0.27053	0.805	0.09310	N	0.999998	B	0.06786	0.001	B	0.04013	0.001	T	0.24835	-1.0149	10	0.51188	T	0.08	-1.4147	9.7024	0.40196	0.0:0.5863:0.2433:0.1704	.	77	Q5H9L4	TAF7L_HUMAN	T	77	ENSP00000361998:A77T	ENSP00000361998:A77T	A	-	1	0	TAF7L	100434461	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.202000	0.03023	-2.983000	0.00282	-0.340000	0.08031	GCC	.	.	none		0.557	TAF7L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057526.2			T	100547805	C	T	100547805	3	4	25	1	0	0	0	0	1	0	0	0	15548	739	26	2	1211	2	TAF7L	23	100547805	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1	100547805	54722755	846	9755	120	3									
TAF7L	54457	hgsc.bcm.edu	37	chrX	100547806	100547806	+	Missense_Mutation	SNP	C	C	A																															tcctggaagttttctggggcCtgggcagcagcctgggcgct																										TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:100547806C>A	ENST00000372907.3	-	1	239	c.228G>T	c.(226-228)caG>caT	p.Q76H	TAF7L_ENST00000356784.1_5'Flank|TAF7L_ENST00000372905.2_De_novo_Start_OutOfFrame	NM_024885.3	NP_079161.3	Q5H9L4	TAF7L_HUMAN	TAF7-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 50kDa	76					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						TTTCTGGGGCCTGGGCAGCAG	0.557																																					p.Q76H	Ovarian(104;431 1530 3210 15406 18594)	Atlas-SNP	.											.	TAF7L	64	.	0			c.G228T						PASS	.						70	71	71					X																	100547806		2203	4300	6503	SO:0001583	missense	54457	exon1			TGGGGCCTGGGCA	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.228G>T	X.37:g.100547806C>A	ENSP00000361998:p.Gln76His	53	0	0		46	44	0.956522	NM_024885	Q5H9L6|Q86XI4|Q9BXU5|Q9H5R0	Missense_Mutation	SNP	ENST00000372907.3	37	CCDS35347.1	.	.	.	.	.	.	.	.	.	.	C	8.598	0.886065	0.17540	.	.	ENSG00000102387	ENST00000372907	T	0.16597	2.33	3.17	-2.29	0.06805	.	5.716450	0.00953	N	0.002982	T	0.08714	0.0216	N	0.14661	0.345	0.09310	N	0.999993	P	0.39964	0.697	B	0.32465	0.146	T	0.13683	-1.0500	10	0.51188	T	0.08	6.1498	3.8568	0.08979	0.0:0.284:0.4115:0.3044	.	76	Q5H9L4	TAF7L_HUMAN	H	76	ENSP00000361998:Q76H	ENSP00000361998:Q76H	Q	-	3	2	TAF7L	100434462	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.793000	0.04589	-0.640000	0.05495	-0.340000	0.08031	CAG	.	.	none		0.557	TAF7L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057526.2			A	100547806	C	A	100547806	3	1	25	1	0	0	0	0	1	0	0	0	15548	680	24	4	1212	4	TAF7L	23	100547806	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1	100547806	54722754	847	9756	120	3									
MORC4	79710	hgsc.bcm.edu	37	chrX	106221323	106221323	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tactcaccttcacctggcacCccaccttctcaaaagatttt	10	12	3	16	0	3	1	3	0	1	1	4	1	3	1	5	1	1	1	5	1	3	5			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:106221323C>A	ENST00000355610.4	-	8	1317	c.1043G>T	c.(1042-1044)gGg>gTg	p.G348V	MORC4_ENST00000255495.7_Missense_Mutation_p.G348V|MORC4_ENST00000535534.1_Missense_Mutation_p.G96V	NM_001085354.2|NM_024657.4	NP_001078823.1|NP_078933.3	Q8TE76	MORC4_HUMAN	MORC family CW-type zinc finger 4	348						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						CACCTGGCACCCCACCTTCTC	0.383																																					p.G348V		Atlas-SNP	.											.	MORC4	155	.	0			c.G1043T						PASS	.						160	159	160					X																	106221323		2203	4300	6503	SO:0001583	missense	79710	exon8			TGGCACCCCACCT	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.1043G>T	X.37:g.106221323C>A	ENSP00000347821:p.Gly348Val	67	0	0		71	61	0.859155	NM_001085354	A1YR23|A1YR24|H7BXF1|Q5JUK7|Q96MZ2|Q9HAI7	Missense_Mutation	SNP	ENST00000355610.4	37	CCDS14525.2	.	.	.	.	.	.	.	.	.	.	C	19.17	3.775432	0.70107	.	.	ENSG00000133131	ENST00000355610;ENST00000535534;ENST00000255495	T;T;T	0.37752	2.41;1.18;2.41	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.59582	0.2204	M	0.72118	2.19	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	0.63739	-0.6569	10	0.87932	D	0	-13.769	15.1835	0.72978	0.0:1.0:0.0:0.0	.	96;348;348	A1YR24;A1YR23;Q8TE76	.;.;MORC4_HUMAN	V	348;96;348	ENSP00000347821:G348V;ENSP00000440359:G96V;ENSP00000255495:G348V	ENSP00000255495:G348V	G	-	2	0	MORC4	106107979	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	5.777000	0.68931	2.393000	0.81446	0.538000	0.68166	GGG	.	.	none		0.383	MORC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057816.3	NM_024657		A	106221323	C	A	106221323	3	1	25	1	0	0	0	0	1	0	0	0	9713	623	22	4	1810	4	MORC4	23	106221323	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	5673517	106221323	49049237	848	9757											
LAMP2	3920	hgsc.bcm.edu	37	chrX	119576455	119576455	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggccagtgctttgcttaccGgagccattaaccaaatacat	12	10	8	11	1	0	0	0	0	0	0	0	1	0	1	4	2	6	2	4	2	4	4	rs73219144	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:119576455G>A	ENST00000200639.4	-	7	1063	c.927C>T	c.(925-927)tcC>tcT	p.S309S	LAMP2_ENST00000434600.2_Splice_Site_p.S309S|LAMP2_ENST00000540603.1_Splice_Site_p.S262S|LAMP2_ENST00000538785.1_Splice_Site_p.S198S|LAMP2_ENST00000371335.4_Splice_Site_p.S309S			P13473	LAMP2_HUMAN	lysosomal-associated membrane protein 2	309	Second lumenal domain.				blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	enzyme binding (GO:0019899)			endometrium(4)|large_intestine(2)|lung(5)|ovary(2)|urinary_tract(2)	15						TTTGCTTACCGGAGCCATTAA	0.358													G|||	50	0.013245	0.0	0.0072	3775	,	,		13506	0.0		0.0398	False		,,,				2504	0.0051				p.S309S		Atlas-SNP	.											.	LAMP2	101	.	0			c.C927T						PASS	.	G	,,	29,3806		0,24,5,1608,566	254	242	246		927,927,927	0.9	1	X	dbSNP_130	246	274,6454		6,187,75,2235,1797	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	LAMP2	NM_001122606.1,NM_002294.2,NM_013995.2	,,	6,211,80,3843,2363	AA,AG,A,GG,G		4.0725,0.7562,2.8685	,,	309/412,309/411,309/411	119576455	303,10260	2203	4300	6503	SO:0001630	splice_region_variant	3920	exon7			CTTACCGGAGCCA	X77196	CCDS14599.1, CCDS14600.1, CCDS48159.1	Xq24-q25	2014-09-17			ENSG00000005893	ENSG00000005893		"CD molecules"	6501	protein-coding gene	gene with protein product		309060					Standard	NM_002294		Approved	CD107b	uc004ess.4	P13473	OTTHUMG00000022301	ENST00000200639.4:c.928+1C>T	X.37:g.119576455G>A		44	0	0		44	44	1	NM_013995	A8K4X5|D3DTF0|Q16641|Q6Q3G8|Q96J30|Q99534|Q9UD93	Silent	SNP	ENST00000200639.4	37	CCDS14599.1																																																																																			G|0.975;A|0.025	0.025	strong		0.358	LAMP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058099.1		Silent	A	119576455	G	A	119576455	5	1	25	1	0	0	0	0	0	0	1	0	8627	1130	39	1	608	1	LAMP2	23	119576455	Splice_Site	SNP	G	TCGA-G8-6906-01A-11D-2210-10	13355132	119576455	35694105	849	9758											
RBMX	27316	hgsc.bcm.edu	37	chrX	135961560	135961560	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttaagcccaccaatgaagagCtttcctgggcgatctgcttc	9	11	9	12	1	1	2	0	1	1	1	3	3	2	2	3	1	3	2	3	1	3	3	rs80321628		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:135961560C>G	ENST00000320676.7	-	2	181	c.27G>C	c.(25-27)aaG>aaC	p.K9N	RBMX_ENST00000565438.1_Intron|RBMX_ENST00000570135.1_5'UTR|RBMX_ENST00000562646.1_Missense_Mutation_p.K9N|SNORD61_ENST00000384252.1_RNA|RBMX_ENST00000431446.3_Missense_Mutation_p.K9N	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	9	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				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)	p.K9N(1)		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)					CAATGAAGAGCTTTCCTGGGC	0.413																																					p.K9N		Atlas-SNP	.											.	RBMX	149	.	1	Substitution - Missense(1)	pancreas(1)	c.G27C						PASS	.						109	103	105					X																	135961560		2203	4300	6503	SO:0001583	missense	27316	exon2			GAAGAGCTTTCCT		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.27G>C	X.37:g.135961560C>G	ENSP00000359645:p.Lys9Asn	123	0	0		158	35	0.221519	NM_001164803	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	Missense_Mutation	SNP	ENST00000320676.7	37	CCDS14661.1	.	.	.	.	.	.	.	.	.	.	.	19.30	3.801463	0.70682	.	.	ENSG00000147274	ENST00000431446;ENST00000320676;ENST00000449161	D;D	0.89050	-2.46;-2.46	4.66	3.78	0.43462	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.000000	0.85682	U	0.000000	D	0.88507	0.6455	L	0.56340	1.77	0.09310	P	0.9999999999999992	P;B;P	0.46656	0.882;0.278;0.868	P;B;B	0.50270	0.636;0.142;0.311	D	0.91729	0.5395	9	0.72032	D	0.01	.	8.8627	0.35267	0.0:0.7507:0.0:0.2493	.	9;9;9	B4E3U4;P38159;Q8N8Y7	.;HNRPG_HUMAN;.	N	9	ENSP00000411989:K9N;ENSP00000359645:K9N	ENSP00000359645:K9N	K	-	3	2	RBMX	135789226	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.970000	0.29383	1.905000	0.55150	0.508000	0.49915	AAG	.	.	weak		0.413	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058507.1	NM_002139		G	135961560	C	G	135961560	3	3	25	1	0	0	0	0	1	0	0	0	13166	796	28	4	1235	4	RBMX	23	135961560	Missense_Mutation	SNP	C	TCGA-G8-6906-01A-11D-2210-10	16385105	135961560	19309000	850	9759											
CDR1	1038	hgsc.bcm.edu	37	chrX	139866424	139866441	+	In_Frame_Del	DEL	GTCTTCCAACAAAGGTAC	GTCTTCCAACAAAGGTAC	-																															atgtcttccagcctacttgtGtcttccaacaaaggtacgtc																										TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GTCTTCCAACAAAGGTAC	GTCTTCCAACAAAGGTAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:139866424_139866441delGTCTTCCAACAAAGGTAC	ENST00000370532.2	-	1	282_299	c.91_108delGTACCTTTGTTGGAAGAC	c.(91-108)gtacctttgttggaagacdel	p.VPLLED31del		NM_004065.2	NP_004056.2	P51861	CDR1_HUMAN	cerebellar degeneration-related protein 1, 34kDa	31	23 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)				GCCTACTTGTGTCTTCCAACAAAGGTACGTCTTCCAAC	0.44																																					p.31_37del		Atlas-Indel	.											.	CDR1	58	.	0			c.92_109del						PASS	.			205,3516		5,155,40,1432,497						-2.7	0			152	40,6440		8,5,19,2342,1751	no	coding	CDR1	NM_004065.2		13,160,59,3774,2248	A1A1,A1R,A1,RR,R		0.6173,5.5093,2.4017				245,9956				SO:0001651	inframe_deletion	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.91_108delGTACCTTTGTTGGAAGAC	X.37:g.139866424_139866441delGTCTTCCAACAAAGGTAC	ENSP00000359563:p.Val31_Asp36del	251	0	0		195	104	0.533333	NM_004065	Q5JXH6	In_Frame_Del	DEL	ENST00000370532.2	37	CCDS14670.1																																																																																			.	.	none		0.44	CDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058583.1	NM_004065		-	139866441	GTCTTCCAACAAAGGTAC	-	139866424	7	5	25	1	0	1	0	1	0	0	0	0	3173	1368	48	0	684	0	CDR1	23	139866424	In_Frame_Del	DEL	GTCTTCCAACAAAGGTAC	TCGA-G8-6906-01A-11D-2210-10	3904864	139866424	15404136	851	9760											
FMR1	2332	hgsc.bcm.edu	37	chrX	146993715	146993715	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagatggaggagctggtggtGgaagtgcggggctccaatgg	9	7	20	5	1	0	1	0	0	0	1	1	4	1	4	1	8	2	2	1	8	3	0	rs111485627	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:146993715G>T	ENST00000370475.4	+	1	146	c.18G>T	c.(16-18)gtG>gtT	p.V6V	FMR1-AS1_ENST00000598667.1_RNA|FMR1-AS1_ENST00000596112.1_RNA|FMR1_ENST00000370471.3_Silent_p.V6V|FMR1_ENST00000439526.2_Silent_p.V6V|FMR1_ENST00000370477.1_Silent_p.V6V|FMR1_ENST00000370470.1_Silent_p.V6V|FMR1-AS1_ENST00000594922.1_RNA|FMR1_ENST00000218200.8_Silent_p.V6V|FMR1_ENST00000334557.6_Silent_p.V6V	NM_002024.5	NP_002015.1	Q06787	FMR1_HUMAN	fragile X mental retardation 1	6	Agenet-like 1.				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)					AGCTGGTGGTGGAAGTGCGGG	0.677									Fragile X syndrome				G|||	15	0.00397351	0.0	0.0029	3775	,	,		5155	0.0		0.0129	False		,,,				2504	0.0				p.V6V		Atlas-SNP	.											.	FMR1	93	.	0			c.G18T						PASS	.	G	,,,,	6,3525		0,6,0,1538,443	76	50	59		18,18,18,18,18	4	1	X	dbSNP_132	59	79,6026		0,62,17,2208,1548	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FMR1	NM_001185075.1,NM_001185076.1,NM_001185081.1,NM_001185082.1,NM_002024.5	,,,,	0,68,17,3746,1991	TT,TG,T,GG,G		1.294,0.1699,0.8821	,,,,	6/538,6/612,6/517,6/587,6/633	146993715	85,9551	1987	3835	5822	SO:0001819	synonymous_variant	2332	exon1	Familial Cancer Database	Martin-Bell syndrome, FRAXA syndrome	GGTGGTGGAAGTG	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.18G>T	X.37:g.146993715G>T		94	0	0		114	113	0.991228	NM_002024	A6NNH4|D3DWT0|D3DWT1|D3DWT2|G8JL90|Q16578|Q5PQZ6|Q99054	Silent	SNP	ENST00000370475.4	37	CCDS14682.1																																																																																			C|0.000;G|0.987;T|0.013	0.013	strong		0.677	FMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058655.1	NM_002024		T	146993715	G	T	146993715	2	4	25	1	0	0	0	0	0	0	0	1	5968	1335	47	4		4	FMR1	23	146993715	Silent	SNP	G	TCGA-G8-6906-01A-11D-2210-10	7127291	146993715	8276845	852	9761											
MAGEA6	4105	hgsc.bcm.edu	37	chrX	151870117	151870117	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagtgatcctgcatgctaTgagttcctgtggggtccaag	7	11	14	9	0	0	2	0	2	0	0	3	2	3	2	3	3	2	4	3	3	2	2	rs369345489		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:151870117T>C	ENST00000329342.5	+	3	1032	c.807T>C	c.(805-807)taT>taC	p.Y269Y		NM_005363.2	NP_005354.1	P43360	MAGA6_HUMAN	melanoma antigen family A, 6	269	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									breast(1)|endometrium(3)|large_intestine(3)|lung(16)|prostate(3)|skin(1)|urinary_tract(1)	28	Acute lymphoblastic leukemia(192;6.56e-05)					CTGCATGCTATGAGTTCCTGT	0.527																																					p.Y269Y		Atlas-SNP	.											.	MAGEA6	53	.	0			c.T807C						PASS	.	T	,	0,3834		0,0,0,1632,570	139	136	137		807,807	-1.8	0	X		137	2,6726		0,1,1,2427,1871	no	coding-synonymous,coding-synonymous	MAGEA6	NM_005363.2,NM_175868.1	,	0,1,1,4059,2441	CC,CT,C,TT,T		0.0297,0.0,0.0189	,	269/315,269/315	151870117	2,10560	2202	4300	6502	SO:0001819	synonymous_variant	4105	exon3			ATGCTATGAGTTC		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.807T>C	X.37:g.151870117T>C		119	0	0		92	91	0.98913	NM_005363	A8IF93|Q6NW44	Silent	SNP	ENST00000329342.5	37	CCDS14708.1																																																																																			.	.	weak		0.527	MAGEA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058747.2	NM_005363		C	151870117	T	C	151870117	2	2	25	1	0	0	0	0	0	0	0	1	9179	1471	51	3		3	MAGEA6	23	151870117	Silent	SNP	T	TCGA-G8-6906-01A-11D-2210-10	4876402	151870117	3400443	853	9762											
TKTL1	8277	hgsc.bcm.edu	37	chrX	153537783	153537783	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcatatactggcaagtacttCgacagggccaggtgaggttc	10	9	13	9	1	0	1	0	1	0	0	2	2	0	1	1	4	2	4	1	4	4	5			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:153537783C>T	ENST00000369915.3	+	3	528	c.339C>T	c.(337-339)ttC>ttT	p.F113F	TKTL1_ENST00000217905.7_Intron|TKTL1_ENST00000369912.2_Silent_p.F57F	NM_001145933.1|NM_012253.3	NP_001139405.1|NP_036385.3	P51854	TKTL1_HUMAN	transketolase-like 1	113					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)	p.F113F(1)		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)					GCAAGTACTTCGACAGGGCCA	0.537																																					p.F113F		Atlas-SNP	.											.	TKTL1	61	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C339T						PASS	.						252	213	226					X																	153537783		2203	4300	6503	SO:0001819	synonymous_variant	8277	exon3			GTACTTCGACAGG	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.339C>T	X.37:g.153537783C>T		56	0	0		53	53	1	NM_012253	A8K896|Q5TYJ8|Q5TYJ9|Q8TC75	Silent	SNP	ENST00000369915.3	37	CCDS35448.1	.	.	.	.	.	.	.	.	.	.	C	4.122	0.020848	0.08006	.	.	ENSG00000007350	ENST00000426203	.	.	.	4.64	-1.03	0.10102	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.2143	4.8078	0.13328	0.0:0.2949:0.1505:0.5547	.	.	.	.	X	96	.	.	R	+	1	2	TKTL1	153190977	0.998000	0.40836	0.927000	0.36925	0.416000	0.31233	0.367000	0.20382	-0.364000	0.08088	-0.380000	0.06706	CGA	.	.	none		0.537	TKTL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058923.1	NM_012253		T	153537783	C	T	153537783	2	4	25	1	0	0	0	0	0	0	0	1	15950	883	31	1		1	TKTL1	23	153537783	Silent	SNP	C	TCGA-G8-6906-01A-11D-2210-10	1667666	153537783	1732777	854	9763											
AGRN	375790	hgsc.bcm.edu	37	chr1	985377	985377	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cccgagggtggtgctcagtgCgagtgccccctggggcgtga	4	7	18	12	3	1	1	1	1	0	0	1	3	1	1	3	4	3	1	3	4	0	0	rs113020870	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:985377C>T	ENST00000379370.2	+	27	4889	c.4839C>T	c.(4837-4839)tgC>tgT	p.C1613C		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	1613	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)		GTGCTCAGTGCGAGTGCCCCC	0.716													C|||	6	0.00119808	0.0	0.0043	5008	,	,		7759	0.0		0.002	False		,,,				2504	0.001				p.C1613C		Atlas-SNP	.											.	AGRN	110	.	0			c.C4839T						PASS	.	C		6,4366		0,6,2180	16	17	16		4839	0.6	0.7	1	dbSNP_132	16	26,8532		0,26,4253	no	coding-synonymous	AGRN	NM_198576.3		0,32,6433	TT,TC,CC		0.3038,0.1372,0.2475		1613/2046	985377	32,12898	2186	4279	6465	SO:0001819	synonymous_variant	375790	exon27			TCAGTGCGAGTGC	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.4839C>T	1.37:g.985377C>T		67	0	0		65	41	0.630769	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Silent	SNP	ENST00000379370.2	37	CCDS30551.1																																																																																			C|0.998;T|0.002	0.002	strong		0.716	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576		T	985377	C	T	985377	2	4	26	1	0	0	0	0	0	0	0	1	397	776	27	1		1	AGRN	1	985377	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10		985377	248265244	1	9764											
AGRN	375790	hgsc.bcm.edu	37	chr1	989207	989207	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaggggctggtgctctggaGtggcaaggccacggagcggg	6	5	21	9	2	1	0	0	0	1	0	1	2	1	2	1	8	2	4	1	8	1	0	rs74685771	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:989207G>C	ENST00000379370.2	+	34	5776	c.5726G>C	c.(5725-5727)aGt>aCt	p.S1909T	RP11-54O7.14_ENST00000418300.1_RNA	NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	1931	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				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)		GTGCTCTGGAGTGGCAAGGCC	0.652													G|||	45	0.00898562	0.0	0.0519	5008	,	,		19298	0.0089		0.0	False		,,,				2504	0.0				p.S1909T		Atlas-SNP	.											.	AGRN	110	.	0			c.G5726C						PASS	.	G	THR/SER	7,4393	9.9+/-24.2	0,7,2193	44	36	39		5726	-0.8	0.2	1	dbSNP_132	39	5,8587	5.0+/-18.6	0,5,4291	yes	missense	AGRN	NM_198576.3	58	0,12,6484	CC,CG,GG		0.0582,0.1591,0.0924	benign	1909/2046	989207	12,12980	2200	4296	6496	SO:0001583	missense	375790	exon34			TCTGGAGTGGCAA	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.5726G>C	1.37:g.989207G>C	ENSP00000368678:p.Ser1909Thr	205	0	0		237	123	0.518987	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Missense_Mutation	SNP	ENST00000379370.2	37	CCDS30551.1	19|19	0.0086996336996337|0.0086996336996337	0|0	0.0|0.0	13|13	0.03591160220994475|0.03591160220994475	6|6	0.01048951048951049|0.01048951048951049	0|0	0.0|0.0	G|G	1.487|1.487	-0.555666|-0.555666	0.03967|0.03967	0.001591|0.001591	5.82E-4|5.82E-4	ENSG00000188157|ENSG00000188157	ENST00000419249|ENST00000379370;ENST00000379364	.|T	.|0.78595	.|-1.19	3.95|3.95	-0.779|-0.779	0.10973|0.10973	.|Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	.|0.141330	.|0.44902	.|D	.|0.000411	T|T	0.43166|0.43166	0.1235|0.1235	L|L	0.45285|0.45285	1.41|1.41	0.40815|0.40815	D|D	0.98345|0.98345	.|B	.|0.22346	.|0.068	.|B	.|0.42422	.|0.387	T|T	0.49495|0.49495	-0.8934|-0.8934	5|10	.|0.09338	.|T	.|0.73	-3.2936|-3.2936	12.7066|12.7066	0.57063|0.57063	0.0:0.0:0.4308:0.5692|0.0:0.0:0.4308:0.5692	.|.	.|1909	.|O00468	.|AGRIN_HUMAN	D|T	230|1909;271	.|ENSP00000368678:S1909T	.|ENSP00000368671:S271T	E|S	+|+	3|2	2|0	AGRN|AGRN	979070|979070	1.000000|1.000000	0.71417|0.71417	0.215000|0.215000	0.23724|0.23724	0.135000|0.135000	0.20990|0.20990	4.270000|4.270000	0.58896|0.58896	-0.358000|-0.358000	0.08162|0.08162	-0.521000|-0.521000	0.04368|0.04368	GAG|AGT	G|0.997;C|0.003	0.003	strong		0.652	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576		C	989207	G	C	989207	3	2	26	1	0	0	0	0	1	0	0	0	397	1029	36	4	5860	4	AGRN	1	989207	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	3830	989207	248261414	2	9765											
MEGF6	1953	hgsc.bcm.edu	37	chr1	3418428	3418428	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccgtgaccccgtggcaggggGcccccccacaggagcaggag	7	2	16	16	2	0	1	0	1	0	0	0	3	0	3	6	5	1	2	6	5	0	0	rs200472001	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:3418428G>A	ENST00000356575.4	-	18	2472	c.2246C>T	c.(2245-2247)gCc>gTc	p.A749V	MEGF6_ENST00000294599.4_Missense_Mutation_p.A644V	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	749	EGF-like 12. {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)		GTGGCAGGGGGCCCCCCCACA	0.697													G|||	9	0.00179712	0.0	0.0	5008	,	,		14048	0.0		0.001	False		,,,				2504	0.0082				p.A749V	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.C2246T						PASS	.	G	VAL/ALA	0,3974		0,0,1987	21	30	27		2246	2.6	0.1	1		27	8,8250		0,8,4121	yes	missense	MEGF6	NM_001409.3	64	0,8,6108	AA,AG,GG		0.0969,0.0,0.0654	probably-damaging	749/1542	3418428	8,12224	1987	4129	6116	SO:0001583	missense	1953	exon18			CAGGGGGCCCCCC	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.2246C>T	1.37:g.3418428G>A	ENSP00000348982:p.Ala749Val	251	1	0.00398406		250	137	0.548	NM_001409	Q4AC86|Q5VV39	Missense_Mutation	SNP	ENST00000356575.4	37	CCDS41237.1	.	.	.	.	.	.	.	.	.	.	G	12.47	1.947341	0.34377	0.0	9.69E-4	ENSG00000162591	ENST00000294599;ENST00000356575	T;T	0.33438	1.41;1.41	3.58	2.61	0.31194	EGF-like, laminin (1);Epidermal growth factor-like, type 3 (1);	0.071934	0.53938	U	0.000043	T	0.59702	0.2213	M	0.91038	3.17	0.32858	D	0.507526	D;D	0.76494	0.999;0.999	D;D	0.72982	0.979;0.979	T	0.73177	-0.4065	10	0.66056	D	0.02	-11.9588	11.1649	0.48537	0.0:0.1871:0.8129:0.0	.	749;644	O75095;O75095-2	MEGF6_HUMAN;.	V	644;749	ENSP00000294599:A644V;ENSP00000348982:A749V	ENSP00000294599:A644V	A	-	2	0	MEGF6	3408288	0.993000	0.37304	0.112000	0.21494	0.318000	0.28184	4.377000	0.59562	0.548000	0.28955	0.455000	0.32223	GCC	G|0.996;A|0.004	0.004	strong		0.697	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409		A	3418428	G	A	3418428	3	1	26	1	0	0	0	0	1	0	0	0	9471	1203	42	2	2459	2	MEGF6	1	3418428	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	2429221	3418428	245832193	3	9766											
NPHP4	261734	hgsc.bcm.edu	37	chr1	5935096	5935096	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgatgctctcggccttcgtgCgttcccggtaggcggcgatg	3	10	15	13	7	1	0	0	0	1	0	4	2	2	0	2	4	2	3	2	4	1	3	rs183885357	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:5935096C>T	ENST00000378156.4	-	21	3147	c.2882G>A	c.(2881-2883)cGc>cAc	p.R961H	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	961			R -> H (in NPHP4; dbSNP:rs183885357). {ECO:0000269|PubMed:15776426}.		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)		GGCCTTCGTGCGTTCCCGGTA	0.652													c|||	6	0.00119808	0.0	0.0029	5008	,	,		17500	0.0		0.004	False		,,,				2504	0.0				p.R961H		Atlas-SNP	.											.	NPHP4	119	.	0			c.G2882A	GRCh37	CM051580	NPHP4	M	rs183885357	PASS	.		HIS/ARG	6,4380	11.4+/-27.6	0,6,2187	63	78	73		2882	4.9	0.9	1		73	35,8527	23.4+/-69.3	0,35,4246	yes	missense	NPHP4	NM_015102.3	29	0,41,6433	TT,TC,CC		0.4088,0.1368,0.3167	possibly-damaging	961/1427	5935096	41,12907	2193	4281	6474	SO:0001583	missense	261734	exon21			TTCGTGCGTTCCC	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.2882G>A	1.37:g.5935096C>T	ENSP00000367398:p.Arg961His	61	0	0		72	33	0.458333	NM_015102	Q8IWC0	Missense_Mutation	SNP	ENST00000378156.4	37	CCDS44052.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	2	0.0034965034965034965	3	0.00395778364116095	c	12.12	1.841986	0.32513	0.001368	0.004088	ENSG00000131697	ENST00000378156	D	0.88431	-2.38	4.88	4.88	0.63580	.	0.074186	0.53938	D	0.000041	D	0.90188	0.6933	M	0.75264	2.295	0.48511	D	0.999666	D	0.56746	0.977	P	0.48840	0.592	D	0.90860	0.4738	10	0.56958	D	0.05	.	12.536	0.56142	0.0:0.9169:0.0:0.0831	.	961	O75161	NPHP4_HUMAN	H	961	ENSP00000367398:R961H	ENSP00000367398:R961H	R	-	2	0	NPHP4	5857683	1.000000	0.71417	0.923000	0.36655	0.015000	0.08874	3.579000	0.53900	2.272000	0.75746	0.550000	0.68814	CGC	C|0.996;T|0.004	0.004	strong		0.652	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2			T	5935096	C	T	5935096	3	4	26	1	0	0	0	0	1	0	0	0	10590	768	27	1	1438	1	NPHP4	1	5935096	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	2516668	5935096	243315525	4	9767											
TNFRSF9	3604	hgsc.bcm.edu	37	chr1	7995152	7995152	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagatggtccacagaccacGtccctctccttcgtcccatt	7	10	8	16	2	1	2	0	0	1	2	6	3	4	2	5	2	0	0	5	2	0	2	rs373859958		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:7995152G>A	ENST00000377507.3	-	6	631	c.465C>T	c.(463-465)gaC>gaT	p.D155D		NM_001561.5	NP_001552.2	Q07011	TNR9_HUMAN	tumor necrosis factor receptor superfamily, member 9	155					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19	Ovarian(185;0.0634)|all_lung(157;0.151)	all_epithelial(116;9.63e-21)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.000625)|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;2.93e-71)|GBM - Glioblastoma multiforme(8;3.72e-37)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;7.71e-06)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000419)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00103)|READ - Rectum adenocarcinoma(331;0.0649)		CACAGACCACGTCCCTCTCCT	0.502																																					p.D155D		Atlas-SNP	.											.	TNFRSF9	50	.	0			c.C465T						PASS	.						105	88	94					1																	7995152		2203	4300	6503	SO:0001819	synonymous_variant	3604	exon7			GACCACGTCCCTC	L12964	CCDS92.1	1p36	2008-02-05			ENSG00000049249	ENSG00000049249		"Tumor necrosis factor receptor superfamily", "CD molecules"	11924	protein-coding gene	gene with protein product		602250		ILA		8262389, 8639902	Standard	NM_001561		Approved	CD137, 4-1BB	uc001aot.3	Q07011	OTTHUMG00000001223	ENST00000377507.3:c.465C>T	1.37:g.7995152G>A		137	0	0		130	56	0.430769	NM_001561		Silent	SNP	ENST00000377507.3	37	CCDS92.1																																																																																			.	.	none		0.502	TNFRSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003622.1			A	7995152	G	A	7995152	2	1	26	1	0	0	0	0	0	0	0	1	16315	1136	40	1		1	TNFRSF9	1	7995152	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	2060056	7995152	241255469	5	9768											
RERE	473	hgsc.bcm.edu	37	chr1	8421186	8421186	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggatgtgggtgtggggaacaGgcgctgtgggagcctgtggc	5	8	22	6	1	0	0	0	0	0	0	0	3	0	3	1	7	2	1	1	7	1	0	rs201922249	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:8421186G>A	ENST00000337907.3	-	19	3015	c.2381C>T	c.(2380-2382)cCt>cTt	p.P794L	RERE_ENST00000400907.2_Intron|RERE_ENST00000476556.1_Missense_Mutation_p.P240L|RERE_ENST00000377464.1_Missense_Mutation_p.P526L|RERE_ENST00000400908.2_Missense_Mutation_p.P794L	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	794	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)		GTGGGGAACAGGCGCTGTGGG	0.731													G|||	25	0.00499201	0.0	0.0101	5008	,	,		12737	0.0		0.0159	False		,,,				2504	0.002				p.P794L		Atlas-SNP	.											.	RERE	129	.	0			c.C2381T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO	16,4116		0,16,2050	8	9	9		2381,719,2381	4.2	0	1		9	135,8059		1,133,3963	yes	missense,missense,missense	RERE	NM_012102.3,NM_001042682.1,NM_001042681.1	98,98,98	1,149,6013	AA,AG,GG		1.6475,0.3872,1.2251	benign,benign,benign	794/1567,240/1013,794/1567	8421186	151,12175	2066	4097	6163	SO:0001583	missense	473	exon19			GGAACAGGCGCTG	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.2381C>T	1.37:g.8421186G>A	ENSP00000338629:p.Pro794Leu	21	0	0		19	13	0.684211	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Missense_Mutation	SNP	ENST00000337907.3	37	CCDS95.1	14	0.00641025641025641	0	0.0	5	0.013812154696132596	0	0.0	9	0.011873350923482849	G	20.8	4.057756	0.76074	0.003872	0.016475	ENSG00000142599	ENST00000337907;ENST00000377464;ENST00000476556;ENST00000400908	T;T;T	0.46063	0.88;0.89;0.88	5.15	4.24	0.50183	.	.	.	.	.	T	0.22513	0.0543	L	0.44542	1.39	0.37189	D	0.903842	B;B	0.27910	0.193;0.005	B;B	0.31390	0.129;0.038	T	0.35599	-0.9782	9	0.54805	T	0.06	-2.2502	12.4483	0.55664	0.0824:0.0:0.9176:0.0	.	526;794	B1AKN3;Q9P2R6	.;RERE_HUMAN	L	794;526;240;794	ENSP00000338629:P794L;ENSP00000366684:P526L;ENSP00000383700:P794L	ENSP00000338629:P794L	P	-	2	0	RERE	8343773	0.692000	0.27719	0.002000	0.10522	0.010000	0.07245	4.289000	0.59013	1.299000	0.44798	0.561000	0.74099	CCT	G|0.994;A|0.006	0.006	strong		0.731	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1			A	8421186	G	A	8421186	3	1	26	1	0	0	0	0	1	0	0	0	13246	1000	35	2	2343	2	RERE	1	8421186	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	426034	8421186	240829435	6	9769											
DFFA	1676	hgsc.bcm.edu	37	chr1	10529326	10529326	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtaatcgtcatcatccactAtggtgccatcctctgccagg	9	11	8	13	1	3	0	2	0	1	0	6	0	5	0	4	2	2	1	4	2	2	2	rs138842024	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:10529326A>G	ENST00000377038.3	-	2	273	c.206T>C	c.(205-207)aTa>aCa	p.I69T	DFFA_ENST00000377036.2_Missense_Mutation_p.I69T	NM_004401.2	NP_004392.1	O00273	DFFA_HUMAN	DNA fragmentation factor, 45kDa, alpha polypeptide	69	CIDE-N. {ECO:0000255|PROSITE- ProRule:PRU00447}.				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)		ATCATCCACTATGGTGCCATC	0.423													A|||	11	0.00219649	0.0	0.0043	5008	,	,		21849	0.0		0.006	False		,,,				2504	0.002				p.I69T		Atlas-SNP	.											.	DFFA	24	.	0			c.T206C						PASS	.	A	THR/ILE,THR/ILE	5,4401	9.9+/-24.2	0,5,2198	152	132	139		206,206	5.5	1	1	dbSNP_134	139	38,8562	25.7+/-73.6	0,38,4262	yes	missense,missense	DFFA	NM_004401.2,NM_213566.1	89,89	0,43,6460	GG,GA,AA		0.4419,0.1135,0.3306	probably-damaging,probably-damaging	69/332,69/269	10529326	43,12963	2203	4300	6503	SO:0001583	missense	1676	exon2			TCCACTATGGTGC	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.206T>C	1.37:g.10529326A>G	ENSP00000366237:p.Ile69Thr	225	0	0		272	135	0.496324	NM_004401	Q5T6G5|Q5T6G6|Q96I97|Q9Y6C6	Missense_Mutation	SNP	ENST00000377038.3	37	CCDS118.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	A	19.98	3.927190	0.73327	0.001135	0.004419	ENSG00000160049	ENST00000377038;ENST00000377036	.	.	.	5.49	5.49	0.81192	Caspase-activated nuclease CIDE-N (3);	0.000000	0.85682	D	0.000000	T	0.66752	0.2821	L	0.48362	1.52	0.58432	D	0.999998	D;D	0.89917	0.999;1.0	D;D	0.97110	0.991;1.0	T	0.69639	-0.5091	9	0.37606	T	0.19	-14.8227	15.6132	0.76744	1.0:0.0:0.0:0.0	.	69;69	O00273-2;O00273	.;DFFA_HUMAN	T	69	.	ENSP00000366235:I69T	I	-	2	0	DFFA	10451913	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.677000	0.84024	2.076000	0.62316	0.533000	0.62120	ATA	A|0.997;G|0.003	0.003	strong		0.423	DFFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005418.1	NM_004401		G	10529326	A	G	10529326	3	3	26	1	0	0	0	0	1	0	0	0	4454	449	16	3	833	3	DFFA	1	10529326	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	2108140	10529326	238721295	7	9770											
SPEN	23013	hgsc.bcm.edu	37	chr1	16255799	16255799	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcaaaaaagcagcctgacGtgtcctctagagaggtcatt	12	11	9	9	1	3	2	2	1	1	1	4	3	4	2	2	1	2	1	2	1	4	3	rs115566585	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:16255799G>A	ENST00000375759.3	+	11	3268	c.3064G>A	c.(3064-3066)Gtg>Atg	p.V1022M		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1022					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)		GCAGCCTGACGTGTCCTCTAG	0.423													G|||	12	0.00239617	0.0	0.0115	5008	,	,		20147	0.0		0.004	False		,,,				2504	0.0				p.V1022M		Atlas-SNP	.											.	SPEN	374	.	0			c.G3064A						PASS	.	G	MET/VAL	2,4404	2.1+/-5.4	0,2,2201	46	53	51		3064	-5.8	0	1	dbSNP_132	51	31,8569	18.5+/-59.3	0,31,4269	yes	missense	SPEN	NM_015001.2	21	0,33,6470	AA,AG,GG		0.3605,0.0454,0.2537	benign	1022/3665	16255799	33,12973	2203	4300	6503	SO:0001583	missense	23013	exon11			CCTGACGTGTCCT		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.3064G>A	1.37:g.16255799G>A	ENSP00000364912:p.Val1022Met	129	0	0		149	75	0.503356	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	5	0.0022893772893772895	0	0.0	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	0.012	-1.676123	0.00751	4.54E-4	0.003605	ENSG00000065526	ENST00000375759	T	0.09445	2.98	5.13	-5.85	0.02311	.	.	.	.	.	T	0.02304	0.0071	N	0.03608	-0.345	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.41233	-0.9520	9	0.42905	T	0.14	6.4781	3.6799	0.08306	0.2371:0.3302:0.3421:0.0907	.	1022	Q96T58	MINT_HUMAN	M	1022	ENSP00000364912:V1022M	ENSP00000364912:V1022M	V	+	1	0	SPEN	16128386	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	-1.308000	0.02730	-0.807000	0.04393	-0.150000	0.13652	GTG	G|0.998;A|0.002	0.002	strong		0.423	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		A	16255799	G	A	16255799	3	1	26	1	0	0	0	0	1	0	0	0	15053	1145	40	1	3106	1	SPEN	1	16255799	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	5726473	16255799	232994822	8	9771											
EPHA2	1969	hgsc.bcm.edu	37	chr1	16456763	16456763	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttgagggagtcaggggcaCgaatgagcttgtccaggatg	9	9	16	7	1	2	2	1	2	1	0	3	5	3	4	1	4	1	2	1	4	1	2	rs35903225	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:16456763C>T	ENST00000358432.5	-	15	2781	c.2627G>A	c.(2626-2628)cGt>cAt	p.R876H		NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2	876	Mediates interaction with ARHGEF16 and ELMO2.		R -> H (in dbSNP:rs35903225). {ECO:0000269|PubMed:17344846}.		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)	GTCAGGGGCACGAATGAGCTT	0.582													C|||	39	0.00778754	0.0015	0.0144	5008	,	,		17836	0.002		0.0239	False		,,,				2504	0.001				p.R876H		Atlas-SNP	.											.	EPHA2	102	.	0			c.G2627A						PASS	.	C	HIS/ARG	34,4372	39.2+/-71.8	0,34,2169	99	93	95		2627	5.6	1	1	dbSNP_126	95	220,8380	92.8+/-154.8	0,220,4080	yes	missense	EPHA2	NM_004431.3	29	0,254,6249	TT,TC,CC		2.5581,0.7717,1.9529	probably-damaging	876/977	16456763	254,12752	2203	4300	6503	SO:0001583	missense	1969	exon15			GGGGCACGAATGA	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.2627G>A	1.37:g.16456763C>T	ENSP00000351209:p.Arg876His	253	0	0		309	148	0.478964	NM_004431	B5A968|Q8N3Z2	Missense_Mutation	SNP	ENST00000358432.5	37	CCDS169.1	23	0.010531135531135532	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	16	0.021108179419525065	C	29.2	4.986612	0.93106	0.007717	0.025581	ENSG00000142627	ENST00000358432	T	0.62364	0.03	5.63	5.63	0.86233	Protein kinase-like domain (1);	0.000000	0.49305	D	0.000155	T	0.56775	0.2008	M	0.84326	2.69	0.80722	D	1	D	0.76494	0.999	P	0.55112	0.769	T	0.74671	-0.3587	10	0.87932	D	0	.	18.2443	0.89979	0.0:1.0:0.0:0.0	rs35903225;rs61731099	876	P29317	EPHA2_HUMAN	H	876	ENSP00000351209:R876H	ENSP00000351209:R876H	R	-	2	0	EPHA2	16329350	1.000000	0.71417	0.962000	0.40283	0.926000	0.56050	4.709000	0.61867	2.670000	0.90874	0.655000	0.94253	CGT	C|0.983;T|0.017	0.017	strong		0.582	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	NM_004431		T	16456763	C	T	16456763	3	4	26	1	0	0	0	0	1	0	0	0	5169	536	19	1	315	1	EPHA2	1	16456763	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	200964	16456763	232793858	9	9772											
SPATA21	374955	hgsc.bcm.edu	37	chr1	16748432	16748432	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgcttttttaggtccaggCgtggatggcaggaaggggtt	6	14	16	5	1	0	0	0	0	0	0	1	2	1	2	1	7	1	3	1	7	2	5	rs114456729	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:16748432C>T	ENST00000335496.1	-	4	551	c.69G>A	c.(67-69)acG>acA	p.T23T	SPATA21_ENST00000540400.1_Intron|SPATA21_ENST00000466212.1_5'UTR	NM_198546.1	NP_940948.1	Q7Z572	SPT21_HUMAN	spermatogenesis associated 21	23							calcium ion binding (GO:0005509)	p.T23T(1)		breast(1)|endometrium(2)|lung(8)|ovary(2)|pancreas(3)|stomach(1)|urinary_tract(2)	19		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;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;4.2e-05)|Kidney(64;0.000183)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.0122)|READ - Rectum adenocarcinoma(331;0.0651)		TAGGTCCAGGCGTGGATGGCA	0.562													C|||	122	0.024361	0.0015	0.036	5008	,	,		19316	0.001		0.0726	False		,,,				2504	0.0215				p.T23T		Atlas-SNP	.											SPATA21,NS,carcinoma,-1,2	SPATA21	47	2	1	Substitution - coding silent(1)	pancreas(1)	c.G69A						PASS	.	C		57,4349	54.9+/-90.9	0,57,2146	219	207	211		69	-2.2	0	1	dbSNP_132	211	600,8000	158.9+/-212.3	23,554,3723	no	coding-synonymous	SPATA21	NM_198546.1		23,611,5869	TT,TC,CC		6.9767,1.2937,5.0515		23/470	16748432	657,12349	2203	4300	6503	SO:0001819	synonymous_variant	374955	exon4			TCCAGGCGTGGAT		CCDS172.1	1p36.13	2013-01-10			ENSG00000187144	ENSG00000187144		"EF-hand domain containing"	28026	protein-coding gene	gene with protein product							Standard	NM_198546		Approved	spergen-2, spergen2	uc001ayn.3	Q7Z572	OTTHUMG00000002312	ENST00000335496.1:c.69G>A	1.37:g.16748432C>T		96	0	0		129	73	0.565891	NM_198546	B9EK40|F5GXP5	Silent	SNP	ENST00000335496.1	37	CCDS172.1																																																																																			C|0.954;T|0.046	0.046	strong		0.562	SPATA21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006677.2	NM_198546		T	16748432	C	T	16748432	2	4	26	1	0	0	0	0	0	0	0	1	15022	755	27	1		1	SPATA21	1	16748432	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	291669	16748432	232502189	10	9773											
IGSF21	84966	hgsc.bcm.edu	37	chr1	18692089	18692089	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgtggaagtacgtgccctgCtcacctggaccctcaaccca	8	8	9	16	1	2	0	2	0	0	0	2	2	2	2	4	2	4	2	4	2	3	1			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:18692089C>T	ENST00000251296.1	+	6	1296	c.913C>T	c.(913-915)Ctc>Ttc	p.L305F		NM_032880.4	NP_116269.3	Q96ID5	IGS21_HUMAN	immunoglobin superfamily, member 21	305						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)		ACGTGCCCTGCTCACCTGGAC	0.647																																					p.L305F		Atlas-SNP	.											.	IGSF21	87	.	0			c.C913T						PASS	.						117	95	103					1																	18692089		2203	4300	6503	SO:0001583	missense	84966	exon6			GCCCTGCTCACCT	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.913C>T	1.37:g.18692089C>T	ENSP00000251296:p.Leu305Phe	150	0	0		194	97	0.5	NM_032880	Q8NBR8	Missense_Mutation	SNP	ENST00000251296.1	37	CCDS184.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.6|25.6	4.654766|4.654766	0.88056|0.88056	.|.	.|.	ENSG00000117154|ENSG00000117154	ENST00000412684|ENST00000251296	.|T	.|0.31510	.|1.49	4.28|4.28	4.28|4.28	0.50868|0.50868	.|Immunoglobulin-like fold (1);	.|0.120807	.|0.56097	.|D	.|0.000037	T|T	0.35451|0.35451	0.0932|0.0932	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	.|D	.|0.65815	.|0.995	.|P	.|0.56278	.|0.795	T|T	0.03231|0.03231	-1.1058|-1.1058	5|10	.|0.22109	.|T	.|0.4	-13.5806|-13.5806	15.7859|15.7859	0.78304|0.78304	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|305	.|Q96ID5	.|IGS21_HUMAN	V|F	257|305	.|ENSP00000251296:L305F	.|ENSP00000251296:L305F	A|L	+|+	2|1	0|0	IGSF21|IGSF21	18564676|18564676	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.976000|0.976000	0.68499|0.68499	4.004000|4.004000	0.57068|0.57068	2.383000|2.383000	0.81215|0.81215	0.561000|0.561000	0.74099|0.74099	GCT|CTC	.	.	none		0.647	IGSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006924.1	NM_032880		T	18692089	C	T	18692089	3	4	26	1	0	0	0	0	1	0	0	0	7608	797	28	2	935	2	IGSF21	1	18692089	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1943657	18692089	230558532	11	9774											
HSPG2	3339	hgsc.bcm.edu	37	chr1	22169926	22169926	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcagcctcagcagtgggccGtggacctggccaaggtgggg	6	7	17	11	1	2	0	2	0	0	0	2	1	2	1	4	6	2	1	4	6	1	1	rs62642513	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:22169926G>A	ENST00000374695.3	-	66	8701	c.8622C>T	c.(8620-8622)caC>caT	p.H2874H		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2874	Ig-like C2-type 14.				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)	GCAGTGGGCCGTGGACCTGGC	0.652													G|||	251	0.0501198	0.1589	0.0274	5008	,	,		16760	0.0		0.0189	False		,,,				2504	0.0031				p.H2874H		Atlas-SNP	.											.	HSPG2	311	.	0			c.C8622T						PASS	.	G		716,3690	288.1+/-279.7	60,596,1547	33	35	34		8622	-3	0.7	1	dbSNP_129	34	170,8430	75.4+/-138.0	2,166,4132	no	coding-synonymous	HSPG2	NM_005529.5		62,762,5679	AA,AG,GG		1.9767,16.2506,6.8122		2874/4392	22169926	886,12120	2203	4300	6503	SO:0001819	synonymous_variant	3339	exon66			TGGGCCGTGGACC	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.8622C>T	1.37:g.22169926G>A		110	0	0		138	62	0.449275	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																			G|0.935;A|0.065	0.065	strong		0.652	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		A	22169926	G	A	22169926	2	1	26	1	0	0	0	0	0	0	0	1	7439	1136	40	1		1	HSPG2	1	22169926	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	3477837	22169926	227080695	12	9775											
HSPG2	3339	hgsc.bcm.edu	37	chr1	22182115	22182115	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggctcgacagctggcaggcGcaggatgccgccgtggattt	6	7	17	11	4	0	0	0	0	0	0	1	3	0	2	2	5	2	4	2	5	0	1	rs2229474	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:22182115G>A	ENST00000374695.3	-	46	5834	c.5755C>T	c.(5755-5757)Cgc>Tgc	p.R1919C	HSPG2_ENST00000430507.1_5'Flank	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	1919	Ig-like C2-type 4.		R -> C (in dbSNP:rs2229474).		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)	GCTGGCAGGCGCAGGATGCCG	0.687													G|||	10	0.00199681	0.0	0.0014	5008	,	,		13927	0.001		0.008	False		,,,				2504	0.0				p.R1919C		Atlas-SNP	.											.	HSPG2	311	.	0			c.C5755T						PASS	.	G	CYS/ARG	9,4359		0,9,2175	13	13	13		5755	5.1	1	1	dbSNP_98	13	74,8476		0,74,4201	no	missense	HSPG2	NM_005529.5	180	0,83,6376	AA,AG,GG		0.8655,0.206,0.6425	probably-damaging	1919/4392	22182115	83,12835	2184	4275	6459	SO:0001583	missense	3339	exon46			GCAGGCGCAGGAT	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.5755C>T	1.37:g.22182115G>A	ENSP00000363827:p.Arg1919Cys	82	0	0		52	28	0.538462	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	9	0.004120879120879121	2	0.0040650406504065045	1	0.0027624309392265192	1	0.0017482517482517483	5	0.006596306068601583	G	14.28	2.487173	0.44249	0.00206	0.008655	ENSG00000142798	ENST00000374695	T	0.69435	-0.4	5.12	5.12	0.69794	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.181406	0.26939	N	0.021731	T	0.80385	0.4613	M	0.89353	3.025	0.41354	D	0.987383	D	0.89917	1.0	D	0.91635	0.999	D	0.85946	0.1461	10	0.72032	D	0.01	.	16.0425	0.80695	0.0:0.0:1.0:0.0	rs2229474	1919	P98160	PGBM_HUMAN	C	1919	ENSP00000363827:R1919C	ENSP00000363827:R1919C	R	-	1	0	HSPG2	22054702	1.000000	0.71417	1.000000	0.80357	0.027000	0.11550	2.974000	0.49272	2.399000	0.81585	0.462000	0.41574	CGC	G|0.994;A|0.006	0.006	strong		0.687	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		A	22182115	G	A	22182115	3	1	26	1	0	0	0	0	1	0	0	0	7439	1087	38	1	7628	1	HSPG2	1	22182115	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	12189	22182115	227068506	13	9776											
HSPG2	3339	hgsc.bcm.edu	37	chr1	22200998	22200998	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggctggcactgctcacacCgagggccctccgtgtgatgc	5	8	13	15	2	1	1	1	1	0	0	2	2	2	1	3	3	2	3	3	3	0	0	rs2229481	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:22200998C>T	ENST00000374695.3	-	28	3636	c.3557G>A	c.(3556-3558)cGg>cAg	p.R1186Q		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	1186	Laminin EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00460}.		R -> Q (in dbSNP:rs2229481).		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)	CTGCTCACACCGAGGGCCCTC	0.682													C|||	320	0.0638978	0.1967	0.0432	5008	,	,		17120	0.0		0.0219	False		,,,				2504	0.0082				p.R1186Q		Atlas-SNP	.											.	HSPG2	311	.	0			c.G3557A						PASS	.	C	GLN/ARG	768,3638	290.1+/-280.8	57,654,1492	31	31	31		3557	0.2	1	1	dbSNP_98	31	256,8344	96.1+/-157.9	4,248,4048	yes	missense	HSPG2	NM_005529.5	43	61,902,5540	TT,TC,CC		2.9767,17.4308,7.8733	benign	1186/4392	22200998	1024,11982	2203	4300	6503	SO:0001583	missense	3339	exon28			TCACACCGAGGGC	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.3557G>A	1.37:g.22200998C>T	ENSP00000363827:p.Arg1186Gln	133	0	0		188	91	0.484043	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	152	0.0695970695970696	97	0.19715447154471544	22	0.06077348066298342	6	0.01048951048951049	27	0.03562005277044855	C	11.48	1.651776	0.29336	0.174308	0.029767	ENSG00000142798	ENST00000374695	T	0.61859	0.07	4.93	0.185	0.15096	EGF-like, laminin (4);	0.899723	0.09017	N	0.860725	T	0.00039	0.0001	N	0.04768	-0.165	0.44966	P	0.0020120000000000138	B	0.09022	0.002	B	0.10450	0.005	T	0.14476	-1.0471	9	0.25106	T	0.35	.	8.6369	0.33953	0.0:0.242:0.0:0.758	rs2229481;rs58148193;rs2229481	1186	P98160	PGBM_HUMAN	Q	1186	ENSP00000363827:R1186Q	ENSP00000363827:R1186Q	R	-	2	0	HSPG2	22073585	0.005000	0.15991	0.982000	0.44146	0.734000	0.41952	-0.080000	0.11339	-0.211000	0.10124	-0.480000	0.04831	CGG	C|0.915;T|0.085	0.085	strong		0.682	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		T	22200998	C	T	22200998	3	4	26	1	0	0	0	0	1	0	0	0	7439	652	23	1	9898	1	HSPG2	1	22200998	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	18883	22200998	227049623	14	9777											
C1orf38	9473	hgsc.bcm.edu	37	chr1	28203156	28203156	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctccacgggggacctgatcaAggtcacccaggtccgcctcc	7	6	11	17	2	2	1	2	1	0	0	5	2	5	2	6	4	0	0	6	4	1	0			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:28203156A>G	ENST00000373921.3	+	2	156	c.152A>G	c.(151-153)aAg>aGg	p.K51R	THEMIS2_ENST00000373925.1_Missense_Mutation_p.K51R|THEMIS2_ENST00000328928.7_Missense_Mutation_p.K51R|THEMIS2_ENST00000373927.3_Missense_Mutation_p.K51R	NM_001105556.1	NP_001099026.1	Q5TEJ8	THMS2_HUMAN	thymocyte selection associated family member 2	51	CABIT 1.				cell adhesion (GO:0007155)|inflammatory response (GO:0006954)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											GACCTGATCAAGGTCACCCAG	0.592																																					p.K51R		Atlas-SNP	.											.	.	.	.	0			c.A152G						PASS	.						88	86	87					1																	28203156		2203	4300	6503	SO:0001583	missense	9473	exon2			TGATCAAGGTCAC	AF044896	CCDS30653.1, CCDS30654.1, CCDS41290.1, CCDS65461.1	1p35.2	2012-07-10	2012-07-10	2012-07-10	ENSG00000130775	ENSG00000130775			16839	protein-coding gene	gene with protein product	"induced by contact to basement membrane 1"		"chromosome 1 open reading frame 38"	C1orf38		16219472	Standard	XM_005246041		Approved	ICB-1, Icb-1	uc001bpc.4	Q5TEJ8	OTTHUMG00000003735	ENST00000373921.3:c.152A>G	1.37:g.28203156A>G	ENSP00000363031:p.Lys51Arg	57	0	0		63	39	0.619048	NM_001039477	A2RTZ3|B4DZT9|B4DZY3|O60560|Q5TEJ1|Q5TEJ9|Q5TEK1|Q68DP4|Q9BYB6|Q9NS90	Missense_Mutation	SNP	ENST00000373921.3	37	CCDS41290.1	.	.	.	.	.	.	.	.	.	.	A	19.45	3.829475	0.71258	.	.	ENSG00000130775	ENST00000373925;ENST00000328928;ENST00000373927;ENST00000442118;ENST00000373921	T;T;T;T;T	0.15017	2.46;2.46;2.46;2.46;2.46	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.45054	0.1323	M	0.81802	2.56	0.46564	D	0.999102	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;0.991;0.989	T	0.47623	-0.9103	10	0.72032	D	0.01	-42.0968	14.6767	0.68986	1.0:0.0:0.0:0.0	.	51;51;51;51;51	Q5TEJ8-5;Q5TEJ8-6;Q5TEJ8;Q5TEJ8-4;Q5TEJ8-2	.;.;THMS2_HUMAN;.;.	R	51	ENSP00000363035:K51R;ENSP00000329862:K51R;ENSP00000363037:K51R;ENSP00000413725:K51R;ENSP00000363031:K51R	ENSP00000329862:K51R	K	+	2	0	C1orf38	28075743	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.414000	0.73318	2.146000	0.66826	0.528000	0.53228	AAG	.	.	none		0.592	THEMIS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011148.1	NM_004848		G	28203156	A	G	28203156	3	3	26	1	0	0	0	0	1	0	0	0	2041	72	3	3	158	3	C1orf38	1	28203156	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	6002158	28203156	221047465	15	9778											
ZNF362	149076	hgsc.bcm.edu	37	chr1	33764617	33764617	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccagaggacggagtccccCggcatcccggtgcgaatctc	7	5	12	17	4	1	1	0	0	1	1	4	4	3	3	5	4	1	1	5	4	1	0	rs55887741	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:33764617C>T	ENST00000539719.1	+	9	1403	c.1233C>T	c.(1231-1233)ccC>ccT	p.P411P	ZNF362_ENST00000373428.5_Silent_p.P411P	NM_152493.2	NP_689706.2	Q5T0B9	ZN362_HUMAN	zinc finger protein 362	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)			endometrium(3)|kidney(1)|large_intestine(4)|lung(2)	10		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				CGGAGTCCCCCGGCATCCCGG	0.657											OREG0013343	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	7	0.00139776	0.0	0.0014	5008	,	,		16576	0.0		0.006	False		,,,				2504	0.0				p.P411P	Pancreas(162;1431 2676 35353 38425)	Atlas-SNP	.											.	ZNF362	31	.	0			c.C1233T						PASS	.	C		8,4398	14.3+/-33.2	0,8,2195	70	68	69		1233	3.3	1	1	dbSNP_129	69	75,8525	43.1+/-100.9	0,75,4225	no	coding-synonymous	ZNF362	NM_152493.2		0,83,6420	TT,TC,CC		0.8721,0.1816,0.6382		411/421	33764617	83,12923	2203	4300	6503	SO:0001819	synonymous_variant	149076	exon9			GTCCCCCGGCATC		CCDS377.1	1p35.1	2013-01-08			ENSG00000160094	ENSG00000160094		"Zinc fingers, C2H2-type"	18079	protein-coding gene	gene with protein product	"rotund homolog (Drosophila)"						Standard	NM_152493		Approved	FLJ25476, lin-29, RN	uc001bxc.1	Q5T0B9	OTTHUMG00000004124	ENST00000539719.1:c.1233C>T	1.37:g.33764617C>T		58	0	0	842	59	32	0.542373	NM_152493	Q8WYU4	Silent	SNP	ENST00000539719.1	37	CCDS377.1																																																																																			C|0.997;T|0.003	0.003	strong		0.657	ZNF362-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011857.2	NM_152493		T	33764617	C	T	33764617	2	4	26	1	0	0	0	0	0	0	0	1	17883	639	23	1		1	ZNF362	1	33764617	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	5561461	33764617	215486004	16	9779											
GRIK3	2899	hgsc.bcm.edu	37	chr1	37356579	37356579	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctctgtatgtcataggtcaaGgttgtgttgggcagcagagt	8	13	14	6	0	3	1	2	0	1	1	3	1	3	1	0	3	1	5	0	3	3	4			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	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						PASS	.						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	1.37:g.37356579G>T		168	0	0		222	105	0.472973	NM_000831	A9Z1Z8|B1AMS6|Q13004|Q16136	Silent	SNP	ENST00000373091.3	37	CCDS416.1																																																																																			.	.	none		0.547	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012053.1	NM_000831		T	37356579	G	T	37356579	2	4	26	1	0	0	0	0	0	0	0	1	6784	987	35	4		4	GRIK3	1	37356579	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	3591962	37356579	211894042	17	9780											
WDR65	149465	hgsc.bcm.edu	37	chr1	43647424	43647424	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaatacctattggctcagaCgtcacctccagagtcaaatc	13	9	6	13	1	3	2	3	0	0	2	5	2	4	2	3	1	1	1	3	1	4	3	rs138300205	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:43647424C>T	ENST00000372492.4	+	3	701	c.377C>T	c.(376-378)aCg>aTg	p.T126M	WDR65_ENST00000528956.1_Missense_Mutation_p.T126M	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		126										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)				TTGGCTCAGACGTCACCTCCA	0.423													C|||	28	0.00559105	0.0015	0.0	5008	,	,		17818	0.0		0.0159	False		,,,				2504	0.0102				p.T126M		Atlas-SNP	.											.	WDR65	76	.	0			c.C377T						PASS	.	C	MET/THR,MET/THR,MET/THR	12,4394	20.2+/-43.8	0,12,2191	81	86	84		377,377,377	5.6	1	1	dbSNP_134	84	150,8450	72.6+/-135.2	0,150,4150	yes	missense,missense,missense	WDR65	NM_001167965.1,NM_001167966.1,NM_152498.3	81,81,81	0,162,6341	TT,TC,CC		1.7442,0.2724,1.2456	probably-damaging,probably-damaging,probably-damaging	126/699,126/699,126/699	43647424	162,12844	2203	4300	6503	SO:0001583	missense	149465	exon3			CTCAGACGTCACC																												ENST00000372492.4:c.377C>T	1.37:g.43647424C>T	ENSP00000361570:p.Thr126Met	151	0	0		163	75	0.460123	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Missense_Mutation	SNP	ENST00000372492.4	37		13	0.005952380952380952	1	0.0020325203252032522	0	0.0	0	0.0	12	0.0158311345646438	C	20.1	3.937291	0.73557	0.002724	0.017442	ENSG00000243710	ENST00000372492;ENST00000528956;ENST00000529956	T;T;T	0.38401	4.93;1.14;4.93	5.57	5.57	0.84162	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.153918	0.64402	D	0.000017	T	0.43100	0.1232	M	0.66939	2.045	0.47862	D	0.999536	D;D	0.76494	0.999;0.998	P;D	0.67900	0.899;0.954	T	0.50931	-0.8769	10	0.48119	T	0.1	.	19.1541	0.93503	0.0:1.0:0.0:0.0	.	126;126	Q96MR6;Q96MR6-2	WDR65_HUMAN;.	M	126	ENSP00000361570:T126M;ENSP00000435310:T126M;ENSP00000434133:T126M	ENSP00000361570:T126M	T	+	2	0	WDR65	43420011	1.000000	0.71417	0.999000	0.59377	0.588000	0.36517	5.291000	0.65667	2.626000	0.88956	0.557000	0.71058	ACG	C|0.990;T|0.010	0.010	strong		0.423	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1			T	43647424	C	T	43647424	3	4	26	1	0	0	0	0	1	0	0	0	17331	536	19	1	383	1	WDR65	1	43647424	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	6290845	43647424	205603197	18	9781											
TMEM125	128218	hgsc.bcm.edu	37	chr1	43738760	43738760	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtgctgctcagtggcctcGtgctgctggtcaccggcctg	2	11	15	13	2	2	0	2	0	0	0	3	0	2	0	3	4	4	4	3	4	0	0	rs143350378	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:43738760G>A	ENST00000432792.2	+	4	937	c.367G>A	c.(367-369)Gtg>Atg	p.V123M	TMEM125_ENST00000439858.1_Missense_Mutation_p.V123M			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													G|||	5	0.000998403	0.0008	0.0014	5008	,	,		15058	0.0		0.003	False		,,,				2504	0.0				p.V123M		Atlas-SNP	.											.	TMEM125	18	.	0			c.G367A						PASS	.	G	MET/VAL	5,4391		0,5,2193	22	24	23		367	5.2	0.9	1	dbSNP_134	23	33,8553		1,31,4261	no	missense	TMEM125	NM_144626.2	21	1,36,6454	AA,AG,GG		0.3843,0.1137,0.2927	possibly-damaging	123/220	43738760	38,12944	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>A	1.37:g.43738760G>A	ENSP00000429275:p.Val123Met	13	0	0		24	13	0.541667	NM_144626	D3DPX1	Missense_Mutation	SNP	ENST00000432792.2	37	CCDS480.1	.	.	.	.	.	.	.	.	.	.	G	17.47	3.397316	0.62177	0.001137	0.003843	ENSG00000179178	ENST00000439858;ENST00000432792	T;T	0.47177	0.85;0.85	5.24	5.24	0.73138	.	0.350030	0.29059	N	0.013275	T	0.46268	0.1384	L	0.27053	0.805	0.30773	N	0.742775	D	0.69078	0.997	P	0.53360	0.724	T	0.52946	-0.8507	10	0.62326	D	0.03	.	12.2066	0.54355	0.0783:0.0:0.9217:0.0	.	123	Q96AQ2	TM125_HUMAN	M	123	ENSP00000429775:V123M;ENSP00000429275:V123M	ENSP00000429275:V123M	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	0.003	strong		0.721	TMEM125-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019032.2	NM_144626		A	43738760	G	A	43738760	3	1	26	1	0	0	0	0	1	0	0	0	16052	1145	40	1	369	1	TMEM125	1	43738760	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	91336	43738760	205511861	19	9782											
C1orf210	149466	hgsc.bcm.edu	37	chr1	43748763	43748763	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cagacgctgtggggagctccGaaggcccaacaagtgctgca	10	5	14	12	2	0	1	0	0	0	1	1	3	1	2	2	3	4	4	2	3	3	0	rs35465732	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:43748763G>A	ENST00000523677.1	-	3	268	c.35C>T	c.(34-36)tCg>tTg	p.S12L	C1orf210_ENST00000423420.1_Missense_Mutation_p.S12L	NM_001164829.1|NM_182517.2	NP_001158301.1|NP_872323.1	Q8IVY1	CA210_HUMAN	chromosome 1 open reading frame 210	12			S -> L (in dbSNP:rs35465732).			integral component of membrane (GO:0016021)				breast(1)	1	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GGGGAGCTCCGAAGGCCCAAC	0.642													G|||	29	0.00579073	0.0008	0.0029	5008	,	,		15217	0.0		0.0189	False		,,,				2504	0.0072				p.S12L		Atlas-SNP	.											C1orf210,NS,carcinoma,+1,1	C1orf210	9	1	0			c.C35T						PASS	.	G	LEU/SER,LEU/SER	16,4390	24.3+/-50.5	0,16,2187	25	27	26		35,35	2	0	1	dbSNP_126	26	158,8442	71.6+/-134.2	0,158,4142	yes	missense,missense	C1orf210	NM_001164829.1,NM_182517.2	145,145	0,174,6329	AA,AG,GG		1.8372,0.3631,1.3378	possibly-damaging,possibly-damaging	12/114,12/114	43748763	174,12832	2203	4300	6503	SO:0001583	missense	149466	exon3			AGCTCCGAAGGCC	BC041633	CCDS481.1	1p34.2	2006-03-22			ENSG00000253313	ENSG00000253313			28755	protein-coding gene	gene with protein product						12477932	Standard	NM_182517		Approved	MGC52423	uc001cit.4	Q8IVY1	OTTHUMG00000007289	ENST00000523677.1:c.35C>T	1.37:g.43748763G>A	ENSP00000430918:p.Ser12Leu	98	0	0		137	67	0.489051	NM_182517	D3DPX2	Missense_Mutation	SNP	ENST00000523677.1	37	CCDS481.1	18	0.008241758241758242	0	0.0	2	0.0055248618784530384	0	0.0	16	0.021108179419525065	G	17.71	3.457811	0.63401	0.003631	0.018372	ENSG00000253313	ENST00000523677;ENST00000423420	T;T	0.47869	0.83;0.83	4.96	2.04	0.26737	.	0.670270	0.13234	N	0.403431	T	0.18593	0.0446	L	0.36672	1.1	0.09310	N	1	B	0.17465	0.022	B	0.09377	0.004	T	0.23154	-1.0196	10	0.72032	D	0.01	.	3.4949	0.07651	0.2809:0.0:0.5414:0.1777	rs35465732	12	Q8IVY1	CA210_HUMAN	L	12	ENSP00000430918:S12L;ENSP00000429399:S12L	ENSP00000429399:S12L	S	-	2	0	C1orf210	43521350	0.129000	0.22400	0.008000	0.14137	0.346000	0.29079	0.752000	0.26362	0.277000	0.22141	0.561000	0.74099	TCG	G|0.989;A|0.011	0.011	strong		0.642	C1orf210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019035.2	NM_182517		A	43748763	G	A	43748763	3	1	26	1	0	0	0	0	1	0	0	0	2031	1059	37	1	310	1	C1orf210	1	43748763	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	10003	43748763	205501858	20	9783											
EPS15	2060	hgsc.bcm.edu	37	chr1	51829575	51829575	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggtcttgttggagttccgatCtttggtggcagtgctggggg	3	14	18	6	1	2	0	0	0	2	0	3	2	3	1	1	6	1	4	1	6	0	4			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:51829575C>T	ENST00000371733.3	-	23	2418	c.2322G>A	c.(2320-2322)aaG>aaA	p.K774K	EPS15_ENST00000396122.4_Silent_p.K451K|EPS15_ENST00000371730.2_Silent_p.K640K	NM_001981.2	NP_001972.1	P42566	EPS15_HUMAN	epidermal growth factor receptor pathway substrate 15	774	15 X 3 AA repeats of D-P-F.|Pro-rich.				cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|protein transport (GO:0015031)|vesicle organization (GO:0016050)	AP-2 adaptor complex (GO:0030122)|ciliary membrane (GO:0060170)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|polyubiquitin binding (GO:0031593)	p.0?(2)		endometrium(3)|kidney(5)|large_intestine(8)|lung(13)|prostate(2)|skin(1)|stomach(1)|urinary_tract(2)	35						GAGTTCCGATCTTTGGTGGCA	0.448			T	MLL	ALL																																p.K774K		Atlas-SNP	.		Dom	yes		1	1p32	2060	epidermal growth factor receptor pathway substrate 15 (AF1p)		L	EPS15,right_upper_lobe,carcinoma,0,1	EPS15	72	1	2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)	c.G2322A						PASS	.						215	194	201					1																	51829575		2203	4300	6503	SO:0001819	synonymous_variant	2060	exon23			TCCGATCTTTGGT	BC054006	CCDS557.1	1p32	2013-01-10			ENSG00000085832	ENSG00000085832		"EF-hand domain containing"	3419	protein-coding gene	gene with protein product		600051				8183552	Standard	NM_001159969		Approved	AF-1P, MLLT5	uc001csq.1	P42566	OTTHUMG00000008192	ENST00000371733.3:c.2322G>A	1.37:g.51829575C>T		255	1	0.00392157		236	106	0.449153	NM_001981	B2R8J7|D3DPJ2|Q5SRH4	Silent	SNP	ENST00000371733.3	37	CCDS557.1																																																																																			.	.	none		0.448	EPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022422.1	NM_001981		T	51829575	C	T	51829575	2	4	26	1	0	0	0	0	0	0	0	1	5194	912	32	2		2	EPS15	1	51829575	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	8080812	51829575	197421046	21	9784											
USP24	23358	hgsc.bcm.edu	37	chr1	55563349	55563349	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	attaggtgaattaccaagacGctaggtaaagatttaataca	17	11	8	5	1	0	3	0	1	0	2	0	3	0	3	1	2	2	2	1	2	9	7	rs75297697	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:55563349G>A	ENST00000294383.6	-	48	5636	c.5637C>T	c.(5635-5637)agC>agT	p.S1879S	USP24_ENST00000407756.1_Silent_p.S1719S	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	1879	USP.				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						TTACCAAGACGCTAGGTAAAG	0.333													G|||	10	0.00199681	0.0045	0.0029	5008	,	,		17063	0.0		0.002	False		,,,				2504	0.0				p.S1879S		Atlas-SNP	.											.	USP24	323	.	0			c.C5637T						PASS	.	G		27,3571		0,27,1772	38	34	35		5637	-2.3	1	1	dbSNP_132	35	18,8108		0,18,4045	no	coding-synonymous	USP24	NM_015306.2		0,45,5817	AA,AG,GG		0.2215,0.7504,0.3838		1879/2621	55563349	45,11679	1799	4063	5862	SO:0001819	synonymous_variant	23358	exon48			CAAGACGCTAGGT	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.5637C>T	1.37:g.55563349G>A		132	0	0		132	69	0.522727	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Silent	SNP	ENST00000294383.6	37	CCDS44154.2																																																																																			G|0.997;A|0.003	0.003	strong		0.333	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			A	55563349	G	A	55563349	2	1	26	1	0	0	0	0	0	0	0	1	17070	1078	38	1		1	USP24	1	55563349	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	3733774	55563349	193687272	22	9785											
ATG4C	84938	hgsc.bcm.edu	37	chr1	63299751	63299751	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtgggtattattggtggcAaacctaaacagtcatattac	12	13	10	6	0	1	0	1	0	0	0	1	0	1	0	1	3	3	2	1	3	7	6	rs146422144	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:63299751A>C	ENST00000317868.4	+	8	1183	c.976A>C	c.(976-978)Aaa>Caa	p.K326Q	ATG4C_ENST00000371120.3_Missense_Mutation_p.K326Q	NM_032852.3	NP_116241.2	Q96DT6	ATG4C_HUMAN	autophagy related 4C, cysteine peptidase	326					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						TATTGGTGGCAAACCTAAACA	0.299													A|||	5	0.000998403	0.0	0.0014	5008	,	,		17562	0.0		0.004	False		,,,				2504	0.0				p.K326Q		Atlas-SNP	.											.	ATG4C	96	.	0			c.A976C						PASS	.	A	GLN/LYS,GLN/LYS	4,4402	8.1+/-20.4	0,4,2199	186	196	193		976,976	6	1	1	dbSNP_134	193	21,8579	14.6+/-50.1	0,21,4279	yes	missense,missense	ATG4C	NM_032852.3,NM_178221.2	53,53	0,25,6478	CC,CA,AA		0.2442,0.0908,0.1922	probably-damaging,probably-damaging	326/459,326/459	63299751	25,12981	2203	4300	6503	SO:0001583	missense	84938	exon8			GGTGGCAAACCTA	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.976A>C	1.37:g.63299751A>C	ENSP00000322159:p.Lys326Gln	95	0	0		94	43	0.457447	NM_178221	A6NLR8|D3DQ58|Q96K04	Missense_Mutation	SNP	ENST00000317868.4	37	CCDS623.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	21.5	4.159289	0.78226	9.08E-4	0.002442	ENSG00000125703	ENST00000317868;ENST00000371120;ENST00000540025;ENST00000414558	T;T	0.48836	0.8;0.8	5.97	5.97	0.96955	.	0.042802	0.85682	D	0.000000	T	0.67683	0.2919	M	0.87547	2.89	0.80722	D	1	D	0.67145	0.996	D	0.70716	0.97	T	0.74562	-0.3624	10	0.72032	D	0.01	-20.3301	16.4534	0.84003	1.0:0.0:0.0:0.0	.	326	Q96DT6	ATG4C_HUMAN	Q	326;326;326;70	ENSP00000322159:K326Q;ENSP00000360161:K326Q	ENSP00000322159:K326Q	K	+	1	0	ATG4C	63072339	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.285000	0.76669	0.477000	0.44152	AAA	A|0.998;C|0.002	0.002	strong		0.299	ATG4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025332.2	NM_032852		C	63299751	A	C	63299751	3	2	26	1	0	0	0	0	1	0	0	0	1098	131	5	5	1002	5	ATG4C	1	63299751	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	7736402	63299751	185950870	23	9786											
C1orf141	400757	hgsc.bcm.edu	37	chr1	67561087	67561087	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttttatattaaaatcgttcAtctgtggagatttttttctg	9	21	6	5	1	3	1	1	0	2	1	4	2	3	1	0	1	0	1	0	1	4	8	rs145227724		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:67561087A>C	ENST00000371007.2	-	7	543	c.434T>G	c.(433-435)aTg>aGg	p.M145R	C1orf141_ENST00000544837.1_Missense_Mutation_p.M145R|C1orf141_ENST00000371006.1_Missense_Mutation_p.M145R	NM_001276351.1	NP_001263280.1	Q5JVX7	CA141_HUMAN	chromosome 1 open reading frame 141	145										NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|skin(1)	18						AAAATCGTTCATCTGTGGAGA	0.368													A|||	1	0.000199681	0.0	0.0	5008	,	,		19847	0.0		0.0	False		,,,				2504	0.001				p.M145R		Atlas-SNP	.											.	C1orf141	58	.	0			c.T434G						PASS	.	A	ARG/MET	0,4404		0,0,2202	47	44	45		434	-4	0	1	dbSNP_134	45	17,8579		0,17,4281	yes	missense	C1orf141	NM_001013674.1	91	0,17,6483	CC,CA,AA		0.1978,0.0,0.1308	possibly-damaging	145/401	67561087	17,12983	2202	4298	6500	SO:0001583	missense	400757	exon7			TCGTTCATCTGTG	BC090886	CCDS30745.1, CCDS72804.1	1p31.2	2012-07-23			ENSG00000203963	ENSG00000203963			32044	protein-coding gene	gene with protein product							Standard	NM_001276351		Approved		uc001ddm.2	Q5JVX7	OTTHUMG00000009406	ENST00000371007.2:c.434T>G	1.37:g.67561087A>C	ENSP00000360046:p.Met145Arg	75	0	0		93	41	0.44086	NM_001276351	Q0P5P5|Q5JVX5	Missense_Mutation	SNP	ENST00000371007.2	37	CCDS30745.1	.	.	.	.	.	.	.	.	.	.	A	12.89	2.073770	0.36566	0.0	0.001978	ENSG00000203963	ENST00000371007;ENST00000371006;ENST00000544837;ENST00000371005;ENST00000448166	T;T;T	0.29397	1.57;1.57;1.57	5.76	-3.98	0.04082	.	0.801389	0.10895	N	0.622204	T	0.06962	0.0177	N	0.19112	0.55	0.09310	N	1	D	0.54601	0.967	P	0.52217	0.693	T	0.07829	-1.0752	10	0.10902	T	0.67	1.1288	2.2939	0.04145	0.3772:0.1336:0.3596:0.1296	.	145	Q5JVX7	CA141_HUMAN	R	145;145;145;216;216	ENSP00000360046:M145R;ENSP00000360045:M145R;ENSP00000444018:M145R	ENSP00000360044:M216R	M	-	2	0	C1orf141	67333675	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.277000	0.08502	-0.490000	0.06707	-0.263000	0.10527	ATG	A|0.999;C|0.001	0.001	strong		0.368	C1orf141-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026096.2	NM_001013674		C	67561087	A	C	67561087	3	2	26	1	0	0	0	0	1	0	0	0	2003	217	8	5	776	5	C1orf141	1	67561087	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	4261336	67561087	181689534	24	9787											
C1orf173	127254	hgsc.bcm.edu	37	chr1	75037385	75037385	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tagaacttccacagccacaaCccttcctcctcccatgccct	9	9	3	20	0	0	1	0	0	0	1	4	1	4	1	7	0	4	0	7	0	3	3	rs200080388		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:75037385C>T	ENST00000326665.5	-	14	4227	c.4009G>A	c.(4009-4011)Gtt>Att	p.V1337I	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		1337	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						ACAGCCACAACCCTTCCTCCT	0.562																																					p.V1337I		Atlas-SNP	.											.	C1orf173	380	.	0			c.G4009A						PASS	.	C	ILE/VAL	0,4406		0,0,2203	254	238	243		4009	2.1	0	1		243	1,8599	1.2+/-3.3	0,1,4299	yes	missense	C1orf173	NM_001002912.4	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	1337/1531	75037385	1,13005	2203	4300	6503	SO:0001583	missense	127254	exon14			CCACAACCCTTCC																												ENST00000326665.5:c.4009G>A	1.37:g.75037385C>T	ENSP00000322609:p.Val1337Ile	130	0	0		134	72	0.537313	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	37	CCDS30755.1	.	.	.	.	.	.	.	.	.	.	C	11.88	1.771644	0.31320	0.0	1.16E-4	ENSG00000178965	ENST00000326665	T	0.13901	2.55	4.1	2.14	0.27477	.	.	.	.	.	T	0.02727	0.0082	N	0.19112	0.55	0.09310	N	0.999999	P	0.36535	0.557	B	0.35971	0.215	T	0.42068	-0.9473	9	0.38643	T	0.18	.	7.5396	0.27731	0.0:0.734:0.1688:0.0972	.	1337	Q5RHP9	CA173_HUMAN	I	1337	ENSP00000322609:V1337I	ENSP00000322609:V1337I	V	-	1	0	C1orf173	74809973	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.090000	0.15025	0.187000	0.20147	0.462000	0.41574	GTT	.	.	weak		0.562	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			T	75037385	C	T	75037385	3	4	26	1	0	0	0	0	1	0	0	0	2016	507	18	2	587	2	C1orf173	1	75037385	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	7476298	75037385	174213236	25	9788											
C1orf173	127254	hgsc.bcm.edu	37	chr1	75078423	75078423	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagcttaacctgttcacctgCatcccattcaggaaaaaggt	12	10	8	11	0	2	0	2	0	0	0	3	2	3	1	3	2	3	3	3	2	3	3	rs150709786	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:75078423C>T	ENST00000326665.5	-	9	1289	c.1071G>A	c.(1069-1071)atG>atA	p.M357I	RP4-612J11.1_ENST00000416017.1_RNA|C1orf173_ENST00000420661.2_Missense_Mutation_p.M160I	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		357										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						TGTTCACCTGCATCCCATTCA	0.423													C|||	7	0.00139776	0.0	0.0014	5008	,	,		18608	0.0		0.001	False		,,,				2504	0.0051				p.M357I		Atlas-SNP	.											C1orf173,NS,lymphoid_neoplasm,-2,1	C1orf173	380	1	0			c.G1071A						PASS	.	C	ILE/MET	2,4404	4.2+/-10.8	0,2,2201	99	95	97		1071	-6.5	0.9	1	dbSNP_134	97	14,8586	9.8+/-36.6	0,14,4286	yes	missense	C1orf173	NM_001002912.4	10	0,16,6487	TT,TC,CC		0.1628,0.0454,0.123	benign	357/1531	75078423	16,12990	2203	4300	6503	SO:0001583	missense	127254	exon9			CACCTGCATCCCA																												ENST00000326665.5:c.1071G>A	1.37:g.75078423C>T	ENSP00000322609:p.Met357Ile	64	0	0		72	38	0.527778	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	37	CCDS30755.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	11.61	1.691085	0.30052	4.54E-4	0.001628	ENSG00000178965	ENST00000326665;ENST00000420661	T;T	0.16073	2.87;2.37	5.63	-6.51	0.01878	.	.	.	.	.	T	0.01287	0.0042	N	0.17474	0.49	0.30304	N	0.789207	B;B	0.16396	0.001;0.017	B;B	0.12837	0.003;0.008	T	0.33854	-0.9852	9	0.02654	T	1	-0.6393	1.2823	0.02043	0.2419:0.2826:0.0937:0.3818	.	160;357	Q5RHP9-3;Q5RHP9	.;CA173_HUMAN	I	357;160	ENSP00000322609:M357I;ENSP00000398581:M160I	ENSP00000322609:M357I	M	-	3	0	C1orf173	74851011	0.009000	0.17119	0.871000	0.34182	0.994000	0.84299	-0.981000	0.03766	-1.229000	0.02564	-0.140000	0.14226	ATG	C|0.999;T|0.001	0.001	strong		0.423	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			T	75078423	C	T	75078423	3	4	26	1	0	0	0	0	1	0	0	0	2016	710	25	2	3545	2	C1orf173	1	75078423	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	41038	75078423	174172198	26	9789											
SH3GLB1	51100	hgsc.bcm.edu	37	chr1	87170606	87170606	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aatatcatggacttcaacgtGaagaagctggcggccgacgc	12	7	12	10	4	2	2	2	1	0	1	2	4	2	3	1	3	2	1	1	3	5	2	rs150324653	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:87170606G>A	ENST00000370558.4	+	1	348	c.24G>A	c.(22-24)gtG>gtA	p.V8V	SH3GLB1_ENST00000535010.1_5'UTR|RP4-612B15.3_ENST00000565575.1_RNA|SH3GLB1_ENST00000482504.1_Silent_p.V8V	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	8	Membrane-binding amphipathic helix.				'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)		ACTTCAACGTGAAGAAGCTGG	0.716													G|||	28	0.00559105	0.0008	0.0058	5008	,	,		12901	0.0		0.0179	False		,,,				2504	0.0051				p.V8V		Atlas-SNP	.											.	SH3GLB1	57	.	0			c.G24A						PASS	.	G	,,,	10,4384		0,10,2187	13	16	15		24,24,,24	1.6	1	1	dbSNP_134	15	87,8499		0,87,4206	no	coding-synonymous,coding-synonymous,utr-5,coding-synonymous	SH3GLB1	NM_001206651.1,NM_001206652.1,NM_001206653.1,NM_016009.4	,,,	0,97,6393	AA,AG,GG		1.0133,0.2276,0.7473	,,,	8/395,8/387,,8/366	87170606	97,12883	2197	4293	6490	SO:0001819	synonymous_variant	51100	exon1			CAACGTGAAGAAG	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.24G>A	1.37:g.87170606G>A		29	0	0		40	21	0.525	NM_001206652	B4E182|Q5H8U5|Q9H3Z0|Q9NR47|Q9NYA9	Silent	SNP	ENST00000370558.4	37	CCDS710.1																																																																																			G|0.993;A|0.007	0.007	strong		0.716	SH3GLB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028287.2	NM_016009		A	87170606	G	A	87170606	2	1	26	1	0	0	0	0	0	0	0	1	14268	1277	45	2		2	SH3GLB1	1	87170606	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	12092183	87170606	162080015	27	9790											
FRRS1	391059	hgsc.bcm.edu	37	chr1	100182997	100182997	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgcttcaccaagcaagaaaGcttttgaccaaactggcttg	12	10	8	11	0	1	2	1	1	0	1	1	2	1	2	2	1	4	4	2	1	4	4	rs149801998		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:100182997G>C	ENST00000414213.1	-	11	1806	c.1205C>G	c.(1204-1206)gCt>gGt	p.A402G	FRRS1_ENST00000287474.5_Missense_Mutation_p.A402G|FRRS1_ENST00000492943.1_5'Flank			Q6ZNA5	FRRS1_HUMAN	ferric-chelate reductase 1	402	Cytochrome b561. {ECO:0000255|PROSITE- ProRule:PRU00242}.					integral component of membrane (GO:0016021)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	26		all_epithelial(167;2.09e-06)|all_lung(203;0.000435)|Lung NSC(277;0.00201)		Epithelial(280;0.0718)|all cancers(265;0.126)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.206)		AAGCAAGAAAGCTTTTGACCA	0.398													G|||	1	0.000199681	0.0	0.0	5008	,	,		22156	0.0		0.001	False		,,,				2504	0.0				p.A402G		Atlas-SNP	.											.	FRRS1	50	.	0			c.C1205G						PASS	.	G	GLY/ALA	0,4406		0,0,2203	163	157	159		1205	3.2	0.6	1	dbSNP_134	159	12,8588	9.1+/-34.3	0,12,4288	yes	missense	FRRS1	NM_001013660.2	60	0,12,6491	CC,CG,GG		0.1395,0.0,0.0923	benign	402/627	100182997	12,12994	2203	4300	6503	SO:0001583	missense	391059	exon11			AAGAAAGCTTTTG	AK131302	CCDS30780.1	1p21.3	2009-11-30	2006-02-22	2006-02-22	ENSG00000156869	ENSG00000156869			27622	protein-coding gene	gene with protein product		611578	"stromal cell derived factor receptor 2 homolog (mouse)"	SDFR2			Standard	NM_001013660		Approved	SDR2	uc001dsh.1	Q6ZNA5	OTTHUMG00000010768	ENST00000414213.1:c.1205C>G	1.37:g.100182997G>C	ENSP00000393884:p.Ala402Gly	87	0	0		96	39	0.40625	NM_001013660	A6NLN7	Missense_Mutation	SNP	ENST00000414213.1	37		2	9.157509157509158E-4	0	0.0	0	0.0	1	0.0017482517482517483	1	0.0013192612137203166	G	11.14	1.550414	0.27739	0.0	0.001395	ENSG00000156869	ENST00000414213;ENST00000287474	.	.	.	5.03	3.16	0.36331	.	0.744958	0.13319	N	0.396864	T	0.23054	0.0557	L	0.54323	1.7	0.09310	N	0.99999	B	0.15930	0.015	B	0.19666	0.026	T	0.26538	-1.0100	9	0.40728	T	0.16	-1.6172	9.3248	0.37986	0.2357:0.0:0.7643:0.0	.	402	Q6ZNA5-2	.	G	402	.	ENSP00000287474:A402G	A	-	2	0	FRRS1	99955585	0.017000	0.18338	0.612000	0.29024	0.767000	0.43475	1.388000	0.34442	0.633000	0.30452	0.561000	0.74099	GCT	G|0.999;C|0.001	0.001	strong		0.398	FRRS1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001013660		C	100182997	G	C	100182997	3	2	26	1	0	0	0	0	1	0	0	0	6068	971	34	4	703	4	FRRS1	1	100182997	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	13012391	100182997	149067624	28	9791											
AMY2B	280	hgsc.bcm.edu	37	chr1	104117892	104117892	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccttctgacagagcacttgTctttgtggataaccatgaca	10	12	9	10	0	2	3	0	2	2	1	2	4	2	4	2	1	2	1	2	1	1	4	rs140209167	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:104117892T>C	ENST00000361355.4	+	8	1542	c.926T>C	c.(925-927)gTc>gCc	p.V309A	AMY2B_ENST00000491397.1_3'UTR	NM_020978.3	NP_066188.1	P19961	AMY2B_HUMAN	amylase, alpha 2B (pancreatic)	309					carbohydrate metabolic process (GO:0005975)|digestion (GO:0007586)	extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|metal ion binding (GO:0046872)			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)		AGAGCACTTGTCTTTGTGGAT	0.408													.|||	6	0.00119808	0.0	0.0014	5008	,	,		14681	0.0		0.005	False		,,,				2504	0.0				p.V309A		Atlas-SNP	.											.	AMY2B	80	.	0			c.T926C						PASS	.	T	ALA/VAL	2,4404	4.2+/-10.8	0,2,2201	275	274	275		926	4.1	1	1	dbSNP_134	275	30,8566	21.0+/-64.5	0,30,4268	no	missense	AMY2B	NM_020978.3	64	0,32,6469	CC,CT,TT		0.349,0.0454,0.2461	probably-damaging	309/512	104117892	32,12970	2203	4298	6501	SO:0001583	missense	280	exon8			CACTTGTCTTTGT	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.926T>C	1.37:g.104117892T>C	ENSP00000354610:p.Val309Ala	192	0	0		261	137	0.524904	NM_020978	B3KTI1|B3KXB7|D3DT76|Q9UBH3	Missense_Mutation	SNP	ENST00000361355.4	37	CCDS782.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	T	22.1	4.248687	0.80024	4.54E-4	0.00349	ENSG00000240038	ENST00000361355	D	0.98400	-4.91	5.26	4.12	0.48240	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	0.98372	0.9459	M	0.82323	2.585	0.80722	D	1	P	0.40681	0.727	P	0.57204	0.815	D	0.99818	1.1045	10	0.66056	D	0.02	.	11.3322	0.49484	0.0:0.0734:0.0:0.9266	.	309	P19961	AMY2B_HUMAN	A	309	ENSP00000354610:V309A	ENSP00000354610:V309A	V	+	2	0	AMY2B	103919415	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.096000	0.64535	1.992000	0.58205	0.456000	0.33151	GTC	T|0.998;C|0.002	0.002	strong		0.408	AMY2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030318.1	NM_020978		C	104117892	T	C	104117892	3	2	26	1	0	0	0	0	1	0	0	0	595	1667	58	3	948	3	AMY2B	1	104117892	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	3934895	104117892	145132729	29	9792											
MAN1A2	10905	hgsc.bcm.edu	37	chr1	117945057	117945067	+	Splice_Site	DEL	TAAAGAGGTAA	TAAAGAGGTAA	-																															agagagaaaagggaaaaaatTaaagaggtaataagctgagt																										TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TAAAGAGGTAA	TAAAGAGGTAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:117945057_117945067delTAAAGAGGTAA	ENST00000356554.3	+	2	1287_1293	c.552_558delTAAAGAGGTAA	c.(550-558)attaaagag>at	p.IKE184fs	MAN1A2_ENST00000482811.1_Intron	NM_006699.3	NP_006690.1	O60476	MA1A2_HUMAN	mannosidase, alpha, class 1A, member 2	184					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)		GGGAAAAAATTAAAGAGGTAATAAGCTGAGT	0.36																																					p.184_186del	Ovarian(33;199 881 8228 13687 31538)	Pindel,Atlas-Indel	.											.	MAN1A2	50	.	0			c.551_558del						PASS	.																																			SO:0001630	splice_region_variant	10905	exon2			.	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.558+1TAAAGAGGTAA>-	1.37:g.117945057_117945067delTAAAGAGGTAA		114	0	.		95	30	0.316	NM_006699	Q9H510	Frame_Shift_Del	DEL	ENST00000356554.3	37	CCDS895.1																																																																																			.	.	none		0.36	MAN1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033593.1	NM_006699	Frame_Shift_Del	-	117945067	TAAAGAGGTAA	-	117945057	8	5	26	1	0	1	0	1	0	0	1	0	9220	1742	61	0	558	0	MAN1A2	1	117945057	Splice_Site	DEL	TAAAGAGGTAA	TCGA-G8-6907-01A-11D-2210-10	13827165	117945057	131305564	30	9793											
MRPS21	54460	hgsc.bcm.edu	37	chr1	150280546	150280546	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtattatgagaagccatgcCgccggcgacagagggaaagc	12	5	15	9	3	0	2	0	1	0	2	0	5	0	3	3	3	3	1	3	3	4	2	rs10480	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:150280546C>T	ENST00000369084.5	+	2	595	c.148C>T	c.(148-150)Cgc>Tgc	p.R50C	MRPS21_ENST00000309092.7_Missense_Mutation_p.R50C	NM_018997.3	NP_061870.1	P82921	RT21_HUMAN	mitochondrial ribosomal protein S21	50			R -> C (in dbSNP:rs10480).		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)			GAAGCCATGCCGCCGGCGACA	0.493													C|||	48	0.00958466	0.0008	0.0216	5008	,	,		17027	0.0		0.0249	False		,,,				2504	0.0072				p.R50C		Atlas-SNP	.											.	MRPS21	8	.	0			c.C148T						PASS	.	C	CYS/ARG,CYS/ARG	28,4378	35.2+/-66.4	0,28,2175	50	47	48		148,148	4.9	1	1	dbSNP_52	48	289,8311	106.6+/-167.4	8,273,4019	no	missense,missense	MRPS21	NM_018997.2,NM_031901.4	180,180	8,301,6194	TT,TC,CC		3.3605,0.6355,2.4373	benign,benign	50/88,50/88	150280546	317,12689	2203	4300	6503	SO:0001583	missense	54460	exon2			CCATGCCGCCGGC	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.148C>T	1.37:g.150280546C>T	ENSP00000358080:p.Arg50Cys	203	1	0.00492611		202	108	0.534653	NM_018997	Q5TB11|Q9BST6	Missense_Mutation	SNP	ENST00000369084.5	37	CCDS950.1	21	0.009615384615384616	0	0.0	6	0.016574585635359115	0	0.0	15	0.01978891820580475	C	14.33	2.504529	0.44558	0.006355	0.033605	ENSG00000187145	ENST00000309092;ENST00000369084	T;T	0.30182	1.54;1.54	4.93	4.93	0.64822	.	.	.	.	.	T	0.12732	0.0309	.	.	.	0.53005	D	0.999962	B	0.20780	0.048	B	0.15484	0.013	T	0.02991	-1.1085	8	0.36615	T	0.2	.	12.9741	0.58529	0.1618:0.8382:0.0:0.0	rs10480;rs10480	50	P82921	RT21_HUMAN	C	50	ENSP00000312395:R50C;ENSP00000358080:R50C	ENSP00000312395:R50C	R	+	1	0	MRPS21	148547170	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.309000	0.43699	2.567000	0.86603	0.650000	0.86243	CGC	C|0.979;T|0.021	0.021	strong		0.493	MRPS21-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035813.1	NM_018997		T	150280546	C	T	150280546	3	4	26	1	0	0	0	0	1	0	0	0	9841	652	23	1	154	1	MRPS21	1	150280546	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	32335489	150280546	98970075	31	9794											
ADAMTSL4	54507	hgsc.bcm.edu	37	chr1	150526270	150526270	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gcccccctcacccacgcactCcttaggagaaggtggcttct	7	8	9	17	1	2	1	1	0	1	1	3	2	3	1	5	3	0	2	5	3	2	2	rs41317517	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:150526270C>T	ENST00000369038.2	+	4	1004	c.803C>T	c.(802-804)tCc>tTc	p.S268F	ADAMTSL4_ENST00000271643.4_Missense_Mutation_p.S268F|ADAMTSL4_ENST00000369041.5_Missense_Mutation_p.S268F|MIR4257_ENST00000581735.1_RNA|ADAMTSL4_ENST00000369039.5_Missense_Mutation_p.S268F|RP11-54A4.2_ENST00000442435.2_RNA			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	268					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)			CCCACGCACTCCTTAGGAGAA	0.657													C|||	17	0.00339457	0.0015	0.0072	5008	,	,		15387	0.001		0.008	False		,,,				2504	0.001				p.S268F		Atlas-SNP	.											.	ADAMTSL4	101	.	0			c.C803T						PASS	.	C	PHE/SER,PHE/SER	16,4390	23.3+/-48.9	0,16,2187	50	49	49		803,803	0.4	0	1	dbSNP_127	49	100,8500	55.2+/-116.2	1,98,4201	yes	missense,missense	ADAMTSL4	NM_019032.4,NM_025008.3	155,155	1,114,6388	TT,TC,CC		1.1628,0.3631,0.8919	possibly-damaging,possibly-damaging	268/1075,268/878	150526270	116,12890	2203	4300	6503	SO:0001583	missense	54507	exon6			CGCACTCCTTAGG	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.803C>T	1.37:g.150526270C>T	ENSP00000358034:p.Ser268Phe	103	0	0		143	73	0.51049	NM_019032	B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Missense_Mutation	SNP	ENST00000369038.2	37	CCDS955.1	13	0.005952380952380952	1	0.0020325203252032522	5	0.013812154696132596	1	0.0017482517482517483	6	0.0079155672823219	C	8.618	0.890660	0.17613	0.003631	0.011628	ENSG00000143382	ENST00000369041;ENST00000271643;ENST00000369039;ENST00000369038	T;T;T;T	0.64085	0.02;-0.08;0.2;-0.08	4.73	0.378	0.16204	.	.	.	.	.	T	0.26304	0.0642	L	0.29908	0.895	0.09310	N	1	B;B;B;B	0.12013	0.001;0.005;0.002;0.005	B;B;B;B	0.09377	0.002;0.004;0.002;0.004	T	0.32851	-0.9891	9	0.72032	D	0.01	.	7.3289	0.26571	0.0:0.5416:0.0:0.4584	rs41317517	268;268;268;268	B7ZMJ3;F8WAD0;Q6UY14;Q6UY14-2	.;.;ATL4_HUMAN;.	F	268	ENSP00000358037:S268F;ENSP00000271643:S268F;ENSP00000358035:S268F;ENSP00000358034:S268F	ENSP00000271643:S268F	S	+	2	0	ADAMTSL4	148792894	0.000000	0.05858	0.000000	0.03702	0.064000	0.16182	-0.115000	0.10741	0.034000	0.15491	0.484000	0.47621	TCC	C|0.991;T|0.009	0.009	strong		0.657	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032		T	150526270	C	T	150526270	3	4	26	1	0	0	0	0	1	0	0	0	277	855	30	2	817	2	ADAMTSL4	1	150526270	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	245724	150526270	98724351	32	9795											
FLG	2312	hgsc.bcm.edu	37	chr1	152283267	152283267	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgagtgtctggagctgtcTgctgactgctggtggcggga	4	11	17	9	1	2	2	0	2	2	0	2	4	2	4	1	4	3	3	1	4	0	0	rs11581451	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:152283267T>A	ENST00000368799.1	-	3	4130	c.4095A>T	c.(4093-4095)gcA>gcT	p.A1365A	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1365	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)			TGGAGCTGTCTGCTGACTGCT	0.537									Ichthyosis				T|||	37	0.00738818	0.0	0.0072	5008	,	,		21371	0.001		0.0119	False		,,,				2504	0.0194				p.A1365A		Atlas-SNP	.											FLG,NS,carcinoma,-2,1	FLG	900	1	0			c.A4095T						scavenged	.	T		14,4392	21.2+/-45.6	0,14,2189	392	369	377		4095	-8.4	0	1	dbSNP_120	377	98,8498	55.2+/-116.2	1,96,4201	no	coding-synonymous	FLG	NM_002016.1		1,110,6390	AA,AT,TT		1.1401,0.3177,0.8614		1365/4062	152283267	112,12890	2203	4298	6501	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GCTGTCTGCTGAC	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.4095A>T	1.37:g.152283267T>A		147	1	0.00680272		176	91	0.517045	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			T|0.993;A|0.007	0.007	strong		0.537	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152283267	T	A	152283267	2	1	26	1	0	0	0	0	0	0	0	1	5930	1567	55	5		5	FLG	1	152283267	Silent	SNP	T	TCGA-G8-6907-01A-11D-2210-10	1756997	152283267	96967354	33	9796											
FLG	2312	hgsc.bcm.edu	37	chr1	152283605	152283605	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccccgatgattgttcctgtcCcacctgtgagtgtctagagc	6	12	10	13	1	1	3	0	2	1	1	3	4	3	3	5	0	1	1	5	0	1	3	rs199895224		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:152283605C>A	ENST00000368799.1	-	3	3792	c.3757G>T	c.(3757-3759)Gga>Tga	p.G1253*	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1253	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)			TGTTCCTGTCCCACCTGTGAG	0.557									Ichthyosis																												p.G1253X		Atlas-SNP	.											.	FLG	900	.	0			c.G3757T						PASS	.						276	263	267					1																	152283605		2203	4300	6503	SO:0001587	stop_gained	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CCTGTCCCACCTG	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.3757G>T	1.37:g.152283605C>A	ENSP00000357789:p.Gly1253*	226	0	0		223	101	0.452915	NM_002016	Q01720|Q5T583|Q9UC71	Nonsense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	38	6.749215	0.97809	.	.	ENSG00000143631	ENST00000368799	.	.	.	2.72	0.669	0.17918	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.19147	T	0.46	.	5.0097	0.14306	0.0:0.6754:0.0:0.3246	.	.	.	.	X	1253	.	ENSP00000357789:G1253X	G	-	1	0	FLG	150550229	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.711000	0.05019	0.347000	0.23924	0.186000	0.17326	GGA	.	.	weak		0.557	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152283605	C	A	152283605	4	1	26	1	0	0	0	0	0	1	0	0	5930	632	22	4	8432	4	FLG	1	152283605	Nonsense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	338	152283605	96967016	34	9797											
LCE1F	353137	hgsc.bcm.edu	37	chr1	152748962	152748962	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	agtgtccccctaagtgccctCctgtctcttcctgctgcagc	4	12	8	17	0	1	0	0	0	1	0	5	0	4	0	5	0	4	2	5	0	1	2	rs116630978		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:152748962C>T	ENST00000334371.2	+	1	115	c.115C>T	c.(115-117)Cct>Tct	p.P39S		NM_178354.2	NP_848131.1	Q5T754	LCE1F_HUMAN	late cornified envelope 1F	39	Pro-rich.				keratinization (GO:0031424)			p.P39A(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)			taagtgccctccTGTCTCTTC	0.677													.|||	1	0.000199681	0.0008	0.0	5008	,	,		14646	0.0		0.0	False		,,,				2504	0.0				p.P39S		Atlas-SNP	.											LCE1F,NS,carcinoma,0,2	LCE1F	42	2	1	Substitution - Missense(1)	prostate(1)	c.C115T						PASS	.	C	SER/PRO	1,4405	2.1+/-5.4	0,1,2202	58	60	59		115	4.6	0.9	1	dbSNP_132	59	0,8600		0,0,4300	no	missense	LCE1F	NM_178354.2	74	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	39/119	152748962	1,13005	2203	4300	6503	SO:0001583	missense	353137	exon1			TGCCCTCCTGTCT		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.115C>T	1.37:g.152748962C>T	ENSP00000334187:p.Pro39Ser	132	0	0		145	7	0.0482759	NM_178354		Missense_Mutation	SNP	ENST00000334371.2	37	CCDS1023.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	10.13	1.264799	0.23136	2.27E-4	0.0	ENSG00000240386	ENST00000334371	T	0.04119	3.7	4.56	4.56	0.56223	.	.	.	.	.	T	0.02848	0.0085	L	0.39326	1.205	0.24725	N	0.993127	B	0.28760	0.221	B	0.34138	0.176	T	0.30736	-0.9968	9	0.87932	D	0	.	13.0238	0.58804	0.0:1.0:0.0:0.0	.	39	Q5T754	LCE1F_HUMAN	S	39	ENSP00000334187:P39S	ENSP00000334187:P39S	P	+	1	0	LCE1F	151015586	0.776000	0.28616	0.936000	0.37596	0.529000	0.34654	2.029000	0.41098	2.516000	0.84829	0.557000	0.71058	CCT	C|0.998;T|0.002	0.002	strong		0.677	LCE1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034523.2	NM_178354		T	152748962	C	T	152748962	3	4	26	1	0	0	0	0	1	0	0	0	8673	855	30	2	117	2	LCE1F	1	152748962	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	465357	152748962	96501659	35	9798											
SPRR3	6707	hgsc.bcm.edu	37	chr1	152975810	152975810	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	taccaaggtccctgagccagGctacaccaaggtccctgaac	11	6	9	15	0	0	2	0	2	0	0	2	2	2	2	5	3	4	1	5	3	5	2	rs72704847|rs527966074	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:152975810G>A	ENST00000295367.4	+	2	356	c.314G>A	c.(313-315)gGc>gAc	p.G105D	SPRR3_ENST00000331860.3_Missense_Mutation_p.G105D|SPRR3_ENST00000542696.1_Missense_Mutation_p.G97D	NM_001097589.1	NP_001091058.1	Q9UBC9	SPRR3_HUMAN	small proline-rich protein 3	105	14 X 8 AA approximate tandem repeats.		Missing.		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)			CCTGAGCCAGGCTACACCAAG	0.572													-|||	33	0.00658946	0.0008	0.0159	5008	,	,		20523	0.0		0.0209	False		,,,				2504	0.0				p.G105D		Atlas-SNP	.											.	SPRR3	45	.	0			c.G314A						PASS	.	G	ASP/GLY,ASP/GLY	27,4379	32.6+/-62.9	0,27,2176	99	80	87		314,314	1	0	1	dbSNP_131	87	142,8458	71.0+/-133.6	1,140,4159	yes	missense,missense	SPRR3	NM_001097589.1,NM_005416.2	94,94	1,167,6335	AA,AG,GG		1.6512,0.6128,1.2994	probably-damaging,probably-damaging	105/170,105/170	152975810	169,12837	2203	4300	6503	SO:0001583	missense	6707	exon2			AGCCAGGCTACAC	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.314G>A	1.37:g.152975810G>A	ENSP00000295367:p.Gly105Asp	109	0	0		154	65	0.422078	NM_001097589	A5YKK8|B2R4G8|D3DV32|O75597|Q4ZGI7|Q5T525|Q8NET7|Q9UDG3	Missense_Mutation	SNP	ENST00000295367.4	37	CCDS1033.1	21	0.009615384615384616	0	0.0	8	0.022099447513812154	0	0.0	13	0.017150395778364115	G	10.84	1.465063	0.26335	0.006128	0.016512	ENSG00000163209	ENST00000331860;ENST00000443178;ENST00000295367;ENST00000542696	T;T;T;T	0.11385	2.78;2.78;2.78;2.78	5.31	0.967	0.19674	.	.	.	.	.	T	0.05823	0.0152	L	0.31664	0.95	0.09310	N	1	D;P	0.62365	0.991;0.606	D;B	0.65233	0.933;0.177	T	0.29912	-0.9996	9	0.12766	T	0.61	.	8.245	0.31682	0.0767:0.0:0.5068:0.4165	.	97;105	F5GZ12;Q9UBC9	.;SPRR3_HUMAN	D	105;105;105;97	ENSP00000330391:G105D;ENSP00000402016:G105D;ENSP00000295367:G105D;ENSP00000441477:G97D	ENSP00000295367:G105D	G	+	2	0	SPRR3	151242434	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.009000	0.12765	0.242000	0.21303	-0.321000	0.08615	GGC	G|0.988;A|0.012	0.012	strong		0.572	SPRR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038910.1	NM_005416		A	152975810	G	A	152975810	3	1	26	1	0	0	0	0	1	0	0	0	15118	1203	42	2	316	2	SPRR3	1	152975810	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	226848	152975810	96274811	36	9799											
ILF2	3608	hgsc.bcm.edu	37	chr1	153635022	153635022	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatcccaggtagatatttcAgaagcaagatctaggaaaga	16	8	9	8	0	2	4	1	0	1	4	3	5	3	5	2	2	1	2	2	2	6	4			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:153635022A>G	ENST00000361891.4	-	14	1148	c.1023T>C	c.(1021-1023)tcT>tcC	p.S341S	ILF2_ENST00000480213.1_5'UTR	NM_001267809.1|NM_004515.3	NP_001254738.1|NP_004506.2	Q12905	ILF2_HUMAN	interleukin enhancer binding factor 2	341	DZF. {ECO:0000255|PROSITE- ProRule:PRU01040}.				immune response (GO:0006955)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|transferase activity (GO:0016740)			cervix(1)|kidney(1)|lung(4)|skin(1)	7	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			TAGATATTTCAGAAGCAAGAT	0.393																																					p.S341S		Atlas-SNP	.											.	ILF2	25	.	0			c.T1023C						PASS	.						121	120	120					1																	153635022		2203	4300	6503	SO:0001819	synonymous_variant	3608	exon14			TATTTCAGAAGCA	U10323	CCDS1050.1, CCDS72919.1	1q21.3	2012-12-04	2012-12-04		ENSG00000143621	ENSG00000143621			6037	protein-coding gene	gene with protein product		603181	"interleukin enhancer binding factor 2, 45kD", "interleukin enhancer binding factor 2, 45kDa"			7519613	Standard	NM_004515		Approved	NF45	uc001fcr.4	Q12905	OTTHUMG00000037087	ENST00000361891.4:c.1023T>C	1.37:g.153635022A>G		87	0	0		152	71	0.467105	NM_004515	A6NDB0|B2R8G7|Q5SR10|Q5SR11|Q7L7R3|Q9BWD4|Q9P1N0	Silent	SNP	ENST00000361891.4	37	CCDS1050.1																																																																																			.	.	none		0.393	ILF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090040.1	NM_004515		G	153635022	A	G	153635022	2	3	26	1	0	0	0	0	0	0	0	1	7720	175	7	3		3	ILF2	1	153635022	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	659212	153635022	95615599	37	9800											
ADAR	103	hgsc.bcm.edu	37	chr1	154573526	154573526	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtctcttaccgaggttcaTggggtggtccactctgctct	4	14	12	11	1	4	0	1	0	3	0	6	1	5	0	2	5	2	2	2	5	1	2			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:154573526T>C	ENST00000368474.4	-	2	1791	c.1592A>G	c.(1591-1593)cAt>cGt	p.H531R	ADAR_ENST00000368471.3_Missense_Mutation_p.H236R|ADAR_ENST00000292205.5_Missense_Mutation_p.H574R|ADAR_ENST00000471068.1_5'Flank	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	531	DRBM 1. {ECO:0000255|PROSITE- ProRule:PRU00266}.				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)		CCGAGGTTCATGGGGTGGTCC	0.527																																					p.H531R		Atlas-SNP	.											ADAR,NS,malignant_melanoma,-1,1	ADAR	113	1	0			c.A1592G						PASS	.						108	115	113					1																	154573526		2203	4300	6503	SO:0001583	missense	103	exon2			GGTTCATGGGGTG	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.1592A>G	1.37:g.154573526T>C	ENSP00000357459:p.His531Arg	211	0	0		242	102	0.421488	NM_015840	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Missense_Mutation	SNP	ENST00000368474.4	37	CCDS1071.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.978122	0.74360	.	.	ENSG00000160710	ENST00000292205;ENST00000368474;ENST00000368471;ENST00000529168	D;D;D;D	0.81499	-1.5;-1.5;-1.5;-1.5	4.77	3.62	0.41486	Double-stranded RNA-binding (3);Double-stranded RNA-binding-like (1);	0.154749	0.56097	D	0.000026	D	0.88332	0.6408	M	0.91354	3.2	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;0.997	D;D;D	0.91635	0.999;0.999;0.994	D	0.89488	0.3755	10	0.66056	D	0.02	-17.755	10.7753	0.46346	0.1421:0.0:0.0:0.8579	.	531;531;531	P55265-3;P55265-2;P55265	.;.;DSRAD_HUMAN	R	574;531;236;526	ENSP00000292205:H574R;ENSP00000357459:H531R;ENSP00000357456:H236R;ENSP00000431794:H526R	ENSP00000292205:H574R	H	-	2	0	ADAR	152840150	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	7.312000	0.78968	0.815000	0.34398	0.459000	0.35465	CAT	.	.	none		0.527	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111		C	154573526	T	C	154573526	3	2	26	1	0	0	0	0	1	0	0	0	281	1464	51	3	2144	3	ADAR	1	154573526	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	938504	154573526	94677095	38	9801											
FAM189B	10712	hgsc.bcm.edu	37	chr1	155217614	155217614	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccccgttgaggctgaggcTgtgggggcgggtaccacgct	4	7	18	12	3	0	2	0	2	0	0	0	2	0	2	3	5	1	5	3	5	1	2	rs553505679		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:155217614T>C	ENST00000361361.2	-	12	2475	c.1966A>G	c.(1966-1968)Agc>Ggc	p.S656G	FAM189B_ENST00000368368.3_Missense_Mutation_p.S638G|FAM189B_ENST00000350210.2_Missense_Mutation_p.S560G|FAM189B_ENST00000472550.1_5'Flank	NM_006589.2	NP_006580.2	P81408	F189B_HUMAN	family with sequence similarity 189, member B	656						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						AGGCTGAGGCTGTGGGGGCGG	0.647													T|||	1	0.000199681	0.0008	0.0	5008	,	,		14418	0.0		0.0	False		,,,				2504	0.0				p.S656G		Atlas-SNP	.											.	FAM189B	51	.	0			c.A1966G						PASS	.						11	11	11					1																	155217614		2144	4211	6355	SO:0001583	missense	10712	exon12			TGAGGCTGTGGGG	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.1966A>G	1.37:g.155217614T>C	ENSP00000354958:p.Ser656Gly	373	0	0		400	205	0.5125	NM_006589	B1AVS5|Q8IXL3|Q9BR66	Missense_Mutation	SNP	ENST00000361361.2	37	CCDS1103.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.066640	0.76301	.	.	ENSG00000160767	ENST00000350210;ENST00000368368;ENST00000361361	T;T;T	0.03272	3.99;3.99;3.99	4.51	4.51	0.55191	.	0.000000	0.64402	D	0.000008	T	0.03959	0.0111	N	0.19112	0.55	0.31239	N	0.695389	D;P;P;P	0.59767	0.986;0.924;0.954;0.924	D;P;D;P	0.70935	0.971;0.878;0.916;0.827	T	0.21348	-1.0248	10	0.87932	D	0	.	12.1475	0.54031	0.0:0.0:0.0:1.0	.	421;638;560;656	B1AVS2;B1AVS5;P81408-2;P81408	.;.;.;F189B_HUMAN	G	560;638;656	ENSP00000307128:S560G;ENSP00000357352:S638G;ENSP00000354958:S656G	ENSP00000307128:S560G	S	-	1	0	FAM189B	153484238	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.099000	0.64554	2.037000	0.60232	0.529000	0.55759	AGC	.	.	none		0.647	FAM189B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087224.1	NM_006589		C	155217614	T	C	155217614	3	2	26	1	0	0	0	0	1	0	0	0	5522	1580	55	3	44	3	FAM189B	1	155217614	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	644088	155217614	94033007	39	9802											
PRCC	5546	hgsc.bcm.edu	37	chr1	156761540	156761540	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aggacccggccctggtccccCcccaggaaattgccccagat	8	5	10	18	1	0	1	0	0	0	1	1	3	1	3	8	4	1	0	8	4	1	1	rs17850664	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:156761540C>A	ENST00000271526.4	+	4	1407	c.1135C>A	c.(1135-1137)Ccc>Acc	p.P379T	PRCC_ENST00000491853.1_3'UTR|PRCC_ENST00000353233.3_Intron	NM_005973.4	NP_005964.3	Q92733	PRCC_HUMAN	papillary renal cell carcinoma (translocation-associated)	379					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)					CCTGGTCCCCCCCCAGGAAAT	0.512			T	TFE3	papillary renal								C|||	21	0.00419329	0.0008	0.0043	5008	,	,		16912	0.0		0.0099	False		,,,				2504	0.0072				p.P379T		Atlas-SNP	.		Dom	yes		1	1q21.1	5546	papillary renal cell carcinoma (translocation-associated)		E	.	PRCC	39	.	0			c.C1135A						PASS	.	C	THR/PRO	12,4394	19.1+/-41.9	0,12,2191	74	74	74		1135	-1	0.2	1	dbSNP_123	74	84,8516	48.1+/-107.5	0,84,4216	yes	missense	PRCC	NM_005973.4	38	0,96,6407	AA,AC,CC		0.9767,0.2724,0.7381	benign	379/492	156761540	96,12910	2203	4300	6503	SO:0001583	missense	5546	exon4			GTCCCCCCCCAGG	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.1135C>A	1.37:g.156761540C>A	ENSP00000271526:p.Pro379Thr	154	0	0		163	86	0.527607	NM_005973	A8K1F7|O00665|O00724|Q5SZ06	Missense_Mutation	SNP	ENST00000271526.4	37	CCDS1157.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	7.049	0.564048	0.13498	0.002724	0.009767	ENSG00000143294	ENST00000271526;ENST00000368201	T	0.44482	0.92	5.39	-1.04	0.10068	.	0.674960	0.15238	N	0.273053	T	0.07458	0.0188	N	0.14661	0.345	0.32356	N	0.557795	B	0.11235	0.004	B	0.08055	0.003	T	0.30090	-0.9990	10	0.20519	T	0.43	-0.1729	6.3416	0.21327	0.1139:0.5723:0.0:0.3138	rs17850664	379	Q92733	PRCC_HUMAN	T	379;355	ENSP00000271526:P379T	ENSP00000271526:P379T	P	+	1	0	PRCC	155028164	0.001000	0.12720	0.160000	0.22671	0.907000	0.53573	-0.090000	0.11163	-0.094000	0.12374	0.655000	0.94253	CCC	C|0.993;A|0.007	0.007	strong		0.512	PRCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098941.2	NM_005973		A	156761540	C	A	156761540	3	1	26	1	0	0	0	0	1	0	0	0	12459	623	22	4	1149	4	PRCC	1	156761540	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1543926	156761540	92489081	40	9803											
FCRL5	83416	hgsc.bcm.edu	37	chr1	157488567	157488567	+	Frame_Shift_Del	DEL	G	G	-																															cttgggagtccgagtctgaaGggctcctgtgagacagagaa																										TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:157488567delG	ENST00000361835.3	-	14	2823	c.2666delC	c.(2665-2667)cctfs	p.P889fs	FCRL5_ENST00000461387.1_5'UTR|FCRL5_ENST00000356953.4_Frame_Shift_Del_p.P889fs	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	889					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)				CGAGTCTGAAGGGCTCCTGTG	0.493																																					p.P889fs		Pindel,Atlas-Indel	.											FCRL5,NS,carcinoma,-1,1	FCRL5	177	1	0			c.2667delT						PASS	.						93	91	92					1																	157488567		2203	4300	6503	SO:0001589	frameshift_variant	83416	exon14			.	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.2666delC	1.37:g.157488567delG	ENSP00000354691:p.Pro889fs	171	0	.		209	52	0.249	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Frame_Shift_Del	DEL	ENST00000361835.3	37	CCDS1165.1																																																																																			.	.	none		0.493	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281		-	157488567	G	-	157488567	7	5	26	1	0	1	0	1	0	0	0	0	5806	1000	35	0	283	0	FCRL5	1	157488567	Frame_Shift_Del	DEL	G	TCGA-G8-6907-01A-11D-2210-10	727027	157488567	91762054	41	9804											
FCGR3A	2214	hgsc.bcm.edu	37	chr1	161512873	161512873	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttgttgagcttcgaatgtTtgtcttcacagagaaatata	11	16	8	6	1	3	2	1	1	2	1	4	4	3	2	0	0	1	3	0	0	4	7	rs115866423	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:161512873T>A	ENST00000436743.1	-	6	848	c.694A>T	c.(694-696)Aac>Tac	p.N232Y	RP11-25K21.6_ENST00000537821.2_RNA|FCGR3A_ENST00000476031.1_5'Flank|FCGR3A_ENST00000443193.1_Missense_Mutation_p.N267Y|FCGR3A_ENST00000367969.3_Missense_Mutation_p.N268Y|FCGR3A_ENST00000540048.1_Missense_Mutation_p.N232Y	NM_001127593.1|NM_001127595.1|NM_001127596.1	NP_001121065.1|NP_001121067.1|NP_001121068.1	P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)	232					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)	CTTCGAATGTTTGTCTTCACA	0.443													T|||	29	0.00579073	0.0	0.0086	5008	,	,		22717	0.0		0.0099	False		,,,				2504	0.0133				p.N268Y		Atlas-SNP	.											.	FCGR3A	38	.	0			c.A802T						PASS	.	T	TYR/ASN,TYR/ASN,TYR/ASN,TYR/ASN,TYR/ASN	11,4395	19.1+/-41.9	0,11,2192	151	149	150		691,694,694,799,802	-2.9	0	1	dbSNP_132	150	100,8500	56.4+/-117.6	2,96,4202	no	missense,missense,missense,missense,missense	FCGR3A	NM_001127596.1,NM_001127595.1,NM_001127593.1,NM_001127592.1,NM_000569.6	143,143,143,143,143	2,107,6394	AA,AT,TT		1.1628,0.2497,0.8535	benign,benign,benign,benign,benign	231/254,232/255,232/255,267/290,268/291	161512873	111,12895	2203	4300	6503	SO:0001583	missense	2214	exon5			GAATGTTTGTCTT	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	ENST00000436743.1:c.694A>T	1.37:g.161512873T>A	ENSP00000416607:p.Asn232Tyr	417	0	0		407	196	0.481572	NM_000569	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000436743.1	37	CCDS44266.1	9|9	0.004120879120879121|0.004120879120879121	0|0	0.0|0.0	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	7|7	0.009234828496042216|0.009234828496042216	T|T	9.319|9.319	1.057646|1.057646	0.19907|0.19907	0.002497|0.002497	0.011628|0.011628	ENSG00000203747|ENSG00000203747	ENST00000367969;ENST00000443193;ENST00000436743;ENST00000367967;ENST00000540048|ENST00000426740	T;T;T;T;T|.	0.01484|.	4.84;4.84;4.89;4.89;4.89|.	3.88|3.88	-2.9|-2.9	0.05648|0.05648	.|.	14.258800|.	0.00166|.	U|.	0.000000|.	T|T	0.12860|0.12860	0.0312|0.0312	L|L	0.38175|0.38175	1.15|1.15	0.09310|0.09310	N|N	1|1	B;P;P|.	0.37864|.	0.087;0.61;0.49|.	B;B;B|.	0.31812|.	0.029;0.101;0.136|.	T|T	0.33979|0.33979	-0.9847|-0.9847	10|5	0.66056|.	D|.	0.02|.	.|.	4.9176|4.9176	0.13853|0.13853	0.0:0.3545:0.157:0.4885|0.0:0.3545:0.157:0.4885	.|.	232;267;232|.	P08637;E9PG94;Q9UPY7|.	FCG3A_HUMAN;.;.|.	Y|H	268;267;232;232;232|248	ENSP00000356946:N268Y;ENSP00000392047:N267Y;ENSP00000416607:N232Y;ENSP00000356944:N232Y;ENSP00000444971:N232Y|.	ENSP00000356944:N232Y|.	N|Q	-|-	1|3	0|2	FCGR3A|FCGR3A	159779497|159779497	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	-1.623000|-1.623000	0.02040|0.02040	-0.510000|-0.510000	0.06523|0.06523	0.482000|0.482000	0.46254|0.46254	AAC|CAA	T|0.993;A|0.007	0.007	strong		0.443	FCGR3A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102169.2	NM_000569		A	161512873	T	A	161512873	3	1	26	1	0	0	0	0	1	0	0	0	5792	1841	64	5	74	5	FCGR3A	1	161512873	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	4024306	161512873	87737748	42	9805											
KIAA1614	57710	hgsc.bcm.edu	37	chr1	180897634	180897634	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccacgcatctgctgcagcGtgcccgcatgaaggccagga	9	5	13	14	3	1	1	0	1	1	0	1	2	1	2	3	2	5	4	3	2	1	0	rs140222211	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:180897634G>A	ENST00000367588.4	+	4	1185	c.1130G>A	c.(1129-1131)cGt>cAt	p.R377H	KIAA1614_ENST00000367587.1_5'UTR	NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	377										NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						CTGCTGCAGCGTGCCCGCATG	0.687													G|||	14	0.00279553	0.0	0.0029	5008	,	,		14999	0.001		0.005	False		,,,				2504	0.0061				p.R377H		Atlas-SNP	.											.	KIAA1614	75	.	0			c.G1130A						PASS	.	G	HIS/ARG	5,4137		0,5,2066	49	56	54		1130	1.1	1	1	dbSNP_134	54	54,8378		1,52,4163	yes	missense	KIAA1614	NM_020950.1	29	1,57,6229	AA,AG,GG		0.6404,0.1207,0.4692	probably-damaging	377/1191	180897634	59,12515	2071	4216	6287	SO:0001583	missense	57710	exon4			TGCAGCGTGCCCG	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.1130G>A	1.37:g.180897634G>A	ENSP00000356560:p.Arg377His	177	0	0		202	95	0.470297	NM_020950	Q5VZ45|Q9HCF8	Missense_Mutation	SNP	ENST00000367588.4	37	CCDS41442.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	14.72	2.618956	0.46736	0.001207	0.006404	ENSG00000135835	ENST00000367588	T	0.22336	1.96	5.56	1.09	0.20402	.	0.498887	0.17274	N	0.180243	T	0.14874	0.0359	L	0.58101	1.795	0.37966	D	0.933112	B	0.13145	0.007	B	0.10450	0.005	T	0.13872	-1.0493	9	0.72032	D	0.01	-0.6487	9.816	0.40853	0.2886:0.0:0.7114:0.0	.	377	Q5VZ46	K1614_HUMAN	H	377	ENSP00000356560:R377H	ENSP00000356560:R377H	R	+	2	0	KIAA1614	179164257	0.993000	0.37304	0.971000	0.41717	0.997000	0.91878	2.386000	0.44380	0.254000	0.21573	0.650000	0.86243	CGT	G|0.997;A|0.003	0.003	strong		0.687	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531		A	180897634	G	A	180897634	3	1	26	1	0	0	0	0	1	0	0	0	8257	1145	40	1	1144	1	KIAA1614	1	180897634	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	19384761	180897634	68352987	43	9806											
KIF21B	23046	hgsc.bcm.edu	37	chr1	200978422	200978422	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggccagcaccgtggcattaTagccctcgaagcagccctcg	9	6	11	15	3	0	0	0	0	0	0	2	1	0	0	4	2	4	3	4	2	3	2			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:200978422T>C	ENST00000422435.2	-	2	552	c.236A>G	c.(235-237)tAt>tGt	p.Y79C	KIF21B_ENST00000332129.2_Missense_Mutation_p.Y79C|KIF21B_ENST00000461742.2_Missense_Mutation_p.Y79C|KIF21B_ENST00000360529.5_Missense_Mutation_p.Y79C	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	79	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						CGTGGCATTATAGCCCTCGAA	0.557																																					p.Y79C		Atlas-SNP	.											.	KIF21B	208	.	0			c.A236G						PASS	.						106	96	99					1																	200978422		2203	4300	6503	SO:0001583	missense	23046	exon2			GCATTATAGCCCT	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.236A>G	1.37:g.200978422T>C	ENSP00000411831:p.Tyr79Cys	170	0	0		211	116	0.549763	NM_017596	B2RP62|B7ZMI0|Q5T4J3	Missense_Mutation	SNP	ENST00000422435.2	37	CCDS58056.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.296788	0.81025	.	.	ENSG00000116852	ENST00000332129;ENST00000360529;ENST00000461742;ENST00000422435;ENST00000539858	T;T;T;T	0.75154	-0.91;-0.91;-0.91;-0.91	4.67	4.67	0.58626	Kinesin, motor domain (5);	0.000000	0.85682	D	0.000000	D	0.86497	0.5947	M	0.82630	2.6	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	0.88783	0.3272	10	0.87932	D	0	.	14.2798	0.66202	0.0:0.0:0.0:1.0	.	79;79;79;79	B7ZMI0;B2RP62;O75037;O75037-2	.;.;KI21B_HUMAN;.	C	79	ENSP00000328494:Y79C;ENSP00000353724:Y79C;ENSP00000433808:Y79C;ENSP00000411831:Y79C	ENSP00000328494:Y79C	Y	-	2	0	KIF21B	199245045	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.841000	0.86834	1.967000	0.57214	0.528000	0.53228	TAT	.	.	none		0.557	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332		C	200978422	T	C	200978422	3	2	26	1	0	0	0	0	1	0	0	0	8298	1406	49	3	4770	3	KIF21B	1	200978422	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	20080788	200978422	48272199	44	9807											
C4BPA	722	hgsc.bcm.edu	37	chr1	207287446	207287446	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctcattttggtgtccaggCaattgtggtcctccacccac	6	14	8	13	0	1	0	1	0	1	0	5	0	4	0	4	3	0	1	4	3	1	4			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:207287446C>G	ENST00000367070.3	+	3	338	c.144C>G	c.(142-144)ggC>ggG	p.G48G		NM_000715.3	NP_000706.1	P04003	C4BPA_HUMAN	complement component 4 binding protein, alpha	48					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						GGTGTCCAGGCAATTGTGGTC	0.443																																					p.G48G		Atlas-SNP	.											.	C4BPA	70	.	0			c.C144G						PASS	.						182	169	174					1																	207287446		2203	4300	6503	SO:0001630	splice_region_variant	722	exon3			TCCAGGCAATTGT	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.143-1C>G	1.37:g.207287446C>G		137	0	0		144	69	0.479167	NM_000715	Q5VVQ8	Silent	SNP	ENST00000367070.3	37	CCDS1477.1																																																																																			.	.	none		0.443	C4BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088089.3		Silent	G	207287446	C	G	207287446	5	3	26	1	0	0	0	0	0	0	1	0	2251	724	25	4	150	4	C4BPA	1	207287446	Splice_Site	SNP	C	TCGA-G8-6907-01A-11D-2210-10	6309024	207287446	41963175	45	9808											
CR2	1380	hgsc.bcm.edu	37	chr1	207648456	207648456	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catattcccacaatgacataGtgtatgttgactgcaatcct	12	13	6	10	0	0	2	0	2	0	0	2	2	2	2	2	0	1	3	2	0	5	5	rs144572703	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:207648456G>T	ENST00000367058.3	+	13	2623	c.2434G>T	c.(2434-2436)Gtg>Ttg	p.V812L	CR2_ENST00000367057.3_Missense_Mutation_p.V871L|CR2_ENST00000367059.3_Missense_Mutation_p.V812L|CR2_ENST00000458541.2_Missense_Mutation_p.V785L	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	812	Sushi 13. {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						CAATGACATAGTGTATGTTGA	0.448													G|||	10	0.00199681	0.0008	0.0014	5008	,	,		23285	0.0		0.002	False		,,,				2504	0.0061				p.V871L		Atlas-SNP	.											.	CR2	164	.	0			c.G2611T						PASS	.	G	LEU/VAL,LEU/VAL	18,4388	26.2+/-53.5	0,18,2185	177	156	163		2611,2434	0.4	0	1	dbSNP_134	163	49,8551	32.3+/-84.9	0,49,4251	yes	missense,missense	CR2	NM_001006658.2,NM_001877.4	32,32	0,67,6436	TT,TG,GG		0.5698,0.4085,0.5151	benign,benign	871/1093,812/1034	207648456	67,12939	2203	4300	6503	SO:0001583	missense	1380	exon14			GACATAGTGTATG	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.2434G>T	1.37:g.207648456G>T	ENSP00000356025:p.Val812Leu	159	0	0		173	83	0.479769	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Missense_Mutation	SNP	ENST00000367058.3	37	CCDS1478.1	4	0.0018315018315018315	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	5.431	0.264713	0.10294	0.004085	0.005698	ENSG00000117322	ENST00000367058;ENST00000367057;ENST00000367059;ENST00000458541	T;T;T;T	0.68331	-0.32;-0.32;-0.32;-0.32	4.7	0.427	0.16489	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.49287	0.1548	L	0.60845	1.875	0.09310	N	1	B;B;B	0.21520	0.039;0.012;0.057	B;B;B	0.27796	0.083;0.027;0.05	T	0.52215	-0.8605	9	0.56958	D	0.05	.	2.2553	0.04053	0.1786:0.1505:0.516:0.1549	.	812;812;871	Q5SR47;P20023;P20023-3	.;CR2_HUMAN;.	L	812;871;812;785	ENSP00000356025:V812L;ENSP00000356024:V871L;ENSP00000356026:V812L;ENSP00000404222:V785L	ENSP00000356024:V871L	V	+	1	0	CR2	205715079	0.006000	0.16342	0.000000	0.03702	0.195000	0.23768	0.157000	0.16402	-0.007000	0.14345	0.655000	0.94253	GTG	G|0.996;T|0.004	0.004	strong		0.448	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877		T	207648456	G	T	207648456	3	4	26	1	0	0	0	0	1	0	0	0	3844	1029	36	4	2665	4	CR2	1	207648456	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	361010	207648456	41602165	46	9809											
WNT9A	7483	hgsc.bcm.edu	37	chr1	228113073	228113073	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atgctcacggcctccaccagCgtctctgccacgcccgggtc	5	7	10	19	4	2	0	1	0	1	0	5	0	3	0	5	2	3	1	5	2	0	0	rs8192628	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:228113073C>G	ENST00000272164.5	-	2	253	c.243G>C	c.(241-243)acG>acC	p.T81T		NM_003395.2	NP_003386.1	O14904	WNT9A_HUMAN	wingless-type MMTV integration site family, member 9A	81					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)				CCTCCACCAGCGTCTCTGCCA	0.701													C|||	10	0.00199681	0.0	0.0	5008	,	,		16240	0.0		0.008	False		,,,				2504	0.002				p.T81T		Atlas-SNP	.											.	WNT9A	39	.	0			c.G243C						PASS	.	C		8,4394		0,8,2193	17	18	17		243	-6.8	0.9	1	dbSNP_117	17	82,8506		0,82,4212	no	coding-synonymous	WNT9A	NM_003395.2		0,90,6405	GG,GC,CC		0.9548,0.1817,0.6928		81/366	228113073	90,12900	2201	4294	6495	SO:0001819	synonymous_variant	7483	exon2			CACCAGCGTCTCT	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.243G>C	1.37:g.228113073C>G		82	0	0		56	26	0.464286	NM_003395	A6NLW2|Q2M2J3|Q5VWU0|Q96S50	Silent	SNP	ENST00000272164.5	37	CCDS31045.1																																																																																			G|0.005;C|0.995	0.005	strong		0.701	WNT9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091646.1	NM_003395		G	228113073	C	G	228113073	2	3	26	1	0	0	0	0	0	0	0	1	17413	755	27	4		4	WNT9A	1	228113073	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	20464617	228113073	21137548	47	9810											
GALNT2	2590	hgsc.bcm.edu	37	chr1	230386238	230386238	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtgggctgtttgtgatggAtaagttctattttgaagaac	9	16	13	3	0	1	3	0	2	1	1	1	4	1	4	0	3	1	3	0	3	4	6	rs78164071	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:230386238A>C	ENST00000366672.4	+	10	1013	c.941A>C	c.(940-942)gAt>gCt	p.D314A	GALNT2_ENST00000541865.1_Intron|GALNT2_ENST00000543760.1_Missense_Mutation_p.D276A	NM_004481.3	NP_004472.1	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2	314	Catalytic subdomain B.				cellular protein metabolic process (GO:0044267)|immunoglobulin biosynthetic process (GO:0002378)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(5)|skin(2)	32	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				TTTGTGATGGATAAGTTCTAT	0.488													A|||	6	0.00119808	0.0	0.0014	5008	,	,		19543	0.0		0.005	False		,,,				2504	0.0				p.D314A		Atlas-SNP	.											.	GALNT2	83	.	0			c.A941C						PASS	.	A	ALA/ASP	4,4402	9.9+/-24.2	0,4,2199	176	157	164		941	4.4	1	1	dbSNP_133	164	30,8570	22.2+/-67.0	0,30,4270	yes	missense	GALNT2	NM_004481.3	126	0,34,6469	CC,CA,AA		0.3488,0.0908,0.2614	benign	314/572	230386238	34,12972	2203	4300	6503	SO:0001583	missense	2590	exon10			TGATGGATAAGTT	BC041120	CCDS1582.1	1q41-q42	2014-03-13	2014-03-13		ENSG00000143641	ENSG00000143641	2.4.1.41	"Glycosyltransferase family 2 domain containing"	4124	protein-coding gene	gene with protein product	"polypeptide GalNAc transferase 2"	602274	"UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)"			9592121, 7592619	Standard	NM_004481		Approved	GalNAc-T2	uc010pwa.1	Q10471	OTTHUMG00000037771	ENST00000366672.4:c.941A>C	1.37:g.230386238A>C	ENSP00000355632:p.Asp314Ala	118	0	0		136	69	0.507353	NM_004481	A8K1Y3|B7Z8V8|C5HU00|Q9NPY4	Missense_Mutation	SNP	ENST00000366672.4	37	CCDS1582.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	A	16.68	3.189190	0.57909	9.08E-4	0.003488	ENSG00000143641	ENST00000543760;ENST00000366672;ENST00000543291	T;T	0.59772	0.24;0.24	4.43	4.43	0.53597	.	0.000000	0.85682	D	0.000000	T	0.50514	0.1620	M	0.80746	2.51	0.80722	D	1	B;B	0.32573	0.376;0.213	B;B	0.28305	0.088;0.018	T	0.63479	-0.6628	10	0.66056	D	0.02	.	13.6391	0.62239	1.0:0.0:0.0:0.0	.	314;276	Q10471;G3V1S6	GALT2_HUMAN;.	A	276;314;195	ENSP00000445017:D276A;ENSP00000355632:D314A	ENSP00000355632:D314A	D	+	2	0	GALNT2	228452861	1.000000	0.71417	0.986000	0.45419	0.977000	0.68977	8.799000	0.91895	1.761000	0.52028	0.379000	0.24179	GAT	A|0.997;C|0.003	0.003	strong		0.488	GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092158.1	NM_004481		C	230386238	A	C	230386238	3	2	26	1	0	0	0	0	1	0	0	0	6221	333	12	5	979	5	GALNT2	1	230386238	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	2273165	230386238	18864383	48	9811											
TRIM67	440730	hgsc.bcm.edu	37	chr1	231344908	231344908	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggccagcgtggtcaaggacAtgatgctgggcaaggatgac	10	6	17	8	1	1	2	1	2	0	0	1	4	1	4	1	5	2	2	1	5	2	0	rs114415891	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:231344908A>G	ENST00000366653.5	+	8	2035	c.2035A>G	c.(2035-2037)Atg>Gtg	p.M679V	TRIM67_ENST00000449018.3_Missense_Mutation_p.M617V|TRIM67_ENST00000444294.3_Missense_Mutation_p.M677V|TRIM67_ENST00000366652.2_Missense_Mutation_p.M679V			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67	679	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.			M -> V (in Ref. 3; BAC86689). {ECO:0000305}.	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)	p.M679V(1)		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)				GGTCAAGGACATGATGCTGGG	0.617													A|||	30	0.00599042	0.0	0.0072	5008	,	,		20231	0.0		0.0229	False		,,,				2504	0.002				p.M679V		Atlas-SNP	.											TRIM67_ENST00000366653,colon,carcinoma,-1,7	TRIM67	160	7	1	Substitution - Missense(1)	breast(1)	c.A2035G						PASS	.	A	VAL/MET	20,4368	26.2+/-53.5	0,20,2174	91	99	96		2035	5.7	1	1	dbSNP_132	96	142,8458	68.7+/-131.2	1,140,4159	yes	missense	TRIM67	NM_001004342.3	21	1,160,6333	GG,GA,AA		1.6512,0.4558,1.2473	benign	679/784	231344908	162,12826	2194	4300	6494	SO:0001583	missense	440730	exon8			AAGGACATGATGC	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.2035A>G	1.37:g.231344908A>G	ENSP00000355613:p.Met679Val	230	1	0.00434783		263	127	0.48289	NM_001004342	Q5TER7|Q5TER8|Q7Z4K7	Missense_Mutation	SNP	ENST00000366653.5	37	CCDS44333.1	19	0.0086996336996337	0	0.0	4	0.011049723756906077	0	0.0	15	0.01978891820580475	A	4.607	0.112797	0.08831	0.004558	0.016512	ENSG00000119283	ENST00000444294;ENST00000366652;ENST00000449018;ENST00000366653	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	5.73	5.73	0.89815	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.85682	D	0.000000	T	0.28400	0.0702	N	0.02721	-0.515	0.46981	D	0.999274	B	0.14012	0.009	B	0.17098	0.017	T	0.27739	-1.0065	10	0.28530	T	0.3	.	16.3197	0.82945	1.0:0.0:0.0:0.0	.	679	Q6ZTA4	TRI67_HUMAN	V	677;679;617;679	ENSP00000412124:M677V;ENSP00000355612:M679V;ENSP00000400163:M617V;ENSP00000355613:M679V	ENSP00000355612:M679V	M	+	1	0	TRIM67	229411531	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.313000	0.65798	2.302000	0.77476	0.533000	0.62120	ATG	A|0.990;G|0.010	0.010	strong		0.617	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	NM_001004342		G	231344908	A	G	231344908	3	3	26	1	0	0	0	0	1	0	0	0	16555	217	8	3	2065	3	TRIM67	1	231344908	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	958670	231344908	17905713	49	9812											
KIAA1383	54627	hgsc.bcm.edu	37	chr1	232943775	232943775	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tacctgccttcaaatgtgtcCgaacttaatgtcctggatag	10	13	8	10	1	1	0	1	0	0	0	3	2	3	1	4	1	3	0	4	1	5	4	rs147903928		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:232943775C>T	ENST00000418460.1	+	1	3133	c.3006C>T	c.(3004-3006)tcC>tcT	p.S1002S		NM_019090.2	NP_061963.2	Q9P2G4	MAP10_HUMAN	microtubule-associated protein 10	860					cytoplasmic microtubule organization (GO:0031122)|positive regulation of cytokinesis (GO:0032467)|regulation of microtubule-based process (GO:0032886)|spindle midzone assembly involved in mitosis (GO:0051256)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)	microtubule binding (GO:0008017)										CAAATGTGTCCGAACTTAATG	0.378													C|||	1	0.000199681	0.0	0.0	5008	,	,		17059	0.0		0.001	False		,,,				2504	0.0				p.S1002S		Atlas-SNP	.											.	.	.	.	0			c.C3006T						PASS	.	C		0,3776		0,0,1888	133	133	133		3006	-2.9	1	1	dbSNP_134	133	10,8194		0,10,4092	no	coding-synonymous	KIAA1383	NM_019090.2		0,10,5980	TT,TC,CC		0.1219,0.0,0.0835		1002/1048	232943775	10,11970	1888	4102	5990	SO:0001819	synonymous_variant	54627	exon1			TGTGTCCGAACTT	AB037804	CCDS44334.1	1q42.2	2013-02-12	2013-02-12	2013-02-12	ENSG00000212916	ENSG00000212916			29265	protein-coding gene	gene with protein product	"microtubule regulator 120 KDa"		"KIAA1383"	KIAA1383		23264731	Standard	NM_019090		Approved	MTR120	uc001hvh.2	Q9P2G4	OTTHUMG00000037819	ENST00000418460.1:c.3006C>T	1.37:g.232943775C>T		249	1	0.00401606		294	138	0.469388	NM_019090	A8K2F1|Q32MI1|Q58EZ9|Q5VV83	Silent	SNP	ENST00000418460.1	37	CCDS44334.1																																																																																			C|0.999;T|0.001	0.001	strong		0.378	MAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092317.3	NM_019090		T	232943775	C	T	232943775	2	4	26	1	0	0	0	0	0	0	0	1	8237	639	23	1		1	KIAA1383	1	232943775	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1598867	232943775	16306846	50	9813											
LYST	1130	hgsc.bcm.edu	37	chr1	235907279	235907279	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgtaattaatttacttacAatagatactttgaatccttc	14	17	3	7	0	0	2	0	1	0	1	2	2	1	2	1	0	3	1	1	0	8	9	rs201045270		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:235907279A>G	ENST00000389794.3	-	30	8325	c.8151T>C	c.(8149-8151)atT>atC	p.I2717I	LYST_ENST00000389793.2_Splice_Site_p.I2717I			Q99698	LYST_HUMAN	lysosomal trafficking regulator	2717					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)			ATTTACTTACAATAGATACTT	0.279																																					p.I2717I		Atlas-SNP	.											.	LYST	370	.	0			c.T8151C						PASS	.	A		0,4382		0,0,2191	31	36	34		8151	5.5	1	1		34	1,8567		0,1,4283	no	coding-synonymous-near-splice	LYST	NM_000081.2		0,1,6474	GG,GA,AA		0.0117,0.0,0.0077		2717/3802	235907279	1,12949	2191	4284	6475	SO:0001630	splice_region_variant	1130	exon30			ACTTACAATAGAT	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.8151+1T>C	1.37:g.235907279A>G		182	0	0		196	78	0.397959	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	37	CCDS31062.1																																																																																			.	.	weak		0.279	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		Silent	G	235907279	A	G	235907279	5	3	26	1	0	0	0	0	0	0	1	0	9137	144	5	3	3350	3	LYST	1	235907279	Splice_Site	SNP	A	TCGA-G8-6907-01A-11D-2210-10	2963504	235907279	13343342	51	9814											
NLRP3	114548	hgsc.bcm.edu	37	chr1	247588140	247588140	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gagcacggcctctgcgcccaCctctgggggctctgctcttt	3	10	12	16	2	4	0	0	0	4	0	4	1	4	0	3	3	3	3	3	3	0	1	rs111400208	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:247588140C>T	ENST00000336119.3	+	3	2141	c.1395C>T	c.(1393-1395)caC>caT	p.H465H	NLRP3_ENST00000366497.2_Silent_p.H465H|NLRP3_ENST00000348069.2_Silent_p.H465H|NLRP3_ENST00000366496.2_Silent_p.H465H|NLRP3_ENST00000391828.3_Silent_p.H465H|NLRP3_ENST00000474792.1_3'UTR|NLRP3_ENST00000391827.2_Silent_p.H465H	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	465	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				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)			TCTGCGCCCACCTCTGGGGGC	0.592													C|||	7	0.00139776	0.0	0.0014	5008	,	,		19340	0.0		0.006	False		,,,				2504	0.0				p.H465H		Atlas-SNP	.											.	NLRP3	286	.	0			c.C1395T						PASS	.	C	,,,,	4,4402	8.1+/-20.4	0,4,2199	28	28	28	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1395,1395,1395,1395,1395	3.2	0	1	dbSNP_132	28	47,8553	29.6+/-80.5	0,47,4253	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP3	NM_001079821.2,NM_001127461.2,NM_001127462.2,NM_004895.4,NM_183395.2	,,,,	0,51,6452	TT,TC,CC		0.5465,0.0908,0.3921	,,,,	465/1037,465/980,465/980,465/1037,465/923	247588140	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	114548	exon3			CGCCCACCTCTGG	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.1395C>T	1.37:g.247588140C>T		29	0	0		41	18	0.439024	NM_183395	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Silent	SNP	ENST00000336119.3	37	CCDS1632.1																																																																																			C|0.997;T|0.003	0.003	strong		0.592	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895		T	247588140	C	T	247588140	2	4	26	1	0	0	0	0	0	0	0	1	10487	506	18	2		2	NLRP3	1	247588140	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	11680861	247588140	1662481	52	9815											
OR2T3	343173	hgsc.bcm.edu	37	chr1	248637447	248637447	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttccttctacacctacatgCtcccgagttcctaccacaca	9	11	3	18	1	1	0	0	0	1	0	4	1	4	0	5	0	4	2	5	0	3	6	rs369769145		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248637447C>T	ENST00000359594.2	+	1	821	c.796C>T	c.(796-798)Ctc>Ttc	p.L266F		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	266						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)			CACCTACATGCTCCCGAGTTC	0.547																																					p.L266F		Atlas-SNP	.											.	OR2T3	79	.	0			c.C796T						PASS	.	C	PHE/LEU	0,4406		0,0,2203	363	338	347		796	1.4	0	1		347	1,8599	1.2+/-3.3	0,1,4299	no	missense	OR2T3	NM_001005495.1	22	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	266/319	248637447	1,13005	2203	4300	6503	SO:0001583	missense	343173	exon1			TACATGCTCCCGA		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.796C>T	1.37:g.248637447C>T	ENSP00000352604:p.Leu266Phe	856	0	0		957	292	0.30512	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	37	CCDS31117.1	.	.	.	.	.	.	.	.	.	.	c	11.19	1.565845	0.27915	0.0	1.16E-4	ENSG00000196539	ENST00000359594	T	0.37235	1.21	2.37	1.42	0.22433	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.31638	0.0803	L	0.33189	0.99	0.09310	N	1	P	0.41848	0.763	P	0.51016	0.656	T	0.17837	-1.0356	9	0.16420	T	0.52	.	3.9402	0.09323	0.0:0.593:0.2477:0.1593	.	266	Q8NH03	OR2T3_HUMAN	F	266	ENSP00000352604:L266F	ENSP00000352604:L266F	L	+	1	0	OR2T3	246704070	0.000000	0.05858	0.011000	0.14972	0.280000	0.26924	-1.065000	0.03458	0.109000	0.17891	0.186000	0.17326	CTC	.	.	none		0.547	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495		T	248637447	C	T	248637447	3	4	26	1	0	0	0	0	1	0	0	0	11032	797	28	2	798	2	OR2T3	1	248637447	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1049307	248637447	613174	53	9816											
TTC15	51112	hgsc.bcm.edu	37	chr2	3425749	3425749	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggctgctcaccagccacaCgacagattcactgcaggtga	10	6	11	14	2	2	2	2	1	0	1	2	3	2	2	2	2	3	3	2	2	0	1	rs145733257		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:3425749C>T	ENST00000324266.5	+	4	1457	c.1262C>T	c.(1261-1263)aCg>aTg	p.T421M	TRAPPC12_ENST00000382110.2_Missense_Mutation_p.T421M	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	421					vesicle-mediated transport (GO:0016192)												ACCAGCCACACGACAGATTCA	0.587													C|||	1	0.000199681	0.0	0.0	5008	,	,		20473	0.0		0.001	False		,,,				2504	0.0				p.T421M		Atlas-SNP	.											.	.	.	.	0			c.C1262T						PASS	.	C	MET/THR	1,4405	2.1+/-5.4	0,1,2202	28	27	28		1262	4.7	0.8	2	dbSNP_134	28	19,8581	12.6+/-44.7	0,19,4281	yes	missense	TTC15	NM_016030.5	81	0,20,6483	TT,TC,CC		0.2209,0.0227,0.1538	probably-damaging	421/736	3425749	20,12986	2203	4300	6503	SO:0001583	missense	51112	exon4			GCCACACGACAGA	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.1262C>T	2.37:g.3425749C>T	ENSP00000324318:p.Thr421Met	108	0	0		161	74	0.459627	NM_016030	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Missense_Mutation	SNP	ENST00000324266.5	37	CCDS1652.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	C|C	24.4|24.4	4.524474|4.524474	0.85600|0.85600	2.27E-4|2.27E-4	0.002209|0.002209	ENSG00000171853|ENSG00000171853	ENST00000441983|ENST00000382110;ENST00000304601;ENST00000324266	.|T;T	.|0.54866	.|0.55;0.55	4.72|4.72	4.72|4.72	0.59763|0.59763	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.72906	.|0.3519	M|M	0.78637|0.78637	2.42|2.42	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.73380	.|0.964;0.98	.|T	.|0.76942	.|-0.2772	.|10	.|0.66056	.|D	.|0.02	.|.	16.8604|16.8604	0.86016|0.86016	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|404;421	.|E7ENL7;Q8WVT3	.|.;TPC12_HUMAN	X|M	101|421;404;421	.|ENSP00000371544:T421M;ENSP00000324318:T421M	.|ENSP00000303612:T404M	R|T	+|+	1|2	2|0	TTC15|TTC15	3404756|3404756	1.000000|1.000000	0.71417|0.71417	0.841000|0.841000	0.33234|0.33234	0.976000|0.976000	0.68499|0.68499	7.133000|7.133000	0.77259|0.77259	2.439000|2.439000	0.82584|0.82584	0.563000|0.563000	0.77884|0.77884	CGA|ACG	C|0.999;T|0.001	0.001	strong		0.587	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030		T	3425749	C	T	3425749	3	4	26	1	0	0	0	0	1	0	0	0	16697	536	19	1	1272	1	TTC15	2	3425749	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10		3425749	239773624	54	9817											
NOL10	79954	hgsc.bcm.edu	37	chr2	10740989	10740989	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcaccttaccttaactttcTttttccatgtagatttctgc	7	20	3	11	0	3	1	1	0	2	1	4	1	4	1	3	0	3	1	3	0	3	8	rs115424813	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:10740989T>C	ENST00000381685.5	-	17	1517	c.1412A>G	c.(1411-1413)aAg>aGg	p.K471R	AC092687.5_ENST00000414538.1_RNA|NOL10_ENST00000538384.1_Missense_Mutation_p.K445R|NOL10_ENST00000345985.3_Missense_Mutation_p.K421R|NOL10_ENST00000542668.1_Missense_Mutation_p.K421R	NM_024894.3	NP_079170.2	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	471						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)		CTTAACTTTCTTTTTCCATGT	0.303													T|||	5	0.000998403	0.0008	0.0	5008	,	,		14204	0.0		0.004	False		,,,				2504	0.0				p.K471R		Atlas-SNP	.											.	NOL10	22	.	0			c.A1412G						PASS	.	T	ARG/LYS	1,4363		0,1,2181	147	126	133		1412	5.4	1	2	dbSNP_133	133	34,8502		0,34,4234	yes	missense	NOL10	NM_024894.2	26	0,35,6415	CC,CT,TT		0.3983,0.0229,0.2713	benign	471/689	10740989	35,12865	2182	4268	6450	SO:0001583	missense	79954	exon17			ACTTTCTTTTTCC	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.1412A>G	2.37:g.10740989T>C	ENSP00000371101:p.Lys471Arg	150	0	0		140	71	0.507143	NM_024894	A8K3R5|B4DLV0|Q53RC9|Q96TA5|Q9H7Y7|Q9H855	Missense_Mutation	SNP	ENST00000381685.5	37	CCDS1673.2	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	12.48	1.950627	0.34377	2.29E-4	0.003983	ENSG00000115761	ENST00000345985;ENST00000381685;ENST00000542668;ENST00000538384	T;T;T;T	0.48522	0.81;2.21;1.42;2.21	5.39	5.39	0.77823	.	0.041560	0.85682	D	0.000000	T	0.35248	0.0925	L	0.41573	1.285	0.53688	D	0.999975	B;B;B	0.12630	0.001;0.003;0.006	B;B;B	0.15052	0.007;0.012;0.005	T	0.15492	-1.0435	10	0.11182	T	0.66	-7.9689	10.455	0.44546	0.0:0.0825:0.0:0.9174	.	445;471;421	B4DLV0;Q9BSC4;Q9BSC4-2	.;NOL10_HUMAN;.	R	421;471;421;445	ENSP00000263837:K421R;ENSP00000371101:K471R;ENSP00000437625:K421R;ENSP00000439663:K445R	ENSP00000263837:K421R	K	-	2	0	NOL10	10658440	1.000000	0.71417	1.000000	0.80357	0.404000	0.30871	4.072000	0.57563	2.170000	0.68504	0.460000	0.39030	AAG	T|0.998;C|0.002	0.002	strong		0.303	NOL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239227.1	NM_024894		C	10740989	T	C	10740989	3	2	26	1	0	0	0	0	1	0	0	0	10529	1609	56	3	674	3	NOL10	2	10740989	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	7315240	10740989	232458384	55	9818											
MATN3	4148	hgsc.bcm.edu	37	chr2	20202930	20202930	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacaggcctcacctgaacacGttttcttgtcggcattcaag	9	11	8	13	2	3	1	2	1	1	0	4	1	3	1	2	2	1	2	2	2	2	4	rs77245812	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:20202930G>A	ENST00000407540.3	-	3	970	c.908C>T	c.(907-909)aCg>aTg	p.T303M	AC079145.4_ENST00000416575.1_RNA|MATN3_ENST00000421259.2_Intron	NM_002381.4	NP_002372.1	O15232	MATN3_HUMAN	matrilin 3	303	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.		T -> M (in dbSNP:rs28939676). {ECO:0000269|PubMed:12736871, ECO:0000269|PubMed:14729835, ECO:0000269|PubMed:15459972}.		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)					ACCTGAACACGTTTTCTTGTC	0.527													G|||	70	0.0139776	0.0	0.0101	5008	,	,		18855	0.001		0.0159	False		,,,				2504	0.047				p.T303M		Atlas-SNP	.											.	MATN3	28	.	0			c.C908T	GRCh37	CM031237	MATN3	M	rs77245812	PASS	.	G	MET/THR	20,4030		0,20,2005	127	118	121	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	908	5.5	0.4	2	dbSNP_131	121	122,8220		0,122,4049	yes	missense	MATN3	NM_002381.4	81	0,142,6054	AA,AG,GG		1.4625,0.4938,1.1459	probably-damaging	303/487	20202930	142,12250	2025	4171	6196	SO:0001583	missense	4148	exon3			GAACACGTTTTCT	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.908C>T	2.37:g.20202930G>A	ENSP00000383894:p.Thr303Met	111	0	0		171	65	0.380117	NM_002381	B2CPU0|Q4ZG02	Missense_Mutation	SNP	ENST00000407540.3	37	CCDS46226.1	17	0.007783882783882784	0	0.0	5	0.013812154696132596	0	0.0	12	0.0158311345646438	G	22.5	4.298303	0.81025	0.004938	0.014625	ENSG00000132031	ENST00000407540	D	0.88201	-2.35	5.5	5.5	0.81552	Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.93106	0.7805	H	0.95539	3.685	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93432	0.6786	10	0.72032	D	0.01	-21.4112	16.1448	0.81559	0.0:0.0:1.0:0.0	rs28939676;rs52790166	303	O15232	MATN3_HUMAN	M	303	ENSP00000383894:T303M	ENSP00000383894:T303M	T	-	2	0	MATN3	20066411	1.000000	0.71417	0.415000	0.26534	0.782000	0.44232	8.518000	0.90559	2.596000	0.87737	0.650000	0.86243	ACG	G|0.990;A|0.010	0.010	strong		0.527	MATN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323925.1	NM_002381		A	20202930	G	A	20202930	3	1	26	1	0	0	0	0	1	0	0	0	9344	1145	40	1	576	1	MATN3	2	20202930	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	9461941	20202930	222996443	56	9819											
HS1BP3	64342	hgsc.bcm.edu	37	chr2	20840851	20840851	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gactccccaacaaacaggacCttcctgggtagtggggggag	10	6	14	11	0	0	0	0	0	0	0	2	3	2	2	4	5	2	1	4	5	3	2	rs148915944		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:20840851C>T	ENST00000304031.3	-	3	313	c.288G>A	c.(286-288)aaG>aaA	p.K96K	HS1BP3_ENST00000402541.1_Silent_p.K96K|HS1BP3_ENST00000406618.3_Silent_p.K96K	NM_022460.3	NP_071905.3	Q53T59	H1BP3_HUMAN	HCLS1 binding protein 3	96	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.						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)					CAAACAGGACCTTCCTGGGTA	0.552													C|||	1	0.000199681	0.0	0.0014	5008	,	,		20113	0.0		0.0	False		,,,				2504	0.0				p.K96K		Atlas-SNP	.											.	HS1BP3	33	.	0			c.G288A						PASS	.	C		0,4406		0,0,2203	166	168	167		288	3.7	1	2	dbSNP_134	167	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	HS1BP3	NM_022460.3		0,4,6499	TT,TC,CC		0.0465,0.0,0.0308		96/393	20840851	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	64342	exon3			CAGGACCTTCCTG		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.288G>A	2.37:g.20840851C>T		43	0	0		41	19	0.463415	NM_022460	B2RAW2|D6W529|Q86VC2|Q8N367	Silent	SNP	ENST00000304031.3	37	CCDS1700.1																																																																																			C|0.999;T|0.001	0.001	strong		0.552	HS1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242863.1	NM_022460		T	20840851	C	T	20840851	2	4	26	1	0	0	0	0	0	0	0	1	7370	680	24	2		2	HS1BP3	2	20840851	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	637921	20840851	222358522	57	9820											
NCOA1	8648	hgsc.bcm.edu	37	chr2	24980955	24980955	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tacgaatgttcagaacatgaAcccaatgatggcccagatgc	14	8	9	10	1	1	4	1	2	0	2	1	5	1	4	2	1	4	1	2	1	5	2	rs150066931	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:24980955A>G	ENST00000406961.1	+	21	4647	c.3995A>G	c.(3994-3996)aAc>aGc	p.N1332S	NCOA1_ENST00000395856.3_Missense_Mutation_p.N1332S|NCOA1_ENST00000405141.1_Missense_Mutation_p.N1332S|NCOA1_ENST00000348332.3_Missense_Mutation_p.N1332S|NCOA1_ENST00000538539.1_Missense_Mutation_p.N1332S|NCOA1_ENST00000288599.5_Missense_Mutation_p.N1332S|NCOA1_ENST00000407230.1_Missense_Mutation_p.N1181S			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	1332					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)					CAGAACATGAACCCAATGATG	0.527			T	PAX3	alveolar rhadomyosarcoma								A|||	29	0.00579073	0.0	0.0072	5008	,	,		15823	0.0		0.001	False		,,,				2504	0.0235				p.N1332S		Atlas-SNP	.		Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	NCOA1	210	.	0			c.A3995G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN	0,4406		0,0,2203	161	132	142		3995,3995,3995	3.8	1	2	dbSNP_134	142	9,8591	7.1+/-27.0	0,9,4291	yes	missense,missense,missense	NCOA1	NM_003743.4,NM_147223.2,NM_147233.2	46,46,46	0,9,6494	GG,GA,AA		0.1047,0.0,0.0692	probably-damaging,probably-damaging,probably-damaging	1332/1442,1332/1400,1332/1441	24980955	9,12997	2203	4300	6503	SO:0001583	missense	8648	exon19			ACATGAACCCAAT	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.3995A>G	2.37:g.24980955A>G	ENSP00000385216:p.Asn1332Ser	226	0	0		272	130	0.477941	NM_147223	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Missense_Mutation	SNP	ENST00000406961.1	37	CCDS1712.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	A	19.15	3.771069	0.69992	0.0	0.001047	ENSG00000084676	ENST00000406961;ENST00000405141;ENST00000407230;ENST00000538539;ENST00000348332;ENST00000288599;ENST00000395856	T;T;T;T;T;T;T	0.02369	4.44;4.42;4.32;4.42;4.44;4.42;4.44	5.01	3.82	0.43975	.	0.165920	0.53938	D	0.000052	T	0.06872	0.0175	L	0.47716	1.5	0.41217	D	0.986487	D;D;P;D;D	0.61697	0.982;0.99;0.586;0.99;0.982	P;P;B;P;P	0.54889	0.584;0.763;0.28;0.763;0.584	T	0.18085	-1.0348	10	0.62326	D	0.03	.	10.6256	0.45506	0.9228:0.0:0.0771:0.0	.	1332;1332;1332;1332;1181	A8K1V4;Q15788-3;Q15788;Q15788-2;B5MCN7	.;.;NCOA1_HUMAN;.;.	S	1332;1332;1181;1332;1332;1332;1332	ENSP00000385216:N1332S;ENSP00000385097:N1332S;ENSP00000385195:N1181S;ENSP00000444039:N1332S;ENSP00000320940:N1332S;ENSP00000288599:N1332S;ENSP00000379197:N1332S	ENSP00000288599:N1332S	N	+	2	0	NCOA1	24834459	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.694000	0.61760	0.897000	0.36392	0.477000	0.44152	AAC	A|0.999;G|0.001	0.001	strong		0.527	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223		G	24980955	A	G	24980955	3	3	26	1	0	0	0	0	1	0	0	0	10237	43	2	3	4061	3	NCOA1	2	24980955	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	4140104	24980955	218218418	58	9821											
ADCY3	109	hgsc.bcm.edu	37	chr2	25062875	25062875	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccacacgcatgtccacccCagtcttggtcttctcccgca	6	9	6	20	2	3	0	0	0	3	0	5	0	4	0	6	1	0	2	6	1	0	2	rs201606553	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:25062875C>T	ENST00000260600.5	-	6	2073	c.1222G>A	c.(1222-1224)Ggg>Agg	p.G408R	ADCY3_ENST00000405392.1_Missense_Mutation_p.G19R	NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	408					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)					ATGTCCACCCCAGTCTTGGTC	0.642													C|||	4	0.000798722	0.0	0.0058	5008	,	,		18860	0.0		0.0	False		,,,				2504	0.0				p.G408R		Atlas-SNP	.											.	ADCY3	114	.	0			c.G1222A						PASS	.	C	ARG/GLY	0,4406		0,0,2203	94	100	98		1222	5.1	0.5	2		98	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ADCY3	NM_004036.3	125	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	408/1145	25062875	1,13005	2203	4300	6503	SO:0001583	missense	109	exon6			CCACCCCAGTCTT	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.1222G>A	2.37:g.25062875C>T	ENSP00000260600:p.Gly408Arg	93	0	0		125	60	0.48	NM_004036	B3KT86|Q53T54|Q9UDB1	Missense_Mutation	SNP	ENST00000260600.5	37	CCDS1715.1	.	.	.	.	.	.	.	.	.	.	C	17.55	3.417937	0.62622	0.0	1.16E-4	ENSG00000138031	ENST00000260600;ENST00000405392;ENST00000415879;ENST00000454027;ENST00000427849;ENST00000435135	D;D;D;D;D	0.84589	-1.87;-1.87;-1.87;-1.87;-1.87	5.05	5.05	0.67936	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.248631	0.39759	N	0.001263	D	0.83188	0.5200	N	0.20986	0.625	0.22827	N	0.998681	P;P;D	0.52996	0.843;0.843;0.957	P;P;P	0.55455	0.673;0.673;0.776	T	0.76016	-0.3113	10	0.44086	T	0.13	.	12.4747	0.55807	0.0:0.9179:0.0:0.0821	.	408;408;19	B7ZLX9;O60266;B3KT86	.;ADCY3_HUMAN;.	R	408;19;383;34;164;358	ENSP00000260600:G408R;ENSP00000384484:G19R;ENSP00000410120:G34R;ENSP00000399275:G164R;ENSP00000389799:G358R	ENSP00000260600:G408R	G	-	1	0	ADCY3	24916379	0.021000	0.18746	0.474000	0.27266	0.995000	0.86356	1.371000	0.34250	2.325000	0.78763	0.549000	0.68633	GGG	.	.	weak		0.642	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211574.2			T	25062875	C	T	25062875	3	4	26	1	0	0	0	0	1	0	0	0	295	594	21	2	2276	2	ADCY3	2	25062875	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	81920	25062875	218136498	59	9822											
ASXL2	55252	hgsc.bcm.edu	37	chr2	25972936	25972936	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttctcagattcctgttcagCagaggtgactggcttctgct	6	14	10	11	0	3	3	2	1	2	2	5	3	4	3	1	2	2	4	1	2	0	4	rs192716734	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:25972936C>T	ENST00000435504.4	-	12	1782	c.1489G>A	c.(1489-1491)Gct>Act	p.A497T	ASXL2_ENST00000404843.1_Missense_Mutation_p.A237T|ASXL2_ENST00000336112.4_Missense_Mutation_p.A469T|ASXL2_ENST00000272341.4_Missense_Mutation_p.A237T			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	497					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)					TCCTGTTCAGCAGAGGTGACT	0.453													C|||	7	0.00139776	0.0	0.0058	5008	,	,		20730	0.0		0.003	False		,,,				2504	0.0				p.A497T		Atlas-SNP	.											.	ASXL2	217	.	0			c.G1489A						PASS	.	C	THR/ALA	2,3826		0,2,1912	173	158	163		1489	4.2	1	2		163	44,8222		1,42,4090	yes	missense	ASXL2	NM_018263.4	58	1,44,6002	TT,TC,CC		0.5323,0.0522,0.3804	benign	497/1436	25972936	46,12048	1914	4133	6047	SO:0001583	missense	55252	exon11			GTTCAGCAGAGGT			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.1489G>A	2.37:g.25972936C>T	ENSP00000391447:p.Ala497Thr	129	0	0		158	76	0.481013	NM_018263	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Missense_Mutation	SNP	ENST00000435504.4	37		3	0.0013736263736263737	0	0.0	3	0.008287292817679558	0	0.0	0	0.0	C	11.46	1.644550	0.29246	5.22E-4	0.005323	ENSG00000143970	ENST00000435504;ENST00000336112;ENST00000404843;ENST00000272341	T;T;T;T	0.18338	2.24;2.24;2.22;2.22	6.01	4.22	0.49857	.	0.445872	0.26951	N	0.021661	T	0.10208	0.0250	L	0.48362	1.52	0.26143	N	0.980241	B;B	0.17852	0.006;0.024	B;B	0.13407	0.005;0.009	T	0.19811	-1.0294	10	0.14252	T	0.57	-2.402	11.1814	0.48631	0.0:0.8518:0.0:0.1482	.	237;497	Q76L83-2;Q76L83	.;ASXL2_HUMAN	T	497;469;237;237	ENSP00000391447:A497T;ENSP00000337250:A469T;ENSP00000383920:A237T;ENSP00000272341:A237T	ENSP00000272341:A237T	A	-	1	0	ASXL2	25826440	0.000000	0.05858	1.000000	0.80357	0.627000	0.37826	0.440000	0.21592	1.566000	0.49654	-0.142000	0.14014	GCT	C|0.997;T|0.003	0.003	strong		0.453	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263		T	25972936	C	T	25972936	3	4	26	1	0	0	0	0	1	0	0	0	1067	710	25	2	2826	2	ASXL2	2	25972936	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	910061	25972936	217226437	60	9823											
EIF2B4	8890	hgsc.bcm.edu	37	chr2	27590415	27590415	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgctgacaggggacggcacTgagtcaggaagctataatac	12	7	13	9	2	1	2	1	2	0	0	2	4	1	4	0	4	2	3	0	4	4	3			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:27590415T>C	ENST00000347454.4	-	9	965	c.794A>G	c.(793-795)cAg>cGg	p.Q265R	SNX17_ENST00000233575.2_5'Flank|EIF2B4_ENST00000493344.2_Missense_Mutation_p.Q286R|EIF2B4_ENST00000451130.2_Missense_Mutation_p.Q285R|AC074117.10_ENST00000412749.1_RNA|EIF2B4_ENST00000445933.2_Missense_Mutation_p.Q264R	NM_001034116.1|NM_015636.3	NP_001029288.1|NP_056451.3	Q9UI10	EI2BD_HUMAN	eukaryotic translation initiation factor 2B, subunit 4 delta, 67kDa	265					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)					GGGACGGCACTGAGTCAGGAA	0.433																																					p.Q285R		Atlas-SNP	.											.	EIF2B4	48	.	0			c.A854G						PASS	.						108	104	105					2																	27590415		2203	4300	6503	SO:0001583	missense	8890	exon8			CGGCACTGAGTCA	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.794A>G	2.37:g.27590415T>C	ENSP00000233552:p.Gln265Arg	64	0	0		62	28	0.451613	NM_172195	Q53RY7|Q5BJF4|Q9BUV9|Q9UBG4|Q9UIQ9|Q9UJ95	Missense_Mutation	SNP	ENST00000347454.4	37	CCDS33164.1	.	.	.	.	.	.	.	.	.	.	T	15.84	2.953247	0.53293	.	.	ENSG00000115211	ENST00000347454;ENST00000414437;ENST00000445933;ENST00000451130;ENST00000493344	D;D;D;D	0.92495	-3.05;-3.05;-3.05;-3.05	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	D	0.90793	0.7109	L	0.60455	1.87	0.80722	D	1	B;B;B;B	0.31790	0.34;0.34;0.071;0.057	B;B;B;B	0.36922	0.108;0.236;0.055;0.032	D	0.88128	0.2836	10	0.21014	T	0.42	-20.7409	15.2744	0.73732	0.0:0.0:0.0:1.0	.	262;264;265;285	F5H6W1;Q9UI10-3;Q9UI10;Q9UI10-2	.;.;EI2BD_HUMAN;.	R	265;262;264;285;286	ENSP00000233552:Q265R;ENSP00000394397:Q264R;ENSP00000394869:Q285R;ENSP00000429323:Q286R	ENSP00000233552:Q265R	Q	-	2	0	EIF2B4	27443919	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.460000	0.80816	2.288000	0.76882	0.533000	0.62120	CAG	.	.	none		0.433	EIF2B4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324448.1			C	27590415	T	C	27590415	3	2	26	1	0	0	0	0	1	0	0	0	5005	1580	55	3	797	3	EIF2B4	2	27590415	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	1617479	27590415	215608958	61	9824											
FAM179A	165186	hgsc.bcm.edu	37	chr2	29259543	29259543	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctctccatcatcatcactgTtgcagacaacctcaactcca	11	10	4	16	0	5	1	4	0	1	1	7	1	6	1	3	0	3	3	3	0	2	1	rs72788155	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:29259543T>C	ENST00000379558.4	+	18	2906	c.2555T>C	c.(2554-2556)gTt>gCt	p.V852A	FAM179A_ENST00000465300.1_3'UTR|FAM179A_ENST00000403861.2_Missense_Mutation_p.V797A	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	852										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						ATCATCACTGTTGCAGACAAC	0.562													T|||	18	0.00359425	0.0008	0.0014	5008	,	,		19875	0.0		0.0129	False		,,,				2504	0.0031				p.V852A		Atlas-SNP	.											.	FAM179A	106	.	0			c.T2555C						PASS	.	T	ALA/VAL	21,4385	29.0+/-57.7	0,21,2182	125	94	104		2555	3.7	0.4	2	dbSNP_130	104	191,8409	84.2+/-146.7	2,187,4111	yes	missense	FAM179A	NM_199280.2	64	2,208,6293	CC,CT,TT		2.2209,0.4766,1.63	benign	852/1020	29259543	212,12794	2203	4300	6503	SO:0001583	missense	165186	exon18			TCACTGTTGCAGA	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.2555T>C	2.37:g.29259543T>C	ENSP00000368876:p.Val852Ala	159	0	0		151	76	0.503311	NM_199280	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	37	CCDS1769.2	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	T	15.18	2.757343	0.49468	0.004766	0.022209	ENSG00000189350	ENST00000379558;ENST00000403861	T;T	0.69040	-0.37;-0.37	6.04	3.68	0.42216	Armadillo-like helical (1);Armadillo-type fold (1);	0.350805	0.24774	N	0.035714	T	0.37839	0.1018	L	0.38531	1.155	0.24198	N	0.995528	B;B;B	0.25390	0.096;0.125;0.082	B;B;B	0.25140	0.039;0.041;0.058	T	0.31024	-0.9958	10	0.34782	T	0.22	.	9.9505	0.41636	0.0:0.128:0.0:0.872	.	797;852;150	F8W8E4;Q6ZUX3;Q6ZUX3-3	.;F179A_HUMAN;.	A	852;797	ENSP00000368876:V852A;ENSP00000384699:V797A	ENSP00000368876:V852A	V	+	2	0	FAM179A	29113047	0.951000	0.32395	0.374000	0.26016	0.893000	0.52053	3.920000	0.56446	0.540000	0.28808	0.459000	0.35465	GTT	T|0.988;C|0.012	0.012	strong		0.562	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280		C	29259543	T	C	29259543	3	2	26	1	0	0	0	0	1	0	0	0	5510	1725	60	3	2621	3	FAM179A	2	29259543	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	1669128	29259543	213939830	62	9825											
LBH	81606	hgsc.bcm.edu	37	chr2	30480466	30480466	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gataactgcgaagagacagcGaaagaaaataaagagcagta	21	4	11	5	2	0	3	0	0	0	3	0	7	0	3	0	0	4	2	0	0	8	3	rs372905950		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:30480466G>A	ENST00000395323.3	+	3	505	c.297G>A	c.(295-297)gcG>gcA	p.A99A	LBH_ENST00000407930.2_Silent_p.A82A|LBH_ENST00000401506.1_Silent_p.A105A|LBH_ENST00000406087.1_3'UTR|LBH_ENST00000467242.1_3'UTR|LBH_ENST00000404397.1_Intron	NM_030915.3	NP_112177.2	Q53QV2	LBH_HUMAN	limb bud and heart development	99					multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|large_intestine(1)|lung(2)	5	Acute lymphoblastic leukemia(172;0.155)					AAGAGACAGCGAAAGAAAATA	0.542													G|||	1	0.000199681	0.0	0.0	5008	,	,		16752	0.0		0.0	False		,,,				2504	0.001				p.A99A		Atlas-SNP	.											.	LBH	14	.	0			c.G297A						PASS	.	G		0,4406		0,0,2203	43	45	44		297	2	0.1	2		44	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	LBH	NM_030915.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		99/106	30480466	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	81606	exon3			GACAGCGAAAGAA	AF110224	CCDS33173.1	2p23.1	2012-12-07	2012-12-07		ENSG00000213626	ENSG00000213626			29532	protein-coding gene	gene with protein product		611763	"limb bud and heart development homolog (mouse)"			11230166, 11336496	Standard	NM_030915		Approved		uc002rne.2	Q53QV2	OTTHUMG00000152051	ENST00000395323.3:c.297G>A	2.37:g.30480466G>A		68	0	0		69	34	0.492754	NM_030915	B2RBC2|Q9H0Q1	Silent	SNP	ENST00000395323.3	37	CCDS33173.1																																																																																			.	.	weak		0.542	LBH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325091.1	NM_030915		A	30480466	G	A	30480466	2	1	26	1	0	0	0	0	0	0	0	1	8659	1045	37	1		1	LBH	2	30480466	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1220923	30480466	212718907	63	9826											
PRKD3	23683	hgsc.bcm.edu	37	chr2	37505108	37505108	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gattgtacaaccctcattagCggaatattattgcttgttga	11	15	8	7	1	1	1	1	1	0	0	1	3	1	2	1	1	4	3	1	1	6	8	rs116096831	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:37505108C>T	ENST00000379066.1	-	9	1959	c.1197G>A	c.(1195-1197)ccG>ccA	p.P399P	PRKD3_ENST00000234179.2_Silent_p.P399P			O94806	KPCD3_HUMAN	protein kinase D3	399					intracellular signal transduction (GO:0035556)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)			breast(3)|central_nervous_system(2)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33		all_hematologic(82;0.21)				CCCTCATTAGCGGAATATTAT	0.368													C|||	10	0.00199681	0.0	0.0029	5008	,	,		16204	0.0		0.005	False		,,,				2504	0.0031				p.P399P	Melanoma(80;621 1355 8613 11814 51767)	Atlas-SNP	.											.	PRKD3	170	.	0			c.G1197A						PASS	.	C		3,4403	8.1+/-20.4	0,3,2200	191	157	168		1197	-6	0.9	2	dbSNP_132	168	46,8554	30.1+/-81.4	0,46,4254	no	coding-synonymous	PRKD3	NM_005813.3		0,49,6454	TT,TC,CC		0.5349,0.0681,0.3767		399/891	37505108	49,12957	2203	4300	6503	SO:0001819	synonymous_variant	23683	exon8			CATTAGCGGAATA	AB015982	CCDS1789.1	2p21	2013-01-10	2004-10-28	2004-10-30	ENSG00000115825	ENSG00000115825		"Pleckstrin homology (PH) domain containing"	9408	protein-coding gene	gene with protein product		607077	"protein kinase C, nu"	PRKCN		10231560	Standard	NM_005813		Approved	EPK2	uc002rqd.3	O94806	OTTHUMG00000100961	ENST00000379066.1:c.1197G>A	2.37:g.37505108C>T		155	0	0		140	82	0.585714	NM_005813	D6W587|Q53TR7|Q8NEL8	Silent	SNP	ENST00000379066.1	37	CCDS1789.1																																																																																			C|0.996;T|0.004	0.004	strong		0.368	PRKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218570.3	NM_005813		T	37505108	C	T	37505108	2	4	26	1	0	0	0	0	0	0	0	1	12532	755	27	1		1	PRKD3	2	37505108	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	7024642	37505108	205694265	64	9827											
GPR75	10936	hgsc.bcm.edu	37	chr2	54081548	54081548	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atggaaagtgaagcagaaagCatccgggatactactggctg	14	7	13	7	1	0	2	0	1	0	1	1	4	1	4	1	3	4	3	1	3	5	2	rs34000641	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:54081548C>T	ENST00000394705.2	-	2	616	c.346G>A	c.(346-348)Gct>Act	p.A116T	GPR75-ASB3_ENST00000352846.3_Intron|ASB3_ENST00000498475.2_Intron|ASB3_ENST00000406625.2_Intron	NM_006794.3	NP_006785.1	O95800	GPR75_HUMAN	G protein-coupled receptor 75	116	Phe-rich.		A -> T (in dbSNP:rs34000641). {ECO:0000269|PubMed:11466257}.		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)			AAGCAGAAAGCATCCGGGATA	0.517													C|||	82	0.0163738	0.0015	0.0331	5008	,	,		22590	0.0		0.0358	False		,,,				2504	0.0215				p.A116T		Atlas-SNP	.											.	GPR75	55	.	0			c.G346A						PASS	.	C	,THR/ALA	25,4381	30.8+/-60.4	0,25,2178	78	79	79		,346	1.9	0	2	dbSNP_126	79	288,8312	107.0+/-167.8	4,280,4016	yes	intron,missense	GPR75,GPR75-ASB3	NM_001164165.1,NM_006794.3	,58	4,305,6194	TT,TC,CC		3.3488,0.5674,2.4066	,benign	,116/541	54081548	313,12693	2203	4300	6503	SO:0001583	missense	10936	exon2			AGAAAGCATCCGG	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.346G>A	2.37:g.54081548C>T	ENSP00000378195:p.Ala116Thr	110	0	0		154	77	0.5	NM_006794	B2RC02|Q6NWR2	Missense_Mutation	SNP	ENST00000394705.2	37	CCDS1849.1	41	0.018772893772893772	3	0.006097560975609756	13	0.03591160220994475	0	0.0	25	0.032981530343007916	C	11.13	1.546930	0.27652	0.005674	0.033488	ENSG00000119737	ENST00000394705	T	0.73789	-0.78	5.75	1.93	0.25924	GPCR, rhodopsin-like superfamily (1);	0.420647	0.28057	N	0.016775	T	0.23926	0.0579	.	.	.	0.26102	N	0.980802	B	0.02656	0.0	B	0.09377	0.004	T	0.10177	-1.0641	9	0.17369	T	0.5	0.8186	10.2743	0.43501	0.0:0.6632:0.0:0.3368	rs34000641	116	O95800	GPR75_HUMAN	T	116	ENSP00000378195:A116T	ENSP00000378195:A116T	A	-	1	0	GPR75	53935052	0.005000	0.15991	0.026000	0.17262	0.978000	0.69477	0.367000	0.20382	0.073000	0.16731	0.561000	0.74099	GCT	C|0.975;T|0.025	0.025	strong		0.517	GPR75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251403.2			T	54081548	C	T	54081548	3	4	26	1	0	0	0	0	1	0	0	0	6716	710	25	2	1280	2	GPR75	2	54081548	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	16576440	54081548	189117825	65	9828											
SPTBN1	6711	hgsc.bcm.edu	37	chr2	54858435	54858435	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctctctaggacccagacagCgatcgcctcggaggacatgc	9	6	12	14	3	1	1	0	0	1	1	4	5	1	4	2	3	2	1	2	3	1	1	rs377200533		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:54858435C>T	ENST00000356805.4	+	16	3532	c.3251C>T	c.(3250-3252)gCg>gTg	p.A1084V	SPTBN1_ENST00000333896.5_Missense_Mutation_p.A1071V	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1084					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)			ACCCAGACAGCGATCGCCTCG	0.587																																					p.A1084V		Atlas-SNP	.											.	SPTBN1	378	.	0			c.C3251T						PASS	.	C	VAL/ALA,VAL/ALA	0,4406		0,0,2203	91	87	88		3212,3251	5.6	1	2		88	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	SPTBN1	NM_178313.2,NM_003128.2	64,64	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	1071/2156,1084/2365	54858435	1,13005	2203	4300	6503	SO:0001583	missense	6711	exon16			AGACAGCGATCGC		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.3251C>T	2.37:g.54858435C>T	ENSP00000349259:p.Ala1084Val	113	0	0		116	56	0.482759	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	37	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	C	18.79	3.699502	0.68501	0.0	1.16E-4	ENSG00000115306	ENST00000356805;ENST00000333896	T;T	0.49432	0.78;0.78	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.49609	0.1567	L	0.49640	1.575	0.80722	D	1	B;B	0.22800	0.029;0.075	B;B	0.29598	0.046;0.104	T	0.45425	-0.9262	10	0.54805	T	0.06	.	19.5376	0.95260	0.0:1.0:0.0:0.0	.	1071;1084	Q01082-3;Q01082	.;SPTB2_HUMAN	V	1084;1071	ENSP00000349259:A1084V;ENSP00000334156:A1071V	ENSP00000334156:A1071V	A	+	2	0	SPTBN1	54711939	1.000000	0.71417	0.997000	0.53966	0.709000	0.40893	4.910000	0.63321	2.620000	0.88729	0.655000	0.94253	GCG	.	.	weak		0.587	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3			T	54858435	C	T	54858435	3	4	26	1	0	0	0	0	1	0	0	0	15134	768	27	1	3422	1	SPTBN1	2	54858435	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	776887	54858435	188340938	66	9829											
CCT4	10575	hgsc.bcm.edu	37	chr2	62103327	62103327	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctctcttctcgcagcactcGgtccatctgggcatagtcag	6	12	9	14	2	5	0	1	0	4	0	9	0	6	0	1	2	1	3	1	2	1	2	rs115496486	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:62103327G>T	ENST00000394440.3	-	8	1116	c.820C>A	c.(820-822)Cga>Aga	p.R274R	CCT4_ENST00000544079.1_Silent_p.R244R|CCT4_ENST00000538252.1_Silent_p.R218R|AC107081.5_ENST00000425779.1_RNA|CCT4_ENST00000544185.1_Silent_p.R124R|CCT4_ENST00000461540.2_5'UTR	NM_006430.3	NP_006421.2	P50991	TCPD_HUMAN	chaperonin containing TCP1, subunit 4 (delta)	274					'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)			CGCAGCACTCGGTCCATCTGG	0.328													G|||	14	0.00279553	0.0	0.0058	5008	,	,		16234	0.0		0.0099	False		,,,				2504	0.0				p.R274R		Atlas-SNP	.											.	CCT4	38	.	0			c.C820A						PASS	.	G		6,4400	11.4+/-27.6	0,6,2197	103	107	106		820	2.1	1	2	dbSNP_132	106	44,8556	29.0+/-79.6	0,44,4256	no	coding-synonymous	CCT4	NM_006430.2		0,50,6453	TT,TG,GG		0.5116,0.1362,0.3844		274/540	62103327	50,12956	2203	4300	6503	SO:0001819	synonymous_variant	10575	exon8			GCACTCGGTCCAT		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.820C>A	2.37:g.62103327G>T		150	0	0		231	87	0.376623	NM_006430	B2R6I3|B7Z8B1|F5H5W3|O14870|Q53QP9|Q96C51	Silent	SNP	ENST00000394440.3	37	CCDS33206.1																																																																																			G|0.996;T|0.004	0.004	strong		0.328	CCT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325548.2			T	62103327	G	T	62103327	2	4	26	1	0	0	0	0	0	0	0	1	2957	1124	39	4		4	CCT4	2	62103327	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	7244892	62103327	181096046	67	9830											
C2orf42	54980	hgsc.bcm.edu	37	chr2	70387826	70387826	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctatacgaccgtaggtttCtgctatgctttctacttcca	7	17	6	11	2	3	0	0	0	3	0	4	1	4	0	2	1	4	4	2	1	5	9			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:70387826C>A	ENST00000264434.2	-	9	1826	c.1447G>T	c.(1447-1449)Gaa>Taa	p.E483*	C2orf42_ENST00000420306.1_Nonsense_Mutation_p.E483*	NM_017880.1	NP_060350.1	Q9NWW7	CB042_HUMAN	chromosome 2 open reading frame 42	483										endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(1)	12						CCGTAGGTTTCTGCTATGCTT	0.418																																					p.E483X		Atlas-SNP	.											.	C2orf42	30	.	0			c.G1447T						PASS	.						156	154	154					2																	70387826		2203	4300	6503	SO:0001587	stop_gained	54980	exon9			AGGTTTCTGCTAT	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.1447G>T	2.37:g.70387826C>A	ENSP00000264434:p.Glu483*	262	0	0		370	247	0.667568	NM_017880	D6W5G3|Q9H629	Nonsense_Mutation	SNP	ENST00000264434.2	37	CCDS1899.1	.	.	.	.	.	.	.	.	.	.	C	37	6.198271	0.97367	.	.	ENSG00000115998	ENST00000264434;ENST00000420306	.	.	.	5.24	5.24	0.73138	.	0.212745	0.47852	D	0.000210	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-25.1419	17.5771	0.87953	0.0:1.0:0.0:0.0	.	.	.	.	X	483	.	ENSP00000264434:E483X	E	-	1	0	C2orf42	70241330	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.278000	0.65592	2.726000	0.93360	0.650000	0.86243	GAA	.	.	none		0.418	C2orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251840.1	NM_017880		A	70387826	C	A	70387826	4	1	26	1	0	0	0	0	0	1	0	0	2168	922	32	4	285	4	C2orf42	2	70387826	Nonsense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	8284499	70387826	172811547	68	9831											
DYSF	8291	hgsc.bcm.edu	37	chr2	71871177	71871195	+	Splice_Site	DEL	ATTTTGACACCCTGAAGGT	ATTTTGACACCCTGAAGGT	-																															cggctcctacctggagaaggAttttgacaccctgaaggtaa																								rs7573406|rs199861501|rs200809348	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	ATTTTGACACCCTGAAGGT	ATTTTGACACCCTGAAGGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:71871177_71871195delATTTTGACACCCTGAAGGT	ENST00000258104.3	+	41	4770_4786	c.4493_4509delATTTTGACACCCTGAAGGT	c.(4492-4509)gattttgacaccctgaag>g	p.DFDTLK1498fs	DYSF_ENST00000410020.3_Splice_Site_p.DFDTLK1537fs|DYSF_ENST00000429174.2_Splice_Site_p.DFDTLK1519fs|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000409744.1_Splice_Site_p.DFDTLK1506fs|DYSF_ENST00000409651.1_Splice_Site_p.DFDTLK1530fs|DYSF_ENST00000394120.2_Splice_Site_p.DFDTLK1499fs|DYSF_ENST00000413539.2_Splice_Site_p.DFDTLK1529fs|DYSF_ENST00000409582.3_Splice_Site_p.DFDTLK1536fs|DYSF_ENST00000410041.1_Splice_Site_p.DFDTLK1516fs|DYSF_ENST00000409762.1_Splice_Site_p.DFDTLK1515fs|DYSF_ENST00000409366.1_Splice_Site_p.DFDTLK1520fs	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1498					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						CTGGAGAAGGATTTTGACACCCTGAAGGTAAGGCCTCTC	0.493																																					p.1537_1542del		Pindel,Atlas-Indel	.											.	DYSF	536	.	0			c.4609_4626del	GRCh37	CD031501	DYSF	D		PASS	.																																			SO:0001630	splice_region_variant	8291	exon42			.	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.4509+1ATTTTGACACCCTGAAGGT>-	2.37:g.71871177_71871195delATTTTGACACCCTGAAGGT		180	0	.		211	57	0.27	NM_001130987	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	In_Frame_Del	DEL	ENST00000258104.3	37	CCDS1918.1																																																																																			.	.	none		0.493	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	Frame_Shift_Del	-	71871195	ATTTTGACACCCTGAAGGT	-	71871177	8	5	26	1	0	1	0	1	0	0	1	0	4861	333	12	0	4914	0	DYSF	2	71871177	Splice_Site	DEL	ATTTTGACACCCTGAAGGT	TCGA-G8-6907-01A-11D-2210-10	1483351	71871177	171328196	69	9832											
ALMS1	7840	hgsc.bcm.edu	37	chr2	73681184	73681184	+	Frame_Shift_Del	DEL	A	A	-																															gaggaagaggaaagccgggtAcgagcacatggtaagaagaa																										TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:73681184delA	ENST00000264448.6	+	8	7638	c.7527delA	c.(7525-7527)gtafs	p.V2509fs	ALMS1_ENST00000377715.1_Frame_Shift_Del_p.V2509fs|ALMS1_ENST00000409009.1_Frame_Shift_Del_p.V2467fs|ALMS1-IT1_ENST00000441587.2_RNA	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2509					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						AAAGCCGGGTACGAGCACATG	0.368																																					p.V2509fs		Pindel,Atlas-Indel	.											ALMS1,NS,carcinoma,0,1	ALMS1	384	1	0			c.7526delT						PASS	.						34	32	33					2																	73681184		1889	4102	5991	SO:0001589	frameshift_variant	7840	exon8			.	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.7527delA	2.37:g.73681184delA	ENSP00000264448:p.Val2509fs	92	0	.		135	30	0.222	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Frame_Shift_Del	DEL	ENST00000264448.6	37	CCDS42697.1																																																																																			.	.	none		0.368	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		-	73681184	A	-	73681184	7	5	26	1	0	1	0	1	0	0	0	0	535	378	14	0	7557	0	ALMS1	2	73681184	Frame_Shift_Del	DEL	A	TCGA-G8-6907-01A-11D-2210-10	1810007	73681184	169518189	70	9833											
GGCX	2677	hgsc.bcm.edu	37	chr2	85783341	85783341	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatagttccaaaggggcacGtgggcattcctcctatgggc	8	9	13	11	1	0	0	0	0	0	0	3	0	3	0	3	4	0	4	3	4	3	4	rs76767923	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:85783341G>A	ENST00000233838.4	-	5	662	c.582C>T	c.(580-582)caC>caT	p.H194H	GGCX_ENST00000473665.1_5'Flank|GGCX_ENST00000430215.3_Silent_p.H137H	NM_000821.5	NP_000812.2	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase	194					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)	AAAGGGGCACGTGGGCATTCC	0.557													G|||	7	0.00139776	0.0	0.0014	5008	,	,		14470	0.0		0.006	False		,,,				2504	0.0				p.H194H		Atlas-SNP	.											.	GGCX	44	.	0			c.C582T						PASS	.	G	,	7,4399	11.4+/-27.6	0,7,2196	127	93	104		582,411	-11.9	0.5	2	dbSNP_131	104	43,8557	27.9+/-77.7	0,43,4257	no	coding-synonymous,coding-synonymous	GGCX	NM_000821.5,NM_001142269.2	,	0,50,6453	AA,AG,GG		0.5,0.1589,0.3844	,	194/759,137/702	85783341	50,12956	2203	4300	6503	SO:0001819	synonymous_variant	2677	exon5			GGGCACGTGGGCA		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.582C>T	2.37:g.85783341G>A		48	0	0		51	22	0.431373	NM_000821	B4DMC5|E9PEE1|Q14415|Q6GU45	Silent	SNP	ENST00000233838.4	37	CCDS1978.1																																																																																			G|0.996;A|0.004	0.004	strong		0.557	GGCX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252490.3	NM_000821		A	85783341	G	A	85783341	2	1	26	1	0	0	0	0	0	0	0	1	6364	1136	40	1		1	GGCX	2	85783341	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	12102157	85783341	157416032	71	9834											
FAHD2B	151313	hgsc.bcm.edu	37	chr2	97749730	97749730	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aatacaccgacacctgggggGgtcccagttaggatgacatc	11	7	12	11	1	0	1	0	1	0	0	2	3	1	2	3	4	1	1	3	4	3	2	rs113222096	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:97749730G>T	ENST00000414820.1	-	8	1107	c.837C>A	c.(835-837)acC>acA	p.T279T	FAHD2B_ENST00000272610.3_Silent_p.T279T|FAHD2B_ENST00000468548.1_5'Flank|FAHD2B_ENST00000440566.2_Silent_p.T279T			Q6P2I3	FAH2B_HUMAN	fumarylacetoacetate hydrolase domain containing 2B	279							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			kidney(5)|large_intestine(2)|lung(3)|skin(2)	12						CACCTGGGGGGGTCCCAGTTA	0.557													g|||	25	0.00499201	0.0	0.0014	5008	,	,		21137	0.0		0.0209	False		,,,				2504	0.0031				p.T279T		Atlas-SNP	.											.	FAHD2B	34	.	0			c.C837A						PASS	.	G		22,4384	26.2+/-53.5	0,22,2181	31	32	32		837	-2.4	1	2	dbSNP_132	32	159,8437	73.8+/-136.5	0,159,4139	no	coding-synonymous	FAHD2B	NM_199336.1		0,181,6320	TT,TG,GG		1.8497,0.4993,1.3921		279/315	97749730	181,12821	2203	4298	6501	SO:0001819	synonymous_variant	151313	exon7			TGGGGGGGTCCCA		CCDS2030.1	2q11.2	2012-06-29			ENSG00000144199	ENSG00000144199			25318	protein-coding gene	gene with protein product							Standard	NM_199336		Approved	DKFZp434N062	uc002sxm.3	Q6P2I3	OTTHUMG00000130533	ENST00000414820.1:c.837C>A	2.37:g.97749730G>T		151	0	0		162	74	0.45679	NM_199336	D3DXH7|Q8NDK1	Silent	SNP	ENST00000414820.1	37	CCDS2030.1																																																																																			G|0.987;T|0.013	0.013	strong		0.557	FAHD2B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339482.1	NM_199336		T	97749730	G	T	97749730	2	4	26	1	0	0	0	0	0	0	0	1	5379	1219	43	4		4	FAHD2B	2	97749730	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	11966389	97749730	145449643	72	9835											
GCC2	9648	hgsc.bcm.edu	37	chr2	109087167	109087167	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	attaatgtttgaaatacaggGtcttaaggaacagtgtgaaa	16	12	10	3	0	1	2	0	2	1	0	1	3	1	3	0	2	2	1	0	2	6	4			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:109087167G>T	ENST00000309863.6	+	6	2096	c.1382G>T	c.(1381-1383)gGt>gTt	p.G461V		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	461					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						GAAATACAGGGTCTTAAGGAA	0.294																																					p.G461V		Atlas-SNP	.											GCC2,NS,carcinoma,-1,1	GCC2	129	1	0			c.G1382T						PASS	.						35	37	37					2																	109087167		2203	4289	6492	SO:0001583	missense	9648	exon6			TACAGGGTCTTAA	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.1382G>T	2.37:g.109087167G>T	ENSP00000307939:p.Gly461Val	124	0	0		153	58	0.379085	NM_181453	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Missense_Mutation	SNP	ENST00000309863.6	37	CCDS33268.1	.	.	.	.	.	.	.	.	.	.	G	9.716	1.158335	0.21454	.	.	ENSG00000135968	ENST00000309863;ENST00000409896;ENST00000393318	T	0.31247	1.5	5.41	4.51	0.55191	.	0.374008	0.26163	N	0.025964	T	0.25344	0.0616	L	0.57536	1.79	0.44330	D	0.99721	B	0.30763	0.294	B	0.30251	0.113	T	0.07770	-1.0755	10	0.30078	T	0.28	.	5.137	0.14939	0.1494:0.0:0.6492:0.2014	.	461	Q8IWJ2	GCC2_HUMAN	V	461;424;206	ENSP00000307939:G461V	ENSP00000307939:G461V	G	+	2	0	GCC2	108453599	1.000000	0.71417	1.000000	0.80357	0.601000	0.36947	2.328000	0.43867	2.688000	0.91661	0.655000	0.94253	GGT	.	.	none		0.294	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635		T	109087167	G	T	109087167	3	4	26	1	0	0	0	0	1	0	0	0	6294	1261	44	4	1404	4	GCC2	2	109087167	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	11337437	109087167	134112206	73	9836											
GLI2	2736	hgsc.bcm.edu	37	chr2	121742124	121742124	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctccggaagcatgtgaaaacGgtccacggcccagatgccca	11	5	11	14	3	0	2	0	1	0	1	2	3	2	3	4	3	3	1	4	3	3	0	rs61732852	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:121742124G>A	ENST00000452319.1	+	12	1821	c.1761G>A	c.(1759-1761)acG>acA	p.T587T	GLI2_ENST00000435313.2_3'UTR|GLI2_ENST00000361492.4_Silent_p.T587T|GLI2_ENST00000314490.11_Silent_p.T259T					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)				ATGTGAAAACGGTCCACGGCC	0.597													G|||	22	0.00439297	0.0	0.0043	5008	,	,		19759	0.0		0.0139	False		,,,				2504	0.0051				p.T587T		Atlas-SNP	.											.	GLI2	187	.	0			c.G1761A						PASS	.	G		13,4393	19.1+/-41.9	0,13,2190	154	147	149		1761	-9	0.3	2	dbSNP_129	149	117,8483	61.7+/-123.6	0,117,4183	no	coding-synonymous	GLI2	NM_005270.4		0,130,6373	AA,AG,GG		1.3605,0.2951,0.9995		587/1587	121742124	130,12876	2203	4300	6503	SO:0001819	synonymous_variant	2736	exon11			GAAAACGGTCCAC		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.1761G>A	2.37:g.121742124G>A		179	0	0		199	82	0.41206	NM_005270		Silent	SNP	ENST00000452319.1	37	CCDS33283.1																																																																																			G|0.991;A|0.009	0.009	strong		0.597	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		A	121742124	G	A	121742124	2	1	26	1	0	0	0	0	0	0	0	1	6446	1103	39	1		1	GLI2	2	121742124	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	12654957	121742124	121457249	74	9837											
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125660582	125660582	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcgccatgccactgtcgCgcctgtgactgtccatggga	5	9	12	15	3	0	1	0	1	0	0	2	2	1	2	5	1	2	0	5	1	0	0			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:125660582C>T	ENST00000431078.1	+	22	3921	c.3557C>T	c.(3556-3558)gCg>gTg	p.A1186V		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	1186	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)		GCCACTGTCGCGCCTGTGACT	0.537																																					p.A1186V		Atlas-SNP	.											CNTNAP5,caecum,carcinoma,-1,1	CNTNAP5	405	1	0			c.C3557T						PASS	.						62	62	62					2																	125660582		2131	4255	6386	SO:0001583	missense	129684	exon22			CTGTCGCGCCTGT	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.3557C>T	2.37:g.125660582C>T	ENSP00000399013:p.Ala1186Val	144	0	0		127	62	0.488189	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	37	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	C	11.23	1.578109	0.28180	.	.	ENSG00000155052	ENST00000431078	D	0.88354	-2.37	5.5	3.64	0.41730	Laminin G domain (1);	0.279884	0.24698	N	0.036332	D	0.86932	0.6052	M	0.69248	2.105	0.36478	D	0.867685	P	0.52842	0.956	B	0.40782	0.34	D	0.87606	0.2500	10	0.46703	T	0.11	.	13.6352	0.62219	0.2828:0.7172:0.0:0.0	.	1186	Q8WYK1	CNTP5_HUMAN	V	1186	ENSP00000399013:A1186V	ENSP00000399013:A1186V	A	+	2	0	CNTNAP5	125377052	0.980000	0.34600	0.439000	0.26833	0.015000	0.08874	3.047000	0.49854	0.652000	0.30806	-0.181000	0.13052	GCG	.	.	none		0.537	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			T	125660582	C	T	125660582	3	4	26	1	0	0	0	0	1	0	0	0	3652	768	27	1	3643	1	CNTNAP5	2	125660582	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	3918458	125660582	117538791	75	9838											
POTEF	728378	hgsc.bcm.edu	37	chr2	130832545	130832545	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcacagcctggatggccaCgtacatggctggggtgttga	8	8	15	10	1	0	1	0	1	0	0	0	2	0	2	2	5	3	4	2	5	1	2	rs199777567	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:130832545C>T	ENST00000409914.2	-	17	2899	c.2500G>A	c.(2500-2502)Gtg>Atg	p.V834M	POTEF_ENST00000357462.5_Missense_Mutation_p.V834M	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	834	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						TGGATGGCCACGTACATGGCT	0.592													.|||	6	0.00119808	0.0	0.0014	5008	,	,		20796	0.0		0.005	False		,,,				2504	0.0				p.V834M		Atlas-SNP	.											.	POTEF	140	.	0			c.G2500A						PASS	.	C	MET/VAL	2,4392		0,2,2195	104	125	118		2500		0.3	2		118	26,8544		0,26,4259	no	missense	POTEF	NM_001099771.2	21	0,28,6454	TT,TC,CC		0.3034,0.0455,0.216	probably-damaging	834/1076	130832545	28,12936	2197	4285	6482	SO:0001583	missense	728378	exon17			TGGCCACGTACAT	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.2500G>A	2.37:g.130832545C>T	ENSP00000386786:p.Val834Met	217	0	0		145	73	0.503448	NM_001099771	A6NC34	Missense_Mutation	SNP	ENST00000409914.2	37	CCDS46409.1	.	.	.	.	.	.	.	.	.	.	.	15.44	2.834922	0.50951	4.55E-4	0.003034	ENSG00000196604	ENST00000357462;ENST00000409914	D;D	0.94723	-3.5;-3.5	.	.	.	.	.	.	.	.	D	0.95695	0.8600	M	0.88570	2.965	0.80722	D	1	D	0.57257	0.979	P	0.55055	0.767	D	0.93384	0.6746	8	0.87932	D	0	.	5.9051	0.18992	0.0:0.9992:0.0:8.0E-4	.	834	A5A3E0	POTEF_HUMAN	M	834	ENSP00000350052:V834M;ENSP00000386786:V834M	ENSP00000350052:V834M	V	-	1	0	POTEF	130549015	1.000000	0.71417	0.299000	0.25016	0.302000	0.27658	3.653000	0.54446	0.119000	0.18210	0.121000	0.15741	GTG	C|0.993;T|0.007	0.007	strong		0.592	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771		T	130832545	C	T	130832545	3	4	26	1	0	0	0	0	1	0	0	0	12274	536	19	1	731	1	POTEF	2	130832545	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	5171963	130832545	112366828	76	9839											
POTEE	445582	hgsc.bcm.edu	37	chr2	132020976	132020976	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acgtcttgcatgaaaatagtAcgttgcgggaagaaattgcc	13	10	11	7	3	1	2	0	1	1	1	1	3	1	3	1	1	4	3	1	1	6	5			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:132020976A>G	ENST00000356920.5	+	15	2042	c.1948A>G	c.(1948-1950)Acg>Gcg	p.T650A	PLEKHB2_ENST00000404460.1_Intron|POTEE_ENST00000358087.5_3'UTR|PLEKHB2_ENST00000303908.3_Intron	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	650					retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)											TGAAAATAGTACGTTGCGGGA	0.353																																					p.T650A		Atlas-SNP	.											ENSG00000188219,NS,carcinoma,-1,1	.	.	1	0			c.A1948G						scavenged	.						25	26	26					2																	132020976		1927	4158	6085	SO:0001583	missense	445582	exon15			AATAGTACGTTGC	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.1948A>G	2.37:g.132020976A>G	ENSP00000439189:p.Thr650Ala	428	1	0.00233645		404	162	0.40099	NM_001083538	Q6S8J4|Q6S8J5|Q6S8J8	Missense_Mutation	SNP	ENST00000356920.5	37	CCDS46414.1	.	.	.	.	.	.	.	.	.	.	.	2.826	-0.243795	0.05906	.	.	ENSG00000188219	ENST00000356920	T	0.14144	2.53	0.993	0.993	0.19825	.	.	.	.	.	T	0.07999	0.0200	N	0.19112	0.55	0.09310	N	0.999999	B	0.10296	0.003	B	0.01281	0.0	T	0.31336	-0.9947	9	0.72032	D	0.01	.	4.2424	0.10654	1.0:0.0:0.0:0.0	.	650	Q6S8J3	POTEE_HUMAN	A	650	ENSP00000439189:T650A	ENSP00000439189:T650A	T	+	1	0	AC131180.1	131737446	0.001000	0.12720	0.030000	0.17652	0.008000	0.06430	1.083000	0.30815	0.705000	0.31890	0.155000	0.16302	ACG	.	.	none		0.353	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538		G	132020976	A	G	132020976	3	3	26	1	0	0	0	0	1	0	0	0	12273	391	14	3	2006	3	POTEE	2	132020976	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	1188431	132020976	111178397	77	9840											
POTEE	445582	hgsc.bcm.edu	37	chr2	132021908	132021908	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cggttccgctgccccgaggcGctcttccagccttgcttcct	2	11	10	18	4	1	0	0	0	1	0	4	1	4	0	6	2	3	4	6	2	0	4	rs201238743	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:132021908G>A	ENST00000356920.5	+	15	2974	c.2880G>A	c.(2878-2880)gcG>gcA	p.A960A	PLEKHB2_ENST00000404460.1_Intron|POTEE_ENST00000358087.5_3'UTR|PLEKHB2_ENST00000303908.3_Intron	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	960	Actin-like.				retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)											GCCCCGAGGCGCTCTTCCAGC	0.592																																					p.A960A		Atlas-SNP	.											.	.	.	.	0			c.G2880A						PASS	.						2	1	1					2																	132021908		762	1288	2050	SO:0001819	synonymous_variant	445582	exon15			CGAGGCGCTCTTC	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.2880G>A	2.37:g.132021908G>A		165	0	0		184	41	0.222826	NM_001083538	Q6S8J4|Q6S8J5|Q6S8J8	Silent	SNP	ENST00000356920.5	37	CCDS46414.1																																																																																			A|1.000;|0.000	1.000	weak		0.592	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538		A	132021908	G	A	132021908	2	1	26	1	0	0	0	0	0	0	0	1	12273	1074	38	1		1	POTEE	2	132021908	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	932	132021908	111177465	78	9841											
NCKAP5	344148	hgsc.bcm.edu	37	chr2	133538703	133538703	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttgagtactgatagagctGccgatgagacaggagccctg	10	8	13	10	1	0	4	0	3	0	2	0	7	0	5	3	1	4	2	3	1	2	3	rs61742426	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:133538703G>A	ENST00000409261.1	-	15	5344	c.4971C>T	c.(4969-4971)ggC>ggT	p.G1657G	NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000317721.6_Silent_p.G1657G|NCKAP5_ENST00000473859.1_5'UTR	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1657										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						TGATAGAGCTGCCGATGAGAC	0.458													G|||	8	0.00159744	0.0	0.0	5008	,	,		17507	0.0		0.008	False		,,,				2504	0.0				p.G1657G		Atlas-SNP	.											.	NCKAP5	322	.	0			c.C4971T						PASS	.	G	,	5,3821		0,5,1908	94	97	96		4971,	5.3	0	2	dbSNP_129	96	55,8203		1,53,4075	no	coding-synonymous,intron	NCKAP5	NM_207363.2,NM_207481.3	,	1,58,5983	AA,AG,GG		0.666,0.1307,0.4965	,	1657/1910,	133538703	60,12024	1913	4129	6042	SO:0001819	synonymous_variant	344148	exon15			AGAGCTGCCGATG	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.4971C>T	2.37:g.133538703G>A		358	0	0		434	219	0.504608	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Silent	SNP	ENST00000409261.1	37	CCDS46418.1																																																																																			G|0.996;A|0.004	0.004	strong		0.458	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481		A	133538703	G	A	133538703	2	1	26	1	0	0	0	0	0	0	0	1	10232	1306	46	2		2	NCKAP5	2	133538703	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1516795	133538703	109660670	79	9842											
RBM43	375287	hgsc.bcm.edu	37	chr2	152112161	152112161	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaagtggctcttcactaataCggccaataattgatcactaa	14	11	7	9	1	3	1	2	1	1	0	3	2	3	1	1	2	1	1	1	2	6	6	rs147060862	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:152112161C>G	ENST00000331426.5	-	2	251	c.100G>C	c.(100-102)Gta>Cta	p.V34L		NM_198557.2	NP_940959.1	Q6ZSC3	RBM43_HUMAN	RNA binding motif protein 43	34	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.						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)		TTCACTAATACGGCCAATAAT	0.408													C|||	72	0.014377	0.0151	0.0245	5008	,	,		13812	0.001		0.0288	False		,,,				2504	0.0051				p.V34L		Atlas-SNP	.											RBM43,colon,carcinoma,0,1	RBM43	35	1	0			c.G100C						PASS	.	C	LEU/VAL	60,4346	56.8+/-93.2	0,60,2143	131	130	130		100	-1.3	0	2	dbSNP_134	130	251,8349	99.5+/-161.0	5,241,4054	yes	missense	RBM43	NM_198557.2	32	5,301,6197	GG,GC,CC		2.9186,1.3618,2.3912	benign	34/358	152112161	311,12695	2203	4300	6503	SO:0001583	missense	375287	exon2			CTAATACGGCCAA	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.100G>C	2.37:g.152112161C>G	ENSP00000331211:p.Val34Leu	188	0	0		213	111	0.521127	NM_198557	B2RMT5	Missense_Mutation	SNP	ENST00000331426.5	37	CCDS2191.1	34	0.015567765567765568	6	0.012195121951219513	9	0.024861878453038673	1	0.0017482517482517483	18	0.023746701846965697	C	2.210	-0.380974	0.05000	0.013618	0.029186	ENSG00000184898	ENST00000331426	T	0.42131	0.98	4.25	-1.31	0.09230	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.899723	0.09370	N	0.811424	T	0.05593	0.0147	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.23119	-1.0197	10	0.09843	T	0.71	-0.7126	4.1354	0.10169	0.0:0.414:0.209:0.377	.	34	Q6ZSC3	RBM43_HUMAN	L	34	ENSP00000331211:V34L	ENSP00000331211:V34L	V	-	1	0	RBM43	151820407	0.000000	0.05858	0.025000	0.17156	0.004000	0.04260	0.426000	0.21363	-0.071000	0.12886	-2.222000	0.00295	GTA	C|0.974;G|0.026	0.026	strong		0.408	RBM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254816.2	NM_198557		G	152112161	C	G	152112161	3	3	26	1	0	0	0	0	1	0	0	0	13152	536	19	4	985	4	RBM43	2	152112161	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	18573458	152112161	91087212	80	9843											
PKP4	8502	hgsc.bcm.edu	37	chr2	159517926	159517926	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gactcactgttgtatgtgatCcacacgtgtgtgaacacatc	10	12	9	10	1	1	2	1	2	0	0	3	3	2	2	1	0	1	2	1	0	2	2	rs112890651	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:159517926C>T	ENST00000389759.3	+	13	2287	c.2175C>T	c.(2173-2175)atC>atT	p.I725I	PKP4_ENST00000389757.3_Silent_p.I725I|AC005042.4_ENST00000342892.4_RNA	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	725					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						TGTATGTGATCCACACGTGTG	0.587										HNSCC(62;0.18)			C|||	18	0.00359425	0.0	0.0058	5008	,	,		20670	0.0		0.0129	False		,,,				2504	0.001				p.I725I		Atlas-SNP	.											.	PKP4	133	.	0			c.C2175T						PASS	.	C	,	5,4401	9.9+/-24.2	0,5,2198	127	113	118		2175,2175	5.7	1	2	dbSNP_132	118	103,8497	56.4+/-117.6	2,99,4199	no	coding-synonymous,coding-synonymous	PKP4	NM_001005476.1,NM_003628.3	,	2,104,6397	TT,TC,CC		1.1977,0.1135,0.8304	,	725/1150,725/1193	159517926	108,12898	2203	4300	6503	SO:0001819	synonymous_variant	8502	exon13			TGTGATCCACACG	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.2175C>T	2.37:g.159517926C>T		37	0	0		55	28	0.509091	NM_001005476	Q86W91	Silent	SNP	ENST00000389759.3	37	CCDS33305.1																																																																																			C|0.990;T|0.010	0.010	strong		0.587	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333250.1			T	159517926	C	T	159517926	2	4	26	1	0	0	0	0	0	0	0	1	11996	845	30	2		2	PKP4	2	159517926	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	7405765	159517926	83681447	81	9844											
PLA2R1	22925	hgsc.bcm.edu	37	chr2	160885432	160885432	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagcgtgttcatccagctgaTtgaggcccatccacacctcc	8	9	8	16	1	1	2	1	2	0	0	4	2	4	2	5	1	2	2	5	1	0	2	rs139957604	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:160885432T>C	ENST00000283243.7	-	5	1090	c.884A>G	c.(883-885)aAt>aGt	p.N295S	PLA2R1_ENST00000392771.1_Missense_Mutation_p.N295S	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	295	C-type lectin 1. {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						ATCCAGCTGATTGAGGCCCAT	0.468																																					p.N295S		Atlas-SNP	.											.	PLA2R1	153	.	0			c.A884G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN	0,4406		0,0,2203	119	94	103		884,884,884	5.8	1	2	dbSNP_134	103	11,8589	7.7+/-29.5	0,11,4289	yes	missense,missense,missense	PLA2R1	NM_001007267.2,NM_001195641.1,NM_007366.4	46,46,46	0,11,6492	CC,CT,TT		0.1279,0.0,0.0846	probably-damaging,probably-damaging,probably-damaging	295/1325,295/1462,295/1464	160885432	11,12995	2203	4300	6503	SO:0001583	missense	22925	exon5			AGCTGATTGAGGC	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.884A>G	2.37:g.160885432T>C	ENSP00000283243:p.Asn295Ser	263	0	0		298	155	0.520134	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Missense_Mutation	SNP	ENST00000283243.7	37	CCDS33309.1	.	.	.	.	.	.	.	.	.	.	T	15.77	2.932188	0.52866	0.0	0.001279	ENSG00000153246	ENST00000283243;ENST00000392771	T;T	0.15718	2.4;2.4	5.83	5.83	0.93111	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.85682	D	0.000000	T	0.35711	0.0941	L	0.48935	1.535	0.58432	D	0.999993	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.995;0.998;0.999	T	0.02498	-1.1150	10	0.48119	T	0.1	.	15.1831	0.72975	0.0:0.0:0.0:1.0	.	295;295;295	B7ZML4;Q13018-2;Q13018	.;.;PLA2R_HUMAN	S	295	ENSP00000283243:N295S;ENSP00000376524:N295S	ENSP00000283243:N295S	N	-	2	0	PLA2R1	160593678	1.000000	0.71417	0.998000	0.56505	0.093000	0.18481	4.310000	0.59141	2.227000	0.72691	0.528000	0.53228	AAT	T|0.999;C|0.001	0.001	strong		0.468	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1			C	160885432	T	C	160885432	3	2	26	1	0	0	0	0	1	0	0	0	12019	1493	52	3	3619	3	PLA2R1	2	160885432	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	1367506	160885432	82313941	82	9845											
IFIH1	64135	hgsc.bcm.edu	37	chr2	163124637	163124637	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gacgtgatgcattttctcaaTtacatggatatcttccccag	10	14	7	10	1	2	1	1	1	2	0	4	3	3	2	2	1	2	1	2	1	3	5	rs35667974	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:163124637T>C	ENST00000263642.2	-	14	3162	c.2767A>G	c.(2767-2769)Att>Gtt	p.I923V		NM_022168.3	NP_071451.2	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	923					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						ATTTTCTCAATTACATGGATA	0.398													T|||	12	0.00239617	0.0008	0.0	5008	,	,		18807	0.0		0.0099	False		,,,				2504	0.001				p.I923V		Atlas-SNP	.											.	IFIH1	102	.	0			c.A2767G						PASS	.	T	VAL/ILE	11,4395	17.9+/-39.9	0,11,2192	128	128	128	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2767	5.1	0.9	2	dbSNP_126	128	140,8460	70.7+/-133.2	4,132,4164	yes	missense	IFIH1	NM_022168.2	29	4,143,6356	CC,CT,TT		1.6279,0.2497,1.161	benign	923/1026	163124637	151,12855	2203	4300	6503	SO:0001583	missense	64135	exon14			TCTCAATTACATG	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.2767A>G	2.37:g.163124637T>C	ENSP00000263642:p.Ile923Val	183	0	0		226	103	0.455752	NM_022168	Q2NKL6|Q6DC96|Q86X56|Q96MX8|Q9H3G6	Missense_Mutation	SNP	ENST00000263642.2	37	CCDS2217.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	T	17.27	3.347761	0.61183	0.002497	0.016279	ENSG00000115267	ENST00000263642;ENST00000543192	T	0.29917	1.55	5.13	5.13	0.70059	C-terminal domain of RIG-I (1);	0.048848	0.85682	D	0.000000	T	0.29684	0.0741	L	0.50919	1.6	0.50313	D	0.999862	D	0.53151	0.958	P	0.61397	0.888	T	0.09015	-1.0694	10	0.33141	T	0.24	-8.4883	14.9508	0.71071	0.0:0.0:0.0:1.0	rs35667974	923	Q9BYX4	IFIH1_HUMAN	V	923	ENSP00000263642:I923V	ENSP00000263642:I923V	I	-	1	0	IFIH1	162832883	1.000000	0.71417	0.917000	0.36280	0.768000	0.43524	7.427000	0.80284	1.932000	0.55993	0.528000	0.53228	ATT	T|0.991;C|0.009	0.009	strong		0.398	IFIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255078.2	NM_022168		C	163124637	T	C	163124637	3	2	26	1	0	0	0	0	1	0	0	0	7529	1493	52	3	322	3	IFIH1	2	163124637	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	2239205	163124637	80074736	83	9846											
LRP2	4036	hgsc.bcm.edu	37	chr2	170002322	170002322	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccaagggttcactaccagcGttttctctttctttccttgc	5	16	7	13	1	3	0	1	0	2	0	5	0	4	0	3	1	3	2	3	1	2	7	rs543890594		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:170002322G>A	ENST00000263816.3	-	70	13208	c.12923C>T	c.(12922-12924)aCg>aTg	p.T4308M		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	4308					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)"	CACTACCAGCGTTTTCTCTTT	0.388																																					p.T4308M		Atlas-SNP	.											LRP2,right_lower_lobe,carcinoma,+1,1	LRP2	751	1	0			c.C12923T						PASS	.						108	100	103					2																	170002322		2203	4300	6503	SO:0001583	missense	4036	exon70			ACCAGCGTTTTCT		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.12923C>T	2.37:g.170002322G>A	ENSP00000263816:p.Thr4308Met	64	0	0		69	40	0.57971	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	G	4.856	0.159199	0.09236	.	.	ENSG00000081479	ENST00000263816	D	0.91894	-2.93	5.38	3.0	0.34707	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.626869	0.17107	N	0.186765	D	0.85084	0.5616	L	0.37507	1.11	0.80722	D	1	B	0.18741	0.03	B	0.06405	0.002	T	0.75399	-0.3331	10	0.31617	T	0.26	.	5.8816	0.18858	0.7744:0.0:0.0793:0.1463	.	4308	P98164	LRP2_HUMAN	M	4308	ENSP00000263816:T4308M	ENSP00000263816:T4308M	T	-	2	0	LRP2	169710568	0.992000	0.36948	0.281000	0.24762	0.093000	0.18481	7.437000	0.80417	0.434000	0.26340	-1.087000	0.02190	ACG	.	.	none		0.388	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		A	170002322	G	A	170002322	3	1	26	1	0	0	0	0	1	0	0	0	8965	1145	40	1	1084	1	LRP2	2	170002322	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	6877685	170002322	73197051	84	9847											
TTN	7273	hgsc.bcm.edu	37	chr2	179582853	179582853	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttctttataccaagaaattcTaatttctggagttccatcca	12	16	4	9	0	3	1	0	0	3	1	5	2	5	2	3	1	1	1	3	1	5	8	rs72648982	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179582853T>C	ENST00000591111.1	-	84	24153	c.23929A>G	c.(23929-23931)Aga>Gga	p.R7977G	TTN_ENST00000589042.1_Missense_Mutation_p.R8294G|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.R7050G			Q8WZ42	TITIN_HUMAN	titin	12168	Ig-like 62.				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)			CAAGAAATTCTAATTTCTGGA	0.378													T|||	61	0.0121805	0.0023	0.013	5008	,	,		21179	0.001		0.0278	False		,,,				2504	0.0204				p.R8294G		Atlas-SNP	.											.	TTN	18412	.	0			c.A24880G						PASS	.	T	,,,GLY/ARG	21,3687		0,21,1833	118	109	112		,,,21148	5	1	2	dbSNP_130	112	253,7959		2,249,3855	yes	intron,intron,intron,missense	TTN	NM_003319.4,NM_133432.3,NM_133437.3,NM_133378.4	,,,125	2,270,5688	CC,CT,TT		3.0809,0.5663,2.2987	,,,benign	,,,7050/33424	179582853	274,11646	1854	4106	5960	SO:0001583	missense	7273	exon86			AAATTCTAATTTC	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.23929A>G	2.37:g.179582853T>C	ENSP00000465570:p.Arg7977Gly	45	0	0		50	30	0.6	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	37		28	0.01282051282051282	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	20	0.026385224274406333	T	9.326	1.059350	0.19987	0.005663	0.030809	ENSG00000155657	ENST00000342992	T	0.67523	-0.27	6.16	4.99	0.66335	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.42539	0.1207	M	0.70595	2.14	0.58432	D	0.999996	B	0.26577	0.153	B	0.24394	0.053	T	0.58725	-0.7586	9	0.87932	D	0	.	13.6119	0.62083	0.0:0.0:0.1293:0.8707	.	7977	Q8WZ42	TITIN_HUMAN	G	7050	ENSP00000343764:R7050G	ENSP00000343764:R7050G	R	-	1	2	TTN	179291098	0.010000	0.17322	0.992000	0.48379	0.963000	0.63663	1.356000	0.34079	1.113000	0.41760	0.528000	0.53228	AGA	T|0.981;C|0.019	0.019	strong		0.378	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179582853	T	C	179582853	3	2	26	1	0	0	0	0	1	0	0	0	16750	1530	53	3	79757	3	TTN	2	179582853	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	9580531	179582853	63616520	85	9848											
TTN	7273	hgsc.bcm.edu	37	chr2	179590329	179590329	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtaattcagcaggctctcCggctacaacagtgaggctgt	9	11	11	10	1	2	1	1	1	1	0	3	1	2	1	1	3	3	5	1	3	3	4	rs17355460	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179590329C>T	ENST00000591111.1	-	69	19875	c.19651G>A	c.(19651-19653)Gga>Aga	p.G6551R	TTN_ENST00000589042.1_Missense_Mutation_p.G6868R|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.G5624R|RP11-171I2.1_ENST00000590024.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12154	Ig-like 47.				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)			GCAGGCTCTCCGGCTACAACA	0.433													C|||	33	0.00658946	0.0008	0.0086	5008	,	,		20718	0.0		0.0209	False		,,,				2504	0.0051				p.G6868R		Atlas-SNP	.											.	TTN	18412	.	0			c.G20602A						PASS	.	C	ARG/GLY,,,	13,3713		0,13,1850	88	80	83		16870,,,	5.9	1	2	dbSNP_123	83	142,8056		2,138,3959	yes	missense,intron,intron,intron	TTN	NM_133378.4,NM_003319.4,NM_133432.3,NM_133437.3	125,,,	2,151,5809	TT,TC,CC		1.7321,0.3489,1.2999	probably-damaging,,,	5624/33424,,,	179590329	155,11769	1863	4099	5962	SO:0001583	missense	7273	exon71			GCTCTCCGGCTAC	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.19651G>A	2.37:g.179590329C>T	ENSP00000465570:p.Gly6551Arg	133	0	0		150	65	0.433333	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	37		19	0.0086996336996337	0	0.0	4	0.011049723756906077	0	0.0	15	0.01978891820580475	C	13.86	2.363340	0.41902	0.003489	0.017321	ENSG00000155657	ENST00000342992	T	0.81330	-1.48	5.86	5.86	0.93980	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.89515	0.6737	H	0.96748	3.875	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.92012	0.5619	9	0.87932	D	0	.	20.5632	0.99335	0.0:1.0:0.0:0.0	rs17355460;rs52829777;rs17355460	6551	Q8WZ42	TITIN_HUMAN	R	5624	ENSP00000343764:G5624R	ENSP00000343764:G5624R	G	-	1	0	TTN	179298574	0.989000	0.36119	0.998000	0.56505	0.450000	0.32258	3.002000	0.49496	2.937000	0.99478	0.650000	0.86243	GGA	C|0.991;T|0.009	0.009	strong		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179590329	C	T	179590329	3	4	26	1	0	0	0	0	1	0	0	0	16750	661	23	1	84095	1	TTN	2	179590329	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	7476	179590329	63609044	86	9849											
CWC22	57703	hgsc.bcm.edu	37	chr2	180835443	180835443	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	agtgaattgatcatcttcttCcaccaaatcaagaccttcta	13	13	4	11	0	5	3	2	2	3	1	6	3	6	3	3	0	0	0	3	0	4	5	rs143785942	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:180835443C>G	ENST00000410053.3	-	10	1380	c.1081G>C	c.(1081-1083)Gaa>Caa	p.E361Q	CWC22_ENST00000295749.6_Missense_Mutation_p.E361Q	NM_020943.2	NP_065994.1	Q9HCG8	CWC22_HUMAN	CWC22 spliceosome-associated protein	361					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						TCATCTTCTTCCACCAAATCA	0.403													C|||	4	0.000798722	0.0	0.0014	5008	,	,		14767	0.0		0.001	False		,,,				2504	0.002				p.E361Q		Atlas-SNP	.											.	CWC22	62	.	0			c.G1081C						PASS	.	C	GLN/GLU	0,3776		0,0,1888	96	91	92		1081	5.9	1	2	dbSNP_134	92	10,8210		0,10,4100	yes	missense	CWC22	NM_020943.2	29	0,10,5988	GG,GC,CC		0.1217,0.0,0.0834	possibly-damaging	361/909	180835443	10,11986	1888	4110	5998	SO:0001583	missense	57703	exon10			CTTCTTCCACCAA		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.1081G>C	2.37:g.180835443C>G	ENSP00000387006:p.Glu361Gln	170	0	0		161	76	0.47205	NM_020943	Q05DC2|Q4G135|Q52LF0|Q6PEX2|Q7Z6I0|Q9H5L3|Q9H6Q6	Missense_Mutation	SNP	ENST00000410053.3	37	CCDS46465.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	27.9	4.873213	0.91664	0.0	0.001217	ENSG00000163510	ENST00000410053;ENST00000295749;ENST00000404136	T;T;T	0.30448	1.78;1.77;1.53	5.95	5.95	0.96441	Armadillo-type fold (1);	0.047002	0.85682	D	0.000000	T	0.62392	0.2424	M	0.88570	2.965	0.80722	D	1	D	0.76494	0.999	P	0.62649	0.905	T	0.67825	-0.5570	10	0.72032	D	0.01	-23.3839	19.3813	0.94536	0.0:1.0:0.0:0.0	.	361	Q9HCG8	CWC22_HUMAN	Q	361	ENSP00000387006:E361Q;ENSP00000295749:E361Q;ENSP00000384159:E361Q	ENSP00000295749:E361Q	E	-	1	0	CWC22	180543688	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.818000	0.86416	2.824000	0.97209	0.655000	0.94253	GAA	C|1.000;G|0.000	0.000	strong		0.403	CWC22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334537.1	NM_020943		G	180835443	C	G	180835443	3	3	26	1	0	0	0	0	1	0	0	0	4070	864	30	4	1689	4	CWC22	2	180835443	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1245114	180835443	62363930	87	9850											
UBE2E3	10477	hgsc.bcm.edu	37	chr2	181846844	181846844	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttcagatgcggaccagcgAgacccagccgctccagagcc	10	4	12	15	3	1	3	1	0	0	3	2	5	2	4	5	1	4	2	5	1	0	1	rs146744789	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:181846844A>T	ENST00000410062.4	+	2	468	c.75A>T	c.(73-75)cgA>cgT	p.R25R	AC104076.3_ENST00000428080.1_RNA|UBE2E3_ENST00000602710.1_Silent_p.R25R|UBE2E3_ENST00000392415.2_Silent_p.R25R|UBE2E3_ENST00000602475.1_Silent_p.R25R|UBE2E3_ENST00000602632.1_Silent_p.R25R|UBE2E3_ENST00000602959.1_Silent_p.R25R	NM_006357.2	NP_006348.1	Q969T4	UB2E3_HUMAN	ubiquitin-conjugating enzyme E2E 3	25					protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|endometrium(3)|lung(4)|ovary(1)|skin(1)	11						CGGACCAGCGAGACCCAGCCG	0.507													A|||	47	0.00938498	0.0008	0.0086	5008	,	,		15694	0.0		0.0169	False		,,,				2504	0.0235				p.R25R		Atlas-SNP	.											.	UBE2E3	26	.	0			c.A75T						PASS	.	A	,	11,4393	14.3+/-33.2	0,11,2191	37	45	42		75,75	0.9	1	2	dbSNP_134	42	146,8416	70.3+/-132.9	0,146,4135	no	coding-synonymous,coding-synonymous	UBE2E3	NM_006357.2,NM_182678.1	,	0,157,6326	TT,TA,AA		1.7052,0.2498,1.2109	,	25/208,25/208	181846844	157,12809	2202	4281	6483	SO:0001819	synonymous_variant	10477	exon2			CCAGCGAGACCCA	AB017644	CCDS2282.1	2q31.3	2011-05-19	2011-05-19		ENSG00000170035	ENSG00000170035		"Ubiquitin-conjugating enzymes E2"	12479	protein-coding gene	gene with protein product		604151	"ubiquitin-conjugating enzyme E2E 3 (homologous to yeast UBC4/5)", "ubiquitin-conjugating enzyme E2E 3 (UBC4/5 homolog, yeast)"			10343118	Standard	NM_006357		Approved	UbcH9	uc002unq.1	Q969T4	OTTHUMG00000132585	ENST00000410062.4:c.75A>T	2.37:g.181846844A>T		181	0	0		203	189	0.931035	NM_006357	B2RAD6|D3DPG3|Q5U0R7|Q7Z4W4	Silent	SNP	ENST00000410062.4	37	CCDS2282.1																																																																																			A|0.985;T|0.015	0.015	weak		0.507	UBE2E3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255795.6	NM_006357		T	181846844	A	T	181846844	2	4	26	1	0	0	0	0	0	0	0	1	16869	291	11	5		5	UBE2E3	2	181846844	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	1011401	181846844	61352529	88	9851											
PGAP1	80055	hgsc.bcm.edu	37	chr2	197781288	197781288	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaagtcaatgtcctctgcttTtctaagtgcaatggagccaa	11	12	9	9	0	3	0	1	0	2	0	4	2	4	1	2	1	3	2	2	1	5	3	rs142320636	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:197781288T>C	ENST00000354764.4	-	3	445	c.331A>G	c.(331-333)Aaa>Gaa	p.K111E	PGAP1_ENST00000409188.1_Missense_Mutation_p.K69E|PGAP1_ENST00000409475.1_Missense_Mutation_p.K111E|PGAP1_ENST00000485830.1_5'UTR	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	111					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						TCCTCTGCTTTTCTAAGTGCA	0.388													T|||	4	0.000798722	0.0	0.0014	5008	,	,		18296	0.0		0.003	False		,,,				2504	0.0				p.K111E		Atlas-SNP	.											.	PGAP1	84	.	0			c.A331G						PASS	.	T	GLU/LYS	2,4404	4.2+/-10.8	0,2,2201	77	71	73		331	5.6	1	2	dbSNP_134	73	13,8587	9.8+/-36.6	0,13,4287	yes	missense	PGAP1	NM_024989.3	56	0,15,6488	CC,CT,TT		0.1512,0.0454,0.1153	possibly-damaging	111/923	197781288	15,12991	2203	4300	6503	SO:0001583	missense	80055	exon3			CTGCTTTTCTAAG		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.331A>G	2.37:g.197781288T>C	ENSP00000346809:p.Lys111Glu	119	0	0		128	58	0.453125	NM_024989	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Missense_Mutation	SNP	ENST00000354764.4	37	CCDS2318.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	24.3	4.516548	0.85495	4.54E-4	0.001512	ENSG00000197121	ENST00000354764;ENST00000409475;ENST00000409188	D;D;D	0.85955	-2.05;-2.05;-2.05	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.91503	0.7317	M	0.79123	2.44	0.80722	D	1	P;D	0.76494	0.873;0.999	B;D	0.83275	0.403;0.996	D	0.89403	0.3697	10	0.18276	T	0.48	-17.7348	16.0983	0.81144	0.0:0.0:0.0:1.0	.	111;111	Q75T13-3;Q75T13	.;PGAP1_HUMAN	E	111;111;69	ENSP00000346809:K111E;ENSP00000387028:K111E;ENSP00000386802:K69E	ENSP00000346809:K111E	K	-	1	0	PGAP1	197489533	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.643000	0.83403	2.256000	0.74724	0.524000	0.50904	AAA	T|0.999;C|0.001	0.001	strong		0.388	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989		C	197781288	T	C	197781288	3	2	26	1	0	0	0	0	1	0	0	0	11786	1850	64	3	2537	3	PGAP1	2	197781288	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	15934444	197781288	45418085	89	9852											
CLK1	1195	hgsc.bcm.edu	37	chr2	201728858	201728858	+	Intron	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccacagctgcttggctcaCgcacattctggaaccccagc	8	7	8	18	1	2	0	1	0	1	0	2	1	2	1	4	2	4	4	4	2	1	2	rs140874256	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:201728858C>T	ENST00000321356.4	-	1	136				Y_RNA_ENST00000516950.1_RNA|CLK1_ENST00000434813.2_Missense_Mutation_p.R31H|CLK1_ENST00000492793.1_Intron	NM_004071.3	NP_004062.2	P49759	CLK1_HUMAN	CDC-like kinase 1						cell proliferation (GO:0008283)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			NS(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(12)|ovary(1)|pancreas(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33						GCTTGGCTCACGCACATTCTG	0.587													C|||	6	0.00119808	0.0	0.0029	5008	,	,		15982	0.001		0.002	False		,,,				2504	0.001				p.R31H		Atlas-SNP	.											.	CLK1	103	.	0			c.G92A						PASS	.	C	HIS/ARG,	0,1384		0,0,692	100	89	92		92,	-2.6	0	2	dbSNP_134	92	3,3179		0,3,1588	yes	missense,intron	CLK1	NM_001162407.1,NM_004071.3	29,	0,3,2280	TT,TC,CC		0.0943,0.0,0.0657	,	31/527,	201728858	3,4563	692	1591	2283	SO:0001627	intron_variant	1195	exon1			GGCTCACGCACAT	L29219	CCDS2331.1, CCDS54427.1	2q33	2008-05-02			ENSG00000013441	ENSG00000013441		"CDC-like kinases"	2068	protein-coding gene	gene with protein product		601951				9856501	Standard	NM_004071		Approved		uc002uwe.2	P49759	OTTHUMG00000132784	ENST00000321356.4:c.0+428G>A	2.37:g.201728858C>T		71	0	0		74	44	0.594595	NM_001162407	B4DFW7|Q0P694|Q8N5V8	Missense_Mutation	SNP	ENST00000321356.4	37	CCDS2331.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	1	0.0017482517482517483	2	0.002638522427440633	C	6.751	0.507366	0.12883	0.0	9.43E-4	ENSG00000013441	ENST00000434813	T	0.70631	-0.5	2.28	-2.64	0.06114	.	.	.	.	.	T	0.43077	0.1231	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.11916	-1.0568	9	0.46703	T	0.11	.	2.9621	0.05896	0.1488:0.4118:0.3218:0.1176	.	31	B4DFW7	.	H	31	ENSP00000394734:R31H	ENSP00000394734:R31H	R	-	2	0	CLK1	201437103	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.543000	0.00436	-1.305000	0.02327	-2.739000	0.00128	CGT	C|0.998;T|0.002	0.002	strong		0.587	CLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256192.2			T	201728858	C	T	201728858	1	4	26	0	1	0	0	0	0	0	0	0	3538	536	19	1		1	CLK1	2	201728858	Intron	SNP	C	TCGA-G8-6907-01A-11D-2210-10	3947570	201728858	41470515	90	9853											
PIKFYVE	200576	hgsc.bcm.edu	37	chr2	209190070	209190070	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcaagctaagaggaggctcTgattatgagctggctcgagt	11	10	13	7	1	2	3	1	2	1	1	3	5	2	4	0	3	2	4	0	3	3	2	rs138885638	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:209190070T>C	ENST00000264380.4	+	20	2693	c.2535T>C	c.(2533-2535)tcT>tcC	p.S845S		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	845					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						GAGGAGGCTCTGATTATGAGC	0.378													T|||	3	0.000599042	0.0015	0.0	5008	,	,		20316	0.0		0.001	False		,,,				2504	0.0				p.S845S		Atlas-SNP	.											.	PIKFYVE	223	.	0			c.T2535C						PASS	.	T		2,4404	4.2+/-10.8	0,2,2201	97	91	93		2535	1.9	1	2	dbSNP_134	93	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous	PIKFYVE	NM_015040.3		0,15,6488	CC,CT,TT		0.1512,0.0454,0.1153		845/2099	209190070	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	200576	exon20			AGGCTCTGATTAT	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.2535T>C	2.37:g.209190070T>C		104	0	0		101	51	0.504951	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Silent	SNP	ENST00000264380.4	37	CCDS2382.1																																																																																			T|0.999;C|0.001	0.001	strong		0.378	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040		C	209190070	T	C	209190070	2	2	26	1	0	0	0	0	0	0	0	1	11933	1567	55	3		3	PIKFYVE	2	209190070	Silent	SNP	T	TCGA-G8-6907-01A-11D-2210-10	7461212	209190070	34009303	91	9854											
TNS1	7145	hgsc.bcm.edu	37	chr2	218758200	218758200	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacattgtgagggtctgcatTgagccatgtgtccatggcct	7	12	13	9	0	1	2	0	2	1	0	2	3	2	2	3	2	2	1	3	2	0	2	rs61745748	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:218758200T>G	ENST00000171887.4	-	8	756	c.304A>C	c.(304-306)Aat>Cat	p.N102H	TNS1_ENST00000419504.1_Missense_Mutation_p.N102H|TNS1_ENST00000310858.6_Missense_Mutation_p.N133H|TNS1_ENST00000430930.1_Missense_Mutation_p.N102H	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	102	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)		GGGTCTGCATTGAGCCATGTG	0.562													T|||	63	0.0125799	0.0023	0.0086	5008	,	,		19412	0.0		0.0199	False		,,,				2504	0.0348				p.N102H		Atlas-SNP	.											.	TNS1	251	.	0			c.A304C						PASS	.	T	HIS/ASN	19,4387	26.2+/-53.5	0,19,2184	144	113	123		304	5.1	1	2	dbSNP_129	123	190,8410	85.0+/-147.5	0,190,4110	yes	missense	TNS1	NM_022648.4	68	0,209,6294	GG,GT,TT		2.2093,0.4312,1.607	possibly-damaging	102/1736	218758200	209,12797	2203	4300	6503	SO:0001583	missense	7145	exon8			CTGCATTGAGCCA	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.304A>C	2.37:g.218758200T>G	ENSP00000171887:p.Asn102His	122	0	0		152	77	0.506579	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	26	0.011904761904761904	3	0.006097560975609756	4	0.011049723756906077	0	0.0	19	0.025065963060686015	T	18.57	3.652558	0.67472	0.004312	0.022093	ENSG00000079308	ENST00000171887;ENST00000419504;ENST00000430930;ENST00000446903;ENST00000413554;ENST00000310858;ENST00000413280	D;D;D;D;D;D;D	0.98617	-5.03;-5.03;-5.03;-5.03;-5.03;-5.03;-5.03	5.09	5.09	0.68999	Phosphatase tensin type (1);	0.098933	0.64402	D	0.000002	D	0.96361	0.8813	L	0.49350	1.555	0.54753	D	0.99998	D;B;D;D;D;D	0.89917	0.988;0.086;1.0;0.976;0.963;0.963	P;B;D;P;P;P	0.91635	0.819;0.112;0.999;0.867;0.498;0.498	D	0.92353	0.5891	10	0.72032	D	0.01	.	14.6945	0.69110	0.0:0.0:0.0:1.0	.	102;156;133;102;102;102	B2RU35;A1L0S7;Q6IPI5;Q9HBL0;E9PGF5;E9PF55	.;.;.;TENS1_HUMAN;.;.	H	102;102;102;227;170;133;102	ENSP00000171887:N102H;ENSP00000408724:N102H;ENSP00000406016:N102H;ENSP00000405460:N227H;ENSP00000400383:N170H;ENSP00000308321:N133H;ENSP00000395615:N102H	ENSP00000171887:N102H	N	-	1	0	TNS1	218466445	1.000000	0.71417	0.961000	0.40146	0.927000	0.56198	6.097000	0.71452	2.142000	0.66516	0.460000	0.39030	AAT	T|0.986;G|0.014	0.014	strong		0.562	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		G	218758200	T	G	218758200	3	3	26	1	0	0	0	0	1	0	0	0	16358	1812	63	5	5007	5	TNS1	2	218758200	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	9568130	218758200	24441173	92	9855											
SPHKAP	80309	hgsc.bcm.edu	37	chr2	228855993	228855993	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atgggaaggtggcttaccctCtgtgctttctgactgtcctt	5	15	11	10	0	2	1	0	1	2	0	3	2	3	2	2	3	2	2	2	3	2	3	rs61752221	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:228855993C>T	ENST00000392056.3	-	10	4817	c.4771G>A	c.(4771-4773)Gag>Aag	p.E1591K	SPHKAP_ENST00000344657.5_Missense_Mutation_p.E1562K	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1591						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)		GGCTTACCCTCTGTGCTTTCT	0.418													C|||	24	0.00479233	0.0015	0.0086	5008	,	,		19744	0.0		0.0159	False		,,,				2504	0.0				p.E1591K		Atlas-SNP	.											.	SPHKAP	750	.	0			c.G4771A						PASS	.	C	LYS/GLU,LYS/GLU	8,4398	14.3+/-33.2	0,8,2195	184	175	178		4771,4684	4.2	0.9	2	dbSNP_129	178	121,8479	63.5+/-125.6	0,121,4179	yes	missense,missense	SPHKAP	NM_001142644.1,NM_030623.3	56,56	0,129,6374	TT,TC,CC		1.407,0.1816,0.9918	benign,benign	1591/1701,1562/1672	228855993	129,12877	2203	4300	6503	SO:0001583	missense	80309	exon10			TACCCTCTGTGCT		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.4771G>A	2.37:g.228855993C>T	ENSP00000375909:p.Glu1591Lys	198	0	0		237	102	0.43038	NM_001142644	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	16	0.007326007326007326	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	11	0.014511873350923483	C	12.78	2.039722	0.35989	0.001816	0.01407	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.12147	2.73;2.71	6.17	4.25	0.50352	.	0.480270	0.24755	N	0.035878	T	0.05547	0.0146	N	0.22421	0.69	0.33424	D	0.580224	B;B	0.15473	0.011;0.013	B;B	0.18561	0.022;0.013	T	0.23940	-1.0174	10	0.19590	T	0.45	.	6.1421	0.20265	0.0:0.7401:0.0:0.2599	rs61752221	1591;1562	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	K	1591;1562	ENSP00000375909:E1591K;ENSP00000339886:E1562K	ENSP00000339886:E1562K	E	-	1	0	SPHKAP	228564237	0.988000	0.35896	0.850000	0.33497	0.996000	0.88848	2.406000	0.44557	0.778000	0.33520	0.655000	0.94253	GAG	C|0.991;T|0.009	0.009	strong		0.418	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		T	228855993	C	T	228855993	3	4	26	1	0	0	0	0	1	0	0	0	15063	922	32	2	343	2	SPHKAP	2	228855993	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	10097793	228855993	14343380	93	9856											
NCL	4691	hgsc.bcm.edu	37	chr2	232325382	232325384	+	In_Frame_Del	DEL	TCC	TCC	-																															agaatctaatttaagtacctTcctcctcctcttcttcctcc																								rs140018754		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:232325382_232325384delTCC	ENST00000322723.4	-	4	1047_1049	c.807_809delGGA	c.(805-810)gaggaa>gaa	p.269_270EE>E	SNORD82_ENST00000365530.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	269	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)		TTAAGTACCTTCCTCCTCCTCTT	0.409																																					p.270_270del		Pindel,Atlas-Indel	.											.	NCL	80	.	0			c.808_810del						PASS	.			1,0,4265		0,0,1,0,0,2132						4.7	0.3			220	4,5,8245		0,0,4,0,5,4118	no	codingComplex	NCL	NM_005381.2		0,0,5,0,5,6250	A1A1,A1A2,A1R,A2A2,A2R,RR		0.109,0.0234,0.0799				5,5,12510				SO:0001651	inframe_deletion	4691	exon4			.		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.807_809delGGA	2.37:g.232325388_232325390delTCC	ENSP00000318195:p.Glu271del	142	0	.		153	50	0.327	NM_005381	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	In_Frame_Del	DEL	ENST00000322723.4	37	CCDS33397.1																																																																																			.	.	none		0.409	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381		-	232325384	TCC	-	232325382	7	5	26	1	0	1	0	1	0	0	0	0	10235	1783	62	0	1367	0	NCL	2	232325382	In_Frame_Del	DEL	TCC	TCGA-G8-6907-01A-11D-2210-10	3469389	232325382	10873991	94	9857											
ALPP	250	hgsc.bcm.edu	37	chr2	233243793	233243793	+	Silent	SNP	C	C	T																															aacctcatcatcttcctgggCgatggtgagtgagccaggcc																								rs1130337	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:233243793C>T	ENST00000392027.2	+	2	458	c.189C>T	c.(187-189)ggC>ggT	p.G63G	AC068134.8_ENST00000439072.1_RNA|AC068134.8_ENST00000441266.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	63					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)		TCTTCCTGGGCGATGGTGAGT	0.677													C|||	57	0.0113818	0.0008	0.0101	5008	,	,		17685	0.0		0.0249	False		,,,				2504	0.0245				p.G63G		Atlas-SNP	.											.	ALPP	53	.	0			c.C189T						PASS	.	T		10,4396		0,10,2193	71	79	76		189	-5	0	2	dbSNP_86	76	137,8463		3,131,4166	no	coding-synonymous	ALPP	NM_001632.3		3,141,6359	TT,TC,CC		1.593,0.227,1.1302		63/536	233243793	147,12859	2203	4300	6503	SO:0001819	synonymous_variant	250	exon2			CCTGGGCGATGGT	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.189C>T	2.37:g.233243793C>T		95	0	0		88	36	0.409091	NM_001632	P05188|P06861|Q53S78|Q96DB7	Silent	SNP	ENST00000392027.2	37	CCDS2490.1																																																																																			C|0.996;G|0.001;T|0.003	0.003	strong		0.677	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632		T	233243793	C	T	233243793	2	4	26	1	0	0	0	0	0	0	0	1	548	755	27	1		1	ALPP	2	233243793	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	918411	233243793	9955580	95	9858	121	2									
ALPP	250	hgsc.bcm.edu	37	chr2	233243796	233243796	+	Splice_Site	SNP	T	T	C																															ctcatcatcttcctgggcgaTggtgagtgagccaggccttc																								rs200958062|rs1130338	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:233243796T>C	ENST00000392027.2	+	2	461	c.192T>C	c.(190-192)gaT>gaC	p.D64D	AC068134.8_ENST00000439072.1_RNA|AC068134.8_ENST00000441266.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	64					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)		TCCTGGGCGATGGTGAGTGAG	0.667													t|||	60	0.0119808	0.0008	0.0101	5008	,	,		17060	0.0		0.0258	False		,,,				2504	0.0266				p.D64D		Atlas-SNP	.											.	ALPP	53	.	0			c.T192C						PASS	.	C		9,4397		0,9,2194	72	79	77		192	-5	0	2		77	144,8456		4,136,4160	no	coding-synonymous-near-splice	ALPP	NM_001632.3		4,145,6354	CC,CT,TT		1.6744,0.2043,1.1764		64/536	233243796	153,12853	2203	4300	6503	SO:0001630	splice_region_variant	250	exon2			GGGCGATGGTGAG	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.193+1T>C	2.37:g.233243796T>C		94	0	0		85	33	0.388235	NM_001632	P05188|P06861|Q53S78|Q96DB7	Silent	SNP	ENST00000392027.2	37	CCDS2490.1																																																																																			T|0.989;C|0.011	0.011	strong		0.667	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632	Silent	C	233243796	T	C	233243796	5	2	26	1	0	0	0	0	0	0	1	0	548	1478	51	3	198	3	ALPP	2	233243796	Splice_Site	SNP	T	TCGA-G8-6907-01A-11D-2210-10	3	233243796	9955577	96	9859	121	2									
GIGYF2	26058	hgsc.bcm.edu	37	chr2	233712223	233712223	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcgtcagcagcagcagcTgccacagcagcagcagcagc	11	2	13	15	1	1	0	1	0	0	0	1	0	1	0	1	0	11	9	1	0	0	0	rs114013774|rs527464858	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:233712223T>A	ENST00000409547.1	+	29	3937	c.3626T>A	c.(3625-3627)cTg>cAg	p.L1209Q	GIGYF2_ENST00000409196.3_Missense_Mutation_p.L1203Q|GIGYF2_ENST00000373563.4_Missense_Mutation_p.L1209Q|GIGYF2_ENST00000373566.3_Missense_Mutation_p.L1231Q|GIGYF2_ENST00000409480.1_Missense_Mutation_p.L1231Q|GIGYF2_ENST00000409451.3_Missense_Mutation_p.L1230Q	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	1209	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)		cagcagcagctgccacagcag	0.557																																					p.L1230Q		Atlas-SNP	.											.	GIGYF2	288	.	0			c.T3689A						PASS	.						14	16	15					2																	233712223		2161	4224	6385	SO:0001583	missense	26058	exon29			AGCAGCTGCCACA	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.3626T>A	2.37:g.233712223T>A	ENSP00000386537:p.Leu1209Gln	42	0	0		38	9	0.236842	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	37	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	T	0.021	-1.427088	0.01117	.	.	ENSG00000204120	ENST00000373566;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000409196;ENST00000409451	T;T;T;T;T;T	0.61859	0.07;0.07;0.07;0.07;0.07;0.07	1.39	-2.77	0.05877	.	.	.	.	.	T	0.25344	0.0616	N	0.04959	-0.14	0.39400	D	0.966566	B;B;B	0.12630	0.0;0.006;0.0	B;B;B	0.08055	0.0;0.003;0.0	T	0.32322	-0.9911	9	0.13108	T	0.6	-0.0091	3.5635	0.07890	0.3937:0.4039:0.0:0.2024	.	1230;1209;1203	A6H8W4;Q6Y7W6;E9PBB0	.;PERQ2_HUMAN;.	Q	1231;1209;1231;1209;1203;1230	ENSP00000362667:L1231Q;ENSP00000362664:L1209Q;ENSP00000386765:L1231Q;ENSP00000386537:L1209Q;ENSP00000387070:L1203Q;ENSP00000387170:L1230Q	ENSP00000362664:L1209Q	L	+	2	0	GIGYF2	233420467	0.003000	0.15002	0.361000	0.25849	0.026000	0.11368	0.028000	0.13644	-2.729000	0.00385	-2.797000	0.00114	CTG	T|0.966;A|0.034	0.034	strong		0.557	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		A	233712223	T	A	233712223	3	1	26	1	0	0	0	0	1	0	0	0	6386	1580	55	5	3794	5	GIGYF2	2	233712223	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	468427	233712223	9487150	97	9860											
USP40	55230	hgsc.bcm.edu	37	chr2	234433190	234433190	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcagcaatttcagtttcaCacagtgtcagttcatcccct	10	13	5	13	0	5	0	5	0	0	0	6	0	6	0	2	0	1	3	2	0	1	3	rs200068889		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:234433190C>G	ENST00000427112.2	-	14	1861	c.1826G>C	c.(1825-1827)tGt>tCt	p.C609S	USP40_ENST00000450966.1_Missense_Mutation_p.C621S|USP40_ENST00000251722.6_Missense_Mutation_p.C609S			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	609					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)		TTCAGTTTCACACAGTGTCAG	0.378																																					p.C621S		Atlas-SNP	.											.	USP40	174	.	0			c.G1862C						PASS	.	C	SER/CYS	1,3723		0,1,1861	84	78	80		1862	2.4	0.1	2		80	2,8252		0,2,4125	yes	missense	USP40	NM_018218.2	112	0,3,5986	GG,GC,CC		0.0242,0.0269,0.025	benign	621/1248	234433190	3,11975	1862	4127	5989	SO:0001583	missense	55230	exon14			GTTTCACACAGTG	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.1826G>C	2.37:g.234433190C>G	ENSP00000387898:p.Cys609Ser	123	0	0		131	60	0.458015	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	37	CCDS46547.1	.	.	.	.	.	.	.	.	.	.	C	6.767	0.510490	0.12883	2.69E-4	2.42E-4	ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112	T;T;T	0.41065	1.01;1.01;1.01	5.68	2.38	0.29361	.	2.175690	0.01523	N	0.018456	T	0.31606	0.0802	L	0.27053	0.805	0.09310	N	0.999999	B;B	0.11235	0.002;0.004	B;B	0.11329	0.002;0.006	T	0.14254	-1.0479	10	0.21014	T	0.42	.	6.3009	0.21111	0.1483:0.6338:0.0:0.2179	.	609;621	Q9NVE5;Q9NVE5-3	UBP40_HUMAN;.	S	621;609;609	ENSP00000415434:C621S;ENSP00000251722:C609S;ENSP00000387898:C609S	ENSP00000251722:C609S	C	-	2	0	USP40	234097929	0.190000	0.23276	0.056000	0.19401	0.988000	0.76386	0.707000	0.25704	0.709000	0.31976	0.563000	0.77884	TGT	.	.	weak		0.378	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294		G	234433190	C	G	234433190	3	3	26	1	0	0	0	0	1	0	0	0	17087	478	17	4	1953	4	USP40	2	234433190	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	720967	234433190	8766183	98	9861											
USP40	55230	hgsc.bcm.edu	37	chr2	234449358	234449358	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcttgttccaagatattcCtatctttttcaaaagtttct	9	20	3	9	0	4	1	1	0	3	1	6	1	6	1	2	0	0	2	2	0	5	9	rs202235068		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:234449358C>G	ENST00000427112.2	-	9	1152	c.1117G>C	c.(1117-1119)Gga>Cga	p.G373R	USP40_ENST00000450966.1_Missense_Mutation_p.G385R|USP40_ENST00000251722.6_Missense_Mutation_p.G373R			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	373	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)		CAAGATATTCCTATCTTTTTC	0.388																																					p.G385R		Atlas-SNP	.											.	USP40	174	.	0			c.G1153C						PASS	.	C	ARG/GLY	1,3697		0,1,1848	180	168	172		1153	5.1	1	2		172	2,8216		0,2,4107	yes	missense	USP40	NM_018218.2	125	0,3,5955	GG,GC,CC		0.0243,0.027,0.0252	probably-damaging	385/1248	234449358	3,11913	1849	4109	5958	SO:0001583	missense	55230	exon9			ATATTCCTATCTT	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.1117G>C	2.37:g.234449358C>G	ENSP00000387898:p.Gly373Arg	226	0	0		221	109	0.493213	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	37	CCDS46547.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.026869	0.75390	2.7E-4	2.43E-4	ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112	T;T;T	0.07021	3.23;3.24;3.24	5.09	5.09	0.68999	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	13.261800	0.00166	N	0.000000	T	0.31796	0.0808	M	0.66939	2.045	0.53005	D	0.999963	D;D	0.69078	0.997;0.996	D;D	0.77557	0.99;0.982	T	0.00540	-1.1681	10	0.87932	D	0	.	10.533	0.44988	0.0:0.8747:0.0:0.1253	.	373;385	Q9NVE5;Q9NVE5-3	UBP40_HUMAN;.	R	385;373;373	ENSP00000415434:G385R;ENSP00000251722:G373R;ENSP00000387898:G373R	ENSP00000251722:G373R	G	-	1	0	USP40	234114097	1.000000	0.71417	0.993000	0.49108	0.877000	0.50540	4.295000	0.59049	2.526000	0.85167	0.561000	0.74099	GGA	.	.	weak		0.388	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294		G	234449358	C	G	234449358	3	3	26	1	0	0	0	0	1	0	0	0	17087	690	24	4	2682	4	USP40	2	234449358	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	16168	234449358	8750015	99	9862											
HDAC4	9759	hgsc.bcm.edu	37	chr2	240078400	240078400	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tcgtacattcccaggaccggGtggttataggaggtcgacac	9	9	13	10	3	0	0	0	0	0	0	3	3	1	2	2	5	1	2	2	5	3	4	rs148880349	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:240078400G>A	ENST00000345617.3	-	7	1472	c.681C>T	c.(679-681)caC>caT	p.H227H	HDAC4_ENST00000543185.1_5'Flank|HDAC4_ENST00000553145.1_5'Flank|HDAC4_ENST00000541256.1_Silent_p.H196H	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	227	Interaction with MEF2A.				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)		CCAGGACCGGGTGGTTATAGG	0.567																																					p.H227H		Atlas-SNP	.											.	HDAC4	127	.	0			c.C681T						PASS	.	G		3,4403	6.2+/-15.9	0,3,2200	126	120	122		681	3.5	1	2	dbSNP_134	122	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous	HDAC4	NM_006037.3		0,12,6491	AA,AG,GG		0.1047,0.0681,0.0923		227/1085	240078400	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	9759	exon7			GACCGGGTGGTTA	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.681C>T	2.37:g.240078400G>A		57	0	0		77	42	0.545455	NM_006037	Q9UND6	Silent	SNP	ENST00000345617.3	37	CCDS2529.1																																																																																			G|0.999;A|0.001	0.001	strong		0.567	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037		A	240078400	G	A	240078400	2	1	26	1	0	0	0	0	0	0	0	1	7018	1252	44	2		2	HDAC4	2	240078400	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	5629042	240078400	3120973	100	9863											
PASK	23178	hgsc.bcm.edu	37	chr2	242080119	242080119	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagtgcagtttacttgtacaAatattctgggcagccagtga	11	12	10	8	0	1	1	0	1	1	0	1	1	1	1	1	1	4	4	1	1	4	6			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:242080119A>C	ENST00000405260.1	-	3	944	c.246T>G	c.(244-246)atT>atG	p.I82M	PASK_ENST00000539818.1_Intron|PASK_ENST00000544142.1_Intron|PASK_ENST00000234040.4_Missense_Mutation_p.I82M|PASK_ENST00000403638.3_Missense_Mutation_p.I82M|PASK_ENST00000358649.4_Missense_Mutation_p.I82M	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	82					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)		TACTTGTACAAATATTCTGGG	0.557																																					p.I82M		Atlas-SNP	.											.	PASK	230	.	0			c.T246G						PASS	.						70	70	70					2																	242080119		2203	4300	6503	SO:0001583	missense	23178	exon3			TGTACAAATATTC	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.246T>G	2.37:g.242080119A>C	ENSP00000384016:p.Ile82Met	426	0	0		483	211	0.436853	NM_001252122	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Missense_Mutation	SNP	ENST00000405260.1	37	CCDS2545.1	.	.	.	.	.	.	.	.	.	.	A	12.70	2.015499	0.35511	.	.	ENSG00000115687	ENST00000234040;ENST00000405260;ENST00000358649;ENST00000403638;ENST00000452907	T;T;T;T	0.74842	-0.88;-0.88;-0.84;0.1	4.54	-2.86	0.05717	.	0.000000	0.52532	D	0.000076	T	0.78572	0.4304	M	0.61703	1.905	0.42674	D	0.993524	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.87578	0.981;0.998;0.982;0.981	T	0.75470	-0.3306	10	0.87932	D	0	.	6.5076	0.22204	0.4255:0.1261:0.4485:0.0	.	82;82;82;82	B7Z7R6;Q96RG2-2;G5E9F1;Q96RG2	.;.;.;PASK_HUMAN	M	82	ENSP00000234040:I82M;ENSP00000384016:I82M;ENSP00000351475:I82M;ENSP00000384438:I82M	ENSP00000234040:I82M	I	-	3	3	PASK	241728792	0.204000	0.23447	0.036000	0.18154	0.265000	0.26407	-0.645000	0.05409	-0.426000	0.07360	-0.464000	0.05259	ATT	.	.	none		0.557	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148		C	242080119	A	C	242080119	3	2	26	1	0	0	0	0	1	0	0	0	11481	10	1	5	3789	5	PASK	2	242080119	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	2001719	242080119	1119254	101	9864											
SUMF1	285362	hgsc.bcm.edu	37	chr3	4508802	4508802	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaacccgcaagggaccccGcgcccgcaccggtcccggcc	8	1	12	20	6	0	1	0	0	0	1	1	2	1	2	7	3	1	2	7	3	3	0	rs200789939	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:4508802G>A	ENST00000272902.5	-	1	163	c.128C>T	c.(127-129)gCg>gTg	p.A43V	SUMF1_ENST00000534863.1_Missense_Mutation_p.A43V|SUMF1_ENST00000458465.2_Missense_Mutation_p.A43V|SUMF1_ENST00000383843.5_Missense_Mutation_p.A43V|SUMF1_ENST00000405420.2_Missense_Mutation_p.A43V	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													G|||	2	0.000399361	0.0	0.0	5008	,	,		13188	0.0		0.002	False		,,,				2504	0.0				p.A43V		Atlas-SNP	.											.	SUMF1	23	.	0			c.C128T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA	0,4178		0,0,2089	5	7	6		128,128,128	2.7	0	3		6	3,8223		0,3,4110	no	missense,missense,missense	SUMF1	NM_001164674.1,NM_001164675.1,NM_182760.3	64,64,64	0,3,6199	AA,AG,GG		0.0365,0.0,0.0242	benign,benign,benign	43/350,43/355,43/375	4508802	3,12401	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>T	3.37:g.4508802G>A	ENSP00000272902:p.Ala43Val	18	0	0		19	12	0.631579	NM_001164675	B4DXK5|B7XD05|E9PGL0|G5E9B0|Q0VAC6|Q0VAC7|Q2NL78|Q53ZE4|Q6UY39|Q96AK5|Q96DK8	Missense_Mutation	SNP	ENST00000272902.5	37	CCDS2564.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	11.94	1.790063	0.31685	0.0	3.65E-4	ENSG00000144455	ENST00000534982;ENST00000534863;ENST00000272902;ENST00000383843;ENST00000458465;ENST00000405420	D;D;D;D;D	0.92805	-2.68;-3.11;-3.09;-2.33;-3.11	4.54	2.71	0.32032	.	0.485588	0.20903	N	0.083614	D	0.87418	0.6172	L	0.59436	1.845	0.09310	N	1	B;B;B;B	0.19200	0.034;0.023;0.014;0.014	B;B;B;B	0.12156	0.003;0.007;0.005;0.005	T	0.75808	-0.3187	10	0.34782	T	0.22	-14.8698	5.3757	0.16164	0.1034:0.0:0.6962:0.2003	.	43;43;43;43	E9PF05;G5E9B0;E9PGL0;Q8NBK3	.;.;.;SUMF1_HUMAN	V	43	ENSP00000440421:A43V;ENSP00000272902:A43V;ENSP00000373355:A43V;ENSP00000410060:A43V;ENSP00000384977:A43V	ENSP00000272902:A43V	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	0.001	strong		0.711	SUMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206591.2	NM_182760		A	4508802	G	A	4508802	3	1	26	1	0	0	0	0	1	0	0	0	15400	1087	38	1	1032	1	SUMF1	3	4508802	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10		4508802	193513628	102	9865											
TTLL3	26140	hgsc.bcm.edu	37	chr3	9874914	9874914	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagtccctctgctgacccagCgaggctctggggaaggcaag	8	6	14	13	1	2	1	0	1	2	0	3	3	3	2	2	4	2	3	2	4	2	0	rs115917139	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:9874914C>T	ENST00000547186.1	+	11	1897	c.1681C>T	c.(1681-1683)Cga>Tga	p.R561*	ARPC4-TTLL3_ENST00000397256.1_Intron|TTLL3_ENST00000455274.1_Intron|TTLL3_ENST00000427853.3_Intron|TTLL3_ENST00000397241.1_Intron|TTLL3_ENST00000426895.4_Nonsense_Mutation_p.R704*|TTLL3_ENST00000430793.1_Nonsense_Mutation_p.R349*|TTLL3_ENST00000383827.1_Intron	NM_001025930.3	NP_001021100.3	Q9Y4R7	TTLL3_HUMAN	tubulin tyrosine ligase-like family, member 3	561					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)					GCTGACCCAGCGAGGCTCTGG	0.647													C|||	115	0.0229633	0.0	0.0231	5008	,	,		16546	0.001		0.0408	False		,,,				2504	0.0583				p.R704X		Atlas-SNP	.											.	TTLL3	51	.	0			c.C2110T						PASS	.	C	stop/ARG,	28,3784		0,28,1878	29	31	30		2110,	3.6	0.3	3	dbSNP_132	30	360,7860		10,340,3760	yes	stop-gained,intron	TTLL3,ARPC4-TTLL3	NM_001025930.3,NM_001198793.1	,	10,368,5638	TT,TC,CC		4.3796,0.7345,3.2247	,	704/916,	9874914	388,11644	1906	4110	6016	SO:0001587	stop_gained	26140	exon11			ACCCAGCGAGGCT		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.1681C>T	3.37:g.9874914C>T	ENSP00000446659:p.Arg561*	87	0	0		92	50	0.543478	NM_001025930	Q4KMS8|Q6AWA3|Q6ZU95|Q8NDN8|Q96GG8|Q9H876|Q9UI99	Nonsense_Mutation	SNP	ENST00000547186.1	37		43	0.019688644688644688	0	0.0	11	0.03038674033149171	0	0.0	32	0.04221635883905013	C	38	6.974468	0.97975	0.007345	0.043796	ENSG00000214021	ENST00000426895;ENST00000547186;ENST00000443148;ENST00000430793	.	.	.	5.39	3.58	0.41010	.	0.000000	0.27782	U	0.017874	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.6056	0.33771	0.3092:0.5413:0.1495:0.0	rs3208837;rs17407417	.	.	.	X	704;561;499;349	.	ENSP00000392549:R704X	R	+	1	2	TTLL3	9849914	0.009000	0.17119	0.270000	0.24601	0.659000	0.38960	0.677000	0.25262	0.639000	0.30564	-0.152000	0.13540	CGA	C|0.975;T|0.025	0.025	strong		0.647	TTLL3-203	KNOWN	basic	protein_coding	protein_coding		NM_001025930.2		T	9874914	C	T	9874914	4	4	26	1	0	0	0	0	0	1	0	0	16743	760	27	1	1719	1	TTLL3	3	9874914	Nonsense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	5366112	9874914	188147516	103	9866											
TATDN2	9797	hgsc.bcm.edu	37	chr3	10312633	10312633	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttaaggcaccctaaggctgtGgcatttggagaaatgggctt	10	11	13	7	0	0	1	0	0	0	1	0	2	0	1	1	5	0	4	1	5	3	4	rs115984909	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:10312633G>A	ENST00000287652.4	+	4	2818	c.1767G>A	c.(1765-1767)gtG>gtA	p.V589V	TATDN2_ENST00000448281.2_Silent_p.V589V|RP11-438J1.1_ENST00000450534.1_3'UTR	NM_014760.3	NP_055575.3	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	589					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						CTAAGGCTGTGGCATTTGGAG	0.473													G|||	5	0.000998403	0.0	0.0	5008	,	,		20193	0.0		0.004	False		,,,				2504	0.001				p.V589V		Atlas-SNP	.											.	TATDN2	59	.	0			c.G1767A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	107	114	112		1767	0.4	1	3	dbSNP_132	112	19,8581	13.3+/-46.6	0,19,4281	no	coding-synonymous	TATDN2	NM_014760.3		0,20,6483	AA,AG,GG		0.2209,0.0227,0.1538		589/762	10312633	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	9797	exon4			GGCTGTGGCATTT	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.1767G>A	3.37:g.10312633G>A		28	0	0		30	18	0.6	NM_014760	Q3MIL9|Q5BKU0	Silent	SNP	ENST00000287652.4	37	CCDS33698.1																																																																																			G|0.998;A|0.002	0.002	strong		0.473	TATDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339641.1	XM_376203		A	10312633	G	A	10312633	2	1	26	1	0	0	0	0	0	0	0	1	15607	1335	47	2		2	TATDN2	3	10312633	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	437719	10312633	187709797	104	9867											
RPL32	6161	hgsc.bcm.edu	37	chr3	12877704	12877704	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttggaggaaacattgtgagcGatctcggcacagtaagatct	12	10	12	7	2	2	2	0	1	2	1	3	5	2	4	0	3	2	2	0	3	2	3	rs6497	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:12877704G>A	ENST00000429711.2	-	4	396	c.297C>T	c.(295-297)atC>atT	p.I99I	RPL32_ENST00000273223.6_Silent_p.I117I|RPL32_ENST00000435983.1_Silent_p.I99I|RPL32_ENST00000396953.2_Silent_p.I99I|RPL32_ENST00000396957.1_Silent_p.I99I	NM_000994.3	NP_000985.1	P62910	RL32_HUMAN	ribosomal protein L32	99					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)|structural constituent of ribosome (GO:0003735)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)	6						CATTGTGAGCGATCTCGGCAC	0.517													G|||	119	0.023762	0.0461	0.0072	5008	,	,		20645	0.0109		0.0249	False		,,,				2504	0.0174				p.I99I		Atlas-SNP	.											RPL32,NS,carcinoma,0,1	RPL32	11	1	0			c.C297T						scavenged	.	G	,,	183,4223	113.8+/-151.8	1,181,2021	67	58	61		297,297,297	-1	1	3	dbSNP_52	61	243,8357	93.8+/-155.7	5,233,4062	no	coding-synonymous,coding-synonymous,coding-synonymous	RPL32	NM_000994.3,NM_001007073.1,NM_001007074.1	,,	6,414,6083	AA,AG,GG		2.8256,4.1534,3.2754	,,	99/136,99/136,99/136	12877704	426,12580	2203	4300	6503	SO:0001819	synonymous_variant	6161	exon4			GTGAGCGATCTCG	CA436299, CF124158, CR608027	CCDS2614.1	3q13.3-q21	2011-04-06			ENSG00000144713	ENSG00000144713		"L ribosomal proteins"	10336	protein-coding gene	gene with protein product						9284913	Standard	NM_001007073		Approved	L32	uc003bxl.3	P62910	OTTHUMG00000129804	ENST00000429711.2:c.297C>T	3.37:g.12877704G>A		8	0	0		12	3	0.25	NM_001007073	B2R4Q3|P02433	Silent	SNP	ENST00000429711.2	37	CCDS2614.1																																																																																			G|0.971;A|0.029	0.029	strong		0.517	RPL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252032.2	NM_000994		A	12877704	G	A	12877704	2	1	26	1	0	0	0	0	0	0	0	1	13597	1048	37	1		1	RPL32	3	12877704	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	2565071	12877704	185144726	105	9868											
SLC4A7	9497	hgsc.bcm.edu	37	chr3	27436597	27436597	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tatgatccaccctctctctgGatgagtaggctgttaaaaaa	12	12	8	9	0	2	2	0	2	2	0	4	3	3	3	2	2	0	3	2	2	5	3	rs114662202	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:27436597G>A	ENST00000295736.5	-	19	2756	c.2686C>T	c.(2686-2688)Cca>Tca	p.P896S	SLC4A7_ENST00000437179.1_Missense_Mutation_p.P777S|SLC4A7_ENST00000455077.1_Missense_Mutation_p.P777S|SLC4A7_ENST00000446700.1_Missense_Mutation_p.P888S|SLC4A7_ENST00000388777.4_Missense_Mutation_p.P446S|SLC4A7_ENST00000428386.1_Missense_Mutation_p.P772S|SLC4A7_ENST00000454389.1_Missense_Mutation_p.P905S|SLC4A7_ENST00000435667.2_Missense_Mutation_p.P781S|SLC4A7_ENST00000425128.2_3'UTR|SLC4A7_ENST00000445684.1_Missense_Mutation_p.P892S|SLC4A7_ENST00000440156.1_Missense_Mutation_p.P892S	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	896					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)	CCTCTCTCTGGATGAGTAGGC	0.358													G|||	35	0.00698882	0.0106	0.0086	5008	,	,		17732	0.0		0.0129	False		,,,				2504	0.002				p.P896S		Atlas-SNP	.											SLC4A7,rectum,carcinoma,+2,4	SLC4A7	119	4	0			c.C2686T						scavenged	.	G	SER/PRO	50,4356	51.6+/-87.1	0,50,2153	60	59	59		2686	3	1	3	dbSNP_132	59	144,8456	66.7+/-129.0	2,140,4158	yes	missense	SLC4A7	NM_003615.3	74	2,190,6311	AA,AG,GG		1.6744,1.1348,1.4916	benign	896/1215	27436597	194,12812	2203	4300	6503	SO:0001583	missense	9497	exon19			TCTCTGGATGAGT	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.2686C>T	3.37:g.27436597G>A	ENSP00000295736:p.Pro896Ser	179	1	0.00558659		154	64	0.415584	NM_003615	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Missense_Mutation	SNP	ENST00000295736.5	37	CCDS33721.1	13	0.005952380952380952	4	0.008130081300813009	3	0.008287292817679558	0	0.0	6	0.0079155672823219	G	10.88	1.475427	0.26511	0.011348	0.016744	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	0.78595	-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19	6.06	2.95	0.34219	Bicarbonate transporter, C-terminal (1);	0.308279	0.38217	N	0.001764	T	0.49406	0.1555	N	0.25890	0.77	0.80722	D	1	B;B;B;B;B;B;B;B;B	0.19445	0.033;0.033;0.014;0.036;0.033;0.005;0.026;0.033;0.033	B;B;B;B;B;B;B;B;B	0.29176	0.099;0.04;0.04;0.099;0.099;0.015;0.06;0.099;0.04	T	0.53556	-0.8422	10	0.36615	T	0.2	.	9.3212	0.37966	0.0:0.1003:0.3472:0.5525	.	892;777;888;892;905;446;772;896;777	E9PFN4;B5M452;E9PGC1;B5M453;E9PDL9;F8W7E6;Q9Y6M7-2;Q9Y6M7;B2CI53	.;.;.;.;.;.;.;S4A7_HUMAN;.	S	447;896;772;905;892;777;888;777;892;781;446;792	ENSP00000411031:P447S;ENSP00000295736:P896S;ENSP00000416368:P772S;ENSP00000390394:P905S;ENSP00000414797:P892S;ENSP00000394252:P777S;ENSP00000406605:P888S;ENSP00000407382:P777S;ENSP00000406804:P892S;ENSP00000395336:P781S;ENSP00000373429:P446S;ENSP00000388703:P792S	ENSP00000295736:P896S	P	-	1	0	SLC4A7	27411601	1.000000	0.71417	0.992000	0.48379	0.649000	0.38597	1.998000	0.40796	0.842000	0.35045	0.655000	0.94253	CCA	G|0.988;A|0.012	0.012	strong		0.358	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615		A	27436597	G	A	27436597	3	1	26	1	0	0	0	0	1	0	0	0	14673	1174	41	2	986	2	SLC4A7	3	27436597	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	14558893	27436597	170585833	106	9869											
UBP1	7342	hgsc.bcm.edu	37	chr3	33467112	33467112	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ataagtaagcgtttcatcatGcagttttactgctggtgacg	10	14	10	7	2	2	1	2	1	0	0	2	1	2	1	0	1	4	5	0	1	3	5	rs61751640	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:33467112G>A	ENST00000283629.3	-	2	764	c.235C>T	c.(235-237)Cat>Tat	p.H79Y	UBP1_ENST00000283628.5_Missense_Mutation_p.H79Y|UBP1_ENST00000447368.2_Missense_Mutation_p.H79Y	NM_001128161.1|NM_014517.4	NP_001121633.1|NP_055332.3	Q9NZI7	UBIP1_HUMAN	upstream binding protein 1 (LBP-1a)	79					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						GTTTCATCATGCAGTTTTACT	0.388													G|||	8	0.00159744	0.0	0.0014	5008	,	,		16266	0.0		0.006	False		,,,				2504	0.001				p.H79Y		Atlas-SNP	.											.	UBP1	42	.	0			c.C235T						PASS	.	G	TYR/HIS,TYR/HIS,TYR/HIS	11,4395	19.1+/-41.9	0,11,2192	87	72	77		235,235,235	5.9	1	3	dbSNP_129	77	89,8511	50.6+/-110.7	0,89,4211	yes	missense,missense,missense	UBP1	NM_001128160.1,NM_001128161.1,NM_014517.4	83,83,83	0,100,6403	AA,AG,GG		1.0349,0.2497,0.7689	benign,benign,benign	79/505,79/541,79/541	33467112	100,12906	2203	4300	6503	SO:0001583	missense	7342	exon2			CATCATGCAGTTT	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.235C>T	3.37:g.33467112G>A	ENSP00000283629:p.His79Tyr	80	0	0		86	35	0.406977	NM_001128160	Q68CT0|Q86Y57|Q9H8V0|Q9UD76|Q9UD78	Missense_Mutation	SNP	ENST00000283629.3	37	CCDS2659.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	G	16.88	3.243954	0.58995	0.002497	0.010349	ENSG00000153560	ENST00000283629;ENST00000447368;ENST00000283628;ENST00000456378	T;T;T;T	0.18016	2.24;2.24;2.24;2.24	5.92	5.92	0.95590	CP2 transcription factor (1);	0.048704	0.85682	D	0.000000	T	0.12646	0.0307	L	0.41573	1.285	0.58432	D	0.999994	B;B	0.13145	0.006;0.007	B;B	0.23852	0.005;0.049	T	0.01587	-1.1318	10	0.56958	D	0.05	-21.3838	13.9369	0.64029	0.0778:0.0:0.9222:0.0	rs61751640	79;79	Q9NZI7-4;Q9NZI7	.;UBIP1_HUMAN	Y	79	ENSP00000283629:H79Y;ENSP00000395558:H79Y;ENSP00000283628:H79Y;ENSP00000401614:H79Y	ENSP00000283628:H79Y	H	-	1	0	UBP1	33442116	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.723000	0.74742	2.810000	0.96702	0.585000	0.79938	CAT	G|0.994;A|0.006	0.006	strong		0.388	UBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253249.2	NM_014517		A	33467112	G	A	33467112	3	1	26	1	0	0	0	0	1	0	0	0	16910	1319	46	2	1447	2	UBP1	3	33467112	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	6030515	33467112	164555318	107	9870											
CLASP2	23122	hgsc.bcm.edu	37	chr3	33543195	33543195	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tttagttcatcaccaattacCgcatgaacagccaccaggca	13	9	6	13	1	2	1	2	1	0	0	2	1	2	1	4	1	3	3	4	1	4	4	rs111990025	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:33543195C>T	ENST00000468888.2	-	38	4453	c.4407G>A	c.(4405-4407)gcG>gcA	p.A1469A	CLASP2_ENST00000399362.4_Silent_p.A1468A|CLASP2_ENST00000480013.1_Silent_p.A1248A|CLASP2_ENST00000539981.1_3'UTR|CLASP2_ENST00000359576.5_Silent_p.A1460A|CLASP2_ENST00000461133.3_Silent_p.A1228A|CLASP2_ENST00000307312.7_Silent_p.A950A			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	1249					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						CACCAATTACCGCATGAACAG	0.443													C|||	57	0.0113818	0.0008	0.0072	5008	,	,		19135	0.001		0.0219	False		,,,				2504	0.0286				p.A1470A		Atlas-SNP	.											.	CLASP2	138	.	0			c.G4410A						PASS	.	C	,	24,3892		0,24,1934	141	135	137		3747,4410	-6.2	0.4	3	dbSNP_132	137	206,8106		3,200,3953	no	coding-synonymous,coding-synonymous	CLASP2	NM_001207044.1,NM_015097.2	,	3,224,5887	TT,TC,CC		2.4783,0.6129,1.8809	,	1249/1295,1470/1516	33543195	230,11998	1958	4156	6114	SO:0001819	synonymous_variant	23122	exon38			AATTACCGCATGA	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.4407G>A	3.37:g.33543195C>T		61	0	0		71	32	0.450704	NM_015097	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Silent	SNP	ENST00000468888.2	37		22	0.010073260073260074	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	20	0.026385224274406333	C	6.469	0.454728	0.12283	0.006129	0.024783	ENSG00000163539	ENST00000487553	.	.	.	5.7	-6.15	0.02105	.	.	.	.	.	T	0.29126	0.0724	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52953	-0.8506	4	.	.	.	-6.566	11.4283	0.50025	0.085:0.3006:0.0:0.6144	.	.	.	.	S	175	.	.	G	-	1	0	CLASP2	33518199	0.000000	0.05858	0.395000	0.26283	0.793000	0.44817	-2.319000	0.01120	-1.720000	0.01380	-2.945000	0.00085	GGT	C|0.987;T|0.013	0.013	strong		0.443	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044		T	33543195	C	T	33543195	2	4	26	1	0	0	0	0	0	0	0	1	3457	639	23	1		1	CLASP2	3	33543195	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	76083	33543195	164479235	108	9871											
ITGA9	3680	hgsc.bcm.edu	37	chr3	37550109	37550109	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attaagatctttcaagcatcAggtaaaaaggtgaggttctt	14	13	9	5	0	4	2	2	1	2	1	4	2	4	2	0	3	1	3	0	3	5	5			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:37550109A>G	ENST00000264741.5	+	8	1144	c.888A>G	c.(886-888)tcA>tcG	p.S296S	ITGA9_ENST00000422441.1_Silent_p.S296S	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	296					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)		TTCAAGCATCAGGTAAAAAGG	0.338																																					p.S296S		Atlas-SNP	.											.	ITGA9	98	.	0			c.A888G						PASS	.						100	105	103					3																	37550109		2203	4300	6503	SO:0001819	synonymous_variant	3680	exon8			AGCATCAGGTAAA	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.888A>G	3.37:g.37550109A>G		144	0	0		160	80	0.5	NM_002207	Q14638	Silent	SNP	ENST00000264741.5	37	CCDS2669.1																																																																																			.	.	none		0.338	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207		G	37550109	A	G	37550109	2	3	26	1	0	0	0	0	0	0	0	1	7892	175	7	3		3	ITGA9	3	37550109	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	4006914	37550109	160472321	109	9872											
CSRNP1	64651	hgsc.bcm.edu	37	chr3	39185525	39185525	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagccacaggggaatgctGtgtggtccatctgcagagaa	11	7	14	9	0	1	1	0	0	1	1	2	3	2	2	2	3	4	3	2	3	2	0	rs375810664		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:39185525G>A	ENST00000273153.5	-	5	968	c.791C>T	c.(790-792)aCa>aTa	p.T264I	CSRNP1_ENST00000514182.1_Missense_Mutation_p.T264I	NM_033027.3	NP_149016.2	Q96S65	CSRN1_HUMAN	cysteine-serine-rich nuclear protein 1	264	Cys-rich.				apoptotic process (GO:0006915)|face morphogenesis (GO:0060325)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)	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)			central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|skin(3)	24						GGGGAATGCTGTGTGGTCCAT	0.552																																					p.T264I		Atlas-SNP	.											.	CSRNP1	59	.	0			c.C791T						PASS	.	G	ILE/THR	0,4406		0,0,2203	39	39	39		791	4.5	0.9	3		39	1,8599	1.2+/-3.3	0,1,4299	no	missense	CSRNP1	NM_033027.3	89	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	264/590	39185525	1,13005	2203	4300	6503	SO:0001583	missense	64651	exon5			AATGCTGTGTGGT	AB053121	CCDS2682.1	3p22	2009-04-17	2009-04-17	2009-04-17	ENSG00000144655	ENSG00000144655			14300	protein-coding gene	gene with protein product		606458	"AXIN1 up-regulated 1"	AXUD1		11526492, 17726538	Standard	NM_033027		Approved	URAX1, DKFZp566F164, FAM130B, TAIP-3	uc003cjg.3	Q96S65	OTTHUMG00000131293	ENST00000273153.5:c.791C>T	3.37:g.39185525G>A	ENSP00000273153:p.Thr264Ile	36	0	0		52	21	0.403846	NM_033027	Q69YY5	Missense_Mutation	SNP	ENST00000273153.5	37	CCDS2682.1	.	.	.	.	.	.	.	.	.	.	G	16.31	3.087702	0.55968	0.0	1.16E-4	ENSG00000144655	ENST00000273153;ENST00000514182	T;T	0.14516	2.5;2.5	4.48	4.48	0.54585	.	0.061123	0.64402	D	0.000003	T	0.28599	0.0708	L	0.51422	1.61	0.36804	D	0.885495	D	0.67145	0.996	P	0.59889	0.865	T	0.10042	-1.0647	10	0.46703	T	0.11	-16.1823	17.7133	0.88328	0.0:0.0:1.0:0.0	.	264	Q96S65	CSRN1_HUMAN	I	264	ENSP00000273153:T264I;ENSP00000422532:T264I	ENSP00000273153:T264I	T	-	2	0	CSRNP1	39160529	0.997000	0.39634	0.946000	0.38457	0.905000	0.53344	2.532000	0.45659	2.475000	0.83589	0.561000	0.74099	ACA	.	.	weak		0.552	CSRNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254061.1	NM_033027		A	39185525	G	A	39185525	3	1	26	1	0	0	0	0	1	0	0	0	3965	1377	48	2	982	2	CSRNP1	3	39185525	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1635416	39185525	158836905	110	9873											
CCDC13	152206	hgsc.bcm.edu	37	chr3	42787467	42787467	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gacccctccaggtccctggcGaagataggagctgctgaacg	9	6	13	13	2	0	2	0	1	0	1	2	5	2	3	4	3	3	2	4	3	3	1	rs141737119	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:42787467G>A	ENST00000310232.6	-	7	856	c.773C>T	c.(772-774)tCg>tTg	p.S258L	CCDC13-AS1_ENST00000446950.1_RNA|CCDC13-AS1_ENST00000418161.1_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						GGTCCCTGGCGAAGATAGGAG	0.512																																					p.S258L		Atlas-SNP	.											CCDC13,colon,carcinoma,+1,1	CCDC13	71	1	0			c.C773T						PASS	.	G	LEU/SER	1,4405	2.1+/-5.4	0,1,2202	92	89	90		773	3.3	0.4	3	dbSNP_134	90	2,8598	2.2+/-6.3	0,2,4298	no	missense	CCDC13	NM_144719.3	145	0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231	benign	258/716	42787467	3,13003	2203	4300	6503	SO:0001583	missense	152206	exon7			CCTGGCGAAGATA	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.773C>T	3.37:g.42787467G>A	ENSP00000309836:p.Ser258Leu	110	0	0		75	42	0.56	NM_144719		Missense_Mutation	SNP	ENST00000310232.6	37	CCDS2705.1	.	.	.	.	.	.	.	.	.	.	G	8.690	0.907306	0.17833	2.27E-4	2.33E-4	ENSG00000244607	ENST00000310232	T	0.25085	1.82	5.08	3.27	0.37495	.	0.461691	0.22580	N	0.058238	T	0.22399	0.0540	L	0.52905	1.665	0.18873	N	0.999983	B	0.16396	0.017	B	0.12156	0.007	T	0.18777	-1.0326	10	0.26408	T	0.33	.	9.0645	0.36455	0.0787:0.0:0.7746:0.1466	.	258	Q8IYE1	CCD13_HUMAN	L	258	ENSP00000309836:S258L	ENSP00000309836:S258L	S	-	2	0	CCDC13	42762471	0.405000	0.25336	0.434000	0.26772	0.186000	0.23388	0.648000	0.24828	0.539000	0.28788	-0.137000	0.14449	TCG	G|1.000;A|0.000	0.000	strong		0.512	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719		A	42787467	G	A	42787467	3	1	26	1	0	0	0	0	1	0	0	0	2767	1059	37	1	1414	1	CCDC13	3	42787467	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	3601942	42787467	155234963	111	9874											
C3orf39	84892	hgsc.bcm.edu	37	chr3	43122702	43122702	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcggcagatgcggtctgtGtgcgtgcggcccgtgcacac	6	7	16	12	5	1	1	0	0	1	1	1	1	1	1	1	3	5	2	1	3	1	0	rs141040291		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:43122702G>A	ENST00000344697.2	-	2	567	c.222C>T	c.(220-222)caC>caT	p.H74H	POMGNT2_ENST00000441964.1_Silent_p.H74H	NM_032806.5	NP_116195.2	Q8NAT1	PMGT2_HUMAN	protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)	74					protein O-linked glycosylation (GO:0006493)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein O-GlcNAc transferase activity (GO:0097363)										TGCGGTCTGTGTGCGTGCGGC	0.607																																					p.H74H		Atlas-SNP	.											.	.	.	.	0			c.C222T						PASS	.	G		0,4406		0,0,2203	83	73	76		222	4.9	1	3	dbSNP_134	76	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	C3orf39	NM_032806.4		0,3,6500	AA,AG,GG		0.0349,0.0,0.0231		74/581	43122702	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	84892	exon2			GTCTGTGTGCGTG	AK092147	CCDS2709.1	3p22.1	2014-07-15	2013-08-22	2013-08-22	ENSG00000144647	ENSG00000144647			25902	protein-coding gene	gene with protein product		614828	"chromosome 3 open reading frame 39", "glycosyltransferase-like domain containing 2"	C3orf39, GTDC2		12477932	Standard	NM_032806		Approved	FLJ14566, AGO61	uc003cmr.2	Q8NAT1	OTTHUMG00000133038	ENST00000344697.2:c.222C>T	3.37:g.43122702G>A		85	0	0		109	57	0.522936	NM_032806	B3KWC3|Q96SY3	Silent	SNP	ENST00000344697.2	37	CCDS2709.1																																																																																			G|1.000;A|0.000	0.000	weak		0.607	POMGNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256643.1	NM_032806		A	43122702	G	A	43122702	2	1	26	1	0	0	0	0	0	0	0	1	2231	1368	48	2		2	C3orf39	3	43122702	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	335235	43122702	154899728	112	9875											
NBEAL2	23218	hgsc.bcm.edu	37	chr3	47033970	47033970	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cccacttccccacagctgtaCctgcagtcccgggcgccccc	5	6	8	22	2	0	0	0	0	0	0	2	0	2	0	7	1	3	3	7	1	1	2	rs201015016	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:47033970C>T	ENST00000450053.3	+	10	1217	c.1038C>T	c.(1036-1038)taC>taT	p.Y346Y	NBEAL2_ENST00000292309.5_Silent_p.Y346Y|NBEAL2_ENST00000383740.2_5'UTR	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	346					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)		CACAGCTGTACCTGCAGTCCC	0.642													C|||	2	0.000399361	0.0	0.0014	5008	,	,		17796	0.0		0.001	False		,,,				2504	0.0				p.Y346Y		Atlas-SNP	.											.	NBEAL2	267	.	0			c.C1038T						PASS	.	C		3,3859		0,3,1928	26	28	27		1038	3.4	1	3		27	23,8219		0,23,4098	no	coding-synonymous	NBEAL2	NM_015175.1		0,26,6026	TT,TC,CC		0.2791,0.0777,0.2148		346/2755	47033970	26,12078	1931	4121	6052	SO:0001819	synonymous_variant	23218	exon10			GCTGTACCTGCAG	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.1038C>T	3.37:g.47033970C>T		96	0	0		88	37	0.420455	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Silent	SNP	ENST00000450053.3	37	CCDS46817.1																																																																																			C|0.998;T|0.002	0.002	weak		0.642	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064		T	47033970	C	T	47033970	2	4	26	1	0	0	0	0	0	0	0	1	10198	518	18	2		2	NBEAL2	3	47033970	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	3911268	47033970	150988460	113	9876											
NCKIPSD	51517	hgsc.bcm.edu	37	chr3	48716536	48716536	+	Missense_Mutation	SNP	G	G	A																															caggttcacgcagaggtccgGcagctgctctgtggtgtcca																								rs75577765	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:48716536G>A	ENST00000294129.2	-	10	1770	c.1651C>T	c.(1651-1653)Ccg>Tcg	p.P551S	NCKIPSD_ENST00000341520.4_Missense_Mutation_p.P551S|NCKIPSD_ENST00000416649.2_Missense_Mutation_p.P544S	NM_016453.2	NP_057537.1	Q9NZQ3	SPN90_HUMAN	NCK interacting protein with SH3 domain	551	Leu-rich.				cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|NLS-bearing protein import into nucleus (GO:0006607)|signal transduction (GO:0007165)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	cytoskeletal protein binding (GO:0008092)			endometrium(1)|large_intestine(3)|lung(6)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CAGAGGTCCGGCAGCTGCTCT	0.652													G|||	26	0.00519169	0.0	0.0029	5008	,	,		16917	0.0		0.0139	False		,,,				2504	0.0102				p.P551S		Atlas-SNP	.											.	NCKIPSD	52	.	0			c.C1651T						PASS	.	G	SER/PRO,SER/PRO	16,4390	22.3+/-47.3	0,16,2187	53	54	54		1651,1630	5.4	1	3	dbSNP_131	54	112,8488	52.3+/-112.8	0,112,4188	yes	missense,missense	NCKIPSD	NM_016453.2,NM_184231.1	74,74	0,128,6375	AA,AG,GG		1.3023,0.3631,0.9842	probably-damaging,probably-damaging	551/723,544/716	48716536	128,12878	2203	4300	6503	SO:0001583	missense	51517	exon10			GGTCCGGCAGCTG	AF178432	CCDS2776.1, CCDS46827.1	3p21	2008-07-18			ENSG00000213672	ENSG00000213672			15486	protein-coding gene	gene with protein product	"dia interacting protein", "diaphanous protein interacting protein", "SH3 protein interacting with Nck, 90 kDa"	606671				10648423, 10619843	Standard	NM_016453		Approved	AF3P21, SPIN90, ORF1, WISH, WASLBP, DIP1	uc003cun.3	Q9NZQ3	OTTHUMG00000133542	ENST00000294129.2:c.1651C>T	3.37:g.48716536G>A	ENSP00000294129:p.Pro551Ser	121	0	0		148	71	0.47973	NM_016453	B4DFL5|Q6GU34|Q6SPF3|Q8TC10|Q9UGM8	Missense_Mutation	SNP	ENST00000294129.2	37	CCDS2776.1	11|11	0.005036630036630037|0.005036630036630037	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	10|10	0.013192612137203167|0.013192612137203167	G|G	26.1|26.1	4.700036|4.700036	0.88924|0.88924	0.003631|0.003631	0.013023|0.013023	ENSG00000213672|ENSG00000213672	ENST00000415281|ENST00000341520;ENST00000416649;ENST00000294129;ENST00000413374	.|T;T;T;T	.|0.64260	.|1.02;-0.09;-0.09;1.02	5.37|5.37	5.37|5.37	0.77165|0.77165	.|Domain of unknown function DUF2013 (1);	.|0.000000	.|0.85682	.|U	.|0.000000	T|T	0.71813|0.71813	0.3384|0.3384	M|M	0.76328|0.76328	2.33|2.33	0.80722|0.80722	D|D	1|1	.|D;D	.|0.62365	.|0.991;0.989	.|D;P	.|0.66497	.|0.944;0.906	T|T	0.72067|0.72067	-0.4402|-0.4402	5|10	.|0.25106	.|T	.|0.35	.|.	19.105|19.105	0.93291|0.93291	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|551;544	.|Q9NZQ3;Q9NZQ3-3	.|SPN90_HUMAN;.	V|S	259|551;544;551;7	.|ENSP00000342621:P551S;ENSP00000389059:P544S;ENSP00000294129:P551S;ENSP00000396683:P7S	.|ENSP00000294129:P551S	A|P	-|-	2|1	0|0	NCKIPSD|NCKIPSD	48691540|48691540	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.839000|0.839000	0.47603|0.47603	9.307000|9.307000	0.96226|0.96226	2.498000|2.498000	0.84270|0.84270	0.650000|0.650000	0.86243|0.86243	GCC|CCG	G|0.990;A|0.010	0.010	strong		0.652	NCKIPSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257520.1	NM_016453		A	48716536	G	A	48716536	3	1	26	1	0	0	0	0	1	0	0	0	10234	1203	42	2	533	2	NCKIPSD	3	48716536	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1682566	48716536	149305894	114	9877	122	2									
NCKIPSD	51517	hgsc.bcm.edu	37	chr3	48716537	48716537	+	Silent	SNP	C	C	A																															aggttcacgcagaggtccggCagctgctctgtggtgtccaa																								rs76815705	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:48716537C>A	ENST00000294129.2	-	10	1769	c.1650G>T	c.(1648-1650)ctG>ctT	p.L550L	NCKIPSD_ENST00000341520.4_Silent_p.L550L|NCKIPSD_ENST00000416649.2_Silent_p.L543L	NM_016453.2	NP_057537.1	Q9NZQ3	SPN90_HUMAN	NCK interacting protein with SH3 domain	550	Leu-rich.				cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|NLS-bearing protein import into nucleus (GO:0006607)|signal transduction (GO:0007165)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	cytoskeletal protein binding (GO:0008092)			endometrium(1)|large_intestine(3)|lung(6)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		AGAGGTCCGGCAGCTGCTCTG	0.652													C|||	26	0.00519169	0.0	0.0029	5008	,	,		17050	0.0		0.0139	False		,,,				2504	0.0102				p.L550L		Atlas-SNP	.											.	NCKIPSD	52	.	0			c.G1650T						PASS	.	C	,	16,4390	22.3+/-47.3	0,16,2187	53	54	54		1650,1629	4.5	1	3	dbSNP_132	54	112,8488	52.3+/-112.8	0,112,4188	no	coding-synonymous,coding-synonymous	NCKIPSD	NM_016453.2,NM_184231.1	,	0,128,6375	AA,AC,CC		1.3023,0.3631,0.9842	,	550/723,543/716	48716537	128,12878	2203	4300	6503	SO:0001819	synonymous_variant	51517	exon10			GTCCGGCAGCTGC	AF178432	CCDS2776.1, CCDS46827.1	3p21	2008-07-18			ENSG00000213672	ENSG00000213672			15486	protein-coding gene	gene with protein product	"dia interacting protein", "diaphanous protein interacting protein", "SH3 protein interacting with Nck, 90 kDa"	606671				10648423, 10619843	Standard	NM_016453		Approved	AF3P21, SPIN90, ORF1, WISH, WASLBP, DIP1	uc003cun.3	Q9NZQ3	OTTHUMG00000133542	ENST00000294129.2:c.1650G>T	3.37:g.48716537C>A		122	0	0		153	73	0.477124	NM_016453	B4DFL5|Q6GU34|Q6SPF3|Q8TC10|Q9UGM8	Silent	SNP	ENST00000294129.2	37	CCDS2776.1	11	0.005036630036630037	0	0.0	1	0.0027624309392265192	0	0.0	10	0.013192612137203167	C	7.195	0.592354	0.13812	0.003631	0.013023	ENSG00000213672	ENST00000415281	.	.	.	5.37	4.49	0.54785	.	.	.	.	.	T	0.47728	0.1461	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50406	-0.8832	4	.	.	.	.	6.1236	0.20167	0.1406:0.6518:0.1354:0.0721	.	.	.	.	S	259	.	.	A	-	1	0	NCKIPSD	48691541	0.999000	0.42202	1.000000	0.80357	0.841000	0.47740	0.710000	0.25748	1.236000	0.43740	0.650000	0.86243	GCC	C|0.989;A|0.011	0.011	strong		0.652	NCKIPSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257520.1	NM_016453		A	48716537	C	A	48716537	2	1	26	1	0	0	0	0	0	0	0	1	10234	697	25	4		4	NCKIPSD	3	48716537	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1	48716537	149305893	115	9878	122	2									
BSN	8927	hgsc.bcm.edu	37	chr3	49698115	49698115	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctgctccgggagctggaccGggacctgcggctggtggagc	4	6	18	13	3	0	0	0	0	0	0	1	4	1	4	4	6	4	3	4	6	0	0	rs116113662	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:49698115G>A	ENST00000296452.4	+	6	8951	c.8837G>A	c.(8836-8838)cGg>cAg	p.R2946Q		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	2946					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)		GAGCTGGACCGGGACCTGCGG	0.642													G|||	24	0.00479233	0.0	0.0029	5008	,	,		18137	0.0		0.0139	False		,,,				2504	0.0082				p.R2946Q		Atlas-SNP	.											BSN,NS,carcinoma,-1,1	BSN	272	1	0			c.G8837A						PASS	.	G	GLN/ARG	16,4376		0,16,2180	23	24	24		8837	4.5	1	3	dbSNP_132	24	113,8475		0,113,4181	yes	missense	BSN	NM_003458.3	43	0,129,6361	AA,AG,GG		1.3158,0.3643,0.9938	probably-damaging	2946/3927	49698115	129,12851	2196	4294	6490	SO:0001583	missense	8927	exon6			TGGACCGGGACCT	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.8837G>A	3.37:g.49698115G>A	ENSP00000296452:p.Arg2946Gln	92	0	0		120	54	0.45	NM_003458	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	37	CCDS2800.1	12	0.005494505494505495	0	0.0	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	G	14.70	2.614137	0.46631	0.003643	0.013158	ENSG00000164061	ENST00000296452	T	0.24151	1.87	4.5	4.5	0.54988	.	0.080992	0.49305	D	0.000146	T	0.38026	0.1025	M	0.64404	1.975	0.43338	D	0.995383	D	0.76494	0.999	P	0.61275	0.886	T	0.46317	-0.9200	10	0.66056	D	0.02	-17.5126	17.2151	0.86941	0.0:0.0:1.0:0.0	.	2946	Q9UPA5	BSN_HUMAN	Q	2946	ENSP00000296452:R2946Q	ENSP00000296452:R2946Q	R	+	2	0	BSN	49673119	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.338000	0.59316	2.043000	0.60533	0.561000	0.74099	CGG	G|0.990;A|0.010	0.010	strong		0.642	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		A	49698115	G	A	49698115	3	1	26	1	0	0	0	0	1	0	0	0	1532	1116	39	1	8859	1	BSN	3	49698115	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	981578	49698115	148324315	116	9879											
SEMA3G	56920	hgsc.bcm.edu	37	chr3	52476246	52476246	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agggcacaggtgggctggaaGgccccagtgccacaggctag	9	4	17	11	0	0	0	0	0	0	0	0	1	0	1	3	6	1	3	3	6	2	1	rs34900551	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:52476246G>A	ENST00000231721.2	-	4	413	c.414C>T	c.(412-414)gcC>gcT	p.A138A		NM_020163.1	NP_064548.1	Q9NS98	SEM3G_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G	138	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				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)		TGGGCTGGAAGGCCCCAGTGC	0.657													G|||	49	0.00978435	0.0008	0.0101	5008	,	,		16416	0.0		0.0358	False		,,,				2504	0.0051				p.A138A		Atlas-SNP	.											.	SEMA3G	58	.	0			c.C414T						PASS	.	G		35,4371	40.0+/-72.8	0,35,2168	47	45	45		414	4.7	1	3	dbSNP_126	45	325,8275	112.0+/-172.2	3,319,3978	no	coding-synonymous	SEMA3G	NM_020163.1		3,354,6146	AA,AG,GG		3.7791,0.7944,2.768		138/783	52476246	360,12646	2203	4300	6503	SO:0001819	synonymous_variant	56920	exon4			CTGGAAGGCCCCA		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.414C>T	3.37:g.52476246G>A		183	0	0		211	109	0.516588	NM_020163	Q7L9D9|Q9H7Q3	Silent	SNP	ENST00000231721.2	37	CCDS2856.1																																																																																			G|0.978;A|0.022	0.022	strong		0.657	SEMA3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351354.1	NM_020163		A	52476246	G	A	52476246	2	1	26	1	0	0	0	0	0	0	0	1	14045	987	35	2		2	SEMA3G	3	52476246	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	2778131	52476246	145546184	117	9880											
PBRM1	55193	hgsc.bcm.edu	37	chr3	52676038	52676038	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ttgtaattgctgataaacgaCctccttgtactgctctttta	9	17	6	9	1	1	1	0	1	1	0	2	2	2	1	2	0	4	4	2	0	5	8	rs200106731		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:52676038C>G	ENST00000296302.7	-	10	1020	c.1019G>C	c.(1018-1020)gGt>gCt	p.G340A	PBRM1_ENST00000356770.4_Missense_Mutation_p.G308A|PBRM1_ENST00000409057.1_Missense_Mutation_p.G340A|PBRM1_ENST00000337303.4_Missense_Mutation_p.G340A|PBRM1_ENST00000409767.1_Missense_Mutation_p.G340A|PBRM1_ENST00000410007.1_Missense_Mutation_p.G340A|PBRM1_ENST00000394830.3_Missense_Mutation_p.G340A|PBRM1_ENST00000409114.3_Missense_Mutation_p.G340A			Q86U86	PB1_HUMAN	polybromo 1	340			G -> A (found in a malignant melanoma cell line). {ECO:0000269|PubMed:21248752}.		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)		TGATAAACGACCTCCTTGTAC	0.363			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.G340A		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.G1019C						PASS	.	C	ALA/GLY,ALA/GLY,ALA/GLY	0,4406		0,0,2203	260	245	250		923,1019,1019	4.8	1	3		250	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense	PBRM1	NM_018165.4,NM_018313.4,NM_181042.3	60,60,60	0,3,6500	GG,GC,CC		0.0349,0.0,0.0231	benign,benign,benign	308/1603,340/1583,340/1583	52676038	3,13003	2203	4300	6503	SO:0001583	missense	55193	exon11			AAACGACCTCCTT	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.1019G>C	3.37:g.52676038C>G	ENSP00000296302:p.Gly340Ala	97	0	0		102	54	0.529412	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Missense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	C	15.82	2.945034	0.53079	0.0	3.49E-4	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103	T;T;T;T;T;T;T;T;T;T	0.33216	1.45;1.43;1.46;1.42;1.43;1.42;1.89;1.42;1.43;1.44	5.71	4.83	0.62350	Bromodomain (1);	0.049850	0.85682	D	0.000000	T	0.13543	0.0328	N	0.08118	0	0.46113	D	0.998875	B;B;B;B;B;B;B;B;B	0.23377	0.03;0.03;0.058;0.066;0.017;0.082;0.084;0.066;0.066	B;B;B;B;B;B;B;B;B	0.29267	0.019;0.02;0.031;0.046;0.024;0.1;0.034;0.046;0.046	T	0.20806	-1.0264	10	0.11794	T	0.64	-18.8331	5.4588	0.16606	0.0:0.7329:0.0:0.2671	.	340;340;340;340;340;340;340;308;340	Q86U86-9;Q86U86-6;Q86U86-4;Q86U86-2;Q86U86-8;Q86U86-7;Q86U86;Q86U86-3;Q86U86-5	.;.;.;.;.;.;PB1_HUMAN;.;.	A	308;340;340;340;340;340;340;340;340;284	ENSP00000349213:G308A;ENSP00000378307:G340A;ENSP00000296302:G340A;ENSP00000338302:G340A;ENSP00000386593:G340A;ENSP00000386529:G340A;ENSP00000386643:G340A;ENSP00000386601:G340A;ENSP00000387775:G340A;ENSP00000397662:G284A	ENSP00000296302:G340A	G	-	2	0	PBRM1	52651078	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.354000	0.66040	2.700000	0.92200	0.650000	0.86243	GGT	C|0.999;G|0.001	0.001	weak		0.363	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		G	52676038	C	G	52676038	3	3	26	1	0	0	0	0	1	0	0	0	11500	507	18	4	3965	4	PBRM1	3	52676038	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	199792	52676038	145346392	118	9881											
CNTN3	5067	hgsc.bcm.edu	37	chr3	74334458	74334458	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaatcagaatatacttacgcGttttcttggtggttacatta	12	16	7	6	2	2	1	1	0	1	1	2	1	2	1	0	2	3	2	0	2	7	8	rs141921900	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:74334458G>A	ENST00000263665.6	-	19	2729	c.2702C>T	c.(2701-2703)aCg>aTg	p.T901M		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	901	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)		ATACTTACGCGTTTTCTTGGT	0.438													G|||	18	0.00359425	0.0	0.0043	5008	,	,		17726	0.0		0.0139	False		,,,				2504	0.001				p.T901M		Atlas-SNP	.											CNTN3,NS,lymphoid_neoplasm,+1,1	CNTN3	174	1	0			c.C2702T						PASS	.	G	MET/THR	7,4399	12.9+/-30.5	0,7,2196	116	124	121		2702	2.2	0.5	3	dbSNP_134	121	97,8503	54.4+/-115.2	1,95,4204	yes	missense	CNTN3	NM_020872.1	81	1,102,6400	AA,AG,GG		1.1279,0.1589,0.7996	benign	901/1029	74334458	104,12902	2203	4300	6503	SO:0001583	missense	5067	exon19			TTACGCGTTTTCT	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.2702C>T	3.37:g.74334458G>A	ENSP00000263665:p.Thr901Met	96	0	0		113	61	0.539823	NM_020872	B9EK50|Q9H039	Missense_Mutation	SNP	ENST00000263665.6	37	CCDS33790.1	10	0.004578754578754579	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	G	11.68	1.709735	0.30322	0.001589	0.011279	ENSG00000113805	ENST00000263665	T	0.54675	0.56	5.4	2.15	0.27550	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.290390	0.38720	N	0.001587	T	0.27098	0.0664	N	0.16656	0.425	0.34827	D	0.73933	B	0.11235	0.004	B	0.16289	0.015	T	0.38866	-0.9641	10	0.62326	D	0.03	.	10.8289	0.46649	0.2572:0.0:0.7428:0.0	.	901	Q9P232	CNTN3_HUMAN	M	901	ENSP00000263665:T901M	ENSP00000263665:T901M	T	-	2	0	CNTN3	74417148	1.000000	0.71417	0.483000	0.27378	0.537000	0.34900	4.561000	0.60809	0.762000	0.33152	-0.126000	0.14955	ACG	G|0.995;A|0.005	0.005	strong		0.438	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872		A	74334458	G	A	74334458	3	1	26	1	0	0	0	0	1	0	0	0	3644	1145	40	1	400	1	CNTN3	3	74334458	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	21658420	74334458	123687972	119	9882											
OR5H2	79310	hgsc.bcm.edu	37	chr3	98002527	98002527	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cacttatcttcatgtatttgCgccctgcatctccacaagca	9	13	5	14	1	3	0	1	0	2	0	4	0	3	0	2	0	3	3	2	0	3	4	rs17787561	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:98002527C>T	ENST00000355273.2	+	1	796	c.796C>T	c.(796-798)Cgc>Tgc	p.R266C	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005482.1	NP_001005482.1	Q8NGV7	OR5H2_HUMAN	olfactory receptor, family 5, subfamily H, member 2	266			R -> C (in dbSNP:rs17787561).			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						CATGTATTTGCGCCCTGCATC	0.398													C|||	19	0.00379393	0.0	0.0058	5008	,	,		17042	0.0		0.0089	False		,,,				2504	0.0061				p.R266C		Atlas-SNP	.											.	OR5H2	63	.	0			c.C796T						PASS	.	C	CYS/ARG	6,4400	9.9+/-24.2	0,6,2197	87	83	84		796	-1.1	0	3	dbSNP_123	84	80,8520	47.2+/-106.3	1,78,4221	yes	missense	OR5H2	NM_001005482.1	180	1,84,6418	TT,TC,CC		0.9302,0.1362,0.6612	benign	266/315	98002527	86,12920	2203	4300	6503	SO:0001583	missense	79310	exon1			TATTTGCGCCCTG		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.796C>T	3.37:g.98002527C>T	ENSP00000347418:p.Arg266Cys	118	0	0		141	69	0.489362	NM_001005482	Q6IF87	Missense_Mutation	SNP	ENST00000355273.2	37	CCDS33801.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	C	0.635	-0.815604	0.02776	0.001362	0.009302	ENSG00000197938	ENST00000355273	T	0.35789	1.29	3.03	-1.07	0.09968	GPCR, rhodopsin-like superfamily (1);	0.410613	0.17855	U	0.159738	T	0.22742	0.0549	M	0.69523	2.12	0.09310	N	1	B	0.21688	0.059	B	0.19148	0.024	T	0.24728	-1.0152	10	0.62326	D	0.03	.	3.5217	0.07744	0.1797:0.3604:0.0:0.4599	rs17787561;rs52823927;rs17787561	266	Q8NGV7	OR5H2_HUMAN	C	266	ENSP00000347418:R266C	ENSP00000347418:R266C	R	+	1	0	OR5H2	99485217	0.000000	0.05858	0.003000	0.11579	0.006000	0.05464	-0.227000	0.09126	-0.440000	0.07211	-0.495000	0.04643	CGC	C|0.993;T|0.007	0.007	strong		0.398	OR5H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359113.2			T	98002527	C	T	98002527	3	4	26	1	0	0	0	0	1	0	0	0	11171	768	27	1	798	1	OR5H2	3	98002527	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	23668069	98002527	100019903	120	9883											
MORC1	27136	hgsc.bcm.edu	37	chr3	108677910	108677910	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctggaagagaagattatcttCtttaagcaaagcttctaaat	15	13	7	6	0	3	2	0	0	3	2	3	4	3	3	0	1	2	2	0	1	7	6	rs78212601	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:108677910C>T	ENST00000483760.1	-	27	2837	c.2794G>A	c.(2794-2796)Gaa>Aaa	p.E932K	MORC1_ENST00000232603.5_Missense_Mutation_p.E953K					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						AGATTATCTTCTTTAAGCAAA	0.378													C|||	40	0.00798722	0.0	0.0101	5008	,	,		15018	0.001		0.0288	False		,,,				2504	0.0031				p.E953K		Atlas-SNP	.											.	MORC1	211	.	0			c.G2857A						PASS	.	C	LYS/GLU	18,4388	20.2+/-43.8	0,18,2185	46	48	47		2857	5.2	1	3	dbSNP_131	47	191,8407	78.4+/-141.0	2,187,4110	yes	missense	MORC1	NM_014429.3	56	2,205,6295	TT,TC,CC		2.2214,0.4085,1.6072	probably-damaging	953/985	108677910	209,12795	2203	4299	6502	SO:0001583	missense	27136	exon28			TATCTTCTTTAAG	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.2794G>A	3.37:g.108677910C>T	ENSP00000417282:p.Glu932Lys	87	0	0		105	44	0.419048	NM_014429		Missense_Mutation	SNP	ENST00000483760.1	37		31	0.014194139194139194	0	0.0	8	0.022099447513812154	0	0.0	23	0.030343007915567283	C	22.9	4.346692	0.82022	0.004085	0.022214	ENSG00000114487	ENST00000232603;ENST00000483760	T;T	0.10005	2.92;2.92	5.2	5.2	0.72013	.	0.143592	0.32640	N	0.005834	T	0.04092	0.0114	L	0.32530	0.975	0.29995	N	0.816578	P;P	0.46784	0.884;0.884	P;P	0.46419	0.516;0.516	T	0.01048	-1.1469	10	0.44086	T	0.13	-17.6497	14.1073	0.65099	0.0:1.0:0.0:0.0	.	932;953	E7ERX1;Q86VD1	.;MORC1_HUMAN	K	953;932	ENSP00000232603:E953K;ENSP00000417282:E932K	ENSP00000232603:E953K	E	-	1	0	MORC1	110160600	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.944000	0.40263	2.716000	0.92895	0.650000	0.86243	GAA	C|0.984;T|0.016	0.016	strong		0.378	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1			T	108677910	C	T	108677910	3	4	26	1	0	0	0	0	1	0	0	0	9710	922	32	2	101	2	MORC1	3	108677910	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	10675383	108677910	89344520	121	9884											
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113376113	113376113	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcttgttgttgttgctgttgCtgctgctgctgctgctgctg	0	18	14	9	0	0	0	0	0	0	0	0	0	0	0	0	0	8	13	0	0	0	5	rs62265537|rs59601191|rs112313093|rs59990801|rs397990842|rs10606566		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:113376113C>T	ENST00000478658.1	-	5	4433	c.4416G>A	c.(4414-4416)caG>caA	p.Q1472Q	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Silent_p.Q1472Q			Q68DE3	K2018_HUMAN	KIAA2018	1472	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						gttgctgttgctgctgctgct	0.502																																					p.Q1472Q		Atlas-SNP	.											KIAA2018,rectum,carcinoma,0,1	KIAA2018	180	1	0			c.G4416A						scavenged	.						68	71	70					3																	113376113		2188	4274	6462	SO:0001819	synonymous_variant	205717	exon7			CTGTTGCTGCTGC	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.4416G>A	3.37:g.113376113C>T		45	1	0.0222222		104	24	0.230769	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	37	CCDS43133.1																																																																																			.	.	weak		0.502	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		T	113376113	C	T	113376113	2	4	26	1	0	0	0	0	0	0	0	1	8277	796	28	2		2	KIAA2018	3	113376113	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	4698203	113376113	84646317	122	9885											
POLQ	10721	hgsc.bcm.edu	37	chr3	121252048	121252048	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagacagagaactggctagaTctgcctgactgtaaaaaaac	16	8	9	8	0	1	4	0	1	1	3	1	5	1	4	1	1	3	2	1	1	7	3	rs73179915	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:121252048T>G	ENST00000264233.5	-	6	877	c.749A>C	c.(748-750)gAt>gCt	p.D250A	POLQ_ENST00000488282.1_5'UTR	NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	250	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				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)		ACTGGCTAGATCTGCCTGACT	0.368								DNA polymerases (catalytic subunits)					T|||	3	0.000599042	0.0	0.0	5008	,	,		18003	0.0		0.003	False		,,,				2504	0.0				p.D250A	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.A749C						PASS	.	T	ALA/ASP	1,4405	2.1+/-5.4	0,1,2202	78	77	77		749	1.6	0.9	3	dbSNP_130	77	19,8581	14.0+/-48.4	0,19,4281	yes	missense	POLQ	NM_199420.3	126	0,20,6483	GG,GT,TT		0.2209,0.0227,0.1538	benign	250/2591	121252048	20,12986	2203	4300	6503	SO:0001583	missense	10721	exon6			GCTAGATCTGCCT	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.749A>C	3.37:g.121252048T>G	ENSP00000264233:p.Asp250Ala	149	0	0		139	65	0.467626	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	5.065	0.197617	0.09652	2.27E-4	0.002209	ENSG00000051341	ENST00000264233;ENST00000393672	T	0.49139	0.79	5.3	1.56	0.23342	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	1.695750	0.02414	N	0.081944	T	0.29749	0.0743	N	0.11364	0.135	0.09310	N	1	B	0.21452	0.056	B	0.24394	0.053	T	0.20505	-1.0273	10	0.12103	T	0.63	.	8.008	0.30336	0.0:0.3139:0.0:0.6861	.	250	O75417	DPOLQ_HUMAN	A	250;385	ENSP00000264233:D250A	ENSP00000264233:D250A	D	-	2	0	POLQ	122734738	0.029000	0.19370	0.855000	0.33649	0.438000	0.31896	0.913000	0.28611	0.393000	0.25203	0.383000	0.25322	GAT	T|0.999;G|0.001	0.001	strong		0.368	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		G	121252048	T	G	121252048	3	3	26	1	0	0	0	0	1	0	0	0	12217	1435	50	5	7123	5	POLQ	3	121252048	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	7875935	121252048	76770382	123	9886											
CHST13	166012	hgsc.bcm.edu	37	chr3	126260791	126260791	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgctgagcggccaagcccgCggcgacccgcgcgccatctc	5	3	14	19	8	1	1	0	1	1	0	2	2	1	1	4	2	2	1	4	2	1	0			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:126260791C>T	ENST00000319340.2	+	3	446	c.396C>T	c.(394-396)cgC>cgT	p.R132R		NM_152889.2	NP_690849.1	Q8NET6	CHSTD_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 13	132					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)		GCCAAGCCCGCGGCGACCCGC	0.726																																					p.R132R		Atlas-SNP	.											.	CHST13	21	.	0			c.C396T						PASS	.						16	13	14					3																	126260791		2183	4262	6445	SO:0001819	synonymous_variant	166012	exon3			AGCCCGCGGCGAC	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.396C>T	3.37:g.126260791C>T		4	0	0		5	5	1	NM_152889	Q3SYA3|Q3SYA5	Silent	SNP	ENST00000319340.2	37	CCDS3039.1																																																																																			.	.	none		0.726	CHST13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370201.2	NM_152889		T	126260791	C	T	126260791	2	4	26	1	0	0	0	0	0	0	0	1	3403	755	27	1		1	CHST13	3	126260791	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	5008743	126260791	71761639	124	9887											
COL6A6	131873	hgsc.bcm.edu	37	chr3	130380710	130380710	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	agccatgctccccccgacttCctacccaacactcagaagag	11	6	6	18	1	1	2	1	0	0	2	3	3	3	2	6	0	4	1	6	0	3	2	rs201325545	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:130380710C>T	ENST00000358511.6	+	34	6091	c.6060C>T	c.(6058-6060)ttC>ttT	p.F2020F	COL6A6_ENST00000453409.2_Silent_p.F2020F	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	2020	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						CCCCCGACTTCCTACCCAACA	0.512													C|||	2	0.000399361	0.0	0.0	5008	,	,		18044	0.0		0.0	False		,,,				2504	0.002				p.F2020F		Atlas-SNP	.											.	COL6A6	497	.	0			c.C6060T						PASS	.	C		1,3759		0,1,1879	56	54	55		6060	4.1	1	3		55	10,8210		0,10,4100	no	coding-synonymous	COL6A6	NM_001102608.1		0,11,5979	TT,TC,CC		0.1217,0.0266,0.0918		2020/2264	130380710	11,11969	1880	4110	5990	SO:0001819	synonymous_variant	131873	exon34			CGACTTCCTACCC	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.6060C>T	3.37:g.130380710C>T		113	0	0		141	58	0.411348	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Silent	SNP	ENST00000358511.6	37	CCDS46911.1																																																																																			C|0.996;T|0.004	0.004	strong		0.512	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		T	130380710	C	T	130380710	2	4	26	1	0	0	0	0	0	0	0	1	3705	854	30	2		2	COL6A6	3	130380710	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	4119919	130380710	67641720	125	9888											
NPHP3	27031	hgsc.bcm.edu	37	chr3	132401603	132401603	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cgaggatgcatccgacccagGctatcttcataaatctttaa	12	11	7	11	2	3	0	1	0	2	0	4	3	4	1	2	2	1	2	2	2	4	5	rs143451766	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:132401603G>C	ENST00000337331.5	-	26	3842	c.3756C>G	c.(3754-3756)agC>agG	p.S1252R	NPHP3_ENST00000326682.8_3'UTR	NM_153240.4	NP_694972.3	Q7Z494	NPHP3_HUMAN	nephronophthisis 3 (adolescent)	1252			S -> R (in NPHP3; dbSNP:rs143451766). {ECO:0000269|PubMed:12872122}.		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						TCCGACCCAGGCTATCTTCAT	0.348													G|||	2	0.000399361	0.0	0.0	5008	,	,		18145	0.0		0.002	False		,,,				2504	0.0				p.S1252R		Atlas-SNP	.											.	NPHP3	110	.	0			c.C3756G	GRCh37	CM032020	NPHP3	M	rs143451766	PASS	.	G	ARG/SER	3,4403	6.2+/-15.9	0,3,2200	109	115	113		3756	4.4	1	3	dbSNP_134	113	8,8592	6.4+/-24.3	0,8,4292	yes	missense	NPHP3	NM_153240.4	110	0,11,6492	CC,CG,GG		0.093,0.0681,0.0846	probably-damaging	1252/1331	132401603	11,12995	2203	4300	6503	SO:0001583	missense	27031	exon26			ACCCAGGCTATCT	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.3756C>G	3.37:g.132401603G>C	ENSP00000338766:p.Ser1252Arg	179	0	0		177	70	0.39548	NM_153240	Q5JPE3|Q5JPE6|Q68D99|Q6NVH3|Q7Z492|Q7Z493|Q8N9R2|Q8NCM5|Q96N70|Q96NK2	Missense_Mutation	SNP	ENST00000337331.5	37	CCDS3078.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	16.67	3.188670	0.57909	6.81E-4	9.3E-4	ENSG00000113971	ENST00000393144;ENST00000393156;ENST00000337331	T	0.76839	-1.05	6.16	4.38	0.52667	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.77267	0.4105	N	0.20881	0.62	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.83275	0.996;0.966	T	0.72057	-0.4405	10	0.21014	T	0.42	-24.6133	9.7792	0.40639	0.2093:0.0:0.7907:0.0	.	1252;134	Q7Z494;Q7Z491	NPHP3_HUMAN;.	R	532;314;1252	ENSP00000338766:S1252R	ENSP00000338766:S1252R	S	-	3	2	NPHP3	133884293	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	2.446000	0.44908	0.937000	0.37394	0.650000	0.86243	AGC	G|0.999;C|0.001	0.001	strong		0.348	NPHP3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357020.2	NM_153240		C	132401603	G	C	132401603	3	2	26	1	0	0	0	0	1	0	0	0	10589	1194	42	4	244	4	NPHP3	3	132401603	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	2020893	132401603	65620827	126	9889											
KY	339855	hgsc.bcm.edu	37	chr3	134322877	134322877	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggtgcagctggaagatgtaGcgccgctgtgtctcctcagt	6	10	14	11	3	2	1	1	0	1	1	3	2	2	2	2	2	3	4	2	2	2	1	rs35316983	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:134322877G>A	ENST00000423778.2	-	11	1591	c.1530C>T	c.(1528-1530)cgC>cgT	p.R510R	KY_ENST00000503669.1_3'UTR|KY_ENST00000508956.1_Silent_p.R489R	NM_178554.4	NP_848649.3	Q8NBH2	KY_HUMAN	kyphoscoliosis peptidase	510					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						GGAAGATGTAGCGCCGCTGTG	0.592													G|||	25	0.00499201	0.0	0.0058	5008	,	,		19389	0.0		0.0209	False		,,,				2504	0.0				p.R510R		Atlas-SNP	.											KY_ENST00000423778,NS,carcinoma,-2,2	KY	92	2	0			c.C1530T						PASS	.	G		14,4172		0,14,2079	48	51	50		1530	4.6	1	3	dbSNP_126	50	191,8247		3,185,4031	yes	coding-synonymous	KY	NM_178554.4		3,199,6110	AA,AG,GG		2.2636,0.3344,1.6239		510/662	134322877	205,12419	2093	4219	6312	SO:0001819	synonymous_variant	339855	exon11			GATGTAGCGCCGC	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.1530C>T	3.37:g.134322877G>A		86	0	0		116	57	0.491379	NM_178554	B7Z1S4|Q6ZT15	Silent	SNP	ENST00000423778.2	37	CCDS46920.1																																																																																			G|0.989;A|0.011	0.011	strong		0.592	KY-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357320.1	NM_178554		A	134322877	G	A	134322877	2	1	26	1	0	0	0	0	0	0	0	1	8595	958	34	2		2	KY	3	134322877	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1921274	134322877	63699553	127	9890											
C3orf58	205428	hgsc.bcm.edu	37	chr3	143708645	143708645	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tccaggctgcaaaagaactgCgtgaatacctagcacaatta	15	8	8	10	1	0	2	0	1	0	1	1	2	1	2	2	1	5	3	2	1	8	3			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:143708645C>A	ENST00000315691.3	+	3	1790	c.1255C>A	c.(1255-1257)Cgt>Agt	p.R419S	C3orf58_ENST00000493396.1_Intron|C3orf58_ENST00000495414.1_Missense_Mutation_p.R210S|C3orf58_ENST00000441925.2_Missense_Mutation_p.R181S	NM_173552.3	NP_775823.1	Q8NDZ4	DIA1_HUMAN	chromosome 3 open reading frame 58	419					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						AAAAGAACTGCGTGAATACCT	0.448																																					p.R419S		Atlas-SNP	.											.	C3orf58	36	.	0			c.C1255A						PASS	.						69	73	72					3																	143708645		2203	4300	6503	SO:0001583	missense	205428	exon3			GAACTGCGTGAAT	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.1255C>A	3.37:g.143708645C>A	ENSP00000320081:p.Arg419Ser	104	0	0		90	48	0.533333	NM_173552	B2RCF2|B7Z1W3	Missense_Mutation	SNP	ENST00000315691.3	37	CCDS3130.1	.	.	.	.	.	.	.	.	.	.	C	17.43	3.387226	0.61956	.	.	ENSG00000181744	ENST00000315691;ENST00000495414;ENST00000441925	T	0.32272	1.46	6.17	4.35	0.52113	.	0.000000	0.85682	D	0.000000	T	0.46718	0.1407	L	0.45581	1.43	0.58432	D	0.999997	B;D	0.63046	0.168;0.992	B;D	0.72982	0.077;0.979	T	0.22730	-1.0208	10	0.21540	T	0.41	.	15.7877	0.78319	0.2489:0.7511:0.0:0.0	.	210;419	B7Z1W3;Q8NDZ4	.;CC058_HUMAN	S	419;210;181	ENSP00000320081:R419S	ENSP00000320081:R419S	R	+	1	0	C3orf58	145191335	1.000000	0.71417	0.991000	0.47740	0.998000	0.95712	4.658000	0.61497	0.900000	0.36469	0.655000	0.94253	CGT	.	.	none		0.448	C3orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355038.1	NM_173552		A	143708645	C	A	143708645	3	1	26	1	0	0	0	0	1	0	0	0	2238	768	27	4	1299	4	C3orf58	3	143708645	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	9385768	143708645	54313785	128	9891											
IGSF10	285313	hgsc.bcm.edu	37	chr3	151161330	151161330	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtggaggaccaatgttccgTcaaccgtcaccacagcctgc	9	8	10	14	2	2	0	2	0	0	0	3	2	3	2	5	2	3	1	5	2	2	1	rs35736581	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:151161330T>A	ENST00000282466.3	-	5	5404	c.5405A>T	c.(5404-5406)gAc>gTc	p.D1802V	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	1802	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)			CAATGTTCCGTCAACCGTCAC	0.493													T|||	5	0.000998403	0.0	0.0014	5008	,	,		20951	0.0		0.004	False		,,,				2504	0.0				p.D1802V		Atlas-SNP	.											.	IGSF10	279	.	0			c.A5405T						PASS	.	T	VAL/ASP	9,4397	15.5+/-35.6	0,9,2194	93	83	87		5405	5.3	0.1	3	dbSNP_126	87	44,8556	29.0+/-79.6	0,44,4256	yes	missense	IGSF10	NM_178822.4	152	0,53,6450	AA,AT,TT		0.5116,0.2043,0.4075	probably-damaging	1802/2624	151161330	53,12953	2203	4300	6503	SO:0001583	missense	285313	exon5			GTTCCGTCAACCG	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.5405A>T	3.37:g.151161330T>A	ENSP00000282466:p.Asp1802Val	222	0	0		238	128	0.537815	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	37	CCDS3160.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	T	11.28	1.592435	0.28357	0.002043	0.005116	ENSG00000152580	ENST00000282466;ENST00000544042	T	0.79653	-1.29	5.26	5.26	0.73747	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.128349	0.34291	N	0.004098	D	0.84456	0.5476	M	0.79475	2.455	0.80722	D	1	P	0.50943	0.94	P	0.62885	0.908	D	0.86437	0.1764	9	.	.	.	.	12.3129	0.54938	0.0:0.0:0.1409:0.8591	rs35736581	1802	Q6WRI0	IGS10_HUMAN	V	1802;429	ENSP00000282466:D1802V	.	D	-	2	0	IGSF10	152644020	0.991000	0.36638	0.052000	0.19188	0.038000	0.13279	2.679000	0.46909	1.993000	0.58246	0.482000	0.46254	GAC	T|0.996;A|0.004	0.004	strong		0.493	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		A	151161330	T	A	151161330	3	1	26	1	0	0	0	0	1	0	0	0	7606	1667	58	5	2522	5	IGSF10	3	151161330	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	7452685	151161330	46861100	129	9892											
PLCH1	23007	hgsc.bcm.edu	37	chr3	155203301	155203301	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atcttgatctcttgtggcctCggacacagaatcctttatct	8	15	7	11	1	3	2	0	1	3	1	6	3	4	3	2	2	0	0	2	2	2	4	rs143905522	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:155203301C>T	ENST00000340059.7	-	22	2841	c.2842G>A	c.(2842-2844)Gag>Aag	p.E948K	PLCH1_ENST00000334686.6_Missense_Mutation_p.E910K|PLCH1_ENST00000494598.1_Missense_Mutation_p.E928K|PLCH1_ENST00000460012.1_Missense_Mutation_p.E910K|PLCH1_ENST00000414191.1_Missense_Mutation_p.E910K|PLCH1_ENST00000447496.2_Missense_Mutation_p.E948K|PLCH1-AS2_ENST00000472913.1_RNA	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	948					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)			CTTGTGGCCTCGGACACAGAA	0.517																																					p.E948K		Atlas-SNP	.											PLCH1_ENST00000340059,bladder,carcinoma,+1,2	PLCH1	406	2	0			c.G2842A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU	2,4404	4.2+/-10.8	0,2,2201	154	144	147		2842,2842,2728	5.9	1	3	dbSNP_134	147	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense,missense	PLCH1	NM_001130960.1,NM_001130961.1,NM_014996.2	56,56,56	0,7,6496	TT,TC,CC		0.0581,0.0454,0.0538	benign,benign,benign	948/1694,948/1003,910/1656	155203301	7,12999	2203	4300	6503	SO:0001583	missense	23007	exon22			TGGCCTCGGACAC	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.2842G>A	3.37:g.155203301C>T	ENSP00000345988:p.Glu948Lys	167	0	0		200	100	0.5	NM_001130960	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Missense_Mutation	SNP	ENST00000340059.7	37	CCDS46939.1	.	.	.	.	.	.	.	.	.	.	C	17.41	3.382670	0.61845	4.54E-4	5.81E-4	ENSG00000114805	ENST00000494598;ENST00000460012;ENST00000447496;ENST00000340059;ENST00000334686;ENST00000414191	T;T;T;T;T;T	0.34275	1.8;1.65;1.37;1.68;1.65;1.65	5.88	5.88	0.94601	.	0.244558	0.40385	N	0.001102	T	0.35941	0.0949	L	0.54323	1.7	0.80722	D	1	B;P;B	0.52061	0.222;0.95;0.039	B;B;B	0.37601	0.099;0.254;0.031	T	0.19679	-1.0298	10	0.39692	T	0.17	.	20.2228	0.98330	0.0:1.0:0.0:0.0	.	910;948;948	Q4KWH8-2;Q4KWH8;Q4KWH8-3	.;PLCH1_HUMAN;.	K	928;910;948;948;910;910	ENSP00000419100:E928K;ENSP00000417502:E910K;ENSP00000402759:E948K;ENSP00000345988:E948K;ENSP00000335469:E910K;ENSP00000412977:E910K	ENSP00000335469:E910K	E	-	1	0	PLCH1	156685995	0.993000	0.37304	0.975000	0.42487	0.446000	0.32137	3.168000	0.50801	2.789000	0.95967	0.655000	0.94253	GAG	C|1.000;T|0.000	0.000	strong		0.517	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996		T	155203301	C	T	155203301	3	4	26	1	0	0	0	0	1	0	0	0	12046	893	31	1	2262	1	PLCH1	3	155203301	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	4041971	155203301	42819129	130	9893											
ZNF721	170960	hgsc.bcm.edu	37	chr4	436991	436991	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaatccaaaggctctgccaCgatcttcacatgtgtagggt	11	10	9	11	1	3	0	1	0	2	0	4	1	4	0	2	2	1	2	2	2	3	2	rs376220761		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:436991C>T	ENST00000338977.5	-	2	1277	c.1229G>A	c.(1228-1230)cGt>cAt	p.R410H	ZNF721_ENST00000506646.1_Intron|ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000511833.2_Missense_Mutation_p.R422H|ZNF721_ENST00000507078.1_Intron			Q8TF20	ZN721_HUMAN	zinc finger protein 721	410				R -> C (in Ref. 1; CAH10687). {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(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						GGCTCTGCCACGATCTTCACA	0.378																																					p.P422H		Atlas-SNP	.											ZNF721_ENST00000511833,NS,carcinoma,-1,2	ZNF721	205	2	0			c.C1265A						scavenged	.	C	HIS/ARG	0,4098		0,0,2049	75	78	77		1265	1	0	4		77	1,8439		0,1,4219	no	missense	ZNF721	NM_133474.2	29	0,1,6268	TT,TC,CC		0.0118,0.0,0.0080	possibly-damaging	422/924	436991	1,12537	2049	4220	6269	SO:0001583	missense	170960	exon3			CTGCCACGATCTT	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.1229G>A	4.37:g.436991C>T	ENSP00000340524:p.Arg410His	47	1	0.0212766		39	16	0.410256	NM_133474	Q69YG7	Missense_Mutation	SNP	ENST00000338977.5	37		.	.	.	.	.	.	.	.	.	.	C	12.31	1.900631	0.33535	0.0	1.18E-4	ENSG00000182903	ENST00000338977;ENST00000511833	T;T	0.17854	2.25;2.25	1.03	1.03	0.20045	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13798	0.0334	N	0.25647	0.755	0.09310	N	1	D;D;D	0.62365	0.991;0.975;0.985	B;B;P	0.45881	0.208;0.301;0.496	T	0.17961	-1.0352	9	0.87932	D	0	.	7.9579	0.30053	0.0:1.0:0.0:0.0	.	410;422;422	Q8TF20;D9N162;Q8TF20-2	ZN721_HUMAN;.;.	H	410;422	ENSP00000340524:R410H;ENSP00000428878:R422H	ENSP00000340524:R410H	R	-	2	0	ZNF721	426991	0.888000	0.30383	0.003000	0.11579	0.003000	0.03518	2.751000	0.47508	0.890000	0.36211	0.194000	0.17425	CGT	.	.	weak		0.378	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474		T	436991	C	T	436991	3	4	26	1	0	0	0	0	1	0	0	0	18137	536	19	1	1510	1	ZNF721	4	436991	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10		436991	190717285	131	9894											
CPZ	8532	hgsc.bcm.edu	37	chr4	8621167	8621167	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cccaagaactttattcatggGctgcggaggactgggcccca	9	8	12	12	1	1	1	1	0	0	1	1	3	1	3	3	4	2	1	3	4	3	3	rs9342	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:8621167G>A	ENST00000360986.4	+	11	1956	c.1782G>A	c.(1780-1782)ggG>ggA	p.G594G	CPZ_ENST00000429646.2_Silent_p.G202G|CPZ_ENST00000315782.6_Silent_p.G583G|CPZ_ENST00000382480.2_Silent_p.G457G	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	594					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						TTATTCATGGGCTGCGGAGGA	0.652													G|||	300	0.0599042	0.1354	0.0331	5008	,	,		14230	0.0288		0.0507	False		,,,				2504	0.0184				p.G594G		Atlas-SNP	.											.	CPZ	95	.	0			c.G1782A						PASS	.	G	,,	498,3908	230.4+/-244.6	36,426,1741	49	50	49		1782,1371,1749	-0.6	0	4	dbSNP_52	49	413,8187	129.8+/-187.9	8,397,3895	no	coding-synonymous,coding-synonymous,coding-synonymous	CPZ	NM_001014447.2,NM_001014448.2,NM_003652.3	,,	44,823,5636	AA,AG,GG		4.8023,11.3028,7.0045	,,	594/653,457/516,583/642	8621167	911,12095	2203	4300	6503	SO:0001819	synonymous_variant	8532	exon11			TCATGGGCTGCGG	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.1782G>A	4.37:g.8621167G>A		204	1	0.00490196		255	136	0.533333	NM_001014447	O00520|Q96MX2	Silent	SNP	ENST00000360986.4	37	CCDS33953.1																																																																																			G|0.936;A|0.064	0.064	strong		0.652	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652		A	8621167	G	A	8621167	2	1	26	1	0	0	0	0	0	0	0	1	3841	1190	42	2		2	CPZ	4	8621167	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	8184176	8621167	182533109	132	9895											
STIM2	57620	hgsc.bcm.edu	37	chr4	27024524	27024524	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggaagccccaagtgttgccaGaataagcagcatcccacatg	13	6	10	12	0	0	1	0	0	0	1	1	2	1	2	4	1	4	3	4	1	4	2	rs147362228	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:27024524G>A	ENST00000467087.1	+	12	2675	c.2147G>A	c.(2146-2148)aGa>aAa	p.R716K	STIM2_ENST00000412829.2_3'UTR|STIM2_ENST00000382009.3_Missense_Mutation_p.R811K|STIM2_ENST00000237364.5_Missense_Mutation_p.R803K|STIM2_ENST00000467011.1_3'UTR|STIM2_ENST00000465503.1_Missense_Mutation_p.R724K			Q9P246	STIM2_HUMAN	stromal interaction molecule 2	716					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)				AGTGTTGCCAGAATAAGCAGC	0.458													G|||	3	0.000599042	0.0008	0.0	5008	,	,		20105	0.0		0.002	False		,,,				2504	0.0				p.R724K		Atlas-SNP	.											.	STIM2	77	.	0			c.G2171A						PASS	.	G	LYS/ARG,LYS/ARG,	0,4406		0,0,2203	99	100	99		2171,2147,	5	1	4	dbSNP_134	99	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,utr-3	STIM2	NM_001169118.1,NM_020860.3,NM_001169117.1	26,26,	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	possibly-damaging,possibly-damaging,	724/755,716/747,	27024524	3,13003	2203	4300	6503	SO:0001583	missense	57620	exon13			TTGCCAGAATAAG	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	ENST00000467087.1:c.2147G>A	4.37:g.27024524G>A	ENSP00000419073:p.Arg716Lys	90	0	0		126	64	0.507937	NM_001169118	A6H8L7|B7ZVY0|Q96BF1|Q9BQH2|Q9H8R1	Missense_Mutation	SNP	ENST00000467087.1	37	CCDS3440.2	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	14.37	2.515082	0.44763	0.0	3.49E-4	ENSG00000109689	ENST00000467087;ENST00000382009;ENST00000237364;ENST00000465503	T;T;T;T	0.76968	-1.03;-1.06;-1.06;-1.04	5.87	5.02	0.67125	.	0.254762	0.44902	D	0.000414	T	0.67813	0.2933	N	0.24115	0.695	0.80722	D	1	P;P	0.48640	0.858;0.913	B;B	0.42593	0.22;0.392	T	0.71856	-0.4466	10	0.54805	T	0.06	.	14.2358	0.65925	0.0:0.0:0.7287:0.2713	.	811;803	E9PGD0;F5GXJ4	.;.	K	716;811;803;724	ENSP00000419073:R716K;ENSP00000371439:R811K;ENSP00000237364:R803K;ENSP00000417569:R724K	ENSP00000237364:R803K	R	+	2	0	STIM2	26633622	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.921000	0.48852	1.583000	0.49898	0.655000	0.94253	AGA	G|0.999;A|0.001	0.001	strong		0.458	STIM2-001	KNOWN	non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215063.2	NM_020860		A	27024524	G	A	27024524	3	1	26	1	0	0	0	0	1	0	0	0	15299	942	33	2	2262	2	STIM2	4	27024524	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	18403357	27024524	164129752	133	9896											
PCDH7	5099	hgsc.bcm.edu	37	chr4	30725858	30725859	+	Frame_Shift_Ins	INS	-	-	A																															aaaagcctaaaaaggacaagINSaaaaacaaaaaatctaagca																										TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:30725858_30725859insA	ENST00000361762.2	+	1	3822_3823	c.2814_2815insA	c.(2815-2817)aaafs	p.K939fs	PCDH7_ENST00000543491.1_Frame_Shift_Ins_p.K939fs	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	939					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						AAAAGGACAAGAAAAACAAAAA	0.401																																					p.K938fs		Pindel,Atlas-Indel	.											.	PCDH7	215	.	0			c.2814_2815insA						PASS	.																																			SO:0001589	frameshift_variant	5099	exon1			.	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.2819dupA	4.37:g.30725863_30725863dupA	ENSP00000355243:p.Lys939fs	60	0	.		91	38	0.418	NM_032457	O60246|O60247|Q4W5C4	Frame_Shift_Ins	INS	ENST00000361762.2	37	CCDS33971.1																																																																																			.	.	none		0.401	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589		A	30725859	-	A	30725858	7	5	26	1	0	1	1	0	0	0	0	0	11525	933	33	0	2816	0	PCDH7	4	30725858	Frame_Shift_Ins	INS	-	TCGA-G8-6907-01A-11D-2210-10	3701334	30725858	160428418	134	9897											
N4BP2	55728	hgsc.bcm.edu	37	chr4	40122453	40122453	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	caaagactggtttaagtgagCccaacctagaaattggaaca	16	8	9	8	0	0	3	0	1	0	2	0	4	0	4	2	2	3	1	2	2	6	4	rs78417585	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:40122453C>T	ENST00000261435.6	+	9	3138	c.2722C>T	c.(2722-2724)Ccc>Tcc	p.P908S		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	908					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)	p.P908S(1)		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						TTTAAGTGAGCCCAACCTAGA	0.398													C|||	14	0.00279553	0.0	0.0058	5008	,	,		22081	0.0		0.0099	False		,,,				2504	0.0				p.P908S		Atlas-SNP	.											N4BP2,NS,carcinoma,0,1	N4BP2	166	1	1	Substitution - Missense(1)	pancreas(1)	c.C2722T						PASS	.	C	SER/PRO	13,4393	19.1+/-41.9	0,13,2190	50	48	49		2722	1.6	0.2	4	dbSNP_131	49	82,8518	46.3+/-105.2	1,80,4219	yes	missense	N4BP2	NM_018177.4	74	1,93,6409	TT,TC,CC		0.9535,0.2951,0.7304	benign	908/1771	40122453	95,12911	2203	4300	6503	SO:0001583	missense	55728	exon9			AGTGAGCCCAACC	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.2722C>T	4.37:g.40122453C>T	ENSP00000261435:p.Pro908Ser	254	0	0		263	132	0.501901	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	37	CCDS3457.1	11|11	0.005036630036630037|0.005036630036630037	0|0	0.0|0.0	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	8|8	0.010554089709762533|0.010554089709762533	C|C	0.446|0.446	-0.896370|-0.896370	0.02472|0.02472	0.002951|0.002951	0.009535|0.009535	ENSG00000078177|ENSG00000078177	ENST00000513269|ENST00000261435;ENST00000381804	.|T	.|0.14391	.|2.51	5.48|5.48	1.64|1.64	0.23874|0.23874	.|.	.|0.866997	.|0.10353	.|N	.|0.684921	T|T	0.06962|0.06962	0.0177|0.0177	L|L	0.45581|0.45581	1.43|1.43	0.09310|0.09310	N|N	1|1	.|B;B	.|0.14438	.|0.01;0.006	.|B;B	.|0.08055	.|0.003;0.001	T|T	0.41928|0.41928	-0.9481|-0.9481	5|10	.|0.10636	.|T	.|0.68	-0.6285|-0.6285	4.8249|4.8249	0.13410|0.13410	0.0:0.4947:0.1599:0.3453|0.0:0.4947:0.1599:0.3453	.|.	.|908;908	.|Q86UW6-2;Q86UW6	.|.;N4BP2_HUMAN	V|S	554|908;828	.|ENSP00000261435:P908S	.|ENSP00000261435:P908S	A|P	+|+	2|1	0|0	N4BP2|N4BP2	39798848|39798848	0.000000|0.000000	0.05858|0.05858	0.230000|0.230000	0.23976|0.23976	0.286000|0.286000	0.27126|0.27126	0.125000|0.125000	0.15749|0.15749	0.803000|0.803000	0.34113|0.34113	0.655000|0.655000	0.94253|0.94253	GCC|CCC	C|0.992;T|0.008	0.008	strong		0.398	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177		T	40122453	C	T	40122453	3	4	26	1	0	0	0	0	1	0	0	0	10119	739	26	2	2748	2	N4BP2	4	40122453	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	9396595	40122453	151031823	135	9898											
LIMCH1	22998	hgsc.bcm.edu	37	chr4	41687843	41687843	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgagtctcccagtgaaaggCggaagtgagtaaccagacac	13	6	12	10	2	1	3	0	2	1	1	3	5	1	4	2	2	1	1	2	2	3	1	rs76461603	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:41687843C>T	ENST00000313860.7	+	23	2986	c.2932C>T	c.(2932-2934)Cgg>Tgg	p.R978W	LIMCH1_ENST00000509277.1_Missense_Mutation_p.R811W|LIMCH1_ENST00000396595.3_Missense_Mutation_p.R823W|LIMCH1_ENST00000503057.1_Missense_Mutation_p.R1362W|LIMCH1_ENST00000514096.1_Missense_Mutation_p.R818W|LIMCH1_ENST00000508501.1_Missense_Mutation_p.R977W|LIMCH1_ENST00000513024.1_Missense_Mutation_p.R831W|LIMCH1_ENST00000381753.4_Missense_Mutation_p.R811W|LIMCH1_ENST00000512632.1_Missense_Mutation_p.R901W|LIMCH1_ENST00000512820.1_Missense_Mutation_p.R990W|LIMCH1_ENST00000511496.1_Missense_Mutation_p.R818W|LIMCH1_ENST00000512946.1_Missense_Mutation_p.R978W	NM_014988.2	NP_055803.2	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1	978					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						CAGTGAAAGGCGGAAGTGAGT	0.433													C|||	11	0.00219649	0.0	0.0043	5008	,	,		20909	0.0069		0.001	False		,,,				2504	0.0				p.R978W		Atlas-SNP	.											.	LIMCH1	233	.	0			c.C2932T						PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	83	71	75		2932,2929,2467,2431,2932	4.6	1	4	dbSNP_131	75	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense,missense	LIMCH1	NM_001112717.1,NM_001112718.1,NM_001112719.1,NM_001112720.1,NM_014988.2	101,101,101,101,101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	978/1058,977/1057,823/903,811/891,978/1084	41687843	1,13005	2203	4300	6503	SO:0001583	missense	22998	exon23			GAAAGGCGGAAGT	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.2932C>T	4.37:g.41687843C>T	ENSP00000316891:p.Arg978Trp	116	0	0		127	16	0.125984	NM_014988	A8MXC3|E9PHM7|Q503B5|Q5CZB1|Q5CZB6|Q5H9S8|Q68E07|Q6PJ44|Q7Z3G5|Q8N3S9|Q8N6M2	Missense_Mutation	SNP	ENST00000313860.7	37	CCDS33977.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	5	0.008741258741258742	1	0.0013192612137203166	C	14.03	2.414116	0.42817	0.0	1.16E-4	ENSG00000064042	ENST00000513024;ENST00000508501;ENST00000512946;ENST00000313860;ENST00000512632;ENST00000512820;ENST00000503057;ENST00000511496;ENST00000313875;ENST00000514096;ENST00000509277;ENST00000396595;ENST00000381753;ENST00000537405	T;T;T;T;T;T;T;T;T;T;T;T	0.49720	0.82;1.38;1.39;1.38;0.8;1.39;0.79;0.79;0.79;0.77;0.8;0.79	5.51	4.61	0.57282	.	0.066428	0.64402	D	0.000014	T	0.53642	0.1809	L	0.60455	1.87	0.34467	D	0.702395	D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.999;0.999;0.998;1.0;1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0	P;P;P;D;D;D;D;D;D;D;D;D	0.79108	0.642;0.88;0.719;0.99;0.949;0.949;0.992;0.947;0.981;0.958;0.981;0.958	T	0.68969	-0.5269	10	0.87932	D	0	-20.9146	10.6354	0.45563	0.2036:0.7964:0.0:0.0	.	818;728;811;901;811;823;1362;831;990;977;978;978	E7EPK0;B7Z3G0;E9PDJ9;D6RD46;Q9UPQ0-9;Q9UPQ0-6;G5EA03;Q9UPQ0-5;Q9UPQ0-4;E9PHM7;Q9UPQ0-2;Q9UPQ0	.;.;.;.;.;.;.;.;.;.;.;LIMC1_HUMAN	W	831;977;978;978;901;990;1362;818;1361;818;811;823;811;330	ENSP00000425222:R831W;ENSP00000424825:R977W;ENSP00000424645:R978W;ENSP00000316891:R978W;ENSP00000427045:R901W;ENSP00000424437:R990W;ENSP00000425631:R1362W;ENSP00000421242:R818W;ENSP00000426334:R818W;ENSP00000422864:R811W;ENSP00000379840:R823W;ENSP00000371172:R811W	ENSP00000316891:R978W	R	+	1	2	LIMCH1	41382600	1.000000	0.71417	1.000000	0.80357	0.660000	0.38997	1.469000	0.35343	2.873000	0.98535	0.561000	0.74099	CGG	C|0.999;T|0.001	0.001	strong		0.433	LIMCH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361249.2	NM_014988		T	41687843	C	T	41687843	3	4	26	1	0	0	0	0	1	0	0	0	8806	759	27	1	3050	1	LIMCH1	4	41687843	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1565390	41687843	149466433	136	9899											
PDGFRA	5156	hgsc.bcm.edu	37	chr4	55130078	55130078	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccagaccatcccatttaaTgtttatgctttaaaaggtac	12	15	5	9	0	0	1	0	0	0	1	2	1	2	1	3	1	2	3	3	1	5	8	rs2229307	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:55130078T>C	ENST00000257290.5	+	4	943	c.612T>C	c.(610-612)aaT>aaC	p.N204N	PDGFRA_ENST00000508170.1_Silent_p.N204N|FIP1L1_ENST00000507166.1_Intron	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	204	Ig-like C2-type 3.				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)	TCCCATTTAATGTTTATGCTT	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)			C|||	1183	0.236222	0.2776	0.3487	5008	,	,		19351	0.2034		0.1233	False		,,,				2504	0.2505				p.N204N	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.T612C						PASS	.	C		1102,3304	719.5+/-408.9	128,846,1229	73	73	73		612	-3.1	0	4	dbSNP_98	73	1044,7556	771.5+/-407.7	67,910,3323	no	coding-synonymous	PDGFRA	NM_006206.4		195,1756,4552	CC,CT,TT		12.1395,25.0113,16.5001		204/1090	55130078	2146,10860	2203	4300	6503	SO:0001819	synonymous_variant	5156	exon4	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	ATTTAATGTTTAT	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.612T>C	4.37:g.55130078T>C		37	0	0		48	27	0.5625	NM_006206	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Silent	SNP	ENST00000257290.5	37	CCDS3495.1																																																																																			T|0.828;C|0.172	0.172	strong		0.393	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206		C	55130078	T	C	55130078	2	2	26	1	0	0	0	0	0	0	0	1	11670	1461	51	3		3	PDGFRA	4	55130078	Silent	SNP	T	TCGA-G8-6907-01A-11D-2210-10	13442235	55130078	136024198	137	9900											
PDGFRA	5156	hgsc.bcm.edu	37	chr4	55143577	55143577	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgggtcttggggtctggagcGtttgggaaggtggttgaagg	5	11	21	4	2	2	1	0	1	2	0	2	3	2	3	0	8	1	2	0	8	2	3	rs10028020	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:55143577G>A	ENST00000257290.5	+	13	2140	c.1809G>A	c.(1807-1809)gcG>gcA	p.A603A	FIP1L1_ENST00000507166.1_Silent_p.A363A	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	603	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)	GGTCTGGAGCGTTTGGGAAGG	0.532			"Mis, O, T"	FIP1L1	"GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)			G|||	1142	0.228035	0.3366	0.2666	5008	,	,		16391	0.1726		0.1064	False		,,,				2504	0.2362				p.A603A	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.G1809A						PASS	.	G		1306,3100	441.2+/-346.3	179,948,1076	141	145	144		1809	-11.3	0.1	4	dbSNP_119	144	855,7745	193.8+/-239.4	54,747,3499	no	coding-synonymous	PDGFRA	NM_006206.4		233,1695,4575	AA,AG,GG		9.9419,29.6414,16.6154		603/1090	55143577	2161,10845	2203	4300	6503	SO:0001819	synonymous_variant	5156	exon13	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	TGGAGCGTTTGGG	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.1809G>A	4.37:g.55143577G>A		252	0	0		267	117	0.438202	NM_006206	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Silent	SNP	ENST00000257290.5	37	CCDS3495.1																																																																																			A|0.170;C|0.000;G|0.830	0.170	strong		0.532	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206		A	55143577	G	A	55143577	2	1	26	1	0	0	0	0	0	0	0	1	11670	1132	40	1		1	PDGFRA	4	55143577	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	13499	55143577	136010699	138	9901											
PDGFRA	5156	hgsc.bcm.edu	37	chr4	55152040	55152040	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gatctggctgctcgcaacgtCctcctggcacaaggaaaaat	11	8	10	12	2	1	0	0	0	1	0	4	2	3	1	2	3	2	4	2	3	4	0	rs2228230	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:55152040C>T	ENST00000257290.5	+	18	2803	c.2472C>T	c.(2470-2472)gtC>gtT	p.V824V	FIP1L1_ENST00000507166.1_Silent_p.V584V	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	824	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)	p.V824V(15)		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)	CTCGCAACGTCCTCCTGGCAC	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)			C|||	1204	0.240415	0.3449	0.2767	5008	,	,		22168	0.1726		0.1451	False		,,,				2504	0.2413				p.V824V	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,NS,carcinoma,0,17	PDGFRA	1583	17	15	Substitution - coding silent(15)	soft_tissue(11)|central_nervous_system(3)|endometrium(1)	c.C2472T						PASS	.	C		1381,3025	455.5+/-351.0	211,959,1033	186	168	174		2472	2.4	1	4	dbSNP_98	174	1198,7402	241.0+/-271.5	95,1008,3197	no	coding-synonymous	PDGFRA	NM_006206.4		306,1967,4230	TT,TC,CC		13.9302,31.3436,19.8293		824/1090	55152040	2579,10427	2203	4300	6503	SO:0001819	synonymous_variant	5156	exon18	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	CAACGTCCTCCTG	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.2472C>T	4.37:g.55152040C>T		66	0	0		64	24	0.375	NM_006206	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Silent	SNP	ENST00000257290.5	37	CCDS3495.1																																																																																			C|0.801;T|0.199	0.199	strong		0.498	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206		T	55152040	C	T	55152040	2	4	26	1	0	0	0	0	0	0	0	1	11670	842	30	2		2	PDGFRA	4	55152040	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	8463	55152040	136002236	139	9902											
MUC7	4589	hgsc.bcm.edu	37	chr4	71347050	71347050	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgccccacccacaccttctGcaactacacaagctccacca	11	6	3	21	0	1	0	0	0	1	0	2	0	2	0	6	0	5	2	6	0	3	2	rs144679944	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:71347050G>A	ENST00000304887.5	+	3	779	c.589G>A	c.(589-591)Gca>Aca	p.A197T	MUC7_ENST00000413702.1_Missense_Mutation_p.A197T|MUC7_ENST00000456088.1_Missense_Mutation_p.A197T	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted	197	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)			CACACCTTCTGCAACTACACA	0.592													G|||	7	0.00139776	0.0	0.0	5008	,	,		20060	0.0		0.007	False		,,,				2504	0.0				p.A197T		Atlas-SNP	.											.	MUC7	91	.	0			c.G589A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	3,4403	6.2+/-15.9	0,3,2200	428	344	372		589,589,589	-4.1	0	4	dbSNP_134	372	48,8552	31.2+/-83.2	0,48,4252	no	missense,missense,missense	MUC7	NM_152291.2,NM_001145007.1,NM_001145006.1	58,58,58	0,51,6452	AA,AG,GG		0.5581,0.0681,0.3921	benign,benign,benign	197/378,197/378,197/378	71347050	51,12955	2203	4300	6503	SO:0001583	missense	4589	exon4			CCTTCTGCAACTA	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.589G>A	4.37:g.71347050G>A	ENSP00000302021:p.Ala197Thr	270	0	0		359	149	0.415042	NM_001145007	Q9UCD7|Q9UCD8	Missense_Mutation	SNP	ENST00000304887.5	37	CCDS3541.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	G	5.104	0.204826	0.09704	6.81E-4	0.005581	ENSG00000171195	ENST00000413702;ENST00000456088;ENST00000304887	T;T;T	0.48836	0.8;0.8;0.8	2.05	-4.1	0.03940	.	.	.	.	.	T	0.19565	0.0470	L	0.27053	0.805	0.09310	N	1	B	0.16396	0.017	B	0.12837	0.008	T	0.14337	-1.0476	8	.	.	.	-1.511	4.8329	0.13449	0.4757:0.3088:0.2155:0.0	.	197	Q8TAX7	MUC7_HUMAN	T	197	ENSP00000407422:A197T;ENSP00000400585:A197T;ENSP00000302021:A197T	.	A	+	1	0	MUC7	71381639	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-6.631000	0.00059	-1.559000	0.01688	-0.136000	0.14681	GCA	G|0.996;A|0.004	0.004	strong		0.592	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291		A	71347050	G	A	71347050	3	1	26	1	0	0	0	0	1	0	0	0	9990	1319	46	2	595	2	MUC7	4	71347050	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	16195010	71347050	119807226	140	9903											
THAP6	152815	hgsc.bcm.edu	37	chr4	76452302	76452302	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaaaacgttttcagaaatcaTtgaggaagacaatcagggaa	19	8	9	5	1	3	3	3	1	0	2	3	5	3	5	0	2	1	1	0	2	6	3	rs150566447		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:76452302T>A	ENST00000311638.3	+	5	615	c.547T>A	c.(547-549)Ttg>Atg	p.L183M	THAP6_ENST00000504190.1_Intron|THAP6_ENST00000514480.1_Missense_Mutation_p.L183M|THAP6_ENST00000507556.1_Intron|THAP6_ENST00000507885.1_Intron|THAP6_ENST00000380837.3_Missense_Mutation_p.L141M|THAP6_ENST00000502620.1_Intron|THAP6_ENST00000507557.1_Intron	NM_144721.4	NP_653322.1	Q8TBB0	THAP6_HUMAN	THAP domain containing 6	183						microtubule cytoskeleton (GO:0015630)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			lung(5)	5			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			TCAGAAATCATTGAGGAAGAC	0.398													T|||	1	0.000199681	0.0	0.0	5008	,	,		19622	0.0		0.001	False		,,,				2504	0.0				p.L183M		Atlas-SNP	.											.	THAP6	14	.	0			c.T547A						PASS	.	T	MET/LEU	1,4405	2.1+/-5.4	0,1,2202	114	118	117		547	-3.8	0.7	4	dbSNP_134	117	27,8573	18.5+/-59.3	0,27,4273	yes	missense	THAP6	NM_144721.4	15	0,28,6475	AA,AT,TT		0.314,0.0227,0.2153	probably-damaging	183/223	76452302	28,12978	2203	4300	6503	SO:0001583	missense	152815	exon5			AAATCATTGAGGA	BC022989	CCDS3568.1	4q21.21	2013-01-25			ENSG00000174796	ENSG00000174796		"THAP (C2CH-type zinc finger) domain containing"	23189	protein-coding gene	gene with protein product		612535				12575992	Standard	NM_144721		Approved	MGC30052	uc003him.3	Q8TBB0	OTTHUMG00000130108	ENST00000311638.3:c.547T>A	4.37:g.76452302T>A	ENSP00000309007:p.Leu183Met	213	1	0.00469484		250	129	0.516	NM_144721	B4E146|Q5HYJ7|Q5JPC6	Missense_Mutation	SNP	ENST00000311638.3	37	CCDS3568.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	T	17.57	3.422570	0.62622	2.27E-4	0.00314	ENSG00000174796	ENST00000311638;ENST00000380837;ENST00000514480	D;D;D	0.98666	-5.06;-2.37;-5.06	4.67	-3.82	0.04281	.	0.149661	0.28828	N	0.014010	D	0.97102	0.9053	N	0.19112	0.55	0.21445	N	0.999684	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.963	D	0.93524	0.6864	10	0.33141	T	0.24	-10.7559	11.1423	0.48411	0.0:0.5762:0.0:0.4238	.	141;183	Q8TBB0-2;Q8TBB0	.;THAP6_HUMAN	M	183;141;183	ENSP00000309007:L183M;ENSP00000370217:L141M;ENSP00000423720:L183M	ENSP00000309007:L183M	L	+	1	2	THAP6	76671326	0.071000	0.21146	0.716000	0.30569	0.983000	0.72400	-1.212000	0.02994	-0.636000	0.05524	0.533000	0.62120	TTG	T|0.998;A|0.002	0.002	strong		0.398	THAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252414.1	NM_144721		A	76452302	T	A	76452302	3	1	26	1	0	0	0	0	1	0	0	0	15863	1490	52	5	561	5	THAP6	4	76452302	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	5105252	76452302	114701974	141	9904											
BMP3	651	hgsc.bcm.edu	37	chr4	81967240	81967240	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctcataggatttaacattaCgtccaagggacgccagctgc	11	9	9	12	2	1	0	1	0	0	0	2	2	2	2	3	2	4	1	3	2	4	4	rs34505126	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:81967240C>T	ENST00000282701.2	+	2	985	c.665C>T	c.(664-666)aCg>aTg	p.T222M		NM_001201.2	NP_001192.2	P12645	BMP3_HUMAN	bone morphogenetic protein 3	222			T -> M (in dbSNP:rs34505126).		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						TTTAACATTACGTCCAAGGGA	0.433													C|||	125	0.0249601	0.0847	0.0115	5008	,	,		20614	0.0		0.001	False		,,,				2504	0.0041				p.T222M		Atlas-SNP	.											.	BMP3	59	.	0			c.C665T						PASS	.	C	MET/THR	273,4133	154.4+/-187.8	5,263,1935	115	123	120		665	5.1	0.3	4	dbSNP_126	120	6,8594	4.3+/-15.6	0,6,4294	yes	missense	BMP3	NM_001201.2	81	5,269,6229	TT,TC,CC		0.0698,6.1961,2.1452	probably-damaging	222/473	81967240	279,12727	2203	4300	6503	SO:0001583	missense	651	exon2			ACATTACGTCCAA	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.665C>T	4.37:g.81967240C>T	ENSP00000282701:p.Thr222Met	51	0	0		88	40	0.454545	NM_001201	Q4VAS5	Missense_Mutation	SNP	ENST00000282701.2	37	CCDS3588.1	43	0.019688644688644688	38	0.07723577235772358	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	C	9.519	1.107725	0.20714	0.061961	6.98E-4	ENSG00000152785	ENST00000282701	T	0.74632	-0.86	5.08	5.08	0.68730	.	0.361129	0.33610	N	0.004726	T	0.27349	0.0671	M	0.68952	2.095	0.09310	N	1	D	0.89917	1.0	D	0.69307	0.963	T	0.54866	-0.8229	10	0.56958	D	0.05	.	14.6465	0.68764	0.1459:0.8541:0.0:0.0	rs34505126;rs61679463	222	P12645	BMP3_HUMAN	M	222	ENSP00000282701:T222M	ENSP00000282701:T222M	T	+	2	0	BMP3	82186264	0.293000	0.24371	0.254000	0.24359	0.004000	0.04260	2.015000	0.40961	2.806000	0.96561	0.655000	0.94253	ACG	C|0.975;T|0.025	0.025	strong		0.433	BMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252634.1			T	81967240	C	T	81967240	3	4	26	1	0	0	0	0	1	0	0	0	1461	536	19	1	671	1	BMP3	4	81967240	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	5514938	81967240	109187036	142	9905											
RASGEF1B	153020	hgsc.bcm.edu	37	chr4	82355804	82355804	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacactcacctcaaaattgaCatggccattgggaaggcggt	12	8	10	11	1	2	1	2	1	0	0	2	2	2	2	2	4	0	0	2	4	3	2	rs34211143	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:82355804C>T	ENST00000264400.2	-	11	1340	c.1189G>A	c.(1189-1191)Gtc>Atc	p.V397I	RASGEF1B_ENST00000335927.7_Missense_Mutation_p.V355I|RASGEF1B_ENST00000509081.1_Missense_Mutation_p.V396I	NM_152545.1	NP_689758.1	Q0VAM2	RGF1B_HUMAN	RasGEF domain family, member 1B	397	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				positive regulation of Ras GTPase activity (GO:0032320)|small GTPase mediated signal transduction (GO:0007264)	endosome (GO:0005768)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)			endometrium(2)|kidney(5)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	26						TCAAAATTGACATGGCCATTG	0.453													C|||	30	0.00599042	0.0008	0.0159	5008	,	,		17128	0.0		0.0179	False		,,,				2504	0.0				p.V397I		Atlas-SNP	.											RASGEF1B,NS,carcinoma,+2,1	RASGEF1B	44	1	0			c.G1189A						PASS	.	C	ILE/VAL	17,4389	24.3+/-50.5	0,17,2186	74	68	70		1189	3.7	1	4	dbSNP_126	70	131,8469	64.9+/-127.2	1,129,4170	yes	missense	RASGEF1B	NM_152545.1	29	1,146,6356	TT,TC,CC		1.5233,0.3858,1.1379	benign	397/474	82355804	148,12858	2203	4300	6503	SO:0001583	missense	153020	exon11			AATTGACATGGCC	AK056257	CCDS34022.1, CCDS75151.1, CCDS75152.1	4q21.21	2013-09-24				ENSG00000138670			24881	protein-coding gene	gene with protein product		614532				12488504	Standard	XM_005262776		Approved	GPIG4, FLJ31695	uc003hmi.1	Q0VAM2		ENST00000264400.2:c.1189G>A	4.37:g.82355804C>T	ENSP00000264400:p.Val397Ile	127	0	0		135	70	0.518519	NM_152545	Q0VAM1|Q4W5L7|Q4W5M3|Q96MY8	Missense_Mutation	SNP	ENST00000264400.2	37	CCDS34022.1	18	0.008241758241758242	0	0.0	6	0.016574585635359115	0	0.0	12	0.0158311345646438	C	4.202	0.036168	0.08148	0.003858	0.015233	ENSG00000138670	ENST00000509081;ENST00000264400;ENST00000335927	T;T;T	0.26373	1.74;1.74;1.74	4.62	3.69	0.42338	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine-nucleotide exchange factor, conserved site (1);Ras guanine nucleotide exchange factor, domain (1);	0.122271	0.53938	D	0.000046	T	0.03783	0.0107	N	0.01809	-0.71	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.002;0.001	T	0.19063	-1.0317	10	0.02654	T	1	.	12.9491	0.58389	0.0:0.9062:0.0:0.0938	rs34211143	355;396;397	Q0VAM2-2;Q0VAM2-3;Q0VAM2	.;.;RGF1B_HUMAN	I	396;397;355	ENSP00000425393:V396I;ENSP00000264400:V397I;ENSP00000338437:V355I	ENSP00000264400:V397I	V	-	1	0	RASGEF1B	82574828	0.941000	0.31946	0.997000	0.53966	0.997000	0.91878	1.302000	0.33459	2.413000	0.81919	0.585000	0.79938	GTC	C|0.989;T|0.011	0.011	strong		0.453	RASGEF1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362830.1	NM_152545		T	82355804	C	T	82355804	3	4	26	1	0	0	0	0	1	0	0	0	13085	478	17	2	248	2	RASGEF1B	4	82355804	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	388564	82355804	108798472	143	9906											
MANBA	4126	hgsc.bcm.edu	37	chr4	103553372	103553372	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcttcctacatccaaccaaaCaaagggagcgacagctgagg	14	5	10	12	1	0	1	0	1	0	0	2	3	2	2	3	2	5	2	3	2	4	2	rs75826658	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:103553372C>T	ENST00000226578.4	-	17	2581	c.2482G>A	c.(2482-2484)Gtt>Att	p.V828I	MANBA_ENST00000505239.1_Missense_Mutation_p.V771I	NM_005908.3	NP_005899.3	O00462	MANBA_HUMAN	mannosidase, beta A, lysosomal	828					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)		TCCAACCAAACAAAGGGAGCG	0.423													C|||	32	0.00638978	0.0008	0.0101	5008	,	,		20461	0.0		0.0239	False		,,,				2504	0.0				p.V828I		Atlas-SNP	.											.	MANBA	78	.	0			c.G2482A						PASS	.	C	ILE/VAL	17,4389	24.3+/-50.5	0,17,2186	102	106	105		2482	5.2	1	4	dbSNP_131	105	151,8449	74.5+/-137.1	1,149,4150	yes	missense	MANBA	NM_005908.3	29	1,166,6336	TT,TC,CC		1.7558,0.3858,1.2917	probably-damaging	828/880	103553372	168,12838	2203	4300	6503	SO:0001583	missense	4126	exon17			ACCAAACAAAGGG		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.2482G>A	4.37:g.103553372C>T	ENSP00000226578:p.Val828Ile	224	0	0		238	101	0.42437	NM_005908	Q96BC3|Q9NYX9	Missense_Mutation	SNP	ENST00000226578.4	37	CCDS3658.1	26	0.011904761904761904	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	20	0.026385224274406333	C	25.5	4.645483	0.87859	0.003858	0.017558	ENSG00000109323	ENST00000226578;ENST00000505239	T;T	0.77098	-1.06;-1.07	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.77644	0.4161	M	0.86740	2.835	0.58432	D	0.999992	D;D	0.76494	0.997;0.999	P;D	0.70016	0.907;0.967	D	0.85752	0.1344	10	0.72032	D	0.01	-22.6841	16.8489	0.85988	0.0:1.0:0.0:0.0	.	771;828	E9PFW2;O00462	.;MANBA_HUMAN	I	828;771	ENSP00000226578:V828I;ENSP00000427322:V771I	ENSP00000226578:V828I	V	-	1	0	MANBA	103772420	1.000000	0.71417	0.997000	0.53966	0.852000	0.48524	5.317000	0.65822	2.404000	0.81709	0.460000	0.39030	GTT	C|0.986;T|0.014	0.014	strong		0.423	MANBA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253803.2			T	103553372	C	T	103553372	3	4	26	1	0	0	0	0	1	0	0	0	9228	478	17	2	161	2	MANBA	4	103553372	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	21197568	103553372	87600904	144	9907											
LRIT3	345193	hgsc.bcm.edu	37	chr4	110791290	110791290	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagaatggaagtaagcttcCtccagccagcacaagtaaga	17	6	9	9	0	0	2	0	0	0	2	2	3	2	3	3	1	3	4	3	1	6	3	rs201097191		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:110791290C>T	ENST00000594814.1	+	4	1385	c.1385C>T	c.(1384-1386)cCt>cTt	p.P462L	LRIT3_ENST00000327908.3_Missense_Mutation_p.P279L|LRIT3_ENST00000409621.2_Missense_Mutation_p.P279L|LRIT3_ENST00000379920.3_Missense_Mutation_p.P417L	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	462					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)		AGTAAGCTTCCTCCAGCCAGC	0.468													C|||	1	0.000199681	0.0	0.0	5008	,	,		22471	0.0		0.001	False		,,,				2504	0.0				p.P462L		Atlas-SNP	.											.	LRIT3	107	.	0			c.C1385T						PASS	.						67	68	68					4																	110791290		2203	4300	6503	SO:0001583	missense	345193	exon4			AGCTTCCTCCAGC	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.1385C>T	4.37:g.110791290C>T	ENSP00000469759:p.Pro462Leu	106	0	0		121	61	0.504132	NM_198506	C9J1C2|Q6ZTG1	Missense_Mutation	SNP	ENST00000594814.1	37	CCDS3688.3	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	12.59	1.982265	0.34942	.	.	ENSG00000183423	ENST00000327908;ENST00000379920;ENST00000409621	T;T;T	0.57752	0.38;0.55;0.38	5.06	4.22	0.49857	.	0.662798	0.13364	N	0.393444	T	0.42630	0.1211	L	0.43152	1.355	0.42468	D	0.992817	B;B	0.17667	0.006;0.023	B;B	0.16722	0.005;0.016	T	0.28996	-1.0026	10	0.36615	T	0.2	.	6.7454	0.23458	0.223:0.686:0.0:0.091	.	417;279	Q3SXY7;Q3SXY7-2	LRIT3_HUMAN;.	L	279;417;279	ENSP00000328222:P279L;ENSP00000369252:P417L;ENSP00000386734:P279L	ENSP00000328222:P279L	P	+	2	0	LRIT3	111010739	0.070000	0.21116	0.179000	0.23059	0.105000	0.19272	3.151000	0.50670	1.121000	0.41925	0.655000	0.94253	CCT	C|1.000;T|0.000	0.000	strong		0.468	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506		T	110791290	C	T	110791290	3	4	26	1	0	0	0	0	1	0	0	0	8958	681	24	2	1260	2	LRIT3	4	110791290	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	7237918	110791290	80362986	145	9908											
FAT4	79633	hgsc.bcm.edu	37	chr4	126412106	126412106	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agcccctttctccaaatcttCtacgttctatagaaacagcc	11	12	4	14	1	4	1	0	0	4	1	5	1	4	1	4	0	4	1	4	0	5	6	rs147662558	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:126412106C>G	ENST00000394329.3	+	17	14142	c.14129C>G	c.(14128-14130)tCt>tGt	p.S4710C	FAT4_ENST00000335110.5_Missense_Mutation_p.S2951C	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4710	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						TCCAAATCTTCTACGTTCTAT	0.483													C|||	30	0.00599042	0.0008	0.0058	5008	,	,		20671	0.0		0.0179	False		,,,				2504	0.0072				p.S4710C		Atlas-SNP	.											.	FAT4	1752	.	0			c.C14129G						PASS	.	C	CYS/SER	22,4384	30.8+/-60.4	0,22,2181	103	109	107		14129	4.9	0.3	4	dbSNP_134	107	177,8423	80.6+/-143.3	1,175,4124	yes	missense	FAT4	NM_024582.4	112	1,197,6305	GG,GC,CC		2.0581,0.4993,1.5301	probably-damaging	4710/4982	126412106	199,12807	2203	4300	6503	SO:0001583	missense	79633	exon17			AATCTTCTACGTT	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.14129C>G	4.37:g.126412106C>G	ENSP00000377862:p.Ser4710Cys	95	0	0		117	56	0.478632	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	20	0.009157509157509158	0	0.0	5	0.013812154696132596	0	0.0	15	0.01978891820580475	C	15.14	2.744809	0.49151	0.004993	0.020581	ENSG00000196159	ENST00000394329;ENST00000335110	T;D	0.82081	-1.36;-1.57	4.93	4.93	0.64822	.	0.000000	0.33732	U	0.004612	T	0.73760	0.3628	L	0.36672	1.1	0.41081	D	0.985527	D;D;D	0.61697	0.982;0.983;0.99	P;P;P	0.53313	0.639;0.533;0.723	T	0.82729	-0.0313	10	0.72032	D	0.01	.	17.1555	0.86791	0.0:1.0:0.0:0.0	.	2951;4710;4709	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	C	4710;2951	ENSP00000377862:S4710C;ENSP00000335169:S2951C	ENSP00000335169:S2951C	S	+	2	0	FAT4	126631556	0.998000	0.40836	0.267000	0.24556	0.798000	0.45092	5.643000	0.67895	2.283000	0.76528	0.561000	0.74099	TCT	C|0.986;G|0.014	0.014	strong		0.483	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		G	126412106	C	G	126412106	3	3	26	1	0	0	0	0	1	0	0	0	5700	913	32	4	14195	4	FAT4	4	126412106	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	15620816	126412106	64742170	146	9909											
SCLT1	132320	hgsc.bcm.edu	37	chr4	129864289	129864289	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttctctctctcagactccaaTacattttgaagtttctgaat	10	17	4	10	0	4	3	1	2	3	1	7	3	5	3	1	0	1	1	1	0	4	5	rs144333168	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:129864289T>C	ENST00000281142.5	-	17	1997	c.1494A>G	c.(1492-1494)gtA>gtG	p.V498V	SCLT1_ENST00000502495.1_5'UTR|SCLT1_ENST00000503215.1_Intron|SCLT1_ENST00000434680.1_Intron|SCLT1_ENST00000439369.2_Intron	NM_144643.2	NP_653244.2	Q96NL6	SCLT1_HUMAN	sodium channel and clathrin linker 1	498					cilium assembly (GO:0042384)|clustering of voltage-gated sodium channels (GO:0045162)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|clathrin complex (GO:0071439)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)	sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	29						CAGACTCCAATACATTTTGAA	0.348													T|||	3	0.000599042	0.0	0.0	5008	,	,		17091	0.0		0.002	False		,,,				2504	0.001				p.V498V		Atlas-SNP	.											.	SCLT1	136	.	0			c.A1494G						PASS	.	T		2,4402	4.2+/-10.8	0,2,2200	79	75	76		1494	-10.6	0	4	dbSNP_134	76	22,8574	16.0+/-53.3	0,22,4276	no	coding-synonymous	SCLT1	NM_144643.2		0,24,6476	CC,CT,TT		0.2559,0.0454,0.1846		498/689	129864289	24,12976	2202	4298	6500	SO:0001819	synonymous_variant	132320	exon17			CTCCAATACATTT	AK055217	CCDS3740.1	4q28.2	2008-05-02			ENSG00000151466	ENSG00000151466			26406	protein-coding gene	gene with protein product		611399				15797711	Standard	XM_005262732		Approved	hCAP-1A, FLJ30655	uc003igp.2	Q96NL6	OTTHUMG00000133346	ENST00000281142.5:c.1494A>G	4.37:g.129864289T>C		127	0	0		132	66	0.5	NM_144643	A4QN04|Q0VAH2|Q6P2M4	Silent	SNP	ENST00000281142.5	37	CCDS3740.1																																																																																			T|0.999;C|0.001	0.001	strong		0.348	SCLT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257176.2	NM_144643		C	129864289	T	C	129864289	2	2	26	1	0	0	0	0	0	0	0	1	13921	1393	49	3		3	SCLT1	4	129864289	Silent	SNP	T	TCGA-G8-6907-01A-11D-2210-10	3452183	129864289	61289987	147	9910											
ELF2	1998	hgsc.bcm.edu	37	chr4	140046466	140046466	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaatcactgctggatattcAgaaaccttttcactttccta	12	14	4	11	0	3	1	3	0	0	1	4	2	4	2	2	1	2	1	2	1	4	6	rs115767880	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:140046466A>C	ENST00000394235.2	-	4	592	c.90T>G	c.(88-90)tcT>tcG	p.S30S	ELF2_ENST00000265495.4_Silent_p.S30S|ELF2_ENST00000379550.1_Silent_p.S30S	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)					CTGGATATTCAGAAACCTTTT	0.373													a|||	6	0.00119808	0.0	0.0	5008	,	,		17185	0.0		0.006	False		,,,				2504	0.0				p.E30E		Atlas-SNP	.											.	ELF2	43	.	0			c.G90G						PASS	.	A		3,4403	8.1+/-20.4	0,3,2200	102	100	100		90	3	1	4	dbSNP_132	100	51,8549	32.8+/-85.7	0,51,4249	no	coding-synonymous	ELF2	NM_201999.1		0,54,6449	CC,CA,AA		0.593,0.0681,0.4152		30/582	140046466	54,12952	2203	4300	6503	SO:0001819	synonymous_variant	1998	exon3			ATATTCAGAAACC	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.90T>G	4.37:g.140046466A>C		126	0	0		134	59	0.440298	NM_201999		Silent	SNP	ENST00000394235.2	37	CCDS3744.1																																																																																			A|0.997;C|0.003	0.003	strong		0.373	ELF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257233.2	NM_006874		C	140046466	A	C	140046466	2	2	26	1	0	0	0	0	0	0	0	1	5056	175	7	5		5	ELF2	4	140046466	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	10182177	140046466	51107810	148	9911											
NAA15	80155	hgsc.bcm.edu	37	chr4	140278638	140278638	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agccatctattgctttggagTacataaatactgctattgaa	13	14	7	7	0	1	1	0	1	1	0	1	2	1	2	1	1	5	3	1	1	7	8			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:140278638T>G	ENST00000296543.5	+	11	1509	c.1186T>G	c.(1186-1188)Tac>Gac	p.Y396D	NAA15_ENST00000398947.1_Missense_Mutation_p.Y396D	NM_057175.3	NP_476516.1	Q9BXJ9	NAA15_HUMAN	N(alpha)-acetyltransferase 15, NatA auxiliary subunit	396					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)	p.Y396H(1)		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						TGCTTTGGAGTACATAAATAC	0.338																																					p.Y396D		Atlas-SNP	.											NAA15,NS,carcinoma,0,1	NAA15	88	1	1	Substitution - Missense(1)	endometrium(1)	c.T1186G						PASS	.						83	76	78					4																	140278638		1854	4087	5941	SO:0001583	missense	80155	exon11			TTGGAGTACATAA	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.1186T>G	4.37:g.140278638T>G	ENSP00000296543:p.Tyr396Asp	118	0	0		133	55	0.413534	NM_057175	D3DNY6|Q52LG9|Q8IWH4|Q8NEV2|Q9H8P6	Missense_Mutation	SNP	ENST00000296543.5	37	CCDS43270.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.795402	0.90453	.	.	ENSG00000164134	ENST00000296543;ENST00000544077;ENST00000398947	T;T	0.49720	0.77;0.77	5.71	5.71	0.89125	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.72518	0.3470	M	0.90082	3.085	0.80722	D	1	P	0.46220	0.874	P	0.59889	0.865	T	0.77327	-0.2629	10	0.54805	T	0.06	-6.2825	15.994	0.80228	0.0:0.0:0.0:1.0	.	396	Q9BXJ9	NAA15_HUMAN	D	396;270;396	ENSP00000296543:Y396D;ENSP00000381920:Y396D	ENSP00000296543:Y396D	Y	+	1	0	NAA15	140498088	1.000000	0.71417	0.996000	0.52242	0.990000	0.78478	5.959000	0.70339	2.168000	0.68352	0.528000	0.53228	TAC	.	.	none		0.338	NAA15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000267839.2	NM_057175		G	140278638	T	G	140278638	3	3	26	1	0	0	0	0	1	0	0	0	10127	1638	57	5	1228	5	NAA15	4	140278638	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	232172	140278638	50875638	149	9912											
GAB1	2549	hgsc.bcm.edu	37	chr4	144359490	144359490	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tattagttatgacattcctcCaacacctggtaatacttatc	12	15	4	10	0	0	1	0	1	0	0	3	1	2	1	3	1	2	2	3	1	7	7	rs28925904	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:144359490C>T	ENST00000262994.4	+	4	1234	c.932C>T	c.(931-933)cCa>cTa	p.P311L	GAB1_ENST00000262995.4_Missense_Mutation_p.P311L|GAB1_ENST00000505913.1_Missense_Mutation_p.P208L	NM_002039.3	NP_002030.2	Q13480	GAB1_HUMAN	GRB2-associated binding protein 1	311			P -> L (in dbSNP:rs28925904). {ECO:0000269|Ref.2}.		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)					GACATTCCTCCAACACCTGGT	0.423													C|||	39	0.00778754	0.0	0.0173	5008	,	,		15521	0.0		0.0249	False		,,,				2504	0.002				p.P311L		Atlas-SNP	.											.	GAB1	80	.	0			c.C932T						PASS	.	C	LEU/PRO,LEU/PRO	20,4386	28.1+/-56.4	0,20,2183	96	87	90		932,932	5.8	1	4	dbSNP_125	90	175,8425	80.4+/-143.0	0,175,4125	yes	missense,missense	GAB1	NM_002039.3,NM_207123.2	98,98	0,195,6308	TT,TC,CC		2.0349,0.4539,1.4993	probably-damaging,probably-damaging	311/695,311/725	144359490	195,12811	2203	4300	6503	SO:0001583	missense	2549	exon4			TTCCTCCAACACC	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.932C>T	4.37:g.144359490C>T	ENSP00000262994:p.Pro311Leu	115	0	0		117	56	0.478632	NM_207123	A8K152|Q4W5G2|Q6P1W2	Missense_Mutation	SNP	ENST00000262994.4	37	CCDS3759.1	23	0.010531135531135532	0	0.0	6	0.016574585635359115	0	0.0	17	0.022427440633245383	C	33	5.225676	0.95173	0.004539	0.020349	ENSG00000109458	ENST00000262995;ENST00000262994;ENST00000505913	T;T;T	0.42131	0.98;0.98;0.98	5.8	5.8	0.92144	.	0.048415	0.85682	D	0.000000	T	0.35653	0.0939	M	0.65975	2.015	0.80722	D	1	P;P	0.52577	0.954;0.947	B;P	0.46320	0.439;0.512	T	0.48570	-0.9024	10	0.59425	D	0.04	1.2408	20.063	0.97692	0.0:1.0:0.0:0.0	rs28925904;rs28925904	311;311	Q13480;Q13480-2	GAB1_HUMAN;.	L	311;311;208	ENSP00000262995:P311L;ENSP00000262994:P311L;ENSP00000424554:P208L	ENSP00000262994:P311L	P	+	2	0	GAB1	144578940	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.564000	0.67359	2.735000	0.93741	0.655000	0.94253	CCA	C|0.986;T|0.014	0.014	strong		0.423	GAB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364998.1	NM_002039		T	144359490	C	T	144359490	3	4	26	1	0	0	0	0	1	0	0	0	6156	594	21	2	946	2	GAB1	4	144359490	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	4080852	144359490	46794786	150	9913											
KIAA0922	23240	hgsc.bcm.edu	37	chr4	154388363	154388363	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	attttttggtgttcctgcagCgattgagccgttgccgaacg	6	14	12	9	4	0	1	0	1	0	0	1	3	1	1	3	1	5	3	3	1	1	6	rs78441178	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:154388363C>T	ENST00000409663.3	+	2	177	c.125C>T	c.(124-126)gCg>gTg	p.A42V	KIAA0922_ENST00000440693.1_Splice_Site_p.A42V|KIAA0922_ENST00000409959.3_Splice_Site_p.A42V	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	42						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)				GTTCCTGCAGCGATTGAGCCG	0.577													c|||	2	0.000399361	0.0	0.0	5008	,	,		18938	0.0		0.002	False		,,,				2504	0.0				p.A42V		Atlas-SNP	.											.	KIAA0922	214	.	0			c.C125T						PASS	.		VAL/ALA,VAL/ALA	1,1383		0,1,691	198	177	183		125,125	4.2	1	4	dbSNP_131	183	15,3167		0,15,1576	yes	missense-near-splice,missense-near-splice	KIAA0922	NM_001131007.1,NM_015196.3	64,64	0,16,2267	TT,TC,CC		0.4714,0.0723,0.3504	benign,benign	42/1611,42/1610	154388363	16,4550	692	1591	2283	SO:0001630	splice_region_variant	23240	exon2			CTGCAGCGATTGA	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.125-1C>T	4.37:g.154388363C>T		210	0	0		218	104	0.477064	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	37	CCDS3783.2	.	.	.	.	.	.	.	.	.	.	c	15.31	2.796674	0.50208	7.23E-4	0.004714	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959	T;T;T	0.28255	1.89;1.62;1.9	5.23	4.19	0.49359	.	.	.	.	.	T	0.27798	0.0684	L	0.55481	1.735	0.27301	N	0.957589	B;B	0.32526	0.374;0.257	B;B	0.29942	0.109;0.051	T	0.08827	-1.0703	8	.	.	.	.	10.079	0.42377	0.0:0.8247:0.0:0.1753	.	42;42	A2VDJ0-5;A2VDJ0	.;T131L_HUMAN	V	42	ENSP00000386574:A42V;ENSP00000409663:A42V;ENSP00000386787:A42V	.	A	+	2	0	KIAA0922	154607813	0.991000	0.36638	1.000000	0.80357	0.988000	0.76386	1.197000	0.32211	2.442000	0.82660	0.550000	0.68814	GCG	.	.	weak		0.577	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196	Missense_Mutation	T	154388363	C	T	154388363	5	4	26	1	0	0	0	0	0	0	1	0	8210	782	27	1	131	1	KIAA0922	4	154388363	Splice_Site	SNP	C	TCGA-G8-6907-01A-11D-2210-10	10028873	154388363	36765913	151	9914											
TLR2	7097	hgsc.bcm.edu	37	chr4	154625042	154625042	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttttacttattttatgatcTgagcactttatattcactta	10	21	4	6	0	2	2	1	2	1	0	2	2	2	2	0	0	2	2	0	0	6	10			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:154625042T>G	ENST00000260010.6	+	1	2391	c.983T>G	c.(982-984)cTg>cGg	p.L328R		NM_003264.3	NP_003255.2	O60603	TLR2_HUMAN	toll-like receptor 2	328					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)	TTTTATGATCTGAGCACTTTA	0.323																																					p.L328R		Atlas-SNP	.											.	TLR2	84	.	0			c.T983G						PASS	.						58	63	61					4																	154625042		2203	4299	6502	SO:0001583	missense	7097	exon3			ATGATCTGAGCAC	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.983T>G	4.37:g.154625042T>G	ENSP00000260010:p.Leu328Arg	80	0	0		115	57	0.495652	NM_003264	B3Y612|D1CS45|D1CS48|D1CS49|O15454|Q8NI00	Missense_Mutation	SNP	ENST00000260010.6	37	CCDS3784.1	.	.	.	.	.	.	.	.	.	.	T	18.84	3.708432	0.68615	.	.	ENSG00000137462	ENST00000260010	T	0.60424	0.19	6.06	4.88	0.63580	.	0.583671	0.16992	N	0.191252	T	0.72382	0.3453	M	0.77103	2.36	0.09310	N	0.999999	P	0.48407	0.91	P	0.57244	0.816	T	0.65726	-0.6098	10	0.87932	D	0	.	12.394	0.55374	0.0:0.0653:0.0:0.9347	.	328	O60603	TLR2_HUMAN	R	328	ENSP00000260010:L328R	ENSP00000260010:L328R	L	+	2	0	TLR2	154844492	0.709000	0.27886	0.013000	0.15412	0.020000	0.10135	5.184000	0.65070	1.116000	0.41820	-0.263000	0.10527	CTG	.	.	none		0.323	TLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365205.1			G	154625042	T	G	154625042	3	3	26	1	0	0	0	0	1	0	0	0	15966	1580	55	5	985	5	TLR2	4	154625042	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	236679	154625042	36529234	152	9915											
DCHS2	54798	hgsc.bcm.edu	37	chr4	155298432	155298432	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttagcttccaccaggagatcAtaggtagctggatccctttc	9	12	9	11	0	1	1	1	0	0	1	4	3	3	2	3	3	2	3	3	3	3	5			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:155298432A>G	ENST00000357232.4	-	3	398	c.399T>C	c.(397-399)taT>taC	p.Y133Y	DCHS2_ENST00000339452.1_Silent_p.Y739Y	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	133	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)		CCAGGAGATCATAGGTAGCTG	0.443																																					p.Y739Y		Atlas-SNP	.											.	DCHS2	594	.	0			c.T2217C						PASS	.						134	121	126					4																	155298432		2203	4300	6503	SO:0001819	synonymous_variant	54798	exon2			GAGATCATAGGTA	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.399T>C	4.37:g.155298432A>G		92	0	0		88	38	0.431818	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	37	CCDS3785.1																																																																																			.	.	none		0.443	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		G	155298432	A	G	155298432	2	3	26	1	0	0	0	0	0	0	0	1	4290	224	8	3		3	DCHS2	4	155298432	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	673390	155298432	35855844	153	9916											
LRRC14B	389257	hgsc.bcm.edu	37	chr5	192467	192467	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accccctcctcgcctccatcGcccgggagctcagcaagatg	7	6	9	19	3	1	1	1	0	0	1	5	2	3	2	6	1	2	2	6	1	1	0	rs78454293	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:192467G>A	ENST00000328278.3	+	1	842	c.814G>A	c.(814-816)Gcc>Acc	p.A272T		NM_001080478.1	NP_001073947.1	A6NHZ5	LR14B_HUMAN	leucine rich repeat containing 14B	272										endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)|upper_aerodigestive_tract(2)	10						CGCCTCCATCGCCCGGGAGCT	0.682													G|||	10	0.00199681	0.0008	0.0029	5008	,	,		17788	0.0		0.007	False		,,,				2504	0.0				p.A272T		Atlas-SNP	.											.	LRRC14B	30	.	0			c.G814A						PASS	.	G	THR/ALA	13,4271		0,13,2129	9	12	11		814	4.4	1	5	dbSNP_131	11	61,8449		0,61,4194	yes	missense	LRRC14B	NM_001080478.1	58	0,74,6323	AA,AG,GG		0.7168,0.3035,0.5784	possibly-damaging	272/515	192467	74,12720	2142	4255	6397	SO:0001583	missense	389257	exon1			TCCATCGCCCGGG		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.814G>A	5.37:g.192467G>A	ENSP00000327675:p.Ala272Thr	132	0	0		189	102	0.539683	NM_001080478		Missense_Mutation	SNP	ENST00000328278.3	37	CCDS47184.1	9	0.004120879120879121	0	0.0	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	G	17.09	3.300830	0.60195	0.003035	0.007168	ENSG00000185028	ENST00000328278	T	0.55052	0.54	5.33	4.43	0.53597	.	0.149049	0.64402	D	0.000010	T	0.42314	0.1197	L	0.38838	1.175	0.36111	D	0.844832	D	0.62365	0.991	P	0.52109	0.69	T	0.51779	-0.8662	10	0.18276	T	0.48	.	12.8535	0.57871	0.0:0.0:0.8357:0.1643	.	272	A6NHZ5	LR14B_HUMAN	T	272	ENSP00000327675:A272T	ENSP00000327675:A272T	A	+	1	0	LRRC14B	245467	1.000000	0.71417	0.987000	0.45799	0.131000	0.20780	7.463000	0.80869	1.185000	0.42971	0.462000	0.41574	GCC	G|0.996;A|0.004	0.004	strong		0.682	LRRC14B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000365393.2	NM_001080478		A	192467	G	A	192467	3	1	26	1	0	0	0	0	1	0	0	0	8978	1087	38	1	816	1	LRRC14B	5	192467	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10		192467	180722793	154	9917											
SDHA	6389	hgsc.bcm.edu	37	chr5	256508	256508	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aacgaggctgactgtgccacCgtcccgccagccattcgctc	7	7	10	17	4	0	1	0	1	0	0	3	2	1	1	5	1	3	2	5	1	1	1	rs3211499		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:256508C>T	ENST00000264932.6	+	15	2083	c.1968C>T	c.(1966-1968)acC>acT	p.T656T	SDHA_ENST00000510361.1_Silent_p.T608T|SDHA_ENST00000507522.1_3'UTR|SDHA_ENST00000504309.1_Silent_p.T575T	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	656					cellular metabolic process (GO:0044237)|nervous system development (GO:0007399)|oxidation-reduction process (GO:0055114)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|tricarboxylic acid cycle (GO:0006099)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|succinate dehydrogenase (ubiquinone) activity (GO:0008177)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|liver(2)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	40			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	ACTGTGCCACCGTCCCGCCAG	0.438									Familial Paragangliomas																												p.T656T		Atlas-SNP	.											SDHA,NS,carcinoma,+2,1	SDHA	80	1	0			c.C1968T						scavenged	.						70	78	75					5																	256508		2203	4300	6503	SO:0001819	synonymous_variant	6389	exon15	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	TGCCACCGTCCCG	BC001380	CCDS3853.1	5p15	2014-09-17			ENSG00000073578	ENSG00000073578		"Mitochondrial respiratory chain complex / Complex II"	10680	protein-coding gene	gene with protein product		600857		SDH2		7798181	Standard	XM_005248329		Approved	FP, SDHF	uc003jao.4	P31040	OTTHUMG00000090275	ENST00000264932.6:c.1968C>T	5.37:g.256508C>T		137	0	0		144	6	0.0416667	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Silent	SNP	ENST00000264932.6	37	CCDS3853.1																																																																																			.	.	weak		0.438	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168		T	256508	C	T	256508	2	4	26	1	0	0	0	0	0	0	0	1	13978	639	23	1		1	SDHA	5	256508	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	64041	256508	180658752	155	9918											
SLC12A7	10723	hgsc.bcm.edu	37	chr5	1065514	1065514	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgactggatcaggtgggacAtgccatcccgcaggctggac	8	6	14	13	2	1	0	1	0	0	0	2	4	2	3	3	5	1	2	3	5	0	0	rs56350427	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:1065514A>G	ENST00000264930.5	-	18	2364	c.2321T>C	c.(2320-2322)aTg>aCg	p.M774T	MIR4635_ENST00000583759.1_RNA	NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	774					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)	CAGGTGGGACATGCCATCCCG	0.627													A|||	26	0.00519169	0.0	0.0014	5008	,	,		18614	0.0		0.0209	False		,,,				2504	0.0041				p.M774T		Atlas-SNP	.											.	SLC12A7	97	.	0			c.T2321C						PASS	.	A	THR/MET	14,4392	21.2+/-45.6	0,14,2189	67	69	68		2321	0.5	0.8	5	dbSNP_129	68	195,8405	85.6+/-148.0	4,187,4109	yes	missense	SLC12A7	NM_006598.2	81	4,201,6298	GG,GA,AA		2.2674,0.3177,1.607	benign	774/1084	1065514	209,12797	2203	4300	6503	SO:0001583	missense	10723	exon18			TGGGACATGCCAT	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.2321T>C	5.37:g.1065514A>G	ENSP00000264930:p.Met774Thr	118	0	0		145	66	0.455172	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Missense_Mutation	SNP	ENST00000264930.5	37	CCDS34129.1	21	0.009615384615384616	0	0.0	2	0.0055248618784530384	0	0.0	19	0.025065963060686015	a	8.557	0.876903	0.17395	0.003177	0.022674	ENSG00000113504	ENST00000264930	D	0.93426	-3.22	4.49	0.507	0.16967	.	0.552015	0.20357	N	0.093925	T	0.64349	0.2590	N	0.10645	0.015	0.24364	N	0.994864	B	0.02656	0.0	B	0.04013	0.001	T	0.64588	-0.6372	10	0.33141	T	0.24	.	7.1786	0.25760	0.5848:0.0:0.4152:0.0	rs56350427	774	Q9Y666	S12A7_HUMAN	T	774	ENSP00000264930:M774T	ENSP00000264930:M774T	M	-	2	0	SLC12A7	1118514	0.090000	0.21635	0.789000	0.31954	0.693000	0.40251	1.824000	0.39072	-0.143000	0.11334	0.383000	0.25322	ATG	A|0.987;G|0.013	0.013	strong		0.627	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598		G	1065514	A	G	1065514	3	3	26	1	0	0	0	0	1	0	0	0	14403	217	8	3	958	3	SLC12A7	5	1065514	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	809006	1065514	179849746	156	9919											
TERT	7015	hgsc.bcm.edu	37	chr5	1253918	1253918	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agggcagtcagcgtcgtcccCgggagcttccgactcagctg	6	7	14	14	4	2	0	2	0	0	0	5	2	4	1	3	2	3	3	3	2	0	1	rs35033501	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:1253918C>T	ENST00000310581.5	-	16	3381	c.3324G>A	c.(3322-3324)ccG>ccA	p.P1108P	TERT_ENST00000334602.6_Silent_p.P1045P|TERT_ENST00000296820.5_3'UTR	NM_001193376.1|NM_198253.2	NP_001180305.1|NP_937983.2	O14746	TERT_HUMAN	telomerase reverse transcriptase	1108	CTE.				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)	GCGTCGTCCCCGGGAGCTTCC	0.657									TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis				c|||	36	0.0071885	0.0	0.0101	5008	,	,		16253	0.0		0.0288	False		,,,				2504	0.0				p.P1108P		Atlas-SNP	.											.	TERT	2594	.	0			c.G3324A						PASS	.	C	,	23,4331		0,23,2154	22	31	28		3135,3324	-6.8	0	5	dbSNP_126	28	208,8314		1,206,4054	no	coding-synonymous,coding-synonymous	TERT	NM_001193376.1,NM_198253.2	,	1,229,6208	TT,TC,CC		2.4407,0.5282,1.794	,	1045/1070,1108/1133	1253918	231,12645	2177	4261	6438	SO:0001819	synonymous_variant	7015	exon16	Familial Cancer Database	;Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia;Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	CGTCCCCGGGAGC	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.3324G>A	5.37:g.1253918C>T		116	0	0		126	64	0.507937	NM_198253	O14783|Q2XS35|Q8N6C3|Q8NG38|Q8NG46	Silent	SNP	ENST00000310581.5	37	CCDS3861.2																																																																																			C|0.985;T|0.015	0.015	strong		0.657	TERT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206729.2			T	1253918	C	T	1253918	2	4	26	1	0	0	0	0	0	0	0	1	15779	639	23	1		1	TERT	5	1253918	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	188404	1253918	179661342	157	9920											
FASTKD3	79072	hgsc.bcm.edu	37	chr5	7867027	7867027	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaaaagtttctgccactgcAttgaggatgggttttgaaag	12	12	11	6	0	1	2	0	2	1	0	1	3	1	3	1	2	2	3	1	2	3	4	rs77130393	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:7867027A>G	ENST00000264669.5	-	2	1306	c.1170T>C	c.(1168-1170)aaT>aaC	p.N390N	MTRR_ENST00000502509.1_Intron|MTRR_ENST00000341013.6_5'Flank|FASTKD3_ENST00000513658.1_Intron|MTRR_ENST00000264668.2_5'Flank|MTRR_ENST00000440940.2_5'Flank	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	390					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						CTGCCACTGCATTGAGGATGG	0.438													A|||	32	0.00638978	0.0	0.0173	5008	,	,		18240	0.0		0.0189	False		,,,				2504	0.001				p.N390N		Atlas-SNP	.											.	FASTKD3	88	.	0			c.T1170C						PASS	.	A		24,4382	30.8+/-60.4	0,24,2179	63	64	63		1170	-5.6	0	5	dbSNP_134	63	199,8401	87.1+/-149.5	1,197,4102	no	coding-synonymous	FASTKD3	NM_024091.3		1,221,6281	GG,GA,AA		2.314,0.5447,1.7146		390/663	7867027	223,12783	2203	4300	6503	SO:0001819	synonymous_variant	79072	exon2			CACTGCATTGAGG	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.1170T>C	5.37:g.7867027A>G		137	0	0		176	81	0.460227	NM_024091	Q9BVD3	Silent	SNP	ENST00000264669.5	37	CCDS3873.1																																																																																			A|0.984;G|0.016	0.016	strong		0.438	FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1	NM_024091		G	7867027	A	G	7867027	2	3	26	1	0	0	0	0	0	0	0	1	5695	214	8	3		3	FASTKD3	5	7867027	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	6613109	7867027	173048233	158	9921											
MTRR	4552	hgsc.bcm.edu	37	chr5	7892933	7892933	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaggttctgcggaagggagtAtgtacaggctggctggcctt	7	10	17	7	1	1	0	0	0	1	0	1	3	1	2	1	6	2	5	1	6	3	4	rs35890938	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:7892933A>G	ENST00000264668.2	+	11	1575	c.1545A>G	c.(1543-1545)gtA>gtG	p.V515V	MTRR_ENST00000440940.2_Silent_p.V488V	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	515	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				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)	GGAAGGGAGTATGTACAGGCT	0.473													G|||	40	0.00798722	0.0015	0.0245	5008	,	,		18051	0.0		0.0189	False		,,,				2504	0.002				p.V515V		Atlas-SNP	.											.	MTRR	74	.	0			c.A1545G						PASS	.	G	,	46,4360	822.1+/-416.4	0,46,2157	150	129	136		1464,1545	0.7	0.5	5	dbSNP_126	136	207,8393	810.1+/-407.1	2,203,4095	no	coding-synonymous,coding-synonymous	MTRR	NM_002454.2,NM_024010.2	,	2,249,6252	GG,GA,AA		2.407,1.044,1.9453	,	488/699,515/726	7892933	253,12753	2203	4300	6503	SO:0001819	synonymous_variant	4552	exon11			GGGAGTATGTACA	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.1545A>G	5.37:g.7892933A>G		158	0	0		186	93	0.5	NM_024010	O60471|Q32MA9|Q7Z4M8	Silent	SNP	ENST00000264668.2	37	CCDS3874.1																																																																																			A|0.981;G|0.019	0.019	strong		0.473	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1			G	7892933	A	G	7892933	2	3	26	1	0	0	0	0	0	0	0	1	9970	436	16	3		3	MTRR	5	7892933	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	25906	7892933	173022327	159	9922											
MTRR	4552	hgsc.bcm.edu	37	chr5	7893005	7893005	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	catgcatcccatgaagacagCgggaaagccctggctcctaa	12	6	10	13	1	0	2	0	1	0	1	2	3	2	3	3	2	3	2	3	2	3	1	rs34172797	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:7893005C>T	ENST00000264668.2	+	11	1647	c.1617C>T	c.(1615-1617)agC>agT	p.S539S	MTRR_ENST00000440940.2_Silent_p.S512S	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	539	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				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)	ATGAAGACAGCGGGAAAGCCC	0.458													C|||	45	0.00898562	0.0045	0.0259	5008	,	,		18337	0.0		0.0189	False		,,,				2504	0.002				p.S539S		Atlas-SNP	.											.	MTRR	74	.	0			c.C1617T						PASS	.	C	,	66,4340	61.7+/-98.7	0,66,2137	84	71	75		1536,1617	0.2	0	5	dbSNP_126	75	207,8393	89.4+/-151.6	2,203,4095	no	coding-synonymous,coding-synonymous	MTRR	NM_002454.2,NM_024010.2	,	2,269,6232	TT,TC,CC		2.407,1.498,2.099	,	512/699,539/726	7893005	273,12733	2203	4300	6503	SO:0001819	synonymous_variant	4552	exon11			AGACAGCGGGAAA	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.1617C>T	5.37:g.7893005C>T		89	0	0		118	58	0.491525	NM_024010	O60471|Q32MA9|Q7Z4M8	Silent	SNP	ENST00000264668.2	37	CCDS3874.1																																																																																			C|0.981;T|0.019	0.019	strong		0.458	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1			T	7893005	C	T	7893005	2	4	26	1	0	0	0	0	0	0	0	1	9970	767	27	1		1	MTRR	5	7893005	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	72	7893005	173022255	160	9923											
CCT5	22948	hgsc.bcm.edu	37	chr5	10261764	10261764	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gctggtcttgtacaggagatCtcatttgggacaactaagga	11	11	12	7	0	2	1	1	0	2	1	3	4	2	3	0	4	2	2	0	4	3	4	rs141675330	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:10261764C>G	ENST00000280326.4	+	8	1506	c.1086C>G	c.(1084-1086)atC>atG	p.I362M	CTD-2256P15.4_ENST00000606194.1_RNA|CCT5_ENST00000515390.1_Missense_Mutation_p.I307M|CCT5_ENST00000515676.1_Missense_Mutation_p.I324M|CCT5_ENST00000506600.1_Missense_Mutation_p.I269M|CCT5_ENST00000503026.1_Missense_Mutation_p.I341M	NM_012073.3	NP_036205.1	P48643	TCPE_HUMAN	chaperonin containing TCP1, subunit 5 (epsilon)	362					'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						TACAGGAGATCTCATTTGGGA	0.478													C|||	15	0.00299521	0.0008	0.0144	5008	,	,		19303	0.0		0.004	False		,,,				2504	0.0				p.I362M		Atlas-SNP	.											.	CCT5	49	.	0			c.C1086G						PASS	.	C	MET/ILE	8,4398	14.3+/-33.2	0,8,2195	146	154	151		1086	3.6	1	5	dbSNP_134	151	57,8543	36.4+/-91.3	0,57,4243	yes	missense	CCT5	NM_012073.3	10	0,65,6438	GG,GC,CC		0.6628,0.1816,0.4998	benign	362/542	10261764	65,12941	2203	4300	6503	SO:0001583	missense	22948	exon8			GGAGATCTCATTT	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.1086C>G	5.37:g.10261764C>G	ENSP00000280326:p.Ile362Met	374	1	0.0026738		376	196	0.521277	NM_012073	A8JZY8|A8K2X8|B4DYD8	Missense_Mutation	SNP	ENST00000280326.4	37	CCDS3877.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	C	13.57	2.278030	0.40294	0.001816	0.006628	ENSG00000150753	ENST00000280326;ENST00000503026;ENST00000515390;ENST00000440011;ENST00000515676;ENST00000506600	T;T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18;-1.18	5.39	3.59	0.41128	.	0.045544	0.85682	D	0.000000	T	0.59959	0.2232	L	0.28014	0.82	0.58432	D	0.999999	B;B;B;B;B;B	0.25772	0.113;0.012;0.134;0.006;0.006;0.006	B;B;B;B;B;B	0.34722	0.188;0.079;0.049;0.049;0.049;0.049	T	0.62286	-0.6886	10	0.45353	T	0.12	-30.4305	9.1905	0.37195	0.0:0.7727:0.0:0.2273	.	269;307;211;360;362;362	B4DYD8;E7ENZ3;B4DZY9;Q9BU08;A8K2X8;P48643	.;.;.;.;.;TCPE_HUMAN	M	362;341;307;335;324;269	ENSP00000280326:I362M;ENSP00000423318:I341M;ENSP00000426923:I307M;ENSP00000427297:I324M;ENSP00000423052:I269M	ENSP00000280326:I362M	I	+	3	3	CCT5	10314764	1.000000	0.71417	0.997000	0.53966	0.985000	0.73830	1.786000	0.38694	1.266000	0.44231	0.558000	0.71614	ATC	C|0.996;G|0.004	0.004	strong		0.478	CCT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253688.2			G	10261764	C	G	10261764	3	3	26	1	0	0	0	0	1	0	0	0	2958	903	32	4	1116	4	CCT5	5	10261764	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	2368759	10261764	170653496	161	9924											
DNAH5	1767	hgsc.bcm.edu	37	chr5	13830749	13830749	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cggaaatccatctggtctgaAcaattgaaaaccacgacgta	15	8	8	10	3	2	2	0	2	2	0	3	4	3	3	2	2	2	1	2	2	6	2	rs368456533		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:13830749A>G	ENST00000265104.4	-	36	6122	c.6018T>C	c.(6016-6018)tgT>tgC	p.C2006C		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2006	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)					TCTGGTCTGAACAATTGAAAA	0.473									Kartagener syndrome																												p.C2006C		Atlas-SNP	.											.	DNAH5	868	.	0			c.T6018C						PASS	.	A		0,4406		0,0,2203	129	126	127		6018	1.7	1	5		127	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	DNAH5	NM_001369.2		0,2,6501	GG,GA,AA		0.0233,0.0,0.0154		2006/4625	13830749	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon36	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GTCTGAACAATTG	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.6018T>C	5.37:g.13830749A>G		107	0	0		110	59	0.536364	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			.	.	weak		0.473	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		G	13830749	A	G	13830749	2	3	26	1	0	0	0	0	0	0	0	1	4606	41	2	3		3	DNAH5	5	13830749	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	3568985	13830749	167084511	162	9925											
MTMR12	54545	hgsc.bcm.edu	37	chr5	32263316	32263316	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acaccagtccttaagtgtgtCaaacattacggtatggttct	11	13	8	9	1	2	0	1	0	1	0	3	0	3	0	2	2	2	2	2	2	4	4	rs61748194	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:32263316C>T	ENST00000382142.3	-	7	786	c.616G>A	c.(616-618)Gac>Aac	p.D206N	MTMR12_ENST00000280285.5_Missense_Mutation_p.D206N|MTMR12_ENST00000264934.5_Missense_Mutation_p.D206N	NM_001040446.1	NP_001035536.1	Q9C0I1	MTMRC_HUMAN	myotubularin related protein 12	206	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.					cytoplasm (GO:0005737)	phosphatase activity (GO:0016791)			breast(3)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						TTAAGTGTGTCAAACATTACG	0.398													C|||	37	0.00738818	0.0008	0.0173	5008	,	,		21370	0.0		0.0219	False		,,,				2504	0.002				p.D206N		Atlas-SNP	.											.	MTMR12	76	.	0			c.G616A						PASS	.	C	ASN/ASP	21,4385	29.0+/-57.7	0,21,2182	274	225	241		616	5.5	1	5	dbSNP_129	241	196,8404	86.1+/-148.5	3,190,4107	yes	missense	MTMR12	NM_001040446.1	23	3,211,6289	TT,TC,CC		2.2791,0.4766,1.6685	possibly-damaging	206/748	32263316	217,12789	2203	4300	6503	SO:0001583	missense	54545	exon7			GTGTGTCAAACAT	AB051469	CCDS34138.1, CCDS75230.1	5p15.33	2011-06-09	2005-04-07	2005-04-07	ENSG00000150712	ENSG00000150712		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"	18191	protein-coding gene	gene with protein product		606501	"phosphatidylinositol-3-phosphate associated protein"	PIP3AP		11504939, 12495846	Standard	XM_005248313		Approved	3-PAP, FLJ20476, KIAA1682, 3PAP	uc003jhq.3	Q9C0I1	OTTHUMG00000161978	ENST00000382142.3:c.616G>A	5.37:g.32263316C>T	ENSP00000371577:p.Asp206Asn	370	1	0.0027027		348	151	0.433908	NM_001040446	Q69YJ4|Q6PFW3|Q96QU2|Q9NX27	Missense_Mutation	SNP	ENST00000382142.3	37	CCDS34138.1	25	0.011446886446886446	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	20	0.026385224274406333	C	19.09	3.760426	0.69763	0.004766	0.022791	ENSG00000150712	ENST00000280285;ENST00000382142;ENST00000264934	D;D;D	0.89681	-2.55;-2.55;-2.55	5.47	5.47	0.80525	Myotubularin phosphatase domain (1);	0.343414	0.29087	N	0.013200	T	0.78233	0.4251	M	0.62723	1.935	0.51767	D	0.999935	P;P;P	0.37370	0.592;0.592;0.457	B;B;B	0.42959	0.403;0.403;0.227	T	0.81867	-0.0735	10	0.19147	T	0.46	.	19.3518	0.94392	0.0:1.0:0.0:0.0	rs61748194	206;206;206	Q9C0I1-3;Q9C0I1-2;Q9C0I1	.;.;MTMRC_HUMAN	N	206	ENSP00000280285:D206N;ENSP00000371577:D206N;ENSP00000264934:D206N	ENSP00000264934:D206N	D	-	1	0	MTMR12	32299073	1.000000	0.71417	1.000000	0.80357	0.790000	0.44656	2.746000	0.47467	2.571000	0.86741	0.650000	0.86243	GAC	C|0.985;T|0.015	0.015	strong		0.398	MTMR12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366579.1	NM_019061		T	32263316	C	T	32263316	3	4	26	1	0	0	0	0	1	0	0	0	9950	826	29	2	1667	2	MTMR12	5	32263316	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	18432567	32263316	148651944	163	9926											
SKP2	6502	hgsc.bcm.edu	37	chr5	36163858	36163858	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	taagaggtggtatcgcctagCgtaagtatttttcacccctt	9	14	9	9	2	1	1	1	0	0	1	2	1	1	1	3	2	1	3	3	2	5	8			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:36163858C>T	ENST00000274255.6	+	3	588	c.392C>T	c.(391-393)gCg>gTg	p.A131V	SKP2_ENST00000274254.5_Splice_Site_p.A131V|SKP2_ENST00000508514.1_Intron|SKP2_ENST00000546211.1_Intron	NM_005983.3	NP_005974.2	Q13309	SKP2_HUMAN	S-phase kinase-associated protein 2, E3 ubiquitin protein ligase	131	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|cellular response to cell-matrix adhesion (GO:0071460)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein polyubiquitination (GO:0000209)|regulation of cell cycle (GO:0051726)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)	identical protein binding (GO:0042802)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(2)|ovary(1)	4	all_lung(31;5.63e-05)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TATCGCCTAGCGTAAGTATTT	0.458																																					p.A131V		Atlas-SNP	.											.	SKP2	70	.	0			c.C392T						PASS	.						118	101	107					5																	36163858		2203	4300	6503	SO:0001630	splice_region_variant	6502	exon3			GCCTAGCGTAAGT	U33761	CCDS3915.1, CCDS3916.1, CCDS58944.1	5p13	2012-02-23	2012-02-23		ENSG00000145604	ENSG00000145604		"F-boxes / Leucine-rich repeats"	10901	protein-coding gene	gene with protein product		601436	"S-phase kinase-associated protein 2 (p45)"			8646875	Standard	NM_005983		Approved	FBXL1, FBL1, p45	uc003jkc.2	Q13309	OTTHUMG00000131106	ENST00000274255.6:c.392+1C>T	5.37:g.36163858C>T		173	0	0		185	95	0.513514	NM_032637	A8K5E0|B4DJT4|Q8TDZ0|Q8TDZ1|Q9BV69	Missense_Mutation	SNP	ENST00000274255.6	37	CCDS3916.1	.	.	.	.	.	.	.	.	.	.	C	14.54	2.565020	0.45694	.	.	ENSG00000145604	ENST00000274254;ENST00000274255;ENST00000308927;ENST00000513151	T;T;T	0.55930	0.49;0.49;0.49	4.92	4.05	0.47172	F-box domain, cyclin-like (2);F-box domain, Skp2-like (1);	0.382188	0.30723	N	0.009015	T	0.37376	0.1001	N	0.24115	0.695	0.80722	D	1	B;B	0.23806	0.059;0.091	B;B	0.09377	0.003;0.004	T	0.31223	-0.9951	10	0.72032	D	0.01	-7.66	11.5359	0.50636	0.0:0.9161:0.0:0.0839	.	131;131	Q13309-2;Q13309	.;SKP2_HUMAN	V	131;131;97;131	ENSP00000274254:A131V;ENSP00000274255:A131V;ENSP00000423188:A131V	ENSP00000274254:A131V	A	+	2	0	SKP2	36199615	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.113000	0.57851	1.437000	0.47472	0.650000	0.86243	GCG	.	.	none		0.458	SKP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253769.2	NM_005983	Missense_Mutation	T	36163858	C	T	36163858	5	4	26	1	0	0	0	0	0	0	1	0	14377	782	27	1	402	1	SKP2	5	36163858	Splice_Site	SNP	C	TCGA-G8-6907-01A-11D-2210-10	3900542	36163858	144751402	164	9927											
IL6ST	3572	hgsc.bcm.edu	37	chr5	55248135	55248135	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcctggtccatcagcatataCtggagtaactgttatcaaat	12	13	7	9	0	2	0	2	0	0	0	4	1	4	1	2	2	3	3	2	2	5	4	rs34417936	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:55248135C>T	ENST00000381298.2	-	12	1807	c.1495G>A	c.(1495-1497)Gta>Ata	p.V499I	IL6ST_ENST00000381286.3_Intron|IL6ST_ENST00000536319.1_3'UTR|IL6ST_ENST00000522633.2_3'UTR|IL6ST_ENST00000381287.4_3'UTR|IL6ST_ENST00000336909.5_Missense_Mutation_p.V499I|IL6ST_ENST00000502326.3_Missense_Mutation_p.V499I|IL6ST_ENST00000381294.3_Missense_Mutation_p.V438I|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	499	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.		V -> I (in dbSNP:rs34417936).		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)				TCAGCATATACTGGAGTAACT	0.363			O		hepatocellular ca								C|||	54	0.0107827	0.003	0.0259	5008	,	,		18030	0.0		0.0258	False		,,,				2504	0.0061				p.V499I		Atlas-SNP	.		Dom	yes		5	5q11	3572	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"		E	.	IL6ST	75	.	0			c.G1495A						PASS	.	C	ILE/VAL,ILE/VAL,	25,4381	29.9+/-59.1	0,25,2178	97	94	95		1312,1495,	5.9	0.8	5	dbSNP_126	95	259,8341	101.0+/-162.3	4,251,4045	yes	missense,missense,utr-3	IL6ST	NM_001190981.1,NM_002184.3,NM_175767.2	29,29,	4,276,6223	TT,TC,CC		3.0116,0.5674,2.1836	benign,benign,	438/858,499/919,	55248135	284,12722	2203	4300	6503	SO:0001583	missense	3572	exon12			CATATACTGGAGT	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.1495G>A	5.37:g.55248135C>T	ENSP00000370698:p.Val499Ile	144	0	0		113	59	0.522124	NM_002184	A0N0L4|Q5FC04|Q9UQ41	Missense_Mutation	SNP	ENST00000381298.2	37	CCDS3971.1	30	0.013736263736263736	2	0.0040650406504065045	14	0.03867403314917127	0	0.0	14	0.018469656992084433	C	11.85	1.761705	0.31228	0.005674	0.030116	ENSG00000134352	ENST00000381298;ENST00000336909;ENST00000381294	T;T;T	0.55234	0.53;0.53;1.12	5.93	5.93	0.95920	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.131931	0.53938	D	0.000041	T	0.11623	0.0283	L	0.31926	0.97	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	0.07578	-1.0765	10	0.12766	T	0.61	.	10.6199	0.45474	0.1248:0.6405:0.2347:0.0	rs34417936	499;438;499	Q17RA0;Q5FC04;P40189	.;.;IL6RB_HUMAN	I	499;499;438	ENSP00000370698:V499I;ENSP00000338799:V499I;ENSP00000370694:V438I	ENSP00000338799:V499I	V	-	1	0	IL6ST	55283892	0.919000	0.31177	0.836000	0.33094	0.996000	0.88848	0.610000	0.24253	2.826000	0.97356	0.655000	0.94253	GTA	C|0.980;T|0.020	0.020	strong		0.363	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184		T	55248135	C	T	55248135	3	4	26	1	0	0	0	0	1	0	0	0	7712	565	20	2	1285	2	IL6ST	5	55248135	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	19084277	55248135	125667125	165	9928											
MAP3K1	4214	hgsc.bcm.edu	37	chr5	56177843	56177843	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cagcatttcagtaggaccttCtagttcaacaacaacaacaa	16	9	5	11	0	3	0	2	0	1	0	3	1	3	1	1	1	5	3	1	1	7	5	rs45556841	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:56177843C>G	ENST00000399503.3	+	14	2816	c.2816C>G	c.(2815-2817)tCt>tGt	p.S939C		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	939					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)		GTAGGACCTTCTAGTTcaaca	0.423													C|||	37	0.00738818	0.0015	0.0259	5008	,	,		20934	0.0		0.0139	False		,,,				2504	0.0031				p.S939C		Atlas-SNP	.											.	MAP3K1	355	.	0			c.C2816G						PASS	.	C	CYS/SER	20,3788		0,20,1884	73	70	71		2816	3.9	1	5	dbSNP_127	71	191,8093		5,181,3956	yes	missense	MAP3K1	NM_005921.1	112	5,201,5840	GG,GC,CC		2.3056,0.5252,1.745	benign	939/1513	56177843	211,11881	1904	4142	6046	SO:0001583	missense	4214	exon14			GACCTTCTAGTTC	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.2816C>G	5.37:g.56177843C>G	ENSP00000382423:p.Ser939Cys	146	0	0		139	75	0.539568	NM_005921		Missense_Mutation	SNP	ENST00000399503.3	37	CCDS43318.1	23	0.010531135531135532	1	0.0020325203252032522	13	0.03591160220994475	0	0.0	9	0.011873350923482849	C	11.21	1.571845	0.28003	0.005252	0.023056	ENSG00000095015	ENST00000399503	T	0.32272	1.46	5.71	3.87	0.44632	.	0.150855	0.47093	D	0.000259	T	0.04182	0.0116	N	0.08118	0	0.26331	N	0.977519	B	0.24368	0.102	B	0.27262	0.078	T	0.15578	-1.0432	10	0.87932	D	0	.	13.0984	0.59206	0.1278:0.7495:0.1227:0.0	rs45556841	939	Q13233	M3K1_HUMAN	C	939	ENSP00000382423:S939C	ENSP00000382423:S939C	S	+	2	0	MAP3K1	56213600	0.989000	0.36119	0.986000	0.45419	0.965000	0.64279	2.061000	0.41403	1.414000	0.47017	0.655000	0.94253	TCT	C|0.985;G|0.015	0.015	strong		0.423	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066		G	56177843	C	G	56177843	3	3	26	1	0	0	0	0	1	0	0	0	9252	913	32	4	2870	4	MAP3K1	5	56177843	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	929708	56177843	124737417	166	9929											
DMGDH	29958	hgsc.bcm.edu	37	chr5	78338202	78338202	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgataggaccattgacaacaTtgatgatgtcagcctttttc	11	14	8	8	0	1	4	1	4	0	0	2	5	1	5	2	1	2	0	2	1	2	5	rs77116243	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:78338202T>C	ENST00000255189.3	-	7	1125	c.1097A>G	c.(1096-1098)aAt>aGt	p.N366S	DMGDH_ENST00000380311.4_Missense_Mutation_p.N165S|DMGDH_ENST00000540686.1_Intron	NM_013391.2	NP_037523.2	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase	366					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)		ATTGACAACATTGATGATGTC	0.458													T|||	38	0.00758786	0.0	0.0072	5008	,	,		18599	0.0		0.0179	False		,,,				2504	0.0153				p.N366S		Atlas-SNP	.											.	DMGDH	88	.	0			c.A1097G						PASS	.	T	SER/ASN	8,4398	12.9+/-30.5	0,8,2195	128	117	120		1097	3	0.5	5	dbSNP_131	120	112,8488	61.0+/-122.8	1,110,4189	yes	missense	DMGDH	NM_013391.2	46	1,118,6384	CC,CT,TT		1.3023,0.1816,0.9227	benign	366/867	78338202	120,12886	2203	4300	6503	SO:0001583	missense	29958	exon7			ACAACATTGATGA	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.1097A>G	5.37:g.78338202T>C	ENSP00000255189:p.Asn366Ser	177	0	0		204	96	0.470588	NM_013391	B2RBN0|B4E1J9	Missense_Mutation	SNP	ENST00000255189.3	37	CCDS4044.1	20	0.009157509157509158	0	0.0	4	0.011049723756906077	0	0.0	16	0.021108179419525065	T	11.11	1.541978	0.27563	0.001816	0.013023	ENSG00000132837	ENST00000255189;ENST00000523732;ENST00000380311;ENST00000539598	T;T;T	0.80824	-1.42;-1.42;-1.42	5.44	3.01	0.34805	FAD dependent oxidoreductase (1);	0.194937	0.52532	D	0.000068	T	0.33644	0.0870	N	0.01649	-0.78	0.80722	D	1	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.09377	0.004;0.002;0.002	T	0.15235	-1.0444	10	0.10377	T	0.69	.	8.0518	0.30583	0.0:0.0714:0.1365:0.7921	.	165;216;366	F8W6P8;F5H1C7;Q9UI17	.;.;M2GD_HUMAN	S	366;205;165;216	ENSP00000255189:N366S;ENSP00000430972:N205S;ENSP00000369667:N165S	ENSP00000255189:N366S	N	-	2	0	DMGDH	78373958	1.000000	0.71417	0.481000	0.27354	0.903000	0.53119	3.289000	0.51747	0.366000	0.24427	0.529000	0.55759	AAT	T|0.990;C|0.010	0.010	strong		0.458	DMGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226963.3	NM_013391		C	78338202	T	C	78338202	3	2	26	1	0	0	0	0	1	0	0	0	4583	1493	52	3	1543	3	DMGDH	5	78338202	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	22160359	78338202	102577058	167	9930											
THBS4	7060	hgsc.bcm.edu	37	chr5	79374957	79374957	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccagacagatgatgactatgCaggctttatctttggctacc	10	12	9	10	0	1	4	0	2	1	2	1	4	1	4	2	2	2	3	2	2	3	5			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:79374957C>T	ENST00000350881.2	+	19	2577	c.2387C>T	c.(2386-2388)gCa>gTa	p.A796V	THBS4_ENST00000504720.1_3'UTR|THBS4_ENST00000511733.1_Missense_Mutation_p.A705V|CTD-2201I18.1_ENST00000514042.1_RNA|CTD-2201I18.1_ENST00000503007.1_RNA	NM_003248.4	NP_003239.2	P35443	TSP4_HUMAN	thrombospondin 4	796	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				behavioral response to pain (GO:0048266)|endothelial cell-cell adhesion (GO:0071603)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|positive regulation of cell division (GO:0051781)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of tissue remodeling (GO:0034103)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)|tissue remodeling (GO:0048771)	basement membrane (GO:0005604)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)|integrin binding (GO:0005178)			breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|stomach(3)	34		Lung NSC(167;0.00328)|all_lung(232;0.00355)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-45)|Epithelial(54;1.77e-39)|all cancers(79;3.2e-34)		GATGACTATGCAGGCTTTATC	0.473																																					p.A796V		Atlas-SNP	.											.	THBS4	82	.	0			c.C2387T						PASS	.						138	128	131					5																	79374957		2203	4300	6503	SO:0001583	missense	7060	exon19			ACTATGCAGGCTT		CCDS4049.1	5q13	2008-05-15			ENSG00000113296	ENSG00000113296			11788	protein-coding gene	gene with protein product		600715				7852353	Standard	NM_003248		Approved		uc021yaw.1	P35443	OTTHUMG00000108173	ENST00000350881.2:c.2387C>T	5.37:g.79374957C>T	ENSP00000339730:p.Ala796Val	207	0	0		229	125	0.545852	NM_003248	B2R909|Q86TG2	Missense_Mutation	SNP	ENST00000350881.2	37	CCDS4049.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.987130	0.93106	.	.	ENSG00000113296	ENST00000350881;ENST00000511733	D;D	0.94280	-3.39;-3.39	5.06	5.06	0.68205	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.91181	0.7222	N	0.16478	0.41	0.80722	D	1	D	0.71674	0.998	P	0.53266	0.722	D	0.89639	0.3861	10	0.25751	T	0.34	-23.1552	18.977	0.92742	0.0:1.0:0.0:0.0	.	796	P35443	TSP4_HUMAN	V	796;705	ENSP00000339730:A796V;ENSP00000422298:A705V	ENSP00000339730:A796V	A	+	2	0	THBS4	79410713	1.000000	0.71417	0.858000	0.33744	0.991000	0.79684	7.609000	0.82925	2.782000	0.95742	0.655000	0.94253	GCA	.	.	none		0.473	THBS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226977.1			T	79374957	C	T	79374957	3	4	26	1	0	0	0	0	1	0	0	0	15871	710	25	2	2461	2	THBS4	5	79374957	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1036755	79374957	101540303	168	9931											
MSH3	4437	hgsc.bcm.edu	37	chr5	80109479	80109479	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctacataaaacaagttgcatTgattaccatcatggctcaga	15	11	6	9	0	2	2	2	1	0	1	2	2	2	2	1	1	4	3	1	1	5	5	rs41545019	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:80109479T>G	ENST00000265081.6	+	20	2812	c.2732T>G	c.(2731-2733)tTg>tGg	p.L911W		NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	911					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)		CAAGTTGCATTGATTACCATC	0.413								Mismatch excision repair (MMR)					T|||	5	0.000998403	0.0	0.0014	5008	,	,		18784	0.0		0.004	False		,,,				2504	0.0				p.L911W	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											.	MSH3	129	.	0			c.T2732G						PASS	.	T	TRP/LEU	2,4404	4.2+/-10.8	0,2,2201	192	187	188		2732	5.6	0.2	5	dbSNP_127	188	41,8559	27.4+/-76.7	0,41,4259	yes	missense	MSH3	NM_002439.3	61	0,43,6460	GG,GT,TT		0.4767,0.0454,0.3306	probably-damaging	911/1138	80109479	43,12963	2203	4300	6503	SO:0001583	missense	4437	exon20			TTGCATTGATTAC	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.2732T>G	5.37:g.80109479T>G	ENSP00000265081:p.Leu911Trp	196	1	0.00510204		229	120	0.524017	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	37	CCDS34195.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	17.41	3.383061	0.61845	4.54E-4	0.004767	ENSG00000113318	ENST00000265081;ENST00000535995	D	0.88896	-2.44	5.57	5.57	0.84162	DNA mismatch repair protein MutS, C-terminal (2);	0.000000	0.64402	D	0.000001	D	0.95968	0.8687	H	0.94698	3.57	0.47245	D	0.999368	D	0.89917	1.0	D	0.72625	0.978	D	0.97127	0.9815	9	.	.	.	-4.0755	15.7269	0.77766	0.0:0.0:0.0:1.0	rs41545019;rs61749610	911	P20585	MSH3_HUMAN	W	911;902	ENSP00000265081:L911W	.	L	+	2	0	MSH3	80145235	1.000000	0.71417	0.203000	0.23512	0.261000	0.26267	8.032000	0.88838	2.123000	0.65237	0.482000	0.46254	TTG	T|0.997;G|0.003	0.003	strong		0.413	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		G	80109479	T	G	80109479	3	3	26	1	0	0	0	0	1	0	0	0	9880	1821	63	5	2810	5	MSH3	5	80109479	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	734522	80109479	100805781	169	9932											
VDAC1	7416	hgsc.bcm.edu	37	chr5	133328003	133328003	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttggacaacttaccaatccAttctcagattttgttttcaa	11	16	5	9	0	2	1	2	0	1	1	4	2	3	2	2	1	2	2	2	1	4	7	rs142141751	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:133328003A>G	ENST00000265333.3	-	3	355	c.111T>C	c.(109-111)aaT>aaC	p.N37N	VDAC1_ENST00000395044.3_Silent_p.N37N|VDAC1_ENST00000466080.1_5'UTR|VDAC1_ENST00000395047.2_Silent_p.N37N	NM_003374.2	NP_003365.1	P21796	VDAC1_HUMAN	voltage-dependent anion channel 1	37					anion transport (GO:0006820)|apoptotic process (GO:0006915)|behavioral fear response (GO:0001662)|epithelial cell differentiation (GO:0030855)|learning (GO:0007612)|neuron-neuron synaptic transmission (GO:0007270)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|pore complex (GO:0046930)	porin activity (GO:0015288)|protein kinase binding (GO:0019901)|voltage-gated anion channel activity (GO:0008308)			endometrium(1)|large_intestine(1)|lung(1)|skin(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00806)|Kidney(363;0.02)		Dihydroxyaluminium(DB01375)	TTACCAATCCATTCTCAGATT	0.308													A|||	2	0.000399361	0.0	0.0	5008	,	,		16993	0.0		0.002	False		,,,				2504	0.0				p.N37N	NSCLC(127;1776 1806 35523 41489 48154)	Atlas-SNP	.											.	VDAC1	17	.	0			c.T111C						PASS	.	A		5,4399	8.1+/-20.4	0,5,2197	48	48	48		111	4.4	1	5	dbSNP_134	48	25,8575	18.5+/-59.3	0,25,4275	no	coding-synonymous	VDAC1	NM_003374.2		0,30,6472	GG,GA,AA		0.2907,0.1135,0.2307		37/284	133328003	30,12974	2202	4300	6502	SO:0001819	synonymous_variant	7416	exon3			CAATCCATTCTCA		CCDS4168.1	5q31	2011-11-15			ENSG00000213585	ENSG00000213585		"Voltage-dependent anion channels"	12669	protein-coding gene	gene with protein product		604492				7517385	Standard	NM_003374		Approved	MGC111064, PORIN	uc003kyr.2	P21796	OTTHUMG00000129118	ENST00000265333.3:c.111T>C	5.37:g.133328003A>G		153	0	0		156	75	0.480769	NM_003374	B3KVK4|D3DQ93|Q5FVE7|Q9UIQ5|Q9UPL0	Silent	SNP	ENST00000265333.3	37	CCDS4168.1																																																																																			A|0.997;G|0.003	0.003	strong		0.308	VDAC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259208.1			G	133328003	A	G	133328003	2	3	26	1	0	0	0	0	0	0	0	1	17161	214	8	3		3	VDAC1	5	133328003	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	53218524	133328003	47587257	170	9933											
CATSPER3	347732	hgsc.bcm.edu	37	chr5	134332143	134332143	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agttcacttacctgtatatcGctgatggcatgcagtccctg	8	13	9	11	1	1	1	1	1	0	0	3	1	2	1	2	1	2	5	2	1	3	4	rs114447625	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:134332143G>A	ENST00000282611.6	+	3	519	c.433G>A	c.(433-435)Gct>Act	p.A145T		NM_178019.2	NP_821138.1	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	145					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)			CCTGTATATCGCTGATGGCAT	0.547													G|||	43	0.00858626	0.0008	0.0101	5008	,	,		20081	0.0		0.0258	False		,,,				2504	0.0092				p.A145T		Atlas-SNP	.											.	CATSPER3	38	.	0			c.G433A						PASS	.	G	THR/ALA	20,4386	27.2+/-55.0	0,20,2183	135	117	123		433	4.1	0	5	dbSNP_132	123	264,8336	102.9+/-164.1	6,252,4042	yes	missense	CATSPER3	NM_178019.2	58	6,272,6225	AA,AG,GG		3.0698,0.4539,2.1836	probably-damaging	145/399	134332143	284,12722	2203	4300	6503	SO:0001583	missense	347732	exon3			TATATCGCTGATG	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.433G>A	5.37:g.134332143G>A	ENSP00000282611:p.Ala145Thr	107	0	0		113	54	0.477876	NM_178019	Q86XS6	Missense_Mutation	SNP	ENST00000282611.6	37	CCDS4181.1	24	0.01098901098901099	0	0.0	3	0.008287292817679558	0	0.0	21	0.027704485488126648	G	13.19	2.164341	0.38217	0.004539	0.030698	ENSG00000152705	ENST00000282611	D	0.98550	-4.99	4.14	4.14	0.48551	Ion transport (1);	0.256502	0.27886	N	0.017445	D	0.91676	0.7369	M	0.63843	1.955	0.09310	N	1	P	0.51537	0.946	B	0.41174	0.349	D	0.88435	0.3038	10	0.66056	D	0.02	-7.0009	12.2204	0.54431	0.0:0.0:1.0:0.0	.	145	Q86XQ3	CTSR3_HUMAN	T	145	ENSP00000282611:A145T	ENSP00000282611:A145T	A	+	1	0	CATSPER3	134360042	0.001000	0.12720	0.008000	0.14137	0.158000	0.22134	1.002000	0.29796	2.587000	0.87381	0.561000	0.74099	GCT	G|0.981;A|0.019	0.019	strong		0.547	CATSPER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251191.2	NM_178019		A	134332143	G	A	134332143	3	1	26	1	0	0	0	0	1	0	0	0	2691	1087	38	1	443	1	CATSPER3	5	134332143	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1004140	134332143	46583117	171	9934											
KDM3B	51780	hgsc.bcm.edu	37	chr5	137754808	137754808	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agacagttcggcatcaaataGcaatagtgaactgaaagcca	17	7	9	8	1	1	3	1	2	0	1	2	3	1	3	1	1	3	3	1	1	6	3	rs7706614	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:137754808G>A	ENST00000314358.5	+	14	3802	c.3602G>A	c.(3601-3603)aGc>aAc	p.S1201N	KDM3B_ENST00000508386.1_3'UTR|KDM3B_ENST00000542866.1_Missense_Mutation_p.S233N|KDM3B_ENST00000394866.1_Missense_Mutation_p.S857N	NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	1201			S -> N (in dbSNP:rs7706614).		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						GCATCAAATAGCAATAGTGAA	0.532													G|||	299	0.0597045	0.0764	0.0187	5008	,	,		17731	0.0208		0.0318	False		,,,				2504	0.135				p.S1201N		Atlas-SNP	.											.	KDM3B	177	.	0			c.G3602A						PASS	.	G	ASN/SER	242,4164	143.1+/-178.2	8,226,1969	83	78	79		3602	5.6	1	5	dbSNP_116	79	279,8321	104.8+/-165.8	4,271,4025	yes	missense	KDM3B	NM_016604.3	46	12,497,5994	AA,AG,GG		3.2442,5.4925,4.0058	benign	1201/1762	137754808	521,12485	2203	4300	6503	SO:0001583	missense	51780	exon14			CAAATAGCAATAG	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.3602G>A	5.37:g.137754808G>A	ENSP00000326563:p.Ser1201Asn	239	0	0		289	142	0.491349	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Missense_Mutation	SNP	ENST00000314358.5	37	CCDS34242.1	84	0.038461538461538464	39	0.07926829268292683	6	0.016574585635359115	10	0.017482517482517484	29	0.03825857519788918	G	13.74	2.328710	0.41197	0.054925	0.032442	ENSG00000120733	ENST00000314358;ENST00000545151;ENST00000394866;ENST00000542866	T;T;T	0.71341	0.03;-0.56;-0.54	5.63	5.63	0.86233	.	0.216515	0.56097	D	0.000039	T	0.06050	0.0157	L	0.27053	0.805	0.39818	D	0.972792	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.13791	-1.0496	10	0.19147	T	0.46	-5.3037	13.3783	0.60752	0.0814:0.0:0.9186:0.0	rs7706614;rs17460129;rs56548578;rs57723304;rs7706614	857;1201	Q7LBC6-2;Q7LBC6	.;KDM3B_HUMAN	N	1201;991;857;233	ENSP00000326563:S1201N;ENSP00000378335:S857N;ENSP00000439462:S233N	ENSP00000326563:S1201N	S	+	2	0	KDM3B	137782707	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.336000	0.52113	2.665000	0.90641	0.650000	0.86243	AGC	G|0.953;A|0.047	0.047	strong		0.532	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604		A	137754808	G	A	137754808	3	1	26	1	0	0	0	0	1	0	0	0	8136	971	34	2	3656	2	KDM3B	5	137754808	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	3422665	137754808	43160452	172	9935											
KDM3B	51780	hgsc.bcm.edu	37	chr5	137766066	137766066	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgcaaggctgggctattgtGcagttcctaggtgatgctgt	6	13	15	7	0	0	1	0	1	0	0	1	1	1	1	1	3	3	6	1	3	3	4	rs61749634	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:137766066G>A	ENST00000314358.5	+	22	5222	c.5022G>A	c.(5020-5022)gtG>gtA	p.V1674V	KDM3B_ENST00000542866.1_Silent_p.V706V|KDM3B_ENST00000394866.1_Silent_p.V1330V	NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	1674	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						GGGCTATTGTGCAGTTCCTAG	0.532																																					p.V1674V		Atlas-SNP	.											.	KDM3B	177	.	0			c.G5022A						PASS	.	G		242,4164	143.1+/-178.2	8,226,1969	161	147	152		5022	3.9	1	5	dbSNP_129	152	279,8321	104.8+/-165.8	4,271,4025	yes	coding-synonymous	KDM3B	NM_016604.3		12,497,5994	AA,AG,GG		3.2442,5.4925,4.0058		1674/1762	137766066	521,12485	2203	4300	6503	SO:0001819	synonymous_variant	51780	exon22			TATTGTGCAGTTC	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.5022G>A	5.37:g.137766066G>A		169	0	0		184	95	0.516304	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Silent	SNP	ENST00000314358.5	37	CCDS34242.1																																																																																			A|0.040;C|0.000;G|0.960;T|0.000	0.040	strong		0.532	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604		A	137766066	G	A	137766066	2	1	26	1	0	0	0	0	0	0	0	1	8136	1306	46	2		2	KDM3B	5	137766066	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	11258	137766066	43149194	173	9936											
PAIP2	51247	hgsc.bcm.edu	37	chr5	138700404	138700404	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttaatgaccttgttatcaGtgatggctcttctctggaag	8	16	10	7	0	3	2	1	2	2	0	4	3	3	3	1	2	0	3	1	2	3	5	rs151194423	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:138700404G>A	ENST00000394795.2	+	3	1281	c.290G>A	c.(289-291)aGt>aAt	p.S97N	PAIP2_ENST00000511706.1_Intron|PAIP2_ENST00000510080.1_Missense_Mutation_p.S97N|PAIP2_ENST00000511381.1_3'UTR|CTB-43P18.1_ENST00000503553.3_RNA|PAIP2_ENST00000265192.4_Missense_Mutation_p.S97N			Q9BPZ3	PAIP2_HUMAN	poly(A) binding protein interacting protein 2	97					memory (GO:0007613)|negative regulation of translational initiation (GO:0045947)|regulation of long-term synaptic potentiation (GO:1900271)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mRNA binding (GO:0003729)|translation repressor activity (GO:0030371)			kidney(1)|large_intestine(2)|lung(2)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CTTGTTATCAGTGATGGCTCT	0.398													G|||	2	0.000399361	0.0	0.0029	5008	,	,		20179	0.0		0.0	False		,,,				2504	0.0				p.S97N		Atlas-SNP	.											.	PAIP2	10	.	0			c.G290A						PASS	.						108	94	99					5																	138700404		2203	4300	6503	SO:0001583	missense	51247	exon3			TTATCAGTGATGG	AF151052	CCDS4211.1	5q32	2008-02-05			ENSG00000120727	ENSG00000120727			17970	protein-coding gene	gene with protein product		605604				11172725, 16804161	Standard	NM_016480		Approved	PAIP2A	uc003led.3	Q9BPZ3	OTTHUMG00000129227	ENST00000394795.2:c.290G>A	5.37:g.138700404G>A	ENSP00000378275:p.Ser97Asn	123	0	0		143	66	0.461538	NM_001033112	B2RBI1|D3DQC6|Q49A06|Q9H0Y5|Q9P0Q8	Missense_Mutation	SNP	ENST00000394795.2	37	CCDS4211.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	G	13.16	2.153214	0.38021	.	.	ENSG00000120727	ENST00000265192;ENST00000394795;ENST00000510080	.	.	.	5.93	3.13	0.36017	.	0.483405	0.25916	N	0.027466	T	0.27629	0.0679	L	0.34521	1.04	0.35331	D	0.785643	B	0.02656	0.0	B	0.01281	0.0	T	0.22034	-1.0228	8	.	.	.	-10.2094	6.1013	0.20049	0.2021:0.2583:0.5396:0.0	.	97	Q9BPZ3	PAIP2_HUMAN	N	97	.	.	S	+	2	0	PAIP2	138728303	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.347000	0.44036	0.381000	0.24851	-0.165000	0.13383	AGT	G|0.999;A|0.001	0.001	strong		0.398	PAIP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373002.1	NM_016480		A	138700404	G	A	138700404	3	1	26	1	0	0	0	0	1	0	0	0	11406	1029	36	2	296	2	PAIP2	5	138700404	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	934338	138700404	42214856	174	9937											
PCDHA4	56144	hgsc.bcm.edu	37	chr5	140188353	140188353	+	Silent	SNP	G	G	A																															cagccgctggaccacgaggaGctagagctgctgcagtttca																								rs561061447	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140188353G>A	ENST00000530339.1	+	1	1581	c.1581G>A	c.(1579-1581)gaG>gaA	p.E527E	PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000356878.4_Silent_p.E527E|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Silent_p.E527E	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	527	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)			ACCACGAGGAGCTAGAGCTGC	0.652													.|||	115	0.0229633	0.003	0.0389	5008	,	,		17480	0.0		0.0755	False		,,,				2504	0.0082				p.E527E		Atlas-SNP	.											.	PCDHA4	419	.	0			c.G1581A						PASS	.						71	76	74					5																	140188353		2203	4300	6503	SO:0001819	synonymous_variant	56144	exon1			CGAGGAGCTAGAG	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.1581G>A	5.37:g.140188353G>A		107	0	0		58	15	0.258621	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			.	.	none		0.652	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		A	140188353	G	A	140188353	2	1	26	1	0	0	0	0	0	0	0	1	11535	962	34	2		2	PCDHA4	5	140188353	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1487949	140188353	40726907	175	9938	123	3									
PCDHA4	56144	hgsc.bcm.edu	37	chr5	140188354	140188354	+	Missense_Mutation	SNP	C	C	G																															agccgctggaccacgaggagCtagagctgctgcagtttcag																								rs142480630	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140188354C>G	ENST00000530339.1	+	1	1582	c.1582C>G	c.(1582-1584)Cta>Gta	p.L528V	PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000356878.4_Missense_Mutation_p.L528V|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Missense_Mutation_p.L528V	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	528	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)			CCACGAGGAGCTAGAGCTGCT	0.652													.|||	115	0.0229633	0.003	0.0389	5008	,	,		17618	0.0		0.0755	False		,,,				2504	0.0082				p.L528V		Atlas-SNP	.											PCDHA4_ENST00000530339,NS,carcinoma,0,8	PCDHA4	419	8	0			c.C1582G						scavenged	.						70	75	74					5																	140188354		2203	4300	6503	SO:0001583	missense	56144	exon1			GAGGAGCTAGAGC	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.1582C>G	5.37:g.140188354C>G	ENSP00000435300:p.Leu528Val	107	1	0.00934579		56	13	0.232143	NM_031500	O75285|Q2M253	Missense_Mutation	SNP	ENST00000530339.1	37	CCDS54916.1	.	.	.	.	.	.	.	.	.	.	c	11.23	1.577307	0.28092	.	.	ENSG00000204967	ENST00000512229;ENST00000356878;ENST00000530339	T;T;T	0.51325	0.71;0.71;0.71	4.18	2.19	0.27852	Cadherin (5);Cadherin-like (1);	0.000000	0.28952	U	0.013601	T	0.34948	0.0915	N	0.25332	0.735	0.20764	N	0.999854	P;B;B	0.43662	0.814;0.101;0.207	B;B;B	0.43508	0.422;0.421;0.214	T	0.15150	-1.0447	10	0.51188	T	0.08	.	8.8809	0.35374	0.2588:0.4914:0.2498:0.0	.	528;528;528	Q9UN74-2;Q9UN74;D6RA20	.;PCDA4_HUMAN;.	V	528	ENSP00000423470:L528V;ENSP00000349344:L528V;ENSP00000435300:L528V	ENSP00000349344:L528V	L	+	1	2	PCDHA4	140168538	0.000000	0.05858	1.000000	0.80357	0.984000	0.73092	-1.847000	0.01675	0.874000	0.35823	0.580000	0.79431	CTA	C|0.999;G|0.001	0.001	weak		0.652	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		G	140188354	C	G	140188354	3	3	26	1	0	0	0	0	1	0	0	0	11535	796	28	4	1584	4	PCDHA4	5	140188354	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1	140188354	40726906	176	9939	123	3									
PCDHA4	56144	hgsc.bcm.edu	37	chr5	140188356	140188356	+	Silent	SNP	A	A	G																															ccgctggaccacgaggagctAgagctgctgcagtttcaggt																								rs144593807	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140188356A>G	ENST00000530339.1	+	1	1584	c.1584A>G	c.(1582-1584)ctA>ctG	p.L528L	PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000356878.4_Silent_p.L528L|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Silent_p.L528L	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	528	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)			ACGAGGAGCTAGAGCTGCTGC	0.652													.|||	115	0.0229633	0.003	0.0389	5008	,	,		17817	0.0		0.0755	False		,,,				2504	0.0082				p.L528L		Atlas-SNP	.											PCDHA4_ENST00000530339,NS,carcinoma,+2,8	PCDHA4	419	8	0			c.A1584G						scavenged	.	A	,,,,,	11,4395		0,11,2192	70	75	73		,,,1584,,1584	1.3	1	5	dbSNP_134	73	57,8543		9,39,4252	no	intron,intron,intron,coding-synonymous,intron,coding-synonymous	PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_031411.1,NM_031500.1	,,,,,	9,50,6444	GG,GA,AA		0.6628,0.2497,0.5228	,,,,,	,,,528/948,,528/799	140188356	68,12938	2203	4300	6503	SO:0001819	synonymous_variant	56144	exon1			GGAGCTAGAGCTG	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.1584A>G	5.37:g.140188356A>G		107	0	0		60	15	0.25	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			A|0.976;G|0.024	0.024	strong		0.652	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		G	140188356	A	G	140188356	2	3	26	1	0	0	0	0	0	0	0	1	11535	407	15	3		3	PCDHA4	5	140188356	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	2	140188356	40726904	177	9940	123	3									
PCDHA10	56139	hgsc.bcm.edu	37	chr5	140237158	140237158	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cgctgtcgagctacgtgtcgGtgcacgcggagagcggcaag	7	6	17	11	7	0	1	0	0	0	1	2	3	0	1	0	3	4	4	0	3	2	1	rs142356019	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140237158G>A	ENST00000307360.5	+	1	1525	c.1525G>A	c.(1525-1527)Gtg>Atg	p.V509M	PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|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|PCDHA10_ENST00000506939.2_Missense_Mutation_p.V509M|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	509	Cadherin 5. {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)			CTACGTGTCGGTGCACGCGGA	0.697													.|||	119	0.023762	0.0121	0.0346	5008	,	,		14546	0.0		0.0716	False		,,,				2504	0.0072				p.V509M		Atlas-SNP	.											.	PCDHA10	358	.	0			c.G1525A						PASS	.	G	,MET/VAL,,,,,,,,,,,MET/VAL,MET/VAL	120,4272		4,112,2080	66	73	71		,1525,,,,,,,,,,,1525,1525	3.6	1	5	dbSNP_134	71	477,8069		47,383,3843	no	intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,missense	PCDHA9,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031859.1,NM_031860.1	,21,,,,,,,,,,,21,21	51,495,5923	AA,AG,GG		5.5816,2.7322,4.6143	,,,,,,,,,,,,,	,509/949,,,,,,,,,,,509/845,509/686	140237158	597,12341	2196	4273	6469	SO:0001583	missense	56139	exon1			GTGTCGGTGCACG	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.1525G>A	5.37:g.140237158G>A	ENSP00000304234:p.Val509Met	202	0	0		123	66	0.536585	NM_031859	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	37	CCDS54921.1	87	0.03983516483516483	9	0.018292682926829267	19	0.052486187845303865	0	0.0	59	0.07783641160949868	G	14.28	2.487603	0.44249	0.027322	0.055816	ENSG00000250120	ENST00000506939;ENST00000307360	T;T	0.67698	-0.28;-0.28	3.63	3.63	0.41609	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.17323	0.0416	M	0.64404	1.975	0.43489	P	0.004271000000000025	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.993	T	0.65446	-0.6166	8	0.59425	D	0.04	.	9.6727	0.40021	0.0974:0.0:0.9026:0.0	.	509;509;509	Q9Y5I2-3;Q9Y5I2;Q9Y5I2-2	.;PCDAA_HUMAN;.	M	509	ENSP00000421030:V509M;ENSP00000304234:V509M	ENSP00000304234:V509M	V	+	1	0	PCDHA10	140217342	.	.	0.998000	0.56505	0.648000	0.38561	.	.	2.007000	0.58848	0.561000	0.74099	GTG	G|0.957;A|0.043	0.043	strong		0.697	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		A	140237158	G	A	140237158	3	1	26	1	0	0	0	0	1	0	0	0	11529	1261	44	2	1527	2	PCDHA10	5	140237158	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	48802	140237158	40678102	178	9941											
PCDHAC2	56134	hgsc.bcm.edu	37	chr5	140347902	140347902	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggagattcaagggctgccAgtcacctcctatgtctccat	9	10	10	12	0	3	1	2	0	1	1	5	2	4	1	4	2	1	1	4	2	2	2	rs144335538	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140347902A>T	ENST00000289269.5	+	1	2083	c.1551A>T	c.(1549-1551)ccA>ccT	p.P517P	PCDHA6_ENST00000529310.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA11_ENST00000398640.2_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	517	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)			AAGGGCTGCCAGTCACCTCCT	0.507													A|||	11	0.00219649	0.0015	0.0014	5008	,	,		22726	0.0		0.008	False		,,,				2504	0.0				p.P517P	Melanoma(190;638 2083 3390 11909 52360)	Atlas-SNP	.											.	PCDHAC2	142	.	0			c.A1551T						PASS	.	A	,,,,,,,,,,,,,,,,,,	15,4391	21.2+/-45.6	0,15,2188	92	88	89		,1551,,,,,,,,,,,,,,,,,1551	3.6	1	5	dbSNP_134	89	94,8506	54.0+/-114.7	1,92,4207	no	intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHAC2,PCDHAC1,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018898.3,NM_018899.5,NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018904.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031883.2	,,,,,,,,,,,,,,,,,,	1,107,6395	TT,TA,AA		1.093,0.3404,0.8381	,,,,,,,,,,,,,,,,,,	,517/1008,,,,,,,,,,,,,,,,,517/885	140347902	109,12897	2203	4300	6503	SO:0001819	synonymous_variant	56134	exon1			GCTGCCAGTCACC	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.1551A>T	5.37:g.140347902A>T		130	0	0		167	86	0.51497	NM_031883	Q2M3V1|Q9Y5F4	Silent	SNP	ENST00000289269.5	37	CCDS4242.1																																																																																			A|0.993;T|0.007	0.007	strong		0.507	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899		T	140347902	A	T	140347902	2	4	26	1	0	0	0	0	0	0	0	1	11542	175	7	5		5	PCDHAC2	5	140347902	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	110744	140347902	40567358	179	9942											
PCDHB5	26167	hgsc.bcm.edu	37	chr5	140517034	140517034	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagccctacctgccgctgcCggaggcggccccggcccagg	4	3	14	20	4	0	0	0	0	0	0	0	1	0	1	8	5	4	1	8	5	1	1	rs139801121	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140517034C>G	ENST00000231134.5	+	1	2235	c.2018C>G	c.(2017-2019)cCg>cGg	p.P673R		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	673					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)			CTGCCGCTGCCGGAGGCGGCC	0.692													C|||	46	0.0091853	0.0008	0.0159	5008	,	,		14307	0.0		0.0318	False		,,,				2504	0.002				p.P673R		Atlas-SNP	.											.	PCDHB5	184	.	0			c.C2018G						PASS	.	C	ARG/PRO	11,4325		0,11,2157	53	60	58		2018	4.7	0.1	5	dbSNP_134	58	155,8307		1,153,4077	no	missense	PCDHB5	NM_015669.2	103	1,164,6234	GG,GC,CC		1.8317,0.2537,1.2971	possibly-damaging	673/796	140517034	166,12632	2168	4231	6399	SO:0001583	missense	26167	exon1			CGCTGCCGGAGGC	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.2018C>G	5.37:g.140517034C>G	ENSP00000231134:p.Pro673Arg	28	0	0		18	9	0.5	NM_015669	Q549F4|Q9UFU9	Missense_Mutation	SNP	ENST00000231134.5	37	CCDS4247.1	40	0.018315018315018316	4	0.008130081300813009	11	0.03038674033149171	0	0.0	25	0.032981530343007916	C	14.58	2.579289	0.46006	0.002537	0.018317	ENSG00000113209	ENST00000231134	T	0.50277	0.75	4.71	4.71	0.59529	.	.	.	.	.	T	0.48589	0.1508	M	0.86028	2.79	0.09310	N	1	D	0.67145	0.996	D	0.69654	0.965	T	0.56902	-0.7902	9	0.72032	D	0.01	.	15.1203	0.72438	0.0:0.7833:0.2167:0.0	.	673	Q9Y5E4	PCDB5_HUMAN	R	673	ENSP00000231134:P673R	ENSP00000231134:P673R	P	+	2	0	PCDHB5	140497218	0.000000	0.05858	0.064000	0.19789	0.138000	0.21146	0.604000	0.24164	2.337000	0.79520	0.430000	0.28490	CCG	C|0.986;G|0.014	0.014	strong		0.692	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669		G	140517034	C	G	140517034	3	3	26	1	0	0	0	0	1	0	0	0	11554	652	23	4	2020	4	PCDHB5	5	140517034	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	169132	140517034	40398226	180	9943											
PCDHGB1	56104	hgsc.bcm.edu	37	chr5	140730384	140730384	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaaggaaagtcctgatggaaGtaaatatccggtattactgc	14	10	11	6	1	0	1	0	1	0	0	2	4	2	3	2	3	2	2	2	3	8	4	rs62378414	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140730384G>T	ENST00000523390.1	+	1	557	c.557G>T	c.(556-558)aGt>aTt	p.S186I	PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018922.2|NM_032095.1	NP_061745.1|NP_115266.1	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1	186	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)			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)			CCTGATGGAAGTAAATATCCG	0.468													.|||	118	0.0235623	0.0356	0.0288	5008	,	,		20557	0.001		0.0298	False		,,,				2504	0.0204				p.S186I		Atlas-SNP	.											.	PCDHGB1	198	.	0			c.G557T						PASS	.	G	,,,ILE/SER,ILE/SER	118,3644		2,114,1765	151	148	149		,,,557,557	1.3	1	5	dbSNP_129	149	241,7983		3,235,3874	yes	intron,intron,intron,missense,missense	PCDHGB1,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018922.2,NM_032095.1	,,,142,142	5,349,5639	TT,TG,GG		2.9304,3.1366,2.9952	,,,,	,,,186/928,186/811	140730384	359,11627	1881	4112	5993	SO:0001583	missense	56104	exon1			ATGGAAGTAAATA	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.557G>T	5.37:g.140730384G>T	ENSP00000429273:p.Ser186Ile	108	0	0		134	47	0.350746	NM_018922	Q3SY75|Q9Y5C8	Missense_Mutation	SNP	ENST00000523390.1	37	CCDS54923.1	53	0.024267399267399268	16	0.032520325203252036	16	0.04419889502762431	0	0.0	21	0.027704485488126648	.	12.14	1.849715	0.32699	0.031366	0.029304	ENSG00000254221	ENST00000523390	T	0.22336	1.96	5.36	1.34	0.21922	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.04452	0.0122	M	0.62088	1.915	0.09310	N	1	B;B	0.32467	0.125;0.372	B;B	0.35727	0.094;0.209	T	0.24764	-1.0151	9	0.40728	T	0.16	.	1.2756	0.02030	0.2205:0.1214:0.4089:0.2492	rs62378414	186;186	Q9Y5G3-2;Q9Y5G3	.;PCDGD_HUMAN	I	186	ENSP00000429273:S186I	ENSP00000429273:S186I	S	+	2	0	PCDHGB1	140710568	0.000000	0.05858	0.998000	0.56505	0.897000	0.52465	-0.393000	0.07305	0.019000	0.15079	-0.253000	0.11424	AGT	G|0.975;T|0.025	0.025	strong		0.468	PCDHGB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374740.1	NM_018922		T	140730384	G	T	140730384	3	4	26	1	0	0	0	0	1	0	0	0	11571	1029	36	4	559	4	PCDHGB1	5	140730384	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	213350	140730384	40184876	181	9944											
PCDHGB1	56104	hgsc.bcm.edu	37	chr5	140731022	140731022	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacctcgaagaattattacAagctggtgattgctggagcc	11	10	10	10	1	0	2	0	1	0	1	1	4	0	3	3	2	4	2	3	2	5	3	rs77250251	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140731022A>G	ENST00000523390.1	+	1	1195	c.1195A>G	c.(1195-1197)Aag>Gag	p.K399E	PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018922.2|NM_032095.1	NP_061745.1|NP_115266.1	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1	399	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)			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)			GAATTATTACAAGCTGGTGAT	0.478													.|||	118	0.0235623	0.0356	0.0288	5008	,	,		20579	0.001		0.0298	False		,,,				2504	0.0204				p.K399E		Atlas-SNP	.											.	PCDHGB1	198	.	0			c.A1195G						PASS	.	A	,,,GLU/LYS,GLU/LYS	120,3818		2,116,1851	54	57	56		,,,1195,1195	3	0.6	5	dbSNP_132	56	243,8063		3,237,3913	yes	intron,intron,intron,missense,missense	PCDHGB1,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018922.2,NM_032095.1	,,,56,56	5,353,5764	GG,GA,AA		2.9256,3.0472,2.9647	,,,,	,,,399/928,399/811	140731022	363,11881	1969	4153	6122	SO:0001583	missense	56104	exon1			TATTACAAGCTGG	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.1195A>G	5.37:g.140731022A>G	ENSP00000429273:p.Lys399Glu	110	0	0		106	48	0.45283	NM_018922	Q3SY75|Q9Y5C8	Missense_Mutation	SNP	ENST00000523390.1	37	CCDS54923.1	53	0.024267399267399268	16	0.032520325203252036	16	0.04419889502762431	0	0.0	21	0.027704485488126648	.	10.77	1.444408	0.25987	0.030472	0.029256	ENSG00000254221	ENST00000523390	T	0.01705	4.68	5.49	2.97	0.34412	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.01156	0.0038	M	0.69463	2.115	0.19300	N	0.999972	P;P	0.48998	0.918;0.835	P;P	0.51385	0.668;0.612	T	0.20273	-1.0280	9	0.66056	D	0.02	.	12.1998	0.54319	0.7302:0.2698:0.0:0.0	.	399;399	Q9Y5G3-2;Q9Y5G3	.;PCDGD_HUMAN	E	399	ENSP00000429273:K399E	ENSP00000429273:K399E	K	+	1	0	PCDHGB1	140711206	0.000000	0.05858	0.646000	0.29493	0.241000	0.25554	0.720000	0.25896	0.406000	0.25560	0.460000	0.39030	AAG	A|0.975;G|0.025	0.025	strong		0.478	PCDHGB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374740.1	NM_018922		G	140731022	A	G	140731022	3	3	26	1	0	0	0	0	1	0	0	0	11571	131	5	3	1197	3	PCDHGB1	5	140731022	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	638	140731022	40184238	182	9945											
PCDHGA10	56106	hgsc.bcm.edu	37	chr5	140794750	140794750	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cgctcaccgtggccgtggccGacagcatcccccaagtcctg	6	6	11	18	4	1	0	1	0	0	0	3	1	3	0	6	2	1	2	6	2	1	0	rs201831693		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140794750G>A	ENST00000398610.2	+	1	2008	c.2008G>A	c.(2008-2010)Gac>Aac	p.D670N	PCDHGB7_ENST00000398594.2_5'Flank|PCDHGB4_ENST00000519479.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_018913.2|NM_032090.1	NP_061736.1|NP_114479.1	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10	670	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)			GGCCGTGGCCGACAGCATCCC	0.652													g|||	1	0.000199681	0.0	0.0014	5008	,	,		17360	0.0		0.0	False		,,,				2504	0.0				p.D670N		Atlas-SNP	.											.	PCDHGA10	114	.	0			c.G2008A						PASS	.	G	,,ASN/ASP,,,,,,,,,,,,,,ASN/ASP	0,4400		0,0,2200	48	58	54		,,2008,,,,,,,,,,,,,,2008	5.6	1	5		54	5,8583		0,5,4289	no	intron,intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHGB4,PCDHGA8,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018913.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_032088.1,NM_032090.1	,,23,,,,,,,,,,,,,,23	0,5,6489	AA,AG,GG		0.0582,0.0,0.0385	,,,,,,,,,,,,,,,,	,,670/937,,,,,,,,,,,,,,670/851	140794750	5,12983	2200	4294	6494	SO:0001583	missense	56106	exon1			GTGGCCGACAGCA		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.2008G>A	5.37:g.140794750G>A	ENSP00000381611:p.Asp670Asn	145	0	0		140	69	0.492857	NM_032090	Q9Y5E0	Missense_Mutation	SNP	ENST00000398610.2	37	CCDS47292.1	.	.	.	.	.	.	.	.	.	.	g	12.26	1.885612	0.33255	0.0	5.82E-4	ENSG00000253846	ENST00000398610	D	0.84298	-1.83	5.57	5.57	0.84162	Cadherin (3);Cadherin-like (1);	.	.	.	.	D	0.87916	0.6298	M	0.82630	2.6	0.32335	N	0.560538	P;P	0.39717	0.684;0.557	B;B	0.39119	0.291;0.152	D	0.90719	0.4633	9	0.51188	T	0.08	.	19.1633	0.93543	0.0:0.0:1.0:0.0	.	670;670	Q9Y5H3-2;Q9Y5H3	.;PCDGA_HUMAN	N	670	ENSP00000381611:D670N	ENSP00000381611:D670N	D	+	1	0	PCDHGA10	140774934	1.000000	0.71417	0.972000	0.41901	0.015000	0.08874	7.703000	0.84585	2.621000	0.88768	0.655000	0.94253	GAC	G|0.999;A|0.001	0.001	weak		0.652	PCDHGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374747.1	NM_018913		A	140794750	G	A	140794750	3	1	26	1	0	0	0	0	1	0	0	0	11560	1058	37	1	2010	1	PCDHGA10	5	140794750	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	63728	140794750	40120510	183	9946											
TCERG1	10915	hgsc.bcm.edu	37	chr5	145838647	145838647	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gctcaggctcaggcccaggcCcaggcccaggcccaggccca	7	2	13	19	0	2	0	2	0	0	0	2	0	2	0	5	6	0	2	5	6	0	0	rs187468589		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:145838647C>T	ENST00000296702.5	+	4	677	c.639C>T	c.(637-639)gcC>gcT	p.A213A	TCERG1_ENST00000394421.2_Silent_p.A213A	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	213	Ala/Gln-rich.				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)			aggcccaggcccaggcccagg	0.731																																					p.A213A		Atlas-SNP	.											TCERG1,NS,neuroblastoma,0,1	TCERG1	148	1	0			c.C639T						scavenged	.						10	14	12					5																	145838647		2183	4260	6443	SO:0001819	synonymous_variant	10915	exon4			CCAGGCCCAGGCC	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.639C>T	5.37:g.145838647C>T		17	0	0		17	10	0.588235	NM_006706	Q2NKN2|Q59EA1	Silent	SNP	ENST00000296702.5	37	CCDS4282.1																																																																																			C|0.974;T|0.026	0.026	strong		0.731	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006		T	145838647	C	T	145838647	2	4	26	1	0	0	0	0	0	0	0	1	15700	610	22	2		2	TCERG1	5	145838647	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	5043897	145838647	35076613	184	9947											
ABLIM3	22885	hgsc.bcm.edu	37	chr5	148596546	148596546	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagggaagcactaccacccaAcctgtgccaggtgtgtacgc	10	6	12	13	1	0	0	0	0	0	0	0	2	0	1	4	2	5	2	4	2	4	2	rs148615457	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:148596546A>G	ENST00000506113.1	+	7	1176	c.694A>G	c.(694-696)Acc>Gcc	p.T232A	ABLIM3_ENST00000309868.7_Missense_Mutation_p.T232A|ABLIM3_ENST00000504238.1_Missense_Mutation_p.T232A|RP11-331K21.1_ENST00000512647.2_RNA|ABLIM3_ENST00000508983.1_Missense_Mutation_p.T232A|ABLIM3_ENST00000356541.3_Missense_Mutation_p.T232A|ABLIM3_ENST00000326685.7_Missense_Mutation_p.T232A|RP11-331K21.1_ENST00000522685.1_RNA|AC012613.2_ENST00000523176.1_RNA			O94929	ABLM3_HUMAN	actin binding LIM protein family, member 3	232	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|cilium assembly (GO:0042384)|lamellipodium assembly (GO:0030032)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTACCACCCAACCTGTGCCAG	0.517																																					p.T232A		Atlas-SNP	.											.	ABLIM3	91	.	0			c.A694G						PASS	.	A	ALA/THR	1,4405	2.1+/-5.4	0,1,2202	94	80	85		694	2.8	1	5	dbSNP_134	85	9,8591	7.1+/-27.0	0,9,4291	yes	missense	ABLIM3	NM_014945.2	58	0,10,6493	GG,GA,AA		0.1047,0.0227,0.0769	benign	232/684	148596546	10,12996	2203	4300	6503	SO:0001583	missense	22885	exon8			CACCCAACCTGTG	AB020650	CCDS4294.1	5q33.1	2008-02-05			ENSG00000173210	ENSG00000173210			29132	protein-coding gene	gene with protein product		611305					Standard	XM_005268392		Approved	KIAA0843	uc003lpy.2	O94929	OTTHUMG00000129932	ENST00000506113.1:c.694A>G	5.37:g.148596546A>G	ENSP00000425394:p.Thr232Ala	82	0	0		127	68	0.535433	NM_014945	A8K121|Q19VH3|Q658S1|Q68CI5|Q9BV32	Missense_Mutation	SNP	ENST00000506113.1	37	CCDS4294.1	.	.	.	.	.	.	.	.	.	.	A	15.03	2.710883	0.48517	2.27E-4	0.001047	ENSG00000173210	ENST00000326685;ENST00000356541;ENST00000309868;ENST00000506113;ENST00000504238;ENST00000508983	D;D;D;D;D;D	0.86865	-2.18;-2.18;-2.18;-2.18;-2.18;-2.18	5.49	2.84	0.33178	Zinc finger, LIM-type (5);	0.416904	0.28192	N	0.016242	T	0.80037	0.4550	L	0.38175	1.15	0.26146	N	0.980218	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.11329	0.0;0.0;0.006	T	0.72204	-0.4361	10	0.62326	D	0.03	.	9.5085	0.39062	0.8081:0.0:0.1919:0.0	.	232;232;232	O94929-3;O94929-2;O94929	.;.;ABLM3_HUMAN	A	232	ENSP00000315841:T232A;ENSP00000348938:T232A;ENSP00000310309:T232A;ENSP00000425394:T232A;ENSP00000421183:T232A;ENSP00000420855:T232A	ENSP00000310309:T232A	T	+	1	0	ABLIM3	148576739	0.953000	0.32496	0.990000	0.47175	0.990000	0.78478	3.238000	0.51352	1.013000	0.39391	-0.264000	0.10439	ACC	A|0.999;G|0.001	0.001	strong		0.517	ABLIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373435.1	NM_014945		G	148596546	A	G	148596546	3	3	26	1	0	0	0	0	1	0	0	0	96	43	2	3	720	3	ABLIM3	5	148596546	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	2757899	148596546	32318714	185	9948											
IL17B	27190	hgsc.bcm.edu	37	chr5	148754153	148754153	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cacggggatacggctggggtCgtggttgatgctgcagggag	6	8	20	7	3	0	1	0	1	0	0	1	3	0	3	0	7	3	4	0	7	1	2			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:148754153C>T	ENST00000261796.3	-	3	372	c.322G>A	c.(322-324)Gac>Aac	p.D108N	RP11-394O4.3_ENST00000521756.1_RNA|IL17B_ENST00000505432.1_5'UTR	NM_014443.2	NP_055258.1	Q9UHF5	IL17B_HUMAN	interleukin 17B	108					cell-cell signaling (GO:0007267)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)|urinary_tract(1)	8			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGCTGGGGTCGTGGTTGATG	0.607																																					p.D108N		Atlas-SNP	.											.	IL17B	15	.	0			c.G322A						PASS	.						23	23	23					5																	148754153		2197	4291	6488	SO:0001583	missense	27190	exon3			TGGGGTCGTGGTT	AF184969	CCDS4297.1	5q33.1	2011-07-14			ENSG00000127743	ENSG00000127743		"Interleukins and interleukin receptors"	5982	protein-coding gene	gene with protein product	"neuronal interleukin-17-related factor"	604627				10639155	Standard	NM_014443		Approved	IL-17B, ZCYTO7, IL-20, MGC138900, MGC138901, NIRF	uc003lqo.3	Q9UHF5	OTTHUMG00000130051	ENST00000261796.3:c.322G>A	5.37:g.148754153C>T	ENSP00000261796:p.Asp108Asn	47	0	0		71	36	0.507042	NM_014443	Q14CE5	Missense_Mutation	SNP	ENST00000261796.3	37	CCDS4297.1	.	.	.	.	.	.	.	.	.	.	C	16.83	3.231424	0.58777	.	.	ENSG00000127743	ENST00000261796	T	0.64260	-0.09	4.68	4.68	0.58851	.	0.159823	0.42420	D	0.000720	T	0.76659	0.4018	L	0.58583	1.82	0.50813	D	0.999891	D	0.89917	1.0	D	0.91635	0.999	T	0.78851	-0.2041	10	0.62326	D	0.03	-20.8315	17.807	0.88604	0.0:1.0:0.0:0.0	.	108	Q9UHF5	IL17B_HUMAN	N	108	ENSP00000261796:D108N	ENSP00000261796:D108N	D	-	1	0	IL17B	148734346	1.000000	0.71417	1.000000	0.80357	0.092000	0.18411	5.794000	0.69067	2.423000	0.82170	0.561000	0.74099	GAC	.	.	none		0.607	IL17B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252330.1	NM_014443		T	148754153	C	T	148754153	3	4	26	1	0	0	0	0	1	0	0	0	7644	884	31	1	224	1	IL17B	5	148754153	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	157607	148754153	32161107	186	9949											
PPARGC1B	133522	hgsc.bcm.edu	37	chr5	149212590	149212590	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctccccaaggcctgcagcaaCccctcccagcaggtcagatc	9	5	8	19	0	1	1	1	0	0	1	4	1	3	1	6	2	4	3	6	2	2	0	rs144195384	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:149212590C>T	ENST00000309241.5	+	5	986	c.954C>T	c.(952-954)aaC>aaT	p.N318N	PPARGC1B_ENST00000394320.3_Silent_p.N318N|PPARGC1B_ENST00000403750.1_Silent_p.N254N|PPARGC1B_ENST00000360453.4_Silent_p.N279N	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	318					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)			CCTGCAGCAACCCCTCCCAGC	0.627													C|||	12	0.00239617	0.0068	0.0014	5008	,	,		16493	0.0		0.0	False		,,,				2504	0.002				p.N318N		Atlas-SNP	.											.	PPARGC1B	74	.	0			c.C954T						PASS	.	C	,,	25,4381	31.7+/-61.6	0,25,2178	46	52	50		837,762,954	5.6	1	5	dbSNP_134	50	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	PPARGC1B	NM_001172698.1,NM_001172699.1,NM_133263.3	,,	0,25,6478	TT,TC,CC		0.0,0.5674,0.1922	,,	279/985,254/960,318/1024	149212590	25,12981	2203	4300	6503	SO:0001819	synonymous_variant	133522	exon5			CAGCAACCCCTCC	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.954C>T	5.37:g.149212590C>T		180	0	0		188	95	0.505319	NM_133263	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Silent	SNP	ENST00000309241.5	37	CCDS4298.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	0.907	-0.720352	0.03182	0.005674	0.0	ENSG00000155846	ENST00000434684	.	.	.	5.61	5.61	0.85477	.	.	.	.	.	T	0.69967	0.3170	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.71879	-0.4459	4	.	.	.	-7.6835	19.6373	0.95740	0.0:1.0:0.0:0.0	.	.	.	.	S	5	.	.	P	+	1	0	PPARGC1B	149192783	1.000000	0.71417	1.000000	0.80357	0.234000	0.25298	2.309000	0.43699	2.636000	0.89361	0.655000	0.94253	CCC	C|0.998;T|0.002	0.002	strong		0.627	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263		T	149212590	C	T	149212590	2	4	26	1	0	0	0	0	0	0	0	1	12310	506	18	2		2	PPARGC1B	5	149212590	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	458437	149212590	31702670	187	9950											
PDE6A	5145	hgsc.bcm.edu	37	chr5	149264117	149264117	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catgctcatgctgtcgacgaTtgaggttttgaaagatattc	10	14	10	7	2	1	3	1	2	0	1	3	5	1	3	0	1	2	3	0	1	2	5	rs149380104	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:149264117T>C	ENST00000255266.5	-	16	2071	c.1952A>G	c.(1951-1953)aAt>aGt	p.N651S		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	651					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)	CTGTCGACGATTGAGGTTTTG	0.438													T|||	5	0.000998403	0.0	0.0029	5008	,	,		14804	0.0		0.0	False		,,,				2504	0.0031				p.N651S		Atlas-SNP	.											.	PDE6A	98	.	0			c.A1952G						PASS	.	T	SER/ASN	0,4406		0,0,2203	96	96	96		1952	4.6	1	5	dbSNP_134	96	3,8597	3.0+/-9.4	0,3,4297	yes	missense	PDE6A	NM_000440.2	46	0,3,6500	CC,CT,TT		0.0349,0.0,0.0231	benign	651/861	149264117	3,13003	2203	4300	6503	SO:0001583	missense	5145	exon16			CGACGATTGAGGT		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.1952A>G	5.37:g.149264117T>C	ENSP00000255266:p.Asn651Ser	165	1	0.00606061		227	161	0.709251	NM_000440	Q0P638	Missense_Mutation	SNP	ENST00000255266.5	37	CCDS4299.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	T	11.92	1.781228	0.31502	0.0	3.49E-4	ENSG00000132915	ENST00000255266	T	0.74737	-0.87	5.72	4.56	0.56223	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.096275	0.64402	N	0.000002	T	0.57257	0.2041	N	0.20328	0.56	0.44079	D	0.996839	P	0.36438	0.553	B	0.40782	0.34	T	0.55604	-0.8115	10	0.02654	T	1	.	9.7477	0.40457	0.0:0.0815:0.0:0.9185	.	651	P16499	PDE6A_HUMAN	S	651	ENSP00000255266:N651S	ENSP00000255266:N651S	N	-	2	0	PDE6A	149244310	1.000000	0.71417	0.997000	0.53966	0.971000	0.66376	3.597000	0.54031	1.011000	0.39340	0.455000	0.32223	AAT	T|1.000;C|0.000	0.000	strong		0.438	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2			C	149264117	T	C	149264117	3	2	26	1	0	0	0	0	1	0	0	0	11654	1493	52	3	658	3	PDE6A	5	149264117	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	51527	149264117	31651143	188	9951											
TNIP1	10318	hgsc.bcm.edu	37	chr5	150441711	150441711	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggatggaggcttctggactgGtgctggcttgtcactggggc	4	11	18	8	0	2	0	1	0	1	0	2	3	2	3	0	8	1	3	0	8	0	2			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:150441711G>C	ENST00000389378.2	-	4	922	c.334C>G	c.(334-336)Cca>Gca	p.P112A	TNIP1_ENST00000522226.1_Missense_Mutation_p.P112A|TNIP1_ENST00000523338.1_Missense_Mutation_p.P112A|TNIP1_ENST00000518977.1_Missense_Mutation_p.P112A|TNIP1_ENST00000520931.1_Missense_Mutation_p.P59A|TNIP1_ENST00000521591.1_Missense_Mutation_p.P112A|TNIP1_ENST00000315050.7_Missense_Mutation_p.P112A|TNIP1_ENST00000524280.1_Missense_Mutation_p.P112A|TNIP1_ENST00000523200.1_Missense_Mutation_p.P112A	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	112	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)			TTCTGGACTGGTGCTGGCTTG	0.498																																					p.P112A		Atlas-SNP	.											.	TNIP1	51	.	0			c.C334G						PASS	.						115	102	106					5																	150441711		2203	4300	6503	SO:0001583	missense	10318	exon4			GGACTGGTGCTGG	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.334C>G	5.37:g.150441711G>C	ENSP00000374029:p.Pro112Ala	132	0	0		133	68	0.511278	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	37	CCDS34280.1	.	.	.	.	.	.	.	.	.	.	G	12.55	1.971545	0.34754	.	.	ENSG00000145901	ENST00000520931;ENST00000389378;ENST00000315050;ENST00000523338;ENST00000544828;ENST00000417127;ENST00000539213;ENST00000522226;ENST00000521591;ENST00000518977;ENST00000524280;ENST00000523200;ENST00000545840;ENST00000522100;ENST00000520695;ENST00000521001	T;T;T;T;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;1.36;1.36;1.36;1.36	4.96	-1.53	0.08611	.	0.304128	0.34484	N	0.003934	T	0.23649	0.0572	L	0.56769	1.78	0.09310	N	1	B;B;B;B;B;B;B	0.23377	0.081;0.052;0.084;0.052;0.052;0.028;0.015	B;B;B;B;B;B;B	0.20184	0.028;0.011;0.022;0.017;0.024;0.015;0.015	T	0.09143	-1.0688	10	0.30078	T	0.28	-0.1324	1.0768	0.01634	0.2623:0.2792:0.3156:0.1429	.	112;66;66;112;112;112;112	B7Z8K2;A4F1X9;A4F1X7;E7EPY1;E7ET96;A4F1W9;Q15025	.;.;.;.;.;.;TNIP1_HUMAN	A	59;112;112;112;69;69;74;112;112;112;112;112;69;59;112;112	ENSP00000429891:P59A;ENSP00000374029:P112A;ENSP00000317891:P112A;ENSP00000428243:P112A;ENSP00000428187:P112A;ENSP00000430760:P112A;ENSP00000430971:P112A;ENSP00000429912:P112A;ENSP00000431105:P112A;ENSP00000428487:P59A;ENSP00000430279:P112A;ENSP00000428404:P112A	ENSP00000317891:P112A	P	-	1	0	TNIP1	150421904	0.527000	0.26306	0.003000	0.11579	0.632000	0.37999	1.069000	0.30641	0.009000	0.14813	-0.142000	0.14014	CCA	.	.	none		0.498	TNIP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374914.1	NM_006058		C	150441711	G	C	150441711	3	2	26	1	0	0	0	0	1	0	0	0	16329	1261	44	4	1636	4	TNIP1	5	150441711	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1177594	150441711	30473549	189	9952											
FAT2	2196	hgsc.bcm.edu	37	chr5	150947162	150947162	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtccacaatgtcaatgaccAccacggtggaggcctggccc	10	6	11	14	1	1	1	1	1	0	0	2	2	2	2	5	4	0	0	5	4	2	0	rs114337863	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:150947162A>G	ENST00000261800.5	-	1	1343	c.1331T>C	c.(1330-1332)gTg>gCg	p.V444A		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	444	Cadherin 3. {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)			GTCAATGACCACCACGGTGGA	0.542													A|||	39	0.00778754	0.0	0.0187	5008	,	,		18868	0.0		0.0209	False		,,,				2504	0.0051				p.V444A		Atlas-SNP	.											.	FAT2	465	.	0			c.T1331C						PASS	.	A	ALA/VAL	24,4382	31.7+/-61.6	0,24,2179	138	134	135		1331	5.7	0.1	5	dbSNP_132	135	222,8378	91.9+/-153.9	5,212,4083	yes	missense	FAT2	NM_001447.2	64	5,236,6262	GG,GA,AA		2.5814,0.5447,1.8914	probably-damaging	444/4350	150947162	246,12760	2203	4300	6503	SO:0001583	missense	2196	exon1			ATGACCACCACGG	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.1331T>C	5.37:g.150947162A>G	ENSP00000261800:p.Val444Ala	165	0	0		213	90	0.422535	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	23	0.010531135531135532	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	15	0.01978891820580475	A	15.30	2.791763	0.50102	0.005447	0.025814	ENSG00000086570	ENST00000261800	T	0.69435	-0.4	5.72	5.72	0.89469	Cadherin (3);Cadherin-like (1);	0.000000	0.56097	D	0.000024	T	0.62171	0.2406	M	0.82132	2.575	0.58432	D	0.999999	D	0.67145	0.996	P	0.60473	0.875	T	0.76911	-0.2784	10	0.62326	D	0.03	.	16.0156	0.80439	1.0:0.0:0.0:0.0	.	444	Q9NYQ8	FAT2_HUMAN	A	444	ENSP00000261800:V444A	ENSP00000261800:V444A	V	-	2	0	FAT2	150927355	1.000000	0.71417	0.116000	0.21606	0.171000	0.22731	9.262000	0.95591	2.189000	0.69895	0.533000	0.62120	GTG	A|0.983;G|0.017	0.017	strong		0.542	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		G	150947162	A	G	150947162	3	3	26	1	0	0	0	0	1	0	0	0	5698	159	6	3	11810	3	FAT2	5	150947162	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	505451	150947162	29968098	190	9953											
STK10	6793	hgsc.bcm.edu	37	chr5	171523512	171523512	+	Missense_Mutation	SNP	G	G	A																															tcacctcggccttggcctcaGccaccagctcccgcagagcc																										TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:171523512G>A	ENST00000176763.5	-	8	1266	c.923C>T	c.(922-924)gCt>gTt	p.A308V	STK10_ENST00000517775.1_5'Flank	NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	308					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)			CTTGGCCTCAGCCACCAGCTC	0.622																																					p.A308V		Atlas-SNP	.											.	STK10	100	.	0			c.C923T						PASS	.						109	104	106					5																	171523512		2203	4300	6503	SO:0001583	missense	6793	exon8			GCCTCAGCCACCA	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.923C>T	5.37:g.171523512G>A	ENSP00000176763:p.Ala308Val	47	0	0		62	7	0.112903	NM_005990	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Missense_Mutation	SNP	ENST00000176763.5	37	CCDS34290.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.433688	0.83776	.	.	ENSG00000072786	ENST00000176763;ENST00000545839	T	0.69435	-0.4	4.96	4.96	0.65561	Protein kinase-like domain (1);	0.061568	0.64402	D	0.000005	T	0.73636	0.3612	M	0.74647	2.275	0.80722	D	1	D	0.56746	0.977	P	0.49922	0.626	T	0.76424	-0.2964	10	0.45353	T	0.12	.	15.7705	0.78164	0.0:0.0:1.0:0.0	.	308	O94804	STK10_HUMAN	V	308	ENSP00000176763:A308V	ENSP00000176763:A308V	A	-	2	0	STK10	171456117	1.000000	0.71417	0.947000	0.38551	0.941000	0.58515	9.834000	0.99428	2.320000	0.78422	0.485000	0.47835	GCT	.	.	none		0.622	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990		A	171523512	G	A	171523512	3	1	26	1	0	0	0	0	1	0	0	0	15301	971	34	2	2031	2	STK10	5	171523512	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	20576350	171523512	9391748	191	9954	124	2									
STK10	6793	hgsc.bcm.edu	37	chr5	171523513	171523513	+	Missense_Mutation	SNP	C	C	A																															cacctcggccttggcctcagCcaccagctcccgcagagcct																										TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:171523513C>A	ENST00000176763.5	-	8	1265	c.922G>T	c.(922-924)Gct>Tct	p.A308S	STK10_ENST00000517775.1_5'Flank	NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	308					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)			TTGGCCTCAGCCACCAGCTCC	0.622																																					p.A308S		Atlas-SNP	.											.	STK10	100	.	0			c.G922T						PASS	.						109	105	106					5																	171523513		2203	4300	6503	SO:0001583	missense	6793	exon8			CCTCAGCCACCAG	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.922G>T	5.37:g.171523513C>A	ENSP00000176763:p.Ala308Ser	46	0	0		62	7	0.112903	NM_005990	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Missense_Mutation	SNP	ENST00000176763.5	37	CCDS34290.1	.	.	.	.	.	.	.	.	.	.	C	19.94	3.920058	0.73098	.	.	ENSG00000072786	ENST00000176763;ENST00000545839	T	0.68479	-0.33	4.96	4.96	0.65561	Protein kinase-like domain (1);	0.061568	0.64402	N	0.000005	T	0.72495	0.3467	M	0.74647	2.275	0.80722	D	1	B	0.27140	0.169	B	0.41510	0.359	T	0.67492	-0.5657	10	0.14656	T	0.56	.	15.7705	0.78164	0.0:1.0:0.0:0.0	.	308	O94804	STK10_HUMAN	S	308	ENSP00000176763:A308S	ENSP00000176763:A308S	A	-	1	0	STK10	171456118	1.000000	0.71417	0.997000	0.53966	0.953000	0.61014	7.791000	0.85805	2.320000	0.78422	0.485000	0.47835	GCT	.	.	none		0.622	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990		A	171523513	C	A	171523513	3	1	26	1	0	0	0	0	1	0	0	0	15301	739	26	4	2032	4	STK10	5	171523513	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1	171523513	9391747	192	9955	124	2									
CDHR2	54825	hgsc.bcm.edu	37	chr5	176011444	176011444	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtggtgaaggcctgggacgCggaccagacggaagccaaca	11	3	16	11	4	0	2	0	1	0	1	0	5	0	5	3	5	2	0	3	5	3	0	rs115050587	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:176011444C>T	ENST00000510636.1	+	19	2436	c.2162C>T	c.(2161-2163)gCg>gTg	p.A721V	CDHR2_ENST00000261944.5_Missense_Mutation_p.A721V|CDHR2_ENST00000506348.1_Missense_Mutation_p.A721V	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	721	Cadherin 7. {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						GCCTGGGACGCGGACCAGACG	0.637													C|||	9	0.00179712	0.0015	0.0014	5008	,	,		18356	0.0		0.005	False		,,,				2504	0.001				p.A721V		Atlas-SNP	.											.	CDHR2	152	.	0			c.C2162T						PASS	.	C	VAL/ALA,VAL/ALA	14,4392	21.2+/-45.6	0,14,2189	93	96	95		2162,2162	4.2	0.1	5	dbSNP_132	95	119,8481	61.0+/-122.8	0,119,4181	yes	missense,missense	CDHR2	NM_001171976.1,NM_017675.4	64,64	0,133,6370	TT,TC,CC		1.3837,0.3177,1.0226	probably-damaging,probably-damaging	721/1311,721/1311	176011444	133,12873	2203	4300	6503	SO:0001583	missense	54825	exon19			GGGACGCGGACCA	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.2162C>T	5.37:g.176011444C>T	ENSP00000424565:p.Ala721Val	115	0	0		136	76	0.558824	NM_017675	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	37	CCDS34297.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	13.57	2.277159	0.40294	0.003177	0.013837	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.55413	0.52;0.52;0.52	5.12	4.24	0.50183	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.66470	0.2792	M	0.91920	3.255	0.33621	D	0.604834	D	0.67145	0.996	P	0.59546	0.859	T	0.81061	-0.1103	9	0.36615	T	0.2	-11.2568	12.946	0.58373	0.2944:0.7056:0.0:0.0	.	721	Q9BYE9	CDHR2_HUMAN	V	721	ENSP00000424565:A721V;ENSP00000261944:A721V;ENSP00000421078:A721V	ENSP00000261944:A721V	A	+	2	0	CDHR2	175944050	0.874000	0.30092	0.079000	0.20413	0.097000	0.18754	1.646000	0.37249	1.248000	0.43934	0.549000	0.68633	GCG	C|0.991;T|0.009	0.009	strong		0.637	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675		T	176011444	C	T	176011444	3	4	26	1	0	0	0	0	1	0	0	0	3121	768	27	1	2232	1	CDHR2	5	176011444	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	4487931	176011444	4903816	193	9956											
DSP	1832	hgsc.bcm.edu	37	chr6	7581032	7581032	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcaggagcaagaactgacaCgcctgaggatcgactatgaa	14	7	11	9	2	1	4	1	3	0	1	2	7	1	6	1	2	2	1	1	2	4	2	rs28763967	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:7581032C>T	ENST00000379802.3	+	23	4950	c.4609C>T	c.(4609-4611)Cgc>Tgc	p.R1537C	DSP_ENST00000418664.2_Intron	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	1537	Central fibrous rod domain.		R -> C (in dbSNP:rs28763967). {ECO:0000269|PubMed:19863551, ECO:0000269|PubMed:20031617}.		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)		AGAACTGACACGCCTGAGGAT	0.493													C|||	18	0.00359425	0.0008	0.0014	5008	,	,		21149	0.0		0.0159	False		,,,				2504	0.0				p.R1537C		Atlas-SNP	.											.	DSP	306	.	0			c.C4609T						PASS	.	C	,CYS/ARG	13,4393	20.2+/-43.8	0,13,2190	120	121	120		,4609	5.8	1	6	dbSNP_125	120	123,8477	62.8+/-124.8	3,117,4180	yes	intron,missense	DSP	NM_001008844.1,NM_004415.2	,180	3,130,6370	TT,TC,CC		1.4302,0.2951,1.0457	,probably-damaging	,1537/2872	7581032	136,12870	2203	4300	6503	SO:0001583	missense	1832	exon23			CTGACACGCCTGA	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.4609C>T	6.37:g.7581032C>T	ENSP00000369129:p.Arg1537Cys	72	0	0		81	28	0.345679	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	37	CCDS4501.1	12	0.005494505494505495	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	C	16.80	3.224244	0.58668	0.002951	0.014302	ENSG00000096696	ENST00000379802	T	0.74737	-0.87	5.85	5.85	0.93711	.	0.000000	0.64402	D	0.000009	T	0.76047	0.3933	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.69654	0.965	T	0.77800	-0.2452	10	0.59425	D	0.04	.	15.812	0.78571	0.1441:0.8559:0.0:0.0	rs28763967	1537	P15924	DESP_HUMAN	C	1537	ENSP00000369129:R1537C	ENSP00000369129:R1537C	R	+	1	0	DSP	7526031	0.859000	0.29813	0.966000	0.40874	0.971000	0.66376	2.051000	0.41307	2.772000	0.95346	0.655000	0.94253	CGC	C|0.992;T|0.008	0.008	strong		0.493	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		T	7581032	C	T	7581032	3	4	26	1	0	0	0	0	1	0	0	0	4783	536	19	1	4699	1	DSP	6	7581032	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10		7581032	163534035	194	9957											
HFE	3077	hgsc.bcm.edu	37	chr6	26093141	26093141	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaagagcagagatatacgtGccaggtggagcacccaggcc	12	4	15	10	1	0	2	0	0	0	2	0	5	0	4	3	4	4	2	3	4	3	2	rs1800562	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:26093141G>A	ENST00000357618.5	+	4	967	c.845G>A	c.(844-846)tGc>tAc	p.C282Y	HFE_ENST00000461397.1_Missense_Mutation_p.C268Y|HFE_ENST00000470149.1_Missense_Mutation_p.C279Y|HFE_ENST00000317896.7_Missense_Mutation_p.C190Y|HFE_ENST00000336625.8_Missense_Mutation_p.C176Y|HFE_ENST00000397022.3_Missense_Mutation_p.C259Y|HFE_ENST00000353147.5_Missense_Mutation_p.C102Y|HFE_ENST00000352392.4_Intron|HFE_ENST00000309234.6_Missense_Mutation_p.C282Y|HFE_ENST00000488199.1_Missense_Mutation_p.C180Y|HFE_ENST00000349999.4_Missense_Mutation_p.C194Y	NM_000410.3|NM_139006.2	NP_000401.1|NP_620575.1	Q30201	HFE_HUMAN	hemochromatosis	282	Alpha-3.|Ig-like C1-type.		C -> Y (in HFE1; associated with susceptibility to porphyria cutanea tarda; associated with increased serum transferrin levels; higher frequency in patients with type 2 diabetes than in controls; dbSNP:rs1800562). {ECO:0000269|PubMed:10094552, ECO:0000269|PubMed:10194428, ECO:0000269|PubMed:11069625, ECO:0000269|PubMed:11423500, ECO:0000269|PubMed:12542741, ECO:0000269|PubMed:14633868, ECO:0000269|PubMed:18157833, ECO:0000269|PubMed:8696333, ECO:0000269|PubMed:9024376, ECO:0000269|PubMed:9106528, ECO:0000269|PubMed:9620340, ECO:0000269|Ref.8}.		antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular iron ion homeostasis (GO:0006879)|cellular response to iron ion starvation (GO:0010106)|female pregnancy (GO:0007565)|hormone biosynthetic process (GO:0042446)|immune response (GO:0006955)|iron ion import into cell (GO:0097459)|multicellular organismal iron ion homeostasis (GO:0060586)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein complex assembly (GO:0006461)	apical part of cell (GO:0045177)|basal part of cell (GO:0045178)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|MHC class I protein complex (GO:0042612)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	peptide antigen binding (GO:0042605)|receptor binding (GO:0005102)			endometrium(3)|large_intestine(3)|liver(2)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						AGATATACGTGCCAGGTGGAG	0.547									Hemochromatosis				G|||	63	0.0125799	0.0023	0.0216	5008	,	,		19430	0.0		0.0427	False		,,,				2504	0.002				p.C282Y		Atlas-SNP	.											.	HFE	37	.	0			c.G845A	GRCh37	CM004391|CM960828	HFE	M	rs1800562	PASS	.	G	TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS,	67,4339		1,65,2137	84	81	82	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	845,527,569,803,581,539,776,305,	5.3	1	6	dbSNP_89	82	551,8049		18,515,3767	yes	missense,missense,missense,missense,missense,missense,missense,missense,intron	HFE	NM_000410.3,NM_139003.2,NM_139004.2,NM_139006.2,NM_139007.2,NM_139008.2,NM_139009.2,NM_139010.2,NM_139011.2	194,194,194,194,194,194,194,194,	19,580,5904	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	6.407,1.5207,4.7517	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,	282/349,176/243,190/257,268/335,194/261,180/247,259/326,102/169,	26093141	618,12388	2203	4300	6503	SO:0001583	missense	3077	exon4	Familial Cancer Database		ATACGTGCCAGGT		CCDS4578.1, CCDS4579.1, CCDS4580.1, CCDS4581.1, CCDS4582.1, CCDS47386.1, CCDS47387.1, CCDS54974.1, CCDS54975.1, CCDS75412.1	6p21.3	2014-09-17			ENSG00000010704	ENSG00000010704		"Immunoglobulin superfamily / C1-set domain containing"	4886	protein-coding gene	gene with protein product	"high Fe"	613609				3460331	Standard	XR_241893		Approved	HLA-H	uc003nfx.1	Q30201	OTTHUMG00000016348	ENST00000357618.5:c.845G>A	6.37:g.26093141G>A	ENSP00000417404:p.Cys282Tyr	228	0	0		192	87	0.453125	NM_000410	B2CKL0|O75929|O75930|O75931|Q17RT0|Q96KU5|Q96KU6|Q96KU7|Q96KU8|Q9HC64|Q9HC68|Q9HC70|Q9HC83	Missense_Mutation	SNP	ENST00000357618.5	37	CCDS4578.1	43	0.019688644688644688	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	35	0.04617414248021108	.	17.19	3.326013	0.60743	0.015207	0.06407	ENSG00000010704	ENST00000349999;ENST00000397022;ENST00000317896;ENST00000353147;ENST00000357618;ENST00000470149;ENST00000336625;ENST00000461397;ENST00000488199;ENST00000309234	D;D;D;D;D;D;D;D;D;D	0.95342	-3.68;-3.68;-3.68;-3.68;-3.68;-3.68;-3.68;-3.68;-3.68;-3.68	5.35	5.35	0.76521	Immunoglobulin/major histocompatibility complex, conserved site (1);Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000003	D	0.98557	0.9518	H	0.99143	4.445	0.80722	A	1	D;D;D;D;D;P;D;D;D	0.89917	0.982;1.0;1.0;1.0;1.0;0.951;0.996;0.993;0.961	P;D;D;D;D;P;P;D;P	0.91635	0.756;0.999;0.999;0.999;0.999;0.56;0.826;0.917;0.667	D	0.98784	1.0733	9	0.87932	D	0	.	14.7506	0.69522	0.0:0.0:1.0:0.0	rs1800562;rs4134660;rs17530654;rs58044250;rs1800562	279;102;180;190;176;268;194;259;282	Q6B0J5;Q30201-6;Q30201-4;Q30201-7;Q30201-10;Q30201-3;Q30201-2;Q30201-5;Q30201	.;.;.;.;.;.;.;.;HFE_HUMAN	Y	194;259;190;102;282;279;176;268;180;282	ENSP00000259699:C194Y;ENSP00000380217:C259Y;ENSP00000313776:C190Y;ENSP00000312342:C102Y;ENSP00000417404:C282Y;ENSP00000419725:C279Y;ENSP00000337819:C176Y;ENSP00000420802:C268Y;ENSP00000420559:C180Y;ENSP00000311698:C282Y	ENSP00000311698:C282Y	C	+	2	0	HFE	26201120	1.000000	0.71417	0.993000	0.49108	0.351000	0.29236	4.282000	0.58971	2.941000	0.99782	0.655000	0.94253	TGC	G|0.966;A|0.034	0.034	strong		0.547	HFE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356133.1			A	26093141	G	A	26093141	3	1	26	1	0	0	0	0	1	0	0	0	7090	1319	46	2	859	2	HFE	6	26093141	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	18512109	26093141	145021926	195	9958											
MOG	4340	hgsc.bcm.edu	37	chr6	29638101	29638101	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctggaagataaccctgttTgtaattgtgccggttcttgg	7	15	12	7	1	1	1	0	0	1	1	1	2	1	2	2	3	3	4	2	3	3	6	rs112913018	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:29638101T>C	ENST00000376917.3	+	6	865	c.636T>C	c.(634-636)ttT>ttC	p.F212F	MOG_ENST00000376902.3_3'UTR|MOG_ENST00000396701.2_Intron|MOG_ENST00000376888.2_Silent_p.F96F|MOG_ENST00000376894.4_Silent_p.F212F|MOG_ENST00000533330.2_3'UTR|MOG_ENST00000494692.1_Intron|MOG_ENST00000490427.1_Intron|MOG_ENST00000396704.3_Intron|MOG_ENST00000416766.2_Silent_p.F174F|MOG_ENST00000376891.4_Intron|MOG_ENST00000376898.3_Silent_p.F212F|MOG_ENST00000431798.2_Intron|MOG_ENST00000483013.1_Intron	NM_002433.4|NM_206809.3	NP_002424.3|NP_996532.2	Q16653	MOG_HUMAN	myelin oligodendrocyte glycoprotein	212					cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|positive regulation of MyD88-dependent toll-like receptor signaling pathway (GO:0034126)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)|skin(2)	19						TAACCCTGTTTGTAATTGTGC	0.527													T|||	5	0.000998403	0.0	0.0014	5008	,	,		18756	0.0		0.004	False		,,,				2504	0.0				p.F212F		Atlas-SNP	.											.	MOG	47	.	0			c.T636C						PASS	.						220	211	214					6																	29638101		2203	4300	6503	SO:0001819	synonymous_variant	4340	exon6			CCTGTTTGTAATT		CCDS4667.1, CCDS34366.1, CCDS34367.1, CCDS34368.1, CCDS34369.1, CCDS34370.1, CCDS47394.1, CCDS47395.1, CCDS47395.2, CCDS54977.1	6p22.1	2014-01-16			ENSG00000204655	ENSG00000204655		"Immunoglobulin superfamily / V-set domain containing", "Butyrophilins"	7197	protein-coding gene	gene with protein product		159465					Standard	NM_002433		Approved	BTN6, BTNL11	uc003nne.3	Q16653	OTTHUMG00000031099	ENST00000376917.3:c.636T>C	6.37:g.29638101T>C		406	0	0		423	209	0.49409	NM_002433	A6NDR4|A6NNJ9|A8MY31|B0UZR9|E9PGF0|F8W9D5|O00713|O00714|O00715|Q13054|Q13055|Q14855|Q29ZN8|Q56UY0|Q5JNX7|Q5JNY1|Q5JNY2|Q5JNY4|Q5SSB5|Q5SSB6|Q5STL9|Q5STM0|Q5STM1|Q5STM2|Q5STM5|Q5SUK5|Q5SUK7|Q5SUK8|Q5SUK9|Q5SUL0|Q5SUL1|Q8IYG5|Q92891|Q92892|Q92893|Q92894|Q92895|Q93053|Q96KU9|Q96KV0|Q96KV1|Q99605	Silent	SNP	ENST00000376917.3	37	CCDS34370.1																																																																																			A|0.002;C|0.001;T|0.997	0.001	strong		0.527	MOG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076160.3	NM_002433		C	29638101	T	C	29638101	2	2	26	1	0	0	0	0	0	0	0	1	9702	1809	63	3		3	MOG	6	29638101	Silent	SNP	T	TCGA-G8-6907-01A-11D-2210-10	3544960	29638101	141476966	196	9959											
ABCF1	23	hgsc.bcm.edu	37	chr6	30545879	30545879	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaaagcgagatacccgaaaAggcaggcggaagaaggatgt	18	3	14	6	3	0	2	0	0	0	2	0	6	0	4	1	4	2	1	1	4	7	1	rs113473909	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30545879A>G	ENST00000326195.8	+	4	355	c.243A>G	c.(241-243)aaA>aaG	p.K81K	ABCF1_ENST00000376545.3_Silent_p.K81K|ABCF1_ENST00000396515.4_Silent_p.K81K	NM_001025091.1	NP_001020262.1	Q8NE71	ABCF1_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 1	81					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						ATACCCGAAAAGGCAGGCGGA	0.493													A|||	37	0.00738818	0.0	0.0043	5008	,	,		19009	0.006		0.004	False		,,,				2504	0.0245				p.K81K		Atlas-SNP	.											.	ABCF1	61	.	0			c.A243G						PASS	.	A	,	8,4398	14.3+/-33.2	0,8,2195	88	93	91		243,243	3.2	1	6	dbSNP_132	91	90,8510	42.6+/-100.3	1,88,4211	no	coding-synonymous,coding-synonymous	ABCF1	NM_001025091.1,NM_001090.2	,	1,96,6406	GG,GA,AA		1.0465,0.1816,0.7535	,	81/846,81/808	30545879	98,12908	2203	4300	6503	SO:0001819	synonymous_variant	23	exon4			CCGAAAAGGCAGG	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.243A>G	6.37:g.30545879A>G		94	0	0		93	47	0.505376	NM_001090	A2BF75|O14897|Q69YP6	Silent	SNP	ENST00000326195.8	37	CCDS34380.1																																																																																			A|0.993;G|0.007	0.007	strong		0.493	ABCF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076137.3			G	30545879	A	G	30545879	2	3	26	1	0	0	0	0	0	0	0	1	65	69	3	3		3	ABCF1	6	30545879	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	907778	30545879	140569188	197	9960											
MUC21	394263	hgsc.bcm.edu	37	chr6	30954309	30954309	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctccagtggggccagcacAgccaccaactctgagtccag	10	5	10	16	0	1	1	0	1	1	0	3	1	3	1	6	2	3	1	6	2	1	0	rs150035336		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954309A>T	ENST00000376296.3	+	2	598	c.357A>T	c.(355-357)acA>acT	p.T119T	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	119	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						GGGCCAGCACAGCCACCAACT	0.597																																					p.T119T		Atlas-SNP	.											.	MUC21	98	.	0			c.A357T						PASS	.						180	166	171					6																	30954309		2203	4298	6501	SO:0001819	synonymous_variant	394263	exon2			CAGCACAGCCACC	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.357A>T	6.37:g.30954309A>T		107	0	0		166	15	0.0903614	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																			.	.	weak		0.597	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909		T	30954309	A	T	30954309	2	4	26	1	0	0	0	0	0	0	0	1	9986	175	7	5		5	MUC21	6	30954309	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	408430	30954309	140160758	198	9961			1	43		4	4	286	N	G_C_A	3.939491e-08
MUC21	394263	hgsc.bcm.edu	37	chr6	30954327	30954327	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acagccaccaactctgagtcCagcacaccctccagtggggc	10	5	9	17	0	1	1	0	1	1	0	3	1	3	1	5	2	3	1	5	2	1	0	rs149194643	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954327C>T	ENST00000376296.3	+	2	616	c.375C>T	c.(373-375)tcC>tcT	p.S125S	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	125	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						ACTCTGAGTCCAGCACACCCT	0.592																																					p.S125S		Atlas-SNP	.											.	MUC21	98	.	0			c.C375T						PASS	.						174	162	166					6																	30954327		2203	4299	6502	SO:0001819	synonymous_variant	394263	exon2			TGAGTCCAGCACA	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.375C>T	6.37:g.30954327C>T		94	0	0		151	12	0.0794702	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																			C|0.989;T|0.011	0.011	strong		0.592	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909		T	30954327	C	T	30954327	2	4	26	1	0	0	0	0	0	0	0	1	9986	581	21	2		2	MUC21	6	30954327	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	18	30954327	140160740	199	9962			1	43		4	4	286	N	G_C_A	3.939491e-08
MUC21	394263	hgsc.bcm.edu	37	chr6	30954560	30954560	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	caactctgagtccagcacaaCctccagtggggccagcacag	11	5	10	15	0	1	1	0	1	1	0	3	1	3	1	4	2	4	2	4	2	2	0	rs531044924	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954560C>T	ENST00000376296.3	+	2	849	c.608C>T	c.(607-609)aCc>aTc	p.T203I	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	203	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						TCCAGCACAACCTCCAGTGGG	0.617													c|||	192	0.0383387	0.0401	0.0533	5008	,	,		25680	0.0337		0.0308	False		,,,				2504	0.0378				p.T203I		Atlas-SNP	.											.	MUC21	98	.	0			c.C608T						PASS	.						160	154	156					6																	30954560		2203	4300	6503	SO:0001583	missense	394263	exon2			GCACAACCTCCAG	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.608C>T	6.37:g.30954560C>T	ENSP00000365473:p.Thr203Ile	94	0	0		142	13	0.0915493	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	c	9.167	1.020156	0.19433	.	.	ENSG00000204544	ENST00000376296	T	0.11385	2.78	4.1	1.24	0.21308	.	.	.	.	.	T	0.03095	0.0091	L	0.27053	0.805	0.09310	N	1	P	0.44044	0.825	P	0.44897	0.463	T	0.42292	-0.9460	8	.	.	.	.	7.7906	0.29119	0.0:0.7057:0.0:0.2943	.	203	Q5SSG8	MUC21_HUMAN	I	203	ENSP00000365473:T203I	.	T	+	2	0	MUC21	31062539	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.733000	0.04898	0.127000	0.18452	0.491000	0.48974	ACC	.	.	none		0.617	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909		T	30954560	C	T	30954560	3	4	26	1	0	0	0	0	1	0	0	0	9986	507	18	2	614	2	MUC21	6	30954560	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	233	30954560	140160507	200	9963			1	43		4	4	286	N	G_C_A	3.939491e-08
MUC21	394263	hgsc.bcm.edu	37	chr6	30954594	30954594	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcacagccaccaactctgaGtccagaacgacctccaatgg	13	5	8	15	1	1	2	0	1	1	1	3	3	3	2	5	1	4	1	5	1	3	0			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954594G>C	ENST00000376296.3	+	2	883	c.642G>C	c.(640-642)gaG>gaC	p.E214D	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	214	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						CCAACTCTGAGTCCAGAACGA	0.612																																					p.E214D		Atlas-SNP	.											.	MUC21	98	.	0			c.G642C						PASS	.						154	152	153					6																	30954594		2203	4300	6503	SO:0001583	missense	394263	exon2			CTCTGAGTCCAGA	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.642G>C	6.37:g.30954594G>C	ENSP00000365473:p.Glu214Asp	95	0	0		120	6	0.05	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	G	3.066	-0.192132	0.06299	.	.	ENSG00000204544	ENST00000376296	T	0.01787	4.64	3.54	-7.08	0.01558	.	.	.	.	.	T	0.00384	0.0012	N	0.19112	0.55	0.09310	N	1	B	0.12013	0.005	B	0.08055	0.003	T	0.43196	-0.9406	8	.	.	.	.	10.9515	0.47332	0.1259:0.5078:0.3663:0.0	.	214	Q5SSG8	MUC21_HUMAN	D	214	ENSP00000365473:E214D	.	E	+	3	2	MUC21	31062573	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.756000	0.04777	-2.750000	0.00375	-0.349000	0.07799	GAG	.	.	none		0.612	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909		C	30954594	G	C	30954594	3	2	26	1	0	0	0	0	1	0	0	0	9986	1020	36	4	648	4	MUC21	6	30954594	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	34	30954594	140160473	201	9964			1	43		4	4	286	N	G_C_A	3.939491e-08
HLA-B	3106	hgsc.bcm.edu	37	chr6	31323286	31323286	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggtcagtgtgatctccgCagggtagaaacccagggccc	9	6	13	13	1	2	2	1	1	1	1	3	2	2	2	4	3	1	2	4	3	2	1	rs146555925		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31323286C>T	ENST00000412585.2	-	4	731	c.703G>A	c.(703-705)Gcg>Acg	p.A235T		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	235	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						GTGATCTCCGCAGGGTAGAAA	0.592									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.A235T		Atlas-SNP	.											.	HLA-B	54	.	0			c.G703A						PASS	.						83	81	82					6																	31323286		2203	4298	6501	SO:0001583	missense	3106	exon4	Familial Cancer Database	;Lichen Sclerosis, Familial	TCTCCGCAGGGTA	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.703G>A	6.37:g.31323286C>T	ENSP00000399168:p.Ala235Thr	112	0	0		162	10	0.0617284	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	11.65	1.701624	0.30142	.	.	ENSG00000234745	ENST00000412585;ENST00000428231;ENST00000452596;ENST00000434333	T;T	0.14766	2.48;2.48	3.06	-1.02	0.10135	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.402479	0.17716	U	0.164428	T	0.16727	0.0402	H	0.95780	3.72	0.09310	N	1	B	0.28820	0.224	B	0.41619	0.361	T	0.25847	-1.0120	10	0.87932	D	0	.	6.9863	0.24731	0.0:0.3733:0.0:0.6267	rs1050335;rs3190627	235	P01889	1B07_HUMAN	T	235;114;114;246	ENSP00000399168:A235T;ENSP00000405931:A246T	ENSP00000399168:A235T	A	-	1	0	HLA-B	31431265	0.000000	0.05858	0.023000	0.16930	0.855000	0.48748	-0.862000	0.04263	-0.113000	0.11958	0.442000	0.29010	GCG	C|0.999;T|0.001	0.001	weak		0.592	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514		T	31323286	C	T	31323286	3	4	26	1	0	0	0	0	1	0	0	0	7205	710	25	2	401	2	HLA-B	6	31323286	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	368692	31323286	139791781	202	9965											
HLA-DRB1	3123	hgsc.bcm.edu	37	chr6	32552000	32552000	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gctgttccagtactcagcgtCaggccgccccagctccgtca	6	8	10	17	3	3	0	3	0	0	0	5	0	5	0	5	1	3	4	5	1	1	2	rs17880292	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32552000C>T	ENST00000360004.5	-	2	361	c.256G>A	c.(256-258)Gac>Aac	p.D86N		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	86	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)|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)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						TACTCAGCGTCAGGCCGCCCC	0.632										Multiple Myeloma(14;0.17)			C|||	334	0.0666933	0.0938	0.0591	5008	,	,		7793	0.1002		0.0487	False		,,,				2504	0.0194				p.D86N		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.G256A						PASS	.																																			SO:0001583	missense	3123	exon2			CAGCGTCAGGCCG	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.256G>A	6.37:g.32552000C>T	ENSP00000353099:p.Asp86Asn	33	0	0		50	16	0.32	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	13.25	2.179960	0.38511	.	.	ENSG00000196126	ENST00000360004	T	0.00224	8.51	3.52	-1.57	0.08506	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (3);MHC classes I/II-like antigen recognition protein (1);	11.458300	0.00979	N	0.003354	T	0.00073	0.0002	M	0.63428	1.95	0.09310	N	1	B	0.21606	0.058	B	0.28385	0.089	T	0.33777	-0.9855	10	0.72032	D	0.01	.	3.0064	0.06030	0.3359:0.2318:0.0:0.4323	rs17880292	86	P01911	2B1F_HUMAN	N	86	ENSP00000353099:D86N	ENSP00000353099:D86N	D	-	1	0	HLA-DRB1	32659978	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-4.770000	0.00188	-0.268000	0.09312	0.453000	0.30009	GAC	C|0.989;T|0.011	0.011	strong		0.632	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124		T	32552000	C	T	32552000	3	4	26	1	0	0	0	0	1	0	0	0	7217	826	29	2	564	2	HLA-DRB1	6	32552000	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1228714	32552000	138563067	203	9966											
PSMB8	5696	hgsc.bcm.edu	37	chr6	32809947	32809947	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagatcatactgcccatagaGaggcccatgccccggtactg	10	7	10	14	1	1	2	1	0	0	2	1	3	1	2	4	2	4	1	4	2	3	3	rs11540143	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32809947G>A	ENST00000374882.3	-	4	551	c.501C>T	c.(499-501)ctC>ctT	p.L167L	PSMB8_ENST00000374881.2_Silent_p.L163L|TAPSAR1_ENST00000453426.1_lincRNA|PSMB9_ENST00000395330.1_5'Flank|PSMB8_ENST00000395339.3_Silent_p.L143L	NM_148919.3	NP_683720.2	P28062	PSB8_HUMAN	proteasome (prosome, macropain) subunit, beta type, 8	167					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)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|fat cell differentiation (GO:0045444)|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)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	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)			NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(1)	11					Carfilzomib(DB08889)	TGCCCATAGAGAGGCCCATGC	0.532													G|||	6	0.00119808	0.0	0.0029	5008	,	,		20162	0.001		0.003	False		,,,				2504	0.0				p.L167L	NSCLC(48;53 1172 10859 13624 22883)	Atlas-SNP	.											.	PSMB8	42	.	0			c.C501T						PASS	.	G	,	0,3022		0,0,1511	133	117	122		489,501	4.2	1	6	dbSNP_120	122	35,5383		0,35,2674	no	coding-synonymous,coding-synonymous	PSMB8	NM_004159.4,NM_148919.3	,	0,35,4185	AA,AG,GG		0.646,0.0,0.4147	,	163/273,167/277	32809947	35,8405	1511	2709	4220	SO:0001819	synonymous_variant	5696	exon4			CATAGAGAGGCCC		CCDS4756.1, CCDS4757.1	6p21.3	2013-03-27	2013-03-27		ENSG00000204264	ENSG00000204264		"Proteasome (prosome, macropain) subunits"	9545	protein-coding gene	gene with protein product		177046	"proteasome (prosome, macropain) subunit, beta type, 8 (large multifunctional protease 7)", "large multifunctional peptidase 7"	LMP7		1529427, 10329130	Standard	XM_005275000		Approved	RING10, D6S216E, PSMB5i, beta5i	uc003oce.3	P28062	OTTHUMG00000031285	ENST00000374882.3:c.501C>T	6.37:g.32809947G>A		116	0	0		119	54	0.453782	NM_148919	B0UZC0|Q29824|Q5JNW6|Q5QNR8|Q96J48	Silent	SNP	ENST00000374882.3	37	CCDS4757.1																																																																																			G|0.996;A|0.004	0.004	strong		0.532	PSMB8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076617.3	NM_148919		A	32809947	G	A	32809947	2	1	26	1	0	0	0	0	0	0	0	1	12695	929	33	2		2	PSMB8	6	32809947	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	257947	32809947	138305120	204	9967											
BRPF3	27154	hgsc.bcm.edu	37	chr6	36185759	36185759	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaatgtagtttgggtctcAgtggtggactggcatttgaa	8	14	14	5	0	1	2	1	2	1	0	2	3	1	3	0	4	0	3	0	4	3	3	rs145016452	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:36185759A>G	ENST00000357641.6	+	9	3308	c.3055A>G	c.(3055-3057)Agt>Ggt	p.S1019G	BRPF3_ENST00000543502.1_Missense_Mutation_p.S749G|BRPF3_ENST00000534694.1_Intron|BRPF3_ENST00000339717.7_Missense_Mutation_p.S749G|BRPF3_ENST00000443324.2_Intron|BRPF3_ENST00000534400.1_Missense_Mutation_p.S1019G	NM_015695.2	NP_056510.2	Q9ULD4	BRPF3_HUMAN	bromodomain and PHD finger containing, 3	1019					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						TTTGGGTCTCAGTGGTGGACT	0.498													A|||	4	0.000798722	0.0008	0.0029	5008	,	,		21651	0.0		0.001	False		,,,				2504	0.0				p.S1019G		Atlas-SNP	.											.	BRPF3	93	.	0			c.A3055G						PASS	.	A	GLY/SER	3,4403	6.2+/-15.9	0,3,2200	183	146	159		3055	3.4	1	6	dbSNP_134	159	27,8573	19.2+/-60.6	0,27,4273	yes	missense	BRPF3	NM_015695.2	56	0,30,6473	GG,GA,AA		0.314,0.0681,0.2307	benign	1019/1206	36185759	30,12976	2203	4300	6503	SO:0001583	missense	27154	exon9			GGTCTCAGTGGTG	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.3055A>G	6.37:g.36185759A>G	ENSP00000350267:p.Ser1019Gly	174	0	0		243	99	0.407407	NM_015695	A6ND56|A6NJE2|B7ZLN5|E7EX85|Q17RB6|Q5R3K8	Missense_Mutation	SNP	ENST00000357641.6	37	CCDS34437.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	A	14.27	2.484908	0.44147	6.81E-4	0.00314	ENSG00000096070	ENST00000357641;ENST00000339717;ENST00000543502;ENST00000534400	T;T;T;T	0.19394	2.27;2.28;2.28;2.15	6.05	3.37	0.38596	.	0.607803	0.19087	N	0.123094	T	0.05135	0.0137	N	0.24115	0.695	0.80722	D	1	B;B	0.17465	0.022;0.0	B;B	0.18263	0.021;0.0	T	0.17501	-1.0367	10	0.25751	T	0.34	.	8.2232	0.31554	0.7652:0.0:0.2348:0.0	.	749;1019	Q17RB6;Q9ULD4	.;BRPF3_HUMAN	G	1019;749;749;1019	ENSP00000350267:S1019G;ENSP00000345419:S749G;ENSP00000445352:S749G;ENSP00000436504:S1019G	ENSP00000345419:S749G	S	+	1	0	BRPF3	36293737	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.870000	0.39529	1.116000	0.41820	0.528000	0.53228	AGT	A|0.997;G|0.003	0.003	strong		0.498	BRPF3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040335.3	NM_015695		G	36185759	A	G	36185759	3	3	26	1	0	0	0	0	1	0	0	0	1523	188	7	3	3085	3	BRPF3	6	36185759	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	3375812	36185759	134929308	205	9968											
TREML4	285852	hgsc.bcm.edu	37	chr6	41196733	41196733	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtggaatctacaacgcttcCgaaaacatcatcactgttct	12	12	6	11	2	4	0	2	0	2	0	5	2	5	1	1	1	3	2	1	1	5	3	rs147088240	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:41196733C>T	ENST00000341495.2	+	2	449	c.345C>T	c.(343-345)tcC>tcT	p.S115S	TREML4_ENST00000448827.2_Silent_p.S115S	NM_198153.2	NP_937796.1	Q6UXN2	TRML4_HUMAN	triggering receptor expressed on myeloid cells-like 4	115	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)					ACAACGCTTCCGAAAACATCA	0.488													C|||	12	0.00239617	0.0	0.0086	5008	,	,		19933	0.0		0.006	False		,,,				2504	0.0				p.S115S		Atlas-SNP	.											.	TREML4	25	.	0			c.C345T						PASS	.	C		6,4400		0,6,2197	83	80	81		345	-1	0	6	dbSNP_134	81	41,8559		0,41,4259	no	coding-synonymous	TREML4	NM_198153.2		0,47,6456	TT,TC,CC		0.4767,0.1362,0.3614		115/201	41196733	47,12959	2203	4300	6503	SO:0001819	synonymous_variant	285852	exon2			CGCTTCCGAAAAC	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.345C>T	6.37:g.41196733C>T		192	0	0		168	88	0.52381	NM_198153	B7ZL92	Silent	SNP	ENST00000341495.2	37	CCDS34446.1																																																																																			C|0.996;T|0.004	0.004	strong		0.488	TREML4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043873.2			T	41196733	C	T	41196733	2	4	26	1	0	0	0	0	0	0	0	1	16489	639	23	1		1	TREML4	6	41196733	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	5010974	41196733	129918334	206	9969											
TRERF1	55809	hgsc.bcm.edu	37	chr6	42236589	42236589	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	gggcctgcagtggctgtcctCcctgcactggcacctgagcc	4	8	13	16	0	0	1	0	1	0	0	2	1	2	1	5	3	3	4	5	3	0	0			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:42236589C>G	ENST00000372922.4	-	5	1302	c.740G>C	c.(739-741)gGa>gCa	p.G247A	TRERF1_ENST00000354325.2_Missense_Mutation_p.G247A|TRERF1_ENST00000541110.1_Missense_Mutation_p.G247A|TRERF1_ENST00000372917.4_Missense_Mutation_p.G247A|TRERF1_ENST00000340840.2_Missense_Mutation_p.G247A	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	247	Gln-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)			TGGCTGTCCTCCCTGCACTGG	0.602																																					p.G247A		Atlas-SNP	.											.	TRERF1	124	.	0			c.G740C						PASS	.						48	47	47					6																	42236589		2202	4299	6501	SO:0001583	missense	55809	exon5			TGTCCTCCCTGCA	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.740G>C	6.37:g.42236589C>G	ENSP00000362013:p.Gly247Ala	84	0	0		119	60	0.504202	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Missense_Mutation	SNP	ENST00000372922.4	37	CCDS4867.1	.	.	.	.	.	.	.	.	.	.	C	14.82	2.648503	0.47258	.	.	ENSG00000124496	ENST00000541110;ENST00000372917;ENST00000372922;ENST00000340840;ENST00000354325	T;T;T;T;T	0.12465	2.84;2.68;2.84;2.68;2.68	5.54	3.63	0.41609	.	0.268702	0.25566	N	0.029784	T	0.07593	0.0191	N	0.24115	0.695	0.25742	N	0.985152	D;D;D;B;B	0.71674	0.998;0.997;0.997;0.008;0.008	D;D;D;B;B	0.70935	0.971;0.936;0.936;0.015;0.015	T	0.15206	-1.0445	10	0.25106	T	0.35	-6.3785	4.8502	0.13533	0.0:0.4353:0.3986:0.1661	.	247;247;247;86;86	Q96PN7-4;Q05GC8;Q96PN7;Q96PN7-2;Q96PN7-3	.;.;TREF1_HUMAN;.;.	A	247	ENSP00000439689:G247A;ENSP00000362008:G247A;ENSP00000362013:G247A;ENSP00000339438:G247A;ENSP00000346285:G247A	ENSP00000339438:G247A	G	-	2	0	TRERF1	42344567	0.891000	0.30450	0.993000	0.49108	0.992000	0.81027	0.852000	0.27764	1.319000	0.45190	0.462000	0.41574	GGA	.	.	none		0.602	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502		G	42236589	C	G	42236589	3	3	26	1	0	0	0	0	1	0	0	0	16490	855	30	4	2918	4	TRERF1	6	42236589	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1039856	42236589	128878478	207	9970											
CUL9	23113	hgsc.bcm.edu	37	chr6	43174057	43174065	+	Splice_Site	DEL	AGGAGGAAG	AGGAGGAAG	-																															ttgaaatccttctgtccctcAggaggaagaggaggaagagg																								rs542758187	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AGGAGGAAG	AGGAGGAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:43174057_43174065delAGGAGGAAG	ENST00000252050.4	+	26	5106_5113	c.5022_5029delAGGAGGAAG	c.(5020-5031)gaaggaggaaga>gaga	p.GGR1675del	CUL9_ENST00000372647.2_Splice_Site_p.GGR1675del|CUL9_ENST00000354495.3_Splice_Site_p.GGR1565del	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	1675	Glu-rich.				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						TCTGTCCCTCAGGAGGAAGAGGAGGAAGA	0.517														9	0.00179712	0.0	0.0	5008	,	,		22978	0.0		0.004	False		,,,				2504	0.0051				p.1675_1676del		Pindel,Atlas-Indel	.											.	CUL9	248	.	0			c.5023_5028del						PASS	.			3,4261		0,3,2129						3.3	0.9			67	25,8229		0,25,4102	no	coding-near-splice	CUL9	NM_015089.2		0,28,6231	A1A1,A1R,RR		0.3029,0.0704,0.2237				28,12490				SO:0001630	splice_region_variant	23113	exon26			.	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.5023-1AGGAGGAAG>-	6.37:g.43174066_43174074delAGGAGGAAG		66	0	.		50	20	0.4	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	In_Frame_Del	DEL	ENST00000252050.4	37	CCDS4890.1																																																																																			.	.	none		0.517	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	In_Frame_Del	-	43174065	AGGAGGAAG	-	43174057	8	5	26	1	0	1	0	1	0	0	1	0	4063	202	7	0	5119	0	CUL9	6	43174057	Splice_Site	DEL	AGGAGGAAG	TCGA-G8-6907-01A-11D-2210-10	937468	43174057	127941010	208	9971											
CYP39A1	51302	hgsc.bcm.edu	37	chr6	46563779	46563779	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgacaccaggagcttttaaaCgaatggtttccaaaacacac	15	9	7	10	1	0	1	0	1	0	0	1	3	1	2	2	2	3	2	2	2	5	3	rs147961800	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:46563779C>T	ENST00000275016.2	-	8	1213	c.1010G>A	c.(1009-1011)cGt>cAt	p.R337H		NM_016593.3	NP_057677.2	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A, polypeptide 1	337					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						AGCTTTTAAACGAATGGTTTC	0.338													C|||	7	0.00139776	0.0	0.0029	5008	,	,		15087	0.0		0.004	False		,,,				2504	0.001				p.R337H		Atlas-SNP	.											CYP39A1,caecum,carcinoma,-1,1	CYP39A1	41	1	0			c.G1010A						PASS	.	C	HIS/ARG	0,4406		0,0,2203	92	98	96		1010	3.9	0.7	6	dbSNP_134	96	14,8586	10.5+/-38.8	0,14,4286	yes	missense	CYP39A1	NM_016593.3	29	0,14,6489	TT,TC,CC		0.1628,0.0,0.1076	probably-damaging	337/470	46563779	14,12992	2203	4300	6503	SO:0001583	missense	51302	exon8			TTTAAACGAATGG	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.1010G>A	6.37:g.46563779C>T	ENSP00000275016:p.Arg337His	324	1	0.00308642		316	143	0.452532	NM_016593	Q5VTT0|Q96FW5	Missense_Mutation	SNP	ENST00000275016.2	37	CCDS4916.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	21.3	4.127159	0.77549	0.0	0.001628	ENSG00000146233	ENST00000275016	D	0.97505	-4.41	5.7	3.91	0.45181	.	0.141963	0.47455	D	0.000237	D	0.98099	0.9373	M	0.89601	3.045	0.51012	D	0.9999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98321	1.0528	10	0.87932	D	0	-13.1901	9.8571	0.41092	0.0:0.7875:0.1394:0.0731	.	317;337	B7Z786;Q9NYL5	.;CP39A_HUMAN	H	337	ENSP00000275016:R337H	ENSP00000275016:R337H	R	-	2	0	CYP39A1	46671738	0.999000	0.42202	0.739000	0.30968	0.954000	0.61252	4.208000	0.58486	0.746000	0.32786	0.557000	0.71058	CGT	C|0.999;T|0.001	0.001	strong		0.338	CYP39A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040787.1			T	46563779	C	T	46563779	3	4	26	1	0	0	0	0	1	0	0	0	4179	536	19	1	419	1	CYP39A1	6	46563779	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	3389722	46563779	124551288	209	9972											
TDRD6	221400	hgsc.bcm.edu	37	chr6	46658915	46658915	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tattttagaacagttgtcatGtagtattacacaattaagta	15	16	6	4	0	1	1	1	0	0	1	1	1	1	1	0	0	2	4	0	0	9	9	rs140575009	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:46658915G>A	ENST00000316081.6	+	1	3050	c.3050G>A	c.(3049-3051)tGt>tAt	p.C1017Y	TDRD6_ENST00000544460.1_Missense_Mutation_p.C1017Y	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	1017					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)			CAGTTGTCATGTAGTATTACA	0.348																																					p.C1017Y		Atlas-SNP	.											.	TDRD6	205	.	0			c.G3050A						PASS	.	G	TYR/CYS,TYR/CYS	1,4405	2.1+/-5.4	0,1,2202	50	54	53		3050,3050	-1.1	0	6	dbSNP_134	53	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	TDRD6	NM_001010870.2,NM_001168359.1	194,194	0,6,6497	AA,AG,GG		0.0581,0.0227,0.0461	benign,benign	1017/2097,1017/2067	46658915	6,13000	2203	4300	6503	SO:0001583	missense	221400	exon1			TGTCATGTAGTAT	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.3050G>A	6.37:g.46658915G>A	ENSP00000346065:p.Cys1017Tyr	80	0	0		65	28	0.430769	NM_001168359	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Missense_Mutation	SNP	ENST00000316081.6	37	CCDS34470.1	.	.	.	.	.	.	.	.	.	.	G	0.004	-2.250495	0.00268	2.27E-4	5.81E-4	ENSG00000180113	ENST00000544460;ENST00000316081	T;T	0.09073	3.02;3.02	5.36	-1.1	0.09872	Maternal tudor protein (1);	1.918670	0.01499	N	0.017422	T	0.02012	0.0063	N	0.20986	0.625	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.08055	0.002;0.003	T	0.45731	-0.9241	10	0.51188	T	0.08	1.382	8.6227	0.33870	0.6481:0.1225:0.2294:0.0	.	1017;1017	F5H5M3;O60522	.;TDRD6_HUMAN	Y	1017	ENSP00000443299:C1017Y;ENSP00000346065:C1017Y	ENSP00000346065:C1017Y	C	+	2	0	TDRD6	46766874	0.000000	0.05858	0.000000	0.03702	0.985000	0.73830	0.088000	0.14979	-0.617000	0.05664	-0.136000	0.14681	TGT	G|0.999;A|0.001	0.001	strong		0.348	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443		A	46658915	G	A	46658915	3	1	26	1	0	0	0	0	1	0	0	0	15749	1377	48	2	3052	2	TDRD6	6	46658915	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	95136	46658915	124456152	210	9973											
PKHD1	5314	hgsc.bcm.edu	37	chr6	51892977	51892977	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgagtgaatgctgaccccAttgatagagacggaaattct	12	11	11	7	1	1	5	0	4	1	1	1	7	1	6	2	1	1	1	2	1	3	3	rs141574387	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:51892977A>G	ENST00000371117.3	-	30	3812	c.3537T>C	c.(3535-3537)aaT>aaC	p.N1179N	PKHD1_ENST00000340994.4_Silent_p.N1179N	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1179	IPT/TIG 6; atypical.				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)					TGCTGACCCCATTGATAGAGA	0.498													A|||	4	0.000798722	0.0	0.0029	5008	,	,		19364	0.0		0.001	False		,,,				2504	0.001				p.N1179N		Atlas-SNP	.											.	PKHD1	927	.	0			c.T3537C						PASS	.	A	,	0,4406		0,0,2203	144	158	154		3537,3537	2	1	6	dbSNP_134	154	15,8585	11.2+/-40.8	0,15,4285	no	coding-synonymous,coding-synonymous	PKHD1	NM_138694.3,NM_170724.2	,	0,15,6488	GG,GA,AA		0.1744,0.0,0.1153	,	1179/4075,1179/3397	51892977	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	5314	exon30			GACCCCATTGATA	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.3537T>C	6.37:g.51892977A>G		81	0	0		96	58	0.604167	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			A|0.999;G|0.001	0.001	strong		0.498	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		G	51892977	A	G	51892977	2	3	26	1	0	0	0	0	0	0	0	1	11980	214	8	3		3	PKHD1	6	51892977	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	5234062	51892977	119222090	211	9974											
MYO6	4646	hgsc.bcm.edu	37	chr6	76542585	76542585	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aagcttttcgagacatgaagGtgctcaagatgagtcagtct	12	11	11	7	1	3	4	2	2	1	2	4	5	3	4	0	1	2	2	0	1	3	2			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:76542585G>A	ENST00000369977.3	+	6	557	c.418G>A	c.(418-420)Gtg>Atg	p.V140M	MYO6_ENST00000369985.4_Missense_Mutation_p.V140M|MYO6_ENST00000369981.3_Missense_Mutation_p.V140M|MYO6_ENST00000369975.1_Missense_Mutation_p.V140M	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	140	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)		AGACATGAAGGTGCTCAAGAT	0.333																																					p.V140M		Atlas-SNP	.											.	MYO6	124	.	0			c.G418A						PASS	.						85	90	88					6																	76542585		2203	4300	6503	SO:0001583	missense	4646	exon6			ATGAAGGTGCTCA	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.418G>A	6.37:g.76542585G>A	ENSP00000358994:p.Val140Met	56	0	0		50	26	0.52	NM_004999	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Missense_Mutation	SNP	ENST00000369977.3	37	CCDS34487.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.914335	0.92178	.	.	ENSG00000196586	ENST00000428345;ENST00000369981;ENST00000369985;ENST00000369977;ENST00000369975	D;D;D;D	0.87412	-2.25;-2.25;-2.25;-2.25	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	D	0.91002	0.7170	L	0.55990	1.75	0.80722	D	1	D;D	0.69078	0.997;0.996	D;D	0.79784	0.957;0.993	D	0.89801	0.3975	10	0.46703	T	0.11	.	19.6547	0.95831	0.0:0.0:1.0:0.0	.	140;140	Q9UM54-2;Q9UM54-1	.;.	M	140	ENSP00000358998:V140M;ENSP00000359002:V140M;ENSP00000358994:V140M;ENSP00000358992:V140M	ENSP00000358992:V140M	V	+	1	0	MYO6	76599305	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.388000	0.97237	2.717000	0.92951	0.650000	0.86243	GTG	.	.	none		0.333	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999		A	76542585	G	A	76542585	3	1	26	1	0	0	0	0	1	0	0	0	10090	1261	44	2	436	2	MYO6	6	76542585	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	24649608	76542585	94572482	212	9975											
KIAA1009	22832	hgsc.bcm.edu	37	chr6	84884544	84884544	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attttctagttctttctcctTttctgagaatgtggctttaa	7	21	6	7	0	4	1	0	1	4	1	5	2	4	1	1	1	0	2	1	1	3	9	rs149892489		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:84884544T>G	ENST00000403245.3	-	15	2041	c.1927A>C	c.(1927-1929)Aag>Cag	p.K643Q	KIAA1009_ENST00000257766.4_Missense_Mutation_p.K567Q|KIAA1009_ENST00000461137.1_5'UTR	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)		TCTTTCTCCTTTTCTGAGAAT	0.348																																					p.K643Q		Atlas-SNP	.											.	KIAA1009	119	.	0			c.A1927C						PASS	.						78	70	72					6																	84884544		2203	4297	6500	SO:0001583	missense	22832	exon15			TCTCCTTTTCTGA																												ENST00000403245.3:c.1927A>C	6.37:g.84884544T>G	ENSP00000385215:p.Lys643Gln	174	0	0		205	17	0.0829268	NM_014895		Missense_Mutation	SNP	ENST00000403245.3	37	CCDS34494.2	.	.	.	.	.	.	.	.	.	.	T	21.8	4.205158	0.79127	.	.	ENSG00000135315	ENST00000257766;ENST00000403245	T;T	0.24723	1.84;1.85	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.44540	0.1298	M	0.77616	2.38	0.38548	D	0.949389	D	0.89917	1.0	D	0.85130	0.997	T	0.48222	-0.9054	10	0.52906	T	0.07	-30.2168	15.7393	0.77876	0.0:0.0:0.0:1.0	.	643	Q5TB80	QN1_HUMAN	Q	567;643	ENSP00000257766:K567Q;ENSP00000385215:K643Q	ENSP00000257766:K567Q	K	-	1	0	KIAA1009	84941263	1.000000	0.71417	0.993000	0.49108	0.784000	0.44337	5.561000	0.67339	2.184000	0.69523	0.460000	0.39030	AAG	.	.	weak		0.348	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1			G	84884544	T	G	84884544	3	3	26	1	0	0	0	0	1	0	0	0	8212	1850	64	5	2336	5	KIAA1009	6	84884544	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	8341959	84884544	86230523	213	9976											
C6orf162	57150	hgsc.bcm.edu	37	chr6	88046818	88046818	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagaaagagtttcaaagcccAgggctcagaggggtgcgcac	12	5	15	9	1	2	3	2	0	0	3	2	4	2	3	1	3	2	3	1	3	2	1	rs138902411	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:88046818A>G	ENST00000392863.1	+	3	158	c.69A>G	c.(67-69)ccA>ccG	p.P23P	RP1-102H19.8_ENST00000448282.2_Silent_p.P23P|SMIM8_ENST00000608353.1_Silent_p.P23P|SMIM8_ENST00000608868.1_Silent_p.P23P|SMIM8_ENST00000608525.1_Silent_p.P23P|SMIM8_ENST00000229570.5_Silent_p.P23P	NM_001042493.1	NP_001035958.1	Q96KF7	SMIM8_HUMAN	small integral membrane protein 8	23						integral component of membrane (GO:0016021)											TTCAAAGCCCAGGGCTCAGAG	0.408													A|||	2	0.000399361	0.0	0.0	5008	,	,		14790	0.0		0.002	False		,,,				2504	0.0				p.P23P		Atlas-SNP	.											.	.	.	.	0			c.A69G						PASS	.	A	,	5,4401	9.9+/-24.2	0,5,2198	94	96	95		69,69	2.1	1	6	dbSNP_134	95	18,8582	12.6+/-44.7	0,18,4282	no	coding-synonymous,coding-synonymous	C6orf162	NM_001042493.1,NM_020425.4	,	0,23,6480	GG,GA,AA		0.2093,0.1135,0.1768	,	23/98,23/98	88046818	23,12983	2203	4300	6503	SO:0001819	synonymous_variant	57150	exon3			AAGCCCAGGGCTC	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.69A>G	6.37:g.88046818A>G		89	0	0		68	39	0.573529	NM_001042493	B2R4V6|E1P505|Q5TEZ3|Q6NSD2|Q8IZ10	Silent	SNP	ENST00000392863.1	37	CCDS34496.1																																																																																			A|0.998;G|0.002	0.002	strong		0.408	SMIM8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472479.2	NM_020425		G	88046818	A	G	88046818	2	3	26	1	0	0	0	0	0	0	0	1	2342	175	7	3		3	C6orf162	6	88046818	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	3162274	88046818	83068249	214	9977											
LYRM2	57226	hgsc.bcm.edu	37	chr6	90347516	90347516	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcttgcccaatctttcaggTatttgcgatcagaatcattt	9	16	6	10	1	5	1	3	0	2	1	5	2	5	1	1	1	2	1	1	1	3	5	rs151021837	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:90347516T>A	ENST00000523377.1	-	2	167	c.131A>T	c.(130-132)tAc>tTc	p.Y44F	LYRM2_ENST00000517396.1_5'UTR|LYRM2_ENST00000520441.1_Missense_Mutation_p.Y44F|LYRM2_ENST00000520318.1_Missense_Mutation_p.Y44F	NM_020466.4	NP_065199.1	Q9NU23	LYRM2_HUMAN	LYR motif containing 2	44						mitochondrion (GO:0005739)				kidney(1)|large_intestine(1)|lung(1)	3		all_cancers(76;2.76e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;3.72e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0131)		ATCTTTCAGGTATTTGCGATC	0.403													T|||	15	0.00299521	0.0008	0.0014	5008	,	,		16864	0.0		0.0129	False		,,,				2504	0.0				p.Y44F		Atlas-SNP	.											.	LYRM2	6	.	0			c.A131T						PASS	.	T	PHE/TYR	8,4398	14.3+/-33.2	0,8,2195	176	171	173		131	4.9	1	6	dbSNP_134	173	91,8509	51.5+/-111.7	1,89,4210	no	missense	LYRM2	NM_020466.4	22	1,97,6405	AA,AT,TT		1.0581,0.1816,0.7612	probably-damaging	44/89	90347516	99,12907	2203	4300	6503	SO:0001583	missense	57226	exon2			TTCAGGTATTTGC	BC009782	CCDS5023.1	6q15	2006-09-19			ENSG00000083099	ENSG00000083099		"LYR motif containing"	25229	protein-coding gene	gene with protein product						12477932	Standard	NM_020466		Approved	DJ122O8.2	uc003pnm.3	Q9NU23	OTTHUMG00000015203	ENST00000523377.1:c.131A>T	6.37:g.90347516T>A	ENSP00000430025:p.Tyr44Phe	257	0	0		318	161	0.506289	NM_020466	B2R4U2|E1P517	Missense_Mutation	SNP	ENST00000523377.1	37	CCDS5023.1	10	0.004578754578754579	0	0.0	0	0.0	0	0.0	10	0.013192612137203167	T	22.3	4.274655	0.80580	0.001816	0.010581	ENSG00000083099	ENST00000520441;ENST00000523377;ENST00000520318	T;T;T	0.72282	-0.64;-0.64;-0.64	6.03	4.86	0.63082	.	0.188192	0.47455	D	0.000240	T	0.49795	0.1578	.	.	.	0.41428	D	0.987849	B	0.14438	0.01	B	0.20767	0.031	T	0.54002	-0.8358	9	0.59425	D	0.04	.	11.4509	0.50151	0.1342:0.0:0.0:0.8658	.	44	Q9NU23	LYRM2_HUMAN	F	44	ENSP00000427859:Y44F;ENSP00000430025:Y44F;ENSP00000428207:Y44F	ENSP00000430316:Y44F	Y	-	2	0	LYRM2	90404237	1.000000	0.71417	0.999000	0.59377	0.787000	0.44495	4.337000	0.59310	1.083000	0.41159	0.455000	0.32223	TAC	T|0.994;A|0.006	0.006	strong		0.403	LYRM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041498.2	NM_020466		A	90347516	T	A	90347516	3	1	26	1	0	0	0	0	1	0	0	0	9129	1638	57	5	143	5	LYRM2	6	90347516	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	2300698	90347516	80767551	215	9978											
MDN1	23195	hgsc.bcm.edu	37	chr6	90384216	90384216	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcaggcgctctgtccacTgctgcacgccatcctgaggg	5	8	13	15	2	1	1	0	1	1	0	3	1	3	1	3	2	3	5	3	2	0	0			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:90384216T>G	ENST00000369393.3	-	79	12969	c.12854A>C	c.(12853-12855)cAg>cCg	p.Q4285P	RP1-122O8.7_ENST00000438877.1_RNA|MDN1_ENST00000428876.1_Missense_Mutation_p.Q4285P|MDN1_ENST00000468568.1_5'Flank			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4285					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)		CTCTGTCCACTGCTGCACGCC	0.642																																					p.Q4285P		Atlas-SNP	.											.	MDN1	478	.	0			c.A12854C						PASS	.						22	23	23					6																	90384216		2203	4299	6502	SO:0001583	missense	23195	exon79			GTCCACTGCTGCA	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.12854A>C	6.37:g.90384216T>G	ENSP00000358400:p.Gln4285Pro	20	0	0		30	13	0.433333	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	T	13.08	2.129345	0.37630	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03301	3.98;3.98	5.87	5.87	0.94306	.	0.308307	0.33691	N	0.004644	T	0.03263	0.0095	M	0.63428	1.95	0.34397	D	0.694857	P	0.51653	0.947	P	0.44597	0.454	T	0.41179	-0.9523	10	0.48119	T	0.1	.	12.0858	0.53695	0.0:0.0685:0.0:0.9315	.	4285	Q9NU22	MDN1_HUMAN	P	4285	ENSP00000358400:Q4285P;ENSP00000413970:Q4285P	ENSP00000358400:Q4285P	Q	-	2	0	MDN1	90440937	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.651000	0.37302	2.248000	0.74166	0.533000	0.62120	CAG	.	.	none		0.642	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			G	90384216	T	G	90384216	3	3	26	1	0	0	0	0	1	0	0	0	9424	1580	55	5	4032	5	MDN1	6	90384216	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	36700	90384216	80730851	216	9979											
CASP8AP2	9994	hgsc.bcm.edu	37	chr6	90572435	90572435	+	RNA	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggtcacacagtcgagtagActctcaaagtgacaaaaaac	18	6	8	9	1	2	2	2	1	1	1	4	3	2	2	0	1	1	1	0	1	6	1			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:90572435A>C	ENST00000551025.1	+	0	2444									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)		AGTCGAGTAGACTCTCAAAGT	0.348																																					p.D336A	Colon(187;1656 2025 17045 31481 39901)	Atlas-SNP	.											.	CASP8AP2	108	.	0			c.A1007C						PASS	.																																					9994	exon7			GAGTAGACTCTCA	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.90572435A>C		26	0	0		38	14	0.368421	NM_001137667		Missense_Mutation	SNP	ENST00000551025.1	37																																																																																				.	.	none		0.348	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667		C	90572435	A	C	90572435	1	2	26	0	1	0	0	0	0	0	0	0	2680	275	10	5		5	CASP8AP2	6	90572435	RNA	SNP	A	TCGA-G8-6907-01A-11D-2210-10	188219	90572435	80542632	217	9980											
C6orf167	253714	hgsc.bcm.edu	37	chr6	97599674	97599674	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagaagtcagctgggaggaaGgttcttcttctgaccccact	9	10	11	11	0	4	2	1	1	3	1	4	4	4	4	2	3	1	2	2	3	2	3	rs138146580	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:97599674G>A	ENST00000275053.4	-	23	3720	c.3455C>T	c.(3454-3456)cCt>cTt	p.P1152L	MMS22L_ENST00000369251.2_Missense_Mutation_p.P1112L	NM_198468.2	NP_940870.2	Q6ZRQ5	MMS22_HUMAN	MMS22-like, DNA repair protein	1152					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						CTGGGAGGAAGGTTCTTCTTC	0.433													G|||	37	0.00738818	0.0023	0.0058	5008	,	,		15425	0.0		0.0239	False		,,,				2504	0.0061				p.P1152L		Atlas-SNP	.											.	MMS22L	102	.	0			c.C3455T						PASS	.	G	LEU/PRO	17,4389	24.3+/-50.5	0,17,2186	204	203	203		3455	3.6	1	6	dbSNP_134	203	155,8445	73.5+/-136.2	2,151,4147	yes	missense	MMS22L	NM_198468.2	98	2,168,6333	AA,AG,GG		1.8023,0.3858,1.3225	benign	1152/1244	97599674	172,12834	2203	4300	6503	SO:0001583	missense	253714	exon23			GAGGAAGGTTCTT		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.3455C>T	6.37:g.97599674G>A	ENSP00000275053:p.Pro1152Leu	214	1	0.0046729		187	100	0.534759	NM_198468	D6R9Y8|D6RBQ4|E1P529|Q5THT2|Q68CQ6|Q68D32	Missense_Mutation	SNP	ENST00000275053.4	37	CCDS5039.1	26	0.011904761904761904	3	0.006097560975609756	4	0.011049723756906077	0	0.0	19	0.025065963060686015	G	9.389	1.074903	0.20227	0.003858	0.018023	ENSG00000146263	ENST00000275053;ENST00000369251	T;T	0.29655	3.93;1.56	5.44	3.59	0.41128	.	0.290094	0.38492	N	0.001666	T	0.09202	0.0227	L	0.56769	1.78	0.44966	D	0.997984	B;B	0.31548	0.328;0.082	B;B	0.27380	0.079;0.036	T	0.13255	-1.0516	10	0.14252	T	0.57	.	3.4047	0.07336	0.1576:0.1261:0.5698:0.1465	.	1112;1152	E2QRD4;Q6ZRQ5	.;MMS22_HUMAN	L	1152;1112	ENSP00000275053:P1152L;ENSP00000358254:P1112L	ENSP00000275053:P1152L	P	-	2	0	MMS22L	97706395	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	1.175000	0.31944	0.606000	0.29965	0.650000	0.86243	CCT	G|0.987;A|0.013	0.013	strong		0.433	MMS22L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041573.3	NM_198468		A	97599674	G	A	97599674	3	1	26	1	0	0	0	0	1	0	0	0	2344	1000	35	2	288	2	C6orf167	6	97599674	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	7027239	97599674	73515393	218	9981											
SFRS18	25957	hgsc.bcm.edu	37	chr6	99848998	99848998	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttctacgtctctctcgggaAggactccgatttcgtcgtct	5	14	9	13	5	4	0	0	0	4	0	9	3	5	2	1	2	1	0	1	2	2	3	rs369239036		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:99848998A>C	ENST00000369239.5	-	12	2040	c.1836T>G	c.(1834-1836)ccT>ccG	p.P612P	PNISR_ENST00000438806.1_Silent_p.P612P	NM_032870.2	NP_116259.2	Q8TF01	PNISR_HUMAN	PNN-interacting serine/arginine-rich protein	612						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						TCTCTCGGGAAGGACTCCGAT	0.428																																					p.P612P		Atlas-SNP	.											.	PNISR	74	.	0			c.T1836G						PASS	.	A	,	0,4406		0,0,2203	110	98	102		1836,1836	4.2	1	6		102	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	PNISR	NM_015491.1,NM_032870.2	,	0,2,6501	CC,CA,AA		0.0233,0.0,0.0154	,	612/806,612/806	99848998	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	25957	exon11			TCGGGAAGGACTC	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.1836T>G	6.37:g.99848998A>C		113	0	0		164	83	0.506098	NM_015491	A8K540|E1P5D2|Q5T064|Q5T065|Q6P2B4|Q6P2N4|Q6PJ93|Q6PK36|Q7Z640|Q8N2L1|Q8TF00|Q96K10|Q96SI3|Q96SM5|Q9P076|Q9P0C0|Q9Y4N3	Silent	SNP	ENST00000369239.5	37	CCDS5043.1																																																																																			.	.	weak		0.428	PNISR-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041598.1	NM_032870		C	99848998	A	C	99848998	2	2	26	1	0	0	0	0	0	0	0	1	14189	59	3	5		5	SFRS18	6	99848998	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	2249324	99848998	71266069	219	9982											
FAM184A	79632	hgsc.bcm.edu	37	chr6	119341211	119341211	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggttttgcttcgcaaaaaagCtctttcctcttcaagttgag	9	15	8	9	1	3	1	1	1	2	0	5	1	4	1	1	1	2	5	1	1	4	6	rs41292560	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:119341211C>T	ENST00000338891.7	-	4	1707	c.1264G>A	c.(1264-1266)Gct>Act	p.A422T	FAM184A_ENST00000368475.4_Missense_Mutation_p.A302T|FAM184A_ENST00000522284.1_Missense_Mutation_p.A302T|FAM184A_ENST00000521531.1_Missense_Mutation_p.A422T|FAM184A_ENST00000352896.5_Missense_Mutation_p.A302T|RP11-351A11.1_ENST00000518570.1_RNA	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	422						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						CGCAAAAAAGCTCTTTCCTCT	0.398													C|||	20	0.00399361	0.0	0.0029	5008	,	,		15929	0.0		0.0169	False		,,,				2504	0.001				p.A422T		Atlas-SNP	.											.	FAM184A	109	.	0			c.G1264A						PASS	.	C	THR/ALA,THR/ALA	11,3663		0,11,1826	156	142	146		904,1264	2.7	1	6	dbSNP_127	146	96,8068		1,94,3987	yes	missense,missense	FAM184A	NM_001100411.1,NM_024581.4	58,58	1,105,5813	TT,TC,CC		1.1759,0.2994,0.9039	benign,benign	302/972,422/1141	119341211	107,11731	1837	4082	5919	SO:0001583	missense	79632	exon4			AAAAAGCTCTTTC	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.1264G>A	6.37:g.119341211C>T	ENSP00000342604:p.Ala422Thr	183	0	0		224	113	0.504464	NM_024581	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Missense_Mutation	SNP	ENST00000338891.7	37	CCDS43499.1	15	0.006868131868131868	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	13	0.017150395778364115	C	12.19	1.862249	0.32884	0.002994	0.011759	ENSG00000111879	ENST00000338891;ENST00000352896;ENST00000368475;ENST00000521531;ENST00000522284	T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48	5.85	2.69	0.31865	.	0.416381	0.27831	N	0.017672	T	0.05960	0.0155	L	0.36672	1.1	0.27593	N	0.949223	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.11329	0.004;0.002;0.006	T	0.33471	-0.9867	10	0.15066	T	0.55	-3.7601	1.9962	0.03457	0.2501:0.3672:0.0:0.3827	rs41292560	422;302;422	Q8NB25-2;F8W8D6;Q8NB25	.;.;F184A_HUMAN	T	422;302;302;422;302	ENSP00000342604:A422T;ENSP00000326608:A302T;ENSP00000357460:A302T;ENSP00000430442:A422T;ENSP00000429826:A302T	ENSP00000342604:A422T	A	-	1	0	FAM184A	119382910	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.652000	0.46682	0.788000	0.33755	0.557000	0.71058	GCT	C|0.992;T|0.008	0.008	strong		0.398	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581		T	119341211	C	T	119341211	3	4	26	1	0	0	0	0	1	0	0	0	5516	797	28	2	2218	2	FAM184A	6	119341211	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	19492213	119341211	51773856	220	9983											
UTRN	7402	hgsc.bcm.edu	37	chr6	144898276	144898276	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttggaggctgagtggaggaCggtgcaggcctctcgcagag	7	7	18	9	2	1	2	0	1	1	1	2	5	1	5	1	6	1	3	1	6	0	1	rs367807203		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:144898276C>T	ENST00000367545.3	+	50	7331	c.7331C>T	c.(7330-7332)aCg>aTg	p.T2444M		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	2444					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)		GAGTGGAGGACGGTGCAGGCC	0.493																																					p.T2444M		Atlas-SNP	.											.	UTRN	327	.	0			c.C7331T						PASS	.	C	MET/THR	0,4406		0,0,2203	105	86	93		7331	1.1	0	6		93	1,8599	1.2+/-3.3	0,1,4299	no	missense	UTRN	NM_007124.2	81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	2444/3434	144898276	1,13005	2203	4300	6503	SO:0001583	missense	7402	exon50			GGAGGACGGTGCA	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.7331C>T	6.37:g.144898276C>T	ENSP00000356515:p.Thr2444Met	139	0	0		179	89	0.497207	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	C	13.76	2.333825	0.41297	0.0	1.16E-4	ENSG00000152818	ENST00000367545	T	0.60299	0.2	6.03	1.14	0.20703	.	0.371682	0.22724	N	0.056418	T	0.20088	0.0483	L	0.33485	1.01	0.09310	N	1	B	0.20261	0.043	B	0.25291	0.059	T	0.19910	-1.0291	10	0.48119	T	0.1	.	2.8168	0.05458	0.1134:0.528:0.11:0.2486	.	2444	P46939	UTRO_HUMAN	M	2444	ENSP00000356515:T2444M	ENSP00000356515:T2444M	T	+	2	0	UTRN	144939969	0.006000	0.16342	0.001000	0.08648	0.663000	0.39108	0.115000	0.15540	0.134000	0.18681	-0.137000	0.14449	ACG	.	.	weak		0.493	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			T	144898276	C	T	144898276	3	4	26	1	0	0	0	0	1	0	0	0	17118	536	19	1	7529	1	UTRN	6	144898276	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	25557065	144898276	26216791	221	9984											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152457795	152457795	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagcaggccccgccactcCtccagcagagagcacactcg	9	4	10	18	2	0	1	0	0	0	1	3	2	2	1	5	1	4	4	5	1	0	0	rs118187988	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:152457795C>T	ENST00000367255.5	-	141	26218	c.25617G>A	c.(25615-25617)gaG>gaA	p.E8539E	SYNE1_ENST00000356820.4_Silent_p.E3063E|SYNE1_ENST00000539504.1_Silent_p.E694E|SYNE1_ENST00000341594.5_Silent_p.E8151E|SYNE1_ENST00000423061.1_Silent_p.E8491E|SYNE1_ENST00000448038.1_Silent_p.E8491E|SYNE1_ENST00000354674.4_Silent_p.E717E|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000265368.4_Silent_p.E8539E	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8539					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)		CCCGCCACTCCTCCAGCAGAG	0.602										HNSCC(10;0.0054)			C|||	7	0.00139776	0.0	0.0014	5008	,	,		18729	0.001		0.005	False		,,,				2504	0.0				p.E8539E		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G25617A						PASS	.	C	,	2,4404	4.2+/-10.8	0,2,2201	53	49	50		25473,25617	1.8	1	6	dbSNP_133	50	16,8584	12.6+/-44.7	0,16,4284	no	coding-synonymous,coding-synonymous	SYNE1	NM_033071.3,NM_182961.3	,	0,18,6485	TT,TC,CC		0.186,0.0454,0.1384	,	8491/8750,8539/8798	152457795	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	23345	exon141			CCACTCCTCCAGC	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.25617G>A	6.37:g.152457795C>T		65	0	0		100	51	0.51	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																			C|0.998;T|0.002	0.002	strong		0.602	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152457795	C	T	152457795	2	4	26	1	0	0	0	0	0	0	0	1	15460	680	24	2		2	SYNE1	6	152457795	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	7559519	152457795	18657272	222	9985											
TULP4	56995	hgsc.bcm.edu	37	chr6	158910743	158910743	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcccaaaatctccagagctaGcaaatcacccaaactcccaa	16	6	3	16	0	2	1	1	0	1	1	5	1	4	1	4	0	3	2	4	0	6	1	rs61742077	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:158910743G>A	ENST00000367097.3	+	9	2967	c.1610G>A	c.(1609-1611)aGc>aAc	p.S537N	TULP4_ENST00000367094.2_Missense_Mutation_p.S537N	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	537					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)		TCCAGAGCTAGCAAATCACCC	0.473													G|||	9	0.00179712	0.0	0.0058	5008	,	,		19135	0.0		0.004	False		,,,				2504	0.001				p.S537N		Atlas-SNP	.											.	TULP4	137	.	0			c.G1610A						PASS	.	G	ASN/SER,ASN/SER	1,4405	2.1+/-5.4	0,1,2202	131	118	123		1610,1610	4.7	1	6	dbSNP_129	123	66,8534	40.3+/-97.0	0,66,4234	yes	missense,missense	TULP4	NM_001007466.1,NM_020245.3	46,46	0,67,6436	AA,AG,GG		0.7674,0.0227,0.5151	benign,benign	537/679,537/1544	158910743	67,12939	2203	4300	6503	SO:0001583	missense	56995	exon9			GAGCTAGCAAATC		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.1610G>A	6.37:g.158910743G>A	ENSP00000356064:p.Ser537Asn	132	0	0		152	74	0.486842	NM_020245	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Missense_Mutation	SNP	ENST00000367097.3	37	CCDS34561.1	7	0.003205128205128205	0	0.0	4	0.011049723756906077	0	0.0	3	0.00395778364116095	G	17.26	3.344506	0.61073	2.27E-4	0.007674	ENSG00000130338	ENST00000367097;ENST00000367094	T;T	0.61627	0.09;0.89	5.57	4.68	0.58851	Tubby, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.22513	0.0543	N	0.10874	0.06	0.58432	D	0.999991	B;B	0.16166	0.002;0.016	B;B	0.14023	0.009;0.01	T	0.04678	-1.0934	10	0.24483	T	0.36	-30.6907	16.3085	0.82859	0.0:0.1325:0.8675:0.0	rs61742077	537;537	Q9NRJ4-2;Q9NRJ4	.;TULP4_HUMAN	N	537	ENSP00000356064:S537N;ENSP00000356061:S537N	ENSP00000356061:S537N	S	+	2	0	TULP4	158830731	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.437000	0.80417	1.299000	0.44798	0.655000	0.94253	AGC	G|0.996;A|0.004	0.004	strong		0.473	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245		A	158910743	G	A	158910743	3	1	26	1	0	0	0	0	1	0	0	0	16791	971	34	2	1644	2	TULP4	6	158910743	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	6452948	158910743	12204324	223	9986											
FRMD1	79981	hgsc.bcm.edu	37	chr6	168461516	168461516	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggctccttctcatggagccCgtggacctccaagggcacgt	6	8	12	15	3	1	0	1	0	1	0	4	2	3	2	4	4	1	2	4	4	1	1	rs148097635	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:168461516C>T	ENST00000283309.6	-	9	1331	c.1267G>A	c.(1267-1269)Ggg>Agg	p.G423R	FRMD1_ENST00000432403.1_5'UTR|FRMD1_ENST00000440994.2_Missense_Mutation_p.G355R|FRMD1_ENST00000537786.1_Missense_Mutation_p.G194R	NM_024919.3	NP_079195.3	Q8N878	FRMD1_HUMAN	FERM domain containing 1	423						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)		TCATGGAGCCCGTGGACCTCC	0.657													C|||	3	0.000599042	0.0	0.0014	5008	,	,		17850	0.002		0.0	False		,,,				2504	0.0				p.G423R	GBM(50;8 1094 9538 34399)|Ovarian(80;676 1857 8675 49015)	Atlas-SNP	.											.	FRMD1	52	.	0			c.G1267A						PASS	.	C	ARG/GLY,ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	47	42	44		1063,1267	-2.6	0	6	dbSNP_134	44	17,8583	11.2+/-40.8	0,17,4283	yes	missense,missense	FRMD1	NM_001122841.1,NM_024919.3	125,125	0,18,6485	TT,TC,CC		0.1977,0.0227,0.1384	benign,benign	355/482,423/550	168461516	18,12988	2203	4300	6503	SO:0001583	missense	79981	exon9			GGAGCCCGTGGAC		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.1267G>A	6.37:g.168461516C>T	ENSP00000283309:p.Gly423Arg	100	0	0		148	78	0.527027	NM_024919	B2RNV8|B3KUM6|Q5SZU7|Q9UFB0	Missense_Mutation	SNP	ENST00000283309.6	37	CCDS5306.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	1	0.0017482517482517483	0	0.0	C	2.675	-0.276625	0.05679	2.27E-4	0.001977	ENSG00000153303	ENST00000283309;ENST00000440994;ENST00000537786	T;T;T	0.50277	0.75;0.75;0.75	2.48	-2.6	0.06190	.	2.404160	0.02924	U	0.138326	T	0.09642	0.0237	L	0.36672	1.1	0.09310	N	1	B;P;B;B	0.36733	0.076;0.567;0.207;0.262	B;B;B;B	0.22152	0.012;0.038;0.027;0.021	T	0.04053	-1.0981	10	0.10636	T	0.68	.	4.8184	0.13378	0.1237:0.1851:0.5734:0.1178	.	358;423;355;318	B7Z8G9;Q8N878;Q8N878-2;Q5SZU5	.;FRMD1_HUMAN;.;.	R	423;355;194	ENSP00000283309:G423R;ENSP00000414115:G355R;ENSP00000440078:G194R	ENSP00000283309:G423R	G	-	1	0	FRMD1	168204365	0.001000	0.12720	0.000000	0.03702	0.053000	0.15095	0.872000	0.28037	-0.378000	0.07918	0.313000	0.20887	GGG	C|0.999;T|0.001	0.001	strong		0.657	FRMD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362513.2	NM_024919		T	168461516	C	T	168461516	3	4	26	1	0	0	0	0	1	0	0	0	6057	652	23	1	394	1	FRMD1	6	168461516	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	9550773	168461516	2653551	224	9987											
GPER	2852	hgsc.bcm.edu	37	chr7	1132260	1132260	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccctgcaagcagtctttccGccatgcccaccccctcacgg	6	8	7	20	2	2	0	1	0	1	0	4	0	4	0	6	1	3	2	6	1	1	1	rs150960969	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:1132260G>A	ENST00000297469.3	+	2	1587	c.896G>A	c.(895-897)cGc>cAc	p.R299H	GPER1_ENST00000397092.1_Missense_Mutation_p.R299H|GPER1_ENST00000401670.1_Missense_Mutation_p.R299H|GPER1_ENST00000397088.3_Missense_Mutation_p.R299H|C7orf50_ENST00000397100.2_Intron|C7orf50_ENST00000357429.6_Intron|C7orf50_ENST00000488073.1_Intron|C7orf50_ENST00000397098.3_Intron	NM_001505.2	NP_001496.1	Q99527	GPER1_HUMAN	G protein-coupled estrogen receptor 1	299					apoptotic chromosome condensation (GO:0030263)|cell cycle (GO:0007049)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucose stimulus (GO:0071333)|cellular response to mineralocorticoid stimulus (GO:0071389)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytosolic calcium ion homeostasis (GO:0051480)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA metabolic process (GO:0051053)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte activation (GO:0002695)|negative regulation of lipid biosynthetic process (GO:0051055)|neuronal action potential (GO:0019228)|nuclear fragmentation involved in apoptotic nuclear change (GO:0030264)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of gene expression (GO:0010628)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of insulin secretion (GO:0032024)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vasodilation (GO:0045909)|steroid hormone mediated signaling pathway (GO:0043401)	axon (GO:0030424)|axon terminus (GO:0043679)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|dendritic spine head (GO:0044327)|dendritic spine membrane (GO:0032591)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|keratin filament (GO:0045095)|mitochondrial membrane (GO:0031966)|neuronal postsynaptic density (GO:0097481)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	chromatin binding (GO:0003682)|estrogen receptor activity (GO:0030284)|G-protein coupled receptor activity (GO:0004930)|mineralocorticoid receptor activity (GO:0017082)|steroid binding (GO:0005496)										CAGTCTTTCCGCCATGCCCAC	0.627																																					p.R299H		Atlas-SNP	.											.	GPER	25	.	0			c.G896A						PASS	.		HIS/ARG,HIS/ARG,,,HIS/ARG,	1,4405	2.1+/-5.4	0,1,2202	86	68	74		896,896,,,896,	5.7	1	7	dbSNP_134	74	8,8592	6.4+/-24.3	0,8,4292	yes	missense,missense,intron,intron,missense,intron	GPER,C7orf50	NM_001039966.1,NM_001098201.1,NM_001134395.1,NM_001134396.1,NM_001505.2,NM_032350.5	29,29,,,29,	0,9,6494	AA,AG,GG		0.093,0.0227,0.0692	probably-damaging,probably-damaging,,,probably-damaging,	299/376,299/376,,,299/376,	1132260	9,12997	2203	4300	6503	SO:0001583	missense	2852	exon2			CTTTCCGCCATGC	U63917	CCDS5322.1	7p22	2013-08-14	2007-07-03	2013-08-14	ENSG00000164850	ENSG00000164850			4485	protein-coding gene	gene with protein product		601805	"G protein-coupled receptor 30"	CMKRL2, GPR30, GPER		9479505, 17655271	Standard	NM_001098201		Approved	FEG-1, GPCR-Br, LERGU, LERGU2, DRY12, LyGPR, CEPR	uc003skb.2	Q99527	OTTHUMG00000023680	ENST00000297469.3:c.896G>A	7.37:g.1132260G>A	ENSP00000297469:p.Arg299His	75	0	0		71	34	0.478873	NM_001505	A8K6C5|B5BUJ1|O00143|O43494|Q13631|Q6FHL1|Q96F42|Q99981	Missense_Mutation	SNP	ENST00000297469.3	37	CCDS5322.1	.	.	.	.	.	.	.	.	.	.	G	17.40	3.381327	0.61845	2.27E-4	9.3E-4	ENSG00000164850	ENST00000401670;ENST00000397092;ENST00000297469;ENST00000397088;ENST00000508834	T;T;T;T	0.37411	1.2;1.2;1.2;1.2	5.65	5.65	0.86999	GPCR, rhodopsin-like superfamily (1);	0.057131	0.64402	D	0.000001	T	0.51193	0.1660	L	0.37630	1.12	0.54753	D	0.999989	D	0.89917	1.0	D	0.71414	0.973	T	0.39663	-0.9603	10	0.39692	T	0.17	-32.5649	18.7284	0.91724	0.0:0.0:1.0:0.0	.	299	Q99527	GPER_HUMAN	H	299	ENSP00000385151:R299H;ENSP00000380281:R299H;ENSP00000297469:R299H;ENSP00000380277:R299H	ENSP00000297469:R299H	R	+	2	0	GPER	1098786	1.000000	0.71417	1.000000	0.80357	0.371000	0.29859	6.012000	0.70767	2.670000	0.90874	0.655000	0.94253	CGC	G|0.999;A|0.001	0.001	strong		0.627	GPER1-030	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060001.1	NM_001039966		A	1132260	G	A	1132260	3	1	26	1	0	0	0	0	1	0	0	0	6615	1087	38	1	898	1	GPER	7	1132260	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10		1132260	158006403	225	9988											
DGKB	1607	hgsc.bcm.edu	37	chr7	14620536	14620536	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcattgccagtcccaagaggCagaatcgcaactggaggatg	12	7	12	10	1	1	2	1	0	0	2	3	4	2	4	2	3	2	2	2	3	3	1	rs61753128		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:14620536C>A	ENST00000403951.2	-	19	1982	c.1563G>T	c.(1561-1563)ctG>ctT	p.L521L	DGKB_ENST00000402815.1_Silent_p.L520L|DGKB_ENST00000399322.3_Silent_p.L521L|DGKB_ENST00000403963.1_5'UTR|DGKB_ENST00000406247.3_Silent_p.L521L|DGKB_ENST00000258767.5_Silent_p.L521L|DGKB_ENST00000407950.1_Silent_p.L513L|DGKB_ENST00000444700.2_Silent_p.L502L			Q9Y6T7	DGKB_HUMAN	diacylglycerol kinase, beta 90kDa	521	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				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						TCCCAAGAGGCAGAATCGCAA	0.423																																					p.L521L		Atlas-SNP	.											.	DGKB	166	.	0			c.G1563T						PASS	.	C	,	1,3881		0,1,1940	94	84	87		1563,1563	3.9	1	7	dbSNP_129	87	9,8297		0,9,4144	no	coding-synonymous,coding-synonymous	DGKB	NM_004080.2,NM_145695.2	,	0,10,6084	AA,AC,CC		0.1084,0.0258,0.082	,	521/805,521/774	14620536	10,12178	1941	4153	6094	SO:0001819	synonymous_variant	1607	exon18			AAGAGGCAGAATC	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.1563G>T	7.37:g.14620536C>A		98	0	0		140	60	0.428571	NM_145695	A4D116|A4D117|A8MXU2|O75241|Q2M377|Q75MF9|Q75MU7|Q86UI5|Q86UM9|Q9UQ29	Silent	SNP	ENST00000403951.2	37	CCDS47547.1																																																																																			.	.	weak		0.423	DGKB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000326356.2	NM_004080		A	14620536	C	A	14620536	2	1	26	1	0	0	0	0	0	0	0	1	4468	697	25	4		4	DGKB	7	14620536	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	13488276	14620536	144518127	226	9989											
SP8	221833	hgsc.bcm.edu	37	chr7	20825271	20825271	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctggcggaagaagaggaCgaggagcgtttccaggggtg	10	5	19	7	3	0	2	0	0	0	2	1	6	1	5	1	6	2	2	1	6	2	1	rs145875827		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:20825271C>T	ENST00000361443.4	-	3	348	c.111G>A	c.(109-111)tcG>tcA	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.G165A						PASS	.	C	,	1,4405		0,1,2202	46	47	47		165,111	-4.4	1	7	dbSNP_134	47	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	SP8	NM_182700.4,NM_198956.2	,	0,4,6499	TT,TC,CC		0.0349,0.0227,0.0308	,	55/509,37/491	20825271	4,13002	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>A	7.37:g.20825271C>T		54	0	0		62	34	0.548387	NM_182700	Q7Z615|Q7Z616|Q96MJ1	Silent	SNP	ENST00000361443.4	37	CCDS5372.1																																																																																			C|1.000;T|0.000	0.000	weak		0.632	SP8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326904.2			T	20825271	C	T	20825271	2	4	26	1	0	0	0	0	0	0	0	1	14985	523	19	1		1	SP8	7	20825271	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	6204735	20825271	138313392	227	9990											
SP4	6671	hgsc.bcm.edu	37	chr7	21468934	21468934	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agccctctcctctggctttaCtggcagctacttgcagcaaa	8	11	8	14	0	2	0	0	0	2	0	3	0	2	0	2	2	6	5	2	2	3	4			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:21468934C>T	ENST00000222584.3	+	3	369	c.151C>T	c.(151-153)Ctg>Ttg	p.L51L		NM_003112.3	NP_003103.2	Q02446	SP4_HUMAN	Sp4 transcription factor	51					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						TCTGGCTTTACTGGCAGCTAC	0.478																																					p.L51L		Atlas-SNP	.											.	SP4	91	.	0			c.C151T						PASS	.						39	42	41					7																	21468934		2203	4300	6503	SO:0001819	synonymous_variant	6671	exon3			GCTTTACTGGCAG		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.151C>T	7.37:g.21468934C>T		53	0	0		73	31	0.424658	NM_003112	O60402|Q32M52	Silent	SNP	ENST00000222584.3	37	CCDS5373.1																																																																																			.	.	none		0.478	SP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211617.2	NM_003112		T	21468934	C	T	21468934	2	4	26	1	0	0	0	0	0	0	0	1	14981	564	20	2		2	SP4	7	21468934	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	643663	21468934	137669729	228	9991											
STK31	56164	hgsc.bcm.edu	37	chr7	23811822	23811822	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccagtgtggatcacttgctAtccattaagaagacattgaa	13	11	8	9	0	1	3	1	1	0	2	2	4	2	4	2	1	1	1	2	1	4	4	rs147172261		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:23811822A>G	ENST00000355870.3	+	15	2009	c.1890A>G	c.(1888-1890)ctA>ctG	p.L630L	STK31_ENST00000354639.3_Silent_p.L607L|STK31_ENST00000433467.2_Silent_p.L630L|STK31_ENST00000405627.3_3'UTR|STK31_ENST00000428484.1_Silent_p.L607L	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	630						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						ATCACTTGCTATCCATTAAGA	0.313																																					p.L630L		Atlas-SNP	.											STK31,NS,carcinoma,+2,1	STK31	175	1	0			c.A1890G						PASS	.	A	,,	0,4406		0,0,2203	59	61	60		1821,1890,1821	-8.1	0.9	7	dbSNP_134	60	4,8582	3.7+/-12.6	0,4,4289	no	coding-synonymous,coding-synonymous,coding-synonymous	STK31	NM_001122833.1,NM_031414.3,NM_032944.2	,,	0,4,6492	GG,GA,AA		0.0466,0.0,0.0308	,,	607/997,630/1020,607/997	23811822	4,12988	2203	4293	6496	SO:0001819	synonymous_variant	56164	exon15			CTTGCTATCCATT	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.1890A>G	7.37:g.23811822A>G		166	0	0		186	93	0.5	NM_031414	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Silent	SNP	ENST00000355870.3	37	CCDS5386.1																																																																																			A|1.000;G|0.000	0.000	weak		0.313	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414		G	23811822	A	G	23811822	2	3	26	1	0	0	0	0	0	0	0	1	15311	436	16	3		3	STK31	7	23811822	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	2342888	23811822	135326841	229	9992											
CCDC129	223075	hgsc.bcm.edu	37	chr7	31692409	31692409	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aacccctttgtcaaattgtcCtgttggagaaaaggatgcag	12	11	10	8	0	1	1	1	0	0	1	2	3	2	2	3	2	2	2	3	2	4	3	rs34177136	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:31692409C>G	ENST00000407970.3	+	14	3139	c.3101C>G	c.(3100-3102)cCt>cGt	p.P1034R	CCDC129_ENST00000409210.1_Missense_Mutation_p.P942R|CCDC129_ENST00000451887.2_Intron|CCDC129_ENST00000319386.3_Missense_Mutation_p.P886R	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	1034								p.P1034H(1)|p.P886H(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						TCAAATTGTCCTGTTGGAGAA	0.453													C|||	6	0.00119808	0.0008	0.0029	5008	,	,		21006	0.0		0.003	False		,,,				2504	0.0				p.P1044R		Atlas-SNP	.											.	CCDC129	127	.	2	Substitution - Missense(2)	lung(2)	c.C3131G						PASS	.	C	ARG/PRO	1,4405	2.1+/-5.4	0,1,2202	107	98	101		3101	-0.3	0	7	dbSNP_126	101	41,8559	27.4+/-76.7	0,41,4259	yes	missense	CCDC129	NM_194300.2	103	0,42,6461	GG,GC,CC		0.4767,0.0227,0.3229	probably-damaging	1034/1045	31692409	42,12964	2203	4300	6503	SO:0001583	missense	223075	exon15			ATTGTCCTGTTGG	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.3101C>G	7.37:g.31692409C>G	ENSP00000384416:p.Pro1034Arg	216	0	0		275	140	0.509091	NM_001257967	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Missense_Mutation	SNP	ENST00000407970.3	37	CCDS5435.2	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	9.917	1.211175	0.22289	2.27E-4	0.004767	ENSG00000180347	ENST00000319386;ENST00000407970;ENST00000538406;ENST00000409210	T;T;T	0.17691	2.26;2.53;2.27	3.96	-0.303	0.12792	.	1.098150	0.07119	N	0.843657	T	0.11836	0.0288	M	0.63428	1.95	0.09310	N	1	P;P;P	0.43701	0.815;0.815;0.815	B;B;B	0.39935	0.314;0.314;0.314	T	0.19549	-1.0302	10	0.42905	T	0.14	.	3.6334	0.08140	0.1791:0.504:0.0:0.3169	rs34177136	1044;1034;886	F5H2J8;Q6ZRS4;Q6ZRS4-2	.;CC129_HUMAN;.	R	886;1034;1044;942	ENSP00000313062:P886R;ENSP00000384416:P1034R;ENSP00000387214:P942R	ENSP00000313062:P886R	P	+	2	0	CCDC129	31658934	0.000000	0.05858	0.001000	0.08648	0.068000	0.16541	-0.005000	0.12855	-0.187000	0.10516	-0.793000	0.03317	CCT	C|0.997;G|0.003	0.003	strong		0.453	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300		G	31692409	C	G	31692409	3	3	26	1	0	0	0	0	1	0	0	0	2766	681	24	4	3151	4	CCDC129	7	31692409	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	7880587	31692409	127446254	230	9993											
PDE1C	5137	hgsc.bcm.edu	37	chr7	31855625	31855625	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttgcccgtgttccattgaCttgattcttagtttctccag	5	18	8	10	1	2	2	0	2	2	0	4	2	3	2	3	0	1	3	3	0	1	7	rs61736729	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:31855625C>G	ENST00000396191.1	-	15	2181	c.1726G>C	c.(1726-1728)Gtc>Ctc	p.V576L	PDE1C_ENST00000396184.3_Missense_Mutation_p.V576L|PDE1C_ENST00000321453.7_Missense_Mutation_p.V576L|PDE1C_ENST00000479980.1_5'UTR|PDE1C_ENST00000396182.2_Missense_Mutation_p.V576L|PDE1C_ENST00000396193.1_Missense_Mutation_p.V636L	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	576					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)	GTTCCATTGACTTGATTCTTA	0.473													C|||	13	0.00259585	0.0	0.0072	5008	,	,		20836	0.0		0.008	False		,,,				2504	0.0				p.V636L		Atlas-SNP	.											.	PDE1C	465	.	0			c.G1906C						PASS	.	C	LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL	11,4395	17.9+/-39.9	0,11,2192	271	268	269		1726,1726,1906,1726,1726	5.3	1	7	dbSNP_129	269	108,8492	59.1+/-120.7	0,108,4192	yes	missense,missense,missense,missense,missense	PDE1C	NM_001191056.1,NM_001191057.1,NM_001191058.1,NM_001191059.1,NM_005020.2	32,32,32,32,32	0,119,6384	GG,GC,CC		1.2558,0.2497,0.915	benign,benign,benign,benign,benign	576/635,576/710,636/770,576/710,576/635	31855625	119,12887	2203	4300	6503	SO:0001583	missense	5137	exon16			CATTGACTTGATT	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.1726G>C	7.37:g.31855625C>G	ENSP00000379494:p.Val576Leu	254	1	0.00393701		333	168	0.504505	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Missense_Mutation	SNP	ENST00000396191.1	37	CCDS55099.1	9	0.004120879120879121	0	0.0	5	0.013812154696132596	0	0.0	4	0.005277044854881266	C	8.002	0.755676	0.15846	0.002497	0.012558	ENSG00000154678	ENST00000396193;ENST00000396191;ENST00000321453;ENST00000396184;ENST00000396182	T;T;T;T;T	0.72835	-0.69;-0.69;-0.69;-0.65;-0.65	5.34	5.34	0.76211	.	2.382430	0.01786	N	0.032006	T	0.53578	0.1805	N	0.19112	0.55	0.19775	N	0.999959	B;B;B	0.12630	0.006;0.003;0.003	B;B;B	0.13407	0.009;0.004;0.004	T	0.40608	-0.9554	10	0.25751	T	0.34	.	12.0225	0.53352	0.0:0.9176:0.0:0.0824	rs61736729	576;636;576	Q14123-2;E9PE92;Q14123	.;.;PDE1C_HUMAN	L	636;576;576;576;576	ENSP00000379496:V636L;ENSP00000379494:V576L;ENSP00000318105:V576L;ENSP00000379487:V576L;ENSP00000379485:V576L	ENSP00000318105:V576L	V	-	1	0	PDE1C	31822150	0.060000	0.20803	0.993000	0.49108	0.186000	0.23388	1.274000	0.33132	2.779000	0.95612	0.655000	0.94253	GTC	C|0.983;G|0.017	0.017	strong		0.473	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1			G	31855625	C	G	31855625	3	3	26	1	0	0	0	0	1	0	0	0	11644	565	20	4	190	4	PDE1C	7	31855625	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	163216	31855625	127283038	231	9994											
HECW1	23072	hgsc.bcm.edu	37	chr7	43547692	43547692	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tattcgcggaaagagctccaGcgaaacaagctctacgtcac	13	7	9	12	4	2	1	1	0	1	1	4	3	3	2	1	1	5	2	1	1	5	3	rs17172219	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:43547692G>A	ENST00000395891.2	+	23	4433	c.3828G>A	c.(3826-3828)caG>caA	p.Q1276Q	AC011738.4_ENST00000436105.1_RNA|HECW1_ENST00000453890.1_Silent_p.Q1242Q	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1276	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				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						AAGAGCTCCAGCGAAACAAGC	0.547													G|||	20	0.00399361	0.0151	0.0	5008	,	,		20717	0.0		0.0	False		,,,				2504	0.0				p.Q1276Q		Atlas-SNP	.											.	HECW1	540	.	0			c.G3828A						PASS	.	G		74,3858		1,72,1893	76	78	77		3828	5.8	1	7	dbSNP_123	77	1,8287		0,1,4143	no	coding-synonymous	HECW1	NM_015052.3		1,73,6036	AA,AG,GG		0.0121,1.882,0.6137		1276/1607	43547692	75,12145	1966	4144	6110	SO:0001819	synonymous_variant	23072	exon23			GCTCCAGCGAAAC	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.3828G>A	7.37:g.43547692G>A		108	0	0		116	66	0.568965	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	ENST00000395891.2	37	CCDS5469.2																																																																																			G|0.995;A|0.005	0.005	strong		0.547	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052		A	43547692	G	A	43547692	2	1	26	1	0	0	0	0	0	0	0	1	7051	962	34	2		2	HECW1	7	43547692	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	11692067	43547692	115590971	232	9995											
URGCP	55665	hgsc.bcm.edu	37	chr7	43917604	43917604	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgtcccttctgtaggcatcCgagtctttgattttcctggt	4	17	9	11	2	2	1	0	1	2	0	6	2	5	1	3	2	0	2	3	2	1	5	rs2232098	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:43917604C>T	ENST00000453200.1	-	6	1951	c.1458G>A	c.(1456-1458)tcG>tcA	p.S486S	URGCP_ENST00000443736.1_Silent_p.S443S|URGCP_ENST00000497914.1_5'UTR|URGCP_ENST00000447717.3_Silent_p.S443S|URGCP_ENST00000402306.3_Silent_p.S477S|URGCP_ENST00000336086.6_Silent_p.S443S|URGCP_ENST00000223341.7_Silent_p.S443S|URGCP-MRPS24_ENST00000603700.1_Intron			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	486					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						TGTAGGCATCCGAGTCTTTGA	0.587													C|||	92	0.0183706	0.0673	0.0043	5008	,	,		19017	0.0		0.0	False		,,,				2504	0.0				p.S486S		Atlas-SNP	.											.	URGCP	170	.	0			c.G1458A						PASS	.	C	,,,	214,3798		7,200,1799	136	141	140		1458,1329,,1431	-7.3	0	7	dbSNP_98	140	5,8311		0,5,4153	no	coding-synonymous,coding-synonymous,intron,coding-synonymous	URGCP,URGCP-MRPS24	NM_001077663.1,NM_001077664.1,NM_001204871.1,NM_017920.3	,,,	7,205,5952	TT,TC,CC		0.0601,5.334,1.7764	,,,	486/932,443/889,,477/923	43917604	219,12109	2006	4158	6164	SO:0001819	synonymous_variant	55665	exon6			GGCATCCGAGTCT		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.1458G>A	7.37:g.43917604C>T		157	0	0		164	82	0.5	NM_001077663	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Silent	SNP	ENST00000453200.1	37	CCDS47578.1																																																																																			C|0.972;T|0.028	0.028	strong		0.587	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664		T	43917604	C	T	43917604	2	4	26	1	0	0	0	0	0	0	0	1	17041	639	23	1		1	URGCP	7	43917604	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	369912	43917604	115221059	233	9996											
PGAM2	5224	hgsc.bcm.edu	37	chr7	44104896	44104896	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtgcgcaccacaggcagcCacatctggtccgtgccgtcc	8	6	11	16	3	1	0	0	0	1	0	3	0	3	0	5	2	3	2	5	2	1	0	rs10250779	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:44104896C>T	ENST00000297283.3	-	1	290	c.233G>A	c.(232-234)tGg>tAg	p.W78*	AC017116.11_ENST00000445938.1_RNA	NM_000290.3	NP_000281.2	P15259	PGAM2_HUMAN	phosphoglycerate mutase 2 (muscle)	78					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|response to mercury ion (GO:0046689)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|striated muscle contraction (GO:0006941)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity (GO:0046538)|bisphosphoglycerate 2-phosphatase activity (GO:0004083)|bisphosphoglycerate mutase activity (GO:0004082)|cofactor binding (GO:0048037)|phosphoglycerate mutase activity (GO:0004619)			large_intestine(2)|lung(4)|ovary(1)|stomach(1)	8						CACAGGCAGCCACATCTGGTC	0.622													C|||	10	0.00199681	0.0068	0.0014	5008	,	,		16885	0.0		0.0	False		,,,				2504	0.0				p.W78X		Atlas-SNP	.											.	PGAM2	20	.	0			c.G233A	GRCh37	CM930584	PGAM2	M	rs10250779	PASS	.	C	stop/TRP	40,4366	43.8+/-77.6	1,38,2164	85	74	78	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	233	5.9	1	7	dbSNP_119	78	0,8600		0,0,4300	yes	stop-gained	PGAM2	NM_000290.3		1,38,6464	TT,TC,CC		0.0,0.9079,0.3076		78/254	44104896	40,12966	2203	4300	6503	SO:0001587	stop_gained	5224	exon1			GGCAGCCACATCT		CCDS34624.1	7p13-p12	2008-11-17			ENSG00000164708	ENSG00000164708	5.4.2.1, 3.1.3.13, 5.4.2.4		8889	protein-coding gene	gene with protein product		612931					Standard	NM_000290		Approved	PGAM-M	uc003tjs.3	P15259	OTTHUMG00000155355	ENST00000297283.3:c.233G>A	7.37:g.44104896C>T	ENSP00000297283:p.Trp78*	103	0	0		129	66	0.511628	NM_000290		Nonsense_Mutation	SNP	ENST00000297283.3	37	CCDS34624.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	36	5.972079	0.97162	0.009079	0.0	ENSG00000164708	ENST00000297283	.	.	.	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-32.2844	17.8825	0.88844	0.0:1.0:0.0:0.0	rs10250779;rs10250779	.	.	.	X	78	.	ENSP00000297283:W78X	W	-	2	0	PGAM2	44071421	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.674000	0.83992	2.828000	0.97474	0.644000	0.83932	TGG	C|0.997;T|0.003	0.003	strong		0.622	PGAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339614.1			T	44104896	C	T	44104896	4	4	26	1	0	0	0	0	0	1	0	0	11783	595	21	2	540	2	PGAM2	7	44104896	Nonsense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	187292	44104896	115033767	234	9997											
MYO1G	64005	hgsc.bcm.edu	37	chr7	45005249	45005249	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtagtacctgcagaagagtgCgtggcaggtgtcctggaagg	9	8	17	7	1	0	2	0	0	0	2	1	3	1	3	2	4	3	4	2	4	4	2			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:45005249C>T	ENST00000258787.7	-	17	2504	c.2368G>A	c.(2368-2370)Gca>Aca	p.A790T		NM_033054.2	NP_149043.2	B0I1T2	MYO1G_HUMAN	myosin IG	790						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						CAGAAGAGTGCGTGGCAGGTG	0.617																																					p.A790T		Atlas-SNP	.											.	MYO1G	86	.	0			c.G2368A						PASS	.						75	72	73					7																	45005249		2203	4300	6503	SO:0001583	missense	64005	exon17			AGAGTGCGTGGCA	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.2368G>A	7.37:g.45005249C>T	ENSP00000258787:p.Ala790Thr	61	0	0		97	40	0.412371	NM_033054	Q8TEI9|Q8TES2|Q96BE2|Q96RI5|Q96RI6	Missense_Mutation	SNP	ENST00000258787.7	37	CCDS34629.1	.	.	.	.	.	.	.	.	.	.	C	0.298	-0.975870	0.02215	.	.	ENSG00000136286	ENST00000258787	D	0.86956	-2.19	4.37	1.42	0.22433	.	0.867457	0.09344	U	0.815042	T	0.73156	0.3551	N	0.20986	0.625	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.54397	-0.8300	10	0.13470	T	0.59	.	2.1804	0.03873	0.1374:0.4415:0.2463:0.1748	.	790	B0I1T2	MYO1G_HUMAN	T	790	ENSP00000258787:A790T	ENSP00000258787:A790T	A	-	1	0	MYO1G	44971774	0.000000	0.05858	0.000000	0.03702	0.383000	0.30230	-0.095000	0.11077	0.042000	0.15717	0.462000	0.41574	GCA	.	.	none		0.617	MYO1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341832.2			T	45005249	C	T	45005249	3	4	26	1	0	0	0	0	1	0	0	0	10083	768	27	1	712	1	MYO1G	7	45005249	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	900353	45005249	114133414	235	9998											
DDC	1644	hgsc.bcm.edu	37	chr7	50611751	50611751	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccatgtaatccaccatctcCttccctctccttcggaattc	7	13	4	17	1	2	0	0	0	2	0	8	1	4	1	6	1	0	1	6	1	2	4			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:50611751C>T	ENST00000444124.2	-	2	233	c.33G>A	c.(31-33)aaG>aaA	p.K11K	DDC_ENST00000431062.1_Silent_p.K11K|DDC_ENST00000357936.5_Silent_p.K11K|DDC_ENST00000426377.1_Silent_p.K11K|AC018705.5_ENST00000454521.1_RNA|DDC_ENST00000380984.4_Silent_p.K11K	NM_001082971.1	NP_001076440	P20711	DDC_HUMAN	dopa decarboxylase (aromatic L-amino acid decarboxylase)	11					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)			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)	CCACCATCTCCTTCCCTCTCC	0.537																																					p.K11K		Atlas-SNP	.											.	DDC	100	.	0			c.G33A						PASS	.						247	190	209					7																	50611751		2203	4300	6503	SO:0001819	synonymous_variant	1644	exon2			CATCTCCTTCCCT		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.33G>A	7.37:g.50611751C>T		179	0	0		192	95	0.494792	NM_001082971	C9IYA0|E7ER62|E7EU95|Q16723|Q5W5T9|Q75MJ6	Silent	SNP	ENST00000444124.2	37	CCDS5511.1																																																																																			.	.	none		0.537	DDC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342593.1			T	50611751	C	T	50611751	2	4	26	1	0	0	0	0	0	0	0	1	4327	680	24	2		2	DDC	7	50611751	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	5606502	50611751	108526912	236	9999											
EGFR	1956	hgsc.bcm.edu	37	chr7	55224507	55224507	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggaactggatattctgaaaAccgtaaaggaaatcacaggt	17	8	10	6	1	2	1	1	1	1	0	2	4	2	4	1	4	2	1	1	4	7	3			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:55224507A>C	ENST00000275493.2	+	10	1366	c.1189A>C	c.(1189-1191)Acc>Ccc	p.T397P	EGFR_ENST00000344576.2_Missense_Mutation_p.T397P|EGFR_ENST00000442591.1_Missense_Mutation_p.T397P|EGFR_ENST00000420316.2_Missense_Mutation_p.T397P|EGFR_ENST00000454757.2_Missense_Mutation_p.T344P|EGFR_ENST00000455089.1_Missense_Mutation_p.T352P|EGFR_ENST00000342916.3_Missense_Mutation_p.T397P	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	397					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)	TATTCTGAAAACCGTAAAGGA	0.393		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																											p.T397P		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_ENST00000344576,NS,malignant_melanoma,0,2	EGFR	20426	2	0			c.A1189C						PASS	.						94	90	92					7																	55224507		2203	4300	6503	SO:0001583	missense	1956	exon10	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	CTGAAAACCGTAA		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.1189A>C	7.37:g.55224507A>C	ENSP00000275493:p.Thr397Pro	174	0	0		177	78	0.440678	NM_201283	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	A	16.99	3.274643	0.59649	.	.	ENSG00000146648	ENST00000455089;ENST00000342916;ENST00000395504;ENST00000344576;ENST00000420316;ENST00000275493;ENST00000442591;ENST00000454757;ENST00000533450	T;T;T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89;0.89;0.89	5.95	5.95	0.96441	EGF receptor, L domain (1);	0.045464	0.85682	D	0.000000	T	0.69611	0.3130	M	0.91300	3.195	0.58432	D	0.999999	D;D;D;D;D	0.89917	1.0;0.998;1.0;0.997;0.999	D;D;D;D;D	0.87578	0.992;0.982;0.989;0.97;0.998	T	0.76263	-0.3023	10	0.87932	D	0	.	10.478	0.44676	0.855:0.0:0.0:0.145	.	352;397;397;397;397	Q504U8;P00533;P00533-3;P00533-4;P00533-2	.;EGFR_HUMAN;.;.;.	P	352;397;267;397;397;397;397;344;191	ENSP00000415559:T352P;ENSP00000342376:T397P;ENSP00000345973:T397P;ENSP00000413843:T397P;ENSP00000275493:T397P;ENSP00000410031:T397P;ENSP00000395243:T344P	ENSP00000275493:T397P	T	+	1	0	EGFR	55192001	1.000000	0.71417	0.591000	0.28745	0.427000	0.31564	6.996000	0.76263	2.279000	0.76181	0.533000	0.62120	ACC	.	.	none		0.393	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		C	55224507	A	C	55224507	3	2	26	1	0	0	0	0	1	0	0	0	4969	43	2	5	1227	5	EGFR	7	55224507	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	4612756	55224507	103914156	237	10000											
AUTS2	26053	hgsc.bcm.edu	37	chr7	70239034	70239034	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acatccaaccctatcgatgtCgctgctcggcctgggacagt	8	9	10	14	3	0	0	0	0	0	0	4	2	1	1	3	2	2	2	3	2	2	1	rs139965676		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:70239034C>T	ENST00000342771.4	+	12	2172	c.1851C>T	c.(1849-1851)gtC>gtT	p.V617V	AUTS2_ENST00000406775.2_Intron	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	617										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)		CTATCGATGTCGCTGCTCGGC	0.488													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19785	0.0		0.0	False		,,,				2504	0.0				p.V617V		Atlas-SNP	.											AUTS2,NS,carcinoma,0,1	AUTS2	173	1	0			c.C1851T						PASS	.	C	,	0,4406		0,0,2203	132	104	113		,1851	-12.1	0.6	7	dbSNP_134	113	3,8597	3.0+/-9.4	0,3,4297	no	intron,coding-synonymous	AUTS2	NM_001127231.1,NM_015570.2	,	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	,	,617/1260	70239034	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	26053	exon12			CGATGTCGCTGCT	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.1851C>T	7.37:g.70239034C>T		69	0	0		96	45	0.46875	NM_015570	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Silent	SNP	ENST00000342771.4	37	CCDS5539.1	.	.	.	.	.	.	.	.	.	.	C	9.577	1.122506	0.20877	0.0	3.49E-4	ENSG00000158321	ENST00000443672	.	.	.	6.06	-12.1	0.00011	.	.	.	.	.	T	0.41166	0.1147	.	.	.	0.49915	D	0.999835	.	.	.	.	.	.	T	0.52268	-0.8598	4	.	.	.	-18.381	6.7154	0.23300	0.0845:0.4459:0.3111:0.1585	.	.	.	.	L	144	.	.	S	+	2	0	AUTS2	69876970	0.002000	0.14202	0.582000	0.28627	0.972000	0.66771	-1.549000	0.02182	-1.627000	0.01550	-0.768000	0.03414	TCG	C|1.000;T|0.000	0.000	weak		0.488	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2			T	70239034	C	T	70239034	2	4	26	1	0	0	0	0	0	0	0	1	1225	871	31	1		1	AUTS2	7	70239034	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	15014527	70239034	88899629	238	10001											
GTF2I	2969	hgsc.bcm.edu	37	chr7	74105424	74105424	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aataccagaaaggattttcaAaaagattttgtaaaatattg	19	13	6	3	0	1	2	1	0	0	2	1	3	1	3	1	1	1	1	1	1	8	8	rs143931854	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:74105424A>G	ENST00000324896.4	+	3	608	c.219A>G	c.(217-219)caA>caG	p.Q73Q	GTF2I_ENST00000416070.1_Silent_p.Q73Q|AC083884.8_ENST00000450426.2_RNA|GTF2I_ENST00000353920.4_Silent_p.Q73Q|GTF2I_ENST00000443166.1_Silent_p.Q73Q|GTF2I_ENST00000346152.4_Silent_p.Q73Q	NM_032999.2	NP_127492.1	P78347	GTF2I_HUMAN	general transcription factor IIi	73					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						AGGATTTTCAAAAAGATTTTG	0.328													A|||	5	0.000998403	0.0	0.0043	5008	,	,		17800	0.0		0.002	False		,,,				2504	0.0				p.Q73Q		Atlas-SNP	.											.	GTF2I	40	.	0			c.A219G						PASS	.	A	,,,,	2,4404		0,2,2201	68	69	69		219,219,219,219,219	-1.2	1	7	dbSNP_134	69	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GTF2I	NM_001163636.1,NM_001518.3,NM_032999.2,NM_033000.2,NM_033001.2	,,,,	0,2,6501	GG,GA,AA		0.0,0.0454,0.0154	,,,,	73/977,73/958,73/999,73/979,73/978	74105424	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	2969	exon3			TTTTCAAAAAGAT	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.219A>G	7.37:g.74105424A>G		206	0	0		213	97	0.455399	NM_032999	O14743|O15359|O43546|O43588|O43589|Q75M85|Q75M86|Q75M87|Q75M88|Q86U51|Q9BSZ4	Silent	SNP	ENST00000324896.4	37	CCDS5573.1																																																																																			A|0.999;G|0.001	0.001	strong		0.328	GTF2I-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252708.1	NM_032999		G	74105424	A	G	74105424	2	3	26	1	0	0	0	0	0	0	0	1	6876	11	1	3		3	GTF2I	7	74105424	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	3866390	74105424	85033239	239	10002											
HIP1	3092	hgsc.bcm.edu	37	chr7	75187009	75187009	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aacgaatcctccagctctttTttctctcgttccaaatctac	9	15	3	14	2	3	0	0	0	3	0	8	1	6	0	3	0	3	2	3	0	4	5	rs144294774	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:75187009T>C	ENST00000336926.6	-	16	1556	c.1530A>G	c.(1528-1530)aaA>aaG	p.K510K	HIP1_ENST00000434438.2_Silent_p.K510K	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	510					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						CCAGCTCTTTTTTCTCTCGTT	0.537			T	PDGFRB	CMML								T|||	13	0.00259585	0.0098	0.0	5008	,	,		18946	0.0		0.0	False		,,,				2504	0.0				p.K510K		Atlas-SNP	.		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	.	HIP1	91	.	0			c.A1530G						PASS	.	T		55,4351	54.2+/-90.2	0,55,2148	160	155	157		1530	-2	0.9	7	dbSNP_134	157	0,8600		0,0,4300	no	coding-synonymous	HIP1	NM_005338.5		0,55,6448	CC,CT,TT		0.0,1.2483,0.4229		510/1038	75187009	55,12951	2203	4300	6503	SO:0001819	synonymous_variant	3092	exon16			CTCTTTTTTCTCT	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.1530A>G	7.37:g.75187009T>C		127	0	0		142	70	0.492958	NM_005338	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Silent	SNP	ENST00000336926.6	37	CCDS34669.1																																																																																			T|0.996;C|0.004	0.004	strong		0.537	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338		C	75187009	T	C	75187009	2	2	26	1	0	0	0	0	0	0	0	1	7123	1838	64	3		3	HIP1	7	75187009	Silent	SNP	T	TCGA-G8-6907-01A-11D-2210-10	1081585	75187009	83951654	240	10003											
SLC25A40	55972	hgsc.bcm.edu	37	chr7	87483585	87483585	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctccctcttcacagacacaTagatgatccatgagtccatt	11	11	5	14	0	2	4	1	2	1	2	5	4	5	4	4	0	0	0	4	0	1	3	rs150511221	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:87483585T>A	ENST00000341119.5	-	5	544	c.198A>T	c.(196-198)ctA>ctT	p.L66L		NM_018843.3	NP_061331.2	Q8TBP6	S2540_HUMAN	solute carrier family 25, member 40	66					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				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)					CACAGACACATAGATGATCCA	0.343													T|||	36	0.0071885	0.0015	0.0375	5008	,	,		16226	0.0		0.005	False		,,,				2504	0.0031				p.L66L		Atlas-SNP	.											.	SLC25A40	32	.	0			c.A198T						PASS	.	T		7,4399	14.3+/-33.2	0,7,2196	161	150	154		198	-7.1	0.1	7	dbSNP_134	154	106,8494	56.8+/-118.0	0,106,4194	no	coding-synonymous	SLC25A40	NM_018843.3		0,113,6390	AA,AT,TT		1.2326,0.1589,0.8688		66/339	87483585	113,12893	2203	4300	6503	SO:0001819	synonymous_variant	55972	exon5			GACACATAGATGA	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.198A>T	7.37:g.87483585T>A		101	0	0		83	32	0.385542	NM_018843	A8K483|D6W5P6|Q53GB1|Q9UHR1	Silent	SNP	ENST00000341119.5	37	CCDS5610.1																																																																																			T|0.994;A|0.006	0.006	strong		0.343	SLC25A40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253677.5	NM_018843		A	87483585	T	A	87483585	2	1	26	1	0	0	0	0	0	0	0	1	14520	1393	49	5		5	SLC25A40	7	87483585	Silent	SNP	T	TCGA-G8-6907-01A-11D-2210-10	12296576	87483585	71655078	241	10004											
DBF4	10926	hgsc.bcm.edu	37	chr7	87537183	87537183	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttctggtaaaatacatcgaaAagtgaaaataatattaggac	19	11	7	4	1	1	1	0	1	1	0	2	3	1	2	0	2	1	1	0	2	10	6			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:87537183A>G	ENST00000265728.1	+	12	2234	c.1730A>G	c.(1729-1731)aAa>aGa	p.K577R		NM_006716.3	NP_006707.1	Q9UBU7	DBF4A_HUMAN	DBF4 zinc finger	577					DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)	nucleoplasm (GO:0005654)	enzyme activator activity (GO:0008047)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|skin(3)	28	Esophageal squamous(14;0.00202)	Breast(660;0.0334)				ATACATCGAAAAGTGAAAATA	0.333																																					p.K577R		Atlas-SNP	.											.	DBF4	67	.	0			c.A1730G						PASS	.						48	55	52					7																	87537183		2201	4266	6467	SO:0001583	missense	10926	exon12			ATCGAAAAGTGAA	AF160876	CCDS5611.1	7q21.3	2014-02-17	2014-02-17		ENSG00000006634	ENSG00000006634		"Zinc fingers, DBF-type"	17364	protein-coding gene	gene with protein product	"activator of S phase kinase", "chiffon homolog (Drosophila)", "zinc finger, DBF-type containing 1", "DBF4 zinc finger A"	604281	"DBF4 homolog (S. cerevisiae)"			10373557, 10517317	Standard	NM_006716		Approved	ASK, chif, ZDBF1, DBF4A	uc003ujf.1	Q9UBU7	OTTHUMG00000131034	ENST00000265728.1:c.1730A>G	7.37:g.87537183A>G	ENSP00000265728:p.Lys577Arg	234	0	0		297	158	0.531987	NM_006716	A4D1D8|A8K954|O75226|Q75MS6|Q75N01|Q9Y2M6	Missense_Mutation	SNP	ENST00000265728.1	37	CCDS5611.1	.	.	.	.	.	.	.	.	.	.	A	16.90	3.250022	0.59212	.	.	ENSG00000006634	ENST00000265728	T	0.52295	0.67	5.13	5.13	0.70059	.	0.000000	0.64402	D	0.000002	T	0.46718	0.1407	M	0.63843	1.955	0.47905	D	0.999544	P;P	0.52463	0.953;0.802	B;B	0.41036	0.346;0.277	T	0.55798	-0.8084	10	0.87932	D	0	-13.7887	13.5232	0.61580	1.0:0.0:0.0:0.0	.	353;577	B7Z8C6;Q9UBU7	.;DBF4A_HUMAN	R	577	ENSP00000265728:K577R	ENSP00000265728:K577R	K	+	2	0	DBF4	87375119	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.326000	0.59241	1.934000	0.56057	0.528000	0.53228	AAA	.	.	none		0.333	DBF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253678.1	NM_006716		G	87537183	A	G	87537183	3	3	26	1	0	0	0	0	1	0	0	0	4250	14	1	3	1776	3	DBF4	7	87537183	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	53598	87537183	71601480	242	10005											
AKAP9	10142	hgsc.bcm.edu	37	chr7	91730338	91730338	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atgactctttacttcaaactCtgagccctgattctgaacat	11	14	5	11	0	4	4	1	4	3	0	4	4	4	4	1	0	4	0	1	0	3	4			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:91730338C>T	ENST00000359028.2	+	45	11302	c.11077C>T	c.(11077-11079)Ctg>Ttg	p.L3693L	AKAP9_ENST00000358100.2_Silent_p.L3639L|AKAP9_ENST00000356239.3_Silent_p.L3689L			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	3693					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)			ACTTCAAACTCTGAGCCCTGA	0.393			T	BRAF	papillary thyroid																																p.L3689L		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.C11065T						PASS	.						69	69	69					7																	91730338		2203	4300	6503	SO:0001819	synonymous_variant	10142	exon45			CAAACTCTGAGCC	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.11077C>T	7.37:g.91730338C>T		73	0	0		98	4	0.0408163	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Silent	SNP	ENST00000359028.2	37																																																																																				.	.	none		0.393	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		T	91730338	C	T	91730338	2	4	26	1	0	0	0	0	0	0	0	1	459	912	32	2		2	AKAP9	7	91730338	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	4193155	91730338	67408325	243	10006											
CCDC132	55610	hgsc.bcm.edu	37	chr7	92900576	92900576	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tactttggaacagattgaggTaagaagtattatatcctaac	15	13	8	5	0	0	3	0	1	0	2	1	4	1	4	1	2	3	2	1	2	8	8			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:92900576T>G	ENST00000305866.5	+	10	830		c.e10+2		CCDC132_ENST00000541136.1_Splice_Site|CCDC132_ENST00000544910.1_Splice_Site|CCDC132_ENST00000535481.1_Intron|CCDC132_ENST00000317751.6_Splice_Site|CCDC132_ENST00000251739.5_Splice_Site	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132							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)			CAGATTGAGGTAAGAAGTATT	0.294																																					.		Atlas-SNP	.											.	CCDC132	136	.	0			c.702+2T>G						PASS	.						121	129	126					7																	92900576		2203	4298	6501	SO:0001630	splice_region_variant	55610	exon10			TTGAGGTAAGAAG	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.702+2T>G	7.37:g.92900576T>G		101	0	0		111	43	0.387387	NM_017667	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Splice_Site	SNP	ENST00000305866.5	37	CCDS43617.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.030563	0.75504	.	.	ENSG00000004766	ENST00000251739;ENST00000305866;ENST00000544910;ENST00000541136;ENST00000458707	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3837	0.74681	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	CCDC132	92738512	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.413000	0.80104	2.367000	0.80283	0.528000	0.53228	.	.	.	none		0.294	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667	Intron	G	92900576	T	G	92900576	5	3	26	1	0	0	0	0	0	0	1	0	2769	1652	57	5	742	5	CCDC132	7	92900576	Splice_Site	SNP	T	TCGA-G8-6907-01A-11D-2210-10	1170238	92900576	66238087	244	10007											
LRCH4	4034	hgsc.bcm.edu	37	chr7	100175010	100175010	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcccctgccggctcctccCgcctgagggaccaagacagg	6	5	11	19	2	0	2	0	1	0	1	3	3	3	3	8	3	1	1	8	3	1	0	rs140761835	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:100175010C>T	ENST00000310300.6	-	11	1233	c.1181G>A	c.(1180-1182)cGg>cAg	p.R394Q	LRCH4_ENST00000497245.1_5'UTR	NM_002319.3	NP_002310.2	O75427	LRCH4_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 4	394					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)					CGGCTCCTCCCGCCTGAGGGA	0.741													C|||	25	0.00499201	0.0008	0.0115	5008	,	,		13720	0.0		0.0119	False		,,,				2504	0.0041				p.R394Q		Atlas-SNP	.											LRCH4,caecum,carcinoma,+1,1	LRCH4	53	1	0			c.G1181A						PASS	.	C	GLN/ARG	15,4287		0,15,2136	15	19	18		1181	3.2	1	7	dbSNP_134	18	139,8325		1,137,4094	yes	missense	LRCH4	NM_002319.3	43	1,152,6230	TT,TC,CC		1.6422,0.3487,1.2063	benign	394/684	100175010	154,12612	2151	4232	6383	SO:0001583	missense	4034	exon11			TCCTCCCGCCTGA	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.1181G>A	7.37:g.100175010C>T	ENSP00000309689:p.Arg394Gln	34	0	0		28	20	0.714286	NM_002319	A4D2D5|Q8WV85|Q96ID0	Missense_Mutation	SNP	ENST00000310300.6	37	CCDS34706.1	16	0.007326007326007326	0	0.0	6	0.016574585635359115	0	0.0	10	0.013192612137203167	C	13.57	2.276222	0.40294	0.003487	0.016422	ENSG00000077454	ENST00000310300	T	0.34275	1.37	5.21	3.2	0.36748	.	0.501717	0.17581	N	0.169125	T	0.07863	0.0197	N	0.17312	0.475	0.80722	D	1	P	0.48998	0.918	B	0.34180	0.177	T	0.01492	-1.1341	10	0.29301	T	0.29	-22.7983	7.2591	0.26193	0.172:0.565:0.263:0.0	.	394	O75427	LRCH4_HUMAN	Q	394	ENSP00000309689:R394Q	ENSP00000309689:R394Q	R	-	2	0	LRCH4	100012946	1.000000	0.71417	1.000000	0.80357	0.435000	0.31806	0.771000	0.26633	2.460000	0.83146	0.536000	0.68110	CGG	C|0.991;T|0.009	0.009	strong		0.741	LRCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356110.1	NM_002319		T	100175010	C	T	100175010	3	4	26	1	0	0	0	0	1	0	0	0	8944	652	23	1	902	1	LRCH4	7	100175010	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	7274434	100175010	58963653	245	10008											
MUC17	140453	hgsc.bcm.edu	37	chr7	100679715	100679715	+	Missense_Mutation	SNP	C	C	T																															tgaagtcagttcatctcctaCacctgctgaaggtaccagca																								rs143909059	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:100679715C>T	ENST00000306151.4	+	3	5082	c.5018C>T	c.(5017-5019)aCa>aTa	p.T1673I		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1673	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)					TCATCTCCTACACCTGCTGAA	0.498													C|||	3	0.000599042	0.0	0.0	5008	,	,		26255	0.0		0.003	False		,,,				2504	0.0				p.T1673I		Atlas-SNP	.											.	MUC17	804	.	0			c.C5018T						PASS	.	C	ILE/THR	0,4406		0,0,2203	210	221	217		5018	0.9	0	7	dbSNP_134	217	7,8593	4.3+/-15.6	0,7,4293	no	missense	MUC17	NM_001040105.1	89	0,7,6496	TT,TC,CC		0.0814,0.0,0.0538	possibly-damaging	1673/4494	100679715	7,12999	2203	4300	6503	SO:0001583	missense	140453	exon3			CTCCTACACCTGC	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.5018C>T	7.37:g.100679715C>T	ENSP00000302716:p.Thr1673Ile	78	0	0		54	34	0.62963	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	2.860	-0.236376	0.05944	0.0	8.14E-4	ENSG00000169876	ENST00000306151	T	0.03242	4.0	0.932	0.932	0.19466	.	.	.	.	.	T	0.01730	0.0055	N	0.17082	0.46	0.09310	N	1	P	0.42757	0.789	B	0.28849	0.095	T	0.48614	-0.9020	9	0.23891	T	0.37	.	5.3368	0.15961	0.0:1.0:0.0:0.0	.	1673	Q685J3	MUC17_HUMAN	I	1673	ENSP00000302716:T1673I	ENSP00000302716:T1673I	T	+	2	0	MUC17	100466435	0.004000	0.15560	0.001000	0.08648	0.004000	0.04260	1.442000	0.35046	0.857000	0.35407	0.134000	0.15878	ACA	C|1.000;T|0.000	0.000	weak		0.498	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		T	100679715	C	T	100679715	3	4	26	1	0	0	0	0	1	0	0	0	9983	478	17	2	5028	2	MUC17	7	100679715	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	504705	100679715	58458948	246	10009	125	2									
MUC17	140453	hgsc.bcm.edu	37	chr7	100679720	100679720	+	Missense_Mutation	SNP	G	G	A																															tcagttcatctcctacacctGctgaaggtaccagcatgcca																								rs140695064	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:100679720G>A	ENST00000306151.4	+	3	5087	c.5023G>A	c.(5023-5025)Gct>Act	p.A1675T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1675	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)					TCCTACACCTGCTGAAGGTAC	0.493													G|||	4	0.000798722	0.0008	0.0	5008	,	,		26161	0.0		0.003	False		,,,				2504	0.0				p.A1675T		Atlas-SNP	.											.	MUC17	804	.	0			c.G5023A						PASS	.						208	220	216					7																	100679720		2203	4300	6503	SO:0001583	missense	140453	exon3			ACACCTGCTGAAG	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.5023G>A	7.37:g.100679720G>A	ENSP00000302716:p.Ala1675Thr	78	0	0		52	32	0.615385	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	2.769	-0.256106	0.05829	.	.	ENSG00000169876	ENST00000306151	T	0.02085	4.46	0.932	-0.0747	0.13730	.	.	.	.	.	T	0.00998	0.0033	N	0.08118	0	0.09310	N	1	B	0.27286	0.174	B	0.16722	0.016	T	0.47114	-0.9142	9	0.08179	T	0.78	.	3.5105	0.07706	0.297:0.0:0.703:0.0	.	1675	Q685J3	MUC17_HUMAN	T	1675	ENSP00000302716:A1675T	ENSP00000302716:A1675T	A	+	1	0	MUC17	100466440	0.000000	0.05858	0.003000	0.11579	0.005000	0.04900	-3.486000	0.00455	-0.003000	0.14444	0.134000	0.15878	GCT	.	.	weak		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100679720	G	A	100679720	3	1	26	1	0	0	0	0	1	0	0	0	9983	1319	46	2	5033	2	MUC17	7	100679720	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	5	100679720	58458943	247	10010	125	2									
CDHR3	222256	hgsc.bcm.edu	37	chr7	105621474	105621474	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaccaaacatatttgatttgCagatttatgtgaaggatgag	14	13	10	4	0	0	4	0	3	0	1	0	6	0	5	1	1	2	1	1	1	4	5			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:105621474C>T	ENST00000317716.9	+	3	390	c.310C>T	c.(310-312)Cag>Tag	p.Q104*	CDHR3_ENST00000470188.1_3'UTR|CDHR3_ENST00000541203.1_Nonsense_Mutation_p.Q104*|CDHR3_ENST00000343407.5_5'UTR|CDHR3_ENST00000542731.1_Nonsense_Mutation_p.Q104*|CDHR3_ENST00000478080.1_Nonsense_Mutation_p.Q16*	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	104	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(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						ATTTGATTTGCAGATTTATGT	0.418																																					p.Q104X		Atlas-SNP	.											.	CDHR3	153	.	0			c.C310T						PASS	.						88	82	84					7																	105621474		1929	4140	6069	SO:0001587	stop_gained	222256	exon3			GATTTGCAGATTT	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.310C>T	7.37:g.105621474C>T	ENSP00000325954:p.Gln104*	160	0	0		179	72	0.402235	NM_152750	Q8TCI7	Nonsense_Mutation	SNP	ENST00000317716.9	37	CCDS47684.1	.	.	.	.	.	.	.	.	.	.	C	36	5.837584	0.97009	.	.	ENSG00000128536	ENST00000542731;ENST00000317716;ENST00000478080;ENST00000541203	.	.	.	5.02	5.02	0.67125	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	-3.9079	17.6187	0.88075	0.0:1.0:0.0:0.0	.	.	.	.	X	104;104;16;104	.	ENSP00000325954:Q104X	Q	+	1	0	CDHR3	105408710	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	5.065000	0.64344	2.774000	0.95407	0.561000	0.74099	CAG	.	.	none		0.418	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750		T	105621474	C	T	105621474	4	4	26	1	0	0	0	0	0	1	0	0	3122	711	25	2	320	2	CDHR3	7	105621474	Nonsense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	4941754	105621474	53517189	248	10011											
LAMB4	22798	hgsc.bcm.edu	37	chr7	107746265	107746265	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggattaataactcaccatTccaggagggctgaaaacatc	14	10	8	9	0	1	1	1	1	0	0	3	3	2	3	2	3	2	1	2	3	4	4			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:107746265T>C	ENST00000388781.3	-	8	950	c.867A>G	c.(865-867)ggA>ggG	p.G289G	LAMB4_ENST00000418464.1_Silent_p.G289G|LAMB4_ENST00000414450.2_Silent_p.G289G|LAMB4_ENST00000205386.4_Silent_p.G289G|LAMB4_ENST00000388780.3_Silent_p.G289G	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	289	Laminin EGF-like 1. {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						AACTCACCATTCCAGGAGGGC	0.478																																					p.G289G		Atlas-SNP	.											.	LAMB4	253	.	0			c.A867G						PASS	.						80	72	75					7																	107746265		2203	4300	6503	SO:0001819	synonymous_variant	22798	exon8			CACCATTCCAGGA	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.867A>G	7.37:g.107746265T>C		121	0	0		119	48	0.403361	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Silent	SNP	ENST00000388781.3	37	CCDS34732.1																																																																																			.	.	none		0.478	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857		C	107746265	T	C	107746265	2	2	26	1	0	0	0	0	0	0	0	1	8622	1770	62	3		3	LAMB4	7	107746265	Silent	SNP	T	TCGA-G8-6907-01A-11D-2210-10	2124791	107746265	51392398	249	10012											
MET	4233	hgsc.bcm.edu	37	chr7	116339672	116339672	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgtcctgactgtgtggtgagCgccctgggagccaaagtcct	6	10	14	11	1	0	2	0	2	0	0	2	3	2	3	4	2	2	0	4	2	1	0	rs35775721	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:116339672C>T	ENST00000318493.6	+	2	721	c.534C>T	c.(532-534)agC>agT	p.S178S	MET_ENST00000436117.2_Silent_p.S178S|MET_ENST00000397752.3_Silent_p.S178S			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0	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)			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)			GTGTGGTGAGCGCCCTGGGAG	0.473			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				C|||	443	0.0884585	0.1664	0.0303	5008	,	,		20901	0.0526		0.0417	False		,,,				2504	0.1094				p.S178S		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,carcinoma,0,1	MET	412	1	0			c.C534T						scavenged	.	C	,	514,3416		29,456,1480	104	105	105		534,534	-2.6	0.7	7	dbSNP_126	105	337,7949		10,317,3816	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	39,773,5296	TT,TC,CC		4.0671,13.0789,6.9663	,	178/1391,178/1409	116339672	851,11365	1965	4143	6108	SO:0001819	synonymous_variant	4233	exon2	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	GGTGAGCGCCCTG	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.534C>T	7.37:g.116339672C>T		115	1	0.00869565		150	82	0.546667	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			C|0.935;T|0.065	0.065	strong		0.473	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			T	116339672	C	T	116339672	2	4	26	1	0	0	0	0	0	0	0	1	9494	767	27	1		1	MET	7	116339672	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	8593407	116339672	42798991	250	10013											
MET	4233	hgsc.bcm.edu	37	chr7	116340262	116340262	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atatgtcaacgacttcttcaAcaagatcgtcaacaaaaaca	18	9	4	10	2	4	1	3	0	1	1	5	2	4	1	0	0	4	0	0	0	7	3	rs33917957	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:116340262A>G	ENST00000318493.6	+	2	1311	c.1124A>G	c.(1123-1125)aAc>aGc	p.N375S	MET_ENST00000436117.2_Missense_Mutation_p.N375S|MET_ENST00000397752.3_Missense_Mutation_p.N375S			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)	p.N375S(2)		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)			GACTTCTTCAACAAGATCGTC	0.443			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				A|||	165	0.0329473	0.0053	0.0101	5008	,	,		19354	0.0526		0.0209	False		,,,				2504	0.0787				p.N375S		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,carcinoma,0,3	MET	412	3	2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|kidney(1)	c.A1124G						PASS	.	A	SER/ASN,SER/ASN	26,3828		0,26,1901	101	93	96		1124,1124	4.9	1	7	dbSNP_126	96	151,8127		0,151,3988	yes	missense,missense	MET	NM_000245.2,NM_001127500.1	46,46	0,177,5889	GG,GA,AA		1.8241,0.6746,1.459	benign,benign	375/1391,375/1409	116340262	177,11955	1927	4139	6066	SO:0001583	missense	4233	exon2	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	TCTTCAACAAGAT	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.1124A>G	7.37:g.116340262A>G	ENSP00000317272:p.Asn375Ser	39	0	0		56	33	0.589286	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	37	CCDS47689.1	46	0.021062271062271064	0	0.0	3	0.008287292817679558	27	0.0472027972027972	16	0.021108179419525065	A	10.97	1.502020	0.26949	0.006746	0.018241	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000436117	T;T;T	0.04551	3.6;3.6;3.6	6.04	4.91	0.64330	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.135646	0.64402	D	0.000003	T	0.00906	0.0030	L	0.52364	1.645	0.80722	D	1	B;B;B;B;B;B;B;B;B;B;B;B;B	0.21071	0.051;0.044;0.008;0.011;0.024;0.024;0.044;0.044;0.005;0.02;0.025;0.043;0.043	B;B;B;B;B;B;B;B;B;B;B;B;B	0.26310	0.018;0.026;0.047;0.034;0.047;0.026;0.068;0.038;0.007;0.015;0.026;0.026;0.026	T	0.36601	-0.9741	10	0.40728	T	0.16	.	9.6723	0.40019	0.869:0.0:0.131:0.0	rs33917957	375;375;375;375;375;375;375;375;375;375;375;375;375	B5A929;E7EQ94;B5A930;B5A934;B5A936;B5A937;B5A939;B5A941;B5A940;P08581-2;B5A942;P08581;A1L467	.;.;.;.;.;.;.;.;.;.;.;MET_HUMAN;.	S	375	ENSP00000380860:N375S;ENSP00000317272:N375S;ENSP00000410980:N375S	ENSP00000317272:N375S	N	+	2	0	MET	116127498	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	2.866000	0.48420	2.317000	0.78254	0.460000	0.39030	AAC	A|0.977;G|0.023	0.023	strong		0.443	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			G	116340262	A	G	116340262	3	3	26	1	0	0	0	0	1	0	0	0	9494	43	2	3	1126	3	MET	7	116340262	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	590	116340262	42798401	251	10014											
MET	4233	hgsc.bcm.edu	37	chr7	116435768	116435768	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagccccaccttatcctgaCgtaaacacctttgatataac	12	10	6	13	1	0	2	0	2	0	0	1	3	1	3	5	1	3	1	5	1	5	5	rs41736	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:116435768C>T	ENST00000318493.6	+	20	4099	c.3912C>T	c.(3910-3912)gaC>gaT	p.D1304D	MET_ENST00000539704.1_Silent_p.D156D|MET_ENST00000397752.3_Silent_p.D1286D			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)	p.D1304D(1)		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)			CTTATCCTGACGTAAACACCT	0.473			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)		OREG0003446	type=REGULATORY REGION|Gene=MET|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	c|||	1764	0.352236	0.034	0.464	5008	,	,		18610	0.4673		0.4414	False		,,,				2504	0.4928				p.D1304D		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,carcinoma,0,1	MET	412	1	1	Substitution - coding silent(1)	stomach(1)	c.C3912T						scavenged	.	T	,	393,3383		15,363,1510	245	238	240		3858,3912	-10.9	0	7	dbSNP_76	240	3487,4731		756,1975,1378	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	771,2338,2888	TT,TC,CC		42.4312,10.4078,32.3495	,	1286/1391,1304/1409	116435768	3880,8114	1888	4109	5997	SO:0001819	synonymous_variant	4233	exon20	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	TCCTGACGTAAAC	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.3912C>T	7.37:g.116435768C>T		143	1	0.00699301	1473	147	79	0.537415	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			C|0.624;T|0.376	0.376	strong		0.473	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			T	116435768	C	T	116435768	2	4	26	1	0	0	0	0	0	0	0	1	9494	535	19	1		1	MET	7	116435768	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	95506	116435768	42702895	252	10015			2	44		3	3	330	N	G_C	2.553125e-05
MET	4233	hgsc.bcm.edu	37	chr7	116436022	116436022	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctggtgtcccggatatcagcGatcttctctactttcattgg	6	15	9	11	2	4	0	2	0	2	0	6	2	5	1	1	3	2	0	1	3	2	5	rs2023748	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:116436022G>A	ENST00000318493.6	+	21	4258	c.4071G>A	c.(4069-4071)gcG>gcA	p.A1357A	MET_ENST00000539704.1_Silent_p.A209A|MET_ENST00000397752.3_Silent_p.A1339A			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)	p.A1357A(1)		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)			GGATATCAGCGATCTTCTCTA	0.443			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				G|||	1772	0.353834	0.034	0.4697	5008	,	,		21305	0.4673		0.4433	False		,,,				2504	0.4949				p.A1357A		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,carcinoma,0,1	MET	412	1	1	Substitution - coding silent(1)	stomach(1)	c.G4071A						PASS	.	G	,	405,3531		16,373,1579	140	130	133		4017,4071	-11.4	0	7	dbSNP_94	133	3536,4748		773,1990,1379	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	789,2363,2958	AA,AG,GG		42.6847,10.2896,32.2504	,	1339/1391,1357/1409	116436022	3941,8279	1968	4142	6110	SO:0001819	synonymous_variant	4233	exon21	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	ATCAGCGATCTTC	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.4071G>A	7.37:g.116436022G>A		249	0	0		262	132	0.503817	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			G|0.618;A|0.382	0.382	strong		0.443	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			A	116436022	G	A	116436022	2	1	26	1	0	0	0	0	0	0	0	1	9494	1045	37	1		1	MET	7	116436022	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	254	116436022	42702641	253	10016			2	44		3	3	330	N	G_C	2.553125e-05
MET	4233	hgsc.bcm.edu	37	chr7	116436097	116436097	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aacgtaaaatgtgtcgctccGtatccttctctgttgtcatc	8	15	7	11	3	2	0	1	0	1	0	7	0	4	0	2	0	1	4	2	0	4	4	rs41737	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:116436097G>A	ENST00000318493.6	+	21	4333	c.4146G>A	c.(4144-4146)ccG>ccA	p.P1382P	MET_ENST00000539704.1_Silent_p.P234P|MET_ENST00000397752.3_Silent_p.P1364P			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)	p.P1382P(1)		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)			GTGTCGCTCCGTATCCTTCTC	0.468			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				A|||	1776	0.354633	0.0356	0.4726	5008	,	,		19834	0.4673		0.4433	False		,,,				2504	0.4949				p.P1382P		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,carcinoma,0,1	MET	412	1	1	Substitution - coding silent(1)	stomach(1)	c.G4146A						PASS	.	A	,	418,3602		15,388,1607	193	176	181		4092,4146	-3.1	1	7	dbSNP_76	181	3563,4817		777,2009,1404	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	792,2397,3011	AA,AG,GG		42.5179,10.398,32.1048	,	1364/1391,1382/1409	116436097	3981,8419	2010	4190	6200	SO:0001819	synonymous_variant	4233	exon21	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	CGCTCCGTATCCT	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.4146G>A	7.37:g.116436097G>A		173	0	0		192	88	0.458333	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			G|0.615;A|0.385	0.385	strong		0.468	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			A	116436097	G	A	116436097	2	1	26	1	0	0	0	0	0	0	0	1	9494	1132	40	1		1	MET	7	116436097	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	75	116436097	42702566	254	10017			2	44		3	3	330	N	G_C	2.553125e-05
WASL	8976	hgsc.bcm.edu	37	chr7	123332793	123332793	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggtggtggaggtgcagctgTgggagctcttgaaggtggtg	5	10	21	5	1	1	1	0	1	1	0	1	3	1	3	0	7	3	3	0	7	1	1			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:123332793T>A	ENST00000223023.4	-	9	1287	c.955A>T	c.(955-957)Aca>Tca	p.T319S		NM_003941.2	NP_003932.3	O00401	WASL_HUMAN	Wiskott-Aldrich syndrome-like	319	Pro-rich.				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						GGTGCAGCTGTGGGAGCTCTT	0.642																																					p.T319S		Atlas-SNP	.											.	WASL	70	.	0			c.A955T						PASS	.						78	76	77					7																	123332793		2203	4300	6503	SO:0001583	missense	8976	exon9			CAGCTGTGGGAGC	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.955A>T	7.37:g.123332793T>A	ENSP00000223023:p.Thr319Ser	61	0	0		73	5	0.0684932	NM_003941	A1JUI9|Q7Z746	Missense_Mutation	SNP	ENST00000223023.4	37	CCDS34743.1	.	.	.	.	.	.	.	.	.	.	T	8.371	0.835392	0.16820	.	.	ENSG00000106299	ENST00000223023	D	0.91180	-2.8	5.39	2.92	0.33932	.	0.235349	0.41938	N	0.000787	T	0.80352	0.4607	N	0.20881	0.62	0.44067	D	0.996816	B	0.06786	0.001	B	0.04013	0.001	T	0.67197	-0.5731	10	0.06625	T	0.88	-12.2313	10.6239	0.45495	0.2563:0.0:0.0:0.7437	.	319	O00401	WASL_HUMAN	S	319	ENSP00000223023:T319S	ENSP00000223023:T319S	T	-	1	0	WASL	123120029	0.958000	0.32768	0.997000	0.53966	0.999000	0.98932	1.689000	0.37700	0.315000	0.23110	0.524000	0.50904	ACA	.	.	none		0.642	WASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348522.1	NM_003941		A	123332793	T	A	123332793	3	1	26	1	0	0	0	0	1	0	0	0	17271	1696	59	5	574	5	WASL	7	123332793	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	6896696	123332793	35805870	255	10018											
WASL	8976	hgsc.bcm.edu	37	chr7	123349251	123349251	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagttccgatctgctgcataTaactgcaccactgctgaaga	11	10	8	12	1	1	2	0	1	1	1	2	3	2	2	2	0	5	5	2	0	3	3	rs3195229	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:123349251T>C	ENST00000223023.4	-	2	476	c.144A>G	c.(142-144)ttA>ttG	p.L48L		NM_003941.2	NP_003932.3	O00401	WASL_HUMAN	Wiskott-Aldrich syndrome-like	48	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						CTGCTGCATATAACTGCACCA	0.368													T|||	4	0.000798722	0.0	0.0014	5008	,	,		16453	0.0		0.002	False		,,,				2504	0.001				p.L48L		Atlas-SNP	.											.	WASL	70	.	0			c.A144G						PASS	.	T		5,4401	11.4+/-27.6	0,5,2198	76	70	72		144	1.8	1	7	dbSNP_105	72	34,8566	23.4+/-69.3	0,34,4266	no	coding-synonymous	WASL	NM_003941.2		0,39,6464	CC,CT,TT		0.3953,0.1135,0.2999		48/506	123349251	39,12967	2203	4300	6503	SO:0001819	synonymous_variant	8976	exon2			TGCATATAACTGC	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.144A>G	7.37:g.123349251T>C		292	0	0		322	143	0.444099	NM_003941	A1JUI9|Q7Z746	Silent	SNP	ENST00000223023.4	37	CCDS34743.1																																																																																			T|0.998;C|0.002	0.002	strong		0.368	WASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348522.1	NM_003941		C	123349251	T	C	123349251	2	2	26	1	0	0	0	0	0	0	0	1	17271	1403	49	3		3	WASL	7	123349251	Silent	SNP	T	TCGA-G8-6907-01A-11D-2210-10	16458	123349251	35789412	256	10019											
FLNC	2318	hgsc.bcm.edu	37	chr7	128481578	128481578	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccgctgagttcaccattgAtgctcgtgcagctggcaagg	7	9	13	12	2	1	2	1	2	0	0	2	2	1	2	2	2	3	6	2	2	1	2	rs34972246	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:128481578A>C	ENST00000325888.8	+	13	2339	c.2078A>C	c.(2077-2079)gAt>gCt	p.D693A	FLNC_ENST00000346177.6_Missense_Mutation_p.D693A	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	693					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						TTCACCATTGATGCTCGTGCA	0.607													A|||	10	0.00199681	0.0008	0.0014	5008	,	,		20237	0.0		0.005	False		,,,				2504	0.0031				p.D693A		Atlas-SNP	.											.	FLNC	339	.	0			c.A2078C						PASS	.	A	ALA/ASP,ALA/ASP	5,4075		0,5,2035	139	144	142		2078,2078	5.6	1	7	dbSNP_126	142	45,8355		0,45,4155	yes	missense,missense	FLNC	NM_001127487.1,NM_001458.4	126,126	0,50,6190	CC,CA,AA		0.5357,0.1225,0.4006	benign,benign	693/2693,693/2726	128481578	50,12430	2040	4200	6240	SO:0001583	missense	2318	exon13			CCATTGATGCTCG	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.2078A>C	7.37:g.128481578A>C	ENSP00000327145:p.Asp693Ala	109	0	0		167	72	0.431138	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Missense_Mutation	SNP	ENST00000325888.8	37	CCDS43644.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	A	35	5.430186	0.96131	0.001225	0.005357	ENSG00000128591	ENST00000325888;ENST00000346177	D;D	0.85411	-1.98;-1.98	5.57	5.57	0.84162	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.93167	0.7824	H	0.95950	3.745	0.58432	D	0.999999	D;P	0.89917	1.0;0.923	D;P	0.91635	0.999;0.85	D	0.94673	0.7858	10	0.87932	D	0	.	15.7306	0.77800	1.0:0.0:0.0:0.0	rs34972246	693;693	Q14315-2;Q14315	.;FLNC_HUMAN	A	693	ENSP00000327145:D693A;ENSP00000344002:D693A	ENSP00000327145:D693A	D	+	2	0	FLNC	128268814	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	7.035000	0.76517	2.117000	0.64856	0.459000	0.35465	GAT	A|0.996;C|0.004	0.004	strong		0.607	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			C	128481578	A	C	128481578	3	2	26	1	0	0	0	0	1	0	0	0	5943	333	12	5	2128	5	FLNC	7	128481578	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	5132327	128481578	30657085	257	10020											
SMO	6608	hgsc.bcm.edu	37	chr7	128843263	128843263	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gctgctgggcagtgatccagCccctgctgtgtgccgtatac	5	10	13	13	1	0	1	0	1	0	0	1	1	1	1	4	1	5	5	4	1	2	2			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:128843263C>A	ENST00000249373.3	+	2	650	c.370C>A	c.(370-372)Ccc>Acc	p.P124T		NM_005631.4	NP_005622.1	Q99835	SMO_HUMAN	smoothened, frizzled class receptor	124	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				adenohypophysis development (GO:0021984)|anterior/posterior pattern specification (GO:0009952)|atrial septum morphogenesis (GO:0060413)|axon extension involved in axon guidance (GO:0048846)|canonical Wnt signaling pathway (GO:0060070)|cardioblast differentiation (GO:0010002)|cell fate specification (GO:0001708)|cellular response to cholesterol (GO:0071397)|central nervous system neuron differentiation (GO:0021953)|cerebellar cortex morphogenesis (GO:0021696)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|detection of cell density by contact stimulus involved in contact inhibition (GO:0060248)|determination of left/right asymmetry in lateral mesoderm (GO:0003140)|determination of left/right symmetry (GO:0007368)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|epithelial-mesenchymal cell signaling (GO:0060684)|exocrine pancreas development (GO:0031017)|facial nerve development (GO:0021561)|floor plate formation (GO:0021508)|forebrain morphogenesis (GO:0048853)|gonad development (GO:0008406)|hair follicle morphogenesis (GO:0031069)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mammary gland epithelial cell differentiation (GO:0060644)|mesenchymal to epithelial transition involved in metanephric renal vesicle formation (GO:0072285)|midgut development (GO:0007494)|multicellular organism growth (GO:0035264)|muscle cell fate commitment (GO:0042693)|myoblast migration (GO:0051451)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of gene expression (GO:0010629)|negative regulation of hair follicle development (GO:0051799)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate commitment (GO:0048663)|neuron projection regeneration (GO:0031102)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|otolith morphogenesis (GO:0032474)|pancreas morphogenesis (GO:0061113)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gene expression (GO:0010628)|positive regulation of hh target transcription factor activity (GO:0007228)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|protein stabilization (GO:0050821)|regulation of heart morphogenesis (GO:2000826)|regulation of stem cell maintenance (GO:2000036)|renal system development (GO:0072001)|semicircular canal morphogenesis (GO:0048752)|skeletal muscle fiber development (GO:0048741)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021910)|somite development (GO:0061053)|spermatogenesis (GO:0007283)|thalamus development (GO:0021794)|type B pancreatic cell development (GO:0003323)|vasculogenesis (GO:0001570)|ventral midline determination (GO:0007371)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	drug binding (GO:0008144)|G-protein coupled receptor activity (GO:0004930)|patched binding (GO:0005113)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			biliary_tract(1)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(14)|liver(1)|lung(11)|pancreas(2)|prostate(1)|skin(20)|upper_aerodigestive_tract(3)|urinary_tract(1)	64					Fluocinonide(DB01047)|Vismodegib(DB08828)	AGTGATCCAGCCCCTGCTGTG	0.652			Mis		skin basal cell																																p.P124T		Atlas-SNP	.		Dom	yes		7	7q31-q32	6608	smoothened homolog (Drosophila)		E	.	SMO	145	.	0			c.C370A						PASS	.						22	18	19					7																	128843263		2178	4271	6449	SO:0001583	missense	6608	exon2			ATCCAGCCCCTGC	U84401	CCDS5811.1	7q32.1	2014-01-29	2014-01-29	2003-01-17	ENSG00000128602	ENSG00000128602		"GPCR / Class F : Frizzled receptors"	11119	protein-coding gene	gene with protein product	"frizzled family member 11"	601500	"smoothened (Drosophila) homolog", "smoothened homolog (Drosophila)", "smoothened, seven transmembrane spanning receptor", "smoothened, frizzled family receptor"	SMOH		9628830	Standard	NM_005631		Approved	FZD11	uc003vor.3	Q99835	OTTHUMG00000158421	ENST00000249373.3:c.370C>A	7.37:g.128843263C>A	ENSP00000249373:p.Pro124Thr	105	0	0		113	53	0.469027	NM_005631	A4D1K5	Missense_Mutation	SNP	ENST00000249373.3	37	CCDS5811.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.690771	0.88735	.	.	ENSG00000128602	ENST00000249373	T	0.79554	-1.28	5.5	5.5	0.81552	Frizzled domain (5);	0.000000	0.85682	D	0.000000	D	0.90321	0.6972	M	0.82630	2.6	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90922	0.4784	10	0.56958	D	0.05	.	16.9188	0.86158	0.0:1.0:0.0:0.0	.	124	Q99835	SMO_HUMAN	T	124	ENSP00000249373:P124T	ENSP00000249373:P124T	P	+	1	0	SMO	128630499	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.695000	0.84257	2.584000	0.87258	0.563000	0.77884	CCC	.	.	none		0.652	SMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350986.1	NM_005631		A	128843263	C	A	128843263	3	1	26	1	0	0	0	0	1	0	0	0	14815	739	26	4	376	4	SMO	7	128843263	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	361685	128843263	30295400	258	10021											
EXOC4	60412	hgsc.bcm.edu	37	chr7	133692514	133692514	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctggcatcaagaaaatgtgTaggaacatttttgttcttca	12	15	8	6	0	4	1	2	0	2	1	4	2	4	2	0	2	1	3	0	2	5	5			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:133692514T>G	ENST00000253861.4	+	17	2642	c.2613T>G	c.(2611-2613)tgT>tgG	p.C871W	EXOC4_ENST00000545148.1_Missense_Mutation_p.C481W|EXOC4_ENST00000539845.1_Missense_Mutation_p.C770W|EXOC4_ENST00000541309.1_Missense_Mutation_p.C159W	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	871					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)				AGAAAATGTGTAGGAACATTT	0.502																																					p.C871W		Atlas-SNP	.											.	EXOC4	118	.	0			c.T2613G						PASS	.						86	72	77					7																	133692514		2203	4300	6503	SO:0001583	missense	60412	exon17			AATGTGTAGGAAC	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.2613T>G	7.37:g.133692514T>G	ENSP00000253861:p.Cys871Trp	93	0	0		111	50	0.45045	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Missense_Mutation	SNP	ENST00000253861.4	37	CCDS5829.1	.	.	.	.	.	.	.	.	.	.	T	18.38	3.610461	0.66558	.	.	ENSG00000131558	ENST00000253861;ENST00000546185;ENST00000539845;ENST00000545148;ENST00000541309	.	.	.	5.45	-4.48	0.03515	.	0.000000	0.85682	D	0.000000	T	0.79782	0.4505	M	0.82716	2.605	0.80722	D	1	D;D;D	0.89917	0.996;1.0;1.0	P;D;D	0.80764	0.855;0.994;0.987	T	0.81232	-0.1026	9	0.48119	T	0.1	.	17.5564	0.87890	0.0:0.6695:0.0:0.3305	.	403;481;871	B7Z689;F5GZT1;Q96A65	.;.;EXOC4_HUMAN	W	871;490;770;481;159	.	ENSP00000253861:C871W	C	+	3	2	EXOC4	133343054	0.920000	0.31207	0.962000	0.40283	0.983000	0.72400	0.028000	0.13644	-0.786000	0.04516	-0.353000	0.07706	TGT	.	.	none		0.502	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807		G	133692514	T	G	133692514	3	3	26	1	0	0	0	0	1	0	0	0	5308	1644	57	5	2688	5	EXOC4	7	133692514	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	4849251	133692514	25446149	259	10022											
ZC3HAV1	56829	hgsc.bcm.edu	37	chr7	138764741	138764741	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acttgttcctccaagatcagTagccttggacgagcctgagg	9	10	11	11	1	1	2	1	1	0	1	3	4	3	3	4	2	2	2	4	2	2	4	rs142490389	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:138764741T>G	ENST00000242351.5	-	4	1262	c.946A>C	c.(946-948)Act>Cct	p.T316P	ZC3HAV1_ENST00000464606.1_Missense_Mutation_p.T316P|ZC3HAV1_ENST00000471652.1_Missense_Mutation_p.T316P	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	316					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						CCAAGATCAGTAGCCTTGGAC	0.582													T|||	2	0.000399361	0.0	0.0	5008	,	,		19261	0.0		0.002	False		,,,				2504	0.0				p.T316P		Atlas-SNP	.											.	ZC3HAV1	75	.	0			c.A946C						PASS	.	T	PRO/THR,PRO/THR	4,4402	8.1+/-20.4	0,4,2199	51	51	51		946,946	-8.9	0	7	dbSNP_134	51	22,8578	16.0+/-53.3	0,22,4278	yes	missense,missense	ZC3HAV1	NM_020119.3,NM_024625.3	38,38	0,26,6477	GG,GT,TT		0.2558,0.0908,0.1999	benign,benign	316/903,316/700	138764741	26,12980	2203	4300	6503	SO:0001583	missense	56829	exon4			GATCAGTAGCCTT	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.946A>C	7.37:g.138764741T>G	ENSP00000242351:p.Thr316Pro	78	0	0		63	38	0.603175	NM_024625	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Missense_Mutation	SNP	ENST00000242351.5	37	CCDS5851.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	11.79	1.745165	0.30955	9.08E-4	0.002558	ENSG00000105939	ENST00000242351;ENST00000464606;ENST00000471652;ENST00000540247	T;T;T	0.30448	1.53;1.53;1.53	4.47	-8.94	0.00768	.	1.426730	0.04367	N	0.358508	T	0.16896	0.0406	L	0.36672	1.1	0.09310	N	1	B;B	0.21225	0.053;0.001	B;B	0.15484	0.013;0.002	T	0.17592	-1.0364	10	0.48119	T	0.1	.	0.8161	0.01103	0.3267:0.2947:0.2199:0.1588	.	316;316	Q7Z2W4-2;Q7Z2W4	.;ZCCHV_HUMAN	P	316;316;316;76	ENSP00000242351:T316P;ENSP00000418385:T316P;ENSP00000419855:T316P	ENSP00000242351:T316P	T	-	1	0	ZC3HAV1	138415281	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-4.989000	0.00162	-1.691000	0.01430	0.528000	0.53228	ACT	T|0.999;G|0.001	0.001	strong		0.582	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119		G	138764741	T	G	138764741	3	3	26	1	0	0	0	0	1	0	0	0	17590	1638	57	5	1806	5	ZC3HAV1	7	138764741	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	5072227	138764741	20373922	260	10023											
TBXAS1	6916	hgsc.bcm.edu	37	chr7	139715645	139715645	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gcactggccaagcccggagaCcttcaaccctgaaaggtgag	11	5	12	13	1	1	3	1	2	0	1	1	4	1	3	4	3	2	1	4	3	3	1	rs5763	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:139715645C>A	ENST00000336425.5	+	15	1738	c.1349C>A	c.(1348-1350)aCc>aAc	p.T450N	TBXAS1_ENST00000414508.2_Missense_Mutation_p.T451N|TBXAS1_ENST00000411653.1_Missense_Mutation_p.T450N|TBXAS1_ENST00000448866.1_Missense_Mutation_p.T450N|TBXAS1_ENST00000462275.1_3'UTR|TBXAS1_ENST00000436047.2_Missense_Mutation_p.T451N|TBXAS1_ENST00000263552.6_Missense_Mutation_p.T451N|TBXAS1_ENST00000425687.1_Missense_Mutation_p.T383N|TBXAS1_ENST00000458722.1_Missense_Mutation_p.T496N|TBXAS1_ENST00000416849.2_Missense_Mutation_p.T497N			P24557	THAS_HUMAN	thromboxane A synthase 1 (platelet)	450			T -> N (in allele CYP5A1*8; dbSNP:rs5763). {ECO:0000269|PubMed:11465543}.		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)	AGCCCGGAGACCTTCAACCCT	0.602													C|||	27	0.00539137	0.0015	0.0072	5008	,	,		16586	0.0		0.0149	False		,,,				2504	0.0051				p.T497N		Atlas-SNP	.											.	TBXAS1	121	.	0			c.C1490A	GRCh37	CM054133	TBXAS1	M	rs5763	PASS	.	C	ASN/THR,ASN/THR,ASN/THR,ASN/THR,ASN/THR	15,4391	22.3+/-47.3	0,15,2188	53	52	53		1352,1352,1490,1148,1352	0.3	0.1	7	dbSNP_52	53	178,8422	78.6+/-141.3	3,172,4125	yes	missense,missense,missense,missense,missense	TBXAS1	NM_001061.4,NM_001130966.2,NM_001166253.1,NM_001166254.1,NM_030984.3	65,65,65,65,65	3,187,6313	AA,AC,CC		2.0698,0.3404,1.4839	benign,benign,benign,benign,benign	451/535,451/535,497/581,383/467,451/461	139715645	193,12813	2203	4300	6503	SO:0001583	missense	6916	exon12			CGGAGACCTTCAA	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.1349C>A	7.37:g.139715645C>A	ENSP00000338087:p.Thr450Asn	76	0	0		57	25	0.438596	NM_001166253	B4DJG6|E7EMU9|E7EP08|E7ESB5|O14987|Q16843|Q16844|Q8IUN1|Q96CN2|Q9GZW4|Q9HD77|Q9HD78|Q9HD79|Q9HD80|Q9HD81|Q9HD82|Q9HD83|Q9HD84	Missense_Mutation	SNP	ENST00000336425.5	37		14	0.00641025641025641	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	C	3.350	-0.132775	0.06711	0.003404	0.020698	ENSG00000059377	ENST00000425687;ENST00000263552;ENST00000336425;ENST00000416849;ENST00000436047;ENST00000414508;ENST00000448866;ENST00000458722;ENST00000411653	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	4.52	0.297	0.15762	.	0.380726	0.27577	N	0.018760	T	0.37293	0.0998	L	0.47190	1.495	0.80722	D	1	B;B;B;B;B;B;B	0.14805	0.011;0.009;0.003;0.002;0.002;0.004;0.004	B;B;B;B;B;B;B	0.26517	0.025;0.01;0.014;0.007;0.07;0.014;0.009	T	0.33497	-0.9866	10	0.52906	T	0.07	.	4.2042	0.10481	0.459:0.3493:0.0:0.1916	rs5763;rs52807031;rs61074508;rs5763	431;497;402;383;451;451;450	B4DVP1;E7EP08;B4E0M5;E7ESB5;E7EMU9;Q53F23;P24557	.;.;.;.;.;.;THAS_HUMAN	N	383;451;450;497;451;451;450;496;450	ENSP00000388736:T383N;ENSP00000263552:T451N;ENSP00000338087:T450N;ENSP00000389414:T497N;ENSP00000392361:T451N;ENSP00000392702:T451N;ENSP00000402536:T450N;ENSP00000411274:T496N;ENSP00000411326:T450N	ENSP00000263552:T451N	T	+	2	0	TBXAS1	139362114	0.703000	0.27826	0.050000	0.19076	0.020000	0.10135	-0.032000	0.12266	0.039000	0.15632	-0.379000	0.06801	ACC	C|0.988;A|0.012	0.012	strong		0.602	TBXAS1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000348373.1			A	139715645	C	A	139715645	3	1	26	1	0	0	0	0	1	0	0	0	15679	507	18	4	1536	4	TBXAS1	7	139715645	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	950904	139715645	19423018	261	10024											
TAS2R5	54429	hgsc.bcm.edu	37	chr7	141490325	141490325	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cctgggcctggctggctgccGatttctcctgcagtggctga	3	11	14	13	1	1	1	0	1	1	0	2	2	1	1	4	4	2	4	4	4	0	1	rs147887777		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:141490325G>A	ENST00000247883.4	+	1	309	c.164G>A	c.(163-165)cGa>cAa	p.R55Q		NM_018980.2	NP_061853.1	Q9NYW4	TA2R5_HUMAN	taste receptor, type 2, member 5	55					chemosensory behavior (GO:0007635)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)	p.R55Q(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(2)|skin(1)	9	Melanoma(164;0.0171)					GCTGGCTGCCGATTTCTCCTG	0.468													g|||	1	0.000199681	0.0	0.0014	5008	,	,		19581	0.0		0.0	False		,,,				2504	0.0				p.R55Q		Atlas-SNP	.											TAS2R5,colon,carcinoma,0,1	TAS2R5	33	1	1	Substitution - Missense(1)	large_intestine(1)	c.G164A						PASS	.	G	GLN/ARG	3,4403	6.2+/-15.9	0,3,2200	112	107	109		164	1.7	0	7	dbSNP_134	109	17,8583	12.6+/-44.7	0,17,4283	yes	missense	TAS2R5	NM_018980.2	43	0,20,6483	AA,AG,GG		0.1977,0.0681,0.1538	probably-damaging	55/300	141490325	20,12986	2203	4300	6503	SO:0001583	missense	54429	exon1			GCTGCCGATTTCT	AF227132	CCDS5869.1	7q31.3-q32	2012-08-22			ENSG00000127366	ENSG00000127366		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14912	protein-coding gene	gene with protein product		605062					Standard	NM_018980		Approved	T2R5	uc003vwr.1	Q9NYW4	OTTHUMG00000157632	ENST00000247883.4:c.164G>A	7.37:g.141490325G>A	ENSP00000247883:p.Arg55Gln	211	1	0.00473934		236	135	0.572034	NM_018980	Q645W0|Q75MV7	Missense_Mutation	SNP	ENST00000247883.4	37	CCDS5869.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	12.07	1.828778	0.32329	6.81E-4	0.001977	ENSG00000127366	ENST00000247883	T	0.37058	1.22	4.46	1.67	0.24075	.	.	.	.	.	T	0.57989	0.2091	M	0.84683	2.71	0.09310	N	1	D	0.76494	0.999	D	0.70716	0.97	T	0.45249	-0.9274	9	0.87932	D	0	.	6.4583	0.21942	0.3113:0.0:0.6887:0.0	.	55	Q9NYW4	TA2R5_HUMAN	Q	55	ENSP00000247883:R55Q	ENSP00000247883:R55Q	R	+	2	0	TAS2R5	141136794	0.130000	0.22417	0.009000	0.14445	0.033000	0.12548	1.820000	0.39032	0.162000	0.19483	0.561000	0.74099	CGA	G|0.999;A|0.001	0.001	strong		0.468	TAS2R5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349283.1			A	141490325	G	A	141490325	3	1	26	1	0	0	0	0	1	0	0	0	15598	1058	37	1	166	1	TAS2R5	7	141490325	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1774680	141490325	17648338	262	10025											
EZH2	2146	hgsc.bcm.edu	37	chr7	148508727	148508727	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtgccttacctctccacagTattctgagatgaattcattt	10	15	6	10	0	3	2	1	2	2	1	4	3	3	2	3	0	2	1	3	0	3	5	rs267601394		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:148508727T>G	ENST00000460911.1	-	16	2010	c.1922A>C	c.(1921-1923)tAc>tCc	p.Y641S	EZH2_ENST00000320356.2_Missense_Mutation_p.Y646S|EZH2_ENST00000541220.1_Missense_Mutation_p.Y590S|EZH2_ENST00000350995.2_Missense_Mutation_p.Y602S|EZH2_ENST00000478654.1_Missense_Mutation_p.Y590S|EZH2_ENST00000483967.1_Missense_Mutation_p.Y632S|EZH2_ENST00000476773.1_Missense_Mutation_p.Y590S			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	641	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.		Y -> C (in a patient with diffuse large B-cell lymphoma; somatic mutation). {ECO:0000269|PubMed:20081860}.|Y -> F (found in patients with follicular lymphoma; also in diffuse large B-cell lymphoma; somatic mutation). {ECO:0000269|PubMed:20081860}.|Y -> H (found in patients with follicular lymphoma; also in diffuse large B-cell lymphoma; somatic mutation). {ECO:0000269|PubMed:20081860}.|Y -> N (found in patients with follicular lymphoma; also in diffuse large B-cell lymphoma; somatic mutation). {ECO:0000269|PubMed:20081860}.|Y -> S (found in patients with follicular lymphoma; also in diffuse large B-cell lymphoma; somatic mutation). {ECO:0000269|PubMed:20081860}.		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)	p.Y646F(59)|p.Y646S(22)|p.Y602F(8)|p.Y646C(6)|p.Y602S(4)		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)			CTCTCCACAGTATTCTGAGAT	0.378			Mis		DLBCL																																p.Y646S		Atlas-SNP	.		Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	EZH2_ENST00000350995,face,carcinoma,-1,214	EZH2	823	214	99	Substitution - Missense(99)	haematopoietic_and_lymphoid_tissue(99)	c.A1937C						PASS	.						96	89	91					7																	148508727		2203	4300	6503	SO:0001583	missense	2146	exon16			CCACAGTATTCTG		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.1922A>C	7.37:g.148508727T>G	ENSP00000419711:p.Tyr641Ser	46	0	0		57	24	0.421053	NM_004456	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Missense_Mutation	SNP	ENST00000460911.1	37	CCDS56516.1	.	.	.	.	.	.	.	.	.	.	t	25.3	4.619614	0.87460	.	.	ENSG00000106462	ENST00000478654;ENST00000320356;ENST00000460911;ENST00000350995;ENST00000541220;ENST00000476773;ENST00000483967	D;D;D;D;D;D;D	0.93307	-3.2;-1.94;-1.94;-1.94;-3.2;-3.2;-1.94	5.63	5.63	0.86233	SET domain (3);	0.000000	0.85682	D	0.000000	D	0.97654	0.9231	H	0.99516	4.605	0.80722	D	1	D;P;P;D;P	0.63880	0.986;0.918;0.543;0.993;0.688	P;P;B;P;B	0.52481	0.7;0.577;0.395;0.7;0.318	D	0.99066	1.0832	10	0.87932	D	0	.	15.87	0.79108	0.0:0.0:0.0:1.0	.	632;590;641;602;646	Q15910-4;Q15910-5;Q15910;Q15910-3;Q15910-2	.;.;EZH2_HUMAN;.;.	S	590;646;641;602;590;590;632	ENSP00000417062:Y590S;ENSP00000320147:Y646S;ENSP00000419711:Y641S;ENSP00000223193:Y602S;ENSP00000443219:Y590S;ENSP00000419050:Y590S;ENSP00000419856:Y632S	ENSP00000320147:Y646S	Y	-	2	0	EZH2	148139660	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.789000	0.85783	2.145000	0.66743	0.533000	0.62120	TAC	.	.	none		0.378	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456		G	148508727	T	G	148508727	3	3	26	1	0	0	0	0	1	0	0	0	5336	1638	57	5	338	5	EZH2	7	148508727	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	7018402	148508727	10629936	263	10026											
EZH2	2146	hgsc.bcm.edu	37	chr7	148525904	148525904	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtctccatcatcatcatcgtCatcatcattatattgaccaa	12	14	3	12	1	7	1	6	1	1	0	9	1	7	1	2	0	0	0	2	0	3	3	rs2302427	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:148525904C>G	ENST00000460911.1	-	6	641	c.553G>C	c.(553-555)Gac>Cac	p.D185H	EZH2_ENST00000320356.2_Missense_Mutation_p.D185H|EZH2_ENST00000541220.1_Missense_Mutation_p.D176H|EZH2_ENST00000350995.2_Missense_Mutation_p.D146H|EZH2_ENST00000478654.1_Missense_Mutation_p.D176H|EZH2_ENST00000483967.1_Missense_Mutation_p.D176H|EZH2_ENST00000536783.1_Missense_Mutation_p.D76H|EZH2_ENST00000476773.1_Missense_Mutation_p.D176H			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	185	Interaction with DNMT1, DNMT3A and DNMT3B.		D -> H (in dbSNP:rs2302427).		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)			tcatcatcgtcatcatcatta	0.393			Mis		DLBCL								C|||	400	0.0798722	0.0038	0.0461	5008	,	,		19098	0.2063		0.0696	False		,,,				2504	0.0869				p.D185H		Atlas-SNP	.		Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	EZH2_ENST00000350995,NS,carcinoma,+2,2	EZH2	823	2	0			c.G553C						PASS	.	C	HIS/ASP,HIS/ASP,HIS/ASP,HIS/ASP,HIS/ASP	66,4340	60.5+/-97.4	0,66,2137	178	146	157		553,526,526,553,436	5.7	0.9	7	dbSNP_100	157	719,7881	175.3+/-225.4	30,659,3611	yes	missense,missense,missense,missense,missense	EZH2	NM_001203247.1,NM_001203248.1,NM_001203249.1,NM_004456.4,NM_152998.2	81,81,81,81,81	30,725,5748	GG,GC,CC		8.3605,1.498,6.0357	benign,benign,benign,benign,benign	185/747,176/738,176/696,185/752,146/708	148525904	785,12221	2203	4300	6503	SO:0001583	missense	2146	exon6			CATCGTCATCATC		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.553G>C	7.37:g.148525904C>G	ENSP00000419711:p.Asp185His	202	0	0		203	103	0.507389	NM_001203247	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Missense_Mutation	SNP	ENST00000460911.1	37	CCDS56516.1	161	0.07371794871794872	3	0.006097560975609756	21	0.058011049723756904	83	0.1451048951048951	54	0.0712401055408971	C	19.43	3.826662	0.71143	0.01498	0.083605	ENSG00000106462	ENST00000478654;ENST00000320356;ENST00000460911;ENST00000350995;ENST00000541220;ENST00000476773;ENST00000483967;ENST00000536783	D;D;D;D;D;D;D;T	0.94828	-3.46;-3.5;-3.46;-3.5;-3.46;-3.46;-3.53;0.81	5.69	5.69	0.88448	SANT domain, DNA binding (1);	0.168733	0.49916	D	0.000127	T	0.08980	0.0222	L	0.34521	1.04	0.09310	P	0.99999641944	P;B;B;B;P;P	0.47604	0.898;0.348;0.348;0.41;0.659;0.676	P;B;B;B;B;P	0.49226	0.553;0.393;0.393;0.299;0.393;0.603	T	0.59161	-0.7506	9	0.72032	D	0.01	.	19.4235	0.94732	0.0:1.0:0.0:0.0	rs2302427;rs52833659	185;176;176;185;146;185	B7Z8K5;Q15910-4;Q15910-5;Q15910;Q15910-3;Q15910-2	.;.;.;EZH2_HUMAN;.;.	H	176;185;185;146;176;176;176;76	ENSP00000417062:D176H;ENSP00000320147:D185H;ENSP00000419711:D185H;ENSP00000223193:D146H;ENSP00000443219:D176H;ENSP00000419050:D176H;ENSP00000419856:D176H;ENSP00000439305:D76H	ENSP00000320147:D185H	D	-	1	0	EZH2	148156837	1.000000	0.71417	0.919000	0.36401	0.821000	0.46438	7.538000	0.82048	2.682000	0.91365	0.585000	0.79938	GAC	C|0.926;G|0.074	0.074	strong		0.393	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456		G	148525904	C	G	148525904	3	3	26	1	0	0	0	0	1	0	0	0	5336	826	29	4	1762	4	EZH2	7	148525904	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	17177	148525904	10612759	264	10027											
MFHAS1	9258	hgsc.bcm.edu	37	chr8	8748058	8748058	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gacccattcaaaggcttgccCttgggtttattgaggcagta	9	12	11	9	0	1	1	1	1	0	0	1	2	1	1	2	3	1	4	2	3	3	7	rs146502253	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:8748058C>T	ENST00000276282.6	-	1	3097	c.2511G>A	c.(2509-2511)aaG>aaA	p.K837K		NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	837										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)		AAGGCTTGCCCTTGGGTTTAT	0.537													C|||	3	0.000599042	0.0	0.0	5008	,	,		18898	0.0		0.002	False		,,,				2504	0.001				p.K837K	Melanoma(103;1201 2045 17515 28966)	Atlas-SNP	.											.	MFHAS1	58	.	0			c.G2511A						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	73	72	72		2511	4.1	1	8	dbSNP_134	72	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	MFHAS1	NM_004225.2		0,16,6487	TT,TC,CC		0.1628,0.0454,0.123		837/1053	8748058	16,12990	2203	4300	6503	SO:0001819	synonymous_variant	9258	exon1			CTTGCCCTTGGGT	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.2511G>A	8.37:g.8748058C>T		53	0	0		44	24	0.545455	NM_004225	Q96CI0	Silent	SNP	ENST00000276282.6	37	CCDS34844.1																																																																																			C|0.998;T|0.002	0.002	strong		0.537	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225		T	8748058	C	T	8748058	2	4	26	1	0	0	0	0	0	0	0	1	9530	680	24	2		2	MFHAS1	8	8748058	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10		8748058	137615964	265	10028											
GATA4	2626	hgsc.bcm.edu	37	chr8	11606438	11606438	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aactcagtagatatgtttgaCgacttctcagaaggcagaga	14	10	10	7	1	2	4	2	1	1	3	3	6	2	4	0	1	1	3	0	1	4	4	rs192122549	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:11606438C>T	ENST00000335135.4	+	3	1185	c.627C>T	c.(625-627)gaC>gaT	p.D209D	GATA4_ENST00000528712.1_Silent_p.D3D|GATA4_ENST00000532059.1_Silent_p.D210D	NM_002052.3	NP_002043.2	P43694	GATA4_HUMAN	GATA binding protein 4	209					atrial septum morphogenesis (GO:0060413)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|atrioventricular valve morphogenesis (GO:0003181)|blood coagulation (GO:0007596)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac ventricle morphogenesis (GO:0003208)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to glucose stimulus (GO:0071333)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube anterior/posterior pattern specification (GO:0035054)|endocardial cushion development (GO:0003197)|endoderm development (GO:0007492)|endoderm formation (GO:0001706)|epithelial cell fate commitment (GO:0072148)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|intestinal epithelial cell differentiation (GO:0060575)|lung lobe formation (GO:0060464)|male gonad development (GO:0008584)|negative regulation of autophagy (GO:0010507)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|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 cardiac muscle cell contraction (GO:0086004)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to mechanical stimulus (GO:0009612)|seminiferous tubule development (GO:0072520)|Sertoli cell differentiation (GO:0060008)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|enhancer sequence-specific DNA binding (GO:0001158)|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)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(10)	13	all_epithelial(15;0.0839)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.199)		ATATGTTTGACGACTTCTCAG	0.517													C|||	2	0.000399361	0.0	0.0	5008	,	,		20917	0.0		0.002	False		,,,				2504	0.0				p.D209D		Atlas-SNP	.											.	GATA4	29	.	0			c.C627T						PASS	.	C		0,4406		0,0,2203	134	134	134		627	-10.2	0.2	8		134	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	GATA4	NM_002052.3		0,3,6500	TT,TC,CC		0.0349,0.0,0.0231		209/443	11606438	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	2626	exon3			GTTTGACGACTTC	AK097060	CCDS5983.1	8p23.1-p22	2013-01-25	2001-11-28		ENSG00000136574	ENSG00000136574		"GATA zinc finger domain containing"	4173	protein-coding gene	gene with protein product		600576	"GATA-binding protein 4"			7665171	Standard	NM_002052		Approved		uc003wuc.2	P43694	OTTHUMG00000090800	ENST00000335135.4:c.627C>T	8.37:g.11606438C>T		132	0	0		224	105	0.46875	NM_002052	B7ZKX0|B7ZKZ4|Q3MJ45|Q5IFM8	Silent	SNP	ENST00000335135.4	37	CCDS5983.1																																																																																			C|0.999;T|0.001	0.001	strong		0.517	GATA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207587.2	NM_002052		T	11606438	C	T	11606438	2	4	26	1	0	0	0	0	0	0	0	1	6264	535	19	1		1	GATA4	8	11606438	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	2858380	11606438	134757584	266	10029											
FAM86B1	85002	hgsc.bcm.edu	37	chr8	12044264	12044264	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctgcaaggtagagggcggCatcccatgtgaccaggcctg	8	8	14	11	1	1	2	0	1	1	1	2	2	2	2	3	4	1	3	3	4	2	2			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:12044264C>T	ENST00000448228.2	-	4	368	c.319G>A	c.(319-321)Gcc>Acc	p.A107T	FAM86B1_ENST00000321602.8_Start_Codon_SNP_p.M1I|FAM86B1_ENST00000534520.1_Missense_Mutation_p.A107T|FAM86B1_ENST00000533852.2_Missense_Mutation_p.A141T|FAM86B1_ENST00000533513.1_Missense_Mutation_p.A141T	NM_001083537.1	NP_001077006.1	Q8N7N1	F86B1_HUMAN	family with sequence similarity 86, member B1	107										kidney(1)|prostate(1)|stomach(1)	3			STAD - Stomach adenocarcinoma(15;0.033)	COAD - Colon adenocarcinoma(149;0.0965)		TAGAGGGCGGCATCCCATGTG	0.612																																					p.A107T		Atlas-SNP	.											FAM86B1,NS,carcinoma,+2,1	FAM86B1	7	1	0			c.G319A						scavenged	.						1	1	1					8																	12044264		461	1070	1531	SO:0001583	missense	85002	exon4			GGGCGGCATCCCA	BC007983	CCDS59512.1	8p23.1	2014-02-12	2005-08-19		ENSG00000186523	ENSG00000186523			28268	protein-coding gene	gene with protein product						12477932	Standard	NM_001083537		Approved	MGC16279	uc010lse.3	Q8N7N1	OTTHUMG00000165298	ENST00000448228.2:c.319G>A	8.37:g.12044264C>T	ENSP00000407067:p.Ala107Thr	297	0	0		320	27	0.084375	NM_001083537		Missense_Mutation	SNP	ENST00000448228.2	37	CCDS59512.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	11.97|11.97	1.796969|1.796969	0.31777|0.31777	.|.	.|.	ENSG00000186523|ENSG00000186523	ENST00000431227;ENST00000340537;ENST00000448228;ENST00000534520;ENST00000526708;ENST00000524571;ENST00000533513|ENST00000321602;ENST00000526802	T;T;T;T;T|T	0.36340|0.24350	1.26;2.52;1.26;1.56;4.06|1.86	1.17|1.17	1.17|1.17	0.20885|0.20885	.|.	10.022600|.	0.01570|.	U|.	0.020538|.	T|T	0.33731|0.33731	0.0873|0.0873	M|M	0.90309|0.90309	3.105|3.105	0.80722|0.80722	D|D	1|1	P;P|B;B	0.46457|0.15719	0.878;0.749|0.014;0.003	D;P|B;B	0.64144|0.08055	0.922;0.624|0.003;0.002	T|T	0.42050|0.42050	-0.9474|-0.9474	10|9	0.72032|0.87932	D|D	0.01|0	.|.	8.2654|8.2654	0.31810|0.31810	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	107;141|1;38	Q8N7N1;E9PN63|F6QN85;Q4KMP3	F86B1_HUMAN;.|.;.	T|I	141;107;107;107;141;79;141|1;102	ENSP00000342610:A107T;ENSP00000407067:A107T;ENSP00000431362:A107T;ENSP00000432790:A79T;ENSP00000435201:A141T|ENSP00000439686:M1I	ENSP00000342610:A107T|ENSP00000439686:M1I	A|M	-|-	1|3	0|0	FAM86B1|FAM86B1	12081673|12081673	1.000000|1.000000	0.71417|0.71417	0.088000|0.088000	0.20740|0.20740	0.049000|0.049000	0.14656|0.14656	6.283000|6.283000	0.72646|0.72646	0.950000|0.950000	0.37743|0.37743	0.173000|0.173000	0.16961|0.16961	GCC|ATG	.	.	none		0.612	FAM86B1-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000383317.1	NM_032916		T	12044264	C	T	12044264	3	4	26	1	0	0	0	0	1	0	0	0	5652	710	25	2	587	2	FAM86B1	8	12044264	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	437826	12044264	134319758	267	10030											
MTMR7	9108	hgsc.bcm.edu	37	chr8	17157605	17157605	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaaatgatttcatattcccActgtaatcctggggagtgtt	10	14	10	7	0	1	1	1	1	0	0	3	3	3	3	2	3	0	2	2	3	3	5	rs145244130	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:17157605A>C	ENST00000180173.5	-	14	1783	c.1749T>G	c.(1747-1749)agT>agG	p.S583R	MTMR7_ENST00000398099.3_Missense_Mutation_p.S174R|VPS37A_ENST00000521162.1_3'UTR	NM_004686.4	NP_004677.3	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	583					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)		TCATATTCCCACTGTAATCCT	0.453													A|||	6	0.00119808	0.0	0.0	5008	,	,		17679	0.0		0.003	False		,,,				2504	0.0031				p.S583R		Atlas-SNP	.											.	MTMR7	75	.	0			c.T1749G						PASS	.	A	ARG/SER	4,4402	8.1+/-20.4	0,4,2199	193	193	193		1749	-2.7	0.9	8	dbSNP_134	193	36,8564	24.6+/-71.5	1,34,4265	yes	missense	MTMR7	NM_004686.4	110	1,38,6464	CC,CA,AA		0.4186,0.0908,0.3076	possibly-damaging	583/661	17157605	40,12966	2203	4300	6503	SO:0001583	missense	9108	exon14			ATTCCCACTGTAA	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.1749T>G	8.37:g.17157605A>C	ENSP00000180173:p.Ser583Arg	242	0	0		286	141	0.493007	NM_004686	A1L4K9|B4DG87|Q68DX4	Missense_Mutation	SNP	ENST00000180173.5	37	CCDS34851.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	A	12.24	1.877751	0.33162	9.08E-4	0.004186	ENSG00000003987	ENST00000180173;ENST00000398099	D;T	0.92965	-3.14;-1.07	5.32	-2.65	0.06095	.	0.377447	0.33127	N	0.005259	T	0.79476	0.4452	L	0.36672	1.1	0.39153	D	0.96225	B	0.28128	0.201	B	0.19391	0.025	T	0.68507	-0.5390	10	0.15499	T	0.54	.	13.1914	0.59713	0.4371:0.0:0.5629:0.0	.	583	Q9Y216	MTMR7_HUMAN	R	583;174	ENSP00000180173:S583R;ENSP00000381171:S174R	ENSP00000180173:S583R	S	-	3	2	MTMR7	17201976	0.516000	0.26218	0.932000	0.37286	0.971000	0.66376	-0.103000	0.10940	-0.380000	0.07894	-0.326000	0.08463	AGT	A|0.997;C|0.003	0.003	strong		0.453	MTMR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375311.1	NM_004686		C	17157605	A	C	17157605	3	2	26	1	0	0	0	0	1	0	0	0	9957	156	6	5	237	5	MTMR7	8	17157605	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	5113341	17157605	129206417	268	10031											
MTUS1	57509	hgsc.bcm.edu	37	chr8	17611924	17611924	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aggtgcctccttcgagtctgGtatgtttttaagccctcgat	6	15	10	10	2	1	0	0	0	1	0	4	2	2	0	3	2	2	2	3	2	2	5			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:17611924G>A	ENST00000262102.6	-	2	1617	c.1393C>T	c.(1393-1395)Cca>Tca	p.P465S	MTUS1_ENST00000381862.3_Missense_Mutation_p.P465S|MTUS1_ENST00000519263.1_Missense_Mutation_p.P465S|MTUS1_ENST00000381869.3_Missense_Mutation_p.P465S	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	465					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)		TTCGAGTCTGGTATGTTTTTA	0.418																																					p.P465S		Atlas-SNP	.											.	MTUS1	144	.	0			c.C1393T						PASS	.						155	147	149					8																	17611924		1868	4121	5989	SO:0001583	missense	57509	exon2			AGTCTGGTATGTT	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.1393C>T	8.37:g.17611924G>A	ENSP00000262102:p.Pro465Ser	180	0	0		244	48	0.196721	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	.	.	.	.	.	.	.	.	.	.	G	6.988	0.552322	0.13374	.	.	ENSG00000129422	ENST00000381869;ENST00000262102;ENST00000519263;ENST00000381862	T;T;T;T	0.18960	3.16;3.17;3.16;2.18	5.0	-1.15	0.09709	.	0.579128	0.16128	N	0.228351	T	0.09598	0.0236	N	0.16656	0.425	0.09310	N	1	B;B;B	0.23377	0.084;0.041;0.041	B;B;B	0.21917	0.037;0.011;0.011	T	0.18745	-1.0327	10	0.52906	T	0.07	-0.6007	2.2436	0.04025	0.3516:0.1319:0.4048:0.1117	.	465;465;465	Q9ULD2-5;Q9ULD2-2;Q9ULD2	.;.;MTUS1_HUMAN	S	465	ENSP00000371293:P465S;ENSP00000262102:P465S;ENSP00000430167:P465S;ENSP00000371286:P465S	ENSP00000262102:P465S	P	-	1	0	MTUS1	17656204	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.204000	0.17335	-0.351000	0.08249	-1.623000	0.00790	CCA	.	.	none		0.418	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		A	17611924	G	A	17611924	3	1	26	1	0	0	0	0	1	0	0	0	9974	1261	44	2	2794	2	MTUS1	8	17611924	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	454319	17611924	128752098	269	10032											
PCM1	5108	hgsc.bcm.edu	37	chr8	17830005	17830005	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatacaaacggaagaagacGccagtttgatgaagaatcac	18	6	10	7	2	1	6	1	2	0	4	1	7	1	7	1	1	2	1	1	1	6	2	rs17514547	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:17830005G>A	ENST00000519253.1	+	23	4003	c.3752G>A	c.(3751-3753)cGc>cAc	p.R1251H	PCM1_ENST00000524226.1_Missense_Mutation_p.R1252H|PCM1_ENST00000327578.8_5'Flank|PCM1_ENST00000325083.8_Missense_Mutation_p.R1251H			Q15154	PCM1_HUMAN	pericentriolar material 1	1251			R -> H (in dbSNP:rs17514547).		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)		GGAAGAAGACGCCAGTTTGAT	0.378			T	"RET, JAK2"	"papillary thyroid, CML, MPD"								G|||	51	0.0101837	0.0008	0.0086	5008	,	,		17700	0.0		0.0268	False		,,,				2504	0.0174				p.R1251H		Atlas-SNP	.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"E, L"	.	PCM1	120	.	0			c.G3752A						PASS	.	G	HIS/ARG	17,3709		0,17,1846	102	96	98		3752	2	1	8	dbSNP_123	98	250,7948		5,240,3854	yes	missense	PCM1	NM_006197.3	29	5,257,5700	AA,AG,GG		3.0495,0.4563,2.2392	probably-damaging	1251/2025	17830005	267,11657	1863	4099	5962	SO:0001583	missense	5108	exon23			GAAGACGCCAGTT		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.3752G>A	8.37:g.17830005G>A	ENSP00000431099:p.Arg1251His	163	0	0		172	81	0.47093	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	37		27	0.012362637362637362	0	0.0	4	0.011049723756906077	0	0.0	23	0.030343007915567283	G	12.33	1.904852	0.33628	0.004563	0.030495	ENSG00000078674	ENST00000325083;ENST00000519253;ENST00000524226	T;T;T	0.52983	0.64;0.64;0.64	4.81	2.01	0.26516	.	0.261491	0.45126	N	0.000386	T	0.25121	0.0610	N	0.25647	0.755	0.80722	D	1	B;D;B;D	0.89917	0.0;1.0;0.01;1.0	B;D;B;D	0.79784	0.001;0.993;0.007;0.993	T	0.13980	-1.0489	10	0.44086	T	0.13	-0.0745	7.4507	0.27237	0.3627:0.0:0.6373:0.0	rs17514547;rs52805963;rs56506649;rs17514547	113;1251;1252;1251	B4DJ00;E7ETA6;E7EV56;Q15154	.;.;.;PCM1_HUMAN	H	1251;1251;1252	ENSP00000327077:R1251H;ENSP00000431099:R1251H;ENSP00000430521:R1252H	ENSP00000327077:R1251H	R	+	2	0	PCM1	17874285	0.992000	0.36948	1.000000	0.80357	0.174000	0.22865	0.417000	0.21214	0.305000	0.22832	0.313000	0.20887	CGC	G|0.986;A|0.014	0.014	strong		0.378	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197		A	17830005	G	A	17830005	3	1	26	1	0	0	0	0	1	0	0	0	11593	1087	38	1	3834	1	PCM1	8	17830005	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	218081	17830005	128534017	270	10033											
NAT1	9	hgsc.bcm.edu	37	chr8	18080128	18080128	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	caaataccgaaaaatctactCctttactcttaagcctcgaa	15	11	3	12	2	2	0	0	0	2	0	4	2	3	0	3	0	4	0	3	0	8	5	rs141552883		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:18080128C>T	ENST00000517492.1	+	3	1210	c.572C>T	c.(571-573)tCc>tTc	p.S191F	NAT1_ENST00000541942.1_Missense_Mutation_p.S191F|NAT1_ENST00000517441.1_3'UTR|NAT1_ENST00000518029.1_Missense_Mutation_p.S191F|NAT1_ENST00000307719.4_Missense_Mutation_p.S191F|NAT1_ENST00000545197.1_Missense_Mutation_p.S253F|NAT1_ENST00000535084.1_Missense_Mutation_p.S191F|NAT1_ENST00000520546.1_Missense_Mutation_p.S191F|NAT1_ENST00000539092.1_Missense_Mutation_p.S191F			Q8IZM9	S38A6_HUMAN	N-acetyltransferase 1 (arylamine N-acetyltransferase)	0					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(3)|kidney(1)|lung(2)|urinary_tract(1)	9				Colorectal(111;0.0519)|COAD - Colon adenocarcinoma(73;0.208)		AAAATCTACTCCTTTACTCTT	0.358													C|||	1	0.000199681	0.0	0.0	5008	,	,		19441	0.0		0.001	False		,,,				2504	0.0				p.S253F		Atlas-SNP	.											.	NAT1	38	.	0			c.C758T						PASS	.	C	PHE/SER,PHE/SER,PHE/SER,PHE/SER,PHE/SER,PHE/SER,PHE/SER,PHE/SER,PHE/SER	0,4406		0,0,2203	112	115	114		572,572,572,572,572,572,758,758,572	3.1	0.5	8	dbSNP_134	114	1,8599		0,1,4299	no	missense,missense,missense,missense,missense,missense,missense,missense,missense	NAT1	NM_000662.5,NM_001160170.1,NM_001160171.1,NM_001160172.1,NM_001160173.1,NM_001160174.1,NM_001160175.1,NM_001160176.1,NM_001160179.1	155,155,155,155,155,155,155,155,155	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	191/291,191/291,191/291,191/291,191/291,191/291,253/353,253/353,191/291	18080128	1,13005	2203	4300	6503	SO:0001583	missense	9	exon4			TCTACTCCTTTAC	BC047666	CCDS6007.1, CCDS55205.1	8p22	2012-01-18			ENSG00000171428	ENSG00000171428	2.3.1.5		7645	protein-coding gene	gene with protein product		108345		AAC1		7773298	Standard	NM_001160174		Approved		uc003wyt.3	P18440	OTTHUMG00000097001	ENST00000517492.1:c.572C>T	8.37:g.18080128C>T	ENSP00000429407:p.Ser191Phe	116	0	0		138	62	0.449275	NM_001160176	C9JWA6|Q86SY5	Missense_Mutation	SNP	ENST00000517492.1	37	CCDS6007.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	.	7.210	0.595309	0.13875	0.0	1.16E-4	ENSG00000171428	ENST00000535084;ENST00000307719;ENST00000545197;ENST00000539092;ENST00000541942;ENST00000518029;ENST00000517492;ENST00000520546	T;T;T;T;T;T;T;T	0.02177	4.41;4.41;4.41;4.41;4.41;4.41;4.41;4.41	4.05	3.13	0.36017	.	0.492839	0.21479	N	0.073870	T	0.07279	0.0184	M	0.90252	3.1	0.32873	D	0.50949	P;P	0.47409	0.895;0.851	P;P	0.52909	0.713;0.658	T	0.12811	-1.0533	10	0.10111	T	0.7	.	5.0238	0.14374	0.2107:0.6782:0.0:0.1111	.	253;191	F5H5R8;P18440	.;ARY1_HUMAN	F	191;191;253;191;191;191;191;191	ENSP00000444609:S191F;ENSP00000307218:S191F;ENSP00000443194:S253F;ENSP00000440434:S191F;ENSP00000440900:S191F;ENSP00000428270:S191F;ENSP00000429407:S191F;ENSP00000429341:S191F	ENSP00000307218:S191F	S	+	2	0	NAT1	18124408	0.952000	0.32445	0.453000	0.27007	0.784000	0.44337	0.616000	0.24344	0.767000	0.33267	0.460000	0.39030	TCC	C|1.000;T|0.000	0.000	strong		0.358	NAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374828.1	NM_000662		T	18080128	C	T	18080128	3	4	26	1	0	0	0	0	1	0	0	0	10182	855	30	2	768	2	NAT1	8	18080128	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	250123	18080128	128283894	271	10034											
FAM160B2	64760	hgsc.bcm.edu	37	chr8	21954017	21954017	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctgcacgctgggcaaggcCgaggtgggaggccctctgcg	5	6	17	13	3	2	0	0	0	2	0	2	2	2	1	2	5	2	3	2	5	1	0	rs117838157|rs577506980	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:21954017C>T	ENST00000289921.7	+	3	340	c.294C>T	c.(292-294)gcC>gcT	p.A98A		NM_022749.5	NP_073586.5	Q86V87	F16B2_HUMAN	family with sequence similarity 160, member B2	98										endometrium(2)|kidney(1)|lung(2)|prostate(3)|urinary_tract(1)	9						TGGGCAAGGCCGAGGTGGGAG	0.716													c|||	50	0.00998403	0.0219	0.0072	5008	,	,		14888	0.0		0.0139	False		,,,				2504	0.002				p.A98A		Atlas-SNP	.											.	FAM160B2	35	.	0			c.C294T						PASS	.	T		95,3757		2,91,1833	13	16	15		294	-10	0	8	dbSNP_132	15	87,7943		1,85,3929	no	coding-synonymous	FAM160B2	NM_022749.5		3,176,5762	TT,TC,CC		1.0834,2.4663,1.5317		98/744	21954017	182,11700	1926	4015	5941	SO:0001819	synonymous_variant	64760	exon3			CAAGGCCGAGGTG	AK025454	CCDS6021.2	8p21.3	2012-11-30	2008-06-05	2008-06-05	ENSG00000158863	ENSG00000158863			16492	protein-coding gene	gene with protein product			"retinoic acid induced 16"	RAI16		22971576, 15626329	Standard	XR_247128		Approved	FLJ21801	uc011kyx.2	Q86V87	OTTHUMG00000097088	ENST00000289921.7:c.294C>T	8.37:g.21954017C>T		79	0	0		74	48	0.648649	NM_022749	B2RDQ5|B3KNX1|Q2M211|Q71JB5|Q7L3J6|Q969T0|Q9H6W4	Silent	SNP	ENST00000289921.7	37	CCDS6021.2																																																																																			C|0.990;T|0.010	0.010	strong		0.716	FAM160B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375334.2			T	21954017	C	T	21954017	2	4	26	1	0	0	0	0	0	0	0	1	5476	639	23	1		1	FAM160B2	8	21954017	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	3873889	21954017	124410005	272	10035											
NUDT18	79873	hgsc.bcm.edu	37	chr8	21965801	21965801	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctccattctccccgcaggCaggtaccacgacccccggca	7	5	10	19	3	1	0	0	0	1	0	3	1	2	0	6	4	1	5	6	4	1	2	rs184414226	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:21965801C>A	ENST00000309188.6	-	4	337	c.219G>T	c.(217-219)ctG>ctT	p.L73L	NUDT18_ENST00000522405.1_5'UTR|NUDT18_ENST00000521807.2_3'UTR	NM_024815.3	NP_079091.3	Q6ZVK8	NUD18_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 18	73	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				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)		TCCCCGCAGGCAGGTACCACG	0.647													C|||	20	0.00399361	0.0015	0.0159	5008	,	,		17574	0.0		0.005	False		,,,				2504	0.002				p.L73L		Atlas-SNP	.											.	NUDT18	13	.	0			c.G219T						PASS	.	C		3,4253		0,3,2125	29	35	33		221	-6.9	0.4	8		33	74,8356		1,72,4142	yes	coding-synonymous	NUDT18	NM_024815.3		1,75,6267	AA,AC,CC		0.8778,0.0705,0.607		73/324	21965801	77,12609	2128	4215	6343	SO:0001819	synonymous_variant	79873	exon4			CGCAGGCAGGTAC		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.219G>T	8.37:g.21965801C>A		65	0	0		81	48	0.592593	NM_024815	Q8IZ75|Q9H687	Silent	SNP	ENST00000309188.6	37		8	0.003663003663003663	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	0	0.0	C	9.689	1.151432	0.21371	7.05E-4	0.008778	ENSG00000173566	ENST00000522379	.	.	.	5.1	-6.89	0.01660	.	.	.	.	.	T	0.20981	0.0505	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36016	-0.9765	4	.	.	.	.	2.7266	0.05215	0.1919:0.4767:0.2185:0.113	.	.	.	.	S	109	.	.	A	-	1	0	NUDT18	22021746	0.082000	0.21442	0.361000	0.25849	0.984000	0.73092	-0.870000	0.04228	-1.380000	0.02115	0.561000	0.74099	GCC	C|0.996;A|0.004	0.004	strong		0.647	NUDT18-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_024815		A	21965801	C	A	21965801	2	1	26	1	0	0	0	0	0	0	0	1	10744	697	25	4		4	NUDT18	8	21965801	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	11784	21965801	124398221	273	10036											
HR	55806	hgsc.bcm.edu	37	chr8	21976710	21976710	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgccaggcaggcagtggtgTgtcggcatgcaccaggatgc	7	7	17	10	1	0	0	0	0	0	0	1	1	0	1	2	5	3	4	2	5	0	0	rs7014851	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:21976710T>C	ENST00000381418.4	-	15	4544	c.3064A>G	c.(3064-3066)Aca>Gca	p.T1022A	HR_ENST00000312841.8_Missense_Mutation_p.T1022A	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	1022	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.		T -> A (in ALUNC; dbSNP:rs7014851). {ECO:0000269|PubMed:9445480}.		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)		GGCAGTGGTGTGTCGGCATGC	0.642													C|||	392	0.0782748	0.261	0.0418	5008	,	,		15589	0.0		0.0159	False		,,,				2504	0.002				p.T1022A		Atlas-SNP	.											.	HR	71	.	0			c.A3064G	GRCh37	CM983990	HR	M	rs7014851	PASS	.	C	ALA/THR,ALA/THR	1101,3305	718.9+/-408.9	131,839,1233	64	59	61	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3064,3064	4.3	0	8	dbSNP_116	61	138,8462	812.3+/-407.1	1,136,4163	yes	missense,missense	HR	NM_005144.4,NM_018411.4	58,58	132,975,5396	CC,CT,TT		1.6047,24.9887,9.5264	benign,benign	1022/1190,1022/1135	21976710	1239,11767	2203	4300	6503	SO:0001583	missense	55806	exon15			GTGGTGTGTCGGC	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.3064A>G	8.37:g.21976710T>C	ENSP00000370826:p.Thr1022Ala	113	0	0		132	65	0.492424	NM_018411	Q6GS30|Q96H33|Q9NPE1	Missense_Mutation	SNP	ENST00000381418.4	37	CCDS6022.1	164	0.07509157509157509	140	0.2845528455284553	15	0.04143646408839779	0	0.0	9	0.011873350923482849	C	0.021	-1.420024	0.01136	0.249887	0.016047	ENSG00000168453	ENST00000381418;ENST00000312841	T;T	0.69806	-0.43;-0.43	5.18	4.29	0.51040	Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.000000	0.56097	N	0.000034	T	0.00012	0.0000	N	0.00210	-1.845	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.16129	-1.0413	9	0.17832	T	0.49	-2.4672	7.2891	0.26356	0.0:0.7386:0.1695:0.0919	rs7014851;rs7014851	1022;1022	O43593-2;O43593	.;HAIR_HUMAN	A	1022	ENSP00000370826:T1022A;ENSP00000326765:T1022A	ENSP00000326765:T1022A	T	-	1	0	HR	22032655	0.965000	0.33210	0.010000	0.14722	0.026000	0.11368	1.953000	0.40352	0.571000	0.29365	-0.642000	0.03964	ACA	T|0.909;C|0.091	0.091	strong		0.642	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1			C	21976710	T	C	21976710	3	2	26	1	0	0	0	0	1	0	0	0	7356	1696	59	3	525	3	HR	8	21976710	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	10909	21976710	124387312	274	10037											
HR	55806	hgsc.bcm.edu	37	chr8	21978734	21978734	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctggggtctcagcggaatcGggggtctctgtcagggagga	6	8	19	8	2	3	0	2	0	2	0	6	3	3	3	0	7	1	1	0	7	1	0	rs77689228	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:21978734G>A	ENST00000381418.4	-	10	3691	c.2211C>T	c.(2209-2211)ccC>ccT	p.P737P	HR_ENST00000312841.8_Silent_p.P737P	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	737					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)		CAGCGGAATCGGGGGTCTCTG	0.632													G|||	33	0.00658946	0.0083	0.0101	5008	,	,		16735	0.0		0.0129	False		,,,				2504	0.002				p.P737P		Atlas-SNP	.											.	HR	71	.	0			c.C2211T						PASS	.	G	,	42,4364	44.6+/-78.6	0,42,2161	59	72	67		2211,2211	-5.9	0.9	8	dbSNP_132	67	120,8480	61.3+/-123.2	0,120,4180	no	coding-synonymous,coding-synonymous	HR	NM_005144.4,NM_018411.4	,	0,162,6341	AA,AG,GG		1.3953,0.9532,1.2456	,	737/1190,737/1135	21978734	162,12844	2203	4300	6503	SO:0001819	synonymous_variant	55806	exon10			GGAATCGGGGGTC	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.2211C>T	8.37:g.21978734G>A		105	0	0		131	70	0.534351	NM_018411	Q6GS30|Q96H33|Q9NPE1	Silent	SNP	ENST00000381418.4	37	CCDS6022.1																																																																																			G|0.988;A|0.012	0.012	strong		0.632	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1			A	21978734	G	A	21978734	2	1	26	1	0	0	0	0	0	0	0	1	7356	1103	39	1		1	HR	8	21978734	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	2024	21978734	124385288	275	10038											
REEP4	80346	hgsc.bcm.edu	37	chr8	21996453	21996453	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcaccaatgggtggcctcCggtgggacacctggtcctcc	5	8	13	15	1	1	0	1	0	0	0	4	1	4	1	6	5	0	1	6	5	1	0	rs79793560	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:21996453C>T	ENST00000306306.3	-	6	1007	c.539G>A	c.(538-540)cGg>cAg	p.R180Q	REEP4_ENST00000523293.1_Missense_Mutation_p.R180Q|REEP4_ENST00000334530.5_Intron	NM_025232.2	NP_079508.2	Q9H6H4	REEP4_HUMAN	receptor accessory protein 4	180					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)		GGGTGGCCTCCGGTGGGACAC	0.652													C|||	46	0.0091853	0.0053	0.0187	5008	,	,		17285	0.002		0.0209	False		,,,				2504	0.0031				p.R180Q		Atlas-SNP	.											.	REEP4	13	.	0			c.G539A						PASS	.	C	GLN/ARG	24,4382		0,24,2179	25	26	26		539	1.9	0.1	8	dbSNP_131	26	158,8430		1,156,4137	yes	missense	REEP4	NM_025232.2	43	1,180,6316	TT,TC,CC		1.8398,0.5447,1.4006	benign	180/258	21996453	182,12812	2203	4294	6497	SO:0001583	missense	80346	exon6			GGCCTCCGGTGGG	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.539G>A	8.37:g.21996453C>T	ENSP00000303482:p.Arg180Gln	85	0	0		116	64	0.551724	NM_025232	D3DSQ9|Q86VL1|Q9H6I5|Q9HBP4	Missense_Mutation	SNP	ENST00000306306.3	37	CCDS6024.1	29	0.013278388278388278	5	0.01016260162601626	8	0.022099447513812154	2	0.0034965034965034965	14	0.018469656992084433	C	3.815	-0.038862	0.07497	0.005447	0.018398	ENSG00000168476	ENST00000306306;ENST00000523293;ENST00000518664	D;D;D	0.89617	-1.7;-2.39;-2.54	4.86	1.92	0.25849	.	0.768004	0.11073	N	0.602648	T	0.62405	0.2425	N	0.14661	0.345	0.29351	N	0.865351	B	0.10296	0.003	B	0.04013	0.001	T	0.57871	-0.7736	10	0.13853	T	0.58	-14.4627	6.2242	0.20698	0.0:0.6692:0.1536:0.1772	.	180	Q9H6H4	REEP4_HUMAN	Q	180	ENSP00000303482:R180Q;ENSP00000428709:R180Q;ENSP00000428160:R180Q	ENSP00000303482:R180Q	R	-	2	0	REEP4	22052398	0.000000	0.05858	0.147000	0.22382	0.291000	0.27294	-0.823000	0.04443	0.481000	0.27557	-0.749000	0.03505	CGG	C|0.985;T|0.015	0.015	strong		0.652	REEP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254337.2	NM_025232		T	21996453	C	T	21996453	3	4	26	1	0	0	0	0	1	0	0	0	13222	652	23	1	246	1	REEP4	8	21996453	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	17719	21996453	124367569	276	10039											
BMP1	649	hgsc.bcm.edu	37	chr8	22049596	22049596	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacgtccctggacctgtaccGcagccgcctgtgctggtacg	5	8	12	16	4	0	0	0	0	0	0	1	1	1	1	5	2	4	4	5	2	2	2	rs145284541	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:22049596G>A	ENST00000306385.5	+	9	1782	c.1112G>A	c.(1111-1113)cGc>cAc	p.R371H	BMP1_ENST00000354870.5_3'UTR|BMP1_ENST00000397816.3_Missense_Mutation_p.R371H|BMP1_ENST00000306349.8_Missense_Mutation_p.R371H|BMP1_ENST00000397814.3_Missense_Mutation_p.R371H	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1	371	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of cartilage development (GO:0061036)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(3)	30				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)		GACCTGTACCGCAGCCGCCTG	0.632													G|||	17	0.00339457	0.0008	0.0072	5008	,	,		18169	0.0		0.0109	False		,,,				2504	0.0				p.R371H		Atlas-SNP	.											BMP1_ENST00000306349,NS,carcinoma,+1,2	BMP1	131	2	0			c.G1112A						PASS	.	G	HIS/ARG,HIS/ARG	6,4400	11.4+/-27.6	0,6,2197	179	142	155		1112,1112	5.8	1	8	dbSNP_134	155	61,8539	37.8+/-93.5	0,61,4239	yes	missense,missense	BMP1	NM_001199.3,NM_006129.4	29,29	0,67,6436	AA,AG,GG		0.7093,0.1362,0.5151	possibly-damaging,possibly-damaging	371/731,371/987	22049596	67,12939	2203	4300	6503	SO:0001583	missense	649	exon9			TGTACCGCAGCCG		CCDS6026.1, CCDS34856.1	8p21	2013-02-06	2004-08-09		ENSG00000168487	ENSG00000168487	3.4.24.19	"Bone morphogenetic proteins"	1067	protein-coding gene	gene with protein product	"procollagen C-endopeptidase"	112264	"procollagen C-endopeptidase"	PCOLC		2004778	Standard	NM_006129		Approved		uc003xbg.3	P13497	OTTHUMG00000097761	ENST00000306385.5:c.1112G>A	8.37:g.22049596G>A	ENSP00000305714:p.Arg371His	53	0	0		54	18	0.333333	NM_001199	A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Missense_Mutation	SNP	ENST00000306385.5	37	CCDS6026.1	9	0.004120879120879121	0	0.0	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	G	26.4	4.738348	0.89573	0.001362	0.007093	ENSG00000168487	ENST00000306385;ENST00000397816;ENST00000306349;ENST00000397814	T;T;T;T	0.18960	2.18;2.18;2.18;2.18	5.77	5.77	0.91146	CUB (5);	0.000000	0.39274	U	0.001414	T	0.30166	0.0756	L	0.38175	1.15	0.80722	D	1	D;D;D;D	0.89917	0.99;1.0;0.999;0.999	P;D;D;P	0.91635	0.86;0.999;0.949;0.862	T	0.01249	-1.1406	10	0.44086	T	0.13	.	17.4922	0.87707	0.0:0.0:1.0:0.0	.	371;444;371;371	P13497;Q59F71;P13497-2;P13497-6	BMP1_HUMAN;.;.;.	H	371	ENSP00000305714:R371H;ENSP00000380917:R371H;ENSP00000306121:R371H;ENSP00000380915:R371H	ENSP00000306121:R371H	R	+	2	0	BMP1	22105541	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.535000	0.53575	2.724000	0.93272	0.561000	0.74099	CGC	G|0.995;A|0.005	0.005	strong		0.632	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132		A	22049596	G	A	22049596	3	1	26	1	0	0	0	0	1	0	0	0	1456	1087	38	1	1146	1	BMP1	8	22049596	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	53143	22049596	124314426	277	10040											
PPP3CC	5533	hgsc.bcm.edu	37	chr8	22390522	22390522	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctcaggaggcaagcagactAtcgagacaggtgagtatgag	13	7	14	7	1	1	4	1	2	1	2	3	6	1	5	0	3	1	3	0	3	3	2			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:22390522A>G	ENST00000240139.5	+	12	1639	c.1312A>G	c.(1312-1314)Atc>Gtc	p.I438V	PPP3CC_ENST00000289963.8_Missense_Mutation_p.I438V|PPP3CC_ENST00000397775.3_Missense_Mutation_p.I447V	NM_005605.4	NP_005596.2	P48454	PP2BC_HUMAN	protein phosphatase 3, catalytic subunit, gamma isozyme	438					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)		CAAGCAGACTATCGAGACAGG	0.542																																					p.I447V		Atlas-SNP	.											.	PPP3CC	39	.	0			c.A1339G						PASS	.						84	66	72					8																	22390522		2203	4300	6503	SO:0001583	missense	5533	exon13			CAGACTATCGAGA		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.1312A>G	8.37:g.22390522A>G	ENSP00000240139:p.Ile438Val	60	0	0		103	48	0.466019	NM_001243974	B4DRT5|Q9BSS6|Q9H4M5	Missense_Mutation	SNP	ENST00000240139.5	37	CCDS34859.1	.	.	.	.	.	.	.	.	.	.	A	8.509	0.866175	0.17250	.	.	ENSG00000120910	ENST00000240139;ENST00000289963;ENST00000397775	T;T;T	0.05382	3.45;3.45;3.45	5.74	1.72	0.24424	.	0.185247	0.47455	D	0.000236	T	0.04588	0.0125	N	0.15975	0.35	0.34146	D	0.667017	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.12837	0.004;0.008;0.005	T	0.18745	-1.0327	10	0.45353	T	0.12	-16.5588	13.6583	0.62352	0.386:0.614:0.0:0.0	.	447;438;438	B4DRT5;P48454-2;P48454	.;.;PP2BC_HUMAN	V	438;438;447	ENSP00000240139:I438V;ENSP00000289963:I438V;ENSP00000380878:I447V	ENSP00000240139:I438V	I	+	1	0	PPP3CC	22446467	0.826000	0.29277	0.849000	0.33467	0.006000	0.05464	1.656000	0.37355	0.401000	0.25424	-0.313000	0.08912	ATC	.	.	none		0.542	PPP3CC-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375652.1	NM_005605		G	22390522	A	G	22390522	3	3	26	1	0	0	0	0	1	0	0	0	12411	449	16	3	1358	3	PPP3CC	8	22390522	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	340926	22390522	123973500	278	10041											
TNFRSF10D	8793	hgsc.bcm.edu	37	chr8	23002086	23002086	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tatctgttactcagggtctcGttgcgggcattgtcctccgc	4	14	11	12	3	3	0	1	0	2	0	6	0	5	0	2	2	2	3	2	2	2	4	rs117862321	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:23002086G>A	ENST00000312584.3	-	7	925	c.831C>T	c.(829-831)aaC>aaT	p.N277N		NM_003840.4	NP_003831.2	Q9UBN6	TR10D_HUMAN	tumor necrosis factor receptor superfamily, member 10d, decoy with truncated death domain	277					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		TCAGGGTCTCGTTGCGGGCAT	0.572													.|||	21	0.00419329	0.0015	0.0014	5008	,	,		21181	0.0		0.0119	False		,,,				2504	0.0061				p.N277N		Atlas-SNP	.											.	TNFRSF10D	21	.	0			c.C831T						PASS	.	G		12,4394	19.1+/-41.9	0,12,2191	92	87	89		831	-0.3	0	8	dbSNP_132	89	63,8537	38.3+/-94.2	0,63,4237	no	coding-synonymous	TNFRSF10D	NM_003840.3		0,75,6428	AA,AG,GG		0.7326,0.2724,0.5767		277/387	23002086	75,12931	2203	4300	6503	SO:0001819	synonymous_variant	8793	exon7			GGTCTCGTTGCGG	AF029761	CCDS6038.1	8p21	2006-02-22			ENSG00000173530	ENSG00000173530		"Tumor necrosis factor receptor superfamily", "CD molecules"	11907	protein-coding gene	gene with protein product		603614				9382840, 9537512	Standard	NM_003840		Approved	DcR2, TRUNDD, TRAILR4, CD264	uc003xcz.2	Q9UBN6	OTTHUMG00000097845	ENST00000312584.3:c.831C>T	8.37:g.23002086G>A		148	0	0		174	83	0.477012	NM_003840	B2R8W0|Q9Y6Q4	Silent	SNP	ENST00000312584.3	37	CCDS6038.1																																																																																			G|0.995;A|0.005	0.005	strong		0.572	TNFRSF10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215135.1			A	23002086	G	A	23002086	2	1	26	1	0	0	0	0	0	0	0	1	16298	1136	40	1		1	TNFRSF10D	8	23002086	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	611564	23002086	123361936	279	10042											
ADAM28	10863	hgsc.bcm.edu	37	chr8	24167750	24167750	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatcaccacaagcccacaaaTtatggtataacggagtctct	14	9	7	11	1	2	0	1	0	1	0	3	2	2	1	2	2	2	1	2	2	5	3			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:24167750T>G	ENST00000265769.4	+	4	412	c.302T>G	c.(301-303)aTt>aGt	p.I101S	RP11-624C23.1_ENST00000523700.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000518988.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|ADAM28_ENST00000397649.3_De_novo_Start_OutOfFrame|ADAM28_ENST00000437154.2_Missense_Mutation_p.I101S|ADAM28_ENST00000540823.1_De_novo_Start_OutOfFrame	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	101					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)		AGCCCACAAATTATGGTATAA	0.403																																					p.I101S	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											.	ADAM28	100	.	0			c.T302G						PASS	.						84	79	81					8																	24167750		2203	4300	6503	SO:0001583	missense	10863	exon4			CACAAATTATGGT	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.302T>G	8.37:g.24167750T>G	ENSP00000265769:p.Ile101Ser	128	0	0		123	62	0.504065	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Missense_Mutation	SNP	ENST00000265769.4	37	CCDS34865.1	.	.	.	.	.	.	.	.	.	.	T	17.10	3.302338	0.60195	.	.	ENSG00000042980	ENST00000265769;ENST00000437154	T;T	0.05786	3.39;3.39	4.97	3.84	0.44239	Peptidase M12B, propeptide (1);	.	.	.	.	T	0.12860	0.0312	L	0.55990	1.75	0.80722	D	1	D;P	0.62365	0.991;0.837	P;P	0.62089	0.898;0.457	T	0.13019	-1.0525	9	0.16420	T	0.52	.	6.8564	0.24042	0.0:0.101:0.0:0.899	.	101;101	Q9UKQ2;Q9UKQ2-2	ADA28_HUMAN;.	S	101	ENSP00000265769:I101S;ENSP00000393699:I101S	ENSP00000265769:I101S	I	+	2	0	ADAM28	24223695	1.000000	0.71417	1.000000	0.80357	0.538000	0.34931	2.018000	0.40991	2.222000	0.72286	0.477000	0.44152	ATT	.	.	none		0.403	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778		G	24167750	T	G	24167750	3	3	26	1	0	0	0	0	1	0	0	0	246	1493	52	5	316	5	ADAM28	8	24167750	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	1165664	24167750	122196272	280	10043											
EPHX2	2053	hgsc.bcm.edu	37	chr8	27358509	27358509	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actacccggcttatgaaaggAgagatcacactttcccaggt	12	9	9	11	1	1	2	1	1	0	1	2	4	2	3	2	3	1	1	2	3	3	3			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:27358509A>G	ENST00000521400.1	+	2	598	c.168A>G	c.(166-168)ggA>ggG	p.G56G	EPHX2_ENST00000380476.3_Silent_p.G3G|EPHX2_ENST00000520666.1_3'UTR|EPHX2_ENST00000518379.1_Silent_p.G56G|EPHX2_ENST00000521780.1_Intron|EPHX2_ENST00000517536.1_Silent_p.G56G	NM_001979.5	NP_001970.2	P34913	HYES_HUMAN	epoxide hydrolase 2, cytoplasmic	56	Phosphatase.				arachidonic acid metabolic process (GO:0019369)|cellular calcium ion homeostasis (GO:0006874)|cholesterol homeostasis (GO:0042632)|dephosphorylation (GO:0016311)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|inflammatory response (GO:0006954)|phospholipid dephosphorylation (GO:0046839)|positive regulation of gene expression (GO:0010628)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|regulation of blood pressure (GO:0008217)|regulation of cholesterol metabolic process (GO:0090181)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|stilbene catabolic process (GO:0046272)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity (GO:0033885)|epoxide hydrolase activity (GO:0004301)|lipid phosphatase activity (GO:0042577)|magnesium ion binding (GO:0000287)|phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxic substance binding (GO:0015643)			cervix(1)|endometrium(8)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	27		Ovarian(32;2.61e-05)|all_epithelial(46;0.207)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0226)|Epithelial(17;1.12e-09)|Colorectal(74;0.157)		TTATGAAAGGAGAGATCACAC	0.527																																					p.G56G		Atlas-SNP	.											EPHX2,scalp,carcinoma,+2,1	EPHX2	57	1	0			c.A168G						PASS	.						101	94	97					8																	27358509		2203	4300	6503	SO:0001819	synonymous_variant	2053	exon2			GAAAGGAGAGATC	L05779	CCDS6060.1, CCDS59097.1, CCDS59098.1	8p21	2010-04-23			ENSG00000120915	ENSG00000120915	3.3.2.10		3402	protein-coding gene	gene with protein product		132811					Standard	NM_001979		Approved		uc003xfu.4	P34913	OTTHUMG00000102115	ENST00000521400.1:c.168A>G	8.37:g.27358509A>G		67	0	0		72	36	0.5	NM_001979	B2Z3B1|B3KTU8|B3KUA0|G3V134|J3KPH7|Q16764|Q9HBJ1|Q9HBJ2	Silent	SNP	ENST00000521400.1	37	CCDS6060.1	.	.	.	.	.	.	.	.	.	.	A	6.193	0.403741	0.11754	.	.	ENSG00000120915	ENST00000521684	.	.	.	4.33	0.328	0.15918	.	.	.	.	.	T	0.45418	0.1341	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.24404	-1.0161	4	.	.	.	-4.3771	3.8982	0.09149	0.6131:0.1839:0.203:0.0	.	.	.	.	G	56	.	.	E	+	2	0	EPHX2	27414426	0.994000	0.37717	0.854000	0.33618	0.579000	0.36224	0.349000	0.20055	-0.024000	0.13941	0.383000	0.25322	GAG	.	.	none		0.527	EPHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219954.4			G	27358509	A	G	27358509	2	3	26	1	0	0	0	0	0	0	0	1	5182	291	11	3		3	EPHX2	8	27358509	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	3190759	27358509	119005513	281	10044											
SCARA3	51435	hgsc.bcm.edu	37	chr8	27516323	27516323	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaaggacctcacccaggaGtgctacgatgtcaaggctgc	10	7	12	12	1	2	1	2	1	0	0	2	4	2	3	2	3	3	2	2	3	3	1			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:27516323G>A	ENST00000301904.3	+	5	656	c.636G>A	c.(634-636)gaG>gaA	p.E212E	SCARA3_ENST00000337221.4_Silent_p.E212E	NM_016240.2	NP_057324.2	Q6AZY7	SCAR3_HUMAN	scavenger receptor class A, member 3	212					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)		TCACCCAGGAGTGCTACGATG	0.612																																					p.E212E		Atlas-SNP	.											.	SCARA3	93	.	0			c.G636A						PASS	.						38	39	39					8																	27516323		2203	4300	6503	SO:0001819	synonymous_variant	51435	exon5			CCAGGAGTGCTAC	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.636G>A	8.37:g.27516323G>A		86	0	0		118	54	0.457627	NM_182826	Q9UM15|Q9UM16	Silent	SNP	ENST00000301904.3	37	CCDS34871.1																																																																																			.	.	none		0.612	SCARA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376258.2	NM_016240		A	27516323	G	A	27516323	2	1	26	1	0	0	0	0	0	0	0	1	13894	1020	36	2		2	SCARA3	8	27516323	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	157814	27516323	118847699	282	10045											
WRN	7486	hgsc.bcm.edu	37	chr8	30999075	30999075	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gattcttggtagaagtttctCggtataacaaatttatgaag	13	15	9	4	1	2	2	0	1	2	1	3	3	2	2	0	2	1	3	0	2	7	8	rs143954702		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:30999075C>T	ENST00000298139.5	+	25	3346	c.3097C>T	c.(3097-3099)Cgg>Tgg	p.R1033W		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	1033					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)		AGAAGTTTCTCGGTATAACAA	0.423			"Mis, N, F, S"			"osteosarcoma, meningioma, others"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome																												p.R1033W	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.C3097T						PASS	.	C	TRP/ARG	3,4403	6.2+/-15.9	0,3,2200	106	104	105		3097	3.2	0.1	8	dbSNP_134	105	2,8598	2.2+/-6.3	0,2,4298	yes	missense	WRN	NM_000553.4	101	0,5,6498	TT,TC,CC		0.0233,0.0681,0.0384	benign	1033/1433	30999075	5,13001	2203	4300	6503	SO:0001583	missense	7486	exon25	Familial Cancer Database	WS, Adult Progeria	GTTTCTCGGTATA		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.3097C>T	8.37:g.30999075C>T	ENSP00000298139:p.Arg1033Trp	108	0	0		145	77	0.531034	NM_000553	A1KYY9	Missense_Mutation	SNP	ENST00000298139.5	37	CCDS6082.1	.	.	.	.	.	.	.	.	.	.	C	13.66	2.304314	0.40795	6.81E-4	2.33E-4	ENSG00000165392	ENST00000298139	T	0.30448	1.53	5.9	3.15	0.36227	RQC domain (2);	0.406919	0.26176	N	0.025894	T	0.18841	0.0452	L	0.36672	1.1	0.21950	N	0.999455	B;P	0.38565	0.098;0.637	B;B	0.26614	0.044;0.071	T	0.11494	-1.0585	10	0.72032	D	0.01	-1.5776	8.5727	0.33578	0.1396:0.1272:0.7332:0.0	.	443;1033	Q59F09;Q14191	.;WRN_HUMAN	W	1033	ENSP00000298139:R1033W	ENSP00000298139:R1033W	R	+	1	2	WRN	31118617	0.089000	0.21612	0.091000	0.20842	0.002000	0.02628	0.474000	0.22148	0.400000	0.25396	-0.134000	0.14843	CGG	C|1.000;T|0.000	0.000	weak		0.423	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1			T	30999075	C	T	30999075	3	4	26	1	0	0	0	0	1	0	0	0	17417	875	31	1	3191	1	WRN	8	30999075	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	3482752	30999075	115364947	283	10046											
GOT1L1	137362	hgsc.bcm.edu	37	chr8	37797467	37797467	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatatcttgttcgggtaatcAtcttgtttgtaggtctttaa	9	19	8	5	1	4	0	1	0	3	0	5	0	4	0	0	2	0	4	0	2	5	9	rs151011886	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:37797467A>G	ENST00000307599.4	-	1	180	c.81T>C	c.(79-81)gaT>gaC	p.D27D		NM_152413.2	NP_689626.2	Q8NHS2	AATC2_HUMAN	glutamic-oxaloacetic transaminase 1-like 1	27					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)			TCGGGTAATCATCTTGTTTGT	0.458													A|||	4	0.000798722	0.0	0.0	5008	,	,		21029	0.0		0.003	False		,,,				2504	0.001				p.D27D		Atlas-SNP	.											.	GOT1L1	87	.	0			c.T81C						PASS	.	A		2,3874		0,2,1936	141	127	132		81	-10.2	0	8	dbSNP_134	132	35,8205		0,35,4085	no	coding-synonymous	GOT1L1	NM_152413.2		0,37,6021	GG,GA,AA		0.4248,0.0516,0.3054		27/422	37797467	37,12079	1938	4120	6058	SO:0001819	synonymous_variant	137362	exon1			GTAATCATCTTGT	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.81T>C	8.37:g.37797467A>G		224	0	0		196	96	0.489796	NM_152413	A8MWL4	Silent	SNP	ENST00000307599.4	37	CCDS47839.1																																																																																			A|0.999;G|0.001	0.001	strong		0.458	GOT1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376823.1	NM_152413		G	37797467	A	G	37797467	2	3	26	1	0	0	0	0	0	0	0	1	6588	214	8	3		3	GOT1L1	8	37797467	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	6798392	37797467	108566555	284	10047											
PXDNL	137902	hgsc.bcm.edu	37	chr8	52321728	52321728	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcgggctgtgctcagcgcaGgcactgtgtggtccaagtcg	6	8	16	11	3	1	0	1	0	0	0	3	0	2	0	1	3	3	4	1	3	1	0	rs201184283		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:52321728G>C	ENST00000356297.4	-	17	2556	c.2456C>G	c.(2455-2457)cCt>cGt	p.P819R	PXDNL_ENST00000543296.1_Missense_Mutation_p.P819R	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	819					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)				GCTCAGCGCAGGCACTGTGTG	0.677																																					p.P819R		Atlas-SNP	.											PXDNL_ENST00000356297,uveal_tract,malignant_melanoma,0,2	PXDNL	414	2	0			c.C2456G						PASS	.	G	ARG/PRO	0,4240		0,0,2120	15	19	18		2456	2.5	0	8		18	14,8462		0,14,4224	yes	missense	PXDNL	NM_144651.4	103	0,14,6344	CC,CG,GG		0.1652,0.0,0.1101	possibly-damaging	819/1464	52321728	14,12702	2120	4238	6358	SO:0001583	missense	137902	exon17			AGCGCAGGCACTG		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.2456C>G	8.37:g.52321728G>C	ENSP00000348645:p.Pro819Arg	39	0	0		28	15	0.535714	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	G	7.942	0.742913	0.15642	0.0	0.001652	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.67698	-0.28;-0.28	3.4	2.49	0.30216	.	0.143845	0.31989	N	0.006753	T	0.75803	0.3899	M	0.80746	2.51	0.27711	N	0.945471	D	0.58620	0.983	D	0.63703	0.917	T	0.66705	-0.5856	10	0.62326	D	0.03	.	4.3235	0.11029	0.1247:0.0:0.6474:0.2279	.	819	A1KZ92	PXDNL_HUMAN	R	819	ENSP00000348645:P819R;ENSP00000444865:P819R	ENSP00000348645:P819R	P	-	2	0	PXDNL	52484281	0.809000	0.29036	0.007000	0.13788	0.001000	0.01503	2.425000	0.44723	0.516000	0.28340	-0.188000	0.12872	CCT	.	.	weak		0.677	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		C	52321728	G	C	52321728	3	2	26	1	0	0	0	0	1	0	0	0	12863	1000	35	4	1963	4	PXDNL	8	52321728	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	14524261	52321728	94042294	285	10048											
TGS1	96764	hgsc.bcm.edu	37	chr8	56698365	56698365	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcataggcctggatgaaaGtgaacttgattctgaggctg	11	10	14	6	0	1	4	0	4	1	0	1	5	1	5	1	4	1	2	1	4	3	3	rs61753685	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:56698365G>A	ENST00000260129.5	+	3	731	c.254G>A	c.(253-255)aGt>aAt	p.S85N		NM_024831.6	NP_079107.6	Q96RS0	TGS1_HUMAN	trimethylguanosine synthase 1	85					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)			CTGGATGAAAGTGAACTTGAT	0.418													G|||	7	0.00139776	0.0	0.0043	5008	,	,		17006	0.0		0.003	False		,,,				2504	0.001				p.S85N	Esophageal Squamous(34;275 823 4842 34837 48447)	Atlas-SNP	.											.	TGS1	66	.	0			c.G254A						PASS	.	G	ASN/SER	5,4401	11.4+/-27.6	0,5,2198	153	140	145		254	1.6	1	8	dbSNP_129	145	55,8545	34.8+/-89.0	1,53,4246	yes	missense	TGS1	NM_024831.6	46	1,58,6444	AA,AG,GG		0.6395,0.1135,0.4613	benign	85/854	56698365	60,12946	2203	4300	6503	SO:0001583	missense	96764	exon3			ATGAAAGTGAACT	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.254G>A	8.37:g.56698365G>A	ENSP00000260129:p.Ser85Asn	201	0	0		226	112	0.495575	NM_024831	A6NJQ5|Q5GH23|Q8TDG9|Q96QU3|Q9H5V3	Missense_Mutation	SNP	ENST00000260129.5	37	CCDS34894.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	0.835	-0.743908	0.03088	0.001135	0.006395	ENSG00000137574	ENST00000260129	T	0.18338	2.22	5.8	1.61	0.23674	.	0.520508	0.22306	N	0.061787	T	0.06188	0.0160	N	0.25647	0.755	0.27538	N	0.950872	B	0.02656	0.0	B	0.01281	0.0	T	0.34850	-0.9812	10	0.13853	T	0.58	-5.7431	5.868	0.18786	0.3053:0.0:0.5326:0.1621	rs61753685	85	Q96RS0	TGS1_HUMAN	N	85	ENSP00000260129:S85N	ENSP00000260129:S85N	S	+	2	0	TGS1	56860919	0.976000	0.34144	0.996000	0.52242	0.006000	0.05464	0.183000	0.16919	0.382000	0.24878	-0.880000	0.02959	AGT	G|0.995;A|0.005	0.005	strong		0.418	TGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378152.1	NM_024831		A	56698365	G	A	56698365	3	1	26	1	0	0	0	0	1	0	0	0	15852	1029	36	2	264	2	TGS1	8	56698365	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	4376637	56698365	89665657	286	10049											
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77763355	77763355	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgtctacaagtatcgctgtAaccattgtagcttggctttc	9	15	8	9	1	1	0	0	0	1	0	3	0	1	0	1	1	3	6	1	1	5	7			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:77763355A>C	ENST00000521891.2	+	10	4646	c.4198A>C	c.(4198-4200)Aac>Cac	p.N1400H	ZFHX4_ENST00000050961.6_Missense_Mutation_p.N1355H|ZFHX4_ENST00000518282.1_Missense_Mutation_p.N1374H|ZFHX4_ENST00000455469.2_Missense_Mutation_p.N1355H	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	1355					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.N1400D(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)			GTATCGCTGTAACCATTGTAG	0.453										HNSCC(33;0.089)																											p.N1400H		Atlas-SNP	.											ZFHX4,NS,carcinoma,0,1	ZFHX4	878	1	1	Substitution - Missense(1)	lung(1)	c.A4198C						PASS	.						87	82	83					8																	77763355		1894	4118	6012	SO:0001583	missense	79776	exon10			CGCTGTAACCATT		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.4198A>C	8.37:g.77763355A>C	ENSP00000430497:p.Asn1400His	166	0	0		238	108	0.453782	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	A	13.28	2.190004	0.38707	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	4.65	4.65	0.58169	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.48286	U	0.000184	T	0.48077	0.1480	M	0.73962	2.25	0.40800	D	0.98333	P;P;P	0.50528	0.894;0.936;0.936	P;P;P	0.53809	0.548;0.735;0.735	T	0.56414	-0.7983	10	0.72032	D	0.01	.	14.5713	0.68213	1.0:0.0:0.0:0.0	.	1355;1355;1400	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	H	1400;1400;1355;1355;1374	ENSP00000430497:N1400H;ENSP00000399605:N1355H;ENSP00000050961:N1355H;ENSP00000430848:N1374H	ENSP00000050961:N1355H	N	+	1	0	ZFHX4	77925910	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	7.066000	0.76734	2.096000	0.63516	0.454000	0.30748	AAC	.	.	none		0.453	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		C	77763355	A	C	77763355	3	2	26	1	0	0	0	0	1	0	0	0	17650	362	13	5	4232	5	ZFHX4	8	77763355	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	21064990	77763355	68600667	287	10050											
WWP1	11059	hgsc.bcm.edu	37	chr8	87473473	87473473	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgtgaaagagacagacaaTgaagtaagaatgcgactatt	17	10	10	4	1	0	5	0	2	0	3	0	7	0	5	0	0	1	1	0	0	6	4	rs201436587		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:87473473T>C	ENST00000517970.1	+	23	2827	c.2520T>C	c.(2518-2520)aaT>aaC	p.N840N	WWP1_ENST00000341922.2_Silent_p.N710N|WWP1_ENST00000349423.2_Silent_p.N622N|WWP1_ENST00000265428.4_Silent_p.N840N	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	840	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						AGACAGACAATGAAGTAAGAA	0.343													T|||	1	0.000199681	0.0	0.0014	5008	,	,		19862	0.0		0.0	False		,,,				2504	0.0				p.N840N		Atlas-SNP	.											.	WWP1	97	.	0			c.T2520C						PASS	.	T		0,4406		0,0,2203	148	139	142		2520	2.9	1	8		142	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	WWP1	NM_007013.3		0,2,6501	CC,CT,TT		0.0233,0.0,0.0154		840/923	87473473	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	11059	exon23			AGACAATGAAGTA	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.2520T>C	8.37:g.87473473T>C		88	0	0		123	63	0.512195	NM_007013	O00307|Q5YLC1|Q96BP4	Silent	SNP	ENST00000517970.1	37	CCDS6242.1																																																																																			T|1.000;C|0.000	0.000	strong		0.343	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013		C	87473473	T	C	87473473	2	2	26	1	0	0	0	0	0	0	0	1	17430	1461	51	3		3	WWP1	8	87473473	Silent	SNP	T	TCGA-G8-6907-01A-11D-2210-10	9710118	87473473	58890549	288	10051											
RIPK2	8767	hgsc.bcm.edu	37	chr8	90770393	90770393	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tctggcactgtgtcgtccgcCcgccacgcagactggcgcgt	4	8	13	16	6	1	1	0	0	1	1	3	1	2	1	3	2	0	2	3	2	0	0	rs200258974		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:90770393C>T	ENST00000220751.4	+	1	419	c.105C>T	c.(103-105)gcC>gcT	p.A35A	RP11-37B2.1_ENST00000504145.1_lincRNA|RIPK2_ENST00000540020.1_5'UTR	NM_003821.5	NP_003812.1	O43353	RIPK2_HUMAN	receptor-interacting serine-threonine kinase 2	35	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|adaptive immune response (GO:0002250)|apoptotic process (GO:0006915)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|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)|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)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070427)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of immature T cell proliferation (GO:0033091)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-2 production (GO:0032743)|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 peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|response to exogenous dsRNA (GO:0043330)|response to interleukin-1 (GO:0070555)|response to interleukin-12 (GO:0070671)|response to interleukin-18 (GO:0070673)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|T cell proliferation (GO:0042098)|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)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|LIM domain binding (GO:0030274)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(2)	10			BRCA - Breast invasive adenocarcinoma(11;0.0474)			TGTCGTCCGCCCGCCACGCAG	0.677																																					p.A35A		Atlas-SNP	.											RIPK2,NS,malignant_melanoma,+2,1	RIPK2	37	1	0			c.C105T						PASS	.																																			SO:0001819	synonymous_variant	8767	exon1			GTCCGCCCGCCAC	AC004003	CCDS6247.1	8q21	2008-05-02			ENSG00000104312	ENSG00000104312			10020	protein-coding gene	gene with protein product		603455				9575181, 9705938	Standard	XM_005251092		Approved	RICK, RIP2, CARDIAK, CARD3	uc003yee.3	O43353	OTTHUMG00000163809	ENST00000220751.4:c.105C>T	8.37:g.90770393C>T		66	0	0		86	55	0.639535	NM_003821	B7Z748|Q6UWF0	Silent	SNP	ENST00000220751.4	37	CCDS6247.1																																																																																			.	.	weak		0.677	RIPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375686.1			T	90770393	C	T	90770393	2	4	26	1	0	0	0	0	0	0	0	1	13396	610	22	2		2	RIPK2	8	90770393	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	3296920	90770393	55593629	289	10052											
RAD54B	25788	hgsc.bcm.edu	37	chr8	95470507	95470507	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagtcttacctgtatgaggtGgatctaatgttgccagtgta	9	14	11	7	0	2	1	0	1	2	0	2	2	2	2	2	2	2	3	2	2	4	5	rs148525625	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:95470507G>A	ENST00000336148.5	-	3	417	c.293C>T	c.(292-294)cCa>cTa	p.P98L	RAD54B_ENST00000297592.5_Missense_Mutation_p.P98L	NM_012415.3	NP_036547.1	Q9Y620	RA54B_HUMAN	RAD54 homolog B (S. cerevisiae)	98					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)			TGTATGAGGTGGATCTAATGT	0.308								Direct reversal of damage;Homologous recombination																													p.P98L		Atlas-SNP	.											RAD54B,NS,carcinoma,+1,1	RAD54B	88	1	0			c.C293T						PASS	.	G	LEU/PRO,LEU/PRO	0,4406		0,0,2203	163	154	157		293,293	1.4	0	8	dbSNP_134	157	2,8594	2.2+/-6.3	0,2,4296	no	missense,missense	RAD54B	NM_001205262.1,NM_012415.3	98,98	0,2,6499	AA,AG,GG		0.0233,0.0,0.0154	benign,benign	98/118,98/911	95470507	2,13000	2203	4298	6501	SO:0001583	missense	25788	exon3			TGAGGTGGATCTA	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.293C>T	8.37:g.95470507G>A	ENSP00000336606:p.Pro98Leu	133	0	0		148	73	0.493243	NM_001205262	F6WBS8	Missense_Mutation	SNP	ENST00000336148.5	37	CCDS6262.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.989826	0.54041	0.0	2.33E-4	ENSG00000197275	ENST00000336148;ENST00000523839;ENST00000297592	D;T;T	0.87966	-2.32;1.57;1.54	5.44	1.42	0.22433	.	1.455470	0.03871	N	0.275599	D	0.82435	0.5036	L	0.48642	1.525	0.09310	N	1	B;B	0.11235	0.004;0.0	B;B	0.11329	0.006;0.001	T	0.60321	-0.7286	10	0.15066	T	0.55	-28.8344	7.8043	0.29193	0.366:0.0:0.634:0.0	.	98;98	F6WBS8;Q9Y620	.;RA54B_HUMAN	L	98	ENSP00000336606:P98L;ENSP00000428554:P98L;ENSP00000430153:P98L	ENSP00000430153:P98L	P	-	2	0	RAD54B	95539683	0.000000	0.05858	0.000000	0.03702	0.525000	0.34531	-0.063000	0.11655	0.123000	0.18342	0.650000	0.86243	CCA	G|1.000;A|0.000	0.000	strong		0.308	RAD54B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257806.3	NM_012415		A	95470507	G	A	95470507	3	1	26	1	0	0	0	0	1	0	0	0	13007	1348	47	2	2491	2	RAD54B	8	95470507	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	4700114	95470507	50893515	290	10053											
MATN2	4147	hgsc.bcm.edu	37	chr8	99019799	99019799	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcagtgtcctgagggacacGtgctccgcagcgatgggaag	8	7	16	10	3	1	1	1	1	0	0	3	4	3	3	2	2	2	2	2	2	1	0	rs372608950		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:99019799G>A	ENST00000520016.1	+	9	1667	c.1543G>A	c.(1543-1545)Gtg>Atg	p.V515M	MATN2_ENST00000522025.2_Missense_Mutation_p.V231M|MATN2_ENST00000524308.1_Missense_Mutation_p.V474M|MATN2_ENST00000521689.1_Missense_Mutation_p.V515M|MATN2_ENST00000254898.5_Missense_Mutation_p.V515M			O00339	MATN2_HUMAN	matrilin 2	515	EGF-like 7. {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)			TGAGGGACACGTGCTCCGCAG	0.567																																					p.V515M		Atlas-SNP	.											.	MATN2	165	.	0			c.G1543A						PASS	.						143	140	141					8																	99019799		2145	4249	6394	SO:0001583	missense	4147	exon10			GGACACGTGCTCC	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.1543G>A	8.37:g.99019799G>A	ENSP00000430487:p.Val515Met	75	0	0		95	51	0.536842	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Missense_Mutation	SNP	ENST00000520016.1	37	CCDS55264.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.569|6.569	0.473360|0.473360	0.12461|0.12461	.|.	.|.	ENSG00000132561|ENSG00000132561	ENST00000518154|ENST00000521689;ENST00000254898;ENST00000378716;ENST00000524308;ENST00000522025;ENST00000520016	.|D;D;D;T;D	.|0.87887	.|-2.3;-2.3;-2.31;1.5;-2.3	5.65|5.65	2.57|2.57	0.30868|0.30868	.|Epidermal growth factor-like (1);	.|0.695407	.|0.13029	.|N	.|0.419495	T|T	0.80259|0.80259	0.4590|0.4590	L|L	0.41961|0.41961	1.31|1.31	0.21355|0.21355	N|N	0.999711|0.999711	.|B;B;B;B	.|0.21606	.|0.058;0.026;0.02;0.014	.|B;B;B;B	.|0.11329	.|0.006;0.003;0.005;0.003	T|T	0.68157|0.68157	-0.5483|-0.5483	5|10	.|0.45353	.|T	.|0.12	-6.9692|-6.9692	6.4777|6.4777	0.22045|0.22045	0.4096:0.0:0.5904:0.0|0.4096:0.0:0.5904:0.0	.|.	.|474;515;515;515	.|C9JH87;E9PF03;O00339-2;O00339	.|.;.;.;MATN2_HUMAN	H|M	297|515;515;474;474;231;515	.|ENSP00000429977:V515M;ENSP00000254898:V515M;ENSP00000430221:V474M;ENSP00000429010:V231M;ENSP00000430487:V515M	.|ENSP00000254898:V515M	R|V	+|+	2|1	0|0	MATN2|MATN2	99088975|99088975	0.000000|0.000000	0.05858|0.05858	0.315000|0.315000	0.25238|0.25238	0.144000|0.144000	0.21451|0.21451	-0.333000|-0.333000	0.07894|0.07894	0.577000|0.577000	0.29470|0.29470	-0.126000|-0.126000	0.14955|0.14955	CGT|GTG	.	.	weak		0.567	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1			A	99019799	G	A	99019799	3	1	26	1	0	0	0	0	1	0	0	0	9343	1145	40	1	1577	1	MATN2	8	99019799	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	3549292	99019799	47344223	291	10054											
GRHL2	79977	hgsc.bcm.edu	37	chr8	102585965	102585965	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagggggagggccccatgacCtacctcaacaaaggacagtt	12	5	12	12	0	1	1	1	1	0	0	1	3	1	3	4	4	2	1	4	4	3	2	rs55682875	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:102585965C>T	ENST00000251808.3	+	6	1142	c.804C>T	c.(802-804)acC>acT	p.T268T	GRHL2_ENST00000395927.1_Silent_p.T252T	NM_024915.3	NP_079191.2	Q6ISB3	GRHL2_HUMAN	grainyhead-like 2 (Drosophila)	268					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)			GCCCCATGACCTACCTCAACA	0.527													C|||	3	0.000599042	0.0	0.0014	5008	,	,		19445	0.0		0.002	False		,,,				2504	0.0				p.T268T		Atlas-SNP	.											.	GRHL2	68	.	0			c.C804T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	84	70	75		804	4	1	8	dbSNP_129	75	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous	GRHL2	NM_024915.3		0,12,6491	TT,TC,CC		0.1163,0.0454,0.0923		268/626	102585965	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	79977	exon6			CATGACCTACCTC	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.804C>T	8.37:g.102585965C>T		62	0	0		68	36	0.529412	NM_024915	A1L303|Q6NT03|Q9H8B8	Silent	SNP	ENST00000251808.3	37	CCDS34931.1																																																																																			C|0.999;T|0.001	0.001	strong		0.527	GRHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313882.1	NM_024915		T	102585965	C	T	102585965	2	4	26	1	0	0	0	0	0	0	0	1	6773	668	24	2		2	GRHL2	8	102585965	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	3566166	102585965	43778057	292	10055											
ZFPM2	23414	hgsc.bcm.edu	37	chr8	106814029	106814029	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aaaaagcattattgcagcagCcgatggcagcagatggctaa	15	7	11	8	1	0	1	0	0	0	1	0	2	0	1	1	2	5	6	1	2	4	3			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:106814029C>A	ENST00000407775.2	+	8	1969	c.1719C>A	c.(1717-1719)agC>agA	p.S573R	ZFPM2_ENST00000378472.4_Missense_Mutation_p.S304R|RP11-152P17.2_ENST00000524045.2_RNA|RP11-152P17.2_ENST00000521622.1_RNA|ZFPM2_ENST00000517361.1_Missense_Mutation_p.S441R|RP11-152P17.2_ENST00000520594.1_RNA|RP11-152P17.2_ENST00000520433.1_RNA|ZFPM2_ENST00000522296.1_3'UTR|RP11-152P17.2_ENST00000509144.2_RNA|ZFPM2_ENST00000520492.1_Missense_Mutation_p.S441R|RP11-152P17.2_ENST00000518932.1_RNA	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	573					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)			ATTGCAGCAGCCGATGGCAGC	0.448																																					p.S573R		Atlas-SNP	.											.	ZFPM2	219	.	0			c.C1719A						PASS	.						128	131	130					8																	106814029		1929	4136	6065	SO:0001583	missense	23414	exon8			CAGCAGCCGATGG	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.1719C>A	8.37:g.106814029C>A	ENSP00000384179:p.Ser573Arg	125	0	0		185	93	0.502703	NM_012082	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Missense_Mutation	SNP	ENST00000407775.2	37	CCDS47908.1	.	.	.	.	.	.	.	.	.	.	C	15.47	2.842831	0.51057	.	.	ENSG00000169946	ENST00000407775;ENST00000520492;ENST00000517361;ENST00000378472	T;T;T;T	0.25579	1.79;2.28;2.28;3.53	5.86	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.48059	0.1479	M	0.72353	2.195	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.44711	-0.9310	10	0.44086	T	0.13	.	11.619	0.51106	0.0:0.8135:0.0:0.1865	.	573	Q8WW38	FOG2_HUMAN	R	573;441;441;304	ENSP00000384179:S573R;ENSP00000430757:S441R;ENSP00000428720:S441R;ENSP00000367733:S304R	ENSP00000367733:S304R	S	+	3	2	ZFPM2	106883205	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.698000	0.37794	1.485000	0.48380	0.655000	0.94253	AGC	.	.	none		0.448	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1			A	106814029	C	A	106814029	3	1	26	1	0	0	0	0	1	0	0	0	17673	738	26	4	1749	4	ZFPM2	8	106814029	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	4228064	106814029	39549993	293	10056											
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110447469	110447469	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaagtgctggacatgcccccGttgctgtgtccatggctgat	6	11	13	11	1	0	1	0	1	0	0	1	3	1	2	3	2	3	4	3	2	1	1	rs376326343		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:110447469G>A	ENST00000378402.5	+	29	3495	c.3391G>A	c.(3391-3393)Gtt>Att	p.V1131I		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1131	IPT/TIG 4.				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)			ACATGCCCCCGTTGCTGTGTC	0.413										HNSCC(38;0.096)			G|||	1	0.000199681	0.0	0.0	5008	,	,		19159	0.0		0.001	False		,,,				2504	0.0				p.V1131I		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.G3391A						PASS	.	G	ILE/VAL	0,3716		0,0,1858	173	171	172		3391	4.3	0	8		172	3,8233		0,3,4115	no	missense	PKHD1L1	NM_177531.4	29	0,3,5973	AA,AG,GG		0.0364,0.0,0.0251	probably-damaging	1131/4244	110447469	3,11949	1858	4118	5976	SO:0001583	missense	93035	exon29			GCCCCCGTTGCTG	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.3391G>A	8.37:g.110447469G>A	ENSP00000367655:p.Val1131Ile	142	0	0		173	80	0.462428	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	G	5.667	0.307710	0.10733	0.0	3.64E-4	ENSG00000205038	ENST00000378402	T	0.80033	-1.33	6.07	4.28	0.50868	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.146172	0.44902	N	0.000403	T	0.73133	0.3548	L	0.52759	1.655	0.22142	N	0.999333	B	0.12630	0.006	B	0.12156	0.007	T	0.59279	-0.7484	10	0.28530	T	0.3	.	9.7436	0.40433	0.1605:0.0:0.8395:0.0	.	1131	Q86WI1	PKHL1_HUMAN	I	1131	ENSP00000367655:V1131I	ENSP00000367655:V1131I	V	+	1	0	PKHD1L1	110516645	0.934000	0.31675	0.041000	0.18516	0.005000	0.04900	2.374000	0.44274	0.883000	0.36040	-0.150000	0.13652	GTT	.	.	weak		0.413	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		A	110447469	G	A	110447469	3	1	26	1	0	0	0	0	1	0	0	0	11981	1145	40	1	3505	1	PKHD1L1	8	110447469	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	3633440	110447469	35916553	294	10057											
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110447512	110447512	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tggactagcacagaatgtagGgggtgaagagttctactttg	11	11	14	5	0	1	3	0	1	1	2	1	4	1	4	0	3	2	3	0	3	5	5	rs142972518	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:110447512G>C	ENST00000378402.5	+	29	3538	c.3434G>C	c.(3433-3435)gGg>gCg	p.G1145A		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1145	IPT/TIG 4.				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)			CAGAATGTAGGGGGTGAAGAG	0.443										HNSCC(38;0.096)			G|||	58	0.0115815	0.0015	0.0101	5008	,	,		18338	0.0		0.0268	False		,,,				2504	0.0225				p.G1145A		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.G3434C						PASS	.	G	ALA/GLY	15,3743		0,15,1864	197	197	197		3434	-2.3	0	8	dbSNP_134	197	167,8083		3,161,3961	yes	missense	PKHD1L1	NM_177531.4	60	3,176,5825	CC,CG,GG		2.0242,0.3991,1.5157	benign	1145/4244	110447512	182,11826	1879	4125	6004	SO:0001583	missense	93035	exon29			ATGTAGGGGGTGA	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.3434G>C	8.37:g.110447512G>C	ENSP00000367655:p.Gly1145Ala	167	0	0		222	102	0.459459	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	27	0.012362637362637362	0	0.0	5	0.013812154696132596	0	0.0	22	0.029023746701846966	G	2.585	-0.296544	0.05532	0.003991	0.020242	ENSG00000205038	ENST00000378402	D	0.85702	-2.02	6.07	-2.3	0.06785	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.912531	0.09435	N	0.802529	T	0.53142	0.1778	L	0.34521	1.04	0.09310	N	1	B	0.16396	0.017	B	0.21360	0.034	T	0.50074	-0.8870	10	0.12103	T	0.63	.	12.0147	0.53307	0.3405:0.0:0.6595:0.0	.	1145	Q86WI1	PKHL1_HUMAN	A	1145	ENSP00000367655:G1145A	ENSP00000367655:G1145A	G	+	2	0	PKHD1L1	110516688	0.005000	0.15991	0.000000	0.03702	0.004000	0.04260	0.643000	0.24750	-0.303000	0.08856	-0.768000	0.03414	GGG	G|0.986;C|0.014	0.014	strong		0.443	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		C	110447512	G	C	110447512	3	2	26	1	0	0	0	0	1	0	0	0	11981	1232	43	4	3548	4	PKHD1L1	8	110447512	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	43	110447512	35916510	295	10058											
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110492352	110492352	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agaagttgttttgaatgctaCctacatatcactgcaggtaa	13	13	8	7	0	1	2	1	1	0	1	1	2	1	2	1	1	4	5	1	1	6	7	rs117952538	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:110492352C>T	ENST00000378402.5	+	55	9415	c.9311C>T	c.(9310-9312)aCc>aTc	p.T3104I		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3104	G8 2. {ECO:0000255|PROSITE- ProRule:PRU00817}.				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)			TTGAATGCTACCTACATATCA	0.333										HNSCC(38;0.096)			C|||	31	0.0061901	0.0008	0.0086	5008	,	,		17368	0.0		0.0179	False		,,,				2504	0.0061				p.T3104I		Atlas-SNP	.											PKHD1L1,NS,carcinoma,-1,1	PKHD1L1	522	1	0			c.C9311T						PASS	.	C	ILE/THR	8,3650		0,8,1821	50	49	49		9311	5.2	1	8	dbSNP_132	49	106,8056		0,106,3975	yes	missense	PKHD1L1	NM_177531.4	89	0,114,5796	TT,TC,CC		1.2987,0.2187,0.9645	probably-damaging	3104/4244	110492352	114,11706	1829	4081	5910	SO:0001583	missense	93035	exon55			ATGCTACCTACAT	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.9311C>T	8.37:g.110492352C>T	ENSP00000367655:p.Thr3104Ile	141	0	0		122	56	0.459016	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	17	0.007783882783882784	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	13	0.017150395778364115	C	17.97	3.519012	0.64634	0.002187	0.012987	ENSG00000205038	ENST00000378402	D	0.89415	-2.51	5.25	5.25	0.73442	G8 domain (2);	0.139370	0.49305	D	0.000142	D	0.84683	0.5526	M	0.82056	2.57	0.30997	N	0.720711	B	0.29766	0.256	B	0.37989	0.262	D	0.86191	0.1612	10	0.34782	T	0.22	.	16.7128	0.85389	0.0:1.0:0.0:0.0	.	3104	Q86WI1	PKHL1_HUMAN	I	3104	ENSP00000367655:T3104I	ENSP00000367655:T3104I	T	+	2	0	PKHD1L1	110561528	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	3.752000	0.55172	2.604000	0.88044	0.650000	0.86243	ACC	C|0.992;T|0.008	0.008	strong		0.333	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		T	110492352	C	T	110492352	3	4	26	1	0	0	0	0	1	0	0	0	11981	507	18	2	9529	2	PKHD1L1	8	110492352	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	44840	110492352	35871670	296	10059											
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110510964	110510964	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccccatgcaggaatcatgAgttacaatgccatcagtggc	12	8	10	11	0	2	1	2	1	0	0	2	2	2	2	3	2	4	2	3	2	3	1	rs191412861	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:110510964A>C	ENST00000378402.5	+	67	10896	c.10792A>C	c.(10792-10794)Agt>Cgt	p.S3598R		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3598					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)			AGGAATCATGAGTTACAATGC	0.408										HNSCC(38;0.096)			A|||	28	0.00559105	0.0008	0.0072	5008	,	,		16193	0.0		0.005	False		,,,				2504	0.0174				p.S3598R		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.A10792C						PASS	.	A	ARG/SER	2,3744		0,2,1871	81	77	78		10792	6	1	8		78	48,8134		1,46,4044	yes	missense	PKHD1L1	NM_177531.4	110	1,48,5915	CC,CA,AA		0.5867,0.0534,0.4192	probably-damaging	3598/4244	110510964	50,11878	1873	4091	5964	SO:0001583	missense	93035	exon67			ATCATGAGTTACA	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.10792A>C	8.37:g.110510964A>C	ENSP00000367655:p.Ser3598Arg	138	0	0		158	59	0.373418	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	5	0.0022893772893772895	0	0.0	3	0.008287292817679558	0	0.0	2	0.002638522427440633	A	26.4	4.731514	0.89390	5.34E-4	0.005867	ENSG00000205038	ENST00000378402;ENST00000526472	D;D	0.86865	-2.18;-1.99	6.02	6.02	0.97574	.	0.109105	0.64402	D	0.000010	D	0.83723	0.5316	M	0.78637	2.42	0.40619	D	0.981744	B	0.25719	0.132	B	0.22601	0.04	D	0.84175	0.0436	10	0.59425	D	0.04	.	14.5014	0.67724	1.0:0.0:0.0:0.0	.	3598	Q86WI1	PKHL1_HUMAN	R	3598;526	ENSP00000367655:S3598R;ENSP00000437376:S526R	ENSP00000367655:S3598R	S	+	1	0	PKHD1L1	110580140	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	7.683000	0.84093	2.299000	0.77371	0.528000	0.53228	AGT	A|0.997;C|0.003	0.003	strong		0.408	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		C	110510964	A	C	110510964	3	2	26	1	0	0	0	0	1	0	0	0	11981	304	11	5	11058	5	PKHD1L1	8	110510964	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	18612	110510964	35853058	297	10060											
CSMD3	114788	hgsc.bcm.edu	37	chr8	113841971	113841971	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccatcgccaattgtcaaggtAtcatagccaatctccagatc	12	10	6	13	1	3	1	2	0	1	1	6	1	3	1	4	1	1	1	4	1	5	3	rs142880481	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:113841971A>G	ENST00000297405.5	-	12	2047	c.1803T>C	c.(1801-1803)gaT>gaC	p.D601D	CSMD3_ENST00000455883.2_Silent_p.D497D|CSMD3_ENST00000343508.3_Silent_p.D561D|CSMD3_ENST00000352409.3_Silent_p.D601D	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	601	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						TTGTCAAGGTATCATAGCCAA	0.403										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			A|||	6	0.00119808	0.0	0.0014	5008	,	,		15247	0.0		0.005	False		,,,				2504	0.0				p.D601D		Atlas-SNP	.											.	CSMD3	2325	.	0			c.T1803C						PASS	.	A	,,	1,4405	2.1+/-5.4	0,1,2202	108	97	100		1491,1803,1683	-3.2	0.9	8	dbSNP_134	100	18,8582	13.3+/-46.6	0,18,4282	no	coding-synonymous,coding-synonymous,coding-synonymous	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	,,	0,19,6484	GG,GA,AA		0.2093,0.0227,0.1461	,,	497/3539,601/3708,561/3668	113841971	19,12987	2203	4300	6503	SO:0001819	synonymous_variant	114788	exon12			CAAGGTATCATAG	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.1803T>C	8.37:g.113841971A>G		66	0	0		76	35	0.460526	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																			A|0.999;G|0.001	0.001	strong		0.403	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		G	113841971	A	G	113841971	2	3	26	1	0	0	0	0	0	0	0	1	3948	446	16	3		3	CSMD3	8	113841971	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	3331007	113841971	32522051	298	10061											
ENPP2	5168	hgsc.bcm.edu	37	chr8	120575249	120575249	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaatggaactgccttccaCgtacctgaaacaggaaggta	14	7	11	9	1	0	1	0	1	0	0	1	4	1	4	3	4	4	2	3	4	6	3	rs61758149	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:120575249C>T	ENST00000075322.6	-	24	2327	c.2269G>A	c.(2269-2271)Gtg>Atg	p.V757M	ENPP2_ENST00000259486.6_Missense_Mutation_p.V809M|ENPP2_ENST00000522826.1_Missense_Mutation_p.V782M|ENPP2_ENST00000427067.2_Missense_Mutation_p.V778M|ENPP2_ENST00000522167.1_Missense_Mutation_p.V392M	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	757					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)			CTGCCTTCCACGTACCTGAAA	0.443													C|||	7	0.00139776	0.0	0.0014	5008	,	,		20547	0.0		0.002	False		,,,				2504	0.0041				p.V809M	Melanoma(20;305 879 2501 4818 31020)	Atlas-SNP	.											.	ENPP2	254	.	0			c.G2425A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL	1,4405	2.1+/-5.4	0,1,2202	120	101	108		2269,2344,2425	5.7	1	8	dbSNP_129	108	13,8587	9.8+/-36.6	0,13,4287	yes	missense,missense,missense	ENPP2	NM_001040092.1,NM_001130863.1,NM_006209.3	21,21,21	0,14,6489	TT,TC,CC		0.1512,0.0227,0.1076	possibly-damaging,possibly-damaging,possibly-damaging	757/864,782/889,809/916	120575249	14,12992	2203	4300	6503	SO:0001583	missense	5168	exon25			CTTCCACGTACCT	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.2269G>A	8.37:g.120575249C>T	ENSP00000075322:p.Val757Met	79	0	0		124	57	0.459677	NM_006209	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Missense_Mutation	SNP	ENST00000075322.6	37	CCDS34936.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	21.3	4.123821	0.77436	2.27E-4	0.001512	ENSG00000136960	ENST00000259486;ENST00000427067;ENST00000522167;ENST00000522826;ENST00000075322	T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52	5.67	5.67	0.87782	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.000000	0.46442	D	0.000285	T	0.51517	0.1679	L	0.49778	1.585	0.80722	D	1	D;D;D;D;D	0.89917	0.997;0.993;0.999;0.998;1.0	D;P;D;P;D	0.67548	0.952;0.894;0.919;0.896;0.919	T	0.46261	-0.9204	10	0.56958	D	0.05	.	19.7743	0.96385	0.0:1.0:0.0:0.0	rs61758149	295;782;757;809;392	B4DJD3;E9PHP7;Q13822;Q13822-2;E5RIA2	.;.;ENPP2_HUMAN;.;.	M	809;778;392;782;757	ENSP00000259486:V809M;ENSP00000403315:V778M;ENSP00000429476:V392M;ENSP00000428291:V782M;ENSP00000075322:V757M	ENSP00000075322:V757M	V	-	1	0	ENPP2	120644430	1.000000	0.71417	0.993000	0.49108	0.949000	0.60115	5.281000	0.65609	2.663000	0.90544	0.557000	0.71058	GTG	C|0.998;T|0.002	0.002	strong		0.443	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1			T	120575249	C	T	120575249	3	4	26	1	0	0	0	0	1	0	0	0	5132	536	19	1	330	1	ENPP2	8	120575249	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	6733278	120575249	25788773	299	10062											
DSCC1	79075	hgsc.bcm.edu	37	chr8	120850521	120850521	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aatatatggagcaatatcttCttctgtccacttctccctta	10	16	4	11	0	4	0	0	0	4	0	6	1	5	1	2	1	1	1	2	1	6	7			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:120850521C>T	ENST00000313655.4	-	8	1265	c.1051G>A	c.(1051-1053)Gaa>Aaa	p.E351K		NM_024094.2	NP_076999.2	Q9BVC3	DCC1_HUMAN	DNA replication and sister chromatid cohesion 1	351					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)			GCAATATCTTCTTCTGTCCAC	0.338																																					p.E351K		Atlas-SNP	.											.	DSCC1	40	.	0			c.G1051A						PASS	.						82	86	85					8																	120850521		2203	4300	6503	SO:0001583	missense	79075	exon8			TATCTTCTTCTGT		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.1051G>A	8.37:g.120850521C>T	ENSP00000322180:p.Glu351Lys	133	0	0		127	16	0.125984	NM_024094	Q969N5	Missense_Mutation	SNP	ENST00000313655.4	37	CCDS6330.1	.	.	.	.	.	.	.	.	.	.	C	19.67	3.870756	0.72065	.	.	ENSG00000136982	ENST00000313655	T	0.46819	0.86	4.82	4.82	0.62117	.	0.212150	0.48767	D	0.000170	T	0.38321	0.1036	L	0.41079	1.255	0.50039	D	0.99984	P	0.35468	0.503	B	0.30029	0.11	T	0.19976	-1.0289	10	0.19590	T	0.45	-21.7187	18.2534	0.90011	0.0:1.0:0.0:0.0	.	351	Q9BVC3	DCC1_HUMAN	K	351	ENSP00000322180:E351K	ENSP00000322180:E351K	E	-	1	0	DSCC1	120919702	1.000000	0.71417	0.999000	0.59377	0.880000	0.50808	5.923000	0.70045	2.372000	0.80975	0.563000	0.77884	GAA	.	.	none		0.338	DSCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381443.1	NM_024094		T	120850521	C	T	120850521	3	4	26	1	0	0	0	0	1	0	0	0	4772	922	32	2	138	2	DSCC1	8	120850521	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	275272	120850521	25513501	300	10063											
TRAPPC9	83696	hgsc.bcm.edu	37	chr8	141381103	141381103	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccagcgacagactgtagccGggcagcgtttccaggaggag	9	6	15	11	3	0	1	0	0	0	1	2	4	2	3	3	3	3	3	3	3	1	2	rs3735804	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:141381103G>A	ENST00000438773.2	-	8	1444	c.1311C>T	c.(1309-1311)ccC>ccT	p.P437P	TRAPPC9_ENST00000389328.4_Silent_p.P535P|TRAPPC9_ENST00000389327.3_Silent_p.P428P	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	437					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						GACTGTAGCCGGGCAGCGTTT	0.597													G|||	5	0.000998403	0.0	0.0	5008	,	,		17975	0.005		0.0	False		,,,				2504	0.0				p.P535P		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.C1605T						PASS	.						83	83	83					8																	141381103		2203	4300	6503	SO:0001819	synonymous_variant	83696	exon8			GTAGCCGGGCAGC	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.1311C>T	8.37:g.141381103G>A		98	0	0		122	57	0.467213	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Silent	SNP	ENST00000438773.2	37	CCDS55278.1	5	0.0022893772893772895	0	0.0	0	0.0	5	0.008741258741258742	0	0.0	G	7.589	0.670340	0.14776	.	.	ENSG00000167632	ENST00000520857	.	.	.	5.5	-6.88	0.01665	.	.	.	.	.	T	0.43478	0.1249	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55471	-0.8136	4	.	.	.	.	10.8351	0.46683	0.6972:0.0949:0.2079:0.0	rs3735804;rs3735804	.	.	.	W	281	.	.	R	-	1	2	TRAPPC9	141450285	0.044000	0.20184	0.707000	0.30419	0.576000	0.36127	-0.575000	0.05861	-1.330000	0.02255	-0.391000	0.06502	CGG	G|0.996;A|0.004	0.004	strong		0.597	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466		A	141381103	G	A	141381103	2	1	26	1	0	0	0	0	0	0	0	1	16480	1103	39	1		1	TRAPPC9	8	141381103	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	20530582	141381103	4982919	301	10064											
MAFA	389692	hgsc.bcm.edu	37	chr8	144512157	144512157	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggccgctgccgatgagcgcCtccaccgcgtcctcgggcgt	3	7	14	17	7	0	1	0	1	0	0	3	2	2	1	6	2	2	1	6	2	0	0	rs373992315		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:144512157C>T	ENST00000333480.2	-	1	419	c.420G>A	c.(418-420)gaG>gaA	p.E140E	MAFA_ENST00000528185.1_5'Flank	NM_201589.3	NP_963883.2	Q8NHW3	MAFA_HUMAN	v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog A	140					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)			CGATGAGCGCCTCCACCGCGT	0.741										HNSCC(29;0.082)			.|||	1	0.000199681	0.0	0.0	5008	,	,		4841	0.0		0.001	False		,,,				2504	0.0				p.E140E		Atlas-SNP	.											.	MAFA	9	.	0			c.G420A						PASS	.	C		0,4076		0,0,2038	7	5	6		420	2.9	1	8		6	10,7996		0,10,3993	no	coding-synonymous	MAFA	NM_201589.3		0,10,6031	TT,TC,CC		0.1249,0.0,0.0828		140/354	144512157	10,12072	2038	4003	6041	SO:0001819	synonymous_variant	389692	exon1			GAGCGCCTCCACC	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.420G>A	8.37:g.144512157C>T		11	0	0		7	5	0.714286	NM_201589		Silent	SNP	ENST00000333480.2	37	CCDS34955.1																																																																																			.	.	weak		0.741	MAFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381511.2	NM_201589		T	144512157	C	T	144512157	2	4	26	1	0	0	0	0	0	0	0	1	9166	680	24	2		2	MAFA	8	144512157	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	3131054	144512157	1851865	302	10065											
PLEC	5339	hgsc.bcm.edu	37	chr8	144992552	144992552	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggaaggtggaagcccaggcGggggtccacgatgccgccgg	7	3	20	11	4	0	0	0	0	0	0	1	3	1	2	4	7	2	0	4	7	2	0	rs201666443		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:144992552G>A	ENST00000322810.4	-	32	12017	c.11848C>T	c.(11848-11850)Cgc>Tgc	p.R3950C	PLEC_ENST00000354589.3_Missense_Mutation_p.R3813C|PLEC_ENST00000354958.2_Missense_Mutation_p.R3791C|PLEC_ENST00000527096.1_Missense_Mutation_p.R3836C|PLEC_ENST00000357649.2_Missense_Mutation_p.R3817C|PLEC_ENST00000436759.2_Missense_Mutation_p.R3840C|PLEC_ENST00000345136.3_Missense_Mutation_p.R3813C|PLEC_ENST00000356346.3_Missense_Mutation_p.R3799C|PLEC_ENST00000398774.2_Missense_Mutation_p.R3781C	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3950	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						AAGCCCAGGCGGGGGTCCACG	0.652													G|||	1	0.000199681	0.0	0.0	5008	,	,		15094	0.0		0.0	False		,,,				2504	0.001				p.R3950C		Atlas-SNP	.											.	PLEC	1144	.	0			c.C11848T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	0,4044		0,0,2022	12	17	16		11518,11395,11371,11848,11341,11437,11449,11437	3.8	0.6	8		16	2,8328		0,2,4163	yes	missense,missense,missense,missense,missense,missense,missense,missense	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	180,180,180,180,180,180,180,180	0,2,6185	AA,AG,GG		0.024,0.0,0.0162	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	3840/4575,3799/4534,3791/4526,3950/4685,3781/4516,3813/4548,3817/4552,3813/4548	144992552	2,12372	2022	4165	6187	SO:0001583	missense	5339	exon32			CCAGGCGGGGGTC	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.11848C>T	8.37:g.144992552G>A	ENSP00000323856:p.Arg3950Cys	27	0	0		28	11	0.392857	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	G	8.746	0.920155	0.17982	0.0	2.4E-4	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.73789	-0.78;-0.78;-0.78;-0.78;-0.78;-0.78;-0.78;-0.78;-0.78	3.78	3.78	0.43462	.	0.335440	0.24089	U	0.041652	T	0.67135	0.2861	L	0.46157	1.445	0.35517	D	0.801081	P;D;P;P;P;P;P;P	0.54772	0.894;0.968;0.894;0.913;0.894;0.894;0.894;0.894	B;B;B;B;B;B;B;B	0.43990	0.311;0.311;0.311;0.438;0.311;0.311;0.311;0.311	T	0.74300	-0.3710	10	0.38643	T	0.18	.	10.3245	0.43785	0.0:0.0:0.8027:0.1973	.	3840;3799;3791;3950;3781;3813;3817;3813	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	C	3813;3817;3813;3781;3950;3791;3799;3840;3836	ENSP00000344848:R3813C;ENSP00000350277:R3817C;ENSP00000346602:R3813C;ENSP00000381756:R3781C;ENSP00000323856:R3950C;ENSP00000347044:R3791C;ENSP00000348702:R3799C;ENSP00000388180:R3840C;ENSP00000434583:R3836C	ENSP00000323856:R3950C	R	-	1	0	PLEC	145064540	0.957000	0.32711	0.639000	0.29394	0.951000	0.60555	2.993000	0.49425	2.103000	0.63969	0.297000	0.19635	CGC	.	.	weak		0.652	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		A	144992552	G	A	144992552	3	1	26	1	0	0	0	0	1	0	0	0	12061	1116	39	1	2210	1	PLEC	8	144992552	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	480395	144992552	1371470	303	10066											
KIAA0020	9933	hgsc.bcm.edu	37	chr9	2812282	2812282	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcgtactgtatgtgcaggAtctctggggcttagtaagta	8	14	12	7	1	2	0	0	0	2	0	4	1	2	1	0	3	2	6	0	3	5	5	rs142216382	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:2812282A>T	ENST00000397885.2	-	14	1556	c.1350T>A	c.(1348-1350)gaT>gaA	p.D450E		NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020	450	PUM-HD. {ECO:0000255|PROSITE- ProRule:PRU00318}.					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)		TATGTGCAGGATCTCTGGGGC	0.358																																					p.D450E		Atlas-SNP	.											.	KIAA0020	56	.	0			c.T1350A						PASS	.	A	GLU/ASP	1,4405	2.1+/-5.4	0,1,2202	215	193	200		1350	0.9	1	9	dbSNP_134	200	6,8594	5.0+/-18.6	0,6,4294	yes	missense	KIAA0020	NM_014878.4	45	0,7,6496	TT,TA,AA		0.0698,0.0227,0.0538	possibly-damaging	450/649	2812282	7,12999	2203	4300	6503	SO:0001583	missense	9933	exon14			TGCAGGATCTCTG	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.1350T>A	9.37:g.2812282A>T	ENSP00000380982:p.Asp450Glu	214	0	0		229	115	0.502183	NM_014878	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Missense_Mutation	SNP	ENST00000397885.2	37	CCDS6448.2	.	.	.	.	.	.	.	.	.	.	A	21.3	4.134740	0.77662	2.27E-4	6.98E-4	ENSG00000080608	ENST00000397885	T	0.52754	0.65	5.5	0.953	0.19590	CPL (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.134559	0.64402	D	0.000003	T	0.62208	0.2409	M	0.80746	2.51	0.54753	D	0.999989	D;D	0.54397	0.966;0.966	P;P	0.61874	0.861;0.895	T	0.59894	-0.7368	10	0.35671	T	0.21	-21.8403	10.3652	0.44019	0.613:0.0:0.387:0.0	.	310;450	B2RDG4;Q15397	.;K0020_HUMAN	E	450	ENSP00000380982:D450E	ENSP00000380982:D450E	D	-	3	2	KIAA0020	2802282	0.947000	0.32204	1.000000	0.80357	0.997000	0.91878	0.103000	0.15292	0.093000	0.17368	0.482000	0.46254	GAT	A|0.999;T|0.001	0.001	strong		0.358	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878		T	2812282	A	T	2812282	3	4	26	1	0	0	0	0	1	0	0	0	8161	330	12	5	616	5	KIAA0020	9	2812282	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10		2812282	138401149	304	10067											
JAK2	3717	hgsc.bcm.edu	37	chr9	5081828	5081828	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gatcctacacagtttgaagaGagacatttgaaatttctaca	15	12	7	7	0	1	4	0	2	1	2	2	6	2	4	1	0	2	1	1	0	4	5	rs150221602	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:5081828G>C	ENST00000381652.3	+	19	3032	c.2538G>C	c.(2536-2538)gaG>gaC	p.E846D	JAK2_ENST00000544510.1_Missense_Mutation_p.E697D|AL161450.1_ENST00000601793.1_Intron|JAK2_ENST00000539801.1_Missense_Mutation_p.E846D	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	846					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)	AGTTTGAAGAGAGACATTTGA	0.358		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial																												p.E846D		Atlas-SNP	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	35466	.	0			c.G2538C						PASS	.	G	ASP/GLU	1,4405	2.1+/-5.4	0,1,2202	104	104	104		2538	0	1	9	dbSNP_134	104	5,8595	4.3+/-15.6	0,5,4295	yes	missense	JAK2	NM_004972.3	45	0,6,6497	CC,CG,GG		0.0581,0.0227,0.0461	benign	846/1133	5081828	6,13000	2203	4300	6503	SO:0001583	missense	3717	exon19	Familial Cancer Database		TGAAGAGAGACAT		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.2538G>C	9.37:g.5081828G>C	ENSP00000371067:p.Glu846Asp	83	0	0		120	54	0.45	NM_004972	O14636|O75297	Missense_Mutation	SNP	ENST00000381652.3	37	CCDS6457.1	.	.	.	.	.	.	.	.	.	.	G	14.82	2.648097	0.47258	2.27E-4	5.81E-4	ENSG00000096968	ENST00000539801;ENST00000381652;ENST00000544510	D;D;D	0.89123	-2.47;-2.47;-2.47	5.42	0.0118	0.14089	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	D	0.85948	0.5816	M	0.73962	2.25	0.47245	D	0.999367	B	0.31100	0.308	B	0.27076	0.076	T	0.79249	-0.1881	10	0.62326	D	0.03	-17.9695	10.7256	0.46066	0.6272:0.0:0.3728:0.0	.	846	O60674	JAK2_HUMAN	D	846;846;697	ENSP00000440387:E846D;ENSP00000371067:E846D;ENSP00000443103:E697D	ENSP00000371067:E846D	E	+	3	2	JAK2	5071828	1.000000	0.71417	0.992000	0.48379	0.995000	0.86356	0.585000	0.23879	-0.298000	0.08921	0.655000	0.94253	GAG	G|0.999;C|0.001	0.001	strong		0.358	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			C	5081828	G	C	5081828	3	2	26	1	0	0	0	0	1	0	0	0	7947	933	33	4	2604	4	JAK2	9	5081828	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	2269546	5081828	136131603	305	10068											
SNAPC3	6619	hgsc.bcm.edu	37	chr9	15453156	15453156	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgggttttccttacttataCtgtcatcagggagactgtga	8	15	10	8	0	2	2	2	1	0	1	3	3	3	2	1	2	2	1	1	2	3	5			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:15453156C>T	ENST00000380821.3	+	7	1109	c.933C>T	c.(931-933)taC>taT	p.Y311Y	SNAPC3_ENST00000380799.1_Silent_p.Y108Y	NM_001039697.1	NP_001034786.1	Q92966	SNPC3_HUMAN	small nuclear RNA activating complex, polypeptide 3, 50kDa	311					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)		CTTACTTATACTGTCATCAGG	0.368																																					p.Y311Y		Atlas-SNP	.											.	SNAPC3	28	.	0			c.C933T						PASS	.						180	175	177					9																	15453156		2203	4300	6503	SO:0001819	synonymous_variant	6619	exon7			CTTATACTGTCAT	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.933C>T	9.37:g.15453156C>T		222	0	0		215	91	0.423256	NM_001039697	D3DRI8|Q2VPI6|Q5T285	Silent	SNP	ENST00000380821.3	37	CCDS6478.1																																																																																			.	.	none		0.368	SNAPC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051763.2	NM_001039697		T	15453156	C	T	15453156	2	4	26	1	0	0	0	0	0	0	0	1	14851	576	20	2		2	SNAPC3	9	15453156	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	10371328	15453156	125760275	306	10069											
IFNA17	3451	hgsc.bcm.edu	37	chr9	21227821	21227821	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatcacacatgcttccaggtTattcagttgctggtaaagtt	10	15	8	8	0	2	0	2	0	0	0	3	0	3	0	1	2	2	6	1	2	4	7	rs141849715	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:21227821T>C	ENST00000413767.2	-	1	400	c.352A>G	c.(352-354)Aac>Gac	p.N118D		NM_021268.2	NP_067091.1	P01571	IFN17_HUMAN	interferon, alpha 17	118					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(2)|lung(4)|ovary(1)|skin(1)	9				Lung(24;2.13e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)		GCTTCCAGGTTATTCAGTTGC	0.473																																					p.N118D		Atlas-SNP	.											.	IFNA17	17	.	0			c.A352G						PASS	.	T	ASP/ASN	4,4402	4.2+/-10.8	0,4,2199	149	155	153		352	-0.6	0	9	dbSNP_134	153	34,8566	17.9+/-57.8	1,32,4267	no	missense	IFNA17	NM_021268.2	23	1,36,6466	CC,CT,TT		0.3953,0.0908,0.2922	benign	118/190	21227821	38,12968	2203	4300	6503	SO:0001583	missense	3451	exon1			CCAGGTTATTCAG		CCDS6500.1	9p22	2010-12-10			ENSG00000234829	ENSG00000234829		"Interferons"	5422	protein-coding gene	gene with protein product		147583				1385305	Standard	NM_021268		Approved	LEIF2C1, IFN-alphaI	uc003zos.1	P01571	OTTHUMG00000019667	ENST00000413767.2:c.352A>G	9.37:g.21227821T>C	ENSP00000411940:p.Asn118Asp	454	0	0		365	127	0.347945	NM_021268	Q14639|Q4KMT4|Q5VZ53|Q7M4Q4	Missense_Mutation	SNP	ENST00000413767.2	37	CCDS6500.1	7	0.003205128205128205	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	t	0.009	-1.820432	0.00595	9.08E-4	0.003953	ENSG00000234829	ENST00000413767	T	0.02890	4.12	2.87	-0.61	0.11604	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	1.099480	0.06778	N	0.784835	T	0.00356	0.0011	N	0.00014	-2.915	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.50013	-0.8877	10	0.02654	T	1	.	3.954	0.09382	0.0:0.356:0.3901:0.2539	.	118	P01571	IFN17_HUMAN	D	118	ENSP00000411940:N118D	ENSP00000411940:N118D	N	-	1	0	IFNA17	21217821	0.000000	0.05858	0.000000	0.03702	0.060000	0.15804	-0.698000	0.05092	0.082000	0.17018	-0.702000	0.03669	AAC	T|0.997;C|0.003	0.003	strong		0.473	IFNA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051896.1	NM_021268		C	21227821	T	C	21227821	3	2	26	1	0	0	0	0	1	0	0	0	7545	1754	61	3	221	3	IFNA17	9	21227821	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	5774665	21227821	119985610	307	10070											
UNC13B	10497	hgsc.bcm.edu	37	chr9	35398605	35398605	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgcaggtgaaactgaatacgGttctggatgagctcagcatg	11	10	13	7	1	2	3	1	3	1	0	2	4	2	4	0	3	5	4	0	3	3	2	rs41315995	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:35398605G>A	ENST00000378495.3	+	31	3862	c.3640G>A	c.(3640-3642)Gtt>Att	p.V1214I	UNC13B_ENST00000396787.1_Missense_Mutation_p.V1226I|UNC13B_ENST00000481299.1_3'UTR|UNC13B_ENST00000378496.4_Missense_Mutation_p.V1214I	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	1214					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)			ACTGAATACGGTTCTGGATGA	0.527													G|||	40	0.00798722	0.0015	0.0101	5008	,	,		21287	0.0		0.0239	False		,,,				2504	0.0072				p.V1214I		Atlas-SNP	.											.	UNC13B	153	.	0			c.G3640A						PASS	.	G	ILE/VAL	19,4387	26.2+/-53.5	0,19,2184	142	135	138		3640	5.7	1	9	dbSNP_127	138	151,8449	72.9+/-135.5	2,147,4151	yes	missense	UNC13B	NM_006377.3	29	2,166,6335	AA,AG,GG		1.7558,0.4312,1.3071	possibly-damaging	1214/1592	35398605	170,12836	2203	4300	6503	SO:0001583	missense	10497	exon31			AATACGGTTCTGG	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.3640G>A	9.37:g.35398605G>A	ENSP00000367756:p.Val1214Ile	87	0	0		111	51	0.459459	NM_006377	Q5VYM8	Missense_Mutation	SNP	ENST00000378495.3	37	CCDS6579.1	19	0.0086996336996337	0	0.0	5	0.013812154696132596	0	0.0	14	0.018469656992084433	G	31	5.075214	0.94000	0.004312	0.017558	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496;ENST00000535471	T;T;T	0.34472	1.36;1.36;1.36	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.45377	0.1339	M	0.86573	2.825	0.80722	D	1	B;D	0.58268	0.314;0.982	B;P	0.54924	0.068;0.764	T	0.61997	-0.6947	10	0.56958	D	0.05	-16.6564	19.8236	0.96607	0.0:0.0:1.0:0.0	rs41315995	1214;1214	F8W8M9;O14795	.;UN13B_HUMAN	I	1226;1214;1214;801	ENSP00000380006:V1226I;ENSP00000367756:V1214I;ENSP00000367757:V1214I	ENSP00000367756:V1214I	V	+	1	0	UNC13B	35388605	1.000000	0.71417	0.996000	0.52242	0.914000	0.54420	6.586000	0.74067	2.695000	0.91970	0.455000	0.32223	GTT	G|0.987;A|0.013	0.013	strong		0.527	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377		A	35398605	G	A	35398605	3	1	26	1	0	0	0	0	1	0	0	0	17000	1261	44	2	3762	2	UNC13B	9	35398605	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	14170784	35398605	105814826	308	10071											
DCAF10	79269	hgsc.bcm.edu	37	chr9	37861380	37861380	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccaaagaagccagtcccctgCgggtgatccgttctctgtac	8	9	10	14	2	1	2	0	1	1	1	4	2	3	2	5	1	3	2	5	1	3	2			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:37861380C>T	ENST00000377724.3	+	7	1920	c.1555C>T	c.(1555-1557)Cgg>Tgg	p.R519W	DCAF10_ENST00000242323.7_Missense_Mutation_p.R482W|RP11-613M10.9_ENST00000540557.1_Intron|DCAF10_ENST00000483167.1_3'UTR	NM_024345.3	NP_077321.3	Q5QP82	DCA10_HUMAN	DDB1 and CUL4 associated factor 10	519					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						CAGTCCCCTGCGGGTGATCCG	0.483																																					p.R519W		Atlas-SNP	.											DCAF10,NS,carcinoma,0,1	DCAF10	31	1	0			c.C1555T						PASS	.						103	97	99					9																	37861380		2203	4300	6503	SO:0001583	missense	79269	exon7			CCCCTGCGGGTGA	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.1555C>T	9.37:g.37861380C>T	ENSP00000366953:p.Arg519Trp	202	0	0		236	107	0.45339	NM_024345	A4VCJ5|Q32NE2|Q8N2Q5|Q96ET5|Q9BTQ5|Q9H5P6	Missense_Mutation	SNP	ENST00000377724.3	37	CCDS6613.2	.	.	.	.	.	.	.	.	.	.	C	18.69	3.677247	0.68042	.	.	ENSG00000122741	ENST00000377724;ENST00000242323	T;T	0.01388	4.95;4.95	6.06	6.06	0.98353	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.161766	0.56097	D	0.000033	T	0.03783	0.0107	N	0.22421	0.69	0.47698	D	0.99949	P;D	0.65815	0.894;0.995	B;P	0.59703	0.312;0.862	T	0.59862	-0.7374	10	0.56958	D	0.05	.	18.1147	0.89549	0.0:1.0:0.0:0.0	.	482;519	Q5QP82-2;Q5QP82	.;DCA10_HUMAN	W	519;482	ENSP00000366953:R519W;ENSP00000242323:R482W	ENSP00000242323:R482W	R	+	1	2	DCAF10	37851380	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	1.548000	0.36201	2.882000	0.98803	0.655000	0.94253	CGG	.	.	none		0.483	DCAF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052485.2	NM_024345		T	37861380	C	T	37861380	3	4	26	1	0	0	0	0	1	0	0	0	4263	759	27	1	1581	1	DCAF10	9	37861380	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	2462775	37861380	103352051	309	10072											
FAM75A3	727830	hgsc.bcm.edu	37	chr9	40705744	40705744	+	Frame_Shift_Del	DEL	C	C	-																															attgaggactcctcaacttaCcccagtcaggaaaacagaag																										TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:40705744delC	ENST00000356699.5	+	4	3430	c.3401delC	c.(3400-3402)accfs	p.T1134fs	RP11-395E19.5_ENST00000432614.1_lincRNA	NM_001083124.1	NP_001076593.1	Q5VYP0	S31A3_HUMAN	SPATA31 subfamily A, member 3	1134					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CCTCAACTTACCCCAGTCAGG	0.463																																					p.T1134fs		Atlas-Indel	.											.	.	.	.	0			c.3400delA						PASS	.						24	20	21					9																	40705744		919	2111	3030	SO:0001589	frameshift_variant	727830	exon4			.			9p12	2012-10-15	2012-10-12	2012-10-12	ENSG00000147926				32003	protein-coding gene	gene with protein product			"family with sequence similarity 75, member A3"	FAM75A3		20850414	Standard	NM_001083124		Approved	OTTHUMG00000013164, DKFZp434B204	uc010mmj.3	Q5VYP0	OTTHUMG00000013164	ENST00000356699.5:c.3401delC	9.37:g.40705744delC	ENSP00000349132:p.Thr1134fs	207	0	0		504	37	0.0734127	NM_001083124		Frame_Shift_Del	DEL	ENST00000356699.5	37	CCDS47969.1																																																																																			.	.	none		0.463	SPATA31A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036919.1	NM_001083124		-	40705744	C	-	40705744	7	5	26	1	0	1	0	1	0	0	0	0	5629	507	18	0	3415	0	FAM75A3	9	40705744	Frame_Shift_Del	DEL	C	TCGA-G8-6907-01A-11D-2210-10	2844364	40705744	100507687	310	10073											
PRUNE2	158471	hgsc.bcm.edu	37	chr9	79322711	79322711	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatcactgtctatagggacGtccccaaaatcaagacttcg	13	9	7	12	2	3	1	2	0	1	1	5	2	4	2	2	1	0	0	2	1	5	3			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:79322711G>A	ENST00000376718.3	-	8	4602	c.4479C>T	c.(4477-4479)gaC>gaT	p.D1493D	PRUNE2_ENST00000428286.1_Silent_p.D1134D	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	1493					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						CTATAGGGACGTCCCCAAAAT	0.468																																					p.D1493D		Atlas-SNP	.											.	PRUNE2	331	.	0			c.C4479T						PASS	.						43	42	43					9																	79322711		1568	3582	5150	SO:0001819	synonymous_variant	158471	exon8			AGGGACGTCCCCA	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.4479C>T	9.37:g.79322711G>A		83	0	0		100	45	0.45	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Silent	SNP	ENST00000376718.3	37	CCDS47982.1	.	.	.	.	.	.	.	.	.	.	G	3.028	-0.200220	0.06219	.	.	ENSG00000106772	ENST00000426088	.	.	.	5.49	-1.57	0.08506	.	.	.	.	.	T	0.20129	0.0484	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.24404	-1.0161	4	.	.	.	-1.5436	2.2159	0.03959	0.4355:0.2533:0.0685:0.2427	.	.	.	.	C	815	.	.	R	-	1	0	PRUNE2	78512531	0.011000	0.17503	0.001000	0.08648	0.002000	0.02628	0.261000	0.18442	-0.420000	0.07427	-0.238000	0.12139	CGT	.	.	none		0.468	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818		A	79322711	G	A	79322711	2	1	26	1	0	0	0	0	0	0	0	1	12653	1136	40	1		1	PRUNE2	9	79322711	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	38616967	79322711	61890720	311	10074											
TLE1	7088	hgsc.bcm.edu	37	chr9	84302311	84302311	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cggtccagggactccgggatAgtgaacttgaagggctggcc	8	7	16	10	2	0	2	0	2	0	0	2	4	2	4	3	5	1	1	3	5	3	2	rs147523347	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:84302311A>G	ENST00000376499.3	-	2	1127	c.63T>C	c.(61-63)acT>acC	p.T21T	TLE1_ENST00000376472.1_5'UTR|RP11-154D17.1_ENST00000437181.1_lincRNA|TLE1_ENST00000376463.1_5'Flank	NM_005077.3	NP_005068.2	Q04724	TLE1_HUMAN	transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila)	21	Gln-rich.				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						ACTCCGGGATAGTGAACTTGA	0.642											OREG0019267	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	30	0.00599042	0.0	0.0029	5008	,	,		13712	0.0		0.007	False		,,,				2504	0.0215				p.T21T	NSCLC(155;1437 1995 30668 39354 45875)|Melanoma(16;266 781 14000 47728 51870)	Atlas-SNP	.											TLE1,NS,haematopoietic_neoplasm,0,1	TLE1	81	1	0			c.T63C						scavenged	.	A		6,4396	9.9+/-24.2	0,6,2195	25	26	25		63	-3.5	1	9	dbSNP_134	25	55,8545	30.1+/-81.4	2,51,4247	no	coding-synonymous	TLE1	NM_005077.3		2,57,6442	GG,GA,AA		0.6395,0.1363,0.4692		21/771	84302311	61,12941	2201	4300	6501	SO:0001819	synonymous_variant	7088	exon2			CGGGATAGTGAAC		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.63T>C	9.37:g.84302311A>G		97	1	0.0103093	1228	132	61	0.462121	NM_005077	A8K495|Q5T3G4|Q969V9	Silent	SNP	ENST00000376499.3	37	CCDS6661.1																																																																																			A|0.995;G|0.005	0.005	strong		0.642	TLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055407.1	NM_005077		G	84302311	A	G	84302311	2	3	26	1	0	0	0	0	0	0	0	1	15953	407	15	3		3	TLE1	9	84302311	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	4979600	84302311	56911120	312	10075											
KIF27	55582	hgsc.bcm.edu	37	chr9	86474262	86474262	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taagttcaggcgagttgataTtttcaaactatctgtgttta	11	17	8	5	1	3	1	2	1	1	0	3	2	3	1	0	1	1	3	0	1	5	9	rs79324787	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:86474262T>C	ENST00000297814.2	-	14	3102	c.2959A>G	c.(2959-2961)Ata>Gta	p.I987V	RP11-575L7.4_ENST00000590417.1_RNA|RP11-575L7.4_ENST00000591217.1_RNA|KIF27_ENST00000413982.1_Missense_Mutation_p.I921V|RP11-575L7.4_ENST00000592283.1_RNA|KIF27_ENST00000334204.2_Missense_Mutation_p.I890V|RP11-575L7.4_ENST00000589233.1_RNA|RP11-575L7.4_ENST00000589817.1_RNA|RP11-575L7.4_ENST00000586211.1_RNA|RP11-575L7.4_ENST00000608866.1_RNA|RP11-575L7.4_ENST00000590813.1_RNA|RP11-575L7.4_ENST00000590368.1_RNA|RP11-575L7.4_ENST00000421734.3_RNA|RP11-575L7.4_ENST00000586206.1_RNA	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	987					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						CGAGTTGATATTTTCAAACTA	0.378													T|||	54	0.0107827	0.0333	0.0043	5008	,	,		16078	0.001		0.003	False		,,,				2504	0.0031				p.I987V		Atlas-SNP	.											.	KIF27	103	.	0			c.A2959G						PASS	.	T	VAL/ILE	16,4390	9.9+/-24.2	0,16,2187	94	81	85		2959	4.5	1	9	dbSNP_131	85	1,8599		0,1,4299	yes	missense	KIF27	NM_017576.1	29	0,17,6486	CC,CT,TT		0.0116,0.3631,0.1307	benign	987/1402	86474262	17,12989	2203	4300	6503	SO:0001583	missense	55582	exon14			TTGATATTTTCAA	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.2959A>G	9.37:g.86474262T>C	ENSP00000297814:p.Ile987Val	121	0	0		136	11	0.0808824	NM_017576	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Missense_Mutation	SNP	ENST00000297814.2	37	CCDS6665.1	.	.	.	.	.	.	.	.	.	.	T	1.953	-0.440642	0.04636	0.003631	1.16E-4	ENSG00000165115	ENST00000297814;ENST00000413982;ENST00000334204	T;T;T	0.55930	0.49;0.49;0.49	4.49	4.49	0.54785	.	0.125199	0.34067	N	0.004296	T	0.28466	0.0704	N	0.20685	0.6	0.09310	N	0.999999	B;P;P	0.35656	0.049;0.514;0.506	B;B;B	0.36989	0.05;0.238;0.12	T	0.35599	-0.9782	10	0.02654	T	1	.	4.0383	0.09740	0.2382:0.0971:0.0:0.6647	.	890;921;987	Q86VH2-3;Q86VH2-2;Q86VH2	.;.;KIF27_HUMAN	V	987;921;890	ENSP00000297814:I987V;ENSP00000401688:I921V;ENSP00000333928:I890V	ENSP00000297814:I987V	I	-	1	0	KIF27	85664082	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	2.394000	0.44450	1.880000	0.54463	0.397000	0.26171	ATA	T|0.994;C|0.006	0.006	strong		0.378	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576		C	86474262	T	C	86474262	3	2	26	1	0	0	0	0	1	0	0	0	8305	1493	52	3	1266	3	KIF27	9	86474262	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	2171951	86474262	54739169	313	10076											
ZCCHC6	79670	hgsc.bcm.edu	37	chr9	88940359	88940359	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	taaattctaaagcatagaacCgcagcaattccacccagagc	16	7	6	12	1	1	2	0	0	1	2	2	2	2	2	3	0	4	3	3	0	7	5	rs41310053	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:88940359C>T	ENST00000375963.3	-	12	1851	c.1679G>A	c.(1678-1680)cGg>cAg	p.R560Q	ZCCHC6_ENST00000375961.2_Missense_Mutation_p.R560Q|ZCCHC6_ENST00000375960.2_Missense_Mutation_p.R437Q|ZCCHC6_ENST00000277141.6_5'UTR|ZCCHC6_ENST00000469004.1_5'Flank	NM_001185059.1|NM_024617.3	NP_001171988.1|NP_078893.2	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	560	PAP-associated 1.				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						AGCATAGAACCGCAGCAATTC	0.398													C|||	10	0.00199681	0.0	0.0014	5008	,	,		17480	0.0		0.0089	False		,,,				2504	0.0				p.R560Q		Atlas-SNP	.											.	ZCCHC6	105	.	0			c.G1679A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	84	82	83		1679,1310,1679	5.2	1	9	dbSNP_127	83	48,8552	30.7+/-82.3	0,48,4252	yes	missense,missense,missense	ZCCHC6	NM_001185059.1,NM_001185074.1,NM_024617.3	43,43,43	0,50,6453	TT,TC,CC		0.5581,0.0454,0.3844	probably-damaging,probably-damaging,probably-damaging	560/1496,437/1260,560/1496	88940359	50,12956	2203	4300	6503	SO:0001583	missense	79670	exon12			TAGAACCGCAGCA	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.1679G>A	9.37:g.88940359C>T	ENSP00000365130:p.Arg560Gln	108	0	0		136	63	0.463235	NM_024617	Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6	Missense_Mutation	SNP	ENST00000375963.3	37	CCDS35057.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	C	28.5	4.923726	0.92319	4.54E-4	0.005581	ENSG00000083223	ENST00000375960;ENST00000375961;ENST00000375963	T;T;T	0.76709	-1.04;-1.04;-1.04	5.24	5.24	0.73138	PAP/25A-associated (1);	0.000000	0.85682	D	0.000000	D	0.84889	0.5572	M	0.75615	2.305	0.58432	D	0.999993	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.87244	0.2268	10	0.72032	D	0.01	-33.9822	19.0276	0.92939	0.0:1.0:0.0:0.0	rs41310053	437;560	Q5VYS8-4;Q5VYS8	.;TUT7_HUMAN	Q	437;560;560	ENSP00000365127:R437Q;ENSP00000365128:R560Q;ENSP00000365130:R560Q	ENSP00000365127:R437Q	R	-	2	0	ZCCHC6	88130179	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.420000	0.66441	2.745000	0.94114	0.650000	0.86243	CGG	C|0.997;T|0.003	0.003	strong		0.398	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052918.1	NM_024617		T	88940359	C	T	88940359	3	4	26	1	0	0	0	0	1	0	0	0	17607	652	23	1	2872	1	ZCCHC6	9	88940359	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	2466097	88940359	52273072	314	10077											
NOL8	55035	hgsc.bcm.edu	37	chr9	95077289	95077289	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agccacaatctccgcaggacGaatacactgtcggcctctgc	10	7	9	15	3	2	0	0	0	2	0	4	2	2	1	3	2	3	1	3	2	3	1			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:95077289G>A	ENST00000535387.1	-	6	1617	c.1618C>T	c.(1618-1620)Cgt>Tgt	p.R540C	NOL8_ENST00000358855.4_Missense_Mutation_p.R472C|NOL8_ENST00000542053.1_Missense_Mutation_p.R472C|NOL8_ENST00000545558.1_Missense_Mutation_p.R540C|NOL8_ENST00000442668.2_Missense_Mutation_p.R540C					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						TCCGCAGGACGAATACACTGT	0.498																																					p.R540C		Atlas-SNP	.											.	NOL8	118	.	0			c.C1618T						PASS	.						74	70	71					9																	95077289		1855	4090	5945	SO:0001583	missense	55035	exon7			CAGGACGAATACA	AB109030	CCDS47993.1, CCDS59135.1	9q22.32	2013-02-12	2004-01-12	2004-01-14	ENSG00000198000	ENSG00000198000		"RNA binding motif (RRM) containing"	23387	protein-coding gene	gene with protein product		611534	"chromosome 9 open reading frame 34"	C9orf34		12477932	Standard	NM_017948		Approved	FLJ20736, Nop132	uc022bjx.1	Q76FK4	OTTHUMG00000020221	ENST00000535387.1:c.1618C>T	9.37:g.95077289G>A	ENSP00000441300:p.Arg540Cys	143	0	0		139	66	0.47482	NM_017948		Missense_Mutation	SNP	ENST00000535387.1	37	CCDS47993.1	.	.	.	.	.	.	.	.	.	.	G	6.026	0.373204	0.11409	.	.	ENSG00000198000	ENST00000442668;ENST00000375594;ENST00000358855;ENST00000545558;ENST00000535387;ENST00000542053;ENST00000432670	T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91	5.69	-5.16	0.02857	.	1.619260	0.02753	N	0.117648	T	0.20659	0.0497	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.11591	-1.0581	10	0.40728	T	0.16	1.0458	2.1033	0.03685	0.3083:0.0914:0.1236:0.4767	.	540	Q76FK4	NOL8_HUMAN	C	540;542;472;540;540;472;540	ENSP00000401177:R540C;ENSP00000351723:R472C;ENSP00000441140:R540C;ENSP00000441300:R540C;ENSP00000440709:R472C;ENSP00000414112:R540C	ENSP00000351723:R472C	R	-	1	0	NOL8	94117110	0.000000	0.05858	0.004000	0.12327	0.118000	0.20060	-1.388000	0.02533	-0.487000	0.06735	-0.136000	0.14681	CGT	.	.	none		0.498	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948		A	95077289	G	A	95077289	3	1	26	1	0	0	0	0	1	0	0	0	10536	1058	37	1	1929	1	NOL8	9	95077289	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	6136930	95077289	46136142	315	10078											
HEMGN	55363	hgsc.bcm.edu	37	chr9	100692330	100692330	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccttaccttgaggaaaagtAtaagcatctttagcatcttc	12	13	6	10	0	2	1	0	1	2	0	3	2	2	2	2	1	3	3	2	1	6	7	rs35223978	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:100692330A>G	ENST00000259456.3	-	4	1490	c.1347T>C	c.(1345-1347)taT>taC	p.Y449Y		NM_018437.3|NM_197978.2	NP_060907.2|NP_932095.1	Q9BXL5	HEMGN_HUMAN	hemogen	449					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)				GAGGAAAAGTATAAGCATCTT	0.468													A|||	19	0.00379393	0.0	0.0058	5008	,	,		18466	0.0		0.0109	False		,,,				2504	0.0041				p.Y449Y		Atlas-SNP	.											.	HEMGN	55	.	0			c.T1347C						PASS	.	A	,	5,4401	8.1+/-20.4	0,5,2198	221	201	208		1347,1347	0.6	0	9	dbSNP_126	208	69,8531	42.2+/-99.7	1,67,4232	no	coding-synonymous,coding-synonymous	HEMGN	NM_018437.3,NM_197978.1	,	1,72,6430	GG,GA,AA		0.8023,0.1135,0.569	,	449/485,449/485	100692330	74,12932	2203	4300	6503	SO:0001819	synonymous_variant	55363	exon3			AAAAGTATAAGCA	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.1347T>C	9.37:g.100692330A>G		176	0	0		205	89	0.434146	NM_197978	Q6XAR3|Q86XY5|Q9NPC0	Silent	SNP	ENST00000259456.3	37	CCDS6731.1																																																																																			A|0.995;G|0.005	0.005	strong		0.468	HEMGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053344.2	NM_197978		G	100692330	A	G	100692330	2	3	26	1	0	0	0	0	0	0	0	1	7059	456	16	3		3	HEMGN	9	100692330	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	5615041	100692330	40521101	316	10079											
GABBR2	9568	hgsc.bcm.edu	37	chr9	101151192	101151192	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcactggccatgatcatcccGaggatggtgagggcagagag	10	6	16	9	1	1	3	1	2	0	1	2	6	2	4	2	4	0	2	2	4	0	0	rs144313756		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:101151192G>A	ENST00000259455.2	-	10	1932	c.1473C>T	c.(1471-1473)ctC>ctT	p.L491L		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	491					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)	TGATCATCCCGAGGATGGTGA	0.498													G|||	1	0.000199681	0.0	0.0014	5008	,	,		21052	0.0		0.0	False		,,,				2504	0.0				p.L491L		Atlas-SNP	.											.	GABBR2	126	.	0			c.C1473T						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	263	212	229		1473	-6.8	0.7	9	dbSNP_134	229	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous	GABBR2	NM_005458.7		0,15,6488	AA,AG,GG		0.1512,0.0454,0.1153		491/942	101151192	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	9568	exon10			CATCCCGAGGATG	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.1473C>T	9.37:g.101151192G>A		309	0	0		393	203	0.516539	NM_005458	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Silent	SNP	ENST00000259455.2	37	CCDS6736.1																																																																																			G|0.999;A|0.001	0.001	strong		0.498	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1			A	101151192	G	A	101151192	2	1	26	1	0	0	0	0	0	0	0	1	6164	1045	37	1		1	GABBR2	9	101151192	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	458862	101151192	40062239	317	10080											
ALG2	85365	hgsc.bcm.edu	37	chr9	101980707	101980707	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcccaatcttgggatgtcaAtcttccacgcagctgtacta	9	12	7	13	1	3	0	1	0	2	0	5	1	5	1	2	1	2	3	2	1	4	4	rs62562374	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:101980707A>G	ENST00000476832.1	-	2	821	c.760T>C	c.(760-762)Ttg>Ctg	p.L254L	ALG2_ENST00000319033.6_Silent_p.L161L	NM_033087.3	NP_149078.1	O75340	PDCD6_HUMAN	ALG2, alpha-1,3/1,6-mannosyltransferase	0					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(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(11)|ovary(2)|prostate(2)	22		Acute lymphoblastic leukemia(62;0.0559)				TGGGATGTCAATCTTCCACGC	0.463													A|||	8	0.00159744	0.0	0.0014	5008	,	,		22624	0.0		0.007	False		,,,				2504	0.0				p.L254L		Atlas-SNP	.											.	ALG2	37	.	0			c.T760C						PASS	.	A		3,4403	6.2+/-15.9	0,3,2200	153	153	153		760	-2.3	0	9	dbSNP_129	153	48,8552	31.2+/-83.2	0,48,4252	no	coding-synonymous	ALG2	NM_033087.3		0,51,6452	GG,GA,AA		0.5581,0.0681,0.3921		254/417	101980707	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	85365	exon2			ATGTCAATCTTCC	AK027417	CCDS6739.1	9q31.1	2013-02-22	2013-02-22		ENSG00000119523	ENSG00000119523	2.4.1.132, 2.4.1.257	"Glycosyltransferase group 1 domain containing"	23159	protein-coding gene	gene with protein product		607905	"asparagine-linked glycosylation 2 homolog (yeast, alpha-1,3-mannosyltransferase)", "asparagine-linked glycosylation 2, alpha-1,3-mannosyltransferase homolog (S. cerevisiae)"			12684507	Standard	NR_024532		Approved	CDGIi, FLJ14511, hALPG2, NET38	uc004azf.3	Q9H553	OTTHUMG00000020355	ENST00000476832.1:c.760T>C	9.37:g.101980707A>G		185	0	0		188	95	0.505319	NM_033087	B2RD16|E7ESR3|Q2YDC2|Q5TZS0	Silent	SNP	ENST00000476832.1	37	CCDS6739.1																																																																																			A|0.998;C|0.000;G|0.002	0.002	strong		0.463	ALG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215080.1	NM_033087		G	101980707	A	G	101980707	2	3	26	1	0	0	0	0	0	0	0	1	519	98	4	3		3	ALG2	9	101980707	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	829515	101980707	39232724	318	10081											
OR13C5	138799	hgsc.bcm.edu	37	chr9	107361002	107361002	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaggtttgcttctcccctcCgaagagctaattttgaagat	10	13	9	9	1	1	3	0	1	1	2	3	5	2	3	3	1	2	3	3	1	4	5	rs78992791	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:107361002C>G	ENST00000374779.2	-	1	786	c.693G>C	c.(691-693)tcG>tcC	p.S231S		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	231						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						TTCTCCCCTCCGAAGAGCTAA	0.428													G|||	5	0.000998403	0.0	0.0014	5008	,	,		22312	0.0		0.001	False		,,,				2504	0.0031				p.S231S		Atlas-SNP	.											OR13C5,right_upper_lobe,carcinoma,0,2	OR13C5	60	2	0			c.G693C						PASS	.						123	114	117					9																	107361002		2203	4300	6503	SO:0001819	synonymous_variant	138799	exon1			CCCCTCCGAAGAG		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.693G>C	9.37:g.107361002C>G		154	0	0		218	109	0.5	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Silent	SNP	ENST00000374779.2	37	CCDS35091.1																																																																																			C|0.999;G|0.001	0.001	strong		0.428	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482		G	107361002	C	G	107361002	2	3	26	1	0	0	0	0	0	0	0	1	10946	639	23	4		4	OR13C5	9	107361002	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	5380295	107361002	33852429	319	10082											
ZNF462	58499	hgsc.bcm.edu	37	chr9	109685748	109685748	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacattcaggatgtccacacGgcatttctgcagccaactga	11	9	8	13	1	2	1	1	1	1	0	3	2	3	2	2	2	3	2	2	2	1	2			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:109685748G>T	ENST00000277225.5	+	2	373	c.84G>T	c.(82-84)acG>acT	p.T28T	ZNF462_ENST00000457913.1_Silent_p.T28T|RP11-508N12.4_ENST00000451160.2_Silent_p.T28T			Q96JM2	ZN462_HUMAN	zinc finger protein 462	28					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						ATGTCCACACGGCATTTCTGC	0.498																																					p.T28T		Atlas-SNP	.											.	ZNF462	322	.	0			c.G84T						PASS	.						241	216	224					9																	109685748		2203	4300	6503	SO:0001819	synonymous_variant	58499	exon2			CCACACGGCATTT	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.84G>T	9.37:g.109685748G>T		204	0	0		231	81	0.350649	NM_021224	Q5T0T4|Q8N408	Silent	SNP	ENST00000277225.5	37	CCDS35096.1																																																																																			.	.	none		0.498	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224		T	109685748	G	T	109685748	2	4	26	1	0	0	0	0	0	0	0	1	17941	1103	39	4		4	ZNF462	9	109685748	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	2324746	109685748	31527683	320	10083											
PTPN3	5774	hgsc.bcm.edu	37	chr9	112145799	112145799	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccgccgtggttcatgacgtcGgggggatctggccagtactg	5	9	16	11	4	2	1	1	1	1	0	3	2	2	2	3	5	1	2	3	5	1	2	rs2304742	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:112145799G>A	ENST00000374541.2	-	23	2390	c.2286C>T	c.(2284-2286)ccC>ccT	p.P762P	PTPN3_ENST00000412145.1_Silent_p.P631P|PTPN3_ENST00000262539.3_Silent_p.P608P|PTPN3_ENST00000446349.1_Silent_p.P586P|PTPN3_ENST00000394827.3_Silent_p.P230P	NM_001145368.1|NM_002829.3	NP_001138840.1|NP_002820.3	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type 3	762	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						TCATGACGTCGGGGGGATCTG	0.557													G|||	258	0.0515176	0.0008	0.1052	5008	,	,		17925	0.1399		0.0268	False		,,,				2504	0.0164				p.P762P		Atlas-SNP	.											.	PTPN3	106	.	0			c.C2286T						PASS	.	G	,,,,,	30,4376	36.0+/-67.5	0,30,2173	127	119	122		2151,1893,1758,1425,1290,2286	-7.5	0	9	dbSNP_100	122	277,8323	104.8+/-165.8	6,265,4029	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPN3	NM_001145368.1,NM_001145369.1,NM_001145370.1,NM_001145371.1,NM_001145372.1,NM_002829.3	,,,,,	6,295,6202	AA,AG,GG		3.2209,0.6809,2.3604	,,,,,	717/869,631/783,586/738,475/627,430/582,762/914	112145799	307,12699	2203	4300	6503	SO:0001819	synonymous_variant	5774	exon23			GACGTCGGGGGGA		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.2286C>T	9.37:g.112145799G>A		105	0	0		153	85	0.555556	NM_002829	A0AUW9|E7EN99|E9PGU7	Silent	SNP	ENST00000374541.2	37	CCDS6776.1																																																																																			G|0.959;A|0.041	0.041	strong		0.557	PTPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053598.4			A	112145799	G	A	112145799	2	1	26	1	0	0	0	0	0	0	0	1	12804	1103	39	1		1	PTPN3	9	112145799	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	2460051	112145799	29067632	321	10084											
FAM102A	399665	hgsc.bcm.edu	37	chr9	130710489	130710489	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctgggatggagatggacttGgcagtcgatggtggccttgg	6	10	18	7	1	0	1	0	0	0	1	1	5	0	3	2	7	0	1	2	7	0	2	rs144841491	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:130710489G>A	ENST00000373095.1	-	6	852	c.477C>T	c.(475-477)gcC>gcT	p.A159A	FAM102A_ENST00000373084.4_Silent_p.A17A|FAM102A_ENST00000300434.3_Intron	NM_001035254.2	NP_001030331.1	Q5T9C2	F102A_HUMAN	family with sequence similarity 102, member A	159	Ser-rich.									breast(1)|cervix(1)|large_intestine(3)|lung(1)|ovary(4)	10						AGATGGACTTGGCAGTCGATG	0.597													G|||	7	0.00139776	0.0	0.0	5008	,	,		20006	0.0		0.007	False		,,,				2504	0.0				p.A159A		Atlas-SNP	.											.	FAM102A	32	.	0			c.C477T						PASS	.	G	,	4,4402	8.1+/-20.4	0,4,2199	92	82	85		477,51	3.2	1	9	dbSNP_134	85	33,8567	23.4+/-69.3	0,33,4267	no	coding-synonymous,coding-synonymous	FAM102A	NM_001035254.2,NM_203305.2	,	0,37,6466	AA,AG,GG		0.3837,0.0908,0.2845	,	159/385,17/243	130710489	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	399665	exon6			GGACTTGGCAGTC		CCDS6888.1, CCDS35150.1	9q34.11	2012-11-05	2005-11-17	2005-11-17	ENSG00000167106	ENSG00000167106			31419	protein-coding gene	gene with protein product	"sym-3 homolog A (C. elegans)"	610891	"chromosome 9 open reading frame 132"	C9orf132			Standard	NM_001035254		Approved	Eeig1, bA203J24.7, SYM-3A	uc004bsx.2	Q5T9C2	OTTHUMG00000020720	ENST00000373095.1:c.477C>T	9.37:g.130710489G>A		75	0	0		67	38	0.567164	NM_001035254	A2A329|Q8TEL4	Silent	SNP	ENST00000373095.1	37	CCDS35150.1																																																																																			G|0.997;A|0.003	0.003	strong		0.597	FAM102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054298.2			A	130710489	G	A	130710489	2	1	26	1	0	0	0	0	0	0	0	1	5387	1335	47	2		2	FAM102A	9	130710489	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	18564690	130710489	10502942	322	10085											
PTGES2	80142	hgsc.bcm.edu	37	chr9	130886050	130886050	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gcatgagccagtacttattgCcgaactcggtcacctccttg	8	11	9	13	2	1	1	1	1	0	0	3	2	2	1	4	1	4	2	4	1	3	4	rs149102151	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:130886050C>G	ENST00000338961.6	-	4	1361	c.617G>C	c.(616-618)gGc>gCc	p.G206A	PTGES2_ENST00000277462.5_Missense_Mutation_p.G15A|PTGES2_ENST00000483625.1_5'UTR	NM_001256335.1|NM_025072.6	NP_001243264.1|NP_079348.1	Q9H7Z7	PGES2_HUMAN	prostaglandin E synthase 2	206					cell redox homeostasis (GO:0045454)|positive regulation of transcription, DNA-templated (GO:0045893)|prostaglandin biosynthetic process (GO:0001516)|secretion (GO:0046903)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|electron carrier activity (GO:0009055)|glutathione binding (GO:0043295)|heme binding (GO:0020037)|lyase activity (GO:0016829)|prostaglandin-E synthase activity (GO:0050220)|protein disulfide oxidoreductase activity (GO:0015035)			endometrium(1)|large_intestine(1)|lung(2)	4						GTACTTATTGCCGAACTCGGT	0.592													C|||	14	0.00279553	0.0008	0.0029	5008	,	,		14684	0.0		0.007	False		,,,				2504	0.0041				p.G206A		Atlas-SNP	.											.	PTGES2	14	.	0			c.G617C						PASS	.	C	ALA/GLY	4,4402	6.2+/-15.9	0,4,2199	175	125	142		617	4.9	0.9	9	dbSNP_134	142	62,8538	38.8+/-94.9	0,62,4238	yes	missense	PTGES2	NM_025072.5	60	0,66,6437	GG,GC,CC		0.7209,0.0908,0.5075	benign	206/378	130886050	66,12940	2203	4300	6503	SO:0001583	missense	80142	exon4			TTATTGCCGAACT	AK024100	CCDS6891.1	9q34.12	2008-05-06	2002-06-13	2002-06-14	ENSG00000148334	ENSG00000148334			17822	protein-coding gene	gene with protein product		608152	"chromosome 9 open reading frame 15"	C9orf15		11866447	Standard	NM_025072		Approved	FLJ14038	uc004bti.4	Q9H7Z7	OTTHUMG00000020730	ENST00000338961.6:c.617G>C	9.37:g.130886050C>G	ENSP00000345341:p.Gly206Ala	123	0	0		155	83	0.535484	NM_025072	Q53EW9|Q5SYV6|Q96GI0|Q96GL2	Missense_Mutation	SNP	ENST00000338961.6	37	CCDS6891.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	8.598	0.886079	0.17540	9.08E-4	0.007209	ENSG00000148334	ENST00000338961;ENST00000277462;ENST00000449878	T;T;T	0.39787	2.7;1.06;2.7	5.84	4.94	0.65067	Thioredoxin-like fold (1);	0.329789	0.40640	N	0.001045	T	0.19087	0.0458	L	0.28274	0.84	0.30778	N	0.742268	B	0.16603	0.018	B	0.10450	0.005	T	0.19321	-1.0309	10	0.09843	T	0.71	-0.0806	9.3167	0.37939	0.0:0.779:0.0:0.221	.	206	Q9H7Z7	PGES2_HUMAN	A	206;15;171	ENSP00000345341:G206A;ENSP00000277462:G15A;ENSP00000411378:G171A	ENSP00000277462:G15A	G	-	2	0	PTGES2	129925871	1.000000	0.71417	0.937000	0.37676	0.664000	0.39144	1.134000	0.31442	1.485000	0.48380	0.561000	0.74099	GGC	C|0.995;G|0.005	0.005	strong		0.592	PTGES2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054339.1			G	130886050	C	G	130886050	3	3	26	1	0	0	0	0	1	0	0	0	12760	739	26	4	532	4	PTGES2	9	130886050	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	175561	130886050	10327381	323	10086											
DOLPP1	57171	hgsc.bcm.edu	37	chr9	131848488	131848488	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggaggcctcatggccatcGcctggttcatcttcacccag	6	10	10	15	1	4	0	3	0	1	0	5	1	4	1	4	4	0	1	4	4	0	2	rs149976737	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:131848488G>A	ENST00000372546.4	+	6	564	c.532G>A	c.(532-534)Gcc>Acc	p.A178T	DOLPP1_ENST00000540102.1_Intron|DOLPP1_ENST00000406974.3_Intron	NM_020438.4	NP_065171.2	Q86YN1	DOPP1_HUMAN	dolichyldiphosphatase 1	178					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						CATGGCCATCGCCTGGTTCAT	0.622													G|||	5	0.000998403	0.0	0.0	5008	,	,		20902	0.0		0.005	False		,,,				2504	0.0				p.A178T		Atlas-SNP	.											.	DOLPP1	17	.	0			c.G532A						PASS	.	G	,THR/ALA	0,4406		0,0,2203	103	80	87		,532	5.5	1	9	dbSNP_134	87	5,8595	4.3+/-15.6	0,5,4295	yes	intron,missense	DOLPP1	NM_001135917.1,NM_020438.4	,58	0,5,6498	AA,AG,GG		0.0581,0.0,0.0384	,benign	,178/239	131848488	5,13001	2203	4300	6503	SO:0001583	missense	57171	exon6			GCCATCGCCTGGT	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.532G>A	9.37:g.131848488G>A	ENSP00000361625:p.Ala178Thr	88	0	0		85	34	0.4	NM_020438	A8K3U8|B0QZG4|Q96GF8|Q9Y3G1	Missense_Mutation	SNP	ENST00000372546.4	37	CCDS6918.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	17.16	3.317356	0.60524	0.0	5.81E-4	ENSG00000167130	ENST00000372546	T	0.75589	-0.95	5.51	5.51	0.81932	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.107308	0.64402	D	0.000004	T	0.70316	0.3210	L	0.49256	1.55	0.80722	D	1	P	0.50710	0.938	B	0.41571	0.36	T	0.68969	-0.5269	10	0.24483	T	0.36	-10.1792	18.4662	0.90755	0.0:0.0:1.0:0.0	.	178	Q86YN1	DOPP1_HUMAN	T	178	ENSP00000361625:A178T	ENSP00000361625:A178T	A	+	1	0	DOLPP1	130888309	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	7.230000	0.78097	2.604000	0.88044	0.456000	0.33151	GCC	G|0.999;A|0.001	0.001	strong		0.622	DOLPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054548.4	NM_020438		A	131848488	G	A	131848488	3	1	26	1	0	0	0	0	1	0	0	0	4706	1087	38	1	554	1	DOLPP1	9	131848488	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	962438	131848488	9364943	324	10087											
ABL1	25	hgsc.bcm.edu	37	chr9	133759686	133759686	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caatggggctggggtccccaAtggagccctccgggagtccg	6	6	16	13	2	0	0	0	0	0	0	3	2	3	2	5	6	1	1	5	6	2	0	rs61746126	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:133759686A>G	ENST00000318560.5	+	11	2390	c.2009A>G	c.(2008-2010)aAt>aGt	p.N670S		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	670					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)	GGGGTCCCCAATGGAGCCCTC	0.672			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"								A|||	2	0.000399361	0.0008	0.0	5008	,	,		15138	0.0		0.001	False		,,,				2504	0.0				p.N689S		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.A2066G						PASS	.	A	SER/ASN,SER/ASN	0,4366		0,0,2183	17	21	19		2009,2066	5.6	1	9	dbSNP_129	19	2,8516		0,2,4257	no	missense,missense	ABL1	NM_005157.4,NM_007313.2	46,46	0,2,6440	GG,GA,AA		0.0235,0.0,0.0155	possibly-damaging,possibly-damaging	670/1131,689/1150	133759686	2,12882	2183	4259	6442	SO:0001583	missense	25	exon11			TCCCCAATGGAGC	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.2009A>G	9.37:g.133759686A>G	ENSP00000323315:p.Asn670Ser	31	0	0		28	19	0.678571	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Missense_Mutation	SNP	ENST00000318560.5	37	CCDS35166.1	.	.	.	.	.	.	.	.	.	.	A	12.12	1.842721	0.32606	0.0	2.35E-4	ENSG00000097007	ENST00000444970;ENST00000372348;ENST00000318560	T;T	0.12774	2.65;2.65	5.57	5.57	0.84162	.	0.093032	0.64402	D	0.000001	T	0.11495	0.0280	L	0.42245	1.32	0.54753	D	0.999987	B;B	0.33212	0.402;0.402	B;B	0.26864	0.074;0.074	T	0.10428	-1.0630	10	0.11182	T	0.66	.	14.9117	0.70761	1.0:0.0:0.0:0.0	rs61746126	670;707	P00519;Q59FK4	ABL1_HUMAN;.	S	485;689;670	ENSP00000361423:N689S;ENSP00000323315:N670S	ENSP00000323315:N670S	N	+	2	0	ABL1	132749507	0.999000	0.42202	0.997000	0.53966	0.985000	0.73830	4.109000	0.57824	2.117000	0.64856	0.459000	0.35465	AAT	A|0.999;G|0.001	0.001	strong		0.672	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		G	133759686	A	G	133759686	3	3	26	1	0	0	0	0	1	0	0	0	92	101	4	3	2191	3	ABL1	9	133759686	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	1911198	133759686	7453745	325	10088											
AIF1L	83543	hgsc.bcm.edu	37	chr9	133995669	133995669	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgagagcagccccaagccagTtggcccccctccagagagag	10	3	12	16	1	0	3	0	0	0	3	1	5	1	3	7	1	3	2	7	1	1	1	rs112778089	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:133995669T>C	ENST00000247291.3	+	6	501	c.413T>C	c.(412-414)gTt>gCt	p.V138A	AIF1L_ENST00000372302.1_Missense_Mutation_p.V130A|AIF1L_ENST00000372312.3_Missense_Mutation_p.V143A|AIF1L_ENST00000372301.2_Missense_Mutation_p.V82A|AIF1L_ENST00000372300.1_3'UTR|AIF1L_ENST00000372298.1_Intron|AIF1L_ENST00000372297.2_3'UTR|AIF1L_ENST00000372309.3_Missense_Mutation_p.V164A	NM_031426.3	NP_113614.1	Q9BQI0	AIF1L_HUMAN	allograft inflammatory factor 1-like	138						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						CCCAAGCCAGTTGGCCCCCCT	0.542													T|||	3	0.000599042	0.0	0.0014	5008	,	,		14018	0.0		0.002	False		,,,				2504	0.0				p.V164A	Esophageal Squamous(95;611 1423 5044 34794 42333)	Atlas-SNP	.											.	AIF1L	15	.	0			c.T491C						PASS	.	T	ALA/VAL,,ALA/VAL	0,4406		0,0,2203	64	66	65		491,,413	-9	0	9	dbSNP_132	65	23,8577	16.6+/-54.9	0,23,4277	yes	missense,utr-3,missense	AIF1L	NM_001185095.1,NM_001185096.1,NM_031426.3	64,,64	0,23,6480	CC,CT,TT		0.2674,0.0,0.1768	benign,,benign	164/177,,138/151	133995669	23,12983	2203	4300	6503	SO:0001583	missense	83543	exon7			AGCCAGTTGGCCC	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.413T>C	9.37:g.133995669T>C	ENSP00000247291:p.Val138Ala	199	0	0		181	99	0.546961	NM_001185095	B2RBC4|Q6ZR40|Q8NAX7|Q8WU47|Q9H9G0	Missense_Mutation	SNP	ENST00000247291.3	37	CCDS6939.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	6.283	0.420255	0.11928	0.0	0.002674	ENSG00000126878	ENST00000372309;ENST00000247291;ENST00000372302;ENST00000372312;ENST00000372301	T;T;T;T;T	0.61040	0.46;0.3;0.6;0.14;0.44	5.72	-9.04	0.00734	.	1.715750	0.03111	N	0.162504	T	0.34250	0.0891	N	0.25890	0.77	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	0.21177	-1.0253	10	0.08599	T	0.76	-0.9621	6.5492	0.22423	0.1036:0.5225:0.2109:0.1631	.	143;164;138	F5GYC9;Q9BQI0-2;Q9BQI0	.;.;AIF1L_HUMAN	A	164;138;130;143;82	ENSP00000361383:V164A;ENSP00000247291:V138A;ENSP00000361376:V130A;ENSP00000361386:V143A;ENSP00000361375:V82A	ENSP00000247291:V138A	V	+	2	0	AIF1L	132985490	0.000000	0.05858	0.001000	0.08648	0.925000	0.55904	-0.339000	0.07832	-1.647000	0.01511	-2.617000	0.00157	GTT	T|0.998;C|0.002	0.002	strong		0.542	AIF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054703.2	NM_031426		C	133995669	T	C	133995669	3	2	26	1	0	0	0	0	1	0	0	0	425	1725	60	3	517	3	AIF1L	9	133995669	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	235983	133995669	7217762	326	10089											
SEC16A	9919	hgsc.bcm.edu	37	chr9	139370955	139370963	+	In_Frame_Del	DEL	AGCTCCTGA	AGCTCCTGA	-																															ccttggaaaaacatcgccagAgctcctgaagctcctgagtc																								rs545335424	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AGCTCCTGA	AGCTCCTGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:139370955_139370963delAGCTCCTGA	ENST00000371706.3	-	1	604_612	c.571_579delTCAGGAGCT	c.(571-579)tcaggagctdel	p.SGA191del	SEC16A_ENST00000431893.2_In_Frame_Del_p.SGA191del|SEC16A_ENST00000313050.7_In_Frame_Del_p.SGA369del|SEC16A_ENST00000290037.6_In_Frame_Del_p.SGA191del			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	191					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)		p.S369_A371delSGA(1)		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)		ACATCGCCAGAGCTCCTGAAGCTCCTGAG	0.574														13	0.00259585	0.0008	0.0014	5008	,	,		18859	0.0		0.004	False		,,,				2504	0.0072				p.369_372del		Pindel,Atlas-Indel	.											.	SEC16A	249	.	1	Deletion - In frame(1)	breast(1)	c.1106_1114del						PASS	.			7,3561		0,7,1777						1.9	0			19	42,7812		1,40,3886	no	coding	SEC16A	NM_014866.1		1,47,5663	A1A1,A1R,RR		0.5348,0.1962,0.429				49,11373				SO:0001651	inframe_deletion	9919	exon3			.	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.571_579delTCAGGAGCT	9.37:g.139370964_139370972delAGCTCCTGA	ENSP00000360771:p.Ser191_Ala193del	110	0	.		118	32	0.271	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	In_Frame_Del	DEL	ENST00000371706.3	37																																																																																				.	.	none		0.574	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459		-	139370963	AGCTCCTGA	-	139370955	7	5	26	1	0	1	0	1	0	0	0	0	14001	291	11	0	6080	0	SEC16A	9	139370955	In_Frame_Del	DEL	AGCTCCTGA	TCGA-G8-6907-01A-11D-2210-10	5375286	139370955	1842476	327	10090											
NOTCH1	4851	hgsc.bcm.edu	37	chr9	139418260	139418260	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggggttggtgaggcaggcAttgtccaggggtgtcaggca	7	8	19	7	0	1	1	1	1	0	0	2	1	2	1	1	8	0	4	1	8	0	2	rs4489420	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:139418260A>G	ENST00000277541.6	-	3	387	c.312T>C	c.(310-312)aaT>aaC	p.N104N	NOTCH1_ENST00000491649.1_5'UTR	NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	104	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)		TGAGGCAGGCATTGTCCAGGG	0.687			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)			G|||	3706	0.740016	0.9523	0.6037	5008	,	,		12414	0.8363		0.505	False		,,,				2504	0.6922				p.N104N		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	.	NOTCH1	1980	.	0			c.T312C						PASS	.	G		3779,511		1671,437,37	20	32	28		312	-4.3	0	9	dbSNP_111	28	4001,4491		956,2089,1201	yes	coding-synonymous	NOTCH1	NM_017617.3		2627,2526,1238	GG,GA,AA		47.1149,11.9114,39.1332		104/2556	139418260	7780,5002	2145	4246	6391	SO:0001819	synonymous_variant	4851	exon3			GCAGGCATTGTCC	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.312T>C	9.37:g.139418260A>G		112	0	0		137	50	0.364964	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			A|0.323;G|0.677	0.677	strong		0.687	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		G	139418260	A	G	139418260	2	3	26	1	0	0	0	0	0	0	0	1	10556	214	8	3		3	NOTCH1	9	139418260	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	47305	139418260	1795171	328	10091											
FAM166A	401565	hgsc.bcm.edu	37	chr9	140139106	140139106	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tttcctacctggctcttgtcGaattcgtccatggcttgcat	5	16	8	12	2	1	0	0	0	1	0	5	1	3	0	3	2	2	3	3	2	2	5	rs62584882	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:140139106G>A	ENST00000344774.4	-	5	789	c.735C>T	c.(733-735)ttC>ttT	p.F245F		NM_001001710.1	NP_001001710.1	Q6J272	F166A_HUMAN	family with sequence similarity 166, member A	245						nucleus (GO:0005634)				kidney(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(2)	15						GGCTCTTGTCGAATTCGTCCA	0.582													G|||	11	0.00219649	0.0008	0.0	5008	,	,		19622	0.0		0.0089	False		,,,				2504	0.001				p.F245F		Atlas-SNP	.											.	FAM166A	44	.	0			c.C735T						PASS	.	G		6,4392	12.9+/-30.5	0,6,2193	139	119	126		735	-3.4	0.8	9	dbSNP_129	126	94,8504	51.9+/-112.3	1,92,4206	no	coding-synonymous	FAM166A	NM_001001710.1		1,98,6399	AA,AG,GG		1.0933,0.1364,0.7695		245/318	140139106	100,12896	2199	4299	6498	SO:0001819	synonymous_variant	401565	exon5			CTTGTCGAATTCG	BC132916	CCDS35186.1	9q34.3	2008-08-08			ENSG00000188163	ENSG00000188163			33818	protein-coding gene	gene with protein product							Standard	XR_245332		Approved		uc004cmi.1	Q6J272	OTTHUMG00000159545	ENST00000344774.4:c.735C>T	9.37:g.140139106G>A		184	0	0		223	98	0.439462	NM_001001710	A6NND9|Q8N830	Silent	SNP	ENST00000344774.4	37	CCDS35186.1																																																																																			G|0.994;A|0.006	0.006	strong		0.582	FAM166A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356125.1	NM_001001710		A	140139106	G	A	140139106	2	1	26	1	0	0	0	0	0	0	0	1	5486	1049	37	1		1	FAM166A	9	140139106	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	720846	140139106	1074325	329	10092											
PITRM1	10531	hgsc.bcm.edu	37	chr10	3180288	3180288	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtccgaggatggccaggcCgtgtgtgctcttcccagtgc	4	9	16	12	2	1	0	0	0	1	0	3	2	3	1	4	4	2	1	4	4	0	1	rs35779348	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:3180288C>T	ENST00000224949.4	-	27	3083	c.3049G>A	c.(3049-3051)Ggc>Agc	p.G1017S	PITRM1_ENST00000380994.1_Missense_Mutation_p.G575S|PITRM1_ENST00000451104.2_Missense_Mutation_p.G919S|PITRM1_ENST00000464395.1_5'UTR|PITRM1_ENST00000380989.2_Missense_Mutation_p.G1018S			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	1017					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						ATGGCCAGGCCGTGTGTGCTC	0.612													C|||	45	0.00898562	0.0008	0.0231	5008	,	,		17586	0.0		0.0268	False		,,,				2504	0.001				p.G1018S		Atlas-SNP	.											.	PITRM1	109	.	0			c.G3052A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY	26,4230		1,24,2103	48	53	52		3052,2755,3049	3	0	10	dbSNP_126	52	266,8210		6,254,3978	yes	missense,missense,missense	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	56,56,56	7,278,6081	TT,TC,CC		3.1383,0.6109,2.2934	possibly-damaging,possibly-damaging,possibly-damaging	1018/1039,919/940,1017/1038	3180288	292,12440	2128	4238	6366	SO:0001583	missense	10531	exon27			CCAGGCCGTGTGT	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.3049G>A	10.37:g.3180288C>T	ENSP00000224949:p.Gly1017Ser	97	0	0		128	65	0.507812	NM_001242307	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	37	CCDS59208.1	29	0.013278388278388278	0	0.0	8	0.022099447513812154	0	0.0	21	0.027704485488126648	c	15.07	2.724507	0.48728	0.006109	0.031383	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000380994;ENST00000451104	T;T;T;T	0.55760	0.5;0.5;0.5;0.5	5.83	3.02	0.34903	Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.146245	0.64402	N	0.000007	T	0.29223	0.0727	M	0.61703	1.905	0.49798	D	0.99982	P;D;P	0.62365	0.898;0.991;0.87	B;P;B	0.50049	0.312;0.629;0.355	T	0.25187	-1.0139	10	0.23891	T	0.37	-27.4489	9.9005	0.41344	0.0:0.7891:0.0:0.2109	rs35779348	919;1017;952	E7ES23;Q5JRX3;E9PDX7	.;PREP_HUMAN;.	S	1017;1010;1018;575;919	ENSP00000224949:G1017S;ENSP00000370377:G1018S;ENSP00000370382:G575S;ENSP00000401201:G919S	ENSP00000224949:G1017S	G	-	1	0	PITRM1	3170288	0.938000	0.31826	0.006000	0.13384	0.000000	0.00434	3.590000	0.53979	0.394000	0.25230	-1.075000	0.02238	GGC	T|0.016;G|0.000;C|0.984	0.016	strong		0.612	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2			T	3180288	C	T	3180288	3	4	26	1	0	0	0	0	1	0	0	0	11962	652	23	1	68	1	PITRM1	10	3180288	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10		3180288	132354459	330	10093											
AKR1C2	1646	hgsc.bcm.edu	37	chr10	5042789	5042789	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atagaggtcaacatagtccaAttgaagatttttcagtgacc	14	12	8	7	0	2	4	2	2	0	2	3	4	3	4	2	1	1	0	2	1	5	5	rs145355870	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:5042789A>G	ENST00000380753.4	-	3	509	c.322T>C	c.(322-324)Ttg>Ctg	p.L108L	AKR1C2_ENST00000407674.1_Silent_p.L108L|AKR1C2_ENST00000421196.3_Silent_p.L108L|AKR1C2_ENST00000455190.1_Silent_p.L108L	NM_205845.2	NP_995317.1	P52895	AK1C2_HUMAN	aldo-keto reductase family 1, member C2	108					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)	ACATAGTCCAATTGAAGATTT	0.398													A|||	15	0.00299521	0.0015	0.0115	5008	,	,		18331	0.003		0.002	False		,,,				2504	0.0				p.L108L		Atlas-SNP	.											.	AKR1C2	68	.	0			c.T322C						PASS	.	A	,,	7,4399	12.9+/-30.5	0,7,2196	128	118	122		322,322,322	-3	0	10	dbSNP_134	122	30,8570	21.0+/-64.5	0,30,4270	no	coding-synonymous,coding-synonymous,coding-synonymous	AKR1C2	NM_001135241.1,NM_001354.4,NM_205845.1	,,	0,37,6466	GG,GA,AA		0.3488,0.1589,0.2845	,,	108/140,108/324,108/324	5042789	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	1646	exon5			AGTCCAATTGAAG	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.322T>C	10.37:g.5042789A>G		227	1	0.00440529		256	130	0.507812	NM_001354	A8K2N9|B4DKR9|Q14133|Q5SR16|Q7M4N1|Q96A71	Silent	SNP	ENST00000380753.4	37	CCDS7062.1																																																																																			A|0.997;G|0.003	0.003	strong		0.398	AKR1C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046531.1	NM_001354		G	5042789	A	G	5042789	2	3	26	1	0	0	0	0	0	0	0	1	470	98	4	3		3	AKR1C2	10	5042789	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	1862501	5042789	130491958	331	10094											
AKR1C3	8644	hgsc.bcm.edu	37	chr10	5141619	5141619	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctcaacaagccaggactcaAgtacaagcctgtctgcaacc	13	6	7	15	0	3	0	2	0	1	0	3	1	3	1	4	1	6	2	4	1	6	1	rs61730879	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:5141619A>G	ENST00000380554.3	+	5	1200	c.548A>G	c.(547-549)aAg>aGg	p.K183R	AKR1C3_ENST00000439082.2_Missense_Mutation_p.K64R|AKR1C3_ENST00000605149.1_Missense_Mutation_p.K160R	NM_001253908.1|NM_003739.5	NP_001240837.1|NP_003730.4	P42330	AK1C3_HUMAN	aldo-keto reductase family 1, member C3	183					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)	CCAGGACTCAAGTACAAGCCT	0.512													A|||	7	0.00139776	0.0008	0.0029	5008	,	,		17607	0.0		0.004	False		,,,				2504	0.0				p.K183R		Atlas-SNP	.											.	AKR1C3	21	.	0			c.A548G						PASS	.						145	130	135					10																	5141619		2203	4300	6503	SO:0001583	missense	8644	exon5			GACTCAAGTACAA	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.548A>G	10.37:g.5141619A>G	ENSP00000369927:p.Lys183Arg	135	0	0		123	65	0.528455	NM_001253908	A8K2V0|B4DL37|Q5T2L1|Q96DJ1|Q96KI8|Q99530|Q9UCX1|Q9UII3|Q9UKL9	Missense_Mutation	SNP	ENST00000380554.3	37	CCDS7063.1	5	0.0022893772893772895	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	A	14.92	2.680782	0.47886	.	.	ENSG00000196139	ENST00000439082;ENST00000380554	T;T	0.25414	1.8;1.8	2.67	2.67	0.31697	NADP-dependent oxidoreductase domain (3);	0.000000	0.64402	D	0.000003	T	0.23846	0.0577	L	0.36672	1.1	0.42266	D	0.992032	B;B;B	0.22480	0.002;0.07;0.07	B;B;B	0.37239	0.018;0.244;0.244	T	0.08513	-1.0718	10	0.44086	T	0.13	.	8.7963	0.34881	1.0:0.0:0.0:0.0	.	64;183;183	B4DL37;P42330;Q2XPP3	.;AK1C3_HUMAN;.	R	64;183	ENSP00000401327:K64R;ENSP00000369927:K183R	ENSP00000369927:K183R	K	+	2	0	AKR1C3	5131619	1.000000	0.71417	0.997000	0.53966	0.929000	0.56500	5.877000	0.69675	0.992000	0.38840	0.402000	0.26972	AAG	A|0.997;G|0.001;T|0.002	0.001	strong		0.512	AKR1C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046533.2	NM_003739		G	5141619	A	G	5141619	3	3	26	1	0	0	0	0	1	0	0	0	471	72	3	3	566	3	AKR1C3	10	5141619	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	98830	5141619	130393128	332	10095											
KIAA1462	57608	hgsc.bcm.edu	37	chr10	30318345	30318345	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tttaatggaatgggaatttcCgtgcaactcaggctctcggg	9	12	12	8	2	2	0	1	0	1	0	4	2	3	2	1	4	2	2	1	4	4	3	rs11813359	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:30318345C>T	ENST00000375377.1	-	3	833	c.732G>A	c.(730-732)acG>acA	p.T244T		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	244					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						TGGGAATTTCCGTGCAACTCA	0.453													C|||	20	0.00399361	0.0023	0.0029	5008	,	,		21995	0.0		0.0139	False		,,,				2504	0.001				p.T244T		Atlas-SNP	.											KIAA1462,NS,carcinoma,-2,1	KIAA1462	162	1	0			c.G732A						scavenged	.	C		12,3910		0,12,1949	136	139	138		732	0.8	0	10	dbSNP_120	138	113,8169		0,113,4028	no	coding-synonymous	KIAA1462	NM_020848.2		0,125,5977	TT,TC,CC		1.3644,0.306,1.0243		244/1360	30318345	125,12079	1961	4141	6102	SO:0001819	synonymous_variant	57608	exon3			AATTTCCGTGCAA	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.732G>A	10.37:g.30318345C>T		148	1	0.00675676		175	75	0.428571	NM_020848	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Silent	SNP	ENST00000375377.1	37	CCDS41500.1																																																																																			C|0.994;T|0.006	0.006	strong		0.453	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848		T	30318345	C	T	30318345	2	4	26	1	0	0	0	0	0	0	0	1	8243	639	23	1		1	KIAA1462	10	30318345	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	25176726	30318345	105216402	333	10096											
CHAT	1103	hgsc.bcm.edu	37	chr10	50830171	50830171	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccagcctcatctctggtgtaCtcagctacaaggccctgctg	7	10	9	15	0	3	0	2	0	1	0	4	0	3	0	3	2	5	3	3	2	3	2	rs8178990	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:50830171C>T	ENST00000337653.2	+	5	880	c.727C>T	c.(727-729)Ctc>Ttc	p.L243F	CHAT_ENST00000455728.2_Missense_Mutation_p.L125F|CHAT_ENST00000339797.1_Missense_Mutation_p.L125F|CHAT_ENST00000460699.1_3'UTR|CHAT_ENST00000351556.3_Missense_Mutation_p.L125F|CHAT_ENST00000395559.2_Missense_Mutation_p.L125F|CHAT_ENST00000395562.2_Missense_Mutation_p.L161F	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	243			L -> F (in dbSNP:rs8178990).		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)	CTCTGGTGTACTCAGCTACAA	0.622													C|||	126	0.0251597	0.0015	0.0202	5008	,	,		15265	0.0		0.0944	False		,,,				2504	0.0153				p.L243F		Atlas-SNP	.											.	CHAT	162	.	0			c.C727T						PASS	.	C	PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU	49,4357	50.2+/-85.5	1,47,2155	216	167	184		373,481,373,727,373,373,373	4.7	1	10	dbSNP_117	184	546,8054	150.3+/-205.2	29,488,3783	yes	missense,missense,missense,missense,missense,missense,missense	CHAT	NM_001142929.1,NM_001142933.1,NM_001142934.1,NM_020549.4,NM_020984.3,NM_020985.3,NM_020986.3	22,22,22,22,22,22,22	30,535,5938	TT,TC,CC		6.3488,1.1121,4.5748	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	125/631,161/667,125/631,243/749,125/631,125/631,125/631	50830171	595,12411	2203	4300	6503	SO:0001583	missense	1103	exon5			GGTGTACTCAGCT	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.727C>T	10.37:g.50830171C>T	ENSP00000337103:p.Leu243Phe	92	0	0		80	46	0.575	NM_020549	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Missense_Mutation	SNP	ENST00000337653.2	37	CCDS7232.1	80	0.03663003663003663	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	72	0.09498680738786279	C	21.3	4.121133	0.77436	0.011121	0.063488	ENSG00000070748	ENST00000339797;ENST00000351556;ENST00000395559;ENST00000337653;ENST00000395562;ENST00000455728	D;D;D;D;D;D	0.90955	-2.76;-2.76;-2.76;-2.76;-2.76;-2.76	4.74	4.74	0.60224	.	0.245457	0.35096	N	0.003446	T	0.58104	0.2099	M	0.84156	2.68	0.43688	D	0.996133	P;D	0.67145	0.858;0.996	P;D	0.74348	0.637;0.983	T	0.76542	-0.2921	10	0.87932	D	0	-13.929	17.7116	0.88323	0.0:1.0:0.0:0.0	rs8178990;rs61678759;rs8178990	125;243	F8W8I2;P28329	.;CLAT_HUMAN	F	125;125;125;243;161;125	ENSP00000343486:L125F;ENSP00000345878:L125F;ENSP00000378926:L125F;ENSP00000337103:L243F;ENSP00000378929:L161F;ENSP00000390521:L125F	ENSP00000337103:L243F	L	+	1	0	CHAT	50500177	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.979000	0.56888	2.161000	0.67846	0.561000	0.74099	CTC	C|0.955;T|0.045	0.045	strong		0.622	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549		T	50830171	C	T	50830171	3	4	26	1	0	0	0	0	1	0	0	0	3315	565	20	2	789	2	CHAT	10	50830171	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	20511826	50830171	84704576	334	10097											
OGDHL	55753	hgsc.bcm.edu	37	chr10	50953406	50953406	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccacctcaaactcctgcaggGtgactgtgccctcggcaatc	8	8	9	16	1	1	1	1	1	0	0	4	1	2	1	4	2	3	2	4	2	2	0	rs145957744		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:50953406G>T	ENST00000374103.4	-	12	1698	c.1613C>A	c.(1612-1614)aCc>aAc	p.T538N	OGDHL_ENST00000419399.1_Missense_Mutation_p.T481N|OGDHL_ENST00000432695.1_Missense_Mutation_p.T329N	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	538					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						CTCCTGCAGGGTGACTGTGCC	0.592																																					p.T538N		Atlas-SNP	.											.	OGDHL	149	.	0			c.C1613A						PASS	.						72	64	67					10																	50953406		2203	4300	6503	SO:0001583	missense	55753	exon12			TGCAGGGTGACTG	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.1613C>A	10.37:g.50953406G>T	ENSP00000363216:p.Thr538Asn	62	0	0		88	49	0.556818	NM_018245	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Missense_Mutation	SNP	ENST00000374103.4	37	CCDS7234.1	.	.	.	.	.	.	.	.	.	.	G	14.93	2.682876	0.47991	.	.	ENSG00000197444	ENST00000374103;ENST00000419399;ENST00000432695	T;T;D	0.95690	2.45;2.45;-3.78	5.4	5.4	0.78164	Dehydrogenase, E1 component (1);	0.051680	0.85682	D	0.000000	D	0.93903	0.8049	L	0.52011	1.625	0.58432	D	0.999999	B;B;B	0.12013	0.004;0.001;0.005	B;B;B	0.20577	0.012;0.007;0.03	D	0.90070	0.4162	10	0.37606	T	0.19	.	19.5511	0.95322	0.0:0.0:1.0:0.0	.	481;329;538	Q9ULD0-2;Q9ULD0-3;Q9ULD0	.;.;OGDHL_HUMAN	N	538;481;329	ENSP00000363216:T538N;ENSP00000401356:T481N;ENSP00000390240:T329N	ENSP00000363216:T538N	T	-	2	0	OGDHL	50623412	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	4.517000	0.60503	2.704000	0.92352	0.650000	0.86243	ACC	G|1.000;T|0.000	0.000	weak		0.592	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245		T	50953406	G	T	50953406	3	4	26	1	0	0	0	0	1	0	0	0	10849	1261	44	4	1467	4	OGDHL	10	50953406	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	123235	50953406	84581341	335	10098											
DNAJC9	23234	hgsc.bcm.edu	37	chr10	75005896	75005902	+	Frame_Shift_Del	DEL	GTATGTC	GTATGTC	-																															agctcttcttccgaacctttGtatgtcttttcaaaagcttg																								rs36012375	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	GTATGTC	GTATGTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:75005896_75005902delGTATGTC	ENST00000372950.4	-	3	2026_2032	c.354_360delGACATAC	c.(352-360)aagacatacfs	p.KTY118fs	MRPS16_ENST00000479005.1_5'Flank|DNAJC9-AS1_ENST00000513954.1_RNA|DNAJC9_ENST00000453189.2_5'Flank|DNAJC9-AS1_ENST00000440197.2_RNA	NM_015190.3	NP_056005.1	Q8WXX5	DNJC9_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 9	118					social behavior (GO:0035176)	nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|stomach(1)	6	Prostate(51;0.0119)					CCGAACCTTTGTATGTCTTTTCAAAAG	0.382																																					p.119_121del		Pindel,Atlas-Indel	.											.	DNAJC9	19	.	0			c.355_361del						PASS	.																																			SO:0001589	frameshift_variant	23234	exon3			.	AF327347	CCDS7322.1	10q22.3	2011-09-02			ENSG00000213551	ENSG00000213551		"Heat shock proteins / DNAJ (HSP40)"	19123	protein-coding gene	gene with protein product		611206					Standard	NM_015190		Approved	JDD1, SB73	uc001jtr.3	Q8WXX5	OTTHUMG00000018461	ENST00000372950.4:c.354_360delGACATAC	10.37:g.75005896_75005902delGTATGTC	ENSP00000362041:p.Lys118fs	168	0	.		118	20	0.169	NM_015190	B2RMW6	Frame_Shift_Del	DEL	ENST00000372950.4	37	CCDS7322.1																																																																																			.	.	none		0.382	DNAJC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048643.1	NM_015190		-	75005902	GTATGTC	-	75005896	7	5	26	1	0	1	0	1	0	0	0	0	4658	1372	48	0	434	0	DNAJC9	10	75005896	Frame_Shift_Del	DEL	GTATGTC	TCGA-G8-6907-01A-11D-2210-10	24052490	75005896	60528851	336	10099											
TTC18	118491	hgsc.bcm.edu	37	chr10	75053071	75053071	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gttctcattgacttctgcttCaaatgcaaagagttgaagct	11	14	8	8	0	3	3	2	2	2	1	4	3	3	3	0	0	3	5	0	0	3	5			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:75053071C>T	ENST00000310715.3	-	17	2050	c.1930G>A	c.(1930-1932)Gaa>Aaa	p.E644K	TTC18_ENST00000394865.1_Missense_Mutation_p.E644K|TTC18_ENST00000340329.3_Intron|TTC18_ENST00000493787.1_5'UTR|TTC18_ENST00000355577.3_Missense_Mutation_p.E113K|TTC18_ENST00000401621.2_Missense_Mutation_p.E644K	NM_145170.3	NP_660153.3	Q5T0N1	TTC18_HUMAN		644						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)					ACTTCTGCTTCAAATGCAAAG	0.378																																					p.E644K		Atlas-SNP	.											.	TTC18	106	.	0			c.G1930A						PASS	.						121	106	111					10																	75053071		2203	4300	6503	SO:0001583	missense	118491	exon17			CTGCTTCAAATGC																												ENST00000310715.3:c.1930G>A	10.37:g.75053071C>T	ENSP00000310829:p.Glu644Lys	104	0	0		113	5	0.0442478	NM_145170	C9JIZ9|Q5T0M4|Q5T0M9|Q5T0N0|Q69YH9|Q8IYZ8|Q8N7D5|Q8NI30|Q8NI31	Missense_Mutation	SNP	ENST00000310715.3	37	CCDS7324.3	.	.	.	.	.	.	.	.	.	.	C	33	5.207975	0.95033	.	.	ENSG00000156042	ENST00000310715;ENST00000401621;ENST00000355577;ENST00000433268;ENST00000394865	D;D;D;D	0.93488	-3.23;-3.23;-3.23;-3.23	5.63	5.63	0.86233	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	D	0.96191	0.8758	M	0.65498	2.005	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96140	0.9099	10	0.59425	D	0.04	-0.2715	17.1754	0.86840	0.0:1.0:0.0:0.0	.	644	Q5T0N1	TTC18_HUMAN	K	644;644;644;51;644	ENSP00000310829:E644K;ENSP00000384479:E644K;ENSP00000409527:E51K;ENSP00000378334:E644K	ENSP00000310829:E644K	E	-	1	0	TTC18	74723077	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.093000	0.71422	2.632000	0.89209	0.557000	0.71058	GAA	.	.	none		0.378	TTC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				T	75053071	C	T	75053071	3	4	26	1	0	0	0	0	1	0	0	0	16700	835	29	2	1483	2	TTC18	10	75053071	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	47175	75053071	60481676	337	10100											
TSPAN14	81619	hgsc.bcm.edu	37	chr10	82269158	82269158	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaccggttccgggagttcttCgagagcaacatcaagtccta	10	9	11	11	3	2	1	1	0	1	1	5	4	4	2	3	2	2	3	3	2	3	4	rs145582053		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:82269158C>T	ENST00000429989.3	+	5	604	c.381C>T	c.(379-381)ttC>ttT	p.F127F	TSPAN14_ENST00000372158.1_Silent_p.F127F|TSPAN14_ENST00000372156.1_Silent_p.F127F|TSPAN14_ENST00000341863.6_Intron|TSPAN14_ENST00000372164.3_Silent_p.F110F|TSPAN14_ENST00000481124.1_Intron	NM_030927.2	NP_112189.2	Q8NG11	TSN14_HUMAN	tetraspanin 14	127					establishment of protein localization to plasma membrane (GO:0090002)|positive regulation of Notch signaling pathway (GO:0045747)|protein maturation (GO:0051604)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	enzyme binding (GO:0019899)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7			Colorectal(32;0.229)			GGGAGTTCTTCGAGAGCAACA	0.582													C|||	1	0.000199681	0.0	0.0	5008	,	,		19378	0.0		0.001	False		,,,				2504	0.0				p.F127F		Atlas-SNP	.											.	TSPAN14	29	.	0			c.C381T						PASS	.	C	,	3,4403	6.2+/-15.9	0,3,2200	109	93	99		,381	-2.1	1	10	dbSNP_134	99	7,8593	5.7+/-21.5	0,7,4293	no	intron,coding-synonymous	TSPAN14	NM_001128309.1,NM_030927.2	,	0,10,6493	TT,TC,CC		0.0814,0.0681,0.0769	,	,127/271	82269158	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	81619	exon5			GTTCTTCGAGAGC	AF311903	CCDS7369.1, CCDS44448.1	10q23.1	2013-02-14	2005-03-21	2005-03-21	ENSG00000108219	ENSG00000108219		"Tetraspanins"	23303	protein-coding gene	gene with protein product			"transmembrane 4 superfamily member 14"	TM4SF14		11230166	Standard	NM_030927		Approved	DC-TM4F2, MGC11352	uc001kcj.4	Q8NG11	OTTHUMG00000018615	ENST00000429989.3:c.381C>T	10.37:g.82269158C>T		145	0	0		133	70	0.526316	NM_030927	A6NHE1|B4DHY6|D3DWD7|D3DWD8|Q567U7|Q9BU34|Q9H0U1	Silent	SNP	ENST00000429989.3	37	CCDS7369.1																																																																																			C|0.999;T|0.001	0.001	strong		0.582	TSPAN14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049081.2	NM_030927		T	82269158	C	T	82269158	2	4	26	1	0	0	0	0	0	0	0	1	16653	883	31	1		1	TSPAN14	10	82269158	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	7216087	82269158	53265589	338	10101											
SH2D4B	387694	hgsc.bcm.edu	37	chr10	82348395	82348395	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgacattttagaggaaagagGaagaggagaggaagcgagga	17	5	17	2	1	0	5	0	1	0	4	0	11	0	9	0	5	1	0	0	5	4	2	rs140909202		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:82348395G>A	ENST00000470604.2	+	4	502	c.502G>A	c.(502-504)Gaa>Aaa	p.E168K	SH2D4B_ENST00000339284.2_Missense_Mutation_p.E169K|SH2D4B_ENST00000313455.4_Missense_Mutation_p.E120K			Q5SQS7	SH24B_HUMAN	SH2 domain containing 4B	168	Glu-rich.									endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(6)	13			Colorectal(32;0.229)			GAGGAAAGAGGAAGAGGAGAG	0.507													G|||	1	0.000199681	0.0	0.0	5008	,	,		20999	0.0		0.001	False		,,,				2504	0.0				p.E169K		Atlas-SNP	.											.	SH2D4B	44	.	0			c.G505A						PASS	.	G	LYS/GLU,LYS/GLU	3,4403	6.2+/-15.9	0,3,2200	78	73	75		358,505	4.2	1	10	dbSNP_134	75	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	SH2D4B	NM_001145719.1,NM_207372.2	56,56	0,7,6496	AA,AG,GG		0.0465,0.0681,0.0538	probably-damaging,probably-damaging	120/310,169/358	82348395	7,12999	2203	4300	6503	SO:0001583	missense	387694	exon4			AAAGAGGAAGAGG		CCDS7370.1, CCDS44449.1	10q23.1	2013-02-14			ENSG00000178217	ENSG00000178217		"SH2 domain containing"	31440	protein-coding gene	gene with protein product							Standard	NM_207372		Approved		uc001kck.1	Q5SQS7	OTTHUMG00000018617	ENST00000470604.2:c.502G>A	10.37:g.82348395G>A	ENSP00000417953:p.Glu168Lys	21	0	0		32	12	0.375	NM_207372	Q5SQS5|Q6ZVW9|Q6ZVZ3	Missense_Mutation	SNP	ENST00000470604.2	37		1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	17.52	3.409626	0.62399	6.81E-4	4.65E-4	ENSG00000178217	ENST00000339284;ENST00000372147;ENST00000470604;ENST00000313455	T;T;T	0.13657	2.57;2.57;2.57	5.16	4.24	0.50183	.	0.062098	0.64402	D	0.000007	T	0.32194	0.0821	L	0.58669	1.825	0.45930	D	0.998765	D;D	0.89917	0.998;1.0	D;D	0.85130	0.919;0.997	T	0.01829	-1.1265	10	0.45353	T	0.12	-11.6747	13.3192	0.60424	0.0:0.1602:0.8398:0.0	.	120;169	Q5SQS7-3;Q5SQS7-2	.;.	K	169;168;168;120	ENSP00000345295:E169K;ENSP00000417953:E168K;ENSP00000314242:E120K	ENSP00000314242:E120K	E	+	1	0	SH2D4B	82338375	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	4.750000	0.62162	1.143000	0.42306	0.655000	0.94253	GAA	G|0.999;A|0.001	0.001	strong		0.507	SH2D4B-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_351984		A	82348395	G	A	82348395	3	1	26	1	0	0	0	0	1	0	0	0	14251	1175	41	2	560	2	SH2D4B	10	82348395	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	79237	82348395	53186352	339	10102											
PTEN	5728	hgsc.bcm.edu	37	chr10	89690819	89690819	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttagttgtgctgaaagacatTatgacaccgccaaatttaat	14	13	7	7	1	0	3	0	2	0	1	0	3	0	3	2	0	1	2	2	0	5	5			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:89690819T>G	ENST00000371953.3	+	4	1583	c.226T>G	c.(226-228)Tat>Gat	p.Y76D		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	76	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.?(6)|p.R55fs*1(5)|p.Y76fs*1(4)|p.L70fs*7(4)|p.C71fs*6(2)|p.Y76del(2)|p.Y27fs*1(2)|p.H75_T78del(1)|p.F56fs*2(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)		TGAAAGACATTATGACACCGC	0.303		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.Y76D		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,malignant_melanoma,-2,3	PTEN	3652	3	64	Whole gene deletion(37)|Deletion - Frameshift(18)|Unknown(6)|Deletion - In frame(3)	central_nervous_system(17)|prostate(17)|breast(6)|skin(6)|lung(5)|haematopoietic_and_lymphoid_tissue(4)|endometrium(3)|ovary(3)|stomach(1)|soft_tissue(1)|urinary_tract(1)	c.T226G						PASS	.						80	75	77					10																	89690819		2202	4295	6497	SO:0001583	missense	5728	exon4	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.	AGACATTATGACA	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.226T>G	10.37:g.89690819T>G	ENSP00000361021:p.Tyr76Asp	162	0	0		72	60	0.833333	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.697959	0.88830	.	.	ENSG00000171862	ENST00000371953	D	0.98585	-5.01	5.62	5.62	0.85841	Phosphatase tensin type (1);	0.000000	0.85682	D	0.000000	D	0.99102	0.9691	M	0.89904	3.07	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99556	1.0967	9	.	.	.	-12.1246	16.1135	0.81278	0.0:0.0:0.0:1.0	.	76	P60484	PTEN_HUMAN	D	76	ENSP00000361021:Y76D	.	Y	+	1	0	PTEN	89680799	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.586000	0.82596	2.267000	0.75376	0.383000	0.25322	TAT	.	.	none		0.303	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		G	89690819	T	G	89690819	3	3	26	1	0	0	0	0	1	0	0	0	12750	1754	61	5	240	5	PTEN	10	89690819	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	7342424	89690819	45843928	340	10103											
FAS	355	hgsc.bcm.edu	37	chr10	90768672	90768672	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtggaaataaactgcaccCggacccagaataccaagtgc	16	5	9	11	1	0	1	0	0	0	1	0	3	0	3	3	2	4	1	3	2	7	2	rs121913078		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:90768672C>T	ENST00000355279.2	+	4	361	c.361C>T	c.(361-363)Cgg>Tgg	p.R121W	FAS_ENST00000355740.2_Missense_Mutation_p.R121W|FAS_ENST00000313771.5_3'UTR|FAS_ENST00000357339.2_Missense_Mutation_p.R121W|FAS_ENST00000352159.4_Missense_Mutation_p.R121W			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)	AAACTGCACCCGGACCCAGAA	0.393																																					p.R121W		Atlas-SNP	.											FAS,caecum,carcinoma,-1,1	FAS	47	1	0			c.C361T	GRCh37	CM971493	FAS	M	rs121913078	PASS	.						247	274	265					10																	90768672		2203	4300	6503	SO:0001583	missense	355	exon4			TGCACCCGGACCC	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.361C>T	10.37:g.90768672C>T	ENSP00000347426:p.Arg121Trp	115	0	0		71	60	0.84507	NM_152872	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000355279.2	37	CCDS7395.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.235818	0.39498	.	.	ENSG00000026103	ENST00000540197;ENST00000355740;ENST00000352159;ENST00000357339;ENST00000355279;ENST00000371875	D;D;D;D	0.91686	-2.89;-2.89;-2.89;-2.89	4.2	-2.74	0.05932	TNFR/CD27/30/40/95 cysteine-rich region (3);	2.803120	0.00964	N	0.003143	D	0.94879	0.8345	M	0.68593	2.085	0.09310	N	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77557	0.971;0.99;0.983	D	0.84814	0.0792	10	0.66056	D	0.02	0.1313	8.0344	0.30484	0.5264:0.2147:0.2589:0.0	.	121;121;121	P25445-6;Q5T9P3;P25445	.;.;TNR6_HUMAN	W	148;121;121;121;121;121	ENSP00000347979:R121W;ENSP00000345601:R121W;ENSP00000349896:R121W;ENSP00000347426:R121W	ENSP00000345601:R121W	R	+	1	2	FAS	90758652	0.000000	0.05858	0.000000	0.03702	0.502000	0.33828	-1.179000	0.03090	-0.519000	0.06444	0.650000	0.86243	CGG	.	.	weak		0.393	FAS-011	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000049280.2			T	90768672	C	T	90768672	3	4	26	1	0	0	0	0	1	0	0	0	5689	643	23	1	375	1	FAS	10	90768672	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1077853	90768672	44766075	341	10104											
WNT8B	7479	hgsc.bcm.edu	37	chr10	102241724	102241724	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aatgtgggcttcggagaggcGatttccaagcagtttgtcga	9	11	14	7	3	0	1	0	0	0	1	3	4	1	1	1	3	1	3	1	3	2	3	rs76078607	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:102241724G>A	ENST00000343737.5	+	5	551	c.423G>A	c.(421-423)gcG>gcA	p.A141A		NM_003393.3	NP_003384.2	Q93098	WNT8B_HUMAN	wingless-type MMTV integration site family, member 8B	141					cell fate commitment (GO:0045165)|cellular response to retinoic acid (GO:0071300)|determination of dorsal identity (GO:0048263)|gastrulation (GO:0007369)|negative regulation of gene expression (GO:0010629)|nervous system development (GO:0007399)|neuron differentiation (GO:0030182)|positive regulation of gene expression (GO:0010628)|response to estradiol (GO:0032355)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|large_intestine(1)|ovary(1)|skin(1)	4		Colorectal(252;0.117)		Epithelial(162;1.87e-10)|all cancers(201;1.64e-08)		TCGGAGAGGCGATTTCCAAGC	0.607											OREG0020440	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	9	0.00179712	0.0	0.0	5008	,	,		17905	0.0		0.008	False		,,,				2504	0.001				p.A141A		Atlas-SNP	.											.	WNT8B	31	.	0			c.G423A						PASS	.	G		5,4401	9.9+/-24.2	0,5,2198	122	105	111		423	-10.4	0.9	10	dbSNP_132	111	32,8568	22.2+/-67.0	0,32,4268	no	coding-synonymous	WNT8B	NM_003393.3		0,37,6466	AA,AG,GG		0.3721,0.1135,0.2845		141/352	102241724	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	7479	exon5			AGAGGCGATTTCC	X91940	CCDS7494.1	10q24	2003-11-12			ENSG00000075290	ENSG00000075290		"Wingless-type MMTV integration sites"	12789	protein-coding gene	gene with protein product		601396				8661156	Standard	NM_003393		Approved		uc001krb.3	Q93098	OTTHUMG00000018912	ENST00000343737.5:c.423G>A	10.37:g.102241724G>A		92	0	0	1365	68	7	0.102941	NM_003393	O00771|Q5VX55|Q8WYK9	Silent	SNP	ENST00000343737.5	37	CCDS7494.1																																																																																			G|0.998;A|0.002	0.002	strong		0.607	WNT8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049867.1	NM_003393		A	102241724	G	A	102241724	2	1	26	1	0	0	0	0	0	0	0	1	17412	1045	37	1		1	WNT8B	10	102241724	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	11473052	102241724	33293023	342	10105											
AS3MT	57412	hgsc.bcm.edu	37	chr10	104638211	104638211	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aattgggttctgccctccacGtttggtcactgccaatctca	7	13	8	13	1	3	0	2	0	2	0	5	0	4	0	3	2	2	2	3	2	2	3			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:104638211G>A	ENST00000369880.3	+	8	763	c.686G>A	c.(685-687)cGt>cAt	p.R229H	C10orf32-ASMT_ENST00000299353.6_3'UTR	NM_020682.3	NP_065733.2	Q9HBK9	AS3MT_HUMAN	arsenite methyltransferase	229					arsonoacetate metabolic process (GO:0018872)|toxin metabolic process (GO:0009404)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	arsenite methyltransferase activity (GO:0030791)|methylarsonite methyltransferase activity (GO:0030792)			large_intestine(1)|lung(6)	7		Colorectal(252;0.122)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;5.87e-09)|all cancers(201;1.58e-07)|BRCA - Breast invasive adenocarcinoma(275;0.223)		TGCCCTCCACGTTTGGTCACT	0.403																																					p.R229H		Atlas-SNP	.											.	AS3MT	17	.	0			c.G686A						PASS	.						181	173	176					10																	104638211		1886	4134	6020	SO:0001583	missense	57412	exon8			CTCCACGTTTGGT	AF226730	CCDS41567.1	10q24.33	2014-05-09	2014-05-09		ENSG00000214435	ENSG00000214435	2.1.1.137		17452	protein-coding gene	gene with protein product		611806	"arsenic (+3 oxidation state) methyltransferase"			11790780	Standard	NM_020682		Approved	CYT19	uc001kwk.3	Q9HBK9	OTTHUMG00000018972	ENST00000369880.3:c.686G>A	10.37:g.104638211G>A	ENSP00000358896:p.Arg229His	83	0	0		40	38	0.95	NM_020682	A6NP79|Q0VDK3|Q0VDK4|Q5PZ02	Missense_Mutation	SNP	ENST00000369880.3	37	CCDS41567.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.376179	0.82682	.	.	ENSG00000214435	ENST00000369880	T	0.22945	1.93	5.48	3.61	0.41365	.	0.053428	0.64402	D	0.000001	T	0.41994	0.1183	M	0.74881	2.28	0.35290	D	0.782117	D;D;D	0.65815	0.965;0.995;0.995	P;P;P	0.56398	0.548;0.797;0.797	T	0.58042	-0.7706	9	0.40728	T	0.16	-15.267	11.7063	0.51599	0.1505:0.0:0.8495:0.0	.	229;229;229	Q0VDK3;Q9HBK9;Q0VDK4	.;AS3MT_HUMAN;.	H	229	ENSP00000358896:R229H	ENSP00000358896:R229H	R	+	2	0	AS3MT	104628201	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.613000	0.67688	1.314000	0.45095	-0.254000	0.11334	CGT	.	.	none		0.403	AS3MT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050107.1	NM_020682		A	104638211	G	A	104638211	3	1	26	1	0	0	0	0	1	0	0	0	1005	1145	40	1	716	1	AS3MT	10	104638211	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	2396487	104638211	30896536	343	10106											
CCDC147	159686	hgsc.bcm.edu	37	chr10	106214272	106214272	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cggatttcctctcaggtcaaCcaaaatgacgttctaacctg	11	11	7	12	2	3	1	2	1	2	0	5	2	4	2	3	2	2	1	3	2	4	3	rs74741614	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:106214272C>A	ENST00000369704.3	+	18	2737	c.2603C>A	c.(2602-2604)aCc>aAc	p.T868N		NM_001008723.1	NP_001008723.1	Q5T655	CC147_HUMAN		868						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)		CTCAGGTCAACCAAAATGACG	0.458													C|||	26	0.00519169	0.0068	0.0144	5008	,	,		18670	0.0		0.007	False		,,,				2504	0.0				p.T868N		Atlas-SNP	.											.	CCDC147	137	.	0			c.C2603A						PASS	.	C	ASN/THR	36,4370	40.0+/-72.8	2,32,2169	130	122	124		2603	-0.6	0	10	dbSNP_131	124	122,8478	62.8+/-124.8	0,122,4178	yes	missense	CCDC147	NM_001008723.1	65	2,154,6347	AA,AC,CC		1.4186,0.8171,1.2148	benign	868/873	106214272	158,12848	2203	4300	6503	SO:0001583	missense	159686	exon18			GGTCAACCAAAAT																												ENST00000369704.3:c.2603C>A	10.37:g.106214272C>A	ENSP00000358718:p.Thr868Asn	150	0	0		87	7	0.0804598	NM_001008723	D3DRA6|Q8NA27	Missense_Mutation	SNP	ENST00000369704.3	37	CCDS31282.1	18	0.008241758241758242	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	5	0.006596306068601583	C	1.808	-0.475500	0.04414	0.008171	0.014186	ENSG00000120051	ENST00000369704	T	0.31769	1.48	5.47	-0.581	0.11713	.	1.145310	0.06302	N	0.701091	T	0.05090	0.0136	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.24225	-1.0166	10	0.41790	T	0.15	6.1358	1.4035	0.02276	0.2731:0.4062:0.1339:0.1869	.	868	Q5T655	CC147_HUMAN	N	868	ENSP00000358718:T868N	ENSP00000358718:T868N	T	+	2	0	CCDC147	106204262	0.083000	0.21467	0.000000	0.03702	0.006000	0.05464	0.730000	0.26043	0.002000	0.14630	0.650000	0.86243	ACC	C|0.989;A|0.011	0.011	strong		0.458	CCDC147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050216.1			A	106214272	C	A	106214272	3	1	26	1	0	0	0	0	1	0	0	0	2783	507	18	4	2673	4	CCDC147	10	106214272	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1576061	106214272	29320475	344	10107											
BAG3	9531	hgsc.bcm.edu	37	chr10	121429394	121429394	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctctgccaatggcccttcccGggagggctctaggctgccgc	4	8	13	16	2	2	0	0	0	2	0	3	1	3	1	4	4	2	2	4	4	2	2	rs35434411	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:121429394G>T	ENST00000369085.3	+	2	518	c.212G>T	c.(211-213)cGg>cTg	p.R71L		NM_004281.3	NP_004272.2	O95817	BAG3_HUMAN	BCL2-associated athanogene 3	71			R -> Q (in dbSNP:rs35434411). {ECO:0000269|PubMed:21459883}.|R -> W (in CMD1HH). {ECO:0000269|PubMed:21353195}.		brain development (GO:0007420)|cellular response to mechanical stimulus (GO:0071260)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|negative regulation of apoptotic process (GO:0043066)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|protein folding (GO:0006457)|protein stabilization (GO:0050821)|spinal cord development (GO:0021510)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|Z disc (GO:0030018)				endometrium(3)|kidney(1)|large_intestine(3)|liver(2)|lung(5)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	20		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00187)|BRCA - Breast invasive adenocarcinoma(275;0.148)		GGCCCTTCCCGGGAGGGCTCT	0.577																																					p.R71L		Atlas-SNP	.											.	BAG3	42	.	0			c.G212T						PASS	.						83	87	85					10																	121429394		2203	4300	6503	SO:0001583	missense	9531	exon2			CTTCCCGGGAGGG	AF095193	CCDS7615.1	10q25.2-q26.2	2014-09-17			ENSG00000151929	ENSG00000151929			939	protein-coding gene	gene with protein product		603883				9873016, 18094623	Standard	XM_005270287		Approved		uc001lem.3	O95817	OTTHUMG00000019155	ENST00000369085.3:c.212G>T	10.37:g.121429394G>T	ENSP00000358081:p.Arg71Leu	80	0	0		115	66	0.573913	NM_004281	A8K5L8|Q3B763|Q9NT20|Q9P120	Missense_Mutation	SNP	ENST00000369085.3	37	CCDS7615.1	.	.	.	.	.	.	.	.	.	.	G	15.89	2.967365	0.53507	.	.	ENSG00000151929	ENST00000369085;ENST00000450186	T;T	0.75367	-0.93;-0.91	5.4	3.12	0.35913	.	0.417057	0.28219	N	0.016148	T	0.65101	0.2659	L	0.57536	1.79	0.09310	N	1	P;P	0.37276	0.589;0.589	B;B	0.29524	0.103;0.103	T	0.61657	-0.7018	10	0.59425	D	0.04	-12.1508	10.3289	0.43809	0.3064:0.0:0.6936:0.0	.	71;71	O95817;Q53GY1	BAG3_HUMAN;.	L	71;13	ENSP00000358081:R71L;ENSP00000410036:R13L	ENSP00000358081:R71L	R	+	2	0	BAG3	121419384	0.073000	0.21202	0.995000	0.50966	0.981000	0.71138	1.137000	0.31479	1.217000	0.43442	0.561000	0.74099	CGG	G|0.979;A|0.021	.	alt		0.577	BAG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050662.1	NM_004281		T	121429394	G	T	121429394	3	4	26	1	0	0	0	0	1	0	0	0	1288	1116	39	4	218	4	BAG3	10	121429394	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	15215122	121429394	14105353	345	10108											
WDR11	55717	hgsc.bcm.edu	37	chr10	122610983	122610983	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tcggcgcgcaccctcacgggGgccctcaacgcccacaacaa	9	3	10	19	5	2	0	2	0	0	0	3	0	2	0	3	3	2	1	3	3	3	0	rs35692153	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:122610983G>T	ENST00000263461.6	+	1	297	c.51G>T	c.(49-51)ggG>ggT	p.G17G	WDR11-AS1_ENST00000598981.1_RNA	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						CCCTCACGGGGGCCCTCAACG	0.682													G|||	290	0.0579073	0.208	0.0202	5008	,	,		14726	0.0		0.001	False		,,,				2504	0.0				p.G17G		Atlas-SNP	.											.	WDR11	95	.	0			c.G51T						PASS	.	G		707,3685		54,599,1543	18	20	19		51	0.9	1	10	dbSNP_126	19	4,8590		0,4,4293	no	coding-synonymous	WDR11	NM_018117.11		54,603,5836	TT,TG,GG		0.0465,16.0974,5.4751		17/1225	122610983	711,12275	2196	4297	6493	SO:0001819	synonymous_variant	55717	exon1			CACGGGGGCCCTC	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.51G>T	10.37:g.122610983G>T		101	0	0		114	44	0.385965	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	37	CCDS7619.1																																																																																			G|0.952;T|0.048	0.048	strong		0.682	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2			T	122610983	G	T	122610983	2	4	26	1	0	0	0	0	0	0	0	1	17288	1219	43	4		4	WDR11	10	122610983	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1181589	122610983	12923764	346	10109											
WDR11	55717	hgsc.bcm.edu	37	chr10	122668181	122668181	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagcagctggcaaagacttaTtgaatgagcttgagtccccc	11	9	11	10	0	0	4	0	3	0	1	1	5	1	4	2	1	3	4	2	1	3	3	rs34567350	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:122668181T>C	ENST00000263461.6	+	29	3877	c.3631T>C	c.(3631-3633)Ttg>Ctg	p.L1211L	WDR11_ENST00000604509.1_3'UTR	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0	Bromo 1. {ECO:0000255|PROSITE- ProRule:PRU00035}.				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						CAAAGACTTATTGAATGAGCT	0.488													t|||	57	0.0113818	0.0408	0.0043	5008	,	,		18032	0.0		0.0	False		,,,				2504	0.0				p.L1211L		Atlas-SNP	.											.	WDR11	95	.	0			c.T3631C						PASS	.	C		143,4263	101.2+/-139.8	3,137,2063	99	101	100		3631	-7	0	10	dbSNP_126	100	0,8600		0,0,4300	no	coding-synonymous	WDR11	NM_018117.11		3,137,6363	CC,CT,TT		0.0,3.2456,1.0995		1211/1225	122668181	143,12863	2203	4300	6503	SO:0001819	synonymous_variant	55717	exon29			GACTTATTGAATG	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.3631T>C	10.37:g.122668181T>C		141	0	0		153	73	0.477124	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	37	CCDS7619.1																																																																																			T|0.990;C|0.010	0.010	strong		0.488	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2			C	122668181	T	C	122668181	2	2	26	1	0	0	0	0	0	0	0	1	17288	1490	52	3		3	WDR11	10	122668181	Silent	SNP	T	TCGA-G8-6907-01A-11D-2210-10	57198	122668181	12866566	347	10110											
TUBGCP2	10844	hgsc.bcm.edu	37	chr10	135106550	135106550	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcgggcacgcaccgagggaGgccaggatgtccatggtgcg	7	4	19	11	4	0	0	0	0	0	0	1	3	1	2	3	6	1	2	3	6	0	0	rs141042122	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:135106550G>A	ENST00000252936.3	-	6	1056	c.1017C>T	c.(1015-1017)gcC>gcT	p.A339A	TUBGCP2_ENST00000417178.2_Silent_p.A209A|TUBGCP2_ENST00000368562.1_5'Flank|RP11-122K13.12_ENST00000424450.1_RNA|TUBGCP2_ENST00000543663.1_Silent_p.A367A|TUBGCP2_ENST00000368563.2_Silent_p.A339A			Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2	339					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)		CACCGAGGGAGGCCAGGATGT	0.652													G|||	5	0.000998403	0.0	0.0014	5008	,	,		17939	0.0		0.002	False		,,,				2504	0.002				p.A367A		Atlas-SNP	.											.	TUBGCP2	79	.	0			c.C1101T						PASS	.	G		4,4402	8.1+/-20.4	0,4,2199	45	45	45		1017	1.6	1	10	dbSNP_134	45	32,8568	21.6+/-65.8	0,32,4268	no	coding-synonymous	TUBGCP2	NM_006659.2		0,36,6467	AA,AG,GG		0.3721,0.0908,0.2768		339/903	135106550	36,12970	2203	4300	6503	SO:0001819	synonymous_variant	10844	exon8			GAGGGAGGCCAGG	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.1017C>T	10.37:g.135106550G>A		98	0	0		130	67	0.515385	NM_001256617	B4DM18|B7ZKL8|F5H4E0|F5H4L0|O43632|Q5VWX7	Silent	SNP	ENST00000252936.3	37	CCDS7676.1																																																																																			G|0.997;A|0.003	0.003	strong		0.652	TUBGCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051148.1			A	135106550	G	A	135106550	2	1	26	1	0	0	0	0	0	0	0	1	16781	987	35	2		2	TUBGCP2	10	135106550	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	12438369	135106550	428197	348	10111											
RIC8A	60626	hgsc.bcm.edu	37	chr11	210660	210660	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccgcacagaggagttccaCgggtgagaatggggcttttt	9	9	15	8	2	0	2	0	1	0	2	1	5	1	3	2	4	0	3	2	4	1	3	rs34925440	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:210660C>G	ENST00000526104.1	+	4	2160	c.816C>G	c.(814-816)caC>caG	p.H272Q	RIC8A_ENST00000527696.1_Missense_Mutation_p.H266Q|RIC8A_ENST00000325207.5_Missense_Mutation_p.H272Q			Q9NPQ8	RIC8A_HUMAN	RIC8 guanine nucleotide exchange factor A	272					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)		AGGAGTTCCACGGGTGAGAAT	0.587													C|||	30	0.00599042	0.0	0.0144	5008	,	,		19929	0.0		0.0159	False		,,,				2504	0.0041				p.H272Q		Atlas-SNP	.											.	RIC8A	45	.	0			c.C816G						PASS	.	C	GLN/HIS	7,4399	11.4+/-27.6	0,7,2196	81	78	79		816	-5.6	0.9	11	dbSNP_126	79	144,8456	68.4+/-130.8	2,140,4158	yes	missense	RIC8A	NM_021932.4	24	2,147,6354	GG,GC,CC		1.6744,0.1589,1.161	probably-damaging	272/538	210660	151,12855	2203	4300	6503	SO:0001583	missense	60626	exon4			GTTCCACGGGTGA	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.816C>G	11.37:g.210660C>G	ENSP00000432008:p.His272Gln	125	0	0		125	70	0.56	NM_021932	Q0P508|Q2T9J1|Q7Z352|Q96EZ1|Q96SZ2|Q9H064|Q9H5H3|Q9H9E7	Missense_Mutation	SNP	ENST00000526104.1	37		21|21	0.009615384615384616|0.009615384615384616	0|0	0.0|0.0	6|6	0.016574585635359115|0.016574585635359115	0|0	0.0|0.0	15|15	0.01978891820580475|0.01978891820580475	C|C	16.14|16.14	3.038516|3.038516	0.55003|0.55003	0.001589|0.001589	0.016744|0.016744	ENSG00000177963|ENSG00000177963	ENST00000526104;ENST00000325207;ENST00000527696|ENST00000527728	T;T;T|.	0.42513|.	0.97;0.97;0.97|.	4.47|4.47	-5.57|-5.57	0.02521|0.02521	Armadillo-type fold (1);|.	0.047726|.	0.85682|.	N|.	0.000000|.	T|T	0.35624|0.35624	0.0938|0.0938	L|L	0.51853|0.51853	1.615|1.615	0.54753|0.54753	D|D	0.999985|0.999985	P;D;D|.	0.89917|.	0.548;1.0;1.0|.	B;D;D|.	0.97110|.	0.283;1.0;1.0|.	T|T	0.50866|0.50866	-0.8777|-0.8777	10|5	0.26408|.	T|.	0.33|.	-18.6535|-18.6535	8.7496|8.7496	0.34607|0.34607	0.0:0.5309:0.099:0.3701|0.0:0.5309:0.099:0.3701	rs34925440|rs34925440	266;272;272|.	Q9NPQ8-2;Q9NPQ8;Q9NPQ8-3|.	.;RIC8A_HUMAN;.|.	Q|R	272;272;266|167	ENSP00000432008:H272Q;ENSP00000325941:H272Q;ENSP00000434833:H266Q|.	ENSP00000325941:H272Q|.	H|T	+|+	3|2	2|0	RIC8A|RIC8A	200660|200660	0.002000|0.002000	0.14202|0.14202	0.872000|0.872000	0.34217|0.34217	0.678000|0.678000	0.39670|0.39670	-1.433000|-1.433000	0.02428|0.02428	-1.247000|-1.247000	0.02507|0.02507	-1.201000|-1.201000	0.01664|0.01664	CAC|ACG	C|0.988;G|0.012	0.012	strong		0.587	RIC8A-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000384761.1	NM_021932		G	210660	C	G	210660	3	3	26	1	0	0	0	0	1	0	0	0	13370	535	19	4	830	4	RIC8A	11	210660	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10		210660	134795856	349	10112											
ATHL1	80162	hgsc.bcm.edu	37	chr11	290888	290888	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgcaggccaggggagctctGtatacggctcacgcacaggc	8	6	14	13	2	2	0	1	0	1	0	2	1	2	1	1	5	3	5	1	5	2	2	rs150075556	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:290888G>A	ENST00000409548.2	+	4	796	c.681G>A	c.(679-681)ctG>ctA	p.L227L	ATHL1_ENST00000409479.1_Silent_p.L227L|RP11-326C3.2_ENST00000525217.1_RNA|ATHL1_ENST00000409655.1_Silent_p.L50L|RP11-326C3.2_ENST00000534742.1_RNA|RP11-326C3.2_ENST00000533924.1_RNA	NM_025092.4	NP_079368.3	Q32M88	ATHL1_HUMAN	ATH1, acid trehalase-like 1 (yeast)	227					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)		GGGGAGCTCTGTATACGGCTC	0.682													G|||	26	0.00519169	0.0	0.0144	5008	,	,		19309	0.003		0.005	False		,,,				2504	0.0082				p.L227L		Atlas-SNP	.											.	ATHL1	88	.	0			c.G681A						PASS	.	G		5,4401		0,5,2198	45	49	48		681	2.8	0.6	11	dbSNP_134	48	26,8574	7.1+/-27.0	0,26,4274	no	coding-synonymous	ATHL1	NM_025092.4		0,31,6472	AA,AG,GG		0.3023,0.1135,0.2384		227/738	290888	31,12975	2203	4300	6503	SO:0001819	synonymous_variant	80162	exon4			AGCTCTGTATACG	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.681G>A	11.37:g.290888G>A		148	0	0		162	91	0.561728	NM_025092	Q658X8|Q8TEG9|Q9H635	Silent	SNP	ENST00000409548.2	37	CCDS31322.2																																																																																			G|0.995;A|0.005	0.005	strong		0.682	ATHL1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330164.3	NM_025092		A	290888	G	A	290888	2	1	26	1	0	0	0	0	0	0	0	1	1104	1364	48	2		2	ATHL1	11	290888	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	80228	290888	134715628	350	10113											
MUC2	4583	hgsc.bcm.edu	37	chr11	1103855	1103855	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccctgctccaccgtccccgtCaccacggaggtttcgtacgc	5	8	9	19	5	1	0	1	0	0	0	4	1	3	1	6	2	2	3	6	2	1	2			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1103855C>T	ENST00000441003.2	+	48	8181	c.8154C>T	c.(8152-8154)gtC>gtT	p.V2718V		NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	5080					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)	CCGTCCCCGTCACCACGGAGG	0.642																																					p.V2714V		Atlas-SNP	.											.	MUC2	614	.	0			c.C8142T						PASS	.						22	25	24					11																	1103855		2048	4156	6204	SO:0001819	synonymous_variant	4583	exon49			CCCCGTCACCACG	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.8154C>T	11.37:g.1103855C>T		97	0	0		106	62	0.584906	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.	.	none		0.642	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1103855	C	T	1103855	2	4	26	1	0	0	0	0	0	0	0	1	9984	813	29	2		2	MUC2	11	1103855	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	812967	1103855	133902661	351	10114											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1263648	1263648	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcgaccaggtcgggcaggtGctgacctgcagcctggagac	8	6	15	12	2	0	2	0	1	0	1	2	4	0	2	3	4	3	3	3	4	0	0	rs151293115	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1263648G>A	ENST00000529681.1	+	31	5596	c.5538G>A	c.(5536-5538)gtG>gtA	p.V1846V	MUC5B_ENST00000447027.1_Silent_p.V1849V|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1846	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)		TCGGGCAGGTGCTGACCTGCA	0.592													g|||	3	0.000599042	0.0	0.0	5008	,	,		19439	0.0		0.003	False		,,,				2504	0.0				p.V1846V		Atlas-SNP	.											.	MUC5B	473	.	0			c.G5538A						PASS	.			0,4334		0,0,2167	59	72	68		5538	-1.6	0	11	dbSNP_134	68	28,8486		0,28,4229	no	coding-synonymous	MUC5B	NM_002458.2		0,28,6396	AA,AG,GG		0.3289,0.0,0.2179		1846/5763	1263648	28,12820	2167	4257	6424	SO:0001819	synonymous_variant	727897	exon31			GCAGGTGCTGACC	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.5538G>A	11.37:g.1263648G>A		118	0	0		129	52	0.403101	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			G|0.999;A|0.001	0.001	strong		0.592	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		A	1263648	G	A	1263648	2	1	26	1	0	0	0	0	0	0	0	1	9988	1306	46	2		2	MUC5B	11	1263648	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	159793	1263648	133742868	352	10115											
BRSK2	9024	hgsc.bcm.edu	37	chr11	1411572	1411572	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcagtatgttgggccctacCggctggagaagacgctgggc	7	7	16	11	3	0	2	0	0	0	2	0	3	0	2	2	4	1	5	2	4	3	3			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1411572C>T	ENST00000528841.1	+	1	442	c.58C>T	c.(58-60)Cgg>Tgg	p.R20W	BRSK2_ENST00000308230.5_Missense_Mutation_p.R20W|BRSK2_ENST00000526678.1_Missense_Mutation_p.R20W|BRSK2_ENST00000531197.1_Missense_Mutation_p.R20W|BRSK2_ENST00000308219.9_Missense_Mutation_p.R20W			Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2	20	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		TGGGCCCTACCGGCTGGAGAA	0.796																																					p.R20W		Atlas-SNP	.											.	BRSK2	97	.	0			c.C58T						PASS	.						4	6	6					11																	1411572		1915	4006	5921	SO:0001583	missense	9024	exon1			CCCTACCGGCTGG	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.58C>T	11.37:g.1411572C>T	ENSP00000432000:p.Arg20Trp	23	0	0		23	13	0.565217	NM_001256629	B3KVE9|E9PLM7|O60843|O95099|Q5J5B4|Q6ZMQ4|Q8TB60	Missense_Mutation	SNP	ENST00000528841.1	37	CCDS58107.1	.	.	.	.	.	.	.	.	.	.	c	17.64	3.440051	0.63067	.	.	ENSG00000174672	ENST00000308219;ENST00000531197;ENST00000308230;ENST00000528841;ENST00000526678	T;T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26;-0.26	1.54	1.54	0.23209	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	0.78868	0.4351	M	0.86573	2.825	0.80722	D	1	D;D;D;D	0.67145	0.996;0.994;0.988;0.985	P;P;P;P	0.61722	0.721;0.606;0.893;0.828	T	0.79960	-0.1583	9	0.87932	D	0	.	8.6612	0.34093	0.0:1.0:0.0:0.0	.	20;20;20;20	Q8IWQ3-4;Q8IWQ3-3;Q8IWQ3;Q8IWQ3-2	.;.;BRSK2_HUMAN;.	W	20	ENSP00000310697:R20W;ENSP00000431152:R20W;ENSP00000310805:R20W;ENSP00000432000:R20W;ENSP00000433370:R20W	ENSP00000310697:R20W	R	+	1	2	BRSK2	1368148	0.920000	0.31207	1.000000	0.80357	0.993000	0.82548	0.856000	0.27818	0.855000	0.35359	0.409000	0.27619	CGG	.	.	none		0.796	BRSK2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393033.1	NM_003957		T	1411572	C	T	1411572	3	4	26	1	0	0	0	0	1	0	0	0	1526	643	23	1	60	1	BRSK2	11	1411572	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	147924	1411572	133594944	353	10116											
OR56A5	0	hgsc.bcm.edu	37	chr11	5989180	5989180	+	IGR	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tagacacagacacgttagtaCagatgcagttcttgatgatg	13	11	10	7	1	1	5	0	2	1	3	1	5	1	5	0	0	2	4	0	0	3	5	rs147979628	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5989180C>T								OR56A3 (19589 upstream) : OR52L1 (17941 downstream)																							CACGTTAGTACAGATGCAGTT	0.458													.|||	6	0.00119808	0.0	0.0	5008	,	,		23124	0.0		0.006	False		,,,				2504	0.0				p.C182Y		Atlas-SNP	.											.	.	.	.	0			c.G545A						PASS	.	C	TYR/CYS	0,1384		0,0,692	105	86	92		545	2.9	0.9	11	dbSNP_134	92	7,3175		0,7,1584	yes	missense	OR56A5	NM_001146033.1	194	0,7,2276	TT,TC,CC		0.22,0.0,0.1533	possibly-damaging	182/314	5989180	7,4559	692	1591	2283	SO:0001628	intergenic_variant	390084	exon1			TTAGTACAGATGC																													11.37:g.5989180C>T		87	0	0		125	58	0.464	NM_001146033		Missense_Mutation	SNP		37																																																																																				C|0.998;T|0.002	0.002	strong	0	0.458									T	5989180	C	T	5989180	1	4	26	0	1	0	0	0	0	0	0	0	11145	478	17	2		2	OR56A5	11	5989180	IGR	SNP	C	TCGA-G8-6907-01A-11D-2210-10	4577608	5989180	129017336	354	10117											
TRIM3	10612	hgsc.bcm.edu	37	chr11	6486914	6486914	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tctgggccagggctgtcctcCctctttgccatggcgcccac	3	10	11	17	1	2	0	0	0	2	0	4	0	4	0	5	3	1	1	5	3	0	1	rs144521953	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:6486914C>T	ENST00000525074.1	-	2	406	c.12G>A	c.(10-12)agG>agA	p.R4R	TRIM3_ENST00000359518.3_Silent_p.R4R|TRIM3_ENST00000345851.3_Silent_p.R4R|TRIM3_ENST00000536344.1_Intron|TRIM3_ENST00000537602.1_Silent_p.R4R	NM_001248006.1	NP_001234935.1	O75382	TRIM3_HUMAN	tripartite motif containing 3	4					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)		GGCTGTCCTCCCTCTTTGCCA	0.602																																					p.R4R	Melanoma(6;5 510 1540 25169 29084)	Atlas-SNP	.											.	TRIM3	67	.	0			c.G12A						PASS	.	C	,	1,4401	2.1+/-5.4	0,1,2200	148	113	125		12,12	3.3	1	11	dbSNP_134	125	5,8587	4.3+/-15.6	0,5,4291	no	coding-synonymous,coding-synonymous	TRIM3	NM_006458.2,NM_033278.2	,	0,6,6491	TT,TC,CC		0.0582,0.0227,0.0462	,	4/745,4/745	6486914	6,12988	2201	4296	6497	SO:0001819	synonymous_variant	10612	exon2			GTCCTCCCTCTTT	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.12G>A	11.37:g.6486914C>T		92	0	0		106	45	0.424528	NM_001248006	B7Z5E6|F5H2Q8|Q4V9L4|Q9C038|Q9C039	Silent	SNP	ENST00000525074.1	37	CCDS7764.1																																																																																			C|0.999;T|0.001	0.001	strong		0.602	TRIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384224.2	NM_006458		T	6486914	C	T	6486914	2	4	26	1	0	0	0	0	0	0	0	1	16519	622	22	2		2	TRIM3	11	6486914	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	497734	6486914	128519602	355	10118											
OR5P2	120065	hgsc.bcm.edu	37	chr11	7818165	7818165	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccatggcagccagaaggaCgcattcgactgttgcaaaga	12	6	13	10	2	0	2	0	0	0	2	1	4	0	3	2	3	2	4	2	3	2	2	rs569926953	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:7818165C>T	ENST00000329434.2	-	1	355	c.325G>A	c.(325-327)Gtc>Atc	p.V109I	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, 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.V109I(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GCCAGAAGGACGCATTCGACT	0.483																																					p.V109I		Atlas-SNP	.											OR5P2,brain,glioma,0,2	OR5P2	68	2	1	Substitution - Missense(1)	central_nervous_system(1)	c.G325A						scavenged	.						96	111	106					11																	7818165		2105	4292	6397	SO:0001583	missense	120065	exon1			GAAGGACGCATTC	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"GPCR / Class A : Olfactory receptors"	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.325G>A	11.37:g.7818165C>T	ENSP00000331823:p.Val109Ile	64	0	0		60	3	0.05	NM_153444	Q3MIS8	Missense_Mutation	SNP	ENST00000329434.2	37	CCDS7782.1	.	.	.	.	.	.	.	.	.	.	C	6.601	0.479294	0.12581	.	.	ENSG00000183303	ENST00000329434	T	0.01059	5.39	5.5	1.92	0.25849	GPCR, rhodopsin-like superfamily (1);	0.172021	0.42172	N	0.000756	T	0.00724	0.0024	N	0.11000	0.08	0.18873	N	0.999981	B	0.02656	0.0	B	0.04013	0.001	T	0.49214	-0.8963	10	0.49607	T	0.09	-40.3172	3.5462	0.07829	0.6539:0.1394:0.0739:0.1327	.	109	Q8WZ92	OR5P2_HUMAN	I	109	ENSP00000331823:V109I	ENSP00000331823:V109I	V	-	1	0	OR5P2	7774741	0.000000	0.05858	0.991000	0.47740	0.012000	0.07955	-0.165000	0.09968	0.161000	0.19458	-1.921000	0.00515	GTC	.	.	none		0.483	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444		T	7818165	C	T	7818165	3	4	26	1	0	0	0	0	1	0	0	0	11187	536	19	1	647	1	OR5P2	11	7818165	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1331251	7818165	127188351	356	10119											
MICALCL	84953	hgsc.bcm.edu	37	chr11	12379949	12379949	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcgattccttagaggaacaaCgcatcagagaaaaagccgag	16	6	10	9	3	1	2	1	0	0	2	3	6	2	3	2	1	3	1	2	1	5	2	rs34898047	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:12379949C>T	ENST00000256186.2	+	9	2302	c.2011C>T	c.(2011-2013)Cgc>Tgc	p.R671C		NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	671					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)		AGAGGAACAACGCATCAGAGA	0.493													C|||	29	0.00579073	0.0008	0.0101	5008	,	,		17452	0.001		0.0189	False		,,,				2504	0.001				p.R671C		Atlas-SNP	.											.	MICALCL	59	.	0			c.C2011T						PASS	.	C	CYS/ARG	7,3929		0,7,1961	225	225	225		2011	4.3	0.7	11	dbSNP_126	225	132,8158		0,132,4013	yes	missense	MICALCL	NM_032867.2	180	0,139,5974	TT,TC,CC		1.5923,0.1778,1.1369	probably-damaging	671/696	12379949	139,12087	1968	4145	6113	SO:0001583	missense	84953	exon9			GAACAACGCATCA	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.2011C>T	11.37:g.12379949C>T	ENSP00000256186:p.Arg671Cys	78	0	0		76	31	0.407895	NM_032867	Q7RTP7|Q96JU6	Missense_Mutation	SNP	ENST00000256186.2	37	CCDS41620.1	16	0.007326007326007326	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	10	0.013192612137203167	C	17.09	3.301535	0.60195	0.001778	0.015923	ENSG00000133808	ENST00000256186	T	0.53640	0.61	5.33	4.35	0.52113	Domain of unknown function DUF3585 (1);	0.000000	0.26248	U	0.025469	T	0.58722	0.2142	M	0.92604	3.325	0.40653	D	0.982057	D	0.89917	1.0	D	0.83275	0.996	T	0.74870	-0.3517	10	0.87932	D	0	.	10.2888	0.43584	0.3728:0.6272:0.0:0.0	rs34898047	671	Q6ZW33	MICLK_HUMAN	C	671	ENSP00000256186:R671C	ENSP00000256186:R671C	R	+	1	0	MICALCL	12336525	1.000000	0.71417	0.735000	0.30896	0.623000	0.37688	3.076000	0.50081	2.479000	0.83701	0.655000	0.94253	CGC	C|0.986;T|0.014	0.014	strong		0.493	MICALCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386164.1	NM_032867		T	12379949	C	T	12379949	3	4	26	1	0	0	0	0	1	0	0	0	9581	536	19	1	2041	1	MICALCL	11	12379949	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	4561784	12379949	122626567	357	10120											
IGSF22	283284	hgsc.bcm.edu	37	chr11	18735570	18735570	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacttccatgccatccttgtAccatgtcactttgggcagtg	7	13	8	13	0	1	0	1	0	0	0	3	0	3	0	4	1	2	2	4	1	1	4			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:18735570A>G	ENST00000513874.1	-	14	2063	c.1924T>C	c.(1924-1926)Tac>Cac	p.Y642H	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	642	Ig-like 4.									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						CCATCCTTGTACCATGTCACT	0.597																																					p.Y642H		Atlas-SNP	.											.	IGSF22	211	.	0			c.T1924C						PASS	.						118	122	121					11																	18735570		2176	4259	6435	SO:0001583	missense	283284	exon14			CCTTGTACCATGT	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.1924T>C	11.37:g.18735570A>G	ENSP00000421191:p.Tyr642His	227	0	0		250	16	0.064	NM_173588	A6NNA0|D6RGV7	Missense_Mutation	SNP	ENST00000513874.1	37	CCDS41625.2	.	.	.	.	.	.	.	.	.	.	A	13.08	2.131488	0.37630	.	.	ENSG00000179057	ENST00000513874	T	0.47528	0.84	4.11	2.99	0.34606	.	0.000000	0.31519	U	0.007518	T	0.54334	0.1852	L	0.58354	1.805	0.22541	N	0.999007	D	0.65815	0.995	D	0.63283	0.913	T	0.42916	-0.9423	10	0.18710	T	0.47	.	7.6466	0.28323	0.9009:0.0:0.0991:0.0	.	642	D6RGV7	.	H	642	ENSP00000421191:Y642H	ENSP00000322422:Y642H	Y	-	1	0	IGSF22	18692146	1.000000	0.71417	0.964000	0.40570	0.991000	0.79684	2.903000	0.48711	0.655000	0.30866	0.450000	0.29827	TAC	.	.	none		0.597	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588		G	18735570	A	G	18735570	3	3	26	1	0	0	0	0	1	0	0	0	7609	391	14	3	2096	3	IGSF22	11	18735570	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	6355621	18735570	116270946	358	10121											
HTATIP2	10553	hgsc.bcm.edu	37	chr11	20403763	20403763	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttgaagaattaaaatttgatCgttactctgtatttaggcct	12	17	7	5	1	1	3	0	2	1	1	2	3	1	3	1	1	1	2	1	1	7	7	rs376468659		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:20403763C>T	ENST00000451739.2	+	4	922	c.481C>T	c.(481-483)Cgt>Tgt	p.R161C	HTATIP2_ENST00000419348.2_Missense_Mutation_p.R195C|HTATIP2_ENST00000443524.2_Missense_Mutation_p.R161C|HTATIP2_ENST00000531058.1_Missense_Mutation_p.R115C|HTATIP2_ENST00000421577.2_Missense_Mutation_p.R161C	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						AAAATTTGATCGTTACTCTGT	0.343																																					p.R195C		Atlas-SNP	.											.	HTATIP2	30	.	0			c.C583T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	0,4404		0,0,2202	125	141	136		583,481,481,481	5.6	1	11		136	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	HTATIP2	NM_001098520.1,NM_001098521.1,NM_001098522.1,NM_006410.4	180,180,180,180	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	195/277,161/243,161/243,161/243	20403763	1,13003	2202	4300	6502	SO:0001583	missense	10553	exon5			TTTGATCGTTACT	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.481C>T	11.37:g.20403763C>T	ENSP00000394259:p.Arg161Cys	73	0	0		82	4	0.0487805	NM_001098520		Missense_Mutation	SNP	ENST00000451739.2	37	CCDS7852.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.666405	0.88251	0.0	1.16E-4	ENSG00000109854	ENST00000421577;ENST00000443524;ENST00000419348;ENST00000451739;ENST00000531058	T;T;T;T;T	0.32753	1.5;1.5;1.5;1.5;1.44	5.62	5.62	0.85841	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.57007	0.2024	M	0.76838	2.35	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.69654	0.939;0.965	T	0.55438	-0.8141	10	0.46703	T	0.11	-19.1679	17.5131	0.87765	0.0:1.0:0.0:0.0	.	161;195	Q9BUP3;Q9BUP3-3	HTAI2_HUMAN;.	C	161;161;195;161;115	ENSP00000397752:R161C;ENSP00000387876:R161C;ENSP00000392985:R195C;ENSP00000394259:R161C;ENSP00000436729:R115C	ENSP00000392985:R195C	R	+	1	0	HTATIP2	20360339	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.464000	0.53057	2.809000	0.96659	0.655000	0.94253	CGT	.	.	weak		0.343	HTATIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387445.2	NM_001098521		T	20403763	C	T	20403763	3	4	26	1	0	0	0	0	1	0	0	0	7441	884	31	1	700	1	HTATIP2	11	20403763	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1668193	20403763	114602753	359	10122											
DNAJC24	120526	hgsc.bcm.edu	37	chr11	31447864	31447864	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaaatgtaggaccagtagAtgctcaagtatatcttgaag	16	10	10	5	0	2	3	1	1	1	2	2	4	2	4	1	1	1	4	1	1	8	5	rs144649932	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:31447864A>G	ENST00000465995.1	+	4	387	c.281A>G	c.(280-282)gAt>gGt	p.D94G	DNAJC24_ENST00000536040.1_3'UTR	NM_181706.4	NP_859057.4	Q6P3W2	DJC24_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 24	93					chaperone-mediated protein folding (GO:0061077)|oxidation-reduction process (GO:0055114)|peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)|positive regulation of ATPase activity (GO:0032781)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ATPase activator activity (GO:0001671)|ferrous iron binding (GO:0008198)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|skin(1)|upper_aerodigestive_tract(2)	11						GGACCAGTAGATGCTCAAGTA	0.269													A|||	7	0.00139776	0.0	0.0014	5008	,	,		16417	0.0		0.005	False		,,,				2504	0.001				p.D94G		Atlas-SNP	.											.	DNAJC24	23	.	0			c.A281G						PASS	.	A	GLY/ASP	5,3647		0,5,1821	115	111	112		281	4.4	1	11	dbSNP_134	112	28,8128		0,28,4050	yes	missense	DNAJC24	NM_181706.4	94	0,33,5871	GG,GA,AA		0.3433,0.1369,0.2795	benign	94/150	31447864	33,11775	1826	4078	5904	SO:0001583	missense	120526	exon4			CAGTAGATGCTCA	AL833128	CCDS7873.2	11p14.1	2011-09-02	2008-07-03	2008-07-03	ENSG00000170946	ENSG00000170946		"Heat shock proteins / DNAJ (HSP40)"	26979	protein-coding gene	gene with protein product		611072	"zinc finger, CSL-type containing 3", "DPH4 homolog (JJJ3, S. cerevisiae)", "DPH4, JJJ3 homolog (S. cerevisiae)"	ZCSL3, DPH4		15485916	Standard	NM_181706		Approved	JJJ3	uc001msx.3	Q6P3W2	OTTHUMG00000133712	ENST00000465995.1:c.281A>G	11.37:g.31447864A>G	ENSP00000417548:p.Asp94Gly	46	0	0		59	28	0.474576	NM_181706	A8K0V0|B1ALC1|I6L9B4	Missense_Mutation	SNP	ENST00000465995.1	37	CCDS7873.2	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	A	15.76	2.927163	0.52759	0.001369	0.003433	ENSG00000170946	ENST00000465995	T	0.31769	1.48	5.52	4.4	0.53042	Zinc finger, DPH-type (1);	0.143219	0.64402	N	0.000012	T	0.21881	0.0527	L	0.59436	1.845	0.80722	D	1	B	0.14438	0.01	B	0.20577	0.03	T	0.04307	-1.0961	10	0.27785	T	0.31	.	10.0993	0.42495	0.924:0.0:0.076:0.0	.	93	Q6P3W2	DJC24_HUMAN	G	94	ENSP00000417548:D94G	ENSP00000417548:D94G	D	+	2	0	DNAJC24	31404440	1.000000	0.71417	0.999000	0.59377	0.980000	0.70556	5.131000	0.64751	1.037000	0.40024	0.528000	0.53228	GAT	A|0.998;G|0.002	0.002	strong		0.269	DNAJC24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258011.3	NM_181706		G	31447864	A	G	31447864	3	3	26	1	0	0	0	0	1	0	0	0	4644	333	12	3	291	3	DNAJC24	11	31447864	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	11044101	31447864	103558652	360	10123											
ACP2	53	hgsc.bcm.edu	37	chr11	47261762	47261762	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagcagcactatgaggaggaAgaggatggagccacatacag	15	4	15	7	0	0	2	0	1	0	1	0	7	0	6	1	4	4	2	1	4	3	2	rs145420520	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:47261762A>G	ENST00000256997.3	-	11	1293	c.1177T>C	c.(1177-1179)Ttc>Ctc	p.F393L	ACP2_ENST00000529444.1_Missense_Mutation_p.F330L|ACP2_ENST00000533929.1_Missense_Mutation_p.F365L|ACP2_ENST00000537863.1_Missense_Mutation_p.F206L|ACP2_ENST00000527256.1_Missense_Mutation_p.F361L|ACP2_ENST00000525230.1_5'UTR	NM_001610.2	NP_001601.1	P11117	PPAL_HUMAN	acid phosphatase 2, lysosomal	393					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						ATGAGGAGGAAGAGGATGGAG	0.592													A|||	28	0.00559105	0.0015	0.0086	5008	,	,		22440	0.0		0.0149	False		,,,				2504	0.0051				p.F393L	Melanoma(90;262 1440 11488 44828 48531)	Atlas-SNP	.											.	ACP2	36	.	0			c.T1177C						PASS	.	A	LEU/PHE	9,4393	14.3+/-33.2	0,9,2192	121	83	96		1177	5.7	1	11	dbSNP_134	96	85,8511	49.8+/-109.6	1,83,4214	yes	missense	ACP2	NM_001610.2	22	1,92,6406	GG,GA,AA		0.9888,0.2045,0.7232	benign	393/424	47261762	94,12904	2201	4298	6499	SO:0001583	missense	53	exon11			GGAGGAAGAGGAT	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.1177T>C	11.37:g.47261762A>G	ENSP00000256997:p.Phe393Leu	63	0	0		63	29	0.460317	NM_001610	E9PCI1|Q561W5|Q9BTU7	Missense_Mutation	SNP	ENST00000256997.3	37	CCDS7928.1	19	0.0086996336996337	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	13	0.017150395778364115	A	11.49	1.654886	0.29425	0.002045	0.009888	ENSG00000134575	ENST00000256997;ENST00000529444;ENST00000527256;ENST00000537863;ENST00000540414;ENST00000533929	T;T;T;T;T	0.10288	3.17;3.08;3.2;2.89;3.05	5.66	5.66	0.87406	.	0.156460	0.64402	D	0.000019	T	0.02418	0.0074	N	0.08118	0	0.34188	D	0.67174	B;B;B;B	0.12013	0.001;0.005;0.001;0.005	B;B;B;B	0.08055	0.001;0.003;0.001;0.003	T	0.32188	-0.9916	10	0.25106	T	0.35	.	9.2012	0.37260	0.9119:0.0:0.0881:0.0	.	330;361;365;393	E9PHY0;B7Z7D2;E9PQY3;P11117	.;.;.;PPAL_HUMAN	L	393;330;361;206;383;365	ENSP00000256997:F393L;ENSP00000436658:F330L;ENSP00000432205:F361L;ENSP00000441933:F206L;ENSP00000432439:F365L	ENSP00000256997:F393L	F	-	1	0	ACP2	47218338	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.024000	0.57218	2.158000	0.67659	0.482000	0.46254	TTC	A|0.991;G|0.009	0.009	strong		0.592	ACP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392022.2	NM_001610		G	47261762	A	G	47261762	3	3	26	1	0	0	0	0	1	0	0	0	163	72	3	3	98	3	ACP2	11	47261762	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	15813898	47261762	87744754	361	10124											
OR4A5	81318	hgsc.bcm.edu	37	chr11	51412066	51412066	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gccatcaccaccagaaggaaGacctcagccccaccaaagaa	16	2	7	16	0	2	3	2	0	0	3	2	4	2	4	7	1	1	0	7	1	4	0	rs5002409	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:51412066G>C	ENST00000319760.6	-	1	382	c.330C>G	c.(328-330)gtC>gtG	p.V110V		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	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)|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)				CCAGAAGGAAGACCTCAGCCC	0.453													.|||	5	0.000998403	0.0	0.0029	5008	,	,		21048	0.0		0.003	False		,,,				2504	0.0				p.V110V		Atlas-SNP	.											.	OR4A5	116	.	0			c.C330G						PASS	.	A		2,4400		0,2,2199	72	71	71		330	-2	0.8	11	dbSNP_113	71	22,8570		0,22,4274	no	coding-synonymous	OR4A5	NM_001005272.3		0,24,6473	CC,CG,GG		0.2561,0.0454,0.1847		110/316	51412066	24,12970	2201	4296	6497	SO:0001819	synonymous_variant	81318	exon1			AAGGAAGACCTCA	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.330C>G	11.37:g.51412066G>C		112	0	0		142	74	0.521127	NM_001005272	Q6IF84	Silent	SNP	ENST00000319760.6	37	CCDS31497.1																																																																																			C|0.001;G|0.999	0.001	strong		0.453	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272		C	51412066	G	C	51412066	2	2	26	1	0	0	0	0	0	0	0	1	11052	929	33	4		4	OR4A5	11	51412066	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	4150304	51412066	83594450	362	10125											
OR4A15	81328	hgsc.bcm.edu	37	chr11	55136157	55136157	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggaaacgaaaagctttctaCacctgtgcatcccacgtcac	12	8	8	13	2	2	0	1	0	1	0	3	2	3	1	2	1	4	2	2	1	4	2	rs147678504	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55136157C>T	ENST00000314706.3	+	1	798	c.798C>T	c.(796-798)taC>taT	p.Y266Y		NM_001005275.1	NP_001005275.1	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A, member 15	266						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						AAGCTTTCTACACCTGTGCAT	0.423													.|||	7	0.00139776	0.0008	0.0	5008	,	,		20139	0.0		0.005	False		,,,				2504	0.001				p.Y266Y		Atlas-SNP	.											.	OR4A15	161	.	0			c.C798T						PASS	.	C		2,4400		0,2,2199	211	189	197		798	-0.7	0	11	dbSNP_134	197	29,8563		0,29,4267	no	coding-synonymous	OR4A15	NM_001005275.1		0,31,6466	TT,TC,CC		0.3375,0.0454,0.2386		266/345	55136157	31,12963	2201	4296	6497	SO:0001819	synonymous_variant	81328	exon1			TTTCTACACCTGT	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.798C>T	11.37:g.55136157C>T		205	0	0		236	107	0.45339	NM_001005275	Q6IFL4|Q96R65	Silent	SNP	ENST00000314706.3	37	CCDS31500.1																																																																																			C|0.997;T|0.003	0.003	strong		0.423	OR4A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391161.1	NM_001005275		T	55136157	C	T	55136157	2	4	26	1	0	0	0	0	0	0	0	1	11049	489	17	2		2	OR4A15	11	55136157	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	3724091	55136157	79870359	363	10126											
OR4C15	81309	hgsc.bcm.edu	37	chr11	55322099	55322099	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaccattctcagcagccctgCtcttctggtgtctcctatgt	6	14	7	14	0	4	0	1	0	4	0	6	0	4	0	3	1	4	2	3	1	2	3	rs17496724	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55322099C>G	ENST00000314644.2	+	1	317	c.317C>G	c.(316-318)gCt>gGt	p.A106G		NM_001001920.1	NP_001001920.1	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C, member 15	52						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						AGCAGCCCTGCTCTTCTGGTG	0.443										HNSCC(20;0.049)																											p.A106G		Atlas-SNP	.											.	OR4C15	145	.	0			c.C317G						PASS	.						172	137	149					11																	55322099		2201	4296	6497	SO:0001583	missense	81309	exon1			GCCCTGCTCTTCT	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.317C>G	11.37:g.55322099C>G	ENSP00000324958:p.Ala106Gly	66	0	0		77	36	0.467532	NM_001001920	Q6IFE2	Missense_Mutation	SNP	ENST00000314644.2	37	CCDS31501.1	.	.	.	.	.	.	.	.	.	.	C	10.68	1.417099	0.25552	.	.	ENSG00000181939	ENST00000314644	T	0.01092	5.35	4.79	4.79	0.61399	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.01523	0.0049	N	0.20881	0.62	0.09310	N	1	B	0.34264	0.446	B	0.35813	0.211	T	0.54344	-0.8308	9	0.62326	D	0.03	.	15.7279	0.77777	0.0:1.0:0.0:0.0	.	52	Q8NGM1	OR4CF_HUMAN	G	106	ENSP00000324958:A106G	ENSP00000324958:A106G	A	+	2	0	OR4C15	55078675	0.000000	0.05858	0.765000	0.31456	0.191000	0.23601	-0.885000	0.04161	2.665000	0.90641	0.385000	0.25706	GCT	C|0.966;A|0.034	.	alt		0.443	OR4C15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391164.1	NM_001001920		G	55322099	C	G	55322099	3	3	26	1	0	0	0	0	1	0	0	0	11057	797	28	4	319	4	OR4C15	11	55322099	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	185942	55322099	79684417	364	10127											
OR5M3	219482	hgsc.bcm.edu	37	chr11	56237609	56237609	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagaggattcccaattgccAtgtatctatcaaaggccatc	12	10	8	11	0	2	1	1	0	1	1	4	2	3	2	3	2	1	2	3	2	4	4	rs200070203	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56237609A>G	ENST00000312240.2	-	1	405	c.365T>C	c.(364-366)aTg>aCg	p.M122T		NM_001004742.2	NP_001004742.2	Q8NGP4	OR5M3_HUMAN	olfactory receptor, family 5, subfamily M, member 3	122						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)					CCCAATTGCCATGTATCTATC	0.383													a|||	26	0.00519169	0.0	0.0058	5008	,	,		20815	0.0		0.0169	False		,,,				2504	0.0051				p.M122T		Atlas-SNP	.											.	OR5M3	103	.	0			c.T365C						PASS	.						92	86	88					11																	56237609		2201	4280	6481	SO:0001583	missense	219482	exon1			ATTGCCATGTATC	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.365T>C	11.37:g.56237609A>G	ENSP00000312208:p.Met122Thr	146	0	0		85	9	0.105882	NM_001004742	B2RNM7|Q6IEW4|Q96RC0	Missense_Mutation	SNP	ENST00000312240.2	37	CCDS31532.1	.	.	.	.	.	.	.	.	.	.	A	7.717	0.696444	0.15106	.	.	ENSG00000174937	ENST00000312240	T	0.01323	5.01	5.13	4.0	0.46444	GPCR, rhodopsin-like superfamily (1);	0.215738	0.32852	N	0.005578	T	0.01870	0.0059	L	0.43646	1.37	0.28098	N	0.931539	B	0.06786	0.001	B	0.10450	0.005	T	0.30995	-0.9959	10	0.56958	D	0.05	-7.874	9.9755	0.41781	0.9186:0.0:0.0814:0.0	.	122	Q8NGP4	OR5M3_HUMAN	T	122	ENSP00000312208:M122T	ENSP00000312208:M122T	M	-	2	0	OR5M3	55994185	0.001000	0.12720	0.975000	0.42487	0.077000	0.17291	1.595000	0.36708	0.794000	0.33899	-0.536000	0.04276	ATG	.	.	weak		0.383	OR5M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391639.1	NM_001004742		G	56237609	A	G	56237609	3	3	26	1	0	0	0	0	1	0	0	0	11184	217	8	3	560	3	OR5M3	11	56237609	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	915510	56237609	78768907	365	10128											
OR5B12	390191	hgsc.bcm.edu	37	chr11	58207035	58207036	+	Frame_Shift_Del	DEL	AT	AT	-																															tgaatcccaccacaaaaaaaAtaaccatctcactgatgtag																								rs201567144|rs148519730	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:58207035_58207036delAT	ENST00000302572.2	-	1	610_611	c.589_590delAT	c.(589-591)attfs	p.I197fs		NM_001004733.2	NP_001004733.1	Q96R08	OR5BC_HUMAN	olfactory receptor, family 5, subfamily B, member 12	197						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)				CACAAAAAAAATAACCATCTCA	0.391																																					p.197_197del		Atlas-Indel	.											.	OR5B12	80	.	0			c.590_591del						PASS	.																																			SO:0001589	frameshift_variant	390191	exon1			.	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.589_590delAT	11.37:g.58207035_58207036delAT	ENSP00000306657:p.Ile197fs	109	0	0		146	14	0.0958904	NM_001004733	B2RNL2|Q6IEV5	Frame_Shift_Del	DEL	ENST00000302572.2	37	CCDS31551.1																																																																																			.	.	none		0.391	OR5B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394987.1	NM_001004733		-	58207036	AT	-	58207035	7	5	26	1	0	1	0	1	0	0	0	0	11157	101	4	0	358	0	OR5B12	11	58207035	Frame_Shift_Del	DEL	AT	TCGA-G8-6907-01A-11D-2210-10	1969426	58207035	76799481	366	10129	126	2									
OR5B12	390191	hgsc.bcm.edu	37	chr11	58207036	58207036	+	Missense_Mutation	SNP	T	T	A																															gaatcccaccacaaaaaaaaTaaccatctcactgatgtagt																								rs201567144|rs148519730	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:58207036T>A	ENST00000302572.2	-	1	610	c.589A>T	c.(589-591)Att>Ttt	p.I197F		NM_001004733.2	NP_001004733.1	Q96R08	OR5BC_HUMAN	olfactory receptor, family 5, subfamily B, member 12	197						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)				ACAAAAAAAATAACCATCTCA	0.393																																					p.I197F		Atlas-SNP	.											.	OR5B12	80	.	0			c.A589T						PASS	.						69	65	66					11																	58207036		2201	4295	6496	SO:0001583	missense	390191	exon1			AAAAAATAACCAT	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.589A>T	11.37:g.58207036T>A	ENSP00000306657:p.Ile197Phe	112	0	0		136	59	0.433824	NM_001004733	B2RNL2|Q6IEV5	Missense_Mutation	SNP	ENST00000302572.2	37	CCDS31551.1	.	.	.	.	.	.	.	.	.	.	T	8.659	0.900137	0.17686	.	.	ENSG00000172362	ENST00000302572	T	0.00137	8.68	4.3	3.15	0.36227	GPCR, rhodopsin-like superfamily (1);	0.422268	0.20017	N	0.100981	T	0.00178	0.0005	L	0.52573	1.65	0.09310	N	1	B	0.14012	0.009	B	0.17979	0.02	T	0.28038	-1.0056	10	0.54805	T	0.06	-24.7022	9.4514	0.38727	0.1587:0.0:0.0:0.8413	.	197	Q96R08	OR5BC_HUMAN	F	197	ENSP00000306657:I197F	ENSP00000306657:I197F	I	-	1	0	OR5B12	57963612	0.000000	0.05858	0.617000	0.29091	0.689000	0.40095	-5.918000	0.00090	0.772000	0.33382	0.379000	0.24179	ATT	T|0.996;A|0.004	0.004	strong		0.393	OR5B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394987.1	NM_001004733		A	58207036	T	A	58207036	3	1	26	1	0	0	0	0	1	0	0	0	11157	1406	49	5	359	5	OR5B12	11	58207036	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	1	58207036	76799480	367	10130	126	2									
TMEM109	79073	hgsc.bcm.edu	37	chr11	60689534	60689534	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tggctcccgagcctctggggCccaactcgaggccaaggtgc	6	6	14	15	2	1	0	0	0	1	0	3	2	2	0	4	5	3	1	4	5	2	0	rs75070807	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:60689534C>T	ENST00000227525.3	+	4	1032	c.629C>T	c.(628-630)gCc>gTc	p.A210V	TMEM132A_ENST00000005286.4_5'Flank|RP11-881M11.4_ENST00000543907.1_RNA|TMEM132A_ENST00000453848.2_5'Flank|TMEM109_ENST00000536171.1_Missense_Mutation_p.A210V	NM_024092.2	NP_076997.1	Q9BVC6	TM109_HUMAN	transmembrane protein 109	210					cellular response to gamma radiation (GO:0071480)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of cell death (GO:0060548)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)	8						GCCTCTGGGGCCCAACTCGAG	0.706													C|||	48	0.00958466	0.0023	0.0173	5008	,	,		15459	0.0		0.0229	False		,,,				2504	0.0102				p.A210V		Atlas-SNP	.											.	TMEM109	24	.	0			c.C629T						PASS	.	C	VAL/ALA	31,4359		0,31,2164	21	25	24		629	2.8	1	11	dbSNP_131	24	237,8333		2,233,4050	yes	missense	TMEM109	NM_024092.2	64	2,264,6214	TT,TC,CC		2.7655,0.7062,2.0679	benign	210/244	60689534	268,12692	2195	4285	6480	SO:0001583	missense	79073	exon4			CTGGGGCCCAACT		CCDS7996.1	11q12.2	2005-12-22				ENSG00000110108			28771	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_024092		Approved	MGC5508	uc001nqg.3	Q9BVC6		ENST00000227525.3:c.629C>T	11.37:g.60689534C>T	ENSP00000227525:p.Ala210Val	25	0	0		60	37	0.616667	NM_024092		Missense_Mutation	SNP	ENST00000227525.3	37	CCDS7996.1	27	0.012362637362637362	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	19	0.025065963060686015	C	14.68	2.608134	0.46527	0.007062	0.027655	ENSG00000110108	ENST00000227525;ENST00000536171	.	.	.	4.75	2.82	0.32997	.	0.530146	0.18218	N	0.147992	T	0.11452	0.0279	L	0.34521	1.04	0.26459	N	0.975476	B	0.11235	0.004	B	0.14578	0.011	T	0.09314	-1.0680	9	0.39692	T	0.17	-13.8635	8.6821	0.34214	0.0:0.7661:0.1493:0.0847	.	210	Q9BVC6	TM109_HUMAN	V	210	.	ENSP00000227525:A210V	A	+	2	0	TMEM109	60446110	0.001000	0.12720	1.000000	0.80357	0.164000	0.22412	0.816000	0.27267	0.969000	0.38237	0.555000	0.69702	GCC	C|0.983;T|0.017	0.017	strong		0.706	TMEM109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396343.1	NM_024092		T	60689534	C	T	60689534	3	4	26	1	0	0	0	0	1	0	0	0	16040	739	26	2	639	2	TMEM109	11	60689534	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	2482498	60689534	74316982	368	10131											
DAGLA	747	hgsc.bcm.edu	37	chr11	61511794	61511794	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccctcctcgggcatctcaCtctcgccctccttcccgctc	3	10	5	23	3	2	0	1	0	2	0	9	0	5	0	6	1	0	2	6	1	0	1	rs117050893	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:61511794C>G	ENST00000257215.5	+	20	3078	c.2962C>G	c.(2962-2964)Ctc>Gtc	p.L988V	RP11-467L20.10_ENST00000536405.1_lincRNA	NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	988					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)		GGGCATCTCACTCTCGCCCTC	0.667													C|||	33	0.00658946	0.0	0.0331	5008	,	,		16155	0.002		0.006	False		,,,				2504	0.002				p.L988V		Atlas-SNP	.											.	DAGLA	109	.	0			c.C2962G						PASS	.	C	VAL/LEU	18,4386	24.3+/-50.5	0,18,2184	56	62	60		2962	2	0	11	dbSNP_132	60	38,8560	25.7+/-73.6	0,38,4261	yes	missense	DAGLA	NM_006133.2	32	0,56,6445	GG,GC,CC		0.442,0.4087,0.4307	benign	988/1043	61511794	56,12946	2202	4299	6501	SO:0001583	missense	747	exon20			ATCTCACTCTCGC	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.2962C>G	11.37:g.61511794C>G	ENSP00000257215:p.Leu988Val	78	0	0		93	37	0.397849	NM_006133	A7E233|Q6WQJ0	Missense_Mutation	SNP	ENST00000257215.5	37	CCDS31578.1	21	0.009615384615384616	0	0.0	15	0.04143646408839779	1	0.0017482517482517483	5	0.006596306068601583	C	5.197	0.221827	0.09863	0.004087	0.00442	ENSG00000134780	ENST00000257215	T	0.25085	1.82	4.03	1.95	0.26073	.	0.158981	0.41097	D	0.000955	T	0.01905	0.0060	N	0.03608	-0.345	0.18873	N	0.999989	B	0.02656	0.0	B	0.04013	0.001	T	0.32268	-0.9913	10	0.17369	T	0.5	-26.7772	8.6434	0.33991	0.0:0.5927:0.3026:0.1048	.	988	Q9Y4D2	DGLA_HUMAN	V	988	ENSP00000257215:L988V	ENSP00000257215:L988V	L	+	1	0	DAGLA	61268370	0.954000	0.32549	0.008000	0.14137	0.636000	0.38137	1.749000	0.38319	0.815000	0.34398	0.462000	0.41574	CTC	C|0.994;G|0.006	0.006	strong		0.667	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133		G	61511794	C	G	61511794	3	3	26	1	0	0	0	0	1	0	0	0	4228	565	20	4	3036	4	DAGLA	11	61511794	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	822260	61511794	73494722	369	10132											
TUT1	64852	hgsc.bcm.edu	37	chr11	62343667	62343667	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcagggacagcagggagccAcgaagatcccaacaagatac	15	2	12	12	2	0	2	0	0	0	2	1	5	1	4	2	2	4	2	2	2	4	1	rs118073625	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:62343667A>T	ENST00000476907.1	-	9	2215	c.1524T>A	c.(1522-1524)cgT>cgA	p.R508R	MIR3654_ENST00000496634.2_Intron|EEF1G_ENST00000329251.4_5'Flank|EEF1G_ENST00000378019.3_5'Flank|EEF1G_ENST00000532986.1_5'Flank|TUT1_ENST00000308436.7_Silent_p.R546R			Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6 snRNA-specific	508	PAP-associated.				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						GCAGGGAGCCACGAAGATCCC	0.612													A|||	9	0.00179712	0.0	0.0014	5008	,	,		18897	0.0		0.007	False		,,,				2504	0.001				p.R546R		Atlas-SNP	.											.	TUT1	122	.	0			c.T1638A						PASS	.	A		4,4374		0,4,2185	18	20	19		1638	-0.2	1	11	dbSNP_133	19	81,8511		0,81,4215	no	coding-synonymous	TUT1	NM_022830.2		0,85,6400	TT,TA,AA		0.9427,0.0914,0.6554		546/913	62343667	85,12885	2189	4296	6485	SO:0001819	synonymous_variant	64852	exon9			GGAGCCACGAAGA	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.1524T>A	11.37:g.62343667A>T		48	0	0		52	17	0.326923	NM_022830	A1A527|A8K995|Q2NL65|Q7L583|Q9H6H7	Silent	SNP	ENST00000476907.1	37																																																																																				A|0.995;T|0.005	0.005	strong		0.612	TUT1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000351319.2	NM_022830		T	62343667	A	T	62343667	2	4	26	1	0	0	0	0	0	0	0	1	16795	146	6	5		5	TUT1	11	62343667	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	831873	62343667	72662849	370	10133											
TUT1	64852	hgsc.bcm.edu	37	chr11	62359061	62359061	+	5'UTR	DEL	G	G	-																															caacttccgccgatccgataGgaagtgacataaagtcgttc																								rs577382133	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:62359061delG	ENST00000476907.1	-	0	588				MIR3654_ENST00000496634.2_5'Flank|TUT1_ENST00000308436.7_Frame_Shift_Del_p.P4fs			Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6 snRNA-specific						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						CGATCCGATAGGAAGTGACAT	0.572													GG|GG|G|deletion	4	0.000798722	0.0	0.0	5008	,	,		18693	0.0		0.003	False		,,,				2504	0.001				p.P4fs		Pindel,Atlas-Indel	.											.	TUT1	122	.	0			c.12delT						PASS	.			5,4215		0,5,2105	34	46	42			-4.7	0	11		42	32,8150		2,28,4061	no	frameshift	TUT1	NM_022830.2		2,33,6166	A1A1,A1R,RR		0.3911,0.1185,0.2983			62359061	37,12365	692	1591	2283	SO:0001623	5_prime_UTR_variant	64852	exon1			.	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.-104C>-	11.37:g.62359061delG		46	0	.		50	12	0.24	NM_022830	A1A527|A8K995|Q2NL65|Q7L583|Q9H6H7	Frame_Shift_Del	DEL	ENST00000476907.1	37																																																																																				.	.	none		0.572	TUT1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000351319.2	NM_022830		-	62359061	G	-	62359061	6	5	26	0	1	1	0	1	0	0	0	0	16795	1000	35	0		0	TUT1	11	62359061	5'UTR	DEL	G	TCGA-G8-6907-01A-11D-2210-10	15394	62359061	72647455	371	10134											
FERMT3	83706	hgsc.bcm.edu	37	chr11	63974995	63974995	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctgaagattgtggagcagatCagtgagtgtccgctgcccgc	8	9	14	10	2	1	4	1	2	0	2	2	5	2	5	2	1	2	2	2	1	1	1	rs142815441	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:63974995C>G	ENST00000279227.5	+	2	254	c.159C>G	c.(157-159)atC>atG	p.I53M	FERMT3_ENST00000345728.5_Splice_Site_p.I53M	NM_178443.2	NP_848537.1	Q86UX7	URP2_HUMAN	fermitin family member 3	53					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						TGGAGCAGATCAGTGAGTGTC	0.657													C|||	7	0.00139776	0.0	0.0029	5008	,	,		12110	0.0		0.005	False		,,,				2504	0.0				p.I53M		Atlas-SNP	.											.	FERMT3	51	.	0			c.C159G						PASS	.	C	MET/ILE,MET/ILE	4,4398	8.1+/-20.4	0,4,2197	36	40	39		159,159	4.5	1	11	dbSNP_134	39	46,8548	29.6+/-80.5	0,46,4251	yes	missense-near-splice,missense-near-splice	FERMT3	NM_031471.5,NM_178443.2	10,10	0,50,6448	GG,GC,CC		0.5353,0.0909,0.3847	benign,benign	53/664,53/668	63974995	50,12946	2201	4297	6498	SO:0001630	splice_region_variant	83706	exon2			GCAGATCAGTGAG	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.160+1C>G	11.37:g.63974995C>G		96	0	0		123	52	0.422764	NM_031471	Q8IUA1|Q8N207|Q9BT48	Missense_Mutation	SNP	ENST00000279227.5	37	CCDS8060.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	12.17	1.857249	0.32791	9.09E-4	0.005353	ENSG00000149781	ENST00000544997;ENST00000345728;ENST00000279227	T;T;T	0.59083	1.55;0.29;0.29	4.48	4.48	0.54585	.	0.210781	0.37715	N	0.001977	T	0.39627	0.1085	L	0.54323	1.7	0.37691	D	0.923865	P;B	0.45011	0.848;0.031	B;B	0.36885	0.235;0.024	T	0.56183	-0.8021	10	0.49607	T	0.09	-30.3298	10.1956	0.43051	0.3098:0.6902:0.0:0.0	.	53;53	Q86UX7-2;Q86UX7	.;URP2_HUMAN	M	53	ENSP00000445778:I53M;ENSP00000339950:I53M;ENSP00000279227:I53M	ENSP00000279227:I53M	I	+	3	3	FERMT3	63731571	0.223000	0.23663	1.000000	0.80357	0.325000	0.28411	0.067000	0.14510	2.502000	0.84385	0.561000	0.74099	ATC	C|0.997;G|0.003	0.003	strong		0.657	FERMT3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396297.1	NM_031471	Missense_Mutation	G	63974995	C	G	63974995	5	3	26	1	0	0	0	0	0	0	1	0	5827	840	29	4	161	4	FERMT3	11	63974995	Splice_Site	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1615934	63974995	71031521	372	10135											
PLCB3	5331	hgsc.bcm.edu	37	chr11	64031241	64031241	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctcatctacaccgaagcctCggactacattcctgacgacc	10	8	7	16	3	2	1	1	1	1	0	4	4	3	2	4	1	3	1	4	1	3	3	rs35169799	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:64031241C>T	ENST00000540288.1	+	21	2637	c.2534C>T	c.(2533-2535)tCg>tTg	p.S845L	PLCB3_ENST00000279230.6_Missense_Mutation_p.S845L|PLCB3_ENST00000325234.5_Missense_Mutation_p.S778L	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	845				S -> L (in Ref. 6; CAA78903). {ECO:0000305}.	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						ACCGAAGCCTCGGACTACATT	0.667													C|||	114	0.0227636	0.0023	0.0303	5008	,	,		16910	0.0		0.0666	False		,,,				2504	0.0235				p.S845L		Atlas-SNP	.											PLCB3,brain,primitive_neuroectodermal_tumour-medulloblastoma,-1,1	PLCB3	103	1	0			c.C2534T						scavenged	.	C	LEU/SER,LEU/SER	67,4335	59.9+/-96.7	3,61,2137	89	87	88		2534,2333	5.2	1	11	dbSNP_126	88	578,8016	155.5+/-209.5	22,534,3741	yes	missense,missense	PLCB3	NM_000932.2,NM_001184883.1	145,145	25,595,5878	TT,TC,CC		6.7256,1.522,4.9631	benign,benign	845/1235,778/1168	64031241	645,12351	2201	4297	6498	SO:0001583	missense	5331	exon21			AAGCCTCGGACTA	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.2534C>T	11.37:g.64031241C>T	ENSP00000443631:p.Ser845Leu	109	1	0.00917431		96	42	0.4375	NM_000932	A5PKZ6|G5E960|Q8N1A4	Missense_Mutation	SNP	ENST00000540288.1	37	CCDS8064.1	67	0.030677655677655676	2	0.0040650406504065045	15	0.04143646408839779	0	0.0	50	0.06596306068601583	C	15.73	2.918361	0.52546	0.01522	0.067256	ENSG00000149782	ENST00000279230;ENST00000540288;ENST00000325234	T;T;T	0.21932	2.11;2.11;1.98	5.25	5.25	0.73442	C2 calcium/lipid-binding domain, CaLB (1);	0.184175	0.48767	D	0.000167	T	0.01156	0.0038	N	0.25647	0.755	0.36001	D	0.837379	D;P	0.58268	0.982;0.838	B;B	0.42138	0.377;0.177	T	0.05084	-1.0907	10	0.72032	D	0.01	.	13.2818	0.60219	0.1592:0.8407:0.0:0.0	rs35169799;rs61755083;rs35169799	778;845	G5E960;Q01970	.;PLCB3_HUMAN	L	845;845;778	ENSP00000279230:S845L;ENSP00000443631:S845L;ENSP00000324660:S778L	ENSP00000279230:S845L	S	+	2	0	PLCB3	63787817	0.637000	0.27216	0.952000	0.39060	0.334000	0.28698	2.527000	0.45615	2.462000	0.83206	0.561000	0.74099	TCG	C|0.957;T|0.043	0.043	strong		0.667	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1			T	64031241	C	T	64031241	3	4	26	1	0	0	0	0	1	0	0	0	12038	893	31	1	2616	1	PLCB3	11	64031241	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	56246	64031241	70975275	373	10136											
ESRRA	2101	hgsc.bcm.edu	37	chr11	64083273	64083273	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagccggccgggctggcccCggagggggtgctgagcggcg	4	3	22	12	5	0	1	0	1	0	0	0	3	0	2	4	7	3	2	4	7	1	0	rs41294422	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:64083273C>T	ENST00000405666.1	+	7	1341	c.1107C>T	c.(1105-1107)ccC>ccT	p.P369P	PRDX5_ENST00000352435.4_5'Flank|PRDX5_ENST00000347941.4_5'Flank|ESRRA_ENST00000406310.1_Silent_p.P368P|ESRRA_ENST00000000442.6_Silent_p.P369P|PRDX5_ENST00000265462.4_5'Flank	NM_001282450.1	NP_001269379.1	P11474	ERR1_HUMAN	estrogen-related receptor alpha	369	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						GGGCTGGCCCCGGAGGGGGTG	0.672													C|||	18	0.00359425	0.0008	0.0086	5008	,	,		17322	0.0		0.0109	False		,,,				2504	0.0				p.P369P		Atlas-SNP	.											.	ESRRA	56	.	0			c.C1107T						PASS	.	C		12,3752		0,12,1870	25	29	28		1107	-1.3	1	11	dbSNP_127	28	98,8094		1,96,3999	no	coding-synonymous	ESRRA	NM_004451.3		1,108,5869	TT,TC,CC		1.1963,0.3188,0.92		369/424	64083273	110,11846	1882	4096	5978	SO:0001819	synonymous_variant	2101	exon7			TGGCCCCGGAGGG	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.1107C>T	11.37:g.64083273C>T		56	0	0		67	23	0.343284	NM_004451	Q14514	Silent	SNP	ENST00000405666.1	37	CCDS41667.1	15	0.006868131868131868	0	0.0	6	0.016574585635359115	0	0.0	9	0.011873350923482849	C	6.975	0.549876	0.13374	0.003188	0.011963	ENSG00000173153	ENST00000545035	D	0.96396	-4.0	4.36	-1.26	0.09376	.	0.174873	0.28047	N	0.016807	T	0.80221	0.4583	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.74523	-0.3637	7	0.05959	T	0.93	.	5.6486	0.17604	0.0:0.4931:0.1729:0.3339	rs41294422;rs61736654	.	.	.	L	150	ENSP00000444710:P150L	ENSP00000444710:P150L	P	+	2	0	ESRRA	63839849	0.165000	0.22948	0.993000	0.49108	0.953000	0.61014	-1.152000	0.03172	-0.298000	0.08921	-0.291000	0.09656	CCG	C|0.991;T|0.009	0.009	strong		0.672	ESRRA-003	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319304.1	NM_004451		T	64083273	C	T	64083273	2	4	26	1	0	0	0	0	0	0	0	1	5262	639	23	1		1	ESRRA	11	64083273	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	52032	64083273	70923243	374	10137											
CCDC88B	283234	hgsc.bcm.edu	37	chr11	64120703	64120703	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agcgcctgccggctgaccacGcagtgtgaggtgtggctgga	6	7	17	11	3	0	2	0	2	0	0	0	3	0	3	3	4	2	3	3	4	0	0	rs61744422	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:64120703G>A	ENST00000356786.5	+	21	3722	c.3678G>A	c.(3676-3678)acG>acA	p.T1226T	CCDC88B_ENST00000359902.2_Silent_p.T378T|CCDC88B_ENST00000301897.4_5'UTR|CCDC88B_ENST00000463837.1_3'UTR	NM_032251.5	NP_115627.6	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	1226						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						GGCTGACCACGCAGTGTGAGG	0.692													G|||	28	0.00559105	0.0008	0.0101	5008	,	,		13374	0.0		0.0149	False		,,,				2504	0.0051				p.T1226T		Atlas-SNP	.											.	CCDC88B	89	.	0			c.G3678A						PASS	.	G		20,4252		0,20,2116	5	7	6		3678	-8.1	0.9	11	dbSNP_129	6	104,8316		1,102,4107	no	coding-synonymous	CCDC88B	NM_032251.5		1,122,6223	AA,AG,GG		1.2352,0.4682,0.977		1226/1477	64120703	124,12568	2136	4210	6346	SO:0001819	synonymous_variant	283234	exon21			GACCACGCAGTGT	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.3678G>A	11.37:g.64120703G>A		45	0	0		53	31	0.584906	NM_032251	A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1	Silent	SNP	ENST00000356786.5	37	CCDS8072.2																																																																																			G|0.990;A|0.010	0.010	strong		0.692	CCDC88B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104845.1	NM_032251		A	64120703	G	A	64120703	2	1	26	1	0	0	0	0	0	0	0	1	2866	1074	38	1		1	CCDC88B	11	64120703	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	37430	64120703	70885813	375	10138											
SCYL1	57410	hgsc.bcm.edu	37	chr11	65293819	65293819	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagagtggtcagagagaaGtggtgggtgactgggggcag	9	6	22	4	0	1	4	1	1	0	3	1	5	1	4	0	6	0	2	0	6	1	0	rs75169347	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:65293819G>A	ENST00000270176.5	+	4	677	c.600G>A	c.(598-600)aaG>aaA	p.K200K	SCYL1_ENST00000525364.1_Silent_p.K200K|SCYL1_ENST00000524944.1_Silent_p.K200K|SCYL1_ENST00000533862.1_Silent_p.K200K|SCYL1_ENST00000279270.6_Silent_p.K200K|SCYL1_ENST00000527009.1_Silent_p.K57K|SCYL1_ENST00000420247.2_Silent_p.K200K	NM_020680.3	NP_065731.3	Q96KG9	NTKL_HUMAN	SCY1-like 1 (S. cerevisiae)	200	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						TCAGAGAGAAGTGGTGGGTGA	0.657													G|||	91	0.0181709	0.0015	0.0303	5008	,	,		16563	0.0		0.0616	False		,,,				2504	0.0061				p.K200K		Atlas-SNP	.											.	SCYL1	76	.	0			c.G600A						PASS	.	G	,	34,4166		0,34,2066	16	19	18		600,600	-1.8	0.8	11	dbSNP_131	18	504,7942		14,476,3733	no	coding-synonymous,coding-synonymous	SCYL1	NM_001048218.1,NM_020680.3	,	14,510,5799	AA,AG,GG		5.9673,0.8095,4.2543	,	200/792,200/809	65293819	538,12108	2100	4223	6323	SO:0001819	synonymous_variant	57410	exon4			AGAGAAGTGGTGG	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.600G>A	11.37:g.65293819G>A		86	0	0		111	52	0.468468	NM_020680	A6NJF1|Q96G50|Q96KG8|Q96KH1|Q9HAW5|Q9HBL3|Q9NR53	Silent	SNP	ENST00000270176.5	37	CCDS41672.1																																																																																			G|0.968;A|0.032	0.032	strong		0.657	SCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389159.2	NM_020680		A	65293819	G	A	65293819	2	1	26	1	0	0	0	0	0	0	0	1	13962	1020	36	2		2	SCYL1	11	65293819	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1173116	65293819	69712697	376	10139											
EHBP1L1	254102	hgsc.bcm.edu	37	chr11	65349037	65349037	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggcagccagcccaggacacGgcccccaccccagcccctcg	8	1	10	22	2	0	0	0	0	0	0	1	1	0	1	8	3	3	1	8	3	0	0	rs74684453	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:65349037G>A	ENST00000309295.4	+	9	1159	c.894G>A	c.(892-894)acG>acA	p.T298T		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	298						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						CCCAGGACACGGCCCCCACCC	0.677													G|||	34	0.00678914	0.0008	0.0086	5008	,	,		13897	0.0		0.0239	False		,,,				2504	0.0031				p.T298T		Atlas-SNP	.											.	EHBP1L1	64	.	0			c.G894A						PASS	.	G		13,3719		0,13,1853	8	9	9		894	3	0.8	11	dbSNP_134	9	194,7914		2,190,3862	no	coding-synonymous	EHBP1L1	NM_001099409.1		2,203,5715	AA,AG,GG		2.3927,0.3483,1.7483		298/1524	65349037	207,11633	1866	4054	5920	SO:0001819	synonymous_variant	254102	exon9			GGACACGGCCCCC	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.894G>A	11.37:g.65349037G>A		186	0	0		185	89	0.481081	NM_001099409	Q8TB89|Q9H7M7	Silent	SNP	ENST00000309295.4	37	CCDS44649.1																																																																																			G|0.989;A|0.011	0.011	strong		0.677	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658		A	65349037	G	A	65349037	2	1	26	1	0	0	0	0	0	0	0	1	4978	1103	39	1		1	EHBP1L1	11	65349037	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	55218	65349037	69657479	377	10140											
RAB1B	81876	hgsc.bcm.edu	37	chr11	66043586	66043586	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccaccaatgtcgagcaggcGttcatgaccatggctgctga	9	8	12	12	2	1	2	1	2	0	0	2	3	1	2	3	2	2	4	3	2	1	1	rs367843963		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:66043586G>A	ENST00000311481.6	+	6	630	c.483G>A	c.(481-483)gcG>gcA	p.A161A	RP11-867G23.4_ENST00000526951.1_RNA|RAB1B_ENST00000527397.1_Silent_p.A129A|CNIH2_ENST00000311445.6_5'Flank|CNIH2_ENST00000528852.1_5'Flank|RP11-867G23.4_ENST00000528650.1_RNA|RP11-867G23.3_ENST00000501708.1_lincRNA	NM_030981.2	NP_112243.1	Q9H0U4	RAB1B_HUMAN	RAB1B, member RAS oncogene family	161					ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of glycoprotein metabolic process (GO:1903020)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|virion assembly (GO:0019068)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)			large_intestine(2)|lung(1)|ovary(1)|prostate(1)	5						TCGAGCAGGCGTTCATGACCA	0.582																																					p.A161A		Atlas-SNP	.											.	RAB1B	14	.	0			c.G483A						PASS	.	G		0,4400		0,0,2200	46	44	45		483	-7.8	1	11		45	1,8589	1.2+/-3.3	0,1,4294	no	coding-synonymous	RAB1B	NM_030981.2		0,1,6494	AA,AG,GG		0.0116,0.0,0.0077		161/202	66043586	1,12989	2200	4295	6495	SO:0001819	synonymous_variant	81876	exon6			GCAGGCGTTCATG	AJ245875	CCDS31613.1	11q13.1	2008-02-05			ENSG00000174903	ENSG00000174903		"RAB, member RAS oncogene"	18370	protein-coding gene	gene with protein product		612565				9030196	Standard	NM_030981		Approved		uc001ohf.3	Q9H0U4	OTTHUMG00000166916	ENST00000311481.6:c.483G>A	11.37:g.66043586G>A		88	0	0		109	45	0.412844	NM_030981	A8K7S1	Silent	SNP	ENST00000311481.6	37	CCDS31613.1	.	.	.	.	.	.	.	.	.	.	G	8.325	0.825167	0.16749	0.0	1.16E-4	ENSG00000174903	ENST00000314965	.	.	.	3.9	-7.77	0.01227	.	.	.	.	.	T	0.49712	0.1573	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61068	-0.7137	5	0.87932	D	0	.	2.2152	0.03958	0.3414:0.3799:0.1636:0.1151	.	.	.	.	H	161	.	ENSP00000313814:R161H	R	+	2	0	RAB1B	65800162	0.031000	0.19500	0.975000	0.42487	0.825000	0.46686	-0.719000	0.04974	-0.989000	0.03485	0.313000	0.20887	CGT	.	.	weak		0.582	RAB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391886.2	NM_030981		A	66043586	G	A	66043586	2	1	26	1	0	0	0	0	0	0	0	1	12921	1132	40	1		1	RAB1B	11	66043586	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	694549	66043586	68962930	378	10141											
CD248	57124	hgsc.bcm.edu	37	chr11	66083263	66083263	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tctctgtcctctgggaagctCggtctataggccagggcaaa	8	10	12	11	1	3	0	0	0	3	0	6	1	4	1	2	4	1	2	2	4	4	2	rs78560344	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:66083263C>T	ENST00000311330.3	-	1	1252	c.1236G>A	c.(1234-1236)ccG>ccA	p.P412P	RP11-867G23.13_ENST00000534065.1_RNA	NM_020404.2	NP_065137.1	Q9HCU0	CD248_HUMAN	CD248 molecule, endosialin	412	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						CTGGGAAGCTCGGTCTATAGG	0.647													C|||	27	0.00539137	0.0166	0.0029	5008	,	,		17487	0.0		0.003	False		,,,				2504	0.0				p.P412P		Atlas-SNP	.											CD248,NS,carcinoma,-1,1	CD248	69	1	0			c.G1236A						PASS	.	C		62,4338	57.4+/-93.9	0,62,2138	88	91	90		1236	-3.5	0.2	11	dbSNP_131	90	9,8581	7.1+/-27.0	0,9,4286	no	coding-synonymous	CD248	NM_020404.2		0,71,6424	TT,TC,CC		0.1048,1.4091,0.5466		412/758	66083263	71,12919	2200	4295	6495	SO:0001819	synonymous_variant	57124	exon1			GAAGCTCGGTCTA	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.1236G>A	11.37:g.66083263C>T		49	0	0		74	43	0.581081	NM_020404	Q2M2V5|Q3SX55|Q96KB6	Silent	SNP	ENST00000311330.3	37	CCDS8134.1																																																																																			C|0.994;T|0.006	0.006	strong		0.647	CD248-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392922.2	NM_020404		T	66083263	C	T	66083263	2	4	26	1	0	0	0	0	0	0	0	1	2991	871	31	1		1	CD248	11	66083263	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	39677	66083263	68923253	379	10142											
LRP5	4041	hgsc.bcm.edu	37	chr11	68115631	68115631	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aaccgcatcgaggtggccaaCctcaatggcacatcccggaa	12	5	10	14	3	1	0	1	0	0	0	3	2	2	1	4	4	2	2	4	4	4	0			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:68115631C>A	ENST00000294304.7	+	2	514	c.408C>A	c.(406-408)aaC>aaA	p.N136K		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	136	Beta-propeller 1.				adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|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 apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						AGGTGGCCAACCTCAATGGCA	0.642																																					p.N136K		Atlas-SNP	.											.	LRP5	136	.	0			c.C408A						PASS	.						97	93	94					11																	68115631		2200	4294	6494	SO:0001583	missense	4041	exon2			GGCCAACCTCAAT	AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"Low density lipoprotein receptors"	6697	protein-coding gene	gene with protein product		603506	"osteoporosis pseudoglioma syndrome", "exudative vitreoretinopathy 1"	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.408C>A	11.37:g.68115631C>A	ENSP00000294304:p.Asn136Lys	50	0	0		52	22	0.423077	NM_002335	Q96TD6|Q9UES7|Q9UP66	Missense_Mutation	SNP	ENST00000294304.7	37	CCDS8181.1	.	.	.	.	.	.	.	.	.	.	C	12.31	1.900963	0.33535	.	.	ENSG00000162337	ENST00000294304	D	0.83506	-1.73	3.71	2.78	0.32641	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.52532	U	0.000075	T	0.77772	0.4180	L	0.42632	1.34	0.50313	D	0.999863	P	0.45672	0.864	P	0.47376	0.545	T	0.71718	-0.4508	10	0.27785	T	0.31	.	7.2059	0.25907	0.0:0.7283:0.0:0.2717	.	136	O75197	LRP5_HUMAN	K	136	ENSP00000294304:N136K	ENSP00000294304:N136K	N	+	3	2	LRP5	67872207	0.792000	0.28813	0.998000	0.56505	0.307000	0.27823	-0.168000	0.09925	0.888000	0.36160	0.561000	0.74099	AAC	.	.	none		0.642	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1	NM_002335		A	68115631	C	A	68115631	3	1	26	1	0	0	0	0	1	0	0	0	8969	506	18	4	414	4	LRP5	11	68115631	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	2032368	68115631	66890885	380	10143											
FADD	8772	hgsc.bcm.edu	37	chr11	70049752	70049752	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcccgggcacaccgagctcCtgcgcgagctgctcgcctcc	5	5	12	19	5	0	0	0	0	0	0	3	2	2	0	5	1	5	4	5	1	0	0			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:70049752C>T	ENST00000301838.4	+	1	484	c.187C>T	c.(187-189)Ctg>Ttg	p.L63L	RP11-805J14.5_ENST00000526174.1_RNA|RP11-805J14.5_ENST00000527232.1_RNA	NM_003824.3	NP_003815.1	Q13158	FADD_HUMAN	Fas (TNFRSF6)-associated via death domain	63	DED. {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)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|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)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|motor neuron apoptotic process (GO:0097049)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic signaling pathway (GO:0097527)|negative regulation of activation-induced cell death of T cells (GO:0070236)|negative regulation of necroptotic process (GO:0060546)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of apoptotic process (GO:0043065)|positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000454)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of proteolysis (GO:0045862)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|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)|protein heterooligomerization (GO:0051291)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|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)|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)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|ripoptosome (GO:0097342)	death effector domain binding (GO:0035877)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|tumor necrosis factor receptor superfamily binding (GO:0032813)			endometrium(1)|lung(4)|ovary(1)|pancreas(1)|urinary_tract(2)	9	Esophageal squamous(2;1.19e-45)		LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			CACCGAGCTCCTGCGCGAGCT	0.736																																					p.L63L		Atlas-SNP	.											.	FADD	14	.	0			c.C187T						PASS	.						18	23	21					11																	70049752		2140	4217	6357	SO:0001819	synonymous_variant	8772	exon1			GAGCTCCTGCGCG	U24231	CCDS8196.1	11q13.3	2014-09-17			ENSG00000168040	ENSG00000168040			3573	protein-coding gene	gene with protein product	"Fas-associating protein with death domain", "Fas-associating death domain-containing protein", "mediator of receptor-induced toxicity", "growth-inhibiting gene 3 protein"	602457				7536190, 7538907	Standard	NM_003824		Approved	MORT1, GIG3	uc001opm.2	Q13158	OTTHUMG00000167264	ENST00000301838.4:c.187C>T	11.37:g.70049752C>T		65	0	0		62	33	0.532258	NM_003824	Q14866|Q6IBR4	Silent	SNP	ENST00000301838.4	37	CCDS8196.1																																																																																			.	.	none		0.736	FADD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393902.1	NM_003824		T	70049752	C	T	70049752	2	4	26	1	0	0	0	0	0	0	0	1	5369	680	24	2		2	FADD	11	70049752	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1934121	70049752	64956764	381	10144											
LRTOMT	220074	hgsc.bcm.edu	37	chr11	71800166	71800166	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	atatgaacacttcggtacagGagccccctcttgactactcc	10	10	7	14	1	1	2	0	2	1	0	3	3	2	3	3	2	4	1	3	2	4	5	rs146942815	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:71800166G>A	ENST00000289488.2	+	3	415	c.37G>A	c.(37-39)Gag>Aag	p.E13K	LRTOMT_ENST00000539271.1_Intron|LRTOMT_ENST00000439209.1_Missense_Mutation_p.E13K|LRTOMT_ENST00000536917.1_Missense_Mutation_p.E13K|LRTOMT_ENST00000538478.1_Missense_Mutation_p.E13K|LRTOMT_ENST00000539587.1_Intron|LAMTOR1_ENST00000545249.1_Intron|LRTOMT_ENST00000324866.7_Missense_Mutation_p.E13K|LRTOMT_ENST00000447974.1_Missense_Mutation_p.E13K|LRTOMT_ENST00000419228.1_5'UTR|LRTOMT_ENST00000541614.1_Missense_Mutation_p.E13K|LRTOMT_ENST00000435085.1_5'UTR|LRTOMT_ENST00000307198.7_Intron|LRTOMT_ENST00000423494.2_Intron	NM_001271471.2|NM_145309.5	NP_001258400.1|NP_660352.1	Q96E66	LRC51_HUMAN	leucine rich transmembrane and O-methyltransferase domain containing	13						cytoplasm (GO:0005737)				large_intestine(2)|lung(1)|ovary(1)	4						TTCGGTACAGGAGCCCCCTCT	0.547													G|||	8	0.00159744	0.0008	0.0029	5008	,	,		17430	0.0		0.004	False		,,,				2504	0.001				p.E13K		Atlas-SNP	.											.	LRTOMT	20	.	0			c.G37A						PASS	.	G	LYS/GLU,,,LYS/GLU	3,4397	6.2+/-15.9	0,3,2197	146	121	129		37,,,37	4.8	1	11	dbSNP_134	129	54,8532	34.8+/-89.0	1,52,4240	yes	missense,intron,intron,missense	LRTOMT	NM_001145307.2,NM_001145308.2,NM_001205138.1,NM_145309.3	56,,,56	1,55,6437	AA,AG,GG		0.6289,0.0682,0.4389	possibly-damaging,,,possibly-damaging	13/159,,,13/193	71800166	57,12929	2200	4293	6493	SO:0001583	missense	220074	exon3			GTACAGGAGCCCC		CCDS8208.1, CCDS44667.1, CCDS44668.1, CCDS55778.1, CCDS59227.1	11q13.4	2014-09-05	2013-08-19	2008-11-27	ENSG00000184154	ENSG00000184154			25033	protein-coding gene	gene with protein product		612414	"leucine rich repeat containing 51", "deafness, autosomal recessive 63"	LRRC51, DFNB63		18794526, 18953341	Standard	NM_145309		Approved	COMT2, CFAP111	uc010rqw.2	Q8WZ04	OTTHUMG00000154887	ENST00000289488.2:c.37G>A	11.37:g.71800166G>A	ENSP00000289488:p.Glu13Lys	82	0	0		80	34	0.425	NM_001271471	B2R7X1|B6CZ35|B6CZ36|B6CZ37|B6CZ38|B6CZ39|B7Z5I4	Missense_Mutation	SNP	ENST00000289488.2	37	CCDS8208.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	23.4	4.410355	0.83340	6.82E-4	0.006289	ENSG00000184154	ENST00000538413;ENST00000289488;ENST00000447974;ENST00000538478;ENST00000324866;ENST00000439209;ENST00000542846;ENST00000541614;ENST00000537483;ENST00000536917	T;T;T	0.30182	2.54;2.54;1.54	4.77	4.77	0.60923	.	0.057240	0.64402	D	0.000001	T	0.25306	0.0615	L	0.53249	1.67	0.80722	D	1	P;P	0.43352	0.628;0.804	B;B	0.40066	0.318;0.318	T	0.08889	-1.0700	10	0.46703	T	0.11	-25.2568	17.0634	0.86553	0.0:0.0:1.0:0.0	.	13;13	Q96E66-2;Q96E66	.;LRC51_HUMAN	K	13	ENSP00000289488:E13K;ENSP00000444583:E13K;ENSP00000395139:E13K	ENSP00000289488:E13K	E	+	1	0	LRTOMT	71477814	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	5.266000	0.65525	2.643000	0.89663	0.655000	0.94253	GAG	G|0.996;A|0.004	0.004	strong		0.547	LRTOMT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337504.1	NM_145309		A	71800166	G	A	71800166	3	1	26	1	0	0	0	0	1	0	0	0	9055	1175	41	2	39	2	LRTOMT	11	71800166	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1750414	71800166	63206350	382	10145											
POLD3	10714	hgsc.bcm.edu	37	chr11	74347244	74347244	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tatcctctgaccttttagagCtcaagtggagaaaacaaaag	15	10	8	8	0	2	3	1	1	1	2	3	4	3	3	2	1	2	1	2	1	7	3	rs35745457	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:74347244C>T	ENST00000263681.2	+	11	1251	c.1122C>T	c.(1120-1122)agC>agT	p.S374S	POLD3_ENST00000527458.1_Silent_p.S335S|POLD3_ENST00000532497.1_Silent_p.S268S	NM_006591.2	NP_006582.1	Q15054	DPOD3_HUMAN	polymerase (DNA-directed), delta 3, accessory subunit	374					base-excision repair (GO:0006284)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|mismatch repair (GO:0006298)|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)	delta DNA polymerase complex (GO:0043625)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|stomach(1)	18	Breast(11;3.21e-06)					CCTTTTAGAGCTCAAGTGGAG	0.343													C|||	20	0.00399361	0.0015	0.0014	5008	,	,		20618	0.0		0.0159	False		,,,				2504	0.001				p.S374S		Atlas-SNP	.											.	POLD3	87	.	0			c.C1122T						PASS	.	C		9,4391	15.5+/-35.6	0,9,2191	70	67	68		1122	2	1	11	dbSNP_126	68	110,8476	57.9+/-119.4	1,108,4184	no	coding-synonymous	POLD3	NM_006591.1		1,117,6375	TT,TC,CC		1.2812,0.2045,0.9164		374/467	74347244	119,12867	2200	4293	6493	SO:0001819	synonymous_variant	10714	exon11			TTAGAGCTCAAGT	D26018	CCDS8233.1	11q14	2014-06-13			ENSG00000077514	ENSG00000077514		"DNA polymerases"	20932	protein-coding gene	gene with protein product	"DNA polymerase delta subunit p66", "Pol delta C subunit (p66)", "protein phosphatase 1, regulatory subunit 128"	611415				10219083	Standard	NM_006591		Approved	P66, KIAA0039, P68, PPP1R128	uc001ovf.2	Q15054	OTTHUMG00000165621	ENST00000263681.2:c.1122C>T	11.37:g.74347244C>T		139	0	0		159	73	0.459119	NM_006591	B7ZAI6|Q32MZ9|Q32N00	Silent	SNP	ENST00000263681.2	37	CCDS8233.1	13	0.005952380952380952	1	0.0020325203252032522	0	0.0	0	0.0	12	0.0158311345646438	C	12.52	1.961262	0.34565	0.002045	0.012812	ENSG00000077514	ENST00000524752	.	.	.	5.92	1.96	0.26148	.	.	.	.	.	T	0.41465	0.1160	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37033	-0.9723	4	.	.	.	-38.8421	8.8571	0.35234	0.0:0.7328:0.0:0.2672	rs35745457;rs61749198	.	.	.	V	98	.	.	A	+	2	0	POLD3	74024892	0.626000	0.27120	0.979000	0.43373	0.990000	0.78478	0.375000	0.20518	0.113000	0.18004	0.561000	0.74099	GCT	C|0.990;T|0.010	0.010	strong		0.343	POLD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385376.1	NM_006591		T	74347244	C	T	74347244	2	4	26	1	0	0	0	0	0	0	0	1	12201	796	28	2		2	POLD3	11	74347244	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	2547078	74347244	60659272	383	10146											
HEPHL1	341208	hgsc.bcm.edu	37	chr11	93839219	93839219	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgaacgaagatacaatgacaAactggtatttgttagggata	16	11	10	4	1	0	3	0	2	0	1	0	5	0	4	0	2	3	2	0	2	8	5	rs200078708		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:93839219A>C	ENST00000315765.9	+	17	2976	c.2968A>C	c.(2968-2970)Aac>Cac	p.N990H		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	990	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)				TACAATGACAAACTGGTATTT	0.348																																					p.N990H		Atlas-SNP	.											.	HEPHL1	144	.	0			c.A2968C						PASS	.	A	HIS/ASN	0,3770		0,0,1885	127	125	126		2968	4.8	1	11		126	5,8207		0,5,4101	yes	missense	HEPHL1	NM_001098672.1	68	0,5,5986	CC,CA,AA		0.0609,0.0,0.0417	possibly-damaging	990/1160	93839219	5,11977	1885	4106	5991	SO:0001583	missense	341208	exon17			ATGACAAACTGGT	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.2968A>C	11.37:g.93839219A>C	ENSP00000313699:p.Asn990His	189	0	0		203	122	0.600985	NM_001098672	Q3C1W7	Missense_Mutation	SNP	ENST00000315765.9	37	CCDS44710.1	.	.	.	.	.	.	.	.	.	.	A	16.31	3.088343	0.55968	0.0	6.09E-4	ENSG00000181333	ENST00000315765	D	0.99660	-6.32	5.95	4.84	0.62591	Cupredoxin (2);Multicopper oxidase, type 2 (1);	0.232485	0.50627	D	0.000102	D	0.99055	0.9676	L	0.38649	1.16	0.29801	N	0.832439	D	0.56968	0.978	D	0.64687	0.928	D	0.97256	0.9901	10	0.37606	T	0.19	-8.3966	11.4972	0.50415	0.9307:0.0:0.0693:0.0	.	990	Q6MZM0	HPHL1_HUMAN	H	990	ENSP00000313699:N990H	ENSP00000313699:N990H	N	+	1	0	HEPHL1	93478867	0.993000	0.37304	1.000000	0.80357	0.982000	0.71751	2.852000	0.48310	2.279000	0.76181	0.533000	0.62120	AAC	.	.	weak		0.348	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947		C	93839219	A	C	93839219	3	2	26	1	0	0	0	0	1	0	0	0	7064	14	1	5	3034	5	HEPHL1	11	93839219	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	19491975	93839219	41167297	384	10147											
AASDHPPT	60496	hgsc.bcm.edu	37	chr11	105950335	105950335	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccgaatttcaactttaacAtctctcatcaaggagactat	14	12	4	11	1	4	1	3	0	1	1	5	3	4	1	1	1	2	0	1	1	5	4	rs528924003		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:105950335A>G	ENST00000278618.4	+	2	547	c.325A>G	c.(325-327)Atc>Gtc	p.I109V	KBTBD3_ENST00000534815.1_5'Flank|KBTBD3_ENST00000531837.1_5'Flank|KBTBD3_ENST00000526793.1_5'Flank	NM_015423.2	NP_056238.2	Q9NRN7	ADPPT_HUMAN	aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase	109	Coenzyme A binding.				macromolecule biosynthetic process (GO:0009059)|pantothenate metabolic process (GO:0015939)|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)	holo-[acyl-carrier-protein] synthase activity (GO:0008897)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)	17		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.78e-05)|Epithelial(105;0.00622)|all cancers(92;0.041)		CAACTTTAACATCTCTCATCA	0.393																																					p.I109V		Atlas-SNP	.											.	AASDHPPT	40	.	0			c.A325G						PASS	.						116	115	115					11																	105950335		2201	4299	6500	SO:0001583	missense	60496	exon2			TTTAACATCTCTC	AF302110	CCDS31664.1	11q22	2010-12-09			ENSG00000149313	ENSG00000149313	1.2.1.31		14235	protein-coding gene	gene with protein product		607756				12815048, 11286508	Standard	NM_015423		Approved	LYS5, CGI-80, AASD-PPT	uc001pjc.1	Q9NRN7	OTTHUMG00000166253	ENST00000278618.4:c.325A>G	11.37:g.105950335A>G	ENSP00000278618:p.Ile109Val	144	0	0		138	72	0.521739	NM_015423	B2R6D1|B4DDW7|Q9C068|Q9P0Q3|Q9UG80|Q9Y389	Missense_Mutation	SNP	ENST00000278618.4	37	CCDS31664.1	.	.	.	.	.	.	.	.	.	.	A	2.118	-0.402119	0.04865	.	.	ENSG00000149313	ENST00000533423;ENST00000524411;ENST00000278618	.	.	.	5.91	3.59	0.41128	4&apos (1);-phosphopantetheinyl transferase (1);	0.472007	0.24312	N	0.039629	T	0.16428	0.0395	N	0.01817	-0.705	0.36736	D	0.881978	B	0.02656	0.0	B	0.01281	0.0	T	0.20472	-1.0274	9	0.05620	T	0.96	.	7.3013	0.26422	0.6388:0.0:0.3612:0.0	.	109	Q9NRN7	ADPPT_HUMAN	V	44;44;109	.	ENSP00000278618:I109V	I	+	1	0	AASDHPPT	105455545	0.998000	0.40836	1.000000	0.80357	0.985000	0.73830	1.307000	0.33516	0.485000	0.27652	0.533000	0.62120	ATC	.	.	none		0.393	AASDHPPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388734.1	NM_015423		G	105950335	A	G	105950335	3	3	26	1	0	0	0	0	1	0	0	0	23	217	8	3	331	3	AASDHPPT	11	105950335	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	12111116	105950335	29056181	385	10148											
PPP2R1B	5519	hgsc.bcm.edu	37	chr11	111608216	111608216	+	IGR	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgggtcttgggaagtggtTcttgtcagcccgagggacac	6	11	16	8	1	3	0	1	0	2	0	3	3	3	2	1	4	1	1	1	4	1	3	rs61756429	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:111608216T>A	ENST00000527614.1	-	0	5587				PPP2R1B_ENST00000311129.5_Missense_Mutation_p.N623Y|PPP2R1B_ENST00000426998.2_Missense_Mutation_p.N559Y|PPP2R1B_ENST00000530787.1_5'Flank	NM_001177562.1|NM_002716.4	NP_001171033.1|NP_002707.3	P30154	2AAB_HUMAN	protein phosphatase 2, regulatory subunit A, beta						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)		GGGAAGTGGTTCTTGTCAGCC	0.597													T|||	10	0.00199681	0.0	0.0043	5008	,	,		20031	0.0		0.007	False		,,,				2504	0.0				p.N623Y		Atlas-SNP	.											.	PPP2R1B	44	.	0			c.A1867T						PASS	.	T	TYR/ASN,TYR/ASN	13,4389	21.2+/-45.6	0,13,2188	155	128	137		1867,1675	4.1	1	11	dbSNP_129	137	86,8508	48.9+/-108.6	0,86,4211	yes	missense,missense	PPP2R1B	NM_181699.2,NM_181700.1	143,143	0,99,6399	AA,AT,TT		1.0007,0.2953,0.7618	possibly-damaging,possibly-damaging	623/668,559/604	111608216	99,12897	2201	4297	6498	SO:0001628	intergenic_variant	5519	exon15			AGTGGTTCTTGTC	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		11.37:g.111608216T>A		101	0	0		126	55	0.436508	NM_181699	A8MY67|B0YJ69|B4DGQ6|B4DK91|B4DWW5|F8W8G1|O75620|Q8NHV8	Missense_Mutation	SNP	ENST00000527614.1	37	CCDS8349.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	T	10.82	1.458179	0.26161	0.002953	0.010007	ENSG00000137713	ENST00000311129;ENST00000426998	.	.	.	5.25	4.13	0.48395	.	0.617749	0.15812	N	0.243438	T	0.27933	0.0688	N	0.08118	0	0.80722	D	1	P;D	0.54207	0.94;0.965	P;P	0.51135	0.459;0.66	T	0.18493	-1.0335	9	0.87932	D	0	-10.7806	7.9175	0.29827	0.0:0.0914:0.0:0.9086	rs61756429	559;623	B4DWW5;P30154-2	.;.	Y	623;559	.	ENSP00000311344:N623Y	N	-	1	0	PPP2R1B	111113426	1.000000	0.71417	0.991000	0.47740	0.214000	0.24535	1.866000	0.39489	1.132000	0.42129	0.496000	0.49642	AAC	T|0.992;A|0.008	0.008	strong		0.597	PPP2R1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391298.1	NM_002716		A	111608216	T	A	111608216	1	1	26	0	1	0	0	0	0	0	0	0	12395	1783	62	5		5	PPP2R1B	11	111608216	IGR	SNP	T	TCGA-G8-6907-01A-11D-2210-10	5657881	111608216	23398300	386	10149											
FAM55D	54827	hgsc.bcm.edu	37	chr11	114453549	114453549	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atggtggctgtgctatgtgtGgcgctggtggtggtgttcac	3	14	18	6	1	1	0	1	0	0	0	1	0	1	0	0	6	1	4	0	6	1	2	rs371147789		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:114453549G>A	ENST00000375478.3	-	3	471	c.291C>T	c.(289-291)gcC>gcT	p.A97A	NXPE4_ENST00000424261.2_5'UTR	NM_001077639.1	NP_001071107.1	Q6UWF7	NXPE4_HUMAN	neurexophilin and PC-esterase domain family, member 4	97						extracellular vesicular exosome (GO:0070062)											TGCTATGTGTGGCGCTGGTGG	0.537																																					p.A97A		Atlas-SNP	.											FAM55D,NS,carcinoma,-2,1	.	.	1	0			c.C291T						PASS	.	G	,	1,4331		0,1,2165	251	250	250		291,	-1	0	11		250	2,8546		0,2,4272	no	coding-synonymous,utr-5	FAM55D	NM_001077639.1,NM_017678.2	,	0,3,6437	AA,AG,GG		0.0234,0.0231,0.0233	,	97/545,	114453549	3,12877	2166	4274	6440	SO:0001819	synonymous_variant	54827	exon3			ATGTGTGGCGCTG	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.291C>T	11.37:g.114453549G>A		251	0	0		325	142	0.436923	NM_001077639	Q6QDB4|Q9NXP5	Silent	SNP	ENST00000375478.3	37	CCDS41718.1																																																																																			.	.	weak		0.537	NXPE4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399179.1	NM_017678		A	114453549	G	A	114453549	2	1	26	1	0	0	0	0	0	0	0	1	5595	1335	47	2		2	FAM55D	11	114453549	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	2845333	114453549	20552967	387	10150											
IL10RA	3587	hgsc.bcm.edu	37	chr11	117864062	117864062	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccgcaaatgacacatatgaAagcatcttcagtcacttccg	13	9	6	13	2	3	2	2	2	1	0	4	2	4	2	2	0	1	2	2	0	3	3			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:117864062A>G	ENST00000227752.3	+	4	594	c.474A>G	c.(472-474)gaA>gaG	p.E158E	IL10RA_ENST00000545409.1_Silent_p.E9E|IL10RA_ENST00000541785.1_Silent_p.E138E|IL10RA_ENST00000533700.1_3'UTR	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	158					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)		ACACATATGAAAGCATCTTCA	0.542																																					p.E158E		Atlas-SNP	.											.	IL10RA	46	.	0			c.A474G						PASS	.						97	86	90					11																	117864062		2200	4296	6496	SO:0001819	synonymous_variant	3587	exon4			ATATGAAAGCATC	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.474A>G	11.37:g.117864062A>G		121	0	0		102	52	0.509804	NM_001558	A8K6I0|B0YJ27	Silent	SNP	ENST00000227752.3	37	CCDS8388.1																																																																																			.	.	none		0.542	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1			G	117864062	A	G	117864062	2	3	26	1	0	0	0	0	0	0	0	1	7629	11	1	3		3	IL10RA	11	117864062	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	3410513	117864062	17142454	388	10151											
CXCR5	643	hgsc.bcm.edu	37	chr11	118765108	118765108	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atcttcctggacaccctggcGaggctgaaggccgtggacaa	9	7	13	12	2	1	1	0	1	1	0	2	4	2	3	3	5	0	1	3	5	2	1	rs113967672	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:118765108G>A	ENST00000292174.4	+	2	1031	c.855G>A	c.(853-855)gcG>gcA	p.A285A	BCL9L_ENST00000334801.3_3'UTR	NM_001716.4|NM_032966.2	NP_001707.1|NP_116743.1	P32302	CXCR5_HUMAN	chemokine (C-X-C motif) receptor 5	285					B cell activation (GO:0042113)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of cytokinesis (GO:0032467)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|G-protein coupled receptor activity (GO:0004930)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(5)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	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)		ACACCCTGGCGAGGCTGAAGG	0.602													G|||	5	0.000998403	0.0	0.0014	5008	,	,		22112	0.0		0.004	False		,,,				2504	0.0				p.A285A		Atlas-SNP	.											CXCR5,NS,carcinoma,+1,1	CXCR5	34	1	0			c.G855A						PASS	.	G	,	3,4397	8.1+/-20.4	0,3,2197	142	108	119		855,720	-2.9	0	11	dbSNP_132	119	36,8554	24.0+/-70.4	0,36,4259	no	coding-synonymous,coding-synonymous	CXCR5	NM_001716.4,NM_032966.2	,	0,39,6456	AA,AG,GG		0.4191,0.0682,0.3002	,	285/373,240/328	118765108	39,12951	2200	4295	6495	SO:0001819	synonymous_variant	643	exon2			CCTGGCGAGGCTG	X68829	CCDS8402.1	11q23.3	2012-08-08	2008-01-22	2008-01-22	ENSG00000160683	ENSG00000160683		"CD molecules", "GPCR / Class A : Chemokine receptors : C-X-C motif"	1060	protein-coding gene	gene with protein product		601613	"Burkitt lymphoma receptor 1, GTP-binding protein", "Burkitt lymphoma receptor 1, GTP binding protein (chemokine (C-X-C motif) receptor 5)"	BLR1		1425907	Standard	NM_001716		Approved	MDR15, CD185	uc001pue.4	P32302	OTTHUMG00000166345	ENST00000292174.4:c.855G>A	11.37:g.118765108G>A		140	0	0		135	62	0.459259	NM_001716	Q14811	Silent	SNP	ENST00000292174.4	37	CCDS8402.1																																																																																			G|0.997;A|0.003	0.003	strong		0.602	CXCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389309.1	NM_001716		A	118765108	G	A	118765108	2	1	26	1	0	0	0	0	0	0	0	1	4096	1045	37	1		1	CXCR5	11	118765108	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	901046	118765108	16241408	389	10152											
TRIM29	23650	hgsc.bcm.edu	37	chr11	119998151	119998151	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcatccatgatcaccttcaCttggtccacagcatcctgct	9	11	6	15	0	2	1	2	1	0	0	5	1	5	1	4	1	3	3	4	1	0	2	rs146343820	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:119998151C>G	ENST00000341846.5	-	3	1448	c.1027G>C	c.(1027-1029)Gtg>Ctg	p.V343L	TRIM29_ENST00000528870.1_5'Flank|TRIM29_ENST00000529044.1_Missense_Mutation_p.V82L|TRIM29_ENST00000541857.1_Missense_Mutation_p.V76L	NM_012101.3	NP_036233.2	Q14134	TRI29_HUMAN	tripartite motif containing 29	343					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)		ATCACCTTCACTTGGTCCACA	0.587																																					p.V343L		Atlas-SNP	.											.	TRIM29	78	.	0			c.G1027C						PASS	.	C	LEU/VAL	4,4394	8.1+/-20.4	0,4,2195	181	148	159		1027	4.2	0.9	11	dbSNP_134	159	9,8581	7.1+/-27.0	0,9,4286	yes	missense	TRIM29	NM_012101.3	32	0,13,6481	GG,GC,CC		0.1048,0.091,0.1001	benign	343/589	119998151	13,12975	2199	4295	6494	SO:0001583	missense	23650	exon3			CCTTCACTTGGTC	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.1027G>C	11.37:g.119998151C>G	ENSP00000343129:p.Val343Leu	174	0	0		197	90	0.456853	NM_012101	Q96AA9|Q9BZY7	Missense_Mutation	SNP	ENST00000341846.5	37	CCDS8428.1	.	.	.	.	.	.	.	.	.	.	C	15.46	2.840150	0.51057	9.1E-4	0.001048	ENSG00000137699	ENST00000341846;ENST00000541857;ENST00000529044	T	0.35605	1.3	5.14	4.23	0.50019	.	0.220732	0.32147	N	0.006505	T	0.20659	0.0497	N	0.19112	0.55	0.36728	D	0.881557	B;B;B	0.21452	0.003;0.011;0.056	B;B;B	0.17433	0.009;0.017;0.018	T	0.14035	-1.0487	9	.	.	.	.	8.188	0.31350	0.0:0.7621:0.0:0.2379	.	76;82;343	B7Z8U9;E9PRL4;Q14134	.;.;TRI29_HUMAN	L	343;76;82	ENSP00000343129:V343L	.	V	-	1	0	TRIM29	119503361	0.533000	0.26354	0.908000	0.35775	0.971000	0.66376	0.465000	0.22004	1.183000	0.42943	0.655000	0.94253	GTG	C|0.999;G|0.001	0.001	strong		0.587	TRIM29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277108.2	NM_012101		G	119998151	C	G	119998151	3	3	26	1	0	0	0	0	1	0	0	0	16518	565	20	4	767	4	TRIM29	11	119998151	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1233043	119998151	15008365	390	10153											
ARHGEF12	23365	hgsc.bcm.edu	37	chr11	120317731	120317731	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgcagagcgagacaaggaccGattgactttggagaaggagc	13	6	15	7	2	0	4	0	1	0	3	0	9	0	6	1	3	3	1	1	3	2	2	rs138160103	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:120317731G>A	ENST00000397843.2	+	18	1692	c.1526G>A	c.(1525-1527)cGa>cAa	p.R509Q	ARHGEF12_ENST00000532993.1_Missense_Mutation_p.R406Q|ARHGEF12_ENST00000356641.3_Missense_Mutation_p.R490Q	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	509	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)		GACAAGGACCGATTGACTTTG	0.443			T	MLL	AML								G|||	4	0.000798722	0.0	0.0	5008	,	,		22212	0.0		0.003	False		,,,				2504	0.001				p.R509Q		Atlas-SNP	.		Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	.	ARHGEF12	133	.	0			c.G1526A						PASS	.	G	GLN/ARG,GLN/ARG	2,3952		0,2,1975	137	128	131		1469,1526	5.4	1	11	dbSNP_134	131	18,8334		0,18,4158	yes	missense,missense	ARHGEF12	NM_001198665.1,NM_015313.2	43,43	0,20,6133	AA,AG,GG		0.2155,0.0506,0.1625	probably-damaging,probably-damaging	490/1526,509/1545	120317731	20,12286	1977	4176	6153	SO:0001583	missense	23365	exon18			AGGACCGATTGAC	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.1526G>A	11.37:g.120317731G>A	ENSP00000380942:p.Arg509Gln	166	0	0		180	96	0.533333	NM_015313	O15086|Q6P526	Missense_Mutation	SNP	ENST00000397843.2	37	CCDS41727.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	37	6.004474	0.97195	5.06E-4	0.002155	ENSG00000196914	ENST00000397843;ENST00000356641;ENST00000532993	D;D;D	0.83837	-1.77;-1.77;-1.77	5.44	5.44	0.79542	Regulator of G protein signalling superfamily (1);Regulator of G protein signalling-like fold (1);	0.000000	0.41712	D	0.000824	D	0.90086	0.6903	M	0.76328	2.33	0.58432	D	0.999997	D;D;D	0.71674	0.998;0.987;0.989	P;P;P	0.60173	0.87;0.742;0.832	D	0.90454	0.4441	10	0.62326	D	0.03	-16.9171	19.6363	0.95735	0.0:0.0:1.0:0.0	.	406;490;509	B4DGW2;Q9NZN5-2;Q9NZN5	.;.;ARHGC_HUMAN	Q	509;490;406	ENSP00000380942:R509Q;ENSP00000349056:R490Q;ENSP00000432984:R406Q	ENSP00000349056:R490Q	R	+	2	0	ARHGEF12	119822941	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	7.416000	0.80143	2.714000	0.92807	0.650000	0.86243	CGA	G|0.998;A|0.002	0.002	strong		0.443	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	NM_015313		A	120317731	G	A	120317731	3	1	26	1	0	0	0	0	1	0	0	0	897	1058	37	1	1596	1	ARHGEF12	11	120317731	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	319580	120317731	14688785	391	10154											
OR10G4	390264	hgsc.bcm.edu	37	chr11	123886902	123886902	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacattgggatagtggcctcAggctgctttgtcctgatagt	7	13	13	8	0	1	1	1	1	0	0	2	3	2	2	2	3	1	2	2	3	2	4	rs144455396	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:123886902A>G	ENST00000320891.4	+	1	621	c.621A>G	c.(619-621)tcA>tcG	p.S207S		NM_001004462.1	NP_001004462.1	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G, member 4	207						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)		TAGTGGCCTCAGGCTGCTTTG	0.557													a|||	4	0.000798722	0.0	0.0014	5008	,	,		22457	0.0		0.003	False		,,,				2504	0.0				p.S207S		Atlas-SNP	.											.	OR10G4	77	.	0			c.A621G						PASS	.	G		4,4398	8.1+/-20.4	0,4,2197	293	244	261		621	-6.4	0	11	dbSNP_134	261	18,8580	13.3+/-46.6	0,18,4281	no	coding-synonymous	OR10G4	NM_001004462.1		0,22,6478	GG,GA,AA		0.2094,0.0909,0.1692		207/312	123886902	22,12978	2201	4299	6500	SO:0001819	synonymous_variant	390264	exon1			GGCCTCAGGCTGC	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.621A>G	11.37:g.123886902A>G		403	1	0.00248139		510	243	0.476471	NM_001004462	Q6IEW0	Silent	SNP	ENST00000320891.4	37	CCDS31702.1																																																																																			A|0.998;G|0.002	0.002	strong		0.557	OR10G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387268.1	NM_001004462		G	123886902	A	G	123886902	2	3	26	1	0	0	0	0	0	0	0	1	10910	175	7	3		3	OR10G4	11	123886902	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	3569171	123886902	11119614	392	10155											
OR10G7	390265	hgsc.bcm.edu	37	chr11	123908971	123908971	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggccaaagaagcaaaggacCacgatacagtgggaggcaca	16	2	14	9	1	0	1	0	0	0	1	0	4	0	3	2	4	2	2	2	4	4	1	rs142080661	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:123908971C>T	ENST00000330487.5	-	1	746	c.738G>A	c.(736-738)gtG>gtA	p.V246V		NM_001004463.1	NP_001004463.1	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G, member 7	246						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)		AGCAAAGGACCACGATACAGT	0.567													C|||	12	0.00239617	0.0	0.0	5008	,	,		18724	0.0		0.0	False		,,,				2504	0.0123				p.V246V		Atlas-SNP	.											.	OR10G7	103	.	0			c.G738A						PASS	.	C		0,4400		0,0,2200	110	95	100		738	2.4	1	11	dbSNP_134	100	8,8590	6.4+/-24.3	0,8,4291	no	coding-synonymous	OR10G7	NM_001004463.1		0,8,6491	TT,TC,CC		0.093,0.0,0.0615		246/312	123908971	8,12990	2200	4299	6499	SO:0001819	synonymous_variant	390265	exon1			AAGGACCACGATA	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.738G>A	11.37:g.123908971C>T		186	0	0		196	103	0.52551	NM_001004463	Q6IFE8	Silent	SNP	ENST00000330487.5	37	CCDS31705.1																																																																																			C|1.000;T|0.000	0.000	strong		0.567	OR10G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387271.1	NM_001004463		T	123908971	C	T	123908971	2	4	26	1	0	0	0	0	0	0	0	1	10911	581	21	2		2	OR10G7	11	123908971	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	22069	123908971	11097545	393	10156											
OR8G5	219865	hgsc.bcm.edu	37	chr11	124135619	124135619	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtacctgcagccatcatcTgtcagctccatggaccaggg	9	9	10	13	0	3	0	2	0	1	0	4	1	4	1	4	2	4	3	4	2	1	1			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:124135619T>C	ENST00000524943.2	+	1	897	c.897T>C	c.(895-897)tcT>tcC	p.S299S	OR8G1_ENST00000341493.2_RNA	NM_001005198.1	NP_001005198.1	Q8NG78	OR8G5_HUMAN	olfactory receptor, family 8, subfamily G, member 5	299						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)		AGCCATCATCTGTCAGCTCCA	0.507																																					p.S299S	Ovarian(169;523 1969 8640 31295 51256)	Atlas-SNP	.											.	.	.	.	0			c.T897C						PASS	.						106	104	105					11																	124135619		2109	4260	6369	SO:0001819	synonymous_variant	219865	exon1			ATCATCTGTCAGC	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.897T>C	11.37:g.124135619T>C		260	0	0		311	22	0.0707396	NM_001005198	B2RND3|Q6IEU6	Silent	SNP	ENST00000524943.2	37																																																																																				.	.	none		0.507	OR8G5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387283.2	NM_001005198		C	124135619	T	C	124135619	2	2	26	1	0	0	0	0	0	0	0	1	11245	1567	55	3		3	OR8G5	11	124135619	Silent	SNP	T	TCGA-G8-6907-01A-11D-2210-10	226648	124135619	10870897	394	10157											
KCNJ1	3758	hgsc.bcm.edu	37	chr11	128709126	128709126	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttctcattataaaggcacAtggcacagtgaggggtctcc	10	11	10	10	0	2	1	1	1	2	0	4	1	2	1	1	4	0	2	1	4	3	3	rs59172778	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:128709126A>G	ENST00000392664.2	-	2	1186	c.1070T>C	c.(1069-1071)aTg>aCg	p.M357T	KCNJ1_ENST00000392666.1_Missense_Mutation_p.M338T|KCNJ1_ENST00000392665.2_Missense_Mutation_p.M338T|KCNJ1_ENST00000324036.3_Missense_Mutation_p.M338T|KCNJ1_ENST00000440599.2_Missense_Mutation_p.M338T	NM_000220.4	NP_000211.1	P48048	KCNJ1_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 1	357			M -> T (in BS2; dbSNP:rs59172778). {ECO:0000269|PubMed:8841184}.		cardiovascular system development (GO:0072358)|excretion (GO:0007588)|kidney development (GO:0001822)|post-embryonic development (GO:0009791)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of G-protein activated inward rectifier potassium channel activity (GO:1900128)|renal sodium ion absorption (GO:0070294)|synaptic transmission (GO:0007268)|tissue homeostasis (GO:0001894)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|inward rectifier potassium channel activity (GO:0005242)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(2)|endometrium(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)	23	all_hematologic(175;0.0641)	all_lung(97;4.89e-06)|Lung NSC(97;9.34e-06)|Breast(109;0.00123)|all_hematologic(192;0.00793)|Renal(330;0.0112)|all_neural(223;0.0189)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;4.05e-06)|LUSC - Lung squamous cell carcinoma(976;0.008)|Lung(977;0.00942)	Bethanidine(DB00217)|Glimepiride(DB00222)|Glyburide(DB01016)|Glycodiazine(DB01382)|Minoxidil(DB00350)|Tolazamide(DB00839)|Tolbutamide(DB01124)|Yohimbine(DB01392)	ATAAAGGCACATGGCACAGTG	0.438													A|||	14	0.00279553	0.0	0.0029	5008	,	,		21343	0.0		0.0119	False		,,,				2504	0.0				p.M357T		Atlas-SNP	.											.	KCNJ1	68	.	0			c.T1070C	GRCh37	CM960893	KCNJ1	M	rs59172778	PASS	.	A	THR/MET,THR/MET,THR/MET,THR/MET,THR/MET	8,4394	14.3+/-33.2	0,8,2193	119	114	115	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1070,1013,1013,1013,1013	5.9	1	11	dbSNP_129	115	81,8513	46.7+/-105.8	1,79,4217	yes	missense,missense,missense,missense,missense	KCNJ1	NM_000220.2,NM_153764.1,NM_153765.1,NM_153766.1,NM_153767.2	81,81,81,81,81	1,87,6410	GG,GA,AA		0.9425,0.1817,0.6848	benign,benign,benign,benign,benign	357/392,338/373,338/373,338/373,338/373	128709126	89,12907	2201	4297	6498	SO:0001583	missense	3758	exon2			AGGCACATGGCAC	BC063109	CCDS8476.1, CCDS8477.1	11q24	2011-07-05			ENSG00000151704	ENSG00000151704		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Inwardly rectifying"	6255	protein-coding gene	gene with protein product		600359				7680431, 8190102, 16382105	Standard	NM_153765		Approved	Kir1.1, ROMK1	uc001qeo.2	P48048	OTTHUMG00000048247	ENST00000392664.2:c.1070T>C	11.37:g.128709126A>G	ENSP00000376432:p.Met357Thr	100	0	0		126	64	0.507937	NM_000220	B2RMR4|Q6LD67	Missense_Mutation	SNP	ENST00000392664.2	37	CCDS8476.1	11	0.005036630036630037	0	0.0	1	0.0027624309392265192	0	0.0	10	0.013192612137203167	A	8.138	0.784569	0.16189	0.001817	0.009425	ENSG00000151704	ENST00000392665;ENST00000392666;ENST00000440599;ENST00000324036;ENST00000392664	D;D;D;D;D	0.93488	-3.23;-3.23;-3.23;-3.23;-3.23	5.9	5.9	0.94986	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.432611	0.29212	N	0.012803	D	0.86280	0.5895	N	0.24115	0.695	0.25998	N	0.982157	B	0.11235	0.004	B	0.22753	0.041	T	0.80714	-0.1259	10	0.72032	D	0.01	.	16.3245	0.82970	1.0:0.0:0.0:0.0	rs59172778;rs62625013	357	P48048	IRK1_HUMAN	T	338;338;338;338;357	ENSP00000376433:M338T;ENSP00000376434:M338T;ENSP00000406320:M338T;ENSP00000316233:M338T;ENSP00000376432:M357T	ENSP00000316233:M338T	M	-	2	0	KCNJ1	128214336	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.870000	0.63035	2.254000	0.74563	0.460000	0.39030	ATG	A|0.993;G|0.007	0.007	strong		0.438	KCNJ1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386233.1	NM_000220		G	128709126	A	G	128709126	3	3	26	1	0	0	0	0	1	0	0	0	8052	217	8	3	109	3	KCNJ1	11	128709126	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	4573507	128709126	6297390	395	10158											
ARHGAP32	9743	hgsc.bcm.edu	37	chr11	128839550	128839550	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	catggcctccgtgatggtggGctctgtccatctctgcctcg	3	12	12	14	2	2	1	0	1	2	0	6	1	4	1	4	3	1	1	4	3	0	0			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:128839550G>T	ENST00000310343.9	-	22	5515	c.5516C>A	c.(5515-5517)gCc>gAc	p.A1839D	ARHGAP32_ENST00000524655.1_3'UTR|ARHGAP32_ENST00000527272.1_Missense_Mutation_p.A1490D|ARHGAP32_ENST00000392657.3_Missense_Mutation_p.A1490D	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	1839	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						GTGATGGTGGGCTCTGTCCAT	0.622																																					p.A1839D		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.C5516A						PASS	.						72	65	67					11																	128839550		2201	4297	6498	SO:0001583	missense	9743	exon22			TGGTGGGCTCTGT	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.5516C>A	11.37:g.128839550G>T	ENSP00000310561:p.Ala1839Asp	65	0	0		59	26	0.440678	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Missense_Mutation	SNP	ENST00000310343.9	37	CCDS44769.1	.	.	.	.	.	.	.	.	.	.	G	9.632	1.136685	0.21123	.	.	ENSG00000134909	ENST00000310343;ENST00000392657;ENST00000527272	T;T;T	0.10099	2.93;2.91;2.91	5.95	4.11	0.48088	.	0.273133	0.35525	N	0.003151	T	0.14270	0.0345	M	0.62723	1.935	0.34234	D	0.676855	B	0.13594	0.008	B	0.10450	0.005	T	0.05989	-1.0852	10	0.87932	D	0	.	12.7738	0.57436	0.1319:0.0:0.8681:0.0	.	1839	A7KAX9	RHG32_HUMAN	D	1839;1490;1490	ENSP00000310561:A1839D;ENSP00000376425:A1490D;ENSP00000432862:A1490D	ENSP00000310561:A1839D	A	-	2	0	ARHGAP32	128344760	0.998000	0.40836	0.111000	0.21465	0.020000	0.10135	2.664000	0.46783	0.875000	0.35847	-0.126000	0.14955	GCC	.	.	none		0.622	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715		T	128839550	G	T	128839550	3	4	26	1	0	0	0	0	1	0	0	0	881	1203	42	4	751	4	ARHGAP32	11	128839550	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	130424	128839550	6166966	396	10159											
ST14	6768	hgsc.bcm.edu	37	chr11	130079574	130079574	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cagggtgattccgggggaccCctgtccagcgtggaggcgga	6	6	18	11	3	0	1	0	1	0	0	2	4	2	4	4	6	1	0	4	6	0	1	rs116956726	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:130079574C>T	ENST00000278742.5	+	19	2842	c.2424C>T	c.(2422-2424)ccC>ccT	p.P808P		NM_021978.3	NP_068813.1	Q9Y5Y6	ST14_HUMAN	suppression of tumorigenicity 14 (colon carcinoma)	808	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				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)	CCGGGGGACCCCTGTCCAGCG	0.716													C|||	36	0.0071885	0.0	0.0101	5008	,	,		12333	0.0		0.0159	False		,,,				2504	0.0133				p.P808P		Atlas-SNP	.											.	ST14	82	.	0			c.C2424T						PASS	.	C		13,4389	17.9+/-39.9	0,13,2188	41	43	42		2424	-4.3	1	11	dbSNP_132	42	108,8486	56.4+/-117.6	0,108,4189	no	coding-synonymous	ST14	NM_021978.3		0,121,6377	TT,TC,CC		1.2567,0.2953,0.9311		808/856	130079574	121,12875	2201	4297	6498	SO:0001819	synonymous_variant	6768	exon19			GGGACCCCTGTCC	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.2424C>T	11.37:g.130079574C>T		41	0	0		44	23	0.522727	NM_021978	Q9BS01|Q9H3S0|Q9HB36|Q9HCA3	Silent	SNP	ENST00000278742.5	37	CCDS8487.1																																																																																			C|0.993;T|0.007	0.007	strong		0.716	ST14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386119.1			T	130079574	C	T	130079574	2	4	26	1	0	0	0	0	0	0	0	1	15226	610	22	2		2	ST14	11	130079574	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1240024	130079574	4926942	397	10160											
B4GALNT3	283358	hgsc.bcm.edu	37	chr12	644351	644351	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggtacggcagctggagagaActggccaaggctctggccag	9	5	17	10	1	1	1	0	0	1	1	1	3	1	2	2	6	3	4	2	6	3	1			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:644351A>G	ENST00000266383.5	+	2	202	c.189A>G	c.(187-189)gaA>gaG	p.E63E		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	63					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)			GCTGGAGAGAACTGGCCAAGG	0.567																																					p.E63E		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.A189G						PASS	.						50	46	47					12																	644351		2203	4300	6503	SO:0001819	synonymous_variant	283358	exon2			GAGAGAACTGGCC	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.189A>G	12.37:g.644351A>G		43	0	0		46	4	0.0869565	NM_173593	Q6ZNC1|Q8N7T6	Silent	SNP	ENST00000266383.5	37	CCDS8504.1																																																																																			.	.	none		0.567	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593		G	644351	A	G	644351	2	3	26	1	0	0	0	0	0	0	0	1	1268	40	2	3		3	B4GALNT3	12	644351	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10		644351	133207544	398	10161											
CACNA2D4	93589	hgsc.bcm.edu	37	chr12	1965211	1965211	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtccttcctggtgaggaagcGgatcatggcctctagctggc	6	10	14	11	1	2	1	1	1	1	0	4	3	4	3	3	5	2	1	3	5	2	2	rs369720566		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:1965211G>A	ENST00000382722.5	-	22	2481	c.2119C>T	c.(2119-2121)Cgc>Tgc	p.R707C	CACNA2D4_ENST00000539048.2_5'UTR|CACNA2D4_ENST00000586184.1_Missense_Mutation_p.R707C|CACNA2D4_ENST00000585732.1_Missense_Mutation_p.R568C|CACNA2D4_ENST00000588077.1_Missense_Mutation_p.R643C|CACNA2D4_ENST00000585708.1_Missense_Mutation_p.R643C|CACNA2D4_ENST00000587995.1_Missense_Mutation_p.R682C	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	707					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)		GTGAGGAAGCGGATCATGGCC	0.547																																					p.R707C	Colon(2;101 179 21030 23310 28141)	Atlas-SNP	.											.	CACNA2D4	220	.	0			c.C2119T						PASS	.	G	CYS/ARG	0,4086		0,0,2043	66	74	71		2119	3.3	0.8	12		71	1,8377		0,1,4188	no	missense	CACNA2D4	NM_172364.4	180	0,1,6231	AA,AG,GG		0.0119,0.0,0.0080	probably-damaging	707/1138	1965211	1,12463	2043	4189	6232	SO:0001583	missense	93589	exon22			GGAAGCGGATCAT	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.2119C>T	12.37:g.1965211G>A	ENSP00000372169:p.Arg707Cys	84	0	0		104	52	0.5	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Missense_Mutation	SNP	ENST00000382722.5	37	CCDS44785.1	.	.	.	.	.	.	.	.	.	.	G	13.27	2.188538	0.38609	0.0	1.19E-4	ENSG00000151062	ENST00000456077;ENST00000280663;ENST00000382722	T	0.31510	1.49	4.2	3.29	0.37713	.	0.257496	0.39909	N	0.001236	T	0.48995	0.1531	M	0.76002	2.32	0.31211	N	0.698629	D;D	0.76494	0.997;0.999	P;P	0.61397	0.888;0.8	T	0.57963	-0.7720	10	0.66056	D	0.02	.	10.5365	0.45007	0.0:0.0:0.6495:0.3505	.	707;707	Q7Z3S7-2;Q7Z3S7	.;CA2D4_HUMAN	C	643;707;707	ENSP00000372169:R707C	ENSP00000280663:R707C	R	-	1	0	CACNA2D4	1835472	0.445000	0.25657	0.765000	0.31456	0.218000	0.24690	3.494000	0.53273	0.867000	0.35654	0.462000	0.41574	CGC	.	.	weak		0.547	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2			A	1965211	G	A	1965211	3	1	26	1	0	0	0	0	1	0	0	0	2553	1116	39	1	1362	1	CACNA2D4	12	1965211	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1320860	1965211	131886684	399	10162											
ANO2	57101	hgsc.bcm.edu	37	chr12	5841701	5841701	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	catacctcatcgccacactcCgtcgtgtttgtttccaattt	7	15	5	14	3	1	0	1	0	0	0	5	0	3	0	4	0	1	2	4	0	2	4			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:5841701C>T	ENST00000356134.5	-	16	1604	c.1533G>A	c.(1531-1533)acG>acA	p.T511T	ANO2_ENST00000546188.1_Silent_p.T511T|ANO2_ENST00000327087.8_Silent_p.T510T|ANO2_ENST00000538154.1_5'UTR	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	515					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						CGCCACACTCCGTCGTGTTTG	0.463																																					p.T510T		Atlas-SNP	.											ANO2_ENST00000327087,NS,carcinoma,0,2	ANO2	309	2	0			c.G1530A						PASS	.						110	110	110					12																	5841701		2074	4205	6279	SO:0001819	synonymous_variant	57101	exon15			ACACTCCGTCGTG	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.1533G>A	12.37:g.5841701C>T		155	0	0		185	89	0.481081	NM_020373	C4N787|Q9H847	Silent	SNP	ENST00000356134.5	37																																																																																				.	.	none		0.463	ANO2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399019.4	NM_020373		T	5841701	C	T	5841701	2	4	26	1	0	0	0	0	0	0	0	1	697	639	23	1		1	ANO2	12	5841701	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	3876490	5841701	128010194	400	10163											
MRPL51	51258	hgsc.bcm.edu	37	chr12	6601475	6601475	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcggttaaagtgtttgtagaGatagcggatgcgtttattaa	11	15	12	3	3	0	1	0	0	0	1	1	3	0	2	0	2	2	4	0	2	6	7	rs11380	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:6601475G>A	ENST00000229238.3	-	3	810	c.349C>T	c.(349-351)Ctc>Ttc	p.L117F	NCAPD2_ENST00000545962.1_5'Flank|MRPL51_ENST00000543703.1_Missense_Mutation_p.L21F|NCAPD2_ENST00000315579.5_5'Flank|MRPL51_ENST00000543164.1_5'UTR	NM_016497.3	NP_057581.2	Q4U2R6	RM51_HUMAN	mitochondrial ribosomal protein L51	117					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrial ribosome (GO:0005761)	structural constituent of ribosome (GO:0003735)			kidney(2)|large_intestine(1)|lung(3)	6						TGTTTGTAGAGATAGCGGATG	0.433													G|||	2	0.000399361	0.0	0.0	5008	,	,		21574	0.0		0.002	False		,,,				2504	0.0				p.L117F		Atlas-SNP	.											MRPL51,NS,carcinoma,0,1	MRPL51	17	1	0			c.C349T						PASS	.	G	PHE/LEU	2,4404	4.2+/-10.8	0,2,2201	232	220	224		349	5.3	1	12	dbSNP_52	224	9,8591	7.1+/-27.0	0,9,4291	yes	missense	MRPL51	NM_016497.3	22	0,11,6492	AA,AG,GG		0.1047,0.0454,0.0846	probably-damaging	117/129	6601475	11,12995	2203	4300	6503	SO:0001583	missense	51258	exon3			TGTAGAGATAGCG	AB051355	CCDS8547.1	12p13.3-p13.1	2014-02-19	2002-01-07	2002-01-11		ENSG00000111639		"Mitochondrial ribosomal proteins / large subunits"	14044	protein-coding gene	gene with protein product		611855	"mitochondrial ribosomal protein 64"	MRP64		11551941, 11543634	Standard	NM_016497		Approved	CDA09, HSPC241, bMRP64	uc001qom.2	Q4U2R6		ENST00000229238.3:c.349C>T	12.37:g.6601475G>A	ENSP00000229238:p.Leu117Phe	326	0	0		331	166	0.501511	NM_016497	Q96Q57|Q9BQ36|Q9P0N7	Missense_Mutation	SNP	ENST00000229238.3	37	CCDS8547.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	26.9	4.780307	0.90195	4.54E-4	0.001047	ENSG00000111639	ENST00000229238	T	0.63255	-0.03	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.81128	0.4758	M	0.90483	3.12	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84217	0.0459	10	0.87932	D	0	-15.4554	10.5659	0.45173	0.1242:0.0:0.8758:0.0	rs11380;rs52796309	117	Q4U2R6	RM51_HUMAN	F	117	ENSP00000229238:L117F	ENSP00000229238:L117F	L	-	1	0	MRPL51	6471736	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.291000	0.65667	2.478000	0.83669	0.462000	0.41574	CTC	G|0.999;A|0.001	0.001	strong		0.433	MRPL51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399956.1	NM_016497		A	6601475	G	A	6601475	3	1	26	1	0	0	0	0	1	0	0	0	9824	942	33	2	41	2	MRPL51	12	6601475	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	759774	6601475	127250420	401	10164											
GPR162	27239	hgsc.bcm.edu	37	chr12	6934804	6934804	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgcacagtgtgggagcaatgCgtggccatcatgtctgagga	9	8	15	9	2	2	1	1	1	1	0	2	3	2	3	1	3	2	2	1	3	1	0	rs148277722	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:6934804C>T	ENST00000311268.3	+	3	1810	c.1023C>T	c.(1021-1023)tgC>tgT	p.C341C	GPR162_ENST00000428545.2_Silent_p.C57C|LEPREL2_ENST00000606935.1_RNA|GPR162_ENST00000382315.3_Silent_p.C37C|LEPREL2_ENST00000396725.2_RNA|LEPREL2_ENST00000251761.8_RNA	NM_019858.1	NP_062832.1	Q16538	GP162_HUMAN	G protein-coupled receptor 162	341						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						GGGAGCAATGCGTGGCCATCA	0.607											OREG0021636	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	4	0.000798722	0.0015	0.0	5008	,	,		-128	0.0		0.0	False		,,,				2504	0.002				p.C341C		Atlas-SNP	.											.	GPR162	55	.	0			c.C1023T						PASS	.	C	,	2,4400		0,2,2199	92	56	68		171,1023	0.7	1	12	dbSNP_134	68	17,8577		0,17,4280	no	coding-synonymous,coding-synonymous	GPR162	NM_014449.1,NM_019858.1	,	0,19,6479	TT,TC,CC		0.1978,0.0454,0.1462	,	57/305,341/589	6934804	19,12977	2201	4297	6498	SO:0001819	synonymous_variant	27239	exon3			GCAATGCGTGGCC	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.1023C>T	12.37:g.6934804C>T		97	0	0	637	140	71	0.507143	NM_019858	Q16664|Q59EH5|Q66K56	Silent	SNP	ENST00000311268.3	37	CCDS8563.1																																																																																			C|0.999;T|0.001	0.001	strong		0.607	GPR162-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399478.1	NM_019858		T	6934804	C	T	6934804	2	4	26	1	0	0	0	0	0	0	0	1	6674	776	27	1		1	GPR162	12	6934804	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	333329	6934804	126917091	402	10165											
CLEC9A	283420	hgsc.bcm.edu	37	chr12	10217412	10217412	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcaggatggacacagcggaCgctggctttggcaagatggc	9	7	15	10	2	1	1	1	0	0	1	1	4	1	4	0	6	1	3	0	6	1	1	rs147713876	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:10217412C>T	ENST00000355819.1	+	8	1166	c.553C>T	c.(553-555)Cgc>Tgc	p.R185C		NM_207345.2	NP_997228.1	Q6UXN8	CLC9A_HUMAN	C-type lectin domain family 9, member A	185	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				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						ACACAGCGGACGCTGGCTTTG	0.438																																					p.R185C		Atlas-SNP	.											.	CLEC9A	41	.	0			c.C553T						PASS	.	C	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	125	116	119		553	-3	0	12	dbSNP_134	119	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CLEC9A	NM_207345.2	180	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	probably-damaging	185/242	10217412	3,13003	2203	4300	6503	SO:0001583	missense	283420	exon8			AGCGGACGCTGGC		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.553C>T	12.37:g.10217412C>T	ENSP00000348074:p.Arg185Cys	119	0	0		139	71	0.510791	NM_207345	B0ZBM2	Missense_Mutation	SNP	ENST00000355819.1	37	CCDS8611.1	.	.	.	.	.	.	.	.	.	.	C	16.08	3.021102	0.54576	2.27E-4	2.33E-4	ENSG00000197992	ENST00000355819	T	0.19394	2.15	5.24	-3.0	0.05480	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.955151	0.08603	N	0.921157	T	0.22551	0.0544	M	0.64997	1.995	0.09310	N	1	D	0.53312	0.959	P	0.48901	0.594	T	0.18903	-1.0322	10	0.59425	D	0.04	.	1.5356	0.02544	0.1565:0.2573:0.1343:0.4519	.	185	Q6UXN8	CLC9A_HUMAN	C	185	ENSP00000348074:R185C	ENSP00000348074:R185C	R	+	1	0	CLEC9A	10108679	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.238000	0.02919	-0.348000	0.08286	0.655000	0.94253	CGC	C|1.000;T|0.000	0.000	strong		0.438	CLEC9A-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000399564.1	NM_207345		T	10217412	C	T	10217412	3	4	26	1	0	0	0	0	1	0	0	0	3524	536	19	1	571	1	CLEC9A	12	10217412	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	3282608	10217412	123634483	403	10166											
TAS2R31	259290	hgsc.bcm.edu	37	chr12	11183035	11183035	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gaaggcttctctcctttcacCcagtacctcacttgccgcaa	8	11	6	16	1	3	0	2	0	1	0	5	1	4	0	4	1	2	3	4	1	3	4	rs78820764	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:11183035C>T	ENST00000390675.2	-	1	971	c.900G>A	c.(898-900)tgG>tgA	p.W300*	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176885.2	NP_795366.2	P59538	T2R31_HUMAN	taste receptor, type 2, member 31	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)			kidney(1)|lung(6)	7						CTCCTTTCACCCAGTACCTCA	0.408																																					p.W300X		Atlas-SNP	.											.	TAS2R31	24	.	0			c.G900A						PASS	.																																			SO:0001587	stop_gained	259290	exon1			TTTCACCCAGTAC	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.900G>A	12.37:g.11183035C>T	ENSP00000375093:p.Trp300*	314	0	0		263	16	0.0608365	NM_176885	P59547|Q17R84|Q645X5	Nonsense_Mutation	SNP	ENST00000390675.2	37	CCDS53747.1	.	.	.	.	.	.	.	.	.	.	.	10.72	1.429329	0.25726	.	.	ENSG00000256436	ENST00000390675	.	.	.	2.5	-1.35	0.09114	.	.	.	.	.	.	.	.	.	.	.	0.20196	N	0.99993	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.4522	0.16570	0.2085:0.3805:0.4109:0.0	rs3759247	.	.	.	X	300	.	ENSP00000375093:W300X	W	-	3	0	TAS2R31	11074302	0.000000	0.05858	0.001000	0.08648	0.038000	0.13279	-2.133000	0.01308	-0.040000	0.13580	-1.271000	0.01417	TGG	C|0.989;T|0.011	0.011	strong		0.408	TAS2R31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400233.1	NM_176885		T	11183035	C	T	11183035	4	4	26	1	0	0	0	0	0	1	0	0	15589	624	22	2	33	2	TAS2R31	12	11183035	Nonsense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	965623	11183035	122668860	404	10167											
PTPRO	5800	hgsc.bcm.edu	37	chr12	15699555	15699555	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aacaaaacccagacttcagtGactttgctgtgggtggaaga	13	9	11	8	0	1	3	1	1	0	2	1	4	1	4	1	2	3	1	1	2	4	2			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:15699555G>C	ENST00000281171.4	+	13	2547	c.2217G>C	c.(2215-2217)gtG>gtC	p.V739V	PTPRO_ENST00000442921.2_5'UTR|PTPRO_ENST00000348962.2_Silent_p.V739V|PTPRO_ENST00000445537.2_5'UTR|PTPRO_ENST00000544244.1_5'UTR|PTPRO_ENST00000542557.1_5'UTR	NM_030667.2	NP_109592.1	Q16827	PTPRO_HUMAN	protein tyrosine phosphatase, receptor type, O	739	Fibronectin type-III 8. {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)				AGACTTCAGTGACTTTGCTGT	0.393																																					p.V739V		Atlas-SNP	.											.	PTPRO	148	.	0			c.G2217C						PASS	.						98	94	96					12																	15699555		2203	4300	6503	SO:0001819	synonymous_variant	5800	exon13			TTCAGTGACTTTG	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.2217G>C	12.37:g.15699555G>C		183	0	0		160	73	0.45625	NM_002848	A0AV39|Q13101|Q8IYG3|Q9UBF0|Q9UBT5	Silent	SNP	ENST00000281171.4	37	CCDS8675.1																																																																																			.	.	none		0.393	PTPRO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401079.1			C	15699555	G	C	15699555	2	2	26	1	0	0	0	0	0	0	0	1	12824	1277	45	4		4	PTPRO	12	15699555	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	4516520	15699555	118152340	405	10168											
BCAT1	586	hgsc.bcm.edu	37	chr12	24970966	24970966	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gatagcacaattgtccagtcGctctcttctcttccatactg	8	14	6	13	1	2	0	0	0	2	0	7	1	4	0	2	0	2	2	2	0	3	5	rs117200620	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:24970966G>A	ENST00000261192.7	-	11	1663	c.1137C>T	c.(1135-1137)agC>agT	p.S379S	BCAT1_ENST00000538118.1_Silent_p.S378S|BCAT1_ENST00000539282.1_Silent_p.S391S|BCAT1_ENST00000342945.5_Silent_p.S318S|BCAT1_ENST00000539780.1_Silent_p.S342S	NM_001178091.1|NM_005504.6	NP_001171562.1|NP_005495.2	P54687	BCAT1_HUMAN	branched chain amino-acid transaminase 1, cytosolic	379					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)	TTGTCCAGTCGCTCTCTTCTC	0.398													G|||	71	0.0141773	0.003	0.0058	5008	,	,		21169	0.001		0.0099	False		,,,				2504	0.0532				p.S391S		Atlas-SNP	.											BCAT1,NS,carcinoma,0,1	BCAT1	44	1	0			c.C1173T						scavenged	.	G	,,,,	24,3794		0,24,1885	165	153	157		1026,954,1173,1134,1137	-5.2	0.8	12	dbSNP_132	157	101,8187		1,99,4044	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BCAT1	NM_001178091.1,NM_001178092.1,NM_001178093.1,NM_001178094.1,NM_005504.6	,,,,	1,123,5929	AA,AG,GG		1.2186,0.6286,1.0325	,,,,	342/350,318/326,391/399,378/386,379/387	24970966	125,11981	1909	4144	6053	SO:0001819	synonymous_variant	586	exon11			CCAGTCGCTCTCT		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.1137C>T	12.37:g.24970966G>A		202	1	0.00495049		240	114	0.475	NM_001178093	B3KY27|B7Z2M5|B7Z5L0|F5H5E4|Q68DQ7|Q96MY9	Silent	SNP	ENST00000261192.7	37	CCDS44845.1																																																																																			G|0.992;A|0.008	0.008	strong		0.398	BCAT1-001	KNOWN	upstream_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402080.1	NM_005504		A	24970966	G	A	24970966	2	1	26	1	0	0	0	0	0	0	0	1	1354	1078	38	1		1	BCAT1	12	24970966	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	9271411	24970966	108880929	406	10169											
TMTC1	83857	hgsc.bcm.edu	37	chr12	29671406	29671406	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaaagaaagggaactttaccGcttgtaccattcttcagcca	14	10	7	10	1	2	1	1	0	1	1	2	2	2	2	3	1	4	2	3	1	6	6	rs192684476		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:29671406G>A	ENST00000539277.1	-	13	2081	c.2023C>T	c.(2023-2025)Cgc>Tgc	p.R675C	TMTC1_ENST00000319685.8_5'UTR|TMTC1_ENST00000256062.5_Splice_Site_p.R567C|TMTC1_ENST00000551659.1_Splice_Site_p.R737C|TMTC1_ENST00000552618.1_Splice_Site_p.R699C|RP11-310I24.1_ENST00000549070.1_RNA	NM_001193451.1	NP_001180380.1	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	675						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)					GAACTTTACCGCTTGTACCAT	0.458													G|||	1	0.000199681	0.0	0.0	5008	,	,		18068	0.001		0.0	False		,,,				2504	0.0				p.R675C		Atlas-SNP	.											.	TMTC1	147	.	0			c.C2023T						PASS	.						170	155	160					12																	29671406		2203	4300	6503	SO:0001630	splice_region_variant	83857	exon13			TTTACCGCTTGTA		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.2024+1C>T	12.37:g.29671406G>A		172	0	0		204	88	0.431373	NM_001193451	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	Missense_Mutation	SNP	ENST00000539277.1	37	CCDS53772.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	16.48	3.135053	0.56828	.	.	ENSG00000133687	ENST00000540901;ENST00000256062;ENST00000551659;ENST00000552618;ENST00000539277	T;T;T;T	0.59638	0.25;0.25;0.46;0.25	4.79	3.89	0.44902	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.059624	0.64402	D	0.000007	T	0.80287	0.4595	H	0.94620	3.56	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.993	D	0.84100	0.0395	9	.	.	.	-18.2441	10.3987	0.44216	0.0:0.0:0.6447:0.3553	.	675;737	Q8IUR5;F8VTQ9	TMTC1_HUMAN;.	C	438;567;737;699;675	ENSP00000256062:R567C;ENSP00000448112:R737C;ENSP00000449043:R699C;ENSP00000442046:R675C	.	R	-	1	0	TMTC1	29562673	1.000000	0.71417	1.000000	0.80357	0.602000	0.36980	1.784000	0.38674	1.370000	0.46153	0.655000	0.94253	CGC	G|1.000;A|0.000	0.000	strong		0.458	TMTC1-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403509.1	NM_031920	Missense_Mutation	A	29671406	G	A	29671406	5	1	26	1	0	0	0	0	0	0	1	0	16275	1101	38	1	649	1	TMTC1	12	29671406	Splice_Site	SNP	G	TCGA-G8-6907-01A-11D-2210-10	4700440	29671406	104180489	407	10170											
PKP2	5318	hgsc.bcm.edu	37	chr12	33021917	33021917	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgtatgaaagtagctgcagCagaaatcctggatggcagca	13	8	12	8	0	0	2	0	1	0	1	1	3	1	3	1	2	4	7	1	2	4	2	rs200586695		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:33021917C>G	ENST00000070846.6	-	4	1138	c.1114G>C	c.(1114-1116)Gct>Cct	p.A372P	PKP2_ENST00000340811.4_Missense_Mutation_p.A372P	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	372			A -> P. {ECO:0000269|PubMed:20031617, ECO:0000269|PubMed:21062920}.		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)					GTAGCTGCAGCAGAAATCCTG	0.498																																					p.A372P		Atlas-SNP	.											.	PKP2	110	.	0			c.G1114C						PASS	.	C	PRO/ALA,PRO/ALA	0,4406		0,0,2203	118	106	110		1114,1114	4.2	0	12		110	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	PKP2	NM_001005242.2,NM_004572.3	27,27	0,6,6497	GG,GC,CC		0.0698,0.0,0.0461	benign,benign	372/838,372/882	33021917	6,13000	2203	4300	6503	SO:0001583	missense	5318	exon4			CTGCAGCAGAAAT	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.1114G>C	12.37:g.33021917C>G	ENSP00000070846:p.Ala372Pro	74	0	0		81	42	0.518519	NM_004572	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Missense_Mutation	SNP	ENST00000070846.6	37	CCDS8731.1	.	.	.	.	.	.	.	.	.	.	C	11.66	1.703879	0.30232	0.0	6.98E-4	ENSG00000057294	ENST00000340811;ENST00000070846;ENST00000537278	T;T	0.52754	0.65;0.65	5.09	4.2	0.49525	Armadillo-like helical (1);Armadillo-type fold (1);	2.116220	0.01794	N	0.032478	T	0.55940	0.1952	L	0.55481	1.735	0.31883	N	0.618224	P;P;P	0.43662	0.676;0.548;0.814	P;B;P	0.47015	0.506;0.309;0.534	T	0.41556	-0.9502	10	0.30854	T	0.27	-1.899	11.5273	0.50586	0.0:0.9155:0.0:0.0845	.	372;372;372	Q99959-2;A0AV37;Q99959	.;.;PKP2_HUMAN	P	372	ENSP00000342800:A372P;ENSP00000070846:A372P	ENSP00000070846:A372P	A	-	1	0	PKP2	32913184	0.805000	0.28982	0.017000	0.16124	0.333000	0.28666	2.159000	0.42339	1.136000	0.42199	0.650000	0.86243	GCT	C|0.999;G|0.001	0.001	weak		0.498	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572		G	33021917	C	G	33021917	3	3	26	1	0	0	0	0	1	0	0	0	11994	710	25	4	1575	4	PKP2	12	33021917	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	3350511	33021917	100829978	408	10171											
SLC38A1	81539	hgsc.bcm.edu	37	chr12	46622959	46622959	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaagtaggattccagtgttTgccagggcaaaggcgagtcc	12	8	13	8	1	0	0	0	0	0	0	2	2	2	1	3	3	1	3	3	3	4	3	rs61928115	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:46622959T>C	ENST00000398637.5	-	5	985	c.291A>G	c.(289-291)gcA>gcG	p.A97A	SLC38A1_ENST00000549633.1_5'UTR|SLC38A1_ENST00000549049.1_Silent_p.A97A|SLC38A1_ENST00000552197.1_Silent_p.A97A|SLC38A1_ENST00000546893.1_Silent_p.A97A|SLC38A1_ENST00000439706.1_Silent_p.A97A	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	97					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)			TTCCAGTGTTTGCCAGGGCAA	0.408													T|||	42	0.00838658	0.0023	0.0101	5008	,	,		16884	0.0		0.0278	False		,,,				2504	0.0041				p.A97A		Atlas-SNP	.											.	SLC38A1	58	.	0			c.A291G						PASS	.	T	,	15,3751		0,15,1868	57	52	54		291,291	-1.7	1	12	dbSNP_129	54	215,7997		2,211,3893	no	coding-synonymous,coding-synonymous	SLC38A1	NM_001077484.1,NM_030674.3	,	2,226,5761	CC,CT,TT		2.6181,0.3983,1.9202	,	97/488,97/488	46622959	230,11748	1883	4106	5989	SO:0001819	synonymous_variant	81539	exon5			AGTGTTTGCCAGG	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.291A>G	12.37:g.46622959T>C		47	0	0		44	20	0.454545	NM_030674	Q8NC61|Q8NCF8|Q96JX2|Q9H2Q2	Silent	SNP	ENST00000398637.5	37	CCDS41774.1																																																																																			T|0.985;C|0.015	0.015	strong		0.408	SLC38A1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404218.2			C	46622959	T	C	46622959	2	2	26	1	0	0	0	0	0	0	0	1	14616	1799	63	3		3	SLC38A1	12	46622959	Silent	SNP	T	TCGA-G8-6907-01A-11D-2210-10	13601042	46622959	87228936	409	10172											
LALBA	3906	hgsc.bcm.edu	37	chr12	48961801	48961801	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agagggctttatgggccaacCtgataatggagaagggggac	12	7	16	6	0	0	3	0	1	0	2	0	5	0	4	2	5	1	1	2	5	4	3			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:48961801C>A	ENST00000301046.2	-	4	394		c.e4-1		LALBA_ENST00000549817.1_3'UTR	NM_002289.2	NP_002280.1	P00709	LALBA_HUMAN	lactalbumin, alpha-						apoptotic process (GO:0006915)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|lactose biosynthetic process (GO:0005989)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|lactose synthase activity (GO:0004461)			large_intestine(1)|stomach(2)	3						ATGGGCCAACCTGATAATGGA	0.512																																					.		Atlas-SNP	.											.	LALBA	9	.	0			c.369-1G>T						PASS	.						112	85	94					12																	48961801		2203	4300	6503	SO:0001630	splice_region_variant	3906	exon5			GCCAACCTGATAA		CCDS8765.1	12q13	2012-10-02				ENSG00000167531			6480	protein-coding gene	gene with protein product		149750					Standard	XM_006719395		Approved	LYZL7	uc001rrt.3	P00709	OTTHUMG00000170391	ENST00000301046.2:c.369-1G>T	12.37:g.48961801C>A		88	0	0		109	53	0.486239	NM_002289	Q6FGX0|Q9UDK4	Splice_Site	SNP	ENST00000301046.2	37	CCDS8765.1	.	.	.	.	.	.	.	.	.	.	c	15.72	2.916330	0.52546	.	.	ENSG00000167531	ENST00000301046	.	.	.	4.88	4.88	0.63580	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.4099	0.60935	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	LALBA	47248068	0.960000	0.32886	0.996000	0.52242	0.794000	0.44872	2.823000	0.48081	2.539000	0.85634	0.461000	0.40582	.	.	.	none		0.512	LALBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408836.1	NM_002289	Intron	A	48961801	C	A	48961801	5	1	26	1	0	0	0	0	0	0	1	0	8613	695	24	4	64	4	LALBA	12	48961801	Splice_Site	SNP	C	TCGA-G8-6907-01A-11D-2210-10	2338842	48961801	84890094	410	10173											
LIMA1	51474	hgsc.bcm.edu	37	chr12	50571069	50571069	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagctgttatcatcttcatcGgagtctgcaccattttctac	9	15	6	11	1	5	0	2	0	3	0	6	1	5	1	1	1	3	3	1	1	3	5	rs35414607	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:50571069G>A	ENST00000341247.4	-	11	2207	c.2058C>T	c.(2056-2058)tcC>tcT	p.S686S	LIMA1_ENST00000552783.1_Silent_p.S527S|LIMA1_ENST00000552823.1_Silent_p.S526S|LIMA1_ENST00000552909.1_Silent_p.S525S|LIMA1_ENST00000547825.1_Silent_p.S384S|LIMA1_ENST00000552491.1_Silent_p.S383S|LIMA1_ENST00000394943.3_Silent_p.S687S	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	686					actin filament bundle assembly (GO:0051017)|negative regulation of actin filament depolymerization (GO:0030835)|ruffle organization (GO:0031529)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(2)	44						CATCTTCATCGGAGTCTGCAC	0.408													G|||	57	0.0113818	0.0401	0.0058	5008	,	,		21645	0.0		0.0	False		,,,				2504	0.0				p.S687S		Atlas-SNP	.											.	LIMA1	67	.	0			c.C2061T						PASS	.	G	,,	121,4285	89.7+/-128.4	2,117,2084	283	278	279		2061,1581,2058	0	0.2	12	dbSNP_126	279	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	LIMA1	NM_001113546.1,NM_001113547.1,NM_016357.4	,,	2,118,6383	AA,AG,GG		0.0116,2.7463,0.938	,,	687/761,527/601,686/760	50571069	122,12884	2203	4300	6503	SO:0001819	synonymous_variant	51474	exon11			TTCATCGGAGTCT	AF198454	CCDS8802.1, CCDS44877.1, CCDS55826.1, CCDS58230.1	12q13.12	2006-04-12				ENSG00000050405			24636	protein-coding gene	gene with protein product	"epithelial protein lost in neoplasm beta"	608364				10806352, 10618726, 12566430	Standard	NM_016357		Approved	EPLIN	uc001rwk.4	Q9UHB6		ENST00000341247.4:c.2058C>T	12.37:g.50571069G>A		590	0	0		620	304	0.490323	NM_001113546	B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Silent	SNP	ENST00000341247.4	37	CCDS8802.1																																																																																			G|0.986;A|0.014	0.014	strong		0.408	LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357		A	50571069	G	A	50571069	2	1	26	1	0	0	0	0	0	0	0	1	8805	1103	39	1		1	LIMA1	12	50571069	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1609268	50571069	83280826	411	10174											
SLC11A2	4891	hgsc.bcm.edu	37	chr12	51386017	51386017	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagtcattcatccctgttaGatgctctacatcttggaaga	12	13	7	9	0	4	2	2	0	2	2	5	3	5	3	1	1	2	2	1	1	4	4	rs144863268	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:51386017G>T	ENST00000262051.7	-	13	1390	c.1303C>A	c.(1303-1305)Cta>Ata	p.L435I	SLC11A2_ENST00000541174.2_Missense_Mutation_p.L435I|SLC11A2_ENST00000547688.1_Missense_Mutation_p.L464I|SLC11A2_ENST00000546743.1_Missense_Mutation_p.L356I|SLC11A2_ENST00000262052.5_Missense_Mutation_p.L435I|SLC11A2_ENST00000547198.1_Missense_Mutation_p.L435I|SLC11A2_ENST00000394904.3_Missense_Mutation_p.L464I|SLC11A2_ENST00000545993.2_Missense_Mutation_p.L431I	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	435			L -> I (in dbSNP:rs144863268). {ECO:0000269|PubMed:9642100}.		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						ATCCCTGTTAGATGCTCTACA	0.468													G|||	3	0.000599042	0.0015	0.0	5008	,	,		21375	0.0		0.001	False		,,,				2504	0.0				p.L464I		Atlas-SNP	.											.	SLC11A2	51	.	0			c.C1390A						PASS	.	G	ILE/LEU,ILE/LEU,ILE/LEU,ILE/LEU,ILE/LEU,ILE/LEU,ILE/LEU	1,4405	2.1+/-5.4	0,1,2202	152	126	135		1303,1390,1303,1303,1303,1303,1291	4.7	0.9	12	dbSNP_134	135	25,8575	17.3+/-56.4	0,25,4275	yes	missense,missense,missense,missense,missense,missense,missense	SLC11A2	NM_000617.2,NM_001174125.1,NM_001174126.1,NM_001174127.1,NM_001174128.1,NM_001174129.1,NM_001174130.1	5,5,5,5,5,5,5	0,26,6477	TT,TG,GG		0.2907,0.0227,0.1999	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	435/562,464/591,435/569,435/569,435/562,435/562,431/558	51386017	26,12980	2203	4300	6503	SO:0001583	missense	4891	exon13			CTGTTAGATGCTC	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.1303C>A	12.37:g.51386017G>T	ENSP00000262051:p.Leu435Ile	101	0	0		93	39	0.419355	NM_001174125	B3KT08|B4DK84|F5H741|O43288|O60932|O94801|Q498Z5|Q8IUD7|Q96J35	Missense_Mutation	SNP	ENST00000262051.7	37	CCDS53792.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	G	19.37	3.814690	0.70912	2.27E-4	0.002907	ENSG00000110911	ENST00000262051;ENST00000547198;ENST00000262052;ENST00000394904;ENST00000547688;ENST00000541174;ENST00000545993;ENST00000546743	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	5.59	4.67	0.58626	.	0.000000	0.85682	D	0.000000	T	0.73361	0.3577	L	0.49256	1.55	0.58432	D	0.999993	D;D;D;D;D;P	0.64830	0.985;0.981;0.994;0.994;0.985;0.883	D;D;D;D;D;P	0.67382	0.951;0.919;0.919;0.919;0.951;0.665	T	0.72191	-0.4365	9	.	.	.	-6.39	9.6058	0.39632	0.1786:0.0:0.8214:0.0	.	398;431;464;435;284;435	B7Z9M2;F5H741;P49281-3;P49281-2;B3KY44;P49281	.;.;.;.;.;NRAM2_HUMAN	I	435;435;435;464;464;435;431;356	ENSP00000262051:L435I;ENSP00000446769:L435I;ENSP00000262052:L435I;ENSP00000378364:L464I;ENSP00000449200:L464I;ENSP00000444542:L435I;ENSP00000442810:L431I;ENSP00000446914:L356I	.	L	-	1	2	SLC11A2	49672284	1.000000	0.71417	0.949000	0.38748	0.975000	0.68041	2.010000	0.40913	1.408000	0.46895	0.655000	0.94253	CTA	G|0.998;T|0.002	0.002	strong		0.468	SLC11A2-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404383.1			T	51386017	G	T	51386017	3	4	26	1	0	0	0	0	1	0	0	0	14396	933	33	4	480	4	SLC11A2	12	51386017	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	814948	51386017	82465878	412	10175											
SLC4A8	9498	hgsc.bcm.edu	37	chr12	51856159	51856159	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ctggcggggattgatgagttCctagaccaggtgacggtgct	7	10	16	8	2	0	4	0	3	0	1	1	5	1	5	2	5	1	2	2	5	1	3	rs71449805	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:51856159C>T	ENST00000453097.2	+	10	1384	c.1167C>T	c.(1165-1167)ttC>ttT	p.F389F	SLC4A8_ENST00000358657.3_Silent_p.F416F|SLC4A8_ENST00000514353.3_Silent_p.F336F|SLC4A8_ENST00000535225.2_Silent_p.F336F|SLC4A8_ENST00000394856.1_Silent_p.F336F	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)		TTGATGAGTTCCTAGACCAGG	0.473													C|||	48	0.00958466	0.0015	0.0187	5008	,	,		18122	0.0		0.0278	False		,,,				2504	0.0051				p.F389F		Atlas-SNP	.											.	SLC4A8	292	.	0			c.C1167T						PASS	.	C	,	36,4370	41.6+/-74.8	0,36,2167	123	118	120		1167,1167	4.3	1	12	dbSNP_130	120	351,8249	118.5+/-177.9	5,341,3954	no	coding-synonymous,coding-synonymous	SLC4A8	NM_001039960.1,NM_004858.2	,	5,377,6121	TT,TC,CC		4.0814,0.8171,2.9755	,	389/1094,389/1045	51856159	387,12619	2203	4300	6503	SO:0001819	synonymous_variant	9498	exon10			TGAGTTCCTAGAC	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.1167C>T	12.37:g.51856159C>T		101	0	0		109	58	0.53211	NM_001039960		Silent	SNP	ENST00000453097.2	37	CCDS44890.1																																																																																			C|0.974;T|0.026	0.026	strong		0.473	SLC4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404356.1	NM_004858		T	51856159	C	T	51856159	2	4	26	1	0	0	0	0	0	0	0	1	14674	854	30	2		2	SLC4A8	12	51856159	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	470142	51856159	81995736	413	10176											
ATF7	11016	hgsc.bcm.edu	37	chr12	53925573	53925573	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcagggtgctggatgagaatCtggctctgctctgggcgggc	5	10	17	9	1	4	1	1	1	3	1	4	3	4	2	0	5	2	3	0	5	1	0	rs139241958	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:53925573C>T	ENST00000548446.2	-	9	1027	c.915G>A	c.(913-915)caG>caA	p.Q305Q	ATF7_ENST00000420353.2_Silent_p.Q294Q|ATF7_ENST00000328463.7_Silent_p.Q305Q|ATF7_ENST00000415113.1_Silent_p.Q273Q|RP11-793H13.10_ENST00000591834.1_Silent_p.Q294Q|ATF7_ENST00000456903.4_Silent_p.Q294Q			P17544	ATF7_HUMAN	activating transcription factor 7	305					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)	GGATGAGAATCTGGCTCTGCT	0.517													C|||	27	0.00539137	0.0008	0.0144	5008	,	,		14364	0.0		0.0149	False		,,,				2504	0.001				p.Q294Q		Atlas-SNP	.											.	ATF7	51	.	0			c.G882A						PASS	.	C	,,	14,4046		0,14,2016	68	76	73		915,819,882	5.4	1	12	dbSNP_134	73	131,8225		2,127,4049	no	coding-synonymous,coding-synonymous,coding-synonymous	ATF7	NM_001130059.1,NM_001130060.1,NM_006856.2	,,	2,141,6065	TT,TC,CC		1.5677,0.3448,1.1678	,,	305/495,273/463,294/484	53925573	145,12271	2030	4178	6208	SO:0001819	synonymous_variant	11016	exon9			GAGAATCTGGCTC	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.915G>A	12.37:g.53925573C>T		52	0	0		63	34	0.539683	NM_006856	A5D6Y4|B2RMP1|B4DQL4|Q13814|Q8IVR8|Q9UD83	Silent	SNP	ENST00000548446.2	37																																																																																				C|0.991;T|0.009	0.009	strong		0.517	ATF7-007	KNOWN	NMD_exception|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000406302.2	NM_001130059		T	53925573	C	T	53925573	2	4	26	1	0	0	0	0	0	0	0	1	1086	912	32	2		2	ATF7	12	53925573	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	2069414	53925573	79926322	414	10177											
METTL7B	196410	hgsc.bcm.edu	37	chr12	56077599	56077599	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctctcatccctcccagggAggtgtgctctttttctggga	4	14	10	13	0	4	0	1	0	3	0	7	2	6	2	2	3	1	1	2	3	0	2	rs73117273	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:56077599A>T	ENST00000394252.3	+	2	710	c.501A>T	c.(499-501)ggA>ggT	p.G167G		NM_152637.2	NP_689850.2	Q6UX53	MET7B_HUMAN	methyltransferase like 7B	167							methyltransferase activity (GO:0008168)			kidney(1)|large_intestine(1)|lung(4)	6						CCTCCCAGGGAGGTGTGCTCT	0.527													A|||	25	0.00499201	0.0008	0.0043	5008	,	,		18463	0.0		0.0179	False		,,,				2504	0.0031				p.G167G		Atlas-SNP	.											.	METTL7B	35	.	0			c.A501T						PASS	.	A		12,4394	20.2+/-43.8	0,12,2191	129	127	128		501	2.8	1	12	dbSNP_130	128	67,8533	41.7+/-99.0	1,65,4234	no	coding-synonymous	METTL7B	NM_152637.2		1,77,6425	TT,TA,AA		0.7791,0.2724,0.6074		167/245	56077599	79,12927	2203	4300	6503	SO:0001819	synonymous_variant	196410	exon2			CCAGGGAGGTGTG		CCDS8887.2	12q13.2	2012-06-12			ENSG00000170439	ENSG00000170439			28276	protein-coding gene	gene with protein product	"associated with lipid droplets 1"					17004324	Standard	NM_152637		Approved	MGC17301, ALDI	uc010spr.2	Q6UX53	OTTHUMG00000152665	ENST00000394252.3:c.501A>T	12.37:g.56077599A>T		265	0	0		250	126	0.504	NM_152637	A8K247|Q8WUI1	Silent	SNP	ENST00000394252.3	37	CCDS8887.2																																																																																			A|0.993;T|0.007	0.007	strong		0.527	METTL7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327271.1	NM_152637		T	56077599	A	T	56077599	2	4	26	1	0	0	0	0	0	0	0	1	9515	291	11	5		5	METTL7B	12	56077599	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	2152026	56077599	77774296	415	10178											
COQ10A	93058	hgsc.bcm.edu	37	chr12	56664041	56664041	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagcgtcgggcagccaccaaGtttggtccagaaacagccat	11	6	12	12	2	0	1	0	0	0	1	2	2	1	1	4	2	4	2	4	2	2	1	rs11543260	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:56664041G>A	ENST00000308197.5	+	5	945	c.684G>A	c.(682-684)aaG>aaA	p.K228K	COQ10A_ENST00000546544.1_Silent_p.K211K|COQ10A_ENST00000433805.2_Silent_p.K196K|RP11-977G19.14_ENST00000546464.1_RNA	NM_144576.3	NP_653177.3	Q96MF6	CQ10A_HUMAN	coenzyme Q10 homolog A (S. cerevisiae)	228						mitochondrial inner membrane (GO:0005743)				cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	8						CAGCCACCAAGTTTGGTCCAG	0.527													G|||	43	0.00858626	0.0038	0.0115	5008	,	,		20738	0.0		0.0278	False		,,,				2504	0.002				p.K228K		Atlas-SNP	.											.	COQ10A	20	.	0			c.G684A						PASS	.	G	,	36,3956		0,36,1960	127	126	126		588,684	4.8	1	12	dbSNP_120	126	172,8168		3,166,4001	no	coding-synonymous,coding-synonymous	COQ10A	NM_001099337.1,NM_144576.3	,	3,202,5961	AA,AG,GG		2.0624,0.9018,1.6867	,	196/216,228/248	56664041	208,12124	1996	4170	6166	SO:0001819	synonymous_variant	93058	exon5			CACCAAGTTTGGT	AK057003	CCDS41796.1, CCDS44921.1	12q13.3	2011-09-16	2006-04-04		ENSG00000135469	ENSG00000135469			26515	protein-coding gene	gene with protein product			"coenzyme Q10 homolog A (yeast)"				Standard	NM_144576		Approved	FLJ32452	uc001sko.4	Q96MF6	OTTHUMG00000170283	ENST00000308197.5:c.684G>A	12.37:g.56664041G>A		111	0	0		120	57	0.475	NM_144576	Q6GMR6|Q6UWB9|Q86X16|Q8TAL2|Q96MF1|Q9BUP4	Silent	SNP	ENST00000308197.5	37	CCDS41796.1	23	0.010531135531135532	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	19	0.025065963060686015	G	1.929	-0.446438	0.04604	0.009018	0.020624	ENSG00000135469	ENST00000553234;ENST00000551814	.	.	.	4.85	4.85	0.62838	.	.	.	.	.	T	0.41190	0.1148	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53158	-0.8478	4	.	.	.	.	13.5848	0.61924	0.0:0.1571:0.8428:0.0	rs11543260;rs11543260	.	.	.	N	134;45	.	.	S	+	2	0	COQ10A	54950308	1.000000	0.71417	1.000000	0.80357	0.278000	0.26855	0.701000	0.25616	2.675000	0.91044	0.655000	0.94253	AGT	G|0.986;A|0.014	0.014	strong		0.527	COQ10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408332.1	NM_144576		A	56664041	G	A	56664041	2	1	26	1	0	0	0	0	0	0	0	1	3745	1020	36	2		2	COQ10A	12	56664041	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	586442	56664041	77187854	416	10179											
STAT2	6773	hgsc.bcm.edu	37	chr12	56740738	56740738	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcacaaagcccatgatgcGtctggagcacagagagcagc	13	5	11	12	1	2	2	1	1	1	1	2	4	2	3	1	1	5	2	1	1	1	0			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:56740738G>A	ENST00000314128.4	-	20	1749	c.1726C>T	c.(1726-1728)Cgc>Tgc	p.R576C	STAT2_ENST00000556539.1_5'UTR|STAT2_ENST00000557235.1_Splice_Site_p.R572C			P52630	STAT2_HUMAN	signal transducer and activator of transcription 2, 113kDa	576	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|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)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|skin(3)	31						CCCATGATGCGTCTGGAGCAC	0.607																																					p.R576C		Atlas-SNP	.											.	STAT2	70	.	0			c.C1726T						PASS	.						63	56	58					12																	56740738		2203	4300	6503	SO:0001630	splice_region_variant	6773	exon20			TGATGCGTCTGGA	BC051284	CCDS8917.1, CCDS55836.1	12q13.2	2013-02-14	2002-08-29			ENSG00000170581		"SH2 domain containing"	11363	protein-coding gene	gene with protein product		600556	"signal transducer and activator of transcription 2, 113kD"			7885841	Standard	NM_005419		Approved	STAT113	uc001slc.3	P52630		ENST00000314128.4:c.1725-1C>T	12.37:g.56740738G>A		77	0	0		100	48	0.48	NM_005419	B4DLC7|G3V2M6|Q16430|Q16431|Q9UDL4	Missense_Mutation	SNP	ENST00000314128.4	37	CCDS8917.1	.	.	.	.	.	.	.	.	.	.	G	10.90	1.480269	0.26598	.	.	ENSG00000170581	ENST00000314128;ENST00000557235	D;D	0.96459	-4.02;-4.02	5.76	1.27	0.21489	SH2 motif (2);EF-hand-like domain (1);	0.907952	0.09678	N	0.770112	D	0.89681	0.6785	N	0.08118	0	0.09310	N	0.999993	B;B	0.17465	0.0;0.022	B;B	0.15484	0.002;0.013	T	0.79610	-0.1732	10	0.36615	T	0.2	3.6003	9.3617	0.38199	0.3354:0.0:0.6646:0.0	.	572;576	G3V2M6;P52630	.;STAT2_HUMAN	C	576;572	ENSP00000315768:R576C;ENSP00000450751:R572C	ENSP00000315768:R576C	R	-	1	0	STAT2	55027005	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	0.091000	0.15046	0.031000	0.15407	-0.229000	0.12294	CGC	.	.	none		0.607	STAT2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410277.1	NM_005419	Missense_Mutation	A	56740738	G	A	56740738	5	1	26	1	0	0	0	0	0	0	1	0	15280	1159	40	1	849	1	STAT2	12	56740738	Splice_Site	SNP	G	TCGA-G8-6907-01A-11D-2210-10	76697	56740738	77111157	417	10180											
NACA	4666	hgsc.bcm.edu	37	chr12	57114435	57114435	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgggggggtgttgggaccCgcagtcttttgagaagaggt	6	11	18	6	1	2	2	0	1	2	2	2	4	2	3	1	5	0	2	1	5	1	3	rs376706368		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:57114435C>T	ENST00000454682.1	-	3	1160	c.879G>A	c.(877-879)gcG>gcA	p.A293A	NACA_ENST00000546392.1_Intron|NACA_ENST00000552540.1_Intron|NACA_ENST00000551793.1_Intron|NACA_ENST00000393891.4_Intron|NACA_ENST00000550952.1_Silent_p.A293A|NACA_ENST00000548563.1_Intron|NACA_ENST00000356769.3_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	293	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						TGTTGGGACCCGCAGTCTTTT	0.502			T	BCL6	NHL																																p.A293A		Atlas-SNP	.		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	.	NACA	131	.	0			c.G879A						PASS	.		,,,	0,3136		0,0,1568	61	61	61		,,879,	2.6	0	12		61	1,7163		0,1,3581	no	intron,intron,coding-synonymous,intron	NACA	NM_001113201.1,NM_001113202.1,NM_001113203.2,NM_005594.4	,,,	0,1,5149	TT,TC,CC		0.014,0.0,0.0097	,,,	,,293/926,	57114435	1,10299	1568	3582	5150	SO:0001819	synonymous_variant	4666	exon3			GGGACCCGCAGTC	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.879G>A	12.37:g.57114435C>T		38	0	0		46	23	0.5	NM_001113203		Silent	SNP	ENST00000454682.1	37																																																																																				.	.	weak		0.502	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594		T	57114435	C	T	57114435	2	4	26	1	0	0	0	0	0	0	0	1	10142	639	23	1		1	NACA	12	57114435	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	373697	57114435	76737460	418	10181											
ARHGAP9	64333	hgsc.bcm.edu	37	chr12	57869681	57869681	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctctgtctcgtggtccgactGcagcaggaactcgtggccag	6	9	13	13	3	2	0	0	0	2	0	5	2	3	1	2	3	3	2	2	3	1	0			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:57869681G>A	ENST00000356411.2	-	10	1384	c.1246C>T	c.(1246-1248)Cag>Tag	p.Q416*	ARHGAP9_ENST00000393797.2_Nonsense_Mutation_p.Q487*|ARHGAP9_ENST00000550454.1_5'Flank|ARHGAP9_ENST00000424809.2_Nonsense_Mutation_p.Q416*|ARHGAP9_ENST00000550288.1_Nonsense_Mutation_p.Q495*|ARHGAP9_ENST00000393791.3_Nonsense_Mutation_p.Q416*|ARHGAP9_ENST00000430041.2_Nonsense_Mutation_p.Q232*			Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9	416	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)			TGGTCCGACTGCAGCAGGAAC	0.647																																					p.Q416X		Atlas-SNP	.											.	ARHGAP9	79	.	0			c.C1246T						PASS	.						27	30	29					12																	57869681		2201	4296	6497	SO:0001587	stop_gained	64333	exon9			CCGACTGCAGCAG	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.1246C>T	12.37:g.57869681G>A	ENSP00000348782:p.Gln416*	120	0	0		117	47	0.401709	NM_001080157	B4DVI3|E9PDX9|Q8NAF3|Q8TCJ3|Q8WYR0|Q96EZ2|Q96S74	Nonsense_Mutation	SNP	ENST00000356411.2	37		.	.	.	.	.	.	.	.	.	.	G	40	7.946108	0.98574	.	.	ENSG00000123329	ENST00000393791;ENST00000356411;ENST00000423291;ENST00000424809;ENST00000393797;ENST00000340423;ENST00000430041;ENST00000548139	.	.	.	3.97	3.97	0.46021	.	0.139059	0.48767	D	0.000170	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	13.468	0.61266	0.0:0.0:1.0:0.0	.	.	.	.	X	416;416;86;416;487;465;232;232	.	ENSP00000344852:Q465X	Q	-	1	0	ARHGAP9	56155948	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	5.206000	0.65192	2.235000	0.73313	0.561000	0.74099	CAG	.	.	none		0.647	ARHGAP9-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_032496		A	57869681	G	A	57869681	4	1	26	1	0	0	0	0	0	1	0	0	889	1328	46	2	985	2	ARHGAP9	12	57869681	Nonsense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	755246	57869681	75982214	419	10182											
OS9	10956	hgsc.bcm.edu	37	chr12	58114677	58114677	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagggcacaggggacctggaCgaatttgacttctgagacca	11	7	14	9	1	1	2	0	2	1	1	1	7	1	4	2	4	0	1	2	4	1	2	rs564358823		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:58114677C>T	ENST00000315970.7	+	15	2030	c.1989C>T	c.(1987-1989)gaC>gaT	p.D663D	OS9_ENST00000552285.1_Silent_p.D608D|OS9_ENST00000413095.2_Silent_p.D402D|RP11-571M6.8_ENST00000548410.2_RNA|OS9_ENST00000389142.5_Silent_p.D593D|OS9_ENST00000389146.6_Silent_p.D648D|OS9_ENST00000439210.2_Silent_p.D534D|RP11-571M6.7_ENST00000549477.1_RNA|OS9_ENST00000435406.2_Silent_p.D556D|OS9_ENST00000551035.1_Silent_p.D576D|OS9_ENST00000257966.8_Silent_p.D609D	NM_001017958.2|NM_006812.3	NP_001017958.1|NP_006803.1	Q13438	OS9_HUMAN	osteosarcoma amplified 9, endoplasmic reticulum lectin	663					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)			GGGACCTGGACGAATTTGACT	0.607																																					p.D663D		Atlas-SNP	.											.	OS9	55	.	0			c.C1989T						PASS	.						74	78	77					12																	58114677		2203	4300	6503	SO:0001819	synonymous_variant	10956	exon15			CCTGGACGAATTT	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.1989C>T	12.37:g.58114677C>T		111	0	0		112	59	0.526786	NM_006812	A6NDD1|A6NFR7|A6NLB2|A8K5Q9|B4DE28|B4DPX1|B4E1I6|E7ENT8|E7EW91|F8VUH2|G3XA88|O00579|Q6IBL2|Q8IZ58|Q9BW99	Silent	SNP	ENST00000315970.7	37	CCDS31843.1																																																																																			.	.	none		0.607	OS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408344.1	NM_006812		T	58114677	C	T	58114677	2	4	26	1	0	0	0	0	0	0	0	1	11281	535	19	1		1	OS9	12	58114677	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	244996	58114677	75737218	420	10183											
HELB	92797	hgsc.bcm.edu	37	chr12	66704098	66704098	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atcaggtggctgctttggaaAtgatttgctccaatcctgtg	8	14	11	8	0	1	1	1	1	0	0	3	2	3	2	2	3	2	3	2	3	2	2			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:66704098A>G	ENST00000247815.4	+	4	1449	c.1390A>G	c.(1390-1392)Atg>Gtg	p.M464V		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	464					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)		TGCTTTGGAAATGATTTGCTC	0.428																																					p.M464V		Atlas-SNP	.											HELB,NS,carcinoma,-2,1	HELB	90	1	0			c.A1390G						PASS	.						90	90	90					12																	66704098		2203	4300	6503	SO:0001583	missense	92797	exon4			TTGGAAATGATTT	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.1390A>G	12.37:g.66704098A>G	ENSP00000247815:p.Met464Val	70	0	0		93	45	0.483871	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Missense_Mutation	SNP	ENST00000247815.4	37	CCDS8976.1	.	.	.	.	.	.	.	.	.	.	A	14.62	2.589061	0.46110	.	.	ENSG00000127311	ENST00000247815	T	0.40476	1.03	6.04	6.04	0.98038	.	0.083556	0.85682	D	0.000000	T	0.34629	0.0904	L	0.28344	0.845	0.28916	N	0.892402	P	0.40144	0.704	B	0.42462	0.388	T	0.28964	-1.0027	9	.	.	.	-27.9413	13.0143	0.58749	0.8657:0.1343:0.0:0.0	.	464	Q8NG08	HELB_HUMAN	V	464	ENSP00000247815:M464V	.	M	+	1	0	HELB	64990365	1.000000	0.71417	0.993000	0.49108	0.790000	0.44656	5.571000	0.67404	2.317000	0.78254	0.459000	0.35465	ATG	.	.	none		0.428	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1			G	66704098	A	G	66704098	3	3	26	1	0	0	0	0	1	0	0	0	7054	101	4	3	1404	3	HELB	12	66704098	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	8589421	66704098	67147797	421	10184											
MDM1	56890	hgsc.bcm.edu	37	chr12	68708979	68708979	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttctggggctgttcttccacGatatttcctttttcttctgg	3	20	8	10	1	4	0	0	0	4	0	6	1	6	0	2	3	0	2	2	3	1	8	rs139553308	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:68708979G>A	ENST00000303145.7	-	9	1334	c.1248C>T	c.(1246-1248)atC>atT	p.I416I	MDM1_ENST00000540418.1_Silent_p.I136I|MDM1_ENST00000411698.2_Silent_p.I381I	NM_017440.4	NP_059136.2	Q8TC05	MDM1_HUMAN	Mdm1 nuclear protein homolog (mouse)	416					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)		GTTCTTCCACGATATTTCCTT	0.423													G|||	12	0.00239617	0.0008	0.0029	5008	,	,		18479	0.0		0.008	False		,,,				2504	0.001				p.I416I		Atlas-SNP	.											.	MDM1	74	.	0			c.C1248T						PASS	.	G	,	9,4397	15.5+/-35.6	0,9,2194	83	86	85		1143,1248	-2.7	0	12	dbSNP_134	85	99,8501	54.8+/-115.7	0,99,4201	no	coding-synonymous,coding-synonymous	MDM1	NM_001205028.1,NM_017440.4	,	0,108,6395	AA,AG,GG		1.1512,0.2043,0.8304	,	381/680,416/715	68708979	108,12898	2203	4300	6503	SO:0001819	synonymous_variant	56890	exon9			TTCCACGATATTT	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.1248C>T	12.37:g.68708979G>A		163	0	0		171	79	0.461988	NM_017440	B4DM65|E7EPQ3|O43406|Q8WTV9|Q9NR04	Silent	SNP	ENST00000303145.7	37	CCDS8983.1																																																																																			G|0.991;A|0.009	0.009	strong		0.423	MDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402402.1	NM_020128		A	68708979	G	A	68708979	2	1	26	1	0	0	0	0	0	0	0	1	9421	1048	37	1		1	MDM1	12	68708979	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	2004881	68708979	65142916	422	10185											
NUP107	57122	hgsc.bcm.edu	37	chr12	69090624	69090624	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	atgagtatgttttctgatttCctgcagtcttttctgaagca	8	18	8	7	0	3	3	0	3	3	0	4	3	4	3	1	0	2	4	1	0	2	6			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:69090624C>T	ENST00000229179.4	+	6	806	c.474C>T	c.(472-474)ttC>ttT	p.F158F	NUP107_ENST00000539906.1_Silent_p.F129F|NUP107_ENST00000378905.2_Silent_p.F7F	NM_020401.2	NP_065134.1	P57740	NU107_HUMAN	nucleoporin 107kDa	158					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 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)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|structural constituent of nuclear pore (GO:0017056)		NUP107/LGR5(2)	breast(3)|endometrium(4)|kidney(4)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(2)	39	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)			TTTCTGATTTCCTGCAGTCTT	0.363																																					p.F158F		Atlas-SNP	.											.	NUP107	88	.	0			c.C474T						PASS	.						129	113	118					12																	69090624		2203	4300	6503	SO:0001819	synonymous_variant	57122	exon6			TGATTTCCTGCAG	AK055629	CCDS8985.1	12q14	2004-03-19			ENSG00000111581	ENSG00000111581			29914	protein-coding gene	gene with protein product		607617				12552102, 12705868	Standard	XM_005269037		Approved	NUP84	uc001suf.3	P57740	OTTHUMG00000169265	ENST00000229179.4:c.474C>T	12.37:g.69090624C>T		81	0	0		56	4	0.0714286	NM_020401	B4DZ67|Q6PJE1	Silent	SNP	ENST00000229179.4	37	CCDS8985.1																																																																																			.	.	none		0.363	NUP107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403195.1	NM_020401		T	69090624	C	T	69090624	2	4	26	1	0	0	0	0	0	0	0	1	10762	854	30	2		2	NUP107	12	69090624	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	381645	69090624	64761271	423	10186											
ALX1	8092	hgsc.bcm.edu	37	chr12	85674221	85674221	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccctgccccgcgccgagcAtcacgtgcgcttggagagga	7	5	13	16	5	1	1	1	0	0	1	1	4	1	2	5	2	3	2	5	2	0	1	rs115440539	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:85674221A>G	ENST00000316824.3	+	1	337	c.182A>G	c.(181-183)cAt>cGt	p.H61R		NM_006982.2	NP_008913.2	Q15699	ALX1_HUMAN	ALX homeobox 1	61					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)		CGCGCCGAGCATCACGTGCGC	0.637													A|||	24	0.00479233	0.0	0.0043	5008	,	,		14543	0.0		0.0169	False		,,,				2504	0.0041				p.H61R		Atlas-SNP	.											.	ALX1	61	.	0			c.A182G						PASS	.	A	ARG/HIS	10,4396	16.8+/-37.8	0,10,2193	34	36	35		182	5.5	1	12	dbSNP_132	35	95,8505	51.5+/-111.7	1,93,4206	yes	missense	ALX1	NM_006982.2	29	1,103,6399	GG,GA,AA		1.1047,0.227,0.8073	benign	61/327	85674221	105,12901	2203	4300	6503	SO:0001583	missense	8092	exon1			CCGAGCATCACGT	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.182A>G	12.37:g.85674221A>G	ENSP00000315417:p.His61Arg	66	0	0		60	33	0.55	NM_006982	Q546C8|Q96FH4	Missense_Mutation	SNP	ENST00000316824.3	37	CCDS9028.1	16	0.007326007326007326	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	12	0.0158311345646438	A	16.30	3.084377	0.55861	0.00227	0.011047	ENSG00000180318	ENST00000316824	D	0.91686	-2.89	5.47	5.47	0.80525	.	0.165804	0.53938	D	0.000051	T	0.75642	0.3877	N	0.19112	0.55	0.50467	D	0.999873	B	0.24186	0.099	B	0.19946	0.027	T	0.77474	-0.2574	10	0.31617	T	0.26	.	12.1271	0.53922	0.8569:0.143:0.0:0.0	.	61	Q15699	ALX1_HUMAN	R	61	ENSP00000315417:H61R	ENSP00000315417:H61R	H	+	2	0	ALX1	84198352	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.410000	0.52664	2.069000	0.61940	0.528000	0.53228	CAT	A|0.991;G|0.009	0.009	strong		0.637	ALX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406072.1	NM_006982		G	85674221	A	G	85674221	3	3	26	1	0	0	0	0	1	0	0	0	556	217	8	3	184	3	ALX1	12	85674221	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	16583597	85674221	48177674	424	10187											
SCYL2	55681	hgsc.bcm.edu	37	chr12	100732822	100732822	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taatggggacacagatgaacGtgataggacaatctgctttt	13	11	11	6	1	1	3	0	2	1	1	1	5	1	5	0	3	2	1	0	3	4	4	rs117356610	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:100732822G>A	ENST00000360820.2	+	18	3099	c.2662G>A	c.(2662-2664)Gtg>Atg	p.V888M		NM_017988.4	NP_060458.3	Q6P3W7	SCYL2_HUMAN	SCY1-like 2 (S. cerevisiae)	888	Necessary for interaction with AP2 complex and clathrin, interaction with clathrin is necessary for its targeting to the TGN and endosomal membranes.				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						ACAGATGAACGTGATAGGACA	0.438													G|||	6	0.00119808	0.0	0.0	5008	,	,		20321	0.001		0.004	False		,,,				2504	0.001				p.V888M		Atlas-SNP	.											SCYL2,NS,carcinoma,-2,1	SCYL2	99	1	0			c.G2662A						PASS	.	G	MET/VAL	4,4402	8.1+/-20.4	0,4,2199	185	178	181		2662	-7.1	0.4	12	dbSNP_132	181	38,8562	26.3+/-74.7	0,38,4262	yes	missense	SCYL2	NM_017988.4	21	0,42,6461	AA,AG,GG		0.4419,0.0908,0.3229	benign	888/930	100732822	42,12964	2203	4300	6503	SO:0001583	missense	55681	exon18			ATGAACGTGATAG	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.2662G>A	12.37:g.100732822G>A	ENSP00000354061:p.Val888Met	153	0	0		184	79	0.429348	NM_017988	A8KAB5|Q96EF4|Q96ST4|Q9H7V5|Q9NVH3|Q9P2I7	Missense_Mutation	SNP	ENST00000360820.2	37	CCDS9076.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	3.958	-0.010846	0.07727	9.08E-4	0.004419	ENSG00000136021	ENST00000360820	T	0.28454	1.61	5.8	-7.11	0.01542	.	0.675157	0.16660	N	0.204822	T	0.08891	0.0220	N	0.02916	-0.46	0.23314	N	0.99793	B	0.02656	0.0	B	0.01281	0.0	T	0.15983	-1.0418	10	0.30078	T	0.28	0.0271	7.2695	0.26248	0.3732:0.0:0.4283:0.1985	.	888	Q6P3W7	SCYL2_HUMAN	M	888	ENSP00000354061:V888M	ENSP00000354061:V888M	V	+	1	0	SCYL2	99256953	0.922000	0.31269	0.385000	0.26158	0.940000	0.58332	0.731000	0.26058	-1.435000	0.01972	-0.300000	0.09419	GTG	G|0.997;A|0.003	0.003	strong		0.438	SCYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408493.2	NM_017988		A	100732822	G	A	100732822	3	1	26	1	0	0	0	0	1	0	0	0	13963	1145	40	1	2728	1	SCYL2	12	100732822	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	15058601	100732822	33119073	425	10188											
WSCD2	9671	hgsc.bcm.edu	37	chr12	108641799	108641799	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcgtgaggaactatgccccGtggtgggccactcacacact	8	9	11	13	2	1	1	1	1	0	0	2	2	1	2	3	3	2	0	3	3	2	2	rs144706841	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:108641799G>A	ENST00000332082.4	+	10	2195	c.1377G>A	c.(1375-1377)ccG>ccA	p.P459P	WSCD2_ENST00000261400.3_Silent_p.P479P|WSCD2_ENST00000547525.1_Silent_p.P459P|WSCD2_ENST00000549903.1_Silent_p.P479P			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	459						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						ACTATGCCCCGTGGTGGGCCA	0.567													G|||	4	0.000798722	0.0008	0.0	5008	,	,		19841	0.0		0.003	False		,,,				2504	0.0				p.P459P		Atlas-SNP	.											.	WSCD2	125	.	0			c.G1377A						PASS	.	G		2,4082		0,2,2040	62	65	64		1377	-3.8	1	12	dbSNP_134	64	20,8424		0,20,4202	no	coding-synonymous	WSCD2	NM_014653.2		0,22,6242	AA,AG,GG		0.2369,0.049,0.1756		459/566	108641799	22,12506	2042	4222	6264	SO:0001819	synonymous_variant	9671	exon9			TGCCCCGTGGTGG		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.1377G>A	12.37:g.108641799G>A		73	0	0		125	58	0.464	NM_014653	B2RN48|B4DES1|Q8IY35|Q9Y4B7	Silent	SNP	ENST00000332082.4	37	CCDS41828.1																																																																																			G|0.998;A|0.002	0.002	strong		0.567	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405554.1	NM_014653		A	108641799	G	A	108641799	2	1	26	1	0	0	0	0	0	0	0	1	17422	1132	40	1		1	WSCD2	12	108641799	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	7908977	108641799	25210096	426	10189											
ACACB	32	hgsc.bcm.edu	37	chr12	109577344	109577344	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaaacctcatcccgagccAggagccctttccagcctctg	9	7	8	17	1	2	0	1	0	1	0	4	2	4	1	6	1	5	1	6	1	1	1	rs139767464	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:109577344A>G	ENST00000338432.7	+	2	253	c.134A>G	c.(133-135)cAg>cGg	p.Q45R	ACACB_ENST00000377848.3_Missense_Mutation_p.Q45R|ACACB_ENST00000377854.5_Missense_Mutation_p.Q45R			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	45					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)	ATCCCGAGCCAGGAGCCCTTT	0.557													A|||	3	0.000599042	0.0	0.0014	5008	,	,		15671	0.0		0.002	False		,,,				2504	0.0				p.Q45R		Atlas-SNP	.											.	ACACB	330	.	0			c.A134G						PASS	.	A	ARG/GLN	4,4402	6.2+/-15.9	0,4,2199	76	80	79		134	0.2	0.9	12	dbSNP_134	79	23,8577	17.3+/-56.4	0,23,4277	yes	missense	ACACB	NM_001093.3	43	0,27,6476	GG,GA,AA		0.2674,0.0908,0.2076	benign	45/2459	109577344	27,12979	2203	4300	6503	SO:0001583	missense	32	exon1			CGAGCCAGGAGCC	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.134A>G	12.37:g.109577344A>G	ENSP00000341044:p.Gln45Arg	101	0	0		132	66	0.5	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	9.803	1.181034	0.21787	9.08E-4	0.002674	ENSG00000076555	ENST00000338432;ENST00000539864;ENST00000377848;ENST00000377854	D;D;D	0.95307	-3.67;-3.67;-3.67	5.53	0.147	0.14838	.	0.427648	0.19984	N	0.101719	D	0.83737	0.5319	N	0.14661	0.345	0.44579	D	0.997548	B	0.02656	0.0	B	0.04013	0.001	T	0.69172	-0.5215	10	0.15499	T	0.54	.	4.3681	0.11233	0.4845:0.3353:0.1802:0.0	.	45	O00763	ACACB_HUMAN	R	45;20;45;45	ENSP00000341044:Q45R;ENSP00000367079:Q45R;ENSP00000367085:Q45R	ENSP00000341044:Q45R	Q	+	2	0	ACACB	108061727	0.310000	0.24527	0.936000	0.37596	0.137000	0.21094	0.076000	0.14712	0.361000	0.24292	0.528000	0.53228	CAG	A|0.998;G|0.002	0.002	strong		0.557	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		G	109577344	A	G	109577344	3	3	26	1	0	0	0	0	1	0	0	0	107	188	7	3	136	3	ACACB	12	109577344	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	935545	109577344	24274551	427	10190											
MED13L	23389	hgsc.bcm.edu	37	chr12	116446355	116446355	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gactccgggttcgagggcctAatcccacaatataaggctgt	10	9	11	11	2	0	0	0	0	0	0	3	2	2	0	3	3	0	2	3	3	4	4	rs61748071	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:116446355A>G	ENST00000281928.3	-	10	2069	c.1863T>C	c.(1861-1863)atT>atC	p.I621I		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	621						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)		TCGAGGGCCTAATCCCACAAT	0.532													A|||	15	0.00299521	0.0	0.0043	5008	,	,		20935	0.0		0.0099	False		,,,				2504	0.002				p.I621I		Atlas-SNP	.											.	MED13L	193	.	0			c.T1863C						PASS	.	A		7,4399	12.9+/-30.5	0,7,2196	62	55	57		1863	-0.3	1	12	dbSNP_129	57	46,8554	30.1+/-81.4	0,46,4254	no	coding-synonymous	MED13L	NM_015335.4		0,53,6450	GG,GA,AA		0.5349,0.1589,0.4075		621/2211	116446355	53,12953	2203	4300	6503	SO:0001819	synonymous_variant	23389	exon10			GGGCCTAATCCCA	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.1863T>C	12.37:g.116446355A>G		226	0	0		242	127	0.524793	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Silent	SNP	ENST00000281928.3	37	CCDS9177.1																																																																																			A|0.996;G|0.004	0.004	strong		0.532	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3			G	116446355	A	G	116446355	2	3	26	1	0	0	0	0	0	0	0	1	9440	358	13	3		3	MED13L	12	116446355	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	6869011	116446355	17405540	428	10191											
SRRM4	84530	hgsc.bcm.edu	37	chr12	119568596	119568596	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagtccagtcgcccgcccaGtcaacccctccagatgcttg	7	7	8	19	2	1	1	1	0	0	1	4	1	3	1	7	0	2	1	7	0	1	1	rs7297606	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:119568596G>A	ENST00000267260.4	+	8	1116	c.728G>A	c.(727-729)aGt>aAt	p.S243N	SRRM4_ENST00000537597.1_3'UTR	NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	243	Ser-rich.		S -> N (in dbSNP:rs7297606).		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						CGCCCGCCCAGTCAACCCCTC	0.627													G|||	500	0.0998403	0.2042	0.1124	5008	,	,		15715	0.0268		0.0547	False		,,,				2504	0.0716				p.S243N		Atlas-SNP	.											.	SRRM4	131	.	0			c.G728A						PASS	.	G	ASN/SER	638,3266		55,528,1369	25	31	29		728	3.3	1	12	dbSNP_116	29	626,7648		17,592,3528	yes	missense	SRRM4	NM_194286.3	46	72,1120,4897	AA,AG,GG		7.5659,16.3422,10.3794	benign	243/612	119568596	1264,10914	1952	4137	6089	SO:0001583	missense	84530	exon8			CGCCCAGTCAACC	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.728G>A	12.37:g.119568596G>A	ENSP00000267260:p.Ser243Asn	19	0	0		30	17	0.566667	NM_194286	A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	Missense_Mutation	SNP	ENST00000267260.4	37	CCDS44994.1	191	0.08745421245421245	94	0.1910569105691057	36	0.09944751381215469	20	0.03496503496503497	41	0.05408970976253298	G	7.164	0.586356	0.13749	0.163422	0.075659	ENSG00000139767	ENST00000267260	T	0.24538	1.85	5.21	3.34	0.38264	.	0.747332	0.13340	N	0.395235	T	0.00039	0.0001	L	0.44542	1.39	0.41880	P	0.009688999999999948	B	0.30281	0.275	B	0.29942	0.109	T	0.23440	-1.0188	9	0.12430	T	0.62	-8.2941	11.354	0.49605	0.0752:0.1274:0.7974:0.0	rs7297606;rs52809663;rs58175205;rs7297606	243	A7MD48	SRRM4_HUMAN	N	243	ENSP00000267260:S243N	ENSP00000267260:S243N	S	+	2	0	SRRM4	118052979	1.000000	0.71417	0.992000	0.48379	0.053000	0.15095	1.326000	0.33735	0.207000	0.20607	-1.688000	0.00730	AGT	G|0.908;A|0.092	0.092	strong		0.627	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	NM_194286		A	119568596	G	A	119568596	3	1	26	1	0	0	0	0	1	0	0	0	15186	1029	36	2	758	2	SRRM4	12	119568596	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	3122241	119568596	14283299	429	10192											
HNF1A	6927	hgsc.bcm.edu	37	chr12	121437114	121437114	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtggcccagtacacccacacGggcctgctcccgcagactat	8	6	10	17	2	0	1	0	0	0	1	1	1	1	1	4	2	2	3	4	2	2	2	rs55834942	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:121437114G>A	ENST00000257555.6	+	8	1771	c.1545G>A	c.(1543-1545)acG>acA	p.T515T	HNF1A_ENST00000544413.1_Silent_p.T515T|HNF1A_ENST00000541395.1_Silent_p.T515T|RP11-216P16.2_ENST00000606238.1_RNA			P20823	HNF1A_HUMAN	HNF1 homeobox A	515					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)					ACACCCACACGGGCCTGCTCC	0.677									Hepatic Adenoma, Familial Clustering of				.|||	315	0.0628994	0.0121	0.1095	5008	,	,		16172	0.001		0.1988	False		,,,				2504	0.0225				p.T515T		Atlas-SNP	.											HNF1A,brain,glioma,0,4	HNF1A	302	4	0			c.G1545A						scavenged	.	G		175,4231	113.3+/-151.4	4,167,2032	68	70	70		1545	-7.7	0.9	12	dbSNP_129	70	1654,6944	303.3+/-306.4	156,1342,2801	yes	coding-synonymous	HNF1A	NM_000545.5		160,1509,4833	AA,AG,GG		19.237,3.9719,14.0649		515/632	121437114	1829,11175	2203	4299	6502	SO:0001819	synonymous_variant	6927	exon8	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CCACACGGGCCTG	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.1545G>A	12.37:g.121437114G>A		184	1	0.00543478		175	80	0.457143	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Silent	SNP	ENST00000257555.6	37	CCDS9209.1																																																																																			G|0.860;A|0.140	0.140	strong		0.677	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		A	121437114	G	A	121437114	2	1	26	1	0	0	0	0	0	0	0	1	7260	1103	39	1		1	HNF1A	12	121437114	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1868518	121437114	12414781	430	10193											
MPHOSPH9	10198	hgsc.bcm.edu	37	chr12	123678972	123678974	+	In_Frame_Del	DEL	TTT	TTT	-																															tcttgttttagttgagcttcTttatcatctgagagtttgta																										TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TTT	TTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:123678972_123678974delTTT	ENST00000606320.1	-	13	2406_2408	c.2200_2202delAAA	c.(2200-2202)aaadel	p.K734del	MPHOSPH9_ENST00000392425.3_In_Frame_Del_p.K582del|MPHOSPH9_ENST00000302349.5_In_Frame_Del_p.K582del|MPHOSPH9_ENST00000541076.2_In_Frame_Del_p.K704del			Q99550	MPP9_HUMAN	M-phase phosphoprotein 9	734						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(18)|prostate(2)|skin(1)	33	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000182)|Epithelial(86;0.00046)|BRCA - Breast invasive adenocarcinoma(302;0.169)		GTTGAGCTTCTTTATCATCTGAG	0.305																																					p.582_583del		Pindel,Atlas-Indel	.											.	MPHOSPH9	75	.	0			c.1745_1747del						PASS	.																																			SO:0001651	inframe_deletion	10198	exon9			.	X98258	CCDS9243.1, CCDS9243.2	12q24	2008-03-03			ENSG00000051825	ENSG00000051825			7215	protein-coding gene	gene with protein product		605501				8885239	Standard	NM_022782		Approved	MPP9	uc001uel.3	Q99550	OTTHUMG00000168849	ENST00000606320.1:c.2200_2202delAAA	12.37:g.123678972_123678974delTTT	ENSP00000475489:p.Lys734del	142	0	.		162	50	0.309	NM_022782	A1L486|A6NEE2|B3KR87|Q9H976|U3KQ28	In_Frame_Del	DEL	ENST00000606320.1	37																																																																																				.	.	none		0.305	MPHOSPH9-030	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000471390.2			-	123678974	TTT	-	123678972	7	5	26	1	0	1	0	1	0	0	0	0	9737	1606	56	0	1397	0	MPHOSPH9	12	123678972	In_Frame_Del	DEL	TTT	TCGA-G8-6907-01A-11D-2210-10	2241858	123678972	10172923	431	10194											
TMEM132D	121256	hgsc.bcm.edu	37	chr12	130184612	130184612	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gcgtcttccctgacgcagtcCcctctctcaccccctgggtg	3	10	9	19	2	3	1	1	1	2	0	6	1	5	1	5	1	0	1	5	1	0	1	rs140064887	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:130184612C>T	ENST00000422113.2	-	2	1037	c.711G>A	c.(709-711)ggG>ggA	p.G237G	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	237					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)		TGACGCAGTCCCCTCTCTCAC	0.667													C|||	15	0.00299521	0.0015	0.0029	5008	,	,		15848	0.0		0.0099	False		,,,				2504	0.001				p.G237G		Atlas-SNP	.											.	TMEM132D	299	.	0			c.G711A						PASS	.	C		8,4398	12.9+/-30.5	0,8,2195	81	74	76		711	-7.6	0	12	dbSNP_134	76	66,8534	39.8+/-96.3	0,66,4234	no	coding-synonymous	TMEM132D	NM_133448.2		0,74,6429	TT,TC,CC		0.7674,0.1816,0.569		237/1100	130184612	74,12932	2203	4300	6503	SO:0001819	synonymous_variant	121256	exon2			GCAGTCCCCTCTC	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.711G>A	12.37:g.130184612C>T		94	0	0		108	53	0.490741	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Silent	SNP	ENST00000422113.2	37	CCDS9266.1																																																																																			C|0.995;T|0.005	0.005	strong		0.667	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448		T	130184612	C	T	130184612	2	4	26	1	0	0	0	0	0	0	0	1	16062	610	22	2		2	TMEM132D	12	130184612	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	6505640	130184612	3667283	432	10195											
SFRS8	6433	hgsc.bcm.edu	37	chr12	132240010	132240010	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tcttcctccagaaagaagggGgcgatagcatgcaggtacgt	11	8	13	9	2	1	2	0	0	1	2	3	3	3	2	2	3	3	3	2	3	4	3	rs34541796	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:132240010G>A	ENST00000261674.4	+	10	1675	c.1534G>A	c.(1534-1536)Ggc>Agc	p.G512S	SFSWAP_ENST00000541286.1_Missense_Mutation_p.G512S|RP11-495K9.5_ENST00000537032.1_lincRNA	NM_004592.3	NP_004583.2	Q12872	SFSWA_HUMAN	splicing factor, suppressor of white-apricot family	512			G -> S (in dbSNP:rs34541796).		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						GAAAGAAGGGGGCGATAGCAT	0.473											OREG0022261	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	14	0.00279553	0.0	0.0029	5008	,	,		20123	0.0		0.0119	False		,,,				2504	0.0				p.G512S		Atlas-SNP	.											SFSWAP,colon,carcinoma,-2,1	SFSWAP	69	1	0			c.G1534A						PASS	.	G	SER/GLY	23,4383	29.9+/-59.1	0,23,2180	84	82	83		1534	2.7	0	12	dbSNP_126	83	222,8378	92.1+/-154.2	3,216,4081	yes	missense	SFSWAP	NM_004592.2	56	3,239,6261	AA,AG,GG		2.5814,0.522,1.8837	benign	512/952	132240010	245,12761	2203	4300	6503	SO:0001583	missense	6433	exon10			GAAGGGGGCGATA	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.1534G>A	12.37:g.132240010G>A	ENSP00000261674:p.Gly512Ser	35	0	0	1593	45	22	0.488889	NM_001261411	B2RN45|B7ZM97|F5H6B8|Q6PJF7	Missense_Mutation	SNP	ENST00000261674.4	37	CCDS9273.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	G	5.528	0.282302	0.10458	0.00522	0.025814	ENSG00000061936	ENST00000261674;ENST00000544623;ENST00000535236;ENST00000541286	T;T;T	0.24538	2.84;1.85;2.87	5.49	2.69	0.31865	.	0.412335	0.27946	N	0.017203	T	0.03220	0.0094	N	0.12746	0.255	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.34153	-0.9840	10	0.09084	T	0.74	-12.0835	5.7966	0.18389	0.3482:0.1294:0.5224:0.0	rs34541796	512;512	F5H6B8;Q12872	.;SFSWA_HUMAN	S	512;449;305;512	ENSP00000261674:G512S;ENSP00000443045:G305S;ENSP00000437738:G512S	ENSP00000261674:G512S	G	+	1	0	SFSWAP	130805963	0.000000	0.05858	0.007000	0.13788	0.312000	0.27988	0.482000	0.22276	0.294000	0.22547	0.561000	0.74099	GGC	G|0.987;A|0.013	0.013	strong		0.473	SFSWAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399276.1	NM_004592		A	132240010	G	A	132240010	3	1	26	1	0	0	0	0	1	0	0	0	14198	1232	43	2	1572	2	SFRS8	12	132240010	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	2055398	132240010	1611885	433	10196											
EP400	57634	hgsc.bcm.edu	37	chr12	132445675	132445675	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagccctacagggggcttcGtggatgccagcgtgctggtg	5	8	17	11	2	0	0	0	0	0	0	1	1	0	1	2	4	5	3	2	4	1	2	rs61745448	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:132445675G>A	ENST00000333577.4	+	2	620	c.511G>A	c.(511-513)Gtg>Atg	p.V171M	EP400_ENST00000332482.4_Missense_Mutation_p.V171M|EP400_ENST00000389561.2_Missense_Mutation_p.V171M|EP400_ENST00000330386.6_Missense_Mutation_p.V171M|EP400_ENST00000389562.2_Missense_Mutation_p.V171M			Q96L91	EP400_HUMAN	E1A binding protein p400	171					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)		AGGGGGCTTCGTGGATGCCAG	0.672													G|||	61	0.0121805	0.0008	0.0231	5008	,	,		15923	0.0		0.0408	False		,,,				2504	0.0031				p.V171M		Atlas-SNP	.											.	EP400	370	.	0			c.G511A						PASS	.	G	MET/VAL	44,4360	43.8+/-77.6	0,44,2158	55	42	46		511	4.9	1	12	dbSNP_129	46	411,8187	121.7+/-180.7	15,381,3903	no	missense	EP400	NM_015409.4	21	15,425,6061	AA,AG,GG		4.7802,0.9991,3.4995	probably-damaging	171/3124	132445675	455,12547	2202	4299	6501	SO:0001583	missense	57634	exon2			GGCTTCGTGGATG	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.511G>A	12.37:g.132445675G>A	ENSP00000333602:p.Val171Met	426	0	0		478	237	0.495816	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	37		42	0.019230769230769232	0	0.0	10	0.027624309392265192	0	0.0	32	0.04221635883905013	G	6.433	0.448071	0.12223	0.009991	0.047802	ENSG00000183495	ENST00000537902;ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000423130;ENST00000541296;ENST00000542457	D;D;D;D;D	0.94232	-3.23;-3.38;-3.38;-3.38;-3.38	5.79	4.9	0.64082	.	0.000000	0.85682	D	0.000000	D	0.83312	0.5227	M	0.75447	2.3	0.37260	D	0.906958	D;D;D;D;D	0.67145	0.996;0.996;0.996;0.995;0.996	P;P;P;P;P	0.59487	0.753;0.753;0.753;0.858;0.753	D	0.87512	0.2440	10	0.87932	D	0	.	15.0397	0.71781	0.0684:0.0:0.9316:0.0	rs61745448	171;171;171;171;171	Q96L91-2;Q96L91-4;Q96L91-5;F8WCN8;Q96L91-3	.;.;.;.;.	M	171	ENSP00000333602:V171M;ENSP00000374212:V171M;ENSP00000374213:V171M;ENSP00000331737:V171M;ENSP00000330620:V171M	ENSP00000330620:V171M	V	+	1	0	EP400	131011628	1.000000	0.71417	0.961000	0.40146	0.048000	0.14542	9.461000	0.97646	1.453000	0.47775	0.563000	0.77884	GTG	G|0.976;A|0.024	0.024	strong		0.672	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		A	132445675	G	A	132445675	3	1	26	1	0	0	0	0	1	0	0	0	5151	1145	40	1	513	1	EP400	12	132445675	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	205665	132445675	1406220	434	10197											
POLE	5426	hgsc.bcm.edu	37	chr12	133233812	133233812	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agttttttgtgcagccagtcGgggtgtttgacacgtggcac	6	13	14	8	2	0	1	0	1	0	0	1	1	0	1	1	3	2	4	1	3	0	4			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:133233812G>A	ENST00000320574.5	-	29	3535	c.3492C>T	c.(3490-3492)ccC>ccT	p.P1164P	POLE_ENST00000535270.1_Silent_p.P1137P	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	1164					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)	GCAGCCAGTCGGGGTGTTTGA	0.532								DNA polymerases (catalytic subunits)																													p.P1164P		Atlas-SNP	.											.	POLE	416	.	0			c.C3492T						PASS	.						100	98	99					12																	133233812		2203	4300	6503	SO:0001819	synonymous_variant	5426	exon29			CCAGTCGGGGTGT		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.3492C>T	12.37:g.133233812G>A		160	0	0		201	101	0.502488	NM_006231	Q13533|Q86VH9	Silent	SNP	ENST00000320574.5	37	CCDS9278.1																																																																																			.	.	none		0.532	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231		A	133233812	G	A	133233812	2	1	26	1	0	0	0	0	0	0	0	1	12205	1103	39	1		1	POLE	12	133233812	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	788137	133233812	618083	435	10198											
PXMP2	5827	hgsc.bcm.edu	37	chr12	133272590	133272590	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaccgcctcgtctttgcaccGgccttcctcatgttgttctt	3	15	8	15	3	3	0	1	0	2	0	5	1	4	0	5	1	1	3	5	1	0	5	rs145883118	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:133272590G>T	ENST00000317479.3	+	3	422	c.357G>T	c.(355-357)ccG>ccT	p.P119P	PXMP2_ENST00000539093.1_Intron|PXMP2_ENST00000543589.1_Intron|RP13-672B3.2_ENST00000537262.1_Intron|PXMP2_ENST00000545677.1_Intron|PXMP2_ENST00000428960.2_Silent_p.P26P	NM_018663.1	NP_061133.1	Q9NR77	PXMP2_HUMAN	peroxisomal membrane protein 2, 22kDa	119						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|protein complex (GO:0043234)				large_intestine(1)|liver(2)|lung(1)	4	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.86e-08)|Epithelial(86;2.47e-07)|all cancers(50;6.85e-06)		TCTTTGCACCGGCCTTCCTCA	0.537													G|||	3	0.000599042	0.0	0.0	5008	,	,		16181	0.0		0.002	False		,,,				2504	0.001				p.P119P		Atlas-SNP	.											.	PXMP2	15	.	0			c.G357T						PASS	.						89	85	87					12																	133272590		2203	4300	6503	SO:0001819	synonymous_variant	5827	exon3			TGCACCGGCCTTC		CCDS9279.1	12q24	2010-08-18	2002-08-29		ENSG00000176894	ENSG00000176894			9716	protein-coding gene	gene with protein product			"peroxisomal membrane protein 2 (22kD)"			11590176	Standard	NM_018663		Approved	PMP22	uc001ukt.3	Q9NR77	OTTHUMG00000168019	ENST00000317479.3:c.357G>T	12.37:g.133272590G>T		108	0	0		122	57	0.467213	NM_018663		Silent	SNP	ENST00000317479.3	37	CCDS9279.1																																																																																			G|0.999;T|0.001	0.001	strong		0.537	PXMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397553.1	NM_018663		T	133272590	G	T	133272590	2	4	26	1	0	0	0	0	0	0	0	1	12865	1103	39	4		4	PXMP2	12	133272590	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	38778	133272590	579305	436	10199											
ZDHHC20	253832	hgsc.bcm.edu	37	chr13	21955582	21955582	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaactattacctgatttgaCgatgccttcttcagctccat	10	14	6	11	1	2	3	1	2	1	1	3	4	3	3	3	0	4	1	3	0	3	5	rs185661667	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:21955582C>T	ENST00000400590.3	-	11	1249	c.1051G>A	c.(1051-1053)Gtc>Atc	p.V351I	ZDHHC20_ENST00000415724.1_Missense_Mutation_p.V351I|ZDHHC20_ENST00000542645.1_Missense_Mutation_p.V288I|ZDHHC20_ENST00000382466.3_Missense_Mutation_p.V350I|ZDHHC20_ENST00000494731.1_5'UTR|ZDHHC20_ENST00000320220.9_3'UTR			Q5W0Z9	ZDH20_HUMAN	zinc finger, DHHC-type containing 20	351					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)		CCTGATTTGACGATGCCTTCT	0.368													c|||	3	0.000599042	0.0008	0.0	5008	,	,		14111	0.001		0.001	False		,,,				2504	0.0				p.V350I		Atlas-SNP	.											.	ZDHHC20	36	.	0			c.G1048A						PASS	.	T	ILE/VAL	8,3764		0,8,1878	79	75	76		1048	-2.7	0	13		76	13,8195		0,13,4091	yes	missense	ZDHHC20	NM_153251.3	29	0,21,5969	TT,TC,CC		0.1584,0.2121,0.1753	benign	350/355	21955582	21,11959	1886	4104	5990	SO:0001583	missense	253832	exon11			ATTTGACGATGCC	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.1051G>A	13.37:g.21955582C>T	ENSP00000383433:p.Val351Ile	46	0	0		57	37	0.649123	NM_153251	A8MTV9|C9JG20|I6L9D4|Q2TB82|Q6NVU8	Missense_Mutation	SNP	ENST00000400590.3	37		3	0.0013736263736263737	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	1	0.0013192612137203166	c	0.034	-1.315557	0.01331	0.002121	0.001584	ENSG00000180776	ENST00000400590;ENST00000382466;ENST00000542645;ENST00000415724	T;T;T;T	0.52057	0.96;0.94;0.68;0.96	5.24	-2.7	0.06004	.	2.147630	0.01524	N	0.018465	T	0.41858	0.1177	L	0.47716	1.5	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.23511	-1.0186	10	0.22706	T	0.39	-10.2651	11.1755	0.48596	0.0:0.493:0.0:0.507	.	288;350	B4DRN8;Q5W0Z9-3	.;.	I	351;350;288;351	ENSP00000383433:V351I;ENSP00000371905:V350I;ENSP00000443236:V288I;ENSP00000401232:V351I	ENSP00000371905:V350I	V	-	1	0	ZDHHC20	20853582	0.000000	0.05858	0.000000	0.03702	0.486000	0.33341	0.041000	0.13927	-0.958000	0.03622	-0.735000	0.03563	GTC	C|0.998;T|0.002	0.002	strong		0.368	ZDHHC20-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000045994.1	NM_153251		T	21955582	C	T	21955582	3	4	26	1	0	0	0	0	1	0	0	0	17626	536	19	1	24	1	ZDHHC20	13	21955582	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10		21955582	93214296	437	10200											
FREM2	341640	hgsc.bcm.edu	37	chr13	39263218	39263218	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gagggtgaaacagtgcccatCctgcccctttccctgagtgc	7	9	11	14	0	0	2	0	2	0	0	2	3	2	2	5	1	4	0	5	1	1	1	rs144811771		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:39263218C>T	ENST00000280481.7	+	1	1953	c.1737C>T	c.(1735-1737)atC>atT	p.I579I		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	579					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)		CAGTGCCCATCCTGCCCCTTT	0.532																																					p.I579I		Atlas-SNP	.											.	FREM2	385	.	0			c.C1737T						PASS	.	C		0,4406		0,0,2203	126	122	123		1737	3.5	1	13	dbSNP_134	123	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FREM2	NM_207361.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		579/3170	39263218	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	341640	exon1			GCCCATCCTGCCC	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.1737C>T	13.37:g.39263218C>T		51	0	0		18	17	0.944444	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																			C|1.000;T|0.000	0.000	weak		0.532	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39263218	C	T	39263218	2	4	26	1	0	0	0	0	0	0	0	1	6053	845	30	2		2	FREM2	13	39263218	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	17307636	39263218	75906660	438	10201											
NUFIP1	26747	hgsc.bcm.edu	37	chr13	45563215	45563215	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctatcagaagactgtctccaAtaccacgatgtggaagcatg	13	9	9	10	1	2	2	1	0	1	2	3	4	2	3	2	1	2	1	2	1	5	2	rs116755008	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:45563215A>G	ENST00000379161.4	-	1	403	c.357T>C	c.(355-357)taT>taC	p.Y119Y	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	119					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)		ACTGTCTCCAATACCACGATG	0.552													A|||	13	0.00259585	0.0008	0.0043	5008	,	,		19062	0.0		0.0089	False		,,,				2504	0.0				p.Y119Y		Atlas-SNP	.											.	NUFIP1	41	.	0			c.T357C						PASS	.	A		3,4403	6.2+/-15.9	0,3,2200	47	45	46		357	2.2	1	13	dbSNP_132	46	45,8549	28.5+/-78.6	0,45,4252	yes	coding-synonymous	NUFIP1	NM_012345.2		0,48,6452	GG,GA,AA		0.5236,0.0681,0.3692		119/496	45563215	48,12952	2203	4297	6500	SO:0001819	synonymous_variant	26747	exon1			TCTCCAATACCAC	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.357T>C	13.37:g.45563215A>G		312	0	0		166	145	0.873494	NM_012345	Q8WVM5|Q96SG1	Silent	SNP	ENST00000379161.4	37	CCDS9393.1																																																																																			A|0.997;G|0.003	0.003	strong		0.552	NUFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044755.2	NM_012345		G	45563215	A	G	45563215	2	3	26	1	0	0	0	0	0	0	0	1	10757	108	4	3		3	NUFIP1	13	45563215	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	6299997	45563215	69606663	439	10202											
RB1	5925	hgsc.bcm.edu	37	chr13	48947553	48947553	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccctctaggactgttatgaaCactatccaacaattaatgat	14	12	5	10	0	1	2	0	2	1	0	2	3	2	3	2	1	2	1	2	1	7	4	rs117865557		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:48947553C>T	ENST00000267163.4	+	12	1278	c.1140C>T	c.(1138-1140)aaC>aaT	p.N380N		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	380	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)		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)"	CTGTTATGAACACTATCCAAC	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)			C|||	1	0.000199681	0.0	0.0	5008	,	,		14986	0.001		0.0	False		,,,				2504	0.0				p.N380N		Atlas-SNP	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	.	RB1	1068	.	23	Whole gene deletion(15)|Unknown(8)	bone(11)|breast(5)|central_nervous_system(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	c.C1140T						PASS	.	C		0,4406		0,0,2203	103	110	107		1140	4.3	1	13	dbSNP_132	107	3,8577	3.0+/-9.4	0,3,4287	no	coding-synonymous	RB1	NM_000321.2		0,3,6490	TT,TC,CC		0.035,0.0,0.0231		380/929	48947553	3,12983	2203	4290	6493	SO:0001819	synonymous_variant	5925	exon12	Familial Cancer Database		TATGAACACTATC	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.1140C>T	13.37:g.48947553C>T		334	0	0		135	118	0.874074	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Silent	SNP	ENST00000267163.4	37	CCDS31973.1																																																																																			C|1.000;T|0.000	0.000	strong		0.294	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			T	48947553	C	T	48947553	2	4	26	1	0	0	0	0	0	0	0	1	13113	477	17	2		2	RB1	13	48947553	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	3384338	48947553	66222325	440	10203											
RB1	5925	hgsc.bcm.edu	37	chr13	49039405	49039405	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caagtttcctagttcaccctTacggattcctggagggaaca	10	11	9	11	1	1	0	1	0	0	0	3	3	3	3	3	3	2	2	3	3	4	5			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:49039405T>A	ENST00000267163.4	+	23	2528	c.2390T>A	c.(2389-2391)tTa>tAa	p.L797*		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	797	Domain C; mediates interaction with E4F1.|Interaction with LIMD1.				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.?(11)|p.L797fs*1(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)"	AGTTCACCCTTACGGATTCCT	0.403		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.L797X		Atlas-SNP	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"L, E, M, O"	.	RB1	1068	.	27	Whole gene deletion(15)|Unknown(11)|Deletion - Frameshift(1)	bone(11)|haematopoietic_and_lymphoid_tissue(4)|breast(4)|adrenal_gland(1)|eye(1)|soft_tissue(1)|endometrium(1)|urinary_tract(1)|lung(1)|ovary(1)|liver(1)	c.T2390A	GRCh37	CM023820	RB1	M		PASS	.						131	133	133					13																	49039405		2203	4300	6503	SO:0001587	stop_gained	5925	exon23	Familial Cancer Database		CACCCTTACGGAT	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.2390T>A	13.37:g.49039405T>A	ENSP00000267163:p.Leu797*	131	0	0		80	7	0.0875	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Nonsense_Mutation	SNP	ENST00000267163.4	37	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	T	39	7.903488	0.98554	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	.	.	.	5.87	5.87	0.94306	.	0.091849	0.44902	D	0.000409	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.7061	0.51597	0.0:0.0:0.158:0.842	.	.	.	.	X	776;797	.	ENSP00000267163:L797X	L	+	2	0	RB1	47937406	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	5.593000	0.67550	2.242000	0.73789	0.482000	0.46254	TTA	.	.	none		0.403	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1			A	49039405	T	A	49039405	4	1	26	1	0	0	0	0	0	1	0	0	13113	1764	61	5	2480	5	RB1	13	49039405	Nonsense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	91852	49039405	66130473	441	10204											
TBC1D4	9882	hgsc.bcm.edu	37	chr13	76055726	76055726	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gctgcgcctgcggatctcggCcatgagccagggcagcatag	7	6	15	13	3	1	1	0	1	1	0	2	2	1	2	3	3	4	3	3	3	1	1			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:76055726C>T	ENST00000377636.3	-	1	524	c.178G>A	c.(178-180)Gcc>Acc	p.A60T	TBC1D4_ENST00000425511.1_5'UTR|TBC1D4_ENST00000431480.2_Missense_Mutation_p.A60T|TBC1D4_ENST00000377625.2_Missense_Mutation_p.A60T	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	60	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)		CGGATCTCGGCCATGAGCCAG	0.716																																					p.A60T		Atlas-SNP	.											.	TBC1D4	142	.	0			c.G178A						PASS	.						9	11	11					13																	76055726		1891	4103	5994	SO:0001583	missense	9882	exon1			TCTCGGCCATGAG	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.178G>A	13.37:g.76055726C>T	ENSP00000366863:p.Ala60Thr	63	0	0		52	4	0.0769231	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Missense_Mutation	SNP	ENST00000377636.3	37	CCDS41901.1	.	.	.	.	.	.	.	.	.	.	C	34	5.373372	0.95923	.	.	ENSG00000136111	ENST00000377636;ENST00000431480;ENST00000377625	T;T;T	0.55930	0.49;0.49;0.49	3.95	3.95	0.45737	Phosphotyrosine interaction domain (1);Pleckstrin homology-type (1);	0.000000	0.49916	D	0.000138	T	0.70386	0.3218	M	0.68593	2.085	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;0.996	T	0.75459	-0.3310	10	0.72032	D	0.01	-9.0239	16.1706	0.81812	0.0:1.0:0.0:0.0	.	60;60;60	O60343-2;O60343-3;O60343	.;.;TBCD4_HUMAN	T	60	ENSP00000366863:A60T;ENSP00000395986:A60T;ENSP00000366852:A60T	ENSP00000366852:A60T	A	-	1	0	TBC1D4	74953727	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.673000	0.74482	2.017000	0.59298	0.561000	0.74099	GCC	.	.	none		0.716	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832		T	76055726	C	T	76055726	3	4	26	1	0	0	0	0	1	0	0	0	15637	739	26	2	3802	2	TBC1D4	13	76055726	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	27016321	76055726	39114152	442	10205											
LMO7	4008	hgsc.bcm.edu	37	chr13	76370783	76370783	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttttaaggttttgataacAttgtactggctgggaagaaa	12	16	10	3	0	0	2	0	1	0	1	0	3	0	3	0	3	2	3	0	3	5	8			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:76370783A>G	ENST00000341547.4	+	7	1776	c.516A>G	c.(514-516)acA>acG	p.T172T	LMO7_ENST00000321797.8_5'UTR|RP11-29G8.3_ENST00000563635.1_RNA|LMO7_ENST00000526202.1_Silent_p.T81T|LMO7_ENST00000377534.3_Silent_p.T172T|LMO7_ENST00000357063.3_Silent_p.T172T|LMO7_ENST00000465261.2_5'UTR	NM_005358.5	NP_005349.3	Q8WWI1	LMO7_HUMAN	LIM domain 7	172					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)	p.T172T(2)		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)		TTTTGATAACATTGTACTGGC	0.363																																					p.T172T		Atlas-SNP	.											LMO7_ENST00000357063,NS,carcinoma,0,2	LMO7	334	2	2	Substitution - coding silent(2)	breast(2)	c.A516G						PASS	.						80	75	77					13																	76370783		2203	4300	6503	SO:0001819	synonymous_variant	4008	exon7			GATAACATTGTAC	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	ENST00000341547.4:c.516A>G	13.37:g.76370783A>G		61	0	0		78	35	0.448718	NM_005358	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Silent	SNP	ENST00000341547.4	37	CCDS9454.1																																																																																			.	.	none		0.363	LMO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045297.1	NM_005358		G	76370783	A	G	76370783	2	3	26	1	0	0	0	0	0	0	0	1	8864	204	8	3		3	LMO7	13	76370783	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	315057	76370783	38799095	443	10206											
TMTC4	84899	hgsc.bcm.edu	37	chr13	101266580	101266580	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctttctgtacctgtattgtcGaggagtataatcatgttgtt	8	18	9	6	1	2	0	1	0	1	0	3	2	2	1	1	1	1	5	1	1	4	8			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:101266580G>A	ENST00000376234.3	-	15	2073	c.1884C>T	c.(1882-1884)ctC>ctT	p.L628L	TMTC4_ENST00000328767.5_Silent_p.L517L|TMTC4_ENST00000342624.5_Silent_p.L647L	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	628						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)					CTGTATTGTCGAGGAGTATAA	0.463																																					p.L647L		Atlas-SNP	.											.	TMTC4	103	.	0			c.C1941T						PASS	.						166	143	151					13																	101266580		2203	4300	6503	SO:0001819	synonymous_variant	84899	exon16			ATTGTCGAGGAGT		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.1884C>T	13.37:g.101266580G>A		288	1	0.00347222		305	141	0.462295	NM_032813	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Silent	SNP	ENST00000376234.3	37	CCDS41904.1																																																																																			.	.	none		0.463	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813		A	101266580	G	A	101266580	2	1	26	1	0	0	0	0	0	0	0	1	16278	1045	37	1		1	TMTC4	13	101266580	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	24895797	101266580	13903298	444	10207											
C13orf39	196541	hgsc.bcm.edu	37	chr13	103339363	103339363	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atttttgcatcttggaaattCaattcctcggcatgttcctc	8	17	6	10	1	2	0	1	0	1	0	6	1	4	1	2	2	1	3	2	2	2	6	rs148307139	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:103339363C>G	ENST00000267273.6	-	3	332	c.327G>C	c.(325-327)ttG>ttC	p.L109F		NM_001010977.1	NP_001010977.1	Q5VZV1	MT21C_HUMAN	methyltransferase like 21C	109					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						CTTGGAAATTCAATTCCTCGG	0.388																																					p.L109F		Atlas-SNP	.											METTL21C,NS,carcinoma,0,1	METTL21C	23	1	0			c.G327C						PASS	.	C	PHE/LEU	0,4406		0,0,2203	83	77	79		327	2.1	1	13	dbSNP_134	79	10,8590	7.7+/-29.5	0,10,4290	yes	missense	METTL21C	NM_001010977.1	22	0,10,6493	GG,GC,CC		0.1163,0.0,0.0769	benign	109/265	103339363	10,12996	2203	4300	6503	SO:0001583	missense	196541	exon3			GAAATTCAATTCC		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.327G>C	13.37:g.103339363C>G	ENSP00000267273:p.Leu109Phe	87	0	0		66	28	0.424242	NM_001010977		Missense_Mutation	SNP	ENST00000267273.6	37	CCDS32003.1	.	.	.	.	.	.	.	.	.	.	C	11.15	1.554827	0.27739	0.0	0.001163	ENSG00000139780	ENST00000267273	T	0.06528	3.29	5.96	2.13	0.27403	.	0.144833	0.48286	D	0.000182	T	0.04543	0.0124	N	0.20766	0.605	0.31573	N	0.656042	B	0.22541	0.071	B	0.22152	0.038	T	0.23833	-1.0177	10	0.20046	T	0.44	-0.0013	12.4417	0.55629	0.0:0.2593:0.6587:0.082	.	109	Q5VZV1	MT21C_HUMAN	F	109	ENSP00000267273:L109F	ENSP00000267273:L109F	L	-	3	2	METTL21C	102137364	0.993000	0.37304	0.974000	0.42286	0.493000	0.33554	0.487000	0.22356	0.381000	0.24851	0.650000	0.86243	TTG	C|0.999;G|0.001	0.001	strong		0.388	METTL21C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045682.2	NM_001010977		G	103339363	C	G	103339363	3	3	26	1	0	0	0	0	1	0	0	0	1734	825	29	4	475	4	C13orf39	13	103339363	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	2072783	103339363	11830515	445	10208											
ATP11A	23250	hgsc.bcm.edu	37	chr13	113481026	113481026	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	agttcctcaaggcattcacgGacttcctggccttcatggtc	7	12	9	13	1	3	0	3	0	0	0	6	1	5	1	3	4	0	2	3	4	1	4			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:113481026G>A	ENST00000487903.1	+	12	1130	c.1042G>A	c.(1042-1044)Gac>Aac	p.D348N	ATP11A_ENST00000375630.2_Missense_Mutation_p.D348N|ATP11A_ENST00000375645.3_Missense_Mutation_p.D348N|ATP11A_ENST00000283558.8_Missense_Mutation_p.D348N			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	348					phospholipid translocation (GO:0045332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	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(6)|kidney(4)|large_intestine(12)|lung(17)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	51	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_lung(25;0.134)|all_epithelial(44;0.141)				GGCATTCACGGACTTCCTGGC	0.547																																					p.D348N		Atlas-SNP	.											.	ATP11A	225	.	0			c.G1042A						PASS	.						118	104	109					13																	113481026		2203	4300	6503	SO:0001583	missense	23250	exon12			TTCACGGACTTCC	AB028944	CCDS32011.1	13q34	2010-04-20	2007-09-19		ENSG00000068650	ENSG00000068650	3.6.3.1	"ATPases / P-type"	13552	protein-coding gene	gene with protein product	"potential phospholipid-transporting ATPase IH", "phospholipid-translocating ATPase"	605868	"ATPase, Class VI, type 11A"			11015572	Standard	NM_032189		Approved	ATPIH, ATPIS, KIAA1021	uc001vsj.4	P98196	OTTHUMG00000017371	ENST00000487903.1:c.1042G>A	13.37:g.113481026G>A	ENSP00000420387:p.Asp348Asn	197	0	0		259	132	0.509652	NM_032189	Q5VXT2	Missense_Mutation	SNP	ENST00000487903.1	37	CCDS32011.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.006318	0.74932	.	.	ENSG00000068650	ENST00000487903;ENST00000375630;ENST00000375645;ENST00000283558	D;D;D;D	0.90620	-2.7;-2.7;-2.7;-2.7	5.05	5.05	0.67936	ATPase, P-type, ATPase-associated domain (1);	0.000000	0.85682	D	0.000000	D	0.93048	0.7787	L	0.45744	1.44	0.80722	D	1	D;P;B	0.89917	1.0;0.887;0.217	D;P;B	0.97110	1.0;0.733;0.444	D	0.90323	0.4346	10	0.15499	T	0.54	.	18.4296	0.90620	0.0:0.0:1.0:0.0	.	348;348;348	E9PCW5;E9PEJ6;P98196	.;.;AT11A_HUMAN	N	348	ENSP00000420387:D348N;ENSP00000364781:D348N;ENSP00000364796:D348N;ENSP00000283558:D348N	ENSP00000283558:D348N	D	+	1	0	ATP11A	112529027	1.000000	0.71417	0.933000	0.37362	0.121000	0.20230	9.445000	0.97587	2.341000	0.79615	0.557000	0.71058	GAC	.	.	none		0.547	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205		A	113481026	G	A	113481026	3	1	26	1	0	0	0	0	1	0	0	0	1119	1174	41	2	1088	2	ATP11A	13	113481026	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	10141663	113481026	1688852	446	10209											
OR11H6	122748	hgsc.bcm.edu	37	chr14	20692353	20692353	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggaagttctgtataattcTggtctgtgtatgctgggtag	7	16	14	4	0	3	0	0	0	3	0	3	1	3	1	0	3	1	5	0	3	5	6	rs146076639	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:20692353T>C	ENST00000315519.2	+	1	563	c.485T>C	c.(484-486)cTg>cCg	p.L162P		NM_001004480.1	NP_001004480.1	Q8NGC7	O11H6_HUMAN	olfactory receptor, family 11, subfamily H, member 6	162						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)		TGTATAATTCTGGTCTGTGTA	0.463													t|||	9	0.00179712	0.0015	0.0029	5008	,	,		21313	0.0		0.004	False		,,,				2504	0.001				p.L162P		Atlas-SNP	.											.	OR11H6	60	.	0			c.T485C						PASS	.	T	PRO/LEU	4,4402	8.1+/-20.4	0,4,2199	101	99	100		485	5	1	14	dbSNP_134	100	34,8566	23.4+/-69.3	0,34,4266	yes	missense	OR11H6	NM_001004480.1	98	0,38,6465	CC,CT,TT		0.3953,0.0908,0.2922	probably-damaging	162/331	20692353	38,12968	2203	4300	6503	SO:0001583	missense	122748	exon1			TAATTCTGGTCTG		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.485T>C	14.37:g.20692353T>C	ENSP00000319071:p.Leu162Pro	150	0	0		104	56	0.538462	NM_001004480	Q6IF08	Missense_Mutation	SNP	ENST00000315519.2	37	CCDS32033.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	T	9.989	1.230400	0.22542	9.08E-4	0.003953	ENSG00000176219	ENST00000315519	T	0.45276	0.9	4.97	4.97	0.65823	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40818	N	0.001011	T	0.69142	0.3078	H	0.97240	3.965	0.23809	N	0.996783	D	0.89917	1.0	D	0.87578	0.998	T	0.72121	-0.4386	10	0.87932	D	0	.	12.6331	0.56669	0.0:0.0:0.0:1.0	.	162	Q8NGC7	O11H6_HUMAN	P	162	ENSP00000319071:L162P	ENSP00000319071:L162P	L	+	2	0	OR11H6	19762193	0.774000	0.28592	0.996000	0.52242	0.144000	0.21451	4.003000	0.57061	2.077000	0.62373	0.363000	0.22086	CTG	T|0.998;C|0.002	0.002	strong		0.463	OR11H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410676.1			C	20692353	T	C	20692353	3	2	26	1	0	0	0	0	1	0	0	0	10938	1580	55	3	487	3	OR11H6	14	20692353	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10		20692353	86657187	447	10210											
OR10G3	26533	hgsc.bcm.edu	37	chr14	22038731	22038731	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagccttgggtctgcccagaCagtgattaaaataagcaggt	12	9	12	8	0	1	2	0	1	1	1	1	3	1	2	2	2	3	1	2	2	3	3	rs12886819	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:22038731C>G	ENST00000303532.1	-	1	144	c.145G>C	c.(145-147)Gtc>Ctc	p.V49L		NM_001005465.1	NP_001005465.1	Q8NGC4	O10G3_HUMAN	olfactory receptor, family 10, subfamily G, member 3	49						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(4)|lung(7)	15	all_cancers(95;0.000987)			GBM - Glioblastoma multiforme(265;0.0139)		TCTGCCCAGACAGTGATTAAA	0.463													C|||	42	0.00838658	0.0023	0.0101	5008	,	,		21952	0.0		0.0298	False		,,,				2504	0.002				p.V49L		Atlas-SNP	.											.	OR10G3	40	.	0			c.G145C						PASS	.	C	LEU/VAL	28,4378	34.3+/-65.2	0,28,2175	75	73	74		145	3.4	1	14	dbSNP_121	74	231,8369	95.2+/-157.0	2,227,4071	yes	missense	OR10G3	NM_001005465.1	32	2,255,6246	GG,GC,CC		2.686,0.6355,1.9914	benign	49/314	22038731	259,12747	2203	4300	6503	SO:0001583	missense	26533	exon1			CCCAGACAGTGAT		CCDS32046.1	14q11.2	2013-09-24			ENSG00000169208	ENSG00000169208		"GPCR / Class A : Olfactory receptors"	8171	protein-coding gene	gene with protein product						8188290	Standard	NM_001005465		Approved		uc010tmb.2	Q8NGC4	OTTHUMG00000168886	ENST00000303532.1:c.145G>C	14.37:g.22038731C>G	ENSP00000302437:p.Val49Leu	69	0	0		83	43	0.518072	NM_001005465	Q6IET7|Q96R77	Missense_Mutation	SNP	ENST00000303532.1	37	CCDS32046.1	27	0.012362637362637362	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	21	0.027704485488126648	C	11.04	1.521943	0.27211	0.006355	0.02686	ENSG00000169208	ENST00000303532	T	0.03124	4.04	4.33	3.44	0.39384	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42053	D	0.000763	T	0.02342	0.0072	M	0.84846	2.72	0.23070	N	0.99835	B	0.22346	0.068	B	0.27380	0.079	T	0.16719	-1.0393	10	0.87932	D	0	-33.6789	7.2391	0.26086	0.0:0.7924:0.0:0.2076	rs12886819;rs12886819	49	Q8NGC4	O10G3_HUMAN	L	49	ENSP00000302437:V49L	ENSP00000302437:V49L	V	-	1	0	OR10G3	21108571	0.014000	0.17966	0.997000	0.53966	0.860000	0.49131	0.027000	0.13621	0.943000	0.37553	-0.224000	0.12420	GTC	C|0.975;G|0.025	0.025	strong		0.463	OR10G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401521.1			G	22038731	C	G	22038731	3	3	26	1	0	0	0	0	1	0	0	0	10909	478	17	4	799	4	OR10G3	14	22038731	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1346378	22038731	85310809	448	10211											
LRRC16B	90668	hgsc.bcm.edu	37	chr14	24534916	24534916	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tcacggtgttgcccttcccgGgttggaaagagccaagggtt	7	10	14	10	2	1	1	1	0	0	1	2	2	2	2	3	4	2	3	3	4	2	4	rs79328356	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:24534916G>T	ENST00000342740.5	+	34	3636	c.3482G>T	c.(3481-3483)gGg>gTg	p.G1161V	LRRC16B_ENST00000334420.7_Intron	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	1161						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)		GCCCTTCCCGGGTTGGAAAGA	0.617													G|||	98	0.0195687	0.003	0.0245	5008	,	,		17823	0.003		0.0616	False		,,,				2504	0.0123				p.G1161V		Atlas-SNP	.											LRRC16B,NS,carcinoma,+1,1	LRRC16B	120	1	0			c.G3482T						PASS	.	G	VAL/GLY	63,4343	58.7+/-95.3	1,61,2141	123	109	114		3482	4.5	1	14	dbSNP_131	114	574,8026	154.6+/-208.8	26,522,3752	yes	missense	LRRC16B	NM_138360.3	109	27,583,5893	TT,TG,GG		6.6744,1.4299,4.8977	probably-damaging	1161/1373	24534916	637,12369	2203	4300	6503	SO:0001583	missense	90668	exon34			TTCCCGGGTTGGA	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.3482G>T	14.37:g.24534916G>T	ENSP00000340467:p.Gly1161Val	72	0	0		99	51	0.515152	NM_138360	Q8TEF7|Q96HS9	Missense_Mutation	SNP	ENST00000342740.5	37	CCDS32054.1	60	0.027472527472527472	2	0.0040650406504065045	10	0.027624309392265192	1	0.0017482517482517483	47	0.06200527704485488	G	18.54	3.645209	0.67358	0.014299	0.066744	ENSG00000186648	ENST00000342740	T	0.17854	2.25	5.4	4.51	0.55191	.	0.141061	0.33161	N	0.005214	T	0.01835	0.0058	N	0.19112	0.55	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.00950	-1.1503	10	0.72032	D	0.01	-15.7681	9.7564	0.40506	0.0947:0.0:0.9053:0.0	.	1161	Q8ND23	LR16B_HUMAN	V	1161	ENSP00000340467:G1161V	ENSP00000340467:G1161V	G	+	2	0	LRRC16B	23604756	0.964000	0.33143	0.972000	0.41901	0.867000	0.49689	1.806000	0.38892	1.272000	0.44329	0.655000	0.94253	GGG	G|0.958;T|0.042	0.042	strong		0.617	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360		T	24534916	G	T	24534916	3	4	26	1	0	0	0	0	1	0	0	0	8981	1232	43	4	3616	4	LRRC16B	14	24534916	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	2496185	24534916	82814624	449	10212											
TM9SF1	10548	hgsc.bcm.edu	37	chr14	24662296	24662296	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgcactgaaacattggcaaaTataattcggtctccatggaa	14	10	8	9	2	1	1	0	1	1	0	3	2	1	2	1	3	1	2	1	3	5	4	rs62621251	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:24662296T>C	ENST00000261789.4	-	3	883	c.525A>G	c.(523-525)atA>atG	p.I175M	TM9SF1_ENST00000556387.1_Missense_Mutation_p.I384M|TM9SF1_ENST00000528669.1_Missense_Mutation_p.I175M|RP11-468E2.2_ENST00000561419.1_5'Flank|TM9SF1_ENST00000530611.1_Missense_Mutation_p.I384M|TM9SF1_ENST00000396854.4_Missense_Mutation_p.I175M|TM9SF1_ENST00000524835.1_Missense_Mutation_p.I88M	NM_006405.5	NP_006396.2	O15321	TM9S1_HUMAN	transmembrane 9 superfamily member 1	175					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)		CATTGGCAAATATAATTCGGT	0.522													T|||	19	0.00379393	0.0	0.0086	5008	,	,		20446	0.0		0.0129	False		,,,				2504	0.0				p.I175M		Atlas-SNP	.											.	TM9SF1	58	.	0			c.A525G						PASS	.	T	MET/ILE,MET/ILE	9,4397	16.8+/-37.8	0,9,2194	103	99	100		525,525	3.9	1	14	dbSNP_129	100	87,8513	49.4+/-109.1	0,87,4213	yes	missense,missense	TM9SF1	NM_001014842.1,NM_006405.5	10,10	0,96,6407	CC,CT,TT		1.0116,0.2043,0.7381	possibly-damaging,possibly-damaging	175/490,175/607	24662296	96,12910	2203	4300	6503	SO:0001583	missense	10548	exon3			GGCAAATATAATT	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.525A>G	14.37:g.24662296T>C	ENSP00000261789:p.Ile175Met	131	0	0		180	82	0.455556	NM_001014842	D3DS65|Q86SZ6|Q96FI8	Missense_Mutation	SNP	ENST00000261789.4	37	CCDS9617.1	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	T	17.64	3.439673	0.63067	0.002043	0.010116	ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000254692	ENST00000261789;ENST00000528669;ENST00000556387;ENST00000524835;ENST00000396854;ENST00000528895;ENST00000530563;ENST00000530468;ENST00000525592;ENST00000528010;ENST00000530611	T;T;T;T;T;T;T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58	5.1	3.94	0.45596	.	0.052007	0.64402	D	0.000001	T	0.54498	0.1862	M	0.65320	2	0.58432	D	0.999998	P;P;B	0.51791	0.948;0.494;0.016	P;B;B	0.59643	0.861;0.297;0.101	T	0.62765	-0.6785	10	0.72032	D	0.01	-10.9909	9.0359	0.36287	0.0:0.0:0.2919:0.7081	rs62621251	175;175;175	E9PJM1;Q86SZ6;O15321	.;.;TM9S1_HUMAN	M	175;175;384;88;175;175;88;175;175;175;384	ENSP00000261789:I175M;ENSP00000432997:I175M;ENSP00000451949:I384M;ENSP00000434387:I88M;ENSP00000380063:I175M;ENSP00000431447:I175M;ENSP00000437127:I88M;ENSP00000435857:I175M;ENSP00000432435:I175M;ENSP00000433792:I175M;ENSP00000433967:I384M	ENSP00000433967:I384M	I	-	3	3	TM9SF1;RP11-468E2.1	23732136	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.136000	0.50554	2.137000	0.66172	0.533000	0.62120	ATA	T|0.994;C|0.006	0.006	strong		0.522	TM9SF1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073136.2	NM_006405		C	24662296	T	C	24662296	3	2	26	1	0	0	0	0	1	0	0	0	15992	1396	49	3	1354	3	TM9SF1	14	24662296	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	127380	24662296	82687244	450	10213											
NFKBIA	4792	hgsc.bcm.edu	37	chr14	35871232	35871232	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgcgctcataacgtcagaCgctggcctccaaacacacag	11	8	8	14	3	2	1	2	0	0	1	3	1	3	1	2	1	3	2	2	1	2	2	rs142970414	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:35871232C>T	ENST00000216797.5	-	6	1042	c.941G>A	c.(940-942)cGt>cAt	p.R314H	NFKBIA_ENST00000557140.1_Missense_Mutation_p.R271H|NFKBIA_ENST00000557389.1_Missense_Mutation_p.R224H|NFKBIA_ENST00000557100.1_5'Flank	NM_020529.2	NP_065390.1	P25963	IKBA_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha	314					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)	TAACGTCAGACGCTGGCCTCC	0.413																																					p.R314H		Atlas-SNP	.											.	NFKBIA	28	.	0			c.G941A						PASS	.	C	HIS/ARG	1,4405		0,1,2202	90	96	94		941	5.9	1	14	dbSNP_134	94	0,8600		0,0,4300	no	missense	NFKBIA	NM_020529.2	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	314/318	35871232	1,13005	2203	4300	6503	SO:0001583	missense	4792	exon6			GTCAGACGCTGGC		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.941G>A	14.37:g.35871232C>T	ENSP00000216797:p.Arg314His	202	0	0		184	75	0.407609	NM_020529	B2R8L6	Missense_Mutation	SNP	ENST00000216797.5	37	CCDS9656.1	.	.	.	.	.	.	.	.	.	.	C	15.55	2.866682	0.51588	2.27E-4	0.0	ENSG00000100906	ENST00000216797;ENST00000557140;ENST00000557389	T;T;T	0.50001	0.76;0.82;0.97	5.91	5.91	0.95273	.	.	.	.	.	T	0.29749	0.0743	N	0.14661	0.345	0.42889	D	0.994191	B;B	0.17465	0.022;0.013	B;B	0.09377	0.004;0.002	T	0.10894	-1.0610	9	0.41790	T	0.15	-16.9643	9.1946	0.37220	0.0:0.8795:0.0:0.1205	.	271;314	G3V3I4;P25963	.;IKBA_HUMAN	H	314;271;224	ENSP00000216797:R314H;ENSP00000451257:R271H;ENSP00000450514:R224H	ENSP00000216797:R314H	R	-	2	0	NFKBIA	34940983	0.999000	0.42202	0.995000	0.50966	0.865000	0.49528	2.991000	0.49409	2.808000	0.96608	0.655000	0.94253	CGT	C|1.000;T|0.000	0.000	strong		0.413	NFKBIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276683.1	NM_020529		T	35871232	C	T	35871232	3	4	26	1	0	0	0	0	1	0	0	0	10386	536	19	1	16	1	NFKBIA	14	35871232	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	11208936	35871232	71478308	451	10214											
KIAA0586	9786	hgsc.bcm.edu	37	chr14	58943847	58943847	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caccatcctctcagggtagaGcaagaaataatgtcaagaat	16	8	8	9	0	2	3	2	0	1	3	4	3	3	3	2	1	1	2	2	1	6	2	rs373201020		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:58943847G>A	ENST00000556134.1	+	21	3061	c.2787G>A	c.(2785-2787)gaG>gaA	p.E929E	KIAA0586_ENST00000538571.2_3'UTR|KIAA0586_ENST00000354386.6_Silent_p.E997E|KIAA0586_ENST00000423743.3_Silent_p.E900E|KIAA0586_ENST00000261244.5_Silent_p.E868E	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	Q9BVV6	TALD3_HUMAN	KIAA0586	929					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						TCAGGGTAGAGCAAGAAATAA	0.388																																					p.E997E		Atlas-SNP	.											.	KIAA0586	180	.	0			c.G2991A						PASS	.	G		0,3666		0,0,1833	84	73	76		2604	-0.5	1	14		76	1,8181		0,1,4090	no	coding-synonymous	KIAA0586	NM_014749.3		0,1,5923	AA,AG,GG		0.0122,0.0,0.0084		868/1473	58943847	1,11847	1833	4091	5924	SO:0001819	synonymous_variant	9786	exon22			GGTAGAGCAAGAA	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.2787G>A	14.37:g.58943847G>A		72	0	0		88	39	0.443182	NM_001244189	B4DZB6|E7EWM8|J3KQH9|O60328|Q6NYC6|Q6UV20	Silent	SNP	ENST00000556134.1	37	CCDS58321.1																																																																																			.	.	weak		0.388	KIAA0586-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411887.1	NM_014749		A	58943847	G	A	58943847	2	1	26	1	0	0	0	0	0	0	0	1	8195	962	34	2		2	KIAA0586	14	58943847	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	23072615	58943847	48405693	452	10215											
DAAM1	23002	hgsc.bcm.edu	37	chr14	59792755	59792755	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acacatagtgaagcttacccGcatttcatgtccatcctgca	11	11	6	13	1	1	1	1	1	0	0	3	1	3	1	3	0	3	3	3	0	3	3	rs61755642	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:59792755G>A	ENST00000395125.1	+	9	1157	c.1134G>A	c.(1132-1134)ccG>ccA	p.P378P	DAAM1_ENST00000360909.3_Silent_p.P378P|DAAM1_ENST00000351081.1_Silent_p.P378P	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	378	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)		AAGCTTACCCGCATTTCATGT	0.443													G|||	9	0.00179712	0.0	0.0014	5008	,	,		19975	0.0		0.007	False		,,,				2504	0.001				p.P378P		Atlas-SNP	.											.	DAAM1	95	.	0			c.G1134A						PASS	.	G		5,4401	9.9+/-24.2	0,5,2198	161	122	135		1134	-0.9	1	14	dbSNP_129	135	54,8546	35.3+/-89.8	0,54,4246	no	coding-synonymous	DAAM1	NM_014992.1		0,59,6444	AA,AG,GG		0.6279,0.1135,0.4536		378/1079	59792755	59,12947	2203	4300	6503	SO:0001819	synonymous_variant	23002	exon10			TTACCCGCATTTC	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.1134G>A	14.37:g.59792755G>A		153	0	0		192	101	0.526042	NM_001270520	Q86U34|Q8N1Z8|Q8TB39	Silent	SNP	ENST00000395125.1	37	CCDS9737.1																																																																																			G|0.995;A|0.005	0.005	strong		0.443	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992		A	59792755	G	A	59792755	2	1	26	1	0	0	0	0	0	0	0	1	4217	1074	38	1		1	DAAM1	14	59792755	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	848908	59792755	47556785	453	10216											
PCNX	22990	hgsc.bcm.edu	37	chr14	71500217	71500217	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttattagtggcagtgtcttaCcatctcagccgacaaagcag	11	11	9	10	1	2	0	1	0	2	0	3	1	2	0	2	1	3	2	2	1	4	3	rs71425297	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:71500217C>T	ENST00000304743.2	+	17	4076	c.3630C>T	c.(3628-3630)taC>taT	p.Y1210Y	PCNX_ENST00000238570.5_Silent_p.Y1210Y|PCNX_ENST00000439984.3_Silent_p.Y1099Y	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1210						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)		CAGTGTCTTACCATCTCAGCC	0.338													C|||	18	0.00359425	0.0	0.0	5008	,	,		15944	0.0		0.0179	False		,,,				2504	0.0				p.Y1210Y		Atlas-SNP	.											.	PCNX	198	.	0			c.C3630T						PASS	.	C		10,4396	16.8+/-37.8	1,8,2194	153	138	143		3630	0.5	1	14	dbSNP_130	143	87,8513	49.4+/-109.1	0,87,4213	no	coding-synonymous	PCNX	NM_014982.2		1,95,6407	TT,TC,CC		1.0116,0.227,0.7458		1210/2342	71500217	97,12909	2203	4300	6503	SO:0001819	synonymous_variant	22990	exon17			GTCTTACCATCTC	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.3630C>T	14.37:g.71500217C>T		145	0	0		187	82	0.438503	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Silent	SNP	ENST00000304743.2	37	CCDS9806.1	14	0.00641025641025641	0	0.0	0	0.0	0	0.0	14	0.018469656992084433	C	8.208	0.799745	0.16397	0.00227	0.010116	ENSG00000100731	ENST00000554691	.	.	.	5.72	0.525	0.17072	.	.	.	.	.	T	0.39886	0.1095	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38286	-0.9668	4	.	.	.	.	9.1872	0.37178	0.0:0.3569:0.0:0.6431	.	.	.	.	I	269	.	.	T	+	2	0	PCNX	70569970	1.000000	0.71417	0.997000	0.53966	0.954000	0.61252	1.090000	0.30902	0.105000	0.17753	-0.300000	0.09419	ACC	C|0.992;T|0.008	0.008	strong		0.338	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		T	71500217	C	T	71500217	2	4	26	1	0	0	0	0	0	0	0	1	11600	518	18	2		2	PCNX	14	71500217	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	11707462	71500217	35849323	454	10217											
HEATR4	399671	hgsc.bcm.edu	37	chr14	73961982	73961982	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gtgttagtggtccttgttctCctttgggtttcaagtaaaca	7	17	10	7	0	2	0	1	0	1	0	4	0	3	0	2	2	1	4	2	2	4	6	rs76429074	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:73961982C>T	ENST00000553558.1	-	16	3056	c.2735G>A	c.(2734-2736)gGa>gAa	p.G912E	HEATR4_ENST00000560393.1_Missense_Mutation_p.G865E|C14orf169_ENST00000531973.1_RNA|HEATR4_ENST00000334988.2_Missense_Mutation_p.G912E	NM_001220484.1	NP_001207413.1	Q86WZ0	HEAT4_HUMAN	HEAT repeat containing 4	912										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)		TCCTTGTTCTCCTTTGGGTTT	0.443													C|||	46	0.0091853	0.0015	0.0101	5008	,	,		18401	0.0		0.0258	False		,,,				2504	0.0112				p.G912E		Atlas-SNP	.											.	HEATR4	126	.	0			c.G2735A						PASS	.	C	GLU/GLY,GLU/GLY	24,4382	30.8+/-60.4	0,24,2179	235	195	209		2735,2735	1.1	0	14	dbSNP_131	209	254,8346	99.9+/-161.4	9,236,4055	yes	missense,missense	HEATR4	NM_001220484.1,NM_203309.2	98,98	9,260,6234	TT,TC,CC		2.9535,0.5447,2.1375	probably-damaging,probably-damaging	912/1027,912/1027	73961982	278,12728	2203	4300	6503	SO:0001583	missense	399671	exon15			TGTTCTCCTTTGG	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.2735G>A	14.37:g.73961982C>T	ENSP00000450444:p.Gly912Glu	153	0	0		153	66	0.431373	NM_203309	B7Z7V9|E9KL41	Missense_Mutation	SNP	ENST00000553558.1	37	CCDS9815.2	27	0.012362637362637362	0	0.0	6	0.016574585635359115	0	0.0	21	0.027704485488126648	C	0.004	-2.369551	0.00209	0.005447	0.029535	ENSG00000187105	ENST00000553558;ENST00000334988	T	0.20332	2.08	4.96	1.12	0.20585	.	0.699661	0.12884	N	0.431159	T	0.01730	0.0055	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38308	-0.9667	10	0.02654	T	1	-2.6044	5.0448	0.14477	0.0:0.0995:0.3604:0.5401	.	912	Q86WZ0	HEAT4_HUMAN	E	912;865	ENSP00000450444:G912E	ENSP00000335447:G865E	G	-	2	0	HEATR4	73031735	0.000000	0.05858	0.045000	0.18777	0.010000	0.07245	-0.069000	0.11542	0.027000	0.15297	-0.302000	0.09304	GGA	C|0.982;T|0.018	0.018	strong		0.443	HEATR4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414422.2	NM_203309		T	73961982	C	T	73961982	3	4	26	1	0	0	0	0	1	0	0	0	7039	855	30	2	357	2	HEATR4	14	73961982	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	2461765	73961982	33387558	455	10218											
GSTZ1	2954	hgsc.bcm.edu	37	chr14	77793237	77793237	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccatcaatctcataaaggatGggggccaacaggtaagaagg	15	6	12	8	0	2	1	2	0	1	1	3	2	2	2	2	5	1	1	2	5	6	2	rs7972	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:77793237G>A	ENST00000556627.1	+	3	255	c.124G>A	c.(124-126)Ggg>Agg	p.G42R	GSTZ1_ENST00000393734.1_5'UTR|GSTZ1_ENST00000349555.3_Missense_Mutation_p.G42R|GSTZ1_ENST00000557053.1_5'UTR|GSTZ1_ENST00000554279.1_Missense_Mutation_p.G42R|GSTZ1_ENST00000216465.5_Missense_Mutation_p.G42R|GSTZ1_ENST00000557639.1_5'UTR|GSTZ1_ENST00000553586.1_Missense_Mutation_p.G43R|GSTZ1_ENST00000361389.4_5'UTR			O43708	MAAI_HUMAN	glutathione S-transferase zeta 1	42	GST N-terminal.		R -> G (in allele GSTZ1*B and allele GSTZ1*C; dbSNP:rs7972). {ECO:0000269|PubMed:10373324, ECO:0000269|PubMed:10739172, ECO:0000269|PubMed:12508121, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9417084, ECO:0000269|PubMed:9925947, ECO:0000269|Ref.6, ECO:0000269|Ref.7, ECO:0000269|Ref.9}.		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)	CATAAAGGATGGGGGCCAACA	0.567													G|||	153	0.0305511	0.0038	0.0274	5008	,	,		21279	0.0		0.1113	False		,,,				2504	0.0174				p.G42R		Atlas-SNP	.											.	GSTZ1	35	.	0			c.G124A						PASS	.	G	,ARG/GLY,ARG/GLY	78,4326	62.9+/-100.1	0,78,2124	43	35	37		,124,124	5.6	1	14	dbSNP_52	37	707,7893	164.3+/-216.7	41,625,3634	yes	utr-5,missense,missense	GSTZ1	NM_001513.3,NM_145870.2,NM_145871.2	,125,125	41,703,5758	AA,AG,GG		8.2209,1.7711,6.0366	,benign,benign	,42/217,42/175	77793237	785,12219	2202	4300	6502	SO:0001583	missense	2954	exon3			AAGGATGGGGGCC	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.124G>A	14.37:g.77793237G>A	ENSP00000450487:p.Gly42Arg	59	0	0		69	27	0.391304	NM_145871	A6NED0|A6NNB8|A8MWD7|B2RCK3|O15308|O75430|Q6IB17|Q7Z610|Q9BV63	Missense_Mutation	SNP	ENST00000556627.1	37		109	0.04990842490842491	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	96	0.1266490765171504	G	28.3	4.909294	0.92107	0.017711	0.082209	ENSG00000100577	ENST00000216465;ENST00000554279;ENST00000349555;ENST00000556627;ENST00000553586	T;T;T;T;T	0.18810	4.45;3.14;2.19;2.36;4.44	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.00637	0.0021	.	.	.	0.09310	P	1.0	D	0.89917	1.0	D	0.83275	0.996	T	0.00335	-1.1808	8	0.72032	D	0.01	-6.8373	16.4581	0.84029	0.0:0.0:1.0:0.0	rs7972;rs1128968;rs2266617;rs3177429;rs3186383;rs11551317;rs17353483;rs17750846;rs52835763;rs58270987;rs7972	42	A6NED0	.	R	42;42;42;42;43	ENSP00000216465:G42R;ENSP00000452498:G42R;ENSP00000314404:G42R;ENSP00000450487:G42R;ENSP00000451976:G43R	ENSP00000216465:G42R	G	+	1	0	GSTZ1	76862990	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	5.705000	0.68355	2.614000	0.88457	0.655000	0.94253	GGG	G|0.949;A|0.051	0.051	strong		0.567	GSTZ1-012	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000414090.1	NM_145870		A	77793237	G	A	77793237	3	1	26	1	0	0	0	0	1	0	0	0	6857	1348	47	2	134	2	GSTZ1	14	77793237	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	3831255	77793237	29556303	456	10219											
ISM2	145501	hgsc.bcm.edu	37	chr14	77944624	77944624	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcattgcgggccaggagctTccactcctcactggggaggc	7	7	14	13	1	1	0	1	0	0	0	3	2	3	2	3	5	3	2	3	5	0	2	rs149849326	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:77944624T>C	ENST00000342219.4	-	6	1215	c.1159A>G	c.(1159-1161)Aag>Gag	p.K387E	ISM2_ENST00000412904.1_Missense_Mutation_p.K306E|ISM2_ENST00000493585.1_Silent_p.G271G|ISM2_ENST00000393684.3_Missense_Mutation_p.K299E|ISM2_ENST00000429906.1_Missense_Mutation_p.K306E	NM_199296.2	NP_954993.1	Q6H9L7	ISM2_HUMAN	isthmin 2	387						extracellular region (GO:0005576)				endometrium(3)|large_intestine(4)|lung(11)|prostate(1)|skin(1)|urinary_tract(1)	21						GCCAGGAGCTTCCACTCCTCA	0.637													T|||	41	0.0081869	0.003	0.0086	5008	,	,		19142	0.0		0.0159	False		,,,				2504	0.0153				p.K387E		Atlas-SNP	.											.	ISM2	68	.	0			c.A1159G						PASS	.	T	,GLU/LYS	12,4394	17.9+/-39.9	0,12,2191	160	139	146		813,1159	4	0.1	14	dbSNP_134	146	179,8421	81.8+/-144.4	4,171,4125	yes	coding-synonymous,missense	ISM2	NM_182509.3,NM_199296.2	,56	4,183,6316	CC,CT,TT		2.0814,0.2724,1.4686	,benign	271/293,387/572	77944624	191,12815	2203	4300	6503	SO:0001583	missense	145501	exon6			GGAGCTTCCACTC	AK056709	CCDS9864.1, CCDS45143.1	14q24.3	2013-05-15	2013-05-15	2008-12-23	ENSG00000100593	ENSG00000100593			23176	protein-coding gene	gene with protein product	"thrombospondin and AMOP containing isthmin-like 1"	612684	"thrombospondin, type I domain-containing 3", "thrombospondin, type I, domain containing 3", "isthmin 2 homolog (zebrafish)"	THSD3		15194193	Standard	NM_199296		Approved	FLJ32147, TAIL1	uc001xtz.3	Q6H9L7	OTTHUMG00000158563	ENST00000342219.4:c.1159A>G	14.37:g.77944624T>C	ENSP00000341490:p.Lys387Glu	141	0	0		156	72	0.461538	NM_199296	A8K6D5|O95432|Q495U5|Q68CN3|Q86TQ7|Q86TW3|Q86TW4|Q8N501|Q8NBL0	Missense_Mutation	SNP	ENST00000342219.4	37	CCDS9864.1	16	0.007326007326007326	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	10	0.013192612137203167	T	0.025	-1.384359	0.01194	0.002724	0.020814	ENSG00000100593	ENST00000342219;ENST00000412904;ENST00000429906;ENST00000393684	T;T;T;T	0.21734	1.99;2.0;2.0;2.31	4.91	4.02	0.46733	.	0.727256	0.11876	N	0.520968	T	0.07188	0.0182	.	.	.	0.09310	N	1	B;B	0.14012	0.009;0.005	B;B	0.11329	0.006;0.003	T	0.24119	-1.0169	9	0.23302	T	0.38	-16.3633	10.822	0.46610	0.0:0.0:0.8104:0.1896	.	306;387	Q6H9L7-5;Q6H9L7	.;ISM2_HUMAN	E	387;306;306;299	ENSP00000341490:K387E;ENSP00000416773:K306E;ENSP00000395387:K306E;ENSP00000377289:K299E	ENSP00000341490:K387E	K	-	1	0	ISM2	77014377	0.530000	0.26330	0.071000	0.20095	0.024000	0.10985	1.079000	0.30766	1.071000	0.40834	-0.384000	0.06662	AAG	T|0.987;C|0.013	0.013	strong		0.637	ISM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351309.1	NM_182509		C	77944624	T	C	77944624	3	2	26	1	0	0	0	0	1	0	0	0	7870	1792	62	3	564	3	ISM2	14	77944624	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	151387	77944624	29404916	457	10220											
C14orf102	55051	hgsc.bcm.edu	37	chr14	90745442	90745442	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttctgaagtgctttgtagaaTacacctttgcttctttcttt	7	20	6	8	0	3	2	0	1	3	1	3	2	3	2	1	0	3	3	1	0	4	8	rs141933992	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:90745442T>C	ENST00000354366.3	-	13	3565	c.3333A>G	c.(3331-3333)gtA>gtG	p.V1111V	NRDE2_ENST00000357904.3_Silent_p.V880V	NM_017970.3	NP_060440.2	Q9H7Z3	NRDE2_HUMAN	NRDE-2, necessary for RNA interference, domain containing	1111																	CTTTGTAGAATACACCTTTGC	0.458													T|||	8	0.00159744	0.0	0.0	5008	,	,		23470	0.0		0.006	False		,,,				2504	0.002				p.V1111V		Atlas-SNP	.											.	.	.	.	0			c.A3333G						PASS	.	T	,	1,4405	2.1+/-5.4	0,1,2202	230	214	220		3333,2640	-0.1	1	14	dbSNP_134	220	35,8565	22.8+/-68.1	0,35,4265	no	coding-synonymous,coding-synonymous	C14orf102	NM_017970.3,NM_199043.1	,	0,36,6467	CC,CT,TT		0.407,0.0227,0.2768	,	1111/1165,880/934	90745442	36,12970	2203	4300	6503	SO:0001819	synonymous_variant	55051	exon13			GTAGAATACACCT	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.3333A>G	14.37:g.90745442T>C		96	0	0		107	46	0.429907	NM_017970	B4DH71|Q4G0A7|Q9NWH6	Silent	SNP	ENST00000354366.3	37	CCDS9890.1																																																																																			T|0.998;C|0.002	0.002	strong		0.458	NRDE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411264.1	NM_017970		C	90745442	T	C	90745442	2	2	26	1	0	0	0	0	0	0	0	1	1737	1393	49	3		3	C14orf102	14	90745442	Silent	SNP	T	TCGA-G8-6907-01A-11D-2210-10	12800818	90745442	16604098	458	10221											
ASB2	51676	hgsc.bcm.edu	37	chr14	94417531	94417531	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgcggttgcagcggtggtTggtgtctgcattgtgctgca	3	12	17	9	3	1	0	0	0	1	0	1	0	1	0	1	4	5	6	1	4	0	3	rs11555542	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:94417531T>C	ENST00000315988.4	-	4	1038	c.550A>G	c.(550-552)Aac>Gac	p.N184D	ASB2_ENST00000556337.1_Intron|ASB2_ENST00000555019.1_Missense_Mutation_p.N232D|MIR4506_ENST00000584693.1_RNA	NM_016150.4	NP_057234.2	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box containing 2	184					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)		CAGCGGTGGTTGGTGTCTGCA	0.632													T|||	104	0.0207668	0.0023	0.0605	5008	,	,		19972	0.001		0.0567	False		,,,				2504	0.001				p.N232D		Atlas-SNP	.											.	ASB2	71	.	0			c.A694G						PASS	.	T	ASP/ASN,ASP/ASN	50,4356	50.9+/-86.3	0,50,2153	76	63	67		694,550	5.6	1	14	dbSNP_120	67	469,8131	139.0+/-195.8	10,449,3841	yes	missense,missense	ASB2	NM_001202429.1,NM_016150.4	23,23	10,499,5994	CC,CT,TT		5.4535,1.1348,3.9905	possibly-damaging,possibly-damaging	232/636,184/588	94417531	519,12487	2203	4300	6503	SO:0001583	missense	51676	exon6			GGTGGTTGGTGTC	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.550A>G	14.37:g.94417531T>C	ENSP00000320675:p.Asn184Asp	53	0	0		71	42	0.591549	NM_001202429	B2RDP9|B4E166|Q9NSU5|Q9Y567	Missense_Mutation	SNP	ENST00000315988.4	37	CCDS9915.1	67	0.030677655677655676	2	0.0040650406504065045	25	0.06906077348066299	1	0.0017482517482517483	39	0.051451187335092345	T	27.5	4.840814	0.91197	0.011348	0.054535	ENSG00000100628	ENST00000555019;ENST00000434324;ENST00000315988;ENST00000543546;ENST00000555507;ENST00000556062	T;T;T;T	0.73789	-0.5;-0.5;-0.5;-0.78	5.62	5.62	0.85841	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.25044	0.0608	N	0.25201	0.72	0.54753	D	0.999986	P;D;P	0.76494	0.922;0.999;0.922	P;D;P	0.83275	0.841;0.996;0.677	T	0.60742	-0.7203	10	0.30078	T	0.28	-2.7607	15.8384	0.78818	0.0:0.0:0.0:1.0	rs11555542;rs11555542	200;232;184	B3KPZ6;B4E166;Q96Q27	.;.;ASB2_HUMAN	D	232;200;184;130;130;78	ENSP00000451575:N232D;ENSP00000320675:N184D;ENSP00000450940:N130D;ENSP00000451694:N78D	ENSP00000320675:N184D	N	-	1	0	ASB2	93487284	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.258000	0.72487	2.137000	0.66172	0.459000	0.35465	AAC	T|0.964;C|0.036	0.036	strong		0.632	ASB2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412845.1			C	94417531	T	C	94417531	3	2	26	1	0	0	0	0	1	0	0	0	1023	1812	63	3	1233	3	ASB2	14	94417531	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	3672089	94417531	12932009	459	10222											
ATG2B	55102	hgsc.bcm.edu	37	chr14	96769560	96769560	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctggaatcacaatcaggtttGcatggcgggtagacttcatg	10	11	12	8	1	3	1	3	0	0	1	3	2	3	2	0	4	1	3	0	4	3	3			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:96769560G>C	ENST00000359933.4	-	33	5768	c.4875C>G	c.(4873-4875)tgC>tgG	p.C1625W	ATG2B_ENST00000261834.5_5'UTR	NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	1625					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)		AATCAGGTTTGCATGGCGGGT	0.438																																					p.C1625W		Atlas-SNP	.											.	ATG2B	169	.	0			c.C4875G						PASS	.						88	89	89					14																	96769560		2203	4300	6503	SO:0001583	missense	55102	exon33			AGGTTTGCATGGC	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.4875C>G	14.37:g.96769560G>C	ENSP00000353010:p.Cys1625Trp	104	0	0		117	52	0.444444	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	37	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	G	12.66	2.005762	0.35415	.	.	ENSG00000066739	ENST00000359933	T	0.09445	2.98	5.74	3.72	0.42706	.	0.435774	0.22296	N	0.061922	T	0.04227	0.0117	N	0.08118	0	0.23896	N	0.996539	P	0.49358	0.923	B	0.36289	0.221	T	0.33599	-0.9862	10	0.66056	D	0.02	.	4.7681	0.13142	0.3198:0.1534:0.5267:0.0	.	1625	Q96BY7	ATG2B_HUMAN	W	1625	ENSP00000353010:C1625W	ENSP00000261834:C269W	C	-	3	2	ATG2B	95839313	0.002000	0.14202	0.011000	0.14972	0.693000	0.40251	1.215000	0.32431	0.742000	0.32697	0.563000	0.77884	TGC	.	.	none		0.438	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		C	96769560	G	C	96769560	3	2	26	1	0	0	0	0	1	0	0	0	1094	1311	46	4	1401	4	ATG2B	14	96769560	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	2352029	96769560	10579980	460	10223											
DEGS2	51466	hgsc.bcm.edu	37	chr14	100613197	100613197	+	IGR	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagcaccttcacccaggaGtggtgctgcggcaggtggtc	7	7	15	12	1	1	1	1	0	0	1	2	2	1	2	2	5	3	3	2	5	0	1	rs140696950	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:100613197G>A	ENST00000402714.2	+	0	2353				DEGS2_ENST00000553834.1_Missense_Mutation_p.L44F|DEGS2_ENST00000305631.5_Silent_p.H291H|DEGS2_ENST00000557117.1_5'Flank			Q9UI08	EVL_HUMAN	Enah/Vasp-like						actin filament organization (GO:0007015)|actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ruffle assembly (GO:1900028)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of stress fiber assembly (GO:0051496)|protein homotetramerization (GO:0051289)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|membrane (GO:0016020)	profilin binding (GO:0005522)|SH3 domain binding (GO:0017124)			cervix(1)|large_intestine(5)|lung(3)|ovary(3)|urinary_tract(2)	14		Melanoma(154;0.152)				TCACCCAGGAGTGGTGCTGCG	0.637													G|||	14	0.00279553	0.0008	0.0058	5008	,	,		18492	0.0		0.004	False		,,,				2504	0.0051				p.H291H		Atlas-SNP	.											.	DEGS2	25	.	0			c.C873T						PASS	.	G		4,4402	8.1+/-20.4	0,4,2199	119	114	116		873	3.8	1	14	dbSNP_134	116	18,8582	13.3+/-46.6	0,18,4282	no	coding-synonymous	DEGS2	NM_206918.2		0,22,6481	AA,AG,GG		0.2093,0.0908,0.1692		291/324	100613197	22,12984	2203	4300	6503	SO:0001628	intergenic_variant	123099	exon3			CCAGGAGTGGTGC	AF112209	CCDS9955.1	14q32.2	2014-08-13			ENSG00000196405	ENSG00000196405			20234	protein-coding gene	gene with protein product						10945997, 10993894	Standard	NM_016337		Approved	RNB6	uc001ygu.3	Q9UI08	OTTHUMG00000171530		14.37:g.100613197G>A		123	0	0		104	57	0.548077	NM_206918	A8K105|O95884|Q7Z522|Q8TBV1|Q9UF25|Q9UIC2	Silent	SNP	ENST00000402714.2	37		3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	14.12	2.441563	0.43326	9.08E-4	0.002093	ENSG00000168350	ENST00000553834	T	0.58210	0.35	4.86	3.75	0.43078	.	.	.	.	.	T	0.37183	0.0994	.	.	.	0.23519	N	0.997508	.	.	.	.	.	.	T	0.22906	-1.0203	5	.	.	.	-28.8619	8.174	0.31270	0.1037:0.2977:0.5986:0.0	.	.	.	.	F	44	ENSP00000450637:L44F	.	L	-	1	0	DEGS2	99682950	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	0.611000	0.24268	2.251000	0.74343	0.561000	0.74099	CTC	G|0.998;A|0.002	0.002	strong		0.637	EVL-006	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000413958.1			A	100613197	G	A	100613197	1	1	26	0	1	0	0	0	0	0	0	0	4425	1020	36	2		2	DEGS2	14	100613197	IGR	SNP	G	TCGA-G8-6907-01A-11D-2210-10	3843637	100613197	6736343	461	10224											
SLC25A29	123096	hgsc.bcm.edu	37	chr14	100759690	100759690	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cccgcggtactgaggcttctCcacgctctggacctgaagcc	6	8	11	16	3	2	2	0	2	2	0	3	3	2	3	4	3	2	3	4	3	2	2	rs200054689		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:100759690C>T	ENST00000359232.3	-	3	403	c.103G>A	c.(103-105)Gag>Aag	p.E35K	SLC25A29_ENST00000556505.1_5'UTR|SLC25A29_ENST00000392908.3_Missense_Mutation_p.G20E|AL157871.2_ENST00000553954.1_RNA|SLC25A29_ENST00000539621.1_5'UTR|SLC25A29_ENST00000555927.1_5'UTR|RP11-638I2.6_ENST00000556458.1_lincRNA|SLC25A29_ENST00000554912.1_5'UTR	NM_001039355.1	NP_001034444.1	Q8N8R3	MCATL_HUMAN	solute carrier family 25 (mitochondrial carnitine/acylcarnitine carrier), member 29	35						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)	TGAGGCTTCTCCACGCTCTGG	0.632													C|||	1	0.000199681	0.0	0.0	5008	,	,		17380	0.0		0.001	False		,,,				2504	0.0				p.E35K		Atlas-SNP	.											.	SLC25A29	14	.	0			c.G103A						PASS	.						73	49	57					14																	100759690		2202	4300	6502	SO:0001583	missense	123096	exon3			GCTTCTCCACGCT	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.103G>A	14.37:g.100759690C>T	ENSP00000352167:p.Glu35Lys	64	0	0		96	57	0.59375	NM_001039355	A3KMR5|Q541V0	Missense_Mutation	SNP	ENST00000359232.3	37	CCDS32156.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	C|C	7.062|7.062	0.566669|0.566669	0.13560|0.13560	.|.	.|.	ENSG00000197119|ENSG00000197119	ENST00000359232|ENST00000392908;ENST00000554060	T|.	0.78595|.	-1.19|.	4.41|4.41	4.41|4.41	0.53225|0.53225	Mitochondrial carrier domain (2);|.	0.175049|.	0.49305|.	D|.	0.000143|.	T|T	0.34135|0.34135	0.0887|0.0887	N|N	0.02334|0.02334	-0.595|-0.595	0.80722|0.80722	D|D	1|1	B|.	0.11235|.	0.004|.	B|.	0.15052|.	0.012|.	T|T	0.48536|0.48536	-0.9027|-0.9027	10|6	0.09590|0.87932	T|D	0.72|0	-26.801|-26.801	12.1754|12.1754	0.54182|0.54182	0.1709:0.8291:0.0:0.0|0.1709:0.8291:0.0:0.0	.|.	35|.	Q8N8R3|.	MCATL_HUMAN|.	K|E	35|20	ENSP00000352167:E35K|.	ENSP00000352167:E35K|ENSP00000376640:G20E	E|G	-|-	1|2	0|0	SLC25A29|SLC25A29	99829443|99829443	1.000000|1.000000	0.71417|0.71417	0.669000|0.669000	0.29828|0.29828	0.005000|0.005000	0.04900|0.04900	3.411000|3.411000	0.52672|0.52672	2.020000|2.020000	0.59435|0.59435	0.591000|0.591000	0.81541|0.81541	GAG|GGA	C|1.000;T|0.000	0.000	strong		0.632	SLC25A29-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072449.3			T	100759690	C	T	100759690	3	4	26	1	0	0	0	0	1	0	0	0	14507	864	30	2	816	2	SLC25A29	14	100759690	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	146493	100759690	6589850	462	10225											
C14orf68	283600	hgsc.bcm.edu	37	chr14	100793603	100793603	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtgtcttttggcacctacCgccactgcctggcgcacatc	5	10	9	17	3	1	0	0	0	1	0	2	0	1	0	5	2	2	2	5	2	1	3			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:100793603C>T	ENST00000361529.3	+	4	301	c.223C>T	c.(223-225)Cgc>Tgc	p.R75C	SLC25A47_ENST00000557052.1_5'UTR	NM_207117.2	NP_997000.2	Q6Q0C1	S2547_HUMAN	solute carrier family 25, member 47	75					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|prostate(1)|skin(2)|urinary_tract(1)	13						TGGCACCTACCGCCACTGCCT	0.657																																					p.R75C	GBM(11;1289 1351)	Atlas-SNP	.											.	SLC25A47	36	.	0			c.C223T						PASS	.						102	101	101					14																	100793603		2203	4300	6503	SO:0001583	missense	283600	exon4			ACCTACCGCCACT		CCDS9959.1	14q32.2	2013-05-22	2010-07-19	2010-07-19	ENSG00000140107	ENSG00000140107		"Solute carriers"	20115	protein-coding gene	gene with protein product		609911	"chromosome 14 open reading frame 68"	C14orf68			Standard	NM_207117		Approved		uc001yhc.3	Q6Q0C1	OTTHUMG00000171571	ENST00000361529.3:c.223C>T	14.37:g.100793603C>T	ENSP00000354886:p.Arg75Cys	46	0	0		61	33	0.540984	NM_207117	B2RP39|Q68CL2|Q6PZD8|Q86U14	Missense_Mutation	SNP	ENST00000361529.3	37	CCDS9959.1	.	.	.	.	.	.	.	.	.	.	C	15.40	2.821452	0.50633	.	.	ENSG00000140107	ENST00000361529	T	0.79352	-1.26	4.7	3.73	0.42828	Mitochondrial carrier domain (2);	0.267820	0.33959	N	0.004392	T	0.78065	0.4225	M	0.85197	2.74	0.80722	D	1	B	0.20052	0.041	B	0.21546	0.035	T	0.78725	-0.2092	10	0.59425	D	0.04	2.8807	9.8376	0.40980	0.3148:0.6851:0.0:0.0	.	75	Q6Q0C1	S2547_HUMAN	C	75	ENSP00000354886:R75C	ENSP00000354886:R75C	R	+	1	0	SLC25A47	99863356	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	1.291000	0.33330	2.465000	0.83290	0.485000	0.47835	CGC	.	.	none		0.657	SLC25A47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414231.1			T	100793603	C	T	100793603	3	4	26	1	0	0	0	0	1	0	0	0	1780	652	23	1	237	1	C14orf68	14	100793603	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	33913	100793603	6555937	463	10226											
ZNF839	55778	hgsc.bcm.edu	37	chr14	102805556	102805556	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcccttgcatgctttggcCgctggtgagggtaaaatgct	7	11	14	9	1	0	1	0	1	0	0	0	1	0	1	2	4	3	5	2	4	2	3	rs199523800		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:102805556C>T	ENST00000558850.1	+	7	1925	c.1575C>T	c.(1573-1575)gcC>gcT	p.A525A	ZNF839_ENST00000442396.2_Silent_p.A641A|ZNF839_ENST00000262236.5_Silent_p.A525A|AL137229.1_ENST00000577622.1_RNA|ZNF839_ENST00000420933.2_3'UTR|ZNF839_ENST00000559185.1_Silent_p.A525A	NM_001267827.1	NP_001254756.1	A8K0R7	ZN839_HUMAN	zinc finger protein 839	525							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						ATGCTTTGGCCGCTGGTGAGG	0.552													C|||	1	0.000199681	0.0	0.0	5008	,	,		19149	0.0		0.001	False		,,,				2504	0.0				p.A641A		Atlas-SNP	.											.	ZNF839	41	.	0			c.C1923T						PASS	.	C		0,3844		0,0,1922	52	54	53		1923	-5.2	0	14		53	5,8281		0,5,4138	no	coding-synonymous	ZNF839	NM_018335.3		0,5,6060	TT,TC,CC		0.0603,0.0,0.0412		641/928	102805556	5,12125	1922	4143	6065	SO:0001819	synonymous_variant	55778	exon7			TTTGGCCGCTGGT	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.1575C>T	14.37:g.102805556C>T		194	0	0		196	87	0.443878	NM_018335	B3KSD2|Q53FH5|Q6GPI5|Q86TU1|Q9BQ86|Q9NUU3	Silent	SNP	ENST00000558850.1	37	CCDS58336.1																																																																																			C|0.998;T|0.002	0.002	weak		0.552	ZNF839-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415492.2	NM_018335		T	102805556	C	T	102805556	2	4	26	1	0	0	0	0	0	0	0	1	18203	639	23	1		1	ZNF839	14	102805556	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	2011953	102805556	4543984	464	10227											
AKT1	207	hgsc.bcm.edu	37	chr14	105239894	105239894	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggtcctcggagaacacacgCtcccgggacaggtggaagaa	11	4	14	12	4	0	2	0	0	0	2	3	5	2	4	2	5	1	1	2	5	3	0	rs1130233	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:105239894C>T	ENST00000554581.1	-	8	2206	c.726G>A	c.(724-726)gaG>gaA	p.E242E	AKT1_ENST00000544168.1_Silent_p.E180E|AKT1_ENST00000554585.1_5'Flank|AKT1_ENST00000555458.1_5'Flank|AKT1_ENST00000554192.1_5'Flank|AKT1_ENST00000555528.1_Silent_p.E242E|AKT1_ENST00000554848.1_Silent_p.E242E|AKT1_ENST00000402615.2_Silent_p.E242E|AKT1_ENST00000407796.2_Silent_p.E242E|AKT1_ENST00000349310.3_Silent_p.E242E			P31749	AKT1_HUMAN	v-akt murine thymoma viral oncogene homolog 1	242	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)	AGAACACACGCTCCCGGGACA	0.652		1	Mis		"breast, colorectal, ovarian, NSCLC"								C|||	1615	0.322484	0.0787	0.4222	5008	,	,		14497	0.6002		0.2425	False		,,,				2504	0.3773				p.E242E		Atlas-SNP	.		Dom	yes		14	14q32.32	207	v-akt murine thymoma viral oncogene homolog 1		E	.	AKT1	379	.	0			c.G726A	GRCh37	CM081515	AKT1	M	rs1130233	PASS	.	C	,,	507,3897	216.1+/-234.9	33,441,1728	31	26	28		726,726,726	4.8	0.9	14	dbSNP_86	28	2115,6485	334.9+/-321.2	269,1577,2454	no	coding-synonymous,coding-synonymous,coding-synonymous	AKT1	NM_001014431.1,NM_001014432.1,NM_005163.2	,,	302,2018,4182	TT,TC,CC		24.593,11.5123,20.163	,,	242/481,242/481,242/481	105239894	2622,10382	2202	4300	6502	SO:0001819	synonymous_variant	207	exon9			CACACGCTCCCGG	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.726G>A	14.37:g.105239894C>T		149	0	0		138	56	0.405797	NM_005163	B2RAM5|B7Z5R1|Q9BWB6	Silent	SNP	ENST00000554581.1	37	CCDS9994.1																																																																																			C|0.769;T|0.231	0.231	strong		0.652	AKT1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410418.1	NM_005163		T	105239894	C	T	105239894	2	4	26	1	0	0	0	0	0	0	0	1	478	796	28	2		2	AKT1	14	105239894	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	2434338	105239894	2109646	465	10228											
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105416994	105416994	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggtccagcttggggcccttAacatctatctggggcccctt	6	11	11	13	0	2	0	0	0	2	0	3	0	3	0	4	5	2	1	4	5	2	4	rs191772734	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:105416994A>G	ENST00000333244.5	-	7	4913	c.4794T>C	c.(4792-4794)gtT>gtC	p.V1598V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1598						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)			TGGGGCCCTTAACATCTATCT	0.602													.|||	51	0.0101837	0.0015	0.013	5008	,	,		15713	0.0		0.0268	False		,,,				2504	0.0133				p.V1598V		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T4794C						PASS	.	G		12,3588		0,12,1788	105	116	113		4794	-3.1	0	14		113	131,7909		8,115,3897	no	coding-synonymous	AHNAK2	NM_138420.2		8,127,5685	GG,GA,AA		1.6294,0.3333,1.2285		1598/5796	105416994	143,11497	1800	4020	5820	SO:0001819	synonymous_variant	113146	exon7			GCCCTTAACATCT	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.4794T>C	14.37:g.105416994A>G		169	0	0		165	81	0.490909	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.991;G|0.009	0.009	strong		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		G	105416994	A	G	105416994	2	3	26	1	0	0	0	0	0	0	0	1	415	349	13	3		3	AHNAK2	14	105416994	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	177100	105416994	1932546	466	10229											
ARHGAP11A	9824	hgsc.bcm.edu	37	chr15	32925226	32925226	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatctcagagttcactctcTcctgtactcattggtggaaa	9	14	7	11	0	5	1	4	0	2	1	8	2	6	2	1	2	1	2	1	2	2	3	rs77143444	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:32925226T>G	ENST00000361627.3	+	9	1874	c.1152T>G	c.(1150-1152)tcT>tcG	p.S384S	ARHGAP11A_ENST00000563864.1_Intron|ARHGAP11A_ENST00000567348.1_Silent_p.S384S|ARHGAP11A_ENST00000543522.1_Silent_p.S195S|ARHGAP11A_ENST00000565905.1_Silent_p.S195S	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	384					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)		GTTCACTCTCTCCTGTACTCA	0.393													T|||	15	0.00299521	0.0	0.0014	5008	,	,		16649	0.0		0.0129	False		,,,				2504	0.001				p.S384S	Colon(45;757 1134 30003 36652)	Atlas-SNP	.											.	ARHGAP11A	84	.	0			c.T1152G						PASS	.	T	,	5,4397		0,5,2196	159	154	156		1152,1152	2.1	1	15	dbSNP_131	156	63,8537		1,61,4238	no	coding-synonymous,coding-synonymous	ARHGAP11A	NM_014783.3,NM_199357.1	,	1,66,6434	GG,GT,TT		0.7326,0.1136,0.523	,	384/1024,384/502	32925226	68,12934	2201	4300	6501	SO:0001819	synonymous_variant	9824	exon9			ACTCTCTCCTGTA	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.1152T>G	15.37:g.32925226T>G		154	0	0		165	81	0.490909	NM_199357	B4DZN9|Q6PI96|Q9Y3S6	Silent	SNP	ENST00000361627.3	37	CCDS10028.1																																																																																			T|0.995;G|0.005	0.005	strong		0.393	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783		G	32925226	T	G	32925226	2	3	26	1	0	0	0	0	0	0	0	1	863	1538	54	5		5	ARHGAP11A	15	32925226	Silent	SNP	T	TCGA-G8-6907-01A-11D-2210-10		32925226	69606166	467	10230											
RYR3	6263	hgsc.bcm.edu	37	chr15	33842400	33842400	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatggggccaggctttccgActccggcatctcaccacagg	8	7	12	14	2	1	1	1	0	1	1	4	2	3	1	4	5	0	2	4	5	0	1	rs41279202	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:33842400A>T	ENST00000389232.4	+	10	925	c.855A>T	c.(853-855)cgA>cgT	p.R285R	RYR3_ENST00000415757.3_Silent_p.R285R	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	285	MIR 4. {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)			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)		AGGCTTTCCGACTCCGGCATC	0.483													A|||	68	0.0135783	0.0	0.0187	5008	,	,		17879	0.001		0.0447	False		,,,				2504	0.0092				p.R285R		Atlas-SNP	.											.	RYR3	760	.	0			c.A855T						PASS	.	A		34,4350	34.3+/-65.2	0,34,2158	40	42	41		855	-1.1	1	15	dbSNP_127	41	369,8219	120.2+/-179.5	8,353,3933	no	coding-synonymous	RYR3	NM_001036.3		8,387,6091	TT,TA,AA		4.2967,0.7755,3.1067		285/4871	33842400	403,12569	2192	4294	6486	SO:0001819	synonymous_variant	6263	exon10			TTTCCGACTCCGG		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.855A>T	15.37:g.33842400A>T		94	0	0		95	48	0.505263	NM_001243996	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			A|0.970;T|0.030	0.030	strong		0.483	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			T	33842400	A	T	33842400	2	4	26	1	0	0	0	0	0	0	0	1	13785	262	10	5		5	RYR3	15	33842400	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	917174	33842400	68688992	468	10231											
DNAJC17	55192	hgsc.bcm.edu	37	chr15	41068771	41068771	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtcctggtgctccggctcTcctcttcctcctcactctcc	1	14	7	19	1	4	0	1	0	3	0	10	0	8	0	6	2	1	2	6	2	0	1	rs79709714	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:41068771T>G	ENST00000220496.4	-	5	380	c.350A>C	c.(349-351)gAg>gCg	p.E117A		NM_018163.2	NP_060633.1	Q9NVM6	DJC17_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 17	117	Poly-Glu.				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)		GCTCCGGCTCTCCTCTTCCTC	0.622													T|||	42	0.00838658	0.0	0.0173	5008	,	,		14514	0.0		0.0258	False		,,,				2504	0.0041				p.E117A		Atlas-SNP	.											.	DNAJC17	18	.	0			c.A350C						PASS	.	T	ALA/GLU	26,4380	34.3+/-65.2	1,24,2178	156	128	138		350	4.5	1	15	dbSNP_131	138	239,8361	95.9+/-157.7	1,237,4062	yes	missense	DNAJC17	NM_018163.2	107	2,261,6240	GG,GT,TT		2.7791,0.5901,2.0375	benign	117/305	41068771	265,12741	2203	4300	6503	SO:0001583	missense	55192	exon5			CGGCTCTCCTCTT	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.350A>C	15.37:g.41068771T>G	ENSP00000220496:p.Glu117Ala	114	0	0		69	57	0.826087	NM_018163		Missense_Mutation	SNP	ENST00000220496.4	37	CCDS10065.1	30	0.013736263736263736	0	0.0	6	0.016574585635359115	0	0.0	24	0.0316622691292876	T	10.51	1.369675	0.24771	0.005901	0.027791	ENSG00000104129	ENST00000220496	T	0.21191	2.02	4.46	4.46	0.54185	.	0.262954	0.42548	D	0.000681	T	0.06096	0.0158	L	0.55481	1.735	0.39777	D	0.972244	B	0.12630	0.006	B	0.10450	0.005	T	0.05550	-1.0878	10	0.10377	T	0.69	.	10.0697	0.42325	0.0:0.0:0.0:1.0	.	117	Q9NVM6	DJC17_HUMAN	A	117	ENSP00000220496:E117A	ENSP00000220496:E117A	E	-	2	0	DNAJC17	38856063	1.000000	0.71417	0.964000	0.40570	0.954000	0.61252	6.100000	0.71473	1.889000	0.54706	0.459000	0.35465	GAG	T|0.984;G|0.016	0.016	strong		0.622	DNAJC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252356.2	NM_018163		G	41068771	T	G	41068771	3	3	26	1	0	0	0	0	1	0	0	0	4638	1551	54	5	592	5	DNAJC17	15	41068771	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	7226371	41068771	61462621	469	10232											
ZFYVE19	84936	hgsc.bcm.edu	37	chr15	41105942	41105942	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcttccctggatgaggcaaGtggctttaacatccctgcag	9	10	11	11	0	0	1	0	1	0	0	2	2	2	2	2	3	3	4	2	3	2	3	rs34516375	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:41105942G>A	ENST00000355341.4	+	9	1643	c.1142G>A	c.(1141-1143)aGt>aAt	p.S381N	ZFYVE19_ENST00000570108.1_Missense_Mutation_p.S358N|ZFYVE19_ENST00000299173.10_Missense_Mutation_p.S313N|ZFYVE19_ENST00000564258.1_Missense_Mutation_p.S206N|ZFYVE19_ENST00000336455.5_Missense_Mutation_p.S371N	NM_001077268.1	NP_001070736.1	Q96K21	ANCHR_HUMAN	zinc finger, FYVE domain containing 19	381					abscission (GO:0009838)|cell division (GO:0051301)|cytokinesis checkpoint (GO:0031565)|negative regulation of cytokinesis (GO:0032466)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|midbody (GO:0030496)	phosphatidylinositol-3-phosphate binding (GO:0032266)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	9		all_cancers(109;3.31e-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;2.76e-05)|COAD - Colon adenocarcinoma(120;0.151)|BRCA - Breast invasive adenocarcinoma(123;0.164)		GATGAGGCAAGTGGCTTTAAC	0.597													G|||	7	0.00139776	0.0	0.0	5008	,	,		20274	0.0		0.006	False		,,,				2504	0.001				p.S381N		Atlas-SNP	.											.	ZFYVE19	31	.	0			c.G1142A						PASS	.	G	ASN/SER	2,4120		0,2,2059	50	56	54		1142	5.3	1	15	dbSNP_126	54	32,8382		0,32,4175	yes	missense	ZFYVE19	NM_001077268.1	46	0,34,6234	AA,AG,GG		0.3803,0.0485,0.2712	possibly-damaging	381/472	41105942	34,12502	2061	4207	6268	SO:0001583	missense	84936	exon9			AGGCAAGTGGCTT	AK027746	CCDS42025.1, CCDS58353.1, CCDS58354.1, CCDS58355.1	15q14	2008-05-02				ENSG00000166140		"Zinc fingers, FYVE domain containing"	20758	protein-coding gene	gene with protein product							Standard	NM_001077268		Approved	FLJ14840	uc031qrk.1	Q96K21		ENST00000355341.4:c.1142G>A	15.37:g.41105942G>A	ENSP00000347498:p.Ser381Asn	87	0	0		52	51	0.980769	NM_001077268	B3KVB2|C9JNF4|H3BUF9|Q86WC2|Q8WU96	Missense_Mutation	SNP	ENST00000355341.4	37	CCDS42025.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	32	5.125010	0.94429	4.85E-4	0.003803	ENSG00000166140	ENST00000355341;ENST00000299173;ENST00000336455	T;T;T	0.35048	1.33;1.33;1.33	5.27	5.27	0.74061	.	0.078430	0.85682	D	0.000000	T	0.51890	0.1701	M	0.72894	2.215	0.49389	D	0.999784	D;D;P	0.89917	1.0;0.981;0.753	D;P;B	0.87578	0.998;0.725;0.352	T	0.52631	-0.8550	10	0.36615	T	0.2	-14.0194	17.8147	0.88628	0.0:0.0:1.0:0.0	rs34516375	371;313;381	Q96K21-2;Q96K21-3;Q96K21	.;.;ZFY19_HUMAN	N	381;313;371	ENSP00000347498:S381N;ENSP00000299173:S313N;ENSP00000337824:S371N	ENSP00000299173:S313N	S	+	2	0	ZFYVE19	38893234	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	8.753000	0.91637	2.742000	0.94016	0.455000	0.32223	AGT	G|0.997;A|0.003	0.003	strong		0.597	ZFYVE19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418996.1	NM_032850		A	41105942	G	A	41105942	3	1	26	1	0	0	0	0	1	0	0	0	17680	1029	36	2	1176	2	ZFYVE19	15	41105942	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	37171	41105942	61425450	470	10233											
CAPN3	825	hgsc.bcm.edu	37	chr15	42679977	42679977	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctatggagagtgggtggaCgtggttatagatgactgcct	8	11	16	6	2	0	3	0	1	0	2	0	5	0	4	1	4	1	2	1	4	3	3	rs144383442		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:42679977C>T	ENST00000397163.3	+	4	744	c.525C>T	c.(523-525)gaC>gaT	p.D175D	RP11-164J13.1_ENST00000495723.1_RNA|CAPN3_ENST00000349748.3_Silent_p.D175D|CAPN3_ENST00000318023.7_Silent_p.D175D|CAPN3_ENST00000357568.3_Silent_p.D175D|CAPN3_ENST00000356316.3_Silent_p.D88D	NM_000070.2	NP_000061.1	P20807	CAN3_HUMAN	calpain 3, (p94)	175	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				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)		AGTGGGTGGACGTGGTTATAG	0.493													C|||	1	0.000199681	0.0	0.0	5008	,	,		21839	0.0		0.0	False		,,,				2504	0.001				p.D175D		Atlas-SNP	.											CAPN3_ENST00000356316,NS,carcinoma,0,2	CAPN3	172	2	0			c.C525T						PASS	.	C	,,	3,4403	6.2+/-15.9	0,3,2200	310	251	271		525,525,525	-5.8	0.9	15	dbSNP_134	271	15,8583	9.8+/-36.6	0,15,4284	yes	coding-synonymous,coding-synonymous,coding-synonymous	CAPN3	NM_000070.2,NM_024344.1,NM_173087.1	,,	0,18,6484	TT,TC,CC		0.1745,0.0681,0.1384	,,	175/822,175/816,175/730	42679977	18,12986	2203	4299	6502	SO:0001819	synonymous_variant	825	exon4			GGTGGACGTGGTT	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.525C>T	15.37:g.42679977C>T		217	0	0		137	129	0.941606	NM_000070	A6H8K6|Q7L4R0|Q9BQC8|Q9BTU4|Q9Y5S6|Q9Y5S7	Silent	SNP	ENST00000397163.3	37	CCDS45245.1																																																																																			C|0.999;T|0.001	0.001	strong		0.493	CAPN3-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421075.1			T	42679977	C	T	42679977	2	4	26	1	0	0	0	0	0	0	0	1	2630	535	19	1		1	CAPN3	15	42679977	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1574035	42679977	59851415	471	10234											
B2M	567	hgsc.bcm.edu	37	chr15	45003770	45003770	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgctccgtggccttagctgTgctcgcgctactctctcttt	2	15	9	15	4	2	0	0	0	2	0	6	0	3	0	2	1	3	4	2	1	2	3			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:45003770T>A	ENST00000558401.1	+	1	96	c.26T>A	c.(25-27)gTg>gAg	p.V9E	B2M_ENST00000559916.1_Missense_Mutation_p.V9E|B2M_ENST00000544417.1_Missense_Mutation_p.V9E|PATL2_ENST00000558573.1_5'Flank	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	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 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 exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|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 T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|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)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		GCCTTAGCTGTGCTCGCGCTA	0.617																																					p.V9E		Atlas-SNP	.											.	B2M	99	.	0			c.T26A						PASS	.						132	95	108					15																	45003770		2198	4298	6496	SO:0001583	missense	567	exon1			TAGCTGTGCTCGC	AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"Immunoglobulin superfamily / C1-set domain containing"	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.26T>A	15.37:g.45003770T>A	ENSP00000452780:p.Val9Glu	98	0	0		57	52	0.912281	NM_004048	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Missense_Mutation	SNP	ENST00000558401.1	37	CCDS10113.1	.	.	.	.	.	.	.	.	.	.	T	14.32	2.499636	0.44455	.	.	ENSG00000166710	ENST00000349264;ENST00000544417;ENST00000396754	T	0.01430	4.9	5.35	4.23	0.50019	.	0.532223	0.09808	U	0.753127	T	0.01976	0.0062	L	0.46157	1.445	0.09310	N	1	B;B;B	0.30973	0.302;0.201;0.201	B;B;B	0.26969	0.075;0.073;0.055	T	0.45775	-0.9238	10	0.87932	D	0	.	7.8636	0.29524	0.0:0.0912:0.0:0.9088	.	9;9;9	F5H6I0;A6XMH4;P61769	.;.;B2MG_HUMAN	E	9	ENSP00000437604:V9E	ENSP00000340858:V9E	V	+	2	0	B2M	42791062	0.003000	0.15002	0.002000	0.10522	0.005000	0.04900	1.408000	0.34668	1.166000	0.42689	0.533000	0.62120	GTG	.	.	none		0.617	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048		A	45003770	T	A	45003770	3	1	26	1	0	0	0	0	1	0	0	0	1244	1696	59	5	28	5	B2M	15	45003770	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	2323793	45003770	57527622	472	10235											
CCPG1	9236	hgsc.bcm.edu	37	chr15	55652969	55652969	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttatcttccaatattctaatCtgttctcttagtttgtttaa	9	22	3	7	0	4	0	0	0	4	0	6	0	5	0	1	0	0	3	1	0	6	10	rs200417770		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:55652969C>G	ENST00000310958.6	-	8	1300	c.1002G>C	c.(1000-1002)caG>caC	p.Q334H	CCPG1_ENST00000569205.1_Missense_Mutation_p.Q334H|CCPG1_ENST00000425574.3_Intron|CCPG1_ENST00000442196.3_Missense_Mutation_p.Q334H|DYX1C1-CCPG1_ENST00000565113.1_RNA	NM_001204450.1|NM_001204451.1|NM_004748.4|NM_020739.3	NP_001191379.1|NP_001191380.1|NP_004739.3|NP_065790.2	Q9ULG6	CCPG1_HUMAN	cell cycle progression 1	334					cell cycle (GO:0007049)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001106)	integral component of membrane (GO:0016021)				autonomic_ganglia(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|stomach(3)	30				all cancers(107;0.0354)		ATATTCTAATCTGTTCTCTTA	0.343																																					p.Q334H		Atlas-SNP	.											CCPG1,NS,carcinoma,0,1	CCPG1	74	1	0			c.G1002C						scavenged	.						124	115	118					15																	55652969		1815	4071	5886	SO:0001583	missense	9236	exon8			TCTAATCTGTTCT	AF212228	CCDS42039.1, CCDS55966.1, CCDS55967.1	15q21.1	2011-04-20				ENSG00000260916			24227	protein-coding gene	gene with protein product		611326				9383053, 10574462	Standard	NM_004748		Approved	KIAA1254, CPR8	uc010bfk.2	Q9ULG6		ENST00000310958.6:c.1002G>C	15.37:g.55652969C>G	ENSP00000311656:p.Gln334His	179	1	0.00558659		161	57	0.354037	NM_020739	A0PJH3|A8K9T0|O14712|Q05DG4|Q5U5S7|Q8IYV8|Q9BY53|Q9HA17	Missense_Mutation	SNP	ENST00000310958.6	37	CCDS42039.1	.	.	.	.	.	.	.	.	.	.	C	15.32	2.799689	0.50208	.	.	ENSG00000256061	ENST00000310958;ENST00000442196	T;T	0.36157	1.27;1.27	5.72	2.86	0.33363	.	0.153716	0.64402	D	0.000014	T	0.53546	0.1803	M	0.66939	2.045	0.47214	D	0.999356	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.75484	0.986;0.976;0.986;0.979	T	0.52109	-0.8619	10	0.72032	D	0.01	.	9.2561	0.37584	0.0:0.6926:0.0:0.3074	.	334;334;334;190	A8K9T0;Q9ULG6-4;Q9ULG6;Q9ULG6-2	.;.;CCPG1_HUMAN;.	H	334	ENSP00000311656:Q334H;ENSP00000403400:Q334H	ENSP00000311656:Q334H	Q	-	3	2	DYX1C1	53440261	1.000000	0.71417	0.997000	0.53966	0.943000	0.58893	0.759000	0.26461	0.450000	0.26774	-0.145000	0.13849	CAG	C|0.999;G|0.001	0.001	weak		0.343	CCPG1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419850.1	NM_004748		G	55652969	C	G	55652969	3	3	26	1	0	0	0	0	1	0	0	0	2940	912	32	4	1275	4	CCPG1	15	55652969	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	10649199	55652969	46878423	473	10236											
DYX1C1	161582	hgsc.bcm.edu	37	chr15	55722956	55722956	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggatggatcaatcttaagtGccgcttcataatcctgtagg	10	13	10	8	1	3	0	2	0	1	0	4	2	4	2	2	3	1	2	2	3	4	4			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:55722956G>A	ENST00000321149.3	-	10	1542	c.1175C>T	c.(1174-1176)gCa>gTa	p.A392V	DYX1C1_ENST00000457155.2_Missense_Mutation_p.H357Y|DYX1C1_ENST00000348518.3_Missense_Mutation_p.H357Y|DYX1C1_ENST00000380679.1_Intron|DYX1C1-CCPG1_ENST00000565113.1_RNA|DYX1C1_ENST00000448430.2_Intron	NM_130810.3	NP_570722.2	Q8WXU2	DYXC1_HUMAN	dyslexia susceptibility 1 candidate 1	392					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)		AATCTTAAGTGCCGCTTCATA	0.294																																					p.A392V		Atlas-SNP	.											DYX1C1,NS,carcinoma,-1,1	DYX1C1	54	1	0			c.C1175T						PASS	.						126	123	124					15																	55722956		2192	4290	6482	SO:0001583	missense	161582	exon10			TTAAGTGCCGCTT		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.1175C>T	15.37:g.55722956G>A	ENSP00000323275:p.Ala392Val	130	0	0		125	60	0.48	NM_130810	Q6P5Y9|Q8N1S6	Missense_Mutation	SNP	ENST00000321149.3	37	CCDS10154.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	32|32	5.120950|5.120950	0.94385|0.94385	.|.	.|.	ENSG00000256061|ENSG00000256061	ENST00000321149|ENST00000457155;ENST00000348518	D|T;T	0.82803|0.27557	-1.65|1.66;1.66	5.6|5.6	5.6|5.6	0.85130|0.85130	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);|.	0.000000|.	0.85682|.	U|.	0.000000|.	T|T	0.19846|0.19846	0.0477|0.0477	.|.	.|.	.|.	0.34596|0.34596	D|D	0.715963|0.715963	D|B	0.89917|0.29766	1.0|0.256	D|B	0.91635|0.34138	0.999|0.176	T|T	0.05632|0.05632	-1.0873|-1.0873	9|8	0.66056|0.02654	D|T	0.02|1	.|.	18.6754|18.6754	0.91526|0.91526	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	392|357	Q8WXU2|Q8WXU2-3	DYXC1_HUMAN|.	V|Y	392|357	ENSP00000323275:A392V|ENSP00000402640:H357Y;ENSP00000299561:H357Y	ENSP00000323275:A392V|ENSP00000299561:H357Y	A|H	-|-	2|1	0|0	DYX1C1|DYX1C1	53510248|53510248	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.977000|7.977000	0.88081|0.88081	2.650000|2.650000	0.89964|0.89964	0.558000|0.558000	0.71614|0.71614	GCA|CAC	.	.	none		0.294	DYX1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254976.1	NM_130810		A	55722956	G	A	55722956	3	1	26	1	0	0	0	0	1	0	0	0	4864	1319	46	2	194	2	DYX1C1	15	55722956	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	69987	55722956	46808436	474	10237											
PRTG	283659	hgsc.bcm.edu	37	chr15	55964778	55964778	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacatcttgctgccacctcaCagaaatggtggtacagttca	11	11	8	11	0	3	1	2	0	1	1	3	1	3	1	2	2	4	3	2	2	3	4	rs149494002	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:55964778C>G	ENST00000389286.4	-	11	1953	c.1906G>C	c.(1906-1908)Gtg>Ctg	p.V636L		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)		TGCCACCTCACAGAAATGGTG	0.458													C|||	12	0.00239617	0.0008	0.0029	5008	,	,		16822	0.0		0.008	False		,,,				2504	0.001				p.V636L		Atlas-SNP	.											.	PRTG	110	.	0			c.G1906C						PASS	.	C	LEU/VAL	8,3802		0,8,1897	78	74	75		1906	5.6	1	15	dbSNP_134	75	82,8162		0,82,4040	yes	missense	PRTG	NM_173814.4	32	0,90,5937	GG,GC,CC		0.9947,0.21,0.7466	benign	636/1151	55964778	90,11964	1905	4122	6027	SO:0001583	missense	283659	exon11			ACCTCACAGAAAT	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.1906G>C	15.37:g.55964778C>G	ENSP00000373937:p.Val636Leu	128	0	0		152	66	0.434211	NM_173814		Missense_Mutation	SNP	ENST00000389286.4	37	CCDS42040.1	9	0.004120879120879121	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	15.36	2.810509	0.50421	0.0021	0.009947	ENSG00000166450	ENST00000389286	T	0.22336	1.96	5.62	5.62	0.85841	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.232951	0.37483	N	0.002061	T	0.16685	0.0401	L	0.43701	1.375	0.80722	D	1	B	0.22541	0.071	B	0.22152	0.038	T	0.01537	-1.1330	10	0.40728	T	0.16	-15.7028	18.6782	0.91537	0.0:1.0:0.0:0.0	.	636	Q2VWP7	PRTG_HUMAN	L	636	ENSP00000373937:V636L	ENSP00000373937:V636L	V	-	1	0	PRTG	53752070	1.000000	0.71417	1.000000	0.80357	0.742000	0.42306	4.585000	0.60977	2.648000	0.89879	0.650000	0.86243	GTG	C|0.994;G|0.006	0.006	strong		0.458	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814		G	55964778	C	G	55964778	3	3	26	1	0	0	0	0	1	0	0	0	12650	478	17	4	1586	4	PRTG	15	55964778	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	241822	55964778	46566614	475	10238											
MNS1	55329	hgsc.bcm.edu	37	chr15	56736681	56736681	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcttcctaacaatttcatcaAtcatgagtttctcttttagc	10	18	3	10	0	5	1	3	1	2	0	7	1	6	1	1	0	2	1	1	0	4	6	rs35775595	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:56736681A>G	ENST00000260453.3	-	5	811	c.647T>C	c.(646-648)aTt>aCt	p.I216T	TEX9_ENST00000352903.2_Intron|TEX9_ENST00000537232.1_Intron	NM_018365.2	NP_060835.1	Q8NEH6	MNS1_HUMAN	meiosis-specific nuclear structural 1	216	Glu-rich.		I -> T (in dbSNP:rs35775595).		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)		AATTTCATCAATCATGAGTTT	0.328													A|||	30	0.00599042	0.0008	0.013	5008	,	,		18617	0.0		0.0169	False		,,,				2504	0.0031				p.I216T		Atlas-SNP	.											.	MNS1	39	.	0			c.T647C						PASS	.	A	THR/ILE,	23,4361	29.9+/-59.1	0,23,2169	114	107	110		647,	5.4	1	15	dbSNP_126	110	234,8348	95.6+/-157.4	0,234,4057	yes	missense,intron	MNS1,TEX9	NM_018365.2,NM_198524.1	89,	0,257,6226	GG,GA,AA		2.7266,0.5246,1.9821	possibly-damaging,	216/496,	56736681	257,12709	2192	4291	6483	SO:0001583	missense	55329	exon5			TCATCAATCATGA	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.647T>C	15.37:g.56736681A>G	ENSP00000260453:p.Ile216Thr	134	0	0		168	74	0.440476	NM_018365	Q8IYT6|Q9NUP4	Missense_Mutation	SNP	ENST00000260453.3	37	CCDS10158.1	20	0.009157509157509158	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	15	0.01978891820580475	A	24.5	4.537928	0.85917	0.005246	0.027266	ENSG00000138587	ENST00000260453	T	0.11385	2.78	5.43	5.43	0.79202	.	0.154112	0.56097	D	0.000023	T	0.10594	0.0259	M	0.81497	2.545	0.50171	D	0.99985	D	0.52996	0.957	P	0.54431	0.752	T	0.00583	-1.1659	10	0.42905	T	0.14	-5.7208	14.6574	0.68844	1.0:0.0:0.0:0.0	rs35775595	216	Q8NEH6	MNS1_HUMAN	T	216	ENSP00000260453:I216T	ENSP00000260453:I216T	I	-	2	0	MNS1	54523973	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.070000	0.93974	2.053000	0.61076	0.523000	0.50628	ATT	A|0.984;G|0.016	0.016	strong		0.328	MNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255047.2	NM_018365		G	56736681	A	G	56736681	3	3	26	1	0	0	0	0	1	0	0	0	9686	101	4	3	864	3	MNS1	15	56736681	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	771903	56736681	45794711	476	10239											
USP3	9960	hgsc.bcm.edu	37	chr15	63855190	63855190	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttattttatgttgtttggaaGattatgccaaactttaggta	11	19	8	3	0	0	1	0	0	0	1	0	2	0	2	1	2	2	3	1	2	7	9	rs61751106	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:63855190G>A	ENST00000380324.3	+	8	873	c.744G>A	c.(742-744)aaG>aaA	p.K248K	USP3-AS1_ENST00000560350.1_RNA|USP3_ENST00000268049.7_Silent_p.K226K|USP3_ENST00000559711.1_Silent_p.K159K|USP3-AS1_ENST00000559861.1_RNA|USP3_ENST00000539772.1_5'UTR|USP3_ENST00000536001.1_3'UTR|USP3-AS1_ENST00000559357.1_RNA|USP3_ENST00000558285.1_Silent_p.K231K|USP3_ENST00000540797.1_Silent_p.K204K	NM_006537.3	NP_006528.2	Q9Y6I4	UBP3_HUMAN	ubiquitin specific peptidase 3	248	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)		TTGTTTGGAAGATTATGCCAA	0.338													G|||	26	0.00519169	0.0008	0.0086	5008	,	,		18673	0.0		0.0119	False		,,,				2504	0.0072				p.K248K		Atlas-SNP	.											.	USP3	37	.	0			c.G744A						PASS	.	G		11,4395	16.8+/-37.8	0,11,2192	111	112	111		744	4	1	15	dbSNP_129	111	133,8467	62.1+/-124.0	2,129,4169	no	coding-synonymous	USP3	NM_006537.2		2,140,6361	AA,AG,GG		1.5465,0.2497,1.1072		248/521	63855190	144,12862	2203	4300	6503	SO:0001819	synonymous_variant	9960	exon8			TTGGAAGATTATG	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.744G>A	15.37:g.63855190G>A		75	0	0		68	31	0.455882	NM_006537	B4DVU5|F5H1A6|Q8WVD0	Silent	SNP	ENST00000380324.3	37	CCDS32265.1																																																																																			G|0.990;A|0.010	0.010	strong		0.338	USP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417773.1			A	63855190	G	A	63855190	2	1	26	1	0	0	0	0	0	0	0	1	17075	933	33	2		2	USP3	15	63855190	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	7118509	63855190	38676202	477	10240											
DPP8	54878	hgsc.bcm.edu	37	chr15	65790319	65790319	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggcataattttggatccaTccgtatgttgggacaactag	11	12	11	7	1	0	0	0	0	0	0	2	2	2	2	2	3	1	3	2	3	4	6			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:65790319T>C	ENST00000341861.5	-	5	2226	c.646A>G	c.(646-648)Atg>Gtg	p.M216V	DPP8_ENST00000300141.6_Missense_Mutation_p.M200V|DPP8_ENST00000321118.7_Missense_Mutation_p.M216V|DPP8_ENST00000559233.1_Missense_Mutation_p.M216V|DPP8_ENST00000321147.6_Missense_Mutation_p.M216V|DPP8_ENST00000358939.4_Missense_Mutation_p.M200V|DPP8_ENST00000339244.5_Missense_Mutation_p.M216V	NM_197960.2	NP_932064.1	Q6V1X1	DPP8_HUMAN	dipeptidyl-peptidase 8	216					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						TTTGGATCCATCCGTATGTTG	0.383																																					p.M216V		Atlas-SNP	.											.	DPP8	78	.	0			c.A646G						PASS	.						158	128	138					15																	65790319		2201	4299	6500	SO:0001583	missense	54878	exon6			GATCCATCCGTAT	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.646A>G	15.37:g.65790319T>C	ENSP00000339208:p.Met216Val	140	0	0		136	59	0.433824	NM_197960	Q7Z4C8|Q7Z4D3|Q7Z4E1|Q8IWG7|Q8NEM5|Q96JX1|Q9HBM2|Q9HBM3|Q9HBM4|Q9HBM5|Q9NXF4	Missense_Mutation	SNP	ENST00000341861.5	37	CCDS10207.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.240676	0.79912	.	.	ENSG00000074603	ENST00000341861;ENST00000358939;ENST00000300141;ENST00000321147;ENST00000321118;ENST00000339244;ENST00000395652	T;T;T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54;1.54;1.54	5.39	5.39	0.77823	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.51329	0.1668	L	0.61036	1.89	0.25881	N	0.983587	B;P;B;B	0.43578	0.178;0.811;0.178;0.213	B;P;B;B	0.60789	0.108;0.879;0.07;0.173	T	0.45338	-0.9268	10	0.44086	T	0.13	-21.8947	15.4176	0.74983	0.0:0.0:0.0:1.0	.	200;200;216;216	Q6V1X1-3;Q6V1X1-4;Q6V1X1-2;Q6V1X1	.;.;.;DPP8_HUMAN	V	216;200;200;216;216;216;216	ENSP00000339208:M216V;ENSP00000351817:M200V;ENSP00000300141:M200V;ENSP00000318111:M216V;ENSP00000316373:M216V;ENSP00000341230:M216V;ENSP00000379013:M216V	ENSP00000300141:M200V	M	-	1	0	DPP8	63577372	1.000000	0.71417	0.989000	0.46669	0.997000	0.91878	7.119000	0.77145	2.027000	0.59764	0.533000	0.62120	ATG	.	.	none		0.383	DPP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256847.1	NM_017743		C	65790319	T	C	65790319	3	2	26	1	0	0	0	0	1	0	0	0	4734	1435	50	3	2114	3	DPP8	15	65790319	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	1935129	65790319	36741073	478	10241											
KIF23	9493	hgsc.bcm.edu	37	chr15	69729049	69729049	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gacaaatgatgattgatgagTttaacaaacaatgtaagggc	17	10	10	4	0	0	4	0	4	0	0	0	5	0	4	0	1	2	2	0	1	5	4	rs17310879	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:69729049T>C	ENST00000260363.4	+	14	1660	c.1543T>C	c.(1543-1545)Ttt>Ctt	p.F515L	KIF23_ENST00000558585.1_Missense_Mutation_p.F332L|KIF23_ENST00000395392.2_Missense_Mutation_p.F515L|KIF23_ENST00000537891.1_Missense_Mutation_p.F332L|KIF23_ENST00000352331.4_Missense_Mutation_p.F515L|KIF23_ENST00000559279.1_Missense_Mutation_p.F515L	NM_138555.2	NP_612565.1	Q02241	KIF23_HUMAN	kinesin family member 23	515			F -> L (in dbSNP:rs17310879).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytokinesis (GO:0000910)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle elongation (GO:0000022)|positive regulation of cytokinesis (GO:0032467)|spindle midzone assembly involved in mitosis (GO:0051256)	centralspindlin complex (GO:0097149)|centrosome (GO:0005813)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercellular bridge (GO:0045171)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(6)|prostate(2)|skin(1)	21						GATTGATGAGTTTAACAAACA	0.338													T|||	32	0.00638978	0.0	0.0101	5008	,	,		17842	0.0		0.0199	False		,,,				2504	0.0051				p.F515L		Atlas-SNP	.											.	KIF23	57	.	0			c.T1543C						PASS	.	T	LEU/PHE,LEU/PHE	12,4386	17.9+/-39.9	0,12,2187	68	59	62		1543,1543	4	0.9	15	dbSNP_123	62	126,8470	61.0+/-122.8	2,122,4174	yes	missense,missense	KIF23	NM_004856.5,NM_138555.2	22,22	2,134,6361	CC,CT,TT		1.4658,0.2729,1.062	benign,benign	515/857,515/961	69729049	138,12856	2199	4298	6497	SO:0001583	missense	9493	exon14			GATGAGTTTAACA	X67155	CCDS32278.1, CCDS32279.1	15q23	2008-03-03	2003-01-13	2003-01-17		ENSG00000137807		"Kinesins"	6392	protein-coding gene	gene with protein product		605064	"kinesin-like 5 (mitotic kinesin-like protein 1)"	KNSL5		1406973	Standard	NM_138555		Approved	MKLP1, MKLP-1	uc002asb.3	Q02241		ENST00000260363.4:c.1543T>C	15.37:g.69729049T>C	ENSP00000260363:p.Phe515Leu	58	0	0		73	37	0.506849	NM_138555	Q8WVP0	Missense_Mutation	SNP	ENST00000260363.4	37	CCDS32278.1	21	0.009615384615384616	0	0.0	5	0.013812154696132596	0	0.0	16	0.021108179419525065	T	6.643	0.487087	0.12641	0.002729	0.014658	ENSG00000137807	ENST00000260363;ENST00000352331;ENST00000395392;ENST00000537891	T;T;T;T	0.62364	0.03;0.03;0.03;0.03	5.11	3.99	0.46301	.	0.276826	0.41500	N	0.000878	T	0.19565	0.0470	N	0.08118	0	0.38724	D	0.953517	B;B;B	0.14012	0.001;0.009;0.0	B;B;B	0.15484	0.001;0.013;0.001	T	0.18209	-1.0344	10	0.02654	T	1	.	9.3049	0.37870	0.0:0.0866:0.0:0.9134	rs17310879;rs52817803;rs17310879	332;515;515	B4E1K0;Q02241-2;Q02241	.;.;KIF23_HUMAN	L	515;515;515;332	ENSP00000260363:F515L;ENSP00000304978:F515L;ENSP00000378790:F515L;ENSP00000442969:F332L	ENSP00000260363:F515L	F	+	1	0	KIF23	67516103	1.000000	0.71417	0.877000	0.34402	0.953000	0.61014	4.650000	0.61440	0.798000	0.33994	0.459000	0.35465	TTT	T|0.988;C|0.012	0.012	strong		0.338	KIF23-201	KNOWN	basic|CCDS	protein_coding	protein_coding				C	69729049	T	C	69729049	3	2	26	1	0	0	0	0	1	0	0	0	8300	1725	60	3	1597	3	KIF23	15	69729049	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	3938730	69729049	32802343	479	10242											
TBC1D2B	23102	hgsc.bcm.edu	37	chr15	78317679	78317679	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagttgcatttcggaggcCggcttcctgatgctgacgct	5	12	13	11	3	0	2	0	2	0	0	2	3	1	3	2	3	3	6	2	3	0	3	rs148026593		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:78317679C>T	ENST00000300584.3	-	5	1007	c.1008G>A	c.(1006-1008)ccG>ccA	p.P336P	TBC1D2B_ENST00000409931.3_Silent_p.P336P	NM_015079.5|NM_144572.1	NP_055894.6|NP_653173.1	Q9UPU7	TBD2B_HUMAN	TBC1 domain family, member 2B	336							Rab GTPase activator activity (GO:0005097)	p.P336P(2)		breast(3)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26						TTTCGGAGGCCGGCTTCCTGA	0.502													c|||	1	0.000199681	0.0	0.0	5008	,	,		13209	0.0		0.001	False		,,,				2504	0.0				p.P336P		Atlas-SNP	.											TBC1D2B_ENST00000300584,NS,carcinoma,0,2	TBC1D2B	104	2	2	Substitution - coding silent(2)	endometrium(2)	c.G1008A						PASS	.	T	,	0,4392		0,0,2196	110	99	103		1008,1008	-8.8	0	15	dbSNP_134	103	4,8582	3.7+/-12.6	0,4,4289	no	coding-synonymous,coding-synonymous	TBC1D2B	NM_015079.5,NM_144572.1	,	0,4,6485	TT,TC,CC		0.0466,0.0,0.0308	,	336/915,336/964	78317679	4,12974	2196	4293	6489	SO:0001819	synonymous_variant	23102	exon5			GGAGGCCGGCTTC	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.1008G>A	15.37:g.78317679C>T		128	0	0		112	66	0.589286	NM_144572	A7MD42|Q8N1F9|Q9NXM0	Silent	SNP	ENST00000300584.3	37	CCDS45314.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	c	5.989	0.366325	0.11352	0.0	4.66E-4	ENSG00000167202	ENST00000418039	.	.	.	5.61	-8.8	0.00817	.	.	.	.	.	T	0.15998	0.0385	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.21177	-1.0253	4	.	.	.	.	3.3969	0.07310	0.0858:0.2262:0.2483:0.4397	.	.	.	.	Q	218	.	.	R	-	2	0	TBC1D2B	76104734	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.861000	0.00177	-1.282000	0.02396	-1.027000	0.02421	CGG	C|0.999;T|0.001	0.001	strong		0.502	TBC1D2B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328369.3	NM_015079		T	78317679	C	T	78317679	2	4	26	1	0	0	0	0	0	0	0	1	15634	639	23	1		1	TBC1D2B	15	78317679	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	8588630	78317679	24213713	480	10243											
ADAMTS7	11173	hgsc.bcm.edu	37	chr15	79058986	79058986	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgtccggtcccctgtcccCgccaggtctagatcgggctc	3	9	13	16	3	1	1	0	0	1	1	6	1	4	1	6	4	0	1	6	4	1	1	rs150434082	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:79058986C>T	ENST00000388820.4	-	19	3477	c.3267G>A	c.(3265-3267)gcG>gcA	p.A1089A	ADAMTS7_ENST00000566303.1_5'Flank	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	1089					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						CCCCTGTCCCCGCCAGGTCTA	0.627													c|||	4	0.000798722	0.0	0.0	5008	,	,		14692	0.0		0.004	False		,,,				2504	0.0				p.A1089A		Atlas-SNP	.											ADAMTS7,NS,carcinoma,-1,1	ADAMTS7	142	1	0			c.G3267A						PASS	.	C		5,4369		0,5,2182	18	24	22		3267	-4.2	0	15	dbSNP_134	22	48,8500		1,46,4227	no	coding-synonymous	ADAMTS7	NM_014272.3		1,51,6409	TT,TC,CC		0.5615,0.1143,0.4102		1089/1687	79058986	53,12869	2187	4274	6461	SO:0001819	synonymous_variant	11173	exon19			TGTCCCCGCCAGG	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.3267G>A	15.37:g.79058986C>T		86	0	0		106	63	0.59434	NM_014272	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	37	CCDS32303.1																																																																																			C|0.996;T|0.004	0.004	strong		0.627	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272		T	79058986	C	T	79058986	2	4	26	1	0	0	0	0	0	0	0	1	271	639	23	1		1	ADAMTS7	15	79058986	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	741307	79058986	23472406	481	10244											
C15orf40	83640	hgsc.bcm.edu	37	chr15	83657894	83657894	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	agtctcctccaattgttgagGaatggaatagcagagctggt	11	11	12	7	0	1	2	0	1	1	1	3	4	2	4	2	3	2	3	2	3	4	3			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:83657894G>A	ENST00000304191.3	+	3	345	c.124G>A	c.(124-126)Gaa>Aaa	p.E42K	C15orf40_ENST00000538348.2_Missense_Mutation_p.P128S|RP11-382A20.5_ENST00000566841.1_RNA	NM_031452.3	NP_113640.1	Q9BTL3	RAM_HUMAN	family with sequence similarity 103, member A1	42	Interaction with RNMT.				7-methylguanosine mRNA capping (GO:0006370)|methylation (GO:0032259)|recruitment of mRNA capping enzyme to RNA polymerase II holoenzyme complex (GO:0036031)	mRNA cap binding complex (GO:0005845)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			prostate(1)	1						AATTGTTGAGGAATGGAATAG	0.418																																					p.P128S		Atlas-SNP	.											.	C15orf40	18	.	0			c.C382T						PASS	.																																			SO:0001583	missense	123207	exon4			GTTGAGGAATGGA	CR597724	CCDS10321.1	15q25.2	2012-06-13			ENSG00000169612	ENSG00000169612			31022	protein-coding gene	gene with protein product	"RNMT-activating mini protein"	614547				22099306	Standard	NM_031452		Approved	HsT19360, C15orf18, MGC2560, RAM	uc002bjl.2	Q9BTL3	OTTHUMG00000147357	ENST00000304191.3:c.124G>A	15.37:g.83657894G>A	ENSP00000307181:p.Glu42Lys	274	0	0		352	151	0.428977	NM_001160116	Q2M1J8	Missense_Mutation	SNP	ENST00000304191.3	37	CCDS10321.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.4|25.4	4.630726|4.630726	0.87660|0.87660	.|.	.|.	ENSG00000169612|ENSG00000169609	ENST00000304191|ENST00000538348	.|.	.|.	.|.	5.8|5.8	5.8|5.8	0.92144|0.92144	.|.	0.167238|.	0.51477|.	D|.	0.000085|.	T|T	0.76659|0.76659	0.4018|0.4018	M|M	0.70595|0.70595	2.14|2.14	0.80722|0.80722	D|D	1|1	P|D	0.42692|0.67145	0.787|0.996	B|P	0.37601|0.61658	0.254|0.892	T|T	0.72350|0.72350	-0.4320|-0.4320	9|8	0.66056|0.29301	D|T	0.02|0.29	-9.1412|-9.1412	19.6657|19.6657	0.95891|0.95891	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	42|128	Q9BTL3|F5GX92	F103A_HUMAN|.	K|S	42|128	.|.	ENSP00000307181:E42K|ENSP00000441077:P128S	E|P	+|-	1|1	0|0	FAM103A1|C15orf40	81448898|81448898	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	7.848000|7.848000	0.86902|0.86902	2.744000|2.744000	0.94065|0.94065	0.655000|0.655000	0.94253|0.94253	GAA|CCT	.	.	none		0.418	FAM103A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304001.1	NM_031452		A	83657894	G	A	83657894	3	1	26	1	0	0	0	0	1	0	0	0	1796	1175	41	2	71	2	C15orf40	15	83657894	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	4598908	83657894	18873498	482	10245											
ALPK3	57538	hgsc.bcm.edu	37	chr15	85382307	85382307	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatcactcatcagggcaaccGccacacactgcagctgtaca	12	6	8	15	1	3	0	3	0	0	0	3	1	3	0	2	1	4	4	2	1	2	1	rs34407151	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:85382307G>A	ENST00000258888.5	+	4	1174	c.1007G>A	c.(1006-1008)cGc>cAc	p.R336H		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	336	Ig-like 1.		R -> H (in dbSNP:rs34407151). {ECO:0000269|PubMed:17344846}.		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)			CAGGGCAACCGCCACACACTG	0.582													G|||	27	0.00539137	0.0015	0.0058	5008	,	,		16839	0.0		0.0129	False		,,,				2504	0.0082				p.R336H		Atlas-SNP	.											.	ALPK3	289	.	0			c.G1007A						PASS	.	G	HIS/ARG	17,4389	22.3+/-47.3	0,17,2186	49	39	42		1007	4.9	1	15	dbSNP_126	42	120,8478	62.4+/-124.4	1,118,4180	yes	missense	ALPK3	NM_020778.4	29	1,135,6366	AA,AG,GG		1.3957,0.3858,1.0535	probably-damaging	336/1908	85382307	137,12867	2203	4299	6502	SO:0001583	missense	57538	exon4			GCAACCGCCACAC	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.1007G>A	15.37:g.85382307G>A	ENSP00000258888:p.Arg336His	73	0	0		103	45	0.436893	NM_020778	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	37	CCDS10333.1	15	0.006868131868131868	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	10	0.013192612137203167	G	18.96	3.732990	0.69189	0.003858	0.013957	ENSG00000136383	ENST00000258888	T	0.68025	-0.3	4.89	4.89	0.63831	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.308968	0.31438	N	0.007658	T	0.68513	0.3009	L	0.45228	1.405	0.32666	N	0.517502	D	0.89917	1.0	D	0.67231	0.95	T	0.78770	-0.2074	10	0.56958	D	0.05	-8.4768	15.5548	0.76184	0.0:0.0:1.0:0.0	rs34407151	336	Q96L96	ALPK3_HUMAN	H	336	ENSP00000258888:R336H	ENSP00000258888:R336H	R	+	2	0	ALPK3	83183311	0.443000	0.25641	0.990000	0.47175	0.998000	0.95712	2.146000	0.42216	2.266000	0.75297	0.491000	0.48974	CGC	G|0.990;A|0.010	0.010	strong		0.582	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778		A	85382307	G	A	85382307	3	1	26	1	0	0	0	0	1	0	0	0	546	1087	38	1	1021	1	ALPK3	15	85382307	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1724413	85382307	17149085	483	10246											
POLG	5428	hgsc.bcm.edu	37	chr15	89862237	89862237	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggtacgtggtatgtcagaCgtagcaatgctctcaagctt	9	11	13	8	2	2	1	2	0	1	1	3	1	2	1	0	3	4	6	0	3	5	4	rs61752780	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:89862237C>T	ENST00000268124.5	-	20	3531	c.3198G>A	c.(3196-3198)acG>acA	p.T1066T	POLG_ENST00000442287.2_Silent_p.T1066T	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma	1066					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)			GTATGTCAGACGTAGCAATGC	0.567								DNA polymerases (catalytic subunits)					C|||	29	0.00579073	0.0008	0.0043	5008	,	,		19589	0.0		0.0089	False		,,,				2504	0.0164				p.T1066T	Colon(73;648 1203 11348 18386 27782)	Atlas-SNP	.											.	POLG	75	.	0			c.G3198A						PASS	.	C	,	13,4387	20.2+/-43.8	0,13,2187	120	105	110		3198,3198	-0.2	0	15	dbSNP_129	110	67,8531	40.8+/-97.7	0,67,4232	no	coding-synonymous,coding-synonymous	POLG	NM_001126131.1,NM_002693.2	,	0,80,6419	TT,TC,CC		0.7793,0.2955,0.6155	,	1066/1240,1066/1240	89862237	80,12918	2200	4299	6499	SO:0001819	synonymous_variant	5428	exon20			GTCAGACGTAGCA	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.3198G>A	15.37:g.89862237C>T		117	0	0		143	69	0.482517	NM_002693	Q8NFM2|Q92515	Silent	SNP	ENST00000268124.5	37	CCDS10350.1																																																																																			C|0.994;T|0.006	0.006	strong		0.567	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000312854.2	NM_002693		T	89862237	C	T	89862237	2	4	26	1	0	0	0	0	0	0	0	1	12209	523	19	1		1	POLG	15	89862237	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	4479930	89862237	12669155	484	10247											
BLM	641	hgsc.bcm.edu	37	chr15	91341535	91341535	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtaggtccttctggaagatTtactatgaatatgctggtcg	9	15	11	6	1	1	2	0	1	1	1	3	3	2	3	1	3	2	2	1	3	6	6			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:91341535T>A	ENST00000355112.3	+	17	3444	c.3326T>A	c.(3325-3327)tTt>tAt	p.F1109Y	BLM_ENST00000560509.1_Missense_Mutation_p.F1109Y|BLM_ENST00000560136.1_3'UTR	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	1109					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)			TCTGGAAGATTTACTATGAAT	0.313			"Mis, N, F"			"leukemia, lymphoma, skin squamous cell , other cancers"		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome																												p.F1109Y		Atlas-SNP	.	yes	Rec		Bloom Syndrome	15	15q26.1	641	Bloom Syndrome		"L, E"	.	BLM	122	.	0			c.T3326A						PASS	.						131	131	131					15																	91341535		2198	4296	6494	SO:0001583	missense	641	exon17	Familial Cancer Database		GAAGATTTACTAT	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.3326T>A	15.37:g.91341535T>A	ENSP00000347232:p.Phe1109Tyr	152	0	0		137	48	0.350365	NM_000057	Q52M96	Missense_Mutation	SNP	ENST00000355112.3	37	CCDS10363.1	.	.	.	.	.	.	.	.	.	.	T	14.42	2.529829	0.45073	.	.	ENSG00000197299	ENST00000355112;ENST00000536925;ENST00000543977	T	0.51325	0.71	5.36	5.36	0.76844	RQC domain (2);	0.134612	0.52532	D	0.000066	T	0.37758	0.1015	N	0.25380	0.74	0.31109	N	0.710145	B;B	0.24882	0.113;0.113	B;B	0.30401	0.115;0.115	T	0.42464	-0.9450	10	0.33141	T	0.24	-20.8792	13.2993	0.60315	0.0:0.0:0.0:1.0	.	1109;1109	B2RAN0;P54132	.;BLM_HUMAN	Y	1109;739;296	ENSP00000347232:F1109Y	ENSP00000347232:F1109Y	F	+	2	0	BLM	89142539	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.846000	0.62860	2.037000	0.60232	0.477000	0.44152	TTT	.	.	none		0.313	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1			A	91341535	T	A	91341535	3	1	26	1	0	0	0	0	1	0	0	0	1445	1841	64	5	3388	5	BLM	15	91341535	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	1479298	91341535	11189857	485	10248											
SV2B	9899	hgsc.bcm.edu	37	chr15	91827271	91827271	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctctacgagcacaagttcAtcaactgtcggtttatcaac	12	11	6	12	2	4	0	3	0	1	0	5	1	4	0	1	1	4	3	1	1	5	4	rs117361551	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:91827271A>G	ENST00000394232.1	+	11	1998	c.1528A>G	c.(1528-1530)Atc>Gtc	p.I510V	SV2B_ENST00000545111.2_Missense_Mutation_p.I359V|SV2B_ENST00000330276.4_Missense_Mutation_p.I510V	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	510					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)			GCACAAGTTCATCAACTGTCG	0.507													A|||	56	0.0111821	0.0008	0.013	5008	,	,		19869	0.0		0.0169	False		,,,				2504	0.0297				p.I510V		Atlas-SNP	.											.	SV2B	98	.	0			c.A1528G						PASS	.	A	VAL/ILE,VAL/ILE	12,4384	19.1+/-41.9	0,12,2186	192	184	187		1075,1528	5.6	1	15	dbSNP_132	187	127,8469	64.9+/-127.2	2,123,4173	yes	missense,missense	SV2B	NM_001167580.1,NM_014848.4	29,29	2,135,6359	GG,GA,AA		1.4774,0.273,1.0699	benign,benign	359/533,510/684	91827271	139,12853	2198	4298	6496	SO:0001583	missense	9899	exon12			AAGTTCATCAACT	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.1528A>G	15.37:g.91827271A>G	ENSP00000377779:p.Ile510Val	141	0	0		178	96	0.539326	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Missense_Mutation	SNP	ENST00000394232.1	37	CCDS10370.1	16	0.007326007326007326	0	0.0	4	0.011049723756906077	0	0.0	12	0.0158311345646438	A	10.16	1.274723	0.23307	0.00273	0.014774	ENSG00000185518	ENST00000545111;ENST00000394232;ENST00000330276	T;T;T	0.41400	1.0;1.0;1.0	5.61	5.61	0.85477	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.099589	0.64402	D	0.000004	T	0.21145	0.0509	L	0.39245	1.2	0.47584	D	0.999462	B	0.23937	0.094	B	0.31016	0.123	T	0.08911	-1.0699	10	0.12766	T	0.61	-31.4023	14.6867	0.69055	1.0:0.0:0.0:0.0	.	510	Q7L1I2	SV2B_HUMAN	V	359;510;510	ENSP00000443243:I359V;ENSP00000377779:I510V;ENSP00000332818:I510V	ENSP00000332818:I510V	I	+	1	0	SV2B	89628275	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.317000	0.43770	2.152000	0.67230	0.477000	0.44152	ATC	A|0.990;G|0.010	0.010	strong		0.507	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848		G	91827271	A	G	91827271	3	3	26	1	0	0	0	0	1	0	0	0	15433	217	8	3	1566	3	SV2B	15	91827271	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	485736	91827271	10704121	486	10249											
DECR2	26063	hgsc.bcm.edu	37	chr16	461554	461554	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gtcaaagggctgccggatttCgcatccttctctgctaagct	7	12	10	12	2	2	0	1	0	1	0	5	1	3	1	2	2	3	4	2	2	2	3	rs370013477		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:461554C>G	ENST00000219481.5	+	8	993	c.855C>G	c.(853-855)ttC>ttG	p.F285L	DECR2_ENST00000461947.1_Intron|DECR2_ENST00000424398.2_Missense_Mutation_p.F273L	NM_020664.3	NP_065715.1	Q9NUI1	DECR2_HUMAN	2,4-dienoyl CoA reductase 2, peroxisomal	285					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)				TGCCGGATTTCGCATCCTTCT	0.622																																					p.F285L		Atlas-SNP	.											.	DECR2	47	.	0			c.C855G						PASS	.	C	LEU/PHE	0,4404		0,0,2202	149	121	131		855	-10.7	0	16		131	1,8599	1.2+/-3.3	0,1,4299	no	missense	DECR2	NM_020664.3	22	0,1,6501	GG,GC,CC		0.0116,0.0,0.0077	benign	285/293	461554	1,13003	2202	4300	6502	SO:0001583	missense	26063	exon8			GGATTTCGCATCC	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.855C>G	16.37:g.461554C>G	ENSP00000219481:p.Phe285Leu	123	0	0		123	64	0.520325	NM_020664	Q6ZRS7|Q96ET0	Missense_Mutation	SNP	ENST00000219481.5	37	CCDS10409.1	.	.	.	.	.	.	.	.	.	.	C	12.63	1.995624	0.35226	0.0	1.16E-4	ENSG00000242612	ENST00000219481;ENST00000424398	T;T	0.80909	-1.43;-1.06	5.34	-10.7	0.00240	.	1.461700	0.03592	N	0.232010	T	0.59004	0.2162	N	0.04297	-0.235	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.55134	-0.8188	10	0.21014	T	0.42	.	15.9692	0.79998	0.0:0.6665:0.1013:0.2322	.	285	Q9NUI1	DECR2_HUMAN	L	285;273	ENSP00000219481:F285L;ENSP00000400374:F273L	ENSP00000219481:F285L	F	+	3	2	DECR2	401555	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.158000	0.03153	-2.920000	0.00305	-1.036000	0.02392	TTC	.	.	weak		0.622	DECR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109069.4	NM_020664		G	461554	C	G	461554	3	3	26	1	0	0	0	0	1	0	0	0	4385	883	31	4	885	4	DECR2	16	461554	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10		461554	89893199	487	10250											
WDR90	197335	hgsc.bcm.edu	37	chr16	716494	716494	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agggcacagacctatggctgGctgccagtggggaccagcgg	8	5	17	11	1	0	1	0	0	0	1	0	2	0	2	3	6	2	3	3	6	1	1	rs373898012		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:716494G>A	ENST00000293879.4	+	38	4780	c.4780G>A	c.(4780-4782)Gct>Act	p.A1594T	RHOT2_ENST00000315082.4_5'Flank|WDR90_ENST00000549091.1_Missense_Mutation_p.A1596T|WDR90_ENST00000315764.4_Intron|WDR90_ENST00000547543.1_3'UTR|WDR90_ENST00000547944.1_Missense_Mutation_p.A193T			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1594										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CCTATGGCTGGCTGCCAGTGG	0.632																																					p.A1594T		Atlas-SNP	.											.	WDR90	107	.	0			c.G4780A						PASS	.	G	THR/ALA	0,4066		0,0,2033	30	40	37		4780	4.5	1	16		37	2,8340		0,2,4169	no	missense	WDR90	NM_145294.4	58	0,2,6202	AA,AG,GG		0.024,0.0,0.0161	probably-damaging	1594/1749	716494	2,12406	2033	4171	6204	SO:0001583	missense	197335	exon38			TGGCTGGCTGCCA	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.4780G>A	16.37:g.716494G>A	ENSP00000293879:p.Ala1594Thr	98	0	0		106	51	0.481132	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	37	CCDS42092.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.919032	0.92249	0.0	2.4E-4	ENSG00000161996	ENST00000549091;ENST00000293879;ENST00000547944	T;T;T	0.62788	1.43;1.4;-0.0	4.49	4.49	0.54785	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.235790	0.42420	D	0.000715	T	0.78534	0.4298	M	0.77486	2.375	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.981	T	0.78352	-0.2237	10	0.33141	T	0.24	.	16.1987	0.82053	0.0:0.0:1.0:0.0	.	193;1594	G3V201;Q96KV7	.;WDR90_HUMAN	T	1596;1594;193	ENSP00000448122:A1596T;ENSP00000293879:A1594T;ENSP00000449576:A193T	ENSP00000293879:A1594T	A	+	1	0	WDR90	656495	1.000000	0.71417	0.981000	0.43875	0.970000	0.65996	6.432000	0.73400	2.045000	0.60652	0.561000	0.74099	GCT	.	.	weak		0.632	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294		A	716494	G	A	716494	3	1	26	1	0	0	0	0	1	0	0	0	17352	1203	42	2	4930	2	WDR90	16	716494	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	254940	716494	89638259	488	10251											
MSLN	10232	hgsc.bcm.edu	37	chr16	816414	816414	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gatgagccctgaggacattcGcaagtggaatgtgacgtccc	10	8	13	10	2	0	3	0	3	0	0	2	6	1	5	2	2	1	1	2	2	2	1	rs150147307		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:816414G>A	ENST00000382862.3	+	12	1249	c.1154G>A	c.(1153-1155)cGc>cAc	p.R385H	MSLN_ENST00000545450.2_Missense_Mutation_p.R385H|MSLN_ENST00000566549.1_Missense_Mutation_p.R385H|MSLN_ENST00000563941.1_Missense_Mutation_p.R385H	NM_013404.4	NP_037536.2	Q13421	MSLN_HUMAN	mesothelin	385					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)				GAGGACATTCGCAAGTGGAAT	0.567																																					p.R385H		Atlas-SNP	.											.	MSLN	109	.	0			c.G1154A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG	0,4380		0,0,2190	88	78	81		1154,1154,1154	-3.5	0	16	dbSNP_134	81	1,8573	1.2+/-3.3	0,1,4286	no	missense,missense,missense	MSLN	NM_001177355.1,NM_005823.5,NM_013404.4	29,29,29	0,1,6476	AA,AG,GG		0.0117,0.0,0.0077	benign,benign,benign	385/623,385/623,385/631	816414	1,12953	2190	4287	6477	SO:0001583	missense	10232	exon13			ACATTCGCAAGTG	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.1154G>A	16.37:g.816414G>A	ENSP00000372313:p.Arg385His	122	0	0		153	65	0.424837	NM_005823	D3DU65|Q14859|Q4VQD5|Q96GR6|Q96KJ5|Q9BR17|Q9BTR2|Q9UCB2|Q9UK57	Missense_Mutation	SNP	ENST00000382862.3	37	CCDS32356.1	.	.	.	.	.	.	.	.	.	.	G	0.244	-1.011226	0.02095	0.0	1.17E-4	ENSG00000102854	ENST00000446427;ENST00000445361;ENST00000545450;ENST00000382862	T;T	0.13420	2.59;2.59	4.97	-3.46	0.04767	.	1.820510	0.02850	N	0.129024	T	0.07279	0.0184	N	0.12569	0.235	0.09310	N	1	B;B;B;B	0.28350	0.029;0.037;0.208;0.029	B;B;B;B	0.16289	0.005;0.014;0.015;0.005	T	0.30679	-0.9970	10	0.13470	T	0.59	-0.7879	11.3272	0.49456	0.3512:0.0:0.6488:0.0	.	384;385;385;385	Q13421-4;Q13421;Q13421-2;Q13421-3	.;MSLN_HUMAN;.;.	H	385	ENSP00000442965:R385H;ENSP00000372313:R385H	ENSP00000372313:R385H	R	+	2	0	MSLN	756415	0.000000	0.05858	0.043000	0.18650	0.104000	0.19210	-1.290000	0.02777	-0.567000	0.06046	0.297000	0.19635	CGC	G|1.000;A|0.000	0.000	weak		0.567	MSLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109253.2			A	816414	G	A	816414	3	1	26	1	0	0	0	0	1	0	0	0	9890	1087	38	1	1196	1	MSLN	16	816414	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	99920	816414	89538339	489	10252											
PKD1	5310	hgsc.bcm.edu	37	chr16	2144160	2144161	+	In_Frame_Ins	INS	-	-	TGG																															ggctgggtggccccagctccINScccagcctctgcagcgccag																										TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2144160_2144161insTGG	ENST00000262304.4	-	35	10758_10759	c.10550_10551insCCA	c.(10549-10551)ggg>ggCCAg	p.3517_3518insQ	RP11-304L19.3_ENST00000565937.1_RNA|RP11-304L19.1_ENST00000570072.1_RNA|PKD1_ENST00000423118.1_In_Frame_Ins_p.3516_3517insQ	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	3517					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						GCCCCAGCTCCCCCAGCCTCTG	0.663																																					p.G3517delinsGQ		Pindel,Atlas-Indel	.											.	PKD1	184	.	0			c.10551_10552insCCA						PASS	.																																			SO:0001652	inframe_insertion	5310	exon35			.	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.10550_10551insCCA	16.37:g.2144160_2144161insTGG	ENSP00000262304:p.Gly3517_Glu3518insGln	167	0	.		217	59	0.272	NM_001009944	Q15140|Q15141	In_Frame_Ins	INS	ENST00000262304.4	37	CCDS32369.1																																																																																			.	.	none		0.663	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			TGG	2144161	-	TGG	2144160	7	5	26	1	0	1	1	0	0	0	0	0	11972	610	22	0	2408	0	PKD1	16	2144160	In_Frame_Ins	INS	-	TCGA-G8-6907-01A-11D-2210-10	1327746	2144160	88210593	490	10253											
DNASE1L2	1775	hgsc.bcm.edu	37	chr16	2287294	2287294	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tacaaggagatgtacctgttCgtgtacaggtgaggggcggg	9	9	17	6	2	0	2	0	1	0	1	1	3	0	2	1	5	3	3	1	5	4	4			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2287294C>T	ENST00000564065.1	+	3	1310	c.309C>T	c.(307-309)ttC>ttT	p.F103F	RP11-304L19.12_ENST00000564055.1_lincRNA|DNASE1L2_ENST00000320700.5_Silent_p.F103F|DNASE1L2_ENST00000382437.4_Silent_p.F103F|DNASE1L2_ENST00000567494.1_Silent_p.F103F			Q92874	DNSL2_HUMAN	deoxyribonuclease I-like 2	103					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						TGTACCTGTTCGTGTACAGGT	0.692																																					p.F103F		Atlas-SNP	.											.	DNASE1L2	14	.	0			c.C309T						PASS	.						13	16	15					16																	2287294		1860	4078	5938	SO:0001819	synonymous_variant	1775	exon4			CCTGTTCGTGTAC	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.309C>T	16.37:g.2287294C>T		33	0	0		17	6	0.352941	NM_001374	E9PBY4|Q6JVM2|Q6JVM3	Silent	SNP	ENST00000564065.1	37	CCDS42105.1																																																																																			.	.	none		0.692	DNASE1L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435236.1	NM_001374		T	2287294	C	T	2287294	2	4	26	1	0	0	0	0	0	0	0	1	4664	883	31	1		1	DNASE1L2	16	2287294	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	143134	2287294	88067459	491	10254											
DCI	1632	hgsc.bcm.edu	37	chr16	2294549	2294549	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggccgagaagacacccgggCggtcctgcagggggagccgg	7	2	19	13	5	0	2	0	0	0	2	1	4	1	3	4	6	2	1	4	6	1	0	rs145543160		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2294549C>T	ENST00000301729.4	-	4	346	c.299G>A	c.(298-300)cGc>cAc	p.R100H	RP11-304L19.11_ENST00000565709.1_RNA|ECI1_ENST00000562238.1_Missense_Mutation_p.R100H|ECI1_ENST00000570258.1_Missense_Mutation_p.R41H	NM_001919.3	NP_001910.2	P42126	ECI1_HUMAN	enoyl-CoA delta isomerase 1	100					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	dodecenoyl-CoA delta-isomerase activity (GO:0004165)|intramolecular oxidoreductase activity (GO:0016860)			endometrium(1)|large_intestine(2)|lung(6)	9						GACACCCGGGCGGTCCTGCAG	0.692													C|||	1	0.000199681	0.0	0.0	5008	,	,		16248	0.0		0.001	False		,,,				2504	0.0				p.R100H		Atlas-SNP	.											ECI1,NS,carcinoma,-1,1	ECI1	20	1	0			c.G299A						PASS	.	C	HIS/ARG,HIS/ARG	3,4349		0,3,2173	20	19	19		299,299	3.1	0	16	dbSNP_134	19	14,8564		0,14,4275	yes	missense,missense	ECI1	NM_001178029.1,NM_001919.3	29,29	0,17,6448	TT,TC,CC		0.1632,0.0689,0.1315	possibly-damaging,possibly-damaging	100/286,100/303	2294549	17,12913	2176	4289	6465	SO:0001583	missense	1632	exon4			CCCGGGCGGTCCT		CCDS10464.1, CCDS58410.1	16p13.3	2011-03-15	2011-03-15	2011-03-15	ENSG00000167969	ENSG00000167969	5.3.3.8		2703	protein-coding gene	gene with protein product	"3,2 trans-enoyl-CoA isomerase"	600305	"dodecenoyl-Coenzyme A delta isomerase (3,2 trans-enoyl-Coenzyme A isomerase)", "dodecenoyl-CoA isomerase"	DCI		7829074	Standard	NM_001178029		Approved		uc002cpr.3	P42126	OTTHUMG00000128830	ENST00000301729.4:c.299G>A	16.37:g.2294549C>T	ENSP00000301729:p.Arg100His	108	0	0		109	42	0.385321	NM_001178029	A8K512|Q13290|Q7Z2L6|Q7Z2L7|Q9BUB8|Q9BW05|Q9UDG6	Missense_Mutation	SNP	ENST00000301729.4	37	CCDS10464.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	9.396	1.076878	0.20227	6.89E-4	0.001632	ENSG00000167969	ENST00000301729	D	0.85702	-2.02	5.1	3.08	0.35506	Crotonase, core (1);	1.086010	0.06745	N	0.778936	T	0.78502	0.4293	L	0.52573	1.65	0.09310	N	1	P;B	0.40476	0.718;0.084	B;B	0.30105	0.111;0.024	T	0.63892	-0.6534	10	0.35671	T	0.21	-4.2812	8.5437	0.33408	0.1653:0.5146:0.3201:0.0	.	100;100	P42126-2;P42126	.;ECI1_HUMAN	H	100	ENSP00000301729:R100H	ENSP00000301729:R100H	R	-	2	0	ECI1	2234550	0.000000	0.05858	0.047000	0.18901	0.030000	0.12068	-0.936000	0.03946	0.697000	0.31718	0.650000	0.86243	CGC	C|0.998;T|0.002	0.002	strong		0.692	ECI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250768.1			T	2294549	C	T	2294549	3	4	26	1	0	0	0	0	1	0	0	0	4291	768	27	1	625	1	DCI	16	2294549	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	7255	2294549	88060204	492	10255											
AMDHD2	752014	hgsc.bcm.edu	37	chr16	2580755	2580755	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctgcctgggcagggcctcGcctgagggagggcctggggc	4	5	19	13	1	0	1	0	1	0	0	1	2	0	2	5	6	1	1	5	6	0	0	rs76722821	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2580755G>C	ENST00000567119.1	-	1	654	c.320C>G	c.(319-321)gCg>gGg	p.A107G	AMDHD2_ENST00000413459.3_Missense_Mutation_p.A594P|AMDHD2_ENST00000565570.1_3'UTR|AMDHD2_ENST00000302956.4_3'UTR|CEMP1_ENST00000565480.1_Intron|CEMP1_ENST00000382350.1_Missense_Mutation_p.A107G|MIR3178_ENST00000581887.1_RNA	NM_001048212.3	NP_001041677.1	Q6PRD7	CEMP1_HUMAN	cementum protein 1	107						cytoplasm (GO:0005737)				lung(1)|skin(1)	2						GCAGGGCCTCGCCTGAGGGAG	0.627													G|||	40	0.00798722	0.0	0.0173	5008	,	,		18584	0.0		0.0258	False		,,,				2504	0.002				p.A594P		Atlas-SNP	.											.	AMDHD2	33	.	0			c.G1780C						PASS	.	G	PRO/ALA,GLY/ALA	12,3928		0,12,1958	31	36	35		1780,320	0.6	0	16	dbSNP_131	35	141,8143		5,131,4006	yes	missense,missense	AMDHD2,CEMP1	NM_001145815.1,NM_001048212.3	27,60	5,143,5964	CC,CG,GG		1.7021,0.3046,1.2516	probably-damaging,probably-damaging	594/595,107/248	2580755	153,12071	1970	4142	6112	SO:0001583	missense	51005	exon11			GGCCTCGCCTGAG	AY584596	CCDS42108.1	16p13.3	2006-09-22							32553	protein-coding gene	gene with protein product	"cementum protein-23"	611113				16263347	Standard	NM_001048212		Approved	CP-23	uc002cqr.3	Q6PRD7		ENST00000567119.1:c.320C>G	16.37:g.2580755G>C	ENSP00000457380:p.Ala107Gly	54	0	0		64	32	0.5	NM_001145815	B2RUY1	Missense_Mutation	SNP	ENST00000567119.1	37	CCDS42108.1	20|20	0.009157509157509158|0.009157509157509158	0|0	0.0|0.0	6|6	0.016574585635359115|0.016574585635359115	0|0	0.0|0.0	14|14	0.018469656992084433|0.018469656992084433	G|G	3.474|3.474	-0.107349|-0.107349	0.06924|0.06924	0.003046|0.003046	0.017021|0.017021	ENSG00000205923|ENSG00000162066	ENST00000382350|ENST00000413459	T|.	0.55234|.	0.53|.	0.559|0.559	0.559|0.559	0.17272|0.17272	.|.	.|.	.|.	.|.	.|.	T|T	0.38241|0.38241	0.1033|0.1033	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	D|D	0.65815|0.56968	0.995|0.978	D|P	0.69142|0.61800	0.962|0.894	T|T	0.28618|0.28618	-1.0038|-1.0038	7|6	0.87932|0.87932	D|D	0|0	.|.	.|.	.|.	.|.	.|.	107|594	Q6PRD7|Q9Y303-3	CEMP1_HUMAN|.	G|P	107|594	ENSP00000371787:A107G|.	ENSP00000371787:A107G|ENSP00000391596:A594P	A|A	-|+	2|1	0|0	CEMP1|AMDHD2	2520756|2520756	0.005000|0.005000	0.15991|0.15991	0.001000|0.001000	0.08648|0.08648	0.002000|0.002000	0.02628|0.02628	-0.342000|-0.342000	0.07801|0.07801	0.556000|0.556000	0.29098|0.29098	0.561000|0.561000	0.74099|0.74099	GCG|GCC	G|0.990;C|0.010	0.010	strong		0.627	CEMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435686.1	NM_001048212		C	2580755	G	C	2580755	3	2	26	1	0	0	0	0	1	0	0	0	568	1087	38	4	1860	4	AMDHD2	16	2580755	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	286206	2580755	87773998	493	10256											
PDPK1	5170	hgsc.bcm.edu	37	chr16	2611896	2611899	+	Frame_Shift_Del	DEL	CGAC	CGAC	-																															ctttacttcacatttcaggaCgacgagaagctgtgtatcct																										TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CGAC	CGAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2611896_2611899delCGAC	ENST00000342085.4	+	4	602_605	c.453_456delCGAC	c.(451-456)gacgacfs	p.DD151fs	PDPK1_ENST00000354836.5_Frame_Shift_Del_p.DD151fs|RP11-20I23.8_ENST00000569852.1_RNA|PDPK1_ENST00000268673.7_Intron|PDPK1_ENST00000441549.3_Frame_Shift_Del_p.DD151fs|PDPK1_ENST00000389224.3_Frame_Shift_Del_p.DD124fs	NM_002613.4	NP_002604.1	O15530	PDPK1_HUMAN	3-phosphoinositide dependent protein kinase 1	151	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway (GO:0097191)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|focal adhesion assembly (GO:0048041)|hyperosmotic response (GO:0006972)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of endothelial cell migration (GO:0010594)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of mast cell degranulation (GO:0043304)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell development (GO:0003323)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	3-phosphoinositide-dependent protein kinase activity (GO:0004676)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)	7		Ovarian(90;0.17)			Celecoxib(DB00482)	CATTTCAGGACGACGAGAAGCTGT	0.52																																					p.151_152del		Atlas-Indel	.											.	PDPK1	37	.	0			c.452_455del	GRCh37	CD072462	PDPK1	D		PASS	.																																			SO:0001589	frameshift_variant	5170	exon4			.	AF017995	CCDS10472.1, CCDS10473.1, CCDS58411.1	16p13.3	2014-03-20	2014-03-20		ENSG00000140992	ENSG00000140992			8816	protein-coding gene	gene with protein product	"PkB kinase"	605213				9094314, 9445477	Standard	NM_002613		Approved	PDK1	uc002cqs.4	O15530	OTTHUMG00000128874	ENST00000342085.4:c.453_456delCGAC	16.37:g.2611896_2611899delCGAC	ENSP00000344220:p.Asp151fs	582	0	0		582	62	0.106529	NM_001261816	H0Y4Z0|Q59EH6|Q6FI20|Q8IV52|Q9BRD5	Frame_Shift_Del	DEL	ENST00000342085.4	37	CCDS10472.1																																																																																			.	.	none		0.52	PDPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250831.3			-	2611899	CGAC	-	2611896	7	5	26	1	0	1	0	1	0	0	0	0	11696	535	19	0	467	0	PDPK1	16	2611896	Frame_Shift_Del	DEL	CGAC	TCGA-G8-6907-01A-11D-2210-10	31141	2611896	87742857	494	10257											
USP7	7874	hgsc.bcm.edu	37	chr16	9057083	9057083	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccttccatctccatgtcctcGggctcgctcaactgctgctc	4	12	7	18	2	2	0	1	0	1	0	8	0	4	0	4	1	3	4	4	1	1	1	rs374020920	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:9057083G>A	ENST00000344836.4	-	1	258	c.60C>T	c.(58-60)ccC>ccT	p.P20P	RP11-77H9.8_ENST00000564485.1_lincRNA	NM_003470.2	NP_003461.2	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7 (herpes virus-associated)	20	Interaction with TSPYL5.				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						CCATGTCCTCGGGCTCGCTCA	0.756													G|||	12	0.00239617	0.0	0.0014	5008	,	,		3991	0.0		0.004	False		,,,				2504	0.0072				p.P20P		Atlas-SNP	.											.	USP7	116	.	0			c.C60T						PASS	.	G		7,2427		0,7,1210	5	6	6		60	1.3	1	16		6	26,4274		0,26,2124	no	coding-synonymous	USP7	NM_003470.2		0,33,3334	AA,AG,GG		0.6047,0.2876,0.4901		20/1103	9057083	33,6701	1217	2150	3367	SO:0001819	synonymous_variant	7874	exon1			GTCCTCGGGCTCG	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.60C>T	16.37:g.9057083G>A		12	0	0		15	11	0.733333	NM_003470	A6NMY8|B7Z815|H0Y3G8	Silent	SNP	ENST00000344836.4	37	CCDS32385.1																																																																																			.	.	weak		0.756	USP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434268.2			A	9057083	G	A	9057083	2	1	26	1	0	0	0	0	0	0	0	1	17103	1103	39	1		1	USP7	16	9057083	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	6445187	9057083	81297670	495	10258											
GRIN2A	2903	hgsc.bcm.edu	37	chr16	9862741	9862741	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagagcaacccaggccggtcGgagcacacgcccgtgaaaca	13	2	12	14	4	0	2	0	1	0	1	1	3	0	3	3	3	4	2	3	3	3	0			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:9862741G>A	ENST00000396573.2	-	13	2871	c.2562C>T	c.(2560-2562)tcC>tcT	p.S854S	GRIN2A_ENST00000396575.2_Silent_p.S854S|GRIN2A_ENST00000404927.2_Silent_p.S854S|GRIN2A_ENST00000562109.1_Silent_p.S854S|GRIN2A_ENST00000535259.1_Silent_p.S697S|GRIN2A_ENST00000330684.3_Silent_p.S854S	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	854					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)	CAGGCCGGTCGGAGCACACGC	0.562																																					p.S854S		Atlas-SNP	.											.	GRIN2A	366	.	0			c.C2562T						PASS	.						89	91	91					16																	9862741		2197	4300	6497	SO:0001819	synonymous_variant	2903	exon13			CCGGTCGGAGCAC		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.2562C>T	16.37:g.9862741G>A		50	0	0		68	28	0.411765	NM_000833	O00669|Q17RZ6	Silent	SNP	ENST00000396573.2	37	CCDS10539.1																																																																																			.	.	none		0.562	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			A	9862741	G	A	9862741	2	1	26	1	0	0	0	0	0	0	0	1	6788	1103	39	1		1	GRIN2A	16	9862741	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	805658	9862741	80492012	496	10259											
PDXDC1	23042	hgsc.bcm.edu	37	chr16	15111265	15111265	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cggtgacactgtataaacacGatgaccctgccttggtaagt	11	10	10	10	2	0	2	0	2	0	0	0	3	0	2	2	2	2	2	2	2	4	4			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:15111265G>A	ENST00000396410.4	+	11	1046	c.949G>A	c.(949-951)Gat>Aat	p.D317N	PDXDC1_ENST00000455313.2_Missense_Mutation_p.D294N|PDXDC1_ENST00000569715.1_Missense_Mutation_p.D290N|PDXDC1_ENST00000563679.1_Missense_Mutation_p.D335N|RP11-680G24.5_ENST00000565178.1_RNA|PDXDC1_ENST00000325823.7_Missense_Mutation_p.D302N|PDXDC1_ENST00000447912.2_Missense_Mutation_p.D226N|PDXDC1_ENST00000535621.2_Missense_Mutation_p.D317N|PDXDC1_ENST00000450288.2_Missense_Mutation_p.D289N	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	317					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						GTATAAACACGATGACCCTGC	0.502																																					p.D317N		Atlas-SNP	.											.	PDXDC1	59	.	0			c.G949A						PASS	.						112	114	113					16																	15111265		2197	4300	6497	SO:0001583	missense	23042	exon11			AAACACGATGACC	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.949G>A	16.37:g.15111265G>A	ENSP00000379691:p.Asp317Asn	110	0	0		147	34	0.231293	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Missense_Mutation	SNP	ENST00000396410.4	37	CCDS32393.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.526001	0.85600	.	.	ENSG00000179889	ENST00000325823;ENST00000447912;ENST00000535621;ENST00000396410;ENST00000450288;ENST00000537781;ENST00000455313	T;T;T;T;T;T	0.21543	2.0;2.0;2.0;2.0;2.0;2.0	5.45	5.45	0.79879	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.044008	0.85682	D	0.000000	T	0.26629	0.0651	L	0.36672	1.1	0.47374	D	0.999404	P;P;P;P;P;P	0.51240	0.88;0.943;0.94;0.88;0.88;0.625	B;P;P;B;B;B	0.49597	0.288;0.463;0.616;0.288;0.288;0.2	T	0.00827	-1.1550	10	0.23891	T	0.37	-11.8011	18.2726	0.90073	0.0:0.0:1.0:0.0	.	289;226;317;289;317;294	E7EPL4;E7EMH5;Q86XE2;B4DR55;Q6P996;Q6P996-2	.;.;.;.;PDXD1_HUMAN;.	N	302;226;317;317;289;23;294	ENSP00000322807:D302N;ENSP00000400310:D226N;ENSP00000437835:D317N;ENSP00000379691:D317N;ENSP00000391147:D289N;ENSP00000406703:D294N	ENSP00000322807:D302N	D	+	1	0	PDXDC1	15018766	1.000000	0.71417	0.619000	0.29118	0.845000	0.48019	8.666000	0.91149	2.546000	0.85860	0.542000	0.68232	GAT	.	.	none		0.502	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027		A	15111265	G	A	15111265	3	1	26	1	0	0	0	0	1	0	0	0	11705	1058	37	1	991	1	PDXDC1	16	15111265	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	5248524	15111265	75243488	497	10260											
MYH11	4629	hgsc.bcm.edu	37	chr16	15814100	15814100	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcaggtccccttccagctTcttctttgctgcagctgcca	4	15	7	15	0	3	0	1	0	2	0	5	0	5	0	4	1	5	4	4	1	0	5	rs34321232		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:15814100T>G	ENST00000300036.5	-	34	4970	c.4861A>C	c.(4861-4863)Aag>Cag	p.K1621Q	MYH11_ENST00000396324.3_Missense_Mutation_p.K1628Q|NDE1_ENST00000396354.1_Intron|MYH11_ENST00000576790.2_Missense_Mutation_p.K1621Q|MYH11_ENST00000452625.2_Missense_Mutation_p.K1628Q|NDE1_ENST00000342673.5_Intron|NDE1_ENST00000396355.1_Intron	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1621					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						CCTTCCAGCTTCTTCTTTGCT	0.577			T	CBFB	AML								T|||	1	0.000199681	0.0	0.0	5008	,	,		20791	0.0		0.0	False		,,,				2504	0.001				p.K1628Q		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	.	MYH11	520	.	0			c.A4882C						PASS	.	T	GLN/LYS,GLN/LYS,,GLN/LYS,,GLN/LYS	0,4394		0,0,2197	121	104	110		4882,4882,,4861,,4861	4.9	1	16	dbSNP_126	110	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,intron,missense,intron,missense	MYH11,NDE1	NM_001040113.1,NM_001040114.1,NM_001143979.1,NM_002474.2,NM_017668.2,NM_022844.2	53,53,,53,,53	0,3,6494	GG,GT,TT		0.0349,0.0,0.0231	probably-damaging,probably-damaging,,probably-damaging,,probably-damaging	1628/1946,1628/1980,,1621/1973,,1621/1939	15814100	3,12991	2197	4300	6497	SO:0001583	missense	4629	exon35			CCAGCTTCTTCTT	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.4861A>C	16.37:g.15814100T>G	ENSP00000300036:p.Lys1621Gln	147	0	0		190	98	0.515789	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.056096	0.76074	0.0	3.49E-4	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	D;D;D;D	0.85955	-2.05;-2.05;-2.05;-2.05	4.95	4.95	0.65309	Myosin tail (1);	0.000000	0.85682	D	0.000000	D	0.92176	0.7519	M	0.87827	2.91	0.80722	D	1	D;P;P;P;P	0.61697	0.99;0.893;0.893;0.742;0.893	D;P;P;P;P	0.63283	0.913;0.732;0.732;0.732;0.732	D	0.93505	0.6848	10	0.87932	D	0	.	13.7947	0.63164	0.0:0.0:0.0:1.0	rs34321232	1628;1621;1628;1621;1628	B1PS43;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;MYH11_HUMAN;.;.;.	Q	1621;1621;1628;1628;1628	ENSP00000300036:K1621Q;ENSP00000345136:K1621Q;ENSP00000379616:K1628Q;ENSP00000407821:K1628Q	ENSP00000300036:K1621Q	K	-	1	0	MYH11	15721601	1.000000	0.71417	1.000000	0.80357	0.573000	0.36030	7.950000	0.87804	1.864000	0.54056	0.528000	0.53228	AAG	T|0.987;G|0.013	0.013	weak		0.577	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		G	15814100	T	G	15814100	3	3	26	1	0	0	0	0	1	0	0	0	10040	1792	62	5	1124	5	MYH11	16	15814100	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	702835	15814100	74540653	498	10261											
MYH11	4629	hgsc.bcm.edu	37	chr16	15818834	15818834	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcgttaagcatccctgtgaCgctctcaacttcattctaag	9	13	6	13	2	3	1	2	1	2	0	6	1	4	1	1	0	2	3	1	0	3	4	rs151058774		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:15818834C>T	ENST00000300036.5	-	29	3983	c.3874G>A	c.(3874-3876)Gtc>Atc	p.V1292I	MYH11_ENST00000396324.3_Missense_Mutation_p.V1299I|NDE1_ENST00000396354.1_3'UTR|MYH11_ENST00000576790.2_Missense_Mutation_p.V1292I|MYH11_ENST00000452625.2_Missense_Mutation_p.V1299I|NDE1_ENST00000342673.5_3'UTR|NDE1_ENST00000396355.1_3'UTR|AF001548.5_ENST00000574212.1_RNA|NDE1_ENST00000571896.1_3'UTR	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1292					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						ATCCCTGTGACGCTCTCAACT	0.542			T	CBFB	AML																																p.V1299I		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"myosin, heavy polypeptide 11, smooth muscle"		L	.	MYH11	520	.	0			c.G3895A						PASS	.						55	46	49					16																	15818834		2197	4300	6497	SO:0001583	missense	4629	exon30			CTGTGACGCTCTC	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.3874G>A	16.37:g.15818834C>T	ENSP00000300036:p.Val1292Ile	80	0	0		100	48	0.48	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	.	.	.	.	.	.	.	.	.	.	C	16.35	3.099342	0.56183	.	.	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	T;T;T;T	0.75367	-0.93;-0.93;-0.93;-0.93	5.17	5.17	0.71159	Myosin tail (1);	0.069264	0.56097	D	0.000021	T	0.73164	0.3552	L	0.45470	1.425	0.80722	D	1	B;B;B;B;B	0.28439	0.104;0.212;0.212;0.104;0.212	B;B;B;B;B	0.35312	0.2;0.103;0.103;0.103;0.146	T	0.72714	-0.4210	10	0.52906	T	0.07	.	17.6819	0.88246	0.0:1.0:0.0:0.0	.	1299;1292;1299;1292;1299	B1PS43;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;MYH11_HUMAN;.;.;.	I	1292;1292;1299;1299;1299	ENSP00000300036:V1292I;ENSP00000345136:V1292I;ENSP00000379616:V1299I;ENSP00000407821:V1299I	ENSP00000300036:V1292I	V	-	1	0	MYH11	15726335	1.000000	0.71417	1.000000	0.80357	0.694000	0.40290	7.818000	0.86416	2.409000	0.81822	0.650000	0.86243	GTC	C|0.999;G|0.001	.	alt		0.542	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113		T	15818834	C	T	15818834	3	4	26	1	0	0	0	0	1	0	0	0	10040	536	19	1	2131	1	MYH11	16	15818834	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	4734	15818834	74535919	499	10262											
DNAH3	55567	hgsc.bcm.edu	37	chr16	20948142	20948142	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctttgatggctcggccaagAttgatgaggctcctccgaac	8	10	11	12	2	0	4	0	3	0	1	3	5	2	4	4	3	1	2	4	3	2	2	rs140126023	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:20948142A>G	ENST00000261383.3	-	60	11687	c.11688T>C	c.(11686-11688)aaT>aaC	p.N3896N	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	3896					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)		CTCGGCCAAGATTGATGAGGC	0.562													A|||	2	0.000399361	0.0	0.0	5008	,	,		17157	0.0		0.001	False		,,,				2504	0.001				p.N3896N		Atlas-SNP	.											.	DNAH3	1142	.	0			c.T11688C						PASS	.	A		6,4396	11.4+/-27.6	0,6,2195	59	52	54		11688	2	0.6	16	dbSNP_134	54	29,8571	21.0+/-64.5	0,29,4271	no	coding-synonymous	DNAH3	NM_017539.1		0,35,6466	GG,GA,AA		0.3372,0.1363,0.2692		3896/4117	20948142	35,12967	2201	4300	6501	SO:0001819	synonymous_variant	55567	exon60			GCCAAGATTGATG	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.11688T>C	16.37:g.20948142A>G		39	0	0		47	15	0.319149	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	37	CCDS10594.1																																																																																			A|0.998;G|0.002	0.002	strong		0.562	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539		G	20948142	A	G	20948142	2	3	26	1	0	0	0	0	0	0	0	1	4605	330	12	3		3	DNAH3	16	20948142	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	5129308	20948142	69406611	500	10263											
CRYM	1428	hgsc.bcm.edu	37	chr16	21272648	21272648	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcacttctcccagctcagcAaagatctcggcctaggaaac	12	8	7	14	1	4	1	2	0	2	1	6	2	4	2	2	2	3	2	2	2	3	2	rs144588424	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:21272648A>G	ENST00000219599.3	-	9	1072	c.807T>C	c.(805-807)ttT>ttC	p.F269F	CRYM_ENST00000543948.1_Silent_p.F269F|CRYM_ENST00000415987.2_Silent_p.F227F|CRYM_ENST00000396023.2_Silent_p.F269F	NM_001888.3	NP_001879.1	Q14894	CRYM_HUMAN	crystallin, mu	269					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|sensory perception of sound (GO:0007605)|thyroid hormone metabolic process (GO:0042403)|thyroid hormone transport (GO:0070327)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|thiomorpholine-carboxylate dehydrogenase activity (GO:0047127)|thyroid hormone binding (GO:0070324)|transcription corepressor activity (GO:0003714)			large_intestine(1)|lung(3)	4				GBM - Glioblastoma multiforme(48;0.0573)		CCAGCTCAGCAAAGATCTCGG	0.507													A|||	9	0.00179712	0.0	0.0043	5008	,	,		17799	0.0		0.004	False		,,,				2504	0.002				p.F269F		Atlas-SNP	.											.	CRYM	13	.	0			c.T807C						PASS	.	A	,	3,4395	4.2+/-10.8	0,3,2196	114	94	101		681,807	-10.2	0.7	16	dbSNP_134	101	51,8549	33.3+/-86.6	1,49,4250	no	coding-synonymous,coding-synonymous	CRYM	NM_001014444.2,NM_001888.3	,	1,52,6446	GG,GA,AA		0.593,0.0682,0.4154	,	227/273,269/315	21272648	54,12944	2199	4300	6499	SO:0001819	synonymous_variant	1428	exon9			CTCAGCAAAGATC		CCDS10597.1	16p12.2	2013-02-14			ENSG00000103316	ENSG00000103316	1.5.1.25		2418	protein-coding gene	gene with protein product	"thiomorpholine-carboxylate dehydrogenase"	123740				1478656, 21332720	Standard	NM_001014444		Approved	DFNA40	uc002dim.3	Q14894	OTTHUMG00000090707	ENST00000219599.3:c.807T>C	16.37:g.21272648A>G		144	0	0		165	81	0.490909	NM_001888	D5MNX0|Q5HYB7	Silent	SNP	ENST00000219599.3	37	CCDS10597.1																																																																																			A|0.996;G|0.004	0.004	strong		0.507	CRYM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207398.1			G	21272648	A	G	21272648	2	3	26	1	0	0	0	0	0	0	0	1	3923	127	5	3		3	CRYM	16	21272648	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	324506	21272648	69082105	501	10264											
HS3ST4	9951	hgsc.bcm.edu	37	chr16	25704441	25704441	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagagccgcacttcttcgacAggaactacgaaaaggggttg	12	8	12	9	3	1	1	0	0	1	1	2	4	1	2	1	3	3	2	1	3	5	5			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:25704441A>G	ENST00000331351.5	+	1	1095	c.703A>G	c.(703-705)Agg>Ggg	p.R235G		NM_006040.2	NP_006031.2	Q9Y661	HS3S4_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	235	Substrate binding. {ECO:0000250}.				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)		CTTCTTCGACAGGAACTACGA	0.677																																					p.R235G		Atlas-SNP	.											.	HS3ST4	120	.	0			c.A703G						PASS	.						21	24	23					16																	25704441		1999	4138	6137	SO:0001583	missense	9951	exon1			TTCGACAGGAACT	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.703A>G	16.37:g.25704441A>G	ENSP00000330606:p.Arg235Gly	116	0	0		76	40	0.526316	NM_006040	Q5QI42|Q8NDC2	Missense_Mutation	SNP	ENST00000331351.5	37	CCDS53995.1	.	.	.	.	.	.	.	.	.	.	.	22.4	4.279999	0.80692	.	.	ENSG00000182601	ENST00000331351	T	0.54866	0.55	4.29	4.29	0.51040	Sulfotransferase domain (1);	0.103409	0.56097	D	0.000029	T	0.72526	0.3471	M	0.86178	2.8	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.76299	-0.3010	10	0.72032	D	0.01	.	10.165	0.42875	0.8331:0.1669:0.0:0.0	.	235	Q9Y661	HS3S4_HUMAN	G	235	ENSP00000330606:R235G	ENSP00000330606:R235G	R	+	1	2	HS3ST4	25611942	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.496000	0.45346	1.560000	0.49568	0.460000	0.39030	AGG	.	.	none		0.677	HS3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133286.2	NM_006040		G	25704441	A	G	25704441	3	3	26	1	0	0	0	0	1	0	0	0	7376	179	7	3	705	3	HS3ST4	16	25704441	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	4431793	25704441	64650312	502	10265											
KIAA0556	23247	hgsc.bcm.edu	37	chr16	27752099	27752099	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacaccaaggagagaccccaGagggcaaccaccaaagtcca	17	1	9	14	0	0	2	0	0	0	2	1	4	1	3	6	2	2	1	6	2	4	0			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:27752099G>T	ENST00000261588.4	+	15	2500	c.2481G>T	c.(2479-2481)caG>caT	p.Q827H		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	827						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						AGAGACCCCAGAGGGCAACCA	0.607																																					p.Q827H		Atlas-SNP	.											.	KIAA0556	348	.	0			c.G2481T						PASS	.						47	49	48					16																	27752099		2197	4300	6497	SO:0001583	missense	23247	exon15			ACCCCAGAGGGCA	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.2481G>T	16.37:g.27752099G>T	ENSP00000261588:p.Gln827His	59	0	0		79	38	0.481013	NM_015202	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	37	CCDS32415.1	.	.	.	.	.	.	.	.	.	.	G	12.03	1.817035	0.32145	.	.	ENSG00000047578	ENST00000261588	T	0.10960	2.82	5.15	-1.1	0.09872	.	0.718739	0.13839	N	0.359178	T	0.12092	0.0294	L	0.50333	1.59	0.09310	N	1	P	0.42649	0.786	P	0.47251	0.542	T	0.15350	-1.0440	10	0.41790	T	0.15	-18.0325	5.0513	0.14511	0.3084:0.4201:0.2715:0.0	.	827	O60303	K0556_HUMAN	H	827	ENSP00000261588:Q827H	ENSP00000261588:Q827H	Q	+	3	2	KIAA0556	27659600	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	0.385000	0.20685	-0.176000	0.10707	-0.305000	0.09177	CAG	.	.	none		0.607	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202		T	27752099	G	T	27752099	3	4	26	1	0	0	0	0	1	0	0	0	8192	933	33	4	2539	4	KIAA0556	16	27752099	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	2047658	27752099	62602654	503	10266											
ZNF768	79724	hgsc.bcm.edu	37	chr16	30536798	30536798	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgcggtgtagacagcagggcCcctgtgggcatctcaaaagg	9	7	15	10	1	1	1	1	0	1	1	2	1	1	1	2	4	2	3	2	4	3	1	rs138236969	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:30536798C>T	ENST00000380412.5	-	2	838	c.663G>A	c.(661-663)ggG>ggA	p.G221G	ZNF768_ENST00000562803.1_Silent_p.G190G	NM_024671.3	NP_078947.3	Q9H5H4	ZN768_HUMAN	zinc finger protein 768	221					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						ACAGCAGGGCCCCTGTGGGCA	0.642													C|||	11	0.00219649	0.0	0.0014	5008	,	,		14345	0.0		0.0099	False		,,,				2504	0.0				p.G221G		Atlas-SNP	.											.	ZNF768	28	.	0			c.G663A						PASS	.	C		7,4387	11.4+/-27.6	0,7,2190	65	70	68		663	2.2	1	16	dbSNP_134	68	77,8523	41.2+/-98.3	0,77,4223	no	coding-synonymous	ZNF768	NM_024671.3		0,84,6413	TT,TC,CC		0.8953,0.1593,0.6465		221/541	30536798	84,12910	2197	4300	6497	SO:0001819	synonymous_variant	79724	exon2			CAGGGCCCCTGTG	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.663G>A	16.37:g.30536798C>T		112	0	0		124	64	0.516129	NM_024671	Q569L7|Q96CX4	Silent	SNP	ENST00000380412.5	37	CCDS10681.2																																																																																			C|0.995;T|0.005	0.005	strong		0.642	ZNF768-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255522.2	NM_024671		T	30536798	C	T	30536798	2	4	26	1	0	0	0	0	0	0	0	1	18156	610	22	2		2	ZNF768	16	30536798	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	2784699	30536798	59817955	504	10267											
ZNF688	146542	hgsc.bcm.edu	37	chr16	30582855	30582855	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcctccggggagaagtacacGgccacgtccgcgaagctcac	9	5	12	15	5	1	1	1	0	0	1	4	3	4	1	4	3	2	2	4	3	3	1			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:30582855G>A	ENST00000223459.6	-	1	1200	c.96C>T	c.(94-96)gcC>gcT	p.A32A	AC002310.7_ENST00000486926.1_RNA|ZNF688_ENST00000395219.1_Intron|ZNF688_ENST00000563707.1_Silent_p.A32A|AC002310.7_ENST00000492040.1_RNA|ZNF688_ENST00000567855.1_Silent_p.A32A	NM_145271.3	NP_660314.1	P0C7X2	ZN688_HUMAN	zinc finger protein 688	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)			endometrium(3)|large_intestine(2)|lung(2)|ovary(1)	8						AGAAGTACACGGCCACGTCCG	0.741																																					p.A32A		Atlas-SNP	.											.	ZNF688	37	.	0			c.C96T						PASS	.						12	14	13					16																	30582855		2187	4293	6480	SO:0001819	synonymous_variant	146542	exon1			GTACACGGCCACG	AK122680	CCDS10684.1	16p11.2	2013-01-08			ENSG00000229809	ENSG00000229809		"Zinc fingers, C2H2-type", "-"	30489	protein-coding gene	gene with protein product						10493829	Standard	XM_005255139		Approved		uc002dys.2	P0C7X2	OTTHUMG00000132408	ENST00000223459.6:c.96C>T	16.37:g.30582855G>A		109	0	0		103	41	0.398058	NM_145271	A8MV39|B3KV51|O75701|Q8IW91|Q8WV14|Q96MN0	Silent	SNP	ENST00000223459.6	37	CCDS10684.1																																																																																			.	.	none		0.741	ZNF688-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255544.2	NM_145271		A	30582855	G	A	30582855	2	1	26	1	0	0	0	0	0	0	0	1	18108	1103	39	1		1	ZNF688	16	30582855	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	46057	30582855	59771898	505	10268											
PRSS53	339105	hgsc.bcm.edu	37	chr16	31097689	31097689	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cctgcaccccaggctgggggCccccacatagcatcccaggc	7	4	11	19	0	0	0	0	0	0	0	1	0	1	0	6	4	2	3	6	4	1	1			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:31097689C>T	ENST00000280606.6	-	5	785	c.632G>A	c.(631-633)gGc>gAc	p.G211D		NM_001039503.2	NP_001034592.1	Q2L4Q9	PRS53_HUMAN	protease, serine, 53	211	Peptidase S1 1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			large_intestine(1)|lung(3)	4						AGGCTGGGGGCCCCCACATAG	0.642																																					p.G211D		Atlas-SNP	.											.	PRSS53	29	.	0			c.G632A						PASS	.						42	48	46					16																	31097689		1877	4102	5979	SO:0001583	missense	339105	exon5			TGGGGGCCCCCAC		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.632G>A	16.37:g.31097689C>T	ENSP00000280606:p.Gly211Asp	63	0	0		100	39	0.39	NM_001039503		Missense_Mutation	SNP	ENST00000280606.6	37	CCDS42153.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.109734	0.77096	.	.	ENSG00000151006	ENST00000280606	D	0.90133	-2.62	5.77	5.77	0.91146	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.36778	U	0.002401	D	0.95385	0.8502	M	0.84773	2.715	0.53688	D	0.999979	D	0.89917	1.0	D	0.97110	1.0	D	0.95533	0.8605	10	0.87932	D	0	.	13.1188	0.59314	0.0:0.8394:0.1606:0.0	.	211	Q2L4Q9	PRS53_HUMAN	D	211	ENSP00000280606:G211D	ENSP00000280606:G211D	G	-	2	0	PRSS53	31005190	0.992000	0.36948	1.000000	0.80357	0.946000	0.59487	3.137000	0.50562	2.723000	0.93209	0.655000	0.94253	GGC	.	.	none		0.642	PRSS53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108580.4	NM_001081268		T	31097689	C	T	31097689	3	4	26	1	0	0	0	0	1	0	0	0	12644	739	26	2	1057	2	PRSS53	16	31097689	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	514834	31097689	59257064	506	10269											
RPGRIP1L	23322	hgsc.bcm.edu	37	chr16	53639448	53639448	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgaaacatgtcggcaaggtcGacgtgagccacgccaatgtc	11	7	12	11	4	0	2	0	2	0	0	3	3	0	2	2	2	2	1	2	2	3	0	rs144924117		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:53639448G>A	ENST00000379925.3	-	26	3830	c.3780C>T	c.(3778-3780)gtC>gtT	p.V1260V	RPGRIP1L_ENST00000563746.1_Silent_p.V1226V|RPGRIP1L_ENST00000262135.4_Silent_p.V1180V|RPGRIP1L_ENST00000564374.1_Silent_p.V1214V	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	1260					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)				CGGCAAGGTCGACGTGAGCCA	0.532													G|||	1	0.000199681	0.0	0.0	5008	,	,		18112	0.0		0.001	False		,,,				2504	0.0				p.V1260V		Atlas-SNP	.											.	RPGRIP1L	118	.	0			c.C3780T						PASS	.	G	,	2,4394	4.2+/-10.8	0,2,2196	181	134	150		3540,3780	-7.5	0	16	dbSNP_134	150	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous,coding-synonymous	RPGRIP1L	NM_001127897.1,NM_015272.2	,	0,9,6489	AA,AG,GG		0.0814,0.0455,0.0693	,	1180/1236,1260/1316	53639448	9,12987	2198	4300	6498	SO:0001819	synonymous_variant	23322	exon26			AAGGTCGACGTGA		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.3780C>T	16.37:g.53639448G>A		86	0	0		105	65	0.619048	NM_015272	A0PJ88|Q9Y2K8	Silent	SNP	ENST00000379925.3	37	CCDS32447.1																																																																																			G|1.000;A|0.000	0.000	strong		0.532	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272		A	53639448	G	A	53639448	2	1	26	1	0	0	0	0	0	0	0	1	13565	1045	37	1		1	RPGRIP1L	16	53639448	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	22541759	53639448	36715305	507	10270											
B3GNT9	80262	hgsc.bcm.edu	37	chr16	67183867	67183867	+	IGR	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggcgcgccagtgggttcgCgcgccctccccaacttcgtc	4	7	13	17	6	0	0	0	0	0	0	4	0	1	0	4	2	1	1	4	2	1	2			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:67183867C>T	ENST00000219139.3	+	0	2865				B3GNT9_ENST00000449549.3_Silent_p.A174A	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)		AGTGGGTTCGCGCGCCCTCCC	0.701																																					p.A174A		Atlas-SNP	.											B3GNT9,NS,carcinoma,-1,1	B3GNT9	25	1	0			c.G522A						scavenged	.						14	15	14					16																	67183867		1889	4052	5941	SO:0001628	intergenic_variant	84752	exon2			GGTTCGCGCGCCC	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		16.37:g.67183867C>T		25	0	0		25	16	0.64	NM_033309	Q9HA86	Silent	SNP	ENST00000219139.3	37	CCDS10828.1																																																																																			.	.	none		0.701	C16orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268829.2	NM_025187		T	67183867	C	T	67183867	1	4	26	0	1	0	0	0	0	0	0	0	1264	755	27	1		1	B3GNT9	16	67183867	IGR	SNP	C	TCGA-G8-6907-01A-11D-2210-10	13544419	67183867	23170886	508	10271											
PLA2G15	23659	hgsc.bcm.edu	37	chr16	68289739	68289739	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	taccagctgtatgggggcccCgtggtgctggttgcccacag	5	9	15	12	1	0	0	0	0	0	0	0	0	0	0	4	4	4	4	4	4	2	3	rs76404867	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:68289739C>T	ENST00000219345.5	+	5	656	c.573C>T	c.(571-573)ccC>ccT	p.P191P	PLA2G15_ENST00000566188.1_Intron|RP11-96D1.7_ENST00000563175.1_RNA|PLA2G15_ENST00000444212.2_Intron|RP11-96D1.7_ENST00000569843.1_RNA|PLA2G15_ENST00000413021.2_Intron	NM_012320.3	NP_036452.1	Q8NCC3	PAG15_HUMAN	phospholipase A2, group XV	191					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						ATGGGGGCCCCGTGGTGCTGG	0.607													C|||	22	0.00439297	0.0015	0.0043	5008	,	,		18228	0.0		0.0169	False		,,,				2504	0.0				p.P191P		Atlas-SNP	.											.	PLA2G15	30	.	0			c.C573T						PASS	.	C		18,4378	24.3+/-50.5	0,18,2180	49	53	52		573	-8	0.6	16	dbSNP_132	52	173,8427	79.8+/-142.4	2,169,4129	yes	coding-synonymous	PLA2G15	NM_012320.3		2,187,6309	TT,TC,CC		2.0116,0.4095,1.4697		191/413	68289739	191,12805	2198	4300	6498	SO:0001819	synonymous_variant	23659	exon5			GGGCCCCGTGGTG	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.573C>T	16.37:g.68289739C>T		120	0	0		168	85	0.505952	NM_012320	B3KMF3|B4DUD1|Q53GZ1|Q9NPQ6|Q9UG04|Q9Y2B3	Silent	SNP	ENST00000219345.5	37	CCDS10864.1																																																																																			C|0.987;T|0.013	0.013	strong		0.607	PLA2G15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268888.2	NM_012320		T	68289739	C	T	68289739	2	4	26	1	0	0	0	0	0	0	0	1	12001	639	23	1		1	PLA2G15	16	68289739	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1105872	68289739	22065014	509	10272											
ZFHX3	463	hgsc.bcm.edu	37	chr16	72992547	72992547	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cctgtcctccagttcctcatCcaactcgcttggaaagagtc	8	11	7	15	1	1	1	1	0	0	1	7	2	5	2	5	1	1	2	5	1	2	2			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:72992547C>A	ENST00000268489.5	-	2	2170	c.1498G>T	c.(1498-1500)Gat>Tat	p.D500Y	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	500					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)				AGTTCCTCATCCAACTCGCTT	0.552																																					p.D500Y		Atlas-SNP	.											ZFHX3,NS,carcinoma,+1,1	ZFHX3	404	1	0			c.G1498T						PASS	.						82	87	85					16																	72992547		2198	4300	6498	SO:0001583	missense	463	exon2			CCTCATCCAACTC	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.1498G>T	16.37:g.72992547C>A	ENSP00000268489:p.Asp500Tyr	76	0	0		90	44	0.488889	NM_006885	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	37	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	C	5.812	0.334030	0.11013	.	.	ENSG00000140836	ENST00000268489	T	0.78246	-1.16	5.01	5.01	0.66863	.	0.250248	0.27513	N	0.019037	T	0.60728	0.2291	N	0.08118	0	0.80722	D	1	P	0.34462	0.454	B	0.24974	0.057	T	0.67432	-0.5672	10	0.72032	D	0.01	.	18.6828	0.91553	0.0:1.0:0.0:0.0	.	500	Q15911	ZFHX3_HUMAN	Y	500	ENSP00000268489:D500Y	ENSP00000268489:D500Y	D	-	1	0	ZFHX3	71550048	1.000000	0.71417	0.991000	0.47740	0.641000	0.38312	1.580000	0.36547	2.487000	0.83934	0.650000	0.86243	GAT	.	.	none		0.552	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		A	72992547	C	A	72992547	3	1	26	1	0	0	0	0	1	0	0	0	17649	855	30	4	9649	4	ZFHX3	16	72992547	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	4702808	72992547	17362206	510	10273											
ZFHX3	463	hgsc.bcm.edu	37	chr16	72992626	72992626	+	Silent	SNP	C	C	T																															tcctcttcttcctcctcctcCtccgcctcttcctcctcctc																										TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:72992626C>T	ENST00000268489.5	-	2	2091	c.1419G>A	c.(1417-1419)gaG>gaA	p.E473E	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	473	Poly-Glu.				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)				cctcctcctcctccgcctctt	0.577																																					p.E473E		Atlas-SNP	.											.	ZFHX3	404	.	0			c.G1419A						PASS	.						41	44	43					16																	72992626		2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			CTCCTCCTCCGCC	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.1419G>A	16.37:g.72992626C>T		38	0	0		57	9	0.157895	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			.	.	none		0.577	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		T	72992626	C	T	72992626	2	4	26	1	0	0	0	0	0	0	0	1	17649	680	24	2		2	ZFHX3	16	72992626	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	79	72992626	17362127	511	10274	127	3									
ZFHX3	463	hgsc.bcm.edu	37	chr16	72992629	72992629	+	Silent	SNP	C	C	T																															tcttcttcctcctcctcctcCgcctcttcctcctcctcttc																										TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:72992629C>T	ENST00000268489.5	-	2	2088	c.1416G>A	c.(1414-1416)gcG>gcA	p.A472A	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	472	Poly-Glu.				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)				cctcctcctccgcctcttcct	0.572																																					p.A472A		Atlas-SNP	.											.	ZFHX3	404	.	0			c.G1416A						PASS	.						39	43	42					16																	72992629		2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			CTCCTCCGCCTCT	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.1416G>A	16.37:g.72992629C>T		36	0	0		53	5	0.0943396	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			.	.	none		0.572	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		T	72992629	C	T	72992629	2	4	26	1	0	0	0	0	0	0	0	1	17649	639	23	1		1	ZFHX3	16	72992629	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	3	72992629	17362124	512	10275	127	3									
ZFHX3	463	hgsc.bcm.edu	37	chr16	72992630	72992630	+	Missense_Mutation	SNP	G	G	T																															cttcttcctcctcctcctccGcctcttcctcctcctcttcc																										TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:72992630G>T	ENST00000268489.5	-	2	2087	c.1415C>A	c.(1414-1416)gCg>gAg	p.A472E	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	472	Poly-Glu.				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)				ctcctcctccgcctcttcctc	0.577																																					p.A472E		Atlas-SNP	.											.	ZFHX3	404	.	0			c.C1415A						PASS	.						38	42	41					16																	72992630		2198	4300	6498	SO:0001583	missense	463	exon2			TCCTCCGCCTCTT	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.1415C>A	16.37:g.72992630G>T	ENSP00000268489:p.Ala472Glu	36	0	0		53	8	0.150943	NM_006885	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	37	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	G	0.252	-1.005988	0.02112	.	.	ENSG00000140836	ENST00000268489	T	0.73258	-0.73	4.63	-9.25	0.00666	.	1.213240	0.06591	N	0.751946	T	0.34048	0.0884	N	0.08118	0	0.54753	D	0.999985	B	0.23490	0.086	B	0.14023	0.01	T	0.29912	-0.9996	10	0.02654	T	1	.	3.1253	0.06405	0.2364:0.0793:0.1273:0.5569	.	472	Q15911	ZFHX3_HUMAN	E	472	ENSP00000268489:A472E	ENSP00000268489:A472E	A	-	2	0	ZFHX3	71550131	0.000000	0.05858	0.020000	0.16555	0.258000	0.26162	-0.323000	0.07997	-1.925000	0.01063	-0.759000	0.03464	GCG	.	.	none		0.577	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		T	72992630	G	T	72992630	3	4	26	1	0	0	0	0	1	0	0	0	17649	1087	38	4	9732	4	ZFHX3	16	72992630	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1	72992630	17362123	513	10276	127	3									
PLCG2	5336	hgsc.bcm.edu	37	chr16	81942028	81942028	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctttgcggcccaggatatacCccctacagaactacattttg	10	11	7	13	1	0	1	0	0	0	1	0	2	0	2	3	2	5	0	3	2	5	7	rs72824905	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:81942028C>G	ENST00000359376.3	+	17	1779	c.1565C>G	c.(1564-1566)cCc>cGc	p.P522R		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	522					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						CAGGATATACCCCCTACAGAA	0.537													C|||	14	0.00279553	0.0	0.0029	5008	,	,		20275	0.0		0.0109	False		,,,				2504	0.001				p.P522R		Atlas-SNP	.											.	PLCG2	276	.	0			c.C1565G						PASS	.	C	ARG/PRO	3,3799		0,3,1898	56	56	56		1565	4.8	1	16	dbSNP_130	56	73,8147		0,73,4037	yes	missense	PLCG2	NM_002661.3	103	0,76,5935	GG,GC,CC		0.8881,0.0789,0.6322	benign	522/1266	81942028	76,11946	1901	4110	6011	SO:0001583	missense	5336	exon17			ATATACCCCCTAC		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.1565C>G	16.37:g.81942028C>G	ENSP00000352336:p.Pro522Arg	59	0	0		61	21	0.344262	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	37	CCDS42204.1	10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	C	6.031	0.373996	0.11409	7.89E-4	0.008881	ENSG00000197943	ENST00000359376	T	0.65364	-0.15	4.85	4.85	0.62838	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (1);SH2 motif (1);	0.750593	0.12934	N	0.427117	T	0.36248	0.0960	N	0.12182	0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.25710	-1.0124	10	0.49607	T	0.09	.	11.0904	0.48113	0.2379:0.7621:0.0:0.0	.	389;522	B4E3H3;P16885	.;PLCG2_HUMAN	R	522	ENSP00000352336:P522R	ENSP00000352336:P522R	P	+	2	0	PLCG2	80499529	0.014000	0.17966	0.979000	0.43373	0.335000	0.28730	2.624000	0.46444	2.249000	0.74217	0.655000	0.94253	CCC	C|0.993;G|0.007	0.007	strong		0.537	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1			G	81942028	C	G	81942028	3	3	26	1	0	0	0	0	1	0	0	0	12045	623	22	4	1627	4	PLCG2	16	81942028	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	8949398	81942028	8412725	514	10277											
PLCG2	5336	hgsc.bcm.edu	37	chr16	81990441	81990441	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggttaaagagttcagtgttAatgagaaccagctccagctg	12	11	11	7	0	1	2	1	1	0	2	2	3	2	2	2	1	3	5	2	1	4	3			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:81990441A>T	ENST00000359376.3	+	32	3926	c.3712A>T	c.(3712-3714)Aat>Tat	p.N1238Y		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	1238					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						GTTCAGTGTTAATGAGAACCA	0.512																																					p.N1238Y		Atlas-SNP	.											.	PLCG2	276	.	0			c.A3712T						PASS	.						99	100	100					16																	81990441		1953	4145	6098	SO:0001583	missense	5336	exon32			AGTGTTAATGAGA		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.3712A>T	16.37:g.81990441A>T	ENSP00000352336:p.Asn1238Tyr	52	0	0		84	34	0.404762	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	37	CCDS42204.1	.	.	.	.	.	.	.	.	.	.	A	18.00	3.525302	0.64747	.	.	ENSG00000197943	ENST00000359376	T	0.67171	-0.25	5.49	5.49	0.81192	.	0.250471	0.46758	D	0.000266	T	0.71082	0.3298	L	0.36672	1.1	0.52099	D	0.999942	D	0.67145	0.996	P	0.59703	0.862	T	0.74414	-0.3673	10	0.72032	D	0.01	.	13.83	0.63375	1.0:0.0:0.0:0.0	.	1238	P16885	PLCG2_HUMAN	Y	1238	ENSP00000352336:N1238Y	ENSP00000352336:N1238Y	N	+	1	0	PLCG2	80547942	1.000000	0.71417	0.990000	0.47175	0.448000	0.32197	6.593000	0.74100	2.078000	0.62432	0.413000	0.27773	AAT	.	.	none		0.512	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1			T	81990441	A	T	81990441	3	4	26	1	0	0	0	0	1	0	0	0	12045	362	13	5	3834	5	PLCG2	16	81990441	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	48413	81990441	8364312	515	10278											
GALNS	2588	hgsc.bcm.edu	37	chr16	88893122	88893122	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaccaacctgtccatcagcCggccctgcaggagggtgggg	7	5	15	14	1	1	0	1	0	0	0	2	1	2	1	5	5	3	2	5	5	1	0	rs150734270	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:88893122C>T	ENST00000268695.5	-	10	1215	c.1127G>A	c.(1126-1128)cGg>cAg	p.R376Q	AC092384.1_ENST00000593752.1_5'Flank|GALNS_ENST00000542788.1_Missense_Mutation_p.R301Q	NM_000512.4	NP_000503.1	P34059	GALNS_HUMAN	galactosamine (N-acetyl)-6-sulfatase	376	Catalytic domain.		R -> Q (in MPS4A; severe form; dbSNP:rs150734270). {ECO:0000269|PubMed:9521421}.		carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	metal ion binding (GO:0046872)|N-acetylgalactosamine-4-sulfatase activity (GO:0003943)|N-acetylgalactosamine-6-sulfatase activity (GO:0043890)|sulfuric ester hydrolase activity (GO:0008484)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(8)	22				BRCA - Breast invasive adenocarcinoma(80;0.0496)		GTCCATCAGCCGGCCCTGCAG	0.662													C|||	7	0.00139776	0.0	0.0029	5008	,	,		14448	0.0		0.005	False		,,,				2504	0.0				p.R376Q	GBM(129;1929 2344 25209 33204)	Atlas-SNP	.											GALNS,bladder,carcinoma,0,1	GALNS	37	1	0			c.G1127A	GRCh37	CM980820	GALNS	M	rs150734270	PASS	.	C	GLN/ARG	1,4393	2.1+/-5.4	0,1,2196	28	29	28		1127	-2.8	0.2	16	dbSNP_134	28	16,8584	10.5+/-38.8	0,16,4284	yes	missense	GALNS	NM_000512.4	43	0,17,6480	TT,TC,CC		0.186,0.0228,0.1308	benign	376/523	88893122	17,12977	2197	4300	6497	SO:0001583	missense	2588	exon10			ATCAGCCGGCCCT	D17629	CCDS10970.1	16q24.3	2014-07-03	2014-07-03		ENSG00000141012	ENSG00000141012	3.1.6.4	"Arylsulfatase family"	4122	protein-coding gene	gene with protein product	"Morquio syndrome", "mucopolysaccharidosis type IVA"	612222	"galactosamine (N-acetyl)-6-sulfate sulfatase"			1755850	Standard	NM_000512		Approved	GAS, GALNAC6S	uc002fly.4	P34059	OTTHUMG00000137862	ENST00000268695.5:c.1127G>A	16.37:g.88893122C>T	ENSP00000268695:p.Arg376Gln	113	0	0		135	70	0.518519	NM_000512	Q86VK3	Missense_Mutation	SNP	ENST00000268695.5	37	CCDS10970.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	6.207	0.406403	0.11754	2.28E-4	0.00186	ENSG00000141012	ENST00000268695;ENST00000542788	D;D	0.93488	-3.23;-3.23	5.43	-2.81	0.05805	Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.908483	0.09491	N	0.794912	T	0.80358	0.4608	N	0.12853	0.265	0.09310	N	1	B;B	0.18310	0.007;0.027	B;B	0.08055	0.003;0.003	T	0.66064	-0.6016	10	0.31617	T	0.26	.	12.0153	0.53311	0.0:0.2983:0.0:0.7017	.	376;376	B2R6P1;P34059	.;GALNS_HUMAN	Q	376;301	ENSP00000268695:R376Q;ENSP00000438197:R301Q	ENSP00000268695:R376Q	R	-	2	0	GALNS	87420623	0.004000	0.15560	0.161000	0.22692	0.072000	0.16883	-0.448000	0.06820	-0.733000	0.04850	-0.755000	0.03482	CGG	C|0.999;T|0.001	0.001	strong		0.662	GALNS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269543.1			T	88893122	C	T	88893122	3	4	26	1	0	0	0	0	1	0	0	0	6214	652	23	1	461	1	GALNS	16	88893122	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	6902681	88893122	1461631	516	10279											
CDH15	1013	hgsc.bcm.edu	37	chr16	89245884	89245884	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaccaccctgtacccctggCgccgggcgcctgccctgagc	4	5	11	21	3	0	1	0	1	0	0	0	1	0	1	8	2	3	1	8	2	1	1			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:89245884C>T	ENST00000289746.2	+	2	168	c.103C>T	c.(103-105)Cgc>Tgc	p.R35C	CDH15_ENST00000521087.1_3'UTR	NM_004933.2	NP_004924.1	P55291	CAD15_HUMAN	cadherin 15, type 1, M-cadherin (myotubule)	35					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)		GTACCCCTGGCGCCGGGCGCC	0.657																																					p.R35C		Atlas-SNP	.											CDH15,NS,carcinoma,-1,2	CDH15	54	2	0			c.C103T						PASS	.						83	82	82					16																	89245884		2198	4300	6498	SO:0001583	missense	1013	exon2			CCCTGGCGCCGGG	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.103C>T	16.37:g.89245884C>T	ENSP00000289746:p.Arg35Cys	125	0	0		147	82	0.557823	NM_004933		Missense_Mutation	SNP	ENST00000289746.2	37	CCDS10976.1	.	.	.	.	.	.	.	.	.	.	C	15.04	2.713980	0.48622	.	.	ENSG00000129910	ENST00000289746	T	0.58940	0.3	4.58	3.57	0.40892	.	0.454073	0.15889	N	0.239671	T	0.49643	0.1569	N	0.14661	0.345	0.58432	D	0.999997	D	0.69078	0.997	P	0.52343	0.696	T	0.54655	-0.8261	10	0.66056	D	0.02	.	11.1776	0.48610	0.1834:0.8166:0.0:0.0	.	35	P55291	CAD15_HUMAN	C	35	ENSP00000289746:R35C	ENSP00000289746:R35C	R	+	1	0	CDH15	87773385	0.038000	0.19896	0.916000	0.36221	0.077000	0.17291	0.119000	0.15626	2.104000	0.64026	0.407000	0.27541	CGC	.	.	none		0.657	CDH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269920.1	NM_004933		T	89245884	C	T	89245884	3	4	26	1	0	0	0	0	1	0	0	0	3102	768	27	1	109	1	CDH15	16	89245884	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	352762	89245884	1108869	517	10280											
SLC43A2	124935	hgsc.bcm.edu	37	chr17	1479963	1479963	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgcagaagggcgaagagcgcGctgatcagagactgcagtcc	11	5	15	10	3	1	4	1	1	0	3	2	6	2	4	1	1	3	3	1	1	2	0	rs142934102		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1479963G>A	ENST00000301335.5	-	13	1564	c.1476C>T	c.(1474-1476)agC>agT	p.S492S	SLC43A2_ENST00000571650.1_Silent_p.S496S|SLC43A2_ENST00000382147.4_Silent_p.S496S|SLC43A2_ENST00000412517.3_Silent_p.S355S	NM_001284498.1|NM_001284499.1	NP_001271427.1|NP_001271428.1	Q8N370	LAT4_HUMAN	solute carrier family 43 (amino acid system L transporter), member 2	492					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-amino acid transmembrane transporter activity (GO:0015179)			endometrium(4)|large_intestine(4)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0883)		CGAAGAGCGCGCTGATCAGAG	0.637													G|||	1	0.000199681	0.0	0.0	5008	,	,		14140	0.0		0.001	False		,,,				2504	0.0				p.S492S		Atlas-SNP	.											.	SLC43A2	37	.	0			c.C1476T						PASS	.	G		0,4406		0,0,2203	46	44	45		1476	-10	0.1	17	dbSNP_134	45	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	SLC43A2	NM_152346.1		0,6,6497	AA,AG,GG		0.0698,0.0,0.0461		492/570	1479963	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	124935	exon13			GAGCGCGCTGATC	BC027923	CCDS11006.1, CCDS67107.1, CCDS67108.1	17p13.3	2013-07-17	2013-07-17		ENSG00000167703	ENSG00000167703		"Solute carriers"	23087	protein-coding gene	gene with protein product		610791				23268354	Standard	NM_001284498		Approved	MGC34680	uc002fsv.3	Q8N370	OTTHUMG00000090345	ENST00000301335.5:c.1476C>T	17.37:g.1479963G>A		36	0	0		25	14	0.56	NM_152346	B7Z6X9|C9JNU8|D3DTH9|Q5CD75|Q6IPM1|Q8NBX1|Q8NC21|Q8WZ00	Silent	SNP	ENST00000301335.5	37	CCDS11006.1																																																																																			G|1.000;A|0.000	0.000	weak		0.637	SLC43A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206717.4	NM_152346		A	1479963	G	A	1479963	2	1	26	1	0	0	0	0	0	0	0	1	14648	1078	38	1		1	SLC43A2	17	1479963	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10		1479963	79715247	518	10281											
WDR81	124997	hgsc.bcm.edu	37	chr17	1634183	1634183	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcctcctccacatcgccCgcctgtatggggagcctgtc	4	9	11	17	2	0	0	0	0	0	0	4	1	2	1	6	2	2	2	6	2	1	1	rs375054918		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1634183C>T	ENST00000409644.1	+	3	3910	c.3910C>T	c.(3910-3912)Cgc>Tgc	p.R1304C	WDR81_ENST00000309182.5_Missense_Mutation_p.R253C|WDR81_ENST00000545662.1_5'UTR|WDR81_ENST00000446363.1_5'UTR|WDR81_ENST00000419248.1_Missense_Mutation_p.R77C|WDR81_ENST00000437219.2_Missense_Mutation_p.R101C|RP11-961A15.1_ENST00000576540.1_RNA	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1304					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)		CCACATCGCCCGCCTGTATGG	0.652																																					p.R1304C		Atlas-SNP	.											.	WDR81	180	.	0			c.C3910T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	0,4406		0,0,2203	68	68	68		757,229,3910,301	-0.5	1	17		68	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	WDR81	NM_152348.3,NM_001163811.1,NM_001163809.1,NM_001163673.1	180,180,180,180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign,benign	253/891,77/715,1304/1942,101/739	1634183	1,13005	2203	4300	6503	SO:0001583	missense	124997	exon3			ATCGCCCGCCTGT	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.3910C>T	17.37:g.1634183C>T	ENSP00000386609:p.Arg1304Cys	98	0	0		117	49	0.418803	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Missense_Mutation	SNP	ENST00000409644.1	37	CCDS54062.1	.	.	.	.	.	.	.	.	.	.	C	13.13	2.146331	0.37923	0.0	1.16E-4	ENSG00000167716	ENST00000455636;ENST00000437219;ENST00000309182;ENST00000419248;ENST00000409644	T;T;T;T	0.50813	2.45;2.45;2.45;0.73	5.69	-0.476	0.12100	.	0.474665	0.24649	N	0.036728	T	0.19967	0.0480	N	0.02011	-0.69	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	0.04840	-1.0923	10	0.38643	T	0.18	.	12.3797	0.55299	0.0:0.5955:0.0:0.4045	.	101;431;253	B7Z579;Q8TEL1;Q562E7	.;.;WDR81_HUMAN	C	101;101;253;77;1304	ENSP00000391074:R101C;ENSP00000312074:R253C;ENSP00000407845:R77C;ENSP00000386609:R1304C	ENSP00000312074:R253C	R	+	1	0	WDR81	1580933	0.804000	0.28969	0.983000	0.44433	0.645000	0.38454	1.280000	0.33202	0.064000	0.16427	0.655000	0.94253	CGC	.	.	weak		0.652	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348		T	1634183	C	T	1634183	3	4	26	1	0	0	0	0	1	0	0	0	17345	652	23	1	3982	1	WDR81	17	1634183	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	154220	1634183	79561027	519	10282											
WDR81	124997	hgsc.bcm.edu	37	chr17	1636950	1636950	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	caccatgcccggcaccgggcCcgagtgggacccccatggtg	6	4	14	17	3	0	0	0	0	0	0	0	2	0	1	6	4	1	1	6	4	0	0	rs11657394	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1636950C>A	ENST00000409644.1	+	7	4619	c.4619C>A	c.(4618-4620)cCc>cAc	p.P1540H	WDR81_ENST00000309182.5_Missense_Mutation_p.P489H|WDR81_ENST00000545662.1_Missense_Mutation_p.P171H|WDR81_ENST00000446363.1_Missense_Mutation_p.P179H|WDR81_ENST00000419248.1_Missense_Mutation_p.P313H|WDR81_ENST00000437219.2_Missense_Mutation_p.P337H|RP11-961A15.1_ENST00000576540.1_RNA	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1540				P -> H (in Ref. 1; BAB84937). {ECO:0000305}.	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)		GGCACCGGGCCCGAGTGGGAC	0.677													C|||	165	0.0329473	0.0295	0.0331	5008	,	,		15625	0.0		0.0716	False		,,,				2504	0.0317				p.P1540H		Atlas-SNP	.											.	WDR81	180	.	0			c.C4619A						PASS	.	C	HIS/PRO,HIS/PRO,HIS/PRO,HIS/PRO	170,4230		6,158,2036	27	31	30		1010,4619,938,1466	3	0.4	17	dbSNP_120	30	646,7940		23,600,3670	yes	missense,missense,missense,missense	WDR81	NM_001163673.1,NM_001163809.1,NM_001163811.1,NM_152348.3	77,77,77,77	29,758,5706	AA,AC,CC		7.5239,3.8636,6.2837	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	337/739,1540/1942,313/715,489/891	1636950	816,12170	2200	4293	6493	SO:0001583	missense	124997	exon7			CCGGGCCCGAGTG	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.4619C>A	17.37:g.1636950C>A	ENSP00000386609:p.Pro1540His	111	0	0		74	42	0.567568	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Missense_Mutation	SNP	ENST00000409644.1	37	CCDS54062.1	80	0.03663003663003663	18	0.036585365853658534	10	0.027624309392265192	0	0.0	52	0.06860158311345646	C	9.979	1.227684	0.22542	0.038636	0.075239	ENSG00000167716	ENST00000437219;ENST00000309182;ENST00000446363;ENST00000419248;ENST00000418841;ENST00000409644;ENST00000354680;ENST00000545662	T;T;T;T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32;-1.32;-1.32;-1.32	4.99	2.99	0.34606	.	0.416547	0.23768	N	0.044749	T	0.12050	0.0293	L	0.38531	1.155	0.09310	N	0.999998	P;P;P	0.39624	0.681;0.681;0.681	B;B;B	0.39971	0.315;0.315;0.215	T	0.10800	-1.0614	9	.	.	.	.	8.0582	0.30617	0.0:0.7513:0.0:0.2487	rs11657394	171;337;489	B7Z6V3;B7Z579;Q562E7	.;.;WDR81_HUMAN	H	337;489;179;313;125;1540;291;171	ENSP00000391074:P337H;ENSP00000312074:P489H;ENSP00000401560:P179H;ENSP00000407845:P313H;ENSP00000395198:P125H;ENSP00000386609:P1540H;ENSP00000442726:P171H	.	P	+	2	0	WDR81	1583700	0.000000	0.05858	0.424000	0.26647	0.467000	0.32768	0.449000	0.21744	0.519000	0.28406	0.563000	0.77884	CCC	C|0.946;A|0.054	0.054	strong		0.677	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348		A	1636950	C	A	1636950	3	1	26	1	0	0	0	0	1	0	0	0	17345	623	22	4	4707	4	WDR81	17	1636950	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	2767	1636950	79558260	520	10283											
SMYD4	114826	hgsc.bcm.edu	37	chr17	1704297	1704297	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atacccatgtgtctgtgctcTgttaatgtctttaagacacg	9	15	8	9	1	3	1	0	0	3	1	3	1	3	1	1	0	2	2	1	0	3	4			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1704297T>C	ENST00000305513.7	-	5	558	c.391A>G	c.(391-393)Aga>Gga	p.R131G		NM_052928.2	NP_443160.2	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	131			R -> I (in dbSNP:rs7224496). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.				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						GTCTGTGCTCTGTTAATGTCT	0.428																																					p.R131G		Atlas-SNP	.											.	SMYD4	50	.	0			c.A391G						PASS	.						131	132	132					17																	1704297		2203	4300	6503	SO:0001583	missense	114826	exon5			GTGCTCTGTTAAT	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.391A>G	17.37:g.1704297T>C	ENSP00000304360:p.Arg131Gly	97	0	0		109	48	0.440367	NM_052928	Q8N1P2|Q8NAT0|Q96LV4|Q96PV2	Missense_Mutation	SNP	ENST00000305513.7	37	CCDS11013.1	.	.	.	.	.	.	.	.	.	.	T	12.27	1.887796	0.33348	.	.	ENSG00000186532	ENST00000305513	T	0.19532	2.14	5.98	4.88	0.63580	Tetratricopeptide-like helical (1);	0.518027	0.24193	N	0.040700	T	0.45935	0.1367	M	0.90705	3.14	0.35409	D	0.792262	D	0.63880	0.993	P	0.62184	0.899	T	0.59762	-0.7393	10	0.34782	T	0.22	-5.7323	7.6552	0.28371	0.0:0.0712:0.1398:0.7889	.	131	Q8IYR2	SMYD4_HUMAN	G	131	ENSP00000304360:R131G	ENSP00000304360:R131G	R	-	1	2	SMYD4	1651047	0.997000	0.39634	0.826000	0.32828	0.064000	0.16182	3.040000	0.49799	1.038000	0.40049	0.528000	0.53228	AGA	.	.	none		0.428	SMYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207108.4	XM_056082		C	1704297	T	C	1704297	3	2	26	1	0	0	0	0	1	0	0	0	14839	1588	55	3	2051	3	SMYD4	17	1704297	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	67347	1704297	79490913	521	10284											
ZZEF1	23140	hgsc.bcm.edu	37	chr17	4017695	4017695	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agttggaggatgtttctataTaagcatagcactttgctact	11	15	9	6	0	1	0	0	0	1	0	1	2	1	2	0	2	4	5	0	2	5	8	rs138134000	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:4017695T>C	ENST00000381638.2	-	4	888	c.764A>G	c.(763-765)tAt>tGt	p.Y255C	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	255	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						TGTTTCTATATAAGCATAGCA	0.438													T|||	11	0.00219649	0.0	0.0	5008	,	,		17608	0.0		0.005	False		,,,				2504	0.0061				p.Y255C		Atlas-SNP	.											ZZEF1,NS,lymphoid_neoplasm,0,1	ZZEF1	195	1	0			c.A764G						PASS	.	T	CYS/TYR	5,4401	9.9+/-24.2	0,5,2198	180	158	166		764	5.1	1	17	dbSNP_134	166	56,8544	35.9+/-90.5	0,56,4244	yes	missense	ZZEF1	NM_015113.3	194	0,61,6442	CC,CT,TT		0.6512,0.1135,0.469	probably-damaging	255/2962	4017695	61,12945	2203	4300	6503	SO:0001583	missense	23140	exon4			TCTATATAAGCAT	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.764A>G	17.37:g.4017695T>C	ENSP00000371051:p.Tyr255Cys	195	0	0		234	111	0.474359	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Missense_Mutation	SNP	ENST00000381638.2	37	CCDS11043.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	T	16.80	3.223085	0.58668	0.001135	0.006512	ENSG00000074755	ENST00000381638	T	0.63580	-0.05	5.12	5.12	0.69794	Anaphase-promoting complex, subunit 10/DOC domain (1);Galactose-binding domain-like (1);	0.367468	0.29028	N	0.013371	T	0.48370	0.1496	N	0.08118	0	0.27369	N	0.955744	D;D	0.63880	0.993;0.967	P;P	0.56788	0.687;0.806	T	0.53892	-0.8374	10	0.41790	T	0.15	-11.0054	14.927	0.70887	0.0:0.0:0.0:1.0	.	255;255	O43149-3;O43149	.;ZZEF1_HUMAN	C	255	ENSP00000371051:Y255C	ENSP00000371051:Y255C	Y	-	2	0	ZZEF1	3964444	1.000000	0.71417	0.981000	0.43875	0.970000	0.65996	3.945000	0.56637	1.912000	0.55364	0.455000	0.32223	TAT	T|0.996;C|0.004	0.004	strong		0.438	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113		C	4017695	T	C	4017695	3	2	26	1	0	0	0	0	1	0	0	0	18270	1406	49	3	8329	3	ZZEF1	17	4017695	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	2313398	4017695	77177515	522	10285											
MINK1	50488	hgsc.bcm.edu	37	chr17	4794407	4794407	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggccggtggagccccaggaGggaccgcacaaggtgagtct	9	4	17	11	2	1	1	0	1	1	0	1	4	1	4	4	6	1	1	4	6	1	0	rs200592676	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:4794407G>C	ENST00000355280.6	+	15	1924	c.1728G>C	c.(1726-1728)gaG>gaC	p.E576D	MINK1_ENST00000453408.3_Missense_Mutation_p.E576D|MINK1_ENST00000347992.7_Missense_Mutation_p.E576D	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						AGCCCCAGGAGGGACCGCACA	0.647													G|||	3	0.000599042	0.0	0.0	5008	,	,		13597	0.0		0.002	False		,,,				2504	0.001				p.E576D		Atlas-SNP	.											.	MINK1	110	.	0			c.G1728C						PASS	.	G	ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU	5,3705		0,5,1850	6	7	6		1728,1728,1728,1728	2.5	1	17		6	22,7980		0,22,3979	yes	missense,missense,missense,missense	MINK1	NM_001024937.3,NM_015716.4,NM_153827.4,NM_170663.4	45,45,45,45	0,27,5829	CC,CG,GG		0.2749,0.1348,0.2305	benign,benign,benign,benign	576/1313,576/1296,576/1333,576/1304	4794407	27,11685	1855	4001	5856	SO:0001583	missense	50488	exon15			CCAGGAGGGACCG	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.1728G>C	17.37:g.4794407G>C	ENSP00000347427:p.Glu576Asp	106	0	0		145	55	0.37931	NM_170663		Missense_Mutation	SNP	ENST00000355280.6	37	CCDS45588.1	.	.	.	.	.	.	.	.	.	.	G	10.75	1.437336	0.25900	0.001348	0.002749	ENSG00000141503	ENST00000355280;ENST00000453408;ENST00000347992	T;T;T	0.73897	-0.79;0.99;-0.79	4.53	2.51	0.30379	.	0.072669	0.53938	D	0.000046	T	0.64918	0.2642	L	0.36672	1.1	0.38630	D	0.951355	P;P;P;P	0.51933	0.949;0.949;0.915;0.949	B;P;B;P	0.49953	0.444;0.627;0.424;0.627	T	0.61342	-0.7082	10	0.16896	T	0.51	.	5.7787	0.18294	0.2429:0.0:0.7571:0.0	.	576;576;576;576	Q8N4C8-2;Q8N4C8-4;Q8N4C8;Q8N4C8-3	.;.;MINK1_HUMAN;.	D	576	ENSP00000347427:E576D;ENSP00000406487:E576D;ENSP00000269296:E576D	ENSP00000269296:E576D	E	+	3	2	MINK1	4735189	0.997000	0.39634	1.000000	0.80357	0.993000	0.82548	0.254000	0.18314	1.229000	0.43630	0.561000	0.74099	GAG	G|0.995;C|0.005	0.005	weak		0.647	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439801.1	NM_015716		C	4794407	G	C	4794407	3	2	26	1	0	0	0	0	1	0	0	0	9596	991	35	4	1525	4	MINK1	17	4794407	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	776712	4794407	76400803	523	10286											
WSCD1	23302	hgsc.bcm.edu	37	chr17	5984001	5984001	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccaaacctttcttccgacTccagaagtttctccgccgaa	9	10	7	15	3	2	1	0	0	2	1	5	3	4	1	6	1	1	1	6	1	3	3	rs199969111	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:5984001T>C	ENST00000574946.1	+	2	413	c.23T>C	c.(22-24)cTc>cCc	p.L8P	WSCD1_ENST00000574232.1_Missense_Mutation_p.L8P|WSCD1_ENST00000573634.1_Intron|WSCD1_ENST00000317744.5_Missense_Mutation_p.L8P|WSCD1_ENST00000539421.1_Missense_Mutation_p.L8P			Q658N2	WSCD1_HUMAN	WSC domain containing 1	8						integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)	35						TTCTTCCGACTCCAGAAGTTT	0.662													T|||	10	0.00199681	0.0	0.0	5008	,	,		16288	0.0		0.002	False		,,,				2504	0.0082				p.L8P		Atlas-SNP	.											.	WSCD1	84	.	0			c.T23C						PASS	.	T	PRO/LEU	0,4242		0,0,2121	42	41	41		23	5.1	1	17		41	6,8158		0,6,4076	yes	missense	WSCD1	NM_015253.1	98	0,6,6197	CC,CT,TT		0.0735,0.0,0.0484	probably-damaging	8/576	5984001	6,12400	2121	4082	6203	SO:0001583	missense	23302	exon2			TCCGACTCCAGAA		CCDS32538.1	17p13.2	2008-02-05				ENSG00000179314			29060	protein-coding gene	gene with protein product							Standard	XM_005256572		Approved	KIAA0523	uc002gcn.3	Q658N2		ENST00000574946.1:c.23T>C	17.37:g.5984001T>C	ENSP00000460825:p.Leu8Pro	176	0	0		186	93	0.5	NM_015253	A8K0N8|D3DTM3|O60276|Q96G45	Missense_Mutation	SNP	ENST00000574946.1	37	CCDS32538.1	.	.	.	.	.	.	.	.	.	.	T	16.23	3.064321	0.55432	0.0	7.35E-4	ENSG00000179314	ENST00000317744;ENST00000539421	D;D	0.83163	-1.69;-1.69	5.07	5.07	0.68467	.	0.088957	0.46145	D	0.000303	D	0.86665	0.5987	L	0.39898	1.24	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.87073	0.2161	10	0.52906	T	0.07	-33.0853	12.7983	0.57571	0.0:0.0:0.0:1.0	.	8	Q658N2	WSCD1_HUMAN	P	8	ENSP00000323087:L8P;ENSP00000446032:L8P	ENSP00000323087:L8P	L	+	2	0	WSCD1	5924725	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.853000	0.62911	1.904000	0.55121	0.455000	0.32223	CTC	T|0.999;C|0.001	0.001	weak		0.662	WSCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438965.4	NM_015253		C	5984001	T	C	5984001	3	2	26	1	0	0	0	0	1	0	0	0	17421	1551	54	3	25	3	WSCD1	17	5984001	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	1189594	5984001	75211209	524	10287											
SENP3	26168	hgsc.bcm.edu	37	chr17	7474729	7474729	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgtctcagccattcagcttCacccagcaggacatgcccaa	10	8	7	16	0	3	0	3	0	1	0	4	1	3	1	3	1	4	2	3	1	1	2			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7474729C>T	ENST00000429205.2	+	12	1702	c.1653C>T	c.(1651-1653)ttC>ttT	p.F551F	SENP3_ENST00000321337.7_Silent_p.F550F|SENP3-EIF4A1_ENST00000579777.1_RNA|EIF4A1_ENST00000577269.1_5'Flank|EIF4A1_ENST00000293831.8_5'Flank|EIF4A1_ENST00000380512.5_5'Flank|SENP3_ENST00000578868.1_3'UTR|EIF4A1_ENST00000582746.1_5'Flank			Q9H4L4	SENP3_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 3	551						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)				CATTCAGCTTCACCCAGCAGG	0.542																																					p.F551F		Atlas-SNP	.											.	SENP3	18	.	0			c.C1653T						PASS	.						101	101	101					17																	7474729		1991	4189	6180	SO:0001819	synonymous_variant	26168	exon12			CAGCTTCACCCAG	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.1653C>T	17.37:g.7474729C>T		120	0	0		120	59	0.491667	NM_015670	Q66K15|Q86VS7|Q96PS4|Q9Y3W9	Silent	SNP	ENST00000429205.2	37																																																																																				.	.	none		0.542	SENP3-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015670		T	7474729	C	T	7474729	2	4	26	1	0	0	0	0	0	0	0	1	14063	825	29	2		2	SENP3	17	7474729	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1490728	7474729	73720481	525	10288											
FXR2	9513	hgsc.bcm.edu	37	chr17	7497292	7497292	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcattgctgatgttctctcGggtgccaacaaaaatgaagg	11	10	12	8	1	1	2	0	2	1	0	3	2	1	2	1	3	3	3	1	3	4	2			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7497292G>A	ENST00000250113.7	-	11	1385	c.1051C>T	c.(1051-1053)Cga>Tga	p.R351*	FXR2_ENST00000573057.1_5'Flank	NM_004860.3	NP_004851.2	P51116	FXR2_HUMAN	fragile X mental retardation, autosomal homolog 2	351						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)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)	26				READ - Rectum adenocarcinoma(115;0.17)		ATGTTCTCTCGGGTGCCAACA	0.502																																					p.R351X		Atlas-SNP	.											FXR2,NS,carcinoma,+2,1	FXR2	44	1	0			c.C1051T						scavenged	.						68	67	67					17																	7497292		1905	4118	6023	SO:0001587	stop_gained	9513	exon11			TCTCTCGGGTGCC	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.1051C>T	17.37:g.7497292G>A	ENSP00000250113:p.Arg351*	55	0	0		73	3	0.0410959	NM_004860	B2R9M2|D3DTQ1|Q86V09|Q8WUM2	Nonsense_Mutation	SNP	ENST00000250113.7	37	CCDS45604.1	.	.	.	.	.	.	.	.	.	.	G	39	7.571676	0.98365	.	.	ENSG00000129245	ENST00000250113	.	.	.	5.52	4.54	0.55810	.	0.209774	0.41605	D	0.000848	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	-0.0119	11.2846	0.49214	0.0:0.0:0.6676:0.3324	.	.	.	.	X	351	.	ENSP00000250113:R351X	R	-	1	2	FXR2	7438017	1.000000	0.71417	1.000000	0.80357	0.844000	0.47949	3.669000	0.54561	1.555000	0.49500	0.563000	0.77884	CGA	.	.	none		0.502	FXR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441084.1			A	7497292	G	A	7497292	4	1	26	1	0	0	0	0	0	1	0	0	6124	1124	39	1	898	1	FXR2	17	7497292	Nonsense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	22563	7497292	73697918	526	10289											
KDM6B	23135	hgsc.bcm.edu	37	chr17	7750010	7750010	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcaggcccctcaggggaggaGggcctcagccctggaggcaa	8	4	16	13	0	3	0	3	0	0	0	3	3	3	3	4	7	1	1	4	7	1	0	rs79548905	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7750010G>C	ENST00000448097.2	+	8	994	c.663G>C	c.(661-663)gaG>gaC	p.E221D	KDM6B_ENST00000254846.5_Missense_Mutation_p.E221D			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	221	Pro-rich.				cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						CAGGGGAGGAGGGCCTCAGCC	0.647													G|||	34	0.00678914	0.0	0.0159	5008	,	,		10042	0.0		0.0199	False		,,,				2504	0.0031				p.E221D		Atlas-SNP	.											.	KDM6B	95	.	0			c.G663C						PASS	.	G	ASP/GLU	25,4381	29.9+/-59.1	0,25,2178	60	63	62		663	1.5	1	17	dbSNP_131	62	250,8350	96.6+/-158.3	3,244,4053	yes	missense	KDM6B	NM_001080424.1	45	3,269,6231	CC,CG,GG		2.907,0.5674,2.1144	benign	221/1683	7750010	275,12731	2203	4300	6503	SO:0001583	missense	23135	exon8			GGAGGAGGGCCTC	AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"Chromatin-modifying enzymes / K-demethylases"	29012	protein-coding gene	gene with protein product		611577	"jumonji domain containing 3", "jumonji domain containing 3, histone lysine demethylase"	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.663G>C	17.37:g.7750010G>C	ENSP00000412513:p.Glu221Asp	75	0	0		87	35	0.402299	NM_001080424	C9IZ40|Q96G33	Missense_Mutation	SNP	ENST00000448097.2	37		23	0.010531135531135532	0	0.0	8	0.022099447513812154	0	0.0	15	0.01978891820580475	G	10.43	1.347466	0.24426	0.005674	0.02907	ENSG00000132510	ENST00000254846;ENST00000448097	T;T	0.38077	1.27;1.16	4.62	1.48	0.22813	.	0.000000	0.53938	D	0.000046	T	0.09291	0.0229	N	0.08118	0	0.23293	N	0.997964	D	0.59767	0.986	P	0.57720	0.826	T	0.11665	-1.0578	10	0.14252	T	0.57	-17.4424	6.792	0.23705	0.3837:0.0:0.6162:0.0	.	221	O15054-1	.	D	221	ENSP00000254846:E221D;ENSP00000412513:E221D	ENSP00000254846:E221D	E	+	3	2	KDM6B	7690735	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.076000	0.41548	0.274000	0.22072	0.561000	0.74099	GAG	G|0.981;C|0.019	0.019	strong		0.647	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272		C	7750010	G	C	7750010	3	2	26	1	0	0	0	0	1	0	0	0	8147	991	35	4	681	4	KDM6B	17	7750010	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	252718	7750010	73445200	527	10290											
DNAH9	1770	hgsc.bcm.edu	37	chr17	11502188	11502188	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgcagtggtctgcggggacCtgcccgcggcacctctggag	4	6	17	14	4	2	0	0	0	2	0	2	2	2	2	3	5	2	2	3	5	0	0			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:11502188C>T	ENST00000262442.4	+	1	441	c.373C>T	c.(373-375)Ctg>Ttg	p.L125L	DNAH9_ENST00000454412.2_Silent_p.L125L|DNAH9_ENST00000579828.1_Silent_p.L125L	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	125	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)		CTGCGGGGACCTGCCCGCGGC	0.701																																					p.L125L		Atlas-SNP	.											.	DNAH9	695	.	0			c.C373T						PASS	.						3	4	4					17																	11502188		1807	3723	5530	SO:0001819	synonymous_variant	1770	exon1			GGGGACCTGCCCG	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.373C>T	17.37:g.11502188C>T		19	0	0		9	6	0.666667	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			.	.	none		0.701	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11502188	C	T	11502188	2	4	26	1	0	0	0	0	0	0	0	1	4610	680	24	2		2	DNAH9	17	11502188	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	3752178	11502188	69693022	528	10291											
DNAH9	1770	hgsc.bcm.edu	37	chr17	11687721	11687721	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagctcggaaacttcccggcGtccctgcagaaatccatccc	10	7	8	16	3	0	1	0	0	0	1	5	2	4	2	4	2	3	2	4	2	3	1	rs16945337	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:11687721G>A	ENST00000262442.4	+	41	7994	c.7926G>A	c.(7924-7926)gcG>gcA	p.A2642A	DNAH9_ENST00000454412.2_Silent_p.A2642A	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2642	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)		ACTTCCCGGCGTCCCTGCAGA	0.542													G|||	239	0.0477236	0.0877	0.0058	5008	,	,		17425	0.002		0.0348	False		,,,				2504	0.0838				p.A2642A		Atlas-SNP	.											DNAH9,NS,carcinoma,+1,1	DNAH9	695	1	0			c.G7926A						PASS	.	G		358,4048	185.0+/-212.2	14,330,1859	177	169	172		7926	-2.6	0	17	dbSNP_123	172	195,8405	86.1+/-148.5	0,195,4105	no	coding-synonymous	DNAH9	NM_001372.3		14,525,5964	AA,AG,GG		2.2674,8.1253,4.2519		2642/4487	11687721	553,12453	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon41			CCCGGCGTCCCTG	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.7926G>A	17.37:g.11687721G>A		190	0	0		219	107	0.488584	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			G|0.956;A|0.044	0.044	strong		0.542	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		A	11687721	G	A	11687721	2	1	26	1	0	0	0	0	0	0	0	1	4610	1132	40	1		1	DNAH9	17	11687721	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	185533	11687721	69507489	529	10292											
ZNF287	57336	hgsc.bcm.edu	37	chr17	16455760	16455760	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcttttccacattcattacAtttataacacttctctccag	10	16	3	12	0	2	0	1	0	1	0	5	0	4	0	2	1	2	1	2	1	3	8			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:16455760A>G	ENST00000395824.1	-	6	2313	c.1696T>C	c.(1696-1698)Tgt>Cgt	p.C566R	ZNF287_ENST00000395825.3_Missense_Mutation_p.C566R			Q9HBT7	ZN287_HUMAN	zinc finger protein 287	559					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)		CATTCATTACATTTATAACAC	0.348																																					p.C566R		Atlas-SNP	.											.	ZNF287	60	.	0			c.T1696C						PASS	.						89	92	91					17																	16455760		2203	4300	6503	SO:0001583	missense	57336	exon6			CATTACATTTATA	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.1696T>C	17.37:g.16455760A>G	ENSP00000379168:p.Cys566Arg	65	0	0		96	4	0.0416667	NM_020653	Q6IAG1	Missense_Mutation	SNP	ENST00000395824.1	37	CCDS11179.2	.	.	.	.	.	.	.	.	.	.	A	17.56	3.420080	0.62622	.	.	ENSG00000141040	ENST00000395825;ENST00000395824	D;D	0.99974	-10.2;-10.2	5.18	5.18	0.71444	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.56097	D	0.000025	D	0.99984	0.9995	H	0.99225	4.475	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99087	1.0839	10	0.87932	D	0	.	13.3294	0.60477	1.0:0.0:0.0:0.0	.	559	Q9HBT7	ZN287_HUMAN	R	566	ENSP00000379169:C566R;ENSP00000379168:C566R	ENSP00000379168:C566R	C	-	1	0	ZNF287	16396485	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.014000	0.93635	2.317000	0.78254	0.459000	0.35465	TGT	.	.	none		0.348	ZNF287-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130504.1			G	16455760	A	G	16455760	3	3	26	1	0	0	0	0	1	0	0	0	17840	217	8	3	593	3	ZNF287	17	16455760	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	4768039	16455760	64739450	530	10293											
LRRC48	83450	hgsc.bcm.edu	37	chr17	17919414	17919414	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atacgattgttaatgctgtcGgggcatcgcacgacatccac	10	10	10	11	4	0	0	0	0	0	0	3	2	1	0	1	2	2	4	1	2	2	3	rs200381151	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:17919414G>A	ENST00000399187.1	+	13	1581	c.1363G>A	c.(1363-1365)Ggg>Agg	p.G455R	LRRC48_ENST00000583995.1_3'UTR|ATPAF2_ENST00000469327.1_5'Flank|LRRC48_ENST00000313838.8_Missense_Mutation_p.G455R	NM_031294.3	NP_112584.3	Q9H069	LRC48_HUMAN	leucine rich repeat containing 48	455						cytoplasm (GO:0005737)				breast(1)|large_intestine(2)|lung(2)|pancreas(1)|urinary_tract(1)	7	all_neural(463;0.228)					TAATGCTGTCGGGGCATCGCA	0.443													G|||	14	0.00279553	0.0038	0.0043	5008	,	,		21102	0.0		0.004	False		,,,				2504	0.002				p.G455R		Atlas-SNP	.											.	LRRC48	49	.	0			c.G1363A						PASS	.	G	ARG/GLY,ARG/GLY	28,3894		0,28,1933	153	145	147		1363,1363	5.5	0.9	17		147	67,8235		0,67,4084	yes	missense,missense	LRRC48	NM_001130090.1,NM_031294.3	125,125	0,95,6017	AA,AG,GG		0.807,0.7139,0.7772	,	455/524,455/524	17919414	95,12129	1961	4151	6112	SO:0001583	missense	83450	exon13			GCTGTCGGGGCAT	AK093317	CCDS45622.1, CCDS45623.1	17p11.2	2014-07-18			ENSG00000171962	ENSG00000171962			25384	protein-coding gene	gene with protein product						11997338, 23354437	Standard	NM_001130090		Approved	DKFZP586M1120	uc021trk.1	Q9H069	OTTHUMG00000059355	ENST00000399187.1:c.1363G>A	17.37:g.17919414G>A	ENSP00000382140:p.Gly455Arg	59	0	0		100	41	0.41	NM_031294	A8KAE6|Q86SF9|Q86W73|Q8IWG0	Missense_Mutation	SNP	ENST00000399187.1	37	CCDS45622.1	4	0.0018315018315018315	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	0	0.0	G	20.0	3.931107	0.73327	0.007139	0.00807	ENSG00000171962	ENST00000313838;ENST00000448396;ENST00000399187;ENST00000399185	T;T	0.52526	0.66;0.66	5.47	5.47	0.80525	.	0.412797	0.28724	N	0.014349	T	0.47581	0.1453	M	0.63428	1.95	0.80722	D	1	D	0.71674	0.998	P	0.55871	0.786	T	0.53380	-0.8447	10	0.45353	T	0.12	-51.1913	8.5414	0.33395	0.1643:0.0:0.8357:0.0	.	455	Q9H069	LRC48_HUMAN	R	455	ENSP00000326870:G455R;ENSP00000382140:G455R	ENSP00000326870:G455R	G	+	1	0	LRRC48	17860139	0.998000	0.40836	0.932000	0.37286	0.749000	0.42624	3.102000	0.50291	2.557000	0.86248	0.563000	0.77884	GGG	G|0.997;A|0.003	0.003	strong		0.443	LRRC48-001	KNOWN	non_canonical_conserved|non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131945.3	NM_031294		A	17919414	G	A	17919414	3	1	26	1	0	0	0	0	1	0	0	0	9014	1116	39	1	1457	1	LRRC48	17	17919414	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1463654	17919414	63275796	531	10294											
SLC47A1	55244	hgsc.bcm.edu	37	chr17	19474875	19474875	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tcagctaaattggaaaaaagCctgtcagcaggtaactatgt	15	10	9	7	0	2	0	2	0	0	0	2	1	2	1	1	2	4	3	1	2	7	4	rs111653425	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:19474875C>T	ENST00000270570.4	+	15	1480	c.1394C>T	c.(1393-1395)gCc>gTc	p.A465V	RP11-1113L8.1_ENST00000574267.1_RNA|SLC47A1_ENST00000457293.1_Missense_Mutation_p.A465V|SLC47A1_ENST00000436810.2_Intron|SLC47A1_ENST00000395585.1_Missense_Mutation_p.A465V|SLC47A1_ENST00000571335.1_Intron|SLC47A1_ENST00000575023.1_Intron	NM_018242.2	NP_060712.2	Q96FL8	S47A1_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 1	465					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)	TGGAAAAAAGCCTGTCAGCAG	0.393													C|||	11	0.00219649	0.0	0.0043	5008	,	,		18046	0.0		0.007	False		,,,				2504	0.001				p.A465V		Atlas-SNP	.											.	SLC47A1	55	.	0			c.C1394T						PASS	.	C	VAL/ALA	17,4389	24.3+/-50.5	0,17,2186	117	110	112		1394	5.4	1	17	dbSNP_132	112	68,8532	41.2+/-98.3	0,68,4232	yes	missense	SLC47A1	NM_018242.2	64	0,85,6418	TT,TC,CC		0.7907,0.3858,0.6535	benign	465/571	19474875	85,12921	2203	4300	6503	SO:0001583	missense	55244	exon15			AAAAAGCCTGTCA		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.1394C>T	17.37:g.19474875C>T	ENSP00000270570:p.Ala465Val	170	0	0		174	92	0.528736	NM_018242	Q53HF5|Q6PD77|Q86VL4|Q9NVA3	Missense_Mutation	SNP	ENST00000270570.4	37	CCDS11209.1	8	0.003663003663003663	0	0.0	3	0.008287292817679558	0	0.0	5	0.006596306068601583	C	14.34	2.506541	0.44558	0.003858	0.007907	ENSG00000142494	ENST00000270570;ENST00000457293;ENST00000395585;ENST00000424755	T;T;T	0.32023	1.48;1.47;1.47	5.4	5.4	0.78164	.	0.273024	0.41001	D	0.000979	T	0.20170	0.0485	L	0.42581	1.335	0.80722	D	1	B;P	0.40794	0.1;0.729	B;B	0.43251	0.109;0.413	T	0.01972	-1.1237	10	0.14656	T	0.56	-19.0703	10.1604	0.42849	0.0:0.9096:0.0:0.0904	.	465;465	Q96FL8;Q96FL8-3	S47A1_HUMAN;.	V	465;465;465;177	ENSP00000270570:A465V;ENSP00000415586:A465V;ENSP00000378951:A465V	ENSP00000270570:A465V	A	+	2	0	SLC47A1	19415467	1.000000	0.71417	0.964000	0.40570	0.629000	0.37895	2.731000	0.47343	2.539000	0.85634	0.655000	0.94253	GCC	C|0.995;T|0.005	0.005	strong		0.393	SLC47A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132250.1	NM_018242		T	19474875	C	T	19474875	3	4	26	1	0	0	0	0	1	0	0	0	14662	739	26	2	1452	2	SLC47A1	17	19474875	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1555461	19474875	61720335	532	10295											
KCNJ12	3768	hgsc.bcm.edu	37	chr17	21319185	21319185	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcatcgactccttcatgatTggtgccatcatggccaagat	10	12	8	11	1	3	2	3	1	0	1	5	3	4	2	3	2	1	0	3	2	1	2	rs149832249	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:21319185T>A	ENST00000583088.1	+	3	1426	c.531T>A	c.(529-531)atT>atA	p.I177I	KCNJ12_ENST00000331718.5_Silent_p.I177I	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	177					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)	CCTTCATGATTGGTGCCATCA	0.637										Prostate(3;0.18)																											p.I177I		Atlas-SNP	.											.	.	.	.	0			c.T531A						PASS	.	T		2,4404		0,2,2201	87	81	83		531	-4	0.9	17	dbSNP_134	83	18,8582	5.7+/-21.5	0,18,4282	no	coding-synonymous	KCNJ12	NM_021012.4		0,20,6483	AA,AT,TT		0.2093,0.0454,0.1538		177/434	21319185	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	100134444	exon3			CATGATTGGTGCC	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.531T>A	17.37:g.21319185T>A		180	0	0		212	23	0.108491	NM_001194958	O43401|Q15756|Q8NG63	Silent	SNP	ENST00000583088.1	37	CCDS11219.1																																																																																			T|0.999;A|0.001	0.001	strong		0.637	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012		A	21319185	T	A	21319185	2	1	26	1	0	0	0	0	0	0	0	1	8055	1800	63	5		5	KCNJ12	17	21319185	Silent	SNP	T	TCGA-G8-6907-01A-11D-2210-10	1844310	21319185	59876025	533	10296											
UNC119	9094	hgsc.bcm.edu	37	chr17	26874803	26874803	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcttttgagtagctggttgcGgaagtagtgcctctcgatca	7	13	13	8	2	2	1	1	1	1	0	3	3	2	2	1	2	3	5	1	2	3	5	rs146916036	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:26874803G>A	ENST00000335765.4	-	4	612	c.502C>T	c.(502-504)Cgc>Tgc	p.R168C	UNC119_ENST00000484980.1_Missense_Mutation_p.R73C|UNC119_ENST00000470125.1_Missense_Mutation_p.R73C|UNC119_ENST00000301032.4_Missense_Mutation_p.R168C	NM_005148.3	NP_005139.1	Q13432	U119A_HUMAN	unc-119 homolog (C. elegans)	168	Required for centrosome localization.				cytokinesis, completion of separation (GO:0007109)|endocytosis (GO:0006897)|lipoprotein transport (GO:0042953)|negative regulation of caveolin-mediated endocytosis (GO:2001287)|negative regulation of clathrin-mediated endocytosis (GO:1900186)|phototransduction (GO:0007602)|positive regulation of protein tyrosine kinase activity (GO:0061098)|synaptic transmission (GO:0007268)|visual perception (GO:0007601)	centrosome (GO:0005813)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	lipid binding (GO:0008289)			breast(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	7	Lung NSC(42;0.00431)					AGCTGGTTGCGGAAGTAGTGC	0.537											OREG0024277	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R168C		Atlas-SNP	.											.	UNC119	27	.	0			c.C502T						PASS	.	G	CYS/ARG,CYS/ARG	0,4406		0,0,2203	173	156	162		502,502	4.8	1	17	dbSNP_134	162	11,8589	8.4+/-32.0	0,11,4289	yes	missense,missense	UNC119	NM_005148.3,NM_054035.2	180,180	0,11,6492	AA,AG,GG		0.1279,0.0,0.0846	probably-damaging,probably-damaging	168/241,168/221	26874803	11,12995	2203	4300	6503	SO:0001583	missense	9094	exon4			GGTTGCGGAAGTA	U40998	CCDS11233.1, CCDS11234.1	17q11.2	2014-09-17	2001-11-28		ENSG00000109103	ENSG00000109103			12565	protein-coding gene	gene with protein product	"POC7 centriolar protein homolog A (Chlamydomonas)"	604011	"unc119 (C.elegans) homolog"			8576185, 9538874	Standard	NM_005148		Approved	HRG4, POC7, POC7A	uc002hbk.2	Q13432	OTTHUMG00000132606	ENST00000335765.4:c.502C>T	17.37:g.26874803G>A	ENSP00000337040:p.Arg168Cys	216	0	0	790	259	122	0.471042	NM_005148	A8K8G4|F1T095|O95126	Missense_Mutation	SNP	ENST00000335765.4	37	CCDS11233.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.221194	0.79464	0.0	0.001279	ENSG00000109103	ENST00000335765;ENST00000301032;ENST00000444148	D;D;D	0.82344	-1.51;-1.59;-1.6	5.81	4.83	0.62350	Immunoglobulin E-set (1);	0.000000	0.85682	D	0.000000	D	0.93259	0.7852	M	0.93241	3.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.988	D	0.95030	0.8168	10	0.87932	D	0	-19.9144	16.2568	0.82522	0.0:0.0:0.8662:0.1338	.	168;168	F1T095;Q13432	.;U119A_HUMAN	C	168;168;161	ENSP00000337040:R168C;ENSP00000301032:R168C;ENSP00000414639:R161C	ENSP00000301032:R168C	R	-	1	0	UNC119	23898930	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.862000	0.56009	1.437000	0.47472	0.462000	0.41574	CGC	G|0.999;A|0.001	0.001	strong		0.537	UNC119-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255842.2			A	26874803	G	A	26874803	3	1	26	1	0	0	0	0	1	0	0	0	16997	1116	39	1	281	1	UNC119	17	26874803	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	5555618	26874803	54320407	534	10297											
SPAG5	10615	hgsc.bcm.edu	37	chr17	26911204	26911204	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtcccgcacctctttggcCaggacagcttgttgctgctg	5	11	12	13	1	1	0	0	0	1	0	2	1	2	1	3	3	3	5	3	3	0	3	rs117510770	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:26911204C>T	ENST00000321765.5	-	13	2708	c.2376G>A	c.(2374-2376)ctG>ctA	p.L792L		NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	792	Interaction with KNSTRN.				chromosome segregation (GO:0007059)|mitotic sister chromatid segregation (GO:0000070)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|microtubule plus-end (GO:0035371)|mitotic spindle (GO:0072686)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43	Lung NSC(42;0.00431)					CCTCTTTGGCCAGGACAGCTT	0.507													C|||	20	0.00399361	0.0008	0.0043	5008	,	,		23516	0.0		0.0159	False		,,,				2504	0.0				p.L792L		Atlas-SNP	.											.	SPAG5	92	.	0			c.G2376A						PASS	.	C		14,4392	22.3+/-47.3	0,14,2189	207	176	186		2376	3.8	1	17	dbSNP_132	186	132,8468	67.0+/-129.4	2,128,4170	no	coding-synonymous	SPAG5	NM_006461.3		2,142,6359	TT,TC,CC		1.5349,0.3177,1.1226		792/1194	26911204	146,12860	2203	4300	6503	SO:0001819	synonymous_variant	10615	exon13			TTTGGCCAGGACA	AF063308	CCDS32594.1	17q11.2	2008-07-18			ENSG00000076382	ENSG00000076382			13452	protein-coding gene	gene with protein product	"mitotic spindle coiled-coil related protein", "astrin", "mitotic spindle associated protein p126"	615562				11549262	Standard	NM_006461		Approved	DEEPEST, MAP126, hMAP126	uc002hbq.3	Q96R06	OTTHUMG00000166586	ENST00000321765.5:c.2376G>A	17.37:g.26911204C>T		97	0	0		96	53	0.552083	NM_006461	O95213|Q9BWE8|Q9NT17|Q9UFE6	Silent	SNP	ENST00000321765.5	37	CCDS32594.1																																																																																			C|0.991;T|0.009	0.009	strong		0.507	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461		T	26911204	C	T	26911204	2	4	26	1	0	0	0	0	0	0	0	1	14996	581	21	2		2	SPAG5	17	26911204	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	36401	26911204	54284006	535	10298											
PHF12	57649	hgsc.bcm.edu	37	chr17	27277200	27277200	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcttctccggggctccttcTcaggcttccgactgcgcttt	2	13	10	16	4	2	0	1	0	2	0	6	1	4	0	3	3	1	4	3	3	0	4			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:27277200T>A	ENST00000332830.4	-	2	941	c.131A>T	c.(130-132)gAg>gTg	p.E44V	PHF12_ENST00000577226.1_Missense_Mutation_p.E44V|PHF12_ENST00000268756.3_Missense_Mutation_p.E44V	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)			GGGCTCCTTCTCAGGCTTCCG	0.622																																					p.E44V		Atlas-SNP	.											.	PHF12	69	.	0			c.A131T						PASS	.						69	66	67					17																	27277200		2203	4300	6503	SO:0001583	missense	57649	exon2			TCCTTCTCAGGCT	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.131A>T	17.37:g.27277200T>A	ENSP00000329933:p.Glu44Val	76	0	0		102	46	0.45098	NM_020889		Missense_Mutation	SNP	ENST00000332830.4	37	CCDS32598.1	.	.	.	.	.	.	.	.	.	.	T	11.87	1.766609	0.31228	.	.	ENSG00000109118	ENST00000332830;ENST00000378879;ENST00000268756	D;D;D	0.94576	-3.45;-3.46;-3.46	4.43	4.43	0.53597	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.187807	0.45867	D	0.000333	D	0.90383	0.6990	L	0.44542	1.39	0.58432	D	0.999998	B;B;B;B;B	0.31611	0.128;0.331;0.202;0.03;0.01	B;B;B;B;B	0.25884	0.026;0.064;0.058;0.012;0.012	D	0.89168	0.3535	10	0.40728	T	0.16	-1.4833	12.955	0.58421	0.0:0.0:0.0:1.0	.	26;44;44;44;44	B4DFE2;A8K5V5;Q96QT6-2;Q2TAK2;Q96QT6	.;.;.;.;PHF12_HUMAN	V	44	ENSP00000329933:E44V;ENSP00000368157:E44V;ENSP00000268756:E44V	ENSP00000268756:E44V	E	-	2	0	PHF12	24301326	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.609000	0.61148	1.978000	0.57642	0.533000	0.62120	GAG	.	.	none		0.622	PHF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255941.1	NM_020889		A	27277200	T	A	27277200	3	1	26	1	0	0	0	0	1	0	0	0	11832	1551	54	5	2965	5	PHF12	17	27277200	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	365996	27277200	53918010	536	10299											
RNF135	84282	hgsc.bcm.edu	37	chr17	29326155	29326155	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cctttgtaccctgccttctgGctgtatggcttacatcctgg	4	15	9	13	0	1	0	0	0	1	0	2	0	2	0	4	3	3	4	4	3	3	5	rs61749868	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:29326155G>T	ENST00000328381.5	+	5	2118	c.1245G>T	c.(1243-1245)tgG>tgT	p.W415C	RNF135_ENST00000535306.2_3'UTR|RNF135_ENST00000443677.2_3'UTR|RNF135_ENST00000324689.4_3'UTR	NM_032322.3	NP_115698.3	Q8IUD6	RN135_HUMAN	ring finger protein 135	415	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		W -> C (in dbSNP:rs61749868). {ECO:0000269|PubMed:19291764}.		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)				CTGCCTTCTGGCTGTATGGCT	0.458													G|||	12	0.00239617	0.0015	0.0	5008	,	,		21128	0.0		0.0099	False		,,,				2504	0.0				p.W415C		Atlas-SNP	.											.	RNF135	19	.	1	Unknown(1)	central_nervous_system(1)	c.G1245T						PASS	.	G	,CYS/TRP,	10,4396	16.8+/-37.8	0,10,2193	104	106	105		,1245,	5.2	1	17	dbSNP_129	105	86,8514	49.4+/-109.1	0,86,4214	yes	utr-3,missense,utr-3	RNF135	NM_001184992.1,NM_032322.3,NM_197939.1	,215,	0,96,6407	TT,TG,GG		1.0,0.227,0.7381	,probably-damaging,	,415/433,	29326155	96,12910	2203	4300	6503	SO:0001583	missense	84282	exon5			CTTCTGGCTGTAT	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.1245G>T	17.37:g.29326155G>T	ENSP00000328340:p.Trp415Cys	78	0	0		102	40	0.392157	NM_032322	A0AVM5|B2R7G9|B6ZLM5|F5GX60|Q9BSE9	Missense_Mutation	SNP	ENST00000328381.5	37	CCDS11262.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	G	15.55	2.867158	0.51588	0.00227	0.01	ENSG00000181481	ENST00000328381;ENST00000535605	T	0.69926	-0.44	5.21	5.21	0.72293	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.176168	0.28072	N	0.016704	T	0.72244	0.3436	L	0.56280	1.765	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73852	-0.3852	10	0.38643	T	0.18	-10.0145	16.6225	0.84934	0.0:0.0:1.0:0.0	rs61749868	415	Q8IUD6	RN135_HUMAN	C	415;234	ENSP00000328340:W415C	ENSP00000328340:W415C	W	+	3	0	RNF135	26350281	1.000000	0.71417	0.995000	0.50966	0.297000	0.27493	6.437000	0.73421	2.613000	0.88420	0.655000	0.94253	TGG	G|0.995;T|0.005	0.005	strong		0.458	RNF135-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256342.3	NM_032322		T	29326155	G	T	29326155	3	4	26	1	0	0	0	0	1	0	0	0	13455	1212	42	4	1332	4	RNF135	17	29326155	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	2048955	29326155	51869055	537	10300											
ZNF207	7756	hgsc.bcm.edu	37	chr17	30677325	30677325	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgggtcgcaagaagaagaaGcagctgaagccgtggtgctg	12	6	16	7	2	0	4	0	1	0	3	1	4	0	4	1	2	4	4	1	2	5	0	rs140451700	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:30677325G>A	ENST00000321233.6	+	1	175	c.21G>A	c.(19-21)aaG>aaA	p.K7K	RP11-227G15.3_ENST00000581915.1_RNA|ZNF207_ENST00000394670.4_Silent_p.K7K|ZNF207_ENST00000342555.6_5'UTR|ZNF207_ENST00000394673.2_Silent_p.K7K|ZNF207_ENST00000577908.1_Silent_p.K7K|MIR632_ENST00000385193.1_RNA|ZNF207_ENST00000341711.6_Silent_p.K7K	NM_003457.3	NP_003448.1	O43670	ZN207_HUMAN	zinc finger protein 207	7	Microtubule-binding region.				attachment of spindle microtubules to kinetochore (GO:0008608)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|protein stabilization (GO:0050821)|regulation of chromosome segregation (GO:0051983)|regulation of transcription, DNA-templated (GO:0006355)	kinetochore (GO:0000776)|microtubule (GO:0005874)|nucleus (GO:0005634)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|lung(3)|urinary_tract(2)	10		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			AGAAGAAGAAGCAGCTGAAGC	0.537													G|||	4	0.000798722	0.0	0.0043	5008	,	,		19354	0.0		0.001	False		,,,				2504	0.0				p.K7K		Atlas-SNP	.											.	ZNF207	32	.	0			c.G21A						PASS	.	G	,,	4,4402	8.1+/-20.4	0,4,2199	209	197	201		21,21,21	3.5	1	17	dbSNP_134	201	65,8535	39.3+/-95.6	0,65,4235	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF207	NM_001032293.2,NM_001098507.1,NM_003457.3	,,	0,69,6434	AA,AG,GG		0.7558,0.0908,0.5305	,,	7/464,7/495,7/479	30677325	69,12937	2203	4300	6503	SO:0001819	synonymous_variant	7756	exon1			GAAGAAGCAGCTG	AF046001	CCDS11271.1, CCDS32614.1, CCDS42294.1	17q11.2	2008-07-10			ENSG00000010244	ENSG00000010244		"Zinc fingers, C2H2-type"	12998	protein-coding gene	gene with protein product		603428				9799612	Standard	NM_001098507		Approved		uc002hhj.4	O43670	OTTHUMG00000132810	ENST00000321233.6:c.21G>A	17.37:g.30677325G>A		298	0	0		322	172	0.534162	NM_003457	A8K6Y6|E1P660|E1P661|E1P662|Q53XS9|Q96HW5|Q9BUQ7	Silent	SNP	ENST00000321233.6	37	CCDS11271.1																																																																																			G|0.996;A|0.004	0.004	strong		0.537	ZNF207-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256251.2			A	30677325	G	A	30677325	2	1	26	1	0	0	0	0	0	0	0	1	17780	962	34	2		2	ZNF207	17	30677325	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1351170	30677325	50517885	538	10301											
SLFN5	162394	hgsc.bcm.edu	37	chr17	33586111	33586111	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atggattctcaggaagctctGgcattcctcaaatgcaggac	11	10	10	10	0	3	0	2	0	2	0	5	3	4	3	1	4	2	3	1	4	2	2	rs141928271	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:33586111G>A	ENST00000299977.4	+	2	550	c.402G>A	c.(400-402)ctG>ctA	p.L134L	SLFN5_ENST00000542451.1_Silent_p.L134L|SLFN5_ENST00000592325.1_Silent_p.L134L	NM_144975.3	NP_659412.3	Q08AF3	SLFN5_HUMAN	schlafen family member 5	134					cell differentiation (GO:0030154)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(8)|liver(2)|lung(6)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	34		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0191)		AGGAAGCTCTGGCATTCCTCA	0.458													G|||	12	0.00239617	0.0008	0.0	5008	,	,		21328	0.0		0.0089	False		,,,				2504	0.002				p.L134L		Atlas-SNP	.											.	SLFN5	92	.	0			c.G402A						PASS	.	G		8,4398	15.5+/-35.6	0,8,2195	115	113	114		402	2.7	0	17	dbSNP_134	114	68,8532	41.2+/-98.3	0,68,4232	no	coding-synonymous	SLFN5	NM_144975.3		0,76,6427	AA,AG,GG		0.7907,0.1816,0.5843		134/892	33586111	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	162394	exon2			AGCTCTGGCATTC	BX647942	CCDS32619.1	17q12	2006-04-05				ENSG00000166750			28286	protein-coding gene	gene with protein product		614952				9846487	Standard	NM_144975		Approved	MGC19764	uc002hjf.4	Q08AF3		ENST00000299977.4:c.402G>A	17.37:g.33586111G>A		201	0	0		198	96	0.484848	NM_144975	Q08AF2|Q8WU54|Q96A82	Silent	SNP	ENST00000299977.4	37	CCDS32619.1																																																																																			G|0.994;A|0.006	0.006	strong		0.458	SLFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448649.2	NM_144975		A	33586111	G	A	33586111	2	1	26	1	0	0	0	0	0	0	0	1	14752	1335	47	2		2	SLFN5	17	33586111	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	2908786	33586111	47609099	539	10302											
C17orf98	388381	hgsc.bcm.edu	37	chr17	36997503	36997503	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgcgggcgtggtagtccTgctgcgcgttgtagggcgga	4	9	19	9	5	0	0	0	0	0	0	1	1	1	1	1	4	4	5	1	4	2	3	rs61752602	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:36997503T>C	ENST00000398575.4	-	1	205	c.140A>G	c.(139-141)cAg>cGg	p.Q47R		NM_001080465.2	NP_001073934.1	A8MV24	CQ098_HUMAN	chromosome 17 open reading frame 98	47								p.Q47R(1)		endometrium(5)|kidney(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(3)	14						GTGGTAGTCCTGCTGCGCGTT	0.617													T|||	64	0.0127796	0.0023	0.0144	5008	,	,		12922	0.0		0.0437	False		,,,				2504	0.0072				p.Q47R		Atlas-SNP	.											C17orf98,NS,carcinoma,0,1	C17orf98	34	1	1	Substitution - Missense(1)	pancreas(1)	c.A140G						PASS	.	T	ARG/GLN	25,3925		0,25,1950	55	55	55		140	1.4	1	17	dbSNP_129	55	343,7973		7,329,3822	yes	missense	C17orf98	NM_001080465.2	43	7,354,5772	CC,CT,TT		4.1246,0.6329,3.0002	benign	47/155	36997503	368,11898	1975	4158	6133	SO:0001583	missense	388381	exon1			TAGTCCTGCTGCG	AC006449, DY654789	CCDS42310.1	17q12	2014-05-06			ENSG00000214556	ENSG00000275489			34492	protein-coding gene	gene with protein product						16625196	Standard	NM_001080465		Approved	LOC388381	uc002hqv.2	A8MV24	OTTHUMG00000188506	ENST00000398575.4:c.140A>G	17.37:g.36997503T>C	ENSP00000381580:p.Gln47Arg	83	0	0		87	37	0.425287	NM_001080465		Missense_Mutation	SNP	ENST00000398575.4	37	CCDS42310.1	38	0.0173992673992674	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	31	0.040897097625329816	T	8.259	0.810759	0.16537	0.006329	0.041246	ENSG00000214556	ENST00000398575	T	0.43294	0.95	5.16	1.35	0.21983	.	1.362360	0.06396	U	0.717920	T	0.05364	0.0142	N	0.16790	0.44	0.23704	N	0.997064	B	0.12013	0.005	B	0.13407	0.009	T	0.16070	-1.0415	10	0.07175	T	0.84	-11.8449	4.455	0.11639	0.518:0.0925:0.0:0.3895	.	47	A8MV24	CQ098_HUMAN	R	47	ENSP00000381580:Q47R	ENSP00000381580:Q47R	Q	-	2	0	C17orf98	34251029	0.913000	0.31002	1.000000	0.80357	0.893000	0.52053	0.142000	0.16096	0.376000	0.24707	0.379000	0.24179	CAG	T|0.971;C|0.029	0.029	strong		0.617	C17orf98-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255469.2	NM_001080465		C	36997503	T	C	36997503	3	2	26	1	0	0	0	0	1	0	0	0	1895	1580	55	3	336	3	C17orf98	17	36997503	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	3411392	36997503	44197707	540	10303											
STARD3	10948	hgsc.bcm.edu	37	chr17	37815305	37815305	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctgtgcctgttttctgcaggGtctgacaatgaatcagatga	9	13	11	8	0	3	4	1	3	2	1	3	4	3	4	1	1	2	2	1	1	2	2	rs144713925		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:37815305G>A	ENST00000336308.5	+	8	866	c.648G>A	c.(646-648)ggG>ggA	p.G216G	STARD3_ENST00000578232.1_3'UTR|STARD3_ENST00000394250.4_Splice_Site_p.G198G|STARD3_ENST00000580611.1_Splice_Site_p.G190G|STARD3_ENST00000544210.2_Splice_Site_p.G216G	NM_001165937.1|NM_006804.3	NP_001159409.1|NP_006795.3	Q14849	STAR3_HUMAN	StAR-related lipid transfer (START) domain containing 3	216	MENTAL. {ECO:0000255|PROSITE- ProRule:PRU00770}.		G -> A (in dbSNP:rs11556624). {ECO:0000269|PubMed:15489334}.		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)			TTTCTGCAGGGTCTGACAATG	0.527													G|||	1	0.000199681	0.0	0.0014	5008	,	,		16693	0.0		0.0	False		,,,				2504	0.0				p.G216G		Atlas-SNP	.											.	STARD3	33	.	0			c.G648A						PASS	.	G	,,	1,4405		0,1,2202	221	216	218		648,594,648	2.7	1	17	dbSNP_134	218	10,8590	3.7+/-12.6	0,10,4290	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	STARD3	NM_001165937.1,NM_001165938.1,NM_006804.3	,,	0,11,6492	AA,AG,GG		0.1163,0.0227,0.0846	,,	216/446,198/428,216/446	37815305	11,12995	2203	4300	6503	SO:0001630	splice_region_variant	10948	exon8			TGCAGGGTCTGAC		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.647-1G>A	17.37:g.37815305G>A		220	0	0		203	92	0.453202	NM_006804	A8MXA4|B4DUY1|F5H0G2|Q53Y53|Q96HM9	Silent	SNP	ENST00000336308.5	37	CCDS11341.1																																																																																			G|0.999;A|0.001	0.001	strong		0.527	STARD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256933.1		Silent	A	37815305	G	A	37815305	5	1	26	1	0	0	0	0	0	0	1	0	15272	1275	44	2	687	2	STARD3	17	37815305	Splice_Site	SNP	G	TCGA-G8-6907-01A-11D-2210-10	817802	37815305	43379905	541	10304											
ERBB2	2064	hgsc.bcm.edu	37	chr17	37879588	37879588	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagccctctgacgtccatcAtctctgcggtggttggcatt	5	12	10	14	2	3	1	1	1	2	0	5	1	4	1	3	3	2	2	3	3	0	2	rs1136201	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:37879588A>G	ENST00000269571.5	+	17	2122	c.1963A>G	c.(1963-1965)Atc>Gtc	p.I655V	ERBB2_ENST00000541774.1_Missense_Mutation_p.I640V|ERBB2_ENST00000584601.1_Missense_Mutation_p.I625V|ERBB2_ENST00000540147.1_Missense_Mutation_p.I625V|ERBB2_ENST00000445658.2_Missense_Mutation_p.I379V|ERBB2_ENST00000406381.2_Missense_Mutation_p.I625V|ERBB2_ENST00000584450.1_Missense_Mutation_p.I655V			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	655			I -> V (in allele B2 and allele B3; dbSNP:rs1136201). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:8095488, ECO:0000269|Ref.3}.		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)	GACGTCCATCATCTCTGCGGT	0.612		1	"A, Mis, O"		"breast, ovarian, other tumour types, NSCLC, gastric"					TCGA GBM(5;<1E-08)			A|||	608	0.121406	0.0098	0.1369	5008	,	,		13960	0.124		0.2455	False		,,,				2504	0.1309				p.I655V		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.A1963G	GRCh37	CM004332	ERBB2	M	rs1136201	PASS	.	A	VAL/ILE,VAL/ILE	212,4194	132.1+/-168.6	5,202,1996	113	103	106	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1873,1963	5	1	17	dbSNP_86	106	1980,6620	346.8+/-326.3	223,1534,2543	yes	missense,missense	ERBB2	NM_001005862.1,NM_004448.2	29,29	228,1736,4539	GG,GA,AA		23.0233,4.8116,16.8538	benign,benign	625/1226,655/1256	37879588	2192,10814	2203	4300	6503	SO:0001583	missense	2064	exon17			TCCATCATCTCTG	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.1963A>G	17.37:g.37879588A>G	ENSP00000269571:p.Ile655Val	181	0	0		204	106	0.519608	NM_004448	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	37	CCDS32642.1	339	0.15521978021978022	5	0.01016260162601626	58	0.16022099447513813	83	0.1451048951048951	193	0.2546174142480211	A	13.67	2.306999	0.40795	0.048116	0.230233	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147	T;T;T;T;T	0.76316	-1.01;-1.01;-0.99;-1.01;-1.01	4.97	4.97	0.65823	Cytochrome c1, transmembrane anchor, C-terminal (1);	.	.	.	.	T	0.00039	0.0001	N	0.25485	0.75	0.09310	P	1.0	B;P;B	0.39576	0.406;0.679;0.406	B;B;B	0.37650	0.108;0.255;0.108	T	0.05920	-1.0856	8	0.22706	T	0.39	.	8.987	0.35999	0.9164:0.0:0.0836:0.0	rs1136201;rs1801200;rs2006406;rs2230699;rs17606815;rs59955961;rs1801200	379;640;655	B4DTR1;P04626-4;P04626	.;.;ERBB2_HUMAN	V	625;640;379;655;625	ENSP00000385185:I625V;ENSP00000446466:I640V;ENSP00000404047:I379V;ENSP00000269571:I655V;ENSP00000443562:I625V	ENSP00000269571:I655V	I	+	1	0	ERBB2	35133114	1.000000	0.71417	0.995000	0.50966	0.892000	0.51952	4.008000	0.57103	1.880000	0.54463	0.459000	0.35465	ATC	A|0.845;G|0.155;N|0.000;T|0.000	0.155	strong		0.612	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2			G	37879588	A	G	37879588	3	3	26	1	0	0	0	0	1	0	0	0	5208	217	8	3	2029	3	ERBB2	17	37879588	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	64283	37879588	43315622	542	10305											
KRTAP4-7	100132476	hgsc.bcm.edu	37	chr17	39240692	39240692	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	acgacctgctgccaccctagGtgctgcatctccagctgctg	6	9	10	16	1	1	0	0	0	1	0	2	1	1	0	4	1	6	5	4	1	1	1			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39240692G>C	ENST00000391417.4	+	1	234	c.234G>C	c.(232-234)agG>agC	p.R78S		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	78	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						gccaccctaggtgctgcatct	0.667																																					p.R78S		Atlas-SNP	.											KRTAP4-9_ENST00000377734,colon,carcinoma,0,2	KRTAP4-7	49	2	0			c.G234C						scavenged	.																																			SO:0001583	missense	100132476	exon1			CCCTAGGTGCTGC	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.234G>C	17.37:g.39240692G>C	ENSP00000375236:p.Arg78Ser	44	1	0.0227273		49	7	0.142857	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	0	-2.666022	0.00105	.	.	ENSG00000240871;ENSG00000212722	ENST00000391417;ENST00000377734	T	0.00547	6.66	2.45	-4.9	0.03094	.	1.381260	0.05066	N	0.480753	T	0.00210	0.0006	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41070	-0.9529	9	0.02654	T	1	.	3.5468	0.07831	0.1616:0.2372:0.4895:0.1118	.	78	Q9BYR0	KRA47_HUMAN	S	78;69	ENSP00000375236:R78S	ENSP00000375236:R78S	R	+	3	2	KRTAP4-9;KRTAP4-7	36494218	0.000000	0.05858	0.005000	0.12908	0.273000	0.26683	-0.900000	0.04097	-0.963000	0.03600	-2.430000	0.00215	AGG	.	.	none		0.667	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1			C	39240692	G	C	39240692	3	2	26	1	0	0	0	0	1	0	0	0	8564	1252	44	4	236	4	KRTAP4-7	17	39240692	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1361104	39240692	41954518	543	10306											
KRTAP4-7	100132476	hgsc.bcm.edu	37	chr17	39240791	39240791	+	Silent	SNP	C	C	G																															tgccagcccacctgctgccgCcccagctgctgccgcccctg																								rs553572799	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39240791C>G	ENST00000391417.4	+	1	333	c.333C>G	c.(331-333)cgC>cgG	p.R111R		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	136	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].		Missing. {ECO:0000269|PubMed:15955084}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.R111_C115delRPSCC(1)|p.?(1)		NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						cctgctgccgccccagctgct	0.662																																					p.R111R		Atlas-SNP	.											KRTAP4-9_ENST00000377734,NS,carcinoma,0,3	KRTAP4-7	49	3	2	Unknown(1)|Deletion - In frame(1)	NS(2)	c.C333G						scavenged	.																																			SO:0001819	synonymous_variant	100132476	exon1			CTGCCGCCCCAGC	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.333C>G	17.37:g.39240791C>G		29	0	0		32	5	0.15625	NM_033061	A0AVM6|A8MQ08|A8MTL4	Silent	SNP	ENST00000391417.4	37	CCDS45673.1																																																																																			.	.	none		0.662	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1			G	39240791	C	G	39240791	2	3	26	1	0	0	0	0	0	0	0	1	8564	726	26	4		4	KRTAP4-7	17	39240791	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	99	39240791	41954419	544	10307	128	2									
KRTAP4-7	100132476	hgsc.bcm.edu	37	chr17	39240796	39240796	+	Missense_Mutation	SNP	G	G	C																															gcccacctgctgccgccccaGctgctgccgcccctgctgct																								rs553572799|rs199957151	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39240796G>C	ENST00000391417.4	+	1	338	c.338G>C	c.(337-339)aGc>aCc	p.S113T		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	138	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].		Missing. {ECO:0000269|PubMed:15955084}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.R111_C115delRPSCC(1)|p.?(1)		NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						tgccgccccagctgctgccgc	0.667																																					p.S113T		Atlas-SNP	.											KRTAP4-7,NS,carcinoma,+1,1	KRTAP4-7	49	1	2	Unknown(1)|Deletion - In frame(1)	NS(2)	c.G338C						scavenged	.																																			SO:0001583	missense	100132476	exon1			GCCCCAGCTGCTG	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.338G>C	17.37:g.39240796G>C	ENSP00000375236:p.Ser113Thr	28	1	0.0357143		41	19	0.463415	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	0.047	-1.263726	0.01433	.	.	ENSG00000240871	ENST00000391417	T	0.00627	6.12	2.73	1.66	0.24008	.	2.038930	0.02697	N	0.111300	T	0.00552	0.0018	.	.	.	0.21290	N	0.999731	B	0.13145	0.007	B	0.12837	0.008	T	0.47222	-0.9134	9	0.17832	T	0.49	.	5.1702	0.15107	0.0:0.2319:0.5315:0.2367	.	168	Q9BYR0	KRA47_HUMAN	T	113	ENSP00000375236:S113T	ENSP00000375236:S113T	S	+	2	0	KRTAP4-7	36494322	0.010000	0.17322	0.067000	0.19924	0.024000	0.10985	-0.517000	0.06275	0.191000	0.20236	0.289000	0.19496	AGC	.	.	weak		0.667	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1			C	39240796	G	C	39240796	3	2	26	1	0	0	0	0	1	0	0	0	8564	971	34	4	340	4	KRTAP4-7	17	39240796	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	5	39240796	41954414	545	10308	128	2									
NAGLU	4669	hgsc.bcm.edu	37	chr17	40695462	40695462	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgggtgaccagctttgccGcccggcggtatggggtctcc	3	9	15	14	3	1	1	0	1	1	0	2	1	1	1	5	5	2	2	5	5	1	2	rs147293270	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:40695462G>A	ENST00000225927.2	+	6	1539	c.1438G>A	c.(1438-1440)Gcc>Acc	p.A480T	RP11-400F19.8_ENST00000585572.1_RNA	NM_000263.3	NP_000254.2	P54802	ANAG_HUMAN	N-acetylglucosaminidase, alpha	480					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)	CAGCTTTGCCGCCCGGCGGTA	0.652													G|||	2	0.000399361	0.0008	0.0	5008	,	,		17281	0.0		0.001	False		,,,				2504	0.0				p.A480T		Atlas-SNP	.											.	NAGLU	36	.	0			c.G1438A						PASS	.	G	THR/ALA	3,4401		0,3,2199	21	19	19		1438	-0.8	0	17	dbSNP_134	19	13,8581		0,13,4284	yes	missense	NAGLU	NM_000263.3	58	0,16,6483	AA,AG,GG		0.1513,0.0681,0.1231	benign	480/744	40695462	16,12982	2202	4297	6499	SO:0001583	missense	4669	exon6			TTTGCCGCCCGGC		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.1438G>A	17.37:g.40695462G>A	ENSP00000225927:p.Ala480Thr	45	0	0		57	31	0.54386	NM_000263		Missense_Mutation	SNP	ENST00000225927.2	37	CCDS11427.1	.	.	.	.	.	.	.	.	.	.	G	0.011	-1.721599	0.00700	6.81E-4	0.001513	ENSG00000108784	ENST00000225927;ENST00000377405	D	0.98550	-4.99	4.37	-0.768	0.11013	Alpha-N-acetylglucosaminidase, C-terminal (1);	2.129420	0.01419	N	0.014306	D	0.94152	0.8124	N	0.25957	0.775	0.09310	N	1	B	0.19706	0.038	B	0.15870	0.014	D	0.89959	0.4085	10	0.08381	T	0.77	0.3738	4.8095	0.13337	0.3302:0.1519:0.518:0.0	.	480	P54802	ANAG_HUMAN	T	480;156	ENSP00000225927:A480T	ENSP00000225927:A480T	A	+	1	0	NAGLU	37948988	0.000000	0.05858	0.000000	0.03702	0.074000	0.17049	0.114000	0.15520	-0.174000	0.10743	0.205000	0.17691	GCC	G|0.999;A|0.001	0.001	strong		0.652	NAGLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450385.1	NM_000263		A	40695462	G	A	40695462	3	1	26	1	0	0	0	0	1	0	0	0	10152	1087	38	1	1460	1	NAGLU	17	40695462	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1454666	40695462	40499748	546	10309											
MPP2	4355	hgsc.bcm.edu	37	chr17	41955315	41955315	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccgtagccccgctggatgcGgctgctctcctccactgtcc	3	9	10	19	3	1	0	0	0	1	0	4	1	3	1	6	2	3	4	6	2	1	1	rs118165424	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:41955315G>A	ENST00000461854.1	-	14	1676	c.1591C>T	c.(1591-1593)Cgc>Tgc	p.R531C	MPP2_ENST00000518766.1_Missense_Mutation_p.R552C|MPP2_ENST00000520305.1_Missense_Mutation_p.R368C|MPP2_ENST00000536246.1_Missense_Mutation_p.R496C|MPP2_ENST00000269095.4_Missense_Mutation_p.R507C|MPP2_ENST00000377184.3_Missense_Mutation_p.R524C|MPP2_ENST00000523501.1_Missense_Mutation_p.R496C			Q14168	MPP2_HUMAN	membrane protein, palmitoylated 2 (MAGUK p55 subfamily member 2)	531	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.			R -> C (in Ref. 3; BAG57760). {ECO:0000305}.	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)		CGCTGGATGCGGCTGCTCTCC	0.622													G|||	18	0.00359425	0.0008	0.0043	5008	,	,		18030	0.0		0.0139	False		,,,				2504	0.0				p.R507C		Atlas-SNP	.											MPP2,NS,carcinoma,+1,1	MPP2	67	1	0			c.C1519T						PASS	.	G	CYS/ARG	15,4391	22.3+/-47.3	0,15,2188	68	55	60		1519	4.2	1	17	dbSNP_132	60	129,8471	66.0+/-128.3	3,123,4174	yes	missense	MPP2	NM_005374.3	180	3,138,6362	AA,AG,GG		1.5,0.3404,1.1072	probably-damaging	507/553	41955315	144,12862	2203	4300	6503	SO:0001583	missense	4355	exon13			GGATGCGGCTGCT		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.1591C>T	17.37:g.41955315G>A	ENSP00000428286:p.Arg531Cys	82	0	0		96	59	0.614583	NM_005374	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Missense_Mutation	SNP	ENST00000461854.1	37		13	0.005952380952380952	0	0.0	3	0.008287292817679558	0	0.0	10	0.013192612137203167	g	15.76	2.928029	0.52759	0.003404	0.015	ENSG00000108852	ENST00000377184;ENST00000269095;ENST00000461854;ENST00000520305;ENST00000523501;ENST00000536246;ENST00000518766	T;T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93;0.93	5.21	4.23	0.50019	.	.	.	.	.	T	0.37376	0.1001	M	0.79475	2.455	0.80722	D	1	P;P	0.42039	0.766;0.769	B;B	0.41271	0.288;0.352	T	0.39643	-0.9604	9	0.37606	T	0.19	.	11.8021	0.52133	0.0858:0.0:0.9142:0.0	.	552;524	E7EV80;Q14168-3	.;.	C	524;507;531;368;496;496;552	ENSP00000366389:R524C;ENSP00000269095:R507C;ENSP00000428286:R531C;ENSP00000428136:R368C;ENSP00000430540:R496C;ENSP00000438012:R496C;ENSP00000428182:R552C	ENSP00000269095:R507C	R	-	1	0	MPP2	39310841	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.339000	0.65953	1.203000	0.43233	0.555000	0.69702	CGC	G|0.991;A|0.009	0.009	strong		0.622	MPP2-003	KNOWN	non_canonical_polymorphism|basic	protein_coding	protein_coding	OTTHUMT00000258388.2	NM_005374		A	41955315	G	A	41955315	3	1	26	1	0	0	0	0	1	0	0	0	9743	1116	39	1	143	1	MPP2	17	41955315	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1259853	41955315	39239895	547	10310											
ITGA2B	3674	hgsc.bcm.edu	37	chr17	42463054	42463054	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcctcctcagtcttttctaGgacgttccagtgctgccagg	6	12	10	13	1	3	0	1	0	2	0	5	1	5	1	4	2	3	2	4	2	1	4	rs76066357	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:42463054G>C	ENST00000262407.5	-	4	470	c.439C>G	c.(439-441)Cta>Gta	p.L147V	ITGA2B_ENST00000377068.3_5'Flank|ITGA2B_ENST00000353281.4_Missense_Mutation_p.L147V	NM_000419.3	NP_000410.2	P08514	ITA2B_HUMAN	integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)	147					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)	GTCTTTTCTAGGACGTTCCAG	0.667													G|||	23	0.00459265	0.0008	0.0101	5008	,	,		11686	0.0		0.0139	False		,,,				2504	0.001				p.L147V		Atlas-SNP	.											.	ITGA2B	88	.	0			c.C439G	GRCh37	CM073147	ITGA2B	M	rs76066357	PASS	.	G	VAL/LEU	14,4386	19.1+/-41.9	0,14,2186	29	36	34		439	3.5	0	17	dbSNP_134	34	113,8485	59.1+/-120.7	1,111,4187	yes	missense	ITGA2B	NM_000419.3	32	1,125,6373	CC,CG,GG		1.3143,0.3182,0.9771	benign	147/1040	42463054	127,12871	2200	4299	6499	SO:0001583	missense	3674	exon4			TTTCTAGGACGTT		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.439C>G	17.37:g.42463054G>C	ENSP00000262407:p.Leu147Val	56	0	0		43	25	0.581395	NM_000419	B2RCY8|O95366|Q14443|Q17R67	Missense_Mutation	SNP	ENST00000262407.5	37	CCDS32665.1	11	0.005036630036630037	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	7	0.009234828496042216	G	11.09	1.537077	0.27475	0.003182	0.013143	ENSG00000005961	ENST00000262407;ENST00000353281	T;T	0.71698	-0.59;-0.59	5.55	3.52	0.40303	.	0.000000	0.28515	N	0.015074	T	0.51126	0.1656	L	0.52573	1.65	0.24187	N	0.995568	B	0.26363	0.147	B	0.20184	0.028	T	0.46884	-0.9159	10	0.37606	T	0.19	.	6.7565	0.23516	0.0824:0.0:0.6063:0.3113	.	147	P08514	ITA2B_HUMAN	V	147	ENSP00000262407:L147V;ENSP00000340536:L147V	ENSP00000262407:L147V	L	-	1	2	ITGA2B	39818580	0.018000	0.18449	0.011000	0.14972	0.617000	0.37484	0.063000	0.14410	0.666000	0.31087	-0.254000	0.11334	CTA	G|0.991;C|0.009	0.009	strong		0.667	ITGA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439823.1			C	42463054	G	C	42463054	3	2	26	1	0	0	0	0	1	0	0	0	7885	991	35	4	2788	4	ITGA2B	17	42463054	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	507739	42463054	38732156	548	10311											
WNT9B	7484	hgsc.bcm.edu	37	chr17	44949945	44949945	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgcggcagccccggcacAgggcggggcccacctgaagc	7	2	15	17	3	0	1	0	1	0	0	0	1	0	1	4	5	3	2	4	5	1	0	rs118185468	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:44949945A>G	ENST00000290015.2	+	2	193	c.140A>G	c.(139-141)cAg>cGg	p.Q47R	WNT9B_ENST00000393461.2_Missense_Mutation_p.Q47R	NM_003396.1	NP_003387.1	O14905	WNT9B_HUMAN	wingless-type MMTV integration site family, member 9B	47					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)			GCCCCGGCACAGGGCGGGGCC	0.687													A|||	17	0.00339457	0.0	0.0	5008	,	,		13354	0.0		0.006	False		,,,				2504	0.0112				p.Q47R		Atlas-SNP	.											.	WNT9B	37	.	0			c.A140G						PASS	.	A	ARG/GLN	5,4395		0,5,2195	37	43	41		140	4.5	0.1	17	dbSNP_133	41	52,8536		1,50,4243	no	missense	WNT9B	NM_003396.1	43	1,55,6438	GG,GA,AA		0.6055,0.1136,0.4389	benign	47/358	44949945	57,12931	2200	4294	6494	SO:0001583	missense	7484	exon2			CGGCACAGGGCGG	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.140A>G	17.37:g.44949945A>G	ENSP00000290015:p.Gln47Arg	115	0	0		93	49	0.526882	NM_003396	Q6UXT4|Q96Q09	Missense_Mutation	SNP	ENST00000290015.2	37	CCDS11506.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	A	7.343	0.621314	0.14193	0.001136	0.006055	ENSG00000158955	ENST00000376843;ENST00000393461;ENST00000290015	T;T	0.78364	-1.17;-0.95	4.48	4.48	0.54585	.	0.507715	0.20964	N	0.082512	T	0.62974	0.2472	L	0.54323	1.7	0.29457	N	0.858057	B;B	0.22604	0.039;0.072	B;B	0.18871	0.011;0.023	T	0.58020	-0.7710	10	0.15952	T	0.53	.	11.5157	0.50520	0.8506:0.1494:0.0:0.0	.	47;47	E7EPC3;O14905	.;WNT9B_HUMAN	R	53;47;47	ENSP00000377105:Q47R;ENSP00000290015:Q47R	ENSP00000290015:Q47R	Q	+	2	0	WNT9B	42304944	.	.	0.080000	0.20451	0.128000	0.20619	.	.	2.013000	0.59113	0.374000	0.22700	CAG	A|0.997;G|0.003	0.003	strong		0.687	WNT9B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440433.1	NM_003396		G	44949945	A	G	44949945	3	3	26	1	0	0	0	0	1	0	0	0	17414	188	7	3	146	3	WNT9B	17	44949945	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	2486891	44949945	36245265	549	10312											
SCRN2	90507	hgsc.bcm.edu	37	chr17	45917703	45917703	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cggctcagaatcacagcgtgCgtcttcgacacctgttccac	8	9	9	15	4	3	1	2	0	1	1	5	2	4	1	2	1	2	2	2	1	1	2	rs11652952	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:45917703C>T	ENST00000290216.9	-	3	335	c.210G>A	c.(208-210)acG>acA	p.T70T	SCRN2_ENST00000584123.1_Silent_p.T78T|SCRN2_ENST00000407215.3_Silent_p.T70T	NM_001145023.1|NM_138355.3	NP_001138495.1|NP_612364.2	Q96FV2	SCRN2_HUMAN	secernin 2	70						extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)			cervix(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	14						TCACAGCGTGCGTCTTCGACA	0.592													C|||	147	0.029353	0.0658	0.0231	5008	,	,		20332	0.0		0.0358	False		,,,				2504	0.0082				p.T70T		Atlas-SNP	.											.	SCRN2	35	.	0			c.G210A						PASS	.	C	,	237,4169	139.2+/-174.8	7,223,1973	103	77	86		210,210	-10.2	0.3	17	dbSNP_120	86	295,8305	108.8+/-169.4	6,283,4011	no	coding-synonymous,coding-synonymous	SCRN2	NM_001145023.1,NM_138355.3	,	13,506,5984	TT,TC,CC		3.4302,5.379,4.0904	,	70/379,70/426	45917703	532,12474	2203	4300	6503	SO:0001819	synonymous_variant	90507	exon3			AGCGTGCGTCTTC	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.210G>A	17.37:g.45917703C>T		142	0	0		185	89	0.481081	NM_138355	A8K3N1|B7Z8S7|E9PBV5|Q96AC3|Q9BU04	Silent	SNP	ENST00000290216.9	37	CCDS11519.1																																																																																			C|0.963;T|0.037	0.037	strong		0.592	SCRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441383.1	NM_138355		T	45917703	C	T	45917703	2	4	26	1	0	0	0	0	0	0	0	1	13954	755	27	1		1	SCRN2	17	45917703	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	967758	45917703	35277507	550	10313											
DGKE	8526	hgsc.bcm.edu	37	chr17	54940127	54940127	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catctctagtacttcggatcAagaagatataaaggcgactg	14	10	9	8	2	2	2	1	0	1	2	4	4	2	3	0	2	1	1	0	2	7	5	rs61751972	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:54940127A>G	ENST00000284061.3	+	12	1859	c.1679A>G	c.(1678-1680)cAa>cGa	p.Q560R		NM_003647.2	NP_003638.1	P52429	DGKE_HUMAN	diacylglycerol kinase, epsilon 64kDa	560					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)					ACTTCGGATCAAGAAGATATA	0.393													A|||	4	0.000798722	0.0	0.0	5008	,	,		18984	0.0		0.004	False		,,,				2504	0.0				p.Q560R		Atlas-SNP	.											.	DGKE	47	.	0			c.A1679G						PASS	.	A	ARG/GLN	2,4404	4.2+/-10.8	0,2,2201	77	70	72		1679	0.8	1	17	dbSNP_129	72	21,8579	16.0+/-53.3	0,21,4279	yes	missense	DGKE	NM_003647.2	43	0,23,6480	GG,GA,AA		0.2442,0.0454,0.1768	benign	560/568	54940127	23,12983	2203	4300	6503	SO:0001583	missense	8526	exon12			CGGATCAAGAAGA	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.1679A>G	17.37:g.54940127A>G	ENSP00000284061:p.Gln560Arg	57	0	0		44	24	0.545455	NM_003647	Q8TBM4|Q9UKQ3	Missense_Mutation	SNP	ENST00000284061.3	37	CCDS11590.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	15.11	2.734675	0.48939	4.54E-4	0.002442	ENSG00000153933	ENST00000284061	T	0.16897	2.31	5.92	0.807	0.18714	.	0.762462	0.13392	N	0.391343	T	0.13114	0.0318	L	0.36672	1.1	0.80722	D	1	B	0.19583	0.037	B	0.19391	0.025	T	0.10753	-1.0616	10	0.27082	T	0.32	.	10.1281	0.42663	0.5593:0.3798:0.061:0.0	rs61751972	560	P52429	DGKE_HUMAN	R	560	ENSP00000284061:Q560R	ENSP00000284061:Q560R	Q	+	2	0	DGKE	52295126	0.990000	0.36364	0.996000	0.52242	0.993000	0.82548	1.290000	0.33319	0.120000	0.18254	0.524000	0.50904	CAA	A|0.998;G|0.002	0.002	strong		0.393	DGKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440601.1	NM_003647		G	54940127	A	G	54940127	3	3	26	1	0	0	0	0	1	0	0	0	4470	130	5	3	1721	3	DGKE	17	54940127	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	9022424	54940127	26255083	551	10314											
MRC2	9902	hgsc.bcm.edu	37	chr17	60767594	60767594	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actccgcgtggattcccttcCgggagcactgctattctttc	5	13	9	14	3	1	0	0	0	1	0	5	2	4	2	3	2	2	2	3	2	1	5	rs147759673		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:60767594C>A	ENST00000303375.5	+	26	4222	c.3820C>A	c.(3820-3822)Cgg>Agg	p.R1274R	MRC2_ENST00000446119.2_Silent_p.R140R	NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	1274	C-type lectin 8. {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						GATTCCCTTCCGGGAGCACTG	0.617																																					p.R1274R		Atlas-SNP	.											.	MRC2	126	.	0			c.C3820A						PASS	.	C		0,4406		0,0,2203	36	44	42		3820	3.8	1	17	dbSNP_134	42	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	MRC2	NM_006039.3		0,6,6497	AA,AC,CC		0.0698,0.0,0.0461		1274/1480	60767594	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	9902	exon26			CCCTTCCGGGAGC	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.3820C>A	17.37:g.60767594C>A		192	0	0		227	116	0.511013	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Silent	SNP	ENST00000303375.5	37	CCDS11634.1																																																																																			C|1.000;A|0.000	0.000	weak		0.617	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1			A	60767594	C	A	60767594	2	1	26	1	0	0	0	0	0	0	0	1	9767	643	23	4		4	MRC2	17	60767594	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	5827467	60767594	20427616	552	10315											
GNA13	10672	hgsc.bcm.edu	37	chr17	63010494	63010494	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtggtggtataagggcttctGttgctggtcccggcgtttgt	3	15	16	7	2	1	0	0	0	1	0	2	0	2	0	1	5	1	5	1	5	2	5			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:63010494G>A	ENST00000439174.2	-	4	1260	c.1015C>T	c.(1015-1017)Cag>Tag	p.Q339*	GNA13_ENST00000541118.1_Nonsense_Mutation_p.Q244*	NM_006572.4	NP_006563.2	Q14344	GNA13_HUMAN	guanine nucleotide binding protein (G protein), alpha 13	339					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						AAGGGCTTCTGTTGCTGGTCC	0.473																																					p.Q339X		Atlas-SNP	.											.	GNA13	69	.	0			c.C1015T						PASS	.						133	107	116					17																	63010494		2203	4300	6503	SO:0001587	stop_gained	10672	exon4			GCTTCTGTTGCTG	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.1015C>T	17.37:g.63010494G>A	ENSP00000400717:p.Gln339*	309	0	0		147	127	0.863946	NM_006572	B2R977|B7Z7R0|F5H1G8|Q8TD70	Nonsense_Mutation	SNP	ENST00000439174.2	37	CCDS11661.1	.	.	.	.	.	.	.	.	.	.	G	36	5.876075	0.97055	.	.	ENSG00000120063	ENST00000439174;ENST00000541118;ENST00000239138	.	.	.	5.93	5.93	0.95920	.	0.048927	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	.	19.949	0.97192	0.0:0.0:1.0:0.0	.	.	.	.	X	339;244;314	.	ENSP00000239138:Q314X	Q	-	1	0	GNA13	60440956	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.664000	0.74437	2.826000	0.97356	0.655000	0.94253	CAG	.	.	none		0.473	GNA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445720.1	NM_006572		A	63010494	G	A	63010494	4	1	26	1	0	0	0	0	0	1	0	0	6509	1386	48	2	122	2	GNA13	17	63010494	Nonsense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	2242900	63010494	18184716	553	10316											
ST6GALNAC2	10610	hgsc.bcm.edu	37	chr17	74562308	74562308	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttttcgttcgaaatagtggtCggaaaatttccagtagttgc	10	15	10	6	3	0	0	0	0	0	0	4	2	1	1	1	2	1	3	1	2	5	7	rs373585653		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:74562308C>T	ENST00000225276.5	-	9	1322	c.1003G>A	c.(1003-1005)Gac>Aac	p.D335N		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	335					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						AAATAGTGGTCGGAAAATTTC	0.473																																					p.D335N		Atlas-SNP	.											.	ST6GALNAC2	29	.	0			c.G1003A						PASS	.	C	ASN/ASP	0,4406		0,0,2203	171	154	160		1003	3.5	0.7	17		160	1,8599	1.2+/-3.3	0,1,4299	no	missense	ST6GALNAC2	NM_006456.2	23	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	335/375	74562308	1,13005	2203	4300	6503	SO:0001583	missense	10610	exon9			AGTGGTCGGAAAA	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.1003G>A	17.37:g.74562308C>T	ENSP00000225276:p.Asp335Asn	76	0	0		82	36	0.439024	NM_006456	Q12971	Missense_Mutation	SNP	ENST00000225276.5	37	CCDS11747.1	.	.	.	.	.	.	.	.	.	.	C	18.54	3.646027	0.67358	0.0	1.16E-4	ENSG00000070731	ENST00000225276	T	0.29397	1.57	5.45	3.47	0.39725	.	0.000000	0.85682	D	0.000000	T	0.43322	0.1242	L	0.54323	1.7	0.50171	D	0.999853	D	0.76494	0.999	P	0.62435	0.902	T	0.13629	-1.0502	10	0.31617	T	0.26	-26.2793	10.7107	0.45982	0.0:0.8435:0.0:0.1565	.	335	Q9UJ37	SIA7B_HUMAN	N	335	ENSP00000225276:D335N	ENSP00000225276:D335N	D	-	1	0	ST6GALNAC2	72073903	1.000000	0.71417	0.683000	0.30040	0.636000	0.38137	5.182000	0.65059	0.681000	0.31386	0.655000	0.94253	GAC	.	.	weak		0.473	ST6GALNAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450650.1	NM_006456		T	74562308	C	T	74562308	3	4	26	1	0	0	0	0	1	0	0	0	15239	884	31	1	125	1	ST6GALNAC2	17	74562308	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	11551814	74562308	6632902	554	10317											
DNAH17	8632	hgsc.bcm.edu	37	chr17	76503585	76503585	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	aagcgctgggagtcccccggGagctgggtgcggatgtcttc	5	8	17	11	3	1	0	0	0	1	0	3	3	2	3	2	4	3	2	2	4	1	1	rs12943086	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:76503585G>C	ENST00000585328.1	-	28	4654	c.4530C>G	c.(4528-4530)ctC>ctG	p.L1510L	DNAH17_ENST00000389840.5_Silent_p.L1509L	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	1509	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)			AGTCCCCCGGGAGCTGGGTGC	0.597													G|||	60	0.0119808	0.0015	0.0317	5008	,	,		19330	0.0		0.0338	False		,,,				2504	0.002				p.L1513L		Atlas-SNP	.											.	DNAH17	347	.	0			c.C4539G						PASS	.	G		19,4133		0,19,2057	45	50	48		4539	-1.1	0.9	17	dbSNP_121	48	286,8196		6,274,3961	no	coding-synonymous	DNAH17	NM_173628.3		6,293,6018	CC,CG,GG		3.3718,0.4576,2.4141		1513/4463	76503585	305,12329	2076	4241	6317	SO:0001819	synonymous_variant	8632	exon28			CCCCGGGAGCTGG	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.4530C>G	17.37:g.76503585G>C		140	0	0		126	59	0.468254	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				G|0.977;C|0.023	0.023	strong		0.597	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		C	76503585	G	C	76503585	2	2	26	1	0	0	0	0	0	0	0	1	4603	1161	41	4		4	DNAH17	17	76503585	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1941277	76503585	4691625	555	10318											
GAA	2548	hgsc.bcm.edu	37	chr17	78078656	78078656	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcccccccaacagccgcttcGattgcgcccctgacaaggcc	7	6	8	20	3	0	1	0	1	0	0	2	2	1	1	7	1	3	1	7	1	2	2	rs1800299	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:78078656G>A	ENST00000302262.3	+	2	490	c.271G>A	c.(271-273)Gat>Aat	p.D91N	GAA_ENST00000390015.3_Missense_Mutation_p.D91N	NM_000152.3	NP_000143.2	P10253	LYAG_HUMAN	glucosidase, alpha; acid	91	P-type. {ECO:0000255|PROSITE- ProRule:PRU00779}.		D -> N (in allele GAA*2; lower affinity for glycogen and starch but not for lower-molecular weight substrates; dbSNP:rs1800299). {ECO:0000269|PubMed:21109266, ECO:0000269|PubMed:2203258, ECO:0000269|PubMed:9521422}.		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)	CAGCCGCTTCGATTGCGCCCC	0.692													G|||	58	0.0115815	0.0053	0.0173	5008	,	,		15176	0.001		0.0278	False		,,,				2504	0.0102				p.D91N		Atlas-SNP	.											.	GAA	66	.	0			c.G271A	GRCh37	CD983801	GAA	D	rs1800299	PASS	.	G	ASN/ASP,ASN/ASP,ASN/ASP	29,4377	34.3+/-65.2	0,29,2174	35	33	34	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	271,271,271	4.9	1	17	dbSNP_89	34	271,8329	100.8+/-162.1	6,259,4035	yes	missense,missense,missense	GAA	NM_000152.3,NM_001079803.1,NM_001079804.1	23,23,23	6,288,6209	AA,AG,GG		3.1512,0.6582,2.3066	probably-damaging,probably-damaging,probably-damaging	91/953,91/953,91/953	78078656	300,12706	2203	4300	6503	SO:0001583	missense	2548	exon3			CGCTTCGATTGCG		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.271G>A	17.37:g.78078656G>A	ENSP00000305692:p.Asp91Asn	132	0	0		122	72	0.590164	NM_001079803	Q09GN4|Q14351|Q16302|Q8IWE7	Missense_Mutation	SNP	ENST00000302262.3	37	CCDS32760.1	34	0.015567765567765568	4	0.008130081300813009	8	0.022099447513812154	0	0.0	22	0.029023746701846966	G	16.20	3.054964	0.55325	0.006582	0.031512	ENSG00000171298	ENST00000302262;ENST00000390015	T;T	0.58210	0.35;0.35	4.94	4.94	0.65067	P-type trefoil, conserved site (1);P-type trefoil (4);	0.000000	0.85682	D	0.000000	T	0.41811	0.1175	L	0.45051	1.395	0.53688	D	0.99997	D	0.89917	1.0	D	0.91635	0.999	T	0.56836	-0.7913	10	0.41790	T	0.15	-47.1701	16.922	0.86166	0.0:0.0:1.0:0.0	rs1800299;rs52818006	91	P10253	LYAG_HUMAN	N	91	ENSP00000305692:D91N;ENSP00000374665:D91N	ENSP00000305692:D91N	D	+	1	0	GAA	75693251	1.000000	0.71417	0.992000	0.48379	0.213000	0.24496	9.466000	0.97665	2.279000	0.76181	0.655000	0.94253	GAT	G|0.979;A|0.021	0.021	strong		0.692	GAA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437441.1			A	78078656	G	A	78078656	3	1	26	1	0	0	0	0	1	0	0	0	6155	1058	37	1	273	1	GAA	17	78078656	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1575071	78078656	3116554	556	10319											
CARD14	79092	hgsc.bcm.edu	37	chr17	78177680	78177680	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcagcagtgcaccgtgacccGcaaggtgaggctccagggag	9	5	15	12	2	1	2	1	2	0	0	2	3	2	3	3	3	2	4	3	3	1	0	rs143600438		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:78177680G>A	ENST00000573882.1	+	18	2815	c.2279G>A	c.(2278-2280)cGc>cAc	p.R760H	CARD14_ENST00000392434.2_3'UTR|RP11-334C17.5_ENST00000573935.1_RNA|RP11-334C17.5_ENST00000570309.1_RNA|RP11-334C17.5_ENST00000572730.1_RNA|CARD14_ENST00000344227.2_Missense_Mutation_p.R760H|RP11-334C17.5_ENST00000576824.1_RNA|RP11-334C17.5_ENST00000573346.1_RNA			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	760					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)			ACCGTGACCCGCAAGGTGAGG	0.672													G|||	1	0.000199681	0.0	0.0	5008	,	,		16335	0.001		0.0	False		,,,				2504	0.0				p.R760H		Atlas-SNP	.											.	CARD14	98	.	0			c.G2279A						PASS	.	G	HIS/ARG	2,4390		0,2,2194	22	21	21		2279	4.1	1	17	dbSNP_134	21	0,8592		0,0,4296	no	missense	CARD14	NM_024110.3	29	0,2,6490	AA,AG,GG		0.0,0.0455,0.0154	probably-damaging	760/1005	78177680	2,12982	2196	4296	6492	SO:0001583	missense	79092	exon16			TGACCCGCAAGGT	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.2279G>A	17.37:g.78177680G>A	ENSP00000458715:p.Arg760His	298	0	0		319	148	0.46395	NM_024110	B8QQJ3|Q9BVB5	Missense_Mutation	SNP	ENST00000573882.1	37	CCDS11768.1	.	.	.	.	.	.	.	.	.	.	G	15.52	2.859093	0.51376	4.55E-4	0.0	ENSG00000141527	ENST00000344227	T	0.05855	3.38	4.12	4.12	0.48240	.	6.592470	0.00481	U	0.000120	T	0.18635	0.0447	M	0.76328	2.33	0.80722	D	1	P	0.42584	0.784	B	0.44224	0.444	T	0.16482	-1.0401	10	0.44086	T	0.13	-13.3243	15.1676	0.72840	0.0:0.0:1.0:0.0	.	760	Q9BXL6	CAR14_HUMAN	H	760	ENSP00000344549:R760H	ENSP00000344549:R760H	R	+	2	0	CARD14	75792275	1.000000	0.71417	1.000000	0.80357	0.276000	0.26787	3.682000	0.54656	1.865000	0.54081	0.485000	0.47835	CGC	G|1.000;A|0.000	0.000	weak		0.672	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1			A	78177680	G	A	78177680	3	1	26	1	0	0	0	0	1	0	0	0	2648	1087	38	1	2502	1	CARD14	17	78177680	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	99024	78177680	3017530	557	10320											
RNF213	57674	hgsc.bcm.edu	37	chr17	78338305	78338305	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ctaggaaccgagagccgcgtCcccgagttacaggggctggt	8	6	15	12	4	0	1	0	0	0	1	1	4	1	2	4	4	3	2	4	4	3	2	rs148958011	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:78338305C>T	ENST00000582970.1	+	42	11966	c.11823C>T	c.(11821-11823)gtC>gtT	p.V3941V	CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000508628.2_Silent_p.V3990V|CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000336301.6_Silent_p.V2014V	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3941					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)			AGAGCCGCGTCCCCGAGTTAC	0.582													C|||	4	0.000798722	0.0	0.0014	5008	,	,		17383	0.0		0.001	False		,,,				2504	0.002				p.V3941V		Atlas-SNP	.											.	RNF213	766	.	0			c.C11823T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	74	70	71		11970	-3.7	0	17	dbSNP_134	71	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	RNF213	NM_020914.4		0,5,6498	TT,TC,CC		0.0465,0.0227,0.0384		3990/5257	78338305	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	57674	exon42			CCGCGTCCCCGAG	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.11823C>T	17.37:g.78338305C>T		102	0	0		137	79	0.576642	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	37	CCDS58606.1																																																																																			C|0.999;T|0.001	0.001	strong		0.582	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		T	78338305	C	T	78338305	2	4	26	1	0	0	0	0	0	0	0	1	13492	842	30	2		2	RNF213	17	78338305	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	160625	78338305	2856905	558	10321											
AATK	9625	hgsc.bcm.edu	37	chr17	79093211	79093211	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcggcgtccgagtcagacacGtgcgtgatggagaagcggga	9	6	17	9	6	1	3	1	1	0	2	3	6	2	4	1	3	2	0	1	3	1	0	rs201255728	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:79093211G>A	ENST00000326724.4	-	13	4077	c.4053C>T	c.(4051-4053)caC>caT	p.H1351H	AATK_ENST00000417379.1_Silent_p.H1248H	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	1351					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)			AGTCAGACACGTGCGTGATGG	0.746													G|||	4	0.000798722	0.0	0.0	5008	,	,		12763	0.0		0.003	False		,,,				2504	0.001				p.H1351H		Atlas-SNP	.											.	AATK	102	.	0			c.C4053T						PASS	.	G	,	2,4040		0,2,2019	15	19	18		4053,3744	-2.3	0.7	17		18	15,8273		0,15,4129	no	coding-synonymous,coding-synonymous	AATK	NM_001080395.2,NM_004920.2	,	0,17,6148	AA,AG,GG		0.181,0.0495,0.1379	,	1351/1375,1248/1272	79093211	17,12313	2021	4144	6165	SO:0001819	synonymous_variant	9625	exon13			AGACACGTGCGTG	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.4053C>T	17.37:g.79093211G>A		22	0	0		15	7	0.466667	NM_001080395	O75136|Q6ZN31|Q86X28	Silent	SNP	ENST00000326724.4	37	CCDS45807.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	5.059	0.196531	0.09599	4.95E-4	0.00181	ENSG00000181409	ENST00000417379	.	.	.	3.52	-2.34	0.06704	.	.	.	.	.	T	0.52289	0.1725	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48547	-0.9026	4	.	.	.	.	8.3273	0.32165	0.0794:0.0:0.3373:0.5832	.	.	.	.	M	1304	.	.	T	-	2	0	AATK	76707806	0.871000	0.30034	0.747000	0.31113	0.083000	0.17756	-0.123000	0.10611	-0.245000	0.09625	0.297000	0.19635	ACG	G|0.999;A|0.001	0.001	strong		0.746	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920		A	79093211	G	A	79093211	2	1	26	1	0	0	0	0	0	0	0	1	26	1136	40	1		1	AATK	17	79093211	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	754906	79093211	2101999	559	10322											
MYOM1	8736	hgsc.bcm.edu	37	chr18	3129297	3129297	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagccgctttctgtggtggCggggtaagctcttcctgaac	5	11	15	10	2	2	1	0	1	2	0	3	2	3	2	2	5	3	3	2	5	2	3	rs72860212	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:3129297C>T	ENST00000356443.4	-	18	3060	c.2727G>A	c.(2725-2727)ccG>ccA	p.P909P	MYOM1_ENST00000400569.3_Silent_p.P909P|MYOM1_ENST00000261606.7_Intron|MYOM1_ENST00000582016.1_5'UTR	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	909					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						TCTGTGGTGGCGGGGTAAGCT	0.493											OREG0024838	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	3	0.000599042	0.0	0.0014	5008	,	,		19213	0.0		0.002	False		,,,				2504	0.0				p.P909P		Atlas-SNP	.											MYOM1,bladder,carcinoma,-1,1	MYOM1	192	1	0			c.G2727A						PASS	.	C	,	0,3830		0,0,1915	112	118	116		2727,	-5.7	0	18	dbSNP_130	116	28,8192		0,28,4082	no	coding-synonymous,intron	MYOM1	NM_003803.3,NM_019856.1	,	0,28,5997	TT,TC,CC		0.3406,0.0,0.2324	,	909/1686,	3129297	28,12022	1915	4110	6025	SO:0001819	synonymous_variant	8736	exon18			TGGTGGCGGGGTA	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.2727G>A	18.37:g.3129297C>T		253	0	0	608	231	121	0.52381	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	37	CCDS45824.1																																																																																			C|0.998;T|0.002	0.002	strong		0.493	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803		T	3129297	C	T	3129297	2	4	26	1	0	0	0	0	0	0	0	1	10100	755	27	1		1	MYOM1	18	3129297	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10		3129297	74947951	560	10323											
CEP192	55125	hgsc.bcm.edu	37	chr18	13015389	13015389	+	5'UTR	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctaaagagtgacctaagccaCactagcttattagaaaatga	17	9	7	8	0	0	4	0	2	0	2	0	4	0	4	2	0	2	1	2	0	8	5	rs117292623	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:13015389C>G	ENST00000325971.8	+	0	662				CEP192_ENST00000506447.1_Missense_Mutation_p.H194Q			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						ACCTAAGCCACACTAGCTTAT	0.398													C|||	12	0.00239617	0.0008	0.0	5008	,	,		21062	0.0		0.006	False		,,,				2504	0.0051				p.H194Q		Atlas-SNP	.											CEP192_ENST00000506447,colon,carcinoma,+2,1	CEP192	340	1	0			c.C582G						PASS	.	C	GLN/HIS	1,1383		0,1,691	179	134	147		582	0.2	0.2	18	dbSNP_132	147	28,3154		0,28,1563	yes	missense	CEP192	NM_032142.3	24	0,29,2254	GG,GC,CC		0.8799,0.0723,0.6351	possibly-damaging	194/2538	13015389	29,4537	692	1591	2283	SO:0001623	5_prime_UTR_variant	55125	exon6			AAGCCACACTAGC	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.-932C>G	18.37:g.13015389C>G		79	0	0		110	59	0.536364	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	9.667	1.145783	0.21288	7.23E-4	0.008799	ENSG00000101639	ENST00000506447	T	0.05855	3.38	4.04	0.238	0.15480	.	.	.	.	.	T	0.02649	0.0080	N	0.24115	0.695	0.21878	N	0.999499	B	0.17268	0.021	B	0.18561	0.022	T	0.43065	-0.9414	9	0.40728	T	0.16	.	3.0221	0.06079	0.0:0.313:0.2373:0.4497	.	194	E9PF99	.	Q	194	ENSP00000427550:H194Q	ENSP00000427550:H194Q	H	+	3	2	CEP192	13005389	0.000000	0.05858	0.151000	0.22473	0.948000	0.59901	0.222000	0.17699	0.037000	0.15575	0.563000	0.77884	CAC	C|0.997;G|0.003	0.003	strong		0.398	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142		G	13015389	C	G	13015389	1	3	26	0	1	0	0	0	0	0	0	0	3253	477	17	4		4	CEP192	18	13015389	5'UTR	SNP	C	TCGA-G8-6907-01A-11D-2210-10	9886092	13015389	65061859	561	10324											
ZNF519	162655	hgsc.bcm.edu	37	chr18	14104957	14104957	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgttgagtaagggttgagcGtctgttaaaagctttgccac	10	13	12	6	1	1	2	0	2	1	0	1	2	1	2	1	1	3	5	1	1	3	5	rs149267105	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:14104957G>A	ENST00000590202.1	-	3	1734	c.1582C>T	c.(1582-1584)Cgc>Tgc	p.R528C	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	528					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						AGGGTTGAGCGTCTGTTAAAA	0.398													G|||	3	0.000599042	0.0008	0.0	5008	,	,		19567	0.0		0.002	False		,,,				2504	0.0				p.R528C		Atlas-SNP	.											.	ZNF519	53	.	0			c.C1582T						PASS	.	G	CYS/ARG	6,4400	11.4+/-27.6	0,6,2197	134	137	136		1582	-2.4	0	18	dbSNP_134	136	29,8571	21.6+/-65.8	0,29,4271	yes	missense	ZNF519	NM_145287.3	180	0,35,6468	AA,AG,GG		0.3372,0.1362,0.2691	probably-damaging	528/541	14104957	35,12971	2203	4300	6503	SO:0001583	missense	162655	exon3			TTGAGCGTCTGTT	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.1582C>T	18.37:g.14104957G>A	ENSP00000464872:p.Arg528Cys	49	0	0		70	38	0.542857	NM_145287		Missense_Mutation	SNP	ENST00000590202.1	37	CCDS32797.1	3	0.0013736263736263737	2	0.0040650406504065045	0	0.0	0	0.0	1	0.0013192612137203166	G	5.238	0.229427	0.09916	0.001362	0.003372	ENSG00000175322	ENST00000309305	.	.	.	1.2	-2.4	0.06583	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.30510	0.0767	M	0.64404	1.975	0.09310	N	1	B	0.32829	0.386	B	0.26416	0.069	T	0.11717	-1.0576	8	0.45353	T	0.12	.	2.7452	0.05264	0.232:0.0:0.2362:0.5318	.	528	Q8TB69	ZN519_HUMAN	C	528	.	ENSP00000307908:R528C	R	-	1	0	ZNF519	14094957	0.000000	0.05858	0.000000	0.03702	0.509000	0.34042	-1.143000	0.03200	-1.216000	0.02607	0.089000	0.15464	CGC	G|0.998;A|0.002	0.002	strong		0.398	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287		A	14104957	G	A	14104957	3	1	26	1	0	0	0	0	1	0	0	0	17979	1145	40	1	44	1	ZNF519	18	14104957	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1089568	14104957	63972291	562	10325											
ZNF521	25925	hgsc.bcm.edu	37	chr18	22805218	22805218	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	taggctgccccacaaatgtcGcagccgtacataggctcaga	11	7	10	13	2	1	1	1	0	0	1	2	1	1	1	3	2	3	4	3	2	4	3	rs35535552	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:22805218G>A	ENST00000361524.3	-	4	2812	c.2664C>T	c.(2662-2664)tgC>tgT	p.C888C	ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000538137.2_Silent_p.C888C|ZNF521_ENST00000584787.1_Silent_p.C668C	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	888					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)					CACAAATGTCGCAGCCGTACA	0.522			T	PAX5	ALL								g|||	10	0.00199681	0.0	0.0072	5008	,	,		19940	0.0		0.004	False		,,,				2504	0.001				p.C888C		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	ZNF521,caecum,carcinoma,0,1	ZNF521	269	1	0			c.C2664T						scavenged	.	A		4,4402	8.1+/-20.4	0,4,2199	121	113	115		2664	-11.7	0	18	dbSNP_126	115	42,8558	27.9+/-77.7	0,42,4258	no	coding-synonymous	ZNF521	NM_015461.2		0,46,6457	AA,AG,GG		0.4884,0.0908,0.3537		888/1312	22805218	46,12960	2203	4300	6503	SO:0001819	synonymous_variant	25925	exon4			AATGTCGCAGCCG	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.2664C>T	18.37:g.22805218G>A		192	1	0.00520833		285	128	0.449123	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Silent	SNP	ENST00000361524.3	37	CCDS32806.1																																																																																			G|0.995;A|0.005	0.005	strong		0.522	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		A	22805218	G	A	22805218	2	1	26	1	0	0	0	0	0	0	0	1	17980	1079	38	1		1	ZNF521	18	22805218	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	8700261	22805218	55272030	563	10326											
DSG3	1830	hgsc.bcm.edu	37	chr18	29054294	29054294	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	aaccatgagaacaaggcattCcactggaggaaccaataagg	17	5	10	9	0	0	1	0	1	0	1	1	4	1	3	3	4	3	1	3	4	6	2	rs111986709	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:29054294C>T	ENST00000257189.4	+	15	2395	c.2312C>T	c.(2311-2313)tCc>tTc	p.S771F		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	771					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)			ACAAGGCATTCCACTGGAGGA	0.493													C|||	58	0.0115815	0.0015	0.013	5008	,	,		18033	0.0		0.0249	False		,,,				2504	0.0225				p.S771F		Atlas-SNP	.											.	DSG3	172	.	0			c.C2312T						PASS	.	C	PHE/SER	40,4366	43.1+/-76.7	0,40,2163	130	127	128		2312	6.1	1	18	dbSNP_132	128	309,8291	111.4+/-171.7	4,301,3995	yes	missense	DSG3	NM_001944.2	155	4,341,6158	TT,TC,CC		3.593,0.9079,2.6834	probably-damaging	771/1000	29054294	349,12657	2203	4300	6503	SO:0001583	missense	1830	exon15			GGCATTCCACTGG	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.2312C>T	18.37:g.29054294C>T	ENSP00000257189:p.Ser771Phe	146	0	0		170	94	0.552941	NM_001944	A8K2V2	Missense_Mutation	SNP	ENST00000257189.4	37	CCDS11898.1	27	0.012362637362637362	0	0.0	4	0.011049723756906077	0	0.0	23	0.030343007915567283	C	16.16	3.045378	0.55110	0.009079	0.03593	ENSG00000134757	ENST00000257189	T	0.63255	-0.03	6.06	6.06	0.98353	.	0.000000	0.50627	D	0.000110	T	0.37732	0.1014	M	0.71581	2.175	0.41681	D	0.989299	P	0.35700	0.516	B	0.41174	0.349	T	0.60712	-0.7209	10	0.59425	D	0.04	.	18.8049	0.92032	0.0:1.0:0.0:0.0	.	771	P32926	DSG3_HUMAN	F	771	ENSP00000257189:S771F	ENSP00000257189:S771F	S	+	2	0	DSG3	27308292	0.993000	0.37304	1.000000	0.80357	0.130000	0.20726	3.179000	0.50887	2.879000	0.98667	0.650000	0.86243	TCC	C|0.975;T|0.025	0.025	strong		0.493	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944		T	29054294	C	T	29054294	3	4	26	1	0	0	0	0	1	0	0	0	4780	855	30	2	2370	2	DSG3	18	29054294	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	6249076	29054294	49022954	564	10327											
MCART2	147407	hgsc.bcm.edu	37	chr18	29340051	29340051	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttaatgggacctcgaaggcCgaaaaacaagacattgctga	15	7	10	9	2	0	2	0	1	0	1	1	5	0	3	2	2	2	1	2	2	5	2			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:29340051C>T	ENST00000579441.2	-	1	573	c.574G>A	c.(574-576)Ggc>Agc	p.G192S	SLC25A52_ENST00000269205.5_Missense_Mutation_p.G202S			Q3SY17	S2552_HUMAN	solute carrier family 25, member 52	192					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)											CCTCGAAGGCCGAAAAACAAG	0.473																																					p.G202S		Atlas-SNP	.											MCART2_ENST00000269205,NS,carcinoma,+1,2	.	.	2	0			c.G604A						scavenged	.						71	70	70					18																	29340051		2203	4297	6500	SO:0001583	missense	147407	exon1			GAAGGCCGAAAAA		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.574G>A	18.37:g.29340051C>T	ENSP00000462754:p.Gly192Ser	211	1	0.00473934		292	19	0.0650685	NM_001034172		Missense_Mutation	SNP	ENST00000579441.2	37		.	.	.	.	.	.	.	.	.	.	C	13.46	2.243739	0.39697	.	.	ENSG00000141437	ENST00000269205;ENST00000535708	T	0.79141	-1.24	1.22	0.273	0.15650	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	T	0.65544	0.2701	L	0.54323	1.7	0.48511	D	0.999667	B	0.24483	0.104	B	0.19391	0.025	T	0.51052	-0.8754	10	0.26408	T	0.33	.	5.5522	0.17097	0.0:0.7844:0.0:0.2156	.	192	Q3SY17	MCAR2_HUMAN	S	202;192	ENSP00000372612:G202S	ENSP00000372612:G202S	G	-	1	0	MCART2	27594049	1.000000	0.71417	0.108000	0.21378	0.927000	0.56198	4.925000	0.63425	0.084000	0.17077	0.505000	0.49811	GGC	.	.	none		0.473	SLC25A52-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_084000		T	29340051	C	T	29340051	3	4	26	1	0	0	0	0	1	0	0	0	9379	652	23	1	323	1	MCART2	18	29340051	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	285757	29340051	48737197	565	10328											
SLC14A2	8170	hgsc.bcm.edu	37	chr18	43204744	43204744	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cgacatccccggatactcacCcagctctgcccctcctggaa	8	7	7	19	2	2	0	1	0	1	0	4	3	4	2	6	2	3	1	6	2	2	1	rs149251757	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:43204744C>G	ENST00000255226.6	+	2	931	c.115C>G	c.(115-117)Cca>Gca	p.P39A	SLC14A2_ENST00000586448.1_Missense_Mutation_p.P39A	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	39					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						GGATACTCACCCAGCTCTGCC	0.567													C|||	3	0.000599042	0.0	0.0	5008	,	,		20005	0.0		0.001	False		,,,				2504	0.002				p.P39A		Atlas-SNP	.											.	SLC14A2	121	.	0			c.C115G						PASS	.	C	ALA/PRO,ALA/PRO	4,4402	8.1+/-20.4	0,4,2199	81	78	79		115,115	4.2	1	18	dbSNP_134	79	14,8586	10.5+/-38.8	0,14,4286	yes	missense,missense	SLC14A2	NM_001242692.1,NM_007163.3	27,27	0,18,6485	GG,GC,CC		0.1628,0.0908,0.1384	benign,benign	39/921,39/921	43204744	18,12988	2203	4300	6503	SO:0001583	missense	8170	exon3			ACTCACCCAGCTC	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.115C>G	18.37:g.43204744C>G	ENSP00000255226:p.Pro39Ala	77	0	0		88	50	0.568182	NM_001242692	A8K8Q7|Q2TBD6|Q96PH5	Missense_Mutation	SNP	ENST00000255226.6	37	CCDS11924.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	10.95	1.496199	0.26861	9.08E-4	0.001628	ENSG00000132874	ENST00000255226;ENST00000323329	T;T	0.54279	1.26;0.58	5.08	4.2	0.49525	.	0.077891	0.49305	D	0.000142	T	0.47820	0.1466	M	0.63428	1.95	0.35661	D	0.812527	P;P	0.40970	0.455;0.734	B;B	0.40165	0.142;0.321	T	0.56469	-0.7974	10	0.25751	T	0.34	-7.9968	9.6267	0.39754	0.0:0.9023:0.0:0.0977	.	39;39	Q15849;E7EPU1	UT2_HUMAN;.	A	39	ENSP00000255226:P39A;ENSP00000320689:P39A	ENSP00000255226:P39A	P	+	1	0	SLC14A2	41458742	0.100000	0.21855	0.995000	0.50966	0.555000	0.35460	0.953000	0.29162	1.269000	0.44280	0.462000	0.41574	CCA	C|0.999;G|0.001	0.001	strong		0.567	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1			G	43204744	C	G	43204744	3	3	26	1	0	0	0	0	1	0	0	0	14412	623	22	4	117	4	SLC14A2	18	43204744	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	13864693	43204744	34872504	566	10329											
CCDC68	80323	hgsc.bcm.edu	37	chr18	52605279	52605279	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	taagcaaatccaaactgcaaCaagaaggatccatttcagaa	19	7	6	9	0	1	2	1	0	0	2	3	3	3	3	2	1	4	2	2	1	7	2	rs72928889	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:52605279C>T	ENST00000591504.1	-	5	528	c.254G>A	c.(253-255)tGt>tAt	p.C85Y	CCDC68_ENST00000432185.1_Missense_Mutation_p.C85Y|CCDC68_ENST00000337363.4_Missense_Mutation_p.C85Y	NM_025214.2	NP_079490.1	Q9H2F9	CCD68_HUMAN	coiled-coil domain containing 68	85										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)		CAAACTGCAACAAGAAGGATC	0.358													C|||	65	0.0129792	0.003	0.0173	5008	,	,		18079	0.0		0.0417	False		,,,				2504	0.0072				p.C85Y		Atlas-SNP	.											.	CCDC68	38	.	0			c.G254A						PASS	.	C	TYR/CYS,TYR/CYS	31,4375	37.6+/-69.7	1,29,2173	98	90	93		254,254	1.1	0	18	dbSNP_130	93	309,8291	111.8+/-172.0	5,299,3996	yes	missense,missense	CCDC68	NM_001143829.1,NM_025214.2	194,194	6,328,6169	TT,TC,CC		3.593,0.7036,2.6142	benign,benign	85/336,85/336	52605279	340,12666	2203	4300	6503	SO:0001583	missense	80323	exon5			CTGCAACAAGAAG		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.254G>A	18.37:g.52605279C>T	ENSP00000466690:p.Cys85Tyr	182	0	0		188	89	0.473404	NM_025214	B2R9I3	Missense_Mutation	SNP	ENST00000591504.1	37	CCDS11959.1	37	0.01694139194139194	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	25	0.032981530343007916	C	14.87	2.663408	0.47572	0.007036	0.03593	ENSG00000166510	ENST00000337363;ENST00000432185	T;T	0.21361	2.01;2.01	5.18	1.09	0.20402	.	0.935721	0.09027	N	0.859369	T	0.03263	0.0095	L	0.46157	1.445	0.09310	N	1	P	0.51351	0.944	B	0.41036	0.346	T	0.14227	-1.0480	10	0.22109	T	0.4	2.9925	2.645	0.04981	0.1348:0.4379:0.2634:0.1639	.	85	Q9H2F9	CCD68_HUMAN	Y	85	ENSP00000337209:C85Y;ENSP00000413406:C85Y	ENSP00000337209:C85Y	C	-	2	0	CCDC68	50756277	0.000000	0.05858	0.009000	0.14445	0.868000	0.49771	-0.460000	0.06720	0.563000	0.29222	-0.181000	0.13052	TGT	C|0.975;T|0.025	0.025	strong		0.358	CCDC68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256006.1	NM_025214		T	52605279	C	T	52605279	3	4	26	1	0	0	0	0	1	0	0	0	2842	478	17	2	785	2	CCDC68	18	52605279	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	9400535	52605279	25471969	567	10330											
CDH19	28513	hgsc.bcm.edu	37	chr18	64176386	64176386	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtttgtacttgtaagtgaCgggattccattgtcggcaat	8	15	12	6	2	0	1	0	1	0	0	2	2	1	2	1	2	1	4	1	2	3	6	rs150353589	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:64176386C>T	ENST00000262150.2	-	11	1966	c.1674G>A	c.(1672-1674)ccG>ccA	p.P558P	CDH19_ENST00000540086.1_Intron	NM_021153.3	NP_066976.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	1833	Cadherin 5. {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)				TTGTAAGTGACGGGATTCCAT	0.448													c|||	21	0.00419329	0.0008	0.0086	5008	,	,		16460	0.0		0.0139	False		,,,				2504	0.0				p.P558P		Atlas-SNP	.											CDH19,mucosal,malignant_melanoma,-2,2	CDH19	141	2	0			c.G1674A						PASS	.	T		6,4400	11.4+/-27.6	0,6,2197	199	172	181		1674	1.3	0.1	18	dbSNP_134	181	58,8542	36.4+/-91.3	0,58,4242	no	coding-synonymous	CDH19	NM_021153.2		0,64,6439	TT,TC,CC		0.6744,0.1362,0.4921		558/773	64176386	64,12942	2203	4300	6503	SO:0001819	synonymous_variant	28513	exon11			AAGTGACGGGATT	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.1674G>A	18.37:g.64176386C>T		210	0	0		221	125	0.565611	NM_021153	O15098	Silent	SNP	ENST00000262150.2	37	CCDS11994.1																																																																																			A|0.000;C|0.996;T|0.004	0.004	strong		0.448	CDH19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256219.1	NM_021153		T	64176386	C	T	64176386	2	4	26	1	0	0	0	0	0	0	0	1	3106	523	19	1		1	CDH19	18	64176386	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	11571107	64176386	13900862	568	10331											
CNDP1	84735	hgsc.bcm.edu	37	chr18	72228136	72228136	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tacctcccatcatcctggccGaactggggagcgatcccacg	8	7	10	16	3	1	0	1	0	0	0	4	3	4	1	5	3	3	0	5	3	2	1	rs150779486	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:72228136G>A	ENST00000358821.3	+	4	577	c.349G>A	c.(349-351)Gaa>Aaa	p.E117K	CNDP1_ENST00000585136.1_Intron|RP11-231E4.3_ENST00000583702.1_RNA|CNDP1_ENST00000582365.1_Missense_Mutation_p.E74K	NM_032649.5	NP_116038	Q96KN2	CNDP1_HUMAN	carnosine dipeptidase 1 (metallopeptidase M20 family)	117						extracellular region (GO:0005576)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27		Esophageal squamous(42;0.129)|Prostate(75;0.157)|Melanoma(33;0.211)		BRCA - Breast invasive adenocarcinoma(31;0.109)		CATCCTGGCCGAACTGGGGAG	0.552													G|||	12	0.00239617	0.0091	0.0	5008	,	,		16481	0.0		0.0	False		,,,				2504	0.0				p.E117K	Melanoma(32;1029 1042 25286 38395 44237)	Atlas-SNP	.											.	CNDP1	98	.	0			c.G349A						PASS	.	G	LYS/GLU	47,4359	48.9+/-83.8	0,47,2156	135	136	136		349	4.2	0.1	18	dbSNP_134	136	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CNDP1	NM_032649.5	56	0,49,6454	AA,AG,GG		0.0233,1.0667,0.3767	possibly-damaging	117/508	72228136	49,12957	2203	4300	6503	SO:0001583	missense	84735	exon4			CTGGCCGAACTGG		CCDS12007.1	18q22.3	2014-07-14			ENSG00000150656	ENSG00000150656	3.4.13.20		20675	protein-coding gene	gene with protein product	"carnosinase 1", "glutamate carboxypeptidase-like protein 2"	609064				12473676	Standard	NM_032649		Approved	MGC10825, CN1, CPGL2, HsT2308	uc002llq.3	Q96KN2	OTTHUMG00000132852	ENST00000358821.3:c.349G>A	18.37:g.72228136G>A	ENSP00000351682:p.Glu117Lys	120	0	0		117	62	0.529915	NM_032649	Q14D40|Q17S05|Q2TBG0|Q6UWK2|Q9BT98	Missense_Mutation	SNP	ENST00000358821.3	37	CCDS12007.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	5.843	0.339732	0.11069	0.010667	2.33E-4	ENSG00000150656	ENST00000358821	T	0.08896	3.04	5.11	4.22	0.49857	.	0.189436	0.45606	D	0.000347	T	0.03564	0.0102	L	0.45228	1.405	0.19300	N	0.99998	P	0.36633	0.562	B	0.14578	0.011	T	0.37641	-0.9697	10	0.13853	T	0.58	-25.2873	9.5834	0.39501	0.0785:0.1446:0.7769:0.0	.	117	Q96KN2	CNDP1_HUMAN	K	117	ENSP00000351682:E117K	ENSP00000351682:E117K	E	+	1	0	CNDP1	70379116	0.997000	0.39634	0.058000	0.19502	0.362000	0.29581	3.719000	0.54926	1.116000	0.41820	0.655000	0.94253	GAA	G|0.996;A|0.004	0.004	strong		0.552	CNDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256326.1	NM_032649		A	72228136	G	A	72228136	3	1	26	1	0	0	0	0	1	0	0	0	3595	1059	37	1	363	1	CNDP1	18	72228136	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	8051750	72228136	5849112	569	10332											
ABCA7	10347	hgsc.bcm.edu	37	chr19	1054583	1054583	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccccagatcgtgctgcctgcCctctttgtgggcctggccct	2	11	11	17	1	1	1	0	0	1	1	2	1	1	1	6	2	3	1	6	2	0	1			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1054583C>T	ENST00000263094.6	+	28	3972	c.3741C>T	c.(3739-3741)gcC>gcT	p.A1247A	ABCA7_ENST00000433129.1_Silent_p.A1247A|ABCA7_ENST00000435683.2_Silent_p.A1109A	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1247					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)		TGCTGCCTGCCCTCTTTGTGG	0.632																																					p.A1247A		Atlas-SNP	.											.	ABCA7	174	.	0			c.C3741T						PASS	.						93	70	78					19																	1054583		2203	4300	6503	SO:0001819	synonymous_variant	10347	exon28			GCCTGCCCTCTTT	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.3741C>T	19.37:g.1054583C>T		53	0	0		80	31	0.3875	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	37	CCDS12055.1																																																																																			.	.	none		0.632	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		T	1054583	C	T	1054583	2	4	26	1	0	0	0	0	0	0	0	1	37	610	22	2		2	ABCA7	19	1054583	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10		1054583	58074400	570	10333											
MUM1	84939	hgsc.bcm.edu	37	chr19	1370742	1370742	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ccgtggtggggtgccccctgGggcagaggcagccctgccgg	3	5	19	14	2	0	1	0	0	0	1	0	1	0	1	5	7	3	2	5	7	0	0	rs34502536	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1370742G>A	ENST00000415183.3	+	11	1680	c.1654G>A	c.(1654-1656)Ggg>Agg	p.G552R	MUM1_ENST00000591806.1_Missense_Mutation_p.G552R|MUM1_ENST00000311401.5_Missense_Mutation_p.G483R|MUM1_ENST00000344663.3_Missense_Mutation_p.G552R			Q2TAK8	MUM1_HUMAN	melanoma associated antigen (mutated) 1	551					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)		GTGCCCCCTGGGGCAGAGGCA	0.662													G|||	35	0.00698882	0.0008	0.013	5008	,	,		13894	0.0		0.0239	False		,,,				2504	0.001				p.G552R		Atlas-SNP	.											.	MUM1	54	.	0			c.G1654A						PASS	.	G	ARG/GLY	17,4093		0,17,2038	7	8	8		1654	2.6	0	19	dbSNP_126	8	131,7971		0,131,3920	no	missense	MUM1	NM_032853.3	125	0,148,5958	AA,AG,GG		1.6169,0.4136,1.2119	possibly-damaging	552/712	1370742	148,12064	2055	4051	6106	SO:0001583	missense	84939	exon12			CCCCTGGGGCAGA	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.1654G>A	19.37:g.1370742G>A	ENSP00000394925:p.Gly552Arg	54	0	0		79	43	0.544304	NM_032853	A1L489|B5ME02|B7ZLY8|J3KQD6|Q13109|Q5XKB9|Q8N2I4|Q96A67	Missense_Mutation	SNP	ENST00000415183.3	37		26	0.011904761904761904	0	0.0	8	0.022099447513812154	0	0.0	18	0.023746701846965697	G	18.07	3.541037	0.65085	0.004136	0.016169	ENSG00000160953	ENST00000344663;ENST00000311401;ENST00000415183	T;T;T	0.40756	1.02;1.02;1.02	5.07	2.57	0.30868	.	0.460401	0.23351	N	0.049132	T	0.37945	0.1022	M	0.66939	2.045	0.09310	N	1	D;D;D;P	0.89917	0.999;1.0;0.993;0.954	D;D;P;P	0.69307	0.946;0.963;0.898;0.548	T	0.21211	-1.0252	10	0.72032	D	0.01	.	5.3578	0.16071	0.2867:0.0:0.7133:0.0	rs34502536	552;552;483;551	B7ZLY8;D6W5Y8;Q2TAK8-2;Q2TAK8	.;.;.;MUM1_HUMAN	R	552;483;552	ENSP00000345789:G552R;ENSP00000309135:G483R;ENSP00000394925:G552R	ENSP00000309135:G483R	G	+	1	0	MUM1	1321742	0.412000	0.25392	0.009000	0.14445	0.086000	0.17979	2.031000	0.41117	1.253000	0.44018	0.561000	0.74099	GGG	G|0.988;A|0.012	0.012	strong		0.662	MUM1-016	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000449510.1	NM_032853		A	1370742	G	A	1370742	3	1	26	1	0	0	0	0	1	0	0	0	9994	1232	43	2	1696	2	MUM1	19	1370742	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	316159	1370742	57758241	571	10334											
PCSK4	92840	hgsc.bcm.edu	37	chr19	1489817	1489817	+	5'Flank	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtttttcttcaggtgcaggCggtggccccagtgcggggtc	3	11	17	10	2	2	0	1	0	1	0	3	0	2	0	2	7	2	2	2	7	0	3	rs12972390	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1489817C>T	ENST00000233596.3	+	0	0				PCSK4_ENST00000300954.5_Missense_Mutation_p.R90H|PCSK4_ENST00000587784.1_Intron	NM_138393.1	NP_612402.1	Q96HR9	REEP6_HUMAN	receptor accessory protein 6						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)				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)		CAGGTGCAGGCGGTGGCCCCA	0.677													C|||	60	0.0119808	0.0015	0.0231	5008	,	,		14349	0.0		0.0268	False		,,,				2504	0.0153				p.R90H		Atlas-SNP	.											.	PCSK4	44	.	0			c.G269A						PASS	.	C	HIS/ARG	21,4373		0,21,2176	21	24	23		269	2	1	19	dbSNP_121	23	316,8284		6,304,3990	yes	missense	PCSK4	NM_017573.3	29	6,325,6166	TT,TC,CC		3.6744,0.4779,2.5935	benign	90/756	1489817	337,12657	2197	4300	6497	SO:0001631	upstream_gene_variant	54760	exon2			TGCAGGCGGTGGC	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		19.37:g.1489817C>T	Exception_encountered	160	0	0		172	96	0.55814	NM_017573	B2RE01|D6W5Z0|Q96LM0	Missense_Mutation	SNP	ENST00000233596.3	37	CCDS12070.1	32	0.014652014652014652	0	0.0	10	0.027624309392265192	0	0.0	22	0.029023746701846966	C	2.756	-0.259014	0.05791	0.004779	0.036744	ENSG00000115257	ENST00000300954	T	0.27720	1.65	3.13	2.03	0.26663	Proteinase inhibitor, propeptide (1);	0.604415	0.14044	N	0.345214	T	0.01976	0.0062	N	0.04203	-0.255	0.28129	N	0.930294	B	0.21688	0.059	B	0.09377	0.004	T	0.32052	-0.9921	10	0.02654	T	1	.	5.578	0.17235	0.0:0.7484:0.0:0.2516	rs12972390;rs12972390	90	Q6UW60	PCSK4_HUMAN	H	90	ENSP00000300954:R90H	ENSP00000300954:R90H	R	-	2	0	PCSK4	1440817	0.000000	0.05858	1.000000	0.80357	0.837000	0.47467	0.348000	0.20031	1.606000	0.50161	0.561000	0.74099	CGC	C|0.980;T|0.020	0.020	strong		0.677	REEP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449623.1	NM_138393		T	1489817	C	T	1489817	1	4	26	0	1	0	0	0	0	0	0	0	11611	768	27	1		1	PCSK4	19	1489817	5'Flank	SNP	C	TCGA-G8-6907-01A-11D-2210-10	119075	1489817	57639166	572	10335											
ATP8B3	148229	hgsc.bcm.edu	37	chr19	1783185	1783185	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggagaaagcatagctggaacGgcgggcacgagactcccggt	11	4	16	10	4	0	2	0	0	0	2	1	5	1	3	1	5	3	3	1	5	3	1			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1783185G>A	ENST00000310127.6	-	29	3983	c.3745C>T	c.(3745-3747)Cgt>Tgt	p.R1249C	ATP8B3_ENST00000539485.1_Missense_Mutation_p.R1259C|ATP8B3_ENST00000525591.1_Missense_Mutation_p.R1212C	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	1249					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)	p.R1259C(1)		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)		TAGCTGGAACGGCGGGCACGA	0.587																																					p.R1249C		Atlas-SNP	.											ATP8B3,caecum,carcinoma,0,1	ATP8B3	108	1	1	Substitution - Missense(1)	large_intestine(1)	c.C3745T						PASS	.						48	49	49					19																	1783185		1993	4151	6144	SO:0001583	missense	148229	exon29			TGGAACGGCGGGC	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.3745C>T	19.37:g.1783185G>A	ENSP00000311336:p.Arg1249Cys	136	0	0		145	67	0.462069	NM_138813	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Missense_Mutation	SNP	ENST00000310127.6	37	CCDS45901.1	.	.	.	.	.	.	.	.	.	.	G	18.38	3.611889	0.66558	.	.	ENSG00000130270	ENST00000310127;ENST00000539485;ENST00000525591	T;T;T	0.65732	-0.17;-0.05;-0.07	4.57	4.57	0.56435	.	0.144065	0.47852	D	0.000201	T	0.78710	0.4326	M	0.76727	2.345	0.54753	D	0.999983	D;D	0.89917	1.0;1.0	D;D	0.79108	0.988;0.992	T	0.82323	-0.0514	10	0.87932	D	0	.	16.3466	0.83134	0.0:0.0:1.0:0.0	.	1249;1212	O60423;Q7Z485	AT8B3_HUMAN;.	C	1249;1259;1212	ENSP00000311336:R1249C;ENSP00000443574:R1259C;ENSP00000437115:R1212C	ENSP00000311336:R1249C	R	-	1	0	ATP8B3	1734185	1.000000	0.71417	0.937000	0.37676	0.253000	0.25986	7.161000	0.77505	2.088000	0.63022	0.549000	0.68633	CGT	.	.	none		0.587	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813		A	1783185	G	A	1783185	3	1	26	1	0	0	0	0	1	0	0	0	1196	1116	39	1	161	1	ATP8B3	19	1783185	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	293368	1783185	57345798	573	10336											
FAM108A1	81926	hgsc.bcm.edu	37	chr19	1881348	1881348	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgtactggaagtcggcaCgctccgtcaggtgcagcttc	6	9	14	12	3	1	0	1	0	0	0	4	1	2	1	1	4	3	6	1	4	2	2			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1881348C>T	ENST00000292577.7	-	2	651	c.218G>A	c.(217-219)cGt>cAt	p.R73H	ABHD17A_ENST00000250974.9_Missense_Mutation_p.R73H|ABHD17A_ENST00000590661.1_Missense_Mutation_p.R73H	NM_001130111.1	NP_001123583.1	Q96GS6	AB17A_HUMAN	abhydrolase domain containing 17A	73						extracellular region (GO:0005576)|membrane (GO:0016020)	hydrolase activity (GO:0016787)										GAAGTCGGCACGCTCCGTCAG	0.716																																					p.R73H		Atlas-SNP	.											FAM108A1,NS,carcinoma,+1,1	FAM108A1	29	1	0			c.G218A						scavenged	.						19	21	20					19																	1881348		2186	4259	6445	SO:0001583	missense	81926	exon2			TCGGCACGCTCCG	BC020512	CCDS32867.1, CCDS45902.1	19p13.3	2013-03-15	2013-03-15	2013-03-15	ENSG00000129968	ENSG00000129968		"Abhydrolase domain containing"	28756	protein-coding gene	gene with protein product			"chromosome 19 open reading frame 27", "family with sequence similarity 108, member A1"	C19orf27, FAM108A1		14702039	Standard	NM_031213		Approved	MGC5244	uc002lug.3	Q96GS6	OTTHUMG00000171872	ENST00000292577.7:c.218G>A	19.37:g.1881348C>T	ENSP00000292577:p.Arg73His	81	0	0		62	9	0.145161	NM_031213	A8K0G8|D6W5Z9|Q6PJU2|Q8WUH9|Q9BWL0|Q9H7Q9	Missense_Mutation	SNP	ENST00000292577.7	37	CCDS45902.1	.	.	.	.	.	.	.	.	.	.	c	17.49	3.402578	0.62288	.	.	ENSG00000129968	ENST00000250974;ENST00000292577	T;T	0.48201	0.82;0.95	3.76	3.76	0.43208	.	0.000000	0.85682	D	0.000000	T	0.53883	0.1824	M	0.78344	2.41	0.58432	D	0.999999	B;B;P;D	0.61080	0.014;0.325;0.857;0.989	B;B;B;P	0.45310	0.013;0.139;0.273;0.476	T	0.67031	-0.5773	10	0.87932	D	0	-24.7831	15.1068	0.72326	0.0:1.0:0.0:0.0	.	73;73;73;73	Q96GS6;Q96GS6-2;Q96GS6-3;Q96GS6-4	F18A1_HUMAN;.;.;.	H	73	ENSP00000250974:R73H;ENSP00000292577:R73H	ENSP00000250974:R73H	R	-	2	0	FAM108A1	1832348	1.000000	0.71417	0.927000	0.36925	0.901000	0.52897	7.466000	0.80914	2.108000	0.64289	0.561000	0.74099	CGT	.	.	none		0.716	ABHD17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415556.2	NM_031213		T	1881348	C	T	1881348	3	4	26	1	0	0	0	0	1	0	0	0	5396	536	19	1	887	1	FAM108A1	19	1881348	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	98163	1881348	57247635	574	10337											
PIP5K1C	23396	hgsc.bcm.edu	37	chr19	3644220	3644220	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctagcaaggctccgccgcGccccttcttggagggcgagg	6	6	15	14	4	1	0	0	0	1	0	2	2	2	1	4	4	2	3	4	4	2	3			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:3644220G>A	ENST00000335312.3	-	12	1463	c.1375C>T	c.(1375-1377)Cgc>Tgc	p.R459C	PIP5K1C_ENST00000539785.1_Missense_Mutation_p.R459C|PIP5K1C_ENST00000537021.1_Missense_Mutation_p.R459C|PIP5K1C_ENST00000589578.1_Missense_Mutation_p.R459C	NM_001195733.1|NM_012398.2	NP_001182662.1|NP_036530.1	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, gamma	459					actin cytoskeleton organization (GO:0030036)|adherens junction assembly (GO:0034333)|axon guidance (GO:0007411)|clathrin-mediated endocytosis (GO:0072583)|cytoskeletal anchoring at plasma membrane (GO:0007016)|neutrophil chemotaxis (GO:0030593)|phagocytosis (GO:0006909)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet aggregation (GO:0070527)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle exocytosis (GO:0016079)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|uropod (GO:0001931)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)			large_intestine(3)|ovary(1)|skin(3)|stomach(2)	9		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)		GCTCCGCCGCGCCCCTTCTTG	0.687																																					p.R459C	Esophageal Squamous(135;99 1744 12852 27186 39851)	Atlas-SNP	.											.	PIP5K1C	63	.	0			c.C1375T						PASS	.						28	34	32					19																	3644220		2201	4293	6494	SO:0001583	missense	23396	exon12			CGCCGCGCCCCTT	AB011161	CCDS32872.1, CCDS56074.1, CCDS74257.1	19p13.3	2012-10-02			ENSG00000186111	ENSG00000186111			8996	protein-coding gene	gene with protein product		606102				9535851	Standard	NM_001195733		Approved	PIP5Kgamma, KIAA0589, LCCS3	uc002lyj.2	O60331	OTTHUMG00000180870	ENST00000335312.3:c.1375C>T	19.37:g.3644220G>A	ENSP00000335333:p.Arg459Cys	69	0	0		69	42	0.608696	NM_001195733	B7Z9E7|C6GIJ7|C6GIJ8|Q7LE07	Missense_Mutation	SNP	ENST00000335312.3	37	CCDS32872.1	.	.	.	.	.	.	.	.	.	.	G	12.61	1.990963	0.35131	.	.	ENSG00000186111	ENST00000335312;ENST00000539785;ENST00000537021	T;T;T	0.34275	1.42;1.42;1.37	4.66	3.52	0.40303	.	0.000000	0.85682	D	0.000000	T	0.32882	0.0844	L	0.48642	1.525	0.54753	D	0.999987	B;B	0.32382	0.368;0.252	B;B	0.31614	0.133;0.063	T	0.41378	-0.9512	10	0.87932	D	0	-11.2654	14.5132	0.67802	0.0:0.0:0.843:0.157	.	459;459	O60331-3;O60331	.;PI51C_HUMAN	C	459	ENSP00000335333:R459C;ENSP00000445992:R459C;ENSP00000444779:R459C	ENSP00000335333:R459C	R	-	1	0	PIP5K1C	3595220	1.000000	0.71417	0.785000	0.31869	0.212000	0.24457	6.155000	0.71833	2.146000	0.66826	0.491000	0.48974	CGC	.	.	none		0.687	PIP5K1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453432.2	NM_012398		A	3644220	G	A	3644220	3	1	26	1	0	0	0	0	1	0	0	0	11950	1087	38	1	659	1	PIP5K1C	19	3644220	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1762872	3644220	55484763	575	10338											
RAX2	84839	hgsc.bcm.edu	37	chr19	3771684	3771684	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcttcttgggggcctcctcGcccggccccagacccccacc	3	8	9	21	2	2	1	0	0	2	1	4	1	3	1	8	3	0	0	8	3	0	3			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:3771684G>A	ENST00000555633.1	-	2	397	c.57C>T	c.(55-57)ggC>ggT	p.G19G	RAX2_ENST00000555978.1_Silent_p.G19G			Q96IS3	RAX2_HUMAN	retina and anterior neural fold homeobox 2	19					regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			large_intestine(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00463)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGCCTCCTCGCCCGGCCCCA	0.701																																					p.G19G		Atlas-SNP	.											.	RAX2	4	.	0			c.C57T						PASS	.						45	40	42					19																	3771684		2200	4298	6498	SO:0001819	synonymous_variant	84839	exon2			CTCCTCGCCCGGC	AY211277	CCDS12112.1	19p13.3	2013-06-06	2007-08-28	2007-08-28				"Homeoboxes / PRD class"	18286	protein-coding gene	gene with protein product		610362	"retina and anterior neural fold homeobox like 1"	RAXL1			Standard	NM_032753		Approved	MGC15631, ARMD6, CORD11	uc002lys.3	Q96IS3		ENST00000555633.1:c.57C>T	19.37:g.3771684G>A		43	0	0		49	20	0.408163	NM_032753		Silent	SNP	ENST00000555633.1	37	CCDS12112.1	.	.	.	.	.	.	.	.	.	.	G	14.21	2.466341	0.43839	.	.	ENSG00000173976	ENST00000555978	.	.	.	2.98	-5.96	0.02234	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.1764	0.06570	0.3839:0.0:0.3174:0.2987	.	.	.	.	X	39	.	.	R	-	1	2	RAX2	3722684	0.000000	0.05858	0.160000	0.22671	0.866000	0.49608	-2.379000	0.01067	-1.095000	0.03050	0.491000	0.48974	CGA	.	.	none		0.701	RAX2-001	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411919.2	NM_032753		A	3771684	G	A	3771684	2	1	26	1	0	0	0	0	0	0	0	1	13112	1074	38	1		1	RAX2	19	3771684	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	127464	3771684	55357299	576	10339											
PEX11G	92960	hgsc.bcm.edu	37	chr19	7542168	7542168	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgaggagatggtgcccatgaGgcccactagccacggcggga	9	5	16	11	2	0	3	0	2	0	1	0	5	0	4	3	5	2	0	3	5	1	1	rs11668511	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:7542168G>A	ENST00000221480.1	-	5	654	c.646C>T	c.(646-648)Ctc>Ttc	p.L216F	PEX11G_ENST00000593942.1_Missense_Mutation_p.L146F|PEX11G_ENST00000599519.1_5'UTR	NM_001270539.1|NM_080662.3	NP_001257468.1|NP_542393.1	Q96HA9	PX11C_HUMAN	peroxisomal biogenesis factor 11 gamma	216					peroxisome fission (GO:0016559)|regulation of peroxisome size (GO:0044375)	integral component of peroxisomal membrane (GO:0005779)|intrinsic component of peroxisomal membrane (GO:0031231)|peroxisome (GO:0005777)|protein complex (GO:0043234)				central_nervous_system(1)|cervix(1)|endometrium(1)|lung(1)|ovary(1)|prostate(1)|skin(1)	7						GTGCCCATGAGGCCCACTAGC	0.706													G|||	51	0.0101837	0.0008	0.0115	5008	,	,		14100	0.0		0.0358	False		,,,				2504	0.0061				p.L216F		Atlas-SNP	.											.	PEX11G	16	.	0			c.C646T						PASS	.	G	PHE/LEU	25,4313		0,25,2144	12	15	14		646	5.2	1	19	dbSNP_120	14	286,8238		4,278,3980	yes	missense	PEX11G	NM_080662.2	22	4,303,6124	AA,AG,GG		3.3552,0.5763,2.418	probably-damaging	216/242	7542168	311,12551	2169	4262	6431	SO:0001583	missense	92960	exon5			CCATGAGGCCCAC	BC008780	CCDS12178.1	19p13.2	2008-02-05				ENSG00000104883			20208	protein-coding gene	gene with protein product		607583				12417726	Standard	NM_080662		Approved		uc002mgk.2	Q96HA9		ENST00000221480.1:c.646C>T	19.37:g.7542168G>A	ENSP00000221480:p.Leu216Phe	33	0	0		32	16	0.5	NM_080662	Q8NDM0	Missense_Mutation	SNP	ENST00000221480.1	37	CCDS12178.1	31	0.014194139194139194	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	25	0.032981530343007916	G	20.6	4.010285	0.75046	0.005763	0.033552	ENSG00000104883	ENST00000221480	T	0.52983	0.64	5.2	5.2	0.72013	.	0.065408	0.64402	D	0.000008	T	0.38321	0.1036	M	0.78223	2.4	0.58432	D	0.999999	D	0.71674	0.998	D	0.63113	0.911	T	0.53301	-0.8458	10	0.28530	T	0.3	-20.3419	9.8052	0.40789	0.094:0.0:0.906:0.0	rs11668511	216	Q96HA9	PX11C_HUMAN	F	216	ENSP00000221480:L216F	ENSP00000221480:L216F	L	-	1	0	PEX11G	7448168	1.000000	0.71417	1.000000	0.80357	0.688000	0.40055	4.977000	0.63792	2.405000	0.81733	0.563000	0.77884	CTC	G|0.985;A|0.015	0.015	strong		0.706	PEX11G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458965.1	NM_080662		A	7542168	G	A	7542168	3	1	26	1	0	0	0	0	1	0	0	0	11748	1000	35	2	83	2	PEX11G	19	7542168	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	3770484	7542168	51586815	577	10340											
RAB11B	9230	hgsc.bcm.edu	37	chr19	8468322	8468322	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taccgcatcgtgtcacagaaAcagatcgcagaccgcgctgc	11	6	10	14	5	1	3	1	0	0	3	3	3	1	3	2	0	3	3	2	0	2	1			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:8468322A>G	ENST00000328024.6	+	5	755	c.537A>G	c.(535-537)aaA>aaG	p.K179K		NM_004218.3	NP_004209.2	Q15907	RB11B_HUMAN	RAB11B, member RAS oncogene family	179					cellular response to acidic pH (GO:0071468)|constitutive secretory pathway (GO:0045054)|establishment of protein localization to membrane (GO:0090150)|GTP catabolic process (GO:0006184)|insulin secretion involved in cellular response to glucose stimulus (GO:0035773)|melanosome transport (GO:0032402)|receptor recycling (GO:0001881)|regulated secretory pathway (GO:0045055)|regulation of anion transport (GO:0044070)|regulation of endocytic recycling (GO:2001135)|regulation of protein localization to cell surface (GO:2000008)|retrograde transport, endosome to plasma membrane (GO:1990126)|small GTPase mediated signal transduction (GO:0007264)|transferrin transport (GO:0033572)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|phagocytic vesicle (GO:0045335)|recycling endosome (GO:0055037)|recycling endosome membrane (GO:0055038)|synaptic vesicle (GO:0008021)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			large_intestine(2)|lung(1)|ovary(1)	4						TGTCACAGAAACAGATCGCAG	0.657																																					p.K179K		Atlas-SNP	.											.	RAB11B	15	.	0			c.A537G						PASS	.						134	109	117					19																	8468322		2203	4300	6503	SO:0001819	synonymous_variant	9230	exon5			ACAGAAACAGATC	X79780	CCDS12201.1	19p13.2	2012-07-02			ENSG00000185236	ENSG00000185236		"RAB, member RAS oncogene"	9761	protein-coding gene	gene with protein product		604198				7811277	Standard	NM_004218		Approved	H-YPT3	uc002mju.4	Q15907		ENST00000328024.6:c.537A>G	19.37:g.8468322A>G		114	0	0		126	65	0.515873	NM_004218	A5YM50|B2R7I4|B4DMK0|D6W671|Q2YDT2|Q5U0I1|Q6FHR0|Q6FI42|Q8NI07	Silent	SNP	ENST00000328024.6	37	CCDS12201.1																																																																																			.	.	none		0.657	RAB11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460343.2	NM_004218		G	8468322	A	G	8468322	2	3	26	1	0	0	0	0	0	0	0	1	12907	40	2	3		3	RAB11B	19	8468322	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	926154	8468322	50660661	578	10341											
MUC16	94025	hgsc.bcm.edu	37	chr19	9074697	9074697	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aactggttgcctccatattcGtcactgctgtgtctgcagaa	8	13	9	11	1	2	1	1	0	1	1	4	1	3	1	2	1	4	3	2	1	3	3	rs202216364		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9074697G>A	ENST00000397910.4	-	3	12952	c.12749C>T	c.(12748-12750)aCg>aTg	p.T4250M		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4252	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						CTCCATATTCGTCACTGCTGT	0.478													G|||	1	0.000199681	0.0008	0.0	5008	,	,		24112	0.0		0.0	False		,,,				2504	0.0				p.T4250M		Atlas-SNP	.											.	MUC16	4315	.	0			c.C12749T						PASS	.	G	MET/THR	2,4014		0,2,2006	116	113	114		12749	1.6	0	19		114	11,8319		0,11,4154	yes	missense	MUC16	NM_024690.2	81	0,13,6160	AA,AG,GG		0.1321,0.0498,0.1053	probably-damaging	4250/14508	9074697	13,12333	2008	4165	6173	SO:0001583	missense	94025	exon3			ATATTCGTCACTG	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.12749C>T	19.37:g.9074697G>A	ENSP00000381008:p.Thr4250Met	136	0	0		157	70	0.44586	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	3.052	-0.195075	0.06259	4.98E-4	0.001321	ENSG00000181143	ENST00000397910	T	0.33654	1.4	1.63	1.63	0.23807	.	.	.	.	.	T	0.43809	0.1264	L	0.48642	1.525	.	.	.	D	0.89917	1.0	P	0.61070	0.883	T	0.54430	-0.8295	8	0.87932	D	0	.	6.6867	0.23148	0.0:0.0:1.0:0.0	.	4250	B5ME49	.	M	4250	ENSP00000381008:T4250M	ENSP00000381008:T4250M	T	-	2	0	MUC16	8935697	0.000000	0.05858	0.002000	0.10522	0.043000	0.13939	0.138000	0.16016	1.205000	0.43262	0.205000	0.17691	ACG	.	.	weak		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9074697	G	A	9074697	3	1	26	1	0	0	0	0	1	0	0	0	9982	1145	40	1	31102	1	MUC16	19	9074697	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	606375	9074697	50054286	579	10342											
ZNF560	147741	hgsc.bcm.edu	37	chr19	9578512	9578513	+	Frame_Shift_Del	DEL	TG	TG	-																															tttataaggttttatcccaaTgtgggtttgcatgtgattat																										TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9578512_9578513delTG	ENST00000301480.4	-	10	1323_1324	c.1110_1111delCA	c.(1108-1113)cacattfs	p.I371fs		NM_152476.2	NP_689689.2	Q96MR9	ZN560_HUMAN	zinc finger protein 560	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(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						TTTATCCCAATGTGGGTTTGCA	0.386																																					p.371_371del		Pindel,Atlas-Indel	.											.	ZNF560	162	.	0			c.1111_1112del						PASS	.																																			SO:0001589	frameshift_variant	147741	exon10			.	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.1110_1111delCA	19.37:g.9578514_9578515delTG	ENSP00000301480:p.Ile371fs	233	0	.		238	62	0.261	NM_152476	Q495S9|Q495T1	Frame_Shift_Del	DEL	ENST00000301480.4	37	CCDS12214.1																																																																																			.	.	none		0.386	ZNF560-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449901.1	NM_152476		-	9578513	TG	-	9578512	7	5	26	1	0	1	0	1	0	0	0	0	18006	1464	51	0	1265	0	ZNF560	19	9578512	Frame_Shift_Del	DEL	TG	TCGA-G8-6907-01A-11D-2210-10	503815	9578512	49550471	580	10343											
ZNF426	79088	hgsc.bcm.edu	37	chr19	9639710	9639710	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctttcccacattccttacaTacatagggtttctctccagt	8	15	5	13	0	1	0	0	0	1	0	5	0	4	0	3	1	2	2	3	1	3	6	rs45489098	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9639710T>C	ENST00000535489.1	-	6	1347	c.1011A>G	c.(1009-1011)gtA>gtG	p.V337V	ZNF426_ENST00000253115.2_Silent_p.V337V|ZNF426_ENST00000593003.1_Silent_p.V299V			Q9BUY5	ZN426_HUMAN	zinc finger protein 426	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)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20						ATTCCTTACATACATAGGGTT	0.433													T|||	10	0.00199681	0.0015	0.0043	5008	,	,		22000	0.0		0.005	False		,,,				2504	0.0				p.V337V		Atlas-SNP	.											.	ZNF426	56	.	0			c.A1011G						PASS	.	T		6,4400	12.9+/-30.5	0,6,2197	96	96	96		1011	-0.1	0	19	dbSNP_127	96	55,8545	35.3+/-89.8	0,55,4245	no	coding-synonymous	ZNF426	NM_024106.1		0,61,6442	CC,CT,TT		0.6395,0.1362,0.469		337/555	9639710	61,12945	2203	4300	6503	SO:0001819	synonymous_variant	79088	exon8			CTTACATACATAG	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.1011A>G	19.37:g.9639710T>C		70	0	0		110	54	0.490909	NM_024106	B3KTL2	Silent	SNP	ENST00000535489.1	37	CCDS12215.1																																																																																			T|0.995;C|0.005	0.005	strong		0.433	ZNF426-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449905.1	NM_024106		C	9639710	T	C	9639710	2	2	26	1	0	0	0	0	0	0	0	1	17915	1393	49	3		3	ZNF426	19	9639710	Silent	SNP	T	TCGA-G8-6907-01A-11D-2210-10	61198	9639710	49489273	581	10344											
ZNF490	57474	hgsc.bcm.edu	37	chr19	12691497	12691497	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actccagtgtgacttctttcGtgccttcgaaggtgactgaa	8	13	10	10	2	1	3	0	3	1	0	4	4	2	3	2	1	1	0	2	1	2	3	rs140620156	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:12691497G>A	ENST00000311437.6	-	5	1514	c.1392C>T	c.(1390-1392)caC>caT	p.H464H	ZNF490_ENST00000465656.1_5'Flank|CTD-2192J16.20_ENST00000593682.1_Missense_Mutation_p.T98M	NM_020714.2	NP_065765.1	Q9ULM2	ZN490_HUMAN	zinc finger protein 490	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(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	18						GACTTCTTTCGTGCCTTCGAA	0.418													G|||	5	0.000998403	0.0008	0.0014	5008	,	,		20275	0.0		0.003	False		,,,				2504	0.0				p.H464H		Atlas-SNP	.											.	ZNF490	42	.	0			c.C1392T						PASS	.	G		5,4401	9.9+/-24.2	0,5,2198	129	128	128		1392	-1.5	0	19	dbSNP_134	128	35,8565	24.0+/-70.4	0,35,4265	no	coding-synonymous	ZNF490	NM_020714.2		0,40,6463	AA,AG,GG		0.407,0.1135,0.3076		464/530	12691497	40,12966	2203	4300	6503	SO:0001819	synonymous_variant	57474	exon5			TCTTTCGTGCCTT	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.1392C>T	19.37:g.12691497G>A		94	0	0		102	42	0.411765	NM_020714		Silent	SNP	ENST00000311437.6	37	CCDS12272.1																																																																																			G|0.997;A|0.003	0.003	strong		0.418	ZNF490-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344073.1	NM_020714		A	12691497	G	A	12691497	2	1	26	1	0	0	0	0	0	0	0	1	17956	1136	40	1		1	ZNF490	19	12691497	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	3051787	12691497	46437486	582	10345											
FBXW9	84261	hgsc.bcm.edu	37	chr19	12802009	12802009	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtagatggtcaccttcttgTcataggtgccagtcaccagg	8	11	11	11	1	4	1	3	0	1	1	4	1	4	1	3	3	1	1	3	3	2	4	rs143596846	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:12802009T>C	ENST00000380339.3	-	5	890	c.854A>G	c.(853-855)gAc>gGc	p.D285G	CTD-2659N19.2_ENST00000585742.1_RNA|FBXW9_ENST00000393261.3_Missense_Mutation_p.D285G|FBXW9_ENST00000544494.1_Missense_Mutation_p.D23G|FBXW9_ENST00000587955.1_Missense_Mutation_p.D275G			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	285					SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						CACCTTCTTGTCATAGGTGCC	0.607													T|||	2	0.000399361	0.0	0.0	5008	,	,		18570	0.0		0.002	False		,,,				2504	0.0				p.D285G		Atlas-SNP	.											.	FBXW9	30	.	0			c.A854G						PASS	.	T	GLY/ASP	1,4145		0,1,2072	127	128	127		854	4.7	1	19	dbSNP_134	127	16,8394		0,16,4189	yes	missense	FBXW9	NM_032301.2	94	0,17,6261	CC,CT,TT		0.1902,0.0241,0.1354	probably-damaging	285/459	12802009	17,12539	2073	4205	6278	SO:0001583	missense	84261	exon5			TTCTTGTCATAGG	BC004290	CCDS12278.2	19p13.2	2013-01-09	2007-02-08		ENSG00000132004	ENSG00000132004		"F-boxes / WD-40 domains", "WD repeat domain containing"	28136	protein-coding gene	gene with protein product		609074	"F-box and WD-40 domain protein 9"			12477932	Standard	NM_032301		Approved	MGC10870, Fbw9	uc002mum.1	Q5XUX1	OTTHUMG00000150152	ENST00000380339.3:c.854A>G	19.37:g.12802009T>C	ENSP00000369696:p.Asp285Gly	87	0	0		107	52	0.485981	NM_032301	B3KVP7|Q9BT89	Missense_Mutation	SNP	ENST00000380339.3	37		2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	19.32	3.804178	0.70682	2.41E-4	0.001902	ENSG00000132004	ENST00000544494;ENST00000393261;ENST00000380339	D;T;T	0.89270	-2.49;1.07;1.07	4.66	4.66	0.58398	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	0.90665	0.7072	L	0.32530	0.975	0.58432	D	0.999997	D;P;D	0.89917	1.0;0.872;0.999	D;P;D	0.81914	0.995;0.759;0.96	D	0.91740	0.5403	10	0.87932	D	0	-31.5318	13.2197	0.59881	0.0:0.0:0.0:1.0	.	275;285;285	Q5XUX1-2;Q5XUX1;Q5XUX1-3	.;FBXW9_HUMAN;.	G	23;285;285	ENSP00000442714:D23G;ENSP00000376945:D285G;ENSP00000369696:D285G	ENSP00000369696:D285G	D	-	2	0	FBXW9	12663009	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	6.197000	0.72100	1.957000	0.56846	0.379000	0.24179	GAC	T|0.999;C|0.001	0.001	strong		0.607	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301		C	12802009	T	C	12802009	3	2	26	1	0	0	0	0	1	0	0	0	5779	1667	58	3	546	3	FBXW9	19	12802009	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	110512	12802009	46326974	583	10346											
ZSWIM4	65249	hgsc.bcm.edu	37	chr19	13941255	13941255	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaccactcggccttcgaggcGgcctaccagatcgtgctgga	8	7	12	14	4	0	1	0	0	0	1	3	3	0	2	4	4	3	1	4	4	2	2	rs138305620	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:13941255G>A	ENST00000254323.2	+	13	2550	c.2361G>A	c.(2359-2361)gcG>gcA	p.A787A	ZSWIM4_ENST00000440752.2_Silent_p.A621A	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	787							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)			CCTTCGAGGCGGCCTACCAGA	0.706													G|||	2	0.000399361	0.0	0.0	5008	,	,		15823	0.0		0.002	False		,,,				2504	0.0				p.A787A		Atlas-SNP	.											.	ZSWIM4	69	.	0			c.G2361A						PASS	.	G		0,4406		0,0,2203	68	70	69		2361	-8.3	1	19	dbSNP_134	69	14,8586	9.8+/-36.6	0,14,4286	no	coding-synonymous	ZSWIM4	NM_023072.2		0,14,6489	AA,AG,GG		0.1628,0.0,0.1076		787/990	13941255	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	65249	exon13			CGAGGCGGCCTAC	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.2361G>A	19.37:g.13941255G>A		25	0	0		41	25	0.609756	NM_023072		Silent	SNP	ENST00000254323.2	37	CCDS32924.1																																																																																			G|0.999;A|0.001	0.001	strong		0.706	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457457.1	XM_031342		A	13941255	G	A	13941255	2	1	26	1	0	0	0	0	0	0	0	1	18258	1103	39	1		1	ZSWIM4	19	13941255	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1139246	13941255	45187728	584	10347											
CC2D1A	54862	hgsc.bcm.edu	37	chr19	14040420	14040420	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtaccaggacatcatgcaacGcagccagtggcagagggcac	12	4	13	12	1	1	1	1	0	0	1	1	2	1	2	2	3	4	5	2	3	2	1	rs201921029		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14040420G>A	ENST00000318003.7	+	26	2898	c.2657G>A	c.(2656-2658)cGc>cAc	p.R886H	CC2D1A_ENST00000589606.1_Missense_Mutation_p.R885H	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	886					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)			ATCATGCAACGCAGCCAGTGG	0.657																																					p.R886H		Atlas-SNP	.											.	CC2D1A	67	.	0			c.G2657A						PASS	.	G	HIS/ARG	1,4027		0,1,2013	10	14	12		2657	2.3	1	19		12	11,8333		0,11,4161	yes	missense	CC2D1A	NM_017721.4	29	0,12,6174	AA,AG,GG		0.1318,0.0248,0.097	benign	886/952	14040420	12,12360	2014	4172	6186	SO:0001583	missense	54862	exon26			TGCAACGCAGCCA	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.2657G>A	19.37:g.14040420G>A	ENSP00000313601:p.Arg886His	79	0	0		98	51	0.520408	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Missense_Mutation	SNP	ENST00000318003.7	37	CCDS42512.1	.	.	.	.	.	.	.	.	.	.	G	12.67	2.008455	0.35415	2.48E-4	0.001318	ENSG00000132024	ENST00000318003;ENST00000254346	T	0.20738	2.05	4.89	2.33	0.28932	.	0.066900	0.56097	D	0.000037	T	0.11879	0.0289	L	0.29908	0.895	0.41298	D	0.987024	B;B;B	0.29232	0.088;0.017;0.238	B;B;B	0.18561	0.015;0.005;0.022	T	0.10636	-1.0621	10	0.49607	T	0.09	-17.143	5.6295	0.17501	0.0919:0.1409:0.6232:0.144	.	507;885;886	Q9NX28;Q6P1N0-2;Q6P1N0	.;.;C2D1A_HUMAN	H	886;508	ENSP00000313601:R886H	ENSP00000254346:R508H	R	+	2	0	CC2D1A	13901420	1.000000	0.71417	1.000000	0.80357	0.679000	0.39708	3.033000	0.49743	1.044000	0.40200	-0.440000	0.05779	CGC	.	.	weak		0.657	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721		A	14040420	G	A	14040420	3	1	26	1	0	0	0	0	1	0	0	0	2728	1087	38	1	2759	1	CC2D1A	19	14040420	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	99165	14040420	45088563	585	10348											
IL27RA	9466	hgsc.bcm.edu	37	chr19	14162740	14162740	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccccgctgggtctgggagaaAgttcctgatcctgccaacag	8	8	12	13	1	1	2	0	1	1	1	3	3	3	2	5	2	2	2	5	2	2	1	rs148749814	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14162740A>G	ENST00000263379.2	+	13	1796	c.1671A>G	c.(1669-1671)aaA>aaG	p.K557K		NM_004843.3	NP_004834.1	Q6UWB1	I27RA_HUMAN	interleukin 27 receptor, alpha	557					cell surface receptor signaling pathway (GO:0007166)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T-helper 1 type immune response (GO:0002827)|regulation of isotype switching to IgG isotypes (GO:0048302)	integral component of plasma membrane (GO:0005887)	interleukin-27 receptor activity (GO:0045509)|transmembrane signaling receptor activity (GO:0004888)			breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	26						TCTGGGAGAAAGTTCCTGATC	0.622													a|||	14	0.00279553	0.0	0.0	5008	,	,		13386	0.001		0.001	False		,,,				2504	0.0123				p.K557K	Colon(164;1849 1896 4443 37792 47834)	Atlas-SNP	.											.	IL27RA	56	.	0			c.A1671G						PASS	.	A		0,4402		0,0,2201	32	29	30		1671	-5.4	0.1	19	dbSNP_134	30	8,8582		0,8,4287	no	coding-synonymous	IL27RA	NM_004843.2		0,8,6488	GG,GA,AA		0.0931,0.0,0.0616		557/637	14162740	8,12984	2201	4295	6496	SO:0001819	synonymous_variant	9466	exon13			GGAGAAAGTTCCT	AF053004	CCDS12303.1	19p13.11	2013-02-11				ENSG00000104998		"Interleukins and interleukin receptors", "Fibronectin type III domain containing"	17290	protein-coding gene	gene with protein product	"T-cell cytokine receptor type 1"	605350				9600072, 11057672	Standard	NM_004843		Approved	WSX-1, TCCR, CRL1, WSX1, zcytor1, IL-27R	uc002mxx.4	Q6UWB1		ENST00000263379.2:c.1671A>G	19.37:g.14162740A>G		181	0	0		182	91	0.5	NM_004843	A0N0L1|O60624	Silent	SNP	ENST00000263379.2	37	CCDS12303.1																																																																																			A|0.999;G|0.001	0.001	strong		0.622	IL27RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458539.1	NM_004843		G	14162740	A	G	14162740	2	3	26	1	0	0	0	0	0	0	0	1	7690	69	3	3		3	IL27RA	19	14162740	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	122320	14162740	44966243	586	10349											
LPHN1	22859	hgsc.bcm.edu	37	chr19	14261853	14261853	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gaggtgtagtagatttcgggGgggccggggggtgcgggagg	5	7	25	4	3	0	1	0	0	0	1	1	3	0	2	1	9	1	2	1	9	2	3			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14261853G>A	ENST00000340736.6	-	24	4554	c.4257C>T	c.(4255-4257)ccC>ccT	p.P1419P	CTB-55O6.12_ENST00000588387.1_RNA|CTB-55O6.12_ENST00000588658.1_RNA|LPHN1_ENST00000361434.3_Silent_p.P1414P	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	1419	Poly-Pro.				calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|heterophilic cell-cell adhesion (GO:0007157)|neuropeptide signaling pathway (GO:0007218)|positive regulation of synapse maturation (GO:0090129)	axon (GO:0030424)|cell junction (GO:0030054)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						AGATTTCGGGGGGGCCGGGGG	0.731																																					p.P1419P		Atlas-SNP	.											.	LPHN1	107	.	0			c.C4257T						PASS	.						2	3	3					19																	14261853		1382	3162	4544	SO:0001819	synonymous_variant	22859	exon24			TTCGGGGGGGCCG	AB020628	CCDS12307.1, CCDS32928.1	19p13.2	2014-08-08				ENSG00000072071		"-", "GPCR / Class B : Orphans"	20973	protein-coding gene	gene with protein product						10994649	Standard	NM_014921		Approved	KIAA0821, CIRL1, LEC2	uc010xnn.2	O94910		ENST00000340736.6:c.4257C>T	19.37:g.14261853G>A		48	0	0		33	23	0.69697	NM_001008701	Q96IE7|Q9BU07|Q9HAR3	Silent	SNP	ENST00000340736.6	37	CCDS32928.1																																																																																			.	.	none		0.731	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921		A	14261853	G	A	14261853	2	1	26	1	0	0	0	0	0	0	0	1	8924	1219	43	2		2	LPHN1	19	14261853	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	99113	14261853	44867130	587	10350											
NOTCH3	4854	hgsc.bcm.edu	37	chr19	15299112	15299112	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cccaccgttgacacaggggcTactctgacactcgtcaatgt	9	9	9	14	2	2	2	1	2	1	0	3	2	2	2	2	2	1	2	2	2	2	2			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:15299112T>C	ENST00000263388.2	-	9	1501	c.1426A>G	c.(1426-1428)Agc>Ggc	p.S476G		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	476	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)			ACACAGGGGCTACTCTGACAC	0.592																																					p.S476G		Atlas-SNP	.											.	NOTCH3	340	.	0			c.A1426G						PASS	.						55	46	49					19																	15299112		2203	4300	6503	SO:0001583	missense	4854	exon9			AGGGGCTACTCTG	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.1426A>G	19.37:g.15299112T>C	ENSP00000263388:p.Ser476Gly	83	0	0		96	4	0.0416667	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	37	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	t	16.92	3.255393	0.59321	.	.	ENSG00000074181	ENST00000263388;ENST00000539383	D	0.91686	-2.89	5.04	5.04	0.67666	EGF-like calcium-binding, conserved site (1);EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.38058	N	0.001835	D	0.90823	0.7118	L	0.58101	1.795	0.36208	D	0.851202	P;B	0.35401	0.499;0.256	B;B	0.39617	0.168;0.305	D	0.92578	0.6072	10	0.41790	T	0.15	.	13.7877	0.63119	0.0:0.0:0.0:1.0	.	479;476	Q59FL3;Q9UM47	.;NOTC3_HUMAN	G	476;478	ENSP00000263388:S476G	ENSP00000263388:S476G	S	-	1	0	NOTCH3	15160112	1.000000	0.71417	0.999000	0.59377	0.848000	0.48234	5.718000	0.68455	1.903000	0.55091	0.454000	0.30748	AGC	.	.	none		0.592	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435		C	15299112	T	C	15299112	3	2	26	1	0	0	0	0	1	0	0	0	10559	1522	53	3	5639	3	NOTCH3	19	15299112	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	1037259	15299112	43829871	588	10351											
NWD1	284434	hgsc.bcm.edu	37	chr19	16872794	16872794	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tataccctctctgtagacagCtggtcgaggtggtccgtgag	7	11	13	10	2	1	2	0	1	1	1	4	3	2	2	2	3	2	2	2	3	3	3	rs61995711	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:16872794C>T	ENST00000552788.1	+	6	1978	c.1978C>T	c.(1978-1980)Ctg>Ttg	p.L660L	NWD1_ENST00000379808.3_Silent_p.L660L|NWD1_ENST00000523826.1_Silent_p.L454L|NWD1_ENST00000339803.6_Silent_p.L525L|NWD1_ENST00000524140.2_Silent_p.L660L|NWD1_ENST00000549814.1_Silent_p.L660L			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	660	NACHT.						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						CTGTAGACAGCTGGTCGAGGT	0.582													C|||	33	0.00658946	0.0008	0.0086	5008	,	,		16843	0.0		0.0229	False		,,,				2504	0.0031				p.L660L		Atlas-SNP	.											.	NWD1	303	.	0			c.C1978T						PASS	.	C		17,4389	24.3+/-50.5	0,17,2186	89	70	76		1978	3.3	1	19	dbSNP_129	76	198,8402	86.6+/-149.0	2,194,4104	no	coding-synonymous	NWD1	NM_001007525.3		2,211,6290	TT,TC,CC		2.3023,0.3858,1.6531		660/1433	16872794	215,12791	2203	4300	6503	SO:0001819	synonymous_variant	284434	exon8			AGACAGCTGGTCG	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.1978C>T	19.37:g.16872794C>T		75	0	0		98	44	0.44898	NM_001007525	C9J021|Q68CT3	Silent	SNP	ENST00000552788.1	37																																																																																				C|0.986;T|0.014	0.014	strong		0.582	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525		T	16872794	C	T	16872794	2	4	26	1	0	0	0	0	0	0	0	1	10790	796	28	2		2	NWD1	19	16872794	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1573682	16872794	42256189	589	10352											
MAP1S	55201	hgsc.bcm.edu	37	chr19	17835917	17835917	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctggtgttggctgggccctgCctggaggagacgggggagct	4	8	20	9	1	0	1	0	0	0	1	0	4	0	3	2	7	2	3	2	7	0	1	rs141175074	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:17835917C>T	ENST00000324096.4	+	4	514	c.363C>T	c.(361-363)tgC>tgT	p.C121C	CTD-3149D2.4_ENST00000595363.1_RNA|MAP1S_ENST00000544059.2_Silent_p.C95C|MAP1S_ENST00000597681.1_Intron	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	121	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						CTGGGCCCTGCCTGGAGGAGA	0.612													C|||	2	0.000399361	0.0	0.0014	5008	,	,		19191	0.0		0.0	False		,,,				2504	0.001				p.C121C		Atlas-SNP	.											.	MAP1S	74	.	0			c.C363T						PASS	.	C		0,4406		0,0,2203	95	94	94		363	3.2	1	19	dbSNP_134	94	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MAP1S	NM_018174.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		121/1060	17835917	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	55201	exon4			GCCCTGCCTGGAG	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.363C>T	19.37:g.17835917C>T		93	0	0		109	51	0.46789	NM_018174	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Silent	SNP	ENST00000324096.4	37	CCDS32954.1																																																																																			C|1.000;T|0.000	0.000	strong		0.612	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174		T	17835917	C	T	17835917	2	4	26	1	0	0	0	0	0	0	0	1	9243	747	26	2		2	MAP1S	19	17835917	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	963123	17835917	41293066	590	10353											
SLC5A5	6528	hgsc.bcm.edu	37	chr19	17999239	17999239	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acgctgaccactgtgctgtgCggagccctcatcagctgcct	6	9	11	15	2	2	1	2	1	0	0	2	2	2	2	3	1	5	3	3	1	0	0	rs45602038	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:17999239C>T	ENST00000222248.3	+	13	1973	c.1626C>T	c.(1624-1626)tgC>tgT	p.C542C		NM_000453.2	NP_000444.1	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium/iodide cotransporter), member 5	542					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						CTGTGCTGTGCGGAGCCCTCA	0.587													C|||	66	0.0131789	0.0	0.0274	5008	,	,		15316	0.001		0.0239	False		,,,				2504	0.0225				p.C542C	Melanoma(65;1008 1708 7910 46650)	Atlas-SNP	.											.	SLC5A5	67	.	0			c.C1626T						PASS	.	C		23,4383	29.0+/-57.7	0,23,2180	117	102	107		1626	-4.6	0.7	19	dbSNP_127	107	252,8348	99.5+/-161.0	4,244,4052	no	coding-synonymous	SLC5A5	NM_000453.2		4,267,6232	TT,TC,CC		2.9302,0.522,2.1144		542/644	17999239	275,12731	2203	4300	6503	SO:0001819	synonymous_variant	6528	exon13			GCTGTGCGGAGCC		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.1626C>T	19.37:g.17999239C>T		68	0	0		87	36	0.413793	NM_000453	O43702|Q2M335|Q9NYB6	Silent	SNP	ENST00000222248.3	37	CCDS12368.1																																																																																			C|0.979;T|0.021	0.021	strong		0.587	SLC5A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466690.1			T	17999239	C	T	17999239	2	4	26	1	0	0	0	0	0	0	0	1	14683	776	27	1		1	SLC5A5	19	17999239	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	163322	17999239	41129744	591	10354											
DDX49	54555	hgsc.bcm.edu	37	chr19	19037176	19037176	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacctggtgcacgccatcgaGgagcagatcagtgagtgggg	9	6	16	10	2	1	2	1	1	0	1	2	4	1	3	2	4	2	2	2	4	0	0	rs115860110	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:19037176G>A	ENST00000247003.4	+	10	1159	c.1092G>A	c.(1090-1092)gaG>gaA	p.E364E	DDX49_ENST00000599156.1_3'UTR|AC002985.3_ENST00000596918.1_Intron|DDX49_ENST00000438170.2_3'UTR	NM_019070.4	NP_061943.2	Q9Y6V7	DDX49_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 49	364	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						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)			ACGCCATCGAGGAGCAGATCA	0.627													G|||	22	0.00439297	0.0015	0.0101	5008	,	,		11044	0.0		0.0129	False		,,,				2504	0.0				p.E364E		Atlas-SNP	.											.	DDX49	37	.	0			c.G1092A						PASS	.	G		6,4368		0,6,2181	60	40	47		1092	4.7	1	19	dbSNP_132	47	88,8458		0,88,4185	no	coding-synonymous	DDX49	NM_019070.4		0,94,6366	AA,AG,GG		1.0297,0.1372,0.7276		364/484	19037176	94,12826	2187	4273	6460	SO:0001819	synonymous_variant	54555	exon10			CATCGAGGAGCAG		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.1092G>A	19.37:g.19037176G>A		216	0	0		224	90	0.401786	NM_019070	E7ENA0|Q53FJ1|Q9BVQ8	Silent	SNP	ENST00000247003.4	37	CCDS12390.1																																																																																			G|0.993;A|0.007	0.007	strong		0.627	DDX49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464593.1	NM_019070		A	19037176	G	A	19037176	2	1	26	1	0	0	0	0	0	0	0	1	4368	991	35	2		2	DDX49	19	19037176	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1037937	19037176	40091807	592	10355											
LOC729991-MEF2B	100271849	hgsc.bcm.edu	37	chr19	19260045	19260045	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggggtacctcgaggatgTcagtgttggtgcggctctcg	4	11	16	10	3	2	0	1	0	1	0	4	2	2	1	2	5	2	3	2	5	1	2			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:19260045T>A	ENST00000602424.2	-	5	974	c.248A>T	c.(247-249)gAc>gTc	p.D83V	MEF2B_ENST00000409224.1_Missense_Mutation_p.D83V|MEF2B_ENST00000410050.1_Missense_Mutation_p.D83V|MEF2B_ENST00000409447.2_Missense_Mutation_p.D83V|MEF2BNB-MEF2B_ENST00000444486.3_Missense_Mutation_p.D83V|MEF2BNB-MEF2B_ENST00000514819.3_Missense_Mutation_p.D100V|MEF2BNB-MEF2B_ENST00000602276.1_5'UTR|MEF2B_ENST00000424583.2_Missense_Mutation_p.D83V|MEF2B_ENST00000162023.5_Missense_Mutation_p.D83V	NM_005919.3	NP_005910.1	Q02080	MEF2B_HUMAN	myocyte enhancer factor 2B	83					muscle organ development (GO:0007517)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cell junction (GO:0030054)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D83V(11)|p.D83A(2)		breast(1)|haematopoietic_and_lymphoid_tissue(21)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(5;0.00011)|Epithelial(12;0.00412)			CTCGAGGATGTCAGTGTTGGT	0.607																																					p.D83V		Atlas-SNP	.											MEF2BNB-MEF2B,NS,lymphoid_neoplasm,0,15	MEF2BNB-MEF2B	29	15	13	Substitution - Missense(13)	haematopoietic_and_lymphoid_tissue(13)	c.A248T						PASS	.						126	63	84					19																	19260045		2203	4300	6503	SO:0001583	missense	4207	exon5			AGGATGTCAGTGT	X63380	CCDS12394.1, CCDS46024.1	19p13.11	2010-05-12	2007-04-24					"Myocyte enhancer factors"	6995	protein-coding gene	gene with protein product		600661				1516833, 8575763	Standard	NM_001145785		Approved	RSRFR2	uc002nll.2	Q02080		ENST00000602424.2:c.248A>T	19.37:g.19260045T>A	ENSP00000473308:p.Asp83Val	120	0	0		122	53	0.434426	NM_005919	A0AV80|B4DVH7|B7ZVY1|G5E9M1	Missense_Mutation	SNP	ENST00000602424.2	37	CCDS12394.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.187318	0.78789	.	.	ENSG00000213999	ENST00000409224;ENST00000424583;ENST00000410050;ENST00000444486;ENST00000409447;ENST00000162023	D;D;D;D;D	0.83837	-1.77;-1.77;-1.77;-1.77;-1.77	5.33	5.33	0.75918	Transcription factor, MADS-box (1);	0.000000	0.85682	D	0.000000	D	0.90167	0.6927	M	0.74467	2.265	0.80722	D	1	D;D;D;D;D	0.89917	0.999;0.998;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.963;0.92;0.997;0.997;0.998	D	0.91163	0.4962	10	0.72032	D	0.01	-31.0539	13.2359	0.59969	0.0:0.0:0.0:1.0	.	83;130;83;83;83	Q02080;B8ZZJ5;C9J4J4;G5E9M1;B3KQ23	MEF2B_HUMAN;.;.;.;.	V	83;83;83;83;130;83	ENSP00000386480:D83V;ENSP00000402154:D83V;ENSP00000386374:D83V;ENSP00000390762:D83V;ENSP00000162023:D83V	ENSP00000162023:D83V	D	-	2	0	MEF2B	19121045	1.000000	0.71417	0.999000	0.59377	0.518000	0.34316	7.923000	0.87546	2.024000	0.59613	0.459000	0.35465	GAC	.	.	none		0.607	MEF2B-202	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_005919		A	19260045	T	A	19260045	3	1	26	1	0	0	0	0	1	0	0	0	8898	1667	58	5	873	5	LOC729991-MEF2B	19	19260045	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	222869	19260045	39868938	593	10356											
ZNF486	90649	hgsc.bcm.edu	37	chr19	20308149	20308149	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gatactggagagaaaccataCaaatgtgaagaatgtggcaa	18	7	11	5	0	0	3	0	1	0	2	0	6	0	4	1	2	3	1	1	2	7	2	rs184976796	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:20308149C>G	ENST00000335117.8	+	4	687	c.630C>G	c.(628-630)taC>taG	p.Y210*	CTC-260E6.6_ENST00000586657.1_RNA|CTC-260E6.6_ENST00000585498.1_RNA|CTC-260E6.6_ENST00000593655.1_RNA	NM_052852.3	NP_443084.2	Q96H40	ZN486_HUMAN	zinc finger protein 486	210					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						AGAAACCATACAAATGTGAAG	0.363													C|||	17	0.00339457	0.0	0.0058	5008	,	,		19254	0.0		0.0109	False		,,,				2504	0.002				p.Y210X		Atlas-SNP	.											.	ZNF486	74	.	0			c.C630G						PASS	.	C	stop/TYR	7,4291		0,7,2142	39	42	41		630	0.8	0.1	19		41	54,8492		0,54,4219	no	stop-gained	ZNF486	NM_052852.2		0,61,6361	GG,GC,CC		0.6319,0.1629,0.4749		210/464	20308149	61,12783	2149	4273	6422	SO:0001587	stop_gained	90649	exon4			ACCATACAAATGT	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.630C>G	19.37:g.20308149C>G	ENSP00000335042:p.Tyr210*	20	0	0		32	15	0.46875	NM_052852	Q0VG00	Nonsense_Mutation	SNP	ENST00000335117.8	37	CCDS46029.1	8	0.003663003663003663	0	0.0	5	0.013812154696132596	0	0.0	3	0.00395778364116095	c	10.99	1.507634	0.27036	0.001629	0.006319	ENSG00000256229	ENST00000545779;ENST00000335117	.	.	.	0.814	0.814	0.18756	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.9774	0.24683	0.0:1.0:0.0:0.0	.	.	.	.	X	249;210	.	ENSP00000335042:Y210X	Y	+	3	2	ZNF486	20169149	0.000000	0.05858	0.057000	0.19452	0.056000	0.15407	-0.409000	0.07160	0.183000	0.20059	0.186000	0.17326	TAC	C|0.995;G|0.005	0.005	strong		0.363	ZNF486-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447843.2	NM_052852		G	20308149	C	G	20308149	4	3	26	1	0	0	0	0	0	1	0	0	17954	489	17	4	644	4	ZNF486	19	20308149	Nonsense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1048104	20308149	38820834	594	10357											
ZNF486	90649	hgsc.bcm.edu	37	chr19	20308488	20308488	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actggagagaaaccgtacacGtgtgataaatgtggcaaagc	15	7	12	7	2	0	2	0	1	0	1	0	4	0	3	1	2	3	2	1	2	5	2	rs181719180	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:20308488G>T	ENST00000335117.8	+	4	1026	c.969G>T	c.(967-969)acG>acT	p.T323T	CTC-260E6.6_ENST00000586657.1_RNA|CTC-260E6.6_ENST00000585498.1_RNA|CTC-260E6.6_ENST00000593655.1_RNA	NM_052852.3	NP_443084.2	Q96H40	ZN486_HUMAN	zinc finger protein 486	323					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						AACCGTACACGTGTGATAAAT	0.388													G|||	17	0.00339457	0.0	0.0058	5008	,	,		21939	0.0		0.0109	False		,,,				2504	0.002				p.T323T		Atlas-SNP	.											ZNF486_ENST00000335117,NS,carcinoma,+1,4	ZNF486	74	4	0			c.G969T						PASS	.	G		6,4348		0,6,2171	47	52	50		969	-1.7	0.1	19		50	53,8525		0,53,4236	no	coding-synonymous	ZNF486	NM_052852.2		0,59,6407	TT,TG,GG		0.6179,0.1378,0.4562		323/464	20308488	59,12873	2177	4289	6466	SO:0001819	synonymous_variant	90649	exon4			GTACACGTGTGAT	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.969G>T	19.37:g.20308488G>T		25	0	0		24	9	0.375	NM_052852	Q0VG00	Silent	SNP	ENST00000335117.8	37	CCDS46029.1																																																																																			G|0.995;T|0.005	0.005	strong		0.388	ZNF486-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447843.2	NM_052852		T	20308488	G	T	20308488	2	4	26	1	0	0	0	0	0	0	0	1	17954	1132	40	4		4	ZNF486	19	20308488	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	339	20308488	38820495	595	10358											
RHPN2	85415	hgsc.bcm.edu	37	chr19	33517507	33517507	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagctcagctccagccgcaCttgctcccgcacctttgagt	7	9	9	16	2	1	1	1	1	0	0	3	2	3	1	4	0	4	5	4	0	1	2			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:33517507C>T	ENST00000254260.3	-	3	252	c.217G>A	c.(217-219)Gtg>Atg	p.V73M	RHPN2_ENST00000400226.4_De_novo_Start_OutOfFrame	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	73					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)		p.V73M(2)		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)					TCCAGCCGCACTTGCTCCCGC	0.552																																					p.V73M		Atlas-SNP	.											RHPN2,face,carcinoma,0,2	RHPN2	107	2	2	Substitution - Missense(2)	NS(1)|skin(1)	c.G217A						scavenged	.						84	83	83					19																	33517507		2203	4300	6503	SO:0001583	missense	85415	exon3			GCCGCACTTGCTC	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.217G>A	19.37:g.33517507C>T	ENSP00000254260:p.Val73Met	15	1	0.0666667		39	5	0.128205	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	C	18.08	3.542997	0.65198	.	.	ENSG00000131941	ENST00000254260	T	0.39787	1.06	3.88	3.88	0.44766	.	0.000000	0.85682	D	0.000000	T	0.64853	0.2636	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.71984	-0.4427	10	0.87932	D	0	11.9954	16.025	0.80536	0.0:1.0:0.0:0.0	.	73	Q8IUC4	RHPN2_HUMAN	M	73	ENSP00000254260:V73M	ENSP00000254260:V73M	V	-	1	0	RHPN2	38209347	1.000000	0.71417	1.000000	0.80357	0.343000	0.28985	7.267000	0.78462	2.167000	0.68274	0.557000	0.71058	GTG	.	.	none		0.552	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103		T	33517507	C	T	33517507	3	4	26	1	0	0	0	0	1	0	0	0	13366	565	20	2	1895	2	RHPN2	19	33517507	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	13209019	33517507	25611476	596	10359											
FCGBP	8857	hgsc.bcm.edu	37	chr19	40376811	40376811	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggcaggaggacagtggccCtgtggggctggagaggagcc	7	5	21	8	0	0	1	0	0	0	1	0	5	0	4	2	8	1	2	2	8	0	0	rs4802062	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:40376811C>T	ENST00000221347.6	-	24	11618	c.11611G>A	c.(11611-11613)Ggg>Agg	p.G3871R	FCGBP_ENST00000595713.1_5'Flank	NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	3871	VWFD 9. {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)			GACAGTGGCCCTGTGGGGCTG	0.602																																					p.G3871R		Atlas-SNP	.											FCGBP,NS,carcinoma,+2,1	FCGBP	416	1	0			c.G11611A						scavenged	.						9	14	12					19																	40376811		2097	4111	6208	SO:0001583	missense	8857	exon24			GTGGCCCTGTGGG	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.11611G>A	19.37:g.40376811C>T	ENSP00000221347:p.Gly3871Arg	618	1	0.00161812		785	145	0.184713	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	c	19.42	3.823259	0.71143	.	.	ENSG00000090920	ENST00000221347	T	0.19806	2.12	3.75	3.75	0.43078	von Willebrand factor, type D domain (1);Uncharacterised domain, cysteine-rich (2);	.	.	.	.	T	0.55049	0.1896	M	0.92649	3.33	0.43485	D	0.995715	D	0.89917	1.0	D	0.97110	1.0	T	0.69038	-0.5251	9	0.72032	D	0.01	.	14.6972	0.69132	0.0:1.0:0.0:0.0	rs4802062	3871	Q9Y6R7	FCGBP_HUMAN	R	3871	ENSP00000221347:G3871R	ENSP00000221347:G3871R	G	-	1	0	FCGBP	45068651	0.998000	0.40836	0.523000	0.27875	0.621000	0.37620	3.885000	0.56182	1.792000	0.52537	0.313000	0.20887	GGG	C|0.962;T|0.038	0.038	strong		0.602	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		T	40376811	C	T	40376811	3	4	26	1	0	0	0	0	1	0	0	0	5786	681	24	2	4658	2	FCGBP	19	40376811	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	6859304	40376811	18752172	597	10360											
ZNF780B	163131	hgsc.bcm.edu	37	chr19	40541845	40541845	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaggccatctcacattccctAcatacaaagggtttctcatt	12	12	5	12	0	2	0	2	0	2	0	5	0	3	0	2	2	2	1	2	2	4	5	rs371876870		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:40541845A>G	ENST00000434248.1	-	5	986	c.921T>C	c.(919-921)tgT>tgC	p.C307C	ZNF780B_ENST00000221355.6_Silent_p.C159C	NM_001005851.2	NP_001005851.1	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	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)|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)					CACATTCCCTACATACAAAGG	0.373																																					p.C307C		Atlas-SNP	.											.	ZNF780B	143	.	0			c.T921C						PASS	.	A		0,4406		0,0,2203	116	118	117		921	1.1	0.5	19		117	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ZNF780B	NM_001005851.2		0,1,6502	GG,GA,AA		0.0116,0.0,0.0077		307/834	40541845	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	163131	exon5			TTCCCTACATACA	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.921T>C	19.37:g.40541845A>G		94	0	0		99	38	0.383838	NM_001005851	B9EH00	Silent	SNP	ENST00000434248.1	37	CCDS46077.1																																																																																			.	.	weak		0.373	ZNF780B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338466.1	NM_001005851		G	40541845	A	G	40541845	2	3	26	1	0	0	0	0	0	0	0	1	18168	389	14	3		3	ZNF780B	19	40541845	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	165034	40541845	18587138	598	10361											
LYPD3	27076	hgsc.bcm.edu	37	chr19	43965594	43965594	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tattatggggctgctggggcCccccttttgcaggatactgc	5	12	13	11	0	0	0	0	0	0	0	0	1	0	1	3	5	4	3	3	5	3	5	rs149095976	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:43965594C>T	ENST00000244333.3	-	5	1038	c.950G>A	c.(949-951)gGg>gAg	p.G317E		NM_014400.2	NP_055215.2	O95274	LYPD3_HUMAN	LY6/PLAUR domain containing 3	317					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)				CTGCTGGGGCCCCCCTTTTGC	0.622													C|||	4	0.000798722	0.0	0.0014	5008	,	,		16242	0.0		0.003	False		,,,				2504	0.0				p.G317E		Atlas-SNP	.											.	LYPD3	24	.	0			c.G950A						PASS	.	C	GLU/GLY	2,4404	4.2+/-10.8	0,2,2201	43	46	45		950	0.4	0	19	dbSNP_134	45	11,8589	8.4+/-32.0	0,11,4289	yes	missense	LYPD3	NM_014400.2	98	0,13,6490	TT,TC,CC		0.1279,0.0454,0.1	benign	317/347	43965594	13,12993	2203	4300	6503	SO:0001583	missense	27076	exon5			TGGGGCCCCCCTT	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.950G>A	19.37:g.43965594C>T	ENSP00000244333:p.Gly317Glu	91	0	0		103	48	0.466019	NM_014400	Q9UJ74	Missense_Mutation	SNP	ENST00000244333.3	37	CCDS12620.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	10.42	1.345506	0.24426	4.54E-4	0.001279	ENSG00000124466	ENST00000244333;ENST00000377995	T	0.12879	2.64	5.13	0.434	0.16539	.	0.666605	0.13500	N	0.383293	T	0.07098	0.0180	N	0.14661	0.345	0.09310	N	1	B	0.20368	0.044	B	0.18263	0.021	T	0.31336	-0.9947	10	0.72032	D	0.01	.	4.5533	0.12124	0.3053:0.5268:0.0:0.1679	.	317	O95274	LYPD3_HUMAN	E	317;265	ENSP00000244333:G317E	ENSP00000244333:G317E	G	-	2	0	LYPD3	48657434	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.324000	0.07986	0.018000	0.15052	-0.143000	0.13931	GGG	C|0.999;T|0.001	0.001	strong		0.622	LYPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463177.1	NM_014400		T	43965594	C	T	43965594	3	4	26	1	0	0	0	0	1	0	0	0	9120	623	22	2	94	2	LYPD3	19	43965594	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	3423749	43965594	15163389	599	10362											
ARHGAP35	2909	hgsc.bcm.edu	37	chr19	47422388	47422388	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcagaaacaaatgccagaCggaaagctgctggttgatgg	14	6	14	7	1	0	3	0	1	0	2	0	5	0	4	1	3	5	4	1	3	3	1			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:47422388C>T	ENST00000404338.3	+	1	456	c.456C>T	c.(454-456)gaC>gaT	p.D152D		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	152					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)										AAATGCCAGACGGAAAGCTGC	0.473																																					p.D152D		Atlas-SNP	.											GRLF1_ENST00000317082,NS,carcinoma,+1,2	.	.	2	0			c.C456T						PASS	.						81	76	78					19																	47422388		1933	4138	6071	SO:0001819	synonymous_variant	2909	exon1			GCCAGACGGAAAG	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.456C>T	19.37:g.47422388C>T		110	0	0		104	56	0.538462	NM_004491	A7E2A4|Q14452|Q9C0E1	Silent	SNP	ENST00000404338.3	37	CCDS46127.1																																																																																			.	.	none		0.473	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491		T	47422388	C	T	47422388	2	4	26	1	0	0	0	0	0	0	0	1	6804	535	19	1		1	ARHGAP35	19	47422388	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	3456794	47422388	11706595	600	10363											
DHX34	9704	hgsc.bcm.edu	37	chr19	47858489	47858489	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cgtcctccagcgcctgttgcCcacgcggcctgacctcaagg	5	7	11	18	4	1	1	1	1	0	0	3	1	3	1	6	2	2	1	6	2	1	1	rs34802163	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:47858489C>G	ENST00000328771.4	+	3	1248	c.899C>G	c.(898-900)cCc>cGc	p.P300R		NM_014681.5	NP_055496.2	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	300	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				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)		CGCCTGTTGCCCACGCGGCCT	0.587													C|||	66	0.0131789	0.0008	0.0115	5008	,	,		16986	0.001		0.0318	False		,,,				2504	0.0245				p.P300R		Atlas-SNP	.											DHX34,lower_third,carcinoma,-1,1	DHX34	98	1	0			c.C899G						PASS	.	C	ARG/PRO	21,4385	29.9+/-59.1	1,19,2183	133	115	121		899	4.4	1	19	dbSNP_126	121	258,8342	101.4+/-162.7	3,252,4045	yes	missense	DHX34	NM_014681.5	103	4,271,6228	GG,GC,CC		3.0,0.4766,2.1452	benign	300/1144	47858489	279,12727	2203	4300	6503	SO:0001583	missense	9704	exon3			TGTTGCCCACGCG	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.899C>G	19.37:g.47858489C>G	ENSP00000331907:p.Pro300Arg	137	0	0		143	68	0.475524	NM_014681	B4DMY8	Missense_Mutation	SNP	ENST00000328771.4	37	CCDS12700.1	35	0.016025641025641024	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	27	0.03562005277044855	C	10.91	1.484804	0.26598	0.004766	0.03	ENSG00000134815	ENST00000328771;ENST00000257252	T	0.26373	1.74	4.41	4.41	0.53225	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.359689	0.23656	N	0.045867	T	0.04861	0.0131	N	0.02697	-0.525	0.36709	D	0.880551	B;D	0.62365	0.238;0.991	B;P	0.61658	0.126;0.892	T	0.18398	-1.0338	10	0.35671	T	0.21	0.6401	9.6656	0.39983	0.0:0.9004:0.0:0.0996	rs34802163;rs61750959	300;300	Q14147;B4E3G3	DHX34_HUMAN;.	R	300	ENSP00000331907:P300R	ENSP00000257252:P300R	P	+	2	0	DHX34	52550329	0.920000	0.31207	0.984000	0.44739	0.859000	0.49053	2.414000	0.44627	2.010000	0.58986	0.456000	0.33151	CCC	C|0.979;G|0.021	0.021	strong		0.587	DHX34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314313.3	NM_014681		G	47858489	C	G	47858489	3	3	26	1	0	0	0	0	1	0	0	0	4509	623	22	4	905	4	DHX34	19	47858489	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	436101	47858489	11270494	601	10364											
GRIN2D	2906	hgsc.bcm.edu	37	chr19	48908597	48908597	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agaaccgcacccaccgcggcGagagtctgcataggtgagtg	10	5	14	12	4	1	3	0	1	1	2	1	4	1	3	3	2	2	2	3	2	2	1	rs372406980		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:48908597G>A	ENST00000263269.3	+	3	1160	c.1072G>A	c.(1072-1074)Gag>Aag	p.E358K		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	358					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)	CCACCGCGGCGAGAGTCTGCA	0.622																																					p.E358K		Atlas-SNP	.											.	GRIN2D	76	.	0			c.G1072A						PASS	.						14	15	15					19																	48908597		2201	4295	6496	SO:0001583	missense	2906	exon3			CGCGGCGAGAGTC	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.1072G>A	19.37:g.48908597G>A	ENSP00000263269:p.Glu358Lys	22	0	0		40	25	0.625	NM_000836		Missense_Mutation	SNP	ENST00000263269.3	37	CCDS12719.1	.	.	.	.	.	.	.	.	.	.	G	15.44	2.833830	0.50951	.	.	ENSG00000105464	ENST00000263269	T	0.05319	3.46	4.32	4.32	0.51571	.	0.845492	0.10398	N	0.679577	T	0.06280	0.0162	L	0.31926	0.97	0.42288	D	0.992125	P	0.48230	0.907	B	0.33620	0.167	T	0.50285	-0.8846	10	0.54805	T	0.06	.	15.9622	0.79939	0.0:0.0:1.0:0.0	.	358	O15399	NMDE4_HUMAN	K	358	ENSP00000263269:E358K	ENSP00000263269:E358K	E	+	1	0	GRIN2D	53600409	0.989000	0.36119	0.999000	0.59377	0.911000	0.54048	3.506000	0.53364	2.116000	0.64780	0.561000	0.74099	GAG	.	.	alt		0.622	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1			A	48908597	G	A	48908597	3	1	26	1	0	0	0	0	1	0	0	0	6791	1059	37	1	1078	1	GRIN2D	19	48908597	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1050108	48908597	10220386	602	10365											
LMTK3	114783	hgsc.bcm.edu	37	chr19	49013809	49013809	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caggaaatgaggaccacagcGtagggaggagccagaggagc	14	2	17	8	1	0	2	0	1	0	1	0	7	0	7	2	5	3	1	2	5	2	1			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49013809G>T	ENST00000600059.1	-	2	344	c.117C>A	c.(115-117)taC>taA	p.Y39*	LMTK3_ENST00000270238.3_Nonsense_Mutation_p.Y68*|CTC-273B12.10_ENST00000598924.1_lincRNA			Q96Q04	LMTK3_HUMAN	lemur tyrosine kinase 3	39					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)		GGACCACAGCGTAGGGAGGAG	0.627																																					p.Y68X		Atlas-SNP	.											LMTK3_ENST00000270238,caecum,carcinoma,-1,3	LMTK3	125	3	0			c.C204A						PASS	.						41	57	51					19																	49013809		2064	4205	6269	SO:0001587	stop_gained	114783	exon3			CACAGCGTAGGGA	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.117C>A	19.37:g.49013809G>T	ENSP00000472020:p.Tyr39*	123	0	0		152	67	0.440789	NM_001080434	Q4G0U1	Nonsense_Mutation	SNP	ENST00000600059.1	37		.	.	.	.	.	.	.	.	.	.	g	20.9	4.066456	0.76187	.	.	ENSG00000142235	ENST00000270238	.	.	.	3.95	-2.25	0.06888	.	0.000000	0.64402	U	0.000009	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	.	8.747	0.34591	0.6394:0.0:0.3606:0.0	.	.	.	.	X	68	.	ENSP00000270238:Y68X	Y	-	3	2	LMTK3	53705621	0.797000	0.28877	0.989000	0.46669	0.972000	0.66771	-0.150000	0.10189	-0.406000	0.07588	0.282000	0.19409	TAC	.	.	none		0.627	LMTK3-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000466137.1	NM_052895		T	49013809	G	T	49013809	4	4	26	1	0	0	0	0	0	1	0	0	8869	1140	40	4	4321	4	LMTK3	19	49013809	Nonsense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	105212	49013809	10115174	603	10366											
CA11	770	hgsc.bcm.edu	37	chr19	49143533	49143533	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggtgttgtacaaggttcccCggagctgtgggagaggcggg	6	8	19	8	3	0	1	0	0	0	1	1	3	1	2	2	6	2	4	2	6	2	3			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49143533C>T	ENST00000084798.4	-	4	969	c.290G>A	c.(289-291)cGg>cAg	p.R97Q	SEC1P_ENST00000430145.2_RNA|DBP_ENST00000222122.5_5'Flank|DBP_ENST00000601104.1_5'Flank	NM_001217.3	NP_001208.2	O75493	CAH11_HUMAN	carbonic anhydrase XI	97						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)	CAAGGTTCCCCGGAGCTGTGG	0.552																																					p.R97Q		Atlas-SNP	.											.	CA11	29	.	0			c.G290A						PASS	.						47	47	47					19																	49143533		2203	4300	6503	SO:0001583	missense	770	exon4			GTTCCCCGGAGCT	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.290G>A	19.37:g.49143533C>T	ENSP00000084798:p.Arg97Gln	74	0	0		98	41	0.418367	NM_001217	O60596|Q6FHI1|Q9UEC4	Missense_Mutation	SNP	ENST00000084798.4	37	CCDS12729.1	.	.	.	.	.	.	.	.	.	.	C	19.68	3.872278	0.72180	.	.	ENSG00000063180	ENST00000084798	T	0.67698	-0.28	3.46	3.46	0.39613	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.218732	0.39544	N	0.001325	T	0.48750	0.1517	N	0.10916	0.065	0.36952	D	0.892938	D	0.55385	0.971	P	0.45310	0.476	T	0.60910	-0.7169	10	0.54805	T	0.06	.	10.6521	0.45655	0.0:1.0:0.0:0.0	.	97	O75493	CAH11_HUMAN	Q	97	ENSP00000084798:R97Q	ENSP00000084798:R97Q	R	-	2	0	CA11	53835345	0.995000	0.38212	1.000000	0.80357	0.988000	0.76386	2.667000	0.46808	1.970000	0.57323	0.462000	0.41574	CGG	.	.	none		0.552	CA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466172.1	NM_001217		T	49143533	C	T	49143533	3	4	26	1	0	0	0	0	1	0	0	0	2514	652	23	1	720	1	CA11	19	49143533	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	129724	49143533	9985450	604	10367											
CGB8	94115	hgsc.bcm.edu	37	chr19	49551573	49551573	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggcggcaccgtggccgaagCggctccttggatgcccatgt	5	7	16	13	4	0	0	0	0	0	0	1	2	1	1	4	5	2	2	4	5	1	1	rs151241744	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49551573C>T	ENST00000448456.3	-	2	438	c.72G>A	c.(70-72)ccG>ccA	p.P24P	CGB8_ENST00000355414.2_Silent_p.P22P|CGB1_ENST00000391869.3_Intron	NM_033183.2	NP_149439.1	P01233	CGHB_HUMAN	chorionic gonadotropin, beta polypeptide 8	24			P -> M (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:11861891, ECO:0000269|PubMed:6194155}.		apoptotic process (GO:0006915)|cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|female gamete generation (GO:0007292)|peptide hormone processing (GO:0016486)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			pancreas(1)	1		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)		GTGGCCGAAGCGGCTCCTTGG	0.657																																					p.P24P		Atlas-SNP	.											CGB8,NS,carcinoma,0,1	CGB8	2	1	0			c.G72A						scavenged	.						1	1	1					19																	49551573		258	679	937	SO:0001819	synonymous_variant	94115	exon2			CCGAAGCGGCTCC	BG435249	CCDS12753.1	19q13.32	2011-05-26							16453	protein-coding gene	gene with protein product		608827				6194155	Standard	NM_033183		Approved		uc002pmb.4	P01233		ENST00000448456.3:c.72G>A	19.37:g.49551573C>T		127	0	0		135	25	0.185185	NM_033183	A1A5E0|B9ZVP5|Q13991|Q14000|Q3KPI3|Q3SY41|Q8WTT5|Q8WXL1|Q8WXL2|Q8WXL3|Q8WXL4	Silent	SNP	ENST00000448456.3	37	CCDS12753.1																																																																																			T|1.000;|0.000	1.000	weak		0.657	CGB8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452168.1	NM_033183		T	49551573	C	T	49551573	2	4	26	1	0	0	0	0	0	0	0	1	3303	755	27	1		1	CGB8	19	49551573	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	408040	49551573	9577410	605	10368											
TEAD2	8463	hgsc.bcm.edu	37	chr19	49862722	49862722	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gttcgggtcttccccgttctCagcttgatgtagcgggcgat	4	13	13	11	4	2	1	1	1	2	0	5	2	3	1	2	2	2	4	2	2	1	5			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49862722C>T	ENST00000311227.2	-	3	357	c.267G>A	c.(265-267)ctG>ctA	p.L89L	TEAD2_ENST00000598397.1_5'Flank|TEAD2_ENST00000377214.4_Silent_p.L89L|AC010524.4_ENST00000596488.1_RNA|DKKL1_ENST00000594268.1_5'Flank|TEAD2_ENST00000539846.1_5'UTR|TEAD2_ENST00000598810.1_Silent_p.L89L|TEAD2_ENST00000601519.1_Silent_p.L89L|TEAD2_ENST00000593945.1_Silent_p.L89L	NM_001256659.1|NM_003598.1	NP_001243588.1|NP_003589.1	Q15562	TEAD2_HUMAN	TEA domain family member 2	89					gene expression (GO:0010467)|hippo signaling (GO:0035329)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	29		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)		TCCCCGTTCTCAGCTTGATGT	0.522																																					p.L89L		Atlas-SNP	.											.	TEAD2	70	.	0			c.G267A						PASS	.						254	214	228					19																	49862722		2203	4300	6503	SO:0001819	synonymous_variant	8463	exon3			CGTTCTCAGCTTG	X94440	CCDS12761.1, CCDS58670.1, CCDS58671.1, CCDS59406.1	19q13.3	2008-07-22							11715	protein-coding gene	gene with protein product		601729				9889009, 8702974	Standard	NM_003598		Approved	TEF-4, ETF, TEF4	uc031rls.1	Q15562		ENST00000311227.2:c.267G>A	19.37:g.49862722C>T		145	0	0		197	86	0.436548	NM_001256658	B4DTJ6|M0R1T9|Q8NA25|Q96IG3	Silent	SNP	ENST00000311227.2	37	CCDS12761.1																																																																																			.	.	none		0.522	TEAD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465465.1	NM_003598		T	49862722	C	T	49862722	2	4	26	1	0	0	0	0	0	0	0	1	15754	813	29	2		2	TEAD2	19	49862722	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	311149	49862722	9266261	606	10369											
TBC1D17	79735	hgsc.bcm.edu	37	chr19	50381802	50381802	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctgtagaggaggctggagaTtccacccaaatcctcttctc	9	10	9	13	0	2	2	0	0	2	2	5	4	4	3	4	3	0	2	4	3	2	3	rs373760628		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:50381802T>C	ENST00000221543.5	+	3	467	c.168T>C	c.(166-168)gaT>gaC	p.D56D	AKT1S1_ENST00000391832.3_5'Flank|TBC1D17_ENST00000598789.1_3'UTR|AKT1S1_ENST00000391834.2_5'Flank|AKT1S1_ENST00000482622.1_5'Flank|AKT1S1_ENST00000391831.1_5'Flank|AKT1S1_ENST00000391835.1_5'Flank|AKT1S1_ENST00000344175.5_5'Flank|TBC1D17_ENST00000535102.2_Silent_p.D23D	NM_024682.2	NP_078958	Q9HA65	TBC17_HUMAN	TBC1 domain family, member 17	56					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)		AGGCTGGAGATTCCACCCAAA	0.552													T|||	1	0.000199681	0.0	0.0	5008	,	,		18217	0.0		0.001	False		,,,				2504	0.0				p.D56D		Atlas-SNP	.											TBC1D17,NS,carcinoma,+2,1	TBC1D17	39	1	0			c.T168C						PASS	.	T	,	0,4406		0,0,2203	105	99	101		69,168	2.2	1	19		101	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	TBC1D17	NM_001168222.1,NM_024682.2	,	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	,	23/616,56/649	50381802	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	79735	exon3			TGGAGATTCCACC	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.168T>C	19.37:g.50381802T>C		88	0	0		101	48	0.475248	NM_024682	B4DT12|B9A6L8|F5H1W7	Silent	SNP	ENST00000221543.5	37	CCDS12785.1																																																																																			.	.	weak		0.552	TBC1D17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466404.1	NM_024682		C	50381802	T	C	50381802	2	2	26	1	0	0	0	0	0	0	0	1	15621	1490	52	3		3	TBC1D17	19	50381802	Silent	SNP	T	TCGA-G8-6907-01A-11D-2210-10	519080	50381802	8747181	607	10370											
MYH14	79784	hgsc.bcm.edu	37	chr19	50795617	50795617	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgaaaagcgcctcaagggcCtggaggctgaggtgctgcgg	8	6	18	9	2	1	2	1	2	0	0	1	3	1	3	2	5	3	2	2	5	3	0	rs147447646	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:50795617C>T	ENST00000596571.1	+	34	5104	c.5104C>T	c.(5104-5106)Ctg>Ttg	p.L1702L	MYH14_ENST00000262269.8_Silent_p.L1743L|MYH14_ENST00000440075.2_Silent_p.L1743L|MYH14_ENST00000601313.1_Silent_p.L1743L|MYH14_ENST00000598205.1_Silent_p.L1710L|MYH14_ENST00000425460.1_Silent_p.L1710L|MYH14_ENST00000376970.2_Silent_p.L1735L			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1702					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)		CCTCAAGGGCCTGGAGGCTGA	0.642													C|||	5	0.000998403	0.0	0.0014	5008	,	,		16103	0.0		0.004	False		,,,				2504	0.0				p.L1743L		Atlas-SNP	.											.	MYH14	261	.	0			c.C5227T						PASS	.	C	,,	4,4008		0,4,2002	14	17	16		5128,5227,5104	1.6	1	19	dbSNP_134	16	28,8352		0,28,4162	no	coding-synonymous,coding-synonymous,coding-synonymous	MYH14	NM_001077186.1,NM_001145809.1,NM_024729.3	,,	0,32,6164	TT,TC,CC		0.3341,0.0997,0.2582	,,	1710/2004,1743/2037,1702/1996	50795617	32,12360	2006	4190	6196	SO:0001819	synonymous_variant	79784	exon37			AAGGGCCTGGAGG	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.5104C>T	19.37:g.50795617C>T		72	0	0		97	54	0.556701	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent	SNP	ENST00000596571.1	37	CCDS59411.1																																																																																			C|0.998;T|0.002	0.002	strong		0.642	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		T	50795617	C	T	50795617	2	4	26	1	0	0	0	0	0	0	0	1	10042	680	24	2		2	MYH14	19	50795617	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	413815	50795617	8333366	608	10371											
KLK13	26085	hgsc.bcm.edu	37	chr19	51563265	51563265	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcttctccggtattcagggtGggggatagagtggacaactt	8	11	15	7	1	2	1	1	0	1	1	3	3	2	3	1	5	1	2	1	5	3	5	rs34089525	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51563265G>A	ENST00000595793.1	-	3	367	c.325C>T	c.(325-327)Cac>Tac	p.H109Y	KLK13_ENST00000335422.3_Intron|KLK13_ENST00000595547.1_Intron|KLK13_ENST00000596955.1_Missense_Mutation_p.H109Y	NM_015596.1	NP_056411.1	Q9UKR3	KLK13_HUMAN	kallikrein-related peptidase 13	109	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		H -> Y (in dbSNP:rs34089525).		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)		TATTCAGGGTGGGGGATAGAG	0.582													G|||	56	0.0111821	0.0015	0.0058	5008	,	,		11828	0.0		0.0298	False		,,,				2504	0.0204				p.H109Y		Atlas-SNP	.											.	KLK13	40	.	0			c.C325T						PASS	.	G	TYR/HIS	27,4379	34.3+/-65.2	0,27,2176	88	87	87		325	2.9	1	19	dbSNP_126	87	288,8312	106.0+/-166.9	9,270,4021	yes	missense	KLK13	NM_015596.1	83	9,297,6197	AA,AG,GG		3.3488,0.6128,2.422	probably-damaging	109/278	51563265	315,12691	2203	4300	6503	SO:0001583	missense	26085	exon3			CAGGGTGGGGGAT		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.325C>T	19.37:g.51563265G>A	ENSP00000470555:p.His109Tyr	64	0	0		83	46	0.554217	NM_015596	A7UNK6|Q86VI8|Q9Y433	Missense_Mutation	SNP	ENST00000595793.1	37	CCDS12822.1	31	0.014194139194139194	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	26	0.03430079155672823	G	11.51	1.659191	0.29515	0.006128	0.033488	ENSG00000167759	ENST00000156476	.	.	.	3.91	2.86	0.33363	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.132025	0.34700	N	0.003750	T	0.48607	0.1509	M	0.78049	2.395	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74674	0.984;0.984	T	0.64820	-0.6317	9	0.87932	D	0	.	7.6127	0.28139	0.1196:0.0:0.8804:0.0	rs34089525	109;109	B5BUM9;Q9UKR3	.;KLK13_HUMAN	Y	109	.	ENSP00000156476:H109Y	H	-	1	0	KLK13	56255077	1.000000	0.71417	0.987000	0.45799	0.002000	0.02628	4.613000	0.61176	1.001000	0.39076	-0.145000	0.13849	CAC	G|0.977;A|0.023	0.023	strong		0.582	KLK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464298.2	NM_015596		A	51563265	G	A	51563265	3	1	26	1	0	0	0	0	1	0	0	0	8410	1348	47	2	520	2	KLK13	19	51563265	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	767648	51563265	7565718	609	10372											
HAS1	3036	hgsc.bcm.edu	37	chr19	52217128	52217128	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagcagcacccacagcagcGcccaagggcggcccgcgtag	10	1	13	17	4	0	0	0	0	0	0	0	0	0	0	3	2	4	4	3	2	2	1	rs34682338	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:52217128G>A	ENST00000222115.1	-	5	1323	c.1289C>T	c.(1288-1290)gCg>gTg	p.A430V	HAS1_ENST00000601714.1_Missense_Mutation_p.A437V|HAS1_ENST00000540069.2_Missense_Mutation_p.A429V	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	430					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)		CCACAGCAGCGCCCAAGGGCG	0.697													g|||	10	0.00199681	0.0008	0.0014	5008	,	,		15365	0.0		0.005	False		,,,				2504	0.0031				p.A430V	NSCLC(132;636 2450 45807 47979)	Atlas-SNP	.											HAS1,lower_third,carcinoma,0,1	HAS1	61	1	0			c.C1289T						scavenged	.		VAL/ALA	12,4360		0,12,2174	24	25	25		1289	3.2	1	19	dbSNP_126	25	93,8495		0,93,4201	yes	missense	HAS1	NM_001523.2	64	0,105,6375	AA,AG,GG		1.0829,0.2745,0.8102	possibly-damaging	430/579	52217128	105,12855	2186	4294	6480	SO:0001583	missense	3036	exon5			AGCAGCGCCCAAG	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.1289C>T	19.37:g.52217128G>A	ENSP00000222115:p.Ala430Val	5	0	0		5	3	0.6	NM_001523	Q14470|Q9NS49	Missense_Mutation	SNP	ENST00000222115.1	37	CCDS12838.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	g	13.44	2.236984	0.39498	0.002745	0.010829	ENSG00000105509	ENST00000540069;ENST00000222115	T;T	0.59083	0.29;0.29	3.19	3.19	0.36642	.	0.146701	0.44483	U	0.000446	T	0.27278	0.0669	N	0.22421	0.69	0.33217	D	0.554145	B;P;P	0.42757	0.334;0.789;0.789	B;B;B	0.32928	0.04;0.155;0.155	T	0.53085	-0.8488	10	0.66056	D	0.02	-18.9542	7.85	0.29448	0.0:0.0:0.7525:0.2475	rs34682338	429;430;429	G3V1S7;Q92839;Q8IYH3	.;HAS1_HUMAN;.	V	429;430	ENSP00000445021:A429V;ENSP00000222115:A430V	ENSP00000222115:A430V	A	-	2	0	HAS1	56908940	1.000000	0.71417	1.000000	0.80357	0.270000	0.26580	5.291000	0.65667	1.812000	0.52913	0.165000	0.16767	GCG	G|0.995;A|0.005	0.005	strong		0.697	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523		A	52217128	G	A	52217128	3	1	26	1	0	0	0	0	1	0	0	0	6970	1087	38	1	451	1	HAS1	19	52217128	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	653863	52217128	6911855	610	10373											
ZNF578	147660	hgsc.bcm.edu	37	chr19	53015366	53015366	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agtgtggtaaggctcacaatCacttgattgattcatcaatc	12	13	8	8	0	4	2	4	2	0	0	5	2	4	2	0	2	0	2	0	2	3	4	rs376297084		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:53015366C>T	ENST00000421239.2	+	6	1976	c.1732C>T	c.(1732-1734)Cac>Tac	p.H578Y	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	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)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		GGCTCACAATCACTTGATTGA	0.393																																					p.H578Y		Atlas-SNP	.											.	.	.	.	0			c.C1732T						PASS	.	C	TYR/HIS	1,4397		0,1,2198	55	57	56		1732	0.1	0	19		56	5,8591		0,5,4293	no	missense	ZNF578	NM_001099694.1	83	0,6,6491	TT,TC,CC		0.0582,0.0227,0.0462	possibly-damaging	578/591	53015366	6,12988	2199	4298	6497	SO:0001583	missense	147660	exon6			CACAATCACTTGA	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.1732C>T	19.37:g.53015366C>T	ENSP00000459216:p.His578Tyr	72	0	0		48	25	0.520833	NM_001099694	B4DR51|I3L1Y6	Missense_Mutation	SNP	ENST00000421239.2	37	CCDS54310.1	.	.	.	.	.	.	.	.	.	.	-	0.389	-0.924629	0.02377	2.27E-4	5.82E-4	ENSG00000258405	ENST00000553364	.	.	.	0.0465	0.0465	0.14256	.	.	.	.	.	T	0.15825	0.0381	N	0.13098	0.295	0.09310	N	1	B	0.31485	0.325	B	0.20767	0.031	T	0.18777	-1.0326	6	.	.	.	.	.	.	.	.	578	G3V4F6	.	Y	578	.	.	H	+	1	0	ZNF578	57707178	0.033000	0.19621	0.009000	0.14445	0.011000	0.07611	0.000000	0.12993	0.132000	0.18615	0.134000	0.15878	CAC	.	.	weak		0.393	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472		T	53015366	C	T	53015366	3	4	26	1	0	0	0	0	1	0	0	0	18025	826	29	2	1742	2	ZNF578	19	53015366	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	798238	53015366	6113617	611	10374											
LILRB3	11025	hgsc.bcm.edu	37	chr19	54725907	54725907	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cttcatcagaacaaaatggtGatatcccttctgtgagccac	12	11	7	11	0	3	3	2	2	1	1	4	3	4	3	2	1	2	0	2	1	4	3	rs55662384	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:54725907G>C	ENST00000391750.1	-	5	587	c.451C>G	c.(451-453)Cac>Gac	p.H151D	LILRB3_ENST00000245620.9_Missense_Mutation_p.H151D|CTB-83J4.1_ENST00000601161.1_lincRNA|LILRB3_ENST00000407860.2_Missense_Mutation_p.H151D|LILRA6_ENST00000391735.3_Intron|LILRB3_ENST00000424807.1_Missense_Mutation_p.H151D|LILRA6_ENST00000419410.2_Intron|LILRB3_ENST00000469273.1_5'Flank|LILRA6_ENST00000440558.2_Intron|LILRB3_ENST00000346401.6_Missense_Mutation_p.H151D|LILRA6_ENST00000270464.5_Intron			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	151	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)		ACAAAATGGTGATATCCCTTC	0.607													.|||	412	0.0822684	0.2844	0.0346	5008	,	,		11604	0.0		0.005	False		,,,				2504	0.0072				p.H151D		Atlas-SNP	.											.	LILRB3	67	.	0			c.C451G						PASS	.						21	14	17					19																	54725907		2080	3877	5957	SO:0001583	missense	11025	exon4			AATGGTGATATCC	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.451C>G	19.37:g.54725907G>C	ENSP00000375630:p.His151Asp	130	0	0		224	81	0.361607	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	.	.	.	.	.	.	.	.	.	.	g	0.003	-2.570640	0.00133	.	.	ENSG00000204577	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000445347	T;T;T;T;T;T	0.10960	2.82;2.82;2.82;2.82;2.82;5.85	2.87	-4.31	0.03698	Immunoglobulin-like fold (1);	2.010510	0.02119	N	0.055507	T	0.01905	0.0060	N	0.00128	-2.045	0.09310	N	1	B;B;B;B;B	0.06786	0.0;0.0;0.001;0.001;0.0	B;B;B;B;B	0.09377	0.004;0.0;0.003;0.0;0.001	T	0.48570	-0.9024	10	0.02654	T	1	.	8.7737	0.34749	0.1378:0.4079:0.4543:0.0	rs55662384	151;151;151;151;151	B5MCX0;F8WD89;O75022-2;O75022;O75022-3	.;.;.;LIRB3_HUMAN;.	D	151	ENSP00000375630:H151D;ENSP00000412771:H151D;ENSP00000345184:H151D;ENSP00000245620:H151D;ENSP00000384274:H151D;ENSP00000388199:H151D	ENSP00000245620:H151D	H	-	1	0	LILRB3	59417719	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.740000	0.00378	-0.678000	0.05224	-2.793000	0.00115	CAC	G|0.994;C|0.006	0.006	strong		0.607	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864		C	54725907	G	C	54725907	3	2	26	1	0	0	0	0	1	0	0	0	8801	1290	45	4	1487	4	LILRB3	19	54725907	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1710541	54725907	4403076	612	10375											
LILRA6	79168	hgsc.bcm.edu	37	chr19	54745659	54745659	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cttcatcagaacaaaatggtGatatcccttctgtgagccac	12	11	7	11	0	3	3	2	2	1	1	4	3	4	3	2	1	2	0	2	1	4	3	rs200657736		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:54745659G>C	ENST00000396365.2	-	4	490	c.451C>G	c.(451-453)Cac>Gac	p.H151D	LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000391735.3_Missense_Mutation_p.H151D|LILRA6_ENST00000419410.2_Missense_Mutation_p.H151D|LILRA6_ENST00000245621.5_Missense_Mutation_p.H151D|LILRA6_ENST00000440558.2_Missense_Mutation_p.H151D|LILRA6_ENST00000270464.5_Missense_Mutation_p.H151D	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	151					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)		ACAAAATGGTGATATCCCTTC	0.592																																					p.H151D		Atlas-SNP	.											LILRA6,NS,carcinoma,0,2	LILRA6	75	2	0			c.C451G						scavenged	.						23	37	32					19																	54745659		2100	4266	6366	SO:0001583	missense	79168	exon4			AATGGTGATATCC	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.451C>G	19.37:g.54745659G>C	ENSP00000379651:p.His151Asp	675	1	0.00148148		652	89	0.136503	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	g	0	-2.647560	0.00111	.	.	ENSG00000244482	ENST00000440558;ENST00000270464;ENST00000419410;ENST00000391735;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T;T;T	0.10960	2.82;2.82;2.82;4.04;2.82;2.82	2.64	-5.28	0.02755	Immunoglobulin-like fold (1);	2.010510	0.02119	N	0.055507	T	0.01870	0.0059	N	0.00237	-1.79	0.09310	N	1	B;B;B;B;B;B	0.09022	0.002;0.0;0.002;0.0;0.0;0.0	B;B;B;B;B;B	0.08055	0.003;0.0;0.003;0.001;0.002;0.001	T	0.25537	-1.0129	10	0.02654	T	1	.	3.0381	0.06129	0.2388:0.2899:0.373:0.0983	.	151;151;151;151;151;151	C9JFH3;Q6PI73-2;Q6PI73;F8WCY4;D3YTC4;F8W6G6	.;.;LIRA6_HUMAN;.;.;.	D	151	ENSP00000390120:H151D;ENSP00000270464:H151D;ENSP00000411227:H151D;ENSP00000375615:H151D;ENSP00000379651:H151D;ENSP00000245621:H151D	ENSP00000245621:H151D	H	-	1	0	LILRA6	59437471	.	.	0.000000	0.03702	0.020000	0.10135	.	.	-3.099000	0.00245	-1.962000	0.00476	CAC	G|0.999;C|0.001	0.001	weak		0.592	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318		C	54745659	G	C	54745659	3	2	26	1	0	0	0	0	1	0	0	0	8798	1290	45	4	1014	4	LILRA6	19	54745659	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	19752	54745659	4383324	613	10376											
ZNF667	63934	hgsc.bcm.edu	37	chr19	56952615	56952615	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcccacatttactacattcAtagggtttctctgaagaatg	11	15	6	9	0	2	2	1	1	1	1	4	2	3	2	1	1	2	1	1	1	5	7	rs61740673	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:56952615A>G	ENST00000504904.3	-	7	2468	c.1749T>C	c.(1747-1749)taT>taC	p.Y583Y	ZNF667_ENST00000591790.1_3'UTR|ZNF667_ENST00000292069.6_Silent_p.Y583Y|ZNF667_ENST00000342634.3_Silent_p.Y711Y			Q5HYK9	ZN667_HUMAN	zinc finger protein 667	583					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)		TACTACATTCATAGGGTTTCT	0.398													A|||	158	0.0315495	0.0961	0.0159	5008	,	,		20645	0.0		0.0159	False		,,,				2504	0.0041				p.Y583Y		Atlas-SNP	.											ZNF667,NS,NS,-2,1	ZNF667	95	1	0			c.T1749C						PASS	.	A		393,4013	197.7+/-221.8	16,361,1826	120	115	117		1749	-0.7	0.4	19	dbSNP_129	117	96,8504	53.1+/-113.8	0,96,4204	no	coding-synonymous	ZNF667	NM_022103.3		16,457,6030	GG,GA,AA		1.1163,8.9197,3.7598		583/611	56952615	489,12517	2203	4300	6503	SO:0001819	synonymous_variant	63934	exon5			ACATTCATAGGGT		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.1749T>C	19.37:g.56952615A>G		87	0	0		81	44	0.54321	NM_022103	B2RMS6|B9EK36|Q6B093|Q9H807	Silent	SNP	ENST00000504904.3	37	CCDS12944.1																																																																																			A|0.965;G|0.035	0.035	strong		0.398	ZNF667-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458394.1	NM_022103		G	56952615	A	G	56952615	2	3	26	1	0	0	0	0	0	0	0	1	18089	224	8	3		3	ZNF667	19	56952615	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	2206956	56952615	2176368	614	10377											
USP29	57663	hgsc.bcm.edu	37	chr19	57642413	57642413	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttggggcactgggttctgaCaacccaggaaacaaaaacat	14	7	10	10	0	1	1	0	1	1	0	1	2	1	2	1	4	3	2	1	4	4	2	rs35394887	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:57642413C>A	ENST00000254181.4	+	4	2824	c.2370C>A	c.(2368-2370)gaC>gaA	p.D790E	USP29_ENST00000598197.1_Missense_Mutation_p.D790E	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	790	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)		TGGGTTCTGACAACCCAGGAA	0.468													C|||	23	0.00459265	0.0	0.0072	5008	,	,		20144	0.0		0.006	False		,,,				2504	0.0123				p.D790E		Atlas-SNP	.											.	USP29	186	.	0			c.C2370A						PASS	.	C	GLU/ASP	5,4401	9.9+/-24.2	0,5,2198	50	43	46		2370	-1.5	0	19	dbSNP_126	46	62,8538	37.8+/-93.5	0,62,4238	yes	missense	USP29	NM_020903.2	45	0,67,6436	AA,AC,CC		0.7209,0.1135,0.5151	probably-damaging	790/923	57642413	67,12939	2203	4300	6503	SO:0001583	missense	57663	exon4			TTCTGACAACCCA		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.2370C>A	19.37:g.57642413C>A	ENSP00000254181:p.Asp790Glu	105	0	0		128	60	0.46875	NM_020903		Missense_Mutation	SNP	ENST00000254181.4	37	CCDS33124.1	7	0.003205128205128205	0	0.0	3	0.008287292817679558	0	0.0	4	0.005277044854881266	C	10.17	1.276210	0.23307	0.001135	0.007209	ENSG00000131864	ENST00000254181	T	0.72942	-0.7	2.05	-1.45	0.08828	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	.	.	.	.	T	0.57110	0.2031	L	0.54323	1.7	0.09310	N	1	P	0.47545	0.897	P	0.45946	0.498	T	0.55496	-0.8132	9	0.72032	D	0.01	.	5.8011	0.18414	0.0:0.5297:0.0:0.4703	rs35394887	790	Q9HBJ7	UBP29_HUMAN	E	790	ENSP00000254181:D790E	ENSP00000254181:D790E	D	+	3	2	USP29	62334225	0.862000	0.29867	0.001000	0.08648	0.010000	0.07245	-0.726000	0.04936	-0.484000	0.06763	-0.483000	0.04790	GAC	C|0.996;A|0.004	0.004	strong		0.468	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1			A	57642413	C	A	57642413	3	1	26	1	0	0	0	0	1	0	0	0	17074	477	17	4	2372	4	USP29	19	57642413	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	689798	57642413	1486570	615	10378											
ZNF211	10520	hgsc.bcm.edu	37	chr19	58153465	58153465	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacacgggaaaaaggccttaTcagtgcagtcaatgtgggaa	14	7	12	8	1	2	0	2	0	0	0	2	2	2	2	1	3	1	1	1	3	5	1	rs146505315	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:58153465T>A	ENST00000347302.3	+	3	1790	c.1611T>A	c.(1609-1611)taT>taA	p.Y537*	ZNF211_ENST00000420680.1_Nonsense_Mutation_p.Y541*|ZNF211_ENST00000254182.7_Nonsense_Mutation_p.Y528*|ZNF211_ENST00000391703.3_Nonsense_Mutation_p.Y476*|ZNF211_ENST00000544273.1_Nonsense_Mutation_p.Y549*|ZNF211_ENST00000299871.5_Nonsense_Mutation_p.Y602*|ZNF211_ENST00000240731.4_Nonsense_Mutation_p.Y550*|ZNF211_ENST00000541801.1_Nonsense_Mutation_p.Y528*	NM_198855.2	NP_942152.1	Q13398	ZN211_HUMAN	zinc finger protein 211	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)			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)		AAAGGCCTTATCAGTGCAGTC	0.453													T|||	6	0.00119808	0.0008	0.0014	5008	,	,		21540	0.0		0.004	False		,,,				2504	0.0				p.Y602X		Atlas-SNP	.											.	ZNF211	78	.	0			c.T1806A						PASS	.	T	stop/TYR,stop/TYR	10,4396	16.8+/-37.8	0,10,2193	105	102	103		1650,1611	-4	0	19	dbSNP_134	103	49,8551	31.2+/-83.2	0,49,4251	yes	stop-gained,stop-gained	ZNF211	NM_006385.3,NM_198855.2	,	0,59,6444	AA,AT,TT		0.5698,0.227,0.4536	,	550/578,537/565	58153465	59,12947	2203	4300	6503	SO:0001587	stop_gained	10520	exon5			GCCTTATCAGTGC	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.1611T>A	19.37:g.58153465T>A	ENSP00000339562:p.Tyr537*	43	0	0		53	20	0.377358	NM_001265597	B4DH10|B4DLC9|B4E3C9|B9ZVS7|B9ZVW1|F8WDV2|Q05BQ7|Q2TAL7|Q59EG4|Q59G36|Q5EBL6	Nonsense_Mutation	SNP	ENST00000347302.3	37	CCDS12957.1	5|5	0.0022893772893772895|0.0022893772893772895	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	4|4	0.005277044854881266|0.005277044854881266	t|t	37|37	5.990100|5.990100	0.97179|0.97179	0.00227|0.00227	0.005698|0.005698	ENSG00000121417|ENSG00000121417	ENST00000407202|ENST00000420680;ENST00000347302;ENST00000254182;ENST00000391703;ENST00000541801;ENST00000299871;ENST00000544273;ENST00000240731	.|.	.|.	.|.	2.37|2.37	-4.02|-4.02	0.04034|0.04034	.|.	.|.	.|.	.|.	.|.	T|.	0.10809|.	0.0264|.	.|.	.|.	.|.	0.41247|0.41247	D|D	0.986684|0.986684	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.41484|.	-0.9506|.	4|.	.|0.02654	.|T	.|1	.|.	1.7708|1.7708	0.03011|0.03011	0.1459:0.3803:0.1482:0.3256|0.1459:0.3803:0.1482:0.3256	.|.	.|.	.|.	.|.	T|X	541|541;537;528;476;528;602;549;550	.|.	.|ENSP00000240731:Y550X	S|Y	+|+	1|3	0|2	ZNF211|ZNF211	62845277|62845277	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.940000|0.940000	0.58332|0.58332	-0.503000|-0.503000	0.06383|0.06383	-1.154000|-1.154000	0.02825|0.02825	0.477000|0.477000	0.44152|0.44152	TCA|TAT	T|0.996;A|0.004	0.004	strong		0.453	ZNF211-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397502.1			A	58153465	T	A	58153465	4	1	26	1	0	0	0	0	0	1	0	0	17782	1442	50	5	1664	5	ZNF211	19	58153465	Nonsense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	511052	58153465	975518	616	10379											
ZNF418	147686	hgsc.bcm.edu	37	chr19	58437623	58437623	+	Silent	SNP	A	A	G																															cactcataaggcctttctccAgtgtgtactctcctgtgttc																										TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:58437623A>G	ENST00000396147.1	-	4	2217	c.1926T>C	c.(1924-1926)acT>acC	p.T642T	ZNF418_ENST00000595830.1_Silent_p.T642T|ZNF418_ENST00000599852.1_Silent_p.T557T|ZNF418_ENST00000425570.3_Silent_p.T663T|ZNF418_ENST00000600989.1_Intron|ZNF418_ENST00000599086.1_5'Flank	NM_133460.1	NP_597717.1	Q8TF45	ZN418_HUMAN	zinc finger protein 418	642					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(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	31		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;0.0158)		GCCTTTCTCCAGTGTGTACTC	0.443																																					p.T642T		Atlas-SNP	.											.	ZNF418	76	.	0			c.T1926C						PASS	.						119	121	120					19																	58437623		2202	4300	6502	SO:0001819	synonymous_variant	147686	exon4			TTCTCCAGTGTGT	AB075836, AY695825	CCDS42642.1	19q13.43	2013-01-08				ENSG00000196724		"Zinc fingers, C2H2-type", "-"	20647	protein-coding gene	gene with protein product						11853319	Standard	NM_133460		Approved	KIAA1956, FLJ31551	uc002qqs.1	Q8TF45		ENST00000396147.1:c.1926T>C	19.37:g.58437623A>G		109	0	0		89	16	0.179775	NM_133460	Q2M1S2|Q670L5|Q96N18	Silent	SNP	ENST00000396147.1	37	CCDS42642.1																																																																																			.	.	none		0.443	ZNF418-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466693.1	NM_133460		G	58437623	A	G	58437623	2	3	26	1	0	0	0	0	0	0	0	1	17910	175	7	3		3	ZNF418	19	58437623	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	284158	58437623	691360	617	10380	129	2									
ZNF418	147686	hgsc.bcm.edu	37	chr19	58437629	58437629	+	Silent	SNP	T	T	A																															taaggcctttctccagtgtgTactctcctgtgttcagtaag																								rs147202003	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:58437629T>A	ENST00000396147.1	-	4	2211	c.1920A>T	c.(1918-1920)gtA>gtT	p.V640V	ZNF418_ENST00000595830.1_Silent_p.V640V|ZNF418_ENST00000599852.1_Silent_p.V555V|ZNF418_ENST00000425570.3_Silent_p.V661V|ZNF418_ENST00000600989.1_Intron|ZNF418_ENST00000599086.1_5'Flank	NM_133460.1	NP_597717.1	Q8TF45	ZN418_HUMAN	zinc finger protein 418	640					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(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	31		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;0.0158)		CTCCAGTGTGTACTCTCCTGT	0.438																																					p.V640V		Atlas-SNP	.											.	ZNF418	76	.	0			c.A1920T						PASS	.	A		11,4393		0,11,2191	120	122	121		1920	-3.1	0	19	dbSNP_134	121	120,8480		1,118,4181	no	coding-synonymous	ZNF418	NM_133460.1		1,129,6372	AA,AT,TT		1.3953,0.2498,1.0074		640/677	58437629	131,12873	2202	4300	6502	SO:0001819	synonymous_variant	147686	exon4			AGTGTGTACTCTC	AB075836, AY695825	CCDS42642.1	19q13.43	2013-01-08				ENSG00000196724		"Zinc fingers, C2H2-type", "-"	20647	protein-coding gene	gene with protein product						11853319	Standard	NM_133460		Approved	KIAA1956, FLJ31551	uc002qqs.1	Q8TF45		ENST00000396147.1:c.1920A>T	19.37:g.58437629T>A		114	0	0		88	13	0.147727	NM_133460	Q2M1S2|Q670L5|Q96N18	Silent	SNP	ENST00000396147.1	37	CCDS42642.1																																																																																			T|0.993;A|0.007	0.007	strong		0.438	ZNF418-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466693.1	NM_133460		A	58437629	T	A	58437629	2	1	26	1	0	0	0	0	0	0	0	1	17910	1625	57	5		5	ZNF418	19	58437629	Silent	SNP	T	TCGA-G8-6907-01A-11D-2210-10	6	58437629	691354	618	10381	129	2									
ZNF418	147686	hgsc.bcm.edu	37	chr19	58437791	58437791	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattcataaggcctttctccAgtgtgaactctcctgtgttc	7	15	7	12	0	3	1	1	1	2	0	6	1	3	1	3	1	1	1	3	1	2	4			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:58437791A>G	ENST00000396147.1	-	4	2049	c.1758T>C	c.(1756-1758)acT>acC	p.T586T	ZNF418_ENST00000595830.1_Silent_p.T586T|ZNF418_ENST00000599852.1_Silent_p.T501T|ZNF418_ENST00000425570.3_Silent_p.T607T|ZNF418_ENST00000600989.1_Intron|ZNF418_ENST00000599086.1_5'Flank	NM_133460.1	NP_597717.1	Q8TF45	ZN418_HUMAN	zinc finger protein 418	586					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(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	31		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;0.0158)		GCCTTTCTCCAGTGTGAACTC	0.438																																					p.T586T		Atlas-SNP	.											.	ZNF418	76	.	0			c.T1758C						PASS	.						78	81	80					19																	58437791		2202	4300	6502	SO:0001819	synonymous_variant	147686	exon4			TTCTCCAGTGTGA	AB075836, AY695825	CCDS42642.1	19q13.43	2013-01-08				ENSG00000196724		"Zinc fingers, C2H2-type", "-"	20647	protein-coding gene	gene with protein product						11853319	Standard	NM_133460		Approved	KIAA1956, FLJ31551	uc002qqs.1	Q8TF45		ENST00000396147.1:c.1758T>C	19.37:g.58437791A>G		93	0	0		85	20	0.235294	NM_133460	Q2M1S2|Q670L5|Q96N18	Silent	SNP	ENST00000396147.1	37	CCDS42642.1																																																																																			.	.	none		0.438	ZNF418-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466693.1	NM_133460		G	58437791	A	G	58437791	2	3	26	1	0	0	0	0	0	0	0	1	17910	175	7	3		3	ZNF418	19	58437791	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	162	58437791	691192	619	10382											
SLC27A5	10998	hgsc.bcm.edu	37	chr19	59012675	59012675	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggaatgttacacaagtacCgcaggagctcgcccacatac	12	6	11	12	2	0	0	0	0	0	0	1	2	0	2	2	3	4	4	2	3	5	3	rs142672241	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:59012675C>T	ENST00000263093.2	-	4	1269	c.1160G>A	c.(1159-1161)cGg>cAg	p.R387Q	SLC27A5_ENST00000594786.1_5'Flank|SLC27A5_ENST00000599700.1_5'Flank|SLC27A5_ENST00000601355.1_Missense_Mutation_p.R303Q	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	387					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)		ACACAAGTACCGCAGGAGCTC	0.527													C|||	5	0.000998403	0.0	0.0029	5008	,	,		16011	0.0		0.003	False		,,,				2504	0.0				p.R387Q		Atlas-SNP	.											SLC27A5,NS,carcinoma,0,1	SLC27A5	58	1	0			c.G1160A						scavenged	.	C	GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	128	131	130		1160	3.8	1	19	dbSNP_134	130	25,8575	18.5+/-59.3	0,25,4275	yes	missense	SLC27A5	NM_012254.2	43	0,27,6476	TT,TC,CC		0.2907,0.0454,0.2076	probably-damaging	387/691	59012675	27,12979	2203	4300	6503	SO:0001583	missense	10998	exon4			AAGTACCGCAGGA	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.1160G>A	19.37:g.59012675C>T	ENSP00000263093:p.Arg387Gln	37	0	0		31	2	0.0645161	NM_012254	B3KVP6|B4DPQ1	Missense_Mutation	SNP	ENST00000263093.2	37	CCDS12983.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	25.5	4.648722	0.87958	4.54E-4	0.002907	ENSG00000083807	ENST00000263093	T	0.44482	0.92	4.9	3.85	0.44370	AMP-dependent synthetase/ligase (1);	0.135756	0.49305	N	0.000150	T	0.58119	0.2100	M	0.91038	3.17	0.35105	D	0.765588	D	0.76494	0.999	P	0.62184	0.899	T	0.76852	-0.2806	10	0.87932	D	0	-32.5211	9.865	0.41138	0.0:0.9026:0.0:0.0974	.	387	Q9Y2P5	S27A5_HUMAN	Q	387	ENSP00000263093:R387Q	ENSP00000263093:R387Q	R	-	2	0	SLC27A5	63704487	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	4.953000	0.63624	1.188000	0.43014	0.563000	0.77884	CGG	C|0.997;T|0.003	0.003	strong		0.527	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254		T	59012675	C	T	59012675	3	4	26	1	0	0	0	0	1	0	0	0	14544	652	23	1	940	1	SLC27A5	19	59012675	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	574884	59012675	116308	620	10383											
ZCCHC3	85364	hgsc.bcm.edu	37	chr20	279185	279185	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acttgccaggggccttcttcCtgggggccgagaggggctac	5	8	16	12	1	1	1	0	0	1	1	2	2	2	1	4	6	2	1	4	6	1	4	rs45569040	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:279185C>T	ENST00000382352.3	+	1	1449	c.958C>T	c.(958-960)Ctg>Ttg	p.L320L		NM_033089.6	NP_149080	Q9NUD5	ZCHC3_HUMAN	zinc finger, CCHC domain containing 3	320							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)			GGCCTTCTTCCTGGGGGCCGA	0.632													C|||	20	0.00399361	0.0	0.0029	5008	,	,		16576	0.0		0.0149	False		,,,				2504	0.0031				p.L320L		Atlas-SNP	.											.	ZCCHC3	20	.	0			c.C958T						PASS	.	C		13,3825		0,13,1906	40	47	45		958	2.2	1	20	dbSNP_127	45	144,8088		4,136,3976	no	coding-synonymous	ZCCHC3	NM_033089.6		4,149,5882	TT,TC,CC		1.7493,0.3387,1.3007		320/405	279185	157,11913	1919	4116	6035	SO:0001819	synonymous_variant	85364	exon1			TTCTTCCTGGGGG	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.958C>T	20.37:g.279185C>T		133	0	0		163	163	1	NM_033089	Q3B7J3|Q6NT79	Silent	SNP	ENST00000382352.3	37	CCDS42844.1																																																																																			C|0.995;T|0.005	0.005	strong		0.632	ZCCHC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077447.1			T	279185	C	T	279185	2	4	26	1	0	0	0	0	0	0	0	1	17604	680	24	2		2	ZCCHC3	20	279185	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10		279185	62746335	621	10384											
IDH3B	3420	hgsc.bcm.edu	37	chr20	2641471	2641471	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gttggcaaataagtccaactTacgcctgagggtgggcaggg	10	8	15	8	1	0	1	0	1	0	0	1	1	1	1	2	4	2	3	2	4	4	3			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:2641471T>C	ENST00000380843.4	-	6	433	c.403A>G	c.(403-405)Aag>Gag	p.K135E	IDH3B_ENST00000488299.1_5'UTR|IDH3B_ENST00000380851.5_Missense_Mutation_p.K135E	NM_006899.3	NP_008830.2	O43837	IDH3B_HUMAN	isocitrate dehydrogenase 3 (NAD+) beta	135					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|isocitrate metabolic process (GO:0006102)|NADH metabolic process (GO:0006734)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|isocitrate dehydrogenase (NAD+) activity (GO:0004449)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)			breast(1)|endometrium(3)|kidney(2)|lung(7)|prostate(1)	14						AAGTCCAACTTACGCCTGAGG	0.537																																					p.K135E		Atlas-SNP	.											.	IDH3B	25	.	0			c.A403G						PASS	.						118	110	113					20																	2641471		2203	4300	6503	SO:0001583	missense	3420	exon6			CCAACTTACGCCT		CCDS13031.1, CCDS13032.1, CCDS74696.1	20p13	2013-02-14			ENSG00000101365	ENSG00000101365	1.1.1.41		5385	protein-coding gene	gene with protein product		604526				10575215	Standard	NM_006899		Approved	RP46	uc002wgp.4	O43837	OTTHUMG00000031699	ENST00000380843.4:c.403A>G	20.37:g.2641471T>C	ENSP00000370223:p.Lys135Glu	75	0	0		78	35	0.448718	NM_006899	B2RDR1|D3DVX2|D3DVX3|O95106|Q5JXS8|Q9NQ06|Q9NQ07|Q9NUZ0|Q9UEX0|Q9UG99	Missense_Mutation	SNP	ENST00000380843.4	37	CCDS13032.1	.	.	.	.	.	.	.	.	.	.	T	8.127	0.782172	0.16189	.	.	ENSG00000101365	ENST00000380851;ENST00000380843;ENST00000341825	T;T	0.66638	-0.22;-0.22	5.28	5.28	0.74379	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	T	0.35799	0.0944	N	0.01809	-0.71	0.80722	D	1	B;B	0.10296	0.002;0.003	B;B	0.15052	0.009;0.012	T	0.42050	-0.9474	10	0.02654	T	1	-21.4299	13.2215	0.59890	0.0:0.0:0.0:1.0	.	135;135	O43837-2;O43837	.;IDH3B_HUMAN	E	135	ENSP00000370232:K135E;ENSP00000370223:K135E	ENSP00000343215:K135E	K	-	1	0	IDH3B	2589471	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.457000	0.80775	2.217000	0.71921	0.533000	0.62120	AAG	.	.	none		0.537	IDH3B-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077613.1			C	2641471	T	C	2641471	3	2	26	1	0	0	0	0	1	0	0	0	7506	1763	61	3	942	3	IDH3B	20	2641471	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	2362286	2641471	60384049	622	10385											
PLCB1	23236	hgsc.bcm.edu	37	chr20	8703060	8703060	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgactgtaaaaaatcttcaAtggatgaggtgggtacttag	14	12	11	4	0	2	2	1	2	1	0	2	3	2	3	0	3	1	2	0	3	6	4	rs138851178	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:8703060A>T	ENST00000338037.6	+	15	1600	c.1573A>T	c.(1573-1575)Atg>Ttg	p.M525L	PLCB1_ENST00000378641.3_Missense_Mutation_p.M525L|PLCB1_ENST00000494924.1_3'UTR|PLCB1_ENST00000378637.2_Missense_Mutation_p.M525L	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	525					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						AAAATCTTCAATGGATGAGGT	0.448																																					p.E525X		Atlas-SNP	.											.	PLCB1	394	.	0			c.G1573T						PASS	.						201	160	174					20																	8703060		2203	4300	6503	SO:0001583	missense	23236	exon15			TCTTCAATGGATG	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.1573A>T	20.37:g.8703060A>T	ENSP00000338185:p.Met525Leu	97	0	0		76	33	0.434211	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Nonsense_Mutation	SNP	ENST00000338037.6	37	CCDS13102.1	.	.	.	.	.	.	.	.	.	.	A	16.68	3.190382	0.58017	.	.	ENSG00000182621	ENST00000378641;ENST00000338037;ENST00000378637;ENST00000441163;ENST00000535719	T;T;T	0.49432	0.78;0.78;0.78	5.96	5.96	0.96718	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (1);	0.157283	0.37906	U	0.001882	T	0.42245	0.1194	L	0.44542	1.39	0.52501	D	0.999952	B;B	0.13145	0.0;0.007	B;B	0.16289	0.001;0.015	T	0.19516	-1.0303	10	0.28530	T	0.3	.	15.6296	0.76893	1.0:0.0:0.0:0.0	.	525;525	Q9NQ66;Q9NQ66-2	PLCB1_HUMAN;.	L	525;525;525;445;445	ENSP00000367908:M525L;ENSP00000338185:M525L;ENSP00000367904:M525L	ENSP00000338185:M525L	M	+	1	0	PLCB1	8651060	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	7.524000	0.81866	2.285000	0.76669	0.533000	0.62120	ATG	A|1.000;G|0.000	.	alt		0.448	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3			T	8703060	A	T	8703060	3	4	26	1	0	0	0	0	1	0	0	0	12036	101	4	5	1631	5	PLCB1	20	8703060	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	6061589	8703060	54322460	623	10386											
JAG1	182	hgsc.bcm.edu	37	chr20	10625624	10625624	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgggcaggcagctactgtttCgggctataaaagaagagcag	12	8	14	7	1	0	2	0	0	0	2	1	2	0	2	0	3	3	6	0	3	5	4	rs147809756	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:10625624C>T	ENST00000254958.5	-	18	2746	c.2231G>A	c.(2230-2232)cGa>cAa	p.R744Q	JAG1_ENST00000423891.2_Missense_Mutation_p.R585Q|JAG1_ENST00000488480.1_RNA	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	744	EGF-like 14. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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						GCTACTGTTTCGGGCTATAAA	0.567									Alagille Syndrome				C|||	5	0.000998403	0.0	0.0029	5008	,	,		16903	0.0		0.002	False		,,,				2504	0.001				p.R744Q		Atlas-SNP	.											JAG1_ENST00000254958,NS,malignant_melanoma,-1,6	JAG1	213	6	0			c.G2231A						scavenged	.	C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	149	156	154		2231	6.1	1	20	dbSNP_134	154	9,8591	7.1+/-27.0	0,9,4291	yes	missense	JAG1	NM_000214.2	43	0,10,6493	TT,TC,CC		0.1047,0.0227,0.0769	possibly-damaging	744/1219	10625624	10,12996	2203	4300	6503	SO:0001583	missense	182	exon18	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	CTGTTTCGGGCTA	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.2231G>A	20.37:g.10625624C>T	ENSP00000254958:p.Arg744Gln	77	1	0.012987		116	63	0.543103	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Missense_Mutation	SNP	ENST00000254958.5	37	CCDS13112.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	18.43	3.623272	0.66901	2.27E-4	0.001047	ENSG00000101384	ENST00000254958;ENST00000423891	D;D	0.87256	-2.23;-2.23	6.07	6.07	0.98685	Epidermal growth factor-like, type 3 (1);	0.047287	0.85682	D	0.000000	D	0.83294	0.5223	L	0.49778	1.585	0.58432	D	0.999995	P	0.36768	0.569	B	0.26614	0.071	T	0.80915	-0.1169	10	0.29301	T	0.29	.	20.6439	0.99570	0.0:1.0:0.0:0.0	.	744	P78504	JAG1_HUMAN	Q	744;585	ENSP00000254958:R744Q;ENSP00000389519:R585Q	ENSP00000254958:R744Q	R	-	2	0	JAG1	10573624	0.994000	0.37717	0.999000	0.59377	0.872000	0.50106	4.742000	0.62103	2.884000	0.98904	0.655000	0.94253	CGA	C|0.999;T|0.001	0.001	strong		0.567	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214		T	10625624	C	T	10625624	3	4	26	1	0	0	0	0	1	0	0	0	7943	884	31	1	1461	1	JAG1	20	10625624	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1922564	10625624	52399896	624	10387											
RIN2	54453	hgsc.bcm.edu	37	chr20	19915770	19915770	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acacaattgcctcggagatcGgagaactgaaacaggagatg	15	6	12	8	2	0	4	0	1	0	3	2	7	0	4	1	3	3	0	1	3	3	1	rs78648341	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:19915770G>A	ENST00000255006.6	+	3	381	c.232G>A	c.(232-234)Gga>Aga	p.G78R	RIN2_ENST00000440354.2_Missense_Mutation_p.G29R|RIN2_ENST00000484638.1_3'UTR	NM_001242581.1|NM_018993.3	NP_001229510.1|NP_061866.1	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	29					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						CTCGGAGATCGGAGAACTGAA	0.532													G|||	37	0.00738818	0.0008	0.0101	5008	,	,		17562	0.0		0.0278	False		,,,				2504	0.001				p.G78R		Atlas-SNP	.											.	RIN2	126	.	0			c.G232A						PASS	.	G	ARG/GLY,ARG/GLY	4,3954		0,4,1975	70	68	69		232,85	5.7	1	20	dbSNP_131	69	99,8211		1,97,4057	yes	missense,missense	RIN2	NM_001242581.1,NM_018993.3	125,125	1,101,6032	AA,AG,GG		1.1913,0.1011,0.8396	probably-damaging,probably-damaging	78/945,29/896	19915770	103,12165	1979	4155	6134	SO:0001583	missense	54453	exon3			GAGATCGGAGAAC	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.232G>A	20.37:g.19915770G>A	ENSP00000255006:p.Gly78Arg	83	0	0		67	34	0.507463	NM_001242581	Q00425|Q5TFT8|Q9BQL3|Q9H071	Missense_Mutation	SNP	ENST00000255006.6	37	CCDS56182.1	25	0.011446886446886446	0	0.0	5	0.013812154696132596	0	0.0	20	0.026385224274406333	G	27.9	4.876983	0.91664	0.001011	0.011913	ENSG00000132669	ENST00000255006;ENST00000440354	T;T	0.06933	3.24;3.24	5.71	5.71	0.89125	.	0.059318	0.64402	D	0.000003	T	0.08846	0.0219	L	0.47716	1.5	0.33565	D	0.597839	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.00834	-1.1547	9	.	.	.	-14.9319	18.6285	0.91350	0.0:0.0:1.0:0.0	.	29;29	E7EPJ1;Q8WYP3	.;RIN2_HUMAN	R	78;29	ENSP00000255006:G78R;ENSP00000391239:G29R	.	G	+	1	0	RIN2	19863770	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.995000	0.76257	2.703000	0.92315	0.655000	0.94253	GGA	G|0.987;A|0.013	0.013	strong		0.532	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1			A	19915770	G	A	19915770	3	1	26	1	0	0	0	0	1	0	0	0	13387	1117	39	1	91	1	RIN2	20	19915770	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	9290146	19915770	43109750	625	10388											
C20orf26	26074	hgsc.bcm.edu	37	chr20	20055848	20055848	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accagaaccgtgtataaggcAgtgccagagctgcacttcat	12	8	10	11	1	1	2	1	0	0	2	1	2	1	2	3	1	4	4	3	1	3	3	rs367870948		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:20055848A>G	ENST00000245957.5	+	5	463	c.387A>G	c.(385-387)gcA>gcG	p.A129A	C20orf26_ENST00000451767.2_Silent_p.A129A|C20orf26_ENST00000389656.3_5'UTR|C20orf26_ENST00000377306.1_Silent_p.A129A|C20orf26_ENST00000377309.2_5'UTR	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		129										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)		TGTATAAGGCAGTGCCAGAGC	0.502																																					p.A129A		Atlas-SNP	.											.	C20orf26	188	.	0			c.A387G						PASS	.	A	,	0,4406		0,0,2203	173	147	156		387,387	-11.4	0.4	20		156	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	C20orf26	NM_001167816.1,NM_015585.3	,	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	,	129/471,129/1238	20055848	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	26074	exon5			TAAGGCAGTGCCA																												ENST00000245957.5:c.387A>G	20.37:g.20055848A>G		137	0	0		157	78	0.496815	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Silent	SNP	ENST00000245957.5	37	CCDS33447.1																																																																																			.	.	weak		0.502	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3			G	20055848	A	G	20055848	2	3	26	1	0	0	0	0	0	0	0	1	2108	175	7	3		3	C20orf26	20	20055848	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	140078	20055848	42969672	626	10389											
C20orf70	140683	hgsc.bcm.edu	37	chr20	31761919	31761919	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actccctcatcctggatgtcAaagctgaaccgatcgatgat	11	10	8	12	2	2	2	2	2	0	0	5	5	4	3	3	1	2	1	3	1	2	0	rs17304572	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:31761919A>G	ENST00000253362.2	+	4	483	c.337A>G	c.(337-339)Aaa>Gaa	p.K113E	BPIFA2_ENST00000354932.5_Missense_Mutation_p.K113E			Q96DR5	BPIA2_HUMAN	BPI fold containing family A, member 2	113			K -> E (in dbSNP:rs17304572).			extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)										CCTGGATGTCAAAGCTGAACC	0.507													A|||	36	0.0071885	0.0008	0.0447	5008	,	,		20651	0.0		0.003	False		,,,				2504	0.001				p.K113E		Atlas-SNP	.											.	.	.	.	0			c.A337G						PASS	.	A	GLU/LYS	9,4397	15.5+/-35.6	0,9,2194	190	130	150		337	0.5	0	20	dbSNP_123	150	65,8535	39.3+/-95.6	0,65,4235	yes	missense	BPIFA2	NM_080574.2	56	0,74,6429	GG,GA,AA		0.7558,0.2043,0.569	possibly-damaging	113/250	31761919	74,12932	2203	4300	6503	SO:0001583	missense	140683	exon4			GATGTCAAAGCTG	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.337A>G	20.37:g.31761919A>G	ENSP00000253362:p.Lys113Glu	118	0	0		111	62	0.558559	NM_080574	Q9BQQ0	Missense_Mutation	SNP	ENST00000253362.2	37	CCDS13214.1	15	0.006868131868131868	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	4	0.005277044854881266	A	14.94	2.685424	0.47991	0.002043	0.007558	ENSG00000131050	ENST00000253362;ENST00000354932	T;T	0.05580	3.42;3.42	4.11	0.538	0.17150	.	0.626240	0.15043	N	0.283766	T	0.02767	0.0083	L	0.50919	1.6	0.09310	N	1	P	0.41624	0.757	B	0.43728	0.429	T	0.30001	-0.9993	10	0.15952	T	0.53	-20.1787	3.5768	0.07937	0.5707:0.2098:0.2195:0.0	rs17304572;rs52835642;rs56630818;rs17304572	113	Q96DR5	BPIA2_HUMAN	E	113	ENSP00000253362:K113E;ENSP00000347012:K113E	ENSP00000253362:K113E	K	+	1	0	BPIFA2	31225580	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	0.427000	0.21379	0.060000	0.16281	0.459000	0.35465	AAA	A|0.994;G|0.006	0.006	strong		0.507	BPIFA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257117.1	NM_080574		G	31761919	A	G	31761919	3	3	26	1	0	0	0	0	1	0	0	0	2118	131	5	3	347	3	C20orf70	20	31761919	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	11706071	31761919	31263601	627	10390											
SNTA1	6640	hgsc.bcm.edu	37	chr20	32026766	32026766	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccccacaaaaagggcctctGtctggtcagctgccaatccc	9	7	8	17	0	3	0	1	0	2	0	4	0	4	0	5	2	2	1	5	2	3	0			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:32026766G>A	ENST00000217381.2	-	2	648	c.377C>T	c.(376-378)aCa>aTa	p.T126I		NM_003098.2	NP_003089.1	Q13424	SNTA1_HUMAN	syntrophin, alpha 1	126	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						AAGGGCCTCTGTCTGGTCAGC	0.542																																					p.T126I		Atlas-SNP	.											.	SNTA1	35	.	0			c.C377T						PASS	.						127	124	125					20																	32026766		2203	4300	6503	SO:0001583	missense	6640	exon2			GCCTCTGTCTGGT	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.377C>T	20.37:g.32026766G>A	ENSP00000217381:p.Thr126Ile	96	0	0		98	46	0.469388	NM_003098	A8K7H9|B4DX40|E1P5N1|Q16438	Missense_Mutation	SNP	ENST00000217381.2	37	CCDS13220.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.967218	0.74131	.	.	ENSG00000101400	ENST00000217381	T	0.27256	1.68	5.03	5.03	0.67393	PDZ/DHR/GLGF (4);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	T	0.55114	0.1900	M	0.80028	2.48	0.58432	D	0.999999	D;P	0.89917	1.0;0.918	D;D	0.81914	0.995;0.961	T	0.60757	-0.7200	10	0.87932	D	0	-14.1481	18.1836	0.89786	0.0:0.0:1.0:0.0	.	126;126	B4DX40;Q13424	.;SNTA1_HUMAN	I	126	ENSP00000217381:T126I	ENSP00000217381:T126I	T	-	2	0	SNTA1	31490427	1.000000	0.71417	0.987000	0.45799	0.833000	0.47200	6.092000	0.71414	2.614000	0.88457	0.561000	0.74099	ACA	.	.	none		0.542	SNTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078704.2	NM_003098		A	32026766	G	A	32026766	3	1	26	1	0	0	0	0	1	0	0	0	14886	1377	48	2	1168	2	SNTA1	20	32026766	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	264847	32026766	30998754	628	10391											
CBFA2T2	9139	hgsc.bcm.edu	37	chr20	32210968	32210968	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgctgcactgcgctcgggcGgccaagcagaccccatccca	7	5	11	18	3	0	1	0	0	0	1	2	1	1	1	4	2	4	4	4	2	1	0	rs368919989		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:32210968G>A	ENST00000346541.3	+	6	1122	c.585G>A	c.(583-585)gcG>gcA	p.A195A	CBFA2T2_ENST00000491618.1_3'UTR|CBFA2T2_ENST00000342704.6_Silent_p.A186A|CBFA2T2_ENST00000397800.1_Silent_p.A166A|CBFA2T2_ENST00000344201.3_Silent_p.A166A|CBFA2T2_ENST00000359606.3_Silent_p.A205A|CBFA2T2_ENST00000492345.1_Silent_p.A166A|CBFA2T2_ENST00000375279.2_Silent_p.A195A|CBFA2T2_ENST00000397798.2_Silent_p.A166A	NM_005093.3	NP_005084.1	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 2	195	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						GCGCTCGGGCGGCCAAGCAGA	0.582													G|||	1	0.000199681	0.0008	0.0	5008	,	,		5728	0.0		0.0	False		,,,				2504	0.0				p.A195A	Esophageal Squamous(174;142 1955 14837 21276 28041)	Atlas-SNP	.											.	CBFA2T2	93	.	0			c.G585A						PASS	.						83	70	75					20																	32210968		2203	4300	6503	SO:0001819	synonymous_variant	9139	exon6			TCGGGCGGCCAAG	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.585G>A	20.37:g.32210968G>A		111	0	0		139	67	0.482014	NM_005093	B2RAE6|F8W6D7|Q5TGE4|Q5TGE5|Q5TGE6|Q5TGE7|Q8IWF3|Q96B06|Q96L00|Q9H436|Q9UJP8|Q9UJP9|Q9UP24	Silent	SNP	ENST00000346541.3	37	CCDS13221.1																																																																																			.	.	weak		0.582	CBFA2T2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078708.2	NM_001032999		A	32210968	G	A	32210968	2	1	26	1	0	0	0	0	0	0	0	1	2699	1103	39	1		1	CBFA2T2	20	32210968	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	184202	32210968	30814552	629	10392											
ZNF341	84905	hgsc.bcm.edu	37	chr20	32376748	32376748	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagagacacatgttgatccaCgagcccttcaagaaatacaa	17	7	7	10	1	1	3	1	1	0	2	2	5	2	3	2	0	2	1	2	0	5	3	rs34260449	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:32376748C>T	ENST00000375200.1	+	13	2297	c.1932C>T	c.(1930-1932)caC>caT	p.H644H	ZNF341_ENST00000342427.2_Silent_p.H637H|RP4-553F4.6_ENST00000443171.1_RNA|RP4-553F4.6_ENST00000439444.1_RNA|RP4-553F4.6_ENST00000423074.1_RNA	NM_001282933.1	NP_001269862.1	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	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)			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						TGTTGATCCACGAGCCCTTCA	0.552													C|||	60	0.0119808	0.0	0.0159	5008	,	,		17759	0.001		0.0318	False		,,,				2504	0.0164				p.H637H		Atlas-SNP	.											.	ZNF341	73	.	0			c.C1911T						PASS	.	C		17,4389	25.3+/-52.1	0,17,2186	121	99	106		1911	-4.3	1	20	dbSNP_126	106	180,8420	82.6+/-145.2	2,176,4122	no	coding-synonymous	ZNF341	NM_032819.3		2,193,6308	TT,TC,CC		2.093,0.3858,1.5147		637/848	32376748	197,12809	2203	4300	6503	SO:0001819	synonymous_variant	84905	exon13			GATCCACGAGCCC	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.1932C>T	20.37:g.32376748C>T		180	0	0		210	105	0.5	NM_032819	A2RUF4|B2RXE5|B7ZM09|Q5JXM8|Q96ST5	Silent	SNP	ENST00000375200.1	37																																																																																				C|0.985;T|0.015	0.015	strong		0.552	ZNF341-201	KNOWN	basic	protein_coding	protein_coding				T	32376748	C	T	32376748	2	4	26	1	0	0	0	0	0	0	0	1	17872	535	19	1		1	ZNF341	20	32376748	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	165780	32376748	30648772	630	10393											
ASIP	434	hgsc.bcm.edu	37	chr20	32856838	32856838	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gtggtgcggccccggaccccCctatctgcgccctgcgtggc	2	7	14	18	4	1	0	0	0	1	0	1	1	1	1	6	4	3	0	6	4	1	1	rs36093428	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:32856838C>A	ENST00000568305.1	+	4	466	c.264C>A	c.(262-264)ccC>ccA	p.P88P	ASIP_ENST00000374954.3_Silent_p.P88P|RP4-785G19.5_ENST00000512005.1_RNA			P42127	ASIP_HUMAN	agouti signaling protein	88					adult feeding behavior (GO:0008343)|cell-cell signaling (GO:0007267)|generation of precursor metabolites and energy (GO:0006091)|genetic imprinting (GO:0071514)|hormone-mediated signaling pathway (GO:0009755)|melanin biosynthetic process (GO:0042438)|melanosome organization (GO:0032438)|melanosome transport (GO:0032402)|regulation of molecular function, epigenetic (GO:0040030)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	receptor binding (GO:0005102)			central_nervous_system(1)|lung(2)	3						CCCGGACCCCCCTATCTGCGC	0.706													C|||	31	0.0061901	0.0008	0.0144	5008	,	,		11685	0.0		0.0199	False		,,,				2504	0.0				p.P88P		Atlas-SNP	.											.	ASIP	6	.	0			c.C264A						PASS	.	C		3,4325		0,3,2161	9	11	11		264	-1.8	0	20	dbSNP_126	11	48,8490		0,48,4221	no	coding-synonymous	ASIP	NM_001672.2		0,51,6382	AA,AC,CC		0.5622,0.0693,0.3964		88/133	32856838	51,12815	2164	4269	6433	SO:0001819	synonymous_variant	434	exon3			GACCCCCCTATCT		CCDS13232.1	20q11.2-q12	2010-06-24	2010-06-24		ENSG00000101440	ENSG00000101440			745	protein-coding gene	gene with protein product	"nonagouti homolog (mouse)"	600201	"agouti (mouse)-signaling protein", "agouti signaling protein, nonagouti homolog (mouse)"	AGTIL		7937887, 7757071	Standard	NM_001672		Approved	ASP	uc002xah.1	P42127	OTTHUMG00000032289	ENST00000568305.1:c.264C>A	20.37:g.32856838C>A		53	0	0		68	48	0.705882	NM_001672	Q3SXL2	Silent	SNP	ENST00000568305.1	37	CCDS13232.1																																																																																			C|0.994;A|0.006	0.006	strong		0.706	ASIP-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430541.1			A	32856838	C	A	32856838	2	1	26	1	0	0	0	0	0	0	0	1	1043	610	22	4		4	ASIP	20	32856838	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	480090	32856838	30168682	631	10394											
NCOA6	23054	hgsc.bcm.edu	37	chr20	33342623	33342623	+	Missense_Mutation	SNP	G	G	A																															cctgaccttgcataaagttcGgattggcctgtcctgctgag																								rs144477396	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:33342623G>A	ENST00000374796.2	-	9	4147	c.1577C>T	c.(1576-1578)cCg>cTg	p.P526L	NCOA6_ENST00000359003.2_Missense_Mutation_p.P526L			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	526	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						CATAAAGTTCGGATTGGCCTG	0.493																																					p.P526L		Atlas-SNP	.											.	NCOA6	219	.	0			c.C1577T						PASS	.	G	LEU/PRO,LEU/PRO	0,4406		0,0,2203	117	107	110		1577,1577	3.8	1	20	dbSNP_134	110	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	NCOA6	NM_001242539.1,NM_014071.3	98,98	0,6,6497	AA,AG,GG		0.0698,0.0,0.0461	possibly-damaging,possibly-damaging	526/1071,526/2064	33342623	6,13000	2203	4300	6503	SO:0001583	missense	23054	exon8			AAGTTCGGATTGG	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.1577C>T	20.37:g.33342623G>A	ENSP00000363929:p.Pro526Leu	162	0	0		152	80	0.526316	NM_014071	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	37	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	G	14.37	2.514740	0.44763	0.0	6.98E-4	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.23552	1.9;1.9	5.97	3.84	0.44239	.	0.486738	0.20890	N	0.083855	T	0.09598	0.0236	N	0.08118	0	0.46167	D	0.998908	P	0.45078	0.85	B	0.25614	0.062	T	0.20940	-1.0260	10	0.22706	T	0.39	-0.5866	13.5218	0.61572	0.0:0.0:0.6067:0.3933	.	526	Q14686	NCOA6_HUMAN	L	526	ENSP00000363929:P526L;ENSP00000351894:P526L	ENSP00000351894:P526L	P	-	2	0	NCOA6	32806284	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	1.538000	0.36094	1.470000	0.48102	0.591000	0.81541	CCG	G|0.999;A|0.001	0.001	strong		0.493	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		A	33342623	G	A	33342623	3	1	26	1	0	0	0	0	1	0	0	0	10242	1116	39	1	4646	1	NCOA6	20	33342623	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	485785	33342623	29682897	632	10395	130	2									
NCOA6	23054	hgsc.bcm.edu	37	chr20	33342629	33342629	+	Missense_Mutation	SNP	G	G	C																															cttgcataaagttcggattgGcctgtcctgctgagaagcca																								rs148359628	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:33342629G>C	ENST00000374796.2	-	9	4141	c.1571C>G	c.(1570-1572)gCc>gGc	p.A524G	NCOA6_ENST00000359003.2_Missense_Mutation_p.A524G			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	524	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						GTTCGGATTGGCCTGTCCTGC	0.478																																					p.A524G		Atlas-SNP	.											.	NCOA6	219	.	0			c.C1571G						PASS	.	G	GLY/ALA,GLY/ALA	0,4406		0,0,2203	115	106	109		1571,1571	6	1	20	dbSNP_134	109	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	NCOA6	NM_001242539.1,NM_014071.3	60,60	0,6,6497	CC,CG,GG		0.0698,0.0,0.0461	benign,benign	524/1071,524/2064	33342629	6,13000	2203	4300	6503	SO:0001583	missense	23054	exon8			GGATTGGCCTGTC	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.1571C>G	20.37:g.33342629G>C	ENSP00000363929:p.Ala524Gly	152	0	0		144	76	0.527778	NM_014071	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	37	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	G	14.74	2.626084	0.46840	0.0	6.98E-4	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.25414	1.8;1.8	5.97	5.97	0.96955	.	0.081814	0.51477	D	0.000086	T	0.16685	0.0401	N	0.12182	0.205	0.48901	D	0.999723	B	0.09022	0.002	B	0.10450	0.005	T	0.08249	-1.0731	10	0.27082	T	0.32	-7.7298	15.8466	0.78899	0.0:0.1349:0.865:0.0	.	524	Q14686	NCOA6_HUMAN	G	524	ENSP00000363929:A524G;ENSP00000351894:A524G	ENSP00000351894:A524G	A	-	2	0	NCOA6	32806290	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.652000	0.54439	2.835000	0.97688	0.591000	0.81541	GCC	G|0.999;C|0.001	0.001	strong		0.478	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		C	33342629	G	C	33342629	3	2	26	1	0	0	0	0	1	0	0	0	10242	1203	42	4	4652	4	NCOA6	20	33342629	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	6	33342629	29682891	633	10396	130	2									
RALGAPB	57148	hgsc.bcm.edu	37	chr20	37203571	37203571	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagccagagttttatacttcActtttccaggaggttggact	9	14	10	8	0	1	1	1	0	0	1	2	4	2	3	2	3	2	2	2	3	2	7	rs143567036	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:37203571A>G	ENST00000262879.6	+	30	4730	c.4446A>G	c.(4444-4446)tcA>tcG	p.S1482S	RALGAPB_ENST00000490114.1_3'UTR|RALGAPB_ENST00000397040.1_Silent_p.S1482S|RALGAPB_ENST00000397042.3_Silent_p.S1479S|RALGAPB_ENST00000397038.1_Silent_p.S1261S			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	1482					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						TTTATACTTCACTTTTCCAGG	0.463																																					p.S1482S		Atlas-SNP	.											.	RALGAPB	134	.	0			c.A4446G						PASS	.	A		0,4406		0,0,2203	84	89	87		4446	2.4	1	20	dbSNP_134	87	3,8597	4.3+/-15.6	0,3,4297	no	coding-synonymous	RALGAPB	NM_020336.2		0,3,6500	GG,GA,AA		0.0349,0.0,0.0231		1482/1495	37203571	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	57148	exon30			TACTTCACTTTTC	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.4446A>G	20.37:g.37203571A>G		155	0	0		144	57	0.395833	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Silent	SNP	ENST00000262879.6	37	CCDS13305.1																																																																																			A|0.999;G|0.001	0.001	strong		0.463	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336		G	37203571	A	G	37203571	2	3	26	1	0	0	0	0	0	0	0	1	13030	146	6	3		3	RALGAPB	20	37203571	Silent	SNP	A	TCGA-G8-6907-01A-11D-2210-10	3860942	37203571	25821949	634	10397											
TSHZ2	128553	hgsc.bcm.edu	37	chr20	51872869	51872869	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaaatgaaggacatgaccCgcttgtcagtggaccagcaa	13	7	10	11	1	1	2	1	2	0	0	2	4	2	4	3	2	1	2	3	2	3	1	rs61760185	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:51872869C>A	ENST00000371497.5	+	2	3759	c.2872C>A	c.(2872-2874)Cgc>Agc	p.R958S	TSHZ2_ENST00000603338.2_Missense_Mutation_p.R955S|RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000329613.6_Missense_Mutation_p.R955S	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	958					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)			GGACATGACCCGCTTGTCAGT	0.507													C|||	2	0.000399361	0.0	0.0	5008	,	,		19232	0.0		0.002	False		,,,				2504	0.0				p.R958S		Atlas-SNP	.											.	TSHZ2	209	.	0			c.C2872A						PASS	.	C	SER/ARG,SER/ARG	2,4404	4.2+/-10.8	0,2,2201	77	77	77		2863,2872	4.7	1	20	dbSNP_129	77	25,8575	16.0+/-53.3	0,25,4275	yes	missense,missense	TSHZ2	NM_001193421.1,NM_173485.5	110,110	0,27,6476	AA,AC,CC		0.2907,0.0454,0.2076	probably-damaging,probably-damaging	955/1032,958/1035	51872869	27,12979	2203	4300	6503	SO:0001583	missense	128553	exon2			ATGACCCGCTTGT	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.2872C>A	20.37:g.51872869C>A	ENSP00000360552:p.Arg958Ser	84	0	0		121	75	0.619835	NM_173485	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	37	CCDS33490.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	17.55	3.417888	0.62622	4.54E-4	0.002907	ENSG00000182463	ENST00000371497;ENST00000329613;ENST00000450262	T;T	0.15603	2.42;2.41	5.7	4.7	0.59300	.	0.047245	0.85682	D	0.000000	T	0.14700	0.0355	N	0.22421	0.69	0.52501	D	0.999954	P	0.52842	0.956	P	0.45681	0.49	T	0.00844	-1.1543	10	0.62326	D	0.03	-11.6406	11.9946	0.53194	0.3361:0.6639:0.0:0.0	rs61760185	958	Q9NRE2	TSH2_HUMAN	S	958;955;484	ENSP00000360552:R958S;ENSP00000333114:R955S	ENSP00000333114:R955S	R	+	1	0	TSHZ2	51306276	1.000000	0.71417	1.000000	0.80357	0.756000	0.42949	6.371000	0.73119	2.685000	0.91497	0.643000	0.83706	CGC	C|0.999;A|0.001	0.001	strong		0.507	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485		A	51872869	C	A	51872869	3	1	26	1	0	0	0	0	1	0	0	0	16639	652	23	4	2878	4	TSHZ2	20	51872869	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	14669298	51872869	11152651	635	10398											
STX16	8675	hgsc.bcm.edu	37	chr20	57242602	57242602	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agcttagatccagaagcagcGattggtgtgacaaaacggcc	13	7	12	9	2	0	3	0	1	0	2	1	4	1	3	2	2	4	2	2	2	4	2	rs376636519		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:57242602G>A	ENST00000371141.4	+	3	925	c.201G>A	c.(199-201)gcG>gcA	p.A67A	STX16_ENST00000359617.4_Silent_p.A14A|STX16-NPEPL1_ENST00000530122.1_Silent_p.A67A|STX16_ENST00000358029.4_Silent_p.A63A|STX16_ENST00000361830.3_Silent_p.A67A|STX16_ENST00000361770.5_Silent_p.A50A|STX16_ENST00000496003.1_3'UTR|STX16_ENST00000371132.4_Silent_p.A46A|STX16_ENST00000355957.5_Silent_p.A50A	NM_001001433.2	NP_001001433.1	O14662	STX16_HUMAN	syntaxin 16	67					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)			CAGAAGCAGCGATTGGTGTGA	0.413																																					p.A67A		Atlas-SNP	.											.	STX16	36	.	0			c.G201A						PASS	.	G	,,,,	0,4406		0,0,2203	146	135	139		201,189,150,42,138	-4.6	0.6	20		139	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	STX16	NM_001001433.2,NM_001134772.2,NM_001134773.2,NM_001204868.1,NM_003763.5	,,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,	67/326,63/322,50/309,14/273,46/305	57242602	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8675	exon3			AGCAGCGATTGGT	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.201G>A	20.37:g.57242602G>A		108	0	0		105	54	0.514286	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	37	CCDS13468.1																																																																																			.	.	weak		0.413	STX16-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080517.2	NM_001001433		A	57242602	G	A	57242602	2	1	26	1	0	0	0	0	0	0	0	1	15354	1045	37	1		1	STX16	20	57242602	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	5369733	57242602	5782918	636	10399											
TAF4	6874	hgsc.bcm.edu	37	chr20	60585139	60585139	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtggtcgcccctggtaccGtgcgctgaggagtccccgtc	3	9	15	14	4	0	1	0	1	0	0	3	2	1	2	5	4	2	2	5	4	1	1	rs141880507		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:60585139G>A	ENST00000252996.4	-	4	1723	c.1724C>T	c.(1723-1725)aCg>aTg	p.T575M	TAF4_ENST00000609045.1_5'UTR	NM_003185.3	NP_003176.2	O00268	TAF4_HUMAN	TAF4 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 135kDa	575					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)			CCCTGGTACCGTGCGCTGAGG	0.612													G|||	1	0.000199681	0.0	0.0	5008	,	,		16776	0.001		0.0	False		,,,				2504	0.0				p.T575M		Atlas-SNP	.											.	TAF4	84	.	0			c.C1724T						PASS	.						98	79	85					20																	60585139		2203	4300	6503	SO:0001583	missense	6874	exon4			GGTACCGTGCGCT	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.1724C>T	20.37:g.60585139G>A	ENSP00000252996:p.Thr575Met	33	0	0		40	21	0.525	NM_003185	A6NGD9|Q5TBP6|Q99721|Q9BR40|Q9BX42	Missense_Mutation	SNP	ENST00000252996.4	37	CCDS33500.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	14.17	2.456706	0.43634	.	.	ENSG00000130699	ENST00000252996;ENST00000436129	T;T	0.26660	1.72;1.73	4.8	4.8	0.61643	.	0.550327	0.19671	N	0.108752	T	0.30479	0.0766	L	0.34521	1.04	0.22541	N	0.999006	D	0.69078	0.997	P	0.49332	0.607	T	0.13098	-1.0522	10	0.62326	D	0.03	-4.0056	17.8435	0.88722	0.0:0.0:1.0:0.0	.	575	O00268	TAF4_HUMAN	M	575;439	ENSP00000252996:T575M;ENSP00000399091:T439M	ENSP00000252996:T575M	T	-	2	0	TAF4	60018534	0.969000	0.33509	0.095000	0.20976	0.149000	0.21700	6.757000	0.74924	2.226000	0.72624	0.313000	0.20887	ACG	G|1.000;A|0.000	0.000	strong		0.612	TAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079968.2	NM_003185		A	60585139	G	A	60585139	3	1	26	1	0	0	0	0	1	0	0	0	15541	1145	40	1	1581	1	TAF4	20	60585139	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	3342537	60585139	2440381	637	10400											
LAMA5	3911	hgsc.bcm.edu	37	chr20	60892545	60892545	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catccaggctggcggcgaggCgctccagctcctggaatttg	6	8	14	13	3	0	0	0	0	0	0	3	2	3	1	3	5	1	3	3	5	1	1	rs2427282	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:60892545C>T	ENST00000252999.3	-	55	7433	c.7367G>A	c.(7366-7368)cGc>cAc	p.R2456H		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2456	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)			GGCGGCGAGGCGCTCCAGCTC	0.662													.|||	37	0.00738818	0.0008	0.0115	5008	,	,		15961	0.0		0.0268	False		,,,				2504	0.001				p.R2456H		Atlas-SNP	.											.	LAMA5	268	.	0			c.G7367A						PASS	.		HIS/ARG	30,4310		0,30,2140	20	23	22		7367	-4.2	0.8	20	dbSNP_100	22	232,8314		3,226,4044	yes	missense	LAMA5	NM_005560.3	29	3,256,6184	TT,TC,CC		2.7147,0.6912,2.0332	benign	2456/3696	60892545	262,12624	2170	4273	6443	SO:0001583	missense	3911	exon55			GCGAGGCGCTCCA	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.7367G>A	20.37:g.60892545C>T	ENSP00000252999:p.Arg2456His	107	0	0		103	54	0.524272	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	26	0.011904761904761904	0	0.0	5	0.013812154696132596	0	0.0	21	0.027704485488126648	c	7.206	0.594372	0.13875	0.006912	0.027147	ENSG00000130702	ENST00000252999	T	0.18960	2.18	3.54	-4.23	0.03789	.	0.473582	0.22319	N	0.061639	T	0.01592	0.0051	N	0.01048	-1.04	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39820	-0.9595	10	0.25106	T	0.35	.	10.7393	0.46143	0.0:0.3638:0.0:0.6362	rs2427282	2456	O15230	LAMA5_HUMAN	H	2456	ENSP00000252999:R2456H	ENSP00000252999:R2456H	R	-	2	0	LAMA5	60325940	0.672000	0.27530	0.804000	0.32291	0.108000	0.19459	-0.278000	0.08490	-0.734000	0.04843	0.436000	0.28706	CGC	C|0.984;T|0.016	0.016	strong		0.662	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		T	60892545	C	T	60892545	3	4	26	1	0	0	0	0	1	0	0	0	8618	768	27	1	3824	1	LAMA5	20	60892545	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	307406	60892545	2132975	638	10401											
LAMA5	3911	hgsc.bcm.edu	37	chr20	60898889	60898889	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggcactgggtgcggccgcctCgcaggacacagccctcggcg	5	4	16	16	5	0	0	0	0	0	0	2	1	0	1	3	5	2	2	3	5	0	0	rs372008452		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:60898889C>T	ENST00000252999.3	-	44	5858	c.5792G>A	c.(5791-5793)cGa>cAa	p.R1931Q		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1931	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)			GCGGCCGCCTCGCAGGACACA	0.692																																					p.R1931Q		Atlas-SNP	.											.	LAMA5	268	.	0			c.G5792A						PASS	.	C	GLN/ARG	1,4365		0,1,2182	22	24	23		5792	1.2	0.1	20		23	1,8575		0,1,4287	no	missense	LAMA5	NM_005560.3	43	0,2,6469	TT,TC,CC		0.0117,0.0229,0.0155	probably-damaging	1931/3696	60898889	2,12940	2183	4288	6471	SO:0001583	missense	3911	exon44			CCGCCTCGCAGGA	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.5792G>A	20.37:g.60898889C>T	ENSP00000252999:p.Arg1931Gln	75	0	0		72	41	0.569444	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	C	12.12	1.842202	0.32513	2.29E-4	1.17E-4	ENSG00000130702	ENST00000252999	T	0.63096	-0.02	3.63	1.17	0.20885	EGF-like, laminin (3);	0.328525	0.30101	U	0.010416	T	0.38241	0.1033	L	0.42008	1.315	0.09310	N	1	P	0.42993	0.797	B	0.32022	0.139	T	0.22906	-1.0203	10	0.15952	T	0.53	.	3.2772	0.06902	0.0:0.4524:0.2687:0.2789	.	1931	O15230	LAMA5_HUMAN	Q	1931	ENSP00000252999:R1931Q	ENSP00000252999:R1931Q	R	-	2	0	LAMA5	60332284	0.012000	0.17670	0.069000	0.20011	0.382000	0.30200	0.755000	0.26405	0.466000	0.27193	0.297000	0.19635	CGA	.	.	weak		0.692	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		T	60898889	C	T	60898889	3	4	26	1	0	0	0	0	1	0	0	0	8618	884	31	1	5443	1	LAMA5	20	60898889	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	6344	60898889	2126631	639	10402											
DIDO1	11083	hgsc.bcm.edu	37	chr20	61510849	61510849	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tctcggtcgcggttggcgctCctctcccggtttctgtccca	1	13	11	16	5	3	0	0	0	3	0	8	0	5	0	3	4	0	3	3	4	0	2	rs373321839	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:61510849C>T	ENST00000266070.4	-	16	6784	c.6459G>A	c.(6457-6459)agG>agA	p.R2153R	DIDO1_ENST00000395343.1_Silent_p.R2153R	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	2153	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)					GGTTGGCGCTCCTCTcccggt	0.726													C|||	4	0.000798722	0.0008	0.0014	5008	,	,		12926	0.0		0.002	False		,,,				2504	0.0				p.R2153R	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.G6459A						PASS	.	C	,	1,4315		0,1,2157	17	14	15		6459,6459	-0.3	0	20		15	5,8397		0,5,4196	no	coding-synonymous,coding-synonymous	DIDO1	NM_001193369.1,NM_033081.2	,	0,6,6353	TT,TC,CC		0.0595,0.0232,0.0472	,	2153/2241,2153/2241	61510849	6,12712	2158	4201	6359	SO:0001819	synonymous_variant	11083	exon16			GGCGCTCCTCTCC	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.6459G>A	20.37:g.61510849C>T		33	0	0		13	5	0.384615	NM_001193369	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Silent	SNP	ENST00000266070.4	37	CCDS33506.1																																																																																			.	.	weak		0.726	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		T	61510849	C	T	61510849	2	4	26	1	0	0	0	0	0	0	0	1	4524	854	30	2		2	DIDO1	20	61510849	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	611960	61510849	1514671	640	10403											
BACH1	571	hgsc.bcm.edu	37	chr21	30699557	30699557	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aagtactctgagtactgaagGctgttcaagcaatttggaaa	14	11	10	6	0	2	2	1	2	1	0	2	3	2	3	0	2	3	5	0	2	7	4	rs35766001	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:30699557G>C	ENST00000399921.1	+	3	1655	c.1412G>C	c.(1411-1413)gGc>gCc	p.G471A	BACH1_ENST00000286800.3_Missense_Mutation_p.G471A	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						AGTACTGAAGGCTGTTCAAGC	0.423													G|||	40	0.00798722	0.0015	0.0173	5008	,	,		20941	0.0		0.0119	False		,,,				2504	0.0143				p.G471A		Atlas-SNP	.											.	BACH1	66	.	0			c.G1412C						PASS	.	G	ALA/GLY,ALA/GLY	20,4386	26.2+/-53.5	0,20,2183	124	119	121		1412,1412	2.2	1	21	dbSNP_126	121	141,8459	71.0+/-133.6	1,139,4160	yes	missense,missense	BACH1	NM_001186.2,NM_206866.1	60,60	1,159,6343	CC,CG,GG		1.6395,0.4539,1.2379	benign,benign	471/737,471/737	30699557	161,12845	2203	4300	6503	SO:0001583	missense	571	exon3			CTGAAGGCTGTTC	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.1412G>C	21.37:g.30699557G>C	ENSP00000382805:p.Gly471Ala	194	0	0		190	98	0.515789	NM_206866	Q3MJE2|Q8NCI5	Missense_Mutation	SNP	ENST00000399921.1	37	CCDS13585.1	17|17	0.007783882783882784|0.007783882783882784	0|0	0.0|0.0	9|9	0.024861878453038673|0.024861878453038673	0|0	0.0|0.0	8|8	0.010554089709762533|0.010554089709762533	G|G	12.49|12.49	1.952889|1.952889	0.34471|0.34471	0.004539|0.004539	0.016395|0.016395	ENSG00000156273|ENSG00000156273	ENST00000286800;ENST00000399921|ENST00000422809	T;T|.	0.71461|.	-0.57;-0.57|.	5.48|5.48	2.16|2.16	0.27623|0.27623	.|.	0.249525|.	0.34853|.	N|.	0.003632|.	T|T	0.38931|0.38931	0.1059|0.1059	L|L	0.44542|0.44542	1.39|1.39	0.40301|0.40301	D|D	0.978604|0.978604	B|.	0.20052|.	0.041|.	B|.	0.15052|.	0.012|.	T|T	0.41161|0.41161	-0.9524|-0.9524	10|5	0.05436|.	T|.	0.98|.	-16.108|-16.108	10.9423|10.9423	0.47281|0.47281	0.0764:0.2453:0.6782:0.0|0.0764:0.2453:0.6782:0.0	rs35766001|rs35766001	471|.	O14867|.	BACH1_HUMAN|.	A|S	471|36	ENSP00000286800:G471A;ENSP00000382805:G471A|.	ENSP00000286800:G471A|.	G|R	+|+	2|3	0|2	BACH1|BACH1	29621428|29621428	1.000000|1.000000	0.71417|0.71417	0.982000|0.982000	0.44146|0.44146	0.990000|0.990000	0.78478|0.78478	1.712000|1.712000	0.37940|0.37940	0.648000|0.648000	0.30732|0.30732	-0.176000|-0.176000	0.13171|0.13171	GGC|AGG	G|0.989;C|0.011	0.011	strong		0.423	BACH1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171974.1	NM_206866		C	30699557	G	C	30699557	3	2	26	1	0	0	0	0	1	0	0	0	1283	1203	42	4	1418	4	BACH1	21	30699557	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10		30699557	17430338	641	10404											
GRIK1	2897	hgsc.bcm.edu	37	chr21	30926024	30926024	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccataaaagaaacaaaaaGccttgcatgcaaaagaaatg	21	6	7	7	0	0	2	0	0	0	2	1	2	1	2	2	0	4	2	2	0	8	2	rs363503	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:30926024G>A	ENST00000399907.1	-	17	3020	c.2609C>T	c.(2608-2610)gCt>gTt	p.A870V	GRIK1_ENST00000535441.1_Intron|GRIK1_ENST00000399909.1_Splice_Site_p.A855V|GRIK1_ENST00000399914.1_Intron|GRIK1_ENST00000389125.3_Intron|GRIK1_ENST00000399913.1_Intron|GRIK1_ENST00000389124.2_Intron|GRIK1_ENST00000309434.7_Splice_Site_p.A872V|GRIK1_ENST00000327783.4_Intron	NM_000830.3	NP_000821.1	P39086	GRIK1_HUMAN	glutamate receptor, ionotropic, kainate 1	870			A -> V (in dbSNP:rs363503).		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)	GAAACAAAAAGCCTTGCATGC	0.313													G|||	31	0.0061901	0.0015	0.0072	5008	,	,		16981	0.001		0.005	False		,,,				2504	0.0184				p.A870V		Atlas-SNP	.											.	GRIK1	293	.	0			c.C2609T						PASS	.	G	VAL/ALA,	9,3601		0,9,1796	96	98	97		2609,	4.5	1	21	dbSNP_79	97	58,8104		0,58,4023	yes	missense-near-splice,intron	GRIK1	NM_000830.3,NM_175611.2	64,	0,67,5819	AA,AG,GG		0.7106,0.2493,0.5691	benign,	870/919,	30926024	67,11705	1805	4081	5886	SO:0001630	splice_region_variant	2897	exon17			CAAAAAGCCTTGC		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.2608-1C>T	21.37:g.30926024G>A		90	0	0		73	32	0.438356	NM_000830	Q13001|Q86SU9	Missense_Mutation	SNP	ENST00000399907.1	37	CCDS42913.1	6	0.0027472527472527475	0	0.0	4	0.011049723756906077	0	0.0	2	0.002638522427440633	G	17.20	3.327836	0.60743	0.002493	0.007106	ENSG00000171189	ENST00000399907;ENST00000399909;ENST00000309434	T;T;T	0.11277	2.8;2.79;2.8	5.4	4.52	0.55395	.	.	.	.	.	T	0.04182	0.0116	N	0.08118	0	0.31142	N	0.706501	B	0.20261	0.043	B	0.17433	0.018	T	0.16041	-1.0416	9	0.19147	T	0.46	.	13.6508	0.62310	0.0746:0.0:0.9254:0.0	rs363503	870	P39086	GRIK1_HUMAN	V	870;855;872	ENSP00000382791:A870V;ENSP00000382793:A855V;ENSP00000311646:A872V	ENSP00000311646:A872V	A	-	2	0	GRIK1	29847895	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.782000	0.68973	1.503000	0.48686	0.655000	0.94253	GCT	G|0.997;A|0.003	0.003	strong		0.313	GRIK1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171979.1		Missense_Mutation	A	30926024	G	A	30926024	5	1	26	1	0	0	0	0	0	0	1	0	6782	985	34	2	311	2	GRIK1	21	30926024	Splice_Site	SNP	G	TCGA-G8-6907-01A-11D-2210-10	226467	30926024	17203871	642	10405											
SON	6651	hgsc.bcm.edu	37	chr21	34922804	34922804	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgccagggcccctttctaccCcagtgcctgagttgccaggg	5	9	12	15	0	1	1	0	1	1	0	1	1	1	1	7	2	4	1	7	2	1	3	rs201446136	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:34922804C>T	ENST00000356577.4	+	3	1742	c.1267C>T	c.(1267-1269)Cca>Tca	p.P423S	SON_ENST00000381679.4_Missense_Mutation_p.P423S|SON_ENST00000290239.6_Missense_Mutation_p.P423S|SON_ENST00000300278.4_Missense_Mutation_p.P423S|SON_ENST00000381692.2_Intron	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	423					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						CCTTTCTACCCCAGTGCCTGA	0.652													C|||	2	0.000399361	0.0	0.0	5008	,	,		18430	0.0		0.002	False		,,,				2504	0.0				p.P423S		Atlas-SNP	.											SON_ENST00000300278,right_lower_lobe,carcinoma,0,2	SON	343	2	0			c.C1267T						PASS	.	C	SER/PRO,SER/PRO	0,4406		0,0,2203	40	44	43		1267,1267	3.6	1	21		43	3,8593		0,3,4295	yes	missense,missense	SON	NM_032195.1,NM_138927.1	74,74	0,3,6498	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging,probably-damaging	423/2304,423/2427	34922804	3,12999	2203	4298	6501	SO:0001583	missense	6651	exon3			TCTACCCCAGTGC	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.1267C>T	21.37:g.34922804C>T	ENSP00000348984:p.Pro423Ser	71	0	0		86	41	0.476744	NM_032195	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	37	CCDS13629.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	12.68	2.010597	0.35511	0.0	3.49E-4	ENSG00000159140	ENST00000356577;ENST00000290239;ENST00000300278;ENST00000381679	T;T;T;T	0.12147	2.87;2.95;2.94;2.71	5.44	3.6	0.41247	.	0.239020	0.30219	N	0.010126	T	0.11024	0.0269	L	0.29908	0.895	0.27339	N	0.956563	B;P;B	0.34615	0.33;0.459;0.157	B;B;B	0.34824	0.093;0.19;0.069	T	0.13710	-1.0499	10	0.72032	D	0.01	.	10.8006	0.46487	0.0:0.8335:0.0:0.1665	.	423;423;423	P18583;P18583-3;P18583-6	SON_HUMAN;.;.	S	423	ENSP00000348984:P423S;ENSP00000290239:P423S;ENSP00000300278:P423S;ENSP00000371095:P423S	ENSP00000290239:P423S	P	+	1	0	SON	33844674	0.779000	0.28652	1.000000	0.80357	0.997000	0.91878	2.446000	0.44908	1.438000	0.47492	0.491000	0.48974	CCA	C|1.000;T|0.000	0.000	strong		0.652	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		T	34922804	C	T	34922804	3	4	26	1	0	0	0	0	1	0	0	0	14941	623	22	2	1277	2	SON	21	34922804	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	3996780	34922804	13207091	643	10406											
TMPRSS3	64699	hgsc.bcm.edu	37	chr21	43809092	43809092	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgagactccgtcacatcgagCtatcagctcgatacacttaa	12	9	7	13	4	2	1	2	0	0	1	5	4	3	1	1	0	3	2	1	0	3	3	rs45598239	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:43809092C>T	ENST00000291532.3	-	4	1223	c.268G>A	c.(268-270)Gct>Act	p.A90T	TMPRSS3_ENST00000398405.1_Missense_Mutation_p.A88T|TMPRSS3_ENST00000433957.2_Missense_Mutation_p.A90T|TMPRSS3_ENST00000474596.1_5'UTR|TMPRSS3_ENST00000398397.3_Missense_Mutation_p.A90T|TMPRSS3_ENST00000380399.1_Missense_Mutation_p.A174T	NM_032404.2	NP_115780.1	P57727	TMPS3_HUMAN	transmembrane protease, serine 3	90	LDL-receptor class A. {ECO:0000255|PROSITE-ProRule:PRU00124}.			A -> T (in Ref. 1; AAG37012). {ECO:0000305}.	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						TCACATCGAGCTATCAGCTCG	0.527													C|||	51	0.0101837	0.0038	0.0086	5008	,	,		21045	0.0		0.0358	False		,,,				2504	0.0041				p.A90T		Atlas-SNP	.											.	TMPRSS3	40	.	0			c.G268A	GRCh37	CM054156	TMPRSS3	M	rs45598239	PASS	.	C	THR/ALA,THR/ALA	40,4366	43.8+/-77.6	0,40,2163	93	79	83	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	268,268	5.2	0.1	21	dbSNP_127	83	415,8185	130.3+/-188.3	8,399,3893	yes	missense,missense	TMPRSS3	NM_024022.2,NM_032405.1	58,58	8,439,6056	TT,TC,CC		4.8256,0.9079,3.4984	probably-damaging,probably-damaging	90/455,90/345	43809092	455,12551	2203	4300	6503	SO:0001583	missense	64699	exon4			ATCGAGCTATCAG	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.268G>A	21.37:g.43809092C>T	ENSP00000291532:p.Ala90Thr	54	0	0		78	38	0.487179	NM_001256317	D3DSJ6|Q5USC7|Q6ZMC3	Missense_Mutation	SNP	ENST00000291532.3	37	CCDS13686.1	36	0.016483516483516484	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	28	0.036939313984168866	C	14.53	2.562692	0.45694	0.009079	0.048256	ENSG00000160183	ENST00000291532;ENST00000433957;ENST00000398405;ENST00000380399;ENST00000398397	D;D;D;D;D	0.95412	-3.7;-3.7;-3.7;-3.7;-3.7	5.23	5.23	0.72850	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.138905	0.48286	D	0.000189	D	0.87529	0.6200	M	0.75447	2.3	0.38709	D	0.953168	D;D;D	0.56746	0.967;0.977;0.96	P;P;P	0.57244	0.765;0.787;0.816	D	0.87660	0.2534	9	.	.	.	.	18.8283	0.92127	0.0:1.0:0.0:0.0	rs45598239	90;90;90	P57727-3;P57727-5;P57727	.;.;TMPS3_HUMAN	T	90;90;88;174;90	ENSP00000291532:A90T;ENSP00000411013:A90T;ENSP00000381442:A88T;ENSP00000369762:A174T;ENSP00000381434:A90T	.	A	-	1	0	TMPRSS3	42682161	0.992000	0.36948	0.079000	0.20413	0.008000	0.06430	4.157000	0.58144	2.443000	0.82685	0.561000	0.74099	GCT	C|0.969;T|0.031	0.031	strong		0.527	TMPRSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195347.1			T	43809092	C	T	43809092	3	4	26	1	0	0	0	0	1	0	0	0	16263	797	28	2	1219	2	TMPRSS3	21	43809092	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	8886288	43809092	4320803	644	10407											
TRAPPC10	7109	hgsc.bcm.edu	37	chr21	45502758	45502758	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccgtggtccacgtgggcggcGttttgtgcgttgagataacc	5	11	15	10	5	0	1	0	1	0	1	1	2	1	1	3	3	2	2	3	3	1	4	rs367993178		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:45502758G>A	ENST00000291574.4	+	14	1988	c.1813G>A	c.(1813-1815)Gtt>Att	p.V605I		NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	605					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)	p.V605F(1)		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						CGTGGGCGGCGTTTTGTGCGT	0.483																																					p.V605I		Atlas-SNP	.											TRAPPC10,colon,carcinoma,0,1	TRAPPC10	109	1	1	Substitution - Missense(1)	large_intestine(1)	c.G1813A						PASS	.	G	ILE/VAL	0,4406		0,0,2203	194	163	173		1813	-3	0	21		173	1,8599	1.2+/-3.3	0,1,4299	no	missense	TRAPPC10	NM_003274.4	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	605/1260	45502758	1,13005	2203	4300	6503	SO:0001583	missense	7109	exon14			GGCGGCGTTTTGT	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.1813G>A	21.37:g.45502758G>A	ENSP00000291574:p.Val605Ile	184	0	0		177	72	0.40678	NM_003274	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Missense_Mutation	SNP	ENST00000291574.4	37	CCDS13704.1	.	.	.	.	.	.	.	.	.	.	G	6.340	0.430748	0.12045	0.0	1.16E-4	ENSG00000160218	ENST00000291574	T	0.40756	1.02	5.58	-2.99	0.05497	.	0.845087	0.10694	N	0.644857	T	0.22666	0.0547	N	0.19112	0.55	0.09310	N	1	B	0.12630	0.006	B	0.04013	0.001	T	0.21965	-1.0230	10	0.23891	T	0.37	.	8.3648	0.32380	0.6995:0.0:0.1746:0.1259	.	605	P48553	TPC10_HUMAN	I	605	ENSP00000291574:V605I	ENSP00000291574:V605I	V	+	1	0	TRAPPC10	44327186	0.001000	0.12720	0.000000	0.03702	0.031000	0.12232	1.285000	0.33261	-0.457000	0.07033	-0.768000	0.03414	GTT	.	.	weak		0.483	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274		A	45502758	G	A	45502758	3	1	26	1	0	0	0	0	1	0	0	0	16472	1145	40	1	1867	1	TRAPPC10	21	45502758	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1693666	45502758	2627137	645	10408											
KRTAP10-6	386674	hgsc.bcm.edu	37	chr21	46012259	46012259	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacagcagctctctgggcagTcgtccacctgccaggagtcg	7	7	12	15	2	1	0	0	0	1	0	5	1	2	1	3	2	3	3	3	2	0	0	rs201362069	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:46012259T>G	ENST00000400368.1	-	1	127	c.107A>C	c.(106-108)gAc>gCc	p.D36A	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	36						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						CTCTGGGCAGTCGTCCACCTG	0.687													.|||	62	0.0123802	0.0295	0.0029	5008	,	,		14636	0.002		0.0109	False		,,,				2504	0.0082				p.D36A		Atlas-SNP	.											.	KRTAP10-6	57	.	0			c.A107C						PASS	.	T	ALA/ASP,	103,3931		1,101,1915	46	45	45		107,	2.2	1	21		45	117,8165		2,113,4026	no	missense,intron	TSPEAR,KRTAP10-6	NM_198688.2,NM_144991.2	126,	3,214,5941	GG,GT,TT		1.4127,2.5533,1.7863	possibly-damaging,	36/366,	46012259	220,12096	2017	4141	6158	SO:0001583	missense	386674	exon1			GGGCAGTCGTCCA	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.107A>C	21.37:g.46012259T>G	ENSP00000383219:p.Asp36Ala	78	0	0		80	23	0.2875	NM_198688		Missense_Mutation	SNP	ENST00000400368.1	37	CCDS42959.1	23	0.010531135531135532	13	0.026422764227642278	3	0.008287292817679558	1	0.0017482517482517483	6	0.0079155672823219	t	10.71	1.425617	0.25639	0.025533	0.014127	ENSG00000188155	ENST00000400368	T	0.14893	2.47	3.49	2.18	0.27775	.	.	.	.	.	T	0.05640	0.0148	M	0.63843	1.955	0.26990	N	0.965169	P	0.51791	0.948	B	0.41332	0.354	T	0.09729	-1.0661	9	0.38643	T	0.18	.	7.2248	0.26010	0.0:0.0:0.4041:0.5959	.	36	P60371	KR106_HUMAN	A	36	ENSP00000383219:D36A	ENSP00000383219:D36A	D	-	2	0	KRTAP10-6	44836687	0.979000	0.34478	0.997000	0.53966	0.407000	0.30961	1.226000	0.32563	1.354000	0.45846	0.334000	0.21626	GAC	T|0.993;G|0.007	0.007	strong		0.687	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688		G	46012259	T	G	46012259	3	3	26	1	0	0	0	0	1	0	0	0	8522	1667	58	5	994	5	KRTAP10-6	21	46012259	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	509501	46012259	2117636	646	10409											
MCM3AP	8888	hgsc.bcm.edu	37	chr21	47666744	47666744	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agcccactggctcccaggagGtccttctgtgtctccacagc	6	9	10	16	0	2	0	0	0	2	0	5	1	4	1	4	3	2	1	4	3	0	1	rs17183220	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47666744G>T	ENST00000397708.1	-	22	4601	c.4347C>A	c.(4345-4347)gaC>gaA	p.D1449E	MCM3AP-AS1_ENST00000588753.1_RNA|MCM3AP_ENST00000291688.1_Missense_Mutation_p.D1449E|MCM3AP-AS1_ENST00000590829.1_RNA|AP001469.7_ENST00000444966.1_RNA|MCM3AP_ENST00000467026.1_5'UTR|MCM3AP-AS1_ENST00000414659.1_RNA|MCM3AP-AS1_ENST00000455567.1_RNA			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1449			D -> E (in dbSNP:rs17183220). {ECO:0000269|Ref.2}.		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)					CTCCCAGGAGGTCCTTCTGTG	0.587													G|||	105	0.0209665	0.0045	0.0375	5008	,	,		19253	0.001		0.0666	False		,,,				2504	0.0051				p.D1449E		Atlas-SNP	.											.	MCM3AP	146	.	0			c.C4347A						PASS	.	G	GLU/ASP	72,4334	63.5+/-100.7	1,70,2132	109	105	107		4347	0.8	1	21	dbSNP_123	107	568,8032	152.7+/-207.2	13,542,3745	yes	missense	MCM3AP	NM_003906.3	45	14,612,5877	TT,TG,GG		6.6047,1.6341,4.9208	benign	1449/1981	47666744	640,12366	2203	4300	6503	SO:0001583	missense	8888	exon21			CAGGAGGTCCTTC	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.4347C>A	21.37:g.47666744G>T	ENSP00000380820:p.Asp1449Glu	197	0	0		228	103	0.451754	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Missense_Mutation	SNP	ENST00000397708.1	37	CCDS13734.1	81	0.03708791208791209	6	0.012195121951219513	19	0.052486187845303865	1	0.0017482517482517483	55	0.07255936675461741	G	9.045	0.990724	0.18966	0.016341	0.066047	ENSG00000160294	ENST00000397708;ENST00000291688	T;T	0.03212	4.01;4.01	5.68	0.83	0.18854	.	0.187758	0.56097	N	0.000033	T	0.00178	0.0005	N	0.11927	0.2	0.37779	D	0.926956	B	0.09022	0.002	B	0.09377	0.004	T	0.55547	-0.8124	10	0.18710	T	0.47	-9.1595	0.8098	0.01091	0.217:0.2784:0.2857:0.2189	rs17183220;rs17183220	1449	O60318	MCM3A_HUMAN	E	1449	ENSP00000380820:D1449E;ENSP00000291688:D1449E	ENSP00000291688:D1449E	D	-	3	2	MCM3AP	46491172	0.997000	0.39634	0.998000	0.56505	0.655000	0.38815	0.417000	0.21214	0.080000	0.16959	0.650000	0.86243	GAC	G|0.957;T|0.043	0.043	strong		0.587	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906		T	47666744	G	T	47666744	3	4	26	1	0	0	0	0	1	0	0	0	9397	1252	44	4	1627	4	MCM3AP	21	47666744	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1654485	47666744	463151	647	10410											
MCM3AP	8888	hgsc.bcm.edu	37	chr21	47692531	47692531	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgtagccctggaactccgcTtcgctggcacagaagacacc	9	8	10	14	2	0	2	0	0	0	2	2	3	1	3	3	2	2	4	3	2	3	3	rs17182739	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47692531T>C	ENST00000397708.1	-	9	2663	c.2409A>G	c.(2407-2409)gaA>gaG	p.E803E	MCM3AP_ENST00000291688.1_Silent_p.E803E			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	803	SAC3 homology.				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)					GGAACTCCGCTTCGCTGGCAC	0.478													T|||	97	0.019369	0.0015	0.0346	5008	,	,		21993	0.001		0.0646	False		,,,				2504	0.0051				p.E803E		Atlas-SNP	.											MCM3AP,colon,carcinoma,-2,1	MCM3AP	146	1	0			c.A2409G						PASS	.	T		62,4344	57.4+/-93.9	1,60,2142	170	148	155		2409	-7	0	21	dbSNP_123	155	560,8040	153.3+/-207.7	13,534,3753	no	coding-synonymous	MCM3AP	NM_003906.3		14,594,5895	CC,CT,TT		6.5116,1.4072,4.7824		803/1981	47692531	622,12384	2203	4300	6503	SO:0001819	synonymous_variant	8888	exon8			CTCCGCTTCGCTG	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.2409A>G	21.37:g.47692531T>C		196	0	0		200	95	0.475	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Silent	SNP	ENST00000397708.1	37	CCDS13734.1																																																																																			T|0.959;C|0.041	0.041	strong		0.478	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906		C	47692531	T	C	47692531	2	2	26	1	0	0	0	0	0	0	0	1	9397	1606	56	3		3	MCM3AP	21	47692531	Silent	SNP	T	TCGA-G8-6907-01A-11D-2210-10	25787	47692531	437364	648	10411											
C21orf57	54059	hgsc.bcm.edu	37	chr21	47717493	47717493	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgctggacgagctgggccGacgcacggggacccggctgc	5	4	19	13	5	0	0	0	0	0	0	0	4	0	2	2	6	3	4	2	6	0	0	rs61736728	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47717493G>T	ENST00000329319.3	+	5	847	c.449G>T	c.(448-450)cGa>cTa	p.R150L	YBEY_ENST00000397692.1_Missense_Mutation_p.R62L|YBEY_ENST00000339195.6_Missense_Mutation_p.R107L|YBEY_ENST00000397691.1_Missense_Mutation_p.R150L|YBEY_ENST00000397694.1_Missense_Mutation_p.R105L|YBEY_ENST00000397701.4_Missense_Mutation_p.R150L	NM_058181.1	NP_478061.1	P58557	YBEY_HUMAN	ybeY metallopeptidase (putative)	150					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						GAGCTGGGCCGACGCACGGGG	0.701													G|||	87	0.0173722	0.0015	0.0245	5008	,	,		10890	0.001		0.0626	False		,,,				2504	0.0041				p.R150L		Atlas-SNP	.											YBEY,NS,carcinoma,0,1	YBEY	23	1	0			c.G449T						PASS	.	G	LEU/ARG	49,4099		1,47,2026	6	7	7		449	0.1	0	21	dbSNP_129	7	459,7799		8,443,3678	yes	missense	YBEY	NM_058181.1	102	9,490,5704	TT,TG,GG		5.5582,1.1813,4.0948	probably-damaging	150/168	47717493	508,11898	2074	4129	6203	SO:0001583	missense	54059	exon5			TGGGCCGACGCAC	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.449G>T	21.37:g.47717493G>T	ENSP00000329614:p.Arg150Leu	94	0	0		82	51	0.621951	NM_058181	B7WPA9|B7WPF7|D3DSN2	Missense_Mutation	SNP	ENST00000329319.3	37	CCDS33591.1	70	0.03205128205128205	3	0.006097560975609756	13	0.03591160220994475	1	0.0017482517482517483	53	0.06992084432717678	G	9.562	1.118668	0.20877	0.011813	0.055582	ENSG00000182362	ENST00000397701;ENST00000397694;ENST00000329319;ENST00000339195;ENST00000397692;ENST00000397691	.	.	.	4.96	0.0754	0.14399	.	0.158082	0.35838	N	0.002954	T	0.01029	0.0034	N	0.17594	0.5	0.09310	N	1	P;P;P;P	0.44044	0.462;0.825;0.804;0.704	B;B;B;B	0.43950	0.151;0.437;0.28;0.197	T	0.16364	-1.0405	9	0.02654	T	1	-8.7638	7.6929	0.28577	0.4468:0.0:0.5532:0.0	rs61736728	62;107;105;150	P58557-4;P58557-2;P58557-3;P58557	.;.;.;YBEY_HUMAN	L	150;105;150;107;62;150	.	ENSP00000329614:R150L	R	+	2	0	YBEY	46541921	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.015000	0.13355	-0.096000	0.12329	-1.036000	0.02392	CGA	G|0.968;T|0.032	0.032	strong		0.701	YBEY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207265.1	NM_058181		T	47717493	G	T	47717493	3	4	26	1	0	0	0	0	1	0	0	0	2130	1058	37	4	490	4	C21orf57	21	47717493	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	24962	47717493	412402	649	10412											
PCNT	5116	hgsc.bcm.edu	37	chr21	47766113	47766113	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagatgaggctggcctgcaTcagagtcaggtgacccggcg	9	6	16	10	2	2	4	2	2	0	2	2	5	2	4	2	4	1	2	2	4	1	0	rs34500739	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47766113T>G	ENST00000359568.5	+	4	818	c.711T>G	c.(709-711)caT>caG	p.H237Q	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	237	Glu-rich.				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)					CTGGCCTGCATCAGAGTCAGG	0.602													G|||	128	0.0255591	0.028	0.0303	5008	,	,		16755	0.001		0.0646	False		,,,				2504	0.0041				p.H237Q		Atlas-SNP	.											.	PCNT	283	.	0			c.T711G						PASS	.	G	GLN/HIS	192,4214	807.9+/-415.9	5,182,2016	83	74	77		711	3.3	1	21	dbSNP_126	77	528,8072	795.4+/-407.5	11,506,3783	yes	missense	PCNT	NM_006031.5	24	16,688,5799	GG,GT,TT		6.1395,4.3577,5.5359	benign	237/3337	47766113	720,12286	2203	4300	6503	SO:0001583	missense	5116	exon4			CCTGCATCAGAGT	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.711T>G	21.37:g.47766113T>G	ENSP00000352572:p.His237Gln	122	0	0		150	80	0.533333	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	92	0.04212454212454213	21	0.042682926829268296	16	0.04419889502762431	1	0.0017482517482517483	54	0.0712401055408971	G	2.436	-0.329782	0.05314	0.043577	0.061395	ENSG00000160299	ENST00000359568;ENST00000337772	T	0.01279	5.06	3.27	3.27	0.37495	.	.	.	.	.	T	0.00073	0.0002	N	0.00926	-1.1	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45145	-0.9281	9	0.09084	T	0.74	.	8.0049	0.30319	0.0:0.0:0.7564:0.2436	rs34500739	119;237	O95613-2;O95613	.;PCNT_HUMAN	Q	237;224	ENSP00000352572:H237Q	ENSP00000338675:H224Q	H	+	3	2	PCNT	46590541	0.057000	0.20700	0.965000	0.40720	0.171000	0.22731	0.660000	0.25009	0.988000	0.38734	-0.648000	0.03929	CAT	T|0.949;G|0.051	0.051	strong		0.602	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		G	47766113	T	G	47766113	3	3	26	1	0	0	0	0	1	0	0	0	11599	1432	50	5	725	5	PCNT	21	47766113	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	48620	47766113	363782	650	10413											
PCNT	5116	hgsc.bcm.edu	37	chr21	47831621	47831621	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagagaaatttagaaatcgaCgctctgaaccagcggaaggc	15	6	12	8	3	1	3	0	1	1	2	2	7	1	4	1	2	2	1	1	2	5	2	rs61735811	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47831621C>T	ENST00000359568.5	+	28	5741	c.5634C>T	c.(5632-5634)gaC>gaT	p.D1878D	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1878					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)					TAGAAATCGACGCTCTGAACC	0.642													C|||	119	0.023762	0.0212	0.0303	5008	,	,		15874	0.001		0.0646	False		,,,				2504	0.0041				p.D1878D		Atlas-SNP	.											PCNT,colon,carcinoma,0,1	PCNT	283	1	0			c.C5634T						PASS	.	C		150,4246		2,146,2050	25	28	27		5634	-11.6	0	21	dbSNP_129	27	514,8068		9,496,3786	no	coding-synonymous	PCNT	NM_006031.5		11,642,5836	TT,TC,CC		5.9893,3.4122,5.1164		1878/3337	47831621	664,12314	2198	4291	6489	SO:0001819	synonymous_variant	5116	exon28			AATCGACGCTCTG	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.5634C>T	21.37:g.47831621C>T		64	0	0		58	29	0.5	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			C|0.953;T|0.047	0.047	strong		0.642	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		T	47831621	C	T	47831621	2	4	26	1	0	0	0	0	0	0	0	1	11599	535	19	1		1	PCNT	21	47831621	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	65508	47831621	298274	651	10414											
PCNT	5116	hgsc.bcm.edu	37	chr21	47841933	47841933	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcccggggtcaggaggcccTgaggctcaaactgctggtcc	7	6	15	13	1	2	1	2	1	0	0	3	2	3	2	3	6	3	2	3	6	1	0	rs61735815	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47841933T>C	ENST00000359568.5	+	32	7181	c.7074T>C	c.(7072-7074)ccT>ccC	p.P2358P	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2358					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)					CAGGAGGCCCTGAGGCTCAAA	0.612													T|||	115	0.0229633	0.0151	0.0303	5008	,	,		15470	0.001		0.0686	False		,,,				2504	0.0041				p.P2358P		Atlas-SNP	.											.	PCNT	283	.	0			c.T7074C						PASS	.	T		137,4269	96.2+/-134.9	3,131,2069	74	79	77		7074	-8.4	0	21	dbSNP_129	77	532,8068	148.5+/-203.7	11,510,3779	no	coding-synonymous	PCNT	NM_006031.5		14,641,5848	CC,CT,TT		6.186,3.1094,5.1438		2358/3337	47841933	669,12337	2203	4300	6503	SO:0001819	synonymous_variant	5116	exon32			AGGCCCTGAGGCT	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.7074T>C	21.37:g.47841933T>C		71	0	0		88	34	0.386364	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			T|0.952;C|0.048	0.048	strong		0.612	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		C	47841933	T	C	47841933	2	2	26	1	0	0	0	0	0	0	0	1	11599	1567	55	3		3	PCNT	21	47841933	Silent	SNP	T	TCGA-G8-6907-01A-11D-2210-10	10312	47841933	287962	652	10415											
PCNT	5116	hgsc.bcm.edu	37	chr21	47841989	47841989	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	catctctggaaggtttcagcCgctgccggaagccatgaagg	9	8	13	11	2	2	1	1	1	1	0	3	3	2	3	3	4	3	2	3	4	3	1	rs61735814	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47841989C>T	ENST00000359568.5	+	32	7237	c.7130C>T	c.(7129-7131)cCg>cTg	p.P2377L	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2377					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)					AGGTTTCAGCCGCTGCCGGAA	0.627													C|||	94	0.01877	0.0008	0.0259	5008	,	,		16400	0.001		0.0676	False		,,,				2504	0.0061				p.P2377L		Atlas-SNP	.											PCNT,NS,carcinoma,+1,1	PCNT	283	1	0			c.C7130T						PASS	.	C	LEU/PRO	61,4345	57.4+/-93.9	1,59,2143	55	56	56		7130	-7.7	0	21	dbSNP_129	56	524,8076	147.1+/-202.6	11,502,3787	yes	missense	PCNT	NM_006031.5	98	12,561,5930	TT,TC,CC		6.093,1.3845,4.4979	benign	2377/3337	47841989	585,12421	2203	4300	6503	SO:0001583	missense	5116	exon32			TTCAGCCGCTGCC	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.7130C>T	21.37:g.47841989C>T	ENSP00000352572:p.Pro2377Leu	53	0	0		73	29	0.39726	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	72	0.03296703296703297	2	0.0040650406504065045	13	0.03591160220994475	1	0.0017482517482517483	56	0.07387862796833773	C	10.31	1.315395	0.23908	0.013845	0.06093	ENSG00000160299	ENST00000359568	T	0.01464	4.86	4.05	-7.69	0.01263	.	.	.	.	.	T	0.00109	0.0003	L	0.40543	1.245	0.09310	N	1	B;P	0.41848	0.0;0.763	B;B	0.24155	0.001;0.051	T	0.45101	-0.9284	9	0.25751	T	0.34	.	0.2513	0.00206	0.3263:0.2474:0.2047:0.2216	rs61735814	2259;2377	O95613-2;O95613	.;PCNT_HUMAN	L	2377	ENSP00000352572:P2377L	ENSP00000352572:P2377L	P	+	2	0	PCNT	46666417	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.156000	0.03160	-1.441000	0.01958	-0.397000	0.06425	CCG	C|0.960;T|0.040	0.040	strong		0.627	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		T	47841989	C	T	47841989	3	4	26	1	0	0	0	0	1	0	0	0	11599	652	23	1	7256	1	PCNT	21	47841989	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	56	47841989	287906	653	10416											
PCNT	5116	hgsc.bcm.edu	37	chr21	47847700	47847700	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gaaaggctggagaagatcatCcgtgagcaggtgagtgtcag	12	7	16	6	1	2	4	2	2	0	2	3	6	3	4	1	3	1	2	1	3	2	0	rs61735817	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47847700C>T	ENST00000359568.5	+	34	7592	c.7485C>T	c.(7483-7485)atC>atT	p.I2495I	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2495					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)					AGAAGATCATCCGTGAGCAGG	0.582													c|||	92	0.0183706	0.0008	0.0259	5008	,	,		19242	0.001		0.0676	False		,,,				2504	0.0041				p.I2495I		Atlas-SNP	.											.	PCNT	283	.	0			c.C7485T						PASS	.	T		60,4346	56.8+/-93.2	1,58,2144	57	57	57		7485	0.3	0	21	dbSNP_129	57	523,8077	146.3+/-201.9	10,503,3787	no	coding-synonymous	PCNT	NM_006031.5		11,561,5931	TT,TC,CC		6.0814,1.3618,4.4825		2495/3337	47847700	583,12423	2203	4300	6503	SO:0001819	synonymous_variant	5116	exon34			GATCATCCGTGAG	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.7485C>T	21.37:g.47847700C>T		55	0	0		43	17	0.395349	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			C|0.958;T|0.042	0.042	strong		0.582	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		T	47847700	C	T	47847700	2	4	26	1	0	0	0	0	0	0	0	1	11599	845	30	2		2	PCNT	21	47847700	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	5711	47847700	282195	654	10417											
PRMT2	3275	hgsc.bcm.edu	37	chr21	48068518	48068518	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tctcttctgtgcacactatgCgcggcctagagcggtgagtg	6	11	13	11	3	2	2	0	1	2	1	3	2	2	2	1	2	3	1	1	2	2	3			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:48068518C>T	ENST00000397637.1	+	5	1430	c.476C>T	c.(475-477)gCg>gTg	p.A159V	PRMT2_ENST00000291705.6_Missense_Mutation_p.A159V|PRMT2_ENST00000355680.3_Missense_Mutation_p.A159V|PRMT2_ENST00000451211.2_Missense_Mutation_p.A159V|PRMT2_ENST00000458387.2_Missense_Mutation_p.A159V|PRMT2_ENST00000397628.1_Missense_Mutation_p.A159V|PRMT2_ENST00000440086.1_Missense_Mutation_p.A159V|PRMT2_ENST00000334494.4_Missense_Mutation_p.A159V|PRMT2_ENST00000397638.2_Missense_Mutation_p.A159V|PRMT2_ENST00000491389.1_3'UTR			P55345	ANM2_HUMAN	protein arginine methyltransferase 2	159	Interaction with ESR1.|Interaction with RB1. {ECO:0000250}.|SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				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)	p.A159V(1)		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)		GCACACTATGCGCGGCCTAGA	0.582																																					p.A159V		Atlas-SNP	.											PRMT2,NS,NS,0,1	PRMT2	48	1	1	Substitution - Missense(1)	NS(1)	c.C476T						PASS	.						148	133	138					21																	48068518		2203	4300	6503	SO:0001583	missense	3275	exon5			ACTATGCGCGGCC	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.476C>T	21.37:g.48068518C>T	ENSP00000380759:p.Ala159Val	131	0	0		139	62	0.446043	NM_001242864	B7U630|B7U631|B7U632|P78350|Q498Y5|Q5U7D4|Q6FHF0|Q99781|Q9BW15|Q9UMC2	Missense_Mutation	SNP	ENST00000397637.1	37	CCDS13737.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	31|31	5.064734|5.064734	0.93898|0.93898	.|.	.|.	ENSG00000160310|ENSG00000160310	ENST00000355680;ENST00000397638;ENST00000458387;ENST00000451211;ENST00000291705;ENST00000397637;ENST00000334494;ENST00000397628;ENST00000440086|ENST00000379844;ENST00000455177	T;T;T;T;T;T;T;T;T|.	0.73152|.	0.82;0.82;-0.54;-0.36;-0.6;0.82;-0.72;-0.71;-0.08|.	5.05|5.05	5.05|5.05	0.67936|0.67936	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.79747|0.79747	0.4499|0.4499	M|M	0.84846|0.84846	2.72|2.72	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D|.	0.89917|.	1.0;1.0;0.999;1.0;1.0;1.0|.	D;D;P;D;D;D|.	0.81914|.	0.975;0.994;0.904;0.993;0.987;0.995|.	D|D	0.83443|0.83443	0.0044|0.0044	10|6	0.87932|0.87932	D|D	0|0	-9.6393|-9.6393	16.2791|16.2791	0.82664|0.82664	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	159;159;159;159;45;159|.	B7U632;B7U630;B7U631;Q498Y5;Q49AF9;P55345|.	.;.;.;.;.;ANM2_HUMAN|.	V|C	159|45;99	ENSP00000347906:A159V;ENSP00000380760:A159V;ENSP00000407463:A159V;ENSP00000411984:A159V;ENSP00000291705:A159V;ENSP00000380759:A159V;ENSP00000335490:A159V;ENSP00000380752:A159V;ENSP00000397266:A159V|.	ENSP00000291705:A159V|ENSP00000369173:R45C	A|R	+|+	2|1	0|0	PRMT2|PRMT2	46892946|46892946	0.999000|0.999000	0.42202|0.42202	0.035000|0.035000	0.18076|0.18076	0.008000|0.008000	0.06430|0.06430	5.491000|5.491000	0.66887|0.66887	2.531000|2.531000	0.85337|0.85337	0.655000|0.655000	0.94253|0.94253	GCG|CGC	.	.	none		0.582	PRMT2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207401.1	NM_001535		T	48068518	C	T	48068518	3	4	26	1	0	0	0	0	1	0	0	0	12549	768	27	1	490	1	PRMT2	21	48068518	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	220818	48068518	61377	655	10418											
DGCR6	8214	hgsc.bcm.edu	37	chr22	18898468	18898468	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatcgtcctggagctggaccGgaaggtggctgaccagcaga	9	6	16	10	2	0	2	0	1	0	1	2	6	1	5	3	5	2	3	3	5	1	0	rs139729355		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:18898468G>A	ENST00000331444.6	+	4	592	c.440G>A	c.(439-441)cGg>cAg	p.R147Q	DGCR6_ENST00000413981.1_Missense_Mutation_p.R11Q|DGCR6_ENST00000436645.1_3'UTR	NM_005675.4	NP_005666.2	Q14129	DGCR6_HUMAN	DiGeorge syndrome critical region gene 6	147					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						GAGCTGGACCGGAAGGTGGCT	0.682													.|||	1	0.000199681	0.0	0.0	5008	,	,		14833	0.0		0.001	False		,,,				2504	0.0				p.R147Q		Atlas-SNP	.											.	DGCR6	12	.	0			c.G440A						PASS	.	G	GLN/ARG	1,4405	4.2+/-10.8	0,1,2202	96	79	84		440	3.3	1	22	dbSNP_134	84	40,8558	26.3+/-74.7	0,40,4259	no	missense	DGCR6	NM_005675.4	43	0,41,6461	AA,AG,GG		0.4652,0.0227,0.3153	benign	147/221	18898468	41,12963	2203	4299	6502	SO:0001583	missense	8214	exon4			TGGACCGGAAGGT	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	ENST00000331444.6:c.440G>A	22.37:g.18898468G>A	ENSP00000331681:p.Arg147Gln	105	0	0		102	46	0.45098	NM_005675	B2RCH5|D3DX15|G5E9J8|Q9BY28	Missense_Mutation	SNP	ENST00000331444.6	37	CCDS13753.1	.	.	.	.	.	.	.	.	.	.	g	10.25	1.299748	0.23650	2.27E-4	0.004652	ENSG00000183628	ENST00000331444;ENST00000436645	T	0.24151	1.87	4.31	3.3	0.37823	.	0.058938	0.64402	D	0.000001	T	0.05044	0.0135	N	0.00569	-1.365	0.41386	D	0.987582	B	0.18741	0.03	B	0.12837	0.008	T	0.39035	-0.9633	10	0.02654	T	1	-40.3259	5.9322	0.19144	0.2095:0.0:0.7905:0.0	.	147	Q14129	DGCR6_HUMAN	Q	147;67	ENSP00000331681:R147Q	ENSP00000331681:R147Q	R	+	2	0	DGCR6	17278468	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.351000	0.59398	2.421000	0.82119	0.430000	0.28490	CGG	G|0.997;A|0.003	0.003	strong		0.682	DGCR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316631.2	NM_005675		A	18898468	G	A	18898468	3	1	26	1	0	0	0	0	1	0	0	0	4464	1116	39	1	454	1	DGCR6	22	18898468	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10		18898468	32406098	656	10419											
ARVCF	421	hgsc.bcm.edu	37	chr22	19969495	19969495	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgtgccatcttcggatgtGacaatagacacatgggaagt	11	11	12	7	1	1	2	0	1	1	1	2	4	1	4	1	2	1	1	1	2	3	3	rs33992092	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:19969495G>T	ENST00000263207.3	-	4	621	c.330C>A	c.(328-330)gtC>gtA	p.V110V	ARVCF_ENST00000406522.1_Silent_p.V47V|ARVCF_ENST00000487793.1_5'UTR|ARVCF_ENST00000401994.1_Silent_p.V47V|ARVCF_ENST00000344269.3_Silent_p.V47V|ARVCF_ENST00000406259.1_Silent_p.V110V	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	110					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)					CTTCGGATGTGACAATAGACA	0.652													G|||	108	0.0215655	0.0711	0.0086	5008	,	,		17773	0.0		0.008	False		,,,				2504	0.0				p.V110V		Atlas-SNP	.											.	ARVCF	54	.	0			c.C330A						PASS	.	G		239,4167	138.8+/-174.5	7,225,1971	123	94	104		330	1.3	1	22	dbSNP_126	104	38,8562	26.3+/-74.7	0,38,4262	no	coding-synonymous	ARVCF	NM_001670.2		7,263,6233	TT,TG,GG		0.4419,5.4244,2.1298		110/963	19969495	277,12729	2203	4300	6503	SO:0001819	synonymous_variant	421	exon4			GGATGTGACAATA		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.330C>A	22.37:g.19969495G>T		194	0	0		229	108	0.471616	NM_001670	B7WNV2	Silent	SNP	ENST00000263207.3	37	CCDS13771.1																																																																																			G|0.979;T|0.021	0.021	strong		0.652	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670		T	19969495	G	T	19969495	2	4	26	1	0	0	0	0	0	0	0	1	1003	1277	45	4		4	ARVCF	22	19969495	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1071027	19969495	31335071	657	10420											
ARVCF	421	hgsc.bcm.edu	37	chr22	19969587	19969587	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcctccggcatcgtggccaGtgaggcctggctgcctgggc	3	8	16	14	2	0	1	0	1	0	0	2	1	1	1	5	5	2	2	5	5	0	0	rs372955497		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:19969587G>A	ENST00000263207.3	-	4	529	c.238C>T	c.(238-240)Ctg>Ttg	p.L80L	ARVCF_ENST00000406522.1_Silent_p.L17L|ARVCF_ENST00000487793.1_5'UTR|ARVCF_ENST00000401994.1_Silent_p.L17L|ARVCF_ENST00000344269.3_Silent_p.L17L|ARVCF_ENST00000406259.1_Silent_p.L80L	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	80					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)					ATCGTGGCCAGTGAGGCCTGG	0.642																																					p.L80L		Atlas-SNP	.											.	ARVCF	54	.	0			c.C238T						PASS	.	G		0,4404		0,0,2202	71	62	65		238	2.4	0.9	22		65	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	ARVCF	NM_001670.2		0,3,6499	AA,AG,GG		0.0349,0.0,0.0231		80/963	19969587	3,13001	2202	4300	6502	SO:0001819	synonymous_variant	421	exon4			TGGCCAGTGAGGC		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.238C>T	22.37:g.19969587G>A		88	0	0		118	55	0.466102	NM_001670	B7WNV2	Silent	SNP	ENST00000263207.3	37	CCDS13771.1																																																																																			.	.	weak		0.642	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670		A	19969587	G	A	19969587	2	1	26	1	0	0	0	0	0	0	0	1	1003	1020	36	2		2	ARVCF	22	19969587	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	92	19969587	31334979	658	10421											
MED15	51586	hgsc.bcm.edu	37	chr22	20920813	20920814	+	In_Frame_Ins	INS	-	-	CAGCAGCAGCAG																															tgcagctccaacaacagcaaINScagcagcagcagcagcagca																								rs67182670|rs361923|rs535773989|rs539945336	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:20920813_20920814insCAGCAGCAGCAG	ENST00000263205.7	+	7	819_820	c.750_751insCAGCAGCAGCAG	c.(751-753)cag>CAGCAGCAGCAGcag	p.251_251Q>QQQQQ	MED15_ENST00000425759.2_In_Frame_Ins_p.140_140Q>QQQQQ|MED15_ENST00000382974.2_In_Frame_Ins_p.180_180Q>QQQQQ|MED15_ENST00000542773.1_In_Frame_Ins_p.56_56Q>QQQQQ|MED15_ENST00000478831.1_3'UTR|MED15_ENST00000541476.1_In_Frame_Ins_p.225_225Q>QQQQQ|MED15_ENST00000406969.1_In_Frame_Ins_p.225_225Q>QQQQQ|MED15_ENST00000292733.7_In_Frame_Ins_p.251_251Q>QQQQQ	NM_001003891.1	NP_001003891.1	Q96RN5	MED15_HUMAN	mediator complex subunit 15	251	Poly-Gln.			Missing (in Ref. 3; BAB85034). {ECO:0000305}.	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.Q250_Q251insQ(4)		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)			aacaacagcaacagcagcagca	0.589																																					p.Q250delinsQQQQQ		Atlas-Indel	.											PCQAP,caecum,carcinoma,0,2	MED15	68	2	4	Insertion - In frame(4)	ovary(2)|large_intestine(2)	c.750_751insCAGCAGCAGCAG						PASS	.																																			SO:0001652	inframe_insertion	51586	exon7			.	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.775_786dupCAGCAGCAGCAG	22.37:g.20920813_20920814insCAGCAGCAGCAG	ENSP00000263205:p.GlnGlnGlnGln259dup	62	0	0		70	13	0.185714	NM_015889	D3DX31|D3DX32|O15413|Q6IC31|Q8NF16|Q96CT0|Q96IH7|Q9P1T3	In_Frame_Ins	INS	ENST00000263205.7	37	CCDS33602.1																																																																																			.	.	alt		0.589	MED15-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320177.2	NM_015889		CAGCAGCAGCAG	20920814	-	CAGCAGCAGCAG	20920813	7	5	26	1	0	1	1	0	0	0	0	0	9442	40	2	0	776	0	MED15	22	20920813	In_Frame_Ins	INS	-	TCGA-G8-6907-01A-11D-2210-10	951226	20920813	30383753	659	10422											
SGSM1	129049	hgsc.bcm.edu	37	chr22	25264353	25264353	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggcggcagttgacagcggCgggacagtggtattggtcag	7	8	19	7	3	1	1	1	1	0	0	1	2	1	2	0	6	1	3	0	6	1	3	rs61744681	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:25264353C>T	ENST00000400359.4	+	11	1012	c.1005C>T	c.(1003-1005)ggC>ggT	p.G335G	SGSM1_ENST00000400358.4_Silent_p.G335G	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	335	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						TTGACAGCGGCGGGACAGTGG	0.642													C|||	16	0.00319489	0.0	0.0101	5008	,	,		16926	0.002		0.007	False		,,,				2504	0.0				p.G335G		Atlas-SNP	.											.	SGSM1	150	.	0			c.C1005T						PASS	.	C	,,,	9,4055		0,9,2023	32	37	35		1005,1005,1005,1005	-9.8	0.5	22	dbSNP_129	35	93,8267		2,89,4089	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SGSM1	NM_001039948.2,NM_001098497.1,NM_001098498.1,NM_133454.2	,,,	2,98,6112	TT,TC,CC		1.1124,0.2215,0.821	,,,	335/1149,335/1094,335/1033,335/1088	25264353	102,12322	2032	4180	6212	SO:0001819	synonymous_variant	129049	exon11			CAGCGGCGGGACA	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.1005C>T	22.37:g.25264353C>T		114	0	0		138	64	0.463768	NM_001098497	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Silent	SNP	ENST00000400359.4	37	CCDS46674.1																																																																																			C|0.993;T|0.007	0.007	strong		0.642	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	XM_059318		T	25264353	C	T	25264353	2	4	26	1	0	0	0	0	0	0	0	1	14237	755	27	1		1	SGSM1	22	25264353	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	4343540	25264353	26040213	660	10423											
MYO18B	84700	hgsc.bcm.edu	37	chr22	26304363	26304363	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaccgtgaggaccaggaggaGgaactggaggatgtccgtca	11	5	17	8	2	1	1	1	1	0	0	2	8	2	7	3	6	1	0	3	6	1	0	rs58609797	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:26304363G>A	ENST00000407587.2	+	32	5395	c.5226G>A	c.(5224-5226)gaG>gaA	p.E1742E	MYO18B_ENST00000335473.7_Silent_p.E1741E|MYO18B_ENST00000536101.1_Silent_p.E1741E			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1741	Gln-rich.|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						ACCAGGAGGAGGAACTGGAGG	0.607													G|||	259	0.0517173	0.1589	0.0159	5008	,	,		19484	0.0		0.0219	False		,,,				2504	0.0164				p.E1741E		Atlas-SNP	.											.	MYO18B	322	.	0			c.G5223A						PASS	.	G		439,3823		21,397,1713	54	66	62		5223	-0.9	1	22	dbSNP_129	62	122,8348		2,118,4115	no	coding-synonymous	MYO18B	NM_032608.5		23,515,5828	AA,AG,GG		1.4404,10.3003,4.4062		1741/2568	26304363	561,12171	2131	4235	6366	SO:0001819	synonymous_variant	84700	exon32			GGAGGAGGAACTG	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.5226G>A	22.37:g.26304363G>A		67	0	0		84	40	0.47619	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37																																																																																				G|0.952;A|0.048	0.048	strong		0.607	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		A	26304363	G	A	26304363	2	1	26	1	0	0	0	0	0	0	0	1	10075	991	35	2		2	MYO18B	22	26304363	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1040010	26304363	25000203	661	10424											
KREMEN1	83999	hgsc.bcm.edu	37	chr22	29521353	29521353	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aatgcaacagcgtctgcttcGgggatcacacccaaccctgt	10	8	9	14	2	2	0	1	0	1	0	3	1	2	1	2	2	5	2	2	2	3	1			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:29521353G>A	ENST00000407188.1	+	5	574	c.574G>A	c.(574-576)Ggg>Agg	p.G192R	KREMEN1_ENST00000327813.5_Missense_Mutation_p.G194R|KREMEN1_ENST00000400335.4_Missense_Mutation_p.G194R|KREMEN1_ENST00000400338.2_Missense_Mutation_p.G194R			Q96MU8	KREM1_HUMAN	kringle containing transmembrane protein 1	192	WSC. {ECO:0000255|PROSITE- ProRule:PRU00558}.				cell communication (GO:0007154)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	20						CGTCTGCTTCGGGGATCACAC	0.552																																					p.G194R		Atlas-SNP	.											.	KREMEN1	46	.	0			c.G580A						PASS	.						165	170	168					22																	29521353		2146	4261	6407	SO:0001583	missense	83999	exon5			TGCTTCGGGGATC	AB059618	CCDS43000.1, CCDS13849.1, CCDS43000.2	22q12.1	2008-03-27	2002-11-13	2002-11-15	ENSG00000183762	ENSG00000183762			17550	protein-coding gene	gene with protein product		609898	"kringle containing transmembrane protein"	KREMEN		11267660	Standard	NM_001039570		Approved	KRM1	uc011akm.1	Q96MU8	OTTHUMG00000030987	ENST00000407188.1:c.574G>A	22.37:g.29521353G>A	ENSP00000385431:p.Gly192Arg	116	0	0		146	67	0.458904	NM_001039570	B0QY46|B0QY47|B1AJR5|Q5TIB9|Q6P3X6|Q9BY70|Q9UGS5|Q9UGU1	Missense_Mutation	SNP	ENST00000407188.1	37	CCDS43000.2	.	.	.	.	.	.	.	.	.	.	G	23.7	4.442407	0.83993	.	.	ENSG00000183762	ENST00000400335;ENST00000400338;ENST00000327813;ENST00000407188	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	5.74	4.73	0.59995	Carbohydrate-binding WSC (2);	0.000000	0.64402	D	0.000006	D	0.84906	0.5576	M	0.92970	3.365	0.58432	D	0.999999	D;D;B	0.89917	1.0;1.0;0.357	D;D;B	0.97110	1.0;1.0;0.072	D	0.88314	0.2958	10	0.87932	D	0	.	12.87	0.57960	0.079:0.0:0.921:0.0	.	192;194;194	Q96MU8;Q96MU8-2;Q96MU8-3	KREM1_HUMAN;.;.	R	194;194;194;192	ENSP00000383189:G194R;ENSP00000383192:G194R;ENSP00000331242:G194R;ENSP00000385431:G192R	ENSP00000331242:G194R	G	+	1	0	KREMEN1	27851353	1.000000	0.71417	0.997000	0.53966	0.790000	0.44656	9.146000	0.94640	1.579000	0.49836	0.650000	0.86243	GGG	.	.	none		0.552	KREMEN1-004	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320947.1			A	29521353	G	A	29521353	3	1	26	1	0	0	0	0	1	0	0	0	8451	1116	39	1	598	1	KREMEN1	22	29521353	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	3216990	29521353	21783213	662	10425											
ISX	91464	hgsc.bcm.edu	37	chr22	35478529	35478529	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agaaggaaggaagagcaagcGgagggttcgtaccaccttca	14	5	14	8	2	1	2	1	0	0	2	2	5	1	5	2	4	3	3	2	4	5	3	rs8140287	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:35478529G>A	ENST00000308700.6	+	2	1200	c.248G>A	c.(247-249)cGg>cAg	p.R83Q	ISX_ENST00000404699.2_Missense_Mutation_p.R83Q	NM_001008494.1	NP_001008494.1	Q2M1V0	ISX_HUMAN	intestine-specific homeobox	83			R -> Q (in dbSNP:rs8140287).		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						AAGAGCAAGCGGAGGGTTCGT	0.557													G|||	154	0.0307508	0.0023	0.0317	5008	,	,		20015	0.003		0.0557	False		,,,				2504	0.0716				p.R83Q		Atlas-SNP	.											.	ISX	62	.	0			c.G248A						PASS	.	G	GLN/ARG	51,4355	52.9+/-88.7	0,51,2152	142	115	124		248	4.9	0.7	22	dbSNP_116	124	462,8138	137.6+/-194.5	13,436,3851	yes	missense	ISX	NM_001008494.1	43	13,487,6003	AA,AG,GG		5.3721,1.1575,3.9443	probably-damaging	83/246	35478529	513,12493	2203	4300	6503	SO:0001583	missense	91464	exon2			GCAAGCGGAGGGT	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.248G>A	22.37:g.35478529G>A	ENSP00000311492:p.Arg83Gln	42	0	0		81	45	0.555556	NM_001008494	Q68DJ5	Missense_Mutation	SNP	ENST00000308700.6	37	CCDS33640.1	56	0.02564102564102564	0	0.0	8	0.022099447513812154	1	0.0017482517482517483	47	0.06200527704485488	G	28.4	4.916181	0.92249	0.011575	0.053721	ENSG00000175329	ENST00000308700;ENST00000404699	D;D	0.97209	-4.29;-4.29	4.94	4.94	0.65067	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.47852	D	0.000205	D	0.91878	0.7429	M	0.93898	3.47	0.54753	D	0.99998	D	0.89917	1.0	D	0.91635	0.999	D	0.85305	0.1075	10	0.40728	T	0.16	.	15.6832	0.77388	0.0:0.0:1.0:0.0	rs8140287;rs52820185;rs8140287	83	Q2M1V0	ISX_HUMAN	Q	83	ENSP00000311492:R83Q;ENSP00000386037:R83Q	ENSP00000311492:R83Q	R	+	2	0	ISX	33808529	1.000000	0.71417	0.702000	0.30337	0.788000	0.44548	8.758000	0.91663	2.545000	0.85829	0.650000	0.86243	CGG	G|0.965;A|0.035	0.035	strong		0.557	ISX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320662.1	NM_001008494		A	35478529	G	A	35478529	3	1	26	1	0	0	0	0	1	0	0	0	7874	1116	39	1	254	1	ISX	22	35478529	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	5957176	35478529	15826037	663	10426											
MYH9	4627	hgsc.bcm.edu	37	chr22	36685329	36685329	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tacttggcagagatggtcttCtcctccgccaggagctggga	7	10	13	11	1	2	1	0	0	2	1	4	4	3	3	3	4	2	2	3	4	1	3	rs202127454		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:36685329C>T	ENST00000216181.5	-	32	4589	c.4359G>A	c.(4357-4359)gaG>gaA	p.E1453E		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1453					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						AGATGGTCTTCTCCTCCGCCA	0.677			T	ALK	ALCL		"Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"		Hereditary Macrothrombocytopenia, MYH9-associated				C|||	1	0.000199681	0.0	0.0	5008	,	,		19418	0.0		0.001	False		,,,				2504	0.0				p.E1453E		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"myosin, heavy polypeptide 9, non-muscle"	yes	L	.	MYH9	225	.	0			c.G4359A						PASS	.	C		0,4406		0,0,2203	22	20	21		4359	4	1	22		21	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	MYH9	NM_002473.4		0,5,6498	TT,TC,CC		0.0581,0.0,0.0384		1453/1961	36685329	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	4627	exon32	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	GGTCTTCTCCTCC		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.4359G>A	22.37:g.36685329C>T		55	0	0		57	22	0.385965	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Silent	SNP	ENST00000216181.5	37	CCDS13927.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	9.292	1.050864	0.19827	0.0	5.81E-4	ENSG00000100345	ENST00000397231	.	.	.	5.02	4.01	0.46588	.	.	.	.	.	T	0.31136	0.0787	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.12993	-1.0526	5	0.02654	T	1	.	9.9391	0.41570	0.0:0.8436:0.0:0.1564	.	.	.	.	K	56	.	ENSP00000380408:R56K	R	-	2	0	MYH9	35015275	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.320000	0.51991	1.253000	0.44018	0.491000	0.48974	AGA	C|1.000;T|0.000	0.000	strong		0.677	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473		T	36685329	C	T	36685329	2	4	26	1	0	0	0	0	0	0	0	1	10051	912	32	2		2	MYH9	22	36685329	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1206800	36685329	14619237	664	10427											
MYH9	4627	hgsc.bcm.edu	37	chr22	36708244	36708244	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cagcactcctcgtccagcagGgccagaatgcccggggggcc	7	4	14	16	2	0	1	0	0	0	1	3	1	2	1	5	4	3	2	5	4	1	0	rs201827299		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:36708244G>C	ENST00000216181.5	-	14	1808	c.1578C>G	c.(1576-1578)gcC>gcG	p.A526A		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	526	Myosin motor.				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						CGTCCAGCAGGGCCAGAATGC	0.647			T	ALK	ALCL		"Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"		Hereditary Macrothrombocytopenia, MYH9-associated				G|||	1	0.000199681	0.0	0.0	5008	,	,		16777	0.0		0.001	False		,,,				2504	0.0				p.A526A		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"myosin, heavy polypeptide 9, non-muscle"	yes	L	.	MYH9	225	.	0			c.C1578G						PASS	.						67	60	62					22																	36708244		2203	4300	6503	SO:0001819	synonymous_variant	4627	exon14	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	CAGCAGGGCCAGA		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.1578C>G	22.37:g.36708244G>C		71	0	0		92	50	0.543478	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Silent	SNP	ENST00000216181.5	37	CCDS13927.1																																																																																			G|1.000;C|0.000	0.000	strong		0.647	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473		C	36708244	G	C	36708244	2	2	26	1	0	0	0	0	0	0	0	1	10051	1219	43	4		4	MYH9	22	36708244	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	22915	36708244	14596322	665	10428											
SH3BP1	23616	hgsc.bcm.edu	37	chr22	38044341	38044341	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cttaggtacctgatgaagttCctggcacggctggccgagga	8	9	14	10	2	0	2	0	2	0	0	1	4	1	3	3	5	1	4	3	5	3	3	rs118183308	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:38044341C>T	ENST00000357436.4	+	14	1528	c.1215C>T	c.(1213-1215)ttC>ttT	p.F405F	Z83844.1_ENST00000456099.1_RNA|SH3BP1_ENST00000442465.2_Silent_p.F405F|SH3BP1_ENST00000599616.1_Silent_p.F341F|SH3BP1_ENST00000336738.5_Silent_p.F405F	NM_018957.3	NP_061830.3	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	405	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				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)					TGATGAAGTTCCTGGCACGGC	0.582													C|||	45	0.00898562	0.0008	0.0274	5008	,	,		17464	0.0		0.0239	False		,,,				2504	0.001				p.F405F		Atlas-SNP	.											SH3BP1,NS,haematopoietic_neoplasm,0,1	SH3BP1	41	1	0			c.C1215T						PASS	.	C		14,4384		0,14,2185	42	34	37		1215	4.2	1	22	dbSNP_132	37	161,8435		0,161,4137	no	coding-synonymous	SH3BP1	NM_018957.3		0,175,6322	TT,TC,CC		1.873,0.3183,1.3468		405/702	38044341	175,12819	2199	4298	6497	SO:0001819	synonymous_variant	23616	exon14			GAAGTTCCTGGCA		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.1215C>T	22.37:g.38044341C>T		26	0	0		23	13	0.565217	NM_018957	Q5R3N0|Q6IBZ2|Q6ZVL9|Q96HQ5|Q9NSQ9	Silent	SNP	ENST00000357436.4	37	CCDS13952.2																																																																																			C|0.986;T|0.014	0.014	strong		0.582	SH3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075884.4	NM_018957		T	38044341	C	T	38044341	2	4	26	1	0	0	0	0	0	0	0	1	14259	854	30	2		2	SH3BP1	22	38044341	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1336097	38044341	13260225	666	10429											
SLC16A8	23539	hgsc.bcm.edu	37	chr22	38478666	38478666	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gggccgggcggggacactgaCccgtgccgtagagcatggct	6	5	18	12	4	0	2	0	1	0	1	0	3	0	3	3	5	2	3	3	5	1	1	rs77968014	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:38478666C>G	ENST00000320521.5	-	2	323		c.e2+1		SLC16A8_ENST00000469516.1_Intron	NM_013356.2	NP_037488.2	O95907	MOT3_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 8						blood coagulation (GO:0007596)|cellular metabolic process (GO:0044237)|lactate transmembrane transport (GO:0035873)|lactate transport (GO:0015727)|leukocyte migration (GO:0050900)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lactate transmembrane transporter activity (GO:0015129)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			kidney(1)|large_intestine(1)|prostate(1)	3	Melanoma(58;0.045)				Pyruvic acid(DB00119)	GGGACACTGACCCGTGCCGTA	0.701													C|||	17	0.00339457	0.0	0.0058	5008	,	,		12685	0.0		0.0119	False		,,,				2504	0.001				.		Atlas-SNP	.											.	SLC16A8	13	.	0			c.214+1G>C						PASS	.	C		5,4307		0,5,2151	7	9	8			4.2	1	22	dbSNP_132	8	51,8433		0,51,4191	yes	splice-5	SLC16A8	NM_013356.2		0,56,6342	GG,GC,CC		0.6011,0.116,0.4376			38478666	56,12740	2156	4242	6398	SO:0001630	splice_region_variant	23539	exon3			CACTGACCCGTGC	AF132610	CCDS13966.1	22q12.3-q13.2	2013-07-18	2013-07-18		ENSG00000100156	ENSG00000100156		"Solute carriers"	16270	protein-coding gene	gene with protein product	"monocarboxylate transporter 3"	610409	"solute carrier 16 (monocarboxylic acid transporters), member 8"			10493836	Standard	NM_013356		Approved	MCT3, REMP	uc003auu.3	O95907	OTTHUMG00000151196	ENST00000320521.5:c.214+1G>C	22.37:g.38478666C>G		38	0	0		57	32	0.561404	NM_013356	Q9UBE2	Splice_Site	SNP	ENST00000320521.5	37	CCDS13966.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	21.4	4.146560	0.77888	0.00116	0.006011	ENSG00000100156	ENST00000320521;ENST00000427592	.	.	.	4.23	4.23	0.50019	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.0149	0.86415	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLC16A8	36808612	1.000000	0.71417	0.975000	0.42487	0.835000	0.47333	7.622000	0.83099	2.094000	0.63399	0.485000	0.47835	.	C|0.997;G|0.003	0.003	strong		0.701	SLC16A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321724.1	NM_013356	Intron	G	38478666	C	G	38478666	5	3	26	1	0	0	0	0	0	0	1	0	14429	521	18	4	1315	4	SLC16A8	22	38478666	Splice_Site	SNP	C	TCGA-G8-6907-01A-11D-2210-10	434325	38478666	12825900	667	10430											
TAB1	10454	hgsc.bcm.edu	37	chr22	39813800	39813800	+	Missense_Mutation	SNP	G	G	A																															agagggaaatttcgggagggGccatggccgttgtggcggtc																										TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:39813800G>A	ENST00000216160.6	+	5	558	c.496G>A	c.(496-498)Gcc>Acc	p.A166T	TAB1_ENST00000331454.3_Missense_Mutation_p.A166T	NM_006116.2	NP_006107.1	Q15750	TAB1_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 1	166	PP2C-like.				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						TTCGGGAGGGGCCATGGCCGT	0.577																																					p.A166T		Atlas-SNP	.											.	TAB1	36	.	0			c.G496A						PASS	.						86	73	77					22																	39813800		2203	4300	6503	SO:0001583	missense	10454	exon5			GGAGGGGCCATGG	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.496G>A	22.37:g.39813800G>A	ENSP00000216160:p.Ala166Thr	108	0	0		131	68	0.519084	NM_153497	Q2PP09|Q8IZW2	Missense_Mutation	SNP	ENST00000216160.6	37	CCDS13993.1	.	.	.	.	.	.	.	.	.	.	G	18.07	3.541345	0.65085	.	.	ENSG00000100324	ENST00000216160;ENST00000331454	T;T	0.05382	3.45;3.45	5.34	5.34	0.76211	Protein phosphatase 2C-like (4);	0.225313	0.44097	D	0.000492	T	0.11324	0.0276	N	0.16098	0.37	0.80722	D	1	B;B;D	0.71674	0.017;0.29;0.998	B;B;D	0.81914	0.015;0.173;0.995	T	0.31971	-0.9924	10	0.07030	T	0.85	.	19.0356	0.92976	0.0:0.0:1.0:0.0	.	166;166;310	Q15750-2;Q15750;Q59FT7	.;TAB1_HUMAN;.	T	166	ENSP00000216160:A166T;ENSP00000333049:A166T	ENSP00000216160:A166T	A	+	1	0	TAB1	38143746	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	8.488000	0.90458	2.496000	0.84212	0.655000	0.94253	GCC	.	.	none		0.577	TAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321313.1	NM_153497		A	39813800	G	A	39813800	3	1	26	1	0	0	0	0	1	0	0	0	15510	1203	42	2	514	2	TAB1	22	39813800	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1335134	39813800	11490766	668	10431	131	2									
TAB1	10454	hgsc.bcm.edu	37	chr22	39813801	39813801	+	Missense_Mutation	SNP	C	C	A																															gagggaaatttcgggaggggCcatggccgttgtggcggtcc																										TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:39813801C>A	ENST00000216160.6	+	5	559	c.497C>A	c.(496-498)gCc>gAc	p.A166D	TAB1_ENST00000331454.3_Missense_Mutation_p.A166D	NM_006116.2	NP_006107.1	Q15750	TAB1_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 1	166	PP2C-like.				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						TCGGGAGGGGCCATGGCCGTT	0.577																																					p.A166D		Atlas-SNP	.											.	TAB1	36	.	0			c.C497A						PASS	.						86	73	77					22																	39813801		2203	4300	6503	SO:0001583	missense	10454	exon5			GAGGGGCCATGGC	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.497C>A	22.37:g.39813801C>A	ENSP00000216160:p.Ala166Asp	109	0	0		129	66	0.511628	NM_153497	Q2PP09|Q8IZW2	Missense_Mutation	SNP	ENST00000216160.6	37	CCDS13993.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.967710	0.92855	.	.	ENSG00000100324	ENST00000216160;ENST00000331454	T;T	0.10960	2.82;2.82	5.34	5.34	0.76211	Protein phosphatase 2C-like (4);	0.225313	0.44097	D	0.000492	T	0.36248	0.0960	M	0.76170	2.325	0.80722	D	1	P;P;D	0.89917	0.944;0.814;1.0	P;B;D	0.87578	0.531;0.393;0.998	T	0.10109	-1.0644	10	0.72032	D	0.01	.	19.0356	0.92976	0.0:1.0:0.0:0.0	.	166;166;310	Q15750-2;Q15750;Q59FT7	.;TAB1_HUMAN;.	D	166	ENSP00000216160:A166D;ENSP00000333049:A166D	ENSP00000216160:A166D	A	+	2	0	TAB1	38143747	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.726000	0.74758	2.496000	0.84212	0.655000	0.94253	GCC	.	.	none		0.577	TAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321313.1	NM_153497		A	39813801	C	A	39813801	3	1	26	1	0	0	0	0	1	0	0	0	15510	739	26	4	515	4	TAB1	22	39813801	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	1	39813801	11490765	669	10432	131	2									
TTC38	55020	hgsc.bcm.edu	37	chr22	46669924	46669924	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aacccagccgctgacaaggcGggagcagctgcacgtgtctg	9	5	14	13	3	1	1	0	1	1	0	1	2	1	2	2	2	5	4	2	2	2	0			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:46669924G>A	ENST00000381031.3	+	4	399	c.323G>A	c.(322-324)cGg>cAg	p.R108Q	TTC38_ENST00000445282.2_Missense_Mutation_p.R108Q	NM_017931.2	NP_060401	Q5R3I4	TTC38_HUMAN	tetratricopeptide repeat domain 38	108						extracellular vesicular exosome (GO:0070062)				endometrium(4)|large_intestine(3)|lung(4)|ovary(1)	12						CTGACAAGGCGGGAGCAGCTG	0.602																																					p.R108Q		Atlas-SNP	.											.	TTC38	40	.	0			c.G323A						PASS	.						46	52	50					22																	46669924		2080	4217	6297	SO:0001583	missense	55020	exon4			CAAGGCGGGAGCA		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.323G>A	22.37:g.46669924G>A	ENSP00000370419:p.Arg108Gln	86	0	0		116	56	0.482759	NM_017931	Q8WV27|Q9NWP8	Missense_Mutation	SNP	ENST00000381031.3	37	CCDS43030.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.249754	0.80024	.	.	ENSG00000075234	ENST00000381031;ENST00000445282;ENST00000421359	T;T;T	0.67865	0.97;0.24;-0.29	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.84188	0.5417	M	0.85710	2.77	0.24599	N	0.993783	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.995	T	0.78427	-0.2208	10	0.62326	D	0.03	-0.2222	18.5029	0.90888	0.0:0.0:1.0:0.0	.	108;108	E7ES35;Q5R3I4	.;TTC38_HUMAN	Q	108	ENSP00000370419:R108Q;ENSP00000393960:R108Q;ENSP00000410095:R108Q	ENSP00000370419:R108Q	R	+	2	0	TTC38	45048588	1.000000	0.71417	0.595000	0.28798	0.086000	0.17979	9.017000	0.93651	2.596000	0.87737	0.650000	0.86243	CGG	.	.	none		0.602	TTC38-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000318469.1	NM_017931		A	46669924	G	A	46669924	3	1	26	1	0	0	0	0	1	0	0	0	16721	1116	39	1	337	1	TTC38	22	46669924	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	6856123	46669924	4634642	670	10433											
ALG12	79087	hgsc.bcm.edu	37	chr22	50301430	50301430	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaaggcatagatgatgaagcGtagctccttgtgtggcagga	11	9	15	6	1	0	3	0	2	0	1	1	5	1	4	1	3	2	4	1	3	4	3			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50301430G>A	ENST00000330817.6	-	7	1204	c.931C>T	c.(931-933)Cgc>Tgc	p.R311C		NM_024105.3	NP_077010.1	Q9BV10	ALG12_HUMAN	ALG12, alpha-1,6-mannosyltransferase	311					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|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)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alpha-1,6-mannosyltransferase activity (GO:0000009)|dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase activity (GO:0052917)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(3)	12		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)		BRCA - Breast invasive adenocarcinoma(115;0.199)|LUAD - Lung adenocarcinoma(64;0.247)		ATGATGAAGCGTAGCTCCTTG	0.547																																					p.R311C		Atlas-SNP	.											.	ALG12	35	.	0			c.C931T	GRCh37	CM050360	ALG12	M		PASS	.						125	109	115					22																	50301430		2203	4300	6503	SO:0001583	missense	79087	exon7			TGAAGCGTAGCTC	AJ303120	CCDS14081.1	22q13.33	2013-02-26	2013-02-26		ENSG00000182858	ENSG00000182858	2.4.1.260	"Dolichyl D-mannosyl phosphate dependent mannosyltransferases"	19358	protein-coding gene	gene with protein product	"dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichol alpha-1,6-mannosyltransferase", "dol-P-Man dependent alpha-1,6-mannosyltransferase"	607144	"asparagine-linked glycosylation 12 homolog (yeast, alpha-1,6-mannosyltransferase)", "asparagine-linked glycosylation 12, alpha-1,6-mannosyltransferase homolog (S. cerevisiae)"			11983712	Standard	NM_024105		Approved	ECM39	uc003biy.3	Q9BV10	OTTHUMG00000150289	ENST00000330817.6:c.931C>T	22.37:g.50301430G>A	ENSP00000333813:p.Arg311Cys	145	0	0		167	85	0.508982	NM_024105	A6PWM1|Q4KMH4|Q8NG10|Q96AA4	Missense_Mutation	SNP	ENST00000330817.6	37	CCDS14081.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.35|17.35	3.368561|3.368561	0.61624|0.61624	.|.	.|.	ENSG00000182858|ENSG00000182858	ENST00000330817|ENST00000486602	D|.	0.91351|.	-2.83|.	4.28|4.28	4.28|4.28	0.50868|0.50868	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.87111|0.87111	0.6096|0.6096	H|H	0.95470|0.95470	3.675|3.675	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	D|D	0.91436|0.91436	0.5170|0.5170	10|5	0.87932|.	D|.	0|.	-9.9379|-9.9379	17.2733|17.2733	0.87109|0.87109	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	311|.	Q9BV10|.	ALG12_HUMAN|.	C|M	311|46	ENSP00000333813:R311C|.	ENSP00000333813:R311C|.	R|T	-|-	1|2	0|0	ALG12|ALG12	48687434|48687434	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.041000|0.041000	0.13682|0.13682	9.334000|9.334000	0.96470|0.96470	2.378000|2.378000	0.81104|0.81104	0.655000|0.655000	0.94253|0.94253	CGC|ACG	.	.	none		0.547	ALG12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317405.2	NM_024105		A	50301430	G	A	50301430	3	1	26	1	0	0	0	0	1	0	0	0	514	1145	40	1	551	1	ALG12	22	50301430	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	3631506	50301430	1003136	671	10434											
TUBGCP6	85378	hgsc.bcm.edu	37	chr22	50659025	50659025	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggaaaccacatccgacacagGctcccccaagctgatgctgg	11	5	10	15	1	0	1	0	1	0	0	2	3	2	2	4	3	3	3	4	3	2	0			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50659025G>T	ENST00000248846.5	-	16	3867	c.3763C>A	c.(3763-3765)Cct>Act	p.P1255T	TUBGCP6_ENST00000439308.2_Missense_Mutation_p.P1255T|TUBGCP6_ENST00000491449.1_5'UTR			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	1255	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)		TCCGACACAGGCTCCCCCAAG	0.637																																					p.P1255T		Atlas-SNP	.											.	TUBGCP6	132	.	0			c.C3763A						PASS	.						68	53	58					22																	50659025		2203	4300	6503	SO:0001583	missense	85378	exon16			ACACAGGCTCCCC	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.3763C>A	22.37:g.50659025G>T	ENSP00000248846:p.Pro1255Thr	61	0	0		81	35	0.432099	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Missense_Mutation	SNP	ENST00000248846.5	37	CCDS14087.1	.	.	.	.	.	.	.	.	.	.	g	6.032	0.374231	0.11409	.	.	ENSG00000128159	ENST00000248846;ENST00000439308	T;T	0.11063	3.19;2.81	3.02	-0.545	0.11843	.	2.098260	0.03949	U	0.288172	T	0.05456	0.0144	N	0.08118	0	0.09310	N	1	B;B;B	0.16166	0.016;0.004;0.012	B;B;B	0.18561	0.013;0.013;0.022	T	0.36890	-0.9729	10	0.07644	T	0.81	.	8.0715	0.30691	0.0:0.0962:0.5704:0.3334	.	1247;1255;1255	B2RWN4;Q96RT7;Q96RT7-3	.;GCP6_HUMAN;.	T	1255	ENSP00000248846:P1255T;ENSP00000397387:P1255T	ENSP00000248846:P1255T	P	-	1	0	TUBGCP6	49001152	0.000000	0.05858	0.002000	0.10522	0.010000	0.07245	-0.481000	0.06552	-0.178000	0.10672	-0.578000	0.04140	CCT	.	.	none		0.637	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461		T	50659025	G	T	50659025	3	4	26	1	0	0	0	0	1	0	0	0	16785	1203	42	4	1736	4	TUBGCP6	22	50659025	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	357595	50659025	645541	672	10435											
CSF2RA	1438	hgsc.bcm.edu	37	chrX	1413300	1413300	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggtggaaacagcccaggacCtatcagaagctgtcgtacct	11	7	11	12	2	1	1	1	0	0	1	2	3	1	3	3	3	4	2	3	3	4	2			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:1413300C>A	ENST00000381524.3	+	8	912	c.726C>A	c.(724-726)acC>acA	p.T242T	BX649553.3_ENST00000581137.1_RNA|CSF2RA_ENST00000381500.1_Silent_p.T242T|BX649553.2_ENST00000578699.1_RNA|CSF2RA_ENST00000417535.2_Silent_p.T242T|CSF2RA_ENST00000498153.1_3'UTR|MIR3690_ENST00000580266.1_RNA|CSF2RA_ENST00000494969.2_Intron|CSF2RA_ENST00000355432.3_Silent_p.T242T|CSF2RA_ENST00000432318.2_Silent_p.T242T|CSF2RA_ENST00000355805.2_Intron|CSF2RA_ENST00000381529.3_Silent_p.T242T|BX649553.4_ENST00000580687.1_RNA|CSF2RA_ENST00000361536.3_Silent_p.T242T|CSF2RA_ENST00000501036.2_Silent_p.T109T|CSF2RA_ENST00000381509.3_Silent_p.T242T|BX649553.1_ENST00000583047.1_RNA			P15509	CSF2R_HUMAN	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	242	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)	AGCCCAGGACCTATCAGAAGC	0.597																																					p.T242T	Esophageal Squamous(131;723 1707 25334 40494 41806)	Atlas-SNP	.											.	CSF2RA	153	.	0			c.C726A						PASS	.						330	265	287					X																	1413300		2203	4296	6499	SO:0001819	synonymous_variant	1438	exon6			CAGGACCTATCAG	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.726C>A	X.37:g.1413300C>A		464	0	0		263	13	0.0494297	NM_172247	A7J003|A8KAM1|B4DW68|J3JS76|J3JS77|O00207|Q14429|Q14430|Q14431|Q16564	Silent	SNP	ENST00000381524.3	37	CCDS35191.1																																																																																			.	.	none		0.597	CSF2RA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000035013.2			A	1413300	C	A	1413300	2	1	26	1	0	0	0	0	0	0	0	1	3936	668	24	4		4	CSF2RA	23	1413300	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10		1413300	153857260	673	10436											
IL3RA	3563	hgsc.bcm.edu	37	chrX	1471062	1471062	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgtggatttcttgagctgcaGctgggcggtaggcccggggg	4	9	19	9	3	1	1	0	1	1	0	1	2	1	2	1	6	3	4	1	6	1	3			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:1471062G>C	ENST00000331035.4	+	5	717	c.368G>C	c.(367-369)aGc>aCc	p.S123T	IL3RA_ENST00000381469.2_Missense_Mutation_p.S45T	NM_001267713.1|NM_002183.3	NP_001254642.1|NP_002174.1	P26951	IL3RA_HUMAN	interleukin 3 receptor, alpha (low affinity)	123			S -> T (in dbSNP:rs17883572). {ECO:0000269|Ref.5}.		cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-3 receptor activity (GO:0004912)			lung(1)|skin(2)	3		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)	TTGAGCTGCAGCTGGGCGGTA	0.607													g|||	10	0.00199681	0.0008	0.0043	5008	,	,		15306	0.0		0.006	False		,,,				2504	0.0				p.S123T		Atlas-SNP	.											.	IL3RA	49	.	0			c.G368C						PASS	.	G	THR/SER	3,4399		0,3,2198	120	137	131		368	-1.7	0	X	dbSNP_134	131	34,8558		0,34,4262	no	missense	IL3RA	NM_002183.2	58	0,37,6460	CC,CG,GG		0.3957,0.0682,0.2847	benign	123/379	1471062	37,12957	2201	4296	6497	SO:0001583	missense	3563	exon5			GCTGCAGCTGGGC	M74782	CCDS14113.1, CCDS59158.1	Xp22.3 and Yp13.3	2008-07-21			ENSG00000185291	ENSG00000185291		"Pseudoautosomal regions / PAR1", "Interleukins and interleukin receptors", "CD molecules"	6012	protein-coding gene	gene with protein product		308385, 430000				1833064	Standard	NM_002183		Approved	CD123	uc004cps.3	P26951	OTTHUMG00000021059	ENST00000331035.4:c.368G>C	X.37:g.1471062G>C	ENSP00000327890:p.Ser123Thr	253	0	0		115	107	0.930435	NM_002183	A8K3F3|B9VI81|Q5HYQ7|Q5HYQ8|Q9UEH7	Missense_Mutation	SNP	ENST00000331035.4	37	CCDS14113.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	.	3.020	-0.202042	0.06219	6.82E-4	0.003957	ENSG00000185291	ENST00000331035;ENST00000432757;ENST00000381469	D;D;D	0.82803	-1.65;-1.65;-1.65	1.88	-1.72	0.08107	Interleukin-6 receptor alpha chain, binding (1);Fibronectin, type III (1);Short hematopoietin receptor, family 2, conserved site (1);Immunoglobulin-like fold (1);	12.972700	0.00397	U	0.000044	T	0.64853	0.2636	N	0.10707	0.03	0.09310	N	1	D;P	0.55172	0.97;0.62	P;B	0.53146	0.719;0.388	T	0.61739	-0.7001	10	0.11485	T	0.65	0.013	2.6035	0.04872	0.4136:0.2668:0.3195:0.0	.	44;123	P26951-2;P26951	.;IL3RA_HUMAN	T	123;45;45	ENSP00000327890:S123T;ENSP00000414867:S45T;ENSP00000370878:S45T	ENSP00000327890:S123T	S	+	2	0	IL3RA	1431062	0.115000	0.22152	0.001000	0.08648	0.020000	0.10135	-0.706000	0.05047	-0.389000	0.07786	0.365000	0.22127	AGC	.	.	weak		0.607	IL3RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055600.3			C	1471062	G	C	1471062	3	2	26	1	0	0	0	0	1	0	0	0	7704	971	34	4	382	4	IL3RA	23	1471062	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	57762	1471062	153799498	674	10437											
ZBED1	9189	hgsc.bcm.edu	37	chrX	2408434	2408434	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggccggccttgacggccagCgcgtcctgcccgggctgctg	2	7	16	16	5	0	1	0	1	0	0	1	1	1	1	5	4	3	2	5	4	0	1			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:2408434C>T	ENST00000381223.4	-	2	530	c.327G>A	c.(325-327)gcG>gcA	p.A109A	ZBED1_ENST00000381218.3_Silent_p.A109A|DHRSX_ENST00000334651.5_Intron|ZBED1_ENST00000381222.2_Silent_p.A109A|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	109					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)				TGACGGCCAGCGCGTCCTGCC	0.672																																					p.A109A		Atlas-SNP	.											.	ZBED1	64	.	0			c.G327A						PASS	.						59	59	59					X																	2408434		2203	4296	6499	SO:0001819	synonymous_variant	9189	exon2			GGCCAGCGCGTCC	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.327G>A	X.37:g.2408434C>T		139	0	0		87	79	0.908046	NM_001171135	Q96BY4	Silent	SNP	ENST00000381223.4	37	CCDS14118.1																																																																																			C|0.999;G|0.001	.	alt		0.672	ZBED1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144310.3	NM_004729		T	2408434	C	T	2408434	2	4	26	1	0	0	0	0	0	0	0	1	17532	755	27	1		1	ZBED1	23	2408434	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	937372	2408434	152862126	675	10438											
MXRA5	25878	hgsc.bcm.edu	37	chrX	3241591	3241591	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctttggatgcagaagtctcCttgaagtgttctcttcatct	7	16	8	10	0	4	2	1	1	3	1	6	3	4	3	2	1	1	2	2	1	2	4			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:3241591C>T	ENST00000217939.6	-	5	2289	c.2135G>A	c.(2134-2136)aGg>aAg	p.R712K		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	712						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)				CAGAAGTCTCCTTGAAGTGTT	0.498																																					p.R712K		Atlas-SNP	.											.	MXRA5	815	.	0			c.G2135A						PASS	.						81	72	75					X																	3241591		2203	4300	6503	SO:0001583	missense	25878	exon5			AGTCTCCTTGAAG	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.2135G>A	X.37:g.3241591C>T	ENSP00000217939:p.Arg712Lys	66	0	0		81	73	0.901235	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	c	2.192	-0.385056	0.04966	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.62639	0.01	3.49	-0.704	0.11256	.	0.543747	0.15356	N	0.266696	T	0.37598	0.1009	N	0.17082	0.46	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.13845	-1.0494	10	0.23891	T	0.37	.	5.8602	0.18743	0.0:0.5307:0.2897:0.1795	.	712	Q9NR99	MXRA5_HUMAN	K	712	ENSP00000217939:R712K	ENSP00000217939:R712K	R	-	2	0	MXRA5	3251591	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.256000	0.18351	-0.388000	0.07797	0.529000	0.55759	AGG	.	.	none		0.498	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		T	3241591	C	T	3241591	3	4	26	1	0	0	0	0	1	0	0	0	10012	681	24	2	6363	2	MXRA5	23	3241591	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	833157	3241591	152028969	676	10439											
TMSB4X	7114	hgsc.bcm.edu	37	chrX	12994443	12994444	+	Frame_Shift_Del	DEL	AG	AG	-																															aagtcgaaactgaagaagacAgagacgcaagagaaaaatcc																										TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:12994443_12994444delAG	ENST00000380635.1	+	2	279_280	c.63_64delAG	c.(61-66)acagagfs	p.E22fs	TMSB4X_ENST00000380633.1_Frame_Shift_Del_p.E22fs|TMSB4X_ENST00000451311.2_Frame_Shift_Del_p.E22fs|TMSB4X_ENST00000380636.1_Frame_Shift_Del_p.E22fs			P62328	TYB4_HUMAN	thymosin beta 4, X-linked	22					actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|sequestering of actin monomers (GO:0042989)	cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	poly(A) RNA binding (GO:0044822)			upper_aerodigestive_tract(1)	1						TGAAGAAGACAGAGACGCAAGA	0.54																																					p.21_21del		Pindel,Atlas-Indel	.											.	TMSB4X	3	.	0			c.62_63del						PASS	.			0,3721		0,0,1592,537						4.7	1			58	1,6483		0,1,2356,1770	no	frameshift	TMSB4X	NM_021109.3		0,1,3948,2307	A1A1,A1R,RR,R		0.0154,0.0,0.0098				1,10204				SO:0001589	frameshift_variant	7114	exon2			.		CCDS35202.1	Xp22.2	2013-05-14	2008-02-25		ENSG00000205542	ENSG00000205542			11881	protein-coding gene	gene with protein product		300159	"thymosin, beta 4, X chromosome"	TMSB4		2677145, 9381176	Standard	NM_021109		Approved	TB4X	uc004cvf.3	P62328	OTTHUMG00000021144	ENST00000380635.1:c.63_64delAG	X.37:g.12994445_12994446delAG	ENSP00000370009:p.Glu22fs	177	0	.		186	81	0.435	NM_021109	P01253|P01254|Q546P5|Q63576|Q9UE55	Frame_Shift_Del	DEL	ENST00000380635.1	37	CCDS35202.1																																																																																			.	.	none		0.54	TMSB4X-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000055779.1	NM_021109		-	12994444	AG	-	12994443	7	5	26	1	0	1	0	1	0	0	0	0	16272	175	7	0	65	0	TMSB4X	23	12994443	Frame_Shift_Del	DEL	AG	TCGA-G8-6907-01A-11D-2210-10	9752852	12994443	142276117	677	10440											
CDKL5	6792	hgsc.bcm.edu	37	chrX	18664128	18664128	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttctccccactaactagaCggtggatgtgatggcagaag	10	10	12	9	1	1	3	0	1	1	2	2	4	1	4	2	3	1	2	2	3	3	3	rs201714912		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:18664128C>T	ENST00000379989.3	+	20	3000	c.2715C>T	c.(2713-2715)gaC>gaT	p.D905D	CDKL5_ENST00000379996.3_Splice_Site_p.D905D|RS1_ENST00000379984.3_Intron|RS1_ENST00000476595.1_Intron	NM_001037343.1	NP_001032420.1	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	905					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)	p.D905D(1)		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)					actaactagacggtggatgtg	0.493													A|||	1	0.000264901	0.0	0.0	3775	,	,		14324	0.0		0.001	False		,,,				2504	0.0				p.D905D		Atlas-SNP	.											.	CDKL5	124	.	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C2715T						PASS	.	A	,,	1,3834		0,1,1631,571	140	112	122		,2715,2715	0.6	0.1	X		122	0,6728		0,0,2428,1872	no	intron,coding-synonymous-near-splice,coding-synonymous-near-splice	RS1,CDKL5	NM_000330.3,NM_001037343.1,NM_003159.2	,,	0,1,4059,2443	TT,TC,CC,C		0.0,0.0261,0.0095	,,	,905/1031,905/1031	18664128	1,10562	2203	4300	6503	SO:0001630	splice_region_variant	6792	exon19			ACTAGACGGTGGA	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.2714-1C>T	X.37:g.18664128C>T		39	0	0		49	5	0.102041	NM_003159	G9B9X4|Q14198|Q5H985|Q8IYC7|Q9UJL6	Silent	SNP	ENST00000379989.3	37	CCDS14186.1																																																																																			C|0.999;T|0.001	0.001	strong		0.493	CDKL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055945.2	NM_003159	Silent	T	18664128	C	T	18664128	5	4	26	1	0	0	0	0	0	0	1	0	3159	550	19	1	2785	1	CDKL5	23	18664128	Splice_Site	SNP	C	TCGA-G8-6907-01A-11D-2210-10	5669685	18664128	136606432	678	10441											
MAGEB6	158809	hgsc.bcm.edu	37	chrX	26212334	26212334	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggtgtttcaggctcaaaatAtgatgtggctgccaacggcc	10	10	12	9	1	2	1	2	1	0	0	2	1	2	1	2	4	2	3	2	4	4	2	rs143802048	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:26212334A>C	ENST00000379034.1	+	2	520	c.371A>C	c.(370-372)tAt>tCt	p.Y124S		NM_173523.2	NP_775794.2	Q8N7X4	MAGB6_HUMAN	melanoma antigen family B, 6	124	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						GGCTCAAAATATGATGTGGCT	0.552													.|||	342	0.090596	0.0242	0.0706	3775	,	,		12620	0.0794		0.0646	False		,,,				2504	0.1186				p.Y124S		Atlas-SNP	.											.	MAGEB6	91	.	0			c.A371C						PASS	.	C	SER/TYR	21,3809		1,4,15,1626,553	85	77	80		371	-1.5	0	X	dbSNP_134	80	81,6624		6,7,62,2414,1789	no	missense	MAGEB6	NM_173523.2	144	7,11,77,4040,2342	CC,CA,C,AA,A		1.2081,0.5483,0.9682	benign	124/408	26212334	102,10433	2199	4278	6477	SO:0001583	missense	158809	exon2			CAAAATATGATGT	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.371A>C	X.37:g.26212334A>C	ENSP00000368320:p.Tyr124Ser	89	0	0		22	11	0.5	NM_173523	Q6GS19|Q9H219	Missense_Mutation	SNP	ENST00000379034.1	37	CCDS14217.1	.	.	.	.	.	.	.	.	.	.	C	0.003	-2.460724	0.00171	0.005483	0.012081	ENSG00000176746	ENST00000379034	T	0.01629	4.72	1.23	-1.47	0.08772	.	.	.	.	.	T	0.00468	0.0015	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42292	-0.9460	9	0.02654	T	1	.	2.6776	0.05084	0.2703:0.469:0.0:0.2607	.	124	Q8N7X4	MAGB6_HUMAN	S	124	ENSP00000368320:Y124S	ENSP00000368320:Y124S	Y	+	2	0	MAGEB6	26122255	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.070000	0.03440	-1.353000	0.02191	-2.567000	0.00172	TAT	A|0.980;C|0.020	0.020	strong		0.552	MAGEB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056123.1	NM_173523		C	26212334	A	C	26212334	3	2	26	1	0	0	0	0	1	0	0	0	9188	449	16	5	373	5	MAGEB6	23	26212334	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	7548206	26212334	129058226	679	10442											
FAM47B	170062	hgsc.bcm.edu	37	chrX	34961479	34961479	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagacaaccgaggtacccacCgagtctggtaaatatccctg	13	7	9	12	2	1	1	0	0	1	1	2	3	2	1	4	2	2	2	4	2	6	3	rs149160457		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:34961479C>T	ENST00000329357.5	+	1	567	c.531C>T	c.(529-531)acC>acT	p.T177T		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	177										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						AGGTACCCACCGAGTCTGGTA	0.612																																					p.T177T		Atlas-SNP	.											.	FAM47B	209	.	0			c.C531T						PASS	.	C		1,3832		0,1,1630,571	31	31	31		531	-1.7	0	X	dbSNP_134	31	0,6728		0,0,2428,1872	no	coding-synonymous	FAM47B	NM_152631.2		0,1,4058,2443	TT,TC,CC,C		0.0,0.0261,0.0095		177/646	34961479	1,10560	2202	4300	6502	SO:0001819	synonymous_variant	170062	exon1			ACCCACCGAGTCT	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.531C>T	X.37:g.34961479C>T		85	0	0		124	107	0.862903	NM_152631	Q5JQN5|Q6PIG3	Silent	SNP	ENST00000329357.5	37	CCDS14236.1																																																																																			C|1.000;T|0.000	0.000	weak		0.612	FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056211.1	NM_152631		T	34961479	C	T	34961479	2	4	26	1	0	0	0	0	0	0	0	1	5578	639	23	1		1	FAM47B	23	34961479	Silent	SNP	C	TCGA-G8-6907-01A-11D-2210-10	8749145	34961479	120309081	680	10443											
NHSL2	340527	hgsc.bcm.edu	37	chrX	71359555	71359555	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agtggctactccagccagtcGgaaacaccaacacccactgt	12	6	8	15	1	0	0	0	0	0	0	2	1	1	1	4	2	4	1	4	2	3	1			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:71359555G>A	ENST00000373677.1	+	2	2321	c.1059G>A	c.(1057-1059)tcG>tcA	p.S353S	NHSL2_ENST00000510661.1_Silent_p.S488S|NHSL2_ENST00000535692.1_Silent_p.S353S|NHSL2_ENST00000540800.1_Silent_p.S719S			Q5HYW2	NHSL2_HUMAN	NHS-like 2	353	Ser-rich.									NS(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(10)|lung(7)|stomach(1)	28	Renal(35;0.156)					CCAGCCAGTCGGAAACACCAA	0.592																																					p.S719S		Atlas-SNP	.											.	NHSL2	148	.	0			c.G2157A						PASS	.						70	52	58					X																	71359555		2203	4300	6503	SO:0001819	synonymous_variant	340527	exon6			CCAGTCGGAAACA			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.1059G>A	X.37:g.71359555G>A		60	0	0		84	6	0.0714286	NM_001013627	B2RN94	Silent	SNP	ENST00000373677.1	37																																																																																				.	.	none		0.592	NHSL2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057170.1	NM_001013627		A	71359555	G	A	71359555	2	1	26	1	0	0	0	0	0	0	0	1	10421	1103	39	1		1	NHSL2	23	71359555	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	36398076	71359555	83911005	681	10444											
MAGEE1	57692	hgsc.bcm.edu	37	chrX	75649430	75649430	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggactgagcacctctgtgccGcccaccgcctctgatggatc	6	8	11	16	2	2	2	0	2	2	0	3	4	2	4	5	2	2	1	5	2	0	0			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:75649430G>A	ENST00000361470.2	+	1	1385	c.1107G>A	c.(1105-1107)ccG>ccA	p.P369P		NM_020932.2	NP_065983.1	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	369	Pro-rich.					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						CCTCTGTGCCGCCCACCGCCT	0.672																																					p.P369P		Atlas-SNP	.											.	MAGEE1	236	.	0			c.G1107A						PASS	.						33	26	28					X																	75649430		2203	4297	6500	SO:0001819	synonymous_variant	57692	exon1			TGTGCCGCCCACC	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.1107G>A	X.37:g.75649430G>A		48	0	0		70	64	0.914286	NM_020932	Q5JXC7|Q86TG0|Q8TD92|Q9H216	Silent	SNP	ENST00000361470.2	37	CCDS14433.1																																																																																			.	.	none		0.672	MAGEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057298.1	NM_020932		A	75649430	G	A	75649430	2	1	26	1	0	0	0	0	0	0	0	1	9194	1074	38	1		1	MAGEE1	23	75649430	Silent	SNP	G	TCGA-G8-6907-01A-11D-2210-10	4289875	75649430	79621130	682	10445											
BTK	695	hgsc.bcm.edu	37	chrX	100612565	100612565	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctggatatttgagcctggatAtgagtcctgaaacagagaga	13	10	12	6	0	0	5	0	3	0	2	1	8	1	7	2	2	2	0	2	2	3	3			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:100612565A>G	ENST00000308731.7	-	13	1272	c.1109T>C	c.(1108-1110)aTa>aCa	p.I370T	BTK_ENST00000372880.1_Intron	NM_000061.2	NP_000052.1	Q06187	BTK_HUMAN	Bruton agammaglobulinemia tyrosine kinase	370	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.		I -> M (in XLA). {ECO:0000269|PubMed:7711734}.		adaptive immune response (GO:0002250)|apoptotic signaling pathway (GO:0097190)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|calcium-mediated signaling (GO:0019722)|cell maturation (GO:0048469)|Fc-epsilon receptor signaling pathway (GO:0038095)|histamine secretion by mast cell (GO:0002553)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of B cell apoptotic process (GO:0002902)|regulation of B cell cytokine production (GO:0002721)|response to organic substance (GO:0010033)|response to reactive oxygen species (GO:0000302)|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)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein tyrosine kinase activity (GO:0004713)			breast(4)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(25)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						GAGCCTGGATATGAGTCCTGA	0.498									Agammaglobulinemia, X-linked																												p.I370T		Atlas-SNP	.											.	BTK	87	.	0			c.T1109C						PASS	.						304	239	261					X																	100612565		2203	4300	6503	SO:0001583	missense	695	exon13	Familial Cancer Database	Bruton Type Agammaglobulinemia	CTGGATATGAGTC	AK057105	CCDS14482.1, CCDS76002.1, CCDS76003.1	Xq21.33-q22	2014-09-17			ENSG00000010671	ENSG00000010671	2.7.10.1	"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	1133	protein-coding gene	gene with protein product		300300		AGMX1, IMD1		8380905	Standard	NM_000061		Approved	ATK, XLA, PSCTK1	uc004ehg.2	Q06187	OTTHUMG00000022022	ENST00000308731.7:c.1109T>C	X.37:g.100612565A>G	ENSP00000308176:p.Ile370Thr	124	0	0		150	140	0.933333	NM_000061	B2RAW1|Q32ML5	Missense_Mutation	SNP	ENST00000308731.7	37	CCDS14482.1	.	.	.	.	.	.	.	.	.	.	A	15.88	2.962940	0.53507	.	.	ENSG00000010671	ENST00000372855;ENST00000372859;ENST00000372860;ENST00000395179;ENST00000372869;ENST00000443591;ENST00000308731	D	0.92647	-3.08	5.76	5.76	0.90799	SH2 motif (2);	0.046830	0.85682	D	0.000000	D	0.88941	0.6574	L	0.42008	1.315	0.54753	D	0.999988	B;P;P	0.44734	0.227;0.645;0.842	B;B;B	0.39419	0.114;0.299;0.185	D	0.89837	0.4000	10	0.66056	D	0.02	.	14.7456	0.69488	1.0:0.0:0.0:0.0	.	41;370;370	Q3MS94;B2RAW1;Q06187	.;.;BTK_HUMAN	T	41;41;39;41;41;41;370	ENSP00000308176:I370T	ENSP00000308176:I370T	I	-	2	0	BTK	100499221	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.664000	0.83830	1.943000	0.56356	0.483000	0.47432	ATA	.	.	none		0.498	BTK-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057532.2	NM_000061		G	100612565	A	G	100612565	3	3	26	1	0	0	0	0	1	0	0	0	1559	449	16	3	898	3	BTK	23	100612565	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	24963135	100612565	54657995	683	10446											
GPRASP2	114928	hgsc.bcm.edu	37	chrX	101970123	101970123	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagggcagtaggtggcgctcGttctaaaactgatgccaagg	10	8	14	9	2	1	1	0	1	1	0	2	1	1	1	1	4	2	4	1	4	4	3	rs139789934	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:101970123G>A	ENST00000535209.1	+	4	1157	c.326G>A	c.(325-327)cGt>cAt	p.R109H	GPRASP2_ENST00000332262.5_Missense_Mutation_p.R109H|GPRASP2_ENST00000543253.1_Missense_Mutation_p.R109H			Q96D09	GASP2_HUMAN	G protein-coupled receptor associated sorting protein 2	109						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						GGTGGCGCTCGTTCTAAAACT	0.572													.|||	2	0.000529801	0.0	0.0	3775	,	,		14704	0.0		0.002	False		,,,				2504	0.0				p.R109H		Atlas-SNP	.											.	GPRASP2	89	.	0			c.G326A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	0,3835		0,0,1632,571	84	85	84		326,326,326,326,326,326	3.9	0.9	X	dbSNP_134	84	12,6716		0,12,2416,1872	yes	missense,missense,missense,missense,missense,missense	GPRASP2,ARMCX5-GPRASP2	NM_001004051.3,NM_001184874.2,NM_001184875.2,NM_001184876.2,NM_001199818.1,NM_138437.5	29,29,29,29,29,29	0,12,4048,2443	AA,AG,GG,G		0.1784,0.0,0.1136	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	109/839,109/839,109/839,109/839,109/839,109/839	101970123	12,10551	2203	4300	6503	SO:0001583	missense	114928	exon4			GCGCTCGTTCTAA	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.326G>A	X.37:g.101970123G>A	ENSP00000437394:p.Arg109His	37	0	0		80	73	0.9125	NM_138437	D3DXA0|Q8NAB4	Missense_Mutation	SNP	ENST00000535209.1	37	CCDS14501.1	2	0.0012055455093429777	0	0.0	0	0.0	0	0.0	1	0.0013227513227513227	G	11.74	1.729796	0.30684	0.0	0.001784	ENSG00000158301	ENST00000543253;ENST00000535209;ENST00000332262	T;T;T	0.08008	3.14;3.14;3.14	4.76	3.89	0.44902	.	0.000000	0.44483	D	0.000442	T	0.05502	0.0145	N	0.14661	0.345	0.18873	N	0.999989	P	0.51240	0.943	B	0.43990	0.438	T	0.28681	-1.0036	10	0.45353	T	0.12	.	6.4019	0.21642	0.1059:0.1825:0.7116:0.0	.	109	Q96D09	GASP2_HUMAN	H	109	ENSP00000437872:R109H;ENSP00000437394:R109H;ENSP00000339057:R109H	ENSP00000339057:R109H	R	+	2	0	GPRASP2	101856779	0.993000	0.37304	0.927000	0.36925	0.006000	0.05464	3.248000	0.51430	1.078000	0.41014	0.600000	0.82982	CGT	G|0.999;A|0.001	0.001	strong		0.572	GPRASP2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057626.2	NM_138437		A	101970123	G	A	101970123	3	1	26	1	0	0	0	0	1	0	0	0	6732	1145	40	1	328	1	GPRASP2	23	101970123	Missense_Mutation	SNP	G	TCGA-G8-6907-01A-11D-2210-10	1357558	101970123	53300437	684	10447											
STAG2	10735	hgsc.bcm.edu	37	chrX	123184082	123184082	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgcattgaagagattggcAtttggatgaagatgtatagt	12	15	12	2	0	0	4	0	2	0	2	0	6	0	5	0	2	1	3	0	2	4	6			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:123184082A>G	ENST00000371160.1	+	11	1230	c.940A>G	c.(940-942)Att>Gtt	p.I314V	STAG2_ENST00000354548.5_Missense_Mutation_p.I245V|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Missense_Mutation_p.I314V|STAG2_ENST00000371157.3_Missense_Mutation_p.I314V|STAG2_ENST00000371144.3_Missense_Mutation_p.I314V|STAG2_ENST00000371145.3_Missense_Mutation_p.I314V	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	314	SCD. {ECO:0000255|PROSITE- ProRule:PRU00750}.				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						AGAGATTGGCATTTGGATGAA	0.378																																					p.I314V		Atlas-SNP	.											.	STAG2	309	.	0			c.A940G						PASS	.						283	235	252					X																	123184082		2203	4300	6503	SO:0001583	missense	10735	exon11			ATTGGCATTTGGA	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.940A>G	X.37:g.123184082A>G	ENSP00000360202:p.Ile314Val	121	0	0		231	78	0.337662	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Missense_Mutation	SNP	ENST00000371160.1	37	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	A	5.398	0.258667	0.10239	.	.	ENSG00000101972	ENST00000218089;ENST00000455404;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	T;T;T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48;1.48;1.48	5.54	5.54	0.83059	Stromalin conservative domain (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.149337	0.64402	D	0.000013	T	0.10078	0.0247	N	0.01771	-0.73	0.42561	D	0.993144	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.18304	-1.0341	10	0.02654	T	1	-9.3005	9.4174	0.38530	0.9193:0.0:0.0807:0.0	.	314;314	Q8N3U4-2;Q8N3U4	.;STAG2_HUMAN	V	314;314;245;314;314;314;314	ENSP00000218089:I314V;ENSP00000397265:I314V;ENSP00000346555:I245V;ENSP00000360202:I314V;ENSP00000360199:I314V;ENSP00000360187:I314V;ENSP00000360186:I314V	ENSP00000218089:I314V	I	+	1	0	STAG2	123011763	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.344000	0.65981	1.952000	0.56665	0.486000	0.48141	ATT	.	.	none		0.378	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		G	123184082	A	G	123184082	3	3	26	1	0	0	0	0	1	0	0	0	15258	217	8	3	974	3	STAG2	23	123184082	Missense_Mutation	SNP	A	TCGA-G8-6907-01A-11D-2210-10	21213959	123184082	32086478	685	10448											
SPANXN4	441525	hgsc.bcm.edu	37	chrX	142121809	142121811	+	Splice_Site	DEL	AGA	AGA	-																															cctctccctgtttttttaccAgaagaagaagaatctgcaca																								rs368252596		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:142121809_142121811delAGA	ENST00000446864.1	+	2	175_176	c.78_79delAGA	c.(76-81)aaagaa>aaaa	p.E27del	SPANXN4_ENST00000370504.3_Intron	NM_001009613.2	NP_001009613.1	Q5MJ08	SPXN4_HUMAN	SPANX family, member N4	27										endometrium(2)|large_intestine(2)|lung(3)|ovary(1)	8	Acute lymphoblastic leukemia(192;6.56e-05)					TTTTTTTACCAGAAGAAGAAGAA	0.414																																					.		Pindel,Atlas-Indel	.											.	SPANXN4	10	.	0			.						PASS	.			28,3000		4,16,4,1234,516						0.8	0		dbSNP_131	21	265,5828		10,168,77,2059,1542	no	coding-near-splice	SPANXN4	NM_001009613.2		14,184,81,3293,2058	A1A1,A1R,A1,RR,R		4.3493,0.9247,3.2124				293,8828				SO:0001630	splice_region_variant	441525	.			.	DQ336126	CCDS48178.1	Xq27.3	2009-03-25			ENSG00000189326	ENSG00000189326			33177	protein-coding gene	gene with protein product	"cancer/testis antigen family 11, member 9"	300667				14973187, 17012309	Standard	NM_001009613		Approved	SPANX-N4, CT11.9	uc004fbv.4	Q5MJ08	OTTHUMG00000022575	ENST00000446864.1:c.79-1AGA>-	X.37:g.142121818_142121820delAGA		117	0	.		229	39	0.17	.	Q0ZNK6|Q5W0S6	Splice_Site	DEL	ENST00000446864.1	37	CCDS48178.1																																																																																			.	.	none		0.414	SPANXN4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377539.1	NM_001009613	In_Frame_Del	-	142121811	AGA	-	142121809	8	5	26	1	0	1	0	1	0	0	1	0	15008	202	7	0	83	0	SPANXN4	23	142121809	Splice_Site	DEL	AGA	TCGA-G8-6907-01A-11D-2210-10	18937727	142121809	13148751	686	10449											
MAMLD1	10046	hgsc.bcm.edu	37	chrX	149639035	149639035	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	catgacgtccagcagcaatgCtgccctggggcccgccatgc	7	6	12	16	2	0	1	0	1	0	0	1	1	1	1	4	2	5	3	4	2	1	0			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:149639035C>A	ENST00000370401.2	+	4	1500	c.1190C>A	c.(1189-1191)gCt>gAt	p.A397D	MAMLD1_ENST00000426613.2_Missense_Mutation_p.A372D|MAMLD1_ENST00000432680.2_Missense_Mutation_p.A372D|MAMLD1_ENST00000262858.5_Missense_Mutation_p.A397D|MAMLD1_ENST00000455522.2_5'Flank			Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	397					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)					AGCAGCAATGCTGCCCTGGGG	0.597																																					p.A397D		Atlas-SNP	.											.	MAMLD1	263	.	0			c.C1190A						PASS	.						107	102	104					X																	149639035		2203	4300	6503	SO:0001583	missense	10046	exon3			GCAATGCTGCCCT	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.1190C>A	X.37:g.149639035C>A	ENSP00000359428:p.Ala397Asp	45	0	0		124	20	0.16129	NM_005491	B2RCQ4|B4DG93|B9EGA5	Missense_Mutation	SNP	ENST00000370401.2	37	CCDS14693.2	.	.	.	.	.	.	.	.	.	.	C	7.869	0.727815	0.15507	.	.	ENSG00000013619	ENST00000445612;ENST00000370401;ENST00000432680;ENST00000262858;ENST00000426613	T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57	5.03	3.2	0.36748	.	0.474459	0.21020	N	0.081532	T	0.76054	0.3934	L	0.47716	1.5	0.21290	N	0.999735	D;D;D;D	0.71674	0.996;0.96;0.998;0.96	P;B;D;P	0.66351	0.899;0.408;0.943;0.59	T	0.66228	-0.5976	9	.	.	.	-2.4414	11.1467	0.48434	0.1443:0.7201:0.1356:0.0	.	359;372;372;397	F6WVG1;Q13495-4;Q13495-3;Q13495	.;.;.;MAMD1_HUMAN	D	359;397;372;397;372	ENSP00000359428:A397D;ENSP00000414517:A372D;ENSP00000262858:A397D;ENSP00000397438:A372D	.	A	+	2	0	MAMLD1	149389693	0.101000	0.21875	0.000000	0.03702	0.046000	0.14306	4.214000	0.58527	0.358000	0.24211	0.529000	0.55759	GCT	.	.	none		0.597	MAMLD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060844.2	NM_005491		A	149639035	C	A	149639035	3	1	26	1	0	0	0	0	1	0	0	0	9217	797	28	4	1200	4	MAMLD1	23	149639035	Missense_Mutation	SNP	C	TCGA-G8-6907-01A-11D-2210-10	7517226	149639035	5631525	687	10450											
FLNA	2316	hgsc.bcm.edu	37	chrX	153594932	153594932	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccctggccaagggctcacctTatgagtccccgtcacctcgg	6	8	10	17	2	2	1	2	1	0	0	4	1	3	1	6	3	0	1	6	3	2	1			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:153594932T>G	ENST00000369850.3	-	7	1299	c.1063A>C	c.(1063-1065)Aag>Cag	p.K355Q	FLNA_ENST00000344736.4_Missense_Mutation_p.K355Q|FLNA_ENST00000360319.4_Missense_Mutation_p.K355Q|FLNA_ENST00000422373.1_Missense_Mutation_p.K355Q	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	355					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)					GGGCTCACCTTATGAGTCCCC	0.632																																					p.K355Q		Atlas-SNP	.											.	FLNA	373	.	0			c.A1063C						PASS	.						89	91	91					X																	153594932		2009	4148	6157	SO:0001583	missense	2316	exon7			TCACCTTATGAGT	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.1063A>C	X.37:g.153594932T>G	ENSP00000358866:p.Lys355Gln	98	0	0		231	126	0.545455	NM_001456	E9KL45|Q5HY53|Q5HY55|Q8NF52	Missense_Mutation	SNP	ENST00000369850.3	37	CCDS48194.1	.	.	.	.	.	.	.	.	.	.	T	13.80	2.346167	0.41599	.	.	ENSG00000196924	ENST00000360319;ENST00000369852;ENST00000422373;ENST00000369850;ENST00000344736	D;D;D;D	0.85171	-1.95;-1.95;-1.95;-1.95	4.87	4.87	0.63330	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.85605	0.5735	L	0.50993	1.605	0.80722	D	1	B;B	0.29612	0.251;0.18	B;B	0.42163	0.23;0.378	D	0.84661	0.0706	10	0.51188	T	0.08	.	13.3412	0.60545	0.0:0.0:0.0:1.0	.	355;355	P21333-2;P21333	.;FLNA_HUMAN	Q	355;328;355;355;355	ENSP00000353467:K355Q;ENSP00000416926:K355Q;ENSP00000358866:K355Q;ENSP00000358863:K355Q	ENSP00000358863:K355Q	K	-	1	0	FLNA	153248126	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	6.134000	0.71689	1.607000	0.50170	0.427000	0.28365	AAG	.	.	none		0.632	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3			G	153594932	T	G	153594932	3	3	26	1	0	0	0	0	1	0	0	0	5941	1763	61	5	7048	5	FLNA	23	153594932	Missense_Mutation	SNP	T	TCGA-G8-6907-01A-11D-2210-10	3955897	153594932	1675628	688	10451											
SLC35E2	9906	hgsc.bcm.edu	37	chr1	1663960	1663960	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	actcggtgcagggcctgcggGacctgcaggtgagaggaagc	8	5	18	10	2	0	1	0	1	0	1	1	4	0	3	2	5	4	2	2	5	1	0	rs147265331	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:1663960G>A	ENST00000246421.4	-	6	1150	c.735C>T	c.(733-735)gtC>gtT	p.V245V	SLC35E2_ENST00000475229.1_5'UTR|RP1-283E3.8_ENST00000598846.1_RNA|RP1-283E3.4_ENST00000417099.1_RNA|SLC35E2_ENST00000355439.2_Intron|SLC35E2_ENST00000400924.1_Intron	NM_182838.2	NP_878258.1	P0CK97	S35E2_HUMAN	solute carrier family 35, member E2	245						integral component of membrane (GO:0016021)				endometrium(2)|lung(4)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9	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)		GGGCCTGCGGGACCTGCAGGT	0.607													-|||	25	0.00499201	0.0015	0.0086	5008	,	,		16644	0.0		0.0099	False		,,,				2504	0.0072				p.V245V		Atlas-SNP	.											.	SLC35E2	13	.	0			c.C735T						PASS	.		,	16,4378	23.3+/-48.9	1,14,2182	41	37	38		,735	-2.3	0	1	dbSNP_134	38	168,8396	71.0+/-133.6	5,158,4119	no	intron,coding-synonymous	SLC35E2	NM_001199787.1,NM_182838.2	,	6,172,6301	AA,AG,GG		1.9617,0.3641,1.42	,	,245/267	1663960	184,12774	2197	4282	6479	SO:0001819	synonymous_variant	9906	exon6			CTGCGGGACCTGC	AB007916	CCDS33.1, CCDS55560.1	1p36.33	2013-05-22			ENSG00000215790	ENSG00000215790		"Solute carriers"	20863	protein-coding gene	gene with protein product							Standard	NM_182838		Approved	KIAA0447	uc001aia.2	P0CK97	OTTHUMG00000000823	ENST00000246421.4:c.735C>T	1.37:g.1663960G>A		147	0	0		82	61	0.743902	NM_182838	B3KWR0|O75035|Q2TAY8|Q569F8|Q5CZA4|Q5QPR8|Q9Y3J8	Silent	SNP	ENST00000246421.4	37	CCDS33.1																																																																																			G|0.987;A|0.013	0.013	strong		0.607	SLC35E2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000002210.3	XM_049733		A	1663960	G	A	1663960	2	1	27	1	0	0	0	0	0	0	0	1	14600	1161	41	2		2	SLC35E2	1	1663960	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10		1663960	247586661	1	10452											
KIAA1751	85452	hgsc.bcm.edu	37	chr1	1900225	1900225	+	IGR	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcctcctctttcagaatcCgactgatgatctcctgcttt	7	14	6	14	1	3	3	1	2	2	1	6	4	5	3	4	0	2	1	4	0	1	2	rs72636304	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:1900225C>T								TMEM52 (49513 upstream) : C1orf222 (19337 downstream)																							TTTCAGAATCCGACTGATGAT	0.572													c|||	9	0.00179712	0.0	0.0029	5008	,	,		17712	0.0		0.007	False		,,,				2504	0.0				p.R365Q		Atlas-SNP	.											.	KIAA1751	92	.	0			c.G1094A						PASS	.	C	GLN/ARG	5,4041		0,5,2018	141	150	147		1094	1.7	0	1	dbSNP_130	147	78,8256		0,78,4089	no	missense	KIAA1751	NM_001080484.1	43	0,83,6107	TT,TC,CC		0.9359,0.1236,0.6704	possibly-damaging	365/763	1900225	83,12297	2023	4167	6190	SO:0001628	intergenic_variant	85452	exon11			AGAATCCGACTGA																													1.37:g.1900225C>T		118	0	0		59	17	0.288136	NM_001080484		Missense_Mutation	SNP		37		7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	c	15.07	2.725287	0.48833	0.001236	0.009359	ENSG00000142609	ENST00000270720	.	.	.	3.67	1.74	0.24563	.	0.241675	0.27019	N	0.021330	T	0.19005	0.0456	L	0.41824	1.3	0.18873	N	0.999982	D;D	0.57571	0.973;0.98	B;B	0.41988	0.314;0.372	T	0.09729	-1.0661	9	0.39692	T	0.17	-15.2726	8.0725	0.30697	0.0:0.7846:0.0:0.2154	.	365;365	Q9C0B2-2;Q9C0B2	.;K1751_HUMAN	Q	365	.	ENSP00000270720:R365Q	R	-	2	0	C1orf222	1890085	0.231000	0.23751	0.001000	0.08648	0.004000	0.04260	1.053000	0.30442	0.309000	0.22966	0.556000	0.70494	CGG	C|0.994;T|0.006	0.006	strong	0	0.572									T	1900225	C	T	1900225	1	4	27	0	1	0	0	0	0	0	0	0	8265	652	23	1		1	KIAA1751	1	1900225	IGR	SNP	C	TCGA-G8-6909-01A-11D-2210-10	236265	1900225	247350396	2	10453											
PANK4	55229	hgsc.bcm.edu	37	chr1	2449631	2449631	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tccgcgcccgctgcgccgggCcgagctcgggtgatgcactc	3	6	15	17	7	0	1	0	1	0	0	3	2	1	1	4	2	3	3	4	2	0	0	rs144881953		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:2449631C>G	ENST00000378466.3	-	9	1202	c.1190G>C	c.(1189-1191)gGc>gCc	p.G397A	PANK4_ENST00000435556.3_Missense_Mutation_p.G358A	NM_018216.1	NP_060686.1	Q9NVE7	PANK4_HUMAN	pantothenate kinase 4	397					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)		CTGCGCCGGGCCGAGCTCGGG	0.657																																					p.G397A		Atlas-SNP	.											.	PANK4	64	.	0			c.G1190C						PASS	.						34	37	36					1																	2449631		2198	4297	6495	SO:0001583	missense	55229	exon9			GCCGGGCCGAGCT	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.1190G>C	1.37:g.2449631C>G	ENSP00000367727:p.Gly397Ala	47	0	0		26	8	0.307692	NM_018216	B9DI84|Q53EU3|Q5TA84|Q7RTX3|Q9H3X5	Missense_Mutation	SNP	ENST00000378466.3	37	CCDS42.1	.	.	.	.	.	.	.	.	.	.	C	1.513	-0.548845	0.04024	.	.	ENSG00000157881	ENST00000378466;ENST00000435556	D;D	0.96491	-4.03;-3.75	4.81	2.37	0.29283	.	0.356706	0.32106	N	0.006574	D	0.85296	0.5664	N	0.11560	0.145	0.23023	N	0.99841	B;B	0.13145	0.007;0.0	B;B	0.14023	0.01;0.001	T	0.72354	-0.4319	10	0.02654	T	1	-16.9416	1.8614	0.03189	0.2961:0.4266:0.0:0.2773	.	358;397	E9PHT6;Q9NVE7	.;PANK4_HUMAN	A	397;358	ENSP00000367727:G397A;ENSP00000421433:G358A	ENSP00000367727:G397A	G	-	2	0	PANK4	2439491	1.000000	0.71417	0.974000	0.42286	0.034000	0.12701	2.218000	0.42889	2.226000	0.72624	0.561000	0.74099	GGC	C|1.000;T|0.000	.	alt		0.657	PANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002082.1			G	2449631	C	G	2449631	3	3	27	1	0	0	0	0	1	0	0	0	11428	739	26	4	1175	4	PANK4	1	2449631	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	549406	2449631	246800990	3	10454											
NPHP4	261734	hgsc.bcm.edu	37	chr1	5940243	5940243	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tccatcgtttgagatgacccGagatctggacggtggcaatg	9	10	13	9	3	1	3	0	2	1	2	3	6	2	4	2	3	0	2	2	3	1	1	rs17472401	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:5940243G>A	ENST00000378156.4	-	19	2807	c.2542C>T	c.(2542-2544)Cgg>Tgg	p.R848W	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	848			R -> W (does not affect interaction with RPGRIP1L; dbSNP:rs17472401). {ECO:0000269|PubMed:12205563, ECO:0000269|PubMed:15776426}.		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)		GAGATGACCCGAGATCTGGAC	0.527													G|||	38	0.00758786	0.0015	0.0086	5008	,	,		21450	0.0		0.0278	False		,,,				2504	0.002				p.R848W		Atlas-SNP	.											.	NPHP4	119	.	0			c.C2542T	GRCh37	CM022976	NPHP4	M	rs17472401	PASS	.	G	TRP/ARG	15,4117		0,15,2051	82	89	87		2542	0.8	0.2	1	dbSNP_123	87	184,8206		2,180,4013	yes	missense	NPHP4	NM_015102.3	101	2,195,6064	AA,AG,GG		2.1931,0.363,1.5892	probably-damaging	848/1427	5940243	199,12323	2066	4195	6261	SO:0001583	missense	261734	exon19			TGACCCGAGATCT	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.2542C>T	1.37:g.5940243G>A	ENSP00000367398:p.Arg848Trp	111	0	0		72	26	0.361111	NM_015102	Q8IWC0	Missense_Mutation	SNP	ENST00000378156.4	37	CCDS44052.1	26	0.011904761904761904	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	21	0.027704485488126648	G	12.26	1.883773	0.33255	0.00363	0.021931	ENSG00000131697	ENST00000378156	D	0.88124	-2.34	5.21	0.782	0.18567	.	0.153997	0.41500	D	0.000868	T	0.81059	0.4744	M	0.66939	2.045	0.23070	N	0.99835	D	0.89917	1.0	D	0.74674	0.984	T	0.79652	-0.1714	10	0.72032	D	0.01	.	12.097	0.53761	0.0:0.0:0.4162:0.5838	rs17472401;rs52814007;rs17472401	848	O75161	NPHP4_HUMAN	W	848	ENSP00000367398:R848W	ENSP00000367398:R848W	R	-	1	2	NPHP4	5862830	0.900000	0.30661	0.234000	0.24042	0.013000	0.08279	1.160000	0.31761	0.154000	0.19237	0.561000	0.74099	CGG	G|0.986;A|0.014	0.014	strong		0.527	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2			A	5940243	G	A	5940243	3	1	27	1	0	0	0	0	1	0	0	0	10590	1057	37	1	1786	1	NPHP4	1	5940243	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	3490612	5940243	243310378	4	10455											
ESPN	83715	hgsc.bcm.edu	37	chr1	6500712	6500712	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcaccgacgtgagcctgtcCgagcaggacaaagacggcgc	10	4	14	13	5	0	2	0	1	0	1	1	5	1	3	3	2	3	2	3	2	1	0	rs367944375		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:6500712C>G	ENST00000377828.1	+	4	870	c.702C>G	c.(700-702)tcC>tcG	p.S234S	RP1-202O8.2_ENST00000419034.1_RNA	NM_031475.2	NP_113663.2	B1AK53	ESPN_HUMAN	espin	234					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)		TGAGCCTGTCCGAGCAGGACA	0.741																																					p.S234S		Atlas-SNP	.											.	ESPN	32	.	0			c.C702G						PASS	.						3	5	4					1																	6500712		1942	3924	5866	SO:0001819	synonymous_variant	83715	exon4			CCTGTCCGAGCAG	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.702C>G	1.37:g.6500712C>G		9	0	0		12	10	0.833333	NM_031475	Q6XYB2|Q9H0A2|Q9Y329	Silent	SNP	ENST00000377828.1	37	CCDS70.1																																																																																			.	.	none		0.741	ESPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001887.3	NM_031475		G	6500712	C	G	6500712	2	3	27	1	0	0	0	0	0	0	0	1	5256	639	23	4		4	ESPN	1	6500712	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	560469	6500712	242749909	5	10456											
ESPN	83715	hgsc.bcm.edu	37	chr1	6500762	6500762	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gcacttcgcggcgagccgcgGccacaccaaggtgctcagct	7	5	13	16	5	1	0	1	0	0	0	2	1	1	0	3	3	3	3	3	3	1	1	rs200602012		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:6500762G>A	ENST00000377828.1	+	4	920	c.752G>A	c.(751-753)gGc>gAc	p.G251D	RP1-202O8.2_ENST00000419034.1_RNA	NM_031475.2	NP_113663.2	B1AK53	ESPN_HUMAN	espin	251					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)		GCGAGCCGCGGCCACACCAAG	0.726																																					p.G251D		Atlas-SNP	.											.	ESPN	32	.	0			c.G752A						PASS	.						5	6	5					1																	6500762		1942	3927	5869	SO:0001583	missense	83715	exon4			GCCGCGGCCACAC	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.752G>A	1.37:g.6500762G>A	ENSP00000367059:p.Gly251Asp	12	0	0		35	13	0.371429	NM_031475	Q6XYB2|Q9H0A2|Q9Y329	Missense_Mutation	SNP	ENST00000377828.1	37	CCDS70.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.650081	0.87958	.	.	ENSG00000187017	ENST00000377828;ENST00000418286	T;T	0.72394	-0.65;0.89	3.84	3.84	0.44239	Ankyrin repeat-containing domain (5);	0.233607	0.34959	N	0.003544	T	0.81772	0.4893	M	0.80982	2.52	0.80722	D	1	D	0.65815	0.995	D	0.63283	0.913	D	0.83857	0.0266	10	0.54805	T	0.06	-5.9744	12.6418	0.56714	0.0:0.0:1.0:0.0	.	251	B1AK53	ESPN_HUMAN	D	251;36	ENSP00000367059:G251D;ENSP00000401793:G36D	ENSP00000367059:G251D	G	+	2	0	ESPN	6423349	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.972000	0.93424	1.989000	0.58080	0.430000	0.28490	GGC	G|0.991;A|0.010	0.010	weak		0.726	ESPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001887.3	NM_031475		A	6500762	G	A	6500762	3	1	27	1	0	0	0	0	1	0	0	0	5256	1203	42	2	766	2	ESPN	1	6500762	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	50	6500762	242749859	6	10457											
CASZ1	54897	hgsc.bcm.edu	37	chr1	10703243	10703243	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggggcacgcggtcgaagtTcttccccagcatcctccgca	6	7	13	15	4	1	0	0	0	1	0	5	1	4	0	4	4	1	4	4	4	1	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:10703243T>A	ENST00000377022.3	-	19	4311	c.3994A>T	c.(3994-3996)Aac>Tac	p.N1332Y	RP4-734G22.3_ENST00000606802.1_RNA	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	1332					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)		CGGTCGAAGTTCTTCCCCAGC	0.662																																					p.N1332Y		Atlas-SNP	.											.	CASZ1	150	.	0			c.A3994T						PASS	.						52	60	57					1																	10703243		2085	4210	6295	SO:0001583	missense	54897	exon19			CGAAGTTCTTCCC	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.3994A>T	1.37:g.10703243T>A	ENSP00000366221:p.Asn1332Tyr	59	0	0		51	16	0.313726	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	37	CCDS41246.1	.	.	.	.	.	.	.	.	.	.	T	25.7	4.666405	0.88251	.	.	ENSG00000130940	ENST00000377022	.	.	.	4.77	4.77	0.60923	.	0.000000	0.49305	U	0.000149	T	0.68705	0.3030	L	0.43152	1.355	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.71523	-0.4567	9	0.62326	D	0.03	-26.2009	14.3215	0.66489	0.0:0.0:0.0:1.0	.	1332	Q86V15	CASZ1_HUMAN	Y	1332	.	ENSP00000366221:N1332Y	N	-	1	0	CASZ1	10625830	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.530000	0.81962	1.783000	0.52377	0.459000	0.35465	AAC	.	.	none		0.662	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766		A	10703243	T	A	10703243	3	1	27	1	0	0	0	0	1	0	0	0	2687	1783	62	5	1297	5	CASZ1	1	10703243	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	4202481	10703243	238547378	7	10458											
PADI2	11240	hgsc.bcm.edu	37	chr1	17413152	17413152	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaccacatggtagagcttcCgccggcccaggatgtggata	9	8	13	11	2	0	2	0	1	0	1	1	4	1	4	4	4	1	2	4	4	2	3	rs61749340	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:17413152C>T	ENST00000375486.4	-	7	761	c.698G>A	c.(697-699)cGg>cAg	p.R233Q	PADI2_ENST00000444885.2_Missense_Mutation_p.G152R|PADI2_ENST00000375481.1_Missense_Mutation_p.R233Q	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	233					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)	GTAGAGCTTCCGCCGGCCCAG	0.612													C|||	16	0.00319489	0.0	0.0014	5008	,	,		17851	0.0		0.0119	False		,,,				2504	0.0031				p.R233Q		Atlas-SNP	.											.	PADI2	72	.	0			c.G698A						PASS	.	C	GLN/ARG	25,4381	31.7+/-61.6	1,23,2179	79	84	83		698	0	1	1	dbSNP_129	83	86,8514	49.8+/-109.6	0,86,4214	yes	missense	PADI2	NM_007365.2	43	1,109,6393	TT,TC,CC		1.0,0.5674,0.8535	benign	233/666	17413152	111,12895	2203	4300	6503	SO:0001583	missense	11240	exon7			AGCTTCCGCCGGC	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.698G>A	1.37:g.17413152C>T	ENSP00000364635:p.Arg233Gln	109	0	0		117	58	0.495726	NM_007365	Q96DA7|Q9UPN2	Missense_Mutation	SNP	ENST00000375486.4	37	CCDS177.1	10|10	0.004578754578754579|0.004578754578754579	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	9|9	0.011873350923482849|0.011873350923482849	C|C	6.143|6.143	0.394510|0.394510	0.11638|0.11638	0.005674|0.005674	0.01|0.01	ENSG00000117115|ENSG00000117115	ENST00000444885|ENST00000375486;ENST00000375481	T|T;T	0.06294|0.15834	3.32|2.39;2.39	4.71|4.71	-0.0409|-0.0409	0.13870|0.13870	.|Protein-arginine deiminase (PAD), central domain (2);	.|0.666471	.|0.15848	.|N	.|0.241686	T|T	0.03136|0.03136	0.0092|0.0092	N|N	0.02539|0.02539	-0.55|-0.55	0.22185|0.22185	N|N	0.999304|0.999304	B|B	0.06786|0.02656	0.001|0.0	B|B	0.01281|0.04013	0.0|0.001	T|T	0.42327|0.42327	-0.9458|-0.9458	9|10	0.20519|0.02654	T|T	0.43|1	-11.41|-11.41	8.498|8.498	0.33141|0.33141	0.0:0.3828:0.0:0.6172|0.0:0.3828:0.0:0.6172	rs61749340|rs61749340	152|233	B4DIU3|Q9Y2J8	.|PADI2_HUMAN	R|Q	152|233	ENSP00000405894:G152R|ENSP00000364635:R233Q;ENSP00000364630:R233Q	ENSP00000405894:G152R|ENSP00000364630:R233Q	G|R	-|-	1|2	0|0	PADI2|PADI2	17285739|17285739	0.001000|0.001000	0.12720|0.12720	0.981000|0.981000	0.43875|0.43875	0.988000|0.988000	0.76386|0.76386	-0.161000|-0.161000	0.10026|0.10026	0.067000|0.067000	0.16545|0.16545	0.460000|0.460000	0.39030|0.39030	GGA|CGG	C|0.994;T|0.006	0.006	strong		0.612	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1			T	17413152	C	T	17413152	3	4	27	1	0	0	0	0	1	0	0	0	11387	652	23	1	1339	1	PADI2	1	17413152	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	6709909	17413152	231837469	8	10459											
UBR4	23352	hgsc.bcm.edu	37	chr1	19447882	19447882	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagcagcactggggacacGccctcatccacaaggaaact	12	5	10	14	1	1	0	1	0	0	0	2	2	2	2	2	3	4	3	2	3	2	0	rs34710232	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:19447882G>A	ENST00000375254.3	-	68	9969	c.9942C>T	c.(9940-9942)ggC>ggT	p.G3314G	UBR4_ENST00000375267.2_Silent_p.G3314G|UBR4_ENST00000375226.2_Silent_p.G3290G|UBR4_ENST00000375218.3_5'Flank|UBR4_ENST00000375217.2_Silent_p.G3307G	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	3314					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)		CTGGGGACACGCCCTCATCCA	0.592													G|||	23	0.00459265	0.0008	0.0043	5008	,	,		15686	0.0		0.0159	False		,,,				2504	0.0031				p.G3314G		Atlas-SNP	.											UBR4,right_upper_lobe,carcinoma,-1,1	UBR4	415	1	0			c.C9942T						PASS	.	G		7,4399	12.9+/-30.5	0,7,2196	73	66	68		9942	-6.2	0.9	1	dbSNP_126	68	64,8536	38.8+/-94.9	0,64,4236	no	coding-synonymous	UBR4	NM_020765.2		0,71,6432	AA,AG,GG		0.7442,0.1589,0.5459		3314/5184	19447882	71,12935	2203	4300	6503	SO:0001819	synonymous_variant	23352	exon68			GGACACGCCCTCA	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.9942C>T	1.37:g.19447882G>A		360	1	0.00277778		329	175	0.531915	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	37	CCDS189.1																																																																																			G|0.996;A|0.004	0.004	strong		0.592	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		A	19447882	G	A	19447882	2	1	27	1	0	0	0	0	0	0	0	1	16919	1074	38	1		1	UBR4	1	19447882	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2034730	19447882	229802739	9	10460											
TMCO4	255104	hgsc.bcm.edu	37	chr1	20072082	20072082	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggtgatgtgcagctgcctgcCctccgtcagaggcagaaacg	8	7	14	12	2	1	3	1	1	0	2	2	3	2	3	3	2	5	3	3	2	1	0	rs35760408	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:20072082C>T	ENST00000294543.6	-	10	1061	c.820G>A	c.(820-822)Ggc>Agc	p.G274S	TMCO4_ENST00000375122.2_Intron|TMCO4_ENST00000375127.1_Missense_Mutation_p.G274S	NM_181719.4	NP_859070.3	Q5TGY1	TMCO4_HUMAN	transmembrane and coiled-coil domains 4	274						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)		AGCTGCCTGCCCTCCGTCAGA	0.572													C|||	157	0.0313498	0.0	0.0677	5008	,	,		14564	0.0605		0.0159	False		,,,				2504	0.0337				p.G274S		Atlas-SNP	.											.	TMCO4	46	.	0			c.G820A						PASS	.	C	SER/GLY	16,4390	24.3+/-50.5	0,16,2187	124	122	123		820	5	1	1	dbSNP_126	123	152,8448	73.8+/-136.5	1,150,4149	yes	missense	TMCO4	NM_181719.4	56	1,166,6336	TT,TC,CC		1.7674,0.3631,1.2917	possibly-damaging	274/635	20072082	168,12838	2203	4300	6503	SO:0001583	missense	255104	exon10			GCCTGCCCTCCGT		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.820G>A	1.37:g.20072082C>T	ENSP00000294543:p.Gly274Ser	160	0	0		130	54	0.415385	NM_181719	Q5TGY2|Q6MZN5|Q7Z6K6|Q9UQP4|Q9Y3K1	Missense_Mutation	SNP	ENST00000294543.6	37	CCDS198.1	59	0.027014652014652016	0	0.0	14	0.03867403314917127	34	0.05944055944055944	11	0.014511873350923483	C	33	5.193426	0.94960	0.003631	0.017674	ENSG00000162542	ENST00000294543;ENST00000375127	T;T	0.39997	1.05;1.05	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	T	0.11067	0.0270	L	0.39467	1.215	0.80722	D	1	D	0.54397	0.966	P	0.62885	0.908	T	0.03863	-1.0997	10	0.41790	T	0.15	-17.103	16.2009	0.82078	0.0:1.0:0.0:0.0	rs35760408	274	Q5TGY1	TMCO4_HUMAN	S	274	ENSP00000294543:G274S;ENSP00000364269:G274S	ENSP00000294543:G274S	G	-	1	0	TMCO4	19944669	1.000000	0.71417	0.988000	0.46212	0.950000	0.60333	7.072000	0.76777	2.492000	0.84095	0.455000	0.32223	GGC	C|0.981;T|0.019	0.019	strong		0.572	TMCO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007658.1	NM_181719		T	20072082	C	T	20072082	3	4	27	1	0	0	0	0	1	0	0	0	16013	623	22	2	1112	2	TMCO4	1	20072082	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	624200	20072082	229178539	10	10461											
TMCO4	255104	hgsc.bcm.edu	37	chr1	20073019	20073019	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggctgctgagcccagagcCgctgccccggcgctgccaat	5	5	13	18	4	0	2	0	1	0	1	0	2	0	2	6	2	5	4	6	2	1	0	rs34281331	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:20073019C>T	ENST00000294543.6	-	9	928	c.687G>A	c.(685-687)gcG>gcA	p.A229A	TMCO4_ENST00000375122.2_Silent_p.A229A|TMCO4_ENST00000375127.1_Silent_p.A229A	NM_181719.4	NP_859070.3	Q5TGY1	TMCO4_HUMAN	transmembrane and coiled-coil domains 4	229						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)		AGCCCAGAGCCGCTGCCCCGG	0.587													C|||	207	0.0413339	0.0242	0.0735	5008	,	,		17314	0.0605		0.0179	False		,,,				2504	0.046				p.A229A		Atlas-SNP	.											.	TMCO4	46	.	0			c.G687A						PASS	.	C		86,4320	68.1+/-105.8	0,86,2117	22	22	22		687	-10.3	0	1	dbSNP_126	22	150,8446	66.3+/-128.7	1,148,4149	no	coding-synonymous	TMCO4	NM_181719.4		1,234,6266	TT,TC,CC		1.745,1.9519,1.8151		229/635	20073019	236,12766	2203	4298	6501	SO:0001819	synonymous_variant	255104	exon9			CAGAGCCGCTGCC		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.687G>A	1.37:g.20073019C>T		374	1	0.0026738		372	185	0.497312	NM_181719	Q5TGY2|Q6MZN5|Q7Z6K6|Q9UQP4|Q9Y3K1	Silent	SNP	ENST00000294543.6	37	CCDS198.1																																																																																			C|0.973;T|0.027	0.027	strong		0.587	TMCO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007658.1	NM_181719		T	20073019	C	T	20073019	2	4	27	1	0	0	0	0	0	0	0	1	16013	639	23	1		1	TMCO4	1	20073019	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	937	20073019	229177602	11	10462											
KIF17	57576	hgsc.bcm.edu	37	chr1	21044151	21044151	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcgcagctctcgctcccgctGgttcatgggacggcagcgca	5	7	14	15	5	2	0	1	0	1	0	4	1	3	1	1	3	2	7	1	3	0	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:21044151G>A	ENST00000247986.2	-	1	359	c.49C>T	c.(49-51)Cag>Tag	p.Q17*	KIF17_ENST00000400463.3_Nonsense_Mutation_p.Q17*|KIF17_ENST00000375044.1_5'Flank|SH2D5_ENST00000460804.1_5'Flank			Q9P2E2	KIF17_HUMAN	kinesin family member 17	17	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)		CGCTCCCGCTGGTTCATGGGA	0.741																																					p.Q17X		Atlas-SNP	.											.	KIF17	130	.	0			c.C49T						PASS	.						11	12	12					1																	21044151		2178	4261	6439	SO:0001587	stop_gained	57576	exon1			CCCGCTGGTTCAT	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.49C>T	1.37:g.21044151G>A	ENSP00000247986:p.Gln17*	13	0	0		13	6	0.461538	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Nonsense_Mutation	SNP	ENST00000247986.2	37	CCDS213.1	.	.	.	.	.	.	.	.	.	.	G	39	7.498382	0.98322	.	.	ENSG00000117245	ENST00000400463;ENST00000247986	.	.	.	4.11	3.16	0.36331	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	.	2.572	0.04797	0.1049:0.1814:0.5104:0.2033	.	.	.	.	X	17	.	ENSP00000247986:Q17X	Q	-	1	0	KIF17	20916738	0.969000	0.33509	1.000000	0.80357	0.824000	0.46624	1.130000	0.31393	0.865000	0.35603	0.485000	0.47835	CAG	.	.	none		0.741	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816		A	21044151	G	A	21044151	4	1	27	1	0	0	0	0	0	1	0	0	8288	1357	47	2	3100	2	KIF17	1	21044151	Nonsense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	971132	21044151	228206470	12	10463											
NBPF3	84224	hgsc.bcm.edu	37	chr1	21797221	21797221	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagctcgggcaagctgaggAgctcaggtgagtgggccccc	7	5	18	11	1	1	2	1	2	0	0	2	4	1	4	2	5	3	4	2	5	1	0	rs145790279	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:21797221A>G	ENST00000318249.5	+	4	790	c.440A>G	c.(439-441)gAg>gGg	p.E147G	NBPF3_ENST00000342104.5_Missense_Mutation_p.E147G|NBPF3_ENST00000318220.6_Missense_Mutation_p.E91G|NBPF3_ENST00000454000.2_Missense_Mutation_p.E77G	NM_032264.3	NP_115640.1	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3	147						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)		CAAGCTGAGGAGCTCAGGTGA	0.552													.|||	22	0.00439297	0.0	0.0058	5008	,	,		17610	0.0		0.0129	False		,,,				2504	0.0051				p.T147R		Atlas-SNP	.											.	NBPF3	55	.	0			c.C440G						PASS	.	A	GLY/GLU	6,4400		0,6,2197	42	47	46		440	-2.5	0	1	dbSNP_134	46	108,8492		0,108,4192	yes	missense	NBPF3	NM_032264.2	98	0,114,6389	GG,GA,AA		1.2558,0.1362,0.8765	probably-damaging	147/634	21797221	114,12892	2203	4300	6503	SO:0001583	missense	84224	exon4			CTGAGGAGCTCAG	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.440A>G	1.37:g.21797221A>G	ENSP00000316782:p.Glu147Gly	106	0	0		115	63	0.547826	NM_001256416	A8K965|B4DSP2|I3L0I8|Q3BBW1|Q5VTG2|Q5VTG3|Q5VTG4|Q8IX78|Q8ND86|Q8TC96	Missense_Mutation	SNP	ENST00000318249.5	37	CCDS216.1	11	0.005036630036630037	0	0.0	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	.	9.834	1.189143	0.21954	0.001362	0.012558	ENSG00000142794	ENST00000454000;ENST00000318220;ENST00000318249;ENST00000417552;ENST00000342104;ENST00000434838	T;T;T;T;T	0.03860	3.78;4.03;4.03;4.03;4.03	1.23	-2.46	0.06461	.	.	.	.	.	T	0.07188	0.0182	L	0.47716	1.5	0.09310	N	1	P;D;D	0.64830	0.862;0.994;0.976	B;D;P	0.64877	0.405;0.93;0.696	T	0.10917	-1.0609	9	0.56958	D	0.05	.	5.9408	0.19192	0.3793:0.0:0.6207:0.0	.	77;147;147	B4DSP2;Q9H094-3;Q9H094	.;.;NBPF3_HUMAN	G	77;91;147;91;147;91	ENSP00000415711:E77G;ENSP00000316739:E91G;ENSP00000316782:E147G;ENSP00000340336:E147G;ENSP00000391865:E91G	ENSP00000316739:E91G	E	+	2	0	NBPF3	21669808	0.096000	0.21769	0.001000	0.08648	0.076000	0.17211	-0.001000	0.12947	-0.972000	0.03559	0.327000	0.21459	GAG	A|0.992;G|0.008	0.008	strong		0.552	NBPF3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_032264		G	21797221	A	G	21797221	3	3	27	1	0	0	0	0	1	0	0	0	10206	304	11	3	450	3	NBPF3	1	21797221	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	753070	21797221	227453400	13	10464											
USP48	84196	hgsc.bcm.edu	37	chr1	22033020	22033020	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aacaaatttgggagagaagtCttttgctcgtttgcaatcat	12	14	9	6	1	2	1	1	0	1	1	3	3	2	2	0	1	3	3	0	1	4	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:22033020C>T	ENST00000308271.9	-	17	2799	c.2151G>A	c.(2149-2151)aaG>aaA	p.K717K	USP48_ENST00000374732.3_Silent_p.K255K|USP48_ENST00000400301.1_Silent_p.K717K|USP48_ENST00000529637.1_Silent_p.K729K	NM_032236.5	NP_115612.4	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 48	717	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)			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)		GGAGAGAAGTCTTTTGCTCGT	0.388																																					p.K717K		Atlas-SNP	.											USP48,colon,carcinoma,0,1	USP48	91	1	0			c.G2151A						PASS	.						131	133	132					1																	22033020		2203	4300	6503	SO:0001819	synonymous_variant	84196	exon17			AGAAGTCTTTTGC	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.2151G>A	1.37:g.22033020C>T		198	0	0		199	63	0.316583	NM_032236	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Silent	SNP	ENST00000308271.9	37	CCDS30623.1																																																																																			.	.	none		0.388	USP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021372.1	NM_032236		T	22033020	C	T	22033020	2	4	27	1	0	0	0	0	0	0	0	1	17094	912	32	2		2	USP48	1	22033020	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	235799	22033020	227217601	14	10465											
E2F2	1870	hgsc.bcm.edu	37	chr1	23845566	23845566	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggccttgacggcaatcactGtctgctccttaaagttgcca	8	11	10	12	1	2	1	1	1	1	0	3	1	3	1	3	2	2	3	3	2	3	3	rs139052092	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:23845566G>A	ENST00000361729.2	-	5	1220	c.794C>T	c.(793-795)aCa>aTa	p.T265I	E2F2_ENST00000487237.1_5'UTR	NM_004091.3	NP_004082.1	Q14209	E2F2_HUMAN	E2F transcription factor 2	265	Dimerization. {ECO:0000255}.				intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|lens fiber cell apoptotic process (GO:1990086)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(4)|large_intestine(2)|lung(1)|ovary(3)|skin(2)|urinary_tract(1)	13		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;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.52e-24)|Colorectal(126;6.25e-08)|COAD - Colon adenocarcinoma(152;3.42e-06)|GBM - Glioblastoma multiforme(114;8.98e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00102)|KIRC - Kidney renal clear cell carcinoma(1967;0.00366)|STAD - Stomach adenocarcinoma(196;0.0132)|READ - Rectum adenocarcinoma(331;0.0652)|Lung(427;0.0888)|LUSC - Lung squamous cell carcinoma(448;0.19)		GGCAATCACTGTCTGCTCCTT	0.532													G|||	5	0.000998403	0.0	0.0	5008	,	,		20103	0.0		0.005	False		,,,				2504	0.0				p.T265I		Atlas-SNP	.											.	E2F2	31	.	0			c.C794T						PASS	.	G	ILE/THR	2,4404	4.2+/-10.8	0,2,2201	113	97	103		794	6.1	1	1	dbSNP_134	103	27,8573	19.2+/-60.6	0,27,4273	yes	missense	E2F2	NM_004091.3	89	0,29,6474	AA,AG,GG		0.314,0.0454,0.223	probably-damaging	265/438	23845566	29,12977	2203	4300	6503	SO:0001583	missense	1870	exon5			ATCACTGTCTGCT	L22846	CCDS236.1	1p36	2008-02-05			ENSG00000007968	ENSG00000007968			3114	protein-coding gene	gene with protein product		600426				8246995, 8246996	Standard	NM_004091		Approved	E2F-2	uc001bhe.2	Q14209	OTTHUMG00000003223	ENST00000361729.2:c.794C>T	1.37:g.23845566G>A	ENSP00000355249:p.Thr265Ile	126	0	0		128	64	0.5	NM_004091	B2R9W1|Q7Z6H1	Missense_Mutation	SNP	ENST00000361729.2	37	CCDS236.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	35	5.445078	0.96187	4.54E-4	0.00314	ENSG00000007968	ENST00000361729	D	0.87412	-2.25	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	D	0.89234	0.6657	M	0.63428	1.95	0.80722	D	1	P	0.51240	0.943	P	0.48189	0.57	D	0.88744	0.3245	10	0.49607	T	0.09	-19.7296	19.2232	0.93806	0.0:0.0:1.0:0.0	.	265	Q14209	E2F2_HUMAN	I	265	ENSP00000355249:T265I	ENSP00000355249:T265I	T	-	2	0	E2F2	23718153	1.000000	0.71417	0.992000	0.48379	0.988000	0.76386	9.803000	0.99136	2.885000	0.99019	0.650000	0.86243	ACA	G|0.998;A|0.002	0.002	strong		0.532	E2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008885.1	NM_004091		A	23845566	G	A	23845566	3	1	27	1	0	0	0	0	1	0	0	0	4869	1377	48	2	531	2	E2F2	1	23845566	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1812546	23845566	225405055	15	10466											
TRIM63	84676	hgsc.bcm.edu	37	chr1	26384973	26384973	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagctgctcctggtactgctGgatgagggcctcgatgaagc	7	9	14	11	1	0	2	0	2	0	0	2	4	1	3	2	3	5	4	2	3	2	1	rs148395034		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:26384973G>A	ENST00000374272.3	-	5	877	c.739C>T	c.(739-741)Cag>Tag	p.Q247*	TRIM63_ENST00000483052.1_5'Flank	NM_032588.3	NP_115977.2	Q969Q1	TRI63_HUMAN	tripartite motif containing 63, E3 ubiquitin protein ligase	247					cellular response to dexamethasone stimulus (GO:0071549)|muscle contraction (GO:0006936)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of gene expression (GO:0010468)|response to electrical stimulus involved in regulation of muscle adaptation (GO:0014878)|response to interleukin-1 (GO:0070555)|signal transduction (GO:0007165)|skeletal muscle atrophy (GO:0014732)	contractile fiber (GO:0043292)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|titin binding (GO:0031432)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|ovary(1)|skin(1)|stomach(1)	5		Colorectal(325;3.46e-05)|Lung NSC(340;0.000154)|all_lung(284;0.00021)|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;9.15e-26)|Colorectal(126;3.16e-08)|COAD - Colon adenocarcinoma(152;1.72e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000767)|BRCA - Breast invasive adenocarcinoma(304;0.00101)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		TGGTACTGCTGGATGAGGGCC	0.557													G|||	1	0.000199681	0.0	0.0014	5008	,	,		19266	0.0		0.0	False		,,,				2504	0.0				p.Q247X		Atlas-SNP	.											.	TRIM63	33	.	0			c.C739T						PASS	.	G	stop/GLN	0,4406		0,0,2203	142	129	133		739	5.5	1	1	dbSNP_134	133	6,8594	5.0+/-18.6	0,6,4294	yes	stop-gained	TRIM63	NM_032588.2		0,6,6497	AA,AG,GG		0.0698,0.0,0.0461		247/354	26384973	6,13000	2203	4300	6503	SO:0001587	stop_gained	84676	exon5			ACTGCTGGATGAG	AF353673	CCDS273.1	1p34-p33	2014-09-17	2012-02-23	2004-11-17	ENSG00000158022	ENSG00000158022		"RING-type (C3HC4) zinc fingers", "Tripartite motif containing / Tripartite motif containing"	16007	protein-coding gene	gene with protein product	"muscle-specific RING finger protein 1", "iris ring finger protein", "striated muscle RING zinc finger protein"	606131	"ring finger protein 28", "tripartite motif-containing 63", "tripartite motif containing 63"	RNF28		11243782, 11283016	Standard	NM_032588		Approved	MURF-1, IRF, SMRZ	uc001bli.2	Q969Q1	OTTHUMG00000007510	ENST00000374272.3:c.739C>T	1.37:g.26384973G>A	ENSP00000363390:p.Gln247*	153	0	0		160	73	0.45625	NM_032588	B4DN95|Q5T2I1|Q96BD3|Q96KD9|Q9BYV4	Nonsense_Mutation	SNP	ENST00000374272.3	37	CCDS273.1	.	.	.	.	.	.	.	.	.	.	G	36	5.623049	0.96660	0.0	6.98E-4	ENSG00000158022	ENST00000374272	.	.	.	5.5	5.5	0.81552	.	0.425067	0.28436	N	0.015350	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05620	T	0.96	.	9.3577	0.38177	0.0778:0.1466:0.7756:0.0	.	.	.	.	X	247	.	ENSP00000363390:Q247X	Q	-	1	0	TRIM63	26257560	0.561000	0.26578	1.000000	0.80357	0.968000	0.65278	0.572000	0.23684	2.581000	0.87130	0.561000	0.74099	CAG	G|0.999;A|0.001	0.001	strong		0.557	TRIM63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019750.1	NM_032588		A	26384973	G	A	26384973	4	1	27	1	0	0	0	0	0	1	0	0	16553	1357	47	2	342	2	TRIM63	1	26384973	Nonsense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2539407	26384973	222865648	16	10467											
MAP3K6	9064	hgsc.bcm.edu	37	chr1	27686373	27686373	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	atgtccctgtgcacgatgtgGttgtcgtgcaagtagccaag	8	11	13	9	2	0	0	0	0	0	0	2	1	1	0	2	1	3	4	2	1	3	2	rs138787990		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:27686373G>A	ENST00000493901.1	-	18	2534	c.2295C>T	c.(2293-2295)aaC>aaT	p.N765N	MAP3K6_ENST00000357582.2_Silent_p.N765N|MAP3K6_ENST00000374040.3_Silent_p.N757N	NM_004672.3	NP_004663.3	O95382	M3K6_HUMAN	mitogen-activated protein kinase kinase kinase 6	765	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		GCACGATGTGGTTGTCGTGCA	0.612																																					p.N765N		Atlas-SNP	.											.	MAP3K6	134	.	0			c.C2295T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	115	105	108		2295	2.2	1	1	dbSNP_134	108	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MAP3K6	NM_004672.3		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		765/1289	27686373	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	9064	exon17			GATGTGGTTGTCG	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.2295C>T	1.37:g.27686373G>A		176	0	0		183	89	0.486339	NM_004672	A2ACE8|A2VDG4|A2VDG5|Q59HF4|Q5SSD4|Q75PK3|Q96B75	Silent	SNP	ENST00000493901.1	37	CCDS299.1	.	.	.	.	.	.	.	.	.	.	G	3.628	-0.076203	0.07184	2.27E-4	1.16E-4	ENSG00000142733	ENST00000472410	.	.	.	5.03	2.16	0.27623	.	.	.	.	.	T	0.58004	0.2092	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50625	-0.8806	4	.	.	.	.	9.1199	0.36780	0.243:0.0:0.757:0.0	.	.	.	.	I	489	.	.	T	-	2	0	MAP3K6	27558960	1.000000	0.71417	0.989000	0.46669	0.380000	0.30137	1.262000	0.32992	0.309000	0.22966	0.561000	0.74099	ACC	G|1.000;A|0.000	0.000	weak		0.612	MAP3K6-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013469.2	NM_004672		A	27686373	G	A	27686373	2	1	27	1	0	0	0	0	0	0	0	1	9263	1252	44	2		2	MAP3K6	1	27686373	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1301400	27686373	221564248	17	10468											
PTPRU	10076	hgsc.bcm.edu	37	chr1	29606589	29606589	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ccgacatgccgtcacccctgGgcgagtctgagaacaccatc	9	6	10	16	3	2	1	1	1	1	1	3	4	2	1	5	1	2	0	5	1	1	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:29606589G>C	ENST00000345512.3	+	11	1933	c.1804G>C	c.(1804-1806)Ggc>Cgc	p.G602R	PTPRU_ENST00000356870.3_Missense_Mutation_p.G602R|PTPRU_ENST00000415600.2_3'UTR|PTPRU_ENST00000428026.2_Missense_Mutation_p.G602R|PTPRU_ENST00000460170.2_Missense_Mutation_p.G602R|PTPRU_ENST00000323874.8_Missense_Mutation_p.G602R|PTPRU_ENST00000373779.3_Missense_Mutation_p.G602R	NM_005704.4	NP_005695.3	Q92729	PTPRU_HUMAN	protein tyrosine phosphatase, receptor type, U	602	Fibronectin type-III 4. {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)		GTCACCCCTGGGCGAGTCTGA	0.652																																					p.G602R		Atlas-SNP	.											.	PTPRU	374	.	0			c.G1804C						PASS	.						65	66	65					1																	29606589		2203	4300	6503	SO:0001583	missense	10076	exon11			CCCCTGGGCGAGT	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.1804G>C	1.37:g.29606589G>C	ENSP00000334941:p.Gly602Arg	277	0	0		239	53	0.221757	NM_001195001	A6H8L1|O00197|P78399|Q59HA4|Q5SYU4|Q5SYU5|Q92735|Q92850	Missense_Mutation	SNP	ENST00000345512.3	37	CCDS334.1	.	.	.	.	.	.	.	.	.	.	G	17.62	3.434280	0.62955	.	.	ENSG00000060656	ENST00000345512;ENST00000373779;ENST00000356870;ENST00000323874;ENST00000428026;ENST00000460170	T;T;T;T;T;T	0.31510	1.53;1.55;1.55;1.55;1.49;1.55	5.25	5.25	0.73442	.	0.059602	0.64402	D	0.000002	T	0.24044	0.0582	N	0.25647	0.755	0.38689	D	0.952724	P;P;P;P;P	0.48089	0.905;0.905;0.905;0.846;0.846	B;B;B;B;B	0.43251	0.413;0.413;0.413;0.235;0.235	T	0.04454	-1.0950	9	.	.	.	.	13.2132	0.59836	0.0793:0.0:0.9207:0.0	.	602;602;602;602;602	Q92729-3;Q92729-4;Q92729-2;E9PH42;Q92729	.;.;.;.;PTPRU_HUMAN	R	602	ENSP00000334941:G602R;ENSP00000362884:G602R;ENSP00000349333:G602R;ENSP00000314987:G602R;ENSP00000392332:G602R;ENSP00000432906:G602R	.	G	+	1	0	PTPRU	29479176	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	3.471000	0.53107	2.432000	0.82394	0.544000	0.68410	GGC	.	.	none		0.652	PTPRU-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010447.1			C	29606589	G	C	29606589	3	2	27	1	0	0	0	0	1	0	0	0	12828	1232	43	4	1846	4	PTPRU	1	29606589	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1920216	29606589	219644032	18	10469											
BAI2	576	hgsc.bcm.edu	37	chr1	32221612	32221612	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agactcaccatatctcatctCggttgtgaacagatcattgc	11	12	7	11	1	4	3	3	1	2	2	6	3	4	3	1	1	2	1	1	1	2	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:32221612C>T	ENST00000373658.3	-	4	1167	c.826G>A	c.(826-828)Gag>Aag	p.E276K	BAI2_ENST00000398538.1_Missense_Mutation_p.E264K|BAI2_ENST00000398542.1_Missense_Mutation_p.E264K|BAI2_ENST00000373655.2_Missense_Mutation_p.E276K|BAI2_ENST00000257070.4_Missense_Mutation_p.E276K|BAI2_ENST00000527361.1_Missense_Mutation_p.E276K|MIR4254_ENST00000581063.1_RNA|BAI2_ENST00000398547.1_Missense_Mutation_p.E264K|BAI2_ENST00000398556.3_Missense_Mutation_p.E279K	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	276					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)		TATCTCATCTCGGTTGTGAAC	0.642																																					p.E276K		Atlas-SNP	.											.	BAI2	128	.	0			c.G826A						PASS	.						61	65	64					1																	32221612		2203	4300	6503	SO:0001583	missense	576	exon4			TCATCTCGGTTGT	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.826G>A	1.37:g.32221612C>T	ENSP00000362762:p.Glu276Lys	171	0	0		121	54	0.446281	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Missense_Mutation	SNP	ENST00000373658.3	37	CCDS346.2	.	.	.	.	.	.	.	.	.	.	C	11.52	1.662416	0.29515	.	.	ENSG00000121753	ENST00000398556;ENST00000398547;ENST00000373658;ENST00000373655;ENST00000398542;ENST00000257070;ENST00000527361;ENST00000398538;ENST00000420125;ENST00000533175	T;T;T;T;T;T;T;T;T;T	0.44083	1.61;1.81;0.99;0.99;1.97;0.93;0.93;1.01;1.59;1.45	5.33	5.33	0.75918	.	0.000000	0.42053	D	0.000761	T	0.30479	0.0766	N	0.22421	0.69	0.80722	D	1	B;B;B;B;B;B	0.24426	0.103;0.06;0.012;0.012;0.001;0.007	B;B;B;B;B;B	0.15052	0.01;0.012;0.001;0.006;0.0;0.0	T	0.04870	-1.0921	10	0.29301	T	0.29	.	16.3081	0.82856	0.0:1.0:0.0:0.0	.	264;276;264;264;276;276	A2A3C3;O60241-4;O60241-3;A2A3C1;O60241-2;O60241	.;.;.;.;.;BAI2_HUMAN	K	279;264;276;276;264;276;276;264;269;310	ENSP00000381564:E279K;ENSP00000381555:E264K;ENSP00000362762:E276K;ENSP00000362759:E276K;ENSP00000381550:E264K;ENSP00000257070:E276K;ENSP00000435397:E276K;ENSP00000381548:E264K;ENSP00000410921:E269K;ENSP00000437219:E310K	ENSP00000257070:E276K	E	-	1	0	BAI2	31994199	0.978000	0.34361	1.000000	0.80357	0.996000	0.88848	2.427000	0.44740	2.667000	0.90743	0.561000	0.74099	GAG	.	.	none		0.642	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703		T	32221612	C	T	32221612	3	4	27	1	0	0	0	0	1	0	0	0	1299	893	31	1	4051	1	BAI2	1	32221612	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2615023	32221612	217029009	19	10470											
KIAA1522	57648	hgsc.bcm.edu	37	chr1	33236824	33236824	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccaagcccaggagccctaacCcagctgcccctgctctagcc	8	5	8	20	0	1	0	0	0	1	0	1	1	1	1	7	1	7	2	7	1	3	2	rs199566536	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:33236824C>T	ENST00000373480.1	+	6	1970	c.1867C>T	c.(1867-1869)Cca>Tca	p.P623S	KIAA1522_ENST00000373481.3_Missense_Mutation_p.P634S|KIAA1522_ENST00000294521.3_Intron|KIAA1522_ENST00000401073.2_Missense_Mutation_p.P682S	NM_001198972.1	NP_001185901.1	Q9P206	K1522_HUMAN	KIAA1522	623	Pro-rich.									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)				GAGCCCTAACCCAGCTGCCCC	0.627													C|||	3	0.000599042	0.0008	0.0029	5008	,	,		7970	0.0		0.0	False		,,,				2504	0.0				p.P682S		Atlas-SNP	.											.	KIAA1522	68	.	0			c.C2044T						PASS	.	C	,SER/PRO,SER/PRO	1,3823		0,1,1911	49	56	54		,2044,1867	3.8	0.8	1		54	17,8217		0,17,4100	yes	intron,missense,missense	KIAA1522	NM_001198973.1,NM_020888.2,NM_001198972.1	,74,74	0,18,6011	TT,TC,CC		0.2065,0.0262,0.1493	,benign,benign	,682/1095,623/1036	33236824	18,12040	1912	4117	6029	SO:0001583	missense	57648	exon6			CCTAACCCAGCTG	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.1867C>T	1.37:g.33236824C>T	ENSP00000362579:p.Pro623Ser	77	0	0		71	36	0.507042	NM_020888	B4DQU8|B5MDY0|C9JH84|Q8TCQ0	Missense_Mutation	SNP	ENST00000373480.1	37	CCDS55588.1	5	0.0022893772893772895	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	C	2.344	-0.350520	0.05173	2.62E-4	0.002065	ENSG00000162522	ENST00000401073;ENST00000373481;ENST00000373480	T;T;T	0.12569	2.67;2.69;2.7	3.78	3.78	0.43462	.	0.637153	0.12767	N	0.440802	T	0.05868	0.0153	N	0.22421	0.69	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.09377	0.004;0.004;0.004	T	0.32640	-0.9899	10	0.10111	T	0.7	-0.4029	10.0745	0.42351	0.2011:0.7989:0.0:0.0	.	634;623;682	Q9P206-3;Q9P206;Q9P206-2	.;K1522_HUMAN;.	S	682;634;623	ENSP00000383851:P682S;ENSP00000362580:P634S;ENSP00000362579:P623S	ENSP00000362579:P623S	P	+	1	0	KIAA1522	33009411	0.002000	0.14202	0.843000	0.33291	0.062000	0.15995	1.732000	0.38146	1.802000	0.52723	0.655000	0.94253	CCA	C|0.997;T|0.003	0.003	strong		0.627	KIAA1522-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022130.1			T	33236824	C	T	33236824	3	4	27	1	0	0	0	0	1	0	0	0	8247	623	22	2	2066	2	KIAA1522	1	33236824	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1015212	33236824	216013797	20	10471											
S100PBP	64766	hgsc.bcm.edu	37	chr1	33292008	33292008	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagaaaaattcatcgtacaGcctgggaccagtagctgaga	15	7	11	8	1	1	2	1	1	0	2	2	5	1	3	2	1	3	3	2	1	4	3	rs61739743	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:33292008G>A	ENST00000373475.5	+	3	562	c.308G>A	c.(307-309)aGc>aAc	p.S103N	S100PBP_ENST00000398243.3_Missense_Mutation_p.S103N|S100PBP_ENST00000356689.3_3'UTR|S100PBP_ENST00000373476.1_Missense_Mutation_p.S103N	NM_022753.3	NP_073590.2			S100P binding protein											endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|stomach(1)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				TCATCGTACAGCCTGGGACCA	0.473													G|||	35	0.00698882	0.0182	0.0072	5008	,	,		19748	0.0		0.006	False		,,,				2504	0.0				p.S103N		Atlas-SNP	.											.	S100PBP	31	.	0			c.G308A						PASS	.	G	ASN/SER,ASN/SER	72,4334	62.3+/-99.4	1,70,2132	56	52	53		308,308	0.1	0.1	1	dbSNP_129	53	65,8535	39.8+/-96.3	0,65,4235	yes	missense,missense	S100PBP	NM_001017406.1,NM_022753.2	46,46	1,135,6367	AA,AG,GG		0.7558,1.6341,1.0534	benign,benign	103/342,103/409	33292008	137,12869	2203	4300	6503	SO:0001583	missense	64766	exon3			CGTACAGCCTGGG	BX647916	CCDS30666.1	1p35.1	2008-02-05			ENSG00000116497	ENSG00000116497			25768	protein-coding gene	gene with protein product	"S100P binding protein 1"	611889				12477932	Standard	NM_022753		Approved	FLJ12903, S100PBPR	uc001bwc.4	Q96BU1	OTTHUMG00000003955	ENST00000373475.5:c.308G>A	1.37:g.33292008G>A	ENSP00000362574:p.Ser103Asn	110	0	0		82	36	0.439024	NM_001256121		Missense_Mutation	SNP	ENST00000373475.5	37	CCDS30666.1	16	0.007326007326007326	11	0.022357723577235773	3	0.008287292817679558	0	0.0	2	0.002638522427440633	G	4.857	0.159396	0.09236	0.016341	0.007558	ENSG00000116497	ENST00000530710;ENST00000373476;ENST00000373475;ENST00000531123;ENST00000398243;ENST00000356689;ENST00000526230;ENST00000531256;ENST00000482212	.	.	.	5.32	0.136	0.14780	.	0.673278	0.15732	N	0.247367	T	0.12860	0.0312	N	0.20986	0.625	0.09310	N	0.999997	B;B	0.19583	0.037;0.008	B;B	0.22386	0.039;0.009	T	0.12066	-1.0562	9	0.45353	T	0.12	-0.1643	5.5651	0.17167	0.2246:0.2654:0.51:0.0	rs61739743	103;103	A8MTZ6;Q96BU1	.;S1PBP_HUMAN	N	103	.	ENSP00000349117:S103N	S	+	2	0	S100PBP	33064595	0.603000	0.26924	0.082000	0.20525	0.073000	0.16967	0.412000	0.21131	-0.034000	0.13713	0.655000	0.94253	AGC	G|0.990;A|0.010	0.010	strong		0.473	S100PBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011266.1	NM_022753		A	33292008	G	A	33292008	3	1	27	1	0	0	0	0	1	0	0	0	13806	971	34	2	310	2	S100PBP	1	33292008	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	55184	33292008	215958613	21	10472											
MAP7D1	55700	hgsc.bcm.edu	37	chr1	36636774	36636774	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctaggccagcccccccgcaGgaagagtccccttcctctga	7	6	9	19	1	1	2	0	1	1	1	3	3	3	3	8	2	1	1	8	2	2	2	rs139650826	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:36636774G>A	ENST00000373151.2	+	2	465	c.249G>A	c.(247-249)caG>caA	p.Q83Q	MAP7D1_ENST00000373150.4_Silent_p.Q83Q|MAP7D1_ENST00000316156.4_Silent_p.Q83Q	NM_018067.3	NP_060537.3	Q3KQU3	MA7D1_HUMAN	MAP7 domain containing 1	83	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)				CCCCCCCGCAGGAAGAGTCCC	0.642													G|||	23	0.00459265	0.0008	0.0043	5008	,	,		13296	0.0		0.0179	False		,,,				2504	0.001				p.Q83Q		Atlas-SNP	.											.	MAP7D1	62	.	0			c.G249A						PASS	.	G		12,4394	19.1+/-41.9	0,12,2191	39	43	41		249	2.2	1	1	dbSNP_134	41	125,8475	62.4+/-124.4	1,123,4176	no	coding-synonymous	MAP7D1	NM_018067.3		1,135,6367	AA,AG,GG		1.4535,0.2724,1.0534		83/842	36636774	137,12869	2203	4300	6503	SO:0001819	synonymous_variant	55700	exon2			CCCGCAGGAAGAG	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.249G>A	1.37:g.36636774G>A		72	0	0		82	39	0.47561	NM_018067	D3DPS4|Q7L8J5|Q8N905|Q8TAK0|Q9HBQ2|Q9NW29|Q9ULN3	Silent	SNP	ENST00000373151.2	37	CCDS30673.1																																																																																			G|0.992;A|0.008	0.008	strong		0.642	MAP7D1-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382095.1	NM_018067		A	36636774	G	A	36636774	2	1	27	1	0	0	0	0	0	0	0	1	9276	991	35	2		2	MAP7D1	1	36636774	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	3344766	36636774	212613847	22	10473											
MACF1	23499	hgsc.bcm.edu	37	chr1	39816626	39816626	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaggcgctccaggaagagaCacgtgtggcccagaaggaac	12	4	15	10	2	0	3	0	1	0	2	1	6	1	5	2	4	1	1	2	4	3	0	rs116162513	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:39816626C>A	ENST00000372915.3	+	42	11237	c.11150C>A	c.(11149-11151)aCa>aAa	p.T3717K	MACF1_ENST00000545844.1_Missense_Mutation_p.T1650K|MACF1_ENST00000567887.1_Missense_Mutation_p.T3749K|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000539005.1_Missense_Mutation_p.T1650K|MACF1_ENST00000361689.2_Missense_Mutation_p.T1650K|MACF1_ENST00000564288.1_Missense_Mutation_p.T3712K|MACF1_ENST00000317713.7_Missense_Mutation_p.T1650K|MACF1_ENST00000289893.4_Missense_Mutation_p.T2152K			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	3717					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)			CAGGAAGAGACACGTGTGGCC	0.493																																					p.T1650K		Atlas-SNP	.											.	MACF1	909	.	0			c.C4949A						PASS	.						72	70	71					1																	39816626		2203	4300	6503	SO:0001583	missense	23499	exon39			AAGAGACACGTGT	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.11150C>A	1.37:g.39816626C>A	ENSP00000362006:p.Thr3717Lys	80	0	0		57	14	0.245614	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.97|18.97	3.735836|3.735836	0.69189|0.69189	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000372925|ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000530262;ENST00000289893	.|T;T;T;T;T;T;T	.|0.62232	.|1.27;0.04;1.27;1.27;1.27;1.27;1.07	6.06|6.06	5.15|5.15	0.70609|0.70609	.|.	.|0.190098	.|0.37012	.|N	.|0.002284	T|T	0.70150|0.70150	0.3191|0.3191	L|L	0.60455|0.60455	1.87|1.87	0.44843|0.44843	D|D	0.997855|0.997855	.|B;P;D;B	.|0.54772	.|0.433;0.864;0.968;0.225	.|B;P;P;B	.|0.56343	.|0.375;0.669;0.796;0.155	T|T	0.73075|0.73075	-0.4097|-0.4097	5|10	.|0.66056	.|D	.|0.02	.|.	12.0779|12.0779	0.53655|0.53655	0.0:0.8611:0.0:0.1389|0.0:0.8611:0.0:0.1389	.|.	.|3717;1650;1650;1615	.|Q9UPN3;F8W8Q1;Q9UPN3-2;Q9UPN3-3	.|MACF1_HUMAN;.;.;.	E|K	783|1650;3717;1650;1650;1650;1799;2152	.|ENSP00000439537:T1650K;ENSP00000362006:T3717K;ENSP00000354573:T1650K;ENSP00000313438:T1650K;ENSP00000444364:T1650K;ENSP00000437059:T1799K;ENSP00000289893:T2152K	.|ENSP00000289893:T2152K	D|T	+|+	3|2	2|0	MACF1|MACF1	39589213|39589213	0.985000|0.985000	0.35326|0.35326	0.012000|0.012000	0.15200|0.15200	0.872000|0.872000	0.50106|0.50106	3.723000|3.723000	0.54955|0.54955	1.584000|1.584000	0.49913|0.49913	0.650000|0.650000	0.86243|0.86243	GAC|ACA	C|0.999;T|0.001	.	alt		0.493	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		A	39816626	C	A	39816626	3	1	27	1	0	0	0	0	1	0	0	0	9153	478	17	4	11250	4	MACF1	1	39816626	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3179852	39816626	209433995	23	10474											
ELOVL1	64834	hgsc.bcm.edu	37	chr1	43830438	43830438	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagctcaatgaacttggagaAgaggaagagccaggccaccc	14	4	12	11	0	1	4	1	1	0	3	1	6	1	5	3	3	3	1	3	3	4	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:43830438A>G	ENST00000372458.3	-	5	463	c.346T>C	c.(346-348)Ttc>Ctc	p.F116L	ELOVL1_ENST00000413844.2_Missense_Mutation_p.F89L|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	116					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)				AACTTGGAGAAGAGGAAGAGC	0.498																																					p.F116L		Atlas-SNP	.											.	ELOVL1	18	.	0			c.T346C						PASS	.						112	123	119					1																	43830438		2203	4300	6503	SO:0001583	missense	64834	exon5			TGGAGAAGAGGAA	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.346T>C	1.37:g.43830438A>G	ENSP00000361536:p.Phe116Leu	93	0	0		79	42	0.531646	NM_001256399	B4DP24|Q53HT2|Q5JUY3|Q8WXU3|Q9NVD9|Q9Y396	Missense_Mutation	SNP	ENST00000372458.3	37	CCDS485.1	.	.	.	.	.	.	.	.	.	.	A	15.45	2.837426	0.50951	.	.	ENSG00000066322	ENST00000372458;ENST00000413844	T;T	0.16073	2.37;2.37	5.77	4.65	0.58169	.	0.042915	0.85682	N	0.000000	T	0.18002	0.0432	L	0.45470	1.425	0.80722	D	1	B;B	0.13145	0.001;0.007	B;B	0.28465	0.011;0.09	T	0.02844	-1.1103	10	0.38643	T	0.18	0.4038	10.9623	0.47393	0.9261:0.0:0.0739:0.0	.	89;116	B4DP24;Q9BW60	.;ELOV1_HUMAN	L	116;89	ENSP00000361536:F116L;ENSP00000416024:F89L	ENSP00000361536:F116L	F	-	1	0	ELOVL1	43603025	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	4.126000	0.57937	1.026000	0.39733	0.533000	0.62120	TTC	.	.	none		0.498	ELOVL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019496.1	NM_022821		G	43830438	A	G	43830438	3	3	27	1	0	0	0	0	1	0	0	0	5075	72	3	3	509	3	ELOVL1	1	43830438	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	4013812	43830438	205420183	24	10475											
MKNK1	8569	hgsc.bcm.edu	37	chr1	47028362	47028362	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gccccggtcccagccacagtCggccccgcagtgacccacga	7	3	11	20	4	0	1	0	1	0	0	2	2	1	1	7	2	1	1	7	2	0	0	rs55791614	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:47028362C>T	ENST00000371946.4	-	11	1085	c.922G>A	c.(922-924)Gac>Aac	p.D308N	MKNK1_ENST00000371945.4_Missense_Mutation_p.D267N|MKNK1_ENST00000428112.2_Missense_Mutation_p.D267N|MKNK1_ENST00000371944.4_Missense_Mutation_p.D172N|MKNK1_ENST00000341183.5_Missense_Mutation_p.D267N|MKNK1-AS1_ENST00000602433.1_RNA	NM_003684.5	NP_003675.2	Q9BUB5	MKNK1_HUMAN	MAP kinase interacting serine/threonine kinase 1	308	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		D -> N (in dbSNP:rs55791614). {ECO:0000269|PubMed:17344846}.		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)					CAGCCACAGTCGGCCCCGCAG	0.662													C|||	10	0.00199681	0.0	0.0043	5008	,	,		16040	0.0		0.005	False		,,,				2504	0.002				p.D308N		Atlas-SNP	.											.	MKNK1	36	.	0			c.G922A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP	11,4385		0,11,2187	27	24	25		799,922,799	4.5	1	1	dbSNP_129	25	60,8500		1,58,4221	no	missense,missense,missense	MKNK1	NM_001135553.1,NM_003684.4,NM_198973.2	23,23,23	1,69,6408	TT,TC,CC		0.7009,0.2502,0.548	benign,benign,benign	267/425,308/466,267/348	47028362	71,12885	2198	4280	6478	SO:0001583	missense	8569	exon11			CACAGTCGGCCCC	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.922G>A	1.37:g.47028362C>T	ENSP00000361014:p.Asp308Asn	181	0	0		171	104	0.608187	NM_003684	D3DQ20|D3DQ21|O00312|Q5TC06|Q5TC07|Q6V0N6	Missense_Mutation	SNP	ENST00000371946.4	37	CCDS538.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	15.55	2.866573	0.51588	0.002502	0.007009	ENSG00000079277	ENST00000371946;ENST00000371945;ENST00000371944;ENST00000341183;ENST00000428112	T;T;T;T;T	0.20598	2.06;2.06;2.06;2.06;2.06	5.42	4.49	0.54785	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.086825	0.85682	D	0.000000	T	0.08358	0.0208	N	0.12502	0.225	0.80722	D	1	B;B;B;B;B;P	0.42649	0.102;0.245;0.102;0.083;0.193;0.786	B;B;B;B;B;B	0.37888	0.031;0.054;0.031;0.018;0.09;0.26	T	0.09596	-1.0667	10	0.32370	T	0.25	.	13.8642	0.63578	0.0:0.9252:0.0:0.0748	rs55791614	172;172;267;267;267;308	B4DQK5;Q7Z319;A8K341;Q9BUB5-3;Q9BUB5-2;Q9BUB5	.;.;.;.;.;MKNK1_HUMAN	N	308;267;172;267;267	ENSP00000361014:D308N;ENSP00000361013:D267N;ENSP00000361012:D172N;ENSP00000339573:D267N;ENSP00000411135:D267N	ENSP00000339573:D267N	D	-	1	0	MKNK1	46800949	0.994000	0.37717	0.977000	0.42913	0.672000	0.39443	3.119000	0.50422	2.826000	0.97356	0.563000	0.77884	GAC	C|0.996;T|0.004	0.004	strong		0.662	MKNK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021897.2	NM_003684		T	47028362	C	T	47028362	3	4	27	1	0	0	0	0	1	0	0	0	9613	884	31	1	491	1	MKNK1	1	47028362	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3197924	47028362	202222259	25	10476											
SLC5A9	200010	hgsc.bcm.edu	37	chr1	48705066	48705066	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctggagttctcatacccaGcgccagcctgtggggaggtg	6	9	14	12	1	1	0	1	0	1	0	3	2	2	2	4	4	3	1	4	4	1	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:48705066G>A	ENST00000438567.2	+	12	1586	c.1534G>A	c.(1534-1536)Gcg>Acg	p.A512T	SLC5A9_ENST00000236495.5_Missense_Mutation_p.A537T|SLC5A9_ENST00000533824.1_Missense_Mutation_p.A533T	NM_001011547.2	NP_001011547.2	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 9	512					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						CTCATACCCAGCGCCAGCCTG	0.597																																					p.A537T		Atlas-SNP	.											.	SLC5A9	82	.	0			c.G1609A						PASS	.						172	163	166					1																	48705066		2203	4300	6503	SO:0001583	missense	200010	exon13			TACCCAGCGCCAG	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.1534G>A	1.37:g.48705066G>A	ENSP00000401730:p.Ala512Thr	230	1	0.00434783		194	87	0.448454	NM_001135181	B3KY87|B7ZL45|B7ZL47|E9PAK4|E9PJ08|Q5TET3	Missense_Mutation	SNP	ENST00000438567.2	37	CCDS30709.2	.	.	.	.	.	.	.	.	.	.	G	10.33	1.320633	0.23994	.	.	ENSG00000117834	ENST00000533824;ENST00000438567;ENST00000236495	T;T;T	0.63096	-0.02;-0.02;-0.02	5.18	5.18	0.71444	.	0.458166	0.26086	N	0.026430	T	0.41488	0.1161	N	0.11673	0.155	0.29064	N	0.883691	B;B;B	0.19445	0.036;0.005;0.009	B;B;B	0.13407	0.007;0.009;0.009	T	0.07520	-1.0768	10	0.06757	T	0.87	.	17.85	0.88744	0.0:0.0:1.0:0.0	.	533;512;537	E9PJ08;Q2M3M2;E9PAK4	.;SC5A9_HUMAN;.	T	533;512;537	ENSP00000431900:A533T;ENSP00000401730:A512T;ENSP00000236495:A537T	ENSP00000236495:A537T	A	+	1	0	SLC5A9	48477653	0.000000	0.05858	0.855000	0.33649	0.575000	0.36095	0.380000	0.20602	2.682000	0.91365	0.650000	0.86243	GCG	.	.	none		0.597	SLC5A9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022061.3	XM_117174		A	48705066	G	A	48705066	3	1	27	1	0	0	0	0	1	0	0	0	14687	971	34	2	1659	2	SLC5A9	1	48705066	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1676704	48705066	200545555	26	10477											
EPS15	2060	hgsc.bcm.edu	37	chr1	51869184	51869184	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcagtcacaccagaaggcagTagttcaggactacttcttgc	11	10	9	11	0	4	1	3	0	1	1	4	2	4	2	1	2	2	3	1	2	3	5	rs144030750	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:51869184T>G	ENST00000371733.3	-	17	1794	c.1698A>C	c.(1696-1698)ctA>ctC	p.L566L	EPS15_ENST00000396122.4_Silent_p.L243L|EPS15_ENST00000493793.1_5'UTR|EPS15_ENST00000371730.2_Silent_p.L432L	NM_001981.2	NP_001972.1	P42566	EPS15_HUMAN	epidermal growth factor receptor pathway substrate 15	566					cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|protein transport (GO:0015031)|vesicle organization (GO:0016050)	AP-2 adaptor complex (GO:0030122)|ciliary membrane (GO:0060170)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|polyubiquitin binding (GO:0031593)	p.0?(2)		endometrium(3)|kidney(5)|large_intestine(8)|lung(13)|prostate(2)|skin(1)|stomach(1)|urinary_tract(2)	35						CAGAAGGCAGTAGTTCAGGAC	0.338			T	MLL	ALL																																p.L566L		Atlas-SNP	.		Dom	yes		1	1p32	2060	epidermal growth factor receptor pathway substrate 15 (AF1p)		L	.	EPS15	72	.	2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)	c.A1698C						PASS	.	T	,	2,4404	6.2+/-15.9	0,2,2201	95	92	93		756,1698	2.2	0.8	1	dbSNP_134	93	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	EPS15	NM_001159969.1,NM_001981.2	,	0,3,6500	GG,GT,TT		0.0116,0.0454,0.0231	,	252/583,566/897	51869184	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	2060	exon17			AGGCAGTAGTTCA	BC054006	CCDS557.1	1p32	2013-01-10			ENSG00000085832	ENSG00000085832		"EF-hand domain containing"	3419	protein-coding gene	gene with protein product		600051				8183552	Standard	NM_001159969		Approved	AF-1P, MLLT5	uc001csq.1	P42566	OTTHUMG00000008192	ENST00000371733.3:c.1698A>C	1.37:g.51869184T>G		242	0	0		203	104	0.512315	NM_001981	B2R8J7|D3DPJ2|Q5SRH4	Silent	SNP	ENST00000371733.3	37	CCDS557.1																																																																																			T|0.999;G|0.001	0.001	strong		0.338	EPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022422.1	NM_001981		G	51869184	T	G	51869184	2	3	27	1	0	0	0	0	0	0	0	1	5194	1625	57	5		5	EPS15	1	51869184	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	3164118	51869184	197381437	27	10478											
CC2D1B	200014	hgsc.bcm.edu	37	chr1	52822722	52822722	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgggcatacacctcctccGccttctgggagagtcgcagg	6	8	13	14	2	1	1	0	0	1	1	4	2	3	1	4	3	1	3	4	3	1	2	rs201266966		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:52822722G>A	ENST00000371586.2	-	16	1985	c.1847C>T	c.(1846-1848)gCg>gTg	p.A616V	CC2D1B_ENST00000284376.3_Missense_Mutation_p.A610V|CC2D1B_ENST00000460261.1_5'UTR|CC2D1B_ENST00000438831.1_5'UTR	NM_032449.2	NP_115825.1	Q5T0F9	C2D1B_HUMAN	coiled-coil and C2 domain containing 1B	616						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(6)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	27						CACCTCCTCCGCCTTCTGGGA	0.607													G|||	1	0.000199681	0.0	0.0	5008	,	,		19738	0.0		0.0	False		,,,				2504	0.001				p.A616V		Atlas-SNP	.											CC2D1B,NS,carcinoma,0,1	CC2D1B	73	1	0			c.C1847T						PASS	.						59	57	58					1																	52822722		2202	4300	6502	SO:0001583	missense	200014	exon16			TCCTCCGCCTTCT	AB058739	CCDS30714.1	1p32.3	2008-02-05			ENSG00000154222	ENSG00000154222			29386	protein-coding gene	gene with protein product						11347906	Standard	NM_032449		Approved	KIAA1836	uc001ctq.2	Q5T0F9	OTTHUMG00000008102	ENST00000371586.2:c.1847C>T	1.37:g.52822722G>A	ENSP00000360642:p.Ala616Val	164	0	0		173	84	0.485549	NM_032449	Q49AE8|Q5T0F8|Q5T0G0|Q6ZNQ1|Q96AP3|Q96I04|Q96JJ1	Missense_Mutation	SNP	ENST00000371586.2	37	CCDS30714.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.17|12.17	1.858338|1.858338	0.32791|0.32791	.|.	.|.	ENSG00000154222|ENSG00000154222	ENST00000371586;ENST00000284376;ENST00000371573|ENST00000438021;ENST00000450942	T;T|.	0.28895|.	1.59;1.59|.	5.65|5.65	4.73|4.73	0.59995|0.59995	.|.	0.170245|.	0.51477|.	N|.	0.000082|.	T|T	0.71685|0.71685	0.3369|0.3369	M|M	0.61703|0.61703	1.905|1.905	0.80722|0.80722	D|D	1|1	B;B;B|.	0.21688|.	0.059;0.041;0.024|.	B;B;B|.	0.16722|.	0.012;0.016;0.008|.	T|T	0.69687|0.69687	-0.5078|-0.5078	10|5	0.59425|.	D|.	0.04|.	-3.3081|-3.3081	16.7669|16.7669	0.85526|0.85526	0.0692:0.0:0.9308:0.0|0.0692:0.0:0.9308:0.0	.|.	396;610;616|.	Q5T0G1;Q5T0F9-2;Q5T0F9|.	.;.;C2D1B_HUMAN|.	V|W	616;610;524|397;530	ENSP00000360642:A616V;ENSP00000284376:A610V|.	ENSP00000284376:A610V|.	A|R	-|-	2|1	0|2	CC2D1B|CC2D1B	52595310|52595310	1.000000|1.000000	0.71417|0.71417	0.797000|0.797000	0.32132|0.32132	0.144000|0.144000	0.21451|0.21451	5.830000|5.830000	0.69324|0.69324	0.953000|0.953000	0.37825|0.37825	-0.797000|-0.797000	0.03246|0.03246	GCG|CGG	G|0.997;A|0.003	0.003	weak		0.607	CC2D1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022189.1	NM_032449		A	52822722	G	A	52822722	3	1	27	1	0	0	0	0	1	0	0	0	2729	1087	38	1	765	1	CC2D1B	1	52822722	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	953538	52822722	196427899	28	10479											
CDCP2	200008	hgsc.bcm.edu	37	chr1	54605769	54605769	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcatggccatgtatacctcCtggcattctcctggatgggg	6	11	12	12	1	1	0	0	0	1	0	3	1	2	1	4	5	1	3	4	5	2	3	rs372034165		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:54605769C>T	ENST00000371330.1	-	4	1621	c.774G>A	c.(772-774)caG>caA	p.Q258Q	RP11-446E24.4_ENST00000525949.1_5'Flank|CDCP2_ENST00000530059.1_5'Flank	NM_201546.2	NP_963840.2	Q5VXM1	CDCP2_HUMAN	CUB domain containing protein 2	258	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.					extracellular region (GO:0005576)				kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|stomach(1)	24						TGTATACCTCCTGGCATTCTC	0.612																																					p.Q258Q		Atlas-SNP	.											.	CDCP2	52	.	0			c.G774A						PASS	.	C		0,4218		0,0,2109	39	31	34		774	4	1	1		34	1,8315		0,1,4157	no	coding-synonymous	CDCP2	NM_201546.2		0,1,6266	TT,TC,CC		0.012,0.0,0.0080		258/450	54605769	1,12533	2109	4158	6267	SO:0001819	synonymous_variant	200008	exon4			TACCTCCTGGCAT		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.774G>A	1.37:g.54605769C>T		177	0	0		138	68	0.492754	NM_201546	Q6ZWJ3	Silent	SNP	ENST00000371330.1	37	CCDS588.2																																																																																			.	.	none		0.612	CDCP2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000022209.2	NM_201546		T	54605769	C	T	54605769	2	4	27	1	0	0	0	0	0	0	0	1	3096	680	24	2		2	CDCP2	1	54605769	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1783047	54605769	194644852	29	10480											
PCSK9	255738	hgsc.bcm.edu	37	chr1	55505679	55505679	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acggcctggccgaagcacccGagcacggaaccacagccacc	11	1	11	18	4	0	0	0	0	0	0	0	3	0	1	6	3	4	2	6	3	2	0	rs145886902	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:55505679G>A	ENST00000302118.5	+	1	459	c.169G>A	c.(169-171)Gag>Aag	p.E57K	PCSK9_ENST00000452118.2_Missense_Mutation_p.E57K|PCSK9_ENST00000543384.1_5'Flank	NM_174936.3	NP_777596.2	Q8NBP7	PCSK9_HUMAN	proprotein convertase subtilisin/kexin type 9	57			E -> K. {ECO:0000269|PubMed:16465619}.		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						CGAAGCACCCGAGCACGGAAC	0.716													G|||	5	0.000998403	0.0038	0.0	5008	,	,		14732	0.0		0.0	False		,,,				2504	0.0				p.E57K	Pancreas(137;1454 1827 5886 22361 42375)	Atlas-SNP	.											.	PCSK9	76	.	0			c.G169A	GRCh37	CM060421	PCSK9	M	rs145886902	PASS	.	G	LYS/GLU	11,4359		0,11,2174	29	24	26		169	-4.7	0	1	dbSNP_134	26	2,8534		0,2,4266	yes	missense	PCSK9	NM_174936.3	56	0,13,6440	AA,AG,GG		0.0234,0.2517,0.1007	benign	57/693	55505679	13,12893	2185	4268	6453	SO:0001583	missense	255738	exon1			GCACCCGAGCACG	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.169G>A	1.37:g.55505679G>A	ENSP00000303208:p.Glu57Lys	87	0	0		106	22	0.207547	NM_174936	A8T640|C0JYY9|Q5PSM5|Q5SZQ2	Missense_Mutation	SNP	ENST00000302118.5	37	CCDS603.1	.	.	.	.	.	.	.	.	.	.	G	7.413	0.635044	0.14322	0.002517	2.34E-4	ENSG00000169174	ENST00000302118;ENST00000452118	T;T	0.71461	-0.51;-0.57	3.09	-4.71	0.03279	.	1.506200	0.05619	U	0.579657	T	0.45296	0.1335	N	0.14661	0.345	0.09310	N	0.999991	B	0.02656	0.0	B	0.01281	0.0	T	0.26292	-1.0107	10	0.11794	T	0.64	3.2202	5.4094	0.16341	0.1325:0.2249:0.5426:0.1	.	57	Q8NBP7	PCSK9_HUMAN	K	57	ENSP00000303208:E57K;ENSP00000401598:E57K	ENSP00000303208:E57K	E	+	1	0	PCSK9	55278267	0.000000	0.05858	0.000000	0.03702	0.228000	0.25075	-0.351000	0.07711	-0.725000	0.04901	-0.802000	0.03209	GAG	G|0.999;A|0.001	0.001	strong		0.716	PCSK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022280.1	NM_174936		A	55505679	G	A	55505679	3	1	27	1	0	0	0	0	1	0	0	0	11615	1059	37	1	171	1	PCSK9	1	55505679	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	899910	55505679	193744942	30	10481											
ATG4C	84938	hgsc.bcm.edu	37	chr1	63284834	63284834	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgaaggaaacaattgggaaaTattctgatgatcatgaaatg	17	11	10	3	0	2	4	1	4	1	0	2	6	2	6	0	2	1	0	0	2	6	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:63284834T>A	ENST00000317868.4	+	5	760	c.553T>A	c.(553-555)Tat>Aat	p.Y185N	ATG4C_ENST00000371120.3_Missense_Mutation_p.Y185N	NM_032852.3	NP_116241.2	Q96DT6	ATG4C_HUMAN	autophagy related 4C, cysteine peptidase	185					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						AATTGGGAAATATTCTGATGA	0.363																																					p.Y185N		Atlas-SNP	.											.	ATG4C	96	.	0			c.T553A						PASS	.						106	113	111					1																	63284834		2203	4300	6503	SO:0001583	missense	84938	exon5			GGGAAATATTCTG	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.553T>A	1.37:g.63284834T>A	ENSP00000322159:p.Tyr185Asn	162	0	0		114	26	0.22807	NM_178221	A6NLR8|D3DQ58|Q96K04	Missense_Mutation	SNP	ENST00000317868.4	37	CCDS623.1	.	.	.	.	.	.	.	.	.	.	T	10.07	1.249108	0.22880	.	.	ENSG00000125703	ENST00000317868;ENST00000371120;ENST00000540025;ENST00000371118	.	.	.	5.92	-1.03	0.10102	.	1.091040	0.06854	N	0.797869	T	0.09862	0.0242	L	0.34521	1.04	0.09310	N	1	B	0.02656	0.0	B	0.09377	0.004	T	0.26121	-1.0112	9	0.28530	T	0.3	-1.3461	1.7001	0.02870	0.1081:0.2507:0.2521:0.3891	.	185	Q96DT6	ATG4C_HUMAN	N	185	.	ENSP00000322159:Y185N	Y	+	1	0	ATG4C	63057422	0.000000	0.05858	0.003000	0.11579	0.952000	0.60782	0.067000	0.14510	0.136000	0.18733	0.528000	0.53228	TAT	.	.	none		0.363	ATG4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025332.2	NM_032852		A	63284834	T	A	63284834	3	1	27	1	0	0	0	0	1	0	0	0	1098	1406	49	5	567	5	ATG4C	1	63284834	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	7779155	63284834	185965787	31	10482											
RAVER2	55225	hgsc.bcm.edu	37	chr1	65243466	65243466	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttacatcagaagagtttgaAgaacttgttcgtgcttatgg	11	15	10	5	1	1	4	1	1	0	3	2	4	1	4	0	1	3	3	0	1	5	6	rs41285400	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:65243466A>G	ENST00000294428.3	+	3	555	c.477A>G	c.(475-477)gaA>gaG	p.E159E	RAVER2_ENST00000371072.4_Silent_p.E159E|RAVER2_ENST00000430964.2_5'Flank			Q9HCJ3	RAVR2_HUMAN	ribonucleoprotein, PTB-binding 2	159	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						AAGAGTTTGAAGAACTTGTTC	0.368													A|||	13	0.00259585	0.0015	0.0029	5008	,	,		18846	0.001		0.007	False		,,,				2504	0.001				p.E159E		Atlas-SNP	.											.	RAVER2	56	.	0			c.A477G						PASS	.	A		9,3707		0,9,1849	208	187	194		477	1.4	1	1	dbSNP_127	194	119,8097		0,119,3989	no	coding-synonymous	RAVER2	NM_018211.3		0,128,5838	GG,GA,AA		1.4484,0.2422,1.0727		159/679	65243466	128,11804	1858	4108	5966	SO:0001819	synonymous_variant	55225	exon3			GTTTGAAGAACTT	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.477A>G	1.37:g.65243466A>G		249	0	0		237	120	0.506329	NM_018211	Q6P141|Q9NPV7	Silent	SNP	ENST00000294428.3	37																																																																																				A|0.994;G|0.006	0.006	strong		0.368	RAVER2-201	KNOWN	basic	protein_coding	protein_coding		NM_018211		G	65243466	A	G	65243466	2	3	27	1	0	0	0	0	0	0	0	1	13110	69	3	3		3	RAVER2	1	65243466	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	1958632	65243466	184007155	32	10483											
DIRAS3	9077	hgsc.bcm.edu	37	chr1	68512893	68512893	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgatcttcctgtggggctTgaaggcgcggaggataagca	8	10	15	8	2	2	2	0	2	2	0	3	4	3	4	1	5	1	2	1	5	2	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:68512893T>G	ENST00000370981.1	-	4	724	c.88A>C	c.(88-90)Aag>Cag	p.K30Q	GNG12-AS1_ENST00000413628.1_RNA|GNG12-AS1_ENST00000420587.1_RNA|DIRAS3_ENST00000395201.1_Missense_Mutation_p.K30Q			O95661	DIRA3_HUMAN	DIRAS family, GTP-binding RAS-like 3	30					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						CTGTGGGGCTTGAAGGCGCGG	0.607																																					p.K30Q		Atlas-SNP	.											DIRAS3,NS,carcinoma,+2,1	DIRAS3	31	1	0			c.A88C						scavenged	.						45	50	49					1																	68512893		2203	4300	6503	SO:0001583	missense	9077	exon2			GGGGCTTGAAGGC	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.88A>C	1.37:g.68512893T>G	ENSP00000360020:p.Lys30Gln	100	2	0.02		86	23	0.267442	NM_004675	B3KMP3	Missense_Mutation	SNP	ENST00000370981.1	37	CCDS641.1	.	.	.	.	.	.	.	.	.	.	T	9.916	1.210778	0.22289	.	.	ENSG00000162595	ENST00000370981;ENST00000395201	T;T	0.73258	-0.73;-0.73	3.98	-5.83	0.02325	.	.	.	.	.	T	0.21103	0.0508	N	0.19112	0.55	0.09310	N	1	B	0.26775	0.159	B	0.18263	0.021	T	0.06552	-1.0820	9	0.27082	T	0.32	.	2.268	0.04084	0.1192:0.3611:0.1562:0.3635	.	30	O95661	DIRA3_HUMAN	Q	30	ENSP00000360020:K30Q;ENSP00000378627:K30Q	ENSP00000360020:K30Q	K	-	1	0	DIRAS3	68285481	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.537000	0.06128	-1.117000	0.02965	-0.468000	0.05107	AAG	.	.	none		0.607	DIRAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026354.2	NM_004675		G	68512893	T	G	68512893	3	3	27	1	0	0	0	0	1	0	0	0	4534	1821	63	5	605	5	DIRAS3	1	68512893	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	3269427	68512893	180737728	33	10484											
NEGR1	257194	hgsc.bcm.edu	37	chr1	72748169	72748169	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gcaccctgcaccaacagcatCatgtccatccctgctagggc	9	7	8	17	0	1	0	1	0	0	0	3	0	3	0	4	1	4	4	4	1	2	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:72748169C>G	ENST00000357731.5	-	1	248	c.9G>C	c.(7-9)atG>atC	p.M3I	NEGR1_ENST00000434200.1_Start_Codon_SNP_p.M1I	NM_173808.2	NP_776169.2	Q7Z3B1	NEGR1_HUMAN	neuronal growth regulator 1	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)		CCAACAGCATCATGTCCATCC	0.662																																					p.M3I		Atlas-SNP	.											.	NEGR1	60	.	0			c.G9C						PASS	.						89	68	76					1																	72748169		2203	4300	6503	SO:0001583	missense	257194	exon1			CAGCATCATGTCC	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.9G>C	1.37:g.72748169C>G	ENSP00000350364:p.Met3Ile	295	0	0		273	76	0.278388	NM_173808	Q5VT21|Q6UY06|Q8N440|Q8NAQ3	Missense_Mutation	SNP	ENST00000357731.5	37	CCDS661.1	.	.	.	.	.	.	.	.	.	.	C	7.644	0.681557	0.14907	.	.	ENSG00000172260	ENST00000357731;ENST00000434200	T;T	0.69806	0.85;-0.43	5.14	4.17	0.49024	.	0.093449	0.64402	D	0.000001	T	0.23846	0.0577	N	0.04508	-0.205	0.29795	N	0.832905	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.03887	-1.0995	10	0.15499	T	0.54	-14.4855	14.7993	0.69900	0.0:0.8412:0.1588:0.0	.	1;3	B4DI94;Q7Z3B1	.;NEGR1_HUMAN	I	3;1	ENSP00000350364:M3I;ENSP00000413294:M1I	ENSP00000350364:M3I	M	-	3	0	NEGR1	72520757	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.185000	0.42584	2.385000	0.81259	0.561000	0.74099	ATG	.	.	none		0.662	NEGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026722.4	NM_173808		G	72748169	C	G	72748169	3	3	27	1	0	0	0	0	1	0	0	0	10326	826	29	4	1083	4	NEGR1	1	72748169	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	4235276	72748169	176502452	34	10485											
ASB17	127247	hgsc.bcm.edu	37	chr1	76397871	76397871	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	acagtgatatccccactgacCcaaaaactgtagggagggtc	13	7	10	11	0	0	2	0	2	0	0	2	3	1	3	3	2	1	1	3	2	4	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:76397871C>T	ENST00000284142.6	-	1	245	c.106G>A	c.(106-108)Ggt>Agt	p.G36S		NM_080868.2	NP_543144.1	Q8WXJ9	ASB17_HUMAN	ankyrin repeat and SOCS box containing 17	36					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						CCCCACTGACCCAAAAACTGT	0.388																																					p.G36S		Atlas-SNP	.											.	ASB17	53	.	0			c.G106A						PASS	.						106	106	106					1																	76397871		2203	4300	6503	SO:0001583	missense	127247	exon1			ACTGACCCAAAAA	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.106G>A	1.37:g.76397871C>T	ENSP00000284142:p.Gly36Ser	172	0	0		147	42	0.285714	NM_080868	B1APB8|Q8N0X5	Missense_Mutation	SNP	ENST00000284142.6	37	CCDS671.1	.	.	.	.	.	.	.	.	.	.	C	19.99	3.929346	0.73327	.	.	ENSG00000154007	ENST00000284142	T	0.36340	1.26	6.08	3.06	0.35304	.	0.328218	0.26525	N	0.023882	T	0.09512	0.0234	N	0.19112	0.55	0.32637	N	0.521267	B	0.13594	0.008	B	0.08055	0.003	T	0.08617	-1.0713	10	0.52906	T	0.07	.	7.9022	0.29742	0.0:0.6092:0.3092:0.0817	.	36	Q8WXJ9	ASB17_HUMAN	S	36	ENSP00000284142:G36S	ENSP00000284142:G36S	G	-	1	0	ASB17	76170459	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	1.786000	0.38694	0.901000	0.36495	-0.136000	0.14681	GGT	.	.	none		0.388	ASB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026982.1	NM_080868		T	76397871	C	T	76397871	3	4	27	1	0	0	0	0	1	0	0	0	1021	623	22	2	793	2	ASB17	1	76397871	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3649702	76397871	172852750	35	10486											
CTBS	1486	hgsc.bcm.edu	37	chr1	85029085	85029085	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccggaaagggacttttgcaAtggtacaaacatgatcctag	13	9	10	9	1	0	1	0	1	0	0	1	3	1	3	2	3	3	2	2	3	5	4	rs143993403	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:85029085A>G	ENST00000370630.5	-	6	860	c.812T>C	c.(811-813)aTt>aCt	p.I271T	CTBS_ENST00000477677.1_5'UTR	NM_004388.2	NP_004379.1	Q01459	DIAC_HUMAN	chitobiase, di-N-acetyl-	271					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)		GACTTTTGCAATGGTACAAAC	0.363													A|||	7	0.00139776	0.0	0.0	5008	,	,		12899	0.0		0.007	False		,,,				2504	0.0				p.I271T		Atlas-SNP	.											.	CTBS	24	.	0			c.T812C						PASS	.	A	THR/ILE	2,4394		0,2,2196	42	46	44		812	0.2	1	1	dbSNP_134	44	31,8567		0,31,4268	yes	missense	CTBS	NM_004388.2	89	0,33,6464	GG,GA,AA		0.3605,0.0455,0.254	benign	271/386	85029085	33,12961	2198	4299	6497	SO:0001583	missense	1486	exon6			TTTGCAATGGTAC	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.812T>C	1.37:g.85029085A>G	ENSP00000359664:p.Ile271Thr	120	0	0		97	42	0.43299	NM_004388	Q5VX50	Missense_Mutation	SNP	ENST00000370630.5	37	CCDS698.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	A	15.09	2.730266	0.48939	4.55E-4	0.003605	ENSG00000117151	ENST00000370630	T	0.05081	3.5	5.39	0.206	0.15208	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.218455	0.46758	N	0.000269	T	0.02610	0.0079	L	0.43598	1.365	0.33049	D	0.532445	P	0.38420	0.63	B	0.42625	0.393	T	0.44651	-0.9314	10	0.22109	T	0.4	-10.2359	11.7481	0.51832	0.8713:0.0:0.1287:0.0	.	271	Q01459	DIAC_HUMAN	T	271	ENSP00000359664:I271T	ENSP00000359659:I180T	I	-	2	0	CTBS	84801673	0.997000	0.39634	0.992000	0.48379	0.887000	0.51463	3.142000	0.50601	-0.226000	0.09899	0.528000	0.53228	ATT	A|0.997;G|0.003	0.003	strong		0.363	CTBS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027457.2	NM_004388		G	85029085	A	G	85029085	3	3	27	1	0	0	0	0	1	0	0	0	4001	101	4	3	353	3	CTBS	1	85029085	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	8631214	85029085	164221536	36	10487											
AGL	178	hgsc.bcm.edu	37	chr1	100340286	100340286	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gatccaaaccaacaccttacGattattcaagatcctgaata	16	10	4	11	1	1	2	1	1	0	1	3	4	3	2	4	0	3	0	4	0	7	4	rs369218410		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:100340286G>A	ENST00000294724.4	+	8	1480	c.1002G>A	c.(1000-1002)acG>acA	p.T334T	AGL_ENST00000370163.3_Silent_p.T334T|AGL_ENST00000361302.3_Silent_p.T318T|AGL_ENST00000361915.3_Silent_p.T334T|AGL_ENST00000477753.1_3'UTR|AGL_ENST00000361522.4_Silent_p.T317T|AGL_ENST00000370161.2_Silent_p.T318T|AGL_ENST00000370165.3_Silent_p.T334T	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	334					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)		AACACCTTACGATTATTCAAG	0.343																																					p.T334T		Atlas-SNP	.											.	AGL	137	.	0			c.G1002A						PASS	.	G	,,,,,	1,4405	2.1+/-5.4	0,1,2202	127	111	116		1002,1002,1002,1002,951,954	1.8	1	1		116	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AGL	NM_000028.2,NM_000642.2,NM_000643.2,NM_000644.2,NM_000645.2,NM_000646.2	,,,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,,,	334/1533,334/1533,334/1533,334/1533,317/1516,318/1517	100340286	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	178	exon8			CCTTACGATTATT	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.1002G>A	1.37:g.100340286G>A		78	0	0		75	4	0.0533333	NM_000644	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Silent	SNP	ENST00000294724.4	37	CCDS759.1																																																																																			.	.	none		0.343	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028		A	100340286	G	A	100340286	2	1	27	1	0	0	0	0	0	0	0	1	384	1045	37	1		1	AGL	1	100340286	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	15311201	100340286	148910335	37	10488											
GPR88	54112	hgsc.bcm.edu	37	chr1	101005554	101005554	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tggaggaacgaggagttccgCcgctccgtgcgctcagtcct	6	8	14	13	5	1	0	1	0	0	0	4	4	4	3	4	3	2	3	4	3	1	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:101005554C>A	ENST00000315033.4	+	2	1471	c.1032C>A	c.(1030-1032)cgC>cgA	p.R344R		NM_022049.2	NP_071332.2	Q9GZN0	GPR88_HUMAN	G protein-coupled receptor 88	344					G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuronal action potential (GO:0019228)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			large_intestine(2)|skin(1)	3		all_epithelial(167;1.19e-05)|all_lung(203;0.00159)|Lung NSC(277;0.00171)		Epithelial(280;0.0372)|all cancers(265;0.0558)|COAD - Colon adenocarcinoma(174;0.141)|Colorectal(144;0.156)|Lung(183;0.189)		AGGAGTTCCGCCGCTCCGTGC	0.736																																					p.R344R		Atlas-SNP	.											.	GPR88	17	.	0			c.C1032A						PASS	.						5	6	6					1																	101005554		2049	4046	6095	SO:0001819	synonymous_variant	54112	exon2			GTTCCGCCGCTCC	AB042411	CCDS772.1	1p21.3	2012-08-21	2006-02-15		ENSG00000181656	ENSG00000181656		"GPCR / Class A : Orphans"	4539	protein-coding gene	gene with protein product		607468	"G-protein coupled receptor 88", "G protein coupled receptor 88"				Standard	NM_022049		Approved		uc001dth.3	Q9GZN0	OTTHUMG00000010981	ENST00000315033.4:c.1032C>A	1.37:g.101005554C>A		5	0	0		16	5	0.3125	NM_022049	Q29S24|Q6VN48	Silent	SNP	ENST00000315033.4	37	CCDS772.1																																																																																			.	.	none		0.736	GPR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030212.1	NM_022049		A	101005554	C	A	101005554	2	1	27	1	0	0	0	0	0	0	0	1	6725	726	26	4		4	GPR88	1	101005554	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	665268	101005554	148245067	38	10489											
HIPK1	204851	hgsc.bcm.edu	37	chr1	114514543	114514543	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tatcgagctcaacgcgggggGaccagtgcagcacaaccact	11	5	12	13	3	1	0	1	0	0	0	2	2	1	1	2	3	5	3	2	3	3	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:114514543G>A	ENST00000369558.1	+	15	3343	c.3111G>A	c.(3109-3111)ggG>ggA	p.G1037G	HIPK1_ENST00000369554.2_Silent_p.G992G|HIPK1_ENST00000369559.4_Silent_p.G1037G|HIPK1_ENST00000406344.1_Silent_p.G643G|HIPK1_ENST00000426820.2_Silent_p.G1037G|HIPK1_ENST00000340480.4_Silent_p.G663G|HIPK1_ENST00000369555.2_Silent_p.G992G|HIPK1_ENST00000369561.4_Silent_p.G1003G|HIPK1_ENST00000369553.1_Silent_p.G643G			Q86Z02	HIPK1_HUMAN	homeodomain interacting protein kinase 1	1037	Interaction with TP53.				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)		AACGCGGGGGGACCAGTGCAG	0.542																																					p.G1037G		Atlas-SNP	.											.	HIPK1	195	.	0			c.G3111A						PASS	.						176	143	154					1																	114514543		2203	4300	6503	SO:0001819	synonymous_variant	204851	exon15			CGGGGGGACCAGT	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.3111G>A	1.37:g.114514543G>A		222	1	0.0045045		182	94	0.516484	NM_198268	A6NJ34|O75125|Q5SQL2|Q5SQL4|Q5SQL5|Q8IYD7|Q8NDN5|Q8NEB6|Q8TBZ1	Silent	SNP	ENST00000369558.1	37	CCDS867.1	.	.	.	.	.	.	.	.	.	.	G	0.089	-1.170955	0.01660	.	.	ENSG00000163349	ENST00000361587	.	.	.	5.89	0.0782	0.14411	.	.	.	.	.	T	0.25344	0.0616	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.20706	-1.0267	4	.	.	.	.	1.851	0.03169	0.2593:0.1094:0.4096:0.2218	.	.	.	.	N	318	.	.	D	+	1	0	HIPK1	114316066	0.060000	0.20803	0.994000	0.49952	0.168000	0.22595	-0.497000	0.06428	0.095000	0.17434	0.563000	0.77884	GAC	.	.	none		0.542	HIPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033127.1	NM_198268		A	114514543	G	A	114514543	2	1	27	1	0	0	0	0	0	0	0	1	7125	1161	41	2		2	HIPK1	1	114514543	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	13508989	114514543	134736078	39	10490											
AMPD1	270	hgsc.bcm.edu	37	chr1	115221116	115221116	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcagcagatgtttctggttCatgcaagcggctgcatggat	8	11	13	9	2	2	1	1	0	1	1	2	2	2	2	0	3	4	7	0	3	1	2	rs61752478	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:115221116C>A	ENST00000520113.2	-	8	1044	c.1029G>T	c.(1027-1029)atG>atT	p.M343I	AMPD1_ENST00000353928.6_Missense_Mutation_p.M310I|AMPD1_ENST00000369538.3_Missense_Mutation_p.M339I			P23109	AMPD1_HUMAN	adenosine monophosphate deaminase 1	343					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)	GTTTCTGGTTCATGCAAGCGG	0.393													C|||	13	0.00259585	0.0008	0.0072	5008	,	,		21444	0.0		0.007	False		,,,				2504	0.0				p.M343I		Atlas-SNP	.											.	AMPD1	223	.	0			c.G1029T	GRCh37	CM041236	AMPD1	M	rs61752478	PASS	.	C	ILE/MET,ILE/MET	4,4402	8.1+/-20.4	0,4,2199	98	96	97		1029,1017	5.1	1	1	dbSNP_129	97	46,8554	30.7+/-82.3	0,46,4254	yes	missense,missense	AMPD1	NM_000036.2,NM_001172626.1	10,10	0,50,6453	AA,AC,CC		0.5349,0.0908,0.3844	probably-damaging,probably-damaging	343/781,339/777	115221116	50,12956	2203	4300	6503	SO:0001583	missense	270	exon8			CTGGTTCATGCAA	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.1029G>T	1.37:g.115221116C>A	ENSP00000430075:p.Met343Ile	127	0	0		77	40	0.519481	NM_000036	A8K5N4|B2RAM1|F2Z3B3|Q5TF00|Q5TF02	Missense_Mutation	SNP	ENST00000520113.2	37	CCDS876.2	5	0.0022893772893772895	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	28.9	4.960280	0.92791	9.08E-4	0.005349	ENSG00000116748	ENST00000520113;ENST00000369538;ENST00000353928	D;D;D	0.95482	-3.72;-3.72;-3.72	5.1	5.1	0.69264	Adenosine/AMP deaminase (1);	0.000000	0.85682	D	0.000000	D	0.97573	0.9205	M	0.83384	2.64	0.80722	D	1	P;D	0.57899	0.759;0.981	P;D	0.65773	0.576;0.938	D	0.98134	1.0432	10	0.87932	D	0	-20.3493	18.8767	0.92341	0.0:1.0:0.0:0.0	rs61752478	339;310	Q5TF02;P23109	.;AMPD1_HUMAN	I	343;339;310	ENSP00000430075:M343I;ENSP00000358551:M339I;ENSP00000316520:M310I	ENSP00000316520:M310I	M	-	3	0	AMPD1	115022639	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.776000	0.85560	2.539000	0.85634	0.561000	0.74099	ATG	C|0.997;A|0.003	0.003	strong		0.393	AMPD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032860.4			A	115221116	C	A	115221116	3	1	27	1	0	0	0	0	1	0	0	0	585	826	29	4	1349	4	AMPD1	1	115221116	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	706573	115221116	134029505	40	10491											
CD101	9398	hgsc.bcm.edu	37	chr1	117554247	117554247	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aggtgagccattagccctcaCctgtgaggcatccaaagcca	11	7	10	13	0	1	2	1	2	0	0	2	2	2	2	5	2	3	1	5	2	2	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:117554247C>T	ENST00000256652.4	+	3	558	c.500C>T	c.(499-501)aCc>aTc	p.T167I	CD101_ENST00000369470.1_Missense_Mutation_p.T167I	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	167	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						TTAGCCCTCACCTGTGAGGCA	0.483																																					p.T167I		Atlas-SNP	.											.	CD101	95	.	0			c.C500T						PASS	.						107	93	98					1																	117554247		2203	4300	6503	SO:0001583	missense	9398	exon3			CCCTCACCTGTGA	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.500C>T	1.37:g.117554247C>T	ENSP00000256652:p.Thr167Ile	168	0	0		141	60	0.425532	NM_001256109	Q15856	Missense_Mutation	SNP	ENST00000256652.4	37	CCDS891.1	.	.	.	.	.	.	.	.	.	.	C	12.64	1.999464	0.35320	.	.	ENSG00000134256	ENST00000256652;ENST00000369470	T;T	0.67171	-0.25;-0.25	5.33	4.41	0.53225	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.565464	0.18042	N	0.153594	T	0.73729	0.3624	M	0.82823	2.61	0.33375	D	0.574133	D	0.89917	1.0	D	0.80764	0.994	T	0.76672	-0.2873	10	0.72032	D	0.01	-9.8961	7.5864	0.27995	0.0:0.7445:0.1664:0.0891	.	167	Q93033	IGSF2_HUMAN	I	167	ENSP00000256652:T167I;ENSP00000358482:T167I	ENSP00000256652:T167I	T	+	2	0	CD101	117355770	0.104000	0.21937	0.653000	0.29593	0.026000	0.11368	0.930000	0.28858	1.254000	0.44035	0.650000	0.86243	ACC	.	.	none		0.483	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258		T	117554247	C	T	117554247	3	4	27	1	0	0	0	0	1	0	0	0	2964	507	18	2	510	2	CD101	1	117554247	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2333131	117554247	131696374	41	10492											
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144859792	144859792	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcttgtttccagggtcagTgctggctgggaagttctggt	4	14	15	8	0	2	0	1	0	1	0	3	1	3	1	1	4	2	5	1	4	1	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:144859792T>C	ENST00000369354.3	-	38	6481	c.6292A>G	c.(6292-6294)Act>Gct	p.T2098A	PDE4DIP_ENST00000369356.4_Missense_Mutation_p.T2098A|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.T1992A|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.T2234A|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.T2183A|RP4-791M13.4_ENST00000532137.1_RNA			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2098					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)		CCAGGGTCAGTGCTGGCTGGG	0.572			T	PDGFRB	MPD																																p.T2098A		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A6292G						PASS	.						66	64	65					1																	144859792		2203	4300	6503	SO:0001583	missense	9659	exon38			GGTCAGTGCTGGC	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.6292A>G	1.37:g.144859792T>C	ENSP00000358360:p.Thr2098Ala	143	0	0		151	10	0.0662252	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	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	C	6.344	0.431590	0.12045	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01647	4.71;4.8;4.8;4.8;4.8	4.91	-3.04	0.05412	.	.	.	.	.	T	0.00271	0.0008	N	0.16166	0.38	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43893	-0.9363	9	0.02654	T	1	.	7.2849	0.26333	0.0:0.2735:0.1194:0.6071	.	1992;2098	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	A	1992;2098;2098;2183;2234	ENSP00000327209:T1992A;ENSP00000358360:T2098A;ENSP00000358363:T2098A;ENSP00000435654:T2183A;ENSP00000358366:T2234A	ENSP00000327209:T1992A	T	-	1	0	PDE4DIP	143571149	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.278000	0.02809	-1.197000	0.02673	-1.569000	0.00873	ACT	.	.	none		0.572	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		C	144859792	T	C	144859792	3	2	27	1	0	0	0	0	1	0	0	0	11652	1696	59	3	776	3	PDE4DIP	1	144859792	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	27305545	144859792	104390829	42	10493											
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	144859816	144859816	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgggaagttctggttaaTggaggaggggctgaggctgg	7	9	21	4	0	1	1	0	1	1	0	1	4	1	4	0	9	0	5	0	9	2	2	rs587702923	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:144859816T>C	ENST00000369354.3	-	38	6457	c.6268A>G	c.(6268-6270)Att>Gtt	p.I2090V	PDE4DIP_ENST00000369356.4_Missense_Mutation_p.I2090V|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.I1984V|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.I2226V|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.I2175V|RP4-791M13.4_ENST00000532137.1_RNA			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2090					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)		TTCTGGTTAATGGAGGAGGGG	0.577			T	PDGFRB	MPD																																p.I2090V		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A6268G						PASS	.						65	63	63					1																	144859816		2203	4300	6503	SO:0001583	missense	9659	exon38			GGTTAATGGAGGA	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.6268A>G	1.37:g.144859816T>C	ENSP00000358360:p.Ile2090Val	153	0	0		153	11	0.0718954	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	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	T	0.010	-1.760839	0.00657	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01685	4.69;4.78;4.78;4.8;4.79	4.63	-9.26	0.00662	.	.	.	.	.	T	0.00178	0.0005	N	0.03608	-0.345	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.47058	-0.9146	9	0.02654	T	1	.	5.9795	0.19399	0.0819:0.4615:0.1653:0.2913	.	1984;2090	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	V	1984;2090;2090;2175;2226	ENSP00000327209:I1984V;ENSP00000358360:I2090V;ENSP00000358363:I2090V;ENSP00000435654:I2175V;ENSP00000358366:I2226V	ENSP00000327209:I1984V	I	-	1	0	PDE4DIP	143571173	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.249000	0.00266	-3.114000	0.00240	-1.162000	0.01777	ATT	.	.	none		0.577	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359		C	144859816	T	C	144859816	3	2	27	1	0	0	0	0	1	0	0	0	11652	1464	51	3	800	3	PDE4DIP	1	144859816	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	24	144859816	104390805	43	10494											
GJA8	2703	hgsc.bcm.edu	37	chr1	147380460	147380460	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	actaacggcggcccggaccaGggcagcgtcaagaagagcag	12	2	15	12	4	1	2	1	0	0	2	1	3	1	3	2	4	3	2	2	4	3	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:147380460G>A	ENST00000369235.1	+	1	378	c.378G>A	c.(376-378)caG>caA	p.Q126Q	GJA8_ENST00000240986.4_Silent_p.Q126Q			P48165	CXA8_HUMAN	gap junction protein, alpha 8, 50kDa	126					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)					GCCCGGACCAGGGCAGCGTCA	0.647																																					p.Q126Q	Melanoma(76;1255 1795 8195 52096)	Atlas-SNP	.											GJA8,NS,carcinoma,+2,1	GJA8	108	1	0			c.G378A						PASS	.						46	55	52					1																	147380460		2203	4300	6503	SO:0001819	synonymous_variant	2703	exon2			GGACCAGGGCAGC	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.378G>A	1.37:g.147380460G>A		63	0	0		42	11	0.261905	NM_005267	A7L5M5|Q5VVN9|Q9NP25	Silent	SNP	ENST00000369235.1	37	CCDS30834.1																																																																																			.	.	none		0.647	GJA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060647.1	NM_005267		A	147380460	G	A	147380460	2	1	27	1	0	0	0	0	0	0	0	1	6413	991	35	2		2	GJA8	1	147380460	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2520644	147380460	101870161	44	10495											
MCL1	4170	hgsc.bcm.edu	37	chr1	150550920	150550920	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atggatcatcactcgagacaAcgatttcacatcgtcttcgt	11	12	7	11	4	4	1	3	0	1	1	7	4	4	2	0	1	1	0	0	1	1	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:150550920A>C	ENST00000369026.2	-	2	795	c.736T>G	c.(736-738)Ttg>Gtg	p.L246V	MCL1_ENST00000464132.1_5'UTR|MCL1_ENST00000307940.3_Intron	NM_001197320.1|NM_021960.4	NP_001184249.1|NP_068779.1	Q07820	MCL1_HUMAN	myeloid cell leukemia 1	246					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)			ACTCGAGACAACGATTTCACA	0.478																																					p.L246V		Atlas-SNP	.											.	MCL1	27	.	0			c.T736G						PASS	.						106	108	107					1																	150550920		2203	4300	6503	SO:0001583	missense	4170	exon2			GAGACAACGATTT	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.736T>G	1.37:g.150550920A>C	ENSP00000358022:p.Leu246Val	154	0	0		107	28	0.261682	NM_021960	B2R6B2|D3DV03|D3DV04|Q9HD91|Q9NRQ3|Q9NRQ4|Q9UHR7|Q9UHR8|Q9UHR9|Q9UNJ1	Missense_Mutation	SNP	ENST00000369026.2	37	CCDS957.1	.	.	.	.	.	.	.	.	.	.	A	12.37	1.917467	0.33815	.	.	ENSG00000143384	ENST00000369026;ENST00000439749	T	0.04603	3.59	4.77	1.08	0.20341	Apoptosis regulator, Bcl2-like (1);Apoptosis regulator, Bcl-2, BH (3);	0.298701	0.31601	N	0.007374	T	0.00815	0.0027	N	0.11560	0.145	0.80722	D	1	B	0.06786	0.001	B	0.15484	0.013	T	0.46965	-0.9153	10	0.33141	T	0.24	-5.5956	4.6041	0.12368	0.4735:0.2298:0.2967:0.0	.	246	Q07820	MCL1_HUMAN	V	246;175	ENSP00000358022:L246V	ENSP00000358022:L246V	L	-	1	2	MCL1	148817544	0.087000	0.21565	0.993000	0.49108	0.996000	0.88848	0.574000	0.23714	0.345000	0.23873	0.533000	0.62120	TTG	.	.	none		0.478	MCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084402.1	NM_021960		C	150550920	A	C	150550920	3	2	27	1	0	0	0	0	1	0	0	0	9393	40	2	5	335	5	MCL1	1	150550920	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	3170460	150550920	98699701	45	10496											
SPRR1B	6699	hgsc.bcm.edu	37	chr1	153004942	153005013	+	In_Frame_Del	DEL	TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	-																															tccccaaaaccaaggagcccTgccaccccaaggtgcctgag																								rs2339500|rs145337134|rs201925274|rs367847286|rs12195|rs368848590|rs200829544|rs551505658	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:153004942_153005013delTGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	ENST00000307098.4	+	2	186_257	c.121_192delTGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	c.(121-192)tgccaccccaaggtgcctgagccctgccaccccaaagtgcccgagccctgccagcccaaggttccagagccadel	p.CHPKVPEPCHPKVPEPCQPKVPEP41del	SPRR1B_ENST00000392661.3_Splice_Site_p.CHPKVPEPCHPK41del	NM_003125.2	NP_003116.2	P22528	SPR1B_HUMAN	small proline-rich protein 1B	41	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)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)	p.C41_P64delCHPKVPEPCHPKVPEPCQPKVPEP(1)|p.P43A(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|ovary(2)|skin(2)	9	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)			CAAGGAGCCCTGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCATGCCACCCCA	0.621																																					p.40_64del		Pindel	.											.	SPRR1B	18	.	2	Substitution - Missense(1)|Deletion - In frame(1)	ovary(1)|haematopoietic_and_lymphoid_tissue(1)	c.120_191del						PASS	.																																			SO:0001651	inframe_deletion	6699	exon2			.	M84757	CCDS30863.1	1q21-q22	2010-06-25	2010-06-25		ENSG00000169469	ENSG00000169469			11260	protein-coding gene	gene with protein product	"cornifin"	182266		SPRR1		8325635, 1438308	Standard	NM_003125		Approved	GADD33	uc001fba.3	P22528	OTTHUMG00000013869	ENST00000307098.4:c.121_192delTGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	1.37:g.153004942_153005013delTGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	ENSP00000306461:p.Cys41_Pro64del	104	0	.		78	23	0.295	NM_003125	B2R5H7|P22529|P22530|Q5T524	In_Frame_Del	DEL	ENST00000307098.4	37	CCDS30863.1																																																																																			.	.	none		0.621	SPRR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038906.1	NM_003125		-	153005013	TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	-	153004942	7	5	27	1	0	1	0	1	0	0	0	0	15111	1580	55	0	123	0	SPRR1B	1	153004942	In_Frame_Del	DEL	TGCCACCCCAAGGTGCCTGAGCCCTGCCACCCCAAAGTGCCCGAGCCCTGCCAGCCCAAGGTTCCAGAGCCA	TCGA-G8-6909-01A-11D-2210-10	2454022	153004942	96245679	46	10497											
INTS3	65123	hgsc.bcm.edu	37	chr1	153701188	153701188	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggaggtggaggaggaggagcGggagcaggagccccaggagg	10	1	24	6	1	0	0	0	0	0	0	0	8	0	8	2	10	3	1	2	10	0	0	rs150819290	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:153701188G>A	ENST00000318967.2	+	1	646	c.78G>A	c.(76-78)gcG>gcA	p.A26A	Y_RNA_ENST00000362695.1_RNA|INTS3_ENST00000456435.1_5'UTR|INTS3_ENST00000435409.2_Silent_p.A26A	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	0	Ala/Gly-rich.				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)			gaggaggagcgggagcaggag	0.627													G|||	17	0.00339457	0.0	0.0043	5008	,	,		11478	0.0		0.0139	False		,,,				2504	0.0				p.A26A		Atlas-SNP	.											.	INTS3	83	.	0			c.G78A						PASS	.	G		7,4393		0,7,2193	34	45	41		78	4.1	1	1	dbSNP_134	41	106,8494		0,106,4194	no	coding-synonymous	INTS3	NM_023015.3		0,113,6387	AA,AG,GG		1.2326,0.1591,0.8692		26/1043	153701188	113,12887	2200	4300	6500	SO:0001819	synonymous_variant	65123	exon1			AGGAGCGGGAGCA	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.78G>A	1.37:g.153701188G>A		151	0	0		137	70	0.510949	NM_023015	A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Silent	SNP	ENST00000318967.2	37	CCDS1052.1																																																																																			G|0.994;A|0.006	0.006	strong		0.627	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015		A	153701188	G	A	153701188	2	1	27	1	0	0	0	0	0	0	0	1	7788	1103	39	1		1	INTS3	1	153701188	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	696246	153701188	95549433	47	10498											
NUP210L	91181	hgsc.bcm.edu	37	chr1	153982536	153982536	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgaactgtacatggcacagCatgagggtcgctggaagaag	12	7	14	8	1	0	3	0	2	0	1	1	4	0	4	0	3	3	4	0	3	4	1	rs199611847		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:153982536C>T	ENST00000368559.3	-	35	4913	c.4842G>A	c.(4840-4842)atG>atA	p.M1614I	NUP210L_ENST00000271854.3_Missense_Mutation_p.M1614I|NUP210L_ENST00000368553.1_Missense_Mutation_p.M547I	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	1614					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)			CATGGCACAGCATGAGGGTCG	0.423																																					p.M1614I		Atlas-SNP	.											.	NUP210L	181	.	0			c.G4842A						PASS	.	T	ILE/MET,ILE/MET	0,3736		0,0,1868	148	141	143		4842,4842	2.4	0.2	1		143	3,8209		0,3,4103	yes	missense,missense	NUP210L	NM_001159484.1,NM_207308.2	10,10	0,3,5971	TT,TC,CC		0.0365,0.0,0.0251	benign,benign	1614/1737,1614/1889	153982536	3,11945	1868	4106	5974	SO:0001583	missense	91181	exon35			GCACAGCATGAGG	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.4842G>A	1.37:g.153982536C>T	ENSP00000357547:p.Met1614Ile	58	0	0		67	29	0.432836	NM_001159484	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Missense_Mutation	SNP	ENST00000368559.3	37	CCDS41399.1	.	.	.	.	.	.	.	.	.	.	c	0.029	-1.345824	0.01266	0.0	3.65E-4	ENSG00000143552	ENST00000368559;ENST00000368553;ENST00000271854	T;T;T	0.18810	3.68;2.19;3.5	5.24	2.39	0.29439	.	1.290600	0.05075	N	0.482321	T	0.04092	0.0114	L	0.39898	1.24	0.20403	N	0.999903	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.31586	-0.9938	10	0.02654	T	1	-12.129	5.8719	0.18809	0.1534:0.6865:0.0:0.1601	.	1614;1614	E7EP56;Q5VU65	.;P210L_HUMAN	I	1614;547;1614	ENSP00000357547:M1614I;ENSP00000357541:M547I;ENSP00000271854:M1614I	ENSP00000271854:M1614I	M	-	3	0	NUP210L	152249160	0.666000	0.27475	0.235000	0.24058	0.484000	0.33280	0.687000	0.25407	0.370000	0.24538	-0.224000	0.12420	ATG	.	.	weak		0.423	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308		T	153982536	C	T	153982536	3	4	27	1	0	0	0	0	1	0	0	0	10770	710	25	2	848	2	NUP210L	1	153982536	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	281348	153982536	95268085	48	10499											
NUP210L	91181	hgsc.bcm.edu	37	chr1	154031134	154031134	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaaacaaagatcatagacCtccaaggtaaaaaatccagg	19	5	7	10	0	1	2	1	0	0	2	3	2	3	2	4	2	1	1	4	2	7	2	rs201928881		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:154031134C>A	ENST00000368559.3	-	21	2957	c.2886G>T	c.(2884-2886)gaG>gaT	p.E962D	NUP210L_ENST00000368553.1_5'Flank|NUP210L_ENST00000271854.3_Missense_Mutation_p.E962D	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	962					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)			GATCATAGACCTCCAAGGTAA	0.433																																					p.E962D		Atlas-SNP	.											.	NUP210L	181	.	0			c.G2886T						PASS	.	C	ASP/GLU,ASP/GLU	3,3683		0,3,1840	92	82	85		2886,2886	-0.5	1	1		85	19,8163		0,19,4072	yes	missense,missense	NUP210L	NM_001159484.1,NM_207308.2	45,45	0,22,5912	AA,AC,CC		0.2322,0.0814,0.1854	benign,benign	962/1737,962/1889	154031134	22,11846	1843	4091	5934	SO:0001583	missense	91181	exon21			ATAGACCTCCAAG	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.2886G>T	1.37:g.154031134C>A	ENSP00000357547:p.Glu962Asp	95	0	0		66	32	0.484848	NM_001159484	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	Missense_Mutation	SNP	ENST00000368559.3	37	CCDS41399.1	.	.	.	.	.	.	.	.	.	.	C	9.212	1.031090	0.19590	8.14E-4	0.002322	ENSG00000143552	ENST00000368559;ENST00000271854	T;T	0.07021	3.49;3.23	4.44	-0.504	0.11997	.	0.135069	0.33959	N	0.004391	T	0.02012	0.0063	L	0.44542	1.39	0.34482	D	0.703977	P;P	0.39665	0.651;0.682	B;B	0.32980	0.115;0.156	T	0.51787	-0.8661	10	0.33141	T	0.24	-24.0406	7.5347	0.27704	0.0:0.4383:0.0:0.5617	.	962;962	E7EP56;Q5VU65	.;P210L_HUMAN	D	962	ENSP00000357547:E962D;ENSP00000271854:E962D	ENSP00000271854:E962D	E	-	3	2	NUP210L	152297758	0.993000	0.37304	0.999000	0.59377	0.737000	0.42083	0.083000	0.14871	-0.010000	0.14271	0.591000	0.81541	GAG	.	.	weak		0.433	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308		A	154031134	C	A	154031134	3	1	27	1	0	0	0	0	1	0	0	0	10770	680	24	4	2860	4	NUP210L	1	154031134	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	48598	154031134	95219487	49	10500											
PRCC	5546	hgsc.bcm.edu	37	chr1	156756948	156756948	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acatatggcgatgccaatgcCgctggtgcttattatcaggt	9	12	11	9	2	1	0	1	0	0	0	1	1	1	0	2	3	3	2	2	3	4	3	rs201827573		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:156756948C>T	ENST00000271526.4	+	3	1337	c.1065C>T	c.(1063-1065)gcC>gcT	p.A355A	PRCC_ENST00000491853.1_3'UTR|PRCC_ENST00000353233.3_Silent_p.A355A	NM_005973.4	NP_005964.3	Q92733	PRCC_HUMAN	papillary renal cell carcinoma (translocation-associated)	355					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)					ATGCCAATGCCGCTGGTGCTT	0.532			T	TFE3	papillary renal								C|||	1	0.000199681	0.0	0.0	5008	,	,		14844	0.0		0.001	False		,,,				2504	0.0				p.A355A		Atlas-SNP	.		Dom	yes		1	1q21.1	5546	papillary renal cell carcinoma (translocation-associated)		E	.	PRCC	39	.	0			c.C1065T						PASS	.	C		0,4406		0,0,2203	116	121	119		1065	-2.6	1	1		119	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	PRCC	NM_005973.4		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		355/492	156756948	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	5546	exon3			CAATGCCGCTGGT	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.1065C>T	1.37:g.156756948C>T		405	0	0		327	157	0.480122	NM_005973	A8K1F7|O00665|O00724|Q5SZ06	Silent	SNP	ENST00000271526.4	37	CCDS1157.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	7.757	0.704598	0.15172	0.0	2.33E-4	ENSG00000143294	ENST00000454659	.	.	.	5.15	-2.57	0.06248	.	.	.	.	.	T	0.30665	0.0772	.	.	.	0.52501	D	0.999954	.	.	.	.	.	.	T	0.32455	-0.9906	4	.	.	.	-9.8382	4.9292	0.13909	0.0964:0.5476:0.0971:0.2588	.	.	.	.	L	89	.	.	P	+	2	0	PRCC	155023572	0.271000	0.24162	0.973000	0.42090	0.986000	0.74619	-0.613000	0.05610	-0.687000	0.05162	-1.094000	0.02160	CCG	C|0.999;T|0.001	0.001	strong		0.532	PRCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098941.2	NM_005973		T	156756948	C	T	156756948	2	4	27	1	0	0	0	0	0	0	0	1	12459	639	23	1		1	PRCC	1	156756948	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2725814	156756948	92493673	50	10501											
IGSF8	93185	hgsc.bcm.edu	37	chr1	160064697	160064697	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgctgtagctgcccaggtagCgggtatcagtggagggggtg	6	8	19	8	2	1	0	1	0	0	0	1	1	1	1	1	5	3	5	1	5	3	3	rs200550632		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:160064697C>T	ENST00000368086.1	-	2	620	c.404G>A	c.(403-405)cGc>cAc	p.R135H	IGSF8_ENST00000460351.1_5'UTR|IGSF8_ENST00000314485.7_Missense_Mutation_p.R135H			Q969P0	IGSF8_HUMAN	immunoglobulin superfamily, member 8	135	Ig-like C2-type 1.				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)			GCCCAGGTAGCGGGTATCAGT	0.627													C|||	1	0.000199681	0.0	0.0	5008	,	,		18151	0.0		0.001	False		,,,				2504	0.0				p.R135H		Atlas-SNP	.											.	IGSF8	59	.	0			c.G404A						PASS	.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	34	37	36		404,404	-1.3	0.9	1		36	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	IGSF8	NM_001206665.2,NM_052868.4	29,29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	135/614,135/614	160064697	1,13005	2203	4300	6503	SO:0001583	missense	93185	exon2			AGGTAGCGGGTAT	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.404G>A	1.37:g.160064697C>T	ENSP00000357065:p.Arg135His	69	0	0		86	54	0.627907	NM_052868	Q8NG09|Q96DP4|Q9BTG9	Missense_Mutation	SNP	ENST00000368086.1	37	CCDS1195.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.12	3.552769	0.65425	0.0	1.16E-4	ENSG00000162729	ENST00000314485;ENST00000368086;ENST00000358475;ENST00000448417	T;T;T	0.10382	3.47;3.47;2.88	4.89	-1.29	0.09288	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.619503	0.14945	N	0.289261	T	0.03390	0.0098	L	0.42245	1.32	0.26281	N	0.978279	P	0.48694	0.914	B	0.43251	0.413	T	0.35101	-0.9802	10	0.56958	D	0.05	-5.5588	6.2467	0.20823	0.0:0.2743:0.1448:0.5809	.	135	Q969P0	IGSF8_HUMAN	H	135	ENSP00000316664:R135H;ENSP00000357065:R135H;ENSP00000397464:R135H	ENSP00000316664:R135H	R	-	2	0	IGSF8	158331321	0.085000	0.21516	0.917000	0.36280	0.965000	0.64279	-0.605000	0.05661	-0.104000	0.12154	0.563000	0.77884	CGC	C|1.000;T|0.000	0.000	strong		0.627	IGSF8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060636.1	NM_052868		T	160064697	C	T	160064697	3	4	27	1	0	0	0	0	1	0	0	0	7613	768	27	1	1457	1	IGSF8	1	160064697	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3307749	160064697	89185924	51	10502											
UFC1	51506	hgsc.bcm.edu	37	chr1	161123901	161123901	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgaaggaggaatatcagtcCcttatccgggttagttgtgt	9	13	12	7	1	1	1	1	1	0	0	3	3	3	3	2	3	0	2	2	3	5	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:161123901C>G	ENST00000368003.5	+	1	360	c.114C>G	c.(112-114)tcC>tcG	p.S38S	UFC1_ENST00000473766.1_3'UTR|RP11-297K8.2_ENST00000420498.1_RNA	NM_016406.3	NP_057490.2	Q9Y3C8	UFC1_HUMAN	ubiquitin-fold modifier conjugating enzyme 1	38					protein ufmylation (GO:0071569)|response to endoplasmic reticulum stress (GO:0034976)	extracellular vesicular exosome (GO:0070062)	UFM1 conjugating enzyme activity (GO:0071568)			endometrium(1)|lung(9)	10	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)			AATATCAGTCCCTTATCCGGG	0.537																																					p.S38S		Atlas-SNP	.											.	UFC1	16	.	0			c.C114G						PASS	.						179	157	165					1																	161123901		2203	4300	6503	SO:0001819	synonymous_variant	51506	exon1			TCAGTCCCTTATC	AF161504	CCDS1220.1	1q23.3	2008-02-05			ENSG00000143222	ENSG00000143222			26941	protein-coding gene	gene with protein product		610554				15071506, 11042152	Standard	NM_016406		Approved	HSPC155	uc001fyd.4	Q9Y3C8	OTTHUMG00000033155	ENST00000368003.5:c.114C>G	1.37:g.161123901C>G		123	0	0		96	11	0.114583	NM_016406	A8K9R1|D3DVF9|Q549X0|Q5VTX1|Q9BS96|Q9P009	Silent	SNP	ENST00000368003.5	37	CCDS1220.1																																																																																			.	.	none		0.537	UFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080810.1	NM_016406		G	161123901	C	G	161123901	2	3	27	1	0	0	0	0	0	0	0	1	16949	610	22	4		4	UFC1	1	161123901	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1059204	161123901	88126720	52	10503											
HSPA6	3310	hgsc.bcm.edu	37	chr1	161495344	161495344	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtggacttctacacgtccaTcactcgtgcccgctttgagg	6	11	10	14	4	2	1	1	1	1	0	4	2	3	2	2	2	2	1	2	2	1	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:161495344T>C	ENST00000309758.4	+	1	1309	c.896T>C	c.(895-897)aTc>aCc	p.I299T	RP11-25K21.6_ENST00000537821.2_RNA	NM_002155.3	NP_002146.2	P17066	HSP76_HUMAN	heat shock 70kDa protein 6 (HSP70B')	299					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)			TACACGTCCATCACTCGTGCC	0.647																																					p.I299T		Atlas-SNP	.											.	HSPA6	53	.	0			c.T896C						PASS	.						29	32	31					1																	161495344		2203	4300	6503	SO:0001583	missense	3310	exon1			CGTCCATCACTCG		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.896T>C	1.37:g.161495344T>C	ENSP00000310219:p.Ile299Thr	101	0	0		75	17	0.226667	NM_002155	Q1HBA8|Q8IYK7|Q9BT95	Missense_Mutation	SNP	ENST00000309758.4	37	CCDS1231.1	.	.	.	.	.	.	.	.	.	.	.	15.17	2.755454	0.49362	.	.	ENSG00000173110	ENST00000309758;ENST00000545155	T	0.01165	5.24	3.12	3.12	0.35913	.	0.000000	0.39475	U	0.001354	T	0.09774	0.0240	H	0.99806	4.795	0.43953	D	0.996624	P	0.43885	0.82	D	0.74023	0.982	T	0.00206	-1.1920	10	0.87932	D	0	.	9.3095	0.37895	0.0:0.0:0.0:1.0	.	299	P17066	HSP76_HUMAN	T	299;275	ENSP00000310219:I299T	ENSP00000310219:I299T	I	+	2	0	HSPA6	159761968	1.000000	0.71417	0.972000	0.41901	0.619000	0.37552	5.244000	0.65400	1.264000	0.44198	0.443000	0.29094	ATC	.	.	none		0.647	HSPA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083308.1	NM_002155		C	161495344	T	C	161495344	3	2	27	1	0	0	0	0	1	0	0	0	7424	1435	50	3	898	3	HSPA6	1	161495344	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	371443	161495344	87755277	53	10504											
C1orf110	339512	hgsc.bcm.edu	37	chr1	162824960	162824960	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgcccttgctggggtctacGtccttagatggattcacaga	8	12	11	10	1	2	2	1	0	1	2	3	3	3	3	2	3	3	1	2	3	2	4	rs190249067	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:162824960G>A	ENST00000367910.1	-	4	624	c.504C>T	c.(502-504)gaC>gaT	p.D168D	C1orf110_ENST00000367912.2_Silent_p.D167D|C1orf110_ENST00000367911.2_Silent_p.D163D|C1orf110_ENST00000524691.1_Intron	NM_178550.4	NP_848645.3	Q86UF4	CA110_HUMAN	chromosome 1 open reading frame 110	168										endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	12						TGGGGTCTACGTCCTTAGATG	0.463													G|||	3	0.000599042	0.0	0.0	5008	,	,		20117	0.002		0.001	False		,,,				2504	0.0				p.D168D		Atlas-SNP	.											.	C1orf110	22	.	0			c.C504T						PASS	.	G		2,3840		0,2,1919	274	261	265		504	-0.1	0	1		265	33,8235		0,33,4101	no	coding-synonymous	C1orf110	NM_178550.4		0,35,6020	AA,AG,GG		0.3991,0.0521,0.289		168/303	162824960	35,12075	1921	4134	6055	SO:0001819	synonymous_variant	339512	exon4			GTCTACGTCCTTA	BC040018	CCDS44269.1	1q23.3	2012-06-26			ENSG00000185860	ENSG00000185860			28736	protein-coding gene	gene with protein product						12477932	Standard	NM_178550		Approved	MGC48998	uc001gck.2	Q86UF4	OTTHUMG00000034421	ENST00000367910.1:c.504C>T	1.37:g.162824960G>A		242	0	0		215	103	0.47907	NM_178550	Q5JSG1|Q6ZW57	Silent	SNP	ENST00000367910.1	37	CCDS44269.1																																																																																			G|0.999;A|0.001	0.001	strong		0.463	C1orf110-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083211.2	NM_178550		A	162824960	G	A	162824960	2	1	27	1	0	0	0	0	0	0	0	1	1985	1136	40	1		1	C1orf110	1	162824960	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1329616	162824960	86425661	54	10505											
DARS2	55157	hgsc.bcm.edu	37	chr1	173822936	173822936	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atctgtgaatcttctaggccCgtagccaacactatgacttg	10	12	8	11	1	3	2	0	2	3	0	3	2	3	2	2	1	2	1	2	1	5	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:173822936C>T	ENST00000361951.4	+	15	2294	c.1567C>T	c.(1567-1569)Cgt>Tgt	p.R523C	DARS2_ENST00000471476.1_Intron|DARS2_ENST00000239457.5_Intron	NM_018122.4	NP_060592.2	Q6PI48	SYDM_HUMAN	aspartyl-tRNA synthetase 2, mitochondrial	523					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)	p.R523S(1)		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)	CTTCTAGGCCCGTAGCCAACA	0.388																																					p.R523C		Atlas-SNP	.											.	DARS2	61	.	1	Substitution - Missense(1)	lung(1)	c.C1567T						PASS	.						101	105	103					1																	173822936		2203	4300	6503	SO:0001583	missense	55157	exon15			TAGGCCCGTAGCC	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.1567C>T	1.37:g.173822936C>T	ENSP00000355086:p.Arg523Cys	93	0	0		63	15	0.238095	NM_018122		Missense_Mutation	SNP	ENST00000361951.4	37	CCDS1311.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.384482	0.82792	.	.	ENSG00000117593	ENST00000361951	T	0.80123	-1.34	4.65	4.65	0.58169	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (D/K/N) (1);	0.055932	0.64402	D	0.000001	D	0.92492	0.7616	H	0.96777	3.88	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94831	0.7996	10	0.72032	D	0.01	-15.4489	16.6683	0.85259	0.0:1.0:0.0:0.0	.	523	Q6PI48	SYDM_HUMAN	C	523	ENSP00000355086:R523C	ENSP00000355086:R523C	R	+	1	0	DARS2	172089559	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.614000	0.67695	2.304000	0.77564	0.591000	0.81541	CGT	.	.	none		0.388	DARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084220.1	NM_018122		T	173822936	C	T	173822936	3	4	27	1	0	0	0	0	1	0	0	0	4244	652	23	1	1625	1	DARS2	1	173822936	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	10997976	173822936	75427685	55	10506											
FAM5B	57795	hgsc.bcm.edu	37	chr1	177242695	177242695	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gactcagtcagttctgtcttGgtacagagtccagagaacaa	12	10	10	9	0	4	2	2	0	2	2	5	4	5	2	1	1	2	2	1	1	3	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:177242695G>T	ENST00000361539.4	+	5	1053	c.741G>T	c.(739-741)ttG>ttT	p.L247F	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	247	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)	extracellular region (GO:0005576)											GTTCTGTCTTGGTACAGAGTC	0.448																																					p.L247F		Atlas-SNP	.											.	FAM5B	191	.	0			c.G741T						PASS	.						85	77	79					1																	177242695		2203	4300	6503	SO:0001583	missense	57795	exon5			TGTCTTGGTACAG		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.741G>T	1.37:g.177242695G>T	ENSP00000354481:p.Leu247Phe	209	0	0		190	35	0.184211	NM_021165	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	37	CCDS1320.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.015662	0.75161	.	.	ENSG00000198797	ENST00000361539	T	0.27402	1.67	5.39	4.44	0.53790	Membrane attack complex component/perforin (MACPF) domain (1);	0.000000	0.64402	D	0.000002	T	0.54647	0.1871	M	0.74647	2.275	0.58432	D	0.999999	D;D	0.71674	0.995;0.998	D;D	0.83275	0.954;0.996	T	0.58940	-0.7547	10	0.87932	D	0	-11.3146	13.6873	0.62524	0.0:0.0:0.7267:0.2733	.	142;247	Q9C0B6-2;Q9C0B6	.;FAM5B_HUMAN	F	247	ENSP00000354481:L247F	ENSP00000354481:L247F	L	+	3	2	FAM5B	175509318	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	2.030000	0.41108	2.537000	0.85549	0.655000	0.94253	TTG	.	.	none		0.448	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165		T	177242695	G	T	177242695	3	4	27	1	0	0	0	0	1	0	0	0	5601	1339	47	4	755	4	FAM5B	1	177242695	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	3419759	177242695	72007926	56	10507											
TOR3A	64222	hgsc.bcm.edu	37	chr1	179064145	179064145	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttgtgaaggaaaacctgaTtgactacttcatccccttcc	10	13	6	12	0	2	3	1	3	1	0	4	4	4	4	4	1	2	0	4	1	4	5	rs138598531	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:179064145T>C	ENST00000367627.3	+	6	1738	c.986T>C	c.(985-987)aTt>aCt	p.I329T	TOR3A_ENST00000352445.6_Intron	NM_022371.3	NP_071766.2	Q9H497	TOR3A_HUMAN	torsin family 3, member A	329					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						GAAAACCTGATTGACTACTTC	0.502													T|||	3	0.000599042	0.0	0.0	5008	,	,		20059	0.0		0.003	False		,,,				2504	0.0				p.I329T		Atlas-SNP	.											.	TOR3A	28	.	0			c.T986C						PASS	.	T	THR/ILE	1,4405	2.1+/-5.4	0,1,2202	207	183	191		986	5.6	1	1	dbSNP_134	191	8,8592	6.4+/-24.3	0,8,4292	yes	missense	TOR3A	NM_022371.3	89	0,9,6494	CC,CT,TT		0.093,0.0227,0.0692	possibly-damaging	329/398	179064145	9,12997	2203	4300	6503	SO:0001583	missense	64222	exon6			ACCTGATTGACTA	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.986T>C	1.37:g.179064145T>C	ENSP00000356599:p.Ile329Thr	213	0	0		192	98	0.510417	NM_022371	B4DSY0|B7ZB65|Q5M7Y7|Q8WVA7|Q8WWM2|Q9H495|Q9H6E7	Missense_Mutation	SNP	ENST00000367627.3	37	CCDS1329.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	23.6	4.433498	0.83776	2.27E-4	9.3E-4	ENSG00000186283	ENST00000367627	T	0.60797	0.16	5.62	5.62	0.85841	.	0.102990	0.64402	D	0.000005	T	0.67998	0.2953	M	0.90650	3.135	0.80722	D	1	P	0.46706	0.883	B	0.42827	0.399	T	0.76567	-0.2912	10	0.62326	D	0.03	-9.8442	15.0006	0.71469	0.0:0.0:0.0:1.0	.	329	Q9H497	TOR3A_HUMAN	T	329	ENSP00000356599:I329T	ENSP00000356599:I329T	I	+	2	0	TOR3A	177330768	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	7.662000	0.83803	2.134000	0.65973	0.496000	0.49642	ATT	T|0.999;C|0.001	0.001	strong		0.502	TOR3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084927.1	NM_022371		C	179064145	T	C	179064145	3	2	27	1	0	0	0	0	1	0	0	0	16391	1493	52	3	1008	3	TOR3A	1	179064145	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	1821450	179064145	70186476	57	10508											
DHX9	1660	hgsc.bcm.edu	37	chr1	182850520	182850520	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaaacagattttctgatcacGtagcccttttatcagtattc	11	15	6	9	1	3	2	2	1	1	1	4	3	3	2	1	0	2	2	1	0	4	7			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:182850520G>A	ENST00000367549.3	+	23	2856	c.2746G>A	c.(2746-2748)Gta>Ata	p.V916I	DHX9_ENST00000485081.1_3'UTR	NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	916					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						TTCTGATCACGTAGCCCTTTT	0.433																																					p.V916I	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.G2746A						PASS	.						149	140	143					1																	182850520		1865	4107	5972	SO:0001583	missense	1660	exon23			GATCACGTAGCCC	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.2746G>A	1.37:g.182850520G>A	ENSP00000356520:p.Val916Ile	134	0	0		117	62	0.529915	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Missense_Mutation	SNP	ENST00000367549.3	37	CCDS41444.1	.	.	.	.	.	.	.	.	.	.	G	31	5.082905	0.94050	.	.	ENSG00000135829	ENST00000367549	T	0.27557	1.66	5.76	5.76	0.90799	Helicase-associated domain (2);	0.000000	0.85682	D	0.000000	T	0.36580	0.0972	N	0.17379	0.485	0.80722	D	1	D;D	0.60575	0.969;0.988	P;P	0.58077	0.572;0.832	T	0.07028	-1.0794	10	0.30854	T	0.27	.	19.5961	0.95538	0.0:0.0:1.0:0.0	.	195;916	B3KU66;Q08211	.;DHX9_HUMAN	I	916	ENSP00000356520:V916I	ENSP00000356520:V916I	V	+	1	0	DHX9	181117143	1.000000	0.71417	0.999000	0.59377	0.931000	0.56810	7.251000	0.78297	2.706000	0.92434	0.655000	0.94253	GTA	.	.	none		0.433	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588		A	182850520	G	A	182850520	3	1	27	1	0	0	0	0	1	0	0	0	4518	1145	40	1	2832	1	DHX9	1	182850520	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	3786375	182850520	66400101	58	10509											
HMCN1	83872	hgsc.bcm.edu	37	chr1	186121995	186121995	+	Missense_Mutation	SNP	A	A	T																															ttcagtcacctgctgaagtcActgtaaaggtaaaatgccag																								rs114364265	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:186121995A>T	ENST00000271588.4	+	96	15239	c.15010A>T	c.(15010-15012)Act>Tct	p.T5004S	HMCN1_ENST00000367492.2_Missense_Mutation_p.T5004S	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	5004	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						TGCTGAAGTCACTGTAAAGGT	0.438													A|||	9	0.00179712	0.0	0.0	5008	,	,		18499	0.0		0.008	False		,,,				2504	0.001				p.T5004S		Atlas-SNP	.											.	HMCN1	797	.	0			c.A15010T						PASS	.	A	SER/THR	3,4403	4.2+/-10.8	0,3,2200	196	170	179		15010	0.8	0.1	1	dbSNP_133	179	28,8572	9.1+/-34.3	1,26,4273	yes	missense	HMCN1	NM_031935.2	58	1,29,6473	TT,TA,AA		0.3256,0.0681,0.2384	benign	5004/5636	186121995	31,12975	2203	4300	6503	SO:0001583	missense	83872	exon96			GAAGTCACTGTAA	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.15010A>T	1.37:g.186121995A>T	ENSP00000271588:p.Thr5004Ser	215	0	0		170	87	0.511765	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	A	2.871	-0.233991	0.05983	6.81E-4	0.003256	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.32988	1.43;1.43	5.9	0.836	0.18891	G2 nidogen/fibulin G2F (2);Green fluorescent protein-like (1);	0.929918	0.09308	N	0.819936	T	0.08582	0.0213	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.32161	-0.9917	10	0.05833	T	0.94	.	6.2405	0.20787	0.6238:0.1195:0.2567:0.0	.	5004	Q96RW7	HMCN1_HUMAN	S	5004	ENSP00000271588:T5004S;ENSP00000356462:T5004S	ENSP00000271588:T5004S	T	+	1	0	HMCN1	184388618	0.001000	0.12720	0.065000	0.19835	0.779000	0.44077	0.806000	0.27126	-0.101000	0.12219	-0.263000	0.10527	ACT	A|0.996;T|0.004	0.004	strong		0.438	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		T	186121995	A	T	186121995	3	4	27	1	0	0	0	0	1	0	0	0	7229	159	6	5	15392	5	HMCN1	1	186121995	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	3271475	186121995	63128626	59	10510	132	2									
HMCN1	83872	hgsc.bcm.edu	37	chr1	186121996	186121996	+	Missense_Mutation	SNP	C	C	T																															tcagtcacctgctgaagtcaCtgtaaaggtaaaatgccagg																								rs114629728	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:186121996C>T	ENST00000271588.4	+	96	15240	c.15011C>T	c.(15010-15012)aCt>aTt	p.T5004I	HMCN1_ENST00000367492.2_Missense_Mutation_p.T5004I	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	5004	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						GCTGAAGTCACTGTAAAGGTA	0.433													C|||	10	0.00199681	0.0	0.0014	5008	,	,		18553	0.0		0.008	False		,,,				2504	0.001				p.T5004I		Atlas-SNP	.											.	HMCN1	797	.	0			c.C15011T						PASS	.	C	ILE/THR	4,4402	2.1+/-5.4	0,4,2199	196	170	179		15011	2.9	0	1	dbSNP_133	179	29,8571	9.1+/-34.3	1,27,4272	yes	missense	HMCN1	NM_031935.2	89	1,31,6471	TT,TC,CC		0.3372,0.0908,0.2537	benign	5004/5636	186121996	33,12973	2203	4300	6503	SO:0001583	missense	83872	exon96			AAGTCACTGTAAA	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.15011C>T	1.37:g.186121996C>T	ENSP00000271588:p.Thr5004Ile	215	0	0		170	88	0.517647	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	8.698	0.909113	0.17833	9.08E-4	0.003372	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.31510	1.49;1.49	5.9	2.9	0.33743	G2 nidogen/fibulin G2F (2);Green fluorescent protein-like (1);	0.929918	0.09308	N	0.819936	T	0.12603	0.0306	N	0.08118	0	0.09310	N	1	B	0.27316	0.175	B	0.30855	0.121	T	0.34601	-0.9822	10	0.29301	T	0.29	.	9.0753	0.36517	0.4557:0.2514:0.2928:0.0	.	5004	Q96RW7	HMCN1_HUMAN	I	5004	ENSP00000271588:T5004I;ENSP00000356462:T5004I	ENSP00000271588:T5004I	T	+	2	0	HMCN1	184388619	0.000000	0.05858	0.026000	0.17262	0.758000	0.43043	0.220000	0.17660	0.314000	0.23086	0.650000	0.86243	ACT	C|0.996;T|0.004	0.004	strong		0.433	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		T	186121996	C	T	186121996	3	4	27	1	0	0	0	0	1	0	0	0	7229	565	20	2	15393	2	HMCN1	1	186121996	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1	186121996	63128625	60	10511	132	2									
CFHR2	3080	hgsc.bcm.edu	37	chr1	196918741	196918741	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttttggactcgcataacgtGcgcagaagaaggatggtcac	11	9	12	9	3	1	2	1	0	0	2	2	4	1	4	0	3	2	2	0	3	3	3	rs79351096	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:196918741G>A	ENST00000367415.5	+	2	315	c.215G>A	c.(214-216)tGc>tAc	p.C72Y	CFHR2_ENST00000496448.1_Intron|CFHR2_ENST00000476712.2_Missense_Mutation_p.C72Y|CFHR2_ENST00000367421.3_Missense_Mutation_p.C72Y	NM_005666.2	NP_005657.1	P36980	FHR2_HUMAN	complement factor H-related 2	72	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.					extracellular region (GO:0005576)				large_intestine(2)|ovary(1)|skin(3)	6						CGCATAACGTGCGCAGAAGAA	0.403													g|||	76	0.0151757	0.0015	0.0288	5008	,	,		18573	0.0		0.0189	False		,,,				2504	0.0358				p.C72Y		Atlas-SNP	.											CFHR2_ENST00000367415,NS,carcinoma,-1,1	CFHR2	73	1	0			c.G215A						PASS	.	G	TYR/CYS	30,4376		0,30,2173	101	89	93		215	3.3	0	1	dbSNP_133	93	220,8380		2,216,4082	no	missense	CFHR2	NM_005666.2	194	2,246,6255	AA,AG,GG		2.5581,0.6809,1.9222	probably-damaging	72/271	196918741	250,12756	2203	4300	6503	SO:0001583	missense	3080	exon2			TAACGTGCGCAGA	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	ENST00000367415.5:c.215G>A	1.37:g.196918741G>A	ENSP00000356385:p.Cys72Tyr	247	0	0		213	103	0.483568	NM_005666	Q14310|Q5T9T1	Missense_Mutation	SNP	ENST00000367415.5	37	CCDS30959.1	33	0.01510989010989011	1	0.0020325203252032522	14	0.03867403314917127	0	0.0	18	0.023746701846965697	.	13.46	2.242600	0.39598	0.006809	0.025581	ENSG00000080910	ENST00000367421;ENST00000367415	D;D	0.98090	-4.71;-4.71	3.33	3.33	0.38152	Complement control module (2);Sushi/SCR/CCP (2);	0.000000	0.36893	N	0.002344	D	0.94305	0.8170	M	0.84082	2.675	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	D	0.86843	0.2018	10	0.87932	D	0	.	10.313	0.43721	0.0:0.0:1.0:0.0	.	72	P36980	FHR2_HUMAN	Y	72	ENSP00000356391:C72Y;ENSP00000356385:C72Y	ENSP00000356385:C72Y	C	+	2	0	CFHR2	195185364	0.417000	0.25432	0.004000	0.12327	0.001000	0.01503	3.949000	0.56668	1.825000	0.53177	0.508000	0.49915	TGC	G|0.983;A|0.017	0.017	strong		0.403	CFHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088815.2	NM_005666		A	196918741	G	A	196918741	3	1	27	1	0	0	0	0	1	0	0	0	3287	1319	46	2	221	2	CFHR2	1	196918741	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	10796745	196918741	52331880	61	10512											
ASPM	259266	hgsc.bcm.edu	37	chr1	197069640	197069640	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacttctagcttgaataatgAtaacactgcttctgatctgt	11	16	6	8	0	3	3	0	3	3	0	3	3	3	3	0	0	4	2	0	0	5	7	rs200856894		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:197069640A>G	ENST00000367409.4	-	18	8997	c.8741T>C	c.(8740-8742)aTc>aCc	p.I2914T	ASPM_ENST00000367408.1_Intron|ASPM_ENST00000294732.7_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2914	IQ 33. {ECO:0000255|PROSITE- ProRule:PRU00116}.				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						TTGAATAATGATAACACTGCT	0.299																																					p.I2914T		Atlas-SNP	.											ASPM,NS,carcinoma,+1,1	ASPM	444	1	0			c.T8741C						PASS	.	A	,THR/ILE	0,4406		0,0,2203	59	62	61		,8741	2.7	0	1		61	2,8590	2.2+/-6.3	0,2,4294	yes	intron,missense	ASPM	NM_001206846.1,NM_018136.4	,89	0,2,6497	GG,GA,AA		0.0233,0.0,0.0154	,benign	,2914/3478	197069640	2,12996	2203	4296	6499	SO:0001583	missense	259266	exon18			ATAATGATAACAC	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.8741T>C	1.37:g.197069640A>G	ENSP00000356379:p.Ile2914Thr	88	0	0		48	17	0.354167	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	37	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	A	12.05	1.822080	0.32237	0.0	2.33E-4	ENSG00000066279	ENST00000367409;ENST00000367406	T	0.73897	-0.79	5.09	2.7	0.31948	.	0.360702	0.26708	N	0.022904	T	0.80778	0.4688	M	0.68317	2.08	0.09310	N	0.999996	B;D	0.71674	0.024;0.998	B;D	0.65987	0.012;0.94	T	0.70029	-0.4984	10	0.52906	T	0.07	.	7.9874	0.30220	0.7908:0.1371:0.0721:0.0	.	900;2914	E7EQ84;Q8IZT6	.;ASPM_HUMAN	T	2914;900	ENSP00000356379:I2914T	ENSP00000356376:I900T	I	-	2	0	ASPM	195336263	0.020000	0.18652	0.001000	0.08648	0.465000	0.32709	2.427000	0.44740	0.341000	0.23771	0.460000	0.39030	ATC	A|0.999;G|0.001	0.001	weak		0.299	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		G	197069640	A	G	197069640	3	3	27	1	0	0	0	0	1	0	0	0	1056	333	12	3	1736	3	ASPM	1	197069640	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	150899	197069640	52180981	62	10513											
KIF21B	23046	hgsc.bcm.edu	37	chr1	200978027	200978027	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgatgccctgctcctcctccGacgttgccatgtcaaagcca	7	10	8	16	2	1	1	1	1	0	0	4	2	4	1	6	0	4	2	6	0	1	1	rs140589352	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:200978027G>A	ENST00000422435.2	-	3	633	c.317C>T	c.(316-318)tCg>tTg	p.S106L	KIF21B_ENST00000360529.5_Missense_Mutation_p.S106L|KIF21B_ENST00000332129.2_Missense_Mutation_p.S106L|KIF21B_ENST00000461742.2_Missense_Mutation_p.S106L	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	106	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						CTCCTCCTCCGACGTTGCCAT	0.642													G|||	42	0.00838658	0.0	0.013	5008	,	,		20340	0.0		0.0179	False		,,,				2504	0.0153				p.S106L		Atlas-SNP	.											.	KIF21B	208	.	0			c.C317T						PASS	.	G	LEU/SER	13,4393	20.2+/-43.8	0,13,2190	118	103	108		317	4.7	0	1	dbSNP_134	108	193,8407	85.0+/-147.5	3,187,4110	yes	missense	KIF21B	NM_017596.2	145	3,200,6300	AA,AG,GG		2.2442,0.2951,1.5839	benign	106/1625	200978027	206,12800	2203	4300	6503	SO:0001583	missense	23046	exon3			TCCTCCGACGTTG	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.317C>T	1.37:g.200978027G>A	ENSP00000411831:p.Ser106Leu	42	0	0		51	26	0.509804	NM_017596	B2RP62|B7ZMI0|Q5T4J3	Missense_Mutation	SNP	ENST00000422435.2	37	CCDS58056.1	19	0.0086996336996337	0	0.0	4	0.011049723756906077	0	0.0	15	0.01978891820580475	G	10.10	1.257053	0.22965	0.002951	0.022442	ENSG00000116852	ENST00000332129;ENST00000360529;ENST00000461742;ENST00000422435;ENST00000539858	T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83	5.57	4.66	0.58398	Kinesin, motor domain (4);	0.322422	0.29073	N	0.013235	T	0.52208	0.1720	M	0.68952	2.095	0.09310	N	0.999999	P;P;B;P	0.42248	0.774;0.774;0.0;0.733	B;B;B;B	0.31869	0.094;0.137;0.002;0.131	T	0.55296	-0.8163	10	0.27082	T	0.32	.	14.3505	0.66699	0.0714:0.0:0.9286:0.0	.	106;106;106;106	B7ZMI0;B2RP62;O75037;O75037-2	.;.;KI21B_HUMAN;.	L	106	ENSP00000328494:S106L;ENSP00000353724:S106L;ENSP00000433808:S106L;ENSP00000411831:S106L	ENSP00000328494:S106L	S	-	2	0	KIF21B	199244650	0.791000	0.28800	0.014000	0.15608	0.324000	0.28378	4.731000	0.62022	1.348000	0.45733	0.650000	0.86243	TCG	G|0.987;A|0.013	0.013	strong		0.642	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332		A	200978027	G	A	200978027	3	1	27	1	0	0	0	0	1	0	0	0	8298	1059	37	1	4685	1	KIF21B	1	200978027	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	3908387	200978027	48272594	63	10514											
CACNA1S	779	hgsc.bcm.edu	37	chr1	201058530	201058530	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctgccattgatggtgcaccgGcgccctgagcccgtcctggc	4	8	13	16	3	0	2	0	2	0	0	1	2	1	2	5	3	3	1	5	3	0	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:201058530G>A	ENST00000362061.3	-	6	982	c.756C>T	c.(754-756)cgC>cgT	p.R252R	CACNA1S_ENST00000367338.3_Silent_p.R252R	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	252					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)	TGGTGCACCGGCGCCCTGAGC	0.617																																					p.R252R		Atlas-SNP	.											CACNA1S,colon,carcinoma,-2,1	CACNA1S	249	1	0			c.C756T						PASS	.						50	45	47					1																	201058530		2203	4300	6503	SO:0001819	synonymous_variant	779	exon6			GCACCGGCGCCCT	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.756C>T	1.37:g.201058530G>A		133	0	0		117	72	0.615385	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Silent	SNP	ENST00000362061.3	37	CCDS1407.1																																																																																			.	.	none		0.617	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069		A	201058530	G	A	201058530	2	1	27	1	0	0	0	0	0	0	0	1	2549	1190	42	2		2	CACNA1S	1	201058530	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	80503	201058530	48192091	64	10515											
IGFN1	91156	hgsc.bcm.edu	37	chr1	201163305	201163305	+	De_novo_Start_OutOfFrame	SNP	C	C	A																															agctccggaagtcccacatcCctggagtgagcatctggcag																								rs189690117	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:201163305C>A	ENST00000295591.8	+	0	161				IGFN1_ENST00000335211.4_Missense_Mutation_p.P11T|IGFN1_ENST00000451870.2_Missense_Mutation_p.P11T			Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1							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						GTCCCACATCCCTGGAGTGAG	0.607													C|||	7	0.00139776	0.0015	0.0014	5008	,	,		18650	0.0		0.004	False		,,,				2504	0.0				p.P11T		Atlas-SNP	.											.	IGFN1	220	.	0			c.C31A						PASS	.						30	36	34					1																	201163305		692	1591	2283			91156	exon3			CACATCCCTGGAG	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	ENST00000295591.8:c.-8490C>A	1.37:g.201163305C>A		123	0	0		116	116	1	NM_001164586	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000295591.8	37		2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	C	15.73	2.921085	0.52653	.	.	ENSG00000163395	ENST00000335211;ENST00000451870	T;T	0.63096	0.23;-0.02	4.55	4.55	0.56014	.	.	.	.	.	T	0.69287	0.3094	L	0.55481	1.735	0.80722	D	1	.	.	.	.	.	.	T	0.72620	-0.4238	7	0.62326	D	0.03	.	14.2363	0.65929	0.0:1.0:0.0:0.0	.	.	.	.	T	11	ENSP00000334714:P11T;ENSP00000398386:P11T	ENSP00000334714:P11T	P	+	1	0	IGFN1	199429928	0.289000	0.24334	0.730000	0.30809	0.517000	0.34286	2.800000	0.47900	2.058000	0.61347	0.637000	0.83480	CCT	C|0.999;A|0.001	0.001	strong		0.607	IGFN1-201	KNOWN	basic	protein_coding	protein_coding		NM_178275		A	201163305	C	A	201163305	1	1	27	1	0	1	0	0	0	0	0	0	7599	623	22	4		4	IGFN1	1	201163305	De_novo_Start_OutOfFrame	SNP	C	TCGA-G8-6909-01A-11D-2210-10	104775	201163305	48087316	65	10516	133	2									
IGFN1	91156	hgsc.bcm.edu	37	chr1	201163306	201163306	+	Missense_Mutation	SNP	C	C	G																															gctccggaagtcccacatccCtggagtgagcatctggcagc																								rs41313898	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:201163306C>G	ENST00000335211.4	+	3	162	c.32C>G	c.(31-33)cCt>cGt	p.P11R	IGFN1_ENST00000295591.8_5'UTR|IGFN1_ENST00000451870.2_Missense_Mutation_p.P11R	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	11						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						TCCCACATCCCTGGAGTGAGC	0.607													C|||	7	0.00139776	0.0015	0.0014	5008	,	,		18751	0.0		0.004	False		,,,				2504	0.0				p.P11R		Atlas-SNP	.											.	IGFN1	220	.	0			c.C32G						PASS	.						30	36	34					1																	201163306		692	1591	2283	SO:0001583	missense	91156	exon3			ACATCCCTGGAGT	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.32C>G	1.37:g.201163306C>G	ENSP00000334714:p.Pro11Arg	122	0	0		116	116	1	NM_001164586	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000335211.4	37	CCDS53455.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	C	11.13	1.547817	0.27652	.	.	ENSG00000163395	ENST00000335211;ENST00000451870	T;T	0.62788	0.24;0.0	4.55	3.61	0.41365	.	.	.	.	.	T	0.66723	0.2818	L	0.55481	1.735	0.80722	D	1	.	.	.	.	.	.	T	0.68146	-0.5486	7	0.87932	D	0	.	10.9911	0.47549	0.1992:0.8008:0.0:0.0	rs41313898	.	.	.	R	11	ENSP00000334714:P11R;ENSP00000398386:P11R	ENSP00000334714:P11R	P	+	2	0	IGFN1	199429929	0.281000	0.24258	0.781000	0.31783	0.577000	0.36160	2.171000	0.42453	0.840000	0.34995	0.637000	0.83480	CCT	C|0.999;G|0.001	0.001	strong		0.607	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275		G	201163306	C	G	201163306	3	3	27	1	0	0	0	0	1	0	0	0	7599	681	24	4	38	4	IGFN1	1	201163306	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1	201163306	48087315	66	10517	133	2									
PPFIA4	8497	hgsc.bcm.edu	37	chr1	203044777	203044777	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgcgggagcaccacggtcgcGgcggcatgctcagcgcttcc	5	5	15	16	7	1	0	1	0	0	0	3	1	2	1	2	4	3	4	2	4	0	1	rs12130501	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:203044777G>A	ENST00000447715.2	+	34	3841	c.3400G>A	c.(3400-3402)Ggc>Agc	p.G1134S	PPFIA4_ENST00000414050.2_Missense_Mutation_p.G863S|PPFIA4_ENST00000599966.1_Missense_Mutation_p.G641S|PPFIA4_ENST00000367240.2_Missense_Mutation_p.G1135S|PPFIA4_ENST00000272198.6_Missense_Mutation_p.G650S|PPFIA4_ENST00000295706.4_Missense_Mutation_p.G641S			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	1134				G -> A (in Ref. 5; AAC26102). {ECO:0000305}.	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						CCACGGTCGCGGCGGCATGCT	0.716													g|||	32	0.00638978	0.0	0.0115	5008	,	,		11140	0.0		0.0189	False		,,,				2504	0.0051				p.G650S		Atlas-SNP	.											PPFIA4_ENST00000272198,colon,carcinoma,-1,2	PPFIA4	139	2	0			c.G1948A						PASS	.		SER/GLY	15,3733		0,15,1859	11	14	13		1948	-0.2	0	1	dbSNP_120	13	228,7910		2,224,3843	no	missense	PPFIA4	NM_015053.1	56	2,239,5702	AA,AG,GG		2.8017,0.4002,2.0444	benign	650/702	203044777	243,11643	1874	4069	5943	SO:0001583	missense	8497	exon16			GGTCGCGGCGGCA	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.3400G>A	1.37:g.203044777G>A	ENSP00000402576:p.Gly1134Ser	13	0	0		26	12	0.461538	NM_015053	A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Missense_Mutation	SNP	ENST00000447715.2	37		16	0.007326007326007326	0	0.0	5	0.013812154696132596	0	0.0	11	0.014511873350923483	g	12.32	1.901775	0.33535	0.004002	0.028017	ENSG00000143847	ENST00000367240;ENST00000447715;ENST00000295706;ENST00000414050;ENST00000272198	T;T;T;T;T	0.21734	2.32;2.0;1.99;2.0;1.99	4.58	-0.158	0.13383	.	1.035160	0.07805	U	0.957214	T	0.03564	0.0102	N	0.17474	0.49	0.09310	N	1	B;B;B;B;B	0.17038	0.0;0.0;0.005;0.02;0.012	B;B;B;B;B	0.16722	0.0;0.0;0.002;0.016;0.007	T	0.34875	-0.9811	10	0.32370	T	0.25	-0.3686	4.4121	0.11438	0.4118:0.2651:0.3231:0.0	rs12130501	863;1134;336;641;650	B4DIS5;B1N949;B3KN22;O75335-2;O75335	.;.;.;.;LIPA4_HUMAN	S	1135;1134;641;863;650	ENSP00000356209:G1135S;ENSP00000402576:G1134S;ENSP00000295706:G641S;ENSP00000400379:G863S;ENSP00000272198:G650S	ENSP00000272198:G650S	G	+	1	0	PPFIA4	201311400	0.948000	0.32251	0.014000	0.15608	0.413000	0.31143	1.380000	0.34351	-0.369000	0.08028	0.298000	0.19748	GGC	G|0.992;A|0.008	0.008	strong		0.716	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000462949.1	NM_015053		A	203044777	G	A	203044777	3	1	27	1	0	0	0	0	1	0	0	0	12321	1116	39	1	2010	1	PPFIA4	1	203044777	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1881471	203044777	46205844	67	10518											
BTG2	7832	hgsc.bcm.edu	37	chr1	203274826	203274826	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggacccggggctgcgtgaGcgagcagaggcttaaggtct	8	6	18	9	3	1	2	0	1	1	1	1	5	1	3	1	5	3	3	1	5	1	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:203274826G>A	ENST00000290551.4	+	1	163	c.92G>A	c.(91-93)aGc>aAc	p.S31N	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	31					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			GGCTGCGTGAGCGAGCAGAGG	0.711																																					p.S31N		Atlas-SNP	.											.	BTG2	16	.	0			c.G92A						PASS	.						16	16	16					1																	203274826		2157	4238	6395	SO:0001583	missense	7832	exon1			GCGTGAGCGAGCA		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.92G>A	1.37:g.203274826G>A	ENSP00000290551:p.Ser31Asn	132	0	0		165	44	0.266667	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	G	9.276	1.046979	0.19748	.	.	ENSG00000159388	ENST00000290551	T	0.22539	1.95	4.66	3.75	0.43078	Anti-proliferative protein (3);	0.175253	0.47455	N	0.000221	T	0.11324	0.0276	N	0.17800	0.525	0.32144	N	0.585114	B	0.02656	0.0	B	0.04013	0.001	T	0.18272	-1.0342	10	0.14656	T	0.56	-0.1987	8.0794	0.30735	0.1867:0.0:0.8133:0.0	.	31	P78543	BTG2_HUMAN	N	31	ENSP00000290551:S31N	ENSP00000290551:S31N	S	+	2	0	BTG2	201541449	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	2.876000	0.48498	1.194000	0.43101	0.478000	0.44815	AGC	.	.	none		0.711	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		A	203274826	G	A	203274826	3	1	27	1	0	0	0	0	1	0	0	0	1556	971	34	2	94	2	BTG2	1	203274826	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	230049	203274826	45975795	68	10519											
ATP2B4	493	hgsc.bcm.edu	37	chr1	203669371	203669371	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gatggaatcctgatccaaggGaatgatctgaagattgatga	14	10	12	5	0	1	6	0	5	1	1	3	9	3	8	2	2	0	0	2	2	4	1	rs2228446	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:203669371G>A	ENST00000357681.5	+	5	1810	c.687G>A	c.(685-687)ggG>ggA	p.G229G	ATP2B4_ENST00000391954.2_Silent_p.G229G|ATP2B4_ENST00000367219.3_Silent_p.G229G|ATP2B4_ENST00000367218.3_Silent_p.G229G|ATP2B4_ENST00000341360.2_Silent_p.G229G	NM_001684.4	NP_001675.3	P23634	AT2B4_HUMAN	ATPase, Ca++ transporting, plasma membrane 4	229					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)			TGATCCAAGGGAATGATCTGA	0.517													G|||	25	0.00499201	0.0008	0.0072	5008	,	,		20092	0.0		0.0139	False		,,,				2504	0.0051				p.G229G		Atlas-SNP	.											.	ATP2B4	226	.	0			c.G687A						PASS	.	G	,	12,4394	19.1+/-41.9	0,12,2191	114	110	112		687,687	-9.8	0.8	1	dbSNP_98	112	171,8429	78.6+/-141.3	0,171,4129	no	coding-synonymous,coding-synonymous	ATP2B4	NM_001001396.2,NM_001684.4	,	0,183,6320	AA,AG,GG		1.9884,0.2724,1.407	,	229/1171,229/1206	203669371	183,12823	2203	4300	6503	SO:0001819	synonymous_variant	493	exon5			CCAAGGGAATGAT	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.687G>A	1.37:g.203669371G>A		108	0	0		97	49	0.505155	NM_001001396	B1APW5|B1APW6|Q13450|Q13452|Q13455|Q16817|Q7Z3S1	Silent	SNP	ENST00000357681.5	37	CCDS1440.1																																																																																			G|0.987;A|0.013	0.013	strong		0.517	ATP2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087462.1	NM_001001396		A	203669371	G	A	203669371	2	1	27	1	0	0	0	0	0	0	0	1	1142	1161	41	2		2	ATP2B4	1	203669371	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	394545	203669371	45581250	69	10520											
SLC45A3	85414	hgsc.bcm.edu	37	chr1	205628616	205628616	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctcacccaccaccacacgtaCggagacatcacaggcagagg	13	3	9	16	2	2	2	2	0	0	2	2	3	2	2	3	3	1	2	3	3	1	1	rs137949511	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:205628616C>T	ENST00000367145.3	-	5	1703	c.1408G>A	c.(1408-1410)Gta>Ata	p.V470I	SLC45A3_ENST00000460934.1_5'UTR	NM_033102.2	NP_149093.1	Q96JT2	S45A3_HUMAN	solute carrier family 45, member 3	470					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)			SLC45A3/BRAF(2)|SLC45A3/ELK4(18)|SLC45A3/ETV1(3)|SLC45A3/ETV5_ENST00000306376(2)|SLC45A3/ERG(50)	cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(7)|ovary(3)|prostate(5)	21	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0194)			ACCACACGTACGGAGACATCA	0.677			T	"ETV1, ETV5, ELK4, ERG"	prostate						OREG0014161	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	21	0.00419329	0.0	0.0043	5008	,	,		18353	0.0		0.0119	False		,,,				2504	0.0061				p.V470I		Atlas-SNP	.		Dom	yes		1	1q32	85414	"solute carrier family 45, member 3"		E	.	SLC45A3	54	.	0			c.G1408A						PASS	.	C	ILE/VAL	8,4396	14.3+/-33.2	0,8,2194	38	38	38		1408	-1.4	0.4	1	dbSNP_134	38	78,8520	44.5+/-102.8	0,78,4221	yes	missense	SLC45A3	NM_033102.2	29	0,86,6415	TT,TC,CC		0.9072,0.1817,0.6614	benign	470/554	205628616	86,12916	2202	4299	6501	SO:0001583	missense	85414	exon5			CACGTACGGAGAC	AF109301	CCDS1458.1	1q32.1	2013-05-22	2005-10-04	2005-10-04	ENSG00000158715	ENSG00000158715		"Solute carriers"	8642	protein-coding gene	gene with protein product		605097	"prostate cancer associated protein 6", "prostate cancer associated protein 2", "prostate cancer associated protein 8"	PCANAP6, PCANAP2, PCANAP8		10613842, 11245466	Standard	XM_005245556		Approved	IPCA-6, prostein, IPCA-2, IPCA-8	uc001hda.1	Q96JT2	OTTHUMG00000037223	ENST00000367145.3:c.1408G>A	1.37:g.205628616C>T	ENSP00000356113:p.Val470Ile	115	0	0	2153	128	71	0.554688	NM_033102	A8K2U9	Missense_Mutation	SNP	ENST00000367145.3	37	CCDS1458.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	2.983	-0.209897	0.06140	0.001817	0.009072	ENSG00000158715	ENST00000367145	T	0.44482	0.92	5.48	-1.36	0.09085	.	0.387498	0.26341	N	0.024935	T	0.13072	0.0317	N	0.14661	0.345	0.09310	N	1	B	0.22211	0.066	B	0.13407	0.009	T	0.20538	-1.0272	10	0.14656	T	0.56	-17.1135	7.4464	0.27213	0.0:0.4405:0.1634:0.3962	.	470	Q96JT2	S45A3_HUMAN	I	470	ENSP00000356113:V470I	ENSP00000356113:V470I	V	-	1	0	SLC45A3	203895239	0.023000	0.18921	0.369000	0.25952	0.167000	0.22549	-0.027000	0.12371	-0.144000	0.11314	-0.339000	0.08088	GTA	C|0.994;T|0.006	0.006	strong		0.677	SLC45A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090619.1	NM_033102		T	205628616	C	T	205628616	3	4	27	1	0	0	0	0	1	0	0	0	14657	536	19	1	257	1	SLC45A3	1	205628616	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1959245	205628616	43622005	70	10521											
CR1	1378	hgsc.bcm.edu	37	chr1	207669708	207669708	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tccctgctggcggttgtggtGctgcttgcgctgccggtggc	0	12	17	12	3	0	0	0	0	0	0	1	0	1	0	2	5	5	5	2	5	0	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:207669708G>A	ENST00000367049.4	+	1	96	c.96G>A	c.(94-96)gtG>gtA	p.V32V	CR1_ENST00000367051.1_Silent_p.V32V|CR1_ENST00000367053.1_Silent_p.V32V|CR1_ENST00000400960.2_Silent_p.V32V|CR1_ENST00000367052.1_Silent_p.V32V|CR1_ENST00000367050.4_3'UTR	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	32					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						CGGTTGTGGTGCTGCTTGCGC	0.741																																					p.V32V		Atlas-SNP	.											.	CR1	354	.	0			c.G96A						PASS	.						10	13	12					1																	207669708		1820	4065	5885	SO:0001819	synonymous_variant	1378	exon1			TGTGGTGCTGCTT	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.96G>A	1.37:g.207669708G>A		39	0	0		44	15	0.340909	NM_000573	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Silent	SNP	ENST00000367049.4	37	CCDS44308.1	.	.	.	.	.	.	.	.	.	.	G	11.17	1.559458	0.27827	.	.	ENSG00000203710	ENST00000529814	.	.	.	3.59	2.67	0.31697	.	.	.	.	.	T	0.55433	0.1920	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50338	-0.8840	4	.	.	.	.	7.0064	0.24838	0.1239:0.0:0.8761:0.0	.	.	.	.	Y	8	.	.	C	+	2	0	CR1	205736331	0.998000	0.40836	0.834000	0.33040	0.918000	0.54935	3.349000	0.52217	1.078000	0.41014	0.591000	0.81541	TGC	.	.	none		0.741	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573		A	207669708	G	A	207669708	2	1	27	1	0	0	0	0	0	0	0	1	3842	1306	46	2		2	CR1	1	207669708	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2041092	207669708	41580913	71	10522											
USH2A	7399	hgsc.bcm.edu	37	chr1	215848914	215848914	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggaagagaaactgacgattCaaaccagagtactccaggaa	17	5	10	9	2	1	3	1	1	0	2	2	7	2	5	2	2	3	1	2	2	5	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:215848914C>A	ENST00000307340.3	-	63	12725	c.12339G>T	c.(12337-12339)ttG>ttT	p.L4113F	USH2A_ENST00000366943.2_Missense_Mutation_p.L4113F	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	4113	Fibronectin type-III 26. {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)		ACTGACGATTCAAACCAGAGT	0.507										HNSCC(13;0.011)																											p.L4113F		Atlas-SNP	.											.	USH2A	1168	.	0			c.G12339T						PASS	.						69	65	67					1																	215848914		2203	4300	6503	SO:0001583	missense	7399	exon63			ACGATTCAAACCA	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.12339G>T	1.37:g.215848914C>A	ENSP00000305941:p.Leu4113Phe	128	0	0		138	29	0.210145	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	C	1.035	-0.680618	0.03353	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.54279	0.58;0.58	5.25	1.15	0.20763	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.220262	0.22515	N	0.059043	T	0.41351	0.1155	M	0.72894	2.215	0.09310	N	1	B	0.23735	0.09	B	0.20384	0.029	T	0.21861	-1.0233	10	0.18710	T	0.47	.	2.3656	0.04318	0.1182:0.4436:0.2314:0.2067	.	4113	O75445	USH2A_HUMAN	F	4113	ENSP00000305941:L4113F;ENSP00000355910:L4113F	ENSP00000305941:L4113F	L	-	3	2	USH2A	213915537	0.001000	0.12720	0.000000	0.03702	0.084000	0.17831	0.243000	0.18106	0.205000	0.20568	-0.143000	0.13931	TTG	.	.	none		0.507	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		A	215848914	C	A	215848914	3	1	27	1	0	0	0	0	1	0	0	0	17051	825	29	4	3309	4	USH2A	1	215848914	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	8179206	215848914	33401707	72	10523											
USH2A	7399	hgsc.bcm.edu	37	chr1	215956140	215956140	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcttcaagattgtctatttTggtccacgtagggggactca	9	14	10	8	1	4	1	2	0	2	1	5	2	5	2	1	3	0	1	1	3	3	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:215956140T>G	ENST00000307340.3	-	53	10911	c.10525A>C	c.(10525-10527)Aaa>Caa	p.K3509Q	USH2A_ENST00000366943.2_Missense_Mutation_p.K3509Q	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3509	Fibronectin type-III 20. {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)		TTGTCTATTTTGGTCCACGTA	0.403										HNSCC(13;0.011)																											p.K3509Q		Atlas-SNP	.											.	USH2A	1168	.	0			c.A10525C						PASS	.						99	94	95					1																	215956140		2203	4300	6503	SO:0001583	missense	7399	exon53			CTATTTTGGTCCA	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.10525A>C	1.37:g.215956140T>G	ENSP00000305941:p.Lys3509Gln	125	0	0		97	30	0.309278	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	T	14.66	2.602549	0.46423	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.53206	0.63;0.63	5.43	5.43	0.79202	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.313381	0.22314	U	0.061685	T	0.42359	0.1199	L	0.45137	1.4	0.23739	N	0.996979	P	0.50272	0.933	B	0.42386	0.386	T	0.35624	-0.9781	10	0.22706	T	0.39	.	15.4862	0.75569	0.0:0.0:0.0:1.0	.	3509	O75445	USH2A_HUMAN	Q	3509	ENSP00000305941:K3509Q;ENSP00000355910:K3509Q	ENSP00000305941:K3509Q	K	-	1	0	USH2A	214022763	1.000000	0.71417	0.021000	0.16686	0.401000	0.30781	3.818000	0.55678	2.063000	0.61619	0.533000	0.62120	AAA	.	.	none		0.403	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		G	215956140	T	G	215956140	3	3	27	1	0	0	0	0	1	0	0	0	17051	1821	63	5	5163	5	USH2A	1	215956140	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	107226	215956140	33294481	73	10524											
MIA3	375056	hgsc.bcm.edu	37	chr1	222823669	222823669	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttctgagaagttgaagactAtcatgaaagaaaatacagaa	19	10	8	4	0	2	6	1	3	1	4	2	7	2	6	0	0	1	1	0	0	8	4	rs201134844		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:222823669A>G	ENST00000344922.5	+	9	3692	c.3667A>G	c.(3667-3669)Atc>Gtc	p.I1223V	MIA3_ENST00000344507.1_Intron|MIA3_ENST00000340535.7_Missense_Mutation_p.I101V|MIA3_ENST00000344441.6_Missense_Mutation_p.I1223V	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	1223					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)		GTTGAAGACTATCATGAAAGA	0.274																																					p.I1223V		Atlas-SNP	.											.	MIA3	167	.	0			c.A3667G						PASS	.	A	VAL/ILE	0,3618		0,0,1809	33	34	34		3667	-6.1	0	1		34	7,8113		0,7,4053	yes	missense	MIA3	NM_198551.2	29	0,7,5862	GG,GA,AA		0.0862,0.0,0.0596	possibly-damaging	1223/1908	222823669	7,11731	1809	4060	5869	SO:0001583	missense	375056	exon9			AAGACTATCATGA		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.3667A>G	1.37:g.222823669A>G	ENSP00000340900:p.Ile1223Val	152	0	0		102	48	0.470588	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Missense_Mutation	SNP	ENST00000344922.5	37	CCDS41470.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	8.974|8.974	0.973738|0.973738	0.18736|0.18736	0.0|0.0	8.62E-4|8.62E-4	ENSG00000154305|ENSG00000154305	ENST00000344922;ENST00000344441;ENST00000320831;ENST00000340535;ENST00000284471|ENST00000354906	T;T;T|.	0.28666|.	1.6;1.6;1.6|.	5.75|5.75	-6.14|-6.14	0.02111|0.02111	.|.	.|.	.|.	.|.	.|.	T|T	0.27524|0.27524	0.0676|0.0676	L|L	0.31294|0.31294	0.92|0.92	0.09310|0.09310	N|N	1|1	P;B;B|.	0.39022|.	0.655;0.012;0.081|.	B;B;B|.	0.35039|.	0.194;0.015;0.017|.	T|T	0.36311|0.36311	-0.9753|-0.9753	9|5	0.49607|.	T|.	0.09|.	.|.	7.868|7.868	0.29549|0.29549	0.1682:0.4854:0.0:0.3464|0.1682:0.4854:0.0:0.3464	.|.	1223;101;1223|.	Q5JRA6-2;Q5JRA6-4;Q5JRA6|.	.;.;MIA3_HUMAN|.	V|C	1223;1223;1223;101;101|805	ENSP00000340900:I1223V;ENSP00000340587:I1223V;ENSP00000345866:I101V|.	ENSP00000284471:I101V|.	I|Y	+|+	1|2	0|0	MIA3|MIA3	220890292|220890292	0.177000|0.177000	0.23109|0.23109	0.000000|0.000000	0.03702|0.03702	0.048000|0.048000	0.14542|0.14542	1.442000|1.442000	0.35046|0.35046	-0.870000|-0.870000	0.04047|0.04047	0.482000|0.482000	0.46254|0.46254	ATC|TAT	A|0.999;G|0.001	0.001	weak		0.274	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551		G	222823669	A	G	222823669	3	3	27	1	0	0	0	0	1	0	0	0	9574	449	16	3	3701	3	MIA3	1	222823669	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	6867529	222823669	26426952	74	10525											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228452016	228452016	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggaggctggtggtgcaggaGgcaggccaggcggacgccgg	6	3	22	10	4	0	0	0	0	0	0	0	3	0	3	2	10	1	3	2	10	0	0	rs185523702	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228452016G>C	ENST00000422127.1	+	16	4829	c.4785G>C	c.(4783-4785)gaG>gaC	p.E1595D	OBSCN_ENST00000570156.2_Missense_Mutation_p.E1779D|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Missense_Mutation_p.E1595D|OBSCN_ENST00000359599.6_Missense_Mutation_p.E251D	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1595	Ig-like 16.				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)				TGGTGCAGGAGGCAGGCCAGG	0.642													G|||	20	0.00399361	0.0008	0.0086	5008	,	,		18329	0.0		0.0119	False		,,,				2504	0.001				p.E1779D		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G5337C						PASS	.	G	ASP/GLU,ASP/GLU	12,4228		0,12,2108	44	52	50		4785,4785	3.8	1	1		50	165,8287		3,159,4064	no	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	45,45	3,171,6172	CC,CG,GG		1.9522,0.283,1.3946	possibly-damaging,possibly-damaging	1595/7969,1595/6621	228452016	177,12515	2120	4226	6346	SO:0001583	missense	84033	exon18			GCAGGAGGCAGGC	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.4785G>C	1.37:g.228452016G>C	ENSP00000409493:p.Glu1595Asp	319	0	0		309	147	0.475728	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	37	CCDS58065.1	15	0.006868131868131868	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	9	0.011873350923482849	.	1.509	-0.549977	0.03996	0.00283	0.019522	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000359599	T;T;T	0.04317	3.65;3.65;3.65	4.69	3.77	0.43336	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.306226	0.28595	N	0.014790	T	0.01387	0.0045	N	0.16037	0.36	0.80722	D	1	B;B	0.30439	0.018;0.279	B;B	0.23716	0.029;0.048	T	0.52403	-0.8580	10	0.11794	T	0.64	.	13.1743	0.59617	0.1471:0.0:0.8529:0.0	.	1595;1595	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	D	1595;1595;251	ENSP00000284548:E1595D;ENSP00000409493:E1595D;ENSP00000352613:E251D	ENSP00000284548:E1595D	E	+	3	2	OBSCN	226518639	0.000000	0.05858	0.996000	0.52242	0.001000	0.01503	-0.150000	0.10189	0.601000	0.29879	-1.579000	0.00862	GAG	G|0.990;C|0.010	0.010	strong		0.642	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		C	228452016	G	C	228452016	3	2	27	1	0	0	0	0	1	0	0	0	10821	991	35	4	4843	4	OBSCN	1	228452016	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	5628347	228452016	20798605	75	10526											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228464303	228464303	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aggggcccacgtgccacctgGctgtgcggggccccatgcac	5	5	15	16	2	0	0	0	0	0	0	0	0	0	0	5	5	3	2	5	5	0	0	rs75280352	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228464303G>T	ENST00000422127.1	+	22	6417	c.6373G>T	c.(6373-6375)Gct>Tct	p.A2125S	RP5-1139B12.3_ENST00000602947.1_RNA|RP5-1139B12.3_ENST00000602529.1_RNA|RP5-1139B12.2_ENST00000602517.1_RNA|OBSCN_ENST00000359599.6_Missense_Mutation_p.A972S|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000284548.11_Missense_Mutation_p.A2125S|OBSCN_ENST00000570156.2_Missense_Mutation_p.A2500S|OBSCN_ENST00000366709.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	2125	Ig-like 21.				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)				GTGCCACCTGGCTGTGCGGGG	0.672													G|||	23	0.00459265	0.0008	0.0101	5008	,	,		15176	0.0		0.0139	False		,,,				2504	0.001				p.A2500S		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G7498T						PASS	.	G	SER/ALA,SER/ALA	19,4145		0,19,2063	16	21	20		6373,6373	1.9	0.1	1	dbSNP_131	20	234,8182		4,226,3978	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	99,99	4,245,6041	TT,TG,GG		2.7804,0.4563,2.0111	benign,benign	2125/7969,2125/6621	228464303	253,12327	2082	4208	6290	SO:0001583	missense	84033	exon26			CACCTGGCTGTGC	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.6373G>T	1.37:g.228464303G>T	ENSP00000409493:p.Ala2125Ser	234	0	0		232	134	0.577586	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	37	CCDS58065.1	15	0.006868131868131868	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	9	0.011873350923482849	G	10.48	1.363003	0.24684	0.004563	0.027804	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000359599	T;T;T	0.04234	3.67;3.67;3.67	5.23	1.86	0.25419	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.356983	0.26203	N	0.025723	T	0.00724	0.0024	N	0.13168	0.305	0.20403	N	0.999906	P;P	0.44816	0.844;0.499	B;B	0.39152	0.292;0.069	T	0.39901	-0.9591	10	0.08599	T	0.76	.	4.5827	0.12266	0.298:0.0:0.5441:0.1578	.	2125;2125	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	S	2125;2125;972	ENSP00000284548:A2125S;ENSP00000409493:A2125S;ENSP00000352613:A972S	ENSP00000284548:A2125S	A	+	1	0	OBSCN	226530926	0.038000	0.19896	0.075000	0.20258	0.026000	0.11368	1.268000	0.33062	1.193000	0.43086	0.549000	0.68633	GCT	G|0.993;T|0.007	0.007	strong		0.672	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228464303	G	T	228464303	3	4	27	1	0	0	0	0	1	0	0	0	10821	1203	42	4	6455	4	OBSCN	1	228464303	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	12287	228464303	20786318	76	10527											
TRIM11	81559	hgsc.bcm.edu	37	chr1	228589861	228589861	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagtgacttctccagcttcGcctgcgggagaggccaggca	7	7	13	14	2	1	2	0	1	1	1	3	3	1	2	4	3	2	2	4	3	0	2	rs143926476		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:228589861G>A	ENST00000284551.6	-	2	688	c.410C>T	c.(409-411)gCg>gTg	p.A137V	TRIM11_ENST00000366699.3_Splice_Site_p.A137V|TRIM11_ENST00000460651.1_5'Flank|TRIM11_ENST00000493030.2_Missense_Mutation_p.A12V	NM_145214.2	NP_660215.1	Q96F44	TRI11_HUMAN	tripartite motif containing 11	137					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)				CTCCAGCTTCGCCTGCGGGAG	0.597																																					p.A137V		Atlas-SNP	.											.	TRIM11	38	.	0			c.C410T						PASS	.	G	VAL/ALA	2,4404	4.2+/-10.8	0,2,2201	57	48	51		410	0.3	0.4	1	dbSNP_134	51	0,8600		0,0,4300	no	missense-near-splice	TRIM11	NM_145214.2	64	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	benign	137/469	228589861	2,13004	2203	4300	6503	SO:0001630	splice_region_variant	81559	exon2			AGCTTCGCCTGCG	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.409-1C>T	1.37:g.228589861G>A		143	0	0		132	31	0.234848	NM_145214	A6NKE2|B2RB82|B3KUS3|B4DX88|Q5VSU1|Q8NCA6|Q9C022	Missense_Mutation	SNP	ENST00000284551.6	37	CCDS31048.1	.	.	.	.	.	.	.	.	.	.	G	10.19	1.281017	0.23392	4.54E-4	0.0	ENSG00000154370	ENST00000284551;ENST00000366699	T;T	0.57436	0.4;0.4	4.56	0.332	0.15938	.	0.734180	0.11649	N	0.542981	T	0.16342	0.0393	N	0.00605	-1.335	0.09310	N	0.999998	B;B;B	0.17465	0.0;0.022;0.0	B;B;B	0.14578	0.001;0.011;0.0	T	0.18085	-1.0348	10	0.34782	T	0.22	.	1.8017	0.03073	0.3285:0.3588:0.2048:0.1079	.	137;137;137	Q96F44-3;Q96F44-2;Q96F44	.;.;TRI11_HUMAN	V	137	ENSP00000284551:A137V;ENSP00000355660:A137V	ENSP00000284551:A137V	A	-	2	0	TRIM11	226656484	0.001000	0.12720	0.445000	0.26908	0.054000	0.15201	-0.571000	0.05889	0.469000	0.27268	-0.252000	0.11476	GCG	G|1.000;A|0.000	0.000	weak		0.597	TRIM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095995.3	NM_145214	Missense_Mutation	A	228589861	G	A	228589861	5	1	27	1	0	0	0	0	0	0	1	0	16502	1101	38	1	1016	1	TRIM11	1	228589861	Splice_Site	SNP	G	TCGA-G8-6909-01A-11D-2210-10	125558	228589861	20660760	77	10528											
ARID4B	51742	hgsc.bcm.edu	37	chr1	235416122	235416122	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttctcatctccgtcatcaaAaactatgagagggggtaaaa	14	10	8	9	1	4	1	3	1	2	1	6	2	4	1	1	2	1	1	1	2	5	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:235416122A>G	ENST00000264183.3	-	6	774	c.277T>C	c.(277-279)Ttt>Ctt	p.F93L	ARID4B_ENST00000349213.3_Missense_Mutation_p.F93L|ARID4B_ENST00000366603.2_Missense_Mutation_p.F93L	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	93					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)			CCGTCATCAAAAACTATGAGA	0.373																																					p.F93L		Atlas-SNP	.											.	ARID4B	142	.	0			c.T277C						PASS	.						63	63	63					1																	235416122		2203	4300	6503	SO:0001583	missense	51742	exon6			CATCAAAAACTAT	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.277T>C	1.37:g.235416122A>G	ENSP00000264183:p.Phe93Leu	168	0	0		172	36	0.209302	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	37	CCDS31061.1	.	.	.	.	.	.	.	.	.	.	A	32	5.147074	0.94603	.	.	ENSG00000054267	ENST00000391856;ENST00000349213;ENST00000366603;ENST00000264183;ENST00000439834;ENST00000418304	T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11	5.73	5.73	0.89815	Tudor domain (1);	0.000000	0.85682	D	0.000000	T	0.80773	0.4687	M	0.83603	2.65	0.80722	D	1	D;D;D;D	0.71674	0.974;0.99;0.998;0.982	D;D;D;D	0.76071	0.953;0.979;0.987;0.952	D	0.83844	0.0259	10	0.87932	D	0	-14.2235	15.7063	0.77583	1.0:0.0:0.0:0.0	.	93;93;93;93	F8WB31;Q4LE39-3;Q4LE39-2;Q4LE39	.;.;.;ARI4B_HUMAN	L	93	ENSP00000264184:F93L;ENSP00000355562:F93L;ENSP00000264183:F93L;ENSP00000391497:F93L	ENSP00000264183:F93L	F	-	1	0	ARID4B	233482745	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	8.951000	0.93025	2.197000	0.70478	0.533000	0.62120	TTT	.	.	none		0.373	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374		G	235416122	A	G	235416122	3	3	27	1	0	0	0	0	1	0	0	0	920	14	1	3	3737	3	ARID4B	1	235416122	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	6826261	235416122	13834499	78	10529											
CHRM3	1131	hgsc.bcm.edu	37	chr1	240070855	240070855	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcccccgggaaccgtcaCtcatttcggcagctacaatg	8	8	10	15	3	2	0	2	0	0	0	3	1	2	1	3	2	4	3	3	2	3	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:240070855C>G	ENST00000255380.4	+	5	883	c.104C>G	c.(103-105)aCt>aGt	p.T35S		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	35					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)	GGAACCGTCACTCATTTCGGC	0.552																																					p.T35S		Atlas-SNP	.											.	CHRM3	118	.	0			c.C104G						PASS	.						77	77	77					1																	240070855		2203	4300	6503	SO:0001583	missense	1131	exon5			CCGTCACTCATTT	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.104C>G	1.37:g.240070855C>G	ENSP00000255380:p.Thr35Ser	138	0	0		123	32	0.260163	NM_000740	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Missense_Mutation	SNP	ENST00000255380.4	37	CCDS1616.1	.	.	.	.	.	.	.	.	.	.	C	3.466	-0.108946	0.06924	.	.	ENSG00000133019	ENST00000255380;ENST00000448020	T;T	0.58210	0.35;1.64	5.6	5.6	0.85130	.	0.663883	0.14104	N	0.341213	T	0.29882	0.0747	N	0.02011	-0.69	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.06338	-1.0832	10	0.19590	T	0.45	-4.5748	18.1624	0.89712	0.0:1.0:0.0:0.0	.	35	P20309	ACM3_HUMAN	S	35	ENSP00000255380:T35S;ENSP00000404764:T35S	ENSP00000255380:T35S	T	+	2	0	CHRM3	238137478	0.026000	0.19158	0.441000	0.26858	0.202000	0.24057	2.791000	0.47829	2.788000	0.95919	0.650000	0.86243	ACT	.	.	none		0.552	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740		G	240070855	C	G	240070855	3	3	27	1	0	0	0	0	1	0	0	0	3380	565	20	4	106	4	CHRM3	1	240070855	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	4654733	240070855	9179766	79	10530											
CNST	163882	hgsc.bcm.edu	37	chr1	246829147	246829147	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tttgcagacaacatggacttCtattacactaagttacttca	13	14	5	9	0	2	1	1	0	1	1	2	2	2	2	0	1	4	2	0	1	5	7	rs138848173		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:246829147C>G	ENST00000366513.4	+	11	2387	c.2118C>G	c.(2116-2118)ttC>ttG	p.F706L		NM_152609.2	NP_689822.2	Q6PJW8	CNST_HUMAN	consortin, connexin sorting protein	706					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						ACATGGACTTCTATTACACTA	0.463																																					p.F706L		Atlas-SNP	.											.	CNST	73	.	0			c.C2118G						PASS	.						143	126	132					1																	246829147		2203	4300	6503	SO:0001583	missense	163882	exon11			GGACTTCTATTAC	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.2118C>G	1.37:g.246829147C>G	ENSP00000355470:p.Phe706Leu	137	0	0		128	54	0.421875	NM_152609	Q5VSY9|Q5VTM7|Q8IYA9|Q8N3L5|Q8NB09|Q8TEI2|Q96MR5	Missense_Mutation	SNP	ENST00000366513.4	37	CCDS1628.1	.	.	.	.	.	.	.	.	.	.	C	18.29	3.592013	0.66219	.	.	ENSG00000162852	ENST00000366513	T	0.28255	1.62	5.61	3.73	0.42828	.	0.000000	0.85682	D	0.000000	T	0.49508	0.1561	M	0.77103	2.36	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.51084	-0.8750	10	0.66056	D	0.02	-20.4305	5.088	0.14693	0.1498:0.5976:0.0:0.2526	.	706	Q6PJW8	CNST_HUMAN	L	706	ENSP00000355470:F706L	ENSP00000355470:F706L	F	+	3	2	CNST	244895770	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	0.581000	0.23819	1.366000	0.46076	0.655000	0.94253	TTC	C|1.000;T|0.000	.	alt		0.463	CNST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096780.1	NM_152609		G	246829147	C	G	246829147	3	3	27	1	0	0	0	0	1	0	0	0	3636	912	32	4	2171	4	CNST	1	246829147	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	6758292	246829147	2421474	80	10531											
ZNF695	57116	hgsc.bcm.edu	37	chr1	247162688	247162688	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tctctgtgttcacgttccagGgctctttccttgcctccaga	4	15	8	14	1	3	1	1	0	2	1	7	1	6	1	4	1	1	3	4	1	0	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:247162688G>T	ENST00000339986.7	-	3	368	c.221C>A	c.(220-222)cCc>cAc	p.P74H	ZNF695_ENST00000498046.2_Intron|ZNF695_ENST00000487338.2_Missense_Mutation_p.P74H	NM_020394.4	NP_065127	Q8IW36	ZN695_HUMAN	zinc finger protein 695	74	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)			CACGTTCCAGGGCTCTTTCCT	0.468																																					p.P74H		Atlas-SNP	.											.	ZNF695	55	.	0			c.C221A						PASS	.						116	119	118					1																	247162688		2046	4248	6294	SO:0001583	missense	57116	exon3			TTCCAGGGCTCTT		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.221C>A	1.37:g.247162688G>T	ENSP00000341236:p.Pro74His	124	0	0		107	29	0.271028	NM_001204221	Q5T0N9|Q5T0P1|Q5T0P3|Q7Z2W8|Q7Z648	Missense_Mutation	SNP	ENST00000339986.7	37	CCDS44344.1	.	.	.	.	.	.	.	.	.	.	G	11.68	1.710105	0.30322	.	.	ENSG00000197472	ENST00000487338;ENST00000391780;ENST00000339986	T;T	0.09911	5.35;2.93	0.149	0.149	0.14863	Krueppel-associated box (2);	.	.	.	.	T	0.35624	0.0938	M	0.91612	3.225	0.09310	N	1	D;D;D	0.89917	0.992;1.0;1.0	P;D;D	0.91635	0.893;0.999;0.983	T	0.06862	-1.0803	8	0.87932	D	0	.	.	.	.	.	74;62;74	Q8IW36;F2Z2N8;Q8IW36-1	ZN695_HUMAN;.;.	H	74	ENSP00000429736:P74H;ENSP00000341236:P74H	ENSP00000428213:P62H	P	-	2	0	ZNF695	245229311	0.448000	0.25681	0.339000	0.25562	0.341000	0.28922	1.086000	0.30853	0.192000	0.20272	0.195000	0.17529	CCC	.	.	none		0.468	ZNF695-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097823.5	NM_020394		T	247162688	G	T	247162688	3	4	27	1	0	0	0	0	1	0	0	0	18113	1232	43	4	1334	4	ZNF695	1	247162688	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	333541	247162688	2087933	81	10532											
OR2M3	127062	hgsc.bcm.edu	37	chr1	248366632	248366632	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggccttcaactacctgtctgGcagcaagtccatttctatgg	8	12	9	12	0	3	0	1	0	2	0	4	0	4	0	3	3	3	2	3	3	4	4	rs139107079	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:248366632G>T	ENST00000456743.1	+	1	301	c.263G>T	c.(262-264)gGc>gTc	p.G88V		NM_001004689.1	NP_001004689.1	Q8NG83	OR2M3_HUMAN	olfactory receptor, family 2, subfamily M, member 3	88						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)			TACCTGTCTGGCAGCAAGTCC	0.502													G|||	2	0.000399361	0.0	0.0	5008	,	,		20388	0.0		0.002	False		,,,				2504	0.0				p.G88V		Atlas-SNP	.											.	OR2M3	116	.	0			c.G263T						PASS	.	G	VAL/GLY	2,4404	4.2+/-10.8	0,2,2201	267	265	265		263	0.3	0	1	dbSNP_134	265	2,8598	3.0+/-9.4	0,2,4298	no	missense	OR2M3	NM_001004689.1	109	0,4,6499	TT,TG,GG		0.0233,0.0454,0.0308	probably-damaging	88/313	248366632	4,13002	2203	4300	6503	SO:0001583	missense	127062	exon1			TGTCTGGCAGCAA		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.263G>T	1.37:g.248366632G>T	ENSP00000389625:p.Gly88Val	207	0	0		142	68	0.478873	NM_001004689	B9EH06|Q6IEY0	Missense_Mutation	SNP	ENST00000456743.1	37	CCDS31107.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	8.552	0.875710	0.17395	4.54E-4	2.33E-4	ENSG00000228198	ENST00000456743	T	0.02656	4.21	2.44	0.325	0.15903	GPCR, rhodopsin-like superfamily (1);	0.000000	0.32640	U	0.005825	T	0.05777	0.0151	M	0.81239	2.535	0.09310	N	1	P	0.49783	0.928	P	0.47705	0.555	T	0.21415	-1.0246	10	0.87932	D	0	.	2.9467	0.05848	0.2618:0.0:0.4954:0.2428	.	88	Q8NG83	OR2M3_HUMAN	V	88	ENSP00000389625:G88V	ENSP00000389625:G88V	G	+	2	0	OR2M3	246433255	0.000000	0.05858	0.006000	0.13384	0.038000	0.13279	-0.139000	0.10358	0.312000	0.23038	0.405000	0.27470	GGC	G|0.999;T|0.001	0.001	strong		0.502	OR2M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097355.1	NM_001004689		T	248366632	G	T	248366632	3	4	27	1	0	0	0	0	1	0	0	0	11020	1203	42	4	265	4	OR2M3	1	248366632	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1203944	248366632	883989	82	10533											
OR2T12	127064	hgsc.bcm.edu	37	chr1	248458187	248458187	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtggcaaaggccttcttgcGggcttctgtagagcgcatga	7	10	15	9	2	2	2	0	1	2	1	2	2	2	2	1	4	2	4	1	4	2	4	rs200352170		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr1:248458187G>A	ENST00000317996.1	-	1	693	c.694C>T	c.(694-696)Cgc>Tgc	p.R232C		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	232						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)			GCCTTCTTGCGGGCTTCTGTA	0.522																																					p.R232C		Atlas-SNP	.											.	OR2T12	113	.	0			c.C694T						PASS	.						100	94	96					1																	248458187		2203	4300	6503	SO:0001583	missense	127064	exon1			TCTTGCGGGCTTC	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.694C>T	1.37:g.248458187G>A	ENSP00000324583:p.Arg232Cys	402	0	0		363	97	0.267218	NM_001004692		Missense_Mutation	SNP	ENST00000317996.1	37	CCDS31110.1	.	.	.	.	.	.	.	.	.	.	g	10.81	1.454126	0.26161	.	.	ENSG00000177201	ENST00000317996	T	0.00337	8.05	1.55	0.316	0.15857	GPCR, rhodopsin-like superfamily (1);	0.870947	0.09313	U	0.819284	T	0.00384	0.0012	M	0.85945	2.785	0.09310	N	0.999998	B	0.24368	0.102	B	0.24269	0.052	T	0.31833	-0.9929	10	0.59425	D	0.04	.	7.1649	0.25685	0.0:0.0:0.5344:0.4655	.	232	Q8NG77	O2T12_HUMAN	C	232	ENSP00000324583:R232C	ENSP00000324583:R232C	R	-	1	0	OR2T12	246524810	0.000000	0.05858	0.169000	0.22859	0.670000	0.39368	-0.554000	0.06006	0.645000	0.30675	0.175000	0.17021	CGC	G|0.999;A|0.001	0.001	weak		0.522	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692		A	248458187	G	A	248458187	3	1	27	1	0	0	0	0	1	0	0	0	11028	1116	39	1	271	1	OR2T12	1	248458187	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	91555	248458187	792434	83	10534											
LPIN1	23175	hgsc.bcm.edu	37	chr2	11943082	11943082	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aggagcgcgcagctgccaagCcatcaaacgcaggccacctc	11	3	11	16	3	1	0	1	0	0	0	2	1	1	1	4	2	5	3	4	2	2	0	rs4669781	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:11943082C>T	ENST00000256720.2	+	14	1921	c.1828C>T	c.(1828-1830)Cca>Tca	p.P610S	LPIN1_ENST00000425416.2_Missense_Mutation_p.P616S|LPIN1_ENST00000396097.1_Missense_Mutation_p.P340S|LPIN1_ENST00000396099.1_Missense_Mutation_p.P652S|LPIN1_ENST00000449576.2_Missense_Mutation_p.P695S|LPIN1_ENST00000404113.2_Missense_Mutation_p.P111S	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	610			P -> S (in dbSNP:rs4669781). {ECO:0000269|PubMed:12111372}.		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)		AGCTGCCAAGCCATCAAACGC	0.537													C|||	140	0.0279553	0.0008	0.0476	5008	,	,		20971	0.0		0.0378	False		,,,				2504	0.0695				p.P695S		Atlas-SNP	.											LPIN1_ENST00000404113,NS,carcinoma,-2,3	LPIN1	99	3	0			c.C2083T						PASS	.	C	SER/PRO	53,4353	51.6+/-87.1	0,53,2150	182	160	167		1828	4.6	1	2	dbSNP_111	167	460,8140	137.5+/-194.4	15,430,3855	yes	missense	LPIN1	NM_145693.1	74	15,483,6005	TT,TC,CC		5.3488,1.2029,3.9443	benign	610/891	11943082	513,12493	2203	4300	6503	SO:0001583	missense	23175	exon16			GCCAAGCCATCAA	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.1828C>T	2.37:g.11943082C>T	ENSP00000256720:p.Pro610Ser	63	0	0		44	17	0.386364	NM_001261428	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Missense_Mutation	SNP	ENST00000256720.2	37	CCDS1682.1	49	0.022435897435897436	1	0.0020325203252032522	19	0.052486187845303865	0	0.0	29	0.03825857519788918	C	7.475	0.647393	0.14516	0.012029	0.053488	ENSG00000134324	ENST00000449576;ENST00000396099;ENST00000425416;ENST00000256720;ENST00000396097;ENST00000404113;ENST00000454151	T;T;T;T;T;T;T	0.80480	-1.38;-1.37;-1.36;-1.35;-1.19;-0.35;0.53	4.56	4.56	0.56223	.	0.053133	0.85682	D	0.000000	T	0.24736	0.0600	N	0.17312	0.475	0.36110	D	0.844742	B;B;B	0.31705	0.0;0.336;0.002	B;B;B	0.33454	0.003;0.164;0.008	T	0.57100	-0.7869	10	0.07175	T	0.84	-19.8574	13.5335	0.61635	0.1567:0.8433:0.0:0.0	rs4669781;rs4669781	111;695;610	B4DET9;F5GY24;Q14693	.;.;LPIN1_HUMAN	S	695;652;616;610;340;111;137	ENSP00000397908:P695S;ENSP00000379406:P652S;ENSP00000401522:P616S;ENSP00000256720:P610S;ENSP00000379404:P340S;ENSP00000386120:P111S;ENSP00000413714:P137S	ENSP00000256720:P610S	P	+	1	0	LPIN1	11860533	1.000000	0.71417	0.984000	0.44739	0.046000	0.14306	2.155000	0.42301	2.240000	0.73641	0.462000	0.41574	CCA	C|0.968;T|0.032	0.032	strong		0.537	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693		T	11943082	C	T	11943082	3	4	27	1	0	0	0	0	1	0	0	0	8927	739	26	2	1878	2	LPIN1	2	11943082	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10		11943082	231256291	84	10535											
NBAS	51594	hgsc.bcm.edu	37	chr2	15607853	15607853	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccttttcctttttattcttGgcaggctcttcatcaggtgg	4	19	8	10	0	4	0	2	0	2	0	6	0	6	0	2	4	0	2	2	4	1	8			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:15607853G>A	ENST00000281513.5	-	18	1978	c.1953C>T	c.(1951-1953)gcC>gcT	p.A651A	NBAS_ENST00000441750.1_Silent_p.A651A	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	651					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						TTTTATTCTTGGCAGGCTCTT	0.343																																					p.A651A		Atlas-SNP	.											.	NBAS	246	.	0			c.C1953T						PASS	.						106	99	101					2																	15607853		2202	4299	6501	SO:0001819	synonymous_variant	51594	exon18			ATTCTTGGCAGGC	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.1953C>T	2.37:g.15607853G>A		211	1	0.00473934		246	136	0.552846	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Silent	SNP	ENST00000281513.5	37	CCDS1685.1																																																																																			.	.	none		0.343	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909		A	15607853	G	A	15607853	2	1	27	1	0	0	0	0	0	0	0	1	10195	1335	47	2		2	NBAS	2	15607853	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	3664771	15607853	227591520	85	10536											
RAD51AP2	729475	hgsc.bcm.edu	37	chr2	17697635	17697635	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggaattttttcatatgttTcaaaaatcggaaaacctgta	14	14	8	5	1	2	0	2	0	0	0	3	2	2	2	1	3	1	2	1	3	7	6	rs181531922	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:17697635T>C	ENST00000399080.2	-	1	2071	c.2048A>G	c.(2047-2049)gAa>gGa	p.E683G		NM_001099218.2	NP_001092688.1	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	683										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)					TTCATATGTTTCAAAAATCGG	0.289													T|||	13	0.00259585	0.0008	0.0043	5008	,	,		17559	0.0		0.0089	False		,,,				2504	0.0				p.E683G		Atlas-SNP	.											.	RAD51AP2	134	.	0			c.A2048G						PASS	.	T	GLY/GLU	10,3590		0,10,1790	38	36	37		2048	4.6	0	2		37	115,7961		0,115,3923	yes	missense	RAD51AP2	NM_001099218.2	98	0,125,5713	CC,CT,TT		1.424,0.2778,1.0706	possibly-damaging	683/1160	17697635	125,11551	1800	4038	5838	SO:0001583	missense	729475	exon1			TATGTTTCAAAAA	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.2048A>G	2.37:g.17697635T>C	ENSP00000382030:p.Glu683Gly	113	0	0		84	50	0.595238	NM_001099218		Missense_Mutation	SNP	ENST00000399080.2	37	CCDS42656.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	T	5.534	0.283387	0.10458	0.002778	0.01424	ENSG00000214842	ENST00000399080	T	0.25250	1.81	4.62	4.62	0.57501	.	.	.	.	.	T	0.15089	0.0364	N	0.14661	0.345	0.09310	N	1	P	0.44429	0.835	P	0.47645	0.553	T	0.05801	-1.0863	9	0.66056	D	0.02	-0.2662	8.6213	0.33861	0.0:0.0886:0.0:0.9114	.	683	Q09MP3	R51A2_HUMAN	G	683	ENSP00000382030:E683G	ENSP00000382030:E683G	E	-	2	0	RAD51AP2	17561116	0.532000	0.26346	0.003000	0.11579	0.009000	0.06853	2.814000	0.48010	2.012000	0.59069	0.482000	0.46254	GAA	T|0.994;C|0.006	0.006	strong		0.289	RAD51AP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323801.3	NM_001099218		C	17697635	T	C	17697635	3	2	27	1	0	0	0	0	1	0	0	0	13002	1783	62	3	1443	3	RAD51AP2	2	17697635	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	2089782	17697635	225501738	86	10537											
SLC30A3	7781	hgsc.bcm.edu	37	chr2	27481661	27481661	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagacaaagcaaacggcacaGgcagcatatagctgcctccg	15	4	10	12	2	0	1	0	0	0	1	1	1	1	1	2	2	5	5	2	2	5	2	rs41288821	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:27481661G>A	ENST00000233535.4	-	2	589	c.237C>T	c.(235-237)gcC>gcT	p.A79A	SLC30A3_ENST00000447008.2_Silent_p.A74A	NM_003459.4	NP_003450.2	Q99726	ZNT3_HUMAN	solute carrier family 30 (zinc transporter), member 3	79					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)					AAACGGCACAGGCAGCATATA	0.602													G|||	13	0.00259585	0.0008	0.0072	5008	,	,		18488	0.0		0.006	False		,,,				2504	0.001				p.A79A		Atlas-SNP	.											.	SLC30A3	39	.	0			c.C237T						PASS	.	G		10,4396	11.4+/-27.6	0,10,2193	58	62	61		237	4.4	1	2	dbSNP_127	61	84,8516	47.2+/-106.3	0,84,4216	no	coding-synonymous	SLC30A3	NM_003459.4		0,94,6409	AA,AG,GG		0.9767,0.227,0.7227		79/389	27481661	94,12912	2203	4300	6503	SO:0001819	synonymous_variant	7781	exon2			GGCACAGGCAGCA	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.237C>T	2.37:g.27481661G>A		84	0	0		91	62	0.681319	NM_003459	Q8TC03	Silent	SNP	ENST00000233535.4	37	CCDS1743.1																																																																																			G|0.993;A|0.007	0.007	strong		0.602	SLC30A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250189.2			A	27481661	G	A	27481661	2	1	27	1	0	0	0	0	0	0	0	1	14571	987	35	2		2	SLC30A3	2	27481661	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	9784026	27481661	215717712	87	10538											
GCKR	2646	hgsc.bcm.edu	37	chr2	27741665	27741665	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccttttcagaagttccagcGtgagctaagcaccaaatggg	11	9	10	11	1	1	2	1	1	0	1	2	2	2	2	3	1	3	3	3	1	3	4	rs141361209	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:27741665G>A	ENST00000264717.2	+	17	1496	c.1433G>A	c.(1432-1434)cGt>cAt	p.R478H	GCKR_ENST00000424318.2_Missense_Mutation_p.R288H	NM_001486.3	NP_001477.2	Q14397	GCKR_HUMAN	glucokinase (hexokinase 4) regulator	478	SIS 2. {ECO:0000255|PROSITE- ProRule:PRU00797}.				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)	p.R478L(1)		breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(2)	29	Acute lymphoblastic leukemia(172;0.155)					AAGTTCCAGCGTGAGCTAAGC	0.473													G|||	4	0.000798722	0.0	0.0029	5008	,	,		19790	0.0		0.002	False		,,,				2504	0.0				p.R478H		Atlas-SNP	.											GCKR,NS,carcinoma,0,1	GCKR	73	1	1	Substitution - Missense(1)	lung(1)	c.G1433A						PASS	.	G	HIS/ARG	1,4405		0,1,2202	105	101	103		1433	1.2	1	2	dbSNP_134	103	3,8597	3.7+/-12.6	0,3,4297	yes	missense	GCKR	NM_001486.3	29	0,4,6499	AA,AG,GG		0.0349,0.0227,0.0308	benign	478/626	27741665	4,13002	2203	4300	6503	SO:0001583	missense	2646	exon17			TCCAGCGTGAGCT	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.1433G>A	2.37:g.27741665G>A	ENSP00000264717:p.Arg478His	107	0	0		123	46	0.373984	NM_001486	A1L4C2|B4DPQ2|Q53RY6|Q99522	Missense_Mutation	SNP	ENST00000264717.2	37	CCDS1757.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	7.777	0.708592	0.15239	2.27E-4	3.49E-4	ENSG00000084734	ENST00000264717;ENST00000424318	D;D	0.83419	-1.72;-1.72	3.76	1.18	0.20946	Sugar isomerase (SIS) (1);	0.265072	0.33075	N	0.005308	T	0.58793	0.2147	N	0.25144	0.715	0.28844	N	0.896431	B;B;B	0.10296	0.003;0.001;0.001	B;B;B	0.06405	0.002;0.0;0.0	T	0.47045	-0.9147	10	0.11182	T	0.66	0.0223	9.1221	0.36793	0.1699:0.0:0.8301:0.0	.	288;476;478	F5H1P6;A8K731;Q14397	.;.;GCKR_HUMAN	H	478;288	ENSP00000264717:R478H;ENSP00000409109:R288H	ENSP00000264717:R478H	R	+	2	0	GCKR	27595169	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.557000	0.36299	0.269000	0.21961	0.561000	0.74099	CGT	G|0.999;A|0.001	0.001	strong		0.473	GCKR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250214.1	NM_001486		A	27741665	G	A	27741665	3	1	27	1	0	0	0	0	1	0	0	0	6302	1145	40	1	1499	1	GCKR	2	27741665	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	260004	27741665	215457708	88	10539											
C2orf16	84226	hgsc.bcm.edu	37	chr2	27799712	27799712	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagcaaactataaaatctgtGgaattagcaccagggtcact	15	9	8	9	0	2	0	1	0	1	0	2	1	2	1	1	2	3	2	1	2	6	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:27799712G>A	ENST00000408964.2	+	1	324	c.273G>A	c.(271-273)gtG>gtA	p.V91V		NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	91						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)					TAAAATCTGTGGAATTAGCAC	0.393																																					p.V91V		Atlas-SNP	.											.	C2orf16	357	.	0			c.G273A						PASS	.						65	60	61					2																	27799712		1873	4107	5980	SO:0001819	synonymous_variant	84226	exon1			ATCTGTGGAATTA	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.273G>A	2.37:g.27799712G>A		147	0	0		185	89	0.481081	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Silent	SNP	ENST00000408964.2	37	CCDS42666.1																																																																																			.	.	none		0.393	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		A	27799712	G	A	27799712	2	1	27	1	0	0	0	0	0	0	0	1	2159	1335	47	2		2	C2orf16	2	27799712	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	58047	27799712	215399661	89	10540											
C2orf16	84226	hgsc.bcm.edu	37	chr2	27804547	27804547	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccctctcagaggagccatcGtggtccctctgagagaagac	9	8	11	13	1	2	4	1	1	2	3	6	6	4	5	3	2	1	0	3	2	1	0	rs201164610	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:27804547G>A	ENST00000408964.2	+	1	5159	c.5108G>A	c.(5107-5109)cGt>cAt	p.R1703H	ZNF512_ENST00000355467.4_5'Flank|AC074091.1_ENST00000408604.1_RNA|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000556601.1_5'Flank|ZNF512_ENST00000413371.2_5'Flank|ZNF512_ENST00000379717.1_5'Flank|ZNF512_ENST00000416005.2_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1703	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)					AGGAGCCATCGTGGTCCCTCT	0.587													g|||	16	0.00319489	0.0	0.0	5008	,	,		20437	0.0		0.0	False		,,,				2504	0.0164				p.R1703H		Atlas-SNP	.											.	C2orf16	357	.	0			c.G5108A						PASS	.						156	159	158					2																	27804547		1929	4134	6063	SO:0001583	missense	84226	exon1			GCCATCGTGGTCC	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.5108G>A	2.37:g.27804547G>A	ENSP00000386190:p.Arg1703His	65	0	0		72	24	0.333333	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	g	8.649	0.897869	0.17686	.	.	ENSG00000221843	ENST00000408964	T	0.05447	3.44	3.34	-4.16	0.03869	.	.	.	.	.	T	0.02533	0.0077	N	0.19112	0.55	0.09310	N	1	B	0.32800	0.385	B	0.21708	0.036	T	0.39921	-0.9590	9	0.33940	T	0.23	.	0.1461	0.00088	0.2733:0.2564:0.2106:0.2596	.	1703	Q68DN1	CB016_HUMAN	H	1703	ENSP00000386190:R1703H	ENSP00000386190:R1703H	R	+	2	0	C2orf16	27658051	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.454000	0.01004	-1.009000	0.03400	-1.402000	0.01139	CGT	G|0.999;A|0.001	0.001	weak		0.587	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266		A	27804547	G	A	27804547	3	1	27	1	0	0	0	0	1	0	0	0	2159	1145	40	1	5110	1	C2orf16	2	27804547	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	4835	27804547	215394826	90	10541											
XDH	7498	hgsc.bcm.edu	37	chr2	31588395	31588395	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacggtccagcatgcatcgCacagggcggccggtcctggg	6	6	15	14	4	1	0	1	0	0	0	4	0	3	0	3	5	2	3	3	5	0	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:31588395C>T	ENST00000379416.3	-	23	2520	c.2472G>A	c.(2470-2472)gtG>gtA	p.V824V		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	824					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)	GCATGCATCGCACAGGGCGGC	0.567																																					p.V824V	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.G2472A						PASS	.						115	100	105					2																	31588395		2203	4300	6503	SO:0001819	synonymous_variant	7498	exon23			GCATCGCACAGGG	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.2472G>A	2.37:g.31588395C>T		140	0	0		135	45	0.333333	NM_000379	Q16681|Q16712|Q4PJ16	Silent	SNP	ENST00000379416.3	37	CCDS1775.1																																																																																			.	.	none		0.567	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379		T	31588395	C	T	31588395	2	4	27	1	0	0	0	0	0	0	0	1	17441	697	25	2		2	XDH	2	31588395	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3783848	31588395	211610978	91	10542											
SPAST	6683	hgsc.bcm.edu	37	chr2	32289034	32289034	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcccctccgcccgagtcgcCgcataagcggaacctgtact	7	6	11	17	5	0	0	0	0	0	0	2	2	1	1	6	2	3	2	6	2	3	2	rs121908517		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:32289034C>A	ENST00000315285.3	+	1	259	c.134C>A	c.(133-135)cCg>cAg	p.P45Q	SPAST_ENST00000345662.1_Missense_Mutation_p.P45Q	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)					cccgAGTCGCCGCATAAGCGG	0.716																																					p.P45Q		Atlas-SNP	.											SPAST,NS,carcinoma,-1,2	SPAST	61	2	0			c.C134A	GRCh37	CM045939	SPAST	M	rs121908517	PASS	.	C	,GLN/PRO,GLN/PRO	0,4402		0,0,2201	24	25	25	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,134,134	3.2	1	2	dbSNP_133	25	3,8597	2.2+/-6.3	0,3,4297	yes	intron,missense,missense	SPAST,HP11026	XM_003403507.1,NM_199436.1,NM_014946.3	,76,76	0,3,6498	AA,AC,CC		0.0349,0.0,0.0231	,benign,benign	,45/585,45/617	32289034	3,12999	2201	4300	6501	SO:0001583	missense	6683	exon1			AGTCGCCGCATAA	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.134C>A	2.37:g.32289034C>A	ENSP00000320885:p.Pro45Gln	35	0	0		61	25	0.409836	NM_199436		Missense_Mutation	SNP	ENST00000315285.3	37	CCDS1778.1	.	.	.	.	.	.	.	.	.	.	c	10.58	1.390692	0.25118	0.0	3.49E-4	ENSG00000021574	ENST00000345662;ENST00000315285	D;D	0.93426	-3.22;-3.15	4.15	3.25	0.37280	.	0.196102	0.35235	N	0.003354	D	0.84279	0.5437	N	0.14661	0.345	0.35379	A	0.789784	B;B	0.22276	0.067;0.067	B;B	0.14578	0.011;0.011	T	0.81831	-0.0752	9	0.59425	D	0.04	-20.6852	6.4706	0.22005	0.1824:0.722:0.0:0.0957	.	45;45	E5KRP6;Q9UBP0	.;SPAST_HUMAN	Q	45	ENSP00000340817:P45Q;ENSP00000320885:P45Q	ENSP00000320885:P45Q	P	+	2	0	SPAST	32142538	1.000000	0.71417	0.998000	0.56505	0.046000	0.14306	1.604000	0.36804	0.846000	0.35142	0.637000	0.83480	CCG	C|1.000;A|0.000	0.000	weak		0.716	SPAST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250253.1	NM_199436		A	32289034	C	A	32289034	3	1	27	1	0	0	0	0	1	0	0	0	15012	652	23	4	136	4	SPAST	2	32289034	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	700639	32289034	210910339	92	10543											
LTBP1	4052	hgsc.bcm.edu	37	chr2	33623567	33623567	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aagccaaactactgcactccGttgaataccgccttgaattt	12	11	6	12	2	0	2	0	2	0	0	1	2	1	2	4	0	5	2	4	0	6	5	rs138835287		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:33623567G>A	ENST00000404816.2	+	34	5474	c.5121G>A	c.(5119-5121)ccG>ccA	p.P1707P	LTBP1_ENST00000390003.4_Silent_p.P1382P|LTBP1_ENST00000402934.1_Silent_p.P1326P|LTBP1_ENST00000354476.3_Silent_p.P1708P|LTBP1_ENST00000407925.1_Silent_p.P1381P|LTBP1_ENST00000418533.2_Silent_p.P1339P|LTBP1_ENST00000272273.5_Silent_p.P605P|LTBP1_ENST00000404525.1_Silent_p.P1328P			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1707					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)	p.P1708P(1)		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)				ACTGCACTCCGTTGAATACCG	0.458													G|||	1	0.000199681	0.0	0.0014	5008	,	,		21600	0.0		0.0	False		,,,				2504	0.0				p.P1707P		Atlas-SNP	.											LTBP1_ENST00000407925,NS,carcinoma,0,3	LTBP1	317	3	1	Substitution - coding silent(1)	lung(1)	c.G5121A						PASS	.	G	,,,,	0,4406		0,0,2203	123	99	107		4143,4017,3984,3858,5121	-9.1	0	2	dbSNP_134	107	21,8579	15.3+/-51.7	0,21,4279	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LTBP1	NM_000627.3,NM_001166264.1,NM_001166265.1,NM_001166266.1,NM_206943.2	,,,,	0,21,6482	AA,AG,GG		0.2442,0.0,0.1615	,,,,	1381/1396,1339/1354,1328/1343,1286/1301,1707/1722	33623567	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	4052	exon34			CACTCCGTTGAAT		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.5121G>A	2.37:g.33623567G>A		138	0	0		107	55	0.514019	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Silent	SNP	ENST00000404816.2	37	CCDS33177.2																																																																																			G|0.999;A|0.001	0.001	strong		0.458	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		A	33623567	G	A	33623567	2	1	27	1	0	0	0	0	0	0	0	1	9082	1132	40	1		1	LTBP1	2	33623567	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1334533	33623567	209575806	93	10544											
VIT	5212	hgsc.bcm.edu	37	chr2	36970364	36970364	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatggcactgacgtgtatgcAtcctactccagtgtgtgtgg	7	13	12	9	1	0	1	0	1	0	0	2	1	2	1	2	2	2	3	2	2	3	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:36970364A>G	ENST00000389975.3	+	4	542	c.240A>G	c.(238-240)gcA>gcG	p.A80A	VIT_ENST00000379241.3_Silent_p.A80A|VIT_ENST00000379242.3_Silent_p.A80A|VIT_ENST00000457137.2_Silent_p.A80A|VIT_ENST00000404084.1_Silent_p.A58A|VIT_ENST00000401530.1_Silent_p.A80A|VIT_ENST00000497382.1_5'UTR	NM_001177969.1|NM_001177970.1	NP_001171440.1|NP_001171441.1	Q6UXI7	VITRN_HUMAN	vitrin	80	LCCL. {ECO:0000255|PROSITE- ProRule:PRU00123}.			A -> T (in Ref. 1; AAL18263). {ECO:0000305}.	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)				ACGTGTATGCATCCTACTCCA	0.493																																					p.A80A		Atlas-SNP	.											.	VIT	138	.	0			c.A240G						PASS	.						142	117	125					2																	36970364		2203	4300	6503	SO:0001819	synonymous_variant	5212	exon4			GTATGCATCCTAC	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.240A>G	2.37:g.36970364A>G		129	0	0		98	45	0.459184	NM_001177969	A1A526|A6NKI9|A8K7Y4|E9PF47|Q6P7T3|Q96DM8|Q96DT1|Q9UDN0	Silent	SNP	ENST00000389975.3	37	CCDS54347.1																																																																																			.	.	none		0.493	VIT-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding				G	36970364	A	G	36970364	2	3	27	1	0	0	0	0	0	0	0	1	17186	204	8	3		3	VIT	2	36970364	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	3346797	36970364	206229009	94	10545											
CDKL4	344387	hgsc.bcm.edu	37	chr2	39440541	39440541	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cattagaaaatgttacttacGttatgtatatgacagaaatt	16	15	6	4	1	0	3	0	1	0	2	0	3	0	3	0	0	2	3	0	0	9	7	rs375514414		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:39440541G>A	ENST00000395035.3	-	3	362	c.363C>T	c.(361-363)aaC>aaT	p.N121N	CDKL4_ENST00000378803.1_Splice_Site_p.N121N			Q5MAI5	CDKL4_HUMAN	cyclin-dependent kinase-like 4	121	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(1)|large_intestine(2)|liver(1)|lung(7)|ovary(1)	12		all_hematologic(82;0.248)				TGTTACTTACGTTATGTATAT	0.328													G|||	1	0.000199681	0.0	0.0	5008	,	,		18274	0.001		0.0	False		,,,				2504	0.0				p.N121N		Atlas-SNP	.											CDKL4,NS,carcinoma,0,1	CDKL4	30	1	0			c.C363T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	71	78	75		363	-4.6	0.9	2		75	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous-near-splice	CDKL4	NM_001009565.1		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		121/316	39440541	2,13004	2203	4300	6503	SO:0001630	splice_region_variant	344387	exon3			ACTTACGTTATGT		CCDS33184.1	2p22.3	2011-11-04			ENSG00000205111	ENSG00000205111		"Cyclin-dependent kinases"	19287	protein-coding gene	gene with protein product							Standard	NM_001009565		Approved		uc002rrm.3	Q5MAI5	OTTHUMG00000133574	ENST00000395035.3:c.363+1C>T	2.37:g.39440541G>A		173	0	0		328	67	0.204268	NM_001009565	Q2NME9	Silent	SNP	ENST00000395035.3	37																																																																																				.	.	weak		0.328	CDKL4-002	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000331655.1	XM_293029	Silent	A	39440541	G	A	39440541	5	1	27	1	0	0	0	0	0	0	1	0	3158	1159	40	1	608	1	CDKL4	2	39440541	Splice_Site	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2470177	39440541	203758832	95	10546											
SLC8A1	6546	hgsc.bcm.edu	37	chr2	40656756	40656756	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccaggagatatgacagacAaaataatgtaaagccaggtg	18	6	10	7	0	0	3	0	1	0	2	0	4	0	3	2	2	1	1	2	2	6	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:40656756A>T	ENST00000403092.1	-	2	698	c.665T>A	c.(664-666)tTg>tAg	p.L222*	SLC8A1_ENST00000406785.2_Nonsense_Mutation_p.L222*|SLC8A1_ENST00000408028.2_Nonsense_Mutation_p.L222*|SLC8A1_ENST00000402441.1_Nonsense_Mutation_p.L222*|SLC8A1_ENST00000405901.3_Nonsense_Mutation_p.L222*|SLC8A1_ENST00000332839.4_Nonsense_Mutation_p.L222*|SLC8A1_ENST00000406391.2_Nonsense_Mutation_p.L222*|SLC8A1_ENST00000542756.1_Nonsense_Mutation_p.L222*|SLC8A1_ENST00000542024.1_Nonsense_Mutation_p.L222*|SLC8A1_ENST00000405269.1_Nonsense_Mutation_p.L222*			P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 1	222					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)	TATGACAGACAAAATAATGTA	0.473																																					p.L222X		Atlas-SNP	.											.	SLC8A1	221	.	0			c.T665A						PASS	.						52	56	55					2																	40656756		2203	4300	6503	SO:0001587	stop_gained	6546	exon1			ACAGACAAAATAA		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.665T>A	2.37:g.40656756A>T	ENSP00000384763:p.Leu222*	54	0	0		100	15	0.15	NM_001252624	A8K6N1|D6W595|O95849|Q4QQG6|Q587I6|Q59GN4|Q9UBL8|Q9UD55|Q9UDN1|Q9UDN2|Q9UKX6	Nonsense_Mutation	SNP	ENST00000403092.1	37	CCDS1806.1	.	.	.	.	.	.	.	.	.	.	A	25.4	4.631169	0.87660	.	.	ENSG00000183023	ENST00000406785;ENST00000378715;ENST00000542756;ENST00000403092;ENST00000405901;ENST00000402441;ENST00000405269;ENST00000332839;ENST00000408028;ENST00000535962;ENST00000406391;ENST00000542024	.	.	.	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.4743	0.61299	1.0:0.0:0.0:0.0	.	.	.	.	X	222	.	ENSP00000332931:L222X	L	-	2	0	SLC8A1	40510260	1.000000	0.71417	0.954000	0.39281	0.928000	0.56348	9.151000	0.94674	2.076000	0.62316	0.460000	0.39030	TTG	.	.	none		0.473	SLC8A1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326065.1	NM_021097		T	40656756	A	T	40656756	4	4	27	1	0	0	0	0	0	1	0	0	14721	131	5	5	2404	5	SLC8A1	2	40656756	Nonsense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	1216215	40656756	202542617	96	10547											
LRPPRC	10128	hgsc.bcm.edu	37	chr2	44201315	44201315	+	Missense_Mutation	SNP	A	A	T																															catagtcacacagtgttgtaAaaagaaactgccaaagacac																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:44201315A>T	ENST00000260665.7	-	9	1186	c.1129T>A	c.(1129-1131)Tta>Ata	p.L377I	LRPPRC_ENST00000409659.1_Missense_Mutation_p.L377I|LRPPRC_ENST00000409946.1_Missense_Mutation_p.L377I	NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	377					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)				CAGTGTTGTAAAAAGAAACTG	0.358																																					p.L377I		Atlas-SNP	.											.	LRPPRC	105	.	0			c.T1129A						PASS	.						98	96	97					2																	44201315		2203	4300	6503	SO:0001583	missense	10128	exon9			GTTGTAAAAAGAA	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.1129T>A	2.37:g.44201315A>T	ENSP00000260665:p.Leu377Ile	342	0	0		550	65	0.118182	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Missense_Mutation	SNP	ENST00000260665.7	37	CCDS33189.1	.	.	.	.	.	.	.	.	.	.	A	15.67	2.901542	0.52227	.	.	ENSG00000138095	ENST00000465633;ENST00000260665;ENST00000409946;ENST00000409659;ENST00000447246	T;T;T;T	0.70399	0.32;0.26;0.29;-0.48	6.08	1.21	0.21127	.	0.000000	0.64402	D	0.000004	T	0.69753	0.3146	L	0.46157	1.445	0.47621	D	0.999471	P;B;D	0.67145	0.955;0.097;0.996	P;B;P	0.59703	0.753;0.054;0.862	T	0.64659	-0.6355	10	0.40728	T	0.16	-13.0937	4.796	0.13272	0.5914:0.0:0.2803:0.1283	.	277;351;377	F5H4J6;C9JCA9;P42704	.;.;LPPRC_HUMAN	I	277;377;377;377;351	ENSP00000260665:L377I;ENSP00000386234:L377I;ENSP00000386562:L377I;ENSP00000403637:L351I	ENSP00000260665:L377I	L	-	1	2	LRPPRC	44054819	1.000000	0.71417	0.456000	0.27044	0.944000	0.59088	3.419000	0.52728	0.194000	0.20326	0.482000	0.46254	TTA	.	.	none		0.358	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259		T	44201315	A	T	44201315	3	4	27	1	0	0	0	0	1	0	0	0	8974	11	1	5	3175	5	LRPPRC	2	44201315	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	3544559	44201315	198998058	97	10548	134	2									
LRPPRC	10128	hgsc.bcm.edu	37	chr2	44201317	44201317	+	Missense_Mutation	SNP	A	A	C																															tagtcacacagtgttgtaaaAagaaactgccaaagacactt																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:44201317A>C	ENST00000260665.7	-	9	1184	c.1127T>G	c.(1126-1128)tTt>tGt	p.F376C	LRPPRC_ENST00000409659.1_Missense_Mutation_p.F376C|LRPPRC_ENST00000409946.1_Missense_Mutation_p.F376C	NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	376					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)				GTGTTGTAAAAAGAAACTGCC	0.358																																					p.F376C		Atlas-SNP	.											.	LRPPRC	105	.	0			c.T1127G						PASS	.						98	97	97					2																	44201317		2203	4300	6503	SO:0001583	missense	10128	exon9			TGTAAAAAGAAAC	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.1127T>G	2.37:g.44201317A>C	ENSP00000260665:p.Phe376Cys	347	0	0		555	64	0.115315	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Missense_Mutation	SNP	ENST00000260665.7	37	CCDS33189.1	.	.	.	.	.	.	.	.	.	.	A	23.3	4.396960	0.83120	.	.	ENSG00000138095	ENST00000465633;ENST00000260665;ENST00000409946;ENST00000409659;ENST00000447246	T;T;T;T	0.70516	0.2;0.21;0.22;-0.49	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	D	0.83704	0.5312	M	0.82630	2.6	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.987;0.998	D	0.84275	0.0491	10	0.42905	T	0.14	-11.3834	11.417	0.49958	0.8652:0.0:0.0:0.1348	.	276;350;376	F5H4J6;C9JCA9;P42704	.;.;LPPRC_HUMAN	C	276;376;376;376;350	ENSP00000260665:F376C;ENSP00000386234:F376C;ENSP00000386562:F376C;ENSP00000403637:F350C	ENSP00000260665:F376C	F	-	2	0	LRPPRC	44054821	1.000000	0.71417	0.969000	0.41365	0.952000	0.60782	7.100000	0.76989	2.333000	0.79357	0.482000	0.46254	TTT	.	.	none		0.358	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259		C	44201317	A	C	44201317	3	2	27	1	0	0	0	0	1	0	0	0	8974	14	1	5	3177	5	LRPPRC	2	44201317	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	2	44201317	198998056	98	10549	134	2									
C2orf61	285051	hgsc.bcm.edu	37	chr2	47357129	47357129	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaactgttgagcgaaatacaCagctcctatatttcaaaata	16	11	6	8	1	1	1	1	1	0	0	2	3	2	1	1	0	4	2	1	0	8	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:47357129C>T	ENST00000445927.2	-	5	596	c.470G>A	c.(469-471)tGt>tAt	p.C157Y	C2orf61_ENST00000294947.2_Missense_Mutation_p.C157Y|RP11-761B3.1_ENST00000422269.1_3'UTR	NM_001163561.1	NP_001157033.1	Q8N801	CB061_HUMAN	chromosome 2 open reading frame 61	157										endometrium(1)|kidney(1)|lung(2)	4		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)	Lung(47;0.0792)|LUSC - Lung squamous cell carcinoma(58;0.114)			GCGAAATACACAGCTCCTATA	0.259																																					p.C157Y		Atlas-SNP	.											.	C2orf61	31	.	0			c.G470A						PASS	.						77	81	80					2																	47357129		2203	4300	6503	SO:0001583	missense	285051	exon5			AATACACAGCTCC	AK097491	CCDS1831.1, CCDS54356.1	2p21	2008-02-05			ENSG00000239605	ENSG00000239605			26850	protein-coding gene	gene with protein product							Standard	NM_173649		Approved	FLJ40172	uc010yog.2	Q8N801	OTTHUMG00000128851	ENST00000445927.2:c.470G>A	2.37:g.47357129C>T	ENSP00000408527:p.Cys157Tyr	93	0	0		186	27	0.145161	NM_173649	H7C2Z2	Missense_Mutation	SNP	ENST00000445927.2	37	CCDS54356.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.371|7.371	0.626725|0.626725	0.14257|0.14257	.|.	.|.	ENSG00000239605|ENSG00000239605	ENST00000445927;ENST00000294947|ENST00000449846	T;T|.	0.29397|.	1.57;1.6|.	5.07|5.07	0.0874|0.0874	0.14450|0.14450	.|.	0.377447|.	0.22845|.	N|.	0.054930|.	T|T	0.16171|0.16171	0.0389|0.0389	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	0.999995|0.999995	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.21552|0.21552	-1.0242|-1.0242	10|5	0.02654|.	T|.	1|.	-5.7694|-5.7694	0.8202|0.8202	0.01110|0.01110	0.4569:0.1806:0.1051:0.2573|0.4569:0.1806:0.1051:0.2573	.|.	157|.	Q8N801|.	CB061_HUMAN|.	Y|M	157|37	ENSP00000408527:C157Y;ENSP00000294947:C157Y|.	ENSP00000294947:C157Y|.	C|V	-|-	2|1	0|0	C2orf61|C2orf61	47210633|47210633	0.159000|0.159000	0.22864|0.22864	0.705000|0.705000	0.30386|0.30386	0.479000|0.479000	0.33129|0.33129	0.539000|0.539000	0.23175|0.23175	0.794000|0.794000	0.33899|0.33899	-0.521000|-0.521000	0.04368|0.04368	TGT|GTG	.	.	none		0.259	C2orf61-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173649		T	47357129	C	T	47357129	3	4	27	1	0	0	0	0	1	0	0	0	2182	478	17	2	303	2	C2orf61	2	47357129	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3155812	47357129	195842244	99	10550											
KCNK12	56660	hgsc.bcm.edu	37	chr2	47748558	47748558	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gtgctggctgctcaccaggtCcccgaagccgatggtgctga	6	8	14	13	2	1	1	1	1	0	0	2	3	2	1	4	3	4	4	4	3	1	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:47748558C>T	ENST00000327876.4	-	2	1388	c.781G>A	c.(781-783)Gac>Aac	p.D261N	MSH2_ENST00000461394.1_Intron	NM_022055.1	NP_071338.1	Q9HB15	KCNKC_HUMAN	potassium channel, subfamily K, member 12	261						integral component of membrane (GO:0016021)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.0?(2)|p.?(2)		NS(1)|endometrium(1)|lung(3)|ovary(1)	6		all_hematologic(82;0.0495)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CTCACCAGGTCCCCGAAGCCG	0.632																																					p.D261N		Atlas-SNP	.											.	KCNK12	11	.	4	Whole gene deletion(2)|Unknown(2)	haematopoietic_and_lymphoid_tissue(3)|prostate(1)	c.G781A						PASS	.						41	39	40					2																	47748558		2203	4299	6502	SO:0001583	missense	56660	exon2			CCAGGTCCCCGAA	AF287302	CCDS1835.1	2p16.3	2012-03-07			ENSG00000184261	ENSG00000184261		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6274	protein-coding gene	gene with protein product		607366				11060316	Standard	NM_022055		Approved	THIK-2, THIK2, K2p12.1	uc002rwb.3	Q9HB15	OTTHUMG00000129131	ENST00000327876.4:c.781G>A	2.37:g.47748558C>T	ENSP00000327611:p.Asp261Asn	74	0	0		170	43	0.252941	NM_022055		Missense_Mutation	SNP	ENST00000327876.4	37	CCDS1835.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.172527	0.78452	.	.	ENSG00000184261	ENST00000327876	T	0.41758	0.99	4.1	3.22	0.36961	Ion transport 2 (1);	0.000000	0.85682	D	0.000000	T	0.72391	0.3454	H	0.95004	3.61	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80885	-0.1182	10	0.87932	D	0	.	13.8032	0.63214	0.0:0.8451:0.1549:0.0	.	261	Q9HB15	KCNKC_HUMAN	N	261	ENSP00000327611:D261N	ENSP00000327611:D261N	D	-	1	0	KCNK12	47602062	1.000000	0.71417	0.991000	0.47740	0.950000	0.60333	5.915000	0.69973	0.922000	0.37019	0.305000	0.20034	GAC	.	.	none		0.632	KCNK12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251182.2	NM_022055		T	47748558	C	T	47748558	3	4	27	1	0	0	0	0	1	0	0	0	8069	855	30	2	515	2	KCNK12	2	47748558	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	391429	47748558	195450815	100	10551											
KLRAQ1	129285	hgsc.bcm.edu	37	chr2	48687054	48687054	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagaacgacaaggctaaactAgaagtaagccccattgtgag	16	6	10	9	1	0	3	0	1	0	2	0	4	0	3	2	1	3	2	2	1	7	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:48687054A>C	ENST00000294952.8	+	5	694	c.537A>C	c.(535-537)ctA>ctC	p.L179L	PPP1R21_ENST00000281394.4_Silent_p.L179L|PPP1R21_ENST00000449090.2_Silent_p.L179L	NM_001135629.2	NP_001129101.1	Q6ZMI0	PPR21_HUMAN	protein phosphatase 1, regulatory subunit 21	179						membrane (GO:0016020)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(4)|lung(9)	15						AGGCTAAACTAGAAGTAAGCC	0.433																																					p.L179L		Atlas-SNP	.											.	PPP1R21	47	.	0			c.A537C						PASS	.						59	56	57					2																	48687054		2203	4300	6503	SO:0001819	synonymous_variant	129285	exon5			TAAACTAGAAGTA	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.537A>C	2.37:g.48687054A>C		166	0	0		334	33	0.0988024	NM_152994	B7ZKY5|B7ZKY7|E1B6W7|Q2TA78|Q6ZMI6|Q8IW83|Q8J029|Q96ES8	Silent	SNP	ENST00000294952.8	37	CCDS46278.1																																																																																			.	.	none		0.433	PPP1R21-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251238.4	NM_152994		C	48687054	A	C	48687054	2	2	27	1	0	0	0	0	0	0	0	1	8422	407	15	5		5	KLRAQ1	2	48687054	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	938496	48687054	194512319	101	10552											
NRXN1	9378	hgsc.bcm.edu	37	chr2	50464109	50464109	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaagatatatgtcgtcccagCtggaaaacaaaaaccaaaac	20	6	6	9	1	0	1	0	0	0	1	2	2	1	2	2	1	4	1	2	1	9	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:50464109C>A	ENST00000406316.2	-	18	4841		c.e18-1		NRXN1_ENST00000406859.3_Splice_Site|NRXN1_ENST00000401710.1_Splice_Site|NRXN1_ENST00000401669.2_Splice_Site|NRXN1_ENST00000402717.3_Splice_Site|NRXN1_ENST00000405472.3_Splice_Site|NRXN1_ENST00000404971.1_Splice_Site|NRXN1_ENST00000331040.5_Splice_Site|NRXN1_ENST00000342183.5_Splice_Site	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)			GTCGTCCCAGCTGGAAAACAA	0.413																																					.		Atlas-SNP	.											.	NRXN1	1118	.	0			c.3485-1G>T						PASS	.						79	76	77					2																	50464109		2203	4300	6503	SO:0001630	splice_region_variant	9378	exon20			TCCCAGCTGGAAA	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.3365-1G>T	2.37:g.50464109C>A		80	0	0		160	35	0.21875	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Splice_Site	SNP	ENST00000406316.2	37	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.488228	0.84854	.	.	ENSG00000179915	ENST00000342183;ENST00000536347;ENST00000401710;ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859	.	.	.	5.68	5.68	0.88126	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.7969	0.96490	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	NRXN1	50317613	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	7.731000	0.84895	2.679000	0.91253	0.650000	0.86243	.	.	.	none		0.413	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2		Intron	A	50464109	C	A	50464109	5	1	27	1	0	0	0	0	0	0	1	0	10674	811	28	4	1183	4	NRXN1	2	50464109	Splice_Site	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1777055	50464109	192735264	102	10553											
NRXN1	9378	hgsc.bcm.edu	37	chr2	50779939	50779939	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccatggctaaataagatgagGccatttggctctgttgtacg	10	12	11	8	1	1	2	0	1	1	1	1	2	1	2	2	3	1	4	2	3	4	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:50779939G>A	ENST00000406316.2	-	9	3021	c.1545C>T	c.(1543-1545)ggC>ggT	p.G515G	NRXN1_ENST00000406859.3_Silent_p.G515G|NRXN1_ENST00000401669.2_Silent_p.G515G|NRXN1_ENST00000402717.3_Silent_p.G507G|NRXN1_ENST00000405472.3_Silent_p.G507G|NRXN1_ENST00000404971.1_Silent_p.G555G|NRXN1_ENST00000331040.5_5'UTR	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	515	Laminin G-like 3. {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)			ATAAGATGAGGCCATTTGGCT	0.433																																					p.G555G		Atlas-SNP	.											NRXN1_ENST00000536085,rectum,carcinoma,0,6	NRXN1	1118	6	0			c.C1665T						PASS	.						162	151	154					2																	50779939		1904	4114	6018	SO:0001819	synonymous_variant	9378	exon10			GATGAGGCCATTT	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.1545C>T	2.37:g.50779939G>A		134	0	0		261	55	0.210728	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	37	CCDS54360.1																																																																																			.	.	none		0.433	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			A	50779939	G	A	50779939	2	1	27	1	0	0	0	0	0	0	0	1	10674	1190	42	2		2	NRXN1	2	50779939	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	315830	50779939	192419434	103	10554											
MTIF2	4528	hgsc.bcm.edu	37	chr2	55470662	55470662	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaattgatctcttcttccacAgtagatggccatacttctca	10	14	6	11	0	3	2	1	1	3	1	6	3	4	2	2	1	1	1	2	1	3	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:55470662A>G	ENST00000263629.4	-	12	1769	c.1454T>C	c.(1453-1455)cTg>cCg	p.L485P	MTIF2_ENST00000403721.1_Missense_Mutation_p.L485P|MTIF2_ENST00000394600.3_Missense_Mutation_p.L485P	NM_002453.2	NP_002444.2	P46199	IF2M_HUMAN	mitochondrial translational initiation factor 2	485					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						CTTCTTCCACAGTAGATGGCC	0.383																																					p.L485P		Atlas-SNP	.											.	MTIF2	64	.	0			c.T1454C						PASS	.						188	184	185					2																	55470662		2203	4300	6503	SO:0001583	missense	4528	exon12			TTCCACAGTAGAT	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.1454T>C	2.37:g.55470662A>G	ENSP00000263629:p.Leu485Pro	256	0	0		422	328	0.777251	NM_002453	D6W5D0	Missense_Mutation	SNP	ENST00000263629.4	37	CCDS1853.1	.	.	.	.	.	.	.	.	.	.	A	4.188	0.033551	0.08101	.	.	ENSG00000085760	ENST00000403721;ENST00000263629;ENST00000394600;ENST00000418823	T;T;T;T	0.58358	0.34;0.34;0.34;0.87	5.6	1.63	0.23807	.	0.432007	0.27700	N	0.018206	T	0.28267	0.0698	N	0.08118	0	0.38365	D	0.944718	B	0.16802	0.019	B	0.22601	0.04	T	0.05784	-1.0864	10	0.36615	T	0.2	0.6749	7.0519	0.25077	0.2056:0.0:0.2629:0.5315	.	485	P46199	IF2M_HUMAN	P	485;485;485;163	ENSP00000384481:L485P;ENSP00000263629:L485P;ENSP00000378099:L485P;ENSP00000403492:L163P	ENSP00000263629:L485P	L	-	2	0	MTIF2	55324166	1.000000	0.71417	0.995000	0.50966	0.052000	0.14988	0.787000	0.26858	0.381000	0.24851	-0.275000	0.10095	CTG	.	.	none		0.383	MTIF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251486.4	NM_002453		G	55470662	A	G	55470662	3	3	27	1	0	0	0	0	1	0	0	0	9943	188	7	3	749	3	MTIF2	2	55470662	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	4690723	55470662	187728711	104	10555											
APLF	200558	hgsc.bcm.edu	37	chr2	68765205	68765205	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgagtgcccagggcgactcaCttcaggatgagtctcaaggg	9	7	14	11	2	3	1	3	1	1	0	4	4	3	2	1	3	1	0	1	3	1	1	rs13404469	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:68765205C>T	ENST00000303795.4	+	7	1177	c.1006C>T	c.(1006-1008)Ctt>Ttt	p.L336F	APLF_ENST00000471727.1_3'UTR	NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	336			L -> F (in dbSNP:rs13404469).		cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of DNA ligation (GO:0051106)|regulation of isotype switching (GO:0045191)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|endodeoxyribonuclease activity (GO:0004520)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	25						GGGCGACTCACTTCAGGATGA	0.423													T|||	395	0.0788738	0.1483	0.0735	5008	,	,		18007	0.005		0.0726	False		,,,				2504	0.0716				p.L336F		Atlas-SNP	.											.	APLF	69	.	0			c.C1006T						PASS	.	T	PHE/LEU	637,3769		51,535,1617	92	86	88		1006	4	0	2	dbSNP_121	88	695,7905		33,629,3638	yes	missense	APLF	NM_173545.2	22	84,1164,5255	TT,TC,CC		8.0814,14.4576,10.2414	benign	336/512	68765205	1332,11674	2203	4300	6503	SO:0001583	missense	200558	exon7			GACTCACTTCAGG	BC030711	CCDS1888.1	2p14	2014-02-20	2008-10-01	2008-10-01	ENSG00000169621	ENSG00000169621			28724	protein-coding gene	gene with protein product	"XRCC1-interacting protein 1", "zinc finger, CX5CX6HX5H motif containing 1"	611035	"chromosome 2 open reading frame 13"	C2orf13		18474613, 18077224, 17353262	Standard	NM_173545		Approved	MGC47799, Xip1, ZCCHH1	uc002sep.3	Q8IW19	OTTHUMG00000129566	ENST00000303795.4:c.1006C>T	2.37:g.68765205C>T	ENSP00000307004:p.Leu336Phe	203	1	0.00492611		187	94	0.502674	NM_173545	A8K476|Q53P47|Q53PB9|Q53QU0	Missense_Mutation	SNP	ENST00000303795.4	37	CCDS1888.1	151	0.06913919413919414	62	0.12601626016260162	28	0.07734806629834254	4	0.006993006993006993	57	0.07519788918205805	.	0.181	-1.061812	0.01950	0.144576	0.080814	ENSG00000169621	ENST00000303795	T	0.23950	1.88	5.19	4.0	0.46444	.	1.310930	0.04804	N	0.434102	T	0.00073	0.0002	N	0.00289	-1.7	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30475	-0.9977	9	0.26408	T	0.33	.	8.0877	0.30782	0.0:0.1667:0.0:0.8333	rs13404469;rs52799369;rs13404469	336	Q8IW19	APLF_HUMAN	F	336	ENSP00000307004:L336F	ENSP00000307004:L336F	L	+	1	0	APLF	68618709	0.006000	0.16342	0.002000	0.10522	0.063000	0.16089	0.651000	0.24873	0.274000	0.22072	-0.381000	0.06696	CTT	C|0.910;T|0.090	0.090	strong		0.423	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545		T	68765205	C	T	68765205	3	4	27	1	0	0	0	0	1	0	0	0	776	565	20	2	1032	2	APLF	2	68765205	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	13294543	68765205	174434168	105	10556											
APLF	200558	hgsc.bcm.edu	37	chr2	68805143	68805143	+	Frame_Shift_Del	DEL	A	A	-																															aagaagcaaaaaggtttatgAaaagaaaatagtaactaact																								rs149897324	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:68805143delA	ENST00000303795.4	+	10	1696	c.1525delA	c.(1525-1527)aaafs	p.K509fs	APLF_ENST00000471727.1_Intron	NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	509					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of DNA ligation (GO:0051106)|regulation of isotype switching (GO:0045191)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|endodeoxyribonuclease activity (GO:0004520)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	25						AAGGTTTATGAAAAGAAAATA	0.358													AAAA|AAAA|AAA|deletion	23	0.00459265	0.0008	0.0058	5008	,	,		20808	0.0		0.0119	False		,,,				2504	0.0061				p.M508fs		Pindel,Atlas-Indel	.											.	APLF	69	.	0			c.1524delG						PASS	.			15,4251		0,15,2118	68	74	72			2.8	1	2	dbSNP_134	73	121,8127		3,115,4006	no	frameshift	APLF	NM_173545.2		3,130,6124	A1A1,A1R,RR		1.467,0.3516,1.0868			68805143	136,12378	2203	4299	6502	SO:0001589	frameshift_variant	200558	exon10			.	BC030711	CCDS1888.1	2p14	2014-02-20	2008-10-01	2008-10-01	ENSG00000169621	ENSG00000169621			28724	protein-coding gene	gene with protein product	"XRCC1-interacting protein 1", "zinc finger, CX5CX6HX5H motif containing 1"	611035	"chromosome 2 open reading frame 13"	C2orf13		18474613, 18077224, 17353262	Standard	NM_173545		Approved	MGC47799, Xip1, ZCCHH1	uc002sep.3	Q8IW19	OTTHUMG00000129566	ENST00000303795.4:c.1525delA	2.37:g.68805143delA	ENSP00000307004:p.Lys509fs	79	0	.		50	20	0.4	NM_173545	A8K476|Q53P47|Q53PB9|Q53QU0	Frame_Shift_Del	DEL	ENST00000303795.4	37	CCDS1888.1																																																																																			A|0.991;-|0.009	0.009	strong		0.358	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545		-	68805143	A	-	68805143	7	5	27	1	0	1	0	1	0	0	0	0	776	247	9	0	1563	0	APLF	2	68805143	Frame_Shift_Del	DEL	A	TCGA-G8-6909-01A-11D-2210-10	39938	68805143	174394230	106	10557											
LRRTM1	347730	hgsc.bcm.edu	37	chr2	80529595	80529595	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	aggctggctgggaaacacttCcaggacacgtagagcaccag	12	5	13	11	1	0	1	0	0	0	1	1	3	1	3	2	4	2	4	2	4	2	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:80529595C>T	ENST00000295057.3	-	2	2006	c.1350G>A	c.(1348-1350)tgG>tgA	p.W450*	LRRTM1_ENST00000409148.1_Nonsense_Mutation_p.W450*|CTNNA2_ENST00000541047.1_Intron|CTNNA2_ENST00000402739.4_Intron|CTNNA2_ENST00000466387.1_Intron|CTNNA2_ENST00000361291.4_Intron|CTNNA2_ENST00000496558.1_Intron|CTNNA2_ENST00000540488.1_Intron	NM_178839.4	NP_849161.2	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	450					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						GGAAACACTTCCAGGACACGT	0.577										HNSCC(69;0.2)																											p.W450X		Atlas-SNP	.											.	LRRTM1	251	.	0			c.G1350A						PASS	.						100	89	93					2																	80529595		2203	4300	6503	SO:0001587	stop_gained	347730	exon2			ACACTTCCAGGAC	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.1350G>A	2.37:g.80529595C>T	ENSP00000295057:p.Trp450*	83	0	0		91	22	0.241758	NM_178839	A8K397|D6W5K1|Q96DN1	Nonsense_Mutation	SNP	ENST00000295057.3	37	CCDS1966.1	.	.	.	.	.	.	.	.	.	.	C	38	7.112766	0.98070	.	.	ENSG00000162951	ENST00000295057;ENST00000409148	.	.	.	5.18	5.18	0.71444	.	0.077796	0.56097	U	0.000031	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.6948	0.91596	0.0:1.0:0.0:0.0	.	.	.	.	X	450	.	.	W	-	3	0	LRRTM1	80383106	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.803000	0.62546	2.383000	0.81215	0.561000	0.74099	TGG	.	.	none		0.577	LRRTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313614.1	NM_178839		T	80529595	C	T	80529595	4	4	27	1	0	0	0	0	0	1	0	0	9048	856	30	2	222	2	LRRTM1	2	80529595	Nonsense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	11724452	80529595	162669778	107	10558											
GGCX	2677	hgsc.bcm.edu	37	chr2	85788528	85788528	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgagctgggcgaggtccgCgcggacccggcagacaccgc	6	3	16	16	6	0	2	0	1	0	1	1	4	1	3	4	4	1	2	4	4	0	0	rs371622780		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:85788528C>T	ENST00000233838.4	-	1	104	c.24G>A	c.(22-24)gcG>gcA	p.A8A	VAMP8_ENST00000432071.1_5'Flank|GGCX_ENST00000430215.3_Silent_p.A8A	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)	GCGAGGTCCGCGCGGACCCGG	0.697																																					p.A8A		Atlas-SNP	.											.	GGCX	44	.	0			c.G24A						PASS	.	C	,	0,4272		0,0,2136	6	8	8		24,24	1.2	0.1	2		8	5,8413		0,5,4204	no	coding-synonymous,coding-synonymous	GGCX	NM_000821.5,NM_001142269.2	,	0,5,6340	TT,TC,CC		0.0594,0.0,0.0394	,	8/759,8/702	85788528	5,12685	2136	4209	6345	SO:0001819	synonymous_variant	2677	exon1			GGTCCGCGCGGAC		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.24G>A	2.37:g.85788528C>T		126	0	0		137	67	0.489051	NM_000821	B4DMC5|E9PEE1|Q14415|Q6GU45	Silent	SNP	ENST00000233838.4	37	CCDS1978.1																																																																																			.	.	weak		0.697	GGCX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252490.3	NM_000821		T	85788528	C	T	85788528	2	4	27	1	0	0	0	0	0	0	0	1	6364	755	27	1		1	GGCX	2	85788528	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	5258933	85788528	157410845	108	10559											
USP39	10713	hgsc.bcm.edu	37	chr2	85843348	85843348	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggtctaagcgggagtctcgCggttccactcgcgggaagcg	6	7	16	12	7	2	0	0	0	2	0	5	2	3	2	1	4	2	1	1	4	2	2	rs11544042	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:85843348C>T	ENST00000323701.6	+	1	40	c.30C>T	c.(28-30)cgC>cgT	p.R10R	USP39_ENST00000409025.1_Silent_p.R10R|USP39_ENST00000409470.1_Silent_p.R10R|USP39_ENST00000459775.1_Intron|USP39_ENST00000409766.3_Silent_p.R10R|USP39_ENST00000450066.2_Intron	NM_006590.3	NP_006581.2	Q53GS9	SNUT2_HUMAN	ubiquitin specific peptidase 39	10	Arg-rich.				cell cycle (GO:0007049)|cell division (GO:0051301)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|ubiquitin-dependent protein catabolic process (GO:0006511)	spliceosomal complex (GO:0005681)	ubiquitinyl hydrolase activity (GO:0036459)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	19						GGGAGTCTCGCGGTTCCACTC	0.706													C|||	267	0.0533147	0.1036	0.0548	5008	,	,		12680	0.001		0.0775	False		,,,				2504	0.0133				p.R10R		Atlas-SNP	.											.	USP39	33	.	0			c.C30T						PASS	.	C		365,3963		13,339,1812	7	8	8		30	-4.3	1	2	dbSNP_120	8	528,7964		12,504,3730	no	coding-synonymous	USP39	NM_006590.2		25,843,5542	TT,TC,CC		6.2176,8.4335,6.9657		10/566	85843348	893,11927	2164	4246	6410	SO:0001819	synonymous_variant	10713	exon1			GTCTCGCGGTTCC	AF132955	CCDS33234.1, CCDS58716.1, CCDS58717.1, CCDS74534.1	2p11.2	2009-01-06	2005-08-08		ENSG00000168883	ENSG00000168883		"Ubiquitin-specific peptidases"	20071	protein-coding gene	gene with protein product	"snRNP assembly defective 1 homolog (S.cerevisiae)", "small nuclear ribonucleoprotein 65kDa (U4/U6.U5)"	611594	"ubiquitin specific protease 39"			12838346	Standard	NM_006590		Approved	SAD1, CGI-21, SNRNP65	uc002sqg.4	Q53GS9	OTTHUMG00000153090	ENST00000323701.6:c.30C>T	2.37:g.85843348C>T		50	0	0		60	33	0.55	NM_001256725	A8K086|B3KM40|B4DHT4|D6W5L4|G5E9H0|Q6NX47|Q96RK9|Q9BV89|Q9H381|Q9P050|Q9Y310	Silent	SNP	ENST00000323701.6	37	CCDS33234.1																																																																																			C|0.936;T|0.064	0.064	strong		0.706	USP39-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329892.1	NM_006590		T	85843348	C	T	85843348	2	4	27	1	0	0	0	0	0	0	0	1	17085	755	27	1		1	USP39	2	85843348	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	54820	85843348	157356025	109	10560											
EIF2AK3	9451	hgsc.bcm.edu	37	chr2	88926522	88926522	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctctgtctcatcgtctggttCcggaccccgaggctcctgct	3	12	10	16	3	3	0	1	0	3	0	7	2	5	1	4	3	1	3	4	3	0	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:88926522C>A	ENST00000303236.3	-	1	572	c.271G>T	c.(271-273)Gaa>Taa	p.E91*	AC062029.1_ENST00000606164.1_RNA|AC062029.1_ENST00000453008.2_RNA|EIF2AK3_ENST00000419748.1_5'Flank	NM_004836.5	NP_004827.4	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 3	91					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						TCGTCTGGTTCCGGACCCCGA	0.731																																					p.E91X	GBM(138;671 1851 16235 39058 45249)	Atlas-SNP	.											.	EIF2AK3	160	.	0			c.G271T						PASS	.						15	18	17					2																	88926522		2023	4091	6114	SO:0001587	stop_gained	9451	exon1			CTGGTTCCGGACC	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.271G>T	2.37:g.88926522C>A	ENSP00000307235:p.Glu91*	59	0	0		71	24	0.338028	NM_004836	A0AVH1|A0AVH2|B2RCU9|O95846|Q53QY0|Q53SB1	Nonsense_Mutation	SNP	ENST00000303236.3	37	CCDS33241.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.692593	0.88735	.	.	ENSG00000172071	ENST00000303236	.	.	.	4.2	4.2	0.49525	.	0.382598	0.20874	N	0.084102	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	-8.9866	12.3586	0.55190	0.0:1.0:0.0:0.0	.	.	.	.	X	91	.	ENSP00000307235:E91X	E	-	1	0	EIF2AK3	88707637	0.245000	0.23899	0.013000	0.15412	0.003000	0.03518	3.145000	0.50623	2.032000	0.59987	0.561000	0.74099	GAA	.	.	none		0.731	EIF2AK3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000338233.2	NM_004836		A	88926522	C	A	88926522	4	1	27	1	0	0	0	0	0	1	0	0	5000	864	30	4	3147	4	EIF2AK3	2	88926522	Nonsense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3083174	88926522	154272851	110	10561											
EIF2AK3	9451	hgsc.bcm.edu	37	chr2	88926536	88926536	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggttccggaccccgaggcTcctgctctcccgcggctgcc	2	8	12	19	4	1	0	0	0	1	0	4	2	3	1	6	4	2	4	6	4	0	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:88926536T>C	ENST00000303236.3	-	1	558	c.257A>G	c.(256-258)gAg>gGg	p.E86G	AC062029.1_ENST00000606164.1_RNA|AC062029.1_ENST00000453008.2_RNA|EIF2AK3_ENST00000419748.1_5'Flank	NM_004836.5	NP_004827.4	Q9NZJ5	E2AK3_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 3	86					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						ACCCCGAGGCTCCTGCTCTCc	0.731																																					p.E86G	GBM(138;671 1851 16235 39058 45249)	Atlas-SNP	.											.	EIF2AK3	160	.	0			c.A257G						PASS	.						11	14	13					2																	88926536		1978	4004	5982	SO:0001583	missense	9451	exon1			CGAGGCTCCTGCT	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.257A>G	2.37:g.88926536T>C	ENSP00000307235:p.Glu86Gly	44	0	0		55	19	0.345455	NM_004836	A0AVH1|A0AVH2|B2RCU9|O95846|Q53QY0|Q53SB1	Missense_Mutation	SNP	ENST00000303236.3	37	CCDS33241.1	.	.	.	.	.	.	.	.	.	.	T	9.820	1.185631	0.21870	.	.	ENSG00000172071	ENST00000303236	T	0.73258	-0.73	3.67	3.67	0.42095	.	0.229807	0.30011	N	0.010633	T	0.57932	0.2087	L	0.44542	1.39	0.20074	N	0.999937	B	0.31318	0.319	B	0.29440	0.102	T	0.48163	-0.9059	10	0.29301	T	0.29	-6.3314	8.8508	0.35199	0.0:0.0:0.0:1.0	.	86	Q9NZJ5	E2AK3_HUMAN	G	86	ENSP00000307235:E86G	ENSP00000307235:E86G	E	-	2	0	EIF2AK3	88707651	0.289000	0.24334	0.051000	0.19133	0.018000	0.09664	3.014000	0.49590	1.651000	0.50673	0.459000	0.35465	GAG	.	.	none		0.731	EIF2AK3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000338233.2	NM_004836		C	88926536	T	C	88926536	3	2	27	1	0	0	0	0	1	0	0	0	5000	1551	54	3	3161	3	EIF2AK3	2	88926536	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	14	88926536	154272837	111	10562											
GPAT2	150763	hgsc.bcm.edu	37	chr2	96688916	96688916	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgcaaaggccttgagcagcGggctgagcaggcggcagagg	9	4	19	9	2	0	3	0	2	0	1	0	3	0	3	1	5	4	5	1	5	1	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:96688916G>A	ENST00000434632.1	-	20	2546	c.2087C>T	c.(2086-2088)cCg>cTg	p.P696L	FAHD2CP_ENST00000607780.1_RNA|GPAT2_ENST00000359548.4_Missense_Mutation_p.P696L|GPAT2_ENST00000453542.1_Missense_Mutation_p.P625L|GPAT2_ENST00000377137.3_Intron			Q6NUI2	GPAT2_HUMAN	glycerol-3-phosphate acyltransferase 2, mitochondrial	696					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						CTTGAGCAGCGGGCTGAGCAG	0.652																																					p.P696L		Atlas-SNP	.											GPAT2,NS,carcinoma,+1,1	GPAT2	46	1	0			c.C2087T						scavenged	.						12	15	14					2																	96688916		1813	4047	5860	SO:0001583	missense	150763	exon19			AGCAGCGGGCTGA	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.2087C>T	2.37:g.96688916G>A	ENSP00000389395:p.Pro696Leu	339	1	0.00294985		264	29	0.109848	NM_207328	Q6P2E4|Q6ZNI3|Q6ZNI5|Q6ZWJ4	Missense_Mutation	SNP	ENST00000434632.1	37	CCDS42714.1	.	.	.	.	.	.	.	.	.	.	g	23.0	4.365252	0.82463	.	.	ENSG00000186281	ENST00000359548;ENST00000434632;ENST00000453542	D;D;T	0.83419	-1.72;-1.72;-0.81	5.44	5.44	0.79542	.	0.141914	0.49916	D	0.000123	D	0.89894	0.6847	M	0.64404	1.975	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.91635	0.996;0.932;0.999;0.995	D	0.90665	0.4593	10	0.87932	D	0	-13.903	16.7485	0.85479	0.0:0.0:1.0:0.0	.	625;702;696;625	E9PE95;Q6NUI2-4;Q6NUI2;B4DNZ9	.;.;GPAT2_HUMAN;.	L	696;696;625	ENSP00000352547:P696L;ENSP00000389395:P696L;ENSP00000393770:P625L	ENSP00000352547:P696L	P	-	2	0	GPAT2	96052643	1.000000	0.71417	0.905000	0.35620	0.705000	0.40729	7.030000	0.76484	2.569000	0.86673	0.637000	0.83480	CCG	.	.	none		0.652	GPAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338786.1	NM_207328		A	96688916	G	A	96688916	3	1	27	1	0	0	0	0	1	0	0	0	6597	1116	39	1	316	1	GPAT2	2	96688916	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	7762380	96688916	146510457	112	10563											
DUSP2	1844	hgsc.bcm.edu	37	chr2	96810085	96810085	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	actgcagctgcccaggaacaGgtagggcaagatctccacag	12	5	12	12	0	1	1	0	0	1	1	2	2	1	2	2	3	4	4	2	3	3	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:96810085G>C	ENST00000288943.4	-	3	623	c.538C>G	c.(538-540)Ctg>Gtg	p.L180V	AC012307.2_ENST00000449242.1_lincRNA	NM_004418.3	NP_004409.1	Q05923	DUS2_HUMAN	dual specificity phosphatase 2	180					endoderm formation (GO:0001706)|inactivation of MAPK activity (GO:0000188)|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)|protein tyrosine/threonine phosphatase activity (GO:0008330)			NS(1)|breast(1)|lung(2)|skin(1)	5		Ovarian(717;0.0228)				CCCAGGAACAGGTAGGGCAAG	0.662																																					p.L180V		Atlas-SNP	.											.	DUSP2	20	.	0			c.C538G						PASS	.						39	42	41					2																	96810085		2203	4300	6503	SO:0001583	missense	1844	exon3			GGAACAGGTAGGG	L11329	CCDS2016.1	2q11	2011-06-09			ENSG00000158050	ENSG00000158050		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3068	protein-coding gene	gene with protein product		603068				7806236, 7590752, 12673251	Standard	NM_004418		Approved	PAC-1	uc002svk.4	Q05923	OTTHUMG00000130456	ENST00000288943.4:c.538C>G	2.37:g.96810085G>C	ENSP00000288943:p.Leu180Val	76	0	0		61	10	0.163934	NM_004418	Q53T45	Missense_Mutation	SNP	ENST00000288943.4	37	CCDS2016.1	.	.	.	.	.	.	.	.	.	.	g	18.49	3.636287	0.67130	.	.	ENSG00000158050	ENST00000288943	D	0.86627	-2.15	4.56	1.77	0.24775	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.000000	0.64402	D	0.000013	D	0.91998	0.7465	M	0.83953	2.67	0.49687	D	0.999815	D	0.56035	0.974	D	0.80764	0.994	D	0.90547	0.4506	10	0.66056	D	0.02	.	7.8982	0.29719	0.2871:0.0:0.7129:0.0	.	180	Q05923	DUS2_HUMAN	V	180	ENSP00000288943:L180V	ENSP00000288943:L180V	L	-	1	2	DUSP2	96173812	1.000000	0.71417	0.980000	0.43619	0.696000	0.40369	2.783000	0.47766	0.680000	0.31366	0.550000	0.68814	CTG	.	.	none		0.662	DUSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252847.1	NM_004418		C	96810085	G	C	96810085	3	2	27	1	0	0	0	0	1	0	0	0	4821	991	35	4	414	4	DUSP2	2	96810085	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	121169	96810085	146389288	113	10564											
DUSP2	1844	hgsc.bcm.edu	37	chr2	96810609	96810609	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cgggacagcagccctggaagCcgtcgaagcctcctgcaagg	9	4	14	14	3	0	0	0	0	0	0	2	3	1	2	4	3	5	2	4	3	3	0	rs572028879		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:96810609C>T	ENST00000288943.4	-	2	486	c.401G>A	c.(400-402)gGc>gAc	p.G134D	AC012307.2_ENST00000449242.1_lincRNA	NM_004418.3	NP_004409.1	Q05923	DUS2_HUMAN	dual specificity phosphatase 2	134	Rhodanese. {ECO:0000255|PROSITE- ProRule:PRU00173}.				endoderm formation (GO:0001706)|inactivation of MAPK activity (GO:0000188)|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)|protein tyrosine/threonine phosphatase activity (GO:0008330)			NS(1)|breast(1)|lung(2)|skin(1)	5		Ovarian(717;0.0228)				GCCCTGGAAGCCGTCGAAGCC	0.697													C|||	1	0.000199681	0.0008	0.0	5008	,	,		11195	0.0		0.0	False		,,,				2504	0.0				p.G134D		Atlas-SNP	.											.	DUSP2	20	.	0			c.G401A						PASS	.						15	20	18					2																	96810609		2094	4175	6269	SO:0001583	missense	1844	exon2			TGGAAGCCGTCGA	L11329	CCDS2016.1	2q11	2011-06-09			ENSG00000158050	ENSG00000158050		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3068	protein-coding gene	gene with protein product		603068				7806236, 7590752, 12673251	Standard	NM_004418		Approved	PAC-1	uc002svk.4	Q05923	OTTHUMG00000130456	ENST00000288943.4:c.401G>A	2.37:g.96810609C>T	ENSP00000288943:p.Gly134Asp	66	0	0		80	26	0.325	NM_004418	Q53T45	Missense_Mutation	SNP	ENST00000288943.4	37	CCDS2016.1	.	.	.	.	.	.	.	.	.	.	C	3.560	-0.089892	0.07053	.	.	ENSG00000158050	ENST00000288943	T	0.26373	1.74	4.31	2.38	0.29361	Rhodanese-like (5);	0.285507	0.32736	N	0.005712	T	0.26774	0.0655	L	0.58101	1.795	0.25586	N	0.986743	B	0.31459	0.324	B	0.37091	0.241	T	0.14504	-1.0470	10	0.28530	T	0.3	.	10.6808	0.45813	0.0:0.5226:0.4774:0.0	.	134	Q05923	DUS2_HUMAN	D	134	ENSP00000288943:G134D	ENSP00000288943:G134D	G	-	2	0	DUSP2	96174336	0.037000	0.19845	0.471000	0.27229	0.207000	0.24258	0.181000	0.16880	0.349000	0.23975	0.456000	0.33151	GGC	.	.	none		0.697	DUSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252847.1	NM_004418		T	96810609	C	T	96810609	3	4	27	1	0	0	0	0	1	0	0	0	4821	739	26	2	555	2	DUSP2	2	96810609	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	524	96810609	146388764	114	10565											
ANKRD36	375248	hgsc.bcm.edu	37	chr2	97790211	97790211	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttagatcagccctcatacAtgctgttactcttggagaaa	11	14	7	9	0	3	2	2	0	1	2	3	3	3	2	1	1	4	2	1	1	4	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:97790211A>T	ENST00000461153.2	+	5	852	c.608A>T	c.(607-609)cAt>cTt	p.H203L	ANKRD36_ENST00000420699.2_Missense_Mutation_p.H203L			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	203								p.H203L(2)		endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						GCCCTCATACATGCTGTTACT	0.323																																					p.H203L		Atlas-SNP	.											ANKRD36_ENST00000420699,extremity,malignant_melanoma,0,2	ANKRD36	170	2	2	Substitution - Missense(2)	NS(1)|skin(1)	c.A608T						scavenged	.						79	60	65					2																	97790211		692	1589	2281	SO:0001583	missense	375248	exon5			TCATACATGCTGT	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.608A>T	2.37:g.97790211A>T	ENSP00000419530:p.His203Leu	200	2	0.01		198	13	0.0656566	NM_001164315	B4E3I8|Q6UX02|Q86X62|Q9HCD1	Missense_Mutation	SNP	ENST00000461153.2	37	CCDS54379.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.781271	0.00634	.	.	ENSG00000135976	ENST00000461153;ENST00000420699;ENST00000393513;ENST00000455519	T;T	0.60920	0.15;0.15	0.946	-0.341	0.12639	Ankyrin repeat-containing domain (4);	.	.	.	.	T	0.16642	0.0400	N	0.00855	-1.145	0.47511	D	0.999447	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.37384	-0.9708	9	0.02654	T	1	.	3.0347	0.06118	0.3942:0.0:0.0:0.6058	.	203;203	A6QL64;F2Z332	AN36A_HUMAN;.	L	203	ENSP00000419530:H203L;ENSP00000391950:H203L	ENSP00000377149:H203L	H	+	2	0	ANKRD36	97153938	0.990000	0.36364	0.731000	0.30826	0.427000	0.31564	0.125000	0.15749	-0.131000	0.11578	-1.495000	0.00966	CAT	.	.	none		0.323	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339154.5			T	97790211	A	T	97790211	3	4	27	1	0	0	0	0	1	0	0	0	665	217	8	5	626	5	ANKRD36	2	97790211	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	979602	97790211	145409162	115	10566											
VWA3B	200403	hgsc.bcm.edu	37	chr2	98928323	98928323	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctgctttcctcttctggcCactgaaagaagcggacacgc	8	10	9	14	2	3	2	0	1	3	1	4	3	4	3	2	2	2	1	2	2	2	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:98928323C>T	ENST00000477737.1	+	27	3767	c.3563C>T	c.(3562-3564)cCa>cTa	p.P1188L	VWA3B_ENST00000490947.2_3'UTR	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	1188										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						CTCTTCTGGCCACTGAAAGAA	0.587																																					p.P1188L		Atlas-SNP	.											.	VWA3B	138	.	0			c.C3563T						PASS	.						24	30	28					2																	98928323		1936	4132	6068	SO:0001583	missense	200403	exon27			TCTGGCCACTGAA	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.3563C>T	2.37:g.98928323C>T	ENSP00000417955:p.Pro1188Leu	219	0	0		202	53	0.262376	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	37	CCDS42718.1	.	.	.	.	.	.	.	.	.	.	C	11.57	1.676780	0.29783	.	.	ENSG00000168658	ENST00000477737;ENST00000358269	T	0.08458	3.09	3.79	2.9	0.33743	.	.	.	.	.	T	0.06096	0.0158	N	0.22421	0.69	0.09310	N	0.99999	B;B	0.32829	0.386;0.164	B;B	0.30716	0.119;0.056	T	0.33979	-0.9847	9	0.46703	T	0.11	.	8.715	0.34405	0.2264:0.7736:0.0:0.0	.	580;1188	Q502W6-5;Q502W6	.;VWA3B_HUMAN	L	1188;310	ENSP00000417955:P1188L	ENSP00000351009:P310L	P	+	2	0	VWA3B	98294755	0.053000	0.20554	0.002000	0.10522	0.008000	0.06430	1.626000	0.37039	1.155000	0.42497	0.491000	0.48974	CCA	.	.	none		0.587	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992		T	98928323	C	T	98928323	3	4	27	1	0	0	0	0	1	0	0	0	17256	594	21	2	3665	2	VWA3B	2	98928323	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1138112	98928323	144271050	116	10567											
CHST10	9486	hgsc.bcm.edu	37	chr2	101009869	101009869	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagggatagtcgggtatgaCaccaggtggtcaatgccagc	10	7	16	8	1	1	1	1	1	0	0	2	3	1	3	2	5	2	1	2	5	3	2	rs148920749	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:101009869C>T	ENST00000264249.3	-	7	1294	c.909G>A	c.(907-909)gtG>gtA	p.V303V	CHST10_ENST00000542617.1_Silent_p.V351V|CHST10_ENST00000409701.1_Silent_p.V303V	NM_004854.4	NP_004845.1	O43529	CHSTA_HUMAN	carbohydrate sulfotransferase 10	303					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						TCGGGTATGACACCAGGTGGT	0.522													C|||	16	0.00319489	0.0	0.0014	5008	,	,		17713	0.0		0.0099	False		,,,				2504	0.0051				p.V303V		Atlas-SNP	.											.	CHST10	42	.	0			c.G909A						PASS	.	C		7,4399	12.9+/-30.5	0,7,2196	174	143	154		909	1.6	1	2	dbSNP_134	154	95,8505	53.6+/-114.3	0,95,4205	no	coding-synonymous	CHST10	NM_004854.4		0,102,6401	TT,TC,CC		1.1047,0.1589,0.7843		303/357	101009869	102,12904	2203	4300	6503	SO:0001819	synonymous_variant	9486	exon7			GTATGACACCAGG	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.909G>A	2.37:g.101009869C>T		296	0	0		249	117	0.46988	NM_004854	Q53T18	Silent	SNP	ENST00000264249.3	37	CCDS2047.1																																																																																			C|0.993;T|0.007	0.007	strong		0.522	CHST10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253162.1	NM_004854		T	101009869	C	T	101009869	2	4	27	1	0	0	0	0	0	0	0	1	3400	465	17	2		2	CHST10	2	101009869	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2081546	101009869	142189504	117	10568											
MAP4K4	9448	hgsc.bcm.edu	37	chr2	102314984	102314984	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtggttggaaatggcacctAtggacaagtctataaggtcg	12	10	13	6	1	1	0	0	0	1	0	2	2	1	2	1	5	0	2	1	5	5	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:102314984A>T	ENST00000347699.4	+	2	107	c.107A>T	c.(106-108)tAt>tTt	p.Y36F	MAP4K4_ENST00000456652.1_Missense_Mutation_p.Y36F|MAP4K4_ENST00000413150.2_Missense_Mutation_p.Y36F|MAP4K4_ENST00000425019.1_Missense_Mutation_p.Y36F|MAP4K4_ENST00000324219.4_Missense_Mutation_p.Y36F|MAP4K4_ENST00000302217.5_Missense_Mutation_p.Y36F|MAP4K4_ENST00000350198.4_Missense_Mutation_p.Y36F	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4	36	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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						AATGGCACCTATGGACAAGTC	0.488																																					p.Y36F		Atlas-SNP	.											.	MAP4K4	111	.	0			c.A107T						PASS	.						247	242	244					2																	102314984		1880	4108	5988	SO:0001583	missense	9448	exon2			GCACCTATGGACA	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.107A>T	2.37:g.102314984A>T	ENSP00000314363:p.Tyr36Phe	402	1	0.00248756		312	90	0.288462	NM_004834	O75172|Q9NST7	Missense_Mutation	SNP	ENST00000347699.4	37	CCDS56130.1	.	.	.	.	.	.	.	.	.	.	A	18.54	3.645786	0.67358	.	.	ENSG00000071054	ENST00000427603;ENST00000425019;ENST00000324219;ENST00000350198;ENST00000302217;ENST00000413150;ENST00000456652;ENST00000347699	T;T;T;T;T;T;T;T	0.17691	3.68;2.26;2.26;2.26;2.26;2.26;2.26;2.26	4.26	4.26	0.50523	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	0.49305	U	0.000157	T	0.17023	0.0409	N	0.02345	-0.59	0.80722	D	1	D;P;P;P;P;P;P;P	0.64830	0.994;0.939;0.809;0.939;0.939;0.475;0.925;0.925	D;D;P;D;D;P;D;D	0.67548	0.942;0.952;0.739;0.952;0.952;0.634;0.92;0.92	T	0.43360	-0.9396	10	0.72032	D	0.01	.	13.0603	0.59003	1.0:0.0:0.0:0.0	.	36;36;36;36;36;36;36;36	B7Z3V5;C9J840;O95819-4;O95819;E7EN19;G3XAA2;O95819-2;G5E948	.;.;.;M4K4_HUMAN;.;.;.;.	F	36	ENSP00000403016:Y36F;ENSP00000392830:Y36F;ENSP00000313644:Y36F;ENSP00000281111:Y36F;ENSP00000303600:Y36F;ENSP00000389752:Y36F;ENSP00000387370:Y36F;ENSP00000314363:Y36F	ENSP00000303600:Y36F	Y	+	2	0	MAP4K4	101681416	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	8.623000	0.90957	1.544000	0.49359	0.482000	0.46254	TAT	.	.	none		0.488	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834		T	102314984	A	T	102314984	3	4	27	1	0	0	0	0	1	0	0	0	9271	449	16	5	113	5	MAP4K4	2	102314984	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	1305115	102314984	140884389	118	10569											
LIMS1	3987	hgsc.bcm.edu	37	chr2	109276110	109276110	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttgcgagcgctgcaagggcGgctttgcgcccgctgagaag	6	7	16	12	5	0	1	0	1	0	1	0	3	0	1	1	2	4	4	1	2	2	2	rs146149508	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:109276110G>A	ENST00000393310.1	+	2	213	c.46G>A	c.(46-48)Ggc>Agc	p.G16S	LIMS1_ENST00000542845.1_Missense_Mutation_p.G78S|LIMS1_ENST00000332345.6_Missense_Mutation_p.G16S|LIMS1_ENST00000409441.1_Missense_Mutation_p.G53S|LIMS1_ENST00000393314.2_Missense_Mutation_p.G78S|LIMS1_ENST00000338045.3_Missense_Mutation_p.G16S|LIMS1_ENST00000410093.1_Missense_Mutation_p.G20S|LIMS1_ENST00000544547.1_Missense_Mutation_p.G28S|LIMS1_ENST00000462817.1_3'UTR	NM_001193488.1	NP_001180417.1	P48059	LIMS1_HUMAN	LIM and senescent cell antigen-like domains 1	16	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell aging (GO:0007569)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cell-matrix adhesion (GO:0007160)|cellular response to transforming growth factor beta stimulus (GO:0071560)|chordate embryonic development (GO:0043009)|establishment or maintenance of cell polarity (GO:0007163)|negative regulation of apoptotic process (GO:0043066)|negative regulation of hepatocyte proliferation (GO:2000346)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of integrin-mediated signaling pathway (GO:2001046)|protein heterooligomerization (GO:0051291)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)	10						CTGCAAGGGCGGCTTTGCGCC	0.572													G|||	11	0.00219649	0.0	0.0043	5008	,	,		24021	0.0		0.008	False		,,,				2504	0.0				p.G78S		Atlas-SNP	.											.	LIMS1	38	.	0			c.G232A						PASS	.	G	SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY,SER/GLY	9,4397	14.3+/-33.2	0,9,2194	117	90	99		58,82,157,232,46,46	4.6	0.8	2	dbSNP_134	99	93,8507	52.3+/-112.8	0,93,4207	no	missense,missense,missense,missense,missense,missense	LIMS1	NM_001193482.1,NM_001193483.2,NM_001193484.1,NM_001193485.2,NM_001193488.1,NM_004987.5	56,56,56,56,56,56	0,102,6401	AA,AG,GG		1.0814,0.2043,0.7843	benign,benign,benign,benign,benign,benign	20/330,28/338,53/363,78/388,16/326,16/326	109276110	102,12904	2203	4300	6503	SO:0001583	missense	3987	exon2			AAGGGCGGCTTTG		CCDS2078.1, CCDS54382.1, CCDS54383.1, CCDS54384.1, CCDS54385.1	2q12.3	2008-05-23			ENSG00000169756	ENSG00000169756			6616	protein-coding gene	gene with protein product		602567				7517666, 10022929	Standard	NM_001193482		Approved	PINCH, PINCH1	uc002tek.4	P48059	OTTHUMG00000130983	ENST00000393310.1:c.46G>A	2.37:g.109276110G>A	ENSP00000376987:p.Gly16Ser	630	0	0		859	303	0.352736	NM_001193485	B2RAJ4|B7Z483|B7Z7R3|B7Z907|Q53TE0|Q9BS44	Missense_Mutation	SNP	ENST00000393310.1	37	CCDS2078.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.017490	0.75161	0.002043	0.010814	ENSG00000169756	ENST00000544547;ENST00000428064;ENST00000332345;ENST00000393310;ENST00000410093;ENST00000409441;ENST00000338045;ENST00000542845;ENST00000393314	D;D;D;D;D;D;D;D;D	0.87256	-2.23;-2.23;-2.23;-2.23;-2.23;-2.23;-2.23;-2.23;-2.23	4.63	4.63	0.57726	Zinc finger, LIM-type (5);	0.160833	0.41605	D	0.000860	T	0.81978	0.4937	L	0.45744	1.44	0.80722	D	1	P;P;B;B	0.44946	0.846;0.53;0.377;0.377	P;B;B;B	0.45195	0.473;0.124;0.087;0.087	T	0.83289	-0.0034	10	0.33141	T	0.24	.	17.6679	0.88208	0.0:0.0:1.0:0.0	.	78;53;16;28	B7Z7R3;B7Z907;P48059;B7Z483	.;.;LIMS1_HUMAN;.	S	28;28;16;16;20;53;16;78;78	ENSP00000437912:G28S;ENSP00000390862:G28S;ENSP00000331775:G16S;ENSP00000376987:G16S;ENSP00000386926:G20S;ENSP00000387264:G53S;ENSP00000337598:G16S;ENSP00000446121:G78S;ENSP00000376990:G78S	ENSP00000331775:G16S	G	+	1	0	LIMS1	108642542	1.000000	0.71417	0.842000	0.33263	0.932000	0.56968	6.498000	0.73679	2.392000	0.81423	0.563000	0.77884	GGC	G|0.994;A|0.006	0.006	strong		0.572	LIMS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253596.1	NM_004987		A	109276110	G	A	109276110	3	1	27	1	0	0	0	0	1	0	0	0	8812	1116	39	1	48	1	LIMS1	2	109276110	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	6961126	109276110	133923263	119	10570											
EN1	2019	hgsc.bcm.edu	37	chr2	119600674	119600674	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgggactcgttgaggctgAgttcctgggccagggtctgc	4	11	16	10	1	2	2	0	2	2	0	4	3	3	3	2	4	1	3	2	4	0	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:119600674A>C	ENST00000295206.6	-	2	1529	c.1019T>G	c.(1018-1020)cTc>cGc	p.L340R	EN1_ENST00000546667.1_5'Flank	NM_001426.3	NP_001417.3	Q05925	HME1_HUMAN	engrailed homeobox 1	340					anatomical structure morphogenesis (GO:0009653)|dorsal/ventral pattern formation (GO:0009953)|embryonic forelimb morphogenesis (GO:0035115)|hindbrain development (GO:0030902)|midbrain development (GO:0030901)|midbrain-hindbrain boundary development (GO:0030917)|multicellular organism growth (GO:0035264)|neuron development (GO:0048666)|pigmentation (GO:0043473)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|response to cocaine (GO:0042220)|skeletal system development (GO:0001501)	membrane (GO:0016020)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	9						GTTGAGGCTGAGTTCCTGGGC	0.612																																					p.L340R		Atlas-SNP	.											.	EN1	33	.	0			c.T1019G						PASS	.						69	63	65					2																	119600674		2203	4300	6503	SO:0001583	missense	2019	exon2			AGGCTGAGTTCCT	L12699	CCDS2123.1	2q14.2	2011-06-20	2007-02-15		ENSG00000163064	ENSG00000163064		"Homeoboxes / ANTP class : NKL subclass"	3342	protein-coding gene	gene with protein product		131290				8094370	Standard	NM_001426		Approved		uc002tlm.3	Q05925	OTTHUMG00000131401	ENST00000295206.6:c.1019T>G	2.37:g.119600674A>C	ENSP00000295206:p.Leu340Arg	89	0	0		96	33	0.34375	NM_001426	Q4ZG44	Missense_Mutation	SNP	ENST00000295206.6	37	CCDS2123.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.267128	0.80469	.	.	ENSG00000163064	ENST00000295206	D	0.98280	-4.84	4.89	4.89	0.63831	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99432	0.9799	H	0.99169	4.455	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98029	1.0375	10	0.87932	D	0	-14.1387	14.1743	0.65529	1.0:0.0:0.0:0.0	.	340	Q05925	HME1_HUMAN	R	340	ENSP00000295206:L340R	ENSP00000295206:L340R	L	-	2	0	EN1	119317144	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.330000	0.96422	1.831000	0.53308	0.454000	0.30748	CTC	.	.	none		0.612	EN1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254191.3			C	119600674	A	C	119600674	3	2	27	1	0	0	0	0	1	0	0	0	5111	304	11	5	163	5	EN1	2	119600674	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	10324564	119600674	123598699	120	10571											
SCTR	6344	hgsc.bcm.edu	37	chr2	120199139	120199139	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccaagactactcacctcccCattgaggaagcagtagagga	13	6	9	13	0	1	3	1	1	0	2	2	5	2	5	4	2	2	2	4	2	4	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:120199139C>T	ENST00000019103.5	-	12	1444	c.1177G>A	c.(1177-1179)Ggg>Agg	p.G393R		NM_002980.2	NP_002971.2	P47872	SCTR_HUMAN	secretin receptor	393					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)	CTCACCTCCCCATTGAGGAAG	0.602																																					p.G393R		Atlas-SNP	.											.	SCTR	45	.	0			c.G1177A						PASS	.						81	67	72					2																	120199139		2203	4300	6503	SO:0001583	missense	6344	exon12			CCTCCCCATTGAG		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.1177G>A	2.37:g.120199139C>T	ENSP00000019103:p.Gly393Arg	53	0	0		48	23	0.479167	NM_002980	Q12961|Q13213|Q53T00	Missense_Mutation	SNP	ENST00000019103.5	37	CCDS2127.1	.	.	.	.	.	.	.	.	.	.	C	17.75	3.466290	0.63625	.	.	ENSG00000080293	ENST00000019103	T	0.79454	-1.27	4.78	2.02	0.26589	GPCR, family 2, secretin-like, conserved site (1);	0.104147	0.42420	N	0.000703	D	0.86818	0.6024	M	0.84511	2.7	0.46654	D	0.999149	D	0.89917	1.0	D	0.83275	0.996	D	0.85446	0.1158	10	0.87932	D	0	.	8.9316	0.35675	0.0:0.7531:0.0:0.2469	.	393	P47872	SCTR_HUMAN	R	393	ENSP00000019103:G393R	ENSP00000019103:G393R	G	-	1	0	SCTR	119915609	0.823000	0.29233	0.748000	0.31131	0.800000	0.45204	1.860000	0.39428	0.237000	0.21200	-0.140000	0.14226	GGG	.	.	none		0.602	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2			T	120199139	C	T	120199139	3	4	27	1	0	0	0	0	1	0	0	0	13958	594	21	2	153	2	SCTR	2	120199139	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	598465	120199139	123000234	121	10572											
IWS1	55677	hgsc.bcm.edu	37	chr2	128244216	128244216	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccttgcacgggcacagaaTccaggatctccaggtctaag	11	7	10	13	1	2	1	0	0	2	1	4	2	3	2	3	3	1	2	3	3	2	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:128244216T>C	ENST00000295321.4	-	13	2500	c.2241A>G	c.(2239-2241)ggA>ggG	p.G747G	AC010976.2_ENST00000595561.1_RNA|AC010976.2_ENST00000454503.2_RNA|AC010976.2_ENST00000598065.1_RNA|AC010976.2_ENST00000596439.1_RNA|AC010976.2_ENST00000599001.1_RNA	NM_017969.2	NP_060439.2	Q96ST2	IWS1_HUMAN	IWS1 homolog (S. cerevisiae)	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)		GGGCACAGAATCCAGGATCTC	0.517																																					p.G747G		Atlas-SNP	.											.	IWS1	61	.	0			c.A2241G						PASS	.						96	89	91					2																	128244216		2203	4300	6503	SO:0001819	synonymous_variant	55677	exon13			ACAGAATCCAGGA	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.2241A>G	2.37:g.128244216T>C		121	0	0		142	29	0.204225	NM_017969	Q2TB65|Q6P157|Q8N3E8|Q96MI7|Q9NV97|Q9NWH8	Silent	SNP	ENST00000295321.4	37	CCDS2146.1																																																																																			.	.	none		0.517	IWS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254384.2	NM_017969		C	128244216	T	C	128244216	2	2	27	1	0	0	0	0	0	0	0	1	7940	1422	50	3		3	IWS1	2	128244216	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	8045077	128244216	114955157	122	10573											
R3HDM1	23518	hgsc.bcm.edu	37	chr2	136467084	136467084	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcaccatgcagttcccagcaGcttcaaggccaccaatgtac	11	8	7	15	0	2	0	2	0	0	0	3	0	3	0	4	1	4	5	4	1	3	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:136467084G>A	ENST00000264160.4	+	21	2806	c.2436G>A	c.(2434-2436)caG>caA	p.Q812Q	R3HDM1_ENST00000409606.1_Silent_p.Q813Q|R3HDM1_ENST00000410054.1_Silent_p.Q757Q|R3HDM1_ENST00000329971.3_Silent_p.Q683Q|R3HDM1_ENST00000409478.1_Silent_p.Q684Q	NM_001282798.1|NM_015361.2	NP_001269727.1|NP_056176.2	Q15032	R3HD1_HUMAN	R3H domain containing 1	812							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)		GTTCCCAGCAGCTTCAAGGCC	0.383																																					p.Q812Q		Atlas-SNP	.											.	R3HDM1	84	.	0			c.G2436A						PASS	.						123	107	112					2																	136467084		2203	4300	6503	SO:0001819	synonymous_variant	23518	exon21			CCAGCAGCTTCAA	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.2436G>A	2.37:g.136467084G>A		425	1	0.00235294		307	149	0.485342	NM_015361	A8K1V0|B3KXQ9|E9PBB4|E9PG42|G5E9G8|Q8IW32	Silent	SNP	ENST00000264160.4	37	CCDS2177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.684|8.684	0.905766|0.905766	0.17760|0.17760	.|.	.|.	ENSG00000048991|ENSG00000048991	ENST00000429703|ENST00000445855	.|.	.|.	.|.	5.61|5.61	4.72|4.72	0.59763|0.59763	.|.	.|.	.|.	.|.	.|.	T|T	0.60612|0.60612	0.2282|0.2282	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.57329|0.57329	-0.7830|-0.7830	4|4	.|.	.|.	.|.	0.2051|0.2051	9.5268|9.5268	0.39169|0.39169	0.0734:0.0:0.7872:0.1394|0.0734:0.0:0.7872:0.1394	.|.	.|.	.|.	.|.	T|N	536|108	.|.	.|.	A|S	+|+	1|2	0|0	R3HDM1|R3HDM1	136183554|136183554	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	2.615000|2.615000	0.46368|0.46368	2.647000|2.647000	0.89833|0.89833	0.644000|0.644000	0.83932|0.83932	GCT|AGC	.	.	none		0.383	R3HDM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254659.1	NM_015361		A	136467084	G	A	136467084	2	1	27	1	0	0	0	0	0	0	0	1	12902	962	34	2		2	R3HDM1	2	136467084	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	8222868	136467084	106732289	123	10574											
LCT	3938	hgsc.bcm.edu	37	chr2	136547204	136547204	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagccattgcatcggaccaCagaggcgtagaacttcgctg	11	7	12	11	3	0	2	0	0	0	2	2	4	0	3	2	2	3	3	2	2	3	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:136547204C>T	ENST00000264162.2	-	16	5510	c.5500G>A	c.(5500-5502)Gtg>Atg	p.V1834M		NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	1834	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)	CATCGGACCACAGAGGCGTAG	0.552																																					p.V1834M		Atlas-SNP	.											.	LCT	309	.	0			c.G5500A						PASS	.						102	96	98					2																	136547204		2203	4300	6503	SO:0001583	missense	3938	exon16			GGACCACAGAGGC	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.5500G>A	2.37:g.136547204C>T	ENSP00000264162:p.Val1834Met	156	0	0		101	32	0.316832	NM_002299	Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	37	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	C	14.22	2.469955	0.43839	.	.	ENSG00000115850	ENST00000264162	T	0.37752	1.18	5.74	-4.63	0.03359	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.267610	0.39687	N	0.001286	T	0.25344	0.0616	L	0.33792	1.035	0.09310	N	1	B	0.24092	0.097	B	0.32624	0.149	T	0.29366	-1.0014	10	0.87932	D	0	-3.5549	10.4645	0.44600	0.0:0.1835:0.0967:0.7198	.	1834	P09848	LPH_HUMAN	M	1834	ENSP00000264162:V1834M	ENSP00000264162:V1834M	V	-	1	0	LCT	136263674	0.000000	0.05858	0.001000	0.08648	0.814000	0.46013	-0.379000	0.07437	-0.868000	0.04058	0.563000	0.77884	GTG	.	.	none		0.552	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		T	136547204	C	T	136547204	3	4	27	1	0	0	0	0	1	0	0	0	8702	478	17	2	291	2	LCT	2	136547204	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	80120	136547204	106652169	124	10575											
RIF1	55183	hgsc.bcm.edu	37	chr2	152311612	152311612	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcatatttctttgccttctAtgatccgaaaaatatttgca	11	16	6	8	1	2	1	0	1	2	0	3	2	3	1	2	1	2	2	2	1	5	7	rs61750444	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:152311612A>G	ENST00000243326.5	+	21	3031	c.2548A>G	c.(2548-2550)Atg>Gtg	p.M850V	RIF1_ENST00000453091.2_Missense_Mutation_p.M850V|RIF1_ENST00000430328.2_Missense_Mutation_p.M850V|RIF1_ENST00000428287.2_Missense_Mutation_p.M850V|RIF1_ENST00000444746.2_Missense_Mutation_p.M850V			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)		TTTGCCTTCTATGATCCGAAA	0.353													A|||	85	0.0169728	0.0371	0.0072	5008	,	,		17680	0.0		0.0268	False		,,,				2504	0.0041				p.M850V		Atlas-SNP	.											RIF1,NS,carcinoma,-2,1	RIF1	244	1	0			c.A2548G						scavenged	.	A	VAL/MET,VAL/MET,VAL/MET,VAL/MET	156,4250	106.0+/-144.5	5,146,2052	109	108	108		2548,2548,2548,2548	-1.1	1	2	dbSNP_129	108	167,8433	78.4+/-141.0	2,163,4135	yes	missense,missense,missense,missense	RIF1	NM_001177663.1,NM_001177664.1,NM_001177665.1,NM_018151.4	21,21,21,21	7,309,6187	GG,GA,AA		1.9419,3.5406,2.4835	benign,benign,benign,benign	850/2447,850/2447,850/2447,850/2473	152311612	323,12683	2203	4300	6503	SO:0001583	missense	55183	exon22			CCTTCTATGATCC	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.2548A>G	2.37:g.152311612A>G	ENSP00000243326:p.Met850Val	179	1	0.00558659		143	76	0.531469	NM_018151	A0AVS0|Q9NS16	Missense_Mutation	SNP	ENST00000243326.5	37	CCDS2194.1	48|48	0.02197802197802198|0.02197802197802198	22|22	0.044715447154471545|0.044715447154471545	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	24|24	0.0316622691292876|0.0316622691292876	A|A	1.477|1.477	-0.558248|-0.558248	0.03967|0.03967	0.035406|0.035406	0.019419|0.019419	ENSG00000080345|ENSG00000080345	ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000430328|ENST00000414861	T;T;T;T;T|.	0.63744|.	-0.06;-0.06;-0.06;-0.06;-0.06|.	5.55|5.55	-1.09|-1.09	0.09904|0.09904	.|.	0.463720|.	0.26324|.	N|.	0.025028|.	T|T	0.19644|0.19644	0.0472|0.0472	L|L	0.38838|0.38838	1.175|1.175	0.80722|0.80722	D|D	1|1	B;B|.	0.06786|.	0.001;0.001|.	B;B|.	0.04013|.	0.001;0.001|.	T|T	0.16012|0.16012	-1.0417|-1.0417	10|5	0.11794|.	T|.	0.64|.	-3.1534|-3.1534	11.2086|11.2086	0.48784|0.48784	0.4305:0.0:0.5695:0.0|0.4305:0.0:0.5695:0.0	rs61750444|rs61750444	850;850|.	Q5UIP0;Q5UIP0-2|.	RIF1_HUMAN;.|.	V|C	850|841	ENSP00000390181:M850V;ENSP00000414615:M850V;ENSP00000415691:M850V;ENSP00000243326:M850V;ENSP00000416123:M850V|.	ENSP00000243326:M850V|.	M|Y	+|+	1|2	0|0	RIF1|RIF1	152019858|152019858	0.939000|0.939000	0.31865|0.31865	0.997000|0.997000	0.53966|0.53966	0.982000|0.982000	0.71751|0.71751	0.435000|0.435000	0.21510|0.21510	-0.136000|-0.136000	0.11475|0.11475	0.533000|0.533000	0.62120|0.62120	ATG|TAT	A|0.976;G|0.024	0.024	strong		0.353	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3			G	152311612	A	G	152311612	3	3	27	1	0	0	0	0	1	0	0	0	13374	449	16	3	2630	3	RIF1	2	152311612	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	15764408	152311612	90887761	125	10576											
NEB	4703	hgsc.bcm.edu	37	chr2	152382759	152382759	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gttcctctttccttgacatgTttctctttgtatttcagctt	4	22	5	10	0	3	1	1	1	2	0	6	1	5	1	2	0	1	4	2	0	1	8	rs61730765	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:152382759T>C	ENST00000172853.10	-	121	17007	c.16860A>G	c.(16858-16860)aaA>aaG	p.K5620K	NEB_ENST00000427231.2_Silent_p.K7321K|NEB_ENST00000409198.1_Silent_p.K5620K|NEB_ENST00000397345.3_Silent_p.K7321K|NEB_ENST00000603639.1_Silent_p.K7321K|NEB_ENST00000604864.1_Silent_p.K7321K			P20929	NEBU_HUMAN	nebulin	5620					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)		CCTTGACATGTTTCTCTTTGT	0.488													T|||	107	0.0213658	0.0537	0.0072	5008	,	,		16984	0.0		0.0268	False		,,,				2504	0.0041				p.K7356K		Atlas-SNP	.											.	NEB	1697	.	0			c.A22068G						PASS	.	T	,,	176,3694		7,162,1766	64	65	65		21963,21963,16860	-3.7	1	2	dbSNP_129	65	159,8093		2,155,3969	no	coding-synonymous,coding-synonymous,coding-synonymous	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	,,	9,317,5735	CC,CT,TT		1.9268,4.5478,2.7636	,,	7321/8526,7321/8526,5620/6670	152382759	335,11787	1935	4126	6061	SO:0001819	synonymous_variant	4703	exon150			GACATGTTTCTCT	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.16860A>G	2.37:g.152382759T>C		130	0	0		103	47	0.456311	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				T|0.975;C|0.025	0.025	strong		0.488	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		C	152382759	T	C	152382759	2	2	27	1	0	0	0	0	0	0	0	1	10311	1722	60	3		3	NEB	2	152382759	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	71147	152382759	90816614	126	10577											
NEB	4703	hgsc.bcm.edu	37	chr2	152389991	152389991	+	Intron	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgaattgtagagagcagtcaAcatatctggacgcagaattt	14	10	10	7	2	2	2	1	0	1	2	2	5	2	3	0	1	2	3	0	1	5	4	rs114218081	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:152389991A>G	ENST00000172853.10	-	115	16462				NEB_ENST00000427231.2_Intron|NEB_ENST00000409198.1_Intron|NEB_ENST00000397345.3_Silent_p.L7128L|NEB_ENST00000603639.1_Silent_p.L7128L|NEB_ENST00000604864.1_Intron			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)		AGAGCAGTCAACATATCTGGA	0.413													A|||	88	0.0175719	0.0393	0.0072	5008	,	,		22891	0.0		0.0268	False		,,,				2504	0.0041				p.L7163L		Atlas-SNP	.											.	NEB	1697	.	0			c.T21487C						PASS	.	A	,,	55,1329		3,49,640	218	170	185		,21382,	6.2	1	2	dbSNP_132	185	66,3116		0,66,1525	no	intron,coding-synonymous,intron	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	,,	3,115,2165	GG,GA,AA		2.0742,3.974,2.65	,,	,7128/8526,	152389991	121,4445	692	1591	2283	SO:0001627	intron_variant	4703	exon144			CAGTCAACATATC	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.16314+737T>C	2.37:g.152389991A>G		127	0	0		102	46	0.45098	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				A|0.979;G|0.021	0.021	strong		0.413	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		G	152389991	A	G	152389991	1	3	27	0	1	0	0	0	0	0	0	0	10311	40	2	3		3	NEB	2	152389991	Intron	SNP	A	TCGA-G8-6909-01A-11D-2210-10	7232	152389991	90809382	127	10578											
CACNB4	785	hgsc.bcm.edu	37	chr2	152955482	152955482	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctgcgaggtgggggagtgcGgcccgtccgcggtcccgttc	2	7	18	14	6	0	0	0	0	0	0	3	2	2	1	4	5	2	1	4	5	0	1	rs200662010	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:152955482G>C	ENST00000539935.1	-	1	111	c.44C>G	c.(43-45)cCg>cGg	p.P15R	AC079790.2_ENST00000420365.1_RNA|CACNB4_ENST00000201943.5_Missense_Mutation_p.P15R|CACNB4_ENST00000427385.1_5'Flank	NM_000726.3|NM_001145798.1	NP_000717.2|NP_001139270.1	O00305	CACB4_HUMAN	calcium channel, voltage-dependent, beta 4 subunit	15					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)	GGGGGAGTGCGGCCCGTCCGC	0.721													G|||	2	0.000399361	0.0	0.0029	5008	,	,		9469	0.0		0.0	False		,,,				2504	0.0				p.P15R		Atlas-SNP	.											.	CACNB4	108	.	0			c.C44G						PASS	.	G	ARG/PRO,ARG/PRO	4,3898		0,4,1947	11	16	14		44,44	-0.1	1	2		14	26,8102		0,26,4038	yes	missense,missense	CACNB4	NM_000726.3,NM_001145798.1	103,103	0,30,5985	CC,CG,GG		0.3199,0.1025,0.2494	benign,benign	15/521,15/459	152955482	30,12000	1951	4064	6015	SO:0001583	missense	785	exon1			GAGTGCGGCCCGT	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.44C>G	2.37:g.152955482G>C	ENSP00000438949:p.Pro15Arg	117	0	0		124	61	0.491935	NM_001145798	A7BJ74|A8K1Y4|B4DG40|O60515|Q6B000|Q96L40	Missense_Mutation	SNP	ENST00000539935.1	37	CCDS46426.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	4.250	0.045444	0.08196	0.001025	0.003199	ENSG00000182389	ENST00000539935;ENST00000201943;ENST00000339254	T;T	0.71461	-0.57;-0.57	4.55	-0.0829	0.13696	.	0.952431	0.08719	N	0.903787	T	0.49321	0.1550	N	0.14661	0.345	0.80722	D	1	B;B	0.20671	0.0;0.047	B;B	0.19148	0.0;0.024	T	0.36962	-0.9726	10	0.52906	T	0.07	-4.6977	4.2846	0.10848	0.0937:0.2947:0.4771:0.1345	.	15;15	A7BJ74;O00305	.;CACB4_HUMAN	R	15	ENSP00000438949:P15R;ENSP00000201943:P15R	ENSP00000201943:P15R	P	-	2	0	CACNB4	152663728	0.980000	0.34600	0.997000	0.53966	0.024000	0.10985	-0.208000	0.09371	0.025000	0.15241	-0.176000	0.13171	CCG	G|1.000;C|0.000	0.000	strong		0.721	CACNB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000338385.4	NM_000726.3		C	152955482	G	C	152955482	3	2	27	1	0	0	0	0	1	0	0	0	2557	1116	39	4	1636	4	CACNB4	2	152955482	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	565491	152955482	90243891	128	10579											
FMNL2	114793	hgsc.bcm.edu	37	chr2	153378487	153378487	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctacctcctgacaaagccAggttactgcggcagtatgat	11	9	9	12	1	0	2	0	2	0	0	1	2	1	2	4	2	4	3	4	2	4	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:153378487A>T	ENST00000288670.9	+	2	515	c.148A>T	c.(148-150)Agg>Tgg	p.R50W		NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	50	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						TGACAAAGCCAGGTTACTGCG	0.363																																					p.R50W		Atlas-SNP	.											.	FMNL2	75	.	0			c.A148T						PASS	.						84	80	81					2																	153378487		1847	4093	5940	SO:0001583	missense	114793	exon2			AAAGCCAGGTTAC	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.148A>T	2.37:g.153378487A>T	ENSP00000288670:p.Arg50Trp	127	0	0		107	21	0.196262	NM_052905	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Missense_Mutation	SNP	ENST00000288670.9	37	CCDS46429.1	.	.	.	.	.	.	.	.	.	.	A	17.49	3.402207	0.62288	.	.	ENSG00000157827	ENST00000288670	D	0.90261	-2.64	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	D	0.94918	0.8357	M	0.73962	2.25	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.95337	0.8435	10	0.87932	D	0	.	15.3697	0.74554	1.0:0.0:0.0:0.0	.	50	Q96PY5-3	.	W	50	ENSP00000288670:R50W	ENSP00000288670:R50W	R	+	1	2	FMNL2	153086733	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.999000	0.57031	2.270000	0.75569	0.482000	0.46254	AGG	.	.	none		0.363	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905		T	153378487	A	T	153378487	3	4	27	1	0	0	0	0	1	0	0	0	5960	179	7	5	154	5	FMNL2	2	153378487	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	423005	153378487	89820886	129	10580											
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160241785	160241785	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttcagtaagctcagtttgTccacagtgggcttccataaa	10	13	8	10	0	2	0	2	0	0	0	4	0	4	0	2	1	1	4	2	1	3	5	rs372315034		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:160241785T>C	ENST00000392783.2	-	23	4062	c.3567A>G	c.(3565-3567)ggA>ggG	p.G1189G	BAZ2B_ENST00000392782.1_Silent_p.G1153G|AC008277.1_ENST00000420020.1_RNA|BAZ2B_ENST00000355831.2_Silent_p.G1155G|BAZ2B_ENST00000343439.5_Silent_p.G1089G	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	1189					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						GCTCAGTTTGTCCACAGTGGG	0.428													T|||	1	0.000199681	0.0	0.0	5008	,	,		15755	0.0		0.001	False		,,,				2504	0.0				p.G1189G		Atlas-SNP	.											.	BAZ2B	196	.	0			c.A3567G						PASS	.	T		2,3722		0,2,1860	120	117	118		3567	2	1	2		118	12,8192		0,12,4090	no	coding-synonymous	BAZ2B	NM_013450.2		0,14,5950	CC,CT,TT		0.1463,0.0537,0.1174		1189/2169	160241785	14,11914	1862	4102	5964	SO:0001819	synonymous_variant	29994	exon23			AGTTTGTCCACAG	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.3567A>G	2.37:g.160241785T>C		96	0	0		135	60	0.444444	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Silent	SNP	ENST00000392783.2	37	CCDS2209.2																																																																																			.	.	weak		0.428	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			C	160241785	T	C	160241785	2	2	27	1	0	0	0	0	0	0	0	1	1332	1654	58	3		3	BAZ2B	2	160241785	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	6863298	160241785	82957588	130	10581											
LY75	4065	hgsc.bcm.edu	37	chr2	160732019	160732019	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gacaggggtcatcaggcttaGgggatgcttcttcaggccca	8	9	14	10	0	4	0	3	0	1	0	4	2	4	1	1	6	1	2	1	6	1	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:160732019G>C	ENST00000263636.4	-	12	1937	c.1910C>G	c.(1909-1911)cCt>cGt	p.P637R	LY75-CD302_ENST00000504764.1_Missense_Mutation_p.P637R|LY75_ENST00000554112.1_Missense_Mutation_p.P637R|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.P637R|LY75_ENST00000553424.1_Missense_Mutation_p.P637R	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	637					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)		ATCAGGCTTAGGGGATGCTTC	0.463																																					p.P637R		Atlas-SNP	.											.	LY75	151	.	0			c.C1910G						PASS	.						119	126	123					2																	160732019		2203	4300	6503	SO:0001583	missense	4065	exon12			GGCTTAGGGGATG	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.1910C>G	2.37:g.160732019G>C	ENSP00000263636:p.Pro637Arg	123	0	0		99	58	0.585859	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	G	18.02	3.529779	0.64860	.	.	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.08720	3.06;3.06;3.06;3.06;3.06	4.77	4.77	0.60923	C-type lectin-like (1);	0.000000	0.34959	N	0.003545	T	0.27384	0.0672	M	0.64630	1.985	0.80722	D	1	D;D;D;D	0.89917	0.983;1.0;1.0;1.0	D;D;D;D	0.97110	0.928;1.0;0.999;0.999	T	0.01033	-1.1474	10	0.66056	D	0.02	-9.9671	16.9332	0.86196	0.0:0.0:1.0:0.0	.	255;637;637;637	Q59H44;O60449-3;O60449;O60449-2	.;.;LY75_HUMAN;.	R	637	ENSP00000451511:P637R;ENSP00000451446:P637R;ENSP00000263636:P637R;ENSP00000423463:P637R;ENSP00000421035:P637R	ENSP00000423463:P637R	P	-	2	0	LY75;LY75-CD302	160440265	1.000000	0.71417	0.987000	0.45799	0.952000	0.60782	4.393000	0.59665	2.356000	0.79943	0.455000	0.32223	CCT	.	.	none		0.463	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1			C	160732019	G	C	160732019	3	2	27	1	0	0	0	0	1	0	0	0	9108	1000	35	4	3354	4	LY75	2	160732019	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	490234	160732019	82467354	131	10582											
DPP4	1803	hgsc.bcm.edu	37	chr2	162876789	162876789	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgacttcccaggtgcctttTgtaataaatgtgcagtcctg	9	14	9	9	0	0	1	0	1	0	0	2	1	2	1	3	1	2	2	3	1	3	5	rs200990780		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:162876789T>C	ENST00000360534.3	-	14	1754	c.1194A>G	c.(1192-1194)acA>acG	p.T398T	DPP4_ENST00000491591.1_5'Flank	NM_001935.3	NP_001926.2	P27487	DPP4_HUMAN	dipeptidyl-peptidase 4	398					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)	AGGTGCCTTTTGTAATAAATG	0.323																																					p.T398T		Atlas-SNP	.											.	DPP4	90	.	0			c.A1194G						PASS	.						95	90	92					2																	162876789		2203	4300	6503	SO:0001819	synonymous_variant	1803	exon14			GCCTTTTGTAATA	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.1194A>G	2.37:g.162876789T>C		85	0	0		73	35	0.479452	NM_001935	Q53TN1	Silent	SNP	ENST00000360534.3	37	CCDS2216.1																																																																																			.	.	weak		0.323	DPP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255079.2			C	162876789	T	C	162876789	2	2	27	1	0	0	0	0	0	0	0	1	4731	1799	63	3		3	DPP4	2	162876789	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	2144770	162876789	80322584	132	10583											
FIGN	55137	hgsc.bcm.edu	37	chr2	164467750	164467750	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggtgctggctggctactatAagtagaatgcaaatatgatc	13	11	11	6	0	0	2	0	1	0	1	1	2	0	2	0	3	3	5	0	3	7	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:164467750A>T	ENST00000333129.3	-	3	906	c.592T>A	c.(592-594)Tat>Aat	p.Y198N	FIGN_ENST00000409634.1_Intron|FIGN_ENST00000482917.1_5'Flank	NM_018086.2	NP_060556.2	Q5HY92	FIGN_HUMAN	fidgetin	198					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						TGGCTACTATAAGTAGAATGC	0.537																																					p.Y198N		Atlas-SNP	.											.	FIGN	106	.	0			c.T592A						PASS	.						70	76	74					2																	164467750		2038	4192	6230	SO:0001583	missense	55137	exon3			TACTATAAGTAGA	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.592T>A	2.37:g.164467750A>T	ENSP00000333836:p.Tyr198Asn	120	0	0		105	30	0.285714	NM_018086	B3KWM0|Q9H6M5|Q9NVZ9	Missense_Mutation	SNP	ENST00000333129.3	37	CCDS2221.2	.	.	.	.	.	.	.	.	.	.	A	17.94	3.511293	0.64522	.	.	ENSG00000182263	ENST00000333129	T	0.40225	1.04	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.60689	0.2288	M	0.66939	2.045	0.80722	D	1	D	0.69078	0.997	P	0.60789	0.879	T	0.60510	-0.7249	10	0.48119	T	0.1	-9.4916	16.8061	0.85666	1.0:0.0:0.0:0.0	.	198	Q5HY92	FIGN_HUMAN	N	198	ENSP00000333836:Y198N	ENSP00000333836:Y198N	Y	-	1	0	FIGN	164175996	1.000000	0.71417	0.972000	0.41901	0.984000	0.73092	9.339000	0.96797	2.367000	0.80283	0.528000	0.53228	TAT	.	.	none		0.537	FIGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157220.2	NM_018086		T	164467750	A	T	164467750	3	4	27	1	0	0	0	0	1	0	0	0	5899	362	13	5	1691	5	FIGN	2	164467750	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	1590961	164467750	78731623	133	10584											
TTC21B	79809	hgsc.bcm.edu	37	chr2	166771842	166771842	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgcttaaagcccgttcaatAtctccttgggctagagcaag	11	11	9	10	1	2	1	1	0	1	1	3	1	2	1	2	1	3	4	2	1	6	5	rs138449110		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:166771842A>G	ENST00000243344.7	-	15	2144	c.2007T>C	c.(2005-2007)gaT>gaC	p.D669D		NM_024753.4	NP_079029.3	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	669				D -> G (in Ref. 4; BAB71404). {ECO:0000305}.	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						CCCGTTCAATATCTCCTTGGG	0.413																																					p.D669D		Atlas-SNP	.											.	TTC21B	130	.	0			c.T2007C						PASS	.	A		0,4406		0,0,2203	153	154	154		2007	0.6	0.6	2	dbSNP_134	154	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TTC21B	NM_024753.3		0,2,6501	GG,GA,AA		0.0233,0.0,0.0154		669/1317	166771842	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	79809	exon15			TTCAATATCTCCT	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.2007T>C	2.37:g.166771842A>G		74	0	0		86	37	0.430233	NM_024753	A8MUZ3|Q3LIE4|Q53T84|Q6P4A1|Q6PIF5|Q8NCN3|Q96MA4|Q9HAK8	Silent	SNP	ENST00000243344.7	37	CCDS33315.1																																																																																			A|1.000;G|0.000	0.000	weak		0.413	TTC21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333770.1	NM_024753		G	166771842	A	G	166771842	2	3	27	1	0	0	0	0	0	0	0	1	16703	446	16	3		3	TTC21B	2	166771842	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	2304092	166771842	76427531	134	10585											
SCN9A	6335	hgsc.bcm.edu	37	chr2	167144980	167144980	+	Frame_Shift_Del	DEL	T	T	-																															tgctcttttttaagacggtcTaacatctgttgaaattctaa																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:167144980delT	ENST00000409435.1	-	9	1280	c.1281delA	c.(1279-1281)ttafs	p.L427fs	SCN9A_ENST00000375387.4_Frame_Shift_Del_p.L428fs|AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Frame_Shift_Del_p.L428fs|SCN9A_ENST00000409672.1_Frame_Shift_Del_p.L427fs			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	427					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)	TAAGACGGTCTAACATCTGTT	0.383																																					p.D428fs		Atlas-Indel	.											.	SCN9A	296	.	0			c.1282delG						PASS	.						146	154	151					2																	167144980		1841	4092	5933	SO:0001589	frameshift_variant	6335	exon10			.	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.1281delA	2.37:g.167144980delT	ENSP00000386330:p.Leu427fs	78	0	0		79	12	0.151899	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Frame_Shift_Del	DEL	ENST00000409435.1	37	CCDS46441.1																																																																																			.	.	none		0.383	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		-	167144980	T	-	167144980	7	5	27	1	0	1	0	1	0	0	0	0	13940	1519	53	0	4724	0	SCN9A	2	167144980	Frame_Shift_Del	DEL	T	TCGA-G8-6909-01A-11D-2210-10	373138	167144980	76054393	135	10586											
FASTKD1	79675	hgsc.bcm.edu	37	chr2	170387132	170387133	+	Frame_Shift_Ins	INS	-	-	T																															cccagaatttccaaatgtcgINSttttttcatagcagattttc																								rs148187838|rs566862006	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:170387132_170387133insT	ENST00000453153.2	-	14	2752_2753	c.2406_2407insA	c.(2404-2409)aaacgafs	p.R803fs	FASTKD1_ENST00000495505.1_5'UTR|FASTKD1_ENST00000453929.2_Frame_Shift_Ins_p.R760fs	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	803	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						TCCAAATGTCGTTTTTTCATAG	0.342													TTTTTT|TTTTTT|TTTTTTT|insertion	18	0.00359425	0.0008	0.0029	5008	,	,		15503	0.0		0.007	False		,,,				2504	0.0082				p.R803fs		Pindel,Atlas-Indel	.											.	FASTKD1	86	.	0			c.2407_2408insA						PASS	.			8,4258		0,8,2125						3.3	1			159	99,8155		1,97,4029	no	frameshift	FASTKD1	NM_024622.3		1,105,6154	A1A1,A1R,RR		1.1994,0.1875,0.8546				107,12413				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.2407dupA	2.37:g.170387138_170387138dupT	ENSP00000400513:p.Arg803fs	213	0	.		206	69	0.335	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Frame_Shift_Ins	INS	ENST00000453153.2	37	CCDS33318.1																																																																																			.	.	none		0.342	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622		T	170387133	-	T	170387132	7	5	27	1	0	1	1	0	0	0	0	0	5693	1153	40	0	144	0	FASTKD1	2	170387132	Frame_Shift_Ins	INS	-	TCGA-G8-6909-01A-11D-2210-10	3242152	170387132	72812241	136	10587											
FASTKD1	79675	hgsc.bcm.edu	37	chr2	170403106	170403106	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggtcacactgtggtaaaacGgcttcaattcgggatatccc	11	10	10	10	2	2	0	2	0	0	0	4	1	3	1	1	4	1	2	1	4	4	4	rs16857030	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:170403106G>A	ENST00000453153.2	-	8	1669	c.1323C>T	c.(1321-1323)gcC>gcT	p.A441A	FASTKD1_ENST00000453929.2_Silent_p.A441A	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	441					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						GTGGTAAAACGGCTTCAATTC	0.428													G|||	494	0.0986422	0.2496	0.0764	5008	,	,		19180	0.003		0.0636	False		,,,				2504	0.045				p.A441A		Atlas-SNP	.											.	FASTKD1	86	.	0			c.C1323T						PASS	.	G		878,3528	338.9+/-305.5	90,698,1415	70	72	72		1323	-1.6	0.9	2	dbSNP_123	72	483,8117	139.5+/-196.2	10,463,3827	no	coding-synonymous	FASTKD1	NM_024622.3		100,1161,5242	AA,AG,GG		5.6163,19.9274,10.4644		441/848	170403106	1361,11645	2203	4300	6503	SO:0001819	synonymous_variant	79675	exon8			TAAAACGGCTTCA	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.1323C>T	2.37:g.170403106G>A		225	0	0		220	92	0.418182	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Silent	SNP	ENST00000453153.2	37	CCDS33318.1																																																																																			G|0.902;A|0.098	0.098	strong		0.428	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622		A	170403106	G	A	170403106	2	1	27	1	0	0	0	0	0	0	0	1	5693	1103	39	1		1	FASTKD1	2	170403106	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	15974	170403106	72796267	137	10588											
GAD1	2571	hgsc.bcm.edu	37	chr2	171716266	171716266	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atggagtcaggtacgaccatGgttggctaccagccccaagg	10	7	13	11	1	1	0	1	0	0	0	1	2	1	1	4	5	3	3	4	5	3	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:171716266G>C	ENST00000358196.3	+	17	2209	c.1659G>C	c.(1657-1659)atG>atC	p.M553I		NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	553					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						GTACGACCATGGTTGGCTACC	0.493																																					p.M553I		Atlas-SNP	.											.	GAD1	79	.	0			c.G1659C						PASS	.						78	71	73					2																	171716266		2203	4300	6503	SO:0001583	missense	2571	exon17			GACCATGGTTGGC		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.1659G>C	2.37:g.171716266G>C	ENSP00000350928:p.Met553Ile	99	0	0		90	19	0.211111	NM_000817	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Missense_Mutation	SNP	ENST00000358196.3	37	CCDS2239.1	.	.	.	.	.	.	.	.	.	.	G	26.9	4.785893	0.90282	.	.	ENSG00000128683	ENST00000358196	T	0.36520	1.25	5.47	5.47	0.80525	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	T	0.63803	0.2542	M	0.93328	3.405	0.80722	D	1	P	0.50528	0.936	P	0.51016	0.656	T	0.74914	-0.3502	10	0.87932	D	0	-23.7109	19.6956	0.96023	0.0:0.0:1.0:0.0	.	553	Q99259	DCE1_HUMAN	I	553	ENSP00000350928:M553I	ENSP00000350928:M553I	M	+	3	0	GAD1	171424512	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.420000	0.97426	2.729000	0.93468	0.585000	0.79938	ATG	.	.	none		0.493	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2			C	171716266	G	C	171716266	3	2	27	1	0	0	0	0	1	0	0	0	6187	1348	47	4	1762	4	GAD1	2	171716266	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1313160	171716266	71483107	138	10589											
MTX2	10651	hgsc.bcm.edu	37	chr2	177194090	177194090	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatcatattttggcctatcAaaaacagtgggaagtcaaac	16	10	8	7	0	3	0	3	0	0	0	3	2	3	1	1	2	2	0	1	2	7	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:177194090A>G	ENST00000249442.6	+	8	690	c.479A>G	c.(478-480)cAa>cGa	p.Q160R	MTX2_ENST00000443241.1_Missense_Mutation_p.Q104R|MTX2_ENST00000392529.2_Missense_Mutation_p.Q150R	NM_006554.4	NP_006545.1	O75431	MTX2_HUMAN	metaxin 2	160					cellular protein metabolic process (GO:0044267)|mitochondrial transport (GO:0006839)|protein targeting to mitochondrion (GO:0006626)	mitochondrial outer membrane (GO:0005741)				breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(117;0.00365)|Epithelial(96;0.0654)|all cancers(119;0.181)			TTGGCCTATCAAAAACAGTGG	0.403																																					p.Q160R		Atlas-SNP	.											.	MTX2	25	.	0			c.A479G						PASS	.						110	109	110					2																	177194090		2203	4300	6503	SO:0001583	missense	10651	exon8			CCTATCAAAAACA	AF053551	CCDS2272.1	2q31.1	2012-02-07			ENSG00000128654	ENSG00000128654			7506	protein-coding gene	gene with protein product		608555				10381257, 17624330	Standard	NM_006554		Approved		uc002ukx.3	O75431	OTTHUMG00000132514	ENST00000249442.6:c.479A>G	2.37:g.177194090A>G	ENSP00000249442:p.Gln160Arg	219	0	0		222	111	0.5	NM_006554	A8JZZ4|Q53S50|Q53SQ2|Q5M7Z6|Q8IZ68	Missense_Mutation	SNP	ENST00000249442.6	37	CCDS2272.1	.	.	.	.	.	.	.	.	.	.	A	10.81	1.456513	0.26161	.	.	ENSG00000128654	ENST00000249442;ENST00000392529;ENST00000443241	T;T;T	0.41758	0.99;0.99;0.99	5.19	5.19	0.71726	Glutathione S-transferase, C-terminal-like (1);	0.059658	0.64402	D	0.000001	T	0.26376	0.0644	N	0.17594	0.5	0.58432	D	0.999999	B;B	0.14012	0.002;0.009	B;B	0.09377	0.004;0.003	T	0.08700	-1.0709	10	0.09843	T	0.71	-0.1211	15.031	0.71708	1.0:0.0:0.0:0.0	.	160;150	O75431;Q8IZ68	MTX2_HUMAN;.	R	160;150;104	ENSP00000249442:Q160R;ENSP00000376314:Q150R;ENSP00000414176:Q104R	ENSP00000249442:Q160R	Q	+	2	0	MTX2	176902336	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	9.172000	0.94808	1.948000	0.56530	0.455000	0.32223	CAA	.	.	none		0.403	MTX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255695.4	NM_006554		G	177194090	A	G	177194090	3	3	27	1	0	0	0	0	1	0	0	0	9977	130	5	3	509	3	MTX2	2	177194090	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	5477824	177194090	66005283	139	10590											
TTC30A	92104	hgsc.bcm.edu	37	chr2	178482771	178482771	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacctagctcaggatgctggCggatgccacgctcaataatc	10	8	10	13	2	2	0	2	0	0	0	3	2	2	2	2	3	3	3	2	3	3	2	rs59353759	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:178482771C>T	ENST00000355689.5	-	1	923	c.659G>A	c.(658-660)cGc>cAc	p.R220H	AC073834.3_ENST00000357045.4_RNA	NM_152275.3	NP_689488.3	Q86WT1	TT30A_HUMAN	tetratricopeptide repeat domain 30A	220					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)			AGGATGCTGGCGGATGCCACG	0.542													C|||	171	0.0341454	0.0408	0.013	5008	,	,		21101	0.0109		0.0199	False		,,,				2504	0.0787				p.R220H		Atlas-SNP	.											.	TTC30A	60	.	0			c.G659A						PASS	.	C	HIS/ARG	184,4222	119.6+/-157.3	4,176,2023	71	70	70		659	5.8	1	2	dbSNP_129	70	154,8446	73.8+/-136.5	2,150,4148	no	missense	TTC30A	NM_152275.3	29	6,326,6171	TT,TC,CC		1.7907,4.1761,2.5988	benign	220/666	178482771	338,12668	2203	4300	6503	SO:0001583	missense	92104	exon1			TGCTGGCGGATGC	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.659G>A	2.37:g.178482771C>T	ENSP00000347915:p.Arg220His	161	0	0		166	81	0.487952	NM_152275	A8K8N0|Q8IVP2	Missense_Mutation	SNP	ENST00000355689.5	37	CCDS2276.1	40	0.018315018315018316	14	0.028455284552845527	7	0.019337016574585635	5	0.008741258741258742	14	0.018469656992084433	C	11.45	1.642016	0.29157	0.041761	0.017907	ENSG00000197557	ENST00000355689	T	0.21543	2.0	5.78	5.78	0.91487	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.138754	0.64402	D	0.000006	T	0.05731	0.0150	M	0.71920	2.185	0.51482	D	0.99992	B	0.28512	0.214	B	0.21917	0.037	T	0.01626	-1.1309	10	0.59425	D	0.04	.	9.433	0.38622	0.0:0.8764:0.0:0.1236	rs59353759;rs61997200	220	Q86WT1	TT30A_HUMAN	H	220	ENSP00000347915:R220H	ENSP00000347915:R220H	R	-	2	0	TTC30A	178191017	1.000000	0.71417	1.000000	0.80357	0.692000	0.40212	2.932000	0.48940	2.755000	0.94549	0.549000	0.68633	CGC	C|0.974;T|0.026	0.026	strong		0.542	TTC30A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255728.2	NM_152275		T	178482771	C	T	178482771	3	4	27	1	0	0	0	0	1	0	0	0	16713	768	27	1	1342	1	TTC30A	2	178482771	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1288681	178482771	64716602	140	10591											
PDE11A	50940	hgsc.bcm.edu	37	chr2	178528641	178528641	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	aatccactccagttgcaaccGaggcagttcatccttccggt	9	10	8	14	2	1	0	1	0	0	0	5	1	5	0	5	2	2	4	5	2	2	3	rs61306957	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:178528641G>C	ENST00000286063.6	-	19	2916	c.2599C>G	c.(2599-2601)Cgg>Ggg	p.R867G	PDE11A_ENST00000450799.2_Missense_Mutation_p.R58G|PDE11A_ENST00000358450.4_Missense_Mutation_p.R617G|PDE11A_ENST00000389683.3_Missense_Mutation_p.R423G|PDE11A_ENST00000409504.1_Missense_Mutation_p.R509G|PDE11A_ENST00000449286.2_Missense_Mutation_p.R509G	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	867	Catalytic. {ECO:0000250}.		R -> G (in dbSNP:rs61306957). {ECO:0000269|PubMed:16767104}.		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)	AGTTGCAACCGAGGCAGTTCA	0.453									Primary Pigmented Nodular Adrenocortical Disease, Familial				G|||	160	0.0319489	0.0393	0.0115	5008	,	,		18868	0.0109		0.0199	False		,,,				2504	0.0706				p.R867G		Atlas-SNP	.											.	PDE11A	283	.	0			c.C2599G	GRCh37	CM067442	PDE11A	M	rs61306957	PASS	.	G	GLY/ARG,GLY/ARG,GLY/ARG,GLY/ARG	190,4216	122.1+/-159.5	5,180,2018	114	100	104		1267,1849,1525,2599	4.1	1	2	dbSNP_129	104	149,8451	72.3+/-134.9	2,145,4153	yes	missense,missense,missense,missense	PDE11A	NM_001077196.1,NM_001077197.1,NM_001077358.1,NM_016953.3	125,125,125,125	7,325,6171	CC,CG,GG		1.7326,4.3123,2.6065	benign,benign,benign,benign	423/490,617/684,509/576,867/934	178528641	339,12667	2203	4300	6503	SO:0001583	missense	50940	exon19	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	GCAACCGAGGCAG	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.2599C>G	2.37:g.178528641G>C	ENSP00000286063:p.Arg867Gly	111	0	0		70	34	0.485714	NM_016953	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Missense_Mutation	SNP	ENST00000286063.6	37	CCDS33334.1	38|38	0.0173992673992674|0.0173992673992674	14|14	0.028455284552845527|0.028455284552845527	5|5	0.013812154696132596|0.013812154696132596	5|5	0.008741258741258742|0.008741258741258742	14|14	0.018469656992084433|0.018469656992084433	G|G	10.44|10.44	1.352134|1.352134	0.24512|0.24512	0.043123|0.043123	0.017326|0.017326	ENSG00000128655|ENSG00000128655	ENST00000286063;ENST00000358450;ENST00000450799;ENST00000409504;ENST00000389683;ENST00000449286|ENST00000436700	T;T;T;T;T;T|.	0.76578|.	-1.03;-1.03;-1.03;-1.03;-1.03;-1.03|.	6.07|6.07	4.14|4.14	0.48551|0.48551	5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);|.	0.101356|.	0.64402|.	D|.	0.000003|.	T|T	0.11836|0.11836	0.0288|0.0288	N|N	0.12569|0.12569	0.235|0.235	0.41027|0.41027	D|D	0.985121|0.985121	B;B|.	0.06786|.	0.001;0.001|.	B;B|.	0.08055|.	0.001;0.003|.	T|T	0.05767|0.05767	-1.0865|-1.0865	10|5	0.23302|.	T|.	0.38|.	.|.	11.939|11.939	0.52890|0.52890	0.0:0.1083:0.6827:0.2089|0.0:0.1083:0.6827:0.2089	rs61306957|rs61306957	617;867|.	Q9HCR9-2;Q9HCR9|.	.;PDE11_HUMAN|.	G|W	867;617;58;509;423;509|69	ENSP00000286063:R867G;ENSP00000351232:R617G;ENSP00000387964:R58G;ENSP00000386539:R509G;ENSP00000374333:R423G;ENSP00000390599:R509G|.	ENSP00000286063:R867G|.	R|S	-|-	1|2	2|0	PDE11A|PDE11A	178236887|178236887	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	2.923000|2.923000	0.48868|0.48868	1.529000|1.529000	0.49120|0.49120	0.655000|0.655000	0.94253|0.94253	CGG|TCG	G|0.975;C|0.025	0.025	strong		0.453	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2			C	178528641	G	C	178528641	3	2	27	1	0	0	0	0	1	0	0	0	11640	1057	37	4	210	4	PDE11A	2	178528641	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	45870	178528641	64670732	141	10592											
DFNB59	494513	hgsc.bcm.edu	37	chr2	179325714	179325714	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttttgtccttttagatagaAgagtgatggatgtcatttct	9	19	9	4	0	2	4	1	1	1	3	3	5	3	5	1	1	0	0	1	1	3	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179325714A>G	ENST00000409117.3	+	7	1128	c.772A>G	c.(772-774)Aga>Gga	p.R258G	DFNB59_ENST00000375129.4_Missense_Mutation_p.R258G	NM_001042702.3	NP_001036167.1	Q0ZLH3	PJVK_HUMAN	deafness, autosomal recessive 59	258					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)			TTTAGATAGAAGAGTGATGGA	0.323																																					p.R258G		Atlas-SNP	.											.	DFNB59	37	.	0			c.A772G						PASS	.						186	164	171					2																	179325714		1845	4095	5940	SO:0001583	missense	494513	exon7			GATAGAAGAGTGA	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.772A>G	2.37:g.179325714A>G	ENSP00000386647:p.Arg258Gly	84	0	0		71	4	0.056338	NM_001042702	A0PK14|B9EJE2	Missense_Mutation	SNP	ENST00000409117.3	37	CCDS42787.1	.	.	.	.	.	.	.	.	.	.	A	14.69	2.610445	0.46527	.	.	ENSG00000204311	ENST00000409117;ENST00000375129	T;T	0.62788	0.0;0.0	6.04	6.04	0.98038	.	0.105144	0.33959	U	0.004397	T	0.54062	0.1835	L	0.47716	1.5	0.51012	D	0.999909	B	0.09022	0.002	B	0.12156	0.007	T	0.49283	-0.8956	10	0.22706	T	0.39	-25.5225	12.3569	0.55180	0.9331:0.0:0.0669:0.0	.	258	Q0ZLH3	PJVK_HUMAN	G	258	ENSP00000386647:R258G;ENSP00000364271:R258G	ENSP00000364271:R258G	R	+	1	2	DFNB59	179033960	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	2.839000	0.48207	2.317000	0.78254	0.460000	0.39030	AGA	.	.	none		0.323	DFNB59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335160.1			G	179325714	A	G	179325714	3	3	27	1	0	0	0	0	1	0	0	0	4458	64	3	3	794	3	DFNB59	2	179325714	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	797073	179325714	63873659	142	10593											
TTN	7273	hgsc.bcm.edu	37	chr2	179393691	179393691	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttcttctgatgcctgtgatGttttagtgatttcctcatgg	5	19	9	8	0	3	3	1	3	2	0	4	3	4	3	2	1	1	1	2	1	1	5	rs55842557	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179393691G>A	ENST00000591111.1	-	310	102088	c.101864C>T	c.(101863-101865)aCa>aTa	p.T33955I	TTN-AS1_ENST00000587576.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.T33028I|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.T26531I|TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.T35596I|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T26656I|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T26723I|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000592161.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000585487.1_RNA			Q8WZ42	TITIN_HUMAN	titin	33955			T -> I. {ECO:0000269|PubMed:17344846}.		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)			TGCCTGTGATGTTTTAGTGAT	0.398													G|||	19	0.00379393	0.0	0.0043	5008	,	,		22209	0.0		0.0159	False		,,,				2504	0.0				p.T35596I		Atlas-SNP	.											.	TTN	18412	.	0			c.C106787T						PASS	.	G	ILE/THR,ILE/THR,ILE/THR,ILE/THR	3,3779		0,3,1888	147	135	139		80168,79967,99083,79592	4.7	1	2	dbSNP_129	139	56,8158		1,54,4052	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	89,89,89,89	1,57,5940	AA,AG,GG		0.6818,0.0793,0.4918	benign,benign,benign,benign	26723/27119,26656/27052,33028/33424,26531/26927	179393691	59,11937	1891	4107	5998	SO:0001583	missense	7273	exon360			TGTGATGTTTTAG	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.101864C>T	2.37:g.179393691G>A	ENSP00000465570:p.Thr33955Ile	229	0	0		202	80	0.39604	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	37		17	0.007783882783882784	0	0.0	3	0.008287292817679558	0	0.0	14	0.018469656992084433	G	14.74	2.624609	0.46840	7.93E-4	0.006818	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.62941	-0.01;0.25;0.23;0.22	5.69	4.74	0.60224	Ribonuclease H-like (1);	.	.	.	.	T	0.32763	0.0840	N	0.24115	0.695	0.25561	N	0.986992	B;B;B;B;B	0.29805	0.026;0.026;0.026;0.026;0.257	B;B;B;B;B	0.26310	0.029;0.029;0.029;0.029;0.068	T	0.42565	-0.9444	9	0.87932	D	0	.	13.2479	0.60033	0.0:0.0:0.7689:0.2311	rs55842557	26531;26656;26723;33955;33028	D3DPF9;E7EQE6;E7ET18;Q8WZ42;A6NKB1	.;.;.;TITIN_HUMAN;.	I	33028;26531;26723;26656;26528	ENSP00000343764:T33028I;ENSP00000434586:T26531I;ENSP00000340554:T26723I;ENSP00000352154:T26656I	ENSP00000340554:T26723I	T	-	2	0	TTN	179101937	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.452000	0.52971	2.677000	0.91161	0.655000	0.94253	ACA	G|0.993;A|0.007	0.007	strong		0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179393691	G	A	179393691	3	1	27	1	0	0	0	0	1	0	0	0	16750	1377	48	2	1204	2	TTN	2	179393691	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	67977	179393691	63805682	143	10594											
TTN	7273	hgsc.bcm.edu	37	chr2	179396573	179396573	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acttcatacttcctttctgaTgtcttctgagtttttaaagc	8	19	5	9	0	4	2	1	2	3	0	5	2	5	2	1	0	2	1	1	0	3	8	rs56375087	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179396573T>G	ENST00000591111.1	-	308	100070	c.99846A>C	c.(99844-99846)acA>acC	p.T33282T	TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000342992.6_Silent_p.T32355T|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN_ENST00000460472.2_Silent_p.T25858T|TTN-AS1_ENST00000431259.2_RNA|TTN_ENST00000589042.1_Silent_p.T34923T|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN_ENST00000359218.5_Silent_p.T25983T|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342175.6_Silent_p.T26050T|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000585487.1_RNA			Q8WZ42	TITIN_HUMAN	titin	33282					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)			TCCTTTCTGATGTCTTCTGAG	0.458													T|||	19	0.00379393	0.0	0.0043	5008	,	,		21340	0.0		0.0159	False		,,,				2504	0.0				p.T34923T		Atlas-SNP	.											.	TTN	18412	.	0			c.A104769C						PASS	.	T	,,,	2,3864		0,2,1931	51	49	50		77574,97065,77949,78150	-2.6	1	2	dbSNP_129	50	56,8214		1,54,4080	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	1,56,6011	GG,GT,TT		0.6771,0.0517,0.4779	,,,	25858/26927,32355/33424,25983/27052,26050/27119	179396573	58,12078	1933	4135	6068	SO:0001819	synonymous_variant	7273	exon358			TTCTGATGTCTTC	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.99846A>C	2.37:g.179396573T>G		143	0	0		126	57	0.452381	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	37																																																																																				T|0.993;G|0.007	0.007	strong		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179396573	T	G	179396573	2	3	27	1	0	0	0	0	0	0	0	1	16750	1451	51	5		5	TTN	2	179396573	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	2882	179396573	63802800	144	10595											
TTN	7273	hgsc.bcm.edu	37	chr2	179482633	179482633	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tcagtaacagttgcagacagGtcttcagctctcacagtcat	11	11	8	11	0	5	1	4	0	2	1	6	1	5	1	0	1	3	4	0	1	1	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179482633G>T	ENST00000591111.1	-	203	42746	c.42522C>A	c.(42520-42522)gaC>gaA	p.D14174E	TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.D13247E|TTN_ENST00000460472.2_Missense_Mutation_p.D6750E|TTN_ENST00000589042.1_Missense_Mutation_p.D15815E|RP11-171I2.4_ENST00000605334.1_lincRNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.D6875E|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.D6942E|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000604956.1_RNA|TTN-AS1_ENST00000592750.1_RNA			Q8WZ42	TITIN_HUMAN	titin	14174	Fibronectin type-III 2. {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)			TTGCAGACAGGTCTTCAGCTC	0.463																																					p.D15815E		Atlas-SNP	.											.	TTN	18412	.	0			c.C47445A						PASS	.						184	178	180					2																	179482633		1997	4162	6159	SO:0001583	missense	7273	exon253			AGACAGGTCTTCA	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.42522C>A	2.37:g.179482633G>T	ENSP00000465570:p.Asp14174Glu	323	0	0		276	76	0.275362	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	37		.	.	.	.	.	.	.	.	.	.	G	10.34	1.324434	0.24080	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.56611	0.45;0.45;0.45;0.45	5.63	-0.558	0.11796	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.25865	0.0630	N	0.03999	-0.3	0.33357	D	0.571856	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	0.13415	-1.0510	9	0.87932	D	0	.	5.0288	0.14398	0.3413:0.0:0.3539:0.3048	.	6750;6875;6942;14174	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	E	13247;6750;6942;6875;6750	ENSP00000343764:D13247E;ENSP00000434586:D6750E;ENSP00000340554:D6942E;ENSP00000352154:D6875E	ENSP00000340554:D6942E	D	-	3	2	TTN	179190878	0.751000	0.28327	0.993000	0.49108	0.985000	0.73830	-0.159000	0.10056	-0.079000	0.12707	0.655000	0.94253	GAC	.	.	none		0.463	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179482633	G	T	179482633	3	4	27	1	0	0	0	0	1	0	0	0	16750	1252	44	4	60688	4	TTN	2	179482633	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	86060	179482633	63716740	145	10596											
TTN	7273	hgsc.bcm.edu	37	chr2	179643775	179643775	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gtatacgcagactagctctgCcatcttgtagaaagtccatt	11	12	8	10	1	2	2	0	0	2	2	3	2	3	2	2	0	3	4	2	0	5	6	rs36021856	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:179643775C>T	ENST00000591111.1	-	24	4258	c.4034G>A	c.(4033-4035)gGc>gAc	p.G1345D	TTN_ENST00000342992.6_Missense_Mutation_p.G1345D|TTN_ENST00000460472.2_Missense_Mutation_p.G1299D|TTN_ENST00000589042.1_Missense_Mutation_p.G1345D|TTN_ENST00000359218.5_Missense_Mutation_p.G1299D|RP11-88L24.4_ENST00000582038.2_RNA|TTN_ENST00000360870.5_Missense_Mutation_p.G1345D|TTN_ENST00000342175.6_Missense_Mutation_p.G1299D			Q8WZ42	TITIN_HUMAN	titin	33541	Ig-like 5.		G -> D (in dbSNP:rs36021856). {ECO:0000269|PubMed:17344846}.		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)			ACTAGCTCTGCCATCTTGTAG	0.398													C|||	19	0.00379393	0.0	0.0043	5008	,	,		21020	0.0		0.0159	False		,,,				2504	0.0				p.G1345D		Atlas-SNP	.											.	TTN	18412	.	0			c.G4034A						PASS	.	C	ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY	3,4403	6.2+/-15.9	0,3,2200	136	120	125		3896,4034,4034,3896,3896	5.7	1	2	dbSNP_126	125	63,8537	38.8+/-94.9	1,61,4238	yes	missense,missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	94,94,94,94,94	1,64,6438	TT,TC,CC		0.7326,0.0681,0.5075	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	1299/26927,1345/33424,1345/5605,1299/27052,1299/27119	179643775	66,12940	2203	4300	6503	SO:0001583	missense	7273	exon24			GCTCTGCCATCTT	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.4034G>A	2.37:g.179643775C>T	ENSP00000465570:p.Gly1345Asp	174	0	0		144	76	0.527778	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	37		17	0.007783882783882784	0	0.0	3	0.008287292817679558	0	0.0	14	0.018469656992084433	C	17.13	3.311645	0.60414	6.81E-4	0.007326	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24;-0.24	5.72	5.72	0.89469	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.73194	0.3556	M	0.77616	2.38	0.49389	D	0.999784	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	0.80845	-0.1200	9	0.87932	D	0	.	19.8946	0.96949	0.0:1.0:0.0:0.0	rs36021856	1299;1299;1299;1345;1345	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	D	1345;1299;1299;1299;1299;1345	ENSP00000343764:G1345D;ENSP00000434586:G1299D;ENSP00000340554:G1299D;ENSP00000352154:G1299D;ENSP00000354117:G1345D	ENSP00000340554:G1299D	G	-	2	0	TTN	179352020	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.781000	0.85668	2.711000	0.92665	0.655000	0.94253	GGC	C|0.993;T|0.007	0.007	strong		0.398	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179643775	C	T	179643775	3	4	27	1	0	0	0	0	1	0	0	0	16750	739	26	2	107310	2	TTN	2	179643775	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	161142	179643775	63555598	146	10597											
ITGA4	3676	hgsc.bcm.edu	37	chr2	182392096	182392096	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaaacgtgcatggtggagaaAatgaacttaactttccatgt	14	11	10	6	1	0	2	0	1	0	1	1	4	1	2	1	2	4	1	1	2	5	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:182392096A>G	ENST00000397033.2	+	22	2842	c.2412A>G	c.(2410-2412)aaA>aaG	p.K804K		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	804					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)	TGGTGGAGAAAATGAACTTAA	0.333																																					p.K804K		Atlas-SNP	.											.	ITGA4	142	.	0			c.A2412G						PASS	.						91	87	88					2																	182392096		1891	4125	6016	SO:0001819	synonymous_variant	3676	exon22			GGAGAAAATGAAC		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.2412A>G	2.37:g.182392096A>G		84	0	0		58	32	0.551724	NM_000885	D3DPG4|Q7Z4L6	Silent	SNP	ENST00000397033.2	37	CCDS42788.1																																																																																			.	.	none		0.333	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1			G	182392096	A	G	182392096	2	3	27	1	0	0	0	0	0	0	0	1	7887	11	1	3		3	ITGA4	2	182392096	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	2748321	182392096	60807277	147	10598											
ZNF804A	91752	hgsc.bcm.edu	37	chr2	185800768	185800768	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agacacaaaatcggcttttcTtttgcatttccaaagaaagc	14	12	6	9	1	1	2	0	0	1	2	3	2	2	2	1	1	2	2	1	1	4	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:185800768T>C	ENST00000302277.6	+	4	1239	c.645T>C	c.(643-645)tcT>tcC	p.S215S		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	215							metal ion binding (GO:0046872)	p.S215S(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						TCGGCTTTTCTTTTGCATTTC	0.433																																					p.S215S		Atlas-SNP	.											ZNF804A,colon,carcinoma,0,1	ZNF804A	322	1	1	Substitution - coding silent(1)	large_intestine(1)	c.T645C						PASS	.						66	67	66					2																	185800768		2203	4300	6503	SO:0001819	synonymous_variant	91752	exon4			CTTTTCTTTTGCA	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.645T>C	2.37:g.185800768T>C		106	0	0		71	20	0.28169	NM_194250	A7E253|Q6ZN26	Silent	SNP	ENST00000302277.6	37	CCDS2291.1																																																																																			.	.	none		0.433	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		C	185800768	T	C	185800768	2	2	27	1	0	0	0	0	0	0	0	1	18185	1596	56	3		3	ZNF804A	2	185800768	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	3408672	185800768	57398605	148	10599											
ZNF804A	91752	hgsc.bcm.edu	37	chr2	185801871	185801871	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atacaacaaaataaggttgaAagagacccatgaatactggt	19	8	8	6	0	0	3	0	2	0	1	0	4	0	3	1	2	3	1	1	2	8	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:185801871A>T	ENST00000302277.6	+	4	2342	c.1748A>T	c.(1747-1749)aAa>aTa	p.K583I		NM_194250.1	NP_919226.1	Q7Z570	Z804A_HUMAN	zinc finger protein 804A	583							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						ATAAGGTTGAAAGAGACCCAT	0.294																																					p.K583I		Atlas-SNP	.											.	ZNF804A	322	.	0			c.A1748T						PASS	.						34	41	39					2																	185801871		2180	4278	6458	SO:0001583	missense	91752	exon4			GGTTGAAAGAGAC	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.1748A>T	2.37:g.185801871A>T	ENSP00000303252:p.Lys583Ile	69	0	0		60	20	0.333333	NM_194250	A7E253|Q6ZN26	Missense_Mutation	SNP	ENST00000302277.6	37	CCDS2291.1	.	.	.	.	.	.	.	.	.	.	A	18.55	3.647690	0.67358	.	.	ENSG00000170396	ENST00000302277	T	0.10005	2.92	5.5	5.5	0.81552	.	0.097775	0.44902	D	0.000416	T	0.29491	0.0735	L	0.58101	1.795	0.34076	D	0.659021	D	0.89917	1.0	D	0.73380	0.98	T	0.40459	-0.9562	10	0.87932	D	0	-23.4158	14.793	0.69857	1.0:0.0:0.0:0.0	.	583	Q7Z570	Z804A_HUMAN	I	583	ENSP00000303252:K583I	ENSP00000303252:K583I	K	+	2	0	ZNF804A	185510116	1.000000	0.71417	0.489000	0.27452	0.972000	0.66771	3.815000	0.55651	2.083000	0.62718	0.528000	0.53228	AAA	.	.	none		0.294	ZNF804A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255871.1	NM_194250		T	185801871	A	T	185801871	3	4	27	1	0	0	0	0	1	0	0	0	18185	14	1	5	1762	5	ZNF804A	2	185801871	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	1103	185801871	57397502	149	10600											
PMS1	5378	hgsc.bcm.edu	37	chr2	190728798	190728798	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgaaccttgcttgatccacaAtctcaggtttcctgatgcat	9	14	7	11	0	1	3	1	3	1	0	4	3	3	3	3	1	3	3	3	1	2	3	rs201205478		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:190728798A>G	ENST00000441310.2	+	10	2419	c.2186A>G	c.(2185-2187)aAt>aGt	p.N729S	PMS1_ENST00000409823.3_Missense_Mutation_p.N690S|PMS1_ENST00000432292.3_Missense_Mutation_p.N553S|PMS1_ENST00000447232.2_Intron|PMS1_ENST00000421722.1_3'UTR|PMS1_ENST00000418224.3_Missense_Mutation_p.N553S	NM_000534.4	NP_000525.1	P54277	PMS1_HUMAN	PMS1 postmeiotic segregation increased 1 (S. cerevisiae)	729					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)			TTGATCCACAATCTCAGGTTT	0.333			"Mis, N"			"colorectal, endometrial, ovarian"		Direct reversal of damage;Mismatch excision repair (MMR)																													p.N729S		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.A2186G						PASS	.	A	SER/ASN,SER/ASN,	0,4406		0,0,2203	113	122	119		2186,2069,	3.1	1	2		119	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,intron	PMS1	NM_000534.4,NM_001128143.1,NM_001128144.1	46,46,	0,2,6501	GG,GA,AA		0.0233,0.0,0.0154	benign,benign,	729/933,690/894,	190728798	2,13004	2203	4300	6503	SO:0001583	missense	5378	exon10			TCCACAATCTCAG		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.2186A>G	2.37:g.190728798A>G	ENSP00000406490:p.Asn729Ser	155	0	0		186	85	0.456989	NM_000534	D3DPI1|Q4VAL4|Q5FBZ3|Q5FBZ6|Q5FBZ8	Missense_Mutation	SNP	ENST00000441310.2	37	CCDS2302.1	.	.	.	.	.	.	.	.	.	.	A	9.300	1.052870	0.19907	0.0	2.33E-4	ENSG00000064933	ENST00000392338;ENST00000441310;ENST00000418224;ENST00000409823;ENST00000432292;ENST00000424307;ENST00000452382	T;T;T;T;D;T	0.85955	2.0;2.0;2.0;2.0;-2.05;2.02	5.45	3.11	0.35812	.	0.489617	0.25535	N	0.030017	T	0.64338	0.2589	N	0.04043	-0.29	0.19300	N	0.999974	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.52449	-0.8574	10	0.36615	T	0.2	-11.736	4.1444	0.10209	0.6036:0.0:0.2516:0.1448	.	729;690;729	Q4VAL4;Q5FBZ3;P54277	.;.;PMS1_HUMAN	S	553;729;553;690;553;668;117	ENSP00000406490:N729S;ENSP00000404492:N553S;ENSP00000387125:N690S;ENSP00000398378:N553S;ENSP00000389938:N668S;ENSP00000396232:N117S	ENSP00000376149:N553S	N	+	2	0	PMS1	190437043	0.996000	0.38824	1.000000	0.80357	0.975000	0.68041	0.494000	0.22467	0.528000	0.28580	0.524000	0.50904	AAT	.	.	weak		0.333	PMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255918.2			G	190728798	A	G	190728798	3	3	27	1	0	0	0	0	1	0	0	0	12151	101	4	3	2220	3	PMS1	2	190728798	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	4926927	190728798	52470575	150	10601											
PGAP1	80055	hgsc.bcm.edu	37	chr2	197711870	197711870	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctctgacaagttaaaatgacGgcatctaattctggtaacaa	15	11	7	8	1	3	2	0	2	3	0	3	2	3	2	0	2	1	3	0	2	6	4	rs149815494	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:197711870G>A	ENST00000354764.4	-	22	2121	c.2007C>T	c.(2005-2007)gcC>gcT	p.A669A		NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	669					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						TTAAAATGACGGCATCTAATT	0.373													G|||	17	0.00339457	0.0	0.0	5008	,	,		16262	0.0		0.0169	False		,,,				2504	0.0				p.A669A		Atlas-SNP	.											.	PGAP1	84	.	0			c.C2007T						PASS	.	G		10,4396	16.8+/-37.8	0,10,2193	138	143	141		2007	3.1	1	2	dbSNP_134	141	87,8513	49.8+/-109.6	1,85,4214	no	coding-synonymous	PGAP1	NM_024989.3		1,95,6407	AA,AG,GG		1.0116,0.227,0.7458		669/923	197711870	97,12909	2203	4300	6503	SO:0001819	synonymous_variant	80055	exon22			AATGACGGCATCT		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.2007C>T	2.37:g.197711870G>A		204	0	0		147	59	0.401361	NM_024989	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Silent	SNP	ENST00000354764.4	37	CCDS2318.1																																																																																			G|0.993;A|0.007	0.007	strong		0.373	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989		A	197711870	G	A	197711870	2	1	27	1	0	0	0	0	0	0	0	1	11786	1103	39	1		1	PGAP1	2	197711870	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	6983072	197711870	45487503	151	10602											
SF3B1	23451	hgsc.bcm.edu	37	chr2	198257075	198257075	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atataggtgttcttatcatcGttgtagattcttgggtaatg	9	18	10	4	1	3	1	1	0	2	1	4	1	3	1	0	2	0	4	0	2	5	9	rs78516934	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:198257075G>A	ENST00000335508.6	-	25	3958	c.3867C>T	c.(3865-3867)aaC>aaT	p.N1289N		NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	1289					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)			TCTTATCATCGTTGTAGATTC	0.358			Mis		myelodysplastic syndrome								G|||	16	0.00319489	0.0008	0.0014	5008	,	,		17476	0.0		0.0139	False		,,,				2504	0.0				p.N1289N		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1	1038	.	0			c.C3867T						PASS	.	G		5,4401	9.9+/-24.2	0,5,2198	122	121	121		3867	0.9	1	2	dbSNP_132	121	86,8514	49.8+/-109.6	0,86,4214	no	coding-synonymous	SF3B1	NM_012433.2		0,91,6412	AA,AG,GG		1.0,0.1135,0.6997		1289/1305	198257075	91,12915	2203	4300	6503	SO:0001819	synonymous_variant	23451	exon25			ATCATCGTTGTAG	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.3867C>T	2.37:g.198257075G>A		111	0	0		106	40	0.377358	NM_012433	E9PCH3	Silent	SNP	ENST00000335508.6	37	CCDS33356.1																																																																																			G|0.993;A|0.007	0.007	strong		0.358	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			A	198257075	G	A	198257075	2	1	27	1	0	0	0	0	0	0	0	1	14164	1136	40	1		1	SF3B1	2	198257075	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	545205	198257075	44942298	152	10603											
RFTN2	130132	hgsc.bcm.edu	37	chr2	198460748	198460748	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagctgaattccacataacTggcctctgaaggaatacgat	13	9	9	10	1	1	2	0	2	1	0	2	4	2	3	2	2	3	2	2	2	5	3	rs77442629	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:198460748T>G	ENST00000295049.4	-	8	1736	c.1200A>C	c.(1198-1200)ccA>ccC	p.P400P		NM_144629.2	NP_653230.2	Q52LD8	RFTN2_HUMAN	raftlin family member 2	400					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						TCCACATAACTGGCCTCTGAA	0.328													T|||	12	0.00239617	0.0008	0.0	5008	,	,		17368	0.0		0.0109	False		,,,				2504	0.0				p.P400P		Atlas-SNP	.											.	RFTN2	68	.	0			c.A1200C						PASS	.	T		5,4401	9.9+/-24.2	0,5,2198	100	90	93		1200	-4.7	0	2	dbSNP_132	93	64,8536	38.8+/-94.9	0,64,4236	no	coding-synonymous	RFTN2	NM_144629.2		0,69,6434	GG,GT,TT		0.7442,0.1135,0.5305		400/502	198460748	69,12937	2203	4300	6503	SO:0001819	synonymous_variant	130132	exon8			CATAACTGGCCTC	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.1200A>C	2.37:g.198460748T>G		83	0	0		65	30	0.461538	NM_144629	Q14DH4|Q2TA69|Q53QE0|Q53SE1|Q96NM3	Silent	SNP	ENST00000295049.4	37	CCDS2323.1																																																																																			T|0.995;G|0.005	0.005	strong		0.328	RFTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256106.2	NM_144629		G	198460748	T	G	198460748	2	3	27	1	0	0	0	0	0	0	0	1	13274	1567	55	5		5	RFTN2	2	198460748	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	203673	198460748	44738625	153	10604											
FASTKD2	22868	hgsc.bcm.edu	37	chr2	207631446	207631446	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aactttgaagccatttggaaGtgtttcagtggagagcaaaa	14	11	11	5	0	1	2	1	1	0	1	1	4	1	3	1	2	3	2	1	2	5	3	rs147727753	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:207631446G>C	ENST00000236980.6	+	2	377	c.29G>C	c.(28-30)aGt>aCt	p.S10T	MDH1B_ENST00000374412.3_5'Flank|FASTKD2_ENST00000402774.3_Missense_Mutation_p.S10T|MDH1B_ENST00000392214.2_5'Flank|MDH1B_ENST00000454776.2_5'Flank|FASTKD2_ENST00000403094.3_Missense_Mutation_p.S10T|MDH1B_ENST00000449792.1_5'Flank	NM_014929.3	NP_055744.2	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	10					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)		CCATTTGGAAGTGTTTCAGTG	0.398													G|||	14	0.00279553	0.0	0.0029	5008	,	,		17193	0.0		0.0089	False		,,,				2504	0.0031				p.S10T		Atlas-SNP	.											.	FASTKD2	49	.	0			c.G29C						PASS	.	G	THR/SER,THR/SER,THR/SER	15,4391	22.3+/-47.3	0,15,2188	63	69	67		29,29,29	3.3	0.4	2	dbSNP_134	67	60,8540	35.9+/-90.5	1,58,4241	yes	missense,missense,missense	FASTKD2	NM_001136193.1,NM_001136194.1,NM_014929.3	58,58,58	1,73,6429	CC,CG,GG		0.6977,0.3404,0.5767	possibly-damaging,possibly-damaging,possibly-damaging	10/711,10/711,10/711	207631446	75,12931	2203	4300	6503	SO:0001583	missense	22868	exon2			TTGGAAGTGTTTC	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.29G>C	2.37:g.207631446G>C	ENSP00000236980:p.Ser10Thr	174	0	0		148	79	0.533784	NM_001136193	Q9NVX6|Q9Y2H7	Missense_Mutation	SNP	ENST00000236980.6	37	CCDS2371.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	G	16.23	3.065708	0.55539	0.003404	0.006977	ENSG00000118246	ENST00000236980;ENST00000418289;ENST00000402774;ENST00000403094	T;T;T;T	0.50548	2.41;0.74;2.41;2.41	4.14	3.26	0.37387	.	1.872060	0.02814	N	0.124770	T	0.37812	0.1017	L	0.40543	1.245	0.09310	N	1	P;P	0.46512	0.879;0.808	P;B	0.46076	0.503;0.242	T	0.42327	-0.9458	10	0.87932	D	0	-2.845	4.6425	0.12556	0.1112:0.0:0.6698:0.219	.	10;10	Q9NYY8-2;Q9NYY8	.;FAKD2_HUMAN	T	10	ENSP00000236980:S10T;ENSP00000409927:S10T;ENSP00000385990:S10T;ENSP00000384929:S10T	ENSP00000236980:S10T	S	+	2	0	FASTKD2	207339691	0.019000	0.18553	0.385000	0.26158	0.482000	0.33219	1.205000	0.32308	2.316000	0.78162	0.491000	0.48974	AGT	G|0.996;C|0.004	0.004	strong		0.398	FASTKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256428.2	NM_014929		C	207631446	G	C	207631446	3	2	27	1	0	0	0	0	1	0	0	0	5694	1029	36	4	31	4	FASTKD2	2	207631446	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	9170698	207631446	35567927	154	10605											
BARD1	580	hgsc.bcm.edu	37	chr2	215657089	215657089	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaatcatgctgtccagttgtCtatttatcttcaagtcttgt	8	18	7	8	0	5	0	2	0	3	0	6	1	6	0	1	0	1	2	1	0	4	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:215657089C>T	ENST00000260947.4	-	3	430	c.296G>A	c.(295-297)aGa>aAa	p.R99K	BARD1_ENST00000449967.2_Intron|BARD1_ENST00000471787.1_Intron	NM_000465.2|NM_001282543.1|NM_001282545.1|NM_001282548.1	NP_000456.2|NP_001269472.1|NP_001269474.1|NP_001269477.1	Q99728	BARD1_HUMAN	BRCA1 associated RING domain 1	99	Interaction with BRCA1.				cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA 3'-end processing (GO:0031441)|negative regulation of protein export from nucleus (GO:0046826)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein catabolic process (GO:0045732)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of phosphorylation (GO:0042325)|tissue homeostasis (GO:0001894)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	kinase binding (GO:0019900)|ligase activity (GO:0016874)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(14)|prostate(4)|upper_aerodigestive_tract(1)	35		Renal(323;0.0243)		Epithelial(149;3.2e-06)|all cancers(144;0.000461)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		GTCCAGTTGTCTATTTATCTT	0.363									Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.R99K		Atlas-SNP	.											.	BARD1	138	.	0			c.G296A						PASS	.						139	137	138					2																	215657089		2203	4300	6503	SO:0001583	missense	580	exon3	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	AGTTGTCTATTTA		CCDS2397.1, CCDS74645.1, CCDS74646.1, CCDS74647.1, CCDS74648.1	2q34-q35	2013-01-10			ENSG00000138376	ENSG00000138376		"Ankyrin repeat domain containing"	952	protein-coding gene	gene with protein product		601593				8944023, 9425226, 15159397	Standard	NM_001282548		Approved		uc002veu.2	Q99728	OTTHUMG00000133016	ENST00000260947.4:c.296G>A	2.37:g.215657089C>T	ENSP00000260947:p.Arg99Lys	153	0	0		109	5	0.0458716	NM_000465	F6MDH7|F6MDH8|F6MDH9|O43574|Q53SS5	Missense_Mutation	SNP	ENST00000260947.4	37	CCDS2397.1	.	.	.	.	.	.	.	.	.	.	C	17.13	3.312107	0.60414	.	.	ENSG00000138376	ENST00000260947	T	0.75938	-0.98	5.29	4.42	0.53409	Zinc finger, RING/FYVE/PHD-type (1);	0.047598	0.85682	N	0.000000	T	0.70133	0.3189	L	0.53249	1.67	0.80722	D	1	B	0.25390	0.125	B	0.22152	0.038	T	0.70400	-0.4882	10	0.87932	D	0	-23.2173	14.0072	0.64470	0.0:0.9269:0.0:0.0731	.	99	Q99728	BARD1_HUMAN	K	99	ENSP00000260947:R99K	ENSP00000260947:R99K	R	-	2	0	BARD1	215365334	1.000000	0.71417	0.962000	0.40283	0.949000	0.60115	2.583000	0.46094	1.368000	0.46115	0.557000	0.71058	AGA	.	.	none		0.363	BARD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256602.1	NM_000465		T	215657089	C	T	215657089	3	4	27	1	0	0	0	0	1	0	0	0	1312	913	32	2	2073	2	BARD1	2	215657089	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	8025643	215657089	27542284	155	10606											
PLCD4	84812	hgsc.bcm.edu	37	chr2	219492952	219492952	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcagcgtcgagggatatataCggtgcagtggtggtagagaa	11	8	17	5	3	0	1	0	0	0	1	1	4	0	2	0	4	3	3	0	4	5	4	rs61733653	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:219492952C>T	ENST00000450993.2	+	7	1312	c.973C>T	c.(973-975)Cgg>Tgg	p.R325W	PLCD4_ENST00000417849.1_Splice_Site_p.R325W|PLCD4_ENST00000432688.1_Splice_Site_p.R325W	NM_032726.3	NP_116115.1	Q9BRC7	PLCD4_HUMAN	phospholipase C, delta 4	325	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				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)		GGGATATATACGGTGCAGTGG	0.517													C|||	17	0.00339457	0.0008	0.0058	5008	,	,		20599	0.0		0.0089	False		,,,				2504	0.0031				p.R325W		Atlas-SNP	.											.	PLCD4	51	.	0			c.C973T						PASS	.	C	TRP/ARG	17,4047		0,17,2015	121	116	117		973	2.9	1	2	dbSNP_129	117	95,8281		1,93,4094	yes	missense-near-splice	PLCD4	NM_032726.3	101	1,110,6109	TT,TC,CC		1.1342,0.4183,0.9003	probably-damaging	325/763	219492952	112,12328	2032	4188	6220	SO:0001630	splice_region_variant	84812	exon7			TATATACGGTGCA	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.974+1C>T	2.37:g.219492952C>T		107	0	0		80	45	0.5625	NM_032726	Q53FS8	Missense_Mutation	SNP	ENST00000450993.2	37	CCDS46516.1	7	0.003205128205128205	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	C	17.58	3.425437	0.62733	0.004183	0.011342	ENSG00000115556	ENST00000450993;ENST00000251959;ENST00000417849;ENST00000432688	T;T;T	0.64618	-0.11;-0.11;-0.11	4.7	2.91	0.33838	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);Phospholipase C, phosphatidylinositol-specific , X domain (3);	0.112622	0.56097	N	0.000021	T	0.70613	0.3244	M	0.86651	2.83	0.38031	D	0.935157	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.74717	-0.3571	10	0.87932	D	0	.	4.4431	0.11584	0.2899:0.5284:0.0:0.1817	rs61733653	325;325	B7Z5V4;Q9BRC7	.;PLCD4_HUMAN	W	325	ENSP00000388631:R325W;ENSP00000396942:R325W;ENSP00000396185:R325W	ENSP00000251959:R325W	R	+	1	2	PLCD4	219201196	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	1.641000	0.37197	0.600000	0.29862	-0.262000	0.10625	CGG	C|0.994;T|0.006	0.006	strong		0.517	PLCD4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336876.1		Missense_Mutation	T	219492952	C	T	219492952	5	4	27	1	0	0	0	0	0	0	1	0	12042	550	19	1	995	1	PLCD4	2	219492952	Splice_Site	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3835863	219492952	23706421	156	10607											
BCS1L	617	hgsc.bcm.edu	37	chr2	219527857	219527857	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctttccctgtcttctctcagGctggaccctgccctgatacg	4	13	8	16	1	3	1	1	1	2	0	5	2	4	2	3	2	2	1	3	2	1	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:219527857G>A	ENST00000431802.1	+	8	1707	c.1008G>A	c.(1006-1008)agG>agA	p.R336R	BCS1L_ENST00000439945.1_Splice_Site_p.R336R|BCS1L_ENST00000392110.2_Splice_Site_p.R336R|BCS1L_ENST00000465706.1_3'UTR|BCS1L_ENST00000392109.1_Splice_Site_p.R336R|BCS1L_ENST00000392111.2_Splice_Site_p.R336R|BCS1L_ENST00000359273.3_Splice_Site_p.R336R|BCS1L_ENST00000412366.1_Splice_Site_p.R336R			Q9Y276	BCS1_HUMAN	BC1 (ubiquinol-cytochrome c reductase) synthesis-like	336					mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrial respiratory chain complex III assembly (GO:0034551)|mitochondrial respiratory chain complex IV assembly (GO:0033617)|mitochondrion organization (GO:0007005)	mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	8		Renal(207;0.0474)		Epithelial(149;7.12e-07)|all cancers(144;0.000131)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTTCTCTCAGGCTGGACCCTG	0.602																																					p.R336R		Atlas-SNP	.											.	BCS1L	22	.	0			c.G1008A						PASS	.						73	76	75					2																	219527857		2203	4300	6503	SO:0001630	splice_region_variant	617	exon9			TCTCAGGCTGGAC	AF026849	CCDS2419.1	2q35	2014-09-17	2012-10-12		ENSG00000074582	ENSG00000074582		"ATPases / AAA-type", "Mitochondrial respiratory chain complex assembly factors"	1020	protein-coding gene	gene with protein product	"GRACILE syndrome", "Bjornstad syndrome"	603647	"BCS1 (yeast homolog)-like", "BCS1-like (yeast)", "BCS1-like (S. cerevisiae)"			9878253, 17314340	Standard	NM_001079866		Approved	Hs.6719, BCS, h-BCS, BJS	uc002viq.3	Q9Y276	OTTHUMG00000133114	ENST00000431802.1:c.1008-1G>A	2.37:g.219527857G>A		184	0	0		146	39	0.267123	NM_001257343	B3KTW9|Q7Z2V7	Silent	SNP	ENST00000431802.1	37	CCDS2419.1	.	.	.	.	.	.	.	.	.	.	G	4.628	0.116645	0.08881	.	.	ENSG00000074582	ENST00000426649	.	.	.	5.12	2.05	0.26809	.	.	.	.	.	T	0.57651	0.2068	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49542	-0.8929	4	.	.	.	.	8.9926	0.36033	0.2679:0.0:0.7321:0.0	.	.	.	.	T	118	.	.	A	+	1	0	BCS1L	219236101	1.000000	0.71417	0.998000	0.56505	0.156000	0.22039	3.543000	0.53633	0.207000	0.20607	-0.291000	0.09656	GCT	.	.	none		0.602	BCS1L-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336756.1	NM_004328	Silent	A	219527857	G	A	219527857	5	1	27	1	0	0	0	0	0	0	1	0	1389	1217	42	2	1034	2	BCS1L	2	219527857	Splice_Site	SNP	G	TCGA-G8-6909-01A-11D-2210-10	34905	219527857	23671516	157	10608											
DOCK10	55619	hgsc.bcm.edu	37	chr2	225670845	225670845	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcagaagatctcaagtacctGctatggaatttaaaacatct	15	12	6	8	0	3	2	2	0	2	2	4	3	3	3	1	1	3	2	1	1	7	4	rs375740801		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:225670845G>T	ENST00000258390.7	-	34	3879	c.3812C>A	c.(3811-3813)gCa>gAa	p.A1271E	DOCK10_ENST00000409592.3_Missense_Mutation_p.A1265E	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	1271					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)		TCAAGTACCTGCTATGGAATT	0.343																																					p.A1271E		Atlas-SNP	.											.	DOCK10	308	.	0			c.C3812A						PASS	.	G	GLU/ALA	0,3708		0,0,1854	104	103	103		3812	6	1	2		103	3,8181		0,3,4089	no	missense	DOCK10	NM_014689.2	107	0,3,5943	TT,TG,GG		0.0367,0.0,0.0252	benign	1271/2187	225670845	3,11889	1854	4092	5946	SO:0001583	missense	55619	exon34			GTACCTGCTATGG	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.3812C>A	2.37:g.225670845G>T	ENSP00000258390:p.Ala1271Glu	76	0	0		99	46	0.464646	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Missense_Mutation	SNP	ENST00000258390.7	37	CCDS46528.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.3|25.3	4.622605|4.622605	0.87460|0.87460	0.0|0.0	3.67E-4|3.67E-4	ENSG00000135905|ENSG00000135905	ENST00000409592;ENST00000258390|ENST00000422684	T;T|.	0.21361|.	3.53;2.01|.	5.96|5.96	5.96|5.96	0.96718|0.96718	.|.	0.049031|.	0.85682|.	D|.	0.000000|.	T|T	0.72653|0.72653	0.3487|0.3487	L|L	0.53249|0.53249	1.67|1.67	0.58432|0.58432	D|D	0.999996|0.999996	D;P;P|.	0.59767|.	0.986;0.799;0.745|.	P;B;B|.	0.55455|.	0.776;0.343;0.276|.	T|T	0.67051|0.67051	-0.5768|-0.5768	10|5	0.45353|.	T|.	0.12|.	.|.	20.4008|20.4008	0.98991|0.98991	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1271;134;1265|.	Q96BY6;B4DF07;B3FL70|.	DOC10_HUMAN;.;.|.	E|K	1265;1271|162	ENSP00000386694:A1265E;ENSP00000258390:A1271E|.	ENSP00000258390:A1271E|.	A|Q	-|-	2|1	0|0	DOCK10|DOCK10	225379089|225379089	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	8.442000|8.442000	0.90317|0.90317	2.826000|2.826000	0.97356|0.97356	0.655000|0.655000	0.94253|0.94253	GCA|CAG	.	.	weak		0.343	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			T	225670845	G	T	225670845	3	4	27	1	0	0	0	0	1	0	0	0	4687	1319	46	4	2840	4	DOCK10	2	225670845	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	6142988	225670845	17528528	158	10609											
SLC19A3	80704	hgsc.bcm.edu	37	chr2	228563835	228563835	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctctgctgggttttgcatgaAaaaacatgcttttcttgggc	8	15	10	8	0	2	1	0	1	2	0	2	1	2	1	0	2	4	4	0	2	3	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:228563835A>C	ENST00000258403.3	-	3	667	c.596T>G	c.(595-597)tTt>tGt	p.F199C	SLC19A3_ENST00000409287.1_Intron|SLC19A3_ENST00000541617.1_Missense_Mutation_p.F195C	NM_025243.3	NP_079519.1	Q9BZV2	S19A3_HUMAN	solute carrier family 19 (thiamine transporter), member 3	199					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)	TTTTGCATGAAAAAACATGCT	0.433																																					p.F199C		Atlas-SNP	.											.	SLC19A3	62	.	0			c.T596G						PASS	.						91	83	86					2																	228563835		2203	4300	6503	SO:0001583	missense	80704	exon3			GCATGAAAAAACA	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.596T>G	2.37:g.228563835A>C	ENSP00000258403:p.Phe199Cys	117	0	0		90	23	0.255556	NM_025243		Missense_Mutation	SNP	ENST00000258403.3	37	CCDS2468.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.308304	0.81247	.	.	ENSG00000135917	ENST00000258403;ENST00000541617	D;D	0.91295	-2.82;-2.82	5.77	5.77	0.91146	Major facilitator superfamily domain, general substrate transporter (1);	0.044924	0.85682	D	0.000000	D	0.95996	0.8696	M	0.88979	2.995	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.994;0.998	D	0.96405	0.9300	10	0.59425	D	0.04	-19.6375	16.0872	0.81065	1.0:0.0:0.0:0.0	.	195;199	F5H2M8;Q9BZV2	.;S19A3_HUMAN	C	199;195	ENSP00000258403:F199C;ENSP00000445519:F195C	ENSP00000258403:F199C	F	-	2	0	SLC19A3	228272079	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	7.160000	0.77495	2.202000	0.70862	0.533000	0.62120	TTT	.	.	none		0.433	SLC19A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256894.1			C	228563835	A	C	228563835	3	2	27	1	0	0	0	0	1	0	0	0	14445	14	1	5	910	5	SLC19A3	2	228563835	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	2892990	228563835	14635538	159	10610											
ALPI	248	hgsc.bcm.edu	37	chr2	233322286	233322286	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcctcaggtgatccttggCggaggccgcaagtacatgtt	7	11	13	10	2	1	1	1	1	0	0	3	2	3	2	3	4	1	3	3	4	2	3	rs139371546		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:233322286C>T	ENST00000295463.3	+	6	737	c.660C>T	c.(658-660)ggC>ggT	p.G220G		NM_001631.3	NP_001622.2	P09923	PPBI_HUMAN	alkaline phosphatase, intestinal	220					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)		TGATCCTTGGCGGAGGCCGCA	0.642													C|||	1	0.000199681	0.0	0.0014	5008	,	,		19244	0.0		0.0	False		,,,				2504	0.0				p.G220G		Atlas-SNP	.											.	ALPI	64	.	0			c.C660T						PASS	.	C		2,4404	2.1+/-5.4	0,2,2201	56	59	58		660	-11.2	0	2	dbSNP_134	58	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous	ALPI	NM_001631.3		0,12,6491	TT,TC,CC		0.1163,0.0454,0.0923		220/529	233322286	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	248	exon6			CCTTGGCGGAGGC	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.660C>T	2.37:g.233322286C>T		240	1	0.00416667		228	129	0.565789	NM_001631	B2R7Y4|Q53S80|Q9UBV5|Q9UCL2	Silent	SNP	ENST00000295463.3	37	CCDS2492.1																																																																																			C|0.999;T|0.001	0.001	strong		0.642	ALPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257035.2	NM_001631		T	233322286	C	T	233322286	2	4	27	1	0	0	0	0	0	0	0	1	543	755	27	1		1	ALPI	2	233322286	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	4758451	233322286	9877087	160	10611											
GIGYF2	26058	hgsc.bcm.edu	37	chr2	233697708	233697708	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaaaggagctggaggtccagCggcagaaggagttaatgcgc	12	5	17	7	2	0	1	0	0	0	1	1	5	1	4	1	5	3	3	1	5	3	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:233697708C>T	ENST00000409547.1	+	24	2982	c.2671C>T	c.(2671-2673)Cgg>Tgg	p.R891W	GIGYF2_ENST00000409451.3_Missense_Mutation_p.R912W|GIGYF2_ENST00000452341.2_Missense_Mutation_p.R722W|GIGYF2_ENST00000373566.3_Missense_Mutation_p.R913W|GIGYF2_ENST00000373563.4_Missense_Mutation_p.R891W|GIGYF2_ENST00000409196.3_Missense_Mutation_p.R885W|GIGYF2_ENST00000409480.1_Missense_Mutation_p.R913W	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	891	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)		GGAGGTCCAGCGGCAGAAGGA	0.587																																					p.R912W		Atlas-SNP	.											.	GIGYF2	288	.	0			c.C2734T						PASS	.						21	21	21					2																	233697708		2188	4277	6465	SO:0001583	missense	26058	exon24			GTCCAGCGGCAGA	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.2671C>T	2.37:g.233697708C>T	ENSP00000386537:p.Arg891Trp	68	0	0		77	29	0.376623	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	37	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	C	15.37	2.812568	0.50527	.	.	ENSG00000204120	ENST00000373566;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000409196;ENST00000409451;ENST00000452341	T;T;T;T;T;T;T	0.77098	-0.88;-0.88;-0.88;-0.88;-0.88;-0.88;-1.07	5.36	3.43	0.39272	.	0.054543	0.64402	D	0.000001	D	0.83589	0.5287	L	0.50333	1.59	0.46609	D	0.999126	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;P;P;P	0.76071	0.987;0.908;0.908;0.908	D	0.84996	0.0897	10	0.87932	D	0	-21.7548	12.8794	0.58008	0.4371:0.5629:0.0:0.0	.	722;912;891;885	E9PC50;A6H8W4;Q6Y7W6;E9PBB0	.;.;PERQ2_HUMAN;.	W	913;891;913;891;885;912;722	ENSP00000362667:R913W;ENSP00000362664:R891W;ENSP00000386765:R913W;ENSP00000386537:R891W;ENSP00000387070:R885W;ENSP00000387170:R912W;ENSP00000411505:R722W	ENSP00000362664:R891W	R	+	1	2	GIGYF2	233405952	0.993000	0.37304	1.000000	0.80357	0.815000	0.46073	1.280000	0.33202	1.188000	0.43014	0.655000	0.94253	CGG	.	.	none		0.587	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146		T	233697708	C	T	233697708	3	4	27	1	0	0	0	0	1	0	0	0	6386	759	27	1	2819	1	GIGYF2	2	233697708	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	375422	233697708	9501665	161	10612											
USP40	55230	hgsc.bcm.edu	37	chr2	234442134	234442134	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tctttccataccttcaggggGtctctgcaactgggatttcc	6	14	9	12	0	3	0	1	0	2	0	6	1	5	1	3	3	3	1	3	3	2	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:234442134G>C	ENST00000427112.2	-	10	1494	c.1459C>G	c.(1459-1461)Ccc>Gcc	p.P487A	USP40_ENST00000251722.6_Missense_Mutation_p.P487A|USP40_ENST00000450966.1_Missense_Mutation_p.P499A			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	487					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)		CCTTCAGGGGGTCTCTGCAAC	0.348																																					p.P499A		Atlas-SNP	.											.	USP40	174	.	0			c.C1495G						PASS	.						101	97	98					2																	234442134		1836	4076	5912	SO:0001583	missense	55230	exon10			CAGGGGGTCTCTG	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.1459C>G	2.37:g.234442134G>C	ENSP00000387898:p.Pro487Ala	128	0	0		125	32	0.256	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	37	CCDS46547.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.207921	0.79240	.	.	ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112	T;T;T	0.05513	3.43;3.43;3.43	5.23	5.23	0.72850	.	0.763029	0.12385	N	0.473527	T	0.26955	0.0660	M	0.74258	2.255	0.80722	D	1	D;D	0.71674	0.997;0.998	P;D	0.68039	0.904;0.955	T	0.00567	-1.1667	10	0.40728	T	0.16	.	18.8586	0.92264	0.0:0.0:1.0:0.0	.	487;499	Q9NVE5;Q9NVE5-3	UBP40_HUMAN;.	A	499;487;487	ENSP00000415434:P499A;ENSP00000251722:P487A;ENSP00000387898:P487A	ENSP00000251722:P487A	P	-	1	0	USP40	234106873	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.406000	0.97321	2.458000	0.83093	0.586000	0.80456	CCC	.	.	none		0.348	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294		C	234442134	G	C	234442134	3	2	27	1	0	0	0	0	1	0	0	0	17087	1261	44	4	2336	4	USP40	2	234442134	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	744426	234442134	8757239	162	10613											
SH3BP4	23677	hgsc.bcm.edu	37	chr2	235951183	235951183	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctctctgacttcacgctgcgGgttcaggtgaaggacgacca	8	9	12	12	3	3	2	2	2	1	0	4	4	3	3	1	3	1	2	1	3	1	2	rs140262787	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:235951183G>A	ENST00000409212.1	+	4	2277	c.1770G>A	c.(1768-1770)cgG>cgA	p.R590R	SH3BP4_ENST00000392011.2_Silent_p.R590R|SH3BP4_ENST00000344528.4_Silent_p.R590R			Q9P0V3	SH3B4_HUMAN	SH3-domain binding protein 4	590					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)		TCACGCTGCGGGTTCAGGTGA	0.587													G|||	39	0.00778754	0.0	0.0029	5008	,	,		16535	0.0		0.0149	False		,,,				2504	0.0225				p.R590R		Atlas-SNP	.											SH3BP4,NS,carcinoma,+2,1	SH3BP4	109	1	0			c.G1770A						PASS	.	G		8,4398	14.3+/-33.2	0,8,2195	60	64	63		1770	5.1	1	2	dbSNP_134	63	92,8508	51.5+/-111.7	1,90,4209	no	coding-synonymous	SH3BP4	NM_014521.2		1,98,6404	AA,AG,GG		1.0698,0.1816,0.7689		590/964	235951183	100,12906	2203	4300	6503	SO:0001819	synonymous_variant	23677	exon4			GCTGCGGGTTCAG	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.1770G>A	2.37:g.235951183G>A		104	0	0		73	38	0.520548	NM_014521	O95082|Q309A3|Q53QD0|Q53TD1	Silent	SNP	ENST00000409212.1	37	CCDS2513.1																																																																																			G|0.992;A|0.008	0.008	strong		0.587	SH3BP4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329763.1			A	235951183	G	A	235951183	2	1	27	1	0	0	0	0	0	0	0	1	14261	1219	43	2		2	SH3BP4	2	235951183	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1509049	235951183	7248190	163	10614											
AGAP1	116987	hgsc.bcm.edu	37	chr2	236817442	236817442	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgagaaccactgtgaaagtcCcagggaagaggccaccccga	13	4	12	12	1	0	3	0	2	0	2	1	6	1	4	5	2	1	0	5	2	3	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:236817442C>T	ENST00000304032.8	+	11	1796	c.1216C>T	c.(1216-1218)Cca>Tca	p.P406S	AGAP1_ENST00000409538.1_Missense_Mutation_p.P671S|AGAP1_ENST00000428334.2_Missense_Mutation_p.P245S|AGAP1_ENST00000336665.5_Missense_Mutation_p.P406S	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	406	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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						TGTGAAAGTCCCAGGGAAGAG	0.468																																					p.P406S		Atlas-SNP	.											.	AGAP1	95	.	0			c.C1216T						PASS	.						73	68	70					2																	236817442		2203	4300	6503	SO:0001583	missense	116987	exon11			AAAGTCCCAGGGA	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.1216C>T	2.37:g.236817442C>T	ENSP00000307634:p.Pro406Ser	116	0	0		153	20	0.130719	NM_014914	B2RTX7|Q541S5|Q6P9D7|Q9NV93	Missense_Mutation	SNP	ENST00000304032.8	37	CCDS33408.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	32|32	5.116727|5.116727	0.94385|0.94385	.|.	.|.	ENSG00000157985|ENSG00000157985	ENST00000448025|ENST00000304032;ENST00000336665;ENST00000409538;ENST00000428334	.|T;T;T;T	.|0.75367	.|-0.93;-0.93;-0.93;-0.93	4.66|4.66	4.66|4.66	0.58398|0.58398	.|Pleckstrin homology domain (3);	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	D|D	0.87350|0.87350	0.6155|0.6155	M|M	0.84082|0.84082	2.675|2.675	0.80722|0.80722	D|D	1|1	.|D;D	.|0.76494	.|0.998;0.999	.|D;D	.|0.91635	.|0.948;0.999	D|D	0.88666|0.88666	0.3192|0.3192	6|10	.|0.56958	.|D	.|0.05	.|.	18.4385|18.4385	0.90654|0.90654	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|406;406	.|Q9UPQ3-2;Q9UPQ3	.|.;AGAP1_HUMAN	L|S	39|406;406;671;245	.|ENSP00000307634:P406S;ENSP00000338378:P406S;ENSP00000386897:P671S;ENSP00000411824:P245S	.|ENSP00000307634:P406S	P|P	+|+	2|1	0|0	AGAP1|AGAP1	236482181|236482181	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.610000|7.610000	0.82949|0.82949	2.527000|2.527000	0.85204|0.85204	0.655000|0.655000	0.94253|0.94253	CCC|CCA	.	.	none		0.468	AGAP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257076.2	NM_014914		T	236817442	C	T	236817442	3	4	27	1	0	0	0	0	1	0	0	0	366	623	22	2	1258	2	AGAP1	2	236817442	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	866259	236817442	6381931	164	10615											
PRR21	643905	hgsc.bcm.edu	37	chr2	240982389	240982389	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gatgaagagctgtggatgaaCaggcatgcatgtggccaagg	12	7	16	6	0	0	3	0	2	0	1	0	5	0	4	1	4	3	3	1	4	3	0	rs143417758		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:240982389C>G	ENST00000408934.1	-	1	10	c.11G>C	c.(10-12)tGt>tCt	p.C4S		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	4										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						TGTGGATGAACAGGCATGCAT	0.567																																					p.C4S		Atlas-SNP	.											.	PRR21	53	.	0			c.G11C						PASS	.						73	62	65					2																	240982389		2172	4269	6441	SO:0001583	missense	643905	exon1			GATGAACAGGCAT	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.11G>C	2.37:g.240982389C>G	ENSP00000386166:p.Cys4Ser	29	0	0		12	7	0.583333	NM_001080835		Missense_Mutation	SNP	ENST00000408934.1	37	CCDS33417.1	.	.	.	.	.	.	.	.	.	.	c	5.954	0.359922	0.11296	.	.	ENSG00000221961	ENST00000408934;ENST00000486799	T;T	0.37752	1.18;1.18	0.149	0.149	0.14863	.	.	.	.	.	T	0.18173	0.0436	N	0.08118	0	0.19945	N	0.999941	P	0.37500	0.597	B	0.39119	0.291	T	0.15435	-1.0437	8	0.42905	T	0.14	.	.	.	.	.	4	Q8WXC7	PRR21_HUMAN	S	4	ENSP00000386166:C4S;ENSP00000418240:C4S	ENSP00000386166:C4S	C	-	2	0	PRR21	240631062	0.000000	0.05858	0.009000	0.14445	0.017000	0.09413	-0.776000	0.04674	0.192000	0.20272	0.195000	0.17529	TGT	.	.	weak		0.567	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835		G	240982389	C	G	240982389	3	3	27	1	0	0	0	0	1	0	0	0	12604	478	17	4	1161	4	PRR21	2	240982389	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	4164947	240982389	2216984	165	10616											
PPP1R7	5510	hgsc.bcm.edu	37	chr2	242122130	242122130	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagccaggagcctggagacAgtgtacctggagcggaaccc	10	4	16	11	1	0	1	0	0	0	1	0	6	0	5	4	5	5	1	4	5	2	1	rs113069444	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:242122130A>G	ENST00000234038.6	+	10	1449	c.975A>G	c.(973-975)acA>acG	p.T325T	PPP1R7_ENST00000407025.1_Silent_p.T325T|PPP1R7_ENST00000272983.8_Silent_p.T282T	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	325					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)		GCCTGGAGACAGTGTACCTGG	0.602													A|||	3	0.000599042	0.0	0.0	5008	,	,		19210	0.0		0.003	False		,,,				2504	0.0				p.T325T	NSCLC(62;446 1299 5417 11238 27640)	Atlas-SNP	.											PPP1R7,NS,carcinoma,+2,1	PPP1R7	35	1	0			c.A975G						PASS	.	A		3,4403	6.2+/-15.9	0,3,2200	127	116	120		975	-10.4	0.1	2	dbSNP_132	120	26,8574	18.5+/-59.3	0,26,4274	no	coding-synonymous	PPP1R7	NM_002712.1		0,29,6474	GG,GA,AA		0.3023,0.0681,0.223		325/361	242122130	29,12977	2203	4300	6503	SO:0001819	synonymous_variant	5510	exon10			GGAGACAGTGTAC	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.975A>G	2.37:g.242122130A>G		81	0	0		64	26	0.40625	NM_002712	B4DFD4|B5MCY6|Q9UQE5|Q9UQE6|Q9Y6K4	Silent	SNP	ENST00000234038.6	37	CCDS2546.1	3|3	0.0013736263736263737|0.0013736263736263737	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	3|3	0.00395778364116095|0.00395778364116095	A|A	6.902|6.902	0.536047|0.536047	0.13188|0.13188	6.81E-4|6.81E-4	0.003023|0.003023	ENSG00000115685|ENSG00000115685	ENST00000450367|ENST00000415769	.|.	.|.	.|.	5.19|5.19	-10.4|-10.4	0.00318|0.00318	.|.	.|.	.|.	.|.	.|.	T|T	0.41373|0.41373	0.1156|0.1156	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.54002|0.54002	-0.8358|-0.8358	4|4	.|.	.|.	.|.	-12.923|-12.923	5.0645|5.0645	0.14574|0.14574	0.3682:0.4119:0.0765:0.1434|0.3682:0.4119:0.0765:0.1434	.|.	.|.	.|.	.|.	R|G	300|47	.|.	.|.	Q|S	+|+	2|1	0|0	PPP1R7|PPP1R7	241770803|241770803	0.000000|0.000000	0.05858|0.05858	0.124000|0.124000	0.21820|0.21820	0.701000|0.701000	0.40568|0.40568	-5.138000|-5.138000	0.00147|0.00147	-3.714000|-3.714000	0.00117|0.00117	-1.258000|-1.258000	0.01471|0.01471	CAG|AGT	A|0.997;G|0.002;T|0.000	0.002	strong		0.602	PPP1R7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257244.4	NM_002712		G	242122130	A	G	242122130	2	3	27	1	0	0	0	0	0	0	0	1	12388	175	7	3		3	PPP1R7	2	242122130	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	1139741	242122130	1077243	166	10617											
ANO7	50636	hgsc.bcm.edu	37	chr2	242147054	242147054	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttgcctcgactgccctttctGgctgctctccagcgcctgtg	2	13	10	16	2	2	0	0	0	2	0	4	1	2	0	4	1	4	2	4	1	0	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr2:242147054G>A	ENST00000274979.8	+	11	1311	c.1208G>A	c.(1207-1209)tGg>tAg	p.W403*	ANO7_ENST00000402430.3_Nonsense_Mutation_p.W402*	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	403					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						TGCCCTTTCTGGCTGCTCTCC	0.617																																					p.W403X		Atlas-SNP	.											.	ANO7	136	.	0			c.G1208A						PASS	.						108	102	104					2																	242147054		2203	4300	6503	SO:0001587	stop_gained	50636	exon11			CTTTCTGGCTGCT	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.1208G>A	2.37:g.242147054G>A	ENSP00000274979:p.Trp403*	50	0	0		49	11	0.22449	NM_001001891	Q6IWH6	Nonsense_Mutation	SNP	ENST00000274979.8	37	CCDS33423.1	.	.	.	.	.	.	.	.	.	.	G	19.35	3.809907	0.70797	.	.	ENSG00000146205	ENST00000274979;ENST00000402430	.	.	.	2.49	2.49	0.30216	.	0.451423	0.21800	U	0.068929	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.4445	0.55643	0.0:0.0:1.0:0.0	.	.	.	.	X	403;402	.	ENSP00000274979:W403X	W	+	2	0	ANO7	241795727	1.000000	0.71417	1.000000	0.80357	0.400000	0.30750	6.347000	0.73004	1.315000	0.45114	0.313000	0.20887	TGG	.	.	none		0.617	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891		A	242147054	G	A	242147054	4	1	27	1	0	0	0	0	0	1	0	0	702	1357	47	2	1322	2	ANO7	2	242147054	Nonsense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	24924	242147054	1052319	167	10618											
IL5RA	3568	hgsc.bcm.edu	37	chr3	3139910	3139910	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acttggtatgaccttaaacgTgaataattgtcttctgtagt	11	16	8	6	1	2	2	0	2	2	0	2	2	2	2	1	1	1	2	1	1	6	7	rs141948767	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:3139910T>C	ENST00000446632.2	-	6	1006	c.432A>G	c.(430-432)tcA>tcG	p.S144S	IL5RA_ENST00000383846.1_Silent_p.S144S|IL5RA_ENST00000445864.2_Intron|IL5RA_ENST00000311981.8_Silent_p.S144S|IL5RA_ENST00000430514.2_Silent_p.S144S|IL5RA_ENST00000438560.1_Silent_p.S144S|IL5RA_ENST00000256452.3_Silent_p.S144S|IL5RA_ENST00000456302.1_Silent_p.S144S|IL5RA_ENST00000418488.2_Silent_p.S144S	NM_175726.3	NP_783853.1	Q01344	IL5RA_HUMAN	interleukin 5 receptor, alpha	144					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)		ACCTTAAACGTGAATAATTGT	0.423													T|||	5	0.000998403	0.0	0.0029	5008	,	,		21487	0.0		0.003	False		,,,				2504	0.0				p.S144S	GBM(169;430 2801 24955 28528)	Atlas-SNP	.											.	IL5RA	55	.	0			c.A432G						PASS	.	T	,,,,,	5,4401	9.9+/-24.2	0,5,2198	208	215	213		432,432,432,432,432,432	-8.4	0	3	dbSNP_134	213	23,8577	16.6+/-54.9	0,23,4277	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IL5RA	NM_000564.4,NM_175724.2,NM_175725.2,NM_175726.3,NM_175727.2,NM_175728.2	,,,,,	0,28,6475	CC,CT,TT		0.2674,0.1135,0.2153	,,,,,	144/421,144/334,144/336,144/421,144/334,144/336	3139910	28,12978	2203	4300	6503	SO:0001819	synonymous_variant	3568	exon6			TAAACGTGAATAA	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.432A>G	3.37:g.3139910T>C		268	0	0		244	109	0.446721	NM_001243099	B3IU77|B4E2G0|Q14633|Q15469|Q6ISX9	Silent	SNP	ENST00000446632.2	37	CCDS2559.1																																																																																			T|0.998;C|0.002	0.002	strong		0.423	IL5RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337537.2			C	3139910	T	C	3139910	2	2	27	1	0	0	0	0	0	0	0	1	7709	1683	59	3		3	IL5RA	3	3139910	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10		3139910	194882520	168	10619											
IL5RA	3568	hgsc.bcm.edu	37	chr3	3146610	3146610	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tttcatcaggaagtaagtcaGcttgcagtatctcagtggcc	10	12	10	9	0	4	0	4	0	1	0	5	1	4	1	1	2	2	4	1	2	3	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:3146610G>A	ENST00000446632.2	-	3	633	c.59C>T	c.(58-60)gCt>gTt	p.A20V	IL5RA_ENST00000311981.8_Missense_Mutation_p.A20V|SNORA43_ENST00000517240.1_RNA|IL5RA_ENST00000256452.3_Missense_Mutation_p.A20V|IL5RA_ENST00000430514.2_Missense_Mutation_p.A20V|IL5RA_ENST00000456302.1_Missense_Mutation_p.A20V|IL5RA_ENST00000445864.2_Missense_Mutation_p.A20V|IL5RA_ENST00000438560.1_Missense_Mutation_p.A20V|IL5RA_ENST00000418488.2_Missense_Mutation_p.A20V|IL5RA_ENST00000383846.1_Missense_Mutation_p.A20V	NM_175726.3	NP_783853.1	Q01344	IL5RA_HUMAN	interleukin 5 receptor, alpha	20					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)		AAGTAAGTCAGCTTGCAGTAT	0.348																																					p.A20V	GBM(169;430 2801 24955 28528)	Atlas-SNP	.											IL5RA,caecum,carcinoma,0,1	IL5RA	55	1	0			c.C59T						PASS	.						102	100	101					3																	3146610		2203	4300	6503	SO:0001583	missense	3568	exon3			AAGTCAGCTTGCA	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.59C>T	3.37:g.3146610G>A	ENSP00000412209:p.Ala20Val	186	0	0		178	44	0.247191	NM_001243099	B3IU77|B4E2G0|Q14633|Q15469|Q6ISX9	Missense_Mutation	SNP	ENST00000446632.2	37	CCDS2559.1	.	.	.	.	.	.	.	.	.	.	G	12.16	1.853768	0.32791	.	.	ENSG00000091181	ENST00000446632;ENST00000438560;ENST00000256452;ENST00000418488;ENST00000445864;ENST00000383846;ENST00000311981;ENST00000430514;ENST00000456302;ENST00000445701;ENST00000427088	D;D;D;T;T;T;T;T;T;T	0.88664	-2.41;-2.31;-2.41;1.08;1.37;1.14;1.14;1.15;1.15;1.41	5.6	0.812	0.18744	.	0.640598	0.15081	N	0.281648	T	0.79695	0.4490	L	0.31926	0.97	0.09310	N	1	B;B;B;B;B;B	0.33637	0.028;0.047;0.047;0.028;0.42;0.084	B;B;B;B;B;B	0.28465	0.024;0.022;0.032;0.01;0.09;0.028	T	0.66594	-0.5884	10	0.44086	T	0.13	-6.1116	8.1152	0.30940	0.4066:0.0:0.5934:0.0	.	20;20;20;20;20;20	B4E2G0;Q01344-3;Q01344-2;Q01344;B3IU77;E7ERY4	.;.;.;IL5RA_HUMAN;.;.	V	20	ENSP00000412209:A20V;ENSP00000390753:A20V;ENSP00000256452:A20V;ENSP00000388858:A20V;ENSP00000402598:A20V;ENSP00000373358:A20V;ENSP00000309196:A20V;ENSP00000400400:A20V;ENSP00000392059:A20V;ENSP00000398117:A20V	ENSP00000256452:A20V	A	-	2	0	IL5RA	3121610	0.016000	0.18221	0.000000	0.03702	0.030000	0.12068	0.998000	0.29744	-0.062000	0.13088	0.650000	0.86243	GCT	.	.	none		0.348	IL5RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337537.2			A	3146610	G	A	3146610	3	1	27	1	0	0	0	0	1	0	0	0	7709	971	34	2	1269	2	IL5RA	3	3146610	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	6700	3146610	194875820	169	10620											
GHRL	51738	hgsc.bcm.edu	37	chr3	10331519	10331519	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggagccagcctgctagagctCggggctgcagcttggctggt	5	8	17	11	1	0	1	0	0	0	1	1	2	0	2	2	5	6	6	2	5	1	2	rs34911341	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:10331519C>T	ENST00000335542.8	-	4	1022	c.152G>A	c.(151-153)cGa>cAa	p.R51Q	GHRL_ENST00000450603.1_Missense_Mutation_p.R51Q|GHRL_ENST00000430179.1_Missense_Mutation_p.R50Q|GHRL_ENST00000422159.1_Missense_Mutation_p.R51Q|GHRL_ENST00000457360.1_Missense_Mutation_p.R51Q|GHRL_ENST00000439975.2_Intron|GHRL_ENST00000449554.2_Missense_Mutation_p.R50Q|GHRL_ENST00000476283.1_5'Flank|GHRLOS_ENST00000439539.3_RNA|GHRLOS_ENST00000605014.1_RNA|GHRLOS_ENST00000603771.1_RNA|GHRL_ENST00000287656.7_Missense_Mutation_p.R50Q|GHRL_ENST00000449238.2_Missense_Mutation_p.R38Q|GHRL_ENST00000437422.2_Missense_Mutation_p.R39Q|GHRL_ENST00000446937.2_Intron|GHRLOS_ENST00000605105.1_RNA|GHRL_ENST00000429122.1_Missense_Mutation_p.R51Q			Q9UBU3	GHRL_HUMAN	ghrelin/obestatin prepropeptide	51					actin polymerization or depolymerization (GO:0008154)|activation of MAPK activity (GO:0000187)|adult feeding behavior (GO:0008343)|cartilage development (GO:0051216)|cellular protein metabolic process (GO:0044267)|cortisol secretion (GO:0043400)|decidualization (GO:0046697)|dendrite development (GO:0016358)|G-protein coupled receptor signaling pathway (GO:0007186)|gastric acid secretion (GO:0001696)|glucose metabolic process (GO:0006006)|growth hormone secretion (GO:0030252)|hormone-mediated signaling pathway (GO:0009755)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of circadian sleep/wake cycle, REM sleep (GO:0042322)|negative regulation of endothelial cell proliferation (GO:0001937)|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 locomotion (GO:0040013)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of appetite (GO:0032100)|positive regulation of circadian sleep/wake cycle, non-REM sleep (GO:0046010)|positive regulation of corticotropin secretion (GO:0051461)|positive regulation of cortisol secretion (GO:0051464)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of growth hormone secretion (GO:0060124)|positive regulation of insulin secretion (GO:0032024)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of synapse assembly (GO:0051965)|regulation of cell proliferation (GO:0042127)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|response to estrogen (GO:0043627)|response to hormone (GO:0009725)	axon (GO:0030424)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|secretory granule lumen (GO:0034774)	G-protein coupled receptor binding (GO:0001664)|ghrelin receptor binding (GO:0031768)|growth hormone-releasing hormone activity (GO:0016608)|protein tyrosine kinase activator activity (GO:0030296)			breast(2)|large_intestine(1)|lung(1)|ovary(1)	5						TGCTAGAGCTCGGGGCTGCAG	0.567													C|||	13	0.00259585	0.0	0.0014	5008	,	,		17746	0.005		0.007	False		,,,				2504	0.0				p.R51Q		Atlas-SNP	.											.	GHRL	8	.	0			c.G152A	GRCh37	CM012814	GHRL	M	rs34911341	PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG,,GLN/ARG	7,4399	14.3+/-33.2	0,7,2196	140	150	147	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	149,116,113,,152	4.9	1	3	dbSNP_126	147	53,8547	34.8+/-89.0	0,53,4247	yes	missense,missense,missense,intron,missense	GHRL	NM_001134941.1,NM_001134944.1,NM_001134945.1,NM_001134946.1,NM_016362.3	43,43,43,,43	0,60,6443	TT,TC,CC		0.6163,0.1589,0.4613	probably-damaging,probably-damaging,probably-damaging,,probably-damaging	50/117,39/106,38/105,,51/118	10331519	60,12946	2203	4300	6503	SO:0001583	missense	51738	exon3			AGAGCTCGGGGCT	AF296558	CCDS33700.1, CCDS46747.1, CCDS46748.1, CCDS46749.1, CCDS46750.1	3p26-p25	2013-02-26	2008-07-02		ENSG00000157017	ENSG00000157017		"Endogenous ligands"	18129	protein-coding gene	gene with protein product	"prepro-appetite regulatory hormone"	605353	"ghrelin, growth hormone secretagogue receptor ligand"			10930375, 10604470, 16284174	Standard	NR_024133		Approved	MTLRP, ghrelin, obestatin	uc010hdj.2	Q9UBU3	OTTHUMG00000155360	ENST00000335542.8:c.152G>A	3.37:g.10331519C>T	ENSP00000335074:p.Arg51Gln	92	0	0		110	57	0.518182	NM_016362	A8CF34|A8CF38|A8CF42|A8DN29|A8DN30|Q86YP8|Q8TAT9|Q9H3R3	Missense_Mutation	SNP	ENST00000335542.8	37	CCDS33700.1	6	0.0027472527472527475	0	0.0	0	0.0	1	0.0017482517482517483	5	0.006596306068601583	C	26.4	4.737997	0.89573	0.001589	0.006163	ENSG00000157017	ENST00000335542;ENST00000430179;ENST00000450603;ENST00000449554;ENST00000422159;ENST00000449238;ENST00000437422;ENST00000287656;ENST00000457360;ENST00000429122	T;T;T;T;T;T;T;T;T;T	0.62364	0.63;0.63;0.63;0.63;0.03;0.43;0.42;0.63;0.63;0.63	4.88	4.88	0.63580	Motilin/ghrelin (1);	0.000000	0.49305	D	0.000160	T	0.68796	0.3040	M	0.62088	1.915	0.43003	D	0.994528	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;0.996;0.998;0.996;0.999	T	0.73329	-0.4017	10	0.48119	T	0.1	-12.7683	13.3995	0.60874	0.0:1.0:0.0:0.0	rs34911341	38;39;51;50;51	Q9UBU3-4;Q9UBU3-3;Q9UBU3;Q9UBU3-2;Q86YP8	.;.;GHRL_HUMAN;.;.	Q	51;50;51;50;51;38;39;50;51;51	ENSP00000335074:R51Q;ENSP00000399922:R50Q;ENSP00000389192:R51Q;ENSP00000415521:R50Q;ENSP00000405464:R51Q;ENSP00000388145:R38Q;ENSP00000416768:R39Q;ENSP00000287656:R50Q;ENSP00000391406:R51Q;ENSP00000414819:R51Q	ENSP00000287656:R50Q	R	-	2	0	GHRL	10306519	0.997000	0.39634	0.981000	0.43875	0.957000	0.61999	3.731000	0.55013	2.531000	0.85337	0.655000	0.94253	CGA	C|0.996;T|0.004	0.004	strong		0.567	GHRL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000339625.1	NM_016362		T	10331519	C	T	10331519	3	4	27	1	0	0	0	0	1	0	0	0	6382	884	31	1	213	1	GHRL	3	10331519	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	7184909	10331519	187690911	170	10621											
NUP210	23225	hgsc.bcm.edu	37	chr3	13364836	13364836	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttagagcttctgtctcccaCggcaacaatcactttggagg	9	11	10	11	1	3	1	1	0	2	1	4	2	3	2	1	3	2	3	1	3	3	3	rs199752879		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:13364836C>T	ENST00000254508.5	-	34	4823	c.4741G>A	c.(4741-4743)Gtg>Atg	p.V1581M		NM_024923.2	NP_079199.2	Q8TEM1	PO210_HUMAN	nucleoporin 210kDa	1581					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)		p.V1581M(1)		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)					CTGTCTCCCACGGCAACAATC	0.582																																					p.V1581M		Atlas-SNP	.											NUP210,NS,carcinoma,0,1	NUP210	182	1	1	Substitution - Missense(1)	liver(1)	c.G4741A						PASS	.	C	MET/VAL	0,4406		0,0,2203	138	139	139		4741	-4.2	0	3		139	5,8595	4.3+/-15.6	0,5,4295	yes	missense	NUP210	NM_024923.2	21	0,5,6498	TT,TC,CC		0.0581,0.0,0.0384	possibly-damaging	1581/1888	13364836	5,13001	2203	4300	6503	SO:0001583	missense	23225	exon34			CTCCCACGGCAAC	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.4741G>A	3.37:g.13364836C>T	ENSP00000254508:p.Val1581Met	78	0	0		64	23	0.359375	NM_024923	A6NN56|O94980|Q6NXG6|Q8NBJ1|Q9H6C8|Q9UFP3	Missense_Mutation	SNP	ENST00000254508.5	37	CCDS33704.1	.	.	.	.	.	.	.	.	.	.	C	11.56	1.674605	0.29693	0.0	5.81E-4	ENSG00000132182	ENST00000254508	T	0.04970	3.52	5.54	-4.17	0.03857	.	0.660669	0.15319	N	0.268660	T	0.04182	0.0116	L	0.46157	1.445	0.09310	N	1	B	0.17268	0.021	B	0.08055	0.003	T	0.36212	-0.9757	10	0.48119	T	0.1	-10.586	0.6247	0.00784	0.3136:0.1703:0.125:0.3911	.	1581	Q8TEM1	PO210_HUMAN	M	1581	ENSP00000254508:V1581M	ENSP00000254508:V1581M	V	-	1	0	NUP210	13339836	0.028000	0.19301	0.020000	0.16555	0.749000	0.42624	-0.160000	0.10041	-0.685000	0.05177	-0.137000	0.14449	GTG	.	.	weak		0.582	NUP210-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340085.1	NM_024923		T	13364836	C	T	13364836	3	4	27	1	0	0	0	0	1	0	0	0	10769	536	19	1	950	1	NUP210	3	13364836	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3033317	13364836	184657594	171	10622											
SLC6A6	6533	hgsc.bcm.edu	37	chr3	14489107	14489107	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caggtatcggctatgcctccGttgtaattgtgtccctcctg	5	14	10	12	2	0	0	0	0	0	0	4	0	3	0	4	2	1	4	4	2	3	5	rs62233560	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:14489107G>A	ENST00000454876.2	+	5	711	c.382G>A	c.(382-384)Gtt>Att	p.V128I	SLC6A6_ENST00000416216.2_Missense_Mutation_p.V128I|SLC6A6_ENST00000360861.3_Missense_Mutation_p.V128I|SLC6A6_ENST00000484191.1_3'UTR			P31641	SC6A6_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 6	128					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						CTATGCCTCCGTTGTAATTGT	0.547													A|||	27	0.00539137	0.0	0.0101	5008	,	,		21505	0.001		0.0129	False		,,,				2504	0.0061				p.V128I		Atlas-SNP	.											.	SLC6A6	58	.	0			c.G382A						PASS	.	A	ILE/VAL,ILE/VAL,ILE/VAL	12,4394	825.1+/-416.5	0,12,2191	410	392	398		382,382,382	5.1	1	3	dbSNP_129	398	72,8528	816.0+/-406.9	2,68,4230	yes	missense,missense,missense	SLC6A6	NM_001134367.1,NM_001134368.1,NM_003043.3	29,29,29	2,80,6421	AA,AG,GG		0.8372,0.2724,0.6459	benign,benign,benign	128/621,128/201,128/621	14489107	84,12922	2203	4300	6503	SO:0001583	missense	6533	exon5			GCCTCCGTTGTAA		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.382G>A	3.37:g.14489107G>A	ENSP00000398063:p.Val128Ile	134	0	0		118	57	0.483051	NM_003043	B2RNU7|Q9BRI2|Q9BXB0	Missense_Mutation	SNP	ENST00000454876.2	37	CCDS33705.1	15	0.006868131868131868	0	0.0	4	0.011049723756906077	1	0.0017482517482517483	10	0.013192612137203167	A	5.409	0.260708	0.10239	0.002724	0.008372	ENSG00000131389	ENST00000454876;ENST00000360861;ENST00000416216	T;T;T	0.75938	-0.98;-0.98;-0.98	5.05	5.05	0.67936	.	0.106550	0.64402	N	0.000007	T	0.44414	0.1292	N	0.05608	-0.01	0.09310	N	0.999997	B	0.02656	0.0	B	0.04013	0.001	T	0.26018	-1.0115	10	0.17832	T	0.49	.	10.8576	0.46808	0.9255:0.0:0.0745:0.0	rs62233560	128	P31641	SC6A6_HUMAN	I	128	ENSP00000398063:V128I;ENSP00000354107:V128I;ENSP00000401167:V128I	ENSP00000354107:V128I	V	+	1	0	SLC6A6	14464111	1.000000	0.71417	0.999000	0.59377	0.076000	0.17211	2.449000	0.44935	0.778000	0.33520	-0.434000	0.05882	GTT	G|0.992;A|0.008	0.008	strong		0.547	SLC6A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340507.1	NM_003043		A	14489107	G	A	14489107	3	1	27	1	0	0	0	0	1	0	0	0	14703	1145	40	1	392	1	SLC6A6	3	14489107	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1124271	14489107	183533323	172	10623											
EAF1	85403	hgsc.bcm.edu	37	chr3	15477861	15477861	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tattccagagctgagggctgAagttgacattattgaacaaa	14	11	10	6	0	0	5	0	4	0	1	1	5	1	5	1	1	2	3	1	1	5	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:15477861A>G	ENST00000396842.2	+	5	964	c.539A>G	c.(538-540)gAa>gGa	p.E180G	EAF1-AS1_ENST00000594820.1_RNA|EAF1-AS1_ENST00000595975.1_RNA|EAF1-AS1_ENST00000597949.1_RNA|EAF1-AS1_ENST00000596371.1_RNA|EAF1-AS1_ENST00000494875.3_RNA|EAF1-AS1_ENST00000595627.1_RNA|EAF1-AS1_ENST00000608780.1_RNA|EAF1-AS1_ENST00000609310.1_RNA|EAF1-AS1_ENST00000593876.1_RNA|EAF1_ENST00000432764.2_Missense_Mutation_p.E79G	NM_033083.6	NP_149074.3	Q96JC9	EAF1_HUMAN	ELL associated factor 1	180					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ELL-EAF complex (GO:0032783)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|urinary_tract(1)	7						CTGAGGGCTGAAGTTGACATT	0.473																																					p.E180G		Atlas-SNP	.											.	EAF1	16	.	0			c.A539G						PASS	.						45	46	45					3																	15477861		2203	4300	6503	SO:0001583	missense	85403	exon5			GGGCTGAAGTTGA	AF272973	CCDS2626.1	3p25.1	2011-06-10			ENSG00000144597	ENSG00000144597			20907	protein-coding gene	gene with protein product		608315				11418481	Standard	NM_033083		Approved		uc003bzu.3	Q96JC9	OTTHUMG00000162544	ENST00000396842.2:c.539A>G	3.37:g.15477861A>G	ENSP00000380054:p.Glu180Gly	151	0	0		161	32	0.198758	NM_033083	B4E3F5|Q8IW10	Missense_Mutation	SNP	ENST00000396842.2	37	CCDS2626.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.523059	0.85600	.	.	ENSG00000144597	ENST00000396842;ENST00000432764	.	.	.	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.78848	0.4348	M	0.78637	2.42	0.80722	D	1	D;D	0.71674	0.989;0.998	D;D	0.70487	0.969;0.968	T	0.81678	-0.0824	9	0.72032	D	0.01	-27.7472	14.8502	0.70292	1.0:0.0:0.0:0.0	.	79;180	B4E3F5;Q96JC9	.;EAF1_HUMAN	G	180;79	.	ENSP00000380054:E180G	E	+	2	0	EAF1	15452865	1.000000	0.71417	0.898000	0.35279	0.924000	0.55760	8.962000	0.93254	2.150000	0.67090	0.397000	0.26171	GAA	.	.	none		0.473	EAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252100.4	NM_033083		G	15477861	A	G	15477861	3	3	27	1	0	0	0	0	1	0	0	0	4877	246	9	3	557	3	EAF1	3	15477861	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	988754	15477861	182544569	173	10624											
EAF1	85403	hgsc.bcm.edu	37	chr3	15477872	15477872	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgagggctgaagttgacattAttgaacaaatgagcagcagc	14	9	12	6	0	0	5	0	5	0	0	0	5	0	5	0	1	4	4	0	1	4	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:15477872A>C	ENST00000396842.2	+	5	975	c.550A>C	c.(550-552)Att>Ctt	p.I184L	EAF1-AS1_ENST00000594820.1_RNA|EAF1-AS1_ENST00000595975.1_RNA|EAF1-AS1_ENST00000597949.1_RNA|EAF1-AS1_ENST00000596371.1_RNA|EAF1-AS1_ENST00000494875.3_RNA|EAF1-AS1_ENST00000595627.1_RNA|EAF1-AS1_ENST00000608780.1_RNA|EAF1-AS1_ENST00000609310.1_RNA|EAF1-AS1_ENST00000593876.1_RNA|EAF1_ENST00000432764.2_Missense_Mutation_p.I83L	NM_033083.6	NP_149074.3	Q96JC9	EAF1_HUMAN	ELL associated factor 1	184	Necessary for transactivation activity.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ELL-EAF complex (GO:0032783)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|urinary_tract(1)	7						AGTTGACATTATTGAACAAAT	0.483																																					p.I184L		Atlas-SNP	.											.	EAF1	16	.	0			c.A550C						PASS	.						46	47	47					3																	15477872		2203	4300	6503	SO:0001583	missense	85403	exon5			GACATTATTGAAC	AF272973	CCDS2626.1	3p25.1	2011-06-10			ENSG00000144597	ENSG00000144597			20907	protein-coding gene	gene with protein product		608315				11418481	Standard	NM_033083		Approved		uc003bzu.3	Q96JC9	OTTHUMG00000162544	ENST00000396842.2:c.550A>C	3.37:g.15477872A>C	ENSP00000380054:p.Ile184Leu	158	0	0		168	35	0.208333	NM_033083	B4E3F5|Q8IW10	Missense_Mutation	SNP	ENST00000396842.2	37	CCDS2626.1	.	.	.	.	.	.	.	.	.	.	A	28.0	4.885242	0.91814	.	.	ENSG00000144597	ENST00000396842;ENST00000432764	.	.	.	5.67	5.67	0.87782	.	0.091650	0.64402	D	0.000001	T	0.62368	0.2422	M	0.65975	2.015	0.58432	D	0.999999	B;B	0.15473	0.013;0.011	B;B	0.17722	0.019;0.003	T	0.60347	-0.7281	9	0.49607	T	0.09	-10.8435	14.8972	0.70651	1.0:0.0:0.0:0.0	.	83;184	B4E3F5;Q96JC9	.;EAF1_HUMAN	L	184;83	.	ENSP00000380054:I184L	I	+	1	0	EAF1	15452876	1.000000	0.71417	0.966000	0.40874	0.886000	0.51366	8.962000	0.93254	2.159000	0.67721	0.454000	0.30748	ATT	.	.	none		0.483	EAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252100.4	NM_033083		C	15477872	A	C	15477872	3	2	27	1	0	0	0	0	1	0	0	0	4877	449	16	5	568	5	EAF1	3	15477872	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	11	15477872	182544558	174	10625											
ZCWPW2	152098	hgsc.bcm.edu	37	chr3	28454627	28454627	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatggattcctcagtggaaaAcatgtatgtaaacaaagtgt	16	11	9	5	0	1	0	1	0	0	0	2	2	2	2	1	2	2	2	1	2	7	3	rs148504648	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:28454627A>G	ENST00000383768.2	+	3	256	c.68A>G	c.(67-69)aAc>aGc	p.N23S	ZCWPW2_ENST00000421010.1_Missense_Mutation_p.N23S			Q504Y3	ZCPW2_HUMAN	zinc finger, CW type with PWWP domain 2	23							zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(6)|ovary(2)	17						TCAGTGGAAAACATGTATGTA	0.323													A|||	2	0.000399361	0.0	0.0	5008	,	,		19875	0.0		0.002	False		,,,				2504	0.0				p.N23S		Atlas-SNP	.											.	ZCWPW2	49	.	0			c.A68G						PASS	.	A	SER/ASN	6,4400	9.9+/-24.2	0,6,2197	109	107	108		68	0.1	0	3	dbSNP_134	108	25,8575	17.3+/-56.4	0,25,4275	yes	missense	ZCWPW2	NM_001040432.1	46	0,31,6472	GG,GA,AA		0.2907,0.1362,0.2384	benign	23/357	28454627	31,12975	2203	4300	6503	SO:0001583	missense	152098	exon2			TGGAAAACATGTA	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.68A>G	3.37:g.28454627A>G	ENSP00000373278:p.Asn23Ser	131	0	0		83	28	0.337349	NM_001040432		Missense_Mutation	SNP	ENST00000383768.2	37	CCDS33723.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	16.03	3.007777	0.54361	0.001362	0.002907	ENSG00000206559	ENST00000420223;ENST00000383768;ENST00000421010	T;T	0.32988	1.43;1.43	5.37	0.0559	0.14317	.	0.328394	0.26474	N	0.024175	T	0.18383	0.0441	L	0.29908	0.895	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.15350	-1.0440	10	0.36615	T	0.2	-2.9798	7.7479	0.28879	0.5196:0.0:0.4804:0.0	.	23	Q504Y3	ZCPW2_HUMAN	S	23	ENSP00000373278:N23S;ENSP00000412386:N23S	ENSP00000373278:N23S	N	+	2	0	ZCWPW2	28429631	0.001000	0.12720	0.033000	0.17914	0.962000	0.63368	-0.160000	0.10041	0.000000	0.14550	0.482000	0.46254	AAC	A|0.998;G|0.002	0.002	strong		0.323	ZCWPW2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341318.1	XM_087384		G	28454627	A	G	28454627	3	3	27	1	0	0	0	0	1	0	0	0	17613	43	2	3	70	3	ZCWPW2	3	28454627	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	12976755	28454627	169567803	175	10626											
OSBPL10	114884	hgsc.bcm.edu	37	chr3	32022622	32022622	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cacggctgctgctgcggctgCtgctgttgctacccccgccg	2	9	13	17	4	0	0	0	0	0	0	0	0	0	0	3	2	7	8	3	2	1	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:32022622C>T	ENST00000396556.2	-	1	172	c.50G>A	c.(49-51)aGc>aAc	p.S17N	OSBPL10_ENST00000438237.2_Missense_Mutation_p.S17N|ZNF860_ENST00000360311.4_5'Flank	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	17					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)		gctgcggctgctgctgttgct	0.791																																					p.S17N		Atlas-SNP	.											.	OSBPL10	160	.	0			c.G50A						PASS	.						2	3	2					3																	32022622		662	1473	2135	SO:0001583	missense	114884	exon1			CGGCTGCTGCTGT	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.50G>A	3.37:g.32022622C>T	ENSP00000379804:p.Ser17Asn	8	0	0		21	12	0.571429	NM_017784	B4E212|Q9BTU5	Missense_Mutation	SNP	ENST00000396556.2	37	CCDS2651.1	.	.	.	.	.	.	.	.	.	.	C	13.12	2.141933	0.37825	.	.	ENSG00000144645	ENST00000396556;ENST00000438237	T;T	0.26518	1.73;2.07	3.91	3.91	0.45181	.	2.901820	0.03061	N	0.155841	T	0.22898	0.0553	N	0.19112	0.55	0.26378	N	0.976786	B;B	0.27498	0.18;0.18	B;B	0.23716	0.048;0.048	T	0.23119	-1.0197	10	0.51188	T	0.08	.	13.8256	0.63348	0.0:1.0:0.0:0.0	.	17;17	B4E212;Q9BXB5	.;OSB10_HUMAN	N	17	ENSP00000379804:S17N;ENSP00000406124:S17N	ENSP00000379804:S17N	S	-	2	0	OSBPL10	31997626	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	2.460000	0.45031	2.196000	0.70406	0.298000	0.19748	AGC	.	.	none		0.791	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2			T	32022622	C	T	32022622	3	4	27	1	0	0	0	0	1	0	0	0	11284	797	28	2	2292	2	OSBPL10	3	32022622	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3567995	32022622	165999808	176	10627											
DCLK3	85443	hgsc.bcm.edu	37	chr3	36759599	36759599	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccctctcagggctgcggaatGggggaaagccacacagcagg	10	4	15	12	1	1	0	1	0	1	0	2	2	1	2	2	5	3	2	2	5	2	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:36759599G>C	ENST00000416516.2	-	4	2145	c.1655C>G	c.(1654-1656)cCa>cGa	p.P552R	DCLK3_ENST00000498047.1_5'UTR	NM_033403.1	NP_208382.1	Q9C098	DCLK3_HUMAN	doublecortin-like kinase 3	552	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						GCTGCGGAATGGGGGAAAGCC	0.552																																					p.P552R		Atlas-SNP	.											.	DCLK3	95	.	0			c.C1655G						PASS	.						157	171	167					3																	36759599		2085	4248	6333	SO:0001583	missense	85443	exon4			CGGAATGGGGGAA	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.1655C>G	3.37:g.36759599G>C	ENSP00000394484:p.Pro552Arg	67	0	0		89	28	0.314607	NM_033403		Missense_Mutation	SNP	ENST00000416516.2	37	CCDS43064.1	.	.	.	.	.	.	.	.	.	.	G	19.91	3.913710	0.72983	.	.	ENSG00000163673	ENST00000416516	T	0.58652	0.32	5.51	5.51	0.81932	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	0.32518	N	0.005993	D	0.86464	0.5939	H	0.98446	4.235	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91296	0.5063	10	0.87932	D	0	.	19.7913	0.96458	0.0:0.0:1.0:0.0	.	552	Q9C098	DCLK3_HUMAN	R	552	ENSP00000394484:P552R	ENSP00000394484:P552R	P	-	2	0	DCLK3	36734603	1.000000	0.71417	0.754000	0.31244	0.213000	0.24496	9.869000	0.99810	2.765000	0.95021	0.555000	0.69702	CCA	.	.	none		0.552	DCLK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341727.1	XM_047355		C	36759599	G	C	36759599	3	2	27	1	0	0	0	0	1	0	0	0	4295	1348	47	4	299	4	DCLK3	3	36759599	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	4736977	36759599	161262831	177	10628											
GOLGA4	2803	hgsc.bcm.edu	37	chr3	37368710	37368710	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccaataccaggagcgcttaaTaaagctagaacatgctgagg	15	7	10	9	1	0	2	0	1	0	1	0	3	0	3	2	2	5	3	2	2	7	4	rs144205536	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:37368710T>A	ENST00000361924.2	+	14	5707	c.5333T>A	c.(5332-5334)aTa>aAa	p.I1778K	GOLGA4_ENST00000444882.1_Intron|GOLGA4_ENST00000356847.4_Missense_Mutation_p.I1800K	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1778	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						GAGCGCTTAATAAAGCTAGAA	0.373													T|||	2	0.000399361	0.0	0.0	5008	,	,		20680	0.0		0.002	False		,,,				2504	0.0				p.I1800K		Atlas-SNP	.											.	GOLGA4	173	.	0			c.T5399A						PASS	.	T	LYS/ILE,LYS/ILE	1,4405	2.1+/-5.4	0,1,2202	98	100	99		5399,5333	-4.5	0	3	dbSNP_134	99	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	GOLGA4	NM_001172713.1,NM_002078.4	102,102	0,4,6499	AA,AT,TT		0.0349,0.0227,0.0308	benign,benign	1800/2244,1778/2231	37368710	4,13002	2203	4300	6503	SO:0001583	missense	2803	exon15			GCTTAATAAAGCT	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.5333T>A	3.37:g.37368710T>A	ENSP00000354486:p.Ile1778Lys	150	0	0		106	52	0.490566	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	37	CCDS2666.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	4.803	0.149256	0.09185	2.27E-4	3.49E-4	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000437131	T;T;T	0.20332	2.08;2.08;2.08	4.59	-4.53	0.03462	.	0.710473	0.11563	N	0.551556	T	0.06917	0.0176	N	0.17474	0.49	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;0.0	T	0.39840	-0.9594	10	0.06099	T	0.92	.	1.6064	0.02684	0.1664:0.2826:0.3456:0.2054	.	1778;1778;1800;1778	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	K	1778;1800;1649	ENSP00000354486:I1778K;ENSP00000349305:I1800K;ENSP00000405842:I1649K	ENSP00000349305:I1800K	I	+	2	0	GOLGA4	37343714	0.000000	0.05858	0.000000	0.03702	0.156000	0.22039	-0.047000	0.11963	-0.318000	0.08665	0.459000	0.35465	ATA	T|0.999;A|0.001	0.001	strong		0.373	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078		A	37368710	T	A	37368710	3	1	27	1	0	0	0	0	1	0	0	0	6563	1406	49	5	5457	5	GOLGA4	3	37368710	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	609111	37368710	160653720	178	10629											
SCN10A	6336	hgsc.bcm.edu	37	chr3	38739416	38739416	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagagagtgtctgcaaagtcCgagagagcagaaaaggtaat	16	6	14	5	1	1	3	0	0	1	3	2	7	2	3	1	1	2	3	1	1	4	1	rs145313578	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:38739416C>T	ENST00000449082.2	-	27	5294	c.5295G>A	c.(5293-5295)tcG>tcA	p.S1765S		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	1765					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)	CTGCAAAGTCCGAGAGAGCAG	0.498													C|||	4	0.000798722	0.0	0.0014	5008	,	,		19894	0.0		0.001	False		,,,				2504	0.002				p.S1765S		Atlas-SNP	.											SCN10A,NS,carcinoma,-1,2	SCN10A	359	2	0			c.G5295A						scavenged	.	C		1,4405	2.1+/-5.4	0,1,2202	76	80	79		5295	-10.8	0.2	3	dbSNP_134	79	12,8588	8.4+/-32.0	0,12,4288	no	coding-synonymous	SCN10A	NM_006514.2		0,13,6490	TT,TC,CC		0.1395,0.0227,0.1		1765/1957	38739416	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	6336	exon27			AAAGTCCGAGAGA	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.5295G>A	3.37:g.38739416C>T		166	2	0.0120482		165	80	0.484848	NM_006514	A6NDQ1	Silent	SNP	ENST00000449082.2	37	CCDS33736.1																																																																																			C|0.999;T|0.001	0.001	strong		0.498	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514		T	38739416	C	T	38739416	2	4	27	1	0	0	0	0	0	0	0	1	13927	639	23	1		1	SCN10A	3	38739416	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1370706	38739416	159283014	179	10630											
TTC21A	199223	hgsc.bcm.edu	37	chr3	39156124	39156124	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	actcagaggccctggaggtgGtgaaccagatcactgtgact	10	8	13	10	0	2	4	2	2	0	2	2	5	2	5	2	4	1	0	2	4	1	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:39156124G>A	ENST00000431162.2	+	6	741	c.607G>A	c.(607-609)Gtg>Atg	p.V203M	TTC21A_ENST00000301819.6_Missense_Mutation_p.V203M|TTC21A_ENST00000440121.1_Missense_Mutation_p.V162M			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	203										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)		CCTGGAGGTGGTGAACCAGAT	0.552																																					p.V203M		Atlas-SNP	.											.	TTC21A	96	.	0			c.G607A						PASS	.						136	133	134					3																	39156124		2028	4185	6213	SO:0001583	missense	199223	exon6			GAGGTGGTGAACC	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.607G>A	3.37:g.39156124G>A	ENSP00000398211:p.Val203Met	141	0	0		128	19	0.148438	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	37	CCDS46800.1	.	.	.	.	.	.	.	.	.	.	G	19.00	3.742688	0.69418	.	.	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.64618	-0.11;-0.11;2.27	5.0	5.0	0.66597	Tetratricopeptide-like helical (1);	0.183014	0.35615	N	0.003092	T	0.73690	0.3619	M	0.72118	2.19	0.28282	N	0.923935	D;D;D;D;D	0.61080	0.967;0.989;0.989;0.981;0.989	P;D;D;P;D	0.63192	0.805;0.912;0.912;0.819;0.912	T	0.69439	-0.5145	10	0.54805	T	0.06	-18.6922	10.7065	0.45958	0.0894:0.0:0.9106:0.0	.	162;203;203;203;203	Q8NDW8-6;Q8NDW8-5;Q8NDW8-7;Q8NDW8;F5H6V8	.;.;.;TT21A_HUMAN;.	M	203;203;203;162	ENSP00000301819:V203M;ENSP00000398211:V203M;ENSP00000410882:V162M	ENSP00000301819:V203M	V	+	1	0	TTC21A	39131128	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.201000	0.51059	2.316000	0.78162	0.561000	0.74099	GTG	.	.	none		0.552	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755		A	39156124	G	A	39156124	3	1	27	1	0	0	0	0	1	0	0	0	16702	1261	44	2	629	2	TTC21A	3	39156124	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	416708	39156124	158866306	180	10631											
CCR8	1237	hgsc.bcm.edu	37	chr3	39374151	39374151	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgtaatgtgcaaagtggtgtCtggcttttattacattggct	8	17	11	5	0	1	0	0	0	1	0	1	0	1	0	0	3	2	4	0	3	4	5	rs144913149		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:39374151C>T	ENST00000326306.4	+	2	467	c.329C>T	c.(328-330)tCt>tTt	p.S110F	CCR8_ENST00000545843.1_Missense_Mutation_p.S27F|CCR8_ENST00000414803.1_Silent_p.V52V	NM_005201.3	NP_005192.1	P51685	CCR8_HUMAN	chemokine (C-C motif) receptor 8	110					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)		AAAGTGGTGTCTGGCTTTTAT	0.493													C|||	1	0.000199681	0.0	0.0	5008	,	,		24185	0.0		0.001	False		,,,				2504	0.0				p.S110F		Atlas-SNP	.											.	CCR8	34	.	0			c.C329T						PASS	.	C	PHE/SER	1,4405	2.1+/-5.4	0,1,2202	248	223	231		329	4.7	1	3	dbSNP_134	231	15,8585	10.5+/-38.8	0,15,4285	yes	missense	CCR8	NM_005201.3	155	0,16,6487	TT,TC,CC		0.1744,0.0227,0.123	probably-damaging	110/356	39374151	16,12990	2203	4300	6503	SO:0001583	missense	1237	exon2			TGGTGTCTGGCTT	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.329C>T	3.37:g.39374151C>T	ENSP00000326432:p.Ser110Phe	416	0	0		354	180	0.508475	NM_005201	B2RC64|Q3KNQ8|Q3KNR3|Q9BYX5	Missense_Mutation	SNP	ENST00000326306.4	37	CCDS2684.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	15.81	2.941871	0.53079	2.27E-4	0.001744	ENSG00000179934	ENST00000326306;ENST00000545843	T;T	0.37584	1.19;1.19	4.67	4.67	0.58626	GPCR, rhodopsin-like superfamily (1);	0.316313	0.30142	N	0.010316	T	0.59252	0.2180	M	0.79343	2.45	0.36556	D	0.872118	D;D	0.71674	0.998;0.998	D;D	0.80764	0.994;0.994	T	0.69676	-0.5081	10	0.87932	D	0	.	12.254	0.54613	0.1705:0.8294:0.0:0.0	.	110;27	P51685;Q3KNR3	CCR8_HUMAN;.	F	110;27	ENSP00000326432:S110F;ENSP00000440474:S27F	ENSP00000326432:S110F	S	+	2	0	CCR8	39349155	0.000000	0.05858	1.000000	0.80357	0.981000	0.71138	0.375000	0.20518	2.429000	0.82318	0.563000	0.77884	TCT	C|0.999;T|0.001	0.001	strong		0.493	CCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254058.2	NM_005201		T	39374151	C	T	39374151	3	4	27	1	0	0	0	0	1	0	0	0	2949	913	32	2	331	2	CCR8	3	39374151	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	218027	39374151	158648279	181	10632											
CCR8	1237	hgsc.bcm.edu	37	chr3	39374514	39374516	+	In_Frame_Del	DEL	ACA	ACA	-																															gctgaagaggtgtcaaaaccAcaacaagaccaaggccatca																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	ACA	ACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:39374514_39374516delACA	ENST00000326306.4	+	2	830_832	c.692_694delACA	c.(691-696)cacaac>cac	p.N232del	CCR8_ENST00000545843.1_In_Frame_Del_p.N149del|CCR8_ENST00000414803.1_3'UTR	NM_005201.3	NP_005192.1	P51685	CCR8_HUMAN	chemokine (C-C motif) receptor 8	232					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)		TGTCAAAACCACAACAAGACCAA	0.429																																					p.231_231del		Pindel,Atlas-Indel	.											.	CCR8	34	.	0			c.691_693del						PASS	.			1,4265		0,1,2132						3.9	1			109	0,8248		0,0,4124	no	coding	CCR8	NM_005201.3		0,1,6256	A1A1,A1R,RR		0.0,0.0234,0.0080				1,12513				SO:0001651	inframe_deletion	1237	exon2			.	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.692_694delACA	3.37:g.39374517_39374519delACA	ENSP00000326432:p.Asn232del	372	0	.		296	57	0.193	NM_005201	B2RC64|Q3KNQ8|Q3KNR3|Q9BYX5	In_Frame_Del	DEL	ENST00000326306.4	37	CCDS2684.1																																																																																			.	.	none		0.429	CCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254058.2	NM_005201		-	39374516	ACA	-	39374514	7	5	27	1	0	1	0	1	0	0	0	0	2949	159	6	0	694	0	CCR8	3	39374514	In_Frame_Del	DEL	ACA	TCGA-G8-6909-01A-11D-2210-10	363	39374514	158647916	182	10633											
CCDC71	64925	hgsc.bcm.edu	37	chr3	49200611	49200616	+	In_Frame_Del	DEL	GCCTTG	GCCTTG	-																															cccgtactgccttggctttaGccttggccttggcccatgct																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GCCTTG	GCCTTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:49200611_49200616delGCCTTG	ENST00000321895.6	-	2	1132_1137	c.1026_1031delCAAGGC	c.(1024-1032)gccaaggct>gct	p.342_344AKA>A		NM_022903.3	NP_075054.3	Q8IV32	CCD71_HUMAN	coiled-coil domain containing 71	342										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)		cttggctttagccttggccttggccc	0.617																																					p.343_344del		Pindel,Atlas-Indel	.											.	CCDC71	33	.	0			c.1027_1032del						PASS	.																																			SO:0001651	inframe_deletion	64925	exon2			.	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.1026_1031delCAAGGC	3.37:g.49200617_49200622delGCCTTG	ENSP00000319006:p.Ala346_Lys347del	69	0	.		86	21	0.244	NM_022903	Q6IPE2|Q9H8H4|Q9H9F1	In_Frame_Del	DEL	ENST00000321895.6	37	CCDS2790.1																																																																																			.	.	none		0.617	CCDC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345980.1	NM_022903		-	49200616	GCCTTG	-	49200611	7	5	27	1	0	1	0	1	0	0	0	0	2846	971	34	0	376	0	CCDC71	3	49200611	In_Frame_Del	DEL	GCCTTG	TCGA-G8-6909-01A-11D-2210-10	9826097	49200611	148821819	183	10634											
BSN	8927	hgsc.bcm.edu	37	chr3	49693972	49693972	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgcaggagccccagctcCtgccccactagctggccaga	7	5	12	17	0	0	1	0	0	0	1	1	2	1	2	6	3	5	4	6	3	1	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:49693972C>T	ENST00000296452.4	+	5	7097	c.6983C>T	c.(6982-6984)cCt>cTt	p.P2328L		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	2328					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)		GCCCCAGCTCCTGCCCCACTA	0.652																																					p.P2328L		Atlas-SNP	.											.	BSN	272	.	0			c.C6983T						PASS	.						8	9	9					3																	49693972		2177	4270	6447	SO:0001583	missense	8927	exon5			CAGCTCCTGCCCC	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.6983C>T	3.37:g.49693972C>T	ENSP00000296452:p.Pro2328Leu	62	0	0		45	18	0.4	NM_003458	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	37	CCDS2800.1	.	.	.	.	.	.	.	.	.	.	C	3.630	-0.075656	0.07184	.	.	ENSG00000164061	ENST00000296452	T	0.17370	2.28	5.38	5.38	0.77491	.	0.902375	0.09734	N	0.762721	T	0.14013	0.0339	N	0.24115	0.695	0.53688	D	0.999974	B	0.27559	0.181	B	0.21708	0.036	T	0.11348	-1.0591	10	0.30854	T	0.27	-0.369	14.5099	0.67776	0.0:1.0:0.0:0.0	.	2328	Q9UPA5	BSN_HUMAN	L	2328	ENSP00000296452:P2328L	ENSP00000296452:P2328L	P	+	2	0	BSN	49668976	0.002000	0.14202	0.055000	0.19348	0.331000	0.28603	1.786000	0.38694	2.813000	0.96785	0.655000	0.94253	CCT	.	.	none		0.652	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		T	49693972	C	T	49693972	3	4	27	1	0	0	0	0	1	0	0	0	1532	681	24	2	7001	2	BSN	3	49693972	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	493361	49693972	148328458	184	10635											
ZMYND10	51364	hgsc.bcm.edu	37	chr3	50379257	50379257	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttaccttcgcgcctgcagccGcaggtcctgctctgaggggc	4	9	13	15	3	1	1	0	1	1	0	3	1	2	1	4	3	4	3	4	3	1	2	rs142613783	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:50379257G>A	ENST00000231749.3	-	10	2377	c.1105C>T	c.(1105-1107)Cgg>Tgg	p.R369W	ZMYND10-AS1_ENST00000440013.1_RNA|RASSF1_ENST00000359365.4_5'Flank|ZMYND10_ENST00000490675.1_5'UTR|RASSF1_ENST00000357043.2_5'Flank|RASSF1_ENST00000488024.1_5'Flank|ZMYND10_ENST00000360165.3_Missense_Mutation_p.R364W	NM_015896.2	NP_056980.2	O75800	ZMY10_HUMAN	zinc finger, MYND-type containing 10	369	Interaction with LRRC6.		R -> W (in dbSNP:rs142613783). {ECO:0000269|Ref.1}.		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)		GCCTGCAGCCGCAGGTCCTGC	0.627										TSP Lung(30;0.18)			G|||	9	0.00179712	0.0	0.0014	5008	,	,		20400	0.0		0.006	False		,,,				2504	0.002				p.R369W		Atlas-SNP	.											.	ZMYND10	37	.	0			c.C1105T						PASS	.	G	TRP/ARG	7,4399	12.9+/-30.5	0,7,2196	42	42	42		1105	2.2	1	3	dbSNP_134	42	67,8533	39.8+/-96.3	0,67,4233	yes	missense	ZMYND10	NM_015896.2	101	0,74,6429	AA,AG,GG		0.7791,0.1589,0.569	probably-damaging	369/441	50379257	74,12932	2203	4300	6503	SO:0001583	missense	51364	exon10			GCAGCCGCAGGTC	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.1105C>T	3.37:g.50379257G>A	ENSP00000231749:p.Arg369Trp	70	0	0		60	31	0.516667	NM_015896	A6NK41|B3KU54|O14570|O75801|Q53FE6|Q8N4R6|Q8NDN6	Missense_Mutation	SNP	ENST00000231749.3	37	CCDS2825.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	12.24	1.879643	0.33162	0.001589	0.007791	ENSG00000004838	ENST00000231749;ENST00000360165	.	.	.	5.11	2.16	0.27623	.	0.226724	0.41194	D	0.000924	T	0.57007	0.2024	M	0.72894	2.215	0.23468	N	0.997615	D;D	0.89917	0.992;1.0	P;D	0.67725	0.765;0.953	T	0.60105	-0.7328	9	0.87932	D	0	-31.184	14.5087	0.67769	0.0:0.0:0.3974:0.6026	.	364;369	O75800-2;O75800	.;ZMY10_HUMAN	W	369;364	.	ENSP00000231749:R369W	R	-	1	2	ZMYND10	50354261	0.663000	0.27448	0.964000	0.40570	0.168000	0.22595	1.029000	0.30140	0.131000	0.18576	0.462000	0.41574	CGG	G|0.995;A|0.005	0.005	strong		0.627	ZMYND10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346376.1	NM_015896		A	50379257	G	A	50379257	3	1	27	1	0	0	0	0	1	0	0	0	17720	1086	38	1	229	1	ZMYND10	3	50379257	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	685285	50379257	147643173	185	10636											
VPRBP	9730	hgsc.bcm.edu	37	chr3	51458204	51458204	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcatcttaatggacagtaaGgacaggagcaccttgatgcc	12	8	12	9	0	1	1	0	1	1	0	1	4	1	4	2	4	2	3	2	4	2	3	rs150385433	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:51458204G>A	ENST00000335891.5	-	7	882	c.873C>T	c.(871-873)tcC>tcT	p.S291S				Q9Y4B6	VPRBP_HUMAN	Vpr (HIV-1) binding protein	740	Protein kinase-like.				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)		TGGACAGTAAGGACAGGAGCA	0.557													G|||	16	0.00319489	0.0015	0.0058	5008	,	,		20267	0.0		0.0099	False		,,,				2504	0.0				p.S687S		Atlas-SNP	.											.	VPRBP	107	.	0			c.C2061T						PASS	.	G	,	3,4027		0,3,2012	224	213	217		2058,2061	-3.6	1	3	dbSNP_134	217	66,8310		0,66,4122	no	coding-synonymous,coding-synonymous	VPRBP	NM_001171904.1,NM_014703.2	,	0,69,6134	AA,AG,GG		0.788,0.0744,0.5562	,	686/1454,687/1455	51458204	69,12337	2015	4188	6203	SO:0001819	synonymous_variant	9730	exon14			CAGTAAGGACAGG	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.873C>T	3.37:g.51458204G>A		153	0	0		121	69	0.570248	NM_014703	Q2YD74|Q8TBD9|Q9HCA1|Q9UG37	Silent	SNP	ENST00000335891.5	37																																																																																				G|0.995;A|0.005	0.005	strong		0.557	VPRBP-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014703		A	51458204	G	A	51458204	2	1	27	1	0	0	0	0	0	0	0	1	17200	987	35	2		2	VPRBP	3	51458204	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1078947	51458204	146564226	186	10637											
CHDH	55349	hgsc.bcm.edu	37	chr3	53855738	53855738	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcagcattcccgatgccagaGagcatgagcagctgtggaga	11	7	13	10	1	1	3	1	1	0	2	2	6	2	3	2	1	5	4	2	1	0	1	rs35064726	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:53855738G>C	ENST00000315251.6	-	5	1358	c.921C>G	c.(919-921)ctC>ctG	p.L307L		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	307					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)	CGATGCCAGAGAGCATGAGCA	0.562													G|||	123	0.0245607	0.0023	0.0216	5008	,	,		19271	0.0		0.0527	False		,,,				2504	0.0532				p.L307L		Atlas-SNP	.											.	CHDH	34	.	0			c.C921G						PASS	.	G		50,4356	50.9+/-86.3	0,50,2153	142	126	131		921	-2.7	0.6	3	dbSNP_126	131	472,8128	138.7+/-195.5	17,438,3845	no	coding-synonymous	CHDH	NM_018397.4		17,488,5998	CC,CG,GG		5.4884,1.1348,4.0135		307/595	53855738	522,12484	2203	4300	6503	SO:0001819	synonymous_variant	55349	exon5			GCCAGAGAGCATG	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.921C>G	3.37:g.53855738G>C		96	0	0		71	38	0.535211	NM_018397	Q9NY17	Silent	SNP	ENST00000315251.6	37	CCDS2873.1																																																																																			G|0.958;C|0.042	0.042	strong		0.562	CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397		C	53855738	G	C	53855738	2	2	27	1	0	0	0	0	0	0	0	1	3335	929	33	4		4	CHDH	3	53855738	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2397534	53855738	144166692	187	10638											
C3orf67	200844	hgsc.bcm.edu	37	chr3	58870321	58870321	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaattttatttcagtttggCgaagtttagtcatgtttagc	9	18	9	5	2	2	0	2	0	0	0	2	2	2	0	0	1	1	3	0	1	5	8	rs116534917	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:58870321C>T	ENST00000482387.1	-	3	386	c.290G>A	c.(289-291)cGc>cAc	p.R97H	RP11-147N17.1_ENST00000463703.1_RNA|RP11-147N17.1_ENST00000492031.1_RNA|C3orf67_ENST00000295966.7_Missense_Mutation_p.R97H|C3orf67_ENST00000472469.1_Missense_Mutation_p.R17H|RP11-147N17.1_ENST00000482372.1_RNA|RP11-147N17.1_ENST00000493123.1_RNA			Q6ZVT6	CC067_HUMAN	chromosome 3 open reading frame 67	97										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)		TTCAGTTTGGCGAAGTTTAGT	0.413													C|||	10	0.00199681	0.0	0.0043	5008	,	,		18406	0.0		0.005	False		,,,				2504	0.002				p.R97H		Atlas-SNP	.											C3orf67,NS,carcinoma,-1,1	C3orf67	45	1	0			c.G290A						PASS	.	C	HIS/ARG	10,4396	16.8+/-37.8	0,10,2193	204	196	199		290	1.8	1	3	dbSNP_132	199	93,8507	52.7+/-113.3	1,91,4208	yes	missense	C3orf67	NM_198463.2	29	1,101,6401	TT,TC,CC		1.0814,0.227,0.7919	benign	97/564	58870321	103,12903	2203	4300	6503	SO:0001583	missense	200844	exon7			GTTTGGCGAAGTT	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.290G>A	3.37:g.58870321C>T	ENSP00000417122:p.Arg97His	188	0	0		170	78	0.458824	NM_198463	B9EKV6|Q6ZV69	Missense_Mutation	SNP	ENST00000482387.1	37		7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	C	14.64	2.594771	0.46318	0.00227	0.010814	ENSG00000163689	ENST00000295966;ENST00000482387;ENST00000472469	T;T;T	0.50277	0.75;0.75;0.75	5.61	1.83	0.25207	.	0.410282	0.27906	N	0.017375	T	0.23886	0.0578	L	0.41824	1.3	0.80722	D	1	B;B	0.22983	0.078;0.045	B;B	0.20384	0.029;0.019	T	0.04607	-1.0939	9	.	.	.	-1.7255	4.7606	0.13106	0.1522:0.6058:0.0:0.242	.	17;97	C9J3M8;Q6ZVT6-2	.;.	H	97;97;17	ENSP00000295966:R97H;ENSP00000417122:R97H;ENSP00000417271:R17H	.	R	-	2	0	C3orf67	58845361	0.994000	0.37717	0.992000	0.48379	0.517000	0.34286	0.505000	0.22642	0.318000	0.23185	-0.140000	0.14226	CGC	C|0.994;T|0.006	0.006	strong		0.413	C3orf67-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000353803.1	NM_198463		T	58870321	C	T	58870321	3	4	27	1	0	0	0	0	1	0	0	0	2243	768	27	1	1441	1	C3orf67	3	58870321	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	5014583	58870321	139152109	188	10639											
MAGI1	9223	hgsc.bcm.edu	37	chr3	65464386	65464386	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tcggggtcgactgcttagagCcagactgaaggctgtgcaag	9	8	15	9	2	0	3	0	1	0	2	2	4	0	3	1	3	3	3	1	3	3	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:65464386C>G	ENST00000497477.2	-	4	637	c.638G>C	c.(637-639)gGc>gCc	p.G213A	MAGI1_ENST00000402939.2_Missense_Mutation_p.G213A|MAGI1_ENST00000470990.1_5'UTR|MAGI1_ENST00000330909.8_Missense_Mutation_p.G213A|MAGI1_ENST00000483466.1_Missense_Mutation_p.G213A			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	213	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				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)		CTGCTTAGAGCCAGACTGAAG	0.527																																					p.G213A		Atlas-SNP	.											.	MAGI1	481	.	0			c.G638C						PASS	.						165	143	151					3																	65464386		2203	4300	6503	SO:0001583	missense	9223	exon4			TTAGAGCCAGACT	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.638G>C	3.37:g.65464386C>G	ENSP00000424369:p.Gly213Ala	169	0	0		146	38	0.260274	NM_001033057	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Missense_Mutation	SNP	ENST00000497477.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.85|10.85	1.467724|1.467724	0.26335|0.26335	.|.	.|.	ENSG00000151276|ENSG00000151276	ENST00000460329|ENST00000402939;ENST00000330909;ENST00000422949;ENST00000463103;ENST00000483466;ENST00000497477	.|T;T;T;T;T	.|0.42900	.|0.96;0.96;2.35;0.96;0.96	5.89|5.89	5.89|5.89	0.94794|0.94794	.|Guanylate kinase/L-type calcium channel (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.52613|0.52613	0.1745|0.1745	L|L	0.35854|0.35854	1.095|1.095	0.80722|0.80722	D|D	1|1	.|P;P;P;P;P;P	.|0.52692	.|0.944;0.907;0.955;0.893;0.951;0.656	.|P;B;P;B;D;P	.|0.63113	.|0.599;0.395;0.725;0.303;0.911;0.465	T|T	0.25257|0.25257	-1.0137|-1.0137	5|10	.|0.11485	.|T	.|0.65	-22.988|-22.988	20.2576|20.2576	0.98430|0.98430	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|213;213;213;213;213;213	.|Q96QZ7-6;Q96QZ7;Q96QZ7-4;Q96QZ7-3;Q96QZ7-2;Q96QZ7-5	.|.;MAGI1_HUMAN;.;.;.;.	P|A	94|213;213;109;88;213;213	.|ENSP00000385450:G213A;ENSP00000331157:G213A;ENSP00000418177:G88A;ENSP00000420323:G213A;ENSP00000424369:G213A	.|ENSP00000331157:G213A	A|G	-|-	1|2	0|0	MAGI1|MAGI1	65439426|65439426	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.770000|5.770000	0.68873|0.68873	2.783000|2.783000	0.95769|0.95769	0.655000|0.655000	0.94253|0.94253	GCT|GGC	.	.	none		0.527	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742		G	65464386	C	G	65464386	3	3	27	1	0	0	0	0	1	0	0	0	9199	739	26	4	4064	4	MAGI1	3	65464386	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	6594065	65464386	132558044	189	10640											
FAM19A4	151647	hgsc.bcm.edu	37	chr3	68782299	68782299	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacctctctcttcgctaccgCgttacctaaaacaaatcaaa	13	10	3	15	3	3	0	1	0	2	0	5	0	3	0	3	0	3	2	3	0	6	4	rs146641270	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:68782299C>T	ENST00000295569.7	-	6	909	c.417G>A	c.(415-417)acG>acA	p.T139T		NM_001005527.2|NM_182522.4	NP_001005527.1|NP_872328.1	Q96LR4	F19A4_HUMAN	family with sequence similarity 19 (chemokine (C-C motif)-like), member A4	139						extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(5)|skin(2)	10		Lung NSC(201;0.0198)		BRCA - Breast invasive adenocarcinoma(55;1.38e-05)|Epithelial(33;0.000124)|LUSC - Lung squamous cell carcinoma(21;0.0248)|KIRC - Kidney renal clear cell carcinoma(39;0.0729)|Kidney(39;0.0904)		TTCGCTACCGCGTTACCTAAA	0.483													C|||	5	0.000998403	0.0	0.0	5008	,	,		18682	0.0		0.001	False		,,,				2504	0.0041				p.T139T		Atlas-SNP	.											.	FAM19A4	23	.	0			c.G417A						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	128	119	122		417,417	-6.3	1	3	dbSNP_134	122	16,8584	11.9+/-42.8	0,16,4284	no	coding-synonymous,coding-synonymous	FAM19A4	NM_001005527.1,NM_182522.3	,	0,17,6486	TT,TC,CC		0.186,0.0227,0.1307	,	139/141,139/141	68782299	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	151647	exon6			CTACCGCGTTACC	AY325117	CCDS2907.1	3p14.1	2014-08-14			ENSG00000163377	ENSG00000163377			21591	protein-coding gene	gene with protein product						15028294, 25109685	Standard	NM_182522		Approved	TAFA-4	uc021xah.1	Q96LR4	OTTHUMG00000158744	ENST00000295569.7:c.417G>A	3.37:g.68782299C>T		81	0	0		62	29	0.467742	NM_182522	A8MVT2	Silent	SNP	ENST00000295569.7	37	CCDS2907.1																																																																																			C|0.999;T|0.001	0.001	strong		0.483	FAM19A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352002.1	NM_182522		T	68782299	C	T	68782299	2	4	27	1	0	0	0	0	0	0	0	1	5539	755	27	1		1	FAM19A4	3	68782299	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3317913	68782299	129240131	190	10641											
TMF1	7110	hgsc.bcm.edu	37	chr3	69073223	69073223	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tactcttagctgagttctaaGtttgggtatctccttcacct	7	17	7	10	0	4	1	1	1	3	0	5	1	4	1	2	1	2	4	2	1	4	7	rs185749329	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:69073223G>A	ENST00000398559.2	-	16	3337	c.3121C>T	c.(3121-3123)Ctt>Ttt	p.L1041F	CTD-2013N24.2_ENST00000597950.1_RNA|CTD-2013N24.2_ENST00000595925.1_RNA|CTD-2013N24.2_ENST00000601735.1_RNA|CTD-2013N24.2_ENST00000482368.2_RNA|CTD-2013N24.2_ENST00000601511.1_RNA|TMF1_ENST00000489370.1_5'Flank|CTD-2013N24.2_ENST00000597366.1_RNA|TMF1_ENST00000543976.1_Missense_Mutation_p.L1044F|CTD-2013N24.2_ENST00000599467.1_RNA|CTD-2013N24.2_ENST00000596732.1_RNA|CTD-2013N24.2_ENST00000596523.1_RNA|CTD-2013N24.2_ENST00000598783.1_RNA			P82094	TMF1_HUMAN	TATA element modulatory factor 1	1041					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)		TGAGTTCTAAGTTTGGGTATC	0.303													G|||	4	0.000798722	0.0	0.0043	5008	,	,		15654	0.0		0.001	False		,,,				2504	0.0				p.L1041F		Atlas-SNP	.											.	TMF1	77	.	0			c.C3121T						PASS	.	G	PHE/LEU	2,3652		0,2,1825	158	144	149		3121	5.6	1	3		149	12,8158		0,12,4073	yes	missense	TMF1	NM_007114.2	22	0,14,5898	AA,AG,GG		0.1469,0.0547,0.1184	probably-damaging	1041/1094	69073223	14,11810	1827	4085	5912	SO:0001583	missense	7110	exon16			TTCTAAGTTTGGG		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.3121C>T	3.37:g.69073223G>A	ENSP00000381567:p.Leu1041Phe	132	0	0		138	70	0.507246	NM_007114	B7ZLJ2|Q17R87|Q59GK0	Missense_Mutation	SNP	ENST00000398559.2	37	CCDS43105.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	18.43	3.621363	0.66787	5.47E-4	0.001469	ENSG00000144747	ENST00000398559;ENST00000543976;ENST00000356248	D;D	0.83591	-1.74;-1.74	5.59	5.59	0.84812	.	0.000000	0.64402	D	0.000001	D	0.91771	0.7397	M	0.88512	2.96	0.58432	D	0.999993	D;D	0.89917	1.0;0.981	D;D	0.91635	0.999;0.91	D	0.92645	0.6128	10	0.72032	D	0.01	-10.3062	12.4791	0.55831	0.1197:0.0:0.8803:0.0	.	1044;1041	P82094-2;P82094	.;TMF1_HUMAN	F	1041;1044;957	ENSP00000381567:L1041F;ENSP00000438706:L1044F	ENSP00000348582:L957F	L	-	1	0	TMF1	69155913	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.905000	0.56333	2.620000	0.88729	0.557000	0.71058	CTT	G|0.999;A|0.001	0.001	strong		0.303	TMF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352106.1	NM_007114		A	69073223	G	A	69073223	3	1	27	1	0	0	0	0	1	0	0	0	16243	1029	36	2	168	2	TMF1	3	69073223	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	290924	69073223	128949207	191	10642											
ROBO2	6092	hgsc.bcm.edu	37	chr3	77607099	77607099	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gagctttattcttcagttttGacagatagacctccacctat	10	15	6	10	0	2	3	1	1	1	2	3	4	3	3	3	0	1	2	3	0	3	8			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:77607099G>C	ENST00000461745.1	+	9	2136	c.1236G>C	c.(1234-1236)ttG>ttC	p.L412F	ROBO2_ENST00000487694.3_Missense_Mutation_p.L428F|ROBO2_ENST00000332191.8_Missense_Mutation_p.L412F	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	412					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)		CTTCAGTTTTGACAGATAGAC	0.413																																					p.L412F		Atlas-SNP	.											.	ROBO2	527	.	0			c.G1236C						PASS	.						67	70	69					3																	77607099		1853	4083	5936	SO:0001583	missense	6092	exon9			AGTTTTGACAGAT	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.1236G>C	3.37:g.77607099G>C	ENSP00000417164:p.Leu412Phe	109	0	0		103	32	0.31068	NM_002942	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	37	CCDS43109.1	.	.	.	.	.	.	.	.	.	.	G	2.000	-0.429551	0.04701	.	.	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191;ENST00000398467	T;T;T	0.65364	-0.15;-0.13;-0.13	5.53	0.656	0.17844	.	0.203361	0.24178	N	0.040830	T	0.61813	0.2377	L	0.31526	0.94	0.43234	D	0.995137	D;D;D	0.69078	0.994;0.997;0.994	D;D;D	0.72075	0.947;0.976;0.921	T	0.63637	-0.6592	9	0.19147	T	0.46	.	9.9156	0.41432	0.4075:0.0:0.5925:0.0	.	428;412;412	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	F	428;428;432;412;412;133	ENSP00000417335:L428F;ENSP00000417164:L412F;ENSP00000327536:L412F	ENSP00000327536:L412F	L	+	3	2	ROBO2	77689789	1.000000	0.71417	0.998000	0.56505	0.232000	0.25224	1.789000	0.38724	0.111000	0.17947	0.585000	0.79938	TTG	.	.	none		0.413	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		C	77607099	G	C	77607099	3	2	27	1	0	0	0	0	1	0	0	0	13529	1281	45	4	1272	4	ROBO2	3	77607099	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	8533876	77607099	120415331	192	10643											
CADM2	253559	hgsc.bcm.edu	37	chr3	85935455	85935455	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagctgatataagatggttCaaaaatgacaaagagattaa	19	9	9	4	0	1	4	1	2	0	2	1	5	1	4	0	1	1	3	0	1	6	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:85935455C>A	ENST00000407528.2	+	4	542	c.480C>A	c.(478-480)ttC>ttA	p.F160L	CADM2_ENST00000405615.2_Missense_Mutation_p.F162L|CADM2_ENST00000383699.3_Missense_Mutation_p.F169L	NM_001167674.1	NP_001161146.1	Q8N3J6	CADM2_HUMAN	cell adhesion molecule 2	160	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)		TAAGATGGTTCAAAAATGACA	0.343																																					p.F169L		Atlas-SNP	.											.	CADM2	195	.	0			c.C507A						PASS	.						56	54	55					3																	85935455		2203	4300	6503	SO:0001583	missense	253559	exon5			ATGGTTCAAAAAT	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.480C>A	3.37:g.85935455C>A	ENSP00000384575:p.Phe160Leu	188	0	0		124	31	0.25	NM_001167675	G3XHN7|G3XHN8|Q3KQY9|Q658Q7|Q8IZP8	Missense_Mutation	SNP	ENST00000407528.2	37	CCDS54614.1	.	.	.	.	.	.	.	.	.	.	C	13.91	2.378550	0.42207	.	.	ENSG00000175161	ENST00000383699;ENST00000407528;ENST00000405615	T;T;T	0.73575	-0.76;-0.76;-0.76	5.3	3.04	0.35103	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.60196	0.2250	L	0.36672	1.1	0.58432	D	0.99999	B;B;B	0.25272	0.009;0.122;0.031	B;B;B	0.24848	0.02;0.056;0.047	T	0.51371	-0.8714	10	0.16896	T	0.51	.	9.3638	0.38212	0.0:0.7276:0.0:0.2724	.	162;169;160	Q8N3J6-3;G3XHN4;Q8N3J6	.;.;CADM2_HUMAN	L	169;160;162	ENSP00000373200:F169L;ENSP00000384575:F160L;ENSP00000384193:F162L	ENSP00000373200:F169L	F	+	3	2	CADM2	86018145	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.963000	0.40452	1.137000	0.42214	0.557000	0.71058	TTC	.	.	none		0.343	CADM2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352822.1	NM_153184		A	85935455	C	A	85935455	3	1	27	1	0	0	0	0	1	0	0	0	2569	825	29	4	565	4	CADM2	3	85935455	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	8328356	85935455	112086975	193	10644											
EPHA3	2042	hgsc.bcm.edu	37	chr3	89391215	89391215	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccaccaagacagtttgctgcGgtcagcatcacaactaatca	13	8	7	13	1	3	1	3	0	0	1	3	1	3	1	2	1	4	3	2	1	3	2	rs56112995	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:89391215G>A	ENST00000336596.2	+	5	1506	c.1281G>A	c.(1279-1281)gcG>gcA	p.A427A	EPHA3_ENST00000494014.1_Silent_p.A427A|EPHA3_ENST00000452448.2_Silent_p.A427A	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	427	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		AGTTTGCTGCGGTCAGCATCA	0.458										TSP Lung(6;0.00050)			G|||	16	0.00319489	0.0	0.0	5008	,	,		18214	0.0		0.008	False		,,,				2504	0.0082				p.A427A		Atlas-SNP	.											EPHA3_ENST00000452448,caecum,carcinoma,0,4	EPHA3	501	4	0			c.G1281A						PASS	.	G	,	3,4403	6.2+/-15.9	0,3,2200	65	54	57		1281,1281	-11.1	0.5	3	dbSNP_129	57	55,8545	33.8+/-87.4	1,53,4246	no	coding-synonymous,coding-synonymous	EPHA3	NM_005233.5,NM_182644.2	,	1,56,6446	AA,AG,GG		0.6395,0.0681,0.4459	,	427/984,427/540	89391215	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	2042	exon5			TGCTGCGGTCAGC	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.1281G>A	3.37:g.89391215G>A		81	0	0		72	31	0.430556	NM_005233	Q9H2V3|Q9H2V4	Silent	SNP	ENST00000336596.2	37	CCDS2922.1																																																																																			G|0.995;A|0.005	0.005	strong		0.458	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		A	89391215	G	A	89391215	2	1	27	1	0	0	0	0	0	0	0	1	5170	1103	39	1		1	EPHA3	3	89391215	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	3455760	89391215	108631215	194	10645											
MINA	84864	hgsc.bcm.edu	37	chr3	97686159	97686159	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	acatctcttccatagtacatCccccggctgcacagactctt	9	11	5	16	1	2	1	0	0	2	1	5	1	4	1	3	1	2	3	3	1	2	4	rs34097037	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:97686159C>T	ENST00000333396.7	-	2	861	c.279G>A	c.(277-279)ggG>ggA	p.G93G	MINA_ENST00000330299.2_Silent_p.G93G|MINA_ENST00000394198.2_Silent_p.G93G|MINA_ENST00000360258.4_Silent_p.G93G	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						CATAGTACATCCCCCGGCTGC	0.473													C|||	10	0.00199681	0.0	0.0043	5008	,	,		18523	0.0		0.007	False		,,,				2504	0.0				p.G93G		Atlas-SNP	.											.	MINA	39	.	0			c.G279A						PASS	.	C	,,	6,4400	11.4+/-27.6	0,6,2197	215	231	226		279,279,279	-6.5	0	3	dbSNP_126	226	52,8548	33.3+/-86.6	0,52,4248	no	coding-synonymous,coding-synonymous,coding-synonymous	MINA	NM_001042533.1,NM_032778.4,NM_153182.2	,,	0,58,6445	TT,TC,CC		0.6047,0.1362,0.4459	,,	93/466,93/465,93/466	97686159	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	84864	exon2			GTACATCCCCCGG	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.279G>A	3.37:g.97686159C>T		103	0	0		107	51	0.476636	NM_001261829		Silent	SNP	ENST00000333396.7	37	CCDS43114.1																																																																																			C|0.996;T|0.004	0.004	strong		0.473	MINA-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359244.3	NM_032778		T	97686159	C	T	97686159	2	4	27	1	0	0	0	0	0	0	0	1	9595	842	30	2		2	MINA	3	97686159	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	8294944	97686159	100336271	195	10646											
OR5H14	403273	hgsc.bcm.edu	37	chr3	97868959	97868959	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttctccacctgtggagctCatctcttatctgtatcttta	6	17	5	13	0	5	0	1	0	4	0	7	1	5	1	3	1	1	2	3	1	3	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:97868959C>A	ENST00000437310.1	+	1	790	c.730C>A	c.(730-732)Cat>Aat	p.H244N	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005514.1	NP_001005514.1	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H, member 14	244						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						CTGTGGAGCTCATCTCTTATC	0.418																																					p.H244N		Atlas-SNP	.											.	OR5H14	56	.	0			c.C730A						PASS	.						57	55	56					3																	97868959		2203	4298	6501	SO:0001583	missense	403273	exon1			GGAGCTCATCTCT		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.730C>A	3.37:g.97868959C>A	ENSP00000401706:p.His244Asn	181	0	0		140	73	0.521429	NM_001005514	B9EH15	Missense_Mutation	SNP	ENST00000437310.1	37	CCDS33798.1	.	.	.	.	.	.	.	.	.	.	C	14.07	2.424491	0.43020	.	.	ENSG00000236032	ENST00000437310	T	0.00314	8.14	2.49	2.49	0.30216	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000194	T	0.01029	0.0034	H	0.97707	4.06	0.28760	N	0.900936	D	0.89917	1.0	D	0.97110	1.0	T	0.04178	-1.0971	10	0.87932	D	0	.	10.6214	0.45483	0.0:1.0:0.0:0.0	.	244	A6NHG9	O5H14_HUMAN	N	244	ENSP00000401706:H244N	ENSP00000401706:H244N	H	+	1	0	OR5H14	99351649	1.000000	0.71417	0.954000	0.39281	0.342000	0.28953	6.703000	0.74633	1.380000	0.46344	0.195000	0.17529	CAT	.	.	none		0.418	OR5H14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359112.1			A	97868959	C	A	97868959	3	1	27	1	0	0	0	0	1	0	0	0	11169	826	29	4	732	4	OR5H14	3	97868959	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	182800	97868959	100153471	196	10647											
OR5H2	79310	hgsc.bcm.edu	37	chr3	98002429	98002429	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcttttcacaatcctaaaaaAgaagtctgttagaggcgtaa	15	12	7	7	1	3	2	1	0	2	2	4	2	4	2	1	1	0	2	1	1	7	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:98002429A>T	ENST00000355273.2	+	1	698	c.698A>T	c.(697-699)aAg>aTg	p.K233M	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005482.1	NP_001005482.1	Q8NGV7	OR5H2_HUMAN	olfactory receptor, family 5, subfamily H, 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)			breast(1)|endometrium(1)|large_intestine(5)|lung(13)|ovary(3)|upper_aerodigestive_tract(1)	24						ATCCTAAAAAAGAAGTCTGTT	0.368																																					p.K233M		Atlas-SNP	.											OR5H2,NS,carcinoma,0,1	OR5H2	63	1	0			c.A698T						PASS	.						84	86	85					3																	98002429		2203	4300	6503	SO:0001583	missense	79310	exon1			TAAAAAAGAAGTC		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.698A>T	3.37:g.98002429A>T	ENSP00000347418:p.Lys233Met	169	0	0		137	39	0.284672	NM_001005482	Q6IF87	Missense_Mutation	SNP	ENST00000355273.2	37	CCDS33801.1	.	.	.	.	.	.	.	.	.	.	A	0.025	-1.380780	0.01204	.	.	ENSG00000197938	ENST00000355273	T	0.00032	8.88	3.03	-5.67	0.02444	GPCR, rhodopsin-like superfamily (1);	0.347490	0.20667	N	0.087917	T	0.00039	0.0001	N	0.00642	-1.3	0.09310	N	1	B	0.29232	0.238	B	0.32211	0.142	T	0.47923	-0.9079	10	0.02654	T	1	.	0.6655	0.00849	0.2024:0.1404:0.235:0.4222	.	233	Q8NGV7	OR5H2_HUMAN	M	233	ENSP00000347418:K233M	ENSP00000347418:K233M	K	+	2	0	OR5H2	99485119	0.000000	0.05858	0.003000	0.11579	0.036000	0.12997	-0.051000	0.11885	-0.806000	0.04398	0.338000	0.21704	AAG	.	.	none		0.368	OR5H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359113.2			T	98002429	A	T	98002429	3	4	27	1	0	0	0	0	1	0	0	0	11171	72	3	5	700	5	OR5H2	3	98002429	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	133470	98002429	100020001	197	10648											
OR5K2	402135	hgsc.bcm.edu	37	chr3	98216586	98216586	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacaggatttacagatcaccCtgagctgaagactctgctgt	11	10	9	11	0	2	4	1	2	1	2	2	5	2	5	1	1	3	2	1	1	2	2	rs143260385	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:98216586C>G	ENST00000427338.1	+	1	139	c.62C>G	c.(61-63)cCt>cGt	p.P21R		NM_001004737.1	NP_001004737.1	Q8NHB8	OR5K2_HUMAN	olfactory receptor, family 5, subfamily K, member 2	21						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P21L(1)		endometrium(2)|large_intestine(1)|lung(10)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						ACAGATCACCCTGAGCTGAAG	0.413													C|||	16	0.00319489	0.0008	0.0	5008	,	,		20316	0.0		0.0149	False		,,,				2504	0.0				p.P21R		Atlas-SNP	.											OR5K2,bladder,carcinoma,0,1	OR5K2	56	1	1	Substitution - Missense(1)	urinary_tract(1)	c.C62G						PASS	.	C	ARG/PRO	15,4391	22.3+/-47.3	0,15,2188	94	95	95		62	2.9	0.9	3	dbSNP_134	95	60,8534	36.9+/-92.0	0,60,4237	no	missense	OR5K2	NM_001004737.1	103	0,75,6425	GG,GC,CC		0.6982,0.3404,0.5769	probably-damaging	21/317	98216586	75,12925	2203	4297	6500	SO:0001583	missense	402135	exon1			ATCACCCTGAGCT	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.62C>G	3.37:g.98216586C>G	ENSP00000393889:p.Pro21Arg	349	0	0		361	170	0.470914	NM_001004737	B2RN70|Q6IF47	Missense_Mutation	SNP	ENST00000427338.1	37	CCDS33804.1	16	0.007326007326007326	0	0.0	0	0.0	0	0.0	16	0.021108179419525065	C	11.04	1.521543	0.27211	0.003404	0.006982	ENSG00000231861	ENST00000427338	T	0.20332	2.08	2.91	2.91	0.33838	.	0.000000	0.41294	D	0.000912	T	0.18257	0.0438	M	0.69523	2.12	0.23896	N	0.99653	P	0.45396	0.857	P	0.49637	0.617	T	0.04360	-1.0957	10	0.66056	D	0.02	-9.1222	12.101	0.53783	0.0:1.0:0.0:0.0	.	21	Q8NHB8	OR5K2_HUMAN	R	21	ENSP00000393889:P21R	ENSP00000393889:P21R	P	+	2	0	OR5K2	99699276	0.000000	0.05858	0.913000	0.36048	0.263000	0.26337	0.179000	0.16840	1.940000	0.56252	0.298000	0.19748	CCT	C|0.994;G|0.006	0.006	strong		0.413	OR5K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359020.2			G	98216586	C	G	98216586	3	3	27	1	0	0	0	0	1	0	0	0	11176	681	24	4	64	4	OR5K2	3	98216586	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	214157	98216586	99805844	198	10649											
NFKBIZ	64332	hgsc.bcm.edu	37	chr3	101571753	101571753	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagaacacagtatcatacAgtgggaaaaggaaagggccc	17	5	12	7	0	1	2	1	1	0	1	1	4	1	4	1	3	2	1	1	3	7	2	rs61730026	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:101571753A>G	ENST00000326172.5	+	4	599	c.484A>G	c.(484-486)Agt>Ggt	p.S162G	NFKBIZ_ENST00000394054.2_Missense_Mutation_p.S62G|NFKBIZ_ENST00000326151.5_Missense_Mutation_p.S162G	NM_031419.3	NP_113607.1	Q9BYH8	IKBZ_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, zeta	162					inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24						AGTATCATACAGTGGGAAAAG	0.383													A|||	2	0.000399361	0.0	0.0014	5008	,	,		17347	0.0		0.001	False		,,,				2504	0.0				p.S162G		Atlas-SNP	.											.	NFKBIZ	55	.	0			c.A484G						PASS	.	A	GLY/SER,GLY/SER	4,4402	8.1+/-20.4	0,4,2199	135	135	135		184,484	2	0.2	3	dbSNP_129	135	17,8583	12.6+/-44.7	0,17,4283	yes	missense,missense	NFKBIZ	NM_001005474.2,NM_031419.3	56,56	0,21,6482	GG,GA,AA		0.1977,0.0908,0.1615	benign,benign	62/619,162/719	101571753	21,12985	2203	4300	6503	SO:0001583	missense	64332	exon4			TCATACAGTGGGA	AF548362	CCDS2946.1, CCDS43123.1	3p12-q12	2013-01-10			ENSG00000144802	ENSG00000144802		"Ankyrin repeat domain containing"	29805	protein-coding gene	gene with protein product	"IL-1 inducible nuclear ankyrin-repeat protein"	608004				12565889, 16513645	Standard	NM_031419		Approved	MAIL, FLJ34463, INAP	uc003dvp.3	Q9BYH8	OTTHUMG00000159194	ENST00000326172.5:c.484A>G	3.37:g.101571753A>G	ENSP00000325663:p.Ser162Gly	180	0	0		155	78	0.503226	NM_031419	B3KNR2|D3DN54|Q8IUL4|Q8NAZ8	Missense_Mutation	SNP	ENST00000326172.5	37	CCDS2946.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	0.009	-1.840705	0.00573	9.08E-4	0.001977	ENSG00000144802	ENST00000483180;ENST00000394054;ENST00000326151;ENST00000326172;ENST00000491281	T;T;T;T	0.55760	0.57;0.53;0.5;0.56	5.62	1.98	0.26296	.	0.734859	0.13799	N	0.361934	T	0.29355	0.0731	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	0.18178	-1.0345	10	0.18276	T	0.48	-12.5889	10.5998	0.45360	0.7332:0.0:0.2668:0.0	rs61730026	162;162	Q9BYH8-3;Q9BYH8	.;IKBZ_HUMAN	G	62;62;162;162;62	ENSP00000419800:S62G;ENSP00000377618:S62G;ENSP00000325593:S162G;ENSP00000325663:S162G	ENSP00000325593:S162G	S	+	1	0	NFKBIZ	103054443	0.619000	0.27059	0.159000	0.22649	0.020000	0.10135	1.190000	0.32126	0.081000	0.16988	-2.096000	0.00365	AGT	A|0.998;G|0.002	0.002	strong		0.383	NFKBIZ-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353793.1	NM_031419		G	101571753	A	G	101571753	3	3	27	1	0	0	0	0	1	0	0	0	10392	188	7	3	498	3	NFKBIZ	3	101571753	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	3355167	101571753	96450677	199	10650											
CD96	10225	hgsc.bcm.edu	37	chr3	111286403	111286403	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atggaacagcaaccatacgaTagaaatagagataaatcaga	21	6	8	6	1	1	3	1	0	0	3	1	6	1	4	1	1	4	1	1	1	8	4	rs147832650	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:111286403T>C	ENST00000283285.5	+	3	583	c.452T>C	c.(451-453)aTa>aCa	p.I151T	CD96_ENST00000352690.4_Missense_Mutation_p.I151T|CD96_ENST00000438817.2_Missense_Mutation_p.I151T	NM_198196.2	NP_937839.1	P40200	TACT_HUMAN	CD96 molecule	151					cell adhesion (GO:0007155)|immune response (GO:0006955)|regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(4)|liver(2)|lung(14)|skin(5)	35						AACCATACGATAGAAATAGAG	0.348									Opitz Trigonocephaly syndrome																												p.I151T		Atlas-SNP	.											.	CD96	75	.	0			c.T452C						PASS	.	T	THR/ILE,THR/ILE	0,4406		0,0,2203	99	90	93		452,452	4.2	1	3	dbSNP_134	93	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	CD96	NM_005816.4,NM_198196.2	89,89	0,4,6499	CC,CT,TT		0.0465,0.0,0.0308	possibly-damaging,possibly-damaging	151/570,151/586	111286403	4,13002	2203	4300	6503	SO:0001583	missense	10225	exon3	Familial Cancer Database	C syndrome, Trigonocephaly syndrome	ATACGATAGAAAT	M88282	CCDS2958.1, CCDS2959.1	3p13-q13.2	2013-01-11	2006-03-28		ENSG00000153283	ENSG00000153283		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	16892	protein-coding gene	gene with protein product		606037	"CD96 antigen"			1313846	Standard	XR_241462		Approved	TACTILE	uc003dxx.3	P40200	OTTHUMG00000159275	ENST00000283285.5:c.452T>C	3.37:g.111286403T>C	ENSP00000283285:p.Ile151Thr	92	0	0		72	43	0.597222	NM_005816	Q5JPB3	Missense_Mutation	SNP	ENST00000283285.5	37	CCDS2959.1	.	.	.	.	.	.	.	.	.	.	T	13.03	2.115390	0.37339	0.0	4.65E-4	ENSG00000153283	ENST00000352690;ENST00000283285;ENST00000438817	T;T;T	0.66995	1.6;-0.24;1.6	5.37	4.19	0.49359	Immunoglobulin subtype (1);	0.297277	0.29587	N	0.011726	T	0.59432	0.2193	L	0.27053	0.805	0.29717	N	0.838913	P;P;P;P	0.51351	0.906;0.944;0.906;0.906	B;P;B;B	0.50617	0.444;0.646;0.444;0.444	T	0.60667	-0.7218	10	0.87932	D	0	-14.79	8.037	0.30499	0.0:0.0921:0.0:0.9079	.	151;151;151;151	E9PEJ1;P40200-2;P40200;Q8WUE2	.;.;TACT_HUMAN;.	T	151	ENSP00000342040:I151T;ENSP00000283285:I151T;ENSP00000389801:I151T	ENSP00000283285:I151T	I	+	2	0	CD96	112769093	1.000000	0.71417	1.000000	0.80357	0.827000	0.46813	1.420000	0.34804	2.262000	0.75019	0.528000	0.53228	ATA	T|1.000;C|0.000	0.000	strong		0.348	CD96-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354312.2			C	111286403	T	C	111286403	3	2	27	1	0	0	0	0	1	0	0	0	3050	1406	49	3	462	3	CD96	3	111286403	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	9714650	111286403	86736027	200	10651											
GCET2	257144	hgsc.bcm.edu	37	chr3	111844089	111844089	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttacctggatgggagtagatGacattctttcatctggagaa	11	13	11	6	0	3	3	1	1	2	2	3	6	3	5	1	3	1	1	1	3	3	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:111844089G>T	ENST00000308910.4	-	5	387	c.203C>A	c.(202-204)tCa>tAa	p.S68*	GCSAM_ENST00000484193.1_Nonsense_Mutation_p.S70*|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	68					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)										GGGAGTAGATGACATTCTTTC	0.388																																					p.S70X		Atlas-SNP	.											.	.	.	.	0			c.C209A						PASS	.						117	117	117					3																	111844089		2203	4300	6503	SO:0001587	stop_gained	257144	exon5			GTAGATGACATTC	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.203C>A	3.37:g.111844089G>T	ENSP00000309487:p.Ser68*	60	0	0		41	8	0.195122	NM_001190259	C9JD17|C9JUG6	Nonsense_Mutation	SNP	ENST00000308910.4	37	CCDS2964.1	.	.	.	.	.	.	.	.	.	.	G	16.18	3.050229	0.55218	.	.	ENSG00000174500	ENST00000308910;ENST00000484193;ENST00000460387;ENST00000488580;ENST00000487901	.	.	.	4.23	4.23	0.50019	.	0.783537	0.10863	N	0.625847	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.8044	12.4209	0.55520	0.0:0.0:1.0:0.0	.	.	.	.	X	68;70;53;51;51	.	ENSP00000309487:S68X	S	-	2	0	GCET2	113326779	0.073000	0.21202	0.007000	0.13788	0.040000	0.13550	3.817000	0.55668	2.656000	0.90262	0.561000	0.74099	TCA	.	.	none		0.388	GCSAM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353967.2	NM_152785		T	111844089	G	T	111844089	4	4	27	1	0	0	0	0	0	1	0	0	6296	1294	45	4	341	4	GCET2	3	111844089	Nonsense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	557686	111844089	86178341	201	10652											
CD200R1	131450	hgsc.bcm.edu	37	chr3	112648107	112648107	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attatgcatctgtaatacccGtcatgagtgatggccacggt	10	12	10	9	2	2	2	1	2	1	0	2	2	2	2	2	2	2	2	2	2	3	3	rs373257099		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:112648107G>A	ENST00000471858.1	-	3	613	c.381C>T	c.(379-381)gaC>gaT	p.D127D	CD200R1_ENST00000308611.3_Silent_p.D150D|CD200R1_ENST00000440122.2_Silent_p.D150D|CD200R1_ENST00000490004.1_Silent_p.D127D|CD200R1_ENST00000295863.4_Silent_p.D105D	NM_170780.2	NP_740750.1	Q8TD46	MO2R1_HUMAN	CD200 receptor 1	127	Ig-like V-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						TGTAATACCCGTCATGAGTGA	0.443													g|||	1	0.000199681	0.0	0.0	5008	,	,		20605	0.0		0.0	False		,,,				2504	0.001				p.D150D		Atlas-SNP	.											CD200R1_ENST00000440122,NS,carcinoma,0,2	CD200R1	91	2	0			c.C450T						PASS	.	A	,,,	0,4406		0,0,2203	164	156	159		450,450,381,381	-10.9	0.2	3		159	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CD200R1	NM_138806.3,NM_138939.2,NM_138940.2,NM_170780.2	,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,	150/349,150/189,127/166,127/326	112648107	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	131450	exon4			ATACCCGTCATGA	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.381C>T	3.37:g.112648107G>A		302	0	0		244	108	0.442623	NM_138806	B3KWZ9|E9PCM9|Q52LJ7|Q6IS95|Q6UW94|Q6WHB8|Q8TD44|Q8TD45|Q8TD52	Silent	SNP	ENST00000471858.1	37	CCDS2970.1																																																																																			.	.	weak		0.443	CD200R1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354467.1	NM_138806		A	112648107	G	A	112648107	2	1	27	1	0	0	0	0	0	0	0	1	2983	1136	40	1		1	CD200R1	3	112648107	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	804018	112648107	85374323	202	10653											
POLQ	10721	hgsc.bcm.edu	37	chr3	121212484	121212484	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cacacagctccctctggatgCcaaacgtaagacgcttctga	11	8	8	14	2	2	2	0	1	2	1	3	3	3	3	2	1	3	3	2	1	2	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:121212484C>T	ENST00000264233.5	-	15	2491	c.2363G>A	c.(2362-2364)gGc>gAc	p.G788D		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	788					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)		CCTCTGGATGCCAAACGTAAG	0.468								DNA polymerases (catalytic subunits)																													p.G788D	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											POLQ,caecum,carcinoma,0,1	POLQ	273	1	0			c.G2363A						scavenged	.						76	74	75					3																	121212484		2203	4300	6503	SO:0001583	missense	10721	exon15			TGGATGCCAAACG	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.2363G>A	3.37:g.121212484C>T	ENSP00000264233:p.Gly788Asp	118	0	0		71	3	0.0422535	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	C	32	5.132722	0.94517	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.72505	-0.66	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.88779	0.6529	M	0.93939	3.475	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.91345	0.5100	10	0.87932	D	0	.	19.3309	0.94288	0.0:1.0:0.0:0.0	.	788	O75417	DPOLQ_HUMAN	D	411;788;924	ENSP00000264233:G788D	ENSP00000264233:G788D	G	-	2	0	POLQ	122695174	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.337000	0.79256	2.648000	0.89879	0.650000	0.86243	GGC	.	.	none		0.468	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		T	121212484	C	T	121212484	3	4	27	1	0	0	0	0	1	0	0	0	12217	739	26	2	5473	2	POLQ	3	121212484	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	8564377	121212484	76809946	203	10654											
FBXO40	51725	hgsc.bcm.edu	37	chr3	121341019	121341019	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaacaagaatgactccgagaAagaacagatttccagtggcc	16	6	10	9	1	0	5	0	1	0	4	2	7	2	5	3	1	2	0	3	1	5	1	rs142436040	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:121341019A>T	ENST00000338040.4	+	3	1157	c.743A>T	c.(742-744)aAa>aTa	p.K248I		NM_016298.3	NP_057382.2	Q9UH90	FBX40_HUMAN	F-box protein 40	248					muscle cell differentiation (GO:0042692)	cytoplasm (GO:0005737)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(11)|lung(19)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	46				GBM - Glioblastoma multiforme(114;0.189)		GACTCCGAGAAAGAACAGATT	0.468													A|||	10	0.00199681	0.0	0.0043	5008	,	,		22737	0.0		0.007	False		,,,				2504	0.0				p.K248I		Atlas-SNP	.											.	FBXO40	108	.	0			c.A743T						PASS	.	A	ILE/LYS	4,4402	8.1+/-20.4	1,2,2200	64	69	67		743	0.2	0	3	dbSNP_134	67	34,8566	23.4+/-69.3	0,34,4266	yes	missense	FBXO40	NM_016298.3	102	1,36,6466	TT,TA,AA		0.3953,0.0908,0.2922	possibly-damaging	248/710	121341019	38,12968	2203	4300	6503	SO:0001583	missense	51725	exon3			CCGAGAAAGAACA	AF204674	CCDS33835.1	3q21.1	2004-08-24			ENSG00000163833	ENSG00000163833		"F-boxes /  "other""	29816	protein-coding gene	gene with protein product		609107				10574462	Standard	NM_016298		Approved	KIAA1195, Fbx40	uc003eeg.2	Q9UH90	OTTHUMG00000159410	ENST00000338040.4:c.743A>T	3.37:g.121341019A>T	ENSP00000337510:p.Lys248Ile	61	0	0		47	28	0.595745	NM_016298	B2RAX7|Q32M70|Q9ULM5	Missense_Mutation	SNP	ENST00000338040.4	37	CCDS33835.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	A	8.429	0.848116	0.17034	9.08E-4	0.003953	ENSG00000163833	ENST00000338040	T	0.49139	0.79	5.51	0.213	0.15244	.	0.880954	0.10192	N	0.704471	T	0.29716	0.0742	L	0.47716	1.5	0.23036	N	0.998398	P	0.42620	0.785	B	0.40940	0.344	T	0.15983	-1.0418	10	0.44086	T	0.13	-7.038	5.3399	0.15979	0.6143:0.1385:0.2472:0.0	.	248	Q9UH90	FBX40_HUMAN	I	248	ENSP00000337510:K248I	ENSP00000337510:K248I	K	+	2	0	FBXO40	122823709	0.008000	0.16893	0.009000	0.14445	0.009000	0.06853	0.391000	0.20784	0.058000	0.16222	0.402000	0.26972	AAA	A|0.997;T|0.003	0.003	strong		0.468	FBXO40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355158.1	NM_016298		T	121341019	A	T	121341019	3	4	27	1	0	0	0	0	1	0	0	0	5757	14	1	5	749	5	FBXO40	3	121341019	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	128535	121341019	76681411	204	10655											
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121386377	121386377	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcagcagccactctttggTctcgttcttcttccagcagc	5	14	7	15	1	5	0	1	0	5	0	8	0	6	0	2	1	4	3	2	1	0	4	rs144495540	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:121386377T>A	ENST00000340645.5	-	20	9610	c.9485A>T	c.(9484-9486)gAc>gTc	p.D3162V	GOLGB1_ENST00000393667.3_Missense_Mutation_p.D3172V	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	3162					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)		CACTCTTTGGTCTCGTTCTTC	0.493																																					p.D3172V		Atlas-SNP	.											.	GOLGB1	319	.	0			c.A9515T						PASS	.	T	VAL/ASP	0,4406		0,0,2203	104	93	97		9485	5.5	1	3	dbSNP_134	97	7,8593	5.7+/-21.5	0,7,4293	yes	missense	GOLGB1	NM_004487.3	152	0,7,6496	AA,AT,TT		0.0814,0.0,0.0538	probably-damaging	3162/3260	121386377	7,12999	2203	4300	6503	SO:0001583	missense	2804	exon20			CTTTGGTCTCGTT	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.9485A>T	3.37:g.121386377T>A	ENSP00000341848:p.Asp3162Val	264	1	0.00378788		248	115	0.46371	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	T	17.05	3.290072	0.59976	0.0	8.14E-4	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.16073	2.37;2.37	5.48	5.48	0.80851	.	0.090168	0.48767	D	0.000177	T	0.23451	0.0567	N	0.24115	0.695	0.54753	D	0.999989	D;D;P	0.55800	0.973;0.973;0.903	P;P;P	0.59546	0.859;0.859;0.65	T	0.01456	-1.1350	10	0.56958	D	0.05	.	11.8745	0.52539	0.0:0.0:0.0:1.0	.	3172;3172;3162	E7EP74;B2ZZ91;Q14789	.;.;GOGB1_HUMAN	V	3162;3172	ENSP00000341848:D3162V;ENSP00000377275:D3172V	ENSP00000341848:D3162V	D	-	2	0	GOLGB1	122869067	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	4.287000	0.59001	2.302000	0.77476	0.528000	0.53228	GAC	T|0.999;A|0.001	0.001	strong		0.493	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		A	121386377	T	A	121386377	3	1	27	1	0	0	0	0	1	0	0	0	6573	1667	58	5	306	5	GOLGB1	3	121386377	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	45358	121386377	76636053	205	10656											
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121410844	121410844	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgccttttgctgaatgtttTcctttttgatggttttcagt	4	22	9	6	0	1	2	1	2	0	0	2	2	2	2	2	1	2	3	2	1	1	8			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:121410844T>G	ENST00000340645.5	-	14	7477	c.7352A>C	c.(7351-7353)gAa>gCa	p.E2451A	GOLGB1_ENST00000393667.3_Missense_Mutation_p.E2456A	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	2451					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)		CTGAATGTTTTCCTTTTTGAT	0.398																																					p.E2456A		Atlas-SNP	.											.	GOLGB1	319	.	0			c.A7367C						PASS	.						172	171	171					3																	121410844		2203	4300	6503	SO:0001583	missense	2804	exon14			ATGTTTTCCTTTT	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.7352A>C	3.37:g.121410844T>G	ENSP00000341848:p.Glu2451Ala	491	0	0		483	236	0.488613	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	T	12.49	1.952731	0.34471	.	.	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.28255	1.62;1.62	5.79	5.79	0.91817	.	0.090631	0.47852	D	0.000201	T	0.44052	0.1275	L	0.56769	1.78	0.43588	D	0.995931	D;P;D	0.61697	0.972;0.925;0.99	P;P;P	0.55391	0.616;0.691;0.775	T	0.21552	-1.0242	10	0.30854	T	0.27	.	14.0831	0.64937	0.0:0.0:0.0:1.0	.	2456;2456;2451	E7EP74;B2ZZ91;Q14789	.;.;GOGB1_HUMAN	A	2451;2456	ENSP00000341848:E2451A;ENSP00000377275:E2456A	ENSP00000341848:E2451A	E	-	2	0	GOLGB1	122893534	1.000000	0.71417	0.908000	0.35775	0.972000	0.66771	5.884000	0.69729	2.208000	0.71279	0.460000	0.39030	GAA	.	.	none		0.398	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		G	121410844	T	G	121410844	3	3	27	1	0	0	0	0	1	0	0	0	6573	1783	62	5	2463	5	GOLGB1	3	121410844	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	24467	121410844	76611586	206	10657											
GOLGB1	2804	hgsc.bcm.edu	37	chr3	121413362	121413362	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttatttccgggttctttcTgagcaccttgtattttctcc	4	21	6	10	1	3	1	0	1	3	0	5	1	4	1	3	1	1	3	3	1	2	9			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:121413362T>C	ENST00000340645.5	-	13	6118	c.5993A>G	c.(5992-5994)cAg>cGg	p.Q1998R	GOLGB1_ENST00000393667.3_Missense_Mutation_p.Q2003R	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	1998					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)		GGGTTCTTTCTGAGCACCTTG	0.378																																					p.Q2003R		Atlas-SNP	.											.	GOLGB1	319	.	0			c.A6008G						PASS	.						166	176	172					3																	121413362		2203	4300	6503	SO:0001583	missense	2804	exon13			TCTTTCTGAGCAC	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.5993A>G	3.37:g.121413362T>C	ENSP00000341848:p.Gln1998Arg	123	0	0		87	41	0.471264	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	.	.	.	.	.	.	.	.	.	.	T	13.84	2.356523	0.41700	.	.	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.25912	1.81;1.77	5.21	5.21	0.72293	.	0.130327	0.35525	N	0.003143	T	0.46444	0.1393	M	0.72894	2.215	0.45837	D	0.998705	D;D;D;D	0.76494	0.996;0.996;0.959;0.999	D;D;P;D	0.75484	0.922;0.986;0.564;0.953	T	0.35549	-0.9784	10	0.17832	T	0.49	.	13.0741	0.59077	0.0:0.0:0.0:1.0	.	1923;2003;2003;1998	F1T0J2;E7EP74;B2ZZ91;Q14789	.;.;.;GOGB1_HUMAN	R	1998;2003	ENSP00000341848:Q1998R;ENSP00000377275:Q2003R	ENSP00000341848:Q1998R	Q	-	2	0	GOLGB1	122896052	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.173000	0.50839	2.174000	0.68829	0.533000	0.62120	CAG	.	.	none		0.378	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		C	121413362	T	C	121413362	3	2	27	1	0	0	0	0	1	0	0	0	6573	1580	55	3	3826	3	GOLGB1	3	121413362	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	2518	121413362	76609068	207	10658											
SLC41A3	54946	hgsc.bcm.edu	37	chr3	125726062	125726062	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttctgcgaggtacagcaggaTtgtcacctgtcagaagggca	10	9	13	9	1	3	1	2	0	1	1	3	3	3	2	1	3	3	3	1	3	2	3	rs79696429	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:125726062T>C	ENST00000315891.6	-	11	1499	c.1261A>G	c.(1261-1263)Atc>Gtc	p.I421V	SLC41A3_ENST00000383598.2_Missense_Mutation_p.I395V|SLC41A3_ENST00000360370.4_Missense_Mutation_p.I421V|SLC41A3_ENST00000346785.5_Missense_Mutation_p.I385V|SLC41A3_ENST00000508835.1_Missense_Mutation_p.I304V	NM_001008485.1|NM_017836.3	NP_001008485|NP_060306.3	Q96GZ6	S41A3_HUMAN	solute carrier family 41, member 3	421						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)		TACAGCAGGATTGTCACCTGT	0.537													T|||	99	0.0197684	0.056	0.0072	5008	,	,		21514	0.0		0.007	False		,,,				2504	0.0133				p.I421V		Atlas-SNP	.											.	SLC41A3	80	.	0			c.A1261G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	242,4164	140.0+/-175.5	8,226,1969	56	52	53		1261,1153,1183,910,1261	4.4	0.8	3	dbSNP_132	53	63,8537	39.3+/-95.6	1,61,4238	yes	missense,missense,missense,missense,missense	SLC41A3	NM_001008485.1,NM_001008486.1,NM_001008487.1,NM_001164475.1,NM_017836.3	29,29,29,29,29	9,287,6207	CC,CT,TT		0.7326,5.4925,2.3451	benign,benign,benign,benign,benign	421/508,385/472,395/462,304/371,421/488	125726062	305,12701	2203	4300	6503	SO:0001583	missense	54946	exon11			GCAGGATTGTCAC		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.1261A>G	3.37:g.125726062T>C	ENSP00000326070:p.Ile421Val	85	0	0		70	27	0.385714	NM_017836	A6ND60|B3KSD9|B7Z4Y2|C9JE96|E7ENY4|Q8N342|Q8NB27|Q9H9I6|Q9HAB1|Q9NX30	Missense_Mutation	SNP	ENST00000315891.6	37	CCDS33843.1	37	0.01694139194139194	27	0.054878048780487805	5	0.013812154696132596	0	0.0	5	0.006596306068601583	T	10.45	1.353842	0.24512	0.054925	0.007326	ENSG00000114544	ENST00000360370;ENST00000346785;ENST00000383598;ENST00000458524;ENST00000315891;ENST00000508835	T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54	5.52	4.37	0.52481	MgtE magnesium transporter, integral membrane (1);	0.088897	0.85682	N	0.000000	T	0.04272	0.0118	L	0.35249	1.045	0.45150	D	0.998169	B;B;B;B;B	0.30439	0.031;0.279;0.236;0.279;0.144	B;B;B;B;B	0.36092	0.058;0.217;0.138;0.217;0.084	T	0.02574	-1.1139	10	0.38643	T	0.18	0.3499	9.4473	0.38706	0.0:0.0848:0.0:0.9152	.	304;421;385;421;395	B7Z4Y2;E7ENY4;Q96GZ6-3;Q96GZ6;Q96GZ6-7	.;.;.;S41A3_HUMAN;.	V	421;385;395;412;421;304	ENSP00000353533:I421V;ENSP00000264471:I385V;ENSP00000373092:I395V;ENSP00000326070:I421V;ENSP00000427409:I304V	ENSP00000326070:I421V	I	-	1	0	SLC41A3	127208752	0.388000	0.25197	0.794000	0.32065	0.903000	0.53119	0.596000	0.24044	0.939000	0.37446	0.482000	0.46254	ATC	T|0.980;C|0.020	0.020	strong		0.537	SLC41A3-024	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370886.1	NM_017836		C	125726062	T	C	125726062	3	2	27	1	0	0	0	0	1	0	0	0	14646	1493	52	3	368	3	SLC41A3	3	125726062	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	4312700	125726062	72296368	208	10659											
NEK11	79858	hgsc.bcm.edu	37	chr3	130799314	130799314	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agaactaaatccaaatgaaaCtgtacaggccaatttggaag	18	8	8	7	0	0	2	0	1	0	1	1	3	1	3	2	2	3	1	2	2	8	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:130799314C>G	ENST00000510769.1	+	3	471	c.218C>G	c.(217-219)aCt>aGt	p.T73S	NEK11_ENST00000508196.1_Missense_Mutation_p.T73S|NEK11_ENST00000383366.4_Missense_Mutation_p.T73S|NEK11_ENST00000507910.1_Missense_Mutation_p.T73S|NEK11_ENST00000510688.1_Missense_Mutation_p.T73S|NEK11_ENST00000511262.1_Missense_Mutation_p.T73S|NEK11_ENST00000356918.4_Missense_Mutation_p.T73S|NEK11_ENST00000412440.2_Intron|NEK11_ENST00000429253.2_Missense_Mutation_p.T73S					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						CCAAATGAAACTGTACAGGCC	0.368																																					p.T73S		Atlas-SNP	.											.	NEK11	76	.	0			c.C218G						PASS	.						76	74	75					3																	130799314		2203	4300	6503	SO:0001583	missense	79858	exon4			ATGAAACTGTACA	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.218C>G	3.37:g.130799314C>G	ENSP00000421549:p.Thr73Ser	77	0	0		70	18	0.257143	NM_024800		Missense_Mutation	SNP	ENST00000510769.1	37		.	.	.	.	.	.	.	.	.	.	C	12.87	2.067808	0.36470	.	.	ENSG00000114670	ENST00000510769;ENST00000429253;ENST00000356918;ENST00000510688;ENST00000511262;ENST00000383366;ENST00000507910;ENST00000508196	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	5.77	4.89	0.63831	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	0.53938	D	0.000050	T	0.49847	0.1581	N	0.21240	0.645	0.80722	D	1	P;P;P;P;B	0.49635	0.573;0.513;0.698;0.926;0.063	B;B;B;B;B	0.39935	0.138;0.287;0.161;0.314;0.037	T	0.55927	-0.8063	10	0.54805	T	0.06	.	17.0528	0.86524	0.0:0.8732:0.1268:0.0	.	73;73;73;73;73	Q8NG66-3;E9PHI8;Q8NG66-4;Q8NG66;Q8NG66-2	.;.;.;NEK11_HUMAN;.	S	73	ENSP00000421549:T73S;ENSP00000397180:T73S;ENSP00000349389:T73S;ENSP00000423458:T73S;ENSP00000425114:T73S;ENSP00000372857:T73S;ENSP00000426662:T73S;ENSP00000421851:T73S	ENSP00000349389:T73S	T	+	2	0	NEK11	132282004	1.000000	0.71417	0.983000	0.44433	0.330000	0.28571	3.946000	0.56644	1.415000	0.47037	0.655000	0.94253	ACT	.	.	none		0.368	NEK11-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000356757.1	NM_024800		G	130799314	C	G	130799314	3	3	27	1	0	0	0	0	1	0	0	0	10332	565	20	4	224	4	NEK11	3	130799314	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	5073252	130799314	67223116	209	10660											
PPP2R3A	5523	hgsc.bcm.edu	37	chr3	135721208	135721208	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggttagcatcctatctgAaaaagttaccatttgaattc	13	13	6	9	0	1	2	0	2	1	0	3	2	2	2	3	1	2	3	3	1	6	5	rs146596318	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:135721208A>G	ENST00000264977.3	+	2	1485	c.868A>G	c.(868-870)Aaa>Gaa	p.K290E	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	290					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						ATCCTATCTGAAAAAGTTACC	0.378																																					p.K290E		Atlas-SNP	.											.	PPP2R3A	114	.	0			c.A868G						PASS	.	A	,GLU/LYS	0,4406		0,0,2203	93	91	91		,868	5.3	1	3	dbSNP_134	91	4,8596	3.7+/-12.6	0,4,4296	yes	intron,missense	PPP2R3A	NM_001190447.1,NM_002718.4	,56	0,4,6499	GG,GA,AA		0.0465,0.0,0.0308	,possibly-damaging	,290/1151	135721208	4,13002	2203	4300	6503	SO:0001583	missense	5523	exon2			TATCTGAAAAAGT	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.868A>G	3.37:g.135721208A>G	ENSP00000264977:p.Lys290Glu	51	0	0		44	22	0.5	NM_002718	A8KAE7|B4DNU1|B7ZAE3|Q06189|Q9NPQ5	Missense_Mutation	SNP	ENST00000264977.3	37	CCDS3087.1	.	.	.	.	.	.	.	.	.	.	A	17.74	3.463519	0.63513	0.0	4.65E-4	ENSG00000073711	ENST00000264977	T	0.16897	2.31	5.34	5.34	0.76211	.	0.102401	0.64402	D	0.000004	T	0.23611	0.0571	L	0.58101	1.795	0.80722	D	1	P	0.45348	0.856	B	0.43754	0.43	T	0.01894	-1.1252	10	0.87932	D	0	.	14.5059	0.67752	1.0:0.0:0.0:0.0	.	290	Q06190	P2R3A_HUMAN	E	290	ENSP00000264977:K290E	ENSP00000264977:K290E	K	+	1	0	PPP2R3A	137203898	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.957000	0.93082	2.010000	0.58986	0.533000	0.62120	AAA	A|1.000;G|0.000	0.000	strong		0.378	PPP2R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357232.1	NM_002718		G	135721208	A	G	135721208	3	3	27	1	0	0	0	0	1	0	0	0	12400	247	9	3	870	3	PPP2R3A	3	135721208	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	4921894	135721208	62301222	210	10661											
PCCB	5096	hgsc.bcm.edu	37	chr3	136012637	136012637	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcactggccctgatgttgtgAagtctgtcaccaatgaggat	9	12	11	9	0	3	3	2	3	1	0	3	4	3	4	2	2	0	1	2	2	2	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:136012637A>T	ENST00000251654.4	+	7	764	c.694A>T	c.(694-696)Aag>Tag	p.K232*	PCCB_ENST00000469217.1_Nonsense_Mutation_p.K252*|PCCB_ENST00000468777.1_Nonsense_Mutation_p.K263*|PCCB_ENST00000483687.1_Nonsense_Mutation_p.K213*|PCCB_ENST00000490504.1_Nonsense_Mutation_p.K175*|PCCB_ENST00000482086.1_Nonsense_Mutation_p.K116*|PCCB_ENST00000474833.1_3'UTR|PCCB_ENST00000478469.1_Nonsense_Mutation_p.K232*|PCCB_ENST00000466072.1_Nonsense_Mutation_p.K232*|PCCB_ENST00000462637.1_Nonsense_Mutation_p.K209*|PCCB_ENST00000471595.1_Nonsense_Mutation_p.K232*	NM_000532.4	NP_000523.2	P05166	PCCB_HUMAN	propionyl CoA carboxylase, beta polypeptide	232	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)	TGATGTTGTGAAGTCTGTCAC	0.507																																					p.K252X		Atlas-SNP	.											.	PCCB	52	.	0			c.A754T						PASS	.						216	204	208					3																	136012637		2203	4300	6503	SO:0001587	stop_gained	5096	exon8			GTTGTGAAGTCTG		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.694A>T	3.37:g.136012637A>T	ENSP00000251654:p.Lys232*	83	0	0		58	17	0.293103	NM_001178014	B7Z2Z4|Q16813|Q96CX0	Nonsense_Mutation	SNP	ENST00000251654.4	37	CCDS3089.1	.	.	.	.	.	.	.	.	.	.	A	36	5.673289	0.96754	.	.	ENSG00000114054	ENST00000251654;ENST00000490504;ENST00000483687;ENST00000468777;ENST00000462637;ENST00000466072;ENST00000482086;ENST00000471595;ENST00000469217;ENST00000478469	.	.	.	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.7115	0.69235	1.0:0.0:0.0:0.0	.	.	.	.	X	232;175;213;263;209;232;116;232;252;232	.	ENSP00000251654:K232X	K	+	1	0	PCCB	137495327	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.520000	0.90566	2.009000	0.58944	0.528000	0.53228	AAG	.	.	none		0.507	PCCB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000357335.1			T	136012637	A	T	136012637	4	4	27	1	0	0	0	0	0	1	0	0	11514	247	9	5	784	5	PCCB	3	136012637	Nonsense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	291429	136012637	62009793	211	10662											
GRK7	131890	hgsc.bcm.edu	37	chr3	141497368	141497368	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agccacagtgcccacgttccGcaaggcggcaaccttcctag	9	6	10	16	3	0	0	0	0	0	0	2	0	2	0	5	2	3	3	5	2	3	3	rs34429284		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:141497368G>A	ENST00000264952.2	+	1	379	c.242G>A	c.(241-243)cGc>cAc	p.R81H		NM_139209.2	NP_631948.1	Q8WTQ7	GRK7_HUMAN	G protein-coupled receptor kinase 7	81	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.		R -> H (in dbSNP:rs34429284). {ECO:0000269|PubMed:17344846}.		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						CCCACGTTCCGCAAGGCGGCA	0.647													G|||	1	0.000199681	0.0	0.0	5008	,	,		18091	0.0		0.0	False		,,,				2504	0.001				p.R81H		Atlas-SNP	.											.	GRK7	65	.	0			c.G242A						PASS	.	G	HIS/ARG	3,4401		0,3,2199	27	26	27		242	-4.7	0	3	dbSNP_126	27	26,8568		0,26,4271	yes	missense	GRK7	NM_139209.2	29	0,29,6470	AA,AG,GG		0.3025,0.0681,0.2231	possibly-damaging	81/554	141497368	29,12969	2202	4297	6499	SO:0001583	missense	131890	exon1			CGTTCCGCAAGGC		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.242G>A	3.37:g.141497368G>A	ENSP00000264952:p.Arg81His	120	0	0		108	46	0.425926	NM_139209		Missense_Mutation	SNP	ENST00000264952.2	37	CCDS3120.1	.	.	.	.	.	.	.	.	.	.	G	3.233	-0.157014	0.06544	6.81E-4	0.003025	ENSG00000114124	ENST00000264952	T	0.02236	4.38	4.33	-4.7	0.03288	Regulator of G protein signalling (3);Regulator of G protein signalling superfamily (1);	0.921148	0.09093	N	0.849577	T	0.01222	0.0040	N	0.08118	0	0.09310	N	1	P	0.45594	0.862	B	0.39562	0.303	T	0.47886	-0.9082	10	0.35671	T	0.21	1.776	7.5979	0.28058	0.3685:0.0:0.4911:0.1404	rs34429284	81	Q8WTQ7	GRK7_HUMAN	H	81	ENSP00000264952:R81H	ENSP00000264952:R81H	R	+	2	0	GRK7	142980058	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.737000	0.04877	-1.006000	0.03412	-0.982000	0.02568	CGC	G|0.998;A|0.002	0.002	strong		0.647	GRK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353168.1	NM_139209		A	141497368	G	A	141497368	3	1	27	1	0	0	0	0	1	0	0	0	6803	1087	38	1	244	1	GRK7	3	141497368	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	5484731	141497368	56525062	212	10663											
TFDP2	7029	hgsc.bcm.edu	37	chr3	141678667	141678667	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcaaaggtgttgtcaaaattGaaaagatactcaaacctgca	17	10	7	7	0	3	2	3	1	0	1	3	2	3	2	1	1	3	2	1	1	7	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:141678667G>A	ENST00000489671.1	-	11	1330	c.900C>T	c.(898-900)ttC>ttT	p.F300F	TFDP2_ENST00000495310.1_Silent_p.F203F|TFDP2_ENST00000486111.1_Silent_p.F240F|TFDP2_ENST00000467072.1_Silent_p.F240F|TFDP2_ENST00000310282.6_Silent_p.F240F|TFDP2_ENST00000477292.1_Silent_p.F164F|TFDP2_ENST00000397991.4_Silent_p.F272F|TFDP2_ENST00000479040.1_Silent_p.F239F|TFDP2_ENST00000499676.2_Silent_p.F240F|TFDP2_ENST00000317104.7_Silent_p.F224F			Q14188	TFDP2_HUMAN	transcription factor Dp-2 (E2F dimerization partner 2)	300	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						TGTCAAAATTGAAAAGATACT	0.403																																					p.F300F		Atlas-SNP	.											.	TFDP2	44	.	0			c.C900T						PASS	.						96	91	92					3																	141678667		1932	4165	6097	SO:0001819	synonymous_variant	7029	exon11			AAAATTGAAAAGA	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.900C>T	3.37:g.141678667G>A		93	0	0		87	4	0.045977	NM_001178139	B7Z8C8|B7Z8L5|D3DNG1|E9PFC3|F8WAI2|Q13331|Q14187|Q6R754|Q8WU88|Q9UG28	Silent	SNP	ENST00000489671.1	37	CCDS54650.1	.	.	.	.	.	.	.	.	.	.	G	9.486	1.099510	0.20552	.	.	ENSG00000114126	ENST00000474279	.	.	.	5.69	-4.06	0.03986	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-5.5996	14.6009	0.68441	0.5011:0.0:0.4989:0.0	.	.	.	.	X	14	.	.	Q	-	1	0	TFDP2	143161357	1.000000	0.71417	0.491000	0.27477	0.959000	0.62525	1.103000	0.31062	-0.748000	0.04753	-0.379000	0.06801	CAA	.	.	none		0.403	TFDP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353294.4	NM_006286		A	141678667	G	A	141678667	2	1	27	1	0	0	0	0	0	0	0	1	15813	1281	45	2		2	TFDP2	3	141678667	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	181299	141678667	56343763	213	10664											
GK5	256356	hgsc.bcm.edu	37	chr3	141884493	141884493	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gttataccaattcatggagcGtttcactgctttggcccagt	8	14	9	10	1	2	0	2	0	0	0	2	1	2	1	2	2	3	3	2	2	3	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:141884493G>A	ENST00000392993.2	-	16	1712	c.1561C>T	c.(1561-1563)Cgc>Tgc	p.R521C		NM_001039547.2	NP_001034636.1	Q6ZS86	GLPK5_HUMAN	glycerol kinase 5 (putative)	521					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						TTCATGGAGCGTTTCACTGCT	0.393																																					p.R521C		Atlas-SNP	.											GK5,NS,carcinoma,+1,1	GK5	45	1	0			c.C1561T						PASS	.						218	199	205					3																	141884493		2203	4300	6503	SO:0001583	missense	256356	exon16			TGGAGCGTTTCAC	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.1561C>T	3.37:g.141884493G>A	ENSP00000418001:p.Arg521Cys	396	0	0		303	148	0.488449	NM_001039547	B2R9I2|D3DNG2|Q8N2A7|Q8N5E6	Missense_Mutation	SNP	ENST00000392993.2	37	CCDS33871.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.493597	0.84962	.	.	ENSG00000175066	ENST00000392993	D	0.91407	-2.84	5.98	5.11	0.69529	.	0.049681	0.85682	D	0.000000	D	0.93216	0.7839	M	0.84948	2.725	0.80722	D	1	D	0.59767	0.986	P	0.50537	0.643	D	0.93320	0.6692	10	0.49607	T	0.09	-12.3259	14.3523	0.66711	0.0723:0.0:0.9277:0.0	.	521	Q6ZS86	GLPK5_HUMAN	C	521	ENSP00000418001:R521C	ENSP00000418001:R521C	R	-	1	0	GK5	143367183	1.000000	0.71417	0.989000	0.46669	0.972000	0.66771	6.503000	0.73699	1.537000	0.49254	0.591000	0.81541	CGC	.	.	none		0.393	GK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353999.1	NM_001039547		A	141884493	G	A	141884493	3	1	27	1	0	0	0	0	1	0	0	0	6430	1145	40	1	32	1	GK5	3	141884493	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	205826	141884493	56137937	214	10665											
SR140	23350	hgsc.bcm.edu	37	chr3	142747227	142747227	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gcccatgtttactataggtgGaagctttattctattctgca	9	16	8	8	0	2	0	0	0	2	0	2	1	2	1	1	2	3	3	1	2	6	9			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:142747227G>A	ENST00000473835.2	+	15	1515	c.1425G>A	c.(1423-1425)tgG>tgA	p.W475*	U2SURP_ENST00000493598.2_Nonsense_Mutation_p.W474*|U2SURP_ENST00000397933.2_Nonsense_Mutation_p.W66*	NM_001080415.1	NP_001073884.1	O15042	SR140_HUMAN	U2 snRNP-associated SURP domain containing	475					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						ACTATAGGTGGAAGCTTTATT	0.313																																					p.W475X		Atlas-SNP	.											.	U2SURP	66	.	0			c.G1425A						PASS	.						75	70	72					3																	142747227		1796	4067	5863	SO:0001587	stop_gained	23350	exon15			TAGGTGGAAGCTT	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.1425G>A	3.37:g.142747227G>A	ENSP00000418563:p.Trp475*	210	0	0		182	43	0.236264	NM_001080415	A0PJ60|Q0D2M1|Q2NKQ7|Q9BR70	Nonsense_Mutation	SNP	ENST00000473835.2	37	CCDS46928.1	.	.	.	.	.	.	.	.	.	.	G	39	7.674541	0.98425	.	.	ENSG00000163714	ENST00000473835;ENST00000319822;ENST00000397933;ENST00000493598;ENST00000480029	.	.	.	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.0436	20.2187	0.98312	0.0:0.0:1.0:0.0	.	.	.	.	X	475;475;66;474;42	.	ENSP00000322376:W475X	W	+	3	0	U2SURP	144229917	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.444000	0.97578	2.780000	0.95670	0.655000	0.94253	TGG	.	.	none		0.313	U2SURP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354603.2	NM_001080415		A	142747227	G	A	142747227	4	1	27	1	0	0	0	0	0	1	0	0	15146	1183	41	2	1483	2	SR140	3	142747227	Nonsense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	862734	142747227	55275203	215	10666											
GPR149	344758	hgsc.bcm.edu	37	chr3	154147336	154147336	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggcggatttaaaaggtcCgtagaattatgattctcttt	10	15	9	7	2	1	2	0	1	1	1	3	3	2	3	2	3	0	1	2	3	5	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:154147336C>T	ENST00000389740.2	-	1	168	c.69G>A	c.(67-69)acG>acA	p.T23T		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	23					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)			TTAAAAGGTCCGTAGAATTAT	0.363																																					p.T23T		Atlas-SNP	.											GPR149,NS,carcinoma,-1,1	GPR149	134	1	0			c.G69A						PASS	.						77	77	77					3																	154147336		1836	4087	5923	SO:0001819	synonymous_variant	344758	exon1			AAGGTCCGTAGAA	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.69G>A	3.37:g.154147336C>T		167	0	0		146	33	0.226027	NM_001038705		Silent	SNP	ENST00000389740.2	37	CCDS43162.1																																																																																			.	.	none		0.363	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580		T	154147336	C	T	154147336	2	4	27	1	0	0	0	0	0	0	0	1	6662	639	23	1		1	GPR149	3	154147336	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	11400109	154147336	43875094	216	10667											
ZBBX	79740	hgsc.bcm.edu	37	chr3	167045779	167045779	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttgttgtcatcatgatttccGgttctccattgacttaacac	8	17	6	10	1	3	2	2	2	1	0	5	2	4	2	2	1	1	2	2	1	1	6	rs375095384		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:167045779G>A	ENST00000392766.2	-	11	1153	c.813C>T	c.(811-813)acC>acT	p.T271T	ZBBX_ENST00000392767.2_Silent_p.T271T|ZBBX_ENST00000469220.1_Intron|ZBBX_ENST00000455345.2_Silent_p.T271T|ZBBX_ENST00000392764.1_Silent_p.T242T|ZBBX_ENST00000307529.5_Silent_p.T271T	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	271						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.T271T(2)		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						CATGATTTCCGGTTCTCCATT	0.378													G|||	1	0.000199681	0.0008	0.0	5008	,	,		15273	0.0		0.0	False		,,,				2504	0.0				p.T271T		Atlas-SNP	.											ZBBX_ENST00000455345,NS,carcinoma,0,2	ZBBX	299	2	2	Substitution - coding silent(2)	endometrium(2)	c.C813T						PASS	.	G	,,	1,3745		0,1,1872	218	199	205		813,726,813	-3.4	0	3		205	0,8220		0,0,4110	no	coding-synonymous,coding-synonymous,coding-synonymous	ZBBX	NM_001199201.1,NM_001199202.1,NM_024687.3	,,	0,1,5982	AA,AG,GG		0.0,0.0267,0.0084	,,	271/840,242/772,271/801	167045779	1,11965	1873	4110	5983	SO:0001819	synonymous_variant	79740	exon11			ATTTCCGGTTCTC	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.813C>T	3.37:g.167045779G>A		170	0	0		123	26	0.211382	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Silent	SNP	ENST00000392766.2	37	CCDS3199.2																																																																																			.	.	weak		0.378	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687		A	167045779	G	A	167045779	2	1	27	1	0	0	0	0	0	0	0	1	17531	1103	39	1		1	ZBBX	3	167045779	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	12898443	167045779	30976651	217	10668											
PARL	55486	hgsc.bcm.edu	37	chr3	183551309	183551309	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agagctcccccaagatgtgcCgcatgatcaaaaaatttcca	14	8	7	12	1	1	3	1	1	0	2	3	3	3	3	4	0	2	2	4	0	4	1	rs140027735		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:183551309C>T	ENST00000317096.4	-	9	1059	c.999G>A	c.(997-999)gcG>gcA	p.A333A	PARL_ENST00000435888.1_Silent_p.A249A|PARL_ENST00000311101.5_Silent_p.A283A	NM_018622.5	NP_061092.3	Q9H300	PARL_HUMAN	presenilin associated, rhomboid-like	333					membrane protein proteolysis (GO:0033619)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|proteolysis (GO:0006508)|regulation of protein targeting to mitochondrion (GO:1903214)|regulation of reactive oxygen species metabolic process (GO:2000377)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(3)|liver(1)|lung(6)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	17	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.21e-41)|Epithelial(37;1.34e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			CAAGATGTGCCGCATGATCAA	0.488																																					p.A333A		Atlas-SNP	.											PARL,NS,carcinoma,-2,1	PARL	32	1	0			c.G999A						PASS	.						117	101	106					3																	183551309		2203	4300	6503	SO:0001819	synonymous_variant	55486	exon9			ATGTGCCGCATGA	AF116692	CCDS3248.1, CCDS33897.1	3q27.3	2008-02-05		2006-02-28	ENSG00000175193	ENSG00000175193			18253	protein-coding gene	gene with protein product	"rhomboid 7 homolog 1 (Drosophila)"	607858		PSARL			Standard	XM_005247587		Approved	PRO2207, PSARL1, RHBDS1	uc003fmd.3	Q9H300	OTTHUMG00000156890	ENST00000317096.4:c.999G>A	3.37:g.183551309C>T		272	0	0		249	79	0.317269	NM_018622	Q96CQ4|Q9BTJ6|Q9P1E3	Silent	SNP	ENST00000317096.4	37	CCDS3248.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.958|9.958	1.222020|1.222020	0.22457|0.22457	.|.	.|.	ENSG00000175193|ENSG00000175193	ENST00000417784|ENST00000418450	.|.	.|.	.|.	5.63|5.63	0.535|0.535	0.17133|0.17133	.|.	.|.	.|.	.|.	.|.	T|T	0.42131|0.42131	0.1189|0.1189	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.24297|0.24297	-1.0164|-1.0164	4|4	.|.	.|.	.|.	-14.8538|-14.8538	1.496|1.496	0.02467|0.02467	0.1357:0.2209:0.1255:0.5179|0.1357:0.2209:0.1255:0.5179	.|.	.|.	.|.	.|.	S|Q	125|66	.|.	.|.	G|R	-|-	1|2	0|0	PARL|PARL	185034003|185034003	0.871000|0.871000	0.30034|0.30034	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	-0.009000|-0.009000	0.12765|0.12765	0.149000|0.149000	0.19098|0.19098	-0.238000|-0.238000	0.12139|0.12139	GGC|CGG	C|1.000;A|0.000	.	alt		0.488	PARL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346465.1	NM_018622		T	183551309	C	T	183551309	2	4	27	1	0	0	0	0	0	0	0	1	11460	639	23	1		1	PARL	3	183551309	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	16505530	183551309	14471121	218	10669											
CHRD	8646	hgsc.bcm.edu	37	chr3	184099050	184099050	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggggtcgccgtaccaggggcCctggcagggtcagctgcaag	6	5	18	12	2	1	0	1	0	0	0	2	0	1	0	3	6	3	4	3	6	2	1	rs34095724	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:184099050C>T	ENST00000204604.1	+	3	526	c.280C>T	c.(280-282)Cct>Tct	p.P94S	EIF2B5_ENST00000444495.1_Intron|CHRD_ENST00000545352.1_5'Flank|CHRD_ENST00000348986.3_Missense_Mutation_p.P94S|CHRD_ENST00000450923.1_Missense_Mutation_p.P94S|CHRD_ENST00000482805.1_3'UTR	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	94	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.		P -> S (in dbSNP:rs34095724).		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)			TACCAGGGGCCCTGGCAGGGT	0.657													C|||	195	0.0389377	0.093	0.0173	5008	,	,		14626	0.002		0.0378	False		,,,				2504	0.0204				p.P94S		Atlas-SNP	.											.	CHRD	149	.	0			c.C280T						PASS	.	C	SER/PRO	410,3994		18,374,1810	21	26	24		280	4.3	1	3	dbSNP_126	24	292,8302		2,288,4007	yes	missense	CHRD	NM_003741.2	74	20,662,5817	TT,TC,CC		3.3977,9.3097,5.4008	benign	94/956	184099050	702,12296	2202	4297	6499	SO:0001583	missense	8646	exon3			AGGGGCCCTGGCA	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.280C>T	3.37:g.184099050C>T	ENSP00000204604:p.Pro94Ser	267	0	0		250	144	0.576	NM_003741	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Missense_Mutation	SNP	ENST00000204604.1	37	CCDS3266.1	92	0.04212454212454213	53	0.10772357723577236	9	0.024861878453038673	1	0.0017482517482517483	29	0.03825857519788918	C	3.315	-0.140029	0.06669	0.093097	0.033977	ENSG00000090539	ENST00000204604;ENST00000450923;ENST00000348986	T;T;T	0.13307	2.83;2.6;2.61	5.18	4.3	0.51218	von Willebrand factor, type C (3);	0.242099	0.43110	D	0.000610	T	0.00144	0.0004	N	0.12182	0.205	0.80722	D	1	B;B	0.11235	0.0;0.004	B;B	0.15870	0.007;0.014	T	0.49960	-0.8883	10	0.20519	T	0.43	-8.4545	7.7367	0.28819	0.0:0.5773:0.3366:0.0861	rs34095724	94;94	E7ESX1;Q9H2X0	.;CHRD_HUMAN	S	94	ENSP00000204604:P94S;ENSP00000408972:P94S;ENSP00000334036:P94S	ENSP00000204604:P94S	P	+	1	0	CHRD	185581744	0.001000	0.12720	1.000000	0.80357	0.678000	0.39670	0.462000	0.21956	1.169000	0.42739	0.561000	0.74099	CCT	C|0.949;T|0.051	0.051	strong		0.657	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741		T	184099050	C	T	184099050	3	4	27	1	0	0	0	0	1	0	0	0	3374	623	22	2	290	2	CHRD	3	184099050	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	547741	184099050	13923380	219	10670											
CHRD	8646	hgsc.bcm.edu	37	chr3	184102814	184102814	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctggacccagcgctgcccGtgcccctagcaggagccctg	5	6	13	17	2	1	0	0	0	1	0	1	2	1	2	5	2	5	2	5	2	1	1	rs138882380		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:184102814G>A	ENST00000204604.1	+	14	1852	c.1606G>A	c.(1606-1608)Gtg>Atg	p.V536M	EIF2B5_ENST00000444495.1_Intron|CHRD_ENST00000545352.1_Missense_Mutation_p.V166M|CHRD_ENST00000348986.3_Missense_Mutation_p.V496M|CHRD_ENST00000450923.1_Missense_Mutation_p.V536M	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	536	CHRD 4. {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)			AGCGCTGCCCGTGCCCCTAGC	0.607													G|||	1	0.000199681	0.0	0.0	5008	,	,		16943	0.0		0.001	False		,,,				2504	0.0				p.V536M		Atlas-SNP	.											.	CHRD	149	.	0			c.G1606A						PASS	.	G	MET/VAL	0,4406		0,0,2203	106	112	110		1606	3.6	1	3	dbSNP_134	110	2,8598	2.2+/-6.3	0,2,4298	no	missense	CHRD	NM_003741.2	21	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	536/956	184102814	2,13004	2203	4300	6503	SO:0001583	missense	8646	exon14			CTGCCCGTGCCCC	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.1606G>A	3.37:g.184102814G>A	ENSP00000204604:p.Val536Met	84	0	0		71	40	0.56338	NM_003741	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Missense_Mutation	SNP	ENST00000204604.1	37	CCDS3266.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	16.85	3.236050	0.58886	0.0	2.33E-4	ENSG00000090539	ENST00000204604;ENST00000450923;ENST00000348986;ENST00000545352;ENST00000342610	T;T;T;T	0.46451	0.87;0.87;0.87;0.87	5.38	3.59	0.41128	CHRD (3);	0.125547	0.52532	D	0.000071	T	0.58250	0.2109	M	0.66939	2.045	0.47183	D	0.99934	D;D;D;D	0.89917	0.999;1.0;0.989;1.0	D;D;P;D	0.76071	0.982;0.987;0.906;0.98	T	0.56153	-0.8026	10	0.45353	T	0.12	-20.6515	9.8593	0.41105	0.1666:0.0:0.8334:0.0	.	166;496;536;536	B7Z6F4;Q9H2X0-5;E7ESX1;Q9H2X0	.;.;.;CHRD_HUMAN	M	536;536;496;166;249	ENSP00000204604:V536M;ENSP00000408972:V536M;ENSP00000334036:V496M;ENSP00000442948:V166M	ENSP00000204604:V536M	V	+	1	0	CHRD	185585508	0.810000	0.29049	0.978000	0.43139	0.744000	0.42396	1.230000	0.32612	0.781000	0.33589	0.655000	0.94253	GTG	G|1.000;A|0.000	0.000	strong		0.607	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741		A	184102814	G	A	184102814	3	1	27	1	0	0	0	0	1	0	0	0	3374	1145	40	1	1660	1	CHRD	3	184102814	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	3764	184102814	13919616	220	10671											
LRRC15	131578	hgsc.bcm.edu	37	chr3	194080174	194080174	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gccagcccgctctgggcctgGgtcatgccccaaacgctgcg	5	6	13	17	3	2	0	1	0	1	0	2	0	2	0	5	2	4	2	5	2	1	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:194080174G>A	ENST00000347624.3	-	2	1684	c.1599C>T	c.(1597-1599)acC>acT	p.T533T	LRRC15_ENST00000428839.1_Silent_p.T539T|LRRC15_ENST00000439944.2_Silent_p.T539T	NM_130830.4	NP_570843.2	Q8TF66	LRC15_HUMAN	leucine rich repeat containing 15	533					negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|positive regulation of cell migration (GO:0030335)|receptor-mediated virion attachment to host cell (GO:0046813)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	collagen binding (GO:0005518)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)			biliary_tract(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(20)|ovary(4)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.94e-05)		TCTGGGCCTGGGTCATGCCCC	0.587																																					p.T539T		Atlas-SNP	.											.	LRRC15	137	.	0			c.C1617T						PASS	.						89	88	88					3																	194080174		2203	4300	6503	SO:0001819	synonymous_variant	131578	exon3			GGCCTGGGTCATG	AB071037	CCDS3306.1, CCDS46984.1	3q29	2008-02-05			ENSG00000172061	ENSG00000172061			20818	protein-coding gene	gene with protein product						12923058	Standard	NM_001135057		Approved	LIB	uc003ftu.3	Q8TF66	OTTHUMG00000156048	ENST00000347624.3:c.1599C>T	3.37:g.194080174G>A		133	0	0		142	45	0.316901	NM_001135057	Q495Q6|Q7RTN7	Silent	SNP	ENST00000347624.3	37	CCDS3306.1																																																																																			.	.	none		0.587	LRRC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342858.2			A	194080174	G	A	194080174	2	1	27	1	0	0	0	0	0	0	0	1	8979	1219	43	2		2	LRRC15	3	194080174	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	9977360	194080174	3942256	221	10672											
TMEM44	93109	hgsc.bcm.edu	37	chr3	194346704	194346704	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taagtcaatagctgctaggtAggcaccagtgaaaacctggg	13	8	12	8	0	1	1	1	1	0	0	1	1	1	1	2	3	3	4	2	3	7	4	rs140271606	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:194346704A>G	ENST00000392432.2	-	3	485	c.280T>C	c.(280-282)Tac>Cac	p.Y94H	TMEM44_ENST00000347147.4_Missense_Mutation_p.Y94H|TMEM44_ENST00000381975.3_Missense_Mutation_p.Y94H|TMEM44_ENST00000473092.1_Missense_Mutation_p.Y94H|TMEM44_ENST00000330115.3_5'UTR|TMEM44_ENST00000273580.7_Missense_Mutation_p.Y94H	NM_001166305.1	NP_001159777.1	Q2T9K0	TMM44_HUMAN	transmembrane protein 44	94						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)		GCTGCTAGGTAGGCACCAGTG	0.468													A|||	6	0.00119808	0.0	0.0014	5008	,	,		20623	0.0		0.003	False		,,,				2504	0.002				p.Y94H		Atlas-SNP	.											.	TMEM44	42	.	0			c.T280C						PASS	.	A	HIS/TYR,HIS/TYR,HIS/TYR,HIS/TYR	1,4405		0,1,2202	149	129	135		280,280,280,280	4.9	1	3	dbSNP_134	135	17,8583	12.6+/-44.7	0,17,4283	yes	missense,missense,missense,missense	TMEM44	NM_001011655.2,NM_001166305.1,NM_001166306.1,NM_138399.4	83,83,83,83	0,18,6485	GG,GA,AA		0.1977,0.0227,0.1384	probably-damaging,probably-damaging,probably-damaging,probably-damaging	94/429,94/476,94/397,94/439	194346704	18,12988	2203	4300	6503	SO:0001583	missense	93109	exon3			CTAGGTAGGCACC	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.280T>C	3.37:g.194346704A>G	ENSP00000376227:p.Tyr94His	218	0	0		195	90	0.461538	NM_138399	A1L3V7|B7ZLZ5|B7ZLZ6|C9JJ62|E9PGA9|Q0P6F7|Q6ZT47|Q8IXR1|Q8N4G3	Missense_Mutation	SNP	ENST00000392432.2	37	CCDS54699.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	14.86	2.662149	0.47572	2.27E-4	0.001977	ENSG00000145014	ENST00000392432;ENST00000273580;ENST00000347147;ENST00000381975;ENST00000473092	T;T;T;T;T	0.35973	1.28;1.28;1.28;1.28;1.28	4.94	4.94	0.65067	.	0.104825	0.38837	N	0.001559	T	0.54191	0.1843	L	0.60455	1.87	0.42318	D	0.992247	D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;1.0	D;D;D;D;D	0.87578	0.997;0.998;0.998;0.996;0.998	T	0.58081	-0.7699	10	0.87932	D	0	-18.408	11.2784	0.49180	1.0:0.0:0.0:0.0	.	94;94;94;94;94	E9PGA9;Q2T9K0;Q2T9K0-4;Q2T9K0-2;Q2T9K0-6	.;TMM44_HUMAN;.;.;.	H	94	ENSP00000376227:Y94H;ENSP00000273580:Y94H;ENSP00000333355:Y94H;ENSP00000371402:Y94H;ENSP00000418674:Y94H	ENSP00000273580:Y94H	Y	-	1	0	TMEM44	195827993	1.000000	0.71417	1.000000	0.80357	0.339000	0.28857	4.194000	0.58393	1.980000	0.57719	0.459000	0.35465	TAC	A|0.998;G|0.002	0.002	strong		0.468	TMEM44-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000342750.1	NM_138399		G	194346704	A	G	194346704	3	3	27	1	0	0	0	0	1	0	0	0	16183	420	15	3	1217	3	TMEM44	3	194346704	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	266530	194346704	3675726	222	10673											
MUC4	4585	hgsc.bcm.edu	37	chr3	195505247	195505247	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgctgggaatggtggaaatGatggtctgggaggttgtggg	7	11	21	2	0	1	1	0	1	1	0	1	4	1	4	0	7	1	2	0	7	2	1	rs76650792	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:195505247G>T	ENST00000346145.4	-	2	201	c.162C>A	c.(160-162)atC>atA	p.I54I	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000463781.3_Silent_p.I4290I|MUC4_ENST00000475231.1_Silent_p.I4290I	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	1047					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)		TGGTGGAAATGATGGTCTGGG	0.592													.|||	112	0.0223642	0.0121	0.0562	5008	,	,		8996	0.005		0.0497	False		,,,				2504	0.002				p.I4290I		Atlas-SNP	.											.	MUC4	1505	.	0			c.C12870A						PASS	.	G	,,	66,4336	60.5+/-97.4	2,62,2137	225	175	192		162,12870,	-4.7	0	3	dbSNP_131	192	379,8209	123.9+/-182.7	9,361,3924	no	coding-synonymous,coding-synonymous,intron	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	,,	11,423,6061	TT,TG,GG		4.4131,1.4993,3.4257	,,	54/1177,4290/5413,	195505247	445,12545	2201	4294	6495	SO:0001819	synonymous_variant	4585	exon3			GGAAATGATGGTC	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.162C>A	3.37:g.195505247G>T		296	0	0		285	136	0.477193	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	37	CCDS3310.1																																																																																			G|0.967;T|0.033	0.033	strong		0.592	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406		T	195505247	G	T	195505247	2	4	27	1	0	0	0	0	0	0	0	1	9987	1280	45	4		4	MUC4	3	195505247	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1158543	195505247	2517183	223	10674											
SENP5	205564	hgsc.bcm.edu	37	chr3	196612959	196612959	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctaaagacccttcttgtcggCatcagccgtactttccagat	9	12	7	13	2	2	2	1	0	1	2	4	2	3	2	3	1	2	2	3	1	3	5	rs151102982	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr3:196612959C>T	ENST00000323460.5	+	2	1156	c.907C>T	c.(907-909)Cat>Tat	p.H303Y	SENP5_ENST00000419026.1_Intron|SENP5_ENST00000445299.2_Missense_Mutation_p.H303Y	NM_152699.4	NP_689912.2	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	303					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)		TTCTTGTCGGCATCAGCCGTA	0.532													C|||	12	0.00239617	0.0	0.0029	5008	,	,		19282	0.0		0.007	False		,,,				2504	0.0031				p.H303Y	Ovarian(47;891 1095 11174 13858 51271)	Atlas-SNP	.											.	SENP5	68	.	0			c.C907T						PASS	.	C	TYR/HIS	3,4403	6.2+/-15.9	0,3,2200	90	86	87		907	4.5	0.9	3	dbSNP_134	87	68,8532	40.8+/-97.7	1,66,4233	yes	missense	SENP5	NM_152699.4	83	1,69,6433	TT,TC,CC		0.7907,0.0681,0.5459	benign	303/756	196612959	71,12935	2203	4300	6503	SO:0001583	missense	205564	exon2			TGTCGGCATCAGC	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.907C>T	3.37:g.196612959C>T	ENSP00000327197:p.His303Tyr	69	0	0		55	21	0.381818	NM_152699	B4DY82|Q96SA5	Missense_Mutation	SNP	ENST00000323460.5	37	CCDS3322.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	12.93	2.086414	0.36855	6.81E-4	0.007907	ENSG00000119231	ENST00000323460;ENST00000445299	T;T	0.34275	1.37;1.37	5.37	4.49	0.54785	.	0.432451	0.21815	N	0.068702	T	0.12135	0.0295	N	0.14661	0.345	0.80722	D	1	P;B	0.47350	0.894;0.167	B;B	0.38562	0.276;0.04	T	0.08764	-1.0706	10	0.05351	T	0.99	-0.0265	11.2608	0.49083	0.0:0.9096:0.0:0.0904	.	303;303	B4DY82;Q96HI0	.;SENP5_HUMAN	Y	303	ENSP00000327197:H303Y;ENSP00000390231:H303Y	ENSP00000327197:H303Y	H	+	1	0	SENP5	198097356	0.364000	0.24997	0.863000	0.33907	0.985000	0.73830	2.003000	0.40844	1.381000	0.46364	0.655000	0.94253	CAT	C|0.993;T|0.007	0.007	strong		0.532	SENP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340524.1	NM_152699		T	196612959	C	T	196612959	3	4	27	1	0	0	0	0	1	0	0	0	14064	710	25	2	909	2	SENP5	3	196612959	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1107712	196612959	1409471	224	10675											
CRIPAK	285464	hgsc.bcm.edu	37	chr4	1388944	1388944	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctgctcacacgtgcccatGtggagtgttcgcctgctcac	5	10	11	15	2	2	0	2	0	0	0	3	1	2	1	3	1	3	3	3	1	0	1	rs200759023	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:1388944G>A	ENST00000324803.4	+	1	3605	c.645G>A	c.(643-645)atG>atA	p.M215I		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	215					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			ACGTGCCCATGTGGAGTGTTC	0.657													N|||	445	0.0888578	0.1619	0.0677	5008	,	,		12756	0.001		0.0934	False		,,,				2504	0.091				p.M215I		Atlas-SNP	.											.	CRIPAK	185	.	0			c.G645A						PASS	.	G	ILE/MET	423,3903		140,143,1880	215	149	173		645	0.5	0	4		173	744,6886		259,226,3330	no	missense	CRIPAK	NM_175918.3	10	399,369,5210	AA,AG,GG		9.751,9.7781,9.7608	benign	215/447	1388944	1167,10789	2163	3815	5978	SO:0001583	missense	285464	exon1			GCCCATGTGGAGT	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"cysteine-rich PAK1inhibitor"			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.645G>A	4.37:g.1388944G>A	ENSP00000323978:p.Met215Ile	61	0	0		12	12	1	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	g	4.551	0.102411	0.08731	0.097781	0.09751	ENSG00000179979	ENST00000324803	T	0.17528	2.27	1.41	0.509	0.16977	Post-SET domain (1);	.	.	.	.	T	0.00210	0.0006	N	0.08118	0	0.09310	N	1	B	0.17852	0.024	B	0.12156	0.007	T	0.42865	-0.9426	9	0.18710	T	0.47	.	4.0015	0.09582	0.431:0.0:0.569:0.0	.	215	Q8N1N5	CRPAK_HUMAN	I	215	ENSP00000323978:M215I	ENSP00000323978:M215I	M	+	3	0	CRIPAK	1378944	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.348000	0.02629	0.169000	0.19679	-0.506000	0.04501	ATG	.	.	weak		0.657	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918		A	1388944	G	A	1388944	3	1	27	1	0	0	0	0	1	0	0	0	3879	1377	48	2	647	2	CRIPAK	4	1388944	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10		1388944	189765332	225	10676											
CRIPAK	285464	hgsc.bcm.edu	37	chr4	1389046	1389046	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cacgtgcccatgtggagtgcCcgcctgctcacgtgccgatg	5	8	13	15	4	1	0	1	0	0	0	1	2	1	1	4	1	4	1	4	1	0	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:1389046C>T	ENST00000324803.4	+	1	3707	c.747C>T	c.(745-747)gcC>gcT	p.A249A		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	249					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			TGTGGAGTGCCCGCCTGCTCA	0.692																																					p.A249A		Atlas-SNP	.											CRIPAK,colon,carcinoma,0,1	CRIPAK	185	1	0			c.C747T						PASS	.						148	130	136					4																	1389046		2202	4299	6501	SO:0001819	synonymous_variant	285464	exon1			GAGTGCCCGCCTG	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"cysteine-rich PAK1inhibitor"			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.747C>T	4.37:g.1389046C>T		82	0	0		59	9	0.152542	NM_175918	Q8NB03	Silent	SNP	ENST00000324803.4	37	CCDS3349.1																																																																																			.	.	none		0.692	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918		T	1389046	C	T	1389046	2	4	27	1	0	0	0	0	0	0	0	1	3879	610	22	2		2	CRIPAK	4	1389046	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	102	1389046	189765230	226	10677											
FGFR3	2261	hgsc.bcm.edu	37	chr4	1801511	1801511	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgacgaagacggggaggaCgaggctgaggacacaggtgt	12	4	19	6	3	0	3	0	2	0	1	0	9	0	6	0	6	0	1	0	6	1	0	rs3135867	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:1801511C>T	ENST00000260795.2	+	3	519	c.417C>T	c.(415-417)gaC>gaT	p.D139D	FGFR3_ENST00000352904.1_Silent_p.D139D|FGFR3_ENST00000481110.2_Silent_p.D139D|FGFR3_ENST00000340107.4_Silent_p.D139D|FGFR3_ENST00000440486.2_Silent_p.D139D|FGFR3_ENST00000412135.2_Silent_p.D139D			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	139					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)	ACGGGGAGGACGAGGCTGAGG	0.677		1	"Mis, T"	"IGH@, ETV6"	"bladder, MM, T-cell lymphoma"		"Hypochondroplasia, Thanatophoric dysplasia"		Saethre-Chotzen syndrome;Muenke syndrome				c|||	101	0.0201677	0.0015	0.0331	5008	,	,		17142	0.0		0.0487	False		,,,				2504	0.0276				p.D139D		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"L, E"	.	FGFR3	3320	.	0			c.C417T						PASS	.	C	,,	38,4360	42.3+/-75.8	1,36,2162	88	69	75		417,417,417	-1.1	1	4	dbSNP_103	75	447,8147	134.1+/-191.5	10,427,3860	no	coding-synonymous,coding-synonymous,coding-synonymous	FGFR3	NM_000142.4,NM_001163213.1,NM_022965.3	,,	11,463,6022	TT,TC,CC		5.2013,0.864,3.7331	,,	139/807,139/809,139/695	1801511	485,12507	2199	4297	6496	SO:0001819	synonymous_variant	2261	exon4	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	GGAGGACGAGGCT	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.417C>T	4.37:g.1801511C>T		196	0	0		156	78	0.5	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Silent	SNP	ENST00000260795.2	37	CCDS3353.1																																																																																			C|0.965;T|0.035	0.035	strong		0.677	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142		T	1801511	C	T	1801511	2	4	27	1	0	0	0	0	0	0	0	1	5875	535	19	1		1	FGFR3	4	1801511	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	412465	1801511	189352765	227	10678											
HTT	3064	hgsc.bcm.edu	37	chr4	3107140	3107140	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aggtttgctgagctggctcaCctggttcggcctcagaaatg	7	11	13	10	1	2	2	2	1	0	1	3	2	2	2	2	4	2	5	2	4	1	2	rs184820567		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:3107140C>T	ENST00000355072.5	+	5	730	c.585C>T	c.(583-585)caC>caT	p.H195H		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	195					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)		AGCTGGCTCACCTGGTTCGGC	0.527													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18849	0.0		0.0	False		,,,				2504	0.0				p.H195H		Atlas-SNP	.											.	HTT	221	.	0			c.C585T						PASS	.	C		0,4288		0,0,2144	111	116	114		585	3.4	1	4		114	3,8537		0,3,4267	no	coding-synonymous	HTT	NM_002111.6		0,3,6411	TT,TC,CC		0.0351,0.0,0.0234		195/3143	3107140	3,12825	2144	4270	6414	SO:0001819	synonymous_variant	3064	exon5			GGCTCACCTGGTT	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.585C>T	4.37:g.3107140C>T		182	0	0		145	70	0.482759	NM_002111	Q9UQB7	Silent	SNP	ENST00000355072.5	37	CCDS43206.1																																																																																			C|0.999;T|0.001	0.001	strong		0.527	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111		T	3107140	C	T	3107140	2	4	27	1	0	0	0	0	0	0	0	1	7466	506	18	2		2	HTT	4	3107140	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1305629	3107140	188047136	228	10679											
SLIT2	9353	hgsc.bcm.edu	37	chr4	20487867	20487867	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagactttctgtggcaagttTcaaccatatgcctaaactta	12	14	6	9	0	2	1	1	0	1	1	2	1	2	1	2	1	3	2	2	1	7	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:20487867T>C	ENST00000504154.1	+	7	836	c.584T>C	c.(583-585)tTc>tCc	p.F195S	SLIT2_ENST00000503823.1_Missense_Mutation_p.F195S|SLIT2_ENST00000503837.1_Missense_Mutation_p.F195S|SLIT2_ENST00000273739.5_Missense_Mutation_p.F195S	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	195					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						GTGGCAAGTTTCAACCATATG	0.289																																					p.F195S		Atlas-SNP	.											.	SLIT2	290	.	0			c.T584C						PASS	.						76	77	77					4																	20487867		2202	4299	6501	SO:0001583	missense	9353	exon7			CAAGTTTCAACCA	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.584T>C	4.37:g.20487867T>C	ENSP00000422591:p.Phe195Ser	269	0	0		163	45	0.276074	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation	SNP	ENST00000504154.1	37	CCDS3426.1	.	.	.	.	.	.	.	.	.	.	T	27.8	4.867172	0.91511	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	T;T;T;T	0.70749	-0.51;-0.51;-0.51;-0.51	5.3	5.3	0.74995	.	0.090982	0.85682	D	0.000000	D	0.88175	0.6366	H	0.94620	3.56	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.75484	0.986;0.978	D	0.91139	0.4944	10	0.59425	D	0.04	.	15.5307	0.75960	0.0:0.0:0.0:1.0	.	195;195	O94813-3;O94813	.;SLIT2_HUMAN	S	195	ENSP00000427548:F195S;ENSP00000422591:F195S;ENSP00000273739:F195S;ENSP00000422261:F195S	ENSP00000273739:F195S	F	+	2	0	SLIT2	20096965	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.997000	0.88414	2.120000	0.65058	0.459000	0.35465	TTC	.	.	none		0.289	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			C	20487867	T	C	20487867	3	2	27	1	0	0	0	0	1	0	0	0	14755	1783	62	3	610	3	SLIT2	4	20487867	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	17380727	20487867	170666409	229	10680											
SLIT2	9353	hgsc.bcm.edu	37	chr4	20493415	20493415	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttatggctccttcttgtagTgttttgcactgccctgccgc	3	17	9	12	1	1	0	0	0	1	0	2	0	2	0	3	1	3	4	3	1	2	7			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:20493415T>A	ENST00000504154.1	+	9	1059	c.807T>A	c.(805-807)agT>agA	p.S269R	SLIT2_ENST00000503823.1_Missense_Mutation_p.S269R|SLIT2_ENST00000503837.1_Missense_Mutation_p.S273R|SLIT2_ENST00000273739.5_Missense_Mutation_p.S273R	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	269	LRRNT 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						CTTCTTGTAGTGTTTTGCACT	0.408																																					p.S269R		Atlas-SNP	.											.	SLIT2	290	.	0			c.T807A						PASS	.						132	132	132					4																	20493415		2203	4300	6503	SO:0001583	missense	9353	exon9			TTGTAGTGTTTTG	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.807T>A	4.37:g.20493415T>A	ENSP00000422591:p.Ser269Arg	147	0	0		106	32	0.301887	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation	SNP	ENST00000504154.1	37	CCDS3426.1	.	.	.	.	.	.	.	.	.	.	T	19.90	3.912535	0.72983	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	T;T;T;T	0.81247	-1.45;-1.47;-1.38;-1.44	5.63	-10.6	0.00265	.	0.000000	0.85682	D	0.000000	T	0.71719	0.3373	N	0.17764	0.52	0.54753	D	0.999988	P;D	0.55172	0.801;0.97	P;P	0.53912	0.578;0.737	D	0.85392	0.1126	10	0.48119	T	0.1	.	17.9392	0.89022	0.0:0.5825:0.0:0.4175	.	269;269	O94813-3;O94813	.;SLIT2_HUMAN	R	269;269;273;273;273	ENSP00000427548:S269R;ENSP00000422591:S269R;ENSP00000273739:S273R;ENSP00000422261:S273R	ENSP00000273739:S273R	S	+	3	2	SLIT2	20102513	0.076000	0.21285	0.120000	0.21714	0.952000	0.60782	-0.425000	0.07017	-2.280000	0.00675	-0.146000	0.13790	AGT	.	.	none		0.408	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2			A	20493415	T	A	20493415	3	1	27	1	0	0	0	0	1	0	0	0	14755	1693	59	5	841	5	SLIT2	4	20493415	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	5548	20493415	170660861	230	10681											
KLB	152831	hgsc.bcm.edu	37	chr4	39436192	39436192	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaaatgtttcacttaatttAagagaagcgctgaactggat	15	12	8	6	1	1	2	1	1	0	1	1	4	1	3	0	1	2	2	0	1	6	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:39436192A>C	ENST00000257408.4	+	2	1285	c.1188A>C	c.(1186-1188)ttA>ttC	p.L396F		NM_175737.3	NP_783864.1	Q86Z14	KLOTB_HUMAN	klotho beta	396	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						CACTTAATTTAAGAGAAGCGC	0.418																																					p.L396F		Atlas-SNP	.											.	KLB	95	.	0			c.A1188C						PASS	.						105	105	105					4																	39436192		2203	4300	6503	SO:0001583	missense	152831	exon2			TAATTTAAGAGAA	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.1188A>C	4.37:g.39436192A>C	ENSP00000257408:p.Leu396Phe	81	0	0		43	12	0.27907	NM_175737	Q2M3K8	Missense_Mutation	SNP	ENST00000257408.4	37	CCDS3451.1	.	.	.	.	.	.	.	.	.	.	A	13.59	2.283680	0.40394	.	.	ENSG00000134962	ENST00000257408	T	0.44482	0.92	6.06	-0.216	0.13153	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.64402	D	0.000001	T	0.52581	0.1743	L	0.49699	1.58	0.42547	D	0.993094	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.50030	-0.8875	10	0.56958	D	0.05	-15.1023	10.3696	0.44046	0.412:0.0:0.588:0.0	.	396;396	B7ZL50;Q86Z14	.;KLOTB_HUMAN	F	396	ENSP00000257408:L396F	ENSP00000257408:L396F	L	+	3	2	KLB	39112587	1.000000	0.71417	0.945000	0.38365	0.055000	0.15305	1.488000	0.35551	-0.025000	0.13918	-0.250000	0.11733	TTA	.	.	none		0.418	KLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250429.1	NM_175737		C	39436192	A	C	39436192	3	2	27	1	0	0	0	0	1	0	0	0	8341	359	13	5	1194	5	KLB	4	39436192	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	18942777	39436192	151718084	231	10682											
CHRNA9	55584	hgsc.bcm.edu	37	chr4	40339250	40339250	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaagaaaccaaattctgacTgcttatttgtggatccgcca	13	11	8	9	1	1	2	0	1	1	1	2	4	2	3	3	1	2	1	3	1	4	3	rs55998310	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:40339250T>C	ENST00000310169.2	+	3	373	c.234T>C	c.(232-234)acT>acC	p.T78T		NM_017581.3	NP_060051.2	Q9UGM1	ACHA9_HUMAN	cholinergic receptor, nicotinic, alpha 9 (neuronal)	78					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)	AAATTCTGACTGCTTATTTGT	0.468													T|||	20	0.00399361	0.0008	0.0014	5008	,	,		20941	0.0		0.0149	False		,,,				2504	0.0031				p.T78T	Esophageal Squamous(115;1297 1602 22235 25158 43327)	Atlas-SNP	.											.	CHRNA9	53	.	0			c.T234C						PASS	.	T		3,4403	6.2+/-15.9	0,3,2200	103	80	88		234	-11.7	0	4	dbSNP_129	88	93,8507	51.9+/-112.3	0,93,4207	no	coding-synonymous	CHRNA9	NM_017581.2		0,96,6407	CC,CT,TT		1.0814,0.0681,0.7381		78/480	40339250	96,12910	2203	4300	6503	SO:0001819	synonymous_variant	55584	exon3			TCTGACTGCTTAT	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.234T>C	4.37:g.40339250T>C		137	0	0		156	70	0.448718	NM_017581	Q14CY7|Q4W5A2|Q9NYV2	Silent	SNP	ENST00000310169.2	37	CCDS3459.1																																																																																			T|0.993;C|0.007	0.007	strong		0.468	CHRNA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216822.1			C	40339250	T	C	40339250	2	2	27	1	0	0	0	0	0	0	0	1	3391	1567	55	3		3	CHRNA9	4	40339250	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	903058	40339250	150815026	232	10683											
SPATA18	132671	hgsc.bcm.edu	37	chr4	52946016	52946016	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gatatgttgcattgcctttgCaatgcaggccttagaaccac	10	12	9	10	0	0	1	0	0	0	1	0	2	0	1	3	1	5	4	3	1	4	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:52946016C>A	ENST00000295213.4	+	9	1660	c.1286C>A	c.(1285-1287)gCa>gAa	p.A429E	SPATA18_ENST00000419395.2_Missense_Mutation_p.A397E	NM_145263.2	NP_660306.1	Q8TC71	MIEAP_HUMAN	spermatogenesis associated 18	429					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)			ATTGCCTTTGCAATGCAGGCC	0.443																																					p.A429E		Atlas-SNP	.											.	SPATA18	222	.	0			c.C1286A						PASS	.						250	234	240					4																	52946016		2203	4300	6503	SO:0001583	missense	132671	exon9			CCTTTGCAATGCA	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.1286C>A	4.37:g.52946016C>A	ENSP00000295213:p.Ala429Glu	227	0	0		191	45	0.235602	NM_145263	B4E2R0|E5RLK1|Q8IY48|Q8N7D7	Missense_Mutation	SNP	ENST00000295213.4	37	CCDS3489.1	.	.	.	.	.	.	.	.	.	.	C	16.34	3.096593	0.56075	.	.	ENSG00000163071	ENST00000295213;ENST00000419395	T;T	0.32023	1.47;1.48	5.35	5.35	0.76521	.	0.051108	0.85682	D	0.000000	T	0.46367	0.1389	L	0.39633	1.23	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.87578	0.964;0.964;0.998	T	0.09618	-1.0666	10	0.27785	T	0.31	-16.3661	16.606	0.84830	0.0:1.0:0.0:0.0	.	397;429;429	Q8TC71-2;Q8TC71;Q96M13	.;MIEAP_HUMAN;.	E	429;397	ENSP00000295213:A429E;ENSP00000415309:A397E	ENSP00000295213:A429E	A	+	2	0	SPATA18	52640773	1.000000	0.71417	0.974000	0.42286	0.600000	0.36913	5.025000	0.64097	2.789000	0.95967	0.655000	0.94253	GCA	.	.	none		0.443	SPATA18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250597.2	NM_145263		A	52946016	C	A	52946016	3	1	27	1	0	0	0	0	1	0	0	0	15018	710	25	4	1320	4	SPATA18	4	52946016	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	12606766	52946016	138208260	233	10684											
SCFD2	152579	hgsc.bcm.edu	37	chr4	54218834	54218834	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagtatggagtgcagtgagcGctatcatgttaaccatcaca	12	10	10	9	1	2	1	2	1	0	0	2	2	2	2	1	1	3	4	1	1	3	3	rs147606542	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:54218834G>A	ENST00000401642.3	-	2	1071	c.938C>T	c.(937-939)gCg>gTg	p.A313V	SCFD2_ENST00000388940.4_Missense_Mutation_p.A313V	NM_152540.3	NP_689753.2	Q8WU76	SCFD2_HUMAN	sec1 family domain containing 2	313					protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)			p.A313V(1)		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)			TGCAGTGAGCGCTATCATGTT	0.428													G|||	64	0.0127796	0.0008	0.0	5008	,	,		19473	0.0		0.001	False		,,,				2504	0.0634				p.A313V		Atlas-SNP	.											SCFD2,NS,NS,0,1	SCFD2	78	1	1	Substitution - Missense(1)	pancreas(1)	c.C938T						scavenged	.	G	VAL/ALA	2,4404	4.2+/-10.8	0,2,2201	182	157	166		938	4.2	0.9	4	dbSNP_134	166	21,8579	16.0+/-53.3	0,21,4279	yes	missense	SCFD2	NM_152540.3	64	0,23,6480	AA,AG,GG		0.2442,0.0454,0.1768	benign	313/685	54218834	23,12983	2203	4300	6503	SO:0001583	missense	152579	exon2			GTGAGCGCTATCA	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.938C>T	4.37:g.54218834G>A	ENSP00000384182:p.Ala313Val	207	1	0.00483092		196	90	0.459184	NM_152540	Q8N5F3|Q8N8H0|Q96ED3	Missense_Mutation	SNP	ENST00000401642.3	37	CCDS33984.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	9.740	1.164726	0.21538	4.54E-4	0.002442	ENSG00000184178	ENST00000401642;ENST00000388940;ENST00000503450	D;D	0.85629	-2.01;-2.01	5.33	4.15	0.48705	.	0.060828	0.64402	D	0.000005	T	0.70081	0.3183	N	0.08118	0	0.21553	N	0.999646	B;B	0.13594	0.008;0.005	B;B	0.12837	0.008;0.003	T	0.56890	-0.7904	10	0.30078	T	0.28	.	11.6001	0.50997	0.0:0.0:0.1497:0.8503	.	313;313	Q8WU76-2;Q8WU76	.;SCFD2_HUMAN	V	313;313;6	ENSP00000384182:A313V;ENSP00000373592:A313V	ENSP00000373592:A313V	A	-	2	0	SCFD2	53913591	0.999000	0.42202	0.921000	0.36526	0.006000	0.05464	3.548000	0.53670	0.849000	0.35215	-0.357000	0.07601	GCG	G|0.998;A|0.002	0.002	strong		0.428	SCFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361311.3	NM_152540		A	54218834	G	A	54218834	3	1	27	1	0	0	0	0	1	0	0	0	13905	1087	38	1	1148	1	SCFD2	4	54218834	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1272818	54218834	136935442	234	10685											
KDR	3791	hgsc.bcm.edu	37	chr4	55972946	55972946	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacacttctccattcttcacAagggtatgggtttgtcactg	8	14	8	11	0	4	0	2	0	2	0	5	0	4	0	1	2	0	2	1	2	2	5	rs34231037	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:55972946A>G	ENST00000263923.4	-	11	1739	c.1444T>C	c.(1444-1446)Tgt>Cgt	p.C482R		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	482	Ig-like C2-type 5.		C -> R (in HCI susceptibility; expression of FLT1 in hemangioma endothelial cells is markedly reduced and KDR activity is increased compared to controls; low FLT1 expression in hemangioma cells is caused by reduced activity of a pathway involving ITGB1, ANTXR1, KDR and NFATC2IP; the mutation predicts to result in loss-of-function and disruption of the normal association of these molecules; dbSNP:rs34231037). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:18931684}.		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)	CATTCTTCACAAGGGTATGGG	0.333			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)			A|||	45	0.00898562	0.0015	0.0144	5008	,	,		18156	0.0		0.0308	False		,,,				2504	0.002				p.C482R		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	KDR,middle_lobe,carcinoma,+2,1	KDR	307	1	0			c.T1444C						PASS	.	A	ARG/CYS	23,4383	31.7+/-61.6	0,23,2180	81	85	83	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1444	5.7	0.9	4	dbSNP_126	83	242,8358	97.2+/-158.9	4,234,4062	yes	missense	KDR	NM_002253.2	180	4,257,6242	GG,GA,AA		2.814,0.522,2.0375	probably-damaging	482/1357	55972946	265,12741	2203	4300	6503	SO:0001583	missense	3791	exon11			CTTCACAAGGGTA	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.1444T>C	4.37:g.55972946A>G	ENSP00000263923:p.Cys482Arg	187	0	0		176	89	0.505682	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	37	CCDS3497.1	30	0.013736263736263736	0	0.0	6	0.016574585635359115	0	0.0	24	0.0316622691292876	A	13.84	2.356951	0.41801	0.00522	0.02814	ENSG00000128052	ENST00000263923	T	0.76839	-1.05	5.67	5.67	0.87782	Immunoglobulin subtype (1);Immunoglobulin-like (1);	0.000000	0.85682	D	0.000000	T	0.75436	0.3849	M	0.81497	2.545	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.82382	-0.0485	10	0.40728	T	0.16	.	15.905	0.79419	1.0:0.0:0.0:0.0	rs34231037	482;482	P35968-2;P35968	.;VGFR2_HUMAN	R	482	ENSP00000263923:C482R	ENSP00000263923:C482R	C	-	1	0	KDR	55667703	1.000000	0.71417	0.927000	0.36925	0.088000	0.18126	6.349000	0.73013	2.150000	0.67090	0.533000	0.62120	TGT	A|0.980;G|0.020	0.020	strong		0.333	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			G	55972946	A	G	55972946	3	3	27	1	0	0	0	0	1	0	0	0	8148	130	5	3	2706	3	KDR	4	55972946	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	1754112	55972946	135181330	235	10686											
KDR	3791	hgsc.bcm.edu	37	chr4	55972974	55972974	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggtttgtcactgagacagcTtggctataagaaagagataa	14	10	12	5	0	1	3	1	1	0	3	1	5	1	3	0	2	1	3	0	2	4	5	rs1870377	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:55972974T>A	ENST00000263923.4	-	11	1711	c.1416A>T	c.(1414-1416)caA>caT	p.Q472H		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	472	Ig-like C2-type 5.		Q -> H (in dbSNP:rs1870377). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17344846}.		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)	p.Q472H(1)		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)	CTGAGACAGCTTGGCTATAAG	0.343			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)			T|||	1061	0.211861	0.09	0.1311	5008	,	,		17888	0.4653		0.2346	False		,,,				2504	0.1493				p.Q472H		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	KDR,NS,carcinoma,0,1	KDR	307	1	1	Substitution - Missense(1)	stomach(1)	c.A1416T	GRCh37	CM074306	KDR	M	rs1870377	PASS	.	T	HIS/GLN	485,3921	221.0+/-238.3	28,429,1746	79	82	81		1416	-1.8	0	4	dbSNP_92	81	2037,6563	353.6+/-329.2	246,1545,2509	yes	missense	KDR	NM_002253.2	24	274,1974,4255	AA,AT,TT		23.686,11.0077,19.3911	benign	472/1357	55972974	2522,10484	2203	4300	6503	SO:0001583	missense	3791	exon11			GACAGCTTGGCTA	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.1416A>T	4.37:g.55972974T>A	ENSP00000263923:p.Gln472His	164	0	0		139	66	0.47482	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	37	CCDS3497.1	513	0.2348901098901099	41	0.08333333333333333	52	0.143646408839779	248	0.43356643356643354	172	0.22691292875989447	T	4.227	0.041015	0.08196	0.110077	0.23686	ENSG00000128052	ENST00000263923	T	0.76448	-1.02	5.67	-1.82	0.07857	Immunoglobulin subtype (1);Immunoglobulin-like (1);	0.974058	0.08489	N	0.938324	T	0.00012	0.0000	L	0.49350	1.555	0.80722	P	0.0	P;B	0.52692	0.955;0.003	P;B	0.56514	0.8;0.011	T	0.14699	-1.0463	9	0.25106	T	0.35	.	5.5298	0.16978	0.0:0.2646:0.2451:0.4903	rs1870377;rs52810770;rs1870377	472;472	P35968-2;P35968	.;VGFR2_HUMAN	H	472	ENSP00000263923:Q472H	ENSP00000263923:Q472H	Q	-	3	2	KDR	55667731	0.011000	0.17503	0.005000	0.12908	0.006000	0.05464	-0.046000	0.11983	-0.160000	0.11002	-0.290000	0.09829	CAA	T|0.781;A|0.219	0.219	strong		0.343	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			A	55972974	T	A	55972974	3	1	27	1	0	0	0	0	1	0	0	0	8148	1606	56	5	2734	5	KDR	4	55972974	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	28	55972974	135181302	236	10687											
SRP72	6731	hgsc.bcm.edu	37	chr4	57367891	57367891	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcccacccacctccccaaGacctggcagtgctgcaacag	10	4	8	19	0	0	1	0	0	0	1	1	1	1	1	6	1	4	3	6	1	2	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:57367891G>T	ENST00000342756.5	+	19	2601	c.1880G>T	c.(1879-1881)aGa>aTa	p.R627I	SRP72_ENST00000510663.1_Missense_Mutation_p.R566I	NM_006947.3	NP_008878.3	O76094	SRP72_HUMAN	signal recognition particle 72kDa	627					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)					ACCTCCCCAAGACCTGGCAGT	0.458																																					p.R627I		Atlas-SNP	.											.	SRP72	59	.	0			c.G1880T						PASS	.						57	55	56					4																	57367891		2203	4300	6503	SO:0001583	missense	6731	exon19			CCCCAAGACCTGG	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.1880G>T	4.37:g.57367891G>T	ENSP00000342181:p.Arg627Ile	243	0	0		198	43	0.217172	NM_006947	G5E9Z8|Q7Z3C0	Missense_Mutation	SNP	ENST00000342756.5	37	CCDS3506.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.6|23.6	4.441168|4.441168	0.83993|0.83993	.|.	.|.	ENSG00000174780|ENSG00000174780	ENST00000537129|ENST00000342756;ENST00000510663	.|T;T	.|0.78481	.|-1.13;-1.18	5.8|5.8	5.8|5.8	0.92144|0.92144	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.87273|0.87273	0.6136|0.6136	M|M	0.69823|0.69823	2.125|2.125	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;0.998	.|D;P	.|0.76575	.|0.988;0.896	D|D	0.85985|0.85985	0.1485|0.1485	6|10	0.56958|0.41790	D|T	0.05|0.15	.|.	17.5488|17.5488	0.87870|0.87870	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|566;627	.|G5E9Z8;O76094	.|.;SRP72_HUMAN	Y|I	571|627;566	.|ENSP00000342181:R627I;ENSP00000424576:R566I	ENSP00000445887:D571Y|ENSP00000342181:R627I	D|R	+|+	1|2	0|0	SRP72|SRP72	57062648|57062648	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	6.292000|6.292000	0.72725|0.72725	2.743000|2.743000	0.94032|0.94032	0.455000|0.455000	0.32223|0.32223	GAC|AGA	.	.	none		0.458	SRP72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250782.7			T	57367891	G	T	57367891	3	4	27	1	0	0	0	0	1	0	0	0	15172	942	33	4	1954	4	SRP72	4	57367891	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1394917	57367891	133786385	237	10688											
TMPRSS11F	389208	hgsc.bcm.edu	37	chr4	68930465	68930465	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttttaggtggcaactttataGatgagtctgggaggcaaact	11	13	12	5	0	1	2	0	1	1	1	1	3	1	3	0	4	2	2	0	4	5	5	rs143544573	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:68930465G>A	ENST00000356291.2	-	8	1012	c.953C>T	c.(952-954)tCt>tTt	p.S318F	RP11-35D5.1_ENST00000600441.1_RNA|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	318	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)	p.S318F(1)		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						CAACTTTATAGATGAGTCTGG	0.388													G|||	13	0.00259585	0.0	0.0029	5008	,	,		16858	0.0		0.0109	False		,,,				2504	0.0				p.S318F		Atlas-SNP	.											TMPRSS11F,NS,carcinoma,0,1	TMPRSS11F	79	1	1	Substitution - Missense(1)	prostate(1)	c.C953T						PASS	.	G	PHE/SER	6,4400	12.9+/-30.5	0,6,2197	68	68	68		953	4	1	4	dbSNP_134	68	101,8499	55.6+/-116.7	1,99,4200	yes	missense	TMPRSS11F	NM_207407.2	155	1,105,6397	AA,AG,GG		1.1744,0.1362,0.8227	possibly-damaging	318/439	68930465	107,12899	2203	4300	6503	SO:0001583	missense	389208	exon8			TTTATAGATGAGT	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.953C>T	4.37:g.68930465G>A	ENSP00000348639:p.Ser318Phe	102	0	0		87	51	0.586207	NM_207407	A8MXX2	Missense_Mutation	SNP	ENST00000356291.2	37	CCDS3520.1	11	0.005036630036630037	0	0.0	1	0.0027624309392265192	0	0.0	10	0.013192612137203167	G	14.79	2.641763	0.47153	0.001362	0.011744	ENSG00000198092	ENST00000356291	D	0.89681	-2.55	5.92	4.0	0.46444	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.207319	0.34652	N	0.003800	T	0.78457	0.4286	L	0.28192	0.835	0.42271	D	0.992056	P	0.49090	0.919	B	0.43082	0.407	T	0.83214	-0.0072	10	0.72032	D	0.01	.	12.357	0.55182	0.0:0.0:0.6819:0.3181	.	318	Q6ZWK6	TM11F_HUMAN	F	318	ENSP00000348639:S318F	ENSP00000348639:S318F	S	-	2	0	TMPRSS11F	68613060	0.983000	0.35010	1.000000	0.80357	0.595000	0.36748	1.369000	0.34227	1.488000	0.48433	0.650000	0.86243	TCT	G|0.994;A|0.006	0.006	strong		0.388	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407		A	68930465	G	A	68930465	3	1	27	1	0	0	0	0	1	0	0	0	16258	942	33	2	375	2	TMPRSS11F	4	68930465	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	11562574	68930465	122223811	238	10689											
AMBN	258	hgsc.bcm.edu	37	chr4	71469006	71469006	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atagcccgtttgatttctcaCggaccaatgccacaaaataa	14	10	6	11	2	1	1	1	1	1	0	2	2	1	2	3	1	2	1	3	1	5	4	rs113360877	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:71469006C>T	ENST00000322937.6	+	10	781	c.678C>T	c.(676-678)caC>caT	p.H226H	AMBN_ENST00000449493.2_Silent_p.H211H	NM_016519.5	NP_057603.1	Q9NP70	AMBN_HUMAN	ameloblastin (enamel matrix protein)	226					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)			TGATTTCTCACGGACCAATGC	0.318													C|||	29	0.00579073	0.0008	0.0086	5008	,	,		14320	0.001		0.0179	False		,,,				2504	0.0031				p.H226H		Atlas-SNP	.											.	AMBN	73	.	0			c.C678T						PASS	.	C		14,4390	21.2+/-45.6	0,14,2188	77	74	75		678	1.8	1	4	dbSNP_132	75	186,8406	84.2+/-146.7	1,184,4111	no	coding-synonymous	AMBN	NM_016519.5		1,198,6299	TT,TC,CC		2.1648,0.3179,1.5389		226/448	71469006	200,12796	2202	4296	6498	SO:0001819	synonymous_variant	258	exon10			TTCTCACGGACCA	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.678C>T	4.37:g.71469006C>T		186	0	0		149	65	0.436242	NM_016519	Q3B862|Q9H2X1|Q9H4L1	Silent	SNP	ENST00000322937.6	37	CCDS3543.1																																																																																			C|0.987;T|0.013	0.013	strong		0.318	AMBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252165.1	NM_016519		T	71469006	C	T	71469006	2	4	27	1	0	0	0	0	0	0	0	1	563	535	19	1		1	AMBN	4	71469006	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2538541	71469006	119685270	239	10690											
SLC4A4	8671	hgsc.bcm.edu	37	chr4	72363294	72363294	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cggaggaaacctcgtcgggaAcaactgtaattttgttcctg	10	11	11	9	3	0	0	0	0	0	0	3	3	1	3	2	3	3	2	2	3	4	4	rs35891845	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:72363294A>T	ENST00000264485.5	+	16	2168	c.2051A>T	c.(2050-2052)aAc>aTc	p.N684I	SLC4A4_ENST00000351898.6_Missense_Mutation_p.N684I|SLC4A4_ENST00000340595.3_Missense_Mutation_p.N640I|SLC4A4_ENST00000425175.1_Missense_Mutation_p.N684I	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	684					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)	CTCGTCGGGAACAACTGTAAT	0.378													A|||	2	0.000399361	0.0	0.0	5008	,	,		18419	0.0		0.002	False		,,,				2504	0.0				p.N684I		Atlas-SNP	.											.	SLC4A4	269	.	0			c.A2051T						PASS	.	A	ILE/ASN,ILE/ASN,ILE/ASN	1,4405	2.1+/-5.4	0,1,2202	115	117	116		2051,2051,1919	3	1	4	dbSNP_126	116	24,8576	17.9+/-57.8	0,24,4276	yes	missense,missense,missense	SLC4A4	NM_001098484.2,NM_001134742.1,NM_003759.3	149,149,149	0,25,6478	TT,TA,AA		0.2791,0.0227,0.1922	benign,benign,benign	684/1080,684/1095,640/1036	72363294	25,12981	2203	4300	6503	SO:0001583	missense	8671	exon16			TCGGGAACAACTG	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.2051A>T	4.37:g.72363294A>T	ENSP00000264485:p.Asn684Ile	126	0	0		140	66	0.471429	NM_001098484	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	ENST00000264485.5	37	CCDS43236.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	12.64	1.999658	0.35320	2.27E-4	0.002791	ENSG00000080493	ENST00000264485;ENST00000425175;ENST00000351898;ENST00000340595	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.44	3.02	0.34903	Bicarbonate transporter, C-terminal (1);	0.219123	0.53938	D	0.000044	T	0.73544	0.3600	N	0.14661	0.345	0.48087	D	0.999585	P;D;B;B	0.69078	0.592;0.997;0.313;0.136	P;D;B;B	0.64042	0.477;0.921;0.346;0.353	T	0.72364	-0.4316	10	0.41790	T	0.15	.	9.4956	0.38986	0.8562:0.0:0.1438:0.0	rs35891845	684;684;640;684	A5JJ20;Q9Y6R1-4;Q9Y6R1-2;Q9Y6R1	.;.;.;S4A4_HUMAN	I	684;684;684;640	ENSP00000264485:N684I;ENSP00000393557:N684I;ENSP00000307349:N684I;ENSP00000344272:N640I	ENSP00000264485:N684I	N	+	2	0	SLC4A4	72582158	1.000000	0.71417	1.000000	0.80357	0.241000	0.25554	3.803000	0.55560	1.002000	0.39104	0.533000	0.62120	AAC	A|0.998;T|0.002	0.002	strong		0.378	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759		T	72363294	A	T	72363294	3	4	27	1	0	0	0	0	1	0	0	0	14671	43	2	5	2230	5	SLC4A4	4	72363294	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	894288	72363294	118790982	240	10691											
ALB	213	hgsc.bcm.edu	37	chr4	74285263	74285263	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaacacaagcccaaggcaacAaaagagcaactgaaagctgt	20	3	8	10	0	0	2	0	1	0	1	0	2	0	2	1	1	6	3	1	1	8	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:74285263A>G	ENST00000503124.1	+	11	1449	c.1242A>G	c.(1240-1242)acA>acG	p.T414T	ALB_ENST00000401494.3_Silent_p.T449T|ALB_ENST00000509063.1_Silent_p.T564T|ALB_ENST00000295897.4_Silent_p.T564T|ALB_ENST00000505649.1_3'UTR|ALB_ENST00000415165.2_Silent_p.T372T			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)			CCAAGGCAACAAAAGAGCAAC	0.408																																					p.T564T		Atlas-SNP	.											.	ALB	132	.	0			c.A1692G						PASS	.						93	89	90					4																	74285263		2203	4300	6503	SO:0001819	synonymous_variant	213	exon13			GGCAACAAAAGAG	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.1242A>G	4.37:g.74285263A>G		91	0	0		101	22	0.217822	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000503124.1	37		.	.	.	.	.	.	.	.	.	.	A	10.22	1.290736	0.23564	.	.	ENSG00000163631	ENST00000511370	.	.	.	6.06	-2.4	0.06583	.	.	.	.	.	T	0.21801	0.0525	.	.	.	0.25935	N	0.982943	.	.	.	.	.	.	T	0.31724	-0.9933	4	.	.	.	-29.7385	4.5011	0.11865	0.4432:0.0:0.2016:0.3552	.	.	.	.	E	409	.	.	K	+	1	0	ALB	74504127	0.001000	0.12720	0.046000	0.18839	0.538000	0.34931	-0.230000	0.09083	-0.111000	0.12001	0.533000	0.62120	AAA	.	.	none		0.408	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		G	74285263	A	G	74285263	2	3	27	1	0	0	0	0	0	0	0	1	486	117	5	3		3	ALB	4	74285263	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	1921969	74285263	116869013	241	10692											
RASSF6	166824	hgsc.bcm.edu	37	chr4	74459206	74459206	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctgatgacttcatactagtAaaagaagagaatggcttctc	14	12	8	7	0	3	4	1	2	2	2	4	5	3	4	0	1	1	2	0	1	6	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:74459206A>C	ENST00000342081.3	-	4	475	c.345T>G	c.(343-345)ttT>ttG	p.F115L	RASSF6_ENST00000395777.2_Missense_Mutation_p.F83L|RASSF6_ENST00000335049.5_Missense_Mutation_p.F71L|RASSF6_ENST00000307439.5_Missense_Mutation_p.F83L	NM_201431.2	NP_958834.1	Q6ZTQ3	RASF6_HUMAN	Ras association (RalGDS/AF-6) domain family member 6	115					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)			TCATACTAGTAAAAGAAGAGA	0.363																																					p.F115L		Atlas-SNP	.											.	RASSF6	68	.	0			c.T345G						PASS	.						115	115	115					4																	74459206		2203	4300	6503	SO:0001583	missense	166824	exon4			ACTAGTAAAAGAA	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.345T>G	4.37:g.74459206A>C	ENSP00000340578:p.Phe115Leu	117	0	0		101	20	0.19802	NM_201431	Q68DT2|Q6PDA6|Q86WG9|Q86WH0	Missense_Mutation	SNP	ENST00000342081.3	37	CCDS3558.1	.	.	.	.	.	.	.	.	.	.	A	6.548	0.469333	0.12461	.	.	ENSG00000169435	ENST00000307439;ENST00000342081;ENST00000395777;ENST00000335049	T;T;T;T	0.37235	1.21;1.21;1.21;1.21	4.87	-1.98	0.07480	.	0.620622	0.17776	N	0.162414	T	0.20700	0.0498	L	0.34521	1.04	0.09310	N	0.999999	B;B;B	0.16166	0.013;0.013;0.016	B;B;B	0.19148	0.024;0.014;0.015	T	0.33624	-0.9861	10	0.10636	T	0.68	-3.5922	9.1491	0.36951	0.4954:0.0:0.5046:0.0	.	71;83;115	Q6ZTQ3-3;Q6ZTQ3-4;Q6ZTQ3	.;.;RASF6_HUMAN	L	83;115;83;71	ENSP00000303877:F83L;ENSP00000340578:F115L;ENSP00000379123:F83L;ENSP00000335582:F71L	ENSP00000303877:F83L	F	-	3	2	RASSF6	74678070	0.159000	0.22864	0.029000	0.17559	0.029000	0.11900	-0.191000	0.09601	-0.624000	0.05611	0.443000	0.29094	TTT	.	.	none		0.363	RASSF6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252279.1	NM_177532		C	74459206	A	C	74459206	3	2	27	1	0	0	0	0	1	0	0	0	13105	359	13	5	796	5	RASSF6	4	74459206	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	173943	74459206	116695070	242	10693											
CCDC158	339965	hgsc.bcm.edu	37	chr4	77272155	77272155	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gactggttacttacatgagaCaggaagctggctgtagactg	11	10	13	7	0	0	2	0	1	0	2	0	5	0	3	0	3	3	4	0	3	4	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:77272155C>A	ENST00000388914.3	-	17	2810	c.2658G>T	c.(2656-2658)ctG>ctT	p.L886L		NM_001042784.1	NP_001036249.1	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	886										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						TTACATGAGACAGGAAGCTGG	0.368																																					p.L886L		Atlas-SNP	.											.	CCDC158	114	.	0			c.G2658T						PASS	.						150	147	148					4																	77272155		1960	4149	6109	SO:0001819	synonymous_variant	339965	exon17			ATGAGACAGGAAG	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.2658G>T	4.37:g.77272155C>A		81	0	0		89	18	0.202247	NM_001042784	Q8IYQ1|Q8N7D4|Q8N7E3	Silent	SNP	ENST00000388914.3	37	CCDS43242.1																																																																																			.	.	none		0.368	CCDC158-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362694.2	NM_001042784		A	77272155	C	A	77272155	2	1	27	1	0	0	0	0	0	0	0	1	2792	465	17	4		4	CCDC158	4	77272155	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2812949	77272155	113882121	243	10694											
SHROOM3	57619	hgsc.bcm.edu	37	chr4	77661017	77661017	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatttctgttcagtgcctgAaaatgaggaggatgcctccc	9	11	10	11	0	2	2	1	2	1	0	3	4	3	4	4	2	2	1	4	2	2	2	rs76656494	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:77661017A>C	ENST00000296043.6	+	5	2644	c.1691A>C	c.(1690-1692)gAa>gCa	p.E564A		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	564					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)			TCAGTGCCTGAAAATGAGGAG	0.502													A|||	33	0.00658946	0.0	0.013	5008	,	,		21550	0.0		0.0229	False		,,,				2504	0.001				p.E564A		Atlas-SNP	.											.	SHROOM3	134	.	0			c.A1691C						PASS	.	A	ALA/GLU	14,4392	22.3+/-47.3	0,14,2189	168	168	168		1691	4.4	1	4	dbSNP_131	168	145,8455	70.7+/-133.2	2,141,4157	yes	missense	SHROOM3	NM_020859.3	107	2,155,6346	CC,CA,AA		1.686,0.3177,1.2225	probably-damaging	564/1997	77661017	159,12847	2203	4300	6503	SO:0001583	missense	57619	exon5			TGCCTGAAAATGA	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.1691A>C	4.37:g.77661017A>C	ENSP00000296043:p.Glu564Ala	79	0	0		50	26	0.52	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Missense_Mutation	SNP	ENST00000296043.6	37	CCDS3579.2	23	0.010531135531135532	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	17	0.022427440633245383	A	15.10	2.733513	0.48939	0.003177	0.01686	ENSG00000138771	ENST00000296043	T	0.26660	1.72	5.59	4.39	0.52855	.	0.093877	0.44902	D	0.000410	T	0.31009	0.0783	M	0.71581	2.175	0.35431	D	0.794093	D;P;P	0.76494	0.999;0.89;0.8	D;B;B	0.65987	0.94;0.382;0.153	T	0.57688	-0.7768	10	0.72032	D	0.01	-7.8779	12.7677	0.57401	0.8629:0.1371:0.0:0.0	.	388;564;342	B4E244;Q8TF72;B3KY47	.;SHRM3_HUMAN;.	A	564	ENSP00000296043:E564A	ENSP00000296043:E564A	E	+	2	0	SHROOM3	77880041	1.000000	0.71417	1.000000	0.80357	0.414000	0.31173	1.907000	0.39897	0.925000	0.37094	0.460000	0.39030	GAA	A|0.988;C|0.012	0.012	strong		0.502	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859		C	77661017	A	C	77661017	3	2	27	1	0	0	0	0	1	0	0	0	14310	246	9	5	1709	5	SHROOM3	4	77661017	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	388862	77661017	113493259	244	10695											
FRAS1	80144	hgsc.bcm.edu	37	chr4	79353587	79353587	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttcctctacccgggaagaCagcatggagatctcagtcac	10	8	11	12	1	3	2	2	0	2	2	5	4	4	3	2	3	2	2	2	3	2	2	rs35219594	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:79353587C>G	ENST00000325942.6	+	38	5486	c.5046C>G	c.(5044-5046)gaC>gaG	p.D1682E	FRAS1_ENST00000264895.6_Missense_Mutation_p.D1682E	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	1682					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						CCCGGGAAGACAGCATGGAGA	0.483													C|||	10	0.00199681	0.0008	0.0086	5008	,	,		21025	0.0		0.003	False		,,,				2504	0.0				p.D1682E		Atlas-SNP	.											FRAS1_ENST00000325942,NS,carcinoma,+2,3	FRAS1	779	3	0			c.C5046G						PASS	.	C	GLU/ASP,GLU/ASP	5,3945		0,5,1970	64	65	65		5046,5046	4.5	1	4	dbSNP_126	65	38,8276		0,38,4119	yes	missense,missense	FRAS1	NM_001166133.1,NM_025074.6	45,45	0,43,6089	GG,GC,CC		0.4571,0.1266,0.3506	probably-damaging,probably-damaging	1682/1977,1682/4013	79353587	43,12221	1975	4157	6132	SO:0001583	missense	80144	exon38			GGAAGACAGCATG	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.5046C>G	4.37:g.79353587C>G	ENSP00000326330:p.Asp1682Glu	174	0	0		120	59	0.491667	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	37	CCDS54772.1	3|3	0.0013736263736263737|0.0013736263736263737	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	C|C	13.55|13.55	2.270864|2.270864	0.40194|0.40194	0.001266|0.001266	0.004571|0.004571	ENSG00000138759|ENSG00000138759	ENST00000325942;ENST00000264895;ENST00000545316|ENST00000510944	T;T|.	0.50001|.	0.76;0.76|.	6.17|6.17	4.47|4.47	0.54385|0.54385	.|.	0.048301|.	0.85682|.	D|.	0.000000|.	T|T	0.64450|0.64450	0.2599|0.2599	M|M	0.67517|0.67517	2.055|2.055	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.87578|.	0.982;0.998|.	T|T	0.62167|0.62167	-0.6911|-0.6911	10|5	0.52906|.	T|.	0.07|.	.|.	9.988|9.988	0.41854|0.41854	0.0:0.7975:0.0:0.2025|0.0:0.7975:0.0:0.2025	rs35219594|rs35219594	1682;1682|.	E9PHH6;A2RRR8|.	.;.|.	E|E	1682;1682;102|132	ENSP00000326330:D1682E;ENSP00000264895:D1682E|.	ENSP00000264895:D1682E|.	D|Q	+|+	3|1	2|0	FRAS1|FRAS1	79572611|79572611	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.004000|0.004000	0.04260|0.04260	2.301000|2.301000	0.43628|0.43628	0.954000|0.954000	0.37851|0.37851	-0.136000|-0.136000	0.14681|0.14681	GAC|CAG	C|0.998;G|0.002	0.002	strong		0.483	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2			G	79353587	C	G	79353587	3	3	27	1	0	0	0	0	1	0	0	0	6050	477	17	4	5196	4	FRAS1	4	79353587	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1692570	79353587	111800689	245	10696											
BMP2K	55589	hgsc.bcm.edu	37	chr4	79832870	79832870	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgatgggaaagatagggggAatgtcttacaacctgaggag	13	8	15	5	0	1	3	0	2	1	1	1	6	1	6	1	4	2	0	1	4	5	2	rs116710382	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:79832870A>T	ENST00000335016.5	+	16	3335	c.3169A>T	c.(3169-3171)Aat>Tat	p.N1057Y	PAQR3_ENST00000295462.3_Intron	NM_198892.1	NP_942595.1	Q9NSY1	BMP2K_HUMAN	BMP2 inducible kinase	1057					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)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(3)|prostate(1)|urinary_tract(1)	13						AGATAGGGGGAATGTCTTACA	0.522													A|||	19	0.00379393	0.0	0.0101	5008	,	,		20274	0.0		0.0119	False		,,,				2504	0.0				p.N1057Y		Atlas-SNP	.											.	BMP2K	169	.	0			c.A3169T						PASS	.	A	TYR/ASN	5,3897		0,5,1946	101	101	101		3169	1.3	0	4	dbSNP_132	101	61,8203		0,61,4071	yes	missense	BMP2K	NM_198892.1	143	0,66,6017	TT,TA,AA		0.7381,0.1281,0.5425	benign	1057/1162	79832870	66,12100	1951	4132	6083	SO:0001583	missense	55589	exon16			AGGGGGAATGTCT	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.3169A>T	4.37:g.79832870A>T	ENSP00000334836:p.Asn1057Tyr	151	0	0		135	70	0.518519	NM_198892	O94791|Q4W5H2|Q8IYF2|Q8N2G7|Q8NHG9|Q9NTG8	Missense_Mutation	SNP	ENST00000335016.5	37	CCDS47083.1	13|13	0.005952380952380952|0.005952380952380952	0|0	0.0|0.0	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	9|9	0.011873350923482849|0.011873350923482849	A|A	3.678|3.678	-0.066194|-0.066194	0.07273|0.07273	0.001281|0.001281	0.007381|0.007381	ENSG00000138756|ENSG00000138756	ENST00000502613|ENST00000335016	.|T	.|0.43688	.|0.94	5.41|5.41	1.3|1.3	0.21679|0.21679	.|.	.|1.089200	.|0.07033	.|N	.|0.828802	T|T	0.24198|0.24198	0.0586|0.0586	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	0.999999|0.999999	.|B	.|0.26400	.|0.148	.|B	.|0.18263	.|0.021	T|T	0.25363|0.25363	-1.0134|-1.0134	5|10	.|0.44086	.|T	.|0.13	-1.0317|-1.0317	13.6768|13.6768	0.62458|0.62458	0.4465:0.5535:0.0:0.0|0.4465:0.5535:0.0:0.0	.|.	.|1057	.|Q9NSY1	.|BMP2K_HUMAN	V|Y	749|1057	.|ENSP00000334836:N1057Y	.|ENSP00000334836:N1057Y	E|N	+|+	2|1	0|0	BMP2K|BMP2K	80051894|80051894	0.407000|0.407000	0.25352|0.25352	0.000000|0.000000	0.03702|0.03702	0.011000|0.011000	0.07611|0.07611	2.601000|2.601000	0.46249|0.46249	0.336000|0.336000	0.23639|0.23639	0.397000|0.397000	0.26171|0.26171	GAA|AAT	A|0.993;T|0.007	0.007	strong		0.522	BMP2K-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_017593		T	79832870	A	T	79832870	3	4	27	1	0	0	0	0	1	0	0	0	1460	246	9	5	3269	5	BMP2K	4	79832870	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	479283	79832870	111321406	246	10697											
HPSE	10855	hgsc.bcm.edu	37	chr4	84222157	84222157	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaggtcttagaaggtatttAtccacttgcttgttagaaaa	14	14	8	5	0	1	2	0	0	1	2	2	2	2	2	1	2	1	3	1	2	8	7	rs145560091	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:84222157A>C	ENST00000405413.2	-	12	1564	c.1428T>G	c.(1426-1428)gaT>gaG	p.D476E	HPSE_ENST00000513463.1_Missense_Mutation_p.D418E|HPSE_ENST00000512196.1_Missense_Mutation_p.D402E|HPSE_ENST00000311412.5_Missense_Mutation_p.D476E	NM_006665.5	NP_006656.2	Q9Y251	HPSE_HUMAN	heparanase	476					carbohydrate metabolic process (GO:0005975)|cell-matrix adhesion (GO:0007160)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|positive regulation of blood coagulation (GO:0030194)|positive regulation of hair follicle development (GO:0051798)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation vascular endothelial growth factor production (GO:0010575)|proteoglycan metabolic process (GO:0006029)|regulation of hair follicle development (GO:0051797)|small molecule metabolic process (GO:0044281)|vascular wound healing (GO:0061042)	extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)	beta-glucuronidase activity (GO:0004566)|heparanase activity (GO:0030305)|protein dimerization activity (GO:0046983)|syndecan binding (GO:0045545)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	20		Hepatocellular(203;0.114)		COAD - Colon adenocarcinoma(81;0.141)	Dalteparin(DB06779)|Heparin(DB01109)	GAAGGTATTTATCCACTTGCT	0.348																																					p.D476E		Atlas-SNP	.											.	HPSE	55	.	0			c.T1428G						PASS	.	A	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	0,4406		0,0,2203	114	117	116		1428,1206,1254,1428	-2.4	1	4	dbSNP_134	116	17,8581	12.6+/-44.7	0,17,4282	yes	missense,missense,missense,missense	HPSE	NM_001098540.2,NM_001166498.2,NM_001199830.1,NM_006665.5	45,45,45,45	0,17,6485	CC,CA,AA		0.1977,0.0,0.1307	benign,benign,benign,benign	476/544,402/470,418/486,476/544	84222157	17,12987	2203	4299	6502	SO:0001583	missense	10855	exon11			GTATTTATCCACT	AF144325	CCDS3602.1, CCDS54774.1, CCDS56337.1	4q21.3	2008-02-05			ENSG00000173083	ENSG00000173083			5164	protein-coding gene	gene with protein product		604724				10395325, 10395326	Standard	NM_006665		Approved	HPA, HSE1, HPSE1	uc003hoj.4	Q9Y251	OTTHUMG00000130425	ENST00000405413.2:c.1428T>G	4.37:g.84222157A>C	ENSP00000384262:p.Asp476Glu	120	0	0		133	56	0.421053	NM_001098540	A9JIG7|C7F7I3|C7F7I4|E9PCA9|E9PGR1|Q53GE5|Q9UL39	Missense_Mutation	SNP	ENST00000405413.2	37	CCDS3602.1	.	.	.	.	.	.	.	.	.	.	A	6.169	0.399451	0.11696	0.0	0.001977	ENSG00000173083	ENST00000311412;ENST00000405413;ENST00000512196;ENST00000513463	T;T;T;T	0.38722	1.12;1.12;1.14;1.13	4.56	-2.36	0.06663	.	0.095855	0.64402	D	0.000001	T	0.20981	0.0505	N	0.05199	-0.095	0.35589	D	0.806951	D;B;B;B	0.58620	0.983;0.059;0.097;0.014	P;B;B;B	0.54460	0.753;0.038;0.084;0.009	T	0.44726	-0.9309	10	0.02654	T	1	-21.5243	5.5816	0.17252	0.5796:0.0:0.2952:0.1252	.	402;418;418;476	E9PCA9;A9JIG7;E9PGR1;Q9Y251	.;.;.;HPSE_HUMAN	E	476;476;402;418	ENSP00000308107:D476E;ENSP00000384262:D476E;ENSP00000423265:D402E;ENSP00000421365:D418E	ENSP00000308107:D476E	D	-	3	2	HPSE	84441181	1.000000	0.71417	0.988000	0.46212	0.172000	0.22775	0.482000	0.22276	-0.153000	0.11137	-0.256000	0.11100	GAT	A|0.999;C|0.001	0.001	strong		0.348	HPSE-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252812.2	NM_006665		C	84222157	A	C	84222157	3	2	27	1	0	0	0	0	1	0	0	0	7353	446	16	5	211	5	HPSE	4	84222157	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	4389287	84222157	106932119	247	10698											
FAM190A	401145	hgsc.bcm.edu	37	chr4	92519814	92519814	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cgaggaccgttttaggtattCggcagcggaccagacaagcc	10	7	13	11	4	0	1	0	0	0	1	1	4	0	3	3	4	2	3	3	4	3	4	rs370719096		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:92519814C>T	ENST00000509176.1	+	11	2597	c.2309C>T	c.(2308-2310)tCg>tTg	p.S770L	CCSER1_ENST00000333691.8_Missense_Mutation_p.S770L	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	770																	TTTAGGTATTCGGCAGCGGAC	0.443																																					p.S770L		Atlas-SNP	.											.	.	.	.	0			c.C2309T						PASS	.						58	51	53					4																	92519814		692	1591	2283	SO:0001583	missense	401145	exon11			GGTATTCGGCAGC		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.2309C>T	4.37:g.92519814C>T	ENSP00000425040:p.Ser770Leu	107	0	0		74	21	0.283784	NM_001145065	Q4W5M0|Q86V57	Missense_Mutation	SNP	ENST00000509176.1	37	CCDS47099.1	.	.	.	.	.	.	.	.	.	.	C	14.08	2.429555	0.43122	.	.	ENSG00000184305	ENST00000509176;ENST00000333691	T;T	0.35973	1.28;1.28	5.77	4.93	0.64822	.	.	.	.	.	T	0.25494	0.0620	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.22417	-1.0217	9	0.72032	D	0.01	-2.0E-4	13.2923	0.60278	0.0:0.9256:0.0:0.0744	.	770	Q9C0I3	F190A_HUMAN	L	770	ENSP00000425040:S770L;ENSP00000329482:S770L	ENSP00000329482:S770L	S	+	2	0	FAM190A	92738837	0.154000	0.22792	0.003000	0.11579	0.009000	0.06853	5.253000	0.65452	1.584000	0.49913	-0.157000	0.13467	TCG	.	.	weak		0.443	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065		T	92519814	C	T	92519814	3	4	27	1	0	0	0	0	1	0	0	0	5526	893	31	1	2375	1	FAM190A	4	92519814	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	8297657	92519814	98634462	248	10699											
PDLIM5	10611	hgsc.bcm.edu	37	chr4	95496940	95496940	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gccttcaccccagcccatgcGaccacctcatcacatgcttc	8	8	5	20	1	3	0	3	0	0	0	4	1	3	0	6	0	3	1	6	0	0	2	rs115743950	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:95496940G>A	ENST00000317968.4	+	5	601	c.465G>A	c.(463-465)gcG>gcA	p.A155A	PDLIM5_ENST00000508216.1_Intron|PDLIM5_ENST00000318007.5_Intron|PDLIM5_ENST00000437932.1_Intron|PDLIM5_ENST00000538141.1_Intron|PDLIM5_ENST00000542407.1_Silent_p.A33A|PDLIM5_ENST00000450793.1_Intron|PDLIM5_ENST00000514743.1_Intron|PDLIM5_ENST00000380180.3_Intron	NM_001256428.1|NM_006457.4	NP_001243357.1|NP_006448	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5	155					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)	p.A155A(1)		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)		CAGCCCATGCGACCACCTCAT	0.552													G|||	20	0.00399361	0.0023	0.0043	5008	,	,		20003	0.0		0.0089	False		,,,				2504	0.0051				p.A155A		Atlas-SNP	.											PDLIM5,NS,carcinoma,+1,2	PDLIM5	76	2	1	Substitution - coding silent(1)	kidney(1)	c.G465A						PASS	.	G	,,,	16,4390	24.3+/-50.5	0,16,2187	295	249	265		,,,465	2.9	1	4	dbSNP_132	265	140,8460	70.0+/-132.6	0,140,4160	no	intron,intron,intron,coding-synonymous	PDLIM5	NM_001011513.2,NM_001011515.1,NM_001011516.1,NM_006457.3	,,,	0,156,6347	AA,AG,GG		1.6279,0.3631,1.1994	,,,	,,,155/597	95496940	156,12850	2203	4300	6503	SO:0001819	synonymous_variant	10611	exon5			CCATGCGACCACC	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.465G>A	4.37:g.95496940G>A		203	0	0		205	115	0.560976	NM_006457	A8K6F9|D6RB78|E9PBF5|O60705|Q56VN4|Q5UW38|Q8WVK0	Silent	SNP	ENST00000317968.4	37	CCDS3641.1																																																																																			G|0.991;A|0.009	0.009	strong		0.552	PDLIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253586.1			A	95496940	G	A	95496940	2	1	27	1	0	0	0	0	0	0	0	1	11692	1045	37	1		1	PDLIM5	4	95496940	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2977126	95496940	95657336	249	10700											
MTTP	4547	hgsc.bcm.edu	37	chr4	100503136	100503136	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	ccactgaagttcttcttgatCggggcaaaggaaaactgcaa	13	9	10	9	1	2	2	0	2	2	0	3	3	2	3	1	3	2	3	1	3	5	3	rs141736123	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:100503136C>G	ENST00000265517.5	+	2	339	c.136C>G	c.(136-138)Cgg>Ggg	p.R46G	MTTP_ENST00000422897.2_Missense_Mutation_p.R46G|MTTP_ENST00000511045.1_Missense_Mutation_p.R73G|MTTP_ENST00000457717.1_Missense_Mutation_p.R46G			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	46	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)	TCTTCTTGATCGGGGCAAAGG	0.468													C|||	63	0.0125799	0.0015	0.0115	5008	,	,		19440	0.0		0.0219	False		,,,				2504	0.0317				p.R46G		Atlas-SNP	.											.	MTTP	127	.	0			c.C136G						PASS	.	C	GLY/ARG	13,4393	20.2+/-43.8	0,13,2190	180	151	161		136	4	1	4	dbSNP_134	161	151,8449	73.2+/-135.9	1,149,4150	yes	missense	MTTP	NM_000253.2	125	1,162,6340	GG,GC,CC		1.7558,0.2951,1.261	benign	46/895	100503136	164,12842	2203	4300	6503	SO:0001583	missense	4547	exon3			CTTGATCGGGGCA		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.136C>G	4.37:g.100503136C>G	ENSP00000265517:p.Arg46Gly	163	0	0		151	70	0.463576	NM_000253	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	19	0.0086996336996337	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	15	0.01978891820580475	C	11.83	1.754473	0.31046	0.002951	0.017558	ENSG00000138823	ENST00000506883;ENST00000511045;ENST00000457717;ENST00000265517;ENST00000422897;ENST00000538053	T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03	5.76	3.98	0.46160	Lipid transport protein, beta-sheet shell (1);Lipid transport protein, N-terminal (3);Vitellinogen, beta-sheet N-terminal (1);	0.458166	0.26052	N	0.026639	T	0.16642	0.0400	L	0.38838	1.175	0.33153	D	0.546014	B;B;B	0.09022	0.001;0.001;0.002	B;B;B	0.15484	0.005;0.001;0.013	T	0.25606	-1.0127	10	0.21014	T	0.42	-12.0949	9.6418	0.39844	0.1303:0.5146:0.3551:0.0	.	73;46;46	E9PBP6;P55157;Q6P5T3	.;MTP_HUMAN;.	G	56;73;46;46;46;46	ENSP00000426755:R56G;ENSP00000427679:R73G;ENSP00000400821:R46G;ENSP00000265517:R46G;ENSP00000407350:R46G	ENSP00000265517:R46G	R	+	1	2	MTTP	100722159	1.000000	0.71417	0.996000	0.52242	0.629000	0.37895	1.216000	0.32443	0.733000	0.32492	0.655000	0.94253	CGG	C|0.989;G|0.010;T|0.000	0.010	strong		0.468	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3			G	100503136	C	G	100503136	3	3	27	1	0	0	0	0	1	0	0	0	9973	875	31	4	142	4	MTTP	4	100503136	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	5006196	100503136	90651140	250	10701											
MTTP	4547	hgsc.bcm.edu	37	chr4	100518224	100518224	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgcagtgtatgttttgcagCtctcggagctctggcggtcc	4	13	13	11	2	2	0	0	0	2	0	4	1	3	1	1	3	4	6	1	3	1	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:100518224C>T	ENST00000265517.5	+	8	1113	c.910C>T	c.(910-912)Ctc>Ttc	p.L304F	MTTP_ENST00000511045.1_Splice_Site_p.L331F|MTTP_ENST00000457717.1_Splice_Site_p.L304F|RP11-766F14.1_ENST00000508578.1_RNA			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	304	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)	TGTTTTGCAGCTCTCGGAGCT	0.498																																					p.L304F		Atlas-SNP	.											.	MTTP	127	.	0			c.C910T						PASS	.						101	100	101					4																	100518224		2203	4300	6503	SO:0001630	splice_region_variant	4547	exon9			TTGCAGCTCTCGG		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.910-1C>T	4.37:g.100518224C>T		35	0	0		33	11	0.333333	NM_000253	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	.	.	.	.	.	.	.	.	.	.	C	13.84	2.357959	0.41801	.	.	ENSG00000138823	ENST00000511045;ENST00000457717;ENST00000265517;ENST00000538053	T;T;T	0.55052	0.54;0.54;0.54	5.37	4.53	0.55603	Lipid transport protein, N-terminal (3);Vitellinogen, superhelical (1);	0.061492	0.64402	D	0.000003	T	0.74068	0.3668	M	0.77616	2.38	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.91635	0.995;0.999	T	0.75465	-0.3308	9	.	.	.	-28.4593	18.347	0.90326	0.1216:0.8784:0.0:0.0	.	331;304	E9PBP6;P55157	.;MTP_HUMAN	F	331;304;304;304	ENSP00000427679:L331F;ENSP00000400821:L304F;ENSP00000265517:L304F	.	L	+	1	0	MTTP	100737247	1.000000	0.71417	0.903000	0.35520	0.028000	0.11728	3.706000	0.54830	0.646000	0.30693	-0.808000	0.03180	CTC	.	.	none		0.498	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3		Missense_Mutation	T	100518224	C	T	100518224	5	4	27	1	0	0	0	0	0	0	1	0	9973	811	28	2	940	2	MTTP	4	100518224	Splice_Site	SNP	C	TCGA-G8-6909-01A-11D-2210-10	15088	100518224	90636052	251	10702											
GAR1	54433	hgsc.bcm.edu	37	chr4	110739212	110739212	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaacaaagaacaaattggaaAagtggatgaaatatttggac	21	8	9	3	0	0	2	0	1	0	1	0	5	0	5	0	3	2	0	0	3	8	3	rs143266987		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:110739212A>G	ENST00000226796.6	+	3	599	c.335A>G	c.(334-336)aAa>aGa	p.K112R	RP11-602N24.3_ENST00000609440.1_lincRNA|GAR1_ENST00000394631.3_Missense_Mutation_p.K112R	NM_018983.3	NP_061856.1	Q9NY12	GAR1_HUMAN	GAR1 ribonucleoprotein	112					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						CAAATTGGAAAAGTGGATGAA	0.348													A|||	1	0.000199681	0.0	0.0014	5008	,	,		19750	0.0		0.0	False		,,,				2504	0.0				p.K112R		Atlas-SNP	.											.	GAR1	16	.	0			c.A335G						PASS	.	A	ARG/LYS,ARG/LYS	0,4406		0,0,2203	83	86	85		335,335	4.8	1	4	dbSNP_134	85	6,8594	3.0+/-9.4	0,6,4294	yes	missense,missense	GAR1	NM_018983.3,NM_032993.2	26,26	0,6,6497	GG,GA,AA		0.0698,0.0,0.0461	probably-damaging,probably-damaging	112/218,112/218	110739212	6,13000	2203	4300	6503	SO:0001583	missense	54433	exon3			TTGGAAAAGTGGA	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.335A>G	4.37:g.110739212A>G	ENSP00000226796:p.Lys112Arg	81	0	0		60	30	0.5	NM_018983	Q5MJQ2	Missense_Mutation	SNP	ENST00000226796.6	37	CCDS34050.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.564745	0.86439	0.0	6.98E-4	ENSG00000109534	ENST00000394631;ENST00000226796	.	.	.	4.78	4.78	0.61160	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.000000	0.85682	D	0.000000	T	0.79587	0.4471	M	0.81341	2.54	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.82928	-0.0214	9	0.72032	D	0.01	.	14.6205	0.68582	1.0:0.0:0.0:0.0	.	112;112	Q9NY12-2;Q9NY12	.;GAR1_HUMAN	R	112	.	ENSP00000226796:K112R	K	+	2	0	GAR1	110958661	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.855000	0.92236	1.913000	0.55393	0.533000	0.62120	AAA	A|1.000;G|0.000	0.000	weak		0.348	GAR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363810.2			G	110739212	A	G	110739212	3	3	27	1	0	0	0	0	1	0	0	0	6248	14	1	3	341	3	GAR1	4	110739212	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	10220988	110739212	80415064	252	10703											
LRIT3	345193	hgsc.bcm.edu	37	chr4	110791273	110791273	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaatttaaaggtggcaaaGaatggaagtaagcttcctcc	16	9	10	6	0	0	2	0	0	0	2	2	3	2	3	2	3	1	3	2	3	7	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:110791273G>T	ENST00000594814.1	+	4	1368	c.1368G>T	c.(1366-1368)aaG>aaT	p.K456N	LRIT3_ENST00000409621.2_Missense_Mutation_p.K273N|LRIT3_ENST00000327908.3_Missense_Mutation_p.K273N|LRIT3_ENST00000379920.3_Missense_Mutation_p.K411N	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	456					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)		AGGTGGCAAAGAATGGAAGTA	0.463																																					p.K456N		Atlas-SNP	.											.	LRIT3	107	.	0			c.G1368T						PASS	.						69	71	70					4																	110791273		2203	4300	6503	SO:0001583	missense	345193	exon4			GGCAAAGAATGGA	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.1368G>T	4.37:g.110791273G>T	ENSP00000469759:p.Lys456Asn	110	0	0		73	37	0.506849	NM_198506	C9J1C2|Q6ZTG1	Missense_Mutation	SNP	ENST00000594814.1	37	CCDS3688.3	.	.	.	.	.	.	.	.	.	.	G	0.029	-1.351036	0.01256	.	.	ENSG00000183423	ENST00000327908;ENST00000379920;ENST00000409621	T;T;T	0.58506	0.33;0.5;0.33	5.06	2.14	0.27477	.	0.790373	0.11066	N	0.603446	T	0.38639	0.1048	L	0.29908	0.895	0.09310	N	1	B;B	0.29805	0.097;0.257	B;B	0.26416	0.023;0.069	T	0.17592	-1.0364	10	0.18276	T	0.48	.	6.0052	0.19542	0.2318:0.2504:0.5178:0.0	.	411;273	Q3SXY7;Q3SXY7-2	LRIT3_HUMAN;.	N	273;411;273	ENSP00000328222:K273N;ENSP00000369252:K411N;ENSP00000386734:K273N	ENSP00000328222:K273N	K	+	3	2	LRIT3	111010722	0.000000	0.05858	0.004000	0.12327	0.008000	0.06430	0.171000	0.16685	1.118000	0.41863	0.655000	0.94253	AAG	.	.	none		0.463	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506		T	110791273	G	T	110791273	3	4	27	1	0	0	0	0	1	0	0	0	8958	933	33	4	1243	4	LRIT3	4	110791273	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	52061	110791273	80363003	253	10704											
FAT4	79633	hgsc.bcm.edu	37	chr4	126336201	126336201	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgacctgccacagattccagCctccagattcacaagcactg	11	8	7	15	0	1	3	1	1	0	2	3	3	3	3	5	0	3	1	5	0	1	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:126336201C>T	ENST00000394329.3	+	5	6096	c.6083C>T	c.(6082-6084)gCc>gTc	p.A2028V	FAT4_ENST00000335110.5_Missense_Mutation_p.A326V	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2028	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						CAGATTCCAGCCTCCAGATTC	0.423																																					p.A2028V		Atlas-SNP	.											.	FAT4	1752	.	0			c.C6083T						PASS	.						162	167	165					4																	126336201		2203	4300	6503	SO:0001583	missense	79633	exon5			TTCCAGCCTCCAG	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.6083C>T	4.37:g.126336201C>T	ENSP00000377862:p.Ala2028Val	137	0	0		156	15	0.0961538	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	12.10	1.837537	0.32513	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.53206	0.63;0.63	5.1	4.24	0.50183	Cadherin (4);Cadherin-like (1);	0.239720	0.20285	U	0.095376	T	0.43523	0.1251	L	0.43923	1.385	0.30709	N	0.749492	B;B	0.24675	0.053;0.109	B;B	0.28916	0.096;0.047	T	0.43589	-0.9382	10	0.30854	T	0.27	.	15.7102	0.77620	0.0:0.8632:0.1368:0.0	.	326;2028	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	V	2028;326	ENSP00000377862:A2028V;ENSP00000335169:A326V	ENSP00000335169:A326V	A	+	2	0	FAT4	126555651	0.140000	0.22579	0.932000	0.37286	0.927000	0.56198	2.732000	0.47352	1.111000	0.41721	0.557000	0.71058	GCC	.	.	none		0.423	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126336201	C	T	126336201	3	4	27	1	0	0	0	0	1	0	0	0	5700	739	26	2	6101	2	FAT4	4	126336201	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	15544928	126336201	64818075	254	10705											
FAT4	79633	hgsc.bcm.edu	37	chr4	126336347	126336347	+	Missense_Mutation	SNP	C	C	A																															tcaaagctcaagcaactgacCcagatagtggcccaaacagc																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:126336347C>A	ENST00000394329.3	+	5	6242	c.6229C>A	c.(6229-6231)Cca>Aca	p.P2077T	FAT4_ENST00000335110.5_Missense_Mutation_p.P375T	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2077	Cadherin 20. {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.P2077>?(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						AGCAACTGACCCAGATAGTGG	0.418																																					p.P2077T		Atlas-SNP	.											.	FAT4	1752	.	2	Complex(2)	large_intestine(2)	c.C6229A						PASS	.						138	141	140					4																	126336347		2203	4300	6503	SO:0001583	missense	79633	exon5			ACTGACCCAGATA	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.6229C>A	4.37:g.126336347C>A	ENSP00000377862:p.Pro2077Thr	127	0	0		108	8	0.0740741	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	11.14	1.550366	0.27739	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.52983	0.64;0.64	5.0	4.1	0.47936	Cadherin (4);Cadherin-like (1);	0.000000	0.34314	U	0.004066	T	0.49047	0.1534	L	0.53729	1.69	0.39232	D	0.96369	B;B	0.28783	0.222;0.087	B;B	0.37550	0.253;0.155	T	0.54721	-0.8251	10	0.42905	T	0.14	.	14.821	0.70074	0.0:0.8556:0.1444:0.0	.	375;2077	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	T	2077;375	ENSP00000377862:P2077T;ENSP00000335169:P375T	ENSP00000335169:P375T	P	+	1	0	FAT4	126555797	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	2.603000	0.46266	2.308000	0.77769	0.557000	0.71058	CCA	.	.	none		0.418	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126336347	C	A	126336347	3	1	27	1	0	0	0	0	1	0	0	0	5700	623	22	4	6247	4	FAT4	4	126336347	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	146	126336347	64817929	255	10706	135	2									
FAT4	79633	hgsc.bcm.edu	37	chr4	126336348	126336348	+	Missense_Mutation	SNP	C	C	G																															caaagctcaagcaactgaccCagatagtggcccaaacagct																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:126336348C>G	ENST00000394329.3	+	5	6243	c.6230C>G	c.(6229-6231)cCa>cGa	p.P2077R	FAT4_ENST00000335110.5_Missense_Mutation_p.P375R	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2077	Cadherin 20. {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.P2077>?(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						GCAACTGACCCAGATAGTGGC	0.418																																					p.P2077R		Atlas-SNP	.											.	FAT4	1752	.	2	Complex(2)	large_intestine(2)	c.C6230G						PASS	.						137	140	139					4																	126336348		2203	4300	6503	SO:0001583	missense	79633	exon5			CTGACCCAGATAG	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.6230C>G	4.37:g.126336348C>G	ENSP00000377862:p.Pro2077Arg	126	0	0		107	7	0.0654206	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	2.239	-0.374320	0.05034	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.51574	0.7;0.7	5.0	4.11	0.48088	Cadherin (4);Cadherin-like (1);	0.000000	0.34314	U	0.004066	T	0.32763	0.0840	N	0.17379	0.485	0.42532	D	0.99304	B;B	0.09022	0.002;0.001	B;B	0.12837	0.008;0.004	T	0.10109	-1.0644	10	0.20519	T	0.43	.	16.9703	0.86297	0.0:0.8614:0.1386:0.0	.	375;2077	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	R	2077;375	ENSP00000377862:P2077R;ENSP00000335169:P375R	ENSP00000335169:P375R	P	+	2	0	FAT4	126555798	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	5.908000	0.69916	2.308000	0.77769	0.557000	0.71058	CCA	.	.	none		0.418	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		G	126336348	C	G	126336348	3	3	27	1	0	0	0	0	1	0	0	0	5700	594	21	4	6248	4	FAT4	4	126336348	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1	126336348	64817928	256	10707	135	2									
PCDH18	54510	hgsc.bcm.edu	37	chr4	138452706	138452706	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctcgatattaaaaaaatcAttggcagagagcgagtatgt	16	10	9	6	2	1	1	1	0	0	1	2	4	1	1	1	1	1	2	1	1	6	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:138452706A>T	ENST00000344876.4	-	1	923	c.537T>A	c.(535-537)aaT>aaA	p.N179K	PCDH18_ENST00000511115.1_Intron|PCDH18_ENST00000412923.2_Missense_Mutation_p.N179K|PCDH18_ENST00000507846.1_5'UTR|PCDH18_ENST00000510305.1_Intron	NM_019035.3	NP_061908.1	Q9HCL0	PCD18_HUMAN	protocadherin 18	179	Cadherin 2. {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)					TAAAAAAATCATTGGCAGAGA	0.483																																					p.N179K		Atlas-SNP	.											.	PCDH18	229	.	0			c.T537A						PASS	.						60	59	60					4																	138452706		2203	4300	6503	SO:0001583	missense	54510	exon1			AAAATCATTGGCA	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.537T>A	4.37:g.138452706A>T	ENSP00000355082:p.Asn179Lys	167	0	0		119	31	0.260504	NM_019035	A8K7K3|B7ZKT1|Q52LS2	Missense_Mutation	SNP	ENST00000344876.4	37	CCDS34064.1	.	.	.	.	.	.	.	.	.	.	A	12.89	2.072697	0.36566	.	.	ENSG00000189184	ENST00000344876;ENST00000412923	T;T	0.50813	0.73;0.73	5.89	0.536	0.17138	Cadherin (4);Cadherin-like (1);	0.000000	0.46145	D	0.000304	T	0.65544	0.2701	M	0.87827	2.91	0.80722	D	1	D;D	0.71674	0.998;0.992	P;P	0.61201	0.885;0.739	T	0.69476	-0.5135	10	0.87932	D	0	.	10.9316	0.47222	0.5396:0.0:0.4604:0.0	.	179;179	Q9HCL0-2;Q9HCL0	.;PCD18_HUMAN	K	179	ENSP00000355082:N179K;ENSP00000390688:N179K	ENSP00000355082:N179K	N	-	3	2	PCDH18	138672156	1.000000	0.71417	0.930000	0.37139	0.304000	0.27724	1.063000	0.30567	0.078000	0.16900	0.455000	0.32223	AAT	.	.	none		0.483	PCDH18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364614.1	NM_019035		T	138452706	A	T	138452706	3	4	27	1	0	0	0	0	1	0	0	0	11522	214	8	5	2886	5	PCDH18	4	138452706	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	12116358	138452706	52701570	257	10708											
SMARCA5	8467	hgsc.bcm.edu	37	chr4	144471249	144471249	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaaaaagaaacgaggaccaAagccttcagtaagtattcat	19	7	8	7	1	2	2	2	0	0	2	2	4	2	3	2	1	2	2	2	1	6	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:144471249A>G	ENST00000283131.3	+	23	3547	c.3085A>G	c.(3085-3087)Aag>Gag	p.K1029E		NM_003601.3	NP_003592.3	O60264	SMCA5_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 5	1029					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)					ACGAGGACCAAAGCCTTCAGT	0.358																																					p.K1029E		Atlas-SNP	.											.	SMARCA5	73	.	0			c.A3085G						PASS	.						67	63	64					4																	144471249		2203	4300	6503	SO:0001583	missense	8467	exon23			GGACCAAAGCCTT	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.3085A>G	4.37:g.144471249A>G	ENSP00000283131:p.Lys1029Glu	61	0	0		66	14	0.212121	NM_003601		Missense_Mutation	SNP	ENST00000283131.3	37	CCDS3761.1	.	.	.	.	.	.	.	.	.	.	A	16.07	3.017568	0.54576	.	.	ENSG00000153147	ENST00000283131;ENST00000536484;ENST00000535006	D	0.91011	-2.77	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.81973	0.4936	N	0.08118	0	0.46586	D	0.999116	B	0.26400	0.148	B	0.30029	0.11	T	0.78375	-0.2228	10	0.21014	T	0.42	-12.3435	16.1203	0.81346	1.0:0.0:0.0:0.0	.	1029	O60264	SMCA5_HUMAN	E	1029;972;972	ENSP00000283131:K1029E	ENSP00000283131:K1029E	K	+	1	0	SMARCA5	144690699	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.877000	0.69675	2.274000	0.75844	0.533000	0.62120	AAG	.	.	none		0.358	SMARCA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365077.3			G	144471249	A	G	144471249	3	3	27	1	0	0	0	0	1	0	0	0	14786	15	1	3	3175	3	SMARCA5	4	144471249	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	6018543	144471249	46683027	258	10709											
DCLK2	166614	hgsc.bcm.edu	37	chr4	151141918	151141918	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacctgagcttgaccgttgcAtaagtcctgaaggtagttct	9	12	11	9	1	1	3	0	3	1	0	2	4	2	3	3	1	2	5	3	1	3	5	rs148315360	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:151141918A>C	ENST00000296550.7	+	6	1874	c.1120A>C	c.(1120-1122)Ata>Cta	p.I374L	DCLK2_ENST00000302176.8_Missense_Mutation_p.I391L|DCLK2_ENST00000506325.1_Missense_Mutation_p.I373L	NM_001040260.3	NP_001035350.2	Q8N568	DCLK2_HUMAN	doublecortin-like kinase 2	374					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(1)	26	all_hematologic(180;0.151)					TGACCGTTGCATAAGTCCTGA	0.413													A|||	4	0.000798722	0.0	0.0029	5008	,	,		19679	0.0		0.002	False		,,,				2504	0.0				p.I391L	GBM(195;186 2215 13375 16801 37459)	Atlas-SNP	.											.	DCLK2	168	.	0			c.A1171C						PASS	.	A	LEU/ILE,LEU/ILE	4,4402	8.1+/-20.4	0,4,2199	131	105	114		1120,1171	-6	1	4	dbSNP_134	114	18,8582	13.3+/-46.6	0,18,4282	yes	missense,missense	DCLK2	NM_001040260.3,NM_001040261.4	5,5	0,22,6481	CC,CA,AA		0.2093,0.0908,0.1692	benign,benign	374/767,391/784	151141918	22,12984	2203	4300	6503	SO:0001583	missense	166614	exon7			CGTTGCATAAGTC	BC032726	CCDS34076.1, CCDS47142.1, CCDS47142.2	4q31.3	2008-02-05	2007-04-02	2007-04-02	ENSG00000170390	ENSG00000170390			19002	protein-coding gene	gene with protein product		613166	"doublecortin and CaM kinase-like 2"	DCAMKL2		12477932	Standard	NM_001040260		Approved	MGC45428, DCDC3, DCDC3B, DCK2	uc003ilo.4	Q8N568	OTTHUMG00000161444	ENST00000296550.7:c.1120A>C	4.37:g.151141918A>C	ENSP00000296550:p.Ile374Leu	215	0	0		134	71	0.529851	NM_001040261	C9J5Q9|Q59GC8|Q8N399	Missense_Mutation	SNP	ENST00000296550.7	37	CCDS34076.1	4	0.0018315018315018315	0	0.0	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	A	10.88	1.475306	0.26511	9.08E-4	0.002093	ENSG00000170390	ENST00000296550;ENST00000506325;ENST00000302176	T;T;T	0.63913	0.94;0.94;-0.07	5.49	-5.99	0.02213	.	0.793091	0.12274	N	0.483509	T	0.19327	0.0464	N	0.03608	-0.345	0.09310	N	0.999994	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.39742	-0.9599	10	0.06494	T	0.89	.	8.557	0.33487	0.1693:0.6518:0.08:0.0989	.	391;373;374	Q8N568-3;Q8N568-2;Q8N568	.;.;DCLK2_HUMAN	L	374;373;391	ENSP00000296550:I374L;ENSP00000427235:I373L;ENSP00000303887:I391L	ENSP00000296550:I374L	I	+	1	0	DCLK2	151361368	0.004000	0.15560	0.970000	0.41538	0.777000	0.43975	-1.810000	0.01729	-0.498000	0.06632	0.533000	0.62120	ATA	A|0.998;C|0.002	0.002	strong		0.413	DCLK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364952.1	NM_001040260		C	151141918	A	C	151141918	3	2	27	1	0	0	0	0	1	0	0	0	4294	217	8	5	1142	5	DCLK2	4	151141918	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	6670669	151141918	40012358	259	10710											
GLRB	2743	hgsc.bcm.edu	37	chr4	158060077	158060077	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagatattgaatatggtaacTgtacaaaatactataaaggc	19	11	7	4	0	0	2	0	1	0	1	0	2	0	2	0	2	3	2	0	2	12	8			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:158060077T>A	ENST00000264428.4	+	7	997	c.727T>A	c.(727-729)Tgt>Agt	p.C243S	GLRB_ENST00000509282.1_Missense_Mutation_p.C243S|GLRB_ENST00000512619.1_Intron|GLRB_ENST00000541722.1_Missense_Mutation_p.C243S	NM_000824.4	NP_000815.1	P48167	GLRB_HUMAN	glycine receptor, beta	243					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)	ATATGGTAACTGTACAAAATA	0.313																																					p.C243S		Atlas-SNP	.											GLRB,caecum,carcinoma,-2,1	GLRB	74	1	0			c.T727A						PASS	.						57	62	60					4																	158060077		2203	4295	6498	SO:0001583	missense	2743	exon7			GGTAACTGTACAA	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.727T>A	4.37:g.158060077T>A	ENSP00000264428:p.Cys243Ser	139	0	0		124	20	0.16129	NM_000824	A8K3K2|D3DP23|F5GWE1	Missense_Mutation	SNP	ENST00000264428.4	37	CCDS3796.1	.	.	.	.	.	.	.	.	.	.	T	27.4	4.825550	0.90955	.	.	ENSG00000109738	ENST00000264428;ENST00000541722;ENST00000509282	T;T;T	0.77620	-1.11;-1.11;-1.11	5.5	5.5	0.81552	Neurotransmitter-gated ion-channel ligand-binding (3);	0.093422	0.85682	D	0.000000	D	0.84392	0.5462	L	0.49455	1.56	0.80722	D	1	D	0.54772	0.968	D	0.69824	0.966	D	0.83745	0.0206	10	0.39692	T	0.17	.	15.5984	0.76606	0.0:0.0:0.0:1.0	.	243	P48167	GLRB_HUMAN	S	243	ENSP00000264428:C243S;ENSP00000441873:C243S;ENSP00000427186:C243S	ENSP00000264428:C243S	C	+	1	0	GLRB	158279527	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.961000	0.87903	2.090000	0.63153	0.528000	0.53228	TGT	.	.	none		0.313	GLRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366507.1	NM_000824		A	158060077	T	A	158060077	3	1	27	1	0	0	0	0	1	0	0	0	6466	1580	55	5	749	5	GLRB	4	158060077	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	6918159	158060077	33094199	260	10711											
GRIA2	2891	hgsc.bcm.edu	37	chr4	158242630	158242630	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	attaaaaatccagtttggagGtgcaaatgtctctggatttc	12	14	9	6	0	1	0	0	0	1	0	4	2	2	2	1	3	1	2	1	3	4	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:158242630G>T	ENST00000264426.9	+	6	1040	c.761G>T	c.(760-762)gGt>gTt	p.G254V	GRIA2_ENST00000507898.1_Missense_Mutation_p.G207V|GRIA2_ENST00000449365.1_Missense_Mutation_p.G207V|GRIA2_ENST00000296526.7_Missense_Mutation_p.G254V|GRIA2_ENST00000393815.2_Missense_Mutation_p.G207V	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	254					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)	CAGTTTGGAGGTGCAAATGTC	0.348																																					p.G254V		Atlas-SNP	.											.	GRIA2	358	.	0			c.G761T						PASS	.						192	203	199					4																	158242630		2203	4300	6503	SO:0001583	missense	2891	exon6			TTGGAGGTGCAAA		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.761G>T	4.37:g.158242630G>T	ENSP00000264426:p.Gly254Val	162	0	0		131	29	0.221374	NM_000826	A8MT92|I6L997|Q96FP6	Missense_Mutation	SNP	ENST00000264426.9	37	CCDS43274.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.616977	0.87359	.	.	ENSG00000120251	ENST00000507898;ENST00000393815;ENST00000296526;ENST00000264426;ENST00000449365	D;D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54;-1.54	5.74	5.74	0.90152	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.89150	0.6633	M	0.62723	1.935	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.99;0.94;1.0	D	0.89340	0.3653	10	0.87932	D	0	.	19.9317	0.97122	0.0:0.0:1.0:0.0	.	254;254;207	P42262;P42262-2;A8MT92	GRIA2_HUMAN;.;.	V	207;207;254;254;207	ENSP00000426845:G207V;ENSP00000377403:G207V;ENSP00000296526:G254V;ENSP00000264426:G254V;ENSP00000389837:G207V	ENSP00000264426:G254V	G	+	2	0	GRIA2	158462080	1.000000	0.71417	0.983000	0.44433	0.964000	0.63967	9.238000	0.95380	2.716000	0.92895	0.591000	0.81541	GGT	.	.	none		0.348	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2			T	158242630	G	T	158242630	3	4	27	1	0	0	0	0	1	0	0	0	6777	1261	44	4	783	4	GRIA2	4	158242630	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	182553	158242630	32911646	261	10712											
FNIP2	57600	hgsc.bcm.edu	37	chr4	159780274	159780274	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	taatccagctatggttaggaGgaagaaaattgccataagca	16	9	10	6	0	0	1	0	0	0	1	1	3	1	3	2	3	3	3	2	3	7	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:159780274G>A	ENST00000264433.6	+	9	998	c.923G>A	c.(922-924)aGg>aAg	p.R308K	FNIP2_ENST00000379346.3_Missense_Mutation_p.R331K	NM_020840.1	NP_065891.1	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2	308					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)		ATGGTTAGGAGGAAGAAAATT	0.403																																					p.R308K		Atlas-SNP	.											.	FNIP2	90	.	0			c.G923A						PASS	.						80	78	78					4																	159780274		1843	4097	5940	SO:0001583	missense	57600	exon9			TTAGGAGGAAGAA	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.923G>A	4.37:g.159780274G>A	ENSP00000264433:p.Arg308Lys	345	0	0		339	77	0.227139	NM_020840	Q05DC3|Q96I31|Q9H994	Missense_Mutation	SNP	ENST00000264433.6	37	CCDS47155.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.774472	0.49786	.	.	ENSG00000052795	ENST00000264433;ENST00000512986;ENST00000379346;ENST00000504715	T;T;T;T	0.26373	1.74;1.74;1.74;1.74	5.51	5.51	0.81932	.	.	.	.	.	T	0.25382	0.0617	L	0.34521	1.04	0.53688	D	0.999978	B	0.29162	0.235	B	0.33890	0.172	T	0.03443	-1.1036	8	.	.	.	.	19.4099	0.94667	0.0:0.0:1.0:0.0	.	308	Q9P278	FNIP2_HUMAN	K	308;331;331;173	ENSP00000264433:R308K;ENSP00000421488:R331K;ENSP00000368651:R331K;ENSP00000420841:R173K	.	R	+	2	0	FNIP2	159999724	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.620000	0.61226	2.582000	0.87167	0.655000	0.94253	AGG	.	.	none		0.403	FNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366602.1	NM_020840		A	159780274	G	A	159780274	3	1	27	1	0	0	0	0	1	0	0	0	5984	1000	35	2	957	2	FNIP2	4	159780274	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1537644	159780274	31374002	262	10713											
FSTL5	56884	hgsc.bcm.edu	37	chr4	162680603	162680603	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaagagccaggtgcttgtcAgcattaaaatcatcatattt	13	13	7	8	0	4	1	4	0	0	1	4	1	4	1	1	1	3	2	1	1	4	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:162680603A>T	ENST00000306100.5	-	6	1123	c.687T>A	c.(685-687)gcT>gcA	p.A229A	FSTL5_ENST00000536695.1_Silent_p.A228A|FSTL5_ENST00000379164.4_Silent_p.A228A|FSTL5_ENST00000427802.2_Silent_p.A228A	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	229	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)		GGTGCTTGTCAGCATTAAAAT	0.333																																					p.A229A		Atlas-SNP	.											.	FSTL5	207	.	0			c.T687A						PASS	.						93	101	98					4																	162680603		2203	4300	6503	SO:0001819	synonymous_variant	56884	exon6			CTTGTCAGCATTA	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.687T>A	4.37:g.162680603A>T		239	0	0		210	52	0.247619	NM_020116	E9PCP6|Q9NSW7|Q9ULF7	Silent	SNP	ENST00000306100.5	37	CCDS3802.1																																																																																			.	.	none		0.333	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116		T	162680603	A	T	162680603	2	4	27	1	0	0	0	0	0	0	0	1	6088	175	7	5		5	FSTL5	4	162680603	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	2900329	162680603	28473673	263	10714											
STOX2	56977	hgsc.bcm.edu	37	chr4	184930961	184930961	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcattaacccagacctgaccGtggaaaatgtcatgcggcac	12	7	10	12	2	1	2	1	1	0	1	1	3	1	3	3	2	2	2	3	2	3	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:184930961G>A	ENST00000308497.4	+	3	2405	c.970G>A	c.(970-972)Gtg>Atg	p.V324M	STOX2_ENST00000438269.1_Missense_Mutation_p.V324M	NM_020225.1	NP_064610.1	Q9P2F5	STOX2_HUMAN	storkhead box 2	324					embryo development (GO:0009790)|maternal placenta development (GO:0001893)					breast(1)|endometrium(7)|lung(6)	14		all_lung(41;1.89e-12)|Lung NSC(41;3.48e-12)|Colorectal(36;0.00435)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|all_hematologic(60;0.027)|Prostate(90;0.0283)		all cancers(43;2.85e-26)|Epithelial(43;2.27e-22)|OV - Ovarian serous cystadenocarcinoma(60;3.4e-10)|Colorectal(24;8.23e-06)|GBM - Glioblastoma multiforme(59;1.64e-05)|STAD - Stomach adenocarcinoma(60;3.6e-05)|COAD - Colon adenocarcinoma(29;4.37e-05)|LUSC - Lung squamous cell carcinoma(40;0.008)|READ - Rectum adenocarcinoma(43;0.227)		AGACCTGACCGTGGAAAATGT	0.562																																					p.V324M		Atlas-SNP	.											.	STOX2	142	.	0			c.G970A						PASS	.						24	24	24					4																	184930961		1943	4139	6082	SO:0001583	missense	56977	exon3			CTGACCGTGGAAA	AB037813	CCDS47167.1	4q35.1	2014-09-11			ENSG00000173320	ENSG00000173320			25450	protein-coding gene	gene with protein product							Standard	XM_005263142		Approved	DKFZp762K222	uc003ivz.1	Q9P2F5	OTTHUMG00000160618	ENST00000308497.4:c.970G>A	4.37:g.184930961G>A	ENSP00000311257:p.Val324Met	64	0	0		51	11	0.215686	NM_020225	A6H8U4|Q9NPS8	Missense_Mutation	SNP	ENST00000308497.4	37	CCDS47167.1	.	.	.	.	.	.	.	.	.	.	G	18.39	3.612462	0.66672	.	.	ENSG00000173320	ENST00000308497;ENST00000438269	T;D	0.88741	-1.49;-2.42	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	D	0.94922	0.8358	M	0.79123	2.44	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.987	D	0.94499	0.7708	10	0.87932	D	0	-21.6529	20.6634	0.99662	0.0:0.0:1.0:0.0	.	324;324	Q9P2F5-2;Q9P2F5	.;STOX2_HUMAN	M	324	ENSP00000311257:V324M;ENSP00000390127:V324M	ENSP00000311257:V324M	V	+	1	0	STOX2	185167955	1.000000	0.71417	0.988000	0.46212	0.374000	0.29953	9.869000	0.99810	2.894000	0.99253	0.655000	0.94253	GTG	.	.	none		0.562	STOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361433.3	NM_020225		A	184930961	G	A	184930961	3	1	27	1	0	0	0	0	1	0	0	0	15335	1145	40	1	980	1	STOX2	4	184930961	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	22250358	184930961	6223315	264	10715											
CYP4V2	285440	hgsc.bcm.edu	37	chr4	187118114	187118114	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tactggaaacaaatggcgctCcaggagaaagatgttaacac	16	7	10	8	1	0	2	0	0	0	2	1	4	1	3	1	3	3	2	1	3	5	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:187118114C>T	ENST00000378802.4	+	4	738	c.434C>T	c.(433-435)tCc>tTc	p.S145F		NM_207352.3	NP_997235.3	Q6ZWL3	CP4V2_HUMAN	cytochrome P450, family 4, subfamily V, polypeptide 2	145					fatty acid omega-oxidation (GO:0010430)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	endoplasmic reticulum (GO:0005783)|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)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)|stomach(2)	20		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;1.33e-10)|BRCA - Breast invasive adenocarcinoma(30;3.84e-05)|GBM - Glioblastoma multiforme(59;0.000132)|STAD - Stomach adenocarcinoma(60;0.000293)|LUSC - Lung squamous cell carcinoma(40;0.00242)|READ - Rectum adenocarcinoma(43;0.17)		AAATGGCGCTCCAGGAGAAAG	0.323																																					p.S145F		Atlas-SNP	.											.	CYP4V2	49	.	0			c.C434T						PASS	.						65	69	68					4																	187118114		2203	4298	6501	SO:0001583	missense	285440	exon4			GGCGCTCCAGGAG	AK022114	CCDS34119.1	4q35.2	2004-07-05			ENSG00000145476	ENSG00000145476		"Cytochrome P450s"	23198	protein-coding gene	gene with protein product		608614				15042513	Standard	NM_207352		Approved	CYP4AH1	uc003iyw.4	Q6ZWL3	OTTHUMG00000160379	ENST00000378802.4:c.434C>T	4.37:g.187118114C>T	ENSP00000368079:p.Ser145Phe	66	0	0		55	16	0.290909	NM_207352	B7U6W2|Q6ZTM4	Missense_Mutation	SNP	ENST00000378802.4	37	CCDS34119.1	.	.	.	.	.	.	.	.	.	.	C	15.26	2.780697	0.49891	.	.	ENSG00000145476	ENST00000378802;ENST00000274118	T	0.69806	-0.43	5.42	2.68	0.31781	.	0.512228	0.23803	N	0.044403	T	0.62048	0.2396	L	0.60904	1.88	0.09310	N	1	B	0.27013	0.166	B	0.29267	0.1	T	0.56768	-0.7924	10	0.62326	D	0.03	.	11.3683	0.49686	0.2554:0.6217:0.1229:0.0	.	145	Q6ZWL3	CP4V2_HUMAN	F	145;123	ENSP00000368079:S145F	ENSP00000274118:S123F	S	+	2	0	CYP4V2	187355108	0.014000	0.17966	0.105000	0.21289	0.973000	0.67179	1.809000	0.38922	0.320000	0.23234	-0.182000	0.12963	TCC	.	.	none		0.323	CYP4V2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360398.1	XM_209612		T	187118114	C	T	187118114	3	4	27	1	0	0	0	0	1	0	0	0	4194	855	30	2	448	2	CYP4V2	4	187118114	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2187153	187118114	4036162	265	10716											
FAT1	2195	hgsc.bcm.edu	37	chr4	187629137	187629137	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccgagttggggtttaaactAaagaaatccagttcatttcc	12	12	8	9	1	1	1	1	0	0	1	3	2	3	1	3	2	1	3	3	2	5	6	rs4862726	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:187629137A>G	ENST00000441802.2	-	2	2054	c.1845T>C	c.(1843-1845)ttT>ttC	p.F615F		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	615	Cadherin 5. {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						GGTTTAAACTAAAGAAATCCA	0.433										HNSCC(5;0.00058)			A|||	78	0.0155751	0.0	0.0101	5008	,	,		20191	0.0258		0.0368	False		,,,				2504	0.0082				p.F615F	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T1845C						PASS	.	A		23,3713		0,23,1845	68	63	64		1845	-1.3	0.6	4	dbSNP_111	64	305,7891		4,297,3797	no	coding-synonymous	FAT1	NM_005245.3		4,320,5642	GG,GA,AA		3.7213,0.6156,2.7489		615/4589	187629137	328,11604	1868	4098	5966	SO:0001819	synonymous_variant	2195	exon2			TAAACTAAAGAAA	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.1845T>C	4.37:g.187629137A>G		69	0	0		62	23	0.370968	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			A|0.975;G|0.025	0.025	strong		0.433	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		G	187629137	A	G	187629137	2	3	27	1	0	0	0	0	0	0	0	1	5697	359	13	3		3	FAT1	4	187629137	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	511023	187629137	3525139	266	10717											
ZFP42	132625	hgsc.bcm.edu	37	chr4	188924230	188924230	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acccatcctggaagaggactCactttttgagtccttggaat	10	12	9	10	0	1	2	1	1	0	1	3	5	3	5	3	3	0	0	3	3	2	3	rs149675060		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:188924230C>T	ENST00000326866.4	+	4	677	c.269C>T	c.(268-270)tCa>tTa	p.S90L	ZFP42_ENST00000509524.1_Missense_Mutation_p.S90L	NM_174900.3	NP_777560.2	Q96MM3	ZFP42_HUMAN	ZFP42 zinc finger protein	90					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)		GAAGAGGACTCACTTTTTGAG	0.453													C|||	1	0.000199681	0.0	0.0	5008	,	,		20567	0.0		0.001	False		,,,				2504	0.0				p.S90L		Atlas-SNP	.											.	ZFP42	87	.	0			c.C269T						PASS	.	C	LEU/SER	2,4404	4.2+/-10.8	0,2,2201	83	85	85		269	-1.7	0	4	dbSNP_134	85	6,8594	5.0+/-18.6	0,6,4294	yes	missense	ZFP42	NM_174900.3	145	0,8,6495	TT,TC,CC		0.0698,0.0454,0.0615	benign	90/311	188924230	8,12998	2203	4300	6503	SO:0001583	missense	132625	exon4			AGGACTCACTTTT	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.269C>T	4.37:g.188924230C>T	ENSP00000317686:p.Ser90Leu	64	0	0		89	44	0.494382	NM_174900	D3DP65|Q8WXE2	Missense_Mutation	SNP	ENST00000326866.4	37	CCDS3849.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	0.005	-2.129602	0.00338	4.54E-4	6.98E-4	ENSG00000179059	ENST00000326866;ENST00000509524	T;T	0.62788	0.0;0.0	4.49	-1.68	0.08212	.	0.950524	0.08730	N	0.902147	T	0.42314	0.1197	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.27806	-1.0063	10	0.39692	T	0.17	.	10.2546	0.43390	0.0:0.717:0.0:0.283	.	90	Q96MM3	ZFP42_HUMAN	L	90	ENSP00000317686:S90L;ENSP00000424662:S90L	ENSP00000317686:S90L	S	+	2	0	ZFP42	189161224	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.552000	0.06020	-0.188000	0.10499	0.655000	0.94253	TCA	C|0.999;T|0.001	0.001	strong		0.453	ZFP42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359794.1	NM_174900		T	188924230	C	T	188924230	3	4	27	1	0	0	0	0	1	0	0	0	17665	838	29	2	271	2	ZFP42	4	188924230	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1295093	188924230	2230046	267	10718											
ZFP42	132625	hgsc.bcm.edu	37	chr4	188924523	188924523	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatatgacagtctgagcgcaAtcgcttgtcctcagagtgga	11	10	11	9	2	2	3	1	2	1	1	4	4	3	4	1	1	1	2	1	1	3	2	rs138176771		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr4:188924523A>G	ENST00000326866.4	+	4	970	c.562A>G	c.(562-564)Atc>Gtc	p.I188V	ZFP42_ENST00000509524.1_Missense_Mutation_p.I188V	NM_174900.3	NP_777560.2	Q96MM3	ZFP42_HUMAN	ZFP42 zinc finger protein	188					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)		TCTGAGCGCAATCGCTTGTCC	0.488													A|||	1	0.000199681	0.0	0.0	5008	,	,		17143	0.0		0.001	False		,,,				2504	0.0				p.I188V		Atlas-SNP	.											ZFP42,NS,carcinoma,-2,1	ZFP42	87	1	0			c.A562G						PASS	.	A	VAL/ILE	2,4404	4.2+/-10.8	0,2,2201	107	113	111		562	-7.3	0	4	dbSNP_134	111	5,8595	4.3+/-15.6	0,5,4295	yes	missense	ZFP42	NM_174900.3	29	0,7,6496	GG,GA,AA		0.0581,0.0454,0.0538	benign	188/311	188924523	7,12999	2203	4300	6503	SO:0001583	missense	132625	exon4			AGCGCAATCGCTT	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.562A>G	4.37:g.188924523A>G	ENSP00000317686:p.Ile188Val	89	0	0		87	46	0.528736	NM_174900	D3DP65|Q8WXE2	Missense_Mutation	SNP	ENST00000326866.4	37	CCDS3849.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	6.125	0.391354	0.11581	4.54E-4	5.81E-4	ENSG00000179059	ENST00000326866;ENST00000509524	T;T	0.61742	0.08;0.08	3.64	-7.28	0.01456	Zinc finger, C2H2-like (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.115814	0.53938	D	0.000048	T	0.24044	0.0582	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.04427	-1.0952	10	0.35671	T	0.21	.	3.1416	0.06457	0.1935:0.4611:0.1484:0.197	.	188	Q96MM3	ZFP42_HUMAN	V	188	ENSP00000317686:I188V;ENSP00000424662:I188V	ENSP00000317686:I188V	I	+	1	0	ZFP42	189161517	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-0.764000	0.04735	-3.402000	0.00170	0.533000	0.62120	ATC	A|0.999;G|0.001	0.001	strong		0.488	ZFP42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359794.1	NM_174900		G	188924523	A	G	188924523	3	3	27	1	0	0	0	0	1	0	0	0	17665	101	4	3	564	3	ZFP42	4	188924523	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	293	188924523	2229753	268	10719											
MTRR	4552	hgsc.bcm.edu	37	chr5	7900056	7900056	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatatggccaaggatgtacAtgatgcccttgtgcaaataa	14	10	10	7	0	0	1	0	1	0	0	0	3	0	2	2	2	3	2	2	2	6	4	rs148909799	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:7900056A>G	ENST00000264668.2	+	15	2093	c.2063A>G	c.(2062-2064)cAt>cGt	p.H688R	MTRR_ENST00000440940.2_Missense_Mutation_p.H661R	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	688					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)	AAGGATGTACATGATGCCCTT	0.358													A|||	3	0.000599042	0.0	0.0	5008	,	,		17957	0.0		0.002	False		,,,				2504	0.001				p.H688R		Atlas-SNP	.											.	MTRR	74	.	0			c.A2063G						PASS	.	A	ARG/HIS,ARG/HIS	3,4403	4.2+/-10.8	0,3,2200	100	105	103		1982,2063	3.3	0	5	dbSNP_134	103	24,8576	17.3+/-56.4	1,22,4277	yes	missense,missense	MTRR	NM_002454.2,NM_024010.2	29,29	1,25,6477	GG,GA,AA		0.2791,0.0681,0.2076	benign,benign	661/699,688/726	7900056	27,12979	2203	4300	6503	SO:0001583	missense	4552	exon15			ATGTACATGATGC	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.2063A>G	5.37:g.7900056A>G	ENSP00000264668:p.His688Arg	153	0	0		129	67	0.51938	NM_024010	O60471|Q32MA9|Q7Z4M8	Missense_Mutation	SNP	ENST00000264668.2	37	CCDS3874.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	9.273	1.046111	0.19748	6.81E-4	0.002791	ENSG00000124275	ENST00000264668;ENST00000440940	D;D	0.85629	-2.01;-2.01	5.71	3.29	0.37713	Oxidoreductase FAD/NAD(P)-binding (1);	0.266108	0.46758	D	0.000276	T	0.72399	0.3455	N	0.16862	0.45	0.44316	D	0.997191	B	0.21821	0.061	B	0.24974	0.057	T	0.64228	-0.6457	10	0.27785	T	0.31	-16.3277	9.6534	0.39910	0.7885:0.0:0.2115:0.0	.	688	Q9UBK8	MTRR_HUMAN	R	688;661	ENSP00000264668:H688R;ENSP00000402510:H661R	ENSP00000264668:H688R	H	+	2	0	MTRR	7953056	1.000000	0.71417	0.013000	0.15412	0.988000	0.76386	2.540000	0.45727	0.999000	0.39023	0.533000	0.62120	CAT	A|0.998;G|0.002	0.002	strong		0.358	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1			G	7900056	A	G	7900056	3	3	27	1	0	0	0	0	1	0	0	0	9970	217	8	3	2121	3	MTRR	5	7900056	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10		7900056	173015204	269	10720											
DNAH5	1767	hgsc.bcm.edu	37	chr5	13716796	13716796	+	Missense_Mutation	SNP	C	C	T																															gcggatggtggtccaggagaCaccctgggaaattttataga																								rs138045391	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:13716796C>T	ENST00000265104.4	-	74	12813	c.12709G>A	c.(12709-12711)Gtc>Atc	p.V4237I		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4237					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)					GTCCAGGAGACACCCTGGGAA	0.403									Kartagener syndrome				C|||	2	0.000399361	0.0015	0.0	5008	,	,		16991	0.0		0.0	False		,,,				2504	0.0				p.V4237I		Atlas-SNP	.											.	DNAH5	868	.	0			c.G12709A						PASS	.																																			SO:0001583	missense	1767	exon74	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AGGAGACACCCTG	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.12709G>A	5.37:g.13716796C>T	ENSP00000265104:p.Val4237Ile	88	0	0		103	43	0.417476	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	7.699	0.692759	0.15039	.	.	ENSG00000039139	ENST00000265104	T	0.09538	2.97	5.53	4.67	0.58626	Dynein heavy chain (1);	0.128288	0.51477	N	0.000093	T	0.08537	0.0212	N	0.25426	0.745	0.58432	D	0.999996	B	0.09022	0.002	B	0.23574	0.047	T	0.23619	-1.0183	10	0.20046	T	0.44	.	11.2865	0.49224	0.0:0.8422:0.0:0.1578	.	4237	Q8TE73	DYH5_HUMAN	I	4237	ENSP00000265104:V4237I	ENSP00000265104:V4237I	V	-	1	0	DNAH5	13769796	0.996000	0.38824	0.686000	0.30086	0.589000	0.36550	3.359000	0.52292	1.348000	0.45733	-0.157000	0.13467	GTC	A|0.001;C|0.999	.	weak		0.403	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		T	13716796	C	T	13716796	3	4	27	1	0	0	0	0	1	0	0	0	4606	478	17	2	1189	2	DNAH5	5	13716796	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	5816740	13716796	167198464	270	10721	136	2									
DNAH5	1767	hgsc.bcm.edu	37	chr5	13716797	13716797	+	Silent	SNP	A	A	G																															cggatggtggtccaggagacAccctgggaaattttatagaa																								rs61744054	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:13716797A>G	ENST00000265104.4	-	74	12812	c.12708T>C	c.(12706-12708)ggT>ggC	p.G4236G		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4236					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)					TCCAGGAGACACCCTGGGAAA	0.403									Kartagener syndrome				A|||	174	0.0347444	0.1097	0.0216	5008	,	,		16997	0.001		0.005	False		,,,				2504	0.0082				p.G4236G		Atlas-SNP	.											DNAH5,NS,carcinoma,-1,1	DNAH5	868	1	0			c.T12708C						scavenged	.	A		355,4051	180.5+/-208.7	16,323,1864	57	52	54		12708	-11.1	0	5	dbSNP_129	54	17,8583	12.6+/-44.7	0,17,4283	no	coding-synonymous	DNAH5	NM_001369.2		16,340,6147	GG,GA,AA		0.1977,8.0572,2.8602		4236/4625	13716797	372,12634	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon74	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GGAGACACCCTGG	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.12708T>C	5.37:g.13716797A>G		88	1	0.0113636		101	42	0.415842	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			A|0.971;G|0.029	0.029	strong		0.403	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		G	13716797	A	G	13716797	2	3	27	1	0	0	0	0	0	0	0	1	4606	146	6	3		3	DNAH5	5	13716797	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	1	13716797	167198463	271	10722	136	2									
DNAH5	1767	hgsc.bcm.edu	37	chr5	13883045	13883045	+	Frame_Shift_Del	DEL	C	C	-																															ttcactgctccactgtctgaCccccttagggacactgatga																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:13883045delC	ENST00000265104.4	-	20	3246	c.3142delG	c.(3142-3144)gtcfs	p.V1048fs	CTB-51A17.1_ENST00000503244.1_RNA	NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1048	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)					CACTGTCTGACCCCCTTAGGG	0.507									Kartagener syndrome																												p.V1048fs		Atlas-Indel	.											.	DNAH5	868	.	0			c.3143delT						PASS	.						167	149	155					5																	13883045		2203	4300	6503	SO:0001589	frameshift_variant	1767	exon20	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.3142delG	5.37:g.13883045delC	ENSP00000265104:p.Val1048fs	142	0	0		164	26	0.158537	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Frame_Shift_Del	DEL	ENST00000265104.4	37	CCDS3882.1																																																																																			.	.	none		0.507	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		-	13883045	C	-	13883045	7	5	27	1	0	1	0	1	0	0	0	0	4606	507	18	0	10972	0	DNAH5	5	13883045	Frame_Shift_Del	DEL	C	TCGA-G8-6909-01A-11D-2210-10	166248	13883045	167032215	272	10723											
PRDM9	56979	hgsc.bcm.edu	37	chr5	23527273	23527273	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacacaggggagaagccctaTgtctgcagggagtgtgggcg	9	6	17	9	1	1	1	0	0	1	1	1	3	1	2	1	4	2	1	1	4	2	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:23527273T>C	ENST00000296682.3	+	11	2258	c.2076T>C	c.(2074-2076)taT>taC	p.Y692Y		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	692					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						AGAAGCCCTATGTCTGCAGGG	0.607										HNSCC(3;0.000094)																											p.Y692Y		Atlas-SNP	.											PRDM9,NS,carcinoma,+1,1	PRDM9	344	1	0			c.T2076C						PASS	.						11	8	9					5																	23527273		1606	3274	4880	SO:0001819	synonymous_variant	56979	exon11			GCCCTATGTCTGC	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.2076T>C	5.37:g.23527273T>C		74	0	0		98	26	0.265306	NM_020227	B4DX22|Q27Q50	Silent	SNP	ENST00000296682.3	37	CCDS43307.1																																																																																			.	.	none		0.607	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		C	23527273	T	C	23527273	2	2	27	1	0	0	0	0	0	0	0	1	12475	1471	51	3		3	PRDM9	5	23527273	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	9644228	23527273	157387987	273	10724											
CDH9	1007	hgsc.bcm.edu	37	chr5	26902724	26902724	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atctatatcttccacagataTtttgaccacagctgtatctt	11	16	4	10	0	3	2	0	1	3	1	4	2	4	2	2	0	1	2	2	0	4	8			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:26902724T>G	ENST00000231021.4	-	7	1286	c.1114A>C	c.(1114-1116)Ata>Cta	p.I372L		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	372	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						TCCACAGATATTTTGACCACA	0.403																																					p.I372L	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.A1114C						PASS	.						124	121	122					5																	26902724		2203	4300	6503	SO:0001583	missense	1007	exon7			CAGATATTTTGAC	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.1114A>C	5.37:g.26902724T>G	ENSP00000231021:p.Ile372Leu	120	0	0		147	35	0.238095	NM_016279	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	37	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	T	16.37	3.102931	0.56183	.	.	ENSG00000113100	ENST00000231021	T	0.68181	-0.31	5.62	3.25	0.37280	Cadherin (3);Cadherin-like (1);	0.179874	0.51477	D	0.000089	T	0.70055	0.3180	M	0.83223	2.63	0.36617	D	0.875535	B	0.09022	0.002	B	0.36134	0.218	T	0.66244	-0.5972	9	.	.	.	.	7.5723	0.27915	0.0:0.2391:0.0:0.7609	.	372	Q9ULB4	CADH9_HUMAN	L	372	ENSP00000231021:I372L	.	I	-	1	0	CDH9	26938481	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	1.231000	0.32624	0.426000	0.26116	0.528000	0.53228	ATA	.	.	none		0.403	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		G	26902724	T	G	26902724	3	3	27	1	0	0	0	0	1	0	0	0	3119	1493	52	5	1279	5	CDH9	5	26902724	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	3375451	26902724	154012536	274	10725											
DAB2	1601	hgsc.bcm.edu	37	chr5	39381618	39381618	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgaagagatccagagggttgGgctgcagggctgtaggttgt	8	10	18	5	0	0	3	0	1	0	2	1	4	1	3	1	4	1	6	1	4	2	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:39381618G>A	ENST00000320816.6	-	11	1909	c.1442C>T	c.(1441-1443)cCc>cTc	p.P481L	DAB2_ENST00000339788.6_Missense_Mutation_p.P263L|DAB2_ENST00000545653.1_Missense_Mutation_p.P460L|DAB2_ENST00000509337.1_Missense_Mutation_p.P460L	NM_001343.3	NP_001334.2	P98082	DAB2_HUMAN	Dab, mitogen-responsive phosphoprotein, homolog 2 (Drosophila)	481					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)			CAGAGGGTTGGGCTGCAGGGC	0.532																																					p.P481L		Atlas-SNP	.											.	DAB2	124	.	0			c.C1442T						PASS	.						118	123	121					5																	39381618		2203	4300	6503	SO:0001583	missense	1601	exon11			GGGTTGGGCTGCA	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.1442C>T	5.37:g.39381618G>A	ENSP00000313391:p.Pro481Leu	88	0	0		123	43	0.349593	NM_001343	A6NES5|Q13598|Q9BTY0|Q9UK04	Missense_Mutation	SNP	ENST00000320816.6	37	CCDS34149.1	.	.	.	.	.	.	.	.	.	.	G	13.36	2.212852	0.39102	.	.	ENSG00000153071	ENST00000320816;ENST00000339788;ENST00000545653;ENST00000509337	T;T;T;T	0.37752	1.32;1.18;1.31;1.31	5.87	3.96	0.45880	.	0.775909	0.12796	N	0.438417	T	0.28200	0.0696	L	0.29908	0.895	0.44908	D	0.99792	B;B	0.15719	0.014;0.014	B;B	0.17979	0.013;0.02	T	0.04400	-1.0954	10	0.23891	T	0.37	-1.2282	13.2306	0.59941	0.0:0.1217:0.7521:0.1262	.	481;460	P98082;P98082-3	DAB2_HUMAN;.	L	481;263;460;460	ENSP00000313391:P481L;ENSP00000345508:P263L;ENSP00000439919:P460L;ENSP00000426245:P460L	ENSP00000313391:P481L	P	-	2	0	DAB2	39417375	1.000000	0.71417	0.991000	0.47740	0.841000	0.47740	2.304000	0.43655	1.587000	0.49959	0.655000	0.94253	CCC	.	.	none		0.532	DAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367014.1	NM_001343		A	39381618	G	A	39381618	3	1	27	1	0	0	0	0	1	0	0	0	4220	1232	43	2	886	2	DAB2	5	39381618	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	12478894	39381618	141533642	275	10726											
C7	730	hgsc.bcm.edu	37	chr5	40934471	40934471	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatgggcagtatggaggccaGccttgtgttggaaatgcttt	8	13	14	6	0	0	0	0	0	0	0	0	2	0	2	2	4	2	4	2	4	3	5	rs34196526	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:40934471G>A	ENST00000313164.9	+	4	542	c.183G>A	c.(181-183)caG>caA	p.Q61Q		NM_000587.2	NP_000578.2	P10643	CO7_HUMAN	complement component 7	61	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				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)				ATGGAGGCCAGCCTTGTGTTG	0.458													G|||	35	0.00698882	0.0008	0.0058	5008	,	,		16468	0.0		0.008	False		,,,				2504	0.0225				p.Q61Q		Atlas-SNP	.											.	C7	136	.	0			c.G183A						PASS	.	G		9,3901		0,9,1946	160	165	163		183	-11.8	0	5	dbSNP_126	163	197,8095		3,191,3952	no	coding-synonymous	C7	NM_000587.2		3,200,5898	AA,AG,GG		2.3758,0.2302,1.6882		61/844	40934471	206,11996	1955	4146	6101	SO:0001819	synonymous_variant	730	exon4			AGGCCAGCCTTGT	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.183G>A	5.37:g.40934471G>A		266	0	0		268	162	0.604478	NM_000587	Q6P3T5|Q92489	Silent	SNP	ENST00000313164.9	37	CCDS47201.1																																																																																			G|0.992;A|0.008	0.008	strong		0.458	C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317680.1			A	40934471	G	A	40934471	2	1	27	1	0	0	0	0	0	0	0	1	2377	962	34	2		2	C7	5	40934471	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1552853	40934471	139980789	276	10727											
C6	729	hgsc.bcm.edu	37	chr5	41155088	41155088	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcacgttggcattccacaTccccttgtctccaggtcccg	5	12	7	17	2	2	0	1	0	2	0	7	0	5	0	5	2	0	2	5	2	0	3	rs41271067	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:41155088T>C	ENST00000263413.3	-	14	2351	c.2087A>G	c.(2086-2088)gAt>gGt	p.D696G	C6_ENST00000337836.5_Missense_Mutation_p.D696G	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	696	C5b-binding domain.|CCP 2.|Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				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)				GCATTCCACATCCCCTTGTCT	0.413													T|||	17	0.00339457	0.0	0.0086	5008	,	,		19476	0.001		0.008	False		,,,				2504	0.002				p.D696G		Atlas-SNP	.											.	C6	197	.	0			c.A2087G						PASS	.	T	GLY/ASP,GLY/ASP	8,4398	14.3+/-33.2	0,8,2195	148	138	142		2087,2087	3.5	1	5	dbSNP_127	142	115,8485	60.6+/-122.4	1,113,4186	yes	missense,missense	C6	NM_000065.2,NM_001115131.1	94,94	1,121,6381	CC,CT,TT		1.3372,0.1816,0.9457	benign,benign	696/935,696/935	41155088	123,12883	2203	4300	6503	SO:0001583	missense	729	exon14			TCCACATCCCCTT	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.2087A>G	5.37:g.41155088T>C	ENSP00000263413:p.Asp696Gly	95	0	0		107	38	0.35514	NM_001115131		Missense_Mutation	SNP	ENST00000263413.3	37	CCDS3936.1	12	0.005494505494505495	0	0.0	5	0.013812154696132596	1	0.0017482517482517483	6	0.0079155672823219	T	13.64	2.298824	0.40694	0.001816	0.013372	ENSG00000039537	ENST00000337836;ENST00000263413	T;T	0.41758	0.99;0.99	5.82	3.51	0.40186	Complement control module (2);Sushi/SCR/CCP (2);	0.475155	0.24788	N	0.035595	T	0.26048	0.0635	L	0.47190	1.495	0.34230	D	0.676444	B	0.17852	0.024	B	0.25759	0.063	T	0.36939	-0.9727	10	0.36615	T	0.2	-24.0381	7.4848	0.27425	0.0:0.1133:0.1879:0.6988	rs41271067;rs61733157	696	P13671	CO6_HUMAN	G	696	ENSP00000338861:D696G;ENSP00000263413:D696G	ENSP00000263413:D696G	D	-	2	0	C6	41190845	0.576000	0.26700	0.999000	0.59377	0.992000	0.81027	0.724000	0.25954	2.232000	0.73038	0.528000	0.53228	GAT	T|0.992;C|0.008	0.008	strong		0.413	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1			C	41155088	T	C	41155088	3	2	27	1	0	0	0	0	1	0	0	0	2317	1435	50	3	737	3	C6	5	41155088	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	220617	41155088	139760172	277	10728											
C6	729	hgsc.bcm.edu	37	chr5	41181578	41181578	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccccccctgacttgagaaTgagccttgttgattttcatt	7	15	7	12	0	1	4	1	4	0	1	2	5	2	4	4	0	1	1	4	0	1	6	rs61734263	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:41181578T>A	ENST00000263413.3	-	7	1074	c.810A>T	c.(808-810)tcA>tcT	p.S270S	C6_ENST00000337836.5_Silent_p.S270S|C6_ENST00000475349.1_5'UTR	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	270	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)				GACTTGAGAATGAGCCTTGTT	0.378													T|||	23	0.00459265	0.0	0.0014	5008	,	,		15500	0.0		0.0129	False		,,,				2504	0.0092				p.S270S		Atlas-SNP	.											.	C6	197	.	0			c.A810T						PASS	.	T	,	11,4395	16.8+/-37.8	0,11,2192	81	80	80		810,810	-1.8	0	5	dbSNP_129	80	158,8442	75.7+/-138.4	2,154,4144	no	coding-synonymous,coding-synonymous	C6	NM_000065.2,NM_001115131.1	,	2,165,6336	AA,AT,TT		1.8372,0.2497,1.2994	,	270/935,270/935	41181578	169,12837	2203	4300	6503	SO:0001819	synonymous_variant	729	exon7			TGAGAATGAGCCT	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.810A>T	5.37:g.41181578T>A		146	0	0		154	94	0.61039	NM_001115131		Silent	SNP	ENST00000263413.3	37	CCDS3936.1																																																																																			T|0.980;A|0.020	0.020	strong		0.378	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1			A	41181578	T	A	41181578	2	1	27	1	0	0	0	0	0	0	0	1	2317	1451	51	5		5	C6	5	41181578	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	26490	41181578	139733682	278	10729											
MOCS2	4338	hgsc.bcm.edu	37	chr5	52397199	52397199	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaaatcatacccaagtctatGgaacactgctatgtgtttga	13	12	8	8	0	2	1	1	1	1	0	2	3	2	2	1	1	3	2	1	1	6	4	rs2233218	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:52397199G>A	ENST00000396954.3	-	5	1044	c.367C>T	c.(367-369)Cat>Tat	p.H123Y	MOCS2_ENST00000361377.4_Intron|MOCS2_ENST00000527216.1_3'UTR|MOCS2_ENST00000450852.3_3'UTR|MOCS2_ENST00000508922.1_3'UTR|MOCS2_ENST00000584946.1_3'UTR|MOCS2_ENST00000582677.1_Intron|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)				CCAAGTCTATGGAACACTGCT	0.348													G|||	13	0.00259585	0.0	0.0029	5008	,	,		15837	0.0		0.0109	False		,,,				2504	0.0				p.H123Y		Atlas-SNP	.											.	MOCS2	28	.	0			c.C367T						PASS	.	G	TYR/HIS,	6,4400	11.4+/-27.6	0,6,2197	201	200	200		367,	5.8	1	5	dbSNP_98	200	47,8553	30.1+/-81.4	1,45,4254	yes	missense,utr-3	MOCS2	NM_004531.3,NM_176806.2	83,	1,51,6451	AA,AG,GG		0.5465,0.1362,0.4075	probably-damaging,	123/189,	52397199	53,12953	2203	4300	6503	SO:0001583	missense	4338	exon5			GTCTATGGAACAC	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.367C>T	5.37:g.52397199G>A	ENSP00000380157:p.His123Tyr	126	0	0		148	71	0.47973	NM_004531		Missense_Mutation	SNP	ENST00000396954.3	37	CCDS3958.1	10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	G	26.2	4.718212	0.89205	0.001362	0.005465	ENSG00000164172	ENST00000396954;ENST00000527216	T	0.63744	-0.06	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	D	0.85496	0.5710	H	0.98701	4.305	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91373	0.5121	10	0.87932	D	0	-10.3275	20.1184	0.97949	0.0:0.0:1.0:0.0	rs2233218;rs52802686;rs2233218	123	O96007	MOC2B_HUMAN	Y	123	ENSP00000380157:H123Y	ENSP00000380157:H123Y	H	-	1	0	MOCS2	52432956	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.715000	0.84713	2.775000	0.95449	0.650000	0.86243	CAT	G|0.995;A|0.005	0.005	strong		0.348	MOCS2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214053.3	NM_183418		A	52397199	G	A	52397199	3	1	27	1	0	0	0	0	1	0	0	0	9700	1348	47	2	211	2	MOCS2	5	52397199	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	11215621	52397199	128518061	279	10730											
CDC20B	166979	hgsc.bcm.edu	37	chr5	54424381	54424381	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggttctccccattccagatGtatacagcagagcccagggc	9	9	10	13	0	1	2	0	0	1	2	3	2	2	2	4	2	3	3	4	2	2	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:54424381G>A	ENST00000381375.2	-	7	907	c.762C>T	c.(760-762)taC>taT	p.Y254Y	CDC20B_ENST00000296733.1_Silent_p.Y254Y|CDC20B_ENST00000322374.6_Silent_p.Y254Y|CDC20B_ENST00000334206.5_Silent_p.Y254Y			Q86Y33	CD20B_HUMAN	cell division cycle 20B	254										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)			CATTCCAGATGTATACAGCAG	0.383																																					p.Y254Y		Atlas-SNP	.											.	CDC20B	61	.	0			c.C762T						PASS	.						145	151	149					5																	54424381		2203	4300	6503	SO:0001819	synonymous_variant	166979	exon7			CCAGATGTATACA	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.762C>T	5.37:g.54424381G>A		199	0	0		184	64	0.347826	NM_001170402	B7WNV8|B9EGL8|C9J6X8|C9JHE9|C9JKL5|Q86Y31|Q86Y32|Q8IUZ8|Q8N1S1|Q8NG56	Silent	SNP	ENST00000381375.2	37	CCDS54852.1																																																																																			.	.	none		0.383	CDC20B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369715.1	NM_152623		A	54424381	G	A	54424381	2	1	27	1	0	0	0	0	0	0	0	1	3062	1372	48	2		2	CDC20B	5	54424381	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2027182	54424381	126490879	280	10731											
SKIV2L2	23517	hgsc.bcm.edu	37	chr5	54645455	54645455	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	taatgcaattgattgcttatCcgatgaagataaaaaactcc	16	12	6	7	1	0	3	0	2	0	1	2	4	2	3	2	0	3	2	2	0	7	5	rs142958762	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:54645455C>G	ENST00000230640.5	+	12	1549	c.1295C>G	c.(1294-1296)tCc>tGc	p.S432C	SKIV2L2_ENST00000545714.1_Missense_Mutation_p.S331C	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	432	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)				GATTGCTTATCCGATGAAGAT	0.313													C|||	11	0.00219649	0.0	0.0014	5008	,	,		19133	0.0		0.0099	False		,,,				2504	0.0				p.S432C	Melanoma(2;92 134 23744 29976 33782)	Atlas-SNP	.											.	SKIV2L2	104	.	0			c.C1295G						PASS	.	C	CYS/SER	8,4398	14.3+/-33.2	0,8,2195	72	77	76		1295	5.5	1	5	dbSNP_134	76	40,8560	26.3+/-74.7	0,40,4260	yes	missense	SKIV2L2	NM_015360.4	112	0,48,6455	GG,GC,CC		0.4651,0.1816,0.3691	probably-damaging	432/1043	54645455	48,12958	2203	4300	6503	SO:0001583	missense	23517	exon12			GCTTATCCGATGA	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.1295C>G	5.37:g.54645455C>G	ENSP00000230640:p.Ser432Cys	165	0	0		171	98	0.573099	NM_015360	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Missense_Mutation	SNP	ENST00000230640.5	37	CCDS3967.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	C	26.5	4.743788	0.89663	0.001816	0.004651	ENSG00000039123	ENST00000230640;ENST00000545714	T;T	0.45276	0.9;0.9	5.53	5.53	0.82687	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.65964	0.2742	M	0.90650	3.135	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.74023	0.982;0.947	T	0.76000	-0.3119	10	0.87932	D	0	-21.515	19.8173	0.96576	0.0:1.0:0.0:0.0	.	331;432	F5H7E2;P42285	.;SK2L2_HUMAN	C	432;331	ENSP00000230640:S432C;ENSP00000442583:S331C	ENSP00000230640:S432C	S	+	2	0	SKIV2L2	54681212	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.850000	0.69473	2.763000	0.94921	0.585000	0.79938	TCC	C|0.995;G|0.005	0.005	strong		0.313	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1			G	54645455	C	G	54645455	3	3	27	1	0	0	0	0	1	0	0	0	14375	855	30	4	1341	4	SKIV2L2	5	54645455	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	221074	54645455	126269805	281	10732											
MAP3K1	4214	hgsc.bcm.edu	37	chr5	56155672	56155672	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acgcagtccttctcctggcaActccccatcaggtcgcacag	8	8	8	17	2	2	0	1	0	1	0	6	0	4	0	4	2	1	3	4	2	1	1	rs56069227	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:56155672A>G	ENST00000399503.3	+	3	764	c.764A>G	c.(763-765)aAc>aGc	p.N255S	snoU13_ENST00000459264.1_RNA|AC008937.2_ENST00000415589.1_RNA	NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	255					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)		TCTCCTGGCAACTCCCCATCA	0.488													A|||	83	0.0165735	0.025	0.0216	5008	,	,		15055	0.0		0.0338	False		,,,				2504	0.001				p.N255S		Atlas-SNP	.											.	MAP3K1	355	.	0			c.A764G						PASS	.	A	SER/ASN	79,3755		1,77,1839	42	42	42		764	3.9	0.9	5	dbSNP_129	42	229,8029		5,219,3905	yes	missense	MAP3K1	NM_005921.1	46	6,296,5744	GG,GA,AA		2.7731,2.0605,2.5471	benign	255/1513	56155672	308,11784	1917	4129	6046	SO:0001583	missense	4214	exon3			CTGGCAACTCCCC	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.764A>G	5.37:g.56155672A>G	ENSP00000382423:p.Asn255Ser	225	0	0		206	128	0.621359	NM_005921		Missense_Mutation	SNP	ENST00000399503.3	37	CCDS43318.1	40	0.018315018315018316	6	0.012195121951219513	9	0.024861878453038673	0	0.0	25	0.032981530343007916	A	13.57	2.277282	0.40294	0.020605	0.027731	ENSG00000095015	ENST00000399503	T	0.63255	-0.03	5.72	3.93	0.45458	.	0.316826	0.39544	N	0.001335	T	0.10465	0.0256	N	0.01352	-0.895	0.26121	N	0.98055	B	0.02656	0.0	B	0.01281	0.0	T	0.14448	-1.0472	10	0.02654	T	1	.	11.7667	0.51935	0.1441:0.0:0.8559:0.0	rs56069227;rs61736548	255	Q13233	M3K1_HUMAN	S	255	ENSP00000382423:N255S	ENSP00000382423:N255S	N	+	2	0	MAP3K1	56191429	1.000000	0.71417	0.938000	0.37757	0.734000	0.41952	3.001000	0.49488	0.871000	0.35750	-0.242000	0.12053	AAC	A|0.976;G|0.024	0.024	strong		0.488	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066		G	56155672	A	G	56155672	3	3	27	1	0	0	0	0	1	0	0	0	9252	43	2	3	774	3	MAP3K1	5	56155672	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	1510217	56155672	124759588	282	10733											
BDP1	55814	hgsc.bcm.edu	37	chr5	70818150	70818150	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtatgttcctagttcagcaCaaatgacaagaaggaaattc	15	10	8	8	1	1	2	1	1	0	1	3	3	2	3	1	1	1	4	1	1	6	5	rs12187098	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:70818150C>G	ENST00000358731.4	+	23	5289	c.5026C>G	c.(5026-5028)Caa>Gaa	p.Q1676E	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	1676			Q -> E (in dbSNP:rs12187098).		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)		TAGTTCAGCACAAATGACAAG	0.348													C|||	101	0.0201677	0.0454	0.013	5008	,	,		17087	0.0		0.0298	False		,,,				2504	0.002				p.Q1676E		Atlas-SNP	.											.	BDP1	204	.	0			c.C5026G						PASS	.	C	GLU/GLN	182,3514		3,176,1669	130	127	128		5026	4.5	0.1	5	dbSNP_120	128	196,7988		6,184,3902	yes	missense	BDP1	NM_018429.2	29	9,360,5571	GG,GC,CC		2.3949,4.9242,3.1818	possibly-damaging	1676/2625	70818150	378,11502	1848	4092	5940	SO:0001583	missense	55814	exon23			TCAGCACAAATGA	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.5026C>G	5.37:g.70818150C>G	ENSP00000351575:p.Gln1676Glu	183	0	0		197	67	0.340102	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	37	CCDS43328.1	41	0.018772893772893772	19	0.03861788617886179	5	0.013812154696132596	0	0.0	17	0.022427440633245383	C	8.668	0.902198	0.17760	0.049242	0.023949	ENSG00000145734	ENST00000358731;ENST00000451951	T	0.10477	2.87	5.35	4.48	0.54585	.	1.312210	0.05133	N	0.493011	T	0.01489	0.0048	L	0.47716	1.5	0.49687	D	0.999812	P;P	0.42871	0.557;0.792	B;B	0.37601	0.116;0.254	T	0.48514	-0.9029	10	0.02654	T	1	.	11.1063	0.48205	0.0:0.9126:0.0:0.0874	rs12187098;rs13169583;rs52833258;rs56647603;rs12187098	1676;1676	A6H8Y1;A6H8Y1-2	BDP1_HUMAN;.	E	1676;1256	ENSP00000351575:Q1676E	ENSP00000351575:Q1676E	Q	+	1	0	BDP1	70853906	0.019000	0.18553	0.098000	0.21074	0.052000	0.14988	2.086000	0.41643	1.251000	0.43983	0.555000	0.69702	CAA	C|0.971;G|0.029	0.029	strong		0.348	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429		G	70818150	C	G	70818150	3	3	27	1	0	0	0	0	1	0	0	0	1395	479	17	4	5116	4	BDP1	5	70818150	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	14662478	70818150	110097110	283	10734											
RGNEF	64283	hgsc.bcm.edu	37	chr5	73205337	73205337	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctctatcctccgaggcggccCcttgcaggaccagaagtctc	7	8	10	16	2	2	1	0	0	2	1	5	3	4	2	5	3	1	1	5	3	2	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:73205337C>A	ENST00000426542.2	+	33	4282	c.4262C>A	c.(4261-4263)cCc>cAc	p.P1421H	ARHGEF28_ENST00000513042.2_Missense_Mutation_p.P1421H|ARHGEF28_ENST00000512883.1_Missense_Mutation_p.P341H|ARHGEF28_ENST00000437974.1_Missense_Mutation_p.P1421H|ARHGEF28_ENST00000287898.5_Missense_Mutation_p.P1377H|ARHGEF28_ENST00000545377.1_Missense_Mutation_p.P1421H|ARHGEF28_ENST00000296794.6_Missense_Mutation_p.P1421H|ARHGEF28_ENST00000296799.4_Missense_Mutation_p.P1108H			Q8N1W1	ARG28_HUMAN	Rho guanine nucleotide exchange factor (GEF) 28	1421					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)										CGAGGCGGCCCCTTGCAGGAC	0.642																																					p.P1421H		Atlas-SNP	.											.	.	.	.	0			c.C4262A						PASS	.						17	20	19					5																	73205337		2040	4194	6234	SO:0001583	missense	64283	exon34			GCGGCCCCTTGCA		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.4262C>A	5.37:g.73205337C>A	ENSP00000412175:p.Pro1421His	198	0	0		270	108	0.4	NM_001080479	B2RXG7|B4E3K4|B5MDA3|B7ZW32|E9PC75|Q8NCM7|Q96E37|Q9H6L3|Q9H6W0	Missense_Mutation	SNP	ENST00000426542.2	37	CCDS54870.1	.	.	.	.	.	.	.	.	.	.	C	4.756	0.140576	0.09083	.	.	ENSG00000214944	ENST00000296794;ENST00000545377;ENST00000513042;ENST00000287898;ENST00000437974;ENST00000426542;ENST00000296799;ENST00000512883	T;T;T;T;T;T;T;T	0.21543	2.0;2.0;2.0;2.0;2.0;2.0;2.0;2.0	5.34	1.35	0.21983	.	0.670385	0.11270	U	0.581554	T	0.26011	0.0634	L	0.54323	1.7	0.09310	N	1	D;P;P;D;P	0.54047	0.964;0.836;0.836;0.963;0.898	P;P;P;P;P	0.52424	0.619;0.497;0.497;0.698;0.694	T	0.14008	-1.0488	10	0.56958	D	0.05	.	2.765	0.05317	0.2109:0.2926:0.0:0.4965	.	1108;1421;1421;341;1421	B5MDA3;Q8N1W1;E9PC75;D6RGZ3;Q8N1W1-4	.;RGNEF_HUMAN;.;.;.	H	1421;1421;1421;1377;1421;1421;1108;341	ENSP00000296794:P1421H;ENSP00000441913:P1421H;ENSP00000441436:P1421H;ENSP00000287898:P1377H;ENSP00000411459:P1421H;ENSP00000412175:P1421H;ENSP00000296799:P1108H;ENSP00000421081:P341H	ENSP00000287898:P1377H	P	+	2	0	RP11-428C6.1	73241093	0.038000	0.19896	0.001000	0.08648	0.010000	0.07245	1.372000	0.34261	0.246000	0.21394	-0.324000	0.08512	CCC	.	.	none		0.642	ARHGEF28-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000368975.1			A	73205337	C	A	73205337	3	1	27	1	0	0	0	0	1	0	0	0	13298	623	22	4	4392	4	RGNEF	5	73205337	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2387187	73205337	107709923	284	10735											
F2R	2149	hgsc.bcm.edu	37	chr5	76028669	76028669	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ggtttctggctgtggtgtatCccatgcagtccctctcctgg	3	14	12	12	0	2	0	0	0	2	0	5	0	4	0	3	4	1	4	3	4	1	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:76028669C>T	ENST00000319211.4	+	2	884	c.619C>T	c.(619-621)Ccc>Tcc	p.P207S		NM_001992.3	NP_001983.2	P25116	PAR1_HUMAN	coagulation factor II (thrombin) receptor	207					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPKK activity (GO:0000186)|anatomical structure morphogenesis (GO:0009653)|blood coagulation (GO:0007596)|connective tissue replacement involved in inflammatory response wound healing (GO:0002248)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|G-protein coupled receptor signaling pathway (GO:0007186)|homeostasis of number of cells within a tissue (GO:0048873)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of renin secretion into blood stream (GO:1900134)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|platelet dense granule organization (GO:0060155)|positive regulation of blood coagulation (GO:0030194)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|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 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 ERK1 and ERK2 cascade (GO:0070374)|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 JAK-STAT cascade (GO:0046427)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of Rho protein signal transduction (GO:0035025)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasoconstriction (GO:0045907)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of blood coagulation (GO:0030193)|regulation of interleukin-1 beta production (GO:0032651)|regulation of sensory perception of pain (GO:0051930)|release of sequestered calcium ion into cytosol (GO:0051209)|response to lipopolysaccharide (GO:0032496)|response to wounding (GO:0009611)|STAT protein import into nucleus (GO:0007262)|tyrosine phosphorylation of STAT protein (GO:0007260)	caveola (GO:0005901)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|platelet dense tubular network (GO:0031094)|postsynaptic membrane (GO:0045211)	G-protein alpha-subunit binding (GO:0001965)|G-protein beta-subunit binding (GO:0031681)|G-protein coupled receptor activity (GO:0004930)|receptor binding (GO:0005102)|thrombin receptor activity (GO:0015057)			NS(1)|breast(1)|endometrium(3)|kidney(1)|lung(7)|ovary(3)	16		all_lung(232;0.000414)|Lung NSC(167;0.0011)|Prostate(461;0.00955)|Ovarian(174;0.0129)		all cancers(79;4.43e-43)	Streptokinase(DB00086)	TGTGGTGTATCCCATGCAGTC	0.527																																					p.P207S		Atlas-SNP	.											.	F2R	58	.	0			c.C619T						PASS	.						184	181	182					5																	76028669		2203	4300	6503	SO:0001583	missense	2149	exon2			GTGTATCCCATGC	M62424	CCDS4032.1	5q13	2012-08-08			ENSG00000181104	ENSG00000181104		"GPCR / Class A : Protease activated receptors"	3537	protein-coding gene	gene with protein product		187930				8395910	Standard	NM_001992		Approved	TR, CF2R, PAR1, PAR-1	uc003ken.4	P25116	OTTHUMG00000131299	ENST00000319211.4:c.619C>T	5.37:g.76028669C>T	ENSP00000321326:p.Pro207Ser	249	0	0		250	49	0.196	NM_001992	Q53XV0|Q96RF7|Q9BUN4	Missense_Mutation	SNP	ENST00000319211.4	37	CCDS4032.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.913750	0.92178	.	.	ENSG00000181104	ENST00000319211	T	0.60920	0.15	5.07	5.07	0.68467	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.80849	0.4702	M	0.88181	2.935	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.84195	0.0447	10	0.87932	D	0	-44.8056	19.0012	0.92834	0.0:1.0:0.0:0.0	.	207	P25116	PAR1_HUMAN	S	207	ENSP00000321326:P207S	ENSP00000321326:P207S	P	+	1	0	F2R	76064425	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	7.502000	0.81614	2.786000	0.95864	0.561000	0.74099	CCC	.	.	none		0.527	F2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254068.2			T	76028669	C	T	76028669	3	4	27	1	0	0	0	0	1	0	0	0	5345	855	30	2	625	2	F2R	5	76028669	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2823332	76028669	104886591	285	10736											
DMGDH	29958	hgsc.bcm.edu	37	chr5	78326767	78326767	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accgctactctttgcataacCtgtttatactccgagcccac	9	12	5	15	2	1	0	0	0	1	0	2	1	2	0	4	0	5	3	4	0	4	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:78326767C>T	ENST00000255189.3	-	10	1600	c.1572G>A	c.(1570-1572)caG>caA	p.Q524Q	DMGDH_ENST00000540686.1_Silent_p.Q144Q|DMGDH_ENST00000380311.4_Silent_p.Q323Q	NM_013391.2	NP_037523.2	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase	524					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)		TTTGCATAACCTGTTTATACT	0.423																																					p.Q524Q		Atlas-SNP	.											.	DMGDH	88	.	0			c.G1572A						PASS	.						115	109	111					5																	78326767		2203	4300	6503	SO:0001819	synonymous_variant	29958	exon10			CATAACCTGTTTA	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.1572G>A	5.37:g.78326767C>T		104	0	0		133	85	0.639098	NM_013391	B2RBN0|B4E1J9	Silent	SNP	ENST00000255189.3	37	CCDS4044.1																																																																																			.	.	none		0.423	DMGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226963.3	NM_013391		T	78326767	C	T	78326767	2	4	27	1	0	0	0	0	0	0	0	1	4583	680	24	2		2	DMGDH	5	78326767	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2298098	78326767	102588493	286	10737											
CMYA5	202333	hgsc.bcm.edu	37	chr5	79027030	79027030	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acacaggaatctcaaaagaaAataatcaatgaggcatccca	20	6	6	9	0	2	2	2	1	1	1	4	3	3	3	1	2	0	1	1	2	7	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:79027030A>T	ENST00000446378.2	+	2	2473	c.2442A>T	c.(2440-2442)aaA>aaT	p.K814N		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	814					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)		CTCAAAAGAAAATAATCAATG	0.443																																					p.K814N		Atlas-SNP	.											.	CMYA5	643	.	0			c.A2442T						PASS	.						85	81	83					5																	79027030		1922	4130	6052	SO:0001583	missense	202333	exon2			AAAGAAAATAATC	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.2442A>T	5.37:g.79027030A>T	ENSP00000394770:p.Lys814Asn	139	0	0		100	20	0.2	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	A	12.71	2.018125	0.35606	.	.	ENSG00000164309	ENST00000446378	T	0.39229	1.09	5.41	-3.18	0.05186	.	0.937011	0.08936	N	0.872269	T	0.24431	0.0592	L	0.41236	1.265	0.09310	N	1	B	0.25441	0.126	B	0.22753	0.041	T	0.27331	-1.0077	10	0.29301	T	0.29	.	0.3705	0.00378	0.2947:0.1275:0.2331:0.3446	.	814	Q8N3K9	CMYA5_HUMAN	N	814	ENSP00000394770:K814N	ENSP00000394770:K814N	K	+	3	2	CMYA5	79062786	0.001000	0.12720	0.000000	0.03702	0.009000	0.06853	0.107000	0.15375	-0.130000	0.11599	0.528000	0.53228	AAA	.	.	none		0.443	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		T	79027030	A	T	79027030	3	4	27	1	0	0	0	0	1	0	0	0	3592	11	1	5	2448	5	CMYA5	5	79027030	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	700263	79027030	101888230	287	10738											
CMYA5	202333	hgsc.bcm.edu	37	chr5	79029025	79029025	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccagtaatcaaaacatcatcTtctcagcattcagataaatc	16	11	3	11	0	5	1	4	0	2	1	7	1	5	1	1	0	2	2	1	0	5	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:79029025T>C	ENST00000446378.2	+	2	4468	c.4437T>C	c.(4435-4437)tcT>tcC	p.S1479S		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1479					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)		AAACATCATCTTCTCAGCATT	0.388																																					p.S1479S		Atlas-SNP	.											CMYA5_ENST00000446378,NS,carcinoma,+1,2	CMYA5	643	2	0			c.T4437C						PASS	.						90	88	88					5																	79029025		1853	4095	5948	SO:0001819	synonymous_variant	202333	exon2			ATCATCTTCTCAG	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.4437T>C	5.37:g.79029025T>C		103	0	0		74	16	0.216216	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Silent	SNP	ENST00000446378.2	37	CCDS47238.1																																																																																			.	.	none		0.388	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		C	79029025	T	C	79029025	2	2	27	1	0	0	0	0	0	0	0	1	3592	1596	56	3		3	CMYA5	5	79029025	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	1995	79029025	101886235	288	10739											
ZFYVE16	9765	hgsc.bcm.edu	37	chr5	79735832	79735832	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcaagagtatgtgtagtctgCtatgaaactattagtaaagg	14	12	11	4	0	1	2	0	1	1	1	1	2	1	2	0	1	2	5	0	1	9	6	rs114761271	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:79735832C>T	ENST00000338008.5	+	4	2580	c.2400C>T	c.(2398-2400)tgC>tgT	p.C800C	ZFYVE16_ENST00000505560.1_Silent_p.C800C|ZFYVE16_ENST00000510158.1_Silent_p.C800C	NM_001284236.1|NM_014733.3	NP_001271165.1|NP_055548	Q7Z3T8	ZFY16_HUMAN	zinc finger, FYVE domain containing 16	800					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)		GTGTAGTCTGCTATGAAACTA	0.274													C|||	20	0.00399361	0.0	0.0043	5008	,	,		18426	0.0		0.0159	False		,,,				2504	0.001				p.C800C	Melanoma(150;1452 1854 16018 17851 37292)	Atlas-SNP	.											.	ZFYVE16	100	.	0			c.C2400T						PASS	.	C	,	15,4391	23.3+/-48.9	0,15,2188	149	167	161		2400,2400	5.5	1	5	dbSNP_132	161	160,8440	75.7+/-138.4	1,158,4141	no	coding-synonymous,coding-synonymous	ZFYVE16	NM_001105251.1,NM_014733.3	,	1,173,6329	TT,TC,CC		1.8605,0.3404,1.3455	,	800/1540,800/1540	79735832	175,12831	2203	4300	6503	SO:0001819	synonymous_variant	9765	exon5			AGTCTGCTATGAA	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.2400C>T	5.37:g.79735832C>T		79	0	0		67	23	0.343284	NM_001105251	O15023|Q5H9U2|Q7LAU7|Q86T69|Q8N5L3|Q8NEK3	Silent	SNP	ENST00000338008.5	37	CCDS4050.1																																																																																			C|0.986;T|0.014	0.014	strong		0.274	ZFYVE16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226982.2	NM_014733		T	79735832	C	T	79735832	2	4	27	1	0	0	0	0	0	0	0	1	17679	805	28	2		2	ZFYVE16	5	79735832	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	706807	79735832	101179428	289	10740											
VCAN	1462	hgsc.bcm.edu	37	chr5	82816190	82816190	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atagaagagaaagaacagaaAcactaataccagagatgaga	23	4	9	5	0	0	6	0	1	0	6	0	9	0	6	1	0	3	0	1	0	7	3	rs61754531	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:82816190A>G	ENST00000265077.3	+	7	2630	c.2065A>G	c.(2065-2067)Aca>Gca	p.T689A	VCAN_ENST00000342785.4_Missense_Mutation_p.T689A|VCAN_ENST00000512590.2_Missense_Mutation_p.T641A|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000343200.5_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	689	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)	AAGAACAGAAACACTAATACC	0.328													A|||	16	0.00319489	0.0008	0.0014	5008	,	,		20334	0.0		0.0139	False		,,,				2504	0.0				p.T689A		Atlas-SNP	.											.	VCAN	498	.	0			c.A2065G						PASS	.	A	,,ALA/THR,ALA/THR	8,4372		0,8,2182	51	53	52		,,2065,2065	1.6	0.2	5	dbSNP_129	52	90,8492		0,90,4201	yes	intron,intron,missense,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,,58,58	0,98,6383	GG,GA,AA		1.0487,0.1826,0.7561	,,possibly-damaging,possibly-damaging	,,689/1643,689/3397	82816190	98,12864	2190	4291	6481	SO:0001583	missense	1462	exon7			ACAGAAACACTAA	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.2065A>G	5.37:g.82816190A>G	ENSP00000265077:p.Thr689Ala	88	0	0		64	34	0.53125	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	13	0.005952380952380952	0	0.0	1	0.0027624309392265192	0	0.0	12	0.0158311345646438	A	0.784	-0.761296	0.02996	0.001826	0.010487	ENSG00000038427	ENST00000265077;ENST00000342785;ENST00000512590	T;T;T	0.25579	1.79;1.79;1.79	4.03	1.58	0.23477	.	0.518499	0.17701	N	0.164934	T	0.10637	0.0260	M	0.65975	2.015	0.09310	N	1	B;B	0.33940	0.433;0.307	B;B	0.27887	0.084;0.038	T	0.10590	-1.0623	10	0.23302	T	0.38	.	7.4005	0.26960	0.7289:0.0:0.2711:0.0	rs61754531	689;689	P13611-3;P13611	.;CSPG2_HUMAN	A	689;689;641	ENSP00000265077:T689A;ENSP00000342768:T689A;ENSP00000425959:T641A	ENSP00000265077:T689A	T	+	1	0	VCAN	82851946	0.018000	0.18449	0.153000	0.22517	0.029000	0.11900	1.202000	0.32271	0.336000	0.23639	0.533000	0.62120	ACA	A|0.993;G|0.007	0.007	strong		0.328	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		G	82816190	A	G	82816190	3	3	27	1	0	0	0	0	1	0	0	0	17153	43	2	3	2087	3	VCAN	5	82816190	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	3080358	82816190	98099070	290	10741											
CETN3	1070	hgsc.bcm.edu	37	chr5	89703535	89703535	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctttaattcatgataatctAttgcttcatctttgtctgta	9	20	4	8	0	5	1	2	1	3	0	5	1	5	1	1	0	1	2	1	0	4	9			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:89703535A>C	ENST00000283122.3	-	2	258	c.134T>G	c.(133-135)aTa>aGa	p.I45R	CETN3_ENST00000522565.1_Missense_Mutation_p.I45R|CETN3_ENST00000522083.1_Missense_Mutation_p.I45R|CETN3_ENST00000522842.1_Missense_Mutation_p.I45R|CETN3_ENST00000522864.1_Missense_Mutation_p.I45R	NM_004365.2	NP_004356.2	O15182	CETN3_HUMAN	centrin, EF-hand protein, 3	45	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				centrosome cycle (GO:0007098)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|photoreceptor connecting cilium (GO:0032391)	calcium ion binding (GO:0005509)			lung(3)	3		all_cancers(142;7.93e-09)|all_epithelial(76;2.13e-11)|Lung NSC(167;2.46e-05)|all_lung(232;3.25e-05)|Ovarian(174;0.00832)|Colorectal(57;0.122)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(54;1.42e-32)|Epithelial(54;1.45e-26)|all cancers(79;2.87e-23)		ATGATAATCTATTGCTTCATC	0.269																																					p.I45R		Atlas-SNP	.											.	CETN3	16	.	0			c.T134G						PASS	.						100	96	97					5																	89703535		2200	4291	6491	SO:0001583	missense	1070	exon2			TAATCTATTGCTT	Y12473	CCDS4066.1, CCDS75274.1	5q14.3	2013-01-10	2010-06-24		ENSG00000153140	ENSG00000153140		"EF-hand domain containing"	1868	protein-coding gene	gene with protein product	"CDC31 yeast homolog", "EF-hand superfamily member"	602907	"centrin, EF-hand protein, 3 (CDC31 yeast homolog)"			9256449	Standard	XM_006714521		Approved	CEN3	uc003kjo.3	O15182	OTTHUMG00000131326	ENST00000283122.3:c.134T>G	5.37:g.89703535A>C	ENSP00000283122:p.Ile45Arg	342	0	0		332	122	0.36747	NM_004365	Q53YD2|Q9BS23	Missense_Mutation	SNP	ENST00000283122.3	37	CCDS4066.1	.	.	.	.	.	.	.	.	.	.	A	19.53	3.845429	0.71603	.	.	ENSG00000153140	ENST00000283122;ENST00000522083;ENST00000522864;ENST00000522565;ENST00000522842	T;T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16;-1.16	5.65	4.5	0.54988	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.92156	0.7513	H	0.98738	4.315	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	D	0.93002	0.6424	10	0.87932	D	0	.	10.5918	0.45314	0.925:0.0:0.075:0.0	.	45	O15182	CETN3_HUMAN	R	45	ENSP00000283122:I45R;ENSP00000428259:I45R;ENSP00000430361:I45R;ENSP00000430409:I45R;ENSP00000429875:I45R	ENSP00000283122:I45R	I	-	2	0	CETN3	89739291	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.065000	0.93941	0.975000	0.38392	0.459000	0.35465	ATA	.	.	none		0.269	CETN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254097.1	NM_004365		C	89703535	A	C	89703535	3	2	27	1	0	0	0	0	1	0	0	0	3278	449	16	5	385	5	CETN3	5	89703535	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	6887345	89703535	91211725	291	10742											
GPR98	84059	hgsc.bcm.edu	37	chr5	90086955	90086955	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttgccctgtattcggatcGccagtcaatacttattgggc	8	14	9	10	2	1	0	1	0	0	0	3	1	1	1	2	2	2	1	2	2	4	6	rs41304892	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:90086955G>A	ENST00000405460.2	+	70	14405	c.14309G>A	c.(14308-14310)cGc>cAc	p.R4770H	GPR98_ENST00000425867.2_Missense_Mutation_p.R431H	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4770					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)		TATTCGGATCGCCAGTCAATA	0.453													G|||	7	0.00139776	0.0	0.0029	5008	,	,		19442	0.0		0.005	False		,,,				2504	0.0				p.R4770H		Atlas-SNP	.											.	GPR98	605	.	0			c.G14309A						PASS	.	G	HIS/ARG	1,3827		0,1,1913	105	95	98		14309	-7.1	0	5	dbSNP_127	98	50,8186		0,50,4068	yes	missense	GPR98	NM_032119.3	29	0,51,5981	AA,AG,GG		0.6071,0.0261,0.4227	benign	4770/6307	90086955	51,12013	1914	4118	6032	SO:0001583	missense	84059	exon70			CGGATCGCCAGTC	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.14309G>A	5.37:g.90086955G>A	ENSP00000384582:p.Arg4770His	255	1	0.00392157		269	115	0.427509	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	G	6.244	0.413073	0.11812	2.61E-4	0.006071	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.35236	1.32;1.32	5.77	-7.1	0.01547	.	1.043920	0.07336	N	0.879923	T	0.10423	0.0255	N	0.02539	-0.55	0.09310	N	1	B;B;B	0.10296	0.001;0.003;0.002	B;B;B	0.01281	0.0;0.0;0.0	T	0.36890	-0.9729	10	0.19147	T	0.46	.	16.6102	0.84881	0.6714:0.0:0.3286:0.0	rs41304892;rs61999354	431;4770;431	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	H	4770;4770;431	ENSP00000384582:R4770H;ENSP00000392618:R431H	ENSP00000296619:R4770H	R	+	2	0	GPR98	90122711	0.000000	0.05858	0.000000	0.03702	0.846000	0.48090	-0.098000	0.11024	-1.543000	0.01723	0.561000	0.74099	CGC	G|0.997;A|0.003	0.003	strong		0.453	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		A	90086955	G	A	90086955	3	1	27	1	0	0	0	0	1	0	0	0	6730	1087	38	1	14587	1	GPR98	5	90086955	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	383420	90086955	90828305	292	10743											
PCSK1	5122	hgsc.bcm.edu	37	chr5	95751785	95751785	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaccccgcatttgtgattatTtgcttgcatggcaatttctc	8	16	7	10	1	1	1	0	1	1	0	2	1	1	1	2	1	3	4	2	1	3	5	rs6232	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:95751785T>C	ENST00000311106.3	-	6	898	c.661A>G	c.(661-663)Aat>Gat	p.N221D	CTD-2337A12.1_ENST00000502645.2_RNA|PCSK1_ENST00000508626.1_Missense_Mutation_p.N174D	NM_000439.4|NM_001177876.1	NP_000430.3|NP_001171347.1	P29120	NEC1_HUMAN	proprotein convertase subtilisin/kexin type 1	221	Peptidase S8.		N -> D (associated with susceptibility to obesity; induces a 10.4% reduction of activity (P = 0.03) when compared to the wild-type enzyme; dbSNP:rs6232). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:18604207}.		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)"	TTGTGATTATTTGCTTGCATG	0.373													T|||	105	0.0209665	0.0023	0.0259	5008	,	,		20477	0.002		0.0328	False		,,,				2504	0.0501				p.N221D		Atlas-SNP	.											.	PCSK1	93	.	0			c.A661G	GRCh37	CM083013	PCSK1	M	rs6232	PASS	.	T	ASP/ASN,ASP/ASN	44,4362	45.3+/-79.5	0,44,2159	170	161	164	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	661,520	6.1	1	5	dbSNP_52	164	431,8169	132.5+/-190.1	9,413,3878	yes	missense,missense	PCSK1	NM_000439.4,NM_001177875.1	23,23	9,457,6037	CC,CT,TT		5.0116,0.9986,3.6522	benign,benign	221/754,174/707	95751785	475,12531	2203	4300	6503	SO:0001583	missense	5122	exon6			GATTATTTGCTTG		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.661A>G	5.37:g.95751785T>C	ENSP00000308024:p.Asn221Asp	170	0	0		168	80	0.47619	NM_000439	B7Z8T7|E9PHA1|P78478|Q92532	Missense_Mutation	SNP	ENST00000311106.3	37	CCDS4081.1	39	0.017857142857142856	1	0.0020325203252032522	7	0.019337016574585635	2	0.0034965034965034965	29	0.03825857519788918	T	16.91	3.253847	0.59212	0.009986	0.050116	ENSG00000175426	ENST00000311106;ENST00000508626	D;D	0.87650	-2.28;-2.28	6.06	6.06	0.98353	Peptidase S8/S53, subtilisin/kexin/sedolisin (3);	0.041262	0.85682	D	0.000000	T	0.57460	0.2055	M	0.62088	1.915	0.48040	D	0.999572	B	0.19445	0.036	B	0.23852	0.049	T	0.72760	-0.4196	10	0.36615	T	0.2	-28.6369	16.2708	0.82618	0.0:0.0:0.0:1.0	rs6232;rs17470938;rs57975876;rs6232	221	P29120	NEC1_HUMAN	D	221;174	ENSP00000308024:N221D;ENSP00000421600:N174D	ENSP00000308024:N221D	N	-	1	0	PCSK1	95777541	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.656000	0.67988	2.324000	0.78689	0.533000	0.62120	AAT	T|0.968;C|0.032	0.032	strong		0.373	PCSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242851.1	NM_000439		C	95751785	T	C	95751785	3	2	27	1	0	0	0	0	1	0	0	0	11609	1841	64	3	1636	3	PCSK1	5	95751785	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	5664830	95751785	85163475	293	10744											
SLCO4C1	353189	hgsc.bcm.edu	37	chr5	101592919	101592919	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aactccagatgtgaacagtgCaaacttcattgtgtttttac	12	14	7	8	0	1	2	1	1	0	1	2	2	2	2	1	0	5	2	1	0	4	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:101592919C>T	ENST00000310954.6	-	8	1655	c.1369G>A	c.(1369-1371)Gca>Aca	p.A457T		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)		GTGAACAGTGCAAACTTCATT	0.378																																					p.A457T		Atlas-SNP	.											.	SLCO4C1	113	.	0			c.G1369A						PASS	.						109	108	108					5																	101592919		2203	4300	6503	SO:0001583	missense	353189	exon8			ACAGTGCAAACTT	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.1369G>A	5.37:g.101592919C>T	ENSP00000309741:p.Ala457Thr	410	0	0		355	93	0.261972	NM_180991		Missense_Mutation	SNP	ENST00000310954.6	37	CCDS34205.1	.	.	.	.	.	.	.	.	.	.	C	13.99	2.402413	0.42613	.	.	ENSG00000173930	ENST00000310954	T	0.80393	-1.37	5.78	3.75	0.43078	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.276470	0.30959	N	0.008529	T	0.68375	0.2994	L	0.39566	1.225	0.31887	N	0.617758	B	0.11235	0.004	B	0.18871	0.023	T	0.62520	-0.6837	10	0.19147	T	0.46	.	6.7535	0.23499	0.4703:0.4272:0.0:0.1024	.	457	Q6ZQN7	SO4C1_HUMAN	T	457	ENSP00000309741:A457T	ENSP00000309741:A457T	A	-	1	0	SLCO4C1	101620818	0.994000	0.37717	0.995000	0.50966	0.725000	0.41563	0.657000	0.24963	1.381000	0.46364	0.585000	0.79938	GCA	.	.	none		0.378	SLCO4C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370332.1	NM_180991		T	101592919	C	T	101592919	3	4	27	1	0	0	0	0	1	0	0	0	14745	710	25	2	829	2	SLCO4C1	5	101592919	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	5841134	101592919	79322341	294	10745											
NUDT12	83594	hgsc.bcm.edu	37	chr5	102895169	102895169	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ttgacaattgatctgtcacaCctatagatggaagaaaaaat	17	11	7	6	0	2	4	1	2	1	2	2	5	2	5	1	1	0	0	1	1	7	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:102895169C>T	ENST00000230792.2	-	3	303	c.207G>A	c.(205-207)ggG>ggA	p.G69G	NUDT12_ENST00000507423.1_Splice_Site_p.M51I	NM_031438.2	NP_113626.1	Q9BQG2	NUD12_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 12	69					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)		ATCTGTCACACCTATAGATGG	0.323																																					p.G69G		Atlas-SNP	.											.	NUDT12	27	.	0			c.G207A						PASS	.						34	34	34					5																	102895169		2037	4218	6255	SO:0001630	splice_region_variant	83594	exon3			GTCACACCTATAG	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.207-1G>A	5.37:g.102895169C>T		122	0	0		74	18	0.243243	NM_031438	B3KUW2|Q8TAL7	Silent	SNP	ENST00000230792.2	37	CCDS4096.1	.	.	.	.	.	.	.	.	.	.	C	10.38	1.333868	0.24253	.	.	ENSG00000112874	ENST00000507423	T	0.34072	1.38	5.9	3.17	0.36434	.	.	.	.	.	T	0.29749	0.0743	.	.	.	0.19945	N	0.999946	B	0.09022	0.002	B	0.12837	0.008	T	0.24190	-1.0167	8	0.62326	D	0.03	.	10.3521	0.43943	0.0:0.7281:0.0:0.2719	.	51	E7EM93	.	I	51	ENSP00000424521:M51I	ENSP00000424521:M51I	M	-	3	0	NUDT12	102923068	1.000000	0.71417	0.998000	0.56505	0.533000	0.34776	1.488000	0.35551	0.399000	0.25367	-0.142000	0.14014	ATG	.	.	none		0.323	NUDT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250650.1	NM_031438	Silent	T	102895169	C	T	102895169	5	4	27	1	0	0	0	0	0	0	1	0	10737	521	18	2	1201	2	NUDT12	5	102895169	Splice_Site	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1302250	102895169	78020091	295	10746											
FER	2241	hgsc.bcm.edu	37	chr5	108294979	108294979	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacattcctcaacttatagaTcatcactatacaacaaaaca	19	10	1	11	0	3	1	3	0	0	1	4	1	4	1	1	0	5	0	1	0	9	5	rs34869483	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:108294979T>C	ENST00000281092.4	+	13	1971	c.1587T>C	c.(1585-1587)gaT>gaC	p.D529D	FER_ENST00000438717.2_Silent_p.D354D|FER_ENST00000536402.1_3'UTR	NM_005246.2	NP_005237.2	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	529	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				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)		AACTTATAGATCATCACTATA	0.363													T|||	30	0.00599042	0.0015	0.0043	5008	,	,		15833	0.0		0.0119	False		,,,				2504	0.0133				p.D529D	Colon(146;1051 1799 9836 27344 47401)	Atlas-SNP	.											.	FER	100	.	0			c.T1587C						PASS	.	T		14,4390	21.2+/-45.6	0,14,2188	138	131	133		1587	-7.7	0.9	5	dbSNP_126	133	193,8405	84.8+/-147.2	4,185,4110	no	coding-synonymous	FER	NM_005246.2		4,199,6298	CC,CT,TT		2.2447,0.3179,1.5921		529/823	108294979	207,12795	2202	4299	6501	SO:0001819	synonymous_variant	2241	exon13			TATAGATCATCAC	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.1587T>C	5.37:g.108294979T>C		138	0	0		108	64	0.592593	NM_005246	B2RCR4|B4DSQ2|H2FLB8	Silent	SNP	ENST00000281092.4	37	CCDS4098.1																																																																																			T|0.988;C|0.012	0.012	strong		0.363	FER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250664.1	NM_005246		C	108294979	T	C	108294979	2	2	27	1	0	0	0	0	0	0	0	1	5821	1432	50	3		3	FER	5	108294979	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	5399810	108294979	72620281	296	10747											
ZNF474	133923	hgsc.bcm.edu	37	chr5	121487969	121487969	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcccgcaggcctggattccGggtatgctatatctgtggcc	5	10	14	12	2	1	0	0	0	1	0	2	1	2	1	4	5	1	3	4	5	3	4	rs72786994	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:121487969G>A	ENST00000296600.4	+	2	667	c.284G>A	c.(283-285)cGg>cAg	p.R95Q	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	95							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)		CCTGGATTCCGGGTATGCTAT	0.502													G|||	52	0.0103834	0.0008	0.0086	5008	,	,		17148	0.0		0.0179	False		,,,				2504	0.0276				p.R95Q		Atlas-SNP	.											.	ZNF474	43	.	0			c.G284A						PASS	.	G	GLN/ARG	15,4391	23.3+/-48.9	0,15,2188	74	81	79		284	-1.7	0.1	5	dbSNP_130	79	171,8429	78.6+/-141.3	1,169,4130	yes	missense	ZNF474	NM_207317.1	43	1,184,6318	AA,AG,GG		1.9884,0.3404,1.4301	probably-damaging	95/365	121487969	186,12820	2203	4300	6503	SO:0001583	missense	133923	exon2			GATTCCGGGTATG	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.284G>A	5.37:g.121487969G>A	ENSP00000296600:p.Arg95Gln	104	0	0		91	43	0.472527	NM_207317	A8K4M0|Q96M07	Missense_Mutation	SNP	ENST00000296600.4	37	CCDS4130.1	16	0.007326007326007326	0	0.0	3	0.008287292817679558	0	0.0	13	0.017150395778364115	G	10.15	1.271155	0.23221	0.003404	0.019884	ENSG00000164185	ENST00000296600	T	0.51325	0.71	5.58	-1.72	0.08107	.	3.416030	0.00792	N	0.001340	T	0.30230	0.0758	L	0.52011	1.625	0.19775	N	0.999959	P	0.51147	0.942	P	0.47470	0.548	T	0.34551	-0.9824	10	0.27082	T	0.32	1.9702	6.2544	0.20865	0.5859:0.0:0.2818:0.1323	.	95	Q6S9Z5	ZN474_HUMAN	Q	95	ENSP00000296600:R95Q	ENSP00000296600:R95Q	R	+	2	0	ZNF474	121515868	0.019000	0.18553	0.146000	0.22360	0.062000	0.15995	-0.172000	0.09868	-0.163000	0.10946	-0.123000	0.14984	CGG	G|0.988;A|0.012	0.012	strong		0.502	ZNF474-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250883.2	NM_207317		A	121487969	G	A	121487969	3	1	27	1	0	0	0	0	1	0	0	0	17947	1116	39	1	286	1	ZNF474	5	121487969	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	13192990	121487969	59427291	297	10748											
ADAMTS19	171019	hgsc.bcm.edu	37	chr5	128796860	128796860	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctgcgctctggcgccgggagCcggtggacccggctggcggc	2	5	19	15	6	1	0	0	0	1	0	1	2	1	2	3	7	2	2	3	7	0	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:128796860C>A	ENST00000274487.4	+	2	284	c.139C>A	c.(139-141)Ccg>Acg	p.P47T	ADAMTS19-AS1_ENST00000502827.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	47						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)		GCGCCGGGAGCCGGTGGACCC	0.761																																					p.P47T		Atlas-SNP	.											.	ADAMTS19	216	.	0			c.C139A						PASS	.						1	1	1					5																	128796860		985	2022	3007	SO:0001583	missense	171019	exon2			CGGGAGCCGGTGG	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.139C>A	5.37:g.128796860C>A	ENSP00000274487:p.Pro47Thr	8	0	0		14	13	0.928571	NM_133638		Missense_Mutation	SNP	ENST00000274487.4	37	CCDS4146.1	.	.	.	.	.	.	.	.	.	.	C	13.54	2.266920	0.40095	.	.	ENSG00000145808	ENST00000274487	T	0.64618	-0.11	3.54	2.64	0.31445	.	0.215910	0.23754	N	0.044896	T	0.35566	0.0936	N	0.08118	0	0.24389	N	0.994758	B	0.24186	0.099	B	0.17098	0.017	T	0.16041	-1.0416	9	.	.	.	.	8.9587	0.35834	0.0:0.8863:0.0:0.1137	.	47	Q8TE59	ATS19_HUMAN	T	47	ENSP00000274487:P47T	.	P	+	1	0	ADAMTS19	128824759	1.000000	0.71417	1.000000	0.80357	0.554000	0.35429	1.324000	0.33712	1.043000	0.40175	0.455000	0.32223	CCG	.	.	none		0.761	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		A	128796860	C	A	128796860	3	1	27	1	0	0	0	0	1	0	0	0	264	739	26	4	145	4	ADAMTS19	5	128796860	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	7308891	128796860	52118400	298	10749											
HSPA4	3308	hgsc.bcm.edu	37	chr5	132412424	132412424	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taaatcacttctgtgaagaaTttgggaagaaatacaagcta	17	11	8	5	0	2	3	1	1	1	2	2	4	2	4	0	1	2	1	0	1	9	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:132412424T>C	ENST00000304858.2	+	7	1031	c.742T>C	c.(742-744)Ttt>Ctt	p.F248L	HSPA4_ENST00000504328.1_3'UTR	NM_002154.3	NP_002145.3	P34932	HSP74_HUMAN	heat shock 70kDa protein 4	248					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)			CTGTGAAGAATTTGGGAAGAA	0.373																																					p.F248L	Colon(114;1299 1588 6063 12302 48757)	Atlas-SNP	.											.	HSPA4	68	.	0			c.T742C						PASS	.						106	108	107					5																	132412424		2203	4300	6503	SO:0001583	missense	3308	exon7			GAAGAATTTGGGA	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.742T>C	5.37:g.132412424T>C	ENSP00000302961:p.Phe248Leu	166	0	0		109	19	0.174312	NM_002154	O95756|Q2TAL4|Q9BUK9	Missense_Mutation	SNP	ENST00000304858.2	37	CCDS4166.1	.	.	.	.	.	.	.	.	.	.	T	34	5.399231	0.96030	.	.	ENSG00000170606	ENST00000304858;ENST00000537974	T	0.01295	5.04	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.12263	0.0298	M	0.91561	3.22	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	T	0.00403	-1.1761	10	0.87932	D	0	-10.5177	16.1924	0.82000	0.0:0.0:0.0:1.0	.	248	P34932	HSP74_HUMAN	L	248	ENSP00000302961:F248L	ENSP00000302961:F248L	F	+	1	0	HSPA4	132440323	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.565000	0.82337	2.287000	0.76781	0.482000	0.46254	TTT	.	.	none		0.373	HSPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251011.1	NM_002154, NM_198431		C	132412424	T	C	132412424	3	2	27	1	0	0	0	0	1	0	0	0	7421	1493	52	3	768	3	HSPA4	5	132412424	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	3615564	132412424	48502836	299	10750											
H2AFY	9555	hgsc.bcm.edu	37	chr5	134670756	134670756	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tacaccgttttgatggaagaGgacattgtagacacgaagta	14	10	11	6	2	0	3	0	1	0	2	0	6	0	5	1	2	1	3	1	2	5	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:134670756G>C	ENST00000511689.1	-	9	1622	c.1029C>G	c.(1027-1029)tcC>tcG	p.S343S	H2AFY_ENST00000510038.1_Silent_p.S343S|H2AFY_ENST00000423969.2_Silent_p.S171S|CTC-349C3.1_ENST00000432382.3_Intron|H2AFY_ENST00000312469.4_Silent_p.S340S|H2AFY_ENST00000304332.4_Silent_p.S342S|H2AFY_ENST00000512507.1_5'UTR	NM_001040158.1|NM_138610.2	NP_001035248.1|NP_613258.2	O75367	H2AY_HUMAN	H2A histone family, member Y	343	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				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)			TGATGGAAGAGGACATTGTAG	0.478																																					p.S343S		Atlas-SNP	.											.	H2AFY	61	.	0			c.C1029G						PASS	.						142	129	133					5																	134670756		2203	4300	6503	SO:0001819	synonymous_variant	9555	exon9			GGAAGAGGACATT	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.1029C>G	5.37:g.134670756G>C		250	0	0		236	70	0.29661	NM_138610	O75377|Q503A8|Q7Z5E3|Q96D41|Q9H8P3|Q9UP96	Silent	SNP	ENST00000511689.1	37	CCDS4185.1																																																																																			.	.	none		0.478	H2AFY-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251196.3	NM_004893		C	134670756	G	C	134670756	2	2	27	1	0	0	0	0	0	0	0	1	6938	987	35	4		4	H2AFY	5	134670756	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2258332	134670756	46244504	300	10751											
SPOCK1	6695	hgsc.bcm.edu	37	chr5	136834138	136834138	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actggtcattgtctaggaaaTtgccgtggttggggcccgcg	6	11	15	9	3	2	0	1	0	1	0	2	1	2	1	2	5	1	1	2	5	2	4	rs111393448	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:136834138T>C	ENST00000394945.1	-	2	279	c.110A>G	c.(109-111)aAt>aGt	p.N37S	SPOCK1_ENST00000282223.7_Missense_Mutation_p.N37S	NM_004598.3	NP_004589.1	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1	37					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)			GTCTAGGAAATTGCCGTGGTT	0.682													T|||	19	0.00379393	0.0	0.0058	5008	,	,		9286	0.0		0.0129	False		,,,				2504	0.002				p.N37S		Atlas-SNP	.											.	SPOCK1	58	.	0			c.A110G						PASS	.	T	SER/ASN	9,4397		0,9,2194	22	21	22		110	3.7	1	5	dbSNP_132	22	106,8492		3,100,4196	yes	missense	SPOCK1	NM_004598.3	46	3,109,6390	CC,CT,TT		1.2328,0.2043,0.8843	benign	37/440	136834138	115,12889	2203	4299	6502	SO:0001583	missense	6695	exon2			AGGAAATTGCCGT	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.110A>G	5.37:g.136834138T>C	ENSP00000378401:p.Asn37Ser	43	0	0		40	23	0.575	NM_004598	B3KSW3|Q59EW0|Q8N630|Q9UCL8	Missense_Mutation	SNP	ENST00000394945.1	37	CCDS4191.1	14	0.00641025641025641	0	0.0	2	0.0055248618784530384	0	0.0	12	0.0158311345646438	T	24.2	4.510460	0.85389	0.002043	0.012328	ENSG00000152377	ENST00000394945;ENST00000282223;ENST00000505690	T;T;T	0.58940	0.3;0.3;0.34	3.66	3.66	0.41972	.	0.344437	0.23803	N	0.044419	T	0.33498	0.0865	L	0.51914	1.62	0.27215	N	0.959807	B	0.15930	0.015	B	0.14578	0.011	T	0.44112	-0.9349	10	0.56958	D	0.05	.	10.3639	0.44012	0.0:0.0:0.0:1.0	.	37	Q08629	TICN1_HUMAN	S	37	ENSP00000378401:N37S;ENSP00000282223:N37S;ENSP00000424517:N37S	ENSP00000282223:N37S	N	-	2	0	SPOCK1	136862037	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.481000	0.53179	1.439000	0.47511	0.379000	0.24179	AAT	T|0.991;C|0.009	0.009	strong		0.682	SPOCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251222.1	NM_004598		C	136834138	T	C	136834138	3	2	27	1	0	0	0	0	1	0	0	0	15094	1493	52	3	1249	3	SPOCK1	5	136834138	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	2163382	136834138	44081122	301	10752											
FAM13B	51306	hgsc.bcm.edu	37	chr5	137275968	137275968	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agaacttcaagaagcctaagCttggctttaattttcttgta	12	15	7	7	0	2	2	1	0	1	2	2	2	2	2	1	1	3	3	1	1	6	9	rs201094212	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:137275968C>G	ENST00000033079.3	-	23	3145	c.2694G>C	c.(2692-2694)aaG>aaC	p.K898N	FAM13B_ENST00000425075.2_Missense_Mutation_p.K774N|PKD2L2_ENST00000290431.5_3'UTR|FAM13B_ENST00000420893.2_Missense_Mutation_p.K870N|PKD2L2_ENST00000508638.1_3'UTR|PKD2L2_ENST00000508883.1_Intron|PKD2L2_ENST00000502810.1_3'UTR	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	898					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						GAAGCCTAAGCTTGGCTTTAA	0.348													C|||	2	0.000399361	0.0	0.0014	5008	,	,		18964	0.0		0.001	False		,,,				2504	0.0				p.K898N		Atlas-SNP	.											FAM13B,NS,carcinoma,0,2	FAM13B	46	2	0			c.G2694C						PASS	.						112	110	111					5																	137275968		2203	4300	6503	SO:0001583	missense	51306	exon23			CCTAAGCTTGGCT	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.2694G>C	5.37:g.137275968C>G	ENSP00000033079:p.Lys898Asn	197	0	0		163	83	0.509202	NM_016603	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Missense_Mutation	SNP	ENST00000033079.3	37	CCDS4195.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.29	3.591185	0.66219	.	.	ENSG00000031003	ENST00000033079;ENST00000425075;ENST00000420893	T;T;T	0.37411	2.24;1.2;2.12	5.37	1.84	0.25277	.	0.000000	0.85682	D	0.000000	T	0.52741	0.1753	M	0.72894	2.215	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;0.999	T	0.51028	-0.8757	10	0.87932	D	0	-13.3199	7.0159	0.24887	0.0:0.4207:0.0:0.5793	.	774;870;898	G3V0H9;Q9NYF5-2;Q9NYF5	.;.;FA13B_HUMAN	N	898;774;870	ENSP00000033079:K898N;ENSP00000394669:K774N;ENSP00000388521:K870N	ENSP00000033079:K898N	K	-	3	2	FAM13B	137303867	0.468000	0.25839	1.000000	0.80357	0.997000	0.91878	-0.247000	0.08866	0.446000	0.26666	0.591000	0.81541	AAG	C|0.999;G|0.001	0.001	strong		0.348	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1			G	137275968	C	G	137275968	3	3	27	1	0	0	0	0	1	0	0	0	5458	796	28	4	57	4	FAM13B	5	137275968	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	441830	137275968	43639292	302	10753											
PCDHA10	56139	hgsc.bcm.edu	37	chr5	140235875	140235875	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggaggtaaatctgcagaatgGcattttgtttgtgaattctc	10	15	11	5	0	2	2	0	1	2	1	3	3	2	3	0	3	1	4	0	3	4	5	rs143002904	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140235875G>A	ENST00000307360.5	+	1	242	c.242G>A	c.(241-243)gGc>gAc	p.G81D	PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000506939.2_Missense_Mutation_p.G81D|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	81	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)			CTGCAGAATGGCATTTTGTTT	0.622													.|||	19	0.00379393	0.0	0.0029	5008	,	,		17477	0.0		0.0169	False		,,,				2504	0.0				p.G81D		Atlas-SNP	.											.	PCDHA10	358	.	0			c.G242A						PASS	.	G	,ASP/GLY,,,,,,,,,,,ASP/GLY,ASP/GLY	8,4386	11.4+/-27.6	1,6,2190	104	113	110		,242,,,,,,,,,,,242,242	4.3	1	5	dbSNP_134	110	49,8493	27.4+/-76.7	2,45,4224	no	intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,missense	PCDHA9,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031859.1,NM_031860.1	,94,,,,,,,,,,,94,94	3,51,6414	AA,AG,GG		0.5736,0.1821,0.4406	,,,,,,,,,,,,,	,81/949,,,,,,,,,,,81/845,81/686	140235875	57,12879	2197	4271	6468	SO:0001583	missense	56139	exon1			AGAATGGCATTTT	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.242G>A	5.37:g.140235875G>A	ENSP00000304234:p.Gly81Asp	91	0	0		31	31	1	NM_031859	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	37	CCDS54921.1	11	0.005036630036630037	0	0.0	0	0.0	0	0.0	11	0.014511873350923483	G	23.3	4.399977	0.83120	0.001821	0.005736	ENSG00000250120	ENST00000506939;ENST00000307360	T;T	0.40476	1.03;1.03	4.27	4.27	0.50696	Cadherin, N-terminal (1);Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.74876	0.3774	H	0.99590	4.645	0.51012	D	0.999902	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.88448	0.3047	9	0.87932	D	0	.	17.329	0.87258	0.0:0.0:1.0:0.0	.	81;81;81	Q9Y5I2-3;Q9Y5I2;Q9Y5I2-2	.;PCDAA_HUMAN;.	D	81	ENSP00000421030:G81D;ENSP00000304234:G81D	ENSP00000304234:G81D	G	+	2	0	PCDHA10	140216059	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.573000	0.82421	2.391000	0.81399	0.556000	0.70494	GGC	G|0.995;A|0.005	0.005	strong		0.622	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		A	140235875	G	A	140235875	3	1	27	1	0	0	0	0	1	0	0	0	11529	1203	42	2	244	2	PCDHA10	5	140235875	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2959907	140235875	40679385	303	10754											
PCDHA11	56138	hgsc.bcm.edu	37	chr5	140249884	140249884	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcccttcaagctggtgtccaCcttcaagaattactactcgt	9	13	6	13	1	2	1	2	0	0	1	5	1	4	1	3	1	3	1	3	1	5	4	rs62622798	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140249884C>T	ENST00000398640.2	+	1	1196	c.1196C>T	c.(1195-1197)aCc>aTc	p.T399I	PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529859.1_Intron	NM_018902.3	NP_061725.1	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11	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)			breast(1)|lung(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGTGTCCACCTTCAAGAAT	0.602													.|||	62	0.0123802	0.0008	0.0461	5008	,	,		21105	0.0		0.0149	False		,,,				2504	0.0143				p.T399I		Atlas-SNP	.											.	PCDHA11	209	.	0			c.C1196T						PASS	.	C	,,ILE/THR,,,,,,,,,,,,ILE/THR	34,4372	40.0+/-72.8	0,34,2169	146	134	138		,,1196,,,,,,,,,,,,1196	4.8	1	5	dbSNP_129	138	234,8366	95.6+/-157.4	1,232,4067	no	intron,intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHA9,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018902.3,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031861.1	,,89,,,,,,,,,,,,89	1,266,6236	TT,TC,CC		2.7209,0.7717,2.0606	,,,,,,,,,,,,,,	,,399/950,,,,,,,,,,,,399/811	140249884	268,12738	2203	4300	6503	SO:0001583	missense	56138	exon1			TGTCCACCTTCAA	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.1196C>T	5.37:g.140249884C>T	ENSP00000381636:p.Thr399Ile	239	0	0		178	80	0.449438	NM_018902	B2RN58|O75279	Missense_Mutation	SNP	ENST00000398640.2	37	CCDS47284.1	26	0.011904761904761904	0	0.0	13	0.03591160220994475	0	0.0	13	0.017150395778364115	C	13.18	2.161051	0.38119	0.007717	0.027209	ENSG00000249158	ENST00000398640	T	0.29142	1.58	5.7	4.81	0.61882	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.15522	0.0374	L	0.29908	0.895	0.24765	N	0.992905	D;D	0.76494	0.998;0.999	D;D	0.76575	0.986;0.988	T	0.17410	-1.0370	9	0.87932	D	0	.	15.4515	0.75277	0.14:0.86:0.0:0.0	rs62622798	399;399	Q9Y5I1-2;Q9Y5I1	.;PCDAB_HUMAN	I	399	ENSP00000381636:T399I	ENSP00000381636:T399I	T	+	2	0	PCDHA11	140230068	0.030000	0.19436	0.997000	0.53966	0.560000	0.35617	3.034000	0.49751	1.338000	0.45544	0.563000	0.77884	ACC	C|0.989;T|0.011	0.011	strong		0.602	PCDHA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372885.2	NM_018902		T	140249884	C	T	140249884	3	4	27	1	0	0	0	0	1	0	0	0	11530	507	18	2	1198	2	PCDHA11	5	140249884	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	14009	140249884	40665376	304	10755											
PCDHB8	56128	hgsc.bcm.edu	37	chr5	140559058	140559058	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcgccacagacagagactcGggcaccaacgcccaggtcac	12	2	11	16	3	1	2	1	0	0	2	2	3	1	2	3	2	2	1	3	2	1	0	rs17844495		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140559058G>A	ENST00000239444.2	+	1	1688	c.1443G>A	c.(1441-1443)tcG>tcA	p.S481S	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	481	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)|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)			ACAGAGACTCGGGCACCAACG	0.662																																					p.S481S		Atlas-SNP	.											.	PCDHB8	199	.	0			c.G1443A						PASS	.						85	131	115					5																	140559058		2203	4296	6499	SO:0001819	synonymous_variant	56128	exon1			AGACTCGGGCACC	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.1443G>A	5.37:g.140559058G>A		228	0	0		261	41	0.157088	NM_019120	B9EGV1	Silent	SNP	ENST00000239444.2	37	CCDS4250.1																																																																																			G|0.680;A|0.320	0.320	strong		0.662	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120		A	140559058	G	A	140559058	2	1	27	1	0	0	0	0	0	0	0	1	11557	1103	39	1		1	PCDHB8	5	140559058	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	309174	140559058	40356202	305	10756											
PCDHB8	56128	hgsc.bcm.edu	37	chr5	140559148	140559148	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtctccatcaacacagacaaCggccacctgttcgccctcag	10	7	7	17	2	3	1	2	0	1	1	5	1	3	1	4	1	2	1	4	1	2	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140559148C>T	ENST00000239444.2	+	1	1778	c.1533C>T	c.(1531-1533)aaC>aaT	p.N511N	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	511	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)|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)			ACACAGACAACGGCCACCTGT	0.677																																					p.N511N		Atlas-SNP	.											.	PCDHB8	199	.	0			c.C1533T						PASS	.						94	148	130					5																	140559148		2203	4298	6501	SO:0001819	synonymous_variant	56128	exon1			AGACAACGGCCAC	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.1533C>T	5.37:g.140559148C>T		305	0	0		423	50	0.118203	NM_019120	B9EGV1	Silent	SNP	ENST00000239444.2	37	CCDS4250.1																																																																																			.	.	none		0.677	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120		T	140559148	C	T	140559148	2	4	27	1	0	0	0	0	0	0	0	1	11557	535	19	1		1	PCDHB8	5	140559148	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	90	140559148	40356112	306	10757											
PCDHB12	56124	hgsc.bcm.edu	37	chr5	140590139	140590139	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcgcgtgctggtgctggacGccaacgacaactcgcccttc	6	8	12	15	5	0	0	0	0	0	0	2	2	0	1	2	2	5	2	2	2	2	1	rs145232861	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140590139G>A	ENST00000239450.2	+	1	1849	c.1660G>A	c.(1660-1662)Gcc>Acc	p.A554T	PCDHB12_ENST00000541609.1_Missense_Mutation_p.A217T	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	554	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(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)			GGTGCTGGACGCCAACGACAA	0.711													G|||	11	0.00219649	0.0	0.0014	5008	,	,		16609	0.0		0.0099	False		,,,				2504	0.0				p.A554T		Atlas-SNP	.											.	PCDHB12	179	.	0			c.G1660A						PASS	.	G	THR/ALA	6,4392		0,6,2193	23	27	26		1660	2.5	1	5	dbSNP_134	26	29,8559		0,29,4265	no	missense	PCDHB12	NM_018932.3	58	0,35,6458	AA,AG,GG		0.3377,0.1364,0.2695	benign	554/796	140590139	35,12951	2199	4294	6493	SO:0001583	missense	56124	exon1			CTGGACGCCAACG	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.1660G>A	5.37:g.140590139G>A	ENSP00000239450:p.Ala554Thr	158	0	0		126	73	0.579365	NM_018932	B4DDU1	Missense_Mutation	SNP	ENST00000239450.2	37	CCDS4254.1	.	.	.	.	.	.	.	.	.	.	G	8.941	0.965816	0.18583	0.001364	0.003377	ENSG00000120328	ENST00000541609;ENST00000239450;ENST00000507840	T;T	0.03181	4.02;4.02	3.41	2.5	0.30297	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.02533	0.0077	N	0.13352	0.335	0.09310	N	0.999998	B	0.34015	0.435	B	0.23716	0.048	T	0.46442	-0.9191	9	0.40728	T	0.16	.	12.3896	0.55350	0.0:0.481:0.519:0.0	.	554	Q9Y5F1	PCDBC_HUMAN	T	217;554;174	ENSP00000440199:A217T;ENSP00000239450:A554T	ENSP00000239450:A554T	A	+	1	0	PCDHB12	140570323	0.000000	0.05858	0.953000	0.39169	0.995000	0.86356	0.135000	0.15952	0.525000	0.28522	0.485000	0.47835	GCC	G|0.875;A|0.125	0.125	strong		0.711	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932		A	140590139	G	A	140590139	3	1	27	1	0	0	0	0	1	0	0	0	11546	1087	38	1	1662	1	PCDHB12	5	140590139	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	30991	140590139	40325121	307	10758											
PCDHB14	56122	hgsc.bcm.edu	37	chr5	140604621	140604621	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggacaatggccacctgtttgCcctcaggtcgctggactacg	7	9	12	13	2	1	0	1	0	0	0	2	2	1	2	3	4	2	2	3	4	2	2	rs144421802	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140604621C>T	ENST00000239449.4	+	1	1544	c.1544C>T	c.(1543-1545)gCc>gTc	p.A515V	PCDHB14_ENST00000515856.2_Missense_Mutation_p.A362V	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	515	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)			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)			CACCTGTTTGCCCTCAGGTCG	0.677													c|||	17	0.00339457	0.0	0.0014	5008	,	,		16912	0.0		0.007	False		,,,				2504	0.0092				p.A515V	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.C1544T						PASS	.	C	VAL/ALA	8,4398		0,8,2195	96	100	99		1544	4.2	1	5	dbSNP_134	99	98,8502		0,98,4202	no	missense	PCDHB14	NM_018934.2	64	0,106,6397	TT,TC,CC		1.1395,0.1816,0.815	benign	515/799	140604621	106,12900	2203	4300	6503	SO:0001583	missense	56122	exon1			TGTTTGCCCTCAG	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.1544C>T	5.37:g.140604621C>T	ENSP00000239449:p.Ala515Val	159	0	0		169	92	0.544379	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Missense_Mutation	SNP	ENST00000239449.4	37	CCDS4256.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	-	14.32	2.499118	0.44455	0.001816	0.011395	ENSG00000120327	ENST00000515856;ENST00000239449	T;T	0.01647	4.71;4.71	4.15	4.15	0.48705	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.02083	0.0065	L	0.41124	1.26	0.35681	D	0.814049	P	0.45957	0.869	B	0.43838	0.433	T	0.55835	-0.8078	9	0.62326	D	0.03	.	16.4819	0.84160	0.0:1.0:0.0:0.0	.	515	Q9Y5E9	PCDBE_HUMAN	V	362;515	ENSP00000444518:A362V;ENSP00000239449:A515V	ENSP00000239449:A515V	A	+	2	0	PCDHB14	140584805	0.027000	0.19231	0.956000	0.39512	0.165000	0.22458	1.595000	0.36708	2.048000	0.60808	0.556000	0.70494	GCC	C|0.994;T|0.006	0.006	strong		0.677	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934		T	140604621	C	T	140604621	3	4	27	1	0	0	0	0	1	0	0	0	11548	739	26	2	1546	2	PCDHB14	5	140604621	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	14482	140604621	40310639	308	10759											
PCDHGB4	8641	hgsc.bcm.edu	37	chr5	140769334	140769334	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcgaagtgcgcacagcgcGtgccttaggcgacagggacg	8	4	18	11	6	0	0	0	0	0	0	0	3	0	1	1	3	3	1	1	3	2	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:140769334G>C	ENST00000519479.1	+	1	1883	c.1883G>C	c.(1882-1884)cGt>cCt	p.R628P	PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA7_ENST00000518325.1_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	628	Cadherin 6. {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)			CGCACAGCGCGTGCCTTAGGC	0.692																																					p.R628P		Atlas-SNP	.											.	PCDHGB4	125	.	0			c.G1883C						PASS	.						36	41	39					5																	140769334		2128	4243	6371	SO:0001583	missense	8641	exon1			CAGCGCGTGCCTT	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.1883G>C	5.37:g.140769334G>C	ENSP00000428288:p.Arg628Pro	38	0	0		36	11	0.305556	NM_032098	O15099|Q2M267|Q9UN64	Missense_Mutation	SNP	ENST00000519479.1	37	CCDS54928.1	.	.	.	.	.	.	.	.	.	.	.	15.68	2.906359	0.52333	.	.	ENSG00000253953	ENST00000519479	T	0.54279	0.58	5.05	5.05	0.67936	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.78528	0.4297	H	0.94345	3.525	0.28002	N	0.935256	D;D	0.56521	0.97;0.976	P;P	0.57911	0.793;0.829	T	0.76838	-0.2811	9	0.87932	D	0	.	18.4161	0.90571	0.0:0.0:1.0:0.0	.	628;628	Q9UN71-2;Q9UN71	.;PCDGG_HUMAN	P	628	ENSP00000428288:R628P	ENSP00000428288:R628P	R	+	2	0	PCDHGB4	140749518	0.784000	0.28713	0.057000	0.19452	0.031000	0.12232	4.360000	0.59455	2.503000	0.84419	0.563000	0.77884	CGT	.	.	none		0.692	PCDHGB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374745.1	NM_003736		C	140769334	G	C	140769334	3	2	27	1	0	0	0	0	1	0	0	0	11574	1145	40	4	1885	4	PCDHGB4	5	140769334	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	164713	140769334	40145926	309	10760											
FCHSD1	89848	hgsc.bcm.edu	37	chr5	141026182	141026182	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cacctcacccgatgcccatgGttctggatcttgtagtcacg	7	11	9	14	2	4	0	2	0	2	0	4	2	4	1	3	2	1	2	3	2	1	3	rs3749760	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:141026182G>T	ENST00000435817.2	-	11	1082	c.1032C>A	c.(1030-1032)aaC>aaA	p.N344K	FCHSD1_ENST00000522126.1_Missense_Mutation_p.N268K|FCHSD1_ENST00000522783.1_Missense_Mutation_p.N342K|FCHSD1_ENST00000523856.1_5'UTR	NM_033449.2	NP_258260.1	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	344			N -> K (in dbSNP:rs3749760).						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)			GATGCCCATGGTTCTGGATCT	0.592													G|||	65	0.0129792	0.0015	0.0259	5008	,	,		19308	0.0258		0.0119	False		,,,				2504	0.0072				p.N344K		Atlas-SNP	.											.	FCHSD1	51	.	0			c.C1032A						PASS	.	G	LYS/ASN	8,3962		0,8,1977	33	37	36		1032	2.2	1	5	dbSNP_107	36	131,8141		2,127,4007	yes	missense	FCHSD1	NM_033449.2	94	2,135,5984	TT,TG,GG		1.5837,0.2015,1.1354	benign	344/691	141026182	139,12103	1985	4136	6121	SO:0001583	missense	89848	exon11			CCCATGGTTCTGG	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.1032C>A	5.37:g.141026182G>T	ENSP00000399259:p.Asn344Lys	88	0	0		63	32	0.507937	NM_033449	Q6UX75|Q86Y77|Q9NXX8	Missense_Mutation	SNP	ENST00000435817.2	37	CCDS47295.1	39	0.017857142857142856	3	0.006097560975609756	8	0.022099447513812154	18	0.03146853146853147	10	0.013192612137203167	G	15.12	2.738413	0.49045	0.002015	0.015837	ENSG00000197948	ENST00000435817;ENST00000522126;ENST00000522783	T;T;T	0.39997	1.84;1.05;1.44	5.47	2.22	0.28083	.	0.849984	0.10666	N	0.648098	T	0.09069	0.0224	N	0.22421	0.69	0.80722	D	1	B	0.16396	0.017	B	0.20184	0.028	T	0.08146	-1.0736	10	0.02654	T	1	-17.3402	9.4986	0.39004	0.2876:0.0:0.7124:0.0	rs3749760;rs52802373;rs3749760	344	Q86WN1	FCSD1_HUMAN	K	344;268;342	ENSP00000399259:N344K;ENSP00000427796:N268K;ENSP00000428677:N342K	ENSP00000399259:N344K	N	-	3	2	FCHSD1	141006366	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.933000	0.28897	0.673000	0.31224	0.462000	0.41574	AAC	G|0.981;T|0.019	0.019	strong		0.592	FCHSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375282.2	NM_033449		T	141026182	G	T	141026182	3	4	27	1	0	0	0	0	1	0	0	0	5797	1252	44	4	1080	4	FCHSD1	5	141026182	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	256848	141026182	39889078	310	10761											
FCHSD1	89848	hgsc.bcm.edu	37	chr5	141030640	141030640	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgccaggtctgaaggatgctCagctgttccaggaagcgaag	10	8	14	9	1	2	1	1	1	1	0	3	4	3	3	2	3	4	3	2	3	3	1	rs17287002	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:141030640C>T	ENST00000435817.2	-	2	116	c.66G>A	c.(64-66)ctG>ctA	p.L22L	ARAP3_ENST00000512390.1_5'Flank|FCHSD1_ENST00000522126.1_5'UTR|FCHSD1_ENST00000522783.1_Silent_p.L22L|FCHSD1_ENST00000519800.1_Silent_p.L22L	NM_033449.2	NP_258260.1	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	22	FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.								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)			GAAGGATGCTCAGCTGTTCCA	0.582													C|||	132	0.0263578	0.003	0.0519	5008	,	,		12042	0.0		0.0805	False		,,,				2504	0.0112				p.L22L		Atlas-SNP	.											.	FCHSD1	51	.	0			c.G66A						PASS	.	C		67,3993		0,67,1963	26	28	28		66	1.9	1	5	dbSNP_123	28	616,7746		21,574,3586	no	coding-synonymous	FCHSD1	NM_033449.2		21,641,5549	TT,TC,CC		7.3667,1.6502,5.4983		22/691	141030640	683,11739	2030	4181	6211	SO:0001819	synonymous_variant	89848	exon2			GATGCTCAGCTGT	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.66G>A	5.37:g.141030640C>T		70	0	0		74	32	0.432432	NM_033449	Q6UX75|Q86Y77|Q9NXX8	Silent	SNP	ENST00000435817.2	37	CCDS47295.1																																																																																			C|0.962;T|0.038	0.038	strong		0.582	FCHSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375282.2	NM_033449		T	141030640	C	T	141030640	2	4	27	1	0	0	0	0	0	0	0	1	5797	813	29	2		2	FCHSD1	5	141030640	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	4458	141030640	39884620	311	10762											
PDGFRB	5159	hgsc.bcm.edu	37	chr5	149509446	149509446	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cacctcaaactcctgctcctCctcccagtacgtcacgttag	8	10	5	18	2	2	0	2	0	0	0	6	0	6	0	5	0	3	3	5	0	3	2	rs41287110	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:149509446C>T	ENST00000261799.4	-	10	1922	c.1453G>A	c.(1453-1455)Gag>Aag	p.E485K		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	485	Ig-like C2-type 5.		E -> K (in dbSNP:rs41287110). {ECO:0000269|PubMed:17344846}.		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)	TCCTGCTCCTCCTCCCAGTAC	0.647			T	"ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"	"MPD, AML, CMML, CML"						OREG0016927	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	54	0.0107827	0.0015	0.0216	5008	,	,		23425	0.0		0.0328	False		,,,				2504	0.0041				p.E485K		Atlas-SNP	.		Dom	yes		5	5q31-q32	5159	"platelet-derived growth factor receptor, beta polypeptide"		L	.	PDGFRB	142	.	0			c.G1453A						PASS	.	C	LYS/GLU	21,4385	29.0+/-57.7	0,21,2182	186	118	141		1453	3.7	1	5	dbSNP_127	141	224,8376	93.3+/-155.3	4,216,4080	yes	missense	PDGFRB	NM_002609.3	56	4,237,6262	TT,TC,CC		2.6047,0.4766,1.8837	benign	485/1107	149509446	245,12761	2203	4300	6503	SO:0001583	missense	5159	exon10			GCTCCTCCTCCCA	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.1453G>A	5.37:g.149509446C>T	ENSP00000261799:p.Glu485Lys	175	0	0	1725	123	62	0.504065	NM_002609	B5A957|Q8N5L4	Missense_Mutation	SNP	ENST00000261799.4	37	CCDS4303.1	39	0.017857142857142856	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	27	0.03562005277044855	C	13.36	2.214386	0.39102	0.004766	0.026047	ENSG00000113721	ENST00000261799;ENST00000544453	T	0.75938	-0.98	4.64	3.73	0.42828	.	0.108236	0.40554	N	0.001077	T	0.25754	0.0627	N	0.22421	0.69	0.38651	D	0.951848	B;B	0.25441	0.126;0.126	B;B	0.21360	0.034;0.034	T	0.46219	-0.9207	10	0.23302	T	0.38	.	12.5115	0.56007	0.0:0.8166:0.1834:0.0	rs41287110;rs62620662	485;485	A8KAM8;P09619	.;PGFRB_HUMAN	K	485;155	ENSP00000261799:E485K	ENSP00000261799:E485K	E	-	1	0	PDGFRB	149489639	0.920000	0.31207	0.958000	0.39756	0.940000	0.58332	1.826000	0.39092	2.409000	0.81822	0.462000	0.41574	GAG	C|0.980;T|0.020	0.020	strong		0.647	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609		T	149509446	C	T	149509446	3	4	27	1	0	0	0	0	1	0	0	0	11671	864	30	2	1923	2	PDGFRB	5	149509446	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	8478806	149509446	31405814	312	10763											
PDGFRB	5159	hgsc.bcm.edu	37	chr5	149511636	149511636	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgccaccttcacgcgaacCagtgtcagctctgacacata	10	9	7	15	2	4	1	2	1	2	0	4	2	4	1	3	0	3	1	3	0	2	2	rs2228439	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:149511636C>G	ENST00000261799.4	-	8	1618	c.1149G>C	c.(1147-1149)ctG>ctC	p.L383L		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	383	Ig-like C2-type 4.				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)	TCACGCGAACCAGTGTCAGCT	0.557			T	"ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"	"MPD, AML, CMML, CML"								C|||	24	0.00479233	0.0	0.0115	5008	,	,		20833	0.0		0.0159	False		,,,				2504	0.0				p.L383L		Atlas-SNP	.		Dom	yes		5	5q31-q32	5159	"platelet-derived growth factor receptor, beta polypeptide"		L	.	PDGFRB	142	.	0			c.G1149C						PASS	.	C		9,4397	14.3+/-33.2	0,9,2194	93	80	84		1149	1.1	0.9	5	dbSNP_98	84	100,8500	54.4+/-115.2	0,100,4200	no	coding-synonymous	PDGFRB	NM_002609.3		0,109,6394	GG,GC,CC		1.1628,0.2043,0.8381		383/1107	149511636	109,12897	2203	4300	6503	SO:0001819	synonymous_variant	5159	exon8			GCGAACCAGTGTC	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.1149G>C	5.37:g.149511636C>G		153	0	0		151	68	0.450331	NM_002609	B5A957|Q8N5L4	Silent	SNP	ENST00000261799.4	37	CCDS4303.1																																																																																			C|0.992;G|0.008	0.008	strong		0.557	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609		G	149511636	C	G	149511636	2	3	27	1	0	0	0	0	0	0	0	1	11671	581	21	4		4	PDGFRB	5	149511636	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2190	149511636	31403624	313	10764											
FAT2	2196	hgsc.bcm.edu	37	chr5	150930205	150930205	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgaggtccaattttcccacCgttaccaggacaccactgct	9	9	7	16	2	0	0	0	0	0	0	2	2	2	1	6	2	2	2	6	2	2	3	rs35489594	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:150930205C>T	ENST00000261800.5	-	7	4536	c.4524G>A	c.(4522-4524)acG>acA	p.T1508T		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	1508	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)			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)			ATTTTCCCACCGTTACCAGGA	0.522													C|||	6	0.00119808	0.0	0.0014	5008	,	,		21811	0.0		0.004	False		,,,				2504	0.001				p.T1508T		Atlas-SNP	.											.	FAT2	465	.	0			c.G4524A						PASS	.	C		11,4395	15.5+/-35.6	0,11,2192	96	87	90		4524	-10.5	0.8	5	dbSNP_126	90	73,8527	43.6+/-101.6	0,73,4227	no	coding-synonymous	FAT2	NM_001447.2		0,84,6419	TT,TC,CC		0.8488,0.2497,0.6459		1508/4350	150930205	84,12922	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon7			TCCCACCGTTACC	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.4524G>A	5.37:g.150930205C>T		142	0	0		134	60	0.447761	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																			C|0.995;T|0.005	0.005	strong		0.522	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		T	150930205	C	T	150930205	2	4	27	1	0	0	0	0	0	0	0	1	5698	639	23	1		1	FAT2	5	150930205	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1418569	150930205	29985055	314	10765											
GRIA1	2890	hgsc.bcm.edu	37	chr5	153078582	153078582	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatggaaaatacggagcccgAgaccctgacacgaaggcctg	13	4	13	11	3	0	2	0	1	0	1	0	7	0	4	3	3	2	0	3	3	4	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:153078582A>C	ENST00000285900.5	+	10	1744	c.1401A>C	c.(1399-1401)cgA>cgC	p.R467R	GRIA1_ENST00000340592.5_Silent_p.R467R|GRIA1_ENST00000518142.1_Silent_p.R387R|GRIA1_ENST00000521843.2_Silent_p.R398R|GRIA1_ENST00000518783.1_Silent_p.R477R|GRIA1_ENST00000448073.4_Silent_p.R477R	NM_000827.3|NM_001258019.1	NP_000818.2|NP_001244948.1	P42261	GRIA1_HUMAN	glutamate receptor, ionotropic, AMPA 1	467					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)	ACGGAGCCCGAGACCCTGACA	0.562																																					p.R477R		Atlas-SNP	.											GRIA1_ENST00000544403,NS,carcinoma,+1,2	GRIA1	321	2	0			c.A1431C						PASS	.						66	63	64					5																	153078582		2203	4300	6503	SO:0001819	synonymous_variant	2890	exon10			AGCCCGAGACCCT		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.1401A>C	5.37:g.153078582A>C		126	0	0		104	25	0.240385	NM_001258021	B7Z2S0|B7Z2W8|B7Z3F6|B7Z9G9|D3DQI4|E7ESV8|Q2NKM6	Silent	SNP	ENST00000285900.5	37	CCDS4322.1																																																																																			.	.	none		0.562	GRIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252456.3			C	153078582	A	C	153078582	2	2	27	1	0	0	0	0	0	0	0	1	6776	291	11	5		5	GRIA1	5	153078582	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	2148377	153078582	27836678	315	10766											
CYFIP2	26999	hgsc.bcm.edu	37	chr5	156741411	156741411	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaggagtatcgcgagctcttCgacctagccctgcggggtct	6	9	14	12	4	2	0	0	0	2	0	4	4	2	1	2	3	3	2	2	3	2	3	rs139943836	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:156741411C>T	ENST00000521420.1	+	11	1183	c.1092C>T	c.(1090-1092)ttC>ttT	p.F364F	CYFIP2_ENST00000435847.2_Silent_p.F64F|CYFIP2_ENST00000442283.2_5'UTR|CYFIP2_ENST00000541131.1_Silent_p.F315F|CYFIP2_ENST00000318218.6_Silent_p.F390F|CYFIP2_ENST00000347377.6_Silent_p.F390F|CYFIP2_ENST00000522463.1_Silent_p.F194F|CYFIP2_ENST00000377576.3_Silent_p.F390F					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)			GCGAGCTCTTCGACCTAGCCC	0.597													C|||	4	0.000798722	0.0	0.0014	5008	,	,		16212	0.0		0.003	False		,,,				2504	0.0				p.F390F		Atlas-SNP	.											.	CYFIP2	354	.	0			c.C1170T						PASS	.	C	,,	1,4071		0,1,2035	100	104	103		1170,1170,1170	-0.7	1	5	dbSNP_134	103	27,8355		0,27,4164	no	coding-synonymous,coding-synonymous,coding-synonymous	CYFIP2	NM_001037332.2,NM_001037333.1,NM_014376.2	,,	0,28,6199	TT,TC,CC		0.3221,0.0246,0.2248	,,	390/1254,390/1254,390/1254	156741411	28,12426	2036	4191	6227	SO:0001819	synonymous_variant	26999	exon12			GCTCTTCGACCTA	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.1092C>T	5.37:g.156741411C>T		103	0	0		71	38	0.535211	NM_001037332		Silent	SNP	ENST00000521420.1	37																																																																																				C|0.999;T|0.001	0.001	strong		0.597	CYFIP2-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000373710.1	NM_001037332		T	156741411	C	T	156741411	2	4	27	1	0	0	0	0	0	0	0	1	4140	883	31	1		1	CYFIP2	5	156741411	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3662829	156741411	24173849	316	10767											
ATP10B	23120	hgsc.bcm.edu	37	chr5	160115007	160115007	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagagcagcggtgtggtttcCgatggacaatgggggaagcc	9	7	18	7	2	0	1	0	0	0	1	1	5	1	3	2	5	3	2	2	5	2	1	rs201071012		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:160115007C>T	ENST00000327245.5	-	5	921	c.75G>A	c.(73-75)tcG>tcA	p.S25S	CTC-529G1.1_ENST00000524198.1_RNA|ATP10B_ENST00000518411.1_5'UTR	NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	25					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)			GTGTGGTTTCCGATGGACAAT	0.537													T|||	1	0.000199681	0.0	0.0	5008	,	,		18673	0.0		0.001	False		,,,				2504	0.0				p.S25S		Atlas-SNP	.											.	ATP10B	201	.	0			c.G75A						PASS	.	T		3,4129		0,3,2063	96	98	97		75	1.4	0.9	5		97	20,8428		0,20,4204	no	coding-synonymous	ATP10B	NM_025153.2		0,23,6267	TT,TC,CC		0.2367,0.0726,0.1828		25/1462	160115007	23,12557	2066	4224	6290	SO:0001819	synonymous_variant	23120	exon5			GGTTTCCGATGGA	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.75G>A	5.37:g.160115007C>T		177	1	0.00564972		146	86	0.589041	NM_025153	Q9H725	Silent	SNP	ENST00000327245.5	37	CCDS43394.1																																																																																			C|0.996;T|0.005	0.005	strong		0.537	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153		T	160115007	C	T	160115007	2	4	27	1	0	0	0	0	0	0	0	1	1117	639	23	1		1	ATP10B	5	160115007	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3373596	160115007	20800253	317	10768											
HK3	3101	hgsc.bcm.edu	37	chr5	176314086	176314086	+	Frame_Shift_Del	DEL	G	G	-																															gctcaggccctgcttctgctGgaagtccacgatgcagtcca																								rs534008020	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:176314086delG	ENST00000292432.5	-	13	1865	c.1774delC	c.(1774-1776)cagfs	p.Q593fs		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	593	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)			TGCTTCTGCTGGAAGTCCACG	0.602																																					p.Q592fs		Pindel,Atlas-Indel	.											.	HK3	210	.	0			c.1775delA						PASS	.						84	76	79					5																	176314086		2203	4300	6503	SO:0001589	frameshift_variant	3101	exon13			.		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.1774delC	5.37:g.176314086delG	ENSP00000292432:p.Gln593fs	86	0	.		121	41	0.339	NM_002115	Q8N1E7	Frame_Shift_Del	DEL	ENST00000292432.5	37	CCDS4407.1																																																																																			.	.	none		0.602	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1			-	176314086	G	-	176314086	7	5	27	1	0	1	0	1	0	0	0	0	7201	1357	47	0	1025	0	HK3	5	176314086	Frame_Shift_Del	DEL	G	TCGA-G8-6909-01A-11D-2210-10	16199079	176314086	4601174	318	10769											
NSD1	64324	hgsc.bcm.edu	37	chr5	176637471	176637471	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaagtattctaggtttgctGccacaaacactagggtaaaa	15	11	8	7	0	1	0	0	0	1	0	1	0	1	0	1	2	3	4	1	2	8	7	rs28932177	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:176637471G>A	ENST00000439151.2	+	5	2116	c.2071G>A	c.(2071-2073)Gcc>Acc	p.A691T	NSD1_ENST00000347982.4_Missense_Mutation_p.A422T|NSD1_ENST00000361032.4_Missense_Mutation_p.A588T|NSD1_ENST00000354179.4_Missense_Mutation_p.A422T	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	691			A -> T (in dbSNP:rs28932177). {ECO:0000269|PubMed:12464997}.		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)		TAGGTTTGCTGCCACAAACAC	0.393			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)			G|||	65	0.0129792	0.0045	0.0086	5008	,	,		20290	0.0		0.0249	False		,,,				2504	0.0286				p.A691T		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.G2071A						PASS	.	G	THR/ALA,THR/ALA	28,4378	35.2+/-66.4	1,26,2176	53	56	55		2071,1264	3.3	1	5	dbSNP_125	55	207,8393	89.7+/-151.9	2,203,4095	yes	missense,missense	NSD1	NM_022455.4,NM_172349.2	58,58	3,229,6271	AA,AG,GG		2.407,0.6355,1.8069	benign,benign	691/2697,422/2428	176637471	235,12771	2203	4300	6503	SO:0001583	missense	64324	exon5	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	TTTGCTGCCACAA	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.2071G>A	5.37:g.176637471G>A	ENSP00000395929:p.Ala691Thr	174	0	0		185	69	0.372973	NM_022455	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	37	CCDS4412.1	27	0.012362637362637362	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	21	0.027704485488126648	G	10.58	1.390030	0.25118	0.006355	0.02407	ENSG00000165671	ENST00000354179;ENST00000355783;ENST00000439151;ENST00000347982;ENST00000361032	D;D;D;D	0.92752	-2.98;-2.98;-2.98;-3.1	5.1	3.31	0.37934	.	0.621198	0.16033	N	0.232761	T	0.59362	0.2188	N	0.08118	0	0.21822	N	0.999526	B;B;B	0.12630	0.006;0.006;0.001	B;B;B	0.12156	0.004;0.007;0.002	T	0.58719	-0.7587	9	.	.	.	.	4.2978	0.10910	0.182:0.0:0.592:0.226	rs28932177;rs28932177	422;588;691	Q96L73-2;Q96L73-3;Q96L73	.;.;NSD1_HUMAN	T	422;422;691;422;588	ENSP00000346111:A422T;ENSP00000395929:A691T;ENSP00000343209:A422T;ENSP00000354310:A588T	.	A	+	1	0	NSD1	176570077	0.188000	0.23250	1.000000	0.80357	0.984000	0.73092	0.269000	0.18589	1.504000	0.48704	0.655000	0.94253	GCC	G|0.983;A|0.017	0.017	strong		0.393	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		A	176637471	G	A	176637471	3	1	27	1	0	0	0	0	1	0	0	0	10678	1319	46	2	2085	2	NSD1	5	176637471	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	323385	176637471	4277789	319	10770											
NSD1	64324	hgsc.bcm.edu	37	chr5	176638506	176638506	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aattgcgagatgctttttcaGcccaaatggtaaagaacaca	15	10	8	8	1	1	2	1	0	0	2	1	3	1	2	1	1	4	2	1	1	5	4	rs28932179	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:176638506G>C	ENST00000439151.2	+	5	3151	c.3106G>C	c.(3106-3108)Gcc>Ccc	p.A1036P	NSD1_ENST00000347982.4_Missense_Mutation_p.A767P|NSD1_ENST00000361032.4_Missense_Mutation_p.A933P|NSD1_ENST00000354179.4_Missense_Mutation_p.A767P	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	1036			A -> P (in dbSNP:rs28932179). {ECO:0000269|PubMed:12464997}.		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)		TGCTTTTTCAGCCCAAATGGT	0.458			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.A1036P		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	NSD1_ENST00000439151,NS,carcinoma,-2,2	NSD1	416	2	0			c.G3106C						PASS	.	G	PRO/ALA,PRO/ALA	133,4273	94.8+/-133.5	3,127,2073	122	121	121		3106,2299	-7.9	0	5	dbSNP_125	121	209,8391	89.9+/-152.1	2,205,4093	yes	missense,missense	NSD1	NM_022455.4,NM_172349.2	27,27	5,332,6166	CC,CG,GG		2.4302,3.0186,2.6296	possibly-damaging,possibly-damaging	1036/2697,767/2428	176638506	342,12664	2203	4300	6503	SO:0001583	missense	64324	exon5	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	TTTTCAGCCCAAA	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.3106G>C	5.37:g.176638506G>C	ENSP00000395929:p.Ala1036Pro	136	0	0		144	67	0.465278	NM_022455	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	37	CCDS4412.1	49	0.022435897435897436	24	0.04878048780487805	4	0.011049723756906077	0	0.0	21	0.027704485488126648	G	3.407	-0.121106	0.06838	0.030186	0.024302	ENSG00000165671	ENST00000354179;ENST00000439151;ENST00000347982;ENST00000361032	D;D;D;D	0.93547	-3.13;-3.13;-3.13;-3.24	4.58	-7.92	0.01160	.	0.885835	0.09644	N	0.774583	T	0.52869	0.1761	N	0.24115	0.695	0.09310	N	0.999999	P;P;B	0.40875	0.731;0.729;0.38	B;P;B	0.45232	0.277;0.474;0.147	T	0.72597	-0.4245	9	.	.	.	.	0.8308	0.01130	0.3731:0.1058:0.1991:0.3219	rs28932179	767;933;1036	Q96L73-2;Q96L73-3;Q96L73	.;.;NSD1_HUMAN	P	767;1036;767;933	ENSP00000346111:A767P;ENSP00000395929:A1036P;ENSP00000343209:A767P;ENSP00000354310:A933P	.	A	+	1	0	NSD1	176571112	0.005000	0.15991	0.008000	0.14137	0.473000	0.32948	-0.404000	0.07205	-2.092000	0.00857	0.467000	0.42956	GCC	G|0.975;C|0.025	0.025	strong		0.458	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349		C	176638506	G	C	176638506	3	2	27	1	0	0	0	0	1	0	0	0	10678	971	34	4	3120	4	NSD1	5	176638506	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1035	176638506	4276754	320	10771											
ZNF354C	30832	hgsc.bcm.edu	37	chr5	178506075	178506075	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagatttacccaggaggaaaAcctcacatctgtaatgaatg	15	9	8	9	0	2	2	1	1	1	1	2	4	2	4	2	2	2	1	2	2	5	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:178506075A>T	ENST00000315475.6	+	5	948	c.642A>T	c.(640-642)aaA>aaT	p.K214N		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	214					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)		CAGGAGGAAAACCTCACATCT	0.353																																					p.K214N		Atlas-SNP	.											.	ZNF354C	77	.	0			c.A642T						PASS	.						51	53	52					5																	178506075		2203	4300	6503	SO:0001583	missense	30832	exon5			AGGAAAACCTCAC		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.642A>T	5.37:g.178506075A>T	ENSP00000324064:p.Lys214Asn	62	0	0		71	16	0.225352	NM_014594	Q6P4P9|Q8NFX1	Missense_Mutation	SNP	ENST00000315475.6	37	CCDS4443.1	.	.	.	.	.	.	.	.	.	.	A	13.49	2.254012	0.39896	.	.	ENSG00000177932	ENST00000315475	T	0.35048	1.33	3.94	-4.99	0.03010	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36082	0.0954	M	0.80847	2.515	0.09310	N	1	B	0.19073	0.033	B	0.18871	0.023	T	0.44190	-0.9344	9	0.66056	D	0.02	-3.9769	8.2749	0.31866	0.3087:0.1478:0.5435:0.0	.	214	Q86Y25	Z354C_HUMAN	N	214	ENSP00000324064:K214N	ENSP00000324064:K214N	K	+	3	2	ZNF354C	178438681	0.000000	0.05858	0.000000	0.03702	0.291000	0.27294	-0.409000	0.07160	-1.159000	0.02807	0.482000	0.46254	AAA	.	.	none		0.353	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2			T	178506075	A	T	178506075	3	4	27	1	0	0	0	0	1	0	0	0	17881	40	2	5	656	5	ZNF354C	5	178506075	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	1867569	178506075	2409185	321	10772											
ADAMTS2	9509	hgsc.bcm.edu	37	chr5	178700038	178700038	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	caagggttcgatgaagaactCctcctcctccatccggatca	10	9	8	14	2	1	2	1	1	0	1	7	4	6	3	5	2	1	1	5	2	3	1	rs146064587		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:178700038C>G	ENST00000251582.7	-	3	663	c.562G>C	c.(562-564)Gag>Cag	p.E188Q	ADAMTS2_ENST00000274609.5_Missense_Mutation_p.E188Q	NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	188	Poly-Glu.				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)		ATGAAGAACTCCTCCTCCTCC	0.602																																					p.E188Q		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.G562C						PASS	.	C	GLN/GLU,GLN/GLU	0,4406		0,0,2203	81	78	79		562,562	5	1	5	dbSNP_134	79	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	ADAMTS2	NM_014244.4,NM_021599.2	29,29	0,2,6501	GG,GC,CC		0.0233,0.0,0.0154	possibly-damaging,possibly-damaging	188/1212,188/567	178700038	2,13004	2203	4300	6503	SO:0001583	missense	9509	exon3			AGAACTCCTCCTC	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.562G>C	5.37:g.178700038C>G	ENSP00000251582:p.Glu188Gln	50	0	0		59	25	0.423729	NM_021599		Missense_Mutation	SNP	ENST00000251582.7	37	CCDS4444.1	.	.	.	.	.	.	.	.	.	.	C	23.6	4.430513	0.83776	0.0	2.33E-4	ENSG00000087116	ENST00000251582;ENST00000274609	T;T	0.07327	3.2;3.2	4.96	4.96	0.65561	Peptidase M12B, propeptide (1);	0.000000	0.37178	N	0.002212	T	0.25568	0.0622	M	0.62154	1.92	0.44660	D	0.997649	D;D	0.89917	0.998;1.0	D;D	0.91635	0.994;0.999	T	0.00389	-1.1770	10	0.59425	D	0.04	.	13.7201	0.62720	0.0:1.0:0.0:0.0	.	188;188	O95450-2;O95450	.;ATS2_HUMAN	Q	188	ENSP00000251582:E188Q;ENSP00000274609:E188Q	ENSP00000251582:E188Q	E	-	1	0	ADAMTS2	178632644	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.753000	0.68736	2.284000	0.76573	0.561000	0.74099	GAG	C|1.000;G|0.000	0.000	weak		0.602	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244		G	178700038	C	G	178700038	3	3	27	1	0	0	0	0	1	0	0	0	265	864	30	4	3228	4	ADAMTS2	5	178700038	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	193963	178700038	2215222	322	10773											
CANX	821	hgsc.bcm.edu	37	chr5	179135309	179135309	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggacttgtgttgatgtctcGggccaagcatcatgccatct	8	12	11	10	1	3	1	1	1	2	0	4	2	3	2	2	2	2	2	2	2	1	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:179135309G>A	ENST00000247461.4	+	5	574	c.374G>A	c.(373-375)cGg>cAg	p.R125Q	CANX_ENST00000504734.1_Missense_Mutation_p.R125Q|CANX_ENST00000415618.2_Missense_Mutation_p.R160Q|CANX_ENST00000512607.2_Missense_Mutation_p.R17Q|CANX_ENST00000452673.2_Missense_Mutation_p.R125Q|CANX_ENST00000503126.1_3'UTR	NM_001746.3	NP_001737.1	P27824	CALX_HUMAN	calnexin	125					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)	p.R125L(1)		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)	TTGATGTCTCGGGCCAAGCAT	0.443																																					p.R125Q		Atlas-SNP	.											.	CANX	47	.	1	Substitution - Missense(1)	lung(1)	c.G374A						PASS	.						227	212	217					5																	179135309		2203	4300	6503	SO:0001583	missense	821	exon5			TGTCTCGGGCCAA	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.374G>A	5.37:g.179135309G>A	ENSP00000247461:p.Arg125Gln	202	0	0		246	78	0.317073	NM_001746	B2R5V8|B4DGP8|B4E2T8|D3DWQ3|D6R9K3	Missense_Mutation	SNP	ENST00000247461.4	37	CCDS4447.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.66|19.66	3.869769|3.869769	0.72065|0.72065	.|.	.|.	ENSG00000127022|ENSG00000127022	ENST00000510810;ENST00000508787|ENST00000514383;ENST00000502296;ENST00000504734;ENST00000415618;ENST00000452673;ENST00000247461;ENST00000502498;ENST00000502673;ENST00000506654;ENST00000512607;ENST00000354394;ENST00000376953	.|T;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;0.67	5.81|5.81	5.81|5.81	0.92471|0.92471	.|Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	.|0.060915	.|0.64402	.|D	.|0.000003	T|T	0.39358|0.39358	0.1075|0.1075	L|L	0.35542|0.35542	1.07|1.07	0.52099|0.52099	D|D	0.999942|0.999942	.|B;B;B	.|0.32245	.|0.361;0.292;0.247	.|B;B;B	.|0.21151	.|0.033;0.018;0.03	T|T	0.19712|0.19712	-1.0297|-1.0297	5|10	.|0.46703	.|T	.|0.11	-17.6381|-17.6381	20.071|20.071	0.97724|0.97724	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|160;61;125	.|B4DGP8;Q6ZP56;P27824	.|.;.;CALX_HUMAN	R|Q	94;8|125;125;125;160;125;125;125;61;17;17;117;61	.|ENSP00000424341:R125Q;ENSP00000424745:R125Q;ENSP00000424063:R125Q;ENSP00000394817:R160Q;ENSP00000391646:R125Q;ENSP00000247461:R125Q;ENSP00000425246:R125Q;ENSP00000421107:R61Q;ENSP00000426555:R17Q;ENSP00000423588:R17Q	.|ENSP00000247461:R125Q	G|R	+|+	1|2	0|0	CANX|CANX	179067915|179067915	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.727000|6.727000	0.74764|0.74764	2.754000|2.754000	0.94517|0.94517	0.561000|0.561000	0.74099|0.74099	GGG|CGG	.	.	none		0.443	CANX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253500.2	NM_001024649		A	179135309	G	A	179135309	3	1	27	1	0	0	0	0	1	0	0	0	2620	1116	39	1	388	1	CANX	5	179135309	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	435271	179135309	1779951	323	10774											
MAML1	9794	hgsc.bcm.edu	37	chr5	179201226	179201226	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcagctgcctatgggcagaActctctgggaagctctggcc	7	9	12	13	0	3	1	1	0	2	1	4	2	3	2	2	3	4	3	2	3	3	1	rs148053500	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr5:179201226A>C	ENST00000292599.3	+	5	2662	c.2399A>C	c.(2398-2400)aAc>aCc	p.N800T	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)			TATGGGCAGAACTCTCTGGGA	0.612													A|||	9	0.00179712	0.0015	0.0058	5008	,	,		17029	0.0		0.003	False		,,,				2504	0.0				p.N800T		Atlas-SNP	.											.	MAML1	118	.	0			c.A2399C						PASS	.	A	THR/ASN	4,4402	4.2+/-10.8	0,4,2199	35	36	35		2399	1.3	1	5	dbSNP_134	35	27,8573	19.2+/-60.6	0,27,4273	yes	missense	MAML1	NM_014757.4	65	0,31,6472	CC,CA,AA		0.314,0.0908,0.2384	possibly-damaging	800/1017	179201226	31,12975	2203	4300	6503	SO:0001583	missense	9794	exon5			GGCAGAACTCTCT	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.2399A>C	5.37:g.179201226A>C	ENSP00000292599:p.Asn800Thr	46	0	0		39	25	0.641026	NM_014757		Missense_Mutation	SNP	ENST00000292599.3	37	CCDS34315.1	7	0.003205128205128205	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	3	0.00395778364116095	A	18.11	3.550143	0.65311	9.08E-4	0.00314	ENSG00000161021	ENST00000292599	T	0.25749	1.78	4.94	1.31	0.21738	.	0.192835	0.45606	D	0.000351	T	0.26085	0.0636	L	0.58101	1.795	0.46901	D	0.999241	D	0.69078	0.997	P	0.59056	0.851	T	0.08911	-1.0699	10	0.17832	T	0.49	-16.6951	8.3868	0.32505	0.6881:0.0:0.3119:0.0	.	800	Q92585	MAML1_HUMAN	T	800	ENSP00000292599:N800T	ENSP00000292599:N800T	N	+	2	0	MAML1	179133832	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.050000	0.41297	0.260000	0.21731	0.379000	0.24179	AAC	A|0.997;C|0.003	0.003	strong		0.612	MAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372316.2	NM_014757		C	179201226	A	C	179201226	3	2	27	1	0	0	0	0	1	0	0	0	9214	43	2	5	2417	5	MAML1	5	179201226	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	65917	179201226	1714034	324	10775											
GCNT2	2651	hgsc.bcm.edu	37	chr6	10586727	10586727	+	Intron	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	caggcatttccagactccagGctgacctgaactgtctgaaa	11	9	9	12	0	1	4	0	3	1	1	3	4	3	4	3	2	1	2	3	2	2	1	rs56106312	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:10586727G>A	ENST00000379597.3	+	2	1481				GCNT2_ENST00000495262.1_Intron|GCNT2_ENST00000397423.2_Intron|GCNT2_ENST00000410107.1_Intron|GCNT2_ENST00000316170.3_Intron|GCNT2_ENST00000265012.4_Missense_Mutation_p.A169T			Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)						maintenance of lens transparency (GO:0036438)|negative regulation of cell-substrate adhesion (GO:0010812)|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 ERK1 and ERK2 cascade (GO:0070374)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of protein kinase B signaling (GO:0051897)|posttranscriptional regulation of gene expression (GO:0010608)|protein glycosylation (GO:0006486)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			endometrium(2)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)	12	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		CAGACTCCAGGCTGACCTGAA	0.483													G|||	12	0.00239617	0.0008	0.0058	5008	,	,		19773	0.0		0.006	False		,,,				2504	0.001				p.A169T		Atlas-SNP	.											.	GCNT2	123	.	0			c.G505A						PASS	.	G	,,THR/ALA	3,4403	6.2+/-15.9	0,3,2200	127	123	124	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,,505	5.6	1	6	dbSNP_129	124	45,8555	30.1+/-81.4	0,45,4255	yes	intron,intron,missense	GCNT2	NM_001491.2,NM_145649.4,NM_145655.3	,,58	0,48,6455	AA,AG,GG		0.5233,0.0681,0.3691	,,probably-damaging	,,169/403	10586727	48,12958	2203	4300	6503	SO:0001627	intron_variant	2651	exon1			CTCCAGGCTGACC	L41605	CCDS4512.1, CCDS4513.1, CCDS34338.1	6p24.2	2014-07-18	2006-02-23		ENSG00000111846	ENSG00000111846	2.4.1.150	"Blood group antigens", "Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"	4204	protein-coding gene	gene with protein product	"Ii blood group", "unassigned linkage group 3"	600429	"glucosaminyl (N-acetyl) transferase 5", "glucosaminyl (N-acetyl) transferase 2, I-branching enzyme", "glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (Ii blood group)", "cataract, congenital"	NACGT1, II, GCNT5, CCAT		8449405, 9915862	Standard	NM_145649		Approved	IGNT, NAGCT1, bA421M1.1, bA360O19.2, ULG3	uc003mze.3	Q06430	OTTHUMG00000014244	ENST00000379597.3:c.926-34857G>A	6.37:g.10586727G>A		165	0	0		163	111	0.680982	NM_145655		Missense_Mutation	SNP	ENST00000379597.3	37	CCDS34338.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	G	18.84	3.709073	0.68615	6.81E-4	0.005233	ENSG00000111846	ENST00000265012	T	0.20332	2.08	5.58	5.58	0.84498	.	.	.	.	.	T	0.45836	0.1362	M	0.88842	2.985	0.58432	D	0.999996	D	0.76494	0.999	D	0.77557	0.99	T	0.53920	-0.8370	9	0.87932	D	0	.	14.7518	0.69530	0.0709:0.0:0.9291:0.0	rs56106312	169	Q8NFS9	GNT2C_HUMAN	T	169	ENSP00000265012:A169T	ENSP00000265012:A169T	A	+	1	0	GCNT2	10694713	1.000000	0.71417	1.000000	0.80357	0.110000	0.19582	6.558000	0.73942	2.624000	0.88883	0.655000	0.94253	GCT	G|0.996;A|0.004	0.004	strong		0.483	GCNT2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327912.3	NM_145649		A	10586727	G	A	10586727	1	1	27	0	1	0	0	0	0	0	0	0	6309	1203	42	2		2	GCNT2	6	10586727	Intron	SNP	G	TCGA-G8-6909-01A-11D-2210-10		10586727	160528340	325	10776											
HIVEP1	3096	hgsc.bcm.edu	37	chr6	12124257	12124257	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	attgcagcctccatcttcacCttctcgagtgggagtgactg	7	12	10	12	1	3	1	1	1	2	0	5	3	4	2	3	1	2	1	3	1	0	3	rs372404420		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:12124257C>G	ENST00000379388.2	+	4	4561	c.4229C>G	c.(4228-4230)cCt>cGt	p.P1410R	HIVEP1_ENST00000541134.1_5'Flank	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	1410					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)				CCATCTTCACCTTCTCGAGTG	0.488																																					p.P1410R		Atlas-SNP	.											.	HIVEP1	242	.	0			c.C4229G						PASS	.	C	ARG/PRO	0,4074		0,0,2037	113	116	115		4229	4.9	0.3	6		115	1,8369		0,1,4184	no	missense	HIVEP1	NM_002114.2	103	0,1,6221	GG,GC,CC		0.0119,0.0,0.0080	possibly-damaging	1410/2719	12124257	1,12443	2037	4185	6222	SO:0001583	missense	3096	exon4			CTTCACCTTCTCG	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.4229C>G	6.37:g.12124257C>G	ENSP00000368698:p.Pro1410Arg	104	0	0		97	36	0.371134	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	37	CCDS43426.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.931801	0.73442	0.0	1.19E-4	ENSG00000095951	ENST00000379388	T	0.09538	2.97	5.79	4.93	0.64822	.	0.460558	0.16304	N	0.220330	T	0.08044	0.0201	L	0.57536	1.79	0.80722	D	1	D	0.53462	0.96	P	0.46718	0.525	T	0.14227	-1.0480	9	.	.	.	-6.1734	9.7069	0.40220	0.1398:0.79:0.0:0.0702	.	1410	P15822	ZEP1_HUMAN	R	1410	ENSP00000368698:P1410R	.	P	+	2	0	HIVEP1	12232243	0.278000	0.24230	0.260000	0.24451	0.175000	0.22909	3.441000	0.52893	1.454000	0.47793	0.655000	0.94253	CCT	.	.	weak		0.488	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114		G	12124257	C	G	12124257	3	3	27	1	0	0	0	0	1	0	0	0	7195	681	24	4	4239	4	HIVEP1	6	12124257	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1537530	12124257	158990810	326	10777											
JARID2	3720	hgsc.bcm.edu	37	chr6	15512616	15512616	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagtatgggctttgagaccGccaaggtgagcagagccggc	10	6	15	10	2	0	3	0	2	0	2	0	4	0	3	3	3	2	3	3	3	3	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:15512616G>A	ENST00000341776.2	+	14	3374	c.3130G>A	c.(3130-3132)Gcc>Acc	p.A1044T	JARID2_ENST00000397311.3_Missense_Mutation_p.A872T	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	1044	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)				CTTTGAGACCGCCAAGGTGAG	0.607																																					p.A1044T		Atlas-SNP	.											.	JARID2	135	.	0			c.G3130A						PASS	.						139	133	135					6																	15512616		2203	4300	6503	SO:0001583	missense	3720	exon14			GAGACCGCCAAGG	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.3130G>A	6.37:g.15512616G>A	ENSP00000341280:p.Ala1044Thr	59	0	0		44	13	0.295455	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Missense_Mutation	SNP	ENST00000341776.2	37	CCDS4533.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.520516	0.85495	.	.	ENSG00000008083	ENST00000341776;ENST00000397311	T;T	0.70282	-0.47;-0.47	5.02	4.15	0.48705	Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.000000	0.85682	D	0.000000	T	0.56366	0.1980	L	0.35542	1.07	0.80722	D	1	D	0.67145	0.996	P	0.50136	0.632	T	0.60632	-0.7225	10	0.46703	T	0.11	-15.1615	13.6151	0.62103	0.0757:0.0:0.9243:0.0	.	1044	Q92833	JARD2_HUMAN	T	1044;872	ENSP00000341280:A1044T;ENSP00000380478:A872T	ENSP00000341280:A1044T	A	+	1	0	JARID2	15620595	1.000000	0.71417	0.991000	0.47740	0.956000	0.61745	9.796000	0.99103	1.238000	0.43771	0.609000	0.83330	GCC	.	.	none		0.607	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973		A	15512616	G	A	15512616	3	1	27	1	0	0	0	0	1	0	0	0	7954	1087	38	1	3184	1	JARID2	6	15512616	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	3388359	15512616	155602451	327	10778											
KIF13A	63971	hgsc.bcm.edu	37	chr6	17764896	17764896	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ttcgtctgaatggccagctgGtctgagctgtcactagaagg	8	11	13	9	1	3	3	1	2	2	1	4	3	3	3	1	3	2	2	1	3	3	2	rs41267712	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:17764896G>C	ENST00000259711.6	-	39	4968	c.4863C>G	c.(4861-4863)gaC>gaG	p.D1621E	KIF13A_ENST00000378816.5_Missense_Mutation_p.D1586E|KIF13A_ENST00000378814.5_Missense_Mutation_p.D1573E|KIF13A_ENST00000378826.2_Missense_Mutation_p.D1586E|KIF13A_ENST00000378843.2_Missense_Mutation_p.D1573E	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	1621					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)			TGGCCAGCTGGTCTGAGCTGT	0.537													G|||	17	0.00339457	0.0008	0.0029	5008	,	,		18971	0.0		0.0119	False		,,,				2504	0.002				p.D1621E		Atlas-SNP	.											.	KIF13A	276	.	0			c.C4863G						PASS	.	G	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	7,4099		0,7,2046	76	76	76		4758,4719,4719,4863	-10.1	0.3	6	dbSNP_127	76	89,8313		0,89,4112	yes	missense,missense,missense,missense	KIF13A	NM_001105566.2,NM_001105567.2,NM_001105568.2,NM_022113.5	45,45,45,45	0,96,6158	CC,CG,GG		1.0593,0.1705,0.7675	probably-damaging,probably-damaging,probably-damaging,probably-damaging	1586/1771,1573/1758,1573/1750,1621/1806	17764896	96,12412	2053	4201	6254	SO:0001583	missense	63971	exon39			CAGCTGGTCTGAG	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.4863C>G	6.37:g.17764896G>C	ENSP00000259711:p.Asp1621Glu	83	0	0		67	37	0.552239	NM_022113	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Missense_Mutation	SNP	ENST00000259711.6	37	CCDS47381.1	10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	G	22.2	4.253429	0.80135	0.001705	0.010593	ENSG00000137177	ENST00000378814;ENST00000502297;ENST00000259711;ENST00000378826;ENST00000378843;ENST00000378816	T;T;T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26;-0.26;-0.26	6.08	-10.1	0.00402	.	0.000000	0.85682	D	0.000000	T	0.49677	0.1571	L	0.34521	1.04	0.33165	D	0.54753	D;D;D;D	0.67145	0.996;0.996;0.988;0.996	D;D;P;D	0.77557	0.99;0.99;0.675;0.99	T	0.76876	-0.2797	10	0.05721	T	0.95	.	21.8125	0.99961	0.3087:0.0:0.6913:0.0	rs41267712	1573;1586;1621;1573	Q9H1H9-4;Q9H1H9-2;Q9H1H9;Q9H1H9-3	.;.;KI13A_HUMAN;.	E	1573;625;1621;1586;1573;1586	ENSP00000368091:D1573E;ENSP00000425616:D625E;ENSP00000259711:D1621E;ENSP00000368103:D1586E;ENSP00000368120:D1573E;ENSP00000368093:D1586E	ENSP00000259711:D1621E	D	-	3	2	KIF13A	17872875	0.992000	0.36948	0.342000	0.25602	0.975000	0.68041	0.249000	0.18216	-1.853000	0.01165	-0.423000	0.05987	GAC	G|0.995;C|0.005	0.005	strong		0.537	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4			C	17764896	G	C	17764896	3	2	27	1	0	0	0	0	1	0	0	0	8283	1252	44	4	583	4	KIF13A	6	17764896	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2252280	17764896	153350171	328	10779											
KIAA0319	9856	hgsc.bcm.edu	37	chr6	24576706	24576706	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	caaagtgatggagttttgggGcaaagttatggtgtgatttg	10	14	15	2	0	0	2	0	2	0	0	0	3	0	3	0	4	0	3	0	4	3	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:24576706G>A	ENST00000378214.3	-	10	2148	c.1624C>T	c.(1624-1626)Ccc>Tcc	p.P542S	KIAA0319_ENST00000537886.1_Missense_Mutation_p.P542S|KIAA0319_ENST00000430948.2_Missense_Mutation_p.P497S|KIAA0319_ENST00000535378.1_Missense_Mutation_p.P533S|KIAA0319_ENST00000543707.1_Missense_Mutation_p.P542S	NM_001168375.1|NM_014809.3	NP_001161847.1|NP_055624.2	Q5VV43	K0319_HUMAN	KIAA0319	542	PKD 3. {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						GAGTTTTGGGGCAAAGTTATG	0.498																																					p.P542S		Atlas-SNP	.											.	KIAA0319	117	.	0			c.C1624T						PASS	.						514	503	507					6																	24576706		2203	4300	6503	SO:0001583	missense	9856	exon10			TTTGGGGCAAAGT	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.1624C>T	6.37:g.24576706G>A	ENSP00000367459:p.Pro542Ser	490	0	0		359	65	0.181058	NM_001168377	A7MD37|B2RTU7|B4DHA7|B4DK75|B7ZML3|F5H123|Q9UJC8|Q9Y4G7	Missense_Mutation	SNP	ENST00000378214.3	37	CCDS34348.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.333242	0.81801	.	.	ENSG00000137261	ENST00000537886;ENST00000535378;ENST00000430948;ENST00000378214;ENST00000543707	T;T;T;T;T	0.67523	-0.27;-0.27;-0.27;-0.27;-0.27	3.9	3.9	0.45041	PKD/Chitinase domain (1);PKD/REJ-like protein (1);PKD domain (2);	0.000000	0.64402	D	0.000001	T	0.82268	0.5000	M	0.89968	3.075	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	0.86674	0.1912	10	0.72032	D	0.01	-15.2462	16.4334	0.83861	0.0:0.0:1.0:0.0	.	542;533;542	F5H123;Q5VV43-2;Q5VV43	.;.;K0319_HUMAN	S	542;533;497;542;542	ENSP00000439700:P542S;ENSP00000442403:P533S;ENSP00000401086:P497S;ENSP00000367459:P542S;ENSP00000437656:P542S	ENSP00000367459:P542S	P	-	1	0	KIAA0319	24684685	1.000000	0.71417	0.999000	0.59377	0.952000	0.60782	6.424000	0.73366	2.153000	0.67306	0.655000	0.94253	CCC	.	.	none		0.498	KIAA0319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040009.1	NM_014809		A	24576706	G	A	24576706	3	1	27	1	0	0	0	0	1	0	0	0	8177	1203	42	2	1642	2	KIAA0319	6	24576706	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	6811810	24576706	146538361	329	10780											
HIST1H1C	3006	hgsc.bcm.edu	37	chr6	26056277	26056277	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccccaactggcttcttaggtTtggttccgcccgccttttta	4	15	8	14	2	1	0	0	0	1	0	2	0	2	0	5	3	1	3	5	3	3	7			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26056277T>G	ENST00000343677.2	-	1	422	c.380A>C	c.(379-381)aAa>aCa	p.K127T		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	127					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						CTTCTTAGGTTTGGTTCCGCC	0.557																																					p.K127T		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.A380C						PASS	.						57	68	65					6																	26056277		2202	4299	6501	SO:0001583	missense	3006	exon1			TTAGGTTTGGTTC	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.380A>C	6.37:g.26056277T>G	ENSP00000339566:p.Lys127Thr	153	0	0		127	36	0.283465	NM_005319	A8K4I2	Missense_Mutation	SNP	ENST00000343677.2	37	CCDS4577.1	.	.	.	.	.	.	.	.	.	.	T	12.28	1.890388	0.33348	.	.	ENSG00000187837	ENST00000343677	T	0.19532	2.14	5.54	5.54	0.83059	.	0.120538	0.53938	D	0.000047	T	0.06325	0.0163	N	0.08118	0	0.58432	D	0.999999	B	0.25719	0.132	B	0.25759	0.063	T	0.14392	-1.0474	10	0.62326	D	0.03	-6.0558	15.1351	0.72558	0.0:0.0:0.0:1.0	.	127	P16403	H12_HUMAN	T	127	ENSP00000339566:K127T	ENSP00000339566:K127T	K	-	2	0	HIST1H1C	26164256	1.000000	0.71417	0.961000	0.40146	0.109000	0.19521	3.997000	0.57016	2.229000	0.72834	0.533000	0.62120	AAA	.	.	none		0.557	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319		G	26056277	T	G	26056277	3	3	27	1	0	0	0	0	1	0	0	0	7133	1841	64	5	265	5	HIST1H1C	6	26056277	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	1479571	26056277	145058790	330	10781											
HIST1H2AC	8334	hgsc.bcm.edu	37	chr6	26124563	26124563	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgggccgagtgcaccgcctgCtccgtaaaggcaactacgca	9	6	12	14	4	0	0	0	0	0	0	1	1	1	0	4	2	4	5	4	2	4	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26124563C>G	ENST00000602637.1	+	1	133	c.103C>G	c.(103-105)Ctc>Gtc	p.L35V	HIST1H2BC_ENST00000396984.1_5'Flank|HIST1H2BC_ENST00000314332.5_5'Flank|HIST1H2AC_ENST00000377791.2_Missense_Mutation_p.L35V			Q93077	H2A1C_HUMAN	histone cluster 1, H2ac	35						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(5)	12						GCACCGCCTGCTCCGTAAAGG	0.657																																					p.L35V		Atlas-SNP	.											.	HIST1H2AC	29	.	0			c.C103G						PASS	.						42	44	44					6																	26124563		2203	4300	6503	SO:0001583	missense	8334	exon1			CGCCTGCTCCGTA	Z80778	CCDS4585.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000180573	ENSG00000180573		"Histones / Replication-dependent"	4733	protein-coding gene	gene with protein product		602794	"H2A histone family, member L", "histone 1, H2ac"	H2AFL		9119399, 12408966	Standard	NM_003512		Approved		uc003ngm.3	Q93077	OTTHUMG00000014428	ENST00000602637.1:c.103C>G	6.37:g.26124563C>G	ENSP00000473534:p.Leu35Val	99	0	0		100	32	0.32	NM_003512	B2R4F7|O00775|O00776|O00777|O00778|Q540R1	Missense_Mutation	SNP	ENST00000602637.1	37	CCDS4585.1	.	.	.	.	.	.	.	.	.	.	.	14.39	2.522457	0.44866	.	.	ENSG00000180573	ENST00000377791;ENST00000314088	T;T	0.59224	0.28;0.28	5.6	5.6	0.85130	Histone-fold (2);Histone core (1);Histone H2A (2);	0.000000	0.38897	N	0.001536	T	0.80199	0.4579	H	0.97564	4.03	0.40025	D	0.975457	D	0.64830	0.994	D	0.66351	0.943	D	0.85943	0.1459	10	0.87932	D	0	.	12.3103	0.54925	0.0:0.9229:0.0:0.0771	.	35	Q93077	H2A1C_HUMAN	V	35	ENSP00000367022:L35V;ENSP00000321389:L35V	ENSP00000321389:L35V	L	+	1	0	HIST1H2AC	26232542	1.000000	0.71417	0.810000	0.32431	0.125000	0.20455	3.848000	0.55903	2.793000	0.96121	0.591000	0.81541	CTC	.	.	none		0.657	HIST1H2AC-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468023.1	NM_003512		G	26124563	C	G	26124563	3	3	27	1	0	0	0	0	1	0	0	0	7139	797	28	4	105	4	HIST1H2AC	6	26124563	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	68286	26124563	144990504	331	10782											
HIST1H2AC	8334	hgsc.bcm.edu	37	chr6	26124805	26124805	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttcctaacatccaggccgtGcttctgcctaagaagaccga	10	9	8	14	2	1	2	0	0	1	2	3	3	3	2	5	1	3	1	5	1	3	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26124805G>A	ENST00000602637.1	+	1	375	c.345G>A	c.(343-345)gtG>gtA	p.V115V	HIST1H2BC_ENST00000396984.1_5'Flank|HIST1H2BC_ENST00000314332.5_5'Flank|HIST1H2AC_ENST00000377791.2_Silent_p.V115V			Q93077	H2A1C_HUMAN	histone cluster 1, H2ac	115						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(5)	12						TCCAGGCCGTGCTTCTGCCTA	0.562																																					p.V115V		Atlas-SNP	.											.	HIST1H2AC	29	.	0			c.G345A						PASS	.						82	82	82					6																	26124805		2203	4300	6503	SO:0001819	synonymous_variant	8334	exon1			GGCCGTGCTTCTG	Z80778	CCDS4585.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000180573	ENSG00000180573		"Histones / Replication-dependent"	4733	protein-coding gene	gene with protein product		602794	"H2A histone family, member L", "histone 1, H2ac"	H2AFL		9119399, 12408966	Standard	NM_003512		Approved		uc003ngm.3	Q93077	OTTHUMG00000014428	ENST00000602637.1:c.345G>A	6.37:g.26124805G>A		134	0	0		128	40	0.3125	NM_003512	B2R4F7|O00775|O00776|O00777|O00778|Q540R1	Silent	SNP	ENST00000602637.1	37	CCDS4585.1																																																																																			.	.	none		0.562	HIST1H2AC-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468023.1	NM_003512		A	26124805	G	A	26124805	2	1	27	1	0	0	0	0	0	0	0	1	7139	1306	46	2		2	HIST1H2AC	6	26124805	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	242	26124805	144990262	332	10783											
HIST1H1E	3008	hgsc.bcm.edu	37	chr6	26156817	26156817	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ccgctctcaagaaagcgctgGcagccgctggctatgacgtg	8	7	13	13	4	1	2	1	1	1	1	2	2	1	2	2	2	2	5	2	2	3	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26156817G>A	ENST00000304218.3	+	1	259	c.199G>A	c.(199-201)Gca>Aca	p.A67T	HIST1H2BD_ENST00000377777.4_5'Flank|HIST1H2BD_ENST00000289316.2_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	67	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						GAAAGCGCTGGCAGCCGCTGG	0.617																																					p.A67T		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.G199A						PASS	.						35	38	37					6																	26156817		2203	4300	6503	SO:0001583	missense	3008	exon1			GCGCTGGCAGCCG	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.199G>A	6.37:g.26156817G>A	ENSP00000307705:p.Ala67Thr	90	0	0		72	10	0.138889	NM_005321	Q4VB25	Missense_Mutation	SNP	ENST00000304218.3	37	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	19.26	3.794164	0.70452	.	.	ENSG00000168298	ENST00000304218	T	0.10477	2.87	5.11	5.11	0.69529	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.416196	0.25863	N	0.027820	T	0.15089	0.0364	L	0.60957	1.885	0.53688	D	0.999973	B	0.33379	0.41	P	0.47528	0.549	T	0.01643	-1.1305	10	0.42905	T	0.14	-2.9473	17.8759	0.88825	0.0:0.0:1.0:0.0	.	67	P10412	H14_HUMAN	T	67	ENSP00000307705:A67T	ENSP00000307705:A67T	A	+	1	0	HIST1H1E	26264796	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	5.534000	0.67167	2.542000	0.85734	0.561000	0.74099	GCA	.	.	none		0.617	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321		A	26156817	G	A	26156817	3	1	27	1	0	0	0	0	1	0	0	0	7135	1203	42	2	201	2	HIST1H1E	6	26156817	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	32012	26156817	144958250	333	10784											
HIST1H1E	3008	hgsc.bcm.edu	37	chr6	26157219	26157219	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttaaacccaaggcggctaaaCcaaagaccgccaagcccaag	16	3	8	14	2	0	1	0	0	0	1	0	1	0	1	5	2	3	1	5	2	8	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26157219C>T	ENST00000304218.3	+	1	661	c.601C>T	c.(601-603)Cca>Tca	p.P201S	HIST1H2BD_ENST00000377777.4_5'Flank|HIST1H2BD_ENST00000289316.2_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	201					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						GGCGGCTAAACCAAAGACCGC	0.527																																					p.P201S		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.C601T						PASS	.						32	34	33					6																	26157219		2202	4299	6501	SO:0001583	missense	3008	exon1			GCTAAACCAAAGA	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.601C>T	6.37:g.26157219C>T	ENSP00000307705:p.Pro201Ser	98	0	0		71	10	0.140845	NM_005321	Q4VB25	Missense_Mutation	SNP	ENST00000304218.3	37	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	11.35	1.612147	0.28712	.	.	ENSG00000168298	ENST00000304218	T	0.12672	2.66	5.48	4.56	0.56223	.	0.130977	0.52532	D	0.000076	T	0.07007	0.0178	L	0.59912	1.85	0.37467	D	0.915446	B	0.20261	0.043	B	0.14578	0.011	T	0.06427	-1.0827	10	0.31617	T	0.26	-1.4746	11.1455	0.48428	0.1401:0.7241:0.1358:0.0	.	201	P10412	H14_HUMAN	S	201	ENSP00000307705:P201S	ENSP00000307705:P201S	P	+	1	0	HIST1H1E	26265198	1.000000	0.71417	0.284000	0.24805	0.975000	0.68041	2.111000	0.41883	2.717000	0.92951	0.655000	0.94253	CCA	.	.	none		0.527	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321		T	26157219	C	T	26157219	3	4	27	1	0	0	0	0	1	0	0	0	7135	507	18	2	603	2	HIST1H1E	6	26157219	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	402	26157219	144957848	334	10785											
HIST1H1D	3007	hgsc.bcm.edu	37	chr6	26234735	26234735	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cttcggggtagcggcgccagCcaccttcttgggcttcttgg	3	11	14	13	3	2	0	0	0	2	0	3	0	2	0	3	5	2	2	3	5	1	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26234735C>T	ENST00000244534.5	-	1	481	c.427G>A	c.(427-429)Gct>Act	p.A143T		NM_005320.2	NP_005311.1	P16402	H13_HUMAN	histone cluster 1, H1d	143					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				GCGGCGCCAGCCACCTTCTTG	0.572																																					p.A143T		Atlas-SNP	.											.	HIST1H1D	40	.	0			c.G427A						PASS	.						65	71	69					6																	26234735		2203	4300	6503	SO:0001583	missense	3007	exon1			CGCCAGCCACCTT	M60747	CCDS4597.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000124575	ENSG00000124575		"Histones / Replication-dependent"	4717	protein-coding gene	gene with protein product		142210	"H1 histone family, member 3", "histone 1, H1d"	H1F3		1916825, 12408966	Standard	NM_005320		Approved	H1.3, H1d, H1s-2	uc003nhd.3	P16402	OTTHUMG00000014432	ENST00000244534.5:c.427G>A	6.37:g.26234735C>T	ENSP00000244534:p.Ala143Thr	125	0	0		99	27	0.272727	NM_005320	B2R751|Q2M2I2	Missense_Mutation	SNP	ENST00000244534.5	37	CCDS4597.1	.	.	.	.	.	.	.	.	.	.	.	0.960	-0.703518	0.03255	.	.	ENSG00000124575	ENST00000244534	T	0.14022	2.54	4.7	-4.82	0.03171	.	0.725492	0.13325	N	0.396354	T	0.01061	0.0035	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45396	-0.9264	10	0.06891	T	0.86	-17.2311	5.5857	0.17274	0.2338:0.4156:0.0:0.3506	.	143	P16402	H13_HUMAN	T	143	ENSP00000244534:A143T	ENSP00000244534:A143T	A	-	1	0	HIST1H1D	26342714	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.356000	0.07661	-0.537000	0.06290	-0.295000	0.09555	GCT	.	.	none		0.572	HIST1H1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040095.1	NM_005320		T	26234735	C	T	26234735	3	4	27	1	0	0	0	0	1	0	0	0	7134	739	26	2	242	2	HIST1H1D	6	26234735	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	77516	26234735	144880332	335	10786											
HIST1H3G	8355	hgsc.bcm.edu	37	chr6	26271208	26271208	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcccggaaacctctacgcTctctccccacgaatgcggcg	7	7	9	18	5	2	0	0	0	2	0	4	2	3	1	4	2	4	1	4	2	3	1	rs141036055	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26271208T>C	ENST00000305910.3	-	1	404	c.405A>G	c.(403-405)agA>agG	p.R135R	HIST1H2BI_ENST00000377733.2_5'Flank	NM_003534.2	NP_003525.1	P68431	H31_HUMAN	histone cluster 1, H3g	135				Missing (in Ref. 2; AAA52651). {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)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	12						ACCTCTACGCTCTCTCCCCAC	0.483													T|||	2	0.000399361	0.0	0.0	5008	,	,		17707	0.0		0.0	False		,,,				2504	0.002				p.R135R		Atlas-SNP	.											.	HIST1H3G	20	.	0			c.A405G						PASS	.	T		0,4406		0,0,2203	61	64	63		405	1.5	1	6	dbSNP_134	63	11,8589		0,11,4289	no	coding-synonymous	HIST1H3G	NM_003534.2		0,11,6492	CC,CT,TT		0.1279,0.0,0.0846		135/137	26271208	11,12995	2203	4300	6503	SO:0001819	synonymous_variant	8355	exon1			CTACGCTCTCTCC	Z80785	CCDS4602.1	6p22.1	2011-07-22	2006-10-11	2003-03-14	ENSG00000256018			"Histones / Replication-dependent"	4772	protein-coding gene	gene with protein product		602815	"H3 histone family, member H", "histone 1, H3g"	H3FH		9119399, 12408966	Standard	NM_003534		Approved	H3/h	uc003nhi.3	P68431	OTTHUMG00000014436	ENST00000305910.3:c.405A>G	6.37:g.26271208T>C		84	0	0		50	22	0.44	NM_003534	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000305910.3	37	CCDS4602.1																																																																																			T|0.999;C|0.001	0.001	strong		0.483	HIST1H3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040099.2	NM_003534		C	26271208	T	C	26271208	2	2	27	1	0	0	0	0	0	0	0	1	7170	1548	54	3		3	HIST1H3G	6	26271208	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	36473	26271208	144843859	336	10787											
HIST1H2BI	8346	hgsc.bcm.edu	37	chr6	26273368	26273368	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gtccaccccgacaccggcatCtcgtccaaggctatggggat	8	7	11	15	3	1	0	0	0	1	0	4	2	3	1	5	4	0	2	5	4	2	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:26273368C>G	ENST00000377733.2	+	1	225	c.165C>G	c.(163-165)atC>atG	p.I55M	HIST1H3G_ENST00000305910.3_5'Flank	NM_003525.2	NP_003516.1	P62807	H2B1C_HUMAN	histone cluster 1, H2bi	55					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)			central_nervous_system(1)|cervix(2)|endometrium(3)|large_intestine(1)|lung(8)|urinary_tract(1)	16						ACACCGGCATCTCGTCCAAGG	0.562																																					p.I55M		Atlas-SNP	.											.	HIST1H2BI	29	.	0			c.C165G						PASS	.						215	203	207					6																	26273368		2203	4300	6503	SO:0001583	missense	8346	exon1			CGGCATCTCGTCC	Z80782	CCDS4603.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000168242	ENSG00000278588		"Histones / Replication-dependent"	4756	protein-coding gene	gene with protein product		602807	"H2B histone family, member K", "histone 1, H2bi"	H2BFK		9119399, 12408966	Standard	NM_003525		Approved	H2B/k	uc003nhk.3	P62807	OTTHUMG00000014448	ENST00000377733.2:c.165C>G	6.37:g.26273368C>G	ENSP00000366962:p.Ile55Met	109	0	0		108	22	0.203704	NM_003525	P02278|Q3B872|Q4VB69|Q93078|Q93080	Missense_Mutation	SNP	ENST00000377733.2	37	CCDS4603.1	.	.	.	.	.	.	.	.	.	.	.	16.73	3.205259	0.58234	.	.	ENSG00000168242	ENST00000377733	T	0.73152	-0.72	4.5	2.68	0.31781	.	.	.	.	.	T	0.73401	0.3582	M	0.89904	3.07	0.27866	N	0.940224	.	.	.	.	.	.	T	0.68550	-0.5379	7	0.87932	D	0	.	10.0332	0.42114	0.0:0.8284:0.0:0.1716	.	.	.	.	M	55	ENSP00000366962:I55M	ENSP00000366962:I55M	I	+	3	3	HIST1H2BI	26381347	1.000000	0.71417	1.000000	0.80357	0.677000	0.39632	1.163000	0.31798	0.335000	0.23614	0.563000	0.77884	ATC	.	.	none		0.562	HIST1H2BI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040111.1	NM_003525		G	26273368	C	G	26273368	3	3	27	1	0	0	0	0	1	0	0	0	7157	903	32	4	167	4	HIST1H2BI	6	26273368	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2160	26273368	144841699	337	10788											
HIST1H2BK	85236	hgsc.bcm.edu	37	chr6	27114289	27114289	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcagcaggcgcacggccgTctggatctccctggaggtga	7	6	15	13	3	2	1	0	1	2	0	3	3	2	3	2	5	2	3	2	5	0	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:27114289T>C	ENST00000356950.1	-	1	288	c.289A>G	c.(289-291)Acg>Gcg	p.T97A	MIR3143_ENST00000584253.1_RNA|HIST1H2AH_ENST00000377459.1_5'Flank|HIST1H2BK_ENST00000396891.4_Missense_Mutation_p.T97A			O60814	H2B1K_HUMAN	histone cluster 1, H2bk	97					antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)	extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	13						CGCACGGCCGTCTGGATCTCC	0.622																																					p.T97A		Atlas-SNP	.											.	HIST1H2BK	68	.	0			c.A289G						PASS	.						56	62	60					6																	27114289		2203	4294	6497	SO:0001583	missense	85236	exon1			CGGCCGTCTGGAT	AJ223352	CCDS4621.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000197903	ENSG00000197903		"Histones / Replication-dependent"	13954	protein-coding gene	gene with protein product		615045	"H2B histone family, member T", "histone 1, H2bk"	H2BFT		12408966	Standard	NM_080593		Approved	H2BFAiii	uc003nix.2	O60814	OTTHUMG00000014473	ENST00000356950.1:c.289A>G	6.37:g.27114289T>C	ENSP00000349430:p.Thr97Ala	90	0	0		105	34	0.32381	NM_080593	A8K7P7|Q2VPI7	Missense_Mutation	SNP	ENST00000356950.1	37	CCDS4621.1	.	.	.	.	.	.	.	.	.	.	.	26.7	4.762466	0.89932	.	.	ENSG00000197903	ENST00000396891;ENST00000356950	T;T	0.41758	0.99;0.99	4.05	4.05	0.47172	Histone-fold (2);Histone core (1);	0.000000	0.38548	U	0.001653	T	0.61413	0.2345	M	0.92691	3.335	0.46396	D	0.999028	D	0.57899	0.981	D	0.64042	0.921	T	0.71745	-0.4500	10	0.87932	D	0	.	11.5972	0.50981	0.0:0.0:0.0:1.0	.	97	O60814	H2B1K_HUMAN	A	97	ENSP00000380100:T97A;ENSP00000349430:T97A	ENSP00000349430:T97A	T	-	1	0	HIST1H2BK	27222268	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.391000	0.66266	1.783000	0.52377	0.528000	0.53228	ACG	.	.	none		0.622	HIST1H2BK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040141.1	NM_080593		C	27114289	T	C	27114289	3	2	27	1	0	0	0	0	1	0	0	0	7159	1667	58	3	95	3	HIST1H2BK	6	27114289	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	840921	27114289	144000778	338	10789											
HIST1H4J	8363	hgsc.bcm.edu	37	chr6	27792127	27792128	+	Frame_Shift_Ins	INS	-	-	CACGC																															acgccgtgacctatacagagINScacgccaagcgcaagacggt																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:27792127_27792128insCACGC	ENST00000355057.1	+	1	244_245	c.225_226insCACGC	c.(226-228)cacfs	p.-77fs		NM_021968.3	NP_068803.1	P62805	H4_HUMAN	histone cluster 1, H4j						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(1)|pancreas(1)	4						CCTATACAGAGCACGCCAAGCG	0.624																																					p.E75fs		Atlas-Indel	.											HIST1H4J,NS,carcinoma,+2,1	HIST1H4J	11	1	0			c.225_226insCACGC						PASS	.																																			SO:0001589	frameshift_variant	8363	exon1			.	J00188	CCDS4630.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197238	ENSG00000197238		"Histones / Replication-dependent"	4785	protein-coding gene	gene with protein product		602826	"H4 histone family, member E", "histone 1, H4j"	H4FE		6265100, 9439656, 12408966	Standard	NM_021968		Approved	H4/e, H4F2iv	uc003njp.3	P62805	OTTHUMG00000014487	ENST00000355057.1:c.226_230dupCACGC	6.37:g.27792128_27792132dupCACGC	ENSP00000347168:p.Ala77fs	242	0	0		199	13	0.0653266	NM_021968	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Frame_Shift_Ins	INS	ENST00000355057.1	37	CCDS4630.1																																																																																			.	.	none		0.624	HIST1H4J-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040155.1	NM_021968		CACGC	27792128	-	CACGC	27792127	7	5	27	1	0	1	1	0	0	0	0	0	7183	962	34	0	227	0	HIST1H4J	6	27792127	Frame_Shift_Ins	INS	-	TCGA-G8-6909-01A-11D-2210-10	677838	27792127	143322940	339	10790											
HIST1H2AM	8336	hgsc.bcm.edu	37	chr6	27860579	27860579	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctctcagtcttcttggggaGcagtacggcctggatgttag	6	12	14	9	1	3	0	1	0	3	0	4	2	3	2	1	4	2	4	1	4	2	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:27860579G>A	ENST00000359611.2	-	1	384	c.349C>T	c.(349-351)Ctc>Ttc	p.L117F	HIST1H3J_ENST00000359303.2_5'Flank|HIST1H3J_ENST00000479986.1_5'UTR|HIST1H2BO_ENST00000303806.4_5'Flank	NM_003514.2	NP_003505.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2am	117						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						TTCTTGGGGAGCAGTACGGCC	0.507																																					p.L117F		Atlas-SNP	.											.	HIST1H2AM	27	.	0			c.C349T						PASS	.						131	126	128					6																	27860579		2203	4300	6503	SO:0001583	missense	8336	exon1			TGGGGAGCAGTAC	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.349C>T	6.37:g.27860579G>A	ENSP00000352627:p.Leu117Phe	214	0	0		181	41	0.226519	NM_003514	P02261|Q2M1R2|Q76PA6	Missense_Mutation	SNP	ENST00000359611.2	37	CCDS4639.1	.	.	.	.	.	.	.	.	.	.	G	11.88	1.770382	0.31320	.	.	ENSG00000233224	ENST00000359611	T	0.52057	0.68	4.06	3.19	0.36642	.	0.000000	0.26130	U	0.026178	T	0.48840	0.1522	M	0.79475	2.455	0.32139	N	0.585724	.	.	.	.	.	.	T	0.54351	-0.8307	8	0.87932	D	0	.	11.3928	0.49824	0.0916:0.0:0.9084:0.0	.	.	.	.	F	117	ENSP00000352627:L117F	ENSP00000352627:L117F	L	-	1	0	HIST1H2AM	27968558	1.000000	0.71417	1.000000	0.80357	0.154000	0.21943	3.207000	0.51106	1.298000	0.44778	-0.136000	0.14681	CTC	.	.	none		0.507	HIST1H2AM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040162.1	NM_003514		A	27860579	G	A	27860579	3	1	27	1	0	0	0	0	1	0	0	0	7148	971	34	2	47	2	HIST1H2AM	6	27860579	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	68452	27860579	143254488	340	10791											
ZNF193	7746	hgsc.bcm.edu	37	chr6	28195521	28195521	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtaaagagatggtgcctctAgcagagcagacaccactgac	13	7	11	10	0	1	4	0	1	1	3	1	5	1	4	2	1	3	3	2	1	3	2	rs12197427	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:28195521A>G	ENST00000252207.5	+	3	622	c.474A>G	c.(472-474)ctA>ctG	p.L158L	ZSCAN9_ENST00000531979.1_Silent_p.L158L|ZSCAN9_ENST00000531981.1_3'UTR|ZSCAN9_ENST00000425468.2_Silent_p.L158L|ZSCAN9_ENST00000527436.1_Silent_p.L158L	NM_006299.4	NP_006290.1	O15535	ZSC9_HUMAN	zinc finger and SCAN domain containing 9	158					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)										TGGTGCCTCTAGCAGAGCAGA	0.488													A|||	78	0.0155751	0.0	0.0274	5008	,	,		18815	0.0129		0.0278	False		,,,				2504	0.0184				p.L158L		Atlas-SNP	.											ZNF193,NS,carcinoma,+2,1	.	.	1	0			c.A474G						PASS	.	A	,,	26,4380	32.6+/-62.9	0,26,2177	70	64	66		474,474,474	-3.5	0	6	dbSNP_120	66	313,8287	112.0+/-172.2	8,297,3995	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF193	NM_001199479.1,NM_001199480.1,NM_006299.4	,,	8,323,6172	GG,GA,AA		3.6395,0.5901,2.6065	,,	158/446,158/395,158/395	28195521	339,12667	2203	4300	6503	SO:0001819	synonymous_variant	7746	exon3			GCCTCTAGCAGAG	U62392	CCDS4646.1, CCDS56407.1	6p21	2013-01-09	2013-01-09	2013-01-09	ENSG00000137185	ENSG00000137185		"-", "Zinc fingers, C2H2-type"	12984	protein-coding gene	gene with protein product		602246	"zinc finger protein 193"	ZNF193			Standard	NM_001199479		Approved	PRD51	uc003nkq.2	O15535	OTTHUMG00000014515	ENST00000252207.5:c.474A>G	6.37:g.28195521A>G		200	0	0		160	77	0.48125	NM_006299	B4E1W6|E7EVQ2|Q2TTR1	Silent	SNP	ENST00000252207.5	37	CCDS4646.1																																																																																			A|0.971;G|0.029	0.029	strong		0.488	ZSCAN9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000040183.2	NM_006299		G	28195521	A	G	28195521	2	3	27	1	0	0	0	0	0	0	0	1	17772	407	15	3		3	ZNF193	6	28195521	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	334942	28195521	142919546	341	10792											
ZKSCAN4	387032	hgsc.bcm.edu	37	chr6	28213527	28213527	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tggattctcctgtgtttagtCaggcctgaactttgagcaaa	9	14	10	8	0	2	2	1	2	1	0	3	3	2	3	2	2	2	2	2	2	3	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:28213527C>T	ENST00000377294.2	-	5	1248	c.1005G>A	c.(1003-1005)ctG>ctA	p.L335L	ZKSCAN4_ENST00000423974.2_Silent_p.L180L	NM_019110.3	NP_061983.2	Q969J2	ZKSC4_HUMAN	zinc finger with KRAB and SCAN domains 4	335					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						TGTGTTTAGTCAGGCCTGAAC	0.453																																					p.L335L		Atlas-SNP	.											.	ZKSCAN4	42	.	0			c.G1005A						PASS	.						130	114	119					6																	28213527		2203	4300	6503	SO:0001819	synonymous_variant	387032	exon5			TTTAGTCAGGCCT	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.1005G>A	6.37:g.28213527C>T		152	0	0		138	54	0.391304	NM_019110	B2RE32|Q5U7L4	Silent	SNP	ENST00000377294.2	37	CCDS4647.1																																																																																			.	.	none		0.453	ZKSCAN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040179.1	NM_019110		T	28213527	C	T	28213527	2	4	27	1	0	0	0	0	0	0	0	1	17704	813	29	2		2	ZKSCAN4	6	28213527	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	18006	28213527	142901540	342	10793											
PGBD1	84547	hgsc.bcm.edu	37	chr6	28251890	28251890	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	accatcctgcccaaggagctCcagccctgtgtgaagacata	11	7	9	14	0	0	2	0	1	0	1	2	3	2	3	5	1	3	1	5	1	3	1	rs527450661		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:28251890C>T	ENST00000405948.2	+	2	720	c.300C>T	c.(298-300)ctC>ctT	p.L100L	PGBD1_ENST00000259883.3_Silent_p.L100L	NM_001184743.1|NM_032507.3	NP_001171672.1|NP_115896.1	Q96JS3	PGBD1_HUMAN	piggyBac transposable element derived 1	100	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.					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						CCAAGGAGCTCCAGCCCTGTG	0.532													C|||	1	0.000199681	0.0	0.0	5008	,	,		18052	0.001		0.0	False		,,,				2504	0.0				p.L100L		Atlas-SNP	.											.	PGBD1	106	.	0			c.C300T						PASS	.						101	93	95					6																	28251890		2203	4300	6503	SO:0001819	synonymous_variant	84547	exon2			GGAGCTCCAGCCC	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.300C>T	6.37:g.28251890C>T		81	0	0		88	4	0.0454545	NM_001184743	Q53F43|Q6NTF5|Q8WWS4	Silent	SNP	ENST00000405948.2	37	CCDS4648.1																																																																																			.	.	none		0.532	PGBD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040188.2			T	28251890	C	T	28251890	2	4	27	1	0	0	0	0	0	0	0	1	11789	842	30	2		2	PGBD1	6	28251890	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	38363	28251890	142863177	343	10794											
HLA-A	3105	hgsc.bcm.edu	37	chr6	29910551	29910551	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caggctcccactccatgaggTatttcttcacatccgtgtcc	7	12	7	15	1	2	1	1	1	1	0	6	1	6	1	4	2	0	2	4	2	1	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29910551T>G	ENST00000396634.1	+	4	432	c.91T>G	c.(91-93)Tat>Gat	p.Y31D	HLA-A_ENST00000376802.2_Missense_Mutation_p.Y31D|HLA-A_ENST00000376809.5_Missense_Mutation_p.Y31D|HLA-A_ENST00000376806.5_Missense_Mutation_p.Y31D			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	31	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)			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						CTCCATGAGGTATTTCTTCAC	0.726									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.Y31D		Atlas-SNP	.											.	HLA-A	89	.	0			c.T91G						PASS	.						15	14	15					6																	29910551		2179	4262	6441	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	ATGAGGTATTTCT	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.91T>G	6.37:g.29910551T>G	ENSP00000379873:p.Tyr31Asp	25	0	0		33	15	0.454545	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	9.530	1.110553	0.20714	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.01854	4.6;4.6;4.6;4.6	3.72	2.49	0.30216	MHC class I, alpha chain, alpha1/alpha2 (3);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	0.275088	0.19018	U	0.124883	T	0.19087	0.0458	H	0.99999	5.785	0.09310	N	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	0.48115	-0.9063	10	0.87932	D	0	.	6.2298	0.20728	0.2235:0.0:0.0:0.7765	.	31;31;31;31;31	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	D	31	ENSP00000379873:Y31D;ENSP00000366002:Y31D;ENSP00000366005:Y31D;ENSP00000365998:Y31D	ENSP00000348012:Y31D	Y	+	1	0	HLA-A	30018530	0.000000	0.05858	0.020000	0.16555	0.261000	0.26267	0.438000	0.21559	0.583000	0.29574	0.391000	0.25812	TAT	.	.	none		0.726	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116		G	29910551	T	G	29910551	3	3	27	1	0	0	0	0	1	0	0	0	7204	1638	57	5	97	5	HLA-A	6	29910551	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	1658661	29910551	141204516	344	10795											
HLA-A	3105	hgsc.bcm.edu	37	chr6	29911213	29911213	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcagatcaccaagcgcaagtGggaggcggcccatgaggcgg	10	4	16	11	3	2	2	2	1	0	1	2	3	2	3	2	5	1	1	2	5	2	0	rs199474545		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:29911213G>A	ENST00000396634.1	+	5	853	c.512G>A	c.(511-513)tGg>tAg	p.W171*	HLA-A_ENST00000376802.2_Nonsense_Mutation_p.W171*|HLA-A_ENST00000376809.5_Nonsense_Mutation_p.W171*|HLA-A_ENST00000376806.5_Nonsense_Mutation_p.W171*			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	171	Alpha-2.				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						AAGCGCAAGTGGGAGGCGGCC	0.647									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.W171X		Atlas-SNP	.											.	HLA-A	89	.	0			c.G512A						PASS	.						35	27	30					6																	29911213		1509	2705	4214	SO:0001587	stop_gained	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GCAAGTGGGAGGC	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.512G>A	6.37:g.29911213G>A	ENSP00000379873:p.Trp171*	293	0	0		132	32	0.242424	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Nonsense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	31|31	5.083642|5.083642	0.94050|0.94050	.|.	.|.	ENSG00000206503|ENSG00000206503	ENST00000355767|ENST00000396634;ENST00000376806;ENST00000376809;ENST00000376802	.|.	.|.	.|.	3.78|3.78	-0.515|-0.515	0.11954|0.11954	.|.	.|0.000000	.|0.36815	.|U	.|0.002400	T|.	0.19644|.	0.0472|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.12604|.	-1.0541|.	4|.	0.87932|0.87932	D|D	0|0	.|.	2.0762|2.0762	0.03624|0.03624	0.1916:0.1531:0.4984:0.1569|0.1916:0.1531:0.4984:0.1569	.|.	.|.	.|.	.|.	R|X	146|171	.|.	ENSP00000348012:G146R|ENSP00000365998:W171X	G|W	+|+	1|2	0|0	HLA-A|HLA-A	30019192|30019192	0.184000|0.184000	0.23200|0.23200	0.057000|0.057000	0.19452|0.19452	0.134000|0.134000	0.20937|0.20937	0.137000|0.137000	0.15995|0.15995	-0.240000|-0.240000	0.09696|0.09696	0.485000|0.485000	0.47835|0.47835	GGG|TGG	.	.	weak		0.647	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116		A	29911213	G	A	29911213	4	1	27	1	0	0	0	0	0	1	0	0	7204	1357	47	2	522	2	HLA-A	6	29911213	Nonsense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	662	29911213	141203854	345	10796											
C6orf136	221545	hgsc.bcm.edu	37	chr6	30615413	30615413	+	Intron	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagggcaggggccgagagatTcgtagccctgctgcggcgcc	7	5	17	12	4	0	1	0	0	0	1	1	3	0	1	3	4	3	3	3	4	2	2	rs146616682	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:30615413T>C	ENST00000376473.5	+	1	231				C6orf136_ENST00000376471.4_Intron|C6orf136_ENST00000493705.1_3'UTR|AL662800.2_ENST00000583820.1_RNA|C6orf136_ENST00000293604.6_Silent_p.I135I|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						GCCGAGAGATTCGTAGCCCTG	0.716													T|||	13	0.00259585	0.0	0.0072	5008	,	,		13756	0.001		0.007	False		,,,				2504	0.0				p.I135I		Atlas-SNP	.											.	C6orf136	31	.	0			c.T405C						PASS	.						5	7	7					6																	30615413		669	1552	2221	SO:0001627	intron_variant	221545	exon1			AGAGATTCGTAGC	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+333T>C	6.37:g.30615413T>C		59	0	0		67	44	0.656716	NM_001161376	A9R9P9|F8VX15|Q5SU01|Q6ZSB7|Q8TB84	Silent	SNP	ENST00000376473.5	37	CCDS43443.1																																																																																			T|0.994;C|0.006	0.006	strong		0.716	C6orf136-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076457.4	NM_145029		C	30615413	T	C	30615413	1	2	27	0	1	0	0	0	0	0	0	0	2333	1771	62	3		3	C6orf136	6	30615413	Intron	SNP	T	TCGA-G8-6909-01A-11D-2210-10	704200	30615413	140499654	346	10797											
HLA-C	3107	hgsc.bcm.edu	37	chr6	31238973	31238986	+	Frame_Shift_Del	DEL	TCTGAGCCGCGGTG	TCTGAGCCGCGGTG	-																															ctccaacttgcgctgggtgaTctgagccgcggtgtccgcgg																								rs45578735|rs2308584|rs200155513|rs45622747|rs2308585|rs200892438|rs41541313|rs281860498|rs45505091|rs281860496|rs281860497|rs281860495	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCTGAGCCGCGGTG	TCTGAGCCGCGGTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31238973_31238986delTCTGAGCCGCGGTG	ENST00000376228.5	-	3	497_510	c.483_496delCACCGCGGCTCAGA	c.(481-498)gacaccgcggctcagatcfs	p.TAAQI162fs	HLA-C_ENST00000383329.3_Frame_Shift_Del_p.TAAQI162fs	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	162	Alpha-2.				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)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						CGCTGGGTGATCTGAGCCGCGGTGTCCGCGGCGG	0.692																																					p.162_166del		Atlas-Indel	.											.	HLA-C	92	.	0			c.484_497del						PASS	.																																			SO:0001589	frameshift_variant	3107	exon3			.	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4933	protein-coding gene	gene with protein product		142840	"psoriasis susceptibility 1"	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.483_496delCACCGCGGCTCAGA	6.37:g.31238973_31238986delTCTGAGCCGCGGTG	ENSP00000365402:p.Thr162fs	123	0	0		151	29	0.192053	NM_002117	O02864|O02958|Q29643|Q9MY30	Frame_Shift_Del	DEL	ENST00000376228.5	37	CCDS34393.1																																																																																			.	.	none		0.692	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117		-	31238986	TCTGAGCCGCGGTG	-	31238973	7	5	27	1	0	1	0	1	0	0	0	0	7206	1435	50	0	628	0	HLA-C	6	31238973	Frame_Shift_Del	DEL	TCTGAGCCGCGGTG	TCGA-G8-6909-01A-11D-2210-10	623560	31238973	139876094	347	10798											
MCCD1	401250	hgsc.bcm.edu	37	chr6	31496834	31496834	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tctctcggtaccatttccttCgcctccttctgccctcctgg	2	15	6	18	2	2	0	0	0	2	0	8	0	5	0	6	2	2	1	6	2	1	4	rs146742941	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31496834C>T	ENST00000376191.2	+	1	341	c.43C>T	c.(43-45)Cgc>Tgc	p.R15C	DDX39B_ENST00000462421.1_5'Flank	NM_001011700.2	NP_001011700.2	P59942	MCCD1_HUMAN	mitochondrial coiled-coil domain 1	15						mitochondrion (GO:0005739)				skin(1)	1						CCATTTCCTTCGCCTCCTTCT	0.627																																					p.R15C		Atlas-SNP	.											MCCD1,NS,carcinoma,-1,1	MCCD1	3	1	0			c.C43T						PASS	.	C	CYS/ARG	0,3022		0,0,1511	173	128	144		43	0.8	0.1	6	dbSNP_134	144	2,5416		0,2,2707	yes	missense	MCCD1	NM_001011700.2	180	0,2,4218	TT,TC,CC		0.0369,0.0,0.0237	probably-damaging	15/120	31496834	2,8438	1511	2709	4220	SO:0001583	missense	401250	exon1			TTCCTTCGCCTCC		CCDS34396.1	6p21.3	2003-10-17				ENSG00000204511			20668	protein-coding gene	gene with protein product		609624				14527716	Standard	NM_001011700		Approved		uc003ntp.1	P59942		ENST00000376191.2:c.43C>T	6.37:g.31496834C>T	ENSP00000365362:p.Arg15Cys	68	0	0		46	25	0.543478	NM_001011700	A2AB29|A2RUP7|B0UZB2|Q7RTY2	Missense_Mutation	SNP	ENST00000376191.2	37	CCDS34396.1	.	.	.	.	.	.	.	.	.	.	c	0.103	-1.148811	0.01714	0.0	3.69E-4	ENSG00000204511	ENST00000376191	T	0.25250	1.81	0.748	0.748	0.18376	.	1.197690	0.06338	N	0.707425	T	0.06645	0.0170	N	0.24115	0.695	0.09310	N	1	B	0.10296	0.003	B	0.01281	0.0	T	0.41770	-0.9490	9	0.72032	D	0.01	.	.	.	.	.	15	P59942	MCCD1_HUMAN	C	15	ENSP00000365362:R15C	ENSP00000365362:R15C	R	+	1	0	MCCD1	31604813	0.000000	0.05858	0.062000	0.19696	0.029000	0.11900	-1.047000	0.03521	0.691000	0.31592	0.555000	0.69702	CGC	C|1.000;T|0.000	0.000	strong		0.627	MCCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259099.1			T	31496834	C	T	31496834	3	4	27	1	0	0	0	0	1	0	0	0	9385	884	31	1	45	1	MCCD1	6	31496834	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	257861	31496834	139618233	348	10799											
LTB	4050	hgsc.bcm.edu	37	chr6	31549364	31549364	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgggcagctgggagcccgggGctgagatctgtttctggctc	4	10	17	10	1	2	1	0	1	2	1	3	3	2	2	1	5	2	5	1	5	0	1	rs4647186		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:31549364G>A	ENST00000429299.2	-	3	259	c.252C>T	c.(250-252)agC>agT	p.S84S	LTB_ENST00000446745.2_Missense_Mutation_p.A69V|LTB_ENST00000483972.1_5'UTR	NM_002341.1	NP_002332.1	Q06643	TNFC_HUMAN	lymphotoxin beta (TNF superfamily, member 3)	84			S -> R (in dbSNP:rs4647186). {ECO:0000269|Ref.7}.		cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|signal transduction (GO:0007165)|skin development (GO:0043588)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)	p.S84S(1)		haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	9						GGAGCCCGGGGCTGAGATCTG	0.572													G|||	1	0.000199681	0.0	0.0	5008	,	,		16763	0.0		0.001	False		,,,				2504	0.0				p.A69V		Atlas-SNP	.											LTB,NS,lymphoid_neoplasm,0,1	LTB	19	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C206T						PASS	.						92	108	103					6																	31549364		1510	2709	4219	SO:0001819	synonymous_variant	4050	exon2			CCCGGGGCTGAGA	L11015	CCDS4703.1, CCDS4704.1	6p21.3	2013-05-22			ENSG00000227507	ENSG00000227507		"Tumor necrosis factor (ligand) superfamily"	6711	protein-coding gene	gene with protein product		600978		TNFC		7916655, 1714477	Standard	NM_002341		Approved	p33, TNFSF3	uc003nuk.3	Q06643	OTTHUMG00000031136	ENST00000429299.2:c.252C>T	6.37:g.31549364G>A		144	0	0		92	31	0.336957	NM_009588	P78370|Q52LU8|Q99761	Missense_Mutation	SNP	ENST00000429299.2	37	CCDS4703.1	.	.	.	.	.	.	.	.	.	.	G	15.63	2.889480	0.52014	.	.	ENSG00000227507	ENST00000446745	.	.	.	5.26	-2.05	0.07321	.	.	.	.	.	T	0.10078	0.0247	.	.	.	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.34650	-0.9820	7	0.38643	T	0.18	-10.8294	6.3303	0.21266	0.4617:0.1263:0.412:0.0	.	69	Q52LU8	.	V	69	.	ENSP00000416113:A69V	A	-	2	0	LTB	31657343	0.000000	0.05858	0.002000	0.10522	0.609000	0.37215	0.051000	0.14141	-0.159000	0.11021	-0.783000	0.03347	GCC	G|0.994;C|0.006	.	alt		0.572	LTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076239.3			A	31549364	G	A	31549364	2	1	27	1	0	0	0	0	0	0	0	1	9079	1203	42	2		2	LTB	6	31549364	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	52530	31549364	139565703	349	10800											
HLA-DRB5	3127	hgsc.bcm.edu	37	chr6	32497900	32497900	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcacccacaatgtgcacttAcgtcgggtgtccccagccaa	10	7	9	15	2	0	0	0	0	0	0	2	0	1	0	4	1	4	2	4	1	3	1	rs78612727	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:32497900A>G	ENST00000374975.3	-	1	163		c.e1+1			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						ATGTGCACTTACGTCGGGTGT	0.522																																					.		Atlas-SNP	.											.	HLA-DRB5	31	.	0			c.100+2T>C						PASS	.						99	102	101					6																	32497900		2203	4300	6503	SO:0001630	splice_region_variant	3127	exon2			GCACTTACGTCGG		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.100+1T>C	6.37:g.32497900A>G		123	0	0		86	14	0.162791	NM_002125		Splice_Site	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	8.839	0.941693	0.18281	.	.	ENSG00000198502	ENST00000374975	.	.	.	4.54	3.3	0.37823	.	.	.	.	.	.	.	.	.	.	.	0.35921	D	0.831832	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.4495	0.27229	0.8084:0.0:0.0:0.1916	.	.	.	.	.	-1	.	.	.	-	.	.	HLA-DRB5	32605878	0.985000	0.35326	0.199000	0.23439	0.019000	0.09904	2.123000	0.41996	1.909000	0.55274	0.397000	0.26171	.	A|0.994;G|0.006	0.006	strong		0.522	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	Intron	G	32497900	A	G	32497900	5	3	27	1	0	0	0	0	0	0	1	0	7218	405	14	3	722	3	HLA-DRB5	6	32497900	Splice_Site	SNP	A	TCGA-G8-6909-01A-11D-2210-10	948536	32497900	138617167	350	10801											
HLA-DQB1	3119	hgsc.bcm.edu	37	chr6	32632831	32632831	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tagcacatgcccttaaactgGaacacgaaatcctctgcggg	12	8	9	12	2	1	0	0	0	1	0	2	2	2	1	2	2	5	1	2	2	5	2	rs111588946		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:32632831G>C	ENST00000399084.1	-	3	301	c.123C>G	c.(121-123)ttC>ttG	p.F41L	HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.F41L|XXbac-BPG254F23.6_ENST00000443574.1_RNA|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.F41L|HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.F41L|HLA-DQB1_ENST00000399082.3_Intron			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	41	Beta-1.		Y -> F (in allele DQB1*04:01, allele DQB1*04:02, allele DQB1*04:03, allele DQB1*06:02, allele DQB1*06:10, allele DQB1*06:13, allele DQB1*06:14, allele DQB1*06:15, allele DQB1*06:16, allele DQB1*06:19, allele DQB1*06:20, allele DQB1*06:22, allele DQB1*06:23, allele DQB1*06:24, allele DQB1*06:29, allele DQB1*06:33 and allele DQB1*06:37; dbSNP:rs9274407).|Y -> L (in allele DQB1*06:01 and allele DQB1*06:35; requires 2 nucleotide substitutions).		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)"	CCTTAAACTGGAACACGAAAT	0.647									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia																												p.F41L	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											.	HLA-DQB1	15	.	0			c.C123G						PASS	.						20	21	21					6																	32632831		2088	4185	6273	SO:0001583	missense	3119	exon2	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	AAACTGGAACACG		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.123C>G	6.37:g.32632831G>C	ENSP00000382034:p.Phe41Leu	29	0	0		65	24	0.369231	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	37	CCDS43451.1	.	.	.	.	.	.	.	.	.	.	.	6.750	0.507124	0.12883	.	.	ENSG00000179344	ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084	T;T;T;T	0.04758	3.56;3.56;3.56;3.56	4.13	3.23	0.37069	.	0.154608	0.26359	U	0.024831	T	0.01800	0.0057	L	0.52905	1.665	0.35375	D	0.789428	B;B;B	0.16166	0.016;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.35773	-0.9775	10	0.19147	T	0.46	.	6.6967	0.23203	0.2157:0.0:0.7843:0.0	.	51;41;41	Q59F80;A2AAZ0;Q5Y7D6	.;.;.	L	41	ENSP00000382029:F41L;ENSP00000364080:F41L;ENSP00000407332:F41L;ENSP00000382034:F41L	ENSP00000364080:F41L	F	-	3	2	HLA-DQB1	32740809	0.000000	0.05858	0.071000	0.20095	0.019000	0.09904	0.055000	0.14229	2.161000	0.67846	0.305000	0.20034	TTC	T|1.000;|0.000	.	alt		0.647	HLA-DQB1-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276127.1	NM_002123		C	32632831	G	C	32632831	3	2	27	1	0	0	0	0	1	0	0	0	7215	1165	41	4	678	4	HLA-DQB1	6	32632831	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	134931	32632831	138482236	351	10802											
VPS52	6293	hgsc.bcm.edu	37	chr6	33236826	33236826	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcaccaccagaccatcaacAagctccccaagtttcccccg	11	5	6	19	1	1	1	1	0	0	1	3	1	3	1	7	1	2	3	7	1	3	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33236826A>G	ENST00000445902.2	-	6	731	c.513T>C	c.(511-513)ctT>ctC	p.L171L	VPS52_ENST00000482399.1_3'UTR|VPS52_ENST00000478934.1_5'UTR|VPS52_ENST00000436044.2_Silent_p.L46L|RPS18_ENST00000439602.2_5'Flank	NM_022553.4	NP_072047.4	Q8N1B4	VPS52_HUMAN	vacuolar protein sorting 52 homolog (S. cerevisiae)	171					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						GACCATCAACAAGCTCCCCAA	0.547																																					p.L171L		Atlas-SNP	.											.	VPS52	56	.	0			c.T513C						PASS	.						204	179	188					6																	33236826		1511	2709	4220	SO:0001819	synonymous_variant	6293	exon6			ATCAACAAGCTCC	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.513T>C	6.37:g.33236826A>G		165	0	0		156	64	0.410256	NM_022553	A2BF38|B0UZZ4|B4DNI9|Q53GR4|Q5JPA0|Q5SQW1|Q8IUN6|Q9NPT5	Silent	SNP	ENST00000445902.2	37	CCDS4770.2																																																																																			.	.	none		0.547	VPS52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076598.2	NM_022553		G	33236826	A	G	33236826	2	3	27	1	0	0	0	0	0	0	0	1	17229	117	5	3		3	VPS52	6	33236826	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	603995	33236826	137878241	352	10803											
KIFC1	3833	hgsc.bcm.edu	37	chr6	33374015	33374015	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cccgccagaatcgggctgtgGcccgcacagcccagaatgaa	10	4	12	15	3	0	3	0	1	0	2	1	3	0	3	4	2	1	2	4	2	3	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33374015G>A	ENST00000428849.2	+	8	2029	c.1579G>A	c.(1579-1581)Gcc>Acc	p.A527T		NM_002263.3	NP_002254.2	Q9BW19	KIFC1_HUMAN	kinesin family member C1	527	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic sister chromatid segregation (GO:0000070)|spindle assembly (GO:0051225)	endosome (GO:0005768)|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)|minus-end-directed microtubule motor activity (GO:0008569)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(3)|skin(1)	13						TCGGGCTGTGGCCCGCACAGC	0.597																																					p.A527T		Atlas-SNP	.											.	KIFC1	47	.	0			c.G1579A						PASS	.						60	71	67					6																	33374015		2202	4300	6502	SO:0001583	missense	3833	exon8			GCTGTGGCCCGCA	D14678	CCDS34430.1	6p21.32	2014-05-15	2003-01-09	2003-01-10	ENSG00000237649	ENSG00000237649		"Kinesins"	6389	protein-coding gene	gene with protein product		603763	"kinesin-like 2"	KNSL2		8276466	Standard	NM_002263		Approved	HSET	uc003oef.4	Q9BW19	OTTHUMG00000031209	ENST00000428849.2:c.1579G>A	6.37:g.33374015G>A	ENSP00000393963:p.Ala527Thr	119	0	0		120	52	0.433333	NM_002263	O60887|Q14834|Q4KMP0|Q5SU09|Q6GMS7|Q6P4A5|Q9UQP7	Missense_Mutation	SNP	ENST00000428849.2	37	CCDS34430.1	.	.	.	.	.	.	.	.	.	.	g	25.6	4.651805	0.88056	.	.	ENSG00000237649	ENST00000428849	T	0.49139	0.79	5.29	4.43	0.53597	Kinesin, motor domain (4);	0.000000	0.85682	D	0.000000	T	0.67192	0.2867	M	0.92833	3.35	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.72982	0.979;0.965	T	0.76225	-0.3037	10	0.87932	D	0	-5.1694	11.577	0.50866	0.0857:0.0:0.9143:0.0	.	519;527	B4E063;Q9BW19	.;KIFC1_HUMAN	T	527	ENSP00000393963:A527T	ENSP00000393963:A527T	A	+	1	0	KIFC1	33481993	1.000000	0.71417	0.999000	0.59377	0.871000	0.50021	6.592000	0.74095	1.461000	0.47929	0.558000	0.71614	GCC	.	.	none		0.597	KIFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076417.1	NM_002263		A	33374015	G	A	33374015	3	1	27	1	0	0	0	0	1	0	0	0	8321	1203	42	2	1609	2	KIFC1	6	33374015	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	137189	33374015	137741052	353	10804											
SYNGAP1	8831	hgsc.bcm.edu	37	chr6	33405994	33405994	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgtgcagtcttggagcccGccctgaatgtcaaaggcaag	9	9	13	10	1	2	1	1	1	1	0	2	2	2	2	2	2	2	2	2	2	3	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33405994G>A	ENST00000418600.2	+	8	1413	c.1312G>A	c.(1312-1314)Gcc>Acc	p.A438T	SYNGAP1_ENST00000293748.5_Missense_Mutation_p.A438T|SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000428982.2_Missense_Mutation_p.A379T|MIR5004_ENST00000579078.1_RNA	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	438					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						CTTGGAGCCCGCCCTGAATGT	0.512																																					p.A438T		Atlas-SNP	.											SYNGAP1_ENST00000293748,right_lower_lobe,carcinoma,0,2	SYNGAP1	202	2	0			c.G1312A						scavenged	.						160	155	157					6																	33405994		2203	4300	6503	SO:0001583	missense	8831	exon8			GAGCCCGCCCTGA	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.1312G>A	6.37:g.33405994G>A	ENSP00000403636:p.Ala438Thr	276	2	0.00724638		285	149	0.522807	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Missense_Mutation	SNP	ENST00000418600.2	37	CCDS34434.2	.	.	.	.	.	.	.	.	.	.	G	14.39	2.522340	0.44866	.	.	ENSG00000197283	ENST00000293748;ENST00000418600;ENST00000449372;ENST00000428982	T;T;T	0.16457	2.34;2.43;2.43	4.86	3.99	0.46301	Rho GTPase activation protein (1);Ras GTPase-activating protein (1);	0.246616	0.33712	N	0.004627	T	0.03095	0.0091	N	0.14661	0.345	0.31709	N	0.639723	B;P;P;B	0.36660	0.428;0.564;0.564;0.026	B;B;B;B	0.19666	0.011;0.026;0.026;0.003	T	0.27502	-1.0072	10	0.72032	D	0.01	.	11.1118	0.48237	0.0904:0.0:0.9096:0.0	.	438;438;438;438	Q96PV0;Q96PV0-2;Q96PV0-4;B7ZCA0	SYGP1_HUMAN;.;.;.	T	438;438;438;379	ENSP00000293748:A438T;ENSP00000403636:A438T;ENSP00000412475:A379T	ENSP00000293748:A438T	A	+	1	0	SYNGAP1	33513972	0.968000	0.33430	0.858000	0.33744	0.950000	0.60333	1.961000	0.40432	1.255000	0.44051	0.650000	0.86243	GCC	.	.	none		0.512	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407		A	33405994	G	A	33405994	3	1	27	1	0	0	0	0	1	0	0	0	15462	1087	38	1	1342	1	SYNGAP1	6	33405994	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	31979	33405994	137709073	354	10805											
ITPR3	3710	hgsc.bcm.edu	37	chr6	33658780	33658780	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cgctccatcctgctgacagcCctgctggccctcatcctggt	4	10	9	18	1	1	1	1	1	0	0	4	1	4	1	5	2	3	3	5	2	0	0	rs35506178	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:33658780C>T	ENST00000374316.5	+	53	8179	c.7119C>T	c.(7117-7119)gcC>gcT	p.A2373A	ITPR3_ENST00000605930.1_Silent_p.A2373A			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	2373					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)	TGCTGACAGCCCTGCTGGCCC	0.577													C|||	89	0.0177716	0.003	0.013	5008	,	,		21516	0.0119		0.0517	False		,,,				2504	0.0123				p.A2373A		Atlas-SNP	.											.	ITPR3	409	.	0			c.C7119T						PASS	.	C		58,4348	55.5+/-91.7	1,56,2146	150	122	131		7119	1.8	1	6	dbSNP_126	131	431,8169	132.8+/-190.4	10,411,3879	no	coding-synonymous	ITPR3	NM_002224.3		11,467,6025	TT,TC,CC		5.0116,1.3164,3.7598		2373/2672	33658780	489,12517	2203	4300	6503	SO:0001819	synonymous_variant	3710	exon52			GACAGCCCTGCTG	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.7119C>T	6.37:g.33658780C>T		172	0	0		162	81	0.5	NM_002224	Q14649|Q5TAQ2	Silent	SNP	ENST00000374316.5	37	CCDS4783.1																																																																																			C|0.966;T|0.034	0.034	strong		0.577	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224		T	33658780	C	T	33658780	2	4	27	1	0	0	0	0	0	0	0	1	7931	610	22	2		2	ITPR3	6	33658780	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	252786	33658780	137456287	355	10806											
UHRF1BP1	54887	hgsc.bcm.edu	37	chr6	34826663	34826663	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctctgcttcgcctgaaggagGtgctgcagaggcttcaggag	7	9	15	10	1	2	2	1	1	1	1	3	4	2	4	1	4	3	4	1	4	1	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:34826663G>A	ENST00000192788.5	+	14	2701	c.2530G>A	c.(2530-2532)Gtg>Atg	p.V844M	UHRF1BP1_ENST00000452449.2_Missense_Mutation_p.V844M	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	844							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						CCTGAAGGAGGTGCTGCAGAG	0.537																																					p.V844M		Atlas-SNP	.											.	UHRF1BP1	102	.	0			c.G2530A						PASS	.						123	120	121					6																	34826663		2021	4193	6214	SO:0001583	missense	54887	exon14			AAGGAGGTGCTGC	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.2530G>A	6.37:g.34826663G>A	ENSP00000192788:p.Val844Met	133	0	0		130	32	0.246154	NM_017754	Q9NXE0	Missense_Mutation	SNP	ENST00000192788.5	37	CCDS43455.1	.	.	.	.	.	.	.	.	.	.	G	12.55	1.972845	0.34848	.	.	ENSG00000065060	ENST00000192788;ENST00000452449	T;T	0.17370	2.28;2.28	5.17	5.17	0.71159	.	0.207707	0.41396	D	0.000890	T	0.06600	0.0169	L	0.34521	1.04	0.31062	N	0.713971	B	0.31581	0.329	B	0.27170	0.077	T	0.10870	-1.0611	10	0.52906	T	0.07	-16.6036	13.7912	0.63143	0.0:0.0:0.8469:0.1531	.	844	Q6BDS2	URFB1_HUMAN	M	844	ENSP00000192788:V844M;ENSP00000400628:V844M	ENSP00000192788:V844M	V	+	1	0	UHRF1BP1	34934641	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.028000	0.41088	2.692000	0.91855	0.591000	0.81541	GTG	.	.	none		0.537	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754		A	34826663	G	A	34826663	3	1	27	1	0	0	0	0	1	0	0	0	16983	1261	44	2	2584	2	UHRF1BP1	6	34826663	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1167883	34826663	136288404	356	10807											
PIM1	5292	hgsc.bcm.edu	37	chr6	37138412	37138412	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccgcgccctgcaacgacctgCacgccaccaagctggcgccc	7	3	10	21	5	0	0	0	0	0	0	0	1	0	0	6	1	4	3	6	1	2	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:37138412C>A	ENST00000373509.5	+	1	434	c.61C>A	c.(61-63)Cac>Aac	p.H21N		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	112					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)	CAACGACCTGCACGCCACCAA	0.726			T	BCL6	NHL																																p.H112N		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C334A						PASS	.						25	27	26					6																	37138412		2199	4293	6492	SO:0001583	missense	5292	exon1			GACCTGCACGCCA		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.61C>A	6.37:g.37138412C>A	ENSP00000362608:p.His21Asn	18	0	0		39	11	0.282051	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	13.44	2.236939	0.39498	.	.	ENSG00000137193	ENST00000373509	T	0.68479	-0.33	4.2	3.33	0.38152	.	0.432965	0.20921	N	0.083268	T	0.21468	0.0517	N	0.08118	0	0.29891	N	0.825193	P	0.34615	0.459	B	0.32762	0.152	T	0.17899	-1.0354	10	0.10636	T	0.68	.	12.4383	0.55612	0.0:0.915:0.0:0.085	.	112	P11309	PIM1_HUMAN	N	21	ENSP00000362608:H21N	ENSP00000362608:H21N	H	+	1	0	PIM1	37246390	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.047000	0.41269	1.080000	0.41073	0.542000	0.68232	CAC	.	.	none		0.726	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			A	37138412	C	A	37138412	3	1	27	1	0	0	0	0	1	0	0	0	11936	710	25	4	63	4	PIM1	6	37138412	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2311749	37138412	133976655	357	10808											
GLO1	2739	hgsc.bcm.edu	37	chr6	38650631	38650631	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtggtaactctgggtctcaTcatcttcagtgccccaattg	7	14	9	11	0	5	0	3	0	3	0	6	0	5	0	2	2	2	1	2	2	2	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:38650631T>C	ENST00000373365.4	-	4	415	c.329A>G	c.(328-330)gAt>gGt	p.D110G	GLO1_ENST00000470973.1_5'UTR	NM_006708.2	NP_006699.2	Q04760	LGUL_HUMAN	glyoxalase I	110					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)	CTGGGTCTCATCATCTTCAGT	0.368																																					p.D110G		Atlas-SNP	.											.	GLO1	12	.	0			c.A329G						PASS	.						161	131	141					6																	38650631		2203	4300	6503	SO:0001583	missense	2739	exon4			GTCTCATCATCTT	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.329A>G	6.37:g.38650631T>C	ENSP00000362463:p.Asp110Gly	82	0	0		95	5	0.0526316	NM_006708	B2R6P7|B4DDV0|P78375|Q59EL0|Q5TZW3|Q96FC0|Q96J41	Missense_Mutation	SNP	ENST00000373365.4	37	CCDS4837.1	.	.	.	.	.	.	.	.	.	.	T	28.9	4.959074	0.92726	.	.	ENSG00000124767	ENST00000373365	T	0.69561	-0.41	5.95	5.95	0.96441	Glyoxalase/fosfomycin resistance/dioxygenase (1);	0.043159	0.85682	D	0.000000	T	0.79969	0.4538	M	0.85462	2.755	0.80722	D	1	D	0.61080	0.989	D	0.65773	0.938	D	0.83766	0.0217	10	0.87932	D	0	-26.0981	16.0971	0.81132	0.0:0.0:0.0:1.0	.	110	Q04760	LGUL_HUMAN	G	110	ENSP00000362463:D110G	ENSP00000362463:D110G	D	-	2	0	GLO1	38758609	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.140000	0.77322	2.279000	0.76181	0.533000	0.62120	GAT	.	.	none		0.368	GLO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040438.2	NM_006708		C	38650631	T	C	38650631	3	2	27	1	0	0	0	0	1	0	0	0	6457	1435	50	3	237	3	GLO1	6	38650631	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	1512219	38650631	132464436	358	10809											
DNAH8	1769	hgsc.bcm.edu	37	chr6	38840427	38840428	+	Frame_Shift_Del	DEL	AT	AT	-																															aacagaatgcggaaggcctcAtagagaaatgcgaatgaatc																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:38840427_38840428delAT	ENST00000359357.3	+	48	6709_6710	c.6455_6456delAT	c.(6454-6456)catfs	p.H2152fs	DNAH8_ENST00000449981.2_Frame_Shift_Del_p.H2369fs|DNAH8_ENST00000441566.1_Frame_Shift_Del_p.H2116fs			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	2152	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						GGAAGGCCTCATAGAGAAATGC	0.47																																					p.2369_2369del		Pindel,Atlas-Indel	.											.	DNAH8	1239	.	0			c.7105_7106del						PASS	.																																			SO:0001589	frameshift_variant	1769	exon50			.	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.6455_6456delAT	6.37:g.38840427_38840428delAT	ENSP00000352312:p.His2152fs	117	0	.		128	43	0.336	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Frame_Shift_Del	DEL	ENST00000359357.3	37																																																																																				.	.	none		0.47	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		-	38840428	AT	-	38840427	7	5	27	1	0	1	0	1	0	0	0	0	4609	217	8	0	6637	0	DNAH8	6	38840427	Frame_Shift_Del	DEL	AT	TCGA-G8-6909-01A-11D-2210-10	189796	38840427	132274640	359	10810											
DAAM2	23500	hgsc.bcm.edu	37	chr6	39869657	39869659	+	In_Frame_Del	DEL	GGA	GGA	-																															ctggctgcaggcagctcgctGgaggagggaggagagttcga																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:39869657_39869659delGGA	ENST00000398904.2	+	25	3233_3235	c.3051_3053delGGA	c.(3049-3054)ctggag>ctg	p.E1019del	DAAM2_ENST00000274867.4_In_Frame_Del_p.E1019del|DAAM2_ENST00000538976.1_In_Frame_Del_p.E1018del|RP11-61I13.3_ENST00000437947.1_RNA			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)					GCAGCTCGCTGGAGGAGGGAGGA	0.65																																					p.1017_1018del		Pindel,Atlas-Indel	.											.	DAAM2	101	.	0			c.3050_3052del						PASS	.																																			SO:0001651	inframe_deletion	23500	exon25			.	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.3051_3053delGGA	6.37:g.39869660_39869662delGGA	ENSP00000381876:p.Glu1019del	57	0	.		45	22	0.489	NM_001201427	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	In_Frame_Del	DEL	ENST00000398904.2	37	CCDS56426.1																																																																																			.	.	none		0.65	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1			-	39869659	GGA	-	39869657	7	5	27	1	0	1	0	1	0	0	0	0	4218	1335	47	0	3142	0	DAAM2	6	39869657	In_Frame_Del	DEL	GGA	TCGA-G8-6909-01A-11D-2210-10	1029230	39869657	131245410	360	10811											
MOCS1	4337	hgsc.bcm.edu	37	chr6	39881568	39881568	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cttgtggatgccctccatgaCcttgtggaagcctgggaggg	6	10	15	10	0	0	1	0	1	0	0	1	4	1	4	4	4	2	0	4	4	1	2	rs377241570		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:39881568C>A	ENST00000340692.5	-	5	598	c.595G>T	c.(595-597)Gtc>Ttc	p.V199F	MOCS1_ENST00000373195.3_Missense_Mutation_p.V112F|MOCS1_ENST00000373188.2_Missense_Mutation_p.V199F|MOCS1_ENST00000425303.2_Missense_Mutation_p.V199F|MOCS1_ENST00000373186.4_Missense_Mutation_p.V199F|MOCS1_ENST00000308559.7_Missense_Mutation_p.V199F|MOCS1_ENST00000432280.2_Missense_Mutation_p.V170F|MOCS1_ENST00000373175.4_Missense_Mutation_p.V170F			Q9NZB8	MOCS1_HUMAN	molybdenum cofactor synthesis 1	199	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)					CCCTCCATGACCTTGTGGAAG	0.592																																					p.V199F	NSCLC(84;861 1413 23785 24908 42279)|Melanoma(182;611 2047 9114 11847 26639)	Atlas-SNP	.											.	MOCS1	87	.	0			c.G595T						PASS	.						120	101	107					6																	39881568		2203	4300	6503	SO:0001583	missense	4337	exon4			CCATGACCTTGTG	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.595G>T	6.37:g.39881568C>A	ENSP00000344794:p.Val199Phe	96	0	0		66	16	0.242424	NM_005943	B3KPT7|B4DTP1|O14940|O14941|O75710|Q5J7W0|Q5TCE1|Q5TCE2|Q5TCE6|Q5TCE9|Q5TCF0|Q5TCF1|Q8N418|Q9NZB7|Q9UEM1	Missense_Mutation	SNP	ENST00000340692.5	37		.	.	.	.	.	.	.	.	.	.	C	27.2	4.806025	0.90623	.	.	ENSG00000124615	ENST00000373186;ENST00000308559;ENST00000373175;ENST00000373188;ENST00000373195;ENST00000340692;ENST00000425303;ENST00000432280	T;T;T;T;T;T;T;T	0.80566	-1.39;-1.39;-1.39;-1.39;-1.39;-1.39;-1.39;-1.39	4.84	4.84	0.62591	Elongator protein 3/MiaB/NifB (1);Aldolase-type TIM barrel (1);Radical SAM (1);	0.000000	0.85682	D	0.000000	D	0.93996	0.8077	H	0.99357	4.53	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999	D;D;D;D;D	0.91635	0.999;0.995;0.999;0.999;0.995	D	0.96772	0.9569	9	.	.	.	-19.377	17.5587	0.87900	0.0:1.0:0.0:0.0	.	199;199;199;199;199	Q9NZB8-2;Q9NZB8-5;Q9NZB8;Q9NZB8-8;Q9NZB8-6	.;.;MOCS1_HUMAN;.;.	F	199;199;170;199;112;199;199;170	ENSP00000362282:V199F;ENSP00000309843:V199F;ENSP00000362270:V170F;ENSP00000362284:V199F;ENSP00000362291:V112F;ENSP00000344794:V199F;ENSP00000416478:V199F;ENSP00000410809:V170F	.	V	-	1	0	MOCS1	39989546	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.601000	0.82783	2.245000	0.73994	0.655000	0.94253	GTC	.	.	alt		0.592	MOCS1-005	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000040476.2	NM_005943		A	39881568	C	A	39881568	3	1	27	1	0	0	0	0	1	0	0	0	9699	507	18	4	586	4	MOCS1	6	39881568	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	11911	39881568	131233499	361	10812											
C6orf108	23113	hgsc.bcm.edu	37	chr6	43193877	43193877	+	IGR	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggctgtgtcacttctgccacGaccactgggaggaaagatga	10	8	13	10	1	2	2	1	1	1	1	2	5	2	4	2	3	1	1	2	3	1	1	rs7832	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:43193877G>A	ENST00000252050.4	+	0	7780				DNPH1_ENST00000393987.2_Silent_p.V90V|DNPH1_ENST00000230431.6_Silent_p.V90V|RP3-330M21.5_ENST00000500590.1_RNA	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9						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						CTTCTGCCACGACCACTGGGA	0.592													G|||	208	0.0415335	0.0023	0.0908	5008	,	,		21379	0.003		0.0706	False		,,,				2504	0.0695				p.V90V		Atlas-SNP	.											C6orf108_ENST00000393987,NS,carcinoma,0,2	.	.	2	0			c.C270T						PASS	.	G	,	85,4303		1,83,2110	30	24	26		270,270	-9.2	0	6	dbSNP_52	26	882,7688		43,796,3446	no	coding-synonymous,coding-synonymous	C6orf108	NM_006443.2,NM_199184.1	,	44,879,5556	AA,AG,GG		10.2917,1.9371,7.4626	,	90/175,90/149	43193877	967,11991	2194	4285	6479	SO:0001628	intergenic_variant	10591	exon3			TGCCACGACCACT	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		6.37:g.43193877G>A		40	0	0		27	6	0.222222	NM_006443	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	37	CCDS4890.1																																																																																			G|0.942;A|0.058	0.058	strong		0.592	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089		A	43193877	G	A	43193877	1	1	27	0	1	0	0	0	0	0	0	0	2322	1045	37	1		1	C6orf108	6	43193877	IGR	SNP	G	TCGA-G8-6909-01A-11D-2210-10	3312309	43193877	127921190	362	10813											
XPO5	57510	hgsc.bcm.edu	37	chr6	43514382	43514382	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttacggaagattggatttccActggatgtataacccaccac	12	11	8	10	1	0	1	0	0	0	1	1	4	1	4	3	3	2	1	3	3	4	5	rs567618901		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:43514382A>G	ENST00000265351.7	-	20	2478	c.2268T>C	c.(2266-2268)agT>agC	p.S756S	SCARNA15_ENST00000516409.1_RNA	NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	756					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)			TTGGATTTCCACTGGATGTAT	0.458													A|||	1	0.000199681	0.0	0.0	5008	,	,		15773	0.001		0.0	False		,,,				2504	0.0				p.S756S		Atlas-SNP	.											XPO5,NS,carcinoma,-1,1	XPO5	79	1	0			c.T2268C						PASS	.						54	53	53					6																	43514382		1873	4102	5975	SO:0001819	synonymous_variant	57510	exon20			ATTTCCACTGGAT	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.2268T>C	6.37:g.43514382A>G		142	0	0		98	43	0.438776	NM_020750	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Silent	SNP	ENST00000265351.7	37	CCDS47430.1																																																																																			.	.	none		0.458	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2	NM_020750		G	43514382	A	G	43514382	2	3	27	1	0	0	0	0	0	0	0	1	17462	156	6	3		3	XPO5	6	43514382	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	320505	43514382	127600685	363	10814											
NFKBIE	4794	hgsc.bcm.edu	37	chr6	44232739	44232742	+	Frame_Shift_Del	DEL	GTAA	GTAA	-																															gtgtctccgtcctcggagatGtaagtgagtgcttccagctg																								rs375669043		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GTAA	GTAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:44232739_44232742delGTAA	ENST00000275015.5	-	1	758_761	c.759_762delTTAC	c.(757-762)acttacfs	p.TY253fs		NM_004556.2	NP_004547.2	O00221	IKBE_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, epsilon	253					cytoplasmic sequestering of transcription factor (GO:0042994)|D-serine transport (GO:0042942)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|urinary_tract(1)	10	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)			CCTCGGAGATGTAAGTGAGTGCTT	0.676																																					p.254_255del		Atlas-Indel	.											.	NFKBIE	31	.	0			c.760_763del						PASS	.																																			SO:0001589	frameshift_variant	4794	exon1			.	U91616	CCDS34463.1	6p21.1	2013-01-10			ENSG00000146232	ENSG00000146232		"Ankyrin repeat domain containing"	7799	protein-coding gene	gene with protein product		604548				9135156	Standard	NM_004556		Approved	IKBE	uc003oxe.1	O00221	OTTHUMG00000014762	ENST00000275015.5:c.759_762delTTAC	6.37:g.44232739_44232742delGTAA	ENSP00000275015:p.Thr253fs	44	0	0		35	11	0.314286	NM_004556	Q5T9V9	Frame_Shift_Del	DEL	ENST00000275015.5	37	CCDS34463.1																																																																																			.	.	none		0.676	NFKBIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040733.2			-	44232742	GTAA	-	44232739	7	5	27	1	0	1	0	1	0	0	0	0	10389	1372	48	0	764	0	NFKBIE	6	44232739	Frame_Shift_Del	DEL	GTAA	TCGA-G8-6909-01A-11D-2210-10	718357	44232739	126882328	364	10815											
DEFB110	245913	hgsc.bcm.edu	37	chr6	49986788	49986788	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acattgaccattacctattcTgcactctctcctcaagtcca	10	13	3	15	0	3	1	1	1	2	0	6	1	5	1	4	0	2	1	4	0	3	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:49986788T>A	ENST00000371148.2	-	2	151	c.106A>T	c.(106-108)Aga>Tga	p.R36*	DEFB110_ENST00000393660.2_Intron	NM_001037497.1	NP_001032586.1	Q30KQ9	DB110_HUMAN	defensin, beta 110 locus	36					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(1)|lung(1)|ovary(1)	3	Lung NSC(77;0.042)					TTACCTATTCTGCACTCTCTC	0.393																																					p.R36X		Atlas-SNP	.											.	DEFB110	5	.	0			c.A106T						PASS	.						176	158	164					6																	49986788		2203	4300	6503	SO:0001587	stop_gained	245913	exon2			CTATTCTGCACTC	DQ012014, BC148541	CCDS43473.1, CCDS34475.1	6p12.3	2010-11-26	2010-11-26		ENSG00000203970	ENSG00000203970		"Defensins, beta"	18091	protein-coding gene	gene with protein product			"defensin, beta 110"			11854508, 16033865	Standard	NM_001037728		Approved	DEFB-10, DEFB-11, DEFB111	uc003pac.3	Q30KQ9	OTTHUMG00000160208	ENST00000371148.2:c.106A>T	6.37:g.49986788T>A	ENSP00000360190:p.Arg36*	181	0	0		168	40	0.238095	NM_001037497	Q30KR0	Nonsense_Mutation	SNP	ENST00000371148.2	37	CCDS34475.1	.	.	.	.	.	.	.	.	.	.	T	9.497	1.102324	0.20632	.	.	ENSG00000203970	ENST00000371148	.	.	.	5.03	1.22	0.21188	.	1.271720	0.05234	N	0.510955	.	.	.	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	.	.	.	.	.	.	.	-0.0123	3.4489	0.07491	0.167:0.1849:0.0:0.6482	.	.	.	.	X	36	.	.	R	-	1	2	DEFB110	50094747	0.848000	0.29623	0.483000	0.27378	0.035000	0.12851	1.146000	0.31589	0.390000	0.25115	-0.333000	0.08304	AGA	.	.	none		0.393	DEFB110-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359664.1	NM_001037728		A	49986788	T	A	49986788	4	1	27	1	0	0	0	0	0	1	0	0	4402	1588	55	5	237	5	DEFB110	6	49986788	Nonsense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	5754049	49986788	121128279	365	10816											
PKHD1	5314	hgsc.bcm.edu	37	chr6	51524681	51524681	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aatggcatcagcgctatcaaGaattaggaccacttggtcag	13	9	10	9	1	3	1	3	0	0	1	3	2	3	2	1	3	1	2	1	3	5	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:51524681G>A	ENST00000371117.3	-	61	10518	c.10243C>T	c.(10243-10245)Ctt>Ttt	p.L3415F		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3415					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)	p.L3415F(1)		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)					GCGCTATCAAGAATTAGGACC	0.368																																					p.L3415F		Atlas-SNP	.											PKHD1,NS,carcinoma,0,1	PKHD1	927	1	1	Substitution - Missense(1)	lung(1)	c.C10243T						PASS	.						74	66	69					6																	51524681		2203	4300	6503	SO:0001583	missense	5314	exon61			TATCAAGAATTAG	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.10243C>T	6.37:g.51524681G>A	ENSP00000360158:p.Leu3415Phe	189	0	0		167	42	0.251497	NM_138694	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	G	13.40	2.226393	0.39300	.	.	ENSG00000170927	ENST00000371117	D	0.86497	-2.13	5.48	4.6	0.57074	.	0.000000	0.56097	D	0.000021	D	0.85669	0.5750	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.84345	0.0529	10	0.34782	T	0.22	.	11.1417	0.48406	0.1436:0.0:0.8564:0.0	.	3415	P08F94	PKHD1_HUMAN	F	3415	ENSP00000360158:L3415F	ENSP00000360158:L3415F	L	-	1	0	PKHD1	51632640	1.000000	0.71417	1.000000	0.80357	0.192000	0.23643	1.690000	0.37711	2.580000	0.87095	0.655000	0.94253	CTT	.	.	none		0.368	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51524681	G	A	51524681	3	1	27	1	0	0	0	0	1	0	0	0	11980	942	33	2	2009	2	PKHD1	6	51524681	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1537893	51524681	119590386	366	10817											
PKHD1	5314	hgsc.bcm.edu	37	chr6	51768466	51768466	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttcaggattggagagtccctCggcaccagaaacctggatga	11	8	12	10	1	1	3	1	1	0	2	3	6	2	5	3	4	1	1	3	4	1	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:51768466C>T	ENST00000371117.3	-	43	7200	c.6925G>A	c.(6925-6927)Gag>Aag	p.E2309K	PKHD1_ENST00000340994.4_Missense_Mutation_p.E2309K	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2309					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)	p.E2309K(1)		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)					GAGAGTCCCTCGGCACCAGAA	0.428																																					p.E2309K		Atlas-SNP	.											PKHD1,colon,carcinoma,0,1	PKHD1	927	1	1	Substitution - Missense(1)	large_intestine(1)	c.G6925A						PASS	.						192	174	180					6																	51768466		2203	4300	6503	SO:0001583	missense	5314	exon43			GTCCCTCGGCACC	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.6925G>A	6.37:g.51768466C>T	ENSP00000360158:p.Glu2309Lys	114	0	0		98	34	0.346939	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	C	19.41	3.822784	0.71028	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	T;T	0.80304	-1.36;-1.36	5.87	5.87	0.94306	Pectin lyase fold/virulence factor (1);Pectin lyase fold (1);	0.376162	0.25619	N	0.029438	D	0.85066	0.5612	M	0.71581	2.175	0.40270	D	0.978272	D;D;D	0.71674	0.998;0.992;0.998	P;P;P	0.60609	0.837;0.585;0.877	T	0.83066	-0.0145	10	0.35671	T	0.21	.	17.3804	0.87403	0.0:1.0:0.0:0.0	.	2309;2309;2309	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	K	2309	ENSP00000360158:E2309K;ENSP00000341097:E2309K	ENSP00000341097:E2309K	E	-	1	0	PKHD1	51876425	0.984000	0.35163	0.965000	0.40720	0.368000	0.29767	4.428000	0.59894	2.770000	0.95276	0.650000	0.86243	GAG	.	.	none		0.428	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		T	51768466	C	T	51768466	3	4	27	1	0	0	0	0	1	0	0	0	11980	893	31	1	5438	1	PKHD1	6	51768466	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	243785	51768466	119346601	367	10818											
PKHD1	5314	hgsc.bcm.edu	37	chr6	51890754	51890754	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgaagcctttccccaccaagCttggtgaaggaccacgggcg	9	7	12	13	2	0	2	0	2	0	0	1	3	1	3	5	3	2	1	5	3	3	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:51890754C>T	ENST00000371117.3	-	32	4129	c.3854G>A	c.(3853-3855)aGc>aAc	p.S1285N	PKHD1_ENST00000340994.4_Missense_Mutation_p.S1285N	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1285	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)					CCCCACCAAGCTTGGTGAAGG	0.587																																					p.S1285N		Atlas-SNP	.											.	PKHD1	927	.	0			c.G3854A						PASS	.						88	78	82					6																	51890754		2203	4300	6503	SO:0001583	missense	5314	exon32			ACCAAGCTTGGTG	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.3854G>A	6.37:g.51890754C>T	ENSP00000360158:p.Ser1285Asn	114	0	0		103	27	0.262136	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	C	8.648	0.897477	0.17686	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.87412	-2.05;-2.25	5.79	-0.718	0.11205	Cell surface receptor IPT/TIG (1);	1.934510	0.01638	N	0.023911	T	0.64962	0.2646	M	0.63428	1.95	0.09310	N	1	B;B	0.34015	0.435;0.011	B;B	0.25140	0.058;0.002	T	0.52873	-0.8517	10	0.12766	T	0.61	.	3.7658	0.08622	0.2648:0.4257:0.0:0.3094	.	1285;1285	P08F94-2;P08F94	.;PKHD1_HUMAN	N	1285	ENSP00000360158:S1285N;ENSP00000341097:S1285N	ENSP00000341097:S1285N	S	-	2	0	PKHD1	51998713	0.000000	0.05858	0.000000	0.03702	0.071000	0.16799	-0.748000	0.04818	0.080000	0.16959	-0.169000	0.13324	AGC	.	.	none		0.587	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		T	51890754	C	T	51890754	3	4	27	1	0	0	0	0	1	0	0	0	11980	797	28	2	8553	2	PKHD1	6	51890754	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	122288	51890754	119224313	368	10819											
FAM83B	222584	hgsc.bcm.edu	37	chr6	54735301	54735301	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgatgattcctgtgatgataCcttatcttcagggacctact	9	15	8	9	0	2	4	1	4	1	0	3	5	3	5	3	1	2	0	3	1	3	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:54735301C>G	ENST00000306858.7	+	2	373	c.257C>G	c.(256-258)aCc>aGc	p.T86S		NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	86										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)					TGTGATGATACCTTATCTTCA	0.443																																					p.T86S		Atlas-SNP	.											.	FAM83B	186	.	0			c.C257G						PASS	.						130	131	131					6																	54735301		2203	4300	6503	SO:0001583	missense	222584	exon2			ATGATACCTTATC	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.257C>G	6.37:g.54735301C>G	ENSP00000304078:p.Thr86Ser	131	0	0		128	27	0.210938	NM_001010872	Q2M1P3|Q96DQ2	Missense_Mutation	SNP	ENST00000306858.7	37	CCDS34479.1	.	.	.	.	.	.	.	.	.	.	C	10.88	1.474403	0.26423	.	.	ENSG00000168143	ENST00000306858	T	0.10960	2.82	5.49	3.63	0.41609	.	0.784700	0.12264	N	0.484499	T	0.01765	0.0056	N	0.10782	0.045	0.09310	N	0.99999	B	0.24317	0.101	B	0.25506	0.061	T	0.48151	-0.9060	10	0.18710	T	0.47	-1.312	10.1089	0.42550	0.2692:0.5927:0.1381:0.0	.	86	Q5T0W9	FA83B_HUMAN	S	86	ENSP00000304078:T86S	ENSP00000304078:T86S	T	+	2	0	FAM83B	54843260	0.216000	0.23585	0.731000	0.30826	0.811000	0.45836	2.409000	0.44583	0.732000	0.32470	0.460000	0.39030	ACC	.	.	none		0.443	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139		G	54735301	C	G	54735301	3	3	27	1	0	0	0	0	1	0	0	0	5642	507	18	4	259	4	FAM83B	6	54735301	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2844547	54735301	116379766	369	10820											
DST	667	hgsc.bcm.edu	37	chr6	56327856	56327856	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacaatacctctgcagatggCacgggaaagtctgagcactc	12	8	10	11	1	2	2	0	1	2	1	3	3	2	3	1	2	4	3	1	2	4	2	rs144012429	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:56327856C>T	ENST00000244364.6	-	82	15324	c.15117G>A	c.(15115-15117)gtG>gtA	p.V5039V	DST_ENST00000370769.4_Intron|DST_ENST00000361203.3_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000312431.6_3'UTR|DST_ENST00000370788.2_Intron|DST_ENST00000421834.2_Intron	NM_001144769.2|NM_001144770.1|NM_015548.4|NM_183380.3	NP_001138241.1|NP_001138242.1|NP_056363.2|NP_899236.1	Q03001	DYST_HUMAN	dystonin	7442					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)			CTGCAGATGGCACGGGAAAGT	0.433													C|||	57	0.0113818	0.0015	0.0159	5008	,	,		19060	0.0		0.0268	False		,,,				2504	0.0174				p.V5039V		Atlas-SNP	.											.	DST	1427	.	0			c.G15117A						PASS	.	C		36,3850		0,36,1907	142	133	136		15117	4	1	6	dbSNP_134	136	348,7958		7,334,3812	yes	coding-synonymous	DST	NM_015548.4		7,370,5719	TT,TC,CC		4.1897,0.9264,3.1496		5039/5172	56327856	384,11808	1943	4153	6096	SO:0001819	synonymous_variant	667	exon82			AGATGGCACGGGA	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	ENST00000244364.6:c.15117G>A	6.37:g.56327856C>T		167	0	0		141	78	0.553191	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	ENST00000244364.6	37	CCDS47443.1																																																																																			C|0.983;T|0.017	0.017	strong		0.433	DST-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041022.4	NM_001723		T	56327856	C	T	56327856	2	4	27	1	0	0	0	0	0	0	0	1	4785	697	25	2		2	DST	6	56327856	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1592555	56327856	114787211	370	10821											
DST	667	hgsc.bcm.edu	37	chr6	56420158	56420158	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caaacctgctttctgttcaaCatccttaaatgattttaaga	13	15	4	9	0	2	2	1	1	1	1	3	2	3	2	2	0	3	2	2	0	5	5	rs62621210	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:56420158C>T	ENST00000361203.3	-	56	14495	c.14488G>A	c.(14488-14490)Gtt>Att	p.V4830I	DST_ENST00000370769.4_Missense_Mutation_p.V4832I|DST_ENST00000244364.6_Missense_Mutation_p.V2418I|DST_ENST00000446842.2_Missense_Mutation_p.V4506I|DST_ENST00000370754.5_Missense_Mutation_p.V5010I|DST_ENST00000312431.6_3'UTR|DST_ENST00000370788.2_Missense_Mutation_p.V2744I|DST_ENST00000421834.2_Missense_Mutation_p.V2744I			Q03001	DYST_HUMAN	dystonin	4830					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)			TTCTGTTCAACATCCTTAAAT	0.363													T|||	213	0.0425319	0.115	0.0245	5008	,	,		21783	0.0		0.0278	False		,,,				2504	0.0164				p.V2418I		Atlas-SNP	.											.	DST	1427	.	0			c.G7252A						PASS	.	T	ILE/VAL	434,3276		22,390,1443	98	97	97		7252	4.8	1	6	dbSNP_129	97	356,7848		8,340,3754	yes	missense	DST	NM_015548.4	29	30,730,5197	TT,TC,CC		4.3393,11.6981,6.6309	benign	2418/5172	56420158	790,11124	1855	4102	5957	SO:0001583	missense	667	exon41			GTTCAACATCCTT	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.14488G>A	6.37:g.56420158C>T	ENSP00000354508:p.Val4830Ile	149	0	0		145	72	0.496552	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	37		88	0.040293040293040296	61	0.12398373983739837	10	0.027624309392265192	0	0.0	17	0.022427440633245383	T	12.33	1.907022	0.33628	0.116981	0.043393	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.36520	1.25;1.25;1.25;1.25;1.25;1.25;1.25	5.96	4.8	0.61643	.	0.246447	0.28784	N	0.014144	T	0.05640	0.0148	N	0.02802	-0.49	0.09310	N	1.0	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.11329	0.0;0.002;0.006;0.0;0.001	T	0.23940	-1.0174	9	0.33141	T	0.24	.	7.9146	0.29810	0.0:0.0664:0.2716:0.662	rs62621210	2744;4832;5010;4830;2418	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	I	2418;5010;4832;2744;4506;2744;4830	ENSP00000244364:V2418I;ENSP00000359790:V5010I;ENSP00000359805:V4832I;ENSP00000400883:V2744I;ENSP00000393645:V4506I;ENSP00000359824:V2744I;ENSP00000354508:V4830I	ENSP00000244364:V2418I	V	-	1	0	DST	56528117	1.000000	0.71417	0.997000	0.53966	0.968000	0.65278	2.506000	0.45433	0.505000	0.28104	-0.269000	0.10298	GTT	C|0.959;T|0.041	0.041	strong		0.363	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		T	56420158	C	T	56420158	3	4	27	1	0	0	0	0	1	0	0	0	4785	478	17	2	8439	2	DST	6	56420158	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	92302	56420158	114694909	371	10822											
DST	667	hgsc.bcm.edu	37	chr6	56494071	56494071	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtcaatctgcacatgaacAttttgccacctttcaactaa	12	14	4	11	0	3	1	2	1	1	0	3	1	3	1	2	0	4	1	2	0	4	5	rs112640831	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:56494071A>G	ENST00000361203.3	-	28	3826	c.3819T>C	c.(3817-3819)aaT>aaC	p.N1273N	DST_ENST00000370769.4_Silent_p.N1273N|DST_ENST00000244364.6_Silent_p.N947N|DST_ENST00000446842.2_Silent_p.N947N|DST_ENST00000370754.5_Silent_p.N1451N|DST_ENST00000312431.6_Silent_p.N1273N|DST_ENST00000518935.1_Silent_p.N947N|DST_ENST00000370765.6_Silent_p.N947N|DST_ENST00000370788.2_Silent_p.N1273N|DST_ENST00000421834.2_Silent_p.N1273N			Q03001	DYST_HUMAN	dystonin	1273					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)			GCACATGAACATTTTGCCACC	0.338													A|||	53	0.0105831	0.0015	0.0101	5008	,	,		18282	0.0		0.0268	False		,,,				2504	0.0174				p.N947N		Atlas-SNP	.											.	DST	1427	.	0			c.T2841C						PASS	.	A	,	33,4373	37.6+/-69.7	0,33,2170	276	228	244		2841,2841	-1	1	6	dbSNP_132	244	360,8240	120.2+/-179.5	9,342,3949	no	coding-synonymous,coding-synonymous	DST	NM_001723.5,NM_015548.4	,	9,375,6119	GG,GA,AA		4.186,0.749,3.0217	,	947/2650,947/5172	56494071	393,12613	2203	4300	6503	SO:0001819	synonymous_variant	667	exon18			ATGAACATTTTGC	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.3819T>C	6.37:g.56494071A>G		168	0	0		128	66	0.515625	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	37																																																																																				A|0.974;G|0.026;T|0.000	0.026	strong		0.338	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		G	56494071	A	G	56494071	2	3	27	1	0	0	0	0	0	0	0	1	4785	214	8	3		3	DST	6	56494071	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	73913	56494071	114620996	372	10823											
FAM135A	57579	hgsc.bcm.edu	37	chr6	71195892	71195892	+	Intron	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaggccaacatgcagctcctAtatgagcgtcttctcagaag	12	9	9	11	1	2	2	1	1	2	1	4	2	3	2	2	1	4	2	2	1	5	3	rs142935920		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:71195892A>G	ENST00000418814.2	+	10	1437				FAM135A_ENST00000505868.1_Intron|FAM135A_ENST00000505769.1_Intron|FAM135A_ENST00000370479.3_Silent_p.L239L|FAM135A_ENST00000457062.2_Silent_p.L239L|FAM135A_ENST00000361499.3_Intron	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A											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						TGCAGCTCCTATATGAGCGTC	0.368													A|||	1	0.000199681	0.0	0.0	5008	,	,		16631	0.0		0.001	False		,,,				2504	0.0				p.L239L		Atlas-SNP	.											.	FAM135A	181	.	0			c.A717G						PASS	.	A	,,	0,4406		0,0,2203	88	79	82		,,717	-2.4	1	6	dbSNP_134	82	8,8592	6.4+/-24.3	0,8,4292	no	intron,intron,coding-synonymous	FAM135A	NM_001105531.2,NM_001162529.1,NM_020819.4	,,	0,8,6495	GG,GA,AA		0.093,0.0,0.0615	,,	,,239/1303	71195892	8,12998	2203	4300	6503	SO:0001627	intron_variant	57579	exon9			GCTCCTATATGAG	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.823+4035A>G	6.37:g.71195892A>G		232	0	0		201	94	0.467662	NM_020819	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Silent	SNP	ENST00000418814.2	37	CCDS55028.1																																																																																			A|0.999;G|0.001	0.001	strong		0.368	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819		G	71195892	A	G	71195892	1	3	27	0	1	0	0	0	0	0	0	0	5453	436	16	3		3	FAM135A	6	71195892	Intron	SNP	A	TCGA-G8-6909-01A-11D-2210-10	14701821	71195892	99919175	373	10824											
COL12A1	1303	hgsc.bcm.edu	37	chr6	75887427	75887436	+	Frame_Shift_Del	DEL	AATATTCAGG	AATATTCAGG	-																															tggagtaccaggtcctgagaAatattcaggaattacagata																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AATATTCAGG	AATATTCAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:75887427_75887436delAATATTCAGG	ENST00000322507.8	-	12	2689_2698	c.2380_2389delCCTGAATATT	c.(2380-2391)cctgaatatttcfs	p.PEYF794fs	COL12A1_ENST00000483888.2_Frame_Shift_Del_p.PEYF794fs|COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000416123.2_Frame_Shift_Del_p.PEYF794fs	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	794	Fibronectin type-III 4. {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						GGTCCTGAGAAATATTCAGGAATTACAGAT	0.438																																					p.794_797del		Atlas-Indel	.											.	COL12A1	385	.	0			c.2381_2390del						PASS	.																																			SO:0001589	frameshift_variant	1303	exon12			.	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.2380_2389delCCTGAATATT	6.37:g.75887427_75887436delAATATTCAGG	ENSP00000325146:p.Pro794fs	155	0	0		155	16	0.103226	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Frame_Shift_Del	DEL	ENST00000322507.8	37	CCDS43482.1																																																																																			.	.	none		0.438	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		-	75887436	AATATTCAGG	-	75887427	7	5	27	1	0	1	0	1	0	0	0	0	3671	14	1	0	7022	0	COL12A1	6	75887427	Frame_Shift_Del	DEL	AATATTCAGG	TCGA-G8-6909-01A-11D-2210-10	4691535	75887427	95227640	374	10825											
BCKDHB	594	hgsc.bcm.edu	37	chr6	80816415	80816415	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggtggtgagcggggatggCggttgtagcggcggctgccg	3	7	22	9	6	0	1	0	1	0	0	0	2	0	2	2	8	3	3	2	8	1	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:80816415C>T	ENST00000320393.6	+	1	52	c.5C>T	c.(4-6)gCg>gTg	p.A2V	BCKDHB_ENST00000545529.1_Missense_Mutation_p.A2V|BCKDHB_ENST00000356489.5_Missense_Mutation_p.A2V|BCKDHB_ENST00000369760.4_Missense_Mutation_p.A2V	NM_183050.2	NP_898871.1	P21953	ODBB_HUMAN	branched chain keto acid dehydrogenase E1, beta polypeptide	2					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity (GO:0003863)|alpha-ketoacid dehydrogenase activity (GO:0003826)|carboxy-lyase activity (GO:0016831)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(10)|upper_aerodigestive_tract(1)	15		all_cancers(76;1.38e-05)|Acute lymphoblastic leukemia(125;1.15e-05)|all_hematologic(105;0.00118)|all_epithelial(107;0.0149)		BRCA - Breast invasive adenocarcinoma(397;0.0291)		GCGGGGATGGCGGTTGTAGCG	0.726																																					p.A2V		Atlas-SNP	.											.	BCKDHB	36	.	0			c.C5T						PASS	.						5	6	5					6																	80816415		2025	3958	5983	SO:0001583	missense	594	exon1			GGATGGCGGTTGT	M55575	CCDS4994.1	6q14.1	2008-07-31	2008-07-31		ENSG00000083123	ENSG00000083123			987	protein-coding gene	gene with protein product	"maple syrup urine disease"	248611					Standard	NM_183050		Approved		uc003pje.2	P21953	OTTHUMG00000016430	ENST00000320393.6:c.5C>T	6.37:g.80816415C>T	ENSP00000318351:p.Ala2Val	37	0	0		60	21	0.35	NM_000056	Q5T2J3|Q9BQL0	Missense_Mutation	SNP	ENST00000320393.6	37	CCDS4994.1	.	.	.	.	.	.	.	.	.	.	C	15.45	2.837710	0.50951	.	.	ENSG00000083123	ENST00000369760;ENST00000320393;ENST00000356489;ENST00000545529	D;D;D;D	0.97232	-4.3;-4.22;-4.22;-4.3	5.35	4.46	0.54185	.	0.158692	0.53938	D	0.000046	D	0.87038	0.6078	N	0.08118	0	0.25088	N	0.990873	P	0.50943	0.94	B	0.40636	0.335	D	0.84007	0.0346	10	0.72032	D	0.01	-12.6247	11.7712	0.51960	0.0:0.8233:0.1767:0.0	.	2	P21953	ODBB_HUMAN	V	2	ENSP00000358775:A2V;ENSP00000318351:A2V;ENSP00000348880:A2V;ENSP00000443564:A2V	ENSP00000318351:A2V	A	+	2	0	BCKDHB	80873134	1.000000	0.71417	0.983000	0.44433	0.142000	0.21351	3.221000	0.51215	1.458000	0.47871	0.511000	0.50034	GCG	.	.	none		0.726	BCKDHB-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043911.2	NM_000056		T	80816415	C	T	80816415	3	4	27	1	0	0	0	0	1	0	0	0	1360	768	27	1	7	1	BCKDHB	6	80816415	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	4928988	80816415	90298652	375	10826											
SLC35A1	10559	hgsc.bcm.edu	37	chr6	88218282	88218282	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taaagaaaaaggatttttctAtggttacacatattatgtct	15	16	6	4	0	2	1	0	0	2	1	2	2	2	2	0	2	1	1	0	2	8	7	rs188216651		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:88218282A>G	ENST00000369552.4	+	6	746	c.719A>G	c.(718-720)tAt>tGt	p.Y240C	C6orf165_ENST00000506888.1_3'UTR|SLC35A1_ENST00000369556.3_Intron|SLC35A1_ENST00000544441.1_Missense_Mutation_p.Y106C|SLC35A1_ENST00000464978.1_3'UTR|SLC35A1_ENST00000369557.5_Intron	NM_006416.4	NP_006407.1	P78382	S35A1_HUMAN	solute carrier family 35 (CMP-sialic acid transporter), member A1	240					carbohydrate metabolic process (GO:0005975)|cellular protein modification process (GO:0006464)|CMP-N-acetylneuraminate transport (GO:0015782)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	CMP-N-acetylneuraminate transmembrane transporter activity (GO:0005456)|sugar:proton symporter activity (GO:0005351)			breast(1)|kidney(3)|large_intestine(2)|lung(3)	9		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;0.0429)		GGATTTTTCTATGGTTACACA	0.323																																					p.Y240C	NSCLC(183;214 2117 17033 22638 44782)|Ovarian(87;1008 1343 9644 42916 50932)	Atlas-SNP	.											.	SLC35A1	29	.	0			c.A719G						PASS	.						89	92	91					6																	88218282		2203	4298	6501	SO:0001583	missense	10559	exon6			TTTTCTATGGTTA	D87969	CCDS5010.1, CCDS55043.1	6q15	2013-05-22			ENSG00000164414	ENSG00000164414		"Solute carriers"	11021	protein-coding gene	gene with protein product		605634	"solute carrier family 35 (UDP-galactose transporter), member 1"			9010752, 9644260	Standard	NM_006416		Approved	CMPST, hCST	uc011dzj.2	P78382	OTTHUMG00000015177	ENST00000369552.4:c.719A>G	6.37:g.88218282A>G	ENSP00000358565:p.Tyr240Cys	59	0	0		52	31	0.596154	NM_006416	Q5W1L8	Missense_Mutation	SNP	ENST00000369552.4	37	CCDS5010.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	A|A	15.17|15.17	2.754984|2.754984	0.49362|0.49362	.|.	.|.	ENSG00000164414|ENSG00000164414	ENST00000429605|ENST00000544441;ENST00000369552	.|T;T	.|0.44881	.|0.91;0.91	5.64|5.64	3.21|3.21	0.36854|0.36854	.|.	.|0.214545	.|0.40908	.|U	.|0.000998	T|T	0.42585|0.42585	0.1209|0.1209	M|M	0.68593|0.68593	2.085|2.085	0.48901|0.48901	D|D	0.99972|0.99972	.|D;D	.|0.62365	.|0.991;0.978	.|P;P	.|0.62089	.|0.898;0.762	T|T	0.39800|0.39800	-0.9596|-0.9596	6|10	0.30078|0.54805	T|T	0.28|0.06	-56.8193|-56.8193	7.7786|7.7786	0.29051|0.29051	0.8085:0.0:0.0674:0.1241|0.8085:0.0:0.0674:0.1241	.|.	.|240;106	.|P78382;B4DEM1	.|S35A1_HUMAN;.	V|C	150|106;240	.|ENSP00000438603:Y106C;ENSP00000358565:Y240C	ENSP00000413148:M150V|ENSP00000358565:Y240C	M|Y	+|+	1|2	0|0	SLC35A1|SLC35A1	88275001|88275001	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	2.961000|2.961000	0.49168|0.49168	0.412000|0.412000	0.25729|0.25729	0.459000|0.459000	0.35465|0.35465	ATG|TAT	A|1.000;G|0.000	0.000	strong		0.323	SLC35A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041446.1			G	88218282	A	G	88218282	3	3	27	1	0	0	0	0	1	0	0	0	14585	449	16	3	741	3	SLC35A1	6	88218282	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	7401867	88218282	82896785	376	10827											
KLHL32	114792	hgsc.bcm.edu	37	chr6	97423931	97423931	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgaatctcacaatgacagtGtcctggcagcgctgaatcag	11	8	10	12	2	2	2	2	2	1	0	4	3	3	2	2	1	1	2	2	1	3	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:97423931G>A	ENST00000369261.4	+	3	445	c.82G>A	c.(82-84)Gtc>Atc	p.V28I	KLHL32_ENST00000539200.1_Missense_Mutation_p.V28I|KLHL32_ENST00000544166.1_5'UTR|KLHL32_ENST00000536676.1_Missense_Mutation_p.V28I	NM_052904.3	NP_443136.2	Q96NJ5	KLH32_HUMAN	kelch-like family member 32	28										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)		CAATGACAGTGTCCTGGCAGC	0.493																																					p.V28I		Atlas-SNP	.											.	KLHL32	85	.	0			c.G82A						PASS	.						82	69	73					6																	97423931		2203	4300	6503	SO:0001583	missense	114792	exon3			GACAGTGTCCTGG	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.82G>A	6.37:g.97423931G>A	ENSP00000358265:p.Val28Ile	87	0	0		83	23	0.277108	NM_052904	B7Z346|B7Z4E2|E1P528|Q5THT0|Q96PY7	Missense_Mutation	SNP	ENST00000369261.4	37	CCDS5038.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.181059	0.78677	.	.	ENSG00000186231	ENST00000369261;ENST00000536676;ENST00000539200;ENST00000369254	T;T;T;T	0.70749	-0.51;1.97;1.97;-0.51	5.14	5.14	0.70334	BTB/POZ fold (2);	0.055908	0.64402	N	0.000001	T	0.61438	0.2347	N	0.24115	0.695	0.80722	D	1	P;P;B;P	0.50156	0.517;0.932;0.397;0.9	B;P;B;B	0.61592	0.227;0.891;0.281;0.323	T	0.57740	-0.7759	10	0.07325	T	0.83	.	18.7846	0.91949	0.0:0.0:1.0:0.0	.	28;28;28;28	B7Z4E2;B7Z346;Q96NJ5;Q6IQ08	.;.;KLH32_HUMAN;.	I	28	ENSP00000358265:V28I;ENSP00000440382:V28I;ENSP00000441527:V28I;ENSP00000358258:V28I	ENSP00000358258:V28I	V	+	1	0	KLHL32	97530652	1.000000	0.71417	0.990000	0.47175	0.702000	0.40608	9.263000	0.95617	2.674000	0.91012	0.591000	0.81541	GTC	.	.	none		0.493	KLHL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041570.1	NM_052904		A	97423931	G	A	97423931	3	1	27	1	0	0	0	0	1	0	0	0	8395	1377	48	2	88	2	KLHL32	6	97423931	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	9205649	97423931	73691136	377	10828											
RTN4IP1	84816	hgsc.bcm.edu	37	chr6	107019974	107019974	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtttgttcaataactggcCggatctgtaaaacataagag	14	11	10	6	1	2	1	1	0	1	1	2	2	2	2	1	3	2	3	1	3	5	5	rs372866009		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:107019974C>T	ENST00000369063.3	-	9	1553	c.1088G>A	c.(1087-1089)cGg>cAg	p.R363Q	RTN4IP1_ENST00000539449.1_3'UTR|RTN4IP1_ENST00000498091.1_5'UTR	NM_032730.4	NP_116119.2	Q8WWV3	RT4I1_HUMAN	reticulon 4 interacting protein 1	363						mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)	p.R363L(1)		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)		AATAACTGGCCGGATCTGTAA	0.418																																					p.R363Q		Atlas-SNP	.											RTN4IP1,NS,carcinoma,0,1	RTN4IP1	31	1	1	Substitution - Missense(1)	lung(1)	c.G1088A						PASS	.	C	GLN/ARG	0,4406		0,0,2203	92	95	94		1088	-2.2	0.9	6		94	2,8598	2.2+/-6.3	0,2,4298	no	missense	RTN4IP1	NM_032730.4	43	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	363/397	107019974	2,13004	2203	4300	6503	SO:0001583	missense	84816	exon9			ACTGGCCGGATCT	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.1088G>A	6.37:g.107019974C>T	ENSP00000358059:p.Arg363Gln	96	0	0		71	26	0.366197	NM_032730	Q8N9B3|Q8WZ66|Q9BRA4	Missense_Mutation	SNP	ENST00000369063.3	37	CCDS5056.1	.	.	.	.	.	.	.	.	.	.	C	10.75	1.439632	0.25900	0.0	2.33E-4	ENSG00000130347	ENST00000369063	T	0.24908	1.83	6.02	-2.25	0.06888	.	0.687056	0.15173	N	0.276506	T	0.06645	0.0170	L	0.33245	0.995	0.30421	N	0.7781	B	0.19583	0.037	B	0.12837	0.008	T	0.35847	-0.9772	10	0.31617	T	0.26	-0.4612	12.1462	0.54024	0.0:0.3328:0.0:0.6672	.	363	Q8WWV3	RT4I1_HUMAN	Q	363	ENSP00000358059:R363Q	ENSP00000358059:R363Q	R	-	2	0	RTN4IP1	107126667	0.011000	0.17503	0.894000	0.35097	0.910000	0.53928	-0.027000	0.12371	-0.270000	0.09285	-0.355000	0.07637	CGG	.	.	weak		0.418	RTN4IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041673.1			T	107019974	C	T	107019974	3	4	27	1	0	0	0	0	1	0	0	0	13744	652	23	1	106	1	RTN4IP1	6	107019974	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	9596043	107019974	64095093	378	10829											
AKD1	221264	hgsc.bcm.edu	37	chr6	109827528	109827528	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	accttaaaaagtgctatcttAcctgcttttattctttccag	10	17	4	10	0	2	0	0	0	2	0	3	0	3	0	3	0	3	2	3	0	6	7			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:109827528A>G	ENST00000424296.2	-	35	4926		c.e35+1		RP5-919F19.5_ENST00000423747.2_RNA|AL109947.2_ENST00000517228.1_RNA	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9						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)										GTGCTATCTTACCTGCTTTTA	0.338																																					.		Atlas-SNP	.											C6orf224,NS,carcinoma,-2,2	AKD1	223	2	0			c.4849+2T>C						PASS	.						108	105	106					6																	109827528		2202	4298	6500	SO:0001630	splice_region_variant	221264	exon36			TATCTTACCTGCT	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.4849+1T>C	6.37:g.109827528A>G		131	0	0		78	24	0.307692	NM_001145128	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Splice_Site	SNP	ENST00000424296.2	37	CCDS55048.1	.	.	.	.	.	.	.	.	.	.	A	15.81	2.943658	0.53079	.	.	ENSG00000155085	ENST00000424296;ENST00000470564;ENST00000490722	.	.	.	5.01	5.01	0.66863	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0182	0.71605	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	AKD1	109934221	1.000000	0.71417	0.997000	0.53966	0.685000	0.39939	8.305000	0.89960	1.995000	0.58328	0.533000	0.62120	.	.	.	none		0.338	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128	Intron	G	109827528	A	G	109827528	5	3	27	1	0	0	0	0	0	0	1	0	460	405	14	3	912	3	AKD1	6	109827528	Splice_Site	SNP	A	TCGA-G8-6909-01A-11D-2210-10	2807554	109827528	61287539	379	10830											
REV3L	5980	hgsc.bcm.edu	37	chr6	111631254	111631254	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaatgatgacgtatggcacTcgctccccaacctgaggctc	10	9	9	13	2	0	3	0	3	0	0	3	3	1	3	3	2	1	4	3	2	4	2	rs150392515		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:111631254T>C	ENST00000358835.3	-	31	9298	c.8844A>G	c.(8842-8844)cgA>cgG	p.R2948R	RP5-1112D6.8_ENST00000607434.1_RNA|REV3L_ENST00000435970.1_Silent_p.R2870R|REV3L_ENST00000368805.1_Silent_p.R2948R|REV3L_ENST00000368802.3_Silent_p.R2948R|REV3L_ENST00000462119.1_5'UTR			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2948					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)		CGTATGGCACTCGCTCCCCAA	0.498								DNA polymerases (catalytic subunits)																													p.R2948R		Atlas-SNP	.											REV3L,NS,carcinoma,-2,1	REV3L	386	1	0			c.A8844G						PASS	.	T		0,4406		0,0,2203	74	76	75		8844	0.2	1	6	dbSNP_134	75	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	REV3L	NM_002912.3		0,2,6501	CC,CT,TT		0.0233,0.0,0.0154		2948/3131	111631254	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	5980	exon30			TGGCACTCGCTCC	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.8844A>G	6.37:g.111631254T>C		40	0	0		31	15	0.483871	NM_002912	O43214|Q5TC33	Silent	SNP	ENST00000358835.3	37	CCDS5091.2																																																																																			T|1.000;C|0.000	0.000	weak		0.498	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		C	111631254	T	C	111631254	2	2	27	1	0	0	0	0	0	0	0	1	13255	1538	54	3		3	REV3L	6	111631254	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	1803726	111631254	59483813	380	10831											
SGK1	6446	hgsc.bcm.edu	37	chr6	134494426	134494426	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcatacctctttctttttcaGgattgctttcttctgtaaaa	8	20	4	9	0	6	0	2	0	4	0	6	1	6	1	1	1	2	2	1	1	3	8			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:134494426G>T	ENST00000237305.7	-	5	491	c.403C>A	c.(403-405)Ctg>Atg	p.L135M	SGK1_ENST00000528577.1_Missense_Mutation_p.L163M|SGK1_ENST00000413996.3_Missense_Mutation_p.L149M|SGK1_ENST00000367857.5_Missense_Mutation_p.L125M|SGK1_ENST00000367858.5_Missense_Mutation_p.L230M|SGK1_ENST00000475719.2_Missense_Mutation_p.L135M|SGK1_ENST00000489458.2_5'UTR	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	135	Glu/Lys-rich.|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)		TTCTTTTTCAGGATTGCTTTC	0.378																																					p.L230M		Atlas-SNP	.											.	SGK1	387	.	0			c.C688A						PASS	.						114	113	113					6																	134494426		2203	4300	6503	SO:0001583	missense	6446	exon7			TTTTCAGGATTGC	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.403C>A	6.37:g.134494426G>T	ENSP00000237305:p.Leu135Met	175	0	0		103	31	0.300971	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	16.53	3.149912	0.57151	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719	T;T;T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19;-0.19;1.88	6.17	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	T	0.54481	0.1861	L	0.42686	1.345	0.80722	D	1	B;B;B;B;B;B	0.32918	0.24;0.386;0.389;0.099;0.39;0.121	B;B;P;B;B;B	0.44673	0.179;0.291;0.457;0.111;0.408;0.177	T	0.61262	-0.7098	10	0.54805	T	0.06	.	15.9715	0.80025	0.0648:0.0:0.9352:0.0	.	163;149;135;125;230;135	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	M	230;149;135;125;163;135	ENSP00000356832:L230M;ENSP00000396242:L149M;ENSP00000237305:L135M;ENSP00000356831:L125M;ENSP00000434450:L163M;ENSP00000434302:L135M	ENSP00000237305:L135M	L	-	1	2	SGK1	134536119	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.089000	0.57685	1.599000	0.50093	0.655000	0.94253	CTG	.	.	none		0.378	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			T	134494426	G	T	134494426	3	4	27	1	0	0	0	0	1	0	0	0	14222	991	35	4	924	4	SGK1	6	134494426	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	22863172	134494426	36620641	381	10832			1	45		5	5	1300	N	G_C	1.441812e-07
SGK1	6446	hgsc.bcm.edu	37	chr6	134494619	134494619	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	cctttccaaaactgccctttCcgatcactttcaagaagtga	11	12	5	13	1	2	2	2	1	0	1	4	3	4	2	4	0	2	0	4	0	4	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:134494619C>G	ENST00000237305.7	-	4	402	c.314G>C	c.(313-315)gGa>gCa	p.G105A	SGK1_ENST00000528577.1_Missense_Mutation_p.G133A|SGK1_ENST00000413996.3_Missense_Mutation_p.G119A|SGK1_ENST00000367857.5_Missense_Mutation_p.G95A|SGK1_ENST00000367858.5_Missense_Mutation_p.G200A|SGK1_ENST00000475719.2_Missense_Mutation_p.G105A|SGK1_ENST00000489458.2_5'UTR	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	105	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)		ACTGCCCTTTCCGATCACTTT	0.398																																					p.G200A		Atlas-SNP	.											.	SGK1	387	.	0			c.G599C						PASS	.						63	68	66					6																	134494619		2203	4300	6503	SO:0001583	missense	6446	exon6			CCCTTTCCGATCA	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.314G>C	6.37:g.134494619C>G	ENSP00000237305:p.Gly105Ala	105	0	0		89	19	0.213483	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	C	29.4	5.000125	0.93227	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719	D;D;D;D;D;T	0.82081	-1.57;-1.57;-1.57;-1.57;-1.57;0.61	6.02	6.02	0.97574	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	0.91965	0.7455	M	0.85041	2.73	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;1.0;1.0;0.999;0.999;1.0	D;D;D;D;D;D	0.97110	0.999;0.998;1.0;0.999;0.998;0.999	D	0.91872	0.5508	10	0.87932	D	0	.	20.5407	0.99260	0.0:1.0:0.0:0.0	.	133;119;105;95;200;105	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	A	200;119;105;95;133;105	ENSP00000356832:G200A;ENSP00000396242:G119A;ENSP00000237305:G105A;ENSP00000356831:G95A;ENSP00000434450:G133A;ENSP00000434302:G105A	ENSP00000237305:G105A	G	-	2	0	SGK1	134536312	1.000000	0.71417	0.989000	0.46669	0.951000	0.60555	7.818000	0.86416	2.865000	0.98341	0.655000	0.94253	GGA	.	.	none		0.398	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			G	134494619	C	G	134494619	3	3	27	1	0	0	0	0	1	0	0	0	14222	855	30	4	1017	4	SGK1	6	134494619	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	193	134494619	36620448	382	10833			1	45		5	5	1300	N	G_C	1.441812e-07
SGK1	6446	hgsc.bcm.edu	37	chr6	134494661	134494661	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agtcagatggtttagcatgaGgattggacgacgggccaagg	11	8	16	6	2	1	2	1	1	0	1	1	5	1	4	1	5	1	2	1	5	2	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:134494661G>C	ENST00000237305.7	-	4	360	c.272C>G	c.(271-273)cCt>cGt	p.P91R	SGK1_ENST00000528577.1_Missense_Mutation_p.P119R|SGK1_ENST00000413996.3_Missense_Mutation_p.P105R|SGK1_ENST00000367857.5_Missense_Mutation_p.P81R|SGK1_ENST00000367858.5_Missense_Mutation_p.P186R|SGK1_ENST00000475719.2_Missense_Mutation_p.P91R|SGK1_ENST00000489458.2_5'UTR	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	91					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)	p.P186L(1)|p.P81L(1)|p.P91L(1)		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)		TTTAGCATGAGGATTGGACGA	0.378																																					p.P186R		Atlas-SNP	.											SGK1_ENST00000367858,lymph_node,lymphoid_neoplasm,0,3	SGK1	387	3	3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	c.C557G						PASS	.						73	77	76					6																	134494661		2203	4300	6503	SO:0001583	missense	6446	exon6			GCATGAGGATTGG	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.272C>G	6.37:g.134494661G>C	ENSP00000237305:p.Pro91Arg	90	0	0		70	14	0.2	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	17.43	3.388841	0.61956	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719	T;T;T;T;T;T	0.73152	3.18;3.18;3.18;3.18;3.18;-0.72	6.02	6.02	0.97574	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.79100	0.4389	M	0.62723	1.935	0.80722	D	1	B;D;B;B;P;B	0.67145	0.105;0.996;0.023;0.086;0.503;0.102	B;D;B;B;B;B	0.63703	0.093;0.917;0.046;0.082;0.248;0.059	T	0.75371	-0.3341	10	0.41790	T	0.15	.	20.5407	0.99260	0.0:0.0:1.0:0.0	.	119;105;91;81;186;91	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	R	186;105;91;81;119;91	ENSP00000356832:P186R;ENSP00000396242:P105R;ENSP00000237305:P91R;ENSP00000356831:P81R;ENSP00000434450:P119R;ENSP00000434302:P91R	ENSP00000237305:P91R	P	-	2	0	SGK1	134536354	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	9.790000	0.99075	2.865000	0.98341	0.655000	0.94253	CCT	.	.	none		0.378	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			C	134494661	G	C	134494661	3	2	27	1	0	0	0	0	1	0	0	0	14222	1000	35	4	1059	4	SGK1	6	134494661	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	42	134494661	36620406	383	10834			1	45		5	5	1300	N	G_C	1.441812e-07
SGK1	6446	hgsc.bcm.edu	37	chr6	134495159	134495159	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ttactggaggagaagggttgGcattcataagctcaggctcc	10	10	13	8	0	2	1	2	0	0	1	3	3	3	2	1	5	2	4	1	5	3	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:134495159G>C	ENST00000237305.7	-	3	300	c.212C>G	c.(211-213)gCc>gGc	p.A71G	SGK1_ENST00000528577.1_Missense_Mutation_p.A99G|SGK1_ENST00000413996.3_Missense_Mutation_p.A85G|SGK1_ENST00000367857.5_Missense_Mutation_p.A61G|SGK1_ENST00000367858.5_Missense_Mutation_p.A166G|SGK1_ENST00000475719.2_Missense_Mutation_p.A71G|SGK1_ENST00000489458.2_5'UTR	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	71					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)		AGAAGGGTTGGCATTCATAAG	0.453																																					p.A166G		Atlas-SNP	.											SGK1_ENST00000528577,NS,lymphoid_neoplasm,0,5	SGK1	387	5	0			c.C497G						PASS	.						152	146	148					6																	134495159		2203	4300	6503	SO:0001583	missense	6446	exon5			GGGTTGGCATTCA	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.212C>G	6.37:g.134495159G>C	ENSP00000237305:p.Ala71Gly	82	0	0		58	15	0.258621	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	13.00	2.107682	0.37242	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T	0.72942	-0.69;-0.69;-0.69;-0.67;-0.68;-0.7	5.99	5.12	0.69794	.	0.399737	0.30076	N	0.010479	T	0.40171	0.1106	N	0.22421	0.69	0.80722	D	1	B;B;B;B;B;B	0.27559	0.001;0.0;0.0;0.019;0.181;0.0	B;B;B;B;B;B	0.26693	0.005;0.001;0.001;0.039;0.072;0.001	T	0.36625	-0.9740	10	0.20519	T	0.43	.	14.2908	0.66275	0.0:0.0:0.7295:0.2705	.	99;85;71;61;166;71	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	G	166;85;71;61;99;71;135	ENSP00000356832:A166G;ENSP00000396242:A85G;ENSP00000237305:A71G;ENSP00000356831:A61G;ENSP00000434450:A99G;ENSP00000434302:A71G	ENSP00000237305:A71G	A	-	2	0	SGK1	134536852	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.654000	0.54453	1.523000	0.49018	0.655000	0.94253	GCC	.	.	none		0.453	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			C	134495159	G	C	134495159	3	2	27	1	0	0	0	0	1	0	0	0	14222	1203	42	4	1123	4	SGK1	6	134495159	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	498	134495159	36619908	384	10835			1	45		5	5	1300	N	G_C	1.441812e-07
SGK1	6446	hgsc.bcm.edu	37	chr6	134495725	134495725	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctcctctgcttcatgaaagCtgtggatgaaggaggagaaa	12	9	12	8	0	2	3	1	2	1	1	3	6	3	5	2	3	2	2	2	3	3	1	rs186450029		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:134495725C>T	ENST00000237305.7	-	2	165		c.e2-1		SGK1_ENST00000528577.1_Splice_Site|SGK1_ENST00000413996.3_Splice_Site|SGK1_ENST00000367857.5_Missense_Mutation_p.A16T|SGK1_ENST00000367858.5_Splice_Site|SGK1_ENST00000475719.2_Splice_Site|SGK1_ENST00000489458.2_5'Flank	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)		TTCATGAAAGCTGTGGATGAA	0.433											OREG0017675	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Atlas-SNP	.											SGK1_ENST00000528577,NS,lymphoid_neoplasm,0,4	SGK1	387	4	0			c.77-1G>A						PASS	.						73	73	73					6																	134495725		2203	4300	6503	SO:0001630	splice_region_variant	6446	exon3			TGAAAGCTGTGGA	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.77-1G>A	6.37:g.134495725C>T		84	0	0	1611	36	11	0.305556	NM_005627	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Splice_Site	SNP	ENST00000237305.7	37	CCDS5170.1	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	29.2|29.2	4.985656|4.985656	0.93044|0.93044	.|.	.|.	ENSG00000118515|ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000528577;ENST00000475719;ENST00000461976|ENST00000367857	.|T	.|0.30182	.|1.54	5.89|5.89	5.89|5.89	0.94794|0.94794	.|.	.|.	.|.	.|.	.|.	.|T	.|0.14399	.|0.0348	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|B	.|0.27971	.|0.196	.|B	.|0.25759	.|0.063	.|T	.|0.05419	.|-1.0886	.|7	.|.	.|.	.|.	.|.	20.2576|20.2576	0.98430|0.98430	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|16	.|O00141-4	.|.	.|T	-1|16	.|ENSP00000356831:A16T	.|.	.|A	-|-	.|1	.|0	SGK1|SGK1	134537418|134537418	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.926000|0.926000	0.56050|0.56050	7.818000|7.818000	0.86416|0.86416	2.783000|2.783000	0.95769|0.95769	0.655000|0.655000	0.94253|0.94253	.|GCT	C|1.000;T|0.000	0.000	strong		0.433	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		Intron	T	134495725	C	T	134495725	5	4	27	1	0	0	0	0	0	0	1	0	14222	811	28	2	1263	2	SGK1	6	134495725	Splice_Site	SNP	C	TCGA-G8-6909-01A-11D-2210-10	566	134495725	36619342	385	10836			1	45		5	5	1300	N	G_C	1.441812e-07
ECT2L	345930	hgsc.bcm.edu	37	chr6	139223635	139223635	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatacctcaaatgcttttacAgatgtcaagaatgcatttat	14	15	5	7	0	2	2	2	0	0	2	2	2	2	2	1	0	4	2	1	0	7	6	rs200545869		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:139223635A>T	ENST00000423192.1	+	21	2748		c.e21-1		ECT2L_ENST00000541398.1_Splice_Site|ECT2L_ENST00000367682.2_Splice_Site			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like								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						ATGCTTTTACAGATGTCAAGA	0.289			"N, Splice, Mis"		ETP ALL								A|||	1	0.000199681	0.0	0.0	5008	,	,		18297	0.0		0.001	False		,,,				2504	0.0				.		Atlas-SNP	.		Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	.	ECT2L	75	.	0			c.2588-2A>T						PASS	.	A	,	2,3602		0,2,1800	75	71	72		,	5.6	1	6		72	5,8143		0,5,4069	yes	splice-3,splice-3	ECT2L	NM_001077706.2,NM_001195037.2	,	0,7,5869	TT,TA,AA		0.0614,0.0555,0.0596	,	,	139223635	7,11745	1802	4074	5876	SO:0001630	splice_region_variant	345930	exon21			TTTTACAGATGTC		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.2588-1A>T	6.37:g.139223635A>T		76	0	0		31	12	0.387097	NM_001195037	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Splice_Site	SNP	ENST00000423192.1	37	CCDS43508.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.049498	0.75846	5.55E-4	6.14E-4	ENSG00000203734	ENST00000423192;ENST00000367682;ENST00000541398	.	.	.	5.63	5.63	0.86233	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3602	0.60652	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ECT2L	139265328	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.636000	0.67848	2.145000	0.66743	0.533000	0.62120	.	A|0.999;T|0.001	0.001	weak		0.289	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706	Intron	T	139223635	A	T	139223635	5	4	27	1	0	0	0	0	0	0	1	0	4904	202	7	5	2664	5	ECT2L	6	139223635	Splice_Site	SNP	A	TCGA-G8-6909-01A-11D-2210-10	4727910	139223635	31891432	386	10837											
UTRN	7402	hgsc.bcm.edu	37	chr6	144774982	144774982	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attaaaccaaactggacaaaTccttgtggagcaaatgggaa	17	8	9	7	0	0	0	0	0	0	0	1	3	1	3	2	3	3	1	2	3	6	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:144774982T>G	ENST00000367545.3	+	18	2261	c.2261T>G	c.(2260-2262)aTc>aGc	p.I754S		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	754	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)		ACTGGACAAATCCTTGTGGAG	0.358																																					p.I754S		Atlas-SNP	.											.	UTRN	327	.	0			c.T2261G						PASS	.						90	95	93					6																	144774982		2203	4300	6503	SO:0001583	missense	7402	exon18			GACAAATCCTTGT	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.2261T>G	6.37:g.144774982T>G	ENSP00000356515:p.Ile754Ser	87	0	0		58	30	0.517241	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	T	0.223	-1.027393	0.02045	.	.	ENSG00000152818	ENST00000367529;ENST00000367545	T	0.32988	1.43	5.87	-1.66	0.08265	.	0.697165	0.12797	N	0.438319	T	0.04588	0.0125	N	0.24115	0.695	0.32854	D	0.507058	B	0.21309	0.054	B	0.15484	0.013	T	0.39014	-0.9634	10	0.09084	T	0.74	.	5.6165	0.17434	0.1604:0.2957:0.0:0.5439	.	754	P46939	UTRO_HUMAN	S	754	ENSP00000356515:I754S	ENSP00000356499:I754S	I	+	2	0	UTRN	144816675	0.915000	0.31059	0.238000	0.24106	0.304000	0.27724	0.951000	0.29135	-0.106000	0.12110	-0.290000	0.09829	ATC	.	.	none		0.358	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			G	144774982	T	G	144774982	3	3	27	1	0	0	0	0	1	0	0	0	17118	1435	50	5	2331	5	UTRN	6	144774982	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	5551347	144774982	26340085	387	10838											
SHPRH	257218	hgsc.bcm.edu	37	chr6	146267376	146267376	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgtcttacttacgagggcaTtgaactttttcttttggttc	7	19	8	7	1	2	1	0	1	2	0	3	2	2	1	0	2	3	2	0	2	3	8	rs201477770	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:146267376T>C	ENST00000367505.2	-	7	1578	c.1314A>G	c.(1312-1314)caA>caG	p.Q438Q	SHPRH_ENST00000275233.7_Silent_p.Q438Q|SHPRH_ENST00000367503.3_Silent_p.Q438Q|SHPRH_ENST00000438092.2_Silent_p.Q438Q			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	438	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.		Q -> R (in an ovarian cancer cell line). {ECO:0000269|PubMed:12837266}.		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)		TACGAGGGCATTGAACTTTTT	0.313													T|||	2	0.000399361	0.0015	0.0	5008	,	,		16466	0.0		0.0	False		,,,				2504	0.0				p.Q438Q		Atlas-SNP	.											.	SHPRH	169	.	0			c.A1314G						PASS	.	T	,	0,3650		0,0,1825	165	146	152		1314,1314	-6	0.9	6	dbSNP_134	152	1,8145		0,1,4072	no	coding-synonymous,coding-synonymous	SHPRH	NM_001042683.2,NM_173082.3	,	0,1,5897	CC,CT,TT		0.0123,0.0,0.0085	,	438/1684,438/1660	146267376	1,11795	1825	4073	5898	SO:0001819	synonymous_variant	257218	exon7			AGGGCATTGAACT	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.1314A>G	6.37:g.146267376T>C		57	0	0		20	10	0.5	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Silent	SNP	ENST00000367505.2	37	CCDS43513.2																																																																																			T|1.000;C|0.000	0.000	strong		0.313	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082		C	146267376	T	C	146267376	2	2	27	1	0	0	0	0	0	0	0	1	14306	1490	52	3		3	SHPRH	6	146267376	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	1492394	146267376	24847691	388	10839											
ULBP3	79465	hgsc.bcm.edu	37	chr6	150386752	150386752	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgaactgccaagatccaCggatgtatccatcggcttca	11	9	9	12	2	1	2	1	1	0	1	4	3	3	3	3	2	3	3	3	2	3	2	rs34547018	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:150386752C>T	ENST00000367339.2	-	3	438	c.410G>A	c.(409-411)cGt>cAt	p.R137H	ULBP3_ENST00000438272.2_Missense_Mutation_p.R137H			Q9BZM4	N2DL3_HUMAN	UL16 binding protein 3	137	MHC class I alpha-2 like.				antigen processing and presentation (GO:0019882)|natural killer cell activation (GO:0030101)|natural killer cell mediated cytotoxicity (GO:0042267)|regulation of immune response (GO:0050776)|viral process (GO:0016032)	anchored component of plasma membrane (GO:0046658)|plasma membrane (GO:0005886)	natural killer cell lectin-like receptor binding (GO:0046703)			central_nervous_system(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	9		Ovarian(120;0.12)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.45e-12)		CCAAGATCCACGGATGTATCC	0.517													C|||	25	0.00499201	0.0091	0.0029	5008	,	,		22692	0.0		0.008	False		,,,				2504	0.0031				p.R137H		Atlas-SNP	.											.	ULBP3	22	.	0			c.G410A						PASS	.	C	HIS/ARG	26,4380	32.6+/-62.9	0,26,2177	128	119	122		410	-6.7	0	6	dbSNP_126	122	22,8578	15.3+/-51.7	0,22,4278	yes	missense	ULBP3	NM_024518.1	29	0,48,6455	TT,TC,CC		0.2558,0.5901,0.3691	benign	137/245	150386752	48,12958	2203	4300	6503	SO:0001583	missense	79465	exon3			GATCCACGGATGT	AF304379	CCDS5225.1	6q25	2008-04-11			ENSG00000131019	ENSG00000131019			14895	protein-coding gene	gene with protein product		605699				11239445, 11827464	Standard	NM_024518		Approved	RAET1N	uc003qns.3	Q9BZM4	OTTHUMG00000015811	ENST00000367339.2:c.410G>A	6.37:g.150386752C>T	ENSP00000356308:p.Arg137His	105	0	0		69	19	0.275362	NM_024518	Q5VY82|Q8IZX5|Q8TE75	Missense_Mutation	SNP	ENST00000367339.2	37	CCDS5225.1	10	0.004578754578754579	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	1.414	-0.574714	0.03882	0.005901	0.002558	ENSG00000131019	ENST00000399812;ENST00000253335;ENST00000367339;ENST00000438272	T;T	0.08102	3.13;3.13	3.34	-6.69	0.01772	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	0.01765	0.0056	M	0.71581	2.175	0.09310	N	1	B;B	0.25206	0.12;0.12	B;B	0.11329	0.006;0.006	T	0.24333	-1.0163	9	0.39692	T	0.17	1.34	0.3216	0.00304	0.3017:0.137:0.2037:0.3577	rs34547018	137;137	Q5VY82;Q9BZM4	.;N2DL3_HUMAN	H	88;137;137;137	ENSP00000356308:R137H;ENSP00000403562:R137H	ENSP00000253335:R137H	R	-	2	0	ULBP3	150428445	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.449000	0.01008	-3.228000	0.00210	-1.434000	0.01081	CGT	C|0.997;T|0.003	0.003	strong		0.517	ULBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042678.2			T	150386752	C	T	150386752	3	4	27	1	0	0	0	0	1	0	0	0	16989	536	19	1	331	1	ULBP3	6	150386752	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	4119376	150386752	20728315	389	10840											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152746593	152746593	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtttcatcattttcacatcAtctttggaggctactgagaa	11	15	7	8	0	5	1	4	1	1	1	5	3	5	2	0	2	1	2	0	2	2	5	rs111250109	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:152746593A>T	ENST00000367255.5	-	39	5791	c.5190T>A	c.(5188-5190)gaT>gaA	p.D1730E	SYNE1_ENST00000265368.4_Missense_Mutation_p.D1730E|SYNE1_ENST00000423061.1_Missense_Mutation_p.D1737E|SYNE1_ENST00000448038.1_Missense_Mutation_p.D1737E|SYNE1_ENST00000341594.5_Missense_Mutation_p.D1767E	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1730					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)		TTTTCACATCATCTTTGGAGG	0.363										HNSCC(10;0.0054)			A|||	164	0.0327476	0.0287	0.0288	5008	,	,		18407	0.005		0.0577	False		,,,				2504	0.044				p.D1737E		Atlas-SNP	.											.	SYNE1	3227	.	0			c.T5211A						PASS	.	A	GLU/ASP,GLU/ASP	183,4223	118.8+/-156.5	5,173,2025	153	143	147		5211,5190	-6.3	0.8	6	dbSNP_132	147	444,8156	134.3+/-191.7	18,408,3874	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	45,45	23,581,5899	TT,TA,AA		5.1628,4.1534,4.8209	benign,benign	1737/8750,1730/8798	152746593	627,12379	2203	4300	6503	SO:0001583	missense	23345	exon39			CACATCATCTTTG	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.5190T>A	6.37:g.152746593A>T	ENSP00000356224:p.Asp1730Glu	230	0	0		142	95	0.669014	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	37	CCDS5236.2	68	0.031135531135531136	14	0.028455284552845527	10	0.027624309392265192	2	0.0034965034965034965	42	0.055408970976253295	A	12.76	2.033458	0.35893	0.041534	0.051628	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52	5.71	-6.32	0.01995	.	0.397222	0.23999	N	0.042496	T	0.02230	0.0069	N	0.04959	-0.14	0.80722	D	1	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.0;0.001	T	0.36744	-0.9735	10	0.02654	T	1	.	5.6049	0.17374	0.1571:0.5244:0.1775:0.141	.	1713;1730;1730;1737	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	E	1730;1737;1730;1737;1767	ENSP00000356224:D1730E;ENSP00000396024:D1737E;ENSP00000265368:D1730E;ENSP00000390975:D1737E;ENSP00000341887:D1767E	ENSP00000265368:D1730E	D	-	3	2	SYNE1	152788286	0.003000	0.15002	0.784000	0.31847	0.973000	0.67179	-2.103000	0.01341	-1.475000	0.01876	-0.314000	0.08810	GAT	A|0.951;T|0.049	0.049	strong		0.363	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152746593	A	T	152746593	3	4	27	1	0	0	0	0	1	0	0	0	15460	214	8	5	21708	5	SYNE1	6	152746593	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	2359841	152746593	18368474	390	10841											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152763258	152763258	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcgctccaggccatccagTgtgctctccagcttccgcag	5	9	10	17	2	1	0	0	0	1	0	5	0	4	0	5	1	3	4	5	1	0	1	rs138705766	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:152763258T>C	ENST00000367255.5	-	31	4561	c.3960A>G	c.(3958-3960)acA>acG	p.T1320T	SYNE1_ENST00000265368.4_Silent_p.T1320T|SYNE1_ENST00000423061.1_Silent_p.T1327T|SYNE1_ENST00000448038.1_Silent_p.T1327T|SYNE1_ENST00000367253.4_Silent_p.T1320T|SYNE1_ENST00000367248.3_Silent_p.T1310T|SYNE1_ENST00000413186.2_Silent_p.T1320T|SYNE1_ENST00000341594.5_Silent_p.T1386T	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1320					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)		GGCCATCCAGTGTGCTCTCCA	0.632										HNSCC(10;0.0054)			G|||	64	0.0127796	0.0106	0.0159	5008	,	,		16360	0.001		0.0209	False		,,,				2504	0.0174				p.T1327T		Atlas-SNP	.											.	SYNE1	3227	.	0			c.A3981G						PASS	.	G	,	51,4355		0,51,2152	72	70	71		3981,3960	-1.4	0.7	6	dbSNP_134	71	158,8442		2,154,4144	no	coding-synonymous,coding-synonymous	SYNE1	NM_033071.3,NM_182961.3	,	2,205,6296	CC,CT,TT		1.8372,1.1575,1.607	,	1327/8750,1320/8798	152763258	209,12797	2203	4300	6503	SO:0001819	synonymous_variant	23345	exon31			ATCCAGTGTGCTC	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.3960A>G	6.37:g.152763258T>C		66	0	0		43	33	0.767442	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																			T|0.983;C|0.017	0.017	strong		0.632	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		C	152763258	T	C	152763258	2	2	27	1	0	0	0	0	0	0	0	1	15460	1683	59	3		3	SYNE1	6	152763258	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	16665	152763258	18351809	391	10842											
TIAM2	26230	hgsc.bcm.edu	37	chr6	155500242	155500242	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagatgacaatgttgagtatTgcatccctgcaccatatgaa	13	12	8	8	0	0	4	0	3	0	1	1	4	1	4	2	0	2	4	2	0	5	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:155500242T>C	ENST00000461783.3	+	13	3866	c.2593T>C	c.(2593-2595)Tgc>Cgc	p.C865R	TIAM2_ENST00000360366.4_Missense_Mutation_p.C889R|TIAM2_ENST00000367174.2_Missense_Mutation_p.C241R|TIAM2_ENST00000528391.2_Missense_Mutation_p.C201R|TIAM2_ENST00000456144.1_Missense_Mutation_p.C865R|TIAM2_ENST00000318981.5_Missense_Mutation_p.C865R|TIAM2_ENST00000529824.2_Missense_Mutation_p.C865R|TIAM2_ENST00000456877.2_Missense_Mutation_p.C177R			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	865	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)		TGTTGAGTATTGCATCCCTGC	0.383																																					p.C865R		Atlas-SNP	.											.	TIAM2	161	.	0			c.T2593C						PASS	.						118	107	111					6																	155500242		2203	4300	6503	SO:0001583	missense	26230	exon10			GAGTATTGCATCC		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.2593T>C	6.37:g.155500242T>C	ENSP00000437188:p.Cys865Arg	210	0	0		146	46	0.315068	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Missense_Mutation	SNP	ENST00000461783.3	37	CCDS34558.1	.	.	.	.	.	.	.	.	.	.	T	6.692	0.496320	0.12762	.	.	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000528535;ENST00000456144;ENST00000318981;ENST00000367174;ENST00000360366;ENST00000529824;ENST00000456877;ENST00000528391	T;T;T;T;T;T;T;T;T	0.37411	1.2;1.2;1.2;1.2;1.2;1.2;1.2;1.2;1.2	5.18	1.17	0.20885	Raf-like Ras-binding (2);PDZ/DHR/GLGF (1);	0.495104	0.22584	N	0.058171	T	0.09730	0.0239	L	0.44542	1.39	0.09310	N	0.999997	B;B;B;B	0.09022	0.001;0.002;0.002;0.001	B;B;B;B	0.09377	0.001;0.003;0.004;0.001	T	0.27773	-1.0064	10	0.28530	T	0.3	.	5.0741	0.14622	0.2795:0.0759:0.0:0.6446	.	201;865;889;865	E9PKT1;Q8IVF5-2;Q8IVF5-5;Q8IVF5	.;.;.;TIAM2_HUMAN	R	865;1111;865;865;865;241;889;865;177;201	ENSP00000437188:C865R;ENSP00000434901:C865R;ENSP00000407746:C865R;ENSP00000327315:C865R;ENSP00000356142:C241R;ENSP00000353528:C889R;ENSP00000433348:C865R;ENSP00000407183:C177R;ENSP00000435335:C201R	ENSP00000327315:C865R	C	+	1	0	TIAM2	155541934	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.639000	0.24690	0.379000	0.24794	0.533000	0.62120	TGC	.	.	none		0.383	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454		C	155500242	T	C	155500242	3	2	27	1	0	0	0	0	1	0	0	0	15906	1812	63	3	2623	3	TIAM2	6	155500242	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	2736984	155500242	15614825	392	10843											
FAM120B	84498	hgsc.bcm.edu	37	chr6	170627266	170627266	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttgacaaaaaaggtaacaTcatattagctgtgtcagacc	15	11	7	8	0	2	2	2	1	0	1	2	2	2	2	1	1	2	2	1	1	6	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr6:170627266T>C	ENST00000476287.1	+	2	896	c.788T>C	c.(787-789)aTc>aCc	p.I263T	FAM120B_ENST00000252510.9_Intron|FAM120B_ENST00000540480.1_Missense_Mutation_p.I275T|FAM120B_ENST00000537664.1_Missense_Mutation_p.I286T	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	263					cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		AAAGGTAACATCATATTAGCT	0.373																																					p.I263T		Atlas-SNP	.											.	FAM120B	108	.	0			c.T788C						PASS	.						76	82	80					6																	170627266		2203	4300	6503	SO:0001583	missense	84498	exon2			GTAACATCATATT	AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"PPARgamma constitutive coactivator 1", "constitutive coactivator of PPAR-gamma"	612266	"KIAA1838"	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.788T>C	6.37:g.170627266T>C	ENSP00000417970:p.Ile263Thr	55	0	0		39	15	0.384615	NM_032448	B4DL34|Q86V68|Q96JI9	Missense_Mutation	SNP	ENST00000476287.1	37	CCDS5314.1	.	.	.	.	.	.	.	.	.	.	t	4.546	0.101307	0.08731	.	.	ENSG00000112584	ENST00000540480;ENST00000537664;ENST00000476287	T;T;T	0.08896	3.05;3.04;3.05	5.36	1.33	0.21861	.	1.307360	0.04590	N	0.396515	T	0.02610	0.0079	L	0.41236	1.265	0.09310	N	0.999999	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.44967	-0.9293	10	0.28530	T	0.3	-0.9253	9.4172	0.38528	0.0:0.263:0.0:0.737	.	263;263	Q96EK7;F2Z2E1	F120B_HUMAN;.	T	275;286;263	ENSP00000444125:I275T;ENSP00000440125:I286T;ENSP00000417970:I263T	ENSP00000436640:I263T	I	+	2	0	FAM120B	170469191	0.001000	0.12720	0.002000	0.10522	0.470000	0.32858	0.928000	0.28831	0.426000	0.26116	-0.266000	0.10368	ATC	.	.	none		0.373	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448		C	170627266	T	C	170627266	3	2	27	1	0	0	0	0	1	0	0	0	5422	1435	50	3	790	3	FAM120B	6	170627266	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	15127024	170627266	487801	393	10844											
MICALL2	79778	hgsc.bcm.edu	37	chr7	1477844	1477844	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tatctcctccggggagaggtAgtcggggtgcagctgggaac	7	8	17	9	2	1	1	0	0	1	1	4	3	2	2	2	6	3	3	2	6	3	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:1477844A>G	ENST00000297508.7	-	12	2375	c.2200T>C	c.(2200-2202)Tac>Cac	p.Y734H	MICALL2_ENST00000405088.4_Missense_Mutation_p.Y522H|MICALL2_ENST00000471899.1_5'UTR	NM_182924.3	NP_891554.1	Q8IY33	MILK2_HUMAN	MICAL-like 2	734	Forms an intramolecular interaction with the N-terminal CH and LIM zinc-binding domains-containing region keeping the protein in a closed conformation. {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)		GGGGAGAGGTAGTCGGGGTGC	0.706																																					p.Y734H		Atlas-SNP	.											.	MICALL2	63	.	0			c.T2200C						PASS	.						11	13	12					7																	1477844		2179	4274	6453	SO:0001583	missense	79778	exon12			AGAGGTAGTCGGG	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.2200T>C	7.37:g.1477844A>G	ENSP00000297508:p.Tyr734His	132	0	0		129	103	0.79845	NM_182924	D3YTD2|Q7RTP4|Q7Z655|Q8TEQ4|Q9H5F9	Missense_Mutation	SNP	ENST00000297508.7	37	CCDS5324.1	.	.	.	.	.	.	.	.	.	.	A	11.05	1.525674	0.27299	.	.	ENSG00000164877	ENST00000405088;ENST00000297508	T;T	0.72942	2.19;-0.7	3.95	1.41	0.22369	.	0.269934	0.19725	N	0.107484	T	0.77731	0.4174	M	0.70595	2.14	0.09310	N	0.999999	P;D	0.76494	0.481;0.999	B;D	0.75020	0.373;0.985	T	0.65022	-0.6269	10	0.52906	T	0.07	.	4.6281	0.12488	0.6909:0.1929:0.1162:0.0	.	734;522	Q8IY33;D3YTD2	MILK2_HUMAN;.	H	522;734	ENSP00000385928:Y522H;ENSP00000297508:Y734H	ENSP00000297508:Y734H	Y	-	1	0	MICALL2	1444370	0.990000	0.36364	0.011000	0.14972	0.156000	0.22039	2.693000	0.47027	0.116000	0.18110	0.374000	0.22700	TAC	.	.	none		0.706	MICALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239223.2	NM_182924		G	1477844	A	G	1477844	3	3	27	1	0	0	0	0	1	0	0	0	9583	420	15	3	538	3	MICALL2	7	1477844	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10		1477844	157660819	394	10845											
IQCE	23288	hgsc.bcm.edu	37	chr7	2649686	2649686	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tcatttctgcagacccctctCcctcagggccacaggccttg	6	10	8	17	0	4	1	2	0	2	1	5	1	4	1	5	2	1	1	5	2	0	2	rs368687600		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:2649686C>T	ENST00000402050.2	+	22	2162	c.1978C>T	c.(1978-1980)Ccc>Tcc	p.P660S	IQCE_ENST00000438376.2_Missense_Mutation_p.P644S|IQCE_ENST00000325979.7_Missense_Mutation_p.P595S|IQCE_ENST00000404984.1_Missense_Mutation_p.P609S	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	660						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)		AGACCCCTCTCCCTCAGGGCC	0.597																																					p.P660S		Atlas-SNP	.											.	IQCE	66	.	0			c.C1978T						PASS	.	C	SER/PRO,SER/PRO	0,4082		0,0,2041	65	67	66		1930,1978	0.9	0	7		66	2,8352		0,2,4175	no	missense,missense	IQCE	NM_001100390.1,NM_152558.3	74,74	0,2,6216	TT,TC,CC		0.0239,0.0,0.0161	probably-damaging,probably-damaging	644/680,660/696	2649686	2,12434	2041	4177	6218	SO:0001583	missense	23288	exon22			CCCTCTCCCTCAG	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.1978C>T	7.37:g.2649686C>T	ENSP00000385597:p.Pro660Ser	96	0	0		95	73	0.768421	NM_152558	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Missense_Mutation	SNP	ENST00000402050.2	37	CCDS43542.1	.	.	.	.	.	.	.	.	.	.	C	3.946	-0.013165	0.07727	0.0	2.39E-4	ENSG00000106012	ENST00000402050;ENST00000404984;ENST00000438376;ENST00000325979	T;T;T;T	0.11712	2.77;2.75;2.76;2.76	4.9	0.875	0.19130	.	2.223160	0.02320	N	0.072870	T	0.07413	0.0187	N	0.22421	0.69	0.09310	N	1	B;B	0.13145	0.004;0.007	B;B	0.12837	0.004;0.008	T	0.32745	-0.9895	10	0.09590	T	0.72	.	5.0459	0.14483	0.0:0.4788:0.3314:0.1899	.	660;644	Q6IPM2;Q6IPM2-4	IQCE_HUMAN;.	S	660;609;644;595	ENSP00000385597:P660S;ENSP00000385945:P609S;ENSP00000396178:P644S;ENSP00000313772:P595S	ENSP00000313772:P595S	P	+	1	0	IQCE	2616212	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.116000	0.10724	-0.128000	0.11641	0.561000	0.74099	CCC	.	.	weak		0.597	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558		T	2649686	C	T	2649686	3	4	27	1	0	0	0	0	1	0	0	0	7815	855	30	2	2064	2	IQCE	7	2649686	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1171842	2649686	156488977	395	10846											
KIAA0415	9907	hgsc.bcm.edu	37	chr7	4821352	4821352	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacacgcagaacagccggcaGctgagcctggtggcctccgt	8	5	13	15	3	0	2	0	1	0	1	1	2	1	2	4	3	4	3	4	3	1	0	rs11549840	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:4821352G>C	ENST00000348624.4	+	3	427	c.333G>C	c.(331-333)caG>caC	p.Q111H	AP5Z1_ENST00000401897.1_Missense_Mutation_p.Q111H	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	111					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)											ACAGCCGGCAGCTGAGCCTGG	0.662													G|||	63	0.0125799	0.0015	0.0187	5008	,	,		17920	0.0		0.0249	False		,,,				2504	0.0235				p.Q111H		Atlas-SNP	.											.	.	.	.	0			c.G333C						PASS	.	G	HIS/GLN	13,4247		0,13,2117	21	26	24		333	2.1	0.8	7	dbSNP_120	24	205,8303		4,197,4053	yes	missense	KIAA0415	NM_014855.2	24	4,210,6170	CC,CG,GG		2.4095,0.3052,1.7074	possibly-damaging	111/808	4821352	218,12550	2130	4254	6384	SO:0001583	missense	9907	exon3			CCGGCAGCTGAGC	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.333G>C	7.37:g.4821352G>C	ENSP00000297562:p.Gln111His	116	0	0		124	27	0.217742	NM_014855	Q8N3X2|Q96H80	Missense_Mutation	SNP	ENST00000348624.4	37	CCDS47528.1	33	0.01510989010989011	2	0.0040650406504065045	12	0.03314917127071823	0	0.0	19	0.025065963060686015	G	10.63	1.404230	0.25378	0.003052	0.024095	ENSG00000242802	ENST00000348624;ENST00000401897	T;T	0.44482	0.92;0.92	5.08	2.13	0.27403	.	0.485095	0.20242	N	0.096270	T	0.13970	0.0338	M	0.63428	1.95	0.24747	N	0.993007	B	0.23316	0.083	B	0.20184	0.028	T	0.12941	-1.0528	10	0.27785	T	0.31	.	5.8299	0.18574	0.1763:0.2946:0.5291:0.0	rs11549840	111	O43299	K0415_HUMAN	H	111	ENSP00000297562:Q111H;ENSP00000384980:Q111H	ENSP00000297562:Q111H	Q	+	3	2	KIAA0415	4787878	0.601000	0.26907	0.815000	0.32552	0.847000	0.48162	-0.102000	0.10956	0.256000	0.21614	0.655000	0.94253	CAG	G|0.986;C|0.014	0.014	strong		0.662	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1			C	4821352	G	C	4821352	3	2	27	1	0	0	0	0	1	0	0	0	8184	962	34	4	343	4	KIAA0415	7	4821352	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2171666	4821352	154317311	396	10847											
KIAA0415	9907	hgsc.bcm.edu	37	chr7	4830971	4830971	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgcccctggccctgcgcacGgtcagccggctggtggagag	4	6	16	15	3	1	1	1	0	0	1	1	2	1	1	4	5	3	2	4	5	0	0	rs77393809	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:4830971G>T	ENST00000348624.4	+	17	2473	c.2379G>T	c.(2377-2379)acG>acT	p.T793T	AP5Z1_ENST00000490487.1_3'UTR|MIR4656_ENST00000579503.1_RNA	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	793					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)											CCCTGCGCACGGTCAGCCGGC	0.677													G|||	62	0.0123802	0.0015	0.0187	5008	,	,		17357	0.0		0.0239	False		,,,				2504	0.0235				p.T793T		Atlas-SNP	.											.	.	.	.	0			c.G2379T						PASS	.	G		12,4080		0,12,2034	15	20	18		2379	-9.4	0	7	dbSNP_133	18	204,8148		4,196,3976	no	coding-synonymous	KIAA0415	NM_014855.2		4,208,6010	TT,TG,GG		2.4425,0.2933,1.7358		793/808	4830971	216,12228	2046	4176	6222	SO:0001819	synonymous_variant	9907	exon17			GCGCACGGTCAGC	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.2379G>T	7.37:g.4830971G>T		142	0	0		153	39	0.254902	NM_014855	Q8N3X2|Q96H80	Silent	SNP	ENST00000348624.4	37	CCDS47528.1																																																																																			G|0.985;T|0.015	0.015	strong		0.677	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1			T	4830971	G	T	4830971	2	4	27	1	0	0	0	0	0	0	0	1	8184	1103	39	4		4	KIAA0415	7	4830971	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	9619	4830971	154307692	397	10848											
RADIL	55698	hgsc.bcm.edu	37	chr7	4841614	4841614	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggtgcccgtcaaggaccaCgtggtgcataccctagggag	9	6	14	12	2	1	0	1	0	0	0	1	2	1	2	3	4	3	1	3	4	3	2	rs117943885	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:4841614C>T	ENST00000399583.3	-	12	2699	c.2512G>A	c.(2512-2514)Gtg>Atg	p.V838M	RADIL_ENST00000536091.1_3'UTR|RADIL_ENST00000538469.1_Missense_Mutation_p.V598M	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	838					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)		TCAAGGACCACGTGGTGCATA	0.677													C|||	64	0.0127796	0.0015	0.0187	5008	,	,		13575	0.0		0.0249	False		,,,				2504	0.0245				p.V838M		Atlas-SNP	.											.	RADIL	110	.	0			c.G2512A						PASS	.	C	MET/VAL	10,3304		0,10,1647	5	6	6		2512	-3.5	0	7	dbSNP_132	6	139,6811		3,133,3339	yes	missense	RADIL	NM_018059.4	21	3,143,4986	TT,TC,CC		2.0,0.3018,1.4517	benign	838/1076	4841614	149,10115	1657	3475	5132	SO:0001583	missense	55698	exon12			GGACCACGTGGTG	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.2512G>A	7.37:g.4841614C>T	ENSP00000382492:p.Val838Met	89	0	0		119	22	0.184874	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	34	0.015567765567765568	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	19	0.025065963060686015	C	8.995	0.978733	0.18812	0.003018	0.02	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000544486;ENST00000538469	T;T	0.07114	3.29;3.22	4.15	-3.5	0.04710	.	0.941613	0.08946	N	0.870830	T	0.00815	0.0027	N	0.08118	0	0.09310	N	1	B;B	0.16396	0.017;0.004	B;B	0.06405	0.002;0.0	T	0.41645	-0.9497	10	0.51188	T	0.08	-1.412	5.9949	0.19489	0.0:0.1746:0.2538:0.5716	.	838;146	Q96JH8;Q75LH2	RADIL_HUMAN;.	M	838;809;572;598	ENSP00000382492:V838M;ENSP00000442966:V598M	ENSP00000320946:V809M	V	-	1	0	RADIL	4808140	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.693000	0.05121	-1.147000	0.02851	-1.340000	0.01251	GTG	C|0.984;T|0.016	0.016	strong		0.677	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059		T	4841614	C	T	4841614	3	4	27	1	0	0	0	0	1	0	0	0	13012	536	19	1	731	1	RADIL	7	4841614	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	10643	4841614	154297049	398	10849											
RADIL	55698	hgsc.bcm.edu	37	chr7	4843307	4843307	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agatgctgtcgtccaggcagTtggcttccaagtccacctgg	7	10	12	12	1	0	1	0	0	0	1	4	1	3	1	4	3	1	4	4	3	1	2	rs187128776	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:4843307T>C	ENST00000399583.3	-	11	2556	c.2369A>G	c.(2368-2370)aAc>aGc	p.N790S	RADIL_ENST00000536091.1_3'UTR|RADIL_ENST00000538469.1_Missense_Mutation_p.N550S	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	790					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)		p.N790S(1)		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)		GTCCAGGCAGTTGGCTTCCAA	0.647													T|||	63	0.0125799	0.0015	0.0187	5008	,	,		11788	0.0		0.0239	False		,,,				2504	0.0245				p.N790S		Atlas-SNP	.											RADIL,brain,glioma,0,1	RADIL	110	1	1	Substitution - Missense(1)	central_nervous_system(1)	c.A2369G						scavenged	.						19	26	24					7																	4843307		1977	4092	6069	SO:0001583	missense	55698	exon11			AGGCAGTTGGCTT	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.2369A>G	7.37:g.4843307T>C	ENSP00000382492:p.Asn790Ser	111	1	0.00900901		116	26	0.224138	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	33	0.01510989010989011	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	18	0.023746701846965697	T	0.543	-0.852823	0.02630	.	.	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000544486;ENST00000538469	T;T	0.06449	3.37;3.3	4.27	3.12	0.35913	.	0.502188	0.20854	N	0.084468	T	0.00695	0.0023	N	0.08118	0	0.19300	N	0.999978	B;B	0.09022	0.0;0.002	B;B	0.01281	0.0;0.0	T	0.46925	-0.9156	10	0.23302	T	0.38	-15.6944	6.6406	0.22906	0.0:0.187:0.0:0.813	.	790;98	Q96JH8;Q75LH2	RADIL_HUMAN;.	S	790;761;524;550	ENSP00000382492:N790S;ENSP00000442966:N550S	ENSP00000320946:N761S	N	-	2	0	RADIL	4809833	0.936000	0.31750	0.004000	0.12327	0.026000	0.11368	3.515000	0.53429	0.692000	0.31613	0.459000	0.35465	AAC	T|0.985;C|0.015	0.015	strong		0.647	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059		C	4843307	T	C	4843307	3	2	27	1	0	0	0	0	1	0	0	0	13012	1725	60	3	878	3	RADIL	7	4843307	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	1693	4843307	154295356	399	10850											
RADIL	55698	hgsc.bcm.edu	37	chr7	4856904	4856904	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agacgcactgctggaaggcgTacagcaccacctcctccagc	10	5	10	16	2	0	1	0	0	0	1	2	2	2	2	4	2	4	4	4	2	2	1	rs201312293	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:4856904T>C	ENST00000399583.3	-	7	1881	c.1694A>G	c.(1693-1695)tAc>tGc	p.Y565C	RADIL_ENST00000536091.1_Silent_p.V511V|RADIL_ENST00000538469.1_Missense_Mutation_p.Y325C	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	565	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.				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)		CTGGAAGGCGTACAGCACCAC	0.632													T|||	7	0.00139776	0.0	0.0058	5008	,	,		16847	0.0		0.003	False		,,,				2504	0.0				p.Y565C		Atlas-SNP	.											RADIL,right_upper_lobe,carcinoma,0,1	RADIL	110	1	0			c.A1694G						PASS	.	T	CYS/TYR	9,4395	12.9+/-30.5	0,9,2193	67	74	71		1694	4.5	0.9	7		71	48,8550	30.7+/-82.3	0,48,4251	yes	missense	RADIL	NM_018059.4	194	0,57,6444	CC,CT,TT		0.5583,0.2044,0.4384	probably-damaging	565/1076	4856904	57,12945	2202	4299	6501	SO:0001583	missense	55698	exon7			AAGGCGTACAGCA	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.1694A>G	7.37:g.4856904T>C	ENSP00000382492:p.Tyr565Cys	124	0	0		100	65	0.65	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	t	18.25	3.583364	0.65992	0.002044	0.005583	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000544486;ENST00000538469	T;T	0.42900	0.96;0.96	5.7	4.54	0.55810	Dilute (1);	0.000000	0.85682	D	0.000000	T	0.49321	0.1550	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.52660	-0.8546	10	0.46703	T	0.11	-18.0204	10.6794	0.45804	0.0:0.0759:0.0:0.9241	.	565	Q96JH8	RADIL_HUMAN	C	565;536;299;325	ENSP00000382492:Y565C;ENSP00000442966:Y325C	ENSP00000320946:Y536C	Y	-	2	0	RADIL	4823430	1.000000	0.71417	0.867000	0.34043	0.958000	0.62258	2.542000	0.45744	0.987000	0.38709	0.375000	0.23000	TAC	T|0.997;C|0.003	0.003	strong		0.632	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059		C	4856904	T	C	4856904	3	2	27	1	0	0	0	0	1	0	0	0	13012	1638	57	3	1569	3	RADIL	7	4856904	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	13597	4856904	154281759	400	10851											
SLC29A4	222962	hgsc.bcm.edu	37	chr7	5339049	5339049	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtgttcaacctgtcagacttCgtgggcaaggtgggctgcct	6	11	14	10	1	2	1	2	0	0	1	3	1	2	1	2	3	2	3	2	3	2	2	rs142638970	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:5339049C>T	ENST00000396872.3	+	9	1361	c.1200C>T	c.(1198-1200)ttC>ttT	p.F400F	SLC29A4_ENST00000439491.2_3'UTR|SLC29A4_ENST00000406453.3_Silent_p.F386F|SLC29A4_ENST00000297195.4_Silent_p.F400F			Q7RTT9	S29A4_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 4	400					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nucleoside transmembrane transporter activity (GO:0005337)			breast(1)|cervix(2)|kidney(7)|large_intestine(1)|liver(1)|lung(7)|urinary_tract(1)	20		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0903)|OV - Ovarian serous cystadenocarcinoma(56;2.65e-15)	Metformin(DB00331)	TGTCAGACTTCGTGGGCAAGG	0.657													C|||	3	0.000599042	0.0015	0.0	5008	,	,		18164	0.0		0.001	False		,,,				2504	0.0				p.F400F		Atlas-SNP	.											.	SLC29A4	52	.	0			c.C1200T						PASS	.	C	,	4,4402		0,4,2199	49	37	41		1200,1200	0.2	1	7	dbSNP_134	41	53,8543		0,53,4245	no	coding-synonymous,coding-synonymous	SLC29A4	NM_001040661.1,NM_153247.2	,	0,57,6444	TT,TC,CC		0.6166,0.0908,0.4384	,	400/531,400/531	5339049	57,12945	2203	4298	6501	SO:0001819	synonymous_variant	222962	exon9			AGACTTCGTGGGC	AK075422	CCDS5340.1, CCDS75561.1	7p22.2	2013-07-17	2013-07-17		ENSG00000164638	ENSG00000164638		"Solute carriers"	23097	protein-coding gene	gene with protein product		609149	"solute carrier family 29 (nucleoside transporters), member 4"			12838422	Standard	NM_153247		Approved	FLJ34923, ENT4	uc003soc.3	Q7RTT9	OTTHUMG00000023797	ENST00000396872.3:c.1200C>T	7.37:g.5339049C>T		138	0	0		124	99	0.798387	NM_153247	Q6PJ08|Q86WY8|Q8NAR3|Q8NBM2	Silent	SNP	ENST00000396872.3	37	CCDS5340.1																																																																																			C|0.997;T|0.003	0.003	strong		0.657	SLC29A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060118.6	NM_153247		T	5339049	C	T	5339049	2	4	27	1	0	0	0	0	0	0	0	1	14552	883	31	1		1	SLC29A4	7	5339049	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	482145	5339049	153799614	401	10852											
EIF2AK1	27102	hgsc.bcm.edu	37	chr7	6080686	6080686	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggagctccagggtcgactcaAgttcaccagattctcttatg	9	11	10	11	1	3	1	2	0	1	1	6	3	4	2	2	2	1	2	2	2	2	3	rs34909691	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:6080686A>T	ENST00000199389.6	-	9	1102	c.956T>A	c.(955-957)cTt>cAt	p.L319H	EIF2AK1_ENST00000536084.1_Missense_Mutation_p.L195H|EIF2AK1_ENST00000495565.1_5'UTR	NM_001134335.1|NM_014413.3	NP_001127807.1|NP_055228.2	Q9BQI3	E2AK1_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 1	319	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		L -> H (in dbSNP:rs34909691). {ECO:0000269|PubMed:17344846}.		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)		GGTCGACTCAAGTTCACCAGA	0.458													A|||	45	0.00898562	0.0008	0.0173	5008	,	,		16878	0.0		0.0179	False		,,,				2504	0.0143				p.L319H		Atlas-SNP	.											.	EIF2AK1	76	.	0			c.T956A						PASS	.	A	HIS/LEU,HIS/LEU	15,4391		0,15,2188	164	161	162		953,956	-1.8	0	7	dbSNP_126	162	193,8407		2,189,4109	yes	missense,missense	EIF2AK1	NM_001134335.1,NM_014413.3	99,99	2,204,6297	TT,TA,AA		2.2442,0.3404,1.5993	benign,benign	318/630,319/631	6080686	208,12798	2203	4300	6503	SO:0001583	missense	27102	exon9			GACTCAAGTTCAC	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.956T>A	7.37:g.6080686A>T	ENSP00000199389:p.Leu319His	187	0	0		178	137	0.769663	NM_014413	A8K2R2|Q549K6|Q8NBW3|Q9HC02|Q9NYE0|Q9P0V6|Q9P1J5|Q9P2H8|Q9UHG4	Missense_Mutation	SNP	ENST00000199389.6	37	CCDS5345.1	21	0.009615384615384616	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	12	0.0158311345646438	.	7.886	0.731364	0.15507	0.003404	0.022442	ENSG00000086232	ENST00000199389;ENST00000536084	T;T	0.68624	-0.27;-0.34	5.36	-1.8	0.07907	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.737749	0.14214	N	0.333889	T	0.23649	0.0572	N	0.14661	0.345	0.09310	N	1	B;P;B	0.34826	0.003;0.471;0.401	B;B;B	0.33196	0.005;0.159;0.151	T	0.22208	-1.0223	10	0.15499	T	0.54	-0.6525	6.7447	0.23454	0.2399:0.4967:0.0:0.2635	rs34909691;rs61731539	195;318;319	B4DIP4;Q9BQI3-2;Q9BQI3	.;.;E2AK1_HUMAN	H	319;195	ENSP00000199389:L319H;ENSP00000445784:L195H	ENSP00000199389:L319H	L	-	2	0	EIF2AK1	6047212	0.000000	0.05858	0.013000	0.15412	0.024000	0.10985	0.404000	0.20999	0.018000	0.15052	0.533000	0.62120	CTT	A|0.978;T|0.022	0.022	strong		0.458	EIF2AK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207373.2	NM_014413		T	6080686	A	T	6080686	3	4	27	1	0	0	0	0	1	0	0	0	4998	72	3	5	964	5	EIF2AK1	7	6080686	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	741637	6080686	153057977	402	10853											
CYTH3	9265	hgsc.bcm.edu	37	chr7	6227341	6227341	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcatcacctctgcaatttcAtatttcagcctctgtcaaaa	11	14	4	12	0	7	0	5	0	2	0	7	0	7	0	2	0	2	1	2	0	4	3	rs41282682	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:6227341A>G	ENST00000350796.3	-	3	265	c.129T>C	c.(127-129)taT>taC	p.Y43Y		NM_004227.3	NP_004218.1	O43739	CYH3_HUMAN	cytohesin 3	43					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						CTGCAATTTCATATTTCAGCC	0.408													A|||	48	0.00958466	0.0008	0.0173	5008	,	,		20705	0.0		0.0199	False		,,,				2504	0.0153				p.Y43Y		Atlas-SNP	.											.	CYTH3	44	.	0			c.T129C						PASS	.	A		14,4392	22.3+/-47.3	0,14,2189	157	143	148		129	-4.4	0.8	7	dbSNP_127	148	196,8404	85.8+/-148.2	2,192,4106	no	coding-synonymous	CYTH3	NM_004227.3		2,206,6295	GG,GA,AA		2.2791,0.3177,1.6146		43/400	6227341	210,12796	2203	4300	6503	SO:0001819	synonymous_variant	9265	exon3			AATTTCATATTTC	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.129T>C	7.37:g.6227341A>G		89	0	0		80	58	0.725	NM_004227	A4D2N8	Silent	SNP	ENST00000350796.3	37	CCDS5346.1																																																																																			A|0.986;G|0.014	0.014	strong		0.408	CYTH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207396.2	NM_004227		G	6227341	A	G	6227341	2	3	27	1	0	0	0	0	0	0	0	1	4207	224	8	3		3	CYTH3	7	6227341	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	146655	6227341	152911322	403	10854											
COL28A1	340267	hgsc.bcm.edu	37	chr7	7398423	7398423	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tttccaggcttcaaggcttcCaaacatctaggatctagagt	11	12	8	10	0	3	1	1	0	2	1	5	2	5	2	2	3	1	2	2	3	4	5	rs373840985	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:7398423C>T	ENST00000399429.3	-	35	3359	c.3219G>A	c.(3217-3219)ttG>ttA	p.L1073L		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	1073	BPTI/Kunitz inhibitor. {ECO:0000255|PROSITE-ProRule:PRU00031}.				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)		TCAAGGCTTCCAAACATCTAG	0.358													C|||	2	0.000399361	0.0015	0.0	5008	,	,		18071	0.0		0.0	False		,,,				2504	0.0				p.L1073L		Atlas-SNP	.											.	COL28A1	113	.	0			c.G3219A						PASS	.	C		2,3712		0,2,1855	132	116	121		3219	-3.5	0	7		121	0,8186		0,0,4093	no	coding-synonymous	COL28A1	NM_001037763.2		0,2,5948	TT,TC,CC		0.0,0.0539,0.0168		1073/1126	7398423	2,11898	1857	4093	5950	SO:0001819	synonymous_variant	340267	exon35			GGCTTCCAAACAT	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.3219G>A	7.37:g.7398423C>T		201	0	0		166	40	0.240964	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Silent	SNP	ENST00000399429.3	37	CCDS43553.1																																																																																			.	.	weak		0.358	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763		T	7398423	C	T	7398423	2	4	27	1	0	0	0	0	0	0	0	1	3688	593	21	2		2	COL28A1	7	7398423	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1171082	7398423	151740240	404	10855											
COL28A1	340267	hgsc.bcm.edu	37	chr7	7514293	7514293	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagttggtccttcagaacctTtttcaccctgaaagtacaag	11	12	7	11	0	2	2	2	1	0	1	3	2	3	2	3	1	2	2	3	1	4	5	rs199518824		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:7514293T>C	ENST00000399429.3	-	15	1381	c.1241A>G	c.(1240-1242)aAa>aGa	p.K414R		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	414					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)		TTCAGAACCTTTTTCACCCTG	0.393																																					p.K414R		Atlas-SNP	.											.	COL28A1	113	.	0			c.A1241G						PASS	.	T	ARG/LYS	0,3672		0,0,1836	121	117	118		1241	4.7	1	7		118	4,8194		0,4,4095	yes	missense	COL28A1	NM_001037763.2	26	0,4,5931	CC,CT,TT		0.0488,0.0,0.0337	possibly-damaging	414/1126	7514293	4,11866	1836	4099	5935	SO:0001583	missense	340267	exon15			GAACCTTTTTCAC	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.1241A>G	7.37:g.7514293T>C	ENSP00000382356:p.Lys414Arg	81	0	0		81	63	0.777778	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Missense_Mutation	SNP	ENST00000399429.3	37	CCDS43553.1	.	.	.	.	.	.	.	.	.	.	T	12.72	2.022978	0.35701	0.0	4.88E-4	ENSG00000215018	ENST00000399429;ENST00000399419	D	0.90004	-2.6	4.7	4.7	0.59300	.	0.106321	0.35805	U	0.002969	D	0.88100	0.6346	N	0.25332	0.735	0.32928	D	0.516805	D;D	0.64830	0.994;0.993	D;D	0.72982	0.979;0.968	D	0.84976	0.0885	10	0.10902	T	0.67	-7.2148	10.7486	0.46196	0.0:0.0:0.0:1.0	.	414;414	Q2UY09-2;Q2UY09	.;COSA1_HUMAN	R	414	ENSP00000382356:K414R	ENSP00000382347:K414R	K	-	2	0	COL28A1	7480818	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.768000	0.47645	2.108000	0.64289	0.528000	0.53228	AAA	.	.	weak		0.393	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763		C	7514293	T	C	7514293	3	2	27	1	0	0	0	0	1	0	0	0	3688	1841	64	3	2220	3	COL28A1	7	7514293	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	115870	7514293	151624370	405	10856											
SCIN	85477	hgsc.bcm.edu	37	chr7	12617727	12617727	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgaaagcacagctgctgccAtcttcactgttcagatggat	11	11	9	10	0	3	2	2	1	1	1	3	3	3	3	1	1	4	4	1	1	1	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:12617727A>C	ENST00000297029.5	+	2	339	c.238A>C	c.(238-240)Atc>Ctc	p.I80L		NM_001112706.2	NP_001106177.1	Q9Y6U3	ADSV_HUMAN	scinderin	80	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)		AGCTGCTGCCATCTTCACTGT	0.418																																					p.I80L		Atlas-SNP	.											.	SCIN	105	.	0			c.A238C						PASS	.						116	98	104					7																	12617727		692	1591	2283	SO:0001583	missense	85477	exon2			GCTGCCATCTTCA	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.238A>C	7.37:g.12617727A>C	ENSP00000297029:p.Ile80Leu	144	0	0		148	64	0.432432	NM_001112706	A8K2U8|Q8NBZ6|Q8WU97|Q96JC7|Q96PY2	Missense_Mutation	SNP	ENST00000297029.5	37	CCDS47545.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.275863	0.80580	.	.	ENSG00000006747	ENST00000297029;ENST00000417018	T;T	0.51574	0.7;0.7	4.93	3.76	0.43208	Gelsolin domain (1);	0.000000	0.85682	D	0.000000	T	0.59032	0.2164	M	0.67953	2.075	0.80722	D	1	B	0.26708	0.157	P	0.46026	0.501	T	0.61705	-0.7008	10	0.72032	D	0.01	-9.0734	11.05	0.47880	0.8607:0.0:0.0:0.1393	.	80	Q9Y6U3	ADSV_HUMAN	L	80;107	ENSP00000297029:I80L;ENSP00000404380:I107L	ENSP00000297029:I80L	I	+	1	0	SCIN	12584252	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.286000	0.78671	0.884000	0.36064	-0.481000	0.04817	ATC	.	.	none		0.418	SCIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326041.1	NM_033128		C	12617727	A	C	12617727	3	2	27	1	0	0	0	0	1	0	0	0	13920	217	8	5	244	5	SCIN	7	12617727	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	5103434	12617727	146520936	406	10857											
ABCB5	340273	hgsc.bcm.edu	37	chr7	20767981	20767981	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttattggaagctgttatgcaTtcagccatgcctttatatat	10	17	7	7	0	1	0	1	0	0	0	1	1	1	1	2	1	4	3	2	1	6	8	rs117749018	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:20767981T>C	ENST00000404938.2	+	23	3422	c.2770T>C	c.(2770-2772)Ttc>Ctc	p.F924L	ABCB5_ENST00000258738.6_Missense_Mutation_p.F479L	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	924	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						CTGTTATGCATTCAGCCATGC	0.393													T|||	23	0.00459265	0.0	0.0072	5008	,	,		18255	0.0		0.0109	False		,,,				2504	0.0072				p.F924L		Atlas-SNP	.											.	ABCB5	357	.	0			c.T2770C						PASS	.	T	LEU/PHE,LEU/PHE	13,4393	20.2+/-43.8	0,13,2190	150	154	153		2770,1435	2.7	1	7	dbSNP_132	153	103,8497	56.8+/-118.0	0,103,4197	yes	missense,missense	ABCB5	NM_001163941.1,NM_178559.5	22,22	0,116,6387	CC,CT,TT		1.1977,0.2951,0.8919	benign,benign	924/1258,479/813	20767981	116,12890	2203	4300	6503	SO:0001583	missense	340273	exon23			TATGCATTCAGCC	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.2770T>C	7.37:g.20767981T>C	ENSP00000384881:p.Phe924Leu	160	0	0		134	31	0.231343	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	37	CCDS55090.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	T	11.75	1.732023	0.30684	0.002951	0.011977	ENSG00000004846	ENST00000404938;ENST00000258738	D;D	0.90133	-2.62;-2.62	3.91	2.73	0.32206	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.220353	0.30464	N	0.009574	T	0.73345	0.3575	N	0.17474	0.49	0.29103	N	0.881356	B;B;B	0.16802	0.019;0.0;0.004	B;B;B	0.23150	0.044;0.005;0.02	T	0.64141	-0.6477	10	0.25751	T	0.34	.	4.4745	0.11729	0.1917:0.0:0.2168:0.5914	.	924;102;479	A7BKA4;A0ASV4;Q2M3G0	.;.;ABCB5_HUMAN	L	924;479	ENSP00000384881:F924L;ENSP00000258738:F479L	ENSP00000258738:F479L	F	+	1	0	ABCB5	20734506	0.810000	0.29049	0.998000	0.56505	0.990000	0.78478	1.014000	0.29950	0.827000	0.34685	0.533000	0.62120	TTC	T|0.992;C|0.008	0.008	strong		0.393	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559		C	20767981	T	C	20767981	3	2	27	1	0	0	0	0	1	0	0	0	44	1493	52	3	2897	3	ABCB5	7	20767981	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	8150254	20767981	138370682	407	10858											
RAPGEF5	9771	hgsc.bcm.edu	37	chr7	22233635	22233635	+	5'Flank	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctctttaacctgaacagtcGtcacttcatcatcttgcttt	8	16	5	12	1	5	1	3	1	2	0	6	1	5	1	1	0	3	2	1	0	2	5	rs375862364		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:22233635G>A	ENST00000401957.2	-	0	0				RAPGEF5_ENST00000405243.1_Missense_Mutation_p.T338M|RAPGEF5_ENST00000475788.1_5'UTR|RAPGEF5_ENST00000344041.6_Missense_Mutation_p.T185M			Q92565	RPGF5_HUMAN	Rap guanine nucleotide exchange factor (GEF) 5						nervous system development (GO:0007399)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of Ras GTPase activity (GO:0032320)|small GTPase mediated signal transduction (GO:0007264)	nucleus (GO:0005634)	GTP-dependent protein binding (GO:0030742)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(2)|ovary(1)	6						CTGAACAGTCGTCACTTCATC	0.493																																					p.T185M		Atlas-SNP	.											.	RAPGEF5	96	.	0			c.C554T						PASS	.	G	MET/THR	0,4052		0,0,2026	192	196	195		554	2.4	0.1	7		195	2,8352		0,2,4175	no	missense	RAPGEF5	NM_012294.3	81	0,2,6201	AA,AG,GG		0.0239,0.0,0.0161	possibly-damaging	185/731	22233635	2,12404	2026	4177	6203	SO:0001631	upstream_gene_variant	9771	exon10			ACAGTCGTCACTT	D87467	CCDS55093.1	7p15.3	2004-03-01			ENSG00000136237	ENSG00000136237			16862	protein-coding gene	gene with protein product	"M-Ras-regulated GEF"	609527				9039502, 10486569	Standard	NM_012294		Approved	KIAA0277, GFR, MR-GEF	uc003svg.3	Q92565	OTTHUMG00000152525		7.37:g.22233635G>A	Exception_encountered	103	0	0		77	12	0.155844	NM_012294	A4D140|Q8IXU5	Missense_Mutation	SNP	ENST00000401957.2	37		.	.	.	.	.	.	.	.	.	.	G	11.73	1.724513	0.30593	0.0	2.39E-4	ENSG00000136237	ENST00000344041;ENST00000420196;ENST00000405243	D;D;D	0.85339	-1.97;-1.97;-1.97	5.31	2.44	0.29823	.	4.131740	0.00935	N	0.002779	T	0.82204	0.4986	L	0.40543	1.245	0.09310	N	1	D	0.55385	0.971	B	0.42062	0.374	T	0.69146	-0.5222	10	0.72032	D	0.01	.	9.6692	0.40002	0.0745:0.2663:0.6593:0.0	.	185	A8MQ07	.	M	185;66;338	ENSP00000343656:T185M;ENSP00000395729:T66M;ENSP00000384870:T338M	ENSP00000343656:T185M	T	-	2	0	RAPGEF5	22200160	0.005000	0.15991	0.061000	0.19648	0.976000	0.68499	0.648000	0.24828	0.213000	0.20722	0.563000	0.77884	ACG	.	.	weak		0.493	RAPGEF5-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000326590.2	NM_012294		A	22233635	G	A	22233635	1	1	27	0	1	0	0	0	0	0	0	0	13062	1145	40	1		1	RAPGEF5	7	22233635	5'Flank	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1465654	22233635	136905028	408	10859											
HOXA11	3207	hgsc.bcm.edu	37	chr7	27222437	27222437	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agaggagtggatttgctgagTagtactgtaaacggtctctg	10	12	14	5	1	1	2	0	1	1	1	2	4	1	4	0	3	3	4	0	3	4	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:27222437T>C	ENST00000006015.3	-	2	991	c.920A>G	c.(919-921)tAc>tGc	p.Y307C	HOXA11-AS_ENST00000520395.1_RNA|HOXA10_ENST00000396344.4_5'Flank|RP1-170O19.20_ENST00000470747.4_5'Flank|HOXA11-AS_ENST00000522674.1_RNA|HOXA11-AS_ENST00000520360.1_RNA|HOXA11-AS_ENST00000522863.1_RNA	NM_005523.5	NP_005514.1	P31270	HXA11_HUMAN	homeobox A11	307					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						ATTTGCTGAGTAGTACTGTAA	0.443			T	NUP98	CML																																p.Y307C		Atlas-SNP	.		Dom	yes		7	7p15-p14.2	3207	homeo box A11		L	.	HOXA11	29	.	0			c.A920G						PASS	.						70	70	70					7																	27222437		2203	4300	6503	SO:0001583	missense	3207	exon2			GCTGAGTAGTACT		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.920A>G	7.37:g.27222437T>C	ENSP00000006015:p.Tyr307Cys	68	0	0		63	27	0.428571	NM_005523	A4D190	Missense_Mutation	SNP	ENST00000006015.3	37	CCDS5411.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.23|17.23	3.336101|3.336101	0.60963|0.60963	.|.	.|.	ENSG00000005073|ENSG00000005073	ENST00000517402|ENST00000006015	.|D	.|0.90844	.|-2.74	5.69|5.69	5.69|5.69	0.88448|0.88448	.|.	.|0.000000	.|0.64402	.|D	.|0.000001	D|D	0.92303|0.92303	0.7558|0.7558	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	.|D	.|0.76494	.|0.999	.|D	.|0.76071	.|0.987	D|D	0.93496|0.93496	0.6840|0.6840	5|10	.|0.87932	.|D	.|0	.|.	15.9527|15.9527	0.79855|0.79855	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|307	.|P31270	.|HXA11_HUMAN	A|C	277|307	.|ENSP00000006015:Y307C	.|ENSP00000006015:Y307C	T|Y	-|-	1|2	0|0	HOXA11|HOXA11	27188962|27188962	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	5.017000|5.017000	0.64047|0.64047	2.173000|2.173000	0.68751|0.68751	0.533000|0.533000	0.62120|0.62120	ACT|TAC	.	.	none		0.443	HOXA11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358754.1			C	27222437	T	C	27222437	3	2	27	1	0	0	0	0	1	0	0	0	7299	1638	57	3	25	3	HOXA11	7	27222437	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	4988802	27222437	131916226	409	10860											
FAM188B	84182	hgsc.bcm.edu	37	chr7	30818128	30818128	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacaacagaaatgatcttcgAaaggttttgcatcttgaatt	15	13	7	6	1	2	3	0	2	2	1	3	4	2	3	0	1	3	2	0	1	5	5	rs200053449	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:30818128A>G	ENST00000265299.6	+	2	221	c.144A>G	c.(142-144)cgA>cgG	p.R48R	INMT-FAM188B_ENST00000458257.1_3'UTR	NM_032222.2	NP_115598.2	Q4G0A6	F188B_HUMAN	family with sequence similarity 188, member B	48										endometrium(1)|large_intestine(5)|lung(19)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						ATGATCTTCGAAAGGTTTTGC	0.453													A|||	5	0.000998403	0.0	0.0014	5008	,	,		21808	0.0		0.004	False		,,,				2504	0.0				p.R48R		Atlas-SNP	.											FAM188B,colon,carcinoma,+2,4	FAM188B	62	4	0			c.A144G						PASS	.	A		4,3884		0,4,1940	123	120	121		144	-3.1	1	7		121	62,8220		0,62,4079	no	coding-synonymous	FAM188B	NM_032222.2		0,66,6019	GG,GA,AA		0.7486,0.1029,0.5423		48/758	30818128	66,12104	1944	4141	6085	SO:0001819	synonymous_variant	84182	exon2			TCTTCGAAAGGTT	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.144A>G	7.37:g.30818128A>G		224	0	0		205	47	0.229268	NM_032222	Q71AZ7|Q9H6D2	Silent	SNP	ENST00000265299.6	37	CCDS43565.1																																																																																			A|0.998;G|0.002	0.002	strong		0.453	FAM188B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327962.1	NM_032222		G	30818128	A	G	30818128	2	3	27	1	0	0	0	0	0	0	0	1	5520	233	9	3		3	FAM188B	7	30818128	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	3595691	30818128	128320535	410	10861											
FAM188B	84182	hgsc.bcm.edu	37	chr7	30818142	30818142	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttcgaaaggttttgcatcTtgaatttctctataaggaga	11	16	8	6	1	3	2	0	1	3	1	5	4	3	2	0	2	1	2	0	2	4	7	rs201946407	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:30818142T>G	ENST00000265299.6	+	2	235	c.158T>G	c.(157-159)cTt>cGt	p.L53R	INMT-FAM188B_ENST00000458257.1_3'UTR	NM_032222.2	NP_115598.2	Q4G0A6	F188B_HUMAN	family with sequence similarity 188, member B	53										endometrium(1)|large_intestine(5)|lung(19)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GTTTTGCATCTTGAATTTCTC	0.478													T|||	5	0.000998403	0.0	0.0014	5008	,	,		21672	0.0		0.004	False		,,,				2504	0.0				p.L53R		Atlas-SNP	.											.	FAM188B	62	.	0			c.T158G						PASS	.	T	ARG/LEU	5,3861		0,5,1928	125	120	122		158	4.4	0.9	7		122	62,8212		0,62,4075	yes	missense	FAM188B	NM_032222.2	102	0,67,6003	GG,GT,TT		0.7493,0.1293,0.5519	probably-damaging	53/758	30818142	67,12073	1933	4137	6070	SO:0001583	missense	84182	exon2			TGCATCTTGAATT	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.158T>G	7.37:g.30818142T>G	ENSP00000265299:p.Leu53Arg	226	0	0		209	47	0.22488	NM_032222	Q71AZ7|Q9H6D2	Missense_Mutation	SNP	ENST00000265299.6	37	CCDS43565.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	16.55	3.153666	0.57259	0.001293	0.007493	ENSG00000106125	ENST00000265299	T	0.24723	1.84	4.43	4.43	0.53597	.	0.070363	0.56097	D	0.000037	T	0.41236	0.1150	M	0.77103	2.36	0.58432	D	0.999995	D	0.89917	1.0	D	0.87578	0.998	T	0.49707	-0.8911	10	0.87932	D	0	1.9565	10.2353	0.43280	0.0:0.0:0.0:1.0	.	53	Q4G0A6	F188B_HUMAN	R	53	ENSP00000265299:L53R	ENSP00000265299:L53R	L	+	2	0	FAM188B	30784667	0.997000	0.39634	0.891000	0.34965	0.613000	0.37349	4.603000	0.61105	1.998000	0.58463	0.459000	0.35465	CTT	T|0.998;G|0.002	0.002	strong		0.478	FAM188B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327962.1	NM_032222		G	30818142	T	G	30818142	3	3	27	1	0	0	0	0	1	0	0	0	5520	1609	56	5	164	5	FAM188B	7	30818142	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	14	30818142	128320521	411	10862											
NEUROD6	63974	hgsc.bcm.edu	37	chr7	31378795	31378795	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctttctggcttcttaatttGcttctggtcctcgcattctc	3	19	7	12	1	4	0	0	0	4	0	7	0	5	0	1	2	1	4	1	2	1	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:31378795G>A	ENST00000297142.3	-	2	410	c.88C>T	c.(88-90)Caa>Taa	p.Q30*		NM_022728.2	NP_073565.2	Q96NK8	NDF6_HUMAN	neuronal differentiation 6	30					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						TTCTTAATTTGCTTCTGGTCC	0.433																																					p.Q30X		Atlas-SNP	.											.	NEUROD6	84	.	0			c.C88T						PASS	.						136	148	144					7																	31378795		2203	4300	6503	SO:0001587	stop_gained	63974	exon2			TAATTTGCTTCTG	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.88C>T	7.37:g.31378795G>A	ENSP00000297142:p.Gln30*	82	0	0		61	12	0.196721	NM_022728	Q548T9|Q9H3H6	Nonsense_Mutation	SNP	ENST00000297142.3	37	CCDS5434.1	.	.	.	.	.	.	.	.	.	.	G	37	6.007479	0.97195	.	.	ENSG00000164600	ENST00000297142	.	.	.	5.28	5.28	0.74379	.	0.240470	0.36101	N	0.002799	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	-2.4487	18.9485	0.92632	0.0:0.0:1.0:0.0	.	.	.	.	X	30	.	ENSP00000297142:Q30X	Q	-	1	0	NEUROD6	31345320	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.750000	0.62162	2.485000	0.83878	0.650000	0.86243	CAA	.	.	none		0.433	NEUROD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215050.1	NM_022728		A	31378795	G	A	31378795	4	1	27	1	0	0	0	0	0	1	0	0	10360	1328	46	2	929	2	NEUROD6	7	31378795	Nonsense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	560653	31378795	127759868	412	10863											
GLI3	2737	hgsc.bcm.edu	37	chr7	42007201	42007201	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgtagaactcaccatttccTatgagaggagagaccgcagg	13	8	11	9	1	1	3	1	1	0	3	2	6	2	4	3	2	1	2	3	2	3	3	rs62622373	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:42007201T>C	ENST00000395925.3	-	14	2508	c.2424A>G	c.(2422-2424)atA>atG	p.I808M	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	808			I -> M (in GCPS; dbSNP:rs62622373). {ECO:0000269|PubMed:10441342}.		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						CACCATTTCCTATGAGAGGAG	0.443									Pallister-Hall syndrome;Greig Cephalopolysyndactyly				T|||	3	0.000599042	0.0	0.0014	5008	,	,		18932	0.0		0.002	False		,,,				2504	0.0				p.I808M		Atlas-SNP	.											.	GLI3	312	.	0			c.A2424G	GRCh37	CM990707	GLI3	M	rs62622373	PASS	.	T	MET/ILE	3,4403	6.2+/-15.9	0,3,2200	197	214	208		2424	4.2	1	7	dbSNP_129	208	26,8574	16.6+/-54.9	0,26,4274	yes	missense	GLI3	NM_000168.5	10	0,29,6474	CC,CT,TT		0.3023,0.0681,0.223	possibly-damaging	808/1581	42007201	29,12977	2203	4300	6503	SO:0001583	missense	2737	exon14	Familial Cancer Database	;	ATTTCCTATGAGA		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.2424A>G	7.37:g.42007201T>C	ENSP00000379258:p.Ile808Met	226	1	0.00442478		182	132	0.725275	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Missense_Mutation	SNP	ENST00000395925.3	37	CCDS5465.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	15.74	2.921346	0.52653	6.81E-4	0.003023	ENSG00000106571	ENST00000395925	D	0.92545	-3.06	5.31	4.15	0.48705	.	0.203242	0.52532	D	0.000066	D	0.90428	0.7003	L	0.57536	1.79	0.80722	D	1	D	0.54397	0.966	P	0.48873	0.593	D	0.87818	0.2636	10	0.46703	T	0.11	.	6.3136	0.21178	0.1403:0.0746:0.0:0.7851	rs62622373	808	P10071	GLI3_HUMAN	M	808	ENSP00000379258:I808M	ENSP00000379258:I808M	I	-	3	3	GLI3	41973726	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.344000	0.44010	0.861000	0.35504	0.533000	0.62120	ATA	T|0.999;C|0.001	0.001	strong		0.443	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168		C	42007201	T	C	42007201	3	2	27	1	0	0	0	0	1	0	0	0	6447	1512	53	3	2326	3	GLI3	7	42007201	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	10628406	42007201	117131462	413	10864											
H2AFV	94239	hgsc.bcm.edu	37	chr7	44875203	44875203	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tgcaagctgcaagtgacgcgGagtgatacgctttactttga	10	11	12	8	3	0	3	0	3	0	0	0	4	0	4	0	1	5	4	0	1	4	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:44875203G>C	ENST00000308153.4	-	4	341	c.250C>G	c.(250-252)Ccg>Gcg	p.P84A	H2AFV_ENST00000350771.3_Missense_Mutation_p.P58A|H2AFV_ENST00000349299.3_Missense_Mutation_p.P46A|H2AFV_ENST00000437072.1_Missense_Mutation_p.P46A|H2AFV_ENST00000222690.6_Missense_Mutation_p.P84A|H2AFV_ENST00000446531.1_Missense_Mutation_p.P84A|H2AFV_ENST00000381124.5_Intron|H2AFV_ENST00000521529.1_Intron	NM_012412.4	NP_036544.1	Q71UI9	H2AV_HUMAN	H2A histone family, member V	84						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						AAGTGACGCGGAGTGATACGC	0.453																																					p.P84A		Atlas-SNP	.											.	H2AFV	14	.	0			c.C250G						PASS	.						123	99	107					7																	44875203		2203	4300	6503	SO:0001583	missense	94239	exon4			GACGCGGAGTGAT	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.250C>G	7.37:g.44875203G>C	ENSP00000308405:p.Pro84Ala	87	0	0		56	15	0.267857	NM_012412	A6NFA8|A6NKY0|A6NN01|A8MQC5|Q59GV8|Q6PK98	Missense_Mutation	SNP	ENST00000308153.4	37	CCDS5496.1	.	.	.	.	.	.	.	.	.	.	G	19.56	3.850542	0.71719	.	.	ENSG00000105968	ENST00000222690;ENST00000437072;ENST00000349299;ENST00000308153;ENST00000350771;ENST00000446531	T;T;T;T;T;T	0.70749	-0.51;-0.51;-0.51;-0.51;-0.51;-0.51	5.68	5.68	0.88126	Histone-fold (2);Histone core (1);Histone H2A (2);	.	.	.	.	D	0.84415	0.5467	H	0.94698	3.57	0.80722	D	1	B;P;B;B	0.47302	0.118;0.893;0.083;0.235	B;P;B;B	0.49387	0.247;0.609;0.014;0.122	D	0.88628	0.3167	9	0.87932	D	0	-12.7012	17.2793	0.87124	0.0:0.0:1.0:0.0	.	58;46;84;84	A6NKY0;A6NFA8;Q71UI9;A6NN01	.;.;H2AV_HUMAN;.	A	84;46;46;84;58;84	ENSP00000222690:P84A;ENSP00000397115:P46A;ENSP00000342714:P46A;ENSP00000308405:P84A;ENSP00000340708:P58A;ENSP00000406901:P84A	ENSP00000222690:P84A	P	-	1	0	H2AFV	44841728	1.000000	0.71417	0.671000	0.29857	0.989000	0.77384	9.179000	0.94861	2.698000	0.92095	0.585000	0.79938	CCG	.	.	none		0.453	H2AFV-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251305.1	NM_012412		C	44875203	G	C	44875203	3	2	27	1	0	0	0	0	1	0	0	0	6936	1174	41	4	168	4	H2AFV	7	44875203	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2868002	44875203	114263460	414	10865											
FIGNL1	63979	hgsc.bcm.edu	37	chr7	50513721	50513721	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtaaagatgtctggcctcAacatgggccacacaactatt	13	9	8	11	0	2	1	1	0	1	1	2	1	2	1	2	2	2	1	2	2	5	3	rs146680091	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:50513721A>C	ENST00000419119.1	-	2	2818	c.1265T>G	c.(1264-1266)tTg>tGg	p.L422W	FIGNL1_ENST00000356889.4_Missense_Mutation_p.L422W|FIGNL1_ENST00000433017.1_Missense_Mutation_p.L422W|FIGNL1_ENST00000395556.2_Missense_Mutation_p.L422W			Q6PIW4	FIGL1_HUMAN	fidgetin-like 1	422					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)				GTCTGGCCTCAACATGGGCCA	0.433													A|||	4	0.000798722	0.0	0.0014	5008	,	,		21003	0.0		0.003	False		,,,				2504	0.0				p.L422W		Atlas-SNP	.											.	FIGNL1	73	.	0			c.T1265G						PASS	.	A	TRP/LEU,TRP/LEU	3,4403	6.2+/-15.9	0,3,2200	82	89	86		1265,1265	6	1	7	dbSNP_134	86	33,8567	19.8+/-62.0	0,33,4267	yes	missense,missense	FIGNL1	NM_001042762.1,NM_022116.3	61,61	0,36,6467	CC,CA,AA		0.3837,0.0681,0.2768	probably-damaging,probably-damaging	422/675,422/675	50513721	36,12970	2203	4300	6503	SO:0001583	missense	63979	exon4			GGCCTCAACATGG	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.1265T>G	7.37:g.50513721A>C	ENSP00000410811:p.Leu422Trp	154	0	0		110	75	0.681818	NM_001042762	D3DVM6|Q86V18|Q8ND59|Q9H8P1|Q9H917	Missense_Mutation	SNP	ENST00000419119.1	37	CCDS5510.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	22.2	4.262784	0.80358	6.81E-4	0.003837	ENSG00000132436	ENST00000356889;ENST00000395556;ENST00000433017;ENST00000419119	D;D;D;D	0.95238	-3.65;-3.65;-3.65;-3.65	5.99	5.99	0.97316	.	0.227384	0.36740	N	0.002426	D	0.95652	0.8586	L	0.47190	1.495	0.80722	D	1	D	0.71674	0.998	D	0.65874	0.939	D	0.95189	0.8306	10	0.41790	T	0.15	-3.4226	15.6754	0.77316	1.0:0.0:0.0:0.0	.	422	Q6PIW4	FIGL1_HUMAN	W	422	ENSP00000349356:L422W;ENSP00000378924:L422W;ENSP00000399997:L422W;ENSP00000410811:L422W	ENSP00000349356:L422W	L	-	2	0	FIGNL1	50481215	1.000000	0.71417	0.994000	0.49952	0.995000	0.86356	9.339000	0.96797	2.291000	0.77112	0.533000	0.62120	TTG	A|0.997;C|0.003	0.003	strong		0.433	FIGNL1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342579.1	NM_001042762		C	50513721	A	C	50513721	3	2	27	1	0	0	0	0	1	0	0	0	5900	131	5	5	763	5	FIGNL1	7	50513721	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	5638518	50513721	108624942	415	10866											
EGFR	1956	hgsc.bcm.edu	37	chr7	55238087	55238087	+	Intron	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aatgatggcagcgtgtcccaCcagagcgggagcccagctgc	9	5	14	13	2	0	2	0	1	0	1	1	3	1	3	3	2	5	2	3	2	1	0	rs10258429	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:55238087C>T	ENST00000275493.2	+	16	2057				EGFR_ENST00000454757.2_Intron|EGFR_ENST00000442591.1_Intron|EGFR_ENST00000455089.1_Intron|EGFR_ENST00000344576.2_Silent_p.H656H	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor						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)	GCGTGTCCCACCAGAGCGGGA	0.512		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			C|||	563	0.11242	0.2398	0.049	5008	,	,		20745	0.0496		0.0736	False		,,,				2504	0.09				p.H656H		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.C1968T						PASS	.	C	,	922,3484	352.1+/-311.5	101,720,1382	108	89	95		,1968	2.4	0	7	dbSNP_119	95	606,7994	158.6+/-212.1	23,560,3717	no	intron,coding-synonymous	EGFR	NM_005228.3,NM_201284.1	,	124,1280,5099	TT,TC,CC		7.0465,20.926,11.7484	,	,656/706	55238087	1528,11478	2203	4300	6503	SO:0001627	intron_variant	1956	exon16	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	GTCCCACCAGAGC		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.1881-781C>T	7.37:g.55238087C>T		152	0	0		145	66	0.455172	NM_201284	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																			C|0.889;T|0.111	0.111	strong		0.512	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		T	55238087	C	T	55238087	1	4	27	0	1	0	0	0	0	0	0	0	4969	506	18	2		2	EGFR	7	55238087	Intron	SNP	C	TCGA-G8-6909-01A-11D-2210-10	4724366	55238087	103900576	416	10867											
PSPH	5723	hgsc.bcm.edu	37	chr7	56084977	56084977	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atacattggttgctgggataTtgagctttgaagcaacatgc	11	13	11	6	0	0	2	0	2	0	0	0	3	0	3	0	2	6	4	0	2	4	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:56084977T>C	ENST00000395471.3	-	6	1176	c.371A>G	c.(370-372)aAt>aGt	p.N124S	PSPH_ENST00000459834.1_Intron|PSPH_ENST00000275605.3_Missense_Mutation_p.N124S			P78330	SERB_HUMAN	phosphoserine phosphatase	124					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)			TGCTGGGATATTGAGCTTTGA	0.413																																					p.N124S		Atlas-SNP	.											.	PSPH	23	.	0			c.A371G						PASS	.						95	79	84					7																	56084977		2203	4300	6503	SO:0001583	missense	5723	exon6			GGGATATTGAGCT	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.371A>G	7.37:g.56084977T>C	ENSP00000378854:p.Asn124Ser	548	1	0.00182482		508	130	0.255906	NM_004577	B2RCR5|Q7Z3S5	Missense_Mutation	SNP	ENST00000395471.3	37	CCDS5522.1	.	.	.	.	.	.	.	.	.	.	T	12.28	1.891711	0.33442	.	.	ENSG00000146733	ENST00000275605;ENST00000395471;ENST00000421626	D;D;D	0.84442	-1.85;-1.85;-1.85	4.85	2.45	0.29901	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (2);	0.459751	0.25414	N	0.030855	T	0.74928	0.3781	L	0.33668	1.02	0.23700	N	0.997076	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.64106	-0.6485	10	0.46703	T	0.11	-8.4835	7.6611	0.28404	0.0:0.1848:0.0:0.8152	.	124;124	Q53EY1;P78330	.;SERB_HUMAN	S	124	ENSP00000275605:N124S;ENSP00000378854:N124S;ENSP00000398653:N124S	ENSP00000275605:N124S	N	-	2	0	PSPH	56052471	0.897000	0.30589	0.689000	0.30133	0.972000	0.66771	1.222000	0.32515	0.742000	0.32697	0.472000	0.43445	AAT	.	.	none		0.413	PSPH-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343304.1	NM_004577		C	56084977	T	C	56084977	3	2	27	1	0	0	0	0	1	0	0	0	12729	1493	52	3	318	3	PSPH	7	56084977	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	846890	56084977	103053686	417	10868											
TRIM50	135892	hgsc.bcm.edu	37	chr7	72732848	72732848	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacttgtggtggtcctcattGccgaactgttccagcacaca	9	11	9	12	1	1	0	1	0	0	0	3	1	3	0	3	2	4	2	3	2	2	3	rs201525569	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:72732848G>T	ENST00000333149.2	-	4	899	c.699C>A	c.(697-699)ggC>ggA	p.G233G	TRIM50_ENST00000453152.1_Silent_p.G233G	NM_178125.2	NP_835226.2	Q86XT4	TRI50_HUMAN	tripartite motif containing 50	233						cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)|skin(2)	20						GGTCCTCATTGCCGAACTGTT	0.657													G|||	5	0.000998403	0.0008	0.0043	5008	,	,		17310	0.0		0.001	False		,,,				2504	0.0				p.G233G		Atlas-SNP	.											.	TRIM50	78	.	0			c.C699A						PASS	.						153	138	143					7																	72732848		2203	4300	6503	SO:0001819	synonymous_variant	135892	exon4			CTCATTGCCGAAC	AY081948	CCDS34654.1	7q11.23	2013-01-09	2011-01-25	2006-03-31	ENSG00000146755	ENSG00000146755		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19017	protein-coding gene	gene with protein product		612548	"tripartite motif-containing 50A", "tripartite motif-containing 50"	TRIM50A			Standard	NM_001281450		Approved	FLJ32804	uc003txy.1	Q86XT4	OTTHUMG00000156805	ENST00000333149.2:c.699C>A	7.37:g.72732848G>T		463	0	0		457	32	0.0700219	NM_178125	Q86XT3	Silent	SNP	ENST00000333149.2	37	CCDS34654.1																																																																																			G|0.999;T|0.001	0.001	weak		0.657	TRIM50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345925.1	NM_178125		T	72732848	G	T	72732848	2	4	27	1	0	0	0	0	0	0	0	1	16541	1306	46	4		4	TRIM50	7	72732848	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	16647871	72732848	86405815	418	10869											
LIMK1	3984	hgsc.bcm.edu	37	chr7	73520264	73520264	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catccacgtcggagaccggaTcttggaaatcaatggcacgc	11	7	11	12	4	2	1	1	0	1	1	4	4	3	3	2	4	0	1	2	4	2	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:73520264T>C	ENST00000336180.2	+	6	719	c.668T>C	c.(667-669)aTc>aCc	p.I223T	LIMK1_ENST00000418310.1_Missense_Mutation_p.I253T|LIMK1_ENST00000538333.3_Missense_Mutation_p.I189T	NM_002314.3	NP_002305.1	P53667	LIMK1_HUMAN	LIM domain kinase 1	223	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)	GGAGACCGGATCTTGGAAATC	0.607																																					p.I223T		Atlas-SNP	.											.	LIMK1	55	.	0			c.T668C						PASS	.						104	89	94					7																	73520264		2203	4300	6503	SO:0001583	missense	3984	exon6			ACCGGATCTTGGA	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.668T>C	7.37:g.73520264T>C	ENSP00000336740:p.Ile223Thr	81	0	0		78	16	0.205128	NM_002314	B7Z6I8|D3DXF4|D3DXF5|O15283|Q15820|Q15821|Q75MU3|Q9Y5Q1	Missense_Mutation	SNP	ENST00000336180.2	37	CCDS5563.1	.	.	.	.	.	.	.	.	.	.	T	23.0	4.363859	0.82353	.	.	ENSG00000106683	ENST00000418310;ENST00000419043;ENST00000336180;ENST00000423685;ENST00000538333	T;T;T;T	0.56941	0.43;0.43;0.43;0.43	4.97	4.97	0.65823	PDZ/DHR/GLGF (4);	0.051007	0.85682	D	0.000000	T	0.71685	0.3369	M	0.81341	2.54	0.80722	D	1	P;D;D	0.63046	0.852;0.992;0.992	B;D;D	0.68483	0.433;0.958;0.958	T	0.76356	-0.2989	10	0.87932	D	0	-30.7731	12.6805	0.56918	0.0:0.0:0.0:1.0	.	118;189;223	Q59FA3;B7Z6I8;P53667	.;.;LIMK1_HUMAN	T	253;223;223;189;189	ENSP00000409717:I253T;ENSP00000336740:I223T;ENSP00000396480:I189T;ENSP00000444452:I189T	ENSP00000336740:I223T	I	+	2	0	LIMK1	73158200	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.676000	0.84012	1.898000	0.54952	0.524000	0.50904	ATC	.	.	none		0.607	LIMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252335.2	NM_002314		C	73520264	T	C	73520264	3	2	27	1	0	0	0	0	1	0	0	0	8810	1435	50	3	690	3	LIMK1	7	73520264	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	787416	73520264	85618399	419	10870											
POM121C	100101267	hgsc.bcm.edu	37	chr7	75050958	75050958	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgaaagctccggtggtggcGctggagcctggggtggccac	5	7	18	11	2	0	1	0	1	0	0	1	2	1	2	3	7	2	2	3	7	1	0	rs587702156		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:75050958G>A	ENST00000257665.5	-	11	3302	c.3303C>T	c.(3301-3303)agC>agT	p.S1101S	POM121C_ENST00000453279.2_Silent_p.S859S|POM121C_ENST00000473168.1_5'Flank			A8CG34	P121C_HUMAN	POM121 transmembrane nucleoporin C	1101	Pore side. {ECO:0000255}.				mRNA transport (GO:0051028)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|nuclear pore (GO:0005643)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|urinary_tract(1)	14						CGGTGGTGGCGCTGGAGCCTG	0.637													.|||	1	0.000199681	0.0	0.0	5008	,	,		17160	0.0		0.001	False		,,,				2504	0.0				p.S859S		Atlas-SNP	.											.	POM121C	46	.	0			c.C2577T						PASS	.						7	10	9					7																	75050958		2158	4253	6411	SO:0001819	synonymous_variant	100101267	exon13			GGTGGCGCTGGAG		CCDS47617.1	7q11.23	2012-03-13	2012-03-13		ENSG00000135213	ENSG00000272391			34005	protein-coding gene	gene with protein product		615754	"POM121 membrane glycoprotein C"			17900573	Standard	NM_001099415		Approved		uc003udk.4	A8CG34	OTTHUMG00000156238	ENST00000257665.5:c.3303C>T	7.37:g.75050958G>A		397	1	0.00251889		409	125	0.305623	NM_001099415	O75115|Q9Y2N3|Q9Y4S7	Silent	SNP	ENST00000257665.5	37																																																																																				.	.	none		0.637	POM121C-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000343919.2	NM_001099415		A	75050958	G	A	75050958	2	1	27	1	0	0	0	0	0	0	0	1	12249	1078	38	1		1	POM121C	7	75050958	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1530694	75050958	84087705	420	10871											
PTPN12	5782	hgsc.bcm.edu	37	chr7	77256150	77256150	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tactgtgtggcaggacaatgAtagataccatccaaagccag	14	8	10	9	0	0	2	0	1	0	1	1	3	1	3	3	2	3	1	3	2	5	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:77256150A>G	ENST00000248594.6	+	13	1426	c.1154A>G	c.(1153-1155)gAt>gGt	p.D385G	PTPN12_ENST00000415482.2_Missense_Mutation_p.D266G|PTPN12_ENST00000435495.2_Missense_Mutation_p.D255G	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12	385	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						CAGGACAATGATAGATACCAT	0.458																																					p.D385G		Atlas-SNP	.											.	PTPN12	83	.	0			c.A1154G						PASS	.						94	83	87					7																	77256150		2203	4300	6503	SO:0001583	missense	5782	exon13			ACAATGATAGATA		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.1154A>G	7.37:g.77256150A>G	ENSP00000248594:p.Asp385Gly	189	0	0		178	37	0.207865	NM_002835	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	Missense_Mutation	SNP	ENST00000248594.6	37	CCDS5592.1	.	.	.	.	.	.	.	.	.	.	A	20.3	3.974843	0.74360	.	.	ENSG00000127947	ENST00000248594;ENST00000415482;ENST00000543073;ENST00000435495	T;T;T	0.51574	0.7;0.7;0.7	6.17	5.02	0.67125	.	0.043790	0.85682	N	0.000000	T	0.64627	0.2615	M	0.72894	2.215	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	T	0.62144	-0.6916	10	0.24483	T	0.36	.	12.092	0.53733	0.9337:0.0:0.0663:0.0	.	385	Q05209	PTN12_HUMAN	G	385;266;266;255	ENSP00000248594:D385G;ENSP00000392429:D266G;ENSP00000397991:D255G	ENSP00000248594:D385G	D	+	2	0	PTPN12	77094086	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.871000	0.75531	1.160000	0.42584	0.533000	0.62120	GAT	.	.	none		0.458	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253183.3			G	77256150	A	G	77256150	3	3	27	1	0	0	0	0	1	0	0	0	12794	333	12	3	1204	3	PTPN12	7	77256150	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	2205192	77256150	81882513	421	10872											
PHTF2	57157	hgsc.bcm.edu	37	chr7	77567051	77567051	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttgccctggctccatagtTcccacccaggattagaaaaa	12	10	7	12	0	0	1	0	0	0	1	2	2	2	2	4	2	1	2	4	2	4	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:77567051T>C	ENST00000248550.7	+	12	1439	c.1363T>C	c.(1363-1365)Tcc>Ccc	p.S455P	PHTF2_ENST00000422959.2_Missense_Mutation_p.S421P|PHTF2_ENST00000454592.1_3'UTR|PHTF2_ENST00000424760.1_Missense_Mutation_p.S417P|PHTF2_ENST00000307305.8_Missense_Mutation_p.S417P|PHTF2_ENST00000416283.2_Missense_Mutation_p.S421P|PHTF2_ENST00000275575.7_Missense_Mutation_p.S417P			Q8N3S3	PHTF2_HUMAN	putative homeodomain transcription factor 2	455					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						GCTCCATAGTTCCCACCCAGG	0.289																																					p.S421P		Atlas-SNP	.											.	PHTF2	104	.	0			c.T1261C						PASS	.						53	47	49					7																	77567051		1795	4059	5854	SO:0001583	missense	57157	exon11			CATAGTTCCCACC	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.1363T>C	7.37:g.77567051T>C	ENSP00000248550:p.Ser455Pro	94	0	0		83	5	0.060241	NM_001127357	A0JP04|A0JP05|A4D1C2|E9PEE3|G5E9H7|Q6NW35|Q8TBW4|Q9H099	Missense_Mutation	SNP	ENST00000248550.7	37		.	.	.	.	.	.	.	.	.	.	T	15.62	2.887106	0.52014	.	.	ENSG00000006576	ENST00000427986;ENST00000422959;ENST00000307305;ENST00000424760;ENST00000275575;ENST00000416283;ENST00000248550	.	.	.	5.19	2.81	0.32909	.	0.292942	0.33553	N	0.004795	T	0.38241	0.1033	L	0.38175	1.15	0.39118	D	0.961615	P;P;B;P;P;P	0.50156	0.731;0.918;0.437;0.736;0.49;0.932	B;P;B;B;B;P	0.48571	0.347;0.556;0.244;0.232;0.315;0.582	T	0.18967	-1.0320	9	0.27082	T	0.32	-0.7834	4.84	0.13485	0.1369:0.1486:0.0:0.7145	.	417;280;421;455;417;417	Q8N3S3-4;Q8N5I6;Q8N3S3-2;Q8N3S3;Q8N3S3-3;B3KQZ2	.;.;.;PHTF2_HUMAN;.;.	P	421;421;417;417;417;421;455	.	ENSP00000248550:S455P	S	+	1	0	PHTF2	77404987	1.000000	0.71417	0.979000	0.43373	0.994000	0.84299	1.931000	0.40134	0.391000	0.25143	0.482000	0.46254	TCC	.	.	none		0.289	PHTF2-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000340638.2	NM_020432		C	77567051	T	C	77567051	3	2	27	1	0	0	0	0	1	0	0	0	11872	1783	62	3	1357	3	PHTF2	7	77567051	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	310901	77567051	81571612	422	10873											
GNAT3	346562	hgsc.bcm.edu	37	chr7	80117993	80117993	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaccattcttatggatgatcCtataatttaaacatgaaaag	17	13	5	6	0	1	2	0	2	1	0	2	3	2	3	2	1	2	0	2	1	8	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:80117993C>A	ENST00000398291.3	-	3	255		c.e3-1		CD36_ENST00000435819.1_Intron	NM_001102386.1	NP_001095856.1	A8MTJ3	GNAT3_HUMAN	guanine nucleotide binding protein, alpha transducing 3						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						ATGGATGATCCTATAATTTAA	0.318																																					.		Atlas-SNP	.											.	GNAT3	65	.	0			c.162-1G>T						PASS	.						89	75	80					7																	80117993		1830	4083	5913	SO:0001630	splice_region_variant	346562	exon4			ATGATCCTATAAT		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.162-1G>T	7.37:g.80117993C>A		76	0	0		61	13	0.213115	NM_001102386	A4D1B2|A4D1B3|B9EJG5	Splice_Site	SNP	ENST00000398291.3	37	CCDS47625.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.390611	0.82902	.	.	ENSG00000214415	ENST00000398291	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.7634	0.88470	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GNAT3	79955929	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	7.127000	0.77210	2.720000	0.93068	0.650000	0.86243	.	.	.	none		0.318	GNAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339909.3	XM_294370	Intron	A	80117993	C	A	80117993	5	1	27	1	0	0	0	0	0	0	1	0	6521	695	24	4	925	4	GNAT3	7	80117993	Splice_Site	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2550942	80117993	79020670	423	10874											
SEMA3A	10371	hgsc.bcm.edu	37	chr7	83764113	83764113	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tattagaatactgataccttTtgaaaatccttgatattaac	15	16	4	6	0	0	4	0	3	0	1	1	4	1	4	2	0	3	0	2	0	9	9	rs74349534	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:83764113T>C	ENST00000265362.4	-	2	581	c.267A>G	c.(265-267)caA>caG	p.Q89Q	SEMA3A_ENST00000436949.1_Silent_p.Q89Q	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	89	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						CTGATACCTTTTGAAAATCCT	0.328													t|||	14	0.00279553	0.0008	0.0043	5008	,	,		18311	0.0		0.0099	False		,,,				2504	0.0				p.Q89Q		Atlas-SNP	.											.	SEMA3A	121	.	0			c.A267G						PASS	.	T		12,4394	17.9+/-39.9	0,12,2191	73	73	73		267	3.6	1	7	dbSNP_132	73	101,8499	54.8+/-115.7	1,99,4200	no	coding-synonymous	SEMA3A	NM_006080.2		1,111,6391	CC,CT,TT		1.1744,0.2724,0.8688		89/772	83764113	113,12893	2203	4300	6503	SO:0001819	synonymous_variant	10371	exon2			TACCTTTTGAAAA	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.267A>G	7.37:g.83764113T>C		56	0	0		72	38	0.527778	NM_006080		Silent	SNP	ENST00000265362.4	37	CCDS5599.1																																																																																			T|0.993;C|0.007	0.007	strong		0.328	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080		C	83764113	T	C	83764113	2	2	27	1	0	0	0	0	0	0	0	1	14039	1838	64	3		3	SEMA3A	7	83764113	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	3646120	83764113	75374550	424	10875											
SLC25A13	10165	hgsc.bcm.edu	37	chr7	95761057	95761057	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tccatgggggacactcaccaGctatggcaccagctaagagc	11	6	11	13	0	1	1	1	0	0	1	2	2	2	2	3	3	3	3	3	3	2	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:95761057G>A	ENST00000265631.5	-	15	1725	c.1589C>T	c.(1588-1590)gCt>gTt	p.A530V	SLC25A13_ENST00000416240.2_Missense_Mutation_p.A531V|SLC25A13_ENST00000542654.1_Missense_Mutation_p.A422V			Q9UJS0	CMC2_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 13	530					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)	ACACTCACCAGCTATGGCACC	0.507																																					p.A531V		Atlas-SNP	.											.	SLC25A13	131	.	0			c.C1592T						PASS	.						76	68	70					7																	95761057		2203	4300	6503	SO:0001583	missense	10165	exon15			TCACCAGCTATGG	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.1589C>T	7.37:g.95761057G>A	ENSP00000265631:p.Ala530Val	123	0	0		104	49	0.471154	NM_001160210	O14566|O14575|Q546F9|Q9NZW1|Q9UNI7	Missense_Mutation	SNP	ENST00000265631.5	37	CCDS5645.1	.	.	.	.	.	.	.	.	.	.	G	32	5.127249	0.94473	.	.	ENSG00000004864	ENST00000265631;ENST00000416240;ENST00000542654	D;D;D	0.87256	-2.23;-2.23;-2.23	4.65	4.65	0.58169	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.94719	0.8296	M	0.90252	3.1	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	0.95624	0.8683	10	0.87932	D	0	-12.4191	18.1095	0.89530	0.0:0.0:1.0:0.0	.	422;531;530	F5GX33;Q546F9;Q9UJS0	.;.;CMC2_HUMAN	V	530;531;422	ENSP00000265631:A530V;ENSP00000400101:A531V;ENSP00000440484:A422V	ENSP00000265631:A530V	A	-	2	0	SLC25A13	95598993	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	9.657000	0.98554	2.599000	0.87857	0.655000	0.94253	GCT	.	.	none		0.507	SLC25A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059395.2	NM_014251		A	95761057	G	A	95761057	3	1	27	1	0	0	0	0	1	0	0	0	14490	971	34	2	454	2	SLC25A13	7	95761057	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	11996944	95761057	63377606	425	10876											
TECPR1	25851	hgsc.bcm.edu	37	chr7	97861156	97861156	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	catagtagatgaagaggatgCtgtcccggacgccgtcgtgc	9	8	14	10	4	0	3	0	1	0	2	2	5	1	5	2	2	2	2	2	2	3	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:97861156C>A	ENST00000447648.2	-	13	2233	c.1934G>T	c.(1933-1935)aGc>aTc	p.S645I	TECPR1_ENST00000542604.1_Missense_Mutation_p.S575I|TECPR1_ENST00000379795.3_Missense_Mutation_p.S646I			Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	645	PH.				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						GAAGAGGATGCTGTCCCGGAC	0.657																																					p.S645I		Atlas-SNP	.											.	TECPR1	77	.	0			c.G1934T						PASS	.						88	98	94					7																	97861156		2088	4208	6296	SO:0001583	missense	25851	exon13			AGGATGCTGTCCC		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.1934G>T	7.37:g.97861156C>A	ENSP00000404923:p.Ser645Ile	57	0	0		61	14	0.229508	NM_015395	A8KAD1|B3KPZ1|C9J024|F5GX57|Q96EB0|Q9P2I9|Q9UFR6	Missense_Mutation	SNP	ENST00000447648.2	37	CCDS47648.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.500612	0.85176	.	.	ENSG00000205356	ENST00000447648;ENST00000379795;ENST00000542604	T;T;T	0.38722	1.14;1.12;1.15	5.25	5.25	0.73442	Pleckstrin homology domain (1);	0.043912	0.85682	D	0.000000	T	0.62146	0.2404	L	0.60455	1.87	0.46749	D	0.999184	D;D	0.89917	1.0;0.999	D;D	0.72338	0.977;0.949	T	0.64976	-0.6280	10	0.87932	D	0	-32.2674	17.8224	0.88654	0.0:1.0:0.0:0.0	.	575;645	F5GX57;Q7Z6L1	.;TCPR1_HUMAN	I	645;646;575	ENSP00000404923:S645I;ENSP00000369121:S646I;ENSP00000441121:S575I	ENSP00000369121:S646I	S	-	2	0	TECPR1	97699092	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	4.805000	0.62561	2.459000	0.83118	0.655000	0.94253	AGC	.	.	none		0.657	TECPR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334661.1	NM_015395		A	97861156	C	A	97861156	3	1	27	1	0	0	0	0	1	0	0	0	15758	797	28	4	1619	4	TECPR1	7	97861156	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2100099	97861156	61277507	426	10877											
TRIP6	7205	hgsc.bcm.edu	37	chr7	100465824	100465824	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggccgagctgaatgggggtcGgggtcatgcgtcacggcgac	6	6	19	10	5	2	1	2	1	0	0	3	3	2	1	1	6	2	1	1	6	1	0	rs2437100	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:100465824G>A	ENST00000200457.4	+	3	692	c.332G>A	c.(331-333)cGg>cAg	p.R111Q		NM_003302.2	NP_003293.2	Q15654	TRIP6_HUMAN	thyroid hormone receptor interactor 6	111			R -> Q (in dbSNP:rs2437100). {ECO:0000269|PubMed:15489334}.		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)					AATGGGGGTCGGGGTCATGCG	0.672													G|||	32	0.00638978	0.0008	0.0058	5008	,	,		14361	0.0		0.0268	False		,,,				2504	0.0				p.R111Q		Atlas-SNP	.											.	TRIP6	45	.	0			c.G332A						PASS	.	G	GLN/ARG	21,4385	29.0+/-57.7	0,21,2182	41	41	41		332	4.5	0.8	7	dbSNP_100	41	176,8424	80.6+/-143.3	1,174,4125	yes	missense	TRIP6	NM_003302.2	43	1,195,6307	AA,AG,GG		2.0465,0.4766,1.5147	probably-damaging	111/477	100465824	197,12809	2203	4300	6503	SO:0001583	missense	7205	exon3			GGGGTCGGGGTCA	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.332G>A	7.37:g.100465824G>A	ENSP00000200457:p.Arg111Gln	55	0	0		50	22	0.44	NM_003302	A4D2E7|F2ZC07|F2ZC08|O15170|O15275|Q9BTB2|Q9BUE5|Q9BXP3|Q9UNT4	Missense_Mutation	SNP	ENST00000200457.4	37	CCDS5708.1	26	0.011904761904761904	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	23	0.030343007915567283	G	18.42	3.619897	0.66787	0.004766	0.020465	ENSG00000087077	ENST00000200457	T	0.59502	0.26	4.53	4.53	0.55603	.	0.374538	0.26931	N	0.021774	T	0.33089	0.0851	L	0.47716	1.5	0.28405	N	0.918477	D	0.69078	0.997	P	0.53518	0.728	T	0.40646	-0.9552	10	0.11794	T	0.64	.	12.7393	0.57241	0.0:0.0:1.0:0.0	rs2437100	111	Q15654	TRIP6_HUMAN	Q	111	ENSP00000200457:R111Q	ENSP00000200457:R111Q	R	+	2	0	TRIP6	100303760	0.997000	0.39634	0.757000	0.31301	0.054000	0.15201	3.870000	0.56070	2.074000	0.62210	0.455000	0.32223	CGG	G|0.985;A|0.015	0.015	strong		0.672	TRIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347151.2	NM_003302		A	100465824	G	A	100465824	3	1	27	1	0	0	0	0	1	0	0	0	16574	1116	39	1	342	1	TRIP6	7	100465824	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2604668	100465824	58672839	427	10878											
MUC17	140453	hgsc.bcm.edu	37	chr7	100676968	100676968	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agtatgcctgtcagcaaaacGctgttgaccagttctgaggc	10	10	11	10	1	2	2	1	2	1	0	2	2	2	2	2	1	3	5	2	1	3	3	rs138994021|rs71525818	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:100676968G>A	ENST00000306151.4	+	3	2335	c.2271G>A	c.(2269-2271)acG>acA	p.T757T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	757	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)					TCAGCAAAACGCTGTTGACCA	0.483													A|||	20	0.00399361	0.0045	0.0	5008	,	,		28523	0.0		0.0139	False		,,,				2504	0.0				p.T757T		Atlas-SNP	.											.	MUC17	804	.	0			c.G2271A						PASS	.	G		23,4383	29.0+/-57.7	0,23,2180	300	301	300		2271	-1.3	0	7	dbSNP_134	300	94,8506	52.7+/-113.3	0,94,4206	no	coding-synonymous	MUC17	NM_001040105.1		0,117,6386	AA,AG,GG		1.093,0.522,0.8996		757/4494	100676968	117,12889	2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			CAAAACGCTGTTG	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.2271G>A	7.37:g.100676968G>A		48	0	0		58	29	0.5	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			G|0.991;A|0.009	0.009	strong		0.483	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100676968	G	A	100676968	2	1	27	1	0	0	0	0	0	0	0	1	9983	1074	38	1		1	MUC17	7	100676968	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	211144	100676968	58461695	428	10879											
MUC17	140453	hgsc.bcm.edu	37	chr7	100683796	100683796	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctcctacaactgctgaaggTaccggcataccaatctcaac	12	9	6	14	1	2	1	1	1	2	0	4	1	2	1	3	2	6	3	3	2	7	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:100683796T>C	ENST00000306151.4	+	3	9163	c.9099T>C	c.(9097-9099)ggT>ggC	p.G3033G		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3033	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)					CTGCTGAAGGTACCGGCATAC	0.512																																					p.G3033G		Atlas-SNP	.											MUC17,caecum,carcinoma,+2,2	MUC17	804	2	0			c.T9099C						scavenged	.						265	278	274					7																	100683796		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			TGAAGGTACCGGC	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.9099T>C	7.37:g.100683796T>C		24	0	0		35	2	0.0571429	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			.	.	none		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		C	100683796	T	C	100683796	2	2	27	1	0	0	0	0	0	0	0	1	9983	1625	57	3		3	MUC17	7	100683796	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	6828	100683796	58454867	429	10880											
CUX1	1523	hgsc.bcm.edu	37	chr7	101921292	101921292	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctgcgcgccgacaacatcAagctctttgagaagatcaag	12	7	10	12	3	3	2	2	1	1	2	3	4	3	2	2	0	3	1	2	0	4	1	rs118010189	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:101921292A>C	ENST00000437600.4	+	18	1982	c.1630A>C	c.(1630-1632)Aag>Cag	p.K544Q	CUX1_ENST00000547394.2_Missense_Mutation_p.K530Q|CUX1_ENST00000425244.2_Missense_Mutation_p.K500Q|CUX1_ENST00000560541.1_3'UTR|CUX1_ENST00000292538.4_Missense_Mutation_p.K546Q|CUX1_ENST00000393824.3_Missense_Mutation_p.K507Q	NM_181500.2	NP_852477.1	P39880	CUX1_HUMAN	cut-like homeobox 1	353					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						CGACAACATCAAGCTCTTTGA	0.662													A|||	18	0.00359425	0.0	0.0101	5008	,	,		12632	0.0		0.007	False		,,,				2504	0.0041				p.K546Q		Atlas-SNP	.											.	CUX1	253	.	0			c.A1636C						PASS	.	A	GLN/LYS,GLN/LYS,GLN/LYS,GLN/LYS,GLN/LYS	5,4401	8.1+/-20.4	0,5,2198	42	36	38		1588,1498,1519,1636,1630	4.6	1	7	dbSNP_133	38	88,8510	45.8+/-104.6	0,88,4211	yes	missense,missense,missense,missense,missense	CUX1	NM_001202544.1,NM_001202545.1,NM_001202546.1,NM_001913.3,NM_181500.2	53,53,53,53,53	0,93,6409	CC,CA,AA		1.0235,0.1135,0.7152	,,,,	530/663,500/633,507/640,546/679,544/677	101921292	93,12911	2203	4299	6502	SO:0001583	missense	1523	exon18			AACATCAAGCTCT	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	ENST00000437600.4:c.1630A>C	7.37:g.101921292A>C	ENSP00000414091:p.Lys544Gln	282	0	0		244	120	0.491803	NM_001913	B3KV79|J3KQV9|Q6NYH4|Q75LE5|Q75MT2|Q75MT3|Q86UJ7|Q9UEV5	Missense_Mutation	SNP	ENST00000437600.4	37	CCDS47672.1	9	0.004120879120879121	0	0.0	5	0.013812154696132596	0	0.0	4	0.005277044854881266	A	21.6	4.169486	0.78452	0.001135	0.010235	ENSG00000257923	ENST00000292538;ENST00000547394;ENST00000425244;ENST00000437600	T;T;T;T	0.32753	1.44;1.44;1.44;1.44	4.55	4.55	0.56014	CASP, C-terminal (1);	.	.	.	.	T	0.45796	0.1360	M	0.66560	2.04	0.28388	N	0.919234	D;D;D;D;D	0.89917	1.0;0.999;0.972;1.0;0.998	D;D;P;D;D	0.85130	0.99;0.997;0.861;0.989;0.963	T	0.45220	-0.9276	9	0.52906	T	0.07	.	14.2558	0.66051	1.0:0.0:0.0:0.0	.	507;500;530;544;546	B4DZZ2;B3KV79;G3V1Z6;Q13948-2;Q13948	.;.;.;.;CASP_HUMAN	Q	546;530;500;544	ENSP00000292538:K546Q;ENSP00000449371:K530Q;ENSP00000409745:K500Q;ENSP00000414091:K544Q	ENSP00000292538:K546Q	K	+	1	0	CUX1	101708012	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	8.671000	0.91174	1.849000	0.53698	0.374000	0.22700	AAG	A|0.993;C|0.007	0.007	strong		0.662	CUX1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347534.3	NM_001913		C	101921292	A	C	101921292	3	2	27	1	0	0	0	0	1	0	0	0	4066	131	5	5	5076	5	CUX1	7	101921292	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	1237496	101921292	57217371	430	10881											
CDHR3	222256	hgsc.bcm.edu	37	chr7	105636765	105636765	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acagagctccaggtgaacatCgtgaacctcaacgacgaagt	14	6	10	11	3	1	3	1	2	0	1	3	5	2	3	2	1	4	1	2	1	4	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:105636765C>T	ENST00000317716.9	+	6	758	c.678C>T	c.(676-678)atC>atT	p.I226I	CDHR3_ENST00000470188.1_Intron|CDHR3_ENST00000541203.1_Intron|CDHR3_ENST00000478080.1_Silent_p.I138I|CDHR3_ENST00000542731.1_Silent_p.I226I|CDHR3_ENST00000343407.5_5'UTR	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	226	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)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						AGGTGAACATCGTGAACCTCA	0.587																																					p.I226I		Atlas-SNP	.											.	CDHR3	153	.	0			c.C678T						PASS	.						41	44	43					7																	105636765		2011	4165	6176	SO:0001819	synonymous_variant	222256	exon6			GAACATCGTGAAC	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.678C>T	7.37:g.105636765C>T		42	0	0		51	4	0.0784314	NM_152750	Q8TCI7	Silent	SNP	ENST00000317716.9	37	CCDS47684.1																																																																																			.	.	none		0.587	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750		T	105636765	C	T	105636765	2	4	27	1	0	0	0	0	0	0	0	1	3122	874	31	1		1	CDHR3	7	105636765	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3715473	105636765	53501898	431	10882											
LRRN3	54674	hgsc.bcm.edu	37	chr7	110764596	110764596	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgaatccatcaactgagtatAaaatttgtattgatattccc	14	15	5	7	0	1	3	1	3	0	0	3	3	3	3	2	0	1	2	2	0	7	7			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:110764596A>G	ENST00000422987.3	+	2	2599	c.1768A>G	c.(1768-1770)Aaa>Gaa	p.K590E	IMMP2L_ENST00000437687.1_Intron|IMMP2L_ENST00000447215.1_Intron|LRRN3_ENST00000451085.1_Missense_Mutation_p.K590E|IMMP2L_ENST00000489381.1_Intron|IMMP2L_ENST00000331762.3_Intron|LRRN3_ENST00000308478.5_Missense_Mutation_p.K590E|IMMP2L_ENST00000415362.1_Intron|IMMP2L_ENST00000405709.2_Intron|IMMP2L_ENST00000450877.1_Intron|IMMP2L_ENST00000452895.1_Intron	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	590	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)		AACTGAGTATAAAATTTGTAT	0.348																																					p.K590E		Atlas-SNP	.											.	LRRN3	132	.	0			c.A1768G						PASS	.						44	43	43					7																	110764596		2203	4300	6503	SO:0001583	missense	54674	exon2			GAGTATAAAATTT	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.1768A>G	7.37:g.110764596A>G	ENSP00000412417:p.Lys590Glu	62	0	0		69	22	0.318841	NM_018334	O43377|Q6I9V8|Q8IYQ6	Missense_Mutation	SNP	ENST00000422987.3	37	CCDS5754.1	.	.	.	.	.	.	.	.	.	.	A	0.129	-1.115378	0.01799	.	.	ENSG00000173114	ENST00000308478;ENST00000451085;ENST00000422987	T;T;T	0.55052	0.54;0.54;0.54	5.59	4.41	0.53225	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.190873	0.36303	N	0.002673	T	0.25195	0.0612	N	0.10733	0.035	0.38993	D	0.959181	B	0.10296	0.003	B	0.13407	0.009	T	0.16689	-1.0394	10	0.02654	T	1	.	7.5231	0.27639	0.7855:0.1436:0.0709:0.0	.	590	Q9H3W5	LRRN3_HUMAN	E	590	ENSP00000312001:K590E;ENSP00000397312:K590E;ENSP00000412417:K590E	ENSP00000312001:K590E	K	+	1	0	LRRN3	110551832	0.995000	0.38212	0.997000	0.53966	0.964000	0.63967	2.962000	0.49176	1.033000	0.39918	0.529000	0.55759	AAA	.	.	none		0.348	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334		G	110764596	A	G	110764596	3	3	27	1	0	0	0	0	1	0	0	0	9045	363	13	3	1770	3	LRRN3	7	110764596	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	5127831	110764596	48374067	432	10883											
DOCK4	9732	hgsc.bcm.edu	37	chr7	111375211	111375211	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccaggctccagctgctagggGtggggttcacagctggaagg	7	7	17	10	0	1	0	1	0	0	0	2	1	2	1	2	7	3	5	2	7	2	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:111375211G>C	ENST00000437633.1	-	50	5547	c.5291C>G	c.(5290-5292)aCc>aGc	p.T1764S	DOCK4_ENST00000428084.1_Missense_Mutation_p.T1773S|DOCK4_ENST00000494651.2_Missense_Mutation_p.T647S	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	1764	Ser-rich.				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)				GCTGCTAGGGGTGGGGTTCAC	0.507																																					p.T1764S		Atlas-SNP	.											.	DOCK4	365	.	0			c.C5291G						PASS	.						38	38	38					7																	111375211		1905	4125	6030	SO:0001583	missense	9732	exon50			CTAGGGGTGGGGT		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.5291C>G	7.37:g.111375211G>C	ENSP00000404179:p.Thr1764Ser	44	0	0		37	11	0.297297	NM_014705	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	37	CCDS47688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.24|17.24	3.338601|3.338601	0.60963|0.60963	.|.	.|.	ENSG00000128512|ENSG00000128512	ENST00000445943|ENST00000352877;ENST00000428084;ENST00000494651;ENST00000437633	.|T;T;T	.|0.05717	.|4.13;3.4;4.14	6.04|6.04	5.16|5.16	0.70880|0.70880	.|.	.|0.093637	.|0.85682	.|D	.|0.000000	T|T	0.04182|0.04182	0.0116|0.0116	N|N	0.08118|0.08118	0|0	0.42876|0.42876	D|D	0.994156|0.994156	.|B;B;B;P	.|0.45902	.|0.206;0.146;0.146;0.868	.|B;B;B;B	.|0.41510	.|0.085;0.038;0.026;0.359	T|T	0.59348|0.59348	-0.7471|-0.7471	5|10	.|0.21540	.|T	.|0.41	.|.	14.7566|14.7566	0.69569|0.69569	0.0686:0.0:0.9314:0.0|0.0686:0.0:0.9314:0.0	.|.	.|647;1809;1764;77	.|F5GXW1;Q149N5;Q8N1I0;Q8N1I0-4	.|.;.;DOCK4_HUMAN;.	A|S	1797|1752;1773;647;1764	.|ENSP00000410746:T1773S;ENSP00000440944:T647S;ENSP00000404179:T1764S	.|ENSP00000262421:T1752S	P|T	-|-	1|2	0|0	DOCK4|DOCK4	111162447|111162447	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.062000|7.062000	0.76706|0.76706	2.876000|2.876000	0.98609|0.98609	0.650000|0.650000	0.86243|0.86243	CCC|ACC	.	.	none		0.507	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705		C	111375211	G	C	111375211	3	2	27	1	0	0	0	0	1	0	0	0	4691	1261	44	4	621	4	DOCK4	7	111375211	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	610615	111375211	47763452	433	10884											
DOCK4	9732	hgsc.bcm.edu	37	chr7	111503547	111503547	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccagggtgtcctggaccaagTtggctacttcccggacatca	8	9	11	13	1	1	0	1	0	0	0	3	2	3	2	4	4	1	2	4	4	2	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:111503547T>C	ENST00000437633.1	-	23	2610	c.2354A>G	c.(2353-2355)aAc>aGc	p.N785S	DOCK4_ENST00000428084.1_Missense_Mutation_p.N785S|DOCK4_ENST00000476846.1_5'UTR	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	785					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)				CTGGACCAAGTTGGCTACTTC	0.498																																					p.N785S		Atlas-SNP	.											.	DOCK4	365	.	0			c.A2354G						PASS	.						56	55	55					7																	111503547		1957	4132	6089	SO:0001583	missense	9732	exon23			ACCAAGTTGGCTA		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.2354A>G	7.37:g.111503547T>C	ENSP00000404179:p.Asn785Ser	75	0	0		81	27	0.333333	NM_014705	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	37	CCDS47688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.27|13.27	2.186733|2.186733	0.38609|0.38609	.|.	.|.	ENSG00000128512|ENSG00000128512	ENST00000352877;ENST00000428084;ENST00000437633;ENST00000342288;ENST00000544250|ENST00000423057;ENST00000445943	T;T|.	0.02812|.	4.15;4.15|.	5.23|5.23	4.07|4.07	0.47477|0.47477	.|.	0.213000|.	0.49305|.	D|.	0.000152|.	T|T	0.60843|0.60843	0.2300|0.2300	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	D|D	1|1	B;B;B;B|.	0.17465|.	0.013;0.013;0.013;0.022|.	B;B;B;B|.	0.19666|.	0.017;0.017;0.011;0.026|.	T|T	0.57406|0.57406	-0.7817|-0.7817	10|5	0.09843|.	T|.	0.71|.	.|.	11.1557|11.1557	0.48486|0.48486	0.0:0.0722:0.0:0.9278|0.0:0.0722:0.0:0.9278	.|.	785;785;785;785|.	Q149N2;Q149N5;Q8N1I0;Q8N1I0-2|.	.;.;DOCK4_HUMAN;.|.	S|A	773;785;785;773;784|237;773	ENSP00000410746:N785S;ENSP00000404179:N785S|.	ENSP00000345432:N773S|.	N|T	-|-	2|1	0|0	DOCK4|DOCK4	111290783|111290783	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.861000|0.861000	0.49209|0.49209	4.653000|4.653000	0.61462|0.61462	0.991000|0.991000	0.38814|0.38814	0.460000|0.460000	0.39030|0.39030	AAC|ACT	.	.	none		0.498	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705		C	111503547	T	C	111503547	3	2	27	1	0	0	0	0	1	0	0	0	4691	1725	60	3	3666	3	DOCK4	7	111503547	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	128336	111503547	47635116	434	10885											
CAV1	857	hgsc.bcm.edu	37	chr7	116165140	116165140	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgggggcaaatacgtagaCtcggaggtaggcatccgtgg	9	8	16	8	3	1	1	0	0	1	1	3	2	2	2	1	6	1	4	1	6	4	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:116165140C>A	ENST00000341049.2	+	1	302	c.24C>A	c.(22-24)gaC>gaA	p.D8E	CAV1_ENST00000393470.1_Missense_Mutation_p.D8E|CAV1_ENST00000405348.1_5'Flank|CAV1_ENST00000393468.1_5'Flank|CAV1_ENST00000393467.1_5'Flank	NM_001753.4	NP_001744.2	Q03135	CAV1_HUMAN	caveolin 1, caveolae protein, 22kDa	8					angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|calcium ion homeostasis (GO:0055074)|calcium ion transport (GO:0006816)|caveola assembly (GO:0070836)|caveolin-mediated endocytosis (GO:0072584)|cellular calcium ion homeostasis (GO:0006874)|cellular response to hyperoxia (GO:0071455)|cellular response to starvation (GO:0009267)|cholesterol homeostasis (GO:0042632)|cholesterol transport (GO:0030301)|cytosolic calcium ion homeostasis (GO:0051480)|inactivation of MAPK activity (GO:0000188)|lactation (GO:0007595)|leukocyte migration (GO:0050900)|lipid storage (GO:0019915)|maintenance of protein location in cell (GO:0032507)|mammary gland development (GO:0030879)|mammary gland involution (GO:0060056)|MAPK cascade (GO:0000165)|membrane depolarization (GO:0051899)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of nitric-oxide synthase activity (GO:0051001)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of pinocytosis (GO:0048550)|negative regulation of protein binding (GO:0032091)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|nitric oxide homeostasis (GO:0033484)|nitric oxide metabolic process (GO:0046209)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of vasoconstriction (GO:0045907)|protein homooligomerization (GO:0051260)|protein localization (GO:0008104)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)|regulation of blood coagulation (GO:0030193)|regulation of fatty acid metabolic process (GO:0019217)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidase activity (GO:0052547)|regulation of smooth muscle contraction (GO:0006940)|regulation of the force of heart contraction by chemical signal (GO:0003057)|response to calcium ion (GO:0051592)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|response to ischemia (GO:0002931)|response to progesterone (GO:0032570)|skeletal muscle tissue development (GO:0007519)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|vasculogenesis (GO:0001570)|vasoconstriction (GO:0042310)|vesicle organization (GO:0016050)|viral process (GO:0016032)	acrosomal membrane (GO:0002080)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell cortex (GO:0005938)|cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lipid particle (GO:0005811)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	cholesterol binding (GO:0015485)|enzyme binding (GO:0019899)|nitric-oxide synthase binding (GO:0050998)|patched binding (GO:0005113)|peptidase activator activity (GO:0016504)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)|structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4	all_epithelial(6;1.42e-06)|Lung NSC(10;0.0056)|all_lung(10;0.00609)		STAD - Stomach adenocarcinoma(10;0.00878)			AATACGTAGACTCGGAGGTAG	0.612																																					p.D8E		Atlas-SNP	.											.	CAV1	13	.	0			c.C24A						PASS	.						87	100	96					7																	116165140		2203	4300	6503	SO:0001583	missense	857	exon1			CGTAGACTCGGAG	AF125348	CCDS5767.1, CCDS55156.1	7q31	2006-02-09	2002-08-29		ENSG00000105974	ENSG00000105974			1527	protein-coding gene	gene with protein product		601047	"caveolin 1, caveolae protein, 22kD"	CAV		10087206	Standard	NM_001753		Approved		uc003vif.2	Q03135	OTTHUMG00000023413	ENST00000341049.2:c.24C>A	7.37:g.116165140C>A	ENSP00000339191:p.Asp8Glu	122	0	0		92	37	0.402174	NM_001753	Q9UGP1|Q9UNG1|Q9UQH6	Missense_Mutation	SNP	ENST00000341049.2	37	CCDS5767.1	.	.	.	.	.	.	.	.	.	.	C	16.66	3.184175	0.57800	.	.	ENSG00000105974	ENST00000341049;ENST00000393470	D;D	0.93189	-3.18;-3.06	4.71	2.91	0.33838	.	0.683428	0.14907	N	0.291489	D	0.90307	0.6968	L	0.56769	1.78	0.80722	D	1	B	0.09022	0.002	B	0.09377	0.004	D	0.86138	0.1579	10	0.66056	D	0.02	-15.711	8.0118	0.30357	0.0:0.7413:0.0:0.2587	.	8	Q03135	CAV1_HUMAN	E	8	ENSP00000339191:D8E;ENSP00000377113:D8E	ENSP00000339191:D8E	D	+	3	2	CAV1	115952376	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.667000	0.25112	0.696000	0.31696	0.650000	0.86243	GAC	.	.	none		0.612	CAV1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000059734.4	NM_001753		A	116165140	C	A	116165140	3	1	27	1	0	0	0	0	1	0	0	0	2695	564	20	4	26	4	CAV1	7	116165140	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	4661593	116165140	42973523	435	10886											
MET	4233	hgsc.bcm.edu	37	chr7	116339282	116339282	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagcttcccaacttcaccgcGgaaacacccatccagaatgt	12	7	6	16	2	1	1	1	0	0	1	3	2	3	2	4	1	3	1	4	1	3	2	rs11762213	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:116339282G>A	ENST00000318493.6	+	2	331	c.144G>A	c.(142-144)gcG>gcA	p.A48A	MET_ENST00000436117.2_Silent_p.A48A|MET_ENST00000397752.3_Silent_p.A48A			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0	SAP. {ECO:0000255|PROSITE- ProRule:PRU00186}.				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)			ACTTCACCGCGGAAACACCCA	0.433			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				G|||	77	0.0153754	0.0023	0.0346	5008	,	,		21839	0.0		0.0398	False		,,,				2504	0.0102				p.A48A		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,adenocarcinoma,+1,2	MET	412	2	0			c.G144A						PASS	.	G	,	42,3886		0,42,1922	100	99	99		144,144	-11.8	0	7	dbSNP_120	99	391,7915		6,379,3768	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	6,421,5690	AA,AG,GG		4.7074,1.0692,3.5393	,	48/1391,48/1409	116339282	433,11801	1964	4153	6117	SO:0001819	synonymous_variant	4233	exon2	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	CACCGCGGAAACA	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.144G>A	7.37:g.116339282G>A		126	0	0		136	69	0.507353	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			G|0.974;A|0.026	0.026	strong		0.433	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			A	116339282	G	A	116339282	2	1	27	1	0	0	0	0	0	0	0	1	9494	1103	39	1		1	MET	7	116339282	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	174142	116339282	42799381	436	10887											
CFTR	1080	hgsc.bcm.edu	37	chr7	117199645	117199647	+	In_Frame_Del	DEL	TCT	TCT	-																															caccattaaagaaaatatcaTctttggtgtttcctatgatg																								rs121909001|rs199826652|rs113993960	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:117199645_117199647delTCT	ENST00000003084.6	+	11	1652_1654	c.1520_1522delTCT	c.(1519-1524)atcttt>att	p.F508del	CFTR_ENST00000454343.1_In_Frame_Del_p.F447del|AC000111.3_ENST00000441019.1_RNA	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)	508	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.		F -> C (in dbSNP:rs1800093).|Missing (in CF and CBAVD; most common mutation; 72% of the population; CFTR fails to be properly delivered to plasma membrane).		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)	GAAAATATCATCTTTGGTGTTTC	0.365									Cystic Fibrosis					20	0.00399361	0.0	0.0101	5008	,	,		18625	0.0		0.0089	False		,,,				2504	0.0041				p.507_507del		Pindel,Atlas-Indel	.											.	CFTR	171	.	0			c.1519_1521del	GRCh37	CD890142|CI075604	CFTR	D|I	rs1800093	PASS	.			13,4251		0,13,2119				http://www.ncbi.nlm.nih.gov/sites/varvu?gene		1.9	1		dbSNP_133	89	809,7445		317,175,3635	no	coding	CFTR	NM_000492.3		317,188,5754	A1A1,A1R,RR		9.8013,0.3049,6.5665				822,11696				SO:0001651	inframe_deletion	1080	exon11	Familial Cancer Database	CF	.	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.1520_1522delTCT	7.37:g.117199645_117199647delTCT	ENSP00000003084:p.Phe508del	81	0	.		49	17	0.347	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	In_Frame_Del	DEL	ENST00000003084.6	37	CCDS5773.1																																																																																			TCT|0.994;-|0.006	0.006	strong		0.365	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492		-	117199647	TCT	-	117199645	7	5	27	1	0	1	0	1	0	0	0	0	3296	1435	50	0	1562	0	CFTR	7	117199645	In_Frame_Del	DEL	TCT	TCGA-G8-6909-01A-11D-2210-10	860363	117199645	41939018	437	10888											
SMO	6608	hgsc.bcm.edu	37	chr7	128843277	128843277	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atccagcccctgctgtgtgcCgtatacatgcccaagtgtga	8	10	10	13	1	0	1	0	1	0	0	1	1	1	1	5	0	5	2	5	0	3	2	rs45571737	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:128843277C>T	ENST00000249373.3	+	2	664	c.384C>T	c.(382-384)gcC>gcT	p.A128A		NM_005631.4	NP_005622.1	Q99835	SMO_HUMAN	smoothened, frizzled class receptor	128	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				adenohypophysis development (GO:0021984)|anterior/posterior pattern specification (GO:0009952)|atrial septum morphogenesis (GO:0060413)|axon extension involved in axon guidance (GO:0048846)|canonical Wnt signaling pathway (GO:0060070)|cardioblast differentiation (GO:0010002)|cell fate specification (GO:0001708)|cellular response to cholesterol (GO:0071397)|central nervous system neuron differentiation (GO:0021953)|cerebellar cortex morphogenesis (GO:0021696)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|detection of cell density by contact stimulus involved in contact inhibition (GO:0060248)|determination of left/right asymmetry in lateral mesoderm (GO:0003140)|determination of left/right symmetry (GO:0007368)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|epithelial-mesenchymal cell signaling (GO:0060684)|exocrine pancreas development (GO:0031017)|facial nerve development (GO:0021561)|floor plate formation (GO:0021508)|forebrain morphogenesis (GO:0048853)|gonad development (GO:0008406)|hair follicle morphogenesis (GO:0031069)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mammary gland epithelial cell differentiation (GO:0060644)|mesenchymal to epithelial transition involved in metanephric renal vesicle formation (GO:0072285)|midgut development (GO:0007494)|multicellular organism growth (GO:0035264)|muscle cell fate commitment (GO:0042693)|myoblast migration (GO:0051451)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of gene expression (GO:0010629)|negative regulation of hair follicle development (GO:0051799)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate commitment (GO:0048663)|neuron projection regeneration (GO:0031102)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|otolith morphogenesis (GO:0032474)|pancreas morphogenesis (GO:0061113)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gene expression (GO:0010628)|positive regulation of hh target transcription factor activity (GO:0007228)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|protein stabilization (GO:0050821)|regulation of heart morphogenesis (GO:2000826)|regulation of stem cell maintenance (GO:2000036)|renal system development (GO:0072001)|semicircular canal morphogenesis (GO:0048752)|skeletal muscle fiber development (GO:0048741)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021910)|somite development (GO:0061053)|spermatogenesis (GO:0007283)|thalamus development (GO:0021794)|type B pancreatic cell development (GO:0003323)|vasculogenesis (GO:0001570)|ventral midline determination (GO:0007371)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	drug binding (GO:0008144)|G-protein coupled receptor activity (GO:0004930)|patched binding (GO:0005113)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			biliary_tract(1)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(14)|liver(1)|lung(11)|pancreas(2)|prostate(1)|skin(20)|upper_aerodigestive_tract(3)|urinary_tract(1)	64					Fluocinonide(DB01047)|Vismodegib(DB08828)	TGCTGTGTGCCGTATACATGC	0.667			Mis		skin basal cell								C|||	20	0.00399361	0.0	0.0058	5008	,	,		17322	0.0		0.0119	False		,,,				2504	0.0041				p.A128A		Atlas-SNP	.		Dom	yes		7	7q31-q32	6608	smoothened homolog (Drosophila)		E	.	SMO	145	.	0			c.C384T						PASS	.	C		5,4381		0,5,2188	26	22	23		384	-8.7	0.7	7	dbSNP_127	23	110,8456		0,110,4173	no	coding-synonymous	SMO	NM_005631.4		0,115,6361	TT,TC,CC		1.2841,0.114,0.8879		128/788	128843277	115,12837	2193	4283	6476	SO:0001819	synonymous_variant	6608	exon2			GTGTGCCGTATAC	U84401	CCDS5811.1	7q32.1	2014-01-29	2014-01-29	2003-01-17	ENSG00000128602	ENSG00000128602		"GPCR / Class F : Frizzled receptors"	11119	protein-coding gene	gene with protein product	"frizzled family member 11"	601500	"smoothened (Drosophila) homolog", "smoothened homolog (Drosophila)", "smoothened, seven transmembrane spanning receptor", "smoothened, frizzled family receptor"	SMOH		9628830	Standard	NM_005631		Approved	FZD11	uc003vor.3	Q99835	OTTHUMG00000158421	ENST00000249373.3:c.384C>T	7.37:g.128843277C>T		99	0	0		103	40	0.38835	NM_005631	A4D1K5	Silent	SNP	ENST00000249373.3	37	CCDS5811.1																																																																																			C|0.993;T|0.007	0.007	strong		0.667	SMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350986.1	NM_005631		T	128843277	C	T	128843277	2	4	27	1	0	0	0	0	0	0	0	1	14815	639	23	1		1	SMO	7	128843277	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	11643632	128843277	30295386	438	10889											
ZC3HC1	51530	hgsc.bcm.edu	37	chr7	129664301	129664301	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agccccaccttcctcatacaTtgcgaacatgttatcaggga	11	10	7	13	1	2	0	2	0	0	0	3	2	3	1	4	1	4	1	4	1	3	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:129664301T>C	ENST00000358303.4	-	7	906	c.822A>G	c.(820-822)caA>caG	p.Q274Q	ZC3HC1_ENST00000311873.5_Silent_p.Q253Q|RNA5SP245_ENST00000364239.1_RNA|RP11-306G20.1_ENST00000587038.1_RNA|ZC3HC1_ENST00000481503.1_Intron|ZC3HC1_ENST00000360708.5_Silent_p.Q274Q|RP11-306G20.1_ENST00000480018.1_RNA	NM_016478.3	NP_057562.3	Q86WB0	NIPA_HUMAN	zinc finger, C3HC-type containing 1	274					mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein ubiquitination (GO:0016567)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(6)|large_intestine(10)|lung(2)|prostate(1)|urinary_tract(1)	22	Melanoma(18;0.0435)					TCCTCATACATTGCGAACATG	0.478																																					p.Q274Q	Melanoma(115;540 1606 16325 28853 48167)	Atlas-SNP	.											.	ZC3HC1	45	.	0			c.A822G						PASS	.						73	67	69					7																	129664301		2203	4300	6503	SO:0001819	synonymous_variant	51530	exon7			CATACATTGCGAA	AF151050	CCDS34753.1, CCDS64767.1, CCDS75659.1	7q32.2	2013-01-17			ENSG00000091732	ENSG00000091732		"Zinc fingers, C3HC-type"	29913	protein-coding gene	gene with protein product	"nuclear interaction partner of ALK"					11042152	Standard	XM_005250403		Approved	NIPA	uc003vpi.3	Q86WB0	OTTHUMG00000157648	ENST00000358303.4:c.822A>G	7.37:g.129664301T>C		83	0	0		95	22	0.231579	NM_016478	A6NH66|Q75MF3|Q75MF4|Q8N330|Q96F75|Q9HA34|Q9NVX4|Q9P0R0	Silent	SNP	ENST00000358303.4	37	CCDS34753.1																																																																																			.	.	none		0.478	ZC3HC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349316.1	NM_016478		C	129664301	T	C	129664301	2	2	27	1	0	0	0	0	0	0	0	1	17592	1490	52	3		3	ZC3HC1	7	129664301	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	821024	129664301	29474362	439	10890											
PLXNA4	91584	hgsc.bcm.edu	37	chr7	131883311	131883311	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaaccttgacatgggaggCgatgtcgcgaaattccaggc	11	7	13	10	3	0	1	0	1	0	0	2	4	1	2	2	3	2	1	2	3	2	2	rs62622406	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:131883311C>T	ENST00000359827.3	-	13	3633	c.2671G>A	c.(2671-2673)Gcc>Acc	p.A891T	PLXNA4_ENST00000321063.4_Missense_Mutation_p.A891T			Q9HCM2	PLXA4_HUMAN	plexin A4	891	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						ACATGGGAGGCGATGTCGCGA	0.577													C|||	17	0.00339457	0.0008	0.0014	5008	,	,		19542	0.0		0.0109	False		,,,				2504	0.0041				p.A891T		Atlas-SNP	.											.	PLXNA4	873	.	0			c.G2671A						PASS	.	C	THR/ALA	7,3955		0,7,1974	74	76	75		2671	5.9	1	7	dbSNP_129	75	113,8235		0,113,4061	yes	missense	PLXNA4	NM_020911.1	58	0,120,6035	TT,TC,CC		1.3536,0.1767,0.9748	benign	891/1895	131883311	120,12190	1981	4174	6155	SO:0001583	missense	91584	exon13			GGGAGGCGATGTC	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.2671G>A	7.37:g.131883311C>T	ENSP00000352882:p.Ala891Thr	42	0	0		45	21	0.466667	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	CCDS43646.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	11.07	1.531317	0.27387	0.001767	0.013536	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.75821	-0.97;-0.97	5.94	5.94	0.96194	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.168437	0.52532	D	0.000077	T	0.60586	0.2280	L	0.43923	1.385	0.36252	D	0.853963	P	0.40250	0.709	B	0.37239	0.244	T	0.66693	-0.5859	10	0.13108	T	0.6	.	20.3658	0.98878	0.0:1.0:0.0:0.0	rs62622406	891	Q9HCM2	PLXA4_HUMAN	T	891	ENSP00000323194:A891T;ENSP00000352882:A891T	ENSP00000323194:A891T	A	-	1	0	PLXNA4	131533851	0.986000	0.35501	0.999000	0.59377	0.242000	0.25591	2.642000	0.46596	2.820000	0.97059	0.650000	0.86243	GCC	C|0.991;T|0.009	0.009	strong		0.577	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775		T	131883311	C	T	131883311	3	4	27	1	0	0	0	0	1	0	0	0	12131	768	27	1	3093	1	PLXNA4	7	131883311	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2219010	131883311	27255352	440	10891											
LRGUK	136332	hgsc.bcm.edu	37	chr7	133812351	133812351	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagctggactcggacggagaTgaggaccagggcgagggcga	10	3	20	8	4	0	2	0	1	0	1	1	9	0	5	1	6	1	1	1	6	0	0	rs61732215	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:133812351T>C	ENST00000285928.2	+	1	300	c.231T>C	c.(229-231)gaT>gaC	p.D77D	LRGUK_ENST00000473068.1_3'UTR	NM_144648.1	NP_653249.1	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain containing	77						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						CGGACGGAGATGAGGACCAGG	0.607													C|||	284	0.0567093	0.1717	0.0274	5008	,	,		16505	0.001		0.005	False		,,,				2504	0.0327				p.D77D		Atlas-SNP	.											.	LRGUK	113	.	0			c.T231C						PASS	.	C		710,3696	760.6+/-413.0	61,588,1554	82	79	80		231	-7.9	0	7	dbSNP_129	80	43,8557	817.4+/-406.9	0,43,4257	no	coding-synonymous	LRGUK	NM_144648.1		61,631,5811	CC,CT,TT		0.5,16.1144,5.7896		77/826	133812351	753,12253	2203	4300	6503	SO:0001819	synonymous_variant	136332	exon1			CGGAGATGAGGAC	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.231T>C	7.37:g.133812351T>C		139	0	0		147	73	0.496599	NM_144648	Q2M3I1	Silent	SNP	ENST00000285928.2	37	CCDS5830.1																																																																																			T|0.945;C|0.055	0.055	strong		0.607	LRGUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339442.1	NM_144648		C	133812351	T	C	133812351	2	2	27	1	0	0	0	0	0	0	0	1	8952	1461	51	3		3	LRGUK	7	133812351	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	1929040	133812351	25326312	441	10892											
CNOT4	4850	hgsc.bcm.edu	37	chr7	135047811	135047811	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgtgctgaagggggcgctGtggtgggtctgtgatggagc	4	11	21	5	1	1	2	0	2	1	0	1	3	1	3	0	5	2	2	0	5	1	0	rs200460078	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:135047811G>C	ENST00000451834.1	-	12	2242	c.1959C>G	c.(1957-1959)caC>caG	p.H653Q	CNOT4_ENST00000541284.1_Missense_Mutation_p.H656Q|CNOT4_ENST00000361528.4_Missense_Mutation_p.H582Q|CNOT4_ENST00000473470.1_5'UTR|CNOT4_ENST00000423368.2_Missense_Mutation_p.H585Q			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						AGGGGGCGCTGTGGTGGGTCT	0.587													G|||	4	0.000798722	0.0	0.0	5008	,	,		13429	0.0		0.004	False		,,,				2504	0.0				p.H656Q	Ovarian(51;766 1130 5502 35047 50875)	Atlas-SNP	.											CNOT4_ENST00000541284,NS,carcinoma,0,3	CNOT4	146	3	0			c.C1968G						PASS	.	G	GLN/HIS,GLN/HIS,GLN/HIS,GLN/HIS	3,4123		0,3,2060	115	129	124		1755,1959,1968,1746	5	1	7		124	21,8375		0,21,4177	yes	missense,missense,missense,missense	CNOT4	NM_001190847.1,NM_001190849.1,NM_001190850.1,NM_013316.3	24,24,24,24	0,24,6237	CC,CG,GG		0.2501,0.0727,0.1917	probably-damaging,probably-damaging,probably-damaging,probably-damaging	585/643,653/711,656/714,582/640	135047811	24,12498	2063	4198	6261	SO:0001583	missense	4850	exon12			GGCGCTGTGGTGG	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.1959C>G	7.37:g.135047811G>C	ENSP00000388491:p.His653Gln	110	0	0		139	75	0.539568	NM_001190850	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Missense_Mutation	SNP	ENST00000451834.1	37	CCDS55167.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	18.61	3.662127	0.67700	7.27E-4	0.002501	ENSG00000080802	ENST00000541284;ENST00000451834;ENST00000423368;ENST00000262563;ENST00000361528	T;T;T;T	0.52295	0.67;0.69;0.68;0.68	5.92	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.45657	0.1353	L	0.29908	0.895	0.80722	D	1	P;D;D;D	0.53462	0.932;0.96;0.96;0.96	D;D;D;D	0.69142	0.917;0.962;0.944;0.944	T	0.41124	-0.9526	10	0.14656	T	0.56	-8.6859	15.0604	0.71947	0.0678:0.0:0.9322:0.0	.	653;656;585;582	E7ET38;F8VQP3;O95628-4;O95628-8	.;.;.;.	Q	656;653;585;656;582	ENSP00000445508:H656Q;ENSP00000388491:H653Q;ENSP00000406777:H585Q;ENSP00000354673:H582Q	ENSP00000262563:H656Q	H	-	3	2	CNOT4	134698351	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.869000	0.99810	1.521000	0.48983	0.557000	0.71058	CAC	G|0.998;C|0.002	0.002	strong		0.587	CNOT4-003	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000340670.1	NM_013316		C	135047811	G	C	135047811	3	2	27	1	0	0	0	0	1	0	0	0	3623	1368	48	4	177	4	CNOT4	7	135047811	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1235460	135047811	24090852	442	10893											
CNOT4	4850	hgsc.bcm.edu	37	chr7	135123060	135123060	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	actccacagggtcttccttcGcatcaggactgcgagacatc	9	9	9	14	2	2	1	1	0	1	1	6	3	4	2	2	2	1	1	2	2	0	2	rs17480616	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:135123060G>C	ENST00000315544.5	-	2	299	c.20C>G	c.(19-21)gCg>gGg	p.A7G	CNOT4_ENST00000541284.1_Missense_Mutation_p.A7G|CNOT4_ENST00000361528.4_Missense_Mutation_p.A7G|CNOT4_ENST00000428680.2_Missense_Mutation_p.A7G|CNOT4_ENST00000423368.2_Missense_Mutation_p.A7G|CNOT4_ENST00000356162.4_Missense_Mutation_p.A7G|CNOT4_ENST00000414802.1_Missense_Mutation_p.A7G|CNOT4_ENST00000451834.1_Missense_Mutation_p.A7G	NM_001190848.1	NP_001177777.1	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	7			A -> G (in dbSNP:rs17480616). {ECO:0000269|Ref.3}.		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						GTCTTCCTTCGCATCAGGACT	0.433													G|||	37	0.00738818	0.0023	0.0173	5008	,	,		17128	0.0		0.0209	False		,,,				2504	0.001				p.A7G	Ovarian(51;766 1130 5502 35047 50875)	Atlas-SNP	.											.	CNOT4	146	.	0			c.C20G						PASS	.	G	GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA	17,3759		0,17,1871	67	63	65		20,20,20,20,20,20	1.5	1	7	dbSNP_123	65	228,7992		4,220,3886	yes	missense,missense,missense,missense,missense,missense	CNOT4	NM_001008225.2,NM_001190847.1,NM_001190848.1,NM_001190849.1,NM_001190850.1,NM_013316.3	60,60,60,60,60,60	4,237,5757	CC,CG,GG		2.7737,0.4502,2.0423	benign,benign,benign,benign,benign,benign	7/573,7/643,7/576,7/711,7/714,7/640	135123060	245,11751	1888	4110	5998	SO:0001583	missense	4850	exon2			TCCTTCGCATCAG	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.20C>G	7.37:g.135123060G>C	ENSP00000326731:p.Ala7Gly	163	0	0		98	39	0.397959	NM_001190850	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Missense_Mutation	SNP	ENST00000315544.5	37	CCDS55166.1	27	0.012362637362637362	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	14	0.018469656992084433	G	12.53	1.964625	0.34659	0.004502	0.027737	ENSG00000080802	ENST00000541284;ENST00000451834;ENST00000423368;ENST00000262563;ENST00000361528;ENST00000414802;ENST00000356162;ENST00000428680;ENST00000315544	D;D;D;D;D;D;D;D	0.86164	-2.08;-2.08;-2.08;-2.08;-2.08;-2.08;-2.08;-2.08	5.87	1.55	0.23275	Zinc finger, RING/FYVE/PHD-type (1);	0.373548	0.33938	N	0.004417	T	0.50103	0.1596	N	0.14661	0.345	0.21290	N	0.999735	B;B;B;P;B;B	0.34997	0.211;0.315;0.405;0.479;0.019;0.019	B;B;B;B;B;B	0.31946	0.071;0.138;0.102;0.119;0.022;0.022	T	0.54063	-0.8349	10	0.32370	T	0.25	0.5143	9.3711	0.38254	0.4834:0.0:0.5166:0.0	rs17480616;rs52814664;rs17480616	7;7;7;7;7;7	E7ET38;F8VQP3;O95628;O95628-2;O95628-4;O95628-8	.;.;CNOT4_HUMAN;.;.;.	G	7	ENSP00000445508:A7G;ENSP00000388491:A7G;ENSP00000406777:A7G;ENSP00000354673:A7G;ENSP00000416532:A7G;ENSP00000348485:A7G;ENSP00000399108:A7G;ENSP00000326731:A7G	ENSP00000262563:A7G	A	-	2	0	CNOT4	134773600	0.999000	0.42202	0.976000	0.42696	0.929000	0.56500	1.442000	0.35046	-0.007000	0.14345	0.655000	0.94253	GCG	G|0.983;C|0.017	0.017	strong		0.433	CNOT4-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_013316		C	135123060	G	C	135123060	3	2	27	1	0	0	0	0	1	0	0	0	3623	1087	38	4	2044	4	CNOT4	7	135123060	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	75249	135123060	24015603	443	10894											
KIAA1147	57189	hgsc.bcm.edu	37	chr7	141362558	141362558	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttgggggtctaggcccatGccccgggcatgctctgctgt	3	10	14	14	1	2	0	0	0	2	0	2	0	2	0	4	4	3	3	4	4	1	2	rs375569681		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:141362558G>T	ENST00000536163.1	-	9	1265	c.1266C>A	c.(1264-1266)ggC>ggA	p.G422G	RP5-894A10.6_ENST00000602609.1_RNA|KIAA1147_ENST00000482493.1_Silent_p.G318G	NM_001080392.1	NP_001073861.1	A4D1U4	LCHN_HUMAN	KIAA1147	422										breast(3)|endometrium(4)|kidney(2)|large_intestine(1)|ovary(1)|skin(1)	12	Melanoma(164;0.0171)					CTAGGCCCATGCCCCGGGCAT	0.527																																					p.G422G		Atlas-SNP	.											.	KIAA1147	32	.	0			c.C1266A						PASS	.	G		0,3818		0,0,1909	37	39	38		1266	5.4	1	7		38	2,8234		0,2,4116	no	coding-synonymous	KIAA1147	NM_001080392.1		0,2,6025	TT,TG,GG		0.0243,0.0,0.0166		422/456	141362558	2,12052	1909	4118	6027	SO:0001819	synonymous_variant	57189	exon9			GCCCATGCCCCGG	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.1266C>A	7.37:g.141362558G>T		66	0	0		62	37	0.596774	NM_001080392	Q9ULS3	Silent	SNP	ENST00000536163.1	37	CCDS47726.1																																																																																			.	.	weak		0.527	KIAA1147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349104.1			T	141362558	G	T	141362558	2	4	27	1	0	0	0	0	0	0	0	1	8219	1306	46	4		4	KIAA1147	7	141362558	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	6239498	141362558	17776105	444	10895											
PDIA4	9601	hgsc.bcm.edu	37	chr7	148709061	148709061	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ggtcagaatctccttggaggGaggcccggactgctcgatca	8	8	14	11	2	3	1	2	0	1	1	5	5	3	4	2	5	1	1	2	5	1	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:148709061G>A	ENST00000286091.4	-	6	1088	c.856C>T	c.(856-858)Ccc>Tcc	p.P286S		NM_004911.4	NP_004902.1	P13667	PDIA4_HUMAN	protein disulfide isomerase family A, member 4	286	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)			TCCTTGGAGGGAGGCCCGGAC	0.577																																					p.P286S		Atlas-SNP	.											.	PDIA4	57	.	0			c.C856T						PASS	.						80	76	77					7																	148709061		2203	4300	6503	SO:0001583	missense	9601	exon6			TGGAGGGAGGCCC	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.856C>T	7.37:g.148709061G>A	ENSP00000286091:p.Pro286Ser	70	0	0		60	10	0.166667	NM_004911	A8K4K6|Q549T6	Missense_Mutation	SNP	ENST00000286091.4	37	CCDS5893.1	.	.	.	.	.	.	.	.	.	.	g	12.18	1.862013	0.32884	.	.	ENSG00000155660	ENST00000286091	T	0.19394	2.15	5.14	5.14	0.70334	Thioredoxin-like fold (2);	0.100995	0.64402	D	0.000001	T	0.13114	0.0318	N	0.21583	0.68	0.80722	D	1	P	0.36282	0.546	B	0.22386	0.039	T	0.11567	-1.0582	10	0.16896	T	0.51	.	18.7073	0.91643	0.0:0.0:1.0:0.0	.	286	P13667	PDIA4_HUMAN	S	286	ENSP00000286091:P286S	ENSP00000286091:P286S	P	-	1	0	PDIA4	148339994	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.052000	0.71080	2.423000	0.82170	0.639000	0.83563	CCC	.	.	none		0.577	PDIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317077.1	NM_004911		A	148709061	G	A	148709061	3	1	27	1	0	0	0	0	1	0	0	0	11679	1174	41	2	1101	2	PDIA4	7	148709061	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	7346503	148709061	10429602	445	10896											
SSPO	23145	hgsc.bcm.edu	37	chr7	149520553	149520553	+	RNA	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gacctgccaccctgccagccGggctgctactgccccaaggt	6	6	11	18	1	0	0	0	0	0	0	0	1	0	0	7	2	6	2	7	2	2	1	rs141884347	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:149520553G>A	ENST00000378016.2	+	0	13371							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)			CCTGCCAGCCGGGCTGCTACT	0.627													G|||	48	0.00958466	0.0008	0.013	5008	,	,		17506	0.002		0.0129	False		,,,				2504	0.0235				p.P4457P		Atlas-SNP	.											.	.	.	.	0			c.G13371A						PASS	.	G		5,4069		0,5,2032	34	41	39		13385	-9.9	0.6	7	dbSNP_134	39	118,8248		1,116,4066	yes	coding-notMod3	SSPO	NM_198455.2		1,121,6098	AA,AG,GG		1.4105,0.1227,0.9887			149520553	123,12317	2037	4183	6220			23145	exon92			CCAGCCGGGCTGC	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.149520553G>A		37	0	0		45	18	0.4	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				G|0.990;A|0.010	0.010	strong		0.627	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				A	149520553	G	A	149520553	1	1	27	0	1	0	0	0	0	0	0	0	15204	1103	39	1		1	SSPO	7	149520553	RNA	SNP	G	TCGA-G8-6909-01A-11D-2210-10	811492	149520553	9618110	446	10897											
ABP1	26	hgsc.bcm.edu	37	chr7	150558156	150558156	+	Frame_Shift_Del	DEL	C	C	-																															ttcaacttcttcccagaggaCccctccctggcatccagaga																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:150558156delC	ENST00000493429.1	+	7	2699	c.2115delC	c.(2113-2115)gacfs	p.D705fs	AOC1_ENST00000416793.2_Frame_Shift_Del_p.D724fs|AOC1_ENST00000480582.1_3'UTR|AOC1_ENST00000467291.1_Frame_Shift_Del_p.D705fs|AOC1_ENST00000360937.4_Frame_Shift_Del_p.D705fs			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	705					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)	TCCCAGAGGACCCCTCCCTGG	0.617																																					p.D724fs		Pindel,Atlas-Indel	.											.	ABP1	92	.	0			c.2171delA						PASS	.						63	74	70					7																	150558156		2045	4197	6242	SO:0001589	frameshift_variant	26	exon5			.	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.2115delC	7.37:g.150558156delC	ENSP00000418614:p.Asp705fs	95	0	.		81	17	0.21	NM_001272072	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Frame_Shift_Del	DEL	ENST00000493429.1	37	CCDS43679.1																																																																																			.	.	none		0.617	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091		-	150558156	C	-	150558156	7	5	27	1	0	1	0	1	0	0	0	0	98	506	18	0	2129	0	ABP1	7	150558156	Frame_Shift_Del	DEL	C	TCGA-G8-6909-01A-11D-2210-10	1037603	150558156	8580507	447	10898											
ABCB8	11194	hgsc.bcm.edu	37	chr7	150739054	150739054	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccctcacccacaggagcccGtcctgtttgggacgaccatc	7	7	9	18	2	1	0	1	0	0	0	3	3	2	2	6	2	1	1	6	2	0	1	rs56198402	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:150739054G>A	ENST00000297504.6	+	15	1741	c.1675G>A	c.(1675-1677)Gtc>Atc	p.V559I	ABCB8_ENST00000498578.1_Missense_Mutation_p.V542I|ABCB8_ENST00000356058.4_3'UTR|ABCB8_ENST00000542328.1_Missense_Mutation_p.V454I|ABCB8_ENST00000358849.4_Missense_Mutation_p.V542I			Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 8	559	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)	ACAGGAGCCCGTCCTGTTTGG	0.542													G|||	133	0.0265575	0.0008	0.0476	5008	,	,		19339	0.0208		0.0447	False		,,,				2504	0.0337				p.V542I		Atlas-SNP	.											.	ABCB8	65	.	0			c.G1624A						PASS	.	G	ILE/VAL	34,4372	37.6+/-69.7	0,34,2169	57	59	58		1624	3.8	1	7	dbSNP_129	58	348,8252	118.1+/-177.6	7,334,3959	yes	missense	ABCB8	NM_007188.3	29	7,368,6128	AA,AG,GG		4.0465,0.7717,2.9371	benign	542/719	150739054	382,12624	2203	4300	6503	SO:0001583	missense	11194	exon14			GAGCCCGTCCTGT	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.1675G>A	7.37:g.150739054G>A	ENSP00000297504:p.Val559Ile	31	0	0		42	26	0.619048	NM_007188	A5D8W3|B2RBL8|B3KND2|B4DG02|G3XAP3|O95787|Q53GM0	Missense_Mutation	SNP	ENST00000297504.6	37		67	0.030677655677655676	0	0.0	17	0.04696132596685083	14	0.024475524475524476	36	0.047493403693931395	G	10.61	1.399063	0.25291	0.007717	0.040465	ENSG00000197150	ENST00000358849;ENST00000360651;ENST00000297504;ENST00000542328;ENST00000498578	D;D;D;D	0.90620	-2.7;-2.7;-2.7;-2.7	4.73	3.83	0.44106	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.066008	0.64402	D	0.000013	T	0.45756	0.1358	N	0.10916	0.065	0.80722	D	1	B;B;B;B	0.24963	0.08;0.115;0.099;0.094	B;B;B;B	0.29716	0.047;0.106;0.079;0.079	T	0.65524	-0.6147	10	0.28530	T	0.3	-6.061	11.0243	0.47736	0.093:0.0:0.907:0.0	rs56198402;rs61274547;rs61734191	454;542;559;542	G3XAP3;A5D8W3;Q9NUT2;Q9NUT2-2	.;.;ABCB8_HUMAN;.	I	542;525;559;454;542	ENSP00000351717:V542I;ENSP00000297504:V559I;ENSP00000438776:V454I;ENSP00000418271:V542I	ENSP00000297504:V559I	V	+	1	0	ABCB8	150369987	1.000000	0.71417	1.000000	0.80357	0.487000	0.33371	5.412000	0.66392	2.456000	0.83038	0.462000	0.41574	GTC	G|0.969;A|0.031	0.031	strong		0.542	ABCB8-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351733.2	NM_007188		A	150739054	G	A	150739054	3	1	27	1	0	0	0	0	1	0	0	0	47	1145	40	1	1678	1	ABCB8	7	150739054	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	180898	150739054	8399609	448	10899											
MLL3	58508	hgsc.bcm.edu	37	chr7	151878589	151878589	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttggccttgatatggttccaGgctgggaaaaagcccttgaa	10	11	12	8	0	0	2	0	2	0	0	1	3	1	3	3	4	1	2	3	4	4	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:151878589G>A	ENST00000262189.6	-	36	6574	c.6356C>T	c.(6355-6357)cCt>cTt	p.P2119L	KMT2C_ENST00000355193.2_Missense_Mutation_p.P2119L	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2119	Pro-rich.				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)										TATGGTTCCAGGCTGGGAAAA	0.478																																					p.P2119L		Atlas-SNP	.											.	MLL3	1564	.	0			c.C6356T						PASS	.						104	107	106					7																	151878589		2203	4300	6503	SO:0001583	missense	58508	exon36			GTTCCAGGCTGGG	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.6356C>T	7.37:g.151878589G>A	ENSP00000262189:p.Pro2119Leu	202	0	0		130	74	0.569231	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	G	14.04	2.418230	0.42918	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.84800	-1.9;-1.9	5.11	5.11	0.69529	.	0.157447	0.29551	N	0.011839	D	0.87358	0.6157	L	0.56769	1.78	0.80722	D	1	D;D	0.56521	0.961;0.976	P;P	0.51701	0.617;0.677	D	0.85101	0.0957	10	0.23891	T	0.37	.	18.558	0.91091	0.0:0.0:1.0:0.0	.	2119;1180	Q8NEZ4;Q8NEZ4-2	MLL3_HUMAN;.	L	2119	ENSP00000262189:P2119L;ENSP00000347325:P2119L	ENSP00000262189:P2119L	P	-	2	0	MLL3	151509522	1.000000	0.71417	0.999000	0.59377	0.957000	0.61999	5.577000	0.67444	2.390000	0.81377	0.563000	0.77884	CCT	.	.	none		0.478	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			A	151878589	G	A	151878589	3	1	27	1	0	0	0	0	1	0	0	0	9631	1000	35	2	8475	2	MLL3	7	151878589	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1139535	151878589	7260074	449	10900											
PTPRN2	5799	hgsc.bcm.edu	37	chr7	157929370	157929370	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttggtaaagtctatcatcgtCgtcctgcactccgtcatctg	7	14	8	12	3	4	0	2	0	2	0	8	0	6	0	2	1	1	2	2	1	3	3	rs55645575	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:157929370C>T	ENST00000389418.4	-	8	1159	c.1150G>A	c.(1150-1152)Gac>Aac	p.D384N	PTPRN2_ENST00000404321.2_Missense_Mutation_p.D407N|PTPRN2_ENST00000389416.4_Missense_Mutation_p.D367N|PTPRN2_ENST00000389413.3_Missense_Mutation_p.D384N|PTPRN2_ENST00000409483.1_Missense_Mutation_p.D346N	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	384					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)		CTATCATCGTCGTCCTGCACT	0.443													C|||	27	0.00539137	0.0	0.0072	5008	,	,		17715	0.0		0.0159	False		,,,				2504	0.0061				p.D384N		Atlas-SNP	.											.	PTPRN2	243	.	0			c.G1150A						PASS	.		ASN/ASP,ASN/ASP,ASN/ASP	13,4393	20.2+/-43.8	0,13,2190	194	151	166		1150,1099,1150	-0.7	0	7	dbSNP_129	166	130,8470	66.3+/-128.7	1,128,4171	yes	missense,missense,missense	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	23,23,23	1,141,6361	TT,TC,CC		1.5116,0.2951,1.0995	benign,benign,benign	384/1016,367/999,384/987	157929370	143,12863	2203	4300	6503	SO:0001583	missense	5799	exon8			CATCGTCGTCCTG	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.1150G>A	7.37:g.157929370C>T	ENSP00000374069:p.Asp384Asn	99	0	0		88	32	0.363636	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	14	0.00641025641025641	0	0.0	2	0.0055248618784530384	0	0.0	12	0.0158311345646438	C	4.357	0.065672	0.08388	0.002951	0.015116	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.02916	4.13;4.11;4.13;4.13;4.12	4.47	-0.709	0.11237	.	.	.	.	.	T	0.00695	0.0023	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.10296	0.003;0.002;0.003;0.002;0.002	B;B;B;B;B	0.06405	0.002;0.001;0.002;0.001;0.001	T	0.49194	-0.8965	9	0.17832	T	0.49	.	4.3322	0.11069	0.1523:0.4773:0.0:0.3704	rs55645575	407;346;384;367;384	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	N	346;384;367;384;407	ENSP00000387114:D346N;ENSP00000374064:D384N;ENSP00000374067:D367N;ENSP00000374069:D384N;ENSP00000385464:D407N	ENSP00000374064:D384N	D	-	1	0	PTPRN2	157622131	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.080000	0.14802	-0.123000	0.11745	-1.747000	0.00681	GAC	C|0.989;T|0.011	0.011	strong		0.443	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1			T	157929370	C	T	157929370	3	4	27	1	0	0	0	0	1	0	0	0	12823	884	31	1	1961	1	PTPRN2	7	157929370	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	6050781	157929370	1209293	450	10901											
VIPR2	7434	hgsc.bcm.edu	37	chr7	158828692	158828692	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtccatgcaccgatgcagaCggtggggaggcctgcagaga	10	5	16	10	2	0	2	0	0	0	2	1	5	1	3	3	4	3	3	3	4	0	0	rs145308657		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr7:158828692C>T	ENST00000262178.2	-	8	945	c.760G>A	c.(760-762)Gtc>Atc	p.V254I	VIPR2_ENST00000377633.3_Missense_Mutation_p.V238I|VIPR2_ENST00000402066.1_Missense_Mutation_p.V395I	NM_003382.4	NP_003373.2	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2	254					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)		CCGATGCAGACGGTGGGGAGG	0.612																																					p.V254I	Pancreas(154;1876 1931 2329 17914 20079)	Atlas-SNP	.											.	VIPR2	53	.	0			c.G760A						PASS	.	T	ILE/VAL	0,4406		0,0,2203	66	50	55		760	-2.9	0	7	dbSNP_134	55	2,8598	2.2+/-6.3	0,2,4298	yes	missense	VIPR2	NM_003382.4	29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	254/439	158828692	2,13004	2203	4300	6503	SO:0001583	missense	7434	exon8			TGCAGACGGTGGG	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.760G>A	7.37:g.158828692C>T	ENSP00000262178:p.Val254Ile	68	0	0		56	29	0.517857	NM_003382	Q13053|Q15870|Q53Y09|Q6ZN22|Q9UCW0	Missense_Mutation	SNP	ENST00000262178.2	37	CCDS5950.1	.	.	.	.	.	.	.	.	.	.	c	4.973	0.180779	0.09443	0.0	2.33E-4	ENSG00000106018	ENST00000262178;ENST00000377633;ENST00000402066	T;T;T	0.51574	0.7;0.7;0.7	4.72	-2.87	0.05700	GPCR, family 2-like (1);	0.479321	0.17044	N	0.189218	T	0.23133	0.0559	N	0.16602	0.42	0.09310	N	0.999991	B	0.24882	0.113	B	0.22880	0.042	T	0.16305	-1.0407	9	.	.	.	.	6.6287	0.22845	0.0:0.3749:0.1336:0.4915	.	254	P41587	VIPR2_HUMAN	I	254;238;395	ENSP00000262178:V254I;ENSP00000366860:V238I;ENSP00000384497:V395I	.	V	-	1	0	VIPR2	158521453	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.497000	0.02289	-0.616000	0.05671	-1.616000	0.00795	GTC	C|1.000;T|0.000	0.000	weak		0.612	VIPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322675.1	NM_003382		T	158828692	C	T	158828692	3	4	27	1	0	0	0	0	1	0	0	0	17185	536	19	1	580	1	VIPR2	7	158828692	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	899322	158828692	309971	451	10902											
MFHAS1	9258	hgsc.bcm.edu	37	chr8	8748013	8748013	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcacctcgttctgcacataGcatgggaacttgtaccaagc	10	9	10	12	1	1	0	0	0	1	0	2	1	1	1	2	2	5	5	2	2	4	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:8748013G>C	ENST00000276282.6	-	1	3142	c.2556C>G	c.(2554-2556)tgC>tgG	p.C852W		NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	852										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)		TCTGCACATAGCATGGGAACT	0.507																																					p.C852W	Melanoma(103;1201 2045 17515 28966)	Atlas-SNP	.											.	MFHAS1	58	.	0			c.C2556G						PASS	.						80	76	77					8																	8748013		2203	4300	6503	SO:0001583	missense	9258	exon1			CACATAGCATGGG	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.2556C>G	8.37:g.8748013G>C	ENSP00000276282:p.Cys852Trp	61	0	0		53	30	0.566038	NM_004225	Q96CI0	Missense_Mutation	SNP	ENST00000276282.6	37	CCDS34844.1	.	.	.	.	.	.	.	.	.	.	G	11.37	1.617809	0.28801	.	.	ENSG00000147324	ENST00000276282	T	0.30448	1.53	5.04	4.17	0.49024	.	0.117044	0.64402	D	0.000016	T	0.20210	0.0486	N	0.08118	0	0.58432	D	0.999999	D	0.57571	0.98	P	0.46975	0.533	T	0.04440	-1.0951	10	0.36615	T	0.2	.	12.5332	0.56128	0.0798:0.0:0.9202:0.0	.	852	Q9Y4C4	MFHA1_HUMAN	W	852	ENSP00000276282:C852W	ENSP00000276282:C852W	C	-	3	2	MFHAS1	8785423	1.000000	0.71417	0.973000	0.42090	0.980000	0.70556	5.899000	0.69846	1.359000	0.45940	0.655000	0.94253	TGC	.	.	none		0.507	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225		C	8748013	G	C	8748013	3	2	27	1	0	0	0	0	1	0	0	0	9530	963	34	4	614	4	MFHAS1	8	8748013	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10		8748013	137616009	452	10903			2	46		4	4	1306	N	G_C_A	1.348347e-05
MFHAS1	9258	hgsc.bcm.edu	37	chr8	8748148	8748148	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgggcctggacatgaggcttAagcagcaaccgaatgacatg	12	7	13	9	1	0	2	0	2	0	0	0	4	0	3	2	3	3	3	2	3	3	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:8748148A>C	ENST00000276282.6	-	1	3007	c.2421T>G	c.(2419-2421)ctT>ctG	p.L807L		NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	807										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)		CATGAGGCTTAAGCAGCAACC	0.572																																					p.L807L	Melanoma(103;1201 2045 17515 28966)	Atlas-SNP	.											.	MFHAS1	58	.	0			c.T2421G						PASS	.						67	66	66					8																	8748148		2203	4300	6503	SO:0001819	synonymous_variant	9258	exon1			AGGCTTAAGCAGC	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.2421T>G	8.37:g.8748148A>C		82	0	0		61	35	0.57377	NM_004225	Q96CI0	Silent	SNP	ENST00000276282.6	37	CCDS34844.1																																																																																			.	.	none		0.572	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225		C	8748148	A	C	8748148	2	2	27	1	0	0	0	0	0	0	0	1	9530	349	13	5		5	MFHAS1	8	8748148	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	135	8748148	137615874	453	10904			2	46		4	4	1306	N	G_C_A	1.348347e-05
MFHAS1	9258	hgsc.bcm.edu	37	chr8	8748686	8748686	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtggcgcgggtccctgcagCtaacaggcaacacgggggag	9	4	17	11	3	0	0	0	0	0	0	1	1	1	1	1	5	4	3	1	5	2	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:8748686C>G	ENST00000276282.6	-	1	2469	c.1883G>C	c.(1882-1884)aGc>aCc	p.S628T		NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	628	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)		GTCCCTGCAGCTAACAGGCAA	0.567																																					p.S628T	Melanoma(103;1201 2045 17515 28966)	Atlas-SNP	.											.	MFHAS1	58	.	0			c.G1883C						PASS	.						75	63	67					8																	8748686		2203	4300	6503	SO:0001583	missense	9258	exon1			CTGCAGCTAACAG	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.1883G>C	8.37:g.8748686C>G	ENSP00000276282:p.Ser628Thr	55	0	0		39	15	0.384615	NM_004225	Q96CI0	Missense_Mutation	SNP	ENST00000276282.6	37	CCDS34844.1	.	.	.	.	.	.	.	.	.	.	C	15.29	2.789423	0.49997	.	.	ENSG00000147324	ENST00000276282	D	0.91295	-2.82	5.28	5.28	0.74379	ROC GTPase (1);	0.051489	0.85682	N	0.000000	D	0.90728	0.7090	M	0.71036	2.16	0.58432	D	0.999998	B	0.27791	0.189	B	0.30179	0.112	D	0.89321	0.3640	10	0.66056	D	0.02	.	18.0901	0.89472	0.0:1.0:0.0:0.0	.	628	Q9Y4C4	MFHA1_HUMAN	T	628	ENSP00000276282:S628T	ENSP00000276282:S628T	S	-	2	0	MFHAS1	8786096	1.000000	0.71417	0.992000	0.48379	0.715000	0.41141	7.591000	0.82666	2.736000	0.93811	0.655000	0.94253	AGC	.	.	none		0.567	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225		G	8748686	C	G	8748686	3	3	27	1	0	0	0	0	1	0	0	0	9530	797	28	4	1287	4	MFHAS1	8	8748686	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	538	8748686	137615336	454	10905			2	46		4	4	1306	N	G_C_A	1.348347e-05
MFHAS1	9258	hgsc.bcm.edu	37	chr8	8749318	8749318	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaagtctttcctgcagccttAtgccccatcaggagcagctt	9	11	8	13	0	2	0	1	0	1	0	3	1	3	1	4	1	5	3	4	1	2	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:8749318A>G	ENST00000276282.6	-	1	1837	c.1251T>C	c.(1249-1251)caT>caC	p.H417H		NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	417	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)		CTGCAGCCTTATGCCCCATCA	0.617																																					p.H417H	Melanoma(103;1201 2045 17515 28966)	Atlas-SNP	.											.	MFHAS1	58	.	0			c.T1251C						PASS	.						48	43	44					8																	8749318		2203	4300	6503	SO:0001819	synonymous_variant	9258	exon1			AGCCTTATGCCCC	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.1251T>C	8.37:g.8749318A>G		42	0	0		36	17	0.472222	NM_004225	Q96CI0	Silent	SNP	ENST00000276282.6	37	CCDS34844.1																																																																																			.	.	none		0.617	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225		G	8749318	A	G	8749318	2	3	27	1	0	0	0	0	0	0	0	1	9530	446	16	3		3	MFHAS1	8	8749318	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	632	8749318	137614704	455	10906			2	46		4	4	1306	N	G_C_A	1.348347e-05
RP1L1	94137	hgsc.bcm.edu	37	chr8	10469292	10469292	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggaggtatgggggccggCgagcatgtcctggaccccgc	5	6	19	11	3	0	0	0	0	0	0	1	3	1	2	4	7	1	2	4	7	1	1	rs62490857	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:10469292C>T	ENST00000382483.3	-	4	2539	c.2316G>A	c.(2314-2316)tcG>tcA	p.S772S		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	772					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)		TGGGGGCCGGCGAGCATGTCC	0.662													C|||	152	0.0303514	0.0023	0.0288	5008	,	,		16095	0.001		0.1083	False		,,,				2504	0.0194				p.S772S		Atlas-SNP	.											.	RP1L1	453	.	0			c.G2316A						PASS	.	C		64,3840		0,64,1888	50	57	55		2316	-10.2	0	8	dbSNP_129	55	681,7581		25,631,3475	no	coding-synonymous	RP1L1	NM_178857.5		25,695,5363	TT,TC,CC		8.2426,1.6393,6.1236		772/2401	10469292	745,11421	1952	4131	6083	SO:0001819	synonymous_variant	94137	exon4			GGCCGGCGAGCAT	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.2316G>A	8.37:g.10469292C>T		81	0	0		97	74	0.762887	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																			C|0.945;T|0.055	0.055	strong		0.662	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1			T	10469292	C	T	10469292	2	4	27	1	0	0	0	0	0	0	0	1	13548	755	27	1		1	RP1L1	8	10469292	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1719974	10469292	135894730	456	10907											
C8orf74	203076	hgsc.bcm.edu	37	chr8	10532188	10532188	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggagcgcctgcggaggctTctgaactgggaggagtttga	7	8	18	8	3	1	2	0	2	1	0	1	6	1	6	1	5	3	2	1	5	1	2	rs61729951	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:10532188T>C	ENST00000304519.5	+	2	110	c.81T>C	c.(79-81)ctT>ctC	p.L27L	RP1L1_ENST00000329335.3_Intron|C8orf74_ENST00000524025.1_3'UTR	NM_001040032.1	NP_001035121	Q6P047	CH074_HUMAN	chromosome 8 open reading frame 74	27										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	13				COAD - Colon adenocarcinoma(149;0.0811)		TGCGGAGGCTTCTGAACTGGG	0.577													T|||	23	0.00459265	0.0008	0.0072	5008	,	,		16259	0.0		0.0149	False		,,,				2504	0.002				p.L27L		Atlas-SNP	.											.	C8orf74	28	.	0			c.T81C						PASS	.	T		17,3793		0,17,1888	39	43	42		81	-1.6	0.4	8	dbSNP_129	42	163,8101		3,157,3972	no	coding-synonymous	C8orf74	NM_001040032.1		3,174,5860	CC,CT,TT		1.9724,0.4462,1.4908		27/295	10532188	180,11894	1905	4132	6037	SO:0001819	synonymous_variant	203076	exon2			GAGGCTTCTGAAC	BC038534	CCDS47800.1	8p23.1	2012-04-17			ENSG00000171060	ENSG00000171060			32296	protein-coding gene	gene with protein product							Standard	NM_001040032		Approved		uc003wtd.1	Q6P047	OTTHUMG00000163807	ENST00000304519.5:c.81T>C	8.37:g.10532188T>C		144	0	0		137	105	0.766423	NM_001040032	A2RUD6	Silent	SNP	ENST00000304519.5	37	CCDS47800.1	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	T	1.640	-0.516781	0.04200	0.004462	0.019724	ENSG00000171060	ENST00000521818	.	.	.	5.06	-1.65	0.08291	.	.	.	.	.	T	0.16854	0.0405	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.26950	-1.0088	4	.	.	.	.	7.5808	0.27963	0.0:0.3943:0.3278:0.2779	rs61729951	.	.	.	P	26	.	.	S	+	1	0	C8orf74	10569598	0.002000	0.14202	0.397000	0.26308	0.201000	0.24016	-0.558000	0.05978	-0.316000	0.08690	-0.495000	0.04643	TCT	T|0.992;C|0.008	0.008	strong		0.577	C8orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375675.1	NM_001040032		C	10532188	T	C	10532188	2	2	27	1	0	0	0	0	0	0	0	1	2438	1770	62	3		3	C8orf74	8	10532188	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	62896	10532188	135831834	457	10908											
VPS37A	137492	hgsc.bcm.edu	37	chr8	17123477	17123477	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcaccataaacaacctgacaAttaacattaatatgtgagta	18	11	4	8	0	1	2	1	2	0	0	1	2	1	2	2	0	3	1	2	0	8	5	rs372276569		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:17123477A>G	ENST00000324849.4	+	2	861	c.187A>G	c.(187-189)Att>Gtt	p.I63V	VPS37A_ENST00000324815.3_Missense_Mutation_p.I63V|VPS37A_ENST00000521829.1_Intron	NM_001145152.1|NM_152415.2	NP_001138624.1|NP_689628.2	Q8NEZ2	VP37A_HUMAN	vacuolar protein sorting 37 homolog A (S. cerevisiae)	63					cell death (GO:0008219)|endosomal transport (GO:0016197)|intracellular transport of virus (GO:0075733)|membrane organization (GO:0061024)|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)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|ESCRT I complex (GO:0000813)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)				autonomic_ganglia(1)|breast(1)|kidney(2)|large_intestine(1)|lung(4)|skin(1)	10				Colorectal(111;0.0553)|COAD - Colon adenocarcinoma(73;0.212)		CAACCTGACAATTAACATTAA	0.284																																					p.I63V		Atlas-SNP	.											.	VPS37A	22	.	0			c.A187G						PASS	.	A	,VAL/ILE	1,4405	2.1+/-5.4	0,1,2202	94	96	96		,187	4.8	1	8		96	0,8588		0,0,4294	no	intron,missense	VPS37A	NM_001145152.1,NM_152415.2	,29	0,1,6496	GG,GA,AA		0.0,0.0227,0.0077	,possibly-damaging	,63/398	17123477	1,12993	2203	4294	6497	SO:0001583	missense	137492	exon2			CTGACAATTAACA		CCDS6001.1, CCDS47811.1	8p22	2012-06-29	2006-04-04		ENSG00000155975	ENSG00000155975			24928	protein-coding gene	gene with protein product	"hepatocellular carcinoma related protein 1"	609927	"vacuolar protein sorting 37A (yeast)", "polyglutamine binding protein 2"	PQBP2		15240819, 15218037, 22717650	Standard	NM_152415		Approved	FLJ32642, HCRP1, SPG53	uc003wxj.3	Q8NEZ2	OTTHUMG00000130785	ENST00000324849.4:c.187A>G	8.37:g.17123477A>G	ENSP00000318629:p.Ile63Val	230	0	0		183	42	0.229508	NM_152415	Q336D5|Q6NW27|Q8N3D7|Q8TBL7|Q96DL9	Missense_Mutation	SNP	ENST00000324849.4	37	CCDS6001.1	.	.	.	.	.	.	.	.	.	.	A	13.81	2.348643	0.41599	2.27E-4	0.0	ENSG00000155975	ENST00000324849;ENST00000324815	T	0.56776	0.44	4.77	4.77	0.60923	Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.85682	D	0.000000	T	0.52141	0.1716	M	0.64997	1.995	0.53005	D	0.999963	B	0.33212	0.402	B	0.36186	0.219	T	0.51284	-0.8725	10	0.27785	T	0.31	-20.1891	14.9938	0.71415	1.0:0.0:0.0:0.0	.	63	Q8NEZ2	VP37A_HUMAN	V	63	ENSP00000318629:I63V	ENSP00000318173:I63V	I	+	1	0	VPS37A	17167848	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.108000	0.89559	2.084000	0.62774	0.528000	0.53228	ATT	.	.	weak		0.284	VPS37A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253301.2	NM_152415		G	17123477	A	G	17123477	3	3	27	1	0	0	0	0	1	0	0	0	17220	101	4	3	193	3	VPS37A	8	17123477	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	6591289	17123477	129240545	458	10909											
MTUS1	57509	hgsc.bcm.edu	37	chr8	17611916	17611916	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aggttcacaggtgcctccttCgagtctggtatgtttttaag	7	15	11	8	1	2	0	1	0	1	0	4	1	3	0	2	3	1	3	2	3	2	6	rs61740538	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:17611916C>T	ENST00000262102.6	-	2	1625	c.1401G>A	c.(1399-1401)tcG>tcA	p.S467S	MTUS1_ENST00000519263.1_Silent_p.S467S|MTUS1_ENST00000381869.3_Silent_p.S467S|MTUS1_ENST00000381862.3_Silent_p.S467S	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	467					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)		GTGCCTCCTTCGAGTCTGGTA	0.398													C|||	34	0.00678914	0.0015	0.0086	5008	,	,		19744	0.0		0.0229	False		,,,				2504	0.0031				p.S467S		Atlas-SNP	.											.	MTUS1	144	.	0			c.G1401A						PASS	.	C	,	9,3729		0,9,1860	154	146	149		1401,1401	2.8	0	8	dbSNP_129	149	219,8015		4,211,3902	no	coding-synonymous,coding-synonymous	MTUS1	NM_001001924.2,NM_001001925.2	,	4,220,5762	TT,TC,CC		2.6597,0.2408,1.9044	,	467/1271,467/1217	17611916	228,11744	1869	4117	5986	SO:0001819	synonymous_variant	57509	exon2			CTCCTTCGAGTCT	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.1401G>A	8.37:g.17611916C>T		214	0	0		145	26	0.17931	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Silent	SNP	ENST00000262102.6	37	CCDS43717.1																																																																																			C|0.982;T|0.018	0.018	strong		0.398	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		T	17611916	C	T	17611916	2	4	27	1	0	0	0	0	0	0	0	1	9974	871	31	1		1	MTUS1	8	17611916	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	488439	17611916	128752106	459	10910											
ADAM28	10863	hgsc.bcm.edu	37	chr8	24177788	24177788	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcaggaacatgagaaatacAtagaatattatttggtcctg	15	13	8	5	0	1	2	1	1	0	2	2	4	2	3	1	2	2	0	1	2	7	6	rs200839167		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:24177788A>G	ENST00000265769.4	+	7	726	c.616A>G	c.(616-618)Ata>Gta	p.I206V	ADAM28_ENST00000437154.2_Missense_Mutation_p.I206V|RP11-624C23.1_ENST00000519689.1_RNA|ADAM28_ENST00000397649.3_5'UTR|RP11-624C23.1_ENST00000523700.1_RNA|RP11-624C23.1_ENST00000518988.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAM28_ENST00000540823.1_5'UTR	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	206	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)		TGAGAAATACATAGAATATTA	0.303																																					p.I206V	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											.	ADAM28	100	.	0			c.A616G						PASS	.	A	VAL/ILE,VAL/ILE	0,4406		0,0,2203	88	96	93		616,616	1.7	0.8	8		93	4,8578	3.7+/-12.6	0,4,4287	no	missense,missense	ADAM28	NM_014265.4,NM_021777.3	29,29	0,4,6490	GG,GA,AA		0.0466,0.0,0.0308	benign,benign	206/776,206/541	24177788	4,12984	2203	4291	6494	SO:0001583	missense	10863	exon7			AAATACATAGAAT	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.616A>G	8.37:g.24177788A>G	ENSP00000265769:p.Ile206Val	96	0	0		91	19	0.208791	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Missense_Mutation	SNP	ENST00000265769.4	37	CCDS34865.1	.	.	.	.	.	.	.	.	.	.	A	8.894	0.954625	0.18431	0.0	4.66E-4	ENSG00000042980	ENST00000265769;ENST00000437154	T;T	0.63580	-0.05;-0.05	5.34	1.71	0.24356	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	.	.	.	.	T	0.34454	0.0898	N	0.05351	-0.065	0.58432	D	0.999999	B;B	0.18013	0.02;0.025	B;B	0.29862	0.068;0.108	T	0.21621	-1.0240	9	0.02654	T	1	.	6.5373	0.22361	0.7202:0.0:0.2798:0.0	.	206;206	Q9UKQ2;Q9UKQ2-2	ADA28_HUMAN;.	V	206	ENSP00000265769:I206V;ENSP00000393699:I206V	ENSP00000265769:I206V	I	+	1	0	ADAM28	24233733	0.039000	0.19947	0.825000	0.32803	0.758000	0.43043	0.086000	0.14935	0.429000	0.26202	0.533000	0.62120	ATA	A|0.999;G|0.001	0.001	weak		0.303	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778		G	24177788	A	G	24177788	3	3	27	1	0	0	0	0	1	0	0	0	246	217	8	3	642	3	ADAM28	8	24177788	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	6565872	24177788	122186234	460	10911											
DOCK5	80005	hgsc.bcm.edu	37	chr8	25220581	25220581	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggacttcctcatggaaactTttatcatgttcaaggacctg	11	13	8	9	0	3	0	3	0	0	0	4	3	4	3	2	3	1	1	2	3	3	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:25220581T>A	ENST00000276440.7	+	29	3012	c.2968T>A	c.(2968-2970)Ttt>Att	p.F990I		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	990					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)		CATGGAAACTTTTATCATGTT	0.458																																					p.F990I	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											.	DOCK5	167	.	0			c.T2968A						PASS	.						136	134	135					8																	25220581		2203	4300	6503	SO:0001583	missense	80005	exon29			GAAACTTTTATCA		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.2968T>A	8.37:g.25220581T>A	ENSP00000276440:p.Phe990Ile	120	0	0		84	47	0.559524	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Missense_Mutation	SNP	ENST00000276440.7	37	CCDS6047.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	34|34	5.392449|5.392449	0.96009|0.96009	.|.	.|.	ENSG00000147459|ENSG00000147459	ENST00000276440|ENST00000444569	T|.	0.26223|.	1.75|.	5.68|5.68	5.68|5.68	0.88126|0.88126	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.79281|0.79281	0.4419|0.4419	M|M	0.85542|0.85542	2.76|2.76	0.80722|0.80722	D|D	1|1	P;P;D|.	0.56968|.	0.94;0.898;0.978|.	P;P;P|.	0.57620|.	0.824;0.642;0.824|.	T|T	0.81795|0.81795	-0.0769|-0.0769	10|6	0.72032|.	D|.	0.01|.	.|.	15.9289|15.9289	0.79644|0.79644	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	980;765;990|.	D3DSS6;Q68DL4;Q9H7D0|.	.;.;DOCK5_HUMAN|.	I|Y	990|761	ENSP00000276440:F990I|.	ENSP00000276440:F990I|.	F|F	+|+	1|2	0|0	DOCK5|DOCK5	25276498|25276498	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.977000|0.977000	0.68977|0.68977	7.991000|7.991000	0.88244|0.88244	2.173000|2.173000	0.68751|0.68751	0.528000|0.528000	0.53228|0.53228	TTT|TTT	.	.	none		0.458	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940		A	25220581	T	A	25220581	3	1	27	1	0	0	0	0	1	0	0	0	4692	1841	64	5	3082	5	DOCK5	8	25220581	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	1042793	25220581	121143441	461	10912											
RAB11FIP1	80223	hgsc.bcm.edu	37	chr8	37732509	37732509	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagtccttggtggaagattcGgagagctgcctgtcagaaga	10	9	15	7	1	1	4	1	0	0	4	3	7	2	5	2	3	2	1	2	3	2	2	rs369997427		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:37732509G>A	ENST00000330843.4	-	3	1158	c.1146C>T	c.(1144-1146)tcC>tcT	p.S382S	RAB11FIP1_ENST00000287263.4_Silent_p.S382S|RAB11FIP1_ENST00000523182.1_5'Flank|RAB11FIP1_ENST00000522727.1_Silent_p.S234S|RAB11FIP1_ENST00000524118.1_Silent_p.S234S	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	382					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)			TGGAAGATTCGGAGAGCTGCC	0.567																																					p.S382S		Atlas-SNP	.											.	RAB11FIP1	105	.	0			c.C1146T						PASS	.						59	60	60					8																	37732509		2203	4300	6503	SO:0001819	synonymous_variant	80223	exon3			AGATTCGGAGAGC	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.1146C>T	8.37:g.37732509G>A		90	0	0		87	24	0.275862	NM_025151	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Silent	SNP	ENST00000330843.4	37	CCDS34882.1																																																																																			.	.	weak		0.567	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151		A	37732509	G	A	37732509	2	1	27	1	0	0	0	0	0	0	0	1	12908	1103	39	1		1	RAB11FIP1	8	37732509	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	12511928	37732509	108631513	462	10913											
ADAM32	203102	hgsc.bcm.edu	37	chr8	39044565	39044565	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ataatgaatccagaagttgtGtaagttttaacaatttattt	15	17	6	3	0	0	2	0	1	0	1	1	2	1	2	1	0	1	3	1	0	7	8			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:39044565G>A	ENST00000379907.4	+	11	1179		c.e11+1		ADAM32_ENST00000519315.1_Intron|ADAM32_ENST00000437682.2_Intron	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32							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)			CAGAAGTTGTGTAAGTTTTAA	0.313																																					.		Atlas-SNP	.											.	ADAM32	70	.	0			c.1052+1G>A						PASS	.						72	70	71					8																	39044565		1807	4076	5883	SO:0001630	splice_region_variant	203102	exon11			AGTTGTGTAAGTT	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.1052+1G>A	8.37:g.39044565G>A		44	0	0		38	18	0.473684	NM_145004	Q8TC42	Splice_Site	SNP	ENST00000379907.4	37	CCDS47846.1	.	.	.	.	.	.	.	.	.	.	G	13.48	2.249507	0.39797	.	.	ENSG00000197140	ENST00000379907	.	.	.	5.47	5.47	0.80525	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1764	0.72916	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ADAM32	39163722	1.000000	0.71417	0.992000	0.48379	0.318000	0.28184	4.950000	0.63603	2.734000	0.93682	0.650000	0.86243	.	.	.	none		0.313	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004	Intron	A	39044565	G	A	39044565	5	1	27	1	0	0	0	0	0	0	1	0	249	1391	48	2	1095	2	ADAM32	8	39044565	Splice_Site	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1312056	39044565	107319457	463	10914											
ADAM32	203102	hgsc.bcm.edu	37	chr8	39068684	39068684	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caatccaatggtgtgaagacTtttagcagttgcagtttgag	11	13	11	6	0	0	3	0	2	0	1	1	3	1	3	1	1	2	4	1	1	4	4	rs61753544	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:39068684T>A	ENST00000379907.4	+	12	1201	c.1074T>A	c.(1072-1074)acT>acA	p.T358T	ADAM32_ENST00000519315.1_Intron|ADAM32_ENST00000437682.2_Intron	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	358	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)			GTGTGAAGACTTTTAGCAGTT	0.323													T|||	2	0.000399361	0.0	0.0014	5008	,	,		16759	0.0		0.001	False		,,,				2504	0.0				p.T358T		Atlas-SNP	.											.	ADAM32	70	.	0			c.T1074A						PASS	.	T		5,3635		0,5,1815	102	101	101		1074	-2.5	1	8	dbSNP_129	101	25,8143		0,25,4059	no	coding-synonymous	ADAM32	NM_145004.5		0,30,5874	AA,AT,TT		0.3061,0.1374,0.2541		358/788	39068684	30,11778	1820	4084	5904	SO:0001819	synonymous_variant	203102	exon12			GAAGACTTTTAGC	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.1074T>A	8.37:g.39068684T>A		89	0	0		71	56	0.788732	NM_145004	Q8TC42	Silent	SNP	ENST00000379907.4	37	CCDS47846.1																																																																																			T|0.999;A|0.001	0.001	strong		0.323	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004		A	39068684	T	A	39068684	2	1	27	1	0	0	0	0	0	0	0	1	249	1596	56	5		5	ADAM32	8	39068684	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	24119	39068684	107295338	464	10915											
SLC20A2	6575	hgsc.bcm.edu	37	chr8	42294592	42294592	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caggaggtgaacctcgggtgCgtccttctcctccttctcct	4	12	10	15	2	2	1	0	1	2	0	7	2	4	2	5	3	2	0	5	3	1	2	rs79577461	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:42294592C>T	ENST00000342228.3	-	8	1807	c.1438G>A	c.(1438-1440)Gca>Aca	p.A480T	SLC20A2_ENST00000520179.1_Missense_Mutation_p.A480T|SLC20A2_ENST00000520262.1_Missense_Mutation_p.A480T	NM_006749.4	NP_006740.1	Q08357	S20A2_HUMAN	solute carrier family 20 (phosphate transporter), member 2	480					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)			ACCTCGGGTGCGTCCTTCTCC	0.637													C|||	29	0.00579073	0.0008	0.013	5008	,	,		16739	0.0		0.0159	False		,,,				2504	0.0031				p.A480T		Atlas-SNP	.											.	SLC20A2	64	.	0			c.G1438A						PASS	.	C	THR/ALA	26,4380	32.6+/-62.9	0,26,2177	89	58	69		1438	-4	0	8	dbSNP_132	69	187,8413	83.7+/-146.2	3,181,4116	yes	missense	SLC20A2	NM_006749.3	58	3,207,6293	TT,TC,CC		2.1744,0.5901,1.6377	benign	480/653	42294592	213,12793	2203	4300	6503	SO:0001583	missense	6575	exon8			CGGGTGCGTCCTT		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.1438G>A	8.37:g.42294592C>T	ENSP00000340465:p.Ala480Thr	32	0	0		17	4	0.235294	NM_001257181		Missense_Mutation	SNP	ENST00000342228.3	37	CCDS6132.1	15	0.006868131868131868	0	0.0	6	0.016574585635359115	0	0.0	9	0.011873350923482849	C	4.778	0.144587	0.09134	0.005901	0.021744	ENSG00000168575	ENST00000342228;ENST00000520262;ENST00000520179	D;D;D	0.89746	-2.56;-2.56;-2.56	5.63	-4.0	0.04057	.	0.358640	0.34828	N	0.003654	T	0.44871	0.1314	N	0.01438	-0.865	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.59118	-0.7514	10	0.11485	T	0.65	-2.0977	4.5824	0.12266	0.2622:0.3593:0.0:0.3785	.	480	Q08357	S20A2_HUMAN	T	480	ENSP00000340465:A480T;ENSP00000429754:A480T;ENSP00000429712:A480T	ENSP00000340465:A480T	A	-	1	0	SLC20A2	42413749	0.999000	0.42202	0.015000	0.15790	0.157000	0.22087	0.734000	0.26101	-1.008000	0.03404	-0.482000	0.04802	GCA	C|0.985;T|0.015	0.015	strong		0.637	SLC20A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377578.1			T	42294592	C	T	42294592	3	4	27	1	0	0	0	0	1	0	0	0	14454	768	27	1	536	1	SLC20A2	8	42294592	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3225908	42294592	104069430	465	10916											
PXDNL	137902	hgsc.bcm.edu	37	chr8	52321238	52321238	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcagggcggacagctccgtGgccatcctgttgtgttcccg	4	11	13	13	3	1	0	1	0	0	0	4	1	4	1	4	3	1	3	4	3	0	3	rs141024159	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:52321238G>A	ENST00000356297.4	-	17	3046	c.2946C>T	c.(2944-2946)gcC>gcT	p.A982A	PXDNL_ENST00000543296.1_Silent_p.A982A	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	982					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)				ACAGCTCCGTGGCCATCCTGT	0.647													G|||	29	0.00579073	0.0008	0.0058	5008	,	,		16344	0.0		0.0219	False		,,,				2504	0.002				p.A982A		Atlas-SNP	.											.	PXDNL	414	.	0			c.C2946T						PASS	.	G		9,4085		0,9,2038	17	20	19		2946	-2.5	0	8	dbSNP_134	19	127,8265		1,125,4070	no	coding-synonymous	PXDNL	NM_144651.4		1,134,6108	AA,AG,GG		1.5133,0.2198,1.0892		982/1464	52321238	136,12350	2047	4196	6243	SO:0001819	synonymous_variant	137902	exon17			CTCCGTGGCCATC		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.2946C>T	8.37:g.52321238G>A		75	0	0		67	46	0.686567	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Silent	SNP	ENST00000356297.4	37	CCDS47855.1	23	0.010531135531135532	0	0.0	4	0.011049723756906077	0	0.0	19	0.025065963060686015	G	0.093	-1.164305	0.01673	0.002198	0.015133	ENSG00000147485	ENST00000522933	.	.	.	4.47	-2.51	0.06365	.	.	.	.	.	T	0.16085	0.0387	.	.	.	0.52501	D	0.99995	.	.	.	.	.	.	T	0.21484	-1.0244	4	.	.	.	.	0.455	0.00507	0.3332:0.127:0.2814:0.2584	.	.	.	.	L	101	.	.	P	-	2	0	PXDNL	52483791	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.056000	0.03489	-1.110000	0.02992	-0.175000	0.13238	CCA	G|0.989;A|0.011	0.011	strong		0.647	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		A	52321238	G	A	52321238	2	1	27	1	0	0	0	0	0	0	0	1	12863	1335	47	2		2	PXDNL	8	52321238	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	10026646	52321238	94042784	466	10917											
UBXN2B	137886	hgsc.bcm.edu	37	chr8	59329496	59329496	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacagtcttcaagagcccaCggacaccacctcaacggtaa	13	5	7	16	2	3	1	2	0	1	1	3	2	3	2	4	2	2	1	4	2	3	2	rs373559127	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:59329496C>T	ENST00000399598.2	+	2	294	c.172C>T	c.(172-174)Cgg>Tgg	p.R58W	UBXN2B_ENST00000522978.1_3'UTR	NM_001077619.1	NP_001071087.1	Q14CS0	UBX2B_HUMAN	UBX domain protein 2B	58						endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	13						CAAGAGCCCACGGACACCACC	0.333													C|||	2	0.000399361	0.0	0.0	5008	,	,		15290	0.0		0.0	False		,,,				2504	0.002				p.R58W		Atlas-SNP	.											UBXN2B,NS,carcinoma,-1,1	UBXN2B	36	1	0			c.C172T						PASS	.	C	TRP/ARG	0,3690		0,0,1845	87	75	79		172	2.4	1	8		79	1,8187		0,1,4093	no	missense	UBXN2B	NM_001077619.1	101	0,1,5938	TT,TC,CC		0.0122,0.0,0.0084	probably-damaging	58/332	59329496	1,11877	1845	4094	5939	SO:0001583	missense	137886	exon2			AGCCCACGGACAC	AK054658	CCDS43741.1	8q12.1	2008-08-08			ENSG00000215114	ENSG00000215114		"UBX domain containing"	27035	protein-coding gene	gene with protein product		610686				8619474, 9110174	Standard	NM_001077619		Approved	p37	uc003xtl.3	Q14CS0	OTTHUMG00000164300	ENST00000399598.2:c.172C>T	8.37:g.59329496C>T	ENSP00000382507:p.Arg58Trp	33	0	0		41	14	0.341463	NM_001077619	B3KWZ3	Missense_Mutation	SNP	ENST00000399598.2	37	CCDS43741.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.49|18.49	3.635959|3.635959	0.67130|0.67130	0.0|0.0	1.22E-4|1.22E-4	ENSG00000215114|ENSG00000215114	ENST00000399598|ENST00000521796	T|.	0.48522|.	0.81|.	5.62|5.62	2.44|2.44	0.29823|0.29823	.|.	0.547615|.	0.14599|.	U|.	0.309721|.	T|T	0.49525|0.49525	0.1562|0.1562	L|L	0.54323|0.54323	1.7|1.7	0.29724|0.29724	N|N	0.838446|0.838446	D|.	0.71674|.	0.998|.	P|.	0.53185|.	0.72|.	T|T	0.47774|0.47774	-0.9091|-0.9091	10|5	0.72032|.	D|.	0.01|.	-12.2333|-12.2333	11.203|11.203	0.48751|0.48751	0.6042:0.3958:0.0:0.0|0.6042:0.3958:0.0:0.0	.|.	58|.	Q14CS0|.	UBX2B_HUMAN|.	W|M	58|3	ENSP00000382507:R58W|.	ENSP00000382507:R58W|.	R|T	+|+	1|2	2|0	UBXN2B|UBXN2B	59492050|59492050	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.995000|0.995000	0.86356|0.86356	0.723000|0.723000	0.25939|0.25939	0.670000|0.670000	0.31165|0.31165	0.563000|0.563000	0.77884|0.77884	CGG|ACG	.	.	weak		0.333	UBXN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378184.1	NM_001077619		T	59329496	C	T	59329496	3	4	27	1	0	0	0	0	1	0	0	0	16930	527	19	1	178	1	UBXN2B	8	59329496	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	7008258	59329496	87034526	467	10918											
NSMAF	8439	hgsc.bcm.edu	37	chr8	59508166	59508166	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aactgcagtttggtgatgttAttccaggccagtgttttgct	7	16	11	7	0	0	1	0	1	0	0	1	1	1	1	2	2	3	5	2	2	2	5	rs149564750	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:59508166A>G	ENST00000038176.3	-	22	2057	c.1845T>C	c.(1843-1845)aaT>aaC	p.N615N	NSMAF_ENST00000427130.2_Silent_p.N646N	NM_003580.3	NP_003571.2	Q92636	FAN_HUMAN	neutral sphingomyelinase (N-SMase) activation associated factor	615					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)				TGGTGATGTTATTCCAGGCCA	0.403													A|||	24	0.00479233	0.0	0.0101	5008	,	,		18010	0.0		0.0139	False		,,,				2504	0.0031				p.N646N		Atlas-SNP	.											.	NSMAF	156	.	0			c.T1938C						PASS	.	A	,	6,4400	11.4+/-27.6	0,6,2197	196	181	186		1938,1845	1.1	0.8	8	dbSNP_134	186	79,8521	44.9+/-103.4	1,77,4222	no	coding-synonymous,coding-synonymous	NSMAF	NM_001144772.1,NM_003580.3	,	1,83,6419	GG,GA,AA		0.9186,0.1362,0.6535	,	646/949,615/918	59508166	85,12921	2203	4300	6503	SO:0001819	synonymous_variant	8439	exon22			GATGTTATTCCAG	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.1845T>C	8.37:g.59508166A>G		270	0	0		185	41	0.221622	NM_001144772	B4DFB0|E9PCH0|Q8IW26	Silent	SNP	ENST00000038176.3	37	CCDS6173.1																																																																																			A|0.994;G|0.006	0.006	strong		0.403	NSMAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378384.1	NM_003580		G	59508166	A	G	59508166	2	3	27	1	0	0	0	0	0	0	0	1	10683	446	16	3		3	NSMAF	8	59508166	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	178670	59508166	86855856	468	10919											
NCOA2	10499	hgsc.bcm.edu	37	chr8	71126255	71126255	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaaaatcaactctgcaagttCttctatatatttattttcct	13	18	2	8	0	4	0	1	0	3	0	5	0	5	0	1	0	2	2	1	0	8	9			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:71126255C>T	ENST00000452400.2	-	4	323	c.142G>A	c.(142-144)Gaa>Aaa	p.E48K		NM_006540.2	NP_006531.1	Q15596	NCOA2_HUMAN	nuclear receptor coactivator 2	48	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				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)			TCTGCAAGTTCTTCTATATAT	0.299			T	"RUNXBP2, HEY1"	"AML, Chondrosarcoma"																																p.E48K		Atlas-SNP	.		Dom	yes		8	8q13.1	10499	nuclear receptor coactivator 2 (TIF2)		L	NCOA2,NS,carcinoma,0,1	NCOA2	147	1	0			c.G142A						PASS	.						111	101	104					8																	71126255		1783	4058	5841	SO:0001583	missense	10499	exon4			CAAGTTCTTCTAT	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.142G>A	8.37:g.71126255C>T	ENSP00000399968:p.Glu48Lys	108	0	0		77	4	0.0519481	NM_006540	Q14CD2	Missense_Mutation	SNP	ENST00000452400.2	37	CCDS47872.1	.	.	.	.	.	.	.	.	.	.	C	34	5.304743	0.95601	.	.	ENSG00000140396	ENST00000452400	T	0.02446	4.29	5.53	5.53	0.82687	Helix-loop-helix DNA-binding (4);	0.000000	0.85682	D	0.000000	T	0.19046	0.0457	M	0.82630	2.6	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.00191	-1.1936	10	0.87932	D	0	.	19.466	0.94939	0.0:1.0:0.0:0.0	.	48	Q15596	NCOA2_HUMAN	K	48	ENSP00000399968:E48K	ENSP00000399968:E48K	E	-	1	0	NCOA2	71288809	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.607000	0.88179	0.655000	0.94253	GAA	.	.	none		0.299	NCOA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379696.1			T	71126255	C	T	71126255	3	4	27	1	0	0	0	0	1	0	0	0	10238	922	32	2	4332	2	NCOA2	8	71126255	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	11618089	71126255	75237767	469	10920											
RAD54B	25788	hgsc.bcm.edu	37	chr8	95423464	95423464	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgaaggcttacaccaaacAacactgaaatatttaactag	17	11	5	8	0	0	2	0	2	0	0	0	2	0	2	1	1	4	1	1	1	8	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:95423464A>G	ENST00000336148.5	-	4	508	c.384T>C	c.(382-384)gtT>gtC	p.V128V		NM_012415.3	NP_036547.1	Q9Y620	RA54B_HUMAN	RAD54 homolog B (S. cerevisiae)	128					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)			TACACCAAACAACACTGAAAT	0.328								Direct reversal of damage;Homologous recombination																													p.V128V		Atlas-SNP	.											.	RAD54B	88	.	0			c.T384C						PASS	.						100	101	101					8																	95423464		2202	4297	6499	SO:0001819	synonymous_variant	25788	exon4			CCAAACAACACTG	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.384T>C	8.37:g.95423464A>G		259	0	0		240	111	0.4625	NM_012415	F6WBS8	Silent	SNP	ENST00000336148.5	37	CCDS6262.1																																																																																			.	.	none		0.328	RAD54B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257806.3	NM_012415		G	95423464	A	G	95423464	2	3	27	1	0	0	0	0	0	0	0	1	13007	117	5	3		3	RAD54B	8	95423464	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	24297209	95423464	50940558	470	10921											
PABPC1	26986	hgsc.bcm.edu	37	chr8	101721785	101721785	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tacacttgccattctctgcaTatactggttagtgaggtgag	9	14	10	8	0	1	2	0	2	1	0	2	2	1	2	1	2	4	2	1	2	4	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:101721785T>A	ENST00000318607.5	-	8	2275	c.1147A>T	c.(1147-1149)Atg>Ttg	p.M383L	AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000519596.1_5'UTR|PABPC1_ENST00000522387.1_Missense_Mutation_p.M351L|PABPC1_ENST00000519004.1_Missense_Mutation_p.M338L	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	383					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)			ATTCTCTGCATATACTGGTTA	0.493																																					p.M383L		Atlas-SNP	.											.	PABPC1	76	.	0			c.A1147T						PASS	.						168	142	151					8																	101721785		2203	4300	6503	SO:0001583	missense	26986	exon8			TCTGCATATACTG	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.1147A>T	8.37:g.101721785T>A	ENSP00000313007:p.Met383Leu	256	0	0		220	73	0.331818	NM_002568	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.08|19.08	3.757792|3.757792	0.69648|0.69648	.|.	.|.	ENSG00000070756|ENSG00000070756	ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387|ENST00000519596	T;T;T|.	0.32023|.	1.52;1.47;2.53|.	5.19|5.19	5.19|5.19	0.71726|0.71726	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.76601|0.76601	0.4010|0.4010	M|M	0.84846|0.84846	2.72|2.72	0.58432|0.58432	D|D	0.999995|0.999995	B;B;B|.	0.21452|.	0.043;0.056;0.025|.	B;B;B|.	0.23150|.	0.033;0.044;0.019|.	T|T	0.75736|0.75736	-0.3213|-0.3213	10|6	0.48119|0.23891	T|T	0.1|0.37	.|.	15.3415|15.3415	0.74300|0.74300	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	351;383;383|.	E7ERJ7;B3KT93;P11940|.	.;.;PABP1_HUMAN|.	L|F	383;383;338;351|215	ENSP00000313007:M383L;ENSP00000429594:M338L;ENSP00000429395:M351L|.	ENSP00000313007:M383L|ENSP00000430068:Y215F	M|Y	-|-	1|2	0|0	PABPC1|PABPC1	101790961|101790961	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.968000|7.968000	0.87980|0.87980	2.083000|2.083000	0.62718|0.62718	0.533000|0.533000	0.62120|0.62120	ATG|TAT	.	.	none		0.493	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568		A	101721785	T	A	101721785	3	1	27	1	0	0	0	0	1	0	0	0	11372	1406	49	5	791	5	PABPC1	8	101721785	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	6298321	101721785	44642237	471	10922											
MTSS1	9788	hgsc.bcm.edu	37	chr8	125568485	125568485	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcatcaccctggtggcagcCgatacagtcatgctccgtgg	8	8	12	13	2	2	0	2	0	0	0	3	1	3	0	3	3	4	3	3	3	1	1	rs145509745		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:125568485C>T	ENST00000518547.1	-	12	1865	c.1392G>A	c.(1390-1392)tcG>tcA	p.S464S	MTSS1_ENST00000524090.1_Silent_p.S354S|MTSS1_ENST00000325064.5_Silent_p.S468S|NDUFB9_ENST00000522532.1_Intron|MTSS1_ENST00000354184.4_Silent_p.S182S|MTSS1_ENST00000378017.3_Silent_p.S439S|MTSS1_ENST00000431961.2_Silent_p.S182S|MTSS1_ENST00000523587.1_5'UTR|MTSS1_ENST00000395508.2_Silent_p.S238S	NM_001282971.1|NM_014751.4	NP_001269900.1|NP_055566.3	O43312	MTSS1_HUMAN	metastasis suppressor 1	464					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)			TGGTGGCAGCCGATACAGTCA	0.642																																					p.S464S	Esophageal Squamous(160;622 1893 3862 8546 12509)	Atlas-SNP	.											.	MTSS1	79	.	0			c.G1392A						PASS	.	C		0,4406		0,0,2203	78	66	70		1392	-6.7	0.8	8	dbSNP_134	70	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MTSS1	NM_014751.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		464/756	125568485	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9788	exon12			GGCAGCCGATACA	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.1392G>A	8.37:g.125568485C>T		149	0	0		131	68	0.519084	NM_014751	J3KNK6|Q8TCA2|Q96RX2	Silent	SNP	ENST00000518547.1	37	CCDS6353.1	.	.	.	.	.	.	.	.	.	.	C	8.528	0.870352	0.17322	0.0	1.16E-4	ENSG00000170873	ENST00000519168;ENST00000523179	.	.	.	4.65	-6.73	0.01749	.	.	.	.	.	T	0.37839	0.1018	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39663	-0.9603	4	.	.	.	-9.0128	3.2915	0.06950	0.2562:0.1322:0.0856:0.526	.	.	.	.	S	252;247	.	.	G	-	1	0	MTSS1	125637666	0.000000	0.05858	0.803000	0.32268	0.967000	0.64934	-3.210000	0.00556	-1.401000	0.02058	-0.538000	0.04264	GGC	C|1.000;T|0.000	0.000	weak		0.642	MTSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109625.3	NM_014751		T	125568485	C	T	125568485	2	4	27	1	0	0	0	0	0	0	0	1	9971	639	23	1		1	MTSS1	8	125568485	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	23846700	125568485	20795537	472	10923											
TMEM71	137835	hgsc.bcm.edu	37	chr8	133764112	133764112	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttgtcgcacaggaagctgTcttcagtccaaatatagtag	11	12	9	9	1	2	0	1	0	1	0	4	1	3	1	1	1	1	3	1	1	5	5	rs117725783	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:133764112T>C	ENST00000356838.3	-	4	375	c.233A>G	c.(232-234)gAc>gGc	p.D78G	TMEM71_ENST00000517538.1_5'UTR|TMEM71_ENST00000523829.1_Missense_Mutation_p.D78G|TMEM71_ENST00000377901.4_Missense_Mutation_p.D78G	NM_144649.2	NP_653250.2	Q6P5X7	TMM71_HUMAN	transmembrane protein 71	78						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)			CAGGAAGCTGTCTTCAGTCCA	0.473													T|||	26	0.00519169	0.0	0.0072	5008	,	,		18844	0.0		0.0149	False		,,,				2504	0.0061				p.D78G		Atlas-SNP	.											.	TMEM71	55	.	0			c.A233G						PASS	.	T	GLY/ASP,GLY/ASP	17,4389	23.3+/-48.9	0,17,2186	169	153	158		233,233	5.8	1	8	dbSNP_132	158	176,8424	80.9+/-143.5	4,168,4128	yes	missense,missense	TMEM71	NM_001145153.1,NM_144649.2	94,94	4,185,6314	CC,CT,TT		2.0465,0.3858,1.4839	probably-damaging,probably-damaging	78/233,78/277	133764112	193,12813	2203	4300	6503	SO:0001583	missense	137835	exon4			AAGCTGTCTTCAG	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.233A>G	8.37:g.133764112T>C	ENSP00000349296:p.Asp78Gly	161	0	0		145	27	0.186207	NM_144649	Q3KRC2|Q8WVZ4|Q96LX9	Missense_Mutation	SNP	ENST00000356838.3	37	CCDS6366.1	13	0.005952380952380952	0	0.0	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	T	17.79	3.475998	0.63737	0.003858	0.020465	ENSG00000165071	ENST00000523829;ENST00000356838;ENST00000377901;ENST00000519187;ENST00000519304	.	.	.	5.81	5.81	0.92471	.	0.058994	0.64402	D	0.000003	T	0.66858	0.2832	M	0.77103	2.36	0.47245	D	0.999364	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.971;0.998;0.999	T	0.77638	-0.2513	9	0.87932	D	0	-17.5053	13.9131	0.63881	0.0:0.0:0.0:1.0	.	78;78;78	Q6P5X7;Q6P5X7-3;Q6P5X7-2	TMM71_HUMAN;.;.	G	78	.	ENSP00000349296:D78G	D	-	2	0	TMEM71	133833294	1.000000	0.71417	1.000000	0.80357	0.173000	0.22820	6.769000	0.74985	2.214000	0.71695	0.533000	0.62120	GAC	T|0.988;C|0.012	0.012	strong		0.473	TMEM71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379591.1	NM_144649		C	133764112	T	C	133764112	3	2	27	1	0	0	0	0	1	0	0	0	16215	1667	58	3	682	3	TMEM71	8	133764112	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	8195627	133764112	12599910	473	10924											
TG	7038	hgsc.bcm.edu	37	chr8	133980076	133980076	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tctttctgtcagctcgcagaGataacagagagtgcatcctt	10	12	9	10	1	3	2	1	0	2	2	5	4	4	2	1	0	3	3	1	0	1	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:133980076G>A	ENST00000220616.4	+	31	5764	c.5724G>A	c.(5722-5724)gaG>gaA	p.E1908E	TG_ENST00000377869.1_Silent_p.E1851E|TG_ENST00000519543.1_Silent_p.E62E|TG_ENST00000542445.1_Silent_p.E278E	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1908					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.E1908E(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)		AGCTCGCAGAGATAACAGAGA	0.498																																					p.E1908E		Atlas-SNP	.											TG,colon,carcinoma,0,1	TG	416	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G5724A						PASS	.						83	66	72					8																	133980076		2203	4300	6503	SO:0001819	synonymous_variant	7038	exon31			CGCAGAGATAACA	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.5724G>A	8.37:g.133980076G>A		100	0	0		78	43	0.551282	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	0.014|0.014	-1.571920|-1.571920	0.00895|0.00895	.|.	.|.	ENSG00000042832|ENSG00000042832	ENST00000519178|ENST00000518058	.|.	.|.	.|.	5.87|5.87	0.802|0.802	0.18686|0.18686	.|.	.|.	.|.	.|.	.|.	T|T	0.24470|0.24470	0.0593|0.0593	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.24657|0.24657	-1.0154|-1.0154	4|4	.|.	.|.	.|.	.|.	4.5777|4.5777	0.12241|0.12241	0.1434:0.2262:0.5202:0.1102|0.1434:0.2262:0.5202:0.1102	.|.	.|.	.|.	.|.	N|K	364|40	.|.	.|.	D|R	+|+	1|2	0|0	TG|TG	134049258|134049258	0.111000|0.111000	0.22076|0.22076	0.038000|0.038000	0.18304|0.18304	0.021000|0.021000	0.10359|0.10359	0.030000|0.030000	0.13688|0.13688	-0.039000|-0.039000	0.13602|0.13602	-0.797000|-0.797000	0.03246|0.03246	GAT|AGA	.	.	none		0.498	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		A	133980076	G	A	133980076	2	1	27	1	0	0	0	0	0	0	0	1	15828	933	33	2		2	TG	8	133980076	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	215964	133980076	12383946	474	10925											
ZFAT	57623	hgsc.bcm.edu	37	chr8	135622851	135622851	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcttttcgaggctttttcccGatcatcttccttacacttct	5	19	4	13	2	4	0	1	0	3	0	7	2	6	0	2	1	1	1	2	1	1	7	rs75596750	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:135622851G>A	ENST00000377838.3	-	4	670	c.496C>T	c.(496-498)Cgg>Tgg	p.R166W	ZFAT_ENST00000429442.2_Missense_Mutation_p.R154W|ZFAT_ENST00000520214.1_Missense_Mutation_p.R154W|ZFAT_ENST00000520356.1_Missense_Mutation_p.R154W|ZFAT_ENST00000523399.1_Intron|ZFAT_ENST00000520727.1_Missense_Mutation_p.R154W	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	166					hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|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)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			GCTTTTTCCCGATCATCTTCC	0.448													G|||	2	0.000399361	0.0	0.0	5008	,	,		23535	0.0		0.002	False		,,,				2504	0.0				p.R166W		Atlas-SNP	.											.	ZFAT	265	.	0			c.C496T						PASS	.	G	TRP/ARG,TRP/ARG,,TRP/ARG,TRP/ARG	1,3813		0,1,1906	179	166	170		460,460,,460,496	4.4	1	8	dbSNP_132	170	7,8231		0,7,4112	yes	missense,missense,intron,missense,missense	ZFAT	NM_001029939.3,NM_001167583.2,NM_001174157.1,NM_001174158.1,NM_020863.3	101,101,,101,101	0,8,6018	AA,AG,GG		0.085,0.0262,0.0664	probably-damaging,probably-damaging,,probably-damaging,probably-damaging	154/1232,154/1232,,154/1146,166/1244	135622851	8,12044	1907	4119	6026	SO:0001583	missense	57623	exon4			TTTCCCGATCATC	BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827		"Zinc fingers, C2H2-type"	19899	protein-coding gene	gene with protein product		610931	"zinc finger protein 406"	ZNF406, ZFAT1		10819331, 18329245	Standard	NM_020863		Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.496C>T	8.37:g.135622851G>A	ENSP00000367069:p.Arg166Trp	309	0	0		286	62	0.216783	NM_020863	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Missense_Mutation	SNP	ENST00000377838.3	37	CCDS47924.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	20.3	3.967099	0.74131	2.62E-4	8.5E-4	ENSG00000066827	ENST00000520356;ENST00000520727;ENST00000429442;ENST00000377838;ENST00000520214;ENST00000318135;ENST00000398946;ENST00000522257	T;T;T;T;T;T	0.54279	2.82;2.75;2.76;2.74;2.75;0.58	5.36	4.43	0.53597	.	0.087086	0.48286	D	0.000185	T	0.60392	0.2265	L	0.34521	1.04	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.965;0.999;0.998	T	0.62478	-0.6846	10	0.66056	D	0.02	-7.6436	12.0426	0.53462	0.0:0.0:0.7035:0.2965	.	154;154;166	E9PBN4;Q9P243-3;Q9P243	.;.;ZFAT_HUMAN	W	154;154;154;166;154;154;154;104	ENSP00000427879:R154W;ENSP00000427831:R154W;ENSP00000394501:R154W;ENSP00000367069:R166W;ENSP00000428483:R154W;ENSP00000429983:R104W	ENSP00000326997:R154W	R	-	1	2	ZFAT	135692033	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	3.592000	0.53993	2.498000	0.84270	0.655000	0.94253	CGG	G|0.999;A|0.001	0.001	strong		0.448	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939		A	135622851	G	A	135622851	3	1	27	1	0	0	0	0	1	0	0	0	17647	1057	37	1	3287	1	ZFAT	8	135622851	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1642775	135622851	10741171	475	10926											
LY6K	54742	hgsc.bcm.edu	37	chr8	143783109	143783109	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtgcaaatggacagagccAtactgcgttatagcggccgt	11	8	13	9	3	0	1	0	0	0	1	0	2	0	2	2	3	5	2	2	3	4	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:143783109A>G	ENST00000292430.6	+	2	612	c.195A>G	c.(193-195)ccA>ccG	p.P65P	LY6K_ENST00000518841.1_Silent_p.P65P|LY6K_ENST00000519390.1_3'UTR|LY6K_ENST00000519387.1_Silent_p.P65P|LY6K_ENST00000522591.1_Silent_p.P65P|CTD-2292P10.4_ENST00000520572.1_RNA|LY6K_ENST00000561179.1_Silent_p.P123P			Q17RY6	LY6K_HUMAN	lymphocyte antigen 6 complex, locus K	65	UPAR/Ly6.					anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)	10	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)					GGACAGAGCCATACTGCGTTA	0.502																																					p.P65P		Atlas-SNP	.											.	LY6K	23	.	0			c.A195G						PASS	.						139	130	133					8																	143783109		2203	4300	6503	SO:0001819	synonymous_variant	54742	exon2			AGAGCCATACTGC	AK092545	CCDS6385.1, CCDS6385.2, CCDS59114.1	8q24.3	2009-08-06				ENSG00000160886			24225	protein-coding gene	gene with protein product	"cancer/testis antigen 97"	615093				12516096	Standard	NM_017527		Approved	HSJ001348, FLJ35226, CT97	uc011ljv.2	Q17RY6		ENST00000292430.6:c.195A>G	8.37:g.143783109A>G		193	0	0		179	32	0.178771	NM_001160354	G3V116|O15227|Q9BVD7	Silent	SNP	ENST00000292430.6	37	CCDS6385.2	.	.	.	.	.	.	.	.	.	.	A	2.177	-0.388411	0.04932	.	.	ENSG00000160886	ENST00000522591	.	.	.	1.96	-3.92	0.04155	.	.	.	.	.	T	0.19406	0.0466	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.04029	-1.0983	4	.	.	.	.	2.3733	0.04336	0.2347:0.2455:0.4048:0.1149	.	.	.	.	R	84	.	.	H	+	2	0	LY6K	143780111	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.285000	0.00526	-4.514000	0.00045	-2.025000	0.00428	CAT	.	.	none		0.502	LY6K-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379893.2	NM_017527		G	143783109	A	G	143783109	2	3	27	1	0	0	0	0	0	0	0	1	9107	204	8	3		3	LY6K	8	143783109	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	8160258	143783109	2580913	476	10927											
ZNF623	9831	hgsc.bcm.edu	37	chr8	144733176	144733176	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagaaactctatgaatgtaaCgagtgtgggaaagctttctt	13	12	11	5	1	2	2	0	1	2	1	2	5	2	3	0	1	3	2	0	1	5	4	rs141224385	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:144733176C>T	ENST00000501748.2	+	1	1223	c.1134C>T	c.(1132-1134)aaC>aaT	p.N378N	ZNF623_ENST00000458270.2_Silent_p.N338N|ZNF623_ENST00000526926.1_Silent_p.N338N	NM_014789.3	NP_055604	O75123	ZN623_HUMAN	zinc finger protein 623	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(3)|large_intestine(6)|lung(11)|prostate(1)|stomach(1)|urinary_tract(3)	27	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;2.46e-41)|Epithelial(56;5.28e-40)|all cancers(56;5.23e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			ATGAATGTAACGAGTGTGGGA	0.453													C|||	3	0.000599042	0.0	0.0014	5008	,	,		21487	0.0		0.0	False		,,,				2504	0.002				p.N378N		Atlas-SNP	.											ZNF623,NS,carcinoma,0,1	ZNF623	63	1	0			c.C1134T						scavenged	.	C	,	1,4405	2.1+/-5.4	0,1,2202	71	67	69		1014,1134	-8.1	0	8	dbSNP_134	69	13,8587	9.1+/-34.3	0,13,4287	no	coding-synonymous,coding-synonymous	ZNF623	NM_001082480.1,NM_014789.3	,	0,14,6489	TT,TC,CC		0.1512,0.0227,0.1076	,	338/497,378/537	144733176	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	9831	exon1			ATGTAACGAGTGT	AB014528	CCDS34957.1, CCDS47931.1	8q24.3	2013-01-08				ENSG00000183309		"Zinc fingers, C2H2-type"	29084	protein-coding gene	gene with protein product						9734811	Standard	NM_014789		Approved	KIAA0628	uc003yzd.2	O75123		ENST00000501748.2:c.1134C>T	8.37:g.144733176C>T		32	0	0		35	5	0.142857	NM_014789	A4FU80|B4DGP3|E7ENV5	Silent	SNP	ENST00000501748.2	37	CCDS34957.1																																																																																			C|0.999;T|0.001	0.001	strong		0.453	ZNF623-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382522.3	NM_014789		T	144733176	C	T	144733176	2	4	27	1	0	0	0	0	0	0	0	1	18062	535	19	1		1	ZNF623	8	144733176	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	950067	144733176	1630846	477	10928											
SCRIB	23513	hgsc.bcm.edu	37	chr8	144875168	144875168	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggcaggggcatcctcaggcGggtgagaagtgggcacggcc	7	4	20	10	2	1	1	1	1	0	1	2	2	2	1	2	7	0	3	2	7	1	0	rs202137464	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:144875168G>A	ENST00000320476.3	-	29	4001	c.3995C>T	c.(3994-3996)cCg>cTg	p.P1332L	SCRIB_ENST00000546337.1_5'UTR|RP11-429J17.8_ENST00000534089.1_RNA|SCRIB_ENST00000377533.3_Missense_Mutation_p.P1251L|SCRIB_ENST00000356994.2_Missense_Mutation_p.P1332L|RP11-429J17.8_ENST00000532625.1_RNA|RP11-429J17.8_ENST00000527139.1_RNA	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	1332	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)			ATCCTCAGGCGGGTGAGAAGT	0.716													G|||	10	0.00199681	0.0	0.0	5008	,	,		12252	0.0		0.008	False		,,,				2504	0.002				p.P1332L	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.C3995T						PASS	.	G	LEU/PRO,LEU/PRO	9,4275		0,9,2133	15	16	15		3995,3995	2.2	0	8		15	62,8392		0,62,4165	yes	missense,missense	SCRIB	NM_015356.3,NM_182706.3	98,98	0,71,6298	AA,AG,GG		0.7334,0.2101,0.5574	possibly-damaging,possibly-damaging	1332/1631,1332/1656	144875168	71,12667	2142	4227	6369	SO:0001583	missense	23513	exon29			TCAGGCGGGTGAG	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.3995C>T	8.37:g.144875168G>A	ENSP00000322938:p.Pro1332Leu	100	0	0		110	83	0.754545	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Missense_Mutation	SNP	ENST00000320476.3	37	CCDS6411.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	14.28	2.488712	0.44249	0.002101	0.007334	ENSG00000180900	ENST00000356994;ENST00000320476;ENST00000377533;ENST00000377539	T;T;T	0.37411	1.41;1.36;1.2	4.17	2.25	0.28309	.	.	.	.	.	T	0.41442	0.1159	L	0.56769	1.78	0.09310	N	1	D;D;D	0.89917	0.998;0.999;1.0	P;P;D	0.91635	0.688;0.904;0.999	T	0.16719	-1.0393	9	0.42905	T	0.14	.	5.165	0.15081	0.1014:0.0:0.5328:0.3658	.	1332;1332;1251	Q14160;Q14160-3;Q14160-2	SCRIB_HUMAN;.;.	L	1332;1332;1251;701	ENSP00000349486:P1332L;ENSP00000322938:P1332L;ENSP00000366756:P1251L	ENSP00000322938:P1332L	P	-	2	0	SCRIB	144947156	0.955000	0.32602	0.040000	0.18447	0.028000	0.11728	1.498000	0.35660	0.693000	0.31634	0.195000	0.17529	CCG	G|0.998;A|0.002	0.002	strong		0.716	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356		A	144875168	G	A	144875168	3	1	27	1	0	0	0	0	1	0	0	0	13952	1116	39	1	1008	1	SCRIB	8	144875168	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	141992	144875168	1488854	478	10929											
OPLAH	26873	hgsc.bcm.edu	37	chr8	145107915	145107915	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgatctgcacacggaggcGgatgggggaaccgtcgtcca	8	6	16	11	4	1	1	0	1	1	0	3	4	2	4	2	5	2	2	2	5	1	0	rs200620019	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:145107915G>A	ENST00000426825.1	-	21	3070	c.2989C>T	c.(2989-2991)Cgc>Tgc	p.R997C	OPLAH_ENST00000534424.1_5'UTR|CTD-3065J16.6_ENST00000528912.1_RNA|CTD-3065J16.6_ENST00000561181.1_RNA	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	997					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)			ACACGGAGGCGGATGGGGGAA	0.687													G|||	5	0.000998403	0.0008	0.0014	5008	,	,		14517	0.0		0.002	False		,,,				2504	0.001				p.R997C		Atlas-SNP	.											.	OPLAH	78	.	0			c.C2989T						PASS	.	G	CYS/ARG	1,4293		0,1,2146	19	23	22		2989	0.7	0.9	8		22	8,8440		0,8,4216	yes	missense	OPLAH	NM_017570.3	180	0,9,6362	AA,AG,GG		0.0947,0.0233,0.0706	benign	997/1289	145107915	9,12733	2147	4224	6371	SO:0001583	missense	26873	exon21			GGAGGCGGATGGG	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.2989C>T	8.37:g.145107915G>A	ENSP00000475943:p.Arg997Cys	129	0	0		103	26	0.252427	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Missense_Mutation	SNP	ENST00000426825.1	37		.	.	.	.	.	.	.	.	.	.	G	3.876	-0.026921	0.07589	2.33E-4	9.47E-4	ENSG00000178814	ENST00000426825	.	.	.	4.68	0.665	0.17896	.	0.224693	0.42682	N	0.000665	T	0.28034	0.0691	.	.	.	0.37399	D	0.912761	B	0.06786	0.001	B	0.01281	0.0	T	0.08953	-1.0697	7	0.33940	T	0.23	.	3.9788	0.09486	0.387:0.0:0.4565:0.1565	.	997	O14841	OPLA_HUMAN	C	997	.	ENSP00000412071:R997C	R	-	1	0	OPLAH	145179903	0.886000	0.30341	0.905000	0.35620	0.031000	0.12232	1.258000	0.32944	0.058000	0.16222	-0.480000	0.04831	CGC	.	.	weak		0.687	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570		A	145107915	G	A	145107915	3	1	27	1	0	0	0	0	1	0	0	0	10885	1116	39	1	907	1	OPLAH	8	145107915	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	232747	145107915	1256107	479	10930											
CPSF1	29894	hgsc.bcm.edu	37	chr8	145624578	145624578	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gcacagggtccaatgttcagGatgctgtcacacacctgcgg	9	8	12	12	1	2	0	2	0	0	0	3	1	3	1	2	3	2	3	2	3	1	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:145624578G>A	ENST00000349769.3	-	15	1501	c.1407C>T	c.(1405-1407)atC>atT	p.I469I	MIR1234_ENST00000408875.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	469					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)			CAATGTTCAGGATGCTGTCAC	0.672																																					p.I469I	NSCLC(133;1088 1848 27708 34777 35269)	Atlas-SNP	.											.	CPSF1	92	.	0			c.C1407T						PASS	.						11	12	12					8																	145624578		2196	4290	6486	SO:0001819	synonymous_variant	29894	exon15			GTTCAGGATGCTG	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.1407C>T	8.37:g.145624578G>A		95	0	0		89	40	0.449438	NM_013291	Q96AF0	Silent	SNP	ENST00000349769.3	37	CCDS34966.1																																																																																			.	.	none		0.672	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291		A	145624578	G	A	145624578	2	1	27	1	0	0	0	0	0	0	0	1	3826	1164	41	2		2	CPSF1	8	145624578	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	516663	145624578	739444	480	10931											
PPP1R16A	84988	hgsc.bcm.edu	37	chr8	145722726	145722726	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcccagggcaagaagggtcCtggggagcgtccccggaagg	8	3	19	11	2	0	1	0	0	0	1	2	3	2	3	4	7	1	1	4	7	3	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:145722726C>A	ENST00000292539.4	+	2	1066	c.149C>A	c.(148-150)cCt>cAt	p.P50H	PPP1R16A_ENST00000529009.1_3'UTR|CTD-2517M14.5_ENST00000569326.1_RNA|CTD-2517M22.14_ENST00000532766.1_RNA|PPP1R16A_ENST00000435887.1_Missense_Mutation_p.P50H			Q96I34	PP16A_HUMAN	protein phosphatase 1, regulatory subunit 16A	50				Missing (in Ref. 1; BAC03452). {ECO:0000305}.		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)			AAGAAGGGTCCTGGGGAGCGT	0.652																																					p.P50H		Atlas-SNP	.											.	PPP1R16A	25	.	0			c.C149A						PASS	.						48	43	45					8																	145722726		2203	4299	6502	SO:0001583	missense	84988	exon1			AGGGTCCTGGGGA		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.149C>A	8.37:g.145722726C>A	ENSP00000292539:p.Pro50His	116	0	0		145	80	0.551724	NM_032902	D3DWM5	Missense_Mutation	SNP	ENST00000292539.4	37	CCDS6429.1	.	.	.	.	.	.	.	.	.	.	C	10.05	1.245088	0.22796	.	.	ENSG00000160972	ENST00000292539;ENST00000435887	T;T	0.70986	-0.53;-0.53	4.49	-8.98	0.00754	.	0.960193	0.08687	N	0.908585	T	0.34106	0.0886	N	0.00926	-1.1	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.41698	-0.9494	10	0.42905	T	0.14	.	10.2052	0.43109	0.1214:0.5237:0.3549:0.0	.	50	Q96I34	PP16A_HUMAN	H	50	ENSP00000292539:P50H;ENSP00000391126:P50H	ENSP00000292539:P50H	P	+	2	0	PPP1R16A	145693534	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.717000	0.01876	-1.769000	0.01297	-0.521000	0.04368	CCT	.	.	none		0.652	PPP1R16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382459.1	NM_032902		A	145722726	C	A	145722726	3	1	27	1	0	0	0	0	1	0	0	0	12377	681	24	4	151	4	PPP1R16A	8	145722726	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	98148	145722726	641296	481	10932											
MFSD3	113655	hgsc.bcm.edu	37	chr8	145735120	145735120	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gccggccgaactggggccggGcaataccgtgcaggtggtcg	6	5	18	12	5	0	0	0	0	0	0	1	1	0	0	4	6	3	2	4	6	3	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr8:145735120G>C	ENST00000301327.4	+	1	664	c.404G>C	c.(403-405)gGc>gCc	p.G135A	RECQL4_ENST00000532237.1_5'Flank|CTD-2517M22.17_ENST00000580385.1_RNA	NM_138431.1	NP_612440.1	Q96ES6	MFSD3_HUMAN	major facilitator superfamily domain containing 3	135	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)			CTGGGGCCGGGCAATACCGTG	0.692											OREG0019059	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G135A		Atlas-SNP	.											.	MFSD3	17	.	0			c.G404C						PASS	.						8	8	8					8																	145735120		2127	4210	6337	SO:0001583	missense	113655	exon1			GGCCGGGCAATAC		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.404G>C	8.37:g.145735120G>C	ENSP00000301327:p.Gly135Ala	29	0	0	1696	32	18	0.5625	NM_138431		Missense_Mutation	SNP	ENST00000301327.4	37	CCDS6431.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.053076	0.75960	.	.	ENSG00000167700	ENST00000301327	T	0.47869	0.83	5.02	5.02	0.67125	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	T	0.67002	0.2847	M	0.66506	2.035	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.68322	-0.5439	10	0.52906	T	0.07	-7.8332	16.1659	0.81754	0.0:0.0:1.0:0.0	.	135	Q96ES6	MFSD3_HUMAN	A	135	ENSP00000301327:G135A	ENSP00000301327:G135A	G	+	2	0	MFSD3	145705928	1.000000	0.71417	0.980000	0.43619	0.068000	0.16541	4.514000	0.60482	2.484000	0.83849	0.561000	0.74099	GGC	.	.	none		0.692	MFSD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382478.2	NM_138431		C	145735120	G	C	145735120	3	2	27	1	0	0	0	0	1	0	0	0	9541	1203	42	4	406	4	MFSD3	8	145735120	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	12394	145735120	628902	482	10933											
DOCK8	81704	hgsc.bcm.edu	37	chr9	340230	340230	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgactcctgaaatgctgcccGtgaaaccctttcctgaaaac	11	10	7	13	1	0	4	0	4	0	0	2	4	2	4	4	0	4	1	4	0	4	1	rs373187839		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:340230G>A	ENST00000453981.1	+	14	1700	c.1588G>A	c.(1588-1590)Gtg>Atg	p.V530M	DOCK8_ENST00000469391.1_Missense_Mutation_p.V462M|DOCK8_ENST00000432829.2_Missense_Mutation_p.V462M			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	530					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)		AATGCTGCCCGTGAAACCCTT	0.443																																					p.V530M		Atlas-SNP	.											DOCK8_ENST00000453981,NS,carcinoma,-2,2	DOCK8	401	2	0			c.G1588A						scavenged	.	G	MET/VAL,MET/VAL,MET/VAL	1,4405	2.1+/-5.4	0,1,2202	85	87	86		1384,1384,1588	5.5	0.9	9		86	0,8600		0,0,4300	no	missense,missense,missense	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	21,21,21	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging	462/2000,462/2032,530/2100	340230	1,13005	2203	4300	6503	SO:0001583	missense	81704	exon14			CTGCCCGTGAAAC	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.1588G>A	9.37:g.340230G>A	ENSP00000408464:p.Val530Met	81	1	0.0123457		91	37	0.406593	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	37	CCDS6440.2	.	.	.	.	.	.	.	.	.	.	G	29.2	4.988063	0.93106	2.27E-4	0.0	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391	T;T;T	0.39229	1.09;1.09;1.09	5.49	5.49	0.81192	.	0.128635	0.52532	D	0.000073	T	0.63034	0.2477	M	0.62723	1.935	0.80722	D	1	D;D	0.89917	0.991;1.0	P;D	0.67725	0.878;0.953	T	0.61964	-0.6954	10	0.52906	T	0.07	.	19.7314	0.96182	0.0:0.0:1.0:0.0	.	462;530	E9PH09;Q8NF50	.;DOCK8_HUMAN	M	530;530;462;462	ENSP00000408464:V530M;ENSP00000394888:V462M;ENSP00000419438:V462M	ENSP00000287364:V530M	V	+	1	0	DOCK8	330230	1.000000	0.71417	0.917000	0.36280	0.951000	0.60555	3.219000	0.51200	2.727000	0.93392	0.655000	0.94253	GTG	.	.	weak		0.443	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307		A	340230	G	A	340230	3	1	27	1	0	0	0	0	1	0	0	0	4695	1145	40	1	1642	1	DOCK8	9	340230	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10		340230	140873201	483	10934											
RFX3	5991	hgsc.bcm.edu	37	chr9	3247895	3247895	+	Intron	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttaaggaactcttgcaataActccacagtccctcctggct	10	12	6	13	0	1	0	0	0	1	0	4	1	4	1	3	2	3	2	3	2	4	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:3247895A>G	ENST00000382004.3	-	16	2280				RFX3_ENST00000302303.1_Missense_Mutation_p.V702A|RFX3_ENST00000358730.2_Missense_Mutation_p.V702A	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)		tcttgcaataactccacagtc	0.348																																					p.V702A		Atlas-SNP	.											.	RFX3	156	.	0			c.T2105C						PASS	.						79	80	79					9																	3247895		2203	4300	6503	SO:0001627	intron_variant	5991	exon16			GCAATAACTCCAC	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+136T>C	9.37:g.3247895A>G		25	0	0		22	13	0.590909	NM_002919	A8K0H5|D3DRH8|D3DRH9|Q5JTL7|Q5JTL8|Q6NW13|Q8WTU4|Q95HL5|Q95HL6	Missense_Mutation	SNP	ENST00000382004.3	37	CCDS6449.1	.	.	.	.	.	.	.	.	.	.	A	10.67	1.415133	0.25552	.	.	ENSG00000080298	ENST00000358730;ENST00000302303	T;T	0.59502	0.26;0.26	3.82	-0.0572	0.13802	.	.	.	.	.	T	0.42787	0.1218	.	.	.	0.09310	N	1	B	0.12630	0.006	B	0.09377	0.004	T	0.37957	-0.9683	8	0.87932	D	0	.	5.4108	0.16346	0.5649:0.3387:0.0964:0.0	.	702	P48380-2	.	A	702	ENSP00000351574:V702A;ENSP00000303847:V702A	ENSP00000303847:V702A	V	-	2	0	RFX3	3237895	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.141000	0.10327	-0.009000	0.14296	-0.435000	0.05868	GTT	.	.	none		0.348	RFX3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051545.1	NM_002919		G	3247895	A	G	3247895	1	3	27	0	1	0	0	0	0	0	0	0	13279	43	2	3		3	RFX3	9	3247895	Intron	SNP	A	TCGA-G8-6909-01A-11D-2210-10	2907665	3247895	137965536	484	10935											
KDM4C	23081	hgsc.bcm.edu	37	chr9	6981115	6981115	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaaagtaagaaaagcatcccGaaggtaatgacccctcaccc	16	5	8	12	1	1	2	1	1	0	1	2	4	2	2	4	1	1	3	4	1	6	2	rs35049841	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:6981115G>A	ENST00000381309.3	+	9	1677	c.1112G>A	c.(1111-1113)cGa>cAa	p.R371Q	KDM4C_ENST00000381306.3_Missense_Mutation_p.R371Q|KDM4C_ENST00000442236.2_Missense_Mutation_p.R190Q|RP11-403H13.1_ENST00000445708.1_RNA|KDM4C_ENST00000535193.1_Missense_Mutation_p.R393Q|KDM4C_ENST00000543771.1_Missense_Mutation_p.R371Q|KDM4C_ENST00000536108.1_Missense_Mutation_p.R190Q|KDM4C_ENST00000428870.2_Missense_Mutation_p.R58Q	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	371					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						AAAGCATCCCGAAGGTAATGA	0.453													G|||	2	0.000399361	0.0	0.0014	5008	,	,		19729	0.0		0.001	False		,,,				2504	0.0				p.R393Q		Atlas-SNP	.											.	KDM4C	186	.	0			c.G1178A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	70	62	65		1112,1112,1178,1112	-4.8	0	9	dbSNP_126	65	37,8563	24.6+/-71.5	0,37,4263	yes	missense,missense,missense,missense	KDM4C	NM_001146694.1,NM_001146695.1,NM_001146696.1,NM_015061.3	43,43,43,43	0,37,6466	AA,AG,GG		0.4302,0.0,0.2845	benign,benign,benign,benign	371/1048,371/814,393/836,371/1057	6981115	37,12969	2203	4300	6503	SO:0001583	missense	23081	exon9			CATCCCGAAGGTA	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.1112G>A	9.37:g.6981115G>A	ENSP00000370710:p.Arg371Gln	47	0	0		23	8	0.347826	NM_001146696	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	37	CCDS6471.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	10.47	1.358960	0.24598	0.0	0.004302	ENSG00000107077	ENST00000535193;ENST00000543771;ENST00000381309;ENST00000381306;ENST00000442236;ENST00000536108;ENST00000428870	T;T;T;T;T;T;T	0.19532	2.25;2.26;2.43;2.33;2.64;2.14;3.43	5.47	-4.79	0.03200	.	0.954910	0.08712	N	0.904774	T	0.14657	0.0354	L	0.29908	0.895	0.09310	N	1	B;P;B;B;B	0.47106	0.196;0.89;0.158;0.011;0.045	B;B;B;B;B	0.41466	0.026;0.358;0.039;0.007;0.017	T	0.11275	-1.0594	10	0.13470	T	0.59	-1.4792	15.7963	0.78412	0.7358:0.0:0.2642:0.0	rs35049841;rs61752861	190;371;393;371;371	E7EV17;F5H347;F5H7P0;Q9H3R0;Q9H3R0-2	.;.;.;KDM4C_HUMAN;.	Q	393;371;371;371;190;190;58	ENSP00000442382:R393Q;ENSP00000445427:R371Q;ENSP00000370710:R371Q;ENSP00000370707:R371Q;ENSP00000409353:R190Q;ENSP00000440656:R190Q;ENSP00000405739:R58Q	ENSP00000370707:R371Q	R	+	2	0	KDM4C	6971115	0.001000	0.12720	0.001000	0.08648	0.006000	0.05464	-0.028000	0.12350	-1.432000	0.01979	-0.225000	0.12378	CGA	G|0.998;A|0.002	0.002	strong		0.453	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061		A	6981115	G	A	6981115	3	1	27	1	0	0	0	0	1	0	0	0	8139	1058	37	1	1212	1	KDM4C	9	6981115	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	3733220	6981115	134232316	485	10936											
FREM1	158326	hgsc.bcm.edu	37	chr9	14801725	14801725	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gttggctggctgcttattctCagagaagtctttgctaaacc	8	14	10	9	0	2	1	1	0	2	1	3	2	2	1	1	2	3	5	1	2	4	5	rs61744094	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:14801725C>G	ENST00000380880.3	-	20	4402	c.3619G>C	c.(3619-3621)Gag>Cag	p.E1207Q	FREM1_ENST00000380881.4_Missense_Mutation_p.E1208Q|FREM1_ENST00000422223.2_Missense_Mutation_p.E1207Q			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1207					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)		TGCTTATTCTCAGAGAAGTCT	0.512																																					p.E1207Q		Atlas-SNP	.											.	FREM1	261	.	0			c.G3619C						PASS	.	C	GLN/GLU	1,3989		0,1,1994	147	145	145		3619	1.5	0	9	dbSNP_129	145	2,8356		0,2,4177	no	missense	FREM1	NM_144966.5	29	0,3,6171	GG,GC,CC		0.0239,0.0251,0.0243	benign	1207/2180	14801725	3,12345	1995	4179	6174	SO:0001583	missense	158326	exon21			TATTCTCAGAGAA	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.3619G>C	9.37:g.14801725C>G	ENSP00000370262:p.Glu1207Gln	238	0	0		221	97	0.438914	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	C	0.332	-0.955355	0.02267	2.51E-4	2.39E-4	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.51574	0.7;0.7;0.7	5.51	1.53	0.23141	.	0.815509	0.11476	N	0.560211	T	0.12902	0.0313	N	0.00436	-1.5	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.31166	-0.9953	10	0.11794	T	0.64	0.2002	5.6173	0.17438	0.072:0.2719:0.5253:0.1308	rs61744094	1207	Q5H8C1	FREM1_HUMAN	Q	1208;1207;1207	ENSP00000370263:E1208Q;ENSP00000412940:E1207Q;ENSP00000370262:E1207Q	ENSP00000370257:E1210Q	E	-	1	0	FREM1	14791725	0.011000	0.17503	0.001000	0.08648	0.053000	0.15095	1.753000	0.38359	0.262000	0.21774	-0.340000	0.08031	GAG	C|0.889;G|0.111	0.111	strong		0.512	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		G	14801725	C	G	14801725	3	3	27	1	0	0	0	0	1	0	0	0	6052	835	29	4	3042	4	FREM1	9	14801725	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	7820610	14801725	126411706	486	10937											
TTC39B	158219	hgsc.bcm.edu	37	chr9	15189791	15189791	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aacattcacttctcctgtacCtagaaatttaacaggaaaag	16	11	5	9	0	2	1	1	0	1	1	3	2	2	2	2	1	3	1	2	1	7	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:15189791C>T	ENST00000512701.2	-	12	1142		c.e12-1		TTC39B_ENST00000507993.1_Splice_Site|TTC39B_ENST00000380850.4_Splice_Site|TTC39B_ENST00000355694.2_Splice_Site|TTC39B_ENST00000297615.5_Splice_Site|TTC39B_ENST00000507285.1_Splice_Site			Q5VTQ0	TT39B_HUMAN	tetratricopeptide repeat domain 39B											NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)	21						TCTCCTGTACCTAGAAATTTA	0.408																																					.		Atlas-SNP	.											.	TTC39B	83	.	0			c.1100-1G>A						PASS	.						52	48	49					9																	15189791		2203	4300	6503	SO:0001630	splice_region_variant	158219	exon13			CTGTACCTAGAAA	AK091187	CCDS6477.1, CCDS6477.2, CCDS55294.1, CCDS55295.1, CCDS55296.1	9p22.2	2013-01-11	2008-06-23	2008-06-23	ENSG00000155158	ENSG00000155158		"Tetratricopeptide (TTC) repeat domain containing"	23704	protein-coding gene	gene with protein product		613574	"chromosome 9 open reading frame 52"	C9orf52			Standard	NM_001168339		Approved	FLJ33868	uc003zlr.2	Q5VTQ0	OTTHUMG00000019581	ENST00000512701.2:c.1106-1G>A	9.37:g.15189791C>T		59	0	0		57	11	0.192982	NM_001168339	A5PLN1|B4DQ10|B4DQX4|B4DW93|Q8IVR7|Q8IXZ6|Q8N267	Splice_Site	SNP	ENST00000512701.2	37	CCDS6477.2	.	.	.	.	.	.	.	.	.	.	C	27.7	4.859434	0.91433	.	.	ENSG00000155158	ENST00000380850;ENST00000297615;ENST00000355694;ENST00000512701;ENST00000507285;ENST00000507993	.	.	.	5.72	5.72	0.89469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.8823	0.96903	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TTC39B	15179791	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.261000	0.78400	2.693000	0.91896	0.585000	0.79938	.	.	.	none		0.408	TTC39B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051758.3	NM_152574	Intron	T	15189791	C	T	15189791	5	4	27	1	0	0	0	0	0	0	1	0	16723	695	24	2	1000	2	TTC39B	9	15189791	Splice_Site	SNP	C	TCGA-G8-6909-01A-11D-2210-10	388066	15189791	126023640	487	10938											
TAF1L	138474	hgsc.bcm.edu	37	chr9	32631518	32631518	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cagagattttctgcgaacctCatgcacattctcaattagct	11	13	6	11	1	3	1	2	0	2	1	4	3	3	1	1	0	4	2	1	0	3	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:32631518C>G	ENST00000242310.4	-	1	4149	c.4060G>C	c.(4060-4062)Gag>Cag	p.E1354Q	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	1354					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)		CTGCGAACCTCATGCACATTC	0.403																																					p.E1354Q		Atlas-SNP	.											.	TAF1L	382	.	0			c.G4060C						PASS	.						238	236	236					9																	32631518		2203	4300	6503	SO:0001583	missense	138474	exon1			GAACCTCATGCAC	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.4060G>C	9.37:g.32631518C>G	ENSP00000418379:p.Glu1354Gln	433	1	0.00230947		338	86	0.254438	NM_153809	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	37	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	C	14.20	2.465042	0.43839	.	.	ENSG00000122728	ENST00000242310	T	0.09163	3.01	0.479	0.479	0.16796	.	0.097387	0.64402	D	0.000001	T	0.13415	0.0325	L	0.47190	1.495	0.51233	D	0.999915	D	0.55605	0.972	P	0.52343	0.696	T	0.05716	-1.0868	10	0.40728	T	0.16	.	6.6915	0.23174	0.0:0.9998:0.0:2.0E-4	.	1354	Q8IZX4	TAF1L_HUMAN	Q	1354	ENSP00000418379:E1354Q	ENSP00000418379:E1354Q	E	-	1	0	TAF1L	32621518	1.000000	0.71417	0.942000	0.38095	0.559000	0.35586	4.785000	0.62418	0.507000	0.28148	0.195000	0.17529	GAG	.	.	none		0.403	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2			G	32631518	C	G	32631518	3	3	27	1	0	0	0	0	1	0	0	0	15538	835	29	4	1424	4	TAF1L	9	32631518	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	17441727	32631518	108581913	488	10939											
NOL6	65083	hgsc.bcm.edu	37	chr9	33464897	33464897	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagtgagctcattattgaggTtgacaaagagggggttgttc	10	12	14	5	0	1	4	1	3	0	1	2	4	1	4	0	3	1	4	0	3	2	5	rs142747625	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:33464897T>C	ENST00000379471.2	-	21	2846	c.2759A>G	c.(2758-2760)aAc>aGc	p.N920S	NOL6_ENST00000464829.1_Intron|NOL6_ENST00000455041.2_Missense_Mutation_p.N868S			Q9H6R4	NOL6_HUMAN	nucleolar protein 6 (RNA-associated)	920					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)		ATTATTGAGGTTGACAAAGAG	0.478													T|||	6	0.00119808	0.0	0.0014	5008	,	,		19701	0.0		0.005	False		,,,				2504	0.0				p.N920S		Atlas-SNP	.											.	NOL6	85	.	0			c.A2759G						PASS	.	T	SER/ASN,	1,4405	2.1+/-5.4	0,1,2202	95	100	99		2759,	5.4	1	9	dbSNP_134	99	20,8580	14.6+/-50.1	0,20,4280	yes	missense,intron	NOL6	NM_022917.4,NM_139235.3	46,	0,21,6482	CC,CT,TT		0.2326,0.0227,0.1615	probably-damaging,	920/1147,	33464897	21,12985	2203	4300	6503	SO:0001583	missense	65083	exon21			TTGAGGTTGACAA	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.2759A>G	9.37:g.33464897T>C	ENSP00000368784:p.Asn920Ser	79	0	0		77	34	0.441558	NM_022917	Q5T5M3|Q5T5M4|Q7L4G6|Q8N6I0|Q8TEY9|Q8TEZ0|Q8TEZ1|Q9H675	Missense_Mutation	SNP	ENST00000379471.2	37		5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	T	16.69	3.193496	0.58017	2.27E-4	0.002326	ENSG00000165271	ENST00000297990;ENST00000379471;ENST00000541373;ENST00000325914;ENST00000455041	T;T;T	0.47869	0.83;0.83;0.83	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.58807	0.2148	M	0.78049	2.395	0.80722	D	1	D;D;D;D	0.62365	0.984;0.991;0.981;0.985	P;P;P;P	0.59546	0.794;0.833;0.59;0.859	T	0.68765	-0.5322	10	0.66056	D	0.02	.	15.5171	0.75833	0.0:0.0:0.0:1.0	.	868;917;920;920	B4DF80;Q9H6R4-4;Q9H6R4-2;Q9H6R4	.;.;.;NOL6_HUMAN	S	920;920;476;920;868	ENSP00000297990:N920S;ENSP00000368784:N920S;ENSP00000395915:N868S	ENSP00000297990:N920S	N	-	2	0	NOL6	33454897	1.000000	0.71417	0.993000	0.49108	0.024000	0.10985	7.579000	0.82511	2.059000	0.61396	0.533000	0.62120	AAC	T|0.998;C|0.002	0.002	strong		0.478	NOL6-005	NOVEL	non_canonical_TEC|basic	protein_coding	protein_coding	OTTHUMT00000001019.2	NM_022917		C	33464897	T	C	33464897	3	2	27	1	0	0	0	0	1	0	0	0	10534	1725	60	3	705	3	NOL6	9	33464897	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	833379	33464897	107748534	489	10940											
PAX5	5079	hgsc.bcm.edu	37	chr9	37033983	37033983	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcccgtatcgcggtcctacCtgtcctgctggtccgaggag	5	9	13	14	4	0	0	0	0	0	0	4	2	3	1	5	3	3	2	5	3	2	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:37033983C>G	ENST00000358127.4	-	1	120	c.46G>C	c.(46-48)Gga>Cga	p.G16R	PAX5_ENST00000414447.1_Splice_Site_p.G16R|PAX5_ENST00000377847.2_Splice_Site_p.G16R|PAX5_ENST00000377853.2_Splice_Site_p.G16R|PAX5_ENST00000446742.1_Splice_Site_p.G16R|PAX5_ENST00000523145.1_5'UTR|PAX5_ENST00000520154.1_Splice_Site_p.G16R|PAX5_ENST00000522003.1_5'UTR|PAX5_ENST00000523241.1_Splice_Site_p.G16R|PAX5_ENST00000377852.2_Splice_Site_p.G16R|PAX5_ENST00000520281.1_Splice_Site_p.G16R	NM_001280554.1|NM_001280556.1|NM_016734.1	NP_001267483.1|NP_001267485.1|NP_057953.1	Q02548	PAX5_HUMAN	paired box 5	16	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.				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.?(10)	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)		GCGGTCCTACCTGTCCTGCTG	0.552			"T, Mis, D, F, S"	"IGH@, ETV6, PML, FOXP1, ZNF521, ELN"	"NHL, ALL, B-ALL"																																p.G16R		Atlas-SNP	.		Dom	yes		9	9p13	5079	paired box gene 5 (B-cell lineage specific activator protein)		L	.	PAX5	250	.	10	Unknown(10)	haematopoietic_and_lymphoid_tissue(10)	c.G46C						PASS	.						70	65	66					9																	37033983		2203	4300	6503	SO:0001630	splice_region_variant	5079	exon1			TCCTACCTGTCCT		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.46+1G>C	9.37:g.37033983C>G		72	0	0		98	29	0.295918	NM_016734	A3QVP6|A3QVP7|A3QVP8|C0KTF6|C0KTF7|C0KTF8|C0KTF9|C0KTG0|O75933|Q5SFM2|Q6S728|Q6S729|Q6S730|Q6S731|Q6S732	Missense_Mutation	SNP	ENST00000358127.4	37	CCDS6607.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.650847	0.87958	.	.	ENSG00000196092	ENST00000358127;ENST00000377853;ENST00000377852;ENST00000523241;ENST00000520154;ENST00000520281;ENST00000446742;ENST00000414447;ENST00000377847	D;D;D;D;D;D;D;D;D	0.99474	-5.97;-5.97;-5.97;-5.97;-5.97;-5.97;-5.97;-5.97;-5.97	6.08	6.08	0.98989	Paired box protein, N-terminal (3);	0.000000	0.64402	D	0.000001	D	0.99557	0.9841	M	0.82923	2.615	0.80722	D	1	D;B;P;D;P;P;D;D;D	0.89917	1.0;0.439;0.752;1.0;0.56;0.727;1.0;1.0;1.0	D;B;P;D;P;P;D;D;D	0.91635	0.999;0.196;0.627;0.999;0.533;0.664;0.999;0.999;0.999	D	0.99007	1.0813	9	.	.	.	.	20.2751	0.98485	0.0:1.0:0.0:0.0	.	16;16;16;16;16;16;16;16;16	C0KTF8;C0KTF7;C0KTF9;C0KTF6;E7ERW5;E7EQT0;Q6S730;Q6S731;Q02548	.;.;.;.;.;.;.;.;PAX5_HUMAN	R	16	ENSP00000350844:G16R;ENSP00000367084:G16R;ENSP00000367083:G16R;ENSP00000429637:G16R;ENSP00000429291:G16R;ENSP00000430773:G16R;ENSP00000404687:G16R;ENSP00000412188:G16R;ENSP00000367078:G16R	.	G	-	1	0	PAX5	37023983	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.083000	0.71326	2.890000	0.99128	0.655000	0.94253	GGA	.	.	none		0.552	PAX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052433.1		Missense_Mutation	G	37033983	C	G	37033983	5	3	27	1	0	0	0	0	0	0	1	0	11491	695	24	4	1169	4	PAX5	9	37033983	Splice_Site	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3569086	37033983	104179448	490	10941											
AGTPBP1	23287	hgsc.bcm.edu	37	chr9	88204462	88204462	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaaatggcagatatgttcAtaataattagactctggcat	14	13	8	6	0	2	3	1	1	1	2	2	3	2	3	0	2	0	3	0	2	5	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:88204462A>G	ENST00000357081.3	-	20	2847	c.2703T>C	c.(2701-2703)taT>taC	p.Y901Y	AGTPBP1_ENST00000376109.3_Silent_p.Y913Y|AGTPBP1_ENST00000376083.3_Silent_p.Y861Y|AGTPBP1_ENST00000432218.1_Intron|AGTPBP1_ENST00000337006.4_3'UTR			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	901					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						AGATATGTTCATAATAATTAG	0.378																																					p.Y861Y		Atlas-SNP	.											.	AGTPBP1	128	.	0			c.T2583C						PASS	.						133	129	130					9																	88204462		2203	4300	6503	SO:0001819	synonymous_variant	23287	exon20			ATGTTCATAATAA	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.2703T>C	9.37:g.88204462A>G		142	0	0		119	48	0.403361	NM_015239	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Silent	SNP	ENST00000357081.3	37																																																																																				.	.	none		0.378	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239		G	88204462	A	G	88204462	2	3	27	1	0	0	0	0	0	0	0	1	400	224	8	3		3	AGTPBP1	9	88204462	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	51170479	88204462	53008969	491	10942											
DAPK1	1612	hgsc.bcm.edu	37	chr9	90252966	90252966	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatggtgtttactacctgcaCtcccttcaaatcgcccactt	9	13	5	14	1	1	0	1	0	0	0	3	0	2	0	3	1	3	2	3	1	4	5	rs55800264	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:90252966C>T	ENST00000408954.3	+	4	728	c.393C>T	c.(391-393)caC>caT	p.H131H	DAPK1_ENST00000472284.1_Silent_p.H131H|DAPK1_ENST00000469640.2_Silent_p.H131H|DAPK1_ENST00000358077.5_Silent_p.H131H|DAPK1_ENST00000491893.1_Silent_p.H131H	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	131	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						ACTACCTGCACTCCCTTCAAA	0.408									Chronic Lymphocytic Leukemia, Familial Clustering of				C|||	19	0.00379393	0.0	0.0101	5008	,	,		20103	0.0		0.0089	False		,,,				2504	0.0031				p.H131H		Atlas-SNP	.											.	DAPK1	329	.	0			c.C393T						PASS	.	C		13,3843		0,13,1915	101	94	96		393	0.3	1	9	dbSNP_129	96	140,8146		1,138,4004	no	coding-synonymous	DAPK1	NM_004938.2		1,151,5919	TT,TC,CC		1.6896,0.3371,1.2601		131/1431	90252966	153,11989	1928	4143	6071	SO:0001819	synonymous_variant	1612	exon4	Familial Cancer Database	Familial CLL	CCTGCACTCCCTT	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.393C>T	9.37:g.90252966C>T		110	0	0		75	32	0.426667	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Silent	SNP	ENST00000408954.3	37	CCDS43842.1																																																																																			C|0.991;T|0.009	0.009	strong		0.408	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938		T	90252966	C	T	90252966	2	4	27	1	0	0	0	0	0	0	0	1	4237	564	20	2		2	DAPK1	9	90252966	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2048504	90252966	50960465	492	10943											
LOC645961	645961	hgsc.bcm.edu	37	chr9	90746159	90746159	+	IGR	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggttgacagcaagccaggatCgacgcacactcacggggatc	11	5	13	12	3	1	1	1	1	0	0	3	4	1	3	1	4	2	3	1	4	1	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:90746159C>T								U6 (132909 upstream) : U3 (243024 downstream)																							AAGCCAGGATCGACGCACACT	0.527																																					p.R598Q		Atlas-SNP	.											.	.	.	.	0			c.G1793A						PASS	.						45	38	40					9																	90746159		692	1591	2283	SO:0001628	intergenic_variant	645961	exon4			CAGGATCGACGCA																													9.37:g.90746159C>T		106	0	0		78	20	0.25641	NM_001166137		Missense_Mutation	SNP		37																																																																																				.	.	none	0	0.527									T	90746159	C	T	90746159	1	4	27	0	1	0	0	0	0	0	0	0	8892	884	31	1		1	LOC645961	9	90746159	IGR	SNP	C	TCGA-G8-6909-01A-11D-2210-10	493193	90746159	50467272	493	10944											
NOL8	55035	hgsc.bcm.edu	37	chr9	95069242	95069242	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcaaaacactttgtacaacAttcagggctttctttttttc	10	17	5	9	0	2	0	1	0	1	0	3	0	2	0	0	1	4	3	0	1	4	7	rs375530094		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:95069242A>G	ENST00000535387.1	-	9	2636	c.2637T>C	c.(2635-2637)aaT>aaC	p.N879N	NOL8_ENST00000542053.1_Silent_p.N849N|NOL8_ENST00000545558.1_Silent_p.N917N|NOL8_ENST00000358855.4_Silent_p.N849N|NOL8_ENST00000442668.2_Silent_p.N917N					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						TTTGTACAACATTCAGGGCTT	0.343																																					p.N917N		Atlas-SNP	.											.	NOL8	118	.	0			c.T2751C						PASS	.	A		0,3634		0,0,1817	141	137	139		2751	3.4	0.5	9		139	1,8159		0,1,4079	no	coding-synonymous	NOL8	NM_017948.5		0,1,5896	GG,GA,AA		0.0123,0.0,0.0085		917/1168	95069242	1,11793	1817	4080	5897	SO:0001819	synonymous_variant	55035	exon11			TACAACATTCAGG	AB109030	CCDS47993.1, CCDS59135.1	9q22.32	2013-02-12	2004-01-12	2004-01-14	ENSG00000198000	ENSG00000198000		"RNA binding motif (RRM) containing"	23387	protein-coding gene	gene with protein product		611534	"chromosome 9 open reading frame 34"	C9orf34		12477932	Standard	NM_017948		Approved	FLJ20736, Nop132	uc022bjx.1	Q76FK4	OTTHUMG00000020221	ENST00000535387.1:c.2637T>C	9.37:g.95069242A>G		170	0	0		141	56	0.397163	NM_017948		Silent	SNP	ENST00000535387.1	37	CCDS47993.1																																																																																			.	.	weak		0.343	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948		G	95069242	A	G	95069242	2	3	27	1	0	0	0	0	0	0	0	1	10536	214	8	3		3	NOL8	9	95069242	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	4323083	95069242	46144189	494	10945											
WNK2	65268	hgsc.bcm.edu	37	chr9	96024182	96024182	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaccggctgcggtcctctcGccgcctctgccggaagtgct	3	8	12	18	5	2	0	0	0	2	0	4	1	3	1	6	3	3	2	6	3	1	0	rs12000967	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:96024182G>C	ENST00000297954.4	+	12	3153	c.3153G>C	c.(3151-3153)tcG>tcC	p.S1051S	WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000349097.3_Silent_p.S663S|WNK2_ENST00000395477.2_Silent_p.S1051S|WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000427277.2_Silent_p.S663S	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						CGGTCCTCTCGCCGCCTCTGC	0.692													C|||	665	0.132788	0.2973	0.1124	5008	,	,		13886	0.001		0.1362	False		,,,				2504	0.0573				p.S1051S		Atlas-SNP	.											.	WNK2	277	.	0			c.G3153C						PASS	.	C		1193,3211		166,861,1175	37	35	36		3153	-0.9	1	9	dbSNP_120	36	944,7648		60,824,3412	no	coding-synonymous	WNK2	NM_006648.3		226,1685,4587	CC,CG,GG		10.987,27.089,16.4435		1051/2218	96024182	2137,10859	2202	4296	6498	SO:0001819	synonymous_variant	65268	exon12			CCTCTCGCCGCCT	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.3153G>C	9.37:g.96024182G>C		52	0	0		76	36	0.473684	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Silent	SNP	ENST00000297954.4	37		294|294	0.1346153846153846|0.1346153846153846	144|144	0.2926829268292683|0.2926829268292683	46|46	0.1270718232044199|0.1270718232044199	1|1	0.0017482517482517483|0.0017482517482517483	103|103	0.1358839050131926|0.1358839050131926	C|C	6.678|6.678	0.493719|0.493719	0.12702|0.12702	0.27089|0.27089	0.10987|0.10987	ENSG00000165238|ENSG00000165238	ENST00000411624|ENST00000432730	.|.	.|.	.|.	5.17|5.17	-0.945|-0.945	0.10388|0.10388	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999999084|0.9999999999999084	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.36138|0.36138	-0.9760|-0.9760	3|3	.|.	.|.	.|.	.|.	2.0839|2.0839	0.03641|0.03641	0.177:0.178:0.1227:0.5223|0.177:0.178:0.1227:0.5223	rs12000967|rs12000967	.|.	.|.	.|.	P|P	655|1047	.|.	.|.	A|R	+|+	1|2	0|0	WNK2|WNK2	95064003|95064003	0.613000|0.613000	0.27009|0.27009	0.957000|0.957000	0.39632|0.39632	0.511000|0.511000	0.34104|0.34104	-0.715000|-0.715000	0.04997|0.04997	-0.302000|-0.302000	0.08869|0.08869	-0.647000|-0.647000	0.03941|0.03941	GCC|CGC	G|0.836;C|0.164	0.164	strong		0.692	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648		C	96024182	G	C	96024182	2	2	27	1	0	0	0	0	0	0	0	1	17393	1074	38	4		4	WNK2	9	96024182	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	954940	96024182	45189249	495	10946											
ZNF169	169841	hgsc.bcm.edu	37	chr9	97062852	97062852	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagccctccttctacaccagAggacgcacttggaggagaag	11	7	11	12	1	1	2	0	0	1	2	2	5	2	4	3	3	2	1	3	3	3	4	rs61154129	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:97062852A>T	ENST00000395395.2	+	5	1102	c.1012A>T	c.(1012-1014)Agg>Tgg	p.R338W	ZNF169_ENST00000340911.4_3'UTR	NM_194320.2	NP_919301.2	Q14929	ZN169_HUMAN	zinc finger protein 169	338					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(3)|lung(8)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	24		Acute lymphoblastic leukemia(62;0.136)				TCTACACCAGAGGACGCACTT	0.562													A|||	187	0.0373403	0.0091	0.0706	5008	,	,		20580	0.0833		0.006	False		,,,				2504	0.0368				p.R338W		Atlas-SNP	.											.	ZNF169	60	.	0			c.A1012T						PASS	.	A	TRP/ARG	48,4358	48.9+/-83.8	1,46,2156	99	89	93		1012	1.3	1	9	dbSNP_129	93	92,8508	51.1+/-111.2	1,90,4209	yes	missense	ZNF169	NM_194320.2	101	2,136,6365	TT,TA,AA		1.0698,1.0894,1.0764	probably-damaging	338/604	97062852	140,12866	2203	4300	6503	SO:0001583	missense	169841	exon5			CACCAGAGGACGC	U28322	CCDS6709.2	9q22.32	2014-07-30			ENSG00000175787	ENSG00000175787		"Zinc fingers, C2H2-type", "-"	12957	protein-coding gene	gene with protein product		603404				9186526, 9071574	Standard	NM_001301275		Approved	MGC51961	uc004aum.1	Q14929	OTTHUMG00000020264	ENST00000395395.2:c.1012A>T	9.37:g.97062852A>T	ENSP00000378792:p.Arg338Trp	47	0	0		37	24	0.648649	NM_194320	A2AGP5|A8K127|Q6PI28	Missense_Mutation	SNP	ENST00000395395.2	37	CCDS6709.2	66	0.03021978021978022	5	0.01016260162601626	17	0.04696132596685083	38	0.06643356643356643	6	0.0079155672823219	A	13.18	2.159857	0.38119	0.010894	0.010698	ENSG00000175787	ENST00000395395;ENST00000340911	T	0.25579	1.79	2.53	1.32	0.21799	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07369	0.0186	M	0.93978	3.48	0.09310	P	0.9999999999972624	D	0.71674	0.998	P	0.62813	0.907	T	0.48055	-0.9068	8	0.87932	D	0	.	6.7697	0.23587	0.7458:0.2542:0.0:0.0	rs61154129	338	Q14929	ZN169_HUMAN	W	338;147	ENSP00000378792:R338W	ENSP00000340711:R147W	R	+	1	2	ZNF169	96102673	0.000000	0.05858	0.998000	0.56505	0.364000	0.29643	-0.100000	0.10990	0.372000	0.24591	0.491000	0.48974	AGG	A|0.985;T|0.015	0.015	strong		0.562	ZNF169-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253714.1	NM_194320		T	97062852	A	T	97062852	3	4	27	1	0	0	0	0	1	0	0	0	17757	295	11	5	1026	5	ZNF169	9	97062852	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	1038670	97062852	44150579	496	10947											
C9orf3	84909	hgsc.bcm.edu	37	chr9	97717527	97717527	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tatcaagcatggacttaatcCggagaagatcttcatgcagg	13	10	10	8	1	3	2	2	0	1	2	4	4	4	3	1	3	2	2	1	3	4	3	rs143555020		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:97717527C>T	ENST00000375315.2	+	7	1730	c.1730C>T	c.(1729-1731)cCg>cTg	p.P577L	C9orf3_ENST00000297979.5_Missense_Mutation_p.P478L	NM_001193329.1	NP_001180258.1	Q8N6M6	AMPO_HUMAN	chromosome 9 open reading frame 3	577					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)		GGACTTAATCCGGAGAAGATC	0.398													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20468	0.0		0.0	False		,,,				2504	0.0				p.P577L		Atlas-SNP	.											.	C9orf3	100	.	0			c.C1730T						PASS	.	C	LEU/PRO,LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	125	110	115		1730,1433	4.1	1	9	dbSNP_134	115	0,8600		0,0,4300	no	missense,missense	C9orf3	NM_001193329.1,NM_032823.5	98,98	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	577/820,478/721	97717527	1,13005	2203	4300	6503	SO:0001583	missense	84909	exon7			TTAATCCGGAGAA	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.1730C>T	9.37:g.97717527C>T	ENSP00000364464:p.Pro577Leu	51	0	0		32	7	0.21875	NM_001193329	Q5T9B1|Q5T9B3|Q5T9B4|Q8WUL6|Q96M23|Q96SS1	Missense_Mutation	SNP	ENST00000375315.2	37	CCDS55328.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	10.54	1.377611	0.24944	2.27E-4	0.0	ENSG00000148120	ENST00000297979;ENST00000375315;ENST00000424143;ENST00000428313	T;T;T;T	0.05199	3.48;3.48;3.48;3.48	5.0	4.11	0.48088	.	0.210223	0.39759	N	0.001269	T	0.22781	0.0550	M	0.84082	2.675	0.80722	D	1	D;P;D	0.76494	0.998;0.848;0.999	P;B;P	0.62435	0.835;0.361;0.902	T	0.01508	-1.1337	10	0.87932	D	0	-10.1413	11.284	0.49212	0.0:0.9136:0.0:0.0864	.	577;478;478	Q8N6M6;Q8N6M6-4;Q8N6M6-2	AMPO_HUMAN;.;.	L	478;577;301;359	ENSP00000297979:P478L;ENSP00000364464:P577L;ENSP00000402171:P301L;ENSP00000401854:P359L	ENSP00000297979:P478L	P	+	2	0	C9orf3	96757348	0.442000	0.25633	0.980000	0.43619	0.172000	0.22775	2.770000	0.47662	1.483000	0.48342	-0.126000	0.14955	CCG	C|1.000;T|0.000	0.000	strong		0.398	C9orf3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032823		T	97717527	C	T	97717527	3	4	27	1	0	0	0	0	1	0	0	0	2479	652	23	1	1451	1	C9orf3	9	97717527	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	654675	97717527	43495904	497	10948											
PTCH1	5727	hgsc.bcm.edu	37	chr9	98244242	98244242	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacacttacaggaggtatgcTgtcccagactgtaatttcgc	10	11	9	11	1	0	1	0	0	0	1	2	2	1	2	1	2	2	3	1	2	3	4	rs1805154	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:98244242T>C	ENST00000331920.6	-	5	1034	c.735A>G	c.(733-735)acA>acG	p.T245T	PTCH1_ENST00000429896.2_Silent_p.T94T|PTCH1_ENST00000430669.2_Silent_p.T179T|PTCH1_ENST00000437951.1_Silent_p.T179T|PTCH1_ENST00000418258.1_Silent_p.T94T|PTCH1_ENST00000375274.2_Silent_p.T244T|PTCH1_ENST00000421141.1_Silent_p.T94T|PTCH1_ENST00000548379.1_5'UTR|PTCH1_ENST00000468211.2_Silent_p.T179T	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	245					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)				GGAGGTATGCTGTCCCAGACT	0.388													T|||	47	0.00938498	0.0023	0.0202	5008	,	,		17942	0.0		0.0249	False		,,,				2504	0.0051				p.T245T		Atlas-SNP	.											.	PTCH1	1850	.	0			c.A735G						PASS	.	T	,,,,,,	30,4376	34.3+/-65.2	0,30,2173	84	70	75		735,537,732,282,282,282,282	-2.5	1	9	dbSNP_89	75	329,8271	115.2+/-175.0	4,321,3975	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTCH1	NM_000264.3,NM_001083602.1,NM_001083603.1,NM_001083604.1,NM_001083605.1,NM_001083606.1,NM_001083607.1	,,,,,,	4,351,6148	CC,CT,TT		3.8256,0.6809,2.7603	,,,,,,	245/1448,179/1382,244/1447,94/1297,94/1297,94/1297,94/1297	98244242	359,12647	2203	4300	6503	SO:0001819	synonymous_variant	5727	exon5			GTATGCTGTCCCA	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.735A>G	9.37:g.98244242T>C		91	0	0		94	42	0.446809	NM_000264	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	ENST00000331920.6	37	CCDS6714.1																																																																																			T|0.976;C|0.024	0.024	strong		0.388	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		C	98244242	T	C	98244242	2	2	27	1	0	0	0	0	0	0	0	1	12742	1567	55	3		3	PTCH1	9	98244242	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	526715	98244242	42969189	498	10949											
HSD17B3	3293	hgsc.bcm.edu	37	chr9	99064378	99064378	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgaagaactgttccaggacGtcccccatggctgcactcaa	11	8	9	13	1	1	2	1	1	0	1	3	3	3	3	3	2	2	3	3	2	3	1	rs139582148	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:99064378G>A	ENST00000375263.3	-	1	56	c.9C>T	c.(7-9)gaC>gaT	p.D3D	HSD17B3_ENST00000375262.2_Silent_p.D3D	NM_000197.1	NP_000188.1	P37058	DHB3_HUMAN	hydroxysteroid (17-beta) dehydrogenase 3	3					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)				GTTCCAGGACGTCCCCCATGG	0.567													G|||	8	0.00159744	0.0038	0.0014	5008	,	,		17045	0.0		0.002	False		,,,				2504	0.0				p.D3D		Atlas-SNP	.											.	HSD17B3	32	.	0			c.C9T						PASS	.	G		6,4400	11.4+/-27.6	0,6,2197	82	72	75		9	-6.7	0	9	dbSNP_134	75	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	HSD17B3	NM_000197.1		0,12,6491	AA,AG,GG		0.0698,0.1362,0.0923		3/311	99064378	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	3293	exon1			CAGGACGTCCCCC		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.9C>T	9.37:g.99064378G>A		97	0	0		109	56	0.513761	NM_000197	Q5U0Q6	Silent	SNP	ENST00000375263.3	37	CCDS6716.1																																																																																			G|0.999;A|0.001	0.001	strong		0.567	HSD17B3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053259.1	NM_000197		A	99064378	G	A	99064378	2	1	27	1	0	0	0	0	0	0	0	1	7394	1136	40	1		1	HSD17B3	9	99064378	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	820136	99064378	42149053	499	10950											
KIAA1529	100499483	hgsc.bcm.edu	37	chr9	100122384	100122384	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgactgaactggtctttaccGtaaggaatgggatagggtgg	10	11	15	5	1	1	2	0	2	1	0	1	4	1	4	1	5	2	1	1	5	5	4	rs376419121		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:100122384G>A	ENST00000357054.1	+	37	4463		c.e37+1		RP11-23J9.4_ENST00000534123.1_RNA|CCDC180_ENST00000375202.2_Splice_Site|CCDC180_ENST00000529487.1_Splice_Site|CCDC180_ENST00000395220.1_Splice_Site			Q9P1Z9	CC180_HUMAN	coiled-coil domain containing 180							extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.?(1)									GGTCTTTACCGTAAGGAATGG	0.547																																					.		Atlas-SNP	.											KIAA1529,mouth,carcinoma,0,1	.	.	1	1	Unknown(1)	upper_aerodigestive_tract(1)	c.3615+1G>A						PASS	.	G		0,4406		0,0,2203	100	95	97			3.5	0.9	9		97	1,8599	1.2+/-3.3	0,1,4299	no	splice-5	C9orf174	NM_020893.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077			100122384	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	0	exon26			TTTACCGTAAGGA	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.3528+1G>A	9.37:g.100122384G>A		92	0	0		67	17	0.253731	NM_020893	Q2KHR6|Q5VV25|Q68DP5|Q69YV9|Q6AHY0	Splice_Site	SNP	ENST00000357054.1	37		.	.	.	.	.	.	.	.	.	.	G	12.90	2.075193	0.36662	0.0	1.16E-4	ENSG00000197816	ENST00000357054;ENST00000375202;ENST00000529487	.	.	.	5.31	3.47	0.39725	.	.	.	.	.	.	.	.	.	.	.	0.58432	D	0.999998	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.3386	0.26623	0.1896:0.0:0.8104:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C9orf174	99162205	0.974000	0.33945	0.889000	0.34880	0.044000	0.14063	1.890000	0.39728	1.571000	0.49722	0.561000	0.74099	.	.	.	weak		0.547	CCDC180-201	KNOWN	basic	protein_coding	protein_coding		NM_020893	Intron	A	100122384	G	A	100122384	5	1	27	1	0	0	0	0	0	0	1	0	8249	1159	40	1	3631	1	KIAA1529	9	100122384	Splice_Site	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1058006	100122384	41091047	500	10951											
LPPR1	54886	hgsc.bcm.edu	37	chr9	103947810	103947810	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaacactcaacgaagttatTccatcatcccgtgttttata	13	13	4	11	2	2	0	2	0	0	0	4	1	4	0	2	0	2	2	2	0	6	5	rs41296085	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:103947810T>G	ENST00000374874.3	+	2	473	c.34T>G	c.(34-36)Tcc>Gcc	p.S12A	LPPR1_ENST00000395056.2_Missense_Mutation_p.S12A|LPPR1_ENST00000494890.1_3'UTR	NM_207299.1	NP_997182.1	Q8TBJ4	LPPR1_HUMAN		12					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)										ACGAAGTTATTCCATCATCCC	0.338													T|||	42	0.00838658	0.0	0.0144	5008	,	,		16008	0.0		0.0169	False		,,,				2504	0.0153				p.S12A		Atlas-SNP	.											.	.	.	.	0			c.T34G						PASS	.	T	ALA/SER,ALA/SER	17,4389	24.3+/-50.5	0,17,2186	221	202	208		34,34	5.9	1	9	dbSNP_127	208	133,8467	67.3+/-129.8	1,131,4168	yes	missense,missense	LPPR1	NM_017753.2,NM_207299.1	99,99	1,148,6354	GG,GT,TT		1.5465,0.3858,1.1533	benign,benign	12/326,12/326	103947810	150,12856	2203	4300	6503	SO:0001583	missense	0	exon2			AGTTATTCCATCA																												ENST00000374874.3:c.34T>G	9.37:g.103947810T>G	ENSP00000364008:p.Ser12Ala	246	0	0		227	111	0.488987	NM_207299	Q5VX23|Q9NXE2	Missense_Mutation	SNP	ENST00000374874.3	37	CCDS6751.1	20	0.009157509157509158	0	0.0	6	0.016574585635359115	0	0.0	14	0.018469656992084433	T	15.22	2.768539	0.49680	0.003858	0.015465	ENSG00000148123	ENST00000374874;ENST00000456287;ENST00000374871;ENST00000395056	T;T;T	0.38077	1.16;1.16;1.16	5.93	5.93	0.95920	.	0.431258	0.25774	N	0.028386	T	0.23094	0.0558	M	0.65498	2.005	0.34363	D	0.691192	B	0.02656	0.0	B	0.08055	0.003	T	0.40384	-0.9566	10	0.34782	T	0.22	-32.2815	14.3318	0.66561	0.0:0.0:0.0:1.0	rs41296085;rs61755095	12	Q8TBJ4	LPPR1_HUMAN	A	12	ENSP00000364008:S12A;ENSP00000410223:S12A;ENSP00000378496:S12A	ENSP00000364005:S12A	S	+	1	0	RP11-35N6.1	102987631	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.743000	0.62110	2.271000	0.75665	0.533000	0.62120	TCC	T|0.990;G|0.010	0.010	strong		0.338	LPPR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053425.1			G	103947810	T	G	103947810	3	3	27	1	0	0	0	0	1	0	0	0	8933	1783	62	5	36	5	LPPR1	9	103947810	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	3825426	103947810	37265621	501	10952											
ZNF189	7743	hgsc.bcm.edu	37	chr9	104170796	104170796	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccagagaaggagccttgttaAacatcaaaggattcatacag	16	8	9	8	0	2	1	2	0	0	1	2	4	2	3	2	2	3	1	2	2	5	4	rs370077009		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:104170796A>T	ENST00000339664.2	+	3	875	c.746A>T	c.(745-747)aAa>aTa	p.K249I	ZNF189_ENST00000259395.4_Missense_Mutation_p.K207I|ZNF189_ENST00000374861.3_Missense_Mutation_p.K235I	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	249					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)				AGCCTTGTTAAACATCAAAGG	0.423																																					p.K249I		Atlas-SNP	.											.	ZNF189	79	.	0			c.A746T						PASS	.	A	ILE/LYS,ILE/LYS	0,4406		0,0,2203	183	188	186		746,620	4.7	1	9		186	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	ZNF189	NM_003452.2,NM_197977.1	102,102	0,2,6501	TT,TA,AA		0.0233,0.0,0.0154	benign,benign	249/627,207/585	104170796	2,13004	2203	4300	6503	SO:0001583	missense	7743	exon3			TTGTTAAACATCA	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.746A>T	9.37:g.104170796A>T	ENSP00000342019:p.Lys249Ile	65	0	0		46	27	0.586957	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Missense_Mutation	SNP	ENST00000339664.2	37	CCDS6754.1	.	.	.	.	.	.	.	.	.	.	A	8.404	0.842724	0.16963	0.0	2.33E-4	ENSG00000136870	ENST00000374861;ENST00000339664;ENST00000259395	T;T;T	0.20598	2.06;2.06;2.06	4.67	4.67	0.58626	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.52532	D	0.000079	T	0.12689	0.0308	L	0.28649	0.875	0.31428	N	0.67353	P;B;P	0.43314	0.803;0.136;0.507	B;B;B	0.37304	0.246;0.032;0.205	T	0.06917	-1.0800	10	0.30078	T	0.28	.	7.1431	0.25566	0.9035:0.0:0.0965:0.0	.	234;235;249	B7ZLK9;Q5T7D8;O75820	.;.;ZN189_HUMAN	I	235;249;207	ENSP00000363995:K235I;ENSP00000342019:K249I;ENSP00000259395:K207I	ENSP00000259395:K207I	K	+	2	0	ZNF189	103210617	0.000000	0.05858	1.000000	0.80357	0.998000	0.95712	-2.494000	0.00972	2.324000	0.78689	0.533000	0.62120	AAA	.	.	weak		0.423	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452		T	104170796	A	T	104170796	3	4	27	1	0	0	0	0	1	0	0	0	17769	14	1	5	756	5	ZNF189	9	104170796	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	222986	104170796	37042635	502	10953											
OR13C3	138803	hgsc.bcm.edu	37	chr9	107298270	107298270	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaaatatgatcaccacagtCaggtgagctgagcacgtgga	14	8	11	8	1	2	3	2	3	0	0	2	4	2	4	1	2	2	2	1	2	3	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:107298270C>A	ENST00000374781.2	-	1	867	c.825G>T	c.(823-825)ctG>ctT	p.L275L		NM_001001961.1	NP_001001961.1	Q8NGS6	O13C3_HUMAN	olfactory receptor, family 13, subfamily C, member 3	275						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						TCACCACAGTCAGGTGAGCTG	0.423																																					p.L275L	GBM(86;1248 1274 14222 15028 46219)	Atlas-SNP	.											.	OR13C3	45	.	0			c.G825T						PASS	.						134	126	129					9																	107298270		2203	4300	6503	SO:0001819	synonymous_variant	138803	exon1			CACAGTCAGGTGA		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.825G>T	9.37:g.107298270C>A		141	0	0		108	22	0.203704	NM_001001961	Q5VVG1|Q6IF52	Silent	SNP	ENST00000374781.2	37	CCDS35089.1																																																																																			.	.	none		0.423	OR13C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053477.2			A	107298270	C	A	107298270	2	1	27	1	0	0	0	0	0	0	0	1	10944	813	29	4		4	OR13C3	9	107298270	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3127474	107298270	33915161	503	10954											
MUSK	4593	hgsc.bcm.edu	37	chr9	113449489	113449489	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatggcatttactgctgcaCggccaacaatggtgtgggag	9	10	14	8	1	0	1	0	1	0	0	0	2	0	2	1	4	4	3	1	4	3	2	rs35142681	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:113449489C>T	ENST00000374448.4	+	3	433	c.299C>T	c.(298-300)aCg>aTg	p.T100M	MUSK_ENST00000416899.2_Missense_Mutation_p.T100M|MUSK_ENST00000374439.1_5'Flank|MUSK_ENST00000374440.3_5'UTR|MUSK_ENST00000189978.5_Missense_Mutation_p.T100M	NM_001166281.1|NM_005592.3	NP_001159753.1|NP_005583.1	O15146	MUSK_HUMAN	muscle, skeletal, receptor tyrosine kinase	100	Ig-like 1.		T -> M (in dbSNP:rs35142681). {ECO:0000269|PubMed:17344846}.		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						TACTGCTGCACGGCCAACAAT	0.517													C|||	49	0.00978435	0.0015	0.0216	5008	,	,		17374	0.0		0.0308	False		,,,				2504	0.001				p.T100M		Atlas-SNP	.											.	MUSK	112	.	0			c.C299T						PASS	.	C	MET/THR,MET/THR,MET/THR	29,4035		1,27,2004	181	187	185		299,299,299	-7.1	0	9	dbSNP_126	185	254,8152		3,248,3952	yes	missense,missense,missense	MUSK	NM_001166280.1,NM_001166281.1,NM_005592.3	81,81,81	4,275,5956	TT,TC,CC		3.0217,0.7136,2.2694	benign,benign,benign	100/784,100/774,100/870	113449489	283,12187	2032	4203	6235	SO:0001583	missense	4593	exon3			GCTGCACGGCCAA	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.299C>T	9.37:g.113449489C>T	ENSP00000363571:p.Thr100Met	212	0	0		157	157	1	NM_001166281	Q32MJ8|Q32MJ9|Q5VZW7|Q5VZW8	Missense_Mutation	SNP	ENST00000374448.4	37	CCDS48005.1	29	0.013278388278388278	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	22	0.029023746701846966	C	11.55	1.672850	0.29693	0.007136	0.030217	ENSG00000030304	ENST00000189978;ENST00000374448;ENST00000543335;ENST00000374447;ENST00000545907;ENST00000416899	T	0.68765	-0.35	6.05	-7.08	0.01558	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.734616	0.13377	N	0.392447	T	0.22322	0.0538	N	0.25245	0.725	0.33065	D	0.534608	B;B	0.28233	0.164;0.204	B;B	0.24701	0.055;0.053	T	0.07462	-1.0771	10	0.48119	T	0.1	.	13.5019	0.61462	0.0999:0.6723:0.0:0.2278	rs35142681	100;100	O15146;F5H6T2	MUSK_HUMAN;.	M	100	ENSP00000363571:T100M	ENSP00000189978:T100M	T	+	2	0	MUSK	112489310	0.014000	0.17966	0.006000	0.13384	0.988000	0.76386	0.205000	0.17356	-1.188000	0.02705	-0.355000	0.07637	ACG	C|0.983;T|0.017	0.017	strong		0.517	MUSK-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				T	113449489	C	T	113449489	3	4	27	1	0	0	0	0	1	0	0	0	9998	536	19	1	309	1	MUSK	9	113449489	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	6151219	113449489	27763942	504	10955											
KIAA0368	23392	hgsc.bcm.edu	37	chr9	114124354	114124354	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cttcagtaacgctgctttctCctgcagttcaggtctgctgt	5	15	9	12	1	4	0	2	0	2	0	5	0	4	0	1	1	4	6	1	1	1	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:114124354C>A	ENST00000338205.5	-	49	5695	c.5476G>T	c.(5476-5478)Gag>Tag	p.E1826*	KIAA0368_ENST00000374378.3_Intron|KIAA0368_ENST00000259335.4_Nonsense_Mutation_p.E2004*			Q5VYK3	ECM29_HUMAN	KIAA0368	1832					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						GCTGCTTTCTCCTGCAGTTCA	0.428																																					p.E2004X		Atlas-SNP	.											.	KIAA0368	144	.	0			c.G6010T						PASS	.						130	133	132					9																	114124354		1912	4132	6044	SO:0001587	stop_gained	23392	exon51			CTTTCTCCTGCAG	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.5476G>T	9.37:g.114124354C>A	ENSP00000339889:p.Glu1826*	161	0	0		128	28	0.21875	NM_001080398	O15074|Q8WU82	Nonsense_Mutation	SNP	ENST00000338205.5	37		.	.	.	.	.	.	.	.	.	.	C	47	13.552294	0.99749	.	.	ENSG00000136813	ENST00000338205;ENST00000259335;ENST00000543827	.	.	.	5.93	5.93	0.95920	.	0.090694	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.21540	T	0.41	0.3296	20.3465	0.98790	0.0:1.0:0.0:0.0	.	.	.	.	X	1826;2004;1301	.	ENSP00000259335:E2004X	E	-	1	0	KIAA0368	113164175	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.127000	0.77210	2.798000	0.96311	0.655000	0.94253	GAG	.	.	none		0.428	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686		A	114124354	C	A	114124354	4	1	27	1	0	0	0	0	0	1	0	0	8180	864	30	4	47	4	KIAA0368	9	114124354	Nonsense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	674865	114124354	27089077	505	10956											
KIAA0368	23392	hgsc.bcm.edu	37	chr9	114172438	114172438	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatttctgccaatttcaccCagggctgtgcaggcagcaat	9	10	9	13	0	2	0	1	0	1	0	2	0	2	0	3	2	3	4	3	2	2	2	rs61744546	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:114172438C>T	ENST00000338205.5	-	22	2652	c.2433G>A	c.(2431-2433)ctG>ctA	p.L811L	KIAA0368_ENST00000374378.3_5'Flank|RNA5SP294_ENST00000411306.1_RNA|KIAA0368_ENST00000259335.4_Silent_p.L989L			Q5VYK3	ECM29_HUMAN	KIAA0368	817					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						CAATTTCACCCAGGGCTGTGC	0.443													C|||	16	0.00319489	0.0	0.0043	5008	,	,		18148	0.0		0.0089	False		,,,				2504	0.0041				p.L989L		Atlas-SNP	.											.	KIAA0368	144	.	0			c.G2967A						PASS	.	C		1,3801		0,1,1900	53	53	53		2967	5	1	9	dbSNP_129	53	101,8165		0,101,4032	no	coding-synonymous	KIAA0368	NM_001080398.1		0,102,5932	TT,TC,CC		1.2219,0.0263,0.8452		989/2018	114172438	102,11966	1901	4133	6034	SO:0001819	synonymous_variant	23392	exon24			TTCACCCAGGGCT	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.2433G>A	9.37:g.114172438C>T		212	0	0		159	63	0.396226	NM_001080398	O15074|Q8WU82	Silent	SNP	ENST00000338205.5	37																																																																																				C|0.993;T|0.007	0.007	strong		0.443	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2	NM_014686		T	114172438	C	T	114172438	2	4	27	1	0	0	0	0	0	0	0	1	8180	581	21	2		2	KIAA0368	9	114172438	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	48084	114172438	27040993	506	10957											
HSDL2	84263	hgsc.bcm.edu	37	chr9	115167994	115167994	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtggagaaagccatcaagaAatttggaggtaataccttca	16	9	10	6	0	2	2	2	0	0	2	2	4	2	3	2	3	2	1	2	3	5	4	rs41280175	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:115167994A>T	ENST00000398805.3	+	3	499	c.272A>T	c.(271-273)aAa>aTa	p.K91I	HSDL2_ENST00000398803.1_Missense_Mutation_p.K91I|HSDL2_ENST00000488101.1_3'UTR|HSDL2_ENST00000539114.1_5'UTR|HSDL2_ENST00000262542.7_5'UTR	NM_032303.4	NP_115679.2	Q6YN16	HSDL2_HUMAN	hydroxysteroid dehydrogenase like 2	91						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						GCCATCAAGAAATTTGGAGGT	0.318													A|||	10	0.00199681	0.0008	0.0058	5008	,	,		16111	0.0		0.005	False		,,,				2504	0.0				p.K91I		Atlas-SNP	.											.	HSDL2	24	.	0			c.A272T						PASS	.	A	ILE/LYS,ILE/LYS	7,3743		0,7,1868	128	126	126		272,272	3.2	1	9	dbSNP_127	126	107,8109		1,105,4002	yes	missense,missense	HSDL2	NM_001195822.1,NM_032303.4	102,102	1,112,5870	TT,TA,AA		1.3023,0.1867,0.9527	benign,benign	91/346,91/419	115167994	114,11852	1875	4108	5983	SO:0001583	missense	84263	exon3			TCAAGAAATTTGG	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.272A>T	9.37:g.115167994A>T	ENSP00000381785:p.Lys91Ile	63	0	0		43	26	0.604651	NM_032303	A8K1L4|A8K8X1|A8MSV3|Q658M8|Q9BT58	Missense_Mutation	SNP	ENST00000398805.3	37	CCDS43864.1	8	0.003663003663003663	0	0.0	3	0.008287292817679558	0	0.0	5	0.006596306068601583	A	12.14	1.848888	0.32699	0.001867	0.013023	ENSG00000119471	ENST00000398805;ENST00000398803	D;D	0.88431	-2.38;-2.38	5.57	3.15	0.36227	NAD(P)-binding domain (1);	0.456598	0.25677	N	0.029030	D	0.82296	0.5006	M	0.69823	2.125	0.80722	D	1	P;B	0.45902	0.868;0.064	B;B	0.42138	0.377;0.159	T	0.79027	-0.1971	10	0.39692	T	0.17	.	6.4508	0.21902	0.6281:0.2284:0.1434:0.0	rs41280175	91;91	Q6YN16-2;Q6YN16	.;HSDL2_HUMAN	I	91	ENSP00000381785:K91I;ENSP00000381783:K91I	ENSP00000381783:K91I	K	+	2	0	HSDL2	114207815	0.922000	0.31269	0.991000	0.47740	0.021000	0.10359	0.964000	0.29306	0.369000	0.24510	0.260000	0.18958	AAA	A|0.995;T|0.005	0.005	strong		0.318	HSDL2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053681.1	NM_032303		T	115167994	A	T	115167994	3	4	27	1	0	0	0	0	1	0	0	0	7403	14	1	5	282	5	HSDL2	9	115167994	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	995556	115167994	26045437	507	10958											
FKBP15	23307	hgsc.bcm.edu	37	chr9	115936860	115936860	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttctttttcctttctgagaGgttcttaggaacaagagaac	10	15	8	8	0	3	2	0	1	3	2	4	5	4	3	1	2	2	1	1	2	4	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:115936860G>A	ENST00000238256.3	-	22	2344	c.2227C>T	c.(2227-2229)Ctc>Ttc	p.L743F		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	743					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						CTTTCTGAGAGGTTCTTAGGA	0.443																																					p.L743F		Atlas-SNP	.											FKBP15_ENST00000238256,NS,carcinoma,+1,2	FKBP15	128	2	0			c.C2227T						PASS	.						65	63	64					9																	115936860		1882	4104	5986	SO:0001583	missense	23307	exon22			CTGAGAGGTTCTT	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.2227C>T	9.37:g.115936860G>A	ENSP00000238256:p.Leu743Phe	219	0	0		133	39	0.293233	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Missense_Mutation	SNP	ENST00000238256.3	37	CCDS48007.1	.	.	.	.	.	.	.	.	.	.	g	20.6	4.021430	0.75275	.	.	ENSG00000119321	ENST00000446284;ENST00000238256	T;T	0.29397	1.57;1.58	6.07	6.07	0.98685	.	.	.	.	.	T	0.57227	0.2039	M	0.72894	2.215	0.39987	D	0.974995	D;P	0.89917	1.0;0.788	D;B	0.76575	0.988;0.257	T	0.58194	-0.7679	9	0.72032	D	0.01	-11.325	18.151	0.89674	0.0:0.0:1.0:0.0	.	324;743	B4DVS2;Q5T1M5	.;FKB15_HUMAN	F	768;743	ENSP00000416158:L768F;ENSP00000238256:L743F	ENSP00000238256:L743F	L	-	1	0	FKBP15	114976681	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.051000	0.57412	2.890000	0.99128	0.586000	0.80456	CTC	.	.	none		0.443	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258		A	115936860	G	A	115936860	3	1	27	1	0	0	0	0	1	0	0	0	5913	1000	35	2	1460	2	FKBP15	9	115936860	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	768866	115936860	25276571	508	10959											
ORM1	5004	hgsc.bcm.edu	37	chr9	117087412	117087412	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcattcccaagtcagatgtcGtgtacaccgattggaaaaag	13	9	10	9	2	1	1	1	0	0	1	3	3	2	2	2	1	1	2	2	1	4	3	rs1126801	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:117087412G>A	ENST00000259396.8	+	5	598	c.520G>A	c.(520-522)Gtg>Atg	p.V174M	ORM1_ENST00000477456.1_3'UTR	NM_000607.2	NP_000598.2	P02763	A1AG1_HUMAN	orosomucoid 1	174			V -> M (in allele ORM1*F2; dbSNP:rs1126801). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9050929}.		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)	GTCAGATGTCGTGTACACCGA	0.572													-|||	111	0.0221645	0.0408	0.0187	5008	,	,		23206	0.001		0.0328	False		,,,				2504	0.0102				p.V174M		Atlas-SNP	.											.	ORM1	20	.	0			c.G520A						PASS	.	A	MET/VAL	183,4223		0,183,2020	128	141	136		520	-8.5	0	9	dbSNP_86	136	191,8409		2,187,4111	no	missense	ORM1	NM_000607.2	21	2,370,6131	AA,AG,GG		2.2209,4.1534,2.8756	benign	174/202	117087412	374,12632	2203	4300	6503	SO:0001583	missense	5004	exon5			GATGTCGTGTACA		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.520G>A	9.37:g.117087412G>A	ENSP00000259396:p.Val174Met	150	0	0		128	67	0.523438	NM_000607	B7ZKQ5|Q5T539|Q5U067|Q8TC16	Missense_Mutation	SNP	ENST00000259396.8	37	CCDS6803.1	51	0.023351648351648352	18	0.036585365853658534	8	0.022099447513812154	1	0.0017482517482517483	24	0.0316622691292876	-	3.977	-0.007207	0.07773	0.041534	0.022209	ENSG00000229314	ENST00000259396	T	0.10099	2.91	4.23	-8.47	0.00939	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	1.390010	0.04077	N	0.308987	T	0.00524	0.0017	N	0.02916	-0.46	0.09310	N	0.999999	P	0.37525	0.598	B	0.18263	0.021	T	0.40905	-0.9538	10	0.12103	T	0.63	-0.9597	2.7473	0.05271	0.3979:0.2169:0.2939:0.0913	rs1126801;rs1803078;rs3182058;rs11552134;rs17412027	174	P02763	A1AG1_HUMAN	M	174	ENSP00000259396:V174M	ENSP00000259396:V174M	V	+	1	0	ORM1	116127233	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.459000	0.02370	-2.210000	0.00738	0.197000	0.17608	GTG	G|0.972;A|0.028	0.028	strong		0.572	ORM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055426.1			A	117087412	G	A	117087412	3	1	27	1	0	0	0	0	1	0	0	0	11276	1145	40	1	538	1	ORM1	9	117087412	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1150552	117087412	24126019	509	10960											
PAPPA	5069	hgsc.bcm.edu	37	chr9	119028233	119028233	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgtcacatacatccatggaAgtgggtactgtggcgatggc	9	10	13	9	1	1	0	1	0	0	0	2	2	2	1	1	4	2	1	1	4	3	2	rs117124330	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:119028233A>C	ENST00000328252.3	+	8	3199	c.2830A>C	c.(2830-2832)Agt>Cgt	p.S944R	PAPPA_ENST00000534838.1_5'UTR	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	944			S -> R (in dbSNP:rs117124330). {ECO:0000269|PubMed:7508748, ECO:0000269|PubMed:8620868}.		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						CATCCATGGAAGTGGGTACTG	0.438													A|||	48	0.00958466	0.0	0.0159	5008	,	,		19890	0.0		0.0169	False		,,,				2504	0.0204				p.S944R		Atlas-SNP	.											.	PAPPA	243	.	0			c.A2830C						PASS	.	A	ARG/SER	17,4389	25.3+/-52.1	0,17,2186	103	94	97		2830	2.9	1	9	dbSNP_132	97	154,8446	73.8+/-136.5	1,152,4147	yes	missense	PAPPA	NM_002581.3	110	1,169,6333	CC,CA,AA		1.7907,0.3858,1.3148	possibly-damaging	944/1628	119028233	171,12835	2203	4300	6503	SO:0001583	missense	5069	exon8			CATGGAAGTGGGT		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.2830A>C	9.37:g.119028233A>C	ENSP00000330658:p.Ser944Arg	81	0	0		68	39	0.573529	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Missense_Mutation	SNP	ENST00000328252.3	37	CCDS6813.1	15	0.006868131868131868	0	0.0	4	0.011049723756906077	0	0.0	11	0.014511873350923483	A	12.44	1.939319	0.34189	0.003858	0.017907	ENSG00000182752	ENST00000328252;ENST00000443904	T	0.42513	0.97	5.28	2.88	0.33553	.	0.277336	0.47093	D	0.000259	T	0.29882	0.0747	L	0.45698	1.435	0.80722	D	1	D;P	0.59357	0.985;0.918	P;P	0.56916	0.809;0.475	T	0.06127	-1.0844	10	0.30078	T	0.28	-1.3511	8.9684	0.35890	0.8425:0.0:0.1575:0.0	.	388;944	E7EMD3;Q13219	.;PAPP1_HUMAN	R	944;388	ENSP00000330658:S944R	ENSP00000330658:S944R	S	+	1	0	PAPPA	118068054	1.000000	0.71417	0.995000	0.50966	0.969000	0.65631	1.669000	0.37492	0.306000	0.22856	0.455000	0.32223	AGT	A|0.988;C|0.012	0.012	strong		0.438	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581		C	119028233	A	C	119028233	3	2	27	1	0	0	0	0	1	0	0	0	11441	72	3	5	2860	5	PAPPA	9	119028233	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	1940821	119028233	22185198	510	10961											
DBC1	1620	hgsc.bcm.edu	37	chr9	121930344	121930344	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccaggctgcacatggcgcagCtgttgttcccgcctatcacg	6	9	11	15	3	1	0	1	0	0	0	2	0	2	0	3	2	2	6	3	2	1	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:121930344C>T	ENST00000265922.3	-	8	1765	c.1304G>A	c.(1303-1305)aGc>aAc	p.S435N	BRINP1_ENST00000482797.1_Intron	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	435					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)											CATGGCGCAGCTGTTGTTCCC	0.632																																					p.S435N		Atlas-SNP	.											.	DBC1	194	.	0			c.G1304A						PASS	.						31	31	31					9																	121930344		2203	4300	6503	SO:0001583	missense	1620	exon8			GCGCAGCTGTTGT	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.1304G>A	9.37:g.121930344C>T	ENSP00000265922:p.Ser435Asn	106	0	0		115	16	0.13913	NM_014618	Q6IPV6|Q6P1A0|Q8WU22	Missense_Mutation	SNP	ENST00000265922.3	37	CCDS6822.1	.	.	.	.	.	.	.	.	.	.	C	16.86	3.239289	0.58995	.	.	ENSG00000078725	ENST00000373969;ENST00000265922	T	0.54479	0.57	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.56558	0.1993	L	0.40543	1.245	0.80722	D	1	D	0.53885	0.963	P	0.49853	0.624	T	0.55166	-0.8183	10	0.46703	T	0.11	-29.9476	19.8211	0.96595	0.0:1.0:0.0:0.0	.	435	O60477	DBC1_HUMAN	N	435	ENSP00000265922:S435N	ENSP00000265922:S435N	S	-	2	0	DBC1	120970165	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.947000	0.56652	2.687000	0.91594	0.655000	0.94253	AGC	.	.	none		0.632	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618		T	121930344	C	T	121930344	3	4	27	1	0	0	0	0	1	0	0	0	4249	797	28	2	985	2	DBC1	9	121930344	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2902111	121930344	19283087	511	10962											
C5	727	hgsc.bcm.edu	37	chr9	123776220	123776220	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcttgcgacgacacaacattCagtgaaagctttgatgcatc	12	10	9	10	2	1	2	1	2	0	0	2	4	1	2	0	0	4	3	0	0	2	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:123776220C>T	ENST00000223642.1	-	17	2217	c.2188G>A	c.(2188-2190)Gaa>Aaa	p.E730K		NM_001735.2	NP_001726.2	P01031	CO5_HUMAN	complement component 5	730	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)	ACACAACATTCAGTGAAAGCT	0.438																																					p.E730K		Atlas-SNP	.											.	C5	124	.	0			c.G2188A						PASS	.						170	145	154					9																	123776220		2203	4300	6503	SO:0001583	missense	727	exon17			AACATTCAGTGAA	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.2188G>A	9.37:g.123776220C>T	ENSP00000223642:p.Glu730Lys	153	0	0		131	42	0.320611	NM_001735	Q14CJ0|Q27I61	Missense_Mutation	SNP	ENST00000223642.1	37	CCDS6826.1	.	.	.	.	.	.	.	.	.	.	C	12.08	1.829145	0.32329	.	.	ENSG00000106804	ENST00000223642;ENST00000430906	T	0.24151	1.87	6.06	0.0997	0.14504	Complement C3a/C4a/C5a anaphylatoxin (1);Anaphylatoxin (2);Anaphylatoxin/fibulin (4);	1.861730	0.01962	N	0.043417	T	0.17662	0.0424	L	0.35593	1.075	0.09310	N	1	B	0.30563	0.285	B	0.28916	0.096	T	0.10291	-1.0636	10	0.15952	T	0.53	.	3.2397	0.06777	0.1112:0.4786:0.1091:0.3011	.	730	P01031	CO5_HUMAN	K	730;801	ENSP00000223642:E730K	ENSP00000223642:E730K	E	-	1	0	C5	122816041	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	-0.178000	0.09782	0.088000	0.17205	0.650000	0.86243	GAA	.	.	none		0.438	C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053844.1	NM_001735		T	123776220	C	T	123776220	3	4	27	1	0	0	0	0	1	0	0	0	2282	835	29	2	2942	2	C5	9	123776220	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1845876	123776220	17437211	512	10963											
PTGS1	5742	hgsc.bcm.edu	37	chr9	125154660	125154660	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctccggagtactggaagcCgagcacatttggcggcgagg	8	8	15	10	4	1	0	0	0	1	0	2	4	1	2	2	5	3	2	2	5	2	3	rs200295924		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:125154660C>T	ENST00000362012.2	+	11	1642	c.1637C>T	c.(1636-1638)cCg>cTg	p.P546L	PTGS1_ENST00000373698.5_Missense_Mutation_p.P437L|PTGS1_ENST00000223423.4_Missense_Mutation_p.P509L|PTGS1_ENST00000540753.1_Missense_Mutation_p.P484L	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)	546					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)	TACTGGAAGCCGAGCACATTT	0.527																																					p.P546L		Atlas-SNP	.											.	PTGS1	84	.	0			c.C1637T						PASS	.						112	111	112					9																	125154660		2203	4300	6503	SO:0001583	missense	5742	exon11			GGAAGCCGAGCAC	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.1637C>T	9.37:g.125154660C>T	ENSP00000354612:p.Pro546Leu	272	0	0		230	57	0.247826	NM_000962	A8K1V7|B4DHQ2|B4E2S5|Q15122|Q3HY28|Q3HY29|Q5T7T6|Q5T7T7|Q5T7T8	Missense_Mutation	SNP	ENST00000362012.2	37	CCDS6842.1	.	.	.	.	.	.	.	.	.	.	C	32	5.178609	0.94846	.	.	ENSG00000095303	ENST00000540753;ENST00000362012;ENST00000223423;ENST00000373698	T;T;T;T	0.71103	-0.54;-0.54;-0.54;-0.54	5.41	5.41	0.78517	.	0.096182	0.64402	D	0.000001	D	0.87370	0.6160	M	0.91920	3.255	0.80722	D	1	P;D;D	0.69078	0.939;0.995;0.997	P;D;D	0.68621	0.71;0.959;0.931	D	0.90078	0.4168	10	0.87932	D	0	-4.3937	18.2032	0.89846	0.0:1.0:0.0:0.0	.	484;546;509	B4DHQ2;P23219;P23219-2	.;PGH1_HUMAN;.	L	484;546;509;437	ENSP00000437709:P484L;ENSP00000354612:P546L;ENSP00000223423:P509L;ENSP00000362802:P437L	ENSP00000223423:P509L	P	+	2	0	PTGS1	124194481	1.000000	0.71417	0.878000	0.34440	0.935000	0.57460	7.814000	0.86154	2.539000	0.85634	0.655000	0.94253	CCG	.	.	weak		0.527	PTGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053933.1			T	125154660	C	T	125154660	3	4	27	1	0	0	0	0	1	0	0	0	12768	652	23	1	1679	1	PTGS1	9	125154660	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1378440	125154660	16058771	513	10964											
RC3H2	54542	hgsc.bcm.edu	37	chr9	125639808	125639808	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttcctcgtggacaaccccCttgctgtcgcaaatctcggc	6	11	9	15	3	1	0	0	0	1	0	5	1	2	1	3	2	2	3	3	2	2	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:125639808C>T	ENST00000373670.1	-	8	1867	c.1267G>A	c.(1267-1269)Ggg>Agg	p.G423R	RC3H2_ENST00000423239.2_Missense_Mutation_p.G423R|RC3H2_ENST00000335387.5_Missense_Mutation_p.G423R|SNORD90_ENST00000391145.1_RNA|RC3H2_ENST00000357244.2_Missense_Mutation_p.G423R|RC3H2_ENST00000373665.2_Missense_Mutation_p.G423R			Q9HBD1	RC3H2_HUMAN	ring finger and CCCH-type domains 2	423					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						GGACAACCCCCTTGCTGTCGC	0.418																																					p.G423R		Atlas-SNP	.											.	RC3H2	150	.	0			c.G1267A						PASS	.						276	270	272					9																	125639808		1898	4121	6019	SO:0001583	missense	54542	exon9			AACCCCCTTGCTG	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.1267G>A	9.37:g.125639808C>T	ENSP00000362774:p.Gly423Arg	73	0	0		60	37	0.616667	NM_018835	Q4VXB1|Q5JPD7|Q86ST6|Q8N3D6|Q96F27|Q9H5J2|Q9HBD2|Q9NWN9|Q9NXE1	Missense_Mutation	SNP	ENST00000373670.1	37	CCDS43874.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.810872	0.90707	.	.	ENSG00000056586	ENST00000373670;ENST00000357244;ENST00000373663;ENST00000423239;ENST00000373665;ENST00000335387	T;T;T;T;T	0.75821	-0.97;-0.97;-0.97;-0.97;-0.97	5.54	5.54	0.83059	Zinc finger, CCCH-type (3);	0.109140	0.64402	N	0.000006	D	0.84660	0.5521	M	0.69463	2.115	0.54753	D	0.999985	B;D;D;D	0.76494	0.329;0.988;0.999;0.998	B;D;D;D	0.70487	0.327;0.954;0.969;0.948	T	0.82774	-0.0291	10	0.35671	T	0.21	-10.2029	18.4783	0.90800	0.0:1.0:0.0:0.0	.	423;294;423;423	A6NHN2;Q4VXB0;Q9HBD1;Q9HBD1-4	.;.;RC3H2_HUMAN;.	R	423;423;294;423;423;423	ENSP00000362774:G423R;ENSP00000349783:G423R;ENSP00000411767:G423R;ENSP00000362769:G423R;ENSP00000335150:G423R	ENSP00000335150:G423R	G	-	1	0	RC3H2	124679629	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.043000	0.71004	2.627000	0.88993	0.637000	0.83480	GGG	.	.	none		0.418	RC3H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053966.1	NM_018835		T	125639808	C	T	125639808	3	4	27	1	0	0	0	0	1	0	0	0	13182	681	24	2	2438	2	RC3H2	9	125639808	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	485148	125639808	15573623	514	10965											
WDR38	401551	hgsc.bcm.edu	37	chr9	127618775	127618775	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctcctgggactccaccgtaCacatctgggacctgcggatg	7	8	12	14	2	1	0	0	0	1	0	3	3	3	3	4	3	2	2	4	3	1	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:127618775C>T	ENST00000373574.1	+	6	570	c.514C>T	c.(514-516)Cac>Tac	p.H172Y		NM_001045476.1|NM_001276374.1	NP_001038941.1|NP_001263303.1	Q5JTN6	WDR38_HUMAN	WD repeat domain 38	172			H -> R (in dbSNP:rs2274970). {ECO:0000269|PubMed:15489334}.		hematopoietic progenitor cell differentiation (GO:0002244)					breast(1)|large_intestine(1)|lung(4)|prostate(1)|skin(1)	8						CTCCACCGTACACATCTGGGA	0.637																																					p.H172Y		Atlas-SNP	.											.	WDR38	21	.	0			c.C514T						PASS	.						22	26	25					9																	127618775		2030	4179	6209	SO:0001583	missense	401551	exon6			ACCGTACACATCT		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.514C>T	9.37:g.127618775C>T	ENSP00000362677:p.His172Tyr	56	0	0		61	11	0.180328	NM_001045476	A0PK24	Missense_Mutation	SNP	ENST00000373574.1	37	CCDS43876.1	.	.	.	.	.	.	.	.	.	.	C	9.880	1.201340	0.22121	.	.	ENSG00000136918	ENST00000373574	T	0.59906	0.23	4.68	1.78	0.24846	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.349118	0.25127	N	0.032940	T	0.34337	0.0894	N	0.12887	0.27	0.09310	N	1	B	0.25521	0.128	B	0.26310	0.068	T	0.25152	-1.0140	10	0.87932	D	0	.	5.2255	0.15391	0.165:0.6532:0.0:0.1818	.	172	Q5JTN6	WDR38_HUMAN	Y	172	ENSP00000362677:H172Y	ENSP00000362677:H172Y	H	+	1	0	WDR38	126658596	0.006000	0.16342	0.173000	0.22940	0.446000	0.32137	-0.009000	0.12765	0.193000	0.20303	0.561000	0.74099	CAC	.	.	none		0.637	WDR38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054048.1	NM_001045476		T	127618775	C	T	127618775	3	4	27	1	0	0	0	0	1	0	0	0	17307	478	17	2	536	2	WDR38	9	127618775	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1978967	127618775	13594656	515	10966											
ANGPTL2	23452	hgsc.bcm.edu	37	chr9	129870763	129870763	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctagctcctgcttatgcactCggttctccagaagcacctca	8	11	7	15	1	2	1	1	0	1	1	5	1	3	1	3	1	4	5	3	1	3	3	rs370920897		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:129870763C>T	ENST00000373425.3	-	2	865	c.248G>A	c.(247-249)cGa>cAa	p.R83Q	RALGPS1_ENST00000373434.1_Intron|RALGPS1_ENST00000394022.3_Intron|ANGPTL2_ENST00000373417.1_Intron|RALGPS1_ENST00000424082.2_Intron|ANGPTL2_ENST00000491991.1_5'Flank|RALGPS1_ENST00000373436.1_Intron|RALGPS1_ENST00000259351.5_Intron	NM_012098.2	NP_036230.1	Q9UKU9	ANGL2_HUMAN	angiopoietin-like 2	83					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						CTTATGCACTCGGTTCTCCAG	0.592																																					p.R83Q		Atlas-SNP	.											ANGPTL2,colon,carcinoma,-1,1	ANGPTL2	46	1	0			c.G248A						PASS	.	C	,,,GLN/ARG,	1,4405	2.1+/-5.4	0,1,2202	63	53	56		,,,248,	4.9	1	9		56	0,8600		0,0,4300	no	intron,intron,intron,missense,intron	RALGPS1,ANGPTL2	NM_001190728.1,NM_001190729.1,NM_001190730.1,NM_012098.2,NM_014636.2	,,,43,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,,,probably-damaging,	,,,83/494,	129870763	1,13005	2203	4300	6503	SO:0001583	missense	23452	exon2			TGCACTCGGTTCT	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.248G>A	9.37:g.129870763C>T	ENSP00000362524:p.Arg83Gln	52	0	0		63	14	0.222222	NM_012098	Q5JT58|Q8NCH7	Missense_Mutation	SNP	ENST00000373425.3	37	CCDS6868.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.291664	0.80914	2.27E-4	0.0	ENSG00000136859	ENST00000373425	T	0.40225	1.04	4.87	4.87	0.63330	.	0.119965	0.52532	D	0.000062	T	0.47060	0.1425	M	0.70275	2.135	0.80722	D	1	D	0.53885	0.963	P	0.45660	0.489	T	0.47898	-0.9081	10	0.12103	T	0.63	.	18.0259	0.89269	0.0:1.0:0.0:0.0	.	83	Q9UKU9	ANGL2_HUMAN	Q	83	ENSP00000362524:R83Q	ENSP00000362524:R83Q	R	-	2	0	ANGPTL2	128910584	1.000000	0.71417	0.995000	0.50966	0.749000	0.42624	7.818000	0.86416	2.259000	0.74868	0.655000	0.94253	CGA	.	.	weak		0.592	ANGPTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054129.1	NM_012098		T	129870763	C	T	129870763	3	4	27	1	0	0	0	0	1	0	0	0	614	884	31	1	1249	1	ANGPTL2	9	129870763	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2251988	129870763	11342668	516	10967											
ENG	2022	hgsc.bcm.edu	37	chr9	130586661	130586661	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atcaaggacatgagcagctcCgggctacaagtgtccttggg	10	8	13	10	1	1	1	1	1	0	0	3	2	3	2	2	3	3	3	2	3	3	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:130586661C>T	ENST00000373203.4	-	8	1456	c.1056G>A	c.(1054-1056)ccG>ccA	p.P352P	RP11-228B15.4_ENST00000425991.1_RNA|ENG_ENST00000344849.3_Silent_p.P352P|ENG_ENST00000480266.1_5'UTR|RP11-228B15.4_ENST00000439298.1_RNA	NM_000118.2|NM_001114753.1|NM_001278138.1	NP_000109.1|NP_001108225.1|NP_001265067.1	P17813	EGLN_HUMAN	endoglin	352	Ser/Thr-rich.				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)	p.P352P(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	17						TGAGCAGCTCCGGGCTACAAG	0.597									Juvenile Polyposis;Hereditary Hemorrhagic Telangiectasia																												p.P352P		Atlas-SNP	.											ENG,NS,carcinoma,0,1	ENG	44	1	1	Substitution - coding silent(1)	lung(1)	c.G1056A						scavenged	.						142	116	125					9																	130586661		2203	4300	6503	SO:0001819	synonymous_variant	2022	exon8	Familial Cancer Database	incl.: Juvenile Polyposis of the Stomach;HHT, Rendu-Osler-Weber disease, incl.: Pulmonary arteriovenous malformations, hypertrophic osteoarthropathy and juvenile polyposis,	CAGCTCCGGGCTA	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.1056G>A	9.37:g.130586661C>T		154	1	0.00649351		116	56	0.482759	NM_001114753	Q14248|Q14926|Q5T9C0	Silent	SNP	ENST00000373203.4	37	CCDS48029.1																																																																																			.	.	none		0.597	ENG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054313.1			T	130586661	C	T	130586661	2	4	27	1	0	0	0	0	0	0	0	1	5119	639	23	1		1	ENG	9	130586661	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	715898	130586661	10626770	517	10968											
FAM102A	399665	hgsc.bcm.edu	37	chr9	130742271	130742271	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgaccgccccagctcctacCttgacgacaagctgacaaaa	12	5	8	16	3	0	2	0	2	0	0	1	4	1	2	5	0	3	2	5	0	4	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:130742271C>T	ENST00000373095.1	-	1	521	c.146G>A	c.(145-147)aGg>aAg	p.R49K		NM_001035254.2	NP_001030331.1	Q5T9C2	F102A_HUMAN	family with sequence similarity 102, member A	49										breast(1)|cervix(1)|large_intestine(3)|lung(1)|ovary(4)	10						CAGCTCCTACCTTGACGACAA	0.632																																					p.R49K		Atlas-SNP	.											.	FAM102A	32	.	0			c.G146A						PASS	.						63	67	66					9																	130742271		2203	4300	6503	SO:0001630	splice_region_variant	399665	exon1			TCCTACCTTGACG		CCDS6888.1, CCDS35150.1	9q34.11	2012-11-05	2005-11-17	2005-11-17	ENSG00000167106	ENSG00000167106			31419	protein-coding gene	gene with protein product	"sym-3 homolog A (C. elegans)"	610891	"chromosome 9 open reading frame 132"	C9orf132			Standard	NM_001035254		Approved	Eeig1, bA203J24.7, SYM-3A	uc004bsx.2	Q5T9C2	OTTHUMG00000020720	ENST00000373095.1:c.146+1G>A	9.37:g.130742271C>T		68	0	0		72	17	0.236111	NM_001035254	A2A329|Q8TEL4	Missense_Mutation	SNP	ENST00000373095.1	37	CCDS35150.1	.	.	.	.	.	.	.	.	.	.	C	36	5.857711	0.97030	.	.	ENSG00000167106	ENST00000373095	T	0.39787	1.06	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	T	0.52075	0.1712	M	0.79011	2.435	0.80722	D	1	P	0.45634	0.863	P	0.45538	0.484	T	0.57946	-0.7723	9	.	.	.	-30.8032	16.9987	0.86376	0.0:1.0:0.0:0.0	.	49	Q5T9C2	F102A_HUMAN	K	49	ENSP00000362187:R49K	.	R	-	2	0	FAM102A	129782092	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.487000	0.81328	2.244000	0.73946	0.462000	0.41574	AGG	.	.	none		0.632	FAM102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054298.2		Missense_Mutation	T	130742271	C	T	130742271	5	4	27	1	0	0	0	0	0	0	1	0	5387	695	24	2	1052	2	FAM102A	9	130742271	Splice_Site	SNP	C	TCGA-G8-6909-01A-11D-2210-10	155610	130742271	10471160	518	10969											
FAM102A	399665	hgsc.bcm.edu	37	chr9	130742413	130742413	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cttcttcttcatcaagaaagCcatgagcgagttccctgagt	10	12	8	11	1	4	3	2	2	2	1	5	4	5	3	2	0	2	1	2	0	2	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:130742413C>T	ENST00000373095.1	-	1	379	c.4G>A	c.(4-6)Gct>Act	p.A2T		NM_001035254.2	NP_001030331.1	Q5T9C2	F102A_HUMAN	family with sequence similarity 102, member A	2										breast(1)|cervix(1)|large_intestine(3)|lung(1)|ovary(4)	10						ATCAAGAAAGCCATGAGCGAG	0.517																																					p.A2T		Atlas-SNP	.											.	FAM102A	32	.	0			c.G4A						PASS	.						89	103	98					9																	130742413		2203	4300	6503	SO:0001583	missense	399665	exon1			AGAAAGCCATGAG		CCDS6888.1, CCDS35150.1	9q34.11	2012-11-05	2005-11-17	2005-11-17	ENSG00000167106	ENSG00000167106			31419	protein-coding gene	gene with protein product	"sym-3 homolog A (C. elegans)"	610891	"chromosome 9 open reading frame 132"	C9orf132			Standard	NM_001035254		Approved	Eeig1, bA203J24.7, SYM-3A	uc004bsx.2	Q5T9C2	OTTHUMG00000020720	ENST00000373095.1:c.4G>A	9.37:g.130742413C>T	ENSP00000362187:p.Ala2Thr	75	0	0		68	27	0.397059	NM_001035254	A2A329|Q8TEL4	Missense_Mutation	SNP	ENST00000373095.1	37	CCDS35150.1	.	.	.	.	.	.	.	.	.	.	C	16.50	3.141355	0.57044	.	.	ENSG00000167106	ENST00000373095	.	.	.	4.76	4.76	0.60689	.	0.117104	0.56097	D	0.000025	T	0.54013	0.1832	L	0.43152	1.355	0.80722	D	1	B	0.29162	0.235	B	0.17098	0.017	T	0.55023	-0.8205	9	0.42905	T	0.14	-9.6451	16.7632	0.85517	0.0:1.0:0.0:0.0	.	2	Q5T9C2	F102A_HUMAN	T	2	.	ENSP00000362187:A2T	A	-	1	0	FAM102A	129782234	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.711000	0.54868	2.185000	0.69588	0.462000	0.41574	GCT	.	.	none		0.517	FAM102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054298.2			T	130742413	C	T	130742413	3	4	27	1	0	0	0	0	1	0	0	0	5387	739	26	2	1194	2	FAM102A	9	130742413	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	142	130742413	10471018	519	10970											
ENDOG	2021	hgsc.bcm.edu	37	chr9	131584729	131584729	+	Missense_Mutation	SNP	G	G	T																															aggtgggcaaattgagctccGcacctacgtgatgcccaacg																								rs61737988	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:131584729G>T	ENST00000372642.4	+	3	945	c.734G>T	c.(733-735)cGc>cTc	p.R245L	C9orf114_ENST00000361256.5_3'UTR	NM_004435.2	NP_004426.2	Q14249	NUCG_HUMAN	endonuclease G	245					apoptotic DNA fragmentation (GO:0006309)|DNA recombination (GO:0006310)|in utero embryonic development (GO:0001701)|positive regulation of apoptotic process (GO:0043065)|response to antibiotic (GO:0046677)|response to tumor necrosis factor (GO:0034612)	mitochondrion (GO:0005739)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|nucleic acid binding (GO:0003676)										ATTGAGCTCCGCACCTACGTG	0.587													G|||	5	0.000998403	0.0	0.0014	5008	,	,		21105	0.0		0.001	False		,,,				2504	0.0031				p.R245L		Atlas-SNP	.											.	ENDOG	8	.	0			c.G734T						PASS	.	G	LEU/ARG,	3,4401		0,3,2199	70	61	64		734,	4.7	1	9	dbSNP_129	64	19,8581		0,19,4281	yes	missense,utr-3	ENDOG,C9orf114	NM_004435.2,NM_016390.2	102,	0,22,6480	TT,TG,GG		0.2209,0.0681,0.1692	possibly-damaging,	245/298,	131584729	22,12982	2202	4300	6502	SO:0001583	missense	2021	exon3			AGCTCCGCACCTA	X79444	CCDS6912.1	9q34.1	2008-06-04			ENSG00000167136	ENSG00000167136			3346	protein-coding gene	gene with protein product		600440				7789991	Standard	NM_004435		Approved		uc004bwc.3	Q14249	OTTHUMG00000020763	ENST00000372642.4:c.734G>T	9.37:g.131584729G>T	ENSP00000361725:p.Arg245Leu	147	0	0		143	74	0.517483	NM_004435	Q5T281|Q9BSP2	Missense_Mutation	SNP	ENST00000372642.4	37	CCDS6912.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	18.18	3.566808	0.65651	6.81E-4	0.002209	ENSG00000167136	ENST00000372642	T	0.66995	-0.24	5.63	4.74	0.60224	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.063724	0.64402	D	0.000004	T	0.66157	0.2761	L	0.39633	1.23	0.80722	D	1	P	0.51537	0.946	P	0.49953	0.627	T	0.68232	-0.5463	10	0.52906	T	0.07	-1.808	13.8836	0.63696	0.0731:0.0:0.9269:0.0	rs61737988	245	Q14249	NUCG_HUMAN	L	245	ENSP00000361725:R245L	ENSP00000361725:R245L	R	+	2	0	ENDOG	130624550	1.000000	0.71417	0.977000	0.42913	0.284000	0.27059	6.040000	0.70980	1.384000	0.46424	-0.463000	0.05309	CGC	G|0.998;T|0.002	0.002	strong		0.587	ENDOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054505.1	NM_004435		T	131584729	G	T	131584729	3	4	27	1	0	0	0	0	1	0	0	0	5117	1087	38	4	744	4	ENDOG	9	131584729	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	842316	131584729	9628702	520	10971	137	2									
ENDOG	2021	hgsc.bcm.edu	37	chr9	131584732	131584732	+	Missense_Mutation	SNP	C	C	T																															tgggcaaattgagctccgcaCctacgtgatgcccaacgcac																								rs61737987	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:131584732C>T	ENST00000372642.4	+	3	948	c.737C>T	c.(736-738)aCc>aTc	p.T246I	C9orf114_ENST00000361256.5_3'UTR	NM_004435.2	NP_004426.2	Q14249	NUCG_HUMAN	endonuclease G	246					apoptotic DNA fragmentation (GO:0006309)|DNA recombination (GO:0006310)|in utero embryonic development (GO:0001701)|positive regulation of apoptotic process (GO:0043065)|response to antibiotic (GO:0046677)|response to tumor necrosis factor (GO:0034612)	mitochondrion (GO:0005739)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|nucleic acid binding (GO:0003676)										GAGCTCCGCACCTACGTGATG	0.592													C|||	5	0.000998403	0.0	0.0014	5008	,	,		21151	0.0		0.001	False		,,,				2504	0.0031				p.T246I		Atlas-SNP	.											.	ENDOG	8	.	0			c.C737T						PASS	.	C	ILE/THR,	3,4401		0,3,2199	72	63	66		737,	5.6	1	9	dbSNP_129	66	19,8581		0,19,4281	yes	missense,utr-3	ENDOG,C9orf114	NM_004435.2,NM_016390.2	89,	0,22,6480	TT,TC,CC		0.2209,0.0681,0.1692	benign,	246/298,	131584732	22,12982	2202	4300	6502	SO:0001583	missense	2021	exon3			TCCGCACCTACGT	X79444	CCDS6912.1	9q34.1	2008-06-04			ENSG00000167136	ENSG00000167136			3346	protein-coding gene	gene with protein product		600440				7789991	Standard	NM_004435		Approved		uc004bwc.3	Q14249	OTTHUMG00000020763	ENST00000372642.4:c.737C>T	9.37:g.131584732C>T	ENSP00000361725:p.Thr246Ile	151	0	0		139	71	0.510791	NM_004435	Q5T281|Q9BSP2	Missense_Mutation	SNP	ENST00000372642.4	37	CCDS6912.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	17.73	3.462148	0.63513	6.81E-4	0.002209	ENSG00000167136	ENST00000372642	T	0.29397	1.57	5.63	5.63	0.86233	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.063535	0.64402	D	0.000004	T	0.25344	0.0616	N	0.08118	0	0.80722	D	1	B	0.26002	0.139	B	0.36030	0.216	T	0.22382	-1.0218	10	0.87932	D	0	-0.0021	18.6823	0.91551	0.0:1.0:0.0:0.0	rs61737987	246	Q14249	NUCG_HUMAN	I	246	ENSP00000361725:T246I	ENSP00000361725:T246I	T	+	2	0	ENDOG	130624553	1.000000	0.71417	1.000000	0.80357	0.343000	0.28985	7.227000	0.78070	2.651000	0.90000	0.455000	0.32223	ACC	C|0.998;T|0.002	0.002	strong		0.592	ENDOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054505.1	NM_004435		T	131584732	C	T	131584732	3	4	27	1	0	0	0	0	1	0	0	0	5117	507	18	2	747	2	ENDOG	9	131584732	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3	131584732	9628699	521	10972	137	2									
NUP188	23511	hgsc.bcm.edu	37	chr9	131752487	131752487	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccacgtcttgccattcagctGctgaaacgtctggccacggt	7	10	10	14	3	3	1	1	1	2	0	3	1	3	1	3	2	4	2	3	2	1	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:131752487G>A	ENST00000372577.2	+	25	2643	c.2622G>A	c.(2620-2622)ctG>ctA	p.L874L		NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	874					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						CCATTCAGCTGCTGAAACGTC	0.473																																					p.L874L		Atlas-SNP	.											.	NUP188	140	.	0			c.G2622A						PASS	.						371	316	334					9																	131752487		2203	4300	6503	SO:0001819	synonymous_variant	23511	exon25			TCAGCTGCTGAAA	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.2622G>A	9.37:g.131752487G>A		202	0	0		187	38	0.203209	NM_015354	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Silent	SNP	ENST00000372577.2	37	CCDS35156.1																																																																																			.	.	none		0.473	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2			A	131752487	G	A	131752487	2	1	27	1	0	0	0	0	0	0	0	1	10767	1306	46	2		2	NUP188	9	131752487	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	167755	131752487	9460944	522	10973											
NUP214	8021	hgsc.bcm.edu	37	chr9	134073622	134073622	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tccctgatgccaggacggagGcagtaccacctgcttcctcc	7	8	10	16	1	0	1	0	1	0	0	3	3	3	3	6	3	3	3	6	3	1	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:134073622G>C	ENST00000359428.5	+	29	4885	c.4741G>C	c.(4741-4743)Gca>Cca	p.A1581P	NUP214_ENST00000451030.1_Missense_Mutation_p.A1582P|NUP214_ENST00000483497.2_Missense_Mutation_p.A407P|NUP214_ENST00000411637.2_Missense_Mutation_p.A1571P			P35658	NU214_HUMAN	nucleoporin 214kDa	1581	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)		CAGGACGGAGGCAGTACCACC	0.572			T	"DEK, SET, ABL1"	"AML, T-ALL"																																p.A1581P	Pancreas(4;24 48 25510 30394 32571)	Atlas-SNP	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.G4741C						PASS	.						75	78	77					9																	134073622		2203	4300	6503	SO:0001583	missense	8021	exon29			ACGGAGGCAGTAC	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.4741G>C	9.37:g.134073622G>C	ENSP00000352400:p.Ala1581Pro	98	0	0		106	30	0.283019	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Missense_Mutation	SNP	ENST00000359428.5	37	CCDS6940.1	.	.	.	.	.	.	.	.	.	.	G	12.61	1.989651	0.35131	.	.	ENSG00000126883	ENST00000359428;ENST00000411637;ENST00000451030;ENST00000541375;ENST00000540899;ENST00000438605;ENST00000483497;ENST00000531600;ENST00000541688	T;T;T;T;T	0.50277	0.96;0.79;0.79;0.79;0.75	5.44	2.63	0.31362	.	0.924894	0.08948	N	0.870525	T	0.26593	0.0650	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.10296	0.001;0.001;0.001;0.001;0.003	B;B;B;B;B	0.11329	0.006;0.003;0.003;0.003;0.004	T	0.26503	-1.0101	10	0.22109	T	0.4	-0.1467	7.7656	0.28978	0.0:0.1889:0.4379:0.3732	.	407;1010;1175;1571;1581	B7ZAV2;F5H131;Q5JUP9;P35658-4;P35658	.;.;.;.;NU214_HUMAN	P	1581;1571;1582;1560;1175;1010;407;358;358	ENSP00000352400:A1581P;ENSP00000396576:A1571P;ENSP00000405014:A1582P;ENSP00000436793:A407P;ENSP00000435364:A358P	ENSP00000352400:A1581P	A	+	1	0	NUP214	133063443	0.000000	0.05858	0.033000	0.17914	0.128000	0.20619	-0.086000	0.11233	0.285000	0.22329	-0.475000	0.04921	GCA	.	.	none		0.572	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085		C	134073622	G	C	134073622	3	2	27	1	0	0	0	0	1	0	0	0	10771	1203	42	4	4855	4	NUP214	9	134073622	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2321135	134073622	7139809	523	10974											
RAPGEF1	2889	hgsc.bcm.edu	37	chr9	134503415	134503415	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcagggggagaggcggggCgactctccaccatatgagtg	8	6	17	10	2	1	2	0	1	1	1	2	4	1	2	2	5	1	1	2	5	1	1	rs371503343		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:134503415C>T	ENST00000372189.3	-	9	1158	c.1035G>A	c.(1033-1035)tcG>tcA	p.S345S	RAPGEF1_ENST00000372190.3_Silent_p.S363S|RAPGEF1_ENST00000481260.1_5'UTR|RAPGEF1_ENST00000372195.1_Silent_p.S362S	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1	345					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)		AGAGGCGGGGCGACTCTCCAC	0.547																																					p.S363S		Atlas-SNP	.											.	RAPGEF1	126	.	0			c.G1089A						PASS	.	C	,	0,4264		0,0,2132	28	31	30		1035,1089	-3.3	0.9	9		30	2,8484		0,2,4241	no	coding-synonymous,coding-synonymous	RAPGEF1	NM_005312.2,NM_198679.1	,	0,2,6373	TT,TC,CC		0.0236,0.0,0.0157	,	345/1078,363/1096	134503415	2,12748	2132	4243	6375	SO:0001819	synonymous_variant	2889	exon9			GCGGGGCGACTCT	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.1035G>A	9.37:g.134503415C>T		46	0	0		45	23	0.511111	NM_198679	Q5JUE4|Q8IV73	Silent	SNP	ENST00000372189.3	37	CCDS48047.1																																																																																			.	.	weak		0.547	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312		T	134503415	C	T	134503415	2	4	27	1	0	0	0	0	0	0	0	1	13058	755	27	1		1	RAPGEF1	9	134503415	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	429793	134503415	6710016	524	10975											
SNAPC4	6621	hgsc.bcm.edu	37	chr9	139276448	139276448	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtgccgtagccactgcacAtgggatcgggccacgctgtc	6	8	13	14	3	0	0	0	0	0	0	2	1	0	1	3	2	3	3	3	2	1	1	rs150900916	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139276448A>G	ENST00000298532.2	-	17	2513	c.2145T>C	c.(2143-2145)caT>caC	p.H715H		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)		GCCACTGCACATGGGATCGGG	0.657													A|||	2	0.000399361	0.0	0.0	5008	,	,		17692	0.0		0.002	False		,,,				2504	0.0				p.H715H		Atlas-SNP	.											.	SNAPC4	82	.	0			c.T2145C						PASS	.	A		2,4396		0,2,2197	19	20	20		2145	-8.2	0	9	dbSNP_134	20	11,8579		0,11,4284	no	coding-synonymous	SNAPC4	NM_003086.2		0,13,6481	GG,GA,AA		0.1281,0.0455,0.1001		715/1470	139276448	13,12975	2199	4295	6494	SO:0001819	synonymous_variant	6621	exon17			CTGCACATGGGAT	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.2145T>C	9.37:g.139276448A>G		157	0	0		112	62	0.553571	NM_003086		Silent	SNP	ENST00000298532.2	37	CCDS6998.1																																																																																			A|0.999;G|0.001	0.001	strong		0.657	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086		G	139276448	A	G	139276448	2	3	27	1	0	0	0	0	0	0	0	1	14852	214	8	3		3	SNAPC4	9	139276448	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	4773033	139276448	1936983	525	10976											
NOTCH1	4851	hgsc.bcm.edu	37	chr9	139391636	139391636	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagcaggcagcccttgccGtcctgggacttcttcctccg	4	10	10	17	2	1	0	0	0	1	0	5	1	5	1	6	2	3	2	6	2	0	3	rs2229974	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139391636G>A	ENST00000277541.6	-	34	6630	c.6555C>T	c.(6553-6555)gaC>gaT	p.D2185D		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	2185					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.K2182fs*61(1)|p.S2163_T2283del(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)		AGCCCTTGCCGTCCTGGGACT	0.662			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)			G|||	3481	0.695088	0.6278	0.6542	5008	,	,		16337	0.9494		0.5775	False		,,,				2504	0.6738				p.D2185D		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	.	NOTCH1	1980	.	2	Deletion - Frameshift(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(2)	c.C6555T						PASS	.	G		2777,1589		891,995,297	47	54	52		6555	-0.8	1	9	dbSNP_98	52	4726,3816		1319,2088,864	no	coding-synonymous	NOTCH1	NM_017617.3		2210,3083,1161	AA,AG,GG		44.6734,36.3949,41.8733		2185/2556	139391636	7503,5405	2183	4271	6454	SO:0001819	synonymous_variant	4851	exon34			CTTGCCGTCCTGG	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.6555C>T	9.37:g.139391636G>A		121	0	0		125	56	0.448	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			G|0.341;A|0.659	0.659	strong		0.662	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		A	139391636	G	A	139391636	2	1	27	1	0	0	0	0	0	0	0	1	10556	1136	40	1		1	NOTCH1	9	139391636	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	115188	139391636	1821795	526	10977											
NOTCH1	4851	hgsc.bcm.edu	37	chr9	139407932	139407932	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagggttggattcacactcAttgttgttgatgtcacagtt	9	15	10	7	0	3	1	3	1	0	0	3	2	3	2	0	2	0	4	0	2	1	6	rs2229971|rs587778559	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139407932A>G	ENST00000277541.6	-	14	2340	c.2265T>C	c.(2263-2265)aaT>aaC	p.N755N		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	755	EGF-like 20. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)		ATTCACACTCATTGTTGTTGA	0.602			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)			G|||	2643	0.527756	0.6997	0.4784	5008	,	,		19531	0.7768		0.335	False		,,,				2504	0.272				p.N755N		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	.	NOTCH1	1980	.	0			c.T2265C						PASS	.	G		2695,1683		864,967,358	109	123	118		2265	-2.3	0	9	dbSNP_98	118	2445,6109		358,1729,2190	no	coding-synonymous	NOTCH1	NM_017617.3		1222,2696,2548	GG,GA,AA		28.5831,38.4422,39.7464		755/2556	139407932	5140,7792	2189	4277	6466	SO:0001819	synonymous_variant	4851	exon14			ACACTCATTGTTG	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.2265T>C	9.37:g.139407932A>G		129	0	0		113	51	0.451327	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			A|0.484;G|0.516	0.516	strong		0.602	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		G	139407932	A	G	139407932	2	3	27	1	0	0	0	0	0	0	0	1	10556	214	8	3		3	NOTCH1	9	139407932	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	16296	139407932	1805499	527	10978											
NOTCH1	4851	hgsc.bcm.edu	37	chr9	139413908	139413908	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacgcgcctgtccactctggCgggcagcggcagttgtaggt	5	9	15	12	4	1	0	0	0	1	0	2	0	2	0	2	4	2	4	2	4	2	3	rs2229975	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139413908C>T	ENST00000277541.6	-	5	927	c.852G>A	c.(850-852)ccG>ccA	p.P284P	MIR4673_ENST00000584777.1_RNA	NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	284	EGF-like 7; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				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)		TCCACTCTGGCGGGCAGCGGC	0.617			"T, Mis, O"	TRB@	T-ALL					HNSCC(8;0.001)			C|||	612	0.122204	0.087	0.0793	5008	,	,		16798	0.0962		0.1163	False		,,,				2504	0.2331				p.P284P		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"Notch homolog 1, translocation-associated (Drosophila) (TAN1)"		L	.	NOTCH1	1980	.	0			c.G852A						PASS	.	C		400,3480		29,342,1569	54	68	64		852	-10.4	0	9	dbSNP_98	64	1122,7160		75,972,3094	no	coding-synonymous	NOTCH1	NM_017617.3		104,1314,4663	TT,TC,CC		13.5475,10.3093,12.5144		284/2556	139413908	1522,10640	1940	4141	6081	SO:0001819	synonymous_variant	4851	exon5			CTCTGGCGGGCAG	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.852G>A	9.37:g.139413908C>T		97	0	0		85	38	0.447059	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			T|0.113;G|0.000;C|0.886	0.113	strong		0.617	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617		T	139413908	C	T	139413908	2	4	27	1	0	0	0	0	0	0	0	1	10556	755	27	1		1	NOTCH1	9	139413908	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	5976	139413908	1799523	528	10979											
PHPT1	29085	hgsc.bcm.edu	37	chr9	139744578	139744578	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acaagaagattcacgtgtacGgctattccatggtgagccgc	11	9	11	10	3	1	3	1	1	0	2	2	3	2	3	2	2	2	2	2	2	4	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr9:139744578G>A	ENST00000247665.10	+	2	611	c.274G>A	c.(274-276)Ggc>Agc	p.G92S	MAMDC4_ENST00000317446.2_5'Flank|PHPT1_ENST00000492540.1_3'UTR|PHPT1_ENST00000371661.1_Missense_Mutation_p.G92S|PHPT1_ENST00000545326.1_Missense_Mutation_p.G92S|MAMDC4_ENST00000445819.1_5'Flank	NM_014172.4	NP_054891.2	Q9NRX4	PHP14_HUMAN	phosphohistidine phosphatase 1	92					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)		TCACGTGTACGGCTATTCCAT	0.657																																					p.G92S		Atlas-SNP	.											.	PHPT1	14	.	0			c.G274A						PASS	.						97	90	92					9																	139744578		2202	4300	6502	SO:0001583	missense	29085	exon2			GTGTACGGCTATT	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.274G>A	9.37:g.139744578G>A	ENSP00000247665:p.Gly92Ser	111	0	0		146	39	0.267123	NM_001135861	B1AMX0|B1AMX1|Q9H0Y3	Missense_Mutation	SNP	ENST00000247665.10	37	CCDS7009.1	.	.	.	.	.	.	.	.	.	.	.	35	5.458139	0.96240	.	.	ENSG00000054148	ENST00000371661;ENST00000545326;ENST00000247665	.	.	.	4.61	4.61	0.57282	.	.	.	.	.	D	0.85270	0.5658	M	0.91768	3.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.88984	0.3410	8	0.66056	D	0.02	-0.5277	16.4133	0.83726	0.0:0.0:1.0:0.0	.	92;92	Q9NRX4-2;Q9NRX4	.;PHP14_HUMAN	S	92	.	ENSP00000247665:G92S	G	+	1	0	PHPT1	138864399	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	4.076000	0.57591	2.098000	0.63641	0.455000	0.32223	GGC	.	.	none		0.657	PHPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055150.1	NM_014172		A	139744578	G	A	139744578	3	1	27	1	0	0	0	0	1	0	0	0	11869	1116	39	1	280	1	PHPT1	9	139744578	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	330670	139744578	1468853	529	10980											
PFKP	5214	hgsc.bcm.edu	37	chr10	3178001	3178001	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aacgttatttttcaacctgtGgcagagctgaagaagcaaac	14	10	9	8	1	1	3	1	1	0	2	1	3	1	3	1	1	5	4	1	1	6	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:3178001G>A	ENST00000381125.4	+	21	2272	c.2196G>A	c.(2194-2196)gtG>gtA	p.V732V	PFKP_ENST00000381075.2_Silent_p.V724V|PFKP_ENST00000381072.1_Silent_p.V150V|PITRM1_ENST00000464395.1_5'Flank	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	732	C-terminal regulatory PFK domain 2.				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)		TTCAACCTGTGGCAGAGCTGA	0.403																																					p.V732V		Atlas-SNP	.											.	PFKP	182	.	0			c.G2196A						PASS	.						78	78	78					10																	3178001		2203	4300	6503	SO:0001819	synonymous_variant	5214	exon21			ACCTGTGGCAGAG	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.2196G>A	10.37:g.3178001G>A		112	0	0		118	37	0.313559	NM_002627	B3KS15|Q5VSR7|Q5VSR8	Silent	SNP	ENST00000381125.4	37	CCDS7059.1	.	.	.	.	.	.	.	.	.	.	g	2.795	-0.250360	0.05867	.	.	ENSG00000067057	ENST00000433193	.	.	.	4.92	2.06	0.26882	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.47	0.11708	0.2166:0.0:0.5125:0.271	.	.	.	.	X	85	.	.	W	+	2	0	PFKP	3168001	0.798000	0.28890	0.791000	0.31998	0.487000	0.33371	0.615000	0.24329	0.506000	0.28125	-0.361000	0.07541	TGG	.	.	none		0.403	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627		A	3178001	G	A	3178001	2	1	27	1	0	0	0	0	0	0	0	1	11775	1335	47	2		2	PFKP	10	3178001	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10		3178001	132356746	530	10981											
C10orf18	54906	hgsc.bcm.edu	37	chr10	5803349	5803349	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatcaccagtgtgactctcgAtcatcaacaaaagcagaaat	16	9	6	10	1	4	2	3	1	1	1	5	3	4	2	1	0	2	1	1	0	5	1	rs543461908	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:5803349A>C	ENST00000328090.5	+	19	7714	c.7089A>C	c.(7087-7089)cgA>cgC	p.R2363R		NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	2363																	GTGACTCTCGATCATCAACAA	0.388																																					p.R2363R		Atlas-SNP	.											C10orf18,NS,carcinoma,+2,2	.	.	2	0			c.A7089C						PASS	.						128	120	122					10																	5803349		1889	4118	6007	SO:0001819	synonymous_variant	54906	exon19			CTCTCGATCATCA	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.7089A>C	10.37:g.5803349A>C		119	0	0		120	28	0.233333	NM_017782	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Silent	SNP	ENST00000328090.5	37	CCDS41485.1																																																																																			.	.	none		0.388	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782		C	5803349	A	C	5803349	2	2	27	1	0	0	0	0	0	0	0	1	1598	320	12	5		5	C10orf18	10	5803349	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	2625348	5803349	129731398	531	10982											
MCM10	55388	hgsc.bcm.edu	37	chr10	13230915	13230915	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtcagtaccatgtccaggCtcagtacaagaagctcagcg	11	8	10	12	1	3	1	3	0	0	1	4	1	4	1	2	1	4	4	2	1	4	2	rs35114749	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:13230915C>T	ENST00000484800.2	+	10	1356	c.1253C>T	c.(1252-1254)gCt>gTt	p.A418V	MCM10_ENST00000378694.1_Missense_Mutation_p.A417V|MCM10_ENST00000378714.3_Missense_Mutation_p.A417V			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	418			A -> V (in dbSNP:rs35114749).		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						CATGTCCAGGCTCAGTACAAG	0.547													C|||	49	0.00978435	0.0	0.0086	5008	,	,		18533	0.001		0.0179	False		,,,				2504	0.0245				p.A418V		Atlas-SNP	.											.	MCM10	76	.	0			c.C1253T						PASS	.	C	VAL/ALA,VAL/ALA	8,4398	12.9+/-30.5	0,8,2195	142	131	134		1250,1253	5.9	1	10	dbSNP_126	134	110,8490	58.3+/-119.8	0,110,4190	yes	missense,missense	MCM10	NM_018518.4,NM_182751.2	64,64	0,118,6385	TT,TC,CC		1.2791,0.1816,0.9073	possibly-damaging,possibly-damaging	417/875,418/876	13230915	118,12888	2203	4300	6503	SO:0001583	missense	55388	exon10			TCCAGGCTCAGTA	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.1253C>T	10.37:g.13230915C>T	ENSP00000418268:p.Ala418Val	106	0	0		88	38	0.431818	NM_182751	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Missense_Mutation	SNP	ENST00000484800.2	37	CCDS7096.1	13	0.005952380952380952	0	0.0	0	0.0	1	0.0017482517482517483	12	0.0158311345646438	C	33	5.250184	0.95305	0.001816	0.012791	ENSG00000065328	ENST00000378714;ENST00000361282;ENST00000484800;ENST00000378694	T;T;T	0.45668	0.89;0.89;0.89	5.87	5.87	0.94306	Zinc finger, Mcm10/DnaG-type (1);	0.191044	0.56097	D	0.000036	T	0.30008	0.0751	L	0.54323	1.7	0.80722	D	1	D;P;P	0.55385	0.971;0.827;0.857	P;B;B	0.44696	0.458;0.26;0.378	T	0.09271	-1.0682	10	0.31617	T	0.26	-15.6206	20.5827	0.99408	0.0:1.0:0.0:0.0	rs35114749	417;417;418	Q5T670;Q7L590-2;Q7L590	.;.;MCM10_HUMAN	V	417;418;418;417	ENSP00000367986:A417V;ENSP00000418268:A418V;ENSP00000367966:A417V	ENSP00000354945:A418V	A	+	2	0	MCM10	13270921	1.000000	0.71417	0.990000	0.47175	0.646000	0.38490	6.030000	0.70903	2.941000	0.99782	0.655000	0.94253	GCT	C|0.991;T|0.009	0.009	strong		0.547	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751		T	13230915	C	T	13230915	3	4	27	1	0	0	0	0	1	0	0	0	9394	797	28	2	1287	2	MCM10	10	13230915	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	7427566	13230915	122303832	532	10983											
DCLRE1C	64421	hgsc.bcm.edu	37	chr10	14987181	14987181	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aggtgaacagtatagataaaCcttcaagctgaaaggaaaaa	20	7	9	5	0	1	3	1	2	0	1	1	4	1	4	1	2	3	2	1	2	9	4	rs138077101	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:14987181C>A	ENST00000378278.2	-	3	206	c.169G>T	c.(169-171)Gtt>Ttt	p.V57F	DCLRE1C_ENST00000357717.2_Intron|DCLRE1C_ENST00000378249.1_5'UTR|DCLRE1C_ENST00000378255.1_5'UTR|DCLRE1C_ENST00000378289.4_Missense_Mutation_p.V57F|DCLRE1C_ENST00000453695.2_5'UTR|DCLRE1C_ENST00000378258.1_5'UTR|DCLRE1C_ENST00000378254.1_5'UTR|DCLRE1C_ENST00000378246.2_5'UTR|DCLRE1C_ENST00000396817.2_5'UTR			Q96SD1	DCR1C_HUMAN	DNA cross-link repair 1C	57					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						TATAGATAAACCTTCAAGCTG	0.308								Non-homologous end-joining																													p.V57F		Atlas-SNP	.											.	DCLRE1C	136	.	0			c.G169T						PASS	.	C	PHE/VAL,,,	0,4406		0,0,2203	45	46	46		169,,,	5.2	1	10	dbSNP_134	46	8,8592	5.7+/-21.5	0,8,4292	yes	missense,utr-5,utr-5,utr-5	DCLRE1C	NM_001033855.1,NM_001033857.1,NM_001033858.1,NM_022487.2	50,,,	0,8,6495	AA,AC,CC		0.093,0.0,0.0615	probably-damaging,,,	57/693,,,	14987181	8,12998	2203	4300	6503	SO:0001583	missense	64421	exon3			GATAAACCTTCAA	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.169G>T	10.37:g.14987181C>A	ENSP00000367527:p.Val57Phe	138	0	0		117	53	0.452991	NM_001033855	D3DRT6|Q1HCL2|Q5JSR4|Q5JSR5|Q5JSR7|Q5JSR8|Q5JSR9|Q5JSS0|Q5JSS7|Q6PK14|Q8N101|Q8N132|Q8TBW9|Q9BVW9|Q9HAM4	Missense_Mutation	SNP	ENST00000378278.2	37	CCDS31149.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.843519	0.91197	0.0	9.3E-4	ENSG00000152457	ENST00000378289;ENST00000378278	T;T	0.76316	-1.01;-1.01	5.19	5.19	0.71726	Beta-lactamase-like (1);	0.115748	0.64402	D	0.000016	D	0.83774	0.5327	L	0.47078	1.49	0.80722	D	1	P;P	0.48350	0.897;0.909	P;P	0.60789	0.712;0.879	T	0.82967	-0.0194	10	0.44086	T	0.13	.	18.7242	0.91708	0.0:1.0:0.0:0.0	.	57;57	Q96SD1-4;Q96SD1	.;DCR1C_HUMAN	F	57	ENSP00000367538:V57F;ENSP00000367527:V57F	ENSP00000367527:V57F	V	-	1	0	DCLRE1C	15027187	1.000000	0.71417	0.997000	0.53966	0.941000	0.58515	2.687000	0.46976	2.604000	0.88044	0.573000	0.79308	GTT	C|1.000;A|0.000	0.000	strong		0.308	DCLRE1C-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046934.1	NM_022487		A	14987181	C	A	14987181	3	1	27	1	0	0	0	0	1	0	0	0	4298	507	18	4	1957	4	DCLRE1C	10	14987181	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1756266	14987181	120547566	533	10984											
FAM171A1	221061	hgsc.bcm.edu	37	chr10	15256440	15256440	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgggggcctcggggcggcCgtggctggtgacggacagcg	3	4	22	12	6	0	1	0	1	0	0	1	2	0	2	3	8	1	1	3	8	0	0	rs150647132		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:15256440C>T	ENST00000378116.4	-	8	1153	c.1147G>A	c.(1147-1149)Ggc>Agc	p.G383S	FAM171A1_ENST00000477161.1_5'UTR	NM_001010924.1	NP_001010924.1	Q5VUB5	F1711_HUMAN	family with sequence similarity 171, member A1	383						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						TCGGGGCGGCCGTGGCTGGTG	0.597													C|||	1	0.000199681	0.0008	0.0	5008	,	,		15789	0.0		0.0	False		,,,				2504	0.0				p.G383S		Atlas-SNP	.											.	FAM171A1	252	.	0			c.G1147A						PASS	.	C	SER/GLY	0,4406		0,0,2203	39	45	43		1147	-2.7	0.2	10	dbSNP_134	43	10,8590	7.7+/-29.5	0,10,4290	yes	missense	FAM171A1	NM_001010924.1	56	0,10,6493	TT,TC,CC		0.1163,0.0,0.0769	benign	383/891	15256440	10,12996	2203	4300	6503	SO:0001583	missense	221061	exon8			GGCGGCCGTGGCT	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.1147G>A	10.37:g.15256440C>T	ENSP00000367356:p.Gly383Ser	71	0	0		73	34	0.465753	NM_001010924	D3DRT9|Q32M49|Q8N4I0	Missense_Mutation	SNP	ENST00000378116.4	37	CCDS31154.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	4.340	0.062493	0.08388	0.0	0.001163	ENSG00000148468	ENST00000378116;ENST00000396781	T	0.32023	1.47	4.96	-2.72	0.05968	.	0.300803	0.30695	N	0.009079	T	0.15696	0.0378	N	0.19112	0.55	0.22796	N	0.998728	B	0.15141	0.012	B	0.12156	0.007	T	0.20338	-1.0278	10	0.21014	T	0.42	-16.5191	11.3681	0.49684	0.0:0.4139:0.0:0.5861	.	383	Q5VUB5	F1711_HUMAN	S	383;384	ENSP00000367356:G383S	ENSP00000367356:G383S	G	-	1	0	FAM171A1	15296446	.	.	0.169000	0.22859	0.344000	0.29017	.	.	-0.806000	0.04398	-0.983000	0.02560	GGC	C|0.999;T|0.001	0.001	strong		0.597	FAM171A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046984.1	XM_167709		T	15256440	C	T	15256440	3	4	27	1	0	0	0	0	1	0	0	0	5495	652	23	1	1529	1	FAM171A1	10	15256440	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	269259	15256440	120278307	534	10985											
KIAA1217	56243	hgsc.bcm.edu	37	chr10	24813585	24813585	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acctccactctgcagatgtcGcaggctccgcagtccccaca	8	7	8	18	2	1	1	0	0	1	1	5	1	4	1	5	1	1	4	5	1	0	0	rs145162894	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:24813585G>A	ENST00000376454.3	+	13	2820	c.2790G>A	c.(2788-2790)tcG>tcA	p.S930S	KIAA1217_ENST00000376452.3_Silent_p.S895S|KIAA1217_ENST00000307544.6_Silent_p.S613S|KIAA1217_ENST00000430453.2_Intron|KIAA1217_ENST00000396446.1_Silent_p.S613S|KIAA1217_ENST00000376451.2_Silent_p.S613S|KIAA1217_ENST00000376462.1_Silent_p.S850S|KIAA1217_ENST00000396445.1_Silent_p.S613S|KIAA1217_ENST00000458595.1_Silent_p.S895S	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	930					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						TGCAGATGTCGCAGGCTCCGC	0.592													G|||	8	0.00159744	0.0	0.0	5008	,	,		18873	0.001		0.007	False		,,,				2504	0.0				p.S930S		Atlas-SNP	.											.	KIAA1217	235	.	0			c.G2790A						PASS	.	G	,,	4,4402	8.1+/-20.4	0,4,2199	49	46	47		2550,2685,2790	-8.3	0	10	dbSNP_134	47	49,8551	31.7+/-84.0	0,49,4251	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1217	NM_001098500.1,NM_001098501.1,NM_019590.3	,,	0,53,6450	AA,AG,GG		0.5698,0.0908,0.4075	,,	850/1265,895/1310,930/1944	24813585	53,12953	2203	4300	6503	SO:0001819	synonymous_variant	56243	exon13			GATGTCGCAGGCT	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.2790G>A	10.37:g.24813585G>A		63	0	0		61	32	0.52459	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Silent	SNP	ENST00000376454.3	37	CCDS31165.1																																																																																			G|0.996;A|0.004	0.004	strong		0.592	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		A	24813585	G	A	24813585	2	1	27	1	0	0	0	0	0	0	0	1	8225	1074	38	1		1	KIAA1217	10	24813585	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	9557145	24813585	110721162	535	10986											
ARHGAP21	57584	hgsc.bcm.edu	37	chr10	24889664	24889664	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgaaacaggcattcacagtCggacgtggtgagtcgaaaca	13	7	12	9	3	1	2	1	2	0	0	3	4	1	3	0	3	2	1	0	3	2	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:24889664C>T	ENST00000396432.2	-	14	3529	c.3043G>A	c.(3043-3045)Gac>Aac	p.D1015N	ARHGAP21_ENST00000493154.1_5'UTR|ARHGAP21_ENST00000320481.6_Missense_Mutation_p.D802N	NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	1014	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						CATTCACAGTCGGACGTGGTG	0.478																																					p.D1015N		Atlas-SNP	.											.	ARHGAP21	185	.	0			c.G3043A						PASS	.						118	112	114					10																	24889664		2203	4298	6501	SO:0001583	missense	57584	exon14			CACAGTCGGACGT	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.3043G>A	10.37:g.24889664C>T	ENSP00000379709:p.Asp1015Asn	214	0	0		194	38	0.195876	NM_020824	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000396432.2	37	CCDS7144.2	.	.	.	.	.	.	.	.	.	.	C	23.5	4.427131	0.83667	.	.	ENSG00000107863	ENST00000396432;ENST00000320481;ENST00000376410;ENST00000446003;ENST00000445703	T;T;T;T	0.80033	-1.33;-1.33;-1.33;-1.33	6.02	6.02	0.97574	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	D	0.86961	0.6059	L	0.39467	1.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.995;1.0	D	0.86018	0.1505	10	0.52906	T	0.07	.	20.5407	0.99260	0.0:1.0:0.0:0.0	.	1005;1014	F8W9U9;Q5T5U3	.;RHG21_HUMAN	N	1015;802;1005;1015;850	ENSP00000379709:D1015N;ENSP00000365604:D802N;ENSP00000365592:D1005N;ENSP00000405018:D1015N	ENSP00000365604:D802N	D	-	1	0	ARHGAP21	24929670	1.000000	0.71417	0.892000	0.35008	0.258000	0.26162	7.767000	0.85331	2.865000	0.98341	0.655000	0.94253	GAC	.	.	none		0.478	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824		T	24889664	C	T	24889664	3	4	27	1	0	0	0	0	1	0	0	0	871	884	31	1	2885	1	ARHGAP21	10	24889664	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	76079	24889664	110645083	536	10987											
THNSL1	79896	hgsc.bcm.edu	37	chr10	25314005	25314005	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcaggattttgtagctgactGgtgctctgagggagagtgcc	7	11	16	7	0	1	3	0	2	1	1	1	5	1	4	1	3	3	4	1	3	1	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:25314005G>A	ENST00000524413.1	+	3	2200	c.1853G>A	c.(1852-1854)tGg>tAg	p.W618*	THNSL1_ENST00000376356.4_Nonsense_Mutation_p.W618*			Q8IYQ7	THNS1_HUMAN	threonine synthase-like 1 (S. cerevisiae)	618						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)	GTAGCTGACTGGTGCTCTGAG	0.408																																					p.W618X		Atlas-SNP	.											.	THNSL1	70	.	0			c.G1853A						PASS	.						85	91	89					10																	25314005		2203	4300	6503	SO:0001587	stop_gained	79896	exon3			CTGACTGGTGCTC	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.1853G>A	10.37:g.25314005G>A	ENSP00000434887:p.Trp618*	149	0	0		139	30	0.215827	NM_024838	B3KWL1|D3DRV3|Q5VV21	Nonsense_Mutation	SNP	ENST00000524413.1	37	CCDS7147.1	.	.	.	.	.	.	.	.	.	.	G	40	8.166791	0.98686	.	.	ENSG00000185875	ENST00000524413;ENST00000376356	.	.	.	5.94	5.94	0.96194	.	0.062472	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.9473	20.3632	0.98871	0.0:0.0:1.0:0.0	.	.	.	.	X	618	.	ENSP00000365534:W618X	W	+	2	0	THNSL1	25354011	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	8.861000	0.92277	2.826000	0.97356	0.561000	0.74099	TGG	.	.	none		0.408	THNSL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394913.1	NM_024838		A	25314005	G	A	25314005	4	1	27	1	0	0	0	0	0	1	0	0	15877	1357	47	2	1855	2	THNSL1	10	25314005	Nonsense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	424341	25314005	110220742	537	10988											
PTCHD3	374308	hgsc.bcm.edu	37	chr10	27687437	27687437	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	attgcacatatgcatctaacCaaaactctgtaagattttta	15	14	4	8	0	2	1	0	0	2	1	2	1	2	1	1	0	4	3	1	0	6	7	rs139600575	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:27687437C>A	ENST00000438700.3	-	4	2207	c.2090G>T	c.(2089-2091)tGg>tTg	p.W697L		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	697					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						TGCATCTAACCAAAACTCTGT	0.284																																					p.W697L		Atlas-SNP	.											.	PTCHD3	140	.	0			c.G2090T						PASS	.	C	LEU/TRP	0,4404		0,0,2202	39	41	41		2090	4.2	1	10	dbSNP_134	41	5,8569	3.7+/-12.6	0,5,4282	yes	missense	PTCHD3	NM_001034842.3	61	0,5,6484	AA,AC,CC		0.0583,0.0,0.0385	probably-damaging	697/768	27687437	5,12973	2202	4287	6489	SO:0001583	missense	374308	exon4			TCTAACCAAAACT	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.2090G>T	10.37:g.27687437C>A	ENSP00000417658:p.Trp697Leu	133	0	0		76	35	0.460526	NM_001034842	I3L499|Q6ZU28	Missense_Mutation	SNP	ENST00000438700.3	37	CCDS31173.1	.	.	.	.	.	.	.	.	.	.	C	15.65	2.895630	0.52121	0.0	5.83E-4	ENSG00000182077	ENST00000438700	D	0.89746	-2.56	4.18	4.18	0.49190	.	0.183449	0.51477	D	0.000085	D	0.94548	0.8244	M	0.84326	2.69	0.49130	D	0.999753	D	0.89917	1.0	D	0.87578	0.998	D	0.95493	0.8571	10	0.87932	D	0	-7.4899	16.2851	0.82714	0.0:1.0:0.0:0.0	.	697	Q3KNS1	PTHD3_HUMAN	L	697	ENSP00000417658:W697L	ENSP00000417658:W697L	W	-	2	0	PTCHD3	27727443	1.000000	0.71417	1.000000	0.80357	0.422000	0.31414	3.467000	0.53078	2.169000	0.68431	0.542000	0.68232	TGG	C|0.999;A|0.001	0.001	strong		0.284	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541		A	27687437	C	A	27687437	3	1	27	1	0	0	0	0	1	0	0	0	12746	595	21	4	217	4	PTCHD3	10	27687437	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2373432	27687437	107847310	538	10989											
ANKRD30A	91074	hgsc.bcm.edu	37	chr10	37442545	37442545	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aggatgtgtgtttacccaagGctacacatcaaaaagaaata	17	9	8	7	0	1	1	1	0	0	1	1	2	1	2	1	2	2	2	1	2	7	4	rs200557667		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:37442545G>T	ENST00000602533.1	+	13	1684	c.1585G>T	c.(1585-1587)Gct>Tct	p.A529S	ANKRD30A_ENST00000374660.1_Missense_Mutation_p.A529S|ANKRD30A_ENST00000361713.1_Missense_Mutation_p.A529S			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	585					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						TTTACCCAAGGCTACACATCA	0.294																																					p.A529S		Atlas-SNP	.											ANKRD30A,NS,carcinoma,0,1	ANKRD30A	448	1	0			c.G1585T						scavenged	.	G	SER/ALA	2,3602		0,2,1800	149	148	149		1585	1.5	0	10		149	7,8129		0,7,4061	no	missense	ANKRD30A	NM_052997.2	99	0,9,5861	TT,TG,GG		0.086,0.0555,0.0767	possibly-damaging	529/1342	37442545	9,11731	1802	4068	5870	SO:0001583	missense	91074	exon13			CCCAAGGCTACAC	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.1585G>T	10.37:g.37442545G>T	ENSP00000473551:p.Ala529Ser	779	0	0		714	132	0.184874	NM_052997	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	37		.	.	.	.	.	.	.	.	.	.	.	10.35	1.325943	0.24080	5.55E-4	8.6E-4	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.08458	3.09;3.09	1.47	1.47	0.22746	.	.	.	.	.	T	0.13841	0.0335	L	0.34521	1.04	0.09310	N	1	D	0.58970	0.984	D	0.65443	0.935	T	0.18429	-1.0337	9	0.39692	T	0.17	.	6.4351	0.21819	0.0:0.0:1.0:0.0	.	585	Q9BXX3	AN30A_HUMAN	S	529	ENSP00000354432:A529S;ENSP00000363792:A529S	ENSP00000354432:A529S	A	+	1	0	ANKRD30A	37482551	0.001000	0.12720	0.015000	0.15790	0.022000	0.10575	0.229000	0.17833	1.140000	0.42260	0.384000	0.25694	GCT	G|0.999;T|0.001	0.001	weak		0.294	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		T	37442545	G	T	37442545	3	4	27	1	0	0	0	0	1	0	0	0	658	1203	42	4	1635	4	ANKRD30A	10	37442545	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	9755108	37442545	98092202	539	10990											
ANKRD30A	91074	hgsc.bcm.edu	37	chr10	37486235	37486235	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccgagaagccatctgccttcGaggtatttagttttatgatt	9	15	9	8	2	1	2	0	1	1	1	2	4	1	2	3	1	2	2	3	1	4	7	rs201775035	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:37486235G>A	ENST00000602533.1	+	28	2572	c.2473G>A	c.(2473-2475)Gag>Aag	p.E825K	ANKRD30A_ENST00000374660.1_Missense_Mutation_p.E944K|ANKRD30A_ENST00000361713.1_Missense_Mutation_p.E825K			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	881					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						ATCTGCCTTCGAGGTATTTAG	0.333													.|||	4	0.000798722	0.0	0.0	5008	,	,		18178	0.003		0.001	False		,,,				2504	0.0				p.E825K		Atlas-SNP	.											ANKRD30A,NS,carcinoma,0,1	ANKRD30A	448	1	0			c.G2473A						scavenged	.	G	LYS/GLU	1,3605		0,1,1802	164	139	147		2473	-2.7	0	10		147	3,8151		0,3,4074	no	missense	ANKRD30A	NM_052997.2	56	0,4,5876	AA,AG,GG		0.0368,0.0277,0.034	possibly-damaging	825/1342	37486235	4,11756	1803	4077	5880	SO:0001583	missense	91074	exon28			GCCTTCGAGGTAT	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.2473G>A	10.37:g.37486235G>A	ENSP00000473551:p.Glu825Lys	328	1	0.00304878		292	18	0.0616438	NM_052997	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	37		.	.	.	.	.	.	.	.	.	.	.	0.011	-1.726410	0.00694	2.77E-4	3.68E-4	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.07114	3.22;3.22	1.36	-2.73	0.05950	.	.	.	.	.	T	0.02929	0.0087	N	0.01576	-0.805	0.09310	N	1	P	0.50272	0.933	P	0.52189	0.692	T	0.15838	-1.0423	9	0.02654	T	1	.	2.1426	0.03778	0.4051:0.3297:0.2652:0.0	.	881	Q9BXX3	AN30A_HUMAN	K	825;944	ENSP00000354432:E825K;ENSP00000363792:E944K	ENSP00000354432:E825K	E	+	1	0	ANKRD30A	37526241	0.016000	0.18221	0.008000	0.14137	0.002000	0.02628	-0.757000	0.04772	-0.171000	0.10797	-0.482000	0.04802	GAG	.	.	weak		0.333	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997		A	37486235	G	A	37486235	3	1	27	1	0	0	0	0	1	0	0	0	658	1059	37	1	2583	1	ANKRD30A	10	37486235	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	43690	37486235	98048512	540	10991											
ZNF248	57209	hgsc.bcm.edu	37	chr10	38121631	38121631	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atggaagccttgtccattttTactatactcaaaagattggc	12	14	7	8	0	1	1	1	0	0	1	2	2	2	2	2	2	3	0	2	2	6	7	rs11011379	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:38121631T>C	ENST00000395867.3	-	6	1202	c.652A>G	c.(652-654)Aaa>Gaa	p.K218E	ZNF248_ENST00000494133.1_Intron|ZNF248_ENST00000357328.4_Missense_Mutation_p.K218E|AL135791.1_ENST00000583461.1_RNA|ZNF248_ENST00000374648.3_Intron	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	218			K -> E (in dbSNP:rs11011379).		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						TGTCCATTTTTACTATACTCA	0.353													T|||	38	0.00758786	0.0023	0.0202	5008	,	,		18155	0.0		0.0149	False		,,,				2504	0.0061				p.K218E		Atlas-SNP	.											.	ZNF248	61	.	0			c.A652G						PASS	.	T	GLU/LYS	17,4385	20.2+/-43.8	0,17,2184	53	53	53		652	1.3	0.8	10	dbSNP_120	53	185,8411	78.4+/-141.0	0,185,4113	yes	missense	ZNF248	NM_021045.1	56	0,202,6297	CC,CT,TT		2.1522,0.3862,1.5541	benign	218/580	38121631	202,12796	2201	4298	6499	SO:0001583	missense	57209	exon6			CATTTTTACTATA	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.652A>G	10.37:g.38121631T>C	ENSP00000379208:p.Lys218Glu	90	0	0		56	29	0.517857	NM_001267597	Q8NDV8|Q9UMP3	Missense_Mutation	SNP	ENST00000395867.3	37	CCDS7194.1	19	0.0086996336996337	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	11	0.014511873350923483	T	0.003	-2.502296	0.00157	0.003862	0.021522	ENSG00000198105	ENST00000395867;ENST00000357328	T;T	0.04194	3.68;3.68	4.3	1.32	0.21799	.	0.331549	0.22037	N	0.065510	T	0.00496	0.0016	N	0.00347	-1.61	0.21719	N	0.999574	B	0.02656	0.0	B	0.01281	0.0	T	0.44937	-0.9295	10	0.02654	T	1	.	4.193	0.10430	0.0:0.5858:0.1909:0.2233	rs11011379;rs17662331;rs11011379	218	Q8NDW4	ZN248_HUMAN	E	218	ENSP00000379208:K218E;ENSP00000349882:K218E	ENSP00000349882:K218E	K	-	1	0	ZNF248	38161637	0.935000	0.31712	0.812000	0.32479	0.150000	0.21749	-0.179000	0.09768	0.165000	0.19558	-0.468000	0.05107	AAA	T|0.986;C|0.014	0.014	strong		0.353	ZNF248-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047609.1	NM_021045		C	38121631	T	C	38121631	3	2	27	1	0	0	0	0	1	0	0	0	17808	1763	61	3	1091	3	ZNF248	10	38121631	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	635396	38121631	97413116	541	10992											
RET	5979	hgsc.bcm.edu	37	chr10	43610119	43610119	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggtcagctactcctcttccGgtgcccgccggccctcgctg	2	9	11	19	5	2	0	1	0	1	0	5	0	4	0	5	3	3	2	5	3	1	2	rs1799939	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:43610119G>A	ENST00000355710.3	+	11	2303	c.2071G>A	c.(2071-2073)Ggt>Agt	p.G691S	RET_ENST00000340058.5_Missense_Mutation_p.G691S	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	691			G -> S (in dbSNP:rs1799939). {ECO:0000269|PubMed:14566559, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9223675, ECO:0000269|PubMed:9497256}.		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)	CTCCTCTTCCGGTGCCCGCCG	0.647		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				G|||	847	0.169129	0.0923	0.2565	5008	,	,		18422	0.121		0.1889	False		,,,				2504	0.2403				p.G691S	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_ENST00000340058,adrenal_gland,pheochromocytoma,0,2	RET	916	2	0			c.G2071A	GRCh37	CM023821	RET	M	rs1799939	scavenged	.	G	SER/GLY,SER/GLY	455,3951	216.4+/-235.1	19,417,1767	61	55	57	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2071,2071	-1.1	0	10	dbSNP_89	57	1587,7013	295.7+/-302.5	155,1277,2868	yes	missense,missense	RET	NM_020630.4,NM_020975.4	56,56	174,1694,4635	AA,AG,GG		18.4535,10.3268,15.7004	possibly-damaging,possibly-damaging	691/1073,691/1115	43610119	2042,10964	2203	4300	6503	SO:0001583	missense	5979	exon11	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	TCTTCCGGTGCCC	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.2071G>A	10.37:g.43610119G>A	ENSP00000347942:p.Gly691Ser	75	1	0.0133333		46	20	0.434783	NM_020630	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Missense_Mutation	SNP	ENST00000355710.3	37	CCDS7200.1	338	0.15476190476190477	45	0.09146341463414634	82	0.2265193370165746	60	0.1048951048951049	151	0.19920844327176782	G	8.525	0.869582	0.17322	0.103268	0.184535	ENSG00000165731	ENST00000355710;ENST00000340058	T;T	0.78246	-1.05;-1.16	4.75	-1.08	0.09936	.	0.349618	0.34603	N	0.003826	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.24426	0.062;0.062;0.103	B;B;B	0.16722	0.004;0.007;0.016	T	0.04128	-1.0975	9	0.07990	T	0.79	.	9.2584	0.37597	0.7374:0.0:0.2626:0.0	rs1799939;rs3781260;rs17362555;rs17845010;rs17857772;rs1799939	437;691;691	B4DGX8;P07949;P07949-2	.;RET_HUMAN;.	S	691	ENSP00000347942:G691S;ENSP00000344798:G691S	ENSP00000344798:G691S	G	+	1	0	RET	42930125	1.000000	0.71417	0.000000	0.03702	0.411000	0.31082	4.395000	0.59678	-0.060000	0.13132	0.462000	0.41574	GGT	G|0.839;A|0.161	0.161	strong		0.647	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975		A	43610119	G	A	43610119	3	1	27	1	0	0	0	0	1	0	0	0	13250	1116	39	1	2113	1	RET	10	43610119	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	5488488	43610119	91924628	542	10993											
RET	5979	hgsc.bcm.edu	37	chr10	43615633	43615633	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgtttatgaagaggattcCtacgtgaagaggagccaggt	12	10	14	5	1	0	4	0	2	0	2	1	7	1	6	2	3	2	1	2	3	4	4	rs1800863	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:43615633C>G	ENST00000355710.3	+	15	2944	c.2712C>G	c.(2710-2712)tcC>tcG	p.S904S	RET_ENST00000340058.5_Silent_p.S904S	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	904	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.			S -> P (in Ref. 6; AAA36786). {ECO:0000305}.	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)	AAGAGGATTCCTACGTGAAGA	0.592		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				C|||	864	0.172524	0.1051	0.2536	5008	,	,		15815	0.121		0.1928	False		,,,				2504	0.2382				p.S904S	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.C2712G	GRCh37	CM023822	RET	M	rs1800863	PASS	.	C	,	489,3917	225.2+/-241.2	24,441,1738	64	57	59		2712,2712	3.7	1	10	dbSNP_89	59	1604,6994	293.1+/-301.2	159,1286,2854	no	coding-synonymous,coding-synonymous	RET	NM_020630.4,NM_020975.4	,	183,1727,4592	GG,GC,CC		18.6555,11.0985,16.095	,	904/1073,904/1115	43615633	2093,10911	2203	4299	6502	SO:0001819	synonymous_variant	5979	exon15	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	GGATTCCTACGTG	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.2712C>G	10.37:g.43615633C>G		102	0	0		90	40	0.444444	NM_020630	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Silent	SNP	ENST00000355710.3	37	CCDS7200.1																																																																																			C|0.844;G|0.156	0.156	strong		0.592	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975		G	43615633	C	G	43615633	2	3	27	1	0	0	0	0	0	0	0	1	13250	668	24	4		4	RET	10	43615633	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	5514	43615633	91919114	543	10994											
TMEM72	643236	hgsc.bcm.edu	37	chr10	45430257	45430257	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctctggggacacagagcaaaCctacactttccatggggccc	10	7	10	14	0	1	1	0	0	1	1	2	2	2	2	3	4	3	1	3	4	2	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:45430257C>T	ENST00000544540.1	+	4	633	c.149C>T	c.(148-150)aCc>aTc	p.T50I	TMEM72-AS1_ENST00000450287.2_RNA|RP11-285G1.9_ENST00000425541.2_lincRNA			A0PK05	TMM72_HUMAN	transmembrane protein 72	168						integral component of membrane (GO:0016021)				breast(2)|kidney(1)|large_intestine(2)|lung(10)	15						ACAGAGCAAACCTACACTTTC	0.607																																					p.T168I		Atlas-SNP	.											.	TMEM72	25	.	0			c.C503T						PASS	.						122	130	127					10																	45430257		1568	3582	5150	SO:0001583	missense	643236	exon5			AGCAAACCTACAC	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.149C>T	10.37:g.45430257C>T	ENSP00000439911:p.Thr50Ile	83	0	0		86	37	0.430233	NM_001123376	A1L181|Q5T740	Missense_Mutation	SNP	ENST00000544540.1	37		.	.	.	.	.	.	.	.	.	.	C	14.56	2.570678	0.45798	.	.	ENSG00000187783	ENST00000389583;ENST00000544540	.	.	.	5.28	3.41	0.39046	.	0.000000	0.64402	D	0.000006	T	0.58736	0.2143	M	0.69823	2.125	0.39365	D	0.965998	B	0.15930	0.015	B	0.16722	0.016	T	0.61903	-0.6967	9	0.56958	D	0.05	-28.2717	9.2035	0.37275	0.0:0.8229:0.0:0.1771	.	168	A0PK05	TMM72_HUMAN	I	168;50	.	ENSP00000374234:T168I	T	+	2	0	TMEM72	44750263	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	3.002000	0.49496	1.372000	0.46190	0.563000	0.77884	ACC	.	.	none		0.607	TMEM72-201	KNOWN	basic	protein_coding	protein_coding		NM_001123376		T	45430257	C	T	45430257	3	4	27	1	0	0	0	0	1	0	0	0	16216	507	18	2	521	2	TMEM72	10	45430257	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1814624	45430257	90104490	544	10995											
RBP3	5949	hgsc.bcm.edu	37	chr10	48388508	48388508	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagagcagcgggatggccgtGgagtagctgccagggttgta	8	7	18	8	2	0	1	0	0	0	1	0	3	0	3	2	4	4	5	2	4	2	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:48388508G>C	ENST00000224600.4	-	1	2483	c.2370C>G	c.(2368-2370)tcC>tcG	p.S790S	AL731561.2_ENST00000581861.1_RNA	NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	790	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)	GGATGGCCGTGGAGTAGCTGC	0.617																																					p.S790S		Atlas-SNP	.											.	RBP3	152	.	0			c.C2370G						PASS	.						28	26	27					10																	48388508		2201	4298	6499	SO:0001819	synonymous_variant	5949	exon1			GGCCGTGGAGTAG	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.2370C>G	10.37:g.48388508G>C		153	0	0		144	60	0.416667	NM_002900	Q0QD34|Q5VSR0|Q8IXN0	Silent	SNP	ENST00000224600.4	37	CCDS7218.1																																																																																			.	.	none		0.617	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900		C	48388508	G	C	48388508	2	2	27	1	0	0	0	0	0	0	0	1	13172	1335	47	4		4	RBP3	10	48388508	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2958251	48388508	87146239	545	10996											
HERC4	26091	hgsc.bcm.edu	37	chr10	69695973	69695973	+	Missense_Mutation	SNP	C	C	T																															gctctttcacttctgttgcaCcaaagttttcaactgtgatc																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:69695973C>T	ENST00000395198.3	-	23	2862	c.2615G>A	c.(2614-2616)gGt>gAt	p.G872D	HERC4_ENST00000395187.2_3'UTR|HERC4_ENST00000277817.6_Missense_Mutation_p.G762D|HERC4_ENST00000412272.2_Missense_Mutation_p.G794D|HERC4_ENST00000373700.4_Missense_Mutation_p.G864D	NM_022079.2	NP_071362.1	Q5GLZ8	HERC4_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 4	872	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				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						TTCTGTTGCACCAAAGTTTTC	0.313																																					p.G872D		Atlas-SNP	.											.	HERC4	78	.	0			c.G2615A						PASS	.						141	131	135					10																	69695973		2203	4300	6503	SO:0001583	missense	26091	exon23			GTTGCACCAAAGT	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.2615G>A	10.37:g.69695973C>T	ENSP00000378624:p.Gly872Asp	69	0	0		65	17	0.261538	NM_022079	Q5GC98|Q5GC99|Q5GCA0|Q8IXP9|Q9HCH9	Missense_Mutation	SNP	ENST00000395198.3	37	CCDS41533.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.831789	0.91036	.	.	ENSG00000148634	ENST00000277817;ENST00000412272;ENST00000395198;ENST00000373700	T;T;T;T	0.57107	0.42;0.42;0.42;0.42	5.2	5.2	0.72013	HECT (4);	0.000000	0.85682	D	0.000000	T	0.75391	0.3843	M	0.82323	2.585	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999	D;D;D;D;D	0.91635	0.999;0.999;0.999;0.999;0.992	T	0.75204	-0.3400	10	0.37606	T	0.19	.	19.1052	0.93291	0.0:1.0:0.0:0.0	.	794;762;722;864;872	Q5GLZ8-3;Q5GLZ8-6;Q5VXS9;Q5GLZ8-2;Q5GLZ8	.;.;.;.;HERC4_HUMAN	D	762;794;872;864	ENSP00000277817:G762D;ENSP00000416504:G794D;ENSP00000378624:G872D;ENSP00000362804:G864D	ENSP00000277817:G762D	G	-	2	0	HERC4	69365979	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.364000	0.79526	2.568000	0.86640	0.460000	0.39030	GGT	.	.	none		0.313	HERC4-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359262.1	NM_015601		T	69695973	C	T	69695973	3	4	27	1	0	0	0	0	1	0	0	0	7069	507	18	2	574	2	HERC4	10	69695973	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	21307465	69695973	65838774	546	10997	138	2									
HERC4	26091	hgsc.bcm.edu	37	chr10	69695974	69695974	+	Missense_Mutation	SNP	C	C	T																															ctctttcacttctgttgcacCaaagttttcaactgtgatct																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:69695974C>T	ENST00000395198.3	-	23	2861	c.2614G>A	c.(2614-2616)Ggt>Agt	p.G872S	HERC4_ENST00000395187.2_3'UTR|HERC4_ENST00000277817.6_Missense_Mutation_p.G762S|HERC4_ENST00000412272.2_Missense_Mutation_p.G794S|HERC4_ENST00000373700.4_Missense_Mutation_p.G864S	NM_022079.2	NP_071362.1	Q5GLZ8	HERC4_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 4	872	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				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						TCTGTTGCACCAAAGTTTTCA	0.308																																					p.G872S		Atlas-SNP	.											.	HERC4	78	.	0			c.G2614A						PASS	.						138	129	132					10																	69695974		2203	4300	6503	SO:0001583	missense	26091	exon23			TTGCACCAAAGTT	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.2614G>A	10.37:g.69695974C>T	ENSP00000378624:p.Gly872Ser	68	0	0		62	15	0.241935	NM_022079	Q5GC98|Q5GC99|Q5GCA0|Q8IXP9|Q9HCH9	Missense_Mutation	SNP	ENST00000395198.3	37	CCDS41533.1	.	.	.	.	.	.	.	.	.	.	C	32	5.153248	0.94645	.	.	ENSG00000148634	ENST00000277817;ENST00000412272;ENST00000395198;ENST00000373700	T;T;T;T	0.58210	0.35;0.35;0.35;0.35	5.2	5.2	0.72013	HECT (4);	0.000000	0.85682	D	0.000000	T	0.79587	0.4471	M	0.91872	3.25	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;0.999;0.999;0.999	D	0.84384	0.0551	10	0.87932	D	0	.	19.1052	0.93291	0.0:1.0:0.0:0.0	.	794;762;722;864;872	Q5GLZ8-3;Q5GLZ8-6;Q5VXS9;Q5GLZ8-2;Q5GLZ8	.;.;.;.;HERC4_HUMAN	S	762;794;872;864	ENSP00000277817:G762S;ENSP00000416504:G794S;ENSP00000378624:G872S;ENSP00000362804:G864S	ENSP00000277817:G762S	G	-	1	0	HERC4	69365980	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.364000	0.79526	2.568000	0.86640	0.460000	0.39030	GGT	.	.	none		0.308	HERC4-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359262.1	NM_015601		T	69695974	C	T	69695974	3	4	27	1	0	0	0	0	1	0	0	0	7069	594	21	2	575	2	HERC4	10	69695974	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1	69695974	65838773	547	10998	138	2									
ATOH7	220202	hgsc.bcm.edu	37	chr10	69991266	69991266	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taagcggtcgaaggcagtgtTgagcccctgcatgcggcggc	7	7	16	11	4	0	1	0	1	0	0	1	2	0	1	2	4	4	3	2	4	2	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:69991266T>C	ENST00000373673.3	-	1	605	c.169A>G	c.(169-171)Aac>Gac	p.N57D	RP11-153K11.3_ENST00000444086.1_lincRNA	NM_145178.3	NP_660161.1	Q8N100	ATOH7_HUMAN	atonal homolog 7 (Drosophila)	57	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cell differentiation (GO:0030154)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|neural retina development (GO:0003407)|optic nerve development (GO:0021554)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)										AAGGCAGTGTTGAGCCCCTGC	0.701																																					p.N57D		Atlas-SNP	.											.	ATOH7	4	.	0			c.A169G						PASS	.						38	37	38					10																	69991266		2203	4299	6502	SO:0001583	missense	220202	exon1			CAGTGTTGAGCCC	AF418922	CCDS7276.1	10q22.2	2013-05-21			ENSG00000179774	ENSG00000179774		"Basic helix-loop-helix proteins"	13907	protein-coding gene	gene with protein product		609875				11889557	Standard	NM_145178		Approved	Math5, bHLHa13	uc001jnq.3	Q8N100	OTTHUMG00000018346	ENST00000373673.3:c.169A>G	10.37:g.69991266T>C	ENSP00000362777:p.Asn57Asp	42	0	0		55	32	0.581818	NM_145178		Missense_Mutation	SNP	ENST00000373673.3	37	CCDS7276.1	.	.	.	.	.	.	.	.	.	.	T	19.30	3.800203	0.70567	.	.	ENSG00000179774	ENST00000373673	D	0.99394	-5.82	5.01	2.52	0.30459	Helix-loop-helix DNA-binding (5);	0.043911	0.85682	D	0.000000	D	0.99612	0.9859	H	0.98407	4.225	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.98476	1.0603	9	.	.	.	-34.2974	11.5762	0.50862	0.0:0.0:0.2838:0.7162	.	57	Q8N100	ATOH7_HUMAN	D	57	ENSP00000362777:N57D	.	N	-	1	0	ATOH7	69661272	1.000000	0.71417	0.992000	0.48379	0.079000	0.17450	6.216000	0.72212	0.207000	0.20607	0.459000	0.35465	AAC	.	.	none		0.701	ATOH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048312.1			C	69991266	T	C	69991266	3	2	27	1	0	0	0	0	1	0	0	0	1113	1812	63	3	293	3	ATOH7	10	69991266	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	295292	69991266	65543481	548	10999											
DNA2	1763	hgsc.bcm.edu	37	chr10	70191970	70191970	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gattttagcataccctttagAatgcaggcaactgtatcctt	11	14	7	9	0	0	1	0	0	0	1	1	2	1	1	2	1	4	4	2	1	6	7			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:70191970A>G	ENST00000358410.3	-	12	1916	c.1866T>C	c.(1864-1866)atT>atC	p.I622I	DNA2_ENST00000399180.2_Silent_p.I708I|DNA2_ENST00000399179.2_Silent_p.I622I	NM_001080449.2	NP_001073918.2	P51530	DNA2_HUMAN	DNA replication helicase/nuclease 2	622	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						TACCCTTTAGAATGCAGGCAA	0.323																																					p.I622I		Atlas-SNP	.											.	DNA2	76	.	0			c.T1866C						PASS	.						132	126	128					10																	70191970		1836	4087	5923	SO:0001819	synonymous_variant	1763	exon12			CTTTAGAATGCAG	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.1866T>C	10.37:g.70191970A>G		177	0	0		150	6	0.04	NM_001080449	Q2NKM1|Q5TC49|Q5TC50|Q6P455|Q6PI80|Q7Z6H9|Q8N346	Silent	SNP	ENST00000358410.3	37																																																																																				.	.	none		0.323	DNA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048334.2			G	70191970	A	G	70191970	2	3	27	1	0	0	0	0	0	0	0	1	4598	242	9	3		3	DNA2	10	70191970	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	200704	70191970	65342777	549	11000											
TET1	80312	hgsc.bcm.edu	37	chr10	70332312	70332312	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacccgtgccagtcagaagcCttctgacaagagctggagca	11	6	11	13	1	2	3	1	1	1	2	2	4	2	4	3	1	4	2	3	1	2	1	rs138684329		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:70332312C>T	ENST00000373644.4	+	2	426	c.217C>T	c.(217-219)Ctt>Ttt	p.L73F		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	73					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						AGTCAGAAGCCTTCTGACAAG	0.423													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19958	0.0		0.0	False		,,,				2504	0.0				p.L73F		Atlas-SNP	.											.	TET1	255	.	0			c.C217T						PASS	.	C	PHE/LEU	1,4405	2.1+/-5.4	0,1,2202	71	77	75		217	4.3	1	10	dbSNP_134	75	2,8598	2.2+/-6.3	0,2,4298	yes	missense	TET1	NM_030625.2	22	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	benign	73/2137	70332312	3,13003	2203	4300	6503	SO:0001583	missense	80312	exon2			AGAAGCCTTCTGA	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.217C>T	10.37:g.70332312C>T	ENSP00000362748:p.Leu73Phe	100	0	0		97	43	0.443299	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	14.23	2.472520	0.43942	2.27E-4	2.33E-4	ENSG00000138336	ENST00000373644	T	0.08984	3.03	5.24	4.32	0.51571	.	0.000000	0.44902	D	0.000417	T	0.05135	0.0137	N	0.19112	0.55	0.24628	N	0.993634	B	0.33748	0.423	B	0.31751	0.135	T	0.37865	-0.9687	10	0.27082	T	0.32	.	7.5134	0.27587	0.2035:0.7101:0.0:0.0864	.	73	Q8NFU7	TET1_HUMAN	F	73	ENSP00000362748:L73F	ENSP00000362748:L73F	L	+	1	0	TET1	70002318	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	2.411000	0.44600	1.168000	0.42723	0.563000	0.77884	CTT	C|1.000;T|0.000	0.000	strong		0.423	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		T	70332312	C	T	70332312	3	4	27	1	0	0	0	0	1	0	0	0	15784	681	24	2	219	2	TET1	10	70332312	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	140342	70332312	65202435	550	11001											
STOX1	219736	hgsc.bcm.edu	37	chr10	70641785	70641785	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttgggtgaagttctttgcTgtgctatatctgatatgaat	8	18	10	5	0	2	3	0	3	2	0	2	3	2	3	0	1	2	3	0	1	5	6	rs377656965		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:70641785T>C	ENST00000298596.6	+	2	465	c.382T>C	c.(382-384)Tgt>Cgt	p.C128R	STOX1_ENST00000399165.4_Missense_Mutation_p.C128R|STOX1_ENST00000421961.2_Missense_Mutation_p.C18R|STOX1_ENST00000399162.2_Missense_Mutation_p.C128R|STOX1_ENST00000399169.4_Missense_Mutation_p.C128R	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	128						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						AGTTCTTTGCTGTGCTATATC	0.368																																					p.C128R		Atlas-SNP	.											.	STOX1	75	.	0			c.T382C						PASS	.	T	ARG/CYS,ARG/CYS,ARG/CYS,ARG/CYS,ARG/CYS	0,3730		0,0,1865	166	152	156		382,382,382,52,382	5.6	1	10		156	1,8199		0,1,4099	no	missense,missense,missense,missense,missense	STOX1	NM_001130159.2,NM_001130160.2,NM_001130161.2,NM_001130162.2,NM_152709.4	180,180,180,180,180	0,1,5964	CC,CT,TT		0.0122,0.0,0.0084	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	128/228,128/170,128/990,18/880,128/990	70641785	1,11929	1865	4100	5965	SO:0001583	missense	219736	exon2			CTTTGCTGTGCTA	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.382T>C	10.37:g.70641785T>C	ENSP00000298596:p.Cys128Arg	175	0	0		160	73	0.45625	NM_001130160	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Missense_Mutation	SNP	ENST00000298596.6	37	CCDS41535.1	.	.	.	.	.	.	.	.	.	.	T	13.74	2.328142	0.41197	0.0	1.22E-4	ENSG00000165730	ENST00000399169;ENST00000298596;ENST00000399165;ENST00000399162;ENST00000421961	T;T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98;-0.98	5.57	5.57	0.84162	Storkhead-box protein, winged-helix domain (1);	0.149142	0.45867	U	0.000336	T	0.68970	0.3059	L	0.36672	1.1	0.80722	D	1	P;P;P	0.48503	0.627;0.911;0.627	B;P;B	0.45753	0.216;0.492;0.14	T	0.72381	-0.4311	10	0.59425	D	0.04	.	11.934	0.52864	0.0:0.0702:0.0:0.9298	.	128;128;128	Q6ZVD7-3;Q6ZVD7;Q6ZVD7-2	.;STOX1_HUMAN;.	R	128;128;128;128;18	ENSP00000382121:C128R;ENSP00000298596:C128R;ENSP00000382118:C128R;ENSP00000382115:C128R;ENSP00000394509:C18R	ENSP00000298596:C128R	C	+	1	0	STOX1	70311791	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.709000	0.47160	2.242000	0.73789	0.482000	0.46254	TGT	.	.	none		0.368	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709		C	70641785	T	C	70641785	3	2	27	1	0	0	0	0	1	0	0	0	15334	1580	55	3	388	3	STOX1	10	70641785	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	309473	70641785	64892962	551	11002											
SRGN	5552	hgsc.bcm.edu	37	chr10	70856963	70856963	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aggtgaatccaacaagatccCccgtctgaggactgaccttt	11	9	9	12	1	1	4	0	3	1	1	3	5	3	5	4	2	1	0	4	2	3	1	rs67852477	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:70856963C>G	ENST00000242465.3	+	2	243	c.203C>G	c.(202-204)cCc>cGc	p.P68R	SRGN_ENST00000462445.1_Intron	NM_002727.2	NP_002718.2	P10124	SRGN_HUMAN	serglycin	68					biomineral tissue development (GO:0031214)|blood coagulation (GO:0007596)|granzyme-mediated apoptotic signaling pathway (GO:0008626)|maintenance of granzyme B location in T cell secretory granule (GO:0033382)|maintenance of protease location in mast cell secretory granule (GO:0033373)|mast cell secretory granule organization (GO:0033364)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cytokine secretion (GO:0050710)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein processing (GO:0016485)|T cell secretory granule organization (GO:0033371)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|mast cell granule (GO:0042629)|platelet alpha granule lumen (GO:0031093)|zymogen granule (GO:0042588)				large_intestine(1)|lung(1)|skin(2)|upper_aerodigestive_tract(3)	7						AACAAGATCCCCCGTCTGAGG	0.413													C|||	22	0.00439297	0.0008	0.0029	5008	,	,		16334	0.001		0.0149	False		,,,				2504	0.0031				p.P68R		Atlas-SNP	.											SRGN,NS,carcinoid-endocrine_tumour,0,1	SRGN	15	1	0			c.C203G						PASS	.	C	ARG/PRO	12,4394	19.1+/-41.9	0,12,2191	96	87	90		203	0.2	0	10	dbSNP_130	90	107,8493	57.2+/-118.5	1,105,4194	yes	missense	SRGN	NM_002727.2	103	1,117,6385	GG,GC,CC		1.2442,0.2724,0.915	possibly-damaging	68/159	70856963	119,12887	2203	4300	6503	SO:0001583	missense	5552	exon2			AGATCCCCCGTCT	BC015516	CCDS7285.1	10q22.1	2007-02-16	2007-02-15	2007-02-15	ENSG00000122862	ENSG00000122862		"Proteoglycans / Extracellular Matrix : Other"	9361	protein-coding gene	gene with protein product	"serglycin proteoglycan"	177040	"proteoglycan 1, secretory granule"	PRG, PRG1			Standard	NR_036430		Approved	PPG	uc001joz.3	P10124	OTTHUMG00000018369	ENST00000242465.3:c.203C>G	10.37:g.70856963C>G	ENSP00000242465:p.Pro68Arg	160	0	0		122	62	0.508197	NM_002727	B2R4L7|Q5VW06	Missense_Mutation	SNP	ENST00000242465.3	37	CCDS7285.1	15	0.006868131868131868	0	0.0	2	0.0055248618784530384	1	0.0017482517482517483	12	0.0158311345646438	C	4.802	0.149123	0.09185	0.002724	0.012442	ENSG00000122862	ENST00000242465	T	0.50548	0.74	5.26	0.242	0.15498	.	1.444430	0.04231	N	0.335288	T	0.22704	0.0548	L	0.29908	0.895	0.09310	N	1	B	0.25955	0.138	B	0.32677	0.15	T	0.33292	-0.9874	10	0.59425	D	0.04	-14.8937	4.3284	0.11051	0.0:0.2911:0.1779:0.531	.	68	P10124	SRGN_HUMAN	R	68	ENSP00000242465:P68R	ENSP00000242465:P68R	P	+	2	0	SRGN	70526969	0.002000	0.14202	0.000000	0.03702	0.006000	0.05464	0.360000	0.20250	-0.129000	0.11620	-0.367000	0.07326	CCC	C|0.991;G|0.009	0.009	strong		0.413	SRGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048379.1	NM_002727		G	70856963	C	G	70856963	3	3	27	1	0	0	0	0	1	0	0	0	15163	623	22	4	209	4	SRGN	10	70856963	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	215178	70856963	64677784	552	11003											
PRF1	5551	hgsc.bcm.edu	37	chr10	72360457	72360457	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggtgcaggtgccgtcgggccGcaggaacctttgtgtgtcca	5	9	16	11	3	0	0	0	0	0	0	2	1	1	1	4	4	3	2	4	4	1	1	rs151232299		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:72360457G>A	ENST00000441259.1	-	2	362	c.202C>T	c.(202-204)Cgg>Tgg	p.R68W	PRF1_ENST00000373209.2_Missense_Mutation_p.R68W	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	68	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						CCGTCGGGCCGCAGGAACCTT	0.682			M			"various leukaemia, lymphoma"	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis																												p.R68W		Atlas-SNP	.	yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	PRF1,right_upper_lobe,carcinoma,+2,1	PRF1	64	1	0			c.C202T						PASS	.	G	TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	41	41	41		202,202	1.6	0.9	10	dbSNP_134	41	0,8600		0,0,4300	yes	missense,missense	PRF1	NM_001083116.1,NM_005041.4	101,101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	68/556,68/556	72360457	1,13005	2203	4300	6503	SO:0001583	missense	5551	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	CGGGCCGCAGGAA	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.202C>T	10.37:g.72360457G>A	ENSP00000398568:p.Arg68Trp	252	0	0		239	91	0.380753	NM_001083116	B2R6X4|Q59F57|Q86WX7	Missense_Mutation	SNP	ENST00000441259.1	37	CCDS7305.1	.	.	.	.	.	.	.	.	.	.	G	16.75	3.210912	0.58343	2.27E-4	0.0	ENSG00000180644	ENST00000373209;ENST00000441259;ENST00000318971	D;D	0.91740	-2.9;-2.9	5.7	1.58	0.23477	Membrane attack complex component/perforin (MACPF) domain (1);	0.257519	0.37530	N	0.002057	D	0.93523	0.7933	M	0.83692	2.655	0.18873	N	0.999984	D	0.89917	1.0	P	0.61722	0.893	D	0.86042	0.1520	10	0.87932	D	0	-20.3888	1.6559	0.02782	0.161:0.1295:0.3914:0.3181	.	68	P14222	PERF_HUMAN	W	68	ENSP00000362305:R68W;ENSP00000398568:R68W	ENSP00000316746:R68W	R	-	1	2	PRF1	72030463	0.000000	0.05858	0.910000	0.35882	0.562000	0.35680	0.342000	0.19926	0.014000	0.14944	0.655000	0.94253	CGG	G|1.000;A|0.000	0.000	weak		0.682	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041		A	72360457	G	A	72360457	3	1	27	1	0	0	0	0	1	0	0	0	12490	1086	38	1	1473	1	PRF1	10	72360457	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1503494	72360457	63174290	553	11004											
C10orf27	219793	hgsc.bcm.edu	37	chr10	72534090	72534090	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgagccactgctgtctgcaGgagtcccagagcgaggtctt	7	9	13	12	1	2	2	0	1	2	1	3	4	3	3	2	2	4	2	2	2	0	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:72534090G>T	ENST00000299290.1	-	9	1185	c.796C>A	c.(796-798)Ctg>Atg	p.L266M	TBATA_ENST00000394982.2_5'Flank|TBATA_ENST00000456372.2_Silent_p.S238S	NM_152710.2	NP_689923	Q96M53	TBATA_HUMAN	thymus, brain and testes associated	266					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|nucleus (GO:0005634)											GCTGTCTGCAGGAGTCCCAGA	0.612																																					p.L266M		Atlas-SNP	.											.	.	.	.	0			c.C796A						PASS	.						47	46	46					10																	72534090		2203	4300	6503	SO:0001583	missense	219793	exon9			TCTGCAGGAGTCC	AK057382	CCDS7308.1	10q22.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166220	ENSG00000166220			23511	protein-coding gene	gene with protein product		612640	"chromosome 10 open reading frame 27"	C10orf27		20937703	Standard	NM_152710		Approved	FLJ32820, spatial	uc001jrj.1	Q96M53	OTTHUMG00000018413	ENST00000299290.1:c.796C>A	10.37:g.72534090G>T	ENSP00000299290:p.Leu266Met	84	0	0		77	16	0.207792	NM_152710	A4QPA8|B2RPQ2|Q5T4G2	Missense_Mutation	SNP	ENST00000299290.1	37	CCDS7308.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.85|14.85	2.659135|2.659135	0.47467|0.47467	.|.	.|.	ENSG00000166220|ENSG00000166220	ENST00000299290|ENST00000536955	T|.	0.24151|.	1.87|.	4.94|4.94	4.94|4.94	0.65067|0.65067	.|.	0.000000|.	0.52532|.	D|.	0.000080|.	T|T	0.74635|0.74635	0.3742|0.3742	M|M	0.75447|0.75447	2.3|2.3	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	0.78290|0.78290	-0.2261|-0.2261	10|6	0.72032|0.87932	D|D	0.01|0	-13.863|-13.863	13.674|13.674	0.62443|0.62443	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	265;267;266|.	B7ZMN4;B7ZMN5;Q96M53|.	.;.;SPATL_HUMAN|.	M|H	266|288	ENSP00000299290:L266M|.	ENSP00000299290:L266M|ENSP00000438618:P288H	L|P	-|-	1|2	2|0	C10orf27|C10orf27	72204096|72204096	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.193000|0.193000	0.23685|0.23685	3.298000|3.298000	0.51818|0.51818	2.298000|2.298000	0.77334|0.77334	0.655000|0.655000	0.94253|0.94253	CTG|CCT	.	.	none		0.612	TBATA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048519.1	NM_152710		T	72534090	G	T	72534090	3	4	27	1	0	0	0	0	1	0	0	0	1602	991	35	4	271	4	C10orf27	10	72534090	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	173633	72534090	63000657	554	11005											
ECD	11319	hgsc.bcm.edu	37	chr10	74899209	74899209	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tttgccaacagcttcctgcaGcagctggtccagctgatctg	7	11	10	13	0	1	1	0	1	1	0	3	1	3	1	3	1	7	5	3	1	1	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:74899209G>A	ENST00000372979.4	-	11	1485	c.1279C>T	c.(1279-1281)Ctg>Ttg	p.L427L	ECD_ENST00000430082.2_Silent_p.L460L|ECD_ENST00000454759.2_Silent_p.L384L	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	427					cell proliferation (GO:0008283)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of glycolytic process (GO:0006110)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(51;0.0119)					GCTTCCTGCAGCAGCTGGTCC	0.438																																					p.L460L		Atlas-SNP	.											.	ECD	50	.	0			c.C1378T						PASS	.						89	92	91					10																	74899209		2203	4300	6503	SO:0001819	synonymous_variant	11319	exon12			CCTGCAGCAGCTG	BC000721	CCDS7321.1, CCDS44433.1, CCDS44434.1	10q22.3	2006-02-07				ENSG00000122882			17029	protein-coding gene	gene with protein product						9928932, 15128659	Standard	NM_007265		Approved	hSGT1, GCR2	uc001jtn.3	O95905		ENST00000372979.4:c.1279C>T	10.37:g.74899209G>A		101	0	0		77	18	0.233766	NM_001135752	C9JX46|E9PAW8	Silent	SNP	ENST00000372979.4	37	CCDS7321.1																																																																																			.	.	none		0.438	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265		A	74899209	G	A	74899209	2	1	27	1	0	0	0	0	0	0	0	1	4890	962	34	2		2	ECD	10	74899209	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2365119	74899209	60635538	555	11006											
DNAJC9	23234	hgsc.bcm.edu	37	chr10	75006868	75006868	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ctcgtcggacctcgccgtcgGaggcctcgcgtcgcacgccc	3	6	13	19	9	0	0	0	0	0	0	6	2	0	2	4	3	0	1	4	3	0	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:75006868G>A	ENST00000372950.4	-	1	1752	c.80C>T	c.(79-81)tCc>tTc	p.S27F	MRPS16_ENST00000479005.1_5'Flank|DNAJC9-AS1_ENST00000440197.2_RNA|MRPS16_ENST00000416782.2_3'UTR|DNAJC9-AS1_ENST00000513954.1_RNA	NM_015190.3	NP_056005.1	Q8WXX5	DNJC9_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 9	27	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				social behavior (GO:0035176)	nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|stomach(1)	6	Prostate(51;0.0119)					CTCGCCGTCGGAGGCCTCGCG	0.697																																					p.S27F		Atlas-SNP	.											.	DNAJC9	19	.	0			c.C80T						PASS	.						13	13	13					10																	75006868		2188	4280	6468	SO:0001583	missense	23234	exon1			CCGTCGGAGGCCT	AF327347	CCDS7322.1	10q22.3	2011-09-02			ENSG00000213551	ENSG00000213551		"Heat shock proteins / DNAJ (HSP40)"	19123	protein-coding gene	gene with protein product		611206					Standard	NM_015190		Approved	JDD1, SB73	uc001jtr.3	Q8WXX5	OTTHUMG00000018461	ENST00000372950.4:c.80C>T	10.37:g.75006868G>A	ENSP00000362041:p.Ser27Phe	79	0	0		88	42	0.477273	NM_015190	B2RMW6	Missense_Mutation	SNP	ENST00000372950.4	37	CCDS7322.1	.	.	.	.	.	.	.	.	.	.	g	22.8	4.333978	0.81801	.	.	ENSG00000213551	ENST00000372950	T	0.37058	1.22	5.65	4.74	0.60224	Heat shock protein DnaJ, N-terminal (5);	0.527076	0.21432	N	0.074639	T	0.69522	0.3120	H	0.96518	3.835	0.80722	D	1	D	0.60160	0.987	D	0.65684	0.937	T	0.78851	-0.2041	10	0.87932	D	0	-22.6147	12.6301	0.56653	0.0:0.1665:0.8335:0.0	.	27	Q8WXX5	DNJC9_HUMAN	F	27	ENSP00000362041:S27F	ENSP00000362041:S27F	S	-	2	0	DNAJC9	74676874	0.888000	0.30383	0.842000	0.33263	0.371000	0.29859	4.349000	0.59385	1.377000	0.46286	0.586000	0.80456	TCC	.	.	none		0.697	DNAJC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048643.1	NM_015190		A	75006868	G	A	75006868	3	1	27	1	0	0	0	0	1	0	0	0	4658	1174	41	2	722	2	DNAJC9	10	75006868	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	107659	75006868	60527879	556	11007											
USP54	159195	hgsc.bcm.edu	37	chr10	75258558	75258558	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tctactcttcgaggaccaggGgttcgggaccctggaacagg	8	8	14	11	2	2	0	0	0	2	0	4	4	2	3	2	6	2	1	2	6	2	3	rs61749235	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:75258558G>A	ENST00000339859.4	-	23	4984	c.4884C>T	c.(4882-4884)acC>acT	p.T1628T	USP54_ENST00000408019.1_Silent_p.T1628T|RP11-137L10.6_ENST00000442133.4_RNA|RP11-137L10.6_ENST00000595935.1_RNA|USP54_ENST00000428547.1_Silent_p.T1478T|PPP3CB_ENST00000394829.2_5'Flank|PPP3CB_ENST00000394828.2_5'Flank|RP11-137L10.6_ENST00000597958.1_RNA|RP11-137L10.6_ENST00000600607.1_RNA|RP11-137L10.6_ENST00000593790.1_RNA|PPP3CB_ENST00000342558.3_5'Flank|USP54_ENST00000497106.1_5'UTR|RP11-137L10.6_ENST00000600206.1_RNA|RP11-137L10.6_ENST00000600887.1_RNA|RP11-137L10.6_ENST00000595069.1_RNA|USP54_ENST00000422491.2_Silent_p.T763T|USP54_ENST00000394811.2_Silent_p.T669T|PPP3CB_ENST00000394822.2_5'Flank|PPP3CB_ENST00000360663.5_5'Flank|RP11-137L10.6_ENST00000596320.1_RNA|RP11-137L10.6_ENST00000422977.1_RNA|PPP3CB_ENST00000545874.1_5'Flank			Q70EL1	UBP54_HUMAN	ubiquitin specific peptidase 54	1628					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)					GAGGACCAGGGGTTCGGGACC	0.547													G|||	37	0.00738818	0.0	0.013	5008	,	,		15599	0.0		0.0159	False		,,,				2504	0.0123				p.T1628T	Colon(195;880 2046 8854 25025 38456)	Atlas-SNP	.											.	USP54	178	.	0			c.C4884T						PASS	.	G		22,4384	29.9+/-59.1	0,22,2181	89	87	88		4884	-1	0.6	10	dbSNP_129	88	154,8446	74.2+/-136.8	1,152,4147	no	coding-synonymous	USP54	NM_152586.3		1,174,6328	AA,AG,GG		1.7907,0.4993,1.3532		1628/1685	75258558	176,12830	2203	4300	6503	SO:0001819	synonymous_variant	159195	exon22			ACCAGGGGTTCGG	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.4884C>T	10.37:g.75258558G>A		130	0	0		99	98	0.989899	NM_152586	A1L4Q4|A3KFK3|A3KFK5|A3KFK6|A3KFK7|A6PVS4|A6PVS5|A6PVS6|A6PVS7|B3KVY1|B9ZVM1|Q5F2F4|Q6P1N6|Q6ZSP1|Q6ZSR1|Q6ZTM0|Q8N1X2	Silent	SNP	ENST00000339859.4	37	CCDS7329.2																																																																																			G|0.989;A|0.011	0.011	strong		0.547	USP54-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316563.2	NM_152586		A	75258558	G	A	75258558	2	1	27	1	0	0	0	0	0	0	0	1	17100	1219	43	2		2	USP54	10	75258558	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	251690	75258558	60276189	557	11008											
MYOZ1	58529	hgsc.bcm.edu	37	chr10	75394457	75394457	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gaccagctgtgcccagctgtCcccccactgttggaaggaac	8	7	11	15	0	0	0	0	0	0	0	1	3	1	2	5	2	4	3	5	2	2	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:75394457C>A	ENST00000359322.4	-	4	651	c.287G>T	c.(286-288)gGa>gTa	p.G96V		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)					GCCCAGCTGTCCCCCCACTGT	0.532																																					p.G96V		Atlas-SNP	.											.	MYOZ1	24	.	0			c.G287T						PASS	.						62	60	60					10																	75394457		2203	4300	6503	SO:0001583	missense	58529	exon4			AGCTGTCCCCCCA	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.287G>T	10.37:g.75394457C>A	ENSP00000352272:p.Gly96Val	101	0	0		80	29	0.3625	NM_021245		Missense_Mutation	SNP	ENST00000359322.4	37	CCDS7330.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.251231	0.80135	.	.	ENSG00000177791	ENST00000359322	T	0.66638	-0.22	6.05	6.05	0.98169	.	0.134037	0.64402	D	0.000002	T	0.78027	0.4219	L	0.53249	1.67	0.80722	D	1	D	0.76494	0.999	D	0.73708	0.981	T	0.78455	-0.2197	10	0.72032	D	0.01	-4.7931	14.7834	0.69784	0.0:0.9294:0.0:0.0706	.	96	Q9NP98	MYOZ1_HUMAN	V	96	ENSP00000352272:G96V	ENSP00000352272:G96V	G	-	2	0	MYOZ1	75064463	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.747000	0.62141	2.880000	0.98712	0.655000	0.94253	GGA	.	.	none		0.532	MYOZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048654.1			A	75394457	C	A	75394457	3	1	27	1	0	0	0	0	1	0	0	0	10104	855	30	4	624	4	MYOZ1	10	75394457	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	135899	75394457	60140290	558	11009											
CAMK2G	818	hgsc.bcm.edu	37	chr10	75574956	75574956	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctccccaatcacgtggacGtgtgggtttaggatggtggt	6	12	14	9	2	1	0	1	0	0	0	3	2	3	2	3	5	0	1	3	5	2	2	rs55640406	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:75574956G>A	ENST00000351293.3	-	18	1362	c.1305C>T	c.(1303-1305)caC>caT	p.H435H	CAMK2G_ENST00000372765.1_Silent_p.H456H|CAMK2G_ENST00000322635.3_Silent_p.H467H|CAMK2G_ENST00000423381.1_Silent_p.H528H|CAMK2G_ENST00000322680.3_Silent_p.H496H|CAMK2G_ENST00000394762.2_Silent_p.H473H|RP11-574K11.5_ENST00000434147.1_RNA|CAMK2G_ENST00000305762.7_Silent_p.H469H|CAMK2G_ENST00000472912.1_5'UTR	NM_001222.3|NM_172173.2	NP_001213.2|NP_751913.1	Q13555	KCC2G_HUMAN	calcium/calmodulin-dependent protein kinase II gamma	498					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)	TCACGTGGACGTGTGGGTTTA	0.607													G|||	37	0.00738818	0.0	0.0144	5008	,	,		14899	0.0		0.0169	False		,,,				2504	0.0102				p.H496H		Atlas-SNP	.											.	CAMK2G	79	.	0			c.C1488T						PASS	.	G	,,,,,	25,4381	32.6+/-62.9	0,25,2178	151	123	133		1437,1305,1401,1374,1488,1332	-0.9	0.9	10	dbSNP_129	133	172,8428	79.2+/-141.9	3,166,4131	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CAMK2G	NM_001204492.1,NM_001222.3,NM_172169.2,NM_172170.4,NM_172171.2,NM_172173.2	,,,,,	3,191,6309	AA,AG,GG		2.0,0.5674,1.5147	,,,,,	479/540,435/496,467/528,458/519,496/557,444/505	75574956	197,12809	2203	4300	6503	SO:0001819	synonymous_variant	818	exon20			GTGGACGTGTGGG	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.1305C>T	10.37:g.75574956G>A		195	0	0		143	142	0.993007	NM_172171	O00561|O15378|Q13279|Q13282|Q13556|Q5SQZ3|Q5SQZ4|Q5SWX4|Q7KYX5|Q8N4I3|Q8NIA4	Silent	SNP	ENST00000351293.3	37	CCDS7336.1	18	0.008241758241758242	0	0.0	5	0.013812154696132596	0	0.0	13	0.017150395778364115	G	9.245	1.039308	0.19669	0.005674	0.02	ENSG00000148660	ENST00000441192	.	.	.	5.51	-0.849	0.10723	.	.	.	.	.	T	0.41766	0.1173	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45716	-0.9242	4	.	.	.	.	11.3382	0.49516	0.5165:0.0:0.4835:0.0	rs55640406	.	.	.	C	275	.	.	R	-	1	0	CAMK2G	75244962	0.853000	0.29707	0.880000	0.34516	0.996000	0.88848	-0.037000	0.12164	-0.477000	0.06832	-0.137000	0.14449	CGT	G|0.988;A|0.012	0.012	strong		0.607	CAMK2G-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048715.1	NM_172169		A	75574956	G	A	75574956	2	1	27	1	0	0	0	0	0	0	0	1	2604	1136	40	1		1	CAMK2G	10	75574956	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	180499	75574956	59959791	559	11010											
SAMD8	142891	hgsc.bcm.edu	37	chr10	76910705	76910705	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgaatggtaaaaacaaacAttctgttcgaagattggacc	16	10	8	7	1	1	2	0	1	1	1	2	4	1	3	1	2	2	2	1	2	6	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:76910705A>T	ENST00000542569.1	+	2	522	c.419A>T	c.(418-420)cAt>cTt	p.H140L	SAMD8_ENST00000372690.3_Missense_Mutation_p.H203L|SAMD8_ENST00000372687.4_Missense_Mutation_p.H140L	NM_001174156.1|NM_144660.2	NP_001167627.1|NP_653261.1	Q96LT4	SAMD8_HUMAN	sterile alpha motif domain containing 8	140					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)			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)					AAAAACAAACATTCTGTTCGA	0.373																																					p.H140L		Atlas-SNP	.											.	SAMD8	57	.	0			c.A419T						PASS	.						73	68	69					10																	76910705		2203	4300	6503	SO:0001583	missense	142891	exon2			ACAAACATTCTGT	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.419A>T	10.37:g.76910705A>T	ENSP00000438042:p.His140Leu	115	0	0		88	20	0.227273	NM_144660	Q5JSC5|Q5JSC8|Q66K52	Missense_Mutation	SNP	ENST00000542569.1	37	CCDS53543.1	.	.	.	.	.	.	.	.	.	.	A	12.25	1.881147	0.33255	.	.	ENSG00000156671	ENST00000447533;ENST00000372690;ENST00000542569;ENST00000372687	.	.	.	5.7	5.7	0.88788	.	0.046754	0.85682	D	0.000000	T	0.45276	0.1334	L	0.29908	0.895	0.43141	D	0.994895	P;B	0.36535	0.557;0.007	B;B	0.33620	0.167;0.009	T	0.40117	-0.9580	9	0.23302	T	0.38	-17.3105	15.9627	0.79941	1.0:0.0:0.0:0.0	.	140;140	Q96LT4-2;Q96LT4	.;SAMD8_HUMAN	L	140;203;140;140	.	ENSP00000361772:H140L	H	+	2	0	SAMD8	76580711	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.750000	0.74888	2.179000	0.69175	0.402000	0.26972	CAT	.	.	none		0.373	SAMD8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_144660		T	76910705	A	T	76910705	3	4	27	1	0	0	0	0	1	0	0	0	13840	217	8	5	421	5	SAMD8	10	76910705	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	1335749	76910705	58624042	560	11011											
ZMIZ1	57178	hgsc.bcm.edu	37	chr10	81053248	81053248	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcatggcggctggcatgacGccctcggggatgagcggccc	6	5	17	13	4	0	2	0	2	0	0	1	3	0	3	2	6	2	3	2	6	0	0	rs146995829	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:81053248G>A	ENST00000334512.5	+	12	1640	c.1068G>A	c.(1066-1068)acG>acA	p.T356T	ZMIZ1_ENST00000478357.1_3'UTR	NM_020338.3	NP_065071.1	Q9ULJ6	ZMIZ1_HUMAN	zinc finger, MIZ-type containing 1	356	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)			CTGGCATGACGCCCTCGGGGA	0.701													G|||	26	0.00519169	0.0	0.0029	5008	,	,		10851	0.0		0.0129	False		,,,				2504	0.0112				p.T356T		Atlas-SNP	.											ZMIZ1,NS,carcinoma,+1,1	ZMIZ1	101	1	0			c.G1068A						PASS	.	G		9,4379		0,9,2185	31	41	38		1068	-9.8	0.9	10	dbSNP_134	38	88,8482		0,88,4197	no	coding-synonymous	ZMIZ1	NM_020338.3		0,97,6382	AA,AG,GG		1.0268,0.2051,0.7486		356/1068	81053248	97,12861	2194	4285	6479	SO:0001819	synonymous_variant	57178	exon12			CATGACGCCCTCG	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.1068G>A	10.37:g.81053248G>A		29	0	0		32	13	0.40625	NM_020338	Q5JSH9|Q7Z7E6	Silent	SNP	ENST00000334512.5	37	CCDS7357.1																																																																																			G|0.995;A|0.005	0.005	strong		0.701	ZMIZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048944.2	NM_020338		A	81053248	G	A	81053248	2	1	27	1	0	0	0	0	0	0	0	1	17711	1074	38	1		1	ZMIZ1	10	81053248	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	4142543	81053248	54481499	561	11012											
FAS	355	hgsc.bcm.edu	37	chr10	90771767	90771767	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ttctttcagtgaagagaaagGaagtacagaaaacatgcaga	18	8	10	5	0	2	4	1	1	1	3	2	6	2	5	0	1	3	2	0	1	6	3	rs56006128	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:90771767G>A	ENST00000355279.2	+	7	580	c.580G>A	c.(580-582)Gaa>Aaa	p.E194K	FAS_ENST00000352159.4_Missense_Mutation_p.E194K|FAS_ENST00000357339.2_Missense_Mutation_p.E173K|FAS_ENST00000313771.5_3'UTR|FAS_ENST00000355740.2_Missense_Mutation_p.E194K			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)	GAAGAGAAAGGAAGTACAGAA	0.358													G|||	3	0.000599042	0.0	0.0014	5008	,	,		20137	0.0		0.002	False		,,,				2504	0.0				p.E194K		Atlas-SNP	.											.	FAS	47	.	0			c.G580A	GRCh37	CM065175	FAS	M	rs56006128	PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU	3,4403	6.2+/-15.9	0,3,2200	104	107	106		580,517,580		0	10	dbSNP_129	106	29,8571	19.8+/-62.0	0,29,4271	yes	missense,missense,missense	FAS	NM_000043.4,NM_152871.2,NM_152872.2	56,56,56	0,32,6471	AA,AG,GG		0.3372,0.0681,0.246	benign,benign,benign	194/336,173/315,194/221	90771767	32,12974	2203	4300	6503	SO:0001583	missense	355	exon7			AGAAAGGAAGTAC	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.580G>A	10.37:g.90771767G>A	ENSP00000347426:p.Glu194Lys	83	0	0		54	27	0.5	NM_152872	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000355279.2	37	CCDS7395.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	0.005	-2.233006	0.00277	6.81E-4	0.003372	ENSG00000026103	ENST00000540197;ENST00000355740;ENST00000352159;ENST00000357339;ENST00000355279;ENST00000371875	D;T;D;T	0.92595	-3.07;-0.6;-2.09;-0.49	.	.	.	.	1209.270000	0.00166	U	0.000004	T	0.74489	0.3723	N	0.00583	-1.355	0.09310	N	1	B;B;B	0.14805	0.001;0.0;0.011	B;B;B	0.01281	0.0;0.0;0.0	T	0.69895	-0.5021	8	0.28530	T	0.3	.	.	.	.	rs56006128	173;194;194	P25445-6;Q5T9P3;P25445	.;.;TNR6_HUMAN	K	221;194;194;173;194;194	ENSP00000347979:E194K;ENSP00000345601:E194K;ENSP00000349896:E173K;ENSP00000347426:E194K	ENSP00000345601:E194K	E	+	1	0	FAS	90761747	.	.	0.010000	0.14722	0.014000	0.08584	.	.	0.119000	0.18210	0.121000	0.15741	GAA	G|0.999;A|0.001	0.001	strong		0.358	FAS-011	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000049280.2			A	90771767	G	A	90771767	3	1	27	1	0	0	0	0	1	0	0	0	5689	1175	41	2	606	2	FAS	10	90771767	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	9718519	90771767	44762980	562	11013											
PANK1	53354	hgsc.bcm.edu	37	chr10	91359116	91359116	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tatgggttatcaaggcagtaCggctttttttgacacaattc	10	15	9	7	1	1	1	1	1	0	0	2	1	1	1	0	3	1	4	0	3	5	7	rs11592870	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:91359116C>T	ENST00000307534.4	-	3	1358	c.1203G>A	c.(1201-1203)ccG>ccA	p.P401P	PANK1_ENST00000322191.6_Silent_p.P176P|PANK1_ENST00000342512.3_Silent_p.P176P|PANK1_ENST00000371774.2_Silent_p.P203P	NM_148977.2	NP_683878.1	Q8TE04	PANK1_HUMAN	pantothenate kinase 1	401					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						CAAGGCAGTACGGCTTTTTTT	0.438													C|||	75	0.014976	0.0	0.013	5008	,	,		19072	0.0		0.0408	False		,,,				2504	0.0256				p.P401P		Atlas-SNP	.											PANK1,colon,carcinoma,0,1	PANK1	35	1	0			c.G1203A						scavenged	.	C	,,	30,4376	36.8+/-68.6	0,30,2173	236	213	221		528,1203,528	-4.7	1	10	dbSNP_120	221	250,8350	99.0+/-160.6	1,248,4051	no	coding-synonymous,coding-synonymous,coding-synonymous	PANK1	NM_138316.3,NM_148977.2,NM_148978.2	,,	1,278,6224	TT,TC,CC		2.907,0.6809,2.1529	,,	176/315,401/599,176/374	91359116	280,12726	2203	4300	6503	SO:0001819	synonymous_variant	53354	exon3			GCAGTACGGCTTT	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.1203G>A	10.37:g.91359116C>T		177	1	0.00564972		149	74	0.496644	NM_148977	A6NIP0|Q7RTX6|Q7Z495|Q8TBQ8	Silent	SNP	ENST00000307534.4	37	CCDS31244.1																																																																																			C|0.981;T|0.019	0.019	strong		0.438	PANK1-201	KNOWN	basic|CCDS	protein_coding	protein_coding				T	91359116	C	T	91359116	2	4	27	1	0	0	0	0	0	0	0	1	11425	523	19	1		1	PANK1	10	91359116	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	587349	91359116	44175631	563	11014											
GPR120	338557	hgsc.bcm.edu	37	chr10	95347041	95347041	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcggagagccaccagatccGcgtgtcccagcaggacttcc	8	6	11	16	3	0	2	0	0	0	2	4	4	3	3	5	2	2	1	5	2	0	1	rs116454156	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:95347041G>A	ENST00000371483.4	+	4	865	c.809G>A	c.(808-810)cGc>cAc	p.R270H	FFAR4_ENST00000604414.1_Intron|FFAR4_ENST00000371481.4_Missense_Mutation_p.R254H	NM_181745.3	NP_859529.2	Q5NUL3	FFAR4_HUMAN	free fatty acid receptor 4	270			R -> H (polymorphism associated with increased risk of obesity; dbSNP:rs116454156). {ECO:0000269|PubMed:22343897}.		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)										CACCAGATCCGCGTGTCCCAG	0.562													G|||	75	0.014976	0.0008	0.0072	5008	,	,		18560	0.001		0.0149	False		,,,				2504	0.0542				p.R270H		Atlas-SNP	.											.	.	.	.	0			c.G809A						PASS	.	G	HIS/ARG,HIS/ARG	21,4385	27.2+/-55.0	0,21,2182	110	103	105		761,809	5	1	10	dbSNP_132	105	150,8450	72.9+/-135.5	1,148,4151	yes	missense,missense	O3FAR1	NM_001195755.1,NM_181745.3	29,29	1,169,6333	AA,AG,GG		1.7442,0.4766,1.3148	benign,benign	254/362,270/378	95347041	171,12835	2203	4300	6503	SO:0001583	missense	338557	exon4			AGATCCGCGTGTC		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.809G>A	10.37:g.95347041G>A	ENSP00000360538:p.Arg270His	112	0	0		97	59	0.608247	NM_181745	Q495H1|Q5VY25|Q5VY26|Q7Z605|Q86SM7	Missense_Mutation	SNP	ENST00000371483.4	37	CCDS31248.1	16	0.007326007326007326	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	11	0.014511873350923483	G	15.28	2.785286	0.49997	0.004766	0.017442	ENSG00000186188	ENST00000371481;ENST00000371483	T;T	0.72725	-0.68;-0.68	4.99	4.99	0.66335	GPCR, rhodopsin-like superfamily (1);	0.096786	0.44097	D	0.000500	T	0.48390	0.1497	L	0.57536	1.79	0.29401	N	0.861934	B;B	0.26195	0.07;0.144	B;B	0.18561	0.019;0.022	T	0.60146	-0.7320	10	0.59425	D	0.04	-20.7853	10.4759	0.44665	0.1505:0.0:0.8495:0.0	.	254;270	Q5NUL3-2;Q5NUL3	.;O3FA1_HUMAN	H	254;270	ENSP00000360536:R254H;ENSP00000360538:R270H	ENSP00000360536:R254H	R	+	2	0	O3FAR1	95337031	0.617000	0.27043	0.998000	0.56505	0.924000	0.55760	1.721000	0.38032	2.741000	0.93983	0.555000	0.69702	CGC	G|0.987;A|0.013	0.013	strong		0.562	FFAR4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000083179.1	NM_181745		A	95347041	G	A	95347041	3	1	27	1	0	0	0	0	1	0	0	0	6644	1087	38	1	823	1	GPR120	10	95347041	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	3987925	95347041	40187706	564	11015											
ENTPD7	57089	hgsc.bcm.edu	37	chr10	101458487	101458487	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaggcctcactcaatggcAtatatcaatcgcctattgac	11	10	7	13	1	3	1	3	1	0	0	4	1	3	1	3	2	0	1	3	2	5	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:101458487A>G	ENST00000370489.4	+	10	1385	c.1207A>G	c.(1207-1209)Ata>Gta	p.I403V		NM_020354.3	NP_065087.1	Q9NQZ7	ENTP7_HUMAN	ectonucleoside triphosphate diphosphohydrolase 7	403						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)		ACTCAATGGCATATATCAATC	0.517																																					p.I403V		Atlas-SNP	.											.	ENTPD7	44	.	0			c.A1207G						PASS	.						88	81	83					10																	101458487		2203	4300	6503	SO:0001583	missense	57089	exon10			AATGGCATATATC	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.1207A>G	10.37:g.101458487A>G	ENSP00000359520:p.Ile403Val	247	0	0		153	76	0.496732	NM_020354	B2RB83|B3KP21|D3DR64	Missense_Mutation	SNP	ENST00000370489.4	37	CCDS7480.1	.	.	.	.	.	.	.	.	.	.	A	2.485	-0.318732	0.05386	.	.	ENSG00000198018	ENST00000370489	T	0.08282	3.11	4.79	4.79	0.61399	.	0.069391	0.64402	D	0.000010	T	0.02807	0.0084	N	0.02697	-0.525	0.32828	D	0.503591	B	0.02656	0.0	B	0.04013	0.001	T	0.25779	-1.0122	10	0.02654	T	1	-0.8043	8.8175	0.35004	0.9146:0.0:0.0854:0.0	.	403	Q9NQZ7	ENTP7_HUMAN	V	403	ENSP00000359520:I403V	ENSP00000359520:I403V	I	+	1	0	ENTPD7	101448477	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	2.569000	0.45973	2.022000	0.59522	0.533000	0.62120	ATA	.	.	none		0.517	ENTPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049809.2	NM_020354		G	101458487	A	G	101458487	3	3	27	1	0	0	0	0	1	0	0	0	5146	217	8	3	1241	3	ENTPD7	10	101458487	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	6111446	101458487	34076260	565	11016											
CPN1	1369	hgsc.bcm.edu	37	chr10	101808540	101808540	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ttggttccgcaggacccacgGtcacagttactgtctctggg	6	11	12	12	2	2	0	1	0	1	0	4	1	3	1	2	4	1	3	2	4	1	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:101808540G>A	ENST00000370418.3	-	8	1456	c.1205C>T	c.(1204-1206)aCc>aTc	p.T402I		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	402					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)		AGGACCCACGGTCACAGTTAC	0.512																																					p.T402I		Atlas-SNP	.											.	CPN1	62	.	0			c.C1205T						PASS	.						181	142	156					10																	101808540		2203	4300	6503	SO:0001583	missense	1369	exon8			CCCACGGTCACAG	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.1205C>T	10.37:g.101808540G>A	ENSP00000359446:p.Thr402Ile	137	0	0		113	26	0.230089	NM_001308	B1AP59	Missense_Mutation	SNP	ENST00000370418.3	37	CCDS7486.1	.	.	.	.	.	.	.	.	.	.	G	11.80	1.745365	0.30955	.	.	ENSG00000120054	ENST00000370418;ENST00000441382	T;T	0.49139	0.79;0.79	5.5	4.6	0.57074	Peptidase M14, carboxypeptidase A (1);Carboxypeptidase-like, regulatory domain (1);Carboxypeptidase, regulatory domain (1);	0.099528	0.64402	N	0.000002	T	0.45256	0.1333	M	0.66560	2.04	0.52099	D	0.999945	B	0.14438	0.01	B	0.19148	0.024	T	0.38824	-0.9643	10	0.38643	T	0.18	-16.477	10.2462	0.43343	0.1601:0.0:0.8399:0.0	.	402	P15169	CBPN_HUMAN	I	402;199	ENSP00000359446:T402I;ENSP00000410895:T199I	ENSP00000359446:T402I	T	-	2	0	CPN1	101798530	0.998000	0.40836	0.992000	0.48379	0.342000	0.28953	2.976000	0.49289	1.339000	0.45563	0.644000	0.83932	ACC	.	.	none		0.512	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049828.1	NM_001308		A	101808540	G	A	101808540	3	1	27	1	0	0	0	0	1	0	0	0	3811	1261	44	2	179	2	CPN1	10	101808540	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	350053	101808540	33726207	566	11017											
CWF19L1	55280	hgsc.bcm.edu	37	chr10	101995477	101995477	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtggaaaagcttttctccTgtgtcaagttcaacataaaa	13	13	7	8	0	3	0	2	0	1	0	4	1	3	1	1	1	2	2	1	1	6	4	rs139693285		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:101995477T>G	ENST00000354105.4	-	13	1505	c.1419A>C	c.(1417-1419)acA>acC	p.T473T	CWF19L1_ENST00000370379.1_Silent_p.T188T|RP11-316M21.6_ENST00000444359.1_RNA|CWF19L1_ENST00000478047.1_5'UTR|SNORA12_ENST00000391162.1_RNA	NM_018294.4	NP_060764.3	Q69YN2	C19L1_HUMAN	CWF19-like 1, cell cycle control (S. pombe)	473							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)		GCTTTTCTCCTGTGTCAAGTT	0.328													T|||	1	0.000199681	0.0	0.0	5008	,	,		20611	0.0		0.001	False		,,,				2504	0.0				p.T473T		Atlas-SNP	.											.	CWF19L1	39	.	0			c.A1419C						PASS	.	T		0,4406		0,0,2203	77	79	78		1419	1.6	1	10	dbSNP_134	78	24,8574	17.3+/-56.4	0,24,4275	no	coding-synonymous	CWF19L1	NM_018294.4		0,24,6478	GG,GT,TT		0.2791,0.0,0.1846		473/539	101995477	24,12980	2203	4299	6502	SO:0001819	synonymous_variant	55280	exon13			TTCTCCTGTGTCA	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.1419A>C	10.37:g.101995477T>G		51	0	0		38	16	0.421053	NM_018294	B4DHX1|D3DR66|Q5W0I3|Q96HC3|Q9H865|Q9NV13	Silent	SNP	ENST00000354105.4	37	CCDS7489.1																																																																																			T|0.999;G|0.001	0.001	strong		0.328	CWF19L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018294		G	101995477	T	G	101995477	2	3	27	1	0	0	0	0	0	0	0	1	4073	1567	55	5		5	CWF19L1	10	101995477	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	186937	101995477	33539270	567	11018											
PDCD11	22984	hgsc.bcm.edu	37	chr10	105205260	105205260	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtgcaggcagtcaaggccaAggccctggagtatgtggagg	9	7	17	8	0	1	0	1	0	0	0	1	2	1	2	2	6	1	3	2	6	3	1	rs151054853		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:105205260A>G	ENST00000369797.3	+	36	5664	c.5570A>G	c.(5569-5571)aAg>aGg	p.K1857R		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	1857					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)		GTCAAGGCCAAGGCCCTGGAG	0.587													A|||	1	0.000199681	0.0	0.0	5008	,	,		19265	0.0		0.001	False		,,,				2504	0.0				p.K1857R		Atlas-SNP	.											.	PDCD11	160	.	0			c.A5570G						PASS	.	A	ARG/LYS	1,4405	2.1+/-5.4	0,1,2202	115	96	102		5570	5.6	1	10	dbSNP_134	102	31,8569	19.8+/-62.0	0,31,4269	yes	missense	PDCD11	NM_014976.1	26	0,32,6471	GG,GA,AA		0.3605,0.0227,0.246	probably-damaging	1857/1872	105205260	32,12974	2203	4300	6503	SO:0001583	missense	22984	exon36			AGGCCAAGGCCCT	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.5570A>G	10.37:g.105205260A>G	ENSP00000358812:p.Lys1857Arg	177	0	0		134	78	0.58209	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	37	CCDS31276.1	.	.	.	.	.	.	.	.	.	.	A	19.36	3.812885	0.70912	2.27E-4	0.003605	ENSG00000148843	ENST00000369797	T	0.22743	1.94	5.6	5.6	0.85130	Suppressor of forked (1);	0.087859	0.85682	D	0.000000	T	0.34077	0.0885	L	0.41027	1.25	0.58432	D	0.999993	D	0.89917	1.0	D	0.77557	0.99	T	0.03739	-1.1008	10	0.23302	T	0.38	-26.404	12.0882	0.53710	0.8159:0.1841:0.0:0.0	.	1857	Q14690	RRP5_HUMAN	R	1857	ENSP00000358812:K1857R	ENSP00000358812:K1857R	K	+	2	0	PDCD11	105195250	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	7.030000	0.76484	2.143000	0.66587	0.459000	0.35465	AAG	A|0.998;G|0.002	0.002	strong		0.587	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1			G	105205260	A	G	105205260	3	3	27	1	0	0	0	0	1	0	0	0	11626	72	3	3	5708	3	PDCD11	10	105205260	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	3209783	105205260	30329487	568	11019											
SORCS1	114815	hgsc.bcm.edu	37	chr10	108380256	108380256	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgggccacagcactgccgtcGcattgacctctttgttcttt	5	14	9	13	2	2	1	0	1	2	0	3	1	2	1	3	1	2	3	3	1	0	4	rs144056795	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:108380256G>A	ENST00000263054.6	-	20	2733	c.2726C>T	c.(2725-2727)gCg>gTg	p.A909V	SORCS1_ENST00000369698.1_Missense_Mutation_p.A444V|SORCS1_ENST00000478809.2_5'Flank|SORCS1_ENST00000344440.6_Missense_Mutation_p.A909V	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	909					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)	p.A909V(2)		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)		CACTGCCGTCGCATTGACCTC	0.562													G|||	5	0.000998403	0.0038	0.0	5008	,	,		19875	0.0		0.0	False		,,,				2504	0.0				p.A909V		Atlas-SNP	.											SORCS1_ENST00000344440,right_upper_lobe,carcinoma,+1,3	SORCS1	534	3	2	Substitution - Missense(2)	endometrium(2)	c.C2726T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	18,4388	25.3+/-52.1	0,18,2185	166	135	146		2726,2726,2726,2726,2726,2726	5.8	0.7	10	dbSNP_134	146	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense	SORCS1	NM_001013031.2,NM_001206569.1,NM_001206570.1,NM_001206571.1,NM_001206572.1,NM_052918.4	64,64,64,64,64,64	0,18,6485	AA,AG,GG		0.0,0.4085,0.1384	benign,benign,benign,benign,benign,benign	909/1199,909/1180,909/1131,909/1160,909/1180,909/1169	108380256	18,12988	2203	4300	6503	SO:0001583	missense	114815	exon20			GCCGTCGCATTGA	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.2726C>T	10.37:g.108380256G>A	ENSP00000263054:p.Ala909Val	98	0	0		112	25	0.223214	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	37	CCDS7559.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	11.29	1.594477	0.28445	0.004085	0.0	ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440	T;T;T	0.40476	1.03;1.03;1.03	5.75	5.75	0.90469	PKD/Chitinase domain (1);PKD domain (1);	0.224860	0.40728	N	0.001035	T	0.29556	0.0737	N	0.13043	0.29	0.45962	D	0.998782	B;B;B;B;B	0.19445	0.021;0.036;0.036;0.021;0.036	B;B;B;B;B	0.14023	0.005;0.01;0.01;0.005;0.01	T	0.08576	-1.0715	9	.	.	.	-18.823	19.9548	0.97216	0.0:0.0:1.0:0.0	.	909;909;909;909;909	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	V	444;909;909	ENSP00000358712:A444V;ENSP00000263054:A909V;ENSP00000345964:A909V	.	A	-	2	0	SORCS1	108370246	1.000000	0.71417	0.676000	0.29932	0.232000	0.25224	5.920000	0.70017	2.714000	0.92807	0.655000	0.94253	GCG	G|0.999;A|0.001	0.001	strong		0.562	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		A	108380256	G	A	108380256	3	1	27	1	0	0	0	0	1	0	0	0	14945	1087	38	1	1042	1	SORCS1	10	108380256	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	3174996	108380256	27154491	569	11020											
GPAM	57678	hgsc.bcm.edu	37	chr10	113926224	113926224	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agttttttcgtaacattctaAtaacacctcttgctacactc	11	16	3	11	1	2	0	0	0	2	0	4	0	2	0	1	0	4	3	1	0	4	9	rs35019520	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:113926224A>G	ENST00000348367.4	-	12	1354	c.1157T>C	c.(1156-1158)aTt>aCt	p.I386T	GPAM_ENST00000423155.1_Missense_Mutation_p.I386T|GPAM_ENST00000369425.1_Missense_Mutation_p.I386T			Q9HCL2	GPAT1_HUMAN	glycerol-3-phosphate acyltransferase, mitochondrial	386			I -> T (in dbSNP:rs35019520).		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)		TAACATTCTAATAACACCTCT	0.388													A|||	37	0.00738818	0.0008	0.0086	5008	,	,		20081	0.0		0.0219	False		,,,				2504	0.0082				p.I386T	Ovarian(161;1017 2606 18293 52943)	Atlas-SNP	.											.	GPAM	68	.	0			c.T1157C						PASS	.	A	THR/ILE	11,4395	17.9+/-39.9	0,11,2192	240	207	218		1157	4.7	1	10	dbSNP_126	218	109,8491	59.1+/-120.7	1,107,4192	yes	missense	GPAM	NM_020918.4	89	1,118,6384	GG,GA,AA		1.2674,0.2497,0.9227	benign	386/829	113926224	120,12886	2203	4300	6503	SO:0001583	missense	57678	exon12			ATTCTAATAACAC	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.1157T>C	10.37:g.113926224A>G	ENSP00000265276:p.Ile386Thr	108	0	0		108	38	0.351852	NM_001244949	Q5VW51|Q86TA3	Missense_Mutation	SNP	ENST00000348367.4	37	CCDS7570.1	20	0.009157509157509158	0	0.0	7	0.019337016574585635	0	0.0	13	0.017150395778364115	A	14.69	2.610145	0.46527	0.002497	0.012674	ENSG00000119927	ENST00000348367;ENST00000423155;ENST00000369425	T;T;T	0.42900	0.96;0.96;0.96	5.87	4.69	0.59074	.	0.159420	0.56097	D	0.000036	T	0.12305	0.0299	N	0.08118	0	0.29156	N	0.878052	B;B	0.19817	0.039;0.039	B;B	0.18871	0.023;0.023	T	0.04737	-1.0930	10	0.22706	T	0.39	-19.2312	14.4037	0.67068	0.8693:0.1307:0.0:0.0	rs35019520	386;386	Q5VW52;Q9HCL2	.;GPAT1_HUMAN	T	386	ENSP00000265276:I386T;ENSP00000409242:I386T;ENSP00000358433:I386T	ENSP00000265276:I386T	I	-	2	0	GPAM	113916214	1.000000	0.71417	0.993000	0.49108	0.998000	0.95712	5.730000	0.68546	2.247000	0.74100	0.523000	0.50628	ATT	A|0.990;G|0.010	0.010	strong		0.388	GPAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050377.1	NM_020918		G	113926224	A	G	113926224	3	3	27	1	0	0	0	0	1	0	0	0	6596	101	4	3	1373	3	GPAM	10	113926224	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	5545968	113926224	21608523	570	11021											
ATRNL1	26033	hgsc.bcm.edu	37	chr10	117075140	117075140	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattgcattgaaggttcttcAcggggaccaatgaagcttat	11	12	10	8	1	2	2	1	2	1	0	2	3	2	3	1	3	2	3	1	3	4	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:117075140A>C	ENST00000355044.3	+	18	3057	c.2931A>C	c.(2929-2931)tcA>tcC	p.S977S	ATRNL1_ENST00000423111.2_Silent_p.S74S|ATRNL1_ENST00000303745.7_5'UTR	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)		AAGGTTCTTCACGGGGACCAA	0.458																																					p.S977S		Atlas-SNP	.											.	ATRNL1	219	.	0			c.A2931C						PASS	.						151	134	140					10																	117075140		2203	4300	6503	SO:0001819	synonymous_variant	26033	exon18			TTCTTCACGGGGA	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.2931A>C	10.37:g.117075140A>C		111	0	0		121	27	0.22314	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Silent	SNP	ENST00000355044.3	37	CCDS7592.1	.	.	.	.	.	.	.	.	.	.	A	9.126	1.010135	0.19277	.	.	ENSG00000107518	ENST00000526373	.	.	.	5.34	-3.83	0.04269	.	.	.	.	.	T	0.61974	0.2390	.	.	.	0.53688	D	0.999979	.	.	.	.	.	.	T	0.61806	-0.6987	4	.	.	.	-11.3344	12.8927	0.58080	0.2191:0.6573:0.1236:0.0	.	.	.	.	P	107	.	.	T	+	1	0	ATRNL1	117065130	0.000000	0.05858	0.587000	0.28692	0.980000	0.70556	-2.912000	0.00698	-0.532000	0.06332	0.374000	0.22700	ACG	.	.	none		0.458	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349		C	117075140	A	C	117075140	2	2	27	1	0	0	0	0	0	0	0	1	1207	146	6	5		5	ATRNL1	10	117075140	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	3148916	117075140	18459607	571	11022											
FGFR2	2263	hgsc.bcm.edu	37	chr10	123239112	123239112	+	3'UTR	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcctactggtccacagccaGtacgcacggcaggtgagagg	9	6	14	12	2	0	1	0	1	0	1	2	2	2	1	3	4	3	3	3	4	2	2	rs1047057	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:123239112G>A	ENST00000358487.5	-	0	2997				FGFR2_ENST00000356226.4_3'UTR|FGFR2_ENST00000369061.4_3'UTR|FGFR2_ENST00000478859.1_3'UTR|FGFR2_ENST00000369060.4_3'UTR|FGFR2_ENST00000357555.5_Silent_p.L703L	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2						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)	p.L703L(1)		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)	TCCACAGCCAGTACGCACGGC	0.483		5	Mis		"gastric. NSCLC, endometrial"		"Crouzon, Pfeiffer, and Apert syndromes"		Saethre-Chotzen syndrome;Apert syndrome				G|||	2075	0.414337	0.0938	0.6873	5008	,	,		15689	0.3512		0.5099	False		,,,				2504	0.6207				p.L703L		Atlas-SNP	.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	FGFR2_ENST00000357555,NS,carcinoma,0,1	FGFR2	758	1	1	Substitution - coding silent(1)	stomach(1)	c.C2107T						PASS	.	G	,,,,,,	237,1147		19,199,474	86	84	85		,,2107,,,,	4.5	0.9	10	dbSNP_86	85	1747,1435		500,747,344	no	utr-3,utr-3,coding-synonymous,utr-3,utr-3,utr-3,utr-3	FGFR2	NM_000141.4,NM_001144914.1,NM_001144915.1,NM_001144916.1,NM_001144917.1,NM_001144918.1,NM_022970.3	,,,,,,	519,946,818	AA,AG,GG		45.0974,17.1243,43.4516	,,,,,,	,,703/708,,,,	123239112	1984,2582	692	1591	2283	SO:0001624	3_prime_UTR_variant	2263	exon17	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	CAGCCAGTACGCA	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.*259C>T	10.37:g.123239112G>A		95	0	0		76	35	0.460526	NM_001144915	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	Silent	SNP	ENST00000358487.5	37	CCDS31298.1																																																																																			G|0.609;A|0.391	0.391	strong		0.483	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141		A	123239112	G	A	123239112	1	1	27	0	1	0	0	0	0	0	0	0	5874	1020	36	2		2	FGFR2	10	123239112	3'UTR	SNP	G	TCGA-G8-6909-01A-11D-2210-10	6163972	123239112	12295635	572	11023											
FGFR2	2263	hgsc.bcm.edu	37	chr10	123279643	123279643	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accactgtggaggcatttgcCggcagtccggcttggaggat	7	9	15	10	2	0	0	0	0	0	0	1	3	1	3	3	6	1	3	3	6	0	2	rs138315382		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:123279643C>T	ENST00000358487.5	-	7	1061	c.789G>A	c.(787-789)ccG>ccA	p.P263P	FGFR2_ENST00000346997.2_Silent_p.P263P|FGFR2_ENST00000356226.4_Silent_p.P148P|FGFR2_ENST00000369056.1_Silent_p.P263P|FGFR2_ENST00000351936.6_Silent_p.P263P|FGFR2_ENST00000369059.1_Silent_p.P148P|FGFR2_ENST00000369061.4_Intron|FGFR2_ENST00000478859.1_Silent_p.P35P|FGFR2_ENST00000369060.4_Silent_p.P263P|FGFR2_ENST00000457416.2_Silent_p.P263P|FGFR2_ENST00000490349.1_5'UTR|FGFR2_ENST00000357555.5_Silent_p.P174P|FGFR2_ENST00000360144.3_Silent_p.P174P	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	263	Ig-like C2-type 3.		P -> L (in CS). {ECO:0000269|PubMed:11173845}.		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)	AGGCATTTGCCGGCAGTCCGG	0.552		5	Mis		"gastric. NSCLC, endometrial"		"Crouzon, Pfeiffer, and Apert syndromes"		Saethre-Chotzen syndrome;Apert syndrome				C|||	1	0.000199681	0.0	0.0014	5008	,	,		18486	0.0		0.0	False		,,,				2504	0.0				p.P263P		Atlas-SNP	.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	.	FGFR2	758	.	0			c.G789A						PASS	.	C	,,,,,,,,	0,4406		0,0,2203	81	68	72		789,789,,522,444,789,444,522,789	-11.6	0	10	dbSNP_134	72	1,8599	1.2+/-3.3	0,1,4299	yes	coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FGFR2	NM_000141.4,NM_001144913.1,NM_001144914.1,NM_001144915.1,NM_001144916.1,NM_001144917.1,NM_001144918.1,NM_001144919.1,NM_022970.3	,,,,,,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,,,,,,	263/822,263/770,,174/708,148/707,263/706,148/705,174/681,263/823	123279643	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2263	exon7	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	ATTTGCCGGCAGT	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.789G>A	10.37:g.123279643C>T		78	0	0		63	18	0.285714	NM_022970	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	Silent	SNP	ENST00000358487.5	37	CCDS31298.1																																																																																			C|1.000;T|0.000	0.000	strong		0.552	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141		T	123279643	C	T	123279643	2	4	27	1	0	0	0	0	0	0	0	1	5874	639	23	1		1	FGFR2	10	123279643	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	40531	123279643	12255104	573	11024											
FGFR2	2263	hgsc.bcm.edu	37	chr10	123325034	123325034	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagaggccggagtctctaggCgtggcgccctttatctgcaa	7	10	13	11	3	2	1	0	0	2	1	3	2	2	2	2	4	1	1	2	4	4	4	rs1047101	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:123325034C>T	ENST00000358487.5	-	3	566	c.294G>A	c.(292-294)acG>acA	p.T98T	FGFR2_ENST00000346997.2_Silent_p.T98T|FGFR2_ENST00000356226.4_Intron|FGFR2_ENST00000369056.1_Silent_p.T98T|FGFR2_ENST00000351936.6_Silent_p.T98T|FGFR2_ENST00000369059.1_Intron|FGFR2_ENST00000359354.2_Silent_p.T98T|FGFR2_ENST00000369061.4_Silent_p.T98T|FGFR2_ENST00000369060.4_Silent_p.T98T|FGFR2_ENST00000457416.2_Silent_p.T98T|FGFR2_ENST00000490349.1_5'UTR|FGFR2_ENST00000357555.5_Intron|FGFR2_ENST00000360144.3_Intron	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	98	Ig-like C2-type 1.				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)	AGTCTCTAGGCGTGGCGCCCT	0.537		5	Mis		"gastric. NSCLC, endometrial"		"Crouzon, Pfeiffer, and Apert syndromes"		Saethre-Chotzen syndrome;Apert syndrome				C|||	17	0.00339457	0.0015	0.0058	5008	,	,		17879	0.0		0.0099	False		,,,				2504	0.001				p.T98T		Atlas-SNP	.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	.	FGFR2	758	.	0			c.G294A						PASS	.	C	,,,,,,,,	7,4399	12.9+/-30.5	0,7,2196	175	150	158		294,294,294,,,294,,,294	-0.8	1	10	dbSNP_86	158	79,8521	46.3+/-105.2	1,77,4222	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,intron,coding-synonymous,intron,intron,coding-synonymous	FGFR2	NM_000141.4,NM_001144913.1,NM_001144914.1,NM_001144915.1,NM_001144916.1,NM_001144917.1,NM_001144918.1,NM_001144919.1,NM_022970.3	,,,,,,,,	1,84,6418	TT,TC,CC		0.9186,0.1589,0.6612	,,,,,,,,	98/822,98/770,98/710,,,98/706,,,98/823	123325034	86,12920	2203	4300	6503	SO:0001819	synonymous_variant	2263	exon3	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	TCTAGGCGTGGCG	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.294G>A	10.37:g.123325034C>T		154	0	0		161	87	0.540373	NM_022970	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	Silent	SNP	ENST00000358487.5	37	CCDS31298.1																																																																																			C|0.993;T|0.007	0.007	strong		0.537	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141		T	123325034	C	T	123325034	2	4	27	1	0	0	0	0	0	0	0	1	5874	755	27	1		1	FGFR2	10	123325034	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	45391	123325034	12209713	574	11025											
DMBT1	1755	hgsc.bcm.edu	37	chr10	124358421	124358421	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaccaatgatgccaatgtcGtctgcaggcaactgggctgt	10	9	11	11	1	1	1	0	1	1	0	2	1	1	1	2	2	3	3	2	2	3	0	rs368405942		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:124358421G>A	ENST00000338354.3	+	26	3194	c.3088G>A	c.(3088-3090)Gtc>Atc	p.V1030I	DMBT1_ENST00000368909.3_Missense_Mutation_p.V1030I|DMBT1_ENST00000330163.4_Missense_Mutation_p.V531I|DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000368955.3_Missense_Mutation_p.V1020I|DMBT1_ENST00000344338.3_Missense_Mutation_p.V1020I|DMBT1_ENST00000368956.2_Missense_Mutation_p.V531I			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	1030	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)				TGCCAATGTCGTCTGCAGGCA	0.607													g|||	1	0.000199681	0.0008	0.0	5008	,	,		19742	0.0		0.0	False		,,,				2504	0.0				p.V1030I	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.G3088A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL	0,4072		0,0,2036	260	259	259		1591,3088,3058	2.6	0.9	10		259	2,8420		0,2,4209	no	missense,missense,missense	DMBT1	NM_004406.2,NM_007329.2,NM_017579.2	29,29,29	0,2,6245	AA,AG,GG		0.0237,0.0,0.016	possibly-damaging,possibly-damaging,possibly-damaging	531/1786,1030/2414,1020/2404	124358421	2,12492	2036	4211	6247	SO:0001583	missense	1755	exon26			AATGTCGTCTGCA		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.3088G>A	10.37:g.124358421G>A	ENSP00000342210:p.Val1030Ile	62	0	0		43	14	0.325581	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	37		.	.	.	.	.	.	.	.	.	.	G	16.84	3.233595	0.58886	0.0	2.37E-4	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956	T;T;T;T;T;T	0.39229	1.09;1.09;1.09;1.09;1.09;1.09	3.57	2.63	0.31362	Speract/scavenger receptor (3);Speract/scavenger receptor-related (2);	0.725684	0.11251	N	0.583638	T	0.60143	0.2246	M	0.69248	2.105	0.80722	D	1	D;D;P;P	0.76494	0.99;0.999;0.923;0.938	P;D;B;B	0.74674	0.606;0.984;0.154;0.24	T	0.52540	-0.8562	10	0.38643	T	0.18	.	11.4562	0.50183	0.0924:0.0:0.9076:0.0	.	1030;531;1020;1030	Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;DMBT1_HUMAN	I	1030;1030;1030;1030;1030;1030;531;1020;531;531;1030;1020;531	ENSP00000342210:V1030I;ENSP00000343175:V1020I;ENSP00000327747:V531I;ENSP00000357905:V1030I;ENSP00000357951:V1020I;ENSP00000357952:V531I	ENSP00000331522:V531I	V	+	1	0	DMBT1	124348411	1.000000	0.71417	0.922000	0.36590	0.566000	0.35808	7.239000	0.78182	0.585000	0.29608	0.558000	0.71614	GTC	.	.	none		0.607	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		A	124358421	G	A	124358421	3	1	27	1	0	0	0	0	1	0	0	0	4579	1145	40	1	3190	1	DMBT1	10	124358421	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1033387	124358421	11176326	575	11026											
JAKMIP3	282973	hgsc.bcm.edu	37	chr10	133966522	133966522	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggacagtcctgaccttggccGaaaaggtaacagcagctgtg	11	7	13	10	1	0	1	0	1	0	0	1	3	1	2	3	3	3	3	3	3	3	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:133966522G>A	ENST00000298622.4	+	16	2200	c.2062G>A	c.(2062-2064)Gaa>Aaa	p.E688K	JAKMIP3_ENST00000477275.1_3'UTR	NM_001105521.2	NP_001098991.1	Q5VZ66	JKIP3_HUMAN	Janus kinase and microtubule interacting protein 3	688						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)		GACCTTGGCCGAAAAGGTAAC	0.597																																					p.E688K		Atlas-SNP	.											.	JAKMIP3	69	.	0			c.G2062A						PASS	.						116	81	93					10																	133966522		2200	4293	6493	SO:0001583	missense	282973	exon16			TTGGCCGAAAAGG	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.2062G>A	10.37:g.133966522G>A	ENSP00000298622:p.Glu688Lys	96	0	0		106	27	0.254717	NM_001105521	A6PW00|Q69YM6|Q6ZT29	Missense_Mutation	SNP	ENST00000298622.4	37	CCDS44494.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.366941	0.82463	.	.	ENSG00000188385	ENST00000298622	T	0.30714	1.52	4.01	4.01	0.46588	.	.	.	.	.	T	0.49592	0.1566	M	0.68317	2.08	0.49798	D	0.999825	D;D	0.89917	1.0;0.997	D;P	0.64506	0.926;0.715	T	0.46414	-0.9193	9	0.21540	T	0.41	.	16.1506	0.81618	0.0:0.0:1.0:0.0	.	125;688	Q5VZ66-2;Q5VZ66	.;JKIP3_HUMAN	K	688	ENSP00000298622:E688K	ENSP00000298622:E688K	E	+	1	0	JAKMIP3	133816512	1.000000	0.71417	0.876000	0.34364	0.450000	0.32258	9.219000	0.95173	1.780000	0.52325	0.479000	0.44913	GAA	.	.	none		0.597	JAKMIP3-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051049.3	NM_194303		A	133966522	G	A	133966522	3	1	27	1	0	0	0	0	1	0	0	0	7951	1059	37	1	2124	1	JAKMIP3	10	133966522	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	9608101	133966522	1568225	576	11027											
STK32C	282974	hgsc.bcm.edu	37	chr10	134038809	134038809	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgaaggagtagccggtcccGccgttgacaaaagagtggaa	12	6	14	9	4	0	2	0	1	0	1	2	5	1	4	3	3	1	2	3	3	5	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:134038809G>A	ENST00000368622.1	-	7	834	c.453C>T	c.(451-453)ggC>ggT	p.G151G	STK32C_ENST00000368625.4_Silent_p.G281G					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)		AGCCGGTCCCGCCGTTGACAA	0.632																																					p.G268G		Atlas-SNP	.											.	STK32C	61	.	0			c.C804T						PASS	.						27	29	28					10																	134038809		2200	4296	6496	SO:0001819	synonymous_variant	282974	exon7			GGTCCCGCCGTTG	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.453C>T	10.37:g.134038809G>A		118	0	0		95	49	0.515789	NM_173575		Silent	SNP	ENST00000368622.1	37																																																																																				.	.	none		0.632	STK32C-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000051068.2	NM_173575		A	134038809	G	A	134038809	2	1	27	1	0	0	0	0	0	0	0	1	15314	1074	38	1		1	STK32C	10	134038809	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	72287	134038809	1495938	577	11028											
LRRC27	80313	hgsc.bcm.edu	37	chr10	134151131	134151131	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatttctttcagttgcttccGaacctgacttggctggacct	6	15	9	11	1	2	1	1	1	1	0	3	4	3	2	3	2	2	3	3	2	1	5	rs116451295	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr10:134151131G>T	ENST00000368614.3	+	3	378	c.273G>T	c.(271-273)ccG>ccT	p.P91P	LRRC27_ENST00000368613.4_Silent_p.P91P|LRRC27_ENST00000368612.1_Silent_p.P29P|LRRC27_ENST00000392638.2_Silent_p.P91P|LRRC27_ENST00000368610.3_Silent_p.P29P|LRRC27_ENST00000344079.5_Silent_p.P91P|LRRC27_ENST00000368615.3_Silent_p.P91P|LRRC27_ENST00000356571.4_Silent_p.P91P|LRRC27_ENST00000432555.2_5'UTR	NM_030626.2	NP_085129.1	Q9C0I9	LRC27_HUMAN	leucine rich repeat containing 27	91								p.P91P(2)		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)		AGTTGCTTCCGAACCTGACTT	0.408													G|||	85	0.0169728	0.0015	0.0115	5008	,	,		16328	0.001		0.0129	False		,,,				2504	0.0624				p.P91P		Atlas-SNP	.											LRRC27,rectum,carcinoma,0,2	LRRC27	64	2	2	Substitution - coding silent(2)	large_intestine(1)|pancreas(1)	c.G273T						PASS	.	G	,,,	15,4391	23.3+/-48.9	0,15,2188	105	99	101		273,273,273,273	-9.5	0	10	dbSNP_132	101	198,8402	86.6+/-149.0	5,188,4107	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LRRC27	NM_001143757.1,NM_001143758.1,NM_001143759.1,NM_030626.2	,,,	5,203,6295	TT,TG,GG		2.3023,0.3404,1.6377	,,,	91/531,91/384,91/384,91/531	134151131	213,12793	2203	4300	6503	SO:0001819	synonymous_variant	80313	exon3			GCTTCCGAACCTG	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.273G>T	10.37:g.134151131G>T		146	0	0		118	56	0.474576	NM_001143757	A6NE72|A6NJB4|A6NKD3|D3DRH0|Q5SZH6|Q5SZH8|Q5SZH9|Q86XT5|Q8N7C8|Q8NA21	Silent	SNP	ENST00000368614.3	37	CCDS31316.1	16	0.007326007326007326	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	9	0.011873350923482849	G	0.061	-1.225056	0.01530	0.003404	0.023023	ENSG00000148814	ENST00000450442	.	.	.	4.73	-9.47	0.00594	.	.	.	.	.	T	0.28599	0.0708	.	.	.	0.53005	D	0.999965	.	.	.	.	.	.	T	0.60398	-0.7271	4	.	.	.	-20.1907	6.1334	0.20217	0.2244:0.4943:0.2025:0.0788	.	.	.	.	L	43	.	.	R	+	2	0	LRRC27	134001121	0.957000	0.32711	0.005000	0.12908	0.040000	0.13550	-0.274000	0.08537	-4.666000	0.00037	-1.623000	0.00790	CGA	G|0.984;T|0.016	0.016	strong		0.408	LRRC27-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051058.2	XM_290462		T	134151131	G	T	134151131	2	4	27	1	0	0	0	0	0	0	0	1	8990	1045	37	4		4	LRRC27	10	134151131	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	112322	134151131	1383616	578	11029											
ATHL1	80162	hgsc.bcm.edu	37	chr11	290050	290050	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atgggggagcagctgaccgaGaccttcgccctggacaccaa	10	5	13	13	2	0	2	0	1	0	1	1	5	0	4	4	3	2	2	4	3	1	1	rs139686173	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:290050G>A	ENST00000409548.2	+	2	349	c.234G>A	c.(232-234)gaG>gaA	p.E78E	RP11-326C3.2_ENST00000533924.1_RNA|RP11-326C3.2_ENST00000525217.1_RNA|ATHL1_ENST00000409479.1_Silent_p.E78E|ATHL1_ENST00000409655.1_5'UTR|RP11-326C3.2_ENST00000534742.1_RNA	NM_025092.4	NP_079368.3	Q32M88	ATHL1_HUMAN	ATH1, acid trehalase-like 1 (yeast)	78					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)		AGCTGACCGAGACCTTCGCCC	0.677													G|||	45	0.00898562	0.0015	0.0187	5008	,	,		14729	0.0		0.0149	False		,,,				2504	0.0153				p.E78E		Atlas-SNP	.											.	ATHL1	88	.	0			c.G234A						PASS	.	G		4,1378		0,4,687	25	34	31		234	3.8	0.4	11	dbSNP_134	31	62,3120		0,62,1529	no	coding-synonymous	ATHL1	NM_025092.4		0,66,2216	AA,AG,GG		1.9485,0.2894,1.4461		78/738	290050	66,4498	691	1591	2282	SO:0001819	synonymous_variant	80162	exon2			GACCGAGACCTTC	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.234G>A	11.37:g.290050G>A		36	0	0		52	14	0.269231	NM_025092	Q658X8|Q8TEG9|Q9H635	Silent	SNP	ENST00000409548.2	37	CCDS31322.2																																																																																			G|0.986;A|0.014	0.014	strong		0.677	ATHL1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330164.3	NM_025092		A	290050	G	A	290050	2	1	27	1	0	0	0	0	0	0	0	1	1104	933	33	2		2	ATHL1	11	290050	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10		290050	134716466	579	11030											
HRAS	3265	hgsc.bcm.edu	37	chr11	534242	534242	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gggtcgtattcgtccacaaaAtggttctggatcagctggat	9	12	12	8	2	2	0	1	0	1	0	5	2	3	2	1	4	1	3	1	4	3	3	rs12628	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:534242A>G	ENST00000451590.1	-	2	268	c.81T>C	c.(79-81)caT>caC	p.H27H	HRAS_ENST00000397594.1_Silent_p.H27H|HRAS_ENST00000397596.2_Silent_p.H27H|HRAS_ENST00000311189.7_Silent_p.H27H|HRAS_ENST00000468682.2_5'UTR|HRAS_ENST00000417302.1_Silent_p.H27H	NM_001130442.1|NM_005343.2	NP_001123914.1|NP_005334.1	P01112	RASH_HUMAN	Harvey rat sarcoma viral oncogene homolog	27					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular senescence (GO:0090398)|chemotaxis (GO:0006935)|endocytosis (GO:0006897)|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)|intrinsic apoptotic signaling pathway (GO:0097193)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Rho GTPase activity (GO:0034259)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|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 DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of wound healing (GO:0090303)|protein heterooligomerization (GO:0051291)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein C-terminus binding (GO:0008022)	p.H27H(26)		adrenal_gland(1)|bone(3)|breast(7)|cervix(23)|endometrium(4)|haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|oesophagus(2)|penis(2)|pituitary(10)|prostate(31)|salivary_gland(24)|skin(184)|soft_tissue(38)|stomach(14)|testis(5)|thymus(1)|thyroid(173)|upper_aerodigestive_tract(122)|urinary_tract(225)	901		all_cancers(49;4.37e-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;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)		CGTCCACAAAATGGTTCTGGA	0.642		6	Mis		"infrequent sarcomas, rare other types"	"rhadomyosarcoma, ganglioneuroblastoma, bladder"			Costello syndrome	HNSCC(11;0.0054)			G|||	1488	0.297125	0.3729	0.3646	5008	,	,		18347	0.1726		0.3121	False		,,,				2504	0.2597				p.H27H		Atlas-SNP	.	yes	Dom	yes	Costello syndrome	11	11p15.5	3265	v-Ha-ras Harvey rat sarcoma viral oncogene homolog		"E, L, M"	HRAS,arm,benign_melanocytic_nevus,0,26	HRAS	1232	26	26	Substitution - coding silent(26)	urinary_tract(25)|skin(1)	c.T81C	GRCh37	CM035804	HRAS	M	rs12628	PASS	.	G	,,	1652,2754	653.2+/-399.5	309,1034,860	135	123	127	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	81,81,81	1	1	11	dbSNP_52	127	2959,5641	665.8+/-402.3	510,1939,1851	no	coding-synonymous,coding-synonymous,coding-synonymous	HRAS	NM_001130442.1,NM_005343.2,NM_176795.3	,,	819,2973,2711	GG,GA,AA		34.407,37.4943,35.4529	,,	27/190,27/190,27/171	534242	4611,8395	2203	4300	6503	SO:0001819	synonymous_variant	3265	exon2	Familial Cancer Database	incl.: Facio-Cutaneous-Skeletal syndrome	CACAAAATGGTTC	AJ437024	CCDS7698.1, CCDS7699.1	11p15.5	2014-09-17	2013-07-08		ENSG00000174775	ENSG00000174775			5173	protein-coding gene	gene with protein product		190020	"v-Ha-ras Harvey rat sarcoma viral oncogene homolog"	HRAS1			Standard	NM_176795		Approved		uc010qvx.2	P01112	OTTHUMG00000131919	ENST00000451590.1:c.81T>C	11.37:g.534242A>G		124	0	0		139	104	0.748201	NM_001130442	B5BUA0|Q14080|Q6FHV9|Q9BR65|Q9UCE2	Silent	SNP	ENST00000451590.1	37	CCDS7698.1																																																																																			A|0.663;G|0.337	0.337	strong		0.642	HRAS-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259403.2	NM_176795		G	534242	A	G	534242	2	3	27	1	0	0	0	0	0	0	0	1	7357	98	4	3		3	HRAS	11	534242	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	244192	534242	134472274	580	11031											
MUC6	4588	hgsc.bcm.edu	37	chr11	1027995	1027995	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgcagggttcactgtggcGtggcacctctcgaacaccgt	6	9	14	12	3	2	0	1	0	1	0	3	1	2	0	2	4	2	3	2	4	1	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1027995G>C	ENST00000421673.2	-	15	1868	c.1818C>G	c.(1816-1818)caC>caG	p.H606Q		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	606	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)		TCACTGTGGCGTGGCACCTCT	0.667																																					p.H606Q		Atlas-SNP	.											.	MUC6	408	.	0			c.C1818G						PASS	.						29	34	32					11																	1027995		2115	4236	6351	SO:0001583	missense	4588	exon15			TGTGGCGTGGCAC	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.1818C>G	11.37:g.1027995G>C	ENSP00000406861:p.His606Gln	106	0	0		110	17	0.154545	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	G	7.821	0.717831	0.15372	.	.	ENSG00000184956	ENST00000421673	T	0.79845	-1.31	4.93	-2.13	0.07144	von Willebrand factor, type D domain (1);Uncharacterised domain, cysteine-rich (2);	0.000000	0.31847	U	0.006963	D	0.85575	0.5728	M	0.86420	2.815	0.18873	N	0.999982	D	0.61080	0.989	D	0.66351	0.943	T	0.76277	-0.3018	10	0.87932	D	0	.	3.0196	0.06071	0.3712:0.1112:0.4057:0.112	.	606	Q6W4X9	MUC6_HUMAN	Q	606	ENSP00000406861:H606Q	ENSP00000406861:H606Q	H	-	3	2	MUC6	1017995	0.000000	0.05858	0.008000	0.14137	0.098000	0.18820	-0.761000	0.04751	-0.607000	0.05738	-1.564000	0.00881	CAC	.	.	none		0.667	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540		C	1027995	G	C	1027995	3	2	27	1	0	0	0	0	1	0	0	0	9989	1136	40	4	5577	4	MUC6	11	1027995	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	493753	1027995	133978521	581	11032											
MUC2	4583	hgsc.bcm.edu	37	chr11	1092843	1092843	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaaccccaacacccaccggCacacagaccccaacaacgac	15	0	4	22	2	0	1	0	0	0	1	0	2	0	1	7	1	4	1	7	1	4	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1092843C>G	ENST00000441003.2	+	30	4689	c.4662C>G	c.(4660-4662)ggC>ggG	p.G1554G	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000359061.5_Silent_p.G1555G	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)	CACCCACCGGCACACAGACCC	0.632																																					p.G1554G		Atlas-SNP	.											MUC2_ENST00000441003,trunk,malignant_melanoma,+1,2	MUC2	614	2	0			c.C4662G						PASS	.						88	119	108					11																	1092843		1875	3464	5339	SO:0001819	synonymous_variant	4583	exon30			CACCGGCACACAG	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.4662C>G	11.37:g.1092843C>G		48	0	0		67	5	0.0746269	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.	.	none		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		G	1092843	C	G	1092843	2	3	27	1	0	0	0	0	0	0	0	1	9984	697	25	4		4	MUC2	11	1092843	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	64848	1092843	133913673	582	11033											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1270647	1270647	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtgccgtgcccaggcccaGcctggtgtccccctggggga	4	6	16	15	1	0	0	0	0	0	0	1	2	1	1	6	4	3	0	6	4	0	0	rs185838223	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1270647G>C	ENST00000529681.1	+	31	12595	c.12537G>C	c.(12535-12537)caG>caC	p.Q4179H	MUC5B_ENST00000447027.1_Missense_Mutation_p.Q4182H|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4179	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)		CCCAGGCCCAGCCTGGTGTCC	0.667													G|||	246	0.0491214	0.0598	0.1066	5008	,	,		16942	0.003		0.0497	False		,,,				2504	0.0409				p.Q4179H		Atlas-SNP	.											.	MUC5B	473	.	0			c.G12537C						PASS	.	G	HIS/GLN	237,3547		17,203,1672	44	53	50		12537	-7.2	0	11		50	432,7746		13,406,3670	no	missense	MUC5B	NM_002458.2	24	30,609,5342	CC,CG,GG		5.2825,6.2632,5.5927	benign	4179/5763	1270647	669,11293	1892	4089	5981	SO:0001583	missense	727897	exon31			GGCCCAGCCTGGT	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.12537G>C	11.37:g.1270647G>C	ENSP00000436812:p.Gln4179His	731	0	0		732	153	0.209016	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	96	0.04395604395604396	20	0.04065040650406504	33	0.09116022099447514	0	0.0	43	0.05672823218997362	g	7.941	0.742802	0.15642	0.062632	0.052825	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.17370	2.28;2.28	3.62	-7.25	0.01470	.	.	.	.	.	T	0.00412	0.0013	N	0.05441	-0.05	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.10450	0.005;0.005	T	0.16041	-1.0416	9	0.87932	D	0	.	24.3801	0.99989	0.0:0.8733:0.1267:0.0	.	4652;4182	A7Y9J9;E9PBJ0	.;.	H	4179;4182;4123;4029	ENSP00000436812:Q4179H;ENSP00000415793:Q4182H	ENSP00000343037:Q4123H	Q	+	3	2	MUC5B	1227223	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.783000	0.04638	-1.952000	0.01027	0.393000	0.25936	CAG	G|0.952;C|0.048	0.048	strong		0.667	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		C	1270647	G	C	1270647	3	2	27	1	0	0	0	0	1	0	0	0	9988	962	34	4	12668	4	MUC5B	11	1270647	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	177804	1270647	133735869	583	11034											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1270691	1270691	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggccaggtcgtggaatgcaGcctggactttggcctggtct	5	10	16	10	1	1	0	0	0	1	0	2	2	1	2	3	6	2	1	3	6	1	1	rs201822010		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:1270691G>C	ENST00000529681.1	+	31	12639	c.12581G>C	c.(12580-12582)aGc>aCc	p.S4194T	MUC5B_ENST00000447027.1_Missense_Mutation_p.S4197T|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4194	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)		GTGGAATGCAGCCTGGACTTT	0.637													G|||	1	0.000199681	0.0	0.0	5008	,	,		18430	0.0		0.001	False		,,,				2504	0.0				p.S4194T		Atlas-SNP	.											.	MUC5B	473	.	0			c.G12581C						PASS	.	G	THR/SER	1,3771		0,1,1885	35	44	41		12581	-0.3	0	11		41	14,8120		0,14,4053	no	missense	MUC5B	NM_002458.2	58	0,15,5938	CC,CG,GG		0.1721,0.0265,0.126	possibly-damaging	4194/5763	1270691	15,11891	1886	4067	5953	SO:0001583	missense	727897	exon31			AATGCAGCCTGGA	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.12581G>C	11.37:g.1270691G>C	ENSP00000436812:p.Ser4194Thr	882	1	0.00113379		1023	155	0.151515	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	g	5.081	0.200521	0.09652	2.65E-4	0.001721	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.18810	2.19;2.19	3.69	-0.352	0.12598	.	.	.	.	.	T	0.23330	0.0564	M	0.74467	2.265	0.09310	N	1	P;P	0.42123	0.771;0.771	B;B	0.38562	0.216;0.276	T	0.12268	-1.0554	9	0.87932	D	0	.	8.4625	0.32936	0.6517:0.0:0.3483:0.0	.	4667;4197	A7Y9J9;E9PBJ0	.;.	T	4194;4197;4138;4044	ENSP00000436812:S4194T;ENSP00000415793:S4197T	ENSP00000343037:S4138T	S	+	2	0	MUC5B	1227267	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.695000	0.01913	-0.269000	0.09298	-0.515000	0.04445	AGC	G|0.996;C|0.004	0.004	strong		0.637	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		C	1270691	G	C	1270691	3	2	27	1	0	0	0	0	1	0	0	0	9988	971	34	4	12712	4	MUC5B	11	1270691	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	44	1270691	133735825	584	11035											
TH	7054	hgsc.bcm.edu	37	chr11	2190982	2190982	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccttctcctcaaaggccacAgcctccagggggtccccggg	6	7	11	17	1	2	0	1	0	1	0	6	0	5	0	7	4	1	0	7	4	1	1	rs7950050	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:2190982A>G	ENST00000381178.1	-	3	321	c.303T>C	c.(301-303)gcT>gcC	p.A101A	TH_ENST00000333684.5_Silent_p.A74A|TH_ENST00000381175.1_Silent_p.A97A|TH_ENST00000352909.3_Silent_p.A70A	NM_199292.2	NP_954986.2	P07101	TY3H_HUMAN	tyrosine hydroxylase	101					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)	CAAAGGCCACAGCCTCCAGGG	0.697													G|||	168	0.0335463	0.1233	0.0058	5008	,	,		14629	0.0		0.001	False		,,,				2504	0.0				p.A101A		Atlas-SNP	.											.	TH	43	.	0			c.T303C						PASS	.	G	,,	522,3882	744.0+/-411.5	23,476,1703	32	34	34		210,303,291	-1.3	0.1	11	dbSNP_116	34	13,8583	796.2+/-407.5	0,13,4285	no	coding-synonymous,coding-synonymous,coding-synonymous	TH	NM_000360.3,NM_199292.2,NM_199293.2	,,	23,489,5988	GG,GA,AA		0.1512,11.8529,4.1154	,,	70/498,101/529,97/525	2190982	535,12465	2202	4298	6500	SO:0001819	synonymous_variant	7054	exon3			GGCCACAGCCTCC	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.303T>C	11.37:g.2190982A>G		110	0	0		143	116	0.811189	NM_199292	B7ZL70|B7ZL73|Q0PWM2|Q0PWM3|Q15585|Q15588|Q15589|Q2M3B4	Silent	SNP	ENST00000381178.1	37	CCDS7731.1																																																																																			A|0.952;G|0.048	0.048	strong		0.697	TH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026597.1	NM_000360		G	2190982	A	G	2190982	2	3	27	1	0	0	0	0	0	0	0	1	15853	175	7	3		3	TH	11	2190982	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	920291	2190982	132815534	585	11036											
TH	7054	hgsc.bcm.edu	37	chr11	2191006	2191006	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagggggtccccgggctcCgaggggactgcagcggccgc	4	4	18	15	4	0	0	0	0	0	0	3	2	3	1	5	6	2	2	5	6	0	0	rs34510659	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:2191006C>T	ENST00000381178.1	-	3	297	c.279G>A	c.(277-279)tcG>tcA	p.S93S	TH_ENST00000333684.5_Silent_p.S66S|TH_ENST00000381175.1_Silent_p.S89S|TH_ENST00000352909.3_Silent_p.S62S	NM_199292.2	NP_954986.2	P07101	TY3H_HUMAN	tyrosine hydroxylase	93					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)	CCCCGGGCTCCGAGGGGACTG	0.711													C|||	122	0.024361	0.0893	0.0058	5008	,	,		13970	0.0		0.0	False		,,,				2504	0.0				p.S93S		Atlas-SNP	.											.	TH	43	.	0			c.G279A						PASS	.	C	,,	343,4043		10,323,1860	17	20	19		186,279,267	-1	0	11	dbSNP_126	19	6,8586		0,6,4290	no	coding-synonymous,coding-synonymous,coding-synonymous	TH	NM_000360.3,NM_199292.2,NM_199293.2	,,	10,329,6150	TT,TC,CC		0.0698,7.8203,2.6892	,,	62/498,93/529,89/525	2191006	349,12629	2193	4296	6489	SO:0001819	synonymous_variant	7054	exon3			GGGCTCCGAGGGG	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.279G>A	11.37:g.2191006C>T		75	0	0		107	90	0.841121	NM_199292	B7ZL70|B7ZL73|Q0PWM2|Q0PWM3|Q15585|Q15588|Q15589|Q2M3B4	Silent	SNP	ENST00000381178.1	37	CCDS7731.1																																																																																			C|0.971;T|0.029	0.029	strong		0.711	TH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026597.1	NM_000360		T	2191006	C	T	2191006	2	4	27	1	0	0	0	0	0	0	0	1	15853	639	23	1		1	TH	11	2191006	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	24	2191006	132815510	586	11037											
OR51A4	401666	hgsc.bcm.edu	37	chr11	4967834	4967834	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcttgcaatatctcaagtttCttaaagtgaaagggaaggga	14	12	10	5	0	3	1	1	1	3	0	4	3	3	3	0	2	1	2	0	2	7	4	rs201205025	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:4967834C>G	ENST00000380373.2	-	1	522	c.497G>C	c.(496-498)aGa>aCa	p.R166T	MMP26_ENST00000380390.1_Intron|MMP26_ENST00000477339.1_Intron	NM_001005329.1	NP_001005329.1	Q8NGJ6	O51A4_HUMAN	olfactory receptor, family 51, subfamily A, member 4	166						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)		TCTCAAGTTTCTTAAAGTGAA	0.413													.|||	12	0.00239617	0.003	0.0029	5008	,	,		24981	0.0		0.003	False		,,,				2504	0.0031				p.R166T		Atlas-SNP	.											OR51A4,colon,carcinoma,-1,1	OR51A4	73	1	0			c.G497C						scavenged	.						212	198	203					11																	4967834		2177	4245	6422	SO:0001583	missense	401666	exon1			AAGTTTCTTAAAG	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.497G>C	11.37:g.4967834C>G	ENSP00000369731:p.Arg166Thr	980	0	0		155	11	0.0709677	NM_001005329		Missense_Mutation	SNP	ENST00000380373.2	37	CCDS31367.1	.	.	.	.	.	.	.	.	.	.	C	9.411	1.080491	0.20309	.	.	ENSG00000205497	ENST00000380373	T	0.71817	-0.6	3.44	-3.66	0.04489	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.59046	0.2165	L	0.41027	1.25	0.09310	N	1	B	0.23249	0.082	B	0.27608	0.081	T	0.52041	-0.8628	9	0.66056	D	0.02	.	9.2359	0.37466	0.0:0.303:0.0:0.697	.	166	Q8NGJ6	O51A4_HUMAN	T	166	ENSP00000369731:R166T	ENSP00000369731:R166T	R	-	2	0	OR51A4	4924410	0.000000	0.05858	0.000000	0.03702	0.166000	0.22503	-0.905000	0.04075	-1.059000	0.03193	0.479000	0.44913	AGA	.	.	weak		0.413	OR51A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142821.1	NM_001005329		G	4967834	C	G	4967834	3	3	27	1	0	0	0	0	1	0	0	0	11096	913	32	4	446	4	OR51A4	11	4967834	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2776828	4967834	130038682	587	11038											
OR51B5	282763	hgsc.bcm.edu	37	chr11	5364640	5364640	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaaggagggtgccattgcCaaaaaggatggatatataca	17	7	12	5	0	0	1	0	0	0	1	0	4	0	4	2	4	3	0	2	4	7	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:5364640C>T	ENST00000300773.2	-	1	169	c.115G>A	c.(115-117)Ggc>Agc	p.G39S	HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	39					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)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GTGCCATTGCCAAAAAGGATG	0.478																																					p.G39S		Atlas-SNP	.											.	OR51B5	60	.	0			c.G115A						PASS	.						62	66	65					11																	5364640		2201	4297	6498	SO:0001583	missense	282763	exon5			CATTGCCAAAAAG	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"GPCR / Class A : Olfactory receptors"	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.115G>A	11.37:g.5364640C>T	ENSP00000300773:p.Gly39Ser	63	0	0		67	52	0.776119	NM_001005567	B2RN59	Missense_Mutation	SNP	ENST00000300773.2	37	CCDS31378.1	.	.	.	.	.	.	.	.	.	.	C	16.52	3.145360	0.57044	.	.	ENSG00000242180	ENST00000300773	T	0.00530	6.77	4.78	4.78	0.61160	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40064	N	0.001186	T	0.01156	0.0038	M	0.90870	3.155	0.38694	D	0.952823	P	0.37398	0.593	B	0.37550	0.253	T	0.50118	-0.8865	10	0.72032	D	0.01	.	16.5938	0.84789	0.0:1.0:0.0:0.0	.	39	Q9H339	O51B5_HUMAN	S	39	ENSP00000300773:G39S	ENSP00000300773:G39S	G	-	1	0	OR51B5	5321216	0.190000	0.23276	0.966000	0.40874	0.675000	0.39556	2.218000	0.42889	2.482000	0.83794	0.650000	0.86243	GGC	.	.	none		0.478	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567		T	5364640	C	T	5364640	3	4	27	1	0	0	0	0	1	0	0	0	11100	594	21	2	827	2	OR51B5	11	5364640	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	396806	5364640	129641876	588	11039											
OR52H1	390067	hgsc.bcm.edu	37	chr11	5566076	5566076	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acagcacagaggatgtgtgcGtaggaaacagcaatgagaat	16	6	13	6	1	0	2	0	1	0	2	0	5	0	4	0	2	4	3	0	2	4	1	rs139835065	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:5566076G>A	ENST00000322653.4	-	1	703	c.678C>T	c.(676-678)taC>taT	p.Y226Y	HBG2_ENST00000380259.2_Intron	NM_001005289.1	NP_001005289.1	Q8NGJ2	O52H1_HUMAN	olfactory receptor, family 52, subfamily H, member 1	226						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)		GGATGTGTGCGTAGGAAACAG	0.502													G|||	6	0.00119808	0.0	0.0	5008	,	,		23186	0.001		0.003	False		,,,				2504	0.002				p.Y226Y		Atlas-SNP	.											.	OR52H1	46	.	0			c.C678T						PASS	.	G		0,4402		0,0,2201	120	99	106		678	0.2	0	11	dbSNP_134	106	32,8562	22.8+/-68.1	0,32,4265	no	coding-synonymous	OR52H1	NM_001005289.1		0,32,6466	AA,AG,GG		0.3724,0.0,0.2462		226/321	5566076	32,12964	2201	4297	6498	SO:0001819	synonymous_variant	390067	exon1			GTGTGCGTAGGAA	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.678C>T	11.37:g.5566076G>A		108	0	0		123	108	0.878049	NM_001005289	B9EH26|Q6IF79	Silent	SNP	ENST00000322653.4	37	CCDS31386.1																																																																																			G|0.998;A|0.002	0.002	strong		0.502	OR52H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143400.1	NM_001005289		A	5566076	G	A	5566076	2	1	27	1	0	0	0	0	0	0	0	1	11128	1140	40	1		1	OR52H1	11	5566076	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	201436	5566076	129440440	589	11040											
TRIM34	53840	hgsc.bcm.edu	37	chr11	5653866	5653866	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctctgtgatcatcatggagAgaaactcctactcttctgta	10	14	7	10	0	5	2	2	1	3	1	7	4	6	3	1	1	2	1	1	1	3	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:5653866A>G	ENST00000514226.1	+	2	642	c.305A>G	c.(304-306)gAg>gGg	p.E102G	TRIM34_ENST00000429814.2_Missense_Mutation_p.E102G|TRIM6-TRIM34_ENST00000457787.2_Missense_Mutation_p.E102G|HBG2_ENST00000380259.2_Intron|TRIM6-TRIM34_ENST00000354852.5_Missense_Mutation_p.E456G	NM_001003827.1	NP_001003827.1	Q9BYJ4	TRI34_HUMAN	tripartite motif containing 34	102					positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein trimerization (GO:0070206)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			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)		CATCATGGAGAGAAACTCCTA	0.502																																					p.E456G		Atlas-SNP	.											.	TRIM6-TRIM34	68	.	0			c.A1367G						PASS	.						75	69	71					11																	5653866		2201	4297	6498	SO:0001583	missense	445372	exon8			ATGGAGAGAAACT	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.305A>G	11.37:g.5653866A>G	ENSP00000422947:p.Glu102Gly	107	0	0		90	49	0.544444	NM_001003819	D3DQS7|Q9C016|Q9HCR0|Q9HCR1|Q9HCR2	Missense_Mutation	SNP	ENST00000514226.1	37	CCDS31391.1	.	.	.	.	.	.	.	.	.	.	A	18.93	3.727557	0.69074	.	.	ENSG00000258659;ENSG00000258659;ENSG00000258659;ENSG00000258659;ENSG00000258588	ENST00000337072;ENST00000514226;ENST00000429814;ENST00000457787;ENST00000354852	T;T;T;T	0.47869	0.83;0.83;0.83;0.83	3.53	3.53	0.40419	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, B-box (3);	0.232880	0.22139	N	0.064076	T	0.76321	0.3971	H	0.97051	3.93	0.30699	N	0.750484	D;D;D	0.76494	0.999;0.998;0.983	D;D;P	0.76071	0.984;0.987;0.836	T	0.79257	-0.1878	10	0.87932	D	0	.	10.6794	0.45804	1.0:0.0:0.0:0.0	.	102;102;456	Q9BYJ4-2;Q9BYJ4;B2RNG4	.;TRI34_HUMAN;.	G	456;102;102;102;456	ENSP00000422947:E102G;ENSP00000402595:E102G;ENSP00000395982:E102G;ENSP00000346916:E456G	ENSP00000402595:E102G	E	+	2	0	TRIM34;TRIM6-TRIM34	5610442	1.000000	0.71417	1.000000	0.80357	0.680000	0.39746	8.127000	0.89593	1.847000	0.53656	0.454000	0.30748	GAG	.	.	none		0.502	TRIM34-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143357.2	NM_001003827		G	5653866	A	G	5653866	3	3	27	1	0	0	0	0	1	0	0	0	16523	304	11	3	307	3	TRIM34	11	5653866	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	87790	5653866	129352650	590	11041											
OR56A4	120793	hgsc.bcm.edu	37	chr11	6024031	6024031	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agggagaggaggctgagcagGtagtacaggggctggtgcag	10	5	21	5	0	0	2	0	1	0	1	0	4	0	3	0	7	3	6	0	7	2	2	rs143488149	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:6024031G>A	ENST00000330728.4	-	1	393	c.348C>T	c.(346-348)taC>taT	p.Y116Y		NM_001005179.2	NP_001005179.2	Q8NGH8	O56A4_HUMAN	olfactory receptor, family 56, 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)			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)		GGCTGAGCAGGTAGTACAGGG	0.607													.|||	3	0.000599042	0.0	0.0	5008	,	,		20915	0.0		0.003	False		,,,				2504	0.0				p.Y116Y		Atlas-SNP	.											.	OR56A4	66	.	0			c.C348T						PASS	.	G		0,4400		0,0,2200	69	69	69		348	1.7	1	11	dbSNP_134	69	14,8534	10.5+/-38.8	0,14,4260	no	coding-synonymous	OR56A4	NM_001005179.2		0,14,6460	AA,AG,GG		0.1638,0.0,0.1081		116/366	6024031	14,12934	2200	4274	6474	SO:0001819	synonymous_variant	120793	exon1			GAGCAGGTAGTAC	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.348C>T	11.37:g.6024031G>A		132	0	0		160	110	0.6875	NM_001005179	B9EH17	Silent	SNP	ENST00000330728.4	37	CCDS31404.1																																																																																			G|0.999;A|0.001	0.001	strong		0.607	OR56A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383756.2	NM_001005179		A	6024031	G	A	6024031	2	1	27	1	0	0	0	0	0	0	0	1	11144	1256	44	2		2	OR56A4	11	6024031	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	370165	6024031	128982485	591	11042											
OR56A1	120796	hgsc.bcm.edu	37	chr11	6048408	6048408	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcaatgacattttccccaCagtaatggagcagggaagtg	12	10	10	9	0	1	1	1	1	1	0	3	3	2	3	2	2	1	2	2	2	3	3	rs151331727	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:6048408C>A	ENST00000316650.5	-	1	563	c.527G>T	c.(526-528)tGt>tTt	p.C176F		NM_001001917.2	NP_001001917.2	Q8NGH5	O56A1_HUMAN	olfactory receptor, family 56, subfamily A, 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(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(22)|ovary(2)	33		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)		ATTTTCCCCACAGTAATGGAG	0.453													.|||	15	0.00299521	0.0	0.0014	5008	,	,		23480	0.0		0.0139	False		,,,				2504	0.0				p.C176F		Atlas-SNP	.											.	OR56A1	73	.	0			c.G527T						PASS	.	C	PHE/CYS	4,4398	8.1+/-20.4	0,4,2197	107	101	103		527	3.3	0.9	11	dbSNP_134	103	69,8523	41.2+/-98.3	0,69,4227	yes	missense	OR56A1	NM_001001917.2	205	0,73,6424	AA,AC,CC		0.8031,0.0909,0.5618	probably-damaging	176/319	6048408	73,12921	2201	4296	6497	SO:0001583	missense	120796	exon1			TCCCCACAGTAAT	AB065821	CCDS31405.1	11p15.4	2012-08-09			ENSG00000180934	ENSG00000180934		"GPCR / Class A : Olfactory receptors"	14781	protein-coding gene	gene with protein product							Standard	NM_001001917		Approved		uc010qzw.2	Q8NGH5	OTTHUMG00000165377	ENST00000316650.5:c.527G>T	11.37:g.6048408C>A	ENSP00000321246:p.Cys176Phe	133	0	0		163	36	0.220859	NM_001001917	B2RNI2|Q6IFL0	Missense_Mutation	SNP	ENST00000316650.5	37	CCDS31405.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	C	8.479	0.859298	0.17178	9.09E-4	0.008031	ENSG00000180934	ENST00000316650	T	0.00211	8.54	4.27	3.34	0.38264	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46758	D	0.000276	T	0.00300	0.0009	M	0.85945	2.785	0.28249	N	0.925365	B	0.31989	0.35	B	0.44163	0.443	T	0.00860	-1.1537	10	0.72032	D	0.01	.	13.1758	0.59626	0.0:0.8382:0.1618:0.0	.	176	Q8NGH5	O56A1_HUMAN	F	176	ENSP00000321246:C176F	ENSP00000321246:C176F	C	-	2	0	OR56A1	6004984	0.990000	0.36364	0.893000	0.35052	0.276000	0.26787	3.002000	0.49496	1.113000	0.41760	0.655000	0.94253	TGT	C|0.996;A|0.004	0.004	strong		0.453	OR56A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383757.1	NM_001001917		A	6048408	C	A	6048408	3	1	27	1	0	0	0	0	1	0	0	0	11142	478	17	4	433	4	OR56A1	11	6048408	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	24377	6048408	128958108	592	11043											
FAM160A2	84067	hgsc.bcm.edu	37	chr11	6245256	6245256	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ccgccgttcctcgaccccatCcccaagctcatcccattgca	7	8	5	21	3	1	0	1	0	0	0	5	1	4	0	8	0	2	3	8	0	1	2	rs200289464		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:6245256C>T	ENST00000449352.2	-	3	624	c.361G>A	c.(361-363)Gat>Aat	p.D121N	FAM160A2_ENST00000265978.4_Missense_Mutation_p.D121N|FAM160A2_ENST00000524416.1_Missense_Mutation_p.D121N			Q8N612	F16A2_HUMAN	family with sequence similarity 160, member A2	121					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						TCGACCCCATCCCCAAGCTCA	0.607																																					p.D121N		Atlas-SNP	.											.	FAM160A2	100	.	0			c.G361A						PASS	.	C	ASN/ASP,ASN/ASP	0,4402		0,0,2201	54	46	48		361,361	4.1	1	11		48	3,8589	3.0+/-9.4	0,3,4293	yes	missense,missense	FAM160A2	NM_001098794.1,NM_032127.3	23,23	0,3,6494	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging,probably-damaging	121/973,121/987	6245256	3,12991	2201	4296	6497	SO:0001583	missense	84067	exon3			CCCCATCCCCAAG		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.361G>A	11.37:g.6245256C>T	ENSP00000416918:p.Asp121Asn	77	0	0		97	17	0.175258	NM_032127	Q9C0A4|Q9H0N3|Q9H624	Missense_Mutation	SNP	ENST00000449352.2	37	CCDS44530.1	.	.	.	.	.	.	.	.	.	.	C	17.45	3.392996	0.62066	0.0	3.49E-4	ENSG00000051009	ENST00000449352;ENST00000442917;ENST00000265978;ENST00000524416	T;T;T	0.34472	1.36;1.36;1.36	5.05	4.14	0.48551	.	0.244954	0.28914	N	0.013721	T	0.35508	0.0934	N	0.14661	0.345	0.36163	D	0.84822	D;P;P	0.67145	0.996;0.611;0.557	D;B;B	0.66716	0.946;0.257;0.167	T	0.43877	-0.9364	10	0.48119	T	0.1	-17.8004	6.1565	0.20340	0.1851:0.7216:0.0:0.0933	.	121;121;121	E9PJK5;Q8N612;Q8N612-2	.;F16A2_HUMAN;.	N	121;46;121;121	ENSP00000416918:D121N;ENSP00000265978:D121N;ENSP00000431773:D121N	ENSP00000265978:D121N	D	-	1	0	FAM160A2	6201832	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.975000	0.49281	1.364000	0.46038	0.655000	0.94253	GAT	C|0.999;T|0.001	0.001	weak		0.607	FAM160A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383759.1	NM_032127		T	6245256	C	T	6245256	3	4	27	1	0	0	0	0	1	0	0	0	5474	855	30	2	2639	2	FAM160A2	11	6245256	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	196848	6245256	128761260	593	11044											
CCKBR	887	hgsc.bcm.edu	37	chr11	6291466	6291466	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acgtggctgctgtccggactActcatggtgccctaccccgt	5	10	11	15	3	1	0	1	0	0	0	2	1	2	1	4	3	4	2	4	3	2	2	rs77873910	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:6291466A>G	ENST00000334619.2	+	3	745	c.552A>G	c.(550-552)ctA>ctG	p.L184L	CCKBR_ENST00000525014.1_3'UTR|CCKBR_ENST00000525462.1_Silent_p.L184L|CCKBR_ENST00000532715.1_Silent_p.L100L	NM_176875.3	NP_795344.1	P32239	GASR_HUMAN	cholecystokinin B receptor	184					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)	TGTCCGGACTACTCATGGTGC	0.667													A|||	44	0.00878594	0.0045	0.0187	5008	,	,		2100	0.0		0.0159	False		,,,				2504	0.0092				p.L184L		Atlas-SNP	.											CCKBR_ENST00000525462,NS,carcinoma,+2,2	CCKBR	232	2	0			c.A552G						PASS	.	A		32,4370	36.8+/-68.6	0,32,2169	59	49	53		552	3.2	1	11	dbSNP_131	53	155,8437	73.5+/-136.2	1,153,4142	no	coding-synonymous	CCKBR	NM_176875.2		1,185,6311	GG,GA,AA		1.804,0.7269,1.4391		184/448	6291466	187,12807	2201	4296	6497	SO:0001819	synonymous_variant	887	exon3			CGGACTACTCATG	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.552A>G	11.37:g.6291466A>G		70	0	0		77	16	0.207792	NM_176875	A8K7P9|O75824|Q16144|Q92492|Q96LC6|Q9NYK7|Q9UBV1	Silent	SNP	ENST00000334619.2	37	CCDS7761.1																																																																																			A|0.986;G|0.014	0.014	strong		0.667	CCKBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257230.2	NM_176875		G	6291466	A	G	6291466	2	3	27	1	0	0	0	0	0	0	0	1	2883	378	14	3		3	CCKBR	11	6291466	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	46210	6291466	128715050	594	11045											
OR2AG2	338755	hgsc.bcm.edu	37	chr11	6789492	6789492	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gacaagggctttcttcctccCctcatttgatggcatacgaa	9	12	8	12	1	2	1	1	1	1	0	4	3	4	1	3	2	1	2	3	2	3	4	rs143018775	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:6789492C>T	ENST00000338569.2	-	1	794	c.697G>A	c.(697-699)Ggg>Agg	p.G233R		NM_001004490.1	NP_001004490.1	A6NM03	O2AG2_HUMAN	olfactory receptor, family 2, subfamily AG, 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)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(13)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	28		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)		Epithelial(150;2.15e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TTCTTCCTCCCCTCATTTGAT	0.502													C|||	8	0.00159744	0.0	0.0086	5008	,	,		19208	0.0		0.002	False		,,,				2504	0.0				p.G233R		Atlas-SNP	.											.	OR2AG2	55	.	0			c.G697A						PASS	.	C	ARG/GLY	2,4400	4.2+/-10.8	0,2,2199	110	95	100		697	3.5	0.1	11	dbSNP_134	100	19,8573	14.0+/-48.4	0,19,4277	yes	missense	OR2AG2	NM_001004490.1	125	0,21,6476	TT,TC,CC		0.2211,0.0454,0.1616	probably-damaging	233/317	6789492	21,12973	2201	4296	6497	SO:0001583	missense	338755	exon1			TCCTCCCCTCATT	AB065539	CCDS31413.1	11p15.4	2012-08-09		2004-03-10	ENSG00000188124	ENSG00000188124		"GPCR / Class A : Olfactory receptors"	15143	protein-coding gene	gene with protein product				OR2AG2P			Standard	NM_001004490		Approved		uc001meq.1	A6NM03	OTTHUMG00000165868	ENST00000338569.2:c.697G>A	11.37:g.6789492C>T	ENSP00000342697:p.Gly233Arg	199	0	0		179	145	0.810056	NM_001004490		Missense_Mutation	SNP	ENST00000338569.2	37	CCDS31413.1	4	0.0018315018315018315	0	0.0	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	C	12.95	2.092121	0.36952	4.54E-4	0.002211	ENSG00000188124	ENST00000338569	T	0.00295	8.25	4.47	3.55	0.40652	GPCR, rhodopsin-like superfamily (1);	0.000000	0.51477	D	0.000084	T	0.00496	0.0016	M	0.85197	2.74	0.09310	N	1	D	0.89917	1.0	D	0.85130	0.997	T	0.28554	-1.0040	10	0.87932	D	0	.	10.7934	0.46447	0.0:0.9061:0.0:0.0939	.	233	A6NM03	O2AG2_HUMAN	R	233	ENSP00000342697:G233R	ENSP00000342697:G233R	G	-	1	0	OR2AG2	6746068	0.000000	0.05858	0.111000	0.21465	0.605000	0.37080	0.158000	0.16422	1.480000	0.48289	0.655000	0.94253	GGG	C|0.999;T|0.001	0.001	strong		0.502	OR2AG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386775.1	NM_001004490		T	6789492	C	T	6789492	3	4	27	1	0	0	0	0	1	0	0	0	10994	623	22	2	257	2	OR2AG2	11	6789492	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	498026	6789492	128217024	595	11046											
TUB	7275	hgsc.bcm.edu	37	chr11	8122143	8122143	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agagagtctctatccgccccCgcaacgtgagtgtctacccc	8	8	9	16	3	2	2	0	1	2	1	4	3	3	2	5	0	2	1	5	0	3	2	rs139170512	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:8122143C>T	ENST00000299506.2	+	10	1359	c.1210C>T	c.(1210-1212)Cgc>Tgc	p.R404C	TUB_ENST00000305253.4_Missense_Mutation_p.R459C|TUB_ENST00000534099.1_Missense_Mutation_p.R410C	NM_177972.2	NP_813977.1	P50607	TUB_HUMAN	tubby bipartite transcription factor	404					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)		TATCCGCCCCCGCAACGTGAG	0.537													C|||	2	0.000399361	0.0008	0.0	5008	,	,		19350	0.0		0.0	False		,,,				2504	0.001				p.R459C		Atlas-SNP	.											TUB,NS,carcinoma,-1,1	TUB	71	1	0			c.C1375T						PASS	.	C	CYS/ARG,CYS/ARG	0,4402		0,0,2201	142	112	122		1375,1210	4.6	1	11	dbSNP_134	122	1,8591	1.2+/-3.3	0,1,4295	no	missense,missense	TUB	NM_003320.4,NM_177972.2	180,180	0,1,6496	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	459/562,404/507	8122143	1,12993	2201	4296	6497	SO:0001583	missense	7275	exon11			CGCCCCCGCAACG	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.1210C>T	11.37:g.8122143C>T	ENSP00000299506:p.Arg404Cys	81	0	0		79	55	0.696203	NM_003320	D3DQU4|O00293|Q6B007	Missense_Mutation	SNP	ENST00000299506.2	37	CCDS7787.1	.	.	.	.	.	.	.	.	.	.	C	19.20	3.780775	0.70222	0.0	1.16E-4	ENSG00000166402	ENST00000534099;ENST00000305253;ENST00000299506	D;D;D	0.85484	-1.99;-1.99;-1.99	4.59	4.59	0.56863	Tubby, C-terminal (3);	0.055535	0.64402	D	0.000001	D	0.92564	0.7638	M	0.88570	2.965	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.999	D;D;D	0.65874	0.939;0.931;0.935	D	0.93741	0.7050	10	0.66056	D	0.02	-18.1139	14.2881	0.66258	0.1492:0.8507:0.0:0.0	.	410;404;459	E9PQR4;P50607;P50607-2	.;TUB_HUMAN;.	C	410;459;404	ENSP00000434400:R410C;ENSP00000305426:R459C;ENSP00000299506:R404C	ENSP00000299506:R404C	R	+	1	0	TUB	8078719	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	4.811000	0.62606	2.277000	0.76020	0.563000	0.77884	CGC	C|1.000;T|0.000	0.000	weak		0.537	TUB-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385823.1	NM_003320		T	8122143	C	T	8122143	3	4	27	1	0	0	0	0	1	0	0	0	16757	652	23	1	1459	1	TUB	11	8122143	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1332651	8122143	126884373	596	11047											
SWAP70	23075	hgsc.bcm.edu	37	chr11	9685781	9685781	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctggcacgccttcaccgcaCtcgaccaggaccacagcggc	8	5	10	18	4	2	0	1	0	1	0	3	2	2	1	4	3	1	2	4	3	0	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:9685781C>G	ENST00000318950.6	+	1	158	c.55C>G	c.(55-57)Ctc>Gtc	p.L19V	SWAP70_ENST00000447399.2_Missense_Mutation_p.L19V	NM_015055.2	NP_055870.2	Q9UH65	SWP70_HUMAN	SWAP switching B-cell complex 70kDa subunit	19					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)		CTTCACCGCACTCGACCAGGA	0.701																																					p.L19V		Atlas-SNP	.											.	SWAP70	40	.	0			c.C55G						PASS	.						32	26	28					11																	9685781		2187	4288	6475	SO:0001583	missense	23075	exon1			ACCGCACTCGACC	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.55C>G	11.37:g.9685781C>G	ENSP00000315630:p.Leu19Val	161	0	0		251	57	0.227092	NM_015055	D3DQV1|O75135|Q7LCY6|Q9P061|Q9P0Z8	Missense_Mutation	SNP	ENST00000318950.6	37	CCDS31426.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.950471	0.73787	.	.	ENSG00000133789	ENST00000447399;ENST00000318950	D;T	0.86956	-2.19;2.8	5.5	5.5	0.81552	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.93874	0.8040	M	0.81497	2.545	0.53005	D	0.999966	D;P;D	0.69078	0.993;0.748;0.997	D;B;D	0.78314	0.987;0.351;0.991	D	0.94329	0.7560	10	0.87932	D	0	-7.6476	19.0354	0.92974	0.0:1.0:0.0:0.0	.	19;19;19	E7EMB1;Q9UH65;B3KUB9	.;SWP70_HUMAN;.	V	19	ENSP00000399056:L19V;ENSP00000315630:L19V	ENSP00000315630:L19V	L	+	1	0	SWAP70	9642357	1.000000	0.71417	1.000000	0.80357	0.609000	0.37215	3.715000	0.54897	2.584000	0.87258	0.563000	0.77884	CTC	.	.	none		0.701	SWAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386766.2	NM_015055		G	9685781	C	G	9685781	3	3	27	1	0	0	0	0	1	0	0	0	15440	565	20	4	57	4	SWAP70	11	9685781	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1563638	9685781	125320735	597	11048											
EIF4G2	1982	hgsc.bcm.edu	37	chr11	10827592	10827592	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggggttttccccaggaacTcgctgattaataaaaatcag	12	11	9	9	1	1	1	1	1	0	0	3	2	2	2	2	3	1	2	2	3	5	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:10827592T>A	ENST00000526148.1	-	4	620	c.110A>T	c.(109-111)gAg>gTg	p.E37V	EIF4G2_ENST00000525681.1_Missense_Mutation_p.E37V|EIF4G2_ENST00000525995.1_5'UTR|EIF4G2_ENST00000396525.2_Missense_Mutation_p.E37V|EIF4G2_ENST00000339995.5_Missense_Mutation_p.E37V	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)		CCCCAGGAACTCGCTGATTAA	0.403																																					p.E37V		Atlas-SNP	.											.	EIF4G2	89	.	0			c.A110T						PASS	.						97	93	95					11																	10827592		2201	4294	6495	SO:0001583	missense	1982	exon4			AGGAACTCGCTGA	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.110A>T	11.37:g.10827592T>A	ENSP00000433664:p.Glu37Val	203	0	0		205	48	0.234146	NM_001172705		Missense_Mutation	SNP	ENST00000526148.1	37	CCDS31428.1	.	.	.	.	.	.	.	.	.	.	T	28.8	4.949046	0.92660	.	.	ENSG00000110321	ENST00000526148;ENST00000525681;ENST00000339995;ENST00000396525;ENST00000429377;ENST00000531416;ENST00000532082;ENST00000524932;ENST00000532570;ENST00000526591;ENST00000530211;ENST00000527526;ENST00000530702	T;T;T;T;T;T;T;T	0.49139	2.11;2.11;2.11;2.11;1.79;1.82;1.82;0.79	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.52435	0.1734	N	0.24115	0.695	0.51233	D	0.999912	D;D	0.65815	0.995;0.995	P;P	0.60682	0.878;0.878	T	0.64533	-0.6385	9	0.87932	D	0	-8.5634	15.356	0.74428	0.0:0.0:0.0:1.0	.	37;110	P78344;B4DZF2	IF4G2_HUMAN;.	V	37;37;37;37;110;37;37;37;37;37;37;37;15	ENSP00000433664:E37V;ENSP00000433371:E37V;ENSP00000340281:E37V;ENSP00000379778:E37V;ENSP00000431583:E37V;ENSP00000433121:E37V;ENSP00000435523:E37V;ENSP00000431511:E37V	ENSP00000340281:E37V	E	-	2	0	EIF4G2	10784168	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.040000	0.89188	2.023000	0.59567	0.455000	0.32223	GAG	.	.	none		0.403	EIF4G2-006	KNOWN	alternative_5_UTR|non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386603.1	NM_001418		A	10827592	T	A	10827592	3	1	27	1	0	0	0	0	1	0	0	0	5039	1551	54	5	2689	5	EIF4G2	11	10827592	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	1141811	10827592	124178924	598	11049											
PARVA	55742	hgsc.bcm.edu	37	chr11	12540037	12540037	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agctcatgcaagatggagggTtggaaaagccaaaaccgcgg	14	5	14	8	2	1	1	1	0	0	1	1	3	1	3	2	4	4	3	2	4	5	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:12540037T>C	ENST00000550549.1	+	12	1064	c.1015T>C	c.(1015-1017)Ttg>Ctg	p.L339L	PARVA_ENST00000539723.1_Silent_p.L339L|PARVA_ENST00000334956.8_Silent_p.L379L			Q9NVD7	PARVA_HUMAN	parvin, alpha	339	CH 2. {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)		AGATGGAGGGTTGGAAAAGCC	0.512																																					p.L379L		Atlas-SNP	.											.	PARVA	27	.	0			c.T1135C						PASS	.						89	87	87					11																	12540037		1969	4145	6114	SO:0001819	synonymous_variant	55742	exon12			GGAGGGTTGGAAA	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.1015T>C	11.37:g.12540037T>C		221	0	0		189	33	0.174603	NM_018222	Q96C85|Q9HA48	Silent	SNP	ENST00000550549.1	37																																																																																				.	.	none		0.512	PARVA-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_018222		C	12540037	T	C	12540037	2	2	27	1	0	0	0	0	0	0	0	1	11477	1722	60	3		3	PARVA	11	12540037	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	1712445	12540037	122466479	599	11050											
FAR1	84188	hgsc.bcm.edu	37	chr11	13743325	13743325	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaagctatggtgtttcttgaAtatttcacaagtaattcttg	12	17	7	5	0	3	1	1	1	2	0	3	1	3	1	0	1	1	3	0	1	6	8	rs34341612	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:13743325A>G	ENST00000354817.3	+	10	1320	c.1176A>G	c.(1174-1176)gaA>gaG	p.E392E	FAR1_ENST00000532502.1_Silent_p.E16E	NM_032228.5	NP_115604.1	Q8WVX9	FACR1_HUMAN	fatty acyl CoA reductase 1	392					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						TGTTTCTTGAATATTTCACAA	0.303													A|||	31	0.0061901	0.0008	0.0058	5008	,	,		16434	0.0		0.0119	False		,,,				2504	0.0143				p.E392E		Atlas-SNP	.											.	FAR1	40	.	0			c.A1176G						PASS	.	A		9,4387	15.5+/-35.6	0,9,2189	85	84	84		1176	0.2	1	11	dbSNP_126	84	123,8459	63.5+/-125.6	0,123,4168	no	coding-synonymous	FAR1	NM_032228.5		0,132,6357	GG,GA,AA		1.4332,0.2047,1.0171		392/516	13743325	132,12846	2198	4291	6489	SO:0001819	synonymous_variant	84188	exon10			TCTTGAATATTTC	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.1176A>G	11.37:g.13743325A>G		70	0	0		49	32	0.653061	NM_032228	D3DQW8|Q5CZA3	Silent	SNP	ENST00000354817.3	37	CCDS7813.1																																																																																			A|0.990;G|0.010	0.010	strong		0.303	FAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385990.2	NM_032228		G	13743325	A	G	13743325	2	3	27	1	0	0	0	0	0	0	0	1	5682	98	4	3		3	FAR1	11	13743325	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	1203288	13743325	121263191	600	11051											
NAV2	89797	hgsc.bcm.edu	37	chr11	20124807	20124807	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctggccaccataggaattgCgccagtacctgtccaacctt	9	9	8	15	1	0	0	0	0	0	0	1	1	1	1	7	2	3	1	7	2	4	4	rs34329467	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:20124807C>T	ENST00000396087.3	+	36	6700	c.6601C>T	c.(6601-6603)Cgc>Tgc	p.R2201C	NAV2_ENST00000527559.2_Missense_Mutation_p.R2130C|NAV2_ENST00000311043.8_Missense_Mutation_p.R1206C|NAV2_ENST00000533917.1_Missense_Mutation_p.R1206C|NAV2_ENST00000360655.4_Missense_Mutation_p.R2078C|NAV2_ENST00000349880.4_Missense_Mutation_p.R2142C|NAV2_ENST00000396085.1_Missense_Mutation_p.R2145C|NAV2_ENST00000540292.1_Missense_Mutation_p.R2132C	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	2201					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						ATAGGAATTGCGCCAGTACCT	0.567													C|||	3	0.000599042	0.0008	0.0	5008	,	,		23293	0.0		0.002	False		,,,				2504	0.0				p.R2201C		Atlas-SNP	.											.	NAV2	255	.	0			c.C6601T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	4,4402	8.1+/-20.4	0,4,2199	167	130	143		6232,3616,6424,6433	5.6	1	11	dbSNP_126	143	29,8571	19.8+/-62.0	0,29,4271	yes	missense,missense,missense,missense	NAV2	NM_001111018.1,NM_001111019.1,NM_145117.4,NM_182964.5	180,180,180,180	0,33,6470	TT,TC,CC		0.3372,0.0908,0.2537	probably-damaging,probably-damaging,probably-damaging,probably-damaging	2078/2366,1206/1494,2142/2430,2145/2433	20124807	33,12973	2203	4300	6503	SO:0001583	missense	89797	exon35			GAATTGCGCCAGT	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.6601C>T	11.37:g.20124807C>T	ENSP00000379396:p.Arg2201Cys	114	0	0		75	20	0.266667	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Missense_Mutation	SNP	ENST00000396087.3	37	CCDS58126.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	C	23.6	4.432361	0.83776	9.08E-4	0.003372	ENSG00000166833	ENST00000360655;ENST00000396085;ENST00000349880;ENST00000396087;ENST00000527559;ENST00000540292;ENST00000533917;ENST00000311043	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	5.6	5.6	0.85130	.	0.000000	0.64402	D	0.000003	D	0.94988	0.8378	M	0.83384	2.64	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.978;0.984;0.993;0.999	D	0.94611	0.7804	9	.	.	.	.	19.2099	0.93749	0.0:1.0:0.0:0.0	rs34329467	2145;1206;2142;2078	A7E2D6;Q8IVL1-5;Q8IVL1-3;Q8IVL1-4	.;.;.;.	C	2078;2145;2142;2201;2130;2132;1206;1206	ENSP00000353871:R2078C;ENSP00000379394:R2145C;ENSP00000309577:R2142C;ENSP00000379396:R2201C;ENSP00000435395:R2130C;ENSP00000443489:R2132C;ENSP00000437316:R1206C;ENSP00000312169:R1206C	.	R	+	1	0	NAV2	20081383	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	5.954000	0.70298	2.631000	0.89168	0.655000	0.94253	CGC	C|0.997;T|0.003	0.003	strong		0.567	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		T	20124807	C	T	20124807	3	4	27	1	0	0	0	0	1	0	0	0	10193	768	27	1	6672	1	NAV2	11	20124807	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	6381482	20124807	114881709	601	11052											
PAMR1	25891	hgsc.bcm.edu	37	chr11	35463043	35463043	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	agttaccttttatgcagatgGgctgtttccctgaccactct	7	15	8	11	0	1	2	0	1	1	1	2	2	2	2	3	1	2	4	3	1	2	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:35463043G>A	ENST00000378880.2	-	7	1464	c.1019C>T	c.(1018-1020)cCc>cTc	p.P340L	PAMR1_ENST00000532848.1_Missense_Mutation_p.P300L|PAMR1_ENST00000378878.3_Missense_Mutation_p.P229L|PAMR1_ENST00000278360.3_Missense_Mutation_p.P357L	NM_001001991.1	NP_001001991.1	Q6UXH9	PAMR1_HUMAN	peptidase domain containing associated with muscle regeneration 1	340	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.					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						TATGCAGATGGGCTGTTTCCC	0.418																																					p.P357L		Atlas-SNP	.											.	PAMR1	85	.	0			c.C1070T						PASS	.						195	189	191					11																	35463043		2202	4298	6500	SO:0001583	missense	25891	exon8			CAGATGGGCTGTT		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.1019C>T	11.37:g.35463043G>A	ENSP00000368158:p.Pro340Leu	129	0	0		129	65	0.503876	NM_015430	A8MQ58|B7ZA73|Q5EBL7|Q5JPI4|Q6N062|Q71RE9|Q96JW2|Q9Y432	Missense_Mutation	SNP	ENST00000378880.2	37	CCDS31460.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.031221	0.93575	.	.	ENSG00000149090	ENST00000278360;ENST00000378880;ENST00000378878;ENST00000532848;ENST00000527605	T;T;T;T;T	0.77358	-1.09;-1.09;-1.09;-1.09;-1.09	5.84	5.84	0.93424	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.85682	D	0.000000	D	0.92306	0.7559	H	0.95187	3.635	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	0.93784	0.7086	10	0.87932	D	0	.	20.139	0.98050	0.0:0.0:1.0:0.0	.	229;340;357	A8MQ58;Q6UXH9;Q6UXH9-2	.;PAMR1_HUMAN;.	L	357;340;229;300;317	ENSP00000278360:P357L;ENSP00000368158:P340L;ENSP00000368156:P229L;ENSP00000433868:P300L;ENSP00000432591:P317L	ENSP00000278360:P357L	P	-	2	0	PAMR1	35419619	1.000000	0.71417	0.991000	0.47740	0.987000	0.75469	8.755000	0.91646	2.764000	0.94973	0.655000	0.94253	CCC	.	.	none		0.418	PAMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389177.1	NM_015430		A	35463043	G	A	35463043	3	1	27	1	0	0	0	0	1	0	0	0	11422	1232	43	2	1163	2	PAMR1	11	35463043	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	15338236	35463043	99543473	602	11053											
KIAA0652	9776	hgsc.bcm.edu	37	chr11	46690413	46690413	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgcactcagatggctccagcGggggcagcagtggcaatacc	9	6	14	12	1	1	1	1	0	0	1	2	1	2	1	2	4	4	5	2	4	2	1	rs35619591	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:46690413G>A	ENST00000434074.1	+	15	1989	c.1300G>A	c.(1300-1302)Ggg>Agg	p.G434R	ATG13_ENST00000451945.1_Missense_Mutation_p.G397R|ATG13_ENST00000526508.1_Missense_Mutation_p.G434R|ATG13_ENST00000524625.1_Missense_Mutation_p.G397R|ATG13_ENST00000312040.4_Missense_Mutation_p.G434R|ATG13_ENST00000530500.1_Missense_Mutation_p.G318R|ATG13_ENST00000528494.1_Missense_Mutation_p.G467R|ATG13_ENST00000359513.4_Missense_Mutation_p.G434R|ATG13_ENST00000529655.1_Missense_Mutation_p.G397R	NM_001205120.1	NP_001192049.1	O75143	ATG13_HUMAN	autophagy related 13	434					autophagic vacuole assembly (GO:0000045)	ATG1/UKL1 signaling complex (GO:0034273)|cytosol (GO:0005829)|pre-autophagosomal structure (GO:0000407)|ULK1-ATG13-FIP200 complex (GO:0070969)	protein kinase binding (GO:0019901)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|prostate(1)|skin(1)	15						TGGCTCCAGCGGGGGCAGCAG	0.532													G|||	40	0.00798722	0.0	0.0014	5008	,	,		19713	0.001		0.0109	False		,,,				2504	0.0276				p.G467R		Atlas-SNP	.											.	ATG13	60	.	0			c.G1399A						PASS	.	G	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	6,4396	11.4+/-27.6	0,6,2195	136	122	127		1300,1399,1300,1189,952,1189	4.9	0.8	11	dbSNP_126	127	67,8531	41.7+/-99.0	1,65,4233	yes	missense,missense,missense,missense,missense,missense	ATG13	NM_001142673.2,NM_001205119.1,NM_001205120.1,NM_001205121.1,NM_001205122.1,NM_014741.4	125,125,125,125,125,125	1,71,6428	AA,AG,GG		0.7793,0.1363,0.5615	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	434/518,467/551,434/518,397/481,318/402,397/481	46690413	73,12927	2201	4299	6500	SO:0001583	missense	9776	exon16			TCCAGCGGGGGCA	AB014552	CCDS7921.1, CCDS44582.1, CCDS55760.1, CCDS55761.1	11p11.2	2014-02-12	2012-06-06	2010-06-29	ENSG00000175224	ENSG00000175224			29091	protein-coding gene	gene with protein product		615088	"KIAA0652", "ATG13 autophagy related 13 homolog (S. cerevisiae)"	KIAA0652		15169610, 18339812, 17204848	Standard	NM_001205120		Approved		uc001nda.3	O75143	OTTHUMG00000166538	ENST00000434074.1:c.1300G>A	11.37:g.46690413G>A	ENSP00000400642:p.Gly434Arg	26	0	0		24	19	0.791667	NM_001205119	B4DFI4|D3DQQ1|D3DQQ2|E9PQZ8|Q53EN6|Q9BRL3|Q9H8B0	Missense_Mutation	SNP	ENST00000434074.1	37	CCDS44582.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	G	15.32	2.797457	0.50208	0.001363	0.007793	ENSG00000175224	ENST00000434074;ENST00000312040;ENST00000451945;ENST00000529655;ENST00000530500;ENST00000526508;ENST00000524625;ENST00000359513;ENST00000528494;ENST00000525009	.	.	.	5.8	4.88	0.63580	.	0.345068	0.38111	N	0.001815	T	0.33962	0.0881	L	0.29908	0.895	0.41529	D	0.988441	B;B;B;B	0.25390	0.047;0.003;0.014;0.125	B;B;B;B	0.19148	0.005;0.002;0.003;0.024	T	0.23833	-1.0177	9	0.30854	T	0.27	-14.1572	9.9398	0.41574	0.0698:0.0:0.7929:0.1373	rs35619591;rs35619591	318;434;467;397	B4DFI4;O75143;E9PQZ8;O75143-2	.;ATG13_HUMAN;.;.	R	434;434;397;397;318;434;397;434;467;166	.	ENSP00000310321:G434R	G	+	1	0	ATG13	46646989	1.000000	0.71417	0.765000	0.31456	0.721000	0.41392	4.226000	0.58606	1.452000	0.47756	0.655000	0.94253	GGG	G|0.994;A|0.006	0.006	strong		0.532	ATG13-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390300.2	NM_014741		A	46690413	G	A	46690413	3	1	27	1	0	0	0	0	1	0	0	0	8197	1116	39	1	1354	1	KIAA0652	11	46690413	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	11227370	46690413	88316103	603	11054											
OR4A47	403253	hgsc.bcm.edu	37	chr11	48511050	48511050	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagggaggcaaaaagccctcTcaacctgcagttcccacatg	13	6	9	13	0	1	0	1	0	1	0	3	1	2	1	3	2	3	3	3	2	4	1	rs76991989	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:48511050T>C	ENST00000446524.1	+	1	782	c.706T>C	c.(706-708)Tca>Cca	p.S236P		NM_001005512.2	NP_001005512.2	Q6IF82	O4A47_HUMAN	olfactory receptor, family 4, subfamily A, member 47	236						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						AAAAGCCCTCTCAACCTGCAG	0.428													T|||	41	0.0081869	0.0015	0.0086	5008	,	,		18021	0.0		0.0268	False		,,,				2504	0.0061				p.S236P		Atlas-SNP	.											OR4A47,bladder,carcinoma,-1,1	OR4A47	72	1	0			c.T706C						PASS	.	T	PRO/SER	23,4379		0,23,2178	148	144	145		706	2.4	0.1	11	dbSNP_131	145	217,8379		3,211,4084	yes	missense	OR4A47	NM_001005512.2	74	3,234,6262	CC,CT,TT		2.5244,0.5225,1.8464	benign	236/310	48511050	240,12758	2201	4298	6499	SO:0001583	missense	403253	exon1			GCCCTCTCAACCT	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.706T>C	11.37:g.48511050T>C	ENSP00000412752:p.Ser236Pro	143	0	0		116	90	0.775862	NM_001005512		Missense_Mutation	SNP	ENST00000446524.1	37	CCDS31490.1	23	0.010531135531135532	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	17	0.022427440633245383	N	11.71	1.719811	0.30503	0.005225	0.025244	ENSG00000237388	ENST00000446524	T	0.00309	8.16	4.59	2.36	0.29203	GPCR, rhodopsin-like superfamily (1);	0.553031	0.16377	N	0.217096	T	0.00300	0.0009	H	0.98407	4.225	0.09310	N	0.999997	D	0.53462	0.96	P	0.54965	0.765	T	0.40098	-0.9581	10	0.87932	D	0	.	5.4392	0.16498	0.0:0.2998:0.0:0.7002	.	236	Q6IF82	O4A47_HUMAN	P	236	ENSP00000412752:S236P	ENSP00000412752:S236P	S	+	1	0	OR4A47	48467626	0.000000	0.05858	0.139000	0.22197	0.222000	0.24845	0.081000	0.14823	0.225000	0.20959	0.172000	0.16884	TCA	T|0.981;C|0.019	0.019	strong		0.428	OR4A47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390559.1	NM_001005512		C	48511050	T	C	48511050	3	2	27	1	0	0	0	0	1	0	0	0	11051	1551	54	3	708	3	OR4A47	11	48511050	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	1820637	48511050	86495466	604	11055											
OR4C13	283092	hgsc.bcm.edu	37	chr11	49974626	49974626	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgctcctggtctcctgcgtgGtcatactgtactccttaaag	6	14	9	12	1	2	0	1	0	1	0	5	0	4	0	3	2	4	2	3	2	4	3	rs150606357		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:49974626G>A	ENST00000555099.1	+	1	684	c.652G>A	c.(652-654)Gtc>Atc	p.V218I		NM_001001955.2	NP_001001955.2	Q8NGP0	OR4CD_HUMAN	olfactory receptor, family 4, subfamily C, member 13	218						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)|kidney(1)|large_intestine(5)|lung(24)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	43						CTCCTGCGTGGTCATACTGTA	0.488													G|||	1	0.000199681	0.0	0.0	5008	,	,		17462	0.0		0.001	False		,,,				2504	0.0				p.V218I		Atlas-SNP	.											.	OR4C13	96	.	0			c.G652A						PASS	.	G	ILE/VAL	0,4402		0,0,2201	189	153	165		652	0.8	1	11	dbSNP_134	165	10,8582		0,10,4286	yes	missense	OR4C13	NM_001001955.2	29	0,10,6487	AA,AG,GG		0.1164,0.0,0.077	benign	218/310	49974626	10,12984	2201	4296	6497	SO:0001583	missense	283092	exon1			TGCGTGGTCATAC	AB065750	CCDS31495.1	11p11.12	2012-10-03			ENSG00000258817	ENSG00000258817		"GPCR / Class A : Olfactory receptors"	15169	protein-coding gene	gene with protein product							Standard	NM_001001955		Approved		uc010rhz.2	Q8NGP0	OTTHUMG00000166686	ENST00000555099.1:c.652G>A	11.37:g.49974626G>A	ENSP00000452277:p.Val218Ile	219	0	0		157	111	0.707006	NM_001001955	A6NJJ3|B9EH30|Q6IF48|Q96R68	Missense_Mutation	SNP	ENST00000555099.1	37	CCDS31495.1	.	.	.	.	.	.	.	.	.	.	.	3.409	-0.120655	0.06838	0.0	0.001164	ENSG00000258817	ENST00000555099	T	0.00091	8.74	2.7	0.748	0.18376	GPCR, rhodopsin-like superfamily (1);	0.168066	0.28125	N	0.016511	T	0.00144	0.0004	L	0.60957	1.885	0.09310	N	0.999999	B	0.02656	0.0	B	0.17722	0.019	T	0.38714	-0.9648	9	.	.	.	.	2.838	0.05521	0.3033:0.2481:0.4486:0.0	.	218	Q8NGP0	OR4CD_HUMAN	I	218	ENSP00000452277:V218I	.	V	+	1	0	OR4C13	49931202	0.000000	0.05858	0.988000	0.46212	0.089000	0.18198	-2.155000	0.01284	0.474000	0.27392	0.186000	0.17326	GTC	G|0.999;A|0.001	0.001	strong		0.488	OR4C13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391103.1	NM_001001955		A	49974626	G	A	49974626	3	1	27	1	0	0	0	0	1	0	0	0	11056	1261	44	2	654	2	OR4C13	11	49974626	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1463576	49974626	85031890	605	11056											
OR5L1	219437	hgsc.bcm.edu	37	chr11	55579068	55579068	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggagtcacgttgttagccaaCctgggcatgattgcactgat	9	11	12	9	1	1	2	1	2	0	0	1	3	1	3	2	2	3	4	2	2	2	3	rs575553149		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:55579068C>T	ENST00000333973.2	+	1	215	c.126C>T	c.(124-126)aaC>aaT	p.N42N		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	42						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)				TGTTAGCCAACCTGGGCATGA	0.498																																					p.N42N		Atlas-SNP	.											OR5L1,colon,carcinoma,0,3	OR5L1	145	3	0			c.C126T						scavenged	.						325	285	299					11																	55579068		2200	4296	6496	SO:0001819	synonymous_variant	219437	exon1			AGCCAACCTGGGC	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.126C>T	11.37:g.55579068C>T		113	0	0		143	8	0.0559441	NM_001004738	B2RNK6|Q6IFD0	Silent	SNP	ENST00000333973.2	37	CCDS31509.1																																																																																			.	.	none		0.498	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738		T	55579068	C	T	55579068	2	4	27	1	0	0	0	0	0	0	0	1	11179	506	18	2		2	OR5L1	11	55579068	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	5604442	55579068	79427448	606	11057											
OR5T2	219464	hgsc.bcm.edu	37	chr11	56000079	56000079	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agccactgtatgtatagtagCatgtaaaatgccagcaacat	15	10	8	8	0	0	0	0	0	0	0	0	0	0	0	2	0	5	6	2	0	7	5	rs77295387	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:56000079C>T	ENST00000313264.4	-	1	658	c.583G>A	c.(583-585)Gct>Act	p.A195T		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	195						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)					TGTATAGTAGCATGTAAAATG	0.433													c|||	34	0.00678914	0.0015	0.0029	5008	,	,		23389	0.0		0.0268	False		,,,				2504	0.0031				p.A195T		Atlas-SNP	.											.	OR5T2	107	.	0			c.G583A						PASS	.	C	THR/ALA	21,4381	26.2+/-53.5	0,21,2180	193	169	177		583	4.1	0.1	11	dbSNP_131	177	237,8355	96.6+/-158.3	1,235,4060	yes	missense	OR5T2	NM_001004746.1	58	1,256,6240	TT,TC,CC		2.7584,0.4771,1.9855	probably-damaging	195/360	56000079	258,12736	2201	4296	6497	SO:0001583	missense	219464	exon1			TAGTAGCATGTAA	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.583G>A	11.37:g.56000079C>T	ENSP00000323688:p.Ala195Thr	264	0	0		207	157	0.758454	NM_001004746	B9EGX5|Q6IFC8	Missense_Mutation	SNP	ENST00000313264.4	37	CCDS31523.1	21	0.009615384615384616	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	19	0.025065963060686015	C	12.15	1.852226	0.32699	0.004771	0.027584	ENSG00000181718	ENST00000313264	T	0.39056	1.1	5.07	4.13	0.48395	GPCR, rhodopsin-like superfamily (1);	0.184659	0.26013	U	0.026862	T	0.23054	0.0557	L	0.41356	1.27	0.09310	N	1	P	0.45986	0.87	P	0.53102	0.718	T	0.11155	-1.0599	10	0.49607	T	0.09	.	12.8779	0.57999	0.3516:0.6484:0.0:0.0	.	195	Q8NGG2	OR5T2_HUMAN	T	195	ENSP00000323688:A195T	ENSP00000323688:A195T	A	-	1	0	OR5T2	55756655	0.000000	0.05858	0.078000	0.20375	0.029000	0.11900	-0.966000	0.03825	1.207000	0.43291	0.478000	0.44815	GCT	C|0.981;T|0.019	0.019	strong		0.433	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746		T	56000079	C	T	56000079	3	4	27	1	0	0	0	0	1	0	0	0	11191	710	25	2	495	2	OR5T2	11	56000079	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	421011	56000079	79006437	607	11058											
OR8J1	219477	hgsc.bcm.edu	37	chr11	56128031	56128031	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgtgccacccaactgggaggGttcttgttctttattgtatc	6	16	10	9	0	2	0	0	0	2	0	3	1	2	1	2	2	2	3	2	2	3	7			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:56128031G>C	ENST00000303039.3	+	1	341	c.309G>C	c.(307-309)ggG>ggC	p.G103G		NM_001005205.2	NP_001005205.2	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J, member 1	103						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)					AACTGGGAGGGTTCTTGTTCT	0.423																																					p.G103G		Atlas-SNP	.											.	OR8J1	87	.	0			c.G309C						PASS	.						150	140	143					11																	56128031		2201	4296	6497	SO:0001819	synonymous_variant	219477	exon1			GGGAGGGTTCTTG	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.309G>C	11.37:g.56128031G>C		216	0	0		187	49	0.262032	NM_001005205	B2RNQ6|B9EH63|Q6IFC2|Q96RC3	Silent	SNP	ENST00000303039.3	37	CCDS31529.1																																																																																			.	.	none		0.423	OR8J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391606.2	NM_001005205		C	56128031	G	C	56128031	2	2	27	1	0	0	0	0	0	0	0	1	11250	1248	44	4		4	OR8J1	11	56128031	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	127952	56128031	78878485	608	11059											
OR9G1	390174	hgsc.bcm.edu	37	chr11	56468258	56468258	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctccaagcccctgctttatgCccaggccatgtccataaagc	9	9	7	16	0	0	0	0	0	0	0	2	0	2	0	6	1	4	1	6	1	4	3	rs78340277	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:56468258C>T	ENST00000312153.1	+	1	395	c.395C>T	c.(394-396)gCc>gTc	p.A132V		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	132						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						CTGCTTTATGCCCAGGCCATG	0.498													C|||	31	0.0061901	0.0015	0.0029	5008	,	,		19708	0.0		0.0239	False		,,,				2504	0.0031				p.A132V		Atlas-SNP	.											.	.	.	.	0			c.C395T						PASS	.	C	VAL/ALA	16,4386	21.2+/-45.6	0,16,2185	186	171	176		395	4.4	0.8	11	dbSNP_131	176	171,8421	67.7+/-130.1	0,171,4125	yes	missense	OR9G1	NM_001005213.1	64	0,187,6310	TT,TC,CC		1.9902,0.3635,1.4391	possibly-damaging	132/306	56468258	187,12807	2201	4296	6497	SO:0001583	missense	504191	exon1			TTTATGCCCAGGC	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.395C>T	11.37:g.56468258C>T	ENSP00000309012:p.Ala132Val	257	0	0		227	85	0.374449	NM_001013358	Q6IEU9|Q8NGQ0	Missense_Mutation	SNP	ENST00000312153.1	37	CCDS31536.1	16	0.007326007326007326	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	14	0.018469656992084433	C	11.81	1.748637	0.30955	0.003635	0.019902	ENSG00000174914	ENST00000312153	T	0.01572	4.76	4.43	4.43	0.53597	GPCR, rhodopsin-like superfamily (1);	0.696787	0.13040	N	0.418614	T	0.00998	0.0033	L	0.31120	0.905	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.40117	-0.9580	10	0.66056	D	0.02	-6.4294	10.827	0.46638	0.0:0.9106:0.0:0.0894	.	132	Q8NH87	OR9G1_HUMAN	V	132	ENSP00000309012:A132V	ENSP00000309012:A132V	A	+	2	0	OR9G1	56224834	0.000000	0.05858	0.813000	0.32504	0.681000	0.39784	-0.197000	0.09518	2.430000	0.82344	0.585000	0.79938	GCC	C|0.987;T|0.013	0.013	strong		0.498	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213		T	56468258	C	T	56468258	3	4	27	1	0	0	0	0	1	0	0	0	11259	739	26	2	397	2	OR9G1	11	56468258	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	340227	56468258	78538258	609	11060											
TNKS1BP1	85456	hgsc.bcm.edu	37	chr11	57080938	57080938	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tcacccttggcctcctcctcCccgccagatggaaacgtccg	6	8	8	19	3	1	1	1	0	0	1	5	2	5	2	8	2	1	0	8	2	1	1	rs145901431	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:57080938C>A	ENST00000532437.1	-	4	1535	c.1224G>T	c.(1222-1224)ggG>ggT	p.G408G	TNKS1BP1_ENST00000530920.1_5'Flank|TNKS1BP1_ENST00000358252.3_Silent_p.G408G			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	408	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)				CCTCCTCCTCCCCGCCAGATG	0.647													C|||	7	0.00139776	0.0	0.0029	5008	,	,		16354	0.0		0.004	False		,,,				2504	0.001				p.G408G		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.G1224T						PASS	.	C		0,4398		0,0,2199	23	24	24		1224	0.8	0	11	dbSNP_134	24	27,8561		0,27,4267	yes	coding-synonymous	TNKS1BP1	NM_033396.2		0,27,6466	AA,AC,CC		0.3144,0.0,0.2079		408/1730	57080938	27,12959	2199	4294	6493	SO:0001819	synonymous_variant	85456	exon5			CTCCTCCCCGCCA	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.1224G>T	11.37:g.57080938C>A		66	0	0		50	41	0.82	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Silent	SNP	ENST00000532437.1	37	CCDS7951.1																																																																																			C|0.998;A|0.002	0.002	strong		0.647	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396		A	57080938	C	A	57080938	2	1	27	1	0	0	0	0	0	0	0	1	16335	610	22	4		4	TNKS1BP1	11	57080938	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	612680	57080938	77925578	610	11061											
OR10V1	390201	hgsc.bcm.edu	37	chr11	59481214	59481214	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttccaccgaggctggtcagAtacatcatcaggaagaccac	12	8	9	12	1	3	2	3	0	0	2	4	4	4	3	3	3	1	1	3	3	2	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:59481214A>G	ENST00000307552.2	-	1	123	c.105T>C	c.(103-105)taT>taC	p.Y35Y	STX3_ENST00000300150.7_5'UTR	NM_001005324.1	NP_001005324.1	Q8NGI7	O10V1_HUMAN	olfactory receptor, family 10, subfamily V, member 1	35						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						GGCTGGTCAGATACATCATCA	0.438																																					p.Y35Y		Atlas-SNP	.											.	OR10V1	40	.	0			c.T105C						PASS	.						70	66	67					11																	59481214		2201	4295	6496	SO:0001819	synonymous_variant	390201	exon1			GGTCAGATACATC	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.105T>C	11.37:g.59481214A>G		90	0	0		76	24	0.315789	NM_001005324	Q6IFD9|Q96R50	Silent	SNP	ENST00000307552.2	37	CCDS31565.1																																																																																			.	.	none		0.438	OR10V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394517.1	NM_001005324		G	59481214	A	G	59481214	2	3	27	1	0	0	0	0	0	0	0	1	10929	340	12	3		3	OR10V1	11	59481214	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	2400276	59481214	75525302	611	11062											
MS4A14	84689	hgsc.bcm.edu	37	chr11	60183483	60183483	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcccatgtcaaacagtctTctaatctgacagctaatgac	13	11	5	12	0	4	2	1	2	3	0	5	2	5	2	1	0	2	1	1	0	3	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:60183483T>C	ENST00000300187.6	+	5	1319	c.1042T>C	c.(1042-1044)Tct>Cct	p.S348P	MS4A14_ENST00000531787.1_Missense_Mutation_p.S236P|MS4A14_ENST00000395005.2_Missense_Mutation_p.S331P|MS4A14_ENST00000395001.1_3'UTR|MS4A14_ENST00000531783.1_Missense_Mutation_p.S381P	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14	348						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						CAAACAGTCTTCTAATCTGAC	0.443																																					p.S381P		Atlas-SNP	.											.	MS4A14	120	.	0			c.T1141C						PASS	.						133	108	116					11																	60183483		2203	4300	6503	SO:0001583	missense	84689	exon6			CAGTCTTCTAATC	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.1042T>C	11.37:g.60183483T>C	ENSP00000300187:p.Ser348Pro	230	0	0		214	162	0.757009	NM_001261828	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Missense_Mutation	SNP	ENST00000300187.6	37	CCDS31569.1	.	.	.	.	.	.	.	.	.	.	T	7.724	0.697733	0.15106	.	.	ENSG00000166928	ENST00000531787;ENST00000300187;ENST00000395005;ENST00000531783	T;T;T;T	0.32023	1.47;2.69;1.47;3.05	3.68	-1.06	0.10002	.	18.346600	0.00424	N	0.000065	T	0.15609	0.0376	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	0.12811	-1.0533	10	0.30078	T	0.28	-0.6079	3.9787	0.09486	0.2178:0.542:0.0:0.2402	.	331;348	Q96JA4-2;Q96JA4	.;M4A14_HUMAN	P	236;348;331;381	ENSP00000437222:S236P;ENSP00000300187:S348P;ENSP00000378453:S331P;ENSP00000433761:S381P	ENSP00000300187:S348P	S	+	1	0	MS4A14	59940059	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.134000	0.15932	-0.196000	0.10366	0.528000	0.53228	TCT	.	.	none		0.443	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2			C	60183483	T	C	60183483	3	2	27	1	0	0	0	0	1	0	0	0	9867	1783	62	3	1060	3	MS4A14	11	60183483	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	702269	60183483	74823033	612	11063											
C11orf66	220004	hgsc.bcm.edu	37	chr11	61252200	61252200	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacccaggagcacgggcctcAggccatcacggggctggagc	8	3	15	15	2	2	0	2	0	0	0	2	2	2	2	3	6	2	2	3	6	0	0	rs146231065	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:61252200A>G	ENST00000338608.2	+	5	547	c.422A>G	c.(421-423)cAg>cGg	p.Q141R	RP11-286N22.8_ENST00000544880.1_3'UTR|PPP1R32_ENST00000432063.2_Missense_Mutation_p.Q141R	NM_145017.2	NP_659454.2	Q7Z5V6	PPR32_HUMAN	protein phosphatase 1, regulatory subunit 32	141							phosphatase binding (GO:0019902)										CACGGGCCTCAGGCCATCACG	0.642													A|||	25	0.00499201	0.0	0.0	5008	,	,		17677	0.001		0.0089	False		,,,				2504	0.0153				p.Q141R		Atlas-SNP	.											.	.	.	.	0			c.A422G						PASS	.	A	ARG/GLN,ARG/GLN	11,4393	19.1+/-41.9	1,9,2192	32	29	30		422,422	5.3	0.5	11	dbSNP_134	30	63,8535	37.4+/-92.8	0,63,4236	yes	missense,missense	C11orf66	NM_001170753.1,NM_145017.2	43,43	1,72,6428	GG,GA,AA		0.7327,0.2498,0.5691	possibly-damaging,possibly-damaging	141/406,141/426	61252200	74,12928	2202	4299	6501	SO:0001583	missense	220004	exon5			GGCCTCAGGCCAT	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.422A>G	11.37:g.61252200A>G	ENSP00000344140:p.Gln141Arg	106	0	0		84	48	0.571429	NM_001170753	Q4G0P4|Q96M77	Missense_Mutation	SNP	ENST00000338608.2	37	CCDS8008.1	9	0.004120879120879121	0	0.0	0	0.0	0	0.0	9	0.011873350923482849	A	13.34	2.208254	0.39003	0.002498	0.007327	ENSG00000162148	ENST00000432063;ENST00000338608	T;T	0.45276	0.9;1.49	5.33	5.33	0.75918	.	0.548000	0.17786	N	0.162044	T	0.29491	0.0735	M	0.63428	1.95	0.29499	N	0.855042	B;B	0.32829	0.386;0.386	B;B	0.31101	0.124;0.124	T	0.35251	-0.9796	9	.	.	.	-12.7669	7.9832	0.30196	0.9082:0.0:0.0918:0.0	.	141;141	Q7Z5V6-2;Q7Z5V6	.;PPR32_HUMAN	R	141	ENSP00000391560:Q141R;ENSP00000344140:Q141R	.	Q	+	2	0	C11orf66	61008776	0.092000	0.21681	0.540000	0.28089	0.816000	0.46133	1.745000	0.38278	2.028000	0.59812	0.379000	0.24179	CAG	A|0.995;G|0.005	0.005	strong		0.642	PPP1R32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398621.1	NM_145017		G	61252200	A	G	61252200	3	3	27	1	0	0	0	0	1	0	0	0	1658	188	7	3	436	3	C11orf66	11	61252200	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	1068717	61252200	73754316	613	11064											
C11orf66	220004	hgsc.bcm.edu	37	chr11	61253841	61253841	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cctcccaggccagagtgtcaCcaagtcagacttcctcccca	9	7	7	18	0	2	2	2	0	0	2	5	2	5	2	7	1	0	0	7	1	1	1	rs11230707	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:61253841C>A	ENST00000338608.2	+	8	838	c.713C>A	c.(712-714)aCc>aAc	p.T238N	PPP1R32_ENST00000432063.2_Intron|PPP1R32_ENST00000366212.4_5'Flank|PPP1R32_ENST00000538185.1_5'Flank	NM_145017.2	NP_659454.2	Q7Z5V6	PPR32_HUMAN	protein phosphatase 1, regulatory subunit 32	238			T -> N (in dbSNP:rs11230707).				phosphatase binding (GO:0019902)										CAGAGTGTCACCAAGTCAGAC	0.637													C|||	206	0.0411342	0.1392	0.0058	5008	,	,		19286	0.001		0.008	False		,,,				2504	0.0092				p.T238N		Atlas-SNP	.											.	.	.	.	0			c.C713A						PASS	.	C	,ASN/THR	512,3892	233.3+/-246.5	36,440,1726	48	47	47		,713	3.4	1	11	dbSNP_120	47	62,8536	38.3+/-94.2	0,62,4237	yes	intron,missense	C11orf66	NM_001170753.1,NM_145017.2	,65	36,502,5963	AA,AC,CC		0.7211,11.6258,4.4147	,possibly-damaging	,238/426	61253841	574,12428	2202	4299	6501	SO:0001583	missense	220004	exon8			GTGTCACCAAGTC	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.713C>A	11.37:g.61253841C>A	ENSP00000344140:p.Thr238Asn	194	0	0		143	107	0.748252	NM_145017	Q4G0P4|Q96M77	Missense_Mutation	SNP	ENST00000338608.2	37	CCDS8008.1	89	0.04075091575091575	79	0.16056910569105692	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	C	17.86	3.492963	0.64074	0.116258	0.007211	ENSG00000162148	ENST00000338608;ENST00000542951;ENST00000535545	T;T;T	0.44881	1.39;0.91;1.3	4.37	3.39	0.38822	.	0.338132	0.23748	N	0.044945	T	0.00384	0.0012	M	0.73598	2.24	0.09310	P	0.9999999999999436	D	0.67145	0.996	D	0.66847	0.947	T	0.13899	-1.0492	9	0.56958	D	0.05	-0.1502	12.184	0.54227	0.0:0.8279:0.1721:0.0	rs11230707;rs11230707	238	Q7Z5V6	PPR32_HUMAN	N	238;18;5	ENSP00000344140:T238N;ENSP00000441053:T18N;ENSP00000437511:T5N	ENSP00000344140:T238N	T	+	2	0	C11orf66	61010417	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	1.646000	0.37249	2.153000	0.67306	0.650000	0.86243	ACC	C|0.955;A|0.045	0.045	strong		0.637	PPP1R32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398621.1	NM_145017		A	61253841	C	A	61253841	3	1	27	1	0	0	0	0	1	0	0	0	1658	507	18	4	739	4	C11orf66	11	61253841	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1641	61253841	73752675	614	11065											
C11orf66	220004	hgsc.bcm.edu	37	chr11	61254455	61254455	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagaacccagcagcgtgagTcaccagcagtttcagccact	11	6	9	15	1	2	2	2	1	0	1	2	2	2	2	4	0	5	3	4	0	1	1	rs77676987	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:61254455T>C	ENST00000338608.2	+	10	995	c.870T>C	c.(868-870)agT>agC	p.S290S	PPP1R32_ENST00000432063.2_Silent_p.S270S|PPP1R32_ENST00000366212.4_5'Flank|PPP1R32_ENST00000538185.1_5'Flank	NM_145017.2	NP_659454.2	Q7Z5V6	PPR32_HUMAN	protein phosphatase 1, regulatory subunit 32	290							phosphatase binding (GO:0019902)										GCAGCGTGAGTCACCAGCAGT	0.607													C|||	206	0.0411342	0.1392	0.0058	5008	,	,		19523	0.001		0.008	False		,,,				2504	0.0092				p.S290S		Atlas-SNP	.											.	.	.	.	0			c.T870C						PASS	.	C	,	514,3890	778.9+/-414.3	37,440,1725	213	213	213		810,870	2.9	0.1	11	dbSNP_131	213	62,8536	816.5+/-406.9	0,62,4237	no	coding-synonymous,coding-synonymous	C11orf66	NM_001170753.1,NM_145017.2	,	37,502,5962	CC,CT,TT		0.7211,11.6712,4.4301	,	270/406,290/426	61254455	576,12426	2202	4299	6501	SO:0001819	synonymous_variant	220004	exon10			CGTGAGTCACCAG	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.870T>C	11.37:g.61254455T>C		200	1	0.005		148	120	0.810811	NM_145017	Q4G0P4|Q96M77	Silent	SNP	ENST00000338608.2	37	CCDS8008.1																																																																																			T|0.960;C|0.040	0.040	strong		0.607	PPP1R32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398621.1	NM_145017		C	61254455	T	C	61254455	2	2	27	1	0	0	0	0	0	0	0	1	1658	1664	58	3		3	C11orf66	11	61254455	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	614	61254455	73752061	615	11066											
TUT1	64852	hgsc.bcm.edu	37	chr11	62343141	62343141	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctaccctgtcttccccacCgtcccctgcacatccctgct	4	12	4	21	1	2	0	0	0	2	0	5	0	5	0	7	0	3	2	7	0	1	3	rs369889181		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:62343141C>T	ENST00000476907.1	-	9	2741	c.2050G>A	c.(2050-2052)Ggt>Agt	p.G684S	MIR3654_ENST00000496634.2_Intron|TUT1_ENST00000308436.7_Missense_Mutation_p.G722S|EEF1G_ENST00000329251.4_5'Flank|EEF1G_ENST00000378019.3_5'Flank|EEF1G_ENST00000532986.1_5'Flank			Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6 snRNA-specific	684					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						TCTTCCCCACCGTCCCCTGCA	0.577																																					p.G722S		Atlas-SNP	.											.	TUT1	122	.	0			c.G2164A						PASS	.						455	441	446					11																	62343141		2202	4299	6501	SO:0001583	missense	64852	exon9			CCCCACCGTCCCC	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.2050G>A	11.37:g.62343141C>T	ENSP00000419607:p.Gly684Ser	152	0	0		133	111	0.834586	NM_022830	A1A527|A8K995|Q2NL65|Q7L583|Q9H6H7	Missense_Mutation	SNP	ENST00000476907.1	37		.	.	.	.	.	.	.	.	.	.	C	2.734	-0.263855	0.05754	.	.	ENSG00000149016	ENST00000308436;ENST00000476907	T;T	0.34859	1.34;1.35	5.63	2.54	0.30619	.	1.415740	0.03776	N	0.260632	T	0.24314	0.0589	N	0.14661	0.345	0.09310	N	1	B;B	0.12013	0.005;0.005	B;B	0.06405	0.001;0.002	T	0.18745	-1.0327	10	0.17369	T	0.5	-2.5756	10.007	0.41964	0.0:0.2926:0.5678:0.1396	.	684;722	Q9H6E5;F5H0R1	STPAP_HUMAN;.	S	722;684	ENSP00000308000:G722S;ENSP00000419607:G684S	ENSP00000308000:G722S	G	-	1	0	TUT1	62099717	0.003000	0.15002	0.003000	0.11579	0.011000	0.07611	1.233000	0.32648	0.723000	0.32274	-0.165000	0.13383	GGT	.	.	none		0.577	TUT1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000351319.2	NM_022830		T	62343141	C	T	62343141	3	4	27	1	0	0	0	0	1	0	0	0	16795	652	23	1	578	1	TUT1	11	62343141	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1088686	62343141	72663375	616	11067											
GANAB	23193	hgsc.bcm.edu	37	chr11	62397114	62397114	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggacaaaggggcgttccaTgcccccagagcgctgtctca	9	6	12	14	2	1	1	1	0	1	1	3	2	2	2	3	3	2	2	3	3	1	1	rs76572368	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:62397114T>C	ENST00000356638.3	-	15	1796	c.1780A>G	c.(1780-1782)Atg>Gtg	p.M594V	GANAB_ENST00000534779.1_Missense_Mutation_p.M502V|GANAB_ENST00000346178.4_Missense_Mutation_p.M616V|GANAB_ENST00000540933.1_Missense_Mutation_p.M497V	NM_198334.1	NP_938148.1	Q14697	GANAB_HUMAN	glucosidase, alpha; neutral AB	594					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)	GGGCGTTCCATGCCCCCAGAG	0.597													T|||	89	0.0177716	0.0008	0.0389	5008	,	,		20960	0.001		0.0547	False		,,,				2504	0.0051				p.M616V	Melanoma(23;1005 1074 15747 18937)	Atlas-SNP	.											.	GANAB	110	.	0			c.A1846G						PASS	.	T	VAL/MET,VAL/MET	28,4376	31.7+/-61.6	0,28,2174	37	37	37		1780,1846	-4.7	0.1	11	dbSNP_131	37	362,8236	115.7+/-175.5	10,342,3947	yes	missense,missense	GANAB	NM_198334.1,NM_198335.2	21,21	10,370,6121	CC,CT,TT		4.2103,0.6358,2.9995	benign,benign	594/945,616/967	62397114	390,12612	2202	4299	6501	SO:0001583	missense	23193	exon16			GTTCCATGCCCCC	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.1780A>G	11.37:g.62397114T>C	ENSP00000349053:p.Met594Val	193	0	0		151	29	0.192053	NM_198335	A6NC20|Q8WTS9|Q9P0X0	Missense_Mutation	SNP	ENST00000356638.3	37	CCDS8026.1	53	0.024267399267399268	0	0.0	14	0.03867403314917127	0	0.0	39	0.051451187335092345	T	7.943	0.743196	0.15642	0.006358	0.042103	ENSG00000089597	ENST00000346178;ENST00000356638;ENST00000534779;ENST00000540933	D;D;D;D	0.91068	-2.78;-2.78;-2.78;-2.78	5.31	-4.7	0.03288	Glycoside hydrolase, superfamily (1);	0.908173	0.09646	N	0.774318	T	0.25419	0.0618	N	0.00368	-1.59	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	0.53961	-0.8364	10	0.29301	T	0.29	0.5168	8.9385	0.35715	0.0:0.4806:0.1198:0.3996	.	480;502;594;616	B4DIW2;E9PKU7;Q14697;Q14697-2	.;.;GANAB_HUMAN;.	V	616;594;502;497	ENSP00000340466:M616V;ENSP00000349053:M594V;ENSP00000435306:M502V;ENSP00000442962:M497V	ENSP00000340466:M616V	M	-	1	0	GANAB	62153690	0.000000	0.05858	0.133000	0.22050	0.980000	0.70556	-1.352000	0.02619	-0.731000	0.04862	0.533000	0.62120	ATG	T|0.974;C|0.026	0.026	strong		0.597	GANAB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395689.1	NM_198334		C	62397114	T	C	62397114	3	2	27	1	0	0	0	0	1	0	0	0	6241	1464	51	3	1094	3	GANAB	11	62397114	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	53973	62397114	72609402	617	11068											
RTN3	10313	hgsc.bcm.edu	37	chr11	63486204	63486204	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctctttgctctgatgagcCatcttcagaaattatgactt	9	16	6	10	0	4	4	1	3	3	1	5	4	4	4	1	0	2	1	1	0	2	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:63486204C>T	ENST00000377819.5	+	3	384	c.230C>T	c.(229-231)cCa>cTa	p.P77L	RTN3_ENST00000354497.4_Intron|RTN3_ENST00000341307.2_Intron|RTN3_ENST00000356000.3_Intron|RTN3_ENST00000339997.4_Missense_Mutation_p.P58L|RTN3_ENST00000537981.1_Intron|RTN3_ENST00000540798.1_Intron	NM_001265589.1	NP_001252518.1	O95197	RTN3_HUMAN	reticulon 3	77					apoptotic process (GO:0006915)|endoplasmic reticulum tubular network organization (GO:0071786)|response to stress (GO:0006950)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	20						TCTGATGAGCCATCTTCAGAA	0.378																																					p.P77L		Atlas-SNP	.											.	RTN3	104	.	0			c.C230T						PASS	.						44	42	43					11																	63486204		2201	4298	6499	SO:0001583	missense	10313	exon3			ATGAGCCATCTTC	AF059524	CCDS8048.1, CCDS8049.1, CCDS8050.1, CCDS41664.1, CCDS58141.1, CCDS58142.1, CCDS58143.1	11q13	2011-01-14			ENSG00000133318	ENSG00000133318			10469	protein-coding gene	gene with protein product	"neuroendocrine-specific protein-like 2", "NSP-like protein II", "isoforme III", "ASY interacting protein", "homolog of ASY protein"	604249				10331947	Standard	NM_006054		Approved	NSPL2, NSPLII, ASYIP, HAP, RTN3-A1	uc001nxq.3	O95197		ENST00000377819.5:c.230C>T	11.37:g.63486204C>T	ENSP00000367050:p.Pro77Leu	67	0	0		42	12	0.285714	NM_001265589	B3KQS2|B7Z308|B7Z4M0|F5H774|Q147U9|Q496K2|Q53GN3|Q59EP0|Q5UEP2|Q6T930|Q7RTM7|Q7RTM8|Q7RTN3	Missense_Mutation	SNP	ENST00000377819.5	37	CCDS58141.1	.	.	.	.	.	.	.	.	.	.	C	13.42	2.231150	0.39399	.	.	ENSG00000133318	ENST00000377819;ENST00000339997	T;T	0.27104	1.82;1.69	5.84	3.81	0.43845	.	1.261160	0.05469	N	0.552739	T	0.22627	0.0546	L	0.27053	0.805	0.80722	D	1	B;P	0.36535	0.421;0.557	B;B	0.36418	0.04;0.224	T	0.03473	-1.1033	10	0.87932	D	0	-9.0E-4	10.0371	0.42135	0.1446:0.6966:0.1589:0.0	.	77;58	O95197;O95197-2	RTN3_HUMAN;.	L	77;58	ENSP00000367050:P77L;ENSP00000344106:P58L	ENSP00000344106:P58L	P	+	2	0	RTN3	63242780	0.997000	0.39634	1.000000	0.80357	0.466000	0.32739	1.436000	0.34980	1.412000	0.46977	0.591000	0.81541	CCA	.	.	none		0.378	RTN3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000397846.1	NM_006054		T	63486204	C	T	63486204	3	4	27	1	0	0	0	0	1	0	0	0	13742	594	21	2	240	2	RTN3	11	63486204	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1089090	63486204	71520312	618	11069											
PCNXL3	399909	hgsc.bcm.edu	37	chr11	65386029	65386029	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caaacggcagccacccctgcGaagacactctccacctggcc	10	4	8	19	2	1	1	0	0	1	1	2	2	1	1	6	2	3	1	6	2	2	0	rs538665832		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:65386029G>A	ENST00000355703.3	+	6	1735	c.1196G>A	c.(1195-1197)cGa>cAa	p.R399Q		NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	399						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						CCACCCCTGCGAAGACACTCT	0.657													G|||	1	0.000199681	0.0008	0.0	5008	,	,		14826	0.0		0.0	False		,,,				2504	0.0				p.R399Q		Atlas-SNP	.											.	PCNXL3	140	.	0			c.G1196A						PASS	.						17	19	18					11																	65386029		1990	4164	6154	SO:0001583	missense	399909	exon6			CCCTGCGAAGACA	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.1196G>A	11.37:g.65386029G>A	ENSP00000347931:p.Arg399Gln	47	0	0		53	16	0.301887	NM_032223	Q6MZN8	Missense_Mutation	SNP	ENST00000355703.3	37	CCDS44650.1	.	.	.	.	.	.	.	.	.	.	G	11.99	1.802379	0.31869	.	.	ENSG00000197136	ENST00000355703	T	0.01051	5.4	4.47	3.55	0.40652	.	0.000000	0.31381	N	0.007758	T	0.00967	0.0032	L	0.27053	0.805	0.30274	N	0.791956	B	0.13594	0.008	B	0.04013	0.001	T	0.32851	-0.9891	10	0.15499	T	0.54	.	8.6129	0.33813	0.1056:0.0:0.8944:0.0	.	399	Q9H6A9	PCX3_HUMAN	Q	399	ENSP00000347931:R399Q	ENSP00000347931:R399Q	R	+	2	0	PCNXL3	65142605	0.853000	0.29707	0.917000	0.36280	0.882000	0.50991	2.024000	0.41049	1.098000	0.41479	0.462000	0.41574	CGA	.	.	none		0.657	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223		A	65386029	G	A	65386029	3	1	27	1	0	0	0	0	1	0	0	0	11602	1058	37	1	1218	1	PCNXL3	11	65386029	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1899825	65386029	69620487	619	11070											
TMEM151A	256472	hgsc.bcm.edu	37	chr11	66062014	66062014	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccctgctccgatggctacctGtacatcccgctggccttcgt	4	11	9	17	3	0	0	0	0	0	0	3	1	2	0	5	2	3	4	5	2	2	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:66062014G>A	ENST00000327259.4	+	2	441	c.297G>A	c.(295-297)ctG>ctA	p.L99L		NM_153266.3	NP_694998.1	Q8N4L1	T151A_HUMAN	transmembrane protein 151A	99						integral component of membrane (GO:0016021)				central_nervous_system(1)|kidney(4)|lung(6)	11						ATGGCTACCTGTACATCCCGC	0.731																																					p.L99L		Atlas-SNP	.											.	TMEM151A	39	.	0			c.G297A						PASS	.						66	47	53					11																	66062014		2197	4291	6488	SO:0001819	synonymous_variant	256472	exon2			CTACCTGTACATC	BC033898	CCDS8133.1	11q13.2	2007-10-25	2007-10-25	2007-10-25	ENSG00000179292	ENSG00000179292			28497	protein-coding gene	gene with protein product			"transmembrane protein 151"	TMEM151		12477932	Standard	NM_153266		Approved	MGC33486	uc001ohl.3	Q8N4L1	OTTHUMG00000166920	ENST00000327259.4:c.297G>A	11.37:g.66062014G>A		52	0	0		68	38	0.558824	NM_153266	Q8ND14	Silent	SNP	ENST00000327259.4	37	CCDS8133.1																																																																																			.	.	none		0.731	TMEM151A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391897.1	NM_153266		A	66062014	G	A	66062014	2	1	27	1	0	0	0	0	0	0	0	1	16085	1364	48	2		2	TMEM151A	11	66062014	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	675985	66062014	68944502	620	11071											
CCDC87	55231	hgsc.bcm.edu	37	chr11	66358631	66358633	+	In_Frame_Del	DEL	TCT	TCT	-																															ccacaatctccacaggaaccTcttcttcatgcatttgaaag																								rs535066162		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:66358631_66358633delTCT	ENST00000333861.3	-	1	1921_1923	c.1854_1856delAGA	c.(1852-1857)gaagag>gag	p.618_619EE>E	CCS_ENST00000533244.1_5'Flank|CCS_ENST00000310190.4_5'Flank	NM_018219.2	NP_060689.2	Q9NVE4	CCD87_HUMAN	coiled-coil domain containing 87	618					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						CACAGGAACCTCTTCTTCATGCA	0.473																																					p.619_619del		Pindel,Atlas-Indel	.											.	CCDC87	83	.	0			c.1855_1857del						PASS	.			3,4259		0,3,2128						-1.9	0.2			112	18,8232		0,18,4107	no	coding	CCDC87	NM_018219.2		0,21,6235	A1A1,A1R,RR		0.2182,0.0704,0.1678				21,12491				SO:0001651	inframe_deletion	55231	exon1			.	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.1854_1856delAGA	11.37:g.66358634_66358636delTCT	ENSP00000328487:p.Glu619del	229	0	.		180	78	0.433	NM_018219	Q8NE76	In_Frame_Del	DEL	ENST00000333861.3	37	CCDS8145.1																																																																																			.	.	none		0.473	CCDC87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393825.1	NM_018219		-	66358633	TCT	-	66358631	7	5	27	1	0	1	0	1	0	0	0	0	2864	1551	54	0	697	0	CCDC87	11	66358631	In_Frame_Del	DEL	TCT	TCGA-G8-6909-01A-11D-2210-10	296617	66358631	68647885	621	11072											
SPTBN2	6712	hgsc.bcm.edu	37	chr11	66476403	66476403	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccgagatgagccggccctcGcggggcgtgtagaccttctg	5	8	15	13	5	1	3	0	1	1	2	3	4	2	3	4	3	1	1	4	3	1	2	rs74909073	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:66476403G>A	ENST00000533211.1	-	11	1492	c.1161C>T	c.(1159-1161)cgC>cgT	p.R387R	SPTBN2_ENST00000529997.1_Silent_p.R387R|SPTBN2_ENST00000309996.2_Silent_p.R387R			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	387					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						GCCGGCCCTCGCGGGGCGTGT	0.622													G|||	6	0.00119808	0.0	0.0	5008	,	,		15517	0.0		0.006	False		,,,				2504	0.0				p.R387R		Atlas-SNP	.											SPTBN2,colon,carcinoma,-2,3	SPTBN2	188	3	0			c.C1161T						PASS	.	G		3,4397	6.2+/-15.9	0,3,2197	66	66	66		1161	-10.3	0.6	11	dbSNP_134	66	36,8554	25.1+/-72.6	1,34,4260	no	coding-synonymous	SPTBN2	NM_006946.2		1,37,6457	AA,AG,GG		0.4191,0.0682,0.3002		387/2391	66476403	39,12951	2200	4295	6495	SO:0001819	synonymous_variant	6712	exon10			GCCCTCGCGGGGC	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.1161C>T	11.37:g.66476403G>A		96	0	0		95	28	0.294737	NM_006946	O14872|O14873	Silent	SNP	ENST00000533211.1	37	CCDS8150.1																																																																																			G|0.996;A|0.004	0.004	strong		0.622	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946		A	66476403	G	A	66476403	2	1	27	1	0	0	0	0	0	0	0	1	15135	1074	38	1		1	SPTBN2	11	66476403	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	117772	66476403	68530113	622	11073											
CLCF1	23529	hgsc.bcm.edu	37	chr11	67132804	67132804	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gggttcagtcccaggcagcgGctggggcagtgggtagccca	6	6	18	11	1	1	0	1	0	0	0	2	0	2	0	2	6	2	5	2	6	1	2	rs78755659	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:67132804G>A	ENST00000312438.7	-	3	678	c.481C>T	c.(481-483)Ccg>Tcg	p.P161S	AP003419.11_ENST00000543494.1_RNA|CLCF1_ENST00000533438.1_Missense_Mutation_p.P151S|RN7SKP239_ENST00000364814.1_RNA|CLCF1_ENST00000528474.1_Missense_Mutation_p.P151S	NM_013246.2	NP_037378.1	Q9UBD9	CLCF1_HUMAN	cardiotrophin-like cytokine factor 1	161					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)			CCAGGCAGCGGCTGGGGCAGT	0.657													g|||	64	0.0127796	0.0	0.0058	5008	,	,		17140	0.0		0.0179	False		,,,				2504	0.0429				p.P161S		Atlas-SNP	.											.	CLCF1	15	.	0			c.C481T						PASS	.		SER/PRO,SER/PRO	9,4389		0,9,2190	20	21	21		451,481	4.3	1	11	dbSNP_131	21	91,8483		1,89,4197	yes	missense,missense	CLCF1	NM_001166212.1,NM_013246.2	74,74	1,98,6387	AA,AG,GG		1.0613,0.2046,0.7709	benign,benign	151/216,161/226	67132804	100,12872	2199	4287	6486	SO:0001583	missense	23529	exon3			GCAGCGGCTGGGG	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.481C>T	11.37:g.67132804G>A	ENSP00000309338:p.Pro161Ser	86	0	0		81	20	0.246914	NM_013246	B4DNT4|Q6NZA4	Missense_Mutation	SNP	ENST00000312438.7	37	CCDS31617.1	18	0.008241758241758242	0	0.0	2	0.0055248618784530384	0	0.0	16	0.021108179419525065	g	11.26	1.587561	0.28268	0.002046	0.010613	ENSG00000175505	ENST00000312438;ENST00000533438;ENST00000528474	T;T;T	0.75260	-0.92;-0.92;-0.92	4.27	4.27	0.50696	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.000000	0.64402	D	0.000001	T	0.58409	0.2120	L	0.29908	0.895	0.30105	N	0.807084	P	0.45212	0.853	P	0.52109	0.69	T	0.68981	-0.5266	10	0.87932	D	0	-7.0213	13.0463	0.58928	0.0:0.1625:0.8375:0.0	.	161	Q9UBD9	CLCF1_HUMAN	S	161;151;151	ENSP00000309338:P161S;ENSP00000434122:P151S;ENSP00000432553:P151S	ENSP00000309338:P161S	P	-	1	0	CLCF1	66889380	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	3.795000	0.55499	2.320000	0.78422	0.556000	0.70494	CCG	G|0.992;A|0.008	0.008	strong		0.657	CLCF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395478.1	NM_013246		A	67132804	G	A	67132804	3	1	27	1	0	0	0	0	1	0	0	0	3463	1203	42	2	200	2	CLCF1	11	67132804	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	656401	67132804	67873712	623	11074											
LRP5	4041	hgsc.bcm.edu	37	chr11	68193582	68193582	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aagaccaccggggacaagcgGactcgcatccagggccgtgt	10	4	14	13	4	0	1	0	0	0	1	2	3	1	3	4	4	1	1	4	4	2	0	rs117289001	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:68193582G>A	ENST00000294304.7	+	16	3670	c.3564G>A	c.(3562-3564)cgG>cgA	p.R1188R		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	1188	Beta-propeller 4.				adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|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 apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GGGACAAGCGGACTCGCATCC	0.632													G|||	19	0.00379393	0.0	0.0086	5008	,	,		17781	0.0		0.0129	False		,,,				2504	0.0				p.R1188R		Atlas-SNP	.											.	LRP5	136	.	0			c.G3564A						PASS	.	G		11,4389	19.1+/-41.9	0,11,2189	99	86	90		3564	-1	0.8	11	dbSNP_132	90	110,8478	57.9+/-119.4	3,104,4187	no	coding-synonymous	LRP5	NM_002335.2		3,115,6376	AA,AG,GG		1.2809,0.25,0.9316		1188/1616	68193582	121,12867	2200	4294	6494	SO:0001819	synonymous_variant	4041	exon16			CAAGCGGACTCGC	AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"Low density lipoprotein receptors"	6697	protein-coding gene	gene with protein product		603506	"osteoporosis pseudoglioma syndrome", "exudative vitreoretinopathy 1"	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.3564G>A	11.37:g.68193582G>A		65	0	0		52	38	0.730769	NM_002335	Q96TD6|Q9UES7|Q9UP66	Silent	SNP	ENST00000294304.7	37	CCDS8181.1																																																																																			G|0.992;A|0.008	0.008	strong		0.632	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1	NM_002335		A	68193582	G	A	68193582	2	1	27	1	0	0	0	0	0	0	0	1	8969	1161	41	2		2	LRP5	11	68193582	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1060778	68193582	66812934	624	11075											
SAPS3	55291	hgsc.bcm.edu	37	chr11	68377475	68377475	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcgcccaggcctcccagcAgcagtcccgagcagaggtaa	9	3	13	16	3	0	1	0	0	0	1	2	2	2	1	4	3	3	4	4	3	1	1	rs79540432	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:68377475A>G	ENST00000393800.2	+	23	2808	c.2554A>G	c.(2554-2556)Agc>Ggc	p.S852G	PPP6R3_ENST00000529710.1_Missense_Mutation_p.S772G|PPP6R3_ENST00000524904.1_Missense_Mutation_p.S846G|PPP6R3_ENST00000393801.3_Missense_Mutation_p.S858G|PPP6R3_ENST00000534534.1_Missense_Mutation_p.S620G|PPP6R3_ENST00000265636.5_Missense_Mutation_p.S772G|PPP6R3_ENST00000265637.4_Missense_Mutation_p.S806G|PPP6R3_ENST00000524845.1_Missense_Mutation_p.S823G|PPP6R3_ENST00000393799.2_Missense_Mutation_p.S858G|PPP6R3_ENST00000527403.2_Missense_Mutation_p.S817G	NM_001164161.1|NM_001164162.1|NM_001164163.1	NP_001157633.1|NP_001157634.1|NP_001157635.1	Q5H9R7	PP6R3_HUMAN	protein phosphatase 6, regulatory subunit 3	852					regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			breast(2)|endometrium(6)|kidney(3)|large_intestine(10)|liver(2)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						GCCTCCCAGCAGCAGTCCCGA	0.622													A|||	19	0.00379393	0.0008	0.0086	5008	,	,		18142	0.0		0.0119	False		,,,				2504	0.0				p.S858G		Atlas-SNP	.											.	PPP6R3	159	.	0			c.A2572G						PASS	.	A	GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER	10,4390	17.9+/-39.9	0,10,2190	53	52	52		2572,2554,2536,2467,2314,2314	3.8	1	11	dbSNP_131	52	111,8477	58.3+/-119.8	3,105,4186	yes	missense,missense,missense,missense,missense,missense	PPP6R3	NM_001164160.1,NM_001164161.1,NM_001164162.1,NM_001164163.1,NM_001164164.1,NM_018312.4	56,56,56,56,56,56	3,115,6376	GG,GA,AA		1.2925,0.2273,0.9316	benign,benign,benign,benign,benign,benign	858/880,852/874,846/868,823/845,772/792,772/794	68377475	121,12867	2200	4294	6494	SO:0001583	missense	55291	exon24			CCCAGCAGCAGTC	AF264779	CCDS8182.1, CCDS53671.1, CCDS53672.1, CCDS53673.1, CCDS53674.1, CCDS53675.1	11q13	2012-04-17	2010-06-28	2010-06-28	ENSG00000110075	ENSG00000110075		"Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"	1173	protein-coding gene	gene with protein product	"sporulation-induced transcript 4-associated protein"	610879	"chromosome 11 open reading frame 23", "SAPS domain family, member 3"	C11orf23, SAPS3		11401438, 16769727	Standard	NM_018312		Approved	SAPLa, DKFZp781E2374, DKFZp781O2362, DKFZp781E17107, SAP190, SAPL, PP6R3, FLJ11058, FLJ43065, KIAA1558, MGC125711, MGC125712	uc001onv.3	Q5H9R7		ENST00000393800.2:c.2554A>G	11.37:g.68377475A>G	ENSP00000377389:p.Ser852Gly	57	0	0		58	41	0.706897	NM_001164160	Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3	Missense_Mutation	SNP	ENST00000393800.2	37	CCDS53672.1	12	0.005494505494505495	0	0.0	4	0.011049723756906077	0	0.0	8	0.010554089709762533	A	11.52	1.663897	0.29515	0.002273	0.012925	ENSG00000110075	ENST00000393799;ENST00000393800;ENST00000534534;ENST00000524845;ENST00000265637;ENST00000524904;ENST00000393801;ENST00000265636;ENST00000529710;ENST00000527403;ENST00000534190	T;T;T;T;T;T;T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58	4.96	3.76	0.43208	.	0.236035	0.35207	N	0.003362	T	0.38241	0.1033	L	0.47716	1.5	0.38584	D	0.950242	B;B;B;B;B;B;B;B	0.19200	0.031;0.034;0.0;0.0;0.001;0.0;0.0;0.0	B;B;B;B;B;B;B;B	0.24006	0.05;0.011;0.002;0.001;0.004;0.002;0.003;0.001	T	0.48681	-0.9014	10	0.44086	T	0.13	.	12.9887	0.58606	0.8559:0.1441:0.0:0.0	.	535;620;772;823;846;852;858;772	B4DYU6;E9PQP7;Q5H9R7-3;Q5H9R7-6;Q5H9R7-2;Q5H9R7;Q5H9R7-5;Q5H9R7-4	.;.;.;.;.;PP6R3_HUMAN;.;.	G	858;852;620;823;806;846;858;772;772;817;559	ENSP00000377388:S858G;ENSP00000377389:S852G;ENSP00000434429:S620G;ENSP00000431415:S823G;ENSP00000265637:S806G;ENSP00000433058:S846G;ENSP00000377390:S858G;ENSP00000265636:S772G;ENSP00000437329:S772G;ENSP00000433565:S817G;ENSP00000436209:S559G	ENSP00000265636:S772G	S	+	1	0	PPP6R3	68134051	1.000000	0.71417	0.997000	0.53966	0.357000	0.29423	4.276000	0.58933	1.861000	0.53984	0.459000	0.35465	AGC	A|0.992;G|0.008	0.008	strong		0.622	PPP6R3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395275.1	NM_018312		G	68377475	A	G	68377475	3	3	27	1	0	0	0	0	1	0	0	0	13853	188	7	3	2658	3	SAPS3	11	68377475	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	183893	68377475	66629041	625	11076											
USP35	57558	hgsc.bcm.edu	37	chr11	77911745	77911745	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctctctggtcaaggaggactCgaactcggggaccagctgcc	8	7	13	13	2	2	0	1	0	1	0	5	4	2	3	2	5	3	1	2	5	2	0	rs147270370	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:77911745C>T	ENST00000529308.1	+	6	1349	c.1088C>T	c.(1087-1089)tCg>tTg	p.S363L	USP35_ENST00000530535.1_Intron|USP35_ENST00000530267.1_Intron|USP35_ENST00000526425.1_Missense_Mutation_p.S94L|USP35_ENST00000441408.2_5'UTR	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	363					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)			AAGGAGGACTCGAACTCGGGG	0.647													C|||	19	0.00379393	0.0015	0.0014	5008	,	,		17401	0.0		0.008	False		,,,				2504	0.0082				p.S363L		Atlas-SNP	.											USP35_ENST00000263311,rectum,carcinoma,-1,2	USP35	179	2	0			c.C1088T						PASS	.	C	LEU/SER	5,3907		0,5,1951	46	52	50		1088	4.7	1	11	dbSNP_134	50	46,8202		0,46,4078	yes	missense	USP35	NM_020798.2	145	0,51,6029	TT,TC,CC		0.5577,0.1278,0.4194	benign	363/1019	77911745	51,12109	1956	4124	6080	SO:0001583	missense	57558	exon6			AGGACTCGAACTC	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.1088C>T	11.37:g.77911745C>T	ENSP00000431876:p.Ser363Leu	109	0	0		100	20	0.2	NM_020798		Missense_Mutation	SNP	ENST00000529308.1	37	CCDS41693.1	6	0.0027472527472527475	1	0.0020325203252032522	0	0.0	0	0.0	5	0.006596306068601583	C	13.79	2.343705	0.41498	0.001278	0.005577	ENSG00000118369	ENST00000528910;ENST00000529308;ENST00000526425	T;T;T	0.68181	-0.24;-0.31;3.37	4.73	4.73	0.59995	Armadillo-like helical (1);	0.000000	0.52532	D	0.000071	T	0.40448	0.1117	N	0.19112	0.55	0.80722	D	1	B	0.33739	0.422	B	0.22753	0.041	T	0.43925	-0.9361	10	0.18276	T	0.48	-15.0401	17.9135	0.88942	0.0:1.0:0.0:0.0	.	363	Q9P2H5	UBP35_HUMAN	L	119;363;94	ENSP00000436001:S119L;ENSP00000431876:S363L;ENSP00000434942:S94L	ENSP00000434942:S94L	S	+	2	0	USP35	77589393	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.484000	0.66844	2.461000	0.83175	0.561000	0.74099	TCG	C|0.996;T|0.004	0.004	strong		0.647	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	XM_290527		T	77911745	C	T	77911745	3	4	27	1	0	0	0	0	1	0	0	0	17081	893	31	1	1106	1	USP35	11	77911745	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	9534270	77911745	57094771	626	11077											
CCDC89	220388	hgsc.bcm.edu	37	chr11	85396746	85396746	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcttgatgttctcactcttgTattcatccttgaagcggagc	7	15	9	10	1	3	2	2	2	2	0	5	3	4	3	1	1	2	3	1	1	2	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:85396746T>C	ENST00000316398.3	-	1	574	c.428A>G	c.(427-429)tAc>tGc	p.Y143C	CREBZF_ENST00000531515.1_5'Flank|CREBZF_ENST00000534224.1_5'Flank	NM_152723.1	NP_689936.1	Q8N998	CCD89_HUMAN	coiled-coil domain containing 89	143						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)				CTCACTCTTGTATTCATCCTT	0.517																																					p.Y143C		Atlas-SNP	.											.	CCDC89	45	.	0			c.A428G						PASS	.						100	90	93					11																	85396746		2203	4299	6502	SO:0001583	missense	220388	exon1			CTCTTGTATTCAT	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.428A>G	11.37:g.85396746T>C	ENSP00000320649:p.Tyr143Cys	119	0	0		102	85	0.833333	NM_152723		Missense_Mutation	SNP	ENST00000316398.3	37	CCDS8270.1	.	.	.	.	.	.	.	.	.	.	t	13.79	2.340823	0.41498	.	.	ENSG00000179071	ENST00000316398	.	.	.	5.53	5.53	0.82687	.	0.343021	0.33110	N	0.005272	T	0.49779	0.1577	L	0.29908	0.895	0.37455	D	0.914985	D	0.54964	0.969	P	0.49528	0.614	T	0.54077	-0.8347	8	.	.	.	-8.5222	15.664	0.77213	0.0:0.0:0.0:1.0	.	143	Q8N998	CCD89_HUMAN	C	143	.	.	Y	-	2	0	CCDC89	85074394	1.000000	0.71417	0.950000	0.38849	0.578000	0.36192	5.298000	0.65710	2.104000	0.64026	0.529000	0.55759	TAC	.	.	none		0.517	CCDC89-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392182.1	NM_152723		C	85396746	T	C	85396746	3	2	27	1	0	0	0	0	1	0	0	0	2868	1638	57	3	700	3	CCDC89	11	85396746	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	7485001	85396746	49609770	627	11078											
FAT3	120114	hgsc.bcm.edu	37	chr11	92088524	92088524	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggagagatccagtactccatCagggatggcagtggtcttgg	9	9	15	8	0	2	1	1	0	1	1	4	4	4	3	2	5	1	2	2	5	1	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:92088524C>T	ENST00000298047.6	+	1	3263	c.3246C>T	c.(3244-3246)atC>atT	p.I1082I	FAT3_ENST00000541502.1_Silent_p.I1082I|FAT3_ENST00000525166.1_Silent_p.I932I|FAT3_ENST00000409404.2_Silent_p.I1082I			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	1082	Cadherin 10. {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)				AGTACTCCATCAGGGATGGCA	0.463										TCGA Ovarian(4;0.039)																											p.I1082I		Atlas-SNP	.											.	FAT3	1822	.	0			c.C3246T						PASS	.						108	105	106					11																	92088524		2055	4207	6262	SO:0001819	synonymous_variant	120114	exon1			CTCCATCAGGGAT	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.3246C>T	11.37:g.92088524C>T		114	0	0		102	32	0.313726	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				.	.	none		0.463	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		T	92088524	C	T	92088524	2	4	27	1	0	0	0	0	0	0	0	1	5699	816	29	2		2	FAT3	11	92088524	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	6691778	92088524	42917992	628	11079											
CCDC67	159989	hgsc.bcm.edu	37	chr11	93141575	93141575	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctatcaaagccaaataaaagTggaacaaaatgaagagaggt	21	6	9	5	0	1	2	1	1	0	1	1	4	1	3	1	2	2	0	1	2	9	2	rs371785641		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:93141575T>C	ENST00000298050.3	+	12	1605	c.1505T>C	c.(1504-1506)gTg>gCg	p.V502A	AP004242.1_ENST00000408638.1_RNA|CCDC67_ENST00000525646.1_Missense_Mutation_p.V244A	NM_181645.3	NP_857596.2	Q05D60	DEUP1_HUMAN	coiled-coil domain containing 67	502					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)				CAAATAAAAGTGGAACAAAAT	0.294																																					p.V502A		Atlas-SNP	.											CCDC67,NS,carcinoma,+1,1	CCDC67	57	1	0			c.T1505C						scavenged	.	T	ALA/VAL	0,3600		0,0,1800	38	34	35		1505	2.2	0.3	11		35	1,8127		0,1,4063	no	missense	CCDC67	NM_181645.3	64	0,1,5863	CC,CT,TT		0.0123,0.0,0.0085	benign	502/605	93141575	1,11727	1800	4064	5864	SO:0001583	missense	159989	exon12			TAAAAGTGGAACA	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.1505T>C	11.37:g.93141575T>C	ENSP00000298050:p.Val502Ala	110	1	0.00909091		84	19	0.22619	NM_181645	Q8NEF1|Q96LL7	Missense_Mutation	SNP	ENST00000298050.3	37	CCDS44707.1	.	.	.	.	.	.	.	.	.	.	T	14.27	2.485540	0.44147	0.0	1.23E-4	ENSG00000165325	ENST00000534747;ENST00000298050;ENST00000525646	T;T;T	0.16897	2.31;2.31;2.31	5.86	2.18	0.27775	.	0.473884	0.25948	N	0.027261	T	0.07324	0.0185	N	0.08118	0	0.20196	N	0.999929	B;B	0.17465	0.009;0.022	B;B	0.16289	0.009;0.015	T	0.28554	-1.0040	10	0.41790	T	0.15	.	4.9184	0.13858	0.2853:0.0776:0.0:0.6372	.	502;494	Q05D60;Q6ZRU6	CCD67_HUMAN;.	A	502;502;244	ENSP00000432111:V502A;ENSP00000298050:V502A;ENSP00000435079:V244A	ENSP00000298050:V502A	V	+	2	0	CCDC67	92781223	0.992000	0.36948	0.254000	0.24359	0.935000	0.57460	0.381000	0.20619	0.112000	0.17975	0.533000	0.62120	GTG	.	.	weak		0.294	CCDC67-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_181645		C	93141575	T	C	93141575	3	2	27	1	0	0	0	0	1	0	0	0	2841	1696	59	3	1547	3	CCDC67	11	93141575	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	1053051	93141575	41864941	629	11080											
KDM4D	55693	hgsc.bcm.edu	37	chr11	94731905	94731905	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	gacgtggtcgtggtcgccctCctcagaaactgagagctcag	8	8	13	12	3	2	2	2	1	0	2	5	4	3	2	2	2	2	1	2	2	1	0	rs144086807	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:94731905C>G	ENST00000335080.5	+	3	2201	c.1369C>G	c.(1369-1371)Cct>Gct	p.P457A	KDM4D_ENST00000536741.1_Missense_Mutation_p.P457A	NM_018039.2	NP_060509.2	Q6B0I6	KDM4D_HUMAN	lysine (K)-specific demethylase 4D	457					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						TGGTCGCCCTCCTCAGAAACT	0.597													.|||	5	0.000998403	0.0	0.0	5008	,	,		19936	0.0		0.003	False		,,,				2504	0.002				p.P457A		Atlas-SNP	.											.	KDM4D	58	.	0			c.C1369G						PASS	.	C	ALA/PRO	4,4398	8.1+/-20.4	0,4,2197	52	54	53		1369	1.6	0	11	dbSNP_134	53	46,8550	29.0+/-79.6	0,46,4252	yes	missense	KDM4D	NM_018039.2	27	0,50,6449	GG,GC,CC		0.5351,0.0909,0.3847	possibly-damaging	457/524	94731905	50,12948	2201	4298	6499	SO:0001583	missense	55693	exon3			CGCCCTCCTCAGA	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.1369C>G	11.37:g.94731905C>G	ENSP00000334181:p.Pro457Ala	80	0	0		59	48	0.813559	NM_018039	B3KPC4|Q0VF39|Q9NT41|Q9NW76	Missense_Mutation	SNP	ENST00000335080.5	37	CCDS8302.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	10.19	1.281211	0.23392	9.09E-4	0.005351	ENSG00000186280	ENST00000335080	T	0.28666	1.6	3.52	1.58	0.23477	.	0.179179	0.35555	U	0.003127	T	0.11281	0.0275	L	0.32530	0.975	0.09310	N	1	P	0.48407	0.91	B	0.38106	0.265	T	0.13335	-1.0513	10	0.22109	T	0.4	-5.8535	4.7061	0.12849	0.0:0.6512:0.2251:0.1236	.	457	Q6B0I6	KDM4D_HUMAN	A	457	ENSP00000334181:P457A	ENSP00000334181:P457A	P	+	1	0	KDM4D	94371553	0.023000	0.18921	0.001000	0.08648	0.002000	0.02628	0.744000	0.26245	0.462000	0.27095	0.655000	0.94253	CCT	C|0.997;G|0.003	0.003	strong		0.597	KDM4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396558.2	NM_018039		G	94731905	C	G	94731905	3	3	27	1	0	0	0	0	1	0	0	0	8140	855	30	4	1371	4	KDM4D	11	94731905	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1590330	94731905	40274611	630	11081											
MMP13	4322	hgsc.bcm.edu	37	chr11	102825227	102825227	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgatgtcagcaatgccatcGtgaagtctggtaaaattcag	13	11	10	7	1	3	2	2	2	1	0	4	2	3	2	1	1	2	2	1	1	4	2	rs368161332		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:102825227G>A	ENST00000260302.3	-	3	499	c.471C>T	c.(469-471)caC>caT	p.H157H	MMP13_ENST00000340273.4_Silent_p.H157H	NM_002427.3	NP_002418.1	P45452	MMP13_HUMAN	matrix metallopeptidase 13 (collagenase 3)	157					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)	CAATGCCATCGTGAAGTCTGG	0.343																																					p.H157H		Atlas-SNP	.											MMP13,NS,malignant_melanoma,-2,1	MMP13	75	1	0			c.C471T						PASS	.	G		0,4404		0,0,2202	64	64	64		471	-2.8	0	11		64	2,8596	2.2+/-6.3	0,2,4297	no	coding-synonymous	MMP13	NM_002427.3		0,2,6499	AA,AG,GG		0.0233,0.0,0.0154		157/472	102825227	2,13000	2202	4299	6501	SO:0001819	synonymous_variant	4322	exon3			GCCATCGTGAAGT	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.471C>T	11.37:g.102825227G>A		137	0	0		108	70	0.648148	NM_002427	A8K846|B2RCZ3|Q6NWN6	Silent	SNP	ENST00000260302.3	37	CCDS8324.1																																																																																			.	.	weak		0.343	MMP13-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386648.1	NM_002427		A	102825227	G	A	102825227	2	1	27	1	0	0	0	0	0	0	0	1	9661	1136	40	1		1	MMP13	11	102825227	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	8093322	102825227	32181289	631	11082											
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103116000	103116000	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatagtaactttatcacagcTcttgaattagcagtacgttt	12	15	7	7	1	2	1	1	1	1	0	2	2	2	1	0	0	4	5	0	0	6	8	rs192003811	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:103116000T>C	ENST00000375735.2	+	65	10083	c.9939T>C	c.(9937-9939)gcT>gcC	p.A3313A	DYNC2H1_ENST00000398093.3_Silent_p.A3320A|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	3313	AAA 5. {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)		TTATCACAGCTCTTGAATTAG	0.303													T|||	8	0.00159744	0.0008	0.0029	5008	,	,		15868	0.0		0.004	False		,,,				2504	0.001				p.A3320A		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T9960C						PASS	.	T	,	3,3549		0,3,1773	58	51	54		9960,9939	5.6	1	11		54	40,8010		0,40,3985	no	coding-synonymous,coding-synonymous	DYNC2H1	NM_001080463.1,NM_001377.2	,	0,43,5758	CC,CT,TT		0.4969,0.0845,0.3706	,	3320/4315,3313/4308	103116000	43,11559	1776	4025	5801	SO:0001819	synonymous_variant	79659	exon66			CACAGCTCTTGAA	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.9939T>C	11.37:g.103116000T>C		62	0	0		51	8	0.156863	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Silent	SNP	ENST00000375735.2	37	CCDS53701.1																																																																																			T|0.997;C|0.003	0.003	strong		0.303	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		C	103116000	T	C	103116000	2	2	27	1	0	0	0	0	0	0	0	1	4848	1538	54	3		3	DYNC2H1	11	103116000	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	290773	103116000	31890516	632	11083											
CWF19L2	143884	hgsc.bcm.edu	37	chr11	107224415	107224415	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctcagctgctttggagacAaacatgtcatccagggtgta	10	11	10	10	0	2	1	2	0	1	1	4	2	3	1	1	2	3	3	1	2	2	2	rs35543671	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:107224415A>G	ENST00000282251.5	-	13	1947	c.1920T>C	c.(1918-1920)ttT>ttC	p.F640F	CWF19L2_ENST00000433523.1_Silent_p.F640F	NM_152434.2	NP_689647.2	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control (S. pombe)	640							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)		CTTTGGAGACAAACATGTCAT	0.393													A|||	67	0.0133786	0.0023	0.0331	5008	,	,		17536	0.002		0.0278	False		,,,				2504	0.0112				p.F640F		Atlas-SNP	.											.	CWF19L2	135	.	0			c.T1920C						PASS	.	A		17,4385	25.3+/-52.1	0,17,2184	99	97	98		1920	2.4	1	11	dbSNP_126	98	217,8379	89.4+/-151.6	3,211,4084	no	coding-synonymous	CWF19L2	NM_152434.2		3,228,6268	GG,GA,AA		2.5244,0.3862,1.8003		640/895	107224415	234,12764	2201	4298	6499	SO:0001819	synonymous_variant	143884	exon13			GGAGACAAACATG	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.1920T>C	11.37:g.107224415A>G		90	0	0		100	27	0.27	NM_152434	A4FU66|A4FU67|A4FU68|Q6PHW1|Q96MI1	Silent	SNP	ENST00000282251.5	37	CCDS8336.2																																																																																			A|0.983;G|0.017	0.017	strong		0.393	CWF19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328825.2	NM_152434		G	107224415	A	G	107224415	2	3	27	1	0	0	0	0	0	0	0	1	4074	127	5	3		3	CWF19L2	11	107224415	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	4108415	107224415	27782101	633	11084											
ATM	472	hgsc.bcm.edu	37	chr11	108175462	108175462	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttcatgatattttactccaaGatacaaatgaatcatggaga	16	13	6	6	0	2	4	2	2	0	2	3	5	3	4	1	1	2	0	1	1	6	5	rs1801516	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:108175462G>A	ENST00000452508.2	+	38	5746	c.5557G>A	c.(5557-5559)Gat>Aat	p.D1853N	ATM_ENST00000278616.4_Missense_Mutation_p.D1853N			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1853			D -> N (common polymorphism; dbSNP:rs1801516). {ECO:0000269|PubMed:10397742, ECO:0000269|PubMed:10425038, ECO:0000269|PubMed:10534763, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9711876, ECO:0000269|PubMed:9887333}.|D -> V (might contribute to B-cell chronic lymphocytic leukemia; dbSNP:rs1801673). {ECO:0000269|PubMed:10397742, ECO:0000269|PubMed:10817650, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9872980, ECO:0000269|PubMed:9887333}.		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.D1853N(10)		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)	TTTACTCCAAGATACAAATGA	0.388			"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)			G|||	335	0.066893	0.0083	0.0965	5008	,	,		16727	0.0159		0.162	False		,,,				2504	0.0798				p.D1853N		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	ATM_ENST00000278616,colon,carcinoma,-1,17	ATM	1657	17	10	Substitution - Missense(10)	breast(9)|skin(1)	c.G5557A	GRCh37	CM077896	ATM	M	rs1801516	PASS	.	G	ASN/ASP	125,4277	92.5+/-131.2	3,119,2079	75	72	73	http://www.ncbi.nlm.nih.gov/pubmed?term	5557	5.5	1	11	dbSNP_89	73	1205,7391	241.8+/-272.0	99,1007,3192	yes	missense	ATM	NM_000051.3	23	102,1126,5271	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	14.0181,2.8396,10.2323	possibly-damaging	1853/3057	108175462	1330,11668	2201	4298	6499	SO:0001583	missense	472	exon37	Familial Cancer Database	AT, Louis-Bar syndrome	CTCCAAGATACAA	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.5557G>A	11.37:g.108175462G>A	ENSP00000388058:p.Asp1853Asn	126	0	0		91	15	0.164835	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	172	0.07875457875457875	5	0.01016260162601626	40	0.11049723756906077	7	0.012237762237762238	120	0.158311345646438	G	17.18	3.324076	0.60634	0.028396	0.140181	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.73152	-0.72;-0.72	5.52	5.52	0.82312	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.00580	0.0019	L	0.61036	1.89	0.19945	P	0.9999491241	B	0.20368	0.044	B	0.16289	0.015	T	0.10730	-1.0617	9	0.33940	T	0.23	.	19.8041	0.96521	0.0:0.0:1.0:0.0	rs1801516;rs17503060;rs52821794;rs60879649;rs1801516	1853	Q13315	ATM_HUMAN	N	1853	ENSP00000278616:D1853N;ENSP00000388058:D1853N	ENSP00000278616:D1853N	D	+	1	0	ATM	107680672	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.342000	0.72982	2.748000	0.94277	0.591000	0.81541	GAT	G|0.910;A|0.090	0.090	strong		0.388	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		A	108175462	G	A	108175462	3	1	27	1	0	0	0	0	1	0	0	0	1109	942	33	2	5699	2	ATM	11	108175462	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	951047	108175462	26831054	634	11085											
CEP164	22897	hgsc.bcm.edu	37	chr11	117214881	117214881	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cacctctgcctctccttgcaGaaattcttgaatttgcccgg	7	13	7	14	1	3	2	0	1	3	1	4	2	3	2	4	1	3	1	4	1	2	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:117214881G>A	ENST00000278935.3	+	4	229		c.e4-1			NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa						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)		TCTCCTTGCAGAAATTCTTGA	0.453																																					.		Atlas-SNP	.											CEP164,colon,carcinoma,-2,1	CEP164	121	1	0			c.83-1G>A						PASS	.						33	30	31					11																	117214881		2201	4296	6497	SO:0001630	splice_region_variant	22897	exon3			CTTGCAGAAATTC	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.83-1G>A	11.37:g.117214881G>A		183	0	0		157	28	0.178344	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Splice_Site	SNP	ENST00000278935.3	37	CCDS31683.1	.	.	.	.	.	.	.	.	.	.	G	15.58	2.874286	0.51695	.	.	ENSG00000110274	ENST00000525734;ENST00000278935;ENST00000527609;ENST00000533570;ENST00000529538	.	.	.	4.62	4.62	0.57501	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.4489	0.87586	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CEP164	116720091	1.000000	0.71417	1.000000	0.80357	0.398000	0.30690	9.156000	0.94705	2.274000	0.75844	0.563000	0.77884	.	.	.	none		0.453	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956	Intron	A	117214881	G	A	117214881	5	1	27	1	0	0	0	0	0	0	1	0	3251	956	33	2	88	2	CEP164	11	117214881	Splice_Site	SNP	G	TCGA-G8-6909-01A-11D-2210-10	9039419	117214881	17791635	635	11086											
IL10RA	3587	hgsc.bcm.edu	37	chr11	117869642	117869642	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ttcctcctccctgaccctcaCccccaggctgacagaacgct	7	8	6	20	1	1	3	1	2	0	1	4	3	4	3	6	1	1	2	6	1	1	1	rs369418818		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:117869642C>A	ENST00000227752.3	+	7	1143	c.1023C>A	c.(1021-1023)caC>caA	p.H341Q	IL10RA_ENST00000541785.1_Missense_Mutation_p.H321Q|IL10RA_ENST00000545409.1_Missense_Mutation_p.H192Q|IL10RA_ENST00000533700.1_3'UTR	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	341					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)		CTGACCCTCACCCCCAGGCTG	0.617																																					p.H341Q		Atlas-SNP	.											.	IL10RA	46	.	0			c.C1023A						PASS	.	C	GLN/HIS	0,4400		0,0,2200	59	54	56		1023	-2.5	0	11		56	4,8588	3.0+/-9.4	0,4,4292	no	missense	IL10RA	NM_001558.3	24	0,4,6492	AA,AC,CC		0.0466,0.0,0.0308	benign	341/579	117869642	4,12988	2200	4296	6496	SO:0001583	missense	3587	exon7			CCCTCACCCCCAG	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.1023C>A	11.37:g.117869642C>A	ENSP00000227752:p.His341Gln	47	0	0		53	43	0.811321	NM_001558	A8K6I0|B0YJ27	Missense_Mutation	SNP	ENST00000227752.3	37	CCDS8388.1	.	.	.	.	.	.	.	.	.	.	C	10.44	1.350897	0.24512	0.0	4.66E-4	ENSG00000110324	ENST00000227752;ENST00000541785;ENST00000545409;ENST00000536858	T;T;T	0.21031	2.03;2.03;2.03	5.66	-2.55	0.06288	.	1.951570	0.01920	N	0.040455	T	0.17195	0.0413	L	0.56769	1.78	0.09310	N	1	B;B	0.16802	0.019;0.011	B;B	0.15484	0.013;0.006	T	0.13926	-1.0491	10	0.12430	T	0.62	-2.9137	1.8617	0.03190	0.1108:0.3559:0.2405:0.2928	.	321;341	F5GYV8;Q13651	.;I10R1_HUMAN	Q	341;321;192;321	ENSP00000227752:H341Q;ENSP00000441397:H321Q;ENSP00000443019:H192Q	ENSP00000227752:H341Q	H	+	3	2	IL10RA	117374852	0.000000	0.05858	0.001000	0.08648	0.014000	0.08584	-0.122000	0.10627	0.058000	0.16222	0.563000	0.77884	CAC	.	.	weak		0.617	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1			A	117869642	C	A	117869642	3	1	27	1	0	0	0	0	1	0	0	0	7629	506	18	4	1049	4	IL10RA	11	117869642	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	654761	117869642	17136874	636	11087											
TMPRSS4	56649	hgsc.bcm.edu	37	chr11	117979606	117979606	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccctggtctccctgcactGtcttggtgagtacccccaat	5	12	8	16	0	2	1	0	1	2	0	4	1	3	1	4	2	2	2	4	2	2	2	rs45441097	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:117979606G>C	ENST00000437212.3	+	7	792	c.578G>C	c.(577-579)tGt>tCt	p.C193S	TMPRSS4_ENST00000522824.1_Missense_Mutation_p.C188S|TMPRSS4_ENST00000523251.1_Missense_Mutation_p.C153S|TMPRSS4_ENST00000522307.1_Missense_Mutation_p.C46S|TMPRSS4_ENST00000534111.1_Missense_Mutation_p.C191S			Q9NRS4	TMPS4_HUMAN	transmembrane protease, serine 4	193	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)		TCCCTGCACTGTCTTGGTGAG	0.567													G|||	13	0.00259585	0.0	0.0086	5008	,	,		20409	0.0		0.006	False		,,,				2504	0.001				p.C193S		Atlas-SNP	.											.	TMPRSS4	46	.	0			c.G578C						PASS	.	G	SER/CYS,SER/CYS,SER/CYS,SER/CYS	4,4396	8.1+/-20.4	0,4,2196	108	92	97		563,572,458,578	4.9	1	11	dbSNP_127	97	44,8548	28.5+/-78.6	0,44,4252	yes	missense,missense,missense,missense	TMPRSS4	NM_001083947.1,NM_001173551.1,NM_001173552.1,NM_019894.3	112,112,112,112	0,48,6448	CC,CG,GG		0.5121,0.0909,0.3695	probably-damaging,probably-damaging,probably-damaging,probably-damaging	188/433,191/436,153/398,193/438	117979606	48,12944	2200	4296	6496	SO:0001583	missense	56649	exon7			TGCACTGTCTTGG	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.578G>C	11.37:g.117979606G>C	ENSP00000416037:p.Cys193Ser	53	0	0		63	42	0.666667	NM_019894	A8MU84|B0YJB0|B7Z8C5|E7ERX8|Q5XKQ6|Q6UX37|Q9NZA5	Missense_Mutation	SNP	ENST00000437212.3	37	CCDS31684.1	7	0.003205128205128205	0	0.0	3	0.008287292817679558	0	0.0	4	0.005277044854881266	G	20.7	4.036391	0.75617	9.09E-4	0.005121	ENSG00000137648	ENST00000534111;ENST00000522307;ENST00000523251;ENST00000437212;ENST00000522824;ENST00000522151	D;T;D;D;D;D	0.98926	-5.24;0.26;-5.24;-5.24;-5.24;-5.24	4.93	4.93	0.64822	Speract/scavenger receptor-related (2);	0.000000	0.64402	D	0.000007	D	0.98839	0.9608	M	0.88640	2.97	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	0.91635	0.997;0.996;0.997;0.999;0.998	D	0.95989	0.8984	10	0.87932	D	0	.	15.1719	0.72881	0.0:0.0:1.0:0.0	rs45441097	168;153;46;193;191	B7Z900;E7ERX8;E7ESG9;Q9NRS4;Q9NRS4-3	.;.;.;TMPS4_HUMAN;.	S	191;46;153;193;188;140	ENSP00000435184:C191S;ENSP00000428814:C46S;ENSP00000429209:C153S;ENSP00000416037:C193S;ENSP00000430547:C188S;ENSP00000428407:C140S	ENSP00000416037:C193S	C	+	2	0	TMPRSS4	117484816	0.998000	0.40836	0.964000	0.40570	0.803000	0.45373	5.377000	0.66184	2.564000	0.86499	0.561000	0.74099	TGT	G|0.997;C|0.003	0.003	strong		0.567	TMPRSS4-004	KNOWN	non_canonical_polymorphism|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377328.2	NM_019894		C	117979606	G	C	117979606	3	2	27	1	0	0	0	0	1	0	0	0	16264	1377	48	4	604	4	TMPRSS4	11	117979606	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	109964	117979606	17026910	637	11088											
CD3G	917	hgsc.bcm.edu	37	chr11	118219742	118219742	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tctctcttctgtctttacagGtactttggcccagtcaatca	7	16	6	12	0	6	0	2	0	4	0	7	0	6	0	1	2	2	1	1	2	3	5	rs146393315	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:118219742G>A	ENST00000532917.1	+	2	124	c.56G>A	c.(55-57)gGt>gAt	p.G19D	CD3G_ENST00000392883.2_5'UTR|CD3G_ENST00000532903.1_3'UTR	NM_000073.2	NP_000064.1	P09693	CD3G_HUMAN	CD3g molecule, gamma (CD3-TCR complex)	19					cell surface receptor signaling pathway (GO:0007166)|establishment or maintenance of cell polarity (GO:0007163)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)|protein transport (GO:0015031)|regulation of immune response (GO:0050776)|regulation of lymphocyte apoptotic process (GO:0070228)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	alpha-beta T cell receptor complex (GO:0042105)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	protein heterodimerization activity (GO:0046982)|receptor signaling complex scaffold activity (GO:0030159)|T cell receptor binding (GO:0042608)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|kidney(1)|large_intestine(2)|skin(1)	6	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;3.04e-05)	Muromonab(DB00075)	GTCTTTACAGGTACTTTGGCC	0.413													G|||	2	0.000399361	0.0	0.0014	5008	,	,		21792	0.0		0.001	False		,,,				2504	0.0				p.G19D		Atlas-SNP	.											.	CD3G	31	.	0			c.G56A						PASS	.	G	ASP/GLY	0,4400		0,0,2200	183	172	176		56	4.5	0.7	11	dbSNP_134	176	11,8581	8.4+/-32.0	0,11,4285	yes	missense-near-splice	CD3G	NM_000073.2	94	0,11,6485	AA,AG,GG		0.128,0.0,0.0847	probably-damaging	19/183	118219742	11,12981	2200	4296	6496	SO:0001630	splice_region_variant	917	exon2			TTACAGGTACTTT	X60491	CCDS8395.1	11q23	2014-09-17	2006-03-28		ENSG00000160654	ENSG00000160654		"CD molecules"	1675	protein-coding gene	gene with protein product		186740	"CD3g antigen, gamma polypeptide (TiT3 complex)"				Standard	NM_000073		Approved		uc001psu.2	P09693	OTTHUMG00000166971	ENST00000532917.1:c.56-1G>A	11.37:g.118219742G>A		186	0	0		192	43	0.223958	NM_000073	Q2HIZ6	Missense_Mutation	SNP	ENST00000532917.1	37	CCDS8395.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	18.08	3.543791	0.65198	0.0	0.00128	ENSG00000160654	ENST00000532917	T	0.59083	0.29	5.43	4.49	0.54785	.	0.356469	0.27327	N	0.019871	T	0.73644	0.3613	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.75077	-0.3445	9	.	.	.	.	9.1867	0.37174	0.1016:0.0:0.8984:0.0	.	19	P09693	CD3G_HUMAN	D	19	ENSP00000431445:G19D	.	G	+	2	0	CD3G	117724952	0.989000	0.36119	0.731000	0.30826	0.039000	0.13416	2.669000	0.46825	1.461000	0.47929	0.655000	0.94253	GGT	G|0.999;A|0.001	0.001	strong		0.413	CD3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392135.1	NM_000073	Missense_Mutation	A	118219742	G	A	118219742	5	1	27	1	0	0	0	0	0	0	1	0	3015	1275	44	2	62	2	CD3G	11	118219742	Splice_Site	SNP	G	TCGA-G8-6909-01A-11D-2210-10	240136	118219742	16786774	638	11089											
RNF26	79102	hgsc.bcm.edu	37	chr11	119206427	119206427	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccagcagtgctgtggccatgGccatcctcctttggacaccc	6	9	10	16	0	0	0	0	0	0	0	2	1	2	1	6	3	2	2	6	3	0	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:119206427G>A	ENST00000311413.4	+	1	1191	c.595G>A	c.(595-597)Gcc>Acc	p.A199T	RP11-334E6.10_ENST00000501918.2_RNA	NM_032015.4	NP_114404.1	Q9BY78	RNF26_HUMAN	ring finger protein 26	199						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)		TGTGGCCATGGCCATCCTCCT	0.622																																					p.A199T		Atlas-SNP	.											RNF26,NS,carcinoma,-1,1	RNF26	23	1	0			c.G595A						PASS	.						122	102	109					11																	119206427		2199	4295	6494	SO:0001583	missense	79102	exon1			GCCATGGCCATCC	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.595G>A	11.37:g.119206427G>A	ENSP00000312439:p.Ala199Thr	197	0	0		179	46	0.256983	NM_032015	Q542Y8	Missense_Mutation	SNP	ENST00000311413.4	37	CCDS8419.1	.	.	.	.	.	.	.	.	.	.	G	15.99	2.996878	0.54147	.	.	ENSG00000173456	ENST00000311413	T	0.78816	-1.21	5.12	3.22	0.36961	.	0.171581	0.38663	N	0.001619	T	0.67618	0.2912	L	0.43152	1.355	0.37508	D	0.917046	B	0.10296	0.003	B	0.08055	0.003	T	0.64584	-0.6373	10	0.72032	D	0.01	-5.96	7.4994	0.27509	0.0812:0.0:0.593:0.3257	.	199	Q9BY78	RNF26_HUMAN	T	199	ENSP00000312439:A199T	ENSP00000312439:A199T	A	+	1	0	RNF26	118711637	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.146000	0.42216	0.543000	0.28864	0.561000	0.74099	GCC	.	.	none		0.622	RNF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388220.1	NM_032015		A	119206427	G	A	119206427	3	1	27	1	0	0	0	0	1	0	0	0	13501	1203	42	2	597	2	RNF26	11	119206427	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	986685	119206427	15800089	639	11090											
SLC37A2	219855	hgsc.bcm.edu	37	chr11	124951767	124951767	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggggccatgcgaagagcctGctgccatcagcttctttggg	7	9	14	11	1	2	1	1	0	1	1	2	2	2	1	3	3	5	2	3	3	1	2	rs143239155	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:124951767G>A	ENST00000403796.2	+	9	1151	c.850G>A	c.(850-852)Gct>Act	p.A284T	SLC37A2_ENST00000298280.5_Missense_Mutation_p.A284T|SLC37A2_ENST00000308074.4_Missense_Mutation_p.A284T|SLC37A2_ENST00000407458.1_Missense_Mutation_p.A284T	NM_001145290.1	NP_001138762.1	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 2	284					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)		CGAAGAGCCTGCTGCCATCAG	0.557													G|||	2	0.000399361	0.0	0.0	5008	,	,		18767	0.0		0.002	False		,,,				2504	0.0				p.A284T	Melanoma(11;373 620 21213 26083 47768)	Atlas-SNP	.											.	SLC37A2	105	.	0			c.G850A						PASS	.	G	THR/ALA,THR/ALA	0,4402		0,0,2201	54	54	54		850,850	1.5	0.3	11	dbSNP_134	54	19,8579	14.0+/-48.4	0,19,4280	yes	missense,missense	SLC37A2	NM_001145290.1,NM_198277.2	58,58	0,19,6481	AA,AG,GG		0.221,0.0,0.1462	benign,benign	284/502,284/506	124951767	19,12981	2201	4299	6500	SO:0001583	missense	219855	exon9			GAGCCTGCTGCCA	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.850G>A	11.37:g.124951767G>A	ENSP00000384407:p.Ala284Thr	68	0	0		68	53	0.779412	NM_001145290	A8K2P9|Q6P599|Q7Z7P8|Q8TEM2	Missense_Mutation	SNP	ENST00000403796.2	37	CCDS44757.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	2.657	-0.280533	0.05642	0.0	0.00221	ENSG00000134955	ENST00000403796;ENST00000407458;ENST00000298280;ENST00000308074	T;T;T;T	0.58797	0.31;0.31;0.31;0.31	4.54	1.53	0.23141	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.642521	0.15596	N	0.254169	T	0.42653	0.1212	L	0.35341	1.055	0.09310	N	1	B;B	0.12013	0.005;0.003	B;B	0.16722	0.016;0.016	T	0.33548	-0.9864	10	0.51188	T	0.08	0.1127	6.8982	0.24267	0.0824:0.0:0.6082:0.3094	.	284;284	Q8TED4-2;Q8TED4	.;SPX2_HUMAN	T	284	ENSP00000384407:A284T;ENSP00000385126:A284T;ENSP00000298280:A284T;ENSP00000311833:A284T	ENSP00000298280:A284T	A	+	1	0	SLC37A2	124456977	0.002000	0.14202	0.349000	0.25694	0.102000	0.19082	1.264000	0.33015	0.236000	0.21180	-0.182000	0.12963	GCT	G|0.999;A|0.001	0.001	strong		0.557	SLC37A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386837.1	XM_166184		A	124951767	G	A	124951767	3	1	27	1	0	0	0	0	1	0	0	0	14613	1319	46	2	884	2	SLC37A2	11	124951767	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	5745340	124951767	10054749	640	11091											
SLC37A2	219855	hgsc.bcm.edu	37	chr11	124953735	124953735	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctttagtgccaaggaggctgGggacctgtctacactcttcg	7	11	12	11	1	2	0	0	0	2	0	3	2	2	2	2	4	2	1	2	4	3	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:124953735G>A	ENST00000403796.2	+	11	1302	c.1001G>A	c.(1000-1002)gGg>gAg	p.G334E	SLC37A2_ENST00000298280.5_Missense_Mutation_p.G334E|SLC37A2_ENST00000308074.4_Missense_Mutation_p.G334E|SLC37A2_ENST00000525837.1_3'UTR|SLC37A2_ENST00000407458.1_Missense_Mutation_p.G334E	NM_001145290.1	NP_001138762.1	Q8TED4	SPX2_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 2	334					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)		AAGGAGGCTGGGGACCTGTCT	0.557																																					p.G334E	Melanoma(11;373 620 21213 26083 47768)	Atlas-SNP	.											.	SLC37A2	105	.	0			c.G1001A						PASS	.						150	116	127					11																	124953735		2201	4299	6500	SO:0001583	missense	219855	exon11			AGGCTGGGGACCT	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.1001G>A	11.37:g.124953735G>A	ENSP00000384407:p.Gly334Glu	127	0	0		98	4	0.0408163	NM_001145290	A8K2P9|Q6P599|Q7Z7P8|Q8TEM2	Missense_Mutation	SNP	ENST00000403796.2	37	CCDS44757.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.818168	0.90790	.	.	ENSG00000134955	ENST00000403796;ENST00000407458;ENST00000298280;ENST00000308074	T;T;T;T	0.66099	0.02;0.02;-0.19;0.02	4.97	4.97	0.65823	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.84188	0.5417	M	0.92970	3.365	0.80722	D	1	D;D	0.76494	0.999;0.996	D;D	0.83275	0.996;0.979	D	0.88033	0.2776	10	0.72032	D	0.01	-19.5454	18.0204	0.89253	0.0:0.0:1.0:0.0	.	334;334	Q8TED4-2;Q8TED4	.;SPX2_HUMAN	E	334	ENSP00000384407:G334E;ENSP00000385126:G334E;ENSP00000298280:G334E;ENSP00000311833:G334E	ENSP00000298280:G334E	G	+	2	0	SLC37A2	124458945	1.000000	0.71417	0.998000	0.56505	0.959000	0.62525	9.214000	0.95140	2.583000	0.87209	0.655000	0.94253	GGG	.	.	none		0.557	SLC37A2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000386837.1	XM_166184		A	124953735	G	A	124953735	3	1	27	1	0	0	0	0	1	0	0	0	14613	1232	43	2	1043	2	SLC37A2	11	124953735	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1968	124953735	10052781	641	11092											
CDON	50937	hgsc.bcm.edu	37	chr11	125871721	125871721	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cgggtggagaggatgcctggGtgttttttgatgacgctgtt	5	14	17	5	2	0	3	0	2	0	1	0	5	0	4	1	4	1	3	1	4	0	4	rs145983470	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:125871721G>C	ENST00000392693.3	-	11	2178	c.2051C>G	c.(2050-2052)aCc>aGc	p.T684S	CDON_ENST00000263577.7_Missense_Mutation_p.T684S|CDON_ENST00000531738.1_Missense_Mutation_p.T61S	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated	684			T -> S (in HPE11; dbSNP:rs145983470). {ECO:0000269|PubMed:21802063}.		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)		p.T684I(1)		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)		GGATGCCTGGGTGTTTTTTGA	0.393													G|||	9	0.00179712	0.0	0.0	5008	,	,		16120	0.0		0.008	False		,,,				2504	0.001				p.T684S		Atlas-SNP	.											CDON,right_lower_lobe,carcinoma,0,1	CDON	137	1	1	Substitution - Missense(1)	skin(1)	c.C2051G						PASS	.	G	SER/THR	12,4390	19.1+/-41.9	0,12,2189	121	121	121		2051	5.8	1	11	dbSNP_134	121	76,8522	44.9+/-103.4	0,76,4223	yes	missense	CDON	NM_016952.4	58	0,88,6412	CC,CG,GG		0.8839,0.2726,0.6769	benign	684/1265	125871721	88,12912	2201	4299	6500	SO:0001583	missense	50937	exon11			GCCTGGGTGTTTT	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.2051C>G	11.37:g.125871721G>C	ENSP00000376458:p.Thr684Ser	138	0	0		101	77	0.762376	NM_016952	O14631	Missense_Mutation	SNP	ENST00000392693.3	37	CCDS58192.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	G	13.73	2.323686	0.41096	0.002726	0.008839	ENSG00000064309	ENST00000392693;ENST00000531738;ENST00000263577	T;T;T	0.69040	-0.36;0.25;-0.37	5.78	5.78	0.91487	.	0.231330	0.30383	N	0.009752	T	0.52158	0.1717	L	0.32530	0.975	0.41753	D	0.989675	B;P;B	0.36974	0.44;0.576;0.018	B;B;B	0.36845	0.118;0.234;0.016	T	0.56347	-0.7994	10	0.37606	T	0.19	-9.5924	20.3668	0.98882	0.0:0.0:1.0:0.0	.	684;684;61	Q4KMG0;Q4KMG0-2;E9PN78	CDON_HUMAN;.;.	S	684;61;684	ENSP00000376458:T684S;ENSP00000432901:T61S;ENSP00000263577:T684S	ENSP00000263577:T684S	T	-	2	0	CDON	125376931	1.000000	0.71417	0.971000	0.41717	0.478000	0.33099	4.745000	0.62125	2.894000	0.99253	0.655000	0.94253	ACC	G|0.994;C|0.006	0.006	strong		0.393	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952		C	125871721	G	C	125871721	3	2	27	1	0	0	0	0	1	0	0	0	3172	1261	44	4	1783	4	CDON	11	125871721	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	917986	125871721	9134795	642	11093											
ACAD8	27034	hgsc.bcm.edu	37	chr11	134128923	134128923	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aagtgggagtgatgctgcctCtcttctgacctccgctaaga	8	11	11	11	1	2	3	0	2	2	1	4	4	3	4	3	1	2	2	3	1	2	2	rs113488591	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr11:134128923C>G	ENST00000281182.4	+	5	618	c.512C>G	c.(511-513)tCt>tGt	p.S171C	ACAD8_ENST00000524547.1_3'UTR|ACAD8_ENST00000537423.1_Missense_Mutation_p.S94C|ACAD8_ENST00000374752.4_Missense_Mutation_p.S44C|ACAD8_ENST00000543332.1_Missense_Mutation_p.S73C	NM_014384.2	NP_055199.1	Q9UKU7	ACAD8_HUMAN	acyl-CoA dehydrogenase family, member 8	171					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)	GATGCTGCCTCTCTTCTGACC	0.522													C|||	34	0.00678914	0.0023	0.0144	5008	,	,		19971	0.0		0.0199	False		,,,				2504	0.001				p.S171C	GBM(65;238 1125 33403 41853 48889)	Atlas-SNP	.											.	ACAD8	33	.	0			c.C512G	GRCh37	CM070644	ACAD8	M	rs113488591	PASS	.	C	CYS/SER	38,4364	43.1+/-76.7	0,38,2163	113	106	109		512	4.8	1	11	dbSNP_132	109	190,8404	85.6+/-148.0	0,190,4107	yes	missense	ACAD8	NM_014384.2	112	0,228,6270	GG,GC,CC		2.2108,0.8632,1.7544	probably-damaging	171/416	134128923	228,12768	2201	4297	6498	SO:0001583	missense	27034	exon5			CTGCCTCTCTTCT	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.512C>G	11.37:g.134128923C>G	ENSP00000281182:p.Ser171Cys	121	0	0		138	26	0.188406	NM_014384	B7Z5W4|Q6ZWP6|Q9BUS8	Missense_Mutation	SNP	ENST00000281182.4	37	CCDS8498.1	20	0.009157509157509158	0	0.0	4	0.011049723756906077	0	0.0	16	0.021108179419525065	C	23.8	4.453578	0.84209	0.008632	0.022108	ENSG00000151498	ENST00000281182;ENST00000537423;ENST00000543332;ENST00000374752;ENST00000537915	D;D;D;D	0.99129	-5.46;-5.46;-5.46;-5.46	5.73	4.82	0.62117	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, conserved site (1);Acyl-CoA oxidase/dehydrogenase, central domain (2);	0.000000	0.85682	D	0.000000	D	0.98776	0.9588	M	0.92317	3.295	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;1.0;0.999;0.999;1.0;1.0	D;D;D;D;D;D	0.73708	0.964;0.968;0.98;0.974;0.981;0.98	D	0.93512	0.6854	10	0.72032	D	0.01	.	14.7653	0.69634	0.0:0.9304:0.0:0.0696	.	112;94;73;73;44;171	B7Z767;B7Z5W4;B7Z9L5;B7Z7F1;Q6ZWP6;Q9UKU7	.;.;.;.;.;ACAD8_HUMAN	C	171;94;73;44;133	ENSP00000281182:S171C;ENSP00000443763:S94C;ENSP00000438302:S73C;ENSP00000363884:S44C	ENSP00000281182:S171C	S	+	2	0	ACAD8	133634133	1.000000	0.71417	0.987000	0.45799	0.964000	0.63967	7.385000	0.79763	1.421000	0.47157	-0.140000	0.14226	TCT	C|0.985;G|0.015	0.015	strong		0.522	ACAD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393607.1	NM_014384		G	134128923	C	G	134128923	3	3	27	1	0	0	0	0	1	0	0	0	110	913	32	4	530	4	ACAD8	11	134128923	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	8257202	134128923	877593	643	11094											
WNK1	65125	hgsc.bcm.edu	37	chr12	939268	939268	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgcttgagatggctacatCtgaatatccttactcggagt	10	13	9	9	1	1	2	0	2	1	1	3	4	2	3	1	2	3	2	1	2	4	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:939268C>A	ENST00000315939.6	+	4	1896	c.1253C>A	c.(1252-1254)tCt>tAt	p.S418Y	WNK1_ENST00000530271.2_Missense_Mutation_p.S418Y|WNK1_ENST00000537687.1_Missense_Mutation_p.S418Y|WNK1_ENST00000535572.1_Missense_Mutation_p.S418Y|WNK1_ENST00000540360.1_3'UTR	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	418	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)			ATGGCTACATCTGAATATCCT	0.468																																					p.S418Y	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.C1253A						PASS	.						241	202	215					12																	939268		2203	4300	6503	SO:0001583	missense	65125	exon4			CTACATCTGAATA	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.1253C>A	12.37:g.939268C>A	ENSP00000313059:p.Ser418Tyr	280	0	0		293	72	0.245734	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.037262	0.93630	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000530271	T;T;T;T	0.24723	1.84;1.84;1.84;1.84	5.49	5.49	0.81192	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000006	T	0.43700	0.1259	L	0.32530	0.975	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.998	T	0.36890	-0.9729	10	0.87932	D	0	-15.3704	19.3708	0.94484	0.0:1.0:0.0:0.0	.	418;418	F5GWT4;Q9H4A3	.;WNK1_HUMAN	Y	418	ENSP00000441972:S418Y;ENSP00000313059:S418Y;ENSP00000444465:S418Y;ENSP00000433548:S418Y	ENSP00000313059:S418Y	S	+	2	0	WNK1	809529	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	7.818000	0.86416	2.571000	0.86741	0.467000	0.42956	TCT	.	.	none		0.468	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		A	939268	C	A	939268	3	1	27	1	0	0	0	0	1	0	0	0	17392	913	32	4	1267	4	WNK1	12	939268	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10		939268	132912627	644	11095											
WNK1	65125	hgsc.bcm.edu	37	chr12	994030	994030	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caaccacagcagcagccacaGcaccagtccctgcaacaagc	14	2	7	18	0	0	0	0	0	0	0	1	0	1	0	4	0	8	4	4	0	3	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:994030G>A	ENST00000315939.6	+	19	4703	c.4060G>A	c.(4060-4062)Gca>Aca	p.A1354T	WNK1_ENST00000530271.2_Missense_Mutation_p.A1852T|WNK1_ENST00000537687.1_Missense_Mutation_p.A1614T|WNK1_ENST00000535572.1_Missense_Mutation_p.A1107T|WNK1_ENST00000340908.4_Missense_Mutation_p.A947T	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1354					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)			AGCAGCCACAGCACCAGTCCC	0.498																																					p.A1614T	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.G4840A						PASS	.						92	88	89					12																	994030		2203	4300	6503	SO:0001583	missense	65125	exon19			GCCACAGCACCAG	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.4060G>A	12.37:g.994030G>A	ENSP00000313059:p.Ala1354Thr	190	0	0		180	62	0.344444	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	G	7.571	0.666826	0.14710	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000252477;ENST00000530271;ENST00000340908	T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93	5.63	2.65	0.31530	.	0.499734	0.20150	N	0.098164	T	0.22704	0.0548	N	0.14661	0.345	0.18873	N	0.999989	B;B;B	0.19200	0.01;0.034;0.02	B;B;B	0.21708	0.022;0.036;0.016	T	0.14227	-1.0480	10	0.29301	T	0.29	-1.4729	6.408	0.21676	0.2705:0.1226:0.6068:0.0	.	1107;1107;1354	Q9H4A3-2;F5GWT4;Q9H4A3	.;.;WNK1_HUMAN	T	1107;1354;1614;527;1852;947	ENSP00000441972:A1107T;ENSP00000313059:A1354T;ENSP00000444465:A1614T;ENSP00000433548:A1852T;ENSP00000341292:A947T	ENSP00000252477:A527T	A	+	1	0	WNK1	864291	0.191000	0.23288	0.918000	0.36340	0.051000	0.14879	0.566000	0.23593	0.850000	0.35239	0.655000	0.94253	GCA	.	.	none		0.498	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		A	994030	G	A	994030	3	1	27	1	0	0	0	0	1	0	0	0	17392	971	34	2	5636	2	WNK1	12	994030	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	54762	994030	132857865	645	11096											
WNK1	65125	hgsc.bcm.edu	37	chr12	999632	999632	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttacagcctgtgtccatggCggctccaacagcaatcacag	10	9	9	13	1	1	0	1	0	0	0	3	0	3	0	3	2	4	2	3	2	3	2	rs371264719		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:999632C>A	ENST00000315939.6	+	22	6105	c.5462C>A	c.(5461-5463)gCg>gAg	p.A1821E	WNK1_ENST00000530271.2_Missense_Mutation_p.A2319E|WNK1_ENST00000537687.1_Missense_Mutation_p.A2081E|WNK1_ENST00000535572.1_Missense_Mutation_p.A1574E|WNK1_ENST00000340908.4_Missense_Mutation_p.A1414E	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1821					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)			GTGTCCATGGCGGCTCCAACA	0.463																																					p.A2081E	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.C6242A						PASS	.						137	125	129					12																	999632		2203	4300	6503	SO:0001583	missense	65125	exon22			CCATGGCGGCTCC	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.5462C>A	12.37:g.999632C>A	ENSP00000313059:p.Ala1821Glu	312	0	0		249	55	0.220884	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	T	8.007	0.756729	0.15846	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000252477;ENST00000530271;ENST00000340908	T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51	5.06	1.3	0.21679	.	0.576229	0.16749	N	0.201105	T	0.13756	0.0333	N	0.14661	0.345	0.09310	N	0.999997	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.23084	-1.0198	10	0.23891	T	0.37	0.0017	3.5613	0.07884	0.1573:0.2635:0.0:0.5792	.	1574;1574;1821	Q9H4A3-2;F5GWT4;Q9H4A3	.;.;WNK1_HUMAN	E	1574;1821;2081;994;2319;1414	ENSP00000441972:A1574E;ENSP00000313059:A1821E;ENSP00000444465:A2081E;ENSP00000433548:A2319E;ENSP00000341292:A1414E	ENSP00000252477:A994E	A	+	2	0	WNK1	869893	0.996000	0.38824	0.746000	0.31095	0.091000	0.18340	0.353000	0.20130	-0.096000	0.12329	-0.254000	0.11334	GCG	.	.	alt		0.463	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		A	999632	C	A	999632	3	1	27	1	0	0	0	0	1	0	0	0	17392	768	27	4	7050	4	WNK1	12	999632	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	5602	999632	132852263	646	11097											
ITFG2	55846	hgsc.bcm.edu	37	chr12	2930731	2930731	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacggcactgagagtagtggCtctggcctctttgccctgtg	5	11	13	12	1	2	1	0	1	2	1	2	2	2	1	2	3	1	3	2	3	1	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:2930731C>T	ENST00000228799.2	+	8	955	c.816C>T	c.(814-816)ggC>ggT	p.G272G	ITFG2_ENST00000542548.1_Silent_p.G160G|ITFG2_ENST00000419778.2_Silent_p.G95G	NM_018463.3	NP_060933.3	Q969R8	ITFG2_HUMAN	integrin alpha FG-GAP repeat containing 2	272					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)			AGAGTAGTGGCTCTGGCCTCT	0.607																																					p.G272G		Atlas-SNP	.											.	ITFG2	38	.	0			c.C816T						PASS	.						89	78	82					12																	2930731		2203	4300	6503	SO:0001819	synonymous_variant	55846	exon8			TAGTGGCTCTGGC	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.816C>T	12.37:g.2930731C>T		125	0	0		97	4	0.0412371	NM_018463	A8K4Z5|D3DUQ2|Q6PKU5|Q96SX6	Silent	SNP	ENST00000228799.2	37	CCDS8513.1																																																																																			.	.	none		0.607	ITFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253091.1	NM_018463		T	2930731	C	T	2930731	2	4	27	1	0	0	0	0	0	0	0	1	7879	784	28	2		2	ITFG2	12	2930731	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1931099	2930731	130921164	647	11098											
TEAD4	7004	hgsc.bcm.edu	37	chr12	3120180	3120180	+	De_novo_Start_InFrame	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtctctgcaggtcggaacgaGctgattgcccgctacatcaa	9	9	11	12	3	2	1	1	1	1	0	4	3	2	2	1	2	5	3	1	2	3	2	rs147476820		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:3120180G>A	ENST00000397122.2	+	0	135				TEAD4_ENST00000358409.2_Silent_p.E79E|TEAD4_ENST00000359864.2_Silent_p.E79E	NM_201443.2	NP_958851.1	Q15561	TEAD4_HUMAN	TEA domain family member 4						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)			GTCGGAACGAGCTGATTGCCC	0.642													G|||	1	0.000199681	0.0	0.0	5008	,	,		16156	0.0		0.001	False		,,,				2504	0.0				p.E79E		Atlas-SNP	.											.	TEAD4	45	.	0			c.G237A						PASS	.	G	,,	1,4405	2.1+/-5.4	0,1,2202	74	71	72		237,237,	3.3	1	12	dbSNP_134	72	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous,utr-5	TEAD4	NM_003213.3,NM_201441.2,NM_201443.2	,,	0,6,6497	AA,AG,GG		0.0581,0.0227,0.0461	,,	79/435,79/392,	3120180	6,13000	2203	4300	6503			7004	exon4			GAACGAGCTGATT	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			12.37:g.3120180G>A		127	0	0		139	78	0.561151	NM_003213	H0Y308|Q6MZR9|Q8NEV5|Q92883|Q96BK2	Silent	SNP	ENST00000397122.2	37	CCDS41737.1																																																																																			G|0.999;A|0.001	0.001	strong		0.642	TEAD4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398477.1	NM_003213		A	3120180	G	A	3120180	1	1	27	1	0	1	0	0	0	0	0	0	15756	962	34	2		2	TEAD4	12	3120180	De_novo_Start_InFrame	SNP	G	TCGA-G8-6909-01A-11D-2210-10	189449	3120180	130731715	648	11099											
NDUFA9	4704	hgsc.bcm.edu	37	chr12	4768290	4768290	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagttgaaaaattcattcatGtttcacatctgaatgcgaat	14	14	7	6	1	4	2	3	2	1	0	4	4	4	2	0	0	1	2	0	0	4	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:4768290G>A	ENST00000266544.5	+	5	519	c.499G>A	c.(499-501)Gtt>Att	p.V167I	RP11-500M8.7_ENST00000536588.1_3'UTR	NM_005002.4	NP_004993.1	Q16795	NDUA9_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9, 39kDa	167					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						ATTCATTCATGTTTCACATCT	0.358																																					p.V167I	Colon(75;996 1244 23946 25294 29232)	Atlas-SNP	.											.	NDUFA9	45	.	0			c.G499A						PASS	.						69	73	72					12																	4768290		2203	4300	6503	SO:0001583	missense	4704	exon5			ATTCATGTTTCAC	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.499G>A	12.37:g.4768290G>A	ENSP00000266544:p.Val167Ile	101	0	0		67	30	0.447761	NM_005002	Q14076|Q2NKX0	Missense_Mutation	SNP	ENST00000266544.5	37	CCDS8532.1	.	.	.	.	.	.	.	.	.	.	G	11.75	1.731929	0.30684	.	.	ENSG00000139180	ENST00000266544	D	0.93189	-3.18	5.26	3.43	0.39272	NAD(P)-binding domain (1);NmrA-like (1);	0.304583	0.38005	N	0.001857	D	0.85898	0.5804	N	0.17922	0.545	0.80722	D	1	B;B	0.15473	0.013;0.013	B;B	0.25987	0.065;0.065	T	0.76515	-0.2931	10	0.27082	T	0.32	-11.9884	7.2226	0.25997	0.3375:0.0:0.6625:0.0	.	167;167	A8K4V2;Q16795	.;NDUA9_HUMAN	I	167	ENSP00000266544:V167I	ENSP00000266544:V167I	V	+	1	0	NDUFA9	4638551	0.989000	0.36119	0.984000	0.44739	0.576000	0.36127	0.932000	0.28884	0.707000	0.31934	0.585000	0.79938	GTT	.	.	none		0.358	NDUFA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398900.2	NM_005002		A	4768290	G	A	4768290	3	1	27	1	0	0	0	0	1	0	0	0	10281	1377	48	2	517	2	NDUFA9	12	4768290	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1648110	4768290	129083605	649	11100											
NCAPD2	9918	hgsc.bcm.edu	37	chr12	6638197	6638197	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggaagagcctttccacacCatcatgaagtattgctcccc	11	9	8	13	0	1	2	1	1	0	1	3	4	3	3	5	1	2	2	5	1	3	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:6638197C>T	ENST00000315579.5	+	27	4363	c.3564C>T	c.(3562-3564)acC>acT	p.T1188T	NCAPD2_ENST00000545962.1_Silent_p.T1143T	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	1188					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						CTTTCCACACCATCATGAAGT	0.527																																					p.T1188T		Atlas-SNP	.											.	NCAPD2	99	.	0			c.C3564T						PASS	.						55	61	59					12																	6638197		2203	4300	6503	SO:0001819	synonymous_variant	9918	exon27			CCACACCATCATG	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.3564C>T	12.37:g.6638197C>T		84	0	0		67	23	0.343284	NM_014865	D3DUR4|Q8N6U3	Silent	SNP	ENST00000315579.5	37	CCDS8548.1																																																																																			.	.	none		0.527	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865		T	6638197	C	T	6638197	2	4	27	1	0	0	0	0	0	0	0	1	10214	581	21	2		2	NCAPD2	12	6638197	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1869907	6638197	127213698	650	11101											
ING4	51147	hgsc.bcm.edu	37	chr12	6760367	6760367	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tccaaggcccttatctatttCttcttccgttcttgggagca	6	16	7	12	1	4	0	0	0	4	0	6	1	6	1	3	2	1	2	3	2	3	7	rs76327967	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:6760367C>T	ENST00000396807.4	-	8	782	c.744G>A	c.(742-744)aaG>aaA	p.K248K	ING4_ENST00000486287.1_5'UTR|ING4_ENST00000412586.2_Silent_p.K245K|ING4_ENST00000341550.4_Silent_p.K247K|ING4_ENST00000446105.2_Silent_p.K244K|ING4_ENST00000444704.2_Silent_p.K224K|ING4_ENST00000423703.2_3'UTR	NM_001127582.1|NM_001127585.1|NM_001127586.1|NM_016162.3	NP_001121054.1|NP_001121057.1|NP_001121058.1|NP_057246.2	Q9UNL4	ING4_HUMAN	inhibitor of growth family, member 4	248					apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|chromatin organization (GO:0006325)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|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)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|protein acetylation (GO:0006473)	histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	methylated histone binding (GO:0035064)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			central_nervous_system(3)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)	10						TTATCTATTTCTTCTTCCGTT	0.527													C|||	361	0.0720847	0.1815	0.0677	5008	,	,		20926	0.0179		0.0298	False		,,,				2504	0.0266				p.K248K		Atlas-SNP	.											.	ING4	31	.	0			c.G744A						PASS	.	C	,,,,,	762,3644	310.0+/-291.3	54,654,1495	98	89	92		744,735,732,672,,741	4	1	12	dbSNP_131	92	327,8273	113.5+/-173.5	4,319,3977	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,utr-3,coding-synonymous	ING4	NM_001127582.1,NM_001127583.1,NM_001127584.1,NM_001127585.1,NM_001127586.1,NM_016162.3	,,,,,	58,973,5472	TT,TC,CC		3.8023,17.2946,8.3731	,,,,,	248/250,245/247,244/246,224/226,,247/249	6760367	1089,11917	2203	4300	6503	SO:0001819	synonymous_variant	51147	exon8			CTATTTCTTCTTC	AF063594	CCDS8555.1, CCDS44812.1, CCDS44813.1, CCDS44814.1, CCDS44815.1, CCDS44816.1	12p13.32	2013-01-28			ENSG00000111653	ENSG00000111653		"Zinc fingers, PHD-type"	19423	protein-coding gene	gene with protein product		608524				12750254	Standard	NM_001127582		Approved	p29ING4, my036	uc001qpw.4	Q9UNL4	OTTHUMG00000141274	ENST00000396807.4:c.744G>A	12.37:g.6760367C>T		131	0	0		110	45	0.409091	NM_001127582	A4KYM4|A4KYM6|D3DUR8|Q0EF62|Q0EF63|Q4VBQ6|Q96E15|Q9H3J0	Silent	SNP	ENST00000396807.4	37	CCDS44813.1																																																																																			C|0.923;T|0.077	0.077	strong		0.527	ING4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280467.2	NM_198287		T	6760367	C	T	6760367	2	4	27	1	0	0	0	0	0	0	0	1	7747	912	32	2		2	ING4	12	6760367	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	122170	6760367	127091528	651	11102											
C1S	716	hgsc.bcm.edu	37	chr12	7175762	7175762	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ttctctgtgctattccagggGagtatcactgtgctggtaac	7	14	11	9	0	2	0	1	0	1	0	4	1	3	1	1	3	3	4	1	3	3	5	rs150549869		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:7175762G>C	ENST00000406697.1	+	14	1826	c.1198G>C	c.(1198-1200)Gag>Cag	p.E400Q	C1S_ENST00000360817.5_Missense_Mutation_p.E400Q|C1S_ENST00000495061.1_3'UTR|C1S_ENST00000328916.3_Missense_Mutation_p.E400Q|C1S_ENST00000402681.3_Missense_Mutation_p.E233Q			P09871	C1S_HUMAN	complement component 1, s subcomponent	400	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				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)	TATTCCAGGGGAGTATCACTG	0.587																																					p.E400Q	GBM(156;750 1943 12971 24779 31015)	Atlas-SNP	.											.	C1S	93	.	0			c.G1198C						PASS	.	G	GLN/GLU,GLN/GLU	0,4406		0,0,2203	246	189	208		1198,1198	4.4	0.7	12	dbSNP_134	208	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	C1S	NM_001734.3,NM_201442.2	29,29	0,5,6498	CC,CG,GG		0.0581,0.0,0.0384	benign,benign	400/689,400/689	7175762	5,13001	2203	4300	6503	SO:0001583	missense	716	exon11			CCAGGGGAGTATC		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.1198G>C	12.37:g.7175762G>C	ENSP00000385035:p.Glu400Gln	137	0	0		120	56	0.466667	NM_201442	D3DUT4|Q9UCU7|Q9UCU8|Q9UCU9|Q9UCV0|Q9UCV1|Q9UCV2|Q9UCV3|Q9UCV4|Q9UCV5|Q9UM14	Missense_Mutation	SNP	ENST00000406697.1	37	CCDS31735.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	2.603	-0.292472	0.05568	0.0	5.81E-4	ENSG00000182326	ENST00000406697;ENST00000328916;ENST00000360817;ENST00000382222;ENST00000402681	T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15	5.28	4.39	0.52855	Complement control module (2);Sushi/SCR/CCP (3);	0.768045	0.11079	N	0.601989	T	0.57651	0.2068	L	0.55834	1.745	0.09310	N	1	B	0.23650	0.089	B	0.24974	0.057	T	0.47209	-0.9135	10	0.32370	T	0.25	.	10.104	0.42521	0.1176:0.1284:0.7539:0.0	.	400	P09871	C1S_HUMAN	Q	400;400;400;394;233	ENSP00000385035:E400Q;ENSP00000328173:E400Q;ENSP00000354057:E400Q;ENSP00000384171:E233Q	ENSP00000328173:E400Q	E	+	1	0	C1S	7046023	0.001000	0.12720	0.664000	0.29753	0.013000	0.08279	0.933000	0.28897	0.617000	0.30160	-2.178000	0.00318	GAG	G|1.000;C|0.000	0.000	strong		0.587	C1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317481.1	NM_001734		C	7175762	G	C	7175762	3	2	27	1	0	0	0	0	1	0	0	0	1976	1175	41	4	1236	4	C1S	12	7175762	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	415395	7175762	126676133	652	11103											
SLCO1C1	53919	hgsc.bcm.edu	37	chr12	20876168	20876168	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gcagtatggacagtcatcctCcagggccaactttgtgatcg	9	10	11	11	1	1	1	1	1	0	0	4	2	3	2	3	2	1	2	3	2	2	2	rs144285413	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:20876168C>T	ENST00000266509.2	+	9	1534	c.1166C>T	c.(1165-1167)tCc>tTc	p.S389F	SLCO1C1_ENST00000545604.1_Missense_Mutation_p.S389F|SLCO1C1_ENST00000545102.1_Missense_Mutation_p.S271F|SLCO1C1_ENST00000381552.1_Missense_Mutation_p.S389F|SLCO1C1_ENST00000540354.1_Missense_Mutation_p.S340F	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	389					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)	CAGTCATCCTCCAGGGCCAAC	0.443													C|||	20	0.00399361	0.0008	0.0058	5008	,	,		19476	0.0		0.0139	False		,,,				2504	0.001				p.S389F		Atlas-SNP	.											.	SLCO1C1	216	.	0			c.C1166T						PASS	.	C	PHE/SER,PHE/SER,PHE/SER,PHE/SER	8,4398	14.3+/-33.2	0,8,2195	159	138	145		812,1019,1166,1166	4.5	0.9	12	dbSNP_134	145	59,8541	35.9+/-90.5	0,59,4241	yes	missense,missense,missense,missense	SLCO1C1	NM_001145944.1,NM_001145945.1,NM_001145946.1,NM_017435.4	155,155,155,155	0,67,6436	TT,TC,CC		0.686,0.1816,0.5151	probably-damaging,probably-damaging,probably-damaging,probably-damaging	271/613,340/664,389/731,389/713	20876168	67,12939	2203	4300	6503	SO:0001583	missense	53919	exon9			CATCCTCCAGGGC	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.1166C>T	12.37:g.20876168C>T	ENSP00000266509:p.Ser389Phe	296	0	0		213	111	0.521127	NM_017435	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Missense_Mutation	SNP	ENST00000266509.2	37	CCDS8683.1	12	0.005494505494505495	0	0.0	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	C	21.6	4.166506	0.78339	0.001816	0.00686	ENSG00000139155	ENST00000545604;ENST00000540354;ENST00000266509;ENST00000381552;ENST00000545102	T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79	4.54	4.54	0.55810	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	T	0.69387	0.3105	M	0.92026	3.265	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;0.999;0.997;0.997	T	0.80690	-0.1270	10	0.87932	D	0	.	17.8397	0.88712	0.0:1.0:0.0:0.0	.	271;340;389;389	F5GZD6;B7Z3Q3;Q5JPA4;Q9NYB5	.;.;.;SO1C1_HUMAN	F	389;340;389;389;271	ENSP00000444149:S389F;ENSP00000438665:S340F;ENSP00000266509:S389F;ENSP00000370964:S389F;ENSP00000444527:S271F	ENSP00000266509:S389F	S	+	2	0	SLCO1C1	20767435	1.000000	0.71417	0.949000	0.38748	0.767000	0.43475	7.278000	0.78587	2.510000	0.84645	0.561000	0.74099	TCC	C|0.994;T|0.006	0.006	strong		0.443	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435		T	20876168	C	T	20876168	3	4	27	1	0	0	0	0	1	0	0	0	14740	855	30	2	1196	2	SLCO1C1	12	20876168	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	13700406	20876168	112975727	653	11104											
KRAS	3845	hgsc.bcm.edu	37	chr12	25362777	25362777	+	3'UTR	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctttttcttctttttaccAtctttgctcatcttttcttt	3	27	1	10	0	7	0	1	0	6	0	7	0	7	0	1	0	2	1	1	0	1	11	rs1137282	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:25362777A>G	ENST00000256078.4	-	0	706				KRAS_ENST00000557334.1_Silent_p.D60D|KRAS_ENST00000311936.3_Silent_p.D173D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog						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)			TCTTTTTACCATCTTTGCTCA	0.279		119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			A|||	879	0.175519	0.18	0.1931	5008	,	,		18305	0.0923		0.2187	False		,,,				2504	0.1984				p.D173D	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.T519C						PASS	.	A	,	753,3647	305.5+/-289.0	61,631,1508	68	64	65		519,	3.4	1	12	dbSNP_86	65	1853,6727	328.5+/-318.3	168,1517,2605	no	coding-synonymous,utr-3	KRAS	NM_004985.3,NM_033360.2	,	229,2148,4113	GG,GA,AA		21.5967,17.1136,20.077	,	173/189,	25362777	2606,10374	2200	4290	6490	SO:0001624	3_prime_UTR_variant	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	TTTACCATCTTTG	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.*73T>C	12.37:g.25362777A>G		166	0	0		127	126	0.992126	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Silent	SNP	ENST00000256078.4	37	CCDS8703.1																																																																																			T|0.136;G|0.154;C|0.028;A|0.682	0.154	strong		0.279	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		G	25362777	A	G	25362777	1	3	27	0	1	0	0	0	0	0	0	0	8447	214	8	3		3	KRAS	12	25362777	3'UTR	SNP	A	TCGA-G8-6909-01A-11D-2210-10	4486609	25362777	108489118	654	11105											
PTHLH	5744	hgsc.bcm.edu	37	chr12	28116465	28116465	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttgagcggctgctctttgtAcgtctccaccttgttagttt	4	17	9	11	2	2	1	0	1	2	0	3	1	2	1	2	1	3	5	2	1	2	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:28116465A>G	ENST00000545234.1	-	5	880	c.340T>C	c.(340-342)Tac>Cac	p.Y114H	PTHLH_ENST00000535992.1_Missense_Mutation_p.Y114H|PTHLH_ENST00000539239.1_Missense_Mutation_p.Y114H|PTHLH_ENST00000201015.4_Missense_Mutation_p.Y114H|PTHLH_ENST00000395868.3_Missense_Mutation_p.Y114H|RP11-993B23.3_ENST00000538113.1_RNA|PTHLH_ENST00000354417.3_Missense_Mutation_p.Y114H|PTHLH_ENST00000395872.1_Missense_Mutation_p.Y114H|PTHLH_ENST00000538310.1_Missense_Mutation_p.Y114H			P12272	PTHR_HUMAN	parathyroid hormone-like hormone	114					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|cAMP metabolic process (GO:0046058)|cell-cell signaling (GO:0007267)|endochondral ossification (GO:0001958)|endoderm development (GO:0007492)|epidermis development (GO:0008544)|epithelial cell differentiation (GO:0030855)|female pregnancy (GO:0007565)|lung alveolus development (GO:0048286)|mammary gland bud elongation (GO:0060649)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|nipple sheath formation (GO:0060659)|osteoblast development (GO:0002076)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell proliferation (GO:0008284)|protein processing (GO:0016485)|regulation of gene expression (GO:0010468)|skeletal system development (GO:0001501)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	hormone activity (GO:0005179)|peptide hormone receptor binding (GO:0051428)			breast(1)|endometrium(1)|large_intestine(2)|lung(4)|skin(1)|stomach(1)	10	Lung SC(9;0.184)					TGCTCTTTGTACGTCTCCACC	0.517																																					p.Y114H		Atlas-SNP	.											.	PTHLH	36	.	0			c.T340C						PASS	.						160	151	154					12																	28116465		2203	4300	6503	SO:0001583	missense	5744	exon3			CTTTGTACGTCTC		CCDS8715.1, CCDS44853.1	12p12.1-p11.2	2014-01-07			ENSG00000087494	ENSG00000087494		"Endogenous ligands"	9607	protein-coding gene	gene with protein product	"osteostatin", "parathyroid hormone-like hormone preproprotein", "parathyroid hormone-related protein preproprotein"	168470				2708388	Standard	NM_002820		Approved	PTHRP, HHM, PLP, PTHR	uc001ril.3	P12272	OTTHUMG00000169221	ENST00000545234.1:c.340T>C	12.37:g.28116465A>G	ENSP00000441765:p.Tyr114His	214	0	0		169	38	0.224852	NM_198964	Q15251|Q6FH74	Missense_Mutation	SNP	ENST00000545234.1	37	CCDS44853.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.241957	0.79912	.	.	ENSG00000087494	ENST00000395872;ENST00000539239;ENST00000545234;ENST00000538310;ENST00000354417;ENST00000201015;ENST00000535992;ENST00000395868;ENST00000542963	D;D;D;D;D;D;D;D;D	0.84730	-1.89;-1.89;-1.89;-1.89;-1.89;-1.89;-1.89;-1.89;-1.89	5.56	5.56	0.83823	.	0.054525	0.85682	D	0.000000	D	0.88808	0.6537	L	0.39245	1.2	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	D	0.88398	0.3013	10	0.41790	T	0.15	-16.5447	14.8854	0.70564	1.0:0.0:0.0:0.0	.	114	P12272	PTHR_HUMAN	H	114	ENSP00000379213:Y114H;ENSP00000441571:Y114H;ENSP00000441765:Y114H;ENSP00000441890:Y114H;ENSP00000346398:Y114H;ENSP00000201015:Y114H;ENSP00000440613:Y114H;ENSP00000379209:Y114H;ENSP00000444519:Y114H	ENSP00000201015:Y114H	Y	-	1	0	PTHLH	28007732	1.000000	0.71417	0.891000	0.34965	0.917000	0.54804	7.859000	0.86982	2.111000	0.64477	0.477000	0.44152	TAC	.	.	none		0.517	PTHLH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402913.1	NM_198965		G	28116465	A	G	28116465	3	3	27	1	0	0	0	0	1	0	0	0	12774	391	14	3	205	3	PTHLH	12	28116465	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	2753688	28116465	105735430	655	11106											
C12orf72	254013	hgsc.bcm.edu	37	chr12	31815167	31815167	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cccacagtgatccttactggGcaatctactggccaggaggc	9	8	11	13	0	1	1	0	1	1	0	2	2	2	2	3	4	2	1	3	4	3	2	rs61736289	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:31815167G>T	ENST00000357721.3	+	2	495	c.280G>T	c.(280-282)Gca>Tca	p.A94S	METTL20_ENST00000395763.3_Missense_Mutation_p.A94S|METTL20_ENST00000412352.2_Missense_Mutation_p.A94S|METTL20_ENST00000538463.1_Missense_Mutation_p.A94S|METTL20_ENST00000538391.1_Missense_Mutation_p.A94S	NM_001135863.1	NP_001129335.1	Q8IXQ9	MET20_HUMAN	methyltransferase like 20	94						cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			lung(2)|stomach(1)	3						TCCTTACTGGGCAATCTACTG	0.527													G|||	113	0.0225639	0.0023	0.0504	5008	,	,		19695	0.001		0.0596	False		,,,				2504	0.0143				p.A94S		Atlas-SNP	.											.	METTL20	23	.	0			c.G280T						PASS	.	G	SER/ALA,SER/ALA,SER/ALA	40,4366	43.1+/-76.7	0,40,2163	64	67	66		280,280,280	4.4	1	12	dbSNP_129	66	438,8162	133.5+/-191.0	10,418,3872	yes	missense,missense,missense	METTL20	NM_001135863.1,NM_001135864.1,NM_173802.3	99,99,99	10,458,6035	TT,TG,GG		5.093,0.9079,3.6752	probably-damaging,probably-damaging,probably-damaging	94/263,94/263,94/263	31815167	478,12528	2203	4300	6503	SO:0001583	missense	254013	exon2			TACTGGGCAATCT	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.280G>T	12.37:g.31815167G>T	ENSP00000350353:p.Ala94Ser	60	0	0		48	23	0.479167	NM_173802	D3DUW3	Missense_Mutation	SNP	ENST00000357721.3	37	CCDS8724.1	61	0.027930402930402932	1	0.0020325203252032522	16	0.04419889502762431	1	0.0017482517482517483	43	0.05672823218997362	G	26.6	4.751076	0.89753	0.009079	0.05093	ENSG00000139160	ENST00000412352;ENST00000395763;ENST00000538463;ENST00000357721;ENST00000538391	.	.	.	4.4	4.4	0.53042	.	0.000000	0.85682	D	0.000000	T	0.22666	0.0547	M	0.73962	2.25	0.80722	D	1	D	0.54397	0.966	P	0.49140	0.601	T	0.55964	-0.8057	9	0.37606	T	0.19	-10.4463	17.1676	0.86821	0.0:0.0:1.0:0.0	rs61736289	94	Q8IXQ9	MET20_HUMAN	S	94	.	ENSP00000350353:A94S	A	+	1	0	METTL20	31706434	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	8.907000	0.92634	2.277000	0.76020	0.561000	0.74099	GCA	G|0.968;T|0.032	0.032	strong		0.527	METTL20-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402196.1	NM_173802		T	31815167	G	T	31815167	3	4	27	1	0	0	0	0	1	0	0	0	1715	1203	42	4	282	4	C12orf72	12	31815167	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	3698702	31815167	102036728	656	11107											
KIF21A	55605	hgsc.bcm.edu	37	chr12	39716675	39716675	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccatctgagtggtggttcTccttcgggcctagtcaaaga	7	13	11	10	1	3	2	1	1	2	1	6	2	4	2	3	3	0	1	3	3	2	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:39716675T>A	ENST00000361418.5	-	27	3481	c.3466A>T	c.(3466-3468)Aga>Tga	p.R1156*	KIF21A_ENST00000395670.3_Nonsense_Mutation_p.R1156*|KIF21A_ENST00000544797.2_Nonsense_Mutation_p.R1136*|KIF21A_ENST00000541463.2_Nonsense_Mutation_p.R1120*|KIF21A_ENST00000361961.3_Nonsense_Mutation_p.R1143*|KIF21A_ENST00000547745.1_5'Flank			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	1156					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)				GTGGTGGTTCTCCTTCGGGCC	0.453																																					p.R1156X		Atlas-SNP	.											.	KIF21A	238	.	0			c.A3466T						PASS	.						136	129	131					12																	39716675		2203	4300	6503	SO:0001587	stop_gained	55605	exon27			TGGTTCTCCTTCG	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.3466A>T	12.37:g.39716675T>A	ENSP00000354878:p.Arg1156*	107	0	0		117	28	0.239316	NM_001173464	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Nonsense_Mutation	SNP	ENST00000361418.5	37	CCDS53776.1	.	.	.	.	.	.	.	.	.	.	T	37	5.997374	0.97184	.	.	ENSG00000139116	ENST00000361961;ENST00000395670;ENST00000341813;ENST00000545778;ENST00000551264;ENST00000544797;ENST00000361418;ENST00000541463	.	.	.	5.36	5.36	0.76844	.	0.000000	0.64402	D	0.000016	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.3659	0.74523	0.0:0.0:0.0:1.0	.	.	.	.	X	1143;1156;1156;203;197;1136;1156;1120	.	ENSP00000344501:R1156X	R	-	1	2	KIF21A	38002942	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.732000	0.62029	2.020000	0.59435	0.528000	0.53228	AGA	.	.	none		0.453	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641		A	39716675	T	A	39716675	4	1	27	1	0	0	0	0	0	1	0	0	8297	1559	54	5	1606	5	KIF21A	12	39716675	Nonsense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	7901508	39716675	94135220	657	11108											
LRRK2	120892	hgsc.bcm.edu	37	chr12	40677936	40677936	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	taatttaaggaaacaaacaaGtaagtaacaaggagaatatt	22	9	7	3	0	0	1	0	0	0	1	0	3	0	2	0	2	3	2	0	2	10	7			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:40677936G>A	ENST00000298910.7	+	19	2558		c.e19+1		LRRK2_ENST00000343742.2_Splice_Site	NM_198578.3	NP_940980	Q5S007	LRRK2_HUMAN	leucine-rich repeat kinase 2						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)				AAACAAACAAGTAAGTAACAA	0.308																																					.		Atlas-SNP	.											.	LRRK2	763	.	0			c.2500+1G>A						PASS	.						65	71	69					12																	40677936		2202	4300	6502	SO:0001630	splice_region_variant	120892	exon19			AAACAAGTAAGTA	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.2500+1G>A	12.37:g.40677936G>A		39	0	0		43	13	0.302326	NM_198578	A6NJU2|Q6ZS50|Q8NCX9	Splice_Site	SNP	ENST00000298910.7	37	CCDS31774.1	.	.	.	.	.	.	.	.	.	.	G	17.94	3.510681	0.64522	.	.	ENSG00000188906	ENST00000343742;ENST00000298910	.	.	.	5.05	5.05	0.67936	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.7573	0.91837	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	LRRK2	38964203	1.000000	0.71417	0.993000	0.49108	0.716000	0.41182	5.970000	0.70431	2.498000	0.84270	0.591000	0.81541	.	.	.	none		0.308	LRRK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277179.1	XM_058513	Intron	A	40677936	G	A	40677936	5	1	27	1	0	0	0	0	0	0	1	0	9042	1043	36	2	2575	2	LRRK2	12	40677936	Splice_Site	SNP	G	TCGA-G8-6909-01A-11D-2210-10	961261	40677936	93173959	658	11109											
HDAC7	51564	hgsc.bcm.edu	37	chr12	48189061	48189061	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cactggggggcaggggctctGagcgagtccggctcagtggc	5	6	19	11	2	2	1	1	1	1	0	3	2	3	1	1	7	1	3	1	7	0	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:48189061G>A	ENST00000427332.2	-	11	1229	c.1073C>T	c.(1072-1074)tCa>tTa	p.S358L	HDAC7_ENST00000080059.7_Missense_Mutation_p.S397L|HDAC7_ENST00000354334.3_Missense_Mutation_p.S360L|HDAC7_ENST00000552960.1_Missense_Mutation_p.S380L|HDAC7_ENST00000380610.4_Missense_Mutation_p.S414L			Q8WUI4	HDAC7_HUMAN	histone deacetylase 7	358	Transcription repression 2. {ECO:0000250}.				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)		CAGGGGCTCTGAGCGAGTCCG	0.677																																					p.S397L		Atlas-SNP	.											HDAC7,NS,carcinoma,+1,1	HDAC7	71	1	0			c.C1190T						scavenged	.						28	33	31					12																	48189061		2195	4297	6492	SO:0001583	missense	51564	exon11			GGCTCTGAGCGAG	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.1073C>T	12.37:g.48189061G>A	ENSP00000404394:p.Ser358Leu	42	1	0.0238095		46	16	0.347826	NM_015401	B3KY08|B4DWI0|B4E0Q5|Q6P1W9|Q6W9G7|Q7Z4K2|Q7Z5I1|Q96K01|Q9BR73|Q9H7L0|Q9NW41|Q9NWA9|Q9NYK9|Q9UFU7	Missense_Mutation	SNP	ENST00000427332.2	37		.	.	.	.	.	.	.	.	.	.	G	32	5.178706	0.94846	.	.	ENSG00000061273	ENST00000080059;ENST00000354334;ENST00000552960;ENST00000380610;ENST00000427332	T;T;T;T;T	0.74632	-0.66;-0.86;-0.63;-0.78;-0.57	4.37	4.37	0.52481	.	0.000000	0.64402	D	0.000001	D	0.84570	0.5501	M	0.69358	2.11	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	0.86580	0.1853	10	0.87932	D	0	.	16.0096	0.80391	0.0:0.0:1.0:0.0	.	397;380;360	Q8WUI4-5;Q8WUI4-6;Q8WUI4-7	.;.;.	L	397;360;380;414;358	ENSP00000080059:S397L;ENSP00000351326:S360L;ENSP00000448532:S380L;ENSP00000369984:S414L;ENSP00000404394:S358L	ENSP00000080059:S397L	S	-	2	0	HDAC7	46475328	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.065000	0.93941	2.418000	0.82041	0.561000	0.74099	TCA	.	.	none		0.677	HDAC7-013	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000328804.2			A	48189061	G	A	48189061	3	1	27	1	0	0	0	0	1	0	0	0	7021	1294	45	2	1849	2	HDAC7	12	48189061	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	7511125	48189061	85662834	659	11110											
BIN2	51411	hgsc.bcm.edu	37	chr12	51695839	51695839	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggcaacatagatttccaTggtccttacagcctggtcag	9	11	10	11	0	1	1	1	0	0	1	3	1	3	1	3	3	3	1	3	3	3	3	rs143984628		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:51695839T>C	ENST00000267012.4	-	5	434	c.373A>G	c.(373-375)Atg>Gtg	p.M125V	BIN2_ENST00000604560.1_Missense_Mutation_p.M98V|BIN2_ENST00000544402.1_Missense_Mutation_p.M99V|BIN2_ENST00000452142.2_Intron	NM_016293.2	NP_057377.2	Q9UBW5	BIN2_HUMAN	bridging integrator 2	125	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						TAGATTTCCATGGTCCTTACA	0.468													T|||	1	0.000199681	0.0	0.0	5008	,	,		19345	0.0		0.001	False		,,,				2504	0.0				p.M125V		Atlas-SNP	.											.	BIN2	58	.	0			c.A373G						PASS	.	T	VAL/MET	0,4406		0,0,2203	152	121	131		373	5.5	1	12	dbSNP_134	131	4,8596	3.7+/-12.6	0,4,4296	yes	missense	BIN2	NM_016293.2	21	0,4,6499	CC,CT,TT		0.0465,0.0,0.0308	possibly-damaging	125/566	51695839	4,13002	2203	4300	6503	SO:0001583	missense	51411	exon5			TTTCCATGGTCCT	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.373A>G	12.37:g.51695839T>C	ENSP00000267012:p.Met125Val	172	0	0		151	74	0.490066	NM_016293	Q86VV0|Q9NWK4|Q9UKN4	Missense_Mutation	SNP	ENST00000267012.4	37	CCDS8811.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	17.72	3.459720	0.63401	0.0	4.65E-4	ENSG00000110934	ENST00000267012;ENST00000544402	T;T	0.58652	0.32;0.32	5.48	5.48	0.80851	BAR (3);	0.000000	0.85682	D	0.000000	T	0.70029	0.3177	L	0.49778	1.585	0.40090	D	0.976241	D;D	0.69078	0.997;0.997	D;D	0.80764	0.99;0.994	T	0.70132	-0.4956	10	0.40728	T	0.16	-11.2107	14.8673	0.70427	0.0:0.0:0.0:1.0	.	99;125	F5H0W4;Q9UBW5	.;BIN2_HUMAN	V	125;99	ENSP00000267012:M125V;ENSP00000445874:M99V	ENSP00000267012:M125V	M	-	1	0	BIN2	49982106	1.000000	0.71417	1.000000	0.80357	0.716000	0.41182	4.698000	0.61789	2.227000	0.72691	0.460000	0.39030	ATG	T|1.000;C|0.000	0.000	strong		0.468	BIN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000469800.1			C	51695839	T	C	51695839	3	2	27	1	0	0	0	0	1	0	0	0	1433	1464	51	3	1360	3	BIN2	12	51695839	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	3506778	51695839	82156056	660	11111											
KRT84	3890	hgsc.bcm.edu	37	chr12	52777466	52777466	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcacctccaactgcctccgCaggttggtgatgtagctctc	7	10	10	14	1	1	1	0	1	1	0	4	1	3	1	4	2	4	5	4	2	2	2	rs138204915	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:52777466C>A	ENST00000257951.3	-	2	729	c.663G>T	c.(661-663)ctG>ctT	p.L221L	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	221	Coil 1B.|Rod.				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)		ACTGCCTCCGCAGGTTGGTGA	0.542													C|||	7	0.00139776	0.0	0.0	5008	,	,		20929	0.0		0.006	False		,,,				2504	0.001				p.L221L		Atlas-SNP	.											.	KRT84	61	.	0			c.G663T						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	71	68	69		663	1.4	1	12	dbSNP_134	69	22,8578	16.0+/-53.3	0,22,4278	no	coding-synonymous	KRT84	NM_033045.3		0,25,6478	AA,AC,CC		0.2558,0.0681,0.1922		221/601	52777466	25,12981	2203	4300	6503	SO:0001819	synonymous_variant	3890	exon2			CCTCCGCAGGTTG	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.663G>T	12.37:g.52777466C>A		144	0	0		129	69	0.534884	NM_033045	B2RA43|Q6ISB0|Q701L6	Silent	SNP	ENST00000257951.3	37	CCDS8825.1																																																																																			C|0.998;A|0.002	0.002	strong		0.542	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045		A	52777466	C	A	52777466	2	1	27	1	0	0	0	0	0	0	0	1	8507	697	25	4		4	KRT84	12	52777466	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1081627	52777466	81074429	661	11112											
KRT84	3890	hgsc.bcm.edu	37	chr12	52778829	52778829	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctatcataggtaccttgtCaatgaaggaggcaaacttgt	13	11	10	7	0	2	1	2	1	0	0	2	2	2	2	1	3	3	3	1	3	6	5	rs140632920	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:52778829C>A	ENST00000257951.3	-	1	607	c.541G>T	c.(541-543)Gac>Tac	p.D181Y	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	181	Coil 1A.|Rod.				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)		GGTACCTTGTCAATGAAGGAG	0.488													C|||	7	0.00139776	0.0	0.0	5008	,	,		22209	0.0		0.006	False		,,,				2504	0.001				p.D181Y		Atlas-SNP	.											.	KRT84	61	.	0			c.G541T						PASS	.	C	TYR/ASP	3,4403	6.2+/-15.9	0,3,2200	216	219	218		541	5	1	12	dbSNP_134	218	22,8578	16.0+/-53.3	0,22,4278	yes	missense	KRT84	NM_033045.3	160	0,25,6478	AA,AC,CC		0.2558,0.0681,0.1922	probably-damaging	181/601	52778829	25,12981	2203	4300	6503	SO:0001583	missense	3890	exon1			CCTTGTCAATGAA	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.541G>T	12.37:g.52778829C>A	ENSP00000257951:p.Asp181Tyr	111	0	0		98	55	0.561224	NM_033045	B2RA43|Q6ISB0|Q701L6	Missense_Mutation	SNP	ENST00000257951.3	37	CCDS8825.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	21.2	4.119953	0.77323	6.81E-4	0.002558	ENSG00000161849	ENST00000257951	D	0.92299	-3.01	5.03	5.03	0.67393	Filament (1);	0.000000	0.52532	D	0.000066	D	0.97695	0.9244	H	0.97315	3.98	0.58432	D	0.999998	D	0.76494	0.999	D	0.77004	0.989	D	0.98708	1.0703	10	0.87932	D	0	.	18.9362	0.92586	0.0:1.0:0.0:0.0	.	181	Q9NSB2	KRT84_HUMAN	Y	181	ENSP00000257951:D181Y	ENSP00000257951:D181Y	D	-	1	0	KRT84	51065096	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.612000	0.82975	2.790000	0.95986	0.609000	0.83330	GAC	C|0.998;A|0.002	0.002	strong		0.488	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045		A	52778829	C	A	52778829	3	1	27	1	0	0	0	0	1	0	0	0	8507	826	29	4	1297	4	KRT84	12	52778829	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1363	52778829	81073066	662	11113											
KRT84	3890	hgsc.bcm.edu	37	chr12	52779159	52779159	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gactccacagtggatgggccGagagcctacagctgctatcc	9	7	12	13	1	0	1	0	0	0	1	2	4	2	2	4	2	4	2	4	2	2	2	rs145217788	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:52779159G>A	ENST00000257951.3	-	1	277	c.211C>T	c.(211-213)Cgg>Tgg	p.R71W	RP3-416H24.4_ENST00000547174.1_RNA	NM_033045.3	NP_149034.2	Q9NSB2	KRT84_HUMAN	keratin 84	71	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)		TGGATGGGCCGAGAGCCTACA	0.597													G|||	6	0.00119808	0.0	0.0	5008	,	,		18426	0.0		0.005	False		,,,				2504	0.001				p.R71W		Atlas-SNP	.											.	KRT84	61	.	0			c.C211T						PASS	.	G	TRP/ARG	3,4403	6.2+/-15.9	0,3,2200	99	95	96		211	3.3	0.7	12	dbSNP_134	96	21,8579	15.3+/-51.7	0,21,4279	yes	missense	KRT84	NM_033045.3	101	0,24,6479	AA,AG,GG		0.2442,0.0681,0.1845	probably-damaging	71/601	52779159	24,12982	2203	4300	6503	SO:0001583	missense	3890	exon1			TGGGCCGAGAGCC	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.211C>T	12.37:g.52779159G>A	ENSP00000257951:p.Arg71Trp	165	0	0		118	52	0.440678	NM_033045	B2RA43|Q6ISB0|Q701L6	Missense_Mutation	SNP	ENST00000257951.3	37	CCDS8825.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	9.259	1.042600	0.19748	6.81E-4	0.002442	ENSG00000161849	ENST00000257951	D	0.82344	-1.6	5.15	3.33	0.38152	.	0.736856	0.12245	N	0.486182	T	0.79341	0.4429	M	0.69358	2.11	0.09310	N	1	D	0.59357	0.985	B	0.37508	0.252	T	0.72243	-0.4350	10	0.62326	D	0.03	.	12.4648	0.55751	0.1438:0.0:0.8562:0.0	.	71	Q9NSB2	KRT84_HUMAN	W	71	ENSP00000257951:R71W	ENSP00000257951:R71W	R	-	1	2	KRT84	51065426	0.048000	0.20356	0.713000	0.30519	0.014000	0.08584	0.355000	0.20163	1.553000	0.49476	-0.192000	0.12808	CGG	G|0.998;A|0.002	0.002	strong		0.597	KRT84-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405187.1	NM_033045		A	52779159	G	A	52779159	3	1	27	1	0	0	0	0	1	0	0	0	8507	1057	37	1	1627	1	KRT84	12	52779159	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	330	52779159	81072736	663	11114											
KRT82	3888	hgsc.bcm.edu	37	chr12	52788814	52788814	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctagcgtcatgctggatttcCgcccgctcccacagctcagt	6	10	9	16	3	2	0	2	0	0	0	4	1	4	1	3	1	3	3	3	1	1	2	rs61730587	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:52788814C>T	ENST00000257974.2	-	9	1564	c.1487G>A	c.(1486-1488)cGg>cAg	p.R496Q	RP3-416H24.4_ENST00000547174.1_RNA	NM_033033.3	NP_149022.3	Q9NSB4	KRT82_HUMAN	keratin 82	496	Tail.					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)		GCTGGATTTCCGCCCGCTCCC	0.642													c|||	21	0.00419329	0.0023	0.0072	5008	,	,		16513	0.0		0.0089	False		,,,				2504	0.0041				p.R496Q		Atlas-SNP	.											KRT82,NS,carcinoma,-1,1	KRT82	45	1	0			c.G1487A						PASS	.	T	GLN/ARG	14,4392	21.2+/-45.6	0,14,2189	48	48	48		1487	-0.4	0	12	dbSNP_129	48	113,8487	58.7+/-120.3	1,111,4188	yes	missense	KRT82	NM_033033.3	43	1,125,6377	TT,TC,CC		1.314,0.3177,0.9765	benign	496/514	52788814	127,12879	2203	4300	6503	SO:0001583	missense	3888	exon9			GATTTCCGCCCGC	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.1487G>A	12.37:g.52788814C>T	ENSP00000257974:p.Arg496Gln	150	0	0		114	56	0.491228	NM_033033		Missense_Mutation	SNP	ENST00000257974.2	37	CCDS8826.1	11	0.005036630036630037	0	0.0	4	0.011049723756906077	0	0.0	7	0.009234828496042216	c	11.54	1.670563	0.29693	0.003177	0.01314	ENSG00000161850	ENST00000257974	D	0.82255	-1.59	4.59	-0.424	0.12321	.	0.753921	0.10873	N	0.624709	T	0.52933	0.1765	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.04013	0.001	T	0.39800	-0.9596	10	0.25106	T	0.35	.	4.4613	0.11668	0.1481:0.4148:0.0:0.4371	rs61730587	496	Q9NSB4	KRT82_HUMAN	Q	496	ENSP00000257974:R496Q	ENSP00000257974:R496Q	R	-	2	0	KRT82	51075081	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.155000	0.16362	-0.326000	0.08564	-0.215000	0.12644	CGG	C|0.991;T|0.009	0.009	strong		0.642	KRT82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405189.1	NM_033033		T	52788814	C	T	52788814	3	4	27	1	0	0	0	0	1	0	0	0	8505	652	23	1	58	1	KRT82	12	52788814	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	9655	52788814	81063081	664	11115											
KRT73	319101	hgsc.bcm.edu	37	chr12	53002197	53002197	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgctgaatccaaagccagccCctgtgcctgccatcccggcc	7	7	9	18	1	0	1	0	1	0	0	2	1	2	1	8	1	5	1	8	1	2	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:53002197C>T	ENST00000305748.3	-	9	1440	c.1406G>A	c.(1405-1407)gGg>gAg	p.G469E	RP11-641A6.2_ENST00000551089.1_RNA|RP11-641A6.2_ENST00000552364.1_RNA|RP11-641A6.2_ENST00000549180.1_RNA	NM_175068.2	NP_778238.1	Q86Y46	K2C73_HUMAN	keratin 73	469	Tail.					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)		AAAGCCAGCCCCTGTGCCTGC	0.612																																					p.G469E		Atlas-SNP	.											.	KRT73	101	.	0			c.G1406A						PASS	.						41	39	40					12																	53002197		2203	4300	6503	SO:0001583	missense	319101	exon9			CCAGCCCCTGTGC	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.1406G>A	12.37:g.53002197C>T	ENSP00000307014:p.Gly469Glu	75	0	0		69	9	0.130435	NM_175068	Q32MB2	Missense_Mutation	SNP	ENST00000305748.3	37	CCDS8834.1	.	.	.	.	.	.	.	.	.	.	C	18.20	3.570160	0.65765	.	.	ENSG00000186049	ENST00000305748;ENST00000552855	D;D	0.82893	-1.58;-1.66	4.88	4.88	0.63580	.	0.185839	0.26421	N	0.024464	T	0.74473	0.3721	L	0.46819	1.47	0.09310	N	0.999999	P	0.39216	0.664	B	0.35607	0.206	T	0.64287	-0.6443	10	0.09338	T	0.73	.	13.7369	0.62824	0.0:1.0:0.0:0.0	.	469	Q86Y46	K2C73_HUMAN	E	469;214	ENSP00000307014:G469E;ENSP00000449081:G214E	ENSP00000307014:G469E	G	-	2	0	KRT73	51288464	0.031000	0.19500	0.210000	0.23637	0.137000	0.21094	1.906000	0.39887	2.709000	0.92574	0.655000	0.94253	GGG	.	.	none		0.612	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405700.1	NM_175068		T	53002197	C	T	53002197	3	4	27	1	0	0	0	0	1	0	0	0	8495	623	22	2	220	2	KRT73	12	53002197	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	213383	53002197	80849698	665	11116											
KRT73	319101	hgsc.bcm.edu	37	chr12	53012053	53012053	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccccaaggccacactgccaaAcatgctgccagcaaagccac	13	3	7	18	0	0	0	0	0	0	0	0	0	0	0	6	1	6	2	6	1	3	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:53012053A>C	ENST00000305748.3	-	1	290	c.256T>G	c.(256-258)Ttt>Gtt	p.F86V	RP11-641A6.2_ENST00000552364.1_RNA	NM_175068.2	NP_778238.1	Q86Y46	K2C73_HUMAN	keratin 73	86	Gly-rich.|Head.					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)		ACACTGCCAAACATGCTGCCA	0.637																																					p.F86V		Atlas-SNP	.											.	KRT73	101	.	0			c.T256G						PASS	.						107	119	115					12																	53012053		2203	4300	6503	SO:0001583	missense	319101	exon1			TGCCAAACATGCT	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.256T>G	12.37:g.53012053A>C	ENSP00000307014:p.Phe86Val	108	0	0		118	69	0.584746	NM_175068	Q32MB2	Missense_Mutation	SNP	ENST00000305748.3	37	CCDS8834.1	.	.	.	.	.	.	.	.	.	.	A	12.73	2.025490	0.35701	.	.	ENSG00000186049	ENST00000305748	D	0.91351	-2.83	4.64	3.5	0.40072	.	0.114168	0.38959	N	0.001513	D	0.91372	0.7278	M	0.89534	3.04	0.28878	N	0.894598	P	0.38455	0.632	B	0.43155	0.41	D	0.84270	0.0488	10	0.23302	T	0.38	.	6.9916	0.24758	0.7232:0.1908:0.086:0.0	.	86	Q86Y46	K2C73_HUMAN	V	86	ENSP00000307014:F86V	ENSP00000307014:F86V	F	-	1	0	KRT73	51298320	0.193000	0.23313	1.000000	0.80357	0.888000	0.51559	3.442000	0.52900	0.887000	0.36136	0.533000	0.62120	TTT	.	.	none		0.637	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405700.1	NM_175068		C	53012053	A	C	53012053	3	2	27	1	0	0	0	0	1	0	0	0	8495	43	2	5	1402	5	KRT73	12	53012053	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	9856	53012053	80839842	666	11117											
RAB5B	5869	hgsc.bcm.edu	37	chr12	56383858	56383858	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aggggtgcccaagctgcaatCgtggtttacgacattactaa	11	10	11	9	2	0	0	0	0	0	0	1	1	0	0	1	3	5	3	1	3	5	4	rs141101772	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:56383858C>T	ENST00000360299.5	+	3	512	c.291C>T	c.(289-291)atC>atT	p.I97I	RAB5B_ENST00000448789.2_Silent_p.I97I|RAB5B_ENST00000553116.1_Silent_p.I97I	NM_002868.3	NP_002859.1	P61020	RAB5B_HUMAN	RAB5B, member RAS oncogene family	97					antigen processing and presentation (GO:0019882)|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 (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTP-dependent protein binding (GO:0030742)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(1)|liver(2)|lung(4)|upper_aerodigestive_tract(1)	9			UCEC - Uterine corpus endometrioid carcinoma (6;0.0471)|OV - Ovarian serous cystadenocarcinoma(18;0.235)			AAGCTGCAATCGTGGTTTACG	0.488													C|||	2	0.000399361	0.0	0.0014	5008	,	,		23495	0.0		0.001	False		,,,				2504	0.0				p.I97I		Atlas-SNP	.											RAB5B,NS,lymphoid_neoplasm,+2,1	RAB5B	22	1	0			c.C291T						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	100	79	86		291	-4.7	0.9	12	dbSNP_134	86	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous	RAB5B	NM_002868.2		0,12,6491	TT,TC,CC		0.1047,0.0681,0.0923		97/216	56383858	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	5869	exon3			TGCAATCGTGGTT		CCDS8900.1, CCDS58244.1	12q13	2008-07-30						"RAB, member RAS oncogene"	9784	protein-coding gene	gene with protein product		179514				1541686, 10403367	Standard	NM_001252037		Approved		uc001siw.3	P61020		ENST00000360299.5:c.291C>T	12.37:g.56383858C>T		181	0	0		150	67	0.446667	NM_002868	A8K982|B4DKD7|P35239|P35277|Q6PIK9|Q86TH0|Q8IXL2	Silent	SNP	ENST00000360299.5	37	CCDS8900.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	10.22	1.290646	0.23564	6.81E-4	0.001047	ENSG00000111540	ENST00000549218	.	.	.	4.81	-4.69	0.03299	.	.	.	.	.	T	0.50000	0.1590	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48692	-0.9013	4	.	.	.	-8.259	7.6574	0.28383	0.0:0.2762:0.1073:0.6166	.	.	.	.	C	17	.	.	R	+	1	0	RAB5B	54670125	0.398000	0.25279	0.865000	0.33974	0.959000	0.62525	-0.395000	0.07287	-0.990000	0.03481	-1.329000	0.01275	CGT	C|0.999;T|0.001	0.001	strong		0.488	RAB5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405396.1			T	56383858	C	T	56383858	2	4	27	1	0	0	0	0	0	0	0	1	12964	874	31	1		1	RAB5B	12	56383858	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3371805	56383858	77468037	667	11118											
STAT6	6778	hgsc.bcm.edu	37	chr12	57496654	57496654	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacaggatagtggctttggcAttgttgtcttggttgccatg	6	15	13	7	0	1	0	0	0	1	0	1	1	1	1	1	4	1	4	1	4	1	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:57496654A>T	ENST00000300134.3	-	12	1588	c.1263T>A	c.(1261-1263)aaT>aaA	p.N421K	STAT6_ENST00000537215.2_Missense_Mutation_p.N311K|STAT6_ENST00000454075.3_Missense_Mutation_p.N421K|STAT6_ENST00000543873.2_Missense_Mutation_p.N421K|STAT6_ENST00000556155.1_Missense_Mutation_p.N421K|STAT6_ENST00000538913.2_Missense_Mutation_p.N311K	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	421					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						TGGCTTTGGCATTGTTGTCTT	0.522																																					p.N421K		Atlas-SNP	.											.	STAT6	69	.	0			c.T1263A						PASS	.						144	115	125					12																	57496654		2203	4300	6503	SO:0001583	missense	6778	exon12			TTTGGCATTGTTG	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.1263T>A	12.37:g.57496654A>T	ENSP00000300134:p.Asn421Lys	114	0	0		120	14	0.116667	NM_001178079	A8K316|B7ZA27|F5GXI9|Q5FBW5|Q71UP4	Missense_Mutation	SNP	ENST00000300134.3	37	CCDS8931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.7|21.7	4.184980|4.184980	0.78677|0.78677	.|.	.|.	ENSG00000166888|ENSG00000166888	ENST00000553533|ENST00000300134;ENST00000535201;ENST00000538913;ENST00000543873;ENST00000556155;ENST00000537215;ENST00000454075;ENST00000542721;ENST00000542516	.|D;D;D;D;D;D	.|0.87729	.|-2.29;-2.29;-2.29;-2.29;-2.29;-2.29	5.44|5.44	1.65|1.65	0.23941|0.23941	.|STAT transcription factor, DNA-binding (1);p53-like transcription factor, DNA-binding (1);EF-hand-like domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.91593|0.91593	0.7344|0.7344	M|M	0.76838|0.76838	2.35|2.35	0.58432|0.58432	D|D	0.999997|0.999997	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.998;0.999	D|D	0.89559|0.89559	0.3805|0.3805	5|10	.|0.87932	.|D	.|0	-17.2208|-17.2208	8.3744|8.3744	0.32434|0.32434	0.762:0.0:0.238:0.0|0.762:0.0:0.238:0.0	.|.	.|421;421	.|A8K4S9;P42226	.|.;STAT6_HUMAN	S|K	122|421;311;311;421;421;311;421;311;421	.|ENSP00000300134:N421K;ENSP00000445409:N311K;ENSP00000438451:N421K;ENSP00000451742:N421K;ENSP00000444530:N311K;ENSP00000401486:N421K	.|ENSP00000300134:N421K	C|N	-|-	1|3	0|2	STAT6|STAT6	55782921|55782921	0.536000|0.536000	0.26378|0.26378	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	-0.213000|-0.213000	0.09305|0.09305	0.124000|0.124000	0.18369|0.18369	0.528000|0.528000	0.53228|0.53228	TGC|AAT	.	.	none		0.522	STAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412248.3	NM_003153		T	57496654	A	T	57496654	3	4	27	1	0	0	0	0	1	0	0	0	15285	214	8	5	1324	5	STAT6	12	57496654	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	1112796	57496654	76355241	668	11119											
LRP1	4035	hgsc.bcm.edu	37	chr12	57550588	57550588	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catgcctgtgaaaacgaccaGtatgggaagccgggtggctg	10	7	15	9	2	0	1	0	1	0	0	0	3	0	2	3	3	3	2	3	3	4	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:57550588G>A	ENST00000243077.3	+	10	1912	c.1446G>A	c.(1444-1446)caG>caA	p.Q482Q		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	482	EGF-like 3. {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)	AAAACGACCAGTATGGGAAGC	0.632																																					p.Q482Q		Atlas-SNP	.											.	LRP1	428	.	0			c.G1446A						PASS	.						44	40	42					12																	57550588		2203	4300	6503	SO:0001819	synonymous_variant	4035	exon10			CGACCAGTATGGG	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.1446G>A	12.37:g.57550588G>A		57	0	0		47	5	0.106383	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			.	.	none		0.632	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		A	57550588	G	A	57550588	2	1	27	1	0	0	0	0	0	0	0	1	8960	1020	36	2		2	LRP1	12	57550588	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	53934	57550588	76301307	669	11120											
LRP1	4035	hgsc.bcm.edu	37	chr12	57587437	57587437	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcaacggggccgacgactgTggggatggctctgacgagat	8	7	17	9	4	1	2	0	1	1	1	1	6	1	3	1	5	2	2	1	5	1	0	rs34456957	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:57587437T>C	ENST00000243077.3	+	47	8239	c.7773T>C	c.(7771-7773)tgT>tgC	p.C2591C	MIR1228_ENST00000408438.1_RNA	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	2591	LDL-receptor class A 12. {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)	CCGACGACTGTGGGGATGGCT	0.602													T|||	7	0.00139776	0.0	0.0029	5008	,	,		21660	0.0		0.005	False		,,,				2504	0.0				p.C2591C		Atlas-SNP	.											.	LRP1	428	.	0			c.T7773C						PASS	.	T		6,4400	11.4+/-27.6	0,6,2197	94	84	87		7773	-8.4	0.8	12	dbSNP_126	87	63,8537	39.3+/-95.6	0,63,4237	no	coding-synonymous	LRP1	NM_002332.2		0,69,6434	CC,CT,TT		0.7326,0.1362,0.5305		2591/4545	57587437	69,12937	2203	4300	6503	SO:0001819	synonymous_variant	4035	exon47			CGACTGTGGGGAT	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.7773T>C	12.37:g.57587437T>C		71	0	0		64	29	0.453125	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			T|0.996;C|0.004	0.004	strong		0.602	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		C	57587437	T	C	57587437	2	2	27	1	0	0	0	0	0	0	0	1	8960	1702	59	3		3	LRP1	12	57587437	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	36849	57587437	76264458	670	11121											
LRP1	4035	hgsc.bcm.edu	37	chr12	57587714	57587714	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtgggcgagttccgctgcCgggacgggacctgcatcggg	4	7	19	11	5	0	0	0	0	0	0	2	3	1	2	3	4	2	3	3	4	0	1	rs367968116		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:57587714C>T	ENST00000243077.3	+	48	8303	c.7837C>T	c.(7837-7839)Cgg>Tgg	p.R2613W	MIR1228_ENST00000408438.1_RNA	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	2613	LDL-receptor class A 13. {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)	GTTCCGCTGCCGGGACGGGAC	0.607																																					p.R2613W		Atlas-SNP	.											LRP1,NS,lymphoid_neoplasm,-1,1	LRP1	428	1	0			c.C7837T						PASS	.	C	TRP/ARG	0,4406		0,0,2203	97	89	92		7837	4.2	1	12		92	1,8599	1.2+/-3.3	0,1,4299	no	missense	LRP1	NM_002332.2	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	2613/4545	57587714	1,13005	2203	4300	6503	SO:0001583	missense	4035	exon48			CGCTGCCGGGACG	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.7837C>T	12.37:g.57587714C>T	ENSP00000243077:p.Arg2613Trp	108	0	0		105	38	0.361905	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	C	15.34	2.803636	0.50315	0.0	1.16E-4	ENSG00000123384	ENST00000243077	D	0.95690	-3.78	5.09	4.19	0.49359	.	0.164278	0.37261	N	0.002175	D	0.96617	0.8896	M	0.62088	1.915	0.80722	D	1	D	0.76494	0.999	D	0.63283	0.913	D	0.96868	0.9637	10	0.66056	D	0.02	.	14.7368	0.69422	0.0:0.8543:0.1457:0.0	.	2613	Q07954	LRP1_HUMAN	W	2613	ENSP00000243077:R2613W	ENSP00000243077:R2613W	R	+	1	2	LRP1	55873981	1.000000	0.71417	1.000000	0.80357	0.515000	0.34225	1.355000	0.34068	1.368000	0.46115	0.650000	0.86243	CGG	.	.	weak		0.607	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		T	57587714	C	T	57587714	3	4	27	1	0	0	0	0	1	0	0	0	8960	643	23	1	8027	1	LRP1	12	57587714	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	277	57587714	76264181	671	11122											
LRP1	4035	hgsc.bcm.edu	37	chr12	57597023	57597023	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acggccgctgcatcgcggggCgctggaaatgcgatggagac	8	5	17	11	6	0	1	0	0	0	1	1	4	0	2	1	5	2	3	1	5	1	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:57597023C>T	ENST00000243077.3	+	69	11237	c.10771C>T	c.(10771-10773)Cgc>Tgc	p.R3591C		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	3591	LDL-receptor class A 27. {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)	CATCGCGGGGCGCTGGAAATG	0.672																																					p.R3591C		Atlas-SNP	.											LRP1,bladder,carcinoma,-1,1	LRP1	428	1	0			c.C10771T						PASS	.						36	34	35					12																	57597023		2199	4298	6497	SO:0001583	missense	4035	exon69			GCGGGGCGCTGGA	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.10771C>T	12.37:g.57597023C>T	ENSP00000243077:p.Arg3591Cys	112	0	0		89	25	0.280899	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	C	15.80	2.939225	0.52972	.	.	ENSG00000123384	ENST00000243077;ENST00000555124	D;D	0.95656	-3.77;-3.77	5.06	4.15	0.48705	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.151987	0.40385	N	0.001116	D	0.98197	0.9404	H	0.94658	3.565	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98813	1.0744	10	0.59425	D	0.04	.	13.6941	0.62567	0.1557:0.8443:0.0:0.0	.	3591	Q07954	LRP1_HUMAN	C	3591;172	ENSP00000243077:R3591C;ENSP00000451012:R172C	ENSP00000243077:R3591C	R	+	1	0	LRP1	55883290	0.172000	0.23043	1.000000	0.80357	0.384000	0.30261	0.760000	0.26475	1.325000	0.45301	0.650000	0.86243	CGC	.	.	none		0.672	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		T	57597023	C	T	57597023	3	4	27	1	0	0	0	0	1	0	0	0	8960	768	27	1	11045	1	LRP1	12	57597023	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	9309	57597023	76254872	672	11123											
SLC16A7	9194	hgsc.bcm.edu	37	chr12	60168491	60168491	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taaccataattggcaaatacTtctataggaagcgacccatg	15	10	7	9	1	1	0	0	0	1	0	1	2	1	1	2	2	3	1	2	2	7	7			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:60168491T>G	ENST00000261187.4	+	4	579	c.415T>G	c.(415-417)Ttc>Gtc	p.F139V	SLC16A7_ENST00000552024.1_Missense_Mutation_p.F139V|SLC16A7_ENST00000547379.1_Missense_Mutation_p.F139V|SLC16A7_ENST00000543448.1_Missense_Mutation_p.F40V|SLC16A7_ENST00000552432.1_Missense_Mutation_p.F139V	NM_004731.4	NP_004722.2	O60669	MOT2_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 7	139					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)	TGGCAAATACTTCTATAGGAA	0.398																																					p.F139V		Atlas-SNP	.											.	SLC16A7	82	.	0			c.T415G						PASS	.						77	73	74					12																	60168491		2203	4300	6503	SO:0001583	missense	9194	exon5			AAATACTTCTATA	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.415T>G	12.37:g.60168491T>G	ENSP00000261187:p.Phe139Val	257	0	0		209	44	0.210526	NM_001270622	Q8NEM3|Q9UPB3	Missense_Mutation	SNP	ENST00000261187.4	37	CCDS8961.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.592137	0.86953	.	.	ENSG00000118596	ENST00000552432;ENST00000547379;ENST00000552024;ENST00000548610;ENST00000261187;ENST00000543448;ENST00000548444	T;T;T;T;T;T;T	0.60299	0.2;0.2;0.2;0.2;0.2;0.2;0.2	5.87	5.87	0.94306	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.83087	0.5178	H	0.95745	3.715	0.80722	D	1	D	0.71674	0.998	D	0.74023	0.982	D	0.88302	0.2950	9	.	.	.	.	16.2631	0.82557	0.0:0.0:0.0:1.0	.	139	O60669	MOT2_HUMAN	V	139;139;139;139;139;40;24	ENSP00000449547:F139V;ENSP00000448071:F139V;ENSP00000448742:F139V;ENSP00000446722:F139V;ENSP00000261187:F139V;ENSP00000443731:F40V;ENSP00000447814:F24V	.	F	+	1	0	SLC16A7	58454758	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	8.040000	0.89188	2.239000	0.73571	0.528000	0.53228	TTC	.	.	none		0.398	SLC16A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406587.1	NM_004731		G	60168491	T	G	60168491	3	3	27	1	0	0	0	0	1	0	0	0	14428	1609	56	5	425	5	SLC16A7	12	60168491	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	2571468	60168491	73683404	673	11124											
MSRB3	253827	hgsc.bcm.edu	37	chr12	65857078	65857078	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	agtggggtcgccagcccggcCcaggcagacaaagcggagct	9	3	16	13	3	0	1	0	0	0	1	1	2	0	2	3	5	3	2	3	5	1	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:65857078C>T	ENST00000355192.3	+	6	681	c.555C>T	c.(553-555)gcC>gcT	p.A185A	MSRB3_ENST00000535664.1_Silent_p.A178A|MSRB3_ENST00000308259.5_Silent_p.A178A	NM_198080.3	NP_932346.1	Q8IXL7	MSRB3_HUMAN	methionine sulfoxide reductase B3	185					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)		CCAGCCCGGCCCAGGCAGACA	0.473																																					p.A185A		Atlas-SNP	.											.	MSRB3	80	.	0			c.C555T						PASS	.						49	47	48					12																	65857078		2203	4300	6503	SO:0001819	synonymous_variant	253827	exon6			CCCGGCCCAGGCA	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.555C>T	12.37:g.65857078C>T		113	0	0		75	27	0.36	NM_198080	B4DR19|B7ZAQ0|Q6UXS2	Silent	SNP	ENST00000355192.3	37	CCDS8973.1																																																																																			.	.	none		0.473	MSRB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401421.1	NM_198080		T	65857078	C	T	65857078	2	4	27	1	0	0	0	0	0	0	0	1	9898	610	22	2		2	MSRB3	12	65857078	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	5688587	65857078	67994817	674	11125											
PTPRR	5801	hgsc.bcm.edu	37	chr12	71286606	71286606	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgtttgcttacttgagcttcGgaagaggaatggtagctatg	9	13	13	6	2	0	2	0	1	0	1	1	4	0	4	0	3	4	5	0	3	5	6	rs149684669	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:71286606G>A	ENST00000283228.2	-	2	662	c.210C>T	c.(208-210)tcC>tcT	p.S70S		NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	70					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)		CTTGAGCTTCGGAAGAGGAAT	0.458													G|||	10	0.00199681	0.0	0.0014	5008	,	,		18216	0.0		0.006	False		,,,				2504	0.0031				p.S70S		Atlas-SNP	.											.	PTPRR	109	.	0			c.C210T						PASS	.	G		6,4400	11.4+/-27.6	0,6,2197	230	233	232		210	-3.7	0	12	dbSNP_134	232	32,8568	22.8+/-68.1	0,32,4268	no	coding-synonymous	PTPRR	NM_002849.3		0,38,6465	AA,AG,GG		0.3721,0.1362,0.2922		70/658	71286606	38,12968	2203	4300	6503	SO:0001819	synonymous_variant	5801	exon2			AGCTTCGGAAGAG	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.210C>T	12.37:g.71286606G>A		371	0	0		295	139	0.471186	NM_002849	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Silent	SNP	ENST00000283228.2	37	CCDS8998.1																																																																																			G|0.997;A|0.003	0.003	strong		0.458	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849		A	71286606	G	A	71286606	2	1	27	1	0	0	0	0	0	0	0	1	12825	1103	39	1		1	PTPRR	12	71286606	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	5429528	71286606	62565289	675	11126											
NAV3	89795	hgsc.bcm.edu	37	chr12	78574783	78574783	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttccaggcagtcattaggaCtttctctaaacaatttgaac	12	13	6	10	0	2	1	1	1	1	0	4	2	3	2	1	2	2	1	1	2	5	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:78574783C>A	ENST00000397909.2	+	30	5823	c.5650C>A	c.(5650-5652)Ctt>Att	p.L1884I	NAV3_ENST00000266692.7_Missense_Mutation_p.L1685I|NAV3_ENST00000552300.1_3'UTR|NAV3_ENST00000536525.2_Missense_Mutation_p.L1862I|NAV3_ENST00000228327.6_Missense_Mutation_p.L1862I			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1884	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						GTCATTAGGACTTTCTCTAAA	0.488										HNSCC(70;0.22)																											p.L1862I		Atlas-SNP	.											.	NAV3	506	.	0			c.C5584A						PASS	.						116	117	117					12																	78574783		2000	4164	6164	SO:0001583	missense	89795	exon29			TTAGGACTTTCTC	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.5650C>A	12.37:g.78574783C>A	ENSP00000381007:p.Leu1884Ile	120	0	0		103	18	0.174757	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.9|27.9	4.869227|4.869227	0.91587|0.91587	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692;ENST00000378640;ENST00000550788|ENST00000552895	T;T;T;T;T|.	0.32023|.	1.53;1.51;1.52;1.47;2.32|.	6.02|6.02	6.02|6.02	0.97574|0.97574	.|.	0.000000|.	0.36034|.	U|.	0.002827|.	T|T	0.76285|0.76285	0.3966|0.3966	M|M	0.66939|0.66939	2.045|2.045	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.76494|.	0.998;0.996;0.999;0.998|.	D;D;D;D|.	0.83275|.	0.949;0.986;0.996;0.99|.	T|T	0.72404|0.72404	-0.4304|-0.4304	10|5	0.59425|.	D|.	0.04|.	-12.5593|-12.5593	20.547|20.547	0.99278|0.99278	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1862;1685;1884;1862|.	E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2|.	.;.;NAV3_HUMAN;.|.	I|N	1862;1884;1862;1685;476;484|756	ENSP00000446132:L1862I;ENSP00000381007:L1884I;ENSP00000228327:L1862I;ENSP00000266692:L1685I;ENSP00000448303:L484I|.	ENSP00000228327:L1862I|.	L|T	+|+	1|2	0|0	NAV3|NAV3	77098914|77098914	1.000000|1.000000	0.71417|0.71417	0.417000|0.417000	0.26559|0.26559	0.868000|0.868000	0.49771|0.49771	7.487000|7.487000	0.81328|0.81328	2.850000|2.850000	0.98022|0.98022	0.650000|0.650000	0.86243|0.86243	CTT|ACT	.	.	none		0.488	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		A	78574783	C	A	78574783	3	1	27	1	0	0	0	0	1	0	0	0	10194	565	20	4	5698	4	NAV3	12	78574783	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	7288177	78574783	55277112	676	11127											
PPP1R12A	4659	hgsc.bcm.edu	37	chr12	80199958	80199958	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgacttacctgctttgtgtgCctgctgaggaagaacccgtt	7	13	11	10	1	0	3	0	2	0	1	0	4	0	4	3	1	5	3	3	1	3	3	rs61756418	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:80199958C>G	ENST00000450142.2	-	13	2077	c.1811G>C	c.(1810-1812)gGc>gCc	p.G604A	PPP1R12A_ENST00000546369.1_Missense_Mutation_p.G517A|PPP1R12A_ENST00000550107.1_Intron|PPP1R12A_ENST00000437004.2_Missense_Mutation_p.G604A|PPP1R12A_ENST00000261207.5_Missense_Mutation_p.G604A|AC073569.1_ENST00000598624.1_Intron	NM_002480.2	NP_002471.1	O14974	MYPT1_HUMAN	protein phosphatase 1, regulatory subunit 12A	604	Ser/Thr-rich.				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						GCTTTGTGTGCCTGCTGAGGA	0.458													C|||	12	0.00239617	0.0008	0.0058	5008	,	,		18491	0.0		0.007	False		,,,				2504	0.0				p.G604A		Atlas-SNP	.											.	PPP1R12A	76	.	0			c.G1811C						PASS	.	C	ALA/GLY,ALA/GLY,ALA/GLY	3,3917		0,3,1957	290	274	279		1811,1550,1811	5.6	1	12	dbSNP_129	279	61,8257		0,61,4098	yes	missense,missense,missense	PPP1R12A	NM_001143885.1,NM_001143886.1,NM_002480.2	60,60,60	0,64,6055	GG,GC,CC		0.7333,0.0765,0.523	possibly-damaging,possibly-damaging,possibly-damaging	604/1031,517/944,604/1031	80199958	64,12174	1960	4159	6119	SO:0001583	missense	4659	exon13			TGTGTGCCTGCTG	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.1811G>C	12.37:g.80199958C>G	ENSP00000389168:p.Gly604Ala	91	0	0		118	51	0.432203	NM_002480	B4DZ09|F8VWB4|Q2NKL4|Q569H0|Q86WU3|Q8NFR6|Q9BYH0	Missense_Mutation	SNP	ENST00000450142.2	37	CCDS44947.1	6|6	0.0027472527472527475|0.0027472527472527475	0|0	0.0|0.0	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	4|4	0.005277044854881266|0.005277044854881266	C|C	15.42|15.42	2.827657|2.827657	0.50845|0.50845	7.65E-4|7.65E-4	0.007333|0.007333	ENSG00000058272|ENSG00000058272	ENST00000553081|ENST00000261207;ENST00000546189;ENST00000360825;ENST00000312727;ENST00000450142;ENST00000437004;ENST00000546369;ENST00000547330	.|T;T;T;T;T	.|0.36340	.|1.33;1.33;1.37;1.36;1.26	5.62|5.62	5.62|5.62	0.85841|0.85841	.|.	.|0.151958	.|0.64402	.|D	.|0.000009	T|T	0.33585|0.33585	0.0868|0.0868	L|L	0.31065|0.31065	0.9|0.9	0.44871|0.44871	D|D	0.997885|0.997885	.|P;D;P	.|0.56035	.|0.93;0.974;0.956	.|P;P;P	.|0.54499	.|0.459;0.754;0.572	T|T	0.03112|0.03112	-1.1071|-1.1071	5|10	.|0.20046	.|T	.|0.44	.|.	19.6432|19.6432	0.95764|0.95764	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs61756418|rs61756418	.|604;604;604	.|F8W8Q6;O14974-2;O14974	.|.;.;MYPT1_HUMAN	P|A	196|604;604;604;604;604;604;517;604	.|ENSP00000261207:G604A;ENSP00000389168:G604A;ENSP00000416769:G604A;ENSP00000449514:G517A;ENSP00000446816:G604A	.|ENSP00000261207:G604A	A|G	-|-	1|2	0|0	PPP1R12A|PPP1R12A	78724089|78724089	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.058000|3.058000	0.49939|0.49939	2.641000|2.641000	0.89580|0.89580	0.591000|0.591000	0.81541|0.81541	GCA|GGC	C|0.996;G|0.004	0.004	strong		0.458	PPP1R12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407254.2	NM_002480		G	80199958	C	G	80199958	3	3	27	1	0	0	0	0	1	0	0	0	12366	739	26	4	1333	4	PPP1R12A	12	80199958	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1625175	80199958	53651937	677	11128											
LRRIQ1	84125	hgsc.bcm.edu	37	chr12	85459100	85459100	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctccacactggcagagtgtAcaaatcttcagtttctatcc	10	13	6	12	0	4	1	1	0	3	1	6	1	5	1	2	1	1	3	2	1	3	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:85459100A>C	ENST00000393217.2	+	9	2513	c.2452A>C	c.(2452-2454)Aca>Cca	p.T818P		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	818										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)		GGCAGAGTGTACAAATCTTCA	0.398																																					p.T818P		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.A2452C						PASS	.						146	138	141					12																	85459100		2203	4300	6503	SO:0001583	missense	84125	exon9			GAGTGTACAAATC	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.2452A>C	12.37:g.85459100A>C	ENSP00000376910:p.Thr818Pro	105	0	0		82	16	0.195122	NM_001079910	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	37	CCDS41816.1	.	.	.	.	.	.	.	.	.	.	A	8.766	0.924819	0.18056	.	.	ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393217	T	0.09817	2.94	5.6	-8.78	0.00824	.	1.013500	0.07926	N	0.976669	T	0.04272	0.0118	N	0.16833	0.445	0.09310	N	0.999996	B;B	0.12630	0.003;0.006	B;B	0.14578	0.002;0.011	T	0.39165	-0.9627	10	0.38643	T	0.18	.	1.7967	0.03062	0.1469:0.2665:0.1369:0.4496	.	818;793	Q96JM4;C9JI57	LRIQ1_HUMAN;.	P	818;793;818	ENSP00000376910:T818P	ENSP00000256007:T818P	T	+	1	0	LRRIQ1	83983231	0.002000	0.14202	0.150000	0.22450	0.780000	0.44128	-1.292000	0.02772	-1.451000	0.01933	0.477000	0.44152	ACA	.	.	none		0.398	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		C	85459100	A	C	85459100	3	2	27	1	0	0	0	0	1	0	0	0	9038	391	14	5	2482	5	LRRIQ1	12	85459100	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	5259142	85459100	48392795	678	11129											
CEP290	80184	hgsc.bcm.edu	37	chr12	88520192	88520192	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctgatactcaataatttcAtcatctttagaagacaaaat	16	14	4	7	0	4	3	3	1	1	2	4	3	4	3	0	0	2	1	0	0	7	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:88520192A>T	ENST00000552810.1	-	12	1309	c.966T>A	c.(964-966)gaT>gaA	p.D322E	CEP290_ENST00000397838.3_5'UTR|CEP290_ENST00000309041.7_Missense_Mutation_p.D322E	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	322					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						CAATAATTTCATCATCTTTAG	0.294																																					p.D322E		Atlas-SNP	.											.	CEP290	195	.	0			c.T966A						PASS	.						68	62	64					12																	88520192		1794	4063	5857	SO:0001583	missense	80184	exon12			AATTTCATCATCT	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.966T>A	12.37:g.88520192A>T	ENSP00000448012:p.Asp322Glu	234	0	0		197	56	0.284264	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	37	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	A	3.324	-0.138216	0.06669	.	.	ENSG00000198707	ENST00000552810;ENST00000309041;ENST00000536998;ENST00000545139	T;T	0.50813	0.73;0.73	5.26	4.12	0.48240	.	0.239053	0.38897	N	0.001528	T	0.23289	0.0563	N	0.19112	0.55	0.80722	D	1	B;B	0.14805	0.004;0.011	B;B	0.18561	0.009;0.022	T	0.15723	-1.0427	10	0.02654	T	1	.	3.2543	0.06826	0.5547:0.0:0.1648:0.2805	.	322;322	Q05BJ6;O15078	.;CE290_HUMAN	E	322;322;322;224	ENSP00000448012:D322E;ENSP00000308021:D322E	ENSP00000308021:D322E	D	-	3	2	CEP290	87044323	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.545000	0.36169	0.838000	0.34948	0.455000	0.32223	GAT	.	.	none		0.294	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114		T	88520192	A	T	88520192	3	4	27	1	0	0	0	0	1	0	0	0	3255	214	8	5	6645	5	CEP290	12	88520192	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	3061092	88520192	45331703	679	11130											
BTG1	694	hgsc.bcm.edu	37	chr12	92538171	92538171	+	Nonsense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tggttgatgcgaatacaacgGtaacccgatcccttgcatgg	10	10	11	10	3	0	1	0	1	0	0	1	3	1	1	2	3	5	3	2	3	4	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:92538171G>C	ENST00000256015.3	-	2	562	c.201C>G	c.(199-201)taC>taG	p.Y67*	C12orf79_ENST00000551843.1_5'Flank|C12orf79_ENST00000551563.2_5'Flank|RP11-796E2.4_ENST00000501008.2_RNA|C12orf79_ENST00000549802.1_5'Flank|RP11-796E2.4_ENST00000499685.2_RNA|C12orf79_ENST00000546975.1_5'Flank	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	67					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)	p.Y67Y(1)		haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				GAATACAACGGTAACCCGATC	0.458			T	MYC	BCLL						OREG0022024	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y67X		Atlas-SNP	.		Dom	yes		12	12q22	694	"B-cell translocation gene 1, anti-proliferative"		L	BTG1,NS,lymphoid_neoplasm,0,1	BTG1	30	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C201G						PASS	.						131	131	131					12																	92538171		2203	4300	6503	SO:0001587	stop_gained	694	exon2			ACAACGGTAACCC		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.201C>G	12.37:g.92538171G>C	ENSP00000256015:p.Tyr67*	125	0	0	1291	109	20	0.183486	NM_001731	P31607	Nonsense_Mutation	SNP	ENST00000256015.3	37	CCDS9043.1	.	.	.	.	.	.	.	.	.	.	G	37	6.239268	0.97403	.	.	ENSG00000133639	ENST00000256015	.	.	.	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.0719	13.2979	0.60307	0.072:0.0:0.928:0.0	.	.	.	.	X	67	.	ENSP00000256015:Y67X	Y	-	3	2	BTG1	91062302	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.401000	0.66326	2.738000	0.93877	0.655000	0.94253	TAC	.	.	none		0.458	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1			C	92538171	G	C	92538171	4	2	27	1	0	0	0	0	0	1	0	0	1555	1256	44	4	318	4	BTG1	12	92538171	Nonsense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	4017979	92538171	41313724	680	11131											
ANO4	121601	hgsc.bcm.edu	37	chr12	101520847	101520847	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acaccacaacgagtggccgtGaccatgtaggtgagaggtgt	11	7	14	9	2	0	2	0	2	0	1	0	4	0	2	3	3	1	1	3	3	2	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:101520847G>A	ENST00000392977.3	+	27	3077	c.2867G>A	c.(2866-2868)tGa>tAa	p.*956*	ANO4_ENST00000299222.9_Silent_p.*476*|ANO4_ENST00000392979.3_Silent_p.*921*|ANO4_ENST00000550015.1_Silent_p.*476*			Q32M45	ANO4_HUMAN	anoctamin 4	0					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						GAGTGGCCGTGACCATGTAGG	0.483										HNSCC(74;0.22)																											p.X921X		Atlas-SNP	.											.	ANO4	183	.	0			c.G2762A						PASS	.						91	61	71					12																	101520847		2203	4300	6503	SO:0001819	synonymous_variant	121601	exon26			GGCCGTGACCATG	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.2867G>A	12.37:g.101520847G>A		94	0	0		84	22	0.261905	NM_178826	Q8NAJ0|Q8NB39|Q8NB53	Silent	SNP	ENST00000392977.3	37																																																																																				.	.	none		0.483	ANO4-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409295.1	NM_178826		A	101520847	G	A	101520847	2	1	27	1	0	0	0	0	0	0	0	1	699	1285	45	2		2	ANO4	12	101520847	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	8982676	101520847	32331048	681	11132											
UTP20	27340	hgsc.bcm.edu	37	chr12	101674926	101674926	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctgaacgactggggaatgtTaatattgatattattcaccg	12	13	10	6	2	1	2	1	2	0	0	1	4	1	3	1	2	1	2	1	2	6	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:101674926T>G	ENST00000261637.4	+	2	252	c.78T>G	c.(76-78)gtT>gtG	p.V26V		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	26					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						TGGGGAATGTTAATATTGATA	0.303																																					p.V26V		Atlas-SNP	.											.	UTP20	222	.	0			c.T78G						PASS	.						82	83	82					12																	101674926		2203	4299	6502	SO:0001819	synonymous_variant	27340	exon2			GAATGTTAATATT	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.78T>G	12.37:g.101674926T>G		119	0	0		111	31	0.279279	NM_014503	Q9H3H4	Silent	SNP	ENST00000261637.4	37	CCDS9081.1																																																																																			.	.	none		0.303	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		G	101674926	T	G	101674926	2	3	27	1	0	0	0	0	0	0	0	1	17114	1741	61	5		5	UTP20	12	101674926	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	154079	101674926	32176969	682	11133											
CMKLR1	1240	hgsc.bcm.edu	37	chr12	108686572	108686572	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgatcaccagaccattgccCagaatcccgaggaagcagac	14	5	9	13	1	1	4	1	1	0	3	2	6	2	5	4	1	2	1	4	1	2	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:108686572C>T	ENST00000312143.7	-	3	531	c.168G>A	c.(166-168)ctG>ctA	p.L56L	CMKLR1_ENST00000397688.2_Silent_p.L54L|CMKLR1_ENST00000550402.1_Silent_p.L56L|CMKLR1_ENST00000552995.1_Silent_p.L54L|CMKLR1_ENST00000412676.1_Silent_p.L56L	NM_001142344.1|NM_004072.2	NP_001135816.1|NP_004063.1	Q99788	CML1_HUMAN	chemokine-like receptor 1	56					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						GACCATTGCCCAGAATCCCGA	0.517																																					p.L56L		Atlas-SNP	.											CMKLR1,NS,carcinoma,-2,1	CMKLR1	67	1	0			c.G168A						PASS	.						101	100	100					12																	108686572		2010	4173	6183	SO:0001819	synonymous_variant	1240	exon3			ATTGCCCAGAATC	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.168G>A	12.37:g.108686572C>T		169	0	0		117	28	0.239316	NM_001142344	A8K6Y5|O75748|Q3KP37|Q5U0H0|Q99789	Silent	SNP	ENST00000312143.7	37	CCDS44965.1																																																																																			.	.	none		0.517	CMKLR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404867.1			T	108686572	C	T	108686572	2	4	27	1	0	0	0	0	0	0	0	1	3581	581	21	2		2	CMKLR1	12	108686572	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	7011646	108686572	25165323	683	11134											
ANKRD13A	88455	hgsc.bcm.edu	37	chr12	110449872	110449872	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttgctgtttccttgggacaTttggaatctgctcgagtctt	5	17	10	9	1	2	0	0	0	2	0	4	3	3	2	1	2	2	3	1	2	1	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:110449872T>A	ENST00000261739.4	+	2	325	c.159T>A	c.(157-159)caT>caA	p.H53Q	ANKRD13A_ENST00000550404.1_3'UTR	NM_033121.1	NP_149112.1	Q8IZ07	AN13A_HUMAN	ankyrin repeat domain 13A	53						endosome (GO:0005768)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(8)|lung(3)|urinary_tract(1)	16						CCTTGGGACATTTGGAATCTG	0.413																																					p.H53Q		Atlas-SNP	.											.	ANKRD13A	39	.	0			c.T159A						PASS	.						129	115	120					12																	110449872		2203	4300	6503	SO:0001583	missense	88455	exon2			GGGACATTTGGAA	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.159T>A	12.37:g.110449872T>A	ENSP00000261739:p.His53Gln	101	0	0		72	15	0.208333	NM_033121	O60736	Missense_Mutation	SNP	ENST00000261739.4	37	CCDS9140.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.594305	0.86953	.	.	ENSG00000076513	ENST00000261739	T	0.66460	-0.21	6.17	1.29	0.21616	Ankyrin repeat-containing domain (3);	0.043066	0.85682	D	0.000000	T	0.64271	0.2583	L	0.39020	1.185	0.80722	D	1	D;D;D	0.61080	0.966;0.989;0.966	P;P;P	0.55055	0.69;0.767;0.69	T	0.63033	-0.6727	10	0.66056	D	0.02	-17.1926	9.0087	0.36129	0.0:0.3655:0.0:0.6345	.	53;53;53	B4DYP5;Q3ZTS7;Q8IZ07	.;.;AN13A_HUMAN	Q	53	ENSP00000261739:H53Q	ENSP00000261739:H53Q	H	+	3	2	ANKRD13A	108934255	0.996000	0.38824	0.984000	0.44739	0.996000	0.88848	0.671000	0.25172	0.199000	0.20427	0.533000	0.62120	CAT	.	.	none		0.413	ANKRD13A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403430.1	NM_033121		A	110449872	T	A	110449872	3	1	27	1	0	0	0	0	1	0	0	0	641	1490	52	5	165	5	ANKRD13A	12	110449872	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	1763300	110449872	23402023	684	11135											
DTX1	1840	hgsc.bcm.edu	37	chr12	113496151	113496151	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gccaccacattgagaacgtgCtgaaggaggacgctcgcggt	10	6	14	11	4	0	2	0	2	0	1	1	5	0	4	2	3	2	2	2	3	2	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:113496151C>G	ENST00000257600.3	+	1	657	c.154C>G	c.(154-156)Ctg>Gtg	p.L52V		NM_004416.2	NP_004407.2	Q86Y01	DTX1_HUMAN	deltex 1, E3 ubiquitin ligase	52	WWE 1. {ECO:0000255|PROSITE- ProRule:PRU00248}.				cell surface receptor signaling pathway (GO:0007166)|glial cell differentiation (GO:0010001)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of T cell differentiation (GO:0045581)|Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)|regulation of Notch signaling pathway (GO:0008593)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Notch binding (GO:0005112)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	32						TGAGAACGTGCTGAAGGAGGA	0.647																																					p.L52V		Atlas-SNP	.											.	DTX1	83	.	0			c.C154G						PASS	.						121	106	111					12																	113496151		2203	4300	6503	SO:0001583	missense	1840	exon1			AACGTGCTGAAGG	AF053700	CCDS9164.1	12q24	2014-01-28	2014-01-28			ENSG00000135144			3060	protein-coding gene	gene with protein product		602582	"deltex homolog 1 (Drosophila)"			9590294, 12670957	Standard	NM_004416		Approved	hDx-1	uc001tuk.1	Q86Y01	OTTHUMG00000169610	ENST00000257600.3:c.154C>G	12.37:g.113496151C>G	ENSP00000257600:p.Leu52Val	83	0	0		79	13	0.164557	NM_004416	O60630|Q9BS04	Missense_Mutation	SNP	ENST00000257600.3	37	CCDS9164.1	.	.	.	.	.	.	.	.	.	.	C	18.19	3.569791	0.65765	.	.	ENSG00000135144	ENST00000257600	T	0.46819	0.86	3.9	3.9	0.45041	WWE domain (2);WWE domain, subgroup (1);	0.093779	0.43919	U	0.000507	T	0.31606	0.0802	N	0.16478	0.41	0.39022	D	0.95976	B	0.29481	0.245	B	0.28305	0.088	T	0.19128	-1.0315	10	0.25106	T	0.35	-0.2273	14.8783	0.70513	0.0:1.0:0.0:0.0	.	52	Q86Y01	DTX1_HUMAN	V	52	ENSP00000257600:L52V	ENSP00000257600:L52V	L	+	1	2	DTX1	111980534	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	3.362000	0.52314	2.021000	0.59480	0.555000	0.69702	CTG	.	.	none		0.647	DTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405045.2			G	113496151	C	G	113496151	3	3	27	1	0	0	0	0	1	0	0	0	4795	796	28	4	156	4	DTX1	12	113496151	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3046279	113496151	20355744	685	11136											
DTX1	1840	hgsc.bcm.edu	37	chr12	113496182	113496182	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctcgcggttccgtggtccTggggcaggtggacgcccagc	3	7	17	14	5	0	0	0	0	0	0	3	1	2	1	3	6	1	3	3	6	0	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:113496182T>G	ENST00000257600.3	+	1	688	c.185T>G	c.(184-186)cTg>cGg	p.L62R		NM_004416.2	NP_004407.2	Q86Y01	DTX1_HUMAN	deltex 1, E3 ubiquitin ligase	62	WWE 1. {ECO:0000255|PROSITE- ProRule:PRU00248}.				cell surface receptor signaling pathway (GO:0007166)|glial cell differentiation (GO:0010001)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of T cell differentiation (GO:0045581)|Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)|regulation of Notch signaling pathway (GO:0008593)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Notch binding (GO:0005112)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	32						TCCGTGGTCCTGGGGCAGGTG	0.637																																					p.L62R		Atlas-SNP	.											.	DTX1	83	.	0			c.T185G						PASS	.						123	112	116					12																	113496182		2203	4300	6503	SO:0001583	missense	1840	exon1			TGGTCCTGGGGCA	AF053700	CCDS9164.1	12q24	2014-01-28	2014-01-28			ENSG00000135144			3060	protein-coding gene	gene with protein product		602582	"deltex homolog 1 (Drosophila)"			9590294, 12670957	Standard	NM_004416		Approved	hDx-1	uc001tuk.1	Q86Y01	OTTHUMG00000169610	ENST00000257600.3:c.185T>G	12.37:g.113496182T>G	ENSP00000257600:p.Leu62Arg	59	0	0		58	12	0.206897	NM_004416	O60630|Q9BS04	Missense_Mutation	SNP	ENST00000257600.3	37	CCDS9164.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.436253	0.83885	.	.	ENSG00000135144	ENST00000257600	T	0.64438	-0.1	4.05	4.05	0.47172	WWE domain (2);WWE domain, subgroup (1);	0.000000	0.56097	D	0.000033	T	0.81288	0.4791	M	0.89840	3.065	0.47862	D	0.999538	D	0.76494	0.999	D	0.87578	0.998	D	0.85075	0.0942	10	0.87932	D	0	-9.9988	12.1675	0.54138	0.0:0.0:0.0:1.0	.	62	Q86Y01	DTX1_HUMAN	R	62	ENSP00000257600:L62R	ENSP00000257600:L62R	L	+	2	0	DTX1	111980565	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.286000	0.78671	1.710000	0.51325	0.454000	0.30748	CTG	.	.	none		0.637	DTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405045.2			G	113496182	T	G	113496182	3	3	27	1	0	0	0	0	1	0	0	0	4795	1580	55	5	187	5	DTX1	12	113496182	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	31	113496182	20355713	686	11137											
TBX5	6910	hgsc.bcm.edu	37	chr12	114793414	114793414	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	atgaggggatagagtccttgGcacgccatgagagtagagga	12	7	16	6	1	0	4	0	2	0	3	1	7	1	6	2	4	0	2	2	4	2	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:114793414G>A	ENST00000310346.4	-	9	2146	c.1480C>T	c.(1480-1482)Cca>Tca	p.P494S	TBX5_ENST00000349716.5_Missense_Mutation_p.P444S|TBX5_ENST00000405440.2_Missense_Mutation_p.P494S	NM_000192.3	NP_000183.2	Q99593	TBX5_HUMAN	T-box 5	494				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)		AGAGTCCTTGGCACGCCATGA	0.597																																					p.P494S	NSCLC(152;1358 1980 4050 23898 40356)	Atlas-SNP	.											.	TBX5	188	.	0			c.C1480T						PASS	.						57	55	56					12																	114793414		2203	4300	6503	SO:0001583	missense	6910	exon9			TCCTTGGCACGCC	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.1480C>T	12.37:g.114793414G>A	ENSP00000309913:p.Pro494Ser	90	0	0		87	42	0.482759	NM_000192	A6ND77|O15301|Q96TB0|Q9Y4I2	Missense_Mutation	SNP	ENST00000310346.4	37	CCDS9173.1	.	.	.	.	.	.	.	.	.	.	G	3.093	-0.186357	0.06340	.	.	ENSG00000089225	ENST00000349716;ENST00000310346;ENST00000405440	D;D;D	0.86694	-2.15;-2.16;-2.16	5.42	3.6	0.41247	.	0.168870	0.53938	N	0.000057	T	0.76586	0.4008	L	0.31664	0.95	0.49130	D	0.999753	B	0.12013	0.005	B	0.10450	0.005	T	0.64935	-0.6290	10	0.06757	T	0.87	.	11.3993	0.49860	0.145:0.0:0.855:0.0	.	494	Q99593	TBX5_HUMAN	S	444;494;494	ENSP00000337723:P444S;ENSP00000309913:P494S;ENSP00000384152:P494S	ENSP00000309913:P494S	P	-	1	0	TBX5	113277797	1.000000	0.71417	0.916000	0.36221	0.860000	0.49131	5.471000	0.66762	0.667000	0.31107	0.655000	0.94253	CCA	.	.	none		0.597	TBX5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388297.1	NM_080717		A	114793414	G	A	114793414	3	1	27	1	0	0	0	0	1	0	0	0	15676	1203	42	2	80	2	TBX5	12	114793414	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1297232	114793414	19058481	687	11138											
WDR66	144406	hgsc.bcm.edu	37	chr12	122413481	122413481	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acttctactattctcagctcCgcagtcaaggcatcgacaca	11	10	6	14	2	3	0	2	0	2	0	6	1	4	0	1	1	2	3	1	1	3	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:122413481C>T	ENST00000288912.4	+	19	3750	c.2896C>T	c.(2896-2898)Cgc>Tgc	p.R966C		NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	966							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)		TTCTCAGCTCCGCAGTCAAGG	0.438																																					p.R966C	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											.	WDR66	143	.	0			c.C2896T						PASS	.						107	97	101					12																	122413481		1935	4131	6066	SO:0001583	missense	144406	exon19			CAGCTCCGCAGTC	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.2896C>T	12.37:g.122413481C>T	ENSP00000288912:p.Arg966Cys	150	0	0		132	59	0.44697	NM_144668	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	37	CCDS41853.1	.	.	.	.	.	.	.	.	.	.	C	14.04	2.417308	0.42918	.	.	ENSG00000158023	ENST00000288912	T	0.08546	3.08	5.26	5.26	0.73747	.	0.400698	0.27096	N	0.020942	T	0.12092	0.0294	M	0.84326	2.69	0.80722	D	1	P	0.44429	0.835	B	0.35278	0.199	T	0.01702	-1.1292	10	0.54805	T	0.06	.	9.8744	0.41194	0.1397:0.7858:0.0:0.0745	.	966	Q8TBY9	WDR66_HUMAN	C	966	ENSP00000288912:R966C	ENSP00000288912:R966C	R	+	1	0	WDR66	120897864	1.000000	0.71417	1.000000	0.80357	0.763000	0.43281	1.700000	0.37815	2.452000	0.82932	0.561000	0.74099	CGC	.	.	none		0.438	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668		T	122413481	C	T	122413481	3	4	27	1	0	0	0	0	1	0	0	0	17332	652	23	1	3025	1	WDR66	12	122413481	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	7620067	122413481	11438414	688	11139											
BCL7A	605	hgsc.bcm.edu	37	chr12	122460048	122460048	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggagccgggccaaagatgaTatcaagagggtcatggcggc	12	5	16	8	2	2	3	2	1	0	2	2	4	2	4	2	5	1	0	2	5	3	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:122460048T>G	ENST00000261822.4	+	1	257	c.51T>G	c.(49-51)gaT>gaG	p.D17E	BCL7A_ENST00000538010.1_Missense_Mutation_p.D17E|RP11-87C12.5_ENST00000538710.1_lincRNA	NM_001024808.1	NP_001019979.1	Q4VC05	BCL7A_HUMAN	B-cell CLL/lymphoma 7A	17					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)		CCAAAGATGATATCAAGAGGG	0.716			T	MYC	BNHL																																p.D17E	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.T51G						PASS	.						23	23	23					12																	122460048		2201	4297	6498	SO:0001583	missense	605	exon1			AGATGATATCAAG	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.51T>G	12.37:g.122460048T>G	ENSP00000261822:p.Asp17Glu	32	0	0		47	8	0.170213	NM_020993	B4DJN6|B7ZB21|Q13843|Q14CT7	Missense_Mutation	SNP	ENST00000261822.4	37	CCDS53841.1	.	.	.	.	.	.	.	.	.	.	t	12.37	1.916812	0.33815	.	.	ENSG00000110987	ENST00000538010;ENST00000261822	T;T	0.62788	0.0;0.06	4.22	0.427	0.16489	.	0.000000	0.85682	U	0.000000	T	0.63248	0.2495	L	0.42245	1.32	0.46078	D	0.998856	D;P	0.63046	0.992;0.537	D;B	0.76071	0.987;0.391	T	0.58261	-0.7667	10	0.35671	T	0.21	.	3.1649	0.06533	0.1787:0.3071:0.0:0.5142	.	17;17	Q4VC05;Q4VC05-2	BCL7A_HUMAN;.	E	17	ENSP00000445868:D17E;ENSP00000261822:D17E	ENSP00000261822:D17E	D	+	3	2	BCL7A	120944431	1.000000	0.71417	0.996000	0.52242	0.059000	0.15707	1.804000	0.38873	-0.181000	0.10619	-0.570000	0.04155	GAT	.	.	none		0.716	BCL7A-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000401712.1			G	122460048	T	G	122460048	3	3	27	1	0	0	0	0	1	0	0	0	1378	1403	49	5	53	5	BCL7A	12	122460048	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	46567	122460048	11391847	689	11140											
ABCB9	23457	hgsc.bcm.edu	37	chr12	123444265	123444265	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagagcagcttctgcagcGtggccccagacgcctgctcg	7	6	14	14	3	1	2	0	0	1	2	2	3	1	2	3	2	5	4	3	2	0	1	rs114398803	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:123444265G>A	ENST00000542678.1	-	2	3356	c.518C>T	c.(517-519)aCg>aTg	p.T173M	ABCB9_ENST00000392439.3_Missense_Mutation_p.T173M|ABCB9_ENST00000346530.5_Missense_Mutation_p.T173M|ABCB9_ENST00000344275.7_Missense_Mutation_p.T173M|ABCB9_ENST00000280560.8_Missense_Mutation_p.T173M|ABCB9_ENST00000442833.2_Missense_Mutation_p.T173M|ABCB9_ENST00000540285.1_Missense_Mutation_p.T173M|ABCB9_ENST00000442028.2_Missense_Mutation_p.T173M			Q9NP78	ABCB9_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 9	173					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)		CTTCTGCAGCGTGGCCCCAGA	0.706													G|||	2	0.000399361	0.0008	0.0	5008	,	,		11470	0.0		0.001	False		,,,				2504	0.0				p.T173M	Ovarian(49;786 1333 9175 38236)	Atlas-SNP	.											.	ABCB9	50	.	0			c.C518T						PASS	.	G	MET/THR,MET/THR,MET/THR	0,4406		0,0,2203	37	37	37		518,518,518	5.3	1	12	dbSNP_132	37	1,8595	1.2+/-3.3	0,1,4297	no	missense,missense,missense	ABCB9	NM_019624.3,NM_019625.3,NM_203444.3	81,81,81	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	173/724,173/767,173/767	123444265	1,13001	2203	4298	6501	SO:0001583	missense	23457	exon2			TGCAGCGTGGCCC	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.518C>T	12.37:g.123444265G>A	ENSP00000440288:p.Thr173Met	35	0	0		26	10	0.384615	NM_019625	B4E2J0|Q5W9G7|Q769F3|Q769F4|Q96AB1|Q9P208	Missense_Mutation	SNP	ENST00000542678.1	37	CCDS9241.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	16.27	3.076558	0.55753	0.0	1.16E-4	ENSG00000150967	ENST00000280560;ENST00000540285;ENST00000346530;ENST00000392439;ENST00000542678;ENST00000442028	D;D;D;D;D;D	0.90732	-2.39;-2.72;-2.61;-2.39;-2.39;-2.37	5.3	5.3	0.74995	ABC transporter, transmembrane domain, type 1 (1);	0.000000	0.85682	D	0.000000	D	0.93177	0.7827	L	0.55481	1.735	0.50467	D	0.999878	P;D;B;D	0.76494	0.48;0.999;0.287;0.999	B;D;B;P	0.68039	0.079;0.955;0.109;0.875	D	0.92663	0.6143	10	0.48119	T	0.1	-32.5478	14.1825	0.65583	0.0:0.0:0.8504:0.1496	.	173;173;173;173	B4E2J0;Q9NP78-3;Q9NP78-2;Q9NP78	.;.;.;ABCB9_HUMAN	M	173	ENSP00000280560:T173M;ENSP00000441734:T173M;ENSP00000280559:T173M;ENSP00000376234:T173M;ENSP00000440288:T173M;ENSP00000394898:T173M	ENSP00000280560:T173M	T	-	2	0	ABCB9	122010218	1.000000	0.71417	0.999000	0.59377	0.886000	0.51366	6.425000	0.73370	2.653000	0.90120	0.561000	0.74099	ACG	G|0.999;A|0.001	0.001	strong		0.706	ABCB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400956.1	NM_019624		A	123444265	G	A	123444265	3	1	27	1	0	0	0	0	1	0	0	0	48	1145	40	1	1826	1	ABCB9	12	123444265	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	984217	123444265	10407630	690	11141											
GPR133	283383	hgsc.bcm.edu	37	chr12	131475607	131475607	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gccaagcctcttcatgacatCcacagcaagccccgtggtga	10	7	9	15	1	2	2	1	2	1	0	3	2	3	2	5	1	3	1	5	1	2	1	rs137909892	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:131475607C>A	ENST00000261654.5	+	7	1353	c.794C>A	c.(793-795)tCc>tAc	p.S265Y	GPR133_ENST00000535015.1_Missense_Mutation_p.S297Y|RP11-76C10.5_ENST00000542980.1_lincRNA	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	265					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)		TTCATGACATCCACAGCAAGC	0.473													C|||	16	0.00319489	0.0	0.0	5008	,	,		19824	0.0		0.006	False		,,,				2504	0.0102				p.S265Y		Atlas-SNP	.											.	GPR133	136	.	0			c.C794A						PASS	.	C	TYR/SER	4,4402	8.1+/-20.4	0,4,2199	140	105	117		794	3.4	0	12	dbSNP_134	117	53,8547	34.3+/-88.2	1,51,4248	yes	missense	GPR133	NM_198827.3	144	1,55,6447	AA,AC,CC		0.6163,0.0908,0.4383	possibly-damaging	265/875	131475607	57,12949	2203	4300	6503	SO:0001583	missense	283383	exon7			TGACATCCACAGC	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.794C>A	12.37:g.131475607C>A	ENSP00000261654:p.Ser265Tyr	134	0	0		144	75	0.520833	NM_198827	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Missense_Mutation	SNP	ENST00000261654.5	37	CCDS9272.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	10.74	1.435607	0.25813	9.08E-4	0.006163	ENSG00000111452	ENST00000261654;ENST00000542091;ENST00000535015;ENST00000537600	T;T	0.46063	0.88;0.88	4.4	3.41	0.39046	.	0.630854	0.15230	N	0.273456	T	0.20292	0.0488	N	0.19112	0.55	0.22571	N	0.998973	B;P	0.35600	0.343;0.511	B;B	0.31751	0.116;0.135	T	0.18808	-1.0325	10	0.72032	D	0.01	.	11.8911	0.52630	0.0:0.8233:0.1767:0.0	.	297;265	B7ZLF7;Q6QNK2	.;GP133_HUMAN	Y	265;205;297;24	ENSP00000261654:S265Y;ENSP00000444425:S297Y	ENSP00000261654:S265Y	S	+	2	0	GPR133	130041560	0.001000	0.12720	0.006000	0.13384	0.002000	0.02628	0.878000	0.28126	2.395000	0.81488	0.557000	0.71058	TCC	C|0.997;A|0.003	0.003	strong		0.473	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827		A	131475607	C	A	131475607	3	1	27	1	0	0	0	0	1	0	0	0	6651	855	30	4	820	4	GPR133	12	131475607	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	8031342	131475607	2376288	691	11142											
ULK1	8408	hgsc.bcm.edu	37	chr12	132401058	132401058	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccggacgctgcccgacctctCggaggtgggacccttccatg	5	7	13	16	4	1	0	0	0	1	0	3	4	2	3	5	4	1	1	5	4	0	1	rs55815560	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr12:132401058C>T	ENST00000321867.4	+	20	2345	c.1994C>T	c.(1993-1995)tCg>tTg	p.S665L	ULK1_ENST00000540647.1_5'Flank	NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1	665			S -> L (in dbSNP:rs55815560). {ECO:0000269|PubMed:17344846}.		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)		CCCGACCTCTCGGAGGTGGGA	0.697													C|||	5	0.000998403	0.0	0.0	5008	,	,		15038	0.001		0.003	False		,,,				2504	0.001				p.S665L		Atlas-SNP	.											.	ULK1	92	.	0			c.C1994T						PASS	.	C	LEU/SER	1,4397	2.1+/-5.4	0,1,2198	37	43	41		1994	3.8	0.9	12	dbSNP_129	41	22,8572	16.6+/-54.9	0,22,4275	yes	missense	ULK1	NM_003565.2	145	0,23,6473	TT,TC,CC		0.256,0.0227,0.177	benign	665/1051	132401058	23,12969	2199	4297	6496	SO:0001583	missense	8408	exon20			ACCTCTCGGAGGT	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.1994C>T	12.37:g.132401058C>T	ENSP00000324560:p.Ser665Leu	60	0	0		61	30	0.491803	NM_003565	Q9UQ28	Missense_Mutation	SNP	ENST00000321867.4	37	CCDS9274.1	8	0.003663003663003663	3	0.006097560975609756	0	0.0	1	0.0017482517482517483	4	0.005277044854881266	C	11.31	1.599607	0.28534	2.27E-4	0.00256	ENSG00000177169	ENST00000321867;ENST00000541761	T;T	0.29397	1.57;2.5	5.69	3.79	0.43588	.	1.033790	0.07680	N	0.936898	T	0.19685	0.0473	L	0.44542	1.39	0.20873	N	0.999836	B	0.09022	0.002	B	0.04013	0.001	T	0.04165	-1.0972	10	0.35671	T	0.21	-11.4096	7.8361	0.29371	0.365:0.5069:0.1281:0.0	rs55815560	665	O75385	ULK1_HUMAN	L	665;13	ENSP00000324560:S665L;ENSP00000444298:S13L	ENSP00000324560:S665L	S	+	2	0	ULK1	130967011	0.866000	0.29940	0.897000	0.35233	0.013000	0.08279	2.057000	0.41365	2.684000	0.91462	0.655000	0.94253	TCG	C|0.998;T|0.002	0.002	strong		0.697	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397769.3			T	132401058	C	T	132401058	3	4	27	1	0	0	0	0	1	0	0	0	16990	893	31	1	2072	1	ULK1	12	132401058	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	925451	132401058	1450837	692	11143											
SACS	26278	hgsc.bcm.edu	37	chr13	23910850	23910850	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatgactgcctcacacccaCggtttcaaaaagttcgcgga	11	8	9	13	3	2	1	2	1	0	0	3	2	2	2	2	2	1	3	2	2	2	2	rs142869943		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:23910850C>T	ENST00000382292.3	-	9	7438	c.7165G>A	c.(7165-7167)Gtg>Atg	p.V2389M	SACS_ENST00000382298.3_Missense_Mutation_p.V2389M|SACS_ENST00000402364.1_Missense_Mutation_p.V1639M			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2389					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)		CTCACACCCACGGTTTCAAAA	0.353													C|||	1	0.000199681	0.0	0.0	5008	,	,		18298	0.0		0.001	False		,,,				2504	0.0				p.V2389M		Atlas-SNP	.											.	SACS	871	.	0			c.G7165A						PASS	.	C	MET/VAL	0,4406		0,0,2203	35	36	35		7165	4.9	1	13	dbSNP_134	35	2,8596	2.2+/-6.3	0,2,4297	yes	missense	SACS	NM_014363.4	21	0,2,6500	TT,TC,CC		0.0233,0.0,0.0154	benign	2389/4580	23910850	2,13002	2203	4299	6502	SO:0001583	missense	26278	exon10			CACCCACGGTTTC	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.7165G>A	13.37:g.23910850C>T	ENSP00000371729:p.Val2389Met	85	0	0		81	44	0.54321	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	6.390	0.440092	0.12104	0.0	2.33E-4	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.94000	-3.33;-3.33;-3.33	5.84	4.88	0.63580	.	0.248470	0.41500	D	0.000871	D	0.87541	0.6203	L	0.27053	0.805	0.34084	D	0.659888	B	0.23185	0.081	B	0.18871	0.023	D	0.86770	0.1972	10	0.33940	T	0.23	.	12.7477	0.57289	0.0:0.8603:0.0:0.1397	.	2389	Q9NZJ4	SACS_HUMAN	M	2389;1639;2389	ENSP00000371729:V2389M;ENSP00000385844:V1639M;ENSP00000371735:V2389M	ENSP00000371729:V2389M	V	-	1	0	SACS	22808850	1.000000	0.71417	1.000000	0.80357	0.078000	0.17371	3.105000	0.50314	2.779000	0.95612	0.655000	0.94253	GTG	C|1.000;T|0.000	0.000	strong		0.353	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		T	23910850	C	T	23910850	3	4	27	1	0	0	0	0	1	0	0	0	13819	536	19	1	6578	1	SACS	13	23910850	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10		23910850	91259028	693	11144											
ATP12A	479	hgsc.bcm.edu	37	chr13	25255705	25255705	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gggcttctctttcagaaaacCccagaaatttactccgtgga	11	11	8	11	1	2	2	1	0	1	2	4	3	3	3	3	2	2	1	3	2	4	4	rs41288276	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:25255705C>A	ENST00000381946.3	+	2	182	c.15C>A	c.(13-15)acC>acA	p.T5T	ATP12A_ENST00000218548.6_Silent_p.T5T			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	5					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)		TTCAGAAAACCCCAGAAATTT	0.542													C|||	256	0.0511182	0.1044	0.0303	5008	,	,		17355	0.001		0.0477	False		,,,				2504	0.0491				p.T5T	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.C15A						PASS	.	C	,	401,4005	199.8+/-223.2	18,365,1820	51	54	53		15,15	-6.3	0	13	dbSNP_127	53	391,8209	125.5+/-184.1	5,381,3914	no	coding-synonymous,coding-synonymous	ATP12A	NM_001185085.1,NM_001676.5	,	23,746,5734	AA,AC,CC		4.5465,9.1012,6.0895	,	5/1046,5/1040	25255705	792,12214	2203	4300	6503	SO:0001819	synonymous_variant	479	exon2			GAAAACCCCAGAA	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.15C>A	13.37:g.25255705C>A		83	0	0		71	36	0.507042	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Silent	SNP	ENST00000381946.3	37	CCDS31948.1																																																																																			C|0.942;A|0.058	0.058	strong		0.542	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		A	25255705	C	A	25255705	2	1	27	1	0	0	0	0	0	0	0	1	1122	610	22	4		4	ATP12A	13	25255705	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1344855	25255705	89914173	694	11145											
EXOSC8	11340	hgsc.bcm.edu	37	chr13	37577073	37577073	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttgcttatcttttcaggtTcaattagtaccgcagatggt	8	18	8	7	1	3	1	2	0	1	1	3	1	3	1	1	2	2	4	1	2	4	8			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:37577073T>C	ENST00000389704.3	+	4	386	c.121T>C	c.(121-123)Tca>Cca	p.S41P	EXOSC8_ENST00000489088.1_3'UTR|ALG5_ENST00000496689.1_5'Flank	NM_181503.2	NP_852480.1	Q96B26	EXOS8_HUMAN	exosome component 8	41					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)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)			biliary_tract(1)|breast(1)|kidney(2)|pancreas(1)|prostate(1)|skin(1)	7		Lung NSC(96;6.57e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)		all cancers(112;3.67e-07)|Epithelial(112;1.31e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00699)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0411)		CTTTTCAGGTTCAATTAGTAC	0.318																																					p.S41P		Atlas-SNP	.											.	EXOSC8	16	.	0			c.T121C						PASS	.						107	102	103					13																	37577073		2202	4298	6500	SO:0001583	missense	11340	exon4			TCAGGTTCAATTA	AF025438	CCDS31958.1	13q13.1	2010-05-07			ENSG00000120699	ENSG00000120699	3.1.13.-		17035	protein-coding gene	gene with protein product	"CBP-interacting protein 3", "Opa interacting protein 2"	606019				9466265, 11929972	Standard	NM_181503		Approved	OIP2, RRP43, bA421P11.3, Rrp43p, EAP2, p9, CIP3	uc001uwa.3	Q96B26	OTTHUMG00000016742	ENST00000389704.3:c.121T>C	13.37:g.37577073T>C	ENSP00000374354:p.Ser41Pro	153	0	0		120	5	0.0416667	NM_181503	O43480|Q5TBA5	Missense_Mutation	SNP	ENST00000389704.3	37	CCDS31958.1	.	.	.	.	.	.	.	.	.	.	T	18.46	3.629298	0.67015	.	.	ENSG00000120699	ENST00000389704;ENST00000379809	T	0.63255	-0.03	5.65	4.48	0.54585	Ribosomal protein S5 domain 2-type fold (1);Exoribonuclease, phosphorolytic domain 1 (1);	0.108320	0.64402	D	0.000003	T	0.64405	0.2595	L	0.55017	1.72	0.58432	D	0.999998	P;P	0.46064	0.864;0.872	P;P	0.51229	0.663;0.585	T	0.59941	-0.7359	10	0.24483	T	0.36	-15.5735	11.4062	0.49900	0.0:0.0701:0.0:0.9299	.	41;41	Q5JXM0;Q96B26	.;EXOS8_HUMAN	P	41	ENSP00000374354:S41P	ENSP00000369137:S41P	S	+	1	0	EXOSC8	36475073	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.698000	0.84413	1.098000	0.41479	0.533000	0.62120	TCA	.	.	none		0.318	EXOSC8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044535.2	NM_181503		C	37577073	T	C	37577073	3	2	27	1	0	0	0	0	1	0	0	0	5322	1783	62	3	135	3	EXOSC8	13	37577073	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	12321368	37577073	77592805	695	11146											
FOXO1	2308	hgsc.bcm.edu	37	chr13	41134629	41134629	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctccaagatcatcctgttcGgtcataatgggtgagagtct	9	13	10	9	1	4	2	2	1	2	2	7	3	5	2	2	2	0	1	2	2	2	2	rs139436481	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:41134629G>A	ENST00000379561.5	-	2	1383	c.999C>T	c.(997-999)acC>acT	p.T333T	FOXO1_ENST00000473775.1_5'Flank	NM_002015.3	NP_002006.2	Q12778	FOXO1_HUMAN	forkhead box O1	333	Sufficient for interaction with NLK. {ECO:0000250}.				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)		CATCCTGTTCGGTCATAATGG	0.473													G|||	8	0.00159744	0.0008	0.0029	5008	,	,		21916	0.0		0.004	False		,,,				2504	0.001				p.T333T		Atlas-SNP	.											.	FOXO1	110	.	0			c.C999T						PASS	.	G		12,4394	19.1+/-41.9	0,12,2191	153	135	141		999	-3.3	0.7	13	dbSNP_134	141	62,8538	38.3+/-94.2	0,62,4238	no	coding-synonymous	FOXO1	NM_002015.3		0,74,6429	AA,AG,GG		0.7209,0.2724,0.569		333/656	41134629	74,12932	2203	4300	6503	SO:0001819	synonymous_variant	2308	exon2			CTGTTCGGTCATA		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.999C>T	13.37:g.41134629G>A		173	0	0		157	81	0.515924	NM_002015	O43523|Q5VYC7|Q6NSK6	Silent	SNP	ENST00000379561.5	37	CCDS9371.1																																																																																			G|0.996;A|0.004	0.004	strong		0.473	FOXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044634.3	NM_002015		A	41134629	G	A	41134629	2	1	27	1	0	0	0	0	0	0	0	1	6031	1103	39	1		1	FOXO1	13	41134629	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	3557556	41134629	74035249	696	11147											
DGKH	160851	hgsc.bcm.edu	37	chr13	42729463	42729463	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaaggctaatgctgtgtgctGagaacagaaaggagatggag	14	7	16	4	0	0	3	0	1	0	3	0	7	0	4	0	3	3	3	0	3	4	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:42729463G>A	ENST00000337343.4	+	4	442	c.421G>A	c.(421-423)Gag>Aag	p.E141K	DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000538674.1_5'UTR|DGKH_ENST00000536612.1_Missense_Mutation_p.E5K|DGKH_ENST00000540693.1_Missense_Mutation_p.E141K|DGKH_ENST00000261491.5_Missense_Mutation_p.E141K|DGKH_ENST00000379274.2_Missense_Mutation_p.E5K	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	141	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)		GCTGTGTGCTGAGAACAGAAA	0.398																																					p.E141K		Atlas-SNP	.											.	DGKH	106	.	0			c.G421A						PASS	.						157	152	154					13																	42729463		2203	4300	6503	SO:0001583	missense	160851	exon5			TGTGCTGAGAACA	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.421G>A	13.37:g.42729463G>A	ENSP00000337572:p.Glu141Lys	205	0	0		206	42	0.203883	NM_001204504	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Missense_Mutation	SNP	ENST00000337343.4	37	CCDS9381.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.196603	0.79015	.	.	ENSG00000102780	ENST00000540693;ENST00000337343;ENST00000261491;ENST00000379274;ENST00000536612	T;T;T;T;T	0.35605	1.3;1.3;1.3;1.3;1.3	6.04	5.2	0.72013	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.454524	0.24815	N	0.035363	T	0.42720	0.1215	L	0.59967	1.855	0.80722	D	1	B;B	0.26845	0.161;0.065	B;B	0.35607	0.079;0.206	T	0.36040	-0.9764	10	0.52906	T	0.07	.	15.3721	0.74573	0.0664:0.0:0.9336:0.0	.	141;141	Q86XP1-2;Q86XP1	.;DGKH_HUMAN	K	141;141;141;5;5	ENSP00000440823:E141K;ENSP00000337572:E141K;ENSP00000261491:E141K;ENSP00000368576:E5K;ENSP00000445114:E5K	ENSP00000261491:E141K	E	+	1	0	DGKH	41627463	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.837000	0.99465	1.591000	0.50007	-0.236000	0.12185	GAG	.	.	none		0.398	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009		A	42729463	G	A	42729463	3	1	27	1	0	0	0	0	1	0	0	0	4472	1291	45	2	435	2	DGKH	13	42729463	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1594834	42729463	72440415	697	11148											
DGKH	160851	hgsc.bcm.edu	37	chr13	42803315	42803315	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggaaggagcactccacagtcGgaggtgtaatcatattggtg	11	9	14	7	1	1	0	1	0	0	0	3	3	2	3	1	5	1	2	1	5	3	3	rs376522940		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:42803315G>A	ENST00000337343.4	+	30	3675	c.3654G>A	c.(3652-3654)tcG>tcA	p.S1218S	DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000538674.1_3'UTR|DGKH_ENST00000536612.1_Silent_p.S1082S|DGKH_ENST00000261491.5_3'UTR|DGKH_ENST00000379274.2_Silent_p.S1098S	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	1218					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)		CTCCACAGTCGGAGGTGTAAT	0.413																																					p.S1218S		Atlas-SNP	.											.	DGKH	106	.	0			c.G3654A						PASS	.	G	,,,,	1,4405	2.1+/-5.4	0,1,2202	76	77	77		,3294,3246,,3654	-4.6	0	13		77	0,8600		0,0,4300	no	utr-3,coding-synonymous,coding-synonymous,utr-3,coding-synonymous	DGKH	NM_001204504.1,NM_001204505.1,NM_001204506.1,NM_152910.4,NM_178009.3	,,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,,	,1098/1101,1082/1085,,1218/1221	42803315	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	160851	exon30			ACAGTCGGAGGTG	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.3654G>A	13.37:g.42803315G>A		71	0	0		67	10	0.149254	NM_178009	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Silent	SNP	ENST00000337343.4	37	CCDS9381.1																																																																																			.	.	weak		0.413	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009		A	42803315	G	A	42803315	2	1	27	1	0	0	0	0	0	0	0	1	4472	1103	39	1		1	DGKH	13	42803315	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	73852	42803315	72366563	698	11149											
TSC22D1	8848	hgsc.bcm.edu	37	chr13	45147305	45147305	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgacatgatcttacctctcaTcctcgccatccaccaggggt	8	11	7	15	1	2	2	1	2	2	0	6	2	4	2	5	2	1	0	5	2	1	1	rs144252895	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:45147305T>A	ENST00000458659.2	-	1	3396	c.2906A>T	c.(2905-2907)gAt>gTt	p.D969V	TSC22D1_ENST00000501704.2_Intron|TSC22D1_ENST00000460842.1_5'UTR	NM_183422.3	NP_904358.2	Q15714	T22D1_HUMAN	TSC22 domain family, member 1	969					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)		TTACCTCTCATCCTCGCCATC	0.443													T|||	2	0.000399361	0.0	0.0	5008	,	,		19730	0.0		0.002	False		,,,				2504	0.0				p.D969V		Atlas-SNP	.											.	TSC22D1	88	.	0			c.A2906T						PASS	.	T	VAL/ASP	4,4402	8.1+/-20.4	0,4,2199	48	47	47		2906	5.2	1	13	dbSNP_134	47	15,8585	9.8+/-36.6	0,15,4285	yes	missense	TSC22D1	NM_183422.3	152	0,19,6484	AA,AT,TT		0.1744,0.0908,0.1461	benign	969/1074	45147305	19,12987	2203	4300	6503	SO:0001583	missense	8848	exon1			CTCTCATCCTCGC	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.2906A>T	13.37:g.45147305T>A	ENSP00000397435:p.Asp969Val	91	0	0		90	47	0.522222	NM_183422	B3KRL7|B9EGI0|O00666|Q6AHX5|Q6IBU1|Q8NCN1|Q96JS5	Missense_Mutation	SNP	ENST00000458659.2	37	CCDS31966.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	17.27	3.348233	0.61183	9.08E-4	0.001744	ENSG00000102804	ENST00000458659	T	0.35421	1.31	5.16	5.16	0.70880	.	0.000000	0.64402	D	0.000012	T	0.49098	0.1537	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.50499	-0.8821	10	0.62326	D	0.03	.	14.3252	0.66515	0.0:0.0:0.0:1.0	.	969	Q15714	T22D1_HUMAN	V	969	ENSP00000397435:D969V	ENSP00000397435:D969V	D	-	2	0	TSC22D1	44045305	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.659000	0.68010	2.163000	0.67991	0.459000	0.35465	GAT	T|0.998;A|0.002	0.002	strong		0.443	TSC22D1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044743.2	NM_006022		A	45147305	T	A	45147305	3	1	27	1	0	0	0	0	1	0	0	0	16622	1435	50	5	456	5	TSC22D1	13	45147305	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	2343990	45147305	70022573	699	11150											
FNDC3A	22862	hgsc.bcm.edu	37	chr13	49775997	49775997	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tacaaagacttaatgagtcaAcatcctataaattctgtatt	16	14	4	7	0	2	2	1	1	1	1	3	2	3	2	1	0	2	1	1	0	8	7	rs45604939	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:49775997A>G	ENST00000492622.2	+	24	3354	c.3049A>G	c.(3049-3051)Aca>Gca	p.T1017A	FNDC3A_ENST00000398316.3_Missense_Mutation_p.T961A|FNDC3A_ENST00000541916.1_Missense_Mutation_p.T1017A	NM_001079673.1	NP_001073141.1	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	1017	Fibronectin type-III 8. {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)		TAATGAGTCAACATCCTATAA	0.368													A|||	127	0.0253594	0.0008	0.0476	5008	,	,		15155	0.0		0.0676	False		,,,				2504	0.0256				p.T1017A		Atlas-SNP	.											.	FNDC3A	93	.	0			c.A3049G						PASS	.	A	ALA/THR,ALA/THR	52,4354	50.9+/-86.3	0,52,2151	94	95	94		3049,2881	3.7	1	13	dbSNP_127	94	602,7996	158.2+/-211.7	19,564,3716	yes	missense,missense	FNDC3A	NM_001079673.1,NM_014923.3	58,58	19,616,5867	GG,GA,AA		7.0016,1.1802,5.0292	possibly-damaging,possibly-damaging	1017/1199,961/1143	49775997	654,12350	2203	4299	6502	SO:0001583	missense	22862	exon24			GAGTCAACATCCT	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.3049A>G	13.37:g.49775997A>G	ENSP00000417257:p.Thr1017Ala	174	0	0		141	60	0.425532	NM_001079673	B4DYG1|Q5HYC9|Q5JVF8|Q5JVF9|Q6EVH3|Q6EVH4|Q6N020|Q6P9D5|Q6ZME4|Q9H1W1	Missense_Mutation	SNP	ENST00000492622.2	37	CCDS41886.1	68	0.031135531135531136	1	0.0020325203252032522	18	0.049723756906077346	0	0.0	49	0.06464379947229551	A	22.8	4.334633	0.81801	0.011802	0.070016	ENSG00000102531	ENST00000492622;ENST00000337156;ENST00000541916;ENST00000398316	T;T;T	0.61627	0.09;0.09;0.09	6.16	3.66	0.41972	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.079122	0.52532	D	0.000074	T	0.21509	0.0518	M	0.87547	2.89	0.80722	D	1	D;P	0.64830	0.994;0.597	D;P	0.68765	0.96;0.531	T	0.54794	-0.8240	10	0.48119	T	0.1	-24.27	9.0647	0.36455	0.7455:0.1304:0.0:0.1241	rs45604939	961;1017	Q9Y2H6-2;Q9Y2H6	.;FND3A_HUMAN	A	1017;953;1017;961	ENSP00000417257:T1017A;ENSP00000441831:T1017A;ENSP00000381362:T961A	ENSP00000338579:T953A	T	+	1	0	FNDC3A	48673998	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	8.904000	0.92590	0.515000	0.28320	0.528000	0.53228	ACA	A|0.954;G|0.046	0.046	strong		0.368	FNDC3A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354845.2	NM_014923		G	49775997	A	G	49775997	3	3	27	1	0	0	0	0	1	0	0	0	5977	43	2	3	3150	3	FNDC3A	13	49775997	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	4628692	49775997	65393881	700	11151											
CAB39L	81617	hgsc.bcm.edu	37	chr13	49956980	49956980	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccaaaatggccaaattgtCtttcaggattttcacaattt	12	16	5	8	0	3	0	2	0	1	0	4	1	4	1	2	2	0	0	2	2	4	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:49956980C>A	ENST00000355854.4	-	2	564	c.67G>T	c.(67-69)Gac>Tac	p.D23Y	CAB39L_ENST00000476943.1_5'UTR|CAB39L_ENST00000410043.1_Missense_Mutation_p.D23Y|CAB39L_ENST00000409308.1_Missense_Mutation_p.D23Y|CAB39L_ENST00000347776.5_Missense_Mutation_p.D23Y	NM_030925.2	NP_112187.2	Q9H9S4	CB39L_HUMAN	calcium binding protein 39-like	23					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)		GCCAAATTGTCTTTCAGGATT	0.328																																					p.D23Y		Atlas-SNP	.											.	CAB39L	35	.	0			c.G67T						PASS	.						177	159	165					13																	49956980		1834	4084	5918	SO:0001583	missense	81617	exon2			AATTGTCTTTCAG	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.67G>T	13.37:g.49956980C>A	ENSP00000348113:p.Asp23Tyr	225	0	0		254	63	0.248031	NM_030925	Q5TAW6|Q6WG71|Q96FG1|Q9BZ33	Missense_Mutation	SNP	ENST00000355854.4	37	CCDS9416.2	.	.	.	.	.	.	.	.	.	.	C	29.1	4.976567	0.92982	.	.	ENSG00000102547	ENST00000355854;ENST00000347776;ENST00000378341;ENST00000409308;ENST00000410043;ENST00000457041;ENST00000413278;ENST00000409082	T;T;T;T;T;T;T	0.37584	1.19;1.19;1.19;1.19;1.19;1.19;1.19	5.88	5.88	0.94601	Armadillo-type fold (1);	0.189850	0.56097	D	0.000036	T	0.64294	0.2585	M	0.88979	2.995	0.80722	D	1	P	0.43909	0.821	P	0.55455	0.776	T	0.66236	-0.5974	9	.	.	.	-13.9564	19.2196	0.93791	0.0:1.0:0.0:0.0	.	23	Q9H9S4	CB39L_HUMAN	Y	23;23;20;23;23;23;23;23	ENSP00000348113:D23Y;ENSP00000261669:D23Y;ENSP00000386375:D23Y;ENSP00000386328:D23Y;ENSP00000409253:D23Y;ENSP00000404028:D23Y;ENSP00000386979:D23Y	.	D	-	1	0	CAB39L	48854981	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.327000	0.79147	2.789000	0.95967	0.591000	0.81541	GAC	.	.	none		0.328	CAB39L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044908.3	NM_030925		A	49956980	C	A	49956980	3	1	27	1	0	0	0	0	1	0	0	0	2528	913	32	4	978	4	CAB39L	13	49956980	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	180983	49956980	65212898	701	11152											
NEK3	4752	hgsc.bcm.edu	37	chr13	52710320	52710320	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccaaagctgtaagagctgtaTtgggtacatttttctcccac	10	13	8	10	0	1	1	0	0	1	1	2	1	1	1	2	1	3	5	2	1	4	6	rs371075629		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:52710320T>C	ENST00000400357.2	-	11	2348	c.1055A>G	c.(1054-1056)aAt>aGt	p.N352S	NEK3_ENST00000452082.2_Missense_Mutation_p.N373S|NEK3_ENST00000339406.3_Missense_Mutation_p.N369S|NEK3_ENST00000378101.2_Missense_Mutation_p.N369S			P51956	NEK3_HUMAN	NIMA-related kinase 3	369					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)		AAGAGCTGTATTGGGTACATT	0.378																																					p.N369S		Atlas-SNP	.											.	NEK3	41	.	0			c.A1106G						PASS	.	T	SER/ASN,SER/ASN	0,3738		0,0,1869	160	153	156		1055,1105	-11.1	0	13		156	1,8193		0,1,4096	no	missense,missense	NEK3	NM_001146099.1,NM_152720.2	46,46	0,1,5965	CC,CT,TT		0.0122,0.0,0.0084	benign,benign	352/490,369/507	52710320	1,11931	1869	4097	5966	SO:0001583	missense	4752	exon13			GCTGTATTGGGTA	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.1055A>G	13.37:g.52710320T>C	ENSP00000383210:p.Asn352Ser	232	0	0		230	97	0.421739	NM_002498	A8K2J4|Q5TAP2|Q8J023|Q8WUN5	Missense_Mutation	SNP	ENST00000400357.2	37	CCDS53871.1	.	.	.	.	.	.	.	.	.	.	T	2.579	-0.297749	0.05532	0.0	1.22E-4	ENSG00000136098	ENST00000339406;ENST00000378101;ENST00000400357;ENST00000452082;ENST00000547422	T;T;T;T;T	0.70631	-0.34;-0.34;-0.5;-0.36;-0.34	5.57	-11.1	0.00147	.	0.832180	0.11642	N	0.543642	T	0.32882	0.0844	N	0.03608	-0.345	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.06405	0.001;0.001;0.002	T	0.31110	-0.9955	10	0.07175	T	0.84	.	9.6098	0.39657	0.0:0.2182:0.255:0.5268	.	369;373;346	P51956;Q6ZN64;F8VS47	NEK3_HUMAN;.;.	S	369;369;352;373;346	ENSP00000339429:N369S;ENSP00000367341:N369S;ENSP00000383210:N352S;ENSP00000404197:N373S;ENSP00000448716:N346S	ENSP00000339429:N369S	N	-	2	0	NEK3	51608321	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-2.293000	0.01145	-2.658000	0.00420	-0.290000	0.09829	AAT	.	.	weak		0.378	NEK3-002	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045047.3			C	52710320	T	C	52710320	3	2	27	1	0	0	0	0	1	0	0	0	10334	1493	52	3	430	3	NEK3	13	52710320	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	2753340	52710320	62459558	702	11153											
NEK3	4752	hgsc.bcm.edu	37	chr13	52726772	52726772	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatatctctgtgtagcacaCgtttcttgtgaatgtgattt	8	18	9	6	1	2	3	0	3	2	0	3	3	2	3	0	0	1	3	0	0	3	5	rs56190615	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:52726772C>T	ENST00000400357.2	-	4	1658	c.365G>A	c.(364-366)cGt>cAt	p.R122H	NEK3_ENST00000452082.2_Missense_Mutation_p.R143H|NEK3_ENST00000339406.3_Missense_Mutation_p.R122H|NEK3_ENST00000378101.2_Missense_Mutation_p.R122H			P51956	NEK3_HUMAN	NIMA-related kinase 3	122	Interaction with VAV2.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> H (in dbSNP:rs56190615). {ECO:0000269|PubMed:17344846}.		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)		GTGTAGCACACGTTTCTTGTG	0.353													C|||	16	0.00319489	0.0	0.0043	5008	,	,		18153	0.0		0.0089	False		,,,				2504	0.0041				p.R122H		Atlas-SNP	.											.	NEK3	41	.	0			c.G365A						PASS	.	C	HIS/ARG,HIS/ARG	3,3687		0,3,1842	165	150	154		365,365	4.1	1	13	dbSNP_129	154	55,8141		1,53,4044	yes	missense,missense	NEK3	NM_001146099.1,NM_152720.2	29,29	1,56,5886	TT,TC,CC		0.6711,0.0813,0.488	probably-damaging,probably-damaging	122/490,122/507	52726772	58,11828	1845	4098	5943	SO:0001583	missense	4752	exon5			AGCACACGTTTCT	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.365G>A	13.37:g.52726772C>T	ENSP00000383210:p.Arg122His	123	0	0		105	51	0.485714	NM_002498	A8K2J4|Q5TAP2|Q8J023|Q8WUN5	Missense_Mutation	SNP	ENST00000400357.2	37	CCDS53871.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	C	15.21	2.765809	0.49574	8.13E-4	0.006711	ENSG00000136098	ENST00000339406;ENST00000378101;ENST00000400357;ENST00000452082;ENST00000547422	T;T;T;T;T	0.50277	1.82;1.82;1.82;1.82;0.75	5.92	4.1	0.47936	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.106321	0.64402	N	0.000020	T	0.27098	0.0664	.	.	.	0.41280	D	0.986903	B;P;P	0.45348	0.174;0.856;0.727	B;B;B	0.39562	0.12;0.303;0.201	T	0.03268	-1.1054	9	0.19590	T	0.45	.	11.7317	0.51741	0.0:0.849:0.0:0.151	rs56190615	122;143;116	P51956;Q6ZN64;F8VS47	NEK3_HUMAN;.;.	H	122;122;122;143;116	ENSP00000339429:R122H;ENSP00000367341:R122H;ENSP00000383210:R122H;ENSP00000404197:R143H;ENSP00000448716:R116H	ENSP00000448782:R122H	R	-	2	0	NEK3	51624773	1.000000	0.71417	1.000000	0.80357	0.577000	0.36160	2.816000	0.48026	0.741000	0.32674	-0.136000	0.14681	CGT	C|0.995;T|0.005	0.005	strong		0.353	NEK3-002	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045047.3			T	52726772	C	T	52726772	3	4	27	1	0	0	0	0	1	0	0	0	10334	536	19	1	1203	1	NEK3	13	52726772	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	16452	52726772	62443106	703	11154											
HNRNPA1L2	144983	hgsc.bcm.edu	37	chr13	53216666	53216666	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccaaaagagcccgaacagctGaggaagctcttcattggagg	13	6	12	10	1	2	2	1	1	1	1	2	5	2	4	2	3	4	2	2	3	4	2	rs113869751	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:53216666G>A	ENST00000357495.2	+	1	99	c.39G>A	c.(37-39)ctG>ctA	p.L13L	HNRNPA1L2_ENST00000398039.1_Silent_p.L13L|HNRNPA1L2_ENST00000342657.3_Silent_p.L13L			Q32P51	RA1L2_HUMAN	heterogeneous nuclear ribonucleoprotein A1-like 2	13	Globular A domain.				alternative mRNA splicing, via spliceosome (GO:0000380)|mRNA transport (GO:0051028)	cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			cervix(1)|large_intestine(1)|lung(5)	7						CCGAACAGCTGAGGAAGCTCT	0.502													-|||	54	0.0107827	0.0015	0.0144	5008	,	,		19278	0.0		0.0348	False		,,,				2504	0.0072				p.L13L		Atlas-SNP	.											.	HNRNPA1L2	20	.	0			c.G39A						PASS	.	G	,	19,4387	25.3+/-52.1	0,19,2184	68	71	70		39,39	0.3	0.9	13	dbSNP_132	70	266,8334	101.2+/-162.5	5,256,4039	no	coding-synonymous,coding-synonymous	HNRNPA1L2	NM_001011724.1,NM_001011725.1	,	5,275,6223	AA,AG,GG		3.093,0.4312,2.1913	,	13/321,13/321	53216666	285,12721	2203	4300	6503	SO:0001819	synonymous_variant	144983	exon7			ACAGCTGAGGAAG		CCDS31980.1	13q14.3	2013-02-12			ENSG00000139675	ENSG00000139675		"RNA binding motif (RRM) containing"	27067	protein-coding gene	gene with protein product						12477932	Standard	NM_001011724		Approved	LOC144983	uc001vgy.1	Q32P51	OTTHUMG00000016972	ENST00000357495.2:c.39G>A	13.37:g.53216666G>A		63	0	0		54	26	0.481481	NM_001011724	Q5TBS2	Silent	SNP	ENST00000357495.2	37	CCDS31980.1																																																																																			G|0.980;A|0.020	0.020	strong		0.502	HNRNPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045098.1	NM_001011724		A	53216666	G	A	53216666	2	1	27	1	0	0	0	0	0	0	0	1	7267	1277	45	2		2	HNRNPA1L2	13	53216666	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	489894	53216666	61953212	704	11155											
DIAPH3	81624	hgsc.bcm.edu	37	chr13	60413550	60413550	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgaagctgccttcccatctGcctcaaattcttttccagcg	7	14	6	14	1	3	1	1	1	2	0	5	1	5	1	4	0	4	1	4	0	2	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:60413550G>T	ENST00000400324.4	-	23	2990	c.2770C>A	c.(2770-2772)Cag>Aag	p.Q924K	DIAPH3_ENST00000400319.1_Missense_Mutation_p.Q854K|DIAPH3_ENST00000267215.4_Missense_Mutation_p.Q924K|DIAPH3_ENST00000377908.2_Missense_Mutation_p.Q913K|DIAPH3_ENST00000400330.1_Missense_Mutation_p.Q924K|DIAPH3_ENST00000465066.1_5'UTR|DIAPH3_ENST00000400320.1_Missense_Mutation_p.Q878K	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	924	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)		CTTCCCATCTGCCTCAAATTC	0.403																																					p.Q924K		Atlas-SNP	.											.	DIAPH3	139	.	0			c.C2770A						PASS	.						82	77	79					13																	60413550		1842	4094	5936	SO:0001583	missense	81624	exon23			CCATCTGCCTCAA	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.2770C>A	13.37:g.60413550G>T	ENSP00000383178:p.Gln924Lys	68	0	0		52	10	0.192308	NM_001042517	A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Missense_Mutation	SNP	ENST00000400324.4	37	CCDS41898.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.470488	0.84533	.	.	ENSG00000139734	ENST00000400324;ENST00000400330;ENST00000400327;ENST00000413168;ENST00000400329;ENST00000377908;ENST00000400319;ENST00000400320;ENST00000267215;ENST00000267214;ENST00000453990	T;T;T;T;T;T	0.16073	2.37;2.37;2.37;2.37;2.37;2.37	5.19	5.19	0.71726	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.058535	0.64402	D	0.000001	T	0.29223	0.0727	L	0.58969	1.84	0.51482	D	0.999927	B;D	0.55605	0.014;0.972	B;P	0.49361	0.01;0.608	T	0.01397	-1.1365	10	0.48119	T	0.1	.	19.0719	0.93143	0.0:0.0:1.0:0.0	.	661;924	Q9NSV4-1;Q9NSV4	.;DIAP3_HUMAN	K	924;924;913;878;854;913;854;878;924;661;924	ENSP00000383178:Q924K;ENSP00000383184:Q924K;ENSP00000367141:Q913K;ENSP00000383173:Q854K;ENSP00000383174:Q878K;ENSP00000267215:Q924K	ENSP00000267214:Q661K	Q	-	1	0	DIAPH3	59311551	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.414000	0.97362	2.585000	0.87301	0.591000	0.81541	CAG	.	.	none		0.403	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517		T	60413550	G	T	60413550	3	4	27	1	0	0	0	0	1	0	0	0	4522	1328	46	4	855	4	DIAPH3	13	60413550	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	7196884	60413550	54756328	705	11156											
KLHL1	57626	hgsc.bcm.edu	37	chr13	70293616	70293616	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacaccccctctcctcttacAcatgggagcacacatgttcc	9	9	6	17	0	2	0	0	0	2	0	4	2	3	1	4	1	2	2	4	1	1	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:70293616A>T	ENST00000377844.4	-	9	2659	c.1900T>A	c.(1900-1902)Tgt>Agt	p.C634S	KLHL1_ENST00000545028.1_Missense_Mutation_p.C441S	NM_020866.2	NP_065917.1	Q9NR64	KLHL1_HUMAN	kelch-like family member 1	634					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)		CTCCTCTTACACATGGGAGCA	0.458																																					p.C634S		Atlas-SNP	.											.	KLHL1	164	.	0			c.T1900A						PASS	.						124	107	113					13																	70293616		2203	4300	6503	SO:0001583	missense	57626	exon9			TCTTACACATGGG	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.1900T>A	13.37:g.70293616A>T	ENSP00000367075:p.Cys634Ser	106	0	0		82	15	0.182927	NM_020866	A8K5X0|Q5VZ64|Q9H4X4|Q9NR65|Q9P238	Missense_Mutation	SNP	ENST00000377844.4	37	CCDS9445.1	.	.	.	.	.	.	.	.	.	.	A	6.361	0.434642	0.12045	.	.	ENSG00000150361	ENST00000377844;ENST00000545028	T;T	0.64991	-0.13;-0.13	5.82	5.82	0.92795	Galactose oxidase, beta-propeller (1);	0.082942	0.52532	D	0.000067	T	0.24236	0.0587	N	0.00178	-1.915	0.45261	D	0.998261	B;B	0.09022	0.002;0.002	B;B	0.15052	0.012;0.012	T	0.49688	-0.8913	10	0.02654	T	1	.	16.171	0.81817	1.0:0.0:0.0:0.0	.	634;634	Q8TBJ7;Q9NR64	.;KLHL1_HUMAN	S	634;441	ENSP00000367075:C634S;ENSP00000439602:C441S	ENSP00000367075:C634S	C	-	1	0	KLHL1	69191617	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.228000	0.51270	2.211000	0.71520	0.533000	0.62120	TGT	.	.	none		0.458	KLHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045231.3	NM_020866		T	70293616	A	T	70293616	3	4	27	1	0	0	0	0	1	0	0	0	8374	159	6	5	358	5	KLHL1	13	70293616	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	9880066	70293616	44876262	706	11157											
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77740577	77740577	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attttggtccatatcctgaaTtctgaacagttctgacagga	11	14	8	8	0	2	3	0	3	2	0	4	4	4	4	2	2	1	1	2	2	3	5	rs111642157	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:77740577T>C	ENST00000544440.2	-	41	6130	c.6113A>G	c.(6112-6114)aAt>aGt	p.N2038S	MYCBP2_ENST00000407578.2_Missense_Mutation_p.N2076S|MYCBP2_ENST00000357337.6_Missense_Mutation_p.N2038S|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)		ATATCCTGAATTCTGAACAGT	0.398													T|||	16	0.00319489	0.0068	0.0072	5008	,	,		17955	0.0		0.002	False		,,,				2504	0.0				p.N2076S		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.A6227G						PASS	.	T	SER/ASN	24,4382	30.8+/-60.4	0,24,2179	109	107	108		6227	3.3	1	13	dbSNP_132	108	9,8591	7.1+/-27.0	0,9,4291	yes	missense	MYCBP2	NM_015057.4	46	0,33,6470	CC,CT,TT		0.1047,0.5447,0.2537	benign	2076/4679	77740577	33,12973	2203	4300	6503	SO:0001583	missense	23077	exon41			CCTGAATTCTGAA	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.6113A>G	13.37:g.77740577T>C	ENSP00000444596:p.Asn2038Ser	193	0	0		131	73	0.557252	NM_015057		Missense_Mutation	SNP	ENST00000544440.2	37		7	0.003205128205128205	3	0.006097560975609756	4	0.011049723756906077	0	0.0	0	0.0	T	8.715	0.913023	0.17907	0.005447	0.001047	ENSG00000005810	ENST00000357337;ENST00000407578;ENST00000544440	T;T;T	0.28069	1.63;1.63;1.63	5.79	3.27	0.37495	.	0.264107	0.38326	N	0.001731	T	0.05868	0.0153	N	0.01874	-0.695	0.23030	N	0.998406	B	0.02656	0.0	B	0.01281	0.0	T	0.30822	-0.9965	10	0.08599	T	0.76	.	3.9352	0.09302	0.3857:0.1334:0.0:0.4809	.	2038	O75592	MYCB2_HUMAN	S	2038;2076;2038	ENSP00000349892:N2038S;ENSP00000384288:N2076S;ENSP00000444596:N2038S	ENSP00000349892:N2038S	N	-	2	0	MYCBP2	76638578	1.000000	0.71417	0.993000	0.49108	0.943000	0.58893	1.627000	0.37050	0.978000	0.38470	0.528000	0.53228	AAT	T|0.997;C|0.003	0.003	strong		0.398	MYCBP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045326.1	NM_015057		C	77740577	T	C	77740577	3	2	27	1	0	0	0	0	1	0	0	0	10027	1493	52	3	7981	3	MYCBP2	13	77740577	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	7446961	77740577	37429301	707	11158											
SLITRK1	114798	hgsc.bcm.edu	37	chr13	84455214	84455214	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggcccccgggtctatatcTcgtaataaattaaaatcagc	14	10	7	10	2	3	0	1	0	2	0	4	0	3	0	2	2	1	1	2	2	8	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:84455214T>C	ENST00000377084.2	-	1	1314	c.429A>G	c.(427-429)cgA>cgG	p.R143R		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	143					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)		GGTCTATATCTCGTAATAAAT	0.458																																					p.R143R		Atlas-SNP	.											.	SLITRK1	196	.	0			c.A429G						PASS	.						60	65	64					13																	84455214		2203	4300	6503	SO:0001819	synonymous_variant	114798	exon1			TATATCTCGTAAT	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.429A>G	13.37:g.84455214T>C		67	0	0		61	14	0.229508	NM_052910	Q5U5I6|Q96SF9	Silent	SNP	ENST00000377084.2	37	CCDS9464.1																																																																																			.	.	none		0.458	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910		C	84455214	T	C	84455214	2	2	27	1	0	0	0	0	0	0	0	1	14757	1538	54	3		3	SLITRK1	13	84455214	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	6714637	84455214	30714664	708	11159											
HS6ST3	266722	hgsc.bcm.edu	37	chr13	96743584	96743584	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcctccacatccagaagacGgggggcaccactttcggccg	8	7	11	15	3	0	2	0	0	0	2	4	2	3	2	5	4	0	1	5	4	1	2	rs144263527	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:96743584G>T	ENST00000376705.2	+	1	492	c.468G>T	c.(466-468)acG>acT	p.T156T		NM_153456.3	NP_703157.2	Q8IZP7	H6ST3_HUMAN	heparan sulfate 6-O-sulfotransferase 3	156	5'-phosphosulfate-binding. {ECO:0000255}.				heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)	integral component of membrane (GO:0016021)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)	p.T156T(1)		NS(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|pancreas(1)|skin(1)	20	all_neural(89;0.0878)|Medulloblastoma(90;0.163)					TCCAGAAGACGGGGGGCACCA	0.602													c|||	6	0.00119808	0.0015	0.0	5008	,	,		11700	0.0		0.002	False		,,,				2504	0.002				p.T156T		Atlas-SNP	.											HS6ST3,NS,carcinoma,0,1	HS6ST3	54	1	1	Substitution - coding silent(1)	pancreas(1)	c.G468T						PASS	.	G		4,4402		0,4,2199	34	36	36		468	-0.6	1	13	dbSNP_134	36	18,8582		0,18,4282	no	coding-synonymous	HS6ST3	NM_153456.2		0,22,6481	TT,TG,GG		0.2093,0.0908,0.1692		156/472	96743584	22,12984	2203	4300	6503	SO:0001819	synonymous_variant	266722	exon1			GAAGACGGGGGGC	AF539426	CCDS9481.1	13q32.2	2007-12-04			ENSG00000185352	ENSG00000185352		"Sulfotransferases, membrane-bound"	19134	protein-coding gene	gene with protein product		609401					Standard	NM_153456		Approved		uc001vmw.4	Q8IZP7	OTTHUMG00000017232	ENST00000376705.2:c.468G>T	13.37:g.96743584G>T		50	0	0		41	18	0.439024	NM_153456	Q5W0L0|Q68CW6	Silent	SNP	ENST00000376705.2	37	CCDS9481.1																																																																																			G|0.998;T|0.002	0.002	strong		0.602	HS6ST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045517.2	NM_153456		T	96743584	G	T	96743584	2	4	27	1	0	0	0	0	0	0	0	1	7381	1103	39	4		4	HS6ST3	13	96743584	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	12288370	96743584	18426294	709	11160											
OXGR1	27199	hgsc.bcm.edu	37	chr13	97639021	97639021	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caagggttgtttgagtaactAattttctttgcttgctcaag	9	17	9	6	0	2	1	1	1	1	0	2	1	2	1	0	1	3	5	0	1	4	8	rs9584456	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:97639021A>G	ENST00000298440.1	-	4	1236	c.993T>C	c.(991-993)atT>atC	p.I331I	OXGR1_ENST00000543457.1_Silent_p.I331I	NM_080818.3	NP_543008.3	Q96P68	OXGR1_HUMAN	oxoglutarate (alpha-ketoglutarate) receptor 1	331					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)			NS(1)|large_intestine(1)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	15	all_neural(89;0.0982)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.186)			TTGAGTAACTAATTTTCTTTG	0.398													G|||	319	0.0636981	0.2118	0.0288	5008	,	,		21899	0.0		0.0179	False		,,,				2504	0.001				p.I331I		Atlas-SNP	.											.	OXGR1	46	.	0			c.T993C						PASS	.	G		814,3592	740.9+/-411.2	74,666,1463	104	107	106		993	2.4	0	13	dbSNP_119	106	83,8517	814.3+/-407.0	0,83,4217	no	coding-synonymous	OXGR1	NM_080818.3		74,749,5680	GG,GA,AA		0.9651,18.4748,6.8968		331/338	97639021	897,12109	2203	4300	6503	SO:0001819	synonymous_variant	27199	exon4			GTAACTAATTTTC	AF411109	CCDS9482.1	13q32.2	2014-04-09	2004-07-08	2004-07-09	ENSG00000165621	ENSG00000165621		"GPCR / Class A : Orphans"	4531	protein-coding gene	gene with protein product	"2-oxoglutarate receptor 1", "alpha-ketoglutarate receptor 1"	606922	"G protein-coupled receptor 80"	GPR99, GPR80		15141213, 12098360	Standard	NM_080818		Approved	P2RY15, P2Y15, aKGR	uc001vmx.1	Q96P68	OTTHUMG00000017236	ENST00000298440.1:c.993T>C	13.37:g.97639021A>G		53	0	0		34	13	0.382353	NM_080818	Q5T5A7|Q86TL1	Silent	SNP	ENST00000298440.1	37	CCDS9482.1																																																																																			A|0.933;G|0.067	0.067	strong		0.398	OXGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045521.3	NM_080818		G	97639021	A	G	97639021	2	3	27	1	0	0	0	0	0	0	0	1	11341	358	13	3		3	OXGR1	13	97639021	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	895437	97639021	17530857	710	11161											
OXGR1	27199	hgsc.bcm.edu	37	chr13	97639827	97639827	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgctgctcttccaaggtcTcattttgaaaatgtaagtgg	9	14	11	7	0	2	1	1	1	2	0	4	1	3	1	1	3	2	3	1	3	4	4	rs9300380	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:97639827T>G	ENST00000298440.1	-	4	430	c.187A>C	c.(187-189)Aga>Cga	p.R63R	OXGR1_ENST00000543457.1_Silent_p.R63R	NM_080818.3	NP_543008.3	Q96P68	OXGR1_HUMAN	oxoglutarate (alpha-ketoglutarate) receptor 1	63					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)			NS(1)|large_intestine(1)|lung(9)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	15	all_neural(89;0.0982)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.186)			TTCCAAGGTCTCATTTTGAAA	0.473													G|||	317	0.0632987	0.2118	0.0288	5008	,	,		21471	0.0		0.0169	False		,,,				2504	0.0				p.R63R		Atlas-SNP	.											.	OXGR1	46	.	0			c.A187C						PASS	.	G		815,3591	747.9+/-411.9	74,667,1462	121	113	116		187	3.3	1	13	dbSNP_119	116	83,8517	815.3+/-407.0	0,83,4217	no	coding-synonymous	OXGR1	NM_080818.3		74,750,5679	GG,GT,TT		0.9651,18.4975,6.9045		63/338	97639827	898,12108	2203	4300	6503	SO:0001819	synonymous_variant	27199	exon4			AAGGTCTCATTTT	AF411109	CCDS9482.1	13q32.2	2014-04-09	2004-07-08	2004-07-09	ENSG00000165621	ENSG00000165621		"GPCR / Class A : Orphans"	4531	protein-coding gene	gene with protein product	"2-oxoglutarate receptor 1", "alpha-ketoglutarate receptor 1"	606922	"G protein-coupled receptor 80"	GPR99, GPR80		15141213, 12098360	Standard	NM_080818		Approved	P2RY15, P2Y15, aKGR	uc001vmx.1	Q96P68	OTTHUMG00000017236	ENST00000298440.1:c.187A>C	13.37:g.97639827T>G		173	0	0		145	71	0.489655	NM_080818	Q5T5A7|Q86TL1	Silent	SNP	ENST00000298440.1	37	CCDS9482.1																																																																																			T|0.939;G|0.061	0.061	strong		0.473	OXGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045521.3	NM_080818		G	97639827	T	G	97639827	2	3	27	1	0	0	0	0	0	0	0	1	11341	1559	54	5		5	OXGR1	13	97639827	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	806	97639827	17530051	711	11162											
RASA3	22821	hgsc.bcm.edu	37	chr13	114795333	114795333	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cccagtgtctgtgatgacctCgctcagccgcagctccaggt	6	9	11	15	2	2	2	1	2	1	0	4	2	3	2	4	1	2	3	4	1	0	0	rs200024629		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr13:114795333C>T	ENST00000334062.7	-	5	524	c.403G>A	c.(403-405)Gag>Aag	p.E135K	RASA3_ENST00000389544.4_Missense_Mutation_p.E103K|RASA3_ENST00000542651.1_Missense_Mutation_p.R103Q	NM_007368.2	NP_031394.2	Q14644	RASA3_HUMAN	RAS p21 protein activator 3	135	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				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)			GTGATGACCTCGCTCAGCCGC	0.647													c|||	1	0.000199681	0.0008	0.0	5008	,	,		18381	0.0		0.0	False		,,,				2504	0.0				p.E135K		Atlas-SNP	.											.	RASA3	83	.	0			c.G403A						PASS	.						110	66	81					13																	114795333		2201	4297	6498	SO:0001583	missense	22821	exon5			TGACCTCGCTCAG		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.403G>A	13.37:g.114795333C>T	ENSP00000335029:p.Glu135Lys	43	0	0		48	23	0.479167	NM_007368	A6NL15|F8W6X8|Q8IUY2	Missense_Mutation	SNP	ENST00000334062.7	37	CCDS32016.1	1|1	4.578754578754579E-4|4.578754578754579E-4	1|1	0.0020325203252032522|0.0020325203252032522	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	21.5|21.5	4.163421|4.163421	0.78226|0.78226	.|.	.|.	ENSG00000185989|ENSG00000185989	ENST00000334062;ENST00000389544|ENST00000542651	D;D|T	0.86164|0.17054	-1.97;-2.08|2.3	4.5|4.5	4.5|4.5	0.54988|0.54988	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.31606|0.31606	0.0802|0.0802	L|L	0.60455|0.60455	1.87|1.87	0.38497|0.38497	D|D	0.948117|0.948117	P|.	0.40660|.	0.726|.	B|.	0.39503|.	0.301|.	T|T	0.07290|0.07290	-1.0780|-1.0780	9|6	.|.	.|.	.|.	.|.	16.3374|16.3374	0.83068|0.83068	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	135|.	Q14644|.	RASA3_HUMAN|.	K|Q	135;103|103	ENSP00000335029:E135K;ENSP00000374195:E103K|ENSP00000439008:R103Q	.|.	E|R	-|-	1|2	0|0	RASA3|RASA3	113813435|113813435	1.000000|1.000000	0.71417|0.71417	0.990000|0.990000	0.47175|0.47175	0.916000|0.916000	0.54674|0.54674	6.028000|6.028000	0.70889|0.70889	2.207000|2.207000	0.71202|0.71202	0.561000|0.561000	0.74099|0.74099	GAG|CGA	C|1.000;T|0.000	0.000	strong		0.647	RASA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045957.2	NM_007368		T	114795333	C	T	114795333	3	4	27	1	0	0	0	0	1	0	0	0	13077	893	31	1	2181	1	RASA3	13	114795333	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	17155506	114795333	374545	712	11163											
CHD8	57680	hgsc.bcm.edu	37	chr14	21868678	21868678	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cggtagtgtagaagacagtaCacgagaatggcccgacaaat	15	6	12	8	3	0	3	0	0	0	3	0	5	0	3	1	2	1	3	1	2	6	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:21868678C>T	ENST00000557364.1	-	23	4727	c.4464G>A	c.(4462-4464)gtG>gtA	p.V1488V	CHD8_ENST00000430710.3_Silent_p.V1209V|CHD8_ENST00000555962.1_Intron|CHD8_ENST00000399982.2_Silent_p.V1488V			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1488					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)		GAAGACAGTACACGAGAATGG	0.443																																					p.V1488V		Atlas-SNP	.											.	CHD8	339	.	0			c.G4464A						PASS	.						59	58	58					14																	21868678		1858	4104	5962	SO:0001819	synonymous_variant	57680	exon22			ACAGTACACGAGA	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.4464G>A	14.37:g.21868678C>T		70	0	0		54	15	0.277778	NM_001170629	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Silent	SNP	ENST00000557364.1	37	CCDS53885.1	.	.	.	.	.	.	.	.	.	.	C	5.897	0.349646	0.11182	.	.	ENSG00000100888	ENST00000555935	D	0.84660	-1.88	4.82	-4.95	0.03048	.	0.000000	0.85682	D	0.000000	T	0.75117	0.3806	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61133	-0.7124	6	.	.	.	-7.29	1.8525	0.03172	0.1838:0.1552:0.384:0.277	.	.	.	.	I	714	ENSP00000451442:V714I	.	V	-	1	0	CHD8	20938518	0.000000	0.05858	0.744000	0.31058	0.958000	0.62258	-2.646000	0.00860	-1.016000	0.03371	0.650000	0.86243	GTA	.	.	none		0.443	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920		T	21868678	C	T	21868678	2	4	27	1	0	0	0	0	0	0	0	1	3333	465	17	2		2	CHD8	14	21868678	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10		21868678	85480862	713	11164											
ABHD4	63874	hgsc.bcm.edu	37	chr14	23072905	23072905	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cccagtgagatccgtgcaccCccagcctgggtcaaagccgt	8	6	11	16	2	1	1	1	1	0	1	2	2	2	1	6	1	3	1	6	1	1	0	rs540141952		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:23072905C>G	ENST00000428304.2	+	4	631	c.561C>G	c.(559-561)ccC>ccG	p.P187P	ABHD4_ENST00000544562.1_3'UTR	NM_022060.2	NP_071343.2	Q8TB40	ABHD4_HUMAN	abhydrolase domain containing 4	187					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)		TCCGTGCACCCCCAGCCTGGG	0.557																																					p.P187P		Atlas-SNP	.											.	ABHD4	30	.	0			c.C561G						PASS	.						109	102	105					14																	23072905		2203	4300	6503	SO:0001819	synonymous_variant	63874	exon4			TGCACCCCCAGCC	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.561C>G	14.37:g.23072905C>G		198	0	0		183	91	0.497268	NM_022060	B4DDH7|Q9H9E0	Silent	SNP	ENST00000428304.2	37	CCDS9572.1																																																																																			.	.	none		0.557	ABHD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071623.3			G	23072905	C	G	23072905	2	3	27	1	0	0	0	0	0	0	0	1	84	610	22	4		4	ABHD4	14	23072905	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1204227	23072905	84276635	714	11165											
HAUS4	54930	hgsc.bcm.edu	37	chr14	23421593	23421593	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttcacatagtagtccacaaGcaactcttgaatgactctgt	12	12	6	11	0	3	2	1	2	2	0	4	2	4	2	1	0	2	2	1	0	5	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:23421593G>A	ENST00000206474.7	-	4	526	c.274C>T	c.(274-276)Ctt>Ttt	p.L92F	RP11-298I3.5_ENST00000555074.1_Intron|HAUS4_ENST00000342454.8_Missense_Mutation_p.L92F|HAUS4_ENST00000554446.1_5'UTR|HAUS4_ENST00000490506.1_5'UTR|HAUS4_ENST00000555367.1_Missense_Mutation_p.L92F|HAUS4_ENST00000347758.2_Missense_Mutation_p.L92F|RP11-298I3.1_ENST00000548322.1_RNA|HAUS4_ENST00000397409.4_Missense_Mutation_p.L92F|HAUS4_ENST00000541587.1_Missense_Mutation_p.L92F|RP11-298I3.1_ENST00000548819.1_RNA|HAUS4_ENST00000555986.1_Missense_Mutation_p.L92F			Q9H6D7	HAUS4_HUMAN	HAUS augmin-like complex, subunit 4	92					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)				breast(3)|cervix(1)|endometrium(2)|lung(6)|ovary(1)|skin(1)	14						TAGTCCACAAGCAACTCTTGA	0.433																																					p.L92F		Atlas-SNP	.											.	HAUS4	34	.	0			c.C274T						PASS	.						229	218	222					14																	23421593		2203	4300	6503	SO:0001583	missense	54930	exon4			CCACAAGCAACTC	AK000431	CCDS9580.1, CCDS53886.1	14q11.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000092036	ENSG00000092036		"HAUS augmin-like complex subunits"	20163	protein-coding gene	gene with protein product		613431	"chromosome 14 open reading frame 94"	C14orf94		19427217	Standard	NM_017815		Approved	FLJ20424	uc001wht.3	Q9H6D7	OTTHUMG00000028710	ENST00000206474.7:c.274C>T	14.37:g.23421593G>A	ENSP00000206474:p.Leu92Phe	206	0	0		183	97	0.530055	NM_001166270	B7WP17|D3DS34|Q86T15|Q86T16|Q86U43|Q9NX59	Missense_Mutation	SNP	ENST00000206474.7	37	CCDS9580.1	.	.	.	.	.	.	.	.	.	.	G	22.2	4.260380	0.80246	.	.	ENSG00000092036	ENST00000206474;ENST00000541587;ENST00000342454;ENST00000347758;ENST00000397409;ENST00000555367;ENST00000555986;ENST00000555040;ENST00000556915;ENST00000554516;ENST00000557591	.	.	.	5.71	5.71	0.89125	.	0.124104	0.53938	D	0.000054	T	0.69214	0.3086	L	0.59436	1.845	0.32357	N	0.557748	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.85130	0.997;0.996;0.997	T	0.75453	-0.3312	9	0.72032	D	0.01	-7.2977	15.3637	0.74503	0.0:0.0:1.0:0.0	.	92;92;92	Q9H6D7-4;Q9H6D7-2;Q9H6D7	.;.;HAUS4_HUMAN	F	92	.	ENSP00000206474:L92F	L	-	1	0	HAUS4	22491433	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	3.932000	0.56537	2.694000	0.91930	0.655000	0.94253	CTT	.	.	none		0.433	HAUS4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071680.3			A	23421593	G	A	23421593	3	1	27	1	0	0	0	0	1	0	0	0	6977	971	34	2	845	2	HAUS4	14	23421593	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	348688	23421593	83927947	715	11166											
HOMEZ	57594	hgsc.bcm.edu	37	chr14	23746340	23746340	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctggtgaactactgagacCgctggcctctttattaggag	8	11	12	10	2	1	2	0	2	1	1	1	4	1	3	2	3	2	2	2	3	4	4	rs565379852	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:23746340C>T	ENST00000357460.5	-	2	261	c.97G>A	c.(97-99)Ggt>Agt	p.G33S	HOMEZ_ENST00000561013.1_Missense_Mutation_p.G35S|HOMEZ_ENST00000431326.2_Missense_Mutation_p.G35S	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	33					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|lung(7)	12	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00643)		CTACTGAGACCGCTGGCCTCT	0.532													C|||	2	0.000399361	0.0	0.0	5008	,	,		17905	0.002		0.0	False		,,,				2504	0.0				p.G33S		Atlas-SNP	.											.	HOMEZ	80	.	0			c.G97A						PASS	.						76	71	72					14																	23746340		1974	4166	6140	SO:0001583	missense	57594	exon2			TGAGACCGCTGGC	AB037864	CCDS45085.1	14q11.2	2011-06-20	2007-02-15	2007-02-15		ENSG00000215271		"Homeoboxes / ZF class"	20164	protein-coding gene	gene with protein product		608119	"KIAA1443"	KIAA1443		12925734	Standard	NM_020834		Approved		uc001wja.2	Q8IX15		ENST00000357460.5:c.97G>A	14.37:g.23746340C>T	ENSP00000350049:p.Gly33Ser	71	0	0		63	29	0.460317	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	Missense_Mutation	SNP	ENST00000357460.5	37	CCDS45085.1	.	.	.	.	.	.	.	.	.	.	C	1.235	-0.622995	0.03636	.	.	ENSG00000215271	ENST00000357460;ENST00000431326	T;T	0.20200	2.09;2.09	5.95	2.18	0.27775	.	0.152484	0.56097	N	0.000023	T	0.07503	0.0189	N	0.08118	0	0.22835	N	0.998674	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.40478	-0.9561	10	0.02654	T	1	-7.3746	7.1207	0.25442	0.0:0.3237:0.0:0.6763	.	35;33	F8WCA3;Q8IX15	.;HOMEZ_HUMAN	S	33;35	ENSP00000350049:G33S;ENSP00000406579:G35S	ENSP00000350049:G33S	G	-	1	0	HOMEZ	22816180	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	0.878000	0.28126	0.494000	0.27859	-0.290000	0.09829	GGT	.	.	none		0.532	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834		T	23746340	C	T	23746340	3	4	27	1	0	0	0	0	1	0	0	0	7290	652	23	1	1559	1	HOMEZ	14	23746340	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	324747	23746340	83603200	716	11167											
DHRS2	10202	hgsc.bcm.edu	37	chr14	24114437	24114437	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacggggagaacattgcggTggcaggctactccactcggc	9	6	14	12	3	0	1	0	0	0	1	2	2	1	1	1	6	4	2	1	6	3	2	rs146187363	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:24114437T>A	ENST00000250383.6	+	9	1294	c.818T>A	c.(817-819)gTg>gAg	p.V273E	DHRS2_ENST00000344777.7_Missense_Mutation_p.W277R	NM_005794.3	NP_005785.1	Q13268	DHRS2_HUMAN	dehydrogenase/reductase (SDR family) member 2	273					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)		AACATTGCGGTGGCAGGCTAC	0.597													t|||	14	0.00279553	0.0	0.0	5008	,	,		18947	0.0		0.0	False		,,,				2504	0.0143				p.W277R		Atlas-SNP	.											.	DHRS2	78	.	0			c.T829A						PASS	.		GLU/VAL,ARG/TRP	0,4406		0,0,2203	109	93	99		818,829	4.4	0.7	14	dbSNP_134	99	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	DHRS2	NM_005794.3,NM_182908.4	121,101	0,2,6501	AA,AT,TT		0.0233,0.0,0.0154	probably-damaging,probably-damaging	273/281,277/301	24114437	2,13004	2203	4300	6503	SO:0001583	missense	10202	exon9			TTGCGGTGGCAGG		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.818T>A	14.37:g.24114437T>A	ENSP00000250383:p.Val273Glu	108	0	0		84	38	0.452381	NM_182908	D3DS54|Q53GS4|Q7Z789|Q9H2R2	Missense_Mutation	SNP	ENST00000250383.6	37	CCDS9604.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.18|15.18	2.758232|2.758232	0.49468|0.49468	0.0|0.0	2.33E-4|2.33E-4	ENSG00000100867|ENSG00000100867	ENST00000250383|ENST00000344777	T|D	0.39056|0.82526	1.1|-1.62	4.42|4.42	4.42|4.42	0.53409|0.53409	.|.	.|0.473111	.|0.23616	.|N	.|0.046297	D|D	0.88919|0.88919	0.6568|0.6568	.|.	.|.	.|.	0.30039|0.30039	N|N	0.812755|0.812755	D|D	0.89917|0.89917	1.0|1.0	D|D	0.91635|0.69479	0.999|0.964	D|D	0.85869|0.85869	0.1415|0.1415	8|9	0.87932|0.56958	D|D	0|0.05	.|.	11.9261|11.9261	0.52820|0.52820	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	273|255	D3DS54|Q13268-2	.|.	E|R	273|277	ENSP00000250383:V273E|ENSP00000344674:W277R	ENSP00000250383:V273E|ENSP00000344674:W277R	V|W	+|+	2|1	0|0	DHRS2|DHRS2	23184277|23184277	1.000000|1.000000	0.71417|0.71417	0.707000|0.707000	0.30419|0.30419	0.018000|0.018000	0.09664|0.09664	6.595000|6.595000	0.74109|0.74109	1.981000|1.981000	0.57761|0.57761	0.455000|0.455000	0.32223|0.32223	GTG|TGG	T|1.000;A|0.000	0.000	weak		0.597	DHRS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000071842.2	NM_182908		A	24114437	T	A	24114437	3	1	27	1	0	0	0	0	1	0	0	0	4492	1696	59	5	859	5	DHRS2	14	24114437	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	368097	24114437	83235103	717	11168											
NFATC4	4776	hgsc.bcm.edu	37	chr14	24838953	24838953	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctcgagtgtcccagcatcCgcatcacctccatctctccc	6	11	5	19	2	3	0	1	0	2	0	9	1	7	0	5	0	1	2	5	0	0	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:24838953C>T	ENST00000250373.4	+	2	490	c.349C>T	c.(349-351)Cgc>Tgc	p.R117C	NFATC4_ENST00000539237.2_Missense_Mutation_p.R149C|NFATC4_ENST00000553469.1_Missense_Mutation_p.R149C|NFATC4_ENST00000556169.1_Missense_Mutation_p.R105C|NFATC4_ENST00000554050.1_Missense_Mutation_p.R117C|NFATC4_ENST00000557451.1_Missense_Mutation_p.R47C|NFATC4_ENST00000554344.1_Missense_Mutation_p.R47C|NFATC4_ENST00000440487.2_3'UTR|NFATC4_ENST00000553879.1_Missense_Mutation_p.R47C|NFATC4_ENST00000413692.2_Missense_Mutation_p.R180C|NFATC4_ENST00000554591.1_Missense_Mutation_p.R180C|NFATC4_ENST00000554661.1_Missense_Mutation_p.R47C|NFATC4_ENST00000556279.1_Missense_Mutation_p.R149C|NFATC4_ENST00000424781.2_Missense_Mutation_p.R130C|NFATC4_ENST00000554966.1_Missense_Mutation_p.R130C|NFATC4_ENST00000555590.1_Missense_Mutation_p.R130C|NFATC4_ENST00000555453.1_Missense_Mutation_p.R105C|NFATC4_ENST00000422617.3_Missense_Mutation_p.R105C|NFATC4_ENST00000553708.1_Missense_Mutation_p.R117C	NM_004554.4	NP_004545.2	Q14934	NFAC4_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 4	117	Calcineurin-binding.|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)		TCCCAGCATCCGCATCACCTC	0.687																																					p.R180C		Atlas-SNP	.											.	NFATC4	115	.	0			c.C538T						PASS	.						12	14	13					14																	24838953		2190	4254	6444	SO:0001583	missense	4776	exon3			AGCATCCGCATCA	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.349C>T	14.37:g.24838953C>T	ENSP00000250373:p.Arg117Cys	65	0	0		70	4	0.0571429	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	37	CCDS9629.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.491135	0.84962	.	.	ENSG00000100968	ENST00000413692;ENST00000554591;ENST00000555590;ENST00000554966;ENST00000424781;ENST00000539237;ENST00000556279;ENST00000553469;ENST00000554050;ENST00000554903;ENST00000250373;ENST00000553708;ENST00000557674;ENST00000553879;ENST00000554344;ENST00000554661;ENST00000556169;ENST00000557451;ENST00000422617;ENST00000555453	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.16324	2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35;2.35	3.76	3.76	0.43208	.	0.096786	0.44097	D	0.000481	T	0.27384	0.0672	L	0.29908	0.895	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;0.999;1.0;0.999	D;D;D;D;D;D;D;D;D;D;D;D;D;P	0.67725	0.93;0.93;0.93;0.93;0.93;0.93;0.93;0.953;0.953;0.93;0.953;0.93;0.93;0.853	T	0.04579	-1.0941	10	0.87932	D	0	-5.8251	13.1624	0.59552	0.0:1.0:0.0:0.0	.	105;105;149;149;130;130;130;180;180;105;149;94;180;117	Q14934-17;Q14934-9;Q14934-14;Q14934-4;Q14934-15;Q14934-6;Q14934-7;Q14934-2;Q14934-3;Q14934-10;Q14934-5;B4DU09;Q14934-11;Q14934	.;.;.;.;.;.;.;.;.;.;.;.;.;NFAC4_HUMAN	C	180;180;130;130;130;149;149;149;117;117;117;117;94;47;47;47;105;47;105;105	ENSP00000388910:R180C;ENSP00000452039:R180C;ENSP00000451224:R130C;ENSP00000450644:R130C;ENSP00000388668:R130C;ENSP00000439350:R149C;ENSP00000452270:R149C;ENSP00000451502:R149C;ENSP00000451151:R117C;ENSP00000451853:R117C;ENSP00000250373:R117C;ENSP00000450590:R117C;ENSP00000452352:R94C;ENSP00000452349:R47C;ENSP00000450469:R47C;ENSP00000450733:R47C;ENSP00000451454:R105C;ENSP00000451284:R47C;ENSP00000396788:R105C;ENSP00000450686:R105C	ENSP00000250373:R117C	R	+	1	0	NFATC4	23908793	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.890000	0.75633	1.943000	0.56356	0.558000	0.71614	CGC	.	.	none		0.687	NFATC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073206.6	NM_004554		T	24838953	C	T	24838953	3	4	27	1	0	0	0	0	1	0	0	0	10374	652	23	1	548	1	NFATC4	14	24838953	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	724516	24838953	82510587	718	11169											
PRKD1	5587	hgsc.bcm.edu	37	chr14	30066914	30066914	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gtacccaccactgacctccgGaaagacttctctccaatgat	11	9	6	15	1	1	3	0	2	1	1	4	4	3	4	5	1	1	1	5	1	3	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:30066914G>T	ENST00000331968.5	-	16	2446	c.2217C>A	c.(2215-2217)ttC>ttA	p.F739L	PRKD1_ENST00000415220.2_Missense_Mutation_p.F747L	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	739	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)		CTGACCTCCGGAAAGACTTCT	0.488																																					p.F739L		Atlas-SNP	.											.	PRKD1	316	.	0			c.C2217A						PASS	.						68	70	70					14																	30066914		2203	4300	6503	SO:0001583	missense	5587	exon16			CCTCCGGAAAGAC		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.2217C>A	14.37:g.30066914G>T	ENSP00000333568:p.Phe739Leu	60	0	0		38	9	0.236842	NM_002742	A6NL64|B2RAF6	Missense_Mutation	SNP	ENST00000331968.5	37	CCDS9637.1	.	.	.	.	.	.	.	.	.	.	G	18.33	3.600019	0.66332	.	.	ENSG00000184304	ENST00000331968;ENST00000415220	T;T	0.64438	-0.1;-0.1	5.72	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	0.34483	0.0899	N	0.01668	-0.77	0.80722	D	1	P	0.37207	0.587	B	0.37091	0.241	T	0.46498	-0.9187	10	0.56958	D	0.05	-19.8775	10.6337	0.45551	0.2039:0.0:0.7961:0.0	.	739	Q15139	KPCD1_HUMAN	L	739;747	ENSP00000333568:F739L;ENSP00000390535:F747L	ENSP00000333568:F739L	F	-	3	2	PRKD1	29136665	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.672000	0.46850	1.517000	0.48917	0.650000	0.86243	TTC	.	.	none		0.488	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742		T	30066914	G	T	30066914	3	4	27	1	0	0	0	0	1	0	0	0	12530	1165	41	4	533	4	PRKD1	14	30066914	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	5227961	30066914	77282626	719	11170											
FSCB	84075	hgsc.bcm.edu	37	chr14	44975349	44975349	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttcagcaggtctgggctccGctttagcagtggcctcttca	5	12	11	13	1	4	0	2	0	2	0	5	0	5	0	2	3	2	4	2	3	1	4	rs139581441	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:44975349G>A	ENST00000340446.4	-	1	1133	c.842C>T	c.(841-843)gCg>gTg	p.A281V	RP11-163M18.1_ENST00000555433.1_RNA|RP11-163M18.1_ENST00000556228.1_RNA|RP11-163M18.1_ENST00000557465.1_RNA	NM_032135.3	NP_115511.3	Q5H9T9	FSCB_HUMAN	fibrous sheath CABYR binding protein	281						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)		TCTGGGCTCCGCTTTAGCAGT	0.483													G|||	5	0.000998403	0.003	0.0	5008	,	,		16874	0.0		0.001	False		,,,				2504	0.0				p.A281V		Atlas-SNP	.											FSCB,NS,carcinoma,0,1	FSCB	173	1	0			c.C842T						PASS	.	G	VAL/ALA	11,4395	17.9+/-39.9	0,11,2192	55	57	56		842	-7.7	0	14	dbSNP_134	56	30,8570	20.4+/-63.3	1,28,4271	yes	missense	FSCB	NM_032135.3	64	1,39,6463	AA,AG,GG		0.3488,0.2497,0.3152	benign	281/826	44975349	41,12965	2203	4300	6503	SO:0001583	missense	84075	exon1			GGCTCCGCTTTAG	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.842C>T	14.37:g.44975349G>A	ENSP00000344579:p.Ala281Val	109	0	0		89	37	0.41573	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Missense_Mutation	SNP	ENST00000340446.4	37	CCDS9679.1	.	.	.	.	.	.	.	.	.	.	G	0.019	-1.452098	0.01080	0.002497	0.003488	ENSG00000189139	ENST00000340446;ENST00000537803	T	0.25414	1.8	3.86	-7.73	0.01245	.	.	.	.	.	T	0.11623	0.0283	L	0.29908	0.895	0.09310	N	1	B	0.28971	0.229	B	0.15870	0.014	T	0.12066	-1.0562	9	0.18710	T	0.47	1.4119	6.3551	0.21397	0.1309:0.2257:0.5317:0.1117	.	281	Q5H9T9	FSCB_HUMAN	V	281	ENSP00000344579:A281V	ENSP00000344579:A281V	A	-	2	0	FSCB	44045099	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.261000	0.02855	-2.588000	0.00458	-1.224000	0.01588	GCG	G|0.997;A|0.003	0.003	strong		0.483	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135		A	44975349	G	A	44975349	3	1	27	1	0	0	0	0	1	0	0	0	6074	1087	38	1	1639	1	FSCB	14	44975349	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	14908435	44975349	62374191	720	11171											
C14orf37	145407	hgsc.bcm.edu	37	chr14	58605043	58605043	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcatggcttacttgtgctGtctgagacatctccgttctc	5	15	8	13	1	4	1	1	1	3	1	6	2	4	1	2	1	2	3	2	1	1	3	rs61741199	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:58605043G>A	ENST00000267485.7	-	2	1228	c.1034C>T	c.(1033-1035)aCa>aTa	p.T345I	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	345						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						TACTTGTGCTGTCTGAGACAT	0.547													G|||	351	0.0700879	0.1437	0.0432	5008	,	,		20918	0.0		0.0577	False		,,,				2504	0.0746				p.T345I		Atlas-SNP	.											.	C14orf37	87	.	0			c.C1034T						PASS	.	G	ILE/THR	516,3890	237.1+/-249.0	31,454,1718	155	152	153		1034	3.7	0.2	14	dbSNP_129	153	483,8117	140.1+/-196.7	12,459,3829	yes	missense	C14orf37	NM_001001872.2	89	43,913,5547	AA,AG,GG		5.6163,11.7113,7.6811	benign	345/775	58605043	999,12007	2203	4300	6503	SO:0001583	missense	145407	exon2			TGTGCTGTCTGAG		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.1034C>T	14.37:g.58605043G>A	ENSP00000267485:p.Thr345Ile	139	0	0		112	112	1	NM_001001872	A8K8Z8|Q6P5Q1|Q86TY1	Missense_Mutation	SNP	ENST00000267485.7	37	CCDS32089.1	123	0.05631868131868132	62	0.12601626016260162	15	0.04143646408839779	0	0.0	46	0.06068601583113457	G	11.64	1.698404	0.30142	0.117113	0.056163	ENSG00000139971	ENST00000267485;ENST00000438670	T	0.21191	2.02	5.6	3.72	0.42706	.	0.558344	0.18393	N	0.142606	T	0.00144	0.0004	L	0.46157	1.445	0.58432	P	9.000000000036756E-6	B;P;B;B	0.38597	0.084;0.639;0.084;0.084	B;B;B;B	0.32928	0.066;0.155;0.066;0.066	T	0.12400	-1.0549	9	0.11794	T	0.64	-0.2219	6.3844	0.21552	0.1574:0.1953:0.6473:0.0	.	383;345;345;345	B4DMS4;Q86TY3-2;A8K990;Q86TY3	.;.;.;CN037_HUMAN	I	345;383	ENSP00000267485:T345I	ENSP00000267485:T345I	T	-	2	0	C14orf37	57674796	0.050000	0.20438	0.200000	0.23457	0.367000	0.29736	0.079000	0.14782	1.302000	0.44855	0.655000	0.94253	ACA	G|0.928;A|0.072	0.072	strong		0.547	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872		A	58605043	G	A	58605043	3	1	27	1	0	0	0	0	1	0	0	0	1773	1377	48	2	1318	2	C14orf37	14	58605043	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	13629694	58605043	48744497	721	11172											
C14orf37	145407	hgsc.bcm.edu	37	chr14	58605156	58605156	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cactcatcacttaaggcagaGgcagctggaacagctgtgct	11	8	11	11	0	2	1	2	0	0	1	2	2	2	2	0	3	4	5	0	3	2	1	rs61748937	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:58605156G>A	ENST00000267485.7	-	2	1115	c.921C>T	c.(919-921)gcC>gcT	p.A307A	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	307						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						TTAAGGCAGAGGCAGCTGGAA	0.517													G|||	17	0.00339457	0.0015	0.0029	5008	,	,		21146	0.0		0.0109	False		,,,				2504	0.002				p.A307A		Atlas-SNP	.											.	C14orf37	87	.	0			c.C921T						PASS	.	G		8,4398	14.3+/-33.2	0,8,2195	93	97	96		921	0.4	0	14	dbSNP_129	96	134,8466	68.0+/-130.5	1,132,4167	no	coding-synonymous	C14orf37	NM_001001872.2		1,140,6362	AA,AG,GG		1.5581,0.1816,1.0918		307/775	58605156	142,12864	2203	4300	6503	SO:0001819	synonymous_variant	145407	exon2			GGCAGAGGCAGCT		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.921C>T	14.37:g.58605156G>A		218	0	0		175	98	0.56	NM_001001872	A8K8Z8|Q6P5Q1|Q86TY1	Silent	SNP	ENST00000267485.7	37	CCDS32089.1																																																																																			G|0.989;A|0.011	0.011	strong		0.517	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872		A	58605156	G	A	58605156	2	1	27	1	0	0	0	0	0	0	0	1	1773	987	35	2		2	C14orf37	14	58605156	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	113	58605156	48744384	722	11173											
C14orf135	64430	hgsc.bcm.edu	37	chr14	60592491	60592491	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgaaaagtggaaggaagcaAttttacaagaaaagccatac	20	7	9	5	0	0	2	0	1	0	1	0	4	0	4	1	2	4	1	1	2	10	3	rs145320435	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:60592491A>G	ENST00000406854.1	+	10	3771	c.3217A>G	c.(3217-3219)Att>Gtt	p.I1073V	PCNXL4_ENST00000317623.4_Missense_Mutation_p.I839V|PCNXL4_ENST00000406949.1_Missense_Mutation_p.I839V|PCNXL4_ENST00000535349.1_Missense_Mutation_p.I280V|PCNXL4_ENST00000404681.2_Missense_Mutation_p.I1073V			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	1073						integral component of membrane (GO:0016021)											GAAGGAAGCAATTTTACAAGA	0.323													A|||	10	0.00199681	0.0	0.0029	5008	,	,		17125	0.0		0.005	False		,,,				2504	0.0031				p.I839V		Atlas-SNP	.											.	.	.	.	0			c.A2515G						PASS	.	A	VAL/ILE	2,4404	4.2+/-10.8	0,2,2201	67	70	69		2515	-1.6	0.9	14	dbSNP_134	69	38,8562	24.0+/-70.4	0,38,4262	yes	missense	C14orf135	NM_022495.5	29	0,40,6463	GG,GA,AA		0.4419,0.0454,0.3076	benign	839/939	60592491	40,12966	2203	4300	6503	SO:0001583	missense	64430	exon9			GAAGCAATTTTAC	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.3217A>G	14.37:g.60592491A>G	ENSP00000384801:p.Ile1073Val	99	0	0		101	48	0.475248	NM_022495	A8MXM2|Q9BQG8|Q9H9F2	Missense_Mutation	SNP	ENST00000406854.1	37		4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	A	2.385	-0.341295	0.05243	4.54E-4	0.004419	ENSG00000126773	ENST00000317623;ENST00000406854;ENST00000406949;ENST00000404681;ENST00000535349	T;T;T;T;T	0.37411	1.2;1.2;1.2;1.2;1.2	5.26	-1.63	0.08345	.	0.323849	0.32120	N	0.006555	T	0.11537	0.0281	N	0.02266	-0.62	0.32445	N	0.546244	B;B	0.06786	0.001;0.0	B;B	0.06405	0.001;0.002	T	0.43261	-0.9402	10	0.02654	T	1	.	13.3605	0.60652	0.2688:0.0:0.7312:0.0	.	1073;839	Q63HM2;B5MC47	CN135_HUMAN;.	V	839;1073;839;1073;280	ENSP00000317396:I839V;ENSP00000384801:I1073V;ENSP00000385201:I839V;ENSP00000385713:I1073V;ENSP00000445644:I280V	ENSP00000317396:I839V	I	+	1	0	C14orf135	59662244	0.998000	0.40836	0.917000	0.36280	0.928000	0.56348	1.437000	0.34991	-0.407000	0.07576	-0.410000	0.06199	ATT	A|0.998;G|0.002	0.002	strong		0.323	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495		G	60592491	A	G	60592491	3	3	27	1	0	0	0	0	1	0	0	0	1747	101	4	3	2545	3	C14orf135	14	60592491	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	1987335	60592491	46757049	723	11174											
C14orf39	317761	hgsc.bcm.edu	37	chr14	60945066	60945066	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagtaaattggtcctgcataTaatcttcatgtttacgaaaa	14	14	6	7	1	2	0	1	0	1	0	3	1	3	0	1	1	2	3	1	1	7	7			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:60945066T>C	ENST00000321731.3	-	5	434	c.275A>G	c.(274-276)tAt>tGt	p.Y92C		NM_174978.2	NP_777638	Q8N1H7	S6OS1_HUMAN	chromosome 14 open reading frame 39	92					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)		GTCCTGCATATAATCTTCATG	0.279																																					p.Y92C		Atlas-SNP	.											.	C14orf39	79	.	0			c.A275G						PASS	.						78	76	77					14																	60945066		2201	4294	6495	SO:0001583	missense	317761	exon5			TGCATATAATCTT	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.275A>G	14.37:g.60945066T>C	ENSP00000324920:p.Tyr92Cys	200	0	0		166	90	0.542169	NM_174978	Q08AQ4	Missense_Mutation	SNP	ENST00000321731.3	37	CCDS9746.1	.	.	.	.	.	.	.	.	.	.	T	12.70	2.016056	0.35606	.	.	ENSG00000179008	ENST00000321731;ENST00000555476	T;T	0.59364	1.7;0.27	5.56	5.56	0.83823	.	0.000000	0.64402	D	0.000006	T	0.71187	0.3310	M	0.69823	2.125	0.35794	D	0.822654	D	0.89917	1.0	D	0.73380	0.98	T	0.77770	-0.2463	10	0.44086	T	0.13	-10.7904	9.2845	0.37749	0.1605:0.0:0.0:0.8395	.	92	Q8N1H7	S6OS1_HUMAN	C	92;63	ENSP00000324920:Y92C;ENSP00000451665:Y63C	ENSP00000324920:Y92C	Y	-	2	0	C14orf39	60014819	1.000000	0.71417	0.997000	0.53966	0.107000	0.19398	2.294000	0.43567	2.237000	0.73441	0.528000	0.53228	TAT	.	.	none		0.279	C14orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276948.1	NM_174978		C	60945066	T	C	60945066	3	2	27	1	0	0	0	0	1	0	0	0	1774	1406	49	3	1544	3	C14orf39	14	60945066	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	352575	60945066	46404474	724	11175											
ZFP36L1	677	hgsc.bcm.edu	37	chr14	69256848	69256848	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggctgcggagctcgtggatgCcgtgtgcgaactggcacttg	5	9	17	10	4	0	0	0	0	0	0	1	3	0	2	1	4	5	3	1	4	1	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:69256848C>A	ENST00000439696.2	-	2	720	c.419G>T	c.(418-420)gGc>gTc	p.G140V	ZFP36L1_ENST00000555997.1_3'UTR|ZFP36L1_ENST00000336440.3_Missense_Mutation_p.G140V	NM_001244701.1|NM_004926.3	NP_001231630.1|NP_004917.2	Q07352	TISB_HUMAN	ZFP36 ring finger protein-like 1	140					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)		CTCGTGGATGCCGTGTGCGAA	0.647											OREG0022753	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G209V		Atlas-SNP	.											.	ZFP36L1	47	.	0			c.G626T						PASS	.						96	91	93					14																	69256848		2203	4300	6503	SO:0001583	missense	677	exon3			TGGATGCCGTGTG	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.419G>T	14.37:g.69256848C>A	ENSP00000388402:p.Gly140Val	158	0	0	1113	155	27	0.174194	NM_001244701	Q13851	Missense_Mutation	SNP	ENST00000439696.2	37	CCDS9791.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.090153	0.76756	.	.	ENSG00000185650	ENST00000439696;ENST00000336440;ENST00000435246;ENST00000557086;ENST00000557022	T;T;T;T	0.51071	0.72;0.72;0.72;0.72	4.69	4.69	0.59074	Zinc finger, CCCH-type (3);	0.000000	0.85682	D	0.000000	T	0.79209	0.4407	H	0.96460	3.825	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86683	0.1918	10	0.87932	D	0	0.0068	17.8126	0.88620	0.0:1.0:0.0:0.0	.	140	Q07352	TISB_HUMAN	V	140;140;123;146;118	ENSP00000388402:G140V;ENSP00000337386:G140V;ENSP00000450784:G146V;ENSP00000450600:G118V	ENSP00000337386:G140V	G	-	2	0	ZFP36L1	68326601	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.563000	0.82314	2.423000	0.82170	0.585000	0.79938	GGC	.	.	none		0.647	ZFP36L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413227.1			A	69256848	C	A	69256848	3	1	27	1	0	0	0	0	1	0	0	0	17661	739	26	4	601	4	ZFP36L1	14	69256848	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	8311782	69256848	38092692	725	11176											
ZFP36L1	677	hgsc.bcm.edu	37	chr14	69259598	69259598	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aaatgctccgcccccctttaCcttgcataaaacttcgctca	10	11	4	16	2	1	0	1	0	0	0	3	0	2	0	5	0	4	3	5	0	4	5	rs563928424		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:69259598C>T	ENST00000439696.2	-	1	359		c.e1+1		ZFP36L1_ENST00000555997.1_5'Flank|ZFP36L1_ENST00000336440.3_Splice_Site	NM_001244701.1|NM_004926.3	NP_001231630.1|NP_004917.2	Q07352	TISB_HUMAN	ZFP36 ring finger protein-like 1						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)		CCCCCCTTTACCTTGCATAAA	0.517													C|||	1	0.000199681	0.0008	0.0	5008	,	,		14835	0.0		0.0	False		,,,				2504	0.0				.		Atlas-SNP	.											.	ZFP36L1	47	.	0			c.57+1G>A						PASS	.						163	168	166					14																	69259598		2203	4300	6503	SO:0001630	splice_region_variant	677	exon2			CCTTTACCTTGCA	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.57+1G>A	14.37:g.69259598C>T		63	0	0		34	6	0.176471	NM_004926	Q13851	Splice_Site	SNP	ENST00000439696.2	37	CCDS9791.1	.	.	.	.	.	.	.	.	.	.	C	19.73	3.882604	0.72410	.	.	ENSG00000185650	ENST00000439696;ENST00000336440;ENST00000435246;ENST00000553375	.	.	.	4.56	4.56	0.56223	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0951	0.81114	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ZFP36L1	68329351	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.059000	0.64306	2.065000	0.61736	0.561000	0.74099	.	.	.	none		0.517	ZFP36L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413227.1		Intron	T	69259598	C	T	69259598	5	4	27	1	0	0	0	0	0	0	1	0	17661	521	18	2	966	2	ZFP36L1	14	69259598	Splice_Site	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2750	69259598	38089942	726	11177											
ACTN1	87	hgsc.bcm.edu	37	chr14	69341653	69341653	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcacggagtcggggccggTgtagggggccatccgcgcga	5	5	20	11	6	0	0	0	0	0	0	2	2	1	1	3	7	0	2	3	7	1	1	rs11557769	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:69341653T>A	ENST00000193403.6	-	21	2985	c.2602A>T	c.(2602-2604)Acc>Tcc	p.T868S	ACTN1_ENST00000538545.2_Missense_Mutation_p.T906S|ACTN1_ENST00000438964.2_Missense_Mutation_p.T863S|ACTN1_ENST00000376839.3_Missense_Mutation_p.T798S|ACTN1_ENST00000394419.4_Missense_Mutation_p.T890S	NM_001102.3	NP_001093.1	P12814	ACTN1_HUMAN	actinin, alpha 1	868			T -> S (in dbSNP:rs11557769).		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)		TCGGGGCCGGTGTAGGGGGCC	0.662													t|||	31	0.0061901	0.0	0.0159	5008	,	,		14509	0.0		0.0189	False		,,,				2504	0.001				p.T890S		Atlas-SNP	.											ACTN1,NS,carcinoma,+2,1	ACTN1	77	1	0			c.A2668T						PASS	.	T	SER/THR,SER/THR,SER/THR	16,4390	25.3+/-52.1	0,16,2187	42	41	41		2602,2668,2587	-2.7	0.9	14	dbSNP_120	41	142,8458	70.3+/-132.9	0,142,4158	yes	missense,missense,missense	ACTN1	NM_001102.3,NM_001130004.1,NM_001130005.1	58,58,58	0,158,6345	AA,AT,TT		1.6512,0.3631,1.2148	benign,benign,benign	868/893,890/915,863/888	69341653	158,12848	2203	4300	6503	SO:0001583	missense	87	exon22			GGCCGGTGTAGGG	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.2602A>T	14.37:g.69341653T>A	ENSP00000193403:p.Thr868Ser	76	0	0		42	15	0.357143	NM_001130004	B3V8S3|B4DHH3|B7TY16|Q1HE25|Q9BTN1	Missense_Mutation	SNP	ENST00000193403.6	37	CCDS9792.1	18	0.008241758241758242	0	0.0	8	0.022099447513812154	0	0.0	10	0.013192612137203167	T	9.571	1.121108	0.20877	0.003631	0.016512	ENSG00000072110	ENST00000193403;ENST00000394419;ENST00000438964;ENST00000376839;ENST00000538545	T;T;T;T;T	0.39229	1.6;1.09;1.09;1.09;1.09	4.68	-2.72	0.05968	EF-hand, Ca insensitive (1);EF-hand-like domain (1);	0.656003	0.15664	N	0.250756	T	0.09642	0.0237	L	0.28556	0.865	0.22185	N	0.999308	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	0.21690	-1.0238	10	0.08381	T	0.77	.	2.1866	0.03888	0.1289:0.3501:0.1331:0.3879	rs11557769	863;890;868;510	P12814-2;Q1HE25;P12814;B4DFY0	.;.;ACTN1_HUMAN;.	S	868;890;863;798;906	ENSP00000193403:T868S;ENSP00000377941:T890S;ENSP00000414272:T863S;ENSP00000366035:T798S;ENSP00000439828:T906S	ENSP00000193403:T868S	T	-	1	0	ACTN1	68411406	0.003000	0.15002	0.930000	0.37139	0.998000	0.95712	-0.007000	0.12810	-0.578000	0.05959	0.528000	0.53228	ACC	T|0.988;A|0.012	0.012	strong		0.662	ACTN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413233.3	NM_001102		A	69341653	T	A	69341653	3	1	27	1	0	0	0	0	1	0	0	0	204	1696	59	5	80	5	ACTN1	14	69341653	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	82055	69341653	38007887	727	11178											
SLC8A3	6547	hgsc.bcm.edu	37	chr14	70633998	70633998	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgtgcacctcgctcatgctgGaggccttcttggcttgttct	3	15	11	12	1	3	0	1	0	2	0	4	1	3	1	2	3	2	5	2	3	0	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:70633998G>A	ENST00000381269.2	-	2	1895	c.1142C>T	c.(1141-1143)tCc>tTc	p.S381F	SLC8A3_ENST00000357887.3_Missense_Mutation_p.S381F|SLC8A3_ENST00000528359.1_Missense_Mutation_p.S381F|SLC8A3_ENST00000534137.1_Missense_Mutation_p.S381F|SLC8A3_ENST00000356921.2_Missense_Mutation_p.S381F	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 3	381					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)		GCTCATGCTGGAGGCCTTCTT	0.517																																					p.S381F		Atlas-SNP	.											.	SLC8A3	234	.	0			c.C1142T						PASS	.						126	115	119					14																	70633998		2203	4300	6503	SO:0001583	missense	6547	exon2			ATGCTGGAGGCCT	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.1142C>T	14.37:g.70633998G>A	ENSP00000370669:p.Ser381Phe	139	0	0		148	40	0.27027	NM_183002	Q5K3P6|Q5K3P7|Q8IUE9|Q8IUF0|Q8NFI7|Q96QG1|Q96QG2	Missense_Mutation	SNP	ENST00000381269.2	37	CCDS35498.1	.	.	.	.	.	.	.	.	.	.	G	9.140	1.013566	0.19277	.	.	ENSG00000100678	ENST00000356921;ENST00000381269;ENST00000357887;ENST00000534137;ENST00000528359	T;T;T;T;T	0.36699	1.32;1.24;1.38;1.32;1.38	5.83	5.83	0.93111	.	0.446831	0.24891	N	0.034769	T	0.43077	0.1231	L	0.50333	1.59	0.46396	D	0.999023	B;B;B;B	0.32543	0.135;0.083;0.375;0.242	B;B;B;B	0.39590	0.213;0.066;0.304;0.136	T	0.14671	-1.0464	10	0.35671	T	0.21	.	20.1242	0.97973	0.0:0.0:1.0:0.0	.	381;381;381;381	P57103-2;P57103;Q96QG2;Q96QG1	.;NAC3_HUMAN;.;.	F	381	ENSP00000349392:S381F;ENSP00000370669:S381F;ENSP00000350560:S381F;ENSP00000436688:S381F;ENSP00000433531:S381F	ENSP00000349392:S381F	S	-	2	0	SLC8A3	69703751	1.000000	0.71417	0.991000	0.47740	0.909000	0.53808	4.043000	0.57354	2.744000	0.94065	0.643000	0.83706	TCC	.	.	none		0.517	SLC8A3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390736.1			A	70633998	G	A	70633998	3	1	27	1	0	0	0	0	1	0	0	0	14723	1174	41	2	1780	2	SLC8A3	14	70633998	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1292345	70633998	36715542	728	11179											
PCNX	22990	hgsc.bcm.edu	37	chr14	71443816	71443816	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccaccatgttgatcagtcTctgtccagcgcctgtgacac	8	10	8	15	1	2	2	1	2	1	0	4	2	3	2	4	0	1	1	4	0	0	1	rs35702999	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:71443816T>G	ENST00000304743.2	+	6	1208	c.762T>G	c.(760-762)tcT>tcG	p.S254S	PCNX_ENST00000238570.5_Silent_p.S254S|PCNX_ENST00000439984.3_Silent_p.S254S	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	254						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)		TTGATCAGTCTCTGTCCAGCG	0.498													T|||	35	0.00698882	0.0	0.0043	5008	,	,		18137	0.0069		0.0199	False		,,,				2504	0.0051				p.S254S		Atlas-SNP	.											.	PCNX	198	.	0			c.T762G						PASS	.	T		10,4396	16.8+/-37.8	0,10,2193	141	119	126		762	0.8	1	14	dbSNP_126	126	86,8514	48.9+/-108.6	1,84,4215	no	coding-synonymous	PCNX	NM_014982.2		1,94,6408	GG,GT,TT		1.0,0.227,0.7381		254/2342	71443816	96,12910	2203	4300	6503	SO:0001819	synonymous_variant	22990	exon6			TCAGTCTCTGTCC	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.762T>G	14.37:g.71443816T>G		227	0	0		218	94	0.431193	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Silent	SNP	ENST00000304743.2	37	CCDS9806.1																																																																																			T|0.991;G|0.009	0.009	strong		0.498	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		G	71443816	T	G	71443816	2	3	27	1	0	0	0	0	0	0	0	1	11600	1538	54	5		5	PCNX	14	71443816	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	809818	71443816	35905724	729	11180											
PCNX	22990	hgsc.bcm.edu	37	chr14	71502824	71502824	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggtagtatgcattgtaattGgtgtgctgtattttgctatt	7	20	11	3	0	0	0	0	0	0	0	0	0	0	0	0	2	3	7	0	2	5	10	rs117405927	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:71502824G>T	ENST00000304743.2	+	19	4263	c.3817G>T	c.(3817-3819)Ggt>Tgt	p.G1273C	PCNX_ENST00000238570.5_Missense_Mutation_p.G1273C|PCNX_ENST00000439984.3_Missense_Mutation_p.G1162C	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1273						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)		CATTGTAATTGGTGTGCTGTA	0.328													G|||	2	0.000399361	0.0	0.0	5008	,	,		18875	0.0		0.002	False		,,,				2504	0.0				p.G1273C		Atlas-SNP	.											.	PCNX	198	.	0			c.G3817T						PASS	.	G	CYS/GLY	3,4403	6.2+/-15.9	0,3,2200	280	246	257		3817	5.5	1	14	dbSNP_133	257	9,8591	6.4+/-24.3	0,9,4291	yes	missense	PCNX	NM_014982.2	159	0,12,6491	TT,TG,GG		0.1047,0.0681,0.0923	probably-damaging	1273/2342	71502824	12,12994	2203	4300	6503	SO:0001583	missense	22990	exon19			GTAATTGGTGTGC	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.3817G>T	14.37:g.71502824G>T	ENSP00000304192:p.Gly1273Cys	242	0	0		191	98	0.513089	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	37	CCDS9806.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	G|G	17.74|17.74	3.464833|3.464833	0.63513|0.63513	6.81E-4|6.81E-4	0.001047|0.001047	ENSG00000100731|ENSG00000100731	ENST00000304743;ENST00000238570;ENST00000439984|ENST00000554691	T;T;T|.	0.09911|.	3.37;3.37;2.93|.	5.47|5.47	5.47|5.47	0.80525|0.80525	.|.	0.101356|.	0.64402|.	D|.	0.000003|.	T|T	0.60025|0.60025	0.2237|0.2237	L|L	0.31926|0.31926	0.97|0.97	0.58432|0.58432	D|D	0.999997|0.999997	D;D;D|.	0.64830|.	0.975;0.994;0.983|.	P;D;P|.	0.65987|.	0.742;0.94;0.754|.	T|T	0.54050|0.54050	-0.8351|-0.8351	10|5	0.62326|.	D|.	0.03|.	.|.	19.329|19.329	0.94278|0.94278	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1273;1162;1273|.	Q96RV3-3;B2RTR6;Q96RV3|.	.;.;PCX1_HUMAN|.	C|F	1273;1273;1162|331	ENSP00000304192:G1273C;ENSP00000238570:G1273C;ENSP00000396617:G1162C|.	ENSP00000238570:G1273C|.	G|L	+|+	1|3	0|2	PCNX|PCNX	70572577|70572577	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.991000|0.991000	0.79684|0.79684	9.289000|9.289000	0.96061|0.96061	2.565000|2.565000	0.86533|0.86533	0.467000|0.467000	0.42956|0.42956	GGT|TTG	G|0.999;T|0.001	0.001	strong		0.328	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		T	71502824	G	T	71502824	3	4	27	1	0	0	0	0	1	0	0	0	11600	1348	47	4	3891	4	PCNX	14	71502824	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	59008	71502824	35846716	730	11181											
PAPLN	89932	hgsc.bcm.edu	37	chr14	73720604	73720604	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gtgccgggctgcctgggaagCcccctgccattcaggcctgt	4	8	14	15	1	1	0	1	0	0	0	1	1	1	1	6	3	4	1	6	3	1	1	rs146030488	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:73720604C>A	ENST00000554301.1	+	11	1400	c.1237C>A	c.(1237-1239)Ccc>Acc	p.P413T	PAPLN_ENST00000340738.5_Missense_Mutation_p.P386T|PAPLN_ENST00000381166.3_Missense_Mutation_p.P413T|PAPLN_ENST00000427855.1_Missense_Mutation_p.P413T|PAPLN_ENST00000555445.1_Missense_Mutation_p.P413T			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	413	TSP type-1 3. {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)		GCCTGGGAAGCCCCCTGCCAT	0.701													C|||	16	0.00319489	0.0015	0.0058	5008	,	,		17022	0.0		0.0089	False		,,,				2504	0.001				p.P386T		Atlas-SNP	.											.	PAPLN	180	.	0			c.C1156A						PASS	.	C	THR/PRO	4,4398		0,4,2197	27	29	28		1156	4.6	1	14	dbSNP_134	28	40,8558		0,40,4259	yes	missense	PAPLN	NM_173462.3	38	0,44,6456	AA,AC,CC		0.4652,0.0909,0.3385	probably-damaging	386/1252	73720604	44,12956	2201	4299	6500	SO:0001583	missense	89932	exon11			GGGAAGCCCCCTG	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.1237C>A	14.37:g.73720604C>A	ENSP00000451803:p.Pro413Thr	106	0	0		116	55	0.474138	NM_173462	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Missense_Mutation	SNP	ENST00000554301.1	37		14	0.00641025641025641	3	0.006097560975609756	3	0.008287292817679558	0	0.0	8	0.010554089709762533	C	19.78	3.890634	0.72524	9.09E-4	0.004652	ENSG00000100767	ENST00000340738;ENST00000427855;ENST00000381166;ENST00000554301;ENST00000555445	T;T;T;T;T	0.63255	-0.03;-0.03;-0.03;-0.03;-0.03	4.57	4.57	0.56435	.	.	.	.	.	T	0.76506	0.3997	M	0.85945	2.785	0.49798	D	0.999828	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.83565	0.0109	9	0.87932	D	0	.	17.5437	0.87855	0.0:1.0:0.0:0.0	.	413;413;386	O95428-5;O95428;O95428-6	.;PPN_HUMAN;.	T	386;413;413;413;413	ENSP00000345395:P386T;ENSP00000403403:P413T;ENSP00000370558:P413T;ENSP00000451803:P413T;ENSP00000451729:P413T	ENSP00000216658:P413T	P	+	1	0	PAPLN	72790357	1.000000	0.71417	0.998000	0.56505	0.599000	0.36880	7.053000	0.76641	2.385000	0.81259	0.462000	0.41574	CCC	C|0.996;A|0.004	0.004	strong		0.701	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462		A	73720604	C	A	73720604	3	1	27	1	0	0	0	0	1	0	0	0	11437	739	26	4	1194	4	PAPLN	14	73720604	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2217780	73720604	33628936	731	11182											
VSX2	338917	hgsc.bcm.edu	37	chr14	74707911	74707911	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aagatgtttcctccagcgatCgaaaaatgtccaaatctgct	13	11	7	10	2	1	1	0	0	1	1	5	3	4	1	3	0	2	2	3	0	4	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:74707911C>T	ENST00000261980.2	+	2	487	c.397C>T	c.(397-399)Cga>Tga	p.R133*		NM_182894.2	NP_878314.1	P58304	VSX2_HUMAN	visual system homeobox 2	133	Ser/Thr-rich.				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)		CTCCAGCGATCGAAAAATGTC	0.597																																					p.R133X		Atlas-SNP	.											VSX2,right_upper_lobe,carcinoma,-1,1	VSX2	32	1	0			c.C397T						PASS	.						83	85	84					14																	74707911		2203	4300	6503	SO:0001587	stop_gained	338917	exon2			AGCGATCGAAAAA	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.397C>T	14.37:g.74707911C>T	ENSP00000261980:p.Arg133*	36	0	0		49	10	0.204082	NM_182894	A1A4X6	Nonsense_Mutation	SNP	ENST00000261980.2	37	CCDS9827.1	.	.	.	.	.	.	.	.	.	.	C	37	6.112200	0.97296	.	.	ENSG00000119614	ENST00000261980	.	.	.	4.56	2.52	0.30459	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.2645	0.60125	0.3715:0.6285:0.0:0.0	.	.	.	.	X	133	.	ENSP00000261980:R133X	R	+	1	2	VSX2	73777664	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.035000	0.41155	1.126000	0.42016	0.462000	0.41574	CGA	.	.	none		0.597	VSX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412323.1	NM_182894		T	74707911	C	T	74707911	4	4	27	1	0	0	0	0	0	1	0	0	17247	876	31	1	403	1	VSX2	14	74707911	Nonsense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	987307	74707911	32641629	732	11183											
C14orf159	80017	hgsc.bcm.edu	37	chr14	91633706	91633706	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggatgctgccccctcaaggtGctatctcagagaccaggtaa	10	8	11	12	0	2	1	2	0	1	1	3	3	2	2	3	3	3	3	3	3	3	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:91633706G>A	ENST00000523771.1	+	4	844	c.241G>A	c.(241-243)Gct>Act	p.A81T	C14orf159_ENST00000518665.2_Missense_Mutation_p.A81T|C14orf159_ENST00000523816.1_Missense_Mutation_p.A81T|C14orf159_ENST00000519019.1_Missense_Mutation_p.A81T|C14orf159_ENST00000522322.1_Missense_Mutation_p.A81T|C14orf159_ENST00000298858.4_Missense_Mutation_p.A81T|C14orf159_ENST00000520328.1_Missense_Mutation_p.A81T|C14orf159_ENST00000517877.1_Missense_Mutation_p.A81T|C14orf159_ENST00000412671.2_Missense_Mutation_p.A81T|C14orf159_ENST00000518868.1_Missense_Mutation_p.A81T|C14orf159_ENST00000256324.10_Missense_Mutation_p.A81T|C14orf159_ENST00000521077.2_Missense_Mutation_p.A81T|C14orf159_ENST00000428926.2_Missense_Mutation_p.A81T|C14orf159_ENST00000525393.2_Intron			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	81						mitochondrion (GO:0005739)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		CCCTCAAGGTGCTATCTCAGA	0.547																																					p.A81T		Atlas-SNP	.											.	C14orf159	57	.	0			c.G241A						PASS	.						103	99	100					14																	91633706		2203	4300	6503	SO:0001583	missense	80017	exon6			CAAGGTGCTATCT	AK097294	CCDS32141.1, CCDS41979.1, CCDS45150.1, CCDS66693.1, CCDS73677.1	14q32.11	2012-09-26			ENSG00000133943	ENSG00000133943			20498	protein-coding gene	gene with protein product							Standard	NM_001102367		Approved	FLJ39975	uc001xze.2	Q7Z3D6	OTTHUMG00000164980	ENST00000523771.1:c.241G>A	14.37:g.91633706G>A	ENSP00000429655:p.Ala81Thr	107	0	0		106	20	0.188679	NM_001102366	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Missense_Mutation	SNP	ENST00000523771.1	37	CCDS32141.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.773383	0.49786	.	.	ENSG00000133943	ENST00000521334;ENST00000522837;ENST00000518871;ENST00000298858;ENST00000520328;ENST00000256324;ENST00000522170;ENST00000519950;ENST00000523879;ENST00000521077;ENST00000518665;ENST00000518868;ENST00000519019;ENST00000523816;ENST00000517518;ENST00000428926;ENST00000523894;ENST00000522322;ENST00000523771;ENST00000521064;ENST00000412671;ENST00000517877	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.58060	1.52;0.43;1.52;0.77;1.52;1.52;1.52;1.52;0.36;1.52;0.77;1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52;0.78	5.09	2.29	0.28610	.	0.539348	0.18409	N	0.142104	T	0.39835	0.1093	L	0.52126	1.63	0.09310	N	1	P;B;B;B;B;B	0.42203	0.773;0.036;0.036;0.06;0.06;0.06	B;B;B;B;B;B	0.38428	0.273;0.012;0.012;0.028;0.028;0.028	T	0.18461	-1.0336	10	0.17832	T	0.49	.	7.2233	0.26002	0.3591:0.0:0.6409:0.0	.	81;81;81;81;81;81	Q7Z3D6-6;Q7Z3D6;B3KVU6;Q7Z3D6-5;Q7Z3D6-2;Q7Z3D6-3	.;CN159_HUMAN;.;.;.;.	T	81	ENSP00000430022:A81T;ENSP00000427971:A81T;ENSP00000429189:A81T;ENSP00000298858:A81T;ENSP00000429453:A81T;ENSP00000256324:A81T;ENSP00000430666:A81T;ENSP00000428296:A81T;ENSP00000428122:A81T;ENSP00000430137:A81T;ENSP00000429098:A81T;ENSP00000428263:A81T;ENSP00000430318:A81T;ENSP00000428974:A81T;ENSP00000428652:A81T;ENSP00000404343:A81T;ENSP00000429459:A81T;ENSP00000427953:A81T;ENSP00000429655:A81T;ENSP00000429392:A81T;ENSP00000404196:A81T;ENSP00000429949:A81T	ENSP00000256324:A81T	A	+	1	0	C14orf159	90703459	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.029000	0.12329	0.192000	0.20272	0.561000	0.74099	GCT	.	.	none		0.547	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952		A	91633706	G	A	91633706	3	1	27	1	0	0	0	0	1	0	0	0	1757	1319	46	2	247	2	C14orf159	14	91633706	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	16925795	91633706	15715834	733	11184											
CATSPERB	79820	hgsc.bcm.edu	37	chr14	92102819	92102819	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttgccgaacttcttgctgtaGatcgtttcctggggttcgtt	4	17	11	9	3	1	1	0	0	1	1	4	2	2	1	2	2	3	5	2	2	2	7			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:92102819G>A	ENST00000256343.3	-	17	1848	c.1692C>T	c.(1690-1692)atC>atT	p.I564I		NM_024764.2	NP_079040.2	Q9H7T0	CTSRB_HUMAN	catsper channel auxiliary subunit beta	564					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)				TCTTGCTGTAGATCGTTTCCT	0.408																																					p.I564I		Atlas-SNP	.											.	CATSPERB	114	.	0			c.C1692T						PASS	.						174	157	163					14																	92102819		2203	4300	6503	SO:0001819	synonymous_variant	79820	exon17			GCTGTAGATCGTT	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.1692C>T	14.37:g.92102819G>A		212	0	0		180	39	0.216667	NM_024764	A0AV51	Silent	SNP	ENST00000256343.3	37	CCDS32142.1																																																																																			.	.	none		0.408	CATSPERB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411769.1	NM_024764		A	92102819	G	A	92102819	2	1	27	1	0	0	0	0	0	0	0	1	2693	932	33	2		2	CATSPERB	14	92102819	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	469113	92102819	15246721	734	11185											
WDR25	79446	hgsc.bcm.edu	37	chr14	100996337	100996337	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtgctgccctccgtcctcGccacctgctcctggggaggg	2	8	13	18	3	0	0	0	0	0	0	4	1	3	1	7	3	3	2	7	3	0	0	rs144754220		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:100996337G>A	ENST00000335290.6	+	7	1820	c.1594G>A	c.(1594-1596)Gcc>Acc	p.A532T	WDR25_ENST00000554998.1_Missense_Mutation_p.A532T|WDR25_ENST00000557502.1_3'UTR|WDR25_ENST00000402312.3_Missense_Mutation_p.A532T|WDR25_ENST00000542471.2_Missense_Mutation_p.A275T	NM_024515.4	NP_078791.3	Q64LD2	WDR25_HUMAN	WD repeat domain 25	532										central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|skin(1)	20		Melanoma(154;0.212)				CTCCGTCCTCGCCACCTGCTC	0.617																																					p.A532T		Atlas-SNP	.											.	WDR25	37	.	0			c.G1594A						PASS	.	G	THR/ALA,THR/ALA	1,4405	2.1+/-5.4	0,1,2202	75	68	71		1594,1594	4.8	1	14	dbSNP_134	71	0,8600		0,0,4300	no	missense,missense	WDR25	NM_001161476.1,NM_024515.4	58,58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	532/545,532/545	100996337	1,13005	2203	4300	6503	SO:0001583	missense	79446	exon7			GTCCTCGCCACCT	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.1594G>A	14.37:g.100996337G>A	ENSP00000334148:p.Ala532Thr	98	0	0		91	20	0.21978	NM_001161476	A8K7E5|Q6NVV6|Q86TQ4|Q9BTK5	Missense_Mutation	SNP	ENST00000335290.6	37	CCDS32157.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.693621	0.88735	2.27E-4	0.0	ENSG00000176473	ENST00000554998;ENST00000402312;ENST00000335290;ENST00000542471	T;T;T;T	0.70282	4.69;4.69;4.69;-0.47	4.83	4.83	0.62350	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.133172	0.49305	D	0.000150	D	0.85982	0.5824	M	0.92077	3.27	0.58432	D	0.999996	D;D	0.89917	1.0;0.997	P;P	0.59546	0.859;0.834	D	0.89565	0.3809	10	0.62326	D	0.03	-12.8885	17.0452	0.86500	0.0:0.0:1.0:0.0	.	275;532	Q64LD2-2;Q64LD2	.;WDR25_HUMAN	T	532;532;532;275	ENSP00000450661:A532T;ENSP00000385540:A532T;ENSP00000334148:A532T;ENSP00000441903:A275T	ENSP00000334148:A532T	A	+	1	0	WDR25	100066090	1.000000	0.71417	0.964000	0.40570	0.626000	0.37791	9.336000	0.96533	2.388000	0.81334	0.655000	0.94253	GCC	G|1.000;A|0.000	0.000	weak		0.617	WDR25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414312.1	NM_024515		A	100996337	G	A	100996337	3	1	27	1	0	0	0	0	1	0	0	0	17297	1087	38	1	1616	1	WDR25	14	100996337	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	8893518	100996337	6353203	735	11186											
RTL1	388015	hgsc.bcm.edu	37	chr14	101350274	101350274	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atggcctcttctgccacacgCagtgcctggcggtactcaaa	8	9	10	14	2	3	0	1	0	2	0	3	0	3	0	3	3	3	2	3	3	2	2	rs61993320	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:101350274C>T	ENST00000534062.1	-	1	910	c.852G>A	c.(850-852)ctG>ctA	p.L284L	MIR136_ENST00000385207.1_RNA|MIR127_ENST00000384876.1_RNA|MIR433_ENST00000384837.1_RNA|MIR432_ENST00000606207.1_RNA|MIR431_ENST00000385266.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	284					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						CTGCCACACGCAGTGCCTGGC	0.592													C|||	60	0.0119808	0.0008	0.0245	5008	,	,		18928	0.0		0.0328	False		,,,				2504	0.0092				p.L284L		Atlas-SNP	.											.	RTL1	120	.	0			c.G852A						PASS	.	C		6,1378		0,6,686	57	53	54		852	0.5	0.1	14	dbSNP_129	54	104,3078		0,104,1487	no	coding-synonymous	RTL1	NM_001134888.2		0,110,2173	TT,TC,CC		3.2684,0.4335,2.4091		284/1359	101350274	110,4456	692	1591	2283	SO:0001819	synonymous_variant	388015	exon1			CACACGCAGTGCC		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.852G>A	14.37:g.101350274C>T		69	0	0		49	22	0.44898	NM_001134888	E9PKS8	Silent	SNP	ENST00000534062.1	37	CCDS53910.1																																																																																			C|0.983;T|0.017	0.017	strong		0.592	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888		T	101350274	C	T	101350274	2	4	27	1	0	0	0	0	0	0	0	1	13739	697	25	2		2	RTL1	14	101350274	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	353937	101350274	5999266	736	11187											
KIF26A	26153	hgsc.bcm.edu	37	chr14	104643650	104643650	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctagtggctggtgggtcgCgggctctggggccttcggtg	1	10	20	10	3	1	0	0	0	1	0	3	0	1	0	2	7	0	2	2	7	1	2	rs372336742		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:104643650C>T	ENST00000423312.2	+	12	4525	c.4525C>T	c.(4525-4527)Cgg>Tgg	p.R1509W	KIF26A_ENST00000315264.7_Missense_Mutation_p.R1370W	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	1509					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)	p.R1509W(1)		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)		TGGTGGGTCGCGGGCTCTGGG	0.736																																					p.R1509W		Atlas-SNP	.											KIF26A,NS,carcinoma,0,1	KIF26A	84	1	1	Substitution - Missense(1)	endometrium(1)	c.C4525T						PASS	.	C	TRP/ARG	0,3588		0,0,1794	8	11	10		4525	-0.3	0	14		10	1,7821		0,1,3910	no	missense	KIF26A	NM_015656.1	101	0,1,5704	TT,TC,CC		0.0128,0.0,0.0088	probably-damaging	1509/1883	104643650	1,11409	1794	3911	5705	SO:0001583	missense	26153	exon12			GGGTCGCGGGCTC	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.4525C>T	14.37:g.104643650C>T	ENSP00000388241:p.Arg1509Trp	62	0	0		97	58	0.597938	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Missense_Mutation	SNP	ENST00000423312.2	37	CCDS45171.1	.	.	.	.	.	.	.	.	.	.	C	12.07	1.828514	0.32329	0.0	1.28E-4	ENSG00000066735	ENST00000423312;ENST00000315264	T;T	0.80824	-1.42;-1.42	4.09	-0.307	0.12777	.	.	.	.	.	D	0.82393	0.5027	L	0.47716	1.5	0.09310	N	1	D	0.76494	0.999	P	0.62014	0.897	T	0.71629	-0.4535	9	0.87932	D	0	.	8.6301	0.33915	0.5422:0.3597:0.098:0.0	.	1509	Q9ULI4	KI26A_HUMAN	W	1509;1370	ENSP00000388241:R1509W;ENSP00000325452:R1370W	ENSP00000325452:R1370W	R	+	1	2	KIF26A	103713403	0.964000	0.33143	0.001000	0.08648	0.002000	0.02628	2.357000	0.44125	0.113000	0.18004	0.462000	0.41574	CGG	.	.	weak		0.736	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1			T	104643650	C	T	104643650	3	4	27	1	0	0	0	0	1	0	0	0	8303	759	27	1	4571	1	KIF26A	14	104643650	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3293376	104643650	2705890	737	11188											
SIVA1	10572	hgsc.bcm.edu	37	chr14	105222988	105222988	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttcctcatgcgtgcgagccGtggatgggaaggcggtctgc	5	9	17	10	4	2	0	1	0	1	0	3	3	3	2	2	4	4	1	2	4	1	1	rs144031294	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105222988G>A	ENST00000329967.6	+	3	463	c.361G>A	c.(361-363)Gtg>Atg	p.V121M	SIVA1_ENST00000347067.5_Missense_Mutation_p.V56M	NM_006427.3	NP_006418.2	O15304	SIVA_HUMAN	SIVA1, apoptosis-inducing factor	121	Interaction with coxsackievirus B3 VP2.				activation-induced cell death of T cells (GO:0006924)|extrinsic apoptotic signaling pathway (GO:0097191)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|response to virus (GO:0009615)|viral process (GO:0016032)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	CD27 receptor binding (GO:0005175)|metal ion binding (GO:0046872)|virus receptor activity (GO:0001618)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(1)|prostate(1)	3		all_cancers(154;0.14)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00153)|OV - Ovarian serous cystadenocarcinoma(23;0.0148)|Epithelial(46;0.0396)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.173)		CGTGCGAGCCGTGGATGGGAA	0.647																																					p.V121M		Atlas-SNP	.											.	SIVA1	12	.	0			c.G361A						PASS	.	G	MET/VAL,MET/VAL	0,4406		0,0,2203	117	104	108		361,166	2.9	0	14	dbSNP_134	108	15,8585	11.2+/-40.8	0,15,4285	yes	missense,missense	SIVA1	NM_006427.3,NM_021709.2	21,21	0,15,6488	AA,AG,GG		0.1744,0.0,0.1153	possibly-damaging,possibly-damaging	121/176,56/111	105222988	15,12991	2203	4300	6503	SO:0001583	missense	10572	exon3			CGAGCCGTGGATG	U82938	CCDS9992.1, CCDS9993.1	14q32.33	2007-03-19							17712	protein-coding gene	gene with protein product		605567				9177220	Standard	NM_006427		Approved	SIVA, Siva-1, Siva-2, CD27BP	uc001yph.3	O15304		ENST00000329967.6:c.361G>A	14.37:g.105222988G>A	ENSP00000329213:p.Val121Met	134	0	0		135	73	0.540741	NM_006427	Q96P98|Q9UPD6	Missense_Mutation	SNP	ENST00000329967.6	37	CCDS9992.1	.	.	.	.	.	.	.	.	.	.	G	12.18	1.860882	0.32884	0.0	0.001744	ENSG00000184990	ENST00000329967;ENST00000347067;ENST00000553810	.	.	.	4.77	2.9	0.33743	.	1.203960	0.05732	N	0.599742	T	0.56001	0.1956	L	0.56769	1.78	0.09310	N	1	D;D;D	0.67145	0.994;0.996;0.994	P;P;P	0.58130	0.779;0.759;0.833	T	0.38650	-0.9651	9	0.49607	T	0.09	-10.267	9.5779	0.39470	0.1695:0.0:0.8305:0.0	.	121;56;121	B4DTY2;O15304-2;O15304	.;.;SIVA_HUMAN	M	121;56;121	.	ENSP00000329213:V121M	V	+	1	0	SIVA1	104294033	0.011000	0.17503	0.004000	0.12327	0.026000	0.11368	1.844000	0.39269	1.227000	0.43598	0.561000	0.74099	GTG	G|0.998;A|0.002	0.002	strong		0.647	SIVA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410541.1	NM_006427		A	105222988	G	A	105222988	3	1	27	1	0	0	0	0	1	0	0	0	14360	1145	40	1	371	1	SIVA1	14	105222988	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	579338	105222988	2126552	738	11189											
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105410417	105410417	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agtcacatccttgtcggccaGggacaggtccccctccagct	7	8	10	16	1	1	0	1	0	0	0	5	1	4	1	5	3	1	1	5	3	0	1	rs200284292	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105410417G>A	ENST00000333244.5	-	7	11490	c.11371C>T	c.(11371-11373)Ctg>Ttg	p.L3791L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3791						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)			TTGTCGGCCAGGGACAGGTCC	0.582													.|||	177	0.0353435	0.053	0.0231	5008	,	,		20409	0.0417		0.004	False		,,,				2504	0.046				p.L3791L		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C11371T						PASS	.						216	217	217					14																	105410417		1998	4162	6160	SO:0001819	synonymous_variant	113146	exon7			CGGCCAGGGACAG	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.11371C>T	14.37:g.105410417G>A		140	0	0		117	9	0.0769231	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			G|0.993;A|0.007	0.007	strong		0.582	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		A	105410417	G	A	105410417	2	1	27	1	0	0	0	0	0	0	0	1	415	991	35	2		2	AHNAK2	14	105410417	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	187429	105410417	1939123	739	11190											
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105417683	105417683	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gtcagtggtcttgaggtcccCctgcatggaggggaggctca	6	9	16	10	0	3	1	2	1	1	0	4	3	4	3	2	6	1	2	2	6	0	1	rs367930189		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105417683C>T	ENST00000333244.5	-	7	4224	c.4105G>A	c.(4105-4107)Ggg>Agg	p.G1369R	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1369						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)			TTGAGGTCCCCCTGCATGGAG	0.647																																					p.G1369R		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,+2,1	AHNAK2	719	1	0			c.G4105A						PASS	.	C	ARG/GLY	0,3684		0,0,1842	99	74	83		4105	2.3	0	14		83	2,6232		1,0,3116	no	missense	AHNAK2	NM_138420.2	125	1,0,4958	TT,TC,CC		0.0321,0.0,0.0202	probably-damaging	1369/5796	105417683	2,9916	1842	3117	4959	SO:0001583	missense	113146	exon7			GGTCCCCCTGCAT	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.4105G>A	14.37:g.105417683C>T	ENSP00000353114:p.Gly1369Arg	0	0	.		88	4	0.0454545	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	-	15.55	2.867501	0.51588	0.0	3.21E-4	ENSG00000185567	ENST00000333244	T	0.01584	4.75	4.18	2.29	0.28610	.	.	.	.	.	T	0.06188	0.0160	M	0.75264	2.295	0.09310	N	1	D	0.62365	0.991	P	0.61592	0.891	T	0.32745	-0.9895	9	0.25106	T	0.35	.	6.5072	0.22202	0.1794:0.7206:0.0:0.1001	.	1369	Q8IVF2	AHNK2_HUMAN	R	1369	ENSP00000353114:G1369R	ENSP00000353114:G1369R	G	-	1	0	AHNAK2	104488728	0.006000	0.16342	0.000000	0.03702	0.087000	0.18053	1.114000	0.31196	0.237000	0.21200	0.485000	0.47835	GGG	.	.	weak		0.647	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		T	105417683	C	T	105417683	3	4	27	1	0	0	0	0	1	0	0	0	415	623	22	2	13286	2	AHNAK2	14	105417683	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	7266	105417683	1931857	740	11191											
BTBD6	90135	hgsc.bcm.edu	37	chr14	105716854	105716854	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttctacacggccagtgccGtcctggacggcagcgaactc	7	7	11	16	4	1	0	0	0	1	0	3	2	2	1	4	3	4	1	4	3	2	2	rs146426875	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105716854G>A	ENST00000392554.3	+	4	1600	c.1303G>A	c.(1303-1305)Gtc>Atc	p.V435I	BRF1_ENST00000379937.2_Intron|BTBD6_ENST00000463376.2_Missense_Mutation_p.V360I|BRF1_ENST00000546474.1_Intron|BRF1_ENST00000392557.4_5'Flank|BRF1_ENST00000327359.3_Intron|BTBD6_ENST00000536364.1_Missense_Mutation_p.V435I|BRF1_ENST00000446501.2_5'Flank|BTBD6_ENST00000327471.3_Missense_Mutation_p.V360I|BRF1_ENST00000440513.3_Intron			Q96KE9	BTBD6_HUMAN	BTB (POZ) domain containing 6	435						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)		GGCCAGTGCCGTCCTGGACGG	0.572													G|||	8	0.00159744	0.0	0.0	5008	,	,		19762	0.0		0.002	False		,,,				2504	0.0061				p.V435I		Atlas-SNP	.											.	BTBD6	24	.	0			c.G1303A						PASS	.	G	,,,,ILE/VAL	3,4403	6.2+/-15.9	0,3,2200	95	83	87		,,,,1303	3.1	0.6	14	dbSNP_134	87	25,8575	17.9+/-57.8	0,25,4275	yes	intron,intron,intron,intron,missense	BRF1,BTBD6	NM_001242786.1,NM_001242787.1,NM_001242788.1,NM_001519.3,NM_033271.2	,,,,29	0,28,6475	AA,AG,GG		0.2907,0.0681,0.2153	,,,,benign	,,,,435/486	105716854	28,12978	2203	4300	6503	SO:0001583	missense	90135	exon5			AGTGCCGTCCTGG	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.1303G>A	14.37:g.105716854G>A	ENSP00000376337:p.Val435Ile	70	0	0		56	29	0.517857	NM_033271	Q8IVQ7|Q9BR94	Missense_Mutation	SNP	ENST00000392554.3	37	CCDS10002.2	.	.	.	.	.	.	.	.	.	.	G	2.830	-0.242885	0.05906	6.81E-4	0.002907	ENSG00000184887	ENST00000536364;ENST00000392554;ENST00000327471	T;T;T	0.73789	-0.78;-0.78;-0.69	5.16	3.06	0.35304	PHR (1);	0.122234	0.53938	D	0.000047	T	0.43188	0.1236	N	0.02802	-0.49	0.80722	D	1	B	0.16603	0.018	B	0.17979	0.02	T	0.16571	-1.0398	9	.	.	.	-41.9028	4.7344	0.12981	0.3872:0.0:0.6128:0.0	.	435	Q96KE9	BTBD6_HUMAN	I	435;435;360	ENSP00000443091:V435I;ENSP00000376337:V435I;ENSP00000329361:V360I	.	V	+	1	0	BTBD6	104787899	1.000000	0.71417	0.641000	0.29422	0.440000	0.31957	4.545000	0.60698	1.161000	0.42604	0.655000	0.94253	GTC	G|0.997;A|0.003	0.003	strong		0.572	BTBD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074556.4			A	105716854	G	A	105716854	3	1	27	1	0	0	0	0	1	0	0	0	1547	1145	40	1	1317	1	BTBD6	14	105716854	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	299171	105716854	1632686	741	11192											
MTA1	9112	hgsc.bcm.edu	37	chr14	105936204	105936204	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agccggaacctcctgctcaaCgggaagtcctaccccaccaa	11	5	8	17	2	1	0	1	0	0	0	3	2	3	2	7	2	5	1	7	2	5	1	rs373034822		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr14:105936204C>T	ENST00000331320.7	+	20	2086	c.1872C>T	c.(1870-1872)aaC>aaT	p.N624N	MTA1_ENST00000406191.1_Silent_p.N612N|MTA1_ENST00000405646.1_Silent_p.N607N|MTA1_ENST00000435036.2_Silent_p.N164N|RP11-521B24.5_ENST00000552675.1_RNA	NM_001203258.1|NM_004689.3	NP_001190187.1|NP_004680.2	Q13330	MTA1_HUMAN	metastasis associated 1	624					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)		TCCTGCTCAACGGGAAGTCCT	0.682																																					p.N624N		Atlas-SNP	.											.	MTA1	61	.	0			c.C1872T						PASS	.	C	,	0,4384		0,0,2192	27	26	27		,1872	-6	0.9	14		27	1,8585		0,1,4292	no	utr-3,coding-synonymous	MTA1	NM_001203258.1,NM_004689.3	,	0,1,6484	TT,TC,CC		0.0116,0.0,0.0077	,	,624/716	105936204	1,12969	2192	4293	6485	SO:0001819	synonymous_variant	9112	exon20			GCTCAACGGGAAG	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.1872C>T	14.37:g.105936204C>T		102	0	0		97	53	0.546392	NM_004689	A5PLK4|Q86SW2|Q8NFI8|Q96GI8	Silent	SNP	ENST00000331320.7	37	CCDS32169.1	.	.	.	.	.	.	.	.	.	.	C	9.588	1.125368	0.20959	0.0	1.16E-4	ENSG00000182979	ENST00000494981	.	.	.	5.27	-6.01	0.02199	.	.	.	.	.	T	0.51924	0.1703	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55231	-0.8173	4	.	.	.	-33.3685	10.6162	0.45451	0.0:0.1432:0.115:0.7418	.	.	.	.	W	51	.	.	R	+	1	2	MTA1	105007249	0.007000	0.16637	0.911000	0.35937	0.890000	0.51754	-1.491000	0.02302	-1.078000	0.03117	-0.350000	0.07774	CGG	.	.	weak		0.682	MTA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317849.15			T	105936204	C	T	105936204	2	4	27	1	0	0	0	0	0	0	0	1	9917	535	19	1		1	MTA1	14	105936204	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	219350	105936204	1413336	742	11193											
GABRB3	2562	hgsc.bcm.edu	37	chr15	26806154	26806154	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agcttcttctgcctttgaggGcctcttccaaagaaaatgta	10	13	8	10	0	3	2	0	1	3	1	4	2	4	2	3	1	2	2	3	1	4	5	rs74907974	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:26806154G>A	ENST00000311550.5	-	8	1116	c.1005C>T	c.(1003-1005)ggC>ggT	p.G335G	GABRB3_ENST00000545868.1_Silent_p.G250G|GABRB3_ENST00000299267.4_Silent_p.G335G|GABRB3_ENST00000541819.2_Silent_p.G391G|GABRB3_ENST00000400188.3_Silent_p.G264G	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	335					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)	GCCTTTGAGGGCCTCTTCCAA	0.493													G|||	55	0.0109824	0.034	0.0115	5008	,	,		18829	0.0		0.002	False		,,,				2504	0.0				p.G335G		Atlas-SNP	.											GABRB3_ENST00000541819,right_upper_lobe,carcinoma,-2,6	GABRB3	338	6	0			c.C1005T						PASS	.	G	,,,	122,4284	90.6+/-129.3	1,120,2082	156	163	161		1005,750,792,1005	2.1	1	15	dbSNP_131	161	16,8584	11.9+/-42.8	0,16,4284	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GABRB3	NM_000814.5,NM_001191320.1,NM_001191321.1,NM_021912.4	,,,	1,136,6366	AA,AG,GG		0.186,2.769,1.061	,,,	335/474,250/389,264/403,335/474	26806154	138,12868	2203	4300	6503	SO:0001819	synonymous_variant	2562	exon8			TTGAGGGCCTCTT		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.1005C>T	15.37:g.26806154G>A		159	0	0		129	53	0.410853	NM_021912	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Silent	SNP	ENST00000311550.5	37	CCDS10019.1																																																																																			G|0.991;A|0.009	0.009	strong		0.493	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2			A	26806154	G	A	26806154	2	1	27	1	0	0	0	0	0	0	0	1	6176	1190	42	2		2	GABRB3	15	26806154	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10		26806154	75725238	743	11194											
GABRB3	2562	hgsc.bcm.edu	37	chr15	26825545	26825545	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agctcaatcctttccactccGgtaacagccttgtccccgcc	7	10	6	18	2	1	0	1	0	0	0	5	0	5	0	7	1	3	2	7	1	2	3	rs75965657	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:26825545G>A	ENST00000311550.5	-	6	714	c.603C>T	c.(601-603)acC>acT	p.T201T	GABRB3_ENST00000545868.1_Silent_p.T116T|GABRB3_ENST00000299267.4_Silent_p.T201T|GABRB3_ENST00000541819.2_Silent_p.T257T|GABRB3_ENST00000400188.3_Silent_p.T130T	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	201					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)	TTTCCACTCCGGTAACAGCCT	0.537													G|||	90	0.0179712	0.0643	0.0058	5008	,	,		18278	0.0		0.001	False		,,,				2504	0.0				p.T201T		Atlas-SNP	.											.	GABRB3	338	.	0			c.C603T						PASS	.	G	,,,	275,4131	154.8+/-188.1	7,261,1935	122	105	111		603,348,390,603	-10.2	0	15	dbSNP_131	111	18,8582	11.9+/-42.8	0,18,4282	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GABRB3	NM_000814.5,NM_001191320.1,NM_001191321.1,NM_021912.4	,,,	7,279,6217	AA,AG,GG		0.2093,6.2415,2.2528	,,,	201/474,116/389,130/403,201/474	26825545	293,12713	2203	4300	6503	SO:0001819	synonymous_variant	2562	exon6			CACTCCGGTAACA		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.603C>T	15.37:g.26825545G>A		92	0	0		90	43	0.477778	NM_021912	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Silent	SNP	ENST00000311550.5	37	CCDS10019.1																																																																																			G|0.982;A|0.018	0.018	strong		0.537	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2			A	26825545	G	A	26825545	2	1	27	1	0	0	0	0	0	0	0	1	6176	1103	39	1		1	GABRB3	15	26825545	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	19391	26825545	75705847	744	11195											
GABRA5	2558	hgsc.bcm.edu	37	chr15	27182422	27182422	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatggctccagactgaaccAgtaccacctgatggggcaga	12	6	12	11	0	0	5	0	2	0	3	1	5	1	5	4	3	2	3	4	3	2	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:27182422A>T	ENST00000335625.5	+	8	1559	c.671A>T	c.(670-672)cAg>cTg	p.Q224L	GABRB3_ENST00000541819.2_Intron|GABRA5_ENST00000355395.5_Missense_Mutation_p.Q224L|GABRA5_ENST00000400081.3_Missense_Mutation_p.Q224L	NM_000810.3	NP_000801.1	P31644	GBRA5_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 5	224					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)	AGACTGAACCAGTACCACCTG	0.597																																					p.Q224L		Atlas-SNP	.											GABRA5,colon,carcinoma,-1,1	GABRA5	127	1	0			c.A671T						PASS	.						80	84	83					15																	27182422		2112	4220	6332	SO:0001583	missense	2558	exon8			TGAACCAGTACCA		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.671A>T	15.37:g.27182422A>T	ENSP00000335592:p.Gln224Leu	79	0	0		77	32	0.415584	NM_001165037	A8K338|Q14DC2|Q53XL6|Q9NYT3|Q9NYT4|Q9NYT5	Missense_Mutation	SNP	ENST00000335625.5	37	CCDS45194.1	.	.	.	.	.	.	.	.	.	.	A	32	5.143883	0.94603	.	.	ENSG00000186297	ENST00000335625;ENST00000355395;ENST00000400081	T;T;T	0.79141	-1.24;-1.24;-1.24	5.28	5.28	0.74379	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.88966	0.6581	M	0.88704	2.975	0.80722	D	1	D	0.63046	0.992	D	0.66351	0.943	D	0.91133	0.4939	10	0.87932	D	0	.	14.6925	0.69096	1.0:0.0:0.0:0.0	.	224	P31644	GBRA5_HUMAN	L	224	ENSP00000335592:Q224L;ENSP00000347557:Q224L;ENSP00000382953:Q224L	ENSP00000335592:Q224L	Q	+	2	0	GABRA5	24765168	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.084000	0.94076	2.114000	0.64651	0.379000	0.24179	CAG	.	.	none		0.597	GABRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415234.1			T	27182422	A	T	27182422	3	4	27	1	0	0	0	0	1	0	0	0	6172	188	7	5	693	5	GABRA5	15	27182422	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	356877	27182422	75348970	745	11196											
GABRG3	2567	hgsc.bcm.edu	37	chr15	27765249	27765249	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttggatcaaaaaagatgctAcgccagcaagaacagcatta	17	8	8	8	1	1	2	1	0	0	2	1	3	1	3	1	1	5	3	1	1	7	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:27765249A>G	ENST00000333743.6	+	7	1098	c.844A>G	c.(844-846)Acg>Gcg	p.T282A	RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	282					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)	AAAAGATGCTACGCCAGCAAG	0.348																																					p.T282A	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											.	GABRG3	115	.	0			c.A844G						PASS	.						63	59	60					15																	27765249		1840	4106	5946	SO:0001583	missense	2567	exon7			GATGCTACGCCAG		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.844A>G	15.37:g.27765249A>G	ENSP00000331912:p.Thr282Ala	102	0	0		99	4	0.040404	NM_033223	G3V594|Q9HD46|Q9NYT2	Missense_Mutation	SNP	ENST00000333743.6	37	CCDS45195.1	.	.	.	.	.	.	.	.	.	.	A	13.53	2.264631	0.40095	.	.	ENSG00000182256	ENST00000333743;ENST00000554696	D;D	0.86097	-2.07;-2.07	5.39	5.39	0.77823	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.101026	0.64402	D	0.000002	T	0.72946	0.3524	N	0.13168	0.305	0.80722	D	1	B	0.20780	0.048	B	0.28305	0.088	T	0.67448	-0.5668	10	0.25751	T	0.34	.	9.2407	0.37495	0.9204:0.0:0.0795:0.0	.	282	Q99928	GBRG3_HUMAN	A	282;224	ENSP00000331912:T282A;ENSP00000451862:T224A	ENSP00000331912:T282A	T	+	1	0	GABRG3	25438844	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.888000	0.63164	2.260000	0.74910	0.528000	0.53228	ACG	.	.	none		0.348	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2			G	27765249	A	G	27765249	3	3	27	1	0	0	0	0	1	0	0	0	6181	391	14	3	870	3	GABRG3	15	27765249	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	582827	27765249	74766143	746	11197											
TRPM1	4308	hgsc.bcm.edu	37	chr15	31327779	31327779	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttctctaacgccaggctcacGatgtaggagatgacgatcca	11	9	10	11	3	2	2	1	1	1	1	4	5	3	2	2	2	1	2	2	2	2	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:31327779G>A	ENST00000256552.6	-	21	2817	c.2670C>T	c.(2668-2670)atC>atT	p.I890I	RP11-348B17.1_ENST00000558755.1_RNA|RP11-348B17.1_ENST00000561299.1_RNA|TRPM1_ENST00000397795.2_Silent_p.I868I|TRPM1_ENST00000542188.1_Silent_p.I907I	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)		CCAGGCTCACGATGTAGGAGA	0.542																																					p.I907I		Atlas-SNP	.											.	TRPM1	183	.	0			c.C2721T						PASS	.						87	89	88					15																	31327779		2054	4193	6247	SO:0001819	synonymous_variant	4308	exon20			GCTCACGATGTAG	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.2670C>T	15.37:g.31327779G>A		89	0	0		93	5	0.0537634	NM_001252020		Silent	SNP	ENST00000256552.6	37	CCDS58346.1																																																																																			.	.	none		0.542	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420		A	31327779	G	A	31327779	2	1	27	1	0	0	0	0	0	0	0	1	16600	1048	37	1		1	TRPM1	15	31327779	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	3562530	31327779	71203613	747	11198											
RYR3	6263	hgsc.bcm.edu	37	chr15	33954552	33954552	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccttcgatctggtttctaTgacctgctcatcagcatcca	7	14	6	14	1	4	1	2	1	2	0	7	2	6	1	3	1	2	3	3	1	1	3	rs200740143	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:33954552T>C	ENST00000389232.4	+	35	4891	c.4821T>C	c.(4819-4821)taT>taC	p.Y1607Y	RYR3_ENST00000415757.3_Silent_p.Y1607Y	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	1607	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)		CTGGTTTCTATGACCTGCTCA	0.567													T|||	2	0.000399361	0.0	0.0	5008	,	,		20622	0.0		0.002	False		,,,				2504	0.0				p.Y1607Y		Atlas-SNP	.											.	RYR3	760	.	0			c.T4821C						PASS	.	T		6,4026		0,6,2010	72	71	71		4821	3.7	1	15		71	36,8294		0,36,4129	no	coding-synonymous	RYR3	NM_001036.3		0,42,6139	CC,CT,TT		0.4322,0.1488,0.3398		1607/4871	33954552	42,12320	2016	4165	6181	SO:0001819	synonymous_variant	6263	exon35			TTTCTATGACCTG		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.4821T>C	15.37:g.33954552T>C		91	0	0		122	56	0.459016	NM_001243996	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			T|0.999;C|0.001	0.001	strong		0.567	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			C	33954552	T	C	33954552	2	2	27	1	0	0	0	0	0	0	0	1	13785	1471	51	3		3	RYR3	15	33954552	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	2626773	33954552	68576840	748	11199											
RYR3	6263	hgsc.bcm.edu	37	chr15	34130697	34130697	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aggaagcagtacaggaacgtGaaaaagatgactgcgaagga	18	4	14	5	2	0	3	0	2	0	1	0	7	0	6	0	3	4	2	0	3	6	1	rs75286462	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:34130697G>C	ENST00000389232.4	+	89	12586	c.12516G>C	c.(12514-12516)gtG>gtC	p.V4172V	RYR3_ENST00000415757.3_Silent_p.V4167V	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	4172					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)		ACAGGAACGTGAAAAAGATGA	0.512													G|||	81	0.0161741	0.0015	0.0216	5008	,	,		20602	0.0		0.0557	False		,,,				2504	0.0082				p.V4172V		Atlas-SNP	.											.	RYR3	760	.	0			c.G12516C						PASS	.	G		34,3884		0,34,1925	82	89	86		12516	1.6	1	15	dbSNP_132	86	326,7936		5,316,3810	no	coding-synonymous	RYR3	NM_001036.3		5,350,5735	CC,CG,GG		3.9458,0.8678,2.9557		4172/4871	34130697	360,11820	1959	4131	6090	SO:0001819	synonymous_variant	6263	exon89			GAACGTGAAAAAG		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.12516G>C	15.37:g.34130697G>C		196	0	0		185	111	0.6	NM_001036	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			G|0.975;C|0.025	0.025	strong		0.512	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			C	34130697	G	C	34130697	2	2	27	1	0	0	0	0	0	0	0	1	13785	1277	45	4		4	RYR3	15	34130697	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	176145	34130697	68400695	749	11200											
C15orf55	256646	hgsc.bcm.edu	37	chr15	34649336	34649336	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggaagcagaggaagaggatGaggaactctccaactttgct	14	7	13	7	0	1	3	0	1	1	2	2	7	1	7	1	4	4	2	1	4	4	1	rs149177074	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:34649336G>A	ENST00000333756.4	+	7	3198	c.3043G>A	c.(3043-3045)Gag>Aag	p.E1015K	NUTM1_ENST00000438749.3_Missense_Mutation_p.E1033K|NUTM1_ENST00000537011.1_Missense_Mutation_p.E1043K	NM_175741.1	NP_786883	Q86Y26	NUTM1_HUMAN	NUT midline carcinoma, family member 1	1015						cytoplasm (GO:0005737)|nucleus (GO:0005634)											GGAAGAGGATGAGGAACTCTC	0.498													G|||	8	0.00159744	0.0	0.0029	5008	,	,		20984	0.0		0.006	False		,,,				2504	0.0				p.E1015K		Atlas-SNP	.											C15orf55_ENST00000333756,NS,lymphoid_neoplasm,0,1	C15orf55	110	1	0			c.G3043A						PASS	.	G	LYS/GLU	4,4398	9.9+/-24.2	0,4,2197	76	61	66		3043	4.3	1	15	dbSNP_134	66	31,8565	22.8+/-68.1	0,31,4267	yes	missense	C15orf55	NM_175741.1	56	0,35,6464	AA,AG,GG		0.3606,0.0909,0.2693	benign	1015/1133	34649336	35,12963	2201	4298	6499	SO:0001583	missense	256646	exon7			GAGGATGAGGAAC	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.3043G>A	15.37:g.34649336G>A	ENSP00000329448:p.Glu1015Lys	55	0	0		52	27	0.519231	NM_175741	B4DZ00|B7Z7Y4|E7EVE8|F5H4I6|Q86YS8|Q8N7F2|Q9NTB3	Missense_Mutation	SNP	ENST00000333756.4	37	CCDS32190.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	G	15.74	2.923315	0.52653	9.09E-4	0.003606	ENSG00000184507	ENST00000537011;ENST00000438749;ENST00000333756	T;T;T	0.13307	2.62;2.6;2.61	5.2	4.28	0.50868	.	0.557345	0.16563	N	0.208980	T	0.11324	0.0276	L	0.61387	1.9	0.33479	D	0.58722	B;B;B	0.29085	0.232;0.154;0.192	B;B;B	0.27076	0.059;0.076;0.031	T	0.10222	-1.0639	10	0.66056	D	0.02	.	9.6167	0.39696	0.0944:0.0:0.9056:0.0	.	1033;1043;1015	E7EVE8;F5H4I6;Q86Y26	.;.;NUT_HUMAN	K	1043;1033;1015	ENSP00000444896:E1043K;ENSP00000407031:E1033K;ENSP00000329448:E1015K	ENSP00000329448:E1015K	E	+	1	0	C15orf55	32436628	0.965000	0.33210	0.991000	0.47740	0.842000	0.47809	1.928000	0.40104	1.422000	0.47177	0.655000	0.94253	GAG	G|0.998;A|0.002	0.002	strong		0.498	NUTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418026.1	NM_175741		A	34649336	G	A	34649336	3	1	27	1	0	0	0	0	1	0	0	0	1805	1291	45	2	3069	2	C15orf55	15	34649336	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	518639	34649336	67882056	750	11201											
THBS1	7057	hgsc.bcm.edu	37	chr15	39880818	39880818	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cgtagtcgtctctgcaacaaCcccacaccccagtttggagg	9	8	9	15	2	1	0	0	0	1	0	3	1	1	1	4	2	3	3	4	2	3	2	rs41338344	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:39880818C>T	ENST00000260356.5	+	10	1728	c.1563C>T	c.(1561-1563)aaC>aaT	p.N521N		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	521	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				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)		TCTGCAACAACCCCACACCCC	0.537													C|||	64	0.0127796	0.003	0.0274	5008	,	,		20155	0.0		0.0318	False		,,,				2504	0.0092				p.N521N		Atlas-SNP	.											.	THBS1	106	.	0			c.C1563T						PASS	.	C		34,4366	39.2+/-71.8	0,34,2166	94	89	91		1563	4.8	1	15	dbSNP_127	91	301,8293	109.6+/-170.1	4,293,4000	no	coding-synonymous	THBS1	NM_003246.2		4,327,6166	TT,TC,CC		3.5024,0.7727,2.5781		521/1171	39880818	335,12659	2200	4297	6497	SO:0001819	synonymous_variant	7057	exon10			CAACAACCCCACA		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.1563C>T	15.37:g.39880818C>T		76	0	0		70	34	0.485714	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	37	CCDS32194.1																																																																																			C|0.975;T|0.025	0.025	strong		0.537	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		T	39880818	C	T	39880818	2	4	27	1	0	0	0	0	0	0	0	1	15868	506	18	2		2	THBS1	15	39880818	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	5231482	39880818	62650574	751	11202											
VPS18	57617	hgsc.bcm.edu	37	chr15	41191184	41191184	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caaaagttcacaagatgttcCttgaccatactggtaagtaa	15	11	7	8	0	1	2	1	1	0	1	2	2	2	2	2	1	1	4	2	1	6	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:41191184C>T	ENST00000220509.5	+	3	652	c.313C>T	c.(313-315)Ctt>Ttt	p.L105F	VPS18_ENST00000558474.1_Missense_Mutation_p.L105F	NM_020857.2	NP_065908.1	Q9P253	VPS18_HUMAN	vacuolar protein sorting 18 homolog (S. cerevisiae)	105					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)		CAAGATGTTCCTTGACCATAC	0.567																																					p.L105F		Atlas-SNP	.											.	VPS18	67	.	0			c.C313T						PASS	.						117	97	104					15																	41191184		2203	4300	6503	SO:0001583	missense	57617	exon3			ATGTTCCTTGACC	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.313C>T	15.37:g.41191184C>T	ENSP00000220509:p.Leu105Phe	70	0	0		46	24	0.521739	NM_020857	Q8TCG0|Q96DI3|Q9H268	Missense_Mutation	SNP	ENST00000220509.5	37	CCDS10069.1	.	.	.	.	.	.	.	.	.	.	C	15.41	2.824795	0.50739	.	.	ENSG00000104142	ENST00000220509	T	0.55234	0.53	4.77	3.73	0.42828	.	0.000000	0.64402	D	0.000001	T	0.67832	0.2935	M	0.81682	2.555	0.54753	D	0.999982	D	0.71674	0.998	D	0.72338	0.977	T	0.67925	-0.5544	10	0.56958	D	0.05	-14.8434	5.7082	0.17921	0.0:0.6252:0.0:0.3748	.	105	Q9P253	VPS18_HUMAN	F	105	ENSP00000220509:L105F	ENSP00000220509:L105F	L	+	1	0	VPS18	38978476	1.000000	0.71417	1.000000	0.80357	0.589000	0.36550	1.289000	0.33307	1.063000	0.40649	0.455000	0.32223	CTT	.	.	none		0.567	VPS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252443.2			T	41191184	C	T	41191184	3	4	27	1	0	0	0	0	1	0	0	0	17209	681	24	2	323	2	VPS18	15	41191184	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1310366	41191184	61340208	752	11203											
INO80	54617	hgsc.bcm.edu	37	chr15	41277551	41277551	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aataccttctctgcatacttTtcccgcttccgcttgcgctc	5	15	5	16	3	1	0	0	0	1	0	5	0	3	0	3	0	4	4	3	0	3	7	rs61757083	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:41277551T>C	ENST00000361937.3	-	32	4330	c.3906A>G	c.(3904-3906)gaA>gaG	p.E1302E	INO80_ENST00000401393.3_Silent_p.E1302E|INO80_ENST00000561244.1_5'UTR			Q9ULG1	INO80_HUMAN	INO80 complex subunit	1302	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						CTGCATACTTTTCCCGCTTCC	0.502													T|||	15	0.00299521	0.0008	0.0029	5008	,	,		19721	0.0		0.0089	False		,,,				2504	0.0031				p.E1302E		Atlas-SNP	.											.	INO80	122	.	0			c.A3906G						PASS	.	T		4,4402	8.1+/-20.4	0,4,2199	229	179	196		3906	-0.1	1	15	dbSNP_129	196	94,8506	53.6+/-114.3	0,94,4206	no	coding-synonymous	INO80	NM_017553.1		0,98,6405	CC,CT,TT		1.093,0.0908,0.7535		1302/1557	41277551	98,12908	2203	4300	6503	SO:0001819	synonymous_variant	54617	exon32			ATACTTTTCCCGC	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.3906A>G	15.37:g.41277551T>C		159	0	0		99	50	0.50505	NM_017553	A6H8X4|Q9NTG6	Silent	SNP	ENST00000361937.3	37	CCDS10071.1																																																																																			T|0.992;C|0.008	0.008	strong		0.502	INO80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252527.2	NM_017553		C	41277551	T	C	41277551	2	2	27	1	0	0	0	0	0	0	0	1	7755	1838	64	3		3	INO80	15	41277551	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	86367	41277551	61253841	753	11204											
RPAP1	26015	hgsc.bcm.edu	37	chr15	41819466	41819466	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtcacctccagcacgtagcGcagccgaggcagcaggctgg	8	5	14	14	3	1	0	1	0	0	0	2	1	2	0	3	3	4	6	3	3	1	1	rs35981448	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:41819466G>A	ENST00000304330.4	-	13	1761	c.1645C>T	c.(1645-1647)Cgc>Tgc	p.R549C	RPAP1_ENST00000568413.1_5'Flank|RPAP1_ENST00000561603.1_Missense_Mutation_p.R549C	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	549						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)		AGCACGTAGCGCAGCCGAGGC	0.617													G|||	14	0.00279553	0.0008	0.0014	5008	,	,		18252	0.0		0.006	False		,,,				2504	0.0061				p.R549C		Atlas-SNP	.											.	RPAP1	111	.	0			c.C1645T						PASS	.	G	CYS/ARG	7,4399	12.9+/-30.5	0,7,2196	38	42	41		1645	5.3	1	15	dbSNP_126	41	49,8551	30.1+/-81.4	0,49,4251	yes	missense	RPAP1	NM_015540.2	180	0,56,6447	AA,AG,GG		0.5698,0.1589,0.4306	probably-damaging	549/1394	41819466	56,12950	2203	4300	6503	SO:0001583	missense	26015	exon13			CGTAGCGCAGCCG	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.1645C>T	15.37:g.41819466G>A	ENSP00000306123:p.Arg549Cys	91	0	0		74	37	0.5	NM_015540	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Missense_Mutation	SNP	ENST00000304330.4	37	CCDS10079.1	5	0.0022893772893772895	1	0.0020325203252032522	0	0.0	0	0.0	4	0.005277044854881266	G	20.3	3.958716	0.74016	0.001589	0.005698	ENSG00000103932	ENST00000304330	T	0.17691	2.26	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	T	0.32793	0.0841	M	0.69523	2.12	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.10590	-1.0623	10	0.87932	D	0	-18.6742	13.8344	0.63400	0.0:0.0:0.8466:0.1534	rs35981448	549	Q9BWH6	RPAP1_HUMAN	C	549	ENSP00000306123:R549C	ENSP00000306123:R549C	R	-	1	0	RPAP1	39606758	1.000000	0.71417	0.996000	0.52242	0.877000	0.50540	5.777000	0.68931	2.659000	0.90383	0.655000	0.94253	CGC	G|0.996;A|0.004	0.004	strong		0.617	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540		A	41819466	G	A	41819466	3	1	27	1	0	0	0	0	1	0	0	0	13556	1087	38	1	2588	1	RPAP1	15	41819466	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	541915	41819466	60711926	754	11205											
ZFP106	64397	hgsc.bcm.edu	37	chr15	42743209	42743209	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctgtgttggggaattacGtgtttcatcagtttggggct	5	18	13	5	1	3	0	2	0	1	0	3	1	3	1	0	4	1	4	0	4	2	5	rs201738274		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:42743209G>A	ENST00000263805.4	-	2	1518	c.1192C>T	c.(1192-1194)Cgt>Tgt	p.R398C	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	398					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)										GGGGAATTACGTGTTTCATCA	0.408																																					p.R398C		Atlas-SNP	.											.	ZFP106	117	.	0			c.C1192T						PASS	.	G	CYS/ARG	0,4406		0,0,2203	310	293	299		1192	0.3	0	15		299	2,8596	2.2+/-6.3	0,2,4297	no	missense	ZFP106	NM_022473.1	180	0,2,6500	AA,AG,GG		0.0233,0.0,0.0154	benign	398/1884	42743209	2,13002	2203	4299	6502	SO:0001583	missense	64397	exon2			AATTACGTGTTTC	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.1192C>T	15.37:g.42743209G>A	ENSP00000263805:p.Arg398Cys	158	0	0		187	37	0.197861	NM_022473	B4DZ40|E9PE29|Q6NSD9|Q6PEK1|Q86T43|Q86T45|Q86T50|Q86T58|Q86TA9|Q96M37|Q9H7B8	Missense_Mutation	SNP	ENST00000263805.4	37	CCDS32208.1	.	.	.	.	.	.	.	.	.	.	G	3.212	-0.161477	0.06502	0.0	2.33E-4	ENSG00000103994	ENST00000263805	T	0.55760	0.5	5.24	0.285	0.15705	.	1.426730	0.03878	N	0.276673	T	0.29556	0.0737	N	0.08118	0	0.09310	N	1	P;P	0.45078	0.85;0.476	B;B	0.36885	0.235;0.118	T	0.25710	-1.0124	10	0.66056	D	0.02	-0.4934	4.7175	0.12903	0.0:0.4549:0.2139:0.3312	.	181;398	B4DGC7;Q9H2Y7	.;ZF106_HUMAN	C	398	ENSP00000263805:R398C	ENSP00000263805:R398C	R	-	1	0	ZFP106	40530501	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.176000	0.16782	0.120000	0.18254	-0.269000	0.10298	CGT	G|0.999;A|0.001	0.001	weak		0.408	ZNF106-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422587.1	NM_022473		A	42743209	G	A	42743209	3	1	27	1	0	0	0	0	1	0	0	0	17652	1145	40	1	4531	1	ZFP106	15	42743209	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	923743	42743209	59788183	755	11206											
TGM7	116179	hgsc.bcm.edu	37	chr15	43569097	43569097	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	attgatgaggccgcttccttCcagcaccatcgtgcagctgc	7	10	10	14	2	0	2	0	2	0	0	3	2	2	2	4	1	4	4	4	1	0	3	rs146833656	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:43569097C>T	ENST00000452443.2	-	12	1940	c.1936G>A	c.(1936-1938)Gaa>Aaa	p.E646K		NM_052955.2	NP_443187.1	Q96PF1	TGM7_HUMAN	transglutaminase 7	646					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)	CCGCTTCCTTCCAGCACCATC	0.592													C|||	12	0.00239617	0.0008	0.0086	5008	,	,		21418	0.0		0.004	False		,,,				2504	0.001				p.E646K		Atlas-SNP	.											.	TGM7	86	.	0			c.G1936A						PASS	.	C	LYS/GLU	15,4389	22.3+/-47.3	0,15,2187	111	90	97		1936	5.1	1	15	dbSNP_134	97	104,8494	56.8+/-118.0	0,104,4195	yes	missense	TGM7	NM_052955.2	56	0,119,6382	TT,TC,CC		1.2096,0.3406,0.9152	probably-damaging	646/711	43569097	119,12883	2202	4299	6501	SO:0001583	missense	116179	exon12			TTCCTTCCAGCAC	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.1936G>A	15.37:g.43569097C>T	ENSP00000389466:p.Glu646Lys	69	0	0		84	63	0.75	NM_052955		Missense_Mutation	SNP	ENST00000452443.2	37	CCDS32213.1	7	0.003205128205128205	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	3	0.00395778364116095	C	23.4	4.409135	0.83340	0.003406	0.012096	ENSG00000159495	ENST00000452443	T	0.37584	1.19	5.13	5.13	0.70059	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.233909	0.35378	N	0.003260	T	0.55273	0.1910	M	0.86864	2.845	0.44668	D	0.997653	D	0.67145	0.996	D	0.63192	0.912	T	0.68443	-0.5407	10	0.72032	D	0.01	-23.3696	16.0633	0.80853	0.0:1.0:0.0:0.0	.	646	Q96PF1	TGM7_HUMAN	K	646	ENSP00000389466:E646K	ENSP00000389466:E646K	E	-	1	0	TGM7	41356389	1.000000	0.71417	1.000000	0.80357	0.573000	0.36030	5.641000	0.67881	2.375000	0.81037	0.585000	0.79938	GAA	C|0.992;T|0.008	0.008	strong		0.592	TGM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432489.1	NM_052955		T	43569097	C	T	43569097	3	4	27	1	0	0	0	0	1	0	0	0	15850	864	30	2	204	2	TGM7	15	43569097	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	825888	43569097	58962295	756	11207											
MAP1A	4130	hgsc.bcm.edu	37	chr15	43818115	43818115	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ataaagacttggaacaaaagGacagggtcctagaacagaag	19	5	11	6	0	0	3	0	0	0	3	1	5	1	5	1	3	2	0	1	3	8	3	rs145659671	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:43818115G>A	ENST00000300231.5	+	4	4894	c.4444G>A	c.(4444-4446)Gac>Aac	p.D1482N	MAP1A_ENST00000399453.1_Missense_Mutation_p.D1482N|MAP1A_ENST00000382031.1_Missense_Mutation_p.D1720N			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1482					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)	p.D1482N(1)		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)	GGAACAAAAGGACAGGGTCCT	0.448													G|||	11	0.00219649	0.0008	0.0086	5008	,	,		20845	0.0		0.003	False		,,,				2504	0.001				p.D1482N		Atlas-SNP	.											MAP1A,NS,carcinoma,0,1	MAP1A	189	1	1	Substitution - Missense(1)	pancreas(1)	c.G4444A						scavenged	.	G	ASN/ASP	14,3740		0,14,1863	92	92	92		4444	3.9	0.5	15	dbSNP_134	92	124,8086		0,124,3981	yes	missense	MAP1A	NM_002373.5	23	0,138,5844	AA,AG,GG		1.5104,0.3729,1.1535	probably-damaging	1482/2804	43818115	138,11826	1877	4105	5982	SO:0001583	missense	4130	exon4			CAAAAGGACAGGG	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.4444G>A	15.37:g.43818115G>A	ENSP00000300231:p.Asp1482Asn	54	1	0.0185185		83	53	0.638554	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	37	CCDS42031.1	7	0.003205128205128205	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	3	0.00395778364116095	G	12.86	2.064968	0.36470	0.003729	0.015104	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.23552	2.25;1.9;1.9	3.94	3.94	0.45596	.	.	.	.	.	T	0.32793	0.0841	M	0.71581	2.175	0.09310	N	1	D	0.67145	0.996	D	0.79784	0.993	T	0.12041	-1.0563	9	0.56958	D	0.05	-7.9541	13.1289	0.59369	0.0:0.1622:0.8377:0.0	.	1482	P78559	MAP1A_HUMAN	N	1720;1482;1482	ENSP00000371462:D1720N;ENSP00000382380:D1482N;ENSP00000300231:D1482N	ENSP00000300231:D1482N	D	+	1	0	MAP1A	41605407	0.002000	0.14202	0.509000	0.27700	0.039000	0.13416	0.567000	0.23608	2.166000	0.68216	0.563000	0.77884	GAC	G|0.992;A|0.008	0.008	strong		0.448	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373		A	43818115	G	A	43818115	3	1	27	1	0	0	0	0	1	0	0	0	9236	1174	41	2	4446	2	MAP1A	15	43818115	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	249018	43818115	58713277	757	11208											
DUOX2	50506	hgsc.bcm.edu	37	chr15	45400296	45400296	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caccatcccgcagccgtacaAactggtcgaggacaatggca	12	5	10	14	3	0	0	0	0	0	0	2	2	1	1	3	3	3	3	3	3	3	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:45400296A>G	ENST00000603300.1	-	13	1725	c.1523T>C	c.(1522-1524)tTt>tCt	p.F508S	DUOX2_ENST00000389039.6_Missense_Mutation_p.F508S	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	508	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)		CAGCCGTACAAACTGGTCGAG	0.612																																					p.F508S		Atlas-SNP	.											.	DUOX2	137	.	0			c.T1523C						PASS	.						86	87	87					15																	45400296		2198	4298	6496	SO:0001583	missense	50506	exon13			CGTACAAACTGGT	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.1523T>C	15.37:g.45400296A>G	ENSP00000475084:p.Phe508Ser	88	0	0		109	73	0.669725	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Missense_Mutation	SNP	ENST00000603300.1	37	CCDS10117.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.593116	0.86953	.	.	ENSG00000140279	ENST00000389039	.	.	.	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	D	0.86892	0.6042	H	0.95745	3.715	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.90760	0.4664	9	0.87932	D	0	-8.369	14.7402	0.69448	1.0:0.0:0.0:0.0	.	508;70	Q9NRD8;Q59GU9	DUOX2_HUMAN;.	S	508	.	ENSP00000373691:F508S	F	-	2	0	DUOX2	43187588	1.000000	0.71417	1.000000	0.80357	0.742000	0.42306	9.106000	0.94253	2.080000	0.62538	0.533000	0.62120	TTT	.	.	none		0.612	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080		G	45400296	A	G	45400296	3	3	27	1	0	0	0	0	1	0	0	0	4803	14	1	3	3211	3	DUOX2	15	45400296	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	1582181	45400296	57131096	758	11209											
SPATA5L1	79029	hgsc.bcm.edu	37	chr15	45695445	45695445	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	cgccccggcgctgcagggttCccggcctggggagaccgagg	4	4	18	15	5	0	1	0	0	0	1	1	3	1	1	5	6	1	3	5	6	0	1	rs143453038	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:45695445C>G	ENST00000305560.6	+	1	917	c.818C>G	c.(817-819)tCc>tGc	p.S273C	SPATA5L1_ENST00000559860.1_Missense_Mutation_p.S273C|GATM_ENST00000458245.5_5'Flank	NM_024063.2	NP_076968.2	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	273						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)		CTGCAGGGTTCCCGGCCTGGG	0.761													C|||	50	0.00998403	0.0023	0.0202	5008	,	,		12129	0.0		0.0298	False		,,,				2504	0.0031				p.S273C		Atlas-SNP	.											.	SPATA5L1	40	.	0			c.C818G						PASS	.	C	CYS/SER	17,3375		0,17,1679	3	4	4		818	4.9	0.3	15	dbSNP_134	4	149,7059		1,147,3456	no	missense	SPATA5L1	NM_024063.2	112	1,164,5135	GG,GC,CC		2.0671,0.5012,1.566	possibly-damaging	273/754	45695445	166,10434	1696	3604	5300	SO:0001583	missense	79029	exon1			AGGGTTCCCGGCC	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.818C>G	15.37:g.45695445C>G	ENSP00000305494:p.Ser273Cys	5	0	0		22	6	0.272727	NM_024063	C9JHR5|Q9H8W7|Q9HA41	Missense_Mutation	SNP	ENST00000305560.6	37	CCDS10123.1	40	0.018315018315018316	8	0.016260162601626018	9	0.024861878453038673	0	0.0	23	0.030343007915567283	C	20.5	3.999282	0.74818	0.005012	0.020671	ENSG00000171763	ENST00000305560	D	0.93426	-3.22	4.9	4.9	0.64082	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.367137	0.28560	N	0.014910	D	0.89111	0.6622	M	0.68728	2.09	0.20307	N	0.999919	D	0.56035	0.974	P	0.57057	0.812	D	0.85330	0.1089	10	0.87932	D	0	-22.4119	16.8259	0.85931	0.0:1.0:0.0:0.0	.	273	Q9BVQ7	SPA5L_HUMAN	C	273	ENSP00000305494:S273C	ENSP00000305494:S273C	S	+	2	0	SPATA5L1	43482737	0.758000	0.28405	0.314000	0.25224	0.281000	0.26958	7.247000	0.78257	2.536000	0.85505	0.585000	0.79938	TCC	C|0.982;G|0.018	0.018	strong		0.761	SPATA5L1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254218.1	NM_024063		G	45695445	C	G	45695445	3	3	27	1	0	0	0	0	1	0	0	0	15027	855	30	4	820	4	SPATA5L1	15	45695445	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	295149	45695445	56835947	759	11210											
SPPL2A	84888	hgsc.bcm.edu	37	chr15	51017488	51017488	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acactcattactgagaaataGatcagttttggtactctgat	13	14	7	7	0	3	3	2	2	1	2	3	4	3	3	0	1	2	2	0	1	4	5	rs140457962	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:51017488G>T	ENST00000261854.5	-	12	1453	c.1179C>A	c.(1177-1179)atC>atA	p.I393I	SPPL2A_ENST00000559293.1_5'UTR	NM_032802.3	NP_116191.2	Q8TCT8	SPP2A_HUMAN	signal peptide peptidase like 2A	393					membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|regulation of immune response (GO:0050776)	extracellular vesicular exosome (GO:0070062)|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)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15				all cancers(107;0.000712)|GBM - Glioblastoma multiforme(94;0.00314)		CTGAGAAATAGATCAGTTTTG	0.338													G|||	8	0.00159744	0.0008	0.0	5008	,	,		17872	0.0		0.007	False		,,,				2504	0.0				p.I393I	Melanoma(50;790 1209 4069 22965 33125)	Atlas-SNP	.											.	SPPL2A	26	.	0			c.C1179A						PASS	.	G		6,4386	11.4+/-27.6	0,6,2190	104	101	102		1179	-2.8	0.8	15	dbSNP_134	102	77,8511	44.9+/-103.4	0,77,4217	no	coding-synonymous	SPPL2A	NM_032802.3		0,83,6407	TT,TG,GG		0.8966,0.1366,0.6394		393/521	51017488	83,12897	2196	4294	6490	SO:0001819	synonymous_variant	84888	exon12			GAAATAGATCAGT		CCDS10138.1	15q21.2	2012-02-21			ENSG00000138600	ENSG00000138600			30227	protein-coding gene	gene with protein product	"intramembrane protease 3", "presenilin-like protein 2"	608238				12077416, 12139484	Standard	NM_032802		Approved	IMP3, PSL2	uc001zyv.3	Q8TCT8	OTTHUMG00000131647	ENST00000261854.5:c.1179C>A	15.37:g.51017488G>T		229	0	0		223	127	0.569507	NM_032802	B2RDS0|Q8TAW1|Q96SZ8	Silent	SNP	ENST00000261854.5	37	CCDS10138.1																																																																																			G|0.995;T|0.005	0.005	strong		0.338	SPPL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254543.3	NM_032802		T	51017488	G	T	51017488	2	4	27	1	0	0	0	0	0	0	0	1	15103	932	33	4		4	SPPL2A	15	51017488	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	5322043	51017488	51513904	760	11211											
TLN2	83660	hgsc.bcm.edu	37	chr15	62939591	62939591	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgaaccatctacagctgtgTacgatgcgtgtcgagtcatt	9	13	10	9	3	2	1	1	1	1	0	3	3	2	1	1	0	5	2	1	0	3	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:62939591T>C	ENST00000561311.1	+	3	312	c.82T>C	c.(82-84)Tac>Cac	p.Y28H	RP11-625H11.1_ENST00000558940.1_5'Flank|TLN2_ENST00000306829.6_Missense_Mutation_p.Y28H|RP11-625H11.1_ENST00000560347.1_5'Flank			Q9Y4G6	TLN2_HUMAN	talin 2	28					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						TACAGCTGTGTACGATGCGTG	0.493																																					p.Y28H		Atlas-SNP	.											.	TLN2	253	.	0			c.T82C						PASS	.						217	191	200					15																	62939591		2203	4300	6503	SO:0001583	missense	83660	exon1			GCTGTGTACGATG	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.82T>C	15.37:g.62939591T>C	ENSP00000453508:p.Tyr28His	102	0	0		110	7	0.0636364	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	37	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	T	14.05	2.420151	0.42918	.	.	ENSG00000171914	ENST00000306829	T	0.69561	-0.41	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.77239	0.4101	L	0.51914	1.62	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.76724	-0.2854	10	0.42905	T	0.14	-10.8689	15.0808	0.72113	0.0:0.0:0.0:1.0	.	28	Q9Y4G6	TLN2_HUMAN	H	28	ENSP00000303476:Y28H	ENSP00000303476:Y28H	Y	+	1	0	TLN2	60726883	1.000000	0.71417	0.970000	0.41538	0.108000	0.19459	7.988000	0.88194	2.219000	0.72066	0.533000	0.62120	TAC	.	.	none		0.493	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			C	62939591	T	C	62939591	3	2	27	1	0	0	0	0	1	0	0	0	15963	1638	57	3	84	3	TLN2	15	62939591	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	11922103	62939591	39591801	761	11212											
TLN2	83660	hgsc.bcm.edu	37	chr15	62994208	62994208	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	caggtgaccctgcagacactGactacacagctgtgggatgt	10	8	12	11	0	0	3	0	2	0	1	0	4	0	4	1	2	3	2	1	2	1	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:62994208G>A	ENST00000561311.1	+	17	1944	c.1714G>A	c.(1714-1716)Gac>Aac	p.D572N	TLN2_ENST00000306829.6_Missense_Mutation_p.D572N			Q9Y4G6	TLN2_HUMAN	talin 2	572					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						TGCAGACACTGACTACACAGC	0.517																																					p.D572N		Atlas-SNP	.											.	TLN2	253	.	0			c.G1714A						PASS	.						97	77	83					15																	62994208		2203	4300	6503	SO:0001583	missense	83660	exon15			GACACTGACTACA	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.1714G>A	15.37:g.62994208G>A	ENSP00000453508:p.Asp572Asn	104	0	0		129	65	0.503876	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	37	CCDS32261.1	.	.	.	.	.	.	.	.	.	.	G	19.41	3.822336	0.71028	.	.	ENSG00000171914	ENST00000306829	T	0.70282	-0.47	5.1	5.1	0.69264	Talin, central (3);	0.000000	0.85682	D	0.000000	T	0.70141	0.3190	L	0.61387	1.9	0.80722	D	1	B	0.21905	0.062	B	0.23419	0.046	T	0.66006	-0.6030	10	0.30854	T	0.27	-28.968	18.8833	0.92365	0.0:0.0:1.0:0.0	.	572	Q9Y4G6	TLN2_HUMAN	N	572	ENSP00000303476:D572N	ENSP00000303476:D572N	D	+	1	0	TLN2	60781500	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	9.813000	0.99286	2.532000	0.85374	0.561000	0.74099	GAC	.	.	none		0.517	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			A	62994208	G	A	62994208	3	1	27	1	0	0	0	0	1	0	0	0	15963	1290	45	2	1772	2	TLN2	15	62994208	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	54617	62994208	39537184	762	11213											
TLN2	83660	hgsc.bcm.edu	37	chr15	63102153	63102153	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccaccccgatgtcagtgaCgaggtgagaaccagagcctt	10	8	11	12	2	1	3	1	2	0	2	2	6	2	3	5	1	2	0	5	1	1	2	rs150114385	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:63102153C>T	ENST00000561311.1	+	51	6923	c.6693C>T	c.(6691-6693)gaC>gaT	p.D2231D	TLN2_ENST00000306829.6_Silent_p.D2231D			Q9Y4G6	TLN2_HUMAN	talin 2	2231					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						ATGTCAGTGACGAGGTGAGAA	0.547													C|||	3	0.000599042	0.0015	0.0	5008	,	,		22983	0.0		0.001	False		,,,				2504	0.0				p.D2231D		Atlas-SNP	.											.	TLN2	253	.	0			c.C6693T						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	128	94	106		6693	-4.9	0.9	15	dbSNP_134	106	29,8571	20.4+/-63.3	0,29,4271	no	coding-synonymous	TLN2	NM_015059.2		0,32,6471	TT,TC,CC		0.3372,0.0681,0.246		2231/2543	63102153	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	83660	exon49			CAGTGACGAGGTG	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.6693C>T	15.37:g.63102153C>T		180	0	0		201	123	0.61194	NM_015059	A6NLB8	Silent	SNP	ENST00000561311.1	37	CCDS32261.1																																																																																			C|0.997;T|0.003	0.003	strong		0.547	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			T	63102153	C	T	63102153	2	4	27	1	0	0	0	0	0	0	0	1	15963	535	19	1		1	TLN2	15	63102153	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	107945	63102153	39429239	763	11214											
TLN2	83660	hgsc.bcm.edu	37	chr15	63111778	63111778	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctttctccaagcgagtcgccGgcgctgtgacagagctcatc	7	9	11	14	4	2	2	1	1	1	1	5	3	2	2	2	1	2	2	2	1	1	1	rs138463845	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:63111778G>A	ENST00000561311.1	+	52	7065	c.6835G>A	c.(6835-6837)Ggc>Agc	p.G2279S	TLN2_ENST00000306829.6_Missense_Mutation_p.G2279S			Q9Y4G6	TLN2_HUMAN	talin 2	2279					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						GCGAGTCGCCGGCGCTGTGAC	0.562													G|||	8	0.00159744	0.0008	0.0029	5008	,	,		18034	0.0		0.005	False		,,,				2504	0.0				p.G2279S		Atlas-SNP	.											TLN2,NS,carcinoma,-2,2	TLN2	253	2	0			c.G6835A						scavenged	.	G	SER/GLY	8,4398	14.3+/-33.2	0,8,2195	57	60	59		6835	4.5	0	15	dbSNP_134	59	64,8536	39.3+/-95.6	0,64,4236	yes	missense	TLN2	NM_015059.2	56	0,72,6431	AA,AG,GG		0.7442,0.1816,0.5536	benign	2279/2543	63111778	72,12934	2203	4300	6503	SO:0001583	missense	83660	exon50			GTCGCCGGCGCTG	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.6835G>A	15.37:g.63111778G>A	ENSP00000453508:p.Gly2279Ser	45	2	0.0444444		49	29	0.591837	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	37	CCDS32261.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	G	4.821	0.152577	0.09185	0.001816	0.007442	ENSG00000171914	ENST00000306829	T	0.64803	-0.12	5.38	4.46	0.54185	.	0.218055	0.45361	D	0.000378	T	0.23806	0.0576	N	0.02916	-0.46	0.09310	N	0.999999	B	0.14438	0.01	B	0.06405	0.002	T	0.15009	-1.0452	10	0.05620	T	0.96	-15.6397	10.7611	0.46266	0.2001:0.0:0.7999:0.0	.	2279	Q9Y4G6	TLN2_HUMAN	S	2279	ENSP00000303476:G2279S	ENSP00000303476:G2279S	G	+	1	0	TLN2	60898831	0.994000	0.37717	0.029000	0.17559	0.423000	0.31445	4.826000	0.62715	1.270000	0.44297	0.561000	0.74099	GGC	G|0.995;A|0.005	0.005	strong		0.562	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			A	63111778	G	A	63111778	3	1	27	1	0	0	0	0	1	0	0	0	15963	1116	39	1	7033	1	TLN2	15	63111778	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	9625	63111778	39419614	764	11215											
TLN2	83660	hgsc.bcm.edu	37	chr15	63125804	63125804	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaatcggcctcagcagcccaGagggagctggtggcccaagg	10	4	15	12	1	1	1	1	0	0	1	2	2	1	2	3	5	3	2	3	5	2	0	rs142793310	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:63125804G>A	ENST00000561311.1	+	54	7334	c.7104G>A	c.(7102-7104)caG>caA	p.Q2368Q	RP11-1069G10.1_ENST00000558888.1_RNA|TLN2_ENST00000306829.6_Silent_p.Q2368Q|RP11-1069G10.1_ENST00000558404.1_RNA			Q9Y4G6	TLN2_HUMAN	talin 2	2368	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.				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						CAGCAGCCCAGAGGGAGCTGG	0.577																																					p.Q2368Q		Atlas-SNP	.											.	TLN2	253	.	0			c.G7104A						PASS	.	G		0,4406		0,0,2203	77	77	77		7104	5.1	1	15	dbSNP_134	77	7,8593	6.4+/-24.3	0,7,4293	no	coding-synonymous	TLN2	NM_015059.2		0,7,6496	AA,AG,GG		0.0814,0.0,0.0538		2368/2543	63125804	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	83660	exon52			AGCCCAGAGGGAG	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.7104G>A	15.37:g.63125804G>A		130	0	0		84	24	0.285714	NM_015059	A6NLB8	Silent	SNP	ENST00000561311.1	37	CCDS32261.1																																																																																			G|1.000;A|0.000	0.000	strong		0.577	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			A	63125804	G	A	63125804	2	1	27	1	0	0	0	0	0	0	0	1	15963	933	33	2		2	TLN2	15	63125804	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	14026	63125804	39405588	765	11216											
LACTB	114294	hgsc.bcm.edu	37	chr15	63419223	63419223	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acattatgttcccgaattccCagaaaaagaatatgaaggtg	16	10	8	7	1	0	3	0	1	0	2	2	4	2	3	2	1	0	1	2	1	7	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:63419223C>T	ENST00000261893.4	+	3	662	c.590C>T	c.(589-591)cCa>cTa	p.P197L	LACTB_ENST00000413507.2_Missense_Mutation_p.P197L|RPS27L_ENST00000559763.1_Intron	NM_032857.3	NP_116246.2	P83111	LACTB_HUMAN	lactamase, beta	197						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						CCCGAATTCCCAGAAAAAGAA	0.363																																					p.P197L	Melanoma(85;443 1381 6215 27308 35583)	Atlas-SNP	.											.	LACTB	29	.	0			c.C590T						PASS	.						67	58	61					15																	63419223		2203	4300	6503	SO:0001583	missense	114294	exon3			AATTCCCAGAAAA	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.590C>T	15.37:g.63419223C>T	ENSP00000261893:p.Pro197Leu	138	0	0		155	28	0.180645	NM_171846	P83096	Missense_Mutation	SNP	ENST00000261893.4	37	CCDS10182.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.588482	0.86851	.	.	ENSG00000103642	ENST00000261893;ENST00000413507	T;T	0.47177	0.85;0.85	5.5	5.5	0.81552	Beta-lactamase/transpeptidase-like (2);Beta-lactamase-related (1);	0.000000	0.85682	D	0.000000	T	0.69160	0.3080	M	0.70108	2.13	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.71059	-0.4702	10	0.62326	D	0.03	-9.8513	18.3852	0.90464	0.0:1.0:0.0:0.0	.	197	P83111	LACTB_HUMAN	L	197	ENSP00000261893:P197L;ENSP00000392956:P197L	ENSP00000261893:P197L	P	+	2	0	LACTB	61206276	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.616000	0.83018	2.585000	0.87301	0.563000	0.77884	CCA	.	.	none		0.363	LACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256224.1	NM_032857		T	63419223	C	T	63419223	3	4	27	1	0	0	0	0	1	0	0	0	8606	594	21	2	600	2	LACTB	15	63419223	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	293419	63419223	39112169	766	11217											
TLE3	7090	hgsc.bcm.edu	37	chr15	70351154	70351154	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gacccggggcgttgcggggtCctgaaaacacaagtgatgca	10	6	15	10	3	0	2	0	2	0	0	1	3	1	2	2	4	3	2	2	4	3	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:70351154C>T	ENST00000558939.1	-	11	2143	c.766G>A	c.(766-768)Gac>Aac	p.D256N	TLE3_ENST00000559191.1_Intron|TLE3_ENST00000559048.1_Splice_Site_p.D261N|TLE3_ENST00000440567.3_Splice_Site_p.D249N|TLE3_ENST00000317509.8_Splice_Site_p.D256N|TLE3_ENST00000557907.1_Splice_Site_p.D256N|TLE3_ENST00000539550.1_Splice_Site_p.D200N|TLE3_ENST00000558201.1_Splice_Site_p.D262N|TLE3_ENST00000558379.1_Splice_Site_p.D256N|TLE3_ENST00000560589.1_Splice_Site_p.D200N|TLE3_ENST00000451782.2_Splice_Site_p.D256N|TLE3_ENST00000559929.1_Splice_Site_p.D266N|TLE3_ENST00000442299.2_Splice_Site_p.D256N|TLE3_ENST00000557997.1_Splice_Site_p.D256N|TLE3_ENST00000560939.1_Splice_Site_p.D261N	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	256	CCN domain.				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						GTTGCGGGGTCCTGAAAACAC	0.612																																					p.D256N		Atlas-SNP	.											.	TLE3	104	.	0			c.G766A						PASS	.						17	19	18					15																	70351154		1935	4130	6065	SO:0001630	splice_region_variant	7090	exon11			CGGGGTCCTGAAA	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.766-1G>A	15.37:g.70351154C>T		56	0	0		40	15	0.375	NM_001105192	B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Missense_Mutation	SNP	ENST00000558939.1	37	CCDS45293.1	.	.	.	.	.	.	.	.	.	.	C	19.84	3.902492	0.72754	.	.	ENSG00000140332	ENST00000442299;ENST00000451782;ENST00000317509;ENST00000440567;ENST00000539550	T;T;T;T;T	0.53857	0.82;0.87;0.92;0.87;0.6	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.68449	0.3002	L	0.56340	1.77	0.80722	D	1	D;B;B;B;P;B;P;B	0.61080	0.989;0.021;0.264;0.011;0.552;0.053;0.823;0.019	D;B;B;B;B;B;P;B	0.66497	0.944;0.019;0.16;0.02;0.34;0.043;0.733;0.03	T	0.68161	-0.5482	10	0.54805	T	0.06	-0.4451	19.143	0.93452	0.0:1.0:0.0:0.0	.	249;256;256;256;256;256;261;200	F8W964;E9PD64;Q04726-3;Q6PI57;Q04726-2;Q04726;Q04726-4;F5H7D6	.;.;.;.;.;TLE3_HUMAN;.;.	N	256;256;256;249;200	ENSP00000390007:D256N;ENSP00000394717:D256N;ENSP00000319233:D256N;ENSP00000415057:D249N;ENSP00000442594:D200N	ENSP00000319233:D256N	D	-	1	0	TLE3	68138208	1.000000	0.71417	1.000000	0.80357	0.710000	0.40934	7.559000	0.82265	2.764000	0.94973	0.555000	0.69702	GAC	.	.	none		0.612	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416913.1	NM_005078	Missense_Mutation	T	70351154	C	T	70351154	5	4	27	1	0	0	0	0	0	0	1	0	15955	869	30	2	1592	2	TLE3	15	70351154	Splice_Site	SNP	C	TCGA-G8-6909-01A-11D-2210-10	6931931	70351154	32180238	767	11218											
HCN4	10021	hgsc.bcm.edu	37	chr15	73615097	73615097	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagagcgggaaggcagccaTggactcccctgaggagtgcg	10	4	17	10	2	0	2	0	1	0	1	1	6	1	5	3	4	3	1	3	4	2	0	rs142735148	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:73615097T>C	ENST00000261917.3	-	8	4330	c.3337A>G	c.(3337-3339)Atg>Gtg	p.M1113V		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	1113					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)		AAGGCAGCCATGGACTCCCCT	0.716													T|||	41	0.0081869	0.0068	0.0086	5008	,	,		11518	0.0		0.0129	False		,,,				2504	0.0133				p.M1113V		Atlas-SNP	.											.	HCN4	150	.	0			c.A3337G						PASS	.	T	VAL/MET	29,4303		0,29,2137	8	10	9		3337	-5.1	0.3	15	dbSNP_134	9	107,8365		2,103,4131	no	missense	HCN4	NM_005477.2	21	2,132,6268	CC,CT,TT		1.263,0.6694,1.0622	benign	1113/1204	73615097	136,12668	2166	4236	6402	SO:0001583	missense	10021	exon8			CAGCCATGGACTC	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.3337A>G	15.37:g.73615097T>C	ENSP00000261917:p.Met1113Val	24	0	0		33	19	0.575758	NM_005477	Q9UMQ7	Missense_Mutation	SNP	ENST00000261917.3	37	CCDS10248.1	18	0.008241758241758242	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	11	0.014511873350923483	T	0.004	-2.366028	0.00212	0.006694	0.01263	ENSG00000138622	ENST00000261917	D	0.96651	-4.08	3.32	-5.11	0.02901	.	.	.	.	.	T	0.77698	0.4169	N	0.00926	-1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.76063	-0.3096	9	0.02654	T	1	.	10.5547	0.45110	0.0:0.421:0.0:0.579	.	1113	Q9Y3Q4	HCN4_HUMAN	V	1113	ENSP00000261917:M1113V	ENSP00000261917:M1113V	M	-	1	0	HCN4	71402150	0.000000	0.05858	0.260000	0.24451	0.142000	0.21351	-1.800000	0.01744	-1.006000	0.03412	-0.659000	0.03860	ATG	T|0.992;C|0.008	0.008	strong		0.716	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477		C	73615097	T	C	73615097	3	2	27	1	0	0	0	0	1	0	0	0	7008	1464	51	3	278	3	HCN4	15	73615097	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	3263943	73615097	28916295	768	11219											
CCDC33	80125	hgsc.bcm.edu	37	chr15	74625175	74625175	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cccccatcattctgcagcaaCaggccctgccggtaagaggc	9	6	10	16	1	2	1	1	0	1	1	2	1	2	1	4	3	4	3	4	3	2	2	rs200735867		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:74625175C>A	ENST00000398814.3	+	16	2358	c.1927C>A	c.(1927-1929)Cag>Aag	p.Q643K	CCDC33_ENST00000268082.4_Missense_Mutation_p.Q236K|CCDC33_ENST00000321288.5_Missense_Mutation_p.Q846K|CCDC33_ENST00000558821.1_Missense_Mutation_p.Q236K	NM_025055.3	NP_079331.3	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33	846										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						TCTGCAGCAACAGGCCCTGCC	0.592																																					p.Q643K		Atlas-SNP	.											.	CCDC33	160	.	0			c.C1927A						PASS	.	C	LYS/GLN,LYS/GLN	0,3826		0,0,1913	34	41	39		1927,706	5	1	15		39	3,8237		0,3,4117	yes	missense,missense	CCDC33	NM_025055.3,NM_182791.2	53,53	0,3,6030	AA,AC,CC		0.0364,0.0,0.0249	probably-damaging,probably-damaging	643/756,236/368	74625175	3,12063	1913	4120	6033	SO:0001583	missense	80125	exon16			CAGCAACAGGCCC	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.1927C>A	15.37:g.74625175C>A	ENSP00000381795:p.Gln643Lys	59	0	0		66	36	0.545455	NM_025055	A8K3U4|A8MPQ6|A8MV61|A8MVU9|B3KQ49|Q8TAX6|Q9H5Q6	Missense_Mutation	SNP	ENST00000398814.3	37	CCDS42058.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.446257	0.63178	0.0	3.64E-4	ENSG00000140481	ENST00000321288;ENST00000398814;ENST00000321374;ENST00000268082	T;T;T;T	0.34472	1.36;2.14;1.81;1.73	5.04	5.04	0.67666	.	0.277119	0.26126	N	0.026198	T	0.52996	0.1769	M	0.73962	2.25	0.30582	N	0.762407	P;B;P;D	0.64830	0.936;0.29;0.69;0.994	P;B;B;P	0.58013	0.554;0.081;0.292;0.831	T	0.55425	-0.8143	10	0.20046	T	0.44	.	15.3817	0.74661	0.0:1.0:0.0:0.0	.	236;236;846;643	Q8N5R6-4;Q8N5R6-5;C9JFX2;Q8N5R6-6	.;.;.;.	K	846;643;236;236	ENSP00000325012:Q846K;ENSP00000381795:Q643K;ENSP00000325661:Q236K;ENSP00000268082:Q236K	ENSP00000268082:Q236K	Q	+	1	0	CCDC33	72412228	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	4.670000	0.61583	2.354000	0.79902	0.543000	0.68304	CAG	.	.	weak		0.592	CCDC33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419491.2	NM_182791		A	74625175	C	A	74625175	3	1	27	1	0	0	0	0	1	0	0	0	2808	479	17	4	2062	4	CCDC33	15	74625175	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1010078	74625175	27906217	769	11220											
SCAPER	49855	hgsc.bcm.edu	37	chr15	77025687	77025687	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaaacatcatgacgtttattCtgggcttcaagggtatttat	12	15	8	6	1	3	1	2	1	1	0	3	1	3	1	0	2	1	3	0	2	6	7	rs144694379	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:77025687C>T	ENST00000563290.1	-	16	2000	c.1905G>A	c.(1903-1905)caG>caA	p.Q635Q	SCAPER_ENST00000538941.2_Silent_p.Q389Q|SCAPER_ENST00000324767.7_Silent_p.Q635Q			Q9BY12	SCAPE_HUMAN	S-phase cyclin A-associated protein in the ER	635	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						GACGTTTATTCTGGGCTTCAA	0.348													C|||	38	0.00758786	0.0015	0.0187	5008	,	,		19249	0.0		0.0129	False		,,,				2504	0.0102				p.Q635Q		Atlas-SNP	.											SCAPER_ENST00000538941,NS,carcinoma,-2,2	SCAPER	160	2	0			c.G1905A						PASS	.	C	,	22,3630		0,22,1804	106	93	97		1167,1905	4.6	1	15	dbSNP_134	97	207,7951		2,203,3874	no	coding-synonymous,coding-synonymous	SCAPER	NM_001145923.1,NM_020843.2	,	2,225,5678	TT,TC,CC		2.5374,0.6024,1.939	,	389/1155,635/1401	77025687	229,11581	1826	4079	5905	SO:0001819	synonymous_variant	49855	exon15			TTTATTCTGGGCT	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.1905G>A	15.37:g.77025687C>T		180	0	0		189	103	0.544974	NM_020843	F5H7X8|H3BNR7|Q3B7X7|Q96BS9|Q9H3D8|Q9NT03|Q9P274	Silent	SNP	ENST00000563290.1	37	CCDS53962.1																																																																																			C|0.988;T|0.012	0.012	strong		0.348	SCAPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419698.1	NM_020843		T	77025687	C	T	77025687	2	4	27	1	0	0	0	0	0	0	0	1	13893	912	32	2		2	SCAPER	15	77025687	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2400512	77025687	25505705	770	11221											
ZNF592	9640	hgsc.bcm.edu	37	chr15	85326939	85326939	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ccactagaaaaagtatcaagCcatcggacagccctcgtagc	14	6	8	13	2	1	1	1	0	0	1	3	2	1	2	3	1	3	2	3	1	6	3	rs138966830		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:85326939C>A	ENST00000560079.2	+	4	1321	c.1033C>A	c.(1033-1035)Cca>Aca	p.P345T	ZNF592_ENST00000299927.3_Missense_Mutation_p.P345T	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	345					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)	p.P345S(1)		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)			AAGTATCAAGCCATCGGACAG	0.547																																					p.P345T		Atlas-SNP	.											ZNF592,arm,malignant_melanoma,0,1	ZNF592	95	1	1	Substitution - Missense(1)	skin(1)	c.C1033A						PASS	.						72	82	78					15																	85326939		2203	4299	6502	SO:0001583	missense	9640	exon4			ATCAAGCCATCGG	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.1033C>A	15.37:g.85326939C>A	ENSP00000452877:p.Pro345Thr	117	0	0		121	42	0.347107	NM_014630	Q2M1T2|Q504Y9	Missense_Mutation	SNP	ENST00000560079.2	37	CCDS32317.1	.	.	.	.	.	.	.	.	.	.	C	16.61	3.171393	0.57584	.	.	ENSG00000166716	ENST00000299927	T	0.00620	6.17	5.59	5.59	0.84812	.	0.158983	0.56097	D	0.000026	T	0.02494	0.0076	M	0.61703	1.905	0.43771	D	0.996292	D	0.67145	0.996	P	0.59948	0.866	T	0.65467	-0.6161	10	0.40728	T	0.16	-5.8358	17.0815	0.86600	0.0:1.0:0.0:0.0	.	345	Q92610	ZN592_HUMAN	T	345	ENSP00000299927:P345T	ENSP00000299927:P345T	P	+	1	0	ZNF592	83127943	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	5.786000	0.69006	2.628000	0.89032	0.655000	0.94253	CCA	A|0.001;C|0.999	0.001	weak		0.547	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2	NM_014630		A	85326939	C	A	85326939	3	1	27	1	0	0	0	0	1	0	0	0	18037	739	26	4	1035	4	ZNF592	15	85326939	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	8301252	85326939	17204453	771	11222											
KIF7	374654	hgsc.bcm.edu	37	chr15	90195948	90195948	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggggctgaacgcaggcctGgtacacggcctcctgccccg	6	5	15	15	3	0	1	0	1	0	0	1	2	1	1	5	5	3	3	5	5	2	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:90195948G>C	ENST00000394412.3	-	2	290	c.214C>G	c.(214-216)Cag>Gag	p.Q72E		NM_198525.2	NP_940927.2	Q2M1P5	KIF7_HUMAN	kinesin family member 7	72	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				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)			ACGCAGGCCTGGTACACGGCC	0.637																																					p.Q72E		Atlas-SNP	.											.	KIF7	130	.	0			c.C214G						PASS	.						74	79	78					15																	90195948		689	1590	2279	SO:0001583	missense	374654	exon2			AGGCCTGGTACAC	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.214C>G	15.37:g.90195948G>C	ENSP00000377934:p.Gln72Glu	100	0	0		120	71	0.591667	NM_198525	Q3SXY0|Q6UXE9|Q8IW72	Missense_Mutation	SNP	ENST00000394412.3	37	CCDS32325.2	.	.	.	.	.	.	.	.	.	.	G	0.328	-0.957591	0.02267	.	.	ENSG00000166813	ENST00000394412	T	0.70869	-0.52	4.75	3.77	0.43336	Kinesin, motor domain (4);	.	.	.	.	T	0.36082	0.0954	N	0.00864	-1.135	0.24841	N	0.99247	B	0.09022	0.002	B	0.12156	0.007	T	0.24333	-1.0163	9	0.16420	T	0.52	.	7.1539	0.25626	0.0:0.2579:0.4681:0.274	.	72	Q2M1P5	KIF7_HUMAN	E	72	ENSP00000377934:Q72E	ENSP00000377934:Q72E	Q	-	1	0	KIF7	87996952	0.015000	0.18098	1.000000	0.80357	0.464000	0.32679	0.295000	0.19065	2.183000	0.69458	0.655000	0.94253	CAG	.	.	none		0.637	KIF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347782.1	NM_198525		C	90195948	G	C	90195948	3	2	27	1	0	0	0	0	1	0	0	0	8318	1357	47	4	3889	4	KIF7	15	90195948	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	4869009	90195948	12335444	772	11223											
UNC45A	55898	hgsc.bcm.edu	37	chr15	91496233	91496233	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggagcatgagatgatccgccGggcagccacggagtgcatgt	9	6	16	10	3	0	2	0	2	0	1	1	5	1	4	3	3	3	3	3	3	0	0	rs149872991		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr15:91496233G>A	ENST00000418476.2	+	18	2418	c.2378G>A	c.(2377-2379)cGg>cAg	p.R793Q	RCCD1_ENST00000394258.2_5'Flank|UNC45A_ENST00000394275.2_Missense_Mutation_p.R778Q|RCCD1_ENST00000556618.1_5'Flank|RCCD1_ENST00000555155.1_5'Flank|AC068831.6_ENST00000553321.1_RNA	NM_018671.3	NP_061141.2	Q9H3U1	UN45A_HUMAN	unc-45 homolog A (C. elegans)	793					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)			ATGATCCGCCGGGCAGCCACG	0.582													g|||	1	0.000199681	0.0	0.0	5008	,	,		22008	0.0		0.001	False		,,,				2504	0.0				p.R793Q		Atlas-SNP	.											.	UNC45A	57	.	0			c.G2378A						PASS	.		GLN/ARG,GLN/ARG	1,4395	2.1+/-5.4	0,1,2197	83	62	69		2333,2378	4.9	1	15	dbSNP_134	69	7,8589	5.7+/-21.5	0,7,4291	yes	missense,missense	UNC45A	NM_001039675.1,NM_018671.3	43,43	0,8,6488	AA,AG,GG		0.0814,0.0227,0.0616	benign,benign	778/930,793/945	91496233	8,12984	2198	4298	6496	SO:0001583	missense	55898	exon18			TCCGCCGGGCAGC		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.2378G>A	15.37:g.91496233G>A	ENSP00000407487:p.Arg793Gln	73	0	0		74	48	0.648649	NM_018671	A8K6F7|Q7L3Y6|Q9H3U8|Q9NSE8|Q9NSE9	Missense_Mutation	SNP	ENST00000418476.2	37	CCDS10367.1	.	.	.	.	.	.	.	.	.	.	g	15.13	2.742516	0.49151	2.27E-4	8.14E-4	ENSG00000140553	ENST00000394275;ENST00000418476	T;T	0.49720	0.77;0.77	4.88	4.88	0.63580	Armadillo-like helical (1);Armadillo-type fold (1);	0.457993	0.23413	N	0.048457	T	0.28830	0.0715	N	0.25992	0.78	0.37116	D	0.900608	P;P	0.48640	0.913;0.913	B;B	0.33799	0.17;0.17	T	0.30909	-0.9962	10	0.40728	T	0.16	-27.8398	10.8602	0.46823	0.0:0.0:0.7065:0.2935	.	793;778	Q9H3U1;A8K6F7	UN45A_HUMAN;.	Q	778;793	ENSP00000377816:R778Q;ENSP00000407487:R793Q	ENSP00000377816:R778Q	R	+	2	0	UNC45A	89297237	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.880000	0.39628	2.549000	0.85964	0.645000	0.84053	CGG	G|1.000;A|0.000	0.000	strong		0.582	UNC45A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280406.2	NM_018671		A	91496233	G	A	91496233	3	1	27	1	0	0	0	0	1	0	0	0	17003	1116	39	1	2448	1	UNC45A	15	91496233	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1300285	91496233	11035159	773	11224											
WDR90	197335	hgsc.bcm.edu	37	chr16	708308	708308	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acctcgtccaacagagtcgtGgtgctggatgctgtgtcggg	6	10	15	10	3	0	1	0	0	0	1	4	2	1	2	2	3	3	2	2	3	1	0	rs369151964		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:708308G>A	ENST00000293879.4	+	22	2730	c.2730G>A	c.(2728-2730)gtG>gtA	p.V910V	WDR90_ENST00000549091.1_Silent_p.V910V|LA16c-349E10.1_ENST00000573609.1_RNA			Q96KV7	WDR90_HUMAN	WD repeat domain 90	910										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				ACAGAGTCGTGGTGCTGGATG	0.677																																					p.V910V		Atlas-SNP	.											.	WDR90	107	.	0			c.G2730A						PASS	.						57	63	61					16																	708308		2141	4248	6389	SO:0001819	synonymous_variant	197335	exon22			AGTCGTGGTGCTG	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.2730G>A	16.37:g.708308G>A		121	0	0		70	27	0.385714	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Silent	SNP	ENST00000293879.4	37	CCDS42092.1																																																																																			.	.	alt		0.677	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294		A	708308	G	A	708308	2	1	27	1	0	0	0	0	0	0	0	1	17352	1335	47	2		2	WDR90	16	708308	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10		708308	89646445	774	11225											
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1254064	1254064	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cagtgtgccctgccccctgcCcagccccccagcgggcacac	5	4	10	22	1	0	0	0	0	0	0	0	0	0	0	7	1	5	1	7	1	0	0	rs145376050	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1254064C>T	ENST00000348261.5	+	10	2305	c.2057C>T	c.(2056-2058)cCc>cTc	p.P686L	RP11-616M22.3_ENST00000564700.1_RNA|CACNA1H_ENST00000358590.4_Missense_Mutation_p.P686L|CACNA1H_ENST00000565831.1_Missense_Mutation_p.P686L	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	686					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)	TGCCCCCTGCCCAGCCCCCCA	0.701													C|||	7	0.00139776	0.0	0.0014	5008	,	,		14466	0.0		0.006	False		,,,				2504	0.0				p.P686L		Atlas-SNP	.											.	CACNA1H	317	.	0			c.C2057T						PASS	.	C	LEU/PRO,LEU/PRO	1,3833		0,1,1916	8	10	9		2057,2057	4.1	1	16	dbSNP_134	9	9,8195		0,9,4093	yes	missense,missense	CACNA1H	NM_001005407.1,NM_021098.2	98,98	0,10,6009	TT,TC,CC		0.1097,0.0261,0.0831	probably-damaging,probably-damaging	686/2348,686/2354	1254064	10,12028	1917	4102	6019	SO:0001583	missense	8912	exon10			CCCTGCCCAGCCC	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.2057C>T	16.37:g.1254064C>T	ENSP00000334198:p.Pro686Leu	70	0	0		73	13	0.178082	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	15.89	2.965415	0.53507	2.61E-4	0.001097	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.96396	-4.0;-3.95	4.05	4.05	0.47172	.	0.785431	0.10696	U	0.644627	D	0.95526	0.8546	L	0.48642	1.525	0.42385	D	0.992503	D;D	0.53462	0.96;0.958	P;P	0.49252	0.574;0.604	D	0.93067	0.6479	10	0.30854	T	0.27	.	15.3789	0.74637	0.0:1.0:0.0:0.0	.	686;686	O95180-2;O95180	.;CAC1H_HUMAN	L	686	ENSP00000334198:P686L;ENSP00000351401:P686L	ENSP00000334198:P686L	P	+	2	0	CACNA1H	1194065	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	3.108000	0.50337	2.114000	0.64651	0.561000	0.74099	CCC	C|0.998;T|0.002	0.002	strong		0.701	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		T	1254064	C	T	1254064	3	4	27	1	0	0	0	0	1	0	0	0	2547	623	22	2	2091	2	CACNA1H	16	1254064	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	545756	1254064	89100689	775	11226											
CLCN7	1186	hgsc.bcm.edu	37	chr16	1500567	1500567	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagccccgatgagcagggaCgggatgaagaccccggcaga	11	2	16	12	3	0	4	0	2	0	2	0	7	0	6	4	3	2	3	4	3	1	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1500567C>T	ENST00000382745.4	-	17	2153	c.1548G>A	c.(1546-1548)ccG>ccA	p.P516P	LA16c-390E6.4_ENST00000563610.1_RNA|CLCN7_ENST00000448525.1_Silent_p.P492P|CLCN7_ENST00000262318.8_Silent_p.P492P	NM_001287.5	NP_001278.1	P51798	CLCN7_HUMAN	chloride channel, voltage-sensitive 7	516					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)				TGAGCAGGGACGGGATGAAGA	0.687																																					p.P516P		Atlas-SNP	.											.	CLCN7	53	.	0			c.G1548A						PASS	.						38	42	41					16																	1500567		2181	4298	6479	SO:0001819	synonymous_variant	1186	exon17			CAGGGACGGGATG	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.1548G>A	16.37:g.1500567C>T		90	0	0		136	106	0.779412	NM_001287	A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5	Silent	SNP	ENST00000382745.4	37	CCDS32361.1																																																																																			.	.	none		0.687	CLCN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103598.2	NM_001287		T	1500567	C	T	1500567	2	4	27	1	0	0	0	0	0	0	0	1	3470	523	19	1		1	CLCN7	16	1500567	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	246503	1500567	88854186	776	11227											
IFT140	9742	hgsc.bcm.edu	37	chr16	1652418	1652418	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actggggctccaacggagcaCggtgatgtcggctgtgtgtg	6	9	17	9	3	0	1	0	1	0	0	2	2	1	2	1	5	2	3	1	5	1	0	rs146128830	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:1652418C>T	ENST00000426508.2	-	4	685	c.322G>A	c.(322-324)Gtg>Atg	p.V108M	LA16c-395F10.2_ENST00000563162.1_RNA|IFT140_ENST00000439987.2_5'UTR	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	108					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)				CAACGGAGCACGGTGATGTCG	0.582													C|||	14	0.00279553	0.0023	0.0029	5008	,	,		17970	0.0		0.007	False		,,,				2504	0.002				p.V108M		Atlas-SNP	.											IFT140,NS,carcinoma,0,1	IFT140	128	1	0			c.G322A						PASS	.	C	MET/VAL	12,4386	19.1+/-41.9	0,12,2187	110	80	90		322	-1.2	0	16	dbSNP_134	90	81,8519	47.6+/-106.9	0,81,4219	yes	missense	IFT140	NM_014714.3	21	0,93,6406	TT,TC,CC		0.9419,0.2729,0.7155	possibly-damaging	108/1463	1652418	93,12905	2199	4300	6499	SO:0001583	missense	9742	exon4			GGAGCACGGTGAT	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.322G>A	16.37:g.1652418C>T	ENSP00000406012:p.Val108Met	79	0	0		85	15	0.176471	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Missense_Mutation	SNP	ENST00000426508.2	37	CCDS10439.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	11.51	1.660137	0.29515	0.002729	0.009419	ENSG00000187535	ENST00000397417;ENST00000426508;ENST00000439987	T;T	0.60299	0.7;0.2	4.83	-1.19	0.09585	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.456706	0.22233	N	0.062786	T	0.56790	0.2009	M	0.78801	2.425	0.24640	N	0.993577	D	0.59357	0.985	P	0.56042	0.79	T	0.58126	-0.7691	10	0.32370	T	0.25	.	9.8005	0.40761	0.0:0.4051:0.0:0.5949	.	108	Q96RY7	IF140_HUMAN	M	108	ENSP00000380562:V108M;ENSP00000406012:V108M	ENSP00000380562:V108M	V	-	1	0	IFT140	1592419	0.004000	0.15560	0.008000	0.14137	0.004000	0.04260	-0.032000	0.12266	-0.555000	0.06142	0.561000	0.74099	GTG	C|0.993;T|0.007	0.007	strong		0.582	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714		T	1652418	C	T	1652418	3	4	27	1	0	0	0	0	1	0	0	0	7565	536	19	1	4178	1	IFT140	16	1652418	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	151851	1652418	88702335	777	11228											
ZNF598	90850	hgsc.bcm.edu	37	chr16	2048564	2048564	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtcccggcaactcttgtaaTactgggctgcggagatcagg	8	9	14	10	2	2	1	1	0	1	1	3	2	3	1	1	5	3	3	1	5	3	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:2048564T>C	ENST00000563630.1	-	12	2461	c.2219A>G	c.(2218-2220)tAt>tGt	p.Y740C	ZNF598_ENST00000431526.1_Missense_Mutation_p.Y795C|AC005606.15_ENST00000567515.1_lincRNA|ZNF598_ENST00000562103.1_Missense_Mutation_p.Y740C			Q86UK7	ZN598_HUMAN	zinc finger protein 598	795	Pro-rich.						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						ACTCTTGTAATACTGGGCTGC	0.652																																					p.Y795C		Atlas-SNP	.											.	ZNF598	55	.	0			c.A2384G						PASS	.						7	8	8					16																	2048564		1863	4080	5943	SO:0001583	missense	90850	exon14			TTGTAATACTGGG	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.2219A>G	16.37:g.2048564T>C	ENSP00000455882:p.Tyr740Cys	123	0	0		98	49	0.5	NM_178167	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000563630.1	37		.	.	.	.	.	.	.	.	.	.	.	13.41	2.228427	0.39399	.	.	ENSG00000167962	ENST00000431526	T	0.44881	0.91	5.29	4.2	0.49525	.	0.000000	0.85682	D	0.000000	T	0.67429	0.2892	M	0.90650	3.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	T	0.73360	-0.4007	10	0.87932	D	0	-18.8123	9.7829	0.40660	0.0:0.0812:0.0:0.9188	.	795;787	Q86UK7;Q86UK7-2	ZN598_HUMAN;.	C	795	ENSP00000411409:Y795C	ENSP00000411409:Y795C	Y	-	2	0	ZNF598	1988565	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	7.301000	0.78850	2.000000	0.58554	0.379000	0.24179	TAT	.	.	none		0.652	ZNF598-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000434439.1	NM_178167		C	2048564	T	C	2048564	3	2	27	1	0	0	0	0	1	0	0	0	18043	1406	49	3	334	3	ZNF598	16	2048564	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	396146	2048564	88306189	778	11229											
CCDC64B	146439	hgsc.bcm.edu	37	chr16	3085326	3085326	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ggccaacagcaggtctttctCcttctgctgcagctgcaagg	7	10	11	13	0	3	0	0	0	3	0	4	0	3	0	2	3	6	5	2	3	2	2	rs71386699	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:3085326C>T	ENST00000572449.1	-	2	234	c.172G>A	c.(172-174)Gag>Aag	p.E58K	RP11-473M20.5_ENST00000382225.3_RNA|CCDC64B_ENST00000573514.1_5'Flank|CCDC64B_ENST00000389347.4_Missense_Mutation_p.E58K			A1A5D9	BICR2_HUMAN	coiled-coil domain containing 64B	58										breast(1)|endometrium(2)|large_intestine(1)	4						AGGTCTTTCTCCTTCTGCTGC	0.647													C|||	45	0.00898562	0.0023	0.0173	5008	,	,		11912	0.0		0.0258	False		,,,				2504	0.0041				p.E58K		Atlas-SNP	.											.	CCDC64B	19	.	0			c.G172A						PASS	.	C	LYS/GLU	12,3838		0,12,1913	10	11	11		172	5.1	1	16	dbSNP_130	11	204,8038		3,198,3920	yes	missense	CCDC64B	NM_001103175.1	56	3,210,5833	TT,TC,CC		2.4751,0.3117,1.7863	benign	58/509	3085326	216,11876	1925	4121	6046	SO:0001583	missense	146439	exon1			CTTTCTCCTTCTG	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.172G>A	16.37:g.3085326C>T	ENSP00000459043:p.Glu58Lys	132	0	0		132	17	0.128788	NM_001103175	Q658L9	Missense_Mutation	SNP	ENST00000572449.1	37	CCDS45393.1	31	0.014194139194139194	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	20	0.026385224274406333	c	21.5	4.163784	0.78226	0.003117	0.024751	ENSG00000162069	ENST00000389347	T	0.05513	3.43	5.08	5.08	0.68730	.	0.063133	0.64402	D	0.000009	T	0.08088	0.0202	M	0.71036	2.16	0.50813	D	0.999892	D	0.64830	0.994	D	0.63488	0.915	T	0.00044	-1.2219	10	0.62326	D	0.03	-26.8836	15.9724	0.80031	0.0:1.0:0.0:0.0	.	58	A1A5D9	BICR2_HUMAN	K	58	ENSP00000373998:E58K	ENSP00000373998:E58K	E	-	1	0	CCDC64B	3025327	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	6.271000	0.72569	2.361000	0.80049	0.457000	0.33378	GAG	C|0.985;T|0.015	0.015	strong		0.647	CCDC64B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436991.1			T	3085326	C	T	3085326	3	4	27	1	0	0	0	0	1	0	0	0	2838	864	30	2	1390	2	CCDC64B	16	3085326	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1036762	3085326	87269427	779	11230											
ALG1	56052	hgsc.bcm.edu	37	chr16	5132659	5132659	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgctgtttgcctgtgtgtgCtgtgaacttcaagtggtagg	5	15	15	6	0	1	1	1	1	0	0	1	1	1	1	1	2	4	4	1	2	3	3	rs74910062	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:5132659C>T	ENST00000262374.5	+	11	1203	c.1172C>T	c.(1171-1173)gCt>gTt	p.A391V	ALG1_ENST00000588623.1_Missense_Mutation_p.A280V|ALG1_ENST00000544428.1_Missense_Mutation_p.A280V	NM_019109.4	NP_061982.3	Q9BT22	ALG1_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase	391					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)				CCTGTGTGTGCTGTGAACTTC	0.597													C|||	37	0.00738818	0.0212	0.0029	5008	,	,		20282	0.004		0.001	False		,,,				2504	0.002				p.A391V		Atlas-SNP	.											.	ALG1	35	.	0			c.C1172T						PASS	.						95	71	79					16																	5132659		2087	3975	6062	SO:0001583	missense	56052	exon11			TGTGTGCTGTGAA	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.1172C>T	16.37:g.5132659C>T	ENSP00000262374:p.Ala391Val	17	0	0		17	7	0.411765	NM_019109	B4DP08|Q6UVZ9|Q8N5Y4|Q9P2Y2	Missense_Mutation	SNP	ENST00000262374.5	37	CCDS10528.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.214278	0.79352	.	.	ENSG00000033011	ENST00000262374;ENST00000544428	T;T	0.79141	-1.24;-1.24	5.28	5.28	0.74379	Glycosyl transferase, family 1 (1);	0.000000	0.85682	D	0.000000	D	0.90345	0.6979	M	0.90425	3.115	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92258	0.5814	10	0.87932	D	0	-20.3409	17.5165	0.87775	0.0:1.0:0.0:0.0	.	280;391	B4DP08;Q9BT22	.;ALG1_HUMAN	V	391;280	ENSP00000262374:A391V;ENSP00000440019:A280V	ENSP00000262374:A391V	A	+	2	0	ALG1	5072660	1.000000	0.71417	0.702000	0.30337	0.479000	0.33129	7.176000	0.77643	2.474000	0.83562	0.555000	0.69702	GCT	.	.	weak		0.597	ALG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251716.2	NM_019109		T	5132659	C	T	5132659	3	4	27	1	0	0	0	0	1	0	0	0	510	797	28	2	1214	2	ALG1	16	5132659	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2047333	5132659	85222094	780	11231											
TEKT5	146279	hgsc.bcm.edu	37	chr16	10788624	10788624	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgggcaggtagtagggctgaTagcattcctggatcactggc	8	9	15	9	1	1	1	1	1	0	0	2	2	2	2	1	5	1	5	1	5	3	4	rs145995713	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:10788624T>C	ENST00000283025.2	-	1	178	c.107A>G	c.(106-108)tAt>tGt	p.Y36C	RP11-109M19.1_ENST00000576710.1_RNA	NM_144674.1	NP_653275.1	Q96M29	TEKT5_HUMAN	tektin 5	36						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						GTAGGGCTGATAGCATTCCTG	0.562													T|||	19	0.00379393	0.0	0.0043	5008	,	,		17761	0.0		0.0119	False		,,,				2504	0.0041				p.Y36C		Atlas-SNP	.											.	TEKT5	66	.	0			c.A107G						PASS	.	T	CYS/TYR	3,4391		0,3,2194	79	74	75		107	5.3	1	16	dbSNP_134	75	73,8527		0,73,4227	yes	missense	TEKT5	NM_144674.1	194	0,76,6421	CC,CT,TT		0.8488,0.0683,0.5849	probably-damaging	36/486	10788624	76,12918	2197	4300	6497	SO:0001583	missense	146279	exon1			GGCTGATAGCATT		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.107A>G	16.37:g.10788624T>C	ENSP00000283025:p.Tyr36Cys	73	0	0		69	56	0.811594	NM_144674	A1L3Z3	Missense_Mutation	SNP	ENST00000283025.2	37	CCDS10542.1	13	0.005952380952380952	0	0.0	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	.	11.16	1.557014	0.27827	6.83E-4	0.008488	ENSG00000153060	ENST00000283025	T	0.03212	4.01	5.29	5.29	0.74685	.	0.000000	0.56097	D	0.000032	T	0.08846	0.0219	M	0.72894	2.215	0.49483	D	0.999795	D	0.69078	0.997	D	0.63192	0.912	T	0.01356	-1.1376	10	0.39692	T	0.17	-39.6857	8.7187	0.34428	0.0:0.0854:0.0:0.9146	.	36	Q96M29	TEKT5_HUMAN	C	36	ENSP00000283025:Y36C	ENSP00000283025:Y36C	Y	-	2	0	TEKT5	10696125	1.000000	0.71417	1.000000	0.80357	0.389000	0.30415	1.922000	0.40045	1.992000	0.58205	0.533000	0.62120	TAT	T|0.994;C|0.006	0.006	strong		0.562	TEKT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251963.1	NM_144674		C	10788624	T	C	10788624	3	2	27	1	0	0	0	0	1	0	0	0	15771	1406	49	3	1378	3	TEKT5	16	10788624	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	5655965	10788624	79566129	781	11232											
CLEC16A	23274	hgsc.bcm.edu	37	chr16	11272482	11272482	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctgtccacgccggctgccGcctgcacagagcccgtgggc	4	5	14	18	5	0	1	0	0	0	1	1	1	1	1	5	2	3	3	5	2	0	0	rs72650691	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:11272482G>A	ENST00000409790.1	+	24	3327	c.3097G>A	c.(3097-3099)Gcc>Acc	p.A1033T	CLEC16A_ENST00000381822.2_Missense_Mutation_p.A120T	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						GCCGGCTGCCGCCTGCACAGA	0.687													G|||	4	0.000798722	0.0008	0.0029	5008	,	,		15009	0.0		0.001	False		,,,				2504	0.0				p.A1033T		Atlas-SNP	.											CLEC16A,NS,carcinoma,-1,1	CLEC16A	101	1	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.G3097A						PASS	.	G	THR/ALA	2,4080		0,2,2039	10	13	12		3097	1.3	0	16	dbSNP_130	12	20,8320		0,20,4150	yes	missense	CLEC16A	NM_015226.2	58	0,22,6189	AA,AG,GG		0.2398,0.049,0.1771	benign	1033/1054	11272482	22,12400	2041	4170	6211	SO:0001583	missense	23274	exon23			GCTGCCGCCTGCA	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.3097G>A	16.37:g.11272482G>A	ENSP00000387122:p.Ala1033Thr	12	0	0		13	13	1	NM_015226		Missense_Mutation	SNP	ENST00000409790.1	37	CCDS45409.1	.	.	.	.	.	.	.	.	.	.	G	8.999	0.979594	0.18812	4.9E-4	0.002398	ENSG00000038532	ENST00000409790;ENST00000542102;ENST00000381822	T	0.44482	0.92	4.4	1.28	0.21552	.	1.314290	0.04911	N	0.453315	T	0.23846	0.0577	N	0.08118	0	0.09310	N	1	B;B	0.20261	0.043;0.0	B;B	0.10450	0.005;0.0	T	0.19910	-1.0291	10	0.23302	T	0.38	-0.2189	8.3364	0.32217	0.2744:0.0:0.7256:0.0	.	120;1033	Q2KHT3-3;Q2KHT3	.;CL16A_HUMAN	T	1033;1033;120	ENSP00000387122:A1033T	ENSP00000371244:A120T	A	+	1	0	CLEC16A	11179983	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.320000	0.19540	0.440000	0.26502	-0.794000	0.03295	GCC	.	.	weak		0.687	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226		A	11272482	G	A	11272482	3	1	27	1	0	0	0	0	1	0	0	0	3502	1087	38	1	3187	1	CLEC16A	16	11272482	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	483858	11272482	79082271	782	11233											
SOCS1	8651	hgsc.bcm.edu	37	chr16	11348810	11348810	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gatgcgctggcggcacagctCctgcagcggccgcacgcggc	5	4	16	16	6	0	0	0	0	0	0	1	1	1	0	2	4	4	5	2	4	0	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:11348810C>T	ENST00000332029.2	-	2	676	c.526G>A	c.(526-528)Gag>Aag	p.E176K	RMI2_ENST00000572173.1_Intron	NM_003745.1	NP_003736.1	O15524	SOCS1_HUMAN	suppressor of cytokine signaling 1	176	Interaction with Elongin BC complex. {ECO:0000250}.|SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				cellular response to amino acid stimulus (GO:0071230)|cytokine-mediated signaling pathway (GO:0019221)|fat cell differentiation (GO:0045444)|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 insulin receptor signaling pathway (GO:0046627)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of protein phosphorylation (GO:0001932)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)	insulin-like growth factor receptor binding (GO:0005159)|kinase inhibitor activity (GO:0019210)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)	p.E176fs*35(3)|p.Y64fs*1(1)|p.R127_*212del(1)|p.V171_R179del(1)|p.0?(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(66)|lung(3)	71						CGGCACAGCTCCTGCAGCGGC	0.726			"F, O"		"Hodgkin Lymphoma, PMBL"																																p.E176K	Colon(177;456 3548 27231)	Atlas-SNP	.		Rec	yes		16	16p13.13	8651	suppressor of cytokine signaling 1		L	SOCS1,lymph_node,lymphoid_neoplasm,+2,1	SOCS1	84	1	7	Deletion - Frameshift(4)|Deletion - In frame(2)|Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(7)	c.G526A						PASS	.						6	7	7					16																	11348810		2122	4174	6296	SO:0001583	missense	8651	exon2			ACAGCTCCTGCAG	U88326	CCDS10546.1	16p13.13	2013-02-14			ENSG00000185338	ENSG00000185338		"Suppressors of cytokine signaling", "SH2 domain containing"	19383	protein-coding gene	gene with protein product		603597				7796808, 9266833	Standard	NM_003745		Approved	SOCS-1, SSI-1, JAB, TIP3, Cish1	uc002dar.1	O15524	OTTHUMG00000129792	ENST00000332029.2:c.526G>A	16.37:g.11348810C>T	ENSP00000329418:p.Glu176Lys	12	0	0		17	11	0.647059	NM_003745	O15097|Q9NSA7	Missense_Mutation	SNP	ENST00000332029.2	37	CCDS10546.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.726616	0.89298	.	.	ENSG00000185338	ENST00000332029	T	0.45276	0.9	4.13	4.13	0.48395	SOCS protein, C-terminal (4);	0.126789	0.51477	U	0.000085	T	0.56746	0.2006	M	0.77616	2.38	0.53688	D	0.999977	P	0.38677	0.642	P	0.48334	0.574	T	0.64863	-0.6307	10	0.72032	D	0.01	-30.4191	15.5539	0.76177	0.0:1.0:0.0:0.0	.	176	O15524	SOCS1_HUMAN	K	176	ENSP00000329418:E176K	ENSP00000329418:E176K	E	-	1	0	SOCS1	11256311	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.578000	0.46051	2.141000	0.66446	0.462000	0.41574	GAG	.	.	none		0.726	SOCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252018.1			T	11348810	C	T	11348810	3	4	27	1	0	0	0	0	1	0	0	0	14928	864	30	2	113	2	SOCS1	16	11348810	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	76328	11348810	79005943	783	11234											
VWA3A	146177	hgsc.bcm.edu	37	chr16	22144375	22144375	+	Frame_Shift_Del	DEL	C	C	-																															cgccgcctacaaggaggtcaCccgggctgcaggtggccgct																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:22144375delC	ENST00000389398.5	+	20	2123	c.2027delC	c.(2026-2028)accfs	p.T676fs	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	676	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.					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)		AAGGAGGTCACCCGGGCTGCA	0.577																																					p.T676fs		Atlas-Indel	.											.	VWA3A	115	.	0			c.2026delA						PASS	.						38	42	41					16																	22144375		2053	4186	6239	SO:0001589	frameshift_variant	146177	exon20			.	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.2027delC	16.37:g.22144375delC	ENSP00000374049:p.Thr676fs	91	0	0		69	27	0.391304	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Frame_Shift_Del	DEL	ENST00000389398.5	37	CCDS45441.1																																																																																			.	.	none		0.577	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1			-	22144375	C	-	22144375	7	5	27	1	0	1	0	1	0	0	0	0	17255	507	18	0	2105	0	VWA3A	16	22144375	Frame_Shift_Del	DEL	C	TCGA-G8-6909-01A-11D-2210-10	10795565	22144375	68210378	784	11235	139	4									
VWA3A	146177	hgsc.bcm.edu	37	chr16	22144376	22144378	+	In_Frame_Del	DEL	CCG	CCG	-																															gccgcctacaaggaggtcacCcgggctgcaggtggccgctt																								rs200086497|rs371670962		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCG	CCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:22144376_22144378delCCG	ENST00000389398.5	+	20	2124_2126	c.2028_2030delCCG	c.(2026-2031)acccgg>acg	p.R677del	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	677	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.					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)		AGGAGGTCACCCGGGCTGCAGGT	0.576																																					p.676_677del		Pindel	.											.	VWA3A	115	.	0			c.2027_2029del						PASS	.																																			SO:0001651	inframe_deletion	146177	exon20			.	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.2028_2030delCCG	16.37:g.22144376_22144378delCCG	ENSP00000374049:p.Arg677del	90	0	.		71	21	0.296	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	In_Frame_Del	DEL	ENST00000389398.5	37	CCDS45441.1																																																																																			.	.	none		0.576	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1			-	22144378	CCG	-	22144376	7	5	27	1	0	1	0	1	0	0	0	0	17255	610	22	0	2106	0	VWA3A	16	22144376	In_Frame_Del	DEL	CCG	TCGA-G8-6909-01A-11D-2210-10	1	22144376	68210377	785	11236	139	4									
VWA3A	146177	hgsc.bcm.edu	37	chr16	22144377	22144377	+	Silent	SNP	C	C	A																															ccgcctacaaggaggtcaccCgggctgcaggtggccgcttc																								rs371670962		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:22144377C>A	ENST00000389398.5	+	20	2125	c.2029C>A	c.(2029-2031)Cgg>Agg	p.R677R	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	677	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.					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)		GGAGGTCACCCGGGCTGCAGG	0.577																																					p.R677R		Atlas-SNP	.											.	VWA3A	115	.	0			c.C2029A						PASS	.						38	42	40					16																	22144377		2054	4187	6241	SO:0001819	synonymous_variant	146177	exon20			GTCACCCGGGCTG	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.2029C>A	16.37:g.22144377C>A		91	0	0		71	27	0.380282	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Silent	SNP	ENST00000389398.5	37	CCDS45441.1																																																																																			.	.	alt		0.577	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1			A	22144377	C	A	22144377	2	1	27	1	0	0	0	0	0	0	0	1	17255	643	23	4		4	VWA3A	16	22144377	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1	22144377	68210376	786	11237	139	4									
VWA3A	146177	hgsc.bcm.edu	37	chr16	22144378	22144378	+	Missense_Mutation	SNP	G	G	A																															cgcctacaaggaggtcacccGggctgcaggtggccgcttcc																								rs200086497		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:22144378G>A	ENST00000389398.5	+	20	2126	c.2030G>A	c.(2029-2031)cGg>cAg	p.R677Q	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	677	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.					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)		GAGGTCACCCGGGCTGCAGGT	0.577													G|||	1	0.000199681	0.0	0.0	5008	,	,		17694	0.001		0.0	False		,,,				2504	0.0				p.R677Q		Atlas-SNP	.											.	VWA3A	115	.	0			c.G2030A						PASS	.						38	42	41					16																	22144378		2055	4184	6239	SO:0001583	missense	146177	exon20			TCACCCGGGCTGC	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.2030G>A	16.37:g.22144378G>A	ENSP00000374049:p.Arg677Gln	91	0	0		72	27	0.375	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Missense_Mutation	SNP	ENST00000389398.5	37	CCDS45441.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	10.23	1.294063	0.23564	.	.	ENSG00000175267	ENST00000389398;ENST00000299840	T	0.10668	2.85	5.49	-3.57	0.04612	.	0.842998	0.10736	N	0.640019	T	0.04003	0.0112	N	0.04880	-0.145	0.80722	D	1	B;B	0.22080	0.04;0.064	B;B	0.12156	0.003;0.007	T	0.50136	-0.8863	10	0.02654	T	1	.	12.9659	0.58483	0.7034:0.0:0.2966:0.0	.	677;301	A6NCI4;A6NCI4-2	VWA3A_HUMAN;.	Q	677;300	ENSP00000374049:R677Q	ENSP00000299840:R300Q	R	+	2	0	VWA3A	22051879	0.545000	0.26449	0.959000	0.39883	0.756000	0.42949	-0.213000	0.09305	-0.507000	0.06549	-0.157000	0.13467	CGG	G|1.000;A|0.000	0.000	strong		0.577	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1			A	22144378	G	A	22144378	3	1	27	1	0	0	0	0	1	0	0	0	17255	1116	39	1	2108	1	VWA3A	16	22144378	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1	22144378	68210375	787	11238	139	4									
GTF3C1	2975	hgsc.bcm.edu	37	chr16	27499956	27499956	+	Splice_Site	DEL	C	C	-																															attctctgcggcagtgttctCctgtgagacaagcacagcac																								rs560536443		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:27499956delC	ENST00000356183.4	-	22	3445	c.3430delG	c.(3430-3432)gag>ag	p.E1144fs	GTF3C1_ENST00000561623.1_Splice_Site_p.E1144fs	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	1144					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						GCAGTGTTCTCCTGTGAGACA	0.557																																					p.E1144fs		Pindel,Atlas-Indel	.											.	GTF3C1	210	.	0			c.3431delA						PASS	.						97	90	92					16																	27499956		2197	4300	6497	SO:0001630	splice_region_variant	2975	exon22			.	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.3430-1G>-	16.37:g.27499956delC		44	0	.		46	13	0.283	NM_001520	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Frame_Shift_Del	DEL	ENST00000356183.4	37	CCDS32414.1																																																																																			.	.	none		0.557	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520	Frame_Shift_Del	-	27499956	C	-	27499956	8	5	27	1	0	1	0	1	0	0	1	0	6881	869	30	0	2963	0	GTF3C1	16	27499956	Splice_Site	DEL	C	TCGA-G8-6909-01A-11D-2210-10	5355578	27499956	62854797	788	11239											
ATP2A1	487	hgsc.bcm.edu	37	chr16	28898778	28898778	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagccggcaaggccttgggCatcgtggccaccactggtgt	6	7	15	13	2	0	0	0	0	0	0	1	0	0	0	4	5	1	3	4	5	1	1	rs113803159	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:28898778C>G	ENST00000357084.3	+	8	930	c.663C>G	c.(661-663)ggC>ggG	p.G221G	ATP2A1_ENST00000536376.1_Silent_p.G96G|ATP2A1_ENST00000395503.4_Silent_p.G221G	NM_173201.3	NP_775293.1	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	221					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						AGGCCTTGGGCATCGTGGCCA	0.607													C|||	9	0.00179712	0.0	0.0014	5008	,	,		18988	0.0		0.008	False		,,,				2504	0.0				p.G221G		Atlas-SNP	.											.	ATP2A1	116	.	0			c.C663G						PASS	.	C	,	7,4387	12.9+/-30.5	0,7,2190	85	82	83		663,663	3.4	1	16	dbSNP_132	83	72,8528	43.6+/-101.6	1,70,4229	no	coding-synonymous,coding-synonymous	ATP2A1	NM_004320.4,NM_173201.3	,	1,77,6419	GG,GC,CC		0.8372,0.1593,0.608	,	221/995,221/1002	28898778	79,12915	2197	4300	6497	SO:0001819	synonymous_variant	487	exon8			CTTGGGCATCGTG		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.663C>G	16.37:g.28898778C>G		61	0	0		74	43	0.581081	NM_004320	A8K5J9|B3KY17|O14984	Silent	SNP	ENST00000357084.3	37	CCDS10643.1																																																																																			C|0.995;G|0.005	0.005	strong		0.607	ATP2A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254686.2	NM_004320		G	28898778	C	G	28898778	2	3	27	1	0	0	0	0	0	0	0	1	1136	697	25	4		4	ATP2A1	16	28898778	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1398822	28898778	61455975	789	11240											
SPNS1	83985	hgsc.bcm.edu	37	chr16	28995211	28995211	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgttggggcactgggcggCgcagccttcctgggcaccgc	3	9	16	13	3	0	0	0	0	0	0	1	0	1	0	3	5	1	4	3	5	0	3	rs113165798	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:28995211C>T	ENST00000311008.11	+	11	1802	c.1425C>T	c.(1423-1425)ggC>ggT	p.G475G	LAT_ENST00000564277.1_5'Flank|LAT_ENST00000354453.4_5'Flank|LAT_ENST00000360872.5_5'Flank|LAT_ENST00000566177.1_5'Flank|LAT_ENST00000395461.3_5'Flank|SPNS1_ENST00000334536.8_Silent_p.G423G|SPNS1_ENST00000565975.1_Silent_p.G520G|SPNS1_ENST00000352260.7_Silent_p.G401G|SPNS1_ENST00000323081.8_Silent_p.G402G|RP11-264B17.3_ENST00000569969.1_RNA|LAT_ENST00000454369.2_5'Flank|LAT_ENST00000395456.2_5'Flank	NM_032038.2	NP_114427.1	Q9H2V7	SPNS1_HUMAN	spinster homolog 1 (Drosophila)	475					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrial inner membrane (GO:0005743)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)|urinary_tract(1)	21						CACTGGGCGGCGCAGCCTTCC	0.672													C|||	9	0.00179712	0.0	0.0014	5008	,	,		18700	0.0		0.008	False		,,,				2504	0.0				p.G475G		Atlas-SNP	.											.	SPNS1	47	.	0			c.C1425T						PASS	.	C	,,,,	7,4387	12.9+/-30.5	0,7,2190	48	51	50		1425,1203,1206,1269,1425	-9.2	0.1	16	dbSNP_132	50	74,8526	44.0+/-102.2	1,72,4227	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPNS1	NM_001142448.1,NM_001142449.1,NM_001142450.1,NM_001142451.1,NM_032038.2	,,,,	1,79,6417	TT,TC,CC		0.8605,0.1593,0.6234	,,,,	475/529,401/455,402/456,423/477,475/529	28995211	81,12913	2197	4300	6497	SO:0001819	synonymous_variant	83985	exon12			GGGCGGCGCAGCC	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.1425C>T	16.37:g.28995211C>T		56	0	0		65	33	0.507692	NM_001142448	B5MDM9|Q6P182|Q71RB5|Q7L541|Q86VU7|Q8N953|Q8TCS5|Q9BRN5	Silent	SNP	ENST00000311008.11	37	CCDS10646.1																																																																																			C|0.995;T|0.005	0.005	strong		0.672	SPNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254690.2	NM_032038		T	28995211	C	T	28995211	2	4	27	1	0	0	0	0	0	0	0	1	15089	755	27	1		1	SPNS1	16	28995211	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	96433	28995211	61359542	790	11241											
DOC2A	8448	hgsc.bcm.edu	37	chr16	30018351	30018353	+	Splice_Site	DEL	CCT	CCT	-																															catccccatgaggtgcctcaCctccttcagataacaggaga																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:30018351_30018353delCCT	ENST00000350119.4	-	7	903_905	c.713_715delAGG	c.(712-717)gaggtg>gtg	p.E238del	DOC2A_ENST00000564944.1_Splice_Site_p.E238del|DOC2A_ENST00000564979.1_Splice_Site_p.E238del	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	238	Interaction with UNC13D.			E -> D (in Ref. 1; BAA06695). {ECO:0000305}.	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						AGGTGCCTCACCTCCTTCAGATA	0.65																																					p.238_238del		Pindel,Atlas-Indel	.											.	DOC2A	40	.	0			c.714_714del						PASS	.																																			SO:0001630	splice_region_variant	8448	exon7			.	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.714+1AGG>-	16.37:g.30018354_30018356delCCT		139	0	.		184	32	0.174	NM_003586	B4DEJ2|H3BNH6|Q6P4G4|Q7Z5G0|Q8IVX0	Frame_Shift_Del	DEL	ENST00000350119.4	37	CCDS10666.1																																																																																			.	.	none		0.65	DOC2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255148.2	NM_003586	In_Frame_Del	-	30018353	CCT	-	30018351	8	5	27	1	0	1	0	1	0	0	1	0	4685	521	18	0	507	0	DOC2A	16	30018351	Splice_Site	DEL	CCT	TCGA-G8-6909-01A-11D-2210-10	1023140	30018351	60336402	791	11242											
PHKG2	5261	hgsc.bcm.edu	37	chr16	30762886	30762886	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctagtcaccctcatcgattcCtacgagtcttctagcttcat	8	14	5	14	2	5	0	3	0	2	0	7	2	6	0	2	0	2	1	2	0	3	6	rs56029513		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:30762886C>T	ENST00000563588.1	+	4	527	c.288C>T	c.(286-288)tcC>tcT	p.S96S	RP11-2C24.4_ENST00000483578.1_lincRNA|PHKG2_ENST00000424889.3_Silent_p.S96S|PHKG2_ENST00000328273.7_Silent_p.S96S	NM_000294.2	NP_000285.1	P15735	PHKG2_HUMAN	phosphorylase kinase, gamma 2 (testis)	96	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|positive regulation of glycogen catabolic process (GO:0045819)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)	ATP binding (GO:0005524)|phosphorylase kinase activity (GO:0004689)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			ovary(1)|skin(1)	2			Colorectal(24;0.198)			TCATCGATTCCTACGAGTCTT	0.547													c|||	1	0.000199681	0.0008	0.0	5008	,	,		22627	0.0		0.0	False		,,,				2504	0.0				p.S96S		Atlas-SNP	.											.	PHKG2	29	.	0			c.C288T						PASS	.	G	,	3,4391	6.2+/-15.9	0,3,2194	522	465	484		288,288	3.2	1	16	dbSNP_129	484	21,8579	15.3+/-51.7	0,21,4279	no	coding-synonymous,coding-synonymous	PHKG2	NM_000294.2,NM_001172432.1	,	0,24,6473	TT,TC,CC		0.2442,0.0683,0.1847	,	96/407,96/375	30762886	24,12970	2197	4300	6497	SO:0001819	synonymous_variant	5261	exon4			CGATTCCTACGAG	S73483, M31606	CCDS10690.1, CCDS54002.1	16p11.2	2008-02-05			ENSG00000156873	ENSG00000156873			8931	protein-coding gene	gene with protein product		172471				2915644, 8020963	Standard	NM_000294		Approved		uc021tgo.1	P15735	OTTHUMG00000132400	ENST00000563588.1:c.288C>T	16.37:g.30762886C>T		533	1	0.00187617		672	239	0.355655	NM_001172432	A8K0C7|B4DEB7|E9PEU3|P11800	Silent	SNP	ENST00000563588.1	37	CCDS10690.1																																																																																			C|0.997;T|0.003	0.003	strong		0.547	PHKG2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255531.2	NM_000294		T	30762886	C	T	30762886	2	4	27	1	0	0	0	0	0	0	0	1	11856	668	24	2		2	PHKG2	16	30762886	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	744535	30762886	59591867	792	11243											
SALL1	6299	hgsc.bcm.edu	37	chr16	51174432	51174432	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttccgtcttgatgaagggTatgaggcttgggagggttgg	6	13	17	5	1	2	3	0	3	2	0	3	4	3	4	1	5	0	3	1	5	2	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:51174432T>C	ENST00000251020.4	-	2	1734	c.1701A>G	c.(1699-1701)atA>atG	p.I567M	SALL1_ENST00000541611.1_Intron|SALL1_ENST00000440970.1_Missense_Mutation_p.I470M|SALL1_ENST00000566102.1_Intron|SALL1_ENST00000562674.1_5'Flank	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	567					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)			TGATGAAGGGTATGAGGCTTG	0.612																																					p.I567M	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.A1701G						PASS	.						45	50	48					16																	51174432		2198	4300	6498	SO:0001583	missense	6299	exon2			GAAGGGTATGAGG	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.1701A>G	16.37:g.51174432T>C	ENSP00000251020:p.Ile567Met	88	0	0		64	29	0.453125	NM_002968	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	37	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	T	8.110	0.778639	0.16120	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.05996	3.36;3.38	5.32	-10.6	0.00265	.	0.257755	0.45126	D	0.000388	T	0.02156	0.0067	N	0.08118	0	0.09310	N	1	B	0.21225	0.053	B	0.22386	0.039	T	0.29518	-1.0009	10	0.72032	D	0.01	.	6.6511	0.22963	0.0662:0.2679:0.4445:0.2214	.	567	Q9NSC2	SALL1_HUMAN	M	567;470;531	ENSP00000251020:I567M;ENSP00000407914:I470M	ENSP00000251020:I567M	I	-	3	3	SALL1	49731933	0.000000	0.05858	0.164000	0.22755	0.998000	0.95712	-3.833000	0.00355	-2.099000	0.00849	0.455000	0.32223	ATA	.	.	none		0.612	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		C	51174432	T	C	51174432	3	2	27	1	0	0	0	0	1	0	0	0	13825	1628	57	3	2281	3	SALL1	16	51174432	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	20411546	51174432	39180321	793	11244											
CCDC102A	92922	hgsc.bcm.edu	37	chr16	57562804	57562804	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcagtgcagtccgaccaccGgcgcatggtcttctccatct	6	9	11	15	3	3	0	0	0	3	0	5	1	4	0	4	3	1	3	4	3	0	1	rs12935069		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:57562804G>A	ENST00000258214.2	-	2	532	c.286C>T	c.(286-288)Cgg>Tgg	p.R96W		NM_033212.3	NP_149989.2	Q96A19	C102A_HUMAN	coiled-coil domain containing 102A	96				R -> W (in Ref. 2; AAH08285/AAH09941). {ECO:0000305}.						endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)	8						TCCGACCACCGGCGCATGGTC	0.731													A|||	5008	1.0	1.0	1.0	5008	,	,		3757	1.0		1.0	False		,,,				2504	1.0				p.R96W		Atlas-SNP	.											.	CCDC102A	22	.	0			c.C286T						PASS	.						8	10	9					16																	57562804		1834	3717	5551	SO:0001583	missense	92922	exon2			ACCACCGGCGCAT	BC008285	CCDS10784.1	16q13	2008-02-05			ENSG00000135736	ENSG00000135736			28097	protein-coding gene	gene with protein product						12477932	Standard	NM_033212		Approved	MGC10992	uc002elw.3	Q96A19	OTTHUMG00000133472	ENST00000258214.2:c.286C>T	16.37:g.57562804G>A	ENSP00000258214:p.Arg96Trp	0	0	.		4	4	1	NM_033212	Q9BT74	Missense_Mutation	SNP	ENST00000258214.2	37	CCDS10784.1	2180	0.9981684981684982	492	1.0	360	0.994475138121547	570	0.9965034965034965	758	1.0	A	10.17	1.277909	0.23307	.	.	ENSG00000135736	ENST00000258214	T	0.37752	1.18	4.82	4.82	0.62117	.	0.000000	0.64402	N	0.000001	T	0.00012	0.0000	N	0.00049	-2.415	0.40217	P	0.022302999999999962	B	0.02656	0.0	B	0.01281	0.0	T	0.44787	-0.9305	9	0.33141	T	0.24	-23.2491	9.5348	0.39216	0.9152:0.0:0.0848:0.0	rs12935069;rs12935069	96	Q96A19	C102A_HUMAN	W	96	ENSP00000258214:R96W	ENSP00000258214:R96W	R	-	1	2	CCDC102A	56120305	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	6.801000	0.75170	0.698000	0.31739	-0.556000	0.04195	CGG	G|0.001;A|0.999	0.999	strong		0.731	CCDC102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257348.1	NM_033212		A	57562804	G	A	57562804	3	1	27	1	0	0	0	0	1	0	0	0	2738	1115	39	1	1398	1	CCDC102A	16	57562804	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	6388372	57562804	32791949	794	11245											
EXOC3L	283849	hgsc.bcm.edu	37	chr16	67221737	67221737	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgtgtgggacactgcagccGgcactaatgagagtgaaaag	12	7	15	7	1	0	2	0	2	0	1	0	4	0	3	1	2	2	2	1	2	3	1	rs149684674		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:67221737G>A	ENST00000314586.6	-	5	671	c.431C>T	c.(430-432)cCg>cTg	p.P144L	EXOC3L1_ENST00000562887.1_Intron	NM_178516.3	NP_848611.2	Q86VI1	EX3L1_HUMAN	exocyst complex component 3-like 1	144	Mediates interaction with EXOC2, EXOC4 and EXOC5. {ECO:0000250}.				exocytosis (GO:0006887)|peptide hormone secretion (GO:0030072)	exocyst (GO:0000145)|secretory granule (GO:0030141)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	21						CACTGCAGCCGGCACTAATGA	0.592													G|||	1	0.000199681	0.0	0.0014	5008	,	,		19157	0.0		0.0	False		,,,				2504	0.0				p.P144L		Atlas-SNP	.											LOC283849,caecum,carcinoma,0,2	EXOC3L1	52	2	0			c.C431T						PASS	.	G	LEU/PRO	1,4393		0,1,2196	60	70	67		431	5.7	1	16	dbSNP_134	67	12,8588		0,12,4288	yes	missense	EXOC3L1	NM_178516.3	98	0,13,6484	AA,AG,GG		0.1395,0.0228,0.1	probably-damaging	144/747	67221737	13,12981	2197	4300	6497	SO:0001583	missense	283849	exon5			GCAGCCGGCACTA	AK092858	CCDS10832.1	16q22.1	2011-01-31	2011-01-31	2011-01-31	ENSG00000179044	ENSG00000179044			27540	protein-coding gene	gene with protein product		614117	"exocyst complex component 3-like"	EXOC3L		12477932	Standard	NM_178516		Approved	FLJ35539, FLJ35587	uc002erx.1	Q86VI1	OTTHUMG00000137508	ENST00000314586.6:c.431C>T	16.37:g.67221737G>A	ENSP00000325674:p.Pro144Leu	73	0	0		83	45	0.542169	NM_178516	A8K7I9|Q8NAD2|Q8TEN2	Missense_Mutation	SNP	ENST00000314586.6	37	CCDS10832.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	16.54	3.151062	0.57151	2.28E-4	0.001395	ENSG00000179044	ENST00000314586;ENST00000545725;ENST00000314553	T;T	0.22134	2.77;1.97	5.74	5.74	0.90152	.	0.179126	0.49916	D	0.000134	T	0.46288	0.1385	M	0.77103	2.36	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.69307	0.963;0.92;0.95	T	0.34329	-0.9833	10	0.46703	T	0.11	-20.7533	14.2617	0.66090	0.0:0.0:0.8505:0.1495	.	83;83;144	F5H4W1;B7Z6U0;Q86VI1	.;.;EX3L1_HUMAN	L	144;83;88	ENSP00000325674:P144L;ENSP00000439910:P83L	ENSP00000325008:P88L	P	-	2	0	EXOC3L1	65779238	0.976000	0.34144	0.962000	0.40283	0.656000	0.38851	1.800000	0.38833	2.716000	0.92895	0.650000	0.86243	CCG	G|0.999;A|0.001	0.001	strong		0.592	EXOC3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268827.2	NM_178516		A	67221737	G	A	67221737	3	1	27	1	0	0	0	0	1	0	0	0	5306	1116	39	1	1849	1	EXOC3L	16	67221737	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	9658933	67221737	23133016	795	11246											
SLC9A5	6553	hgsc.bcm.edu	37	chr16	67300058	67300058	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gacagttcagagacagagaaGgaggacgatgaggggatcat	15	5	16	5	1	2	3	2	1	0	2	2	10	2	6	0	4	0	1	0	4	1	1	rs61744117	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:67300058G>A	ENST00000299798.11	+	15	2213	c.2148G>A	c.(2146-2148)aaG>aaA	p.K716K	CTC-277H1.7_ENST00000573063.1_RNA	NM_004594.2	NP_004585.1	Q14940	SL9A5_HUMAN	solute carrier family 9, subfamily A (NHE5, cation proton antiporter 5), member 5	716					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00376)|Epithelial(162;0.0173)|all cancers(182;0.116)		AGACAGAGAAGGAGGACGATG	0.562													G|||	4	0.000798722	0.0	0.0014	5008	,	,		20520	0.0		0.003	False		,,,				2504	0.0				p.K716K		Atlas-SNP	.											.	SLC9A5	82	.	0			c.G2148A						PASS	.	G		1,4181		0,1,2090	117	124	121		2148	2.2	1	16	dbSNP_129	121	23,8393		0,23,4185	no	coding-synonymous	SLC9A5	NM_004594.2		0,24,6275	AA,AG,GG		0.2733,0.0239,0.1905		716/897	67300058	24,12574	2091	4208	6299	SO:0001819	synonymous_variant	6553	exon15			AGAGAAGGAGGAC		CCDS42178.1	16q22.1	2013-05-22	2012-03-22		ENSG00000135740	ENSG00000135740		"Solute carriers"	11078	protein-coding gene	gene with protein product		600477	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 5", "solute carrier family 9 (sodium/hydrogen exchanger), member 5"			7759094, 9933642	Standard	NM_004594		Approved	NHE5	uc002esm.3	Q14940	OTTHUMG00000172935	ENST00000299798.11:c.2148G>A	16.37:g.67300058G>A		153	0	0		200	113	0.565	NM_004594	A5PKY7|Q9Y626	Silent	SNP	ENST00000299798.11	37	CCDS42178.1																																																																																			G|0.998;A|0.002	0.002	strong		0.562	SLC9A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421386.1			A	67300058	G	A	67300058	2	1	27	1	0	0	0	0	0	0	0	1	14732	991	35	2		2	SLC9A5	16	67300058	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	78321	67300058	23054695	796	11247											
CDH1	999	hgsc.bcm.edu	37	chr16	68862165	68862165	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaggatgacacccgggacaaCgtttattactatgatgaaga	14	9	11	7	2	0	4	0	3	0	1	0	7	0	6	1	2	2	1	1	2	5	4	rs33964119	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:68862165C>T	ENST00000261769.5	+	14	2444	c.2253C>T	c.(2251-2253)aaC>aaT	p.N751N	CDH1_ENST00000562836.1_3'UTR|CDH1_ENST00000422392.2_Silent_p.N690N	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	751		Cleavage; by caspase-3.			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.N751N(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)		CCCGGGACAACGTTTATTACT	0.507			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer				C|||	273	0.0545128	0.0582	0.0692	5008	,	,		19674	0.0694		0.0348	False		,,,				2504	0.044				p.N751N		Atlas-SNP	.	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	CDH1,colon,carcinoma,0,3	CDH1	535	3	1	Substitution - coding silent(1)	stomach(1)	c.C2253T						PASS	.	C		215,4181	132.1+/-168.6	5,205,1988	98	94	95		2253	-12.1	0	16	dbSNP_126	95	273,8327	104.4+/-165.4	2,269,4029	no	coding-synonymous	CDH1	NM_004360.3		7,474,6017	TT,TC,CC		3.1744,4.8908,3.755		751/883	68862165	488,12508	2198	4300	6498	SO:0001819	synonymous_variant	999	exon14	Familial Cancer Database	HDGC	GGACAACGTTTAT	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.2253C>T	16.37:g.68862165C>T		85	0	0		84	34	0.404762	NM_004360	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Silent	SNP	ENST00000261769.5	37	CCDS10869.1																																																																																			A|0.000;C|0.956;G|0.000;T|0.043	0.043	strong		0.507	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360		T	68862165	C	T	68862165	2	4	27	1	0	0	0	0	0	0	0	1	3097	535	19	1		1	CDH1	16	68862165	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1562107	68862165	21492588	797	11248											
SNTB2	6645	hgsc.bcm.edu	37	chr16	69318149	69318149	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atcaaggaagtctctctaggTagagatgctgactttttatt	11	15	9	6	0	3	2	1	1	2	1	4	4	3	3	0	2	1	2	0	2	5	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:69318149T>C	ENST00000336278.4	+	5	1383		c.e5+2			NM_006750.3	NP_006741.1	Q13425	SNTB2_HUMAN	syntrophin, beta 2 (dystrophin-associated protein A1, 59kDa, basic component 2)							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)		TCTCTCTAGGTAGAGATGCTG	0.423																																					.	NSCLC(58;1458 1722 3262 39967)|Melanoma(111;1698 2173 25379 28738)	Atlas-SNP	.											.	SNTB2	22	.	0			c.1345+2T>C						PASS	.						70	64	66					16																	69318149		2198	4300	6498	SO:0001630	splice_region_variant	6645	exon5			TCTAGGTAGAGAT	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.1345+2T>C	16.37:g.69318149T>C		85	0	0		88	4	0.0454545	NM_006750	Q9BY09	Splice_Site	SNP	ENST00000336278.4	37	CCDS10873.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.346898	0.82022	.	.	ENSG00000168807	ENST00000336278;ENST00000467311	.	.	.	5.23	5.23	0.72850	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.7976	0.69889	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	SNTB2	67875650	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	7.857000	0.86963	1.975000	0.57531	0.533000	0.62120	.	.	.	none		0.423	SNTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268945.1		Intron	C	69318149	T	C	69318149	5	2	27	1	0	0	0	0	0	0	1	0	14888	1652	57	3	1365	3	SNTB2	16	69318149	Splice_Site	SNP	T	TCGA-G8-6909-01A-11D-2210-10	455984	69318149	21036604	798	11249											
WWP2	11060	hgsc.bcm.edu	37	chr16	69922079	69922079	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccccagccacaccggctgaaGgagaggaacccagcacttcg	11	3	11	16	2	0	2	0	1	0	1	1	4	0	3	5	3	3	2	5	3	2	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:69922079G>A	ENST00000359154.2	+	8	942	c.841G>A	c.(841-843)Gga>Aga	p.G281R	WWP2_ENST00000569174.1_Missense_Mutation_p.G281R|WWP2_ENST00000448661.1_Missense_Mutation_p.G281R|WWP2_ENST00000544162.1_3'UTR|WWP2_ENST00000356003.2_Missense_Mutation_p.G281R|WWP2_ENST00000542271.1_Missense_Mutation_p.G165R	NM_001270454.1|NM_007014.4	NP_001257383.1|NP_008945.2	O00308	WWP2_HUMAN	WW domain containing E3 ubiquitin protein ligase 2	281					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						ACCGGCTGAAGGAGAGGAACC	0.622																																					p.G281R		Atlas-SNP	.											.	WWP2	88	.	0			c.G841A						PASS	.						68	67	67					16																	69922079		2198	4300	6498	SO:0001583	missense	11060	exon8			GCTGAAGGAGAGG	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.841G>A	16.37:g.69922079G>A	ENSP00000352069:p.Gly281Arg	95	0	0		127	51	0.401575	NM_001270454	A6NEP1|B2R706|B4DTL5|F5H213|H3BRF3|I3RSG8|Q6ZTQ5|Q96CZ2|Q9BWN6	Missense_Mutation	SNP	ENST00000359154.2	37	CCDS10885.1	.	.	.	.	.	.	.	.	.	.	G	18.45	3.627292	0.66901	.	.	ENSG00000198373	ENST00000359154;ENST00000448661;ENST00000356003;ENST00000544162;ENST00000542271	T;T;T;T	0.32515	1.45;1.45;1.45;1.48	6.07	6.07	0.98685	.	3.592490	0.00447	N	0.000099	T	0.29556	0.0737	N	0.24115	0.695	0.47737	D	0.9995	P	0.34780	0.468	B	0.31191	0.125	T	0.17623	-1.0363	9	.	.	.	.	17.7999	0.88584	0.0:0.0:1.0:0.0	.	281	O00308	WWP2_HUMAN	R	281;281;281;168;165	ENSP00000352069:G281R;ENSP00000396871:G281R;ENSP00000348283:G281R;ENSP00000445616:G165R	.	G	+	1	0	WWP2	68479580	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.845000	0.55880	2.884000	0.98904	0.655000	0.94253	GGA	.	.	none		0.622	WWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268954.1	NM_007014		A	69922079	G	A	69922079	3	1	27	1	0	0	0	0	1	0	0	0	17431	1001	35	2	867	2	WWP2	16	69922079	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	603930	69922079	20432674	799	11250											
FUK	197258	hgsc.bcm.edu	37	chr16	70512349	70512349	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggcaagacccgcctggctcGgaacctgctgcaggtgagct	7	7	14	13	2	0	2	0	1	0	1	1	3	0	3	3	4	4	5	3	4	2	0	rs17886060	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:70512349G>A	ENST00000288078.6	+	21	3048	c.2816G>A	c.(2815-2817)cGg>cAg	p.R939Q	FUK_ENST00000378912.2_Missense_Mutation_p.R945Q|FUK_ENST00000571514.1_Missense_Mutation_p.R430Q	NM_145059.2	NP_659496.2	Q8N0W3	FUK_HUMAN	fucokinase	939			R -> Q (in dbSNP:rs17886060). {ECO:0000269|Ref.3}.|R -> W (in dbSNP:rs17883248). {ECO:0000269|Ref.3}.			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)				CGCCTGGCTCGGAACCTGCTG	0.647													G|||	22	0.00439297	0.0008	0.0043	5008	,	,		18862	0.0		0.0109	False		,,,				2504	0.0072				p.R939Q		Atlas-SNP	.											.	FUK	72	.	0			c.G2816A						PASS	.	G	GLN/ARG	7,4041		0,7,2017	60	65	63		2816	5.7	1	16	dbSNP_124	63	120,8240		1,118,4061	yes	missense	FUK	NM_145059.2	43	1,125,6078	AA,AG,GG		1.4354,0.1729,1.0235	probably-damaging	939/1085	70512349	127,12281	2024	4180	6204	SO:0001583	missense	197258	exon21			TGGCTCGGAACCT		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	ENST00000288078.6:c.2816G>A	16.37:g.70512349G>A	ENSP00000288078:p.Arg939Gln	87	0	0		73	49	0.671233	NM_145059	Q5PSM3|Q5XKL6|Q6ZRA0|Q96MT9	Missense_Mutation	SNP	ENST00000288078.6	37	CCDS10891.2	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	G	16.72	3.200151	0.58126	0.001729	0.014354	ENSG00000157353	ENST00000288078;ENST00000378912;ENST00000538525	D;D	0.93712	-3.27;-3.27	5.65	5.65	0.86999	.	0.050215	0.85682	D	0.000000	D	0.96021	0.8704	M	0.86028	2.79	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74348	0.983;0.926;0.926	D	0.95082	0.8214	10	0.59425	D	0.04	-30.887	19.7405	0.96228	0.0:0.0:1.0:0.0	rs17886060;rs17886060	945;845;939	Q8N0W3-2;B2RDL5;Q8N0W3	.;.;FUK_HUMAN	Q	939;945;253	ENSP00000288078:R939Q;ENSP00000368192:R945Q	ENSP00000288078:R939Q	R	+	2	0	FUK	69069850	1.000000	0.71417	0.996000	0.52242	0.977000	0.68977	6.263000	0.72521	2.655000	0.90218	0.655000	0.94253	CGG	G|0.990;A|0.010	0.010	strong		0.647	FUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157291.2	NM_145059		A	70512349	G	A	70512349	3	1	27	1	0	0	0	0	1	0	0	0	6104	1116	39	1	2894	1	FUK	16	70512349	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	590270	70512349	19842404	800	11251											
CHST4	10164	hgsc.bcm.edu	37	chr16	71570847	71570847	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aagcagagcaccgcctggatGctgcacatggctgtgcggga	9	6	15	11	2	0	1	0	0	0	1	0	3	0	3	2	3	5	5	2	3	1	0	rs148657245	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:71570847G>A	ENST00000338482.5	+	3	610	c.267G>A	c.(265-267)atG>atA	p.M89I	CHST4_ENST00000572450.1_Missense_Mutation_p.M89I|RP11-510M2.5_ENST00000568523.1_RNA|CHST4_ENST00000539698.3_Missense_Mutation_p.M89I|ZNF19_ENST00000568446.1_Intron			Q8NCG5	CHST4_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 4	89					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|immune response (GO:0006955)|inflammatory response (GO:0006954)|leukocyte tethering or rolling (GO:0050901)|N-acetylglucosamine metabolic process (GO:0006044)|protein sulfation (GO:0006477)|sulfur compound metabolic process (GO:0006790)	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)			cervix(1)|kidney(3)|large_intestine(9)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	21						CCGCCTGGATGCTGCACATGG	0.582													G|||	17	0.00339457	0.0	0.0	5008	,	,		17368	0.0		0.0129	False		,,,				2504	0.0041				p.M89I		Atlas-SNP	.											.	CHST4	47	.	0			c.G267A						PASS	.	G	ILE/MET,ILE/MET	7,4389	12.9+/-30.5	0,7,2191	90	93	92		267,267	-2.5	0	16	dbSNP_134	92	95,8505	54.0+/-114.7	1,93,4206	yes	missense,missense	CHST4	NM_001166395.1,NM_005769.2	10,10	1,100,6397	AA,AG,GG		1.1047,0.1592,0.7849	benign,benign	89/387,89/387	71570847	102,12894	2198	4300	6498	SO:0001583	missense	10164	exon2			CTGGATGCTGCAC	AF131235	CCDS10902.1	16q22.2	2008-02-05			ENSG00000140835	ENSG00000140835		"Sulfotransferases, membrane-bound"	1972	protein-coding gene	gene with protein product						10330415	Standard	NM_001166395		Approved	HEC-GLCNAC-6-ST, LSST	uc002fao.3	Q8NCG5	OTTHUMG00000137592	ENST00000338482.5:c.267G>A	16.37:g.71570847G>A	ENSP00000341206:p.Met89Ile	181	0	0		205	131	0.639024	NM_001166395	Q8IV46|Q9Y5R3	Missense_Mutation	SNP	ENST00000338482.5	37	CCDS10902.1	11	0.005036630036630037	0	0.0	0	0.0	0	0.0	11	0.014511873350923483	G	3.265	-0.150351	0.06585	0.001592	0.011047	ENSG00000140835	ENST00000338482;ENST00000539698	D;D	0.81499	-1.5;-1.5	6.0	-2.45	0.06481	Sulfotransferase domain (1);	1.694150	0.02602	N	0.101171	T	0.55353	0.1915	N	0.14661	0.345	0.09310	N	1	B	0.12013	0.005	B	0.08055	0.003	T	0.43845	-0.9366	10	0.34782	T	0.22	-3.2597	3.7124	0.08425	0.1301:0.4236:0.2298:0.2165	.	89	Q8NCG5	CHST4_HUMAN	I	89	ENSP00000341206:M89I;ENSP00000441204:M89I	ENSP00000341206:M89I	M	+	3	0	CHST4	70128348	0.002000	0.14202	0.001000	0.08648	0.002000	0.02628	0.112000	0.15479	-0.681000	0.05204	-0.878000	0.02970	ATG	G|0.993;A|0.007	0.007	strong		0.582	CHST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268992.4	NM_005769		A	71570847	G	A	71570847	3	1	27	1	0	0	0	0	1	0	0	0	3408	1319	46	2	269	2	CHST4	16	71570847	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1058498	71570847	18783906	801	11252											
ZFHX3	463	hgsc.bcm.edu	37	chr16	72993397	72993397	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cccgccagggctgaggtattCgggaaagcctggtctgggcc	6	7	16	12	2	1	1	0	1	1	0	2	2	1	2	4	5	1	2	4	5	2	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:72993397C>T	ENST00000268489.5	-	2	1320	c.648G>A	c.(646-648)ccG>ccA	p.P216P	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	216					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)				CTGAGGTATTCGGGAAAGCCT	0.572																																					p.P216P		Atlas-SNP	.											.	ZFHX3	404	.	0			c.G648A						PASS	.						85	86	85					16																	72993397		2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			GGTATTCGGGAAA	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.648G>A	16.37:g.72993397C>T		96	0	0		100	38	0.38	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			.	.	none		0.572	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885		T	72993397	C	T	72993397	2	4	27	1	0	0	0	0	0	0	0	1	17649	871	31	1		1	ZFHX3	16	72993397	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1422550	72993397	17361356	802	11253											
CNTNAP4	85445	hgsc.bcm.edu	37	chr16	76461498	76461498	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgttcggatgtgcatacagTaagtgtttgtttatccaata	10	16	10	5	1	0	0	0	0	0	0	2	1	1	1	1	1	2	5	1	1	5	7			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:76461498T>G	ENST00000476707.1	+	3	686		c.e3+2		CNTNAP4_ENST00000469589.1_Splice_Site|CNTNAP4_ENST00000377504.4_Splice_Site|CNTNAP4_ENST00000478060.1_Splice_Site|CNTNAP4_ENST00000307431.8_Splice_Site			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4						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						GTGCATACAGTAAGTGTTTGT	0.388																																					.		Atlas-SNP	.											.	CNTNAP4	600	.	0			c.537+2T>G						PASS	.						76	71	73					16																	76461498		2198	4300	6498	SO:0001630	splice_region_variant	85445	exon4			ATACAGTAAGTGT	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.547+2T>G	16.37:g.76461498T>G		134	0	0		168	74	0.440476	NM_033401	E9PFZ6|Q86YZ7	Splice_Site	SNP	ENST00000476707.1	37		.	.	.	.	.	.	.	.	.	.	T	24.5	4.533056	0.85812	.	.	ENSG00000152910	ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707	.	.	.	4.98	4.98	0.66077	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8097	0.69985	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	CNTNAP4	75018999	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.720000	0.84759	2.232000	0.73038	0.533000	0.62120	.	.	.	none		0.388	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401	Intron	G	76461498	T	G	76461498	5	3	27	1	0	0	0	0	0	0	1	0	3651	1652	57	5	567	5	CNTNAP4	16	76461498	Splice_Site	SNP	T	TCGA-G8-6909-01A-11D-2210-10	3468101	76461498	13893255	803	11254											
IRF8	3394	hgsc.bcm.edu	37	chr16	85942659	85942659	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaaccagccacttggaagAcgaggttacgctgtgctttg	9	10	12	10	2	0	2	0	1	0	1	0	4	0	3	2	2	4	3	2	2	3	3	rs397514711		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:85942659A>G	ENST00000268638.5	+	3	660	c.238A>G	c.(238-240)Acg>Gcg	p.T80A	IRF8_ENST00000563180.1_Missense_Mutation_p.T80A	NM_002163.2	NP_002154.1	Q02556	IRF8_HUMAN	interferon regulatory factor 8	80			T -> A (in IMD32A; impairs transcriptional activity by disrupting the interaction between IRF8 and DNA). {ECO:0000269|PubMed:21524210}.		cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	24		Prostate(104;0.0771)				CACTTGGAAGACGAGGTTACG	0.458																																					p.T80A		Atlas-SNP	.											IRF8,NS,neuroblastoma,-1,1	IRF8	65	1	0			c.A238G						PASS	.						74	76	75					16																	85942659		2198	4300	6498	SO:0001583	missense	3394	exon3			TGGAAGACGAGGT	M91196	CCDS10956.1	16q24.1	2014-09-17	2004-11-12	2004-11-12	ENSG00000140968	ENSG00000140968			5358	protein-coding gene	gene with protein product		601565	"interferon consensus sequence binding protein 1"	ICSBP1		1460054, 11997525	Standard	NM_002163		Approved	IRF-8, ICSBP	uc002fjh.3	Q02556	OTTHUMG00000137648	ENST00000268638.5:c.238A>G	16.37:g.85942659A>G	ENSP00000268638:p.Thr80Ala	87	0	0		107	24	0.224299	NM_002163	A0AV82	Missense_Mutation	SNP	ENST00000268638.5	37	CCDS10956.1	.	.	.	.	.	.	.	.	.	.	A	19.11	3.763543	0.69878	.	.	ENSG00000140968	ENST00000268638	D	0.97688	-4.49	4.88	4.88	0.63580	Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (4);	0.046894	0.85682	D	0.000000	D	0.97791	0.9275	L	0.45470	1.425	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.91635	0.999;0.996	D	0.97383	0.9984	10	0.30854	T	0.27	-15.9347	14.7789	0.69751	1.0:0.0:0.0:0.0	.	80;80	B2R8V7;Q02556	.;IRF8_HUMAN	A	80	ENSP00000268638:T80A	ENSP00000268638:T80A	T	+	1	0	IRF8	84500160	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	8.780000	0.91799	1.973000	0.57446	0.397000	0.26171	ACG	.	.	none		0.458	IRF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269100.2	NM_002163		G	85942659	A	G	85942659	3	3	27	1	0	0	0	0	1	0	0	0	7845	275	10	3	244	3	IRF8	16	85942659	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	9481161	85942659	4412094	804	11255											
MC1R	4157	hgsc.bcm.edu	37	chr16	89985950	89985950	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggagcaacgtgctggagaCggccgtcatcctcctgctgg	6	7	15	13	4	1	1	1	0	0	1	3	3	3	2	3	4	4	3	3	4	1	0	rs34158934	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:89985950C>T	ENST00000555147.1	+	1	1664	c.284C>T	c.(283-285)aCg>aTg	p.T95M	RP11-566K11.4_ENST00000554623.1_RNA|TUBB3_ENST00000554444.1_5'Flank|TUBB3_ENST00000556922.1_Missense_Mutation_p.T95M|MC1R_ENST00000555427.1_Missense_Mutation_p.T95M|RP11-566K11.7_ENST00000570217.1_RNA	NM_002386.3	NP_002377.4	Q01726	MSHR_HUMAN	melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor)	95			T -> M (in dbSNP:rs34158934).		G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|intracellular signal transduction (GO:0035556)|melanin biosynthetic process (GO:0042438)|multicellular organismal development (GO:0007275)|negative regulation of tumor necrosis factor production (GO:0032720)|pigmentation (GO:0043473)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sensory perception of pain (GO:0019233)|UV protection (GO:0009650)|UV-damage excision repair (GO:0070914)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled peptide receptor activity (GO:0008528)|melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|ubiquitin protein ligase binding (GO:0031625)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	11		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)		GTGCTGGAGACGGCCGTCATC	0.627									Melanoma, Familial Clustering of				C|||	4	0.000798722	0.0023	0.0014	5008	,	,		19710	0.0		0.0	False		,,,				2504	0.0				p.T95M		Atlas-SNP	.											.	MC1R	20	.	0			c.C284T	GRCh37	CM062826	MC1R	M	rs34158934	PASS	.	C	MET/THR	3,4379		0,3,2188	46	56	52		284	3.9	0.8	16	dbSNP_126	52	5,8569		0,5,4282	yes	missense	MC1R	NM_002386.3	81	0,8,6470	TT,TC,CC		0.0583,0.0685,0.0617		95/318	89985950	8,12948	2191	4287	6478	SO:0001583	missense	4157	exon1	Familial Cancer Database		TGGAGACGGCCGT		CCDS56011.1	16q24.3	2012-10-05			ENSG00000258839	ENSG00000258839		"GPCR / Class A : Melanocortin receptors"	6929	protein-coding gene	gene with protein product		155555				8458079	Standard	NM_002386		Approved	MSH-R		Q01726		ENST00000555147.1:c.284C>T	16.37:g.89985950C>T	ENSP00000451605:p.Thr95Met	114	0	0		115	67	0.582609	NM_002386	Q66K38|Q6UR93|Q8WWX6|Q8WWX7|Q96I33|Q96RU4|Q9UBF7|Q9UN58|Q9UN59|Q9UN60|Q9UN61|Q9UN62	Missense_Mutation	SNP	ENST00000555147.1	37	CCDS56011.1	.	.	.	.	.	.	.	.	.	.	C	15.03	2.711952	0.48517	6.85E-4	5.83E-4	ENSG00000258947;ENSG00000258947;ENSG00000258839	ENST00000555427;ENST00000556922;ENST00000555147	T;T;T	0.01505	4.82;4.82;4.82	4.86	3.91	0.45181	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38959	U	0.001519	T	0.02727	0.0082	L	0.41824	1.3	0.45914	D	0.998756	P	0.47034	0.889	P	0.46796	0.527	T	0.64368	-0.6424	9	.	.	.	.	10.5142	0.44879	0.0:0.836:0.0:0.164	rs34158934	95	Q01726	MSHR_HUMAN	M	95	ENSP00000451760:T95M;ENSP00000451560:T95M;ENSP00000451605:T95M	.	T	+	2	0	MC1R;RP11-566K11.2	88513451	0.902000	0.30710	0.785000	0.31869	0.215000	0.24574	1.867000	0.39499	1.057000	0.40506	0.455000	0.32223	ACG	C|0.995;T|0.005	0.005	strong		0.627	MC1R-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412014.1	NM_002386		T	89985950	C	T	89985950	3	4	27	1	0	0	0	0	1	0	0	0	9372	536	19	1	286	1	MC1R	16	89985950	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	4043291	89985950	368803	805	11256											
DEF8	54849	hgsc.bcm.edu	37	chr16	90028509	90028509	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaccctctgctgttcagctaCgtggaggagctggtggagat	8	10	14	9	1	2	1	1	0	1	1	2	4	2	3	1	4	5	4	1	4	2	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr16:90028509C>T	ENST00000268676.7	+	9	1169	c.1080C>T	c.(1078-1080)taC>taT	p.Y360Y	DEF8_ENST00000563795.1_Silent_p.Y299Y|DEF8_ENST00000563594.1_Silent_p.Y299Y|DEF8_ENST00000563848.1_3'UTR|DEF8_ENST00000570182.1_Silent_p.Y289Y|DEF8_ENST00000569453.1_Silent_p.Y299Y|DEF8_ENST00000567874.1_Silent_p.Y239Y	NM_207514.2	NP_997397.1	Q6ZN54	DEFI8_HUMAN	differentially expressed in FDCP 8 homolog (mouse)	360					intracellular signal transduction (GO:0035556)		zinc ion binding (GO:0008270)			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)		TGTTCAGCTACGTGGAGGAGC	0.662																																					p.Y360Y		Atlas-SNP	.											.	DEF8	28	.	0			c.C1080T						PASS	.						44	36	39					16																	90028509		2198	4300	6498	SO:0001819	synonymous_variant	54849	exon9			CAGCTACGTGGAG	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.1080C>T	16.37:g.90028509C>T		78	0	0		107	74	0.691589	NM_207514	B3KT65|B4DK62|B4E0S9|B7Z3H6|H3BUG7|Q8N8N3|Q9NXL0	Silent	SNP	ENST00000268676.7	37	CCDS10989.1																																																																																			.	.	none		0.662	DEF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000272878.1	NM_207514		T	90028509	C	T	90028509	2	4	27	1	0	0	0	0	0	0	0	1	4389	547	19	1		1	DEF8	16	90028509	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	42559	90028509	326244	806	11257											
SCARF1	8578	hgsc.bcm.edu	37	chr17	1538714	1538714	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgggctttcggagcgggcTggagagctcccctgagcttc	4	10	15	12	2	0	2	0	1	0	1	3	4	1	3	2	4	3	4	2	4	0	3	rs61738531	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:1538714T>G	ENST00000263071.4	-	11	1880	c.1831A>C	c.(1831-1833)Agc>Cgc	p.S611R	SCARF1_ENST00000571272.1_3'UTR|SCARF1_ENST00000348987.3_Missense_Mutation_p.S525R	NM_003693.2|NM_145350.1	NP_003684.2|NP_663325.1	Q14162	SREC_HUMAN	scavenger receptor class F, member 1	611	Pro/Ser-rich.				cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|dendrite development (GO:0016358)|neuron remodeling (GO:0016322)|positive regulation of axon regeneration (GO:0048680)|positive regulation of neuron projection development (GO:0010976)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(3)|kidney(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CGGAGCGGGCTGGAGAGCTCC	0.677													T|||	55	0.0109824	0.0008	0.0101	5008	,	,		15189	0.001		0.0149	False		,,,				2504	0.0317				p.S611R		Atlas-SNP	.											.	SCARF1	46	.	0			c.A1831C						PASS	.	T	ARG/SER,,ARG/SER	21,4385	27.2+/-55.0	0,21,2182	51	55	53		1831,,1573	5.2	1	17	dbSNP_129	53	214,8386	89.2+/-151.4	3,208,4089	yes	missense,utr-3,missense	SCARF1	NM_003693.2,NM_145350.1,NM_145352.2	110,,110	3,229,6271	GG,GT,TT		2.4884,0.4766,1.8069	probably-damaging,,probably-damaging	611/831,,525/745	1538714	235,12771	2203	4300	6503	SO:0001583	missense	8578	exon11			GCGGGCTGGAGAG	D63483	CCDS11007.1, CCDS45564.1	17p13.3	2008-07-18			ENSG00000074660	ENSG00000074660			16820	protein-coding gene	gene with protein product	"scavenger receptor expressed by endothelial cells", "acetyl LDL receptor"	607873				9395444, 8590280	Standard	NM_003693		Approved	SREC, KIAA0149	uc002fsz.2	Q14162	OTTHUMG00000090555	ENST00000263071.4:c.1831A>C	17.37:g.1538714T>G	ENSP00000263071:p.Ser611Arg	88	0	0		77	22	0.285714	NM_003693	A8MQ05|O43701|Q8NHD2|Q8NHD3|Q8NHD4|Q8NHD5	Missense_Mutation	SNP	ENST00000263071.4	37	CCDS11007.1	17	0.007783882783882784	0	0.0	5	0.013812154696132596	1	0.0017482517482517483	11	0.014511873350923483	T	22.4	4.289498	0.80914	0.004766	0.024884	ENSG00000074660	ENST00000263071;ENST00000348987	T;T	0.37411	1.2;1.2	5.21	5.21	0.72293	.	0.124140	0.36628	N	0.002484	T	0.35364	0.0929	M	0.63428	1.95	0.27223	N	0.959619	D;P	0.63046	0.992;0.947	P;P	0.56648	0.803;0.622	T	0.43669	-0.9377	10	0.72032	D	0.01	-22.476	15.1104	0.72351	0.0:0.0:0.0:1.0	.	525;611	Q14162-2;Q14162	.;SREC_HUMAN	R	611;525	ENSP00000263071:S611R;ENSP00000323964:S525R	ENSP00000263071:S611R	S	-	1	0	SCARF1	1485464	1.000000	0.71417	0.998000	0.56505	0.954000	0.61252	4.194000	0.58393	1.965000	0.57142	0.454000	0.30748	AGC	T|0.984;G|0.016	0.016	strong		0.677	SCARF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207081.4	NM_003693		G	1538714	T	G	1538714	3	3	27	1	0	0	0	0	1	0	0	0	13898	1580	55	5	665	5	SCARF1	17	1538714	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10		1538714	79656496	807	11258											
ALOX15	246	hgsc.bcm.edu	37	chr17	4535314	4535314	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggcgggggcagccgcatcGtgcagggtgcattaggcacc	6	7	17	11	3	0	0	0	0	0	0	1	0	0	0	2	5	3	5	2	5	1	2	rs34210653	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:4535314G>A	ENST00000570836.1	-	14	1775	c.1679C>T	c.(1678-1680)aCg>aTg	p.T560M	ALOX15_ENST00000574640.1_Missense_Mutation_p.T521M|ALOX15_ENST00000545513.1_Missense_Mutation_p.T582M|ALOX15_ENST00000293761.3_Missense_Mutation_p.T560M			P16050	LOX15_HUMAN	arachidonate 15-lipoxygenase	560	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.		T -> M (loss of catalytic activity; dbSNP:rs34210653). {ECO:0000269|PubMed:17959182}.		apoptotic cell clearance (GO:0043277)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|cellular response to calcium ion (GO:0071277)|cellular response to interleukin-13 (GO:0035963)|hepoxilin biosynthetic process (GO:0051122)|inflammatory response (GO:0006954)|leukotriene metabolic process (GO:0006691)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxygenase pathway (GO:0019372)|negative regulation of adaptive immune response (GO:0002820)|ossification (GO:0001503)|phosphatidylethanolamine biosynthetic process (GO:0006646)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of engulfment of apoptotic cell (GO:1901074)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|lipid particle (GO:0005811)|membrane (GO:0016020)|plasma membrane (GO:0005886)	arachidonate 12-lipoxygenase activity (GO:0004052)|arachidonate 15-lipoxygenase activity (GO:0050473)|eoxin A4 synthase activity (GO:0097260)|iron ion binding (GO:0005506)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(5)	20				READ - Rectum adenocarcinoma(115;0.0327)		CAGCCGCATCGTGCAGGGTGC	0.607													G|||	63	0.0125799	0.0023	0.0663	5008	,	,		20270	0.0		0.0109	False		,,,				2504	0.0031				p.T560M		Atlas-SNP	.											.	ALOX15	70	.	0			c.C1679T	GRCh37	CM081155	ALOX15	M	rs34210653	PASS	.	G	MET/THR	17,4389	23.3+/-48.9	0,17,2186	59	54	56		1679	3.3	0.9	17	dbSNP_126	56	144,8456	72.0+/-134.6	1,142,4157	yes	missense	ALOX15	NM_001140.3	81	1,159,6343	AA,AG,GG		1.6744,0.3858,1.2379	probably-damaging	560/663	4535314	161,12845	2203	4300	6503	SO:0001583	missense	246	exon13			CGCATCGTGCAGG	M23892	CCDS11049.1	17p13.3	2010-09-24			ENSG00000161905	ENSG00000161905	1.13.11.33	"Arachidonate lipoxygenases"	433	protein-coding gene	gene with protein product		152392				1570320	Standard	NM_001140		Approved	15-LOX-1	uc002fyh.3	P16050	OTTHUMG00000090746	ENST00000570836.1:c.1679C>T	17.37:g.4535314G>A	ENSP00000458832:p.Thr560Met	61	0	0		63	32	0.507937	NM_001140	A8K2P4|B7ZA11|Q8N6R7|Q99657	Missense_Mutation	SNP	ENST00000570836.1	37	CCDS11049.1	32	0.014652014652014652	2	0.0040650406504065045	20	0.055248618784530384	0	0.0	10	0.013192612137203167	G	18.48	3.632894	0.67015	0.003858	0.016744	ENSG00000161905	ENST00000293761;ENST00000545513	T;T	0.78126	-1.15;-1.15	4.33	3.35	0.38373	Lipoxygenase, C-terminal (3);	0.064395	0.64402	D	0.000011	T	0.51924	0.1703	M	0.85197	2.74	0.35074	D	0.762752	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.998;0.999	T	0.80529	-0.1342	10	0.87932	D	0	-1.2213	10.1417	0.42738	0.0:0.2025:0.7975:0.0	rs34210653	582;521;560	F5H0G8;B7ZA11;P16050	.;.;LOX15_HUMAN	M	560;582	ENSP00000293761:T560M;ENSP00000439855:T582M	ENSP00000293761:T560M	T	-	2	0	ALOX15	4482063	1.000000	0.71417	0.938000	0.37757	0.976000	0.68499	4.166000	0.58203	1.028000	0.39785	0.655000	0.94253	ACG	G|0.988;A|0.012	0.012	strong		0.607	ALOX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207487.2			A	4535314	G	A	4535314	3	1	27	1	0	0	0	0	1	0	0	0	538	1145	40	1	317	1	ALOX15	17	4535314	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2996600	4535314	76659896	808	11259											
MINK1	50488	hgsc.bcm.edu	37	chr17	4797910	4797910	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	accagcctggaggcagtgggGacagcatccccatcacaggt	10	5	13	13	0	1	0	1	0	0	0	2	2	2	2	4	5	2	2	4	5	0	0	rs79940062	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:4797910G>A	ENST00000355280.6	+	24	3095	c.2899G>A	c.(2899-2901)Gac>Aac	p.D967N	MINK1_ENST00000347992.7_Missense_Mutation_p.D938N|MINK1_ENST00000453408.3_Missense_Mutation_p.D947N	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						AGGCAGTGGGGACAGCATCCC	0.612													G|||	28	0.00559105	0.0008	0.0029	5008	,	,		20491	0.001		0.0179	False		,,,				2504	0.0061				p.D967N		Atlas-SNP	.											.	MINK1	110	.	0			c.G2899A						PASS	.	G	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	16,4312		0,16,2148	47	51	50		2839,2788,2899,2812	5.3	1	17	dbSNP_133	50	160,8386		1,158,4114	yes	missense,missense,missense,missense	MINK1	NM_001024937.3,NM_015716.4,NM_153827.4,NM_170663.4	23,23,23,23	1,174,6262	AA,AG,GG		1.8722,0.3697,1.3671	benign,benign,benign,benign	947/1313,930/1296,967/1333,938/1304	4797910	176,12698	2164	4273	6437	SO:0001583	missense	50488	exon24			AGTGGGGACAGCA	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.2899G>A	17.37:g.4797910G>A	ENSP00000347427:p.Asp967Asn	103	0	0		95	40	0.421053	NM_153827		Missense_Mutation	SNP	ENST00000355280.6	37	CCDS45588.1	13	0.005952380952380952	1	0.0020325203252032522	1	0.0027624309392265192	1	0.0017482517482517483	10	0.013192612137203167	G	21.1	4.091253	0.76756	0.003697	0.018722	ENSG00000141503	ENST00000355280;ENST00000453408;ENST00000347992	T;T;T	0.74315	-0.83;-0.83;-0.83	5.26	5.26	0.73747	.	0.053262	0.64402	D	0.000001	T	0.73497	0.3594	M	0.65498	2.005	0.58432	D	0.999999	P;D;D;D	0.67145	0.952;0.996;0.993;0.996	P;D;D;D	0.73708	0.643;0.981;0.956;0.981	T	0.75451	-0.3313	10	0.22109	T	0.4	.	16.4095	0.83703	0.0:0.0:1.0:0.0	.	930;947;967;938	Q8N4C8-2;Q8N4C8-4;Q8N4C8;Q8N4C8-3	.;.;MINK1_HUMAN;.	N	967;947;938	ENSP00000347427:D967N;ENSP00000406487:D947N;ENSP00000269296:D938N	ENSP00000269296:D938N	D	+	1	0	MINK1	4738686	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.679000	0.74513	2.735000	0.93741	0.655000	0.94253	GAC	G|0.993;A|0.007	0.007	strong		0.612	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439801.1	NM_015716		A	4797910	G	A	4797910	3	1	27	1	0	0	0	0	1	0	0	0	9596	1174	41	2	2760	2	MINK1	17	4797910	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	262596	4797910	76397300	809	11260											
DHX33	56919	hgsc.bcm.edu	37	chr17	5347788	5347788	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgtgagccaggcagcggcGgacactctccacgtctcctc	6	7	12	16	3	2	1	0	1	2	0	5	2	2	2	3	3	2	2	3	3	0	0	rs75426953	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:5347788G>A	ENST00000225296.3	-	12	2061	c.1861C>T	c.(1861-1863)Cgc>Tgc	p.R621C	DHX33_ENST00000433302.3_Missense_Mutation_p.R397C	NM_001199699.1|NM_020162.3	NP_001186628.1|NP_064547.2	Q9H6R0	DHX33_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 33	621					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						AGGCAGCGGCGGACACTCTCC	0.607													G|||	35	0.00698882	0.0008	0.0086	5008	,	,		19061	0.001		0.0239	False		,,,				2504	0.0031				p.R621C		Atlas-SNP	.											DHX33,NS,carcinoma,0,1	DHX33	41	1	0			c.C1861T						scavenged	.	G	CYS/ARG,CYS/ARG	24,4382	30.8+/-60.4	1,22,2180	74	69	70		1342,1861	4.6	1	17	dbSNP_131	70	203,8397	88.4+/-150.7	2,199,4099	yes	missense,missense	DHX33	NM_001199699.1,NM_020162.3	180,180	3,221,6279	AA,AG,GG		2.3605,0.5447,1.7453	probably-damaging,probably-damaging	448/535,621/708	5347788	227,12779	2203	4300	6503	SO:0001583	missense	56919	exon12			AGCGGCGGACACT	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.1861C>T	17.37:g.5347788G>A	ENSP00000225296:p.Arg621Cys	119	1	0.00840336		96	54	0.5625	NM_020162	B4DHF9|Q4G149|Q5CZ73|Q9H5M9	Missense_Mutation	SNP	ENST00000225296.3	37	CCDS11072.1	24	0.01098901098901099	1	0.0020325203252032522	5	0.013812154696132596	1	0.0017482517482517483	17	0.022427440633245383	G	25.8	4.678553	0.88542	0.005447	0.023605	ENSG00000005100	ENST00000225296;ENST00000433302	T;T	0.02890	4.12;4.12	4.59	4.59	0.56863	Domain of unknown function DUF1605 (1);	0.000000	0.85682	D	0.000000	T	0.08846	0.0219	M	0.85373	2.75	0.80722	D	1	D;P	0.89917	1.0;0.626	D;B	0.81914	0.995;0.287	T	0.00235	-1.1892	10	0.66056	D	0.02	.	16.9197	0.86161	0.0:0.0:1.0:0.0	.	397;621	Q05BE5;Q9H6R0	.;DHX33_HUMAN	C	621;397	ENSP00000225296:R621C;ENSP00000413779:R397C	ENSP00000225296:R621C	R	-	1	0	DHX33	5288512	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	9.073000	0.93992	2.548000	0.85928	0.561000	0.74099	CGC	A|0.014;C|0.000;G|0.986	0.014	strong		0.607	DHX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219826.2	NM_020162		A	5347788	G	A	5347788	3	1	27	1	0	0	0	0	1	0	0	0	4508	1116	39	1	266	1	DHX33	17	5347788	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	549878	5347788	75847422	810	11261											
GUCY2D	3000	hgsc.bcm.edu	37	chr17	7909890	7909890	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gacacggacgcggcgggagaCcggctttttgccacatacat	9	7	13	12	5	0	1	0	0	0	1	0	4	0	2	2	4	2	1	2	4	1	3	rs61749678	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:7909890C>T	ENST00000254854.4	+	4	1386	c.1236C>T	c.(1234-1236)gaC>gaT	p.D412D		NM_000180.3	NP_000171.1	Q02846	GUC2D_HUMAN	guanylate cyclase 2D, membrane (retina-specific)	412					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)				CGGCGGGAGACCGGCTTTTTG	0.677													C|||	2	0.000399361	0.0	0.0	5008	,	,		13052	0.0		0.002	False		,,,				2504	0.0				p.D412D		Atlas-SNP	.											.	GUCY2D	82	.	0			c.C1236T						PASS	.	C		0,4406		0,0,2203	30	29	29	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1236	2	0.2	17	dbSNP_129	29	9,8591	6.4+/-24.3	0,9,4291	no	coding-synonymous	GUCY2D	NM_000180.3		0,9,6494	TT,TC,CC		0.1047,0.0,0.0692		412/1104	7909890	9,12997	2203	4300	6503	SO:0001819	synonymous_variant	3000	exon4			GGGAGACCGGCTT	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.1236C>T	17.37:g.7909890C>T		91	0	0		79	37	0.468354	NM_000180	Q6LEA7	Silent	SNP	ENST00000254854.4	37	CCDS11127.1																																																																																			C|0.999;T|0.001	0.001	strong		0.677	GUCY2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226973.2			T	7909890	C	T	7909890	2	4	27	1	0	0	0	0	0	0	0	1	6906	506	18	2		2	GUCY2D	17	7909890	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2562102	7909890	73285320	811	11262											
ALOX15B	247	hgsc.bcm.edu	37	chr17	7950009	7950009	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgatcccgcacacccgataCaccctgcacatcaacacact	12	6	4	19	2	1	1	1	1	0	0	2	2	2	1	3	0	3	2	3	0	2	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:7950009C>G	ENST00000380183.4	+	9	1363	c.1224C>G	c.(1222-1224)taC>taG	p.Y408*	ALOX15B_ENST00000380173.2_Intron|ALOX15B_ENST00000573359.1_Intron|ALOX15B_ENST00000572022.1_Nonsense_Mutation_p.Y408*	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	408	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						ACACCCGATACACCCTGCACA	0.627																																					p.Y408X		Atlas-SNP	.											.	ALOX15B	66	.	0			c.C1224G						PASS	.						64	54	57					17																	7950009		2203	4300	6503	SO:0001587	stop_gained	247	exon9			CCGATACACCCTG	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.1224C>G	17.37:g.7950009C>G	ENSP00000369530:p.Tyr408*	86	0	0		61	31	0.508197	NM_001141	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Nonsense_Mutation	SNP	ENST00000380183.4	37	CCDS11128.1	.	.	.	.	.	.	.	.	.	.	C	16.09	3.025494	0.54683	.	.	ENSG00000179593	ENST00000380183	.	.	.	4.99	-2.88	0.05682	.	0.264891	0.39020	N	0.001493	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.1679	11.9463	0.52930	0.0:0.5497:0.0:0.4503	.	.	.	.	X	408	.	ENSP00000369530:Y408X	Y	+	3	2	ALOX15B	7890734	0.222000	0.23652	0.004000	0.12327	0.007000	0.05969	0.543000	0.23237	-0.334000	0.08463	-0.140000	0.14226	TAC	.	.	none		0.627	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2			G	7950009	C	G	7950009	4	3	27	1	0	0	0	0	0	1	0	0	539	489	17	4	1258	4	ALOX15B	17	7950009	Nonsense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	40119	7950009	73245201	812	11263											
USP43	124739	hgsc.bcm.edu	37	chr17	9604775	9604775	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catcctcatcatccacctcaAaaggttctgccaggtgggcg	9	9	9	14	1	4	0	3	0	1	0	6	0	6	0	4	3	1	1	4	3	2	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:9604775A>G	ENST00000285199.7	+	12	1865	c.1769A>G	c.(1768-1770)aAa>aGa	p.K590R	USP43_ENST00000570827.2_3'UTR|USP43_ENST00000570475.1_Missense_Mutation_p.K590R	NM_001267576.1|NM_153210.4	NP_001254505.1|NP_694942.3	Q70EL4	UBP43_HUMAN	ubiquitin specific peptidase 43	590	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						ATCCACCTCAAAAGGTTCTGC	0.567																																					p.K590R		Atlas-SNP	.											.	USP43	65	.	0			c.A1769G						PASS	.						34	36	36					17																	9604775		2123	4249	6372	SO:0001583	missense	124739	exon12			ACCTCAAAAGGTT	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.1769A>G	17.37:g.9604775A>G	ENSP00000285199:p.Lys590Arg	76	0	0		44	7	0.159091	NM_001267576	A6NDT9|B7ZLT9|B7ZVX5|Q8N2C5|Q96DQ6	Missense_Mutation	SNP	ENST00000285199.7	37	CCDS45610.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.284577	0.80803	.	.	ENSG00000154914	ENST00000285199	T	0.39229	1.09	5.12	5.12	0.69794	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.72867	0.3514	H	0.94964	3.605	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;0.999;1.0;1.0	T	0.81026	-0.1119	10	0.87932	D	0	-15.7098	13.1508	0.59488	1.0:0.0:0.0:0.0	.	590;279;590;102	B7ZVX5;Q70EL4-3;Q70EL4;Q70EL4-2	.;.;UBP43_HUMAN;.	R	590	ENSP00000285199:K590R	ENSP00000285199:K590R	K	+	2	0	USP43	9545500	1.000000	0.71417	0.691000	0.30163	0.845000	0.48019	8.748000	0.91615	2.040000	0.60383	0.460000	0.39030	AAA	.	.	none		0.567	USP43-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439855.3	NM_153210		G	9604775	A	G	9604775	3	3	27	1	0	0	0	0	1	0	0	0	17089	14	1	3	1815	3	USP43	17	9604775	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	1654766	9604775	71590435	813	11264											
MYH1	4619	hgsc.bcm.edu	37	chr17	10401064	10401064	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agaataccttatcaaagttcCtttgctttttgtccagggcg	9	15	8	9	1	1	1	1	0	0	1	3	1	3	1	3	1	2	2	3	1	4	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:10401064C>A	ENST00000226207.5	-	31	4446	c.4352G>T	c.(4351-4353)aGg>aTg	p.R1451M	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	1451				R -> T (in Ref. 4; CAA27380). {ECO:0000305}.	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						ATCAAAGTTCCTTTGCTTTTT	0.443																																					p.R1451M		Atlas-SNP	.											.	MYH1	403	.	0			c.G4352T						PASS	.						119	117	118					17																	10401064		2203	4300	6503	SO:0001583	missense	4619	exon31			AAGTTCCTTTGCT		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.4352G>T	17.37:g.10401064C>A	ENSP00000226207:p.Arg1451Met	166	0	0		155	40	0.258065	NM_005963	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	37	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	C	16.60	3.169376	0.57584	.	.	ENSG00000109061	ENST00000226207;ENST00000379814	T	0.80393	-1.37	5.65	5.65	0.86999	Myosin tail (1);	0.138860	0.32593	U	0.005888	D	0.91686	0.7372	H	0.96748	3.875	0.41280	D	0.986904	D	0.71674	0.998	D	0.70016	0.967	D	0.92699	0.6173	10	0.87932	D	0	.	7.7121	0.28684	0.0:0.8062:0.0:0.1938	.	1451	P12882	MYH1_HUMAN	M	1451;540	ENSP00000226207:R1451M	ENSP00000226207:R1451M	R	-	2	0	MYH1	10341789	0.929000	0.31497	1.000000	0.80357	0.903000	0.53119	1.648000	0.37271	2.811000	0.96726	0.655000	0.94253	AGG	.	.	none		0.443	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		A	10401064	C	A	10401064	3	1	27	1	0	0	0	0	1	0	0	0	10038	681	24	4	1507	4	MYH1	17	10401064	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	796289	10401064	70794146	814	11265											
DNAH9	1770	hgsc.bcm.edu	37	chr17	11543610	11543610	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctccccggtgcacaagaacAtgcccaccgtggctggcggc	7	6	12	16	3	1	1	0	0	1	1	2	1	1	1	4	4	3	2	4	4	2	0	rs61740059	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:11543610A>G	ENST00000262442.4	+	10	1878	c.1810A>G	c.(1810-1812)Atg>Gtg	p.M604V	DNAH9_ENST00000454412.2_Missense_Mutation_p.M604V	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	604	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)		GCACAAGAACATGCCCACCGT	0.602													A|||	67	0.0133786	0.0015	0.0216	5008	,	,		18384	0.0		0.0219	False		,,,				2504	0.0286				p.M604V		Atlas-SNP	.											.	DNAH9	695	.	0			c.A1810G						PASS	.	A	VAL/MET	16,4390	24.3+/-50.5	0,16,2187	130	123	125		1810	5.4	1	17	dbSNP_129	125	277,8323	104.2+/-165.2	5,267,4028	yes	missense	DNAH9	NM_001372.3	21	5,283,6215	GG,GA,AA		3.2209,0.3631,2.2528	possibly-damaging	604/4487	11543610	293,12713	2203	4300	6503	SO:0001583	missense	1770	exon10			AAGAACATGCCCA	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.1810A>G	17.37:g.11543610A>G	ENSP00000262442:p.Met604Val	73	0	0		66	28	0.424242	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	23	0.010531135531135532	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	17	0.022427440633245383	A	18.65	3.669200	0.67814	0.003631	0.032209	ENSG00000007174	ENST00000262442;ENST00000454412	T;T	0.55930	0.49;0.49	5.4	5.4	0.78164	Dynein heavy chain, domain-1 (1);	0.554792	0.19401	N	0.115180	T	0.47358	0.1441	M	0.86268	2.805	0.80722	D	1	P	0.52316	0.952	P	0.56127	0.792	T	0.66352	-0.5945	10	0.52906	T	0.07	.	13.6437	0.62267	1.0:0.0:0.0:0.0	rs61740059	604	Q9NYC9	DYH9_HUMAN	V	604	ENSP00000262442:M604V;ENSP00000414874:M604V	ENSP00000262442:M604V	M	+	1	0	DNAH9	11484335	1.000000	0.71417	1.000000	0.80357	0.861000	0.49209	5.050000	0.64251	2.049000	0.60858	0.528000	0.53228	ATG	A|0.981;G|0.019	0.019	strong		0.602	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		G	11543610	A	G	11543610	3	3	27	1	0	0	0	0	1	0	0	0	4610	217	8	3	1848	3	DNAH9	17	11543610	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	1142546	11543610	69651600	815	11266											
FBXW10	10517	hgsc.bcm.edu	37	chr17	18682351	18682352	+	Frame_Shift_Del	DEL	AA	AA	-																															cagccaccctgtctcttaagAaagaacggcctcgcatctat																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	AA	AA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:18682351_18682352delAA	ENST00000395665.4	+	14	3120_3121	c.2899_2900delAA	c.(2899-2901)aaafs	p.K967fs	FBXW10_ENST00000301938.4_Frame_Shift_Del_p.K914fs|TVP23B_ENST00000307767.8_5'Flank|FBXW10_ENST00000308799.4_Frame_Shift_Del_p.K976fs|TVP23B_ENST00000476139.1_5'Flank|FBXW10_ENST00000395667.1_Frame_Shift_Del_p.K966fs|TVP23B_ENST00000574226.1_5'Flank			Q5XX13	FBW10_HUMAN	F-box and WD repeat domain containing 10	967								p.K966fs*10(1)		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						GTCTCTTAAGAAAGAACGGCCT	0.53																																					p.966_967del		Atlas-Indel	.											.	FBXW10	82	.	1	Deletion - Frameshift(1)	skin(1)	c.2898_2899del						PASS	.			6,4034		2,2,2016						1.3	0.5			20	27,7731		6,15,3858	no	frameshift	FBXW10	NM_031456.3		8,17,5874	A1A1,A1R,RR		0.348,0.1485,0.2797				33,11765				SO:0001589	frameshift_variant	10517	exon14			.	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.2899_2900delAA	17.37:g.18682351_18682352delAA	ENSP00000379025:p.Lys967fs	343	0	0		153	43	0.281046	NM_001267585	C9JRY8|C9JZD7|Q8TC00|Q9H0F0	Frame_Shift_Del	DEL	ENST00000395665.4	37	CCDS11199.3																																																																																			.	.	none		0.53	FBXW10-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313531.2	NM_031456		-	18682352	AA	-	18682351	7	5	27	1	0	1	0	1	0	0	0	0	5771	247	9	0	2950	0	FBXW10	17	18682351	Frame_Shift_Del	DEL	AA	TCGA-G8-6909-01A-11D-2210-10	7138741	18682351	62512859	816	11267											
ULK2	9706	hgsc.bcm.edu	37	chr17	19720109	19720109	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaccaaaacaaagtcatccGtgtcacaagaagagttcttg	15	8	8	10	1	3	2	2	0	1	2	4	2	4	2	2	0	1	2	2	0	5	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:19720109G>A	ENST00000395544.4	-	13	1548	c.1049C>T	c.(1048-1050)aCg>aTg	p.T350M	ULK2_ENST00000580130.1_Intron|ULK2_ENST00000361658.2_Missense_Mutation_p.T350M	NM_014683.3	NP_055498.3	Q8IYT8	ULK2_HUMAN	unc-51 like autophagy activating kinase 2	350					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)					AAAGTCATCCGTGTCACAAGA	0.408																																					p.T350M		Atlas-SNP	.											.	ULK2	142	.	0			c.C1049T						PASS	.						127	116	120					17																	19720109		2203	4300	6503	SO:0001583	missense	9706	exon13			TCATCCGTGTCAC	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.1049C>T	17.37:g.19720109G>A	ENSP00000378914:p.Thr350Met	161	0	0		113	17	0.150442	NM_001142610	A8MY69|O75119	Missense_Mutation	SNP	ENST00000395544.4	37	CCDS11213.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.333603	0.81801	.	.	ENSG00000083290	ENST00000361658;ENST00000395544	T;T	0.76709	-1.04;-1.04	5.47	4.5	0.54988	.	0.000000	0.85682	D	0.000000	D	0.86859	0.6034	M	0.73962	2.25	0.48762	D	0.999707	D	0.89917	1.0	D	0.83275	0.996	D	0.88117	0.2829	10	0.87932	D	0	-8.4158	13.0776	0.59095	0.0771:0.0:0.9229:0.0	.	350	Q8IYT8	ULK2_HUMAN	M	350	ENSP00000354877:T350M;ENSP00000378914:T350M	ENSP00000354877:T350M	T	-	2	0	ULK2	19660701	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.097000	0.76967	1.281000	0.44480	0.557000	0.71058	ACG	.	.	none		0.408	ULK2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132375.2	NM_014683		A	19720109	G	A	19720109	3	1	27	1	0	0	0	0	1	0	0	0	16991	1145	40	1	2121	1	ULK2	17	19720109	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1037758	19720109	61475101	817	11268											
TMEM97	27346	hgsc.bcm.edu	37	chr17	26646320	26646320	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgctgggcctctacttcCtcagccacatccccatcacc	6	9	7	19	0	3	0	2	0	1	0	5	0	5	0	6	2	3	2	6	2	1	2	rs202198126		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:26646320C>G	ENST00000226230.6	+	1	200	c.55C>G	c.(55-57)Ctc>Gtc	p.L19V	TMEM97_ENST00000583381.1_Intron|TMEM97_ENST00000336687.6_5'Flank|TMEM97_ENST00000582113.1_Missense_Mutation_p.L19V	NM_014573.2	NP_055388.2	Q5BJF2	TMM97_HUMAN	transmembrane protein 97	19					cholesterol homeostasis (GO:0042632)|regulation of cell growth (GO:0001558)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)				endometrium(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	6	all_lung(13;0.000238)|Lung NSC(42;0.000789)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)		CCTCTACTTCCTCAGCCACAT	0.672																																					p.L19V		Atlas-SNP	.											.	TMEM97	27	.	0			c.C55G						PASS	.	C	VAL/LEU	0,4096		0,0,2048	24	31	28		55	2.1	1	17		28	4,8312		0,4,4154	no	missense	TMEM97	NM_014573.2	32	0,4,6202	GG,GC,CC		0.0481,0.0,0.0322	benign	19/177	26646320	4,12408	2048	4158	6206	SO:0001583	missense	27346	exon1			TACTTCCTCAGCC	BC091504	CCDS11226.2	17q11.2	2014-01-28			ENSG00000109084	ENSG00000109084			28106	protein-coding gene	gene with protein product		612912				7694637, 15375745	Standard	NM_014573		Approved	MAC30	uc002hat.3	Q5BJF2	OTTHUMG00000132497	ENST00000226230.6:c.55C>G	17.37:g.26646320C>G	ENSP00000226230:p.Leu19Val	210	0	0		196	88	0.44898	NM_014573	B4DS02|Q07823	Missense_Mutation	SNP	ENST00000226230.6	37	CCDS11226.2	.	.	.	.	.	.	.	.	.	.	C	0.581	-0.836976	0.02692	0.0	4.81E-4	ENSG00000109084	ENST00000226230	.	.	.	5.41	2.06	0.26882	.	0.329557	0.33534	N	0.004806	T	0.36663	0.0975	L	0.31664	0.95	0.80722	D	1	B	0.10296	0.003	B	0.16289	0.015	T	0.21484	-1.0244	9	0.02654	T	1	-18.6822	9.5507	0.39308	0.0:0.4926:0.4306:0.0767	.	19	Q5BJF2	TMM97_HUMAN	V	19	.	ENSP00000226230:L19V	L	+	1	0	TMEM97	23670447	0.921000	0.31238	1.000000	0.80357	0.020000	0.10135	0.970000	0.29383	0.786000	0.33708	0.561000	0.74099	CTC	C|0.999;G|0.001	0.001	weak		0.672	TMEM97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255675.2	NM_014573		G	26646320	C	G	26646320	3	3	27	1	0	0	0	0	1	0	0	0	16239	681	24	4	57	4	TMEM97	17	26646320	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	6926211	26646320	54548890	818	11269											
PIGS	94005	hgsc.bcm.edu	37	chr17	26881923	26881923	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgatcttgcccagaagctgCgccagggaggtaagggtggt	8	8	16	9	1	1	2	0	1	1	1	1	3	1	3	2	4	3	2	2	4	2	2	rs146249165	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:26881923C>T	ENST00000308360.7	-	11	1713	c.1338G>A	c.(1336-1338)gcG>gcA	p.A446A	PIGS_ENST00000395346.2_Silent_p.A438A|PIGS_ENST00000543734.1_Silent_p.A385A|UNC119_ENST00000301032.4_5'Flank|UNC119_ENST00000335765.4_5'Flank	NM_033198.3	NP_149975.1	Q96S52	PIGS_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class S	446					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)					CCAGAAGCTGCGCCAGGGAGG	0.587																																					p.A446A		Atlas-SNP	.											.	PIGS	42	.	0			c.G1338A						PASS	.	C		0,4406		0,0,2203	123	101	109		1338	-2.2	1	17	dbSNP_134	109	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	PIGS	NM_033198.3		0,3,6500	TT,TC,CC		0.0349,0.0,0.0231		446/556	26881923	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	94005	exon11			AAGCTGCGCCAGG		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.1338G>A	17.37:g.26881923C>T		134	0	0		111	53	0.477477	NM_033198	Q6UVX6	Silent	SNP	ENST00000308360.7	37	CCDS11235.1																																																																																			C|1.000;T|0.000	0.000	strong		0.587	PIGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255833.3	NM_033198		T	26881923	C	T	26881923	2	4	27	1	0	0	0	0	0	0	0	1	11907	755	27	1		1	PIGS	17	26881923	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	235603	26881923	54313287	819	11270											
PIPOX	51268	hgsc.bcm.edu	37	chr17	27371919	27371919	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagctcccatggacaaagcCggataatccgaaaggcgtac	14	5	11	11	3	0	0	0	0	0	0	2	4	2	2	3	3	3	2	3	3	5	2	rs543013733		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:27371919C>T	ENST00000323372.4	+	2	483	c.157C>T	c.(157-159)Cgg>Tgg	p.R53W	PIPOX_ENST00000583215.1_3'UTR	NM_016518.2	NP_057602.2	Q9P0Z9	SOX_HUMAN	pipecolic acid oxidase	53					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)	TGGACAAAGCCGGATAATCCG	0.517																																					p.R53W		Atlas-SNP	.											PIPOX,NS,carcinoma,-1,1	PIPOX	42	1	0			c.C157T						PASS	.						123	108	113					17																	27371919		2203	4300	6503	SO:0001583	missense	51268	exon2			CAAAGCCGGATAA	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.157C>T	17.37:g.27371919C>T	ENSP00000317721:p.Arg53Trp	109	0	0		108	18	0.166667	NM_016518	B3KNH0|Q96H28|Q9C070	Missense_Mutation	SNP	ENST00000323372.4	37	CCDS11248.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.484929	0.84854	.	.	ENSG00000179761	ENST00000323372	D	0.81908	-1.55	5.8	4.82	0.62117	FAD dependent oxidoreductase (1);	0.167524	0.51477	D	0.000093	D	0.90556	0.7040	M	0.90542	3.125	0.80722	D	1	D	0.67145	0.996	P	0.58520	0.84	D	0.91764	0.5422	10	0.66056	D	0.02	-12.3601	13.0057	0.58703	0.0:0.9201:0.0:0.0798	.	53	Q9P0Z9	SOX_HUMAN	W	53	ENSP00000317721:R53W	ENSP00000317721:R53W	R	+	1	2	PIPOX	24396045	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.408000	0.44574	2.740000	0.93945	0.650000	0.86243	CGG	.	.	none		0.517	PIPOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255954.1	NM_016518		T	27371919	C	T	27371919	3	4	27	1	0	0	0	0	1	0	0	0	11952	643	23	1	163	1	PIPOX	17	27371919	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	489996	27371919	53823291	820	11271											
GIT1	28964	hgsc.bcm.edu	37	chr17	27903998	27903998	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtcactctggctccgcagAgacagctcgaggttgtctga	8	9	13	11	2	3	2	1	1	2	1	5	4	4	2	1	3	1	4	1	3	0	1	rs144787773		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:27903998A>C	ENST00000225394.3	-	12	1358	c.1110T>G	c.(1108-1110)tcT>tcG	p.S370S	GIT1_ENST00000394869.3_Silent_p.S379S|GIT1_ENST00000579937.1_Silent_p.S370S|GIT1_ENST00000581348.1_Silent_p.S379S|RP11-68I3.2_ENST00000581474.1_RNA	NM_014030.3	NP_054749.2	Q9Y2X7	GIT1_HUMAN	G protein-coupled receptor kinase interacting ArfGAP 1	370	PTK2/FAK1-binding. {ECO:0000250}.				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)		GGCTCCGCAGAGACAGCTCGA	0.627																																					p.S379S	Colon(81;41 1719 20078 35068)	Atlas-SNP	.											.	GIT1	84	.	0			c.T1137G						PASS	.						48	49	49					17																	27903998		2203	4300	6503	SO:0001819	synonymous_variant	28964	exon13			CCGCAGAGACAGC	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.1110T>G	17.37:g.27903998A>C		36	0	0		31	19	0.612903	NM_001085454	B4DGU9|B4DSV3|Q86SS0|Q9BRJ4	Silent	SNP	ENST00000225394.3	37	CCDS11250.1																																																																																			A|0.998;C|0.002	0.002	weak		0.627	GIT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256073.1	NM_014030		C	27903998	A	C	27903998	2	2	27	1	0	0	0	0	0	0	0	1	6404	291	11	5		5	GIT1	17	27903998	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	532079	27903998	53291212	821	11272											
RFFL	117584	hgsc.bcm.edu	37	chr17	33348541	33348541	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggggacaaggtggaggcaCgagtcctgtcctcctgggag	7	7	17	10	1	0	0	0	0	0	0	3	4	3	3	3	6	0	1	3	6	1	0	rs34747500	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:33348541C>T	ENST00000315249.7	-	3	662	c.440G>A	c.(439-441)cGt>cAt	p.R147H	RAD51L3-RFFL_ENST00000593039.1_Intron|RFFL_ENST00000413582.2_Missense_Mutation_p.R147H|RFFL_ENST00000268850.7_Missense_Mutation_p.R147H|RFFL_ENST00000584655.1_Missense_Mutation_p.R147H|RFFL_ENST00000415395.2_Missense_Mutation_p.R147H|RFFL_ENST00000447669.2_Missense_Mutation_p.R147H|RFFL_ENST00000378516.2_Missense_Mutation_p.R147H|RFFL_ENST00000394597.2_Missense_Mutation_p.R147H					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)		GGTGGAGGCACGAGTCCTGTC	0.582													C|||	68	0.0135783	0.0356	0.0029	5008	,	,		19710	0.0188		0.0	False		,,,				2504	0.0				p.R147H		Atlas-SNP	.											.	RFFL	27	.	0			c.G440A						PASS	.	C	HIS/ARG	124,4282	91.6+/-130.3	3,118,2082	81	65	70		440	-4.3	0.4	17	dbSNP_126	70	1,8599	1.2+/-3.3	0,1,4299	yes	missense	RFFL	NM_001017368.1	29	3,119,6381	TT,TC,CC		0.0116,2.8143,0.9611	benign	147/364	33348541	125,12881	2203	4300	6503	SO:0001583	missense	117584	exon3			GAGGCACGAGTCC	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.440G>A	17.37:g.33348541C>T	ENSP00000326170:p.Arg147His	109	0	0		91	4	0.043956	NM_001017368		Missense_Mutation	SNP	ENST00000315249.7	37	CCDS11286.1	31	0.014194139194139194	16	0.032520325203252036	1	0.0027624309392265192	14	0.024475524475524476	0	0.0	C	7.587	0.669935	0.14776	0.028143	1.16E-4	ENSG00000092871	ENST00000315249;ENST00000394597;ENST00000378516;ENST00000268850;ENST00000413582;ENST00000415395	T;T;T;T;T;T	0.46451	0.87;0.87;0.89;0.91;0.89;0.87	5.65	-4.35	0.03656	.	1.494590	0.03679	N	0.245226	T	0.14184	0.0343	L	0.46157	1.445	0.19300	N	0.999975	B;B;B;B	0.10296	0.003;0.003;0.002;0.003	B;B;B;B	0.10450	0.005;0.003;0.001;0.001	T	0.33497	-0.9866	10	0.45353	T	0.12	-0.0021	7.6995	0.28615	0.1025:0.4344:0.0:0.4631	rs34747500	147;147;147;147	C9JN73;Q8WZ73-3;Q8WZ73;Q8WZ73-2	.;.;RFFL_HUMAN;.	H	147	ENSP00000326170:R147H;ENSP00000378096:R147H;ENSP00000367777:R147H;ENSP00000268850:R147H;ENSP00000408513:R147H;ENSP00000412322:R147H	ENSP00000268850:R147H	R	-	2	0	RFFL	30372654	0.000000	0.05858	0.450000	0.26969	0.123000	0.20343	-1.166000	0.03129	-0.526000	0.06383	-0.940000	0.02684	CGT	C|0.986;T|0.014	0.014	strong		0.582	RFFL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256460.2	NM_057178		T	33348541	C	T	33348541	3	4	27	1	0	0	0	0	1	0	0	0	13265	536	19	1	671	1	RFFL	17	33348541	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	5444543	33348541	47846669	822	11273											
PIGW	284098	hgsc.bcm.edu	37	chr17	34893655	34893655	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaacagagtatggagttcaCtggaactttttctttaccat	11	16	7	7	0	2	1	1	0	1	1	2	3	2	3	1	2	3	2	1	2	4	7	rs61755368	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:34893655C>G	ENST00000592983.1	+	2	1285	c.705C>G	c.(703-705)caC>caG	p.H235Q	MYO19_ENST00000268852.9_5'Flank|MYO19_ENST00000544606.1_5'Flank|MYO19_ENST00000590081.1_Intron|MYO19_ENST00000586007.1_5'Flank|PIGW_ENST00000328396.2_Missense_Mutation_p.H235Q|MYO19_ENST00000431794.3_5'Flank			Q7Z7B1	PIGW_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class W	235					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)		ATGGAGTTCACTGGAACTTTT	0.368													C|||	5	0.000998403	0.0	0.0	5008	,	,		20498	0.0		0.005	False		,,,				2504	0.0				p.H235Q		Atlas-SNP	.											.	PIGW	50	.	0			c.C705G						PASS	.	C	GLN/HIS	6,4390	9.9+/-24.2	0,6,2192	75	79	77		705	2.7	1	17	dbSNP_129	77	60,8538	35.3+/-89.8	0,60,4239	yes	missense	PIGW	NM_178517.3	24	0,66,6431	GG,GC,CC		0.6978,0.1365,0.5079	probably-damaging	235/505	34893655	66,12928	2198	4299	6497	SO:0001583	missense	284098	exon2			AGTTCACTGGAAC	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.705C>G	17.37:g.34893655C>G	ENSP00000468778:p.His235Gln	125	0	0		114	57	0.5	NM_178517	Q8N9G3	Missense_Mutation	SNP	ENST00000592983.1	37	CCDS11313.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	16.95	3.262679	0.59431	0.001365	0.006978	ENSG00000184886	ENST00000328396	.	.	.	5.79	2.71	0.32032	.	0.000000	0.85682	D	0.000000	T	0.76543	0.4002	M	0.92604	3.325	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.82206	-0.0572	8	.	.	.	-6.0044	10.914	0.47124	0.0:0.793:0.0:0.207	rs61755368	235	Q7Z7B1	PIGW_HUMAN	Q	235	.	.	H	+	3	2	PIGW	31967768	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.970000	0.29383	0.802000	0.34089	0.561000	0.74099	CAC	C|0.995;G|0.005	0.005	strong		0.368	PIGW-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451318.1	NM_178517		G	34893655	C	G	34893655	3	3	27	1	0	0	0	0	1	0	0	0	11911	564	20	4	707	4	PIGW	17	34893655	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1545114	34893655	46301555	823	11274											
MED24	9862	hgsc.bcm.edu	37	chr17	38189328	38189328	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcatgcgcttcaccatcGtcagctgctccaccagggac	7	8	9	17	2	2	0	2	0	0	0	4	1	3	1	4	1	4	4	4	1	0	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:38189328G>A	ENST00000394128.2	-	8	884	c.803C>T	c.(802-804)aCg>aTg	p.T268M	MED24_ENST00000394126.1_Missense_Mutation_p.T293M|MED24_ENST00000501516.3_Missense_Mutation_p.T287M|MED24_ENST00000479829.1_5'Flank|MED24_ENST00000394127.2_Missense_Mutation_p.T255M|MED24_ENST00000356271.3_Missense_Mutation_p.T255M	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	268					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)					CTTCACCATCGTCAGCTGCTC	0.637																																					p.T268M		Atlas-SNP	.											.	MED24	89	.	0			c.C803T						PASS	.						51	43	46					17																	38189328		2203	4300	6503	SO:0001583	missense	9862	exon8			ACCATCGTCAGCT	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.803C>T	17.37:g.38189328G>A	ENSP00000377686:p.Thr268Met	75	0	0		48	10	0.208333	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Missense_Mutation	SNP	ENST00000394128.2	37	CCDS11359.1	.	.	.	.	.	.	.	.	.	.	G	9.996	1.232071	0.22626	.	.	ENSG00000008838	ENST00000394126;ENST00000356271;ENST00000394128;ENST00000535071;ENST00000394127;ENST00000536318;ENST00000543759;ENST00000431269;ENST00000428757	T;T;T;T	0.48836	0.8;1.02;1.02;1.02	5.58	3.38	0.38709	Mediator complex, subunit Med24, N-terminal (1);	0.164448	0.64402	N	0.000003	T	0.14098	0.0341	N	0.00436	-1.5	0.25784	N	0.984692	B;B;B;B;B;B;B;B	0.13594	0.0;0.001;0.0;0.001;0.0;0.0;0.0;0.008	B;B;B;B;B;B;B;B	0.08055	0.001;0.003;0.0;0.001;0.001;0.0;0.001;0.001	T	0.22487	-1.0215	10	0.22109	T	0.4	-22.9865	8.1246	0.30990	0.8066:0.0:0.0711:0.1223	.	255;218;197;218;178;255;268;210	B9TX65;B4DV99;B4DDR8;F5H5K2;F8W9R9;O75448-2;O75448;F5H0K1	.;.;.;.;.;.;MED24_HUMAN;.	M	268;268;268;218;255;210;242;178;287	ENSP00000377684:T268M;ENSP00000377686:T268M;ENSP00000443344:T218M;ENSP00000377685:T255M	ENSP00000348610:T268M	T	-	2	0	MED24	35442854	1.000000	0.71417	1.000000	0.80357	0.710000	0.40934	5.178000	0.65037	0.416000	0.25844	-1.099000	0.02127	ACG	.	.	none		0.637	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815		A	38189328	G	A	38189328	3	1	27	1	0	0	0	0	1	0	0	0	9451	1145	40	1	2242	1	MED24	17	38189328	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	3295673	38189328	43005882	824	11275											
KRTAP4-11	653240	hgsc.bcm.edu	37	chr17	39274266	39274266	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggagatgcagcatctggggCggcagcaagtgggctggcag	8	6	19	8	1	1	1	0	0	1	1	1	2	1	1	0	6	3	6	0	6	1	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39274266C>T	ENST00000391413.2	-	1	340	c.302G>A	c.(301-303)cGc>cAc	p.R101H		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	101	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)			gcatctggggcggcagcaAGT	0.647																																					p.R101H		Atlas-SNP	.											.	KRTAP4-11	94	.	0			c.G302A						PASS	.						5	9	8					17																	39274266		655	1560	2215	SO:0001583	missense	653240	exon1			CTGGGGCGGCAGC	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.302G>A	17.37:g.39274266C>T	ENSP00000375232:p.Arg101His	37	0	0		32	8	0.25	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	10.07	1.249110	0.22880	.	.	ENSG00000212721	ENST00000391413	T	0.00638	6.04	3.99	1.96	0.26148	.	1.399950	0.05646	U	0.584357	T	0.01189	0.0039	M	0.78456	2.415	0.09310	N	1	B	0.15473	0.013	B	0.08055	0.003	T	0.50550	-0.8815	10	0.42905	T	0.14	.	3.6707	0.08273	0.1929:0.5877:0.0:0.2193	.	101	Q9BYQ6	KR411_HUMAN	H	101	ENSP00000375232:R101H	ENSP00000375232:R101H	R	-	2	0	KRTAP4-11	36527792	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.701000	0.05075	0.180000	0.19960	-0.192000	0.12808	CGC	.	.	none		0.647	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1			T	39274266	C	T	39274266	3	4	27	1	0	0	0	0	1	0	0	0	8558	768	27	1	289	1	KRTAP4-11	17	39274266	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1084938	39274266	41920944	825	11276											
KRTAP4-12	83755	hgsc.bcm.edu	37	chr17	39279944	39279944	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agctgctggagatgcagcagCtggggcggcagcaggtgggc	7	5	20	9	1	0	1	0	0	0	1	0	2	0	1	0	6	6	7	0	6	0	0	rs536638484		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39279944C>G	ENST00000394014.1	-	1	475	c.431G>C	c.(430-432)aGc>aCc	p.S144T		NM_031854.2	NP_114060.1	Q9BQ66	KR412_HUMAN	keratin associated protein 4-12	144	31 X 5 AA repeats of C-C-[GRQVIL]-[SPTR]- [VSTQPC].		Missing (in allele KAP4.12-v1). {ECO:0000269|PubMed:15955084}.			keratin filament (GO:0045095)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	13		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			gatgcagcagctggggcggca	0.672													C|||	1	0.000199681	0.0	0.0	5008	,	,		15496	0.001		0.0	False		,,,				2504	0.0				p.S144T		Atlas-SNP	.											.	KRTAP4-12	32	.	0			c.G431C						PASS	.						18	24	22					17																	39279944		2195	4276	6471	SO:0001583	missense	83755	exon1			CAGCAGCTGGGGC	AJ406943	CCDS32649.1	17q21.2	2013-06-25			ENSG00000213416	ENSG00000213416		"Keratin associated proteins"	16776	protein-coding gene	gene with protein product						11279113	Standard	NM_031854		Approved	KAP4.12	uc002hwa.3	Q9BQ66	OTTHUMG00000133632	ENST00000394014.1:c.431G>C	17.37:g.39279944C>G	ENSP00000377582:p.Ser144Thr	60	0	0		55	16	0.290909	NM_031854	A3KMC5|Q495I0	Missense_Mutation	SNP	ENST00000394014.1	37	CCDS32649.1	.	.	.	.	.	.	.	.	.	.	.	10.81	1.455027	0.26161	.	.	ENSG00000213416	ENST00000394014	T	0.01484	4.84	5.33	-2.99	0.05497	.	3.044690	0.01738	N	0.029234	T	0.02083	0.0065	L	0.39085	1.19	0.09310	N	1	B	0.14438	0.01	B	0.15052	0.012	T	0.48758	-0.9007	10	0.21540	T	0.41	.	9.6148	0.39685	0.0998:0.2179:0.611:0.0713	.	144	Q9BQ66	KR412_HUMAN	T	144	ENSP00000377582:S144T	ENSP00000377582:S144T	S	-	2	0	KRTAP4-12	36533470	0.009000	0.17119	0.062000	0.19696	0.021000	0.10359	-0.260000	0.08708	-0.227000	0.09884	0.561000	0.74099	AGC	.	.	none		0.672	KRTAP4-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257777.1			G	39279944	C	G	39279944	3	3	27	1	0	0	0	0	1	0	0	0	8559	797	28	4	178	4	KRTAP4-12	17	39279944	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	5678	39279944	41915266	826	11277											
KRT37	8688	hgsc.bcm.edu	37	chr17	39580310	39580310	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctggagctcctcgattgtacGgaagtaggactggtagtcgg	8	10	15	8	3	0	0	0	0	0	0	3	4	1	3	1	5	2	4	1	5	4	4	rs142829376		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39580310G>A	ENST00000225550.3	-	1	465	c.466C>T	c.(466-468)Cgt>Tgt	p.R156C	AC003958.2_ENST00000432258.1_RNA	NM_003770.4	NP_003761.3	O76014	KRT37_HUMAN	keratin 37	156	Coil 1B.|Rod.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)	p.R156C(1)		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)				TCGATTGTACGGAAGTAGGAC	0.597																																					p.R156C		Atlas-SNP	.											KRT37,hand,carcinoma,0,1	KRT37	61	1	1	Substitution - Missense(1)	skin(1)	c.C466T						scavenged	.	G	CYS/ARG	0,4406		0,0,2203	87	77	81		466	3.6	0.7	17	dbSNP_134	81	1,8599		0,1,4299	no	missense	KRT37	NM_003770.4	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	156/450	39580310	1,13005	2203	4300	6503	SO:0001583	missense	8688	exon1			TTGTACGGAAGTA	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.466C>T	17.37:g.39580310G>A	ENSP00000225550:p.Arg156Cys	91	1	0.010989		73	47	0.643836	NM_003770		Missense_Mutation	SNP	ENST00000225550.3	37	CCDS32653.1	.	.	.	.	.	.	.	.	.	.	.	12.99	2.103923	0.37145	0.0	1.16E-4	ENSG00000108417	ENST00000225550	D	0.89415	-2.51	4.69	3.62	0.41486	Filament (1);	0.297247	0.23563	N	0.046837	D	0.85885	0.5801	M	0.68593	2.085	0.09310	N	0.999993	B	0.18863	0.031	B	0.12156	0.007	T	0.76075	-0.3092	10	0.38643	T	0.18	.	10.3203	0.43762	0.0:0.1176:0.6892:0.1932	.	156	O76014	KRT37_HUMAN	C	156	ENSP00000225550:R156C	ENSP00000225550:R156C	R	-	1	0	KRT37	36833836	0.000000	0.05858	0.749000	0.31150	0.958000	0.62258	0.157000	0.16402	2.169000	0.68431	0.655000	0.94253	CGT	G|1.000;A|0.000	0.000	weak		0.597	KRT37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257714.2	NM_003770		A	39580310	G	A	39580310	3	1	27	1	0	0	0	0	1	0	0	0	8483	1116	39	1	911	1	KRT37	17	39580310	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	300366	39580310	41614900	827	11278											
KRT9	3857	hgsc.bcm.edu	37	chr17	39727894	39727894	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaaagccacctccagaaccAccaccaaagccacctccaaa	16	2	3	20	0	0	1	0	0	0	1	2	1	2	1	10	0	3	0	10	0	4	0	rs115965791	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39727894A>G	ENST00000246662.4	-	1	416	c.351T>C	c.(349-351)ggT>ggC	p.G117G	KRT9_ENST00000588431.1_Intron	NM_000226.3	NP_000217.2	P35527	K1C9_HUMAN	keratin 9	117	Head.				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)				ctccagaaccaccaccaaagc	0.567													A|||	28	0.00559105	0.0015	0.0043	5008	,	,		12499	0.0		0.0129	False		,,,				2504	0.0102				p.G117G		Atlas-SNP	.											.	KRT9	78	.	0			c.T351C						PASS	.	A		8,4394		0,8,2193	142	171	161		351	-9.1	0	17	dbSNP_132	161	53,8537		0,53,4242	yes	coding-synonymous	KRT9	NM_000226.3		0,61,6435	GG,GA,AA		0.617,0.1817,0.4695		117/624	39727894	61,12931	2201	4295	6496	SO:0001819	synonymous_variant	3857	exon1			AGAACCACCACCA		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.351T>C	17.37:g.39727894A>G		81	0	0		75	37	0.493333	NM_000226	O00109|Q0IJ47|Q14665	Silent	SNP	ENST00000246662.4	37	CCDS32654.1																																																																																			A|0.995;G|0.005	0.005	strong		0.567	KRT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257707.1	NM_000226		G	39727894	A	G	39727894	2	3	27	1	0	0	0	0	0	0	0	1	8510	146	6	3		3	KRT9	17	39727894	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	147584	39727894	41467316	828	11279											
KRT14	3861	hgsc.bcm.edu	37	chr17	39742921	39742921	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggctcccccagaggagaagcGggaggatgagacagacaggc	12	2	17	10	1	0	4	0	1	0	4	1	8	1	6	2	5	1	1	2	5	1	0	rs117484558	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39742921G>A	ENST00000167586.6	-	1	252	c.166C>T	c.(166-168)Cgc>Tgc	p.R56C		NM_000526.4	NP_000517	P02533	K1C14_HUMAN	keratin 14	56	Head.				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)				GAGGAGAAGCGGGAGGATGAG	0.706													G|||	31	0.0061901	0.0008	0.0043	5008	,	,		13635	0.0		0.0149	False		,,,				2504	0.0123				p.R56C		Atlas-SNP	.											KRT14,NS,carcinoma,+1,1	KRT14	65	1	0			c.C166T						PASS	.	G	CYS/ARG	8,4356		0,8,2174	25	30	28		166	3.4	1	17	dbSNP_132	28	57,8505		0,57,4224	no	missense	KRT14	NM_000526.4	180	0,65,6398	AA,AG,GG		0.6657,0.1833,0.5029	benign	56/473	39742921	65,12861	2182	4281	6463	SO:0001583	missense	3861	exon1			AGAAGCGGGAGGA	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.166C>T	17.37:g.39742921G>A	ENSP00000167586:p.Arg56Cys	22	0	0		25	10	0.4	NM_000526	Q14715|Q53XY3|Q9BUE3|Q9UBN2|Q9UBN3|Q9UCY4	Missense_Mutation	SNP	ENST00000167586.6	37	CCDS11400.1	15	0.006868131868131868	0	0.0	3	0.008287292817679558	0	0.0	12	0.0158311345646438	G	7.992	0.753456	0.15778	0.001833	0.006657	ENSG00000186847	ENST00000167586	D	0.84070	-1.8	4.37	3.4	0.38934	.	0.000000	0.53938	D	0.000053	T	0.61726	0.2370	L	0.47716	1.5	0.53005	D	0.999962	B	0.02656	0.0	B	0.01281	0.0	T	0.65623	-0.6123	10	0.36615	T	0.2	.	9.0759	0.36522	0.1706:0.0:0.8294:0.0	.	56	P02533	K1C14_HUMAN	C	56	ENSP00000167586:R56C	ENSP00000167586:R56C	R	-	1	0	KRT14	36996447	0.997000	0.39634	1.000000	0.80357	0.012000	0.07955	0.082000	0.14847	1.210000	0.43336	-0.235000	0.12190	CGC	G|0.994;A|0.006	0.006	strong		0.706	KRT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257289.1	NM_000526		A	39742921	G	A	39742921	3	1	27	1	0	0	0	0	1	0	0	0	8460	1116	39	1	1284	1	KRT14	17	39742921	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	15027	39742921	41452289	829	11280											
KRT17	3872	hgsc.bcm.edu	37	chr17	39777895	39777895	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggttcttctctgccatctTctcatactggtcacgcatct	5	15	7	14	2	6	0	2	0	5	0	8	0	6	0	1	2	2	2	1	2	1	4	rs146900210	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39777895T>A	ENST00000311208.8	-	4	851	c.784A>T	c.(784-786)Aag>Tag	p.K262*	JUP_ENST00000540235.1_Nonsense_Mutation_p.K421*	NM_000422.2	NP_000413.1	Q04695	K1C17_HUMAN	keratin 17	262	Coil 2.|Rod.				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)				TCTGCCATCTTCTCATACTGG	0.617																																					p.K262X	Pancreas(92;1242 2086 39193 50508)	Atlas-SNP	.											.	KRT17	57	.	0			c.A784T						PASS	.	T	stop/LYS	0,4406		0,0,2203	122	105	111		784	1.5	1	17	dbSNP_134	111	5,8595	4.3+/-15.6	0,5,4295	no	stop-gained	KRT17	NM_000422.2		0,5,6498	AA,AT,TT		0.0581,0.0,0.0384		262/433	39777895	5,13001	2203	4300	6503	SO:0001587	stop_gained	3872	exon4			CCATCTTCTCATA	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.784A>T	17.37:g.39777895T>A	ENSP00000308452:p.Lys262*	307	1	0.00325733		347	172	0.495677	NM_000422	A5Z1M9|A5Z1N0|A5Z1N1|A5Z1N2|A6NDV6|A6NKQ2|Q6IP98|Q8N1P6	Nonsense_Mutation	SNP	ENST00000311208.8	37	CCDS11402.1	.	.	.	.	.	.	.	.	.	.	T	26.3	4.726067	0.89298	0.0	5.81E-4	ENSG00000128422;ENSG00000173801	ENST00000311208;ENST00000540235	.	.	.	3.82	1.49	0.22878	.	0.000000	0.49305	D	0.000147	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.9636	0.14080	0.0:0.1718:0.1573:0.6709	.	.	.	.	X	262;421	.	.	K	-	1	0	JUP;KRT17	37031421	0.014000	0.17966	0.998000	0.56505	0.970000	0.65996	0.145000	0.16157	0.160000	0.19432	0.533000	0.62120	AAG	T|1.000;A|0.000	0.000	strong		0.617	KRT17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257460.1	NM_000422		A	39777895	T	A	39777895	4	1	27	1	0	0	0	0	0	1	0	0	8463	1792	62	5	534	5	KRT17	17	39777895	Nonsense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	34974	39777895	41417315	830	11281											
HAP1	9001	hgsc.bcm.edu	37	chr17	39888636	39888636	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggtaacgctctcccagacaGgtgggagaagctggggggga	10	5	18	8	1	1	2	0	0	1	2	2	4	1	3	1	6	2	3	1	6	2	1	rs142535684	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:39888636G>T	ENST00000310778.5	-	3	569	c.560C>A	c.(559-561)cCt>cAt	p.P187H	RN7SL399P_ENST00000471648.2_RNA|HAP1_ENST00000393939.2_Missense_Mutation_p.P187H|HAP1_ENST00000341193.5_Missense_Mutation_p.P195H|JUP_ENST00000540235.1_Intron|HAP1_ENST00000347901.4_Missense_Mutation_p.P187H			P54257	HAP1_HUMAN	huntingtin-associated protein 1	187	HAP1 N-terminal.			Missing (in Ref. 6; CAB82785). {ECO:0000305}.	anterograde axon cargo transport (GO:0008089)|autophagy (GO:0006914)|brain development (GO:0007420)|cell projection organization (GO:0030030)|exocytosis (GO:0006887)|negative regulation of beta-amyloid formation (GO:1902430)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|positive regulation of neurotrophin production (GO:0032901)|positive regulation of nonmotile primary cilium assembly (GO:1902857)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|protein localization (GO:0008104)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|regulation of organelle transport along microtubule (GO:1902513)|retrograde axon cargo transport (GO:0008090)|synaptic transmission (GO:0007268)|vesicle transport along microtubule (GO:0047496)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|inclusion body (GO:0016234)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|synapse (GO:0045202)	brain-derived neurotrophic factor binding (GO:0048403)|ion channel binding (GO:0044325)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(4)|skin(1)	21		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.0677)			CTCCCAGACAGGTGGGAGAAG	0.582													G|||	6	0.00119808	0.0	0.0029	5008	,	,		19039	0.0		0.004	False		,,,				2504	0.0				p.P195H		Atlas-SNP	.											.	HAP1	48	.	0			c.C584A						PASS	.	G	HIS/PRO,HIS/PRO,HIS/PRO	4,4402	4.2+/-10.8	0,4,2199	33	33	33		584,560,560	0.2	0.4	17	dbSNP_134	33	10,8590	7.1+/-27.0	0,10,4290	yes	missense,missense,missense	HAP1	NM_001079870.1,NM_001079871.1,NM_177977.2	77,77,77	0,14,6489	TT,TG,GG		0.1163,0.0908,0.1076	probably-damaging,probably-damaging,probably-damaging	195/603,187/595,187/620	39888636	14,12992	2203	4300	6503	SO:0001583	missense	9001	exon3			CAGACAGGTGGGA	AF040723	CCDS11406.1, CCDS42338.1, CCDS42339.1	17q21.2-q21.3	2008-04-23	2008-04-23		ENSG00000173805	ENSG00000173805			4812	protein-coding gene	gene with protein product	"neuroan 1"	600947		HAP2		7477378, 9668110	Standard	NM_177977		Approved	HLP, hHLP1, HIP5	uc002hxn.1	P54257	OTTHUMG00000133498	ENST00000310778.5:c.560C>A	17.37:g.39888636G>T	ENSP00000309392:p.Pro187His	68	0	0		93	43	0.462366	NM_001079870	A8MQB5|O75358|Q59GK4|Q9H4G3|Q9HA98|Q9NY90	Missense_Mutation	SNP	ENST00000310778.5	37		6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	12.60	1.985337	0.35036	9.08E-4	0.001163	ENSG00000173805	ENST00000393939;ENST00000310778;ENST00000347901;ENST00000341193	T;T;T;T	0.67171	3.0;3.19;3.14;-0.25	3.42	0.204	0.15199	.	.	.	.	.	T	0.49779	0.1577	N	0.22421	0.69	0.09310	N	1	D;D;D;D	0.61697	0.99;0.99;0.971;0.977	P;P;P;P	0.54590	0.642;0.642;0.642;0.756	T	0.45775	-0.9238	9	0.87932	D	0	0.0581	3.2202	0.06712	0.2633:0.2282:0.5085:0.0	.	187;195;187;187	P54257-3;P54257-4;P54257-2;P54257	.;.;.;HAP1_HUMAN	H	187;187;187;195	ENSP00000377513:P187H;ENSP00000309392:P187H;ENSP00000334002:P187H;ENSP00000343170:P195H	ENSP00000309392:P187H	P	-	2	0	HAP1	37142162	0.031000	0.19500	0.391000	0.26233	0.448000	0.32197	0.694000	0.25512	0.254000	0.21573	0.462000	0.41574	CCT	G|0.998;T|0.002	0.002	strong		0.582	HAP1-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000389619.1	NM_003949		T	39888636	G	T	39888636	3	4	27	1	0	0	0	0	1	0	0	0	6962	1000	35	4	1335	4	HAP1	17	39888636	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	110741	39888636	41306574	831	11282											
ATP6V0A1	535	hgsc.bcm.edu	37	chr17	40665913	40665913	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccatggtccaccaggccaTccacaccatcgagtactgcc	10	6	7	18	1	0	0	0	0	0	0	3	1	2	0	7	2	2	1	7	2	1	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:40665913T>C	ENST00000343619.4	+	20	2288	c.2165T>C	c.(2164-2166)aTc>aCc	p.I722T	ATP6V0A1_ENST00000393829.2_Missense_Mutation_p.I716T|RP11-400F19.18_ENST00000591237.1_RNA|ATP6V0A1_ENST00000544137.1_Missense_Mutation_p.I368T|ATP6V0A1_ENST00000546249.1_Missense_Mutation_p.I722T|MIR5010_ENST00000582846.1_RNA|ATP6V0A1_ENST00000537728.1_Missense_Mutation_p.I673T|ATP6V0A1_ENST00000585525.1_Missense_Mutation_p.I679T|ATP6V0A1_ENST00000264649.6_Missense_Mutation_p.I723T	NM_001130021.1	NP_001123493.1	Q93050	VPP1_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a1	722					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)		CACCAGGCCATCCACACCATC	0.577																																					p.I723T		Atlas-SNP	.											.	ATP6V0A1	67	.	0			c.T2168C						PASS	.						207	182	191					17																	40665913		2203	4300	6503	SO:0001583	missense	535	exon19			AGGCCATCCACAC	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.2165T>C	17.37:g.40665913T>C	ENSP00000342951:p.Ile722Thr	210	0	0		193	58	0.300518	NM_001130020	B7Z3B7|Q8N5G7|Q9NSX0	Missense_Mutation	SNP	ENST00000343619.4	37	CCDS45684.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.468889	0.84533	.	.	ENSG00000033627	ENST00000343619;ENST00000546249;ENST00000393829;ENST00000264649;ENST00000537728;ENST00000544137	D;D;D;D;D;D	0.91351	-2.83;-2.83;-2.83;-2.83;-2.83;-2.83	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	D	0.97238	0.9097	H	0.98276	4.19	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	0.97110	1.0;0.999;0.998;0.999;1.0	D	0.98713	1.0705	10	0.87932	D	0	-21.9263	14.7204	0.69302	0.0:0.0:0.0:1.0	.	673;679;723;722;716	B7Z641;B7Z2A9;B7Z3B7;Q93050;Q93050-1	.;.;.;VPP1_HUMAN;.	T	722;722;716;723;673;368	ENSP00000342951:I722T;ENSP00000444676:I722T;ENSP00000377415:I716T;ENSP00000264649:I723T;ENSP00000443991:I673T;ENSP00000446377:I368T	ENSP00000264649:I723T	I	+	2	0	ATP6V0A1	37919439	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.868000	0.87116	2.067000	0.61834	0.459000	0.35465	ATC	.	.	none		0.577	ATP6V0A1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450364.1	NM_001130020		C	40665913	T	C	40665913	3	2	27	1	0	0	0	0	1	0	0	0	1168	1435	50	3	2260	3	ATP6V0A1	17	40665913	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	777277	40665913	40529297	832	11283											
NAGLU	4669	hgsc.bcm.edu	37	chr17	40696120	40696120	+	Missense_Mutation	SNP	A	A	T																															ccaacagcaccagtttgacaAaaatgtcttccaactggagc																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:40696120A>T	ENST00000225927.2	+	6	2197	c.2096A>T	c.(2095-2097)aAa>aTa	p.K699I	RP11-400F19.8_ENST00000585572.1_RNA	NM_000263.3	NP_000254.2	P54802	ANAG_HUMAN	N-acetylglucosaminidase, alpha	699					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)	CAGTTTGACAAAAATGTCTTC	0.577																																					p.K699I		Atlas-SNP	.											.	NAGLU	36	.	0			c.A2096T						PASS	.						48	46	47					17																	40696120		2203	4300	6503	SO:0001583	missense	4669	exon6			TTGACAAAAATGT		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.2096A>T	17.37:g.40696120A>T	ENSP00000225927:p.Lys699Ile	59	0	0		53	17	0.320755	NM_000263		Missense_Mutation	SNP	ENST00000225927.2	37	CCDS11427.1	.	.	.	.	.	.	.	.	.	.	A	14.62	2.590453	0.46214	.	.	ENSG00000108784	ENST00000225927;ENST00000377405	D	0.98777	-5.13	5.03	2.8	0.32819	Alpha-N-acetylglucosaminidase, C-terminal (1);	0.606411	0.18227	N	0.147694	D	0.96059	0.8716	L	0.31526	0.94	0.09310	N	0.99999	P	0.38395	0.629	B	0.41619	0.361	D	0.92173	0.5745	10	0.46703	T	0.11	-5.9234	8.3135	0.32086	0.833:0.0:0.167:0.0	.	699	P54802	ANAG_HUMAN	I	699;375	ENSP00000225927:K699I	ENSP00000225927:K699I	K	+	2	0	NAGLU	37949646	0.903000	0.30736	0.023000	0.16930	0.900000	0.52787	2.106000	0.41835	0.879000	0.35944	0.454000	0.30748	AAA	.	.	none		0.577	NAGLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450385.1	NM_000263		T	40696120	A	T	40696120	3	4	27	1	0	0	0	0	1	0	0	0	10152	14	1	5	2118	5	NAGLU	17	40696120	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	30207	40696120	40499090	833	11284	140	2									
NAGLU	4669	hgsc.bcm.edu	37	chr17	40696122	40696122	+	Missense_Mutation	SNP	A	A	C																															aacagcaccagtttgacaaaAatgtcttccaactggagcag																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:40696122A>C	ENST00000225927.2	+	6	2199	c.2098A>C	c.(2098-2100)Aat>Cat	p.N700H	RP11-400F19.8_ENST00000585572.1_RNA	NM_000263.3	NP_000254.2	P54802	ANAG_HUMAN	N-acetylglucosaminidase, alpha	700					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)	GTTTGACAAAAATGTCTTCCA	0.577																																					p.N700H		Atlas-SNP	.											.	NAGLU	36	.	0			c.A2098C						PASS	.						50	47	48					17																	40696122		2203	4300	6503	SO:0001583	missense	4669	exon6			GACAAAAATGTCT		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.2098A>C	17.37:g.40696122A>C	ENSP00000225927:p.Asn700His	58	0	0		54	18	0.333333	NM_000263		Missense_Mutation	SNP	ENST00000225927.2	37	CCDS11427.1	.	.	.	.	.	.	.	.	.	.	A	11.71	1.720488	0.30503	.	.	ENSG00000108784	ENST00000225927;ENST00000377405	D	0.98649	-5.05	5.03	1.08	0.20341	Alpha-N-acetylglucosaminidase, C-terminal (1);	0.878057	0.10023	N	0.725727	D	0.95868	0.8655	L	0.42245	1.32	0.20074	N	0.999938	B	0.09022	0.002	B	0.08055	0.003	D	0.90986	0.4831	10	0.52906	T	0.07	0.2904	3.5341	0.07788	0.3663:0.2592:0.3745:0.0	.	700	P54802	ANAG_HUMAN	H	700;376	ENSP00000225927:N700H	ENSP00000225927:N700H	N	+	1	0	NAGLU	37949648	0.991000	0.36638	0.010000	0.14722	0.865000	0.49528	3.225000	0.51246	0.354000	0.24105	0.454000	0.30748	AAT	.	.	none		0.577	NAGLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450385.1	NM_000263		C	40696122	A	C	40696122	3	2	27	1	0	0	0	0	1	0	0	0	10152	14	1	5	2120	5	NAGLU	17	40696122	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	2	40696122	40499088	834	11285	140	2									
AOC2	314	hgsc.bcm.edu	37	chr17	40997461	40997461	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agacttgggccagttggaacGggagtttaagtctggccggt	8	10	16	7	2	1	1	0	0	1	1	1	3	1	3	2	5	1	2	2	5	2	4	rs35508987	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:40997461G>A	ENST00000253799.3	+	1	845	c.818G>A	c.(817-819)cGg>cAg	p.R273Q	AOC2_ENST00000452774.2_Missense_Mutation_p.R273Q	NM_009590.2	NP_033720.2	O75106	AOC2_HUMAN	amine oxidase, copper containing 2 (retina-specific)	273			R -> Q (in dbSNP:rs35508987). {ECO:0000269|Ref.4}.		amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	aliphatic-amine oxidase activity (GO:0052595)|aminoacetone:oxygen oxidoreductase(deaminating) activity (GO:0052594)|copper ion binding (GO:0005507)|electron carrier activity (GO:0009055)|phenethylamine:oxygen oxidoreductase (deaminating) activity (GO:0052596)|primary amine oxidase activity (GO:0008131)|quinone binding (GO:0048038)|tryptamine:oxygen oxidoreductase (deaminating) activity (GO:0052593)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(14)|ovary(4)|skin(2)	30		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)		CAGTTGGAACGGGAGTTTAAG	0.572													G|||	14	0.00279553	0.0	0.0029	5008	,	,		18840	0.0		0.0099	False		,,,				2504	0.002				p.R273Q		Atlas-SNP	.											.	AOC2	61	.	0			c.G818A						PASS	.	G	GLN/ARG,GLN/ARG	13,4393	20.2+/-43.8	0,13,2190	81	80	81		818,818	1	0.8	17	dbSNP_126	81	79,8521	47.2+/-106.3	0,79,4221	yes	missense,missense	AOC2	NM_001158.3,NM_009590.2	43,43	0,92,6411	AA,AG,GG		0.9186,0.2951,0.7074	benign,benign	273/730,273/757	40997461	92,12914	2203	4300	6503	SO:0001583	missense	314	exon1			TGGAACGGGAGTT	AF081363	CCDS11443.1, CCDS45690.1	17q21	2012-07-13				ENSG00000131480	1.4.3.21		549	protein-coding gene	gene with protein product		602268				9119395, 9722954	Standard	NM_001158		Approved	RAO, DAO2	uc002ibu.3	O75106		ENST00000253799.3:c.818G>A	17.37:g.40997461G>A	ENSP00000253799:p.Arg273Gln	141	0	0		116	60	0.517241	NM_009590	A5PKW2|O00120|O75105|Q4TTW5|Q9UNY0	Missense_Mutation	SNP	ENST00000253799.3	37	CCDS11443.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	G	5.383	0.255861	0.10185	0.002951	0.009186	ENSG00000131480	ENST00000253799;ENST00000452774	T;T	0.15603	2.41;2.41	5.75	1.03	0.20045	Copper amine oxidase, N2/N3-terminal (1);Copper amine oxidase, N-terminal (1);	1.003210	0.08026	N	0.992717	T	0.05181	0.0138	N	0.08118	0	0.09310	N	1	B;B	0.15141	0.007;0.012	B;B	0.10450	0.002;0.005	T	0.42275	-0.9461	10	0.12766	T	0.61	-24.7701	6.4476	0.21885	0.3468:0.0:0.5339:0.1193	rs35508987	273;273	O75106;O75106-2	AOC2_HUMAN;.	Q	273	ENSP00000253799:R273Q;ENSP00000406134:R273Q	ENSP00000253799:R273Q	R	+	2	0	AOC2	38250987	0.000000	0.05858	0.837000	0.33122	0.916000	0.54674	0.563000	0.23547	0.366000	0.24427	-0.254000	0.11334	CGG	G|0.993;A|0.007	0.007	strong		0.572	AOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452442.1	NM_009590, NM_001158		A	40997461	G	A	40997461	3	1	27	1	0	0	0	0	1	0	0	0	727	1116	39	1	820	1	AOC2	17	40997461	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	301339	40997461	40197749	835	11286											
SPAG9	9043	hgsc.bcm.edu	37	chr17	49067870	49067870	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taggggaagtggcagctcccGtcacaccttctgcagaacaa	11	7	11	12	1	2	1	1	0	1	1	3	2	3	2	2	3	3	3	2	3	4	2	rs534277665		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:49067870G>A	ENST00000262013.7	-	20	2766	c.2558C>T	c.(2557-2559)aCg>aTg	p.T853M	SPAG9_ENST00000510283.1_Missense_Mutation_p.T696M|SPAG9_ENST00000357122.4_Missense_Mutation_p.T839M|SPAG9_ENST00000505279.1_Missense_Mutation_p.T843M	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	853					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)			GGCAGCTCCCGTCACACCTTC	0.468																																					p.T853M		Atlas-SNP	.											.	SPAG9	151	.	0			c.C2558T						PASS	.						112	84	93					17																	49067870		2203	4300	6503	SO:0001583	missense	9043	exon20			GCTCCCGTCACAC	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.2558C>T	17.37:g.49067870G>A	ENSP00000262013:p.Thr853Met	192	0	0		146	75	0.513699	NM_001130528	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Missense_Mutation	SNP	ENST00000262013.7	37	CCDS45740.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.61|14.61	2.587305|2.587305	0.46110|0.46110	.|.	.|.	ENSG00000008294|ENSG00000008294	ENST00000513906|ENST00000262013;ENST00000376407;ENST00000357804;ENST00000357791;ENST00000510283;ENST00000505279;ENST00000357122;ENST00000535445	.|T;T;T;T	.|0.24723	.|1.84;1.85;1.84;1.84	5.9|5.9	3.59|3.59	0.41128|0.41128	.|WD40 repeat-like-containing domain (1);	.|0.377306	.|0.31648	.|N	.|0.007293	T|T	0.23410|0.23410	0.0566|0.0566	L|L	0.34521|0.34521	1.04|1.04	0.09310|0.09310	N|N	1|1	.|P;P;P;P;P;P	.|0.44659	.|0.84;0.72;0.597;0.646;0.592;0.742	.|B;P;B;B;B;B	.|0.44732	.|0.438;0.459;0.336;0.12;0.277;0.191	T|T	0.07158|0.07158	-1.0787|-1.0787	5|10	.|0.51188	.|T	.|0.08	-3.8257|-3.8257	11.9883|11.9883	0.53161|0.53161	0.1577:0.0:0.8423:0.0|0.1577:0.0:0.8423:0.0	.|.	.|839;853;843;853;839;696	.|O60271-5;O60271-3;O60271-2;O60271;O60271-4;E7ENU2	.|.;.;.;JIP4_HUMAN;.;.	W|M	112|853;610;600;390;696;843;839;451	.|ENSP00000262013:T853M;ENSP00000423165:T696M;ENSP00000426900:T843M;ENSP00000349636:T839M	.|ENSP00000262013:T853M	R|T	-|-	1|2	2|0	SPAG9|SPAG9	46422869|46422869	0.997000|0.997000	0.39634|0.39634	0.969000|0.969000	0.41365|0.41365	0.983000|0.983000	0.72400|0.72400	4.424000|4.424000	0.59868|0.59868	1.512000|1.512000	0.48834|0.48834	0.650000|0.650000	0.86243|0.86243	CGG|ACG	.	.	none		0.468	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971		A	49067870	G	A	49067870	3	1	27	1	0	0	0	0	1	0	0	0	15000	1145	40	1	1451	1	SPAG9	17	49067870	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	8070409	49067870	32127340	836	11287											
KIF2B	84643	hgsc.bcm.edu	37	chr17	51901244	51901244	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttggtgtaccagttcaccGcccagccactggtggagtcc	7	9	12	13	1	1	0	1	0	0	0	2	1	2	1	5	3	2	3	5	3	1	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:51901244G>A	ENST00000268919.4	+	1	1006	c.850G>A	c.(850-852)Gcc>Acc	p.A284T		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	284	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						CCAGTTCACCGCCCAGCCACT	0.572																																					p.A284T		Atlas-SNP	.											.	KIF2B	254	.	0			c.G850A						PASS	.						91	79	83					17																	51901244		2203	4300	6503	SO:0001583	missense	84643	exon1			TTCACCGCCCAGC	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.850G>A	17.37:g.51901244G>A	ENSP00000268919:p.Ala284Thr	96	0	0		86	27	0.313953	NM_032559	Q96MA2|Q9BXG6	Missense_Mutation	SNP	ENST00000268919.4	37	CCDS32685.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.686847	0.88639	.	.	ENSG00000141200	ENST00000268919;ENST00000416491	T	0.18502	2.21	5.52	5.52	0.82312	Kinesin, motor domain (4);	0.000000	0.51477	D	0.000092	T	0.18425	0.0442	L	0.43923	1.385	0.58432	D	0.999998	P	0.41784	0.762	B	0.38880	0.284	T	0.01127	-1.1443	10	0.35671	T	0.21	.	18.3543	0.90352	0.0:0.0:1.0:0.0	.	284	Q8N4N8	KIF2B_HUMAN	T	284;172	ENSP00000268919:A284T	ENSP00000268919:A284T	A	+	1	0	KIF2B	49256243	1.000000	0.71417	0.964000	0.40570	0.833000	0.47200	5.606000	0.67641	2.739000	0.93911	0.655000	0.94253	GCC	.	.	none		0.572	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559		A	51901244	G	A	51901244	3	1	27	1	0	0	0	0	1	0	0	0	8307	1087	38	1	852	1	KIF2B	17	51901244	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2833374	51901244	29293966	837	11288											
MSI2	124540	hgsc.bcm.edu	37	chr17	55693404	55693405	+	Frame_Shift_Ins	INS	-	-	T																															ggccgggcccggggactgccINSttacaccatggacgcgttca																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:55693404_55693405insT	ENST00000284073.2	+	9	820_821	c.611_612insT	c.(610-615)ccttacfs	p.Y205fs	MSI2_ENST00000579505.1_3'UTR|MSI2_ENST00000579180.1_Frame_Shift_Ins_p.Y101fs|RN7SL449P_ENST00000464937.2_RNA|MSI2_ENST00000442934.2_Frame_Shift_Ins_p.Y144fs|MSI2_ENST00000322684.3_Frame_Shift_Ins_p.Y201fs|MSI2_ENST00000416426.2_Frame_Shift_Ins_p.Y183fs	NM_138962.2	NP_620412.1	Q96DH6	MSI2H_HUMAN	musashi RNA-binding protein 2	205						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)		CGGGGACTGCCTTACACCATGG	0.559			T	HOXA9	CML																																p.P204fs		Pindel,Atlas-Indel	.		Dom	yes		17	17q23.2	124540	musashi homolog 2 (Drosophila)		L	.	MSI2	52	.	0			c.611_612insT						PASS	.																																			SO:0001589	frameshift_variant	124540	exon9			.	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.613dupT	17.37:g.55693406_55693406dupT	ENSP00000284073:p.Tyr205fs	52	0	.		51	11	0.216	NM_138962	Q7Z6M7|Q8N9T4	Frame_Shift_Ins	INS	ENST00000284073.2	37	CCDS11596.1																																																																																			.	.	none		0.559	MSI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441813.1			T	55693405	-	T	55693404	7	5	27	1	0	1	1	0	0	0	0	0	9885	681	24	0	695	0	MSI2	17	55693404	Frame_Shift_Ins	INS	-	TCGA-G8-6909-01A-11D-2210-10	3792160	55693404	25501806	838	11289											
MKS1	54903	hgsc.bcm.edu	37	chr17	56294075	56294075	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcacaatctcctcctcttcGtcttcctctgggcggtgtcc	4	14	7	16	2	5	0	1	0	4	0	10	0	8	0	4	2	0	0	4	2	1	2	rs142813109	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:56294075G>C	ENST00000393119.2	-	3	287	c.213C>G	c.(211-213)gaC>gaG	p.D71E	LPO_ENST00000582328.1_5'Flank|MKS1_ENST00000313863.6_Missense_Mutation_p.D71E|MKS1_ENST00000546108.1_5'UTR|MKS1_ENST00000537529.2_Missense_Mutation_p.D61E|MKS1_ENST00000337050.7_Missense_Mutation_p.D71E	NM_017777.3	NP_060247.2	Q9NXB0	MKS1_HUMAN	Meckel syndrome, type 1	71					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)		p.D71V(1)		endometrium(5)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						CCTCCTCTTCGTCTTCCTCTG	0.483													G|||	8	0.00159744	0.0	0.0029	5008	,	,		18460	0.0		0.006	False		,,,				2504	0.0				p.D71E		Atlas-SNP	.											MKS1_ENST00000337050,NS,carcinoma,0,2	MKS1	100	2	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.C213G						PASS	.	G	GLU/ASP,GLU/ASP	8,3946		0,8,1969	135	140	138		183,213	-3.3	1	17	dbSNP_134	138	48,8250		0,48,4101	yes	missense,missense	MKS1	NM_001165927.1,NM_017777.3	45,45	0,56,6070	CC,CG,GG		0.5785,0.2023,0.4571	benign,benign	61/550,71/560	56294075	56,12196	1977	4149	6126	SO:0001583	missense	54903	exon3			CTCTTCGTCTTCC	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.213C>G	17.37:g.56294075G>C	ENSP00000376827:p.Asp71Glu	158	0	0		151	71	0.470199	NM_017777	B7WNX4|F5H885|Q284T0|Q96G13	Missense_Mutation	SNP	ENST00000393119.2	37	CCDS11603.2	5|5	0.0022893772893772895|0.0022893772893772895	0|0	0.0|0.0	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	3|3	0.00395778364116095|0.00395778364116095	G|G	11.11|11.11	1.542037|1.542037	0.27563|0.27563	0.002023|0.002023	0.005785|0.005785	ENSG00000011143|ENSG00000011143	ENST00000537529;ENST00000393120;ENST00000393119;ENST00000337050|ENST00000313863	T;T;T;T|.	0.68331|.	-0.32;1.5;-0.27;-0.04|.	5.41|5.41	-3.29|-3.29	0.05017|0.05017	.|.	0.246500|.	0.23866|.	N|.	0.043797|.	T|T	0.10294|0.10294	0.0252|0.0252	N|N	0.02539|0.02539	-0.55|-0.55	0.80722|0.80722	D|D	1|1	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.06405|.	0.002;0.001|.	T|T	0.19877|0.19877	-1.0292|-1.0292	10|5	0.06891|.	T|.	0.86|.	-13.0566|-13.0566	1.4484|1.4484	0.02369|0.02369	0.2305:0.3965:0.1768:0.1963|0.2305:0.3965:0.1768:0.1963	.|.	71;71|.	A8MPP8;Q9NXB0|.	.;MKS1_HUMAN|.	E|R	61;71;71;71|72	ENSP00000442096:D61E;ENSP00000376828:D71E;ENSP00000376827:D71E;ENSP00000338407:D71E|.	ENSP00000338407:D71E|.	D|T	-|-	3|2	2|0	MKS1|MKS1	53649074|53649074	0.123000|0.123000	0.22298|0.22298	0.997000|0.997000	0.53966|0.53966	0.988000|0.988000	0.76386|0.76386	-0.681000|-0.681000	0.05191|0.05191	-0.194000|-0.194000	0.10399|0.10399	-0.323000|-0.323000	0.08544|0.08544	GAC|ACG	G|0.996;C|0.004	0.004	strong		0.483	MKS1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258015.2	NM_017777		C	56294075	G	C	56294075	3	2	27	1	0	0	0	0	1	0	0	0	9618	1136	40	4	1530	4	MKS1	17	56294075	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	600671	56294075	24901135	839	11290											
PPM1E	22843	hgsc.bcm.edu	37	chr17	56833612	56833612	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggggaccaggagcaagaccCggagcccgaggaggaggcgg	10	0	21	10	3	0	1	0	0	0	1	0	7	0	6	3	8	2	1	3	8	1	0	rs116991234	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:56833612C>G	ENST00000308249.2	+	1	383	c.254C>G	c.(253-255)cCg>cGg	p.P85R		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)			gagcaagacccggagcccgag	0.756													c|||	23	0.00459265	0.0	0.0101	5008	,	,		8364	0.0		0.0129	False		,,,				2504	0.0031				p.P85R		Atlas-SNP	.											.	PPM1E	97	.	0			c.C254G						PASS	.		ARG/PRO	4,3962		0,4,1979	8	7	7		254	2.4	1	17	dbSNP_132	7	43,7859		0,43,3908	no	missense	PPM1E	NM_014906.3	103	0,47,5887	GG,GC,CC		0.5442,0.1009,0.396	benign	85/756	56833612	47,11821	1983	3951	5934	SO:0001583	missense	22843	exon1			AAGACCCGGAGCC	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.254C>G	17.37:g.56833612C>G	ENSP00000312411:p.Pro85Arg	46	0	0		57	25	0.438596	NM_014906	Q8N8J9|Q96DB8	Missense_Mutation	SNP	ENST00000308249.2	37	CCDS11613.1	13	0.005952380952380952	0	0.0	5	0.013812154696132596	0	0.0	8	0.010554089709762533	c	11.88	1.770544	0.31320	0.001009	0.005442	ENSG00000175175	ENST00000308249	T	0.27256	1.68	3.53	2.43	0.29744	.	.	.	.	.	T	0.11750	0.0286	N	0.19112	0.55	0.20638	N	0.999879	B	0.26775	0.159	B	0.31614	0.133	T	0.18335	-1.0340	9	0.34782	T	0.22	-3.1579	7.5016	0.27522	0.2562:0.7438:0.0:0.0	.	85	Q8WY54-2	.	R	85	ENSP00000312411:P85R	ENSP00000312411:P85R	P	+	2	0	PPM1E	54188611	.	.	0.997000	0.53966	0.470000	0.32858	.	.	1.690000	0.51089	0.457000	0.33378	CCG	C|0.993;G|0.007	0.007	strong		0.756	PPM1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445458.1	NM_014906		G	56833612	C	G	56833612	3	3	27	1	0	0	0	0	1	0	0	0	12350	652	23	4	256	4	PPM1E	17	56833612	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	539537	56833612	24361598	840	11291											
PRR11	55771	hgsc.bcm.edu	37	chr17	57247133	57247133	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	catgcccaagttcaaacaacGaagacgaaagctaaaagcca	19	4	7	11	2	1	1	1	0	0	1	1	3	1	1	2	0	5	2	2	0	7	2	rs145780567	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:57247133G>A	ENST00000262293.4	+	2	332	c.20G>A	c.(19-21)cGa>cAa	p.R7Q		NM_018304.3	NP_060774.2	Q96HE9	PRR11_HUMAN	proline rich 11	7						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)					TTCAAACAACGAAGACGAAAG	0.338													G|||	15	0.00299521	0.0	0.0058	5008	,	,		14982	0.001		0.0099	False		,,,				2504	0.0				p.R7Q		Atlas-SNP	.											PRR11,NS,carcinoma,+1,1	PRR11	36	1	0			c.G20A						PASS	.	G	GLN/ARG	11,4395	17.9+/-39.9	0,11,2192	62	60	61		20	1.2	0.4	17	dbSNP_134	61	78,8522	43.6+/-101.6	0,78,4222	yes	missense	PRR11	NM_018304.3	43	0,89,6414	AA,AG,GG		0.907,0.2497,0.6843	benign	7/361	57247133	89,12917	2203	4300	6503	SO:0001583	missense	55771	exon2			AACAACGAAGACG		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.20G>A	17.37:g.57247133G>A	ENSP00000262293:p.Arg7Gln	101	0	0		86	47	0.546512	NM_018304	Q9NUZ7|Q9NXE9	Missense_Mutation	SNP	ENST00000262293.4	37	CCDS11614.1	11	0.005036630036630037	0	0.0	4	0.011049723756906077	0	0.0	7	0.009234828496042216	G	4.777	0.144546	0.09134	0.002497	0.00907	ENSG00000068489	ENST00000262293	.	.	.	4.38	1.17	0.20885	.	0.450854	0.18874	N	0.128767	T	0.19765	0.0475	L	0.32530	0.975	0.18873	N	0.999986	B	0.23490	0.086	B	0.14578	0.011	T	0.12319	-1.0552	9	0.49607	T	0.09	-2.239	6.1076	0.20081	0.3479:0.0:0.6521:0.0	.	7	Q96HE9	PRR11_HUMAN	Q	7	.	ENSP00000262293:R7Q	R	+	2	0	PRR11	54601915	1.000000	0.71417	0.357000	0.25798	0.008000	0.06430	0.486000	0.22340	0.182000	0.20032	0.561000	0.74099	CGA	G|0.994;A|0.006	0.006	strong		0.338	PRR11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445949.1	NM_018304		A	57247133	G	A	57247133	3	1	27	1	0	0	0	0	1	0	0	0	12595	1058	37	1	22	1	PRR11	17	57247133	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	413521	57247133	23948077	841	11292											
BCAS3	54828	hgsc.bcm.edu	37	chr17	58952044	58952044	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atccttgtcgtagtcttgcaGgagaaaattgctgcctttga	9	14	10	8	1	1	2	0	1	1	1	3	3	2	2	2	1	3	3	2	1	3	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:58952044G>A	ENST00000390652.5	+	9	637	c.606G>A	c.(604-606)caG>caA	p.Q202Q	BCAS3_ENST00000407086.3_Silent_p.Q202Q|BCAS3_ENST00000408905.3_Silent_p.Q202Q|BCAS3_ENST00000588462.1_Silent_p.Q202Q|BCAS3_ENST00000589222.1_Silent_p.Q202Q	NM_001099432.1	NP_001092902.1			breast carcinoma amplified sequence 3											NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(24)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			TAGTCTTGCAGGAGAAAATTG	0.328																																					p.Q202Q		Atlas-SNP	.											.	BCAS3	90	.	0			c.G606A						PASS	.						110	101	104					17																	58952044		1820	4081	5901	SO:0001819	synonymous_variant	54828	exon9			CTTGCAGGAGAAA	AF361219	CCDS11626.1, CCDS45749.1	17q23.2	2013-06-25			ENSG00000141376	ENSG00000141376		"WD repeat domain containing"	14347	protein-coding gene	gene with protein product		607470				12378525	Standard	NM_017679		Approved	FLJ20128	uc002iyv.4	Q9H6U6	OTTHUMG00000180064	ENST00000390652.5:c.606G>A	17.37:g.58952044G>A		48	0	0		49	25	0.510204	NM_001099432		Silent	SNP	ENST00000390652.5	37	CCDS45749.1																																																																																			.	.	none		0.328	BCAS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449578.1	NM_017679		A	58952044	G	A	58952044	2	1	27	1	0	0	0	0	0	0	0	1	1352	991	35	2		2	BCAS3	17	58952044	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1704911	58952044	22243166	842	11293											
LIMD2	80774	hgsc.bcm.edu	37	chr17	61775992	61775992	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcggccaaacccctcgtcgtAgttgcctttgctcttaaaca	8	11	8	14	3	1	0	0	0	1	0	3	0	1	0	4	1	4	3	4	1	4	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:61775992A>T	ENST00000259006.3	-	5	462	c.304T>A	c.(304-306)Tac>Aac	p.Y102N	LIMD2_ENST00000578061.1_Missense_Mutation_p.Y102N|LIMD2_ENST00000583211.1_Missense_Mutation_p.Y53N|LIMD2_ENST00000578402.1_Missense_Mutation_p.Y102N|LIMD2_ENST00000582055.1_Missense_Mutation_p.Y53N|LIMD2_ENST00000578993.1_Missense_Mutation_p.Y62N	NM_030576.3	NP_085053.1	Q9BT23	LIMD2_HUMAN	LIM domain containing 2	102							zinc ion binding (GO:0008270)			kidney(1)|lung(2)	3						CCCTCGTCGTAGTTGCCTTTG	0.617																																					p.Y102N		Atlas-SNP	.											.	LIMD2	6	.	0			c.T304A						PASS	.						73	58	63					17																	61775992		2203	4300	6503	SO:0001583	missense	80774	exon5			CGTCGTAGTTGCC	AK092301	CCDS11641.1	17q23.3	2006-02-03				ENSG00000136490			28142	protein-coding gene	gene with protein product						12477932	Standard	NM_030576		Approved	MGC10986	uc002jbj.4	Q9BT23		ENST00000259006.3:c.304T>A	17.37:g.61775992A>T	ENSP00000259006:p.Tyr102Asn	94	0	0		102	27	0.264706	NM_030576	D3DU16|Q96S91	Missense_Mutation	SNP	ENST00000259006.3	37	CCDS11641.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.358147	0.82243	.	.	ENSG00000136490	ENST00000259006	T	0.79845	-1.31	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	D	0.90212	0.6940	M	0.86268	2.805	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.91871	0.5507	10	0.87932	D	0	-26.4471	14.5766	0.68252	1.0:0.0:0.0:0.0	.	102	Q9BT23	LIMD2_HUMAN	N	102	ENSP00000259006:Y102N	ENSP00000259006:Y102N	Y	-	1	0	LIMD2	59129724	1.000000	0.71417	1.000000	0.80357	0.480000	0.33159	9.313000	0.96297	2.100000	0.63781	0.533000	0.62120	TAC	.	.	none		0.617	LIMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443877.1	NM_030576		T	61775992	A	T	61775992	3	4	27	1	0	0	0	0	1	0	0	0	8808	420	15	5	83	5	LIMD2	17	61775992	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	2823948	61775992	19419218	843	11294											
GH1	2688	hgsc.bcm.edu	37	chr17	61995189	61995189	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acgttgctgtcagaggcgccGtacaccaggctgttggcgaa	8	8	14	11	4	1	1	1	0	0	1	1	2	1	1	2	3	2	5	2	3	2	3	rs370785603		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:61995189G>A	ENST00000323322.5	-	4	429	c.387C>T	c.(385-387)taC>taT	p.Y129Y	GH1_ENST00000342364.4_Intron|CSHL1_ENST00000392824.4_Intron|GH1_ENST00000351388.4_Silent_p.Y89Y|GH1_ENST00000458650.2_Silent_p.Y114Y	NM_000515.3	NP_000506.2	P01241	SOMA_HUMAN	growth hormone 1	129					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						CAGAGGCGCCGTACACCAGGC	0.607																																					p.Y129Y		Atlas-SNP	.											GH1,caecum,carcinoma,0,1	GH1	39	1	0			c.C387T						scavenged	.	A	,,,,	1,4405	826.1+/-416.6	0,1,2202	67	66	66		387,342,267,,	-4.1	0.6	17		66	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,intron	GH1	NM_000515.3,NM_022559.2,NM_022560.2,NM_022561.2,NM_022562.2	,,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,,	129/218,114/203,89/178,,	61995189	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2688	exon4			GGCGCCGTACACC	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.387C>T	17.37:g.61995189G>A		131	1	0.00763359		101	30	0.29703	NM_000515	A6NEF6|Q14405|Q16631|Q5EB53|Q9HBZ1|Q9UMJ7|Q9UNL5	Silent	SNP	ENST00000323322.5	37	CCDS11653.1																																																																																			.	.	weak		0.607	GH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417708.1	NM_000515		A	61995189	G	A	61995189	2	1	27	1	0	0	0	0	0	0	0	1	6375	1140	40	1		1	GH1	17	61995189	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	219197	61995189	19200021	844	11295											
LRRC37A3	374819	hgsc.bcm.edu	37	chr17	62856646	62856646	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcccttggggctggacttccGagccttttttcttcggcagt	3	15	11	12	2	1	0	0	0	1	0	4	2	3	1	3	4	1	2	3	4	0	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:62856646G>A	ENST00000584306.1	-	11	4148	c.3618C>T	c.(3616-3618)ctC>ctT	p.L1206L	LRRC37A3_ENST00000334962.5_Silent_p.L183L|LRRC37A3_ENST00000400877.3_Silent_p.L244L|LRRC37A3_ENST00000319651.5_Silent_p.L1206L|LRRC37A3_ENST00000339474.5_Silent_p.L324L	NM_199340.2	NP_955372.2	O60309	L37A3_HUMAN	leucine rich repeat containing 37, member A3	1206						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						CTGGACTTCCGAGCCTTTTTT	0.562																																					p.L1206L		Atlas-SNP	.											.	LRRC37A3	75	.	0			c.C3618T						PASS	.																																			SO:0001819	synonymous_variant	374819	exon11			ACTTCCGAGCCTT	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.3618C>T	17.37:g.62856646G>A		38	0	0		38	21	0.552632	NM_199340	Q49A01|Q49A80|Q8NB33	Silent	SNP	ENST00000584306.1	37	CCDS32708.1																																																																																			.	.	none		0.562	LRRC37A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445377.1	NM_199340		A	62856646	G	A	62856646	2	1	27	1	0	0	0	0	0	0	0	1	9002	1045	37	1		1	LRRC37A3	17	62856646	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	861457	62856646	18338564	845	11296											
COG1	9382	hgsc.bcm.edu	37	chr17	71193525	71193525	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctggagaccatcacaggccaGcatcctgccggtgagctctt	8	8	11	14	1	2	2	1	1	1	1	3	3	3	2	4	3	3	2	4	3	0	1	rs117208167	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:71193525G>C	ENST00000299886.4	+	4	983	c.903G>C	c.(901-903)caG>caC	p.Q301H	RP11-143K11.5_ENST00000580671.1_RNA	NM_018714.2	NP_061184.1	Q8WTW3	COG1_HUMAN	component of oligomeric golgi complex 1	301					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)			TCACAGGCCAGCATCCTGCCG	0.522													G|||	15	0.00299521	0.0008	0.0	5008	,	,		18880	0.001		0.0099	False		,,,				2504	0.0031				p.Q301H		Atlas-SNP	.											.	COG1	46	.	0			c.G903C						PASS	.	G	HIS/GLN	6,4400	11.4+/-27.6	0,6,2197	64	62	63		903	3.3	0.9	17	dbSNP_132	63	71,8529	43.1+/-100.9	0,71,4229	yes	missense	COG1	NM_018714.2	24	0,77,6426	CC,CG,GG		0.8256,0.1362,0.592	probably-damaging	301/981	71193525	77,12929	2203	4300	6503	SO:0001583	missense	9382	exon4			AGGCCAGCATCCT		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.903G>C	17.37:g.71193525G>C	ENSP00000299886:p.Gln301His	75	0	0		49	24	0.489796	NM_018714	Q9NPV9|Q9P2G6	Missense_Mutation	SNP	ENST00000299886.4	37	CCDS11692.1	8	0.003663003663003663	0	0.0	0	0.0	1	0.0017482517482517483	7	0.009234828496042216	G	8.408	0.843455	0.16963	0.001362	0.008256	ENSG00000166685	ENST00000438720;ENST00000299886	T;T	0.24908	1.83;1.84	5.31	3.26	0.37387	.	0.492896	0.23176	N	0.051061	T	0.27798	0.0684	M	0.72479	2.2	0.40675	D	0.982259	D;D;D	0.57571	0.98;0.964;0.98	P;P;P	0.52267	0.694;0.679;0.694	T	0.06661	-1.0814	10	0.44086	T	0.13	-3.2025	7.9278	0.29885	0.1457:0.1339:0.7204:0.0	.	301;301;301	E9PBL8;Q8WTW3;Q4G0L8	.;COG1_HUMAN;.	H	301	ENSP00000400111:Q301H;ENSP00000299886:Q301H	ENSP00000299886:Q301H	Q	+	3	2	COG1	68705120	0.612000	0.27000	0.889000	0.34880	0.675000	0.39556	1.226000	0.32563	0.686000	0.31488	0.655000	0.94253	CAG	G|0.994;C|0.006	0.006	strong		0.522	COG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441638.1			C	71193525	G	C	71193525	3	2	27	1	0	0	0	0	1	0	0	0	3659	962	34	4	917	4	COG1	17	71193525	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	8336879	71193525	10001685	846	11297											
GPR142	350383	hgsc.bcm.edu	37	chr17	72367973	72367973	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcggatatcatcatccaggTggtcatcgtgttcgcgggct	6	12	12	11	4	3	0	3	0	0	0	7	1	4	1	1	4	0	2	1	4	1	2	rs148514779	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:72367973T>C	ENST00000335666.4	+	4	671	c.623T>C	c.(622-624)gTg>gCg	p.V208A		NM_181790.1	NP_861455.1	Q7Z601	GP142_HUMAN	G protein-coupled receptor 142	208						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						ATCATCCAGGTGGTCATCGTG	0.657													T|||	8	0.00159744	0.0008	0.0029	5008	,	,		18903	0.0		0.005	False		,,,				2504	0.0				p.V208A		Atlas-SNP	.											.	GPR142	74	.	0			c.T623C						PASS	.	T	ALA/VAL	5,4401	9.9+/-24.2	0,5,2198	84	68	74		623	5	1	17	dbSNP_134	74	46,8554	30.1+/-81.4	0,46,4254	yes	missense	GPR142	NM_181790.1	64	0,51,6452	CC,CT,TT		0.5349,0.1135,0.3921	probably-damaging	208/463	72367973	51,12955	2203	4300	6503	SO:0001583	missense	350383	exon4			TCCAGGTGGTCAT	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.623T>C	17.37:g.72367973T>C	ENSP00000335158:p.Val208Ala	75	0	0		65	39	0.6	NM_181790	A4CYJ8|Q86SL3	Missense_Mutation	SNP	ENST00000335666.4	37	CCDS11698.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	T	25.2	4.615913	0.87359	0.001135	0.005349	ENSG00000257008	ENST00000335666	T	0.38240	1.15	4.99	4.99	0.66335	GPCR, rhodopsin-like superfamily (1);	0.065348	0.64402	D	0.000007	T	0.43188	0.1236	L	0.47716	1.5	0.43007	D	0.994535	D;D	0.58620	0.977;0.983	P;D	0.65233	0.814;0.933	T	0.50734	-0.8793	10	0.72032	D	0.01	-25.2533	14.4349	0.67274	0.0:0.0:0.0:1.0	.	208;1170	Q7Z601;Q8NGB0	GP142_HUMAN;.	A	208	ENSP00000335158:V208A	ENSP00000335158:V208A	V	+	2	0	GPR142	69879568	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.848000	0.69458	2.188000	0.69820	0.529000	0.55759	GTG	T|0.997;C|0.003	0.003	strong		0.657	GPR142-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442545.1	NM_181790		C	72367973	T	C	72367973	3	2	27	1	0	0	0	0	1	0	0	0	6658	1696	59	3	637	3	GPR142	17	72367973	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	1174448	72367973	8827237	847	11298											
HN1	51155	hgsc.bcm.edu	37	chr17	73143748	73143748	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgccaccactagacttggcaCctaaaaatcaaaatatactt	16	10	4	11	0	1	1	1	0	0	1	1	1	1	1	3	1	2	1	3	1	8	6	rs200749518		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:73143748C>G	ENST00000409753.3	-	3	485	c.200G>C	c.(199-201)gGt>gCt	p.G67A	HN1_ENST00000481647.1_Splice_Site_p.G21A|HN1_ENST00000356033.4_Splice_Site_p.G67A|RP11-649A18.4_ENST00000579554.1_RNA|HN1_ENST00000482348.1_Splice_Site_p.G21A|HN1_ENST00000476258.1_Splice_Site_p.G21A|HN1_ENST00000405458.3_Splice_Site_p.G21A|HN1_ENST00000470924.1_Splice_Site_p.G21A|HN1_ENST00000465454.1_5'Flank|Y_RNA_ENST00000516233.1_RNA|HN1_ENST00000392566.2_Splice_Site_p.G21A|HN1_ENST00000581874.1_Splice_Site_p.G67A	NM_016185.2	NP_057269.1	Q9UK76	HN1_HUMAN	hematological and neurological expressed 1	67					developmental process (GO:0032502)	nucleus (GO:0005634)			HN1/USH1G(2)	breast(1)	1	all_lung(278;0.14)|Lung NSC(278;0.168)					AGACTTGGCACCTAAAAATCA	0.453																																					p.G67A		Atlas-SNP	.											.	HN1	17	.	0			c.G200C						PASS	.						58	60	59					17																	73143748		2203	4300	6503	SO:0001630	splice_region_variant	51155	exon3			TTGGCACCTAAAA	AF086910	CCDS32729.1, CCDS45771.1, CCDS45772.1	17q25.1	2013-09-20			ENSG00000189159	ENSG00000189159			14569	protein-coding gene	gene with protein product	"androgen-regulated protein 2"					15094197	Standard	NM_001002032		Approved	ARM2, HN1A	uc002jnb.1	Q9UK76	OTTHUMG00000154521	ENST00000409753.3:c.200-1G>C	17.37:g.73143748C>G		34	0	0		24	14	0.583333	NM_016185	B2R6K3|Q53FG7|Q7Z2D2|Q7Z2F0	Missense_Mutation	SNP	ENST00000409753.3	37	CCDS45771.1	.	.	.	.	.	.	.	.	.	.	C	16.21	3.059740	0.55325	.	.	ENSG00000189159	ENST00000405458;ENST00000409753;ENST00000356033;ENST00000409135;ENST00000392566	.	.	.	4.97	4.0	0.46444	.	0.129701	0.52532	D	0.000061	T	0.63745	0.2537	M	0.63843	1.955	0.46954	D	0.99926	D;P;D	0.56035	0.974;0.827;0.971	P;B;P	0.54499	0.754;0.418;0.721	T	0.65479	-0.6158	9	0.59425	D	0.04	.	9.2449	0.37520	0.0:0.8284:0.0:0.1716	.	67;67;67	B8ZZT7;Q9UK76-2;Q9UK76	.;.;HN1_HUMAN	A	21;67;67;67;21	.	ENSP00000348316:G67A	G	-	2	0	HN1	70655343	1.000000	0.71417	0.999000	0.59377	0.671000	0.39405	3.060000	0.49955	1.208000	0.43306	0.467000	0.42956	GGT	C|0.999;G|0.001	0.001	weak		0.453	HN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335692.1	NM_001002032	Missense_Mutation	G	73143748	C	G	73143748	5	3	27	1	0	0	0	0	0	0	1	0	7258	521	18	4	376	4	HN1	17	73143748	Splice_Site	SNP	C	TCGA-G8-6909-01A-11D-2210-10	775775	73143748	8051462	848	11299											
TSEN54	283989	hgsc.bcm.edu	37	chr17	73520435	73520435	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctttgccctggtggatcatgGtgacatctccttctacagct	6	14	9	12	0	3	1	1	1	2	0	4	2	3	2	2	3	3	1	2	3	1	3	rs200275380		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:73520435G>A	ENST00000333213.6	+	11	1559	c.1523G>A	c.(1522-1524)gGt>gAt	p.G508D	LLGL2_ENST00000578363.1_5'Flank|LLGL2_ENST00000375227.4_5'Flank|LLGL2_ENST00000167462.5_5'Flank|LLGL2_ENST00000392550.3_5'Flank	NM_207346.2	NP_997229.2	Q7Z6J9	SEN54_HUMAN	TSEN54 tRNA splicing endonuclease subunit	508					mRNA processing (GO:0006397)|tRNA splicing, via endonucleolytic cleavage and ligation (GO:0006388)	nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)	13	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)			GTGGATCATGGTGACATCTCC	0.582																																					p.G508D		Atlas-SNP	.											.	TSEN54	27	.	0			c.G1523A						PASS	.						178	144	155					17																	73520435		2203	4300	6503	SO:0001583	missense	283989	exon11			ATCATGGTGACAT	AK097583	CCDS11724.1	17q25.1	2013-08-06	2013-08-06		ENSG00000182173	ENSG00000182173		"tRNA splicing endonuclease subunits"	27561	protein-coding gene	gene with protein product		608755	"tRNA splicing endonuclease 54 homolog (SEN54, S. cerevisiae)", "tRNA splicing endonuclease 54 homolog (S. cerevisiae)"			15109492	Standard	NM_207346		Approved	SEN54, SEN54L	uc002jof.1	Q7Z6J9		ENST00000333213.6:c.1523G>A	17.37:g.73520435G>A	ENSP00000327487:p.Gly508Asp	180	0	0		150	83	0.553333	NM_207346	Q86WV3|Q86XE4|Q8N9H2	Missense_Mutation	SNP	ENST00000333213.6	37	CCDS11724.1	.	.	.	.	.	.	.	.	.	.	G	35	5.485368	0.96323	.	.	ENSG00000182173	ENST00000333213	T	0.60424	0.19	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.77638	0.4160	M	0.74258	2.255	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.79179	-0.1910	10	0.72032	D	0.01	-14.4051	19.6034	0.95572	0.0:0.0:1.0:0.0	.	508	Q7Z6J9	SEN54_HUMAN	D	508	ENSP00000327487:G508D	ENSP00000327487:G508D	G	+	2	0	TSEN54	71032030	1.000000	0.71417	0.970000	0.41538	0.988000	0.76386	9.171000	0.94802	2.637000	0.89404	0.561000	0.74099	GGT	G|0.999;A|0.001	0.001	weak		0.582	TSEN54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447618.1	NM_207346		A	73520435	G	A	73520435	3	1	27	1	0	0	0	0	1	0	0	0	16629	1261	44	2	1565	2	TSEN54	17	73520435	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	376687	73520435	7674775	849	11300											
SFRS2	6427	hgsc.bcm.edu	37	chr17	74732390	74732395	+	In_Frame_Del	DEL	GGACTT	GGACTT	-																															cgagatctggagaccgacgaGgacttggacttggaccttcg																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	GGACTT	GGACTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:74732390_74732395delGGACTT	ENST00000392485.2	-	2	686_691	c.514_519delAAGTCC	c.(514-519)aagtccdel	p.KS172del	MFSD11_ENST00000355954.3_5'Flank|MFSD11_ENST00000586622.1_5'UTR|MFSD11_ENST00000336509.4_5'Flank|MIR636_ENST00000384825.1_RNA|SRSF2_ENST00000359995.5_In_Frame_Del_p.KS172del|MFSD11_ENST00000591864.1_5'Flank|SRSF2_ENST00000508921.3_In_Frame_Del_p.KS160del|MFSD11_ENST00000590514.1_5'Flank|MFSD11_ENST00000593181.1_5'Flank|RP11-318A15.7_ENST00000587459.1_Intron|MFSD11_ENST00000590393.1_5'Flank|MFSD11_ENST00000588460.1_5'UTR	NM_003016.4	NP_003007.2	Q01130	SRSF2_HUMAN	serine/arginine-rich splicing factor 2	172	Arg/Ser-rich (RS domain).				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)|regulation of RNA biosynthetic process (GO:2001141)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular vesicular exosome (GO:0070062)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|transcription corepressor activity (GO:0003714)			haematopoietic_and_lymphoid_tissue(320)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)	329						AGACCGACGAGGACTTGGACTTGGAC	0.617			Mis		"MDS, CLL"																																p.172_174del		Pindel,Atlas-Indel	.		Dom	yes		17	17q25	6427	serine/arginine-rich splicing factor 2		L	.	SRSF2	544	.	0			c.515_520del						PASS	.																																			SO:0001651	inframe_deletion	6427	exon2			.	M90104	CCDS11749.1	17q25.2	2014-09-17	2010-06-22	2010-06-22	ENSG00000161547	ENSG00000161547		"Serine/arginine-rich splicing factors", "RNA binding motif (RRM) containing"	10783	protein-coding gene	gene with protein product	"SR splicing factor 2"	600813	"splicing factor, arginine/serine-rich 2"	SFRS2		8530103, 20516191	Standard	NM_003016		Approved	SC-35, SC35, PR264, SFRS2A	uc002jsv.3	Q01130		ENST00000392485.2:c.514_519delAAGTCC	17.37:g.74732396_74732401delGGACTT	ENSP00000376276:p.Lys172_Ser173del	72	0	.		67	14	0.209	NM_001195427	B3KWD5|B4DN89|H0YG49	In_Frame_Del	DEL	ENST00000392485.2	37	CCDS11749.1																																																																																			.	.	none		0.617	SRSF2-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437489.1	NM_003016		-	74732395	GGACTT	-	74732390	7	5	27	1	0	1	0	1	0	0	0	0	14190	987	35	0	150	0	SFRS2	17	74732390	In_Frame_Del	DEL	GGACTT	TCGA-G8-6909-01A-11D-2210-10	1211955	74732390	6462820	850	11301											
TMC6	11322	hgsc.bcm.edu	37	chr17	76117136	76117136	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccagtaccggggagtcatgcGgctccagggcggccaggaca	8	4	16	13	3	1	0	1	0	0	0	2	2	2	2	4	6	2	2	4	6	1	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:76117136G>A	ENST00000590602.1	-	12	1652	c.1493C>T	c.(1492-1494)cCg>cTg	p.P498L	TMC6_ENST00000592076.1_Intron|TMC6_ENST00000322914.3_Missense_Mutation_p.P498L|TMC6_ENST00000591436.1_Missense_Mutation_p.P137L|TMC6_ENST00000322933.4_Missense_Mutation_p.P137L|TMC6_ENST00000392467.3_Missense_Mutation_p.P498L|TMC6_ENST00000589553.1_Missense_Mutation_p.P271L|TMC6_ENST00000306591.7_Intron			Q7Z403	TMC6_HUMAN	transmembrane channel-like 6	498					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)			GGAGTCATGCGGCTCCAGGGC	0.632																																					p.P498L		Atlas-SNP	.											.	TMC6	42	.	0			c.C1493T						PASS	.						40	39	39					17																	76117136		2203	4300	6503	SO:0001583	missense	11322	exon12			TCATGCGGCTCCA	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.1493C>T	17.37:g.76117136G>A	ENSP00000465261:p.Pro498Leu	117	0	0		129	71	0.550388	NM_001127198	O43284|Q45VJ2|Q8IU98|Q8IUI7|Q8IWU8|Q8TEQ7|Q9HAG5	Missense_Mutation	SNP	ENST00000590602.1	37	CCDS32748.1	.	.	.	.	.	.	.	.	.	.	G	4.500	0.092789	0.08632	.	.	ENSG00000141524	ENST00000322914;ENST00000392467;ENST00000322933	T;T;T	0.70399	-0.1;-0.1;-0.48	3.93	0.273	0.15650	.	0.837178	0.10830	N	0.629444	T	0.44414	0.1292	N	0.19112	0.55	0.33151	D	0.545754	B;P;B;B	0.39094	0.099;0.659;0.09;0.259	B;B;B;B	0.24848	0.033;0.056;0.005;0.027	T	0.48080	-0.9066	10	0.42905	T	0.14	-12.4351	4.296	0.10901	0.0:0.191:0.2303:0.5788	.	271;498;498;137	Q7Z403-4;B3KTU5;Q7Z403;Q7Z403-3	.;.;TMC6_HUMAN;.	L	498;498;137	ENSP00000313408:P498L;ENSP00000376260:P498L;ENSP00000313479:P137L	ENSP00000313408:P498L	P	-	2	0	TMC6	73628731	0.022000	0.18835	0.402000	0.26371	0.729000	0.41735	-0.010000	0.12743	-0.092000	0.12417	0.462000	0.41574	CCG	.	.	none		0.632	TMC6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437146.1			A	76117136	G	A	76117136	3	1	27	1	0	0	0	0	1	0	0	0	16004	1116	39	1	960	1	TMC6	17	76117136	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1384746	76117136	5078074	851	11302											
DNAH17	8632	hgsc.bcm.edu	37	chr17	76490894	76490894	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atggctctcaggccccagtcGtaatgatcctgcgggcagtg	7	9	13	12	2	1	1	1	1	1	0	4	1	2	1	3	3	1	3	3	3	1	1	rs372912923		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:76490894G>A	ENST00000585328.1	-	40	6160	c.6036C>T	c.(6034-6036)taC>taT	p.Y2012Y	DNAH17_ENST00000389840.5_Silent_p.Y2003Y|RP11-559N14.5_ENST00000585969.1_RNA|RP11-559N14.5_ENST00000591373.1_RNA	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	2003	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(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)			GGCCCCAGTCGTAATGATCCT	0.672																																					p.Y2017Y		Atlas-SNP	.											.	DNAH17	347	.	0			c.C6051T						PASS	.	G		0,4330		0,0,2165	18	21	20		6051	-2	0.9	17		20	9,8557		0,9,4274	no	coding-synonymous	DNAH17	NM_173628.3		0,9,6439	AA,AG,GG		0.1051,0.0,0.0698		2017/4463	76490894	9,12887	2165	4283	6448	SO:0001819	synonymous_variant	8632	exon40			CCAGTCGTAATGA	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.6036C>T	17.37:g.76490894G>A		73	0	0		85	42	0.494118	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				.	.	weak		0.672	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		A	76490894	G	A	76490894	2	1	27	1	0	0	0	0	0	0	0	1	4603	1140	40	1		1	DNAH17	17	76490894	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	373758	76490894	4704316	852	11303											
ENGASE	64772	hgsc.bcm.edu	37	chr17	77082174	77082174	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttcctcctctcacaagtcCgttgcttccgaatccactgc	6	12	5	18	2	1	0	1	0	1	0	7	1	6	0	6	0	2	2	6	0	2	3	rs117014247	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:77082174C>T	ENST00000579016.1	+	14	1975	c.1975C>T	c.(1975-1977)Cgt>Tgt	p.R659C		NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	659						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						CTCACAAGTCCGTTGCTTCCG	0.637													C|||	34	0.00678914	0.0015	0.013	5008	,	,		17023	0.0		0.0199	False		,,,				2504	0.0031				p.R659C		Atlas-SNP	.											.	ENGASE	55	.	0			c.C1975T						PASS	.	C	CYS/ARG	17,4281		0,17,2132	58	68	64		1975	2	0.1	17	dbSNP_132	64	185,8325		1,183,4071	yes	missense	ENGASE	NM_001042573.1	180	1,200,6203	TT,TC,CC		2.1739,0.3955,1.5771	benign	659/744	77082174	202,12606	2149	4255	6404	SO:0001583	missense	64772	exon14			CAAGTCCGTTGCT	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.1975C>T	17.37:g.77082174C>T	ENSP00000462333:p.Arg659Cys	70	0	0		63	42	0.666667	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Missense_Mutation	SNP	ENST00000579016.1	37	CCDS42394.1	22	0.010073260073260074	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	15	0.01978891820580475	C	6.060	0.379407	0.11466	0.003955	0.021739	ENSG00000167280	ENST00000545583	.	.	.	4.26	2.01	0.26516	.	0.333614	0.31797	N	0.007049	T	0.16642	0.0400	L	0.56769	1.78	0.09310	N	0.999999	B	0.27594	0.182	B	0.17979	0.02	T	0.20107	-1.0285	9	0.54805	T	0.06	-3.595	2.1577	0.03816	0.4416:0.2981:0.1551:0.1052	.	659	Q8NFI3	ENASE_HUMAN	C	659	.	ENSP00000438577:R659C	R	+	1	0	ENGASE	74593769	0.000000	0.05858	0.093000	0.20910	0.199000	0.23934	-0.105000	0.10907	0.939000	0.37446	0.467000	0.42956	CGT	C|0.982;T|0.018	0.018	strong		0.637	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759		T	77082174	C	T	77082174	3	4	27	1	0	0	0	0	1	0	0	0	5120	652	23	1	2029	1	ENGASE	17	77082174	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	591280	77082174	4113036	853	11304											
RNF213	57674	hgsc.bcm.edu	37	chr17	78237572	78237572	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctgcctcctgcagcccccaTagcaggtgaggcccaggggt	6	6	14	15	0	0	1	0	1	0	0	1	1	1	1	5	4	4	3	5	4	1	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:78237572T>C	ENST00000582970.1	+	2	235	c.92T>C	c.(91-93)aTa>aCa	p.I31T	RNF213_ENST00000508628.2_Missense_Mutation_p.I31T|RNF213_ENST00000456466.1_Missense_Mutation_p.I31T|RNF213_ENST00000319921.4_Missense_Mutation_p.I31T	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	31					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)			GCAGCCCCCATAGCAGGTGAG	0.642																																					p.I31T		Atlas-SNP	.											.	RNF213	766	.	0			c.T92C						PASS	.						39	41	40					17																	78237572		2203	4300	6503	SO:0001583	missense	57674	exon2			CCCCCATAGCAGG	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.92T>C	17.37:g.78237572T>C	ENSP00000464087:p.Ile31Thr	98	0	0		90	4	0.0444444	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	T	8.002	0.755608	0.15846	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000456466;ENST00000319921	T	0.22743	1.94	3.71	-6.01	0.02199	.	.	.	.	.	T	0.07188	0.0182	N	0.08118	0	0.09310	N	0.999995	B	0.21452	0.056	B	0.18263	0.021	T	0.28202	-1.0051	9	0.46703	T	0.11	.	0.4433	0.00489	0.2848:0.2872:0.1455:0.2825	.	31	Q9HCF4-2	.	T	31	ENSP00000425956:I31T	ENSP00000324392:I31T	I	+	2	0	RNF213	75852167	0.000000	0.05858	0.000000	0.03702	0.060000	0.15804	-3.408000	0.00481	-1.514000	0.01786	0.460000	0.39030	ATA	.	.	none		0.642	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		C	78237572	T	C	78237572	3	2	27	1	0	0	0	0	1	0	0	0	13492	1406	49	3	94	3	RNF213	17	78237572	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	1155398	78237572	2957638	854	11305											
RPTOR	57521	hgsc.bcm.edu	37	chr17	78820351	78820351	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tggagaaccgaaacccacccGaacagctgcccatcgtcctg	11	5	9	16	3	0	1	0	0	0	1	2	4	1	1	5	1	5	1	5	1	3	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:78820351G>A	ENST00000306801.3	+	11	1653	c.1291G>A	c.(1291-1293)Gaa>Aaa	p.E431K	RPTOR_ENST00000544334.2_Missense_Mutation_p.E431K|RPTOR_ENST00000575542.1_3'UTR|RPTOR_ENST00000537330.1_Missense_Mutation_p.E246K	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	431					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						AAACCCACCCGAACAGCTGCC	0.627																																					p.E431K		Atlas-SNP	.											.	RPTOR	122	.	0			c.G1291A						PASS	.						145	112	123					17																	78820351		2203	4300	6503	SO:0001583	missense	57521	exon11			CCACCCGAACAGC		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.1291G>A	17.37:g.78820351G>A	ENSP00000307272:p.Glu431Lys	76	0	0		88	27	0.306818	NM_001163034	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Missense_Mutation	SNP	ENST00000306801.3	37	CCDS11773.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.912856	0.92178	.	.	ENSG00000141564	ENST00000537330;ENST00000306801;ENST00000544334	T;T;T	0.34472	1.36;1.36;1.36	4.92	4.92	0.64577	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.68778	0.3038	M	0.92219	3.285	0.80722	D	1	D;D;D	0.89917	0.995;1.0;0.998	D;D;P	0.85130	0.956;0.997;0.843	T	0.74390	-0.3681	10	0.35671	T	0.21	.	17.7008	0.88294	0.0:0.0:1.0:0.0	.	431;246;431	F5H7J5;F5GXV9;Q8N122	.;.;RPTOR_HUMAN	K	246;431;431	ENSP00000440947:E246K;ENSP00000307272:E431K;ENSP00000442479:E431K	ENSP00000307272:E431K	E	+	1	0	RPTOR	76434946	1.000000	0.71417	0.834000	0.33040	0.611000	0.37282	8.736000	0.91554	2.267000	0.75376	0.467000	0.42956	GAA	.	.	none		0.627	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761		A	78820351	G	A	78820351	3	1	27	1	0	0	0	0	1	0	0	0	13680	1059	37	1	1333	1	RPTOR	17	78820351	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	582779	78820351	2374859	855	11306											
CHMP6	79643	hgsc.bcm.edu	37	chr17	78972192	78972192	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atagagctgccagaggttccCtccgagccccttcctgagaa	9	8	10	14	1	0	3	0	1	0	3	3	5	3	3	6	1	3	2	6	1	2	3	rs61752553	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:78972192C>T	ENST00000325167.5	+	7	600	c.522C>T	c.(520-522)ccC>ccT	p.P174P	CTD-2561B21.7_ENST00000577061.2_RNA|CTD-2561B21.7_ENST00000576215.1_RNA	NM_024591.4	NP_078867.2	Q96FZ7	CHMP6_HUMAN	charged multivesicular body protein 6	174	Interaction with VPS4A.				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)			CAGAGGTTCCCTCCGAGCCCC	0.522																																					p.P174P		Atlas-SNP	.											.	CHMP6	16	.	0			c.C522T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	108	110	109		522	-7.9	0	17	dbSNP_129	109	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CHMP6	NM_024591.4		0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231		174/202	78972192	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	79643	exon7			GGTTCCCTCCGAG	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.522C>T	17.37:g.78972192C>T		137	0	0		125	5	0.04	NM_024591	A8K7U0|Q53FU4|Q9HAE8	Silent	SNP	ENST00000325167.5	37	CCDS11774.1																																																																																			C|0.999;T|0.001	0.001	strong		0.522	CHMP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438215.1	NM_024591		T	78972192	C	T	78972192	2	4	27	1	0	0	0	0	0	0	0	1	3362	668	24	2		2	CHMP6	17	78972192	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	151841	78972192	2223018	856	11307											
AATK	9625	hgsc.bcm.edu	37	chr17	79100340	79100340	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccgccacccggcagctccgCaggtagcccttgaggtcccc	5	6	11	19	3	0	1	0	1	0	0	3	1	3	1	7	3	2	4	7	3	1	2	rs139267162	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:79100340C>T	ENST00000326724.4	-	7	666	c.642G>A	c.(640-642)ctG>ctA	p.L214L	MIR657_ENST00000385003.1_RNA|AATK_ENST00000417379.1_Silent_p.L111L|AATK_ENST00000572339.1_5'UTR|MIR338_ENST00000390137.2_RNA	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	214	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)			GGCAGCTCCGCAGGTAGCCCT	0.692													C|||	28	0.00559105	0.0008	0.0144	5008	,	,		15493	0.0		0.0119	False		,,,				2504	0.0051				p.L214L		Atlas-SNP	.											.	AATK	102	.	0			c.G642A						PASS	.	C	,	6,3592		0,6,1793	5	7	6		642,333	2	1	17	dbSNP_134	6	87,7669		1,85,3792	no	coding-synonymous,coding-synonymous	AATK	NM_001080395.2,NM_004920.2	,	1,91,5585	TT,TC,CC		1.1217,0.1668,0.8191	,	214/1375,111/1272	79100340	93,11261	1799	3878	5677	SO:0001819	synonymous_variant	9625	exon7			GCTCCGCAGGTAG	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.642G>A	17.37:g.79100340C>T		60	0	0		59	31	0.525424	NM_001080395	O75136|Q6ZN31|Q86X28	Silent	SNP	ENST00000326724.4	37	CCDS45807.1	14	0.00641025641025641	0	0.0	6	0.016574585635359115	0	0.0	8	0.010554089709762533	C	10.62	1.402433	0.25291	0.001668	0.011217	ENSG00000181409	ENST00000417379	.	.	.	4.07	2.0	0.26442	.	.	.	.	.	T	0.26412	0.0645	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.15925	-1.0420	4	.	.	.	.	1.1434	0.01770	0.162:0.3873:0.2417:0.2089	.	.	.	.	Y	167	.	.	C	-	2	0	AATK	76714935	0.991000	0.36638	0.999000	0.59377	0.919000	0.55068	0.370000	0.20433	0.330000	0.23485	0.467000	0.42956	TGC	C|0.994;T|0.006	0.006	strong		0.692	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920		T	79100340	C	T	79100340	2	4	27	1	0	0	0	0	0	0	0	1	26	697	25	2		2	AATK	17	79100340	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	128148	79100340	2094870	857	11308											
SLC16A3	9123	hgsc.bcm.edu	37	chr17	80195163	80195163	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggcagctgctgcaggacCgctacggctggcggggcggc	4	5	20	12	4	0	0	0	0	0	0	0	1	0	1	1	8	4	6	1	8	1	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:80195163C>T	ENST00000581287.1	+	3	2839	c.517C>T	c.(517-519)Cgc>Tgc	p.R173C	SLC16A3_ENST00000392341.1_Missense_Mutation_p.R173C|SLC16A3_ENST00000582743.1_Missense_Mutation_p.R173C|SLC16A3_ENST00000392339.1_Missense_Mutation_p.R173C	NM_001206951.1|NM_001206952.1	NP_001193880.1|NP_001193881.1	O15427	MOT4_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 3	173					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)	GCTGCAGGACCGCTACGGCTG	0.701																																					p.R173C	Pancreas(52;652 1135 19190 37282 52456)	Atlas-SNP	.											.	SLC16A3	19	.	0			c.C517T						PASS	.						6	6	6					17																	80195163		2142	4199	6341	SO:0001583	missense	9123	exon4			CAGGACCGCTACG	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.517C>T	17.37:g.80195163C>T	ENSP00000463978:p.Arg173Cys	93	0	0		108	34	0.314815	NM_001206950	B3KXG8|Q2M1P8	Missense_Mutation	SNP	ENST00000581287.1	37	CCDS11804.1	.	.	.	.	.	.	.	.	.	.	C	11.76	1.735148	0.30774	.	.	ENSG00000141526	ENST00000392341;ENST00000392339	T;T	0.37584	1.19;1.19	5.69	4.71	0.59529	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.834666	0.11530	N	0.554741	T	0.41419	0.1158	L	0.40543	1.245	0.33977	D	0.647467	P;D	0.53462	0.919;0.96	P;P	0.53062	0.717;0.657	T	0.49293	-0.8955	10	0.56958	D	0.05	.	9.2009	0.37258	0.0:0.6825:0.2372:0.0802	.	173;173	Q53G91;O15427	.;MOT4_HUMAN	C	173	ENSP00000376152:R173C;ENSP00000376150:R173C	ENSP00000376150:R173C	R	+	1	0	SLC16A3	77788452	0.010000	0.17322	0.980000	0.43619	0.812000	0.45895	0.633000	0.24598	2.696000	0.92011	0.655000	0.94253	CGC	.	.	none		0.701	SLC16A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443498.1	NM_004207		T	80195163	C	T	80195163	3	4	27	1	0	0	0	0	1	0	0	0	14424	652	23	1	527	1	SLC16A3	17	80195163	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1094823	80195163	1000047	858	11309											
RAB40B	10966	hgsc.bcm.edu	37	chr17	80616397	80616397	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgccagagccggtccatccCatgccgcagcagcacgatcc	8	4	10	19	4	0	1	0	0	0	1	3	2	3	1	7	1	4	3	7	1	0	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr17:80616397C>T	ENST00000571995.1	-	5	666	c.535G>A	c.(535-537)Ggg>Agg	p.G179R	RAB40B_ENST00000269347.6_5'UTR|RAB40B_ENST00000538809.2_Missense_Mutation_p.M128I|RAB40B_ENST00000571880.1_5'Flank	NM_006822.2	NP_006813.1	Q12829	RB40B_HUMAN	RAB40B, member RAS oncogene family	179	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)			CGGTCCATCCCATGCCGCAGC	0.662																																					p.G179R		Atlas-SNP	.											.	RAB40B	24	.	0			c.G535A						PASS	.						65	66	66					17																	80616397		2203	4300	6503	SO:0001583	missense	10966	exon5			CCATCCCATGCCG	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.535G>A	17.37:g.80616397C>T	ENSP00000461785:p.Gly179Arg	126	0	0		119	31	0.260504	NM_006822	Q8WVG3	Missense_Mutation	SNP	ENST00000571995.1	37	CCDS11816.1	.	.	.	.	.	.	.	.	.	.	C	18.88	3.716630	0.68844	.	.	ENSG00000141542	ENST00000269347;ENST00000538809	.	.	.	4.24	4.24	0.50183	SOCS protein, C-terminal (1);	0.000000	0.64402	D	0.000003	T	0.62600	0.2441	L	0.47716	1.5	0.43412	D	0.995555	B	0.25609	0.13	B	0.36567	0.228	T	0.64702	-0.6345	9	0.51188	T	0.08	.	17.0842	0.86606	0.0:1.0:0.0:0.0	.	179	Q12829	RB40B_HUMAN	R	179;213	.	ENSP00000269347:G179R	G	-	1	0	RAB40B	78209686	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	7.573000	0.82421	2.283000	0.76528	0.591000	0.81541	GGG	.	.	none		0.662	RAB40B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439007.1			T	80616397	C	T	80616397	3	4	27	1	0	0	0	0	1	0	0	0	12956	594	21	2	309	2	RAB40B	17	80616397	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	421234	80616397	578813	859	11310											
DLGAP1	9229	hgsc.bcm.edu	37	chr18	3534224	3534224	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttgttttcccgttcttccCgctccatctgttgacaccac	4	15	7	15	2	2	1	0	1	2	0	5	1	5	1	4	1	0	5	4	1	0	6	rs35822832	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:3534224C>T	ENST00000315677.3	-	10	3042	c.2447G>A	c.(2446-2448)cGg>cAg	p.R816Q	DLGAP1_ENST00000400149.3_Missense_Mutation_p.R506Q|DLGAP1_ENST00000539435.1_Missense_Mutation_p.R524Q|DLGAP1_ENST00000400147.2_Missense_Mutation_p.R514Q|DLGAP1_ENST00000400145.2_Missense_Mutation_p.R514Q|DLGAP1_ENST00000400155.1_Missense_Mutation_p.R522Q|DLGAP1_ENST00000534970.1_Missense_Mutation_p.R500Q|DLGAP1_ENST00000400150.3_Missense_Mutation_p.R532Q|DLGAP1_ENST00000515196.2_Missense_Mutation_p.R816Q|DLGAP1_ENST00000581527.1_Missense_Mutation_p.R816Q|DLGAP1_ENST00000584874.1_Missense_Mutation_p.R816Q|DLGAP1_ENST00000581699.1_Missense_Mutation_p.R522Q	NM_004746.3	NP_004737.2	O14490	DLGP1_HUMAN	discs, large (Drosophila) homolog-associated protein 1	816			R -> Q (in dbSNP:rs35822832).		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)				CCGTTCTTCCCGCTCCATCTG	0.602													C|||	30	0.00599042	0.003	0.0101	5008	,	,		19947	0.0		0.0179	False		,,,				2504	0.001				p.R816Q		Atlas-SNP	.											.	DLGAP1	201	.	0			c.G2447A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	15,4391	22.3+/-47.3	0,15,2188	109	99	103		1541,2447,1499,1613,1565,1541,1571,2447	5.9	1	18	dbSNP_126	103	219,8381	92.1+/-154.2	2,215,4083	yes	missense,missense,missense,missense,missense,missense,missense,missense	DLGAP1	NM_001003809.2,NM_001242761.1,NM_001242762.1,NM_001242763.1,NM_001242764.1,NM_001242765.1,NM_001242766.1,NM_004746.3	43,43,43,43,43,43,43,43	2,230,6271	TT,TC,CC		2.5465,0.3404,1.7992	benign,benign,benign,benign,benign,benign,benign,benign	514/676,816/930,500/662,538/700,522/684,514/628,524/686,816/978	3534224	234,12772	2203	4300	6503	SO:0001583	missense	9229	exon10			TCTTCCCGCTCCA	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.2447G>A	18.37:g.3534224C>T	ENSP00000316377:p.Arg816Gln	160	0	0		160	70	0.4375	NM_001242761	A8MWN8|B2RMU8|B7WPA1|B7Z2H2|B7Z2I2|B7Z9Y4|O14489|P78335	Missense_Mutation	SNP	ENST00000315677.3	37	CCDS11836.1	20	0.009157509157509158	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	12	0.0158311345646438	C	17.14	3.314540	0.60524	0.003404	0.025465	ENSG00000170579	ENST00000315677;ENST00000400147;ENST00000400150;ENST00000400149;ENST00000400155;ENST00000534970;ENST00000539435;ENST00000400145;ENST00000515196	T;T;T;T;T;T;T;T;T	0.17854	2.25;2.25;2.25;2.25;2.25;2.25;2.25;2.25;2.25	5.93	5.93	0.95920	.	0.106561	0.64402	D	0.000004	T	0.03915	0.0110	N	0.11724	0.165	0.45490	D	0.998455	B;B;B;B;B;B;B;B	0.21309	0.054;0.054;0.017;0.054;0.017;0.043;0.017;0.014	B;B;B;B;B;B;B;B	0.14578	0.006;0.011;0.01;0.006;0.01;0.002;0.004;0.006	T	0.24476	-1.0159	10	0.23891	T	0.37	-19.2872	20.3312	0.98718	0.0:1.0:0.0:0.0	rs35822832	816;500;512;522;524;514;816;514	B7Z9Y4;B7Z2H2;B7Z2J5;A8MWN8;B7Z2I2;O14490-3;O14490;O14490-2	.;.;.;.;.;.;DLGP1_HUMAN;.	Q	816;514;532;506;522;500;524;514;816	ENSP00000316377:R816Q;ENSP00000383011:R514Q;ENSP00000383014:R532Q;ENSP00000383013:R506Q;ENSP00000383019:R522Q;ENSP00000437817:R500Q;ENSP00000446312:R524Q;ENSP00000383010:R514Q;ENSP00000445973:R816Q	ENSP00000316377:R816Q	R	-	2	0	DLGAP1	3524224	1.000000	0.71417	0.988000	0.46212	0.986000	0.74619	4.810000	0.62598	2.797000	0.96272	0.655000	0.94253	CGG	C|0.984;T|0.016	0.016	strong		0.602	DLGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254394.4			T	3534224	C	T	3534224	3	4	27	1	0	0	0	0	1	0	0	0	4561	652	23	1	502	1	DLGAP1	18	3534224	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10		3534224	74543024	860	11311											
PTPRM	5797	hgsc.bcm.edu	37	chr18	8253407	8253407	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctacggcttcaaggaggaaTacgaggtgagcacaagctct	12	7	13	9	2	2	1	1	1	1	0	2	4	2	3	0	4	4	4	0	4	5	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:8253407T>A	ENST00000332175.8	+	17	3747	c.2710T>A	c.(2710-2712)Tac>Aac	p.Y904N	PTPRM_ENST00000400053.4_Missense_Mutation_p.Y842N|PTPRM_ENST00000444013.1_Missense_Mutation_p.Y691N|PTPRM_ENST00000580170.1_Missense_Mutation_p.Y917N|PTPRM_ENST00000400060.4_Missense_Mutation_p.Y918N	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	904	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)				CAAGGAGGAATACGAGGTGAG	0.557																																					p.Y917N		Atlas-SNP	.											.	PTPRM	185	.	0			c.T2749A						PASS	.						43	30	34					18																	8253407		2203	4300	6503	SO:0001583	missense	5797	exon19			GAGGAATACGAGG	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.2710T>A	18.37:g.8253407T>A	ENSP00000331418:p.Tyr904Asn	104	0	0		86	19	0.22093	NM_001105244	A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	37	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.243448	0.79912	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	T;T;T;T	0.34072	1.38;1.38;1.38;1.38	5.93	5.93	0.95920	Protein-tyrosine phosphatase, receptor/non-receptor type (2);	0.000000	0.85682	D	0.000000	T	0.72170	0.3427	H	0.95679	3.705	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.992;0.997;0.997	T	0.81466	-0.0920	10	0.87932	D	0	.	16.3695	0.83350	0.0:0.0:0.0:1.0	.	691;917;904	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	N	904;918;842;691	ENSP00000331418:Y904N;ENSP00000382933:Y918N;ENSP00000382927:Y842N;ENSP00000387608:Y691N	ENSP00000331418:Y904N	Y	+	1	0	PTPRM	8243407	1.000000	0.71417	0.693000	0.30195	0.951000	0.60555	8.033000	0.88852	2.261000	0.74972	0.459000	0.35465	TAC	.	.	none		0.557	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1			A	8253407	T	A	8253407	3	1	27	1	0	0	0	0	1	0	0	0	12821	1406	49	5	2823	5	PTPRM	18	8253407	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	4719183	8253407	69823841	861	11312											
NPC1	4864	hgsc.bcm.edu	37	chr18	21140367	21140367	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gcagtcttggcagctacatgGtgctgtgacctcatccacag	8	10	11	12	0	2	1	1	1	1	0	3	1	3	1	2	2	3	4	2	2	1	2	rs80358251	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:21140367G>A	ENST00000269228.5	-	6	1263	c.709C>T	c.(709-711)Cca>Tca	p.P237S	NPC1_ENST00000540608.1_5'UTR|NPC1_ENST00000412552.2_5'Flank	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	237			P -> S (in NPC1; late infantile form; dbSNP:rs80358251). {ECO:0000269|PubMed:11182931, ECO:0000269|PubMed:11333381, ECO:0000269|PubMed:11349231, ECO:0000269|PubMed:12408188, ECO:0000269|PubMed:12955717}.		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)					CAGCTACATGGTGCTGTGACC	0.547													G|||	23	0.00459265	0.0008	0.0043	5008	,	,		16533	0.0		0.0169	False		,,,				2504	0.002				p.P237S		Atlas-SNP	.											.	NPC1	114	.	0			c.C709T	GRCh37	CM990941	NPC1	M	rs80358251	PASS	.	G	SER/PRO	13,4393	20.2+/-43.8	0,13,2190	70	60	63	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	709	5.9	0.3	18	dbSNP_132	63	137,8463	68.7+/-131.2	1,135,4164	yes	missense	NPC1	NM_000271.4	74	1,148,6354	AA,AG,GG		1.593,0.2951,1.1533	benign	237/1279	21140367	150,12856	2203	4300	6503	SO:0001583	missense	4864	exon6			TACATGGTGCTGT	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.709C>T	18.37:g.21140367G>A	ENSP00000269228:p.Pro237Ser	113	0	0		71	70	0.985915	NM_000271	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	37	CCDS11878.1	14	0.00641025641025641	1	0.0020325203252032522	0	0.0	0	0.0	13	0.017150395778364115	G	11.43	1.635647	0.29068	0.002951	0.01593	ENSG00000141458	ENST00000269228;ENST00000540608	D	0.91011	-2.77	5.87	5.87	0.94306	.	0.052444	0.85682	D	0.000000	T	0.79811	0.4510	L	0.39147	1.195	0.80722	D	1	B;B	0.10296	0.002;0.003	B;B	0.04013	0.001;0.001	T	0.78393	-0.2221	10	0.23891	T	0.37	-22.0744	20.206	0.98277	0.0:0.0:1.0:0.0	.	248;237	Q59GR1;O15118	.;NPC1_HUMAN	S	237;82	ENSP00000269228:P237S	ENSP00000269228:P237S	P	-	1	0	NPC1	19394365	1.000000	0.71417	0.333000	0.25482	0.084000	0.17831	8.061000	0.89467	2.785000	0.95823	0.655000	0.94253	CCA	G|0.991;A|0.009	0.009	strong		0.547	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271		A	21140367	G	A	21140367	3	1	27	1	0	0	0	0	1	0	0	0	10579	1261	44	2	3207	2	NPC1	18	21140367	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	12886960	21140367	56936881	862	11313											
LAMA3	3909	hgsc.bcm.edu	37	chr18	21453038	21453038	+	Intron	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcagtgaggcggtcagcctgCagcatgggatggctgtggat	7	8	18	8	1	1	1	1	1	0	0	1	3	1	3	1	5	3	4	1	5	0	0	rs145044428	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:21453038C>T	ENST00000313654.9	+	38	5239				LAMA3_ENST00000399516.3_Intron|LAMA3_ENST00000269217.6_Silent_p.C10C|LAMA3_ENST00000587184.1_Silent_p.C10C	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3						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)					GGTCAGCCTGCAGCATGGGAT	0.612													C|||	5	0.000998403	0.0	0.0014	5008	,	,		19022	0.0		0.003	False		,,,				2504	0.001				p.C10C		Atlas-SNP	.											.	LAMA3	397	.	0			c.C30T						PASS	.	C	,,,	0,4406		0,0,2203	84	81	82		30,,30,	0.3	0	18	dbSNP_134	82	9,8591	7.7+/-29.5	0,9,4291	no	coding-synonymous,intron,coding-synonymous,intron	LAMA3	NM_000227.3,NM_001127717.1,NM_001127718.1,NM_198129.1	,,,	0,9,6494	TT,TC,CC		0.1047,0.0,0.0692	,,,	10/1725,,10/1669,	21453038	9,12997	2203	4300	6503	SO:0001627	intron_variant	3909	exon1			AGCCTGCAGCATG	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.4998+1413C>T	18.37:g.21453038C>T		97	0	0		86	41	0.476744	NM_001127718	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	37	CCDS42419.1																																																																																			C|0.999;T|0.001	0.001	strong		0.612	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		T	21453038	C	T	21453038	1	4	27	0	1	0	0	0	0	0	0	0	8616	718	25	2		2	LAMA3	18	21453038	Intron	SNP	C	TCGA-G8-6909-01A-11D-2210-10	312671	21453038	56624210	863	11314											
DSC1	1823	hgsc.bcm.edu	37	chr18	28710615	28710615	+	Silent	SNP	C	C	A																															cctttgccttcatagttataCgaacaaacgtagtcttcaca																								rs1816634	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:28710615C>A	ENST00000257198.5	-	16	2808	c.2547G>T	c.(2545-2547)tcG>tcT	p.S849S	DSC1_ENST00000257197.3_3'UTR|RP11-408H20.2_ENST00000581836.1_RNA|RP11-408H20.3_ENST00000582307.1_RNA	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	849					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)			CATAGTTATACGAACAAACGT	0.418													C|||	465	0.0928514	0.2542	0.0533	5008	,	,		18467	0.0		0.0467	False		,,,				2504	0.046				p.S849S		Atlas-SNP	.											.	DSC1	240	.	0			c.G2547T						PASS	.	C	,	886,3520	344.1+/-307.9	88,710,1405	133	134	134		,2547	-12.3	0	18	dbSNP_92	134	344,8256	118.1+/-177.6	6,332,3962	no	utr-3,coding-synonymous	DSC1	NM_004948.3,NM_024421.2	,	94,1042,5367	AA,AC,CC		4.0,20.1089,9.4572	,	,849/895	28710615	1230,11776	2203	4300	6503	SO:0001819	synonymous_variant	1823	exon16			GTTATACGAACAA	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.2547G>T	18.37:g.28710615C>A		246	0	0		201	85	0.422886	NM_024421	Q9HB01	Silent	SNP	ENST00000257198.5	37	CCDS11894.1																																																																																			C|0.914;A|0.086	0.086	strong		0.418	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421		A	28710615	C	A	28710615	2	1	27	1	0	0	0	0	0	0	0	1	4767	523	19	4		4	DSC1	18	28710615	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	7257577	28710615	49366633	864	11315	141	2									
DSC1	1823	hgsc.bcm.edu	37	chr18	28710619	28710619	+	Missense_Mutation	SNP	C	C	A																															tgccttcatagttatacgaaCaaacgtagtcttcacaatgt																								rs985861	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:28710619C>A	ENST00000257198.5	-	16	2804	c.2543G>T	c.(2542-2544)tGt>tTt	p.C848F	DSC1_ENST00000257197.3_3'UTR|RP11-408H20.2_ENST00000581836.1_RNA|RP11-408H20.3_ENST00000582307.1_RNA	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	848			C -> F (in dbSNP:rs985861). {ECO:0000269|PubMed:8507556}.		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)			GTTATACGAACAAACGTAGTC	0.413													C|||	467	0.0932508	0.2549	0.0533	5008	,	,		17746	0.0		0.0477	False		,,,				2504	0.046				p.C848F		Atlas-SNP	.											.	DSC1	240	.	0			c.G2543T						PASS	.	C	,PHE/CYS	885,3521	340.5+/-306.2	88,709,1406	132	133	132		,2543	2	0.2	18	dbSNP_86	132	344,8256	117.4+/-177.0	6,332,3962	yes	utr-3,missense	DSC1	NM_004948.3,NM_024421.2	,205	94,1041,5368	AA,AC,CC		4.0,20.0862,9.4495	,benign	,848/895	28710619	1229,11777	2203	4300	6503	SO:0001583	missense	1823	exon16			TACGAACAAACGT	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.2543G>T	18.37:g.28710619C>A	ENSP00000257198:p.Cys848Phe	240	0	0		198	85	0.429293	NM_024421	Q9HB01	Missense_Mutation	SNP	ENST00000257198.5	37	CCDS11894.1	180	0.08241758241758242	125	0.2540650406504065	21	0.058011049723756904	0	0.0	34	0.044854881266490766	C	10.91	1.485333	0.26598	0.200862	0.04	ENSG00000134765	ENST00000257198	T	0.76060	-0.99	6.17	2.05	0.26809	Cadherin, cytoplasmic domain (1);	0.127555	0.35615	N	0.003081	T	0.00012	0.0000	N	0.08118	0	0.58432	P	1.999999999946489E-6	B	0.06786	0.001	B	0.01281	0.0	T	0.05937	-1.0855	9	0.72032	D	0.01	.	6.2715	0.20956	0.4608:0.3859:0.0:0.1532	rs985861;rs52820787;rs985861	848	Q08554	DSC1_HUMAN	F	848	ENSP00000257198:C848F	ENSP00000257198:C848F	C	-	2	0	DSC1	26964617	0.682000	0.27624	0.197000	0.23402	0.663000	0.39108	1.525000	0.35953	0.485000	0.27652	0.655000	0.94253	TGT	C|0.914;A|0.086	0.086	strong		0.413	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421		A	28710619	C	A	28710619	3	1	27	1	0	0	0	0	1	0	0	0	4767	478	17	4	145	4	DSC1	18	28710619	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	4	28710619	49366629	865	11316	141	2									
DSG3	1830	hgsc.bcm.edu	37	chr18	29056063	29056063	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tggttccctcgtgcaaccttCcactgcaggctttgatccac	6	12	8	15	1	0	1	0	1	0	0	4	1	3	1	4	2	3	4	4	2	1	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:29056063C>T	ENST00000257189.4	+	16	2923	c.2840C>T	c.(2839-2841)tCc>tTc	p.S947F		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	947					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)			GTGCAACCTTCCACTGCAGGC	0.517																																					p.S947F		Atlas-SNP	.											.	DSG3	172	.	0			c.C2840T						PASS	.						156	141	146					18																	29056063		2203	4300	6503	SO:0001583	missense	1830	exon16			AACCTTCCACTGC	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.2840C>T	18.37:g.29056063C>T	ENSP00000257189:p.Ser947Phe	89	0	0		67	16	0.238806	NM_001944	A8K2V2	Missense_Mutation	SNP	ENST00000257189.4	37	CCDS11898.1	.	.	.	.	.	.	.	.	.	.	C	19.04	3.750220	0.69533	.	.	ENSG00000134757	ENST00000257189	T	0.80480	-1.38	5.54	5.54	0.83059	.	0.756022	0.11629	N	0.545016	D	0.85066	0.5612	L	0.58510	1.815	0.09310	N	0.999999	D	0.53619	0.961	P	0.57548	0.823	T	0.76553	-0.2917	10	0.87932	D	0	.	10.1776	0.42948	0.0:0.9051:0.0:0.0949	.	947	P32926	DSG3_HUMAN	F	947	ENSP00000257189:S947F	ENSP00000257189:S947F	S	+	2	0	DSG3	27310061	0.016000	0.18221	0.812000	0.32479	0.925000	0.55904	2.776000	0.47709	2.779000	0.95612	0.655000	0.94253	TCC	.	.	none		0.517	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944		T	29056063	C	T	29056063	3	4	27	1	0	0	0	0	1	0	0	0	4780	855	30	2	2902	2	DSG3	18	29056063	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	345444	29056063	49021185	866	11317											
DCC	1630	hgsc.bcm.edu	37	chr18	49867246	49867246	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cagcgcgcatcttcaagtaaCcggtaagtggctctttcctt	8	12	9	12	3	3	0	1	0	2	0	4	0	4	0	2	2	2	4	2	2	3	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:49867246C>T	ENST00000442544.2	+	1	705	c.89C>T	c.(88-90)aCc>aTc	p.T30I	RP11-25O3.1_ENST00000582700.1_lincRNA	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	30	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)		CTTCAAGTAACCGGTAAGTGG	0.493																																					p.T30I		Atlas-SNP	.											.	DCC	360	.	0			c.C89T						PASS	.						180	160	167					18																	49867246		2203	4300	6503	SO:0001583	missense	1630	exon1			AAGTAACCGGTAA	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.89C>T	18.37:g.49867246C>T	ENSP00000389140:p.Thr30Ile	247	0	0		190	37	0.194737	NM_005215		Missense_Mutation	SNP	ENST00000442544.2	37	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	C	12.53	1.964768	0.34659	.	.	ENSG00000187323	ENST00000442544	T	0.50548	0.74	5.73	5.73	0.89815	Immunoglobulin-like (1);	1.199860	0.05969	N	0.642001	T	0.42630	0.1211	N	0.22421	0.69	0.80722	D	1	B	0.06786	0.001	B	0.10450	0.005	T	0.03910	-1.0993	10	0.22706	T	0.39	.	18.6711	0.91512	0.0:1.0:0.0:0.0	.	30	P43146	DCC_HUMAN	I	30	ENSP00000389140:T30I	ENSP00000389140:T30I	T	+	2	0	DCC	48121244	0.992000	0.36948	1.000000	0.80357	0.965000	0.64279	2.219000	0.42899	2.709000	0.92574	0.561000	0.74099	ACC	.	.	none		0.493	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		T	49867246	C	T	49867246	3	4	27	1	0	0	0	0	1	0	0	0	4284	507	18	2	91	2	DCC	18	49867246	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	20811183	49867246	28210002	867	11318											
DCC	1630	hgsc.bcm.edu	37	chr18	50278563	50278563	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgatcaagtggaagaaagaTggcattcatctggccttggg	11	10	14	6	0	3	3	2	1	1	2	3	4	3	4	1	4	0	1	1	4	3	2	rs112141078	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:50278563T>C	ENST00000442544.2	+	2	847	c.231T>C	c.(229-231)gaT>gaC	p.D77D	DCC_ENST00000412726.1_5'UTR	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	77	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)		GGAAGAAAGATGGCATTCATC	0.507													T|||	33	0.00658946	0.0015	0.0115	5008	,	,		17210	0.0		0.0209	False		,,,				2504	0.002				p.D77D		Atlas-SNP	.											.	DCC	360	.	0			c.T231C						PASS	.	T		27,4379	35.2+/-66.4	0,27,2176	104	98	100		231	0.1	1	18	dbSNP_132	100	215,8385	91.1+/-153.3	2,211,4087	no	coding-synonymous	DCC	NM_005215.3		2,238,6263	CC,CT,TT		2.5,0.6128,1.8607		77/1448	50278563	242,12764	2203	4300	6503	SO:0001819	synonymous_variant	1630	exon2			GAAAGATGGCATT	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.231T>C	18.37:g.50278563T>C		110	0	0		98	43	0.438776	NM_005215		Silent	SNP	ENST00000442544.2	37	CCDS11952.1																																																																																			T|0.986;C|0.014	0.014	strong		0.507	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215		C	50278563	T	C	50278563	2	2	27	1	0	0	0	0	0	0	0	1	4284	1461	51	3		3	DCC	18	50278563	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	411317	50278563	27798685	868	11319											
ALPK2	115701	hgsc.bcm.edu	37	chr18	56202470	56202470	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaataaatgccaaggtcttcGctgaggagctagatgagctt	13	10	11	7	1	1	3	0	2	1	1	2	4	1	4	1	2	3	3	1	2	5	4	rs55656447	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:56202470G>A	ENST00000361673.3	-	5	5162	c.4949C>T	c.(4948-4950)gCg>gTg	p.A1650V	RP11-1151B14.4_ENST00000591360.1_RNA	NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	1650						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						CAAGGTCTTCGCTGAGGAGCT	0.453													G|||	26	0.00519169	0.0015	0.0187	5008	,	,		20727	0.0		0.0089	False		,,,				2504	0.002				p.A1650V		Atlas-SNP	.											.	ALPK2	487	.	0			c.C4949T						PASS	.	G	VAL/ALA	19,4387	25.3+/-52.1	0,19,2184	75	79	77		4949	-1.1	0	18	dbSNP_129	77	112,8488	57.9+/-119.4	1,110,4189	yes	missense	ALPK2	NM_052947.3	64	1,129,6373	AA,AG,GG		1.3023,0.4312,1.0072	benign	1650/2171	56202470	131,12875	2203	4300	6503	SO:0001583	missense	115701	exon5			GTCTTCGCTGAGG	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.4949C>T	18.37:g.56202470G>A	ENSP00000354991:p.Ala1650Val	62	0	0		40	21	0.525	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Missense_Mutation	SNP	ENST00000361673.3	37	CCDS11966.2	16	0.007326007326007326	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	8	0.010554089709762533	G	16.95	3.264457	0.59431	0.004312	0.013023	ENSG00000198796	ENST00000361673	T	0.43688	0.94	5.74	-1.14	0.09741	.	2.962290	0.00633	N	0.000494	T	0.11623	0.0283	L	0.48642	1.525	0.09310	N	1	P;P	0.46952	0.887;0.482	B;B	0.32211	0.142;0.04	T	0.28586	-1.0039	10	0.02654	T	1	-0.4975	0.6684	0.00854	0.2374:0.1259:0.2499:0.3868	rs55656447	1645;1650	Q86TB3-2;Q86TB3	.;ALPK2_HUMAN	V	1650	ENSP00000354991:A1650V	ENSP00000354991:A1650V	A	-	2	0	ALPK2	54353450	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.250000	0.18235	0.060000	0.16281	0.655000	0.94253	GCG	G|0.987;A|0.013	0.013	strong		0.453	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		A	56202470	G	A	56202470	3	1	27	1	0	0	0	0	1	0	0	0	545	1087	38	1	1599	1	ALPK2	18	56202470	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	5923907	56202470	21874778	869	11320											
TSHZ1	10194	hgsc.bcm.edu	37	chr18	72998524	72998524	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aggatcagaaagcagcgaacCcgtacgtcacgcccaataac	15	4	9	13	4	2	1	2	0	0	1	2	3	2	2	2	1	5	2	2	1	5	2	rs200266026		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:72998524C>T	ENST00000580243.1	+	2	1510	c.1162C>T	c.(1162-1164)Ccg>Tcg	p.P388S	TSHZ1_ENST00000322038.5_Missense_Mutation_p.P343S			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	388					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)		AGCAGCGAACCCGTACGTCAC	0.627																																					p.P343S		Atlas-SNP	.											.	TSHZ1	104	.	0			c.C1027T						PASS	.						104	109	107					18																	72998524		2203	4300	6503	SO:0001583	missense	10194	exon2			GCGAACCCGTACG	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.1162C>T	18.37:g.72998524C>T	ENSP00000464391:p.Pro388Ser	131	0	0		98	35	0.357143	NM_005786	O60534|Q4LE29|Q53EU4	Missense_Mutation	SNP	ENST00000580243.1	37		.	.	.	.	.	.	.	.	.	.	C	7.820	0.717534	0.15372	.	.	ENSG00000179981	ENST00000322038	T	0.12569	2.67	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.19846	0.0477	M	0.66939	2.045	0.58432	D	0.999994	P	0.48503	0.911	B	0.39840	0.311	T	0.03354	-1.1045	10	0.54805	T	0.06	-26.8549	18.8997	0.92437	0.0:1.0:0.0:0.0	.	388	Q6ZSZ6	TSH1_HUMAN	S	343	ENSP00000323584:P343S	ENSP00000323584:P343S	P	+	1	0	TSHZ1	71127512	1.000000	0.71417	0.995000	0.50966	0.313000	0.28021	7.343000	0.79319	2.452000	0.82932	0.561000	0.74099	CCG	.	.	weak		0.627	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786		T	72998524	C	T	72998524	3	4	27	1	0	0	0	0	1	0	0	0	16638	623	22	2	1029	2	TSHZ1	18	72998524	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	16796054	72998524	5078724	870	11321											
ZNF516	9658	hgsc.bcm.edu	37	chr18	74091766	74091766	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggacctcggggtagtaggtCttgtggctgcagtaaggaca	9	9	16	7	1	1	0	0	0	1	0	2	2	1	2	1	6	1	5	1	6	3	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:74091766C>T	ENST00000443185.2	-	4	2621	c.2304G>A	c.(2302-2304)aaG>aaA	p.K768K	RP11-504I13.3_ENST00000583287.1_RNA|ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	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)			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)		GGTAGTAGGTCTTGTGGCTGC	0.592																																					p.K768K		Atlas-SNP	.											.	ZNF516	102	.	0			c.G2304A						PASS	.						35	40	38					18																	74091766		2038	4187	6225	SO:0001819	synonymous_variant	9658	exon4			GTAGGTCTTGTGG	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.2304G>A	18.37:g.74091766C>T		135	0	0		89	26	0.292135	NM_014643		Silent	SNP	ENST00000443185.2	37																																																																																				.	.	none		0.592	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643		T	74091766	C	T	74091766	2	4	27	1	0	0	0	0	0	0	0	1	17975	912	32	2		2	ZNF516	18	74091766	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1093242	74091766	3985482	871	11322											
CTDP1	9150	hgsc.bcm.edu	37	chr18	77455227	77455227	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccttgtgtttttttgtagagCggttctggtgaggttggaag	5	17	15	4	1	1	2	0	1	1	1	1	3	1	3	1	4	1	4	1	4	2	7	rs115044443	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr18:77455227C>T	ENST00000299543.7	+	2	464	c.317C>T	c.(316-318)gCg>gTg	p.A106V	CTDP1_ENST00000075430.7_Missense_Mutation_p.A106V	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	106					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)		TTTTGTAGAGCGGTTCTGGTG	0.438													C|||	99	0.0197684	0.0613	0.0072	5008	,	,		16271	0.0		0.0119	False		,,,				2504	0.001				p.A106V		Atlas-SNP	.											.	CTDP1	67	.	0			c.C317T						PASS	.	C	,VAL/ALA,VAL/ALA	222,4184	135.7+/-171.8	5,212,1986	121	109	113		,317,317	3.9	0	18	dbSNP_132	113	125,8475	64.2+/-126.4	0,125,4175	yes	utr-5,missense,missense	CTDP1	NM_001202504.1,NM_004715.4,NM_048368.3	,64,64	5,337,6161	TT,TC,CC		1.4535,5.0386,2.668	,benign,benign	,106/962,106/868	77455227	347,12659	2203	4300	6503	SO:0001583	missense	9150	exon2			GTAGAGCGGTTCT	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.317C>T	18.37:g.77455227C>T	ENSP00000299543:p.Ala106Val	193	0	0		119	40	0.336134	NM_004715	A8MY97|Q7Z644|Q96BZ1|Q9Y6F5	Missense_Mutation	SNP	ENST00000299543.7	37	CCDS12017.1	43	0.019688644688644688	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	12	0.0158311345646438	C	14.60	2.584590	0.46110	0.050386	0.014535	ENSG00000060069	ENST00000299543;ENST00000075430	T;T	0.10382	2.9;2.88	4.8	3.86	0.44501	.	0.283877	0.39615	N	0.001318	T	0.01254	0.0041	M	0.65975	2.015	0.21256	N	0.999743	D;P	0.53312	0.959;0.931	B;B	0.40165	0.321;0.171	T	0.20075	-1.0286	10	0.27785	T	0.31	-21.0839	14.1115	0.65123	0.0:0.6821:0.3179:0.0	.	106;106	Q9Y5B0-4;Q9Y5B0	.;CTDP1_HUMAN	V	106	ENSP00000299543:A106V;ENSP00000075430:A106V	ENSP00000075430:A106V	A	+	2	0	CTDP1	75556215	0.964000	0.33143	0.008000	0.14137	0.004000	0.04260	2.608000	0.46308	2.376000	0.81061	0.655000	0.94253	GCG	C|0.977;T|0.023	0.023	strong		0.438	CTDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256432.1	NM_004715		T	77455227	C	T	77455227	3	4	27	1	0	0	0	0	1	0	0	0	4004	768	27	1	323	1	CTDP1	18	77455227	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3363461	77455227	622021	872	11323											
C19orf21	126353	hgsc.bcm.edu	37	chr19	757234	757234	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gagggttggcaggtttaccgCctgggcgccagggatgccca	6	7	17	11	2	0	0	0	0	0	0	0	2	0	1	4	5	2	3	4	5	1	3	rs34384654	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:757234C>T	ENST00000215582.6	+	2	391	c.288C>T	c.(286-288)cgC>cgT	p.R96R		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	96					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											AGGTTTACCGCCTGGGCGCCA	0.667													C|||	41	0.0081869	0.0008	0.0043	5008	,	,		17750	0.0		0.0328	False		,,,				2504	0.0041				p.R96R		Atlas-SNP	.											C19orf21,NS,carcinoma,+2,1	C19orf21	56	1	0			c.C288T						PASS	.	C		14,4392	21.2+/-45.6	0,14,2189	60	53	55		288	1.2	0	19	dbSNP_126	55	188,8412	82.9+/-145.4	2,184,4114	no	coding-synonymous	C19orf21	NM_173481.2		2,198,6303	TT,TC,CC		2.186,0.3177,1.5531		96/680	757234	202,12804	2203	4300	6503	SO:0001819	synonymous_variant	126353	exon2			TTACCGCCTGGGC	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.288C>T	19.37:g.757234C>T		111	0	0		63	31	0.492063	NM_173481		Silent	SNP	ENST00000215582.6	37	CCDS12042.1																																																																																			C|0.986;T|0.014	0.014	strong		0.667	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481		T	757234	C	T	757234	2	4	27	1	0	0	0	0	0	0	0	1	1915	726	26	2		2	C19orf21	19	757234	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10		757234	58371749	873	11324											
JSRP1	126306	hgsc.bcm.edu	37	chr19	2253687	2253687	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcaccaggcacttgttgagcGacaggtctccccagggcagc	8	6	13	14	1	1	1	0	1	1	0	2	2	1	1	3	3	2	4	3	3	0	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:2253687G>A	ENST00000300961.6	-	5	432	c.368C>T	c.(367-369)tCg>tTg	p.S123L	JSRP1_ENST00000586471.2_Missense_Mutation_p.S123L|MIR4321_ENST00000592276.1_RNA	NM_144616.3	NP_653217.1	Q96MG2	JSPR1_HUMAN	junctional sarcoplasmic reticulum protein 1	123	Pro-rich.				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)		CTTGTTGAGCGACAGGTCTCC	0.756																																					p.S123L		Atlas-SNP	.											.	JSRP1	18	.	0			c.C368T						PASS	.						7	10	9					19																	2253687		1985	3928	5913	SO:0001583	missense	126306	exon5			TTGAGCGACAGGT	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.368C>T	19.37:g.2253687G>A	ENSP00000300961:p.Ser123Leu	15	0	0		20	9	0.45	NM_144616		Missense_Mutation	SNP	ENST00000300961.6	37	CCDS12086.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.051013	0.75960	.	.	ENSG00000167476	ENST00000300961	T	0.42513	0.97	4.89	4.89	0.63831	.	1.031560	0.07762	N	0.950312	T	0.30070	0.0753	N	0.19112	0.55	0.09310	N	1	B	0.28584	0.216	B	0.21546	0.035	T	0.12993	-1.0526	10	0.72032	D	0.01	-7.5515	9.2315	0.37439	0.1:0.0:0.9:0.0	.	123	Q96MG2	JSPR1_HUMAN	L	123	ENSP00000300961:S123L	ENSP00000300961:S123L	S	-	2	0	JSRP1	2204687	0.687000	0.27671	0.017000	0.16124	0.777000	0.43975	4.762000	0.62250	2.251000	0.74343	0.561000	0.74099	TCG	.	.	none		0.756	JSRP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451266.2	NM_144616		A	2253687	G	A	2253687	3	1	27	1	0	0	0	0	1	0	0	0	7975	1059	37	1	639	1	JSRP1	19	2253687	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1496453	2253687	56875296	874	11325											
DIRAS1	148252	hgsc.bcm.edu	37	chr19	2717513	2717513	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gatgagcttgtagatgggccCcagctcctccagcgactgct	7	9	12	13	1	0	2	0	1	0	1	2	4	2	2	4	1	4	4	4	1	1	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:2717513C>G	ENST00000323469.4	-	2	475	c.292G>C	c.(292-294)Ggg>Cgg	p.G98R	DIRAS1_ENST00000585334.1_Missense_Mutation_p.G98R	NM_145173.3	NP_660156.1	O95057	DIRA1_HUMAN	DIRAS family, GTP-binding RAS-like 1	98					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)		TAGATGGGCCCCAGCTCCTCC	0.627																																					p.G98R		Atlas-SNP	.											.	DIRAS1	26	.	0			c.G292C						PASS	.						45	40	41					19																	2717513		2203	4297	6500	SO:0001583	missense	148252	exon2			TGGGCCCCAGCTC	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.292G>C	19.37:g.2717513C>G	ENSP00000325836:p.Gly98Arg	84	0	0		71	21	0.295775	NM_145173		Missense_Mutation	SNP	ENST00000323469.4	37	CCDS12092.1	.	.	.	.	.	.	.	.	.	.	C	9.401	1.078074	0.20227	.	.	ENSG00000176490	ENST00000323469	T	0.75477	-0.94	4.07	-0.695	0.11291	Small GTP-binding protein domain (1);	0.169303	0.49305	D	0.000145	T	0.42017	0.1184	N	0.04245	-0.25	0.26980	N	0.965374	B	0.02656	0.0	B	0.06405	0.002	T	0.17745	-1.0359	10	0.20519	T	0.43	.	3.7079	0.08408	0.0:0.3451:0.3048:0.35	.	98	O95057	DIRA1_HUMAN	R	98	ENSP00000325836:G98R	ENSP00000325836:G98R	G	-	1	0	DIRAS1	2668513	1.000000	0.71417	1.000000	0.80357	0.743000	0.42351	1.026000	0.30103	0.692000	0.31613	0.549000	0.68633	GGG	.	.	none		0.627	DIRAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451350.1			G	2717513	C	G	2717513	3	3	27	1	0	0	0	0	1	0	0	0	4532	623	22	4	308	4	DIRAS1	19	2717513	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	463826	2717513	56411470	875	11326											
C19orf29	58509	hgsc.bcm.edu	37	chr19	3612035	3612035	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cactcgcggttgacgatcttGaaagcgatgtcctcgtaggg	8	10	13	10	5	1	2	0	2	1	0	4	4	2	2	1	2	1	2	1	2	2	3	rs61738769		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:3612035G>A	ENST00000429344.2	-	10	2215	c.2163C>T	c.(2161-2163)ttC>ttT	p.F721F	CACTIN-AS1_ENST00000592274.1_RNA|CACTIN_ENST00000248420.5_Silent_p.F721F|CACTIN_ENST00000221899.3_Silent_p.F653F	NM_001080543.1	NP_001074012.1	Q8WUQ7	CATIN_HUMAN	cactin, spliceosome C complex subunit	721					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)										TGACGATCTTGAAAGCGATGT	0.617													G|||	1	0.000199681	0.0	0.0	5008	,	,		17582	0.0		0.001	False		,,,				2504	0.0				p.F721F		Atlas-SNP	.											C19orf29_ENST00000429344,NS,neuroblastoma,0,2	.	.	2	0			c.C2163T						PASS	.	G	,	0,4120		0,0,2060	110	126	121		2163,2163	3.3	1	19	dbSNP_129	121	3,8363		0,3,4180	no	coding-synonymous,coding-synonymous	C19orf29	NM_001080543.1,NM_021231.1	,	0,3,6240	AA,AG,GG		0.0359,0.0,0.024	,	721/759,721/759	3612035	3,12483	2060	4183	6243	SO:0001819	synonymous_variant	58509	exon10			GATCTTGAAAGCG	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.2163C>T	19.37:g.3612035G>A		148	0	0		156	74	0.474359	NM_021231	A6NNA9|A9UL12|O75229|Q7LE08|Q9BTA6|Q9Y5A4	Silent	SNP	ENST00000429344.2	37	CCDS45920.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	15.54	2.863785	0.51482	0.0	3.59E-4	ENSG00000226800	ENST00000447295	.	.	.	4.31	3.27	0.37495	.	.	.	.	.	T	0.54711	0.1875	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48603	-0.9021	5	0.30078	T	0.28	.	7.8484	0.29440	0.1936:0.0:0.8064:0.0	.	.	.	.	K	103	.	ENSP00000412459:E103K	E	+	1	0	C19orf29OS	3563035	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	2.449000	0.44935	1.171000	0.42768	0.643000	0.83706	GAA	G|0.999;A|0.001	0.001	strong		0.617	CACTIN-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457370.2			A	3612035	G	A	3612035	2	1	27	1	0	0	0	0	0	0	0	1	1920	1281	45	2		2	C19orf29	19	3612035	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	894522	3612035	55516948	876	11327											
PIAS4	51588	hgsc.bcm.edu	37	chr19	4037723	4037723	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcatggagaatgggaagccGggcgccgatgtggtggacct	9	6	18	8	3	0	1	0	0	0	1	0	5	0	3	3	5	2	1	3	5	2	0	rs140558761	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:4037723G>A	ENST00000262971.2	+	11	1498	c.1383G>A	c.(1381-1383)ccG>ccA	p.P461P		NM_015897.2	NP_056981.2	Q8N2W9	PIAS4_HUMAN	protein inhibitor of activated STAT, 4	461					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)		ATGGGAAGCCGGGCGCCGATG	0.697													.|||	4	0.000798722	0.0	0.0	5008	,	,		12829	0.0		0.004	False		,,,				2504	0.0				p.P461P		Atlas-SNP	.											.	PIAS4	40	.	0			c.G1383A						PASS	.			1,4391		0,1,2195	22	23	23		1383	-8.8	0	19	dbSNP_134	23	26,8560		0,26,4267	no	coding-synonymous	PIAS4	NM_015897.2		0,27,6462	AA,AG,GG		0.3028,0.0228,0.208		461/511	4037723	27,12951	2196	4293	6489	SO:0001819	synonymous_variant	51588	exon11			GAAGCCGGGCGCC	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.1383G>A	19.37:g.4037723G>A		53	0	0		80	43	0.5375	NM_015897	O75926|Q96G19|Q9UN16	Silent	SNP	ENST00000262971.2	37	CCDS12118.1																																																																																			G|0.998;A|0.002	0.002	strong		0.697	PIAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457496.1	NM_015897		A	4037723	G	A	4037723	2	1	27	1	0	0	0	0	0	0	0	1	11887	1103	39	1		1	PIAS4	19	4037723	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	425688	4037723	55091260	877	11328											
MAP2K2	5605	hgsc.bcm.edu	37	chr19	4117483	4117483	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accaccccgccgttgcccgcGcccagctctgagatcctttc	5	8	8	20	4	1	1	0	1	1	1	3	2	2	1	7	0	2	2	7	0	0	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:4117483G>A	ENST00000262948.5	-	2	490	c.237C>T	c.(235-237)ggC>ggT	p.G79G	MAP2K2_ENST00000394867.4_5'UTR|MAP2K2_ENST00000599345.1_5'UTR	NM_030662.3	NP_109587.1	P36507	MP2K2_HUMAN	mitogen-activated protein kinase kinase 2	79	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)	CGTTGCCCGCGCCCAGCTCTG	0.617																																					p.G79G		Atlas-SNP	.											.	MAP2K2	72	.	0			c.C237T						PASS	.						67	63	64					19																	4117483		2203	4300	6503	SO:0001819	synonymous_variant	5605	exon2			GCCCGCGCCCAGC	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.237C>T	19.37:g.4117483G>A		79	0	0		89	38	0.426966	NM_030662		Silent	SNP	ENST00000262948.5	37	CCDS12120.1																																																																																			.	.	none		0.617	MAP2K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258957.2			A	4117483	G	A	4117483	2	1	27	1	0	0	0	0	0	0	0	1	9246	1074	38	1		1	MAP2K2	19	4117483	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	79760	4117483	55011500	878	11329											
SEMA6B	10501	hgsc.bcm.edu	37	chr19	4555084	4555084	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aatggctaggaagtcggtaaCagtagctgtgaagagcatcc	13	8	13	7	1	0	2	0	1	0	1	2	3	1	3	1	3	3	5	1	3	6	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:4555084C>A	ENST00000586582.1	-	8	896	c.586G>T	c.(586-588)Gtt>Ttt	p.V196F	SEMA6B_ENST00000301293.3_Missense_Mutation_p.V196F|SEMA6B_ENST00000586965.1_Missense_Mutation_p.V196F	NM_032108.3	NP_115484.2	Q9H3T3	SEM6B_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	196	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)		AAGTCGGTAACAGTAGCTGTG	0.587																																					p.V196F		Atlas-SNP	.											.	SEMA6B	51	.	0			c.G586T						PASS	.						109	87	95					19																	4555084		2203	4300	6503	SO:0001583	missense	10501	exon8			CGGTAACAGTAGC	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.586G>T	19.37:g.4555084C>A	ENSP00000467290:p.Val196Phe	59	0	0		46	17	0.369565	NM_032108	A5PKU4|F6IB19|Q9NRK9	Missense_Mutation	SNP	ENST00000586582.1	37	CCDS12131.1	.	.	.	.	.	.	.	.	.	.	C	18.29	3.592476	0.66219	.	.	ENSG00000167680	ENST00000301293;ENST00000301292	T	0.12147	2.71	2.8	2.8	0.32819	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.141549	0.46145	D	0.000304	T	0.39600	0.1084	M	0.85197	2.74	0.51012	D	0.999904	D;D	0.89917	1.0;1.0	D;D	0.97110	0.995;1.0	T	0.50285	-0.8846	10	0.87932	D	0	.	13.2603	0.60101	0.0:1.0:0.0:0.0	.	196;196	B4DT36;Q9H3T3	.;SEM6B_HUMAN	F	196	ENSP00000301293:V196F	ENSP00000301292:V196F	V	-	1	0	SEMA6B	4506084	1.000000	0.71417	0.087000	0.20705	0.468000	0.32798	5.648000	0.67930	1.882000	0.54519	0.455000	0.32223	GTT	.	.	none		0.587	SEMA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458656.2	NM_032108		A	4555084	C	A	4555084	3	1	27	1	0	0	0	0	1	0	0	0	14055	478	17	4	2120	4	SEMA6B	19	4555084	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	437601	4555084	54573899	879	11330											
SAFB2	9667	hgsc.bcm.edu	37	chr19	5622579	5622579	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	caggacgctcttgttgccgcCcgtgtccaggttccgcttct	3	12	11	15	4	2	0	0	0	2	0	4	1	4	1	4	2	1	4	4	2	0	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:5622579C>T	ENST00000252542.4	-	1	412	c.148G>A	c.(148-150)Ggc>Agc	p.G50S	SAFB_ENST00000454510.1_5'Flank|SAFB_ENST00000588852.1_5'Flank|SAFB_ENST00000433404.1_5'Flank|SAFB_ENST00000292123.5_5'Flank|SAFB_ENST00000538656.1_5'Flank|SAFB_ENST00000592224.1_5'Flank	NM_014649.2	NP_055464.1	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	50	SAP. {ECO:0000255|PROSITE- ProRule:PRU00186}.				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)		TTGTTGCCGCCCGTGTCCAGG	0.716																																					p.G50S	Ovarian(127;888 1728 23957 44128 52668)	Atlas-SNP	.											.	SAFB2	90	.	0			c.G148A						PASS	.						26	25	25					19																	5622579		2203	4300	6503	SO:0001583	missense	9667	exon1			TGCCGCCCGTGTC	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.148G>A	19.37:g.5622579C>T	ENSP00000252542:p.Gly50Ser	93	0	0		105	37	0.352381	NM_014649	B4DKG3|Q8TB13	Missense_Mutation	SNP	ENST00000252542.4	37	CCDS32879.1	.	.	.	.	.	.	.	.	.	.	C	12.42	1.932295	0.34096	.	.	ENSG00000130254	ENST00000434962;ENST00000415313;ENST00000394625;ENST00000252542;ENST00000536849	T	0.06528	3.29	3.87	1.73	0.24493	DNA-binding SAP (4);	0.285141	0.24671	N	0.036545	T	0.03520	0.0101	N	0.00621	-1.32	0.41073	D	0.985466	P;D	0.89917	0.529;1.0	P;D	0.87578	0.536;0.998	T	0.50767	-0.8789	10	0.05436	T	0.98	-16.0604	6.3775	0.21515	0.0:0.6753:0.151:0.1737	.	50;50	A0PJ47;Q14151	.;SAFB2_HUMAN	S	50;50;50;50;29	ENSP00000252542:G50S	ENSP00000252542:G50S	G	-	1	0	SAFB2	5573579	0.881000	0.30235	0.979000	0.43373	0.956000	0.61745	0.882000	0.28186	0.420000	0.25954	0.561000	0.74099	GGC	.	.	none		0.716	SAFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451016.1	NM_014649		T	5622579	C	T	5622579	3	4	27	1	0	0	0	0	1	0	0	0	13822	623	22	2	2797	2	SAFB2	19	5622579	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1067495	5622579	53506404	880	11331											
CAPS	8498	hgsc.bcm.edu	37	chr19	5915300	5915300	+	IGR	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgaacacggatgaggagttCgtggccatgatgaccagtgc	11	8	14	8	2	0	4	0	4	0	0	1	6	0	6	2	3	2	1	2	3	1	1	rs147363394	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:5915300C>A	ENST00000340578.6	-	0	3233				AC104532.4_ENST00000591109.1_RNA|CAPS_ENST00000452990.2_Missense_Mutation_p.F152L|CAPS_ENST00000588776.1_Missense_Mutation_p.F265L|CAPS_ENST00000222125.5_Missense_Mutation_p.F179L	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						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						ATGAGGAGTTCGTGGCCATGA	0.657													C|||	5	0.000998403	0.0	0.0043	5008	,	,		16061	0.0		0.002	False		,,,				2504	0.0				p.F179L		Atlas-SNP	.											.	CAPS	14	.	0			c.C537A						PASS	.	C	LEU/PHE,LEU/PHE	1,4401	2.1+/-5.4	0,1,2200	74	59	64		537,456	-10	0.5	19	dbSNP_134	64	11,8589	7.7+/-29.5	0,11,4289	yes	missense,missense	CAPS	NM_004058.3,NM_080590.2	22,22	0,12,6489	AA,AC,CC		0.1279,0.0227,0.0923	probably-damaging,probably-damaging	179/190,152/163	5915300	12,12990	2201	4300	6501	SO:0001628	intergenic_variant	828	exon5			GGAGTTCGTGGCC	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			19.37:g.5915300C>A		97	0	0		111	57	0.513514	NM_004058	B2RAT8|O60405|O75759|O75760|Q9BT47|Q9UG74	Missense_Mutation	SNP	ENST00000340578.6	37	CCDS42478.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	22.2	4.252906	0.80135	2.27E-4	0.001279	ENSG00000105519	ENST00000394521;ENST00000222125;ENST00000452990	T;T	0.69175	-0.25;-0.38	5.3	-10.0	0.00425	EF-hand-like domain (1);	0.000000	0.64402	D	0.000007	T	0.80374	0.4611	M	0.90425	3.115	0.34295	D	0.683746	D;D	0.89917	1.0;1.0	D;D	0.97110	0.992;1.0	D	0.88488	0.3073	10	0.87932	D	0	-13.7929	17.3435	0.87304	0.0:0.6317:0.0:0.3683	.	312;179	Q8NF12;Q13938	.;CAYP1_HUMAN	L	312;179;152	ENSP00000222125:F179L;ENSP00000403263:F152L	ENSP00000222125:F179L	F	+	3	2	CAPS	5866300	0.002000	0.14202	0.526000	0.27913	0.946000	0.59487	-2.224000	0.01213	-2.213000	0.00735	-1.036000	0.02392	TTC	C|0.999;A|0.001	0.001	strong		0.657	RANBP3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452304.1	NM_007322		A	5915300	C	A	5915300	1	1	27	0	1	0	0	0	0	0	0	0	2639	883	31	4		4	CAPS	19	5915300	IGR	SNP	C	TCGA-G8-6909-01A-11D-2210-10	292721	5915300	53213683	881	11332											
MLLT1	4298	hgsc.bcm.edu	37	chr19	6222552	6222552	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggccctcgcccagcttccgCgaggtgtccttggagctttt	3	11	12	15	4	0	0	0	0	0	0	3	2	2	1	4	3	2	2	4	3	0	4	rs139655596	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:6222552C>T	ENST00000252674.7	-	6	853	c.690G>A	c.(688-690)tcG>tcA	p.S230S		NM_005934.3	NP_005925.2	Q03111	ENL_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1	230					negative regulation of protein kinase activity (GO:0006469)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	DNA binding (GO:0003677)			endometrium(3)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|skin(2)	17						CCAGCTTCCGCGAGGTGTCCT	0.647			T	MLL	AL								C|||	64	0.0127796	0.0023	0.0173	5008	,	,		11334	0.004		0.0258	False		,,,				2504	0.0194				p.S230S		Atlas-SNP	.		Dom	yes		19	19p13.3	4298	"myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 1 (ENL)"		L	.	MLLT1	47	.	0			c.G690A						PASS	.	C		23,4381	29.9+/-59.1	0,23,2179	36	35	36		690	-9.6	0	19	dbSNP_134	36	220,8378	90.6+/-152.8	1,218,4080	no	coding-synonymous	MLLT1	NM_005934.3		1,241,6259	TT,TC,CC		2.5587,0.5223,1.8689		230/560	6222552	243,12759	2202	4299	6501	SO:0001819	synonymous_variant	4298	exon6			CTTCCGCGAGGTG		CCDS12160.1	19p13.3	2012-10-04	2001-11-28		ENSG00000130382	ENSG00000130382			7134	protein-coding gene	gene with protein product		159556	"myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 1"				Standard	XM_005259561		Approved	ENL, LTG19, YEATS1	uc002mek.3	Q03111	OTTHUMG00000180757	ENST00000252674.7:c.690G>A	19.37:g.6222552C>T		30	0	0		27	15	0.555556	NM_005934	Q14768	Silent	SNP	ENST00000252674.7	37	CCDS12160.1																																																																																			C|0.981;T|0.019	0.019	strong		0.647	MLLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452909.1	NM_005934		T	6222552	C	T	6222552	2	4	27	1	0	0	0	0	0	0	0	1	9634	755	27	1		1	MLLT1	19	6222552	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	307252	6222552	52906431	882	11333											
TUBB4	10382	hgsc.bcm.edu	37	chr19	6495199	6495199	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccacctcctcctccgcctcCtcctcgaactcgccctcctc	3	9	4	25	3	0	0	0	0	0	0	9	1	6	0	10	0	1	0	10	0	1	0	rs369467354		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:6495199C>T	ENST00000264071.2	-	4	1682	c.1311G>A	c.(1309-1311)gaG>gaA	p.E437E	CTD-2396E7.9_ENST00000599292.1_RNA|TUBB4A_ENST00000540257.1_Silent_p.E437E|CTD-2396E7.10_ENST00000596027.1_RNA			P04350	TBB4A_HUMAN	tubulin, beta 4A class IVa	437					'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)										CCTCCGCCTCCTCCTCGAACT	0.622																																					p.E437E		Atlas-SNP	.											.	.	.	.	0			c.G1311A						PASS	.	C		0,4406		0,0,2203	70	64	66		1311	2.9	1	19		66	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	TUBB4	NM_006087.2		0,6,6497	TT,TC,CC		0.0698,0.0,0.0461		437/445	6495199	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	10382	exon4			CGCCTCCTCCTCG	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.1311G>A	19.37:g.6495199C>T		54	0	0		49	18	0.367347	NM_006087	B3KQP4|Q969E5	Silent	SNP	ENST00000264071.2	37	CCDS12168.1																																																																																			.	.	weak		0.622	TUBB4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457841.1	NM_006087		T	6495199	C	T	6495199	2	4	27	1	0	0	0	0	0	0	0	1	16773	680	24	2		2	TUBB4	19	6495199	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	272647	6495199	52633784	883	11334											
C3	718	hgsc.bcm.edu	37	chr19	6718146	6718146	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggcccacgggtagcagctTgtggttgacggtgaagatcc	7	8	15	11	3	0	3	0	2	0	1	1	3	1	3	3	4	2	4	3	4	2	3	rs147859257	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:6718146T>G	ENST00000245907.6	-	4	555	c.463A>C	c.(463-465)Aag>Cag	p.K155Q		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	155			K -> Q (in ARMD9; results in resistance to proteolytic inactivation by CFH and CFI). {ECO:0000269|PubMed:24036952}.		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)	GGTAGCAGCTTGTGGTTGACG	0.652													T|||	2	0.000399361	0.0	0.0	5008	,	,		18237	0.0		0.002	False		,,,				2504	0.0				p.K155Q		Atlas-SNP	.											.	C3	192	.	0			c.A463C						PASS	.	T	GLN/LYS	1,4405	2.1+/-5.4	0,1,2202	94	88	90		463	1.3	0.4	19	dbSNP_134	90	37,8563	25.1+/-72.6	0,37,4263	yes	missense	C3	NM_000064.2	53	0,38,6465	GG,GT,TT		0.4302,0.0227,0.2922	possibly-damaging	155/1664	6718146	38,12968	2203	4300	6503	SO:0001583	missense	718	exon4			GCAGCTTGTGGTT	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.463A>C	19.37:g.6718146T>G	ENSP00000245907:p.Lys155Gln	97	0	0		87	47	0.54023	NM_000064	A7E236	Missense_Mutation	SNP	ENST00000245907.6	37	CCDS32883.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	9.992	1.231149	0.22626	2.27E-4	0.004302	ENSG00000125730	ENST00000245907	T	0.73681	-0.77	4.56	1.27	0.21489	Alpha-2-macroglobulin, N-terminal (1);	0.839580	0.11137	N	0.595772	T	0.69305	0.3096	L	0.58354	1.805	0.20074	N	0.999934	B	0.25235	0.121	B	0.32022	0.139	T	0.57359	-0.7825	10	0.33940	T	0.23	.	7.5787	0.27952	0.0:0.2731:0.0:0.7269	.	155	P01024	CO3_HUMAN	Q	155	ENSP00000245907:K155Q	ENSP00000245907:K155Q	K	-	1	0	C3	6669146	0.002000	0.14202	0.358000	0.25811	0.607000	0.37147	-0.429000	0.06982	-0.030000	0.13804	0.248000	0.18094	AAG	T|0.998;G|0.002	0.002	strong		0.652	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064		G	6718146	T	G	6718146	3	3	27	1	0	0	0	0	1	0	0	0	2206	1821	63	5	4680	5	C3	19	6718146	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	222947	6718146	52410837	884	11335											
INSR	3643	hgsc.bcm.edu	37	chr19	7150532	7150532	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggtcctcggcaccagtgcctGaagaggtttttctgtggaaa	8	11	13	9	1	1	2	0	1	1	1	3	3	2	3	3	4	1	2	3	4	2	2	rs143523271	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:7150532G>A	ENST00000302850.5	-	11	2385	c.2243C>T	c.(2242-2244)tCa>tTa	p.S748L	INSR_ENST00000341500.5_Intron	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	748					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)"	ACCAGTGCCTGAAGAGGTTTT	0.592																																					p.S748L		Atlas-SNP	.											.	INSR	265	.	0			c.C2243T						PASS	.	G	LEU/SER,	1,4405	2.1+/-5.4	0,1,2202	77	68	71		2243,	4.2	0.5	19	dbSNP_134	71	12,8588	9.1+/-34.3	0,12,4288	yes	missense,intron	INSR	NM_000208.2,NM_001079817.1	145,	0,13,6490	AA,AG,GG		0.1395,0.0227,0.1	benign,	748/1383,	7150532	13,12993	2203	4300	6503	SO:0001583	missense	3643	exon11			GTGCCTGAAGAGG	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.2243C>T	19.37:g.7150532G>A	ENSP00000303830:p.Ser748Leu	51	0	0		51	21	0.411765	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Missense_Mutation	SNP	ENST00000302850.5	37	CCDS12176.1	.	.	.	.	.	.	.	.	.	.	G	5.384	0.256032	0.10185	2.27E-4	0.001395	ENSG00000171105	ENST00000302850	T	0.75704	-0.96	5.23	4.2	0.49525	Fibronectin, type III (2);	0.753844	0.10277	U	0.693994	T	0.63954	0.2555	L	0.34521	1.04	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.54316	-0.8312	10	0.33940	T	0.23	.	9.578	0.39470	0.0959:0.0:0.9041:0.0	.	748	P06213	INSR_HUMAN	L	748	ENSP00000303830:S748L	ENSP00000303830:S748L	S	-	2	0	INSR	7101532	0.977000	0.34250	0.504000	0.27639	0.048000	0.14542	2.692000	0.47018	1.202000	0.43218	0.643000	0.83706	TCA	G|0.999;A|0.001	0.001	strong		0.592	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1			A	7150532	G	A	7150532	3	1	27	1	0	0	0	0	1	0	0	0	7782	1294	45	2	1953	2	INSR	19	7150532	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	432386	7150532	51978451	885	11336											
C19orf45	374877	hgsc.bcm.edu	37	chr19	7569245	7569245	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcaagatcagctatggatcaAcgtgttcggagcagaaacag	14	7	12	8	2	2	2	2	0	0	2	3	4	2	4	0	2	4	4	0	2	4	2	rs145077335		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:7569245A>G	ENST00000361664.2	+	4	871	c.730A>G	c.(730-732)Acg>Gcg	p.T244A	CTD-2207O23.12_ENST00000599312.1_5'Flank	NM_198534.2	NP_940936.2	Q8NA69	CS045_HUMAN	chromosome 19 open reading frame 45	244										endometrium(1)|kidney(1)|liver(1)|lung(2)|ovary(2)|stomach(1)	8						CTATGGATCAACGTGTTCGGA	0.592													a|||	1	0.000199681	0.0	0.0	5008	,	,		16125	0.0		0.001	False		,,,				2504	0.0				p.T244A		Atlas-SNP	.											.	C19orf45	36	.	0			c.A730G						PASS	.	A	ALA/THR	2,4404	6.2+/-15.9	0,2,2201	63	65	64		730	-6.4	0	19	dbSNP_134	64	10,8590	7.1+/-27.0	0,10,4290	yes	missense	C19orf45	NM_198534.2	58	0,12,6491	GG,GA,AA		0.1163,0.0454,0.0923	benign	244/506	7569245	12,12994	2203	4300	6503	SO:0001583	missense	374877	exon4			GGATCAACGTGTT	BC029824	CCDS12179.2	19p13.2	2008-02-05			ENSG00000198723	ENSG00000198723			24745	protein-coding gene	gene with protein product						12477932	Standard	NM_198534		Approved	FLJ35784	uc002mgm.2	Q8NA69	OTTHUMG00000157183	ENST00000361664.2:c.730A>G	19.37:g.7569245A>G	ENSP00000355241:p.Thr244Ala	111	0	0		116	70	0.603448	NM_198534	Q8N115	Missense_Mutation	SNP	ENST00000361664.2	37	CCDS12179.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	a	5.651	0.304727	0.10678	4.54E-4	0.001163	ENSG00000198723	ENST00000361664	T	0.13420	2.59	4.37	-6.39	0.01951	.	2.395820	0.01247	N	0.008772	T	0.07593	0.0191	N	0.22421	0.69	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.21759	-1.0236	10	0.27785	T	0.31	-0.997	2.6616	0.05028	0.2167:0.4136:0.2533:0.1164	.	244	Q8NA69	CS045_HUMAN	A	244	ENSP00000355241:T244A	ENSP00000355241:T244A	T	+	1	0	C19orf45	7475245	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.028000	0.03589	-1.595000	0.01613	-0.549000	0.04216	ACG	A|0.999;G|0.001	0.001	strong		0.592	C19orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347808.1	NM_198534		G	7569245	A	G	7569245	3	3	27	1	0	0	0	0	1	0	0	0	1930	43	2	3	740	3	C19orf45	19	7569245	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	418713	7569245	51559738	886	11337											
FBN3	84467	hgsc.bcm.edu	37	chr19	8145928	8145928	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggtgaagccgggcggacagCggcaggtgaaggcgcccaca	9	2	19	11	4	0	2	0	2	0	0	0	3	0	3	2	6	2	1	2	6	2	0	rs3848570|rs398088717	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:8145928C>T	ENST00000600128.1	-	59	7826	c.7412G>A	c.(7411-7413)cGc>cAc	p.R2471H	FBN3_ENST00000270509.2_Missense_Mutation_p.R2471H|FBN3_ENST00000601739.1_Missense_Mutation_p.R2471H			Q75N90	FBN3_HUMAN	fibrillin 3	2471	EGF-like 40; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.		R -> H (in dbSNP:rs3848570).			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						GGGCGGACAGCGGCAGGTGAA	0.622													C|||	111	0.0221645	0.0083	0.0403	5008	,	,		17290	0.0		0.0467	False		,,,				2504	0.0256				p.R2471H		Atlas-SNP	.											.	FBN3	300	.	0			c.G7412A						PASS	.	C	HIS/ARG	55,4351	51.6+/-87.1	1,53,2149	60	55	56		7412	0.9	1	19	dbSNP_108	56	406,8194	126.0+/-184.5	7,392,3901	yes	missense	FBN3	NM_032447.3	29	8,445,6050	TT,TC,CC		4.7209,1.2483,3.5445	benign	2471/2810	8145928	461,12545	2203	4300	6503	SO:0001583	missense	84467	exon58			GGACAGCGGCAGG		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.7412G>A	19.37:g.8145928C>T	ENSP00000470498:p.Arg2471His	28	0	0		23	9	0.391304	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	55	0.025183150183150184	3	0.006097560975609756	14	0.03867403314917127	0	0.0	38	0.05013192612137203	C	12.22	1.871409	0.33069	0.012483	0.047209	ENSG00000142449	ENST00000270509;ENST00000341066	D	0.92545	-3.06	4.06	0.915	0.19366	EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.310571	0.28436	N	0.015342	T	0.47691	0.1459	N	0.17312	0.475	0.27752	N	0.944128	B;B	0.21452	0.032;0.056	B;B	0.22753	0.041;0.027	T	0.62492	-0.6843	10	0.41790	T	0.15	.	5.5084	0.16866	0.0:0.3205:0.0:0.6795	rs3848570;rs3848570	2471;577	Q75N90;Q6ZNB8	FBN3_HUMAN;.	H	2471;577	ENSP00000270509:R2471H	ENSP00000270509:R2471H	R	-	2	0	FBN3	8051928	1.000000	0.71417	1.000000	0.80357	0.167000	0.22549	3.177000	0.50871	0.551000	0.29008	0.297000	0.19635	CGC	C|0.971;T|0.029	0.029	strong		0.622	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447		T	8145928	C	T	8145928	3	4	27	1	0	0	0	0	1	0	0	0	5712	768	27	1	1041	1	FBN3	19	8145928	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	576683	8145928	50983055	887	11338											
ANGPTL4	51129	hgsc.bcm.edu	37	chr19	8436289	8436289	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctgcagctcactgcacccGtggccggccagctgggcgcc	4	5	14	18	3	1	0	1	0	0	0	1	0	1	0	5	3	4	4	5	3	0	0	rs139998264	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:8436289G>A	ENST00000301455.2	+	6	1093	c.922G>A	c.(922-924)Gtg>Atg	p.V308M	RAB11B-AS1_ENST00000597785.1_RNA|RAB11B-AS1_ENST00000593581.1_RNA|ANGPTL4_ENST00000393962.2_Missense_Mutation_p.V270M|ANGPTL4_ENST00000541807.1_Missense_Mutation_p.V141M	NM_139314.1	NP_647475.1	Q9BY76	ANGL4_HUMAN	angiopoietin-like 4	308	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.		V -> M (in dbSNP:rs139998264). {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						CACTGCACCCGTGGCCGGCCA	0.672													G|||	2	0.000399361	0.0	0.0	5008	,	,		16262	0.001		0.001	False		,,,				2504	0.0				p.V308M		Atlas-SNP	.											.	ANGPTL4	21	.	0			c.G922A						PASS	.	G	MET/VAL,MET/VAL	1,4405	2.1+/-5.4	0,1,2202	43	38	40		808,922	1.6	0.4	19	dbSNP_134	40	7,8591	5.7+/-21.5	0,7,4292	no	missense,missense	ANGPTL4	NM_001039667.1,NM_139314.1	21,21	0,8,6494	AA,AG,GG		0.0814,0.0227,0.0615	benign,benign	270/369,308/407	8436289	8,12996	2203	4299	6502	SO:0001583	missense	51129	exon6			GCACCCGTGGCCG	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.922G>A	19.37:g.8436289G>A	ENSP00000301455:p.Val308Met	92	0	0		81	40	0.493827	NM_139314	A8MY84|B4E089|D6W670|F5H0I2|Q53HQ6|Q53HU1|Q6UXN0|Q9HBV4|Q9NZU4|Q9Y5B3	Missense_Mutation	SNP	ENST00000301455.2	37	CCDS12200.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	5.392	0.257560	0.10239	2.27E-4	8.14E-4	ENSG00000167772	ENST00000301455;ENST00000393962;ENST00000541807	T;T;T	0.76709	-1.04;-1.04;-1.04	5.09	1.65	0.23941	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	2.318390	0.01258	N	0.009095	T	0.73938	0.3651	L	0.45422	1.42	0.09310	N	1	B;B	0.29646	0.253;0.253	B;B	0.34301	0.179;0.126	T	0.56836	-0.7913	10	0.49607	T	0.09	.	6.3492	0.21367	0.168:0.2821:0.5498:0.0	.	270;308	A8MY84;Q9BY76	.;ANGL4_HUMAN	M	308;270;141	ENSP00000301455:V308M;ENSP00000377534:V270M;ENSP00000439833:V141M	ENSP00000301455:V308M	V	+	1	0	ANGPTL4	8342289	0.038000	0.19896	0.434000	0.26772	0.003000	0.03518	1.289000	0.33307	0.130000	0.18549	-0.263000	0.10527	GTG	G|0.999;A|0.001	0.001	strong		0.672	ANGPTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460322.1	NM_139314		A	8436289	G	A	8436289	3	1	27	1	0	0	0	0	1	0	0	0	616	1145	40	1	944	1	ANGPTL4	19	8436289	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	290361	8436289	50692694	888	11339											
MYO1F	4542	hgsc.bcm.edu	37	chr19	8616999	8616999	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gcaagaagttggagatcttgCccccatctggctccccacct	8	9	9	15	0	2	2	0	0	2	2	3	3	3	2	5	2	1	3	5	2	2	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:8616999C>T	ENST00000338257.8	-	7	821	c.554G>A	c.(553-555)gGc>gAc	p.G185D	AC092316.1_ENST00000598703.1_RNA	NM_012335.3	NP_036467.2	O00160	MYO1F_HUMAN	myosin IF	185	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						GGAGATCTTGCCCCCATCTGG	0.562																																					p.G185D		Atlas-SNP	.											.	MYO1F	128	.	0			c.G554A						PASS	.						100	102	102					19																	8616999		1977	4203	6180	SO:0001583	missense	4542	exon7			ATCTTGCCCCCAT	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.554G>A	19.37:g.8616999C>T	ENSP00000344871:p.Gly185Asp	121	0	0		102	23	0.22549	NM_012335	Q8WWN7	Missense_Mutation	SNP	ENST00000338257.8	37	CCDS42494.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.316297	0.81469	.	.	ENSG00000142347	ENST00000305795;ENST00000338257	D	0.95885	-3.84	3.93	3.93	0.45458	Myosin head, motor domain (2);	0.064498	0.64402	D	0.000010	D	0.98695	0.9562	H	0.98721	4.31	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	0.99301	1.0901	10	0.87932	D	0	.	15.1284	0.72500	0.0:1.0:0.0:0.0	.	185;185;185	B4DVP3;B0I1T1;O00160	.;.;MYO1F_HUMAN	D	230;185	ENSP00000344871:G185D	ENSP00000304899:G230D	G	-	2	0	MYO1F	8522999	1.000000	0.71417	0.986000	0.45419	0.850000	0.48378	7.651000	0.83577	2.048000	0.60808	0.460000	0.39030	GGC	.	.	none		0.562	MYO1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342716.2			T	8616999	C	T	8616999	3	4	27	1	0	0	0	0	1	0	0	0	10082	739	26	2	2830	2	MYO1F	19	8616999	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	180710	8616999	50511984	889	11340											
MUC16	94025	hgsc.bcm.edu	37	chr19	8999044	8999044	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgctagtggtgggcacagaGctccgctgtgtgaaacctgc	7	9	14	11	1	0	2	0	1	0	1	1	2	1	2	2	2	4	4	2	2	2	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:8999044G>A	ENST00000397910.4	-	57	41003	c.40800C>T	c.(40798-40800)agC>agT	p.S13600S	MUC16_ENST00000380951.5_Silent_p.S241S	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13602				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						TGGGCACAGAGCTCCGCTGTG	0.547																																					p.S13600S		Atlas-SNP	.											.	MUC16	4315	.	0			c.C40800T						PASS	.						71	71	71					19																	8999044		1988	4149	6137	SO:0001819	synonymous_variant	94025	exon57			CACAGAGCTCCGC	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.40800C>T	19.37:g.8999044G>A		107	0	0		100	22	0.22	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	1.631	-0.518888	0.04171	.	.	ENSG00000181143	ENST00000542240	.	.	.	1.04	1.04	0.20106	.	.	.	.	.	T	0.37348	0.1000	.	.	.	.	.	.	.	.	.	.	.	.	T	0.43523	-0.9386	3	.	.	.	.	5.4159	0.16374	0.0:0.0:1.0:0.0	.	.	.	.	V	440	.	.	A	-	2	0	MUC16	8860044	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-1.186000	0.03070	0.865000	0.35603	0.455000	0.32223	GCT	.	.	none		0.547	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	8999044	G	A	8999044	2	1	27	1	0	0	0	0	0	0	0	1	9982	962	34	2		2	MUC16	19	8999044	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	382045	8999044	50129939	890	11341											
MUC16	94025	hgsc.bcm.edu	37	chr19	9013905	9013905	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggtccactgtggaggtccCaggagctgaaaagagtcctc	11	7	13	10	0	0	2	0	1	0	1	4	4	3	4	3	4	1	1	3	4	3	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:9013905C>G	ENST00000397910.4	-	33	38688	c.38485G>C	c.(38485-38487)Ggg>Cgg	p.G12829R		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12831				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						GTGGAGGTCCCAGGAGCTGAA	0.502																																					p.G12829R		Atlas-SNP	.											.	MUC16	4315	.	0			c.G38485C						PASS	.						68	61	63					19																	9013905		1920	4127	6047	SO:0001583	missense	94025	exon33			AGGTCCCAGGAGC	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.38485G>C	19.37:g.9013905C>G	ENSP00000381008:p.Gly12829Arg	103	0	0		83	18	0.216867	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	9.580	1.123389	0.20959	.	.	ENSG00000181143	ENST00000397910	T	0.01918	4.56	1.48	1.48	0.22813	.	.	.	.	.	T	0.07458	0.0188	M	0.73962	2.25	.	.	.	D	0.71674	0.998	P	0.58520	0.84	T	0.10730	-1.0617	8	0.87932	D	0	.	6.367	0.21461	0.0:1.0:0.0:0.0	.	12829	B5ME49	.	R	12829	ENSP00000381008:G12829R	ENSP00000381008:G12829R	G	-	1	0	MUC16	8874905	0.000000	0.05858	0.075000	0.20258	0.028000	0.11728	-0.025000	0.12413	1.121000	0.41925	0.484000	0.47621	GGG	.	.	none		0.502	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		G	9013905	C	G	9013905	3	3	27	1	0	0	0	0	1	0	0	0	9982	594	21	4	5246	4	MUC16	19	9013905	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	14861	9013905	50115078	891	11342											
ZNF560	147741	hgsc.bcm.edu	37	chr19	9580305	9580305	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ttgttcttcacaaacactcaCcttggagaactcttggcagt	10	13	7	11	0	4	1	2	0	2	1	4	2	4	1	1	2	2	2	1	2	2	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:9580305C>T	ENST00000301480.4	-	8	743		c.e8+1			NM_152476.2	NP_689689.2	Q96MR9	ZN560_HUMAN	zinc finger protein 560						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						CAAACACTCACCTTGGAGAAC	0.458																																					.		Atlas-SNP	.											.	ZNF560	162	.	0			c.529+1G>A						PASS	.						123	103	110					19																	9580305		2203	4300	6503	SO:0001630	splice_region_variant	147741	exon9			CACTCACCTTGGA	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.529+1G>A	19.37:g.9580305C>T		80	0	0		89	4	0.0449438	NM_152476	Q495S9|Q495T1	Splice_Site	SNP	ENST00000301480.4	37	CCDS12214.1	.	.	.	.	.	.	.	.	.	.	C	13.81	2.348351	0.41599	.	.	ENSG00000198028	ENST00000301480	.	.	.	1.87	0.737	0.18314	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.3266	0.26560	0.2623:0.7377:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ZNF560	9441305	0.001000	0.12720	0.544000	0.28141	0.588000	0.36517	0.273000	0.18662	0.301000	0.22738	0.462000	0.41574	.	.	.	none		0.458	ZNF560-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449901.1	NM_152476	Intron	T	9580305	C	T	9580305	5	4	27	1	0	0	0	0	0	0	1	0	18006	521	18	2	1854	2	ZNF560	19	9580305	Splice_Site	SNP	C	TCGA-G8-6909-01A-11D-2210-10	566400	9580305	49548678	892	11343											
ZNF426	79088	hgsc.bcm.edu	37	chr19	9641722	9641722	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gctgaagtatagaccactggGtttcaagtcgcatttcccat	10	12	9	10	1	1	2	1	1	0	1	3	2	2	2	2	1	0	4	2	1	4	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:9641722G>A	ENST00000535489.1	-	5	683	c.347C>T	c.(346-348)aCc>aTc	p.T116I	ZNF426_ENST00000253115.2_Missense_Mutation_p.T116I|ZNF426_ENST00000593003.1_Missense_Mutation_p.T78I|ZNF426_ENST00000589289.1_Intron			Q9BUY5	ZN426_HUMAN	zinc finger protein 426	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)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20						AGACCACTGGGTTTCAAGTCG	0.418																																					p.T116I		Atlas-SNP	.											.	ZNF426	56	.	0			c.C347T						PASS	.						110	104	106					19																	9641722		2203	4300	6503	SO:0001583	missense	79088	exon7			CACTGGGTTTCAA	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.347C>T	19.37:g.9641722G>A	ENSP00000439017:p.Thr116Ile	113	0	0		111	27	0.243243	NM_024106	B3KTL2	Missense_Mutation	SNP	ENST00000535489.1	37	CCDS12215.1	.	.	.	.	.	.	.	.	.	.	G	5.359	0.251581	0.10185	.	.	ENSG00000130818	ENST00000545189;ENST00000253115;ENST00000535489	T;T	0.06608	3.28;3.28	1.53	0.414	0.16406	.	.	.	.	.	T	0.04679	0.0127	L	0.29908	0.895	0.09310	N	1	B;B	0.21688	0.059;0.017	B;B	0.14023	0.01;0.006	T	0.39881	-0.9592	9	0.41790	T	0.15	.	5.6008	0.17353	0.0:0.3499:0.6501:0.0	.	103;116	Q59EH4;Q9BUY5	.;ZN426_HUMAN	I	103;116;116	ENSP00000253115:T116I;ENSP00000439017:T116I	ENSP00000253115:T116I	T	-	2	0	ZNF426	9502722	0.000000	0.05858	0.001000	0.08648	0.036000	0.12997	-0.134000	0.10436	0.183000	0.20059	0.460000	0.39030	ACC	.	.	none		0.418	ZNF426-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449905.1	NM_024106		A	9641722	G	A	9641722	3	1	27	1	0	0	0	0	1	0	0	0	17915	1261	44	2	1325	2	ZNF426	19	9641722	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	61417	9641722	49487261	893	11344											
FDX1L	112812	hgsc.bcm.edu	37	chr19	10426597	10426597	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccggaagtgcccccaggtcTgttccaccaggtgcccctgg	5	7	12	17	1	1	0	0	0	1	0	2	1	2	1	7	4	2	1	7	4	1	1	rs62640397	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10426597T>C	ENST00000393708.3	-	1	94	c.76A>G	c.(76-78)Aga>Gga	p.R26G	FDX1L_ENST00000494368.1_Intron|FDX1L_ENST00000541276.1_Missense_Mutation_p.R29G|CTD-2369P2.12_ENST00000586529.1_Intron|CTD-2369P2.10_ENST00000452032.2_Missense_Mutation_p.R26G|FDX1L_ENST00000492239.1_5'Flank	NM_001031734.2	NP_001026904.1	Q6P4F2	ADXL_HUMAN	ferredoxin 1-like	26					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)			CCCCCAGGTCTGTTCCACCAG	0.677													T|||	106	0.0211661	0.0015	0.0058	5008	,	,		11423	0.0397		0.0328	False		,,,				2504	0.0276				p.R26G		Atlas-SNP	.											.	FDX1L	21	.	0			c.A76G						PASS	.	T	GLY/ARG	36,4366		0,36,2165	19	22	21		76	-2.5	0	19	dbSNP_129	21	269,8329		5,259,4035	yes	missense	FDX1L	NM_001031734.2	125	5,295,6200	CC,CT,TT		3.1286,0.8178,2.3462	benign	26/184	10426597	305,12695	2201	4299	6500	SO:0001583	missense	112812	exon1			CAGGTCTGTTCCA	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.76A>G	19.37:g.10426597T>C	ENSP00000377311:p.Arg26Gly	86	0	0		70	31	0.442857	NM_001031734	Q8N8B8	Missense_Mutation	SNP	ENST00000393708.3	37	CCDS32905.1	56	0.02564102564102564	1	0.0020325203252032522	2	0.0055248618784530384	26	0.045454545454545456	27	0.03562005277044855	T	10.47	1.359917	0.24598	0.008178	0.031286	ENSG00000167807	ENST00000541276;ENST00000393708	.	.	.	4.14	-2.54	0.06307	.	0.296563	0.29956	N	0.010774	T	0.01976	0.0062	N	0.08118	0	0.19775	N	0.999957	B	0.06786	0.001	B	0.04013	0.001	T	0.06935	-1.0799	9	0.87932	D	0	-10.9532	3.6387	0.08158	0.11:0.0955:0.4395:0.355	.	26	Q6P4F2	ADXL_HUMAN	G	29;26	.	ENSP00000341665:R26G	R	-	1	2	FDX1L	10287597	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.952000	0.03881	-0.744000	0.04778	-2.293000	0.00265	AGA	T|0.980;C|0.020	0.020	strong		0.677	FDX1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280567.2			C	10426597	T	C	10426597	3	2	27	1	0	0	0	0	1	0	0	0	5813	1588	55	3	495	3	FDX1L	19	10426597	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	784875	10426597	48702386	894	11345											
RAVER1	125950	hgsc.bcm.edu	37	chr19	10439501	10439501	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcggcttgcccagcaggtcCgacttggcacgggcagccga	7	5	15	14	4	0	0	0	0	0	0	1	2	1	0	3	4	4	4	3	4	0	2	rs3745263	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10439501C>T	ENST00000293677.6	-	3	705	c.624G>A	c.(622-624)tcG>tcA	p.S208S		NM_133452.2	NP_597709.2	Q8IY67	RAVR1_HUMAN	ribonucleoprotein, PTB-binding 1	191	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)			CCAGCAGGTCCGACTTGGCAC	0.632													C|||	108	0.0215655	0.0015	0.0058	5008	,	,		13773	0.0407		0.0338	False		,,,				2504	0.0276				p.S208S		Atlas-SNP	.											.	RAVER1	67	.	0			c.G624A						PASS	.	C		40,4254		0,40,2107	24	30	28		624	-6.7	0.9	19	dbSNP_107	28	275,8223		6,263,3980	no	coding-synonymous	RAVER1	NM_133452.2		6,303,6087	TT,TC,CC		3.2361,0.9315,2.4625		208/757	10439501	315,12477	2147	4249	6396	SO:0001819	synonymous_variant	125950	exon3			CAGGTCCGACTTG		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.624G>A	19.37:g.10439501C>T		249	0	0		187	86	0.459893	NM_133452	A6NMU4|Q8IY60|Q8TF24	Silent	SNP	ENST00000293677.6	37	CCDS45960.1																																																																																			C|0.971;T|0.029	0.029	strong		0.632	RAVER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451227.1	NM_133452		T	10439501	C	T	10439501	2	4	27	1	0	0	0	0	0	0	0	1	13109	639	23	1		1	RAVER1	19	10439501	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	12904	10439501	48689482	895	11346											
RAVER1	125950	hgsc.bcm.edu	37	chr19	10439540	10439540	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtccttcttcatgtactcAgcaaagccatagcccttgga	10	11	8	12	0	3	0	2	0	1	0	4	2	4	1	3	1	4	2	3	1	3	5	rs3745262	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10439540A>G	ENST00000293677.6	-	3	666	c.585T>C	c.(583-585)gcT>gcC	p.A195A		NM_133452.2	NP_597709.2	Q8IY67	RAVR1_HUMAN	ribonucleoprotein, PTB-binding 1	178	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)			TCATGTACTCAGCAAAGCCAT	0.642													G|||	135	0.0269569	0.0234	0.0058	5008	,	,		16733	0.0397		0.0328	False		,,,				2504	0.0276				p.A195A		Atlas-SNP	.											RAVER1_ENST00000293677,caecum,carcinoma,0,2	RAVER1	67	2	0			c.T585C						PASS	.	G		97,4143		0,97,2023	34	40	38		585	-10.1	0.4	19	dbSNP_107	38	274,8204		6,262,3971	yes	coding-synonymous	RAVER1	NM_133452.2		6,359,5994	GG,GA,AA		3.2319,2.2877,2.9171		195/757	10439540	371,12347	2120	4239	6359	SO:0001819	synonymous_variant	125950	exon3			GTACTCAGCAAAG		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.585T>C	19.37:g.10439540A>G		181	0	0		131	50	0.381679	NM_133452	A6NMU4|Q8IY60|Q8TF24	Silent	SNP	ENST00000293677.6	37	CCDS45960.1																																																																																			A|0.972;G|0.028	0.028	strong		0.642	RAVER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451227.1	NM_133452		G	10439540	A	G	10439540	2	3	27	1	0	0	0	0	0	0	0	1	13109	175	7	3		3	RAVER1	19	10439540	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	39	10439540	48689443	896	11347											
ICAM3	3385	hgsc.bcm.edu	37	chr19	10445806	10445806	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agggtcacgttgcagacgatCtcccgggcaccctcctgatc	7	8	11	15	3	2	2	1	1	1	1	5	3	3	2	3	2	1	3	3	2	0	1	rs3181047	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10445806C>T	ENST00000160262.5	-	4	1081	c.873G>A	c.(871-873)gaG>gaA	p.E291E	RAVER1_ENST00000293677.6_5'Flank|ICAM3_ENST00000589261.1_Silent_p.E214E	NM_002162.3	NP_002153.2	P32942	ICAM3_HUMAN	intercellular adhesion molecule 3	291	Ig-like C2-type 3.				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)			TGCAGACGATCTCCCGGGCAC	0.662													C|||	45	0.00898562	0.0	0.0	5008	,	,		14325	0.0377		0.004	False		,,,				2504	0.0031				p.E291E		Atlas-SNP	.											.	ICAM3	29	.	0			c.G873A						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	106	113	110		873	-4.6	0	19	dbSNP_105	110	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	ICAM3	NM_002162.3		0,9,6494	TT,TC,CC		0.0698,0.0681,0.0692		291/548	10445806	9,12997	2203	4300	6503	SO:0001819	synonymous_variant	3385	exon4			GACGATCTCCCGG		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.873G>A	19.37:g.10445806C>T		93	0	0		90	47	0.522222	NM_002162	Q6PD68	Silent	SNP	ENST00000160262.5	37	CCDS12235.1																																																																																			C|0.995;T|0.005	0.005	strong		0.662	ICAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451234.1			T	10445806	C	T	10445806	2	4	27	1	0	0	0	0	0	0	0	1	7490	912	32	2		2	ICAM3	19	10445806	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	6266	10445806	48683177	897	11348											
PDE4A	5141	hgsc.bcm.edu	37	chr19	10531491	10531491	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcctgtctctgtcactgccCgggccccgggagggccaggc	4	6	15	16	2	2	0	1	0	1	0	3	1	2	1	5	4	2	0	5	4	0	0	rs117495488	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10531491C>T	ENST00000352831.6	+	1	161	c.51C>T	c.(49-51)ccC>ccT	p.P17P	PDE4A_ENST00000380702.2_Intron|PDE4A_ENST00000592685.1_Intron	NM_001111307.1	NP_001104777.1	P27815	PDE4A_HUMAN	phosphodiesterase 4A, cAMP-specific	17					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)	TGTCACTGCCCGGGCCCCGGG	0.726													C|||	34	0.00678914	0.0	0.0	5008	,	,		8964	0.0278		0.004	False		,,,				2504	0.002				p.P17P		Atlas-SNP	.											.	PDE4A	236	.	0			c.C51T						PASS	.	C		0,2670		0,0,1335	7	8	8		51	-7.6	0.9	19	dbSNP_132	8	6,6434		0,6,3214	no	coding-synonymous	PDE4A	NM_001111307.1		0,6,4549	TT,TC,CC		0.0932,0.0,0.0659		17/887	10531491	6,9104	1335	3220	4555	SO:0001819	synonymous_variant	5141	exon1			ACTGCCCGGGCCC		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.51C>T	19.37:g.10531491C>T		2	0	0		32	18	0.5625	NM_001111307	O75522|O76092|Q16255|Q16691|Q5DM53|Q6PMT2|Q8IVA7|Q8WUQ3|Q9H3H2	Silent	SNP	ENST00000352831.6	37	CCDS45961.1																																																																																			C|0.987;T|0.013	0.013	strong		0.726	PDE4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451244.1			T	10531491	C	T	10531491	2	4	27	1	0	0	0	0	0	0	0	1	11648	639	23	1		1	PDE4A	19	10531491	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	85685	10531491	48597492	898	11349											
PDE4A	5141	hgsc.bcm.edu	37	chr19	10572271	10572271	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccacctggccgtgggcttcaAgctgctgcaggaggacaact	8	7	13	13	1	1	0	1	0	0	0	1	2	1	2	3	4	4	4	3	4	2	1	rs141379029		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10572271A>G	ENST00000352831.6	+	12	1645	c.1535A>G	c.(1534-1536)aAg>aGg	p.K512R	PDE4A_ENST00000380702.2_Missense_Mutation_p.K490R|PDE4A_ENST00000592685.1_Missense_Mutation_p.K490R|PDE4A_ENST00000440014.2_Missense_Mutation_p.K451R|PDE4A_ENST00000344979.3_Missense_Mutation_p.K273R|PDE4A_ENST00000293683.5_Missense_Mutation_p.K486R	NM_001111307.1	NP_001104777.1	P27815	PDE4A_HUMAN	phosphodiesterase 4A, cAMP-specific	512	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)	GTGGGCTTCAAGCTGCTGCAG	0.632													A|||	1	0.000199681	0.0	0.0	5008	,	,		10749	0.0		0.001	False		,,,				2504	0.0				p.K512R		Atlas-SNP	.											.	PDE4A	236	.	0			c.A1535G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	0,4406		0,0,2203	77	69	72		1535,1457,1352,818	3.9	1	19	dbSNP_134	72	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense,missense,missense	PDE4A	NM_001111307.1,NM_001111308.1,NM_001111309.1,NM_006202.2	26,26,26,26	0,3,6500	GG,GA,AA		0.0349,0.0,0.0231	benign,benign,benign,benign	512/887,486/861,451/826,273/648	10572271	3,13003	2203	4300	6503	SO:0001583	missense	5141	exon12			GCTTCAAGCTGCT		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.1535A>G	19.37:g.10572271A>G	ENSP00000270474:p.Lys512Arg	154	0	0		105	52	0.495238	NM_001111307	O75522|O76092|Q16255|Q16691|Q5DM53|Q6PMT2|Q8IVA7|Q8WUQ3|Q9H3H2	Missense_Mutation	SNP	ENST00000352831.6	37	CCDS45961.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	18.40	3.614645	0.66672	0.0	3.49E-4	ENSG00000065989	ENST00000380702;ENST00000352831;ENST00000293683;ENST00000440014;ENST00000344979;ENST00000380686	D;D;D;D;D	0.81821	-1.54;-1.54;-1.54;-1.54;-1.54	3.92	3.92	0.45320	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.053169	0.64402	D	0.000001	D	0.84433	0.5471	L	0.43701	1.375	0.58432	D	0.999995	B;D;D;D;D	0.64830	0.081;0.994;0.992;0.971;0.989	B;D;D;P;D	0.83275	0.073;0.996;0.988;0.906;0.943	D	0.85413	0.1138	10	0.87932	D	0	.	10.7358	0.46124	1.0:0.0:0.0:0.0	.	178;273;451;486;512	P27815-5;P27815-4;P27815-6;P27815-2;P27815	.;.;.;.;PDE4A_HUMAN	R	490;512;486;451;273;178	ENSP00000370078:K490R;ENSP00000270474:K512R;ENSP00000293683:K486R;ENSP00000394754:K451R;ENSP00000341007:K273R	ENSP00000293683:K486R	K	+	2	0	PDE4A	10433271	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.022000	0.93678	1.652000	0.50683	0.477000	0.44152	AAG	A|1.000;G|0.000	0.000	strong		0.632	PDE4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451244.1			G	10572271	A	G	10572271	3	3	27	1	0	0	0	0	1	0	0	0	11648	72	3	3	2038	3	PDE4A	19	10572271	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	40780	10572271	48556712	899	11350											
S1PR5	53637	hgsc.bcm.edu	37	chr19	10624838	10624838	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggatcggcctgcaggagtaCaggacaggtgcgcgccgggc	7	4	19	11	4	0	0	0	0	0	0	1	3	0	3	2	6	3	2	2	6	1	1	rs150461309	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10624838C>T	ENST00000439028.3	-	2	975	c.850G>A	c.(850-852)Gta>Ata	p.V284I	S1PR5_ENST00000333430.4_Missense_Mutation_p.V284I	NM_001166215.1	NP_001159687.1	Q9H228	S1PR5_HUMAN	sphingosine-1-phosphate receptor 5	284					regulation of neuron differentiation (GO:0045664)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sphingosine-1-phosphate receptor activity (GO:0038036)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	12					Fingolimod(DB08868)	TGCAGGAGTACAGGACAGGTG	0.657													C|||	24	0.00479233	0.0	0.0014	5008	,	,		15614	0.0169		0.004	False		,,,				2504	0.002				p.V284I		Atlas-SNP	.											.	S1PR5	33	.	0			c.G850A						PASS	.	C	ILE/VAL,ILE/VAL	2,4392	2.1+/-5.4	0,2,2195	34	32	32		850,850	1.8	0.2	19	dbSNP_134	32	9,8591	6.4+/-24.3	0,9,4291	yes	missense,missense	S1PR5	NM_001166215.1,NM_030760.4	29,29	0,11,6486	TT,TC,CC		0.1047,0.0455,0.0847	benign,benign	284/399,284/399	10624838	11,12983	2197	4300	6497	SO:0001583	missense	53637	exon2			GGAGTACAGGACA	AK074661	CCDS12240.1	19p13.2	2012-08-08	2008-04-30	2008-04-30		ENSG00000180739		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"	14299	protein-coding gene	gene with protein product		605146	"endothelial differentiation, sphingolipid G-protein-coupled receptor, 8"	EDG8		10799507	Standard	NM_030760		Approved	Edg-8	uc002mou.2	Q9H228		ENST00000439028.3:c.850G>A	19.37:g.10624838C>T	ENSP00000416915:p.Val284Ile	80	0	0		63	30	0.47619	NM_030760	Q6NW11	Missense_Mutation	SNP	ENST00000439028.3	37	CCDS12240.1	17|17	0.007783882783882784|0.007783882783882784	0|0	0.0|0.0	0|0	0.0|0.0	14|14	0.024475524475524476|0.024475524475524476	3|3	0.00395778364116095|0.00395778364116095	C|C	0.204|0.204	-1.041896|-1.041896	0.01997|0.01997	4.55E-4|4.55E-4	0.001047|0.001047	ENSG00000180739|ENSG00000180739	ENST00000359134|ENST00000439028;ENST00000333430	.|T;T	.|0.36878	.|1.23;1.23	5.21|5.21	1.84|1.84	0.25277|0.25277	.|GPCR, rhodopsin-like superfamily (1);	.|0.440276	.|0.20594	.|U	.|0.089285	T|T	0.05318|0.05318	0.0141|0.0141	N|N	0.05230|0.05230	-0.09|-0.09	0.09310|0.09310	N|N	0.999994|0.999994	.|B	.|0.20459	.|0.045	.|B	.|0.18263	.|0.021	T|T	0.25363|0.25363	-1.0134|-1.0134	6|10	0.87932|0.02654	D|T	0|1	.|.	1.7218|1.7218	0.02913|0.02913	0.147:0.4824:0.143:0.2276|0.147:0.4824:0.143:0.2276	.|.	.|284	.|Q9H228	.|S1PR5_HUMAN	Y|I	252|284	.|ENSP00000416915:V284I;ENSP00000328472:V284I	ENSP00000352045:C252Y|ENSP00000328472:V284I	C|V	-|-	2|1	0|0	S1PR5|S1PR5	10485838|10485838	0.000000|0.000000	0.05858|0.05858	0.163000|0.163000	0.22734|0.22734	0.520000|0.520000	0.34377|0.34377	-0.726000|-0.726000	0.04936|0.04936	0.194000|0.194000	0.20326|0.20326	0.491000|0.491000	0.48974|0.48974	TGT|GTA	C|0.997;T|0.003	0.003	strong		0.657	S1PR5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452015.1	NM_030760		T	10624838	C	T	10624838	3	4	27	1	0	0	0	0	1	0	0	0	13812	478	17	2	350	2	S1PR5	19	10624838	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	52567	10624838	48504145	900	11351											
DNM2	1785	hgsc.bcm.edu	37	chr19	10870486	10870486	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctcatcttctcaaaaacAggtaaaatggggcggcctga	13	8	10	10	1	3	1	2	1	2	0	4	1	3	1	1	4	2	2	1	4	4	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:10870486A>G	ENST00000355667.6	+	2	314	c.234A>G	c.(232-234)acA>acG	p.T78T	DNM2_ENST00000314646.5_Splice_Site_p.T78T|DNM2_ENST00000389253.4_Splice_Site_p.T78T|DNM2_ENST00000585892.1_Splice_Site_p.T78T|DNM2_ENST00000359692.6_Splice_Site_p.T78T|DNM2_ENST00000408974.4_Splice_Site_p.T78T	NM_001005360.2|NM_001190716.1	NP_001005360.1|NP_001177645.1	P50570	DYN2_HUMAN	dynamin 2	78	Dynamin-type G.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|endocytosis (GO:0006897)|G2/M transition of mitotic cell cycle (GO:0000086)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|nitric oxide metabolic process (GO:0046209)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic vesicle transport (GO:0048489)|transferrin transport (GO:0033572)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	enzyme binding (GO:0019899)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|microtubule binding (GO:0008017)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	42			Epithelial(33;4.17e-05)|all cancers(31;8.48e-05)			TCTCAAAAACAGGTAAAATGG	0.587			"F, N, Splice, Mis, O"		ETP ALL																																p.T78T		Atlas-SNP	.		Rec	yes		19	19p13.2	1785	dynamin 2		L	.	DNM2	175	.	0			c.A234G						PASS	.						101	107	105					19																	10870486		2203	4300	6503	SO:0001630	splice_region_variant	1785	exon2			AAAAACAGGTAAA		CCDS32907.1, CCDS32908.1, CCDS45968.1, CCDS45969.1, CCDS59351.1	19p	2014-09-17						"Pleckstrin homology (PH) domain containing"	2974	protein-coding gene	gene with protein product	"dynamin II", "cytoskeletal protein"	602378				7590285, 9143510	Standard	NM_001190716		Approved	DYNII, DYN2, CMTDIB, CMTDI1, DI-CMTB	uc002mps.2	P50570		ENST00000355667.6:c.235+1A>G	19.37:g.10870486A>G		122	0	0		102	43	0.421569	NM_001005361	A8K1B6|E7EV30|E9PEQ4|K7ESI9|Q5I0Y0|Q7Z5S3|Q9UPH4	Silent	SNP	ENST00000355667.6	37	CCDS45968.1																																																																																			.	.	none		0.587	DNM2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452592.1	NM_004945	Silent	G	10870486	A	G	10870486	5	3	27	1	0	0	0	0	0	0	1	0	4674	202	7	3	240	3	DNM2	19	10870486	Splice_Site	SNP	A	TCGA-G8-6909-01A-11D-2210-10	245648	10870486	48258497	901	11352											
KANK2	25959	hgsc.bcm.edu	37	chr19	11303618	11303618	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctccaccacctcctggctgcGgaacacaggtgggctctcag	7	7	11	16	1	1	0	1	0	1	0	4	1	3	1	4	4	2	2	4	4	1	0	rs144821191		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:11303618G>A	ENST00000586659.1	-	4	1452	c.1138C>T	c.(1138-1140)Cgc>Tgc	p.R380C	KANK2_ENST00000589359.1_Missense_Mutation_p.R380C|KANK2_ENST00000432929.2_Missense_Mutation_p.R380C|KANK2_ENST00000589894.1_Missense_Mutation_p.R380C|KANK2_ENST00000355150.5_Missense_Mutation_p.R380C			Q63ZY3	KANK2_HUMAN	KN motif and ankyrin repeat domains 2	380					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						TCCTGGCTGCGGAACACAGGT	0.642													G|||	1	0.000199681	0.0	0.0	5008	,	,		16197	0.0		0.001	False		,,,				2504	0.0				p.R380C		Atlas-SNP	.											.	KANK2	47	.	0			c.C1138T						PASS	.	G	CYS/ARG,CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	70	74	72		1138,1138	0.2	1	19	dbSNP_134	72	10,8590	7.7+/-29.5	0,10,4290	yes	missense,missense	KANK2	NM_001136191.2,NM_015493.6	180,180	0,11,6492	AA,AG,GG		0.1163,0.0227,0.0846	benign,benign	380/852,380/860	11303618	11,12995	2203	4300	6503	SO:0001583	missense	25959	exon2			GGCTGCGGAACAC	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.1138C>T	19.37:g.11303618G>A	ENSP00000465650:p.Arg380Cys	165	0	0		131	65	0.496183	NM_015493	B0I1P4|Q3KQZ3|Q6GUF5|Q9H8S4|Q9NUP0|Q9P210	Missense_Mutation	SNP	ENST00000586659.1	37	CCDS12255.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	6.976	0.550018	0.13374	2.27E-4	0.001163	ENSG00000197256	ENST00000432929;ENST00000355150	T;T	0.37235	1.21;1.21	4.11	0.147	0.14838	.	0.085848	0.43747	D	0.000540	T	0.24774	0.0601	L	0.45581	1.43	0.33354	D	0.571462	B;B;B	0.13145	0.001;0.001;0.007	B;B;B	0.06405	0.002;0.0;0.002	T	0.10474	-1.0628	10	0.37606	T	0.19	-34.2083	5.155	0.15031	0.305:0.0:0.546:0.149	.	380;380;380	Q63ZY3-3;Q63ZY3;Q63ZY3-2	.;KANK2_HUMAN;.	C	380	ENSP00000395650:R380C;ENSP00000347276:R380C	ENSP00000347276:R380C	R	-	1	0	KANK2	11164618	0.023000	0.18921	0.998000	0.56505	0.366000	0.29705	0.248000	0.18198	0.224000	0.20940	-0.448000	0.05591	CGC	G|0.999;A|0.001	0.001	strong		0.642	KANK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453066.2	NM_015493		A	11303618	G	A	11303618	3	1	27	1	0	0	0	0	1	0	0	0	7986	1116	39	1	1481	1	KANK2	19	11303618	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	433132	11303618	47825365	902	11353											
ZNF136	7695	hgsc.bcm.edu	37	chr19	12298164	12298164	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cagttatctcccctcccttcGactacatgaaagaattcaca	12	11	4	14	1	2	2	1	1	1	1	5	3	3	2	3	0	1	1	3	0	4	4	rs200700405		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:12298164G>A	ENST00000343979.4	+	4	1111	c.971G>A	c.(970-972)cGa>cAa	p.R324Q	ZNF136_ENST00000398616.2_Missense_Mutation_p.R258Q	NM_003437.3	NP_003428.1	P52737	ZN136_HUMAN	zinc finger protein 136	324					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)|transcription corepressor activity (GO:0003714)			NS(1)|biliary_tract(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	18						CCCTCCCTTCGACTACATGAA	0.428																																					p.R324Q		Atlas-SNP	.											ZNF136,colon,carcinoma,+1,1	ZNF136	57	1	0			c.G971A						PASS	.						92	93	92					19																	12298164		2203	4300	6503	SO:0001583	missense	7695	exon4			CCCTTCGACTACA	U09367	CCDS32916.1	19p13.2	2013-01-08	2006-06-13		ENSG00000196646	ENSG00000196646		"Zinc fingers, C2H2-type", "-"	12920	protein-coding gene	gene with protein product		604078	"zinc finger protein 136 (clone pHZ-20)"			7557990	Standard	NM_003437		Approved	pHZ-20	uc002mti.3	P52737	OTTHUMG00000156429	ENST00000343979.4:c.971G>A	19.37:g.12298164G>A	ENSP00000344162:p.Arg324Gln	36	0	0		39	22	0.564103	NM_003437		Missense_Mutation	SNP	ENST00000343979.4	37	CCDS32916.1	.	.	.	.	.	.	.	.	.	.	G	11.56	1.676518	0.29783	.	.	ENSG00000196646	ENST00000343979;ENST00000398616	T;T	0.07444	3.19;3.19	1.25	0.00598	0.14064	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02571	0.0078	N	0.10685	0.025	0.09310	N	1	B	0.33857	0.429	B	0.15052	0.012	T	0.42292	-0.9460	8	.	.	.	.	1.9912	0.03447	0.4876:0.0:0.254:0.2584	.	324	P52737	ZN136_HUMAN	Q	324;258	ENSP00000344162:R324Q;ENSP00000381617:R258Q	.	R	+	2	0	ZNF136	12159164	0.000000	0.05858	0.007000	0.13788	0.997000	0.91878	-1.017000	0.03630	-0.007000	0.14345	0.655000	0.94253	CGA	G|0.999;A|0.001	0.001	weak		0.428	ZNF136-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344151.2	NM_003437		A	12298164	G	A	12298164	3	1	27	1	0	0	0	0	1	0	0	0	17741	1058	37	1	985	1	ZNF136	19	12298164	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	994546	12298164	46830819	903	11354											
ZNF563	147837	hgsc.bcm.edu	37	chr19	12429509	12429509	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttattcggcccatctcccgTatgcattaccatatgtcttc	7	16	5	13	2	2	0	0	0	2	0	5	0	2	0	3	1	2	2	3	1	4	7			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:12429509T>C	ENST00000293725.5	-	4	1535	c.1330A>G	c.(1330-1332)Acg>Gcg	p.T444A		NM_145276.2	NP_660319.1	Q8TA94	ZN563_HUMAN	zinc finger protein 563	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(4)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						CCATCTCCCGTATGCATTACC	0.428																																					p.T444A	GBM(39;623 795 5132 29510 31476)	Atlas-SNP	.											ZNF563,colon,carcinoma,+2,1	ZNF563	77	1	0			c.A1330G						scavenged	.						187	173	178					19																	12429509		2203	4300	6503	SO:0001583	missense	147837	exon4			CTCCCGTATGCAT	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.1330A>G	19.37:g.12429509T>C	ENSP00000293725:p.Thr444Ala	72	0	0		46	3	0.0652174	NM_145276	B2R9E7|Q8NAT7	Missense_Mutation	SNP	ENST00000293725.5	37	CCDS12270.1	.	.	.	.	.	.	.	.	.	.	T	14.31	2.498724	0.44455	.	.	ENSG00000188868	ENST00000293725	T	0.26518	1.73	0.537	0.537	0.17144	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41442	0.1159	L	0.58510	1.815	0.20403	N	0.999909	D	0.89917	1.0	D	0.87578	0.998	T	0.13469	-1.0508	9	0.72032	D	0.01	.	6.6537	0.22977	0.0:0.0:0.0:1.0	.	444	Q8TA94	ZN563_HUMAN	A	444	ENSP00000293725:T444A	ENSP00000293725:T444A	T	-	1	0	ZNF563	12290509	0.454000	0.25728	0.020000	0.16555	0.065000	0.16274	1.380000	0.34351	0.454000	0.26884	0.260000	0.18958	ACG	.	.	none		0.428	ZNF563-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344114.1	NM_145276		C	12429509	T	C	12429509	3	2	27	1	0	0	0	0	1	0	0	0	18009	1638	57	3	104	3	ZNF563	19	12429509	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	131345	12429509	46699474	904	11355											
ZNF442	79973	hgsc.bcm.edu	37	chr19	12461745	12461745	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgaaataaactaggccaaaaAaaggctttcccacacaactt	18	7	5	11	1	0	0	0	0	0	0	1	1	1	0	2	2	2	1	2	2	8	4	rs117398535	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:12461745A>G	ENST00000242804.4	-	6	1236	c.654T>C	c.(652-654)ttT>ttC	p.F218F	ZNF442_ENST00000438182.1_Silent_p.F149F|CTD-3105H18.13_ENST00000563695.2_lincRNA	NM_030824.2	NP_110451.1	Q9H7R0	ZN442_HUMAN	zinc finger protein 442	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)			breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	31						TAGGCCAAAAAAAGGCTTTCC	0.403													A|||	10	0.00199681	0.0015	0.0014	5008	,	,		22597	0.0		0.007	False		,,,				2504	0.0				p.F218F		Atlas-SNP	.											ZNF442,middle_lobe,carcinoma,0,1	ZNF442	102	1	0			c.T654C						PASS	.	A		4,4402	8.1+/-20.4	0,4,2199	138	134	135		654	-1.5	0	19	dbSNP_132	135	56,8544	35.9+/-90.5	0,56,4244	no	coding-synonymous	ZNF442	NM_030824.2		0,60,6443	GG,GA,AA		0.6512,0.0908,0.4613		218/628	12461745	60,12946	2203	4300	6503	SO:0001819	synonymous_variant	79973	exon6			CCAAAAAAAGGCT	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.654T>C	19.37:g.12461745A>G		54	0	0		46	18	0.391304	NM_030824	B4DJ48	Silent	SNP	ENST00000242804.4	37	CCDS12271.1																																																																																			A|0.995;G|0.005	0.005	strong		0.403	ZNF442-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344109.1	NM_030824		G	12461745	A	G	12461745	2	3	27	1	0	0	0	0	0	0	0	1	17930	11	1	3		3	ZNF442	19	12461745	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	32236	12461745	46667238	905	11356											
FARSA	2193	hgsc.bcm.edu	37	chr19	13041558	13041558	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtggaccgaagttcagcctcGatgacctagagggaaatgtg	11	8	14	8	2	1	2	1	1	0	1	2	6	1	4	3	2	1	1	3	2	3	2	rs373756496		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:13041558G>A	ENST00000314606.4	-	2	171	c.153C>T	c.(151-153)atC>atT	p.I51I	CTC-425F1.2_ENST00000592636.1_RNA|FARSA_ENST00000588025.1_Silent_p.I91I|FARSA_ENST00000423140.2_Silent_p.I51I	NM_004461.2	NP_004452.1	Q9Y285	SYFA_HUMAN	phenylalanyl-tRNA synthetase, alpha subunit	51					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)	GTTCAGCCTCGATGACCTAGA	0.622																																					p.I51I		Atlas-SNP	.											.	FARSA	46	.	0			c.C153T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	44	46	45		153	-6	0.9	19		45	0,8600		0,0,4300	no	coding-synonymous	FARSA	NM_004461.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		51/509	13041558	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2193	exon2			AGCCTCGATGACC	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.153C>T	19.37:g.13041558G>A		23	0	0		14	9	0.642857	NM_004461	B4E363|Q9NSD8|Q9Y4W8	Silent	SNP	ENST00000314606.4	37	CCDS12287.1																																																																																			.	.	weak		0.622	FARSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451935.1	NM_004461		A	13041558	G	A	13041558	2	1	27	1	0	0	0	0	0	0	0	1	5687	1048	37	1		1	FARSA	19	13041558	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	579813	13041558	46087425	906	11357											
NFIX	4784	hgsc.bcm.edu	37	chr19	13183882	13183882	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atccggacaatcagatagttCaaaccagcaaggagatgcgg	15	6	11	9	2	2	2	2	0	0	2	3	4	3	3	2	3	3	2	2	3	4	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:13183882C>G	ENST00000592199.1	+	3	581	c.581C>G	c.(580-582)tCa>tGa	p.S194*	NFIX_ENST00000585575.1_Nonsense_Mutation_p.S186*|NFIX_ENST00000587760.1_Nonsense_Mutation_p.S186*|NFIX_ENST00000358552.3_Nonsense_Mutation_p.S193*|NFIX_ENST00000397661.2_Nonsense_Mutation_p.S194*|NFIX_ENST00000360105.4_Nonsense_Mutation_p.S197*|NFIX_ENST00000587260.1_Nonsense_Mutation_p.S193*|AC007787.2_ENST00000588095.1_RNA|NFIX_ENST00000588228.1_Nonsense_Mutation_p.S147*|NFIX_ENST00000588680.1_3'UTR			Q14938	NFIX_HUMAN	nuclear factor I/X (CCAAT-binding transcription factor)	194					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)			TCAGATAGTTCAAACCAGCAA	0.557																																					p.S202X		Atlas-SNP	.											.	NFIX	61	.	0			c.C605G						PASS	.						142	144	143					19																	13183882		2032	4166	6198	SO:0001587	stop_gained	4784	exon3			ATAGTTCAAACCA	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.581C>G	19.37:g.13183882C>G	ENSP00000467512:p.Ser194*	120	0	0		105	27	0.257143	NM_001271043	B4DM25|O60413|Q0VG09|Q12859|Q13050|Q13052|Q5U094|Q9UPH1|Q9Y6R8	Nonsense_Mutation	SNP	ENST00000592199.1	37		.	.	.	.	.	.	.	.	.	.	C	35	5.568508	0.96540	.	.	ENSG00000008441	ENST00000397661;ENST00000360105;ENST00000264825;ENST00000438869;ENST00000358552	.	.	.	4.59	4.59	0.56863	.	0.156010	0.44483	D	0.000442	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	.	14.6799	0.69009	0.0:1.0:0.0:0.0	.	.	.	.	X	194;194;197;147;193	.	ENSP00000264825:S197X	S	+	2	0	NFIX	13044882	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.505000	0.73708	2.280000	0.76307	0.462000	0.41574	TCA	.	.	none		0.557	NFIX-013	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000452763.1	NM_002501		G	13183882	C	G	13183882	4	3	27	1	0	0	0	0	0	1	0	0	10383	838	29	4	591	4	NFIX	19	13183882	Nonsense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	142324	13183882	45945101	907	11358											
CYP4F3	4051	hgsc.bcm.edu	37	chr19	15760035	15760035	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atgtttgagcacatcagcctCatgaccttggacagtctgca	10	11	9	11	0	3	2	2	2	1	0	3	3	3	3	2	1	3	3	2	1	0	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:15760035C>G	ENST00000221307.8	+	6	638	c.591C>G	c.(589-591)ctC>ctG	p.L197L	CYP4F3_ENST00000591058.1_Silent_p.L197L|CYP4F3_ENST00000586182.2_Silent_p.L197L|CYP4F3_ENST00000585846.1_Silent_p.L197L	NM_000896.2	NP_000887.2	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 3	197					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						ACATCAGCCTCATGACCTTGG	0.577																																					p.L197L		Atlas-SNP	.											.	CYP4F3	69	.	0			c.C591G						PASS	.						124	107	113					19																	15760035		2203	4300	6503	SO:0001819	synonymous_variant	4051	exon6			CAGCCTCATGACC	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.591C>G	19.37:g.15760035C>G		105	0	0		125	36	0.288	NM_001199209	B7Z8Z3|O60634|Q5U740	Silent	SNP	ENST00000221307.8	37	CCDS12332.1																																																																																			.	.	none		0.577	CYP4F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460819.3	NM_000896		G	15760035	C	G	15760035	2	3	27	1	0	0	0	0	0	0	0	1	4192	813	29	4		4	CYP4F3	19	15760035	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2576153	15760035	43368948	908	11359											
MYO9B	4650	hgsc.bcm.edu	37	chr19	17306074	17306074	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggacaagagcaaaccatgtGgcagcccaagggttcaggaa	15	4	13	9	0	1	1	1	0	0	1	1	3	1	3	2	4	3	3	2	4	4	1	rs112900956	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17306074G>A	ENST00000594824.1	+	22	3985	c.3838G>A	c.(3838-3840)Ggc>Agc	p.G1280S	MYO9B_ENST00000595618.1_Missense_Mutation_p.G1280S|MYO9B_ENST00000397274.2_Missense_Mutation_p.G1280S			Q13459	MYO9B_HUMAN	myosin IXB	1280	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						CAAACCATGTGGCAGCCCAAG	0.701													G|||	19	0.00379393	0.0008	0.0029	5008	,	,		13079	0.0		0.0129	False		,,,				2504	0.0031				p.G1280S		Atlas-SNP	.											MYO9B_ENST00000319396,adrenal_gland,adrenal_cortical_adenoma,0,2	MYO9B	264	2	0			c.G3838A						PASS	.	G	SER/GLY,SER/GLY	11,3783		0,11,1886	20	27	25		3838,3838	-3.2	0	19	dbSNP_132	25	119,8027		0,119,3954	yes	missense,missense	MYO9B	NM_001130065.1,NM_004145.3	56,56	0,130,5840	AA,AG,GG		1.4608,0.2899,1.0888	benign,benign	1280/2023,1280/2158	17306074	130,11810	1897	4073	5970	SO:0001583	missense	4650	exon22			CCATGTGGCAGCC		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.3838G>A	19.37:g.17306074G>A	ENSP00000471367:p.Gly1280Ser	38	0	0		57	29	0.508772	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Missense_Mutation	SNP	ENST00000594824.1	37		12	0.005494505494505495	0	0.0	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	G	5.753	0.323409	0.10900	0.002899	0.014608	ENSG00000099331	ENST00000397274	D	0.83673	-1.75	5.28	-3.16	0.05217	.	1.740110	0.03022	N	0.150866	T	0.65123	0.2661	L	0.34521	1.04	0.09310	N	1	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.06405	0.0;0.0;0.002	T	0.56932	-0.7897	10	0.07030	T	0.85	.	10.5091	0.44851	0.645:0.0:0.355:0.0	.	1280;1280;1286	Q13459;B0I1T6;Q4LE74	MYO9B_HUMAN;.;.	S	1280	ENSP00000380444:G1280S	ENSP00000380444:G1280S	G	+	1	0	MYO9B	17167074	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.479000	0.06567	-0.339000	0.08401	-0.367000	0.07326	GGC	G|0.994;A|0.006	0.006	strong		0.701	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1			A	17306074	G	A	17306074	3	1	27	1	0	0	0	0	1	0	0	0	10094	1348	47	2	3920	2	MYO9B	19	17306074	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1546039	17306074	41822909	909	11360											
ANO8	57719	hgsc.bcm.edu	37	chr19	17439450	17439450	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ctcctcgtcgtcctcgtcctCctccttgccccctggaggcc	1	11	8	21	3	0	0	0	0	0	0	8	1	5	1	8	2	1	0	8	2	0	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17439450C>T	ENST00000159087.4	-	13	1905	c.1747G>A	c.(1747-1749)Gag>Aag	p.E583K		NM_020959.2	NP_066010.1	Q9HCE9	ANO8_HUMAN	anoctamin 8	583	Glu-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						tcctcgtcctcctcctTGCCC	0.741																																					p.E583K		Atlas-SNP	.											.	ANO8	67	.	0			c.G1747A						PASS	.						7	6	6					19																	17439450		2003	3931	5934	SO:0001583	missense	57719	exon13			CGTCCTCCTCCTT	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.1747G>A	19.37:g.17439450C>T	ENSP00000159087:p.Glu583Lys	25	0	0		22	4	0.181818	NM_020959	A6NIJ0	Missense_Mutation	SNP	ENST00000159087.4	37	CCDS32949.1	.	.	.	.	.	.	.	.	.	.	C	16.10	3.027094	0.54683	.	.	ENSG00000074855	ENST00000159087	T	0.61859	0.07	5.3	5.3	0.74995	.	0.247398	0.27836	N	0.017658	T	0.46112	0.1376	N	0.08118	0	0.38121	D	0.937857	P	0.37914	0.611	P	0.45998	0.5	T	0.52200	-0.8607	10	0.31617	T	0.26	.	14.4449	0.67342	0.0:1.0:0.0:0.0	.	583	Q9HCE9	ANO8_HUMAN	K	583	ENSP00000159087:E583K	ENSP00000159087:E583K	E	-	1	0	ANO8	17300450	0.150000	0.22732	0.996000	0.52242	0.352000	0.29268	0.878000	0.28126	2.489000	0.83994	0.484000	0.47621	GAG	.	.	none		0.741	ANO8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462943.1	XM_050644		T	17439450	C	T	17439450	3	4	27	1	0	0	0	0	1	0	0	0	703	864	30	2	1975	2	ANO8	19	17439450	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	133376	17439450	41689533	910	11361											
UNC13A	23025	hgsc.bcm.edu	37	chr19	17749893	17749893	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gacccatctggagtctcaccGggtctgtctggtactcccgg	5	10	12	14	2	4	0	1	0	4	0	6	2	5	1	3	4	1	1	3	4	1	1	rs200328448	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:17749893G>A	ENST00000519716.2	-	25	3079	c.3080C>T	c.(3079-3081)cCg>cTg	p.P1027L	UNC13A_ENST00000252773.7_Splice_Site_p.P1027L|UNC13A_ENST00000551649.1_Splice_Site_p.P1027L|UNC13A_ENST00000428389.2_Splice_Site_p.P1115L|UNC13A_ENST00000552293.1_Splice_Site_p.P1027L|UNC13A_ENST00000550896.1_Splice_Site_p.P1025L	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	1027					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						GAGTCTCACCGGGTCTGTCTG	0.517													G|||	3	0.000599042	0.0	0.0029	5008	,	,		16830	0.0		0.001	False		,,,				2504	0.0				p.P1027L		Atlas-SNP	.											UNC13A_ENST00000519716,NS,carcinoma,0,2	UNC13A	299	2	0			c.C3080T						PASS	.	G	LEU/PRO	7,3979		0,7,1986	27	28	28		3080	1	0	19		28	54,8314		0,54,4130	yes	missense-near-splice	UNC13A	NM_001080421.2	98	0,61,6116	AA,AG,GG		0.6453,0.1756,0.4938	possibly-damaging	1027/1704	17749893	61,12293	1993	4184	6177	SO:0001630	splice_region_variant	23025	exon24			CTCACCGGGTCTG	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.3081+1C>T	19.37:g.17749893G>A		86	0	0		67	39	0.58209	NM_001080421	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	37	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	G	11.97	1.796712	0.31777	0.001756	0.006453	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	T;T;T;T;T;T	0.81247	-1.45;-1.47;-1.45;-1.32;-1.33;-1.46	3.39	1.0	0.19881	Calcium-dependent secretion activator (1);	0.182504	0.35262	U	0.003331	T	0.57873	0.2083	L	0.34521	1.04	0.58432	D	0.999999	P	0.48089	0.905	B	0.36808	0.233	T	0.60525	-0.7246	10	0.66056	D	0.02	.	9.4402	0.38664	0.0:0.0:0.6171:0.3828	.	1027	Q9UPW8	UN13A_HUMAN	L	1027;1115;1027;1027;1027;1025	ENSP00000429562:P1027L;ENSP00000400409:P1115L;ENSP00000252773:P1027L;ENSP00000447236:P1027L;ENSP00000447572:P1027L;ENSP00000446831:P1025L	ENSP00000252773:P1027L	P	-	2	0	UNC13A	17610893	1.000000	0.71417	0.020000	0.16555	0.803000	0.45373	7.588000	0.82629	0.066000	0.16515	0.478000	0.44815	CCG	G|0.996;A|0.004	0.004	strong		0.517	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604	Missense_Mutation	A	17749893	G	A	17749893	5	1	27	1	0	0	0	0	0	0	1	0	16999	1130	39	1	2107	1	UNC13A	19	17749893	Splice_Site	SNP	G	TCGA-G8-6909-01A-11D-2210-10	310443	17749893	41379090	911	11362											
KCNN1	3780	hgsc.bcm.edu	37	chr19	18096220	18096220	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacggcgacatggtgccccaCacctactgcgggaagggtgt	8	7	14	12	3	0	0	0	0	0	0	0	2	0	1	3	4	4	0	3	4	3	2	rs76273600		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:18096220C>T	ENST00000222249.9	+	6	1336	c.1017C>T	c.(1015-1017)caC>caT	p.H339H		NM_002248.3	NP_002239.2	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	339					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)	TGGTGCCCCACACCTACTGCG	0.597													C|||	1	0.000199681	0.0	0.0	5008	,	,		21197	0.0		0.001	False		,,,				2504	0.0				p.H339H		Atlas-SNP	.											.	KCNN1	74	.	0			c.C1017T						PASS	.	C		0,4346		0,0,2173	91	98	96		1017	2.7	1	19	dbSNP_131	96	5,8567	4.3+/-15.6	0,5,4281	no	coding-synonymous	KCNN1	NM_002248.3		0,5,6454	TT,TC,CC		0.0583,0.0,0.0387		339/544	18096220	5,12913	2173	4286	6459	SO:0001819	synonymous_variant	3780	exon6			GCCCCACACCTAC	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.1017C>T	19.37:g.18096220C>T		143	0	0		187	104	0.55615	NM_002248	Q5KR10|Q6DJU4	Silent	SNP	ENST00000222249.9	37																																																																																				C|0.998;T|0.002	0.002	weak		0.597	KCNN1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471896.2	NM_002248		T	18096220	C	T	18096220	2	4	27	1	0	0	0	0	0	0	0	1	8087	477	17	2		2	KCNN1	19	18096220	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	346327	18096220	41032763	912	11363											
NCAN	1463	hgsc.bcm.edu	37	chr19	19335135	19335135	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtatcctatcacccagtcccGtcctggttgctatggcgacc	6	11	9	15	2	1	0	1	0	0	0	4	1	4	0	5	2	1	3	5	2	3	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:19335135G>A	ENST00000252575.6	+	5	770	c.671G>A	c.(670-672)cGt>cAt	p.R224H	NCAN_ENST00000538881.1_5'Flank	NM_004386.2	NP_004377.2	O14594	NCAN_HUMAN	neurocan	224	Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323}.				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)	ACCCAGTCCCGTCCTGGTTGC	0.587																																					p.R224H		Atlas-SNP	.											.	NCAN	277	.	0			c.G671A						PASS	.						157	140	146					19																	19335135		2203	4300	6503	SO:0001583	missense	1463	exon5			AGTCCCGTCCTGG	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.671G>A	19.37:g.19335135G>A	ENSP00000252575:p.Arg224His	111	0	0		88	20	0.227273	NM_004386	Q9UPK6	Missense_Mutation	SNP	ENST00000252575.6	37	CCDS12397.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.996086	0.93167	.	.	ENSG00000130287	ENST00000539499;ENST00000252575	T	0.13657	2.57	4.83	4.83	0.62350	C-type lectin fold (1);Link (5);C-type lectin-like (1);	0.000000	0.34853	N	0.003626	T	0.49338	0.1551	H	0.94734	3.575	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.65026	-0.6268	10	0.87932	D	0	-14.3002	15.4278	0.75069	0.0:0.0:1.0:0.0	.	224	O14594	NCAN_HUMAN	H	238;224	ENSP00000252575:R224H	ENSP00000252575:R224H	R	+	2	0	NCAN	19196135	0.943000	0.32029	0.642000	0.29436	0.926000	0.56050	4.868000	0.63021	2.240000	0.73641	0.561000	0.74099	CGT	.	.	none		0.587	NCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460111.2	NM_004386		A	19335135	G	A	19335135	3	1	27	1	0	0	0	0	1	0	0	0	10213	1145	40	1	685	1	NCAN	19	19335135	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1238915	19335135	39793848	913	11364											
SF4	57794	hgsc.bcm.edu	37	chr19	19427402	19427402	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	caaaccaccggttagcctttCctggggagggaaaaggagta	12	7	13	9	1	0	0	0	0	0	0	1	3	1	3	4	5	2	2	4	5	5	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:19427402C>T	ENST00000247001.5	-	2	382	c.35G>A	c.(34-36)gGa>gAa	p.G12E	SUGP1_ENST00000585763.1_5'UTR|SUGP1_ENST00000334782.5_Splice_Site_p.G12E	NM_172231.3	NP_757386.2	Q8IWZ8	SUGP1_HUMAN	SURP and G patch domain containing 1	12					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(7)|ovary(1)|prostate(1)|stomach(2)|urinary_tract(2)	22						GTTAGCCTTTCCTGGGGAGGG	0.483																																					p.G12E		Atlas-SNP	.											.	SUGP1	63	.	0			c.G35A						PASS	.						61	55	57					19																	19427402		2203	4300	6503	SO:0001630	splice_region_variant	57794	exon2			GCCTTTCCTGGGG	AF521128	CCDS12399.1	19p13	2013-01-28	2010-08-10	2010-08-10		ENSG00000105705		"G patch domain containing"	18643	protein-coding gene	gene with protein product		607992	"splicing factor 4"	SF4		12594045	Standard	NM_172231		Approved	F23858, DKFZp434E2216, RBP	uc002nmh.3	Q8IWZ8		ENST00000247001.5:c.35-1G>A	19.37:g.19427402C>T		141	0	0		91	4	0.043956	NM_172231	O60378|Q6P3X9|Q8TCQ4|Q8WWT4|Q8WWT5|Q9NTG3	Missense_Mutation	SNP	ENST00000247001.5	37	CCDS12399.1	.	.	.	.	.	.	.	.	.	.	C	19.80	3.894791	0.72639	.	.	ENSG00000105705	ENST00000247001;ENST00000535070;ENST00000334782	T	0.35048	1.33	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.58581	0.2132	M	0.63843	1.955	0.51767	D	0.999935	D	0.89917	1.0	D	0.91635	0.999	T	0.62397	-0.6863	10	0.87932	D	0	.	16.9497	0.86242	0.0:1.0:0.0:0.0	.	12	Q8IWZ8	SUGP1_HUMAN	E	12	ENSP00000247001:G12E	ENSP00000247001:G12E	G	-	2	0	SUGP1	19288402	1.000000	0.71417	0.998000	0.56505	0.695000	0.40330	4.890000	0.63178	2.425000	0.82216	0.561000	0.74099	GGA	.	.	none		0.483	SUGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460128.4	NM_021164	Missense_Mutation	T	19427402	C	T	19427402	5	4	27	1	0	0	0	0	0	0	1	0	14170	869	30	2	1954	2	SF4	19	19427402	Splice_Site	SNP	C	TCGA-G8-6909-01A-11D-2210-10	92267	19427402	39701581	914	11365											
GMIP	51291	hgsc.bcm.edu	37	chr19	19745962	19745962	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtgtccgggctgggagccGcctgtgtccacagaggatca	6	7	17	11	2	1	1	1	0	0	1	3	3	3	3	4	4	1	1	4	4	0	0	rs372547969		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:19745962G>A	ENST00000203556.4	-	16	1758	c.1621C>T	c.(1621-1623)Cgg>Tgg	p.R541W	GMIP_ENST00000586269.1_5'UTR|GMIP_ENST00000445806.2_Missense_Mutation_p.R512W|GMIP_ENST00000587238.1_Missense_Mutation_p.R515W	NM_016573.2	NP_057657.2	Q9P107	GMIP_HUMAN	GEM interacting protein	541					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						GCTGGGAGCCGCCTGTGTCCA	0.607																																					p.R541W		Atlas-SNP	.											.	GMIP	55	.	0			c.C1621T						PASS	.	G	TRP/ARG	0,4406		0,0,2203	29	31	30		1621	1.2	0.8	19		30	1,8599	1.2+/-3.3	0,1,4299	no	missense	GMIP	NM_016573.2	101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	541/971	19745962	1,13005	2203	4300	6503	SO:0001583	missense	51291	exon16			GGAGCCGCCTGTG	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.1621C>T	19.37:g.19745962G>A	ENSP00000203556:p.Arg541Trp	122	0	0		94	6	0.0638298	NM_016573	A0AVN9|B7ZLZ0	Missense_Mutation	SNP	ENST00000203556.4	37	CCDS12408.1	.	.	.	.	.	.	.	.	.	.	G	16.31	3.086928	0.55861	0.0	1.16E-4	ENSG00000089639	ENST00000203556;ENST00000445806	T;T	0.23147	1.93;1.92	4.93	1.24	0.21308	.	0.558941	0.13840	N	0.359079	T	0.25901	0.0631	N	0.14661	0.345	0.35031	D	0.758787	D;D;D	0.71674	0.998;0.998;0.998	P;P;P	0.56648	0.803;0.702;0.803	T	0.41787	-0.9489	10	0.87932	D	0	-14.6413	11.5425	0.50675	0.0:0.0:0.2902:0.7098	.	512;515;541	E7ERB7;B7ZLZ0;Q9P107	.;.;GMIP_HUMAN	W	541;512	ENSP00000203556:R541W;ENSP00000397075:R512W	ENSP00000203556:R541W	R	-	1	2	GMIP	19606962	1.000000	0.71417	0.752000	0.31206	0.569000	0.35902	4.044000	0.57361	0.419000	0.25927	0.462000	0.41574	CGG	.	.	weak		0.607	GMIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460551.1	NM_016573		A	19745962	G	A	19745962	3	1	27	1	0	0	0	0	1	0	0	0	6499	1086	38	1	1315	1	GMIP	19	19745962	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	318560	19745962	39383021	915	11366											
ZNF93	81931	hgsc.bcm.edu	37	chr19	20026163	20026163	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tgcctggacactgcacagcgGaatctatataggaatgtgat	12	10	11	8	1	1	1	0	1	1	0	1	4	1	4	1	3	3	1	1	3	5	3	rs150804499	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:20026163G>C	ENST00000343769.5	+	2	106	c.78G>C	c.(76-78)cgG>cgC	p.R26R	ZNF93_ENST00000591366.1_Silent_p.R26R|ZNF93_ENST00000592160.1_Silent_p.R26R|AC007204.2_ENST00000592245.1_lincRNA	NM_031218.3	NP_112495.2	P35789	ZNF93_HUMAN	zinc finger protein 93	26	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(6)|kidney(2)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	24						CTGCACAGCGGAATCTATATA	0.398													g|||	44	0.00878594	0.0008	0.0115	5008	,	,		15681	0.0		0.0119	False		,,,				2504	0.0235				p.R26R		Atlas-SNP	.											.	ZNF93	81	.	0			c.G78C						PASS	.	G		11,4395	17.9+/-39.9	0,11,2192	144	147	146		78	-1.7	0.3	19	dbSNP_134	146	98,8502	55.2+/-116.2	1,96,4203	no	coding-synonymous	ZNF93	NM_031218.3		1,107,6395	CC,CG,GG		1.1395,0.2497,0.8381		26/621	20026163	109,12897	2203	4300	6503	SO:0001819	synonymous_variant	81931	exon2			ACAGCGGAATCTA	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.78G>C	19.37:g.20026163G>C		27	0	0		27	14	0.518519	NM_031218	A6NMY2|B9EGT2|Q8N8Q4|Q9H9X5|Q9Y2N8	Silent	SNP	ENST00000343769.5	37	CCDS32973.1																																																																																			G|0.991;C|0.009	0.009	strong		0.398	ZNF93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460808.2	NM_031218		C	20026163	G	C	20026163	2	2	27	1	0	0	0	0	0	0	0	1	18217	1161	41	4		4	ZNF93	19	20026163	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	280201	20026163	39102820	916	11367											
ZNF93	81931	hgsc.bcm.edu	37	chr19	20044886	20044886	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattacaaatgtgaagaatgTggcaaagccttcatttggtc	13	12	9	7	0	1	2	1	1	0	1	2	2	1	2	1	2	2	1	1	2	5	3	rs10401345	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:20044886T>C	ENST00000343769.5	+	4	1150	c.1122T>C	c.(1120-1122)tgT>tgC	p.C374C	AC007204.2_ENST00000592245.1_lincRNA	NM_031218.3	NP_112495.2	P35789	ZNF93_HUMAN	zinc finger protein 93	374					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)	p.C374C(1)		endometrium(6)|kidney(2)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	24						GTGAAGAATGTGGCAAAGCCT	0.388													t|||	601	0.120008	0.2534	0.0447	5008	,	,		22657	0.0506		0.0437	False		,,,				2504	0.1431				p.C374C		Atlas-SNP	.											ZNF93,NS,carcinoma,0,1	ZNF93	81	1	1	Substitution - coding silent(1)	stomach(1)	c.T1122C						PASS	.	T		928,3478	355.1+/-312.9	98,732,1373	89	89	89		1122	0.9	0.5	19	dbSNP_119	89	281,8319	105.4+/-166.3	2,277,4021	no	coding-synonymous	ZNF93	NM_031218.3		100,1009,5394	CC,CT,TT		3.2674,21.0622,9.2957		374/621	20044886	1209,11797	2203	4300	6503	SO:0001819	synonymous_variant	81931	exon4			AGAATGTGGCAAA	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.1122T>C	19.37:g.20044886T>C		56	0	0		36	36	1	NM_031218	A6NMY2|B9EGT2|Q8N8Q4|Q9H9X5|Q9Y2N8	Silent	SNP	ENST00000343769.5	37	CCDS32973.1																																																																																			T|0.908;C|0.092	0.092	strong		0.388	ZNF93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460808.2	NM_031218		C	20044886	T	C	20044886	2	2	27	1	0	0	0	0	0	0	0	1	18217	1702	59	3		3	ZNF93	19	20044886	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	18723	20044886	39084097	917	11368											
ZNF85	7639	hgsc.bcm.edu	37	chr19	21132453	21132453	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	atgtgaaaaatgtggaaaagCctttaatcatttctcacacc	15	12	6	8	0	2	1	2	1	1	0	3	2	2	2	2	1	1	0	2	1	5	3	rs146063134	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:21132453C>G	ENST00000328178.8	+	4	1246	c.1133C>G	c.(1132-1134)gCc>gGc	p.A378G	ZNF85_ENST00000345030.6_Missense_Mutation_p.A345G|ZNF85_ENST00000601023.1_Missense_Mutation_p.A319G	NM_001256173.1|NM_003429.4	NP_001243102.1|NP_003420.2	Q03923	ZNF85_HUMAN	zinc finger protein 85	378					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						TGTGGAAAAGCCTTTAATCAT	0.348													.|||	2	0.000399361	0.0	0.0	5008	,	,		19410	0.0		0.001	False		,,,				2504	0.001				p.A408G		Atlas-SNP	.											.	ZNF85	72	.	0			c.C1223G						PASS	.	C	GLY/ALA	0,4394		0,0,2197	39	42	41		1133	1.4	0	19	dbSNP_134	41	6,8586		0,6,4290	no	missense	ZNF85	NM_003429.4	60	0,6,6487	GG,GC,CC		0.0698,0.0,0.0462	possibly-damaging	378/596	21132453	6,12980	2197	4296	6493	SO:0001583	missense	7639	exon5			GAAAAGCCTTTAA	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.1133C>G	19.37:g.21132453C>G	ENSP00000329793:p.Ala378Gly	41	0	0		18	8	0.444444	NM_001256171	B9ZVP4|Q6NVI0	Missense_Mutation	SNP	ENST00000328178.8	37	CCDS32977.1	.	.	.	.	.	.	.	.	.	.	.	12.01	1.809319	0.31961	0.0	6.98E-4	ENSG00000105750	ENST00000328178;ENST00000345030;ENST00000421385	T;T	0.19669	2.13;2.13	1.35	1.35	0.21983	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.31071	0.0785	L	0.41573	1.285	0.58432	D	0.999999	B;D;P	0.63046	0.289;0.992;0.898	B;D;P	0.77004	0.17;0.989;0.808	T	0.05632	-1.0873	9	0.66056	D	0.02	.	6.8304	0.23907	0.0:0.4775:0.5225:0.0	.	345;319;378	Q03923-2;Q49A12;Q03923	.;.;ZNF85_HUMAN	G	378;345;253	ENSP00000329793:A378G;ENSP00000342340:A345G	ENSP00000329793:A378G	A	+	2	0	ZNF85	20924293	0.001000	0.12720	0.039000	0.18376	0.129000	0.20672	0.077000	0.14738	0.681000	0.31386	0.462000	0.41574	GCC	C|0.999;G|0.001	0.001	strong		0.348	ZNF85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463430.1	NM_003429		G	21132453	C	G	21132453	3	3	27	1	0	0	0	0	1	0	0	0	18208	739	26	4	1147	4	ZNF85	19	21132453	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1087567	21132453	37996530	918	11369											
ZNF91	7644	hgsc.bcm.edu	37	chr19	23542626	23542626	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgctttgccacattcttcaCacttgtaaggtttctctcca	8	16	5	12	0	3	0	1	0	2	0	5	0	4	0	2	1	2	3	2	1	1	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:23542626C>T	ENST00000300619.7	-	4	3360	c.3155G>A	c.(3154-3156)tGt>tAt	p.C1052Y	ZNF91_ENST00000397082.2_Missense_Mutation_p.C1020Y|ZNF91_ENST00000599743.1_Intron|ZNF91_ENST00000596528.1_5'Flank	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	1052					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)				ACATTCTTCACACTTGTAAGG	0.358																																					p.C1052Y		Atlas-SNP	.											.	ZNF91	349	.	0			c.G3155A						PASS	.						65	70	68					19																	23542626		2185	4292	6477	SO:0001583	missense	7644	exon4			TCTTCACACTTGT	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.3155G>A	19.37:g.23542626C>T	ENSP00000300619:p.Cys1052Tyr	34	0	0		25	12	0.48	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	37	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	C	12.28	1.889340	0.33348	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	D;D	0.85088	-1.94;-1.94	1.31	-0.339	0.12647	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.94032	0.8088	H	0.97962	4.115	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.83578	0.0116	9	0.87932	D	0	.	7.5061	0.27545	0.2521:0.7479:0.0:0.0	.	1020;1052	Q05481-2;Q05481	.;ZNF91_HUMAN	Y	1052;1020	ENSP00000300619:C1052Y;ENSP00000380272:C1020Y	ENSP00000300619:C1052Y	C	-	2	0	ZNF91	23334466	0.951000	0.32395	0.119000	0.21687	0.692000	0.40212	2.703000	0.47110	0.676000	0.31285	0.196000	0.17591	TGT	.	.	none		0.358	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		T	23542626	C	T	23542626	3	4	27	1	0	0	0	0	1	0	0	0	18215	478	17	2	424	2	ZNF91	19	23542626	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2410173	23542626	35586357	919	11370											
ZNF536	9745	hgsc.bcm.edu	37	chr19	31039939	31039939	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caacaaggagcctgatggaaAggcccactctgaagaggatg	14	5	13	9	0	1	3	0	2	1	1	1	6	1	6	2	4	2	0	2	4	4	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:31039939A>G	ENST00000355537.3	+	4	3560	c.3413A>G	c.(3412-3414)aAg>aGg	p.K1138R		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	1138					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)					CCTGATGGAAAGGCCCACTCT	0.532																																					p.K1138R		Atlas-SNP	.											.	ZNF536	424	.	0			c.A3413G						PASS	.						74	72	73					19																	31039939		2203	4300	6503	SO:0001583	missense	9745	exon4			ATGGAAAGGCCCA		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.3413A>G	19.37:g.31039939A>G	ENSP00000347730:p.Lys1138Arg	107	0	0		93	4	0.0430108	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	37	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	A	9.828	1.187633	0.21870	.	.	ENSG00000198597	ENST00000355537	T	0.09445	2.98	5.59	4.57	0.56435	.	0.454568	0.26428	N	0.024436	T	0.07863	0.0197	L	0.29908	0.895	0.28208	N	0.927077	B;P	0.44734	0.001;0.842	B;B	0.36922	0.001;0.236	T	0.13818	-1.0495	10	0.30078	T	0.28	-26.8781	11.4985	0.50424	0.9295:0.0:0.0705:0.0	.	1138;1138	A7E228;O15090	.;ZN536_HUMAN	R	1138	ENSP00000347730:K1138R	ENSP00000347730:K1138R	K	+	2	0	ZNF536	35731779	0.971000	0.33674	0.989000	0.46669	0.505000	0.33919	3.797000	0.55514	0.940000	0.37473	0.533000	0.62120	AAG	.	.	none		0.532	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		G	31039939	A	G	31039939	3	3	27	1	0	0	0	0	1	0	0	0	17989	72	3	3	3423	3	ZNF536	19	31039939	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	7497313	31039939	28089044	920	11371											
LRP3	4037	hgsc.bcm.edu	37	chr19	33696647	33696647	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggggaccgcctgctgcagaCgctgtcctaccgcagcaacc	7	5	12	17	4	0	1	0	0	0	1	1	2	1	2	5	2	5	5	5	2	2	1	rs368108554		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:33696647C>T	ENST00000253193.7	+	5	1173	c.971C>T	c.(970-972)aCg>aTg	p.T324M	CTD-2540B15.13_ENST00000609744.1_RNA	NM_002333.3	NP_002324.2	O75074	LRP3_HUMAN	low density lipoprotein receptor-related protein 3	324	CUB 2. {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)					CTGCTGCAGACGCTGTCCTAC	0.736																																					p.T324M		Atlas-SNP	.											.	LRP3	46	.	0			c.C971T						PASS	.	C	MET/THR	0,4284		0,0,2142	8	12	10		971	5	1	19		10	1,8407		0,1,4203	no	missense	LRP3	NM_002333.3	81	0,1,6345	TT,TC,CC		0.0119,0.0,0.0079	probably-damaging	324/771	33696647	1,12691	2142	4204	6346	SO:0001583	missense	4037	exon5			TGCAGACGCTGTC	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.971C>T	19.37:g.33696647C>T	ENSP00000253193:p.Thr324Met	29	0	0		36	15	0.416667	NM_002333	B3KQD6|B4DKF2	Missense_Mutation	SNP	ENST00000253193.7	37	CCDS12430.1	.	.	.	.	.	.	.	.	.	.	C	15.91	2.972764	0.53614	0.0	1.19E-4	ENSG00000130881	ENST00000431491;ENST00000253193	D	0.87334	-2.24	5.02	5.02	0.67125	CUB (5);	0.218511	0.42548	D	0.000688	D	0.92113	0.7500	M	0.63843	1.955	0.40643	D	0.981969	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.70935	0.96;0.971;0.96	D	0.92597	0.6088	10	0.51188	T	0.08	-22.6449	17.3303	0.87261	0.0:1.0:0.0:0.0	.	198;324;242	C9J8W0;O75074;B7ZAJ9	.;LRP3_HUMAN;.	M	198;324	ENSP00000253193:T324M	ENSP00000253193:T324M	T	+	2	0	LRP3	38388487	0.906000	0.30813	0.994000	0.49952	0.732000	0.41865	2.288000	0.43514	2.341000	0.79615	0.313000	0.20887	ACG	.	.	weak		0.736	LRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450842.4			T	33696647	C	T	33696647	3	4	27	1	0	0	0	0	1	0	0	0	8967	536	19	1	989	1	LRP3	19	33696647	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2656708	33696647	25432336	921	11372											
PDCD2L	84306	hgsc.bcm.edu	37	chr19	34895647	34895647	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggtgtattgcccgctggaaGgctccccgtttcaccgtctg	5	11	12	13	3	2	0	1	0	1	0	3	1	3	1	4	3	1	4	4	3	2	3	rs141960904	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:34895647G>A	ENST00000246535.3	+	2	249	c.202G>A	c.(202-204)Ggc>Agc	p.G68S	PDCD2L_ENST00000587065.2_5'Flank|RP11-618P17.4_ENST00000606020.1_Missense_Mutation_p.G63S	NM_032346.1	NP_115722.1	Q9BRP1	PDD2L_HUMAN	programmed cell death 2-like	68					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)			CCCGCTGGAAGGCTCCCCGTT	0.706													G|||	10	0.00199681	0.0	0.0072	5008	,	,		14816	0.0		0.005	False		,,,				2504	0.0				p.G68S		Atlas-SNP	.											.	PDCD2L	27	.	0			c.G202A						PASS	.	G	SER/GLY	2,4400	2.1+/-5.4	0,2,2199	23	22	22		202	4	1	19	dbSNP_134	22	28,8566	14.0+/-48.4	0,28,4269	yes	missense	PDCD2L	NM_032346.1	56	0,30,6468	AA,AG,GG		0.3258,0.0454,0.2308	probably-damaging	68/359	34895647	30,12966	2201	4297	6498	SO:0001583	missense	84306	exon2			CTGGAAGGCTCCC	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.202G>A	19.37:g.34895647G>A	ENSP00000246535:p.Gly68Ser	68	0	0		76	37	0.486842	NM_032346		Missense_Mutation	SNP	ENST00000246535.3	37	CCDS12438.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	G	21.4	4.141095	0.77775	4.54E-4	0.003258	ENSG00000126249	ENST00000246535	.	.	.	5.04	4.0	0.46444	.	0.111834	0.64402	N	0.000014	T	0.33818	0.0876	L	0.49640	1.575	0.33769	D	0.622826	D	0.53151	0.958	P	0.45071	0.468	T	0.50825	-0.8782	9	0.16896	T	0.51	-20.8332	11.295	0.49274	0.0866:0.0:0.9134:0.0	.	68	Q9BRP1	PDD2L_HUMAN	S	68	.	ENSP00000246535:G68S	G	+	1	0	PDCD2L	39587487	1.000000	0.71417	0.995000	0.50966	0.337000	0.28794	5.910000	0.69931	1.095000	0.41419	0.313000	0.20887	GGC	G|0.998;A|0.002	0.002	strong		0.706	PDCD2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459251.3	NM_032346		A	34895647	G	A	34895647	3	1	27	1	0	0	0	0	1	0	0	0	11629	1000	35	2	208	2	PDCD2L	19	34895647	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1199000	34895647	24233336	922	11373											
GRAMD1A	57655	hgsc.bcm.edu	37	chr19	35504539	35504539	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccaagcccagtgggttcgCgccgtggccatgtcacgccc	6	6	13	16	4	1	0	1	0	0	0	2	0	1	0	5	2	2	1	5	2	1	1	rs201394899		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:35504539C>T	ENST00000317991.5	+	9	1006	c.814C>T	c.(814-816)Cgc>Tgc	p.R272C	GRAMD1A_ENST00000411896.2_Missense_Mutation_p.R265C|GRAMD1A_ENST00000504615.2_Missense_Mutation_p.R38C|GRAMD1A_ENST00000599564.1_Missense_Mutation_p.R359C|CTD-2527I21.14_ENST00000605640.1_RNA	NM_020895.3	NP_065946.2	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A	272						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)			AGTGGGTTCGCGCCGTGGCCA	0.647																																					p.R272C		Atlas-SNP	.											.	GRAMD1A	39	.	0			c.C814T						PASS	.	C	CYS/ARG,CYS/ARG	2,4180		0,2,2089	26	31	29		793,814	2.5	0.2	19		29	9,8429		0,9,4210	yes	missense,missense	GRAMD1A	NM_001136199.1,NM_020895.3	180,180	0,11,6299	TT,TC,CC		0.1067,0.0478,0.0872	probably-damaging,probably-damaging	265/714,272/725	35504539	11,12609	2091	4219	6310	SO:0001583	missense	57655	exon9			GGTTCGCGCCGTG	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.814C>T	19.37:g.35504539C>T	ENSP00000441032:p.Arg272Cys	92	0	0		101	57	0.564356	NM_020895	A6NKY7|Q8NC77|Q9P1Z5	Missense_Mutation	SNP	ENST00000317991.5	37	CCDS42546.1	.	.	.	.	.	.	.	.	.	.	C	11.00	1.509632	0.27036	4.78E-4	0.001067	ENSG00000089351	ENST00000453966;ENST00000504615;ENST00000317991;ENST00000411896	T;T;T	0.52754	0.65;1.91;1.9	4.71	2.5	0.30297	.	0.934879	0.09007	N	0.862100	T	0.52289	0.1725	L	0.29908	0.895	0.09310	N	0.999997	P;D;D;D;P	0.76494	0.675;0.975;0.993;0.999;0.575	B;B;P;D;B	0.65987	0.039;0.249;0.616;0.94;0.068	T	0.37267	-0.9713	10	0.59425	D	0.04	.	6.9609	0.24597	0.1794:0.726:0.0:0.0946	.	272;272;38;265;359	Q96CP6-3;Q96CP6;B3KQF7;Q96CP6-2;F5GZ02	.;GRM1A_HUMAN;.;.;.	C	359;38;272;265	ENSP00000423728:R38C;ENSP00000441032:R272C;ENSP00000439267:R265C	ENSP00000441032:R272C	R	+	1	0	GRAMD1A	40196379	0.680000	0.27605	0.169000	0.22859	0.103000	0.19146	1.547000	0.36190	0.542000	0.28846	0.485000	0.47835	CGC	.	.	weak		0.647	GRAMD1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461557.1	NM_020895		T	35504539	C	T	35504539	3	4	27	1	0	0	0	0	1	0	0	0	6756	768	27	1	848	1	GRAMD1A	19	35504539	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	608892	35504539	23624444	923	11374											
GRAMD1A	57655	hgsc.bcm.edu	37	chr19	35505282	35505282	+	Frame_Shift_Del	DEL	G	G	-																															gtaactcctcttcatccactGgggaggaaggtgaggcaggc																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:35505282delG	ENST00000317991.5	+	10	1252	c.1060delG	c.(1060-1062)gggfs	p.G354fs	GRAMD1A_ENST00000411896.2_Frame_Shift_Del_p.G347fs|GRAMD1A_ENST00000504615.2_Frame_Shift_Del_p.G120fs|GRAMD1A_ENST00000599564.1_Frame_Shift_Del_p.G441fs|CTD-2527I21.14_ENST00000605640.1_RNA	NM_020895.3	NP_065946.2	Q96CP6	GRM1A_HUMAN	GRAM domain containing 1A	354						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)			TTCATCCACTGGGGAGGAAGG	0.607																																					p.T353fs		Pindel,Atlas-Indel	.											.	GRAMD1A	39	.	0			c.1059delT						PASS	.						38	43	41					19																	35505282		1972	4145	6117	SO:0001589	frameshift_variant	57655	exon10			.	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.1060delG	19.37:g.35505282delG	ENSP00000441032:p.Gly354fs	158	0	.		143	43	0.301	NM_020895	A6NKY7|Q8NC77|Q9P1Z5	Frame_Shift_Del	DEL	ENST00000317991.5	37	CCDS42546.1																																																																																			.	.	none		0.607	GRAMD1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461557.1	NM_020895		-	35505282	G	-	35505282	7	5	27	1	0	1	0	1	0	0	0	0	6756	1348	47	0	1098	0	GRAMD1A	19	35505282	Frame_Shift_Del	DEL	G	TCGA-G8-6909-01A-11D-2210-10	743	35505282	23623701	924	11375											
CD22	933	hgsc.bcm.edu	37	chr19	35831986	35831986	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gacaacacaaccatcgcctgCgcagcttgtaatagttggtg	11	9	10	11	2	0	0	0	0	0	0	1	1	0	0	2	1	4	4	2	1	4	4	rs25677	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:35831986C>T	ENST00000085219.5	+	7	1518	c.1452C>T	c.(1450-1452)tgC>tgT	p.C484C	CD22_ENST00000341773.6_Silent_p.C307C|CD22_ENST00000544992.2_Silent_p.C484C|CD22_ENST00000536635.2_Silent_p.C396C|CD22_ENST00000270311.6_Silent_p.C364C|CD22_ENST00000419549.2_Silent_p.C312C|CD22_ENST00000594250.1_Silent_p.C307C	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule	484	Ig-like C2-type 4.				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)			CCATCGCCTGCGCAGCTTGTA	0.607													C|||	294	0.0587061	0.1936	0.0403	5008	,	,		17505	0.0		0.0099	False		,,,				2504	0.0				p.C484C	Ovarian(42;1009 1133 23674 26041)	Atlas-SNP	.											.	CD22	129	.	0			c.C1452T						PASS	.	C	,,,	761,3645	308.0+/-290.3	67,627,1509	95	84	88		1188,1452,921,1452	-2.3	0	19	dbSNP_72	88	105,8495	56.8+/-118.0	1,103,4196	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CD22	NM_001185099.1,NM_001185100.1,NM_001185101.1,NM_001771.3	,,,	68,730,5705	TT,TC,CC		1.2209,17.2719,6.6585	,,,	396/760,484/752,307/671,484/848	35831986	866,12140	2203	4300	6503	SO:0001819	synonymous_variant	933	exon7			CGCCTGCGCAGCT	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.1452C>T	19.37:g.35831986C>T		138	0	0		126	64	0.507937	NM_001185100	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	Silent	SNP	ENST00000085219.5	37	CCDS12457.1																																																																																			A|0.015;C|0.932;T|0.053	0.053	strong		0.607	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466099.1	NM_001771		T	35831986	C	T	35831986	2	4	27	1	0	0	0	0	0	0	0	1	2987	776	27	1		1	CD22	19	35831986	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	326704	35831986	23296997	925	11376											
CD22	933	hgsc.bcm.edu	37	chr19	35835739	35835739	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttctccacccagatagcccGgagaccatcggcaggcgagt	9	7	11	14	3	1	2	0	0	1	2	3	4	1	2	4	3	1	1	4	3	1	2	rs7259477	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:35835739G>A	ENST00000085219.5	+	10	2109	c.2043G>A	c.(2041-2043)ccG>ccA	p.P681P	CD22_ENST00000341773.6_Silent_p.P504P|CD22_ENST00000544992.2_Silent_p.P681P|CD22_ENST00000536635.2_Silent_p.P593P|MIR5196_ENST00000578146.1_RNA|CD22_ENST00000270311.6_Silent_p.P561P|CD22_ENST00000419549.2_Silent_p.P509P|CD22_ENST00000594250.1_Silent_p.P504P	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule	681					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)			CAGATAGCCCGGAGACCATCG	0.617													G|||	14	0.00279553	0.0	0.0072	5008	,	,		18790	0.0		0.0089	False		,,,				2504	0.0				p.P681P	Ovarian(42;1009 1133 23674 26041)	Atlas-SNP	.											.	CD22	129	.	0			c.G2043A						PASS	.	G	,,,	10,4396	16.8+/-37.8	0,10,2193	116	121	120		1779,2043,1512,2043	-9.6	0	19	dbSNP_116	120	81,8519	46.7+/-105.8	0,81,4219	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CD22	NM_001185099.1,NM_001185100.1,NM_001185101.1,NM_001771.3	,,,	0,91,6412	AA,AG,GG		0.9419,0.227,0.6997	,,,	593/760,681/752,504/671,681/848	35835739	91,12915	2203	4300	6503	SO:0001819	synonymous_variant	933	exon10			TAGCCCGGAGACC	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.2043G>A	19.37:g.35835739G>A		76	0	0		62	35	0.564516	NM_001185100	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	Silent	SNP	ENST00000085219.5	37	CCDS12457.1																																																																																			G|0.996;A|0.004	0.004	strong		0.617	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466099.1	NM_001771		A	35835739	G	A	35835739	2	1	27	1	0	0	0	0	0	0	0	1	2987	1103	39	1		1	CD22	19	35835739	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	3753	35835739	23293244	926	11377											
FFAR3	2865	hgsc.bcm.edu	37	chr19	35850408	35850408	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaccagctactgctacagcCgcctggtgtggatcctcggc	6	9	11	15	2	1	0	1	0	0	0	3	1	2	1	4	3	5	2	4	3	2	2	rs138920343	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:35850408C>T	ENST00000327809.4	+	2	817	c.616C>T	c.(616-618)Cgc>Tgc	p.R206C	FFAR3_ENST00000594310.1_Missense_Mutation_p.R206C	NM_005304.3	NP_005295.1	O14843	FFAR3_HUMAN	free fatty acid receptor 3	206					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to fatty acid (GO:0071398)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|mucosal immune response (GO:0002385)|negative regulation of blood pressure (GO:0045776)|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 glucose import in response to insulin stimulus (GO:2001275)|regulation of hormone biosynthetic process (GO:0046885)|regulation of norepinephrine secretion (GO:0014061)|regulation of peptide hormone secretion (GO:0090276)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)			endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|skin(1)|stomach(1)	17	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;1.29e-19)|OV - Ovarian serous cystadenocarcinoma(14;4.63e-18)|all cancers(14;5.19e-17)|LUSC - Lung squamous cell carcinoma(66;0.0221)			CTGCTACAGCCGCCTGGTGTG	0.652																																					p.R206C	Esophageal Squamous(185;1742 2042 21963 24215 27871)	Atlas-SNP	.											.	FFAR3	40	.	0			c.C616T						PASS	.	C	CYS/ARG	7,4375		0,7,2184	14	13	13		616	5.1	1	19	dbSNP_134	13	61,8409		0,61,4174	no	missense	FFAR3	NM_005304.3	180	0,68,6358	TT,TC,CC		0.7202,0.1597,0.5291	probably-damaging	206/347	35850408	68,12784	2191	4235	6426	SO:0001583	missense	2865	exon2			TACAGCCGCCTGG	AF024688	CCDS12459.1	19q13.1	2012-08-08	2006-02-15	2006-02-15	ENSG00000185897	ENSG00000185897		"GPCR / Class A : Fatty acid receptors"	4499	protein-coding gene	gene with protein product		603821	"G protein-coupled receptor 41"	GPR41		9344866, 22493486	Standard	NM_005304		Approved	FFA3R	uc002nzd.3	O14843	OTTHUMG00000172514	ENST00000327809.4:c.616C>T	19.37:g.35850408C>T	ENSP00000328230:p.Arg206Cys	417	0	0		405	113	0.279012	NM_005304	B2RWM8|Q14CM7	Missense_Mutation	SNP	ENST00000327809.4	37	CCDS12459.1	.	.	.	.	.	.	.	.	.	.	C	18.48	3.633388	0.67015	0.001597	0.007202	ENSG00000185897	ENST00000327809	T	0.39592	1.07	5.13	5.13	0.70059	GPCR, rhodopsin-like superfamily (1);	0.264721	0.41001	U	0.000964	T	0.49558	0.1564	M	0.71581	2.175	0.18873	N	0.999988	D	0.76494	0.999	D	0.63033	0.91	T	0.49570	-0.8926	10	0.37606	T	0.19	-16.7142	11.2036	0.48756	0.1836:0.8164:0.0:0.0	.	206	O14843	FFAR3_HUMAN	C	206	ENSP00000328230:R206C	ENSP00000328230:R206C	R	+	1	0	FFAR3	40542248	0.097000	0.21791	1.000000	0.80357	0.990000	0.78478	2.128000	0.42045	2.385000	0.81259	0.455000	0.32223	CGC	C|0.997;T|0.003	0.003	strong		0.652	FFAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418873.2	NM_005304		T	35850408	C	T	35850408	3	4	27	1	0	0	0	0	1	0	0	0	5837	652	23	1	618	1	FFAR3	19	35850408	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	14669	35850408	23278575	927	11378											
NPHS1	4868	hgsc.bcm.edu	37	chr19	36340009	36340009	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cactgcgggccaccgcctggGtgtgctctgtgccccacgct	3	8	13	17	3	1	0	0	0	1	0	1	0	1	0	5	2	3	2	5	2	0	0	rs113825926	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:36340009G>A	ENST00000378910.5	-	8	880	c.881C>T	c.(880-882)aCc>aTc	p.T294I	NPHS1_ENST00000591817.1_5'Flank|NPHS1_ENST00000353632.6_Missense_Mutation_p.T294I	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	294	Ig-like C2-type 3.				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)			CACCGCCTGGGTGTGCTCTGT	0.677													G|||	18	0.00359425	0.0008	0.0029	5008	,	,		18085	0.0		0.0109	False		,,,				2504	0.0041				p.T294I		Atlas-SNP	.											.	NPHS1	165	.	0			c.C881T	GRCh37	CM044680	NPHS1	M	rs113825926	PASS	.	G	ILE/THR	17,4389	23.3+/-48.9	0,17,2186	45	42	43		881	-1	0	19	dbSNP_132	43	102,8496	56.4+/-117.6	1,100,4198	yes	missense	NPHS1	NM_004646.3	89	1,117,6384	AA,AG,GG		1.1863,0.3858,0.9151	benign	294/1242	36340009	119,12885	2203	4299	6502	SO:0001583	missense	4868	exon8			GCCTGGGTGTGCT		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.881C>T	19.37:g.36340009G>A	ENSP00000368190:p.Thr294Ile	58	0	0		48	19	0.395833	NM_004646	A6NDH2|C3RX61	Missense_Mutation	SNP	ENST00000378910.5	37	CCDS32996.1	10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	G	11.76	1.734293	0.30774	0.003858	0.011863	ENSG00000161270	ENST00000378910;ENST00000353632	T;T	0.76578	-1.03;-1.03	5.17	-1.04	0.10068	Immunoglobulin subtype (1);CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.458410	0.04145	N	0.320188	T	0.54191	0.1843	N	0.21583	0.68	0.09310	N	1	B	0.24092	0.097	B	0.27076	0.076	T	0.43702	-0.9375	10	0.24483	T	0.36	-0.2874	3.5633	0.07890	0.373:0.0:0.4437:0.1832	.	294	O60500	NPHN_HUMAN	I	294	ENSP00000368190:T294I;ENSP00000343634:T294I	ENSP00000343634:T294I	T	-	2	0	NPHS1	41031849	0.000000	0.05858	0.011000	0.14972	0.862000	0.49288	0.089000	0.15002	0.224000	0.20940	0.467000	0.42956	ACC	G|0.992;A|0.008	0.008	strong		0.677	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1			A	36340009	G	A	36340009	3	1	27	1	0	0	0	0	1	0	0	0	10591	1261	44	2	2932	2	NPHS1	19	36340009	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	489601	36340009	22788974	928	11379											
TYROBP	7305	hgsc.bcm.edu	37	chr19	36398454	36398454	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcacgatccctgccagcacGcccgggctcaccgtagagca	9	5	10	17	4	2	1	2	0	0	1	3	2	3	1	4	1	3	4	4	1	1	1	rs111477177	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:36398454G>C	ENST00000262629.4	-	3	189	c.123C>G	c.(121-123)ggC>ggG	p.G41G	TYROBP_ENST00000544690.2_Silent_p.G30G|TYROBP_ENST00000589517.1_Silent_p.G41G|TYROBP_ENST00000585901.2_Silent_p.G41G|TYROBP_ENST00000424586.3_Silent_p.G30G	NM_003332.3|NM_198125.2	NP_003323.1|NP_937758.1	O43914	TYOBP_HUMAN	TYRO protein tyrosine kinase binding protein	41					axon guidance (GO:0007411)|cellular defense response (GO:0006968)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|macrophage activation involved in immune response (GO:0002281)|neutrophil activation involved in immune response (GO:0002283)|regulation of immune response (GO:0050776)|regulation of osteoclast development (GO:2001204)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|receptor binding (GO:0005102)|receptor signaling protein activity (GO:0005057)			NS(1)|central_nervous_system(1)|large_intestine(1)|lung(4)|skin(1)	8	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)			CTGCCAGCACGCCCGGGCTCA	0.672													G|||	56	0.0111821	0.0008	0.0202	5008	,	,		16218	0.0		0.0348	False		,,,				2504	0.0061				p.G41G		Atlas-SNP	.											TYROBP,NS,carcinoma,-2,1	TYROBP	15	1	0			c.C123G						PASS	.	G	,,,	36,4370	36.8+/-68.6	0,36,2167	36	38	37		90,90,123,123	-10.3	0	19	dbSNP_132	37	366,8234	115.9+/-175.7	8,350,3942	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TYROBP	NM_001173514.1,NM_001173515.1,NM_003332.3,NM_198125.2	,,,	8,386,6109	CC,CG,GG		4.2558,0.8171,3.0909	,,,	30/103,30/102,41/114,41/113	36398454	402,12604	2203	4300	6503	SO:0001819	synonymous_variant	7305	exon3			CAGCACGCCCGGG	AF019563	CCDS12482.1, CCDS46058.1, CCDS54255.1, CCDS59378.1	19q13.1	2014-09-17				ENSG00000011600			12449	protein-coding gene	gene with protein product	"killer activating receptor associated protein", "DNAX-activation protein 12"	604142		PLOSL		9490415, 10888890	Standard	NM_003332		Approved	DAP12, PLO-SL, KARAP	uc002ocm.3	O43914		ENST00000262629.4:c.123C>G	19.37:g.36398454G>C		76	0	0		68	39	0.573529	NM_198125	A8K2X0|F5H389|Q6FGA5|Q9UMT3	Silent	SNP	ENST00000262629.4	37	CCDS12482.1																																																																																			A|0.000;C|0.024;G|0.976	0.024	strong		0.672	TYROBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457397.1			C	36398454	G	C	36398454	2	2	27	1	0	0	0	0	0	0	0	1	16830	1074	38	4		4	TYROBP	19	36398454	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	58445	36398454	22730529	929	11380											
ZNF461	92283	hgsc.bcm.edu	37	chr19	37130419	37130419	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttaaaggccttcccacattcGttacattcatagcgtttttc	9	16	5	11	2	1	0	1	0	0	0	4	0	2	0	2	1	2	2	2	1	4	8	rs61746298	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:37130419G>A	ENST00000588268.1	-	6	1055	c.828C>T	c.(826-828)aaC>aaT	p.N276N	ZNF461_ENST00000540605.2_5'UTR|ZNF461_ENST00000360357.4_Silent_p.N253N	NM_153257.2	NP_694989.2	Q8TAF7	ZN461_HUMAN	zinc finger protein 461	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(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)			TCCCACATTCGTTACATTCAT	0.368													G|||	73	0.0145767	0.0	0.0317	5008	,	,		20302	0.001		0.0398	False		,,,				2504	0.0102				p.N276N		Atlas-SNP	.											.	ZNF461	73	.	0			c.C828T						PASS	.	G		18,4354	22.3+/-47.3	1,16,2169	56	60	59		828	1	1	19	dbSNP_129	59	265,8305	97.5+/-159.1	5,255,4025	no	coding-synonymous	ZNF461	NM_153257.2		6,271,6194	AA,AG,GG		3.0922,0.4117,2.1867		276/564	37130419	283,12659	2186	4285	6471	SO:0001819	synonymous_variant	92283	exon6			ACATTCGTTACAT	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.828C>T	19.37:g.37130419G>A		99	0	0		81	39	0.481481	NM_153257	A8K9W9|Q6VSF7|Q9ULZ8	Silent	SNP	ENST00000588268.1	37	CCDS54257.1																																																																																			G|0.980;A|0.020	0.020	strong		0.368	ZNF461-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453202.1	NM_153257		A	37130419	G	A	37130419	2	1	27	1	0	0	0	0	0	0	0	1	17940	1136	40	1		1	ZNF461	19	37130419	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	731965	37130419	21998564	930	11381											
ZNF345	25850	hgsc.bcm.edu	37	chr19	37368492	37368492	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcatcagagaattcataccGgtgagaaaccatatatatgt	15	10	9	7	1	2	2	2	1	0	2	2	4	2	2	2	2	2	1	2	2	6	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:37368492G>C	ENST00000529555.1	+	2	1548	c.760G>C	c.(760-762)Ggt>Cgt	p.G254R	ZNF345_ENST00000589046.1_Missense_Mutation_p.G254R|ZNF345_ENST00000420450.1_Missense_Mutation_p.G254R|ZNF345_ENST00000526123.1_Intron|ZNF345_ENST00000432005.2_Intron			Q14585	ZN345_HUMAN	zinc finger protein 345	254					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)			AATTCATACCGGTGAGAAACC	0.423																																					p.G254R		Atlas-SNP	.											.	ZNF345	68	.	0			c.G760C						PASS	.						73	74	74					19																	37368492		2203	4300	6503	SO:0001583	missense	25850	exon4			CATACCGGTGAGA	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.760G>C	19.37:g.37368492G>C	ENSP00000431202:p.Gly254Arg	64	0	0		41	13	0.317073	NM_001242476		Missense_Mutation	SNP	ENST00000529555.1	37	CCDS12497.1	.	.	.	.	.	.	.	.	.	.	G	17.36	3.369349	0.61624	.	.	ENSG00000251247	ENST00000420450;ENST00000529555;ENST00000344705	T;T	0.01629	4.72;4.72	3.96	3.96	0.45880	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07007	0.0178	L	0.55743	1.74	0.32084	N	0.592773	D	0.76494	0.999	D	0.63877	0.919	T	0.02156	-1.1204	9	0.87932	D	0	.	13.8686	0.63603	0.0:0.0:1.0:0.0	.	254	Q14585	ZN345_HUMAN	R	254;254;18	ENSP00000431216:G254R;ENSP00000431202:G254R	ENSP00000442320:G18R	G	+	1	0	ZNF345	42060332	0.974000	0.33945	0.999000	0.59377	0.975000	0.68041	3.047000	0.49854	2.176000	0.68965	0.561000	0.74099	GGT	.	.	none		0.423	ZNF345-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388258.1			C	37368492	G	C	37368492	3	2	27	1	0	0	0	0	1	0	0	0	17874	1116	39	4	762	4	ZNF345	19	37368492	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	238073	37368492	21760491	931	11382											
ZNF568	374900	hgsc.bcm.edu	37	chr19	37440852	37440852	+	Frame_Shift_Del	DEL	T	T	-																															cagtaggaaggaaaatcttaTtacacatcagaaaattcata																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:37440852delT	ENST00000333987.7	+	7	1303	c.797delT	c.(796-798)attfs	p.I266fs	ZNF568_ENST00000427117.1_Intron|ZNF568_ENST00000455427.2_Intron|ZNF568_ENST00000415168.1_Frame_Shift_Del_p.I202fs	NM_001204835.1|NM_198539.3	NP_001191764.1|NP_940941.2	Q3ZCX4	ZN568_HUMAN	zinc finger protein 568	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)			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)			GAAAATCTTATTACACATCAG	0.353																																					p.I266fs		Atlas-Indel	.											.	ZNF568	106	.	0			c.796delA						PASS	.						39	43	41					19																	37440852		2118	4251	6369	SO:0001589	frameshift_variant	374900	exon7			.	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.797delT	19.37:g.37440852delT	ENSP00000334685:p.Ile266fs	30	0	0		45	11	0.244444	NM_198539	B4DS92|E7ER33|Q6N060|Q8NA64	Frame_Shift_Del	DEL	ENST00000333987.7	37	CCDS42558.1																																																																																			.	.	none		0.353	ZNF568-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109572.2	NM_198539		-	37440852	T	-	37440852	7	5	27	1	0	1	0	1	0	0	0	0	18014	1493	52	0	815	0	ZNF568	19	37440852	Frame_Shift_Del	DEL	T	TCGA-G8-6909-01A-11D-2210-10	72360	37440852	21688131	932	11383											
SAMD4B	55095	hgsc.bcm.edu	37	chr19	39873858	39873858	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccacccagactgcccggtTcctgggcctgacctggagat	6	8	11	16	1	0	3	0	1	0	2	2	4	2	3	6	3	1	1	6	3	0	1	rs140996761	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:39873858T>G	ENST00000314471.6	+	15	3018	c.1983T>G	c.(1981-1983)gtT>gtG	p.V661V	SAMD4B_ENST00000598913.1_Silent_p.V661V|SAMD4B_ENST00000596368.1_Intron	NM_018028.2	NP_060498.2	Q5PRF9	SMAG2_HUMAN	sterile alpha motif domain containing 4B	661					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)			ACTGCCCGGTTCCTGGGCCTG	0.562													t|||	12	0.00239617	0.0	0.0014	5008	,	,		20343	0.0		0.0109	False		,,,				2504	0.0				p.V661V		Atlas-SNP	.											.	SAMD4B	48	.	0			c.T1983G						PASS	.	T		4,4402	8.1+/-20.4	0,4,2199	150	116	128		1983	0.1	1	19	dbSNP_134	128	72,8528	42.6+/-100.3	1,70,4229	no	coding-synonymous	SAMD4B	NM_018028.2		1,74,6428	GG,GT,TT		0.8372,0.0908,0.5843		661/695	39873858	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	55095	exon15			CCCGGTTCCTGGG		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.1983T>G	19.37:g.39873858T>G		162	0	0		105	52	0.495238	NM_018028	A5Z0M6|Q6P194	Silent	SNP	ENST00000314471.6	37	CCDS33020.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	T	6.377	0.437719	0.12104	9.08E-4	0.008372	ENSG00000179134	ENST00000429637	.	.	.	4.2	0.092	0.14470	.	.	.	.	.	T	0.47820	0.1466	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54846	-0.8232	5	0.87932	D	0	.	2.9929	0.05989	0.1656:0.441:0.2913:0.1021	.	.	.	.	A	661	.	ENSP00000387732:S661A	S	+	1	0	SAMD4B	44565698	0.999000	0.42202	1.000000	0.80357	0.583000	0.36354	0.404000	0.20999	0.368000	0.24481	-0.805000	0.03199	TCC	T|0.996;G|0.004	0.004	strong		0.562	SAMD4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464467.1	NM_018028		G	39873858	T	G	39873858	2	3	27	1	0	0	0	0	0	0	0	1	13837	1770	62	5		5	SAMD4B	19	39873858	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	2433006	39873858	19255125	933	11384											
LGALS14	56891	hgsc.bcm.edu	37	chr19	40196548	40196548	+	Intron	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atcaatcattccctccagttAtgtccctgacccacaggctt	9	12	5	15	0	2	1	2	1	0	0	5	1	5	1	4	1	0	2	4	1	2	3	rs140242272	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:40196548A>G	ENST00000392052.3	+	2	238				LGALS14_ENST00000360675.3_Start_Codon_SNP_p.M1V	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)			CCCTCCAGTTATGTCCCTGAC	0.478													a|||	2	0.000399361	0.0	0.0014	5008	,	,		21476	0.0		0.001	False		,,,				2504	0.0				p.M1V		Atlas-SNP	.											.	LGALS14	38	.	0			c.A1G						PASS	.	A	,VAL/MET	0,4406		0,0,2203	184	141	156		,1	-0.4	0	19	dbSNP_134	156	7,8593		0,7,4293	no	intron,missense	LGALS14	NM_020129.2,NM_203471.1	,21	0,7,6496	GG,GA,AA		0.0814,0.0,0.0538	,	,1/169	40196548	7,12999	2203	4300	6503	SO:0001627	intron_variant	56891	exon2			CCAGTTATGTCCC	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.16-689A>G	19.37:g.40196548A>G		157	0	0		156	72	0.461538	NM_203471	A8MPV8|B2R530|C5HZ19|Q7Z4X8|Q96KD4|Q96KD5|Q96KD6|Q9NR03	Missense_Mutation	SNP	ENST00000392052.3	37	CCDS46073.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	.	6.163	0.398345	0.11696	0.0	8.14E-4	ENSG00000006659	ENST00000360675	T	0.06933	3.24	0.906	-0.363	0.12556	.	.	.	.	.	T	0.06462	0.0166	.	.	.	0.80722	D	1	B	0.26041	0.14	B	0.26202	0.067	T	0.29119	-1.0022	8	0.62326	D	0.03	.	3.5978	0.08013	0.5843:0.4157:0.0:0.0	.	1	A8MPV8	.	V	1	ENSP00000353893:M1V	ENSP00000353893:M1V	M	+	1	0	LGALS14	44888388	0.000000	0.05858	0.000000	0.03702	0.221000	0.24807	-0.385000	0.07379	-0.203000	0.10251	0.260000	0.18958	ATG	A|0.999;G|0.001	0.001	strong		0.478	LGALS14-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465222.1	NM_020129		G	40196548	A	G	40196548	1	3	27	0	1	0	0	0	0	0	0	0	8750	449	16	3		3	LGALS14	19	40196548	Intron	SNP	A	TCGA-G8-6909-01A-11D-2210-10	322690	40196548	18932435	934	11385											
FCGBP	8857	hgsc.bcm.edu	37	chr19	40399508	40399508	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgctgacgggctggcagcCgtgctggccggatggcagga	5	7	19	10	3	0	1	0	1	0	0	0	3	0	3	2	6	3	5	2	6	0	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:40399508C>T	ENST00000221347.6	-	13	6194	c.6187G>A	c.(6187-6189)Ggc>Agc	p.G2063S		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2063						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)			GGCTGGCAGCCGTGCTGGCCG	0.657																																					p.G2063S		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	1	0			c.G6187A						scavenged	.						1	1	1					19																	40399508		183	426	609	SO:0001583	missense	8857	exon13			GGCAGCCGTGCTG	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.6187G>A	19.37:g.40399508C>T	ENSP00000221347:p.Gly2063Ser	128	0	0		126	22	0.174603	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.485186	0.44147	.	.	ENSG00000090920	ENST00000221347	T	0.05025	3.51	3.01	3.01	0.34805	von Willebrand factor, type D domain (1);	.	.	.	.	T	0.20170	0.0485	M	0.77103	2.36	0.31064	N	0.713759	D	0.76494	0.999	D	0.66196	0.942	T	0.07868	-1.0750	9	0.14656	T	0.56	.	12.9123	0.58187	0.0:1.0:0.0:0.0	.	2063	Q9Y6R7	FCGBP_HUMAN	S	2063	ENSP00000221347:G2063S	ENSP00000221347:G2063S	G	-	1	0	FCGBP	45091348	0.935000	0.31712	0.871000	0.34182	0.831000	0.47069	-0.229000	0.09098	1.536000	0.49237	0.298000	0.19748	GGC	.	.	weak		0.657	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890		T	40399508	C	T	40399508	3	4	27	1	0	0	0	0	1	0	0	0	5786	652	23	1	10126	1	FCGBP	19	40399508	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	202960	40399508	18729475	935	11386											
ARHGEF1	9138	hgsc.bcm.edu	37	chr19	42409189	42409189	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgtgtcggagcggaaaaaGtgagggggggtctgagttct	9	9	18	5	2	2	2	0	2	2	0	3	4	2	4	0	5	1	1	0	5	2	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:42409189G>A	ENST00000354532.3	+	23	2397		c.e23+1		ARHGEF1_ENST00000337665.4_Splice_Site|ARHGEF1_ENST00000347545.4_Splice_Site|ARHGEF1_ENST00000378152.4_Splice_Site|ARHGEF1_ENST00000599846.1_Splice_Site	NM_004706.3	NP_004697.2	Q92888	ARHG1_HUMAN	Rho guanine nucleotide exchange factor (GEF) 1						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)		AGCGGAAAAAGTGAGGGGGGG	0.602																																					.		Atlas-SNP	.											ARHGEF1,NS,carcinoma,+1,1	ARHGEF1	95	1	0			c.2249+1G>A						PASS	.						46	45	45					19																	42409189		2203	4300	6503	SO:0001630	splice_region_variant	9138	exon23			GAAAAAGTGAGGG	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.2249+1G>A	19.37:g.42409189G>A		78	0	0		78	16	0.205128	NM_004706	O00513|Q8N4J4|Q96BF4|Q96F17|Q9BSB1	Splice_Site	SNP	ENST00000354532.3	37	CCDS12591.1	.	.	.	.	.	.	.	.	.	.	G	15.82	2.946544	0.53186	.	.	ENSG00000076928	ENST00000354532;ENST00000347545;ENST00000337665;ENST00000378152	.	.	.	4.53	4.53	0.55603	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1593	0.72771	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARHGEF1	47101029	1.000000	0.71417	0.160000	0.22671	0.018000	0.09664	5.579000	0.67457	2.229000	0.72834	0.585000	0.79938	.	.	.	none		0.602	ARHGEF1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000463360.1	NM_199002	Intron	A	42409189	G	A	42409189	5	1	27	1	0	0	0	0	0	0	1	0	893	1043	36	2	2385	2	ARHGEF1	19	42409189	Splice_Site	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2009681	42409189	16719794	936	11387											
PSG8	440533	hgsc.bcm.edu	37	chr19	43259169	43259169	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcagggtgactgggtaactgCggatgccaccatattggtcc	8	10	13	10	1	1	1	1	1	0	0	2	2	2	2	3	4	3	1	3	4	2	3	rs140722778	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:43259169C>T	ENST00000306511.4	-	4	1056	c.959G>A	c.(958-960)cGc>cAc	p.R320H	PSG8_ENST00000600709.1_Intron|PSG8_ENST00000406636.3_Missense_Mutation_p.R198H|PSG8_ENST00000404209.4_Missense_Mutation_p.R320H|PSG8_ENST00000401467.2_Missense_Mutation_p.R227H	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	320	Ig-like C2-type 2.					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)				TGGGTAACTGCGGATGCCACC	0.488													.|||	4	0.000798722	0.0015	0.0029	5008	,	,		21450	0.0		0.0	False		,,,				2504	0.0				p.R320H		Atlas-SNP	.											PSG8_ENST00000404209,NS,carcinoma,0,5	PSG8	101	5	0			c.G959A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG	8,4398		0,8,2195	180	181	181		959,593,959	-2.8	0	19	dbSNP_134	181	0,8598		0,0,4299	no	missense,missense,missense	PSG8	NM_001130167.1,NM_001130168.1,NM_182707.2	29,29,29	0,8,6494	TT,TC,CC		0.0,0.1816,0.0615	benign,benign,benign	320/420,198/298,320/427	43259169	8,12996	2203	4299	6502	SO:0001583	missense	440533	exon4			TAACTGCGGATGC	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.959G>A	19.37:g.43259169C>T	ENSP00000305005:p.Arg320His	55	0	0		28	15	0.535714	NM_001130167	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Missense_Mutation	SNP	ENST00000306511.4	37	CCDS33037.1	10	0.004578754578754579	2	0.0040650406504065045	2	0.0055248618784530384	5	0.008741258741258742	1	0.0013192612137203166	N	0.102	-1.150122	0.01700	0.001816	0.0	ENSG00000124467	ENST00000404209;ENST00000406636;ENST00000401467;ENST00000426252;ENST00000407488;ENST00000306511	T;T;T;T	0.12672	2.66;2.66;2.66;2.66	1.38	-2.76	0.05896	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.08626	0.0214	L	0.59967	1.855	0.09310	N	1	B;B;B;B;B;B	0.21606	0.029;0.058;0.004;0.005;0.005;0.006	B;B;B;B;B;B	0.27887	0.021;0.084;0.005;0.042;0.005;0.009	T	0.24154	-1.0168	9	0.40728	T	0.16	.	3.1318	0.06425	0.1899:0.3611:0.0:0.4489	.	198;227;320;227;320;320	Q9UQ74-2;B5MCQ0;Q9UQ74;E7ENH0;Q9UQ74-3;A5PKV3	.;.;PSG8_HUMAN;.;.;.	H	320;198;227;132;227;320	ENSP00000385869:R320H;ENSP00000385081:R198H;ENSP00000386090:R227H;ENSP00000305005:R320H	ENSP00000305005:R320H	R	-	2	0	PSG8	47951009	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.062000	0.00623	-3.472000	0.00157	-3.315000	0.00045	CGC	C|0.998;T|0.002	0.002	strong		0.488	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1			T	43259169	C	T	43259169	3	4	27	1	0	0	0	0	1	0	0	0	12673	768	27	1	350	1	PSG8	19	43259169	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	849980	43259169	15869814	937	11388											
PSG8	440533	hgsc.bcm.edu	37	chr19	43262267	43262267	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccaatagaaagagggtcctgTtggtttcagacaactgcaac	13	9	10	9	0	1	3	1	0	0	3	2	3	2	3	2	2	3	3	2	2	5	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:43262267T>C	ENST00000306511.4	-	3	693	c.596A>G	c.(595-597)aAc>aGc	p.N199S	PSG8_ENST00000600709.1_5'UTR|PSG8_ENST00000406636.3_Missense_Mutation_p.N77S|PSG8_ENST00000404209.4_Missense_Mutation_p.N199S|PSG8_ENST00000401467.2_Intron	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	199	Ig-like C2-type 1.					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)				GAGGGTCCTGTTGGTTTCAGA	0.517																																					p.N199S		Atlas-SNP	.											.	PSG8	101	.	0			c.A596G						PASS	.						269	276	274					19																	43262267		2203	4299	6502	SO:0001583	missense	440533	exon3			GTCCTGTTGGTTT	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.596A>G	19.37:g.43262267T>C	ENSP00000305005:p.Asn199Ser	95	0	0		90	39	0.433333	NM_001130167	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Missense_Mutation	SNP	ENST00000306511.4	37	CCDS33037.1	.	.	.	.	.	.	.	.	.	.	t	11.57	1.678127	0.29783	.	.	ENSG00000124467	ENST00000404209;ENST00000292109;ENST00000406636;ENST00000426252;ENST00000306511	T;T;T	0.15017	2.46;2.46;2.46	1.53	1.53	0.23141	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.36936	0.0985	M	0.83223	2.63	0.09310	N	1	P;P;P;P	0.48089	0.624;0.683;0.884;0.905	P;P;P;P	0.62089	0.516;0.73;0.836;0.898	T	0.10291	-1.0636	9	0.87932	D	0	.	5.1071	0.14790	0.0:0.0:0.0:1.0	.	77;199;199;199	Q9UQ74-2;Q9UQ74;Q9UQ74-3;A5PKV3	.;PSG8_HUMAN;.;.	S	199;74;77;11;199	ENSP00000385869:N199S;ENSP00000385081:N77S;ENSP00000305005:N199S	ENSP00000292109:N74S	N	-	2	0	PSG8	47954107	0.019000	0.18553	0.023000	0.16930	0.028000	0.11728	1.962000	0.40442	0.697000	0.31718	0.248000	0.18094	AAC	.	.	none		0.517	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1			C	43262267	T	C	43262267	3	2	27	1	0	0	0	0	1	0	0	0	12673	1725	60	3	717	3	PSG8	19	43262267	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	3098	43262267	15866716	938	11389											
ZNF235	9310	hgsc.bcm.edu	37	chr19	44791537	44791537	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccttcccacactgctgacacGtatagggtttctctcctgtg	6	13	8	14	1	1	1	0	1	1	0	4	1	3	1	3	1	1	3	3	1	2	4	rs149947768		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:44791537G>A	ENST00000291182.4	-	5	2153	c.2051C>T	c.(2050-2052)aCg>aTg	p.T684M	ZNF235_ENST00000589799.1_Intron|ZNF235_ENST00000589248.1_Intron	NM_004234.4	NP_004225.3	Q14590	ZN235_HUMAN	zinc finger protein 235	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)			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)				CTGCTGACACGTATAGGGTTT	0.493													G|||	1	0.000199681	0.0	0.0	5008	,	,		21663	0.0		0.001	False		,,,				2504	0.0				p.T684M		Atlas-SNP	.											.	ZNF235	60	.	0			c.C2051T						PASS	.	G	MET/THR	0,4406		0,0,2203	127	116	120		2051	1.1	0.1	19	dbSNP_134	120	10,8590	7.1+/-27.0	0,10,4290	yes	missense	ZNF235	NM_004234.4	81	0,10,6493	AA,AG,GG		0.1163,0.0,0.0769	benign	684/739	44791537	10,12996	2203	4300	6503	SO:0001583	missense	9310	exon5			TGACACGTATAGG	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.2051C>T	19.37:g.44791537G>A	ENSP00000291182:p.Thr684Met	147	0	0		86	41	0.476744	NM_004234	B4DTQ7|O14898|O14899|Q17RR8	Missense_Mutation	SNP	ENST00000291182.4	37	CCDS33048.1	.	.	.	.	.	.	.	.	.	.	G	6.572	0.473837	0.12521	0.0	0.001163	ENSG00000159917	ENST00000391957;ENST00000291182;ENST00000359844	T	0.19806	2.12	4.97	1.08	0.20341	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.171331	0.28203	N	0.016214	T	0.14270	0.0345	L	0.37697	1.125	0.09310	N	1	B;B	0.28470	0.086;0.213	B;B	0.24701	0.012;0.055	T	0.18493	-1.0335	10	0.62326	D	0.03	-1.4434	7.5912	0.28023	0.0867:0.0:0.5441:0.3692	.	680;684	Q14590-2;Q14590	.;ZN235_HUMAN	M	684;684;576	ENSP00000291182:T684M	ENSP00000291182:T684M	T	-	2	0	ZNF235	49483377	0.000000	0.05858	0.100000	0.21137	0.510000	0.34073	-0.585000	0.05794	0.616000	0.30141	0.313000	0.20887	ACG	G|0.998;A|0.002	0.002	strong		0.493	ZNF235-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460732.1			A	44791537	G	A	44791537	3	1	27	1	0	0	0	0	1	0	0	0	17803	1145	40	1	169	1	ZNF235	19	44791537	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1529270	44791537	14337446	939	11390											
ZNF285	26974	hgsc.bcm.edu	37	chr19	44890651	44890651	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catttataatgtttctctctGctcatgtagtctttgatgag	8	19	7	7	0	4	2	1	2	3	0	5	2	4	2	0	0	1	3	0	0	3	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:44890651G>A	ENST00000330997.4	-	4	1820	c.1756C>T	c.(1756-1758)Cag>Tag	p.Q586*	ZNF285_ENST00000591679.1_Nonsense_Mutation_p.Q593*|ZNF285_ENST00000544719.2_Nonsense_Mutation_p.Q586*|CTC-512J12.6_ENST00000588212.1_Intron	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	586					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						GTTTCTCTCTGCTCATGTAGT	0.433																																					p.Q586X		Atlas-SNP	.											.	ZNF285	86	.	0			c.C1756T						PASS	.						123	103	110					19																	44890651		2203	4300	6503	SO:0001587	stop_gained	26974	exon4			CTCTCTGCTCATG	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.1756C>T	19.37:g.44890651G>A	ENSP00000333595:p.Gln586*	89	0	0		87	18	0.206897	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Nonsense_Mutation	SNP	ENST00000330997.4	37	CCDS12638.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.955111	0.73902	.	.	ENSG00000062370	ENST00000544719;ENST00000330997	.	.	.	3.28	-2.27	0.06846	.	.	.	.	.	.	.	.	.	.	.	0.19775	N	0.999953	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	2.2056	0.03934	0.1362:0.097:0.2974:0.4695	.	.	.	.	X	609;586	.	ENSP00000333595:Q586X	Q	-	1	0	ZNF285	49582491	0.891000	0.30450	0.000000	0.03702	0.024000	0.10985	1.365000	0.34182	-0.266000	0.09339	-0.552000	0.04208	CAG	.	.	none		0.433	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354		A	44890651	G	A	44890651	4	1	27	1	0	0	0	0	0	1	0	0	17837	1328	46	2	20	2	ZNF285	19	44890651	Nonsense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	99114	44890651	14238332	940	11391											
ZNF180	7733	hgsc.bcm.edu	37	chr19	44981009	44981009	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	attctctgatgcataacaagGtgagaactgcggttaaaaga	15	10	10	6	1	1	3	0	2	1	2	2	4	1	3	0	2	4	2	0	2	5	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:44981009G>T	ENST00000221327.4	-	5	1970	c.1689C>A	c.(1687-1689)caC>caA	p.H563Q	ZNF180_ENST00000391956.4_Missense_Mutation_p.H538Q|ZNF180_ENST00000592529.1_Missense_Mutation_p.H536Q|AC069278.4_ENST00000591684.1_lincRNA|ZNF180_ENST00000585514.1_5'Flank	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	563					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)				GCATAACAAGGTGAGAACTGC	0.418																																					p.H563Q	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											.	ZNF180	103	.	0			c.C1689A						PASS	.						103	104	104					19																	44981009		2203	4300	6503	SO:0001583	missense	7733	exon5			AACAAGGTGAGAA	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.1689C>A	19.37:g.44981009G>T	ENSP00000221327:p.His563Gln	90	0	0		81	15	0.185185	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	37	CCDS12639.1	.	.	.	.	.	.	.	.	.	.	G	13.00	2.105656	0.37145	.	.	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.07216	3.21;3.21	5.23	2.97	0.34412	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.44688	D	0.000440	T	0.04272	0.0118	N	0.12961	0.28	0.80722	D	1	P;P;P	0.47545	0.874;0.897;0.897	B;B;B	0.39068	0.191;0.289;0.289	T	0.37430	-0.9706	10	0.51188	T	0.08	-7.8305	6.5992	0.22691	0.1566:0.0:0.6887:0.1546	.	538;562;563	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	Q	563;538	ENSP00000221327:H563Q;ENSP00000375818:H538Q	ENSP00000221327:H563Q	H	-	3	2	ZNF180	49672849	0.000000	0.05858	1.000000	0.80357	0.872000	0.50106	-1.418000	0.02462	2.437000	0.82529	0.467000	0.42956	CAC	.	.	none		0.418	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256		T	44981009	G	T	44981009	3	4	27	1	0	0	0	0	1	0	0	0	17763	1252	44	4	393	4	ZNF180	19	44981009	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	90358	44981009	14147974	941	11392											
CEACAM19	56971	hgsc.bcm.edu	37	chr19	45176003	45176003	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agacaccttccaggacttcaActggtacctgggggaggaga	11	7	13	10	0	1	2	1	0	0	2	2	5	2	4	3	5	2	1	3	5	2	3	rs201929208		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:45176003A>G	ENST00000403660.3	+	2	401	c.191A>G	c.(190-192)aAc>aGc	p.N64S	CTB-171A8.1_ENST00000590796.1_RNA|CEACAM19_ENST00000480278.1_3'UTR|CEACAM19_ENST00000358777.4_Missense_Mutation_p.N64S			Q7Z692	CEA19_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 19	64						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)	11	Lung NSC(12;0.00308)|all_lung(12;0.00806)	Prostate(69;0.0376)				CAGGACTTCAACTGGTACCTG	0.567																																					p.N64S		Atlas-SNP	.											.	CEACAM19	27	.	0			c.A191G						PASS	.						103	75	84					19																	45176003		2203	4300	6503	SO:0001583	missense	56971	exon2			ACTTCAACTGGTA	AF406955	CCDS12641.1, CCDS46108.1	19q13.31	2013-01-11			ENSG00000186567	ENSG00000186567		"Immunoglobulin superfamily / V-set domain containing"	31951	protein-coding gene	gene with protein product		606691					Standard	NM_020219		Approved	CEAL1	uc002ozo.4	Q7Z692	OTTHUMG00000151528	ENST00000403660.3:c.191A>G	19.37:g.45176003A>G	ENSP00000384887:p.Asn64Ser	124	0	0		151	76	0.503311	NM_001127893	Q5XJ15|Q7Z693	Missense_Mutation	SNP	ENST00000403660.3	37	CCDS12641.1	.	.	.	.	.	.	.	.	.	.	A	6.496	0.459717	0.12342	.	.	ENSG00000186567	ENST00000358777;ENST00000403660	T;T	0.62941	-0.01;-0.01	4.18	-0.79	0.10932	Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	0.319679	0.22466	N	0.059684	T	0.34774	0.0909	N	0.17764	0.52	0.21386	N	0.999705	B;B	0.17268	0.021;0.021	B;B	0.18871	0.023;0.023	T	0.08932	-1.0698	10	0.21014	T	0.42	-5.3844	1.0166	0.01509	0.296:0.1476:0.1065:0.4499	.	64;64	Q5XJ15;Q7Z692	.;CEA19_HUMAN	S	64	ENSP00000351627:N64S;ENSP00000384887:N64S	ENSP00000351627:N64S	N	+	2	0	CEACAM19	49867843	0.003000	0.15002	0.944000	0.38274	0.969000	0.65631	-0.536000	0.06135	-0.547000	0.06207	0.454000	0.30748	AAC	.	.	weak		0.567	CEACAM19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323022.1	NM_020219		G	45176003	A	G	45176003	3	3	27	1	0	0	0	0	1	0	0	0	3192	43	2	3	197	3	CEACAM19	19	45176003	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	194994	45176003	13952980	942	11393											
PVRL2	5819	hgsc.bcm.edu	37	chr19	45391553	45391553	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctggacaagatcaaccccAtctatgatgctctgtcctat	11	12	6	12	0	4	2	1	1	3	1	5	3	5	3	3	1	2	1	3	1	4	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:45391553A>G	ENST00000252483.5	+	9	1534	c.1534A>G	c.(1534-1536)Atc>Gtc	p.I512V	TOMM40_ENST00000426677.2_5'Flank|TOMM40_ENST00000252487.5_5'Flank|TOMM40_ENST00000405636.2_5'Flank|TOMM40_ENST00000592434.1_5'Flank|CTB-129P6.4_ENST00000585408.1_RNA	NM_001042724.1	NP_001036189.1	Q92692	PVRL2_HUMAN	poliovirus receptor-related 2 (herpesvirus entry mediator B)	512					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)		GATCAACCCCATCTATGATGC	0.577																																					p.I512V		Atlas-SNP	.											.	PVRL2	58	.	0			c.A1534G						PASS	.						100	95	97					19																	45391553		1973	4146	6119	SO:0001583	missense	5819	exon9			AACCCCATCTATG	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.1534A>G	19.37:g.45391553A>G	ENSP00000252483:p.Ile512Val	185	0	0		198	114	0.575758	NM_001042724	A8K5L5|O75455|Q6IBI6|Q96J29	Missense_Mutation	SNP	ENST00000252483.5	37	CCDS42576.1	.	.	.	.	.	.	.	.	.	.	A	6.458	0.452676	0.12283	.	.	ENSG00000130202	ENST00000252483	D	0.89415	-2.51	4.67	2.59	0.31030	.	0.128913	0.36002	N	0.002850	T	0.79782	0.4505	L	0.29908	0.895	0.33232	D	0.556026	B	0.02656	0.0	B	0.08055	0.003	T	0.73248	-0.4043	10	0.31617	T	0.26	.	7.5527	0.27806	0.8183:0.0:0.1817:0.0	.	512	Q92692	PVRL2_HUMAN	V	512	ENSP00000252483:I512V	ENSP00000252483:I512V	I	+	1	0	PVRL2	50083393	1.000000	0.71417	1.000000	0.80357	0.116000	0.19942	1.310000	0.33551	0.392000	0.25172	-0.609000	0.04063	ATC	.	.	none		0.577	PVRL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453231.1	NM_002856		G	45391553	A	G	45391553	3	3	27	1	0	0	0	0	1	0	0	0	12855	217	8	3	1970	3	PVRL2	19	45391553	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	215550	45391553	13737430	943	11394											
SFRS16	11129	hgsc.bcm.edu	37	chr19	45563695	45563695	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggccatcaagcatgccaaGgctcttgaggaggagaaggc	12	5	15	9	0	2	2	1	1	1	1	2	5	2	3	2	5	2	2	2	5	3	1	rs147776329	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:45563695G>A	ENST00000221455.3	+	9	857	c.759G>A	c.(757-759)aaG>aaA	p.K253K	CLASRP_ENST00000391953.4_Silent_p.K191K|CLASRP_ENST00000544944.2_Silent_p.K253K	NM_007056.2	NP_008987	Q8N2M8	CLASR_HUMAN	CLK4-associating serine/arginine rich protein	253					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						AGCATGCCAAGGCTCTTGAGG	0.602													G|||	20	0.00399361	0.0038	0.0058	5008	,	,		18973	0.0		0.0109	False		,,,				2504	0.0				p.K253K		Atlas-SNP	.											.	CLASRP	44	.	0			c.G759A						PASS	.	G		19,4387	26.2+/-53.5	0,19,2184	126	102	110		759	3.6	1	19	dbSNP_134	110	114,8486	61.0+/-122.8	1,112,4187	no	coding-synonymous	CLASRP	NM_007056.2		1,131,6371	AA,AG,GG		1.3256,0.4312,1.0226		253/675	45563695	133,12873	2203	4300	6503	SO:0001819	synonymous_variant	11129	exon9			TGCCAAGGCTCTT	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.759G>A	19.37:g.45563695G>A		89	0	0		86	33	0.383721	NM_007056	B4DDT8|F8WAG9|O96026|Q6UW71|Q96DX2	Silent	SNP	ENST00000221455.3	37	CCDS12652.2																																																																																			G|0.991;A|0.009	0.009	strong		0.602	CLASRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316749.1	NM_007056		A	45563695	G	A	45563695	2	1	27	1	0	0	0	0	0	0	0	1	14187	991	35	2		2	SFRS16	19	45563695	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	172142	45563695	13565288	944	11395											
ERCC2	2068	hgsc.bcm.edu	37	chr19	45855478	45855478	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aggcctcacccggtggaaggGctgtgccatctgccgcagga	7	6	15	13	2	2	0	1	0	1	0	2	2	2	2	4	5	2	2	4	5	1	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:45855478G>A	ENST00000391945.4	-	22	2256	c.2179C>T	c.(2179-2181)Ccc>Tcc	p.P727S	ERCC2_ENST00000391944.3_Missense_Mutation_p.P649S	NM_000400.3	NP_000391.1	P18074	ERCC2_HUMAN	excision repair cross-complementation group 2	727			Missing (in XP-D and TTDP). {ECO:0000269|PubMed:9195225}.		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)		CGGTGGAAGGGCTGTGCCATC	0.652			"Mis, N, F, S"			"skin basal cell, skin squamous cell, melanoma"		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.P727S		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.C2179T						PASS	.						73	55	61					19																	45855478		2203	4300	6503	SO:0001583	missense	2068	exon22	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	GGAAGGGCTGTGC		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.2179C>T	19.37:g.45855478G>A	ENSP00000375809:p.Pro727Ser	91	0	0		114	30	0.263158	NM_000400	Q2TB78|Q2YDY2|Q7KZU6|Q8N721	Missense_Mutation	SNP	ENST00000391945.4	37	CCDS33049.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.159589	0.78226	.	.	ENSG00000104884	ENST00000391941;ENST00000391942;ENST00000391945;ENST00000391944	T;D	0.82984	-1.41;-1.67	5.27	5.27	0.74061	.	0.126130	0.52532	D	0.000065	D	0.87815	0.6272	M	0.91663	3.23	0.80722	D	1	P;P;P	0.46987	0.762;0.756;0.888	B;B;B	0.43194	0.411;0.391;0.343	D	0.90746	0.4653	10	0.66056	D	0.02	-31.7778	16.3902	0.83532	0.0:0.0:1.0:0.0	.	649;727;420	E7EVE9;P18074;Q6ZNQ5	.;ERCC2_HUMAN;.	S	677;703;727;649	ENSP00000375809:P727S;ENSP00000375808:P649S	ENSP00000375805:P677S	P	-	1	0	ERCC2	50547318	1.000000	0.71417	0.998000	0.56505	0.979000	0.70002	8.735000	0.91549	2.461000	0.83175	0.561000	0.74099	CCC	.	.	none		0.652	ERCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109626.2	NM_000400		A	45855478	G	A	45855478	3	1	27	1	0	0	0	0	1	0	0	0	5215	1203	42	2	111	2	ERCC2	19	45855478	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	291783	45855478	13273505	945	11396											
EML2	24139	hgsc.bcm.edu	37	chr19	46127999	46127999	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ttgccccaaacatagaggttCcccccagagtcccccgtgac	9	7	8	17	1	0	3	0	1	0	2	2	3	2	3	7	1	2	1	7	1	2	3	rs36013288	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:46127999C>T	ENST00000245925.3	-	9	869	c.819G>A	c.(817-819)ggG>ggA	p.G273G	EML2_ENST00000589876.1_Silent_p.G273G|EML2_ENST00000587152.1_Silent_p.G474G|EML2_ENST00000536630.1_Silent_p.G420G|EML2_ENST00000586902.1_5'UTR	NM_012155.2	NP_036287.1	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like 2	273	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)		CATAGAGGTTCCCCCCAGAGT	0.532													C|||	37	0.00738818	0.0	0.0115	5008	,	,		20477	0.0		0.0089	False		,,,				2504	0.0204				p.G474G		Atlas-SNP	.											EML2,NS,carcinoma,-1,1	EML2	64	1	0			c.G1422A						scavenged	.		,,	15,4391	21.2+/-45.6	0,15,2188	86	64	71		1422,1260,819	-0.9	1	19	dbSNP_126	71	70,8530	39.8+/-96.3	2,66,4232	no	coding-synonymous,coding-synonymous,coding-synonymous	EML2	NM_001193268.1,NM_001193269.1,NM_012155.2	,,	2,81,6420	TT,TC,CC		0.814,0.3404,0.6535	,,	474/851,420/797,273/650	46127999	85,12921	2203	4300	6503	SO:0001819	synonymous_variant	24139	exon12			GAGGTTCCCCCCA	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.819G>A	19.37:g.46127999C>T		85	1	0.0117647		72	34	0.472222	NM_001193268	B7Z3I2|B7Z3Q9|K7ERL7|Q59EN8|Q8N5A2|Q9UG50	Silent	SNP	ENST00000245925.3	37	CCDS12670.1																																																																																			C|0.993;T|0.007	0.007	strong		0.532	EML2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459608.1	NM_012155		T	46127999	C	T	46127999	2	4	27	1	0	0	0	0	0	0	0	1	5099	842	30	2		2	EML2	19	46127999	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	272521	46127999	13000984	946	11397											
SYMPK	8189	hgsc.bcm.edu	37	chr19	46329624	46329624	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgatgaacagcagggcctggGagcgcacctgaggaggaaga	12	4	17	8	1	0	4	0	3	0	1	0	7	0	7	2	4	3	2	2	4	2	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:46329624G>A	ENST00000245934.7	-	17	2433	c.2189C>T	c.(2188-2190)tCc>tTc	p.S730F	SYMPK_ENST00000598155.1_5'Flank	NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	730					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)		CAGGGCCTGGGAGCGCACCTG	0.547																																					p.S730F		Atlas-SNP	.											.	SYMPK	104	.	0			c.C2189T						PASS	.						89	73	78					19																	46329624		2203	4300	6503	SO:0001583	missense	8189	exon17			GCCTGGGAGCGCA	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.2189C>T	19.37:g.46329624G>A	ENSP00000245934:p.Ser730Phe	64	0	0		53	31	0.584906	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Missense_Mutation	SNP	ENST00000245934.7	37	CCDS12676.2	.	.	.	.	.	.	.	.	.	.	G	15.97	2.990202	0.54041	.	.	ENSG00000125755	ENST00000245934	T	0.34275	1.37	4.17	4.17	0.49024	Armadillo-like helical (1);Armadillo-type fold (1);	0.287715	0.34750	N	0.003702	T	0.35799	0.0944	L	0.55481	1.735	0.50039	D	0.999846	P;B	0.47604	0.898;0.396	P;B	0.44447	0.45;0.212	T	0.25257	-1.0137	10	0.72032	D	0.01	.	9.6197	0.39714	0.0:0.0:0.7915:0.2085	.	745;730	Q4LE61;Q92797	.;SYMPK_HUMAN	F	730	ENSP00000245934:S730F	ENSP00000245934:S730F	S	-	2	0	SYMPK	51021464	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.873000	0.48475	2.339000	0.79563	0.555000	0.69702	TCC	.	.	none		0.547	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819		A	46329624	G	A	46329624	3	1	27	1	0	0	0	0	1	0	0	0	15454	1174	41	2	1679	2	SYMPK	19	46329624	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	201625	46329624	12799359	947	11398											
NANOS2	339345	hgsc.bcm.edu	37	chr19	46417625	46417625	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcgggcagtacttgagcgtAtgggcctggtcaccggtggc	6	8	17	10	3	1	1	1	1	0	0	1	1	1	1	2	5	3	3	2	5	2	3	rs142962668	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:46417625A>G	ENST00000341294.2	-	1	411	c.327T>C	c.(325-327)caT>caC	p.H109H		NM_001029861.2	NP_001025032.1	P60321	NANO2_HUMAN	nanos homolog 2 (Drosophila)	109					germ-line stem cell maintenance (GO:0030718)|mRNA catabolic process (GO:0006402)|multicellular organismal development (GO:0007275)|negative regulation of meiosis (GO:0045835)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	mRNA binding (GO:0003729)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)	6		Ovarian(192;0.0308)|all_neural(266;0.0476)		OV - Ovarian serous cystadenocarcinoma(262;0.00442)|GBM - Glioblastoma multiforme(486;0.0668)|Epithelial(262;0.231)		ACTTGAGCGTATGGGCCTGGT	0.657													A|||	26	0.00519169	0.0008	0.0115	5008	,	,		14495	0.0		0.0149	False		,,,				2504	0.002				p.H109H		Atlas-SNP	.											.	NANOS2	10	.	0			c.T327C						PASS	.	A		8,4398	14.3+/-33.2	0,8,2195	61	56	58		327	2.5	1	19	dbSNP_134	58	92,8508	49.8+/-109.6	1,90,4209	no	coding-synonymous	NANOS2	NM_001029861.2		1,98,6404	GG,GA,AA		1.0698,0.1816,0.7689		109/139	46417625	100,12906	2203	4300	6503	SO:0001819	synonymous_variant	339345	exon1			GAGCGTATGGGCC	BC042883	CCDS33056.1	19q13.32	2003-12-01				ENSG00000188425			23292	protein-coding gene	gene with protein product		608228				12947200, 12690449	Standard	NM_001029861		Approved	NOS2	uc002pdu.3	P60321		ENST00000341294.2:c.327T>C	19.37:g.46417625A>G		106	0	0		78	40	0.512821	NM_001029861	Q17R30|Q4G0P8	Silent	SNP	ENST00000341294.2	37	CCDS33056.1																																																																																			A|0.993;G|0.007	0.007	strong		0.657	NANOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461685.1			G	46417625	A	G	46417625	2	3	27	1	0	0	0	0	0	0	0	1	10161	446	16	3		3	NANOS2	19	46417625	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	88001	46417625	12711358	948	11399											
ZC3H4	23211	hgsc.bcm.edu	37	chr19	47571039	47571039	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ctgaagccgggggtcggctgGacgtctgctgcctcaaggtc	5	8	16	12	3	2	1	1	1	1	0	4	2	2	2	2	5	3	2	2	5	2	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:47571039G>A	ENST00000253048.5	-	15	2523	c.2486C>T	c.(2485-2487)tCc>tTc	p.S829F	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	829							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)		GGGTCGGCTGGACGTCTGCTG	0.622																																					p.S829F		Atlas-SNP	.											.	ZC3H4	96	.	0			c.C2486T						PASS	.						17	19	18					19																	47571039		2045	4167	6212	SO:0001583	missense	23211	exon15			CGGCTGGACGTCT	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.2486C>T	19.37:g.47571039G>A	ENSP00000253048:p.Ser829Phe	46	0	0		33	6	0.181818	NM_015168	Q9Y420	Missense_Mutation	SNP	ENST00000253048.5	37	CCDS42582.1	.	.	.	.	.	.	.	.	.	.	G	16.11	3.029641	0.54790	.	.	ENSG00000130749	ENST00000253048	T	0.19532	2.14	5.58	5.58	0.84498	.	0.329705	0.30201	N	0.010169	T	0.41650	0.1168	L	0.47716	1.5	0.51233	D	0.999918	D	0.71674	0.998	D	0.71870	0.975	T	0.12604	-1.0541	10	0.66056	D	0.02	.	18.3514	0.90339	0.0:0.0:1.0:0.0	.	829	Q9UPT8	ZC3H4_HUMAN	F	829	ENSP00000253048:S829F	ENSP00000253048:S829F	S	-	2	0	ZC3H4	52262879	1.000000	0.71417	0.103000	0.21229	0.293000	0.27360	5.684000	0.68197	2.642000	0.89623	0.655000	0.94253	TCC	.	.	none		0.622	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1			A	47571039	G	A	47571039	3	1	27	1	0	0	0	0	1	0	0	0	17585	1174	41	2	1429	2	ZC3H4	19	47571039	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1153414	47571039	11557944	949	11400											
CCDC9	26093	hgsc.bcm.edu	37	chr19	47774680	47774680	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggtgatgaggaggaaccagcCcaagaccaccaagccccaga	14	2	12	13	0	0	4	0	2	0	2	0	6	0	6	6	3	3	0	6	3	3	0	rs117519030	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:47774680C>G	ENST00000221922.6	+	12	1563	c.1341C>G	c.(1339-1341)gcC>gcG	p.A447A		NM_015603.2	NP_056418.1	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	447							poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	12		all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114)		OV - Ovarian serous cystadenocarcinoma(262;8.51e-95)|Epithelial(262;1.15e-92)|all cancers(93;7.67e-84)|GBM - Glioblastoma multiforme(486;0.024)|STAD - Stomach adenocarcinoma(1328;0.183)		aggaACCAGCCCAAGACCACC	0.612													C|||	36	0.0071885	0.0023	0.0043	5008	,	,		14944	0.0		0.0249	False		,,,				2504	0.0051				p.A447A		Atlas-SNP	.											.	CCDC9	37	.	0			c.C1341G						PASS	.	C		23,4383		0,23,2180	109	105	106		1341	-1.1	0	19	dbSNP_132	106	311,8287		7,297,3995	no	coding-synonymous	CCDC9	NM_015603.2		7,320,6175	GG,GC,CC		3.6171,0.522,2.5684		447/532	47774680	334,12670	2203	4299	6502	SO:0001819	synonymous_variant	26093	exon12			ACCAGCCCAAGAC	AL050284	CCDS12698.1	19q13.33	2008-02-05				ENSG00000105321			24560	protein-coding gene	gene with protein product						11230166	Standard	NM_015603		Approved	DKFZP586M1019	uc010xym.2	Q9Y3X0		ENST00000221922.6:c.1341C>G	19.37:g.47774680C>G		44	0	0		55	30	0.545455	NM_015603		Silent	SNP	ENST00000221922.6	37	CCDS12698.1																																																																																			C|0.978;G|0.022	0.022	strong		0.612	CCDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466917.1	NM_015603		G	47774680	C	G	47774680	2	3	27	1	0	0	0	0	0	0	0	1	2869	610	22	4		4	CCDC9	19	47774680	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	203641	47774680	11354303	950	11401											
KPTN	11133	hgsc.bcm.edu	37	chr19	47978739	47978739	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	aacccctgtagccgacgtctCctctgctccacttgatgtcg	6	11	8	16	3	2	1	0	1	2	0	5	2	3	1	5	0	3	2	5	0	2	2	rs1046273	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:47978739C>T	ENST00000338134.3	-	12	1352	c.1245G>A	c.(1243-1245)agG>agA	p.R415R	KPTN_ENST00000536339.1_Silent_p.R175R	NM_007059.2	NP_008990.2	Q9Y664	KPTN_HUMAN	kaptin (actin binding protein)	415					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)		GCCGACGTCTCCTCTGCTCCA	0.612													C|||	92	0.0183706	0.0008	0.062	5008	,	,		19204	0.0		0.0249	False		,,,				2504	0.0235				p.R415R		Atlas-SNP	.											.	KPTN	34	.	0			c.G1245A						PASS	.	C		13,4085		0,13,2036	35	37	36		1245	2.5	0.9	19	dbSNP_86	36	166,8212		3,160,4026	no	coding-synonymous	KPTN	NM_007059.2		3,173,6062	TT,TC,CC		1.9814,0.3172,1.4348		415/437	47978739	179,12297	2049	4189	6238	SO:0001819	synonymous_variant	11133	exon12			ACGTCTCCTCTGC	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.1245G>A	19.37:g.47978739C>T		82	0	0		95	31	0.326316	NM_007059	B3KN86|B4DQ76|Q96GT1	Silent	SNP	ENST00000338134.3	37	CCDS42583.1																																																																																			C|0.982;T|0.018	0.018	strong		0.612	KPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466672.2			T	47978739	C	T	47978739	2	4	27	1	0	0	0	0	0	0	0	1	8446	854	30	2		2	KPTN	19	47978739	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	204059	47978739	11150244	951	11402											
BCAT2	587	hgsc.bcm.edu	37	chr19	49309776	49309776	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggccggccgccatgccacctGcagggagtagtggaggctgg	6	5	18	12	2	0	0	0	0	0	0	0	2	0	2	5	6	2	3	5	6	1	1	rs117048185	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:49309776G>C	ENST00000316273.6	-	3	310	c.298C>G	c.(298-300)Cag>Gag	p.Q100E	BCAT2_ENST00000402551.1_Missense_Mutation_p.Q60E|BCAT2_ENST00000599246.1_Intron|BCAT2_ENST00000597011.1_Missense_Mutation_p.Q60E|BCAT2_ENST00000598162.1_Missense_Mutation_p.Q100E|BCAT2_ENST00000545387.2_Intron|BCAT2_ENST00000601496.1_5'Flank	NM_001190.3	NP_001181.2	O15382	BCAT2_HUMAN	branched chain amino-acid transaminase 2, mitochondrial	100					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)	CATGCCACCTGCAGGGAGTAG	0.607													G|||	30	0.00599042	0.0008	0.0072	5008	,	,		16606	0.0		0.0229	False		,,,				2504	0.001				p.Q100E		Atlas-SNP	.											.	BCAT2	35	.	0			c.C298G						PASS	.	G	,GLU/GLN	10,4396	15.5+/-35.6	0,10,2193	63	74	71		,298	5.3	1	19	dbSNP_132	71	120,8480	61.7+/-123.6	1,118,4181	yes	intron,missense	BCAT2	NM_001164773.1,NM_001190.3	,29	1,128,6374	CC,CG,GG		1.3953,0.227,0.9995	,benign	,100/393	49309776	130,12876	2203	4300	6503	SO:0001583	missense	587	exon3			CCACCTGCAGGGA	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.298C>G	19.37:g.49309776G>C	ENSP00000322991:p.Gln100Glu	86	0	0		85	45	0.529412	NM_001190	B2RB87|O00269|Q96KG1|Q9BTB6|Q9BUU6	Missense_Mutation	SNP	ENST00000316273.6	37	CCDS12735.1	22	0.010073260073260074	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	16	0.021108179419525065	G	1.762	-0.486562	0.04352	0.00227	0.013953	ENSG00000105552	ENST00000316273;ENST00000402551	T;T	0.30448	1.53;1.53	5.26	5.26	0.73747	.	0.056271	0.64402	D	0.000001	T	0.05410	0.0143	N	0.02721	-0.515	0.43959	D	0.996633	B;B	0.23377	0.084;0.084	B;B	0.18263	0.021;0.021	T	0.13098	-1.0522	10	0.02654	T	1	-20.0097	12.4651	0.55753	0.0:0.1688:0.8312:0.0	.	100;100	Q53EW7;O15382	.;BCAT2_HUMAN	E	100;60	ENSP00000322991:Q100E;ENSP00000385161:Q60E	ENSP00000322991:Q100E	Q	-	1	0	BCAT2	54001588	0.995000	0.38212	1.000000	0.80357	0.499000	0.33736	2.479000	0.45197	2.627000	0.88993	0.555000	0.69702	CAG	G|0.990;C|0.010	0.010	strong		0.607	BCAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466202.1			C	49309776	G	C	49309776	3	2	27	1	0	0	0	0	1	0	0	0	1355	1328	46	4	916	4	BCAT2	19	49309776	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1331037	49309776	9819207	952	11403											
MYH14	79784	hgsc.bcm.edu	37	chr19	50771511	50771511	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcgggggaggctggcagccCgcaagcaggagctggagctg	7	3	20	11	3	0	0	0	0	0	0	0	3	0	3	1	6	4	6	1	6	1	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:50771511C>T	ENST00000596571.1	+	21	2797	c.2797C>T	c.(2797-2799)Cgc>Tgc	p.R933C	MYH14_ENST00000425460.1_Missense_Mutation_p.R941C|MYH14_ENST00000376970.2_Missense_Mutation_p.R966C|MYH14_ENST00000601313.1_Missense_Mutation_p.R974C|MYH14_ENST00000598205.1_Missense_Mutation_p.R941C|MYH14_ENST00000440075.2_Missense_Mutation_p.R974C|MYH14_ENST00000262269.8_Missense_Mutation_p.R974C			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	933			R -> L (in PNMHH). {ECO:0000269|PubMed:21480433}.		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)		GCTGGCAGCCCGCAAGCAGGA	0.657																																					p.R974C		Atlas-SNP	.											.	MYH14	261	.	0			c.C2920T						PASS	.						20	29	26					19																	50771511		2140	4241	6381	SO:0001583	missense	79784	exon24			GCAGCCCGCAAGC	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.2797C>T	19.37:g.50771511C>T	ENSP00000472819:p.Arg933Cys	109	0	0		78	47	0.602564	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	37	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	C	18.37	3.608866	0.66558	.	.	ENSG00000105357	ENST00000301415;ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	D;D;D;D	0.94232	-3.38;-3.38;-3.38;-3.38	3.9	3.9	0.45041	.	.	.	.	.	D	0.90307	0.6968	M	0.75884	2.315	0.80722	D	1	P;P;P	0.44690	0.713;0.59;0.841	B;B;B	0.34180	0.126;0.059;0.177	D	0.90702	0.4621	9	0.72032	D	0.01	.	9.075	0.36515	0.2192:0.7808:0.0:0.0	.	974;933;941	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	C	933;974;966;941;933;974	ENSP00000406273:R974C;ENSP00000366169:R966C;ENSP00000407879:R941C;ENSP00000262269:R974C	ENSP00000262269:R974C	R	+	1	0	MYH14	55463323	0.779000	0.28652	1.000000	0.80357	0.892000	0.51952	2.109000	0.41863	2.180000	0.69256	0.561000	0.74099	CGC	.	.	none		0.657	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		T	50771511	C	T	50771511	3	4	27	1	0	0	0	0	1	0	0	0	10042	652	23	1	3010	1	MYH14	19	50771511	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1461735	50771511	8357472	953	11404											
MYH14	79784	hgsc.bcm.edu	37	chr19	50812315	50812315	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcggcagctggaggaggcCgaggaggaggcatcccgggc	9	2	20	10	3	0	0	0	0	0	0	1	5	1	4	2	8	2	3	2	8	1	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:50812315C>T	ENST00000596571.1	+	39	5718	c.5718C>T	c.(5716-5718)gcC>gcT	p.A1906A	MYH14_ENST00000425460.1_Silent_p.A1914A|MYH14_ENST00000376970.2_Silent_p.A1939A|MYH14_ENST00000601313.1_Silent_p.A1947A|MYH14_ENST00000598205.1_Silent_p.A1914A|CTB-191K22.5_ENST00000595563.1_RNA|MYH14_ENST00000440075.2_Silent_p.A1947A|MYH14_ENST00000262269.8_Silent_p.A1947A			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1906					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)		TGGAGGAGGCCGAGGAGGAGG	0.612																																					p.A1947A		Atlas-SNP	.											.	MYH14	261	.	0			c.C5841T						PASS	.						32	38	36					19																	50812315		2059	4204	6263	SO:0001819	synonymous_variant	79784	exon42			GGAGGCCGAGGAG	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.5718C>T	19.37:g.50812315C>T		187	0	0		196	98	0.5	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent	SNP	ENST00000596571.1	37	CCDS59411.1																																																																																			.	.	none		0.612	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729		T	50812315	C	T	50812315	2	4	27	1	0	0	0	0	0	0	0	1	10042	639	23	1		1	MYH14	19	50812315	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	40804	50812315	8316668	954	11405											
ETFB	2109	hgsc.bcm.edu	37	chr19	51857774	51857774	+	Intron	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccttctctcatccagccatTcctgggtaccagggacatct	7	12	7	15	0	3	0	1	0	2	0	7	1	6	1	5	2	2	1	5	2	1	3	rs143144671	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:51857774T>G	ENST00000309244.4	-	2	149				CTD-2616J11.9_ENST00000600974.1_RNA|CTD-2616J11.11_ENST00000600067.1_Intron|ETFB_ENST00000354232.4_Missense_Mutation_p.E40A	NM_001985.2	NP_001976.1	P38117	ETFB_HUMAN	electron-transfer-flavoprotein, beta polypeptide						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)		ATCCAGCCATTCCTGGGTACC	0.522													t|||	4	0.000798722	0.0	0.0029	5008	,	,		18122	0.0		0.002	False		,,,				2504	0.0				p.E40A		Atlas-SNP	.											.	ETFB	46	.	0			c.A119C						PASS	.	T	ALA/GLU,	3,4403	6.2+/-15.9	0,3,2200	88	83	85		119,	-3.9	0	19	dbSNP_134	85	31,8569	21.6+/-65.8	0,31,4269	yes	missense,intron	ETFB	NM_001014763.1,NM_001985.2	107,	0,34,6469	GG,GT,TT		0.3605,0.0681,0.2614	possibly-damaging,	40/347,	51857774	34,12972	2203	4300	6503	SO:0001627	intron_variant	2109	exon1			AGCCATTCCTGGG	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.58-212A>C	19.37:g.51857774T>G		106	0	0		94	65	0.691489	NM_001014763	A8K766|B3KNY2|Q6IBH7|Q71RF6|Q9Y3S7	Missense_Mutation	SNP	ENST00000309244.4	37	CCDS12828.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	t	12.37	1.918726	0.33908	6.81E-4	0.003605	ENSG00000105379	ENST00000354232	D	0.85339	-1.97	2.49	-3.88	0.04205	.	.	.	.	.	T	0.68430	0.3000	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.50558	-0.8814	7	.	.	.	.	4.1225	0.10112	0.0:0.1914:0.3562:0.4524	.	40	P38117-2	.	A	40	ENSP00000346173:E40A	.	E	-	2	0	ETFB	56549586	0.000000	0.05858	0.000000	0.03702	0.054000	0.15201	-0.697000	0.05098	-1.056000	0.03205	-0.319000	0.08680	GAA	T|0.998;G|0.002	0.002	strong		0.522	ETFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464273.1			G	51857774	T	G	51857774	1	3	27	0	1	0	0	0	0	0	0	0	5272	1783	62	5		5	ETFB	19	51857774	Intron	SNP	T	TCGA-G8-6909-01A-11D-2210-10	1045459	51857774	7271209	955	11406											
CLDND2	125875	hgsc.bcm.edu	37	chr19	51871194	51871194	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccgcagcgactcgccctcgtCgcaccgaatccgcagtccca	7	5	9	20	7	0	0	0	0	0	0	5	2	2	0	5	0	1	3	5	0	1	0	rs61736500	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:51871194C>T	ENST00000291715.1	-	2	681	c.256G>A	c.(256-258)Gac>Aac	p.D86N	CTD-2616J11.10_ENST00000595500.1_RNA|CTD-2616J11.11_ENST00000600067.1_Missense_Mutation_p.D21N|CLDND2_ENST00000601435.1_Missense_Mutation_p.D86N|ETFB_ENST00000309244.4_5'Flank	NM_152353.2	NP_689566.1	Q8NHS1	CLDN2_HUMAN	claudin domain containing 2	86						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(2)	4		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000211)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		TCGCCCTCGTCGCACCGAATC	0.726													C|||	17	0.00339457	0.0008	0.0072	5008	,	,		11998	0.0		0.0089	False		,,,				2504	0.002				p.D86N		Atlas-SNP	.											.	CLDND2	11	.	0			c.G256A						PASS	.	C	ASN/ASP	2,4398		0,2,2198	29	29	29		256	-0.3	0	19	dbSNP_129	29	54,8540		0,54,4243	yes	missense	CLDND2	NM_152353.2	23	0,56,6441	TT,TC,CC		0.6283,0.0455,0.431	benign	86/168	51871194	56,12938	2200	4297	6497	SO:0001583	missense	125875	exon2			CCTCGTCGCACCG	BC029518	CCDS12829.1	19q13.41	2008-02-05				ENSG00000160318			28511	protein-coding gene	gene with protein product						12477932	Standard	NM_152353		Approved	MGC33839	uc002pwi.1	Q8NHS1		ENST00000291715.1:c.256G>A	19.37:g.51871194C>T	ENSP00000291715:p.Asp86Asn	133	0	0		118	68	0.576271	NM_152353		Missense_Mutation	SNP	ENST00000291715.1	37	CCDS12829.1	12	0.005494505494505495	0	0.0	5	0.013812154696132596	0	0.0	7	0.009234828496042216	C	7.665	0.685760	0.14973	4.55E-4	0.006283	ENSG00000160318	ENST00000291715	D	0.88509	-2.39	4.69	-0.277	0.12898	.	1.778600	0.02886	N	0.133517	T	0.67859	0.2938	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.04013	0.001	T	0.62388	-0.6865	10	0.12766	T	0.61	-0.1713	3.1085	0.06350	0.097:0.3345:0.3983:0.1702	.	86	Q8NHS1	CLDN2_HUMAN	N	86	ENSP00000291715:D86N	ENSP00000291715:D86N	D	-	1	0	CLDND2	56563006	0.000000	0.05858	0.010000	0.14722	0.379000	0.30106	0.451000	0.21779	0.081000	0.16988	-0.228000	0.12330	GAC	C|0.995;T|0.005	0.005	strong		0.726	CLDND2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464268.1	NM_152353		T	51871194	C	T	51871194	3	4	27	1	0	0	0	0	1	0	0	0	3496	884	31	1	259	1	CLDND2	19	51871194	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	13420	51871194	7257789	956	11407											
HAS1	3036	hgsc.bcm.edu	37	chr19	52217174	52217174	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgcagcacagtggccgccaCgaagaaggggaacaggccgg	12	1	16	12	4	0	1	0	0	0	1	0	3	0	2	3	5	2	2	3	5	3	0	rs45625331	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:52217174C>T	ENST00000222115.1	-	5	1277	c.1243G>A	c.(1243-1245)Gtg>Atg	p.V415M	HAS1_ENST00000540069.2_Missense_Mutation_p.V414M|HAS1_ENST00000601714.1_Missense_Mutation_p.V422M|HAS1_ENST00000594621.1_3'UTR	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	415					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)		GTGGCCGCCACGAAGAAGGGG	0.672													c|||	5	0.000998403	0.0	0.0029	5008	,	,		16422	0.0		0.002	False		,,,				2504	0.001				p.V415M	NSCLC(132;636 2450 45807 47979)	Atlas-SNP	.											.	HAS1	61	.	0			c.G1243A						PASS	.		MET/VAL	5,4393	8.1+/-20.4	0,5,2194	48	42	44		1243	3.2	1	19	dbSNP_127	44	58,8542	32.8+/-85.7	0,58,4242	yes	missense	HAS1	NM_001523.2	21	0,63,6436	TT,TC,CC		0.6744,0.1137,0.4847	probably-damaging	415/579	52217174	63,12935	2199	4300	6499	SO:0001583	missense	3036	exon5			CCGCCACGAAGAA	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.1243G>A	19.37:g.52217174C>T	ENSP00000222115:p.Val415Met	21	0	0		17	8	0.470588	NM_001523	Q14470|Q9NS49	Missense_Mutation	SNP	ENST00000222115.1	37	CCDS12838.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	c	16.44	3.122752	0.56613	0.001137	0.006744	ENSG00000105509	ENST00000540069;ENST00000222115	T;T	0.59638	0.25;0.25	3.19	3.19	0.36642	.	0.000000	0.64402	U	0.000002	T	0.56093	0.1962	L	0.49778	1.585	0.58432	D	0.999992	D;D;D	0.67145	0.992;0.996;0.996	P;P;P	0.58013	0.63;0.831;0.831	T	0.65919	-0.6051	10	0.72032	D	0.01	-12.5318	12.2755	0.54733	0.0:1.0:0.0:0.0	rs45625331	414;415;414	G3V1S7;Q92839;Q8IYH3	.;HAS1_HUMAN;.	M	414;415	ENSP00000445021:V414M;ENSP00000222115:V415M	ENSP00000222115:V415M	V	-	1	0	HAS1	56908986	1.000000	0.71417	1.000000	0.80357	0.304000	0.27724	3.956000	0.56722	1.812000	0.52913	0.165000	0.16767	GTG	C|0.997;T|0.003	0.003	strong		0.672	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523		T	52217174	C	T	52217174	3	4	27	1	0	0	0	0	1	0	0	0	6970	536	19	1	497	1	HAS1	19	52217174	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	345980	52217174	6911809	957	11408											
LILRB2	10288	hgsc.bcm.edu	37	chr19	54783836	54783836	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctatatagacggtactcctgGgcttcaaggctcccctgaca	9	10	9	13	1	1	2	1	1	0	1	3	2	3	2	3	3	1	3	3	3	5	5	rs111453734	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:54783836G>A	ENST00000391749.4	-	4	436	c.165C>T	c.(163-165)gcC>gcT	p.A55A	LILRB2_ENST00000314446.5_Silent_p.A55A|LILRB2_ENST00000434421.1_Intron|LILRB2_ENST00000391748.1_Silent_p.A55A|MIR4752_ENST00000579672.1_RNA|LILRB2_ENST00000391746.1_Silent_p.A55A|LILRB2_ENST00000471216.1_5'UTR	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	55	Ig-like C2-type 1.				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)		GGTACTCCTGGGCTTCAAGGC	0.547													.|||	8	0.00159744	0.0008	0.0072	5008	,	,		19344	0.0		0.002	False		,,,				2504	0.0				p.A55A		Atlas-SNP	.											.	LILRB2	94	.	0			c.C165T						PASS	.	G	,	6,4400	9.9+/-24.2	0,6,2197	173	172	172		165,165	-4.8	0	19	dbSNP_132	172	26,8574	17.9+/-57.8	0,26,4274	no	coding-synonymous,coding-synonymous	LILRB2	NM_001080978.2,NM_005874.3	,	0,32,6471	AA,AG,GG		0.3023,0.1362,0.246	,	55/598,55/599	54783836	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	10288	exon4			CTCCTGGGCTTCA	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.165C>T	19.37:g.54783836G>A		92	0	0		84	49	0.583333	NM_005874	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Silent	SNP	ENST00000391749.4	37	CCDS12886.1																																																																																			G|0.997;A|0.003	0.003	strong		0.547	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1			A	54783836	G	A	54783836	2	1	27	1	0	0	0	0	0	0	0	1	8800	1219	43	2		2	LILRB2	19	54783836	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2566662	54783836	4345147	958	11409											
LENG8	114823	hgsc.bcm.edu	37	chr19	54967408	54967408	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcctccaggtccccgacgCgccacttccgcagaaggtac	7	6	9	19	4	0	1	0	0	0	1	4	2	4	1	7	2	1	2	7	2	2	2	rs75472495	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:54967408C>T	ENST00000326764.5	+	9	1767	c.1288C>T	c.(1288-1290)Cgc>Tgc	p.R430C	LENG8_ENST00000376514.2_Intron	NM_052925.2	NP_443157.1	Q96PV6	LENG8_HUMAN	leukocyte receptor cluster (LRC) member 8	393										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)		GTCCCCGACGCGCCACTTCCG	0.617													C|||	4	0.000798722	0.0008	0.0	5008	,	,		16004	0.0		0.003	False		,,,				2504	0.0				p.R430C		Atlas-SNP	.											LENG8,colon,carcinoma,-1,1	LENG8	73	1	0			c.C1288T						PASS	.	C	CYS/ARG	2,4404		0,2,2201	96	114	107		1288	3.7	0.6	19	dbSNP_131	107	26,8566		0,26,4270	yes	missense	LENG8	NM_052925.2	180	0,28,6471	TT,TC,CC		0.3026,0.0454,0.2154	probably-damaging	430/801	54967408	28,12970	2203	4296	6499	SO:0001583	missense	114823	exon9			CCGACGCGCCACT	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.1288C>T	19.37:g.54967408C>T	ENSP00000318374:p.Arg430Cys	140	0	0		128	68	0.53125	NM_052925	B0VJY9|Q8IZ27|Q8NCX6	Missense_Mutation	SNP	ENST00000326764.5	37	CCDS12894.1	4	0.0018315018315018315	1	0.0020325203252032522	0	0.0	0	0.0	3	0.00395778364116095	C	17.47	3.397139	0.62177	4.54E-4	0.003026	ENSG00000167615	ENST00000326764;ENST00000301196;ENST00000376526;ENST00000431846	T;T;T	0.37058	1.26;1.25;1.22	4.73	3.68	0.42216	.	0.063133	0.64402	D	0.000016	T	0.41558	0.1164	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	0.999;1.0	P;D	0.72338	0.855;0.977	T	0.18241	-1.0343	10	0.37606	T	0.19	-12.3824	10.6314	0.45538	0.3457:0.6543:0.0:0.0	.	430;393	Q96PV6-2;F8W9Q9	.;.	C	430;393;393;430	ENSP00000318374:R430C;ENSP00000365709:R393C;ENSP00000388053:R430C	ENSP00000301196:R393C	R	+	1	0	LENG8	59659220	0.987000	0.35691	0.550000	0.28217	0.537000	0.34900	2.804000	0.47931	1.111000	0.41721	0.555000	0.69702	CGC	C|0.998;T|0.002	0.002	strong		0.617	LENG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140523.2	NM_052925		T	54967408	C	T	54967408	3	4	27	1	0	0	0	0	1	0	0	0	8733	768	27	1	1318	1	LENG8	19	54967408	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	183572	54967408	4161575	959	11410											
ZSCAN5B	342933	hgsc.bcm.edu	37	chr19	56703286	56703286	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcgggcctggcctgtccccGgatgcatctggttcacagag	5	8	15	13	2	2	1	1	0	1	1	3	2	3	2	4	5	1	2	4	5	0	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:56703286G>A	ENST00000586855.2	-	3	834	c.521C>T	c.(520-522)cCg>cTg	p.P174L	ZSCAN5B_ENST00000358992.3_Missense_Mutation_p.P174L			A6NJL1	ZSA5B_HUMAN	zinc finger and SCAN domain containing 5B	174					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)|endometrium(5)|large_intestine(3)|lung(23)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						GCCTGTCCCCGGATGCATCTG	0.632																																					p.P174L		Atlas-SNP	.											.	ZSCAN5B	160	.	0			c.C521T						PASS	.						33	35	34					19																	56703286		2203	4300	6503	SO:0001583	missense	342933	exon2			GTCCCCGGATGCA		CCDS46203.1	19q13.42	2013-01-08			ENSG00000197213	ENSG00000197213		"-", "Zinc fingers, C2H2-type"	34246	protein-coding gene	gene with protein product							Standard	NM_001080456		Approved	ZNF495B, ZNF371	uc010ygh.2	A6NJL1		ENST00000586855.2:c.521C>T	19.37:g.56703286G>A	ENSP00000466072:p.Pro174Leu	90	0	0		87	33	0.37931	NM_001080456		Missense_Mutation	SNP	ENST00000586855.2	37	CCDS46203.1	.	.	.	.	.	.	.	.	.	.	G	6.658	0.489887	0.12702	.	.	ENSG00000197213	ENST00000358992	T	0.05580	3.42	1.9	0.827	0.18835	.	.	.	.	.	T	0.08358	0.0208	M	0.78049	2.395	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.33085	-0.9882	9	0.34782	T	0.22	.	3.7907	0.08719	0.2493:0.0:0.7507:0.0	.	174	A6NJL1	ZSA5B_HUMAN	L	174	ENSP00000351883:P174L	ENSP00000351883:P174L	P	-	2	0	ZSCAN5B	61395098	0.002000	0.14202	0.001000	0.08648	0.001000	0.01503	0.329000	0.19698	0.345000	0.23873	0.306000	0.20318	CCG	.	.	none		0.632	ZSCAN5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457834.2	NM_001080456		A	56703286	G	A	56703286	3	1	27	1	0	0	0	0	1	0	0	0	18254	1116	39	1	978	1	ZSCAN5B	19	56703286	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1735878	56703286	2425697	960	11411											
ZNF460	10794	hgsc.bcm.edu	37	chr19	57802116	57802116	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctatcccttctcatctggcCttgcctgaggaagtctcact	6	13	7	15	0	3	1	2	1	3	0	6	2	4	2	4	2	1	0	4	2	2	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:57802116C>T	ENST00000360338.3	+	3	529	c.207C>T	c.(205-207)gcC>gcT	p.A69A	ZNF460_ENST00000537645.1_Silent_p.A28A	NM_006635.3	NP_006626.3	Q14592	ZN460_HUMAN	zinc finger protein 460	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)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CTCATCTGGCCTTGCCTGAGG	0.483																																					p.A69A		Atlas-SNP	.											.	ZNF460	59	.	0			c.C207T						PASS	.						71	64	66					19																	57802116		2203	4300	6503	SO:0001819	synonymous_variant	10794	exon3			TCTGGCCTTGCCT	X78931	CCDS12949.1	19q13.4	2013-01-08				ENSG00000197714		"Zinc fingers, C2H2-type", "-"	21628	protein-coding gene	gene with protein product		604755	"zinc finger protein 272"	ZNF272		15004467	Standard	NM_006635		Approved	HZF8	uc002qog.2	Q14592		ENST00000360338.3:c.207C>T	19.37:g.57802116C>T		140	0	0		140	33	0.235714	NM_006635	A4FU64|B4DNX9|Q2VPC7|Q6VSF8	Silent	SNP	ENST00000360338.3	37	CCDS12949.1																																																																																			.	.	none		0.483	ZNF460-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465727.1	NM_006635		T	57802116	C	T	57802116	2	4	27	1	0	0	0	0	0	0	0	1	17939	668	24	2		2	ZNF460	19	57802116	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1098830	57802116	1326867	961	11412											
ZNF304	57343	hgsc.bcm.edu	37	chr19	57868483	57868483	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	actggagaattcataccgggGcaaggccctatgaatgcata	13	8	11	9	1	1	2	1	1	0	1	1	3	1	2	2	4	2	2	2	4	6	4	rs45612632	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:57868483G>A	ENST00000282286.5	+	3	1419	c.1246G>A	c.(1246-1248)Gca>Aca	p.A416T	ZNF304_ENST00000598744.1_Missense_Mutation_p.A374T|ZNF304_ENST00000443917.2_Missense_Mutation_p.A463T|ZNF304_ENST00000391705.3_Missense_Mutation_p.A416T			Q9HCX3	ZN304_HUMAN	zinc finger protein 304	416					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)		TCATACCGGGGCAAGGCCCTA	0.443													G|||	65	0.0129792	0.0015	0.0101	5008	,	,		21870	0.0		0.0358	False		,,,				2504	0.0204				p.A416T		Atlas-SNP	.											.	ZNF304	74	.	0			c.G1246A						PASS	.	G	THR/ALA	19,4387	25.3+/-52.1	1,17,2185	50	53	52		1246	3	0.9	19	dbSNP_127	52	261,8339	99.9+/-161.4	4,253,4043	yes	missense	ZNF304	NM_020657.2	58	5,270,6228	AA,AG,GG		3.0349,0.4312,2.1529	possibly-damaging	416/660	57868483	280,12726	2203	4300	6503	SO:0001583	missense	57343	exon3			ACCGGGGCAAGGC	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.1246G>A	19.37:g.57868483G>A	ENSP00000282286:p.Ala416Thr	67	0	0		73	50	0.684932	NM_020657		Missense_Mutation	SNP	ENST00000282286.5	37	CCDS12950.1	30	0.013736263736263736	0	0.0	3	0.008287292817679558	0	0.0	27	0.03562005277044855	G	20.5	3.996773	0.74818	0.004312	0.030349	ENSG00000131845	ENST00000282286;ENST00000391705;ENST00000443917	T;T;T	0.17213	2.29;2.29;2.29	4.03	2.96	0.34315	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02230	0.0069	N	0.11364	0.135	0.25176	N	0.990242	P;P	0.35272	0.493;0.493	B;B	0.35413	0.202;0.202	T	0.21042	-1.0257	9	0.87932	D	0	.	12.651	0.56761	0.0:0.0:0.8326:0.1674	rs45612632	416;463	Q9HCX3;E7EQD3	ZN304_HUMAN;.	T	416;416;463	ENSP00000282286:A416T;ENSP00000375586:A416T;ENSP00000401642:A463T	ENSP00000282286:A416T	A	+	1	0	ZNF304	62560295	0.976000	0.34144	0.873000	0.34254	0.992000	0.81027	4.167000	0.58209	1.234000	0.43709	0.650000	0.86243	GCA	G|0.981;A|0.019	0.019	strong		0.443	ZNF304-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465785.1			A	57868483	G	A	57868483	3	1	27	1	0	0	0	0	1	0	0	0	17848	1203	42	2	1256	2	ZNF304	19	57868483	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	66367	57868483	1260500	962	11413											
ZNF416	55659	hgsc.bcm.edu	37	chr19	58084605	58084605	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agtgtgtttgtggctggactCtctcctgcattgactccact	5	15	10	11	0	1	1	0	1	1	0	4	2	3	2	2	2	1	3	2	2	0	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:58084605C>G	ENST00000196489.3	-	4	889	c.667G>C	c.(667-669)Gag>Cag	p.E223Q		NM_017879.1	NP_060349.1	Q9BWM5	ZN416_HUMAN	zinc finger protein 416	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)			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)		TGGCTGGACTCTCTCCTGCAT	0.438																																					p.E223Q		Atlas-SNP	.											.	ZNF416	50	.	0			c.G667C						PASS	.						140	142	141					19																	58084605		2203	4300	6503	SO:0001583	missense	55659	exon4			TGGACTCTCTCCT	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.667G>C	19.37:g.58084605C>G	ENSP00000196489:p.Glu223Gln	178	0	0		174	108	0.62069	NM_017879	Q9NWW8	Missense_Mutation	SNP	ENST00000196489.3	37	CCDS12954.1	.	.	.	.	.	.	.	.	.	.	C	8.461	0.855209	0.17106	.	.	ENSG00000083817	ENST00000196489;ENST00000359489;ENST00000428052	T	0.07444	3.19	3.65	1.43	0.22495	.	.	.	.	.	T	0.05502	0.0145	L	0.27053	0.805	0.09310	N	1	B	0.30361	0.277	B	0.25759	0.063	T	0.36720	-0.9736	9	0.66056	D	0.02	.	4.8172	0.13372	0.1732:0.6307:0.0:0.1961	.	223	Q9BWM5	ZN416_HUMAN	Q	223;209;203	ENSP00000196489:E223Q	ENSP00000196489:E223Q	E	-	1	0	ZNF416	62776417	0.000000	0.05858	0.002000	0.10522	0.021000	0.10359	-0.488000	0.06497	0.334000	0.23590	0.655000	0.94253	GAG	.	.	none		0.438	ZNF416-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466787.1	NM_017879		G	58084605	C	G	58084605	3	3	27	1	0	0	0	0	1	0	0	0	17908	922	32	4	1121	4	ZNF416	19	58084605	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	216122	58084605	1044378	963	11414											
ZNF587	84914	hgsc.bcm.edu	37	chr19	58371202	58371202	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtatgtgggaaattatttggCaataagcacagcgtgactat	13	12	11	5	1	0	1	0	1	0	0	0	2	0	2	0	2	2	3	0	2	6	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr19:58371202C>T	ENST00000339656.5	+	3	1604	c.1422C>T	c.(1420-1422)ggC>ggT	p.G474G	ZNF814_ENST00000596604.1_Intron|ZNF587_ENST00000419854.1_Silent_p.G431G|ZNF814_ENST00000597342.1_Intron|ZNF587_ENST00000423137.1_Silent_p.G473G|ZNF814_ENST00000597652.1_5'Flank|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597832.1_Intron	NM_001204817.1|NM_032828.3	NP_001191746.1|NP_116217.1	Q96SQ5	ZN587_HUMAN	zinc finger protein 587	474					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)		AATTATTTGGCAATAAGCACA	0.433																																					p.G474G	Pancreas(59;641 1233 1885 20055 50741)	Atlas-SNP	.											.	ZNF587	53	.	0			c.C1422T						PASS	.						154	150	151					19																	58371202		2203	4300	6503	SO:0001819	synonymous_variant	84914	exon3			ATTTGGCAATAAG	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.1422C>T	19.37:g.58371202C>T		180	0	0		224	13	0.0580357	NM_032828	A0AV72|G3V0H5|Q6ZMK8	Silent	SNP	ENST00000339656.5	37	CCDS12964.1																																																																																			.	.	none		0.433	ZNF587-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337594.2	NM_032828		T	58371202	C	T	58371202	2	4	27	1	0	0	0	0	0	0	0	1	18035	697	25	2		2	ZNF587	19	58371202	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	286597	58371202	757781	964	11415											
CSNK2A1	1457	hgsc.bcm.edu	37	chr20	472938	472938	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	caggacctttgaagtatcggGaagcaactcggacattatat	13	10	10	8	2	0	1	0	1	0	0	2	4	0	4	1	3	2	2	1	3	6	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:472938G>A	ENST00000217244.3	-	9	956	c.581C>T	c.(580-582)tCc>tTc	p.S194F	CSNK2A1_ENST00000349736.5_Missense_Mutation_p.S194F|CSNK2A1_ENST00000400217.2_Missense_Mutation_p.S58F|CSNK2A1_ENST00000400227.3_Missense_Mutation_p.S194F	NM_177559.2	NP_808227.1	P68400	CSK21_HUMAN	casein kinase 2, alpha 1 polypeptide	194	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)			GAAGTATCGGGAAGCAACTCG	0.408																																					p.S194F		Atlas-SNP	.											.	CSNK2A1	36	.	0			c.C581T						PASS	.						87	80	83					20																	472938		2203	4298	6501	SO:0001583	missense	1457	exon8			TATCGGGAAGCAA	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.581C>T	20.37:g.472938G>A	ENSP00000217244:p.Ser194Phe	78	0	0		60	16	0.266667	NM_001895	B4DYS6|D3DVV8|P19138|P20426|Q14013|Q5U065	Missense_Mutation	SNP	ENST00000217244.3	37	CCDS13003.1	.	.	.	.	.	.	.	.	.	.	G	28.2	4.901024	0.92035	.	.	ENSG00000101266	ENST00000400227;ENST00000349736;ENST00000217244;ENST00000381973;ENST00000400217	T;T;T;T	0.54279	3.06;3.06;3.06;0.58	4.84	4.84	0.62591	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.095477	0.85682	D	0.000000	T	0.81083	0.4749	H	0.95574	3.69	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.86825	0.2007	10	0.87932	D	0	-7.1666	17.471	0.87646	0.0:0.0:1.0:0.0	.	194	P68400	CSK21_HUMAN	F	194;194;194;194;58	ENSP00000383086:S194F;ENSP00000339247:S194F;ENSP00000217244:S194F;ENSP00000383076:S58F	ENSP00000217244:S194F	S	-	2	0	CSNK2A1	420938	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.562000	0.98145	2.679000	0.91253	0.655000	0.94253	TCC	.	.	none		0.408	CSNK2A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077466.1	NM_001895		A	472938	G	A	472938	3	1	27	1	0	0	0	0	1	0	0	0	3959	1174	41	2	618	2	CSNK2A1	20	472938	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10		472938	62552582	965	11416											
ADAM33	80332	hgsc.bcm.edu	37	chr20	3652365	3652365	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtagagtccactggcaccaTgtgcggtgcgagcaggctgg	7	7	17	10	2	0	1	0	0	0	1	1	2	1	1	2	5	3	4	2	5	1	1	rs55687415	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:3652365T>C	ENST00000356518.2	-	16	2009	c.1768A>G	c.(1768-1770)Atg>Gtg	p.M590V	ADAM33_ENST00000350009.2_Missense_Mutation_p.M590V|ADAM33_ENST00000379861.4_Missense_Mutation_p.M590V|ADAM33_ENST00000466620.1_5'UTR	NM_025220.2	NP_079496.1	Q9BZ11	ADA33_HUMAN	ADAM metallopeptidase domain 33	590	Cys-rich.				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						ACTGGCACCATGTGCGGTGCG	0.637													T|||	33	0.00658946	0.0227	0.0043	5008	,	,		20795	0.0		0.0	False		,,,				2504	0.0				p.M590V		Atlas-SNP	.											.	ADAM33	76	.	0			c.A1768G						PASS	.	T	VAL/MET,VAL/MET	82,4324		0,82,2121	42	33	36		1768,1768	0.5	0	20	dbSNP_129	36	4,8588		0,4,4292	yes	missense,missense	ADAM33	NM_025220.2,NM_153202.1	21,21	0,86,6413	CC,CT,TT		0.0466,1.8611,0.6616	benign,benign	590/814,590/788	3652365	86,12912	2203	4296	6499	SO:0001583	missense	80332	exon16			GCACCATGTGCGG	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.1768A>G	20.37:g.3652365T>C	ENSP00000348912:p.Met590Val	66	0	0		53	22	0.415094	NM_025220	A0A1K6|Q5JT75|Q5JT76|Q8N0W6	Missense_Mutation	SNP	ENST00000356518.2	37	CCDS13058.1	14	0.00641025641025641	13	0.026422764227642278	1	0.0027624309392265192	0	0.0	0	0.0	T	4.955	0.177362	0.09443	0.018611	4.66E-4	ENSG00000149451	ENST00000356518;ENST00000379861;ENST00000350009;ENST00000428784;ENST00000439201	T;T;T	0.21031	2.03;2.03;2.03	5.46	0.539	0.17156	ADAM, cysteine-rich (2);	.	.	.	.	T	0.01835	0.0058	N	0.00926	-1.1	0.09310	N	0.999999	B;B;B;B	0.19073	0.033;0.001;0.001;0.001	B;B;B;B	0.14578	0.011;0.002;0.004;0.004	T	0.41520	-0.9504	9	0.16420	T	0.52	.	9.2387	0.37481	0.0:0.3775:0.0:0.6225	rs55687415;rs61753555	106;590;590;590	E9PEB2;Q9BZ11-2;Q9BZ11;A2A2L3	.;.;ADA33_HUMAN;.	V	590;590;590;106;470	ENSP00000348912:M590V;ENSP00000369190:M590V;ENSP00000322550:M590V	ENSP00000322550:M590V	M	-	1	0	ADAM33	3600365	0.620000	0.27068	0.003000	0.11579	0.082000	0.17680	0.249000	0.18216	-0.185000	0.10550	0.459000	0.35465	ATG	T|0.992;C|0.008	0.008	strong		0.637	ADAM33-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077763.2	NM_025220		C	3652365	T	C	3652365	3	2	27	1	0	0	0	0	1	0	0	0	250	1464	51	3	701	3	ADAM33	20	3652365	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	3179427	3652365	59373155	966	11417											
POLR3F	10621	hgsc.bcm.edu	37	chr20	18449662	18449662	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatgaaatgcctcatatagAagcccagcagcgggcagtag	14	6	12	9	1	1	2	1	1	0	1	1	3	1	2	2	1	4	3	2	1	6	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:18449662A>C	ENST00000377603.4	+	2	517	c.137A>C	c.(136-138)gAa>gCa	p.E46A	DZANK1_ENST00000329494.5_5'Flank|MIR3192_ENST00000584920.1_RNA|DZANK1_ENST00000262547.5_5'Flank|POLR3F_ENST00000462997.1_3'UTR|DZANK1_ENST00000357236.4_5'Flank	NM_006466.2	NP_006457.2	Q9H1D9	RPC6_HUMAN	polymerase (RNA) III (DNA directed) polypeptide F, 39 kDa	46				HIEAQQRAVA -> QYRSPAAGSS (in Ref. 1; AAB63677). {ECO:0000305}.	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)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|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)			breast(2)	2						CCTCATATAGAAGCCCAGCAG	0.368																																					p.E46A	GBM(69;898 1468 19907 52011)	Atlas-SNP	.											.	POLR3F	14	.	0			c.A137C						PASS	.						100	100	100					20																	18449662		2203	4300	6503	SO:0001583	missense	10621	exon2			ATATAGAAGCCCA	U93869	CCDS13135.1	20p11.23	2013-01-21	2002-08-29		ENSG00000132664	ENSG00000132664		"RNA polymerase subunits"	15763	protein-coding gene	gene with protein product	"RNA polymerase III C39 subunit"		"polymerase (RNA) III (DNA directed) polypeptide F (39 kDa)"			9171375	Standard	NM_006466		Approved	RPC39, RPC6	uc002wqv.3	Q9H1D9	OTTHUMG00000031971	ENST00000377603.4:c.137A>C	20.37:g.18449662A>C	ENSP00000366828:p.Glu46Ala	238	0	0		267	67	0.250936	NM_006466	A8K4C7|O15319	Missense_Mutation	SNP	ENST00000377603.4	37	CCDS13135.1	.	.	.	.	.	.	.	.	.	.	A	14.44	2.534697	0.45073	.	.	ENSG00000132664	ENST00000377603	.	.	.	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.59824	0.2222	L	0.51422	1.61	0.80722	D	1	B	0.25563	0.129	B	0.30251	0.113	T	0.55147	-0.8186	9	0.30078	T	0.28	.	16.3126	0.82898	1.0:0.0:0.0:0.0	.	46	Q9H1D9	RPC6_HUMAN	A	46	.	ENSP00000366828:E46A	E	+	2	0	POLR3F	18397662	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.904000	0.92590	2.333000	0.79357	0.482000	0.46254	GAA	.	.	none		0.368	POLR3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078170.2	NM_006466		C	18449662	A	C	18449662	3	2	27	1	0	0	0	0	1	0	0	0	12242	246	9	5	143	5	POLR3F	20	18449662	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	14797297	18449662	44575858	967	11418											
RIN2	54453	hgsc.bcm.edu	37	chr20	19955713	19955713	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaacatgggaacgtagctctGcctggaacgaaaccaactcc	14	6	9	12	2	1	0	0	0	1	0	2	3	2	2	3	2	7	2	3	2	6	1	rs149398614	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:19955713G>C	ENST00000255006.6	+	8	1340	c.1191G>C	c.(1189-1191)ctG>ctC	p.L397L	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	348					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						ACGTAGCTCTGCCTGGAACGA	0.562													G|||	37	0.00738818	0.0015	0.0058	5008	,	,		333	0.0		0.0298	False		,,,				2504	0.001				p.L397L		Atlas-SNP	.											.	RIN2	126	.	0			c.G1191C						PASS	.	G	,	20,4018		0,20,1999	107	116	113		1191,1044	3.5	0.1	20	dbSNP_134	113	236,8124		5,226,3949	no	coding-synonymous,coding-synonymous	RIN2	NM_001242581.1,NM_018993.3	,	5,246,5948	CC,CG,GG		2.823,0.4953,2.0648	,	397/945,348/896	19955713	256,12142	2019	4180	6199	SO:0001819	synonymous_variant	54453	exon8			AGCTCTGCCTGGA	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.1191G>C	20.37:g.19955713G>C		36	0	0		34	19	0.558824	NM_001242581	Q00425|Q5TFT8|Q9BQL3|Q9H071	Silent	SNP	ENST00000255006.6	37	CCDS56182.1																																																																																			G|0.983;C|0.017	0.017	strong		0.562	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1			C	19955713	G	C	19955713	2	2	27	1	0	0	0	0	0	0	0	1	13387	1306	46	4		4	RIN2	20	19955713	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1506051	19955713	43069807	968	11419											
NAPB	63908	hgsc.bcm.edu	37	chr20	23377815	23377815	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttggctgcctgacaaaatgcGtttcctgcagctgaagaaga	11	10	11	9	1	0	4	0	2	0	2	1	4	1	4	2	1	4	4	2	1	4	2	rs17750862	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:23377815G>A	ENST00000377026.4	-	3	274	c.189C>T	c.(187-189)aaC>aaT	p.N63N	NAPB_ENST00000398425.3_De_novo_Start_InFrame|NAPB_ENST00000432543.2_Intron|NAPB_ENST00000472855.1_Intron	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	63					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)					GACAAAATGCGTTTCCTGCAG	0.478													G|||	110	0.0219649	0.0015	0.0231	5008	,	,		17642	0.001		0.0537	False		,,,				2504	0.0378				p.N63N		Atlas-SNP	.											.	NAPB	22	.	0			c.C189T						PASS	.	G		47,4359	48.2+/-83.0	0,47,2156	71	59	63		189	-2.1	1	20	dbSNP_123	63	440,8160	134.7+/-192.1	18,404,3878	no	coding-synonymous	NAPB	NM_022080.2		18,451,6034	AA,AG,GG		5.1163,1.0667,3.7444		63/299	23377815	487,12519	2203	4300	6503	SO:0001819	synonymous_variant	63908	exon3			AAATGCGTTTCCT	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.189C>T	20.37:g.23377815G>A		84	0	0		62	24	0.387097	NM_022080	B4DK44|Q4G0M0|Q4G187|Q5JXF9|Q8N3C4	Silent	SNP	ENST00000377026.4	37	CCDS13152.1																																																																																			G|0.966;A|0.034	0.034	strong		0.478	NAPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078317.2	NM_022080		A	23377815	G	A	23377815	2	1	27	1	0	0	0	0	0	0	0	1	10171	1136	40	1		1	NAPB	20	23377815	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	3422102	23377815	39647705	969	11420											
CST4	1472	hgsc.bcm.edu	37	chr20	23667738	23667738	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aacgtaccttctgcagttctGgctgttcatggaaggcacag	9	11	11	10	1	3	0	1	0	2	0	3	1	3	1	1	3	3	6	1	3	3	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:23667738G>C	ENST00000217423.3	-	2	399	c.329C>G	c.(328-330)cCa>cGa	p.P110R		NM_001899.2	NP_001890.1	P01036	CYTS_HUMAN	cystatin S	110					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	16	Lung NSC(19;0.0789)|Colorectal(13;0.0993)|all_lung(19;0.169)					CTGCAGTTCTGGCTGTTCATG	0.572																																					p.P110R		Atlas-SNP	.											.	CST4	37	.	0			c.C329G						PASS	.						207	168	181					20																	23667738		2203	4300	6503	SO:0001583	missense	1472	exon2			AGTTCTGGCTGTT		CCDS13159.1	20p11.2	2008-04-15			ENSG00000101441	ENSG00000101441			2476	protein-coding gene	gene with protein product		123857				1801729	Standard	NM_001899		Approved		uc002wto.1	P01036	OTTHUMG00000032083	ENST00000217423.3:c.329C>G	20.37:g.23667738G>C	ENSP00000217423:p.Pro110Arg	242	0	0		194	37	0.190722	NM_001899	Q9UBI5|Q9UCS9	Missense_Mutation	SNP	ENST00000217423.3	37	CCDS13159.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.165362	0.38217	.	.	ENSG00000101441	ENST00000217423	T	0.14516	2.5	1.51	0.516	0.17019	Proteinase inhibitor I25, cystatin (2);	0.298786	0.30959	U	0.008521	T	0.33118	0.0852	M	0.87682	2.9	0.09310	N	0.999999	D	0.69078	0.997	D	0.80764	0.994	T	0.08617	-1.0713	10	0.87932	D	0	.	3.9044	0.09176	0.2423:0.0:0.7577:0.0	.	110	P01036	CYTS_HUMAN	R	110	ENSP00000217423:P110R	ENSP00000217423:P110R	P	-	2	0	CST4	23615738	0.017000	0.18338	0.006000	0.13384	0.644000	0.38419	-0.007000	0.12810	0.190000	0.20209	0.205000	0.17691	CCA	.	.	none		0.572	CST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078349.2	NM_001899		C	23667738	G	C	23667738	3	2	27	1	0	0	0	0	1	0	0	0	3976	1348	47	4	104	4	CST4	20	23667738	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	289923	23667738	39357782	970	11421											
C20orf3	57136	hgsc.bcm.edu	37	chr20	24954303	24954303	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	caagggcccgaaccaaaccgGgcaatggtctctatttcacc	11	7	9	14	2	2	0	1	0	1	0	3	1	2	0	4	3	2	1	4	3	5	2	rs148400044	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:24954303G>C	ENST00000217456.2	-	4	689	c.399C>G	c.(397-399)gcC>gcG	p.A133A	RNU6-1257P_ENST00000384625.1_RNA|APMAP_ENST00000447138.1_Silent_p.A133A	NM_020531.2	NP_065392.1	Q9HDC9	APMAP_HUMAN	adipocyte plasma membrane associated protein	133					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)										AACCAAACCGGGCAATGGTCT	0.448													G|||	3	0.000599042	0.0	0.0	5008	,	,		19675	0.0		0.001	False		,,,				2504	0.002				p.A133A		Atlas-SNP	.											.	APMAP	3	.	0			c.C399G						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	107	92	97		399	0	1	20	dbSNP_134	97	11,8589	9.1+/-34.3	0,11,4289	no	coding-synonymous	C20orf3	NM_020531.2		0,13,6490	CC,CG,GG		0.1279,0.0454,0.1		133/417	24954303	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	57136	exon4			AAACCGGGCAATG	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.399C>G	20.37:g.24954303G>C		131	0	0		116	62	0.534483	NM_020531	A8K514|B4DXG1|Q6UVZ8|Q9GZS8|Q9NUB2	Silent	SNP	ENST00000217456.2	37	CCDS13166.1	.	.	.	.	.	.	.	.	.	.	G	9.501	1.103322	0.20632	4.54E-4	0.001279	ENSG00000101474	ENST00000451442	.	.	.	5.43	0.0444	0.14225	.	.	.	.	.	T	0.50360	0.1611	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33752	-0.9856	4	.	.	.	-17.6727	5.067	0.14587	0.3047:0.2599:0.4354:0.0	.	.	.	.	R	118	.	.	P	-	2	0	C20orf3	24902303	0.804000	0.28969	0.963000	0.40424	0.854000	0.48673	-0.233000	0.09041	-0.200000	0.10300	-0.150000	0.13652	CCC	G|0.998;C|0.002	0.002	strong		0.448	APMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078380.2	NM_020531		C	24954303	G	C	24954303	2	2	27	1	0	0	0	0	0	0	0	1	2111	1219	43	4		4	C20orf3	20	24954303	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1286565	24954303	38071217	971	11422											
TPX2	22974	hgsc.bcm.edu	37	chr20	30381700	30381700	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tcaacctgtgccacattatgGggtgccttttaagccccaaa	10	11	8	12	0	1	0	1	0	0	0	1	0	1	0	5	2	4	0	5	2	4	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:30381700G>A	ENST00000300403.6	+	14	2087	c.1559G>A	c.(1558-1560)gGg>gAg	p.G520E	TPX2_ENST00000340513.4_Missense_Mutation_p.G556E	NM_012112.4	NP_036244.2	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated	520					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)			CCACATTATGGGGTGCCTTTT	0.443																																					p.G520E		Atlas-SNP	.											.	TPX2	61	.	0			c.G1559A						PASS	.						171	176	174					20																	30381700		2203	4300	6503	SO:0001583	missense	22974	exon14			ATTATGGGGTGCC	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.1559G>A	20.37:g.30381700G>A	ENSP00000300403:p.Gly520Glu	184	0	0		158	38	0.240506	NM_012112	Q9H1R4|Q9NRA3|Q9UFN9|Q9UL00|Q9Y2M1	Missense_Mutation	SNP	ENST00000300403.6	37	CCDS13190.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.831487	0.91036	.	.	ENSG00000088325	ENST00000300403;ENST00000340513	T	0.35236	1.32	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.63674	0.2531	M	0.81682	2.555	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	T	0.57015	-0.7883	10	0.25751	T	0.34	-20.3066	19.545	0.95291	0.0:0.0:1.0:0.0	.	556;520	Q96RR5;Q9ULW0	.;TPX2_HUMAN	E	520;556	ENSP00000341145:G556E	ENSP00000300403:G520E	G	+	2	0	TPX2	29845361	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.527000	0.67123	2.861000	0.98227	0.655000	0.94253	GGG	.	.	none		0.443	TPX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078569.2			A	30381700	G	A	30381700	3	1	27	1	0	0	0	0	1	0	0	0	16447	1232	43	2	1605	2	TPX2	20	30381700	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	5427397	30381700	32643820	972	11423											
MYLK2	85366	hgsc.bcm.edu	37	chr20	30414621	30414621	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atcgagggcggagagctcttCgagaggattgtggatgagga	10	8	18	5	3	1	3	0	1	1	2	3	9	1	6	0	5	1	1	0	5	0	2	rs6089088	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:30414621C>T	ENST00000375994.2	+	7	1377	c.1104C>T	c.(1102-1104)ttC>ttT	p.F368F	MYLK2_ENST00000375985.4_Silent_p.F368F|MYLK2_ENST00000468730.1_3'UTR			Q9H1R3	MYLK2_HUMAN	myosin light chain kinase 2	368	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)			GAGAGCTCTTCGAGAGGATTG	0.592													C|||	41	0.0081869	0.0008	0.013	5008	,	,		19225	0.0		0.0209	False		,,,				2504	0.0102				p.F368F		Atlas-SNP	.											.	MYLK2	76	.	0			c.C1104T						PASS	.	C		25,4381	32.6+/-62.9	0,25,2178	124	99	108		1104	1.4	1	20	dbSNP_114	108	186,8414	84.0+/-146.5	0,186,4114	no	coding-synonymous	MYLK2	NM_033118.3		0,211,6292	TT,TC,CC		2.1628,0.5674,1.6223		368/597	30414621	211,12795	2203	4300	6503	SO:0001819	synonymous_variant	85366	exon8			GCTCTTCGAGAGG	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.1104C>T	20.37:g.30414621C>T		175	0	0		159	75	0.471698	NM_033118	Q569L1|Q96I84	Silent	SNP	ENST00000375994.2	37	CCDS13191.1																																																																																			C|0.986;T|0.014	0.014	strong		0.592	MYLK2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078583.2	NM_033118		T	30414621	C	T	30414621	2	4	27	1	0	0	0	0	0	0	0	1	10066	883	31	1		1	MYLK2	20	30414621	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	32921	30414621	32610899	973	11424											
C20orf186	149954	hgsc.bcm.edu	37	chr20	31671411	31671411	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tatggaggccacaggggcctCgggcgatacagggcagcacc	9	4	16	12	2	0	0	0	0	0	0	1	2	0	1	3	6	2	2	3	6	2	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:31671411C>T	ENST00000375483.3	+	3	408	c.408C>T	c.(406-408)ctC>ctT	p.L136L		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	136	Gly-rich.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										ACAGGGGCCTCGGGCGATACA	0.627																																					p.L136L		Atlas-SNP	.											.	.	.	.	0			c.C408T						PASS	.						59	57	58					20																	31671411		2203	4300	6503	SO:0001819	synonymous_variant	149954	exon3			GGGCCTCGGGCGA	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.408C>T	20.37:g.31671411C>T		215	0	0		178	48	0.269663	NM_182519	Q5TDX6	Silent	SNP	ENST00000375483.3	37	CCDS13213.2																																																																																			.	.	none		0.627	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519		T	31671411	C	T	31671411	2	4	27	1	0	0	0	0	0	0	0	1	2100	871	31	1		1	C20orf186	20	31671411	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1256790	31671411	31354109	974	11425											
E2F1	1869	hgsc.bcm.edu	37	chr20	32266134	32266134	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caacccctcaagccgtccgcCgacgcccactgtggtgtggc	6	6	11	18	4	1	0	1	0	0	0	2	1	2	0	6	2	2	0	6	2	2	0	rs35385772	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:32266134C>T	ENST00000343380.5	-	4	737	c.598G>A	c.(598-600)Ggc>Agc	p.G200S	RP1-63M2.5_ENST00000606866.1_RNA	NM_005225.2	NP_005216.1	Q01094	E2F1_HUMAN	E2F transcription factor 1	200	Dimerization. {ECO:0000255}.|Required for interaction with TRIM28.		G -> S (in dbSNP:rs35385772).		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						AGCCGTCCGCCGACGCCCACT	0.652													C|||	64	0.0127796	0.0015	0.0274	5008	,	,		18426	0.0		0.0408	False		,,,				2504	0.002				p.G200S		Atlas-SNP	.											.	E2F1	41	.	0			c.G598A						PASS	.	C	SER/GLY	30,4376	36.0+/-67.5	0,30,2173	36	34	34		598	-3.4	0	20	dbSNP_126	34	224,8374	91.4+/-153.5	0,224,4075	yes	missense	E2F1	NM_005225.2	56	0,254,6248	TT,TC,CC		2.6053,0.6809,1.9532	benign	200/438	32266134	254,12750	2203	4299	6502	SO:0001583	missense	1869	exon4			GTCCGCCGACGCC		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.598G>A	20.37:g.32266134C>T	ENSP00000345571:p.Gly200Ser	115	0	0		98	45	0.459184	NM_005225	Q13143|Q92768	Missense_Mutation	SNP	ENST00000343380.5	37	CCDS13224.1	41	0.018772893772893772	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	32	0.04221635883905013	C	0.011	-1.707208	0.00719	0.006809	0.026053	ENSG00000101412	ENST00000343380	T	0.07908	3.15	5.16	-3.42	0.04825	.	1.060050	0.07264	N	0.867922	T	0.00998	0.0033	N	0.24115	0.695	0.09310	N	1	B	0.17465	0.022	B	0.04013	0.001	T	0.46133	-0.9213	10	0.07644	T	0.81	-2.1827	9.5138	0.39093	0.0:0.2833:0.1035:0.6132	rs35385772;rs61752051	200	Q01094	E2F1_HUMAN	S	200	ENSP00000345571:G200S	ENSP00000345571:G200S	G	-	1	0	E2F1	31729795	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.376000	0.07465	-0.774000	0.04590	-1.945000	0.00491	GGC	C|0.980;T|0.020	0.020	strong		0.652	E2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078731.2			T	32266134	C	T	32266134	3	4	27	1	0	0	0	0	1	0	0	0	4868	652	23	1	731	1	E2F1	20	32266134	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	594723	32266134	30759386	975	11426											
NCOA6	23054	hgsc.bcm.edu	37	chr20	33328372	33328372	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtcctgctgaggcagtgccCgggcccacagggctagaggt	6	6	17	12	1	0	2	0	1	0	1	1	2	1	2	3	5	2	3	3	5	1	1	rs141863711		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:33328372C>T	ENST00000374796.2	-	12	8258	c.5688G>A	c.(5686-5688)ccG>ccA	p.P1896P	NCOA6_ENST00000359003.2_Silent_p.P1896P			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	1896	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						AGGCAGTGCCCGGGCCCACAG	0.602																																					p.P1896P		Atlas-SNP	.											.	NCOA6	219	.	0			c.G5688A						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	53	53	53		,5688	-11.3	0	20	dbSNP_134	53	0,8600		0,0,4300	no	intron,coding-synonymous	NCOA6	NM_001242539.1,NM_014071.3	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	,1896/2064	33328372	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23054	exon11			AGTGCCCGGGCCC	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.5688G>A	20.37:g.33328372C>T		56	0	0		45	16	0.355556	NM_014071	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Silent	SNP	ENST00000374796.2	37	CCDS13241.1																																																																																			C|1.000;T|0.000	0.000	weak		0.602	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071		T	33328372	C	T	33328372	2	4	27	1	0	0	0	0	0	0	0	1	10242	639	23	1		1	NCOA6	20	33328372	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1062238	33328372	29697148	976	11427											
C20orf117	140710	hgsc.bcm.edu	37	chr20	35443768	35443768	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtcgggggcctcatgcagccGgaagtcagcacactcgttgt	7	8	14	12	3	2	0	2	0	0	0	4	1	2	1	2	3	3	3	2	3	1	1	rs201600310		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:35443768G>A	ENST00000357779.3	-	5	1689	c.1363C>T	c.(1363-1365)Cgg>Tgg	p.R455W	SOGA1_ENST00000456801.2_Missense_Mutation_p.R296W|SOGA1_ENST00000237536.4_Missense_Mutation_p.R693W|SOGA1_ENST00000279034.6_Missense_Mutation_p.R455W			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	455					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						TCATGCAGCCGGAAGTCAGCA	0.642																																					p.R693W		Atlas-SNP	.											.	SOGA1	136	.	0			c.C2077T						PASS	.						38	40	39					20																	35443768		2203	4300	6503	SO:0001583	missense	140710	exon5			GCAGCCGGAAGTC	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.1363C>T	20.37:g.35443768G>A	ENSP00000350424:p.Arg455Trp	96	0	0		82	36	0.439024	NM_080627	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Missense_Mutation	SNP	ENST00000357779.3	37		.	.	.	.	.	.	.	.	.	.	G	12.03	1.815128	0.32053	.	.	ENSG00000149639	ENST00000237536;ENST00000279034;ENST00000456801;ENST00000357779	T;T;T;T	0.18960	2.18;2.19;2.18;2.19	4.6	2.45	0.29901	.	0.356930	0.24426	N	0.038636	T	0.28400	0.0702	L	0.29908	0.895	0.22185	N	0.999303	D	0.76494	0.999	D	0.69307	0.963	T	0.02037	-1.1225	10	0.66056	D	0.02	-35.7471	8.495	0.33123	0.0:0.1348:0.5622:0.3029	.	455	O94964-4	.	W	693;455;296;455	ENSP00000237536:R693W;ENSP00000279034:R455W;ENSP00000413886:R296W;ENSP00000350424:R455W	ENSP00000237536:R693W	R	-	1	2	KIAA0889	34877182	0.915000	0.31059	0.960000	0.40013	0.382000	0.30200	1.264000	0.33015	1.137000	0.42214	0.313000	0.20887	CGG	G|0.998;A|0.002	0.002	weak		0.642	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181		A	35443768	G	A	35443768	3	1	27	1	0	0	0	0	1	0	0	0	2085	1115	39	1	3014	1	C20orf117	20	35443768	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2115396	35443768	27581752	977	11428											
SLC32A1	140679	hgsc.bcm.edu	37	chr20	37353743	37353743	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggaggcaggctggaacgtgAccaacgccatccaggtaagc	11	4	15	11	2	0	1	0	1	0	0	1	3	1	3	3	5	3	3	3	5	3	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:37353743A>G	ENST00000217420.1	+	1	639	c.376A>G	c.(376-378)Acc>Gcc	p.T126A		NM_080552.2	NP_542119.1	Q9H598	VIAAT_HUMAN	solute carrier family 32 (GABA vesicular transporter), member 1	126					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)	CTGGAACGTGACCAACGCCAT	0.677																																					p.T126A		Atlas-SNP	.											.	SLC32A1	81	.	0			c.A376G						PASS	.						38	40	39					20																	37353743		2147	4214	6361	SO:0001583	missense	140679	exon1			AACGTGACCAACG	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.376A>G	20.37:g.37353743A>G	ENSP00000217420:p.Thr126Ala	108	0	0		83	25	0.301205	NM_080552	Q8N489	Missense_Mutation	SNP	ENST00000217420.1	37	CCDS13307.1	.	.	.	.	.	.	.	.	.	.	A	23.6	4.436764	0.83885	.	.	ENSG00000101438	ENST00000217420	T	0.02216	4.39	5.19	4.08	0.47627	.	0.152435	0.64402	N	0.000018	T	0.07458	0.0188	M	0.64170	1.965	0.80722	D	1	P	0.51933	0.949	P	0.58331	0.837	T	0.04885	-1.0920	10	0.59425	D	0.04	-41.9776	9.2152	0.37342	0.9126:0.0:0.0874:0.0	.	126	Q9H598	VIAAT_HUMAN	A	126	ENSP00000217420:T126A	ENSP00000217420:T126A	T	+	1	0	SLC32A1	36787157	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.020000	0.93667	0.811000	0.34303	0.459000	0.35465	ACC	.	.	none		0.677	SLC32A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079206.1	NM_080552		G	37353743	A	G	37353743	3	3	27	1	0	0	0	0	1	0	0	0	14580	275	10	3	378	3	SLC32A1	20	37353743	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	1909975	37353743	25671777	978	11429											
PLCG1	5335	hgsc.bcm.edu	37	chr20	39802374	39802374	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaatttgcctttctgcgcttCgtggtgtatgaggaagacat	8	14	12	7	2	1	2	0	1	1	1	2	4	1	3	1	2	2	2	1	2	3	4	rs150104210		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:39802374C>T	ENST00000373271.1	+	29	3882	c.3477C>T	c.(3475-3477)ttC>ttT	p.F1159F	PLCG1_ENST00000244007.3_Silent_p.F1159F|PLCG1_ENST00000373272.2_Silent_p.F1159F|PLCG1_ENST00000608689.1_3'UTR	NM_182811.1	NP_877963.1	P19174	PLCG1_HUMAN	phospholipase C, gamma 1	1159	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				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)				TTCTGCGCTTCGTGGTGTATG	0.507											OREG0025953	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F1159F		Atlas-SNP	.											.	PLCG1	111	.	0			c.C3477T						PASS	.	C	,	0,4406		0,0,2203	137	116	123		3477,3477	-1.6	1	20	dbSNP_134	123	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	PLCG1	NM_002660.2,NM_182811.1	,	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	,	1159/1292,1159/1291	39802374	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	5335	exon29			GCGCTTCGTGGTG	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.3477C>T	20.37:g.39802374C>T		239	0	0	888	226	135	0.597345	NM_182811	B7ZLY7|B9EGH4|E1P5W4|Q2V575	Silent	SNP	ENST00000373271.1	37	CCDS13314.1																																																																																			C|1.000;T|0.000	0.000	weak		0.507	PLCG1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080514.3	NM_182811		T	39802374	C	T	39802374	2	4	27	1	0	0	0	0	0	0	0	1	12044	883	31	1		1	PLCG1	20	39802374	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2448631	39802374	23223146	979	11430											
CHD6	84181	hgsc.bcm.edu	37	chr20	40049579	40049579	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggttcttttcccttgagatgTtagtagtgggctccgtgaga	6	15	13	7	1	1	2	0	2	1	2	3	4	3	2	2	2	0	4	2	2	2	6	rs55864139	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:40049579T>A	ENST00000373233.3	-	31	5873	c.5696A>T	c.(5695-5697)aAc>aTc	p.N1899I		NM_032221.3	NP_115597.3	Q8TD26	CHD6_HUMAN	chromodomain helicase DNA binding protein 6	1899					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)				CCTTGAGATGTTAGTAGTGGG	0.517													T|||	32	0.00638978	0.0008	0.0216	5008	,	,		18821	0.0		0.0159	False		,,,				2504	0.0				p.N1899I		Atlas-SNP	.											.	CHD6	312	.	0			c.A5696T						PASS	.	T	ILE/ASN	18,4388	24.3+/-50.5	0,18,2185	140	139	139		5696	-6.9	0	20	dbSNP_129	139	125,8475	63.9+/-126.0	1,123,4176	yes	missense	CHD6	NM_032221.3	149	1,141,6361	AA,AT,TT		1.4535,0.4085,1.0995	benign	1899/2716	40049579	143,12863	2203	4300	6503	SO:0001583	missense	84181	exon31			GAGATGTTAGTAG	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.5696A>T	20.37:g.40049579T>A	ENSP00000362330:p.Asn1899Ile	281	0	0		252	125	0.496032	NM_032221	Q5JYQ0|Q5TGZ9|Q5TH00|Q5TH01|Q8IZR2|Q8WTY0|Q9H4H6|Q9H6D4|Q9NTT7|Q9P2L1	Missense_Mutation	SNP	ENST00000373233.3	37	CCDS13317.1	13	0.005952380952380952	0	0.0	4	0.011049723756906077	0	0.0	9	0.011873350923482849	T	3.272	-0.148971	0.06585	0.004085	0.014535	ENSG00000124177	ENST00000373233	D	0.85702	-2.02	5.86	-6.91	0.01649	.	1.661450	0.02896	N	0.134718	T	0.58221	0.2107	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.52895	-0.8514	10	0.34782	T	0.22	-0.042	4.3803	0.11290	0.0875:0.369:0.3003:0.2432	rs55864139;rs61752059	1899	Q8TD26	CHD6_HUMAN	I	1899	ENSP00000362330:N1899I	ENSP00000362330:N1899I	N	-	2	0	CHD6	39482993	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-0.483000	0.06536	-0.683000	0.05190	0.533000	0.62120	AAC	T|0.991;A|0.009	0.009	strong		0.517	CHD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079270.1			A	40049579	T	A	40049579	3	1	27	1	0	0	0	0	1	0	0	0	3331	1725	60	5	2479	5	CHD6	20	40049579	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	247205	40049579	22975941	980	11431											
SGK2	10110	hgsc.bcm.edu	37	chr20	42199296	42199296	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gggagcgccggttcctggagCcccgggccaggttctacgct	4	7	16	14	4	1	0	0	0	1	0	2	2	2	2	5	5	3	3	5	5	1	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:42199296C>T	ENST00000341458.4	+	6	799	c.580C>T	c.(580-582)Ccc>Tcc	p.P194S	SGK2_ENST00000373077.1_Missense_Mutation_p.P133S|SGK2_ENST00000485914.1_3'UTR|SGK2_ENST00000373092.3_Missense_Mutation_p.P134S|SGK2_ENST00000426287.1_Missense_Mutation_p.P160S|SGK2_ENST00000373100.1_Missense_Mutation_p.P134S|SGK2_ENST00000423407.3_Missense_Mutation_p.P134S	NM_016276.3	NP_057360.2	Q9HBY8	SGK2_HUMAN	serum/glucocorticoid regulated kinase 2	194	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|ion transmembrane transport (GO:0034220)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|response to oxidative stress (GO:0006979)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|sodium channel regulator activity (GO:0017080)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			GTTCCTGGAGCCCCGGGCCAG	0.627																																					p.P194S		Atlas-SNP	.											.	SGK2	50	.	0			c.C580T						PASS	.						59	61	61					20																	42199296		2203	4300	6503	SO:0001583	missense	10110	exon6			CTGGAGCCCCGGG	AF169034	CCDS13320.1, CCDS13321.1	20q13.2	2008-07-04			ENSG00000101049	ENSG00000101049			13900	protein-coding gene	gene with protein product		607589				10548550	Standard	NM_016276		Approved		uc002xkv.3	Q9HBY8	OTTHUMG00000033054	ENST00000341458.4:c.580C>T	20.37:g.42199296C>T	ENSP00000340608:p.Pro194Ser	77	0	0		87	4	0.045977	NM_016276	Q52PK5|Q5H8Y6|Q5H8Z1|Q5TZR3|Q9UKG6	Missense_Mutation	SNP	ENST00000341458.4	37	CCDS13320.1	.	.	.	.	.	.	.	.	.	.	C	15.50	2.852794	0.51270	.	.	ENSG00000101049	ENST00000373100;ENST00000373092;ENST00000373077;ENST00000412111;ENST00000423407;ENST00000341458;ENST00000426287	T;T;T;T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07;-0.07;-0.07;-0.07	4.92	4.92	0.64577	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.047564	0.85682	N	0.000000	T	0.48114	0.1482	N	0.17764	0.52	0.80722	D	1	B;B;P	0.37015	0.181;0.241;0.578	B;B;B	0.35971	0.049;0.143;0.215	T	0.44559	-0.9320	10	0.24483	T	0.36	.	17.7648	0.88475	0.0:1.0:0.0:0.0	.	160;194;134	Q9HBY8-3;Q9HBY8;Q9HBY8-2	.;SGK2_HUMAN;.	S	134;134;133;133;134;194;160	ENSP00000362192:P134S;ENSP00000362184:P134S;ENSP00000362168:P133S;ENSP00000396222:P133S;ENSP00000392795:P134S;ENSP00000340608:P194S;ENSP00000412214:P160S	ENSP00000340608:P194S	P	+	1	0	SGK2	41632710	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.643000	0.83403	2.658000	0.90341	0.655000	0.94253	CCC	.	.	none		0.627	SGK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080383.1			T	42199296	C	T	42199296	3	4	27	1	0	0	0	0	1	0	0	0	14224	739	26	2	602	2	SGK2	20	42199296	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2149717	42199296	20826224	981	11432											
MYBL2	4605	hgsc.bcm.edu	37	chr20	42338621	42338621	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aggtttgtaaccccagatcaGaagtactccatggacaacac	14	8	8	11	0	1	2	1	0	0	2	2	3	2	3	3	2	3	3	3	2	4	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:42338621G>C	ENST00000217026.4	+	10	1651	c.1524G>C	c.(1522-1524)caG>caC	p.Q508H	MYBL2_ENST00000396863.4_Missense_Mutation_p.Q484H	NM_002466.2	NP_002457.1	P10244	MYBB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 2	508					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)			CCCCAGATCAGAAGTACTCCA	0.622																																					p.Q508H		Atlas-SNP	.											.	MYBL2	82	.	0			c.G1524C						PASS	.						211	213	212					20																	42338621		2203	4300	6503	SO:0001583	missense	4605	exon10			AGATCAGAAGTAC		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.1524G>C	20.37:g.42338621G>C	ENSP00000217026:p.Gln508His	85	0	0		63	25	0.396825	NM_002466	B2RBS5|B7Z8D9|F8W6N6|Q53F07	Missense_Mutation	SNP	ENST00000217026.4	37	CCDS13322.1	.	.	.	.	.	.	.	.	.	.	G	13.61	2.289002	0.40494	.	.	ENSG00000101057	ENST00000396863;ENST00000217026	T;T	0.28069	1.63;1.63	4.86	4.86	0.63082	C-myb, C-terminal (1);	0.198115	0.46442	D	0.000282	T	0.09774	0.0240	N	0.00926	-1.1	0.40656	D	0.982083	B;B	0.33637	0.287;0.42	B;B	0.31686	0.078;0.134	T	0.30707	-0.9969	10	0.11794	T	0.64	-30.2082	12.2911	0.54819	0.0:0.0:0.8302:0.1697	.	484;508	F8W6N6;P10244	.;MYBB_HUMAN	H	484;508	ENSP00000380072:Q484H;ENSP00000217026:Q508H	ENSP00000217026:Q508H	Q	+	3	2	MYBL2	41772035	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.551000	0.60740	2.427000	0.82271	0.467000	0.42956	CAG	.	.	none		0.622	MYBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080408.1	NM_002466		C	42338621	G	C	42338621	3	2	27	1	0	0	0	0	1	0	0	0	10019	933	33	4	1562	4	MYBL2	20	42338621	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	139325	42338621	20686899	982	11433											
RBPJL	11317	hgsc.bcm.edu	37	chr20	43942698	43942698	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atgggcactctgcccaaggaGacttcccaccgcgagagggc	9	5	13	14	2	1	2	0	0	1	2	2	4	2	2	3	3	1	1	3	3	1	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:43942698G>A	ENST00000343694.3	+	8	853	c.781G>A	c.(781-783)Gac>Aac	p.D261N	RBPJL_ENST00000464504.1_3'UTR|RBPJL_ENST00000372743.1_Missense_Mutation_p.D261N|RBPJL_ENST00000372741.3_Missense_Mutation_p.D261N	NM_001281448.1|NM_001281449.1|NM_014276.2	NP_001268377.1|NP_001268378.1|NP_055091.2	Q9UBG7	RBPJL_HUMAN	recombination signal binding protein for immunoglobulin kappa J region-like	261					positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Myeloproliferative disorder(115;0.0122)				TGCCCAAGGAGACTTCCCACC	0.587																																					p.D261N		Atlas-SNP	.											.	RBPJL	67	.	0			c.G781A						PASS	.						129	127	127					20																	43942698		2203	4300	6503	SO:0001583	missense	11317	exon8			CAAGGAGACTTCC	AB024964	CCDS13349.1, CCDS63283.1, CCDS63284.1	20q13.12	2013-10-18	2007-02-26	2007-02-26	ENSG00000124232	ENSG00000124232			13761	protein-coding gene	gene with protein product			"recombining binding protein suppressor of hairless (Drosophila)-like"	RBPSUHL		9929984	Standard	NM_014276		Approved	RBP-L, SUH, SUHL	uc002xns.3	Q9UBG7	OTTHUMG00000033055	ENST00000343694.3:c.781G>A	20.37:g.43942698G>A	ENSP00000341243:p.Asp261Asn	71	0	0		53	22	0.415094	NM_014276	O95723|Q5QPU9|Q5QPV0|Q9ULV9	Missense_Mutation	SNP	ENST00000343694.3	37	CCDS13349.1	.	.	.	.	.	.	.	.	.	.	G	15.14	2.744830	0.49151	.	.	ENSG00000124232	ENST00000372743;ENST00000372741;ENST00000343694	T;T;T	0.29397	1.57;1.57;1.57	5.25	5.25	0.73442	Beta-trefoil (2);	0.129253	0.51477	D	0.000092	T	0.28962	0.0719	N	0.25485	0.75	0.46260	D	0.998959	P;B	0.47484	0.896;0.303	P;B	0.46172	0.506;0.128	T	0.01334	-1.1382	10	0.36615	T	0.2	-39.329	16.168	0.81785	0.0:0.0:1.0:0.0	.	261;261	Q5QPV1;Q9UBG7	.;RBPJL_HUMAN	N	261	ENSP00000361828:D261N;ENSP00000361826:D261N;ENSP00000341243:D261N	ENSP00000341243:D261N	D	+	1	0	RBPJL	43376112	1.000000	0.71417	1.000000	0.80357	0.313000	0.28021	6.631000	0.74277	2.724000	0.93272	0.563000	0.77884	GAC	.	.	none		0.587	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276		A	43942698	G	A	43942698	3	1	27	1	0	0	0	0	1	0	0	0	13177	942	33	2	811	2	RBPJL	20	43942698	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1604077	43942698	19082822	983	11434											
PTGIS	5740	hgsc.bcm.edu	37	chr20	48156249	48156249	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tcaattccgtaaagagtcagGtagccggctctgggggcggc	8	8	15	10	3	3	1	2	0	1	1	4	1	4	1	2	5	1	3	2	5	4	3	rs61322884	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:48156249G>A	ENST00000244043.4	-	5	560	c.531C>T	c.(529-531)taC>taT	p.Y177Y	PTGIS_ENST00000478971.1_5'UTR	NM_000961.3	NP_000952.1	Q16647	PTGIS_HUMAN	prostaglandin I2 (prostacyclin) synthase	177					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)	AAAGAGTCAGGTAGCCGGCTC	0.602													G|||	56	0.0111821	0.0015	0.0173	5008	,	,		16309	0.0		0.0358	False		,,,				2504	0.0061				p.Y177Y		Atlas-SNP	.											.	PTGIS	60	.	0			c.C531T						PASS	.	G		17,4387	21.2+/-45.6	0,17,2185	34	34	34		531	4.2	1	20	dbSNP_129	34	259,8341	98.6+/-160.1	2,255,4043	no	coding-synonymous	PTGIS	NM_000961.3		2,272,6228	AA,AG,GG		3.0116,0.386,2.1224		177/501	48156249	276,12728	2202	4300	6502	SO:0001819	synonymous_variant	5740	exon5			AGTCAGGTAGCCG		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.531C>T	20.37:g.48156249G>A		36	0	0		31	19	0.612903	NM_000961	Q3MII8|Q9HAX2|Q9HAX3|Q9HAX4	Silent	SNP	ENST00000244043.4	37	CCDS13419.1																																																																																			G|0.982;A|0.018	0.018	strong		0.602	PTGIS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080496.2			A	48156249	G	A	48156249	2	1	27	1	0	0	0	0	0	0	0	1	12765	1256	44	2		2	PTGIS	20	48156249	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	4213551	48156249	14869271	984	11435											
ZNF217	7764	hgsc.bcm.edu	37	chr20	52192417	52192417	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgggaggcagcgcctgcgaCggatacacacagtcctgcgg	8	6	15	12	4	0	0	0	0	0	0	1	3	1	2	2	4	4	1	2	4	1	2	rs45439395	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:52192417C>T	ENST00000371471.2	-	4	3311	c.2886G>A	c.(2884-2886)ccG>ccA	p.P962P	RP4-724E16.2_ENST00000424252.1_RNA|ZNF217_ENST00000302342.3_Silent_p.P962P			O75362	ZN217_HUMAN	zinc finger protein 217	962					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)			GCGCCTGCGACGGATACACAC	0.562													C|||	11	0.00219649	0.0	0.0014	5008	,	,		20692	0.0		0.0099	False		,,,				2504	0.0				p.P962P		Atlas-SNP	.											.	ZNF217	227	.	0			c.G2886A						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	141	113	122		2886	-7.8	0	20	dbSNP_127	122	63,8537	39.8+/-96.3	0,63,4237	no	coding-synonymous	ZNF217	NM_006526.2		0,65,6438	TT,TC,CC		0.7326,0.0454,0.4998		962/1049	52192417	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	7764	exon3			CTGCGACGGATAC	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.2886G>A	20.37:g.52192417C>T		106	0	0		99	55	0.555556	NM_006526	E1P5Y6|Q14DB8	Silent	SNP	ENST00000371471.2	37	CCDS13443.1																																																																																			C|0.997;T|0.003	0.003	strong		0.562	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		T	52192417	C	T	52192417	2	4	27	1	0	0	0	0	0	0	0	1	17787	523	19	1		1	ZNF217	20	52192417	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	4036168	52192417	10833103	985	11436											
ZNF217	7764	hgsc.bcm.edu	37	chr20	52193542	52193542	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgagaggacagcgctgccCagaacattctgaaaaacaga	15	5	12	9	1	1	4	0	2	1	3	1	6	1	5	1	2	4	1	1	2	3	1	rs61748380	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:52193542C>T	ENST00000371471.2	-	4	2186	c.1761G>A	c.(1759-1761)ctG>ctA	p.L587L	RP4-724E16.2_ENST00000424252.1_RNA|ZNF217_ENST00000302342.3_Silent_p.L587L			O75362	ZN217_HUMAN	zinc finger protein 217	587					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)			CAGCGCTGCCCAGAACATTCT	0.428													C|||	9	0.00179712	0.0	0.0	5008	,	,		20409	0.0		0.0089	False		,,,				2504	0.0				p.L587L		Atlas-SNP	.											.	ZNF217	227	.	0			c.G1761A						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	121	113	116		1761	1.9	1	20	dbSNP_129	116	24,8576	17.3+/-56.4	0,24,4276	no	coding-synonymous	ZNF217	NM_006526.2		0,27,6476	TT,TC,CC		0.2791,0.0681,0.2076		587/1049	52193542	27,12979	2203	4300	6503	SO:0001819	synonymous_variant	7764	exon3			GCTGCCCAGAACA	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.1761G>A	20.37:g.52193542C>T		126	0	0		122	68	0.557377	NM_006526	E1P5Y6|Q14DB8	Silent	SNP	ENST00000371471.2	37	CCDS13443.1																																																																																			C|0.998;T|0.002	0.002	strong		0.428	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		T	52193542	C	T	52193542	2	4	27	1	0	0	0	0	0	0	0	1	17787	581	21	2		2	ZNF217	20	52193542	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1125	52193542	10831978	986	11437											
ZBP1	81030	hgsc.bcm.edu	37	chr20	56189956	56189956	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggcctacctgggcggtaaatCgtccatgctttggactgctc	6	11	12	12	2	0	0	0	0	0	0	3	1	1	1	3	4	3	3	3	4	3	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:56189956C>T	ENST00000371173.3	-	4	666	c.489G>A	c.(487-489)acG>acA	p.T163T	ZBP1_ENST00000541799.1_Silent_p.T163T|ZBP1_ENST00000343535.4_Silent_p.T163T|ZBP1_ENST00000538947.1_5'Flank|ZBP1_ENST00000395822.3_Silent_p.T88T|ZBP1_ENST00000340462.4_Silent_p.T140T	NM_001160417.1|NM_030776.2	NP_001153889.1|NP_110403.2	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1	163					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)			GGCGGTAAATCGTCCATGCTT	0.552																																					p.T163T		Atlas-SNP	.											ZBP1,NS,carcinoma,0,1	ZBP1	65	1	0			c.G489A						PASS	.						161	127	139					20																	56189956		2203	4300	6503	SO:0001819	synonymous_variant	81030	exon4			GTAAATCGTCCAT	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.489G>A	20.37:g.56189956C>T		187	0	0		135	28	0.207407	NM_001160419	A2A2F7|B3KVA1|F5GYT1|Q5JY39|Q9BYW4	Silent	SNP	ENST00000371173.3	37	CCDS13461.1																																																																																			.	.	none		0.552	ZBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079849.1	NM_030776		T	56189956	C	T	56189956	2	4	27	1	0	0	0	0	0	0	0	1	17536	871	31	1		1	ZBP1	20	56189956	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3996414	56189956	6835564	987	11438											
PHACTR3	116154	hgsc.bcm.edu	37	chr20	58342349	58342349	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgactccctggacagtcCtcccagacctctggagagat	8	8	11	14	0	1	3	0	1	1	2	4	6	4	5	4	3	0	1	4	3	0	0	rs73598372	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:58342349C>T	ENST00000371015.1	+	5	1117	c.650C>T	c.(649-651)cCt>cTt	p.P217L	PHACTR3_ENST00000395636.2_Missense_Mutation_p.P176L|PHACTR3_ENST00000355648.4_Missense_Mutation_p.P176L|PHACTR3_ENST00000395639.4_Intron|PHACTR3_ENST00000361300.4_Intron|PHACTR3_ENST00000359926.3_Missense_Mutation_p.P214L|PHACTR3_ENST00000541461.1_Missense_Mutation_p.P176L	NM_001281507.1|NM_080672.3	NP_001268436.1|NP_542403.1	Q96KR7	PHAR3_HUMAN	phosphatase and actin regulator 3	217	Pro-rich.					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)			CTGGACAGTCCTCCCAGACCT	0.612													C|||	102	0.0203674	0.0	0.0043	5008	,	,		16709	0.0377		0.0129	False		,,,				2504	0.0491				p.P217L		Atlas-SNP	.											.	PHACTR3	104	.	0			c.C650T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,	12,4394	19.1+/-41.9	0,12,2191	42	41	41		641,527,650,527,	3.7	1	20	dbSNP_130	41	104,8496	55.6+/-116.7	0,104,4196	yes	missense,missense,missense,missense,intron	PHACTR3	NM_001199505.1,NM_001199506.1,NM_080672.3,NM_183244.1,NM_183246.1	98,98,98,98,	0,116,6387	TT,TC,CC		1.2093,0.2724,0.8919	benign,benign,benign,benign,	214/557,176/519,217/560,176/519,	58342349	116,12890	2203	4300	6503	SO:0001583	missense	116154	exon5			ACAGTCCTCCCAG	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.650C>T	20.37:g.58342349C>T	ENSP00000360054:p.Pro217Leu	128	0	0		109	58	0.53211	NM_080672	B1AKX0|B1AN68|B1AN69|B2RB46|Q32P33|Q707P6|Q9H4T4	Missense_Mutation	SNP	ENST00000371015.1	37	CCDS13480.1	34	0.015567765567765568	0	0.0	2	0.0055248618784530384	23	0.04020979020979021	9	0.011873350923482849	C	15.45	2.838151	0.50951	0.002724	0.012093	ENSG00000087495	ENST00000359926;ENST00000371015;ENST00000541461;ENST00000355648;ENST00000395636	T;T;T;T;T	0.26518	1.73;1.77;1.79;1.79;1.79	4.7	3.74	0.42951	.	0.297029	0.25714	N	0.028791	T	0.04634	0.0126	L	0.33485	1.01	0.80722	D	1	B;B	0.18461	0.028;0.006	B;B	0.13407	0.009;0.004	T	0.03651	-1.1016	10	0.52906	T	0.07	-9.1105	12.1901	0.54266	0.0:0.9151:0.0:0.0849	.	217;214	Q96KR7;B1AKX0	PHAR3_HUMAN;.	L	214;217;176;176;176	ENSP00000353002:P214L;ENSP00000360054:P217L;ENSP00000442483:P176L;ENSP00000347866:P176L;ENSP00000378998:P176L	ENSP00000347866:P176L	P	+	2	0	PHACTR3	57775744	0.991000	0.36638	1.000000	0.80357	0.991000	0.79684	3.791000	0.55469	2.166000	0.68216	0.460000	0.39030	CCT	C|0.989;T|0.011	0.011	strong		0.612	PHACTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079923.3	NM_080672		T	58342349	C	T	58342349	3	4	27	1	0	0	0	0	1	0	0	0	11820	681	24	2	668	2	PHACTR3	20	58342349	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2152393	58342349	4683171	988	11439											
PPP1R3D	5509	hgsc.bcm.edu	37	chr20	58514312	58514312	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gtgccctcggggcctgcgggCccgcgccaccgcgccaccgc	2	3	15	21	7	0	0	0	0	0	0	1	0	0	0	7	3	2	0	7	3	0	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:58514312C>A	ENST00000370996.3	-	1	1040	c.675G>T	c.(673-675)ggG>ggT	p.G225G	FAM217B_ENST00000358293.3_Intron|FAM217B_ENST00000360816.3_5'Flank	NM_006242.3	NP_006233.1	O95685	PPR3D_HUMAN	protein phosphatase 1, regulatory subunit 3D	225	CBM21. {ECO:0000255|PROSITE- ProRule:PRU00491}.				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)			GGCCTGCGGGCCCGCGCCACC	0.697																																					p.G225G		Atlas-SNP	.											.	PPP1R3D	23	.	0			c.G675T						PASS	.						32	34	33					20																	58514312		2201	4299	6500	SO:0001819	synonymous_variant	5509	exon1			TGCGGGCCCGCGC	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.675G>T	20.37:g.58514312C>A		4	0	0		17	12	0.705882	NM_006242	Q6DK02	Silent	SNP	ENST00000370996.3	37	CCDS13483.1																																																																																			.	.	none		0.697	PPP1R3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079940.2	NM_006242		A	58514312	C	A	58514312	2	1	27	1	0	0	0	0	0	0	0	1	12386	726	26	4		4	PPP1R3D	20	58514312	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	171963	58514312	4511208	989	11440											
ADRM1	11047	hgsc.bcm.edu	37	chr20	60883192	60883192	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagtcgctgccgcagaccgcGgatgagatccagaataccct	10	6	12	13	4	0	3	0	1	0	3	2	6	1	4	4	1	2	2	4	1	2	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:60883192G>A	ENST00000253003.2	+	8	1018	c.972G>A	c.(970-972)gcG>gcA	p.A324A	RP11-157P1.4_ENST00000414042.1_RNA|LAMA5_ENST00000492698.1_5'UTR	NM_007002.2|NM_175573.1	NP_008933.2|NP_783163.1	Q16186	ADRM1_HUMAN	adhesion regulating molecule 1	324					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)			CGCAGACCGCGGATGAGATCC	0.652																																					p.A324A		Atlas-SNP	.											.	ADRM1	28	.	0			c.G972A						PASS	.						39	39	39					20																	60883192		2199	4295	6494	SO:0001819	synonymous_variant	11047	exon8			GACCGCGGATGAG	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.972G>A	20.37:g.60883192G>A		72	0	0		48	12	0.25	NM_175573	A0PKB1|Q96FJ7|Q9H1P2	Silent	SNP	ENST00000253003.2	37	CCDS13496.1																																																																																			.	.	none		0.652	ADRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080007.1			A	60883192	G	A	60883192	2	1	27	1	0	0	0	0	0	0	0	1	345	1103	39	1		1	ADRM1	20	60883192	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2368880	60883192	2142328	990	11441											
LAMA5	3911	hgsc.bcm.edu	37	chr20	60887028	60887028	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gggggcaccatcggcgaagcCcgcttgagttttcacttcag	7	9	13	12	3	2	1	2	1	0	0	3	2	2	1	2	3	1	3	2	3	1	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:60887028C>T	ENST00000252999.3	-	70	9649	c.9583G>A	c.(9583-9585)Ggc>Agc	p.G3195S	LAMA5_ENST00000492698.1_5'Flank	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	3195	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)			TCGGCGAAGCCCGCTTGAGTT	0.647																																					p.G3195S		Atlas-SNP	.											.	LAMA5	268	.	0			c.G9583A						PASS	.						64	69	67					20																	60887028		2203	4298	6501	SO:0001583	missense	3911	exon70			CGAAGCCCGCTTG	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.9583G>A	20.37:g.60887028C>T	ENSP00000252999:p.Gly3195Ser	80	0	0		51	5	0.0980392	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	c	4.219	0.039521	0.08148	.	.	ENSG00000130702	ENST00000252999	T	0.76709	-1.04	4.62	1.51	0.23008	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.886282	0.09702	N	0.766863	T	0.45538	0.1347	N	0.01352	-0.895	0.09310	N	1	B	0.10296	0.003	B	0.17098	0.017	T	0.35574	-0.9783	10	0.06757	T	0.87	.	7.2199	0.25981	0.0:0.4457:0.3986:0.1557	.	3195	O15230	LAMA5_HUMAN	S	3195	ENSP00000252999:G3195S	ENSP00000252999:G3195S	G	-	1	0	LAMA5	60320423	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	-0.515000	0.06290	0.049000	0.15920	0.556000	0.70494	GGC	.	.	none		0.647	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		T	60887028	C	T	60887028	3	4	27	1	0	0	0	0	1	0	0	0	8618	623	22	2	1548	2	LAMA5	20	60887028	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3836	60887028	2138492	991	11442											
LAMA5	3911	hgsc.bcm.edu	37	chr20	60889385	60889385	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caggctgacagctgcgaactGctccccaatgtcctcatcga	9	8	9	15	2	1	1	1	1	0	0	4	3	3	1	3	1	4	3	3	1	2	0	rs117480847	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:60889385G>T	ENST00000252999.3	-	62	8545	c.8479C>A	c.(8479-8481)Cag>Aag	p.Q2827K		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2827	Laminin G-like 1. {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)			GCTGCGAACTGCTCCCCAATG	0.627													.|||	61	0.0121805	0.0	0.0115	5008	,	,		16760	0.0		0.0189	False		,,,				2504	0.0348				p.Q2827K		Atlas-SNP	.											LAMA5,NS,haematopoietic_neoplasm,0,1	LAMA5	268	1	0			c.C8479A						scavenged	.	G	LYS/GLN	21,4383	28.1+/-56.4	0,21,2181	113	97	103		8479	2.6	1	20	dbSNP_132	103	174,8422	79.8+/-142.4	0,174,4124	yes	missense	LAMA5	NM_005560.3	53	0,195,6305	TT,TG,GG		2.0242,0.4768,1.5	benign	2827/3696	60889385	195,12805	2202	4298	6500	SO:0001583	missense	3911	exon62			CGAACTGCTCCCC	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.8479C>A	20.37:g.60889385G>T	ENSP00000252999:p.Gln2827Lys	94	1	0.0106383		75	36	0.48	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	20	0.009157509157509158	0	0.0	5	0.013812154696132596	0	0.0	15	0.01978891820580475	g	8.022	0.759813	0.15846	0.004768	0.020242	ENSG00000130702	ENST00000252999	T	0.78126	-1.15	3.61	2.62	0.31277	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.621906	0.16406	U	0.215834	T	0.51517	0.1679	L	0.40543	1.245	0.80722	D	1	B	0.33345	0.409	B	0.34489	0.184	T	0.49808	-0.8900	10	0.15952	T	0.53	.	11.3438	0.49548	0.0:0.3552:0.6448:0.0	.	2827	O15230	LAMA5_HUMAN	K	2827	ENSP00000252999:Q2827K	ENSP00000252999:Q2827K	Q	-	1	0	LAMA5	60322780	1.000000	0.71417	1.000000	0.80357	0.099000	0.18886	1.300000	0.33436	0.469000	0.27268	0.457000	0.33378	CAG	G|0.986;T|0.014	0.014	strong		0.627	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		T	60889385	G	T	60889385	3	4	27	1	0	0	0	0	1	0	0	0	8618	1328	46	4	2684	4	LAMA5	20	60889385	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2357	60889385	2136135	992	11443											
LAMA5	3911	hgsc.bcm.edu	37	chr20	60898654	60898654	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aagagcaagttggggtcaccGttgccgctgcagtcgcatgg	8	8	15	10	3	1	1	1	0	0	1	2	1	1	1	2	3	3	6	2	3	2	2	rs11696243	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:60898654G>A	ENST00000252999.3	-	45	5988	c.5922C>T	c.(5920-5922)aaC>aaT	p.N1974N		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1974	Laminin EGF-like 19. {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)			TGGGGTCACCGTTGCCGCTGC	0.697													.|||	60	0.0119808	0.0015	0.0216	5008	,	,		13277	0.0		0.0388	False		,,,				2504	0.0041				p.N1974N		Atlas-SNP	.											.	LAMA5	268	.	0			c.C5922T						PASS	.	G		32,4354		0,32,2161	21	29	26		5922	-2.2	0.2	20	dbSNP_120	26	256,8322		4,248,4037	no	coding-synonymous	LAMA5	NM_005560.3		4,280,6198	AA,AG,GG		2.9844,0.7296,2.2215		1974/3696	60898654	288,12676	2193	4289	6482	SO:0001819	synonymous_variant	3911	exon45			GTCACCGTTGCCG	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.5922C>T	20.37:g.60898654G>A		58	0	0		97	47	0.484536	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			G|0.980;A|0.020	0.020	strong		0.697	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		A	60898654	G	A	60898654	2	1	27	1	0	0	0	0	0	0	0	1	8618	1136	40	1		1	LAMA5	20	60898654	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	9269	60898654	2126866	993	11444											
LAMA5	3911	hgsc.bcm.edu	37	chr20	60901762	60901762	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgcagctgcccacggtgaaCgtggccaggcgtggggtatg	6	7	17	11	3	0	1	0	1	0	0	0	1	0	1	2	5	4	3	2	5	2	1	rs11699758	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:60901762C>T	ENST00000252999.3	-	40	5335	c.5269G>A	c.(5269-5271)Gtt>Att	p.V1757I		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1757	Laminin IV type A. {ECO:0000255|PROSITE- ProRule:PRU00458}.				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)			CCACGGTGAACGTGGCCAGGC	0.657													C|||	73	0.0145767	0.0121	0.0231	5008	,	,		18170	0.0		0.0368	False		,,,				2504	0.0041				p.V1757I		Atlas-SNP	.											.	LAMA5	268	.	0			c.G5269A						PASS	.	C	ILE/VAL	99,4307	79.3+/-117.8	2,95,2106	71	54	60		5269	-1	0	20	dbSNP_120	60	254,8344	99.0+/-160.6	3,248,4048	yes	missense	LAMA5	NM_005560.3	29	5,343,6154	TT,TC,CC		2.9542,2.2469,2.7145	benign	1757/3696	60901762	353,12651	2203	4299	6502	SO:0001583	missense	3911	exon40			GGTGAACGTGGCC	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.5269G>A	20.37:g.60901762C>T	ENSP00000252999:p.Val1757Ile	170	0	0		144	79	0.548611	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	42	0.019230769230769232	8	0.016260162601626018	14	0.03867403314917127	0	0.0	20	0.026385224274406333	C	0.464	-0.887824	0.02511	0.022469	0.029542	ENSG00000130702	ENST00000252999	T	0.36157	1.27	5.12	-1.04	0.10068	Laminin B type IV (2);Laminin B, subgroup (1);	0.497398	0.22077	N	0.064941	T	0.03915	0.0110	N	0.17474	0.49	0.09310	N	1	B	0.13145	0.007	B	0.10450	0.005	T	0.13953	-1.0490	10	0.25106	T	0.35	.	7.414	0.27034	0.0:0.4374:0.2158:0.3468	rs11699758	1757	O15230	LAMA5_HUMAN	I	1757	ENSP00000252999:V1757I	ENSP00000252999:V1757I	V	-	1	0	LAMA5	60335157	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.028000	0.12350	-0.054000	0.13266	-0.355000	0.07637	GTT	C|0.974;T|0.026	0.026	strong		0.657	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		T	60901762	C	T	60901762	3	4	27	1	0	0	0	0	1	0	0	0	8618	536	19	1	5982	1	LAMA5	20	60901762	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3108	60901762	2123758	994	11445											
C20orf151	140893	hgsc.bcm.edu	37	chr20	60987921	60987921	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtctgtctcatccagttcgtCggactctggtctcagcactt	5	14	9	13	2	4	0	2	0	4	0	9	1	5	1	1	2	1	2	1	2	0	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:60987921C>T	ENST00000252998.1	-	12	1867	c.1711G>A	c.(1711-1713)Gac>Aac	p.D571N		NM_080833.2	NP_543023.2	Q8NC74	RB8NL_HUMAN	RBBP8 N-terminal like	571						extracellular space (GO:0005615)											TCCAGTTCGTCGGACTCTGGT	0.657																																					p.D571N		Atlas-SNP	.											.	.	.	.	0			c.G1711A						PASS	.						129	106	114					20																	60987921		2203	4300	6503	SO:0001583	missense	140893	exon12			GTTCGTCGGACTC	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.1711G>A	20.37:g.60987921C>T	ENSP00000252998:p.Asp571Asn	110	0	0		81	31	0.382716	NM_080833	B2RP98|Q8N4Z9|Q9BR75|Q9H0Y9	Missense_Mutation	SNP	ENST00000252998.1	37	CCDS13498.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.846159	0.51164	.	.	ENSG00000130701	ENST00000252998	T	0.20598	2.06	3.52	2.56	0.30785	.	0.908502	0.09136	N	0.843633	T	0.19765	0.0475	L	0.46157	1.445	0.09310	N	1	D	0.61080	0.989	P	0.44447	0.45	T	0.12218	-1.0556	10	0.18276	T	0.48	-0.964	8.456	0.32899	0.0:0.8818:0.0:0.1182	.	571	Q8NC74	CT151_HUMAN	N	571	ENSP00000252998:D571N	ENSP00000252998:D571N	D	-	1	0	C20orf151	60421316	0.001000	0.12720	0.001000	0.08648	0.005000	0.04900	1.089000	0.30890	0.783000	0.33636	-0.339000	0.08088	GAC	.	.	none		0.657	RBBP8NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080029.1	NM_080833		T	60987921	C	T	60987921	3	4	27	1	0	0	0	0	1	0	0	0	2093	884	31	1	295	1	C20orf151	20	60987921	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	86159	60987921	2037599	995	11446											
PRIC285	85441	hgsc.bcm.edu	37	chr20	62194238	62194238	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcgccctgcagctgcccctgCggcgtccgtgacgcctccca	3	6	12	20	5	0	1	0	1	0	0	2	1	2	1	6	1	4	2	6	1	0	0	rs34996572	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:62194238C>T	ENST00000467148.1	-	8	6006	c.5937G>A	c.(5935-5937)ccG>ccA	p.P1979P	HELZ2_ENST00000427522.2_Silent_p.P1410P	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	1979					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)										GCTGCCCCTGCGGCGTCCGTG	0.657													C|||	71	0.0141773	0.0008	0.0303	5008	,	,		15702	0.001		0.0408	False		,,,				2504	0.0072				p.P1979P		Atlas-SNP	.											.	.	.	.	0			c.G5937A						PASS	.	C	,	23,4271		0,23,2124	10	11	11		5937,4230	-9.2	0	20	dbSNP_126	11	243,8151		3,237,3957	no	coding-synonymous,coding-synonymous	PRIC285	NM_001037335.2,NM_033405.3	,	3,260,6081	TT,TC,CC		2.8949,0.5356,2.0965	,	1979/2650,1410/2081	62194238	266,12422	2147	4197	6344	SO:0001819	synonymous_variant	85441	exon9			CCCCTGCGGCGTC	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.5937G>A	20.37:g.62194238C>T		83	0	0		99	38	0.383838	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	37	CCDS33508.1																																																																																			C|0.984;T|0.016	0.016	strong		0.657	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		T	62194238	C	T	62194238	2	4	27	1	0	0	0	0	0	0	0	1	12497	755	27	1		1	PRIC285	20	62194238	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1206317	62194238	831282	996	11447											
RTEL1	51750	hgsc.bcm.edu	37	chr20	62294236	62294236	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctgtcatttctacaacaacGtagaaggtacaagcagctgg	13	9	9	10	1	2	1	1	0	1	1	2	1	2	1	1	2	6	4	1	2	7	4	rs184051277	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr20:62294236G>A	ENST00000360203.5	+	6	857	c.532G>A	c.(532-534)Gta>Ata	p.V178I	RTEL1_ENST00000370018.3_Missense_Mutation_p.V178I|RTEL1_ENST00000318100.4_Missense_Mutation_p.V178I|RTEL1_ENST00000508582.2_Missense_Mutation_p.V202I|RTEL1-TNFRSF6B_ENST00000482936.1_Missense_Mutation_p.V178I					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)			CTACAACAACGTAGAAGGTAC	0.577													G|||	2	0.000399361	0.0	0.0014	5008	,	,		18896	0.001		0.0	False		,,,				2504	0.0				p.V202I		Atlas-SNP	.											.	RTEL1	114	.	0			c.G604A						PASS	.						85	74	78					20																	62294236		2203	4300	6503	SO:0001583	missense	51750	exon6			AACAACGTAGAAG	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.532G>A	20.37:g.62294236G>A	ENSP00000353332:p.Val178Ile	69	0	0		83	29	0.349398	NM_032957		Missense_Mutation	SNP	ENST00000360203.5	37		1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	13.04	2.119146	0.37436	.	.	ENSG00000258366	ENST00000370018;ENST00000318100;ENST00000508582;ENST00000360203;ENST00000356810	T;T;T;T;T	0.70986	-0.53;-0.53;-0.53;-0.53;-0.53	5.05	4.1	0.47936	DEAD2 (1);Helicase-like, DEXD box c2 type (1);Helicase, superfamily 1/2, ATP-binding domain, DinG/Rad3-type (1);	0.137530	0.47455	D	0.000232	T	0.63534	0.2519	L	0.49571	1.57	0.42644	D	0.993425	B;B;B;B	0.33637	0.237;0.129;0.42;0.108	B;B;B;B	0.29942	0.105;0.059;0.109;0.015	T	0.64525	-0.6387	10	0.42905	T	0.14	-13.4976	14.0662	0.64831	0.0739:0.0:0.9261:0.0	.	202;202;178;178	Q9NZ71-7;D6RBA3;Q9NZ71;Q9NZ71-6	.;.;RTEL1_HUMAN;.	I	178;178;202;178;228	ENSP00000359035:V178I;ENSP00000322287:V178I;ENSP00000424307:V202I;ENSP00000353332:V178I;ENSP00000349265:V228I	ENSP00000349265:V228I	V	+	1	0	AL353715.1	61764680	1.000000	0.71417	0.746000	0.31095	0.277000	0.26821	4.731000	0.62022	1.266000	0.44231	0.511000	0.50034	GTA	G|1.000;A|0.000	0.000	strong		0.577	RTEL1-011	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000289781.1	NM_032957		A	62294236	G	A	62294236	3	1	27	1	0	0	0	0	1	0	0	0	13735	1145	40	1	550	1	RTEL1	20	62294236	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	99998	62294236	731284	997	11448											
BAGE2	85319	hgsc.bcm.edu	37	chr21	11058316	11058316	+	RNA	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctccaaagtgcttacaaaatGcacatcgctgaaaggggtaa	15	8	9	9	1	0	1	0	1	0	0	2	1	1	1	1	2	3	4	1	2	6	2	rs3877860		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:11058316G>T	ENST00000470054.1	-	0	331							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)		CTTACAAAATGCACATCGCTG	0.388																																					p.H42N		Atlas-SNP	.											.	.	.	.	0			c.C124A						PASS	.																																					85318	exon3			CAAAATGCACATC	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		21.37:g.11058316G>T		198	0	0		238	13	0.0546218	NM_182481	A8K925|Q08ER0	Missense_Mutation	SNP	ENST00000470054.1	37																																																																																				.	.	weak		0.388	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482		T	11058316	G	T	11058316	1	4	27	0	1	0	0	0	0	0	0	0	1292	1319	46	4		4	BAGE2	21	11058316	RNA	SNP	G	TCGA-G8-6909-01A-11D-2210-10		11058316	37071579	998	11449											
SAMSN1	64092	hgsc.bcm.edu	37	chr21	15873026	15873026	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtccacatccccattggtgTtttgcaaataatgtctatga	10	15	7	9	0	1	1	0	1	1	0	3	1	3	1	3	1	1	2	3	1	3	5	rs62227165	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:15873026T>C	ENST00000400566.1	-	6	673	c.592A>G	c.(592-594)Aca>Gca	p.T198A	SAMSN1_ENST00000285670.2_Missense_Mutation_p.T266A|SAMSN1_ENST00000400564.1_Missense_Mutation_p.T30A|SAMSN1_ENST00000463807.1_5'Flank	NM_022136.4	NP_071419.3	Q9NSI8	SAMN1_HUMAN	SAM domain, SH3 domain and nuclear localization signals 1	198	SH3.				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)		CCCATTGGTGTTTTGCAAATA	0.378													T|||	30	0.00599042	0.0008	0.0202	5008	,	,		20252	0.0		0.0149	False		,,,				2504	0.0				p.T266A		Atlas-SNP	.											.	SAMSN1	112	.	0			c.A796G						PASS	.	T	ALA/THR	21,3673		0,21,1826	193	170	177		592	5.8	1	21	dbSNP_129	177	203,8003		2,199,3902	yes	missense	SAMSN1	NM_022136.3	58	2,220,5728	CC,CT,TT		2.4738,0.5685,1.8824	probably-damaging	198/374	15873026	224,11676	1847	4103	5950	SO:0001583	missense	64092	exon7			TTGGTGTTTTGCA	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.592A>G	21.37:g.15873026T>C	ENSP00000383411:p.Thr198Ala	188	0	0		223	141	0.632287	NM_001256370	B3KWJ3|F8WAA1|Q8NFF7|Q9C041	Missense_Mutation	SNP	ENST00000400566.1	37	CCDS42906.1	21	0.009615384615384616	0	0.0	8	0.022099447513812154	0	0.0	13	0.017150395778364115	T	21.6	4.169451	0.78452	0.005685	0.024738	ENSG00000155307	ENST00000285670;ENST00000400566;ENST00000400564	T;T;T	0.29917	3.22;3.22;1.55	5.77	5.77	0.91146	Src homology-3 domain (2);Variant SH3 (1);	0.046352	0.85682	D	0.000000	T	0.26810	0.0656	N	0.21142	0.635	0.44067	D	0.996815	P;D;D	0.71674	0.954;0.998;0.983	P;D;P	0.80764	0.761;0.994;0.895	T	0.26538	-1.0100	10	0.59425	D	0.04	-17.7917	16.0902	0.81086	0.0:0.0:0.0:1.0	rs62227165	30;266;198	Q9NSI8-2;F8WAA1;Q9NSI8	.;.;SAMN1_HUMAN	A	266;198;30	ENSP00000285670:T266A;ENSP00000383411:T198A;ENSP00000383409:T30A	ENSP00000285670:T266A	T	-	1	0	SAMSN1	14794897	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.226000	0.58606	2.194000	0.70268	0.528000	0.53228	ACA	T|0.985;C|0.015	0.015	strong		0.378	SAMSN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157914.1			C	15873026	T	C	15873026	3	2	27	1	0	0	0	0	1	0	0	0	13845	1725	60	3	541	3	SAMSN1	21	15873026	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	4814710	15873026	32256869	999	11450											
ITSN1	6453	hgsc.bcm.edu	37	chr21	35147359	35147359	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaaattgagagcacaaacAaatctagagagttgagaatt	20	8	9	4	0	1	4	0	2	1	4	1	7	1	4	0	0	2	2	0	0	6	4			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:35147359A>C	ENST00000381318.3	+	14	1831	c.1543A>C	c.(1543-1545)Aaa>Caa	p.K515Q	ITSN1_ENST00000399353.1_Missense_Mutation_p.K478Q|ITSN1_ENST00000399352.1_Missense_Mutation_p.K515Q|ITSN1_ENST00000379960.5_Missense_Mutation_p.K515Q|ITSN1_ENST00000399367.3_Missense_Mutation_p.K515Q|ITSN1_ENST00000399349.1_Missense_Mutation_p.K515Q|ITSN1_ENST00000381291.4_Missense_Mutation_p.K515Q|ITSN1_ENST00000437442.2_Missense_Mutation_p.K515Q|ITSN1_ENST00000399338.4_Missense_Mutation_p.K515Q|ITSN1_ENST00000399355.2_Missense_Mutation_p.K515Q|ITSN1_ENST00000399326.3_Missense_Mutation_p.K515Q|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000381285.4_Missense_Mutation_p.K515Q	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	515	KLERQ.				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						GAGCACAAACAAATCTAGAGA	0.368																																					p.K515Q		Atlas-SNP	.											.	ITSN1	166	.	0			c.A1543C						PASS	.						100	103	102					21																	35147359		2203	4300	6503	SO:0001583	missense	6453	exon14			ACAAACAAATCTA	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.1543A>C	21.37:g.35147359A>C	ENSP00000370719:p.Lys515Gln	214	0	0		198	106	0.535354	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	37	CCDS33545.1	.	.	.	.	.	.	.	.	.	.	A	14.52	2.560779	0.45590	.	.	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	0.44881	1.53;0.93;1.0;0.93;1.53;1.53;1.0;1.53;1.53;1.53;1.53;0.91	5.07	5.07	0.68467	.	0.114374	0.56097	D	0.000026	T	0.38825	0.1055	L	0.27053	0.805	0.43936	D	0.996595	P;B;B;B;P;B;B;B;P;B	0.39352	0.539;0.397;0.068;0.264;0.669;0.296;0.245;0.245;0.542;0.397	B;B;B;B;B;B;B;B;P;B	0.45794	0.281;0.209;0.019;0.17;0.19;0.046;0.077;0.077;0.493;0.209	T	0.16660	-1.0395	10	0.31617	T	0.26	.	14.8326	0.70159	1.0:0.0:0.0:0.0	.	478;478;478;515;515;515;515;515;515;478	A8D7D0;A7XZY7;A8CTY7;A8CTY3;F8W7U0;E7ERJ1;A8CTX8;Q15811;Q15811-3;E7ERJ0	.;.;.;.;.;.;.;ITSN1_HUMAN;.;.	Q	478;515;515;515;515;515;515;515;515;515;515;515;515;515	ENSP00000382290:K478Q;ENSP00000370719:K515Q;ENSP00000370691:K515Q;ENSP00000370685:K515Q;ENSP00000382301:K515Q;ENSP00000382289:K515Q;ENSP00000382292:K515Q;ENSP00000382286:K515Q;ENSP00000382275:K515Q;ENSP00000387377:K515Q;ENSP00000382265:K515Q;ENSP00000369294:K515Q	ENSP00000369294:K515Q	K	+	1	0	ITSN1	34069229	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	6.956000	0.76013	1.910000	0.55303	0.482000	0.46254	AAA	.	.	none		0.368	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024		C	35147359	A	C	35147359	3	2	27	1	0	0	0	0	1	0	0	0	7935	131	5	5	1593	5	ITSN1	21	35147359	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	19274333	35147359	12982536	1000	11451											
FAM165B	54065	hgsc.bcm.edu	37	chr21	35757787	35757787	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcttgaaggttcttgagcaCgtgcccctgctgctgtatat	6	15	10	10	1	2	2	0	2	2	0	2	2	2	2	2	1	4	5	2	1	3	6	rs61747964	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:35757787C>T	ENST00000399295.2	+	3	394	c.24C>T	c.(22-24)caC>caT	p.H8H	SMIM11_ENST00000399299.1_Intron|SMIM11_ENST00000481710.1_3'UTR|SMIM11_ENST00000399292.3_Silent_p.H8H			P58511	SIM11_HUMAN	small integral membrane protein 11	8						integral component of membrane (GO:0016021)											TTCTTGAGCACGTGCCCCTGC	0.403													C|||	121	0.0241613	0.0408	0.0245	5008	,	,		20251	0.002		0.0129	False		,,,				2504	0.0358				p.H8H		Atlas-SNP	.											.	.	.	.	0			c.C24T						PASS	.	C		200,4206	126.1+/-163.2	2,196,2005	106	89	95		24	0.4	0.8	21	dbSNP_129	95	269,8331	103.8+/-164.8	4,261,4035	no	coding-synonymous	FAM165B	NM_058182.4		6,457,6040	TT,TC,CC		3.1279,4.5393,3.606		8/59	35757787	469,12537	2203	4300	6503	SO:0001819	synonymous_variant	54065	exon3			TGAGCACGTGCCC	BC015596	CCDS33550.1	21q22.12	2012-12-03	2012-12-03	2012-12-03	ENSG00000205670	ENSG00000205670			1293	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 51", "family with sequence similarity 165, member B"	C21orf51, FAM165B			Standard	NM_058182		Approved		uc002ytu.4	P58511	OTTHUMG00000086193	ENST00000399295.2:c.24C>T	21.37:g.35757787C>T		307	0	0		290	107	0.368966	NM_058182		Silent	SNP	ENST00000399295.2	37	CCDS33550.1																																																																																			C|0.971;T|0.029	0.029	strong		0.403	SMIM11-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194078.1	NM_058182		T	35757787	C	T	35757787	2	4	27	1	0	0	0	0	0	0	0	1	5485	535	19	1		1	FAM165B	21	35757787	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	610428	35757787	12372108	1001	11452											
FAM165B	54065	hgsc.bcm.edu	37	chr21	35757915	35757915	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actggaggctgaaaggaagaAgcaatcagagaaaaaagata	21	4	12	4	0	1	4	1	1	0	3	1	7	1	6	0	3	1	2	0	3	8	1	rs34016792	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:35757915A>G	ENST00000399295.2	+	3	522	c.152A>G	c.(151-153)aAg>aGg	p.K51R	SMIM11_ENST00000399299.1_Intron|SMIM11_ENST00000481710.1_3'UTR|SMIM11_ENST00000399292.3_Missense_Mutation_p.K51R			P58511	SIM11_HUMAN	small integral membrane protein 11	51			K -> R (in dbSNP:rs34016792).			integral component of membrane (GO:0016021)											GAAAGGAAGAAGCAATCAGAG	0.433													A|||	81	0.0161741	0.0113	0.0231	5008	,	,		20372	0.002		0.0129	False		,,,				2504	0.0358				p.K51R		Atlas-SNP	.											.	.	.	.	0			c.A152G						PASS	.	A	ARG/LYS	67,4339	61.1+/-98.1	0,67,2136	51	47	49		152	-3.9	0	21	dbSNP_126	49	269,8331	100.1+/-161.6	4,261,4035	yes	missense	FAM165B	NM_058182.4	26	4,328,6171	GG,GA,AA		3.1279,1.5207,2.5834	benign	51/59	35757915	336,12670	2203	4300	6503	SO:0001583	missense	54065	exon3			GGAAGAAGCAATC	BC015596	CCDS33550.1	21q22.12	2012-12-03	2012-12-03	2012-12-03	ENSG00000205670	ENSG00000205670			1293	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 51", "family with sequence similarity 165, member B"	C21orf51, FAM165B			Standard	NM_058182		Approved		uc002ytu.4	P58511	OTTHUMG00000086193	ENST00000399295.2:c.152A>G	21.37:g.35757915A>G	ENSP00000382234:p.Lys51Arg	120	0	0		119	49	0.411765	NM_058182		Missense_Mutation	SNP	ENST00000399295.2	37	CCDS33550.1	26	0.011904761904761904	4	0.008130081300813009	12	0.03314917127071823	1	0.0017482517482517483	9	0.011873350923482849	A	10.26	1.300114	0.23650	0.015207	0.031279	ENSG00000205670	ENST00000399292;ENST00000399295	T;T	0.36520	1.25;1.25	5.64	-3.86	0.04230	.	.	.	.	.	T	0.04679	0.0127	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.23691	-1.0181	8	0.15952	T	0.53	.	2.0315	0.03530	0.3294:0.3538:0.2024:0.1144	rs34016792	51	P58511	F165B_HUMAN	R	51	ENSP00000382231:K51R;ENSP00000382234:K51R	ENSP00000382231:K51R	K	+	2	0	FAM165B	34679785	0.000000	0.05858	0.000000	0.03702	0.143000	0.21401	0.555000	0.23422	-0.979000	0.03529	-0.371000	0.07208	AAG	A|0.979;G|0.021	0.021	strong		0.433	SMIM11-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194078.1	NM_058182		G	35757915	A	G	35757915	3	3	27	1	0	0	0	0	1	0	0	0	5485	72	3	3	158	3	FAM165B	21	35757915	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	128	35757915	12371980	1002	11453											
TTC3	7267	hgsc.bcm.edu	37	chr21	38534308	38534308	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ccagcctatgttagttgggtCtggaacaacttcagtaactt	10	13	9	9	0	2	0	1	0	1	0	2	1	2	1	2	2	4	3	2	2	5	6	rs377155188		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:38534308C>G	ENST00000399017.2	+	31	5860	c.3113C>G	c.(3112-3114)tCt>tGt	p.S1038C	TTC3_ENST00000355666.1_Missense_Mutation_p.S1038C|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000354749.2_Missense_Mutation_p.S1038C	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1038					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)				TTAGTTGGGTCTGGAACAACT	0.279																																					p.S1038C	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.C3113G						PASS	.	C	CYS/SER,CYS/SER	0,4404		0,0,2202	50	47	48		3113,3113	5.1	1	21		48	1,8573		0,1,4286	no	missense,missense	TTC3	NM_001001894.1,NM_003316.3	112,112	0,1,6488	GG,GC,CC		0.0117,0.0,0.0077	probably-damaging,probably-damaging	1038/2026,1038/2026	38534308	1,12977	2202	4287	6489	SO:0001583	missense	7267	exon31			TTGGGTCTGGAAC	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.3113C>G	21.37:g.38534308C>G	ENSP00000381981:p.Ser1038Cys	165	0	0		145	79	0.544828	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.86|17.86	3.493015|3.493015	0.64186|0.64186	0.0|0.0	1.17E-4|1.17E-4	ENSG00000182670|ENSG00000182670	ENST00000411496|ENST00000418766;ENST00000438055;ENST00000355666;ENST00000399017;ENST00000354749	.|T;T;T;T;T	.|0.15834	.|2.39;2.39;2.68;2.68;2.68	5.06|5.06	5.06|5.06	0.68205|0.68205	.|.	.|0.000000	.|0.64402	.|D	.|0.000013	T|T	0.40222|0.40222	0.1108|0.1108	M|M	0.66939|0.66939	2.045|2.045	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.87578	.|0.998;0.996	T|T	0.19679|0.19679	-1.0298|-1.0298	5|10	.|0.87932	.|D	.|0	-23.3456|-23.3456	14.2622|14.2622	0.66092|0.66092	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|96;1038	.|Q5GIT6;P53804	.|.;TTC3_HUMAN	V|C	194|1038;1020;1038;1038;1038	.|ENSP00000403943:S1038C;ENSP00000391891:S1020C;ENSP00000347889:S1038C;ENSP00000381981:S1038C;ENSP00000346791:S1038C	.|ENSP00000346791:S1038C	L|S	+|+	1|2	2|0	TTC3|TTC3	37456178|37456178	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.964000|0.964000	0.63967|0.63967	3.437000|3.437000	0.52863|0.52863	2.502000|2.502000	0.84385|0.84385	0.557000|0.557000	0.71058|0.71058	CTG|TCT	.	.	weak		0.279	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			G	38534308	C	G	38534308	3	3	27	1	0	0	0	0	1	0	0	0	16712	913	32	4	3231	4	TTC3	21	38534308	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2776393	38534308	9595587	1003	11454											
TTC3	7267	hgsc.bcm.edu	37	chr21	38572565	38572565	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttcctgtgaaatatgccaCgaggtgttcaaatcaaaaaa	16	10	8	7	1	2	1	2	1	0	0	3	2	3	1	2	1	1	2	2	1	6	3	rs150750778	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:38572565C>T	ENST00000399017.2	+	45	8630	c.5883C>T	c.(5881-5883)caC>caT	p.H1961H	TTC3_ENST00000355666.1_Silent_p.H1961H|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000354749.2_Silent_p.H1961H	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1961					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)				AAATATGCCACGAGGTGTTCA	0.433													C|||	14	0.00279553	0.0083	0.0029	5008	,	,		17732	0.0		0.001	False		,,,				2504	0.0				p.H1961H	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.C5883T						PASS	.	C	,	12,4394	19.1+/-41.9	0,12,2191	85	74	78		5883,5883	-11.2	0	21	dbSNP_134	78	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	TTC3	NM_001001894.1,NM_003316.3	,	0,12,6491	TT,TC,CC		0.0,0.2724,0.0923	,	1961/2026,1961/2026	38572565	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	7267	exon45			ATGCCACGAGGTG	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.5883C>T	21.37:g.38572565C>T		240	0	0		287	56	0.195122	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Silent	SNP	ENST00000399017.2	37	CCDS13651.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	C	5.526	0.282044	0.10458	0.002724	0.0	ENSG00000182670	ENST00000428693	.	.	.	5.58	-11.2	0.00127	.	.	.	.	.	.	.	.	.	.	.	0.22684	N	0.99886	.	.	.	.	.	.	.	.	.	.	.	.	.	-6.0597	9.5757	0.39457	0.2457:0.4773:0.0:0.2771	.	.	.	.	X	253	.	.	R	+	1	2	TTC3	37494435	0.000000	0.05858	0.000000	0.03702	0.741000	0.42261	-3.228000	0.00549	-3.780000	0.00108	-1.090000	0.02178	CGA	C|0.998;T|0.002	0.002	strong		0.433	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			T	38572565	C	T	38572565	2	4	27	1	0	0	0	0	0	0	0	1	16712	535	19	1		1	TTC3	21	38572565	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	38257	38572565	9557330	1004	11455											
BRWD1	54014	hgsc.bcm.edu	37	chr21	40608530	40608530	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtttttcttacctccttcttAggcttattttctttctttct	3	25	3	10	0	5	0	0	0	5	0	6	0	6	0	2	1	1	2	2	1	3	10	rs143020455		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:40608530A>C	ENST00000333229.2	-	23	3084	c.2757T>G	c.(2755-2757)ccT>ccG	p.P919P	BRWD1_ENST00000380800.3_Silent_p.P919P|BRWD1_ENST00000342449.3_Silent_p.P919P	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	919					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)				CCTCCTTCTTAGGCTTATTTT	0.328													A|||	1	0.000199681	0.0008	0.0	5008	,	,		21667	0.0		0.0	False		,,,				2504	0.0				p.P919P	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.T2757G						PASS	.	A	,	0,4406		0,0,2203	122	110	114		2757,2757	4.2	1	21	dbSNP_134	114	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous,coding-synonymous	BRWD1	NM_018963.4,NM_033656.3	,	0,8,6495	CC,CA,AA		0.093,0.0,0.0615	,	919/2321,919/2270	40608530	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	54014	exon23			CTTCTTAGGCTTA	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.2757T>G	21.37:g.40608530A>C		107	0	0		115	56	0.486957	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Silent	SNP	ENST00000333229.2	37	CCDS13662.1																																																																																			A|0.999;C|0.001	0.001	strong		0.328	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		C	40608530	A	C	40608530	2	2	27	1	0	0	0	0	0	0	0	1	1527	407	15	5		5	BRWD1	21	40608530	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	2035965	40608530	7521365	1005	11456											
LCA5L	150082	hgsc.bcm.edu	37	chr21	40800368	40800368	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctattgttttctaatgccaCgccgaagaaatgctcatcta	11	13	6	11	2	3	1	1	0	2	1	3	2	3	1	3	0	2	2	3	0	5	6			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:40800368C>T	ENST00000358268.2	-	4	580	c.52G>A	c.(52-54)Gtg>Atg	p.V18M	LCA5L_ENST00000380671.2_Missense_Mutation_p.V18M|LCA5L_ENST00000485895.2_Missense_Mutation_p.V18M|LCA5L_ENST00000288350.3_Missense_Mutation_p.V18M			O95447	LCA5L_HUMAN	Leber congenital amaurosis 5-like	18										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)				TCTAATGCCACGCCGAAGAAA	0.368																																					p.V18M		Atlas-SNP	.											.	LCA5L	57	.	0			c.G52A						PASS	.						112	109	110					21																	40800368		2203	4300	6503	SO:0001583	missense	150082	exon4			ATGCCACGCCGAA	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.52G>A	21.37:g.40800368C>T	ENSP00000351008:p.Val18Met	89	0	0		124	23	0.185484	NM_152505	D3DSI0|Q3ZCT0	Missense_Mutation	SNP	ENST00000358268.2	37	CCDS13665.1	.	.	.	.	.	.	.	.	.	.	c	14.53	2.562098	0.45590	.	.	ENSG00000157578	ENST00000288350;ENST00000380671;ENST00000358268;ENST00000418018;ENST00000448288;ENST00000434281;ENST00000438404;ENST00000411566;ENST00000415863;ENST00000426783;ENST00000456017	T;T;T;T;T;T;T;T;T;T;T	0.66099	0.19;0.19;0.19;0.62;0.58;0.57;0.56;0.56;0.47;0.42;-0.19	5.65	1.67	0.24075	.	1.008340	0.07969	N	0.983624	T	0.65852	0.2731	L	0.47716	1.5	0.09310	N	1	D;D	0.67145	0.993;0.996	P;P	0.61397	0.743;0.888	T	0.51132	-0.8744	10	0.72032	D	0.01	-2.9629	1.7285	0.02927	0.2757:0.4233:0.1428:0.1582	.	18;18	C9JFB6;O95447	.;LCA5L_HUMAN	M	18	ENSP00000288350:V18M;ENSP00000370046:V18M;ENSP00000351008:V18M;ENSP00000404521:V18M;ENSP00000405598:V18M;ENSP00000400086:V18M;ENSP00000405130:V18M;ENSP00000412691:V18M;ENSP00000395593:V18M;ENSP00000414784:V18M;ENSP00000407065:V18M	ENSP00000288350:V18M	V	-	1	0	LCA5L	39722238	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-0.181000	0.09740	0.032000	0.15435	-0.119000	0.15052	GTG	.	.	none		0.368	LCA5L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141807.2	NM_152505		T	40800368	C	T	40800368	3	4	27	1	0	0	0	0	1	0	0	0	8666	536	19	1	1988	1	LCA5L	21	40800368	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	191838	40800368	7329527	1006	11457											
UMODL1	89766	hgsc.bcm.edu	37	chr21	43531345	43531345	+	Intron	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caggagagtaccagccaggcGagccccagccagaggagcac	12	1	14	14	1	0	2	0	0	0	2	0	5	0	3	5	3	5	2	5	3	1	1	rs76618631	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:43531345G>A	ENST00000408910.2	+	11	1899				C21orf128_ENST00000329015.2_5'Flank|UMODL1_ENST00000400427.1_Silent_p.A599A|UMODL1_ENST00000400424.2_Intron|UMODL1_ENST00000408989.2_Silent_p.A671A	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						CCAGCCAGGCGAGCCCCAGCC	0.726													G|||	104	0.0207668	0.0734	0.0072	5008	,	,		10161	0.0		0.002	False		,,,				2504	0.0				p.A671A	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.G2013A						PASS	.	G	,,,	161,3347		2,157,1595	4	7	6		,1797,,2013	0.1	0	21	dbSNP_131	6	1,7635		0,1,3817	no	intron,coding-synonymous,intron,coding-synonymous	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	,,,	2,158,5412	AA,AG,GG		0.0131,4.5895,1.4537	,,,	,599/1375,,671/1447	43531345	162,10982	1754	3818	5572	SO:0001627	intron_variant	89766	exon11			CCAGGCGAGCCCC		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+114G>A	21.37:g.43531345G>A		27	0	0		35	14	0.4	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Silent	SNP	ENST00000408910.2	37	CCDS42936.1																																																																																			G|0.983;A|0.017	0.017	strong		0.726	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2			A	43531345	G	A	43531345	1	1	27	0	1	0	0	0	0	0	0	0	16995	1045	37	1		1	UMODL1	21	43531345	Intron	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2730977	43531345	4598550	1007	11458											
UMODL1	89766	hgsc.bcm.edu	37	chr21	43543098	43543098	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtcagggtgctctgtgagatCgagaaggtggttgtcgccat	7	11	16	7	2	2	2	1	1	1	2	4	4	2	2	1	3	1	2	1	3	1	1	rs58867895	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:43543098C>T	ENST00000408910.2	+	17	2985	c.2985C>T	c.(2983-2985)atC>atT	p.I995I	UMODL1_ENST00000400427.1_Silent_p.I1051I|UMODL1_ENST00000400423.2_3'UTR|UMODL1_ENST00000400424.2_Silent_p.I923I|UMODL1_ENST00000408989.2_Silent_p.I1123I	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	995	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				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						TCTGTGAGATCGAGAAGGTGG	0.632													C|||	142	0.0283546	0.1006	0.0086	5008	,	,		20433	0.0		0.003	False		,,,				2504	0.0				p.I1123I	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.C3369T						PASS	.	C	,,,	370,3912		11,348,1782	75	80	78		2985,3153,2769,3369	-6.2	0.9	21	dbSNP_129	78	6,8496		0,6,4245	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	,,,	11,354,6027	TT,TC,CC		0.0706,8.6408,2.9412	,,,	995/1319,1051/1375,923/1247,1123/1447	43543098	376,12408	2141	4251	6392	SO:0001819	synonymous_variant	89766	exon16			TGAGATCGAGAAG		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.2985C>T	21.37:g.43543098C>T		95	0	0		93	35	0.376344	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Silent	SNP	ENST00000408910.2	37	CCDS42936.1																																																																																			C|0.985;T|0.015	0.015	strong		0.632	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2			T	43543098	C	T	43543098	2	4	27	1	0	0	0	0	0	0	0	1	16995	874	31	1		1	UMODL1	21	43543098	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	11753	43543098	4586797	1008	11459											
CBS	875	hgsc.bcm.edu	37	chr21	44488631	44488631	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcactcacagagctcacactTcaggccgaacttcttcccaa	11	8	6	16	1	4	1	3	0	1	1	5	2	5	1	2	1	2	2	2	1	2	3	rs34040148	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:44488631T>G	ENST00000398165.3	-	4	563	c.304A>C	c.(304-306)Aag>Cag	p.K102Q	CBS_ENST00000359624.3_Missense_Mutation_p.K102Q|CBS_ENST00000398158.1_Missense_Mutation_p.K102Q|CBS_ENST00000398168.1_Missense_Mutation_p.K102Q|CBS_ENST00000544202.1_Missense_Mutation_p.K14Q|CBS_ENST00000470912.1_5'UTR|CBS_ENST00000352178.5_Missense_Mutation_p.K102Q	NM_000071.2	NP_000062.1	P35520	CBS_HUMAN	cystathionine-beta-synthase	102			K -> N (in CBSD; 50% of activity). {ECO:0000269|PubMed:7981678}.|K -> Q (in CBSD; severe form; linked with Arg-77; dbSNP:rs34040148). {ECO:0000269|PubMed:11013450}.		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)	AGCTCACACTTCAGGCCGAAC	0.542													T|||	59	0.0117812	0.0446	0.0	5008	,	,		11993	0.0		0.0	False		,,,				2504	0.0				p.K102Q		Atlas-SNP	.											.	CBS	85	.	0			c.A304C	GRCh37	CM994315	CBS	M	rs34040148	PASS	.	T	GLN/LYS,GLN/LYS,GLN/LYS	167,4239	110.8+/-149.0	1,165,2037	96	93	94		304,304,304	4.8	1	21	dbSNP_126	94	0,8600		0,0,4300	yes	missense,missense,missense	CBS	NM_000071.2,NM_001178008.1,NM_001178009.1	53,53,53	1,165,6337	GG,GT,TT		0.0,3.7903,1.284	probably-damaging,probably-damaging,probably-damaging	102/552,102/552,102/552	44488631	167,12839	2203	4300	6503	SO:0001583	missense	875	exon4			CACACTTCAGGCC	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.304A>C	21.37:g.44488631T>G	ENSP00000381231:p.Lys102Gln	101	0	0		137	51	0.372263	NM_000071	B2R993|D3DSK4|Q99425|Q9BWC5	Missense_Mutation	SNP	ENST00000398165.3	37	CCDS13693.1	24	0.01098901098901099	24	0.04878048780487805	0	0.0	0	0.0	0	0.0	T	15.59	2.878485	0.51801	0.037903	0.0	ENSG00000160200	ENST00000398158;ENST00000398165;ENST00000359624;ENST00000352178;ENST00000398168;ENST00000539520;ENST00000544202;ENST00000441030	D;D;D;D;D;D;D	0.96491	-4.03;-4.03;-4.03;-4.03;-4.03;-4.03;-4.03	4.81	4.81	0.61882	Pyridoxal phosphate-dependent enzyme, beta subunit (2);	0.000000	0.85682	D	0.000000	T	0.80681	0.4669	M	0.66439	2.03	0.48395	D	0.99964	P	0.36495	0.556	B	0.36766	0.232	D	0.84529	0.0632	10	0.38643	T	0.18	-46.6496	12.8977	0.58109	0.0:0.0:0.0:1.0	rs34040148	102	P35520	CBS_HUMAN	Q	102;102;102;102;102;59;14;102	ENSP00000381225:K102Q;ENSP00000381231:K102Q;ENSP00000352643:K102Q;ENSP00000344460:K102Q;ENSP00000381234:K102Q;ENSP00000439332:K14Q;ENSP00000388235:K102Q	ENSP00000344460:K102Q	K	-	1	0	CBS	43361700	1.000000	0.71417	0.998000	0.56505	0.544000	0.35116	3.979000	0.56888	1.917000	0.55516	0.533000	0.62120	AAG	T|0.985;G|0.015	0.015	strong		0.542	CBS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195525.1	NM_000071		G	44488631	T	G	44488631	3	3	27	1	0	0	0	0	1	0	0	0	2713	1792	62	5	1407	5	CBS	21	44488631	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	945533	44488631	3641264	1009	11460											
AIRE	326	hgsc.bcm.edu	37	chr21	45712983	45712983	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagcacctgccggctccgccTtctgcagccccgctgccagg	5	6	11	19	3	1	0	0	0	1	0	2	0	2	0	7	2	5	4	7	2	1	1	rs61737072	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:45712983T>C	ENST00000291582.5	+	10	1330	c.1203T>C	c.(1201-1203)ccT>ccC	p.P401P	AIRE_ENST00000329347.4_Intron|AIRE_ENST00000355347.4_Silent_p.P194P	NM_000383.3	NP_000374.1	O43918	AIRE_HUMAN	autoimmune regulator	401					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)		CGGCTCCGCCTTCTGCAGCCC	0.677									Autoimmune PolyEndocrinopathy Candidiasis Ectodermal Dystrophy				T|||	232	0.0463259	0.1649	0.0202	5008	,	,		10975	0.0		0.0	False		,,,				2504	0.0				p.P401P		Atlas-SNP	.											.	AIRE	61	.	0			c.T1203C						PASS	.	T	,	665,3717		60,545,1586	22	26	24		1203,612	-2.4	0	21	dbSNP_129	24	2,8586		0,2,4292	no	coding-synonymous,coding-synonymous	AIRE	NM_000383.2,NM_000658.2	,	60,547,5878	CC,CT,TT		0.0233,15.1757,5.1426	,	401/546,204/349	45712983	667,12303	2191	4294	6485	SO:0001819	synonymous_variant	326	exon10	Familial Cancer Database	APECED	TCCGCCTTCTGCA	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.1203T>C	21.37:g.45712983T>C		40	0	0		63	24	0.380952	NM_000383	B2RP50|O43922|O43932|O75745	Silent	SNP	ENST00000291582.5	37	CCDS13706.1																																																																																			T|0.951;C|0.049	0.049	strong		0.677	AIRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195842.2			C	45712983	T	C	45712983	2	2	27	1	0	0	0	0	0	0	0	1	437	1596	56	3		3	AIRE	21	45712983	Silent	SNP	T	TCGA-G8-6909-01A-11D-2210-10	1224352	45712983	2416912	1010	11461											
KRTAP10-11	386678	hgsc.bcm.edu	37	chr21	46067194	46067194	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgctgccgcccggcctcctgCgtgtccctcctctgccgccc	0	9	10	22	4	1	0	0	0	1	0	4	0	4	0	8	1	4	1	8	1	0	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:46067194C>T	ENST00000334670.8	+	1	864	c.819C>T	c.(817-819)tgC>tgT	p.C273C	TSPEAR_ENST00000323084.4_Intron	NM_198692.2	NP_941965.2	P60412	KR10B_HUMAN	keratin associated protein 10-11	273						keratin filament (GO:0045095)				NS(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)	12						CGGCCTCCTGCGTGTCCCTCC	0.677																																					p.C273C		Atlas-SNP	.											KRTAP10-11,NS,carcinoma,0,1	KRTAP10-11	36	1	0			c.C819T						scavenged	.						41	52	48					21																	46067194		2199	4293	6492	SO:0001819	synonymous_variant	386678	exon1			CTCCTGCGTGTCC	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.819C>T	21.37:g.46067194C>T		88	1	0.0113636		108	5	0.0462963	NM_198692	A2RRF9	Silent	SNP	ENST00000334670.8	37	CCDS42962.1																																																																																			.	.	none		0.677	KRTAP10-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128029.1	NM_198692		T	46067194	C	T	46067194	2	4	27	1	0	0	0	0	0	0	0	1	8516	776	27	1		1	KRTAP10-11	21	46067194	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	354211	46067194	2062701	1011	11462											
PCNT	5116	hgsc.bcm.edu	37	chr21	47817316	47817316	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aacagctgtctcagcatcgcGggtgtgccaagcaggcggag	9	6	15	11	3	1	0	1	0	1	0	3	1	1	1	1	3	5	3	1	3	2	0	rs143796569	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:47817316G>A	ENST00000359568.5	+	22	4461	c.4354G>A	c.(4354-4356)Ggg>Agg	p.G1452R	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1452			G -> R (found in a patient with mental retardation, no speech, facial and limbs dysmorphisms). {ECO:0000269|PubMed:23033978}.		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)					TCAGCATCGCGGGTGTGCCAA	0.562													G|||	18	0.00359425	0.0	0.0	5008	,	,		20614	0.0		0.001	False		,,,				2504	0.0174				p.G1452R		Atlas-SNP	.											PCNT,NS,carcinoma,-2,1	PCNT	283	1	0			c.G4354A						PASS	.	G	ARG/GLY	2,4404	4.2+/-10.8	0,2,2201	70	68	69		4354	5.5	0	21	dbSNP_134	69	17,8583	12.6+/-44.7	0,17,4283	yes	missense	PCNT	NM_006031.5	125	0,19,6484	AA,AG,GG		0.1977,0.0454,0.1461	probably-damaging	1452/3337	47817316	19,12987	2203	4300	6503	SO:0001583	missense	5116	exon22			CATCGCGGGTGTG	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.4354G>A	21.37:g.47817316G>A	ENSP00000352572:p.Gly1452Arg	93	0	0		100	27	0.27	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	15.43	2.830357	0.50845	4.54E-4	0.001977	ENSG00000160299	ENST00000359568	T	0.58506	0.33	5.46	5.46	0.80206	.	0.511594	0.14699	N	0.303674	T	0.66056	0.2751	L	0.44542	1.39	0.09310	N	0.999996	D;D	0.76494	0.999;0.998	P;P	0.57152	0.814;0.807	T	0.60182	-0.7313	10	0.51188	T	0.08	.	16.8006	0.85613	0.0:0.0:1.0:0.0	.	1334;1452	O95613-2;O95613	.;PCNT_HUMAN	R	1452	ENSP00000352572:G1452R	ENSP00000352572:G1452R	G	+	1	0	PCNT	46641744	0.968000	0.33430	0.009000	0.14445	0.009000	0.06853	4.647000	0.61418	2.560000	0.86352	0.561000	0.74099	GGG	G|0.999;A|0.001	0.001	strong		0.562	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		A	47817316	G	A	47817316	3	1	27	1	0	0	0	0	1	0	0	0	11599	1116	39	1	4440	1	PCNT	21	47817316	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1750122	47817316	312579	1012	11463											
PCNT	5116	hgsc.bcm.edu	37	chr21	47860110	47860110	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaagcacacaccagcaatGtcaaggtaggaacggtgcca	15	4	12	10	1	1	0	1	0	0	0	1	2	1	2	2	4	4	3	2	4	5	1	rs563489032		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr21:47860110G>A	ENST00000359568.5	+	42	9495	c.9388G>A	c.(9388-9390)Gtc>Atc	p.V3130I	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	3130	Interaction with NEK2.				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)					CACCAGCAATGTCAAGGTAGG	0.542																																					p.V3130I		Atlas-SNP	.											.	PCNT	283	.	0			c.G9388A						PASS	.						59	66	63					21																	47860110		2203	4299	6502	SO:0001583	missense	5116	exon42			AGCAATGTCAAGG	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.9388G>A	21.37:g.47860110G>A	ENSP00000352572:p.Val3130Ile	29	0	0		35	12	0.342857	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	5.094|5.094	0.202944|0.202944	0.09704|0.09704	.|.	.|.	ENSG00000160299|ENSG00000160299	ENST00000418394|ENST00000359568	.|T	.|0.01505	.|4.82	4.3|4.3	-4.62|-4.62	0.03370|0.03370	.|.	.|.	.|.	.|.	.|.	T|T	0.01092|0.01092	0.0036|0.0036	N|N	0.17474|0.17474	0.49|0.49	0.09310|0.09310	N|N	1|1	.|B;B	.|0.17038	.|0.02;0.012	.|B;B	.|0.14578	.|0.011;0.005	T|T	0.48269|0.48269	-0.9050|-0.9050	5|9	.|0.16420	.|T	.|0.52	.|.	6.8565|6.8565	0.24044|0.24044	0.5669:0.0:0.3097:0.1234|0.5669:0.0:0.3097:0.1234	.|.	.|2933;3130	.|O95613-2;O95613	.|.;PCNT_HUMAN	I|I	110|3130	.|ENSP00000352572:V3130I	.|ENSP00000352572:V3130I	M|V	+|+	3|1	0|0	PCNT|PCNT	46684538|46684538	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.005000|0.005000	0.04900|0.04900	-1.051000|-1.051000	0.03507|0.03507	-1.138000|-1.138000	0.02884|0.02884	-0.136000|-0.136000	0.14681|0.14681	ATG|GTC	.	.	none		0.542	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031		A	47860110	G	A	47860110	3	1	27	1	0	0	0	0	1	0	0	0	11599	1377	48	2	9554	2	PCNT	21	47860110	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	42794	47860110	269785	1013	11464											
ARVCF	421	hgsc.bcm.edu	37	chr22	19965563	19965563	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcccttcacactcccggagtCgccgccgggcctcagcacca	6	5	10	20	4	2	0	2	0	0	0	4	1	3	1	6	2	1	1	6	2	0	1	rs16982871	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:19965563C>T	ENST00000263207.3	-	8	1907	c.1616G>A	c.(1615-1617)cGa>cAa	p.R539Q	ARVCF_ENST00000406522.1_Missense_Mutation_p.R476Q|ARVCF_ENST00000344269.3_Missense_Mutation_p.R476Q|ARVCF_ENST00000401994.1_Missense_Mutation_p.R476Q|ARVCF_ENST00000406259.1_Missense_Mutation_p.R539Q	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	539			R -> Q (in dbSNP:rs16982871).		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)					CTCCCGGAGTCGCCGCCGGGC	0.667													C|||	11	0.00219649	0.0008	0.0014	5008	,	,		18613	0.0		0.003	False		,,,				2504	0.0061				p.R539Q		Atlas-SNP	.											.	ARVCF	54	.	0			c.G1616A						PASS	.	C	GLN/ARG	9,4397	15.5+/-35.6	0,9,2194	49	45	47		1616	4	1	22	dbSNP_123	47	79,8517	46.7+/-105.8	0,79,4219	yes	missense	ARVCF	NM_001670.2	43	0,88,6413	TT,TC,CC		0.919,0.2043,0.6768	probably-damaging	539/963	19965563	88,12914	2203	4298	6501	SO:0001583	missense	421	exon8			CGGAGTCGCCGCC		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.1616G>A	22.37:g.19965563C>T	ENSP00000263207:p.Arg539Gln	104	0	0		95	36	0.378947	NM_001670	B7WNV2	Missense_Mutation	SNP	ENST00000263207.3	37	CCDS13771.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	30	5.053953	0.93793	0.002043	0.00919	ENSG00000099889	ENST00000263207;ENST00000344269;ENST00000401994;ENST00000406522;ENST00000406259	T;T;T;T;T	0.70986	-0.53;-0.53;-0.53;-0.53;-0.53	4.03	4.03	0.46877	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.70842	0.3270	L	0.37507	1.11	0.58432	D	0.999999	D;D	0.89917	0.995;1.0	P;D	0.79108	0.877;0.992	T	0.73282	-0.4032	9	.	.	.	-9.945	17.0615	0.86548	0.0:1.0:0.0:0.0	rs16982871;rs16982871	539;61	O00192;E7EV58	ARVC_HUMAN;.	Q	539;476;476;476;539	ENSP00000263207:R539Q;ENSP00000342042:R476Q;ENSP00000384341:R476Q;ENSP00000384732:R476Q;ENSP00000385444:R539Q	.	R	-	2	0	ARVCF	18345563	0.394000	0.25246	0.973000	0.42090	0.993000	0.82548	1.722000	0.38042	2.541000	0.85698	0.655000	0.94253	CGA	C|0.995;T|0.005	0.005	strong		0.667	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670		T	19965563	C	T	19965563	3	4	27	1	0	0	0	0	1	0	0	0	1003	884	31	1	1320	1	ARVCF	22	19965563	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10		19965563	31339003	1014	11465											
SERPIND1	3053	hgsc.bcm.edu	37	chr22	21133831	21133831	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagagggggaggaggacgaCgactatctggacctggagaa	12	4	17	8	2	1	2	0	0	1	2	1	9	1	6	2	6	0	0	2	6	2	1	rs5903	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:21133831C>A	ENST00000215727.5	+	2	514	c.231C>A	c.(229-231)gaC>gaA	p.D77E	PI4KA_ENST00000572273.1_Intron|PI4KA_ENST00000466162.1_Intron|PI4KA_ENST00000255882.6_Intron|SERPIND1_ENST00000406799.1_Missense_Mutation_p.D77E	NM_000185.3	NP_000176.2	P05546	HEP2_HUMAN	serpin peptidase inhibitor, clade D (heparin cofactor), member 1	77	2 X 11 AA approximate repeats, Asp/Glu- rich (acidic) (hirudin-like).|Chemotactic activity.				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)	AGGAGGACGACGACTATCTGG	0.507													C|||	17	0.00339457	0.0	0.0043	5008	,	,		20196	0.0		0.0119	False		,,,				2504	0.002				p.D77E		Atlas-SNP	.											.	SERPIND1	92	.	0			c.C231A						PASS	.	C	GLU/ASP,	10,4396	16.8+/-37.8	0,10,2193	79	69	72		231,	-11.5	0.4	22	dbSNP_52	72	83,8517	48.5+/-108.0	0,83,4217	yes	missense,intron	SERPIND1,PI4KA	NM_000185.3,NM_058004.3	45,	0,93,6410	AA,AC,CC		0.9651,0.227,0.7151	benign,	77/500,	21133831	93,12913	2203	4300	6503	SO:0001583	missense	3053	exon2			GGACGACGACTAT	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.231C>A	22.37:g.21133831C>A	ENSP00000215727:p.Asp77Glu	126	0	0		133	65	0.488722	NM_000185	B2RAI1|D3DX34|Q6IBZ5	Missense_Mutation	SNP	ENST00000215727.5	37	CCDS13783.1	.	.	.	.	.	.	.	.	.	.	C	4.885	0.164489	0.09287	0.00227	0.009651	ENSG00000099937	ENST00000215727;ENST00000406799	D;D	0.81739	-1.53;-1.53	5.75	-11.5	0.00074	.	0.295809	0.41500	N	0.000877	T	0.34135	0.0887	N	0.04018	-0.295	0.22034	N	0.999407	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.55579	-0.8119	10	0.02654	T	1	.	7.576	0.27937	0.0539:0.4378:0.3104:0.1979	.	77;77	Q8IVC0;P05546	.;HEP2_HUMAN	E	77	ENSP00000215727:D77E;ENSP00000384050:D77E	ENSP00000215727:D77E	D	+	3	2	SERPIND1	19463831	0.000000	0.05858	0.378000	0.26068	0.923000	0.55619	-2.171000	0.01267	-1.815000	0.01222	-1.021000	0.02439	GAC	A|0.004;C|0.984;T|0.013	0.004	strong		0.507	SERPIND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319961.1	NM_000185		A	21133831	C	A	21133831	3	1	27	1	0	0	0	0	1	0	0	0	14125	535	19	4	233	4	SERPIND1	22	21133831	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1168268	21133831	30170735	1015	11466											
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230312	23230312	+	Silent	SNP	C	C	T																															ccaggcagcgctggcccctgCtgctgctgggtctggccatg																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:23230312C>T	ENST00000526893.1	+	1	353	c.79C>T	c.(79-81)Ctg>Ttg	p.L27L	IGLL5_ENST00000531372.1_Silent_p.L27L|IGLL5_ENST00000532223.2_Silent_p.L27L|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	27						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CTGGCCCCTGCTGCTGCTGGG	0.667																																					p.L27L		Atlas-SNP	.											IGLL5,NS,lymphoid_neoplasm,-2,1	IGLL5	26	1	0			c.C79T						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			CCCCTGCTGCTGC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.79C>T	22.37:g.23230312C>T		152	0	0		159	41	0.257862	NM_001178126		Silent	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.667	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		T	23230312	C	T	23230312	2	4	27	1	0	0	0	0	0	0	0	1	7603	796	28	2		2	IGLL5	22	23230312	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	2096481	23230312	28074254	1016	11467	142	2	3	47		7	5	117	N	G_C	9.023807e-12
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230317	23230317	+	Silent	SNP	G	G	A																															cagcgctggcccctgctgctGctgggtctggccatggtcgc																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:23230317G>A	ENST00000526893.1	+	1	358	c.84G>A	c.(82-84)ctG>ctA	p.L28L	IGLL5_ENST00000531372.1_Silent_p.L28L|IGLL5_ENST00000532223.2_Silent_p.L28L|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	28						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CCCTGCTGCTGCTGGGTCTGG	0.657																																					p.L28L		Atlas-SNP	.											.	IGLL5	26	.	0			c.G84A						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			GCTGCTGCTGGGT	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.84G>A	22.37:g.23230317G>A		153	0	0		158	33	0.208861	NM_001178126		Silent	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.657	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		A	23230317	G	A	23230317	2	1	27	1	0	0	0	0	0	0	0	1	7603	1306	46	2		2	IGLL5	22	23230317	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	5	23230317	28074249	1017	11468	142	2	3	47		7	5	117	N	G_C	9.023807e-12
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230348	23230348	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccatggtcgcccatggcctgCtgcgcccaatggttgcaccg	5	8	12	16	3	0	0	0	0	0	0	1	0	0	0	5	3	3	3	5	3	1	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:23230348C>G	ENST00000526893.1	+	1	389	c.115C>G	c.(115-117)Ctg>Gtg	p.L39V	IGLL5_ENST00000531372.1_Missense_Mutation_p.L39V|IGLL5_ENST00000532223.2_Missense_Mutation_p.L39V|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	39						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CCATGGCCTGCTGCGCCCAAT	0.687																																					p.L39V		Atlas-SNP	.											.	IGLL5	26	.	0			c.C115G						PASS	.																																			SO:0001583	missense	100423062	exon1			GGCCTGCTGCGCC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.115C>G	22.37:g.23230348C>G	ENSP00000431254:p.Leu39Val	149	0	0		143	28	0.195804	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	C	10.65	1.410199	0.25465	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00717	5.79;5.8	3.92	-2.91	0.05631	.	.	.	.	.	T	0.00608	0.0020	L	0.29908	0.895	0.09310	N	1	B	0.21821	0.061	B	0.13407	0.009	T	0.47509	-0.9112	9	0.51188	T	0.08	.	0.7315	0.00958	0.1663:0.3182:0.1632:0.3524	.	39	B9A064	IGLL5_HUMAN	V	39	ENSP00000436353:L39V;ENSP00000431254:L39V	ENSP00000431254:L39V	L	+	1	2	IGLL5	21560348	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.230000	0.09083	-0.436000	0.07254	0.643000	0.83706	CTG	.	.	none		0.687	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		G	23230348	C	G	23230348	3	3	27	1	0	0	0	0	1	0	0	0	7603	796	28	4	117	4	IGLL5	22	23230348	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	31	23230348	28074218	1018	11469			3	47		7	5	117	N	G_C	9.023807e-12
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230394	23230394	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cggggacccagaccctggagCctcagttggaagcagccgat	9	5	14	13	2	1	1	1	0	0	1	1	5	1	4	4	4	3	2	4	4	1	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:23230394C>T	ENST00000526893.1	+	1	435	c.161C>T	c.(160-162)gCc>gTc	p.A54V	IGLL5_ENST00000531372.1_Missense_Mutation_p.A54V|IGLL5_ENST00000532223.2_Missense_Mutation_p.A54V|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	54						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GACCCTGGAGCCTCAGTTGGA	0.667																																					p.A54V		Atlas-SNP	.											.	IGLL5	26	.	0			c.C161T						PASS	.																																			SO:0001583	missense	100423062	exon1			CTGGAGCCTCAGT	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.161C>T	22.37:g.23230394C>T	ENSP00000431254:p.Ala54Val	135	0	0		114	24	0.210526	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	C	15.92	2.975826	0.53720	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00617	6.19;6.19	3.92	-1.07	0.09968	.	.	.	.	.	T	0.00552	0.0018	L	0.29908	0.895	0.09310	N	1	B	0.21821	0.061	B	0.11329	0.006	T	0.47071	-0.9145	9	0.87932	D	0	.	2.5676	0.04787	0.1918:0.3543:0.3485:0.1053	.	54	B9A064	IGLL5_HUMAN	V	54	ENSP00000436353:A54V;ENSP00000431254:A54V	ENSP00000431254:A54V	A	+	2	0	IGLL5	21560394	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.197000	0.17197	-0.079000	0.12707	-0.152000	0.13540	GCC	.	.	none		0.667	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		T	23230394	C	T	23230394	3	4	27	1	0	0	0	0	1	0	0	0	7603	739	26	2	163	2	IGLL5	22	23230394	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	46	23230394	28074172	1019	11470			3	47		7	5	117	N	G_C	9.023807e-12
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230407	23230407	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctggagcctcagttggaagCagccgatccagcctgcggag	8	6	14	13	2	1	0	1	0	0	0	2	4	2	3	5	3	5	2	5	3	1	1	rs538609996	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:23230407C>G	ENST00000526893.1	+	1	448	c.174C>G	c.(172-174)agC>agG	p.S58R	IGLL5_ENST00000531372.1_Missense_Mutation_p.S58R|IGLL5_ENST00000532223.2_Missense_Mutation_p.S58R|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	58						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CAGTTGGAAGCAGCCGATCCA	0.662																																					p.S58R		Atlas-SNP	.											.	IGLL5	26	.	0			c.C174G						PASS	.																																			SO:0001583	missense	100423062	exon1			TGGAAGCAGCCGA	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.174C>G	22.37:g.23230407C>G	ENSP00000431254:p.Ser58Arg	122	0	0		110	22	0.2	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	C	10.98	1.505085	0.26949	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00585	6.4;6.39	3.92	0.621	0.17643	.	.	.	.	.	T	0.00524	0.0017	L	0.32530	0.975	0.09310	N	1	B	0.21225	0.053	B	0.19148	0.024	T	0.46555	-0.9183	9	0.72032	D	0.01	.	4.068	0.09869	0.0:0.5528:0.224:0.2232	.	58	B9A064	IGLL5_HUMAN	R	58	ENSP00000436353:S58R;ENSP00000431254:S58R	ENSP00000431254:S58R	S	+	3	2	IGLL5	21560407	0.001000	0.12720	0.001000	0.08648	0.013000	0.08279	0.487000	0.22356	0.228000	0.21019	-0.152000	0.13540	AGC	.	.	none		0.662	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		G	23230407	C	G	23230407	3	3	27	1	0	0	0	0	1	0	0	0	7603	709	25	4	176	4	IGLL5	22	23230407	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	13	23230407	28074159	1020	11471			3	47		7	5	117	N	G_C	9.023807e-12
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230419	23230419	+	Silent	SNP	C	C	T																															gttggaagcagccgatccagCctgcggagcctgtggggcag																								rs554734650	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:23230419C>T	ENST00000526893.1	+	1	460	c.186C>T	c.(184-186)agC>agT	p.S62S	IGLL5_ENST00000531372.1_Silent_p.S62S|IGLL5_ENST00000532223.2_Silent_p.S62S|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	62						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GCCGATCCAGCCTGCGGAGCC	0.647													C|||	3	0.000599042	0.0008	0.0	5008	,	,		11441	0.001		0.001	False		,,,				2504	0.0				p.A27V		Atlas-SNP	.											.	IGLL5	26	.	0			c.C80T						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			ATCCAGCCTGCGG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.186C>T	22.37:g.23230419C>T		113	0	0		97	25	0.257732	NM_001256296		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.647	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		T	23230419	C	T	23230419	2	4	27	1	0	0	0	0	0	0	0	1	7603	738	26	2		2	IGLL5	22	23230419	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	12	23230419	28074147	1021	11472	143	2	3	47		7	5	117	N	G_C	9.023807e-12
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230428	23230428	+	Missense_Mutation	SNP	C	C	G																															agccgatccagcctgcggagCctgtggggcaggtaaggggc																								rs151173231	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:23230428C>G	ENST00000526893.1	+	1	469	c.195C>G	c.(193-195)agC>agG	p.S65R	IGLL5_ENST00000531372.1_Missense_Mutation_p.S65R|IGLL5_ENST00000532223.2_Missense_Mutation_p.S65R|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	65						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GCCTGCGGAGCCTGTGGGGCA	0.647																																					p.S65R		Atlas-SNP	.											IGLL5,caecum,carcinoma,+1,1	IGLL5	26	1	0			c.C195G						PASS	.																																			SO:0001583	missense	100423062	exon1			GCGGAGCCTGTGG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.195C>G	22.37:g.23230428C>G	ENSP00000431254:p.Ser65Arg	107	0	0		86	22	0.255814	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	C	14.52	2.558610	0.45590	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00576	6.45;6.54	3.92	1.8	0.24995	.	.	.	.	.	T	0.00468	0.0015	N	0.19112	0.55	0.09310	N	1	B	0.15930	0.015	B	0.12837	0.008	T	0.46775	-0.9167	9	0.56958	D	0.05	.	4.9248	0.13887	0.2081:0.6824:0.0:0.1095	.	65	B9A064	IGLL5_HUMAN	R	65	ENSP00000436353:S65R;ENSP00000431254:S65R	ENSP00000431254:S65R	S	+	3	2	IGLL5	21560428	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.510000	0.06328	0.610000	0.30035	0.643000	0.83706	AGC	C|1.000;T|0.000	.	alt		0.647	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		G	23230428	C	G	23230428	3	3	27	1	0	0	0	0	1	0	0	0	7603	738	26	4	197	4	IGLL5	22	23230428	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	9	23230428	28074138	1022	11473	143	2	3	47		7	5	117	N	G_C	9.023807e-12
CABIN1	23523	hgsc.bcm.edu	37	chr22	24487739	24487739	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctgcacgaggaggctgcccGctaccccaagaagatccact	10	5	10	16	2	0	2	0	0	0	2	1	4	1	3	5	2	3	3	5	2	3	1	rs117908385	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:24487739G>A	ENST00000398319.2	+	24	4113	c.3728G>A	c.(3727-3729)cGc>cAc	p.R1243H	CABIN1_ENST00000405822.2_Missense_Mutation_p.R1193H|CABIN1_ENST00000263119.5_Missense_Mutation_p.R1243H	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	1243					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						GAGGCTGCCCGCTACCCCAAG	0.642													G|||	40	0.00798722	0.0015	0.0072	5008	,	,		17045	0.0		0.0328	False		,,,				2504	0.0				p.R1243H		Atlas-SNP	.											.	CABIN1	153	.	0			c.G3728A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG	13,4393	20.2+/-43.8	0,13,2190	69	61	64		3728,3578,3728	5	1	22	dbSNP_132	64	156,8444	72.9+/-135.5	1,154,4145	yes	missense,missense,missense	CABIN1	NM_001199281.1,NM_001201429.1,NM_012295.3	29,29,29	1,167,6335	AA,AG,GG		1.814,0.2951,1.2994	probably-damaging,probably-damaging,probably-damaging	1243/2221,1193/2171,1243/2221	24487739	169,12837	2203	4300	6503	SO:0001583	missense	23523	exon24			CTGCCCGCTACCC	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.3728G>A	22.37:g.24487739G>A	ENSP00000381364:p.Arg1243His	115	0	0		120	60	0.5	NM_001199281	G5E9F3|Q6PHY0|Q9Y460	Missense_Mutation	SNP	ENST00000398319.2	37	CCDS13823.1	32	0.014652014652014652	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	30	0.0395778364116095	G	35	5.482768	0.96307	0.002951	0.01814	ENSG00000099991	ENST00000263119;ENST00000405822;ENST00000398319	T;T;T	0.30182	1.54;1.54;1.54	5.04	5.04	0.67666	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.20170	0.0485	L	0.56769	1.78	0.80722	D	1	D;D	0.89917	1.0;0.999	D;P	0.65773	0.938;0.869	T	0.16571	-1.0398	10	0.52906	T	0.07	.	17.8214	0.88651	0.0:0.0:1.0:0.0	.	1193;1243	G5E9F3;Q9Y6J0	.;CABIN_HUMAN	H	1243;1193;1243	ENSP00000263119:R1243H;ENSP00000384694:R1193H;ENSP00000381364:R1243H	ENSP00000263119:R1243H	R	+	2	0	CABIN1	22817739	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.918000	0.87506	2.531000	0.85337	0.585000	0.79938	CGC	G|0.987;A|0.013	0.013	strong		0.642	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295		A	24487739	G	A	24487739	3	1	27	1	0	0	0	0	1	0	0	0	2530	1087	38	1	3818	1	CABIN1	22	24487739	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1257311	24487739	26816827	1023	11474											
GGT1	2678	hgsc.bcm.edu	37	chr22	25023881	25023881	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caataatgaaatggacgactTcagctctcccagcatcacca	14	8	6	13	1	3	1	2	1	1	0	4	3	3	2	2	1	2	2	2	1	3	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:25023881T>G	ENST00000400382.1	+	13	2026	c.1271T>G	c.(1270-1272)tTc>tGc	p.F424C	GGT1_ENST00000248923.4_Missense_Mutation_p.F424C|GGT1_ENST00000404223.1_Missense_Mutation_p.F80C|GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000400380.1_Missense_Mutation_p.F424C|GGT1_ENST00000404920.1_Missense_Mutation_p.F80C|GGT1_ENST00000403838.1_Missense_Mutation_p.F80C|GGT1_ENST00000401885.1_Missense_Mutation_p.F80C|GGT1_ENST00000400383.1_Missense_Mutation_p.F424C|GGT1_ENST00000406383.2_Missense_Mutation_p.F424C|GGT1_ENST00000404532.1_Missense_Mutation_p.F80C			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	424					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)	ATGGACGACTTCAGCTCTCCC	0.617																																					p.F424C		Atlas-SNP	.											.	GGT1	68	.	0			c.T1271G						PASS	.						75	82	79					22																	25023881		2203	4300	6503	SO:0001583	missense	2678	exon13			ACGACTTCAGCTC	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.1271T>G	22.37:g.25023881T>G	ENSP00000383232:p.Phe424Cys	538	0	0		431	104	0.241299	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Missense_Mutation	SNP	ENST00000400382.1	37	CCDS42992.1	.	.	.	.	.	.	.	.	.	.	.	13.74	2.326429	0.41197	.	.	ENSG00000100031	ENST00000248923;ENST00000412658;ENST00000400382;ENST00000400383;ENST00000400380;ENST00000406383;ENST00000401885;ENST00000404532;ENST00000403838;ENST00000404223;ENST00000404920	T;T;T;T;T;T;T;T;T;T;T	0.12569	2.67;2.67;2.67;2.67;2.67;2.67;2.67;2.67;2.67;2.67;2.67	3.49	3.49	0.39957	.	0.000000	0.85682	D	0.000000	T	0.53834	0.1821	H	0.99357	4.53	0.48511	D	0.999661	D	0.89917	1.0	D	0.81914	0.995	T	0.72001	-0.4422	10	0.87932	D	0	-41.2004	11.6793	0.51448	0.0:0.0:0.0:1.0	.	424	P19440	GGT1_HUMAN	C	424;424;424;424;424;424;80;80;80;80;80	ENSP00000248923:F424C;ENSP00000393537:F424C;ENSP00000383232:F424C;ENSP00000383233:F424C;ENSP00000383231:F424C;ENSP00000385975:F424C;ENSP00000384381:F80C;ENSP00000385445:F80C;ENSP00000384820:F80C;ENSP00000385016:F80C;ENSP00000385001:F80C	ENSP00000248923:F424C	F	+	2	0	GGT1	23353881	1.000000	0.71417	1.000000	0.80357	0.006000	0.05464	3.722000	0.54948	1.593000	0.50029	0.373000	0.22412	TTC	.	.	none		0.617	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430		G	25023881	T	G	25023881	3	3	27	1	0	0	0	0	1	0	0	0	6369	1783	62	5	1305	5	GGT1	22	25023881	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	536142	25023881	26280685	1024	11475											
DUSP18	150290	hgsc.bcm.edu	37	chr22	31059499	31059500	+	Frame_Shift_Del	DEL	CA	CA	-																															actggggaactgaccatgtgCacagtgttcttgccaaacaa																								rs538206035	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:31059499_31059500delCA	ENST00000334679.3	-	2	996_997	c.491_492delTG	c.(490-492)gtgfs	p.V164fs	DUSP18_ENST00000404885.1_Frame_Shift_Del_p.V164fs|DUSP18_ENST00000403268.1_3'UTR|DUSP18_ENST00000461301.1_Intron|DUSP18_ENST00000407308.1_Frame_Shift_Del_p.V164fs	NM_152511.3	NP_689724.3	Q8NEJ0	DUS18_HUMAN	dual specificity phosphatase 18	164					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						TGACCATGTGCACAGTGTTCTT	0.535														9	0.00179712	0.0	0.0	5008	,	,		20452	0.0		0.0089	False		,,,				2504	0.0				p.164_165del		Pindel,Atlas-Indel	.											.	DUSP18	10	.	0			c.492_493del						PASS	.			3,4261		0,3,2129						5.3	0.9		dbSNP_130	115	32,8222		0,32,4095	no	frameshift	DUSP18	NM_152511.3		0,35,6224	A1A1,A1R,RR		0.3877,0.0704,0.2796				35,12483				SO:0001589	frameshift_variant	150290	exon2			.	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.491_492delTG	22.37:g.31059501_31059502delCA	ENSP00000333917:p.Val164fs	128	0	.		119	32	0.269	NM_152511	B3KPA4	Frame_Shift_Del	DEL	ENST00000334679.3	37	CCDS13883.1																																																																																			.	.	weak		0.535	DUSP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321400.1			-	31059500	CA	-	31059499	7	5	27	1	0	1	0	1	0	0	0	0	4819	697	25	0	78	0	DUSP18	22	31059499	Frame_Shift_Del	DEL	CA	TCGA-G8-6909-01A-11D-2210-10	6035618	31059499	20245067	1025	11476											
APOL6	80830	hgsc.bcm.edu	37	chr22	36054944	36054944	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaagcctgctgctctccacCgctggtcaaggtttggcaac	7	9	12	13	1	2	0	1	0	1	0	3	1	2	1	3	4	4	5	3	4	3	1	rs34527373	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:36054944C>T	ENST00000409652.4	+	3	609	c.333C>T	c.(331-333)acC>acT	p.T111T		NM_030641.3	NP_085144.1	Q9BWW8	APOL6_HUMAN	apolipoprotein L, 6	111					lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)			haematopoietic_and_lymphoid_tissue(1)|lung(4)	5						TGCTCTCCACCGCTGGTCAAG	0.572													C|||	106	0.0211661	0.0424	0.013	5008	,	,		17602	0.0		0.0169	False		,,,				2504	0.0245				p.T111T		Atlas-SNP	.											.	APOL6	26	.	0			c.C333T						PASS	.	C		139,4267	98.0+/-136.7	1,137,2065	62	59	60		333	-8.3	0	22	dbSNP_126	60	165,8435	77.5+/-140.1	4,157,4139	no	coding-synonymous	APOL6	NM_030641.3		5,294,6204	TT,TC,CC		1.9186,3.1548,2.3374		111/344	36054944	304,12702	2203	4300	6503	SO:0001819	synonymous_variant	80830	exon3			CTCCACCGCTGGT	AY014879	CCDS13919.1	22q12.3	2013-01-24			ENSG00000221963	ENSG00000221963		"Apolipoproteins"	14870	protein-coding gene	gene with protein product		607256				11374903, 15671246	Standard	NM_030641		Approved	APOL-VI, APOLVI	uc003aoe.3	Q9BWW8	OTTHUMG00000150615	ENST00000409652.4:c.333C>T	22.37:g.36054944C>T		67	0	0		69	41	0.594203	NM_030641	Q5R3S1|Q658J1|Q8IXX6|Q9UGG1	Silent	SNP	ENST00000409652.4	37	CCDS13919.1																																																																																			C|0.975;T|0.025	0.025	strong		0.572	APOL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319081.2	NM_030641		T	36054944	C	T	36054944	2	4	27	1	0	0	0	0	0	0	0	1	810	639	23	1		1	APOL6	22	36054944	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	4995445	36054944	15249622	1026	11477											
APOL6	80830	hgsc.bcm.edu	37	chr22	36055130	36055130	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctggaaagattatctataaTcttagaaacaccttgaagta	16	12	7	6	0	2	3	0	1	2	2	2	4	2	4	1	1	1	2	1	1	8	6	rs5999923	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:36055130T>A	ENST00000409652.4	+	3	795	c.519T>A	c.(517-519)aaT>aaA	p.N173K		NM_030641.3	NP_085144.1	Q9BWW8	APOL6_HUMAN	apolipoprotein L, 6	173			N -> K (in dbSNP:rs5999923). {ECO:0000269|PubMed:17974005}.		lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)			haematopoietic_and_lymphoid_tissue(1)|lung(4)	5						TTATCTATAATCTTAGAAACA	0.493													T|||	120	0.0239617	0.0537	0.0086	5008	,	,		20620	0.002		0.0169	False		,,,				2504	0.0245				p.N173K		Atlas-SNP	.											.	APOL6	26	.	0			c.T519A						PASS	.	T	LYS/ASN	205,4201	124.1+/-161.4	7,191,2005	61	63	62		519	-8.1	0	22	dbSNP_114	62	168,8432	78.1+/-140.7	5,158,4137	yes	missense	APOL6	NM_030641.3	94	12,349,6142	AA,AT,TT		1.9535,4.6527,2.8679	benign	173/344	36055130	373,12633	2203	4300	6503	SO:0001583	missense	80830	exon3			CTATAATCTTAGA	AY014879	CCDS13919.1	22q12.3	2013-01-24			ENSG00000221963	ENSG00000221963		"Apolipoproteins"	14870	protein-coding gene	gene with protein product		607256				11374903, 15671246	Standard	NM_030641		Approved	APOL-VI, APOLVI	uc003aoe.3	Q9BWW8	OTTHUMG00000150615	ENST00000409652.4:c.519T>A	22.37:g.36055130T>A	ENSP00000386280:p.Asn173Lys	61	0	0		54	23	0.425926	NM_030641	Q5R3S1|Q658J1|Q8IXX6|Q9UGG1	Missense_Mutation	SNP	ENST00000409652.4	37	CCDS13919.1	42	0.019230769230769232	26	0.052845528455284556	5	0.013812154696132596	0	0.0	11	0.014511873350923483	T	0.015	-1.542021	0.00934	0.046527	0.019535	ENSG00000221963	ENST00000409652	T	0.03358	3.96	4.05	-8.09	0.01090	.	1.657170	0.04414	N	0.366552	T	0.00440	0.0014	L	0.41632	1.29	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.43523	-0.9386	10	0.14252	T	0.57	-4.2671	1.0684	0.01616	0.2834:0.3061:0.2313:0.1793	rs5999923;rs52798245;rs5999923	173	Q9BWW8	APOL6_HUMAN	K	173	ENSP00000386280:N173K	ENSP00000386280:N173K	N	+	3	2	APOL6	34385076	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.755000	0.00375	-3.583000	0.00137	-1.567000	0.00876	AAT	T|0.973;A|0.027	0.027	strong		0.493	APOL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319081.2	NM_030641		A	36055130	T	A	36055130	3	1	27	1	0	0	0	0	1	0	0	0	810	1432	50	5	525	5	APOL6	22	36055130	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	186	36055130	15249436	1027	11478											
APOBEC3B	9582	hgsc.bcm.edu	37	chr22	39381936	39381936	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtatcctggaccccctgcccGgactgtgtggcgaagctggc	5	8	14	14	2	0	0	0	0	0	0	1	3	1	2	4	4	2	2	4	4	2	1	rs138362043	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:39381936G>A	ENST00000333467.3	+	3	339	c.294G>A	c.(292-294)ccG>ccA	p.P98P	APOBEC3B_ENST00000407298.3_Silent_p.P98P|APOBEC3B_ENST00000402182.3_Silent_p.P98P	NM_001270411.1|NM_004900.4	NP_001257340.1|NP_004891	Q9UH17	ABC3B_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B	98	CMP/dCMP deaminase zinc-binding 1.		P -> L (in dbSNP:rs2076110).		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)					CCCCCTGCCCGGACTGTGTGG	0.557													G|||	2	0.000399361	0.0015	0.0	5008	,	,		15975	0.0		0.0	False		,,,				2504	0.0				p.P98P		Atlas-SNP	.											APOBEC3B,colon,carcinoma,+1,1	APOBEC3B	32	1	0			c.G294A						PASS	.	G		1,4403		0,1,2201	139	133	135		294	-4.2	0	22	dbSNP_134	135	5,8591		0,5,4293	no	coding-synonymous	APOBEC3B	NM_004900.3		0,6,6494	AA,AG,GG		0.0582,0.0227,0.0462		98/383	39381936	6,12994	2202	4298	6500	SO:0001819	synonymous_variant	9582	exon3			CTGCCCGGACTGT	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.294G>A	22.37:g.39381936G>A		244	0	0		168	117	0.696429	NM_004900	B0QYD2|O95618|Q20WL1|Q5IFJ4|Q7Z2N3|Q7Z6D6|Q9UE74	Silent	SNP	ENST00000333467.3	37	CCDS13982.1																																																																																			G|1.000;A|0.000	0.000	weak		0.557	APOBEC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321233.1	NM_004900		A	39381936	G	A	39381936	2	1	27	1	0	0	0	0	0	0	0	1	790	1103	39	1		1	APOBEC3B	22	39381936	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	3326806	39381936	11922630	1028	11479											
SREBF2	6721	hgsc.bcm.edu	37	chr22	42290890	42290890	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagcgagctatagagtcctTggtgaaacctcaggccaaga	12	7	13	9	1	1	3	1	1	0	2	2	5	2	4	3	3	3	1	3	3	4	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:42290890T>C	ENST00000361204.4	+	13	2610	c.2444T>C	c.(2443-2445)tTg>tCg	p.L815S	SREBF2_ENST00000491541.1_3'UTR	NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	815					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						ATAGAGTCCTTGGTGAAACCT	0.572																																					p.L815S		Atlas-SNP	.											.	SREBF2	99	.	0			c.T2444C						PASS	.						82	83	83					22																	42290890		2203	4300	6503	SO:0001583	missense	6721	exon13			AGTCCTTGGTGAA	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.2444T>C	22.37:g.42290890T>C	ENSP00000354476:p.Leu815Ser	60	0	0		73	21	0.287671	NM_004599	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Missense_Mutation	SNP	ENST00000361204.4	37	CCDS14023.1	.	.	.	.	.	.	.	.	.	.	T	29.4	4.999699	0.93227	.	.	ENSG00000198911	ENST00000361204;ENST00000457567	T	0.27104	1.69	5.96	5.96	0.96718	.	0.063149	0.64402	D	0.000005	T	0.47655	0.1457	M	0.69358	2.11	0.80722	D	1	D	0.71674	0.998	P	0.61070	0.883	T	0.47812	-0.9088	10	0.87932	D	0	-12.0099	16.4484	0.83959	0.0:0.0:0.0:1.0	.	815	Q12772	SRBP2_HUMAN	S	815	ENSP00000354476:L815S	ENSP00000354476:L815S	L	+	2	0	SREBF2	40620836	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	7.049000	0.76613	2.285000	0.76669	0.533000	0.62120	TTG	.	.	none		0.572	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599		C	42290890	T	C	42290890	3	2	27	1	0	0	0	0	1	0	0	0	15157	1821	63	3	2494	3	SREBF2	22	42290890	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	2908954	42290890	9013676	1029	11480											
C22orf9	23313	hgsc.bcm.edu	37	chr22	45608215	45608215	+	Intron	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctccactcagcagcagcctGagagcccatgctcccagccc	8	5	8	20	0	1	1	1	1	0	1	3	2	3	1	6	0	6	3	6	0	0	0	rs150665432	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:45608215G>A	ENST00000336156.5	-	2	130				KIAA0930_ENST00000496226.1_5'UTR|KIAA0930_ENST00000492273.1_Nonsense_Mutation_p.Q4*|KIAA0930_ENST00000443310.3_Intron|KIAA0930_ENST00000251993.7_Nonsense_Mutation_p.Q4*|KIAA0930_ENST00000391627.2_Intron	NM_001009880.1	NP_001009880.1	Q6ICG6	K0930_HUMAN	KIAA0930											endometrium(1)|kidney(4)|large_intestine(2)|lung(7)|urinary_tract(1)	15						GCAGCAGCCTGAGAGCCCATG	0.637													G|||	10	0.00199681	0.0015	0.0029	5008	,	,		16127	0.0		0.004	False		,,,				2504	0.002				p.Q4X		Atlas-SNP	.											.	KIAA0930	43	.	0			c.C10T						PASS	.	G	,stop/GLN	3,4401	6.2+/-15.9	0,3,2199	32	32	32		,10	-1.5	0	22	dbSNP_134	32	35,8563	23.4+/-69.3	1,33,4265	yes	intron,stop-gained	KIAA0930	NM_001009880.1,NM_015264.1	,	1,36,6464	AA,AG,GG		0.4071,0.0681,0.2923	,	,4/410	45608215	38,12964	2202	4299	6501	SO:0001627	intron_variant	23313	exon1			CAGCCTGAGAGCC	AK025608	CCDS33665.1, CCDS33666.1	22q13.31	2011-02-23	2011-02-23	2011-02-23	ENSG00000100364	ENSG00000100364			1314	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 9"	C22orf9		10231032	Standard	NM_015264		Approved	bK268H5.C22.1	uc003bfw.1	Q6ICG6	OTTHUMG00000151263	ENST00000336156.5:c.65-227C>T	22.37:g.45608215G>A		123	0	0		85	47	0.552941	NM_015264	B0QY17|B0QY19|B3KT48|Q6ZVE5|Q7Z6K9|Q8IZ76|Q9Y2E2	Nonsense_Mutation	SNP	ENST00000336156.5	37	CCDS33665.1	10	0.004578754578754579	2	0.0040650406504065045	2	0.0055248618784530384	1	0.0017482517482517483	5	0.006596306068601583	G	15.73	2.919233	0.52546	6.81E-4	0.004071	ENSG00000100364	ENST00000251993	.	.	.	2.41	-1.47	0.08772	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.23302	T	0.38	.	4.8647	0.13602	0.1506:0.3861:0.4633:0.0	.	.	.	.	X	4	.	ENSP00000251993:Q4X	Q	-	1	0	KIAA0930	43986879	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.788000	0.04614	-0.192000	0.10432	-0.258000	0.10820	CAG	G|0.996;A|0.004	0.004	strong		0.637	KIAA0930-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321975.2	NM_001009880		A	45608215	G	A	45608215	1	1	27	0	1	0	0	0	0	0	0	0	2153	1299	45	2		2	C22orf9	22	45608215	Intron	SNP	G	TCGA-G8-6909-01A-11D-2210-10	3317325	45608215	5696351	1030	11481											
PKDREJ	10343	hgsc.bcm.edu	37	chr22	46657894	46657894	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggaccctcttatcagaaaaCgctgtcctagagtccttccg	9	11	8	13	2	2	2	1	0	1	2	5	3	5	3	4	1	1	1	4	1	4	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:46657894C>T	ENST00000253255.5	-	1	1325	c.1326G>A	c.(1324-1326)gcG>gcA	p.A442A		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	442	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				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)			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)		TATCAGAAAACGCTGTCCTAG	0.468																																					p.A442A		Atlas-SNP	.											.	PKDREJ	195	.	0			c.G1326A						PASS	.						110	103	105					22																	46657894		2203	4300	6503	SO:0001819	synonymous_variant	10343	exon1			AGAAAACGCTGTC	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.1326G>A	22.37:g.46657894C>T		199	0	0		183	47	0.256831	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																			.	.	none		0.468	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071		T	46657894	C	T	46657894	2	4	27	1	0	0	0	0	0	0	0	1	11979	523	19	1		1	PKDREJ	22	46657894	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1049679	46657894	4646672	1031	11482											
PLXNB2	23654	hgsc.bcm.edu	37	chr22	50726134	50726134	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcatgttctgtggctgggCgctggtgacggccacgcagg	4	9	17	11	3	2	1	1	1	1	0	2	1	2	1	1	5	0	5	1	5	0	1	rs375580670		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chr22:50726134C>T	ENST00000449103.1	-	7	1710	c.1570G>A	c.(1570-1572)Gcc>Acc	p.A524T	PLXNB2_ENST00000359337.4_Missense_Mutation_p.A524T|PLXNB2_ENST00000496720.1_5'Flank			O15031	PLXB2_HUMAN	plexin B2	524					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)		TGTGGCTGGGCGCTGGTGACG	0.746																																					p.A524T		Atlas-SNP	.											.	PLXNB2	172	.	0			c.G1570A						PASS	.	C	THR/ALA	0,3290		0,0,1645	3	4	4		1570	2.7	0	22		4	2,7290		0,2,3644	no	missense	PLXNB2	NM_012401.3	58	0,2,5289	TT,TC,CC		0.0274,0.0,0.0189	possibly-damaging	524/1839	50726134	2,10580	1645	3646	5291	SO:0001583	missense	23654	exon7			GCTGGGCGCTGGT		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.1570G>A	22.37:g.50726134C>T	ENSP00000409171:p.Ala524Thr	21	0	0		37	11	0.297297	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Missense_Mutation	SNP	ENST00000449103.1	37	CCDS43035.1	.	.	.	.	.	.	.	.	.	.	C	9.673	1.147298	0.21288	0.0	2.74E-4	ENSG00000196576	ENST00000449103;ENST00000359337	T;T	0.03272	3.99;3.99	4.84	2.73	0.32206	.	0.106352	0.41712	D	0.000837	T	0.06096	0.0158	M	0.69823	2.125	0.09310	N	0.99999	B	0.13145	0.007	B	0.04013	0.001	T	0.19778	-1.0295	10	0.59425	D	0.04	.	10.3837	0.44127	0.0:0.8373:0.0:0.1627	.	524	O15031	PLXB2_HUMAN	T	524	ENSP00000409171:A524T;ENSP00000352288:A524T	ENSP00000352288:A524T	A	-	1	0	PLXNB2	49068261	0.454000	0.25728	0.005000	0.12908	0.006000	0.05464	0.904000	0.28491	0.759000	0.33084	0.561000	0.74099	GCC	.	.	weak		0.746	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401		T	50726134	C	T	50726134	3	4	27	1	0	0	0	0	1	0	0	0	12133	768	27	1	4070	1	PLXNB2	22	50726134	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	4068240	50726134	578432	1032	11483											
P2RY8	286530	hgsc.bcm.edu	37	chrX	1584817	1584817	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgaggatggtggccgtgtaaCaagccacggtgatcacgaac	11	7	14	9	3	1	2	1	2	0	0	1	4	1	3	2	4	3	1	2	4	3	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:1584817C>T	ENST00000381297.4	-	2	845	c.635G>A	c.(634-636)tGt>tAt	p.C212Y	P2RY8_ENST00000460672.1_5'Flank	NM_178129.4	NP_835230.1	Q86VZ1	P2RY8_HUMAN	purinergic receptor P2Y, G-protein coupled, 8	212						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(13)|prostate(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)				GGCCGTGTAACAAGCCACGGT	0.657			T	CRLF2	"B-ALL, Downs associated ALL"																																p.C212Y		Atlas-SNP	.		Dom	yes		"X,Y"	Xp22.3; Yp11.3	286530	"purinergic receptor P2Y, G-protein coupled, 8"		L	.	P2RY8	53	.	0			c.G635A						PASS	.						102	55	71					X																	1584817		2203	4295	6498	SO:0001583	missense	286530	exon2			GTGTAACAAGCCA	AA804531	CCDS14115.1	Xp22.33 and Yp11.3	2012-08-08			ENSG00000182162	ENSG00000182162		"Pseudoautosomal regions / PAR1", "Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	15524	protein-coding gene	gene with protein product		300525				11004484	Standard	NM_178129		Approved	P2Y8	uc004cpz.2	Q86VZ1	OTTHUMG00000021060	ENST00000381297.4:c.635G>A	X.37:g.1584817C>T	ENSP00000370697:p.Cys212Tyr	84	0	0		68	27	0.397059	NM_178129		Missense_Mutation	SNP	ENST00000381297.4	37	CCDS14115.1	.	.	.	.	.	.	.	.	.	.	c	13.10	2.136811	0.37728	.	.	ENSG00000182162	ENST00000381297	T	0.42131	0.98	2.41	2.41	0.29592	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	U	0.000000	T	0.66557	0.2801	M	0.87682	2.9	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.61436	-0.7063	10	0.87932	D	0	.	12.9335	0.58301	0.0:1.0:0.0:0.0	.	212	Q86VZ1	P2RY8_HUMAN	Y	212	ENSP00000370697:C212Y	ENSP00000370697:C212Y	C	-	2	0	P2RY8	1544817	1.000000	0.71417	0.993000	0.49108	0.058000	0.15608	6.011000	0.70760	0.838000	0.34948	0.279000	0.19357	TGT	.	.	none		0.657	P2RY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055602.1	NM_178129		T	1584817	C	T	1584817	3	4	27	1	0	0	0	0	1	0	0	0	11364	478	17	2	448	2	P2RY8	23	1584817	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10		1584817	153685743	1033	11484											
ARSF	416	hgsc.bcm.edu	37	chrX	3021870	3021870	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	attgtccgatggcctggaaaGgtaccagctggacggttgat	9	10	14	8	2	0	1	0	1	0	0	1	4	1	3	3	5	2	3	3	5	2	3			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:3021870G>T	ENST00000381127.1	+	9	1391	c.1170G>T	c.(1168-1170)aaG>aaT	p.K390N	ARSF_ENST00000359361.2_Missense_Mutation_p.K390N|ARSF_ENST00000537104.1_Missense_Mutation_p.K390N	NM_001201538.1|NM_001201539.1	NP_001188467.1|NP_001188468.1	P54793	ARSF_HUMAN	arylsulfatase F	390					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)				GGCCTGGAAAGGTACCAGCTG	0.473																																					p.K390N		Atlas-SNP	.											.	ARSF	97	.	0			c.G1170T						PASS	.						101	92	95					X																	3021870		2203	4300	6503	SO:0001583	missense	416	exon9			TGGAAAGGTACCA	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.1170G>T	X.37:g.3021870G>T	ENSP00000370519:p.Lys390Asn	248	0	0		152	152	1	NM_004042	Q8TCC5	Missense_Mutation	SNP	ENST00000381127.1	37	CCDS14123.1	.	.	.	.	.	.	.	.	.	.	G	10.14	1.268921	0.23221	.	.	ENSG00000062096	ENST00000381127;ENST00000537104;ENST00000359361	D;D;D	0.98684	-5.07;-5.07;-5.07	3.4	-1.61	0.08399	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.484707	0.19510	U	0.112538	D	0.96414	0.8830	L	0.61387	1.9	0.09310	N	1	B	0.20671	0.047	B	0.32090	0.14	D	0.89916	0.4055	10	0.16896	T	0.51	.	6.4355	0.21821	0.2735:0.1278:0.5988:0.0	.	390	P54793	ARSF_HUMAN	N	390	ENSP00000370519:K390N;ENSP00000445594:K390N;ENSP00000352319:K390N	ENSP00000352319:K390N	K	+	3	2	ARSF	3031870	0.000000	0.05858	0.000000	0.03702	0.115000	0.19883	-1.019000	0.03622	-0.569000	0.06030	0.279000	0.19357	AAG	.	.	none		0.473	ARSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055652.1			T	3021870	G	T	3021870	3	4	27	1	0	0	0	0	1	0	0	0	991	991	35	4	1200	4	ARSF	23	3021870	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1437053	3021870	152248690	1034	11485											
VCX3A	51481	hgsc.bcm.edu	37	chrX	6451834	6451834	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctcctgactcagtggttcCtccacctggctctcctgact	4	13	7	17	0	3	2	1	2	2	0	7	2	5	2	5	2	0	2	5	2	0	1	rs146638597		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:6451834C>T	ENST00000381089.3	-	3	819	c.513G>A	c.(511-513)gaG>gaA	p.E171E	VCX3A_ENST00000398729.1_Silent_p.E151E	NM_016379.3	NP_057463.2	Q9NNX9	VCX3_HUMAN	variable charge, X-linked 3A	171	8 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.|Glu-rich.				brain development (GO:0007420)	nucleolus (GO:0005730)|nucleus (GO:0005634)				NS(1)|lung(2)|pancreas(1)	4						TCAGTGGTTCCTCCACCTGGC	0.587																																					p.E171E		Atlas-SNP	.											.	VCX3A	17	.	0			c.G513A						PASS	.						230	203	212					X																	6451834		2203	4296	6499	SO:0001819	synonymous_variant	51481	exon3			TGGTTCCTCCACC	AF159128	CCDS35199.1	Xp22.31	2008-02-05	2005-01-11	2005-01-12	ENSG00000169059	ENSG00000169059			18159	protein-coding gene	gene with protein product		300533	"variable charge, X-linked 3"	VCX3		10607842	Standard	NM_016379		Approved	VCX-8r, VCX-8R, VCX-A	uc004crs.3	Q9NNX9	OTTHUMG00000021097	ENST00000381089.3:c.513G>A	X.37:g.6451834C>T		1050	0	0		927	82	0.0884574	NM_016379	Q9P0H4	Silent	SNP	ENST00000381089.3	37	CCDS35199.1																																																																																			.	.	weak		0.587	VCX3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055679.1	NM_016379		T	6451834	C	T	6451834	2	4	27	1	0	0	0	0	0	0	0	1	17159	680	24	2		2	VCX3A	23	6451834	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	3429964	6451834	148818726	1035	11486											
VCX	26609	hgsc.bcm.edu	37	chrX	7811760	7811760	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccccctgagtcaggaggcCgagctggaggaaccactgag	10	4	15	12	1	1	2	1	2	0	0	1	7	1	5	4	4	2	1	4	4	1	0	rs202230674		TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:7811760C>A	ENST00000381059.3	+	3	543	c.324C>A	c.(322-324)gcC>gcA	p.A108A	VCX_ENST00000341408.4_Silent_p.A108A	NM_013452.2	NP_038480.2	Q9H320	VCX1_HUMAN	variable charge, X-linked	108	10 X 10 AA tandem repeats of L-S-Q-E-S- [EQ]-V-E-E-P.|Glu-rich.			A -> S (in Ref. 3; AAH98123). {ECO:0000305}.	chromatin organization (GO:0006325)|ribosome assembly (GO:0042255)|spermatogenesis (GO:0007283)	nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(1)|endometrium(4)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	10		Colorectal(8;0.0136)|Medulloblastoma(8;0.184)				GTCAGGAGGCCGAGCTGGAGG	0.662																																					p.A108A		Atlas-SNP	.											.	VCX	28	.	0			c.C324A						PASS	.						83	103	96					X																	7811760		2133	4081	6214	SO:0001819	synonymous_variant	26609	exon3			GGAGGCCGAGCTG	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.324C>A	X.37:g.7811760C>A		127	0	0		77	18	0.233766	NM_013452	A0JNS5|Q4V774|Q9P0H3	Silent	SNP	ENST00000381059.3	37	CCDS14128.1																																																																																			.	.	alt		0.662	VCX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071474.1	NM_013452		A	7811760	C	A	7811760	2	1	27	1	0	0	0	0	0	0	0	1	17157	639	23	4		4	VCX	23	7811760	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1359926	7811760	147458800	1036	11487											
WWC3	55841	hgsc.bcm.edu	37	chrX	10085582	10085582	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgaggggccaggcctgggcGccctagacagactgcgggca	7	4	18	12	2	0	3	0	1	0	2	0	3	0	3	3	5	1	1	3	5	1	1	rs5934750	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:10085582G>A	ENST00000380861.4	+	11	1874	c.1483G>A	c.(1483-1485)Gcc>Acc	p.A495T	WWC3_ENST00000454666.1_Missense_Mutation_p.A495T	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	495			A -> T (in dbSNP:rs5934750).		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						AGGCCTGGGCGCCCTAGACAG	0.716													G|||	103	0.0272848	0.0015	0.1153	3775	,	,		11338	0.0		0.0179	False		,,,				2504	0.0031				p.A495T		Atlas-SNP	.											.	WWC3	142	.	0			c.G1483A						PASS	.	G	THR/ALA	17,3724		0,15,2,1590,529	6	7	7		1483	-1.5	0	X	dbSNP_114	7	117,6434		1,87,28,2309,1729	yes	missense	WWC3	NM_015691.3	58	1,102,30,3899,2258	AA,AG,A,GG,G		1.786,0.4544,1.302	benign	495/1093	10085582	134,10158	2136	4154	6290	SO:0001583	missense	55841	exon11			CTGGGCGCCCTAG	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.1483G>A	X.37:g.10085582G>A	ENSP00000370242:p.Ala495Thr	40	0	0		61	60	0.983607	NM_015691	A8KA96|Q659C1|Q9BTQ1	Missense_Mutation	SNP	ENST00000380861.4	37	CCDS14136.1	43	0.02591922845087402	2	0.0040650406504065045	20	0.057803468208092484	0	0.0	10	0.013333333333333334	G	6.680	0.494023	0.12702	0.004544	0.01786	ENSG00000047644	ENST00000380861;ENST00000454666;ENST00000543293;ENST00000398613	T;T	0.04970	3.52;3.52	5.43	-1.5	0.08691	.	0.930558	0.09241	N	0.829226	T	0.00328	0.0010	N	0.08118	0	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.48525	-0.9028	9	0.13108	T	0.6	-0.0979	4.8631	0.13594	0.3152:0.0:0.4536:0.2312	rs5934750	495	Q9ULE0	WWC3_HUMAN	T	495;495;159;495	ENSP00000370242:A495T;ENSP00000399584:A495T	ENSP00000370242:A495T	A	+	1	0	WWC3	10045582	0.000000	0.05858	0.000000	0.03702	0.567000	0.35839	0.043000	0.13971	-0.495000	0.06659	-0.382000	0.06688	GCC	G|0.973;A|0.027	0.027	strong		0.716	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691		A	10085582	G	A	10085582	3	1	27	1	0	0	0	0	1	0	0	0	17428	1087	38	1	1521	1	WWC3	23	10085582	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	2273822	10085582	145184978	1037	11488											
ARHGAP6	395	hgsc.bcm.edu	37	chrX	11682921	11682921	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcgaggaacaggagaagaCgctgtggagcaggctctgcg	10	4	19	8	3	1	2	0	0	1	2	1	6	1	4	0	5	3	3	0	5	2	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:11682921C>A	ENST00000337414.4	-	1	900	c.28G>T	c.(28-30)Gtc>Ttc	p.V10F	ARHGAP6_ENST00000380732.3_Missense_Mutation_p.V10F|ARHGAP6_ENST00000380718.1_Missense_Mutation_p.V10F	NM_013427.2	NP_038286.2	O43182	RHG06_HUMAN	Rho GTPase activating protein 6	10					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						CAGGAGAAGACGCTGTGGAGC	0.677																																					p.V10F		Atlas-SNP	.											.	ARHGAP6	130	.	0			c.G28T						PASS	.						8	10	10					X																	11682921		1777	3411	5188	SO:0001583	missense	395	exon1			AGAAGACGCTGTG	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.28G>T	X.37:g.11682921C>A	ENSP00000338967:p.Val10Phe	114	0	0		110	37	0.336364	NM_006125	B2RWQ0|O43437|Q9P1B3|Q9UK81|Q9UK82	Missense_Mutation	SNP	ENST00000337414.4	37	CCDS14140.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.634288	0.87660	.	.	ENSG00000047648	ENST00000337414;ENST00000380718;ENST00000380732	T;T;T	0.44881	1.35;1.19;0.91	4.82	4.82	0.62117	.	.	.	.	.	T	0.50548	0.1622	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.997	T	0.56595	-0.7953	9	0.87932	D	0	.	14.4354	0.67277	0.0:1.0:0.0:0.0	.	10;10	O43182-2;O43182	.;RHG06_HUMAN	F	10	ENSP00000338967:V10F;ENSP00000370094:V10F;ENSP00000370108:V10F	ENSP00000338967:V10F	V	-	1	0	ARHGAP6	11592842	1.000000	0.71417	1.000000	0.80357	0.888000	0.51559	3.516000	0.53436	1.987000	0.57996	0.594000	0.82650	GTC	.	.	none		0.677	ARHGAP6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055760.2	NM_013427		A	11682921	C	A	11682921	3	1	27	1	0	0	0	0	1	0	0	0	887	536	19	4	3070	4	ARHGAP6	23	11682921	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	1597339	11682921	143587639	1038	11489											
DMD	1756	hgsc.bcm.edu	37	chrX	32486756	32486756	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atttcagagggcgctttcttCgacatctctttcacagtggt	7	15	9	10	2	4	1	2	0	2	1	6	2	4	1	0	2	0	1	0	2	0	4	rs1800268	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:32486756C>T	ENST00000357033.4	-	23	3227	c.3021G>A	c.(3019-3021)tcG>tcA	p.S1007S	DMD_ENST00000378677.2_Silent_p.S1003S	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	1007					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)				GCGCTTTCTTCGACATCTCTT	0.408													C|||	33	0.00874172	0.0	0.013	3775	,	,		11926	0.0		0.0159	False		,,,				2504	0.0082				p.S1007S		Atlas-SNP	.											.	DMD	2127	.	0			c.G3021A						PASS	.	C	,,,,	15,3818		0,12,3,1619,568	75	68	70		2997,3021,2652,3009,2652	-2.5	0.9	X	dbSNP_89	70	112,6616		0,87,25,2341,1847	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DMD	NM_000109.3,NM_004006.2,NM_004007.2,NM_004009.3,NM_004010.3	,,,,	0,99,28,3960,2415	TT,TC,T,CC,C		1.6647,0.3913,1.2025	,,,,	999/3678,1007/3686,884/3563,1003/3682,884/3563	32486756	127,10434	2202	4300	6502	SO:0001819	synonymous_variant	1756	exon23			TTTCTTCGACATC	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.3021G>A	X.37:g.32486756C>T		420	0	0		238	238	1	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Silent	SNP	ENST00000357033.4	37	CCDS14233.1																																																																																			C|0.989;T|0.011	0.011	strong		0.408	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006		T	32486756	C	T	32486756	2	4	27	1	0	0	0	0	0	0	0	1	4582	871	31	1		1	DMD	23	32486756	Silent	SNP	C	TCGA-G8-6909-01A-11D-2210-10	20803835	32486756	122783804	1039	11490											
RPGR	6103	hgsc.bcm.edu	37	chrX	38145791	38145805	+	Intron	DEL	CCTCTACTTCCCCTC	CCTCTACTTCCCCTC	-																															ttccctctctcctttcccctCctctacttcccctccctcta																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	CCTCTACTTCCCCTC	CCTCTACTTCCCCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:38145791_38145805delCCTCTACTTCCCCTC	ENST00000339363.3	-	14	2688				RPGR_ENST00000338898.3_Intron|RPGR_ENST00000378505.2_In_Frame_Del_p.GGEVE816del|RPGR_ENST00000342811.3_Intron|RPGR_ENST00000318842.7_Intron|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000309513.3_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						cctttcccctcctctacttcccctccctctacttc	0.595														2	0.000529801	0.0	0.0	3775	,	,		7341	0.0		0.002	False		,,,				2504	0.0				p.816_821del		Pindel	.											.	RPGR	175	.	0			c.2448_2462del	GRCh37	CD020354	orf15	D		PASS	.		,	16,2991		1,13,1,1344,290					,	1.2	0			113	16,4996		3,7,3,1902,1185	no	coding,intron	RPGR	NM_001034853.1,NM_000328.2	,	4,20,4,3246,1475	A1A1,A1R,A1,RR,R		0.3192,0.5321,0.3991	,	,		32,7987				SO:0001627	intron_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.2520+541GAGGGGAAGTAGAGG>-	X.37:g.38145791_38145805delCCTCTACTTCCCCTC		197	0	.		33	18	0.545	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	In_Frame_Del	DEL	ENST00000339363.3	37																																																																																				.	.	none		0.595	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328		-	38145805	CCTCTACTTCCCCTC	-	38145791	6	5	27	0	1	1	0	1	0	0	0	0	13563	864	30	0		0	RPGR	23	38145791	Intron	DEL	CCTCTACTTCCCCTC	TCGA-G8-6909-01A-11D-2210-10	5659035	38145791	117124769	1040	11491											
RPGR	6103	hgsc.bcm.edu	37	chrX	38145805	38145805	+	Intron	DEL	C	C	-																															tcccctcctctacttcccctCcctctacttcccctccctcc																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:38145805delC	ENST00000339363.3	-	14	2688				RPGR_ENST00000338898.3_Intron|RPGR_ENST00000378505.2_Frame_Shift_Del_p.G817fs|RPGR_ENST00000342811.3_Intron|RPGR_ENST00000318842.7_Intron|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000309513.3_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						tacttcccctccctctacttc	0.597																																					p.G816fs		Atlas-Indel	.											.	RPGR	175	.	0			c.2448delA						PASS	.						159	119	133					X																	38145805		1802	3474	5276	SO:0001627	intron_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.2520+541G>-	X.37:g.38145805delC		209	0	0		38	17	0.447368	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Frame_Shift_Del	DEL	ENST00000339363.3	37																																																																																				.	.	none		0.597	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328		-	38145805	C	-	38145805	6	5	27	0	1	1	0	1	0	0	0	0	13563	855	30	0		0	RPGR	23	38145805	Intron	DEL	C	TCGA-G8-6909-01A-11D-2210-10	14	38145805	117124755	1041	11492											
BCOR	54880	hgsc.bcm.edu	37	chrX	39932949	39932949	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acgttagtgatgacagcatcGgtgccgcccatgcgcgggca	8	7	14	12	5	0	2	0	2	0	0	1	2	0	2	2	2	3	3	2	2	1	1	rs17145653	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:39932949G>A	ENST00000378444.4	-	4	1878	c.1650C>T	c.(1648-1650)acC>acT	p.T550T	BCOR_ENST00000342274.4_Silent_p.T550T|BCOR_ENST00000397354.3_Silent_p.T550T|BCOR_ENST00000378455.4_Silent_p.T550T	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	550					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						TGACAGCATCGGTGCCGCCCA	0.572			"F, N, S, T"	RARA	"retinoblastoma, AML, APL(translocation)"		oculo-facio-cardio-dental genetic						G|||	11	0.00291391	0.0015	0.0014	3775	,	,		14756	0.0		0.007	False		,,,				2504	0.001				p.T550T		Atlas-SNP	.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	.	0			c.C1650T						PASS	.	G	,,,	5,3828		0,5,0,1626,571	110	70	84		1650,1650,1650,1650	-11.2	0	X	dbSNP_123	84	76,6652		0,58,18,2370,1854	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BCOR	NM_001123383.1,NM_001123384.1,NM_001123385.1,NM_017745.5	,,,	0,63,18,3996,2425	AA,AG,A,GG,G		1.1296,0.1304,0.767	,,,	550/1722,550/1704,550/1756,550/1722	39932949	81,10480	2202	4300	6502	SO:0001819	synonymous_variant	54880	exon4			AGCATCGGTGCCG	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.1650C>T	X.37:g.39932949G>A		119	1	0.00840336		74	73	0.986486	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Silent	SNP	ENST00000378444.4	37	CCDS48093.1																																																																																			0|0.004;A|0.006	0.006	strong		0.572	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745		A	39932949	G	A	39932949	2	1	27	1	0	0	0	0	0	0	0	1	1386	1103	39	1		1	BCOR	23	39932949	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	1787144	39932949	115337611	1042	11493											
KCND1	3750	hgsc.bcm.edu	37	chrX	48826490	48826490	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccgagctgcccagcaaggtGtctgggtagcggtccagcgt	6	8	15	12	3	1	0	0	0	1	0	3	1	3	0	3	3	5	3	3	3	2	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:48826490G>A	ENST00000218176.3	-	1	1486	c.189C>T	c.(187-189)gaC>gaT	p.D63D	KCND1_ENST00000376477.1_5'Flank	NM_004979.4	NP_004970.3	Q9NSA2	KCND1_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 1	63					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)	CCAGCAAGGTGTCTGGGTAGC	0.567																																					p.D63D		Atlas-SNP	.											.	KCND1	63	.	0			c.C189T						PASS	.						46	31	36					X																	48826490		2203	4300	6503	SO:0001819	synonymous_variant	3750	exon1			CAAGGTGTCTGGG	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.189C>T	X.37:g.48826490G>A		254	0	0		166	53	0.319277	NM_004979	A6NEF1|B2RCG0|O75671	Silent	SNP	ENST00000218176.3	37	CCDS14314.1																																																																																			.	.	none		0.567	KCND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060774.1	NM_004979		A	48826490	G	A	48826490	2	1	27	1	0	0	0	0	0	0	0	1	8027	1368	48	2		2	KCND1	23	48826490	Silent	SNP	G	TCGA-G8-6909-01A-11D-2210-10	8893541	48826490	106444070	1043	11494											
WNK3	65267	hgsc.bcm.edu	37	chrX	54265469	54265469	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcagatgaatggctccacCgcttgacacagcagcaggat	11	7	11	12	1	0	3	0	2	0	1	1	4	1	4	2	2	3	5	2	2	1	1			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:54265469C>T	ENST00000375159.2	-	17	3714	c.3715G>A	c.(3715-3717)Ggt>Agt	p.G1239S	WNK3_ENST00000354646.2_Missense_Mutation_p.G1239S|WNK3_ENST00000375169.3_Missense_Mutation_p.G1239S			Q9BYP7	WNK3_HUMAN	WNK lysine deficient protein kinase 3	1239					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						ATGGCTCCACCGCTTGACACA	0.448																																					p.G1239S		Atlas-SNP	.											.	WNK3	218	.	0			c.G3715A						PASS	.						63	59	60					X																	54265469		2203	4300	6503	SO:0001583	missense	65267	exon18			CTCCACCGCTTGA	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.3715G>A	X.37:g.54265469C>T	ENSP00000364301:p.Gly1239Ser	63	0	0		50	34	0.68	NM_001002838	B1AKG2|Q5JRC1|Q6JP76|Q8TCX6|Q9HCK6	Missense_Mutation	SNP	ENST00000375159.2	37	CCDS14357.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.486242	0.44147	.	.	ENSG00000196632	ENST00000375169;ENST00000354646;ENST00000375159	T;T;T	0.72167	-0.44;-0.63;-0.63	5.02	3.2	0.36748	.	0.584613	0.15074	N	0.282037	T	0.65491	0.2696	L	0.27053	0.805	0.19300	N	0.999975	D;D	0.76494	0.999;0.995	P;P	0.58454	0.839;0.492	T	0.53648	-0.8409	10	0.08837	T	0.75	0.202	8.816	0.34996	0.0:0.7647:0.1477:0.0875	.	1239;1239	Q9BYP7-3;Q9BYP7	.;WNK3_HUMAN	S	1239	ENSP00000364312:G1239S;ENSP00000346667:G1239S;ENSP00000364301:G1239S	ENSP00000346667:G1239S	G	-	1	0	WNK3	54282194	0.002000	0.14202	0.507000	0.27676	0.736000	0.42039	0.569000	0.23638	0.342000	0.23796	0.538000	0.68166	GGT	.	.	none		0.448	WNK3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056799.2	NM_020922		T	54265469	C	T	54265469	3	4	27	1	0	0	0	0	1	0	0	0	17394	652	23	1	1715	1	WNK3	23	54265469	Missense_Mutation	SNP	C	TCGA-G8-6909-01A-11D-2210-10	5438979	54265469	101005091	1044	11495											
HEPH	9843	hgsc.bcm.edu	37	chrX	65390579	65390579	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagcctctggacagtgacaTgtaggtttaatttcttgtgg	8	14	11	8	0	2	1	0	1	2	0	2	2	2	2	2	3	1	2	2	3	2	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:65390579T>C	ENST00000343002.2	+	1	831	c.167T>C	c.(166-168)aTa>aCa	p.I56T	HEPH_ENST00000374727.3_Splice_Site_p.I59T|HEPH_ENST00000519389.1_Splice_Site_p.I110T|HEPH_ENST00000336279.5_Intron|HEPH_ENST00000441993.2_Splice_Site_p.I59T|HEPH_ENST00000419594.1_Splice_Site_p.I59T			Q9BQS7	HEPH_HUMAN	hephaestin	56	Plastocyanin-like 1.			DI -> QR (in Ref. 7; BAA31673). {ECO:0000305}.	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						GACAGTGACATGTAGGTTTAA	0.522																																					p.I110T		Atlas-SNP	.											.	HEPH	224	.	0			c.T329C						PASS	.						83	52	63					X																	65390579		2203	4300	6503	SO:0001630	splice_region_variant	9843	exon2			GTGACATGTAGGT	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.167+1T>C	X.37:g.65390579T>C		200	0	0		158	54	0.341772	NM_138737	B1AJX8|D3DVT7|E9PHN8|O75180|Q6UW45|Q9C058	Missense_Mutation	SNP	ENST00000343002.2	37		.	.	.	.	.	.	.	.	.	.	T	2.827	-0.243436	0.05906	.	.	ENSG00000089472	ENST00000519389;ENST00000374727;ENST00000458621;ENST00000441993;ENST00000419594;ENST00000343002;ENST00000425114	D;D;D;D;D;D;D	0.98807	-5.15;-5.15;-5.15;-5.15;-5.15;-5.15;-5.15	5.01	-4.52	0.03472	Cupredoxin (2);	1.081160	0.07043	N	0.830517	D	0.91123	0.7205	N	0.04508	-0.205	0.28301	N	0.923116	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	D	0.88495	0.3078	10	0.09590	T	0.72	.	0.9233	0.01319	0.3612:0.1545:0.1092:0.3751	.	110;59;56	E9PHN8;E7ES21;Q9BQS7	.;.;HEPH_HUMAN	T	110;59;56;59;59;56;56	ENSP00000430620:I110T;ENSP00000363859:I59T;ENSP00000396907:I56T;ENSP00000411687:I59T;ENSP00000413211:I59T;ENSP00000343939:I56T;ENSP00000398078:I56T	ENSP00000343939:I56T	I	+	2	0	HEPH	65307304	0.002000	0.14202	0.871000	0.34182	0.557000	0.35523	-2.384000	0.01063	-0.859000	0.04105	-0.438000	0.05819	ATA	.	.	none		0.522	HEPH-002	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000056995.1	NM_138737	Missense_Mutation	C	65390579	T	C	65390579	5	2	27	1	0	0	0	0	0	0	1	0	7063	1478	51	3	335	3	HEPH	23	65390579	Splice_Site	SNP	T	TCGA-G8-6909-01A-11D-2210-10	11125110	65390579	89879981	1045	11496											
TAF1	6872	hgsc.bcm.edu	37	chrX	70612454	70612455	+	In_Frame_Ins	INS	-	-	ATT																															ggaacaccacaagggccttcINSattgctgccatgaagggcaa																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:70612454_70612455insATT	ENST00000373790.4	+	19	2865_2866	c.2814_2815insATT	c.(2815-2817)att>ATTatt	p.939_939I>II	TAF1_ENST00000449580.1_In_Frame_Ins_p.939_939I>II|TAF1_ENST00000423759.1_In_Frame_Ins_p.960_960I>II|TAF1_ENST00000276072.3_In_Frame_Ins_p.960_960I>II	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	939	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)				CAAGGGCCTTCATTGCTGCCAT	0.49																																					p.F959delinsFI		Pindel,Atlas-Indel	.											.	TAF1	439	.	0			c.2877_2878insATT						PASS	.																																			SO:0001652	inframe_insertion	6872	exon19			.		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.2815_2817dupATT	X.37:g.70612455_70612457dupATT	ENSP00000362895:p.Ile939dup	127	0	.		118	27	0.229	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	In_Frame_Ins	INS	ENST00000373790.4	37	CCDS35325.1																																																																																			.	.	none		0.49	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606		ATT	70612455	-	ATT	70612454	7	5	27	1	0	1	1	0	0	0	0	0	15528	825	29	0	2951	0	TAF1	23	70612454	In_Frame_Ins	INS	-	TCGA-G8-6909-01A-11D-2210-10	5221875	70612454	84658106	1046	11497											
KLHL13	90293	hgsc.bcm.edu	37	chrX	117035896	117035896	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcatttgttcttggattgtaAcattctactgtggctgttaa	8	19	8	6	0	3	0	1	0	2	0	3	1	3	1	0	2	2	4	0	2	3	8			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:117035896A>G	ENST00000262820.3	-	6	2289	c.1380T>C	c.(1378-1380)tgT>tgC	p.C460C	KLHL13_ENST00000469946.1_Silent_p.C409C|KLHL13_ENST00000539496.1_Silent_p.C463C|KLHL13_ENST00000541812.1_Silent_p.C444C|KLHL13_ENST00000545703.1_Silent_p.C418C|KLHL13_ENST00000540167.1_Silent_p.C444C|KLHL13_ENST00000371882.1_Silent_p.C409C|KLHL13_ENST00000371876.1_Silent_p.C409C|KLHL13_ENST00000371878.1_Silent_p.C409C	NM_033495.3	NP_277030.2	Q9P2N7	KLH13_HUMAN	kelch-like family member 13	460					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						TTGGATTGTAACATTCTACTG	0.318																																					p.C463C		Atlas-SNP	.											.	KLHL13	87	.	0			c.T1389C						PASS	.						133	112	119					X																	117035896		2203	4300	6503	SO:0001819	synonymous_variant	90293	exon7			ATTGTAACATTCT	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.1380T>C	X.37:g.117035896A>G		157	0	0		112	34	0.303571	NM_001168299	B3KV78|B3KWM7|B7Z3S9|B7Z5P2|B7Z802|D3DWH6|Q6P2E3|Q96QI7|Q9UDN9	Silent	SNP	ENST00000262820.3	37	CCDS14571.1																																																																																			.	.	none		0.318	KLHL13-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_033495		G	117035896	A	G	117035896	2	3	27	1	0	0	0	0	0	0	0	1	8378	41	2	3		3	KLHL13	23	117035896	Silent	SNP	A	TCGA-G8-6909-01A-11D-2210-10	46423442	117035896	38234664	1047	11498											
STAG2	10735	hgsc.bcm.edu	37	chrX	123176493	123176493	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaatgactgaagaattcgatGaggtaacttactaccttaag	16	11	8	6	1	0	4	0	3	0	1	1	5	0	4	1	1	3	1	1	1	7	5			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:123176493G>A	ENST00000371160.1	+	7	750	c.460G>A	c.(460-462)Gag>Aag	p.E154K	STAG2_ENST00000371144.3_Missense_Mutation_p.E154K|STAG2_ENST00000371145.3_Missense_Mutation_p.E154K|STAG2_ENST00000371157.3_Missense_Mutation_p.E154K|STAG2_ENST00000354548.5_Missense_Mutation_p.E85K|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Missense_Mutation_p.E154K	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	154					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						AGAATTCGATGAGGTAACTTA	0.323																																					p.E154K		Atlas-SNP	.											.	STAG2	309	.	0			c.G460A						PASS	.						78	73	74					X																	123176493		2203	4300	6503	SO:0001583	missense	10735	exon7			TTCGATGAGGTAA	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.460G>A	X.37:g.123176493G>A	ENSP00000360202:p.Glu154Lys	446	1	0.00224215		257	68	0.264591	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Missense_Mutation	SNP	ENST00000371160.1	37	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	G	35	5.463084	0.96257	.	.	ENSG00000101972	ENST00000218089;ENST00000455404;ENST00000354548;ENST00000371160;ENST00000435103;ENST00000371157;ENST00000371145;ENST00000371144;ENST00000428941;ENST00000435215	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	5.74	5.74	0.90152	STAG (1);	0.000000	0.85682	D	0.000000	T	0.75087	0.3802	M	0.92077	3.27	0.80722	D	1	D;D	0.55605	0.966;0.972	P;P	0.61940	0.747;0.896	T	0.79264	-0.1875	10	0.44086	T	0.13	-12.9428	18.9534	0.92649	0.0:0.0:1.0:0.0	.	154;154	Q8N3U4-2;Q8N3U4	.;STAG2_HUMAN	K	154;154;85;154;154;154;154;154;154;154	ENSP00000218089:E154K;ENSP00000397265:E154K;ENSP00000346555:E85K;ENSP00000360202:E154K;ENSP00000360199:E154K;ENSP00000360187:E154K;ENSP00000360186:E154K;ENSP00000392118:E154K	ENSP00000218089:E154K	E	+	1	0	STAG2	123004174	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	9.740000	0.98839	2.425000	0.82216	0.522000	0.50473	GAG	.	.	none		0.323	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603		A	123176493	G	A	123176493	3	1	27	1	0	0	0	0	1	0	0	0	15258	1291	45	2	478	2	STAG2	23	123176493	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	6140597	123176493	32094067	1048	11499											
AFF2	2334	hgsc.bcm.edu	37	chrX	148048494	148048494	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttccaccatcacctctaccAtcactactggcctcatggat	9	12	4	16	0	4	0	3	0	1	0	5	1	5	1	5	2	2	0	5	2	2	3	rs149653283	byFrequency	TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:148048494A>C	ENST00000370460.2	+	14	3567	c.3088A>C	c.(3088-3090)Atc>Ctc	p.I1030L	AFF2_ENST00000286437.5_Missense_Mutation_p.I671L|AFF2_ENST00000342251.3_Missense_Mutation_p.I997L|AFF2_ENST00000370457.5_Missense_Mutation_p.I995L	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	1030					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)					cacctctaccatcactacTGG	0.567													A|||	2	0.000529801	0.0	0.0014	3775	,	,		13632	0.0		0.001	False		,,,				2504	0.0				p.I1030L		Atlas-SNP	.											.	AFF2	679	.	0			c.A3088C						PASS	.	A	LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE,LEU/ILE	1,3834		0,0,1,1632,570	380	264	304		2983,3058,2983,2971,2011,3088	4.2	1	X	dbSNP_134	304	5,6723		0,4,1,2424,1871	yes	missense,missense,missense,missense,missense,missense	AFF2	NM_001169122.1,NM_001169123.1,NM_001169124.1,NM_001169125.1,NM_001170628.1,NM_002025.3	5,5,5,5,5,5	0,4,2,4056,2441	CC,CA,C,AA,A		0.0743,0.0261,0.0568	benign,benign,benign,benign,benign,benign	995/1277,1020/1302,995/1277,991/1273,671/953,1030/1312	148048494	6,10557	2203	4300	6503	SO:0001583	missense	2334	exon14			TCTACCATCACTA	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.3088A>C	X.37:g.148048494A>C	ENSP00000359489:p.Ile1030Leu	147	0	0		91	89	0.978022	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	ENST00000370460.2	37	CCDS14684.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	A	14.61	2.587998	0.46110	2.61E-4	7.43E-4	ENSG00000155966	ENST00000370460;ENST00000370457;ENST00000342251;ENST00000286437	T;T;T;T	0.71934	-0.01;-0.27;-0.27;-0.61	4.18	4.18	0.49190	.	0.089728	0.42053	D	0.000773	T	0.47710	0.1460	N	0.08118	0	0.24214	N	0.995466	P;P;P;P;P;P	0.38473	0.633;0.579;0.579;0.579;0.579;0.633	B;B;B;B;B;B	0.40782	0.34;0.23;0.23;0.23;0.23;0.34	T	0.32851	-0.9891	10	0.27785	T	0.31	.	5.4451	0.16531	0.8777:0.0:0.1223:0.0	.	671;995;995;991;1020;1030	B4DXD5;P51816-6;P51816-3;P51816-2;P51816-5;P51816	.;.;.;.;.;AFF2_HUMAN	L	1030;995;997;671	ENSP00000359489:I1030L;ENSP00000359486:I995L;ENSP00000345459:I997L;ENSP00000286437:I671L	ENSP00000286437:I671L	I	+	1	0	AFF2	147856188	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.240000	0.51368	1.860000	0.53959	0.417000	0.27973	ATC	A|1.000;C|0.000	0.000	strong		0.567	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025		C	148048494	A	C	148048494	3	2	27	1	0	0	0	0	1	0	0	0	357	217	8	5	3197	5	AFF2	23	148048494	Missense_Mutation	SNP	A	TCGA-G8-6909-01A-11D-2210-10	24872001	148048494	7222066	1049	11500											
MAGEA4	4103	hgsc.bcm.edu	37	chrX	151092968	151092968	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agttcctgtggggtccaaggGctctggctgaaaccagctat	8	10	13	10	0	1	1	0	1	1	0	3	1	3	1	3	4	2	4	3	4	3	2			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:151092968G>T	ENST00000360243.2	+	3	1099	c.832G>T	c.(832-834)Gct>Tct	p.A278S	MAGEA4_ENST00000393921.1_Missense_Mutation_p.A278S|MAGEA4_ENST00000370340.3_Missense_Mutation_p.A278S|MAGEA4_ENST00000276344.2_Missense_Mutation_p.A278S|MAGEA4_ENST00000393920.1_Missense_Mutation_p.A278S|MAGEA4_ENST00000370335.1_Missense_Mutation_p.A278S|MAGEA4_ENST00000370337.4_Missense_Mutation_p.A278S	NM_001011550.1	NP_001011550.1	P43358	MAGA4_HUMAN	melanoma antigen family A, 4	278	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									breast(2)|central_nervous_system(4)|endometrium(1)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)	27	Acute lymphoblastic leukemia(192;6.56e-05)					GGGTCCAAGGGCTCTGGCTGA	0.547																																					p.A278S		Atlas-SNP	.											.	MAGEA4	68	.	0			c.G832T						PASS	.						130	128	129					X																	151092968		2203	4300	6503	SO:0001583	missense	4103	exon3			CCAAGGGCTCTGG		CCDS14702.1	Xq28	2009-03-13			ENSG00000147381	ENSG00000147381			6802	protein-coding gene	gene with protein product	"melanoma-associated antigen 4", "cancer/testis antigen family 1, member 4"	300175		MAGE4		8575766	Standard	XM_005274677		Approved	MAGE4A, MAGE4B, MAGE-41, MAGE-X2, MGC21336, CT1.4	uc004ffa.3	P43358	OTTHUMG00000024174	ENST00000360243.2:c.832G>T	X.37:g.151092968G>T	ENSP00000353379:p.Ala278Ser	158	0	0		95	32	0.336842	NM_001011548	Q14798	Missense_Mutation	SNP	ENST00000360243.2	37	CCDS14702.1	.	.	.	.	.	.	.	.	.	.	G	14.39	2.519751	0.44866	.	.	ENSG00000147381	ENST00000276344;ENST00000393921;ENST00000370337;ENST00000393920;ENST00000370340;ENST00000370335;ENST00000360243	T;T;T;T;T;T;T	0.05717	3.4;3.4;3.4;3.4;3.4;3.4;3.4	2.55	1.68	0.24146	.	0.050169	0.85682	D	0.000000	T	0.19725	0.0474	M	0.83692	2.655	0.09310	N	1	D	0.56968	0.978	D	0.68943	0.961	T	0.02893	-1.1097	9	.	.	.	.	4.7785	0.13190	0.1844:0.0:0.8156:0.0	.	278	P43358	MAGA4_HUMAN	S	278	ENSP00000276344:A278S;ENSP00000377498:A278S;ENSP00000359362:A278S;ENSP00000377497:A278S;ENSP00000359365:A278S;ENSP00000359360:A278S;ENSP00000353379:A278S	.	A	+	1	0	MAGEA4	150843624	0.192000	0.23301	0.009000	0.14445	0.021000	0.10359	0.444000	0.21661	0.500000	0.27991	0.292000	0.19580	GCT	.	.	none		0.547	MAGEA4-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060898.1	NM_002362		T	151092968	G	T	151092968	3	4	27	1	0	0	0	0	1	0	0	0	9177	1203	42	4	834	4	MAGEA4	23	151092968	Missense_Mutation	SNP	G	TCGA-G8-6909-01A-11D-2210-10	3044474	151092968	4177592	1050	11501											
TREX2	11219	hgsc.bcm.edu	37	chrX	152710185	152710185	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggccctggtgctcaggccTccaggctggggtcatcaggc	4	8	16	13	0	3	0	3	0	0	0	4	0	4	0	3	7	1	2	3	7	0	0			TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrX:152710185T>G	ENST00000334497.2	-	11	1974	c.833A>C	c.(832-834)gAg>gCg	p.E278A	TREX2_ENST00000330912.2_Missense_Mutation_p.E235A|TREX2_ENST00000338525.2_Missense_Mutation_p.E235A|TREX2_ENST00000370231.2_Missense_Mutation_p.E235A|TREX2_ENST00000414588.1_Missense_Mutation_p.E277A|TREX2_ENST00000402951.1_Missense_Mutation_p.E278A|TREX2_ENST00000393862.2_Missense_Mutation_p.E235A|HAUS7_ENST00000484394.1_5'Flank|TREX2_ENST00000370232.1_Missense_Mutation_p.E278A			Q9BQ50	TREX2_HUMAN	three prime repair exonuclease 2	278					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)					TGCTCAGGCCTCCAGGCTGGG	0.692								Editing and processing nucleases																													p.E235A		Atlas-SNP	.											.	TREX2	36	.	0			c.A704C						PASS	.						13	10	11					X																	152710185		2176	4263	6439	SO:0001583	missense	11219	exon2			CAGGCCTCCAGGC	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.833A>C	X.37:g.152710185T>G	ENSP00000334993:p.Glu278Ala	139	0	0		50	18	0.36	NM_080701	Q45F08|Q9UN77	Missense_Mutation	SNP	ENST00000334497.2	37		.	.	.	.	.	.	.	.	.	.	T	14.14	2.445525	0.43429	.	.	ENSG00000183479	ENST00000393862;ENST00000330912;ENST00000338525;ENST00000334497;ENST00000370232;ENST00000402951;ENST00000414588;ENST00000370231	T;T;T;T;T;T;T;T	0.53640	0.81;0.81;0.81;0.65;0.65;0.65;0.61;0.81	4.35	4.35	0.52113	.	0.576106	0.12955	U	0.425475	T	0.33818	0.0876	L	0.27053	0.805	0.09310	N	1	P;P	0.46987	0.888;0.608	B;B	0.38985	0.287;0.08	T	0.17018	-1.0383	10	0.87932	D	0	-15.0026	9.2945	0.37806	0.0:0.0:0.0:1.0	.	277;278	Q06S70;Q9BQ50	.;TREX2_HUMAN	A	235;235;235;278;278;278;277;235	ENSP00000377442:E235A;ENSP00000333441:E235A;ENSP00000345218:E235A;ENSP00000334993:E278A;ENSP00000359252:E278A;ENSP00000386078:E278A;ENSP00000401692:E277A;ENSP00000359251:E235A	ENSP00000333441:E235A	E	-	2	0	TREX2	152363379	0.010000	0.17322	0.007000	0.13788	0.003000	0.03518	1.834000	0.39171	1.523000	0.49018	0.381000	0.24937	GAG	.	.	none		0.692	TREX2-001	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000060966.1	NM_080701		G	152710185	T	G	152710185	3	3	27	1	0	0	0	0	1	0	0	0	16492	1551	54	5	9	5	TREX2	23	152710185	Missense_Mutation	SNP	T	TCGA-G8-6909-01A-11D-2210-10	1617217	152710185	2560375	1051	11502											
NLGN4Y	22829	hgsc.bcm.edu	37	chrY	16952663	16952663	+	3'UTR	DEL	C	C	-																															aggaccctcacaaaacagggCccgaggacacaactgtcctc																										TCGA-G8-6909-01A-11D-2210-10	TCGA-G8-6909-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e77b3e68-2caa-4d71-9b83-8c8de72ef6e8	b21ffba7-e2de-4285-baa3-fd0984c6c6ea	g.chrY:16952663delC	ENST00000476359.1	+	0	2517							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						CAAAACAGGGCCCGAGGACAC	0.532																																					p.G657fs		Pindel,Atlas-Indel	.											.	NLGN4Y	44	.	0			c.1971delG						PASS	.																																			SO:0001624	3_prime_UTR_variant	22829	exon6			.		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.*2514C>-	Y.37:g.16952663delC		3	0	.		79	41	0.519	NM_014893	F5H6W0|Q14D08|Q7Z3T5|Q8N5B6|Q9Y2F8	Frame_Shift_Del	DEL	ENST00000476359.1	37																																																																																				.	.	none		0.532	NLGN4Y-004	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000089064.2	NM_014893		-	16952663	C	-	16952663	6	5	27	0	1	1	0	1	0	0	0	0	10474	739	26	0		0	NLGN4Y	24	16952663	3'UTR	DEL	C	TCGA-G8-6909-01A-11D-2210-10		16952663	42420903	1052	11503											
TAS1R3	83756	hgsc.bcm.edu	37	chr1	1268462	1268462	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aggttcaacggcagcctcagGacagagcgcctgaagatccg	11	5	13	12	3	2	3	2	1	0	2	3	4	3	4	3	3	3	2	3	3	2	1	rs138915131	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1268462G>A	ENST00000339381.5	+	4	1469	c.1437G>A	c.(1435-1437)agG>agA	p.R479R		NM_152228.1	NP_689414	Q7RTX0	TS1R3_HUMAN	taste receptor, type 1, member 3	479					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of sweet taste (GO:0050916)|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)			kidney(2)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	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;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.88e-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;0.146)		GCAGCCTCAGGACAGAGCGCC	0.667													g|||	17	0.00339457	0.0015	0.0058	5008	,	,		15673	0.0		0.0109	False		,,,				2504	0.0				p.R479R		Atlas-SNP	.											.	TAS1R3	39	.	0			c.G1437A						PASS	.	G		6,4396	14.3+/-33.2	0,6,2195	48	45	46		1437	-1.7	0	1	dbSNP_134	46	113,8475	58.7+/-120.3	0,113,4181	no	coding-synonymous	TAS1R3	NM_152228.1		0,119,6376	AA,AG,GG		1.3158,0.1363,0.9161		479/853	1268462	119,12871	2201	4294	6495	SO:0001819	synonymous_variant	83756	exon4			CCTCAGGACAGAG	AC026283	CCDS30556.1	1p36	2012-08-22			ENSG00000169962	ENSG00000169962		"Taste receptors / Type 1", "GPCR / Unclassified : Taste receptors"	15661	protein-coding gene	gene with protein product		605865				11319557	Standard	XM_006710939		Approved	T1R3	uc010nyk.2	Q7RTX0	OTTHUMG00000003071	ENST00000339381.5:c.1437G>A	1.37:g.1268462G>A		74	0	0		88	43	0.488636	NM_152228	Q5TA49|Q8NGW9	Silent	SNP	ENST00000339381.5	37	CCDS30556.1																																																																																			G|0.994;A|0.006	0.006	strong		0.667	TAS1R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008493.1			A	1268462	G	A	1268462	2	1	28	1	0	0	0	0	0	0	0	1	15579	1165	41	2		2	TAS1R3	1	1268462	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10		1268462	247982159	1	11504											
MIB2	142678	hgsc.bcm.edu	37	chr1	1564064	1564064	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgcccctggtggctgatgggGccgggggggacccagggccc	3	5	20	13	1	0	1	0	1	0	0	0	2	0	2	5	8	1	1	5	8	0	0	rs201947158		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1564064G>A	ENST00000357210.4	+	16	2554	c.2338G>A	c.(2338-2340)Gcc>Acc	p.A780T	MIB2_ENST00000378712.1_Missense_Mutation_p.A657T|MIB2_ENST00000520777.1_Missense_Mutation_p.A833T|MIB2_ENST00000505820.2_Missense_Mutation_p.A837T|MIB2_ENST00000504599.1_Missense_Mutation_p.A736T|MIB2_ENST00000518681.1_Missense_Mutation_p.A772T|MIB2_ENST00000360522.4_Missense_Mutation_p.A745T|MIB2_ENST00000378708.1_Missense_Mutation_p.A686T|MIB2_ENST00000355826.5_Missense_Mutation_p.A823T|MIB2_ENST00000378710.3_Missense_Mutation_p.A744T	NM_080875.2	NP_543151.2	Q96AX9	MIB2_HUMAN	mindbomb E3 ubiquitin protein ligase 2	780					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)		GGCTGATGGGGCCGGGGGGGA	0.716													.|||	1	0.000199681	0.0	0.0	5008	,	,		15533	0.0		0.001	False		,,,				2504	0.0				p.A837T		Atlas-SNP	.											.	MIB2	62	.	0			c.G2509A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	3,3915		0,3,1956	7	10	9		2497,2467,2314,1969,2509	2.9	1	1		9	26,8118		0,26,4046	yes	missense,missense,missense,missense,missense	MIB2	NM_001170686.1,NM_001170687.1,NM_001170688.1,NM_001170689.1,NM_080875.2	58,58,58,58,58	0,29,6002	AA,AG,GG		0.3193,0.0766,0.2404	benign,benign,benign,benign,benign	833/1067,823/1057,772/1006,657/754,837/1071	1564064	29,12033	1959	4072	6031	SO:0001583	missense	142678	exon16			GATGGGGCCGGGG	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.2338G>A	1.37:g.1564064G>A	ENSP00000349741:p.Ala780Thr	102	0	0		136	66	0.485294	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	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.810|8.810	0.934982|0.934982	0.18206|0.18206	7.66E-4|7.66E-4	0.003193|0.003193	ENSG00000197530|ENSG00000197530	ENST00000520777;ENST00000357210;ENST00000360522;ENST00000378710;ENST00000355826;ENST00000518681;ENST00000505820;ENST00000378712;ENST00000504599;ENST00000378708|ENST00000514234	T;T;T;T;T;T;T;T;T;T|T	0.66995|0.35421	1.26;1.28;1.27;1.28;1.27;1.27;1.26;-0.24;1.28;1.3|1.31	3.83|3.83	2.91|2.91	0.33838|0.33838	Ankyrin repeat-containing domain (1);|.	0.626746|.	0.15520|.	N|.	0.258115|.	T|T	0.32645|0.32645	0.0836|0.0836	L|L	0.36672|0.36672	1.1|1.1	0.26411|0.26411	N|N	0.976259|0.976259	B;B;B;B;P;P;B|.	0.37122|.	0.433;0.011;0.126;0.011;0.583;0.575;0.015|.	B;B;B;B;B;B;B|.	0.36845|.	0.234;0.013;0.05;0.021;0.08;0.108;0.014|.	T|T	0.21895|0.21895	-1.0232|-1.0232	10|7	0.29301|0.56958	T|D	0.29|0.05	-2.4025|-2.4025	7.3783|7.3783	0.26841|0.26841	0.217:0.0:0.783:0.0|0.217:0.0:0.783:0.0	.|.	745;686;657;772;833;766;780|.	Q96AX9-5;F2Z2L2;B3KXY1;E9PHQ1;E9PGU1;Q96AX9-2;Q96AX9|.	.;.;.;.;.;.;MIB2_HUMAN|.	T|D	833;780;745;744;823;772;837;657;736;686|595	ENSP00000428660:A833T;ENSP00000349741:A780T;ENSP00000353713:A745T;ENSP00000367982:A744T;ENSP00000348081:A823T;ENSP00000428264:A772T;ENSP00000426103:A837T;ENSP00000367984:A657T;ENSP00000426128:A736T;ENSP00000367980:A686T|ENSP00000427680:G595D	ENSP00000348081:A823T|ENSP00000427680:G595D	A|G	+|+	1|2	0|0	MIB2|MIB2	1553927|1553927	0.894000|0.894000	0.30519|0.30519	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	0.434000|0.434000	0.21494|0.21494	0.817000|0.817000	0.34445|0.34445	0.491000|0.491000	0.48974|0.48974	GCC|GGC	.	.	weak		0.716	MIB2-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_080875		A	1564064	G	A	1564064	3	1	28	1	0	0	0	0	1	0	0	0	9576	1203	42	2	2571	2	MIB2	1	1564064	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	295602	1564064	247686557	2	11505											
MEGF6	1953	hgsc.bcm.edu	37	chr1	3417545	3417545	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgtacctctctggcagctaaAgccggtccacccgggggcac	7	6	12	16	3	1	0	0	0	1	0	3	0	2	0	4	4	3	4	4	4	3	2	rs41303857	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:3417545A>G	ENST00000356575.4	-	20	2786	c.2560T>C	c.(2560-2562)Ttt>Ctt	p.F854L	MEGF6_ENST00000294599.4_Missense_Mutation_p.F749L	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	854	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)		TGGCAGCTAAAGCCGGTCCAC	0.652													A|||	5	0.000998403	0.0	0.0029	5008	,	,		18548	0.0		0.003	False		,,,				2504	0.0				p.F854L	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.T2560C						PASS	.	A	LEU/PHE	4,3954		0,4,1975	36	45	42		2560	1.7	1	1	dbSNP_127	42	27,8299		0,27,4136	yes	missense	MEGF6	NM_001409.3	22	0,31,6111	GG,GA,AA		0.3243,0.1011,0.2524	benign	854/1542	3417545	31,12253	1979	4163	6142	SO:0001583	missense	1953	exon20			AGCTAAAGCCGGT	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.2560T>C	1.37:g.3417545A>G	ENSP00000348982:p.Phe854Leu	83	0	0		127	57	0.448819	NM_001409	Q4AC86|Q5VV39	Missense_Mutation	SNP	ENST00000356575.4	37	CCDS41237.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	1.886	-0.456687	0.04540	0.001011	0.003243	ENSG00000162591	ENST00000294599;ENST00000356575	T;T	0.24538	1.85;1.85	4.98	1.73	0.24493	EGF-like, laminin (2);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	0.277593	0.32703	N	0.005760	T	0.06416	0.0165	N	0.00686	-1.255	0.24354	N	0.994905	B;B	0.02656	0.0;0.0	B;B	0.11329	0.006;0.002	T	0.32981	-0.9886	10	0.27082	T	0.32	-9.1415	6.1992	0.20567	0.241:0.0:0.6099:0.1491	rs41303857;rs61744087	854;749	O75095;O75095-2	MEGF6_HUMAN;.	L	749;854	ENSP00000294599:F749L;ENSP00000348982:F854L	ENSP00000294599:F749L	F	-	1	0	MEGF6	3407405	0.024000	0.19004	0.996000	0.52242	0.611000	0.37282	1.115000	0.31209	1.072000	0.40860	-0.366000	0.07423	TTT	A|0.998;G|0.002	0.002	strong		0.652	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409		G	3417545	A	G	3417545	3	3	28	1	0	0	0	0	1	0	0	0	9471	72	3	3	2137	3	MEGF6	1	3417545	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	1853481	3417545	245833076	3	11506											
CHD5	26038	hgsc.bcm.edu	37	chr1	6188596	6188596	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgcttcttctttgcactggcGgccaagttcccccctttgga	4	14	9	14	1	2	0	0	0	2	0	3	1	3	1	4	3	2	3	4	3	1	5			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:6188596G>A	ENST00000262450.3	-	24	3792	c.3693C>T	c.(3691-3693)gcC>gcT	p.A1231A	CHD5_ENST00000378021.1_Silent_p.A88A	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)		TTGCACTGGCGGCCAAGTTCC	0.627																																					p.A1231A		Atlas-SNP	.											.	CHD5	267	.	0			c.C3693T						PASS	.						59	62	61					1																	6188596		2203	4300	6503	SO:0001819	synonymous_variant	26038	exon24			ACTGGCGGCCAAG	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.3693C>T	1.37:g.6188596G>A		75	0	0		75	41	0.546667	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Silent	SNP	ENST00000262450.3	37	CCDS57.1																																																																																			.	.	none		0.627	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557		A	6188596	G	A	6188596	2	1	28	1	0	0	0	0	0	0	0	1	3330	1103	39	1		1	CHD5	1	6188596	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2771051	6188596	243062025	4	11507											
LZIC	84328	hgsc.bcm.edu	37	chr1	9995633	9995633	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcattaaattcacttagttGctccagagtttcctttttgg	9	18	6	8	0	2	1	2	0	0	1	4	1	4	1	2	1	1	3	2	1	3	7			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:9995633G>A	ENST00000377223.1	-	4	401	c.154C>T	c.(154-156)Caa>Taa	p.Q52*	LZIC_ENST00000541052.1_Nonsense_Mutation_p.Q73*|LZIC_ENST00000400903.2_Nonsense_Mutation_p.Q52*|LZIC_ENST00000377213.1_Nonsense_Mutation_p.Q52*	NM_032368.3	NP_115744.2	Q8WZA0	LZIC_HUMAN	leucine zipper and CTNNBIP1 domain containing	52					response to ionizing radiation (GO:0010212)					breast(1)|endometrium(2)|large_intestine(2)|lung(1)|skin(1)	7		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;5.29e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;0.000242)|BRCA - Breast invasive adenocarcinoma(304;0.000299)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|STAD - Stomach adenocarcinoma(132;0.00842)|READ - Rectum adenocarcinoma(331;0.0419)		TCACTTAGTTGCTCCAGAGTT	0.333																																					p.Q52X		Atlas-SNP	.											.	LZIC	11	.	0			c.C154T						PASS	.						151	157	155					1																	9995633		2203	4299	6502	SO:0001587	stop_gained	84328	exon3			TTAGTTGCTCCAG	AB060688	CCDS107.1	1p36.22	2008-02-05			ENSG00000162441	ENSG00000162441			17497	protein-coding gene	gene with protein product		610458				11712074	Standard	NM_032368		Approved	MGC15436	uc001aqm.3	Q8WZA0	OTTHUMG00000001804	ENST00000377223.1:c.154C>T	1.37:g.9995633G>A	ENSP00000366430:p.Gln52*	100	0	0		98	5	0.0510204	NM_032368	B2R6F0|B4E2N0|Q96IU1	Nonsense_Mutation	SNP	ENST00000377223.1	37	CCDS107.1	.	.	.	.	.	.	.	.	.	.	G	39	7.297898	0.98196	.	.	ENSG00000162441	ENST00000377223;ENST00000400903;ENST00000541052;ENST00000377213	.	.	.	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6655	0.95891	0.0:0.0:1.0:0.0	.	.	.	.	X	52;52;73;52	.	.	Q	-	1	0	LZIC	9918220	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.716000	0.98752	2.652000	0.90054	0.491000	0.48974	CAA	.	.	none		0.333	LZIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005037.1	NM_032368		A	9995633	G	A	9995633	4	1	28	1	0	0	0	0	0	1	0	0	9144	1328	46	2	438	2	LZIC	1	9995633	Nonsense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	3807037	9995633	239254988	5	11508											
KIF1B	23095	hgsc.bcm.edu	37	chr1	10364260	10364260	+	Intron	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaataaagaagagagccaagAaaaagggggtaaaggagctt	20	4	14	3	0	0	3	0	0	0	3	0	6	0	4	1	3	2	2	1	3	9	3	rs148481786	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:10364260A>G	ENST00000377086.1	+	22	2317				KIF1B_ENST00000377083.1_Missense_Mutation_p.E1006G|RN7SL731P_ENST00000584329.1_RNA|KIF1B_ENST00000377093.4_Missense_Mutation_p.E1006G|KIF1B_ENST00000263934.6_Intron|KIF1B_ENST00000377081.1_Intron			O60333	KIF1B_HUMAN	kinesin family member 1B						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)		GAGAGCCAAGAAAAAGGGGGT	0.423													A|||	11	0.00219649	0.0	0.0029	5008	,	,		20281	0.0		0.007	False		,,,				2504	0.002				p.E1006G		Atlas-SNP	.											.	KIF1B	242	.	0			c.A3017G						PASS	.	A	,GLY/GLU	2,4404	2.1+/-5.4	0,2,2201	108	117	114		,3017	4.4	0.9	1	dbSNP_134	114	52,8548	30.7+/-82.3	1,50,4249	yes	intron,missense	KIF1B	NM_015074.3,NM_183416.3	,98	1,52,6450	GG,GA,AA		0.6047,0.0454,0.4152	,	,1006/1154	10364260	54,12952	2203	4300	6503	SO:0001627	intron_variant	23095	exon21			GCCAAGAAAAAGG	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.2115+6956A>G	1.37:g.10364260A>G		70	0	0		71	43	0.605634	NM_183416	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	37		7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	A	11.72	1.722702	0.30503	4.54E-4	0.006047	ENSG00000054523	ENST00000377093;ENST00000377083	T;T	0.73152	-0.72;-0.72	5.48	4.36	0.52297	.	.	.	.	.	T	0.55513	0.1925	.	.	.	0.80722	D	1	B	0.34290	0.447	B	0.33690	0.168	T	0.61038	-0.7143	8	0.66056	D	0.02	.	9.7928	0.40717	0.9228:0.0:0.0772:0.0	.	1006	O60333-3	.	G	1006	ENSP00000366297:E1006G;ENSP00000366287:E1006G	ENSP00000366287:E1006G	E	+	2	0	KIF1B	10286847	0.933000	0.31639	0.938000	0.37757	0.716000	0.41182	1.714000	0.37961	0.931000	0.37242	0.533000	0.62120	GAA	A|0.994;G|0.006	0.006	strong		0.423	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1			G	10364260	A	G	10364260	1	3	28	0	1	0	0	0	0	0	0	0	8293	246	9	3		3	KIF1B	1	10364260	Intron	SNP	A	TCGA-G8-6914-01A-11D-2210-10	368627	10364260	238886361	6	11509											
PTCHD2	57540	hgsc.bcm.edu	37	chr1	11561577	11561577	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgagccccccgcgtcatcccCgcggcctcactcggtggccc	3	5	11	22	6	2	0	2	0	0	0	4	1	3	0	7	3	1	0	7	3	0	0	rs181120200	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:11561577C>T	ENST00000294484.6	+	2	666	c.528C>T	c.(526-528)ccC>ccT	p.P176P	PTCHD2_ENST00000389575.3_Silent_p.P176P	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	176					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)		GCGTCATCCCCGCGGCCTCAC	0.692													C|||	11	0.00219649	0.0015	0.0014	5008	,	,		14434	0.0		0.008	False		,,,				2504	0.0				p.P176P		Atlas-SNP	.											.	PTCHD2	193	.	0			c.C528T						PASS	.	C		2,3818		0,2,1908	12	15	14		528	-8.6	0	1		14	51,8167		0,51,4058	no	coding-synonymous	PTCHD2	NM_020780.1		0,53,5966	TT,TC,CC		0.6206,0.0524,0.4403		176/1393	11561577	53,11985	1910	4109	6019	SO:0001819	synonymous_variant	57540	exon2			CATCCCCGCGGCC	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.528C>T	1.37:g.11561577C>T		45	0	0		48	22	0.458333	NM_020780	Q5VTU9|Q9UJD6	Silent	SNP	ENST00000294484.6	37	CCDS41247.1																																																																																			C|0.997;T|0.003	0.003	strong		0.692	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561		T	11561577	C	T	11561577	2	4	28	1	0	0	0	0	0	0	0	1	12745	639	23	1		1	PTCHD2	1	11561577	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1197317	11561577	237689044	7	11510											
AGMAT	79814	hgsc.bcm.edu	37	chr1	15905471	15905471	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccggcggaagggcgccccGtggtagagcttctctcctag	6	7	14	14	4	1	1	0	0	1	1	3	2	2	2	4	4	1	2	4	4	3	3	rs116813534	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:15905471G>T	ENST00000375826.3	-	4	745	c.603C>A	c.(601-603)caC>caA	p.H201Q	DNAJC16_ENST00000483270.1_Intron	NM_024758.4	NP_079034.3	Q9BSE5	SPEB_HUMAN	agmatine ureohydrolase (agmatinase)	201					agmatine biosynthetic process (GO:0097055)|cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|putrescine biosynthetic process from arginine (GO:0033388)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	agmatinase activity (GO:0008783)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(6)|lung(2)|skin(1)	12		Breast(348;0.000207)|Colorectal(325;0.000258)|Lung NSC(340;0.000359)|all_lung(284;0.000486)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.93e-07)|COAD - Colon adenocarcinoma(227;3.91e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000121)|KIRC - Kidney renal clear cell carcinoma(229;0.00257)|STAD - Stomach adenocarcinoma(313;0.00734)|READ - Rectum adenocarcinoma(331;0.0649)		AGGGCGCCCCGTGGTAGAGCT	0.627																																					p.H201Q	NSCLC(126;1678 1780 25805 43508 49531)	Atlas-SNP	.											.	AGMAT	25	.	0			c.C603A						PASS	.						66	64	64					1																	15905471		2203	4300	6503	SO:0001583	missense	79814	exon4			CGCCCCGTGGTAG	AY057097	CCDS160.1	1p36.13	2009-01-05			ENSG00000116771	ENSG00000116771			18407	protein-coding gene	gene with protein product						11804860, 14648699, 11914032	Standard	NM_024758		Approved	FLJ23384	uc001awv.2	Q9BSE5	OTTHUMG00000002357	ENST00000375826.3:c.603C>A	1.37:g.15905471G>T	ENSP00000364986:p.His201Gln	86	0	0		84	51	0.607143	NM_024758	Q5TDH1|Q9H5J3	Missense_Mutation	SNP	ENST00000375826.3	37	CCDS160.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.029886	0.75504	.	.	ENSG00000116771	ENST00000375826	D	0.88354	-2.37	5.87	-5.21	0.02815	Ureohydrolase domain (1);	0.000000	0.85682	D	0.000000	D	0.96281	0.8787	H	0.99312	4.51	0.50813	D	0.999893	D	0.89917	1.0	D	0.97110	1.0	D	0.95290	0.8394	10	0.87932	D	0	-29.7251	16.7644	0.85521	0.7501:0.0:0.2499:0.0	.	201	Q9BSE5	SPEB_HUMAN	Q	201	ENSP00000364986:H201Q	ENSP00000364986:H201Q	H	-	3	2	AGMAT	15778058	0.088000	0.21588	0.767000	0.31495	0.884000	0.51177	-0.576000	0.05854	-1.114000	0.02977	-0.142000	0.14014	CAC	A|0.007;G|0.993;T|0.000	0.000	strong		0.627	AGMAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006763.1	NM_024758		T	15905471	G	T	15905471	3	4	28	1	0	0	0	0	1	0	0	0	385	1136	40	4	471	4	AGMAT	1	15905471	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	4343894	15905471	233345150	8	11511											
EPHA2	1969	hgsc.bcm.edu	37	chr1	16458339	16458339	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	taggaaatggcctccggggcGgtccagcggatggggatctt	7	8	17	9	3	1	0	0	0	1	0	3	3	3	3	3	8	1	0	3	8	2	2	rs112285834	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16458339G>A	ENST00000358432.5	-	14	2506	c.2352C>T	c.(2350-2352)acC>acT	p.T784T		NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2	784	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)	CCTCCGGGGCGGTCCAGCGGA	0.647													G|||	14	0.00279553	0.0	0.0014	5008	,	,		17168	0.0		0.0129	False		,,,				2504	0.0				p.T784T		Atlas-SNP	.											.	EPHA2	102	.	0			c.C2352T						PASS	.	G		14,4392	21.2+/-45.6	0,14,2189	49	46	47		2352	-8.9	0.7	1	dbSNP_132	47	138,8462	68.0+/-130.5	0,138,4162	no	coding-synonymous	EPHA2	NM_004431.3		0,152,6351	AA,AG,GG		1.6047,0.3177,1.1687		784/977	16458339	152,12854	2203	4300	6503	SO:0001819	synonymous_variant	1969	exon14			CGGGGCGGTCCAG	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.2352C>T	1.37:g.16458339G>A		53	0	0		79	28	0.35443	NM_004431	B5A968|Q8N3Z2	Silent	SNP	ENST00000358432.5	37	CCDS169.1																																																																																			G|0.990;A|0.010	0.010	strong		0.647	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	NM_004431		A	16458339	G	A	16458339	2	1	28	1	0	0	0	0	0	0	0	1	5169	1103	39	1		1	EPHA2	1	16458339	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	552868	16458339	232792282	9	11512											
ARHGEF19	128272	hgsc.bcm.edu	37	chr1	16525657	16525657	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccctcaccgtcactggtccAggtcctcactgacaggatgt	7	9	9	16	1	3	1	3	1	0	0	5	2	5	2	5	3	0	0	5	3	0	0	rs148325785	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16525657A>G	ENST00000270747.3	-	15	2375	c.2239T>C	c.(2239-2241)Tgg>Cgg	p.W747R	ARHGEF19-AS1_ENST00000457809.1_RNA|ARHGEF19_ENST00000478117.1_5'UTR	NM_153213.3	NP_694945.2	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19	747	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				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)		TCACTGGTCCAGGTCCTCACT	0.562													A|||	25	0.00499201	0.0	0.0115	5008	,	,		19556	0.0		0.0159	False		,,,				2504	0.001				p.W747R		Atlas-SNP	.											.	ARHGEF19	49	.	0			c.T2239C						PASS	.	A	ARG/TRP	11,4395	17.9+/-39.9	0,11,2192	125	98	107		2239	-0.1	1	1	dbSNP_134	107	106,8494	57.9+/-119.4	1,104,4195	yes	missense	ARHGEF19	NM_153213.3	101	1,115,6387	GG,GA,AA		1.2326,0.2497,0.8996	benign	747/803	16525657	117,12889	2203	4300	6503	SO:0001583	missense	128272	exon15			TGGTCCAGGTCCT	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.2239T>C	1.37:g.16525657A>G	ENSP00000270747:p.Trp747Arg	161	0	0		144	72	0.5	NM_153213	A6NJ04|Q5TEV2|Q6PJQ4|Q8N244	Missense_Mutation	SNP	ENST00000270747.3	37	CCDS170.1	18	0.008241758241758242	0	0.0	6	0.016574585635359115	0	0.0	12	0.0158311345646438	A	4.292	0.053391	0.08291	0.002497	0.012326	ENSG00000142632	ENST00000270747	T	0.43294	0.95	4.57	-0.0683	0.13756	Src homology-3 domain (4);	0.268702	0.27604	N	0.018633	T	0.03011	0.0089	N	0.00170	-1.935	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28933	-1.0028	10	0.06236	T	0.91	.	4.4685	0.11701	0.2021:0.0:0.4709:0.327	.	747	Q8IW93	ARHGJ_HUMAN	R	747	ENSP00000270747:W747R	ENSP00000270747:W747R	W	-	1	0	ARHGEF19	16398244	0.005000	0.15991	0.963000	0.40424	0.929000	0.56500	0.455000	0.21843	0.151000	0.19162	-0.366000	0.07423	TGG	A|0.991;G|0.009	0.009	strong		0.562	ARHGEF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006289.1	NM_153213		G	16525657	A	G	16525657	3	3	28	1	0	0	0	0	1	0	0	0	902	188	7	3	177	3	ARHGEF19	1	16525657	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	67318	16525657	232724964	10	11513											
ARHGEF19	128272	hgsc.bcm.edu	37	chr1	16535487	16535487	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tggcacactgctacagggtgGtgggcagtgccaggtggccc	6	7	17	11	0	0	0	0	0	0	0	0	0	0	0	2	6	3	3	2	6	1	1	rs143314517	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16535487G>C	ENST00000270747.3	-	2	199	c.63C>G	c.(61-63)caC>caG	p.H21Q	ARHGEF19_ENST00000478117.1_5'Flank	NM_153213.3	NP_694945.2	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19	21					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)		CTACAGGGTGGTGGGCAGTGC	0.642													G|||	14	0.00279553	0.0	0.0029	5008	,	,		17289	0.0		0.0119	False		,,,				2504	0.0				p.H21Q		Atlas-SNP	.											.	ARHGEF19	49	.	0			c.C63G						PASS	.	G	GLN/HIS	9,4395		0,9,2193	17	19	18		63	1	0	1	dbSNP_134	18	114,8482		0,114,4184	no	missense	ARHGEF19	NM_153213.3	24	0,123,6377	CC,CG,GG		1.3262,0.2044,0.9462	benign	21/803	16535487	123,12877	2202	4298	6500	SO:0001583	missense	128272	exon2			AGGGTGGTGGGCA	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.63C>G	1.37:g.16535487G>C	ENSP00000270747:p.His21Gln	62	0	0		72	35	0.486111	NM_153213	A6NJ04|Q5TEV2|Q6PJQ4|Q8N244	Missense_Mutation	SNP	ENST00000270747.3	37	CCDS170.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	G	5.788	0.329777	0.10956	0.002044	0.013262	ENSG00000142632	ENST00000270747;ENST00000421561;ENST00000375607	T;T	0.39592	1.07;1.07	5.12	1.02	0.19986	.	0.844696	0.10118	N	0.713769	T	0.16471	0.0396	N	0.14661	0.345	0.09310	N	1	B	0.17667	0.023	B	0.14023	0.01	T	0.19516	-1.0303	10	0.52906	T	0.07	.	3.3172	0.07038	0.3042:0.0:0.5128:0.1829	.	21	Q8IW93	ARHGJ_HUMAN	Q	21	ENSP00000270747:H21Q;ENSP00000396001:H21Q	ENSP00000270747:H21Q	H	-	3	2	ARHGEF19	16408074	0.761000	0.28439	0.015000	0.15790	0.010000	0.07245	0.817000	0.27281	-0.076000	0.12775	0.462000	0.41574	CAC	G|0.993;C|0.007	0.007	strong		0.642	ARHGEF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006289.1	NM_153213		C	16535487	G	C	16535487	3	2	28	1	0	0	0	0	1	0	0	0	902	1252	44	4	2405	4	ARHGEF19	1	16535487	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	9830	16535487	232715134	11	11514											
FBXO42	54455	hgsc.bcm.edu	37	chr1	16641797	16641797	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gacctattatgtctagtctcCtcagcctccaatactgggtg	8	13	8	12	0	3	0	1	0	2	0	5	1	4	0	4	1	2	0	4	1	5	4	rs61753288	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16641797C>T	ENST00000375592.3	-	2	333	c.117G>A	c.(115-117)gaG>gaA	p.E39E	FBXO42_ENST00000478089.1_5'UTR	NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	39										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)		GTCTAGTCTCCTCAGCCTCCA	0.502													C|||	14	0.00279553	0.0	0.0029	5008	,	,		17411	0.0		0.0119	False		,,,				2504	0.0				p.E39E		Atlas-SNP	.											.	FBXO42	53	.	0			c.G117A						PASS	.	C		8,4398	14.3+/-33.2	0,8,2195	120	100	107		117	-3.5	0	1	dbSNP_129	107	115,8485	60.2+/-122.0	0,115,4185	no	coding-synonymous	FBXO42	NM_018994.1		0,123,6380	TT,TC,CC		1.3372,0.1816,0.9457		39/718	16641797	123,12883	2203	4300	6503	SO:0001819	synonymous_variant	54455	exon2			AGTCTCCTCAGCC	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.117G>A	1.37:g.16641797C>T		219	0	0		246	110	0.447154	NM_018994	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	Silent	SNP	ENST00000375592.3	37	CCDS30613.1																																																																																			C|0.993;T|0.007	0.007	strong		0.502	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006285.1			T	16641797	C	T	16641797	2	4	28	1	0	0	0	0	0	0	0	1	5759	680	24	2		2	FBXO42	1	16641797	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	106310	16641797	232608824	12	11515											
SPATA21	374955	hgsc.bcm.edu	37	chr1	16736327	16736327	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttggagctgaggtgggcaccGgggtcagggtcctgggcgac	5	7	20	9	2	1	1	1	1	0	0	2	3	2	2	2	7	1	2	2	7	0	1	rs41269197	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16736327G>A	ENST00000335496.1	-	6	838	c.356C>T	c.(355-357)cCg>cTg	p.P119L	SPATA21_ENST00000466212.1_5'UTR|SPATA21_ENST00000540400.1_Missense_Mutation_p.P96L	NM_198546.1	NP_940948.1	Q7Z572	SPT21_HUMAN	spermatogenesis associated 21	119	Pro-rich.						calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|lung(8)|ovary(2)|pancreas(3)|stomach(1)|urinary_tract(2)	19		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;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;4.2e-05)|Kidney(64;0.000183)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.0122)|READ - Rectum adenocarcinoma(331;0.0651)		GGTGGGCACCGGGGTCAGGGT	0.682													G|||	116	0.0231629	0.0015	0.0346	5008	,	,		13933	0.001		0.0686	False		,,,				2504	0.0204				p.P119L		Atlas-SNP	.											.	SPATA21	47	.	0			c.C356T						PASS	.	G	LEU/PRO	53,4353	49.6+/-84.7	0,53,2150	31	39	36		356	2.2	0	1	dbSNP_127	36	550,8050	148.6+/-203.8	22,506,3772	yes	missense	SPATA21	NM_198546.1	98	22,559,5922	AA,AG,GG		6.3953,1.2029,4.6363	probably-damaging	119/470	16736327	603,12403	2203	4300	6503	SO:0001583	missense	374955	exon6			GGCACCGGGGTCA		CCDS172.1	1p36.13	2013-01-10			ENSG00000187144	ENSG00000187144		"EF-hand domain containing"	28026	protein-coding gene	gene with protein product							Standard	NM_198546		Approved	spergen-2, spergen2	uc001ayn.3	Q7Z572	OTTHUMG00000002312	ENST00000335496.1:c.356C>T	1.37:g.16736327G>A	ENSP00000335612:p.Pro119Leu	48	0	0		84	36	0.428571	NM_198546	B9EK40|F5GXP5	Missense_Mutation	SNP	ENST00000335496.1	37	CCDS172.1	68	0.031135531135531136	1	0.0020325203252032522	12	0.03314917127071823	1	0.0017482517482517483	54	0.0712401055408971	G	13.99	2.401897	0.42613	0.012029	0.063953	ENSG00000187144	ENST00000335496;ENST00000540400	T;T	0.69806	-0.39;-0.43	4.07	2.16	0.27623	.	0.145674	0.32401	N	0.006141	T	0.07908	0.0198	L	0.29908	0.895	0.09310	N	1	D;P	0.57899	0.981;0.943	P;B	0.46253	0.509;0.235	T	0.08146	-1.0736	10	0.87932	D	0	-3.4136	7.2518	0.26154	0.1024:0.1774:0.7202:0.0	rs41269197	96;119	F5GXP5;Q7Z572	.;SPT21_HUMAN	L	119;96	ENSP00000335612:P119L;ENSP00000440046:P96L	ENSP00000335612:P119L	P	-	2	0	SPATA21	16608914	0.016000	0.18221	0.007000	0.13788	0.010000	0.07245	1.688000	0.37690	1.049000	0.40321	-0.527000	0.04329	CCG	G|0.960;A|0.040	0.040	strong		0.682	SPATA21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006677.2	NM_198546		A	16736327	G	A	16736327	3	1	28	1	0	0	0	0	1	0	0	0	15022	1116	39	1	1085	1	SPATA21	1	16736327	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	94530	16736327	232514294	13	11516											
SPATA21	374955	hgsc.bcm.edu	37	chr1	16748432	16748432	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgcttttttaggtccaggCgtggatggcaggaaggggtt	6	14	16	5	1	0	0	0	0	0	0	1	2	1	2	1	7	1	3	1	7	2	5	rs114456729	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16748432C>T	ENST00000335496.1	-	4	551	c.69G>A	c.(67-69)acG>acA	p.T23T	SPATA21_ENST00000466212.1_5'UTR|SPATA21_ENST00000540400.1_Intron	NM_198546.1	NP_940948.1	Q7Z572	SPT21_HUMAN	spermatogenesis associated 21	23							calcium ion binding (GO:0005509)	p.T23T(1)		breast(1)|endometrium(2)|lung(8)|ovary(2)|pancreas(3)|stomach(1)|urinary_tract(2)	19		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;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;4.2e-05)|Kidney(64;0.000183)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.0122)|READ - Rectum adenocarcinoma(331;0.0651)		TAGGTCCAGGCGTGGATGGCA	0.562													C|||	122	0.024361	0.0015	0.036	5008	,	,		19316	0.001		0.0726	False		,,,				2504	0.0215				p.T23T		Atlas-SNP	.											SPATA21,NS,carcinoma,-1,2	SPATA21	47	2	1	Substitution - coding silent(1)	pancreas(1)	c.G69A						PASS	.	C		57,4349	54.9+/-90.9	0,57,2146	219	207	211		69	-2.2	0	1	dbSNP_132	211	600,8000	158.9+/-212.3	23,554,3723	no	coding-synonymous	SPATA21	NM_198546.1		23,611,5869	TT,TC,CC		6.9767,1.2937,5.0515		23/470	16748432	657,12349	2203	4300	6503	SO:0001819	synonymous_variant	374955	exon4			TCCAGGCGTGGAT		CCDS172.1	1p36.13	2013-01-10			ENSG00000187144	ENSG00000187144		"EF-hand domain containing"	28026	protein-coding gene	gene with protein product							Standard	NM_198546		Approved	spergen-2, spergen2	uc001ayn.3	Q7Z572	OTTHUMG00000002312	ENST00000335496.1:c.69G>A	1.37:g.16748432C>T		109	0	0		93	46	0.494624	NM_198546	B9EK40|F5GXP5	Silent	SNP	ENST00000335496.1	37	CCDS172.1																																																																																			C|0.954;T|0.046	0.046	strong		0.562	SPATA21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006677.2	NM_198546		T	16748432	C	T	16748432	2	4	28	1	0	0	0	0	0	0	0	1	15022	755	27	1		1	SPATA21	1	16748432	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	12105	16748432	232502189	14	11517											
KLHDC7A	127707	hgsc.bcm.edu	37	chr1	18807523	18807523	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gactggcatttggatatgcaGctgaccggcaaggtggtgct	8	10	15	8	1	0	1	0	1	0	0	0	3	0	2	1	5	3	5	1	5	2	2	rs377259272		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:18807523G>A	ENST00000400664.1	+	1	100	c.48G>A	c.(46-48)caG>caA	p.Q16Q		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	16						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)		TGGATATGCAGCTGACCGGCA	0.592																																					p.Q16Q		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.G48A						PASS	.	G		1,4111		0,1,2055	51	57	55		48	4.9	1	1		55	0,8434		0,0,4217	no	coding-synonymous	KLHDC7A	NM_152375.2		0,1,6272	AA,AG,GG		0.0,0.0243,0.0080		16/778	18807523	1,12545	2056	4217	6273	SO:0001819	synonymous_variant	127707	exon1			TATGCAGCTGACC	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.48G>A	1.37:g.18807523G>A		236	1	0.00423729		218	113	0.518349	NM_152375	Q8N8W6	Silent	SNP	ENST00000400664.1	37	CCDS185.2																																																																																			.	.	none		0.592	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375		A	18807523	G	A	18807523	2	1	28	1	0	0	0	0	0	0	0	1	8369	962	34	2		2	KLHDC7A	1	18807523	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2059091	18807523	230443098	15	11518											
DDOST	1650	hgsc.bcm.edu	37	chr1	20980799	20980799	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggagccgctgaagatgacGcgggcattgttcctggcctg	7	8	16	10	3	0	3	0	2	0	1	1	4	1	4	3	3	1	3	3	3	1	2	rs34189097	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:20980799G>A	ENST00000375048.3	-	7	867	c.762C>T	c.(760-762)cgC>cgT	p.R254R	DDOST_ENST00000602624.2_Silent_p.R237R|PINK1-AS_ENST00000451424.1_RNA|DDOST_ENST00000415136.2_Silent_p.R217R	NM_005216.4	NP_005207	P39656	OST48_HUMAN	dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit (non-catalytic)	254					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)		TGAAGATGACGCGGGCATTGT	0.602													G|||	3	0.000599042	0.0008	0.0014	5008	,	,		17003	0.0		0.0	False		,,,				2504	0.001				p.R254R		Atlas-SNP	.											DDOST,caecum,carcinoma,-1,1	DDOST	30	1	0			c.C762T						PASS	.	G		1,4391		0,1,2195	50	42	45		762	-2	1	1	dbSNP_126	45	9,8553		0,9,4272	no	coding-synonymous	DDOST	NM_005216.4		0,10,6467	AA,AG,GG		0.1051,0.0228,0.0772		254/457	20980799	10,12944	2196	4281	6477	SO:0001819	synonymous_variant	1650	exon7			GATGACGCGGGCA	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.762C>T	1.37:g.20980799G>A		104	0	0		106	31	0.292453	NM_005216	B2RDQ4|B4DJE3|B4DLI2|O43244|Q5VWA5|Q8NI93|Q9BUI2	Silent	SNP	ENST00000375048.3	37	CCDS212.1																																																																																			G|0.999;A|0.001	0.001	strong		0.602	DDOST-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007961.2	NM_005216		A	20980799	G	A	20980799	2	1	28	1	0	0	0	0	0	0	0	1	4337	1074	38	1		1	DDOST	1	20980799	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2173276	20980799	228269822	16	11519											
HSPG2	3339	hgsc.bcm.edu	37	chr1	22214040	22214040	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcaggggcctgacggaaccGggaagcaggggctgaggagc	9	2	21	9	2	0	2	0	2	0	0	0	5	0	5	2	8	3	3	2	8	2	0	rs41310388	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:22214040G>A	ENST00000374695.3	-	8	910	c.831C>T	c.(829-831)ccC>ccT	p.P277P		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	277					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)	p.P277P(1)		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)	TGACGGAACCGGGAAGCAGGG	0.647													G|||	29	0.00579073	0.0008	0.0029	5008	,	,		14680	0.0		0.0179	False		,,,				2504	0.0082				p.P277P		Atlas-SNP	.											HSPG2,NS,carcinoma,0,1	HSPG2	311	1	1	Substitution - coding silent(1)	prostate(1)	c.C831T						PASS	.	G		14,4392	20.2+/-43.8	0,14,2189	81	99	93		831	-4.3	0	1	dbSNP_127	93	138,8462	66.7+/-129.0	1,136,4163	no	coding-synonymous	HSPG2	NM_005529.5		1,150,6352	AA,AG,GG		1.6047,0.3177,1.1687		277/4392	22214040	152,12854	2203	4300	6503	SO:0001819	synonymous_variant	3339	exon8			GGAACCGGGAAGC	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.831C>T	1.37:g.22214040G>A		145	0	0		129	58	0.449612	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1	17	0.007783882783882784	0	0.0	2	0.0055248618784530384	0	0.0	15	0.01978891820580475	G	16.74	3.206474	0.58343	0.003177	0.016047	ENSG00000142798	ENST00000412328;ENST00000374673	T;D	0.92249	0.51;-3.0	4.62	-4.32	0.03688	.	0.000000	0.37623	N	0.002018	T	0.72503	0.3468	.	.	.	0.49915	D	0.999833	B	0.20780	0.048	B	0.17098	0.017	T	0.55805	-0.8083	9	0.27785	T	0.31	.	7.5881	0.28004	0.6013:0.1275:0.2712:0.0	rs41310388	200	Q5SZI5	.	L	200;104	ENSP00000405412:P200L;ENSP00000363805:P104L	ENSP00000363805:P104L	P	-	2	0	HSPG2	22086627	0.011000	0.17503	0.000000	0.03702	0.013000	0.08279	-0.065000	0.11617	-1.198000	0.02669	-0.379000	0.06801	CCG	G|0.989;A|0.011	0.011	strong		0.647	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		A	22214040	G	A	22214040	2	1	28	1	0	0	0	0	0	0	0	1	7439	1103	39	1		1	HSPG2	1	22214040	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1233241	22214040	227036581	17	11520											
TCEA3	6920	hgsc.bcm.edu	37	chr1	23720501	23720501	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cggttccggtacttcatgtcCgtgctcttgagctcttggta	4	15	11	11	3	3	1	1	1	2	0	5	1	5	1	2	3	3	5	2	3	2	6			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:23720501C>T	ENST00000450454.2	-	8	796	c.690G>A	c.(688-690)acG>acA	p.T230T		NM_003196.1	NP_003187.1	O75764	TCEA3_HUMAN	transcription elongation factor A (SII), 3	230	TFIIS central. {ECO:0000255|PROSITE- ProRule:PRU00651}.				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)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|urinary_tract(1)	7		Colorectal(325;3.46e-05)|Lung NSC(340;4.16e-05)|all_lung(284;6.68e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.0054)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.6e-25)|Colorectal(126;8.32e-08)|COAD - Colon adenocarcinoma(152;4.29e-06)|GBM - Glioblastoma multiforme(114;9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00424)|STAD - Stomach adenocarcinoma(196;0.0145)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0963)|LUSC - Lung squamous cell carcinoma(448;0.198)		ACTTCATGTCCGTGCTCTTGA	0.632																																					p.T230T		Atlas-SNP	.											.	TCEA3	20	.	0			c.G690A						PASS	.						68	69	69					1																	23720501		1970	4143	6113	SO:0001819	synonymous_variant	6920	exon8			CATGTCCGTGCTC	AJ223473	CCDS44086.1	1p36.11	2011-01-25			ENSG00000204219	ENSG00000204219			11615	protein-coding gene	gene with protein product		604128				9790746	Standard	NM_003196		Approved	TFIIS.H	uc021oig.1	O75764	OTTHUMG00000003233	ENST00000450454.2:c.690G>A	1.37:g.23720501C>T		92	0	0		109	26	0.238532	NM_003196	A8K2K7|Q5DR83	Silent	SNP	ENST00000450454.2	37	CCDS44086.1																																																																																			.	.	none		0.632	TCEA3-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008911.2	NM_003196		T	23720501	C	T	23720501	2	4	28	1	0	0	0	0	0	0	0	1	15684	639	23	1		1	TCEA3	1	23720501	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1506461	23720501	225530120	18	11521											
TCEA3	6920	hgsc.bcm.edu	37	chr1	23743859	23743859	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctctttcctctccttttTctccttttgggggtccaggg	1	20	8	12	0	3	0	0	0	3	0	8	0	5	0	4	3	0	0	4	3	0	6	rs192746462	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:23743859T>C	ENST00000450454.2	-	4	369	c.263A>G	c.(262-264)gAa>gGa	p.E88G	TCEA3_ENST00000461794.1_Missense_Mutation_p.E51G|TCEA3_ENST00000374601.3_Missense_Mutation_p.E88G	NM_003196.1	NP_003187.1	O75764	TCEA3_HUMAN	transcription elongation factor A (SII), 3	88					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)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|urinary_tract(1)	7		Colorectal(325;3.46e-05)|Lung NSC(340;4.16e-05)|all_lung(284;6.68e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.0054)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.6e-25)|Colorectal(126;8.32e-08)|COAD - Colon adenocarcinoma(152;4.29e-06)|GBM - Glioblastoma multiforme(114;9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00424)|STAD - Stomach adenocarcinoma(196;0.0145)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0963)|LUSC - Lung squamous cell carcinoma(448;0.198)		ctctcctttttctcctTTTGG	0.493													T|||	9	0.00179712	0.0	0.0043	5008	,	,		19825	0.0		0.004	False		,,,				2504	0.002				p.E88G		Atlas-SNP	.											.	TCEA3	20	.	0			c.A263G						PASS	.	T	GLY/GLU	2,3698		0,2,1848	92	90	90		263	5	1	1		90	43,8161		0,43,4059	yes	missense	TCEA3	NM_003196.1	98	0,45,5907	CC,CT,TT		0.5241,0.0541,0.378	possibly-damaging	88/349	23743859	45,11859	1850	4102	5952	SO:0001583	missense	6920	exon4			CCTTTTTCTCCTT	AJ223473	CCDS44086.1	1p36.11	2011-01-25			ENSG00000204219	ENSG00000204219			11615	protein-coding gene	gene with protein product		604128				9790746	Standard	NM_003196		Approved	TFIIS.H	uc021oig.1	O75764	OTTHUMG00000003233	ENST00000450454.2:c.263A>G	1.37:g.23743859T>C	ENSP00000406293:p.Glu88Gly	131	0	0		143	71	0.496504	NM_003196	A8K2K7|Q5DR83	Missense_Mutation	SNP	ENST00000450454.2	37	CCDS44086.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	T	13.93	2.384002	0.42308	5.41E-4	0.005241	ENSG00000204219	ENST00000450454;ENST00000374601	.	.	.	5.02	5.02	0.67125	Transcription factor IIS, N-terminal (2);	0.911073	0.09406	N	0.806532	T	0.24661	0.0598	N	0.24115	0.695	0.24955	N	0.991769	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.09143	-1.0688	9	0.48119	T	0.1	-12.8917	11.3324	0.49484	0.0:0.0:0.0:1.0	.	88;88	A8K2K7;O75764	.;TCEA3_HUMAN	G	88	.	ENSP00000363729:E88G	E	-	2	0	TCEA3	23616446	1.000000	0.71417	1.000000	0.80357	0.810000	0.45777	1.690000	0.37711	2.244000	0.73946	0.533000	0.62120	GAA	T|0.998;C|0.002	0.002	strong		0.493	TCEA3-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008911.2	NM_003196		C	23743859	T	C	23743859	3	2	28	1	0	0	0	0	1	0	0	0	15684	1783	62	3	815	3	TCEA3	1	23743859	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	23358	23743859	225506762	19	11522											
IL28RA	163702	hgsc.bcm.edu	37	chr1	24496085	24496085	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcgcgccaccgtctacgggtGggagagctgggggaggagag	7	5	20	9	4	1	2	0	0	1	2	2	5	1	3	2	5	2	1	2	5	1	1	rs34654982	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:24496085G>A	ENST00000327535.1	-	3	201	c.189C>T	c.(187-189)ccC>ccT	p.P63P	IFNLR1_ENST00000374421.3_Silent_p.P63P|IFNLR1_ENST00000374418.3_Silent_p.P63P|IFNLR1_ENST00000327575.2_Silent_p.P63P|IFNLR1_ENST00000374419.1_5'UTR	NM_170743.3|NM_173064.2	NP_734464.1|NP_775087.1	Q8IU57	INLR1_HUMAN	interferon, lambda receptor 1	63	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)											GTCTACGGGTGGGAGAGCTGG	0.552													G|||	582	0.116214	0.289	0.0432	5008	,	,		21000	0.0327		0.0417	False		,,,				2504	0.0971				p.P63P		Atlas-SNP	.											.	.	.	.	0			c.C189T						PASS	.	G	,,	1063,3343	387.5+/-326.5	126,811,1266	62	62	62		189,189,189	-4.2	0	1	dbSNP_126	62	315,8285	112.3+/-172.5	3,309,3988	no	coding-synonymous,coding-synonymous,coding-synonymous	IL28RA	NM_170743.3,NM_173064.2,NM_173065.2	,,	129,1120,5254	AA,AG,GG		3.6628,24.1262,10.5951	,,	63/521,63/492,63/245	24496085	1378,11628	2203	4300	6503	SO:0001819	synonymous_variant	163702	exon3			ACGGGTGGGAGAG	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.189C>T	1.37:g.24496085G>A		75	0	0		84	41	0.488095	NM_170743	Q5VTX5|Q5VTX7|Q5VTX8|Q6ZML8|Q8IV66|Q8IZI7|Q8IZI8	Silent	SNP	ENST00000327535.1	37	CCDS248.1																																																																																			G|0.897;A|0.103	0.103	strong		0.552	IFNLR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000008402.1	NM_170743		A	24496085	G	A	24496085	2	1	28	1	0	0	0	0	0	0	0	1	7693	1335	47	2		2	IL28RA	1	24496085	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	752226	24496085	224754536	20	11523											
FCN3	8547	hgsc.bcm.edu	37	chr1	27699671	27699671	+	Frame_Shift_Del	DEL	G	G	-																															catgtcacaaaagactgggaGggccctgccctcaggtaggc																								rs28357092|rs532781899	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:27699671delG	ENST00000270879.4	-	5	354	c.349delC	c.(349-351)ctcfs	p.L117fs	FCN3_ENST00000354982.2_Frame_Shift_Del_p.L106fs	NM_003665.2	NP_003656.2	O75636	FCN3_HUMAN	ficolin (collagen/fibrinogen domain containing) 3	117	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)		AAGACTGGGAGGGCCCTGCCC	0.632													GGG|GGG|GG|deletion	94	0.01877	0.0242	0.013	5008	,	,		16176	0.0		0.0268	False		,,,				2504	0.0266				p.L117fs		Pindel,Atlas-Indel	.											.	FCN3	30	.	0			c.350delT	GRCh37	CD052457	FCN3	D		PASS	.		,	117,4149		4,109,2020	51	57	55	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,	3.1	0	1	dbSNP_125	56	147,8107		6,135,3986	no	frameshift,frameshift	FCN3	NM_173452.1,NM_003665.2	,	10,244,6006	A1A1,A1R,RR		1.781,2.7426,2.1086	,	,	27699671	264,12256	2202	4300	6502	SO:0001589	frameshift_variant	8547	exon5			.	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.349delC	1.37:g.27699671delG	ENSP00000270879:p.Leu117fs	184	0	.		175	50	0.286	NM_003665	Q6IBJ5|Q8WW86	Frame_Shift_Del	DEL	ENST00000270879.4	37	CCDS300.1																																																																																			G|0.985;-|0.015	0.015	strong		0.632	FCN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000015667.1			-	27699671	G	-	27699671	7	5	28	1	0	1	0	1	0	0	0	0	5801	1000	35	0	566	0	FCN3	1	27699671	Frame_Shift_Del	DEL	G	TCGA-G8-6914-01A-11D-2210-10	3203586	27699671	221550950	21	11524											
XKR8	55113	hgsc.bcm.edu	37	chr1	28290132	28290132	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgcggctcttcgagaccttcTtggagacggcaccacagctc	7	9	11	14	3	2	2	0	0	2	2	4	4	2	2	2	3	2	3	2	3	0	3	rs61743136	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:28290132T>C	ENST00000373884.5	+	2	1026	c.418T>C	c.(418-420)Ttg>Ctg	p.L140L		NM_018053.2	NP_060523.2	Q9H6D3	XKR8_HUMAN	XK, Kell blood group complex subunit-related family, member 8	140					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)		CGAGACCTTCTTGGAGACGGC	0.632													T|||	40	0.00798722	0.0129	0.0101	5008	,	,		17747	0.0		0.0159	False		,,,				2504	0.0				p.L140L		Atlas-SNP	.											.	XKR8	15	.	0			c.T418C						PASS	.	T		79,4327	64.7+/-102.0	1,77,2125	29	25	27		418	-3.5	0.9	1	dbSNP_129	27	90,8510	47.2+/-106.3	0,90,4210	no	coding-synonymous	XKR8	NM_018053.2		1,167,6335	CC,CT,TT		1.0465,1.793,1.2994		140/396	28290132	169,12837	2203	4300	6503	SO:0001819	synonymous_variant	55113	exon2			ACCTTCTTGGAGA	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.418T>C	1.37:g.28290132T>C		100	0	0		106	45	0.424528	NM_018053		Silent	SNP	ENST00000373884.5	37	CCDS315.1																																																																																			T|0.987;C|0.013	0.013	strong		0.632	XKR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011175.1	NM_018053		C	28290132	T	C	28290132	2	2	28	1	0	0	0	0	0	0	0	1	17452	1606	56	3		3	XKR8	1	28290132	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	590461	28290132	220960489	22	11525											
YARS	8565	hgsc.bcm.edu	37	chr1	33246709	33246709	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggatgggatgacctcctcTggttctgaattcttggcagg	6	12	14	9	1	3	2	0	2	3	0	4	4	4	4	2	5	0	2	2	5	1	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:33246709T>C	ENST00000373477.4	-	10	1988	c.1080A>G	c.(1078-1080)ccA>ccG	p.P360P	YARS_ENST00000469100.1_5'UTR	NM_003680.3	NP_003671.1	P54577	SYYC_HUMAN	tyrosyl-tRNA synthetase	360					apoptotic process (GO:0006915)|gene expression (GO:0010467)|signal transduction (GO:0007165)|tRNA aminoacylation for protein translation (GO:0006418)|tyrosyl-tRNA aminoacylation (GO:0006437)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	ATP binding (GO:0005524)|interleukin-8 receptor binding (GO:0005153)|poly(A) RNA binding (GO:0044822)|signal transducer activity (GO:0004871)|tRNA binding (GO:0000049)|tyrosine-tRNA ligase activity (GO:0004831)			endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|skin(2)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)			L-Tyrosine(DB00135)	TGACCTCCTCTGGTTCTGAAT	0.527																																					p.P360P		Atlas-SNP	.											.	YARS	34	.	0			c.A1080G						PASS	.						128	117	120					1																	33246709		2203	4300	6503	SO:0001819	synonymous_variant	8565	exon10			CTCCTCTGGTTCT	U89436	CCDS368.1	1p35.1	2014-09-17			ENSG00000134684	ENSG00000134684	6.1.1.1	"Aminoacyl tRNA synthetases / Class I"	12840	protein-coding gene	gene with protein product	"tyrosine tRNA ligase 1, cytoplasmic"	603623				8552597, 9162081	Standard	NM_003680		Approved	YTS, YRS, tyrRS	uc001bvy.1	P54577	OTTHUMG00000003933	ENST00000373477.4:c.1080A>G	1.37:g.33246709T>C		53	0	0		62	31	0.5	NM_003680	B3KWK4|D3DPQ4|O43276|Q53EN1	Silent	SNP	ENST00000373477.4	37	CCDS368.1																																																																																			.	.	none		0.527	YARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011225.1	NM_003680		C	33246709	T	C	33246709	2	2	28	1	0	0	0	0	0	0	0	1	17482	1567	55	3		3	YARS	1	33246709	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	4956577	33246709	216003912	23	11526											
GJB4	127534	hgsc.bcm.edu	37	chr1	35226963	35226963	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atctttcgtgtgctggtgtaCgtggtggcagcggaggaggt	5	12	18	6	3	1	0	0	0	1	0	2	2	1	2	0	6	3	3	0	6	1	2	rs142720849	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:35226963C>T	ENST00000339480.1	+	2	478	c.108C>T	c.(106-108)taC>taT	p.Y36Y	RP1-34M23.5_ENST00000542839.1_RNA	NM_153212.2	NP_694944.1	Q9NTQ9	CXB4_HUMAN	gap junction protein, beta 4, 30.3kDa	36					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)				TGCTGGTGTACGTGGTGGCAG	0.582													C|||	7	0.00139776	0.0008	0.0029	5008	,	,		23419	0.001		0.003	False		,,,				2504	0.0				p.Y36Y		Atlas-SNP	.											GJB4,NS,carcinoma,0,1	GJB4	51	1	0			c.C108T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	235	160	186		108	0.9	1	1	dbSNP_134	186	53,8547	33.8+/-87.4	0,53,4247	no	coding-synonymous	GJB4	NM_153212.2		0,55,6448	TT,TC,CC		0.6163,0.0454,0.4229		36/267	35226963	55,12951	2203	4300	6503	SO:0001819	synonymous_variant	127534	exon2			GGTGTACGTGGTG		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.108C>T	1.37:g.35226963C>T		139	0	0		125	63	0.504	NM_153212	B3KQ82	Silent	SNP	ENST00000339480.1	37	CCDS383.1																																																																																			C|0.996;T|0.004	0.004	strong		0.582	GJB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011560.1	NM_153212		T	35226963	C	T	35226963	2	4	28	1	0	0	0	0	0	0	0	1	6418	547	19	1		1	GJB4	1	35226963	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1980254	35226963	214023658	24	11527											
KIAA0319L	79932	hgsc.bcm.edu	37	chr1	35944609	35944609	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctggaaagaggcctggggggTaggggtagcataactgtagg	10	7	19	5	0	0	1	0	0	0	1	0	2	0	2	1	8	2	4	1	8	5	4	rs34372241	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:35944609T>C	ENST00000325722.3	-	4	1105	c.871A>G	c.(871-873)Acc>Gcc	p.T291A		NM_024874.4	NP_079150.3	Q8IZA0	K319L_HUMAN	KIAA0319-like	291						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)				GCCTGGGGGGTAGGGGTAGCA	0.488													T|||	10	0.00199681	0.0	0.0014	5008	,	,		17721	0.0		0.0089	False		,,,				2504	0.0				p.T291A		Atlas-SNP	.											.	KIAA0319L	156	.	0			c.A871G						PASS	.	T	ALA/THR	9,4397	15.5+/-35.6	0,9,2194	80	85	84		871	-1.9	0	1	dbSNP_126	84	86,8514	49.4+/-109.1	1,84,4215	yes	missense	KIAA0319L	NM_024874.4	58	1,93,6409	CC,CT,TT		1.0,0.2043,0.7304	benign	291/1050	35944609	95,12911	2203	4300	6503	SO:0001583	missense	79932	exon4			GGGGGGTAGGGGT	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.871A>G	1.37:g.35944609T>C	ENSP00000318406:p.Thr291Ala	46	0	0		46	21	0.456522	NM_024874	B1AN13|D3DPR8|O95010|Q6PJJ7|Q7L1C9|Q8N2B3|Q8NDA0|Q8WY39|Q8WYZ5|Q96IC3|Q96JJ0|Q9BUW6|Q9H7V0	Missense_Mutation	SNP	ENST00000325722.3	37	CCDS390.1	7|7	0.003205128205128205|0.003205128205128205	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	6|6	0.0079155672823219|0.0079155672823219	T|T	3.559|3.559	-0.090063|-0.090063	0.07053|0.07053	0.002043|0.002043	0.01|0.01	ENSG00000142687|ENSG00000142687	ENST00000325722;ENST00000426982;ENST00000440579;ENST00000373258|ENST00000431916	T;T;T;T|.	0.34667|.	3.24;3.24;2.68;1.35|.	5.65|5.65	-1.92|-1.92	0.07618|0.07618	Fibronectin, type III (1);|.	0.784679|.	0.11712|.	N|.	0.536788|.	T|T	0.18045|0.18045	0.0433|0.0433	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	B;B;B|.	0.09022|.	0.002;0.0;0.0|.	B;B;B|.	0.11329|.	0.006;0.0;0.001|.	T|T	0.27365|0.27365	-1.0076|-1.0076	10|5	0.45353|.	T|.	0.12|.	-3.0E-4|-3.0E-4	10.2654|10.2654	0.43452|0.43452	0.0:0.5192:0.0:0.4807|0.0:0.5192:0.0:0.4807	rs34372241|rs34372241	291;291;291|.	B4DYG9;B1AN14;Q8IZA0|.	.;.;K319L_HUMAN|.	A|C	291|154	ENSP00000318406:T291A;ENSP00000395883:T291A;ENSP00000407576:T291A;ENSP00000362355:T291A|.	ENSP00000318406:T291A|.	T|Y	-|-	1|2	0|0	KIAA0319L|KIAA0319L	35717196|35717196	0.012000|0.012000	0.17670|0.17670	0.001000|0.001000	0.08648|0.08648	0.016000|0.016000	0.09150|0.09150	0.013000|0.013000	0.13310|0.13310	-0.368000|-0.368000	0.08040|0.08040	-0.297000|-0.297000	0.09499|0.09499	ACC|TAC	T|0.994;C|0.006	0.006	strong		0.488	KIAA0319L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012684.2	NM_024874		C	35944609	T	C	35944609	3	2	28	1	0	0	0	0	1	0	0	0	8178	1638	57	3	2350	3	KIAA0319L	1	35944609	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	717646	35944609	213306012	25	11528											
GNL2	29889	hgsc.bcm.edu	37	chr1	38061396	38061396	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttggacgggttgatggtgcTccgtcctttgtacttgggct	3	15	14	9	2	0	1	0	1	0	0	2	2	2	2	2	4	2	4	2	4	1	5			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:38061396T>C	ENST00000373062.3	-	1	126	c.28A>G	c.(28-30)Agc>Ggc	p.S10G		NM_013285.2	NP_037417.1	Q13823	NOG2_HUMAN	guanine nucleotide binding protein-like 2 (nucleolar)	10					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)				TTGATGGTGCTCCGTCCTTTG	0.587																																					p.S10G		Atlas-SNP	.											.	GNL2	58	.	0			c.A28G						PASS	.						143	112	123					1																	38061396		2203	4300	6503	SO:0001583	missense	29889	exon1			TGGTGCTCCGTCC	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.28A>G	1.37:g.38061396T>C	ENSP00000362153:p.Ser10Gly	156	0	0		165	9	0.0545455	NM_013285	Q9BWN7	Missense_Mutation	SNP	ENST00000373062.3	37	CCDS421.1	.	.	.	.	.	.	.	.	.	.	T	17.87	3.494496	0.64186	.	.	ENSG00000134697	ENST00000373062	T	0.24723	1.84	5.01	5.01	0.66863	.	0.073396	0.85682	D	0.000000	T	0.21186	0.0510	L	0.51422	1.61	0.54753	D	0.999985	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.003	T	0.08207	-1.0733	10	0.33141	T	0.24	-17.281	6.6224	0.22810	0.1386:0.0758:0.0:0.7856	.	10;10	Q5T0F3;Q13823	.;NOG2_HUMAN	G	10	ENSP00000362153:S10G	ENSP00000362153:S10G	S	-	1	0	GNL2	37833983	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.138000	0.42140	2.102000	0.63906	0.533000	0.62120	AGC	.	.	none		0.587	GNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012478.1	NM_013285		C	38061396	T	C	38061396	3	2	28	1	0	0	0	0	1	0	0	0	6544	1551	54	3	2231	3	GNL2	1	38061396	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	2116787	38061396	211189225	26	11529											
PPIE	10450	hgsc.bcm.edu	37	chr1	40207580	40207580	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttggcaggatgctgcagcagCtatcgacaacatggtatggc	10	9	13	9	1	0	0	0	0	0	0	1	2	0	1	0	4	5	6	0	4	3	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:40207580C>T	ENST00000324379.5	+	4	207	c.188C>T	c.(187-189)gCt>gTt	p.A63V	PPIE_ENST00000470213.1_Missense_Mutation_p.A63V|PPIE_ENST00000372830.1_Missense_Mutation_p.A63V|PPIE_ENST00000480169.1_3'UTR|PPIE_ENST00000356511.2_Missense_Mutation_p.A63V	NM_006112.3	NP_006103.1	Q9UNP9	PPIE_HUMAN	peptidylprolyl isomerase E (cyclophilin E)	63	Poly-Ala.|RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of viral genome replication (GO:0045070)|protein folding (GO:0006457)|regulation of transcription, DNA-templated (GO:0006355)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|nucleotide binding (GO:0000166)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			kidney(3)|large_intestine(2)|lung(2)|prostate(1)|urinary_tract(1)	9	all_cancers(7;1.63e-13)|all_lung(5;2.27e-16)|all_epithelial(6;1.35e-15)|Lung NSC(20;1.49e-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;1.87e-18)|Epithelial(16;2.7e-17)|all cancers(16;5.5e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			GCTGCAGCAGCTATCGACAAC	0.423																																					p.A63V		Atlas-SNP	.											.	PPIE	33	.	0			c.C188T						PASS	.						146	146	146					1																	40207580		2203	4300	6503	SO:0001583	missense	10450	exon4			CAGCAGCTATCGA	AF042385	CCDS442.1, CCDS443.1, CCDS53299.1	1p32	2013-02-12			ENSG00000084072	ENSG00000084072		"RNA binding motif (RRM) containing"	9258	protein-coding gene	gene with protein product	"peptidyl-prolyl cis-trans isomerase E", "cyclophilin 33", "cyclophilin E", "PPIase E", "rotamase E", "peptidylprolyl isomerase E, isoform 1"	602435				9747881	Standard	NM_203456		Approved	CyP-33, MGC3736, MGC111222	uc001cdw.3	Q9UNP9	OTTHUMG00000009248	ENST00000324379.5:c.188C>T	1.37:g.40207580C>T	ENSP00000312769:p.Ala63Val	149	0	0		182	81	0.445055	NM_006112	B2R971|O43634|O43635|Q32Q72|Q3S611|Q5TGA0|Q5TGA2|Q5TGA3|Q9UIZ5	Missense_Mutation	SNP	ENST00000324379.5	37	CCDS443.1	.	.	.	.	.	.	.	.	.	.	C	33	5.255577	0.95336	.	.	ENSG00000084072	ENST00000324379;ENST00000356511;ENST00000470213;ENST00000372830	D;D;D;D	0.87412	-2.25;-2.25;-2.25;-2.25	4.7	4.7	0.59300	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	D	0.93716	0.7992	M	0.84082	2.675	0.80722	D	1	D;D;D	0.76494	0.999;0.971;0.995	D;P;D	0.74023	0.982;0.783;0.951	D	0.94503	0.7711	10	0.87932	D	0	-15.1861	17.7685	0.88485	0.0:1.0:0.0:0.0	.	63;63;63	Q5TGA3;Q9UNP9-2;Q9UNP9	.;.;PPIE_HUMAN	V	63	ENSP00000312769:A63V;ENSP00000348904:A63V;ENSP00000431714:A63V;ENSP00000361918:A63V	ENSP00000312769:A63V	A	+	2	0	PPIE	39980167	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	6.808000	0.75206	2.619000	0.88677	0.561000	0.74099	GCT	.	.	none		0.423	PPIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025642.2	NM_006112		T	40207580	C	T	40207580	3	4	28	1	0	0	0	0	1	0	0	0	12334	797	28	2	202	2	PPIE	1	40207580	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2146184	40207580	209043041	27	11530											
NFYC	4802	hgsc.bcm.edu	37	chr1	41232588	41232588	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcttaccatcttgttctcaAggggcaaagaaatgcaagtc	12	11	8	10	0	3	1	1	0	3	1	5	1	3	1	1	2	2	3	1	2	5	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:41232588A>G	ENST00000308733.5	+	8	834		c.e8-1		NFYC_ENST00000483091.1_Splice_Site|NFYC_ENST00000425457.2_Splice_Site|NFYC_ENST00000447388.3_Intron|NFYC_ENST00000456393.2_Intron|NFYC_ENST00000440226.3_Intron|NFYC_ENST00000372652.1_Intron|NFYC_ENST00000372651.1_Intron|NFYC_ENST00000427410.2_Intron|NFYC_ENST00000372653.1_Intron|NFYC_ENST00000372654.1_Intron			Q13952	NFYC_HUMAN	nuclear transcription factor Y, gamma						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)			CTTGTTCTCAAGGGGCAAAGA	0.498																																					.		Atlas-SNP	.											.	NFYC	39	.	0			c.829-2A>G						PASS	.						85	83	84					1																	41232588		692	1591	2283	SO:0001630	splice_region_variant	4802	exon9			TTCTCAAGGGGCA	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.829-1A>G	1.37:g.41232588A>G		63	0	0		69	5	0.0724638	NM_001142588	B4DUS6|B4DW63|D3DPV9|F8VWM3|Q59GY4|Q5T6K8|Q5T6K9|Q5T6L1|Q5TZR6|Q92869|Q9HBX1|Q9NXB5|Q9UM67|Q9UML0|Q9UMT7	Splice_Site	SNP	ENST00000308733.5	37		.	.	.	.	.	.	.	.	.	.	A	7.622	0.677071	0.14841	.	.	ENSG00000066136	ENST00000425457;ENST00000308733	.	.	.	5.43	1.91	0.25777	.	.	.	.	.	.	.	.	.	.	.	0.21355	N	0.999718	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.7246	0.23348	0.7231:0.0:0.2769:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NFYC	41005175	0.005000	0.15991	0.003000	0.11579	0.043000	0.13939	0.938000	0.28965	0.077000	0.16863	0.379000	0.24179	.	.	.	none		0.498	NFYC-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000020802.1	NM_014223	Intron	G	41232588	A	G	41232588	5	3	28	1	0	0	0	0	0	0	1	0	10400	86	3	3	857	3	NFYC	1	41232588	Splice_Site	SNP	A	TCGA-G8-6914-01A-11D-2210-10	1025008	41232588	208018033	28	11531											
KIAA0467	23334	hgsc.bcm.edu	37	chr1	43909129	43909129	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcatgggcccccagagacctCtggaccccctgacgggcagg	7	4	14	16	1	1	2	0	1	1	1	1	4	1	3	5	4	0	2	5	4	0	0	rs372395617		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:43909129C>T	ENST00000562955.1	+	60	8435	c.8435C>T	c.(8434-8436)tCt>tTt	p.S2812F	SZT2_ENST00000372442.1_Missense_Mutation_p.S1970F	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	2869					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						CCAGAGACCTCTGGACCCCCT	0.617																																					p.S2812F		Atlas-SNP	.											SZT2_ENST00000562955,NS,carcinoma,-1,3	SZT2	383	3	0			c.C8435T						PASS	.	C	PHE/SER	0,4406		0,0,2203	35	37	36		8435	2.3	0.8	1		36	1,8599	1.2+/-3.3	0,1,4299	no	missense	SZT2	NM_015284.3	155	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	2812/3376	43909129	1,13005	2203	4300	6503	SO:0001583	missense	23334	exon60			AGACCTCTGGACC	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.8435C>T	1.37:g.43909129C>T	ENSP00000457168:p.Ser2812Phe	93	0	0		81	33	0.407407	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Missense_Mutation	SNP	ENST00000562955.1	37	CCDS30694.2	.	.	.	.	.	.	.	.	.	.	C	9.750	1.167172	0.21621	0.0	1.16E-4	ENSG00000198198	ENST00000372442	.	.	.	5.4	2.26	0.28386	.	0.695263	0.14386	N	0.322843	T	0.25269	0.0614	N	0.08118	0	0.09310	N	1	B	0.31351	0.32	B	0.38056	0.264	T	0.24154	-1.0168	9	0.11485	T	0.65	.	12.9384	0.58329	0.0:0.52:0.48:0.0	.	2812	Q5T011-5	.	F	1970	.	ENSP00000361519:S1970F	S	+	2	0	SZT2	43681716	0.011000	0.17503	0.770000	0.31555	0.933000	0.57130	0.549000	0.23329	0.604000	0.29930	0.655000	0.94253	TCT	.	.	none		0.617	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		T	43909129	C	T	43909129	3	4	28	1	0	0	0	0	1	0	0	0	8187	913	32	2	6083	2	KIAA0467	1	43909129	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2676541	43909129	205341492	29	11532											
KDM4A	9682	hgsc.bcm.edu	37	chr1	44170034	44170035	+	Frame_Shift_Ins	INS	-	-	GGAGTAGGTGCTTCCA																															gcactataccgggccatcatINSggagtaggtgcttccagggt																										TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:44170034_44170035insGGAGTAGGTGCTTCCA	ENST00000372396.3	+	22	3322_3323	c.3188_3189insGGAGTAGGTGCTTCCA	c.(3187-3192)atggagfs	p.-1064fs	KDM4A-AS1_ENST00000418149.1_RNA|KDM4A-AS1_ENST00000453015.1_RNA|KDM4A-AS1_ENST00000434346.1_RNA|KDM4A-AS1_ENST00000398804.3_RNA|KDM4A-AS1_ENST00000439057.1_RNA	NM_014663.2	NP_055478.2	O75164	KDM4A_HUMAN	lysine (K)-specific demethylase 4A						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						CGGGCCATCATGGAGTAGGTGC	0.49																																					p.M1063_E1064delinsMEX		Pindel	.											.	KDM4A	74	.	0			c.3188_3189insGGAGTAGGTGCTTCCA						PASS	.																																			SO:0001589	frameshift_variant	9682	exon22			.	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.3189_3204dupGGAGTAGGTGCTTCCA	1.37:g.44170034_44170035insGGAGTAGGTGCTTCCA	ENSP00000361473:p.Glu1064fs	89	0	.		68	15	0.221	NM_014663	Q5VVB1	Frame_Shift_Ins	INS	ENST00000372396.3	37	CCDS491.1																																																																																			.	.	none		0.49	KDM4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019960.1	NM_014663		GGAGTAGGTGCTTCCA	44170035	-	GGAGTAGGTGCTTCCA	44170034	7	5	28	1	0	1	1	0	0	0	0	0	8137	1464	51	0	3270	0	KDM4A	1	44170034	Frame_Shift_Ins	INS	-	TCGA-G8-6914-01A-11D-2210-10	260905	44170034	205080587	30	11533											
TTC39A	22996	hgsc.bcm.edu	37	chr1	51754619	51754619	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtagtggtcatatttaatcTtcttttcactgcagaacaga	12	15	7	7	0	4	2	2	0	2	2	4	2	4	2	0	1	2	2	0	1	4	7	rs138509677	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:51754619T>C	ENST00000447632.2	-	17	1658	c.1610A>G	c.(1609-1611)aAg>aGg	p.K537R	TTC39A_ENST00000530004.1_Missense_Mutation_p.K145R|TTC39A_ENST00000413473.2_Missense_Mutation_p.K505R|TTC39A_ENST00000534098.1_5'UTR|TTC39A_ENST00000451380.1_Missense_Mutation_p.K501R|TTC39A_ENST00000262675.7_Missense_Mutation_p.K474R|TTC39A_ENST00000371750.5_Missense_Mutation_p.K502R			Q5SRH9	TT39A_HUMAN	tetratricopeptide repeat domain 39A	537								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						ATATTTAATCTTCTTTTCACT	0.488													T|||	4	0.000798722	0.0	0.0029	5008	,	,		21512	0.0		0.001	False		,,,				2504	0.001				p.K505R		Atlas-SNP	.											.	TTC39A	40	.	2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)	c.A1514G						PASS	.	T	ARG/LYS,ARG/LYS	2,3792		0,2,1895	44	45	45		1505,1514	4.6	1	1	dbSNP_134	45	26,8194		0,26,4084	yes	missense,missense	TTC39A	NM_001080494.2,NM_001144832.1	26,26	0,28,5979	CC,CT,TT		0.3163,0.0527,0.2331	benign,benign	502/579,505/582	51754619	28,11986	1897	4110	6007	SO:0001583	missense	22996	exon17			TTAATCTTCTTTT	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.1610A>G	1.37:g.51754619T>C	ENSP00000393952:p.Lys537Arg	101	0	0		130	70	0.538462	NM_001144832	B7Z782|E7EQY9|G3XAF8|O43417|O75040|Q5SRH5|Q5SRH6|Q5SRH7|Q5SRH8|Q5SRI0|Q5SRI1|Q5SRI2|Q5T7S1|Q6PIU8|Q9BT24	Missense_Mutation	SNP	ENST00000447632.2	37		2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	10.05	1.242909	0.22796	5.27E-4	0.003163	ENSG00000085831	ENST00000530004;ENST00000447632;ENST00000413473;ENST00000262675;ENST00000451380;ENST00000371750	T;T;T;T;T;T	0.63580	-0.05;0.73;0.75;0.76;0.75;0.75	5.75	4.57	0.56435	Tetratricopeptide-like helical (1);	0.146555	0.64402	N	0.000009	T	0.43144	0.1234	N	0.24115	0.695	0.33034	D	0.530583	B;B;B;B;B	0.09022	0.0;0.002;0.002;0.001;0.002	B;B;B;B;B	0.12837	0.003;0.003;0.008;0.006;0.007	T	0.46034	-0.9220	10	0.16420	T	0.52	-26.6932	8.059	0.30623	0.0:0.1678:0.0:0.8322	.	505;501;474;537;502	Q5SRH9-4;E7EQY9;D3DQ30;Q5SRH9;G3XAF8	.;.;.;TT39A_HUMAN;.	R	145;537;505;474;501;502	ENSP00000431228:K145R;ENSP00000393952:K537R;ENSP00000406144:K505R;ENSP00000262675:K474R;ENSP00000397207:K501R;ENSP00000360815:K502R	ENSP00000262675:K474R	K	-	2	0	TTC39A	51527207	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.926000	0.56491	0.938000	0.37419	0.533000	0.62120	AAG	T|0.999;C|0.001	0.001	strong		0.488	TTC39A-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000022434.2			C	51754619	T	C	51754619	3	2	28	1	0	0	0	0	1	0	0	0	16722	1609	56	3	239	3	TTC39A	1	51754619	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	7584585	51754619	197496002	31	11534											
C1orf175	374977	hgsc.bcm.edu	37	chr1	55119637	55119637	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gactccagcctcctgttcagCgacacctccaccttgacgct	7	9	7	18	2	1	1	1	1	0	0	4	3	4	1	6	0	2	2	6	0	0	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:55119637C>G	ENST00000421030.2	+	3	1323	c.1038C>G	c.(1036-1038)agC>agG	p.S346R	MROH7_ENST00000454855.2_Intron|MROH7-TTC4_ENST00000414150.2_Missense_Mutation_p.S346R|MROH7_ENST00000472987.1_3'UTR|MROH7_ENST00000545244.1_Intron|MROH7_ENST00000339553.5_Missense_Mutation_p.S346R|MROH7_ENST00000395690.2_Missense_Mutation_p.S346R|MROH7_ENST00000409996.1_Intron	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	346	Ser-rich.					extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											TCCTGTTCAGCGACACCTCCA	0.562																																					p.S346R		Atlas-SNP	.											.	.	.	.	0			c.C1038G						PASS	.						99	98	98					1																	55119637		2139	4231	6370	SO:0001583	missense	374977	exon3			GTTCAGCGACACC	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.1038C>G	1.37:g.55119637C>G	ENSP00000396622:p.Ser346Arg	171	0	0		147	77	0.52381	NM_001039464	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Missense_Mutation	SNP	ENST00000421030.2	37	CCDS41342.2	.	.	.	.	.	.	.	.	.	.	C	9.694	1.152800	0.21371	.	.	ENSG00000184313	ENST00000421030;ENST00000414867;ENST00000339553;ENST00000395690	T;T;T	0.04454	3.62;3.62;3.62	3.89	-7.78	0.01223	.	0.164918	0.29113	N	0.013103	T	0.09818	0.0241	L	0.27053	0.805	0.31997	N	0.603917	D;D;D	0.89917	0.996;0.989;1.0	D;P;D	0.75484	0.944;0.875;0.986	T	0.34104	-0.9842	10	0.87932	D	0	.	19.0946	0.93244	0.0:0.7723:0.0:0.2277	.	346;346;346	F8W8P2;Q68CQ1;Q68CQ1-4	.;HEAT8_HUMAN;.	R	346	ENSP00000396622:S346R;ENSP00000343211:S346R;ENSP00000379044:S346R	ENSP00000343211:S346R	S	+	3	2	HEATR8	54892225	0.000000	0.05858	0.261000	0.24466	0.379000	0.30106	-7.901000	0.00028	-2.926000	0.00302	-1.916000	0.00518	AGC	.	.	none		0.562	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547		G	55119637	C	G	55119637	3	3	28	1	0	0	0	0	1	0	0	0	2018	767	27	4	1040	4	C1orf175	1	55119637	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	3365018	55119637	194130984	32	11535											
IL12RB2	3595	hgsc.bcm.edu	37	chr1	67833643	67833643	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gagagagctccatccaggggGtgacacacaggtccctctaa	11	6	12	12	0	1	2	0	1	1	1	4	4	4	2	3	3	1	1	3	3	1	1	rs2307153	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:67833643G>A	ENST00000262345.1	+	10	2034	c.1394G>A	c.(1393-1395)gGt>gAt	p.G465D	IL12RB2_ENST00000544434.1_Missense_Mutation_p.G465D|IL12RB2_ENST00000371000.1_Missense_Mutation_p.G465D|IL12RB2_ENST00000541374.1_Missense_Mutation_p.G465D	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	465	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.		G -> D (in dbSNP:rs2307153). {ECO:0000269|Ref.3}.		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						CATCCAGGGGGTGACACACAG	0.527													G|||	37	0.00738818	0.0015	0.0101	5008	,	,		18311	0.001		0.0268	False		,,,				2504	0.0				p.G465D		Atlas-SNP	.											.	IL12RB2	94	.	0			c.G1394A						PASS	.	G	ASP/GLY	19,4387	26.2+/-53.5	0,19,2184	155	138	144		1394	-3.2	0	1	dbSNP_100	144	163,8437	77.2+/-139.8	0,163,4137	yes	missense	IL12RB2	NM_001559.2	94	0,182,6321	AA,AG,GG		1.8953,0.4312,1.3994	benign	465/863	67833643	182,12824	2203	4300	6503	SO:0001583	missense	3595	exon10			CAGGGGGTGACAC	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.1394G>A	1.37:g.67833643G>A	ENSP00000262345:p.Gly465Asp	89	0	0		80	34	0.425	NM_001559	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Missense_Mutation	SNP	ENST00000262345.1	37	CCDS638.1	23	0.010531135531135532	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	19	0.025065963060686015	G	6.679	0.493890	0.12702	0.004312	0.018953	ENSG00000081985	ENST00000262345;ENST00000371000;ENST00000541374;ENST00000544434	T;T;T;T	0.56444	0.46;0.46;0.46;0.46	5.02	-3.19	0.05171	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.541502	0.22419	N	0.060316	T	0.14960	0.0361	L	0.58101	1.795	0.09310	N	1	B;B;B;B	0.29301	0.011;0.0;0.241;0.002	B;B;B;B	0.26693	0.025;0.002;0.072;0.014	T	0.32929	-0.9888	10	0.16896	T	0.51	0.5509	2.0862	0.03646	0.2949:0.3687:0.22:0.1163	rs2307153;rs17097322;rs52799399;rs2307153	465;465;465;465	B4DGA4;F5H7L6;Q99665-2;Q99665	.;.;.;I12R2_HUMAN	D	465	ENSP00000262345:G465D;ENSP00000360039:G465D;ENSP00000445276:G465D;ENSP00000442443:G465D	ENSP00000262345:G465D	G	+	2	0	IL12RB2	67606231	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.673000	0.05239	-0.876000	0.04017	-0.122000	0.15005	GGT	G|0.986;A|0.014	0.014	strong		0.527	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559		A	67833643	G	A	67833643	3	1	28	1	0	0	0	0	1	0	0	0	7636	1261	44	2	1428	2	IL12RB2	1	67833643	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	12714006	67833643	181416978	33	11536											
LRRC40	55631	hgsc.bcm.edu	37	chr1	70616830	70616830	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctattaaaggaaagattgaTcgtttgcagtcttaccagtg	12	13	9	7	1	1	2	0	1	1	1	2	3	1	3	2	1	2	2	2	1	5	5	rs3180401	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:70616830T>C	ENST00000370952.3	-	13	1577	c.1498A>G	c.(1498-1500)Atc>Gtc	p.I500V		NM_017768.4	NP_060238.3	Q9H9A6	LRC40_HUMAN	leucine rich repeat containing 40	500			I -> V (in dbSNP:rs3180401).			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						GAAAGATTGATCGTTTGCAGT	0.294													T|||	18	0.00359425	0.0015	0.0014	5008	,	,		14238	0.0		0.0149	False		,,,				2504	0.0				p.I500V		Atlas-SNP	.											.	LRRC40	66	.	0			c.A1498G						PASS	.	T	VAL/ILE	21,4377	27.2+/-55.0	0,21,2178	58	58	58		1498	5.7	0.9	1	dbSNP_105	58	141,8447	69.0+/-131.5	1,139,4154	yes	missense	LRRC40	NM_017768.4	29	1,160,6332	CC,CT,TT		1.6418,0.4775,1.2475	benign	500/603	70616830	162,12824	2199	4294	6493	SO:0001583	missense	55631	exon13			GATTGATCGTTTG		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.1498A>G	1.37:g.70616830T>C	ENSP00000359990:p.Ile500Val	204	0	0		199	94	0.472362	NM_017768	Q9BTR7|Q9NSK1|Q9NXC1	Missense_Mutation	SNP	ENST00000370952.3	37	CCDS646.1	10	0.004578754578754579	1	0.0020325203252032522	0	0.0	0	0.0	9	0.011873350923482849	T	9.540	1.113220	0.20795	0.004775	0.016418	ENSG00000066557	ENST00000370952	T	0.53640	0.61	5.74	5.74	0.90152	.	0.097488	0.64402	D	0.000001	T	0.21590	0.0520	L	0.37561	1.115	0.38436	D	0.946563	B	0.29805	0.257	B	0.23018	0.043	T	0.14309	-1.0477	10	0.51188	T	0.08	.	10.3913	0.44171	0.0:0.0727:0.0:0.9273	rs3180401;rs3210316;rs17414609;rs52834337;rs3180401	500	Q9H9A6	LRC40_HUMAN	V	500	ENSP00000359990:I500V	ENSP00000359990:I500V	I	-	1	0	LRRC40	70389418	0.993000	0.37304	0.911000	0.35937	0.431000	0.31685	2.354000	0.44098	2.168000	0.68352	0.533000	0.62120	ATC	T|0.991;C|0.009	0.009	strong		0.294	LRRC40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025914.1	NM_017768		C	70616830	T	C	70616830	3	2	28	1	0	0	0	0	1	0	0	0	9007	1435	50	3	322	3	LRRC40	1	70616830	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	2783187	70616830	178633791	34	11537											
BTBD8	284697	hgsc.bcm.edu	37	chr1	92554283	92554283	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gggaagaattccatacagatGttaccttctctgtgggttgt	9	14	11	7	0	1	2	0	0	1	2	3	3	2	3	2	2	2	2	2	2	4	5	rs34856868	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:92554283G>A	ENST00000342818.3	+	2	414	c.178G>A	c.(178-180)Gtt>Att	p.V60I	BTBD8_ENST00000540648.1_Missense_Mutation_p.V60I|BTBD8_ENST00000370382.3_Missense_Mutation_p.V60I	NM_183242.3	NP_899065.2	Q5XKL5	BTBD8_HUMAN	BTB (POZ) domain containing 8	60	BTB 1. {ECO:0000255|PROSITE- ProRule:PRU00037}.		V -> I (in dbSNP:rs34856868).			nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)	16		all_lung(203;0.0484)|Lung NSC(277;0.126)|Glioma(108;0.222)		all cancers(265;0.0153)|Epithelial(280;0.0982)		CCATACAGATGTTACCTTCTC	0.323													G|||	41	0.0081869	0.0	0.013	5008	,	,		15123	0.0		0.0298	False		,,,				2504	0.002				p.V60I		Atlas-SNP	.											.	BTBD8	32	.	0			c.G178A						PASS	.	G	ILE/VAL	26,4380	32.6+/-62.9	0,26,2177	96	96	96		178	3.4	0.9	1	dbSNP_126	96	260,8340	101.0+/-162.3	6,248,4046	yes	missense	BTBD8	NM_183242.3	29	6,274,6223	AA,AG,GG		3.0233,0.5901,2.199	benign	60/379	92554283	286,12720	2203	4300	6503	SO:0001583	missense	284697	exon2			ACAGATGTTACCT	AY346333	CCDS737.1	1p22.1	2013-01-08			ENSG00000189195	ENSG00000189195		"BTB/POZ domain containing"	21019	protein-coding gene	gene with protein product						14654994	Standard	NM_183242		Approved		uc001doo.3	Q5XKL5	OTTHUMG00000010289	ENST00000342818.3:c.178G>A	1.37:g.92554283G>A	ENSP00000343686:p.Val60Ile	75	0	0		89	40	0.449438	NM_183242	Q6V9S5	Missense_Mutation	SNP	ENST00000342818.3	37	CCDS737.1	28	0.01282051282051282	0	0.0	5	0.013812154696132596	0	0.0	23	0.030343007915567283	G	13.65	2.301359	0.40694	0.005901	0.030233	ENSG00000189195	ENST00000370382;ENST00000342818;ENST00000540648	T;T;T	0.76316	-1.01;-1.01;-1.01	5.31	3.42	0.39159	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.247350	0.28273	N	0.015951	T	0.54822	0.1882	L	0.59967	1.855	0.23003	N	0.99845	B	0.24963	0.115	B	0.27076	0.076	T	0.49031	-0.8981	10	0.33940	T	0.23	-10.1214	8.3882	0.32512	0.2616:0.0:0.7384:0.0	rs34856868	60	Q5XKL5	BTBD8_HUMAN	I	60	ENSP00000359408:V60I;ENSP00000343686:V60I;ENSP00000443397:V60I	ENSP00000343686:V60I	V	+	1	0	BTBD8	92326871	1.000000	0.71417	0.859000	0.33776	0.832000	0.47134	1.026000	0.30103	0.718000	0.32166	0.591000	0.81541	GTT	G|0.980;A|0.020	0.020	strong		0.323	BTBD8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028372.1	NM_183242		A	92554283	G	A	92554283	3	1	28	1	0	0	0	0	1	0	0	0	1549	1377	48	2	184	2	BTBD8	1	92554283	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	21937453	92554283	156696338	35	11538											
DPYD	1806	hgsc.bcm.edu	37	chr1	97547947	97547947	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttgatacacatttcttcaTcaatcatagccacaacttgc	13	13	4	11	0	4	1	3	1	1	0	4	1	4	1	1	0	4	1	1	0	4	6	rs67376798	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:97547947T>A	ENST00000370192.3	-	22	2946	c.2846A>T	c.(2845-2847)gAt>gTt	p.D949V		NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	949	4Fe-4S ferredoxin-type 2. {ECO:0000255|PROSITE-ProRule:PRU00711}.				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)	CATTTCTTCATCAATCATAGC	0.388													T|||	11	0.00219649	0.0008	0.0029	5008	,	,		18701	0.0		0.007	False		,,,				2504	0.001				p.D949V		Atlas-SNP	.											.	DPYD	219	.	0			c.A2846T	GRCh37	CM003590	DPYD	M	rs67376798	PASS	.	T	VAL/ASP	4,4402	9.9+/-24.2	0,4,2199	242	220	228		2846	5.8	1	1	dbSNP_130	228	47,8553	30.7+/-82.3	1,45,4254	yes	missense	DPYD	NM_000110.3	152	1,49,6453	AA,AT,TT		0.5465,0.0908,0.3921	probably-damaging	949/1026	97547947	51,12955	2203	4300	6503	SO:0001583	missense	1806	exon22			TCTTCATCAATCA	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.2846A>T	1.37:g.97547947T>A	ENSP00000359211:p.Asp949Val	141	0	0		128	62	0.484375	NM_000110	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	37	CCDS30777.1	8	0.003663003663003663	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	T	23.4	4.406204	0.83230	9.08E-4	0.005465	ENSG00000188641	ENST00000370192	D	0.93019	-3.15	5.82	5.82	0.92795	4Fe-4S ferredoxin, iron-sulpur binding domain (1);	0.000000	0.85682	D	0.000000	D	0.97170	0.9075	M	0.93763	3.455	0.80722	D	1	D	0.76494	0.999	D	0.66602	0.945	D	0.98134	1.0432	10	0.87932	D	0	-25.8976	16.1779	0.81874	0.0:0.0:0.0:1.0	.	949	Q12882	DPYD_HUMAN	V	949	ENSP00000359211:D949V	ENSP00000359211:D949V	D	-	2	0	DPYD	97320535	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	7.841000	0.86834	2.216000	0.71823	0.533000	0.62120	GAT	T|0.996;A|0.004	0.004	strong		0.388	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110		A	97547947	T	A	97547947	3	1	28	1	0	0	0	0	1	0	0	0	4747	1435	50	5	239	5	DPYD	1	97547947	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	4993664	97547947	151702674	36	11539											
VAV3	10451	hgsc.bcm.edu	37	chr1	108417534	108417534	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tataattacctttccaaagtCacgaacatcaaacaagtcaa	18	10	3	10	1	3	0	3	0	0	0	4	1	4	0	2	0	3	0	2	0	8	4			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:108417534C>T	ENST00000370056.4	-	2	584	c.310G>A	c.(310-312)Gac>Aac	p.D104N	VAV3_ENST00000371846.4_Missense_Mutation_p.D39N|VAV3_ENST00000527011.1_Missense_Mutation_p.D104N	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	104	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)		TTTCCAAAGTCACGAACATCA	0.353																																					p.D104N		Atlas-SNP	.											.	VAV3	176	.	0			c.G310A						PASS	.						78	74	76					1																	108417534		2203	4300	6503	SO:0001583	missense	10451	exon2			CAAAGTCACGAAC	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.310G>A	1.37:g.108417534C>T	ENSP00000359073:p.Asp104Asn	151	0	0		190	92	0.484211	NM_006113	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Missense_Mutation	SNP	ENST00000370056.4	37	CCDS785.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.850961	0.91277	.	.	ENSG00000134215	ENST00000370056;ENST00000527011;ENST00000371846	T;T;T	0.41758	0.99;0.99;0.99	6.08	6.08	0.98989	Calponin homology domain (5);	0.229124	0.43416	D	0.000580	T	0.40423	0.1116	N	0.20328	0.56	0.58432	D	0.99999	B;B;D	0.54397	0.004;0.272;0.966	B;B;D	0.70487	0.023;0.322;0.969	T	0.09773	-1.0659	10	0.22706	T	0.39	.	19.2273	0.93822	0.0:1.0:0.0:0.0	.	104;104;104	B7ZLR1;E9PQ97;Q9UKW4	.;.;VAV3_HUMAN	N	104;104;39	ENSP00000359073:D104N;ENSP00000432540:D104N;ENSP00000360912:D39N	ENSP00000359073:D104N	D	-	1	0	VAV3	108219057	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.302000	0.78861	2.894000	0.99253	0.655000	0.94253	GAC	.	.	none		0.353	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113		T	108417534	C	T	108417534	3	4	28	1	0	0	0	0	1	0	0	0	17148	826	29	2	2362	2	VAV3	1	108417534	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	10869587	108417534	140833087	37	11540											
ANKRD35	148741	hgsc.bcm.edu	37	chr1	145555699	145555699	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggctctggaccaggtggagaGatggaaccgccatgatcaga	11	6	15	9	1	2	3	1	1	1	2	2	7	2	6	3	5	1	1	3	5	1	0	rs141350599	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:145555699G>A	ENST00000355594.4	+	2	134	c.47G>A	c.(46-48)aGa>aAa	p.R16K	ANKRD35_ENST00000544626.1_Missense_Mutation_p.R16K	NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	16										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)					CAGGTGGAGAGATGGAACCGC	0.562													G|||	7	0.00139776	0.0	0.0029	5008	,	,		18080	0.0		0.005	False		,,,				2504	0.0				p.R16K	Melanoma(9;127 754 22988 51047)	Atlas-SNP	.											.	ANKRD35	96	.	0			c.G47A						PASS	.	G	LYS/ARG	1,4405	2.1+/-5.4	0,1,2202	56	52	54		47	0.3	1	1	dbSNP_134	54	42,8558	26.3+/-74.7	0,42,4258	yes	missense	ANKRD35	NM_144698.3	26	0,43,6460	AA,AG,GG		0.4884,0.0227,0.3306	benign	16/1002	145555699	43,12963	2203	4300	6503	SO:0001583	missense	148741	exon2			TGGAGAGATGGAA	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.47G>A	1.37:g.145555699G>A	ENSP00000347802:p.Arg16Lys	76	0	0		67	38	0.567164	NM_144698	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	37	CCDS919.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	G	10.69	1.420552	0.25639	2.27E-4	0.004884	ENSG00000198483	ENST00000355594;ENST00000544626	T;T	0.63417	-0.04;2.52	5.99	0.277	0.15668	.	0.660459	0.13934	N	0.352680	T	0.13157	0.0319	N	0.02011	-0.69	0.19775	N	0.999952	B	0.10296	0.003	B	0.10450	0.005	T	0.34800	-0.9814	10	0.30854	T	0.27	-4.0648	8.8959	0.35465	0.4511:0.0:0.5489:0.0	.	16	Q8N283	ANR35_HUMAN	K	16	ENSP00000347802:R16K;ENSP00000442671:R16K	ENSP00000347802:R16K	R	+	2	0	ANKRD35	144267056	0.998000	0.40836	0.999000	0.59377	0.978000	0.69477	0.259000	0.18405	0.126000	0.18424	0.655000	0.94253	AGA	G|0.998;A|0.002	0.002	strong		0.562	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698		A	145555699	G	A	145555699	3	1	28	1	0	0	0	0	1	0	0	0	664	942	33	2	53	2	ANKRD35	1	145555699	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	37138165	145555699	103694922	38	11541											
ZNF687	5298	hgsc.bcm.edu	37	chr1	151263677	151263678	+	IGR	INS	-	-	ACA																															tcggcagggggctgttggggINSacaactagtctccaaggcct																								rs145032688	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:151263677_151263678insACA	ENST00000368873.1	-	0	3340				ZNF687_ENST00000368879.2_3'UTR			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)			GGCTGTTGGGGACAACTAGTCT	0.584														82	0.0163738	0.0023	0.0144	5008	,	,		16222	0.0		0.0547	False		,,,				2504	0.0143				p.D1236delinsDN	Colon(154;765 1838 9854 28443 37492)	Pindel,Atlas-Indel	.											.	ZNF687	94	.	0			c.3706_3707insACA						PASS	.			59,4025		4,51,1987						4.7	1		dbSNP_134	30	528,7434		53,422,3506	no	coding	ZNF687	NM_020832.1		57,473,5493	A1A1,A1R,RR		6.6315,1.4447,4.873				587,11459				SO:0001628	intergenic_variant	57592	exon9			.	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.151263678_151263680dupACA		23	0	.		27	10	0.37	NM_020832	B4DGI2|O15096|P78405|Q5VWB9|Q5VWC0|Q5VWC1|Q9BWR6	In_Frame_Ins	INS	ENST00000368873.1	37																																																																																				-|0.977;ACA|0.023	0.023	strong		0.584	PI4KB-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000034400.3	NM_002651		ACA	151263678	-	ACA	151263677	6	5	28	0	1	1	1	0	0	0	0	0	18107	1174	41	0		0	ZNF687	1	151263677	IGR	INS	-	TCGA-G8-6914-01A-11D-2210-10	5707978	151263677	97986944	39	11542											
ZBTB7B	51043	hgsc.bcm.edu	37	chr1	154987363	154987363	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agctgtcatgggggccggggGtagcgggacggccactgggg	5	5	22	9	3	1	0	1	0	0	0	1	1	1	1	2	8	2	2	2	8	1	1	rs145349387	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:154987363G>T	ENST00000368426.3	+	3	364	c.227G>T	c.(226-228)gGt>gTt	p.G76V	ZBTB7B_ENST00000417934.2_Missense_Mutation_p.G110V|ZBTB7B_ENST00000487542.1_3'UTR|ZBTB7B_ENST00000535420.1_Missense_Mutation_p.G76V|ZBTB7B_ENST00000292176.2_Missense_Mutation_p.G76V	NM_001256455.1	NP_001243384.1	O15156	ZBT7B_HUMAN	zinc finger and BTB domain containing 7B	76	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				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)			GGGGCCGGGGGTAGCGGGACG	0.622													G|||	7	0.00139776	0.0	0.0101	5008	,	,		15973	0.0		0.0	False		,,,				2504	0.0				p.G110V		Atlas-SNP	.											.	ZBTB7B	69	.	0			c.G329T						PASS	.	G	VAL/GLY	0,4406		0,0,2203	33	39	37		227	3.7	0.9	1	dbSNP_134	37	14,8586	8.4+/-32.0	0,14,4286	yes	missense	ZBTB7B	NM_015872.2	109	0,14,6489	TT,TG,GG		0.1628,0.0,0.1076	benign	76/540	154987363	14,12992	2203	4300	6503	SO:0001583	missense	51043	exon4			CCGGGGGTAGCGG	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.227G>T	1.37:g.154987363G>T	ENSP00000357411:p.Gly76Val	50	0	0		77	30	0.38961	NM_001252406	B4E3K5|D3DV83|J3KQQ3|Q68DR2|Q96EP2	Missense_Mutation	SNP	ENST00000368426.3	37	CCDS1081.1	3	0.0013736263736263737	0	0.0	3	0.008287292817679558	0	0.0	0	0.0	G	8.561	0.877867	0.17395	0.0	0.001628	ENSG00000160685	ENST00000535420;ENST00000368426;ENST00000417934;ENST00000292176	T;T;T;T	0.10099	2.96;2.96;2.91;2.96	3.66	3.66	0.41972	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.847359	0.09620	N	0.777684	T	0.10380	0.0254	N	0.19112	0.55	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.76071	0.987;0.966;0.987	T	0.24905	-1.0147	10	0.39692	T	0.17	.	10.7167	0.46017	0.0:0.0:1.0:0.0	.	76;76;110	A8K6F4;O15156;B4E3K5	.;ZBT7B_HUMAN;.	V	76;76;110;76	ENSP00000438647:G76V;ENSP00000357411:G76V;ENSP00000406286:G110V;ENSP00000292176:G76V	ENSP00000292176:G76V	G	+	2	0	ZBTB7B	153253987	0.978000	0.34361	0.893000	0.35052	0.005000	0.04900	0.651000	0.24873	1.867000	0.54127	0.455000	0.32223	GGT	G|0.999;T|0.001	0.001	strong		0.622	ZBTB7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091083.1	NM_015872		T	154987363	G	T	154987363	3	4	28	1	0	0	0	0	1	0	0	0	17569	1261	44	4	229	4	ZBTB7B	1	154987363	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	3723686	154987363	94263258	40	11543											
CLK2	1196	hgsc.bcm.edu	37	chr1	155239302	155239302	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agatgagcggctaaatgtccGgctgcgcctcctccgccgtc	6	8	12	15	5	0	2	0	1	0	1	4	2	3	2	5	2	2	2	5	2	2	1	rs375441160		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:155239302G>A	ENST00000368361.4	-	3	691	c.376C>T	c.(376-378)Cgg>Tgg	p.R126W	CLK2_ENST00000497188.1_5'Flank|CLK2_ENST00000361168.5_Missense_Mutation_p.R126W|CLK2_ENST00000355560.4_Missense_Mutation_p.R125W|CLK2_ENST00000536801.1_Missense_Mutation_p.R126W			P49760	CLK2_HUMAN	CDC-like kinase 2	126					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)			CTAAATGTCCGGCTGCGCCTC	0.597								Other conserved DNA damage response genes					G|||	1	0.000199681	0.0008	0.0	5008	,	,		18555	0.0		0.0	False		,,,				2504	0.0				p.R126W		Atlas-SNP	.											.	CLK2	55	.	0			c.C376T						PASS	.	G	TRP/ARG	0,4406		0,0,2203	69	63	65		376	3	1	1		65	2,8598		0,2,4298	no	missense	CLK2	NM_003993.2	101	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	126/499	155239302	2,13004	2203	4300	6503	SO:0001583	missense	1196	exon3			ATGTCCGGCTGCG	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.376C>T	1.37:g.155239302G>A	ENSP00000357345:p.Arg126Trp	34	0	0		58	20	0.344828	NM_003993	B1AVS9|B5MBX6|Q96CQ0	Missense_Mutation	SNP	ENST00000368361.4	37		.	.	.	.	.	.	.	.	.	.	.	17.04	3.286501	0.59867	0.0	2.33E-4	ENSG00000176444	ENST00000361168;ENST00000368361;ENST00000355560;ENST00000536801	T;T;T;T	0.55760	0.51;0.51;0.5;0.51	4.96	3.05	0.35203	.	0.567586	0.20018	N	0.100976	T	0.47893	0.1470	L	0.59436	1.845	0.58432	D	0.999999	D;D	0.69078	0.995;0.997	P;P	0.53401	0.535;0.725	T	0.51980	-0.8636	10	0.56958	D	0.05	.	13.0486	0.58942	0.0:0.0:0.7088:0.2911	.	126;126	P49760;P49760-3	CLK2_HUMAN;.	W	126;126;125;126	ENSP00000354856:R126W;ENSP00000357345:R126W;ENSP00000347759:R125W;ENSP00000441023:R126W	ENSP00000347759:R125W	R	-	1	2	CLK2	153505926	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.717000	0.54911	0.671000	0.31185	0.650000	0.86243	CGG	.	.	none		0.597	CLK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000087391.1	NM_003993		A	155239302	G	A	155239302	3	1	28	1	0	0	0	0	1	0	0	0	3539	1115	39	1	1164	1	CLK2	1	155239302	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	251939	155239302	94011319	41	11544											
ARHGEF11	9826	hgsc.bcm.edu	37	chr1	156941607	156941607	+	Intron	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggctatagacctcacagataCgctagggatgggtgaggagg	11	7	16	7	1	1	3	1	1	0	2	1	5	1	5	1	5	1	2	1	5	4	4	rs537664586		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:156941607C>T	ENST00000361409.2	-	8	1325				ARHGEF11_ENST00000368194.3_Splice_Site_p.R195H	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11						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)					CTCACAGATACGCTAGGGATG	0.567													C|||	1	0.000199681	0.0	0.0	5008	,	,		17391	0.0		0.0	False		,,,				2504	0.001				p.R195H		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.G584A						PASS	.						46	48	47					1																	156941607		2203	4300	6503	SO:0001627	intron_variant	9826	exon8			CAGATACGCTAGG	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.583-1772G>A	1.37:g.156941607C>T		42	0	0		64	33	0.515625	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Missense_Mutation	SNP	ENST00000361409.2	37	CCDS1162.1	.	.	.	.	.	.	.	.	.	.	C	10.83	1.461360	0.26248	.	.	ENSG00000132694	ENST00000368194	T	0.66460	-0.21	5.32	1.87	0.25490	.	0.440313	0.21740	N	0.069832	T	0.32376	0.0827	.	.	.	0.80722	D	1	B	0.12013	0.005	B	0.06405	0.002	T	0.13629	-1.0502	9	0.33141	T	0.24	-4.1001	7.6746	0.28478	0.0:0.5815:0.0:0.4185	.	195	O15085-2	.	H	195	ENSP00000357177:R195H	ENSP00000357177:R195H	R	-	2	0	ARHGEF11	155208231	0.878000	0.30173	1.000000	0.80357	0.995000	0.86356	0.424000	0.21330	0.622000	0.30249	0.655000	0.94253	CGT	.	.	none		0.567	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236		T	156941607	C	T	156941607	1	4	28	0	1	0	0	0	0	0	0	0	896	550	19	1		1	ARHGEF11	1	156941607	Intron	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1702305	156941607	92309014	42	11545											
OR10K2	391107	hgsc.bcm.edu	37	chr1	158390378	158390378	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggatggcacagcccaggaaAgaaatggtcttcttctggga	11	9	13	8	0	3	1	0	0	3	1	3	4	3	4	1	5	1	1	1	5	2	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:158390378A>T	ENST00000314902.2	-	1	278	c.279T>A	c.(277-279)tcT>tcA	p.S93S		NM_001004476.1	NP_001004476.1	Q6IF99	O10K2_HUMAN	olfactory receptor, family 10, subfamily K, member 2	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(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)					AGCCCAGGAAAGAAATGGTCT	0.478																																					p.S93S		Atlas-SNP	.											OR10K2,rectum,carcinoma,-1,1	OR10K2	69	1	0			c.T279A						PASS	.						176	172	174					1																	158390378		2203	4300	6503	SO:0001819	synonymous_variant	391107	exon1			CAGGAAAGAAATG	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.279T>A	1.37:g.158390378A>T		175	1	0.00571429		231	139	0.601732	NM_001004476		Silent	SNP	ENST00000314902.2	37	CCDS30896.1																																																																																			.	.	none		0.478	OR10K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051854.1	NM_001004476		T	158390378	A	T	158390378	2	4	28	1	0	0	0	0	0	0	0	1	10923	59	3	5		5	OR10K2	1	158390378	Silent	SNP	A	TCGA-G8-6914-01A-11D-2210-10	1448771	158390378	90860243	43	11546											
SLAMF8	56833	hgsc.bcm.edu	37	chr1	159799824	159799825	+	Frame_Shift_Del	DEL	CT	CT	-																															tttccgaggctccctggagaCtctgtaccattcccgcttcc																										TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:159799824_159799825delCT	ENST00000289707.5	+	2	358_359	c.209_210delCT	c.(208-210)actfs	p.T70fs	SLAMF8_ENST00000368104.4_Intron|SLAMF8_ENST00000471286.1_3'UTR	NM_020125.2	NP_064510.1	Q9P0V8	SLAF8_HUMAN	SLAM family member 8	70					cellular response to drug (GO:0035690)|defense response to bacterium (GO:0042742)|phagosome acidification (GO:0090383)|regulation of kinase activity (GO:0043549)|regulation of NAD(P)H oxidase activity (GO:0033860)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			endometrium(2)|large_intestine(4)|lung(6)	12	all_hematologic(112;0.0597)					TCCCTGGAGACTCTGTACCATT	0.629																																					p.70_70del		Pindel,Atlas-Indel	.											.	SLAMF8	30	.	0			c.208_209del						PASS	.			0,4266		0,0,2133						4.4	1			106	3,8249		0,3,4123	no	frameshift	SLAMF8	NM_020125.2		0,3,6256	A1A1,A1R,RR		0.0364,0.0,0.024				3,12515				SO:0001589	frameshift_variant	56833	exon2			.	AF146761	CCDS1188.1	1q23.1	2013-01-11			ENSG00000158714	ENSG00000158714		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	21391	protein-coding gene	gene with protein product		606620				11313408	Standard	NM_020125		Approved	BLAME, SBBI42, CD353	uc001fue.4	Q9P0V8	OTTHUMG00000035433	ENST00000289707.5:c.209_210delCT	1.37:g.159799826_159799827delCT	ENSP00000289707:p.Thr70fs	69	0	.		96	42	0.438	NM_020125	Q32MC6|Q5VU15	Frame_Shift_Del	DEL	ENST00000289707.5	37	CCDS1188.1																																																																																			.	.	none		0.629	SLAMF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085983.1	NM_020125		-	159799825	CT	-	159799824	7	5	28	1	0	1	0	1	0	0	0	0	14385	565	20	0	215	0	SLAMF8	1	159799824	Frame_Shift_Del	DEL	CT	TCGA-G8-6914-01A-11D-2210-10	1409446	159799824	89450797	44	11547											
FCRLB	127943	hgsc.bcm.edu	37	chr1	161697068	161697068	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gacccggcctccaccaccgcCccagctccatgggccgcagc	6	3	10	22	3	0	0	0	0	0	0	2	1	2	0	9	2	2	2	9	2	0	0			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:161697068C>T	ENST00000367948.2	+	8	1112	c.897C>T	c.(895-897)gcC>gcT	p.A299A	FCRLB_ENST00000367946.3_Missense_Mutation_p.P251L|FCRLB_ENST00000392158.1_Silent_p.A299A|FCRLB_ENST00000495397.1_3'UTR|FCRLB_ENST00000367944.3_Missense_Mutation_p.P258S|FCRLB_ENST00000367945.1_Missense_Mutation_p.P244L|FCRLB_ENST00000336830.5_Missense_Mutation_p.P265S			Q6BAA4	FCRLB_HUMAN	Fc receptor-like B	299					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)			CCACCACCGCCCCAGCTCCAT	0.662																																					p.A299A		Atlas-SNP	.											.	FCRLB	35	.	0			c.C897T						PASS	.						22	25	24					1																	161697068		2203	4299	6502	SO:0001819	synonymous_variant	127943	exon6			CACCGCCCCAGCT	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.897C>T	1.37:g.161697068C>T		60	0	0		65	4	0.0615385	NM_001002901	A2A3J5|A2A3J7|Q5VXA6|Q6BAA0|Q6BAA1|Q6BAA2|Q6BAA3|Q8IXZ7	Silent	SNP	ENST00000367948.2	37	CCDS30927.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.08|17.08	3.296672|3.296672	0.60086|0.60086	.|.	.|.	ENSG00000162746|ENSG00000162746	ENST00000367946;ENST00000367945|ENST00000336830;ENST00000367944	T;T|T;T	0.02032|0.02369	4.49;4.51|4.32;4.35	4.07|4.07	-3.13|-3.13	0.05266|0.05266	.|.	.|.	.|.	.|.	.|.	T|T	0.00666|0.00666	0.0022|0.0022	.|.	.|.	.|.	0.19300|0.19300	N|N	0.999978|0.999978	B;B|B;B;B	0.06786|0.25312	0.001;0.001|0.123;0.005;0.005	B;B|B;B;B	0.04013|0.20955	0.001;0.001|0.032;0.002;0.002	T|T	0.46610|0.46610	-0.9179|-0.9179	8|8	0.62326|0.87932	D|D	0.03|0	.|.	2.4538|2.4538	0.04524|0.04524	0.143:0.2488:0.4213:0.1869|0.143:0.2488:0.4213:0.1869	.|.	244;251|302;258;265	Q6BAA4-5;Q6BAA4-4|Q96DP6;Q6BAA4-3;Q6BAA4-2	.;.|.;.;.	L|S	251;244|265;258	ENSP00000356923:P251L;ENSP00000356922:P244L|ENSP00000338598:P265S;ENSP00000356921:P258S	ENSP00000356922:P244L|ENSP00000338598:P265S	P|P	+|+	2|1	0|0	FCRLB|FCRLB	159963692|159963692	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.088000|0.088000	0.18126|0.18126	-0.913000|-0.913000	0.04042|0.04042	-0.994000|-0.994000	0.03463|0.03463	-0.519000|-0.519000	0.04390|0.04390	CCC|CCC	.	.	none		0.662	FCRLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083585.1	NM_152378		T	161697068	C	T	161697068	2	4	28	1	0	0	0	0	0	0	0	1	5809	610	22	2		2	FCRLB	1	161697068	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1897244	161697068	87553553	45	11548											
FAM78B	149297	hgsc.bcm.edu	37	chr1	166039512	166039512	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacaaccagaggtggccccCgcttgggcctccacatgagg	8	6	12	15	1	1	2	1	1	0	1	2	2	2	2	5	4	1	1	5	4	1	1	rs138713518		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:166039512C>G	ENST00000338353.3	-	3	1341	c.752G>C	c.(751-753)cGg>cCg	p.R251P	FAM78B_ENST00000354422.3_Missense_Mutation_p.R251P			Q5VT40	FA78B_HUMAN	family with sequence similarity 78, member B	251										central_nervous_system(1)|endometrium(5)|large_intestine(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(923;0.0813)|Acute lymphoblastic leukemia(8;0.155)					AGGTGGCCCCCGCTTGGGCCT	0.597																																					p.R251P		Atlas-SNP	.											FAM78B,NS,carcinoma,+1,1	FAM78B	51	1	0			c.G752C						PASS	.						91	91	91					1																	166039512		2203	4300	6503	SO:0001583	missense	149297	exon2			GGCCCCCGCTTGG	AL626787	CCDS30931.1	1q24.1	2008-02-05			ENSG00000188859	ENSG00000188859			13495	protein-coding gene	gene with protein product							Standard	NM_001017961		Approved		uc021pee.1	Q5VT40	OTTHUMG00000034705	ENST00000338353.3:c.752G>C	1.37:g.166039512C>G	ENSP00000339681:p.Arg251Pro	177	0	0		285	51	0.178947	NM_001017961	B7Z693	Missense_Mutation	SNP	ENST00000338353.3	37	CCDS30931.1	.	.	.	.	.	.	.	.	.	.	C	15.61	2.883574	0.51908	.	.	ENSG00000188859	ENST00000354422;ENST00000338353	D;D	0.94330	-3.4;-3.4	5.96	3.94	0.45596	.	0.049142	0.85682	D	0.000000	D	0.89072	0.6611	L	0.44542	1.39	0.53688	D	0.999975	D	0.53745	0.962	P	0.50049	0.629	D	0.87304	0.2307	9	0.27785	T	0.31	-16.1405	14.0529	0.64749	0.0:0.7123:0.2877:0.0	.	251	Q5VT40	FA78B_HUMAN	P	251	ENSP00000346404:R251P;ENSP00000339681:R251P	ENSP00000339681:R251P	R	-	2	0	FAM78B	164306136	1.000000	0.71417	0.990000	0.47175	0.993000	0.82548	4.646000	0.61411	1.471000	0.48121	0.650000	0.86243	CGG	C|1.000;T|0.000	.	alt		0.597	FAM78B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343108.1	NM_001017961		G	166039512	C	G	166039512	3	3	28	1	0	0	0	0	1	0	0	0	5635	652	23	4	37	4	FAM78B	1	166039512	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	4342444	166039512	83211109	46	11549											
CD247	919	hgsc.bcm.edu	37	chr1	167407839	167407839	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catctcagggtcccggccacGtctcttgtccaaaacatcgt	8	10	8	15	3	2	0	1	0	2	0	7	0	4	0	3	2	1	0	3	2	2	1	rs148513413		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:167407839G>A	ENST00000362089.5	-	4	340	c.268C>T	c.(268-270)Cgt>Tgt	p.R90C	CD247_ENST00000483825.1_5'UTR|CD247_ENST00000392122.3_Missense_Mutation_p.R90C			P20963	CD3Z_HUMAN	CD247 molecule	90					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)	p.R90C(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|skin(1)	6			LUSC - Lung squamous cell carcinoma(543;0.236)		Muromonab(DB00075)	TCCCGGCCACGTCTCTTGTCC	0.552													G|||	1	0.000199681	0.0	0.0	5008	,	,		17232	0.001		0.0	False		,,,				2504	0.0				p.R90C	Ovarian(192;1815 2869 36877 43334)	Atlas-SNP	.											CD247,NS,carcinoma,+1,2	CD247	25	2	1	Substitution - Missense(1)	large_intestine(1)	c.C268T						PASS	.						151	141	145					1																	167407839		2203	4300	6503	SO:0001583	missense	919	exon4			GGCCACGTCTCTT	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.268C>T	1.37:g.167407839G>A	ENSP00000354782:p.Arg90Cys	87	0	0		95	4	0.0421053	NM_198053	B1AK49|Q5VX13|Q8TAX4	Missense_Mutation	SNP	ENST00000362089.5	37	CCDS1261.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	16.10	3.026161	0.54683	.	.	ENSG00000198821	ENST00000392122;ENST00000362089	.	.	.	4.52	2.45	0.29901	.	0.137776	0.28718	U	0.014364	T	0.54224	0.1845	M	0.64997	1.995	0.35719	D	0.816966	D;D;D	0.89917	1.0;0.998;0.997	D;P;P	0.74023	0.982;0.855;0.72	T	0.58978	-0.7540	8	0.72032	D	0.01	.	8.5233	0.33289	0.0:0.1632:0.6634:0.1734	.	90;90;90	Q6KAV0;P20963-3;P20963	.;.;CD3Z_HUMAN	C	90	.	ENSP00000354782:R90C	R	-	1	0	CD247	165674463	0.000000	0.05858	0.115000	0.21578	0.951000	0.60555	0.149000	0.16243	1.096000	0.41439	0.563000	0.77884	CGT	G|1.000;A|0.000	0.000	strong		0.552	CD247-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083707.1	NM_198053		A	167407839	G	A	167407839	3	1	28	1	0	0	0	0	1	0	0	0	2990	1145	40	1	246	1	CD247	1	167407839	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1368327	167407839	81842782	47	11550											
GPR52	9293	hgsc.bcm.edu	37	chr1	174417941	174417941	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacattttcaaaatttgccGtcagcacaccaaagagataa	16	9	5	11	1	2	1	2	0	0	1	2	2	2	1	3	0	2	1	3	0	4	4	rs200286780	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:174417941G>A	ENST00000367685.2	+	1	730	c.692G>A	c.(691-693)cGt>cAt	p.R231H	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	231					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						AAAATTTGCCGTCAGCACACC	0.463													G|||	2	0.000399361	0.0015	0.0	5008	,	,		19971	0.0		0.0	False		,,,				2504	0.0				p.R231H	Ovarian(92;924 1390 1930 16467 40583)	Atlas-SNP	.											.	GPR52	40	.	0			c.G692A						PASS	.	G	HIS/ARG,	4,4402	8.1+/-20.4	0,4,2199	196	181	186		692,	6.2	1	1		186	2,8598	2.2+/-6.3	0,2,4298	yes	missense,intron	GPR52,RABGAP1L	NM_005684.4,NM_014857.4	29,	0,6,6497	AA,AG,GG		0.0233,0.0908,0.0461	probably-damaging,	231/362,	174417941	6,13000	2203	4300	6503	SO:0001583	missense	9293	exon1			TTTGCCGTCAGCA	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.692G>A	1.37:g.174417941G>A	ENSP00000356658:p.Arg231His	99	0	0		122	49	0.401639	NM_005684	O75654|Q4VBL6|Q6ISM0	Missense_Mutation	SNP	ENST00000367685.2	37	CCDS30941.1	.	.	.	.	.	.	.	.	.	.	G	19.26	3.793374	0.70452	9.08E-4	2.33E-4	ENSG00000203737	ENST00000367685	T	0.42513	0.97	6.16	6.16	0.99307	GPCR, rhodopsin-like superfamily (1);	0.089581	0.47093	D	0.000250	T	0.55433	0.1920	L	0.54908	1.71	0.37430	D	0.913987	D	0.65815	0.995	P	0.52793	0.709	T	0.58352	-0.7651	10	0.66056	D	0.02	-9.9631	20.8598	0.99761	0.0:0.0:1.0:0.0	.	231	Q9Y2T5	GPR52_HUMAN	H	231	ENSP00000356658:R231H	ENSP00000356658:R231H	R	+	2	0	GPR52	172684564	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.126000	0.77201	2.937000	0.99478	0.650000	0.86243	CGT	.	.	weak		0.463	GPR52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084511.1	NM_005684		A	174417941	G	A	174417941	3	1	28	1	0	0	0	0	1	0	0	0	6706	1145	40	1	694	1	GPR52	1	174417941	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	7010102	174417941	74832680	48	11551											
SEC16B	89866	hgsc.bcm.edu	37	chr1	177933344	177933344	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcaagcaggctccctggaaAcagctcccccggccactcct	9	5	9	18	1	0	0	0	0	0	0	3	1	3	1	5	3	4	4	5	3	2	0			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:177933344A>G	ENST00000308284.6	-	5	693	c.604T>C	c.(604-606)Ttt>Ctt	p.F202L	SEC16B_ENST00000464631.2_Missense_Mutation_p.F202L|RP4-798P15.3_ENST00000354921.3_RNA	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	202	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						CTCCCTGGAAACAGCTCCCCC	0.557																																					p.F202L		Atlas-SNP	.											.	SEC16B	92	.	0			c.T604C						PASS	.						50	53	52					1																	177933344		1948	4130	6078	SO:0001583	missense	89866	exon5			CTGGAAACAGCTC	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.604T>C	1.37:g.177933344A>G	ENSP00000308339:p.Phe202Leu	61	0	0		91	43	0.472527	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Missense_Mutation	SNP	ENST00000308284.6	37	CCDS44281.1	.	.	.	.	.	.	.	.	.	.	A	0.430	-0.903732	0.02453	.	.	ENSG00000120341	ENST00000308284;ENST00000464631	T;T	0.39229	2.65;1.09	4.91	-4.56	0.03431	.	1.235800	0.05332	N	0.528496	T	0.20455	0.0492	N	0.15975	0.35	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	0.21008	-1.0258	10	0.11485	T	0.65	2.0E-4	6.3453	0.21345	0.4249:0.0:0.4488:0.1264	.	202;202;202	E9PK14;B1AM08;Q96JE7	.;.;SC16B_HUMAN	L	202	ENSP00000308339:F202L;ENSP00000431727:F202L	ENSP00000308339:F202L	F	-	1	0	AL359075.1	176199967	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.207000	0.09384	-0.739000	0.04809	-0.290000	0.09829	TTT	.	.	none		0.557	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127		G	177933344	A	G	177933344	3	3	28	1	0	0	0	0	1	0	0	0	14002	43	2	3	2666	3	SEC16B	1	177933344	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	3515403	177933344	71317277	49	11552											
RASAL2	9462	hgsc.bcm.edu	37	chr1	178442222	178442222	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttgtaggaaaaacggatcGtgtccctggattcagccaac	11	10	11	9	2	1	0	1	0	0	0	3	3	2	3	2	3	3	2	2	3	4	3	rs371002131	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:178442222G>A	ENST00000462775.1	+	16	3393	c.3268G>A	c.(3268-3270)Gtg>Atg	p.V1090M	RASAL2_ENST00000448150.3_Missense_Mutation_p.V1220M|RASAL2_ENST00000367649.3_Missense_Mutation_p.V1231M	NM_004841.3	NP_004832.1	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2	1090					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						AAAACGGATCGTGTCCCTGGA	0.522													G|||	2	0.000399361	0.0	0.0	5008	,	,		21631	0.0		0.0	False		,,,				2504	0.002				p.V1231M		Atlas-SNP	.											.	RASAL2	334	.	0			c.G3691A						PASS	.	G	MET/VAL,MET/VAL	1,4405	2.1+/-5.4	0,1,2202	148	129	136		3268,3691	1.7	1	1		136	0,8600		0,0,4300	no	missense,missense	RASAL2	NM_004841.3,NM_170692.2	21,21	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign	1090/1140,1231/1281	178442222	1,13005	2203	4300	6503	SO:0001583	missense	9462	exon18			CGGATCGTGTCCC	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.3268G>A	1.37:g.178442222G>A	ENSP00000420558:p.Val1090Met	126	0	0		168	105	0.625	NM_170692	F8W755|O95174|Q2TB22|Q5TFU9	Missense_Mutation	SNP	ENST00000462775.1	37	CCDS1322.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.86|12.86	2.064109|2.064109	0.36373|0.36373	2.27E-4|2.27E-4	0.0|0.0	ENSG00000075391|ENSG00000075391	ENST00000367647|ENST00000448150;ENST00000367649;ENST00000462775	.|T;T;T	.|0.12569	.|2.67;2.67;2.67	5.79|5.79	1.68|1.68	0.24146|0.24146	.|.	.|0.649779	.|0.15466	.|N	.|0.260880	T|T	0.05364|0.05364	0.0142|0.0142	N|N	0.08118|0.08118	0|0	0.32851|0.32851	D|D	0.506687|0.506687	.|P;P	.|0.46952	.|0.842;0.887	.|B;B	.|0.39379	.|0.298;0.157	T|T	0.31420|0.31420	-0.9944|-0.9944	6|10	0.87932|0.59425	D|D	0|0.04	.|.	1.8144|1.8144	0.03097|0.03097	0.2871:0.1267:0.4559:0.1303|0.2871:0.1267:0.4559:0.1303	.|.	.|1090;1231	.|Q9UJF2;F8W755	.|NGAP_HUMAN;.	H|M	43|1220;1231;1090	.|ENSP00000407768:V1220M;ENSP00000356621:V1231M;ENSP00000420558:V1090M	ENSP00000356619:R43H|ENSP00000356621:V1231M	R|V	+|+	2|1	0|0	RASAL2|RASAL2	176708845|176708845	0.997000|0.997000	0.39634|0.39634	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	0.793000|0.793000	0.26944|0.26944	0.382000|0.382000	0.24878|0.24878	0.655000|0.655000	0.94253|0.94253	CGT|GTG	.	.	none		0.522	RASAL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000084758.3	NM_170692		A	178442222	G	A	178442222	3	1	28	1	0	0	0	0	1	0	0	0	13079	1145	40	1	3799	1	RASAL2	1	178442222	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	508878	178442222	70808399	50	11553											
CACNA1E	777	hgsc.bcm.edu	37	chr1	181732594	181732594	+	Frame_Shift_Del	DEL	C	C	-																															tctgaagctcttccgagctgCccgcctcataaagctcctgc																										TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:181732594delC	ENST00000367573.2	+	34	4742	c.4742delC	c.(4741-4743)gccfs	p.A1581fs	CACNA1E_ENST00000360108.3_Frame_Shift_Del_p.A1562fs|CACNA1E_ENST00000526775.1_Frame_Shift_Del_p.A1562fs|CACNA1E_ENST00000367570.1_Frame_Shift_Del_p.A1581fs|CACNA1E_ENST00000358338.5_Frame_Shift_Del_p.A1513fs|CACNA1E_ENST00000357570.5_Frame_Shift_Del_p.A1532fs|CACNA1E_ENST00000367567.4_Frame_Shift_Del_p.A1188fs	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1581					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						TTCCGAGCTGCCCGCCTCATA	0.463																																					p.A1581fs		Pindel,Atlas-Indel	.											.	CACNA1E	778	.	0			c.4741delG						PASS	.						84	82	83					1																	181732594		1863	4100	5963	SO:0001589	frameshift_variant	777	exon34			.	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.4742delC	1.37:g.181732594delC	ENSP00000356545:p.Ala1581fs	80	0	.		109	34	0.312	NM_000721	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Frame_Shift_Del	DEL	ENST00000367573.2	37	CCDS55664.1																																																																																			.	.	none		0.463	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721		-	181732594	C	-	181732594	7	5	28	1	0	1	0	1	0	0	0	0	2544	739	26	0	4876	0	CACNA1E	1	181732594	Frame_Shift_Del	DEL	C	TCGA-G8-6914-01A-11D-2210-10	3290372	181732594	67518027	51	11554											
DENND1B	163486	hgsc.bcm.edu	37	chr1	197482049	197482049	+	IGR	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cttcatcatcatatagagcaCcatcaaggctcttaagaggc	13	10	7	11	0	5	2	4	0	1	2	5	2	5	2	1	2	1	2	1	2	4	4			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:197482049C>A								CRB1 (34464 upstream) : DENND1B (39335 downstream)																							ATATAGAGCACCATCAAGGCT	0.368																																					p.G517V		Atlas-SNP	.											.	DENND1B	108	.	0			c.G1550T						PASS	.						115	99	105					1																	197482049		2203	4299	6502	SO:0001628	intergenic_variant	163486	exon21			AGAGCACCATCAA																													1.37:g.197482049C>A		108	0	0		124	90	0.725806	NM_001195215		Missense_Mutation	SNP		37		.	.	.	.	.	.	.	.	.	.	C	6.634	0.485376	0.12641	.	.	ENSG00000213047	ENST00000391979;ENST00000542760;ENST00000450419	T	0.32023	1.47	5.2	5.2	0.72013	.	0.398495	0.23317	U	0.049495	T	0.19248	0.0462	L	0.33189	0.99	0.19575	N	0.999965	B	0.21753	0.06	B	0.23574	0.047	T	0.16660	-1.0395	10	0.16896	T	0.51	.	4.781	0.13202	0.1539:0.6157:0.1487:0.0817	.	517	Q6P3S1-5	.	V	157;517;497	ENSP00000375839:G157V	ENSP00000375839:G157V	G	-	2	0	DENND1B	195748672	0.000000	0.05858	0.053000	0.19242	0.125000	0.20455	0.676000	0.25247	2.578000	0.87016	0.655000	0.94253	GGT	.	.	none	0	0.368									A	197482049	C	A	197482049	1	1	28	0	1	0	0	0	0	0	0	0	4429	507	18	4		4	DENND1B	1	197482049	IGR	SNP	C	TCGA-G8-6914-01A-11D-2210-10	15749455	197482049	51768572	52	11555											
KIF14	9928	hgsc.bcm.edu	37	chr1	200558420	200558420	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttcaagatgctgctttgcCttttctaattcctcaatttt	7	20	5	9	0	3	1	2	0	1	1	4	1	4	1	2	0	3	3	2	0	3	8	rs77213709	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:200558420C>T	ENST00000367350.4	-	18	3477	c.3039G>A	c.(3037-3039)aaG>aaA	p.K1013K		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	1013	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						GCTGCTTTGCCTTTTCTAATT	0.303													C|||	30	0.00599042	0.0	0.0	5008	,	,		19286	0.0		0.007	False		,,,				2504	0.0235				p.K1013K		Atlas-SNP	.											.	KIF14	156	.	0			c.G3039A						PASS	.	C		3,4401	6.2+/-15.9	0,3,2199	158	146	150		3039	3.1	0.3	1	dbSNP_132	150	33,8567	22.2+/-67.0	0,33,4267	no	coding-synonymous	KIF14	NM_014875.2		0,36,6466	TT,TC,CC		0.3837,0.0681,0.2768		1013/1649	200558420	36,12968	2202	4300	6502	SO:0001819	synonymous_variant	9928	exon18			CTTTGCCTTTTCT	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.3039G>A	1.37:g.200558420C>T		216	0	0		303	175	0.577558	NM_014875	Q14CI8|Q4G0A5|Q5T1W3	Silent	SNP	ENST00000367350.4	37	CCDS30963.1																																																																																			C|0.996;T|0.004	0.004	strong		0.303	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875		T	200558420	C	T	200558420	2	4	28	1	0	0	0	0	0	0	0	1	8285	680	24	2		2	KIF14	1	200558420	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	3076371	200558420	48692201	53	11556											
ELF3	1999	hgsc.bcm.edu	37	chr1	201981774	201981774	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cctcctcttcccagaccaggGcagcccctttgcccaggagc	6	7	9	19	0	1	1	0	0	1	1	3	2	3	2	7	2	3	1	7	2	0	2	rs55729978	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:201981774G>A	ENST00000359651.3	+	4	3677	c.485G>A	c.(484-486)gGc>gAc	p.G162D	ELF3_ENST00000367284.5_Missense_Mutation_p.G162D|RP11-510N19.5_ENST00000504773.1_RNA|RP11-465N4.4_ENST00000419190.1_RNA|ELF3_ENST00000367283.3_Missense_Mutation_p.G162D					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						CCAGACCAGGGCAGCCCCTTT	0.642													G|||	364	0.0726837	0.2421	0.0159	5008	,	,		14680	0.0		0.0229	False		,,,				2504	0.0102				p.G162D		Atlas-SNP	.											ELF3_ENST00000359651,NS,carcinoma,0,2	ELF3	92	2	0			c.G485A						PASS	.	G	ASP/GLY,ASP/GLY	690,3716		51,588,1564	28	34	32		485,485	3.3	1	1	dbSNP_129	32	147,8451		1,145,4153	yes	missense,missense	ELF3	NM_001114309.1,NM_004433.4	94,94	52,733,5717	AA,AG,GG		1.7097,15.6605,6.4365	benign,benign	162/372,162/372	201981774	837,12167	2203	4299	6502	SO:0001583	missense	1999	exon5			ACCAGGGCAGCCC	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.485G>A	1.37:g.201981774G>A	ENSP00000352673:p.Gly162Asp	65	0	0		66	41	0.621212	NM_001114309		Missense_Mutation	SNP	ENST00000359651.3	37	CCDS1419.1	157	0.07188644688644688	129	0.2621951219512195	9	0.024861878453038673	0	0.0	19	0.025065963060686015	G	10.76	1.441663	0.25900	0.156605	0.017097	ENSG00000163435	ENST00000359651;ENST00000367284;ENST00000367283;ENST00000310044;ENST00000446188	T;T;T;T	0.56103	2.47;2.47;2.47;0.48	5.2	3.29	0.37713	.	0.821186	0.11026	N	0.607832	T	0.00012	0.0000	L	0.37561	1.115	0.27380	P	0.9554544	B	0.10296	0.003	B	0.09377	0.004	T	0.09796	-1.0658	9	0.37606	T	0.19	.	7.8653	0.29533	0.0862:0.164:0.7499:0.0	rs55729978	162	P78545	ELF3_HUMAN	D	162;162;162;162;160	ENSP00000352673:G162D;ENSP00000356253:G162D;ENSP00000356252:G162D;ENSP00000405162:G160D	ENSP00000311348:G162D	G	+	2	0	ELF3	200248397	0.174000	0.23070	0.988000	0.46212	0.681000	0.39784	0.316000	0.19469	1.168000	0.42723	0.655000	0.94253	GGC	G|0.938;A|0.062	0.062	strong		0.642	ELF3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087360.1	NM_004433		A	201981774	G	A	201981774	3	1	28	1	0	0	0	0	1	0	0	0	5057	1203	42	2	499	2	ELF3	1	201981774	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1423354	201981774	47268847	54	11557											
KDM5B	10765	hgsc.bcm.edu	37	chr1	202715288	202715288	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accgcaatttatatttgtaaGgaggacaggaacacaattct	15	11	8	7	1	1	0	0	0	1	0	1	3	1	3	1	3	1	2	1	3	6	6	rs144876400		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:202715288G>A	ENST00000367265.3	-	15	3344	c.2180C>T	c.(2179-2181)cCt>cTt	p.P727L	KDM5B_ENST00000367264.2_Missense_Mutation_p.P763L	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	727					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						ATATTTGTAAGGAGGACAGGA	0.388																																					p.P727L		Atlas-SNP	.											.	KDM5B	166	.	0			c.C2180T						PASS	.	G	LEU/PRO	0,4406		0,0,2203	122	106	112		2180	5.1	0.9	1	dbSNP_134	112	2,8598	1.2+/-3.3	0,2,4298	yes	missense	KDM5B	NM_006618.3	98	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	727/1545	202715288	2,13004	2203	4300	6503	SO:0001583	missense	10765	exon15			TTGTAAGGAGGAC	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.2180C>T	1.37:g.202715288G>A	ENSP00000356234:p.Pro727Leu	108	0	0		130	52	0.4	NM_006618	O95811|Q15752|Q9Y3Q5	Missense_Mutation	SNP	ENST00000367265.3	37	CCDS30974.1	.	.	.	.	.	.	.	.	.	.	G	12.37	1.916623	0.33815	0.0	2.33E-4	ENSG00000117139	ENST00000367265;ENST00000538292;ENST00000367264;ENST00000235790;ENST00000543924	D;D;D	0.88201	-2.35;-2.35;-2.35	5.97	5.06	0.68205	Zinc finger, C5HC2-type (1);	0.356049	0.34555	N	0.003863	D	0.85106	0.5621	L	0.52905	1.665	0.42064	D	0.991176	B;B	0.16396	0.017;0.005	B;B	0.19148	0.011;0.024	T	0.79704	-0.1692	10	0.34782	T	0.22	-10.6553	10.7795	0.46369	0.1402:0.0:0.8598:0.0	.	763;727	Q9UGL1-2;Q9UGL1	.;KDM5B_HUMAN	L	727;569;763;569;96	ENSP00000356234:P727L;ENSP00000356233:P763L;ENSP00000235790:P569L	ENSP00000235790:P569L	P	-	2	0	KDM5B	200981911	0.987000	0.35691	0.930000	0.37139	0.965000	0.64279	3.717000	0.54911	2.836000	0.97738	0.655000	0.94253	CCT	G|1.000;A|0.000	0.000	weak		0.388	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618		A	202715288	G	A	202715288	3	1	28	1	0	0	0	0	1	0	0	0	8143	1000	35	2	2506	2	KDM5B	1	202715288	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	733514	202715288	46535333	55	11558											
KLHL12	59349	hgsc.bcm.edu	37	chr1	202863792	202863792	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtctgcatatctcccagcatGctccactggtcaatgtttgg	7	13	9	12	0	3	0	1	0	2	0	5	0	4	0	2	2	3	4	2	2	2	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:202863792G>A	ENST00000367261.3	-	9	1439	c.1221C>T	c.(1219-1221)agC>agT	p.S407S	KLHL12_ENST00000435533.3_Silent_p.S445S|KLHL12_ENST00000367259.1_Silent_p.S140S	NM_021633.2	NP_067646.1	Q53G59	KLH12_HUMAN	kelch-like family member 12	407	Interaction with DVL3.				COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|protein monoubiquitination (GO:0006513)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|ER to Golgi transport vesicle (GO:0030134)|Golgi membrane (GO:0000139)				NS(3)|breast(2)|endometrium(1)|large_intestine(1)|lung(6)|stomach(1)	14			BRCA - Breast invasive adenocarcinoma(75;0.166)			CTCCCAGCATGCTCCACTGGT	0.517																																					p.S407S		Atlas-SNP	.											.	KLHL12	50	.	0			c.C1221T						PASS	.						153	147	149					1																	202863792		2203	4300	6503	SO:0001819	synonymous_variant	59349	exon9			CAGCATGCTCCAC	AF190900	CCDS1429.1	1q32.1	2013-01-30	2013-01-30		ENSG00000117153	ENSG00000117153		"Kelch-like", "BTB/POZ domain containing"	19360	protein-coding gene	gene with protein product		614522	"kelch-like 12 (Drosophila)"			12477932	Standard	NM_021633		Approved	C3IP1	uc001gyo.1	Q53G59	OTTHUMG00000041385	ENST00000367261.3:c.1221C>T	1.37:g.202863792G>A		144	0	0		192	71	0.369792	NM_021633	A6NEN8|B7Z7B8|Q9HBX5	Silent	SNP	ENST00000367261.3	37	CCDS1429.1																																																																																			.	.	none		0.517	KLHL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099151.1	NM_021633		A	202863792	G	A	202863792	2	1	28	1	0	0	0	0	0	0	0	1	8377	1310	46	2		2	KLHL12	1	202863792	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	148504	202863792	46386829	56	11559											
MYOG	4656	hgsc.bcm.edu	37	chr1	203054651	203054651	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccgcccccgccccggtagcGgaggtcacgctcctcctggt	3	6	12	20	5	1	0	1	0	0	0	3	1	3	1	7	4	1	2	7	4	1	1	rs61745017	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:203054651G>A	ENST00000241651.4	-	1	513	c.439C>T	c.(439-441)Cgc>Tgc	p.R147C		NM_002479.5	NP_002470.2	P15173	MYOG_HUMAN	myogenin (myogenic factor 4)	147					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						CCCCGGTAGCGGAGGTCACGC	0.701													G|||	60	0.0119808	0.003	0.0202	5008	,	,		15296	0.0		0.0378	False		,,,				2504	0.0041				p.R147C		Atlas-SNP	.											.	MYOG	28	.	0			c.C439T						PASS	.	G	CYS/ARG	32,4374	35.2+/-66.4	0,32,2171	23	26	25		439	4.4	1	1	dbSNP_129	25	268,8332	99.9+/-161.4	5,258,4037	yes	missense	MYOG	NM_002479.4	180	5,290,6208	AA,AG,GG		3.1163,0.7263,2.3066	probably-damaging	147/225	203054651	300,12706	2203	4300	6503	SO:0001583	missense	4656	exon1			GGTAGCGGAGGTC	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.439C>T	1.37:g.203054651G>A	ENSP00000241651:p.Arg147Cys	109	0	0		138	82	0.594203	NM_002479	Q53XW6	Missense_Mutation	SNP	ENST00000241651.4	37	CCDS1433.1	42	0.019230769230769232	1	0.0020325203252032522	10	0.027624309392265192	0	0.0	31	0.040897097625329816	G	18.45	3.626906	0.66901	0.007263	0.031163	ENSG00000122180	ENST00000241651	D	0.98585	-5.01	5.32	4.36	0.52297	Helix-loop-helix DNA-binding (1);	0.215520	0.47852	D	0.000208	D	0.87688	0.6240	L	0.46157	1.445	0.45567	D	0.998512	D	0.58620	0.983	B	0.38296	0.27	D	0.89363	0.3669	10	0.62326	D	0.03	-7.4351	15.9767	0.80071	0.0:0.1461:0.8539:0.0	.	147	P15173	MYOG_HUMAN	C	147	ENSP00000241651:R147C	ENSP00000241651:R147C	R	-	1	0	MYOG	201321274	1.000000	0.71417	0.999000	0.59377	0.978000	0.69477	5.946000	0.70234	2.486000	0.83907	0.563000	0.77884	CGC	G|0.979;A|0.021	0.021	strong		0.701	MYOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100279.1	NM_002479		A	203054651	G	A	203054651	3	1	28	1	0	0	0	0	1	0	0	0	10099	1116	39	1	247	1	MYOG	1	203054651	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	190859	203054651	46195970	57	11560											
TGFB2	7042	hgsc.bcm.edu	37	chr1	218520315	218520315	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagggcggccgcctgcgagcGcgagaggagcgacgaagagt	9	2	20	10	7	0	2	0	0	0	2	0	8	0	3	2	3	3	0	2	3	1	0	rs10482721	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:218520315G>A	ENST00000366930.4	+	1	739	c.272G>A	c.(271-273)cGc>cAc	p.R91H	TGFB2_ENST00000366929.4_Missense_Mutation_p.R91H|RP11-224O19.2_ENST00000414452.1_RNA	NM_003238.3	NP_003229.1	P61812	TGFB2_HUMAN	transforming growth factor, beta 2	91			R -> H (in dbSNP:rs10482721). {ECO:0000269|PubMed:11528528, ECO:0000269|Ref.4}.		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)		GCCTGCGAGCGCGAGAGGAGC	0.577													G|||	4	0.000798722	0.0	0.0029	5008	,	,		17473	0.0		0.002	False		,,,				2504	0.0				p.R91H		Atlas-SNP	.											.	TGFB2	102	.	0			c.G272A						PASS	.	G	HIS/ARG,HIS/ARG	5,4393		0,5,2194	23	21	22		272,272	5.4	1	1	dbSNP_119	22	43,8543		1,41,4251	yes	missense,missense	TGFB2	NM_001135599.2,NM_003238.3	29,29	1,46,6445	AA,AG,GG		0.5008,0.1137,0.3697	possibly-damaging,possibly-damaging	91/443,91/415	218520315	48,12936	2199	4293	6492	SO:0001583	missense	7042	exon1			GCGAGCGCGAGAG	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.272G>A	1.37:g.218520315G>A	ENSP00000355897:p.Arg91His	99	0	0		116	56	0.482759	NM_003238	B4DKC5|P08112|Q15579|Q15581|Q4VAV9	Missense_Mutation	SNP	ENST00000366930.4	37	CCDS1521.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	29.8	5.041172	0.93685	0.001137	0.005008	ENSG00000092969	ENST00000366930;ENST00000366929	T;T	0.64618	-0.11;-0.11	5.45	5.45	0.79879	Transforming growth factor-beta, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.68311	0.2987	L	0.60455	1.87	0.80722	D	1	D;D;D	0.89917	0.995;0.984;1.0	P;P;D	0.81914	0.855;0.767;0.995	T	0.71941	-0.4440	10	0.52906	T	0.07	.	13.7098	0.62661	0.0732:0.0:0.9268:0.0	rs10482721	91;91;92	P61812-2;P61812;Q59EG9	.;TGFB2_HUMAN;.	H	91	ENSP00000355897:R91H;ENSP00000355896:R91H	ENSP00000355896:R91H	R	+	2	0	TGFB2	216586938	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.548000	0.73896	2.837000	0.97791	0.591000	0.81541	CGC	G|0.996;A|0.004	0.004	strong		0.577	TGFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095359.2	NM_003238		A	218520315	G	A	218520315	3	1	28	1	0	0	0	0	1	0	0	0	15833	1087	38	1	274	1	TGFB2	1	218520315	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	15465664	218520315	30730306	58	11561											
HHIPL2	79802	hgsc.bcm.edu	37	chr1	222712108	222712108	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccataagcatagattggcaGaacatcatctgtccaggaga	14	8	10	9	0	2	3	1	0	1	3	3	4	3	3	2	2	2	2	2	2	3	3	rs116359984	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:222712108G>T	ENST00000343410.6	-	5	1517	c.1459C>A	c.(1459-1461)Ctg>Atg	p.L487M		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	487					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)		TAGATTGGCAGAACATCATCT	0.453													G|||	12	0.00239617	0.0	0.0086	5008	,	,		19989	0.0		0.006	False		,,,				2504	0.0				p.L487M		Atlas-SNP	.											.	HHIPL2	122	.	0			c.C1459A						PASS	.	G	MET/LEU	3,4403	6.2+/-15.9	0,3,2200	118	97	104		1459	4.4	1	1	dbSNP_132	104	54,8546	33.3+/-86.6	1,52,4247	yes	missense	HHIPL2	NM_024746.3	15	1,55,6447	TT,TG,GG		0.6279,0.0681,0.4383	probably-damaging	487/725	222712108	57,12949	2203	4300	6503	SO:0001583	missense	79802	exon5			TTGGCAGAACATC	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.1459C>A	1.37:g.222712108G>T	ENSP00000342118:p.Leu487Met	119	0	0		118	63	0.533898	NM_024746	Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Missense_Mutation	SNP	ENST00000343410.6	37	CCDS1530.2	7	0.003205128205128205	0	0.0	3	0.008287292817679558	0	0.0	4	0.005277044854881266	G	17.11	3.306873	0.60305	6.81E-4	0.006279	ENSG00000143512	ENST00000343410	T	0.13778	2.56	5.35	4.43	0.53597	Soluble quinoprotein glucose/sorbosone dehydrogenase (1);Glucose/Sorbosone dehydrogenase (1);Six-bladed beta-propeller, TolB-like (1);	0.153343	0.43416	D	0.000570	T	0.19886	0.0478	L	0.49513	1.565	0.42479	D	0.992857	D	0.89917	1.0	D	0.87578	0.998	T	0.00453	-1.1730	10	0.31617	T	0.26	-6.822	9.5251	0.39160	0.1591:0.0:0.8409:0.0	.	487	Q6UWX4	HIPL2_HUMAN	M	487	ENSP00000342118:L487M	ENSP00000342118:L487M	L	-	1	2	HHIPL2	220778731	1.000000	0.71417	0.994000	0.49952	0.530000	0.34684	6.212000	0.72188	2.472000	0.83506	0.591000	0.81541	CTG	G|0.995;T|0.005	0.005	strong		0.453	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746		T	222712108	G	T	222712108	3	4	28	1	0	0	0	0	1	0	0	0	7103	933	33	4	735	4	HHIPL2	1	222712108	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	4191793	222712108	26538513	59	11562											
TAF1A	9015	hgsc.bcm.edu	37	chr1	222732051	222732051	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttcacagatctcttcatcCgcttaattttcttccctaag	8	18	3	12	1	4	1	2	0	2	1	7	1	6	1	2	0	0	1	2	0	2	8	rs143557200	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:222732051C>T	ENST00000352967.4	-	11	1492	c.1304G>A	c.(1303-1305)cGg>cAg	p.R435Q	TAF1A_ENST00000350027.4_Missense_Mutation_p.R435Q|TAF1A_ENST00000391882.1_Missense_Mutation_p.R321Q|TAF1A_ENST00000366890.1_Missense_Mutation_p.R321Q	NM_005681.3	NP_005672.1	Q15573	TAF1A_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, A, 48kDa	435					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)		TCTCTTCATCCGCTTAATTTT	0.303													C|||	20	0.00399361	0.0	0.0144	5008	,	,		12618	0.0		0.007	False		,,,				2504	0.0031				p.R435Q		Atlas-SNP	.											TAF1A,NS,carcinoma,0,1	TAF1A	35	1	0			c.G1304A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	2,4400	4.2+/-10.8	0,2,2199	82	84	83		1304,1304,962	-3.5	0.8	1	dbSNP_134	83	72,8498	40.8+/-97.7	1,70,4214	yes	missense,missense,missense	TAF1A	NM_001201536.1,NM_005681.3,NM_139352.2	43,43,43	1,72,6413	TT,TC,CC		0.8401,0.0454,0.5705	benign,benign,benign	435/451,435/451,321/337	222732051	74,12898	2201	4285	6486	SO:0001583	missense	9015	exon11			TTCATCCGCTTAA	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.1304G>A	1.37:g.222732051C>T	ENSP00000327072:p.Arg435Gln	90	0	0		90	43	0.477778	NM_001201536	B2RDZ8|D3DTB7|Q9NWA1	Missense_Mutation	SNP	ENST00000352967.4	37	CCDS1531.1	10	0.004578754578754579	0	0.0	5	0.013812154696132596	0	0.0	5	0.006596306068601583	C	10.77	1.444536	0.25987	4.54E-4	0.008401	ENSG00000143498	ENST00000366890;ENST00000350027;ENST00000352967;ENST00000391882	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	5.34	-3.51	0.04696	.	0.878450	0.10066	N	0.720352	T	0.16214	0.0390	N	0.21583	0.68	0.38468	D	0.947394	B	0.15141	0.012	B	0.10450	0.005	T	0.21965	-1.0230	10	0.18276	T	0.48	-18.2737	7.0687	0.25167	0.0:0.2261:0.1415:0.6324	.	435	Q15573	TAF1A_HUMAN	Q	321;435;435;321	ENSP00000355856:R321Q;ENSP00000339976:R435Q;ENSP00000327072:R435Q;ENSP00000375754:R321Q	ENSP00000339976:R435Q	R	-	2	0	TAF1A	220798674	0.035000	0.19736	0.844000	0.33320	0.826000	0.46750	-1.046000	0.03525	-0.257000	0.09459	-0.345000	0.07892	CGG	C|0.994;T|0.006	0.006	strong		0.303	TAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091493.2	NM_005681		T	222732051	C	T	222732051	3	4	28	1	0	0	0	0	1	0	0	0	15534	652	23	1	52	1	TAF1A	1	222732051	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	19943	222732051	26518570	60	11563											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228401329	228401329	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcgccgcctgaccgtgcgCaatgtctcggccgacgacga	7	5	14	15	8	1	1	0	1	1	0	2	5	1	1	4	1	2	1	4	1	1	0	rs185717159	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:228401329C>T	ENST00000422127.1	+	3	1220	c.1176C>T	c.(1174-1176)cgC>cgT	p.R392R	OBSCN_ENST00000570156.2_Silent_p.R392R|OBSCN_ENST00000366707.4_5'UTR|C1orf145_ENST00000295012.5_Silent_p.L11L|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Silent_p.R392R	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	392	Ig-like 4.				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)				TGACCGTGCGCAATGTCTCGG	0.706													C|||	17	0.00339457	0.0	0.0029	5008	,	,		6657	0.0		0.0139	False		,,,				2504	0.001				p.R392R		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C1176T						PASS	.	C	,	1,4053		0,1,2026	12	14	13		1176,1176	1.1	0.1	1		13	61,8229		0,61,4084	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	0,62,6110	TT,TC,CC		0.7358,0.0247,0.5023	,	392/7969,392/6621	228401329	62,12282	2027	4145	6172	SO:0001819	synonymous_variant	84033	exon3			CGTGCGCAATGTC	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.1176C>T	1.37:g.228401329C>T		100	0	0		114	64	0.561404	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			C|0.994;T|0.006	0.006	strong		0.706	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228401329	C	T	228401329	2	4	28	1	0	0	0	0	0	0	0	1	10821	697	25	2		2	OBSCN	1	228401329	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	5669278	228401329	20849292	61	11564											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228476420	228476420	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagctgagcaaggcggccccCgtggagtggaggaaggggcg	8	3	21	9	3	0	1	0	1	0	0	0	5	0	4	2	7	2	2	2	7	2	0	rs56367754		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:228476420C>T	ENST00000422127.1	+	38	10214	c.10170C>T	c.(10168-10170)ccC>ccT	p.P3390P	OBSCN_ENST00000570156.2_Silent_p.P3819P|OBSCN_ENST00000359599.6_Silent_p.P2237P|OBSCN_ENST00000366707.4_Silent_p.P509P|OBSCN_ENST00000284548.11_Silent_p.P3390P|OBSCN_ENST00000366709.4_Silent_p.P509P	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3390	Ig-like 34.				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)				AGGCGGCCCCCGTGGAGTGGA	0.637													C|||	1	0.000199681	0.0	0.0	5008	,	,		21068	0.0		0.001	False		,,,				2504	0.0				p.P3819P		Atlas-SNP	.											OBSCN_ENST00000570156,colon,carcinoma,+1,4	OBSCN	2142	4	0			c.C11457T						PASS	.	C	,	2,4160		0,2,2079	88	98	95		10170,10170	-9.9	0	1	dbSNP_129	95	33,8355		0,33,4161	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	0,35,6240	TT,TC,CC		0.3934,0.0481,0.2789	,	3390/7969,3390/6621	228476420	35,12515	2081	4194	6275	SO:0001819	synonymous_variant	84033	exon43			GGCCCCCGTGGAG	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.10170C>T	1.37:g.228476420C>T		85	0	0		113	56	0.495575	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			C|0.995;T|0.005	0.005	strong		0.637	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228476420	C	T	228476420	2	4	28	1	0	0	0	0	0	0	0	1	10821	639	23	1		1	OBSCN	1	228476420	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	75091	228476420	20774201	62	11565											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228495867	228495867	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcggaggtgacggccgatgaGgatgttgagttcagctgtga	8	9	18	6	3	1	4	1	4	0	0	1	7	1	6	1	4	1	3	1	4	0	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:228495867G>A	ENST00000422127.1	+	47	12566	c.12522G>A	c.(12520-12522)gaG>gaA	p.E4174E	OBSCN_ENST00000570156.2_Silent_p.E5131E|OBSCN_ENST00000366707.4_Silent_p.E1808E|OBSCN_ENST00000284548.11_Silent_p.E4174E|OBSCN_ENST00000366709.4_Silent_p.E1293E	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4174	Ig-like 43.				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)				CGGCCGATGAGGATGTTGAGT	0.597																																					p.E5131E		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G15393A						PASS	.						92	104	100					1																	228495867		2171	4258	6429	SO:0001819	synonymous_variant	84033	exon58			CGATGAGGATGTT	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.12522G>A	1.37:g.228495867G>A		113	0	0		118	53	0.449153	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			.	.	none		0.597	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		A	228495867	G	A	228495867	2	1	28	1	0	0	0	0	0	0	0	1	10821	991	35	2		2	OBSCN	1	228495867	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	19447	228495867	20754754	63	11566											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228554725	228554725	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcacaaaggaaacaagatcTtgtgcgctgccaagttcatc	14	8	9	10	1	2	1	1	0	1	1	3	2	2	2	1	1	4	3	1	1	4	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:228554725T>G	ENST00000422127.1	+	86	19521	c.19477T>G	c.(19477-19479)Ttg>Gtg	p.L6493V	OBSCN_ENST00000570156.2_Missense_Mutation_p.L7450V|OBSCN_ENST00000366707.4_Missense_Mutation_p.L4127V	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	6493	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)				AAACAAGATCTTGTGCGCTGC	0.607																																					p.L7450V		Atlas-SNP	.											.	OBSCN	2142	.	0			c.T22348G						PASS	.						47	50	49					1																	228554725		2026	4164	6190	SO:0001583	missense	84033	exon97			AAGATCTTGTGCG	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.19477T>G	1.37:g.228554725T>G	ENSP00000409493:p.Leu6493Val	105	0	0		106	46	0.433962	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	37	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.92|10.92	1.486513|1.486513	0.26686|0.26686	.|.	.|.	ENSG00000154358|ENSG00000154358	ENST00000441106|ENST00000422127;ENST00000366707	.|T;T	.|0.66099	.|-0.19;-0.19	4.69|4.69	1.05|1.05	0.20165|0.20165	.|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	0.36026|0.36026	0.0952|0.0952	N|N	0.13043|0.13043	0.29|0.29	0.09310|0.09310	N|N	1|1	.|B	.|0.13145	.|0.007	.|B	.|0.18871	.|0.023	T|T	0.17167|0.17167	-1.0378|-1.0378	5|9	.|0.20046	.|T	.|0.44	.|.	1.1263|1.1263	0.01736|0.01736	0.1407:0.236:0.146:0.4773|0.1407:0.236:0.146:0.4773	.|.	.|6493	.|Q5VST9	.|OBSCN_HUMAN	R|V	1109|6493;4127	.|ENSP00000409493:L6493V;ENSP00000355668:L4127V	.|ENSP00000355668:L4127V	L|L	+|+	2|1	0|2	OBSCN|OBSCN	226621348|226621348	0.003000|0.003000	0.15002|0.15002	0.016000|0.016000	0.15963|0.15963	0.385000|0.385000	0.30292|0.30292	0.243000|0.243000	0.18106|0.18106	0.018000|0.018000	0.15052|0.15052	0.402000|0.402000	0.26972|0.26972	CTT|TTG	.	.	none		0.607	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		G	228554725	T	G	228554725	3	3	28	1	0	0	0	0	1	0	0	0	10821	1606	56	5	21025	5	OBSCN	1	228554725	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	58858	228554725	20695896	64	11567											
URB2	9816	hgsc.bcm.edu	37	chr1	229787055	229787055	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcagttatgcgggaagggcGgcagaaggacaaaggtaatt	13	8	15	5	2	1	1	1	0	0	1	1	3	1	3	0	5	1	3	0	5	5	4	rs41310553	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:229787055G>A	ENST00000258243.2	+	8	4359	c.4223G>A	c.(4222-4224)cGg>cAg	p.R1408Q		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	1408						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						CGGGAAGGGCGGCAGAAGGAC	0.388													G|||	41	0.0081869	0.0083	0.0159	5008	,	,		17462	0.0		0.0139	False		,,,				2504	0.0051				p.R1408Q		Atlas-SNP	.											.	URB2	152	.	0			c.G4223A						PASS	.	G	GLN/ARG	58,4348	56.8+/-93.2	0,58,2145	87	84	85		4223	4.9	1	1	dbSNP_127	85	149,8451	72.9+/-135.5	1,147,4152	yes	missense	URB2	NM_014777.2	43	1,205,6297	AA,AG,GG		1.7326,1.3164,1.5916	probably-damaging	1408/1525	229787055	207,12799	2203	4300	6503	SO:0001583	missense	9816	exon8			AAGGGCGGCAGAA	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.4223G>A	1.37:g.229787055G>A	ENSP00000258243:p.Arg1408Gln	130	0	0		101	40	0.39604	NM_014777	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	20	0.009157509157509158	3	0.006097560975609756	7	0.019337016574585635	0	0.0	10	0.013192612137203167	G	25.7	4.661699	0.88154	0.013164	0.017326	ENSG00000135763	ENST00000258243;ENST00000434387	T;T	0.45668	0.89;0.89	5.78	4.86	0.63082	Nucleolar 27S pre-rRNA processing, Urb2/Npa2, C-terminal (1);	0.116848	0.53938	D	0.000042	T	0.46210	0.1381	M	0.69823	2.125	0.40363	D	0.97926	D	0.89917	1.0	D	0.69824	0.966	T	0.59968	-0.7354	9	.	.	.	-18.2991	14.7398	0.69445	0.0695:0.0:0.9305:0.0	rs41310553	1408	Q14146	URB2_HUMAN	Q	1408;24	ENSP00000258243:R1408Q;ENSP00000395107:R24Q	.	R	+	2	0	URB2	227853678	0.967000	0.33354	0.971000	0.41717	0.989000	0.77384	5.262000	0.65501	1.435000	0.47434	0.655000	0.94253	CGG	G|0.986;A|0.014	0.014	strong		0.388	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777		A	229787055	G	A	229787055	3	1	28	1	0	0	0	0	1	0	0	0	17040	1116	39	1	4249	1	URB2	1	229787055	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1232330	229787055	19463566	65	11568											
LYST	1130	hgsc.bcm.edu	37	chr1	235955276	235955276	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctcttctcaataaacccatGgccttactgtttaaaatccc	11	13	4	13	0	2	0	1	0	2	0	4	0	3	0	3	1	2	2	3	1	6	5			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:235955276G>T	ENST00000389794.3	-	12	4440	c.4266C>A	c.(4264-4266)gcC>gcA	p.A1422A	LYST_ENST00000536965.1_Intron|LYST_ENST00000389793.2_Silent_p.A1422A			Q99698	LYST_HUMAN	lysosomal trafficking regulator	1422					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)			ATAAACCCATGGCCTTACTGT	0.458																																					p.A1422A		Atlas-SNP	.											.	LYST	370	.	0			c.C4266A						PASS	.						152	155	154					1																	235955276		2203	4300	6503	SO:0001819	synonymous_variant	1130	exon12			ACCCATGGCCTTA	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.4266C>A	1.37:g.235955276G>T		85	0	0		85	42	0.494118	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	37	CCDS31062.1																																																																																			.	.	none		0.458	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			T	235955276	G	T	235955276	2	4	28	1	0	0	0	0	0	0	0	1	9137	1335	47	4		4	LYST	1	235955276	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	6168221	235955276	13295345	66	11569											
ACTN2	88	hgsc.bcm.edu	37	chr1	236908053	236908053	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caggaccgcgtggagcagatCgcagccatcgcgcaggagct	9	4	15	13	5	0	1	0	0	0	1	2	4	0	4	2	3	3	4	2	3	0	0	rs34827377	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:236908053C>T	ENST00000366578.4	+	12	1549	c.1383C>T	c.(1381-1383)atC>atT	p.I461I	ACTN2_ENST00000492634.1_3'UTR|ACTN2_ENST00000542672.1_Silent_p.I461I|ACTN2_ENST00000546208.1_5'UTR	NM_001103.2|NM_001278343.1	NP_001094.1|NP_001265272.1	P35609	ACTN2_HUMAN	actinin, alpha 2	461					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)			TGGAGCAGATCGCAGCCATCG	0.652													C|||	5	0.000998403	0.0	0.0029	5008	,	,		18183	0.0		0.003	False		,,,				2504	0.0				p.I461I		Atlas-SNP	.											.	ACTN2	191	.	0			c.C1383T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	61	52	55		1383	-9.9	0.1	1	dbSNP_126	55	16,8584	11.9+/-42.8	0,16,4284	yes	coding-synonymous	ACTN2	NM_001103.2		0,17,6486	TT,TC,CC		0.186,0.0227,0.1307		461/895	236908053	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	88	exon12			GCAGATCGCAGCC	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.1383C>T	1.37:g.236908053C>T		100	0	0		110	59	0.536364	NM_001103	B1ANE4|B2RCS5|Q86TF4|Q86TI8	Silent	SNP	ENST00000366578.4	37	CCDS1613.1																																																																																			C|0.998;T|0.002	0.002	strong		0.652	ACTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096628.1	NM_001103		T	236908053	C	T	236908053	2	4	28	1	0	0	0	0	0	0	0	1	205	874	31	1		1	ACTN2	1	236908053	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	952777	236908053	12342568	67	11570											
FMN2	56776	hgsc.bcm.edu	37	chr1	240256668	240256668	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catcaccccctgctacatcaAgaccaccacccggcagctca	11	5	5	20	1	3	1	3	0	0	1	3	1	3	1	5	1	3	3	5	1	2	1	rs146681532	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:240256668A>C	ENST00000319653.9	+	1	1489	c.1259A>C	c.(1258-1260)aAg>aCg	p.K420T		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	420					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)			TGCTACATCAAGACCACCACC	0.677													A|||	7	0.00139776	0.0	0.0029	5008	,	,		11822	0.0		0.003	False		,,,				2504	0.002				p.K420T		Atlas-SNP	.											.	FMN2	451	.	0			c.A1259C						PASS	.	A	THR/LYS	4,4402	8.1+/-20.4	0,4,2199	48	56	54		1259	3	1	1	dbSNP_134	54	55,8545	33.8+/-87.4	0,55,4245	yes	missense	FMN2	NM_020066.4	78	0,59,6444	CC,CA,AA		0.6395,0.0908,0.4536	probably-damaging	420/1723	240256668	59,12947	2203	4300	6503	SO:0001583	missense	56776	exon1			ACATCAAGACCAC	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.1259A>C	1.37:g.240256668A>C	ENSP00000318884:p.Lys420Thr	108	0	0		122	55	0.45082	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	A	12.29	1.892175	0.33442	9.08E-4	0.006395	ENSG00000155816	ENST00000319653	D	0.83591	-1.74	4.15	3.02	0.34903	.	0.084158	0.49305	D	0.000158	T	0.74846	0.3770	L	0.34521	1.04	0.80722	D	1	D	0.63880	0.993	P	0.53266	0.722	T	0.77611	-0.2523	10	0.87932	D	0	.	9.2617	0.37616	0.9135:0.0:0.0865:0.0	.	420	Q9NZ56	FMN2_HUMAN	T	420	ENSP00000318884:K420T	ENSP00000318884:K420T	K	+	2	0	FMN2	238323291	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.340000	0.72973	0.647000	0.30713	0.379000	0.24179	AAG	A|0.997;C|0.003	0.003	strong		0.677	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		C	240256668	A	C	240256668	3	2	28	1	0	0	0	0	1	0	0	0	5958	72	3	5	1261	5	FMN2	1	240256668	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	3348615	240256668	8993953	68	11571											
AHCTF1	25909	hgsc.bcm.edu	37	chr1	247007232	247007232	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggaacctctatttttttagcTaaaaaaagttgaaaaaactg	17	13	6	5	0	1	1	0	1	1	0	1	2	1	2	1	1	3	2	1	1	10	7	rs148600466	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:247007232T>A	ENST00000391829.2	-	34	6515		c.e34-2		AHCTF1_ENST00000366508.1_Splice_Site|AHCTF1_ENST00000470300.1_Splice_Site|AHCTF1_ENST00000326225.3_Splice_Site			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1						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)			TTTTTTTAGCTAAAAAAAGTT	0.303													T|||	19	0.00379393	0.0	0.0101	5008	,	,		13414	0.0		0.0109	False		,,,				2504	0.001				.	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.6419-2A>T						PASS	.	T		19,4381	20.2+/-43.8	0,19,2181	44	44	44			4.2	0.9	1	dbSNP_134	44	102,8494	43.6+/-101.6	1,100,4197	no	splice-3	AHCTF1	NM_015446.4		1,119,6378	AA,AT,TT		1.1866,0.4318,0.9311			247007232	121,12875	2200	4298	6498	SO:0001630	splice_region_variant	25909	exon35			TTTAGCTAAAAAA		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.6392-2A>T	1.37:g.247007232T>A		231	0	0		209	102	0.488038	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Splice_Site	SNP	ENST00000391829.2	37		13	0.005952380952380952	1	0.0020325203252032522	3	0.008287292817679558	1	0.0017482517482517483	8	0.010554089709762533	T	13.05	2.121636	0.37436	0.004318	0.011866	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	.	.	.	5.29	4.17	0.49024	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.8575	0.41094	0.0:0.0781:0.0:0.9219	.	.	.	.	.	-1	.	.	.	-	.	.	AHCTF1	245073855	1.000000	0.71417	0.937000	0.37676	0.546000	0.35178	3.504000	0.53347	0.955000	0.37878	-0.326000	0.08463	.	T|0.992;A|0.008	0.008	strong		0.303	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446	Intron	A	247007232	T	A	247007232	5	1	28	1	0	0	0	0	0	0	1	0	408	1536	53	5	422	5	AHCTF1	1	247007232	Splice_Site	SNP	T	TCGA-G8-6914-01A-11D-2210-10	6750564	247007232	2243389	69	11572											
TPO	7173	hgsc.bcm.edu	37	chr2	1426844	1426844	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaggagtctcgtgtctctaGcgtcttggaggaaagcaagc	9	10	14	8	2	3	1	0	1	3	0	5	4	3	4	0	3	3	1	0	3	3	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:1426844G>T	ENST00000345913.4	+	3	213	c.122G>T	c.(121-123)aGc>aTc	p.S41I	TPO_ENST00000382201.3_Missense_Mutation_p.S41I|TPO_ENST00000349624.3_Missense_Mutation_p.S41I|TPO_ENST00000382198.1_Missense_Mutation_p.S41I|TPO_ENST00000329066.4_Missense_Mutation_p.S41I|TPO_ENST00000346956.3_Missense_Mutation_p.S41I|TPO_ENST00000539820.1_Missense_Mutation_p.S41I|TPO_ENST00000382269.3_Missense_Mutation_p.S41I|TPO_ENST00000497517.2_Intron|TPO_ENST00000337415.3_Missense_Mutation_p.S41I	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	41					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)	CGTGTCTCTAGCGTCTTGGAG	0.572																																					p.S41I		Atlas-SNP	.											.	TPO	224	.	0			c.G122T						PASS	.						124	99	108					2																	1426844		2203	4300	6503	SO:0001583	missense	7173	exon3			TCTCTAGCGTCTT		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.122G>T	2.37:g.1426844G>T	ENSP00000318820:p.Ser41Ile	75	0	0		58	37	0.637931	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	37	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	G	10.16	1.274665	0.23307	.	.	ENSG00000115705	ENST00000382269;ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000539820;ENST00000329066;ENST00000382201;ENST00000423320;ENST00000382198	T;T;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;0.34;0.34	3.72	-0.276	0.12902	.	2.391560	0.01734	N	0.029009	T	0.59865	0.2225	L	0.54323	1.7	0.09310	N	1	P;P;D;P;P	0.65815	0.846;0.545;0.995;0.911;0.761	P;B;P;P;B	0.58172	0.466;0.206;0.834;0.563;0.276	T	0.40001	-0.9586	10	0.33940	T	0.23	-1.8372	3.7622	0.08609	0.3281:0.185:0.4869:0.0	.	41;41;41;41;41	P07202-4;P07202-5;E9PFM6;P07202-2;P07202	.;.;.;.;PERT_HUMAN	I	41	ENSP00000371704:S41I;ENSP00000337263:S41I;ENSP00000318820:S41I;ENSP00000263886:S41I;ENSP00000332044:S41I;ENSP00000444840:S41I;ENSP00000329869:S41I;ENSP00000371636:S41I;ENSP00000390994:S41I;ENSP00000371633:S41I	ENSP00000329869:S41I	S	+	2	0	TPO	1405851	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.511000	0.22739	-0.075000	0.12798	-0.373000	0.07131	AGC	.	.	none		0.572	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		T	1426844	G	T	1426844	3	4	28	1	0	0	0	0	1	0	0	0	16425	971	34	4	128	4	TPO	2	1426844	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10		1426844	241772529	70	11573											
PDIA6	10130	hgsc.bcm.edu	37	chr2	10929938	10929938	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agggcccgggacacgatgtcGgatcttgtccgcccaccgtc	6	7	13	15	5	1	0	0	0	1	0	4	3	2	2	4	3	0	0	4	3	0	1	rs138712410	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:10929938G>A	ENST00000272227.3	-	8	924	c.777C>T	c.(775-777)tcC>tcT	p.S259S	PDIA6_ENST00000404371.2_Silent_p.S311S|PDIA6_ENST00000381611.4_Silent_p.S264S|PDIA6_ENST00000404824.2_Silent_p.S307S|PDIA6_ENST00000540494.1_Silent_p.S256S	NM_001282707.1|NM_005742.2	NP_001269636.1|NP_005733.1	Q15084	PDIA6_HUMAN	protein disulfide isomerase family A, member 6	259	Thioredoxin 2. {ECO:0000255|PROSITE- ProRule:PRU00691}.				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)		ACACGATGTCGGATCTTGTCC	0.458													G|||	40	0.00798722	0.0008	0.0058	5008	,	,		14648	0.0		0.008	False		,,,				2504	0.0276				p.S259S	GBM(73;509 1219 34219 41343 41551)	Atlas-SNP	.											PDIA6,NS,carcinoma,0,1	PDIA6	31	1	0			c.C777T						PASS	.	G		3,4403	6.2+/-15.9	0,3,2200	85	83	84		777	-11.3	0	2	dbSNP_134	84	68,8532	41.7+/-99.0	0,68,4232	no	coding-synonymous	PDIA6	NM_005742.2		0,71,6432	AA,AG,GG		0.7907,0.0681,0.5459		259/441	10929938	71,12935	2203	4300	6503	SO:0001819	synonymous_variant	10130	exon8			GATGTCGGATCTT	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.777C>T	2.37:g.10929938G>A		68	0	0		77	39	0.506494	NM_005742	B3KY95|B5MCQ5|B7Z254|B7Z4M8|F8WA83|Q53RC7|Q6ZSH5|Q99778	Silent	SNP	ENST00000272227.3	37	CCDS1675.1																																																																																			G|0.994;A|0.006	0.006	strong		0.458	PDIA6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206933.1	NM_005742		A	10929938	G	A	10929938	2	1	28	1	0	0	0	0	0	0	0	1	11681	1103	39	1		1	PDIA6	2	10929938	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	9503094	10929938	232269435	71	11574											
GREB1	9687	hgsc.bcm.edu	37	chr2	11750985	11750985	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcagtgcccctgcggccaCgggctcatggtcctgctgcg	5	7	14	15	3	1	0	1	0	0	0	2	0	2	0	4	3	5	3	4	3	1	0	rs374277928		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:11750985C>T	ENST00000381486.2	+	18	3138	c.2838C>T	c.(2836-2838)caC>caT	p.H946H	GREB1_ENST00000396123.1_5'Flank|GREB1_ENST00000234142.5_Silent_p.H946H	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	946						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)		CCTGCGGCCACGGGCTCATGG	0.687																																					p.H946H	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.C2838T						PASS	.	C		0,4120		0,0,2060	29	33	32		2838	4.2	1	2		32	1,8383		0,1,4191	no	coding-synonymous	GREB1	NM_014668.3		0,1,6251	TT,TC,CC		0.0119,0.0,0.0080		946/1950	11750985	1,12503	2060	4192	6252	SO:0001819	synonymous_variant	9687	exon18			CGGCCACGGGCTC		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.2838C>T	2.37:g.11750985C>T		60	0	0		79	46	0.582278	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Silent	SNP	ENST00000381486.2	37	CCDS42655.1																																																																																			.	.	weak		0.687	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		T	11750985	C	T	11750985	2	4	28	1	0	0	0	0	0	0	0	1	6769	535	19	1		1	GREB1	2	11750985	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	821047	11750985	231448388	72	11575											
GREB1	9687	hgsc.bcm.edu	37	chr2	11758536	11758536	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cccctggtgagaaacagaggCcccgggcaagtcaggggcca	10	3	15	13	1	1	2	1	1	0	2	1	3	1	2	5	5	1	1	5	5	2	0	rs61741332	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:11758536C>A	ENST00000381486.2	+	22	3835	c.3535C>A	c.(3535-3537)Ccc>Acc	p.P1179T	GREB1_ENST00000396123.1_Missense_Mutation_p.P177T|GREB1_ENST00000234142.5_Missense_Mutation_p.P1179T	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1179	Ser-rich.					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)		GAAACAGAGGCCCCGGGCAAG	0.721													C|||	32	0.00638978	0.0008	0.0159	5008	,	,		14493	0.001		0.0159	False		,,,				2504	0.0031				p.P1179T	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.C3535A						PASS	.	C	THR/PRO	17,3853		0,17,1918	9	12	11		3535	1.9	0	2	dbSNP_129	11	145,8019		3,139,3940	no	missense	GREB1	NM_014668.3	38	3,156,5858	AA,AC,CC		1.7761,0.4393,1.3462	benign	1179/1950	11758536	162,11872	1935	4082	6017	SO:0001583	missense	9687	exon22			CAGAGGCCCCGGG		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.3535C>A	2.37:g.11758536C>A	ENSP00000370896:p.Pro1179Thr	84	0	0		86	43	0.5	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	37	CCDS42655.1	21	0.009615384615384616	1	0.0020325203252032522	7	0.019337016574585635	1	0.0017482517482517483	12	0.0158311345646438	C	9.915	1.210717	0.22289	0.004393	0.017761	ENSG00000196208	ENST00000381486;ENST00000234142;ENST00000396123	T;T;T	0.21543	3.34;3.34;2.0	4.84	1.93	0.25924	.	2.089630	0.01658	N	0.024926	T	0.04998	0.0134	N	0.03608	-0.345	0.09310	N	1	B	0.22211	0.066	B	0.23419	0.046	T	0.24083	-1.0170	10	0.22109	T	0.4	-25.9697	5.8172	0.18500	0.1667:0.6621:0.0:0.1712	rs61741332	1179	Q4ZG55	GREB1_HUMAN	T	1179;1179;177	ENSP00000370896:P1179T;ENSP00000234142:P1179T;ENSP00000379429:P177T	ENSP00000234142:P1179T	P	+	1	0	GREB1	11675987	0.036000	0.19791	0.000000	0.03702	0.357000	0.29423	1.934000	0.40163	0.084000	0.17077	0.643000	0.83706	CCC	C|0.989;A|0.011	0.011	strong		0.721	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668		A	11758536	C	A	11758536	3	1	28	1	0	0	0	0	1	0	0	0	6769	739	26	4	3725	4	GREB1	2	11758536	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	7551	11758536	231440837	73	11576											
APOB	338	hgsc.bcm.edu	37	chr2	21233099	21233101	+	In_Frame_Del	DEL	TCA	TCA	-																															ttacacggatatgatagtgcTcatcaagactttttaatttt																								rs541497967	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TCA	TCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:21233099_21233101delTCA	ENST00000233242.1	-	26	6766_6768	c.6639_6641delTGA	c.(6637-6642)gatgag>gag	p.D2213del		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2213					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)					ATGATAGTGCTCATCAAGACTTT	0.246														9	0.00179712	0.0	0.0014	5008	,	,		19525	0.0		0.007	False		,,,				2504	0.001				p.2214_2214del		Pindel,Atlas-Indel	.											.	APOB	761	.	0			c.6640_6642del						PASS	.			1,4235		0,1,2117						0.7	0.9		dbSNP_130	33	39,8177		3,33,4072	no	coding	APOB	NM_000384.2		3,34,6189	A1A1,A1R,RR		0.4747,0.0236,0.3212				40,12412				SO:0001651	inframe_deletion	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.6639_6641delTGA	2.37:g.21233102_21233104delTCA	ENSP00000233242:p.Asp2213del	41	0	.		46	17	0.37	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	In_Frame_Del	DEL	ENST00000233242.1	37	CCDS1703.1																																																																																			.	.	none		0.246	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			-	21233101	TCA	-	21233099	7	5	28	1	0	1	0	1	0	0	0	0	785	1551	54	0	7066	0	APOB	2	21233099	In_Frame_Del	DEL	TCA	TCGA-G8-6914-01A-11D-2210-10	9474563	21233099	221966274	74	11577											
POMC	5443	hgsc.bcm.edu	37	chr2	25384113	25384113	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggggccctcgtccttcttcTcggccgccaccagcaggctg	4	8	12	17	3	2	0	0	0	2	0	5	0	3	0	5	4	1	2	5	4	0	2	rs80326661	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:25384113T>C	ENST00000405623.1	-	3	1096	c.641A>G	c.(640-642)gAg>gGg	p.E214G	POMC_ENST00000380794.1_Missense_Mutation_p.E214G|POMC_ENST00000395826.2_Missense_Mutation_p.E214G|RP11-509E16.1_ENST00000567599.1_lincRNA|POMC_ENST00000264708.3_Missense_Mutation_p.E214G			P01189	COLI_HUMAN	proopiomelanocortin	214			E -> G (in dbSNP:rs80326661). {ECO:0000269|PubMed:9768693}.		cell-cell signaling (GO:0007267)|cellular pigmentation (GO:0033059)|cellular protein metabolic process (GO:0044267)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|negative regulation of tumor necrosis factor production (GO:0032720)|neuropeptide signaling pathway (GO:0007218)|peptide hormone processing (GO:0016486)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of appetite (GO:0032098)|regulation of blood pressure (GO:0008217)|regulation of corticosterone secretion (GO:2000852)|regulation of glycogen metabolic process (GO:0070873)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|peroxisomal matrix (GO:0005782)|secretory granule (GO:0030141)|secretory granule lumen (GO:0034774)	G-protein coupled receptor binding (GO:0001664)|hormone activity (GO:0005179)|receptor binding (GO:0005102)|type 1 melanocortin receptor binding (GO:0070996)|type 3 melanocortin receptor binding (GO:0031781)|type 4 melanocortin receptor binding (GO:0031782)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(5)|ovary(1)	12	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Loperamide(DB00836)	GTCCTTCTTCTCGGCCGCCAC	0.697													T|||	7	0.00139776	0.0	0.0	5008	,	,		15787	0.0		0.007	False		,,,				2504	0.0				p.E214G	Colon(110;1515 1566 8452 10082 43216)	Atlas-SNP	.											POMC,colon,carcinoma,-1,1	POMC	33	1	0			c.A641G	GRCh37	CM984056	POMC	M	rs80326661	scavenged	.	T	GLY/GLU,GLY/GLU	6,4400	8.1+/-20.4	0,6,2197	24	26	25		641,641	-2.6	0.3	2	dbSNP_131	25	62,8538	35.9+/-90.5	0,62,4238	yes	missense,missense	POMC	NM_000939.2,NM_001035256.1	98,98	0,68,6435	CC,CT,TT		0.7209,0.1362,0.5228	possibly-damaging,possibly-damaging	214/268,214/268	25384113	68,12938	2203	4300	6503	SO:0001583	missense	5443	exon4			TTCTTCTCGGCCG		CCDS1717.1	2p23	2013-02-25	2008-07-31		ENSG00000115138	ENSG00000115138		"Endogenous ligands"	9201	protein-coding gene	gene with protein product	"adrenocorticotropin", "beta-lipotropin", "alpha-melanocyte stimulating hormone", "beta-melanocyte stimulating hormone", "beta-endorphin", "adrenocorticotropic hormone", "opiomelanocortin prepropeptide"	176830				6254047, 9620771	Standard	NM_001035256		Approved	MSH, POC, CLIP, ACTH, NPP, LPH	uc002rfz.1	P01189	OTTHUMG00000094764	ENST00000405623.1:c.641A>G	2.37:g.25384113T>C	ENSP00000384092:p.Glu214Gly	25	1	0.04		58	29	0.5	NM_001035256	P78442|Q53T23|Q9UD39|Q9UD40	Missense_Mutation	SNP	ENST00000405623.1	37	CCDS1717.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	T	8.778	0.927470	0.18056	0.001362	0.007209	ENSG00000115138	ENST00000380794;ENST00000405623;ENST00000264708;ENST00000395826;ENST00000449220	T;T;T;T;T	0.80033	-1.32;-1.32;-1.32;-1.32;-1.33	4.94	-2.56	0.06268	.	0.859913	0.10550	N	0.661521	T	0.65281	0.2676	M	0.80183	2.485	0.23657	N	0.997187	P	0.36086	0.536	B	0.27380	0.079	T	0.62685	-0.6802	10	0.87932	D	0	-23.9239	1.564	0.02601	0.3754:0.0782:0.2568:0.2896	.	214	P01189	COLI_HUMAN	G	214	ENSP00000370171:E214G;ENSP00000384092:E214G;ENSP00000264708:E214G;ENSP00000379170:E214G;ENSP00000387993:E214G	ENSP00000264708:E214G	E	-	2	0	POMC	25237617	0.001000	0.12720	0.348000	0.25681	0.190000	0.23558	-0.012000	0.12699	-0.317000	0.08677	-0.379000	0.06801	GAG	T|0.996;C|0.004	0.004	strong		0.697	POMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211573.3	NM_001035256		C	25384113	T	C	25384113	3	2	28	1	0	0	0	0	1	0	0	0	12251	1551	54	3	166	3	POMC	2	25384113	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	4151014	25384113	217815260	75	11578											
ASXL2	55252	hgsc.bcm.edu	37	chr2	25991713	25991713	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcattgctgctgctgctTcttctgctgttgctgcttta	2	18	9	12	0	2	0	0	0	2	0	2	0	2	0	1	0	8	9	1	0	1	6	rs190136878	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:25991713T>G	ENST00000435504.4	-	7	822	c.529A>C	c.(529-531)Aag>Cag	p.K177Q	ASXL2_ENST00000336112.4_Missense_Mutation_p.K149Q|ASXL2_ENST00000272341.4_5'UTR|ASXL2_ENST00000497092.1_5'UTR|ASXL2_ENST00000404843.1_5'UTR			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	177	Ser-rich.				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)					tgctgctgcttcttctgctgt	0.393													T|||	4	0.000798722	0.0008	0.0029	5008	,	,		14558	0.0		0.0	False		,,,				2504	0.001				p.K177Q		Atlas-SNP	.											.	ASXL2	217	.	0			c.A529C						PASS	.	T	GLN/LYS	2,4014		0,2,2006	141	143	142		529	6	1	2		142	11,8399		0,11,4194	yes	missense	ASXL2	NM_018263.4	53	0,13,6200	GG,GT,TT		0.1308,0.0498,0.1046	probably-damaging	177/1436	25991713	13,12413	2008	4205	6213	SO:0001583	missense	55252	exon6			GCTGCTTCTTCTG			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.529A>C	2.37:g.25991713T>G	ENSP00000391447:p.Lys177Gln	120	0	0		111	54	0.486486	NM_018263	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Missense_Mutation	SNP	ENST00000435504.4	37		1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	T	18.47	3.630847	0.67015	4.98E-4	0.001308	ENSG00000143970	ENST00000435504;ENST00000336112	T;T	0.19669	2.13;2.13	6.03	6.03	0.97812	.	0.168425	0.53938	D	0.000053	T	0.19604	0.0471	N	0.02011	-0.69	0.35856	D	0.827145	D	0.89917	1.0	D	0.63488	0.915	T	0.50947	-0.8767	10	0.87932	D	0	-15.1812	12.95	0.58394	0.0:0.0:0.0:1.0	.	177	Q76L83	ASXL2_HUMAN	Q	177;149	ENSP00000391447:K177Q;ENSP00000337250:K149Q	ENSP00000337250:K149Q	K	-	1	0	ASXL2	25845217	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.963000	0.49184	2.308000	0.77769	0.533000	0.62120	AAG	T|0.999;G|0.001	0.001	strong		0.393	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263		G	25991713	T	G	25991713	3	3	28	1	0	0	0	0	1	0	0	0	1067	1792	62	5	3806	5	ASXL2	2	25991713	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	607600	25991713	217207660	76	11579											
GPR113	165082	hgsc.bcm.edu	37	chr2	26533898	26533898	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taggtagagccccagggtgaCacctgccaaccccagtgggc	9	5	13	14	0	0	2	0	1	0	1	0	2	0	2	6	3	3	1	6	3	3	2	rs72811754	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:26533898C>T	ENST00000311519.1	-	11	2697	c.2698G>A	c.(2698-2700)Gtc>Atc	p.V900I	GPR113_ENST00000459892.1_5'UTR|GPR113_ENST00000541401.1_Missense_Mutation_p.V503I|GPR113_ENST00000333478.6_Missense_Mutation_p.V701I|GPR113_ENST00000421160.2_Missense_Mutation_p.V831I	NM_001145168.1	NP_001138640.1	Q8IZF5	GP113_HUMAN	G protein-coupled receptor 113	900					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)					CCCAGGGTGACACCTGCCAAC	0.612													C|||	9	0.00179712	0.0	0.0	5008	,	,		17885	0.0		0.006	False		,,,				2504	0.0031				p.V900I		Atlas-SNP	.											.	GPR113	134	.	0			c.G2698A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL	3,4403	6.2+/-15.9	0,3,2200	38	36	36		2698,2491,2101	0.9	0	2	dbSNP_130	36	36,8564	23.4+/-69.3	0,36,4264	yes	missense,missense,missense	GPR113	NM_001145168.1,NM_001145169.1,NM_153835.3	29,29,29	0,39,6464	TT,TC,CC		0.4186,0.0681,0.2999	benign,benign,benign	900/1080,831/998,701/874	26533898	39,12967	2203	4300	6503	SO:0001583	missense	165082	exon11			GGGTGACACCTGC	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.2698G>A	2.37:g.26533898C>T	ENSP00000307831:p.Val900Ile	65	0	0		66	40	0.606061	NM_001145168	B4DF15|E9PEV1|Q53TA5|Q6UXT7|Q6UXX3|Q86SL7|Q8IXD8|Q8TDT3	Missense_Mutation	SNP	ENST00000311519.1	37	CCDS46239.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	0.726	-0.781775	0.02929	6.81E-4	0.004186	ENSG00000173567	ENST00000541401;ENST00000333478;ENST00000421160;ENST00000311519	T;T;T;T	0.37058	1.22;1.22;1.22;1.22	5.78	0.853	0.19001	GPCR, family 2-like (1);	.	.	.	.	T	0.13628	0.0330	N	0.17631	0.505	0.09310	N	1	B;B;B;B	0.06786	0.001;0.001;0.0;0.001	B;B;B;B	0.18871	0.023;0.013;0.023;0.008	T	0.31447	-0.9943	9	0.11485	T	0.65	-4.2378	6.3783	0.21519	0.0:0.5889:0.1217:0.2894	.	831;701;900;503	E9PEV1;Q8IZF5-2;Q8IZF5;F5H1E4	.;.;GP113_HUMAN;.	I	503;701;831;900	ENSP00000445729:V503I;ENSP00000327396:V701I;ENSP00000388537:V831I;ENSP00000307831:V900I	ENSP00000307831:V900I	V	-	1	0	GPR113	26387402	0.000000	0.05858	0.000000	0.03702	0.992000	0.81027	0.166000	0.16583	0.093000	0.17368	0.650000	0.86243	GTC	C|0.998;T|0.002	0.002	strong		0.612	GPR113-004	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316892.1	NM_153835		T	26533898	C	T	26533898	3	4	28	1	0	0	0	0	1	0	0	0	6638	478	17	2	642	2	GPR113	2	26533898	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	542185	26533898	216665475	77	11580											
FNDC4	64838	hgsc.bcm.edu	37	chr2	27716823	27716823	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgaactgtttgaaggtagcCggtcagaacccttgagagtt	10	12	12	7	1	1	4	1	3	0	2	1	5	1	4	2	2	3	3	2	2	4	5			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:27716823C>T	ENST00000264703.3	-	4	819	c.428G>A	c.(427-429)cGg>cAg	p.R143Q	GCKR_ENST00000264717.2_5'Flank|GCKR_ENST00000424318.2_5'Flank	NM_022823.2	NP_073734.1	Q9H6D8	FNDC4_HUMAN	fibronectin type III domain containing 4	143						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|liver(2)|prostate(1)|skin(1)	9	Acute lymphoblastic leukemia(172;0.155)					TGAAGGTAGCCGGTCAGAACC	0.562																																					p.R143Q		Atlas-SNP	.											FNDC4,NS,carcinoma,-1,1	FNDC4	21	1	0			c.G428A						PASS	.						75	81	79					2																	27716823		2203	4300	6503	SO:0001583	missense	64838	exon4			GGTAGCCGGTCAG	AK026015	CCDS1756.1	2p23.3	2013-02-11			ENSG00000115226	ENSG00000115226		"Fibronectin type III domain containing"	20239	protein-coding gene	gene with protein product		611905				12384288	Standard	NM_022823		Approved	FLJ22362, FRCP1	uc002rkx.3	Q9H6D8	OTTHUMG00000097787	ENST00000264703.3:c.428G>A	2.37:g.27716823C>T	ENSP00000264703:p.Arg143Gln	73	0	0		76	24	0.315789	NM_022823	D6W560	Missense_Mutation	SNP	ENST00000264703.3	37	CCDS1756.1	.	.	.	.	.	.	.	.	.	.	C	13.08	2.129221	0.37533	.	.	ENSG00000115226	ENST00000264703	T	0.07444	3.19	5.46	3.68	0.42216	.	0.057087	0.64402	D	0.000002	T	0.04092	0.0114	N	0.24115	0.695	0.44660	D	0.997647	P	0.41710	0.76	B	0.26770	0.073	T	0.54200	-0.8329	10	0.28530	T	0.3	-10.0669	8.5567	0.33485	0.0:0.7609:0.0:0.2391	.	143	Q9H6D8	FNDC4_HUMAN	Q	143	ENSP00000264703:R143Q	ENSP00000264703:R143Q	R	-	2	0	FNDC4	27570327	1.000000	0.71417	1.000000	0.80357	0.524000	0.34500	2.017000	0.40981	0.682000	0.31407	-0.244000	0.11960	CGG	.	.	none		0.562	FNDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215031.1	NM_022823		T	27716823	C	T	27716823	3	4	28	1	0	0	0	0	1	0	0	0	5979	652	23	1	292	1	FNDC4	2	27716823	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1182925	27716823	215482550	78	11581											
FAM179A	165186	hgsc.bcm.edu	37	chr2	29225463	29225463	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacagcaccatcccccgagcCacctctcagaggctgctgag	9	5	9	18	1	1	2	1	1	1	1	3	3	2	2	5	1	3	3	5	1	0	0	rs370488483		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:29225463C>T	ENST00000379558.4	+	5	840	c.489C>T	c.(487-489)gcC>gcT	p.A163A	FAM179A_ENST00000403861.2_Silent_p.A163A	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	163										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						TCCCCCGAGCCACCTCTCAGA	0.632																																					p.A163A		Atlas-SNP	.											.	FAM179A	106	.	0			c.C489T						PASS	.	C		1,3891		0,1,1945	23	28	27		489	-0.5	0.1	2		27	7,8255		0,7,4124	no	coding-synonymous	FAM179A	NM_199280.2		0,8,6069	TT,TC,CC		0.0847,0.0257,0.0658		163/1020	29225463	8,12146	1946	4131	6077	SO:0001819	synonymous_variant	165186	exon5			CCGAGCCACCTCT	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.489C>T	2.37:g.29225463C>T		80	0	0		78	32	0.410256	NM_199280	Q6ZUF5	Silent	SNP	ENST00000379558.4	37	CCDS1769.2																																																																																			.	.	weak		0.632	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280		T	29225463	C	T	29225463	2	4	28	1	0	0	0	0	0	0	0	1	5510	581	21	2		2	FAM179A	2	29225463	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1508640	29225463	213973910	79	11582											
ALK	238	hgsc.bcm.edu	37	chr2	29416366	29416366	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagccccaggttacccctGtcgtgtggctccttctttgc	3	13	9	16	1	1	0	0	0	1	0	4	0	3	0	6	2	3	2	6	2	1	3	rs1881421	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:29416366G>C	ENST00000389048.3	-	29	5493	c.4587C>G	c.(4585-4587)gaC>gaG	p.D1529E	ALK_ENST00000431873.1_Missense_Mutation_p.D359E	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1529			D -> E (in dbSNP:rs1881421). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9053841, ECO:0000269|Ref.4}.		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)	GGTTACCCCTGTCGTGTGGCT	0.547			"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				C|||	2869	0.572883	0.643	0.5706	5008	,	,		17724	0.7292		0.3837	False		,,,				2504	0.5133				p.D1529E		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	.	ALK	533	.	0			c.C4587G						PASS	.	C	GLU/ASP	2681,1725	517.7+/-369.5	834,1013,356	180	196	191		4587	-3.4	0	2	dbSNP_92	191	2957,5643	667.4+/-402.5	508,1941,1851	yes	missense	ALK	NM_004304.4	45	1342,2954,2207	CC,CG,GG		34.3837,39.1512,43.3492	benign	1529/1621	29416366	5638,7368	2203	4300	6503	SO:0001583	missense	238	exon29	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	ACCCCTGTCGTGT	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.4587C>G	2.37:g.29416366G>C	ENSP00000373700:p.Asp1529Glu	271	1	0.00369004		269	127	0.472119	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	ENST00000389048.3	37	CCDS33172.1	1235	0.5654761904761905	327	0.6646341463414634	191	0.5276243093922652	415	0.7255244755244755	302	0.39841688654353563	C	2.203	-0.382484	0.04966	0.608488	0.343837	ENSG00000171094	ENST00000389048;ENST00000431873	T;T	0.26957	1.7;1.7	5.11	-3.42	0.04825	.	0.428474	0.19238	N	0.119246	T	0.00012	0.0000	N	0.00246	-1.78	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31861	-0.9928	9	0.02654	T	1	.	11.8015	0.52130	0.0:0.2641:0.5636:0.1723	rs1881421;rs3738872;rs17007643;rs52821197;rs60882094;rs1881421	1529	Q9UM73	ALK_HUMAN	E	1529;359	ENSP00000373700:D1529E;ENSP00000414027:D359E	ENSP00000373700:D1529E	D	-	3	2	ALK	29269870	0.000000	0.05858	0.000000	0.03702	0.047000	0.14425	-0.022000	0.12480	-1.464000	0.01902	-0.357000	0.07601	GAC	G|0.518;C|0.482	0.482	strong		0.547	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		C	29416366	G	C	29416366	3	2	28	1	0	0	0	0	1	0	0	0	525	1368	48	4	279	4	ALK	2	29416366	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	190903	29416366	213783007	80	11583											
XDH	7498	hgsc.bcm.edu	37	chr2	31593230	31593230	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccaagacttaccttatccttCgcaaagactgtctcatcatt	11	13	4	13	1	2	2	2	0	1	2	5	2	3	2	3	0	1	1	3	0	4	4	rs557103794		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:31593230C>T	ENST00000379416.3	-	18	2019	c.1971G>A	c.(1969-1971)gcG>gcA	p.A657A		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	657					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)	p.A657A(1)		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)	CCTTATCCTTCGCAAAGACTG	0.358																																					p.A657A	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											XDH,colon,carcinoma,0,1	XDH	191	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G1971A						scavenged	.						84	83	83					2																	31593230		2203	4300	6503	SO:0001819	synonymous_variant	7498	exon18			ATCCTTCGCAAAG	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.1971G>A	2.37:g.31593230C>T		48	0	0		63	3	0.047619	NM_000379	Q16681|Q16712|Q4PJ16	Silent	SNP	ENST00000379416.3	37	CCDS1775.1																																																																																			.	.	none		0.358	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379		T	31593230	C	T	31593230	2	4	28	1	0	0	0	0	0	0	0	1	17441	871	31	1		1	XDH	2	31593230	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2176864	31593230	211606143	81	11584											
KCNK12	56660	hgsc.bcm.edu	37	chr2	47748388	47748388	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccgggcagcagcgcgcgcaGcagcggcagctcagcttgcg	6	3	17	15	6	1	0	1	0	0	0	1	0	1	0	1	2	7	7	1	2	0	1	rs115862926	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:47748388G>A	ENST00000327876.4	-	2	1558	c.951C>T	c.(949-951)tgC>tgT	p.C317C	MSH2_ENST00000461394.1_Intron	NM_022055.1	NP_071338.1	Q9HB15	KCNKC_HUMAN	potassium channel, subfamily K, member 12	317						integral component of membrane (GO:0016021)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.0?(2)|p.?(2)		NS(1)|endometrium(1)|lung(3)|ovary(1)	6		all_hematologic(82;0.0495)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AGCGCGCGCAGCAGCGGCAGC	0.697													G|||	3	0.000599042	0.0	0.0014	5008	,	,		11033	0.0		0.001	False		,,,				2504	0.001				p.C317C		Atlas-SNP	.											.	KCNK12	11	.	4	Whole gene deletion(2)|Unknown(2)	haematopoietic_and_lymphoid_tissue(3)|prostate(1)	c.C951T						PASS	.	G		5,4319		0,5,2157	13	15	14		951	3.4	1	2	dbSNP_132	14	15,8443		0,15,4214	no	coding-synonymous	KCNK12	NM_022055.1		0,20,6371	AA,AG,GG		0.1773,0.1156,0.1565		317/431	47748388	20,12762	2162	4229	6391	SO:0001819	synonymous_variant	56660	exon2			CGCGCAGCAGCGG	AF287302	CCDS1835.1	2p16.3	2012-03-07			ENSG00000184261	ENSG00000184261		"Potassium channels", "Voltage-gated ion channels / Potassium channels, Two-P"	6274	protein-coding gene	gene with protein product		607366				11060316	Standard	NM_022055		Approved	THIK-2, THIK2, K2p12.1	uc002rwb.3	Q9HB15	OTTHUMG00000129131	ENST00000327876.4:c.951C>T	2.37:g.47748388G>A		16	0	0		19	12	0.631579	NM_022055		Silent	SNP	ENST00000327876.4	37	CCDS1835.1																																																																																			G|0.998;A|0.002	0.002	strong		0.697	KCNK12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251182.2	NM_022055		A	47748388	G	A	47748388	2	1	28	1	0	0	0	0	0	0	0	1	8069	963	34	2		2	KCNK12	2	47748388	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	16155158	47748388	195450985	82	11585											
FOXN2	3344	hgsc.bcm.edu	37	chr2	48573875	48573875	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaatgttttcagaaagtggaAagaagccatggcaaggtcag	16	8	12	5	0	2	2	2	0	0	2	2	3	2	3	1	3	1	2	1	3	5	2	rs35742253	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:48573875A>G	ENST00000340553.3	+	3	783	c.522A>G	c.(520-522)gaA>gaG	p.E174E		NM_002158.3	NP_002149.2	P32314	FOXN2_HUMAN	forkhead box N2	174					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)			AGAAAGTGGAAAGAAGCCATG	0.418													A|||	16	0.00319489	0.0008	0.0072	5008	,	,		16893	0.0		0.0099	False		,,,				2504	0.0				p.E174E		Atlas-SNP	.											.	FOXN2	39	.	0			c.A522G						PASS	.	A		13,4363		1,11,2176	52	54	53		522	2.9	1	2	dbSNP_126	53	91,8483		0,91,4196	no	coding-synonymous	FOXN2	NM_002158.3		1,102,6372	GG,GA,AA		1.0613,0.2971,0.8031		174/432	48573875	104,12846	2188	4287	6475	SO:0001819	synonymous_variant	3344	exon3			AGTGGAAAGAAGC		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.522A>G	2.37:g.48573875A>G		30	0	0		21	11	0.52381	NM_002158	Q15769|Q6P4Q2	Silent	SNP	ENST00000340553.3	37	CCDS1838.1																																																																																			A|0.992;G|0.008	0.008	strong		0.418	FOXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251240.3	NM_002158		G	48573875	A	G	48573875	2	3	28	1	0	0	0	0	0	0	0	1	6028	11	1	3		3	FOXN2	2	48573875	Silent	SNP	A	TCGA-G8-6914-01A-11D-2210-10	825487	48573875	194625498	83	11586											
TSPYL6	388951	hgsc.bcm.edu	37	chr2	54482271	54482271	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacatgtcggttcctatgaaTgaaggactggggtccatggc	9	10	14	8	1	0	2	0	2	0	0	3	4	2	3	2	5	0	1	2	5	3	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:54482271T>C	ENST00000317802.7	-	1	1138	c.1018A>G	c.(1018-1020)Att>Gtt	p.I340V	ACYP2_ENST00000303536.4_Intron|ACYP2_ENST00000606865.1_Intron|ACYP2_ENST00000394666.3_Intron|ACYP2_ENST00000607452.1_Intron	NM_001003937.2	NP_001003937.2	Q8N831	TSYL6_HUMAN	TSPY-like 6	340					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						TTCCTATGAATGAAGGACTGG	0.498																																					p.I340V		Atlas-SNP	.											.	TSPYL6	54	.	0			c.A1018G						PASS	.						74	79	77					2																	54482271		2124	4267	6391	SO:0001583	missense	388951	exon1			TATGAATGAAGGA	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.1018A>G	2.37:g.54482271T>C	ENSP00000417919:p.Ile340Val	106	0	0		92	47	0.51087	NM_001003937	Q6NUJ3	Missense_Mutation	SNP	ENST00000317802.7	37	CCDS42682.1	.	.	.	.	.	.	.	.	.	.	T	7.246	0.602182	0.13939	.	.	ENSG00000178021	ENST00000317802	T	0.28666	1.6	1.52	0.306	0.15806	.	.	.	.	.	T	0.16938	0.0407	N	0.05177	-0.1	0.09310	N	1	P	0.35192	0.489	P	0.45232	0.474	T	0.36432	-0.9748	9	0.12430	T	0.62	.	5.7092	0.17925	0.0:0.0:0.3027:0.6972	.	340	Q8N831	TSYL6_HUMAN	V	340	ENSP00000417919:I340V	ENSP00000417919:I340V	I	-	1	0	TSPYL6	54335775	0.000000	0.05858	0.006000	0.13384	0.349000	0.29174	-0.527000	0.06200	0.071000	0.16664	0.383000	0.25322	ATT	.	.	none		0.498	TSPYL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324069.3	XM_371494		C	54482271	T	C	54482271	3	2	28	1	0	0	0	0	1	0	0	0	16678	1464	51	3	218	3	TSPYL6	2	54482271	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	5908396	54482271	188717102	84	11587											
SMEK2	57223	hgsc.bcm.edu	37	chr2	55777083	55777085	+	In_Frame_Del	DEL	TTC	TTC	-																															ggtcttttcctgggggacgaTtcttcttcttcatcttcctc																										TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:55777083_55777085delTTC	ENST00000345102.5	-	17	2813_2815	c.2512_2514delGAA	c.(2512-2514)gaadel	p.E838del	SMEK2_ENST00000407823.3_In_Frame_Del_p.E806del|SMEK2_ENST00000272313.5_In_Frame_Del_p.E753del	NM_001122964.1	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	838	Poly-Glu.				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)			TGGGGGACGATTCTTCTTCTTCA	0.369																																					p.838_839del		Pindel,Atlas-Indel	.											SMEK2_ENST00000345102,colon,carcinoma,+1,4	SMEK2	86	4	0			c.2513_2515del						PASS	.		,	1,4265		0,1,2132					,	3	1			95	2,8252		0,2,4125	no	coding,coding	SMEK2	NM_020463.2,NM_001122964.1	,	0,3,6257	A1A1,A1R,RR		0.0242,0.0234,0.024	,	,		3,12517				SO:0001651	inframe_deletion	57223	exon17			.	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.2512_2514delGAA	2.37:g.55777092_55777094delTTC	ENSP00000339769:p.Glu838del	42	0	.		45	15	0.333	NM_001122964	Q6P9B0|Q86XB8|Q9BQJ0|Q9BRK2|Q9H913|Q9P2G0	In_Frame_Del	DEL	ENST00000345102.5	37	CCDS46289.1																																																																																			.	.	none		0.369	SMEK2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251483.1	NM_020463		-	55777085	TTC	-	55777083	7	5	28	1	0	1	0	1	0	0	0	0	14809	1490	52	0	39	0	SMEK2	2	55777083	In_Frame_Del	DEL	TTC	TCGA-G8-6914-01A-11D-2210-10	1294812	55777083	187422290	85	11588											
DYSF	8291	hgsc.bcm.edu	37	chr2	71778829	71778829	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaggtggaggaccttcctgcGgatgacatcctccgggtgga	8	8	15	10	2	0	1	0	1	0	0	3	5	3	5	4	6	1	0	4	6	1	1	rs35984374	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:71778829G>A	ENST00000258104.3	+	19	2008	c.1731G>A	c.(1729-1731)gcG>gcA	p.A577A	DYSF_ENST00000409582.3_Silent_p.A594A|DYSF_ENST00000413539.2_Silent_p.A608A|DYSF_ENST00000409744.1_Silent_p.A564A|DYSF_ENST00000429174.2_Silent_p.A577A|DYSF_ENST00000409762.1_Silent_p.A594A|DYSF_ENST00000410020.3_Silent_p.A595A|DYSF_ENST00000409366.1_Silent_p.A578A|DYSF_ENST00000394120.2_Silent_p.A578A|DYSF_ENST00000410041.1_Silent_p.A595A|DYSF_ENST00000409651.1_Silent_p.A609A	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	577					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						ACCTTCCTGCGGATGACATCC	0.652													G|||	30	0.00599042	0.0008	0.0058	5008	,	,		15341	0.0		0.0249	False		,,,				2504	0.0				p.A609A		Atlas-SNP	.											.	DYSF	536	.	0			c.G1827A						PASS	.	G	,,,,,,,,,,,,,	17,4389	23.3+/-48.9	1,15,2187	73	61	65		1734,1689,1689,1731,1824,1782,1782,1827,1734,1692,1785,1692,1785,1731	-10.9	0	2	dbSNP_126	65	168,8432	76.9+/-139.5	1,166,4133	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DYSF	NM_001130455.1,NM_001130976.1,NM_001130977.1,NM_001130978.1,NM_001130979.1,NM_001130980.1,NM_001130981.1,NM_001130982.1,NM_001130983.1,NM_001130984.1,NM_001130985.1,NM_001130986.1,NM_001130987.1,NM_003494.3	,,,,,,,,,,,,,	2,181,6320	AA,AG,GG		1.9535,0.3858,1.4224	,,,,,,,,,,,,,	578/2082,563/2067,563/2088,577/2102,608/2112,594/2098,594/2119,609/2113,578/2103,564/2089,595/2099,564/2068,595/2120,577/2081	71778829	185,12821	2203	4300	6503	SO:0001819	synonymous_variant	8291	exon20			TCCTGCGGATGAC	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.1731G>A	2.37:g.71778829G>A		42	0	0		47	26	0.553191	NM_001130982	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	37	CCDS1918.1																																																																																			G|0.987;A|0.013	0.013	strong		0.652	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		A	71778829	G	A	71778829	2	1	28	1	0	0	0	0	0	0	0	1	4861	1103	39	1		1	DYSF	2	71778829	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	16001746	71778829	171420544	86	11589											
ALMS1	7840	hgsc.bcm.edu	37	chr2	73829362	73829362	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	atctcccgctctggggagcgGataaagcgcctgaagttaat	10	9	12	10	3	2	1	0	1	2	0	3	3	2	3	2	3	2	2	2	3	4	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:73829362G>A	ENST00000264448.6	+	20	12273	c.12162G>A	c.(12160-12162)cgG>cgA	p.R4054R	ALMS1_ENST00000409009.1_Silent_p.R4012R|ALMS1_ENST00000464408.2_3'UTR	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	4054	ALMS motif.				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						CTGGGGAGCGGATAAAGCGCC	0.483																																					p.R4054R		Atlas-SNP	.											ALMS1,rectum,carcinoma,+2,1	ALMS1	384	1	0			c.G12162A						PASS	.						50	54	52					2																	73829362		2203	4300	6503	SO:0001819	synonymous_variant	7840	exon20			GGAGCGGATAAAG	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.12162G>A	2.37:g.73829362G>A		189	0	0		200	103	0.515	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	37	CCDS42697.1																																																																																			.	.	none		0.483	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		A	73829362	G	A	73829362	2	1	28	1	0	0	0	0	0	0	0	1	535	1161	41	2		2	ALMS1	2	73829362	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2050533	73829362	169370011	87	11590											
DCTN1	1639	hgsc.bcm.edu	37	chr2	74596527	74596527	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttctgggcctcacgaaccCgcgcgcctgccatgtccagc	5	7	11	18	4	2	0	1	0	1	0	3	1	3	0	5	1	3	1	5	1	1	1	rs17721059	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:74596527C>T	ENST00000361874.3	-	14	1801	c.1484G>A	c.(1483-1485)cGg>cAg	p.R495Q	DCTN1_ENST00000394003.3_Missense_Mutation_p.R488Q|DCTN1_ENST00000409438.1_Missense_Mutation_p.R361Q|DCTN1_ENST00000495643.1_5'Flank|DCTN1_ENST00000409567.3_Missense_Mutation_p.R475Q|DCTN1_ENST00000409240.1_Missense_Mutation_p.R458Q|DCTN1_ENST00000407639.2_Missense_Mutation_p.R361Q|DCTN1_ENST00000409868.1_Missense_Mutation_p.R478Q	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						CTCACGAACCCGCGCGCCTGC	0.597													C|||	39	0.00778754	0.0	0.0187	5008	,	,		16682	0.0		0.0239	False		,,,				2504	0.002				p.R495Q		Atlas-SNP	.											.	DCTN1	110	.	0			c.G1484A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	19,4387	25.3+/-52.1	0,19,2184	89	90	90		1424,1082,1373,1463,1484,1082	5	1	2	dbSNP_123	90	160,8440	73.2+/-135.9	1,158,4141	yes	missense,missense,missense,missense,missense,missense	DCTN1	NM_001135040.2,NM_001135041.2,NM_001190836.1,NM_001190837.1,NM_004082.4,NM_023019.3	43,43,43,43,43,43	1,177,6325	TT,TC,CC		1.8605,0.4312,1.3763	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	475/1254,361/1140,458/1237,488/1272,495/1279,361/1145	74596527	179,12827	2203	4300	6503	SO:0001583	missense	1639	exon14			CGAACCCGCGCGC		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.1484G>A	2.37:g.74596527C>T	ENSP00000354791:p.Arg495Gln	131	0	0		180	88	0.488889	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Missense_Mutation	SNP	ENST00000361874.3	37	CCDS1939.1	21	0.009615384615384616	0	0.0	6	0.016574585635359115	0	0.0	15	0.01978891820580475	C	15.10	2.731990	0.48939	0.004312	0.018605	ENSG00000204843	ENST00000361874;ENST00000394003;ENST00000393999;ENST00000407639;ENST00000409438;ENST00000409240;ENST00000409868;ENST00000409567	T;T;T;T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03;-1.03;-0.71;-1.03	5.91	5.03	0.67393	.	0.203082	0.24587	N	0.037257	T	0.43500	0.1250	N	0.25144	0.715	0.50632	D	0.99988	B;P;P;B;B;P	0.46578	0.176;0.88;0.804;0.016;0.136;0.876	B;B;B;B;B;B	0.34138	0.022;0.122;0.123;0.008;0.04;0.176	T	0.54833	-0.8234	10	0.14252	T	0.57	-6.5169	14.0459	0.64704	0.0:0.9269:0.0:0.0731	rs17721059;rs17721059	475;458;495;488;361;361	E9PGE1;E9PFS5;Q14203;A8MY36;Q14203-2;G5E9H4	.;.;DCTN1_HUMAN;.;.;.	Q	495;488;478;361;361;458;478;475	ENSP00000354791:R495Q;ENSP00000377571:R488Q;ENSP00000384844:R361Q;ENSP00000387270:R361Q;ENSP00000386406:R458Q;ENSP00000387327:R478Q;ENSP00000386843:R475Q	ENSP00000354791:R495Q	R	-	2	0	DCTN1	74450035	0.991000	0.36638	0.970000	0.41538	0.394000	0.30568	3.179000	0.50887	1.507000	0.48752	0.655000	0.94253	CGG	C|0.985;T|0.015	0.015	strong		0.597	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082		T	74596527	C	T	74596527	3	4	28	1	0	0	0	0	1	0	0	0	4308	652	23	1	2428	1	DCTN1	2	74596527	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	767165	74596527	168602846	88	11591											
PTCD3	55037	hgsc.bcm.edu	37	chr2	86352925	86352925	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tattattttacagctgatgtAtacacatttaatgcattgat	13	18	5	5	0	0	2	0	2	0	0	0	2	0	2	0	0	4	3	0	0	6	9	rs139474497	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:86352925A>G	ENST00000254630.7	+	12	939	c.873A>G	c.(871-873)gtA>gtG	p.V291V	PTCD3_ENST00000409277.3_3'UTR	NM_017952.5	NP_060422.4	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3	291					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						CAGCTGATGTATACACATTTA	0.338													A|||	28	0.00559105	0.0	0.0086	5008	,	,		20926	0.0		0.0219	False		,,,				2504	0.0				p.V291V		Atlas-SNP	.											.	PTCD3	51	.	0			c.A873G						PASS	.	A		6,4400	11.4+/-27.6	0,6,2197	44	49	47		873	-11.5	0	2	dbSNP_134	47	127,8473	64.6+/-126.8	1,125,4174	no	coding-synonymous	PTCD3	NM_017952.5		1,131,6371	GG,GA,AA		1.4767,0.1362,1.0226		291/690	86352925	133,12873	2203	4300	6503	SO:0001819	synonymous_variant	55037	exon12			TGATGTATACACA		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.873A>G	2.37:g.86352925A>G		113	0	0		86	38	0.44186	NM_017952	A6NHD2|D6W5M1|Q597H0|Q658Y9|Q9BUZ8|Q9NWL0	Silent	SNP	ENST00000254630.7	37	CCDS33235.1																																																																																			A|0.991;G|0.009	0.009	strong		0.338	PTCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329854.1	NM_017952		G	86352925	A	G	86352925	2	3	28	1	0	0	0	0	0	0	0	1	12741	436	16	3		3	PTCD3	2	86352925	Silent	SNP	A	TCGA-G8-6914-01A-11D-2210-10	11756398	86352925	156846448	89	11592											
TEKT4	150483	hgsc.bcm.edu	37	chr2	95539833	95539833	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaggtgcaggctcatccgtaCtccaccaccttccaagagag	10	7	10	14	1	1	1	1	0	0	1	4	3	4	1	5	2	2	3	5	2	2	2	rs111469930	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:95539833C>T	ENST00000295201.4	+	3	830	c.693C>T	c.(691-693)taC>taT	p.Y231Y	AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	231					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						CTCATCCGTACTCCACCACCT	0.662													.|||	28	0.00559105	0.0015	0.0101	5008	,	,		14386	0.0		0.0149	False		,,,				2504	0.0041				p.Y231Y		Atlas-SNP	.											.	TEKT4	72	.	0			c.C693T						PASS	.	C		14,4392		0,14,2189	73	70	71		693	2.2	0	2	dbSNP_132	71	177,8423		1,175,4124	no	coding-synonymous	TEKT4	NM_144705.2		1,189,6313	TT,TC,CC		2.0581,0.3177,1.4686		231/436	95539833	191,12815	2203	4300	6503	SO:0001819	synonymous_variant	150483	exon3			TCCGTACTCCACC	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.693C>T	2.37:g.95539833C>T		94	0	0		65	28	0.430769	NM_144705		Silent	SNP	ENST00000295201.4	37	CCDS2005.1																																																																																			C|0.988;T|0.012	0.012	strong		0.662	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705		T	95539833	C	T	95539833	2	4	28	1	0	0	0	0	0	0	0	1	15770	576	20	2		2	TEKT4	2	95539833	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	9186908	95539833	147659540	90	11593											
VWA3B	200403	hgsc.bcm.edu	37	chr2	98797660	98797660	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaaaccggagaatgagtcCgtgcagaccagtgcggtagg	11	5	15	10	3	0	3	0	1	0	2	1	4	1	3	4	3	3	2	4	3	3	1	rs375244468		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:98797660C>T	ENST00000477737.1	+	9	1500	c.1296C>T	c.(1294-1296)tcC>tcT	p.S432S	VWA3B_ENST00000435344.1_Silent_p.S432S|VWA3B_ENST00000451075.2_Silent_p.S282S	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	432										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						AGAATGAGTCCGTGCAGACCA	0.592																																					p.S432S		Atlas-SNP	.											.	VWA3B	138	.	0			c.C1296T						PASS	.	C		0,4068		0,0,2034	87	90	89		1296	-2.5	0.1	2		89	1,8365		0,1,4182	no	coding-synonymous	VWA3B	NM_144992.4		0,1,6216	TT,TC,CC		0.012,0.0,0.0080		432/1295	98797660	1,12433	2034	4183	6217	SO:0001819	synonymous_variant	200403	exon9			TGAGTCCGTGCAG	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.1296C>T	2.37:g.98797660C>T		154	0	0		168	68	0.404762	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Silent	SNP	ENST00000477737.1	37	CCDS42718.1																																																																																			.	.	weak		0.592	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992		T	98797660	C	T	98797660	2	4	28	1	0	0	0	0	0	0	0	1	17256	639	23	1		1	VWA3B	2	98797660	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	3257827	98797660	144401713	91	11594											
NPAS2	4862	hgsc.bcm.edu	37	chr2	101541736	101541736	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	cgtgttggaaaaggtcatcgGatttttgcagaaacacaatg	13	11	11	6	2	1	1	1	0	0	1	2	3	1	3	0	3	2	2	0	3	4	3	rs138995271		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:101541736G>C	ENST00000335681.5	+	3	446	c.161G>C	c.(160-162)gGa>gCa	p.G54A	NPAS2_ENST00000486017.1_3'UTR|NPAS2_ENST00000542504.1_Missense_Mutation_p.G119A	NM_002518.3	NP_002509.2	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2	54	Sufficient for heterodimer formation with ARNTL/BMAL1, E-box binding and for the effect of NADPH. {ECO:0000250|UniProtKB:P97460}.|bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				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						AAGGTCATCGGATTTTTGCAG	0.498													G|||	1	0.000199681	0.0	0.0	5008	,	,		20410	0.0		0.001	False		,,,				2504	0.0				p.G54A		Atlas-SNP	.											.	NPAS2	88	.	0			c.G161C						PASS	.	G	ALA/GLY	0,4406		0,0,2203	108	101	104		161	5.7	1	2	dbSNP_134	104	10,8590	7.7+/-29.5	0,10,4290	yes	missense	NPAS2	NM_002518.3	60	0,10,6493	CC,CG,GG		0.1163,0.0,0.0769	benign	54/825	101541736	10,12996	2203	4300	6503	SO:0001583	missense	4862	exon3			TCATCGGATTTTT	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.161G>C	2.37:g.101541736G>C	ENSP00000338283:p.Gly54Ala	145	0	0		165	68	0.412121	NM_002518	Q4ZFV9|Q53SQ3|Q86V96|Q99629	Missense_Mutation	SNP	ENST00000335681.5	37	CCDS2048.1	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	11.83|11.83	1.756142|1.756142	0.31137|0.31137	0.0|0.0	0.001163|0.001163	ENSG00000170485|ENSG00000170485	ENST00000427413|ENST00000335681;ENST00000542504;ENST00000451740	.|D;D;D	.|0.97710	.|-4.5;-4.5;-4.5	5.65|5.65	5.65|5.65	0.86999|0.86999	.|Helix-loop-helix DNA-binding (5);	.|0.055781	.|0.64402	.|D	.|0.000001	D|D	0.93680|0.93680	0.7981|0.7981	N|N	0.02751|0.02751	-0.505|-0.505	0.58432|0.58432	D|D	0.999998|0.999998	.|P;P	.|0.37370	.|0.537;0.592	.|B;B	.|0.41174	.|0.237;0.349	D|D	0.93572|0.93572	0.6905|0.6905	5|10	.|0.41790	.|T	.|0.15	.|.	19.7272|19.7272	0.96168|0.96168	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|119;54	.|F5H027;Q99743	.|.;NPAS2_HUMAN	H|A	120|54;119;38	.|ENSP00000338283:G54A;ENSP00000438428:G119A;ENSP00000395265:G38A	.|ENSP00000338283:G54A	D|G	+|+	1|2	0|0	NPAS2|NPAS2	100908168|100908168	1.000000|1.000000	0.71417|0.71417	0.988000|0.988000	0.46212|0.46212	0.994000|0.994000	0.84299|0.84299	6.750000|6.750000	0.74888|0.74888	2.646000|2.646000	0.89796|0.89796	0.655000|0.655000	0.94253|0.94253	GAT|GGA	G|0.999;C|0.001	0.001	strong		0.498	NPAS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253168.3			C	101541736	G	C	101541736	3	2	28	1	0	0	0	0	1	0	0	0	10572	1174	41	4	167	4	NPAS2	2	101541736	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2744076	101541736	141657637	92	11595											
POLR1B	84172	hgsc.bcm.edu	37	chr2	113333238	113333238	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcgatactgtttctgtgcctTatgtttttcggtattttgta	5	22	8	6	2	1	0	0	0	1	0	3	1	1	0	1	1	2	4	1	1	4	9			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:113333238T>C	ENST00000263331.5	+	15	3920	c.3340T>C	c.(3340-3342)Tat>Cat	p.Y1114H	POLR1B_ENST00000409894.3_Missense_Mutation_p.Y931H|POLR1B_ENST00000417433.2_Missense_Mutation_p.Y1058H|POLR1B_ENST00000541869.1_Missense_Mutation_p.Y1152H|POLR1B_ENST00000537335.1_Missense_Mutation_p.Y903H	NM_019014.4	NP_061887.2	Q9H9Y6	RPA2_HUMAN	polymerase (RNA) I polypeptide B, 128kDa	1114					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						TTCTGTGCCTTATGTTTTTCG	0.423																																					p.Y1114H	Ovarian(16;256 576 9537 23969 41147)	Atlas-SNP	.											.	POLR1B	95	.	0			c.T3340C						PASS	.						122	114	117					2																	113333238		2203	4300	6503	SO:0001583	missense	84172	exon15			GTGCCTTATGTTT	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.3340T>C	2.37:g.113333238T>C	ENSP00000263331:p.Tyr1114His	79	0	0		77	4	0.0519481	NM_019014	B7Z6Y7|B7Z823|F5GZX4|F8W898|Q2TAM4|Q585T5|Q6ZRR2|Q9H9D3	Missense_Mutation	SNP	ENST00000263331.5	37	CCDS2097.1	.	.	.	.	.	.	.	.	.	.	T	15.75	2.925462	0.52759	.	.	ENSG00000125630	ENST00000263331;ENST00000541869;ENST00000409894;ENST00000537335;ENST00000417433	T;T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24;-1.24	5.37	5.37	0.77165	RNA polymerase Rpb2, domain 7 (1);	0.108910	0.64402	D	0.000004	D	0.87669	0.6235	M	0.78637	2.42	0.80722	D	1	P;D;B;B	0.76494	0.476;0.999;0.274;0.183	B;D;B;B	0.83275	0.178;0.996;0.225;0.2	D	0.88914	0.3361	10	0.62326	D	0.03	-21.3681	14.3792	0.66900	0.0:0.0:0.0:1.0	.	1152;931;1058;1114	F5GZX4;F8W898;Q9H9Y6-2;Q9H9Y6	.;.;.;RPA2_HUMAN	H	1114;1152;931;903;1058	ENSP00000263331:Y1114H;ENSP00000444136:Y1152H;ENSP00000387143:Y931H;ENSP00000437914:Y903H;ENSP00000405358:Y1058H	ENSP00000263331:Y1114H	Y	+	1	0	POLR1B	113049709	1.000000	0.71417	0.978000	0.43139	0.995000	0.86356	5.887000	0.69751	2.030000	0.59900	0.455000	0.32223	TAT	.	.	none		0.423	POLR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254083.1	NM_019014		C	113333238	T	C	113333238	3	2	28	1	0	0	0	0	1	0	0	0	12219	1754	61	3	3398	3	POLR1B	2	113333238	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	11791502	113333238	129866135	93	11596											
PSD4	23550	hgsc.bcm.edu	37	chr2	113953346	113953346	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgagaagctcgagtgggccGtgtgagtgagactccctttc	7	9	15	10	3	0	3	0	2	0	2	3	6	1	3	2	1	1	1	2	1	1	1	rs370284646	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:113953346G>A	ENST00000245796.6	+	11	2419	c.2224G>A	c.(2224-2226)Gtg>Atg	p.V742M	PSD4_ENST00000441564.3_Splice_Site_p.V714M	NM_012455.2	NP_036587.2	Q8NDX1	PSD4_HUMAN	pleckstrin and Sec7 domain containing 4	742					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						CGAGTGGGCCGTGTGAGTGAG	0.592																																					p.V742M		Atlas-SNP	.											.	PSD4	74	.	0			c.G2224A						PASS	.	G	MET/VAL	0,4406		0,0,2203	152	141	145		2224	-0.4	0.1	2		145	1,8599	1.2+/-3.3	0,1,4299	no	missense-near-splice	PSD4	NM_012455.2	21	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	742/1057	113953346	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	23550	exon11			TGGGCCGTGTGAG	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.2225+1G>A	2.37:g.113953346G>A		74	0	0		57	11	0.192982	NM_012455	A6NEG7|A8K1Y0|O95621|Q4ZG34|Q6GPH8|Q8IYP4	Missense_Mutation	SNP	ENST00000245796.6	37	CCDS33276.1	.	.	.	.	.	.	.	.	.	.	G	11.40	1.627464	0.28978	0.0	1.16E-4	ENSG00000125637	ENST00000245796;ENST00000441564	T;T	0.30182	1.54;1.54	5.65	-0.402	0.12404	SEC7-like, alpha orthogonal bundle (1);SEC7-like (1);	0.449069	0.25267	N	0.031905	T	0.23210	0.0561	L	0.45581	1.43	0.80722	D	1	B;B;B	0.24882	0.113;0.027;0.016	B;B;B	0.22880	0.042;0.015;0.007	T	0.05007	-1.0912	10	0.39692	T	0.17	.	9.3598	0.38188	0.57:0.0:0.43:0.0	.	400;714;742	Q59HG0;Q8NDX1-2;Q8NDX1	.;.;PSD4_HUMAN	M	742;714	ENSP00000245796:V742M;ENSP00000413997:V714M	ENSP00000245796:V742M	V	+	1	0	PSD4	113669817	0.000000	0.05858	0.084000	0.20598	0.906000	0.53458	-0.730000	0.04915	-0.136000	0.11475	-0.140000	0.14226	GTG	.	.	weak		0.592	PSD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330789.1	NM_012455	Missense_Mutation	A	113953346	G	A	113953346	5	1	28	1	0	0	0	0	0	0	1	0	12661	1159	40	1	2262	1	PSD4	2	113953346	Splice_Site	SNP	G	TCGA-G8-6914-01A-11D-2210-10	620108	113953346	129246027	94	11597											
TMEM37	6344	hgsc.bcm.edu	37	chr2	120194682	120194682	+	IGR	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagacctgggccaggcccAtgtgcccgggctggccgtgg	5	5	17	14	2	0	1	0	0	0	1	0	2	0	1	5	5	1	1	5	5	0	0	rs200510439		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:120194682A>C	ENST00000019103.5	-	0	1865				TMEM37_ENST00000465296.1_3'UTR|TMEM37_ENST00000306406.4_Missense_Mutation_p.H80P|TMEM37_ENST00000409826.1_Missense_Mutation_p.H92P	NM_002980.2	NP_002971.2	P47872	SCTR_HUMAN	secretin receptor						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)	GGCCAGGCCCATGTGCCCGGG	0.667													A|||	1	0.000199681	0.0	0.0	5008	,	,		14518	0.0		0.001	False		,,,				2504	0.0				p.H80P		Atlas-SNP	.											.	TMEM37	40	.	0			c.A239C						PASS	.	A	PRO/HIS	0,4406		0,0,2203	51	54	53		239	-1.9	0	2		53	5,8595	4.3+/-15.6	0,5,4295	no	missense	TMEM37	NM_183240.2	77	0,5,6498	CC,CA,AA		0.0581,0.0,0.0384	benign	80/191	120194682	5,13001	2203	4300	6503	SO:0001628	intergenic_variant	140738	exon2			AGGCCCATGTGCC		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		2.37:g.120194682A>C		48	0	0		40	15	0.375	NM_183240	Q12961|Q13213|Q53T00	Missense_Mutation	SNP	ENST00000019103.5	37	CCDS2127.1	.	.	.	.	.	.	.	.	.	.	A	7.689	0.690644	0.15039	0.0	5.81E-4	ENSG00000171227	ENST00000409826;ENST00000306406	.	.	.	4.74	-1.88	0.07713	.	1.326400	0.04832	N	0.438832	T	0.37571	0.1008	L	0.44542	1.39	0.09310	N	1	B	0.32620	0.378	B	0.34931	0.192	T	0.39522	-0.9610	9	0.35671	T	0.21	0.0526	11.2183	0.48840	0.5495:0.0:0.4505:0.0	.	80	Q8WXS4	CCGL_HUMAN	P	92;80	.	ENSP00000303148:H80P	H	+	2	0	TMEM37	119911152	0.000000	0.05858	0.001000	0.08648	0.381000	0.30169	0.049000	0.14099	-0.500000	0.06614	0.459000	0.35465	CAT	.	.	weak		0.667	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2			C	120194682	A	C	120194682	1	2	28	0	1	0	0	0	0	0	0	0	16173	217	8	5		5	TMEM37	2	120194682	IGR	SNP	A	TCGA-G8-6914-01A-11D-2210-10	6241336	120194682	123004691	95	11598											
BIN1	274	hgsc.bcm.edu	37	chr2	127809840	127809840	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgggcacttacttgggcaggCcccggctcggccgtctggct	3	9	15	14	3	1	0	0	0	1	0	2	0	1	0	3	6	1	4	3	6	1	2	rs61748155	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:127809840C>A	ENST00000316724.5	-	15	1773	c.1362G>T	c.(1360-1362)ggG>ggT	p.G454G	BIN1_ENST00000348750.4_Intron|BIN1_ENST00000352848.3_Intron|BIN1_ENST00000259238.4_Intron|BIN1_ENST00000357970.3_Silent_p.G411G|BIN1_ENST00000466111.1_Intron|BIN1_ENST00000409400.1_Intron|BIN1_ENST00000376113.2_Intron|BIN1_ENST00000393041.3_Silent_p.G336G|BIN1_ENST00000351659.3_Silent_p.G367G|BIN1_ENST00000393040.3_Intron|BIN1_ENST00000346226.3_Silent_p.G379G	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	454					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)		CTTGGGCAGGCCCCGGCTCGG	0.692													C|||	73	0.0145767	0.0	0.0144	5008	,	,		14417	0.0		0.0159	False		,,,				2504	0.0481				p.G454G		Atlas-SNP	.											BIN1,brain,glioma,0,1	BIN1	85	1	0			c.G1362T						scavenged	.	C	,,,,,,,,,	14,4288		0,14,2137	9	12	11		,1362,1233,1101,,1137,,1008,,	3.8	1	2	dbSNP_129	11	149,8367		1,147,4110	no	intron,coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous,intron,coding-synonymous,intron,intron	BIN1	NM_004305.3,NM_139343.2,NM_139344.2,NM_139345.2,NM_139346.2,NM_139347.2,NM_139348.2,NM_139349.2,NM_139350.2,NM_139351.2	,,,,,,,,,	1,161,6247	AA,AC,CC		1.7496,0.3254,1.2716	,,,,,,,,,	,454/594,411/551,367/507,,379/519,,336/476,,	127809840	163,12655	2151	4258	6409	SO:0001819	synonymous_variant	274	exon15			GGCAGGCCCCGGC	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.1362G>T	2.37:g.127809840C>A		64	1	0.015625		67	35	0.522388	NM_139343	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Silent	SNP	ENST00000316724.5	37	CCDS2138.1																																																																																			C|0.990;A|0.010	0.010	strong		0.692	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343		A	127809840	C	A	127809840	2	1	28	1	0	0	0	0	0	0	0	1	1432	726	26	4		4	BIN1	2	127809840	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	7615158	127809840	115389533	96	11599											
BIN1	274	hgsc.bcm.edu	37	chr2	127811561	127811561	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caggtccagcagactggcctGctccgagaaaggccccgggg	8	4	15	14	2	0	2	0	0	0	2	2	3	2	2	5	5	2	2	5	5	1	0			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:127811561G>A	ENST00000316724.5	-	13	1570	c.1159C>T	c.(1159-1161)Cag>Tag	p.Q387*	BIN1_ENST00000348750.4_Intron|BIN1_ENST00000352848.3_Intron|BIN1_ENST00000259238.4_Intron|BIN1_ENST00000357970.3_Nonsense_Mutation_p.Q344*|BIN1_ENST00000466111.1_Intron|BIN1_ENST00000409400.1_Intron|BIN1_ENST00000376113.2_Intron|BIN1_ENST00000393041.3_Intron|BIN1_ENST00000351659.3_Intron|BIN1_ENST00000393040.3_Intron|BIN1_ENST00000346226.3_Intron	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	387	Clathrin-binding.				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)		AGACTGGCCTGCTCCGAGAAA	0.642																																					p.Q387X		Atlas-SNP	.											.	BIN1	85	.	0			c.C1159T						PASS	.						22	24	23					2																	127811561		2107	4099	6206	SO:0001587	stop_gained	274	exon13			TGGCCTGCTCCGA	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.1159C>T	2.37:g.127811561G>A	ENSP00000316779:p.Gln387*	173	0	0		162	67	0.41358	NM_139343	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Nonsense_Mutation	SNP	ENST00000316724.5	37	CCDS2138.1	.	.	.	.	.	.	.	.	.	.	G	41	8.932924	0.99008	.	.	ENSG00000136717	ENST00000357970;ENST00000316724	.	.	.	5.36	4.39	0.52855	.	0.765384	0.12406	N	0.471717	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	-22.063	9.5913	0.39548	0.0:0.2271:0.6314:0.1415	.	.	.	.	X	344;387	.	ENSP00000316779:Q387X	Q	-	1	0	BIN1	127528031	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.211000	0.42825	2.533000	0.85409	0.456000	0.33151	CAG	.	.	none		0.642	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343		A	127811561	G	A	127811561	4	1	28	1	0	0	0	0	0	1	0	0	1432	1328	46	2	650	2	BIN1	2	127811561	Nonsense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1721	127811561	115387812	97	11600											
PROC	5624	hgsc.bcm.edu	37	chr2	128186156	128186156	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggccaggagaccctcgtgacGggctggggctaccacagcag	8	4	16	13	2	0	2	0	1	0	1	1	3	0	2	3	5	2	3	3	5	1	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:128186156G>A	ENST00000234071.3	+	9	1107	c.1020G>A	c.(1018-1020)acG>acA	p.T340T	PROC_ENST00000422777.3_Silent_p.T340T|PROC_ENST00000409048.1_Silent_p.T374T|PROC_ENST00000453608.2_Silent_p.T395T	NM_000312.3	NP_000303.1	P04070	PROC_HUMAN	protein C (inactivator of coagulation factors Va and VIIIa)	340	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		T -> M (in THPH3; Vermont-2). {ECO:0000269|PubMed:8292730, ECO:0000269|PubMed:9798967}.		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)	p.T340T(1)		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)	CCCTCGTGACGGGCTGGGGCT	0.632																																					p.T340T		Atlas-SNP	.											.	PROC	31	.	1	Substitution - coding silent(1)	lung(1)	c.G1020A						PASS	.						85	99	94					2																	128186156		2203	4300	6503	SO:0001819	synonymous_variant	5624	exon9			CGTGACGGGCTGG	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.1020G>A	2.37:g.128186156G>A		84	0	0		99	42	0.424242	NM_000312	B4DPQ7|Q15189|Q15190|Q16001|Q53S74|Q9UC55	Silent	SNP	ENST00000234071.3	37	CCDS2145.1	.	.	.	.	.	.	.	.	.	.	G	0.108	-1.142460	0.01728	.	.	ENSG00000115718	ENST00000402125	.	.	.	5.23	-10.5	0.00291	.	.	.	.	.	T	0.32224	0.0822	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41016	-0.9532	4	.	.	.	.	1.6144	0.02700	0.4409:0.2044:0.1371:0.2175	.	.	.	.	Q	115	.	.	R	+	2	0	PROC	127902626	0.000000	0.05858	0.263000	0.24496	0.026000	0.11368	-5.090000	0.00152	-2.914000	0.00307	-1.036000	0.02392	CGG	.	.	none		0.632	PROC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254385.2	NM_000312		A	128186156	G	A	128186156	2	1	28	1	0	0	0	0	0	0	0	1	12557	1103	39	1		1	PROC	2	128186156	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	374595	128186156	115013217	98	11601											
WDR33	55339	hgsc.bcm.edu	37	chr2	128528508	128528508	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cgaggtgcctggtgctggaaCcttggcatatggaaaaaacg	11	8	14	8	2	0	0	0	0	0	0	0	3	0	2	2	5	4	2	2	5	5	2	rs55916728	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:128528508C>T	ENST00000322313.4	-	2	206	c.48G>A	c.(46-48)agG>agA	p.R16R	WDR33_ENST00000409658.3_Silent_p.R16R|WDR33_ENST00000393006.1_Silent_p.R16R	NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	16					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)		GGTGCTGGAACCTTGGCATAT	0.418													C|||	66	0.0131789	0.0008	0.0159	5008	,	,		16418	0.0		0.0527	False		,,,				2504	0.001				p.R16R		Atlas-SNP	.											.	WDR33	136	.	0			c.G48A						PASS	.	C	,,	45,4361	46.0+/-80.4	0,45,2158	102	100	101		48,48,48	5.5	1	2	dbSNP_129	101	389,8211	125.1+/-183.8	14,361,3925	no	coding-synonymous,coding-synonymous,coding-synonymous	WDR33	NM_001006622.2,NM_001006623.2,NM_018383.4	,,	14,406,6083	TT,TC,CC		4.5233,1.0213,3.3369	,,	16/327,16/258,16/1337	128528508	434,12572	2203	4300	6503	SO:0001819	synonymous_variant	55339	exon2			CTGGAACCTTGGC		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.48G>A	2.37:g.128528508C>T		121	0	0		149	75	0.503356	NM_001006623	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Silent	SNP	ENST00000322313.4	37	CCDS2150.1																																																																																			C|0.972;T|0.028	0.028	strong		0.418	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383		T	128528508	C	T	128528508	2	4	28	1	0	0	0	0	0	0	0	1	17302	506	18	2		2	WDR33	2	128528508	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	342352	128528508	114670865	99	11602											
LY75	4065	hgsc.bcm.edu	37	chr2	160661704	160661704	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	taagatacttagtgtggcaaCtatgatagctattgctgtgt	11	15	10	5	0	0	2	0	1	0	1	0	2	0	2	0	1	4	3	0	1	7	7			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:160661704C>T	ENST00000263636.4	-	35	5047	c.5020G>A	c.(5020-5022)Gtt>Att	p.V1674I	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	1674					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)		AGTGTGGCAACTATGATAGCT	0.423																																					p.V1674I		Atlas-SNP	.											.	LY75	151	.	0			c.G5020A						PASS	.						107	98	101					2																	160661704		2203	4300	6503	SO:0001583	missense	4065	exon35			TGGCAACTATGAT	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.5020G>A	2.37:g.160661704C>T	ENSP00000263636:p.Val1674Ile	117	0	0		99	16	0.161616	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	C	8.786	0.929415	0.18131	.	.	ENSG00000054219	ENST00000263636	T	0.08634	3.07	5.38	-5.11	0.02901	.	1.327090	0.05825	N	0.616489	T	0.02970	0.0088	N	0.08118	0	0.24881	N	0.992224	B	0.02656	0.0	B	0.01281	0.0	T	0.44590	-0.9318	10	0.12766	T	0.61	.	2.3409	0.04260	0.3665:0.2775:0.066:0.29	.	1674	O60449	LY75_HUMAN	I	1674	ENSP00000263636:V1674I	ENSP00000263636:V1674I	V	-	1	0	LY75	160369950	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.555000	0.05999	-0.516000	0.06470	-2.451000	0.00208	GTT	.	.	none		0.423	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1			T	160661704	C	T	160661704	3	4	28	1	0	0	0	0	1	0	0	0	9108	565	20	2	152	2	LY75	2	160661704	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	32133196	160661704	82537669	100	11603											
COBLL1	22837	hgsc.bcm.edu	37	chr2	165578602	165578602	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccttatctgtctcatccaCgctcatggatttcactatac	9	14	4	14	1	4	0	3	0	2	0	6	1	5	1	2	1	1	1	2	1	3	4	rs74459242	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:165578602C>T	ENST00000392717.2	-	7	1097	c.1093G>A	c.(1093-1095)Gtg>Atg	p.V365M	COBLL1_ENST00000409184.3_Missense_Mutation_p.V365M|COBLL1_ENST00000375458.2_Missense_Mutation_p.V327M|COBLL1_ENST00000342193.4_Missense_Mutation_p.V327M|COBLL1_ENST00000194871.6_Missense_Mutation_p.V393M|COBLL1_ENST00000491126.2_Intron			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	365						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						GTCTCATCCACGCTCATGGAT	0.458													C|||	63	0.0125799	0.0023	0.0202	5008	,	,		16844	0.0		0.0368	False		,,,				2504	0.0092				p.V327M		Atlas-SNP	.											.	COBLL1	122	.	0			c.G979A						PASS	.	C	MET/VAL	34,4372	40.0+/-72.8	0,34,2169	77	83	81		979	1.4	0.5	2	dbSNP_132	81	421,8179	130.5+/-188.4	13,395,3892	yes	missense	COBLL1	NM_014900.3	21	13,429,6061	TT,TC,CC		4.8953,0.7717,3.4984	probably-damaging	327/1167	165578602	455,12551	2203	4300	6503	SO:0001583	missense	22837	exon6			CATCCACGCTCAT	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.1093G>A	2.37:g.165578602C>T	ENSP00000376478:p.Val365Met	81	0	0		102	58	0.568627	NM_014900	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Missense_Mutation	SNP	ENST00000392717.2	37		41	0.018772893772893772	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	29	0.03825857519788918	C	12.89	2.073757	0.36566	0.007717	0.048953	ENSG00000082438	ENST00000375458;ENST00000342193;ENST00000409184;ENST00000392717;ENST00000194871	D	0.93076	-3.16	6.17	1.37	0.22104	Cordon-bleu domain (1);	0.602245	0.17823	N	0.160815	T	0.75428	0.3848	L	0.47716	1.5	0.21553	N	0.999649	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74023	0.982;0.982;0.968	T	0.76080	-0.3090	10	0.52906	T	0.07	-0.5122	2.5206	0.04679	0.1029:0.3543:0.2961:0.2466	.	365;393;365	Q53SF7;B7Z2P5;Q53SF7-2	COBL1_HUMAN;.;.	M	327;327;365;365;393	ENSP00000194871:V393M	ENSP00000194871:V393M	V	-	1	0	COBLL1	165286848	0.099000	0.21834	0.503000	0.27626	0.406000	0.30931	0.134000	0.15932	0.180000	0.19960	0.655000	0.94253	GTG	C|0.971;T|0.029	0.029	strong		0.458	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900		T	165578602	C	T	165578602	3	4	28	1	0	0	0	0	1	0	0	0	3656	536	19	1	2557	1	COBLL1	2	165578602	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	4916898	165578602	77620771	101	11604											
SCN7A	6332	hgsc.bcm.edu	37	chr2	167284444	167284444	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgaccaagtgaagatccgcGtctgcaacctgtcaagattg	11	10	10	10	2	2	4	1	2	1	2	3	4	3	4	3	0	2	1	3	0	4	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:167284444G>A	ENST00000409855.1	-	17	2833	c.2707C>T	c.(2707-2709)Cgc>Tgc	p.R903C		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	903					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)	GAAGATCCGCGTCTGCAACCT	0.383																																					p.R903C		Atlas-SNP	.											SCN7A_ENST00000409855,NS,carcinoma,+1,6	SCN7A	410	6	0			c.C2707T						PASS	.						90	83	85					2																	167284444		1856	4093	5949	SO:0001583	missense	6332	exon17			ATCCGCGTCTGCA	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.2707C>T	2.37:g.167284444G>A	ENSP00000386796:p.Arg903Cys	92	0	0		96	24	0.25	NM_002976		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	G	14.08	2.428994	0.43122	.	.	ENSG00000136546	ENST00000409855;ENST00000259060	D	0.84730	-1.89	5.2	3.32	0.38043	Sodium ion transport-associated (1);	1.098480	0.06996	N	0.822524	D	0.87700	0.6243	M	0.80616	2.505	0.09310	N	1	D	0.61697	0.99	P	0.51101	0.659	T	0.71537	-0.4563	10	0.33141	T	0.24	.	4.2946	0.10895	0.0858:0.1551:0.5991:0.16	.	903	Q01118	SCN7A_HUMAN	C	903	ENSP00000386796:R903C	ENSP00000259060:R903C	R	-	1	0	SCN7A	166992690	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.174000	0.09839	0.630000	0.30394	0.591000	0.81541	CGC	.	.	none		0.383	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1			A	167284444	G	A	167284444	3	1	28	1	0	0	0	0	1	0	0	0	13938	1145	40	1	2377	1	SCN7A	2	167284444	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1705842	167284444	75914929	102	11605											
XIRP2	129446	hgsc.bcm.edu	37	chr2	168099555	168099555	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttttgaaaacacaaatgaCagttctcaaaaagatctgaa	18	11	6	6	0	2	4	1	3	2	1	3	4	2	4	0	0	1	2	0	0	6	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:168099555C>T	ENST00000409195.1	+	9	1742	c.1653C>T	c.(1651-1653)gaC>gaT	p.D551D	XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000295237.9_Silent_p.D551D|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409273.1_Silent_p.D329D|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409043.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	376					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						ACACAAATGACAGTTCTCAAA	0.398																																					p.D551D		Atlas-SNP	.											.	XIRP2	914	.	0			c.C1653T						PASS	.						43	40	41					2																	168099555		1842	4094	5936	SO:0001819	synonymous_variant	129446	exon9			AAATGACAGTTCT	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.1653C>T	2.37:g.168099555C>T		85	0	0		71	21	0.295775	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	37	CCDS42769.1																																																																																			.	.	none		0.398	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		T	168099555	C	T	168099555	2	4	28	1	0	0	0	0	0	0	0	1	17445	477	17	2		2	XIRP2	2	168099555	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	815111	168099555	75099818	103	11606											
LRP2	4036	hgsc.bcm.edu	37	chr2	170060670	170060670	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaattctttgtgtgtacaaGtcagtccagtaaatatactg	13	15	7	6	0	2	0	1	0	1	0	3	0	3	0	1	0	2	2	1	0	8	7			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:170060670G>C	ENST00000263816.3	-	42	8112	c.7827C>G	c.(7825-7827)gaC>gaG	p.D2609E		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2609					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)"	GTGTGTACAAGTCAGTCCAGT	0.473																																					p.D2609E		Atlas-SNP	.											.	LRP2	751	.	0			c.C7827G						PASS	.						165	174	171					2																	170060670		2203	4300	6503	SO:0001583	missense	4036	exon42			GTACAAGTCAGTC		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.7827C>G	2.37:g.170060670G>C	ENSP00000263816:p.Asp2609Glu	126	0	0		153	48	0.313726	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	G	16.72	3.200151	0.58126	.	.	ENSG00000081479	ENST00000263816	D	0.92446	-3.04	5.78	3.01	0.34805	Six-bladed beta-propeller, TolB-like (1);	0.093401	0.64402	N	0.000001	D	0.93677	0.7980	H	0.95504	3.68	0.80722	D	1	D	0.53745	0.962	P	0.44394	0.448	D	0.91687	0.5363	10	0.87932	D	0	.	7.2942	0.26383	0.1959:0.0:0.6833:0.1207	.	2609	P98164	LRP2_HUMAN	E	2609	ENSP00000263816:D2609E	ENSP00000263816:D2609E	D	-	3	2	LRP2	169768916	1.000000	0.71417	0.553000	0.28255	0.357000	0.29423	3.438000	0.52871	0.364000	0.24374	-0.857000	0.03018	GAC	.	.	none		0.473	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		C	170060670	G	C	170060670	3	2	28	1	0	0	0	0	1	0	0	0	8965	1020	36	4	6292	4	LRP2	2	170060670	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1961115	170060670	73138703	104	11607											
SLC25A12	8604	hgsc.bcm.edu	37	chr2	172671648	172671648	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacctccagcaactgagcccAgagtgaatctgtaagcagac	13	6	9	13	0	1	4	0	2	1	2	2	4	2	4	3	0	4	3	3	0	3	1	rs200754828		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:172671648A>C	ENST00000422440.2	-	10	1032	c.995T>G	c.(994-996)cTg>cGg	p.L332R	SLC25A12_ENST00000392592.4_Missense_Mutation_p.L225R	NM_003705.4	NP_003696.2	O75746	CMC1_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 12	332					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)	AACTGAGCCCAGAGTGAATCT	0.473																																					p.L332R		Atlas-SNP	.											.	SLC25A12	59	.	0			c.T995G						PASS	.						86	81	83					2																	172671648		2203	4300	6503	SO:0001583	missense	8604	exon10			GAGCCCAGAGTGA	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.995T>G	2.37:g.172671648A>C	ENSP00000388658:p.Leu332Arg	189	0	0		215	95	0.44186	NM_003705	B3KR64|Q96AM8	Missense_Mutation	SNP	ENST00000422440.2	37	CCDS33327.1	.	.	.	.	.	.	.	.	.	.	a	23.6	4.440914	0.83993	.	.	ENSG00000115840	ENST00000422440;ENST00000392592	T;T	0.80033	-1.33;-1.33	5.47	5.47	0.80525	Mitochondrial carrier domain (2);	0.140827	0.49305	D	0.000150	D	0.88187	0.6369	M	0.63208	1.945	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.89300	0.3625	10	0.72032	D	0.01	-1.9365	15.5193	0.75854	1.0:0.0:0.0:0.0	.	225;332	B3KR64;O75746	.;CMC1_HUMAN	R	332;225	ENSP00000388658:L332R;ENSP00000376371:L225R	ENSP00000376371:L225R	L	-	2	0	SLC25A12	172379894	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.869000	0.92326	2.054000	0.61138	0.482000	0.46254	CTG	A|0.999;C|0.001	0.001	weak		0.473	SLC25A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259010.2	NM_003705		C	172671648	A	C	172671648	3	2	28	1	0	0	0	0	1	0	0	0	14489	188	7	5	1077	5	SLC25A12	2	172671648	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	2610978	172671648	70527725	105	11608											
TTN	7273	hgsc.bcm.edu	37	chr2	179453429	179453429	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgttgacagggacccatcgtGttgaatgcttttcctttttc	6	17	9	9	1	0	2	0	2	0	0	3	3	1	3	2	1	1	3	2	1	1	6	rs72646850	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179453429G>A	ENST00000591111.1	-	254	58324	c.58100C>T	c.(58099-58101)aCa>aTa	p.T19367I	TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.T11943I|TTN_ENST00000342992.6_Missense_Mutation_p.T18440I|TTN_ENST00000589042.1_Missense_Mutation_p.T21008I|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T12135I|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T12068I|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000590743.1_RNA			Q8WZ42	TITIN_HUMAN	titin	19367	Fibronectin type-III 40. {ECO:0000255|PROSITE-ProRule:PRU00316}.		T -> I. {ECO:0000269|PubMed:17344846}.		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)			GACCCATCGTGTTGAATGCTT	0.428													G|||	29	0.00579073	0.0008	0.0159	5008	,	,		20616	0.0		0.0169	False		,,,				2504	0.0				p.T21008I		Atlas-SNP	.											.	TTN	18412	.	0			c.C63023T						PASS	.	G	ILE/THR,ILE/THR,ILE/THR,ILE/THR	12,3802		0,12,1895	162	152	155		36404,36203,55319,35828	-6.5	0	2	dbSNP_130	155	134,8108		2,130,3989	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	89,89,89,89	2,142,5884	AA,AG,GG		1.6258,0.3146,1.211	benign,benign,benign,benign	12135/27119,12068/27052,18440/33424,11943/26927	179453429	146,11910	1907	4121	6028	SO:0001583	missense	7273	exon304			CATCGTGTTGAAT	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.58100C>T	2.37:g.179453429G>A	ENSP00000465570:p.Thr19367Ile	195	0	0		208	119	0.572115	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	37		21	0.009615384615384616	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	13	0.017150395778364115	G	9.129	1.011021	0.19277	0.003146	0.016258	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	6.16	-6.48	0.01896	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.19765	0.0475	N	0.10874	0.06	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	0.08764	-1.0706	9	0.87932	D	0	.	19.6396	0.95753	0.9305:0.0:0.0695:0.0	.	11943;12068;12135;19367	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	18440;11943;12135;12068;11941	ENSP00000343764:T18440I;ENSP00000434586:T11943I;ENSP00000340554:T12135I;ENSP00000352154:T12068I	ENSP00000340554:T12135I	T	-	2	0	TTN	179161675	0.000000	0.05858	0.000000	0.03702	0.925000	0.55904	1.233000	0.32648	-1.316000	0.02295	-0.312000	0.09012	ACA	G|0.988;A|0.012	0.012	strong		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179453429	G	A	179453429	3	1	28	1	0	0	0	0	1	0	0	0	16750	1377	48	2	45192	2	TTN	2	179453429	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	6781781	179453429	63745944	106	11609											
TTN	7273	hgsc.bcm.edu	37	chr2	179455352	179455352	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccaggtggtttgatgggcCggcaagcttttattggatca	7	13	14	7	1	1	1	1	1	0	0	2	2	2	2	2	5	1	3	2	5	2	4	rs141973925	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179455352C>T	ENST00000591111.1	-	254	56401	c.56177G>A	c.(56176-56178)cGg>cAg	p.R18726Q	TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R11302Q|TTN_ENST00000342992.6_Missense_Mutation_p.R17799Q|TTN_ENST00000589042.1_Missense_Mutation_p.R20367Q|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R11494Q|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R11427Q|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000590743.1_RNA			Q8WZ42	TITIN_HUMAN	titin	18726	Fibronectin type-III 35. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> Q. {ECO:0000269|PubMed:17344846}.		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)			TTTGATGGGCCGGCAAGCTTT	0.433													C|||	6	0.00119808	0.0008	0.0029	5008	,	,		22262	0.0		0.003	False		,,,				2504	0.0				p.R20367Q		Atlas-SNP	.											TTN_ENST00000359218,NS,carcinoma,+1,5	TTN	18412	5	0			c.G61100A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	5,3765		0,5,1880	109	107	107		33905,53396,34280,34481	6.1	1	2	dbSNP_134	107	35,8191		0,35,4078	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	43,43,43,43	0,40,5958	TT,TC,CC		0.4255,0.1326,0.3334	probably-damaging,probably-damaging,probably-damaging,probably-damaging	11302/26927,17799/33424,11427/27052,11494/27119	179455352	40,11956	1885	4113	5998	SO:0001583	missense	7273	exon304			ATGGGCCGGCAAG	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.56177G>A	2.37:g.179455352C>T	ENSP00000465570:p.Arg18726Gln	330	0	0		344	179	0.520349	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	37		3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	15.40	2.821552	0.50633	0.001326	0.004255	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.39056	1.1;1.1;1.1;1.1	6.11	6.11	0.99139	Fibronectin, type III (2);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.60818	0.2298	L	0.43923	1.385	0.80722	D	1	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	0.59101	-0.7517	9	0.87932	D	0	.	20.7342	0.99715	0.0:1.0:0.0:0.0	.	11302;11427;11494;18726	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	Q	17799;11302;11494;11427;11300	ENSP00000343764:R17799Q;ENSP00000434586:R11302Q;ENSP00000340554:R11494Q;ENSP00000352154:R11427Q	ENSP00000340554:R11494Q	R	-	2	0	TTN	179163598	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.976000	0.70484	2.906000	0.99361	0.655000	0.94253	CGG	C|0.999;T|0.001	0.001	strong		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179455352	C	T	179455352	3	4	28	1	0	0	0	0	1	0	0	0	16750	652	23	1	47115	1	TTN	2	179455352	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1923	179455352	63744021	107	11610											
TTN	7273	hgsc.bcm.edu	37	chr2	179611809	179611809	+	Intron	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcctcccctgggggtgtggaAtatcgctctagagtctctcc	5	11	12	13	1	2	1	0	0	2	1	6	2	4	2	4	3	0	1	4	3	3	2	rs397517815|rs569499266		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179611809A>G	ENST00000591111.1	-	46	10585				TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN_ENST00000589042.1_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000360870.5_Silent_p.Y5106Y			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)			GGGGTGTGGAATATCGCTCTA	0.498																																					p.Y5106Y		Atlas-SNP	.											.	TTN	18412	.	0			c.T15318C						PASS	.																																			SO:0001627	intron_variant	7273	exon46			TGTGGAATATCGC	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.10361-5161T>C	2.37:g.179611809A>G		168	0	0		164	12	0.0731707	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	Silent	SNP	ENST00000591111.1	37																																																																																				.	.	none		0.498	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179611809	A	G	179611809	1	3	28	0	1	0	0	0	0	0	0	0	16750	108	4	3		3	TTN	2	179611809	Intron	SNP	A	TCGA-G8-6914-01A-11D-2210-10	156457	179611809	63587564	108	11611			1	48		5	3	76	N	T_C_A	1.532912e-06
TTN	7273	hgsc.bcm.edu	37	chr2	179611847	179611847	+	Intron	SNP	T	T	G																															tcctgggggtgtggagtatcTctccagagtctctcctgggg																								rs141105907|rs397517814	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179611847T>G	ENST00000591111.1	-	46	10585				TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN_ENST00000589042.1_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000360870.5_Silent_p.R5094R			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)			GTGGAGTATCTCTCCAGAGTC	0.537													T|||	5	0.000998403	0.0	0.0029	5008	,	,		15680	0.0		0.003	False		,,,				2504	0.0				p.R5094R		Atlas-SNP	.											.	TTN	18412	.	0			c.A15280C						PASS	.	T	,,,,	0,4406		0,0,2203	62	74	70		,,15280,,	4.4	1	2	dbSNP_134	70	2,8596		0,2,4297	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	0,2,6500	GG,GT,TT		0.0233,0.0,0.0154	,,,,	,,5094/5605,,	179611847	2,13002	2203	4299	6502	SO:0001627	intron_variant	7273	exon46			AGTATCTCTCCAG	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.10361-5199A>C	2.37:g.179611847T>G		132	0	0		148	35	0.236486	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	Silent	SNP	ENST00000591111.1	37																																																																																				T|0.998;G|0.002	0.002	strong		0.537	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179611847	T	G	179611847	1	3	28	0	1	0	0	0	0	0	0	0	16750	1559	54	5		5	TTN	2	179611847	Intron	SNP	T	TCGA-G8-6914-01A-11D-2210-10	38	179611847	63587526	109	11612	144	2	1	48		5	3	76	N	T_C_A	1.532912e-06
TTN	7273	hgsc.bcm.edu	37	chr2	179611851	179611851	+	Intron	SNP	C	C	T																															gggggtgtggagtatctctcCagagtctctcctgggggtgt																								rs72648910	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179611851C>T	ENST00000591111.1	-	46	10585				TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN_ENST00000589042.1_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000360870.5_Silent_p.L5092L			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)			AGTATCTCTCCAGAGTCTCTC	0.527													T|||	200	0.0399361	0.1407	0.013	5008	,	,		15008	0.001		0.003	False		,,,				2504	0.001				p.L5092L		Atlas-SNP	.											TTN_ENST00000360870,NS,carcinoma,-2,1	TTN	18412	1	0			c.G15276A						PASS	.	T	,,,,	323,4077	759.4+/-412.9	21,281,1898	61	73	69		,,15276,,	-10.5	0	2	dbSNP_130	69	6,8592	810.5+/-407.1	0,6,4293	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	21,287,6191	TT,TC,CC		0.0698,7.3409,2.5312	,,,,	,,5092/5605,,	179611851	329,12669	2200	4299	6499	SO:0001627	intron_variant	7273	exon46			TCTCTCCAGAGTC	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.10361-5203G>A	2.37:g.179611851C>T		131	0	0		148	32	0.216216	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	Silent	SNP	ENST00000591111.1	37																																																																																				C|0.965;T|0.035	0.035	strong		0.527	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179611851	C	T	179611851	1	4	28	0	1	0	0	0	0	0	0	0	16750	581	21	2		2	TTN	2	179611851	Intron	SNP	C	TCGA-G8-6914-01A-11D-2210-10	4	179611851	63587522	110	11613	144	2	1	48		5	3	76	N	T_C_A	1.532912e-06
TTN	7273	hgsc.bcm.edu	37	chr2	179611875	179611875	+	Intron	SNP	A	A	G																															gtctctcctgggggtgtggaAtatctctctagagtctctcc																								rs61233923	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179611875A>G	ENST00000591111.1	-	46	10585				TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN_ENST00000589042.1_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000360870.5_Silent_p.Y5084Y			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)			GGGGTGTGGAATATCTCTCTA	0.547													a|||	199	0.0397364	0.1407	0.013	5008	,	,		14705	0.0		0.003	False		,,,				2504	0.001				p.Y5084Y		Atlas-SNP	.											.	TTN	18412	.	0			c.T15252C						PASS	.	G	,,,,	406,4000	178.7+/-207.4	27,352,1824	62	73	69		,,15252,,	-7.1	0	2	dbSNP_129	69	6,8592	1.2+/-3.3	0,6,4293	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	27,358,6117	GG,GA,AA		0.0698,9.2147,3.1683	,,,,	,,5084/5605,,	179611875	412,12592	2203	4299	6502	SO:0001627	intron_variant	7273	exon46			TGTGGAATATCTC	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.10361-5227T>C	2.37:g.179611875A>G		133	0	0		162	20	0.123457	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	Silent	SNP	ENST00000591111.1	37																																																																																				A|0.963;G|0.037	0.037	strong		0.547	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		G	179611875	A	G	179611875	1	3	28	0	1	0	0	0	0	0	0	0	16750	108	4	3		3	TTN	2	179611875	Intron	SNP	A	TCGA-G8-6914-01A-11D-2210-10	24	179611875	63587498	111	11614	145	2	1	48		5	3	76	N	T_C_A	1.532912e-06
TTN	7273	hgsc.bcm.edu	37	chr2	179611884	179611884	+	Intron	SNP	T	T	C																															gggggtgtggaatatctctcTagagtctctcctgggggtgt																										TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179611884T>C	ENST00000591111.1	-	46	10585				TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN_ENST00000589042.1_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000360870.5_Silent_p.L5081L			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)			AATATCTCTCTAGAGTCTCTC	0.552																																					p.L5081L		Atlas-SNP	.											.	TTN	18412	.	0			c.A15243G						PASS	.						63	72	69					2																	179611884		2203	4299	6502	SO:0001627	intron_variant	7273	exon46			TCTCTCTAGAGTC	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.10361-5236A>G	2.37:g.179611884T>C		137	0	0		165	17	0.10303	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	Silent	SNP	ENST00000591111.1	37																																																																																				.	.	none		0.552	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		C	179611884	T	C	179611884	1	2	28	0	1	0	0	0	0	0	0	0	16750	1509	53	3		3	TTN	2	179611884	Intron	SNP	T	TCGA-G8-6914-01A-11D-2210-10	9	179611884	63587489	112	11615	145	2	1	48		5	3	76	N	T_C_A	1.532912e-06
SESTD1	91404	hgsc.bcm.edu	37	chr2	179986553	179986553	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtatgtggtccacattttcTttattttcaatggttacatc	8	20	6	7	0	2	0	1	0	1	0	4	0	3	0	1	2	1	2	1	2	4	8	rs56336305	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179986553T>C	ENST00000428443.3	-	13	1702	c.1386A>G	c.(1384-1386)aaA>aaG	p.K462K		NM_178123.4	NP_835224.3	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1	462							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)			CCACATTTTCTTTATTTTCAA	0.383													T|||	56	0.0111821	0.0	0.0159	5008	,	,		17677	0.0		0.0278	False		,,,				2504	0.0174				p.K462K		Atlas-SNP	.											.	SESTD1	66	.	0			c.A1386G						PASS	.	T		25,4381	32.6+/-62.9	0,25,2178	110	105	107		1386	2.8	1	2	dbSNP_129	107	198,8402	86.9+/-149.2	0,198,4102	no	coding-synonymous	SESTD1	NM_178123.4		0,223,6280	CC,CT,TT		2.3023,0.5674,1.7146		462/697	179986553	223,12783	2203	4300	6503	SO:0001819	synonymous_variant	91404	exon13			ATTTTCTTTATTT	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.1386A>G	2.37:g.179986553T>C		62	0	0		75	32	0.426667	NM_178123	Q53R38|Q53SP3|Q5GM69|Q8N6M1|Q96LQ2	Silent	SNP	ENST00000428443.3	37	CCDS33338.1																																																																																			T|0.982;C|0.018	0.018	strong		0.383	SESTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335916.2	NM_178123		C	179986553	T	C	179986553	2	2	28	1	0	0	0	0	0	0	0	1	14142	1606	56	3		3	SESTD1	2	179986553	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	374669	179986553	63212820	113	11616											
FAM171B	165215	hgsc.bcm.edu	37	chr2	187605000	187605000	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgaatgacatcatcagtcGtcagtacctgagccaagcag	12	8	11	10	1	3	3	3	3	0	0	4	3	3	3	2	1	3	2	2	1	3	1	rs73979354	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:187605000G>A	ENST00000304698.5	+	2	487	c.284G>A	c.(283-285)cGt>cAt	p.R95H		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	95						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						ATCATCAGTCGTCAGTACCTG	0.403													G|||	72	0.014377	0.0393	0.0115	5008	,	,		19566	0.0		0.008	False		,,,				2504	0.0041				p.R95H		Atlas-SNP	.											.	FAM171B	146	.	0			c.G284A						PASS	.	G	HIS/ARG	156,4250	105.6+/-144.1	2,152,2049	106	91	96		284	5.3	1	2	dbSNP_130	96	40,8560	26.8+/-75.7	0,40,4260	yes	missense	FAM171B	NM_177454.3	29	2,192,6309	AA,AG,GG		0.4651,3.5406,1.507	benign	95/827	187605000	196,12810	2203	4300	6503	SO:0001583	missense	165215	exon2			TCAGTCGTCAGTA	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.284G>A	2.37:g.187605000G>A	ENSP00000304108:p.Arg95His	136	0	0		107	55	0.514019	NM_177454	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Missense_Mutation	SNP	ENST00000304698.5	37	CCDS33347.1	30	0.013736263736263736	18	0.036585365853658534	6	0.016574585635359115	0	0.0	6	0.0079155672823219	G	9.869	1.198429	0.22037	0.035406	0.004651	ENSG00000144369	ENST00000304698;ENST00000272804	T	0.31769	1.48	6.16	5.26	0.73747	.	0.252210	0.41938	N	0.000786	T	0.03053	0.0090	N	0.08118	0	0.34129	D	0.665083	B;B	0.19583	0.037;0.037	B;B	0.12837	0.008;0.008	T	0.17623	-1.0363	10	0.22706	T	0.39	-4.6378	7.6817	0.28518	0.227:0.0:0.773:0.0	.	95;96	Q6P995;A8K122	F171B_HUMAN;.	H	95	ENSP00000304108:R95H	ENSP00000272804:R95H	R	+	2	0	FAM171B	187313245	1.000000	0.71417	0.997000	0.53966	0.892000	0.51952	2.871000	0.48459	1.557000	0.49525	0.650000	0.86243	CGT	G|0.987;A|0.013	0.013	strong		0.403	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454		A	187605000	G	A	187605000	3	1	28	1	0	0	0	0	1	0	0	0	5496	1145	40	1	290	1	FAM171B	2	187605000	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	7618447	187605000	55594373	114	11617											
COL3A1	1281	hgsc.bcm.edu	37	chr2	189859312	189859312	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaggagagcccggaccacgtGgtgaacgcgtaagttttact	11	8	13	9	4	0	2	0	1	0	1	0	4	0	3	2	3	3	2	2	3	4	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:189859312G>A	ENST00000304636.3	+	19	1509	c.1339G>A	c.(1339-1341)Ggt>Agt	p.G447S	COL3A1_ENST00000317840.5_Missense_Mutation_p.G447S	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	447	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)	CGGACCACGTGGTGAACGCGT	0.393																																					p.G447S		Atlas-SNP	.											COL3A1,NS,malignant_melanoma,-1,1	COL3A1	292	1	0			c.G1339A						PASS	.						102	101	101					2																	189859312		2203	4300	6503	SO:0001583	missense	1281	exon19			CCACGTGGTGAAC	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.1339G>A	2.37:g.189859312G>A	ENSP00000304408:p.Gly447Ser	110	0	0		122	36	0.295082	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	37	CCDS2297.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.907297	0.92107	.	.	ENSG00000168542	ENST00000304636;ENST00000317840	D;D	0.99607	-6.27;-6.27	6.17	6.17	0.99709	.	0.000000	0.52532	D	0.000067	D	0.99806	0.9916	H	0.96048	3.76	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97394	0.9991	10	0.87932	D	0	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	447	P02461	CO3A1_HUMAN	S	447	ENSP00000304408:G447S;ENSP00000315243:G447S	ENSP00000304408:G447S	G	+	1	0	COL3A1	189567557	1.000000	0.71417	0.983000	0.44433	0.945000	0.59286	9.550000	0.98110	2.941000	0.99782	0.655000	0.94253	GGT	.	.	none		0.393	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090		A	189859312	G	A	189859312	3	1	28	1	0	0	0	0	1	0	0	0	3690	1348	47	2	1413	2	COL3A1	2	189859312	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2254312	189859312	53340061	115	11618											
DNAH7	56171	hgsc.bcm.edu	37	chr2	196922836	196922836	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atttttctttgctggccgatTtatcctgtatgaaaaacatg	10	17	7	7	1	1	1	0	1	1	0	2	2	2	1	2	1	2	2	2	1	4	6	rs72917299	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:196922836T>A	ENST00000312428.6	-	2	120	c.20A>T	c.(19-21)aAa>aTa	p.K7I	DNAH7_ENST00000410072.1_Missense_Mutation_p.K7I	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	7	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						GCTGGCCGATTTATCCTGTAT	0.313													T|||	16	0.00319489	0.0008	0.0029	5008	,	,		16097	0.0		0.0129	False		,,,				2504	0.0				p.K7I		Atlas-SNP	.											.	DNAH7	512	.	0			c.A20T						PASS	.	T	ILE/LYS	10,3592		0,10,1791	181	174	176		20	4.3	0.9	2	dbSNP_130	176	108,8028		1,106,3961	yes	missense	DNAH7	NM_018897.2	102	1,116,5752	AA,AT,TT		1.3274,0.2776,1.0053	possibly-damaging	7/4025	196922836	118,11620	1801	4068	5869	SO:0001583	missense	56171	exon2			GCCGATTTATCCT	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.20A>T	2.37:g.196922836T>A	ENSP00000311273:p.Lys7Ile	110	0	0		94	47	0.5	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	13	0.005952380952380952	0	0.0	2	0.0055248618784530384	1	0.0017482517482517483	10	0.013192612137203167	T	13.85	2.361068	0.41801	0.002776	0.013274	ENSG00000118997	ENST00000312428;ENST00000410072;ENST00000312446	T;T	0.23754	1.89;2.52	4.29	4.29	0.51040	.	.	.	.	.	T	0.26919	0.0659	N	0.22421	0.69	0.31255	N	0.693556	D	0.65815	0.995	D	0.75484	0.986	T	0.19712	-1.0297	9	0.87932	D	0	.	10.1288	0.42665	0.0:0.0:0.0:1.0	.	7	Q8WXX0	DYH7_HUMAN	I	7	ENSP00000311273:K7I;ENSP00000386260:K7I	ENSP00000311273:K7I	K	-	2	0	DNAH7	196631081	0.996000	0.38824	0.876000	0.34364	0.572000	0.35998	3.399000	0.52586	2.155000	0.67459	0.460000	0.39030	AAA	T|0.991;A|0.009	0.009	strong		0.313	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		A	196922836	T	A	196922836	3	1	28	1	0	0	0	0	1	0	0	0	4608	1841	64	5	12310	5	DNAH7	2	196922836	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	7063524	196922836	46276537	116	11619											
NBEAL1	65065	hgsc.bcm.edu	37	chr2	204002925	204002926	+	Frame_Shift_Del	DEL	AG	AG	-																															aatgggcaatctcagaaaacAgagaagcaaaaactaatcca																										TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:204002925_204002926delAG	ENST00000449802.1	+	29	4852_4853	c.4519_4520delAG	c.(4519-4521)agafs	p.R1507fs		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	1507										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						CTCAGAAAACAGAGAAGCAAAA	0.376																																					p.1506_1507del		Pindel,Atlas-Indel	.											.	NBEAL1	266	.	0			c.4518_4519del						PASS	.																																			SO:0001589	frameshift_variant	65065	exon29			.	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.4519_4520delAG	2.37:g.204002927_204002928delAG	ENSP00000399903:p.Arg1507fs	165	0	.		176	58	0.33	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Frame_Shift_Del	DEL	ENST00000449802.1	37	CCDS46495.1																																																																																			.	.	none		0.376	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4			-	204002926	AG	-	204002925	7	5	28	1	0	1	0	1	0	0	0	0	10197	180	7	0	4629	0	NBEAL1	2	204002925	Frame_Shift_Del	DEL	AG	TCGA-G8-6914-01A-11D-2210-10	7080089	204002925	39196448	117	11620											
RAPH1	65059	hgsc.bcm.edu	37	chr2	204306093	204306093	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	taggttgcggggataaagggGgcacaagtgaagtgtagggc	11	7	19	4	1	0	1	0	1	0	0	0	2	0	2	0	6	1	3	0	6	6	4	rs541342499		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:204306093G>A	ENST00000319170.5	-	14	2119	c.1820C>T	c.(1819-1821)cCc>cTc	p.P607L	ABI2_ENST00000295851.5_3'UTR|RAPH1_ENST00000374493.3_Missense_Mutation_p.P659L|RAPH1_ENST00000457812.1_Intron	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	607					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						GGATAAAGGGGGCACAAGTGA	0.517																																					p.P607L		Atlas-SNP	.											.	RAPH1	118	.	0			c.C1820T						PASS	.						32	35	34					2																	204306093		1757	3443	5200	SO:0001583	missense	65059	exon14			AAAGGGGGCACAA	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.1820C>T	2.37:g.204306093G>A	ENSP00000316543:p.Pro607Leu	43	0	0		92	61	0.663043	NM_213589	Q96Q37|Q9C0I2	Missense_Mutation	SNP	ENST00000319170.5	37	CCDS2359.1	.	.	.	.	.	.	.	.	.	.	g	11.68	1.710804	0.30322	.	.	ENSG00000173166	ENST00000319170;ENST00000374493	T;T	0.75154	-0.91;-0.91	3.02	3.02	0.34903	.	1.838130	0.03300	U	0.188852	T	0.63546	0.2520	N	0.14661	0.345	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.25187	-1.0139	10	0.34782	T	0.22	-8.7148	13.4277	0.61035	0.0:0.0:1.0:0.0	.	607	Q70E73	RAPH1_HUMAN	L	607;659	ENSP00000316543:P607L;ENSP00000363617:P659L	ENSP00000316543:P607L	P	-	2	0	RAPH1	204014338	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	4.020000	0.57189	2.008000	0.58898	0.479000	0.44913	CCC	.	.	none		0.517	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2	NM_025252		A	204306093	G	A	204306093	3	1	28	1	0	0	0	0	1	0	0	0	13065	1232	43	2	1936	2	RAPH1	2	204306093	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	303168	204306093	38893280	118	11621											
ZDBF2	57683	hgsc.bcm.edu	37	chr2	207170026	207170026	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagaaacataaagaatcaaaTaggaaatctttacgcatgaa	21	8	6	6	1	2	3	1	1	1	2	2	4	2	4	0	1	2	1	0	1	9	4	rs77622365	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:207170026T>C	ENST00000374423.3	+	5	1160	c.774T>C	c.(772-774)aaT>aaC	p.N258N		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	258							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						AAGAATCAAATAGGAAATCTT	0.368													T|||	115	0.0229633	0.0734	0.0159	5008	,	,		18712	0.0		0.006	False		,,,				2504	0.001				p.N258N		Atlas-SNP	.											.	ZDBF2	531	.	0			c.T774C						PASS	.	T		243,3413		8,227,1593	29	28	29		774	-3.9	0	2	dbSNP_132	29	71,8095		0,71,4012	no	coding-synonymous	ZDBF2	NM_020923.1		8,298,5605	CC,CT,TT		0.8695,6.6466,2.6561		258/2355	207170026	314,11508	1828	4083	5911	SO:0001819	synonymous_variant	57683	exon5			ATCAAATAGGAAA	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.774T>C	2.37:g.207170026T>C		160	0	0		148	67	0.452703	NM_020923	Q6ZNP7|Q6ZSN8	Silent	SNP	ENST00000374423.3	37	CCDS46501.1																																																																																			T|0.979;C|0.021	0.021	strong		0.368	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		C	207170026	T	C	207170026	2	2	28	1	0	0	0	0	0	0	0	1	17614	1403	49	3		3	ZDBF2	2	207170026	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	2863933	207170026	36029347	119	11622											
ZDBF2	57683	hgsc.bcm.edu	37	chr2	207170242	207170242	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatactattgcaaagaaccaTgaggaattcttttctaacat	15	13	6	7	0	2	2	0	1	2	1	2	4	2	3	1	1	4	1	1	1	6	7	rs112075178	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:207170242T>C	ENST00000374423.3	+	5	1376	c.990T>C	c.(988-990)caT>caC	p.H330H		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	330							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						CAAAGAACCATGAGGAATTCT	0.358													T|||	116	0.0231629	0.0741	0.0159	5008	,	,		19800	0.0		0.006	False		,,,				2504	0.001				p.H330H		Atlas-SNP	.											.	ZDBF2	531	.	0			c.T990C						PASS	.	T		248,3394		8,232,1581	47	46	46		990	-1.2	0	2	dbSNP_132	46	70,8096		0,70,4013	no	coding-synonymous	ZDBF2	NM_020923.1		8,302,5594	CC,CT,TT		0.8572,6.8094,2.6931		330/2355	207170242	318,11490	1821	4083	5904	SO:0001819	synonymous_variant	57683	exon5			GAACCATGAGGAA	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.990T>C	2.37:g.207170242T>C		74	0	0		48	25	0.520833	NM_020923	Q6ZNP7|Q6ZSN8	Silent	SNP	ENST00000374423.3	37	CCDS46501.1																																																																																			T|0.979;C|0.021	0.021	strong		0.358	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		C	207170242	T	C	207170242	2	2	28	1	0	0	0	0	0	0	0	1	17614	1461	51	3		3	ZDBF2	2	207170242	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	216	207170242	36029131	120	11623											
ZDBF2	57683	hgsc.bcm.edu	37	chr2	207174559	207174559	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctcaagaaactgttaagaaAagacacccttgtaagaaggt	17	8	8	8	0	1	4	1	0	0	4	1	4	1	4	2	1	1	2	2	1	7	3	rs13408088	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:207174559A>G	ENST00000374423.3	+	5	5693	c.5307A>G	c.(5305-5307)aaA>aaG	p.K1769K		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1769							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						CTGTTAAGAAAAGACACCCTT	0.413													A|||	157	0.0313498	0.1051	0.0159	5008	,	,		20253	0.0		0.006	False		,,,				2504	0.001				p.K1769K		Atlas-SNP	.											.	ZDBF2	531	.	0			c.A5307G						PASS	.	A		352,3382		17,318,1532	55	56	56		5307	2.6	0	2	dbSNP_121	56	71,8127		0,71,4028	no	coding-synonymous	ZDBF2	NM_020923.1		17,389,5560	GG,GA,AA		0.8661,9.4269,3.5451		1769/2355	207174559	423,11509	1867	4099	5966	SO:0001819	synonymous_variant	57683	exon5			TAAGAAAAGACAC	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.5307A>G	2.37:g.207174559A>G		109	0	0		114	54	0.473684	NM_020923	Q6ZNP7|Q6ZSN8	Silent	SNP	ENST00000374423.3	37	CCDS46501.1																																																																																			A|0.970;G|0.030	0.030	strong		0.413	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923		G	207174559	A	G	207174559	2	3	28	1	0	0	0	0	0	0	0	1	17614	11	1	3		3	ZDBF2	2	207174559	Silent	SNP	A	TCGA-G8-6914-01A-11D-2210-10	4317	207174559	36024814	121	11624											
DYTN	391475	hgsc.bcm.edu	37	chr2	207527656	207527656	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctagattgaaggcatccAtaagttttgacaatagttct	12	16	7	6	0	2	3	0	2	2	1	3	3	3	3	1	1	0	3	1	1	5	8	rs201792178	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:207527656A>G	ENST00000452335.2	-	11	1720	c.1604T>C	c.(1603-1605)aTg>aCg	p.M535T		NM_001093730.1	NP_001087199.1	A2CJ06	DYTN_HUMAN	dystrotelin	535						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)		GAAGGCATCCATAAGTTTTGA	0.433													A|||	2	0.000399361	0.0	0.0014	5008	,	,		21916	0.0		0.001	False		,,,				2504	0.0				p.M535T		Atlas-SNP	.											DYTN_ENST00000452335,colon,carcinoma,-1,1	DYTN	168	1	0			c.T1604C						PASS	.	A	THR/MET	5,3917		0,5,1956	277	273	274		1604	-2.1	0	2		274	42,8238		0,42,4098	yes	missense	DYTN	NM_001093730.1	81	0,47,6054	GG,GA,AA		0.5072,0.1275,0.3852	benign	535/579	207527656	47,12155	1961	4140	6101	SO:0001583	missense	391475	exon11			GCATCCATAAGTT	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.1604T>C	2.37:g.207527656A>G	ENSP00000396593:p.Met535Thr	172	0	0		187	88	0.470588	NM_001093730		Missense_Mutation	SNP	ENST00000452335.2	37	CCDS46502.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	A	2.601	-0.292930	0.05568	0.001275	0.005072	ENSG00000232125	ENST00000452335	T	0.14640	2.49	5.13	-2.14	0.07123	.	.	.	.	.	T	0.03695	0.0105	N	0.12182	0.205	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.44267	-0.9339	9	0.15066	T	0.55	-0.1195	4.7275	0.12948	0.392:0.0:0.4418:0.1662	.	535	A2CJ06	DYTN_HUMAN	T	535	ENSP00000396593:M535T	ENSP00000396593:M535T	M	-	2	0	DYTN	207235901	0.114000	0.22134	0.020000	0.16555	0.244000	0.25665	0.144000	0.16135	-0.124000	0.11724	0.533000	0.62120	ATG	A|0.999;G|0.001	0.001	strong		0.433	DYTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336799.1			G	207527656	A	G	207527656	3	3	28	1	0	0	0	0	1	0	0	0	4863	217	8	3	140	3	DYTN	2	207527656	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	353097	207527656	35671717	122	11625											
DYTN	391475	hgsc.bcm.edu	37	chr2	207564537	207564537	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gctgataaccggtggcaggtCgggagccacaggaggatggg	9	5	19	8	2	0	1	0	1	0	0	1	4	0	4	2	7	2	2	2	7	1	1	rs113447424	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:207564537C>T	ENST00000452335.2	-	7	749	c.633G>A	c.(631-633)ccG>ccA	p.P211P	DYTN_ENST00000477734.1_5'UTR|Y_RNA_ENST00000384589.1_RNA	NM_001093730.1	NP_001087199.1	A2CJ06	DYTN_HUMAN	dystrotelin	211						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)		GGTGGCAGGTCGGGAGCCACA	0.532													C|||	16	0.00319489	0.0076	0.0058	5008	,	,		16997	0.0		0.002	False		,,,				2504	0.0				p.P211P		Atlas-SNP	.											DYTN,medulla,primitive_neuroectodermal_tumour-medulloblastoma,-1,1	DYTN	168	1	0			c.G633A						scavenged	.	C		46,3908		1,44,1932	70	76	74		633	-11.8	0	2	dbSNP_132	74	52,8280		0,52,4114	no	coding-synonymous	DYTN	NM_001093730.1		1,96,6046	TT,TC,CC		0.6241,1.1634,0.7977		211/579	207564537	98,12188	1977	4166	6143	SO:0001819	synonymous_variant	391475	exon7			GCAGGTCGGGAGC	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.633G>A	2.37:g.207564537C>T		125	1	0.008		146	71	0.486301	NM_001093730		Silent	SNP	ENST00000452335.2	37	CCDS46502.1																																																																																			C|0.997;T|0.003	0.003	strong		0.532	DYTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336799.1			T	207564537	C	T	207564537	2	4	28	1	0	0	0	0	0	0	0	1	4863	871	31	1		1	DYTN	2	207564537	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	36881	207564537	35634836	123	11626											
DYTN	391475	hgsc.bcm.edu	37	chr2	207564562	207564562	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccacaggaggatgggaggcTcagattggacccaagacagg	12	4	16	9	0	1	2	1	0	0	2	1	6	1	6	2	6	0	1	2	6	1	1	rs112735024	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:207564562T>A	ENST00000452335.2	-	7	724	c.608A>T	c.(607-609)gAg>gTg	p.E203V	DYTN_ENST00000477734.1_5'UTR|Y_RNA_ENST00000384589.1_RNA	NM_001093730.1	NP_001087199.1	A2CJ06	DYTN_HUMAN	dystrotelin	203						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)		GATGGGAGGCTCAGATTGGAC	0.507													T|||	16	0.00319489	0.0076	0.0058	5008	,	,		18067	0.0		0.002	False		,,,				2504	0.0				p.E203V		Atlas-SNP	.											.	DYTN	168	.	0			c.A608T						PASS	.	T	VAL/GLU	44,3860		1,42,1909	76	82	80		608	3.6	1	2	dbSNP_132	80	51,8255		0,51,4102	yes	missense	DYTN	NM_001093730.1	121	1,93,6011	AA,AT,TT		0.614,1.127,0.7781	probably-damaging	203/579	207564562	95,12115	1952	4153	6105	SO:0001583	missense	391475	exon7			GGAGGCTCAGATT	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.608A>T	2.37:g.207564562T>A	ENSP00000396593:p.Glu203Val	139	0	0		166	81	0.487952	NM_001093730		Missense_Mutation	SNP	ENST00000452335.2	37	CCDS46502.1	4	0.0018315018315018315	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	T	16.99	3.273329	0.59649	0.01127	0.00614	ENSG00000232125	ENST00000452335	T	0.77620	-1.11	5.89	3.58	0.41010	EF-hand domain, type 2 (1);	.	.	.	.	D	0.83450	0.5257	M	0.84433	2.695	0.36672	D	0.878551	D	0.89917	1.0	D	0.79784	0.993	D	0.88043	0.2782	9	0.87932	D	0	-12.5875	9.3049	0.37870	0.0:0.1712:0.0:0.8288	.	203	A2CJ06	DYTN_HUMAN	V	203	ENSP00000396593:E203V	ENSP00000396593:E203V	E	-	2	0	DYTN	207272807	1.000000	0.71417	0.998000	0.56505	0.413000	0.31143	2.499000	0.45372	2.254000	0.74563	0.459000	0.35465	GAG	T|0.997;A|0.003	0.003	strong		0.507	DYTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336799.1			A	207564562	T	A	207564562	3	1	28	1	0	0	0	0	1	0	0	0	4863	1551	54	5	1152	5	DYTN	2	207564562	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	25	207564562	35634811	124	11627											
CPO	130749	hgsc.bcm.edu	37	chr2	207834049	207834049	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagaccatggaggctgtgctGtcagtcctggatgatgtgta	8	11	15	7	0	1	2	1	1	0	1	2	5	2	4	2	3	1	3	2	3	1	1	rs139758524	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:207834049G>C	ENST00000272852.3	+	9	1060	c.1014G>C	c.(1012-1014)ctG>ctC	p.L338L		NM_173077.2	NP_775100.1	Q8IVL8	CBPO_HUMAN	carboxypeptidase O	338						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)		AGGCTGTGCTGTCAGTCCTGG	0.542																																					p.L338L		Atlas-SNP	.											.	CPO	42	.	0			c.G1014C						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	164	129	141		1014	-0.4	0.3	2	dbSNP_134	141	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	CPO	NM_173077.2		0,5,6498	CC,CG,GG		0.0465,0.0227,0.0384		338/375	207834049	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	130749	exon9			TGTGCTGTCAGTC		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.1014G>C	2.37:g.207834049G>C		119	0	0		119	59	0.495798	NM_173077	Q2M277|Q7RTW7	Silent	SNP	ENST00000272852.3	37	CCDS2372.1																																																																																			G|1.000;C|0.000	0.000	strong		0.542	CPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202040.2	NM_173077		C	207834049	G	C	207834049	2	2	28	1	0	0	0	0	0	0	0	1	3822	1364	48	4		4	CPO	2	207834049	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	269487	207834049	35365324	125	11628											
IDH1	3417	hgsc.bcm.edu	37	chr2	209108317	209108317	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	attatacatccccatggcaaCaccaccaccttctgtagagg	12	9	6	14	0	1	1	0	0	1	1	2	1	2	1	5	2	2	2	5	2	4	4	rs34218846	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:209108317C>T	ENST00000415913.1	-	6	913	c.532G>A	c.(532-534)Gtt>Att	p.V178I	IDH1_ENST00000345146.2_Missense_Mutation_p.V178I|IDH1_ENST00000446179.1_Missense_Mutation_p.V178I	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	178			V -> I (in dbSNP:rs34218846).		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.V178I(8)		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)		CCCATGGCAACACCACCACCT	0.418			Mis		gliobastoma								C|||	247	0.0493211	0.0893	0.0447	5008	,	,		18161	0.0069		0.0477	False		,,,				2504	0.044				p.V178I	Pancreas(158;264 1958 3300 35450 36047)	Atlas-SNP	.		Dom	yes		2	2q33.3	3417	"isocitrate dehydrogenase 1 (NADP+), soluble"		O	IDH1,colon,carcinoma,0,9	IDH1	6310	9	8	Substitution - Missense(8)	thyroid(8)	c.G532A						PASS	.	C	ILE/VAL	356,4050	182.6+/-210.3	12,332,1859	69	65	66		532	5.5	1	2	dbSNP_126	66	457,8143	137.1+/-194.1	7,443,3850	yes	missense	IDH1	NM_005896.2	29	19,775,5709	TT,TC,CC		5.314,8.0799,6.251	possibly-damaging	178/415	209108317	813,12193	2203	4300	6503	SO:0001583	missense	3417	exon6			TGGCAACACCACC		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.532G>A	2.37:g.209108317C>T	ENSP00000390265:p.Val178Ile	70	0	0		66	33	0.5	NM_005896	Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	90	0.04120879120879121	38	0.07723577235772358	16	0.04419889502762431	2	0.0034965034965034965	34	0.044854881266490766	C	20.3	3.968029	0.74131	0.080799	0.05314	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913	T;T;T	0.77229	-1.08;-1.08;-1.08	5.52	5.52	0.82312	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	T	0.32376	0.0827	L	0.54863	1.705	0.80722	D	1	D	0.63046	0.992	D	0.74674	0.984	T	0.66701	-0.5857	10	0.44086	T	0.13	-13.6312	19.7971	0.96490	0.0:1.0:0.0:0.0	rs34218846	178	O75874	IDHC_HUMAN	I	178	ENSP00000260985:V178I;ENSP00000410513:V178I;ENSP00000390265:V178I	ENSP00000260985:V178I	V	-	1	0	IDH1	208816562	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	6.126000	0.71635	2.762000	0.94881	0.484000	0.47621	GTT	C|0.946;T|0.054	0.054	strong		0.418	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1			T	209108317	C	T	209108317	3	4	28	1	0	0	0	0	1	0	0	0	7503	478	17	2	732	2	IDH1	2	209108317	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1274268	209108317	34091056	126	11629											
PTH2R	5746	hgsc.bcm.edu	37	chr2	209358262	209358262	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcctgccacactctttccacGaggagaccaaggaagatagt	12	7	10	12	1	1	2	0	0	1	2	2	5	2	3	4	2	1	0	4	2	3	2	rs140566891	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:209358262G>A	ENST00000272847.2	+	13	1744	c.1531G>A	c.(1531-1533)Gag>Aag	p.E511K	AC019185.4_ENST00000424628.1_RNA|PTH2R_ENST00000413482.1_3'UTR	NM_005048.2	NP_005039.1	P49190	PTH2R_HUMAN	parathyroid hormone 2 receptor	511					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)	CTCTTTCCACGAGGAGACCAA	0.527													G|||	2	0.000399361	0.0	0.0	5008	,	,		20843	0.0		0.001	False		,,,				2504	0.001				p.E511K		Atlas-SNP	.											.	PTH2R	92	.	0			c.G1531A						PASS	.	G	LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	84	77	80		1531	4.4	0.3	2	dbSNP_134	80	11,8589	8.4+/-32.0	0,11,4289	yes	missense	PTH2R	NM_005048.2	56	0,12,6491	AA,AG,GG		0.1279,0.0227,0.0923	probably-damaging	511/551	209358262	12,12994	2203	4300	6503	SO:0001583	missense	5746	exon13			TTCCACGAGGAGA	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.1531G>A	2.37:g.209358262G>A	ENSP00000272847:p.Glu511Lys	136	0	0		179	96	0.536313	NM_005048	Q8N429	Missense_Mutation	SNP	ENST00000272847.2	37	CCDS2383.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	20.8	4.050399	0.75960	2.27E-4	0.001279	ENSG00000144407	ENST00000272847	T	0.58060	0.36	5.31	4.43	0.53597	.	0.000000	0.36740	U	0.002436	T	0.48750	0.1517	M	0.73962	2.25	0.31256	N	0.693435	P;P	0.51240	0.892;0.943	B;B	0.37144	0.178;0.242	T	0.62358	-0.6871	9	.	.	.	.	11.6752	0.51425	0.0868:0.0:0.9132:0.0	.	400;511	B4DFN8;P49190	.;PTH2R_HUMAN	K	511	ENSP00000272847:E511K	.	E	+	1	0	PTH2R	209066507	1.000000	0.71417	0.276000	0.24689	0.027000	0.11550	4.221000	0.58574	1.236000	0.43740	0.591000	0.81541	GAG	G|0.999;A|0.001	0.001	strong		0.527	PTH2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256519.2	NM_005048		A	209358262	G	A	209358262	3	1	28	1	0	0	0	0	1	0	0	0	12773	1059	37	1	1581	1	PTH2R	2	209358262	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	249945	209358262	33841111	127	11630											
ERBB4	2066	hgsc.bcm.edu	37	chr2	212587119	212587119	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcttattctgttacttacgTggacatttcttgacacagaa	10	17	6	8	1	3	2	0	1	3	1	3	3	3	3	0	1	2	1	0	1	4	7	rs77309171	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:212587119T>C	ENST00000342788.4	-	7	1192	c.882A>G	c.(880-882)ccA>ccG	p.P294P	ERBB4_ENST00000484474.1_5'Flank|ERBB4_ENST00000436443.1_Splice_Site_p.P294P|ERBB4_ENST00000402597.1_Splice_Site_p.P294P	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	294	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)	GTTACTTACGTGGACATTTCT	0.313										TSP Lung(8;0.080)			T|||	10	0.00199681	0.0	0.0029	5008	,	,		16437	0.0		0.005	False		,,,				2504	0.0031				p.P294P		Atlas-SNP	.											.	ERBB4	480	.	0			c.A882G						PASS	.	T	,	1,4405	2.1+/-5.4	0,1,2202	146	133	138		882,882	1.9	1	2	dbSNP_131	138	46,8554	30.1+/-81.4	0,46,4254	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	ERBB4	NM_001042599.1,NM_005235.2	,	0,47,6456	CC,CT,TT		0.5349,0.0227,0.3614	,	294/1293,294/1309	212587119	47,12959	2203	4300	6503	SO:0001630	splice_region_variant	2066	exon7			CTTACGTGGACAT	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.883+1A>G	2.37:g.212587119T>C		132	0	0		109	61	0.559633	NM_001042599	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Silent	SNP	ENST00000342788.4	37	CCDS2394.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	12.44	1.939839	0.34189	2.27E-4	0.005349	ENSG00000178568	ENST00000260943	.	.	.	5.67	1.89	0.25635	.	.	.	.	.	T	0.43765	0.1262	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29119	-1.0022	4	.	.	.	.	4.9983	0.14251	0.2313:0.1302:0.0:0.6385	.	.	.	.	R	294	.	.	H	-	2	0	ERBB4	212295364	0.999000	0.42202	1.000000	0.80357	0.976000	0.68499	0.474000	0.22148	0.078000	0.16900	-0.344000	0.07964	CAC	T|0.997;C|0.003	0.003	strong		0.313	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599	Silent	C	212587119	T	C	212587119	5	2	28	1	0	0	0	0	0	0	1	0	5211	1710	59	3	3132	3	ERBB4	2	212587119	Splice_Site	SNP	T	TCGA-G8-6914-01A-11D-2210-10	3228857	212587119	30612254	128	11631											
TNS1	7145	hgsc.bcm.edu	37	chr2	218686643	218686643	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgctgtccgtgccacagacTccacatagctccggggctct	6	8	10	17	3	1	1	0	0	1	1	4	1	4	1	5	2	2	3	5	2	1	1	rs112371945	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:218686643T>A	ENST00000171887.4	-	23	3532	c.3080A>T	c.(3079-3081)gAg>gTg	p.E1027V	TNS1_ENST00000430930.1_Missense_Mutation_p.E1006V|TNS1_ENST00000419504.1_Missense_Mutation_p.E1014V	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1027					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)		TGCCACAGACTCCACATAGCT	0.627													T|||	3	0.000599042	0.0	0.0	5008	,	,		17582	0.0		0.003	False		,,,				2504	0.0				p.E1027V		Atlas-SNP	.											.	TNS1	251	.	0			c.A3080T						PASS	.	T	VAL/GLU	0,4400		0,0,2200	16	18	17		3080	4.1	1	2	dbSNP_132	17	12,8582		0,12,4285	yes	missense	TNS1	NM_022648.4	121	0,12,6485	AA,AT,TT		0.1396,0.0,0.0924	probably-damaging	1027/1736	218686643	12,12982	2200	4297	6497	SO:0001583	missense	7145	exon23			ACAGACTCCACAT	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.3080A>T	2.37:g.218686643T>A	ENSP00000171887:p.Glu1027Val	95	0	0		126	68	0.539683	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	22	0.010073260073260074	6	0.012195121951219513	2	0.0055248618784530384	6	0.01048951048951049	8	0.010554089709762533	T	22.7	4.320848	0.81469	0.0	0.001396	ENSG00000079308	ENST00000171887;ENST00000446688;ENST00000419504;ENST00000430930	D;T;D;D	0.93859	-3.3;1.79;-3.19;-3.12	4.11	4.11	0.48088	.	0.793281	0.11520	N	0.555860	D	0.92675	0.7672	L	0.32530	0.975	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.984	D;D;P	0.85130	0.997;0.994;0.844	D	0.91199	0.4990	10	0.62326	D	0.03	.	13.4292	0.61044	0.0:0.0:0.0:1.0	.	1027;1006;1014	Q9HBL0;E9PGF5;E9PF55	TENS1_HUMAN;.;.	V	1027;165;1014;1006	ENSP00000171887:E1027V;ENSP00000394171:E165V;ENSP00000408724:E1014V;ENSP00000406016:E1006V	ENSP00000171887:E1027V	E	-	2	0	TNS1	218394888	1.000000	0.71417	0.994000	0.49952	0.792000	0.44763	7.653000	0.83643	1.631000	0.50456	0.459000	0.35465	GAG	T|0.996;A|0.004	0.004	strong		0.627	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		A	218686643	T	A	218686643	3	1	28	1	0	0	0	0	1	0	0	0	16358	1551	54	5	2171	5	TNS1	2	218686643	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	6099524	218686643	24512730	129	11632											
STK36	27148	hgsc.bcm.edu	37	chr2	219553423	219553423	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccctcatgtcacccagatcCtgaaaggcatcttggagggt	9	10	10	12	0	3	2	2	1	1	1	5	3	5	3	3	3	0	1	3	3	1	1	rs45586733	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:219553423C>G	ENST00000295709.3	+	12	1663	c.1384C>G	c.(1384-1386)Ctg>Gtg	p.L462V	STK36_ENST00000440309.1_Missense_Mutation_p.L462V|STK36_ENST00000392105.3_Missense_Mutation_p.L462V|STK36_ENST00000392106.2_Missense_Mutation_p.L462V	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)		CACCCAGATCCTGAAAGGCAT	0.498													C|||	22	0.00439297	0.0	0.0101	5008	,	,		22309	0.0		0.0149	False		,,,				2504	0.0				p.L462V		Atlas-SNP	.											.	STK36	111	.	0			c.C1384G						PASS	.	C	VAL/LEU	17,4389	25.3+/-52.1	0,17,2186	223	210	215		1384	4.5	1	2	dbSNP_127	215	124,8476	66.0+/-128.3	0,124,4176	yes	missense	STK36	NM_015690.4	32	0,141,6362	GG,GC,CC		1.4419,0.3858,1.0841	probably-damaging	462/1316	219553423	141,12865	2203	4300	6503	SO:0001583	missense	27148	exon12			CAGATCCTGAAAG	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.1384C>G	2.37:g.219553423C>G	ENSP00000295709:p.Leu462Val	148	0	0		171	86	0.502924	NM_015690		Missense_Mutation	SNP	ENST00000295709.3	37	CCDS2421.1	13	0.005952380952380952	0	0.0	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	C	17.41	3.382206	0.61845	0.003858	0.014419	ENSG00000163482	ENST00000295709;ENST00000392106;ENST00000392105;ENST00000440309	T;T;T;T	0.78126	-1.15;-1.15;-1.11;-1.15	5.38	4.51	0.55191	.	0.000000	0.34110	N	0.004245	T	0.73976	0.3656	L	0.27053	0.805	0.42723	D	0.993681	D;D	0.71674	0.998;0.997	D;D	0.68765	0.96;0.913	T	0.80125	-0.1513	10	0.72032	D	0.01	-8.883	12.2295	0.54480	0.0:0.9212:0.0:0.0788	rs45586733	462;462	Q9NRP7-2;Q9NRP7	.;STK36_HUMAN	V	462	ENSP00000295709:L462V;ENSP00000375955:L462V;ENSP00000375954:L462V;ENSP00000394095:L462V	ENSP00000295709:L462V	L	+	1	2	STK36	219261667	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	1.753000	0.38359	1.505000	0.48720	-0.140000	0.14226	CTG	C|0.990;G|0.010	0.010	strong		0.498	STK36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256723.2			G	219553423	C	G	219553423	3	3	28	1	0	0	0	0	1	0	0	0	15317	680	24	4	1426	4	STK36	2	219553423	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	866780	219553423	23645950	130	11633											
CUL3	8452	hgsc.bcm.edu	37	chr2	225365109	225365109	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctcaaaagcatgtcttggTgctggtgggatgttgcactt	8	14	12	7	0	2	0	1	0	2	0	3	1	2	1	0	3	3	4	0	3	2	3	rs41373148	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:225365109T>A	ENST00000264414.4	-	11	1919	c.1581A>T	c.(1579-1581)gcA>gcT	p.A527A	CUL3_ENST00000409096.1_Silent_p.A503A|CUL3_ENST00000344951.4_Silent_p.A461A|CUL3_ENST00000409777.1_Silent_p.A503A	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	527					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)		CATGTCTTGGTGCTGGTGGGA	0.403													T|||	27	0.00539137	0.0015	0.0043	5008	,	,		16507	0.0		0.0169	False		,,,				2504	0.0051				p.A533A		Atlas-SNP	.											.	CUL3	96	.	0			c.A1599T						PASS	.	T		18,4388	26.2+/-53.5	0,18,2185	206	186	193		1581	3.6	1	2	dbSNP_127	193	154,8446	74.2+/-136.8	3,148,4149	no	coding-synonymous	CUL3	NM_003590.3		3,166,6334	AA,AT,TT		1.7907,0.4085,1.3225		527/769	225365109	172,12834	2203	4300	6503	SO:0001819	synonymous_variant	8452	exon11			TCTTGGTGCTGGT	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.1581A>T	2.37:g.225365109T>A		96	0	0		87	41	0.471264	NM_001257198	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Silent	SNP	ENST00000264414.4	37	CCDS2462.1																																																																																			T|0.987;A|0.013	0.013	strong		0.403	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2			A	225365109	T	A	225365109	2	1	28	1	0	0	0	0	0	0	0	1	4058	1683	59	5		5	CUL3	2	225365109	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	5811686	225365109	17834264	131	11634											
SP100	6672	hgsc.bcm.edu	37	chr2	231327184	231327184	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gactctgaaggatccactgaCgttgatgagcccttagaagt	11	10	11	9	1	1	5	0	4	1	1	2	7	2	6	2	1	1	1	2	1	3	2	rs35985492	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:231327184C>T	ENST00000264052.5	+	10	1363	c.1008C>T	c.(1006-1008)gaC>gaT	p.D336D	SP100_ENST00000409824.1_Silent_p.D311D|SP100_ENST00000341950.4_Silent_p.D336D|SP100_ENST00000409341.1_Silent_p.D336D|SP100_ENST00000409897.1_Silent_p.D301D|SP100_ENST00000340126.4_Silent_p.D336D|SP100_ENST00000427101.2_Silent_p.D311D|SP100_ENST00000409112.1_Silent_p.D336D	NM_003113.3	NP_003104.2	P23497	SP100_HUMAN	SP100 nuclear antigen	336	Sufficient to mediate interaction with ETS1.				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)		GATCCACTGACGTTGATGAGC	0.493													C|||	18	0.00359425	0.0	0.0086	5008	,	,		19642	0.0		0.0089	False		,,,				2504	0.0031				p.D336D		Atlas-SNP	.											.	SP100	167	.	0			c.C1008T						PASS	.	C	,,,,,	11,4395	17.9+/-39.9	0,11,2192	126	110	115		1008,1008,1008,933,903,1008	-4.5	0	2	dbSNP_126	115	121,8479	62.8+/-124.8	1,119,4180	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SP100	NM_001080391.1,NM_001206701.1,NM_001206702.1,NM_001206703.1,NM_001206704.1,NM_003113.3	,,,,,	1,130,6372	TT,TC,CC		1.407,0.2497,1.0149	,,,,,	336/886,336/689,336/481,311/453,301/446,336/880	231327184	132,12874	2203	4300	6503	SO:0001819	synonymous_variant	6672	exon10			CACTGACGTTGAT	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.1008C>T	2.37:g.231327184C>T		95	0	0		124	54	0.435484	NM_001206702	B4DDX5|B8ZZD8|E7EUA7|E9PH61|F8WFE2|O75450|Q13343|Q8TE34|Q96F70|Q96T24|Q96T95|Q9NP33|Q9UE32	Silent	SNP	ENST00000264052.5	37	CCDS2477.1	9	0.004120879120879121	0	0.0	3	0.008287292817679558	0	0.0	6	0.0079155672823219	C	2.308	-0.358494	0.05138	0.002497	0.01407	ENSG00000067066	ENST00000413284	.	.	.	4.09	-4.5	0.03493	.	.	.	.	.	T	0.15176	0.0366	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.29458	-1.0011	4	.	.	.	.	5.3685	0.16127	0.0:0.3668:0.307:0.3261	rs35985492	.	.	.	M	12	.	.	T	+	2	0	SP100	231035428	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.439000	0.02414	-0.840000	0.04206	-2.265000	0.00278	ACG	C|0.992;T|0.008	0.008	strong		0.493	SP100-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256914.2	NM_003113		T	231327184	C	T	231327184	2	4	28	1	0	0	0	0	0	0	0	1	14975	535	19	1		1	SP100	2	231327184	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	5962075	231327184	11872189	132	11635											
COPS7B	64708	hgsc.bcm.edu	37	chr2	232653358	232653358	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aaaggtaccagtggctcagcCctcactgctctcataagcca	11	8	8	14	0	3	0	3	0	1	0	4	0	3	0	3	2	4	3	3	2	3	2	rs11557625	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:232653358C>T	ENST00000350033.3	+	2	219	c.78C>T	c.(76-78)gcC>gcT	p.A26A	COPS7B_ENST00000410017.1_Silent_p.A26A|COPS7B_ENST00000409295.1_Intron|COPS7B_ENST00000373608.3_Silent_p.A26A|COPS7B_ENST00000409091.1_Intron|COPS7B_ENST00000410024.1_Silent_p.A26A	NM_001282949.1|NM_022730.1	NP_001269878.1|NP_073567.1	Q9H9Q2	CSN7B_HUMAN	COP9 signalosome subunit 7B	26					cullin deneddylation (GO:0010388)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				large_intestine(1)|liver(1)|lung(4)|ovary(1)|skin(1)	8		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Renal(207;0.025)		Epithelial(121;1.36e-12)|BRCA - Breast invasive adenocarcinoma(100;0.00136)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		GTGGCTCAGCCCTCACTGCTC	0.507													C|||	31	0.0061901	0.0	0.0086	5008	,	,		16814	0.0		0.0239	False		,,,				2504	0.001				p.A26A		Atlas-SNP	.											.	COPS7B	14	.	0			c.C78T						PASS	.	C		27,4379	33.5+/-64.1	0,27,2176	84	86	85		78	1.2	1	2	dbSNP_120	85	195,8405	85.8+/-148.2	2,191,4107	no	coding-synonymous	COPS7B	NM_022730.1		2,218,6283	TT,TC,CC		2.2674,0.6128,1.7069		26/265	232653358	222,12784	2203	4300	6503	SO:0001819	synonymous_variant	64708	exon2			CTCAGCCCTCACT	AK022674	CCDS2488.1, CCDS63152.1, CCDS63153.1, CCDS63154.1, CCDS74668.1	2q37.1	2013-03-14	2013-03-14		ENSG00000144524	ENSG00000144524			16760	protein-coding gene	gene with protein product			"COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 7B", "COP9 constitutive photomorphogenic homolog subunit 7B (Arabidopsis)"			9707402	Standard	NM_001282950		Approved	CSN7B	uc002vsg.1	Q9H9Q2	OTTHUMG00000133228	ENST00000350033.3:c.78C>T	2.37:g.232653358C>T		71	0	0		98	47	0.479592	NM_022730	Q53S22|Q5BJG3|Q9H7V6	Silent	SNP	ENST00000350033.3	37	CCDS2488.1																																																																																			C|0.988;T|0.012	0.012	strong		0.507	COPS7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256964.2	NM_022730		T	232653358	C	T	232653358	2	4	28	1	0	0	0	0	0	0	0	1	3741	610	22	2		2	COPS7B	2	232653358	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1326174	232653358	10546015	133	11636											
ALPP	250	hgsc.bcm.edu	37	chr2	233245982	233245982	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctggcccctggcaaggcccGggacaggaaggcctacacgg	8	3	16	14	2	0	0	0	0	0	0	0	2	0	2	4	7	1	2	4	7	3	1	rs143205011	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:233245982G>A	ENST00000392027.2	+	10	1483	c.1214G>A	c.(1213-1215)cGg>cAg	p.R405Q	AC068134.8_ENST00000441266.1_RNA|AC068134.8_ENST00000439072.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	405					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)		GGCAAGGCCCGGGACAGGAAG	0.637													G|||	5	0.000998403	0.0	0.0029	5008	,	,		19588	0.0		0.001	False		,,,				2504	0.002				p.R405Q		Atlas-SNP	.											.	ALPP	53	.	0			c.G1214A						PASS	.	A	GLN/ARG	3,4395		0,3,2196	24	30	28		1214	-4.7	0	2	dbSNP_134	28	41,8505		0,41,4232	no	missense	ALPP	NM_001632.3	43	0,44,6428	AA,AG,GG		0.4798,0.0682,0.3399	benign	405/536	233245982	44,12900	2199	4273	6472	SO:0001583	missense	250	exon10			AGGCCCGGGACAG	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.1214G>A	2.37:g.233245982G>A	ENSP00000375881:p.Arg405Gln	342	0	0		393	121	0.307888	NM_001632	P05188|P06861|Q53S78|Q96DB7	Missense_Mutation	SNP	ENST00000392027.2	37	CCDS2490.1	.	.	.	.	.	.	.	.	.	.	g	1.358	-0.589485	0.03799	6.82E-4	0.004798	ENSG00000163283	ENST00000392027	D	0.96491	-4.03	2.35	-4.69	0.03299	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	2.308210	0.01558	N	0.019990	D	0.85084	0.5616	N	0.02368	-0.58	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.81695	-0.0816	10	0.13108	T	0.6	.	0.4192	0.00453	0.392:0.1279:0.2136:0.2665	.	405	P05187	PPB1_HUMAN	Q	405	ENSP00000375881:R405Q	ENSP00000375881:R405Q	R	+	2	0	ALPP	232954226	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-6.351000	0.00069	-3.004000	0.00275	-3.289000	0.00047	CGG	G|0.999;A|0.001	0.001	strong		0.637	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632		A	233245982	G	A	233245982	3	1	28	1	0	0	0	0	1	0	0	0	548	1116	39	1	1252	1	ALPP	2	233245982	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	592624	233245982	9953391	134	11637											
UGT1A10	54575	hgsc.bcm.edu	37	chr2	234545932	234545932	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atcaatttggttgttgcgaaCggactttgttttggactatc	8	17	10	6	2	1	0	1	0	0	0	2	3	1	2	0	3	2	3	0	3	3	7	rs45574333	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:234545932C>T	ENST00000344644.5	+	1	833	c.764C>T	c.(763-765)aCg>aTg	p.T255M	UGT1A10_ENST00000373445.1_Missense_Mutation_p.T255M|UGT1A1_ENST00000373450.4_Intron	NM_019075.2	NP_061948.1	Q9HAW8	UD110_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A10	255					cellular glucuronidation (GO:0052695)|flavone metabolic process (GO:0051552)	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)|protein kinase C binding (GO:0005080)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(2)|skin(3)	32		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0334)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;1.96e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000468)|Lung(119;0.00381)|LUSC - Lung squamous cell carcinoma(224;0.008)	Acetaminophen(DB00316)|Etodolac(DB00749)|Losartan(DB00678)|Mycophenolate mofetil(DB00688)|Valproic Acid(DB00313)	TTGTTGCGAACGGACTTTGTT	0.433																																					p.T255M		Atlas-SNP	.											.	UGT1A10	71	.	0			c.C764T						PASS	.	C	MET/THR,	1,4405	2.1+/-5.4	0,1,2202	254	253	253		764,	1.5	0.5	2	dbSNP_127	253	11,8589	8.4+/-32.0	0,11,4289	no	missense,intron	UGT1A10,UGT1A8	NM_019075.2,NM_019076.4	81,	0,12,6491	TT,TC,CC		0.1279,0.0227,0.0923	,	255/531,	234545932	12,12994	2203	4300	6503	SO:0001583	missense	54575	exon1			TGCGAACGGACTT	U39550	CCDS33403.1	2q37	2010-03-05	2005-07-20		ENSG00000242515	ENSG00000242515		"UDP glucuronosyltransferases"	12531	other	complex locus constituent		606435	"UDP glycosyltransferase 1 family, polypeptide A10"			9295054, 9325166	Standard	NM_019075		Approved	UGT1J		Q9HAW8	OTTHUMG00000059121	ENST00000344644.5:c.764C>T	2.37:g.234545932C>T	ENSP00000343838:p.Thr255Met	133	0	0		153	71	0.464052	NM_019075	O00474|Q6NT91|Q7Z6H8	Missense_Mutation	SNP	ENST00000344644.5	37	CCDS33403.1	.	.	.	.	.	.	.	.	.	.	C	7.102	0.574235	0.13623	2.27E-4	0.001279	ENSG00000242515	ENST00000344644;ENST00000373445	T;T	0.67345	-0.26;-0.26	3.52	1.53	0.23141	.	.	.	.	.	T	0.69726	0.3143	M	0.84433	2.695	0.09310	N	1	B;B	0.34147	0.234;0.438	B;B	0.42163	0.269;0.378	T	0.63418	-0.6642	9	0.51188	T	0.08	.	3.4103	0.07356	0.3801:0.3993:0.1324:0.0881	rs45574333	255;255	Q9HAW8;Q7Z6H8	UD110_HUMAN;.	M	255	ENSP00000343838:T255M;ENSP00000362544:T255M	ENSP00000343838:T255M	T	+	2	0	UGT1A10	234210671	0.000000	0.05858	0.532000	0.27989	0.802000	0.45316	-2.845000	0.00735	0.254000	0.21573	0.405000	0.27470	ACG	C|0.999;T|0.001	0.001	strong		0.433	UGT1A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130986.1	NM_019075		T	234545932	C	T	234545932	3	4	28	1	0	0	0	0	1	0	0	0	16960	536	19	1	766	1	UGT1A10	2	234545932	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1299950	234545932	8653441	135	11638											
MLPH	79083	hgsc.bcm.edu	37	chr2	238434245	238434245	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	gacagccccatgtgcttagtCcctcacagatgagtcctgct	8	10	9	14	0	1	2	1	1	0	1	3	3	3	2	4	0	3	2	4	0	1	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:238434245C>G	ENST00000264605.3	+	7	971	c.677C>G	c.(676-678)tCc>tGc	p.S226C	MLPH_ENST00000338530.4_Splice_Site_p.S226C|MLPH_ENST00000410032.1_Intron|MLPH_ENST00000468178.1_3'UTR|MLPH_ENST00000445024.2_Splice_Site_p.S226C|MLPH_ENST00000409373.1_Splice_Site_p.S186C	NM_024101.5	NP_077006.1	Q9BV36	MELPH_HUMAN	melanophilin	226					melanocyte differentiation (GO:0030318)|melanosome localization (GO:0032400)|protein targeting (GO:0006605)	cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|microtubule plus-end (GO:0035371)|stress fiber (GO:0001725)	metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(3)|large_intestine(2)|lung(11)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)		TGTGCTTAGTCCCTCACAGAT	0.607																																					p.S226C		Atlas-SNP	.											.	MLPH	41	.	0			c.C677G						PASS	.						42	44	44					2																	238434245		2203	4300	6503	SO:0001630	splice_region_variant	79083	exon7			CTTAGTCCCTCAC	AY358857	CCDS2518.1, CCDS42836.1, CCDS63172.1, CCDS63173.1	2q37.2	2014-09-17			ENSG00000115648	ENSG00000115648			29643	protein-coding gene	gene with protein product		606526				11980908, 11504925	Standard	NM_024101		Approved	l1Rk3, l(1)-3Rk, Slac-2a, ln, exophilin-3	uc002vwt.3	Q9BV36	OTTHUMG00000133298	ENST00000264605.3:c.676-1C>G	2.37:g.238434245C>G		74	0	0		104	51	0.490385	NM_001042467	B3KSS2|B4DKW7|G5E9G5|Q9HA71	Missense_Mutation	SNP	ENST00000264605.3	37	CCDS2518.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.10|10.10	1.256882|1.256882	0.22965|0.22965	.|.	.|.	ENSG00000115648|ENSG00000115648	ENST00000437893|ENST00000264605;ENST00000445024;ENST00000338530;ENST00000409373	T|T;T;T;T	0.30182|0.29655	1.54|1.92;1.91;1.78;1.56	3.35|3.35	1.51|1.51	0.23008|0.23008	.|.	.|2.607010	.|0.01744	.|N	.|0.029577	T|T	0.39655|0.39655	0.1086|0.1086	L|L	0.40543|0.40543	1.245|1.245	0.35469|0.35469	D|D	0.797185|0.797185	.|B;D;B;D;B;B	.|0.71674	.|0.017;0.998;0.085;0.986;0.137;0.021	.|B;P;B;P;B;B	.|0.56216	.|0.017;0.747;0.071;0.794;0.149;0.023	T|T	0.32640|0.32640	-0.9899|-0.9899	7|10	0.87932|0.54805	D|T	0|0.06	-6.1716|-6.1716	4.7792|4.7792	0.13194|0.13194	0.0:0.6545:0.2219:0.1236|0.0:0.6545:0.2219:0.1236	.|.	.|226;110;226;186;226;226	.|B4DKW7;Q6UWC1;A8KA64;B8ZZ97;Q9BV36-2;Q9BV36	.|.;.;.;.;.;MELPH_HUMAN	A|C	33|226;226;226;186	ENSP00000412438:P33A|ENSP00000264605:S226C;ENSP00000414849:S226C;ENSP00000341845:S226C;ENSP00000386780:S186C	ENSP00000412438:P33A|ENSP00000264605:S226C	P|S	+|+	1|2	0|0	MLPH|MLPH	238098984|238098984	0.730000|0.730000	0.28100|0.28100	0.950000|0.950000	0.38849|0.38849	0.777000|0.777000	0.43975|0.43975	-0.133000|-0.133000	0.10451|0.10451	0.424000|0.424000	0.26061|0.26061	0.563000|0.563000	0.77884|0.77884	CCC|TCC	.	.	none		0.607	MLPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257083.2	NM_024101	Missense_Mutation	G	238434245	C	G	238434245	5	3	28	1	0	0	0	0	0	0	1	0	9642	869	30	4	699	4	MLPH	2	238434245	Splice_Site	SNP	C	TCGA-G8-6914-01A-11D-2210-10	3888313	238434245	4765128	136	11639											
LRRFIP1	9208	hgsc.bcm.edu	37	chr2	238662005	238662005	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggctatggtttccaatgcTcagctagacaatgaaaagac	15	9	9	8	0	1	3	1	1	0	2	2	3	2	3	1	2	2	4	1	2	7	3	rs200278632		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:238662005T>C	ENST00000392000.4	+	8	654	c.537T>C	c.(535-537)gcT>gcC	p.A179A	LRRFIP1_ENST00000244815.5_Silent_p.A155A|LRRFIP1_ENST00000289175.6_Silent_p.A123A|LRRFIP1_ENST00000308482.9_Silent_p.A307A	NM_001137552.1	NP_001131024.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1	179					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)		TTTCCAATGCTCAGCTAGACA	0.388																																					p.A307A		Atlas-SNP	.											.	LRRFIP1	171	.	0			c.T921C						PASS	.						89	88	89					2																	238662005		2203	4300	6503	SO:0001819	synonymous_variant	9208	exon15			CAATGCTCAGCTA	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.537T>C	2.37:g.238662005T>C		50	0	0		45	12	0.266667	NM_001137550	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Silent	SNP	ENST00000392000.4	37	CCDS46552.1																																																																																			T|1.000;C|0.000	0.000	strong		0.388	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	NM_004735		C	238662005	T	C	238662005	2	2	28	1	0	0	0	0	0	0	0	1	9036	1538	54	3		3	LRRFIP1	2	238662005	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	227760	238662005	4537368	137	11640											
KLHL30	377007	hgsc.bcm.edu	37	chr2	239059578	239059578	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acgtggagatggaggcctacGacacggttcgggacacctgg	9	6	16	10	4	0	1	0	0	0	1	1	5	0	3	2	6	1	1	2	6	1	2	rs369686635	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:239059578G>A	ENST00000409223.1	+	8	1716	c.1609G>A	c.(1609-1611)Gac>Aac	p.D537N	KLHL30_ENST00000305959.4_Missense_Mutation_p.D519N			Q0D2K2	KLH30_HUMAN	kelch-like family member 30	537										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)		GGAGGCCTACGACACGGTTCG	0.672													G|||	2	0.000399361	0.0	0.0014	5008	,	,		11838	0.001		0.0	False		,,,				2504	0.0				p.D537N		Atlas-SNP	.											.	KLHL30	79	.	0			c.G1609A						PASS	.	G	ASN/ASP	1,4305		0,1,2152	19	27	24		1609	4.7	0.9	2		24	0,8462		0,0,4231	no	missense	KLHL30	NM_198582.3	23	0,1,6383	AA,AG,GG		0.0,0.0232,0.0078	possibly-damaging	537/579	239059578	1,12767	2153	4231	6384	SO:0001583	missense	377007	exon8			GCCTACGACACGG		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.1609G>A	2.37:g.239059578G>A	ENSP00000386389:p.Asp537Asn	138	0	0		138	65	0.471014	NM_198582	Q6ZUS1	Missense_Mutation	SNP	ENST00000409223.1	37	CCDS46555.2	.	.	.	.	.	.	.	.	.	.	G	13.29	2.192615	0.38707	2.32E-4	0.0	ENSG00000168427	ENST00000409223;ENST00000305959	T;T	0.70869	-0.52;-0.52	4.66	4.66	0.58398	Kelch-type beta propeller (1);	0.075656	0.64402	D	0.000008	T	0.61825	0.2378	L	0.52011	1.625	0.41539	D	0.988502	P	0.47841	0.901	B	0.34652	0.187	T	0.67620	-0.5624	10	0.39692	T	0.17	.	16.4605	0.84033	0.0:0.0:1.0:0.0	.	537	Q0D2K2	KLH30_HUMAN	N	537;519	ENSP00000386389:D537N;ENSP00000302386:D519N	ENSP00000302386:D519N	D	+	1	0	KLHL30	238724317	1.000000	0.71417	0.923000	0.36655	0.269000	0.26545	3.349000	0.52217	2.423000	0.82170	0.561000	0.74099	GAC	.	.	weak		0.672	KLHL30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328518.1	NM_198582		A	239059578	G	A	239059578	3	1	28	1	0	0	0	0	1	0	0	0	8393	1058	37	1	1635	1	KLHL30	2	239059578	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	397573	239059578	4139795	138	11641											
HDAC4	9759	hgsc.bcm.edu	37	chr2	240036848	240036848	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcgctctcaatgggctcctgCttcacctgcacgccggcctg	4	10	10	17	3	2	0	2	0	1	0	5	0	3	0	4	2	2	4	4	2	1	1	rs114495208	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:240036848C>T	ENST00000345617.3	-	13	2468	c.1677G>A	c.(1675-1677)aaG>aaA	p.K559K	HDAC4_ENST00000541256.1_Silent_p.K533K|HDAC4_ENST00000543185.1_Silent_p.K143K	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	559					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)		TGGGCTCCTGCTTCACCTGCA	0.687													C|||	13	0.00259585	0.0	0.0072	5008	,	,		16655	0.0		0.007	False		,,,				2504	0.001				p.K559K		Atlas-SNP	.											.	HDAC4	127	.	0			c.G1677A						PASS	.	C		5,4401	9.9+/-24.2	0,5,2198	66	73	71		1677	2.3	1	2	dbSNP_132	71	44,8554	29.0+/-79.6	0,44,4255	no	coding-synonymous	HDAC4	NM_006037.3		0,49,6453	TT,TC,CC		0.5117,0.1135,0.3768		559/1085	240036848	49,12955	2203	4299	6502	SO:0001819	synonymous_variant	9759	exon13			CTCCTGCTTCACC	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.1677G>A	2.37:g.240036848C>T		89	0	0		125	60	0.48	NM_006037	Q9UND6	Silent	SNP	ENST00000345617.3	37	CCDS2529.1																																																																																			C|0.996;T|0.004	0.004	strong		0.687	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037		T	240036848	C	T	240036848	2	4	28	1	0	0	0	0	0	0	0	1	7018	796	28	2		2	HDAC4	2	240036848	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	977270	240036848	3162525	139	11642											
KIF1A	547	hgsc.bcm.edu	37	chr2	241702599	241702599	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcacctctgctccatctcctGcttcatgtcgatgccctgct	4	14	6	17	1	4	0	2	0	2	0	7	1	5	0	4	0	4	3	4	0	0	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:241702599G>A	ENST00000320389.7	-	20	2064	c.1906C>T	c.(1906-1908)Cag>Tag	p.Q636*	KIF1A_ENST00000498729.2_Nonsense_Mutation_p.Q645*	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	636					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)		TCCATCTCCTGCTTCATGTCG	0.672																																					p.Q645X		Atlas-SNP	.											.	KIF1A	152	.	0			c.C1933T						PASS	.						24	27	26					2																	241702599		2151	4252	6403	SO:0001587	stop_gained	547	exon21			TCTCCTGCTTCAT	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.1906C>T	2.37:g.241702599G>A	ENSP00000322791:p.Gln636*	37	0	0		52	16	0.307692	NM_001244008	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Nonsense_Mutation	SNP	ENST00000320389.7	37	CCDS46561.1	.	.	.	.	.	.	.	.	.	.	G	42	9.413377	0.99164	.	.	ENSG00000130294	ENST00000320389;ENST00000498729;ENST00000373308;ENST00000404283	.	.	.	3.81	2.91	0.33838	.	0.000000	0.85682	U	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	.	11.8555	0.52435	0.089:0.0:0.911:0.0	.	.	.	.	X	636;645;645;645	.	ENSP00000322791:Q636X	Q	-	1	0	KIF1A	241351272	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.644000	0.83416	0.695000	0.31675	0.467000	0.42956	CAG	.	.	none		0.672	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483		A	241702599	G	A	241702599	4	1	28	1	0	0	0	0	0	1	0	0	8292	1328	46	2	3278	2	KIF1A	2	241702599	Nonsense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1665751	241702599	1496774	140	11643											
ANO7	50636	hgsc.bcm.edu	37	chr2	242144308	242144308	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acaggctggctcctgccagcGgcagtggtgggcacactggt	6	7	16	12	1	0	0	0	0	0	0	1	0	1	0	2	6	2	4	2	6	0	0	rs139761441	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:242144308G>A	ENST00000274979.8	+	10	1183	c.1080G>A	c.(1078-1080)gcG>gcA	p.A360A	ANO7_ENST00000402430.3_Silent_p.A359A	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	360					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						TCCTGCCAGCGGCAGTGGTGG	0.632													G|||	4	0.000798722	0.0	0.0	5008	,	,		16608	0.0		0.004	False		,,,				2504	0.0				p.A360A		Atlas-SNP	.											.	ANO7	136	.	0			c.G1080A						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	52	55	54		1080	-5.1	0.1	2	dbSNP_134	54	23,8577	16.6+/-54.9	0,23,4277	no	coding-synonymous	ANO7	NM_001001891.3		0,25,6478	AA,AG,GG		0.2674,0.0454,0.1922		360/934	242144308	25,12981	2203	4300	6503	SO:0001819	synonymous_variant	50636	exon10			GCCAGCGGCAGTG	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.1080G>A	2.37:g.242144308G>A		64	0	0		71	37	0.521127	NM_001001891	Q6IWH6	Silent	SNP	ENST00000274979.8	37	CCDS33423.1																																																																																			G|0.998;A|0.002	0.002	strong		0.632	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891		A	242144308	G	A	242144308	2	1	28	1	0	0	0	0	0	0	0	1	702	1103	39	1		1	ANO7	2	242144308	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	441709	242144308	1055065	141	11644											
FARP2	9855	hgsc.bcm.edu	37	chr2	242380734	242380734	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cccagagcatctcattccccGagggattgaggactcctgcc	8	8	10	15	1	1	2	1	1	1	1	4	5	3	4	5	2	2	1	5	2	0	2	rs146443541	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:242380734G>A	ENST00000264042.3	+	13	1344	c.1174G>A	c.(1174-1176)Gag>Aag	p.E392K	FARP2_ENST00000545004.1_Missense_Mutation_p.E392K|FARP2_ENST00000373287.4_Missense_Mutation_p.E392K	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	392					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)		CTCATTCCCCGAGGGATTGAG	0.473													G|||	6	0.00119808	0.0	0.0	5008	,	,		17915	0.0		0.005	False		,,,				2504	0.001				p.E392K		Atlas-SNP	.											.	FARP2	92	.	0			c.G1174A						PASS	.	G	LYS/GLU	2,4404	4.2+/-10.8	0,2,2201	104	98	100		1174	5.3	0.5	2	dbSNP_134	100	19,8581	14.0+/-48.4	0,19,4281	yes	missense	FARP2	NM_014808.2	56	0,21,6482	AA,AG,GG		0.2209,0.0454,0.1615	benign	392/1055	242380734	21,12985	2203	4300	6503	SO:0001583	missense	9855	exon13			TTCCCCGAGGGAT	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.1174G>A	2.37:g.242380734G>A	ENSP00000264042:p.Glu392Lys	74	0	0		74	25	0.337838	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Missense_Mutation	SNP	ENST00000264042.3	37	CCDS33424.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	12.87	2.068509	0.36470	4.54E-4	0.002209	ENSG00000006607	ENST00000264042;ENST00000545004;ENST00000373287;ENST00000413432	T;T;T;D	0.81739	-0.88;-1.46;-1.46;-1.53	5.28	5.28	0.74379	.	0.652894	0.15957	N	0.236471	T	0.64605	0.2613	L	0.34521	1.04	0.47153	D	0.999336	P;P;P	0.52577	0.954;0.907;0.76	B;B;B	0.39840	0.311;0.246;0.091	T	0.68179	-0.5477	10	0.09843	T	0.71	.	18.9095	0.92477	0.0:0.0:1.0:0.0	.	392;392;392	O94887-2;F5GZ84;O94887	.;.;FARP2_HUMAN	K	392;392;392;79	ENSP00000264042:E392K;ENSP00000443876:E392K;ENSP00000362384:E392K;ENSP00000412772:E79K	ENSP00000264042:E392K	E	+	1	0	FARP2	242029407	1.000000	0.71417	0.484000	0.27391	0.024000	0.10985	8.223000	0.89779	2.472000	0.83506	0.655000	0.94253	GAG	G|0.999;A|0.001	0.001	strong		0.473	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1			A	242380734	G	A	242380734	3	1	28	1	0	0	0	0	1	0	0	0	5685	1059	37	1	1220	1	FARP2	2	242380734	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	236426	242380734	818639	142	11645											
CHL1	10752	hgsc.bcm.edu	37	chr3	407785	407785	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcctttgaaattaatggcAcagaagatggcaggtaggta	15	9	12	5	0	0	3	0	1	0	2	0	3	0	3	1	4	1	4	1	4	6	4	rs143907501	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:407785A>G	ENST00000256509.2	+	15	2380	c.1738A>G	c.(1738-1740)Aca>Gca	p.T580A	CHL1-AS1_ENST00000417612.1_RNA|CHL1_ENST00000397491.2_Missense_Mutation_p.T564A|CHL1-AS1_ENST00000608098.1_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)		AATTAATGGCACAGAAGATGG	0.363																																					p.T580A		Atlas-SNP	.											.	CHL1	242	.	0			c.A1738G						PASS	.	A	ALA/THR	0,4406		0,0,2203	115	111	112		1738	4.9	0.8	3	dbSNP_134	112	3,8597	3.0+/-9.4	0,3,4297	no	missense	CHL1	NM_006614.2	58	0,3,6500	GG,GA,AA		0.0349,0.0,0.0231	benign	580/1225	407785	3,13003	2203	4300	6503	SO:0001583	missense	10752	exon13			AATGGCACAGAAG	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.1738A>G	3.37:g.407785A>G	ENSP00000256509:p.Thr580Ala	65	0	0		93	60	0.645161	NM_001253388	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	37	CCDS2556.1	.	.	.	.	.	.	.	.	.	.	A	14.44	2.535747	0.45176	0.0	3.49E-4	ENSG00000134121	ENST00000256509;ENST00000397491	T;T	0.13778	2.56;2.56	4.94	4.94	0.65067	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.056117	0.64402	D	0.000001	T	0.19208	0.0461	L	0.55103	1.725	0.37538	D	0.918193	B;B;B	0.26363	0.003;0.004;0.147	B;B;B	0.35727	0.026;0.016;0.209	T	0.08534	-1.0717	10	0.59425	D	0.04	.	13.1152	0.59295	1.0:0.0:0.0:0.0	.	564;564;580	B3KX75;O00533;O00533-2	.;CHL1_HUMAN;.	A	580;564	ENSP00000256509:T580A;ENSP00000380628:T564A	ENSP00000256509:T580A	T	+	1	0	CHL1	382785	1.000000	0.71417	0.824000	0.32777	0.973000	0.67179	4.982000	0.63825	1.980000	0.57719	0.460000	0.39030	ACA	A|1.000;G|0.000	0.000	strong		0.363	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614		G	407785	A	G	407785	3	3	28	1	0	0	0	0	1	0	0	0	3351	159	6	3	1788	3	CHL1	3	407785	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10		407785	197614645	143	11646											
GPD1L	23171	hgsc.bcm.edu	37	chr3	32181723	32181723	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttggcatccttgtagggcAtagacgagggccccgagggg	7	8	16	10	2	1	1	0	0	1	1	2	3	2	1	3	5	0	3	3	5	2	4	rs72552293	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:32181723A>G	ENST00000282541.5	+	4	571	c.370A>G	c.(370-372)Ata>Gta	p.I124V		NM_015141.3	NP_055956.1	Q8N335	GPD1L_HUMAN	glycerol-3-phosphate dehydrogenase 1-like	124			I -> V (in SIDS; significant reduction of sodium current when coexpressed with SCN5A in HEK cells; dbSNP:rs72552293). {ECO:0000269|PubMed:17967976}.		carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|glycerol-3-phosphate catabolic process (GO:0046168)|glycerophospholipid biosynthetic process (GO:0046474)|NAD metabolic process (GO:0019674)|NADH metabolic process (GO:0006734)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase C signaling (GO:0090038)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate (GO:0002027)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|ventricular cardiac muscle cell action potential (GO:0086005)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycerol-3-phosphate dehydrogenase complex (GO:0009331)|plasma membrane (GO:0005886)	glycerol-3-phosphate dehydrogenase [NAD+] activity (GO:0004367)|ion channel binding (GO:0044325)|NAD binding (GO:0051287)|sodium channel regulator activity (GO:0017080)			large_intestine(4)|lung(7)|ovary(1)	12						CTTGTAGGGCATAGACGAGGG	0.483													A|||	4	0.000798722	0.0	0.0014	5008	,	,		20191	0.0		0.003	False		,,,				2504	0.0				p.I124V		Atlas-SNP	.											.	GPD1L	25	.	0			c.A370G	GRCh37	CM074889	GPD1L	M	rs72552293	PASS	.	A	VAL/ILE	0,4406		0,0,2203	172	184	180	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	370	3.9	1	3	dbSNP_130	180	14,8586	10.5+/-38.8	0,14,4286	yes	missense	GPD1L	NM_015141.3	29	0,14,6489	GG,GA,AA		0.1628,0.0,0.1076	benign	124/352	32181723	14,12992	2203	4300	6503	SO:0001583	missense	23171	exon4			TAGGGCATAGACG	D42047	CCDS33729.1	3p22.3	2014-09-17			ENSG00000152642	ENSG00000152642			28956	protein-coding gene	gene with protein product		611778				7788527	Standard	NM_015141		Approved	KIAA0089	uc003cew.3	Q8N335	OTTHUMG00000155846	ENST00000282541.5:c.370A>G	3.37:g.32181723A>G	ENSP00000282541:p.Ile124Val	92	0	0		110	42	0.381818	NM_015141	A8K9U3|Q14702|Q9BRM5	Missense_Mutation	SNP	ENST00000282541.5	37	CCDS33729.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	1.632	-0.518627	0.04171	0.0	0.001628	ENSG00000152642	ENST00000429432;ENST00000282541;ENST00000425459;ENST00000431009	T;T;T;T	0.59772	0.24;0.24;0.42;0.24	5.06	3.87	0.44632	Glycerol-3-phosphate dehydrogenase, NAD-dependent, N-terminal (1);NAD(P)-binding domain (1);	0.042492	0.85682	D	0.000000	T	0.31979	0.0814	N	0.11818	0.18	0.54753	A	0.999988	B	0.02656	0.0	B	0.04013	0.001	T	0.30679	-0.9970	9	0.10377	T	0.69	-17.6846	7.0731	0.25189	0.7746:0.15:0.0753:0.0	.	124	Q8N335	GPD1L_HUMAN	V	85;124;77;85	ENSP00000393861:I85V;ENSP00000282541:I124V;ENSP00000408770:I77V;ENSP00000416518:I85V	ENSP00000282541:I124V	I	+	1	0	GPD1L	32156727	0.908000	0.30866	0.992000	0.48379	0.825000	0.46686	2.058000	0.41374	0.979000	0.38497	0.533000	0.62120	ATA	A|0.998;G|0.002	0.002	strong		0.483	GPD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341975.2	NM_015141		G	32181723	A	G	32181723	3	3	28	1	0	0	0	0	1	0	0	0	6613	217	8	3	384	3	GPD1L	3	32181723	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	31773938	32181723	165840707	144	11647											
ARPP21	10777	hgsc.bcm.edu	37	chr3	35780947	35780947	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagcccagctatgtaatcGcctctacaggccagcagctt	10	8	9	14	1	1	0	0	0	1	0	2	0	1	0	3	1	6	5	3	1	3	4	rs151173813	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:35780947G>A	ENST00000187397.4	+	17	2239	c.1783G>A	c.(1783-1785)Gcc>Acc	p.A595T	ARPP21_ENST00000444190.1_Missense_Mutation_p.A576T|ARPP21_ENST00000458225.1_Missense_Mutation_p.A596T|ARPP21_ENST00000337271.5_Missense_Mutation_p.A576T|ARPP21_ENST00000417925.1_Missense_Mutation_p.A596T	NM_016300.4	NP_057384.2	Q9UBL0	ARP21_HUMAN	cAMP-regulated phosphoprotein, 21kDa	595	Gln-rich.				cellular response to heat (GO:0034605)	cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)	p.A595T(1)		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						CTATGTAATCGCCTCTACAGG	0.627													G|||	7	0.00139776	0.0	0.0029	5008	,	,		15714	0.0		0.003	False		,,,				2504	0.002				p.A596T		Atlas-SNP	.											ARPP21,NS,NS,0,1	ARPP21	153	1	1	Substitution - Missense(1)	large_intestine(1)	c.G1786A						PASS	.	G	THR/ALA	3,4403	6.2+/-15.9	0,3,2200	58	59	58		1783	4.1	0.4	3	dbSNP_134	58	37,8563	25.7+/-73.6	0,37,4263	yes	missense	ARPP21	NM_016300.4	58	0,40,6463	AA,AG,GG		0.4302,0.0681,0.3076	benign	595/813	35780947	40,12966	2203	4300	6503	SO:0001583	missense	10777	exon16			GTAATCGCCTCTA	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.1783G>A	3.37:g.35780947G>A	ENSP00000187397:p.Ala595Thr	108	0	0		135	76	0.562963	NM_001267619	B4DG96|Q49AK3|Q49AS6|Q4G0V4|Q6NYC3|Q86V31|Q9UF93	Missense_Mutation	SNP	ENST00000187397.4	37	CCDS2661.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	G	11.71	1.719677	0.30503	6.81E-4	0.004302	ENSG00000172995	ENST00000458225;ENST00000337271;ENST00000444190;ENST00000187397;ENST00000417925	T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03	5.96	4.14	0.48551	.	0.068903	0.56097	N	0.000036	T	0.19127	0.0459	L	0.31476	0.935	0.31779	N	0.631164	B;B;B;B	0.32543	0.067;0.375;0.011;0.067	B;B;B;B	0.28385	0.023;0.089;0.006;0.023	T	0.19418	-1.0306	10	0.12103	T	0.63	-7.922	10.8408	0.46715	0.1502:0.0:0.8498:0.0	.	596;118;595;576	Q9UBL0-3;Q9UBL0-5;Q9UBL0;Q9UBL0-4	.;.;ARP21_HUMAN;.	T	596;576;576;595;596	ENSP00000414351:A596T;ENSP00000337792:A576T;ENSP00000405276:A576T;ENSP00000187397:A595T;ENSP00000412326:A596T	ENSP00000187397:A595T	A	+	1	0	ARPP21	35755951	1.000000	0.71417	0.406000	0.26421	0.573000	0.36030	4.374000	0.59543	1.499000	0.48617	0.655000	0.94253	GCC	G|0.997;A|0.003	0.003	strong		0.627	ARPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253334.2	NM_198399		A	35780947	G	A	35780947	3	1	28	1	0	0	0	0	1	0	0	0	978	1087	38	1	1854	1	ARPP21	3	35780947	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	3599224	35780947	162241483	145	11648											
DLEC1	9940	hgsc.bcm.edu	37	chr3	38136476	38136476	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tcaagtgctaccccgacaagGagactgccttctccatcatg	10	9	8	14	1	3	1	2	0	1	1	4	3	3	1	4	1	3	1	4	1	3	2	rs34290809	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:38136476G>A	ENST00000308059.6	+	13	2047	c.2026G>A	c.(2026-2028)Gag>Aag	p.E676K	DLEC1_ENST00000346219.3_Missense_Mutation_p.E676K|DLEC1_ENST00000452631.2_Missense_Mutation_p.E676K					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)		CCCCGACAAGGAGACTGCCTT	0.552													G|||	4	0.000798722	0.0	0.0	5008	,	,		23233	0.0		0.004	False		,,,				2504	0.0				p.E676K		Atlas-SNP	.											.	DLEC1	278	.	0			c.G2026A						PASS	.	G	LYS/GLU,LYS/GLU	1,4115		0,1,2057	84	91	89		2026,2026	5.4	0	3	dbSNP_126	89	21,8383		0,21,4181	yes	missense,missense	DLEC1	NM_007335.2,NM_007337.2	56,56	0,22,6238	AA,AG,GG		0.2499,0.0243,0.1757	possibly-damaging,possibly-damaging	676/1756,676/1779	38136476	22,12498	2058	4202	6260	SO:0001583	missense	9940	exon13			GACAAGGAGACTG	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.2026G>A	3.37:g.38136476G>A	ENSP00000308597:p.Glu676Lys	112	0	0		142	55	0.387324	NM_007337		Missense_Mutation	SNP	ENST00000308059.6	37	CCDS2672.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	11.20	1.569663	0.28003	2.43E-4	0.002499	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.05513	3.45;3.43;3.67	5.39	5.39	0.77823	.	0.244689	0.40908	D	0.000992	T	0.13841	0.0335	M	0.67953	2.075	0.09310	N	1	P;D;P	0.53745	0.804;0.962;0.804	P;P;P	0.52481	0.485;0.7;0.485	T	0.13495	-1.0507	10	0.54805	T	0.06	-14.4509	8.3585	0.32344	0.1685:0.0:0.8315:0.0	rs34290809	676;676;676	F8W6T4;Q9Y238-3;Q9Y238	.;.;DLEC1_HUMAN	K	676	ENSP00000308597:E676K;ENSP00000315914:E676K;ENSP00000410427:E676K	ENSP00000308597:E676K	E	+	1	0	DLEC1	38111480	0.996000	0.38824	0.037000	0.18230	0.085000	0.17905	2.689000	0.46993	2.506000	0.84524	0.655000	0.94253	GAG	G|0.998;A|0.002	0.002	strong		0.552	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		A	38136476	G	A	38136476	3	1	28	1	0	0	0	0	1	0	0	0	4554	1175	41	2	2076	2	DLEC1	3	38136476	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2355529	38136476	159885954	146	11649											
SLC22A14	9389	hgsc.bcm.edu	37	chr3	38357067	38357067	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggggaggatggcctcagacTcaagtggccacgttgtccgg	8	7	16	10	2	2	1	2	0	0	1	3	3	3	3	3	6	0	1	3	6	1	1	rs34256819	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:38357067T>C	ENST00000273173.4	+	8	1488	c.1397T>C	c.(1396-1398)cTc>cCc	p.L466P	SLC22A14_ENST00000448498.1_Missense_Mutation_p.L466P	NM_004803.3	NP_004794.2	Q9Y267	S22AE_HUMAN	solute carrier family 22, member 14	466			L -> P (in dbSNP:rs34256819).		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)		GGCCTCAGACTCAAGTGGCCA	0.587													T|||	4	0.000798722	0.0015	0.0	5008	,	,		19422	0.0		0.002	False		,,,				2504	0.0				p.L466P		Atlas-SNP	.											.	SLC22A14	64	.	0			c.T1397C						PASS	.	T	PRO/LEU	2,4404	4.2+/-10.8	0,2,2201	96	84	88		1397	3.7	0.1	3	dbSNP_126	88	32,8568	22.8+/-68.1	0,32,4268	yes	missense	SLC22A14	NM_004803.3	98	0,34,6469	CC,CT,TT		0.3721,0.0454,0.2614	probably-damaging	466/595	38357067	34,12972	2203	4300	6503	SO:0001583	missense	9389	exon8			TCAGACTCAAGTG	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.1397T>C	3.37:g.38357067T>C	ENSP00000273173:p.Leu466Pro	64	0	0		106	31	0.292453	NM_004803	A0AVS9|A1L4H6|B2RCX3|Q6DJT3	Missense_Mutation	SNP	ENST00000273173.4	37	CCDS2677.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	14.48	2.549489	0.45383	4.54E-4	0.003721	ENSG00000144671	ENST00000448498;ENST00000273173	T;T	0.66815	-0.23;-0.23	3.66	3.66	0.41972	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.270402	0.15269	U	0.271366	T	0.56426	0.1984	N	0.02011	-0.69	0.20638	N	0.999874	D	0.76494	0.999	D	0.69307	0.963	T	0.50276	-0.8847	10	0.87932	D	0	.	8.9423	0.35738	0.0:0.0:0.0:1.0	rs34256819	466	Q9Y267	S22AE_HUMAN	P	466	ENSP00000396283:L466P;ENSP00000273173:L466P	ENSP00000273173:L466P	L	+	2	0	SLC22A14	38332071	0.184000	0.23200	0.067000	0.19924	0.003000	0.03518	0.714000	0.25808	1.873000	0.54277	0.533000	0.62120	CTC	T|0.997;C|0.003	0.003	strong		0.587	SLC22A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253742.3	NM_004803		C	38357067	T	C	38357067	3	2	28	1	0	0	0	0	1	0	0	0	14460	1551	54	3	1427	3	SLC22A14	3	38357067	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	220591	38357067	159665363	147	11650											
ALS2CL	259173	hgsc.bcm.edu	37	chr3	46717175	46717175	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	taaggcaactcgcagcagacCcctgtgagtcaatgagagag	13	6	12	10	1	1	4	1	2	0	2	2	5	1	4	2	1	2	3	2	1	3	1	rs142971127	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:46717175C>T	ENST00000318962.4	-	20	2271	c.2188G>A	c.(2188-2190)Ggt>Agt	p.G730S	ALS2CL_ENST00000383742.3_Splice_Site_p.G77S|ALS2CL_ENST00000415953.1_Splice_Site_p.G730S	NM_147129.3	NP_667340.2	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like	730					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)		CGCAGCAGACCCCTGTGAGTC	0.577													C|||	17	0.00339457	0.0008	0.0086	5008	,	,		20439	0.0		0.0089	False		,,,				2504	0.001				p.G730S		Atlas-SNP	.											.	ALS2CL	78	.	0			c.G2188A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY	9,4397	15.5+/-35.6	0,9,2194	81	76	78		2188,2188,229	4.7	1	3	dbSNP_134	78	89,8511	49.4+/-109.1	1,87,4212	yes	missense-near-splice,missense-near-splice,missense-near-splice	ALS2CL	NM_001190707.1,NM_147129.3,NM_182775.2	56,56,56	1,96,6406	TT,TC,CC		1.0349,0.2043,0.7535	probably-damaging,probably-damaging,probably-damaging	730/954,730/954,77/301	46717175	98,12908	2203	4300	6503	SO:0001630	splice_region_variant	259173	exon20			GCAGACCCCTGTG	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.2187-1G>A	3.37:g.46717175C>T		33	0	0		44	15	0.340909	NM_001190707	Q32MA1|Q6AI56|Q6ZNC5|Q6ZNC7|Q6ZTL4|Q86YD2|Q8N9U1|Q8NAL7	Missense_Mutation	SNP	ENST00000318962.4	37	CCDS2743.1	12	0.005494505494505495	0	0.0	4	0.011049723756906077	0	0.0	8	0.010554089709762533	C	12.27	1.886260	0.33348	0.002043	0.010349	ENSG00000178038	ENST00000318962;ENST00000415953;ENST00000383742	T;T;T	0.30182	1.54;1.54;1.54	4.66	4.66	0.58398	.	0.195229	0.35970	N	0.002863	T	0.31638	0.0803	L	0.60455	1.87	0.45541	D	0.998496	D	0.62365	0.991	P	0.55785	0.784	T	0.06643	-1.0815	10	0.10377	T	0.69	.	13.236	0.59969	0.0:1.0:0.0:0.0	.	730	Q60I27	AL2CL_HUMAN	S	730;730;77	ENSP00000313670:G730S;ENSP00000413223:G730S;ENSP00000373248:G77S	ENSP00000313670:G730S	G	-	1	0	ALS2CL	46692179	1.000000	0.71417	1.000000	0.80357	0.077000	0.17291	1.715000	0.37971	2.592000	0.87571	0.561000	0.74099	GGT	C|0.993;T|0.007	0.007	strong		0.577	ALS2CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250567.3	NM_147129	Missense_Mutation	T	46717175	C	T	46717175	5	4	28	1	0	0	0	0	0	0	1	0	551	637	22	2	701	2	ALS2CL	3	46717175	Splice_Site	SNP	C	TCGA-G8-6914-01A-11D-2210-10	8360108	46717175	151305255	148	11651											
PRSS45	29122	hgsc.bcm.edu	37	chr3	46784532	46784532	+	Intron	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccatgataaacacctcagcCtcctgcagctctggggtcag	9	9	9	14	0	3	1	2	1	1	0	5	1	5	1	4	2	4	2	4	2	2	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:46784532C>T	ENST00000460241.1	-	4	1129				PRSS45_ENST00000442359.2_Silent_p.E108E			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						ACACCTCAGCCTCCTGCAGCT	0.577																																					p.E108E	Pancreas(41;915 1239 11561 17469)	Atlas-SNP	.											.	PRSS45	12	.	0			c.G324A						PASS	.						61	69	66					3																	46784532		2133	4258	6391	SO:0001627	intron_variant	377047	exon3			CTCAGCCTCCTGC	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+5582G>A	3.37:g.46784532C>T		60	0	0		78	45	0.576923	NM_199183		Silent	SNP	ENST00000460241.1	37	CCDS2745.1																																																																																			.	.	none		0.577	PRSS50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354544.1			T	46784532	C	T	46784532	1	4	28	0	1	0	0	0	0	0	0	0	12641	680	24	2		2	PRSS45	3	46784532	Intron	SNP	C	TCGA-G8-6914-01A-11D-2210-10	67357	46784532	151237898	149	11652											
TMEM89	440955	hgsc.bcm.edu	37	chr3	48658924	48658924	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtggcctgtgagcgccgcCgcccctgcagtatcttgcgg	3	9	15	14	4	1	1	0	1	1	0	1	1	1	1	5	3	3	2	5	3	1	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:48658924C>T	ENST00000330862.3	-	1	364	c.266G>A	c.(265-267)cGg>cAg	p.R89Q		NM_001008269.1	NP_001008270.1	A2RUT3	TMM89_HUMAN	transmembrane protein 89	89						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|lung(1)|stomach(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000286)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		TGAGCGCCGCCGCCCCTGCAG	0.622																																					p.R89Q		Atlas-SNP	.											TMEM89,NS,carcinoma,+1,1	TMEM89	10	1	0			c.G266A						PASS	.						31	30	30					3																	48658924		2203	4299	6502	SO:0001583	missense	440955	exon1			CGCCGCCGCCCCT	AX657016	CCDS33751.1	3p21.31	2005-11-02			ENSG00000183396	ENSG00000183396			32372	protein-coding gene	gene with protein product							Standard	NM_001008269		Approved		uc011bbo.2	A2RUT3	OTTHUMG00000156647	ENST00000330862.3:c.266G>A	3.37:g.48658924C>T	ENSP00000329557:p.Arg89Gln	144	0	0		194	108	0.556701	NM_001008269		Missense_Mutation	SNP	ENST00000330862.3	37	CCDS33751.1	.	.	.	.	.	.	.	.	.	.	C	15.01	2.705879	0.48412	.	.	ENSG00000183396	ENST00000330862	T	0.57107	0.42	4.79	4.79	0.61399	.	0.182364	0.26899	N	0.021928	T	0.51483	0.1677	L	0.36672	1.1	0.09310	N	1	D	0.64830	0.994	P	0.51229	0.663	T	0.47222	-0.9134	10	0.44086	T	0.13	-19.7761	13.2009	0.59767	0.0:1.0:0.0:0.0	.	89	A2RUT3	TMM89_HUMAN	Q	89	ENSP00000329557:R89Q	ENSP00000329557:R89Q	R	-	2	0	TMEM89	48633928	.	.	0.011000	0.14972	0.055000	0.15305	.	.	2.492000	0.84095	0.462000	0.41574	CGG	.	.	none		0.622	TMEM89-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345046.1	NM_001008269		T	48658924	C	T	48658924	3	4	28	1	0	0	0	0	1	0	0	0	16228	652	23	1	220	1	TMEM89	3	48658924	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1874392	48658924	149363506	150	11653											
CCDC71	64925	hgsc.bcm.edu	37	chr3	49201140	49201140	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgcatggcagggtagacacCtggataaaggtgggtgggga	10	6	18	7	1	0	1	0	0	0	1	0	3	0	3	2	7	0	3	2	7	3	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:49201140C>T	ENST00000321895.6	-	2	608	c.502G>A	c.(502-504)Ggt>Agt	p.G168S		NM_022903.3	NP_075054.3	Q8IV32	CCD71_HUMAN	coiled-coil domain containing 71	168										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)		GGGTAGACACCTGGATAAAGG	0.587																																					p.G168S		Atlas-SNP	.											.	CCDC71	33	.	0			c.G502A						PASS	.						54	58	56					3																	49201140		2203	4300	6503	SO:0001583	missense	64925	exon2			AGACACCTGGATA	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.502G>A	3.37:g.49201140C>T	ENSP00000319006:p.Gly168Ser	56	0	0		76	16	0.210526	NM_022903	Q6IPE2|Q9H8H4|Q9H9F1	Missense_Mutation	SNP	ENST00000321895.6	37	CCDS2790.1	.	.	.	.	.	.	.	.	.	.	C	16.31	3.086570	0.55861	.	.	ENSG00000177352	ENST00000321895	T	0.36699	1.24	5.44	4.57	0.56435	.	0.068720	0.56097	D	0.000035	T	0.52533	0.1740	M	0.66939	2.045	0.36735	D	0.881929	D	0.60160	0.987	P	0.57425	0.82	T	0.65080	-0.6255	10	0.72032	D	0.01	-30.1272	14.1305	0.65250	0.0:0.9276:0.0:0.0724	.	168	Q8IV32	CCD71_HUMAN	S	168	ENSP00000319006:G168S	ENSP00000319006:G168S	G	-	1	0	CCDC71	49176144	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	3.531000	0.53546	1.313000	0.45069	0.585000	0.79938	GGT	.	.	none		0.587	CCDC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345980.1	NM_022903		T	49201140	C	T	49201140	3	4	28	1	0	0	0	0	1	0	0	0	2846	681	24	2	905	2	CCDC71	3	49201140	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	542216	49201140	148821290	151	11654											
USP4	7375	hgsc.bcm.edu	37	chr3	49321424	49321424	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtcaccatgacccacctgaTtgggaattctacgactgtgt	10	11	9	11	1	2	2	1	2	1	0	2	4	2	3	3	1	1	0	3	1	2	3	rs41290700	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:49321424T>C	ENST00000265560.4	-	19	2582	c.2536A>G	c.(2536-2538)Atc>Gtc	p.I846V	USP4_ENST00000351842.4_Missense_Mutation_p.I799V	NM_003363.3	NP_003354.2	Q13107	UBP4_HUMAN	ubiquitin specific peptidase 4 (proto-oncogene)	846	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)		ACCCACCTGATTGGGAATTCT	0.463													T|||	15	0.00299521	0.0008	0.0058	5008	,	,		22007	0.0		0.005	False		,,,				2504	0.0051				p.I846V		Atlas-SNP	.											.	USP4	72	.	0			c.A2536G						PASS	.	T	VAL/ILE,VAL/ILE	8,4398	14.3+/-33.2	0,8,2195	133	130	131		2536,2395	3.3	1	3	dbSNP_127	131	59,8541	36.9+/-92.0	0,59,4241	yes	missense,missense	USP4	NM_003363.3,NM_199443.2	29,29	0,67,6436	CC,CT,TT		0.686,0.1816,0.5151	benign,benign	846/964,799/917	49321424	67,12939	2203	4300	6503	SO:0001583	missense	7375	exon19			ACCTGATTGGGAA	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.2536A>G	3.37:g.49321424T>C	ENSP00000265560:p.Ile846Val	114	0	0		147	54	0.367347	NM_003363	A8K6Y0|C9IY91|O43452|O43453|Q08AK8	Missense_Mutation	SNP	ENST00000265560.4	37	CCDS2793.1	5|5	0.0022893772893772895|0.0022893772893772895	0|0	0.0|0.0	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	T|T	12.07|12.07	1.827377|1.827377	0.32329|0.32329	0.001816|0.001816	0.00686|0.00686	ENSG00000114316|ENSG00000114316	ENST00000351842;ENST00000265560|ENST00000431357	T;T|.	0.33654|.	1.4;1.4|.	5.63|5.63	3.35|3.35	0.38373|0.38373	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);|.	0.097121|.	0.64402|.	N|.	0.000002|.	T|T	0.31104|0.31104	0.0786|0.0786	N|N	0.26092|0.26092	0.79|0.79	0.80722|0.80722	D|D	1|1	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.12156|.	0.003;0.007;0.003|.	T|T	0.10200|0.10200	-1.0640|-1.0640	10|5	0.29301|.	T|.	0.29|.	.|.	4.7623|4.7623	0.13113|0.13113	0.0:0.5066:0.0:0.4934|0.0:0.5066:0.0:0.4934	rs41290700|rs41290700	799;846;846|.	Q13107-2;Q13107;Q08AK7|.	.;UBP4_HUMAN;.|.	V|S	799;846|584	ENSP00000341028:I799V;ENSP00000265560:I846V|.	ENSP00000265560:I846V|.	I|N	-|-	1|2	0|0	USP4|USP4	49296428|49296428	0.963000|0.963000	0.33076|0.33076	0.998000|0.998000	0.56505|0.56505	0.743000|0.743000	0.42351|0.42351	1.848000|1.848000	0.39309|0.39309	1.176000|1.176000	0.42840|0.42840	-0.408000|-0.408000	0.06270|0.06270	ATC|AAT	T|0.995;C|0.005	0.005	strong		0.463	USP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346069.1	NM_199443		C	49321424	T	C	49321424	3	2	28	1	0	0	0	0	1	0	0	0	17086	1493	52	3	371	3	USP4	3	49321424	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	120284	49321424	148701006	152	11655											
BSN	8927	hgsc.bcm.edu	37	chr3	49689642	49689642	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gccccagacccaggcctgagCctagccaagaaccagcagca	12	2	10	17	0	0	3	0	1	0	2	0	3	0	3	7	1	5	2	7	1	3	1	rs150021639	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:49689642C>T	ENST00000296452.4	+	5	2767	c.2653C>T	c.(2653-2655)Cct>Tct	p.P885S		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	885					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)		CAGGCCTGAGCCTAGCCAAGA	0.652													C|||	34	0.00678914	0.0023	0.0058	5008	,	,		17544	0.0		0.0249	False		,,,				2504	0.002				p.P885S		Atlas-SNP	.											.	BSN	272	.	0			c.C2653T						PASS	.	C	SER/PRO	12,4394	19.1+/-41.9	0,12,2191	25	26	26		2653	1.3	1	3	dbSNP_134	26	152,8446	71.6+/-134.2	0,152,4147	yes	missense	BSN	NM_003458.3	74	0,164,6338	TT,TC,CC		1.7679,0.2724,1.2612	benign	885/3927	49689642	164,12840	2203	4299	6502	SO:0001583	missense	8927	exon5			CCTGAGCCTAGCC	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.2653C>T	3.37:g.49689642C>T	ENSP00000296452:p.Pro885Ser	105	0	0		154	87	0.564935	NM_003458	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	37	CCDS2800.1	24	0.01098901098901099	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	18	0.023746701846965697	C	5.535	0.283703	0.10458	0.002724	0.017679	ENSG00000164061	ENST00000296452	T	0.15256	2.44	4.81	1.26	0.21427	.	1.048100	0.07469	N	0.901973	T	0.02083	0.0065	N	0.02011	-0.69	0.09310	N	0.99999	B	0.02656	0.0	B	0.04013	0.001	T	0.40757	-0.9546	10	0.08179	T	0.78	.	0.9669	0.01407	0.2611:0.3854:0.1373:0.2161	.	885	Q9UPA5	BSN_HUMAN	S	885	ENSP00000296452:P885S	ENSP00000296452:P885S	P	+	1	0	BSN	49664646	0.991000	0.36638	0.979000	0.43373	0.947000	0.59692	1.573000	0.36472	0.253000	0.21552	-0.225000	0.12378	CCT	C|0.987;T|0.013	0.013	strong		0.652	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458		T	49689642	C	T	49689642	3	4	28	1	0	0	0	0	1	0	0	0	1532	739	26	2	2671	2	BSN	3	49689642	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	368218	49689642	148332788	153	11656											
RBM5	10181	hgsc.bcm.edu	37	chr3	50147061	50147061	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcagtgaccaccacctcagcGgctgtagtgtcccagagtcc	8	7	11	15	1	1	2	1	1	0	1	3	2	3	2	5	1	1	3	5	1	1	1	rs116604207	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:50147061G>A	ENST00000347869.3	+	15	1393	c.1218G>A	c.(1216-1218)gcG>gcA	p.A406A	RBM5_ENST00000441812.2_3'UTR	NM_005778.3	NP_005769.1	P52756	RBM5_HUMAN	RNA binding motif protein 5	406	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)		CCACCTCAGCGGCTGTAGTGT	0.488													G|||	2	0.000399361	0.0	0.0	5008	,	,		14240	0.0		0.002	False		,,,				2504	0.0				p.A406A		Atlas-SNP	.											.	RBM5	76	.	0			c.G1218A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	203	183	190		1218	-12.1	0.5	3	dbSNP_132	190	20,8580	14.6+/-50.1	0,20,4280	no	coding-synonymous	RBM5	NM_005778.2		0,21,6482	AA,AG,GG		0.2326,0.0227,0.1615		406/816	50147061	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	10181	exon15			CTCAGCGGCTGTA	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.1218G>A	3.37:g.50147061G>A		167	0	0		193	69	0.357513	NM_005778	B2RA45|B4DM16|B4DMF9|B4DZ63|Q93021|Q9BU14|Q9HDA6|Q9UKY8|Q9UL24	Silent	SNP	ENST00000347869.3	37	CCDS2810.1																																																																																			G|0.998;A|0.002	0.002	strong		0.488	RBM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345797.3	NM_005778		A	50147061	G	A	50147061	2	1	28	1	0	0	0	0	0	0	0	1	13158	1103	39	1		1	RBM5	3	50147061	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	457419	50147061	147875369	154	11657											
SEMA3G	56920	hgsc.bcm.edu	37	chr3	52476899	52476899	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cctgggggcccagaaagatgGcagagcggttggcagacagg	10	4	18	9	1	0	4	0	0	0	4	0	4	0	4	2	6	1	3	2	6	1	1	rs138988057	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:52476899G>A	ENST00000231721.2	-	2	139	c.140C>T	c.(139-141)gCc>gTc	p.A47V		NM_020163.1	NP_064548.1	Q9NS98	SEM3G_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G	47	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				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)		CAGAAAGATGGCAGAGCGGTT	0.617													G|||	10	0.00199681	0.0	0.0	5008	,	,		19476	0.0		0.0099	False		,,,				2504	0.0				p.A47V		Atlas-SNP	.											.	SEMA3G	58	.	0			c.C140T						PASS	.	G	VAL/ALA	0,4404		0,0,2202	54	55	54		140	4.1	1	3	dbSNP_134	54	23,8575		0,23,4276	yes	missense	SEMA3G	NM_020163.1	64	0,23,6478	AA,AG,GG		0.2675,0.0,0.1769	benign	47/783	52476899	23,12979	2202	4299	6501	SO:0001583	missense	56920	exon2			AAGATGGCAGAGC		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.140C>T	3.37:g.52476899G>A	ENSP00000231721:p.Ala47Val	67	0	0		94	57	0.606383	NM_020163	Q7L9D9|Q9H7Q3	Missense_Mutation	SNP	ENST00000231721.2	37	CCDS2856.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	G	7.761	0.705426	0.15172	0.0	0.002675	ENSG00000010319	ENST00000231721;ENST00000475739	T;T	0.20069	2.1;2.1	4.93	4.05	0.47172	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (2);	0.142087	0.47852	D	0.000201	T	0.06371	0.0164	N	0.12182	0.205	0.09310	N	1	B	0.10296	0.003	B	0.12156	0.007	T	0.30475	-0.9977	10	0.13853	T	0.58	.	5.736	0.18067	0.2264:0.0:0.7736:0.0	.	47	Q9NS98	SEM3G_HUMAN	V	47;65	ENSP00000231721:A47V;ENSP00000419181:A65V	ENSP00000231721:A47V	A	-	2	0	SEMA3G	52451939	0.000000	0.05858	0.962000	0.40283	0.733000	0.41908	0.733000	0.26087	2.302000	0.77476	0.561000	0.74099	GCC	G|0.998;A|0.002	0.002	strong		0.617	SEMA3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351354.1	NM_020163		A	52476899	G	A	52476899	3	1	28	1	0	0	0	0	1	0	0	0	14045	1203	42	2	2268	2	SEMA3G	3	52476899	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2329838	52476899	145545531	155	11658											
FLNB	2317	hgsc.bcm.edu	37	chr3	58080639	58080639	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcagcgccgggcaaggagaCgtgatggtgtttgttgagga	9	9	17	6	3	1	3	1	2	0	1	1	5	1	4	1	4	1	3	1	4	1	2	rs141151998	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:58080639C>T	ENST00000295956.4	+	5	1029	c.864C>T	c.(862-864)gaC>gaT	p.D288D	FLNB_ENST00000419752.2_Silent_p.D119D|FLNB_ENST00000358537.3_Silent_p.D288D|FLNB_ENST00000429972.2_Silent_p.D288D|FLNB_ENST00000357272.4_Silent_p.D288D|FLNB_ENST00000348383.5_Silent_p.D288D|FLNB_ENST00000493452.1_Silent_p.D119D|FLNB_ENST00000490882.1_Silent_p.D288D	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	288					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)		GGCAAGGAGACGTGATGGTGT	0.542																																					p.D288D		Atlas-SNP	.											FLNB_ENST00000490882,NS,carcinoma,0,2	FLNB	430	2	0			c.C864T						PASS	.	C	,,,	0,4406		0,0,2203	213	194	201		864,864,864,864	-7.8	0.3	3	dbSNP_134	201	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FLNB	NM_001164317.1,NM_001164318.1,NM_001164319.1,NM_001457.3	,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,	288/2634,288/2592,288/2579,288/2603	58080639	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2317	exon5			AGGAGACGTGATG	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.864C>T	3.37:g.58080639C>T		78	0	0		123	43	0.349593	NM_001457	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Silent	SNP	ENST00000295956.4	37	CCDS2885.1																																																																																			C|0.999;T|0.001	0.001	strong		0.542	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457		T	58080639	C	T	58080639	2	4	28	1	0	0	0	0	0	0	0	1	5942	535	19	1		1	FLNB	3	58080639	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	5603740	58080639	139941791	156	11659											
FAM3D	131177	hgsc.bcm.edu	37	chr3	58639418	58639418	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacccagccagcgtggcagaCggatggttttcatgctgaag	9	8	13	11	2	1	2	1	1	0	1	1	3	1	3	2	3	3	3	2	3	1	2	rs13097314	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:58639418C>T	ENST00000358781.2	-	3	414	c.104G>A	c.(103-105)cGt>cAt	p.R35H		NM_138805.2	NP_620160.1	Q96BQ1	FAM3D_HUMAN	family with sequence similarity 3, member D	35					negative regulation of insulin secretion (GO:0046676)	extracellular region (GO:0005576)	cytokine activity (GO:0005125)			large_intestine(1)|lung(2)	3				BRCA - Breast invasive adenocarcinoma(55;0.000225)|Kidney(10;0.000667)|KIRC - Kidney renal clear cell carcinoma(10;0.000802)|OV - Ovarian serous cystadenocarcinoma(275;0.169)		GCGTGGCAGACGGATGGTTTT	0.572													C|||	13	0.00259585	0.0008	0.0014	5008	,	,		22521	0.0		0.0109	False		,,,				2504	0.0				p.R35H		Atlas-SNP	.											FAM3D,colon,carcinoma,-1,1	FAM3D	29	1	0			c.G104A						PASS	.	C	HIS/ARG	9,4397	15.5+/-35.6	0,9,2194	132	128	129		104	3.4	1	3	dbSNP_121	129	79,8521	45.8+/-104.6	1,77,4222	yes	missense	FAM3D	NM_138805.2	29	1,86,6416	TT,TC,CC		0.9186,0.2043,0.6766	possibly-damaging	35/225	58639418	88,12918	2203	4300	6503	SO:0001583	missense	131177	exon3			GGCAGACGGATGG	AF494381	CCDS2893.1	3p21.1	2008-07-18			ENSG00000198643	ENSG00000198643			18665	protein-coding gene	gene with protein product		608619				12160727	Standard	NM_138805		Approved	EF7, OIT1	uc003dkq.3	Q96BQ1	OTTHUMG00000159148	ENST00000358781.2:c.104G>A	3.37:g.58639418C>T	ENSP00000351632:p.Arg35His	35	0	0		39	17	0.435897	NM_138805	Q547G2	Missense_Mutation	SNP	ENST00000358781.2	37	CCDS2893.1	9	0.004120879120879121	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	16.58	3.163527	0.57476	0.002043	0.009186	ENSG00000198643	ENST00000358781;ENST00000483787;ENST00000498347	T;T;T	0.53857	0.6;1.85;1.44	4.26	3.38	0.38709	.	0.262588	0.30920	N	0.008602	T	0.41190	0.1148	L	0.54323	1.7	0.33744	D	0.619856	D	0.63046	0.992	P	0.49047	0.599	T	0.55611	-0.8114	10	0.13470	T	0.59	-5.3718	9.7791	0.40637	0.2049:0.795:0.0:0.0	rs13097314	35	Q96BQ1	FAM3D_HUMAN	H	35	ENSP00000351632:R35H;ENSP00000417099:R35H;ENSP00000418982:R35H	ENSP00000351632:R35H	R	-	2	0	FAM3D	58614458	0.956000	0.32656	0.971000	0.41717	0.801000	0.45260	1.522000	0.35921	1.156000	0.42514	0.435000	0.28638	CGT	C|0.994;T|0.006	0.006	strong		0.572	FAM3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353494.1	NM_138805		T	58639418	C	T	58639418	3	4	28	1	0	0	0	0	1	0	0	0	5567	536	19	1	602	1	FAM3D	3	58639418	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	558779	58639418	139383012	157	11660											
PTPRG	5793	hgsc.bcm.edu	37	chr3	61975387	61975387	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacattttagaccagtatgcGcgtgttggggaagaatacca	12	10	12	7	2	0	2	0	0	0	2	0	4	0	3	2	2	2	2	2	2	5	5			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:61975387G>A	ENST00000474889.1	+	3	656	c.279G>A	c.(277-279)gcG>gcA	p.A93A	PTPRG_ENST00000295874.10_Silent_p.A93A	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	93	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)		ACCAGTATGCGCGTGTTGGGG	0.483																																					p.A93A		Atlas-SNP	.											PTPRG,NS,carcinoma,0,1	PTPRG	153	1	0			c.G279A						PASS	.						117	107	111					3																	61975387		2203	4300	6503	SO:0001819	synonymous_variant	5793	exon3			GTATGCGCGTGTT	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.279G>A	3.37:g.61975387G>A		76	0	0		108	61	0.564815	NM_002841	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Silent	SNP	ENST00000474889.1	37	CCDS2895.1																																																																																			.	.	none		0.483	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841		A	61975387	G	A	61975387	2	1	28	1	0	0	0	0	0	0	0	1	12817	1074	38	1		1	PTPRG	3	61975387	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	3335969	61975387	136047043	158	11661											
FOXP1	27086	hgsc.bcm.edu	37	chr3	71096114	71096114	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ttgagcaagaggttgaagggGaagggcaggctgcccgggct	9	6	19	7	1	0	3	0	2	0	1	0	4	0	4	1	6	2	5	1	6	3	2	rs146606219		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:71096114G>C	ENST00000318789.4	-	10	1168	c.643C>G	c.(643-645)Ccc>Gcc	p.P215A	FOXP1_ENST00000493089.1_Missense_Mutation_p.P215A|FOXP1_ENST00000491238.1_Missense_Mutation_p.P217A|FOXP1_ENST00000498215.1_Missense_Mutation_p.P215A|FOXP1_ENST00000468577.1_Missense_Mutation_p.P215A|FOXP1_ENST00000472382.1_5'UTR|FOXP1_ENST00000475937.1_Missense_Mutation_p.P215A|FOXP1_ENST00000484350.1_Missense_Mutation_p.P139A	NM_001244810.1|NM_001244813.1|NM_032682.5	NP_001231739.1|NP_001231742.1|NP_116071.2	Q9H334	FOXP1_HUMAN	forkhead box P1	215	Gln-rich.		P -> A (in dbSNP:rs146606219). {ECO:0000269|PubMed:19352412, ECO:0000269|PubMed:20848658, ECO:0000269|PubMed:20950788}.		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)	p.P215S(1)		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)		GGTTGAAGGGGAAGGGCAGGC	0.517			T	PAX5	ALL								G|||	1	0.000199681	0.0	0.0	5008	,	,		19705	0.0		0.001	False		,,,				2504	0.0				p.P217A		Atlas-SNP	.		Dom	yes		3	3p14.1	27086	forkhead box P1		L	FOXP1,NS,carcinoma,0,1	FOXP1	104	1	1	Substitution - Missense(1)	endometrium(1)	c.C649G						PASS	.	G	ALA/PRO	2,4404	4.2+/-10.8	0,2,2201	177	181	180		643	6	1	3	dbSNP_134	180	22,8578	15.3+/-51.7	0,22,4278	yes	missense	FOXP1	NM_032682.5	27	0,24,6479	CC,CG,GG		0.2558,0.0454,0.1845	benign	215/678	71096114	24,12982	2203	4300	6503	SO:0001583	missense	27086	exon5			GAAGGGGAAGGGC	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.643C>G	3.37:g.71096114G>C	ENSP00000318902:p.Pro215Ala	124	0	0		161	90	0.559006	NM_001244815	A3QVP8|B3KV70|G5E9V8|Q8NAN6|Q9BSG9|Q9H332|Q9H333|Q9P0R1	Missense_Mutation	SNP	ENST00000318789.4	37	CCDS2914.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	24.6	4.554029	0.86231	4.54E-4	0.002558	ENSG00000114861	ENST00000318789;ENST00000318796;ENST00000475937;ENST00000339693;ENST00000497355;ENST00000491238;ENST00000493089;ENST00000498215;ENST00000484350;ENST00000468577;ENST00000485326;ENST00000497553	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;1.13	6.03	6.03	0.97812	.	0.195111	0.56097	D	0.000031	T	0.64483	0.2602	L	0.44542	1.39	0.80722	D	1	D;D;D;D	0.67145	0.996;0.996;0.993;0.993	D;D;D;D	0.76071	0.987;0.981;0.956;0.956	T	0.61322	-0.7086	10	0.52906	T	0.07	.	20.5666	0.99351	0.0:0.0:1.0:0.0	.	214;215;139;215	A3KMG1;G5E9V8;Q8NAN6;Q9H334	.;.;.;FOXP1_HUMAN	A	215;115;215;215;111;217;215;215;139;215;115;115	ENSP00000318902:P215A;ENSP00000419393:P215A;ENSP00000418225:P111A;ENSP00000420736:P217A;ENSP00000418524:P215A;ENSP00000418102:P215A;ENSP00000417857:P139A;ENSP00000418883:P215A;ENSP00000417941:P115A;ENSP00000418784:P115A	ENSP00000318902:P215A	P	-	1	0	FOXP1	71178804	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.878000	0.92393	2.854000	0.98071	0.655000	0.94253	CCC	G|0.998;C|0.002	0.002	strong		0.517	FOXP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352250.1	NM_032682		C	71096114	G	C	71096114	3	2	28	1	0	0	0	0	1	0	0	0	6034	1174	41	4	1438	4	FOXP1	3	71096114	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	9120727	71096114	126926316	159	11662											
OR5H14	403273	hgsc.bcm.edu	37	chr3	97868656	97868656	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaccaatggactgtgcatcCggctattaatcttgtcatat	10	14	8	9	1	2	1	1	1	1	0	3	2	3	2	2	2	1	2	2	2	4	4	rs146577101	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:97868656C>T	ENST00000437310.1	+	1	487	c.427C>T	c.(427-429)Cgg>Tgg	p.R143W	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005514.1	NP_001005514.1	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H, member 14	143						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						ACTGTGCATCCGGCTATTAAT	0.388																																					p.R143W		Atlas-SNP	.											.	OR5H14	56	.	0			c.C427T						PASS	.	C	TRP/ARG	107,4297		0,107,2095	118	120	119		427	-0.7	0	3	dbSNP_134	119	163,8435		0,163,4136	no	missense	OR5H14	NM_001005514.1	101	0,270,6231	TT,TC,CC		1.8958,2.4296,2.0766	benign	143/311	97868656	270,12732	2202	4299	6501	SO:0001583	missense	403273	exon1			TGCATCCGGCTAT		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.427C>T	3.37:g.97868656C>T	ENSP00000401706:p.Arg143Trp	357	0	0		529	72	0.136106	NM_001005514	B9EH15	Missense_Mutation	SNP	ENST00000437310.1	37	CCDS33798.1	.	.	.	.	.	.	.	.	.	.	C	5.787	0.329517	0.10956	0.024296	0.018958	ENSG00000236032	ENST00000437310	T	0.00130	8.69	2.49	-0.723	0.11181	GPCR, rhodopsin-like superfamily (1);	1.524830	0.04305	N	0.347965	T	0.00073	0.0002	L	0.39467	1.215	0.09310	N	1	B	0.15930	0.015	B	0.13407	0.009	T	0.23190	-1.0195	10	0.34782	T	0.22	.	3.4429	0.07470	0.0:0.3739:0.2056:0.4205	.	143	A6NHG9	O5H14_HUMAN	W	143	ENSP00000401706:R143W	ENSP00000401706:R143W	R	+	1	2	OR5H14	99351346	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.390000	0.00487	-0.356000	0.08187	0.195000	0.17529	CGG	C|0.936;T|0.064	0.064	strong		0.388	OR5H14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359112.1			T	97868656	C	T	97868656	3	4	28	1	0	0	0	0	1	0	0	0	11169	643	23	1	429	1	OR5H14	3	97868656	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	26772542	97868656	100153774	160	11663											
MORC1	27136	hgsc.bcm.edu	37	chr3	108723983	108723983	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	attctctgctgttgagagttCattttctcctccatagactt	7	18	6	10	0	3	2	1	1	2	2	6	3	4	2	2	0	1	3	2	0	1	7	rs35421732	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:108723983C>T	ENST00000483760.1	-	18	1927	c.1884G>A	c.(1882-1884)atG>atA	p.M628I	MORC1_ENST00000232603.5_Missense_Mutation_p.M649I					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						GTTGAGAGTTCATTTTCTCCT	0.363													C|||	67	0.0133786	0.0	0.0231	5008	,	,		16137	0.0		0.0497	False		,,,				2504	0.001				p.M649I		Atlas-SNP	.											.	MORC1	211	.	0			c.G1947A						PASS	.	C	ILE/MET	42,4362	43.1+/-76.7	0,42,2160	102	105	104		1947	-2	0	3	dbSNP_126	104	401,8199	128.2+/-186.4	14,373,3913	yes	missense	MORC1	NM_014429.3	10	14,415,6073	TT,TC,CC		4.6628,0.9537,3.4066	benign	649/985	108723983	443,12561	2202	4300	6502	SO:0001583	missense	27136	exon19			AGAGTTCATTTTC	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.1884G>A	3.37:g.108723983C>T	ENSP00000417282:p.Met628Ile	58	0	0		79	18	0.227848	NM_014429		Missense_Mutation	SNP	ENST00000483760.1	37		49	0.022435897435897436	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	37	0.048812664907651716	C	4.574	0.106543	0.08780	0.009537	0.046628	ENSG00000114487	ENST00000232603;ENST00000483760	T;T	0.05382	3.5;3.45	4.11	-1.98	0.07480	.	3.152720	0.00941	N	0.002824	T	0.00552	0.0018	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.08055	0.0;0.003	T	0.39251	-0.9623	10	0.31617	T	0.26	5.4385	4.2307	0.10601	0.1623:0.3617:0.0:0.476	rs35421732	628;649	E7ERX1;Q86VD1	.;MORC1_HUMAN	I	649;628	ENSP00000232603:M649I;ENSP00000417282:M628I	ENSP00000232603:M649I	M	-	3	0	MORC1	110206673	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.154000	0.10130	-0.447000	0.07138	0.557000	0.71058	ATG	C|0.965;T|0.035	0.035	strong		0.363	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1			T	108723983	C	T	108723983	3	4	28	1	0	0	0	0	1	0	0	0	9710	826	29	2	1047	2	MORC1	3	108723983	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	10855327	108723983	89298447	161	11664											
POLQ	10721	hgsc.bcm.edu	37	chr3	121207449	121207449	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgataaccttgaagaaaactAtttaattgtgaatcagtaac	17	13	6	5	0	1	4	1	3	0	1	1	4	1	4	1	0	3	1	1	0	8	7			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:121207449A>C	ENST00000264233.5	-	16	4457	c.4329T>G	c.(4327-4329)aaT>aaG	p.N1443K		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1443					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)		GAAGAAAACTATTTAATTGTG	0.348								DNA polymerases (catalytic subunits)																													p.N1443K	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.T4329G						PASS	.						44	46	45					3																	121207449		2201	4296	6497	SO:0001583	missense	10721	exon16			AAAACTATTTAAT	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.4329T>G	3.37:g.121207449A>C	ENSP00000264233:p.Asn1443Lys	87	0	0		107	19	0.17757	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	A	16.42	3.118039	0.56505	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.50548	0.74	6.11	3.38	0.38709	.	0.230437	0.44688	D	0.000425	T	0.48804	0.1520	L	0.34521	1.04	0.28458	N	0.916	D;D	0.67145	0.996;0.975	P;P	0.62740	0.906;0.781	T	0.40608	-0.9554	10	0.54805	T	0.06	.	5.3884	0.16229	0.5847:0.1381:0.2772:0.0	.	1443;615	O75417;O75417-2	DPOLQ_HUMAN;.	K	1066;1443;1579	ENSP00000264233:N1443K	ENSP00000264233:N1443K	N	-	3	2	POLQ	122690139	0.943000	0.32029	1.000000	0.80357	0.899000	0.52679	-0.042000	0.12063	0.392000	0.25172	0.533000	0.62120	AAT	.	.	none		0.348	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		C	121207449	A	C	121207449	3	2	28	1	0	0	0	0	1	0	0	0	12217	446	16	5	3503	5	POLQ	3	121207449	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	12483466	121207449	76814981	162	11665											
KALRN	8997	hgsc.bcm.edu	37	chr3	124157798	124157798	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgaggactggtgtggtggaCgagataagctggggccagca	10	7	18	6	1	0	2	0	1	0	1	0	5	0	4	1	6	2	2	1	6	1	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:124157798C>A	ENST00000240874.3	+	18	3263	c.3106C>A	c.(3106-3108)Cga>Aga	p.R1036R	KALRN_ENST00000360013.3_Silent_p.R1036R|KALRN_ENST00000460856.1_Silent_p.R1027R	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1036					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)	p.R1036*(2)		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						GTGTGGTGGACGAGATAAGCT	0.468																																					p.R1036R		Atlas-SNP	.											KALRN_ENST00000360013,caecum,carcinoma,0,2	KALRN	556	2	2	Substitution - Nonsense(2)	large_intestine(2)	c.C3106A						PASS	.						197	186	190					3																	124157798		2203	4300	6503	SO:0001819	synonymous_variant	8997	exon18			GGTGGACGAGATA	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.3106C>A	3.37:g.124157798C>A		95	0	0		131	72	0.549618	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	37	CCDS3027.1	.	.	.	.	.	.	.	.	.	.	C	10.23	1.292179	0.23564	.	.	ENSG00000160145	ENST00000354186	.	.	.	5.54	3.54	0.40534	.	.	.	.	.	T	0.72011	0.3408	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.71182	-0.4668	4	.	.	.	.	16.5605	0.84565	0.1516:0.8484:0.0:0.0	.	.	.	.	E	1004	.	.	D	+	3	2	KALRN	125640488	0.957000	0.32711	1.000000	0.80357	0.997000	0.91878	1.191000	0.32138	0.683000	0.31428	0.655000	0.94253	GAC	.	.	none		0.468	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		A	124157798	C	A	124157798	2	1	28	1	0	0	0	0	0	0	0	1	7984	528	19	4		4	KALRN	3	124157798	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2950349	124157798	73864632	163	11666											
PLXND1	23129	hgsc.bcm.edu	37	chr3	129297255	129297255	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccaggggtgagagcagggTccgggggcagtcctgagggc	6	5	21	9	1	0	2	0	2	0	1	2	3	2	2	3	6	2	2	3	6	0	0	rs112755880	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:129297255T>C	ENST00000324093.4	-	9	2441	c.2263A>G	c.(2263-2265)Acc>Gcc	p.T755A	PLXND1_ENST00000393239.1_Missense_Mutation_p.T755A	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	755					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						GAGAGCAGGGTCCGGGGGCAG	0.617																																					p.T755A	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.A2263G						PASS	.	T	ALA/THR	5,4399		0,5,2197	32	36	35		2263	4.6	1	3	dbSNP_132	35	30,8566		0,30,4268	yes	missense	PLXND1	NM_015103.2	58	0,35,6465	CC,CT,TT		0.349,0.1135,0.2692	benign	755/1926	129297255	35,12965	2202	4298	6500	SO:0001583	missense	23129	exon9			GCAGGGTCCGGGG	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.2263A>G	3.37:g.129297255T>C	ENSP00000317128:p.Thr755Ala	78	0	0		125	81	0.648	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	37	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	T	10.99	1.505945	0.26949	0.001135	0.00349	ENSG00000004399	ENST00000324093;ENST00000393239	T;T	0.33654	1.45;1.4	4.62	4.62	0.57501	.	0.643158	0.13899	N	0.355056	T	0.23572	0.0570	N	0.14661	0.345	0.23581	N	0.997361	B	0.12630	0.006	B	0.06405	0.002	T	0.16600	-1.0397	10	0.87932	D	0	.	10.4209	0.44350	0.0:0.0:0.0:1.0	.	755	Q9Y4D7	PLXD1_HUMAN	A	755	ENSP00000317128:T755A;ENSP00000376931:T755A	ENSP00000317128:T755A	T	-	1	0	PLXND1	130779945	1.000000	0.71417	1.000000	0.80357	0.483000	0.33249	2.729000	0.47327	1.708000	0.51301	0.459000	0.35465	ACC	T|0.997;C|0.003	0.003	strong		0.617	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103		C	129297255	T	C	129297255	3	2	28	1	0	0	0	0	1	0	0	0	12136	1667	58	3	3626	3	PLXND1	3	129297255	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	5139457	129297255	68725175	164	11667											
NPHP3	27031	hgsc.bcm.edu	37	chr3	132441143	132441143	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcgccgccgcccgccccgtaCgtgtcctcgatcacttcccc	3	8	8	22	7	1	0	1	0	0	0	5	1	3	0	8	0	1	1	8	0	1	2	rs192633696	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:132441143C>G	ENST00000337331.5	-	1	143	c.57G>C	c.(55-57)acG>acC	p.T19T	NPHP3_ENST00000383282.2_Silent_p.T19T|NPHP3-AS1_ENST00000504440.1_RNA|NPHP3_ENST00000326682.8_Silent_p.T19T|NPHP3-AS1_ENST00000489343.1_RNA|NPHP3_ENST00000343113.4_Silent_p.T19T	NM_153240.4	NP_694972.3	Q7Z494	NPHP3_HUMAN	nephronophthisis 3 (adolescent)	19					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						CCGCCCCGTACGTGTCCTCGA	0.721													c|||	46	0.0091853	0.0008	0.0202	5008	,	,		6716	0.001		0.0179	False		,,,				2504	0.0123				p.T19T		Atlas-SNP	.											.	NPHP3	110	.	0			c.G57C						PASS	.			13,3561		0,13,1774	10	12	12		57	0.6	1	3		12	120,7108		3,114,3497	no	coding-synonymous	NPHP3	NM_153240.4		3,127,5271	GG,GC,CC		1.6602,0.3637,1.2313		19/1331	132441143	133,10669	1787	3614	5401	SO:0001819	synonymous_variant	27031	exon1			CCCGTACGTGTCC	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.57G>C	3.37:g.132441143C>G		7	0	0		19	8	0.421053	NM_153240	Q5JPE3|Q5JPE6|Q68D99|Q6NVH3|Q7Z492|Q7Z493|Q8N9R2|Q8NCM5|Q96N70|Q96NK2	Silent	SNP	ENST00000337331.5	37	CCDS3078.1																																																																																			C|0.991;G|0.009	0.009	strong		0.721	NPHP3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357020.2	NM_153240		G	132441143	C	G	132441143	2	3	28	1	0	0	0	0	0	0	0	1	10589	523	19	4		4	NPHP3	3	132441143	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	3143888	132441143	65581287	165	11668											
KY	339855	hgsc.bcm.edu	37	chr3	134369767	134369767	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgcacgatcagcagcatgtcGatagatacagcgttgatgtc	11	10	11	9	3	1	2	1	1	0	1	3	4	1	2	0	0	5	4	0	0	2	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:134369767G>A	ENST00000423778.2	-	1	97	c.36C>T	c.(34-36)atC>atT	p.I12I	KY_ENST00000503669.1_Silent_p.I12I|KY_ENST00000508956.1_Silent_p.I12I	NM_178554.4	NP_848649.3	Q8NBH2	KY_HUMAN	kyphoscoliosis peptidase	12					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						GCAGCATGTCGATAGATACAG	0.647																																					p.I12I		Atlas-SNP	.											.	KY	92	.	0			c.C36T						PASS	.						58	65	63					3																	134369767		2131	4236	6367	SO:0001819	synonymous_variant	339855	exon1			CATGTCGATAGAT	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.36C>T	3.37:g.134369767G>A		107	0	0		190	37	0.194737	NM_178554	B7Z1S4|Q6ZT15	Silent	SNP	ENST00000423778.2	37	CCDS46920.1																																																																																			.	.	none		0.647	KY-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357320.1	NM_178554		A	134369767	G	A	134369767	2	1	28	1	0	0	0	0	0	0	0	1	8595	1048	37	1		1	KY	3	134369767	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1928624	134369767	63652663	166	11669											
FAM194A	131831	hgsc.bcm.edu	37	chr3	150398311	150398311	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgcaaaatgtctggccattCgttgctcctgtttcctacaa	8	15	7	11	1	1	0	0	0	1	0	4	0	3	0	3	1	3	4	3	1	4	5	rs144597450	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:150398311C>A	ENST00000295910.6	-	9	1107	c.1055G>T	c.(1054-1056)cGa>cTa	p.R352L	FAM194A_ENST00000491361.1_Missense_Mutation_p.R206L	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						TCTGGCCATTCGTTGCTCCTG	0.383													C|||	20	0.00399361	0.0008	0.0014	5008	,	,		18752	0.0		0.0089	False		,,,				2504	0.0092				p.R352L		Atlas-SNP	.											.	FAM194A	91	.	0			c.G1055T						PASS	.	C	LEU/ARG	17,4389	23.3+/-48.9	0,17,2186	203	181	189		1055	-0.5	0.3	3	dbSNP_134	189	155,8445	73.8+/-136.5	0,155,4145	yes	missense	FAM194A	NM_152394.3	102	0,172,6331	AA,AC,CC		1.8023,0.3858,1.3225	benign	352/664	150398311	172,12834	2203	4300	6503	SO:0001583	missense	131831	exon9			GCCATTCGTTGCT																												ENST00000295910.6:c.1055G>T	3.37:g.150398311C>A	ENSP00000295910:p.Arg352Leu	95	0	0		112	47	0.419643	NM_152394		Missense_Mutation	SNP	ENST00000295910.6	37	CCDS3151.2	10	0.004578754578754579	1	0.0020325203252032522	0	0.0	0	0.0	9	0.011873350923482849	C	6.981	0.551108	0.13374	0.003858	0.018023	ENSG00000163645	ENST00000295910;ENST00000491361;ENST00000313811	T;T	0.14144	2.73;2.53	4.93	-0.458	0.12182	.	0.483859	0.19089	N	0.123014	T	0.03053	0.0090	N	0.22421	0.69	0.20638	N	0.999872	B	0.13594	0.008	B	0.13407	0.009	T	0.26292	-1.0107	10	0.42905	T	0.14	-6.1936	2.7584	0.05299	0.321:0.1879:0.0:0.491	.	352	Q7L0X2	F194A_HUMAN	L	352;206;310	ENSP00000295910:R352L;ENSP00000419366:R206L	ENSP00000295910:R352L	R	-	2	0	FAM194A	151881001	0.994000	0.37717	0.258000	0.24420	0.019000	0.09904	0.567000	0.23608	-0.140000	0.11394	-0.471000	0.05019	CGA	C|0.990;A|0.010	0.010	strong		0.383	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1			A	150398311	C	A	150398311	3	1	28	1	0	0	0	0	1	0	0	0	5531	884	31	4	960	4	FAM194A	3	150398311	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	16028544	150398311	47624119	167	11670											
MME	4311	hgsc.bcm.edu	37	chr3	154859862	154859862	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgaggaagatgtggttgtttAtgctccagaatatttaacca	12	14	10	5	0	0	3	0	1	0	2	1	4	1	4	2	2	2	3	2	2	5	6	rs138218277		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:154859862A>G	ENST00000460393.1	+	11	1160	c.1040A>G	c.(1039-1041)tAt>tGt	p.Y347C	MME_ENST00000462745.1_Missense_Mutation_p.Y347C|MME_ENST00000492661.1_Missense_Mutation_p.Y347C|MME_ENST00000493237.1_Missense_Mutation_p.Y347C|MME_ENST00000360490.2_Missense_Mutation_p.Y347C	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	347					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)	GTGGTTGTTTATGCTCCAGAA	0.368													A|||	1	0.000199681	0.0	0.0014	5008	,	,		17690	0.0		0.0	False		,,,				2504	0.0				p.Y347C		Atlas-SNP	.											.	MME	133	.	0			c.A1040G						PASS	.	A	CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR	2,4404	4.2+/-10.8	0,2,2201	140	142	142		1040,1040,1040,1040	6	1	3	dbSNP_134	142	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense,missense,missense	MME	NM_000902.3,NM_007287.2,NM_007288.2,NM_007289.2	194,194,194,194	0,8,6495	GG,GA,AA		0.0698,0.0454,0.0615	probably-damaging,probably-damaging,probably-damaging,probably-damaging	347/751,347/751,347/751,347/751	154859862	8,12998	2203	4300	6503	SO:0001583	missense	4311	exon11			TTGTTTATGCTCC		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.1040A>G	3.37:g.154859862A>G	ENSP00000418525:p.Tyr347Cys	121	0	0		151	97	0.642384	NM_007287	A8K6U6|D3DNJ9|Q3MIX4	Missense_Mutation	SNP	ENST00000460393.1	37	CCDS3172.1	.	.	.	.	.	.	.	.	.	.	A	16.81	3.227122	0.58668	4.54E-4	6.98E-4	ENSG00000196549	ENST00000492661;ENST00000460393;ENST00000462745;ENST00000493237;ENST00000360490	T;T;T;T;T	0.74842	-0.88;-0.88;-0.88;-0.88;-0.88	6.02	6.02	0.97574	Peptidase M13 (1);	0.189758	0.47852	D	0.000203	T	0.80824	0.4697	M	0.85197	2.74	0.58432	D	0.999999	P	0.47350	0.894	P	0.47891	0.56	D	0.83807	0.0239	10	0.66056	D	0.02	-17.4255	11.5514	0.50723	0.931:0.0:0.069:0.0	.	347	P08473	NEP_HUMAN	C	347	ENSP00000420389:Y347C;ENSP00000418525:Y347C;ENSP00000419653:Y347C;ENSP00000417079:Y347C;ENSP00000353679:Y347C	ENSP00000353679:Y347C	Y	+	2	0	MME	156342556	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.179000	0.71974	2.306000	0.77630	0.482000	0.46254	TAT	A|0.999;G|0.001	0.001	strong		0.368	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902		G	154859862	A	G	154859862	3	3	28	1	0	0	0	0	1	0	0	0	9654	449	16	3	1078	3	MME	3	154859862	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	4461551	154859862	43162568	168	11671											
SERPINI2	5276	hgsc.bcm.edu	37	chr3	167159968	167159968	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cactcttcccataaacagaaTtgattctagggaaaaaaaaa	19	9	5	8	0	2	2	0	1	2	1	3	3	3	3	1	1	1	0	1	1	8	5			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:167159968T>C	ENST00000476257.1	-	10	1445	c.1147A>G	c.(1147-1149)Att>Gtt	p.I383V	SERPINI2_ENST00000264677.4_Missense_Mutation_p.I383V|SERPINI2_ENST00000471111.1_Missense_Mutation_p.I383V|SERPINI2_ENST00000461846.1_Missense_Mutation_p.I383V			O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin), member 2	383					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						ATAAACAGAATTGATTCTAGG	0.308																																					p.I393V		Atlas-SNP	.											.	SERPINI2	85	.	0			c.A1177G						PASS	.						88	80	83					3																	167159968		2203	4299	6502	SO:0001583	missense	5276	exon10			ACAGAATTGATTC	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.1147A>G	3.37:g.167159968T>C	ENSP00000420621:p.Ile383Val	46	0	0		79	36	0.455696	NM_001012303		Missense_Mutation	SNP	ENST00000476257.1	37	CCDS3200.1	.	.	.	.	.	.	.	.	.	.	T	13.14	2.149400	0.37923	.	.	ENSG00000114204	ENST00000476257;ENST00000461846;ENST00000264677;ENST00000471111	D;D;D;D	0.85411	-1.98;-1.98;-1.98;-1.98	6.17	5.0	0.66597	Serpin domain (3);	0.102768	0.64402	D	0.000004	D	0.83496	0.5267	L	0.60845	1.875	0.80722	D	1	P;P	0.45634	0.863;0.863	P;P	0.45538	0.484;0.484	T	0.81402	-0.0949	10	0.39692	T	0.17	.	9.7406	0.40416	0.1538:0.0:0.0:0.8462	.	383;383	B4DDY9;O75830	.;SPI2_HUMAN	V	383	ENSP00000420621:I383V;ENSP00000417692:I383V;ENSP00000264677:I383V;ENSP00000419407:I383V	ENSP00000264677:I383V	I	-	1	0	SERPINI2	168642662	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	1.916000	0.39986	1.120000	0.41904	0.533000	0.62120	ATT	.	.	none		0.308	SERPINI2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350450.1	NM_006217		C	167159968	T	C	167159968	3	2	28	1	0	0	0	0	1	0	0	0	14134	1493	52	3	74	3	SERPINI2	3	167159968	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	12300106	167159968	30862462	169	11672											
SERPINI2	5276	hgsc.bcm.edu	37	chr3	167170788	167170788	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgttcaaagaatacaaaacGtctttgaagtctactttttg	14	15	6	6	1	3	2	1	1	2	1	3	2	3	2	0	0	3	1	0	0	7	6	rs61750373	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:167170788G>A	ENST00000476257.1	-	7	1198	c.900C>T	c.(898-900)gaC>gaT	p.D300D	SERPINI2_ENST00000264677.4_Silent_p.D300D|SERPINI2_ENST00000471111.1_Silent_p.D300D|SERPINI2_ENST00000461846.1_Silent_p.D300D			O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin), member 2	300					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						AATACAAAACGTCTTTGAAGT	0.279													G|||	7	0.00139776	0.0015	0.0	5008	,	,		15704	0.0		0.004	False		,,,				2504	0.001				p.D310D		Atlas-SNP	.											.	SERPINI2	85	.	0			c.C930T						PASS	.	G		9,4397	15.5+/-35.6	0,9,2194	64	61	62		900	1.5	1	3	dbSNP_129	62	66,8532	39.8+/-96.3	1,64,4234	no	coding-synonymous	SERPINI2	NM_006217.3		1,73,6428	AA,AG,GG		0.7676,0.2043,0.5767		300/406	167170788	75,12929	2203	4299	6502	SO:0001819	synonymous_variant	5276	exon7			CAAAACGTCTTTG	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.900C>T	3.37:g.167170788G>A		184	0	0		204	75	0.367647	NM_001012303		Silent	SNP	ENST00000476257.1	37	CCDS3200.1																																																																																			G|0.996;A|0.004	0.004	strong		0.279	SERPINI2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350450.1	NM_006217		A	167170788	G	A	167170788	2	1	28	1	0	0	0	0	0	0	0	1	14134	1136	40	1		1	SERPINI2	3	167170788	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	10820	167170788	30851642	170	11673											
PIK3CA	5290	hgsc.bcm.edu	37	chr3	178936082	178936082	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctacacgagatcctctctctGaaatcactgagcaggagaaa	14	8	8	11	1	3	4	1	2	2	2	5	6	4	4	1	1	2	1	1	1	3	1	rs121913273		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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,0,745	PIK3CA	8460	745	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						scavenged	.						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	3.37:g.178936082G>A	ENSP00000263967:p.Glu542Lys	275	1	0.00363636		372	85	0.228495	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	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	.	.	weak		0.333	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2			A	178936082	G	A	178936082	3	1	28	1	0	0	0	0	1	0	0	0	11922	1291	45	2	1658	2	PIK3CA	3	178936082	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	11765294	178936082	19086348	171	11674											
KLHL6	89857	hgsc.bcm.edu	37	chr3	183273248	183273248	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagagcgttttccattcgcAgggtttccaggccattctga	7	13	10	11	2	2	2	1	1	1	1	5	2	4	2	3	2	1	3	3	2	0	5	rs148924291	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:183273248A>G	ENST00000341319.3	-	1	229	c.194T>C	c.(193-195)cTg>cCg	p.L65P		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	65					B cell receptor signaling pathway (GO:0050853)|germinal center formation (GO:0002467)			p.L65P(1)		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)			TTCCATTCGCAGGGTTTCCAG	0.498													A|||	2	0.000399361	0.0008	0.0014	5008	,	,		16106	0.0		0.0	False		,,,				2504	0.0				p.L65P		Atlas-SNP	.											KLHL6,NS,lymphoid_neoplasm,-1,2	KLHL6	100	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.T194C						scavenged	.	A	PRO/LEU	0,4406		0,0,2203	140	139	139		194	5.6	0.9	3	dbSNP_134	139	1,8599	1.2+/-3.3	0,1,4299	no	missense	KLHL6	NM_130446.2	98	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	probably-damaging	65/622	183273248	1,13005	2203	4300	6503	SO:0001583	missense	89857	exon1			ATTCGCAGGGTTT	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.194T>C	3.37:g.183273248A>G	ENSP00000341342:p.Leu65Pro	190	2	0.0105263		228	96	0.421053	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Missense_Mutation	SNP	ENST00000341319.3	37	CCDS3245.2	.	.	.	.	.	.	.	.	.	.	A	17.61	3.433538	0.62955	0.0	1.16E-4	ENSG00000172578	ENST00000341319	T	0.75154	-0.91	5.56	5.56	0.83823	BTB/POZ (1);BTB/POZ fold (2);	0.066358	0.64402	D	0.000007	D	0.90487	0.7020	H	0.96142	3.775	0.80722	D	1	D	0.71674	0.998	D	0.75484	0.986	D	0.93464	0.6813	10	0.87932	D	0	.	15.7124	0.77641	1.0:0.0:0.0:0.0	.	65	Q8WZ60	KLHL6_HUMAN	P	65	ENSP00000341342:L65P	ENSP00000341342:L65P	L	-	2	0	KLHL6	184755942	1.000000	0.71417	0.941000	0.38009	0.438000	0.31896	7.483000	0.81158	2.108000	0.64289	0.533000	0.62120	CTG	A|1.000;G|0.000	0.000	weak		0.498	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446		G	183273248	A	G	183273248	3	3	28	1	0	0	0	0	1	0	0	0	8402	188	7	3	1699	3	KLHL6	3	183273248	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	4337166	183273248	14749182	172	11675											
PARL	55486	hgsc.bcm.edu	37	chr3	183580581	183580581	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacttaggttattccaccaCttgttaatctaaaacagaca	14	13	4	10	0	2	1	1	0	1	1	3	1	3	1	2	1	1	2	2	1	5	6			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:183580581C>T	ENST00000317096.4	-	4	531	c.471G>A	c.(469-471)aaG>aaA	p.K157K	PARL_ENST00000311101.5_Silent_p.K157K|PARL_ENST00000435888.1_Silent_p.K157K	NM_018622.5	NP_061092.3	Q9H300	PARL_HUMAN	presenilin associated, rhomboid-like	157					membrane protein proteolysis (GO:0033619)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|proteolysis (GO:0006508)|regulation of protein targeting to mitochondrion (GO:1903214)|regulation of reactive oxygen species metabolic process (GO:2000377)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(3)|liver(1)|lung(6)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	17	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.21e-41)|Epithelial(37;1.34e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			TATTCCACCACTTGTTAATCT	0.393																																					p.K157K		Atlas-SNP	.											.	PARL	32	.	0			c.G471A						PASS	.						108	95	100					3																	183580581		2203	4300	6503	SO:0001819	synonymous_variant	55486	exon4			CCACCACTTGTTA	AF116692	CCDS3248.1, CCDS33897.1	3q27.3	2008-02-05		2006-02-28	ENSG00000175193	ENSG00000175193			18253	protein-coding gene	gene with protein product	"rhomboid 7 homolog 1 (Drosophila)"	607858		PSARL			Standard	XM_005247587		Approved	PRO2207, PSARL1, RHBDS1	uc003fmd.3	Q9H300	OTTHUMG00000156890	ENST00000317096.4:c.471G>A	3.37:g.183580581C>T		46	0	0		72	30	0.416667	NM_018622	Q96CQ4|Q9BTJ6|Q9P1E3	Silent	SNP	ENST00000317096.4	37	CCDS3248.1	.	.	.	.	.	.	.	.	.	.	C	9.171	1.021044	0.19433	.	.	ENSG00000175193	ENST00000449306	.	.	.	5.45	4.51	0.55191	.	.	.	.	.	T	0.61476	0.2350	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57774	-0.7753	4	.	.	.	-19.1355	10.6799	0.45809	0.1449:0.7143:0.1408:0.0	.	.	.	.	M	71	.	.	V	-	1	0	PARL	185063275	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.931000	0.28871	2.690000	0.91761	0.557000	0.71058	GTG	.	.	none		0.393	PARL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346465.1	NM_018622		T	183580581	C	T	183580581	2	4	28	1	0	0	0	0	0	0	0	1	11460	564	20	2		2	PARL	3	183580581	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	307333	183580581	14441849	173	11676											
HTR3C	170572	hgsc.bcm.edu	37	chr3	183777328	183777328	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttctacctgccagcagagagCgagaatcgtgccccattcaa	11	8	9	13	2	2	2	1	0	1	2	3	4	2	2	4	0	5	1	4	0	3	3	rs138181384	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:183777328C>T	ENST00000318351.1	+	7	859	c.825C>T	c.(823-825)agC>agT	p.S275S		NM_130770.2	NP_570126.2	Q8WXA8	5HT3C_HUMAN	5-hydroxytryptamine (serotonin) receptor 3C, ionotropic	275					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)	CAGCAGAGAGCGAGAATCGTG	0.547													C|||	3	0.000599042	0.0	0.0	5008	,	,		17250	0.002		0.001	False		,,,				2504	0.0				p.S275S		Atlas-SNP	.											.	HTR3C	65	.	0			c.C825T						PASS	.	C		0,4406		0,0,2203	150	133	139		825	-3	0	3	dbSNP_134	139	5,8595		0,5,4295	no	coding-synonymous	HTR3C	NM_130770.2		0,5,6498	TT,TC,CC		0.0581,0.0,0.0384		275/448	183777328	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	170572	exon7			AGAGAGCGAGAAT	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	ENST00000318351.1:c.825C>T	3.37:g.183777328C>T		122	0	0		134	44	0.328358	NM_130770	A2RRR5	Silent	SNP	ENST00000318351.1	37	CCDS3250.1																																																																																			C|0.999;T|0.001	0.001	strong		0.547	HTR3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346296.1	NM_130770		T	183777328	C	T	183777328	2	4	28	1	0	0	0	0	0	0	0	1	7455	767	27	1		1	HTR3C	3	183777328	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	196747	183777328	14245102	174	11677											
TM4SF19	116211	hgsc.bcm.edu	37	chr3	196050862	196050862	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagcgaacggtcatacagAtaattcctatcccaaaaaat	17	8	6	10	2	1	2	1	0	0	2	3	3	3	2	2	1	3	0	2	1	7	4	rs36016914	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:196050862A>G	ENST00000273695.3	-	5	581	c.456T>C	c.(454-456)taT>taC	p.Y152Y	TM4SF19-AS1_ENST00000452051.1_RNA|TM4SF19_ENST00000446879.1_Missense_Mutation_p.I151T|TM4SF19_ENST00000442633.1_Silent_p.Y152Y|TM4SF19_ENST00000454715.1_Silent_p.Y126Y|TM4SF19-AS1_ENST00000444939.1_RNA|TM4SF19-AS1_ENST00000420226.1_RNA	NM_001204897.1|NM_138461.3	NP_001191826.1|NP_612470.2	Q96DZ7	T4S19_HUMAN	transmembrane 4 L six family member 19	152						integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(3)|lung(5)	12	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;3.94e-24)|all cancers(36;4.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.53e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		GGTCATACAGATAATTCCTAT	0.552													A|||	32	0.00638978	0.0008	0.0259	5008	,	,		20131	0.0		0.0129	False		,,,				2504	0.0				p.I151T		Atlas-SNP	.											.	TM4SF19	21	.	0			c.T452C						PASS	.	A	THR/ILE,,	14,4392	20.2+/-43.8	0,14,2189	54	52	53		452,378,456	-0.1	0.6	3	dbSNP_126	53	114,8486	61.3+/-123.2	2,110,4188	yes	missense,coding-synonymous,coding-synonymous	TM4SF19	NM_001204897.1,NM_001204898.1,NM_138461.3	89,,	2,124,6377	GG,GA,AA		1.3256,0.3177,0.9842	,,	151/243,126/184,152/210	196050862	128,12878	2203	4300	6503	SO:0001819	synonymous_variant	116211	exon5			ATACAGATAATTC	BC013113	CCDS3316.1, CCDS56299.1	3q29	2005-08-09			ENSG00000145107	ENSG00000145107			25167	protein-coding gene	gene with protein product						12477932	Standard	NM_138461		Approved		uc021xjs.1	Q96DZ7	OTTHUMG00000155675	ENST00000273695.3:c.456T>C	3.37:g.196050862A>G		52	0	0		76	22	0.289474	NM_001204897	B2RV20|E9PH22|Q336K7	Missense_Mutation	SNP	ENST00000273695.3	37	CCDS3316.1	20|20	0.009157509157509158|0.009157509157509158	0|0	0.0|0.0	10|10	0.027624309392265192|0.027624309392265192	0|0	0.0|0.0	10|10	0.013192612137203167|0.013192612137203167	A|A	6.649|6.649	0.488243|0.488243	0.12641|0.12641	0.003177|0.003177	0.013256|0.013256	ENSG00000145107|ENSG00000145107	ENST00000446879|ENST00000440822	T|.	0.27402|.	1.67|.	5.13|5.13	-0.105|-0.105	0.13601|0.13601	.|.	.|.	.|.	.|.	.|.	T|T	0.29945|0.29945	0.0749|0.0749	.|.	.|.	.|.	0.54753|0.54753	D|D	0.99998|0.99998	B|.	0.24132|.	0.098|.	B|.	0.26094|.	0.066|.	T|T	0.27365|0.27365	-1.0076|-1.0076	8|4	0.27082|.	T|.	0.32|.	-5.5124|-5.5124	7.8335|7.8335	0.29358|0.29358	0.5849:0.0:0.415:0.0|0.5849:0.0:0.415:0.0	rs36016914;rs62409180|rs36016914;rs62409180	151|.	C9JCD5|.	.|.	T|P	151|19	ENSP00000395280:I151T|.	ENSP00000395280:I151T|.	I|S	-|-	2|1	0|0	TM4SF19|TM4SF19	197535259|197535259	0.355000|0.355000	0.24921|0.24921	0.565000|0.565000	0.28409|0.28409	0.176000|0.176000	0.22953|0.22953	0.361000|0.361000	0.20267|0.20267	0.002000|0.002000	0.14630|0.14630	0.460000|0.460000	0.39030|0.39030	ATC|TCT	A|0.989;G|0.011	0.011	strong		0.552	TM4SF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341174.1	NM_138461		G	196050862	A	G	196050862	2	3	28	1	0	0	0	0	0	0	0	1	15983	340	12	3		3	TM4SF19	3	196050862	Silent	SNP	A	TCGA-G8-6914-01A-11D-2210-10	12273534	196050862	1971568	175	11678											
MFI2	4241	hgsc.bcm.edu	37	chr3	196742243	196742243	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgtgactcccacctggatcCgctccatgcagtgttggggg	5	9	14	13	2	0	1	0	1	0	0	3	2	3	2	4	3	1	3	4	3	0	1	rs45625439	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:196742243C>T	ENST00000296350.5	-	9	1339	c.1226G>A	c.(1225-1227)cGg>cAg	p.R409Q		NM_005929.5	NP_005920.2	P08582	TRFM_HUMAN	antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5	409	Transferrin-like 2. {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)		CACCTGGATCCGCTCCATGCA	0.657													C|||	23	0.00459265	0.0	0.0043	5008	,	,		18548	0.0		0.0129	False		,,,				2504	0.0072				p.R409Q		Atlas-SNP	.											.	MFI2	88	.	0			c.G1226A						PASS	.	C	GLN/ARG	22,4348		0,22,2163	34	24	27		1226	-3.8	0.9	3	dbSNP_127	27	146,8408		2,142,4133	yes	missense	MFI2	NM_005929.5	43	2,164,6296	TT,TC,CC		1.7068,0.5034,1.2999	benign	409/739	196742243	168,12756	2185	4277	6462	SO:0001583	missense	4241	exon9			TGGATCCGCTCCA		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.1226G>A	3.37:g.196742243C>T	ENSP00000296350:p.Arg409Gln	91	0	0		107	66	0.616822	NM_005929	Q9BQE2	Missense_Mutation	SNP	ENST00000296350.5	37	CCDS3325.1	14	0.00641025641025641	0	0.0	2	0.0055248618784530384	0	0.0	12	0.0158311345646438	C	12.39	1.923379	0.33908	0.005034	0.017068	ENSG00000163975	ENST00000296350	T	0.32272	1.46	5.72	-3.84	0.04256	.	1.025380	0.07685	N	0.937703	T	0.04907	0.0132	N	0.03177	-0.4	0.41333	D	0.987255	B	0.09022	0.002	B	0.08055	0.003	T	0.38001	-0.9681	10	0.14656	T	0.56	-10.756	5.8183	0.18514	0.183:0.3633:0.0:0.4537	rs45625439	409	P08582	TRFM_HUMAN	Q	409	ENSP00000296350:R409Q	ENSP00000296350:R409Q	R	-	2	0	MFI2	198226640	0.027000	0.19231	0.857000	0.33713	0.825000	0.46686	-0.069000	0.11542	-0.368000	0.08040	-1.320000	0.01293	CGG	C|0.991;T|0.009	0.009	strong		0.657	MFI2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340458.1			T	196742243	C	T	196742243	3	4	28	1	0	0	0	0	1	0	0	0	9531	652	23	1	1022	1	MFI2	3	196742243	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	691381	196742243	1280187	176	11679											
FAM193A	8603	hgsc.bcm.edu	37	chr4	2632799	2632800	+	Frame_Shift_Ins	INS	-	-	C																															gcaccatctggcctgcagggINScccgccgcaagcgcaccagt																										TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:2632799_2632800insC	ENST00000324666.5	+	3	419_420	c.68_69insC	c.(67-72)ggcccgfs	p.GP23fs	FAM193A_ENST00000382839.3_Frame_Shift_Ins_p.GP23fs|FAM193A_ENST00000502458.1_Frame_Shift_Ins_p.GP23fs|FAM193A_ENST00000545951.1_Frame_Shift_Ins_p.GP23fs|FAM193A_ENST00000505311.1_Frame_Shift_Ins_p.GP23fs	NM_001256666.1	NP_001243595.1	P78312	F193A_HUMAN	family with sequence similarity 193, member A	23										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						GGCCTGCAGGGCCCGCCGCAAG	0.639																																					p.G23fs		Atlas-Indel	.											.	FAM193A	103	.	0			c.68_69insC						PASS	.																																			SO:0001589	frameshift_variant	8603	exon3			.	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.71dupC	4.37:g.2632802_2632802dupC	ENSP00000324587:p.Gly23fs	113	0	0		127	12	0.0944882	NM_001256666	B7ZM85|B9EGR0|E9PFA1|O43607|P78311|P78313|Q9UEG8	Frame_Shift_Ins	INS	ENST00000324666.5	37	CCDS58875.1																																																																																			.	.	none		0.639	FAM193A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360903.1	NM_003704		C	2632800	-	C	2632799	7	5	28	1	0	1	1	0	0	0	0	0	5529	1203	42	0	70	0	FAM193A	4	2632799	Frame_Shift_Ins	INS	-	TCGA-G8-6914-01A-11D-2210-10		2632799	188521477	177	11680											
LRPAP1	4043	hgsc.bcm.edu	37	chr4	3516560	3516560	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acacgctcgccgtcgcccacGctctctgcgtgcctcagctt	4	9	9	19	6	2	0	1	0	1	0	5	0	2	0	3	0	3	3	3	0	0	1	rs11549512	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:3516560G>A	ENST00000500728.2	-	7	1076	c.930C>T	c.(928-930)agC>agT	p.S310S	LRPAP1_ENST00000296325.5_5'UTR	NM_002337.3	NP_002328.1	P30533	AMRP_HUMAN	low density lipoprotein receptor-related protein associated protein 1	310	LDL receptor binding. {ECO:0000255}.				extracellular negative regulation of signal transduction (GO:1900116)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of protein binding (GO:0032091)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|protein folding (GO:0006457)|receptor-mediated endocytosis (GO:0006898)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|rough endoplasmic reticulum lumen (GO:0048237)|vesicle (GO:0031982)	asialoglycoprotein receptor activity (GO:0004873)|heparin binding (GO:0008201)|low-density lipoprotein particle receptor binding (GO:0050750)|receptor antagonist activity (GO:0048019)|unfolded protein binding (GO:0051082)|very-low-density lipoprotein particle receptor binding (GO:0070326)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(2)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.165)		CGTCGCCCACGCTCTCTGCGT	0.637													.|||	95	0.0189696	0.0023	0.0519	5008	,	,		17011	0.001		0.0497	False		,,,				2504	0.0051				p.S310S		Atlas-SNP	.											.	LRPAP1	29	.	0			c.C930T						PASS	.	G		39,4367	43.8+/-77.6	0,39,2164	127	104	112		930	0.3	0.3	4	dbSNP_120	112	401,8199	127.7+/-186.0	7,387,3906	no	coding-synonymous	LRPAP1	NM_002337.3		7,426,6070	AA,AG,GG		4.6628,0.8852,3.3831		310/358	3516560	440,12566	2203	4300	6503	SO:0001819	synonymous_variant	4043	exon7			GCCCACGCTCTCT		CCDS3371.1	4p16.3	2008-05-02	2003-03-17		ENSG00000163956	ENSG00000163956			6701	protein-coding gene	gene with protein product		104225	"low density lipoprotein-related protein-associated protein 1 (alpha-2-macroglobulin receptor-associated protein 1)"	A2MRAP		1712782	Standard	NM_002337		Approved	HBP44	uc003ghh.4	P30533	OTTHUMG00000090299	ENST00000500728.2:c.930C>T	4.37:g.3516560G>A		96	0	0		125	61	0.488	NM_002337	D3DVR9|Q2M310|Q53HQ3|Q53HS6	Silent	SNP	ENST00000500728.2	37	CCDS3371.1																																																																																			G|0.971;A|0.029	0.029	strong		0.637	LRPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206659.4			A	3516560	G	A	3516560	2	1	28	1	0	0	0	0	0	0	0	1	8973	1078	38	1		1	LRPAP1	4	3516560	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	883761	3516560	187637716	178	11681											
EVC2	132884	hgsc.bcm.edu	37	chr4	5642347	5642347	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttccaggtcacattcagctGtcaatgccaccatcttccga	9	12	6	14	1	4	0	3	0	1	0	6	1	6	0	4	1	2	1	4	1	1	3	rs141287105	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:5642347G>C	ENST00000344408.5	-	10	1417	c.1364C>G	c.(1363-1365)aCa>aGa	p.T455R	EVC2_ENST00000310917.2_Missense_Mutation_p.T375R|EVC2_ENST00000344938.1_Missense_Mutation_p.T455R	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	455					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						ACATTCAGCTGTCAATGCCAC	0.433													G|||	10	0.00199681	0.0	0.0014	5008	,	,		22461	0.0		0.0089	False		,,,				2504	0.0				p.T455R		Atlas-SNP	.											.	EVC2	202	.	0			c.C1364G						PASS	.	G	ARG/THR,ARG/THR	5,4401	9.9+/-24.2	0,5,2198	367	327	341		1124,1364	3.3	0.8	4	dbSNP_134	341	65,8535	39.8+/-96.3	1,63,4236	yes	missense,missense	EVC2	NM_001166136.1,NM_147127.4	71,71	1,68,6434	CC,CG,GG		0.7558,0.1135,0.5382	probably-damaging,probably-damaging	375/1229,455/1309	5642347	70,12936	2203	4300	6503	SO:0001583	missense	132884	exon10			TCAGCTGTCAATG	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.1364C>G	4.37:g.5642347G>C	ENSP00000342144:p.Thr455Arg	149	0	0		151	66	0.437086	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	37	CCDS3382.2	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	G	16.55	3.154339	0.57259	0.001135	0.007558	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.78707	-1.2;-1.2;-1.2	4.25	3.34	0.38264	.	0.344939	0.27677	N	0.018315	T	0.75671	0.3881	M	0.67953	2.075	0.38779	D	0.954725	D	0.56746	0.977	P	0.54544	0.755	T	0.77814	-0.2448	10	0.22706	T	0.39	-4.8253	12.9472	0.58379	0.0:0.0:0.8385:0.1615	.	455	Q86UK5	LBN_HUMAN	R	455;375;455	ENSP00000339954:T455R;ENSP00000311683:T375R;ENSP00000342144:T455R	ENSP00000311683:T375R	T	-	2	0	EVC2	5693248	1.000000	0.71417	0.807000	0.32361	0.767000	0.43475	4.192000	0.58378	2.074000	0.62210	0.591000	0.81541	ACA	G|0.995;C|0.005	0.005	strong		0.433	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127		C	5642347	G	C	5642347	3	2	28	1	0	0	0	0	1	0	0	0	5288	1377	48	4	2614	4	EVC2	4	5642347	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2125787	5642347	185511929	179	11682											
SH3TC1	54436	hgsc.bcm.edu	37	chr4	8229378	8229378	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agctcctgcagctggcgctgCggcgggcggtgggtggccag	3	6	20	12	4	0	0	0	0	0	0	1	0	1	0	2	6	4	4	2	6	0	0	rs139890356	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:8229378C>A	ENST00000245105.3	+	12	2024	c.1957C>A	c.(1957-1959)Cgg>Agg	p.R653R	SH3TC1_ENST00000539824.1_Silent_p.R577R	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	653										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						GCTGGCGCTGCGGCGGGCGGT	0.726																																					p.R653R	NSCLC(145;2298 2623 35616 37297)	Atlas-SNP	.											.	SH3TC1	105	.	0			c.C1957A						PASS	.						12	13	13					4																	8229378		1842	3696	5538	SO:0001819	synonymous_variant	54436	exon12			GCGCTGCGGCGGG	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.1957C>A	4.37:g.8229378C>A		24	0	0		38	21	0.552632	NM_018986	Q4W5G5	Silent	SNP	ENST00000245105.3	37	CCDS3399.1																																																																																			C|0.996;T|0.004	.	alt		0.726	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986		A	8229378	C	A	8229378	2	1	28	1	0	0	0	0	0	0	0	1	14276	759	27	4		4	SH3TC1	4	8229378	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2587031	8229378	182924898	180	11683											
CLNK	116449	hgsc.bcm.edu	37	chr4	10502936	10502936	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgattcctctccaggaagcGtatttttacattgtagactt	9	16	7	9	1	1	2	0	1	1	1	3	3	2	3	2	1	2	2	2	1	4	8	rs190441710	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:10502936G>A	ENST00000226951.6	-	18	1323	c.1084C>T	c.(1084-1086)Cgc>Tgc	p.R362C	CLNK_ENST00000515667.1_Missense_Mutation_p.R100C	NM_052964.2	NP_443196.2	Q7Z7G1	CLNK_HUMAN	cytokine-dependent hematopoietic cell linker	362	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				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						TCCAGGAAGCGTATTTTTACA	0.468													G|||	7	0.00139776	0.0	0.0	5008	,	,		19909	0.0		0.007	False		,,,				2504	0.0				p.R362C	GBM(87;402 1286 6949 13902 35851)	Atlas-SNP	.											.	CLNK	85	.	0			c.C1084T						PASS	.						82	78	79					4																	10502936		1884	4125	6009	SO:0001583	missense	116449	exon18			GGAAGCGTATTTT	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.1084C>T	4.37:g.10502936G>A	ENSP00000226951:p.Arg362Cys	110	0	0		101	50	0.49505	NM_052964	Q05C27|Q9P2U9	Missense_Mutation	SNP	ENST00000226951.6	37	CCDS47024.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	25.4	4.637615	0.87760	.	.	ENSG00000109684	ENST00000226951;ENST00000515667;ENST00000429087	D;D	0.89196	-2.48;-2.48	5.39	5.39	0.77823	SH2 motif (4);	0.000000	0.64402	D	0.000001	D	0.91439	0.7298	M	0.64260	1.97	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92357	0.5894	10	0.87932	D	0	-20.0915	16.6639	0.85247	0.0:0.0:1.0:0.0	.	362	Q7Z7G1	CLNK_HUMAN	C	362;100;326	ENSP00000226951:R362C;ENSP00000427256:R100C	ENSP00000226951:R362C	R	-	1	0	CLNK	10112034	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	8.149000	0.89632	2.515000	0.84797	0.650000	0.86243	CGC	G|0.998;A|0.002	0.002	strong		0.468	CLNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359047.1	NM_052964		A	10502936	G	A	10502936	3	1	28	1	0	0	0	0	1	0	0	0	3549	1145	40	1	210	1	CLNK	4	10502936	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2273558	10502936	180651340	181	11684											
KCNIP4	80333	hgsc.bcm.edu	37	chr4	20751343	20751343	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cattgaacagaaaatgtgcaTatgttgtagagtctgaaatg	15	12	10	4	0	1	4	0	2	1	2	1	4	1	4	0	0	2	3	0	0	6	4			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:20751343T>C	ENST00000382152.2	-	5	538	c.371A>G	c.(370-372)tAt>tGt	p.Y124C	PACRGL_ENST00000507634.1_Intron|KCNIP4_ENST00000509207.1_Missense_Mutation_p.Y62C|KCNIP4_ENST00000447367.2_Missense_Mutation_p.Y90C|KCNIP4_ENST00000382148.3_Missense_Mutation_p.Y99C|KCNIP4_ENST00000359001.5_Missense_Mutation_p.Y62C|KCNIP4_ENST00000382149.4_5'UTR|KCNIP4_ENST00000382150.4_Missense_Mutation_p.Y103C	NM_025221.5	NP_079497.2	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4	124	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.					dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13		Breast(46;0.134)				AAAATGTGCATATGTTGTAGA	0.368																																					p.Y104C		Atlas-SNP	.											.	KCNIP4	85	.	0			c.A311G						PASS	.						114	105	108					4																	20751343		2203	4300	6503	SO:0001583	missense	80333	exon4			TGTGCATATGTTG	AF453244	CCDS3428.1, CCDS43215.1, CCDS43216.1, CCDS43217.1, CCDS47035.1	4p15.32	2013-01-10			ENSG00000185774	ENSG00000185774		"EF-hand domain containing"	30083	protein-coding gene	gene with protein product		608182				11805342, 11847232	Standard	XM_005248190		Approved	CALP, KCHIP4, MGC44947	uc003gqh.1	Q6PIL6	OTTHUMG00000128557	ENST00000382152.2:c.371A>G	4.37:g.20751343T>C	ENSP00000371587:p.Tyr124Cys	53	0	0		48	4	0.0833333	NM_025221	Q3YAB8|Q3YAB9|Q3YAC0|Q3YAC1|Q3YAC2|Q4W5G8|Q8NEU0|Q9BWT2|Q9H294|Q9H2A4	Missense_Mutation	SNP	ENST00000382152.2	37	CCDS43216.1	.	.	.	.	.	.	.	.	.	.	T	18.46	3.628173	0.66901	.	.	ENSG00000185774	ENST00000382148;ENST00000447367;ENST00000382150;ENST00000413487;ENST00000382152;ENST00000509207;ENST00000359001	T;T;T;T;T;T	0.21932	1.98;1.98;1.98;1.98;1.98;1.98	5.24	5.24	0.73138	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.55862	0.1947	M	0.92880	3.355	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;0.999	T	0.67715	-0.5599	10	0.87932	D	0	.	14.1041	0.65078	0.0:0.0:0.0:1.0	.	99;103;107;124	Q3YAB9;Q3YAC0;Q3YAB7;Q6PIL6	.;.;.;KCIP4_HUMAN	C	99;90;103;62;124;62;62	ENSP00000371583:Y99C;ENSP00000399080:Y90C;ENSP00000371585:Y103C;ENSP00000371587:Y124C;ENSP00000423257:Y62C;ENSP00000351892:Y62C	ENSP00000351892:Y62C	Y	-	2	0	KCNIP4	20360441	1.000000	0.71417	0.997000	0.53966	0.725000	0.41563	7.662000	0.83803	1.974000	0.57490	0.482000	0.46254	TAT	.	.	none		0.368	KCNIP4-004	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360407.3	NM_025221		C	20751343	T	C	20751343	3	2	28	1	0	0	0	0	1	0	0	0	8051	1406	49	3	401	3	KCNIP4	4	20751343	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	10248407	20751343	170402933	182	11685											
LGI2	55203	hgsc.bcm.edu	37	chr4	25014048	25014048	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgggctgcgcgatggccacGtacacatcgttcttggagtt	6	11	13	11	4	1	0	0	0	1	0	2	2	1	1	1	3	2	4	1	3	1	4	rs34079294	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:25014048G>A	ENST00000382114.4	-	7	914	c.729C>T	c.(727-729)taC>taT	p.Y243Y		NM_018176.3	NP_060646.2	Q8N0V4	LGI2_HUMAN	leucine-rich repeat LGI family, member 2	243						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)				CGATGGCCACGTACACATCGT	0.468													G|||	12	0.00239617	0.0	0.0043	5008	,	,		21248	0.0		0.0089	False		,,,				2504	0.0				p.Y243Y		Atlas-SNP	.											.	LGI2	62	.	0			c.C729T						PASS	.	G		5,4401	9.9+/-24.2	0,5,2198	145	122	130		729	1	1	4	dbSNP_126	130	60,8540	37.8+/-93.5	0,60,4240	no	coding-synonymous	LGI2	NM_018176.3		0,65,6438	AA,AG,GG		0.6977,0.1135,0.4998		243/546	25014048	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	55203	exon7			GGCCACGTACACA	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.729C>T	4.37:g.25014048G>A		110	0	0		151	67	0.443709	NM_018176	Q3MIN2|Q8NDW6|Q96PX2|Q9NVK4	Silent	SNP	ENST00000382114.4	37	CCDS3431.1																																																																																			G|0.995;A|0.005	0.005	strong		0.468	LGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214978.1			A	25014048	G	A	25014048	2	1	28	1	0	0	0	0	0	0	0	1	8761	1140	40	1		1	LGI2	4	25014048	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	4262705	25014048	166140228	183	11686											
FRYL	285527	hgsc.bcm.edu	37	chr4	48542671	48542671	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caaaaaatggtggccatcaaGttggtaggctcagtagtgga	13	9	13	6	0	2	0	2	0	0	0	2	1	2	1	1	5	0	4	1	5	6	3	rs373260615		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:48542671G>A	ENST00000503238.1	-	43	5993	c.5994C>T	c.(5992-5994)aaC>aaT	p.N1998N	FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000507873.2_5'UTR|FRYL_ENST00000358350.4_Silent_p.N1998N|FRYL_ENST00000537810.1_Silent_p.N1998N			O94915	FRYL_HUMAN	FRY-like	1998					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						TGGCCATCAAGTTGGTAGGCT	0.423																																					p.N1998N		Atlas-SNP	.											.	FRYL	242	.	0			c.C5994T						PASS	.	G		0,3846		0,0,1923	79	78	79		5994	5.3	1	4		79	2,8232		0,2,4115	no	coding-synonymous	FRYL	NM_015030.1		0,2,6038	AA,AG,GG		0.0243,0.0,0.0166		1998/3014	48542671	2,12078	1923	4117	6040	SO:0001819	synonymous_variant	285527	exon46			CATCAAGTTGGTA	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.5994C>T	4.37:g.48542671G>A		132	0	0		117	57	0.487179	NM_015030	O95640|Q8WTZ5|Q9NT40	Silent	SNP	ENST00000503238.1	37	CCDS43227.1	.	.	.	.	.	.	.	.	.	.	G	2.279	-0.365058	0.05103	0.0	2.43E-4	ENSG00000075539	ENST00000514617	.	.	.	6.16	5.33	0.75918	.	.	.	.	.	T	0.62696	0.2449	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61594	-0.7031	4	.	.	.	.	10.6144	0.45441	0.1986:0.0:0.8014:0.0	.	.	.	.	F	868	.	.	L	-	1	0	FRYL	48237428	1.000000	0.71417	0.978000	0.43139	0.571000	0.35966	3.050000	0.49877	1.628000	0.50416	0.650000	0.86243	CTT	.	.	weak		0.423	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2			A	48542671	G	A	48542671	2	1	28	1	0	0	0	0	0	0	0	1	6072	1020	36	2		2	FRYL	4	48542671	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	23528623	48542671	142611605	184	11687											
LRRC66	339977	hgsc.bcm.edu	37	chr4	52862020	52862020	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaagcccccaggctgaaggCgacaaggaatgtgatgaaca	15	4	13	9	1	0	3	0	3	0	0	0	6	0	4	2	3	2	1	2	3	5	0	rs202189181		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:52862020C>G	ENST00000343457.3	-	4	1174	c.1168G>C	c.(1168-1170)Gcc>Ccc	p.A390P		NM_001024611.1	NP_001019782.1	Q68CR7	LRC66_HUMAN	leucine rich repeat containing 66	390						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						AGGCTGAAGGCGACAAGGAAT	0.557													C|||	1	0.000199681	0.0	0.0	5008	,	,		18727	0.0		0.0	False		,,,				2504	0.001				p.A390P		Atlas-SNP	.											.	LRRC66	128	.	0			c.G1168C						PASS	.	C	PRO/ALA	1,3953		0,1,1976	53	54	54		1168	4.7	1	4		54	4,8318		0,4,4157	yes	missense	LRRC66	NM_001024611.1	27	0,5,6133	GG,GC,CC		0.0481,0.0253,0.0407	probably-damaging	390/881	52862020	5,12271	1977	4161	6138	SO:0001583	missense	339977	exon4			TGAAGGCGACAAG	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.1168G>C	4.37:g.52862020C>G	ENSP00000341944:p.Ala390Pro	103	0	0		128	69	0.539062	NM_001024611		Missense_Mutation	SNP	ENST00000343457.3	37	CCDS43229.1	.	.	.	.	.	.	.	.	.	.	C	15.37	2.812710	0.50527	2.53E-4	4.81E-4	ENSG00000188993	ENST00000343457	T	0.49432	0.78	4.67	4.67	0.58626	.	0.000000	0.45867	D	0.000335	T	0.65533	0.2700	M	0.63843	1.955	0.40966	D	0.98466	D	0.89917	1.0	D	0.91635	0.999	T	0.70263	-0.4920	10	0.87932	D	0	-17.3724	14.6507	0.68794	0.0:1.0:0.0:0.0	.	390	Q68CR7	LRC66_HUMAN	P	390	ENSP00000341944:A390P	ENSP00000341944:A390P	A	-	1	0	LRRC66	52556777	0.999000	0.42202	0.997000	0.53966	0.011000	0.07611	4.870000	0.63035	2.306000	0.77630	0.467000	0.42956	GCC	.	.	weak		0.557	LRRC66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361473.1	NM_001024611		G	52862020	C	G	52862020	3	3	28	1	0	0	0	0	1	0	0	0	9027	768	27	4	1478	4	LRRC66	4	52862020	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	4319349	52862020	138292256	185	11688											
UGT2B15	7367	hgsc.bcm.edu	37	chr4	69433479	69433479	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caattggacacacgacttacCtagaacttcactataaaact	16	10	4	11	1	1	1	1	0	0	1	1	3	1	2	1	1	3	0	1	1	7	6	rs145791375	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:69433479C>G	ENST00000317746.2	-	1	766	c.724G>C	c.(724-726)Gga>Cga	p.G242R		NM_001077.3	NP_001068.1	O75795	UDB17_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B17	242					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)	CACGACTTACCTAGAACTTCA	0.323													C|||	2	0.000399361	0.0	0.0	5008	,	,		10536	0.0		0.002	False		,,,				2504	0.0				p.G242R	Melanoma(18;649 833 28984 37818 38500)	Atlas-SNP	.											.	UGT2B17	34	.	0			c.G724C						PASS	.	C	ARG/GLY	2,4188		0,2,2093	100	109	106		724	2.7	0.7	4	dbSNP_134	106	6,7868		2,2,3933	yes	missense-near-splice	UGT2B17	NM_001077.3	125	2,4,6026	GG,GC,CC		0.0762,0.0477,0.0663		242/531	69433479	8,12056	2095	3937	6032	SO:0001630	splice_region_variant	7367	exon1			ACTTACCTAGAAC	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.724+1G>C	4.37:g.69433479C>G		0	0	.		127	59	0.464567	NM_001077		Missense_Mutation	SNP	ENST00000317746.2	37	CCDS3523.1	.	.	.	.	.	.	.	.	.	.	c	14.66	2.602420	0.46423	4.77E-4	7.62E-4	ENSG00000197888	ENST00000317746	T	0.60424	0.19	2.66	2.66	0.31614	.	0.000000	0.64402	U	0.000005	T	0.69967	0.3170	M	0.85777	2.775	0.30173	N	0.801107	.	.	.	.	.	.	T	0.70927	-0.4739	7	.	.	.	.	11.1206	0.48287	0.0:1.0:0.0:0.0	.	.	.	.	R	242	ENSP00000320401:G242R	.	G	-	1	0	UGT2B17	69116074	1.000000	0.71417	0.673000	0.29887	0.022000	0.10575	6.023000	0.70848	1.516000	0.48900	0.499000	0.49734	GGA	C|0.999;G|0.001	0.001	strong		0.323	UGT2B17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251436.1	NM_001077	Missense_Mutation	G	69433479	C	G	69433479	5	3	28	1	0	0	0	0	0	0	1	0	16973	695	24	4	892	4	UGT2B15	4	69433479	Splice_Site	SNP	C	TCGA-G8-6914-01A-11D-2210-10	16571459	69433479	121720797	186	11689											
CNOT6L	246175	hgsc.bcm.edu	37	chr4	78697538	78697538	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	catatttttcctttggcatcCctattagtctgtttaaaaaa	11	18	4	8	0	1	0	0	0	1	0	3	0	3	0	2	1	0	2	2	1	6	8			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:78697538C>T	ENST00000504123.1	-	2	144	c.14G>A	c.(13-15)gGg>gAg	p.G5E	CNOT6L_ENST00000264903.4_Missense_Mutation_p.G5E|CNOT6L_ENST00000506166.1_5'UTR			Q96LI5	CNO6L_HUMAN	CCR4-NOT transcription complex, subunit 6-like	5	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						CTTTGGCATCCCTATTAGTCT	0.358																																					p.G5E		Atlas-SNP	.											.	CNOT6L	57	.	0			c.G14A						PASS	.						60	53	55					4																	78697538		1804	4080	5884	SO:0001583	missense	246175	exon2			GGCATCCCTATTA	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.14G>A	4.37:g.78697538C>T	ENSP00000424896:p.Gly5Glu	79	0	0		79	32	0.405063	NM_144571	Q9UF92	Missense_Mutation	SNP	ENST00000504123.1	37		.	.	.	.	.	.	.	.	.	.	C	19.78	3.890592	0.72524	.	.	ENSG00000138767	ENST00000504123;ENST00000264903;ENST00000512485;ENST00000515441	T;T;T;T	0.35605	1.3;1.3;1.67;1.98	5.72	5.72	0.89469	.	0.000000	0.44285	D	0.000480	T	0.39860	0.1094	L	0.29908	0.895	0.58432	D	0.999993	D;P	0.58268	0.982;0.866	P;P	0.51550	0.622;0.673	T	0.22347	-1.0219	10	0.72032	D	0.01	-2.6931	16.1856	0.81948	0.1336:0.8664:0.0:0.0	.	5;5	B4E2S0;Q96LI5	.;CNO6L_HUMAN	E	5;5;12;5	ENSP00000424896:G5E;ENSP00000264903:G5E;ENSP00000425571:G12E;ENSP00000426269:G5E	ENSP00000264903:G5E	G	-	2	0	CNOT6L	78916562	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.037000	0.70956	2.695000	0.91970	0.557000	0.71058	GGG	.	.	none		0.358	CNOT6L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000362515.1			T	78697538	C	T	78697538	3	4	28	1	0	0	0	0	1	0	0	0	3625	623	22	2	1697	2	CNOT6L	4	78697538	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	9264059	78697538	112456738	187	11690											
MRPL1	65008	hgsc.bcm.edu	37	chr4	78792906	78792906	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttcctttcaagccttgataCatcatcaaaggcatagcctt	11	14	5	11	0	3	1	3	1	0	0	4	1	4	1	3	1	3	1	3	1	4	6	rs373565703		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:78792906C>T	ENST00000315567.8	+	2	369	c.40C>T	c.(40-42)Cat>Tat	p.H14Y		NM_020236.3	NP_064621.3	Q9BYD6	RM01_HUMAN	mitochondrial ribosomal protein L1	14					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						AGCCTTGATACATCATCAAAG	0.303																																					p.H14Y		Atlas-SNP	.											.	MRPL1	37	.	0			c.C40T						PASS	.	C	TYR/HIS	0,4406		0,0,2203	82	77	78		40	2.6	1	4		78	2,8598	2.2+/-6.3	0,2,4298	no	missense	MRPL1	NM_020236.3	83	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	14/326	78792906	2,13004	2203	4300	6503	SO:0001583	missense	65008	exon2			TTGATACATCATC	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.40C>T	4.37:g.78792906C>T	ENSP00000315017:p.His14Tyr	126	0	0		108	51	0.472222	NM_020236	A6NG03|Q4W5B8|Q6IAG4|Q96BW3|Q9H793|Q9NRL5	Missense_Mutation	SNP	ENST00000315567.8	37	CCDS3583.2	.	.	.	.	.	.	.	.	.	.	C	8.711	0.912058	0.17907	0.0	2.33E-4	ENSG00000169288	ENST00000315567	T	0.49139	0.79	5.27	2.62	0.31277	Ribosomal protein L1, chordata (1);	1.288150	0.06367	U	0.712771	T	0.46034	0.1372	L	0.56769	1.78	0.25979	N	0.982403	B	0.30889	0.299	B	0.35278	0.199	T	0.38585	-0.9654	10	0.31617	T	0.26	-0.8796	6.1972	0.20555	0.0:0.6775:0.1532:0.1693	.	14	Q9BYD6	RM01_HUMAN	Y	14	ENSP00000315017:H14Y	ENSP00000315017:H14Y	H	+	1	0	MRPL1	79011930	0.405000	0.25336	0.956000	0.39512	0.721000	0.41392	0.268000	0.18571	0.442000	0.26555	-0.143000	0.13931	CAT	.	.	weak		0.303	MRPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252518.3	NM_020236		T	78792906	C	T	78792906	3	4	28	1	0	0	0	0	1	0	0	0	9783	478	17	2	46	2	MRPL1	4	78792906	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	95368	78792906	112361370	188	11691											
WDFY3	23001	hgsc.bcm.edu	37	chr4	85612823	85612823	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccagtctgcaactgaggtcTgcatagccccaagcaaaagt	12	7	9	13	0	2	1	0	1	2	0	2	1	2	1	3	1	5	3	3	1	5	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:85612823T>C	ENST00000295888.4	-	60	9572	c.9165A>G	c.(9163-9165)gcA>gcG	p.A3055A	WDFY3_ENST00000322366.6_Silent_p.A3038A	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	3055	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)		AACTGAGGTCTGCATAGCCCC	0.413																																					p.A3055A		Atlas-SNP	.											.	WDFY3	314	.	0			c.A9165G						PASS	.						121	108	113					4																	85612823		2203	4300	6503	SO:0001819	synonymous_variant	23001	exon60			GAGGTCTGCATAG	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.9165A>G	4.37:g.85612823T>C		69	0	0		73	25	0.342466	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Silent	SNP	ENST00000295888.4	37	CCDS3609.1																																																																																			.	.	none		0.413	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991		C	85612823	T	C	85612823	2	2	28	1	0	0	0	0	0	0	0	1	17285	1567	55	3		3	WDFY3	4	85612823	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	6819917	85612823	105541453	189	11692											
NUDT9	53343	hgsc.bcm.edu	37	chr4	88344154	88344154	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcgcgctgccgcggcatcCaggcgttcaggtattccacc	5	8	11	17	5	1	0	1	0	0	0	4	0	3	0	5	3	1	4	5	3	1	3	rs146952902	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:88344154C>A	ENST00000302174.4	+	1	421	c.97C>A	c.(97-99)Cag>Aag	p.Q33K	NUDT9_ENST00000473942.1_Intron	NM_024047.4	NP_076952.1	Q9BW91	NUDT9_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 9	33					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)			endometrium(1)|large_intestine(4)|lung(6)	11		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000937)		CCGCGGCATCCAGGCGTTCAG	0.592													C|||	11	0.00219649	0.0	0.0014	5008	,	,		15253	0.0		0.006	False		,,,				2504	0.0041				p.Q33K		Atlas-SNP	.											.	NUDT9	21	.	0			c.C97A						PASS	.	C	LYS/GLN,	5,4401	9.9+/-24.2	0,5,2198	57	57	57		97,	2.7	0	4	dbSNP_134	57	32,8568	22.2+/-67.0	0,32,4268	yes	missense,intron	NUDT9	NM_024047.3,NM_198038.1	53,	0,37,6466	AA,AC,CC		0.3721,0.1135,0.2845	benign,	33/351,	88344154	37,12969	2203	4300	6503	SO:0001583	missense	53343	exon1			GGCATCCAGGCGT	AY026252	CCDS3620.1, CCDS3621.1	4q22.1	2008-08-29			ENSG00000170502	ENSG00000170502		"Nudix motif containing"	8056	protein-coding gene	gene with protein product		606022				11385575, 12427752	Standard	NM_024047		Approved	MGC3037	uc003hqq.3	Q9BW91	OTTHUMG00000130591	ENST00000302174.4:c.97C>A	4.37:g.88344154C>A	ENSP00000303575:p.Gln33Lys	40	0	0		40	11	0.275	NM_001248011	Q8NBN1|Q8NCB9|Q8NG25	Missense_Mutation	SNP	ENST00000302174.4	37	CCDS3620.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	C	9.675	1.147631	0.21288	0.001135	0.003721	ENSG00000170502	ENST00000302174;ENST00000440591	T;T	0.75589	-0.95;2.6	3.56	2.71	0.32032	.	0.536650	0.17871	N	0.159179	T	0.44498	0.1296	N	0.08118	0	0.21897	N	0.99949	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.44726	-0.9309	10	0.51188	T	0.08	0.1088	9.1276	0.36826	0.0:0.7534:0.2466:0.0	.	33;33	Q96KB3;Q9BW91	.;NUDT9_HUMAN	K	33	ENSP00000303575:Q33K;ENSP00000410270:Q33K	ENSP00000303575:Q33K	Q	+	1	0	NUDT9	88563178	0.004000	0.15560	0.008000	0.14137	0.004000	0.04260	0.585000	0.23879	1.048000	0.40298	0.484000	0.47621	CAG	C|0.997;A|0.003	0.003	strong		0.592	NUDT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253035.2			A	88344154	C	A	88344154	3	1	28	1	0	0	0	0	1	0	0	0	10755	595	21	4	99	4	NUDT9	4	88344154	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2731331	88344154	102810122	190	11693											
PKD2	5311	hgsc.bcm.edu	37	chr4	88996673	88996673	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tggaacggctagtacgtgaaGagttggaacgctgggaatcc	11	8	15	7	3	0	2	0	1	0	1	1	5	1	5	1	4	3	4	1	4	6	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:88996673G>A	ENST00000508588.1	+	10	1383	c.988G>A	c.(988-990)Gag>Aag	p.E330K	PKD2_ENST00000237596.2_Missense_Mutation_p.E912K|PKD2_ENST00000511337.1_3'UTR|PKD2_ENST00000502363.1_Missense_Mutation_p.E330K			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)		AGTACGTGAAGAGTTGGAACG	0.517																																					p.E912K		Atlas-SNP	.											.	PKD2	82	.	0			c.G2734A						PASS	.						157	155	155					4																	88996673		2203	4300	6503	SO:0001583	missense	5311	exon15			CGTGAAGAGTTGG	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.988G>A	4.37:g.88996673G>A	ENSP00000427131:p.Glu330Lys	88	0	0		93	20	0.215054	NM_000297	Q8TB08|Q9P0T6|Q9Y3X8	Missense_Mutation	SNP	ENST00000508588.1	37		.	.	.	.	.	.	.	.	.	.	G	34	5.343226	0.95783	.	.	ENSG00000118762	ENST00000237596;ENST00000508588;ENST00000502363	T;D;D	0.94613	-0.82;-3.47;-3.47	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	D	0.96793	0.8953	M	0.68593	2.085	0.80722	D	1	D	0.69078	0.997	D	0.73380	0.98	D	0.97032	0.9751	10	0.59425	D	0.04	-22.2119	18.7273	0.91718	0.0:0.0:1.0:0.0	.	912	Q13563	PKD2_HUMAN	K	912;330;330	ENSP00000237596:E912K;ENSP00000427131:E330K;ENSP00000425289:E330K	ENSP00000237596:E912K	E	+	1	0	PKD2	89215697	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.183000	0.94887	2.409000	0.81822	0.585000	0.79938	GAG	.	.	none		0.517	PKD2-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000363253.2	NM_000297		A	88996673	G	A	88996673	3	1	28	1	0	0	0	0	1	0	0	0	11975	943	33	2	2792	2	PKD2	4	88996673	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	652519	88996673	102157603	191	11694											
UNC5C	8633	hgsc.bcm.edu	37	chr4	96140151	96140151	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acaataaggtgacctcccagCgagttgaagctgccaaatgc	13	7	10	11	1	0	2	0	2	0	0	1	3	1	2	3	1	4	2	3	1	4	2	rs61741188	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:96140151C>T	ENST00000453304.1	-	9	1962	c.1614G>A	c.(1612-1614)tcG>tcA	p.S538S	UNC5C_ENST00000506749.1_Silent_p.S557S	NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	538	ZU5. {ECO:0000255|PROSITE- ProRule:PRU00485}.				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)		GACCTCCCAGCGAGTTGAAGC	0.443													C|||	151	0.0301518	0.0318	0.0202	5008	,	,		20428	0.0		0.0219	False		,,,				2504	0.0746				p.S538S		Atlas-SNP	.											.	UNC5C	141	.	0			c.G1614A						PASS	.	C		134,4272	98.5+/-137.1	0,134,2069	108	86	94		1614	-1.9	0.9	4	dbSNP_129	94	231,8369	94.0+/-155.9	3,225,4072	no	coding-synonymous	UNC5C	NM_003728.3		3,359,6141	TT,TC,CC		2.686,3.0413,2.8064		538/932	96140151	365,12641	2203	4300	6503	SO:0001819	synonymous_variant	8633	exon9			TCCCAGCGAGTTG	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.1614G>A	4.37:g.96140151C>T		91	0	0		89	37	0.41573	NM_003728	Q8IUT0	Silent	SNP	ENST00000453304.1	37	CCDS3643.1																																																																																			C|0.977;T|0.023	0.023	strong		0.443	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728		T	96140151	C	T	96140151	2	4	28	1	0	0	0	0	0	0	0	1	17008	755	27	1		1	UNC5C	4	96140151	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	7143478	96140151	95014125	192	11695											
PPP3CA	5530	hgsc.bcm.edu	37	chr4	101984390	101984390	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcaggattccacaacataccTttttccccaacaaatggaag	14	10	5	12	0	1	0	1	0	0	0	3	2	3	2	4	2	3	0	4	2	5	4			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:101984390T>C	ENST00000394854.3	-	9	1763	c.1080A>G	c.(1078-1080)aaA>aaG	p.K360K	PPP3CA_ENST00000523694.2_Splice_Site_p.K293K|PPP3CA_ENST00000394853.4_Splice_Site_p.K360K|PPP3CA_ENST00000512215.1_Splice_Site_p.K128K|PPP3CA_ENST00000323055.6_Intron|PPP3CA_ENST00000507176.1_Splice_Site_p.K262K	NM_000944.4	NP_000935.1	Q08209	PP2BA_HUMAN	protein phosphatase 3, catalytic subunit, alpha isozyme	360					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)		ACAACATACCTTTTTCCCCAA	0.383																																					p.K360K		Atlas-SNP	.											.	PPP3CA	51	.	0			c.A1080G						PASS	.						86	86	86					4																	101984390		2203	4300	6503	SO:0001630	splice_region_variant	5530	exon9			CATACCTTTTTCC		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.1081+1A>G	4.37:g.101984390T>C		146	0	0		124	26	0.209677	NM_000944	A1A441|A8K3B7|A8W6Z7|A8W6Z8|B5BUA2|Q8TAW9	Silent	SNP	ENST00000394854.3	37	CCDS34037.1																																																																																			.	.	none		0.383	PPP3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258379.2	NM_000944	Silent	C	101984390	T	C	101984390	5	2	28	1	0	0	0	0	0	0	1	0	12409	1623	56	3	509	3	PPP3CA	4	101984390	Splice_Site	SNP	T	TCGA-G8-6914-01A-11D-2210-10	5844239	101984390	89169886	193	11696											
NFKB1	4790	hgsc.bcm.edu	37	chr4	103518700	103518700	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acctctttctagagaaggctAtgcagcttgcaaagaggcat	12	10	10	9	0	2	2	0	0	2	2	2	3	2	2	1	2	3	5	1	2	4	4	rs4648072	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:103518700A>G	ENST00000505458.1	+	15	1793	c.1516A>G	c.(1516-1518)Atg>Gtg	p.M506V	NFKB1_ENST00000394820.4_Missense_Mutation_p.M506V|NFKB1_ENST00000600343.1_Missense_Mutation_p.M326V|NFKB1_ENST00000226574.4_Missense_Mutation_p.M507V			P19838	NFKB1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	506	Interaction with CFLAR.		M -> V (in dbSNP:rs4648072). {ECO:0000269|Ref.8}.		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)	AGAGAAGGCTATGCAGCTTGC	0.483													A|||	69	0.013778	0.0424	0.0072	5008	,	,		22523	0.0		0.008	False		,,,				2504	0.0				p.M507V		Atlas-SNP	.											.	NFKB1	78	.	0			c.A1519G						PASS	.	A	VAL/MET,VAL/MET	181,4225	118.0+/-155.7	4,173,2026	111	101	104		1516,1519	-4.9	0	4	dbSNP_111	104	69,8531	41.7+/-99.0	0,69,4231	yes	missense,missense	NFKB1	NM_001165412.1,NM_003998.3	21,21	4,242,6257	GG,GA,AA		0.8023,4.108,1.9222	benign,benign	506/969,507/970	103518700	250,12756	2203	4300	6503	SO:0001583	missense	4790	exon15			AAGGCTATGCAGC	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.1516A>G	4.37:g.103518700A>G	ENSP00000424790:p.Met506Val	72	0	0		48	48	1	NM_003998	A8K5Y5|B3KVE8|Q68D84|Q86V43|Q8N4X7|Q9NZC0	Missense_Mutation	SNP	ENST00000505458.1	37	CCDS54783.1	26	0.011904761904761904	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	A	7.891	0.732244	0.15507	0.04108	0.008023	ENSG00000109320	ENST00000226574;ENST00000394820;ENST00000505458	T;T;T	0.36157	1.28;1.27;1.27	4.57	-4.88	0.03113	.	0.299368	0.33327	N	0.005038	T	0.07369	0.0186	L	0.56769	1.78	0.18873	N	0.999983	B;B;B	0.20052	0.011;0.011;0.041	B;B;B	0.20955	0.021;0.021;0.032	T	0.10245	-1.0638	10	0.48119	T	0.1	.	10.0045	0.41949	0.2584:0.6027:0.1389:0.0	rs4648072;rs4648072	326;506;507	B3KVE8;P19838;P19838-2	.;NFKB1_HUMAN;.	V	507;506;506	ENSP00000226574:M507V;ENSP00000378297:M506V;ENSP00000424790:M506V	ENSP00000226574:M507V	M	+	1	0	NFKB1	103737738	0.037000	0.19845	0.034000	0.17996	0.916000	0.54674	0.284000	0.18864	-1.114000	0.02977	0.533000	0.62120	ATG	A|0.984;G|0.016	0.016	strong		0.483	NFKB1-003	KNOWN	alternative_5_UTR|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363411.1			G	103518700	A	G	103518700	3	3	28	1	0	0	0	0	1	0	0	0	10384	449	16	3	1573	3	NFKB1	4	103518700	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	1534310	103518700	87635576	194	11697											
C4orf21	55345	hgsc.bcm.edu	37	chr4	113553098	113553098	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtactcactttgtttcctaaGtgagtgatcttcagaattcc	9	16	7	9	0	3	3	2	2	1	1	5	3	5	3	2	0	1	2	2	0	3	6			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:113553098G>A	ENST00000505019.1	-	3	215	c.90C>T	c.(88-90)caC>caT	p.H30H	C4orf21_ENST00000445203.2_5'UTR|C4orf21_ENST00000309071.5_Silent_p.H30H	NM_018392.4	NP_060862.3	Q86YA3	ZGRF1_HUMAN		30						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)		TGTTTCCTAAGTGAGTGATCT	0.323																																					p.H30H		Atlas-SNP	.											.	C4orf21	223	.	0			c.C90T						PASS	.						103	94	97					4																	113553098		2202	4298	6500	SO:0001819	synonymous_variant	55345	exon3			TCCTAAGTGAGTG																												ENST00000505019.1:c.90C>T	4.37:g.113553098G>A		77	0	0		88	4	0.0454545	NM_018392	B3KQX2|B4DSN6|B4DYU8|E9PDE1|G5EA02|Q6ZU11|Q9NSW3|Q9NUJ4	Silent	SNP	ENST00000505019.1	37																																																																																				.	.	none		0.323	C4orf21-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256413.1			A	113553098	G	A	113553098	2	1	28	1	0	0	0	0	0	0	0	1	2256	1020	36	2		2	C4orf21	4	113553098	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	10034398	113553098	77601178	195	11698											
FHDC1	85462	hgsc.bcm.edu	37	chr4	153886104	153886104	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctaaacttttcagaaaaattGcatcatgttcagaagactgc	15	12	6	8	0	3	3	3	0	0	3	3	3	3	3	0	0	3	2	0	0	5	5	rs2018007	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:153886104G>A	ENST00000511601.1	+	9	1265	c.1077G>A	c.(1075-1077)ttG>ttA	p.L359L	FHDC1_ENST00000260008.3_Silent_p.L359L			Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	359	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)					CAGAAAAATTGCATCATGTTC	0.303													G|||	113	0.0225639	0.0749	0.0086	5008	,	,		18165	0.0		0.005	False		,,,				2504	0.0031				p.L359L		Atlas-SNP	.											.	FHDC1	102	.	0			c.G1077A						PASS	.	G		277,4129	152.2+/-185.9	13,251,1939	75	81	79		1077	0.9	0	4	dbSNP_92	79	37,8557	24.6+/-71.5	1,35,4261	no	coding-synonymous	FHDC1	NM_033393.2		14,286,6200	AA,AG,GG		0.4305,6.2869,2.4154		359/1144	153886104	314,12686	2203	4297	6500	SO:0001819	synonymous_variant	85462	exon8			AAAATTGCATCAT	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.1077G>A	4.37:g.153886104G>A		383	1	0.00261097		330	166	0.50303	NM_033393		Silent	SNP	ENST00000511601.1	37	CCDS34081.1																																																																																			G|0.973;A|0.027	0.027	strong		0.303	FHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364981.2	NM_033393		A	153886104	G	A	153886104	2	1	28	1	0	0	0	0	0	0	0	1	5884	1310	46	2		2	FHDC1	4	153886104	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	40333006	153886104	37268172	196	11699											
FSTL5	56884	hgsc.bcm.edu	37	chr4	163032498	163032498	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggttggccttccttccgaCtccagaaaaatgaatccgag	10	11	9	11	2	0	2	0	1	0	1	4	4	4	2	5	2	0	1	5	2	3	4	rs140747357	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:163032498C>G	ENST00000306100.5	-	2	487	c.51G>C	c.(49-51)gaG>gaC	p.E17D	FSTL5_ENST00000379164.4_Missense_Mutation_p.E17D|FSTL5_ENST00000536695.1_Missense_Mutation_p.E17D|FSTL5_ENST00000427802.2_Missense_Mutation_p.E17D	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	17						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)		TTCCTTCCGACTCCAGAAAAA	0.398													C|||	4	0.000798722	0.0	0.0	5008	,	,		14268	0.0		0.004	False		,,,				2504	0.0				p.E17D		Atlas-SNP	.											.	FSTL5	207	.	0			c.G51C						PASS	.	C	ASP/GLU,ASP/GLU,ASP/GLU	7,4399	12.9+/-30.5	0,7,2196	131	125	127		51,51,51	-2.3	0.5	4	dbSNP_134	127	45,8555	29.0+/-79.6	0,45,4255	yes	missense,missense,missense	FSTL5	NM_001128427.1,NM_001128428.1,NM_020116.3	45,45,45	0,52,6451	GG,GC,CC		0.5233,0.1589,0.3998	benign,benign,benign	17/847,17/838,17/848	163032498	52,12954	2203	4300	6503	SO:0001583	missense	56884	exon2			TTCCGACTCCAGA	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.51G>C	4.37:g.163032498C>G	ENSP00000305334:p.Glu17Asp	101	0	0		81	41	0.506173	NM_001128428	E9PCP6|Q9NSW7|Q9ULF7	Missense_Mutation	SNP	ENST00000306100.5	37	CCDS3802.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	2.069	-0.413600	0.04799	0.001589	0.005233	ENSG00000168843	ENST00000306100;ENST00000379164;ENST00000427802;ENST00000536695	T;T;T;T	0.72725	-0.66;-0.65;-0.68;-0.65	5.51	-2.26	0.06867	.	0.753644	0.12056	N	0.503598	T	0.32556	0.0833	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;0.0	T	0.14671	-1.0464	10	0.17832	T	0.49	.	4.3997	0.11381	0.2402:0.3205:0.0:0.4394	.	17;17;17	E9PCP6;F8VZ90;Q8N475	.;.;FSTL5_HUMAN	D	17	ENSP00000305334:E17D;ENSP00000368462:E17D;ENSP00000389270:E17D;ENSP00000440409:E17D	ENSP00000305334:E17D	E	-	3	2	FSTL5	163251948	0.865000	0.29922	0.477000	0.27303	0.010000	0.07245	-0.188000	0.09642	-0.753000	0.04721	-1.975000	0.00460	GAG	C|0.996;G|0.004	0.004	strong		0.398	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116		G	163032498	C	G	163032498	3	3	28	1	0	0	0	0	1	0	0	0	6088	564	20	4	2552	4	FSTL5	4	163032498	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	9146394	163032498	28121778	197	11700											
DDX60	55601	hgsc.bcm.edu	37	chr4	169227551	169227551	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccaggaaaaaatctggtgTctgtacatgcttggaagaag	13	11	11	6	0	2	1	0	0	2	1	3	3	3	3	1	3	2	2	1	3	6	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:169227551T>C	ENST00000393743.3	-	5	876	c.585A>G	c.(583-585)agA>agG	p.R195R		NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	195					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)		AAATCTGGTGTCTGTACATGC	0.378																																					p.R195R		Atlas-SNP	.											.	DDX60	304	.	0			c.A585G						PASS	.						59	59	59					4																	169227551		2203	4300	6503	SO:0001819	synonymous_variant	55601	exon5			CTGGTGTCTGTAC	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.585A>G	4.37:g.169227551T>C		61	0	0		38	4	0.105263	NM_017631	Q6PK35|Q9NVE3	Silent	SNP	ENST00000393743.3	37	CCDS34097.1																																																																																			.	.	none		0.378	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631		C	169227551	T	C	169227551	2	2	28	1	0	0	0	0	0	0	0	1	4380	1664	58	3		3	DDX60	4	169227551	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	6195053	169227551	21926725	198	11701											
GPM6A	2823	hgsc.bcm.edu	37	chr4	176573028	176573028	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatttgctccctccactaaTgtggtgttccggcagatggt	7	13	11	10	1	0	2	0	0	0	2	3	2	3	2	3	3	1	3	3	3	1	3	rs72702639	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:176573028T>C	ENST00000280187.7	-	5	543	c.498A>G	c.(496-498)acA>acG	p.T166T	GPM6A_ENST00000515090.1_Silent_p.T159T|GPM6A_ENST00000393658.2_Silent_p.T166T|GPM6A_ENST00000506894.1_Silent_p.T155T	NM_005277.4	NP_005268.1	P51674	GPM6A_HUMAN	glycoprotein M6A	166					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)		CCTCCACTAATGTGGTGTTCC	0.458													T|||	138	0.0275559	0.0008	0.0072	5008	,	,		18223	0.0		0.0308	False		,,,				2504	0.1033				p.T166T		Atlas-SNP	.											.	GPM6A	70	.	0			c.A498G						PASS	.	T	,,	18,4388	25.3+/-52.1	1,16,2186	142	131	134		498,498,465	-11.2	0	4	dbSNP_130	134	174,8426	78.6+/-141.3	4,166,4130	no	coding-synonymous,coding-synonymous,coding-synonymous	GPM6A	NM_005277.3,NM_201591.1,NM_201592.1	,,	5,182,6316	CC,CT,TT		2.0233,0.4085,1.4762	,,	166/279,166/279,155/268	176573028	192,12814	2203	4300	6503	SO:0001819	synonymous_variant	2823	exon4			CACTAATGTGGTG		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.498A>G	4.37:g.176573028T>C		64	0	0		73	39	0.534247	NM_201591	B7Z642|E9PHI5|Q92602	Silent	SNP	ENST00000280187.7	37	CCDS3824.1																																																																																			T|0.986;C|0.014	0.014	strong		0.458	GPM6A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362163.1			C	176573028	T	C	176573028	2	2	28	1	0	0	0	0	0	0	0	1	6623	1451	51	3		3	GPM6A	4	176573028	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	7345477	176573028	14581248	199	11702											
WWC2	80014	hgsc.bcm.edu	37	chr4	184207192	184207192	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagaaactccaccgaacgcCgcagtttgagggtcaaaagg	13	6	12	10	3	1	2	1	2	0	1	2	4	2	2	3	2	2	2	3	2	4	1	rs148189381		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:184207192C>T	ENST00000403733.3	+	20	3320	c.3121C>T	c.(3121-3123)Cgc>Tgc	p.R1041C	WWC2_ENST00000508747.1_Missense_Mutation_p.R169C|WWC2_ENST00000504005.1_Missense_Mutation_p.R723C|WWC2_ENST00000448232.2_Missense_Mutation_p.R1065C|WWC2_ENST00000513834.1_Missense_Mutation_p.R992C	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	1041					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)		CACCGAACGCCGCAGTTTGAG	0.448																																					p.R1041C		Atlas-SNP	.											.	WWC2	78	.	0			c.C3121T						PASS	.	C	CYS/ARG	0,4404		0,0,2202	73	63	67		3121	4.4	1	4	dbSNP_134	67	1,8599		0,1,4299	no	missense	WWC2	NM_024949.5	180	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	1041/1193	184207192	1,13003	2202	4300	6502	SO:0001583	missense	80014	exon20			GAACGCCGCAGTT	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.3121C>T	4.37:g.184207192C>T	ENSP00000384222:p.Arg1041Cys	52	0	0		80	40	0.5	NM_024949	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Missense_Mutation	SNP	ENST00000403733.3	37	CCDS34109.2	.	.	.	.	.	.	.	.	.	.	C	19.81	3.897272	0.72639	0.0	1.16E-4	ENSG00000151718	ENST00000403733;ENST00000513834;ENST00000448232;ENST00000504005;ENST00000508747	T;T;T;T;T	0.56103	0.48;0.48;0.48;0.48;0.48	5.23	4.39	0.52855	.	0.082358	0.50627	D	0.000117	T	0.71350	0.3329	M	0.82823	2.61	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;0.998	T	0.73672	-0.3909	10	0.54805	T	0.06	-15.2741	9.6331	0.39791	0.1967:0.7307:0.0:0.0726	.	1065;1041;169;992	Q6AWC2-6;Q6AWC2;Q6AWC2-7;Q6AWC2-4	.;WWC2_HUMAN;.;.	C	1041;992;1065;723;169	ENSP00000384222:R1041C;ENSP00000425054:R992C;ENSP00000398577:R1065C;ENSP00000427569:R723C;ENSP00000420835:R169C	ENSP00000384222:R1041C	R	+	1	0	WWC2	184444186	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.516000	0.45520	1.443000	0.47586	0.655000	0.94253	CGC	C|1.000;T|0.000	0.000	weak		0.448	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949		T	184207192	C	T	184207192	3	4	28	1	0	0	0	0	1	0	0	0	17427	652	23	1	3199	1	WWC2	4	184207192	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	7634164	184207192	6947084	200	11703											
SORBS2	8470	hgsc.bcm.edu	37	chr4	186536235	186536235	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggaagatgcccactctcccGtggtgttctccctcatacca	7	10	9	15	1	3	1	1	0	2	1	5	2	3	2	4	2	2	1	4	2	2	2	rs373495088		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:186536235G>A	ENST00000284776.7	-	16	3227	c.2718C>T	c.(2716-2718)caC>caT	p.H906H	SORBS2_ENST00000437304.2_Silent_p.H630H|SORBS2_ENST00000448662.2_Silent_p.H467H|SORBS2_ENST00000449407.2_Silent_p.H450H|SORBS2_ENST00000498125.1_5'UTR|SORBS2_ENST00000393528.3_Silent_p.H472H|SORBS2_ENST00000418609.1_Silent_p.H810H|SORBS2_ENST00000355634.5_Silent_p.H1006H|SORBS2_ENST00000431808.1_Silent_p.H906H|SORBS2_ENST00000319471.9_Silent_p.H537H	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	906	SH3 1. {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)		CCACTCTCCCGTGGTGTTCTC	0.468																																					p.H1006H	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-SNP	.											.	SORBS2	300	.	0			c.C3018T						PASS	.	G	,,,,,,,	0,4406		0,0,2203	145	134	138		1350,1611,1401,1890,2430,894,1416,2718	-6.9	0.3	4		138	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SORBS2	NM_001145670.1,NM_001145671.1,NM_001145672.1,NM_001145673.1,NM_001145674.1,NM_001145675.1,NM_003603.5,NM_021069.4	,,,,,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,,,,	450/645,537/732,467/662,630/825,810/1005,298/493,472/667,906/1101	186536235	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8470	exon19			TCTCCCGTGGTGT		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.2718C>T	4.37:g.186536235G>A		129	0	0		142	71	0.5	NM_001270771	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Silent	SNP	ENST00000284776.7	37	CCDS3845.1																																																																																			.	.	weak		0.468	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603		A	186536235	G	A	186536235	2	1	28	1	0	0	0	0	0	0	0	1	14943	1136	40	1		1	SORBS2	4	186536235	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2329043	186536235	4618041	201	11704											
SDHA	6389	hgsc.bcm.edu	37	chr5	256508	256508	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aacgaggctgactgtgccacCgtcccgccagccattcgctc	7	7	10	17	4	0	1	0	1	0	0	3	2	1	1	5	1	3	2	5	1	1	1	rs3211499		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:256508C>T	ENST00000264932.6	+	15	2083	c.1968C>T	c.(1966-1968)acC>acT	p.T656T	SDHA_ENST00000510361.1_Silent_p.T608T|SDHA_ENST00000504309.1_Silent_p.T575T|SDHA_ENST00000507522.1_3'UTR	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	656					cellular metabolic process (GO:0044237)|nervous system development (GO:0007399)|oxidation-reduction process (GO:0055114)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|tricarboxylic acid cycle (GO:0006099)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|succinate dehydrogenase (ubiquinone) activity (GO:0008177)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|liver(2)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	40			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	ACTGTGCCACCGTCCCGCCAG	0.438									Familial Paragangliomas																												p.T656T		Atlas-SNP	.											SDHA,NS,carcinoma,+2,1	SDHA	80	1	0			c.C1968T						scavenged	.						70	78	75					5																	256508		2203	4300	6503	SO:0001819	synonymous_variant	6389	exon15	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	TGCCACCGTCCCG	BC001380	CCDS3853.1	5p15	2014-09-17			ENSG00000073578	ENSG00000073578		"Mitochondrial respiratory chain complex / Complex II"	10680	protein-coding gene	gene with protein product		600857		SDH2		7798181	Standard	XM_005248329		Approved	FP, SDHF	uc003jao.4	P31040	OTTHUMG00000090275	ENST00000264932.6:c.1968C>T	5.37:g.256508C>T		93	0	0		102	7	0.0686275	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Silent	SNP	ENST00000264932.6	37	CCDS3853.1																																																																																			.	.	weak		0.438	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168		T	256508	C	T	256508	2	4	28	1	0	0	0	0	0	0	0	1	13978	639	23	1		1	SDHA	5	256508	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10		256508	180658752	202	11705											
AHRR	57491	hgsc.bcm.edu	37	chr5	422858	422858	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tttcagacggatgtaatgcaCcagaacatttatgactacat	14	12	7	8	1	1	3	1	1	0	2	1	4	1	4	1	1	3	2	1	1	4	5	rs562253075		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:422858C>G	ENST00000505113.1	+	6	512	c.468C>G	c.(466-468)caC>caG	p.H156Q	AHRR_ENST00000512529.1_Missense_Mutation_p.H2Q|AHRR_ENST00000506456.1_Missense_Mutation_p.H12Q|AHRR_ENST00000316418.5_Missense_Mutation_p.H156Q	NM_001242412.1	NP_001229341.1	A9YTQ3	AHRR_HUMAN	aryl-hydrocarbon receptor repressor	156	PAS. {ECO:0000255|PROSITE- ProRule:PRU00140}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein sumoylation (GO:0033235)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|endometrium(4)|large_intestine(1)|lung(12)|prostate(1)	20			Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)			ATGTAATGCACCAGAACATTT	0.522																																					p.H156Q		Atlas-SNP	.											.	AHRR	67	.	0			c.C468G						PASS	.						92	98	96					5																	422858		1997	4152	6149	SO:0001583	missense	57491	exon6			AATGCACCAGAAC	AB033060	CCDS43297.1, CCDS56355.1	5p15.33	2013-05-21	2003-09-11	2003-09-12	ENSG00000063438	ENSG00000063438		"Basic helix-loop-helix proteins"	346	protein-coding gene	gene with protein product		606517	"aryl hydrocarbon receptor regulator"	AHH, AHHR		1070014, 11423533	Standard	NM_020731		Approved	KIAA1234, bHLHe77	uc003jaw.3	A9YTQ3	OTTHUMG00000162171	ENST00000505113.1:c.468C>G	5.37:g.422858C>G	ENSP00000424601:p.His156Gln	107	0	0		119	53	0.445378	NM_001242412	A7MBN5|D6RAZ1|Q9HAZ3|Q9ULI6	Missense_Mutation	SNP	ENST00000505113.1	37	CCDS56355.1	.	.	.	.	.	.	.	.	.	.	C	12.88	2.070730	0.36566	.	.	ENSG00000063438	ENST00000505113;ENST00000316418;ENST00000512529;ENST00000514523;ENST00000510400;ENST00000506456	T;T;T;T;T	0.36878	2.32;2.32;1.3;2.32;1.23	4.76	0.128	0.14733	PAS (2);PAS fold (1);	0.047043	0.85682	D	0.000000	T	0.51787	0.1695	M	0.72576	2.205	0.58432	D	0.999991	D;D;D	0.76494	0.999;0.993;0.99	D;D;D	0.74023	0.982;0.954;0.923	T	0.49744	-0.8907	10	0.87932	D	0	.	8.2783	0.31885	0.0:0.4437:0.0:0.5563	.	12;156;156	D6RE68;A9YTQ3;A9YTQ3-2	.;AHRR_HUMAN;.	Q	156;156;2;2;152;12	ENSP00000424601:H156Q;ENSP00000323816:H156Q;ENSP00000424880:H2Q;ENSP00000428893:H152Q;ENSP00000426932:H12Q	ENSP00000323816:H156Q	H	+	3	2	AHRR	475858	0.862000	0.29867	0.994000	0.49952	0.918000	0.54935	-0.009000	0.12765	-0.051000	0.13334	0.655000	0.94253	CAC	.	.	none		0.522	AHRR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367720.1	NM_020731		G	422858	C	G	422858	3	3	28	1	0	0	0	0	1	0	0	0	417	506	18	4	490	4	AHRR	5	422858	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	166350	422858	180492402	203	11706											
AHRR	57491	hgsc.bcm.edu	37	chr5	434546	434546	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cagtgacaggagccacccagCcaccttccctaccaggatgc	10	5	9	17	0	0	1	0	1	0	0	1	3	1	3	6	2	4	0	6	2	1	2	rs61757546	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:434546C>T	ENST00000505113.1	+	11	1747	c.1703C>T	c.(1702-1704)gCc>gTc	p.A568V	AHRR_ENST00000512529.1_Missense_Mutation_p.A414V|AHRR_ENST00000506456.1_Missense_Mutation_p.A424V|AHRR_ENST00000316418.5_Missense_Mutation_p.A586V	NM_001242412.1	NP_001229341.1	A9YTQ3	AHRR_HUMAN	aryl-hydrocarbon receptor repressor	568	Needed for transcriptional repression. {ECO:0000250}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein sumoylation (GO:0033235)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|endometrium(4)|large_intestine(1)|lung(12)|prostate(1)	20			Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)			AGCCACCCAGCCACCTTCCCT	0.637													C|||	16	0.00319489	0.0	0.0029	5008	,	,		16396	0.0		0.0129	False		,,,				2504	0.001				p.A586V		Atlas-SNP	.											.	AHRR	67	.	0			c.C1757T						PASS	.	C	VAL/ALA,VAL/ALA	2,4254		0,2,2126	51	58	56		1703,1757	-2.3	0	5	dbSNP_129	56	40,8438		0,40,4199	yes	missense,missense	AHRR	NM_001242412.1,NM_020731.4	64,64	0,42,6325	TT,TC,CC		0.4718,0.047,0.3298	benign,benign	568/702,586/720	434546	42,12692	2128	4239	6367	SO:0001583	missense	57491	exon12			ACCCAGCCACCTT	AB033060	CCDS43297.1, CCDS56355.1	5p15.33	2013-05-21	2003-09-11	2003-09-12	ENSG00000063438	ENSG00000063438		"Basic helix-loop-helix proteins"	346	protein-coding gene	gene with protein product		606517	"aryl hydrocarbon receptor regulator"	AHH, AHHR		1070014, 11423533	Standard	NM_020731		Approved	KIAA1234, bHLHe77	uc003jaw.3	A9YTQ3	OTTHUMG00000162171	ENST00000505113.1:c.1703C>T	5.37:g.434546C>T	ENSP00000424601:p.Ala568Val	44	0	0		43	19	0.44186	NM_020731	A7MBN5|D6RAZ1|Q9HAZ3|Q9ULI6	Missense_Mutation	SNP	ENST00000505113.1	37	CCDS56355.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	C	0.008	-1.892504	0.00522	4.7E-4	0.004718	ENSG00000063438	ENST00000505113;ENST00000316418;ENST00000512529;ENST00000506456	T;T;T;T	0.20069	2.44;2.43;2.11;2.1	4.43	-2.29	0.06805	.	0.629100	0.15903	N	0.238965	T	0.03095	0.0091	N	0.01168	-0.975	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	0.39860	-0.9593	10	0.09590	T	0.72	.	5.5855	0.17272	0.1478:0.4627:0.0:0.3895	rs61757546	424;568;586	D6RE68;A9YTQ3;A9YTQ3-2	.;AHRR_HUMAN;.	V	568;586;414;424	ENSP00000424601:A568V;ENSP00000323816:A586V;ENSP00000424880:A414V;ENSP00000426932:A424V	ENSP00000323816:A586V	A	+	2	0	AHRR	487546	0.000000	0.05858	0.000000	0.03702	0.179000	0.23085	0.002000	0.13061	-0.364000	0.08088	-0.263000	0.10527	GCC	C|0.996;T|0.004	0.004	strong		0.637	AHRR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367720.1	NM_020731		T	434546	C	T	434546	3	4	28	1	0	0	0	0	1	0	0	0	417	739	26	2	1803	2	AHRR	5	434546	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	11688	434546	180480714	204	11707											
DNAH5	1767	hgsc.bcm.edu	37	chr5	13700783	13700783	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	taaatccttatgacaggcatCaactcaaagagcacttttgg	14	11	7	9	0	2	2	2	1	0	1	3	2	3	2	1	2	2	2	1	2	5	4	rs374221053		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:13700783C>G	ENST00000265104.4	-	78	13793	c.13689G>C	c.(13687-13689)ttG>ttC	p.L4563F		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4563					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)					TGACAGGCATCAACTCAAAGA	0.413									Kartagener syndrome																												p.L4563F		Atlas-SNP	.											.	DNAH5	868	.	0			c.G13689C						PASS	.	C	PHE/LEU	0,4406		0,0,2203	183	176	178		13689	2.1	0.8	5		178	1,8599	1.2+/-3.3	0,1,4299	no	missense	DNAH5	NM_001369.2	22	0,1,6502	GG,GC,CC		0.0116,0.0,0.0077	possibly-damaging	4563/4625	13700783	1,13005	2203	4300	6503	SO:0001583	missense	1767	exon78	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AGGCATCAACTCA	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.13689G>C	5.37:g.13700783C>G	ENSP00000265104:p.Leu4563Phe	173	0	0		155	75	0.483871	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	14.00	2.405974	0.42715	0.0	1.16E-4	ENSG00000039139	ENST00000265104	T	0.08896	3.04	5.95	2.1	0.27182	Dynein heavy chain (1);	0.167558	0.46758	D	0.000275	T	0.14013	0.0339	M	0.73430	2.235	0.36463	D	0.866823	P	0.37612	0.602	P	0.45474	0.482	T	0.04427	-1.0952	10	0.51188	T	0.08	.	5.1797	0.15154	0.0:0.4605:0.2582:0.2813	.	4563	Q8TE73	DYH5_HUMAN	F	4563	ENSP00000265104:L4563F	ENSP00000265104:L4563F	L	-	3	2	DNAH5	13753783	0.427000	0.25514	0.788000	0.31933	0.528000	0.34623	0.101000	0.15251	0.095000	0.17434	-0.182000	0.12963	TTG	.	.	weak		0.413	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		G	13700783	C	G	13700783	3	3	28	1	0	0	0	0	1	0	0	0	4606	825	29	4	193	4	DNAH5	5	13700783	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	13266237	13700783	167214477	205	11708											
MYO10	4651	hgsc.bcm.edu	37	chr5	16676247	16676247	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aaatctgttccaccacatccGagttcaggcagttctcctaa	11	11	6	13	1	3	0	1	0	2	0	6	1	5	0	4	1	0	4	4	1	2	4	rs61744227	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:16676247G>A	ENST00000513610.1	-	34	5013	c.4559C>T	c.(4558-4560)tCg>tTg	p.S1520L	MYO10_ENST00000505695.1_Missense_Mutation_p.S859L|MYO10_ENST00000427430.2_Missense_Mutation_p.S877L|MYO10_ENST00000274203.9_Missense_Mutation_p.S877L|MYO10_ENST00000515803.1_Missense_Mutation_p.S859L	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	1520					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						CACCACATCCGAGTTCAGGCA	0.428													G|||	19	0.00379393	0.0	0.0029	5008	,	,		17461	0.0		0.0109	False		,,,				2504	0.0061				p.S1520L		Atlas-SNP	.											.	MYO10	198	.	0			c.C4559T						PASS	.	G	LEU/SER	7,3821		0,7,1907	119	127	125		4559	3.3	0	5	dbSNP_129	125	84,8158		2,80,4039	yes	missense	MYO10	NM_012334.2	145	2,87,5946	AA,AG,GG		1.0192,0.1829,0.7539	benign	1520/2059	16676247	91,11979	1914	4121	6035	SO:0001583	missense	4651	exon34			ACATCCGAGTTCA	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.4559C>T	5.37:g.16676247G>A	ENSP00000421280:p.Ser1520Leu	117	0	0		82	37	0.451219	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	37	CCDS54834.1	10	0.004578754578754579	0	0.0	0	0.0	0	0.0	10	0.013192612137203167	G	10.94	1.493361	0.26774	0.001829	0.010192	ENSG00000145555	ENST00000513610;ENST00000515803;ENST00000274203;ENST00000505695;ENST00000427430	T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93	5.31	3.27	0.37495	.	.	.	.	.	T	0.18425	0.0442	N	0.17674	0.51	0.09310	N	1	B;B;B	0.09022	0.002;0.0;0.001	B;B;B	0.04013	0.001;0.0;0.001	T	0.17289	-1.0374	9	0.27785	T	0.31	.	6.3605	0.21425	0.1845:0.1421:0.6734:0.0	.	399;1160;1520	B4DIJ5;Q69YP8;Q9HD67	.;.;MYO10_HUMAN	L	1520;859;877;859;877	ENSP00000421280:S1520L;ENSP00000425051:S859L;ENSP00000274203:S877L;ENSP00000421170:S859L;ENSP00000391106:S877L	ENSP00000274203:S877L	S	-	2	0	MYO10	16729247	0.013000	0.17824	0.008000	0.14137	0.950000	0.60333	1.891000	0.39738	0.554000	0.29061	0.563000	0.77884	TCG	G|0.994;A|0.006	0.006	strong		0.428	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		A	16676247	G	A	16676247	3	1	28	1	0	0	0	0	1	0	0	0	10071	1059	37	1	1649	1	MYO10	5	16676247	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2975464	16676247	164239013	206	11709											
MYO10	4651	hgsc.bcm.edu	37	chr5	16701796	16701796	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagctcctgctgctccttcAtgcgctgcaggtcctcgatt	5	12	9	15	2	1	0	1	0	0	0	5	1	4	0	3	1	5	5	3	1	0	2	rs112696559	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:16701796A>G	ENST00000513610.1	-	25	3162	c.2708T>C	c.(2707-2709)aTg>aCg	p.M903T	MYO10_ENST00000505695.1_Missense_Mutation_p.M242T|MYO10_ENST00000427430.2_Missense_Mutation_p.M260T|MYO10_ENST00000274203.9_Missense_Mutation_p.M260T|MYO10_ENST00000512061.1_5'Flank|MYO10_ENST00000515803.1_Missense_Mutation_p.M242T	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	903	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						CTGCTCCTTCATGCGCTGCAG	0.587													A|||	28	0.00559105	0.0	0.0029	5008	,	,		18003	0.0		0.0129	False		,,,				2504	0.0133				p.M903T		Atlas-SNP	.											.	MYO10	198	.	0			c.T2708C						PASS	.	A	THR/MET	6,4234		0,6,2114	40	44	43		2708	3.8	1	5	dbSNP_132	43	79,8425		2,75,4175	yes	missense	MYO10	NM_012334.2	81	2,81,6289	GG,GA,AA		0.929,0.1415,0.667	benign	903/2059	16701796	85,12659	2120	4252	6372	SO:0001583	missense	4651	exon25			TCCTTCATGCGCT	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.2708T>C	5.37:g.16701796A>G	ENSP00000421280:p.Met903Thr	131	0	0		133	62	0.466165	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	37	CCDS54834.1	11	0.005036630036630037	0	0.0	0	0.0	0	0.0	11	0.014511873350923483	A	9.654	1.142336	0.21205	0.001415	0.00929	ENSG00000145555	ENST00000513610;ENST00000515803;ENST00000274203;ENST00000505695;ENST00000427430	T;T;T;T;T	0.03982	3.74;3.74;3.74;3.74;3.74	5.0	3.82	0.43975	.	.	.	.	.	T	0.02047	0.0064	N	0.14661	0.345	0.29659	N	0.843378	B;B	0.17667	0.01;0.023	B;B	0.11329	0.004;0.006	T	0.40289	-0.9571	9	0.19147	T	0.46	.	7.2935	0.26380	0.7044:0.1512:0.0:0.1444	.	544;903	Q69YP8;Q9HD67	.;MYO10_HUMAN	T	903;242;260;242;260	ENSP00000421280:M903T;ENSP00000425051:M242T;ENSP00000274203:M260T;ENSP00000421170:M242T;ENSP00000391106:M260T	ENSP00000274203:M260T	M	-	2	0	MYO10	16754796	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	3.753000	0.55180	0.733000	0.32492	-0.460000	0.05396	ATG	A|0.994;G|0.006;T|0.000	0.006	strong		0.587	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		G	16701796	A	G	16701796	3	3	28	1	0	0	0	0	1	0	0	0	10071	217	8	3	3536	3	MYO10	5	16701796	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	25549	16701796	164213464	207	11710											
MYO10	4651	hgsc.bcm.edu	37	chr5	16877739	16877739	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgaccatagtctgtccggaaGacgacgatgccttctgcaca	10	9	10	12	3	2	2	0	1	2	1	3	5	3	3	3	1	2	1	3	1	2	2	rs185323430		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:16877739G>A	ENST00000513610.1	-	2	553	c.99C>T	c.(97-99)gtC>gtT	p.V33V	MYO10_ENST00000507288.1_Silent_p.V33V	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	33					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						CTGTCCGGAAGACGACGATGC	0.498													G|||	1	0.000199681	0.0	0.0	5008	,	,		18799	0.0		0.001	False		,,,				2504	0.0				p.V33V		Atlas-SNP	.											.	MYO10	198	.	0			c.C99T						PASS	.	G		0,4024		0,0,2012	104	105	105		99	2.5	1	5		105	6,8338		0,6,4166	no	coding-synonymous	MYO10	NM_012334.2		0,6,6178	AA,AG,GG		0.0719,0.0,0.0485		33/2059	16877739	6,12362	2012	4172	6184	SO:0001819	synonymous_variant	4651	exon2			CCGGAAGACGACG	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.99C>T	5.37:g.16877739G>A		63	0	0		60	34	0.566667	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	37	CCDS54834.1																																																																																			G|0.999;A|0.001	0.001	strong		0.498	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334		A	16877739	G	A	16877739	2	1	28	1	0	0	0	0	0	0	0	1	10071	929	33	2		2	MYO10	5	16877739	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	175943	16877739	164037521	208	11711											
CDH9	1007	hgsc.bcm.edu	37	chr5	26885964	26885964	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctttccgagtcatgattccTgctgtattatctgggggaga	7	15	11	8	1	3	2	1	1	2	1	5	4	5	2	2	2	1	2	2	2	2	4	rs35328154	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:26885964T>G	ENST00000231021.4	-	11	1813	c.1641A>C	c.(1639-1641)gcA>gcC	p.A547A		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	547	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						TCATGATTCCTGCTGTATTAT	0.318													T|||	49	0.00978435	0.0	0.0187	5008	,	,		17688	0.0		0.0109	False		,,,				2504	0.0256				p.A547A	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.A1641C						PASS	.	T		7,4399	11.4+/-27.6	0,7,2196	55	58	57		1641	-4.3	1	5	dbSNP_126	57	82,8518	44.0+/-102.2	0,82,4218	no	coding-synonymous	CDH9	NM_016279.3		0,89,6414	GG,GT,TT		0.9535,0.1589,0.6843		547/790	26885964	89,12917	2203	4300	6503	SO:0001819	synonymous_variant	1007	exon11			GATTCCTGCTGTA	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.1641A>C	5.37:g.26885964T>G		72	0	0		60	26	0.433333	NM_016279	Q3B7I5	Silent	SNP	ENST00000231021.4	37	CCDS3893.1																																																																																			T|0.992;G|0.008	0.008	strong		0.318	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279		G	26885964	T	G	26885964	2	3	28	1	0	0	0	0	0	0	0	1	3119	1567	55	5		5	CDH9	5	26885964	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	10008225	26885964	154029296	209	11712											
ADAMTS12	81792	hgsc.bcm.edu	37	chr5	33576803	33576803	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctccgaggtaggaccagtatCtgaactggaaacattttcct	11	11	9	10	1	1	1	0	1	1	0	3	4	3	3	3	3	2	2	3	3	4	4			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:33576803C>T	ENST00000504830.1	-	19	3663	c.3328G>A	c.(3328-3330)Gat>Aat	p.D1110N	ADAMTS12_ENST00000504582.1_5'Flank|ADAMTS12_ENST00000352040.3_Missense_Mutation_p.D1025N	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	1110	Spacer 2.				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						GGACCAGTATCTGAACTGGAA	0.507										HNSCC(64;0.19)																											p.D1110N		Atlas-SNP	.											.	ADAMTS12	464	.	0			c.G3328A						PASS	.						95	89	91					5																	33576803		2203	4300	6503	SO:0001583	missense	81792	exon19			CAGTATCTGAACT	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.3328G>A	5.37:g.33576803C>T	ENSP00000422554:p.Asp1110Asn	83	0	0		111	49	0.441441	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	c	8.033	0.762246	0.15914	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.59772	0.25;0.24	5.22	4.33	0.51752	.	1.532230	0.03305	N	0.189648	T	0.45637	0.1352	L	0.27053	0.805	0.21675	N	0.999593	B;B	0.34015	0.435;0.201	B;B	0.30572	0.117;0.055	T	0.35351	-0.9792	10	0.21014	T	0.42	.	8.6051	0.33769	0.0:0.7653:0.1545:0.0802	.	1025;1110	P58397-3;P58397	.;ATS12_HUMAN	N	1110;1025	ENSP00000422554:D1110N;ENSP00000344847:D1025N	ENSP00000344847:D1025N	D	-	1	0	ADAMTS12	33612560	0.000000	0.05858	0.170000	0.22879	0.143000	0.21401	-0.091000	0.11146	1.391000	0.46566	0.651000	0.88453	GAT	.	.	none		0.507	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		T	33576803	C	T	33576803	3	4	28	1	0	0	0	0	1	0	0	0	257	913	32	2	1480	2	ADAMTS12	5	33576803	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	6690839	33576803	147338457	210	11713											
NIPBL	25836	hgsc.bcm.edu	37	chr5	36985274	36985274	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acaactgaatgcaaacaaaaCgagagcaccatagttgagcc	18	5	8	10	1	0	3	0	2	0	1	0	4	0	3	2	0	6	3	2	0	6	2	rs116049172		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:36985274C>T	ENST00000282516.8	+	10	2491	c.1992C>T	c.(1990-1992)aaC>aaT	p.N664N	NIPBL_ENST00000448238.2_Silent_p.N664N|NIPBL_ENST00000504430.1_3'UTR	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	664					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)			GCAAACAAAACGAGAGCACCA	0.338													C|||	1	0.000199681	0.0	0.0	5008	,	,		20570	0.0		0.001	False		,,,				2504	0.0				p.N664N		Atlas-SNP	.											.	NIPBL	513	.	0			c.C1992T						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	97	96	96		1992,1992	0.7	0.9	5	dbSNP_132	96	2,8598	3.0+/-9.4	0,2,4298	no	coding-synonymous,coding-synonymous	NIPBL	NM_015384.4,NM_133433.3	,	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	,	664/2698,664/2805	36985274	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	25836	exon10			ACAAAACGAGAGC	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.1992C>T	5.37:g.36985274C>T		94	0	0		121	68	0.561983	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Silent	SNP	ENST00000282516.8	37	CCDS3920.1																																																																																			C|1.000;T|0.000	0.000	strong		0.338	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384		T	36985274	C	T	36985274	2	4	28	1	0	0	0	0	0	0	0	1	10437	535	19	1		1	NIPBL	5	36985274	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	3408471	36985274	143929986	211	11714											
IL6ST	3572	hgsc.bcm.edu	37	chr5	55251889	55251889	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agggatagttaaaacagctgCatctgatttgccaacaagat	15	10	9	7	0	1	2	0	1	1	1	1	3	1	3	1	1	5	3	1	1	5	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:55251889C>T	ENST00000381298.2	-	10	1543	c.1231G>A	c.(1231-1233)Gca>Aca	p.A411T	IL6ST_ENST00000381294.3_Missense_Mutation_p.A411T|IL6ST_ENST00000381293.2_Intron|IL6ST_ENST00000502326.3_Missense_Mutation_p.A411T|IL6ST_ENST00000336909.5_Missense_Mutation_p.A411T|IL6ST_ENST00000522633.2_3'UTR|IL6ST_ENST00000381286.3_Intron|IL6ST_ENST00000536319.1_3'UTR|IL6ST_ENST00000381287.4_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	411	Fibronectin type-III 3. {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)				AAAACAGCTGCATCTGATTTG	0.413			O		hepatocellular ca																																p.A411T		Atlas-SNP	.		Dom	yes		5	5q11	3572	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"		E	.	IL6ST	75	.	0			c.G1231A						PASS	.						142	131	135					5																	55251889		2203	4300	6503	SO:0001583	missense	3572	exon10			CAGCTGCATCTGA	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.1231G>A	5.37:g.55251889C>T	ENSP00000370698:p.Ala411Thr	119	0	0		141	61	0.432624	NM_002184	A0N0L4|Q5FC04|Q9UQ41	Missense_Mutation	SNP	ENST00000381298.2	37	CCDS3971.1	.	.	.	.	.	.	.	.	.	.	C	1.910	-0.450848	0.04572	.	.	ENSG00000134352	ENST00000381298;ENST00000336909;ENST00000381294	T;T;T	0.43688	0.94;0.94;0.94	5.86	0.727	0.18254	Long hematopoietin receptor, Gp130 family 2, conserved site (1);Fibronectin, type III (2);	0.981590	0.08384	N	0.954070	T	0.40956	0.1138	M	0.71036	2.16	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.06405	0.0;0.002;0.0	T	0.41251	-0.9519	10	0.56958	D	0.05	.	6.7334	0.23395	0.0:0.3836:0.3238:0.2926	.	411;411;411	Q17RA0;Q5FC04;P40189	.;.;IL6RB_HUMAN	T	411	ENSP00000370698:A411T;ENSP00000338799:A411T;ENSP00000370694:A411T	ENSP00000338799:A411T	A	-	1	0	IL6ST	55287646	0.007000	0.16637	0.002000	0.10522	0.162000	0.22319	-0.060000	0.11712	0.166000	0.19597	-0.145000	0.13849	GCA	.	.	none		0.413	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184		T	55251889	C	T	55251889	3	4	28	1	0	0	0	0	1	0	0	0	7712	710	25	2	1557	2	IL6ST	5	55251889	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	18266615	55251889	125663371	212	11715											
MCCC2	64087	hgsc.bcm.edu	37	chr5	70888804	70888804	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	atcagctccatgaacgagtgGagcatataaaactaggtaaa	17	8	9	7	1	1	1	1	1	0	0	2	3	2	2	1	2	4	3	1	2	7	4			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:70888804G>A	ENST00000340941.6	+	2	310	c.181G>A	c.(181-183)Gag>Aag	p.E61K	MCCC2_ENST00000323375.8_Missense_Mutation_p.E61K|MCCC2_ENST00000509358.2_Missense_Mutation_p.E61K	NM_022132.4	NP_071415.1	Q9HCC0	MCCB_HUMAN	methylcrotonoyl-CoA carboxylase 2 (beta)	61	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)	TGAACGAGTGGAGCATATAAA	0.348																																					p.E61K		Atlas-SNP	.											.	MCCC2	47	.	0			c.G181A						PASS	.						69	67	67					5																	70888804		2203	4300	6503	SO:0001583	missense	64087	exon2			CGAGTGGAGCATA	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.181G>A	5.37:g.70888804G>A	ENSP00000343657:p.Glu61Lys	245	0	0		256	137	0.535156	NM_022132	A6NIY9|Q96C27|Q9Y4L7	Missense_Mutation	SNP	ENST00000340941.6	37	CCDS34184.1	.	.	.	.	.	.	.	.	.	.	G	10.36	1.327666	0.24080	.	.	ENSG00000131844	ENST00000340941;ENST00000509358;ENST00000323375	D;D;D	0.98090	-4.71;-4.71;-4.71	4.73	0.197	0.15164	Acetyl-coenzyme A carboxyltransferase, N-terminal (1);	0.297876	0.35903	N	0.002915	D	0.96015	0.8702	M	0.69185	2.1	0.34463	D	0.701963	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	D	0.92607	0.6096	10	0.36615	T	0.2	-1.2046	16.3491	0.83195	0.0:0.3931:0.6069:0.0	.	61;61	D6RDF7;Q9HCC0	.;MCCB_HUMAN	K	61	ENSP00000343657:E61K;ENSP00000420994:E61K;ENSP00000327308:E61K	ENSP00000327308:E61K	E	+	1	0	MCCC2	70924560	0.999000	0.42202	0.001000	0.08648	0.001000	0.01503	0.986000	0.29590	0.062000	0.16340	-0.153000	0.13522	GAG	.	.	none		0.348	MCCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369243.4			A	70888804	G	A	70888804	3	1	28	1	0	0	0	0	1	0	0	0	9384	1175	41	2	187	2	MCCC2	5	70888804	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	15636915	70888804	110026456	213	11716											
POC5	134359	hgsc.bcm.edu	37	chr5	74998489	74998489	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttctgaaggttttcatcagAaacaagaaaatcgctcacaa	16	10	6	9	1	4	3	3	1	1	2	5	3	4	3	0	1	1	2	0	1	6	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:74998489A>G	ENST00000428202.2	-	5	643	c.454T>C	c.(454-456)Tct>Cct	p.S152P	POC5_ENST00000514838.2_Missense_Mutation_p.S124P|POC5_ENST00000510798.1_Missense_Mutation_p.S35P|POC5_ENST00000380475.2_Missense_Mutation_p.S35P|POC5_ENST00000504862.1_5'UTR|POC5_ENST00000446329.2_Missense_Mutation_p.S127P	NM_001099271.1	NP_001092741.1	Q8NA72	POC5_HUMAN	POC5 centriolar protein	152					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						TTTTCATCAGAAACAAGAAAA	0.378																																					p.S152P		Atlas-SNP	.											.	POC5	82	.	0			c.T454C						PASS	.						89	84	86					5																	74998489		1888	4109	5997	SO:0001583	missense	134359	exon5			CATCAGAAACAAG	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.454T>C	5.37:g.74998489A>G	ENSP00000410216:p.Ser152Pro	120	0	0		99	4	0.040404	NM_001099271	B4DJG7|Q494X7|Q494X9|Q6P085	Missense_Mutation	SNP	ENST00000428202.2	37	CCDS47236.1	.	.	.	.	.	.	.	.	.	.	A	12.80	2.046958	0.36085	.	.	ENSG00000152359	ENST00000428202;ENST00000514838;ENST00000380475;ENST00000510798;ENST00000446329;ENST00000503835;ENST00000502826	T;T;T;T;T	0.48836	1.84;1.42;0.8;0.8;1.84	5.78	4.51	0.55191	.	0.325126	0.38492	N	0.001678	T	0.51907	0.1702	L	0.47716	1.5	0.32491	N	0.54012	D;B;B	0.76494	0.999;0.148;0.281	D;B;B	0.64776	0.929;0.07;0.122	T	0.58457	-0.7633	10	0.26408	T	0.33	-9.7843	5.43	0.16448	0.7038:0.0:0.144:0.1522	.	35;152;127	Q8NA72-2;Q8NA72;Q8NA72-3	.;POC5_HUMAN;.	P	152;124;35;35;127;35;35	ENSP00000410216:S152P;ENSP00000420971:S124P;ENSP00000369842:S35P;ENSP00000426796:S35P;ENSP00000399481:S127P	ENSP00000369842:S35P	S	-	1	0	POC5	75034245	1.000000	0.71417	0.975000	0.42487	0.928000	0.56348	0.951000	0.29135	2.205000	0.71048	0.533000	0.62120	TCT	.	.	none		0.378	POC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369124.1	NM_152408		G	74998489	A	G	74998489	3	3	28	1	0	0	0	0	1	0	0	0	12186	246	9	3	1305	3	POC5	5	74998489	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	4109685	74998489	105916771	214	11717											
WDR41	55255	hgsc.bcm.edu	37	chr5	76728996	76728996	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagtcaccattctcctctaaTttttgaaataatcttaaact	14	16	2	9	0	4	1	1	1	3	0	5	1	4	1	2	0	1	0	2	0	6	6	rs72769029	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:76728996T>C	ENST00000296679.4	-	13	1719	c.1344A>G	c.(1342-1344)aaA>aaG	p.K448K	WDR41_ENST00000512033.1_5'UTR|WDR41_ENST00000507029.1_Silent_p.K393K|WDR41_ENST00000414719.2_Silent_p.K194K	NM_018268.2	NP_060738.2	Q9HAD4	WDR41_HUMAN	WD repeat domain 41	448						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)		TCTCCTCTAATTTTTGAAATA	0.368													T|||	83	0.0165735	0.0015	0.0245	5008	,	,		17492	0.0		0.0338	False		,,,				2504	0.0307				p.K448K		Atlas-SNP	.											.	WDR41	29	.	0			c.A1344G						PASS	.	T		21,4383	27.2+/-55.0	0,21,2181	118	121	120		1344	-0.2	1	5	dbSNP_130	120	238,8362	96.8+/-158.5	5,228,4067	no	coding-synonymous	WDR41	NM_018268.2		5,249,6248	CC,CT,TT		2.7674,0.4768,1.9917		448/460	76728996	259,12745	2202	4300	6502	SO:0001819	synonymous_variant	55255	exon13			CTCTAATTTTTGA	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.1344A>G	5.37:g.76728996T>C		135	0	0		201	101	0.502488	NM_018268	B4DT55|Q7Z792|Q8IWG3|Q8IXA9|Q8NDA7|Q9NV62	Silent	SNP	ENST00000296679.4	37	CCDS4038.1																																																																																			T|0.979;C|0.021	0.021	strong		0.368	WDR41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220014.2	NM_018268		C	76728996	T	C	76728996	2	2	28	1	0	0	0	0	0	0	0	1	17309	1490	52	3		3	WDR41	5	76728996	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	1730507	76728996	104186264	215	11718											
FAM151B	167555	hgsc.bcm.edu	37	chr5	79797690	79797690	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gacggtgctgagatcacctgGtatcatgcagctaaccacaa	12	8	10	11	1	2	1	2	1	0	1	2	3	2	1	2	2	4	4	2	2	3	2	rs149355931		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:79797690G>A	ENST00000282226.4	+	2	260	c.105G>A	c.(103-105)tgG>tgA	p.W35*	FAM151B_ENST00000511718.1_3'UTR	NM_205548.2	NP_991111.2	Q6UXP7	F151B_HUMAN	family with sequence similarity 151, member B	35										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)		AGATCACCTGGTATCATGCAG	0.358													G|||	1	0.000199681	0.0	0.0014	5008	,	,		11791	0.0		0.0	False		,,,				2504	0.0				p.W35X		Atlas-SNP	.											.	FAM151B	25	.	0			c.G105A						PASS	.	G	stop/TRP	0,4406		0,0,2203	165	166	166		105	5.9	1	5	dbSNP_134	166	5,8595	4.3+/-15.6	0,5,4295	yes	stop-gained	FAM151B	NM_205548.2		0,5,6498	AA,AG,GG		0.0581,0.0,0.0384		35/277	79797690	5,13001	2203	4300	6503	SO:0001587	stop_gained	167555	exon2			CACCTGGTATCAT		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.105G>A	5.37:g.79797690G>A	ENSP00000282226:p.Trp35*	197	0	0		208	99	0.475962	NM_205548	A2RRE4	Nonsense_Mutation	SNP	ENST00000282226.4	37	CCDS4051.1	.	.	.	.	.	.	.	.	.	.	G	37	6.368955	0.97511	0.0	5.81E-4	ENSG00000152380	ENST00000282226	.	.	.	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.2276	19.0783	0.93171	0.0:0.0:1.0:0.0	.	.	.	.	X	35	.	ENSP00000282226:W35X	W	+	3	0	FAM151B	79833446	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.660000	0.68018	2.803000	0.96430	0.591000	0.81541	TGG	G|1.000;A|0.000	0.000	strong		0.358	FAM151B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254072.1	NM_205548		A	79797690	G	A	79797690	4	1	28	1	0	0	0	0	0	1	0	0	5464	1270	44	2	111	2	FAM151B	5	79797690	Nonsense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	3068694	79797690	101117570	216	11719											
VCAN	1462	hgsc.bcm.edu	37	chr5	82817843	82817843	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cacctctcatcgacagggaaCctggtgaagaaacaaccagt	14	6	9	12	1	1	2	1	1	1	1	3	4	1	3	3	2	3	0	3	2	4	0	rs374590975		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:82817843C>G	ENST00000265077.3	+	7	4283	c.3718C>G	c.(3718-3720)Cct>Gct	p.P1240A	VCAN_ENST00000512590.2_Missense_Mutation_p.P1192A|VCAN_ENST00000343200.5_Intron|VCAN_ENST00000342785.4_Missense_Mutation_p.P1240A|VCAN_ENST00000502527.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1240	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)	CGACAGGGAACCTGGTGAAGA	0.443																																					p.P1240A		Atlas-SNP	.											.	VCAN	498	.	0			c.C3718G						PASS	.	C	ALA/PRO,ALA/PRO,,	0,4406		0,0,2203	134	129	131		3718,3718,,	2.5	0	5		131	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,intron,intron	VCAN	NM_001164098.1,NM_004385.4,NM_001126336.2,NM_001164097.1	27,27,,	0,1,6502	GG,GC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,,	1240/1643,1240/3397,,	82817843	1,13005	2203	4300	6503	SO:0001583	missense	1462	exon7			AGGGAACCTGGTG	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.3718C>G	5.37:g.82817843C>G	ENSP00000265077:p.Pro1240Ala	159	0	0		153	68	0.444444	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	C	10.43	1.348713	0.24426	0.0	1.16E-4	ENSG00000038427	ENST00000265077;ENST00000342785;ENST00000512590	D;D;D	0.87571	-2.2;-2.24;-2.27	5.39	2.49	0.30216	.	0.322422	0.27155	N	0.020667	D	0.86661	0.5986	M	0.68952	2.095	0.24807	N	0.992661	P;D	0.54397	0.944;0.966	P;P	0.50617	0.646;0.583	T	0.77571	-0.2538	10	0.40728	T	0.16	.	6.7264	0.23359	0.1164:0.5654:0.2497:0.0685	.	1240;1240	P13611-3;P13611	.;CSPG2_HUMAN	A	1240;1240;1192	ENSP00000265077:P1240A;ENSP00000342768:P1240A;ENSP00000425959:P1192A	ENSP00000265077:P1240A	P	+	1	0	VCAN	82853599	0.818000	0.29161	0.046000	0.18839	0.310000	0.27922	1.228000	0.32588	0.195000	0.20347	0.650000	0.86243	CCT	.	.	weak		0.443	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385		G	82817843	C	G	82817843	3	3	28	1	0	0	0	0	1	0	0	0	17153	507	18	4	3740	4	VCAN	5	82817843	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	3020153	82817843	98097417	217	11720											
GPR98	84059	hgsc.bcm.edu	37	chr5	90079811	90079811	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaatttctattgctaatccCaattccacaatgattttatc	14	16	2	9	0	1	1	0	1	1	0	4	1	3	1	2	0	1	1	2	0	7	7	rs41311745	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:90079811C>T	ENST00000405460.2	+	67	13686	c.13590C>T	c.(13588-13590)ccC>ccT	p.P4530P	GPR98_ENST00000425867.2_Silent_p.P191P	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4530	Calx-beta 31. {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)		TTGCTAATCCCAATTCCACAA	0.398													C|||	28	0.00559105	0.0008	0.0043	5008	,	,		18649	0.0		0.0219	False		,,,				2504	0.002				p.P4530P		Atlas-SNP	.											.	GPR98	605	.	0			c.C13590T						PASS	.	C		21,3687		0,21,1833	41	41	41		13590	2.7	1	5	dbSNP_127	41	157,8011		2,153,3929	no	coding-synonymous	GPR98	NM_032119.3		2,174,5762	TT,TC,CC		1.9221,0.5663,1.4988		4530/6307	90079811	178,11698	1854	4084	5938	SO:0001819	synonymous_variant	84059	exon67			TAATCCCAATTCC	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.13590C>T	5.37:g.90079811C>T		90	0	0		126	60	0.47619	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	37	CCDS47246.1																																																																																			A|0.001;C|0.992;T|0.006	0.006	strong		0.398	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		T	90079811	C	T	90079811	2	4	28	1	0	0	0	0	0	0	0	1	6730	581	21	2		2	GPR98	5	90079811	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	7261968	90079811	90835449	218	11721											
FAM172A	83989	hgsc.bcm.edu	37	chr5	93159971	93159971	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgttcttcaggagaaccattTtcctataagggaaacaaatg	14	12	8	7	0	2	1	1	0	1	1	3	3	3	2	2	2	2	1	2	2	5	6	rs141777861	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:93159971T>C	ENST00000395965.3	-	8	931	c.789A>G	c.(787-789)gaA>gaG	p.E263E	FAM172A_ENST00000509163.1_Silent_p.E217E|FAM172A_ENST00000505869.1_Silent_p.E153E|FAM172A_ENST00000509739.1_Silent_p.E116E	NM_032042.5	NP_114431.2	Q8WUF8	F172A_HUMAN	family with sequence similarity 172, member A	263						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)				endometrium(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	9						GAGAACCATTTTCCTATAAGG	0.343													T|||	42	0.00838658	0.0	0.0086	5008	,	,		11615	0.0		0.0199	False		,,,				2504	0.0164				p.E263E		Atlas-SNP	.											.	FAM172A	38	.	0			c.A789G						PASS	.	T	,,	28,4378	32.6+/-62.9	0,28,2175	102	100	101		651,459,789	2.3	1	5	dbSNP_134	101	195,8405	84.2+/-146.7	3,189,4108	no	coding-synonymous,coding-synonymous,coding-synonymous	FAM172A	NM_001163417.1,NM_001163418.1,NM_032042.5	,,	3,217,6283	CC,CT,TT		2.2674,0.6355,1.7146	,,	217/371,153/307,263/417	93159971	223,12783	2203	4300	6503	SO:0001819	synonymous_variant	83989	exon8			ACCATTTTCCTAT		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.789A>G	5.37:g.93159971T>C		162	0	0		128	66	0.515625	NM_032042	B2R7C6|B4DJ14|B4DLG5|Q9H0U8	Silent	SNP	ENST00000395965.3	37	CCDS4069.1																																																																																			T|0.986;C|0.015	0.015	strong		0.343	FAM172A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254100.3	NM_032042		C	93159971	T	C	93159971	2	2	28	1	0	0	0	0	0	0	0	1	5497	1838	64	3		3	FAM172A	5	93159971	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	3080160	93159971	87755289	219	11722											
APC	324	hgsc.bcm.edu	37	chr5	112162854	112162854	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagtggactgtgaaatgtaTgggcttactaatgaccacta	13	11	10	7	0	0	2	0	2	0	0	0	3	0	3	1	2	1	2	1	2	6	4	rs2229992	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:112162854T>C	ENST00000457016.1	+	12	1838	c.1458T>C	c.(1456-1458)taT>taC	p.Y486Y	APC_ENST00000257430.4_Silent_p.Y486Y|APC_ENST00000508376.2_Silent_p.Y486Y|CTC-554D6.1_ENST00000520401.1_5'Flank			P25054	APC_HUMAN	adenomatous polyposis coli	486	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)		GTGAAATGTATGGGCTTACTA	0.368		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)			T|||	2554	0.509984	0.1619	0.6671	5008	,	,		17461	0.6647		0.5795	False		,,,				2504	0.638				p.Y486Y	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	1	1	Unknown(1)	skin(1)	c.T1458C	GRCh37	CM990152	APC	M	rs2229992	PASS	.	T	,,	934,3470	356.6+/-313.6	103,728,1371	131	117	122	http://omim.org/entry/114500	1458,1458,1404	0.7	1	5	dbSNP_98	122	5076,3524	632.0+/-398.6	1516,2044,740	no	coding-synonymous,coding-synonymous,coding-synonymous	APC	NM_000038.5,NM_001127510.2,NM_001127511.2	,,	1619,2772,2111	CC,CT,TT		40.9767,21.208,46.2165	,,	486/2844,486/2844,468/2826	112162854	6010,6994	2202	4300	6502	SO:0001819	synonymous_variant	324	exon13	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	AATGTATGGGCTT	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.1458T>C	5.37:g.112162854T>C		98	0	0		119	119	1	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																			A|0.002;C|0.475	0.475	strong		0.368	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		C	112162854	T	C	112162854	2	2	28	1	0	0	0	0	0	0	0	1	763	1471	51	3		3	APC	5	112162854	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	19002883	112162854	68752406	220	11723											
APC	324	hgsc.bcm.edu	37	chr5	112164561	112164561	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	attaatttgcaggttattgcGagtgttttgaggaatttgtc	9	18	11	3	1	0	1	0	1	0	0	1	3	0	2	0	2	2	3	0	2	3	7	rs351771	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:112164561G>A	ENST00000457016.1	+	14	2015	c.1635G>A	c.(1633-1635)gcG>gcA	p.A545A	APC_ENST00000257430.4_Silent_p.A545A|APC_ENST00000508376.2_Silent_p.A545A|CTC-554D6.1_ENST00000520401.1_Missense_Mutation_p.R41Q			P25054	APC_HUMAN	adenomatous polyposis coli	545	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)		AGGTTATTGCGAGTGTTTTGA	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)			A|||	3336	0.666134	0.5166	0.7161	5008	,	,		17820	0.8165		0.5994	False		,,,				2504	0.7464				p.A545A	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.G1635A						PASS	.	A	,,	2321,2083	570.8+/-382.9	619,1083,500	101	105	104	http://omim.org/entry/114500	1635,1635,1581	4.5	1	5	dbSNP_79	104	5305,3295	491.5+/-373.1	1671,1963,666	no	coding-synonymous,coding-synonymous,coding-synonymous	APC	NM_000038.5,NM_001127510.2,NM_001127511.2	,,	2290,3046,1166	AA,AG,GG		38.314,47.2979,41.3565	,,	545/2844,545/2844,527/2826	112164561	7626,5378	2202	4300	6502	SO:0001819	synonymous_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,	TATTGCGAGTGTT	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.1635G>A	5.37:g.112164561G>A		134	0	0		111	111	1	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																			G|0.388;A|0.612	0.612	strong		0.313	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112164561	G	A	112164561	2	1	28	1	0	0	0	0	0	0	0	1	763	1045	37	1		1	APC	5	112164561	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1707	112164561	68750699	221	11724											
APC	324	hgsc.bcm.edu	37	chr5	112176325	112176325	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggagaaggagttagaggaggGgcacagtcaggtgaatttga	13	7	18	3	0	1	4	1	2	0	2	1	7	1	6	0	6	0	2	0	6	3	2	rs42427	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:112176325G>A	ENST00000457016.1	+	16	5414	c.5034G>A	c.(5032-5034)ggG>ggA	p.G1678G	APC_ENST00000257430.4_Silent_p.G1678G|APC_ENST00000508376.2_Silent_p.G1678G|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1678	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)		TTAGAGGAGGGGCACAGTCAG	0.443		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)			g|||	3339	0.666733	0.5189	0.7176	5008	,	,		20292	0.8165		0.6024	False		,,,				2504	0.7423				p.G1678G	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	.	2	Unknown(1)|Deletion - Frameshift(1)	soft_tissue(1)|skin(1)	c.G5034A						PASS	.	T	,,	2333,2071	603.2+/-390.1	625,1083,494	60	59	59	http://omim.org/entry/114500	5034,5034,4980	1.3	0.2	5	dbSNP_76	59	5341,3259	648.4+/-400.5	1692,1957,651	no	coding-synonymous,coding-synonymous,coding-synonymous	APC	NM_000038.5,NM_001127510.2,NM_001127511.2	,,	2317,3040,1145	AA,AG,GG		37.8953,47.0254,40.9874	,,	1678/2844,1678/2844,1660/2826	112176325	7674,5330	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,	AGGAGGGGCACAG	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.5034G>A	5.37:g.112176325G>A		107	0	0		80	80	1	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																			G|0.379;A|0.621	0.621	strong		0.443	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112176325	G	A	112176325	2	1	28	1	0	0	0	0	0	0	0	1	763	1219	43	2		2	APC	5	112176325	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	11764	112176325	68738935	222	11725			2	49		4	4	847	N	T_G	1.28852e-06
APC	324	hgsc.bcm.edu	37	chr5	112176559	112176559	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtccagcaagcatctgcgtcTtcttctgcacccaacaaaaa	12	9	6	14	1	4	0	0	0	4	0	5	0	5	0	2	0	5	3	2	0	4	2	rs866006	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:112176559T>G	ENST00000457016.1	+	16	5648	c.5268T>G	c.(5266-5268)tcT>tcG	p.S1756S	APC_ENST00000257430.4_Silent_p.S1756S|APC_ENST00000508376.2_Silent_p.S1756S|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1756	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)		CATCTGCGTCTTCTTCTGCAC	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)			t|||	3340	0.666933	0.5197	0.7161	5008	,	,		19571	0.8165		0.6004	False		,,,				2504	0.7454				p.S1756S	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	.	2	Unknown(1)|Deletion - Frameshift(1)	soft_tissue(1)|skin(1)	c.T5268G						PASS	.	G	,,	2326,2078	584.6+/-386.1	621,1084,497	55	54	54	http://omim.org/entry/114500	5268,5268,5214	-2.5	0.2	5	dbSNP_86	54	5319,3279	623.8+/-397.5	1680,1959,660	no	coding-synonymous,coding-synonymous,coding-synonymous	APC	NM_000038.5,NM_001127510.2,NM_001127511.2	,,	2301,3043,1157	GG,GT,TT		38.1368,47.1844,41.2014	,,	1756/2844,1756/2844,1738/2826	112176559	7645,5357	2202	4299	6501	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,	TGCGTCTTCTTCT	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.5268T>G	5.37:g.112176559T>G		95	0	0		111	111	1	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																			T|0.384;G|0.616	0.616	strong		0.398	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		G	112176559	T	G	112176559	2	3	28	1	0	0	0	0	0	0	0	1	763	1596	56	5		5	APC	5	112176559	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	234	112176559	68738701	223	11726			2	49		4	4	847	N	T_G	1.28852e-06
APC	324	hgsc.bcm.edu	37	chr5	112176756	112176756	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgaaaaataattccaaggTcttcaatgataagctcccaa	16	12	5	8	0	2	2	1	2	1	0	4	2	4	2	2	1	1	1	2	1	7	5	rs459552	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:112176756T>A	ENST00000457016.1	+	16	5845	c.5465T>A	c.(5464-5466)gTc>gAc	p.V1822D	APC_ENST00000257430.4_Missense_Mutation_p.V1822D|APC_ENST00000508376.2_Missense_Mutation_p.V1822D|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1822	Ser-rich.		V -> D (in dbSNP:rs459552). {ECO:0000269|PubMed:1651562, ECO:0000269|PubMed:1678319, ECO:0000269|PubMed:9950360, ECO:0000269|Ref.4}.		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)		AATTCCAAGGTCTTCAATGAT	0.328		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)			A|||	4334	0.865415	0.9909	0.8184	5008	,	,		19820	0.9008		0.7654	False		,,,				2504	0.7955				p.V1822D	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	.	2	Unknown(1)|Deletion - Frameshift(1)	soft_tissue(1)|skin(1)	c.T5465A	GRCh37	CM990164	APC	M	rs459552	PASS	.	A	ASP/VAL,ASP/VAL,ASP/VAL	4164,238	135.3+/-171.4	1973,218,10	67	63	64	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	5465,5465,5411	3.6	1	5	dbSNP_80	64	6579,2021	339.4+/-323.1	2529,1521,250	yes	missense,missense,missense	APC	NM_000038.5,NM_001127510.2,NM_001127511.2	152,152,152	4502,1739,260	AA,AT,TT		23.5,5.4066,17.3743	benign,benign,benign	1822/2844,1822/2844,1804/2826	112176756	10743,2259	2201	4300	6501	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,	CCAAGGTCTTCAA	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.5465T>A	5.37:g.112176756T>A	ENSP00000413133:p.Val1822Asp	71	0	0		86	84	0.976744	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	1883	0.8621794871794872	486	0.9878048780487805	296	0.8176795580110497	514	0.8986013986013986	587	0.7744063324538258	A	0.069	-1.206578	0.01568	0.945934	0.765	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.87809	-2.3;-2.3;-2.3	6.07	3.59	0.41128	.	0.187419	0.47093	N	0.000244	T	0.00012	0.0000	N	0.01352	-0.895	0.40534	P	0.019048999999999983	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42085	-0.9472	8	.	.	.	-1.4078	9.3995	0.38424	0.6507:0.2365:0.0:0.1128	rs459552;rs52814776;rs56587573;rs459552	1824;1822	Q4LE70;P25054	.;APC_HUMAN	D	1822	ENSP00000413133:V1822D;ENSP00000257430:V1822D;ENSP00000427089:V1822D	.	V	+	2	0	APC	112204655	1.000000	0.71417	0.987000	0.45799	0.796000	0.44982	3.653000	0.54446	0.139000	0.18822	-0.265000	0.10407	GTC	T|0.151;A|0.849	0.849	strong		0.328	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112176756	T	A	112176756	3	1	28	1	0	0	0	0	1	0	0	0	763	1667	58	5	5523	5	APC	5	112176756	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	197	112176756	68738504	224	11727			2	49		4	4	847	N	T_G	1.28852e-06
APC	324	hgsc.bcm.edu	37	chr5	112177171	112177171	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttgctattgaaaatactccGgtttgcttttctcataattc	9	19	5	8	1	1	1	1	1	1	0	4	1	2	1	1	1	3	3	1	1	5	9	rs465899|rs587779801	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:112177171G>A	ENST00000457016.1	+	16	6260	c.5880G>A	c.(5878-5880)ccG>ccA	p.P1960P	APC_ENST00000257430.4_Silent_p.P1960P|APC_ENST00000508376.2_Silent_p.P1960P|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1960	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)		AAAATACTCCGGTTTGCTTTT	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)			A|||	3338	0.666534	0.5212	0.7161	5008	,	,		20489	0.8165		0.5994	False		,,,				2504	0.7423				p.P1960P	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.G5880A						PASS	.	A	,,	2328,2076	560.3+/-380.4	623,1082,497	66	64	65	http://omim.org/entry/114500	5880,5880,5826	-3.7	1	5	dbSNP_80	65	5303,3295	486.2+/-371.8	1668,1967,664	no	coding-synonymous,coding-synonymous,coding-synonymous	APC	NM_000038.5,NM_001127510.2,NM_001127511.2	,,	2291,3049,1161	AA,AG,GG		38.3229,47.139,41.309	,,	1960/2844,1960/2844,1942/2826	112177171	7631,5371	2202	4299	6501	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,	TACTCCGGTTTGC	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.5880G>A	5.37:g.112177171G>A		119	0	0		141	139	0.985816	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																			G|0.332;A|0.668	0.668	strong		0.398	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038		A	112177171	G	A	112177171	2	1	28	1	0	0	0	0	0	0	0	1	763	1103	39	1		1	APC	5	112177171	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	415	112177171	68738089	225	11728			2	49		4	4	847	N	T_G	1.28852e-06
SEMA6A	57556	hgsc.bcm.edu	37	chr5	115782493	115782493	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atggctgggagctgtgcaccTggatggagtccaccctctgc	6	9	14	12	0	1	0	0	0	1	0	2	3	2	3	3	4	3	3	3	4	0	0	rs200578077	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:115782493T>G	ENST00000343348.6	-	19	3696	c.2909A>C	c.(2908-2910)cAg>cCg	p.Q970P	CTB-118N6.3_ENST00000508640.1_RNA|CTB-118N6.3_ENST00000512128.1_RNA|SEMA6A_ENST00000282394.6_Missense_Mutation_p.Q447P|SEMA6A_ENST00000503865.1_Missense_Mutation_p.Q349P|CTB-118N6.3_ENST00000508424.1_RNA|SEMA6A_ENST00000513137.1_Missense_Mutation_p.Q397P|CTB-118N6.3_ENST00000510682.1_RNA|CTB-118N6.3_ENST00000514214.1_RNA|SEMA6A_ENST00000510263.1_Missense_Mutation_p.Q970P|SEMA6A_ENST00000257414.8_Missense_Mutation_p.Q987P	NM_020796.3	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	970					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)		GCTGTGCACCTGGATGGAGTC	0.617																																					p.Q970P		Atlas-SNP	.											.	SEMA6A	93	.	0			c.A2909C						PASS	.	T	PRO/GLN	5,4167		0,5,2081	24	27	26		2909	4.3	1	5		26	62,8402		0,62,4170	yes	missense	SEMA6A	NM_020796.3	76	0,67,6251	GG,GT,TT		0.7325,0.1198,0.5302	probably-damaging	970/1031	115782493	67,12569	2086	4232	6318	SO:0001583	missense	57556	exon19			TGCACCTGGATGG	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.2909A>C	5.37:g.115782493T>G	ENSP00000345512:p.Gln970Pro	65	0	0		75	34	0.453333	NM_020796	Q9P2H9	Missense_Mutation	SNP	ENST00000343348.6	37	CCDS47256.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	T	15.45	2.836504	0.50951	0.001198	0.007325	ENSG00000092421	ENST00000343348;ENST00000257414;ENST00000513137;ENST00000282394;ENST00000503865;ENST00000510263	T;T;T;T;T;T	0.50001	2.11;2.1;0.76;2.59;0.79;2.11	4.27	4.27	0.50696	.	1.559450	0.04430	N	0.369061	T	0.51109	0.1655	L	0.46157	1.445	0.58432	D	0.999996	P;P;D;D;D;D	0.62365	0.936;0.874;0.991;0.974;0.965;0.965	P;B;P;P;P;P	0.55161	0.571;0.439;0.77;0.663;0.567;0.663	T	0.40739	-0.9547	10	0.59425	D	0.04	.	11.7765	0.51989	0.0:0.0:0.0:1.0	.	349;970;514;987;447;397	E9PDV9;Q9H2E6;Q96SM8;Q9H2E6-2;E7ERF3;B3KU01	.;SEM6A_HUMAN;.;.;.;.	P	970;987;397;447;349;970	ENSP00000345512:Q970P;ENSP00000257414:Q987P;ENSP00000422997:Q397P;ENSP00000282394:Q447P;ENSP00000425364:Q349P;ENSP00000424388:Q970P	ENSP00000257414:Q987P	Q	-	2	0	SEMA6A	115810392	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.512000	0.81728	1.793000	0.52555	0.379000	0.24179	CAG	T|0.997;G|0.003	0.003	strong		0.617	SEMA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371270.1	NM_020796		G	115782493	T	G	115782493	3	3	28	1	0	0	0	0	1	0	0	0	14054	1580	55	5	187	5	SEMA6A	5	115782493	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	3605322	115782493	65132767	226	11729											
DMXL1	1657	hgsc.bcm.edu	37	chr5	118454599	118454599	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttaccaaatgattgtttgcTatacggaggtgactgcagcc	10	13	10	8	1	0	2	0	2	0	0	0	3	0	3	2	2	5	3	2	2	4	6	rs200933738		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:118454599T>C	ENST00000311085.8	+	8	913	c.833T>C	c.(832-834)cTa>cCa	p.L278P	DMXL1_ENST00000539542.1_Missense_Mutation_p.L278P	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	278										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)		GATTGTTTGCTATACGGAGGT	0.363																																					p.L278P		Atlas-SNP	.											.	DMXL1	268	.	0			c.T833C						PASS	.	T	PRO/LEU	0,4404		0,0,2202	158	151	154		833	5.4	0.4	5		154	3,8597	3.0+/-9.4	0,3,4297	yes	missense	DMXL1	NM_005509.4	98	0,3,6499	CC,CT,TT		0.0349,0.0,0.0231	probably-damaging	278/3028	118454599	3,13001	2202	4300	6502	SO:0001583	missense	1657	exon8			GTTTGCTATACGG	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.833T>C	5.37:g.118454599T>C	ENSP00000309690:p.Leu278Pro	95	0	0		125	54	0.432	NM_005509		Missense_Mutation	SNP	ENST00000311085.8	37	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	T	15.22	2.770171	0.49680	0.0	3.49E-4	ENSG00000172869	ENST00000503802;ENST00000311085;ENST00000539542	T;T;T	0.28069	1.63;2.67;2.67	5.38	5.38	0.77491	WD40 repeat-like-containing domain (1);	0.000000	0.64402	D	0.000002	T	0.56001	0.1956	M	0.73962	2.25	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.72338	0.977;0.931	T	0.60905	-0.7170	10	0.72032	D	0.01	-1.619	15.3913	0.74747	0.0:0.0:0.0:1.0	.	278;278	F5H269;Q9Y485	.;DMXL1_HUMAN	P	278	ENSP00000427692:L278P;ENSP00000309690:L278P;ENSP00000439479:L278P	ENSP00000309690:L278P	L	+	2	0	DMXL1	118482498	0.940000	0.31905	0.396000	0.26296	0.137000	0.21094	5.757000	0.68766	2.046000	0.60703	0.533000	0.62120	CTA	T|0.999;C|0.001	0.001	weak		0.363	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509		C	118454599	T	C	118454599	3	2	28	1	0	0	0	0	1	0	0	0	4596	1522	53	3	863	3	DMXL1	5	118454599	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	2672106	118454599	62460661	227	11730											
FBN2	2201	hgsc.bcm.edu	37	chr5	127680130	127680130	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agccactattgcaacggcatTtgaagcttccgattgtattt	10	14	8	9	2	0	1	0	1	0	0	1	2	1	1	2	1	4	4	2	1	4	7			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:127680130T>G	ENST00000508053.1	-	31	4264	c.3290A>C	c.(3289-3291)aAa>aCa	p.K1097T	FBN2_ENST00000508989.1_Missense_Mutation_p.K1064T|FBN2_ENST00000262464.4_Missense_Mutation_p.K1097T			P35556	FBN2_HUMAN	fibrillin 2	1097	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)		GCAACGGCATTTGAAGCTTCC	0.423																																					p.K1097T		Atlas-SNP	.											.	FBN2	858	.	0			c.A3290C						PASS	.						144	139	141					5																	127680130		2203	4300	6503	SO:0001583	missense	2201	exon25			CGGCATTTGAAGC	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.3290A>C	5.37:g.127680130T>G	ENSP00000424571:p.Lys1097Thr	86	0	0		72	31	0.430556	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	37	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	T	9.363	1.068611	0.20067	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989	D;D;D	0.86865	-2.18;-2.18;-2.18	4.26	4.26	0.50523	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.076495	0.50627	D	0.000108	T	0.79341	0.4429	N	0.04116	-0.275	0.38313	D	0.943307	P;P	0.47677	0.899;0.503	P;B	0.51701	0.677;0.296	T	0.78884	-0.2028	10	0.17369	T	0.5	.	14.4286	0.67233	0.0:0.0:0.0:1.0	.	1064;1097	D6RJI3;P35556	.;FBN2_HUMAN	T	1097;1097;1064	ENSP00000262464:K1097T;ENSP00000424571:K1097T;ENSP00000425596:K1064T	ENSP00000262464:K1097T	K	-	2	0	FBN2	127708029	0.954000	0.32549	1.000000	0.80357	0.011000	0.07611	1.122000	0.31295	2.148000	0.66965	0.454000	0.30748	AAA	.	.	none		0.423	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999		G	127680130	T	G	127680130	3	3	28	1	0	0	0	0	1	0	0	0	5711	1841	64	5	5612	5	FBN2	5	127680130	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	9225531	127680130	53235130	228	11731											
PCDHA4	56144	hgsc.bcm.edu	37	chr5	140188353	140188353	+	Silent	SNP	G	G	A																															cagccgctggaccacgaggaGctagagctgctgcagtttca																								rs561061447	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140188353G>A	ENST00000530339.1	+	1	1581	c.1581G>A	c.(1579-1581)gaG>gaA	p.E527E	PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Silent_p.E527E|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000356878.4_Silent_p.E527E|PCDHA2_ENST00000526136.1_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	527	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)			ACCACGAGGAGCTAGAGCTGC	0.652													.|||	115	0.0229633	0.003	0.0389	5008	,	,		17480	0.0		0.0755	False		,,,				2504	0.0082				p.E527E		Atlas-SNP	.											.	PCDHA4	419	.	0			c.G1581A						PASS	.						71	76	74					5																	140188353		2203	4300	6503	SO:0001819	synonymous_variant	56144	exon1			CGAGGAGCTAGAG	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.1581G>A	5.37:g.140188353G>A		112	0	0		66	20	0.30303	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			.	.	none		0.652	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		A	140188353	G	A	140188353	2	1	28	1	0	0	0	0	0	0	0	1	11535	962	34	2		2	PCDHA4	5	140188353	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	12508223	140188353	40726907	229	11732	146	3									
PCDHA4	56144	hgsc.bcm.edu	37	chr5	140188354	140188354	+	Missense_Mutation	SNP	C	C	G																															agccgctggaccacgaggagCtagagctgctgcagtttcag																								rs142480630	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140188354C>G	ENST00000530339.1	+	1	1582	c.1582C>G	c.(1582-1584)Cta>Gta	p.L528V	PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Missense_Mutation_p.L528V|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000356878.4_Missense_Mutation_p.L528V|PCDHA2_ENST00000526136.1_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	528	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)			CCACGAGGAGCTAGAGCTGCT	0.652													.|||	115	0.0229633	0.003	0.0389	5008	,	,		17618	0.0		0.0755	False		,,,				2504	0.0082				p.L528V		Atlas-SNP	.											PCDHA4_ENST00000530339,NS,carcinoma,0,8	PCDHA4	419	8	0			c.C1582G						PASS	.						70	75	74					5																	140188354		2203	4300	6503	SO:0001583	missense	56144	exon1			GAGGAGCTAGAGC	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.1582C>G	5.37:g.140188354C>G	ENSP00000435300:p.Leu528Val	110	0	0		65	20	0.307692	NM_031500	O75285|Q2M253	Missense_Mutation	SNP	ENST00000530339.1	37	CCDS54916.1	.	.	.	.	.	.	.	.	.	.	c	11.23	1.577307	0.28092	.	.	ENSG00000204967	ENST00000512229;ENST00000356878;ENST00000530339	T;T;T	0.51325	0.71;0.71;0.71	4.18	2.19	0.27852	Cadherin (5);Cadherin-like (1);	0.000000	0.28952	U	0.013601	T	0.34948	0.0915	N	0.25332	0.735	0.20764	N	0.999854	P;B;B	0.43662	0.814;0.101;0.207	B;B;B	0.43508	0.422;0.421;0.214	T	0.15150	-1.0447	10	0.51188	T	0.08	.	8.8809	0.35374	0.2588:0.4914:0.2498:0.0	.	528;528;528	Q9UN74-2;Q9UN74;D6RA20	.;PCDA4_HUMAN;.	V	528	ENSP00000423470:L528V;ENSP00000349344:L528V;ENSP00000435300:L528V	ENSP00000349344:L528V	L	+	1	2	PCDHA4	140168538	0.000000	0.05858	1.000000	0.80357	0.984000	0.73092	-1.847000	0.01675	0.874000	0.35823	0.580000	0.79431	CTA	C|0.999;G|0.001	0.001	weak		0.652	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		G	140188354	C	G	140188354	3	3	28	1	0	0	0	0	1	0	0	0	11535	796	28	4	1584	4	PCDHA4	5	140188354	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1	140188354	40726906	230	11733	146	3									
PCDHA4	56144	hgsc.bcm.edu	37	chr5	140188356	140188356	+	Silent	SNP	A	A	G																															ccgctggaccacgaggagctAgagctgctgcagtttcaggt																								rs144593807	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140188356A>G	ENST00000530339.1	+	1	1584	c.1584A>G	c.(1582-1584)ctA>ctG	p.L528L	PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Silent_p.L528L|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000356878.4_Silent_p.L528L|PCDHA2_ENST00000526136.1_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	528	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)			ACGAGGAGCTAGAGCTGCTGC	0.652													.|||	115	0.0229633	0.003	0.0389	5008	,	,		17817	0.0		0.0755	False		,,,				2504	0.0082				p.L528L		Atlas-SNP	.											PCDHA4_ENST00000530339,NS,carcinoma,+2,8	PCDHA4	419	8	0			c.A1584G						PASS	.	A	,,,,,	11,4395		0,11,2192	70	75	73		,,,1584,,1584	1.3	1	5	dbSNP_134	73	57,8543		9,39,4252	no	intron,intron,intron,coding-synonymous,intron,coding-synonymous	PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_031411.1,NM_031500.1	,,,,,	9,50,6444	GG,GA,AA		0.6628,0.2497,0.5228	,,,,,	,,,528/948,,528/799	140188356	68,12938	2203	4300	6503	SO:0001819	synonymous_variant	56144	exon1			GGAGCTAGAGCTG	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.1584A>G	5.37:g.140188356A>G		108	0	0		63	20	0.31746	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			A|0.976;G|0.024	0.024	strong		0.652	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		G	140188356	A	G	140188356	2	3	28	1	0	0	0	0	0	0	0	1	11535	407	15	3		3	PCDHA4	5	140188356	Silent	SNP	A	TCGA-G8-6914-01A-11D-2210-10	2	140188356	40726904	231	11734	146	3									
PCDHA5	56143	hgsc.bcm.edu	37	chr5	140203463	140203463	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcaacgtgtacctgatcatCgccatctgtgcggtgtccag	7	11	11	12	3	3	1	2	1	1	0	5	1	4	1	3	1	3	1	3	1	2	1	rs142924665	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140203463C>A	ENST00000529859.1	+	1	2103	c.2103C>A	c.(2101-2103)atC>atA	p.I701I	PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Silent_p.I701I|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000378126.3_Silent_p.I701I|PCDHA2_ENST00000526136.1_Intron	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	701					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)			ACCTGATCATCGCCATCTGTG	0.692													.|||	2	0.000399361	0.0	0.0	5008	,	,		16849	0.0		0.002	False		,,,				2504	0.0				p.I701I		Atlas-SNP	.											.	PCDHA5	361	.	0			c.C2103A						PASS	.	C	,,,,,,	4,4402	8.1+/-20.4	0,4,2199	63	62	62		,,,,2103,,2103	2.2	1	5	dbSNP_134	62	35,8561	23.4+/-69.3	0,35,4263	no	intron,intron,intron,intron,coding-synonymous,intron,coding-synonymous	PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_031411.1,NM_031501.1	,,,,,,	0,39,6462	AA,AC,CC		0.4072,0.0908,0.3	,,,,,,	,,,,701/937,,701/817	140203463	39,12963	2203	4298	6501	SO:0001819	synonymous_variant	56143	exon1			GATCATCGCCATC	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.2103C>A	5.37:g.140203463C>A		154	0	0		159	76	0.477987	NM_018908	O75284|Q8N4R3	Silent	SNP	ENST00000529859.1	37	CCDS54917.1																																																																																			C|0.997;A|0.003	0.003	strong		0.692	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908		A	140203463	C	A	140203463	2	1	28	1	0	0	0	0	0	0	0	1	11536	874	31	4		4	PCDHA5	5	140203463	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	15107	140203463	40711797	232	11735											
PCDHA10	56139	hgsc.bcm.edu	37	chr5	140237158	140237158	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cgctgtcgagctacgtgtcgGtgcacgcggagagcggcaag	7	6	17	11	7	0	1	0	0	0	1	2	3	0	1	0	3	4	4	0	3	2	1	rs142356019	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140237158G>A	ENST00000307360.5	+	1	1525	c.1525G>A	c.(1525-1527)Gtg>Atg	p.V509M	PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000506939.2_Missense_Mutation_p.V509M|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	509	Cadherin 5. {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)			CTACGTGTCGGTGCACGCGGA	0.697													.|||	119	0.023762	0.0121	0.0346	5008	,	,		14546	0.0		0.0716	False		,,,				2504	0.0072				p.V509M		Atlas-SNP	.											.	PCDHA10	358	.	0			c.G1525A						PASS	.	G	,MET/VAL,,,,,,,,,,,MET/VAL,MET/VAL	120,4272		4,112,2080	66	73	71		,1525,,,,,,,,,,,1525,1525	3.6	1	5	dbSNP_134	71	477,8069		47,383,3843	no	intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,missense	PCDHA9,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031859.1,NM_031860.1	,21,,,,,,,,,,,21,21	51,495,5923	AA,AG,GG		5.5816,2.7322,4.6143	,,,,,,,,,,,,,	,509/949,,,,,,,,,,,509/845,509/686	140237158	597,12341	2196	4273	6469	SO:0001583	missense	56139	exon1			GTGTCGGTGCACG	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.1525G>A	5.37:g.140237158G>A	ENSP00000304234:p.Val509Met	73	0	0		160	79	0.49375	NM_031859	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	37	CCDS54921.1	87	0.03983516483516483	9	0.018292682926829267	19	0.052486187845303865	0	0.0	59	0.07783641160949868	G	14.28	2.487603	0.44249	0.027322	0.055816	ENSG00000250120	ENST00000506939;ENST00000307360	T;T	0.67698	-0.28;-0.28	3.63	3.63	0.41609	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.17323	0.0416	M	0.64404	1.975	0.43489	P	0.004271000000000025	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.993	T	0.65446	-0.6166	8	0.59425	D	0.04	.	9.6727	0.40021	0.0974:0.0:0.9026:0.0	.	509;509;509	Q9Y5I2-3;Q9Y5I2;Q9Y5I2-2	.;PCDAA_HUMAN;.	M	509	ENSP00000421030:V509M;ENSP00000304234:V509M	ENSP00000304234:V509M	V	+	1	0	PCDHA10	140217342	.	.	0.998000	0.56505	0.648000	0.38561	.	.	2.007000	0.58848	0.561000	0.74099	GTG	G|0.957;A|0.043	0.043	strong		0.697	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		A	140237158	G	A	140237158	3	1	28	1	0	0	0	0	1	0	0	0	11529	1261	44	2	1527	2	PCDHA10	5	140237158	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	33695	140237158	40678102	233	11736											
PCDHA12	56137	hgsc.bcm.edu	37	chr5	140256729	140256729	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgcaggtgttcgtgctggacGagaacgacaacgcgccggca	9	6	15	11	6	0	1	0	0	0	1	1	4	0	2	1	3	4	4	1	3	2	1	rs543806401	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140256729G>A	ENST00000398631.2	+	1	1672	c.1672G>A	c.(1672-1674)Gag>Aag	p.E558K	PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	558	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(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)			CGTGCTGGACGAGAACGACAA	0.701													.|||	2	0.000399361	0.0	0.0	5008	,	,		17343	0.0		0.0	False		,,,				2504	0.002				p.E558K	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											.	PCDHA12	196	.	0			c.G1672A						PASS	.						144	149	147					5																	140256729		2203	4299	6502	SO:0001583	missense	56137	exon1			CTGGACGAGAACG	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.1672G>A	5.37:g.140256729G>A	ENSP00000381628:p.Glu558Lys	11	0	0		21	8	0.380952	NM_018903	O75278|Q2M1N8	Missense_Mutation	SNP	ENST00000398631.2	37	CCDS47285.1	.	.	.	.	.	.	.	.	.	.	G	16.09	3.023113	0.54683	.	.	ENSG00000251664	ENST00000398631	T	0.60920	0.15	4.92	4.05	0.47172	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.65698	0.2716	M	0.70108	2.13	0.24151	N	0.995691	D;D	0.60575	0.988;0.983	P;B	0.53760	0.734;0.284	T	0.57585	-0.7786	9	0.62326	D	0.03	.	8.9151	0.35576	0.1715:0.0:0.8285:0.0	.	558;558	Q9UN75-2;Q9UN75	.;PCDAC_HUMAN	K	558	ENSP00000381628:E558K	ENSP00000381628:E558K	E	+	1	0	PCDHA12	140236913	0.033000	0.19621	0.956000	0.39512	0.208000	0.24298	0.499000	0.22546	1.060000	0.40578	0.561000	0.74099	GAG	.	.	none		0.701	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		A	140256729	G	A	140256729	3	1	28	1	0	0	0	0	1	0	0	0	11531	1059	37	1	1674	1	PCDHA12	5	140256729	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	19571	140256729	40658531	234	11737											
PCDHA12	56137	hgsc.bcm.edu	37	chr5	140256920	140256920	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcggtcggcgcgcacatcccGttccacgtggggctgtacac	5	7	14	15	6	0	0	0	0	0	0	3	0	2	0	2	4	1	4	2	4	1	2	rs115718636	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140256920G>C	ENST00000398631.2	+	1	1863	c.1863G>C	c.(1861-1863)ccG>ccC	p.P621P	PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	621	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)			CGCACATCCCGTTCCACGTGG	0.672													.|||	111	0.0221645	0.0129	0.0303	5008	,	,		17234	0.0		0.0656	False		,,,				2504	0.0072				p.P621P	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											PCDHA12,colon,carcinoma,0,2	PCDHA12	196	2	0			c.G1863C						PASS	.	G	,,,,,,,,,,,,,,,	117,4289	87.8+/-126.4	0,117,2086	228	205	213		,,,1863,,,,,,,,,,,,1863	-0.7	0.9	5	dbSNP_132	213	437,8161	133.5+/-191.0	11,415,3873	no	intron,intron,intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031864.1	,,,,,,,,,,,,,,,	11,532,5959	CC,CG,GG		5.0826,2.6555,4.2602	,,,,,,,,,,,,,,,	,,,621/942,,,,,,,,,,,,621/793	140256920	554,12450	2203	4299	6502	SO:0001819	synonymous_variant	56137	exon1			CATCCCGTTCCAC	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.1863G>C	5.37:g.140256920G>C		195	0	0		262	124	0.473282	NM_018903	O75278|Q2M1N8	Silent	SNP	ENST00000398631.2	37	CCDS47285.1																																																																																			G|0.959;C|0.041	0.041	strong		0.672	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		C	140256920	G	C	140256920	2	2	28	1	0	0	0	0	0	0	0	1	11531	1132	40	4		4	PCDHA12	5	140256920	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	191	140256920	40658340	235	11738											
PCDHB13	56123	hgsc.bcm.edu	37	chr5	140595831	140595831	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctcctgttcgtggcggtgcgGctgtgtaggaggagcagggc	4	9	19	9	3	0	0	0	0	0	0	2	2	1	2	1	6	2	4	1	6	1	2	rs145378952		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140595831G>T	ENST00000341948.4	+	1	2323	c.2136G>T	c.(2134-2136)cgG>cgT	p.R712R		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	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)			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)			TGGCGGTGCGGCTGTGTAGGA	0.662													G|||	1	0.000199681	0.0	0.0	5008	,	,		15801	0.0		0.001	False		,,,				2504	0.0				p.R712R		Atlas-SNP	.											.	PCDHB13	142	.	0			c.G2136T						PASS	.	G		0,4402		0,0,2201	88	97	94		2136	0.2	0.8	5	dbSNP_134	94	4,8580		0,4,4288	no	coding-synonymous	PCDHB13	NM_018933.2		0,4,6489	TT,TG,GG		0.0466,0.0,0.0308		712/799	140595831	4,12982	2201	4292	6493	SO:0001819	synonymous_variant	56123	exon1			GGTGCGGCTGTGT	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.2136G>T	5.37:g.140595831G>T		67	0	0		95	49	0.515789	NM_018933	A8K9V6	Silent	SNP	ENST00000341948.4	37	CCDS4255.1																																																																																			G|1.000;T|0.000	0.000	strong		0.662	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933		T	140595831	G	T	140595831	2	4	28	1	0	0	0	0	0	0	0	1	11547	1190	42	4		4	PCDHB13	5	140595831	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	338911	140595831	40319429	236	11739											
PCDHGC3	5098	hgsc.bcm.edu	37	chr5	140856349	140856349	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgttggacggagggaccccAgctctctccgccagcctgcc	5	6	13	17	3	1	0	0	0	1	0	3	3	2	3	6	3	3	2	6	3	0	1	rs115808055	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140856349A>G	ENST00000308177.3	+	1	770	c.666A>G	c.(664-666)ccA>ccG	p.P222P	PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|RN7SL68P_ENST00000488078.2_RNA|PCDHGB1_ENST00000523390.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000518882.1_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	222	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)			GAGGGACCCCAGCTCTCTCCG	0.627													A|||	20	0.00399361	0.0008	0.0014	5008	,	,		15671	0.0		0.0179	False		,,,				2504	0.0				p.P222P		Atlas-SNP	.											.	PCDHGC3	173	.	0			c.A666G						PASS	.	A	,,,,,,,,,,,,,,,,,,,,,,	17,4389	23.3+/-48.9	0,17,2186	37	29	32		666,,,,,,,,,,,,,,,,,,,,,666,	-2.9	0.7	5	dbSNP_132	32	100,8500	51.5+/-111.7	2,96,4202	no	coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,intron	PCDHGC3,PCDHGB4,PCDHGA8,PCDHGA12,PCDHGB7,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA11,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_002588.2,NM_003735.2,NM_003736.2,NM_018912.2,NM_018913.2,NM_018914.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_018927.3,NM_032088.1,NM_032092.1,NM_032402.1,NM_032403.1	,,,,,,,,,,,,,,,,,,,,,,	2,113,6388	GG,GA,AA		1.1628,0.3858,0.8996	,,,,,,,,,,,,,,,,,,,,,,	222/935,,,,,,,,,,,,,,,,,,,,,222/864,	140856349	117,12889	2203	4300	6503	SO:0001819	synonymous_variant	5098	exon1			GACCCCAGCTCTC	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.666A>G	5.37:g.140856349A>G		40	0	0		23	16	0.695652	NM_032402	O60622|Q08192|Q9Y5C4	Silent	SNP	ENST00000308177.3	37	CCDS4261.1																																																																																			A|0.990;G|0.010	0.010	strong		0.627	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588		G	140856349	A	G	140856349	2	3	28	1	0	0	0	0	0	0	0	1	11578	175	7	3		3	PCDHGC3	5	140856349	Silent	SNP	A	TCGA-G8-6914-01A-11D-2210-10	260518	140856349	40058911	237	11740											
ARAP3	64411	hgsc.bcm.edu	37	chr5	141041735	141041735	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cccctggtcggagcttcaccGaccgggcatcccgacggaac	7	5	12	17	5	1	0	1	0	0	0	3	4	2	2	5	4	2	2	5	4	1	1	rs536504402		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:141041735G>A	ENST00000239440.4	-	20	2953	c.2888C>T	c.(2887-2889)tCg>tTg	p.S963L	ARAP3_ENST00000508305.1_Intron|ARAP3_ENST00000513878.1_Missense_Mutation_p.S625L|ARAP3_ENST00000512390.1_5'UTR	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	963	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				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						GAGCTTCACCGACCGGGCATC	0.617													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17730	0.0		0.0	False		,,,				2504	0.0				p.S963L		Atlas-SNP	.											.	ARAP3	139	.	0			c.C2888T						PASS	.						116	114	115					5																	141041735		2203	4300	6503	SO:0001583	missense	64411	exon20			TTCACCGACCGGG	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.2888C>T	5.37:g.141041735G>A	ENSP00000239440:p.Ser963Leu	123	0	0		129	31	0.24031	NM_022481	B4DIT1|D3DQE3	Missense_Mutation	SNP	ENST00000239440.4	37	CCDS4266.1	.	.	.	.	.	.	.	.	.	.	G	32	5.167079	0.94768	.	.	ENSG00000120318	ENST00000239440;ENST00000513878	T;T	0.10477	2.87;2.87	5.27	5.27	0.74061	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.129855	0.45606	D	0.000345	T	0.18341	0.0440	L	0.33624	1.015	0.44155	D	0.996956	D;D	0.76494	0.995;0.999	P;P	0.61132	0.884;0.833	T	0.00202	-1.1925	10	0.49607	T	0.09	.	11.6675	0.51383	0.0:0.0:0.7116:0.2884	.	625;963	B4DIT1;Q8WWN8	.;ARAP3_HUMAN	L	963;625	ENSP00000239440:S963L;ENSP00000421468:S625L	ENSP00000239440:S963L	S	-	2	0	ARAP3	141021919	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	6.365000	0.73090	2.741000	0.93983	0.650000	0.86243	TCG	.	.	none		0.617	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481		A	141041735	G	A	141041735	3	1	28	1	0	0	0	0	1	0	0	0	840	1059	37	1	1802	1	ARAP3	5	141041735	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	185386	141041735	39873525	238	11741											
SH3TC2	79628	hgsc.bcm.edu	37	chr5	148388512	148388512	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtcagcttattgaaaatcCggagctcagttctcaccgcc	9	11	8	13	2	3	1	3	1	1	0	5	2	4	2	3	1	2	3	3	1	3	3	rs139192433	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:148388512C>T	ENST00000515425.1	-	15	3481	c.3380G>A	c.(3379-3381)cGg>cAg	p.R1127Q	SH3TC2_ENST00000538184.1_Missense_Mutation_p.R674Q|SH3TC2_ENST00000512049.1_Missense_Mutation_p.R1120Q|SH3TC2_ENST00000502274.1_5'Flank	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	1127					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)			ATTGAAAATCCGGAGCTCAGT	0.522													C|||	2	0.000399361	0.0	0.0	5008	,	,		21382	0.0		0.002	False		,,,				2504	0.0				p.R1127Q		Atlas-SNP	.											.	SH3TC2	178	.	0			c.G3380A						PASS	.	C	GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	134	133	133		3380	5.2	1	5	dbSNP_134	133	19,8581	14.0+/-48.4	0,19,4281	yes	missense	SH3TC2	NM_024577.3	43	0,21,6482	TT,TC,CC		0.2209,0.0454,0.1615	probably-damaging	1127/1289	148388512	21,12985	2203	4300	6503	SO:0001583	missense	79628	exon15			AAAATCCGGAGCT	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.3380G>A	5.37:g.148388512C>T	ENSP00000423660:p.Arg1127Gln	93	0	0		75	35	0.466667	NM_024577	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Missense_Mutation	SNP	ENST00000515425.1	37	CCDS4293.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	33	5.223428	0.95139	4.54E-4	0.002209	ENSG00000169247	ENST00000538184;ENST00000515425;ENST00000512049	T;T;T	0.75821	-0.97;-0.97;-0.95	6.03	5.16	0.70880	Tetratricopeptide-like helical (1);	0.000000	0.64402	D	0.000002	D	0.86083	0.5848	M	0.73962	2.25	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	D	0.87067	0.2157	10	0.52906	T	0.07	-21.7677	17.3176	0.87228	0.0:0.8748:0.1252:0.0	.	1120;1127;1127	Q14CC0;E9PDF1;Q8TF17	.;.;S3TC2_HUMAN	Q	674;1127;1120	ENSP00000441427:R674Q;ENSP00000423660:R1127Q;ENSP00000421860:R1120Q	ENSP00000425627:R1127Q	R	-	2	0	SH3TC2	148368705	0.978000	0.34361	0.959000	0.39883	0.995000	0.86356	7.275000	0.78548	1.530000	0.49136	0.655000	0.94253	CGG	C|0.998;T|0.002	0.002	strong		0.522	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577		T	148388512	C	T	148388512	3	4	28	1	0	0	0	0	1	0	0	0	14277	652	23	1	498	1	SH3TC2	5	148388512	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	7346777	148388512	32526748	239	11742											
FAT2	2196	hgsc.bcm.edu	37	chr5	150947128	150947128	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gaagacctgttgaagaggggGgcatggttgttgcagtccac	9	9	16	7	0	0	3	0	1	0	2	1	4	1	3	2	4	1	5	2	4	2	3	rs34166097	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:150947128G>A	ENST00000261800.5	-	1	1377	c.1365C>T	c.(1363-1365)gcC>gcT	p.A455A		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	455	Cadherin 3. {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)			TGAAGAGGGGGGCATGGTTGT	0.557													G|||	79	0.0157748	0.0008	0.0259	5008	,	,		19350	0.001		0.0527	False		,,,				2504	0.0061				p.A455A		Atlas-SNP	.											.	FAT2	465	.	0			c.C1365T						PASS	.	G		36,4370	41.6+/-74.8	0,36,2167	125	124	125		1365	2.8	1	5	dbSNP_126	125	414,8186	129.5+/-187.6	7,400,3893	no	coding-synonymous	FAT2	NM_001447.2		7,436,6060	AA,AG,GG		4.814,0.8171,3.4599		455/4350	150947128	450,12556	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon1			GAGGGGGGCATGG	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.1365C>T	5.37:g.150947128G>A		116	0	0		152	62	0.407895	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																			G|0.970;A|0.030	0.030	strong		0.557	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		A	150947128	G	A	150947128	2	1	28	1	0	0	0	0	0	0	0	1	5698	1219	43	2		2	FAT2	5	150947128	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2558616	150947128	29968132	240	11743											
GABRA6	2559	hgsc.bcm.edu	37	chr5	161117243	161117243	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacagtttacttccacttgcAaaggaagatgggctacttca	12	11	9	9	0	1	1	1	0	0	1	2	3	2	2	1	2	3	3	1	2	4	6	rs76773579	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:161117243A>G	ENST00000274545.5	+	7	1143	c.710A>G	c.(709-711)cAa>cGa	p.Q237R	GABRA6_ENST00000523217.1_Missense_Mutation_p.Q227R|RP11-348M17.2_ENST00000521984.1_RNA			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	237					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)	TTCCACTTGCAAAGGAAGATG	0.393										TCGA Ovarian(5;0.080)			A|||	4	0.000798722	0.0	0.0014	5008	,	,		19724	0.0		0.002	False		,,,				2504	0.001				p.Q237R		Atlas-SNP	.											.	GABRA6	139	.	0			c.A710G						PASS	.	A	ARG/GLN	1,4405	2.1+/-5.4	0,1,2202	152	135	141		710	5.3	1	5	dbSNP_131	141	35,8565	24.6+/-71.5	0,35,4265	yes	missense	GABRA6	NM_000811.2	43	0,36,6467	GG,GA,AA		0.407,0.0227,0.2768	benign	237/454	161117243	36,12970	2203	4300	6503	SO:0001583	missense	2559	exon7			ACTTGCAAAGGAA		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.710A>G	5.37:g.161117243A>G	ENSP00000274545:p.Gln237Arg	112	0	0		131	65	0.496183	NM_000811	A8K096|Q4VAV2	Missense_Mutation	SNP	ENST00000274545.5	37	CCDS4356.1	3|3	0.0013736263736263737|0.0013736263736263737	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	A|A	14.82|14.82	2.648356|2.648356	0.47258|0.47258	2.27E-4|2.27E-4	0.00407|0.00407	ENSG00000145863|ENSG00000145863	ENST00000520000|ENST00000274545;ENST00000523217;ENST00000517823;ENST00000523691	.|T;T;T;T	.|0.75589	.|-0.95;-0.95;-0.95;-0.95	5.31|5.31	5.31|5.31	0.75309|0.75309	.|Neurotransmitter-gated ion-channel ligand-binding (3);	.|0.053501	.|0.85682	.|D	.|0.000000	T|T	0.57257|0.57257	0.2041|0.2041	N|N	0.04959|0.04959	-0.14|-0.14	0.47778|0.47778	D|D	0.999516|0.999516	.|B	.|0.20052	.|0.041	.|B	.|0.25405	.|0.06	T|T	0.55547|0.55547	-0.8124|-0.8124	5|10	.|0.39692	.|T	.|0.17	.|.	15.2733|15.2733	0.73723|0.73723	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|237	.|Q16445	.|GBRA6_HUMAN	E|R	177|237;227;184;157	.|ENSP00000274545:Q237R;ENSP00000430527:Q227R;ENSP00000430212:Q184R;ENSP00000427989:Q157R	.|ENSP00000274545:Q237R	K|Q	+|+	1|2	0|0	GABRA6|GABRA6	161049821|161049821	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.423000|7.423000	0.80229|0.80229	2.016000|2.016000	0.59253|0.59253	0.533000|0.533000	0.62120|0.62120	AAA|CAA	A|0.997;G|0.003	0.003	strong		0.393	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2			G	161117243	A	G	161117243	3	3	28	1	0	0	0	0	1	0	0	0	6173	130	5	3	736	3	GABRA6	5	161117243	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	10170115	161117243	19798017	241	11744											
DOCK2	1794	hgsc.bcm.edu	37	chr5	169267839	169267839	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacagtcatcaccatgggcCgggatcacattctgattgtg	9	10	12	10	1	4	1	3	1	1	0	4	3	4	3	2	3	0	0	2	3	0	2	rs200070944		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:169267839C>T	ENST00000256935.8	+	27	2862	c.2782C>T	c.(2782-2784)Cgg>Tgg	p.R928W	DOCK2_ENST00000540750.1_5'UTR|DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000520908.1_Missense_Mutation_p.R420W	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	928					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)			CACCATGGGCCGGGATCACAT	0.458																																					p.R928W		Atlas-SNP	.											.	DOCK2	389	.	0			c.C2782T						PASS	.						126	108	114					5																	169267839		2203	4300	6503	SO:0001583	missense	1794	exon27			ATGGGCCGGGATC	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.2782C>T	5.37:g.169267839C>T	ENSP00000256935:p.Arg928Trp	91	0	0		75	42	0.56	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	37	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	C	18.01	3.527368	0.64860	.	.	ENSG00000134516	ENST00000256935;ENST00000343291;ENST00000520908;ENST00000519628	T;T	0.69306	-0.39;-0.39	5.28	5.28	0.74379	.	0.120890	0.56097	D	0.000022	T	0.70518	0.3233	M	0.71036	2.16	0.80722	D	1	D;D	0.65815	0.995;0.959	P;B	0.49387	0.609;0.245	T	0.73202	-0.4057	10	0.49607	T	0.09	.	11.5168	0.50526	0.1792:0.8208:0.0:0.0	.	420;928	E7ERW7;Q92608	.;DOCK2_HUMAN	W	928;309;420;132	ENSP00000256935:R928W;ENSP00000429283:R420W	ENSP00000256935:R928W	R	+	1	2	DOCK2	169200417	0.994000	0.37717	1.000000	0.80357	0.778000	0.44026	3.353000	0.52247	2.460000	0.83146	0.585000	0.79938	CGG	C|0.999;A|0.001	.	alt		0.458	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946		T	169267839	C	T	169267839	3	4	28	1	0	0	0	0	1	0	0	0	4689	643	23	1	2888	1	DOCK2	5	169267839	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	8150596	169267839	11647421	242	11745											
LCP2	3937	hgsc.bcm.edu	37	chr5	169675739	169675739	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgcgttaatgtgcactggtAtctggaacctcggtttttcc	7	15	10	9	2	1	0	0	0	1	0	3	1	2	1	2	3	3	4	2	3	3	4	rs187889192	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:169675739A>G	ENST00000046794.5	-	21	2179	c.1564T>C	c.(1564-1566)Tac>Cac	p.Y522H	LCP2_ENST00000521416.1_Missense_Mutation_p.Y317H|C5orf58_ENST00000517575.1_Intron	NM_005565.3	NP_005556.1	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)	522	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				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)		GTGCACTGGTATCTGGAACCT	0.458													A|||	3	0.000599042	0.0008	0.0	5008	,	,		17968	0.0		0.002	False		,,,				2504	0.0				p.Y522H		Atlas-SNP	.											.	LCP2	133	.	0			c.T1564C						PASS	.	A	HIS/TYR	1,3959		0,1,1979	308	298	302		1564	3.1	1	5		302	42,8248		0,42,4103	yes	missense	LCP2	NM_005565.3	83	0,43,6082	GG,GA,AA		0.5066,0.0253,0.351	possibly-damaging	522/534	169675739	43,12207	1980	4145	6125	SO:0001583	missense	3937	exon21			ACTGGTATCTGGA		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.1564T>C	5.37:g.169675739A>G	ENSP00000046794:p.Tyr522His	157	0	0		159	83	0.522013	NM_005565	A8KA25|Q53XV4	Missense_Mutation	SNP	ENST00000046794.5	37	CCDS47339.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	16.03	3.006340	0.54361	2.53E-4	0.005066	ENSG00000043462	ENST00000046794;ENST00000521416	T;T	0.42513	0.97;0.98	5.82	3.07	0.35406	SH2 motif (1);	0.191452	0.43260	D	0.000595	T	0.12050	0.0293	N	0.01874	-0.695	0.31418	N	0.674662	P;P	0.47910	0.902;0.902	B;B	0.44278	0.445;0.445	T	0.04216	-1.0968	10	0.29301	T	0.29	-19.8141	5.4042	0.16312	0.5846:0.0:0.0818:0.3337	.	317;522	E7ESF6;Q13094	.;LCP2_HUMAN	H	522;317	ENSP00000046794:Y522H;ENSP00000428871:Y317H	ENSP00000046794:Y522H	Y	-	1	0	LCP2	169608317	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.042000	0.41222	0.971000	0.38288	0.482000	0.46254	TAC	A|0.999;G|0.001	0.001	strong		0.458	LCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371727.1	NM_005565		G	169675739	A	G	169675739	3	3	28	1	0	0	0	0	1	0	0	0	8701	449	16	3	41	3	LCP2	5	169675739	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	407900	169675739	11239521	243	11746											
SFXN1	94081	hgsc.bcm.edu	37	chr5	174936102	174936102	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caaagtacatctatgattcaGcttttcatcctgacactggt	11	14	6	10	0	3	2	2	2	1	0	4	2	4	2	1	1	2	2	1	1	3	5			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:174936102G>T	ENST00000321442.5	+	3	486	c.232G>T	c.(232-234)Gct>Tct	p.A78S	SFXN1_ENST00000502393.1_Missense_Mutation_p.A78S	NM_022754.5	NP_073591.2	Q9H9B4	SFXN1_HUMAN	sideroflexin 1	78					erythrocyte differentiation (GO:0030218)|iron ion homeostasis (GO:0055072)|iron ion transport (GO:0006826)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|skin(3)	15	all_cancers(89;0.00922)|Renal(175;0.000269)|Lung NSC(126;0.00515)|all_lung(126;0.00873)	Medulloblastoma(196;0.0399)|all_neural(177;0.0663)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			CTATGATTCAGCTTTTCATCC	0.393																																					p.A78S		Atlas-SNP	.											.	SFXN1	23	.	0			c.G232T						PASS	.						204	192	196					5																	174936102		2203	4300	6503	SO:0001583	missense	94081	exon3			GATTCAGCTTTTC	AF327346	CCDS4394.1	5q35.3	2008-02-05			ENSG00000164466	ENSG00000164466		"Sideroflexins"	16085	protein-coding gene	gene with protein product		615569					Standard	NM_022754		Approved	FLJ12876	uc003mda.2	Q9H9B4	OTTHUMG00000130555	ENST00000321442.5:c.232G>T	5.37:g.174936102G>T	ENSP00000316905:p.Ala78Ser	166	0	0		204	9	0.0441176	NM_022754	B3KPW3|D3DQN2|Q9HA53	Missense_Mutation	SNP	ENST00000321442.5	37	CCDS4394.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.923734	0.92319	.	.	ENSG00000164466	ENST00000507017;ENST00000321442;ENST00000506963	T;T;T	0.36157	1.27;1.27;1.27	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.59362	0.2188	M	0.69248	2.105	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.993	T	0.57277	-0.7839	10	0.39692	T	0.17	-21.0535	17.8038	0.88596	0.0:0.0:1.0:0.0	.	78;78	D6RFI0;Q9H9B4	.;SFXN1_HUMAN	S	78	ENSP00000420961:A78S;ENSP00000316905:A78S;ENSP00000421467:A78S	ENSP00000316905:A78S	A	+	1	0	SFXN1	174868708	1.000000	0.71417	0.048000	0.18961	0.968000	0.65278	9.731000	0.98807	2.444000	0.82710	0.555000	0.69702	GCT	.	.	none		0.393	SFXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252980.2	NM_022754		T	174936102	G	T	174936102	3	4	28	1	0	0	0	0	1	0	0	0	14209	971	34	4	238	4	SFXN1	5	174936102	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	5260363	174936102	5979158	244	11747											
FAM153B	202134	hgsc.bcm.edu	37	chr5	175530780	175530780	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	catccttgggagttccacaaCgtggtacgtattggggaacc	9	10	12	10	2	0	0	0	0	0	0	2	2	2	2	3	4	3	3	3	4	4	5	rs200265244		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:175530780C>T	ENST00000253490.4	+	14	814	c.757C>T	c.(757-759)Cgt>Tgt	p.R253C	FAM153B_ENST00000515817.1_Missense_Mutation_p.R176C|FAM153B_ENST00000512862.1_Missense_Mutation_p.R44C|FAM153B_ENST00000510151.1_Missense_Mutation_p.R176C			P0C7A2	F153B_HUMAN	family with sequence similarity 153, member B	253										endometrium(3)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	16	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)		AGTTCCACAACGTGGTACGTA	0.473																																					p.R176C		Atlas-SNP	.											.	FAM153B	28	.	0			c.C526T						PASS	.	C	CYS/ARG	5,4401	8.1+/-20.4	0,5,2198	78	80	79		757	-2.2	0	5		79	29,8565	15.3+/-51.7	0,29,4268	no	missense	FAM153B	NM_001079529.2	180	0,34,6466	TT,TC,CC		0.3374,0.1135,0.2615	possibly-damaging	253/388	175530780	34,12966	2203	4297	6500	SO:0001583	missense	202134	exon13			CCACAACGTGGTA	AK055006	CCDS43401.1, CCDS43401.2	5q35.2	2010-05-12			ENSG00000182230	ENSG00000182230			27323	protein-coding gene	gene with protein product							Standard	NM_001265615		Approved		uc031smb.1	P0C7A2	OTTHUMG00000163181	ENST00000253490.4:c.757C>T	5.37:g.175530780C>T	ENSP00000253490:p.Arg253Cys	913	1	0.00109529		923	206	0.223185	NM_001265615	A8MTI1	Missense_Mutation	SNP	ENST00000253490.4	37		.	.	.	.	.	.	.	.	.	.	C	4.556	0.103267	0.08731	0.001135	0.003374	ENSG00000182230	ENST00000515817;ENST00000253490	.	.	.	1.12	-2.24	0.06909	.	.	.	.	.	T	0.16642	0.0400	N	0.14661	0.345	0.09310	N	1	B	0.19200	0.034	B	0.04013	0.001	T	0.16748	-1.0392	8	0.51188	T	0.08	.	2.2521	0.04046	0.4486:0.3196:0.2318:0.0	.	253	P0C7A2	F153B_HUMAN	C	176;253	.	ENSP00000253490:R253C	R	+	1	0	FAM153B	175463386	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-2.175000	0.01263	-0.591000	0.05859	-1.402000	0.01139	CGT	C|0.999;T|0.001	0.001	weak		0.473	FAM153B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001079529		T	175530780	C	T	175530780	3	4	28	1	0	0	0	0	1	0	0	0	5466	536	19	1	811	1	FAM153B	5	175530780	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	594678	175530780	5384480	245	11748											
CDHR2	54825	hgsc.bcm.edu	37	chr5	176004680	176004680	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagaacttctccgtcgccAtggtgaccatccaccttaga	9	9	8	15	2	1	3	0	1	1	2	4	3	2	3	6	1	1	0	6	1	2	2	rs34767982	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:176004680A>C	ENST00000510636.1	+	14	1667	c.1393A>C	c.(1393-1395)Atg>Ctg	p.M465L	CDHR2_ENST00000506348.1_Missense_Mutation_p.M465L|CDHR2_ENST00000261944.5_Missense_Mutation_p.M465L	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	465	Cadherin 4. {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						CTCCGTCGCCATGGTGACCAT	0.632													A|||	98	0.0195687	0.0333	0.0072	5008	,	,		18027	0.0		0.0229	False		,,,				2504	0.0266				p.M465L		Atlas-SNP	.											.	CDHR2	152	.	0			c.A1393C						PASS	.	A	LEU/MET,LEU/MET	129,4277	95.3+/-134.0	0,129,2074	90	82	85		1393,1393	-5.5	0	5	dbSNP_126	85	150,8450	73.2+/-135.9	2,146,4152	yes	missense,missense	CDHR2	NM_001171976.1,NM_017675.4	15,15	2,275,6226	CC,CA,AA		1.7442,2.9278,2.1452	benign,benign	465/1311,465/1311	176004680	279,12727	2203	4300	6503	SO:0001583	missense	54825	exon14			GTCGCCATGGTGA	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.1393A>C	5.37:g.176004680A>C	ENSP00000424565:p.Met465Leu	44	0	0		67	33	0.492537	NM_017675	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	37	CCDS34297.1	33	0.01510989010989011	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	14	0.018469656992084433	A	13.81	2.349616	0.41599	0.029278	0.017442	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.59772	0.24;0.24;0.24	4.8	-5.53	0.02552	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.06826	0.0174	N	0.05012	-0.13	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.06250	-1.0837	9	0.44086	T	0.13	0.0331	2.189	0.03894	0.446:0.2189:0.0691:0.266	rs34767982;rs62404700	465	Q9BYE9	CDHR2_HUMAN	L	465	ENSP00000424565:M465L;ENSP00000261944:M465L;ENSP00000421078:M465L	ENSP00000261944:M465L	M	+	1	0	CDHR2	175937286	0.063000	0.20901	0.000000	0.03702	0.408000	0.30992	0.800000	0.27042	-1.193000	0.02688	0.391000	0.25812	ATG	A|0.979;C|0.021	0.021	strong		0.632	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675		C	176004680	A	C	176004680	3	2	28	1	0	0	0	0	1	0	0	0	3121	217	8	5	1443	5	CDHR2	5	176004680	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	473900	176004680	4910580	246	11749											
CDHR2	54825	hgsc.bcm.edu	37	chr5	176005481	176005481	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgctgcaggccacagacggcGggaacctgtcctcctccacc	7	5	11	18	3	0	1	0	0	0	1	3	2	3	2	6	3	2	2	6	3	1	0	rs61743422	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:176005481G>A	ENST00000510636.1	+	16	1964	c.1690G>A	c.(1690-1692)Ggg>Agg	p.G564R	CDHR2_ENST00000506348.1_Missense_Mutation_p.G564R|CDHR2_ENST00000261944.5_Missense_Mutation_p.G564R	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	564	Cadherin 5. {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						CACAGACGGCGGGAACCTGTC	0.617													G|||	53	0.0105831	0.0038	0.0043	5008	,	,		19440	0.0		0.0189	False		,,,				2504	0.0266				p.G564R		Atlas-SNP	.											.	CDHR2	152	.	0			c.G1690A						PASS	.	G	ARG/GLY,ARG/GLY	21,4385	29.0+/-57.7	0,21,2182	80	61	67		1690,1690	5.3	0.1	5	dbSNP_129	67	150,8450	72.9+/-135.5	2,146,4152	yes	missense,missense	CDHR2	NM_001171976.1,NM_017675.4	125,125	2,167,6334	AA,AG,GG		1.7442,0.4766,1.3148	probably-damaging,probably-damaging	564/1311,564/1311	176005481	171,12835	2203	4300	6503	SO:0001583	missense	54825	exon16			GACGGCGGGAACC	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.1690G>A	5.37:g.176005481G>A	ENSP00000424565:p.Gly564Arg	75	0	0		65	38	0.584615	NM_017675	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	37	CCDS34297.1	15	0.006868131868131868	1	0.0020325203252032522	0	0.0	0	0.0	14	0.018469656992084433	G	15.92	2.975766	0.53720	0.004766	0.017442	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.68181	-0.31;-0.31;-0.31	5.33	5.33	0.75918	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.70474	0.3228	M	0.79693	2.465	0.48452	D	0.999658	D	0.89917	1.0	D	0.70935	0.971	T	0.79969	-0.1579	9	0.72032	D	0.01	-27.052	14.6072	0.68489	0.0:0.1456:0.8544:0.0	rs61743422	564	Q9BYE9	CDHR2_HUMAN	R	564	ENSP00000424565:G564R;ENSP00000261944:G564R;ENSP00000421078:G564R	ENSP00000261944:G564R	G	+	1	0	CDHR2	175938087	1.000000	0.71417	0.098000	0.21074	0.041000	0.13682	5.345000	0.65987	2.504000	0.84457	0.542000	0.68232	GGG	G|0.987;A|0.013	0.013	strong		0.617	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675		A	176005481	G	A	176005481	3	1	28	1	0	0	0	0	1	0	0	0	3121	1116	39	1	1748	1	CDHR2	5	176005481	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	801	176005481	4909779	247	11750											
ADAMTS2	9509	hgsc.bcm.edu	37	chr5	178552115	178552115	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcggctgaatgcagcgcacGgagcgcacctgcatgcctgt	8	6	14	13	4	0	1	0	1	0	0	0	2	0	2	2	2	6	5	2	2	1	0	rs201215425		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:178552115G>A	ENST00000251582.7	-	19	2918	c.2817C>T	c.(2815-2817)tcC>tcT	p.S939S		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	939	TSP type-1 3. {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)		TGCAGCGCACGGAGCGCACCT	0.692																																					p.S939S		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.C2817T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	107	106	107		2817	-9.1	0.4	5		107	0,8600		0,0,4300	yes	coding-synonymous	ADAMTS2	NM_014244.4		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		939/1212	178552115	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9509	exon19			GCGCACGGAGCGC	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.2817C>T	5.37:g.178552115G>A		148	0	0		169	70	0.414201	NM_014244		Silent	SNP	ENST00000251582.7	37	CCDS4444.1																																																																																			.	.	weak		0.692	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244		A	178552115	G	A	178552115	2	1	28	1	0	0	0	0	0	0	0	1	265	1103	39	1		1	ADAMTS2	5	178552115	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2546634	178552115	2363145	248	11751											
TXNDC5	81567	hgsc.bcm.edu	37	chr6	7910865	7910865	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctcgccgtctgccgcgggggGcccgtccgccgccgccgccg	0	4	16	21	10	1	0	0	0	1	0	3	0	2	0	8	3	1	0	8	3	0	0	rs183777097	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:7910865G>A	ENST00000379757.4	-	1	182	c.145C>T	c.(145-147)Ccc>Tcc	p.P49S	BLOC1S5-TXNDC5_ENST00000439343.2_Intron|TXNDC5_ENST00000473453.1_5'Flank|TXNDC5_ENST00000539054.1_Intron	NM_030810.3	NP_110437.2	Q8NBS9	TXND5_HUMAN	thioredoxin domain containing 5 (endoplasmic reticulum)	49	Thioredoxin 1. {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)					GCCGCGGGGGGCCCGTccgcc	0.771													g|||	70	0.0139776	0.0023	0.0187	5008	,	,		3218	0.001		0.0408	False		,,,				2504	0.0123				p.P49S	Ovarian(119;1430 1625 3928 26125 34589)	Atlas-SNP	.											.	TXNDC5	33	.	0			c.C145T						PASS	.		SER/PRO	31,3679		1,29,1825	11	11	11		145	-5.6	0	6		11	258,6904		3,252,3326	no	missense	TXNDC5	NM_030810.3	74	4,281,5151	AA,AG,GG		3.6023,0.8356,2.6582	benign	49/433	7910865	289,10583	1855	3581	5436	SO:0001583	missense	81567	exon1			CGGGGGGCCCGTC	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.145C>T	6.37:g.7910865G>A	ENSP00000369081:p.Pro49Ser	7	0	0		11	7	0.636364	NM_030810	B2RDM2|Q5TCQ0|Q8ND33|Q8TCT2|Q9BVH9	Missense_Mutation	SNP	ENST00000379757.4	37	CCDS4505.1	73	0.033424908424908424	19	0.03861788617886179	8	0.022099447513812154	2	0.0034965034965034965	44	0.05804749340369393	.	0.221	-1.028982	0.02045	0.008356	0.036023	ENSG00000239264	ENST00000379757	T	0.03441	3.93	2.8	-5.61	0.02489	Thioredoxin-like fold (1);	0.991997	0.08180	N	0.985621	T	0.00468	0.0015	N	0.11201	0.11	0.09310	N	0.999996	B	0.02656	0.0	B	0.01281	0.0	T	0.45527	-0.9255	10	0.22109	T	0.4	.	5.4918	0.16781	0.3092:0.4165:0.2743:0.0	.	49	Q8NBS9	TXND5_HUMAN	S	49	ENSP00000369081:P49S	ENSP00000369081:P49S	P	-	1	0	TXNDC5	7855864	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-0.769000	0.04710	-3.133000	0.00235	-1.338000	0.01255	CCC	G|0.966;A|0.034	0.034	strong		0.771	TXNDC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039792.1	NM_030810		A	7910865	G	A	7910865	3	1	28	1	0	0	0	0	1	0	0	0	16814	1203	42	2	1193	2	TXNDC5	6	7910865	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10		7910865	163204202	249	11752											
SYCP2L	221711	hgsc.bcm.edu	37	chr6	10964015	10964015	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gatggaccaatttcttccagGttcaattcaactcagacttc	11	13	6	11	0	4	1	3	0	1	1	6	3	5	2	2	2	1	1	2	2	3	5	rs115084361	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:10964015G>A	ENST00000283141.6	+	29	2711	c.2415G>A	c.(2413-2415)agG>agA	p.R805R	SYCP2L_ENST00000465872.1_3'UTR	NM_001040274.2	NP_001035364.2	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like	805						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)			TTTCTTCCAGGTTCAATTCAA	0.358													G|||	49	0.00978435	0.0015	0.0173	5008	,	,		18130	0.0		0.0239	False		,,,				2504	0.0112				p.R805R		Atlas-SNP	.											.	SYCP2L	101	.	0			c.G2415A						PASS	.	G		11,3687		0,11,1838	103	96	98		2415	2.3	0.9	6	dbSNP_132	98	175,8007		1,173,3917	yes	coding-synonymous-near-splice	SYCP2L	NM_001040274.2		1,184,5755	AA,AG,GG		2.1388,0.2975,1.5657		805/813	10964015	186,11694	1849	4091	5940	SO:0001630	splice_region_variant	221711	exon29			TTCCAGGTTCAAT	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.2415-1G>A	6.37:g.10964015G>A		79	0	0		64	32	0.5	NM_001040274	A6NDS5|Q08GK5|Q6ZRM2|Q96EJ2	Silent	SNP	ENST00000283141.6	37	CCDS43423.1																																																																																			G|0.987;A|0.013	0.013	strong		0.358	SYCP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039845.3	NM_194299	Silent	A	10964015	G	A	10964015	5	1	28	1	0	0	0	0	0	0	1	0	15448	1275	44	2	2529	2	SYCP2L	6	10964015	Splice_Site	SNP	G	TCGA-G8-6914-01A-11D-2210-10	3053150	10964015	160151052	250	11753											
HFE	3077	hgsc.bcm.edu	37	chr6	26093141	26093141	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaagagcagagatatacgtGccaggtggagcacccaggcc	12	4	15	10	1	0	2	0	0	0	2	0	5	0	4	3	4	4	2	3	4	3	2	rs1800562	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:26093141G>A	ENST00000357618.5	+	4	967	c.845G>A	c.(844-846)tGc>tAc	p.C282Y	HFE_ENST00000470149.1_Missense_Mutation_p.C279Y|HFE_ENST00000397022.3_Missense_Mutation_p.C259Y|HFE_ENST00000461397.1_Missense_Mutation_p.C268Y|HFE_ENST00000353147.5_Missense_Mutation_p.C102Y|HFE_ENST00000352392.4_Intron|HFE_ENST00000336625.8_Missense_Mutation_p.C176Y|HFE_ENST00000349999.4_Missense_Mutation_p.C194Y|HFE_ENST00000309234.6_Missense_Mutation_p.C282Y|HFE_ENST00000488199.1_Missense_Mutation_p.C180Y|HFE_ENST00000317896.7_Missense_Mutation_p.C190Y	NM_000410.3|NM_139006.2	NP_000401.1|NP_620575.1	Q30201	HFE_HUMAN	hemochromatosis	282	Alpha-3.|Ig-like C1-type.		C -> Y (in HFE1; associated with susceptibility to porphyria cutanea tarda; associated with increased serum transferrin levels; higher frequency in patients with type 2 diabetes than in controls; dbSNP:rs1800562). {ECO:0000269|PubMed:10094552, ECO:0000269|PubMed:10194428, ECO:0000269|PubMed:11069625, ECO:0000269|PubMed:11423500, ECO:0000269|PubMed:12542741, ECO:0000269|PubMed:14633868, ECO:0000269|PubMed:18157833, ECO:0000269|PubMed:8696333, ECO:0000269|PubMed:9024376, ECO:0000269|PubMed:9106528, ECO:0000269|PubMed:9620340, ECO:0000269|Ref.8}.		antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular iron ion homeostasis (GO:0006879)|cellular response to iron ion starvation (GO:0010106)|female pregnancy (GO:0007565)|hormone biosynthetic process (GO:0042446)|immune response (GO:0006955)|iron ion import into cell (GO:0097459)|multicellular organismal iron ion homeostasis (GO:0060586)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein complex assembly (GO:0006461)	apical part of cell (GO:0045177)|basal part of cell (GO:0045178)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|MHC class I protein complex (GO:0042612)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	peptide antigen binding (GO:0042605)|receptor binding (GO:0005102)			endometrium(3)|large_intestine(3)|liver(2)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						AGATATACGTGCCAGGTGGAG	0.547									Hemochromatosis				G|||	63	0.0125799	0.0023	0.0216	5008	,	,		19430	0.0		0.0427	False		,,,				2504	0.002				p.C282Y		Atlas-SNP	.											.	HFE	37	.	0			c.G845A	GRCh37	CM004391|CM960828	HFE	M	rs1800562	PASS	.	G	TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS,	67,4339		1,65,2137	84	81	82	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	845,527,569,803,581,539,776,305,	5.3	1	6	dbSNP_89	82	551,8049		18,515,3767	yes	missense,missense,missense,missense,missense,missense,missense,missense,intron	HFE	NM_000410.3,NM_139003.2,NM_139004.2,NM_139006.2,NM_139007.2,NM_139008.2,NM_139009.2,NM_139010.2,NM_139011.2	194,194,194,194,194,194,194,194,	19,580,5904	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	6.407,1.5207,4.7517	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,	282/349,176/243,190/257,268/335,194/261,180/247,259/326,102/169,	26093141	618,12388	2203	4300	6503	SO:0001583	missense	3077	exon4	Familial Cancer Database		ATACGTGCCAGGT		CCDS4578.1, CCDS4579.1, CCDS4580.1, CCDS4581.1, CCDS4582.1, CCDS47386.1, CCDS47387.1, CCDS54974.1, CCDS54975.1, CCDS75412.1	6p21.3	2014-09-17			ENSG00000010704	ENSG00000010704		"Immunoglobulin superfamily / C1-set domain containing"	4886	protein-coding gene	gene with protein product	"high Fe"	613609				3460331	Standard	XR_241893		Approved	HLA-H	uc003nfx.1	Q30201	OTTHUMG00000016348	ENST00000357618.5:c.845G>A	6.37:g.26093141G>A	ENSP00000417404:p.Cys282Tyr	152	0	0		138	77	0.557971	NM_000410	B2CKL0|O75929|O75930|O75931|Q17RT0|Q96KU5|Q96KU6|Q96KU7|Q96KU8|Q9HC64|Q9HC68|Q9HC70|Q9HC83	Missense_Mutation	SNP	ENST00000357618.5	37	CCDS4578.1	43	0.019688644688644688	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	35	0.04617414248021108	.	17.19	3.326013	0.60743	0.015207	0.06407	ENSG00000010704	ENST00000349999;ENST00000397022;ENST00000317896;ENST00000353147;ENST00000357618;ENST00000470149;ENST00000336625;ENST00000461397;ENST00000488199;ENST00000309234	D;D;D;D;D;D;D;D;D;D	0.95342	-3.68;-3.68;-3.68;-3.68;-3.68;-3.68;-3.68;-3.68;-3.68;-3.68	5.35	5.35	0.76521	Immunoglobulin/major histocompatibility complex, conserved site (1);Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000003	D	0.98557	0.9518	H	0.99143	4.445	0.80722	A	1	D;D;D;D;D;P;D;D;D	0.89917	0.982;1.0;1.0;1.0;1.0;0.951;0.996;0.993;0.961	P;D;D;D;D;P;P;D;P	0.91635	0.756;0.999;0.999;0.999;0.999;0.56;0.826;0.917;0.667	D	0.98784	1.0733	9	0.87932	D	0	.	14.7506	0.69522	0.0:0.0:1.0:0.0	rs1800562;rs4134660;rs17530654;rs58044250;rs1800562	279;102;180;190;176;268;194;259;282	Q6B0J5;Q30201-6;Q30201-4;Q30201-7;Q30201-10;Q30201-3;Q30201-2;Q30201-5;Q30201	.;.;.;.;.;.;.;.;HFE_HUMAN	Y	194;259;190;102;282;279;176;268;180;282	ENSP00000259699:C194Y;ENSP00000380217:C259Y;ENSP00000313776:C190Y;ENSP00000312342:C102Y;ENSP00000417404:C282Y;ENSP00000419725:C279Y;ENSP00000337819:C176Y;ENSP00000420802:C268Y;ENSP00000420559:C180Y;ENSP00000311698:C282Y	ENSP00000311698:C282Y	C	+	2	0	HFE	26201120	1.000000	0.71417	0.993000	0.49108	0.351000	0.29236	4.282000	0.58971	2.941000	0.99782	0.655000	0.94253	TGC	G|0.966;A|0.034	0.034	strong		0.547	HFE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356133.1			A	26093141	G	A	26093141	3	1	28	1	0	0	0	0	1	0	0	0	7090	1319	46	2	859	2	HFE	6	26093141	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	15129126	26093141	145021926	251	11754											
HIST1H2AL	8332	hgsc.bcm.edu	37	chr6	27833378	27833378	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aagacccgcattatcccgcgCcacttgcagctggccatccg	8	7	9	17	4	0	1	0	0	0	1	2	1	2	1	5	1	2	3	5	1	2	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:27833378C>T	ENST00000357320.2	+	1	345	c.246C>T	c.(244-246)cgC>cgT	p.R82R		NM_003511.2	NP_003502.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2al	82						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)			breast(1)|endometrium(1)|large_intestine(2)|lung(3)|urinary_tract(2)	9						TTATCCCGCGCCACTTGCAGC	0.637																																					p.R82R		Atlas-SNP	.											.	HIST1H2AL	14	.	0			c.C246T						PASS	.						112	113	113					6																	27833378		2203	4300	6503	SO:0001819	synonymous_variant	8332	exon1			CCCGCGCCACTTG	X83549	CCDS4634.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000198374	ENSG00000276903		"Histones / Replication-dependent"	4730	protein-coding gene	gene with protein product		602793	"H2A histone family, member I", "histone 1, H2al"	H2AFI		9439656, 9031620, 12408966	Standard	NM_003511		Approved	H2A/i, dJ193B12.9	uc003njw.3	P0C0S8	OTTHUMG00000014492	ENST00000357320.2:c.246C>T	6.37:g.27833378C>T		108	0	0		101	49	0.485149	NM_003511	P02261|Q2M1R2|Q76PA6	Silent	SNP	ENST00000357320.2	37	CCDS4634.1																																																																																			.	.	none		0.637	HIST1H2AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040160.1	NM_003511		T	27833378	C	T	27833378	2	4	28	1	0	0	0	0	0	0	0	1	7147	726	26	2		2	HIST1H2AL	6	27833378	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1740237	27833378	143281689	252	11755											
OR2B3	442184	hgsc.bcm.edu	37	chr6	29054923	29054923	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gccaaatatggtgattgtgtAtgatattaacaggaccacaa	15	11	9	6	0	0	2	0	2	0	0	0	3	0	3	2	2	1	1	2	2	6	5	rs149723131	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29054923A>G	ENST00000377173.2	-	1	167	c.103T>C	c.(103-105)Tac>Cac	p.Y35H		NM_001005226.2	NP_001005226.1	O76000	OR2B3_HUMAN	olfactory receptor, family 2, subfamily B, member 3	35						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						GTGATTGTGTATGATATTAAC	0.408													A|||	10	0.00199681	0.0	0.0	5008	,	,		19983	0.0		0.0099	False		,,,				2504	0.0				p.Y35H		Atlas-SNP	.											OR2B3,NS,carcinoma,+2,1	OR2B3	44	1	0			c.T103C						PASS	.	A	HIS/TYR	15,4391	21.2+/-45.6	0,15,2188	135	124	128		103	2.7	0	6	dbSNP_134	128	87,8513	49.8+/-109.6	0,87,4213	yes	missense	OR2B3	NM_001005226.2	83	0,102,6401	GG,GA,AA		1.0116,0.3404,0.7843	probably-damaging	35/314	29054923	102,12904	2203	4300	6503	SO:0001583	missense	442184	exon1			TTGTGTATGATAT		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.103T>C	6.37:g.29054923A>G	ENSP00000366378:p.Tyr35His	85	0	0		54	25	0.462963	NM_001005226	B0UYQ1|Q5ST41|Q96R13	Missense_Mutation	SNP	ENST00000377173.2	37	CCDS34358.1	9	0.004120879120879121	0	0.0	0	0.0	0	0.0	9	0.011873350923482849	A	14.13	2.442681	0.43326	0.003404	0.010116	ENSG00000204703	ENST00000377173	T	0.04654	3.58	3.9	2.72	0.32119	.	0.000000	0.36854	U	0.002376	T	0.15825	0.0381	H	0.95043	3.615	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.12041	-1.0563	10	0.87932	D	0	.	8.8277	0.35065	0.9058:0.0:0.0942:0.0	.	35	O76000	OR2B3_HUMAN	H	35	ENSP00000366378:Y35H	ENSP00000366378:Y35H	Y	-	1	0	OR2B3	29162902	0.799000	0.28903	0.011000	0.14972	0.799000	0.45148	4.031000	0.57267	0.370000	0.24538	-0.396000	0.06452	TAC	A|0.993;G|0.007	0.007	strong		0.408	OR2B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076469.2			G	29054923	A	G	29054923	3	3	28	1	0	0	0	0	1	0	0	0	10999	449	16	3	842	3	OR2B3	6	29054923	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	1221545	29054923	142060144	253	11756											
KIAA1949	170954	hgsc.bcm.edu	37	chr6	30647035	30647035	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttcctcatcctcttcgtcGtcgggttgggctgctggagg	2	14	13	12	3	3	0	1	0	2	0	8	1	5	1	2	4	1	3	2	4	0	3	rs115169407	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:30647035G>T	ENST00000274853.3	-	2	3619	c.1743C>A	c.(1741-1743)gaC>gaA	p.D581E	PPP1R18_ENST00000399199.3_Missense_Mutation_p.D581E|PPP1R18_ENST00000488324.1_5'UTR	NM_133471.3	NP_597728.1	Q6NYC8	PPR18_HUMAN	protein phosphatase 1, regulatory subunit 18	581						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											CCTCTTCGTCGTCGGGTTGGG	0.667													G|||	7	0.00139776	0.0008	0.0014	5008	,	,		11756	0.0		0.005	False		,,,				2504	0.0				p.D581E		Atlas-SNP	.											KIAA1949,NS,carcinoma,0,1	.	.	1	0			c.C1743A						PASS	.	G	GLU/ASP,GLU/ASP	3,2425		0,3,1211	42	46	45		1743,1743	0.7	1	6	dbSNP_132	45	26,4986		0,26,2480	yes	missense,missense	KIAA1949	NM_001134870.1,NM_133471.3	45,45	0,29,3691	TT,TG,GG		0.5188,0.1236,0.3898	benign,benign	581/614,581/614	30647035	29,7411	1214	2506	3720	SO:0001583	missense	170954	exon3			TTCGTCGTCGGGT	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.1743C>A	6.37:g.30647035G>T	ENSP00000274853:p.Asp581Glu	32	0	0		38	17	0.447368	NM_001134870	A2AB01|A2AIB8|A4UBI6|A6NCB7|A8MSS7|B7ZCV7|Q68CK8|Q6ZTV1|Q6ZUJ6|Q8NDQ4|Q8TF52|Q9BRL9	Missense_Mutation	SNP	ENST00000274853.3	37	CCDS43444.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	G	15.40	2.822116	0.50739	0.001236	0.005188	ENSG00000146112	ENST00000274853;ENST00000399199	T;T	0.25579	1.79;1.79	5.08	0.679	0.17975	.	0.378241	0.23744	N	0.044992	T	0.04998	0.0134	N	0.17474	0.49	0.23076	N	0.998333	P	0.48407	0.91	P	0.45660	0.489	T	0.18366	-1.0339	10	0.34782	T	0.22	-7.4927	0.6512	0.00827	0.3521:0.1647:0.3139:0.1693	.	581	Q6NYC8	PPR18_HUMAN	E	581	ENSP00000274853:D581E;ENSP00000382150:D581E	ENSP00000274853:D581E	D	-	3	2	KIAA1949	30755014	0.253000	0.23982	0.953000	0.39169	0.881000	0.50899	-0.738000	0.04871	0.560000	0.29169	0.650000	0.86243	GAC	G|0.997;T|0.003	0.003	strong		0.667	PPP1R18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076498.2	NM_133471		T	30647035	G	T	30647035	3	4	28	1	0	0	0	0	1	0	0	0	8272	1136	40	4	106	4	KIAA1949	6	30647035	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1592112	30647035	140468032	254	11757											
PSORS1C1	170679	hgsc.bcm.edu	37	chr6	31106489	31106489	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttaacacagatcccagctccGaggaaactcgtcccccccac	11	6	6	18	2	0	1	0	0	0	1	4	3	3	2	5	1	3	1	5	1	2	1	rs1265096	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31106489G>A	ENST00000259881.9	+	5	389	c.100G>A	c.(100-102)Gag>Aag	p.E34K	PSORS1C2_ENST00000259845.4_Intron|PSORS1C1_ENST00000481450.2_Intron|PSORS1C1_ENST00000547221.1_5'UTR	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1	34			E -> K (in dbSNP:rs1265096). {ECO:0000269|PubMed:10545595, ECO:0000269|PubMed:12930300}.|E -> Q. {ECO:0000269|PubMed:12930300}.							kidney(1)|ovary(2)|prostate(1)|skin(1)	5						TCCCAGCTCCGAGGAAACTCG	0.567													G|||	85	0.0169728	0.0053	0.0115	5008	,	,		16762	0.0		0.0656	False		,,,				2504	0.0041				p.E34K		Atlas-SNP	.											.	PSORS1C1	11	.	0			c.G100A						PASS	.	G	LYS/GLU,	50,2972		0,50,1461	141	142	142		100,	0.3	0	6	dbSNP_87	142	361,5057		14,333,2362	yes	missense,intron	PSORS1C1,PSORS1C2	NM_014068.2,NM_014069.2	56,	14,383,3823	AA,AG,GG		6.663,1.6545,4.8697	benign,	34/153,	31106489	411,8029	1511	2709	4220	SO:0001583	missense	170679	exon5			AGCTCCGAGGAAA	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.100G>A	6.37:g.31106489G>A	ENSP00000259881:p.Glu34Lys	103	0	0		103	45	0.436893	NM_014068	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	37	CCDS34390.1	64	0.029304029304029304	3	0.006097560975609756	4	0.011049723756906077	0	0.0	57	0.07519788918205805	G	10.18	1.278140	0.23307	0.016545	0.06663	ENSG00000204540	ENST00000259881	T	0.14266	2.52	2.33	0.351	0.16042	.	.	.	.	.	T	0.01189	0.0039	N	0.08118	0	0.09310	N	1	P	0.44578	0.838	B	0.29353	0.101	T	0.44375	-0.9332	9	0.26408	T	0.33	.	4.9377	0.13948	0.3537:0.0:0.6463:0.0	rs1265096;rs3912054;rs1265096	34	Q9UIG5	PS1C1_HUMAN	K	34	ENSP00000259881:E34K	ENSP00000259881:E34K	E	+	1	0	PSORS1C1	31214468	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-2.035000	0.01423	-0.095000	0.12351	0.297000	0.19635	GAG	G|0.960;A|0.040	0.040	strong		0.567	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068		A	31106489	G	A	31106489	3	1	28	1	0	0	0	0	1	0	0	0	12726	1059	37	1	110	1	PSORS1C1	6	31106489	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	459454	31106489	140008578	255	11758											
HLA-DRB1	3123	hgsc.bcm.edu	37	chr6	32549582	32549582	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgtggtgctgcaggggctggGtctttgaaggatatacagtc	7	12	16	6	0	1	1	0	1	1	0	2	2	1	2	0	5	3	3	0	5	3	3	rs200516145		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32549582G>T	ENST00000360004.5	-	3	509	c.404C>A	c.(403-405)aCc>aAc	p.T135N		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	135	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)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						CAGGGGCTGGGTCTTTGAAGG	0.507										Multiple Myeloma(14;0.17)																											p.T135N		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.C404A						PASS	.						67	84	78					6																	32549582		1510	2709	4219	SO:0001583	missense	3123	exon3			GGCTGGGTCTTTG	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.404C>A	6.37:g.32549582G>T	ENSP00000353099:p.Thr135Asn	145	0	0		172	22	0.127907	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	11.78	1.740603	0.30865	.	.	ENSG00000196126	ENST00000360004	T	0.02863	4.13	3.87	2.92	0.33932	Immunoglobulin-like (1);Immunoglobulin C1-set (1);Immunoglobulin-like fold (1);	0.480425	0.24686	N	0.036424	T	0.06781	0.0173	M	0.76574	2.34	0.26397	N	0.97649	D	0.76494	0.999	D	0.87578	0.998	T	0.02632	-1.1131	10	0.87932	D	0	.	10.9743	0.47456	0.0:0.0:0.8139:0.1861	.	135	P01911	2B1F_HUMAN	N	135	ENSP00000353099:T135N	ENSP00000353099:T135N	T	-	2	0	HLA-DRB1	32657560	0.030000	0.19436	0.762000	0.31397	0.139000	0.21198	1.809000	0.38922	1.883000	0.54544	0.453000	0.30009	ACC	.	.	weak		0.507	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124		T	32549582	G	T	32549582	3	4	28	1	0	0	0	0	1	0	0	0	7217	1261	44	4	412	4	HLA-DRB1	6	32549582	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1443093	32549582	138565485	256	11759											
TAP1	6890	hgsc.bcm.edu	37	chr6	32814856	32814859	+	Frame_Shift_Del	DEL	TGTT	TGTT	-																															ctgcctcacctgtaactggcTgtttgcatccagggcactgg																										TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TGTT	TGTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32814856_32814859delTGTT	ENST00000354258.4	-	10	2367_2370	c.2206_2209delAACA	c.(2206-2211)aacagcfs	p.NS736fs	PSMB8_ENST00000374881.2_5'Flank|TAPSAR1_ENST00000453426.1_lincRNA|TAP1_ENST00000425148.2_Frame_Shift_Del_p.NS475fs|PSMB9_ENST00000395330.1_Intron	NM_000593.5	NP_000584.2	Q03518	TAP1_HUMAN	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	736	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|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)|cytosol to ER transport (GO:0046967)|defense response (GO:0006952)|intracellular transport of viral protein in host cell (GO:0019060)|peptide transport (GO:0015833)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|TAP complex (GO:0042825)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|MHC class Ib protein binding (GO:0023029)|peptide antigen binding (GO:0042605)|peptide transporter activity (GO:0015197)|protein homodimerization activity (GO:0042803)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(4)|prostate(1)|skin(1)	21					Lapatinib(DB01259)	TGTAACTGGCTGTTTGCATCCAGG	0.475																																					p.736_737del		Atlas-Indel	.											.	TAP1	39	.	0			c.2207_2210del						PASS	.																																			SO:0001589	frameshift_variant	6890	exon10			.		CCDS4758.1	6p21.3	2014-09-17			ENSG00000168394	ENSG00000168394		"ATP binding cassette transporters / subfamily B"	43	protein-coding gene	gene with protein product		170260		ABCB2		1529427, 1946428	Standard	NM_000593		Approved	PSF1, RING4, D6S114E	uc003ocg.3	Q03518	OTTHUMG00000031067	ENST00000354258.4:c.2206_2209delAACA	6.37:g.32814856_32814859delTGTT	ENSP00000346206:p.Asn736fs	28	0	0		35	10	0.285714	NM_000593	Q16149|Q96CP4	Frame_Shift_Del	DEL	ENST00000354258.4	37	CCDS4758.1																																																																																			.	.	none		0.475	TAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076087.2	NM_000593		-	32814859	TGTT	-	32814856	7	5	28	1	0	1	0	1	0	0	0	0	15565	1580	55	0	225	0	TAP1	6	32814856	Frame_Shift_Del	DEL	TGTT	TCGA-G8-6914-01A-11D-2210-10	265274	32814856	138300211	257	11760											
COL11A2	1302	hgsc.bcm.edu	37	chr6	33133555	33133555	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgccgagtcttcttgggcatCtgaatgggcagtggctggat	6	11	15	9	2	3	1	0	1	3	0	3	3	3	2	1	4	0	3	1	4	1	2	rs114580597	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:33133555C>T	ENST00000374708.4	-	61	4521	c.4263G>A	c.(4261-4263)caG>caA	p.Q1421Q	COL11A2_ENST00000477772.1_5'UTR|COL11A2_ENST00000374712.1_Silent_p.Q1426Q|COL11A2_ENST00000374713.1_Silent_p.Q1460Q|COL11A2_ENST00000361917.1_Silent_p.Q1400Q|COL11A2_ENST00000395197.1_Silent_p.Q1447Q|COL11A2_ENST00000341947.2_Silent_p.Q1507Q|COL11A2_ENST00000374714.1_Silent_p.Q1481Q|COL11A2_ENST00000357486.1_Silent_p.Q1486Q	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	1507	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						TCTTGGGCATCTGAATGGGCA	0.642													C|||	4	0.000798722	0.0	0.0	5008	,	,		18621	0.0		0.003	False		,,,				2504	0.001				p.Q1507Q	Melanoma(1;90 116 3946 5341 17093)	Atlas-SNP	.											.	COL11A2	124	.	0			c.G4521A						PASS	.	C	,,	4,4402	8.1+/-20.4	0,4,2199	59	60	60		4200,4521,4263	3.8	1	6	dbSNP_132	60	33,8567	19.8+/-62.0	0,33,4267	no	coding-synonymous,coding-synonymous,coding-synonymous	COL11A2	NM_080679.2,NM_080680.2,NM_080681.2	,,	0,37,6466	TT,TC,CC		0.3837,0.0908,0.2845	,,	1400/1630,1507/1737,1421/1651	33133555	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	1302	exon63			GGGCATCTGAATG	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.4263G>A	6.37:g.33133555C>T		18	0	0		17	7	0.411765	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Silent	SNP	ENST00000374708.4	37	CCDS43452.1																																																																																			C|0.998;T|0.002	0.002	strong		0.642	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2			T	33133555	C	T	33133555	2	4	28	1	0	0	0	0	0	0	0	1	3670	912	32	2		2	COL11A2	6	33133555	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	318699	33133555	137981512	258	11761											
SYNGAP1	8831	hgsc.bcm.edu	37	chr6	33391270	33391270	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccagatgtacggggaccctcTatgcaccgaacccaatacgt	11	7	9	14	3	1	1	0	0	1	1	1	3	1	2	4	2	4	2	4	2	5	3	rs587780476|rs142359891	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:33391270T>C	ENST00000418600.2	+	2	185	c.84T>C	c.(82-84)tcT>tcC	p.S28S	SYNGAP1_ENST00000293748.5_Silent_p.S28S|SYNGAP1_ENST00000496374.1_3'UTR	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	28					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						GGGGACCCTCTATGCACCGAA	0.527													T|||	10	0.00199681	0.0	0.0	5008	,	,		20532	0.0		0.006	False		,,,				2504	0.0041				p.S28S		Atlas-SNP	.											.	SYNGAP1	202	.	0			c.T84C						PASS	.	T		16,4390	23.3+/-48.9	0,16,2187	255	222	233		84	3.7	1	6	dbSNP_134	233	101,8499	55.2+/-116.2	0,101,4199	no	coding-synonymous	SYNGAP1	NM_006772.2		0,117,6386	CC,CT,TT		1.1744,0.3631,0.8996		28/1344	33391270	117,12889	2203	4300	6503	SO:0001819	synonymous_variant	8831	exon2			ACCCTCTATGCAC	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.84T>C	6.37:g.33391270T>C		89	0	0		104	52	0.5	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Silent	SNP	ENST00000418600.2	37	CCDS34434.2																																																																																			T|0.993;C|0.007	0.007	strong		0.527	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407		C	33391270	T	C	33391270	2	2	28	1	0	0	0	0	0	0	0	1	15462	1509	53	3		3	SYNGAP1	6	33391270	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	257715	33391270	137723797	259	11762											
ANKS1A	23294	hgsc.bcm.edu	37	chr6	35048829	35048829	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tcagaatgattcctgcactgGgcggtcggcagatctgctgc	7	10	13	11	2	2	3	1	1	1	2	4	3	3	3	1	3	3	3	1	3	1	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:35048829G>A	ENST00000360359.3	+	17	2741	c.2603G>A	c.(2602-2604)gGg>gAg	p.G868E	ANKS1A_ENST00000470698.1_3'UTR|ANKS1A_ENST00000535627.1_Intron	NM_015245.2	NP_056060.2	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1A	868					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						TCCTGCACTGGGCGGTCGGCA	0.617																																					p.G868E		Atlas-SNP	.											.	ANKS1A	123	.	0			c.G2603A						PASS	.						119	102	108					6																	35048829		2203	4300	6503	SO:0001583	missense	23294	exon17			GCACTGGGCGGTC	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.2603G>A	6.37:g.35048829G>A	ENSP00000353518:p.Gly868Glu	80	0	0		100	27	0.27	NM_015245	A2RUC1|B4DQW8|Q5JYI9|Q5SYR2|Q86WQ7	Missense_Mutation	SNP	ENST00000360359.3	37	CCDS4798.1	.	.	.	.	.	.	.	.	.	.	G	15.46	2.838812	0.51057	.	.	ENSG00000064999	ENST00000360359;ENST00000373990	T	0.40756	1.02	5.28	2.37	0.29283	.	0.133303	0.33591	N	0.004742	T	0.49508	0.1561	M	0.68952	2.095	0.80722	D	1	D;B;P	0.67145	0.996;0.104;0.884	D;B;B	0.63703	0.917;0.04;0.432	T	0.59521	-0.7439	10	0.87932	D	0	-8.113	15.4348	0.75137	0.0:0.4714:0.5286:0.0	.	194;194;868	Q49AR9;E7EM84;Q92625	.;.;ANS1A_HUMAN	E	868;194	ENSP00000353518:G868E	ENSP00000353518:G868E	G	+	2	0	ANKS1A	35156807	0.765000	0.28485	0.008000	0.14137	0.101000	0.19017	0.901000	0.28445	0.561000	0.29186	-0.211000	0.12701	GGG	.	.	none		0.617	ANKS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040262.1	XM_166478		A	35048829	G	A	35048829	3	1	28	1	0	0	0	0	1	0	0	0	688	1232	43	2	2669	2	ANKS1A	6	35048829	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1657559	35048829	136066238	260	11763											
CDKN1A	1026	hgsc.bcm.edu	37	chr6	36652228	36652228	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtggacctgtcactgtcttGtacccttgtgcctcgctcag	4	14	10	13	1	3	0	2	0	1	0	4	1	3	1	3	1	2	2	3	1	1	3	rs148679597		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:36652228G>A	ENST00000405375.1	+	2	585	c.350G>A	c.(349-351)tGt>tAt	p.C117Y	CDKN1A_ENST00000244741.5_Missense_Mutation_p.C117Y|CDKN1A_ENST00000478800.1_3'UTR|CDKN1A_ENST00000373711.2_Missense_Mutation_p.C117Y|CDKN1A_ENST00000448526.2_Missense_Mutation_p.C151Y	NM_001220778.1	NP_001207707.1	P38936	CDN1A_HUMAN	cyclin-dependent kinase inhibitor 1A (p21, Cip1)	117					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						TCACTGTCTTGTACCCTTGTG	0.642													G|||	1	0.000199681	0.0	0.0	5008	,	,		19561	0.0		0.001	False		,,,				2504	0.0				p.C117Y		Atlas-SNP	.											.	CDKN1A	27	.	0			c.G350A						PASS	.	G	TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS	3,4403	6.2+/-15.9	0,3,2200	45	44	44		350,350,350,350	5.2	1	6	dbSNP_134	44	30,8570	19.8+/-62.0	0,30,4270	yes	missense,missense,missense,missense	CDKN1A	NM_000389.4,NM_001220777.1,NM_001220778.1,NM_078467.2	194,194,194,194	0,33,6470	AA,AG,GG		0.3488,0.0681,0.2537	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	117/165,117/165,117/165,117/165	36652228	33,12973	2203	4300	6503	SO:0001583	missense	1026	exon2			TGTCTTGTACCCT	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.350G>A	6.37:g.36652228G>A	ENSP00000384849:p.Cys117Tyr	33	0	0		45	17	0.377778	NM_001220778	Q14010|Q6FI05|Q9BUT4	Missense_Mutation	SNP	ENST00000405375.1	37	CCDS4824.1	.	.	.	.	.	.	.	.	.	.	G	14.12	2.441009	0.43326	6.81E-4	0.003488	ENSG00000124762	ENST00000448526;ENST00000244741;ENST00000405375;ENST00000373711	T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14	5.23	5.23	0.72850	.	0.000000	0.64402	D	0.000010	T	0.81240	0.4781	L	0.49126	1.545	0.48040	D	0.999578	D;D;D	0.69078	0.997;0.995;0.997	D;D;D	0.73380	0.98;0.916;0.956	T	0.81911	-0.0716	10	0.56958	D	0.05	-36.2508	14.1752	0.65537	0.0:0.0:1.0:0.0	.	151;117;117	B4DQP9;P38936;Q96LE1	.;CDN1A_HUMAN;.	Y	151;117;117;117	ENSP00000409259:C151Y;ENSP00000244741:C117Y;ENSP00000384849:C117Y;ENSP00000362815:C117Y	ENSP00000244741:C117Y	C	+	2	0	CDKN1A	36760206	0.127000	0.22367	0.981000	0.43875	0.040000	0.13550	1.857000	0.39399	2.724000	0.93272	0.561000	0.74099	TGT	G|0.998;A|0.002	0.002	strong		0.642	CDKN1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040354.1	NM_078467		A	36652228	G	A	36652228	3	1	28	1	0	0	0	0	1	0	0	0	3160	1377	48	2	352	2	CDKN1A	6	36652228	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1603399	36652228	134462839	261	11764											
KCNK17	89822	hgsc.bcm.edu	37	chr6	39267230	39267230	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccttgccacagcctgcagcGtgagcagaaggttccagatg	9	8	12	12	1	0	3	0	1	0	2	2	3	2	3	4	1	5	3	4	1	1	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:39267230G>A	ENST00000373231.4	-	5	1204	c.972C>T	c.(970-972)caC>caT	p.H324H	KCNK17_ENST00000453413.2_3'UTR	NM_031460.3	NP_113648.2	Q96T54	KCNKH_HUMAN	potassium channel, subfamily K, member 17	324					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						aGCCTGCAGCGTGAGCAGAAG	0.547																																					p.H324H		Atlas-SNP	.											.	KCNK17	61	.	0			c.C972T						PASS	.						68	60	63					6																	39267230		2203	4300	6503	SO:0001819	synonymous_variant	89822	exon5			TGCAGCGTGAGCA	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.972C>T	6.37:g.39267230G>A		82	0	0		72	43	0.597222	NM_031460	E9PB46|Q5TCF4|Q8TAW4|Q9BXD1|Q9H592	Silent	SNP	ENST00000373231.4	37	CCDS4842.1																																																																																			.	.	none		0.547	KCNK17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040453.2	NM_031460		A	39267230	G	A	39267230	2	1	28	1	0	0	0	0	0	0	0	1	8073	1136	40	1		1	KCNK17	6	39267230	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2615002	39267230	131847837	262	11765											
ABCC10	89845	hgsc.bcm.edu	37	chr6	43400050	43400050	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	agggtgcgtggcagctgtggCctggatcagccacagcctgg	6	7	17	11	1	1	0	1	0	0	0	1	1	1	1	3	5	4	2	3	5	0	0			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:43400050C>T	ENST00000372530.4	+	3	547	c.332C>T	c.(331-333)gCc>gTc	p.A111V	ABCC10_ENST00000244533.3_Missense_Mutation_p.A68V|ABCC10_ENST00000443426.2_Intron	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	111					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)	GCAGCTGTGGCCTGGATCAGC	0.647																																					p.A111V		Atlas-SNP	.											.	ABCC10	118	.	0			c.C332T						PASS	.						61	61	61					6																	43400050		2203	4300	6503	SO:0001583	missense	89845	exon3			CTGTGGCCTGGAT	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.332C>T	6.37:g.43400050C>T	ENSP00000361608:p.Ala111Val	63	0	0		54	24	0.444444	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Missense_Mutation	SNP	ENST00000372530.4	37	CCDS56430.1	.	.	.	.	.	.	.	.	.	.	C	19.13	3.767863	0.69878	.	.	ENSG00000124574	ENST00000372530;ENST00000244533	T;T	0.41065	1.01;1.01	5.94	5.94	0.96194	.	0.106734	0.64402	D	0.000004	T	0.37758	0.1015	L	0.32530	0.975	0.52099	D	0.999942	D;P	0.55385	0.971;0.952	P;P	0.50825	0.651;0.449	T	0.13361	-1.0512	10	0.56958	D	0.05	-20.1624	20.3633	0.98874	0.0:1.0:0.0:0.0	.	68;111	Q5T3U5-2;Q5T3U5	.;MRP7_HUMAN	V	111;68	ENSP00000361608:A111V;ENSP00000244533:A68V	ENSP00000244533:A68V	A	+	2	0	ABCC10	43508028	1.000000	0.71417	1.000000	0.80357	0.054000	0.15201	7.418000	0.80167	2.826000	0.97356	0.561000	0.74099	GCC	.	.	none		0.647	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450		T	43400050	C	T	43400050	3	4	28	1	0	0	0	0	1	0	0	0	50	739	26	2	205	2	ABCC10	6	43400050	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	4132820	43400050	127715017	263	11766											
TMEM63B	55362	hgsc.bcm.edu	37	chr6	44117619	44117619	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cccatcatcacccagttcttCcccaccctgctgctgtggtg	5	11	7	18	0	3	0	2	0	1	0	4	0	4	0	5	1	2	3	5	1	0	2	rs75310630		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:44117619C>T	ENST00000259746.9	+	16	1620	c.1437C>T	c.(1435-1437)ttC>ttT	p.F479F	TMEM63B_ENST00000323267.6_Silent_p.F479F			Q5T3F8	CSCL2_HUMAN	transmembrane protein 63B	479					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)			CCCAGTTCTTCCCCACCCTGC	0.622													C|||	1	0.000199681	0.0	0.0	5008	,	,		19084	0.0		0.001	False		,,,				2504	0.0				p.F479F		Atlas-SNP	.											.	TMEM63B	77	.	0			c.C1437T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	206	141	163		1437	4.5	1	6	dbSNP_133	163	14,8586	9.1+/-34.3	0,14,4286	no	coding-synonymous	TMEM63B	NM_018426.1		0,15,6488	TT,TC,CC		0.1628,0.0227,0.1153		479/833	44117619	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	55362	exon16			GTTCTTCCCCACC	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.1437C>T	6.37:g.44117619C>T		126	0	0		107	42	0.392523	NM_018426	B9EGU3|Q5T3F9|Q6AHX4|Q6P5A0|Q8N219|Q8NDE1|Q9NSG5	Silent	SNP	ENST00000259746.9	37	CCDS34461.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	10.77	1.443996	0.25987	2.27E-4	0.001628	ENSG00000137216	ENST00000371893	.	.	.	4.49	4.49	0.54785	.	.	.	.	.	T	0.54062	0.1835	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53099	-0.8486	4	.	.	.	.	12.2754	0.54733	0.0:0.9139:0.0:0.0861	.	.	.	.	F	408	.	.	S	+	2	0	TMEM63B	44225597	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.121000	0.50438	2.488000	0.83962	0.549000	0.68633	TCC	C|0.999;T|0.001	0.001	strong		0.622	TMEM63B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040712.2	XM_166410		T	44117619	C	T	44117619	2	4	28	1	0	0	0	0	0	0	0	1	16206	854	30	2		2	TMEM63B	6	44117619	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	717569	44117619	126997448	264	11767											
GPR116	221395	hgsc.bcm.edu	37	chr6	46846060	46846060	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accttcatttcttcatttgcCaaaatttggatgggcataac	11	15	6	9	0	3	0	2	0	1	0	3	1	3	1	2	2	2	1	2	2	3	6			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:46846060C>T	ENST00000283296.7	-	10	1407	c.1119G>A	c.(1117-1119)ttG>ttA	p.L373L	GPR116_ENST00000265417.7_Silent_p.L373L|GPR116_ENST00000456426.2_Intron|GPR116_ENST00000362015.4_Silent_p.L373L	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	373	Ig-like 2.				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)			CTTCATTTGCCAAAATTTGGA	0.358																																					p.L373L	NSCLC(59;410 1274 8751 36715 50546)	Atlas-SNP	.											.	GPR116	133	.	0			c.G1119A						PASS	.						138	123	128					6																	46846060		2202	4300	6502	SO:0001819	synonymous_variant	221395	exon10			ATTTGCCAAAATT	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.1119G>A	6.37:g.46846060C>T		219	0	0		208	54	0.259615	NM_015234	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Silent	SNP	ENST00000283296.7	37	CCDS4919.1																																																																																			.	.	none		0.358	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234		T	46846060	C	T	46846060	2	4	28	1	0	0	0	0	0	0	0	1	6641	593	21	2		2	GPR116	6	46846060	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2728441	46846060	124269007	265	11768											
PKHD1	5314	hgsc.bcm.edu	37	chr6	51771044	51771044	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcatgacctaaaatattgtaGaatacattactgtccacctt	14	13	5	9	0	0	2	0	1	0	1	1	2	1	2	3	0	2	2	3	0	7	7	rs140065359	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:51771044G>A	ENST00000371117.3	-	41	7052	c.6777C>T	c.(6775-6777)ttC>ttT	p.F2259F	PKHD1_ENST00000340994.4_Silent_p.F2259F	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2259					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)	p.F2259L(2)		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)					AAATATTGTAGAATACATTAC	0.438													G|||	11	0.00219649	0.0	0.0014	5008	,	,		17456	0.0		0.0099	False		,,,				2504	0.0				p.F2259F		Atlas-SNP	.											PKHD1_ENST00000340994,NS,carcinoma,0,2	PKHD1	927	2	2	Substitution - Missense(2)	lung(2)	c.C6777T						PASS	.	G	,	3,4403	6.2+/-15.9	0,3,2200	80	79	79		6777,6777	3.7	1	6	dbSNP_134	79	50,8550	32.8+/-85.7	0,50,4250	no	coding-synonymous,coding-synonymous	PKHD1	NM_138694.3,NM_170724.2	,	0,53,6450	AA,AG,GG		0.5814,0.0681,0.4075	,	2259/4075,2259/3397	51771044	53,12953	2203	4300	6503	SO:0001819	synonymous_variant	5314	exon41			ATTGTAGAATACA	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.6777C>T	6.37:g.51771044G>A		36	0	0		20	7	0.35	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			G|0.996;A|0.004	0.004	strong		0.438	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		A	51771044	G	A	51771044	2	1	28	1	0	0	0	0	0	0	0	1	11980	933	33	2		2	PKHD1	6	51771044	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	4924984	51771044	119344023	266	11769											
GSTA4	2941	hgsc.bcm.edu	37	chr6	52850270	52850270	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggttctctccttgaggttcTtgccaaagagattgtgcttg	6	15	12	8	0	2	2	0	1	2	1	4	3	3	2	2	2	2	3	2	2	1	6	rs151284340	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:52850270T>C	ENST00000370959.1	-	4	368	c.251A>G	c.(250-252)aAg>aGg	p.K84R	GSTA4_ENST00000486559.1_5'UTR|GSTA4_ENST00000370960.1_Intron|GSTA4_ENST00000541324.1_Intron			O15217	GSTA4_HUMAN	glutathione S-transferase alpha 4	84					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)	CTTGAGGTTCTTGCCAAAGAG	0.488													T|||	6	0.00119808	0.0	0.0	5008	,	,		19004	0.0		0.006	False		,,,				2504	0.0				p.K84R		Atlas-SNP	.											GSTA4,right_upper_lobe,carcinoma,+1,1	GSTA4	20	1	0			c.A251G						PASS	.	T	ARG/LYS	0,4406		0,0,2203	187	150	162		251	-0.5	0.9	6	dbSNP_134	162	7,8593	5.7+/-21.5	0,7,4293	yes	missense	GSTA4	NM_001512.3	26	0,7,6496	CC,CT,TT		0.0814,0.0,0.0538	benign	84/223	52850270	7,12999	2203	4300	6503	SO:0001583	missense	2941	exon4			AGGTTCTTGCCAA	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.251A>G	6.37:g.52850270T>C	ENSP00000359998:p.Lys84Arg	129	0	0		153	62	0.405229	NM_001512	B2RD15|Q5T7Q8|Q6P4G1|Q9BX18|Q9H414	Missense_Mutation	SNP	ENST00000370959.1	37	CCDS4948.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	T	14.82	2.649056	0.47362	0.0	8.14E-4	ENSG00000170899	ENST00000370963;ENST00000370959	T;T	0.35048	1.33;1.33	5.13	-0.516	0.11950	Glutathione S-transferase, C-terminal-like (1);Thioredoxin-like fold (1);	0.248733	0.46145	N	0.000302	T	0.16214	0.0390	M	0.62016	1.91	0.80722	D	1	B	0.09022	0.002	B	0.15052	0.012	T	0.08493	-1.0719	10	0.48119	T	0.1	-15.3197	8.5879	0.33668	0.0:0.3374:0.0:0.6626	.	84	O15217	GSTA4_HUMAN	R	84	ENSP00000360002:K84R;ENSP00000359998:K84R	ENSP00000359998:K84R	K	-	2	0	GSTA4	52958229	0.443000	0.25641	0.914000	0.36105	0.981000	0.71138	0.582000	0.23834	-0.231000	0.09825	-0.376000	0.06991	AAG	T|0.999;C|0.001	0.001	strong		0.488	GSTA4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040946.1	NM_001512		C	52850270	T	C	52850270	3	2	28	1	0	0	0	0	1	0	0	0	6842	1609	56	3	433	3	GSTA4	6	52850270	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	1079226	52850270	118264797	267	11770											
COL21A1	81578	hgsc.bcm.edu	37	chr6	55925801	55925801	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	attctccttttgatccaatgGcacctcggacaccaggttct	8	13	7	13	1	2	1	0	1	2	0	5	2	3	2	4	3	0	2	4	3	1	4	rs9464337	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:55925801G>T	ENST00000244728.5	-	26	2637	c.2240C>A	c.(2239-2241)gCc>gAc	p.A747D	COL21A1_ENST00000467045.1_5'UTR|COL21A1_ENST00000370808.2_Missense_Mutation_p.A147D|COL21A1_ENST00000370819.1_Missense_Mutation_p.A744D|COL21A1_ENST00000535941.1_Missense_Mutation_p.A747D	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	747	Collagen-like 5.		A -> D (in dbSNP:rs9464337).		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)			TGATCCAATGGCACCTCGGAC	0.483													G|||	209	0.0417332	0.0794	0.0173	5008	,	,		16689	0.0397		0.006	False		,,,				2504	0.047				p.A747D		Atlas-SNP	.											.	COL21A1	201	.	0			c.C2240A						PASS	.	G	ASP/ALA	284,3426		12,260,1583	58	56	57		2240	3.9	0.5	6	dbSNP_119	57	54,8128		1,52,4038	yes	missense	COL21A1	NM_030820.3	126	13,312,5621	TT,TG,GG		0.66,7.655,2.8422	benign	747/958	55925801	338,11554	1855	4091	5946	SO:0001583	missense	81578	exon26			CCAATGGCACCTC	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.2240C>A	6.37:g.55925801G>T	ENSP00000244728:p.Ala747Asp	93	0	0		110	50	0.454545	NM_030820	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Missense_Mutation	SNP	ENST00000244728.5	37	CCDS55025.1	72	0.03296703296703297	45	0.09146341463414634	8	0.022099447513812154	17	0.02972027972027972	2	0.002638522427440633	G	3.291	-0.144886	0.06627	0.07655	0.0066	ENSG00000124749	ENST00000244728;ENST00000370819;ENST00000535941;ENST00000370811;ENST00000370808	D;D;D;T	0.94376	-3.41;-3.41;-3.41;-1.07	4.77	3.9	0.45041	.	0.411176	0.21246	N	0.077734	T	0.68072	0.2961	N	0.12182	0.205	0.09310	N	1	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.10450	0.002;0.003;0.005;0.003	T	0.58405	-0.7642	10	0.13108	T	0.6	.	3.8636	0.09007	0.2009:0.0:0.5938:0.2053	rs9464337;rs52804762;rs9464337	147;747;747;104	Q96P44-2;B7ZLK3;Q96P44;B3KU30	.;.;COLA1_HUMAN;.	D	747;744;747;744;147	ENSP00000244728:A747D;ENSP00000359855:A744D;ENSP00000444384:A747D;ENSP00000359844:A147D	ENSP00000244728:A747D	A	-	2	0	COL21A1	56033760	0.847000	0.29606	0.523000	0.27875	0.413000	0.31143	2.015000	0.40961	1.132000	0.42129	-0.268000	0.10319	GCC	G|0.960;T|0.040	0.040	strong		0.483	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2			T	55925801	G	T	55925801	3	4	28	1	0	0	0	0	1	0	0	0	3682	1203	42	4	653	4	COL21A1	6	55925801	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	3075531	55925801	115189266	268	11771											
KIAA1586	57691	hgsc.bcm.edu	37	chr6	56918933	56918933	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttcaactgcattacagtcaAgatcaactaatattaagaaa	18	12	4	7	0	3	2	3	0	0	2	3	2	3	2	0	0	4	1	0	0	8	5			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:56918933A>G	ENST00000370733.4	+	4	1843	c.1636A>G	c.(1636-1638)Aga>Gga	p.R546G	KIAA1586_ENST00000545356.1_Missense_Mutation_p.R519G	NM_020931.2	NP_065982.1	Q9HCI6	K1586_HUMAN	KIAA1586	546							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)			ATTACAGTCAAGATCAACTAA	0.299																																					p.R546G		Atlas-SNP	.											.	KIAA1586	59	.	0			c.A1636G						PASS	.						30	31	31					6																	56918933		2174	4281	6455	SO:0001583	missense	57691	exon4			CAGTCAAGATCAA	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.1636A>G	6.37:g.56918933A>G	ENSP00000359768:p.Arg546Gly	88	0	0		90	4	0.0444444	NM_020931	A8K4M3|Q8IW25	Missense_Mutation	SNP	ENST00000370733.4	37	CCDS34480.1	.	.	.	.	.	.	.	.	.	.	a	10.50	1.368490	0.24771	.	.	ENSG00000168116	ENST00000370733;ENST00000545356	T;T	0.21191	2.02;2.02	3.84	2.66	0.31614	Ribonuclease H-like (1);	.	.	.	.	T	0.03305	0.0096	N	0.08118	0	0.23107	N	0.998283	B;B	0.11235	0.004;0.004	B;B	0.09377	0.004;0.004	T	0.40831	-0.9542	9	0.62326	D	0.03	-3.9313	5.9809	0.19407	0.8787:0.0:0.1213:0.0	.	519;546	F5H2N6;Q9HCI6	.;K1586_HUMAN	G	546;519	ENSP00000359768:R546G;ENSP00000445507:R519G	ENSP00000359768:R546G	R	+	1	2	KIAA1586	57026892	0.999000	0.42202	0.959000	0.39883	0.992000	0.81027	1.557000	0.36299	0.637000	0.30526	-0.263000	0.10527	AGA	.	.	none		0.299	KIAA1586-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041033.1	NM_020931		G	56918933	A	G	56918933	3	3	28	1	0	0	0	0	1	0	0	0	8254	64	3	3	1650	3	KIAA1586	6	56918933	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	993132	56918933	114196134	269	11772											
TTK	7272	hgsc.bcm.edu	37	chr6	80718167	80718167	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagcaaactgcaagaaatttGcttttgttcatatatctttt	12	17	6	6	0	2	1	1	0	1	1	2	2	2	1	0	0	4	4	0	0	5	8			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:80718167G>A	ENST00000369798.2	+	4	538	c.427G>A	c.(427-429)Gct>Act	p.A143T	TTK_ENST00000230510.3_Missense_Mutation_p.A143T|TTK_ENST00000509894.1_Missense_Mutation_p.A143T	NM_001166691.1|NM_003318.4	NP_001160163.1|NP_003309.2	P33981	TTK_HUMAN	TTK protein kinase	143					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)		CAAGAAATTTGCTTTTGTTCA	0.299																																					p.A143T		Atlas-SNP	.											.	TTK	199	.	0			c.G427A						PASS	.						77	70	73					6																	80718167		2203	4299	6502	SO:0001583	missense	7272	exon4			AAATTTGCTTTTG		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.427G>A	6.37:g.80718167G>A	ENSP00000358813:p.Ala143Thr	50	0	0		47	10	0.212766	NM_003318	A8K8U5|B2RDW2|E1P543|Q15272|Q5TCS0|Q9BW51|Q9NTM0	Missense_Mutation	SNP	ENST00000369798.2	37	CCDS4993.1	.	.	.	.	.	.	.	.	.	.	G	32	5.165323	0.94768	.	.	ENSG00000112742	ENST00000509894;ENST00000230510;ENST00000369798;ENST00000511260;ENST00000504040	D;D;D;D;D	0.89485	-2.52;-2.52;-2.52;-2.52;-2.52	6.16	5.27	0.74061	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	D	0.92328	0.7566	M	0.66939	2.045	0.49213	D	0.999764	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.93231	0.6617	10	0.62326	D	0.03	.	15.8123	0.78573	0.0:0.0:0.8632:0.1368	.	143;143	P33981;A8K8U5	TTK_HUMAN;.	T	143	ENSP00000422936:A143T;ENSP00000230510:A143T;ENSP00000358813:A143T;ENSP00000421636:A143T;ENSP00000427483:A143T	ENSP00000230510:A143T	A	+	1	0	TTK	80774886	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.619000	0.67729	1.557000	0.49525	0.650000	0.86243	GCT	.	.	none		0.299	TTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041316.2			A	80718167	G	A	80718167	3	1	28	1	0	0	0	0	1	0	0	0	16735	1319	46	2	437	2	TTK	6	80718167	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	23799234	80718167	90396900	270	11773											
CNR1	1268	hgsc.bcm.edu	37	chr6	88854166	88854166	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtgaccccgatccagaacatCaggtaggtttcatcaatgtg	11	10	10	10	1	3	2	3	1	0	1	4	3	4	2	3	2	1	2	3	2	3	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:88854166C>T	ENST00000537554.1	-	2	4390	c.828G>A	c.(826-828)ctG>ctA	p.L276L	CNR1_ENST00000369499.2_Silent_p.L276L|CNR1_ENST00000428600.2_Silent_p.L276L|CNR1_ENST00000549890.1_Silent_p.L276L|CNR1_ENST00000549716.1_Silent_p.L215L|CNR1_ENST00000468898.1_Silent_p.L243L|CNR1_ENST00000362094.5_3'UTR|CNR1_ENST00000535130.1_Silent_p.L276L|CNR1_ENST00000369501.2_Silent_p.L276L	NM_001160226.1|NM_001160258.1	NP_001153698.1|NP_001153730.1	P21554	CNR1_HUMAN	cannabinoid receptor 1 (brain)	276					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)	TCCAGAACATCAGGTAGGTTT	0.512																																					p.L276L		Atlas-SNP	.											.	CNR1	91	.	0			c.G828A						PASS	.						83	72	76					6																	88854166		2203	4300	6503	SO:0001819	synonymous_variant	1268	exon4			GAACATCAGGTAG	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.828G>A	6.37:g.88854166C>T		64	0	0		68	34	0.5	NM_001160258	B2R9T4|E1P512|Q13949|Q495Z0|Q4PLI4|Q4VBM6|Q5JVL5|Q5UB37|Q9UNN0	Silent	SNP	ENST00000537554.1	37	CCDS5015.1																																																																																			.	.	none		0.512	CNR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354204.2			T	88854166	C	T	88854166	2	4	28	1	0	0	0	0	0	0	0	1	3633	813	29	2		2	CNR1	6	88854166	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	8135999	88854166	82260901	271	11774											
CASP8AP2	9994	hgsc.bcm.edu	37	chr6	90577650	90577650	+	RNA	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcattgtgaaaatacgacgTgcaacaccatctacctcttc	12	12	5	12	2	3	1	1	1	2	0	4	2	3	1	2	0	4	1	2	0	5	5	rs200433993	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:90577650T>G	ENST00000551025.1	+	0	6078									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)		AAATACGACGTGCAACACCAT	0.443													T|||	5	0.000998403	0.0	0.0	5008	,	,		21746	0.0		0.005	False		,,,				2504	0.0				p.R1547R	Colon(187;1656 2025 17045 31481 39901)	Atlas-SNP	.											CASP8AP2,caecum,carcinoma,+2,1	CASP8AP2	108	1	0			c.T4641G						PASS	.	T	,,	5,3875		0,5,1935	142	128	133		4641,4641,4641	4.3	1	6		133	22,8250		0,22,4114	no	coding-synonymous,coding-synonymous,coding-synonymous	CASP8AP2	NM_001137667.1,NM_001137668.1,NM_012115.3	,,	0,27,6049	GG,GT,TT		0.266,0.1289,0.2222	,,	1547/1967,1547/1967,1547/1967	90577650	27,12125	1940	4136	6076			9994	exon8			ACGACGTGCAACA	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.90577650T>G		89	0	0		96	37	0.385417	NM_001137667		Silent	SNP	ENST00000551025.1	37																																																																																				T|0.996;G|0.004	0.004	strong		0.443	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667		G	90577650	T	G	90577650	1	3	28	0	1	0	0	0	0	0	0	0	2680	1683	59	5		5	CASP8AP2	6	90577650	RNA	SNP	T	TCGA-G8-6914-01A-11D-2210-10	1723484	90577650	80537417	272	11775											
PRDM1	639	hgsc.bcm.edu	37	chr6	106543533	106543533	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atacataccaaagggcacacGttttggacccctaataggtg	13	9	9	10	1	0	0	0	0	0	0	0	1	0	1	3	3	2	2	3	3	5	6			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:106543533G>A	ENST00000369096.4	+	3	569	c.335G>A	c.(334-336)cGt>cAt	p.R112H	PRDM1_ENST00000369091.2_Missense_Mutation_p.R76H	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	112	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				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)		AAGGGCACACGTTTTGGACCC	0.363			"D, N, Mis, F, S"		DLBCL																																p.R112H		Atlas-SNP	.		Rec	yes		6	6q21	639	"PR domain containing 1, with ZNF domain"		L	PRDM1,colon,carcinoma,0,1	PRDM1	195	1	0			c.G335A						PASS	.						97	91	93					6																	106543533		2203	4300	6503	SO:0001583	missense	639	exon3			GCACACGTTTTGG		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.335G>A	6.37:g.106543533G>A	ENSP00000358092:p.Arg112His	63	0	0		68	6	0.0882353	NM_001198	B2REA6|E1P5E0|Q86WM7	Missense_Mutation	SNP	ENST00000369096.4	37	CCDS5054.2	.	.	.	.	.	.	.	.	.	.	G	35	5.532045	0.96446	.	.	ENSG00000057657	ENST00000369091;ENST00000369096;ENST00000456278	T;T	0.73363	-0.74;-0.74	6.06	6.06	0.98353	SET domain (3);	0.052943	0.85682	D	0.000000	D	0.83968	0.5369	M	0.63208	1.945	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83781	0.0225	10	0.87932	D	0	-14.1659	20.6208	0.99490	0.0:0.0:1.0:0.0	.	112	O75626	PRDM1_HUMAN	H	76;112;76	ENSP00000358087:R76H;ENSP00000358092:R112H	ENSP00000358087:R76H	R	+	2	0	PRDM1	106650226	1.000000	0.71417	0.890000	0.34922	0.962000	0.63368	9.869000	0.99810	2.882000	0.98803	0.655000	0.94253	CGT	.	.	none		0.363	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3			A	106543533	G	A	106543533	3	1	28	1	0	0	0	0	1	0	0	0	12462	1145	40	1	345	1	PRDM1	6	106543533	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	15965883	106543533	64571534	273	11776											
PRDM1	639	hgsc.bcm.edu	37	chr6	106554343	106554343	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctgcagaaacactacctggTacacacgggagaaaagccac	15	4	9	13	1	0	2	0	0	0	2	0	3	0	2	3	2	5	2	3	2	5	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:106554343T>A	ENST00000369096.4	+	6	2105	c.1871T>A	c.(1870-1872)gTa>gAa	p.V624E	PRDM1_ENST00000369089.3_Missense_Mutation_p.V490E|PRDM1_ENST00000369091.2_Missense_Mutation_p.V588E	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	624					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)		CACTACCTGGTACACACGGGA	0.512			"D, N, Mis, F, S"		DLBCL																																p.V624E		Atlas-SNP	.		Rec	yes		6	6q21	639	"PR domain containing 1, with ZNF domain"		L	.	PRDM1	195	.	0			c.T1871A						PASS	.						116	96	103					6																	106554343		2203	4300	6503	SO:0001583	missense	639	exon6			ACCTGGTACACAC		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.1871T>A	6.37:g.106554343T>A	ENSP00000358092:p.Val624Glu	54	0	0		57	13	0.22807	NM_001198	B2REA6|E1P5E0|Q86WM7	Missense_Mutation	SNP	ENST00000369096.4	37	CCDS5054.2	.	.	.	.	.	.	.	.	.	.	T	25.0	4.589481	0.86851	.	.	ENSG00000057657	ENST00000369091;ENST00000369096;ENST00000456278;ENST00000369089	T;T;T	0.07688	3.17;3.17;3.17	5.55	5.55	0.83447	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.052469	0.85682	D	0.000000	T	0.14700	0.0355	L	0.50993	1.605	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.994;0.998	T	0.00613	-1.1644	10	0.87932	D	0	-13.8246	12.4582	0.55716	0.0:0.0:0.1492:0.8508	.	490;624	Q86WM7;O75626	.;PRDM1_HUMAN	E	588;624;587;490	ENSP00000358087:V588E;ENSP00000358092:V624E;ENSP00000358085:V490E	ENSP00000358085:V490E	V	+	2	0	PRDM1	106661036	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	6.180000	0.71981	2.118000	0.64928	0.533000	0.62120	GTA	.	.	none		0.512	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3			A	106554343	T	A	106554343	3	1	28	1	0	0	0	0	1	0	0	0	12462	1638	57	5	1906	5	PRDM1	6	106554343	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	10810	106554343	64560724	274	11777											
TSPYL4	23270	hgsc.bcm.edu	37	chr6	116574977	116574977	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggggccacagtcgacaggAtcctgggatgcacccccctc	7	5	13	16	2	0	0	0	0	0	0	3	3	1	2	5	4	1	1	5	4	0	0	rs187133419	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:116574977A>C	ENST00000420283.1	-	1	284	c.195T>G	c.(193-195)gaT>gaG	p.D65E	RP3-486I3.7_ENST00000448740.2_lincRNA|DSE_ENST00000540275.1_5'Flank	NM_021648.4	NP_067680.3	Q9UJ04	TSYL4_HUMAN	TSPY-like 4	65					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)		AGTCGACAGGATCCTGGGATG	0.667													A|||	8	0.00159744	0.0	0.0086	5008	,	,		15829	0.0		0.002	False		,,,				2504	0.0				p.D65E		Atlas-SNP	.											.	TSPYL4	18	.	0			c.T195G						PASS	.	A	GLU/ASP	3,4039		0,3,2018	19	22	21		195	-7.5	0	6		21	36,8334		0,36,4149	yes	missense	TSPYL4	NM_021648.4	45	0,39,6167	CC,CA,AA		0.4301,0.0742,0.3142	possibly-damaging	65/415	116574977	39,12373	2021	4185	6206	SO:0001583	missense	23270	exon1			GACAGGATCCTGG		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.195T>G	6.37:g.116574977A>C	ENSP00000410943:p.Asp65Glu	34	0	0		35	15	0.428571	NM_021648	B4DYQ2|O94828|Q96GW8	Missense_Mutation	SNP	ENST00000420283.1	37	CCDS5106.1	4	0.0018315018315018315	0	0.0	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	A	10.13	1.264700	0.23136	7.42E-4	0.004301	ENSG00000187189	ENST00000420283	T	0.18810	2.19	3.75	-7.5	0.01351	.	.	.	.	.	T	0.03220	0.0094	M	0.63843	1.955	0.09310	N	1	B	0.15930	0.015	B	0.15052	0.012	T	0.43718	-0.9374	9	0.02654	T	1	-2.0876	2.3433	0.04265	0.1299:0.3779:0.1165:0.3757	.	65	Q9UJ04	TSYL4_HUMAN	E	65	ENSP00000410943:D65E	ENSP00000410943:D65E	D	-	3	2	TSPYL4	116681670	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.061000	0.11693	-1.631000	0.01543	-0.648000	0.03929	GAT	A|0.998;C|0.002	0.002	strong		0.667	TSPYL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041934.2			C	116574977	A	C	116574977	3	2	28	1	0	0	0	0	1	0	0	0	16676	330	12	5	1053	5	TSPYL4	6	116574977	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	10020634	116574977	54540090	275	11778											
PERP	64065	hgsc.bcm.edu	37	chr6	138428379	138428379	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgctagactgcaaccagccGcggccggccagcgcgatgat	8	5	13	15	6	0	2	0	1	0	1	1	3	0	2	4	2	4	2	4	2	2	1	rs145663845	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:138428379G>A	ENST00000421351.3	-	1	269	c.99C>T	c.(97-99)cgC>cgT	p.R33R		NM_022121.4	NP_071404.2	Q96FX8	PERP_HUMAN	PERP, TP53 apoptosis effector	33					activation of cysteine-type endopeptidase activity (GO:0097202)|amelogenesis (GO:0097186)|desmosome organization (GO:0002934)|heterotypic cell-cell adhesion (GO:0034113)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of proteolysis (GO:0045862)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(1)|lung(1)|prostate(1)	5	Breast(32;0.0799)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000878)|OV - Ovarian serous cystadenocarcinoma(155;0.000997)		GCAACCAGCCGCGGCCGGCCA	0.682													g|||	24	0.00479233	0.0008	0.0058	5008	,	,		11494	0.0		0.0089	False		,,,				2504	0.0102				p.R33R		Atlas-SNP	.											.	PERP	15	.	0			c.C99T						PASS	.	G		12,4260		0,12,2124	31	39	36		99	-0.4	1	6	dbSNP_134	36	95,8285		0,95,4095	no	coding-synonymous	PERP	NM_022121.4		0,107,6219	AA,AG,GG		1.1337,0.2809,0.8457		33/194	138428379	107,12545	2136	4190	6326	SO:0001819	synonymous_variant	64065	exon1			CCAGCCGCGGCCG	AF317550	CCDS5188.1	6q24	2014-04-29			ENSG00000112378	ENSG00000112378			17637	protein-coding gene	gene with protein product	"keratinocyte associated protein 1"	609301				11062687	Standard	NM_022121		Approved	PIGPC1, dJ496H19.1, KCP1, THW, KRTCAP1	uc003qht.2	Q96FX8	OTTHUMG00000015668	ENST00000421351.3:c.99C>T	6.37:g.138428379G>A		64	0	0		75	37	0.493333	NM_022121	B2RB73|E1P590|Q8IWS3|Q8N1J6|Q8NC16|Q9H1C5|Q9H230	Silent	SNP	ENST00000421351.3	37	CCDS5188.1																																																																																			G|0.993;A|0.007	0.007	strong		0.682	PERP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042423.2	NM_022121		A	138428379	G	A	138428379	2	1	28	1	0	0	0	0	0	0	0	1	11741	1074	38	1		1	PERP	6	138428379	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	21853402	138428379	32686688	276	11779											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152722368	152722368	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgttgttatgtcattaataaActtctccacttgtgtacttt	9	20	5	7	0	2	0	1	0	1	0	3	0	2	0	1	0	2	3	1	0	5	8	rs138004884		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:152722368A>G	ENST00000367255.5	-	47	7535	c.6934T>C	c.(6934-6936)Ttt>Ctt	p.F2312L	SYNE1_ENST00000423061.1_Missense_Mutation_p.F2319L|RP3-398G3.5_ENST00000458194.1_RNA|SYNE1_ENST00000448038.1_Missense_Mutation_p.F2319L|SYNE1_ENST00000341594.5_Missense_Mutation_p.F2349L|SYNE1_ENST00000265368.4_Missense_Mutation_p.F2312L	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2312					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)		TCATTAATAAACTTCTCCACT	0.393										HNSCC(10;0.0054)			A|||	1	0.000199681	0.0	0.0	5008	,	,		19585	0.0		0.001	False		,,,				2504	0.0				p.F2319L		Atlas-SNP	.											.	SYNE1	3227	.	0			c.T6955C						PASS	.	A	LEU/PHE,LEU/PHE	1,4405	2.1+/-5.4	0,1,2202	147	129	135		6955,6934	5.6	1	6	dbSNP_134	135	8,8592	6.4+/-24.3	0,8,4292	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	22,22	0,9,6494	GG,GA,AA		0.093,0.0227,0.0692	benign,benign	2319/8750,2312/8798	152722368	9,12997	2203	4300	6503	SO:0001583	missense	23345	exon47			TAATAAACTTCTC	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.6934T>C	6.37:g.152722368A>G	ENSP00000356224:p.Phe2312Leu	159	0	0		156	63	0.403846	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	37	CCDS5236.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	14.92	2.678770	0.47886	2.27E-4	9.3E-4	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.32515	1.45;1.45;1.45;1.45;1.45	5.58	5.58	0.84498	.	0.101968	0.43919	D	0.000518	T	0.11623	0.0283	L	0.39633	1.23	0.80722	D	1	B;B;B;B	0.15141	0.012;0.002;0.002;0.002	B;B;B;B	0.13407	0.009;0.003;0.003;0.004	T	0.08848	-1.0702	10	0.16896	T	0.51	.	11.6415	0.51235	0.9288:0.0:0.0712:0.0	.	2295;2312;2312;2319	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	L	2312;2319;2312;2319;2349	ENSP00000356224:F2312L;ENSP00000396024:F2319L;ENSP00000265368:F2312L;ENSP00000390975:F2319L;ENSP00000341887:F2349L	ENSP00000265368:F2312L	F	-	1	0	SYNE1	152764061	1.000000	0.71417	0.963000	0.40424	0.921000	0.55340	5.286000	0.65639	2.133000	0.65898	0.482000	0.46254	TTT	A|0.999;G|0.001	0.001	strong		0.393	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		G	152722368	A	G	152722368	3	3	28	1	0	0	0	0	1	0	0	0	15460	43	2	3	19932	3	SYNE1	6	152722368	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	14293989	152722368	18392699	277	11780											
RBM16	22828	hgsc.bcm.edu	37	chr6	155123273	155123273	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccttagaacagggagtctccTttaacaaggtagaaattaaa	16	10	8	7	0	1	2	0	0	1	2	2	3	1	3	2	2	2	1	2	2	8	5			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:155123273T>C	ENST00000367178.3	+	7	1351	c.775T>C	c.(775-777)Ttt>Ctt	p.F259L	SCAF8_ENST00000367186.4_Missense_Mutation_p.F325L|SCAF8_ENST00000417268.1_Missense_Mutation_p.F259L	NM_014892.3	NP_055707.3	Q9UPN6	SCAF8_HUMAN	SR-related CTD-associated factor 8	259	Gln-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase core enzyme binding (GO:0043175)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(15)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	46						GGGAGTCTCCTTTAACAAGGT	0.343																																					p.F259L		Atlas-SNP	.											.	SCAF8	122	.	0			c.T775C						PASS	.						48	45	46					6																	155123273		2203	4300	6503	SO:0001583	missense	22828	exon7			GTCTCCTTTAACA	AB029039	CCDS5247.1, CCDS69226.1, CCDS75541.1	6q25.1-q25.3	2013-02-12	2011-01-10	2011-01-10	ENSG00000213079	ENSG00000213079		"RNA binding motif (RRM) containing"	20959	protein-coding gene	gene with protein product			"RNA binding motif protein 16"	RBM16		10470851	Standard	NM_001286189		Approved	KIAA1116	uc003qpz.3	Q9UPN6	OTTHUMG00000015877	ENST00000367178.3:c.775T>C	6.37:g.155123273T>C	ENSP00000356146:p.Phe259Leu	67	0	0		85	4	0.0470588	NM_014892	B7Z888|Q5TBU6|Q6NSK3|Q9BQN8|Q9BX43	Missense_Mutation	SNP	ENST00000367178.3	37	CCDS5247.1	.	.	.	.	.	.	.	.	.	.	T	17.60	3.430469	0.62844	.	.	ENSG00000213079	ENST00000367178;ENST00000417268;ENST00000367186	T;T;T	0.54675	0.6;0.6;0.56	5.75	5.75	0.90469	.	0.205984	0.41938	U	0.000799	T	0.23289	0.0563	L	0.27053	0.805	0.52501	D	0.999959	B;B;B;B	0.18610	0.029;0.029;0.006;0.015	B;B;B;B	0.17433	0.018;0.018;0.007;0.01	T	0.11131	-1.0600	10	0.35671	T	0.21	.	10.3929	0.44184	0.0:0.073:0.0:0.927	.	304;325;337;259	B7Z876;B7Z888;B7Z3A4;Q9UPN6	.;.;.;SCAF8_HUMAN	L	259;259;325	ENSP00000356146:F259L;ENSP00000413098:F259L;ENSP00000356154:F325L	ENSP00000356146:F259L	F	+	1	0	SCAF8	155164965	1.000000	0.71417	0.995000	0.50966	0.984000	0.73092	5.971000	0.70440	2.188000	0.69820	0.528000	0.53228	TTT	.	.	none		0.343	SCAF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042798.1	NM_014892		C	155123273	T	C	155123273	3	2	28	1	0	0	0	0	1	0	0	0	13133	1609	56	3	801	3	RBM16	6	155123273	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	2400905	155123273	15991794	278	11781											
MAP3K4	4216	hgsc.bcm.edu	37	chr6	161507618	161507618	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ttgtaactgtgatcctaggaCctggaaatagcagcagaatt	13	11	10	7	0	0	2	0	1	0	1	1	4	1	4	2	2	3	3	2	2	5	5	rs145569434	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:161507618C>T	ENST00000392142.4	+	9	2623	c.2475C>T	c.(2473-2475)gaC>gaT	p.D825D	MAP3K4_ENST00000348824.7_Silent_p.D825D|MAP3K4_ENST00000366920.2_Silent_p.D825D|MAP3K4_ENST00000366919.2_Silent_p.D825D	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	825					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)		GATCCTAGGACCTGGAAATAG	0.353													C|||	32	0.00638978	0.0008	0.0346	5008	,	,		19983	0.0		0.006	False		,,,				2504	0.001				p.D825D		Atlas-SNP	.											.	MAP3K4	364	.	0			c.C2475T						PASS	.	C	,	15,4391	22.3+/-47.3	0,15,2188	71	69	70		2475,2475	4.4	1	6	dbSNP_134	70	65,8535	38.8+/-94.9	0,65,4235	no	coding-synonymous,coding-synonymous	MAP3K4	NM_005922.2,NM_006724.2	,	0,80,6423	TT,TC,CC		0.7558,0.3404,0.6151	,	825/1609,825/1559	161507618	80,12926	2203	4300	6503	SO:0001819	synonymous_variant	4216	exon9			CTAGGACCTGGAA	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.2475C>T	6.37:g.161507618C>T		78	0	0		91	45	0.494505	NM_006724	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Silent	SNP	ENST00000392142.4	37	CCDS34565.1																																																																																			C|0.994;T|0.006	0.006	strong		0.353	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			T	161507618	C	T	161507618	2	4	28	1	0	0	0	0	0	0	0	1	9261	506	18	2		2	MAP3K4	6	161507618	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	6384345	161507618	9607449	279	11782											
GPER	2852	hgsc.bcm.edu	37	chr7	1132384	1132384	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aagctgaggctgtacattgaGcagaaaacaaatttgccggc	14	8	11	8	1	0	3	0	2	0	1	0	3	0	3	1	2	5	4	1	2	5	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:1132384G>A	ENST00000297469.3	+	2	1711	c.1020G>A	c.(1018-1020)gaG>gaA	p.E340E	GPER1_ENST00000401670.1_Silent_p.E340E|GPER1_ENST00000397088.3_Silent_p.E340E|C7orf50_ENST00000357429.6_Intron|C7orf50_ENST00000397098.3_Intron|C7orf50_ENST00000488073.1_Intron|C7orf50_ENST00000397100.2_Intron|GPER1_ENST00000397092.1_Silent_p.E340E	NM_001505.2	NP_001496.1	Q99527	GPER1_HUMAN	G protein-coupled estrogen receptor 1	340					apoptotic chromosome condensation (GO:0030263)|cell cycle (GO:0007049)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucose stimulus (GO:0071333)|cellular response to mineralocorticoid stimulus (GO:0071389)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytosolic calcium ion homeostasis (GO:0051480)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA metabolic process (GO:0051053)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte activation (GO:0002695)|negative regulation of lipid biosynthetic process (GO:0051055)|neuronal action potential (GO:0019228)|nuclear fragmentation involved in apoptotic nuclear change (GO:0030264)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of gene expression (GO:0010628)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of insulin secretion (GO:0032024)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vasodilation (GO:0045909)|steroid hormone mediated signaling pathway (GO:0043401)	axon (GO:0030424)|axon terminus (GO:0043679)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|dendritic spine head (GO:0044327)|dendritic spine membrane (GO:0032591)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|keratin filament (GO:0045095)|mitochondrial membrane (GO:0031966)|neuronal postsynaptic density (GO:0097481)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	chromatin binding (GO:0003682)|estrogen receptor activity (GO:0030284)|G-protein coupled receptor activity (GO:0004930)|mineralocorticoid receptor activity (GO:0017082)|steroid binding (GO:0005496)										TGTACATTGAGCAGAAAACAA	0.557																																					p.E340E		Atlas-SNP	.											.	GPER	25	.	0			c.G1020A						PASS	.						93	76	82					7																	1132384		2203	4300	6503	SO:0001819	synonymous_variant	2852	exon2			CATTGAGCAGAAA	U63917	CCDS5322.1	7p22	2013-08-14	2007-07-03	2013-08-14	ENSG00000164850	ENSG00000164850			4485	protein-coding gene	gene with protein product		601805	"G protein-coupled receptor 30"	CMKRL2, GPR30, GPER		9479505, 17655271	Standard	NM_001098201		Approved	FEG-1, GPCR-Br, LERGU, LERGU2, DRY12, LyGPR, CEPR	uc003skb.2	Q99527	OTTHUMG00000023680	ENST00000297469.3:c.1020G>A	7.37:g.1132384G>A		121	0	0		174	64	0.367816	NM_001505	A8K6C5|B5BUJ1|O00143|O43494|Q13631|Q6FHL1|Q96F42|Q99981	Silent	SNP	ENST00000297469.3	37	CCDS5322.1																																																																																			.	.	none		0.557	GPER1-030	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060001.1	NM_001039966		A	1132384	G	A	1132384	2	1	28	1	0	0	0	0	0	0	0	1	6615	962	34	2		2	GPER	7	1132384	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10		1132384	158006279	280	11783											
CARD11	84433	hgsc.bcm.edu	37	chr7	2983886	2983886	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcctcatgaccgccatgttcTtctcctcactgagctgtgcg	5	13	8	15	2	4	2	2	2	2	0	6	2	5	2	4	0	2	2	4	0	0	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:2983886T>G	ENST00000396946.4	-	5	1047	c.644A>C	c.(643-645)aAg>aCg	p.K215T	AC004906.3_ENST00000423194.1_RNA	NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	215					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)		CGCCATGTTCTTCTCCTCACT	0.572			Mis		DLBCL																																p.K215T		Atlas-SNP	.		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	CARD11,colon,carcinoma,-1,6	CARD11	339	6	0			c.A644C						PASS	.						187	114	139					7																	2983886		2203	4300	6503	SO:0001583	missense	84433	exon5			ATGTTCTTCTCCT	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.644A>C	7.37:g.2983886T>G	ENSP00000380150:p.Lys215Thr	178	0	0		251	36	0.143426	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	T	18.82	3.705011	0.68615	.	.	ENSG00000198286	ENST00000396946	T	0.37915	1.17	4.16	4.16	0.48862	.	0.000000	0.85682	D	0.000000	T	0.55016	0.1894	L	0.57536	1.79	0.58432	D	0.999995	D	0.89917	1.0	D	0.83275	0.996	T	0.58836	-0.7566	10	0.66056	D	0.02	-28.1579	13.4982	0.61438	0.0:0.0:0.0:1.0	.	215	Q9BXL7	CAR11_HUMAN	T	215	ENSP00000380150:K215T	ENSP00000380150:K215T	K	-	2	0	CARD11	2950412	1.000000	0.71417	0.991000	0.47740	0.982000	0.71751	5.720000	0.68470	1.650000	0.50662	0.459000	0.35465	AAG	.	.	none		0.572	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		G	2983886	T	G	2983886	3	3	28	1	0	0	0	0	1	0	0	0	2647	1609	56	5	2904	5	CARD11	7	2983886	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	1851502	2983886	156154777	281	11784											
TNRC18	84629	hgsc.bcm.edu	37	chr7	5396866	5396866	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgtcgagcttgcttgccaaCtgctcctggtcgctggccat	4	13	11	13	2	0	0	0	0	0	0	3	1	1	0	3	2	5	4	3	2	1	3	rs200950320		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:5396866C>G	ENST00000430969.1	-	16	5223	c.4875G>C	c.(4873-4875)caG>caC	p.Q1625H	TNRC18_ENST00000399537.4_Missense_Mutation_p.Q1625H	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1625							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)		TGCTTGCCAACTGCTCCTGGT	0.498																																					p.Q1625H		Atlas-SNP	.											.	TNRC18	311	.	0			c.G4875C						PASS	.	C	HIS/GLN	0,4034		0,0,2017	48	48	48		4875	3.4	0.9	7		48	1,8387		0,1,4193	yes	missense	TNRC18	NM_001080495.2	24	0,1,6210	GG,GC,CC		0.0119,0.0,0.0081	probably-damaging	1625/2969	5396866	1,12421	2017	4194	6211	SO:0001583	missense	84629	exon16			TGCCAACTGCTCC	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.4875G>C	7.37:g.5396866C>G	ENSP00000395538:p.Gln1625His	65	0	0		124	47	0.379032	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	37	CCDS47534.1	.	.	.	.	.	.	.	.	.	.	c	11.99	1.803262	0.31869	0.0	1.19E-4	ENSG00000182095	ENST00000399537;ENST00000430969;ENST00000399544;ENST00000440081	T;T;T	0.55052	2.34;2.4;0.54	5.25	3.37	0.38596	.	0.000000	0.37483	N	0.002071	T	0.61123	0.2322	L	0.47016	1.485	0.39858	D	0.973332	D;D	0.71674	0.997;0.998	D;D	0.79784	0.993;0.956	T	0.61441	-0.7062	10	0.66056	D	0.02	.	7.4435	0.27198	0.0:0.7123:0.0:0.2877	.	680;1625	A8MSW5;O15417	.;TNC18_HUMAN	H	1625;1625;680;115	ENSP00000382452:Q1625H;ENSP00000395538:Q1625H;ENSP00000395990:Q115H	ENSP00000382452:Q1625H	Q	-	3	2	TNRC18	5363392	0.999000	0.42202	0.878000	0.34440	0.983000	0.72400	1.017000	0.29989	0.550000	0.28991	0.561000	0.74099	CAG	.	.	weak		0.498	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				G	5396866	C	G	5396866	3	3	28	1	0	0	0	0	1	0	0	0	16354	564	20	4	4091	4	TNRC18	7	5396866	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2412980	5396866	153741797	282	11785											
SP8	221833	hgsc.bcm.edu	37	chr7	20824953	20824953	+	Silent	SNP	G	G	C																															gcggaggagccgccgccgccGcccccgccgccgccgccgct																										TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:20824953G>C	ENST00000361443.4	-	3	666	c.429C>G	c.(427-429)ggC>ggG	p.G143G	SP8_ENST00000418710.2_Silent_p.G161G	NM_198956.2	NP_945194.1	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor	143					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						cgccgccgccgcccccgccgc	0.736																																					p.G161G		Atlas-SNP	.											.	SP8	43	.	0			c.C483G						PASS	.						2	2	2					7																	20824953		584	1454	2038	SO:0001819	synonymous_variant	221833	exon2			GCCGCCGCCCCCG		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.429C>G	7.37:g.20824953G>C		2	0	0		9	9	1	NM_182700	Q7Z615|Q7Z616|Q96MJ1	Silent	SNP	ENST00000361443.4	37	CCDS5372.1																																																																																			.	.	none		0.736	SP8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326904.2			C	20824953	G	C	20824953	2	2	28	1	0	0	0	0	0	0	0	1	14985	1074	38	4		4	SP8	7	20824953	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	15428087	20824953	138313710	283	11786	147	2									
SP8	221833	hgsc.bcm.edu	37	chr7	20824956	20824956	+	Silent	SNP	C	C	G																															gaggagccgccgccgccgccCccgccgccgccgccgctgcc																								rs201180283		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						PASS	.						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	7.37:g.20824956C>G		2	0	0		7	7	1	NM_182700	Q7Z615|Q7Z616|Q96MJ1	Silent	SNP	ENST00000361443.4	37	CCDS5372.1																																																																																			.	.	weak		0.741	SP8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326904.2			G	20824956	C	G	20824956	2	3	28	1	0	0	0	0	0	0	0	1	14985	610	22	4		4	SP8	7	20824956	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	3	20824956	138313707	284	11787	147	2									
FAM126A	84668	hgsc.bcm.edu	37	chr7	23030692	23030692	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatattaccttaaactctgaCaaccattcctccacaacccc	14	10	1	16	0	1	1	0	1	1	0	3	1	3	1	6	0	4	0	6	0	7	4			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:23030692C>T	ENST00000432176.2	-	2	271	c.39G>A	c.(37-39)ttG>ttA	p.L13L	FAM126A_ENST00000409923.1_Silent_p.L13L|FAM126A_ENST00000409763.1_Silent_p.L13L	NM_032581.3	NP_115970.2	Q9BYI3	HYCCI_HUMAN	family with sequence similarity 126, member A	13					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						TAAACTCTGACAACCATTCCT	0.308																																					p.L13L		Atlas-SNP	.											.	FAM126A	53	.	0			c.G39A						PASS	.						107	108	108					7																	23030692		2203	4294	6497	SO:0001819	synonymous_variant	84668	exon2			CTCTGACAACCAT	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.39G>A	7.37:g.23030692C>T		71	0	0		139	106	0.76259	NM_032581	A4D145|Q6N010|Q75MR4|Q7LDZ4|Q96MX1|Q96NQ6	Silent	SNP	ENST00000432176.2	37	CCDS5377.1																																																																																			.	.	none		0.308	FAM126A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250230.1	NM_032581		T	23030692	C	T	23030692	2	4	28	1	0	0	0	0	0	0	0	1	5434	477	17	2		2	FAM126A	7	23030692	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2205736	23030692	136107971	285	11788											
OSBPL3	26031	hgsc.bcm.edu	37	chr7	24905795	24905795	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatggcaatttcattctgaCgatacattctgtggtggcga	10	13	10	8	2	3	1	1	1	2	0	3	3	3	1	0	3	1	1	0	3	2	4	rs201132926	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:24905795C>T	ENST00000313367.2	-	6	894	c.443G>A	c.(442-444)cGt>cAt	p.R148H	OSBPL3_ENST00000396429.1_Missense_Mutation_p.R148H|OSBPL3_ENST00000409069.1_Missense_Mutation_p.R148H|OSBPL3_ENST00000353930.1_Missense_Mutation_p.R148H|OSBPL3_ENST00000352860.1_Missense_Mutation_p.R148H|OSBPL3_ENST00000431825.2_Missense_Mutation_p.R148H|OSBPL3_ENST00000396431.1_Missense_Mutation_p.R148H	NM_015550.2	NP_056365.1	Q9H4L5	OSBL3_HUMAN	oxysterol binding protein-like 3	148					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						TTCATTCTGACGATACATTCT	0.398													C|||	2	0.000399361	0.0008	0.0	5008	,	,		20987	0.0		0.0	False		,,,				2504	0.001				p.R148H		Atlas-SNP	.											.	OSBPL3	100	.	0			c.G443A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	164	135	145		443,443,443,443	5.6	1	7		145	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense	OSBPL3	NM_015550.2,NM_145320.1,NM_145321.1,NM_145322.1	29,29,29,29	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	148/888,148/857,148/852,148/821	24905795	2,13004	2203	4300	6503	SO:0001583	missense	26031	exon6			TTCTGACGATACA	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.443G>A	7.37:g.24905795C>T	ENSP00000315410:p.Arg148His	98	0	0		135	39	0.288889	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	37	CCDS5390.1	.	.	.	.	.	.	.	.	.	.	C	35	5.425170	0.96131	2.27E-4	1.16E-4	ENSG00000070882	ENST00000313367;ENST00000352860;ENST00000353930;ENST00000431825;ENST00000396431;ENST00000396429;ENST00000409069	T;T;T;T;T;T;T	0.55588	1.89;0.51;0.57;1.85;0.51;0.57;1.85	5.63	5.63	0.86233	Pleckstrin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.75012	0.3792	M	0.78637	2.42	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	0.74771	-0.3552	10	0.51188	T	0.08	-2.461	20.0499	0.97621	0.0:1.0:0.0:0.0	.	148;148;148;148	Q9H4L5-4;Q9H4L5-2;Q9H4L5-3;Q9H4L5	.;.;.;OSBL3_HUMAN	H	148	ENSP00000315410:R148H;ENSP00000315331:R148H;ENSP00000315277:R148H;ENSP00000389779:R148H;ENSP00000379708:R148H;ENSP00000379706:R148H;ENSP00000386953:R148H	ENSP00000315410:R148H	R	-	2	0	OSBPL3	24872320	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.752000	0.85141	2.798000	0.96311	0.655000	0.94253	CGT	.	.	weak		0.398	OSBPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214085.2			T	24905795	C	T	24905795	3	4	28	1	0	0	0	0	1	0	0	0	11288	536	19	1	2292	1	OSBPL3	7	24905795	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1875103	24905795	134232868	286	11789											
BMPER	168667	hgsc.bcm.edu	37	chr7	34091570	34091570	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgtacgataactgcacagcTtgtacctgcagggtaaggca	11	9	11	10	1	0	0	0	0	0	0	0	1	0	0	1	2	6	7	1	2	4	5	rs117988035	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:34091570T>G	ENST00000297161.2	+	9	1148	c.774T>G	c.(772-774)gcT>gcG	p.A258A	BMPER_ENST00000426693.1_Silent_p.A258A|BMPER_ENST00000494786.1_3'UTR	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	258	VWFC 4. {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						ACTGCACAGCTTGTACCTGCA	0.478													T|||	36	0.0071885	0.0	0.0173	5008	,	,		22541	0.0		0.0149	False		,,,				2504	0.0092				p.A258A		Atlas-SNP	.											.	BMPER	131	.	0			c.T774G						PASS	.	T		9,4397	15.5+/-35.6	0,9,2194	168	147	154		774	-10.2	0	7	dbSNP_132	154	103,8497	57.2+/-118.5	0,103,4197	no	coding-synonymous	BMPER	NM_133468.3		0,112,6391	GG,GT,TT		1.1977,0.2043,0.8611		258/686	34091570	112,12894	2203	4300	6503	SO:0001819	synonymous_variant	168667	exon9			CACAGCTTGTACC		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.774T>G	7.37:g.34091570T>G		97	0	0		156	43	0.275641	NM_133468	A8K1P8|Q8TF36	Silent	SNP	ENST00000297161.2	37	CCDS5442.1																																																																																			T|0.990;G|0.010	0.010	strong		0.478	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2	NM_133468		G	34091570	T	G	34091570	2	3	28	1	0	0	0	0	0	0	0	1	1468	1596	56	5		5	BMPER	7	34091570	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	9185775	34091570	125047093	287	11790											
SPDYE1	285955	hgsc.bcm.edu	37	chr7	44046900	44046900	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gacatggaggaggacgacgaGgactccaaacaaaacatctt	16	5	11	9	2	1	0	0	0	1	0	2	7	2	4	1	4	2	0	1	4	3	1	rs147853765	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:44046900G>A	ENST00000258704.3	+	5	803	c.666G>A	c.(664-666)gaG>gaA	p.E222E	RP5-1165K10.2_ENST00000454572.1_RNA|AC004951.6_ENST00000447643.1_lincRNA|POLR2J4_ENST00000427076.1_RNA	NM_001099435.2|NM_175064.2	NP_001092905.2|NP_778234.2	Q8NFV5	SPDE1_HUMAN	speedy/RINGO cell cycle regulator family member E1	222										endometrium(1)|kidney(4)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	11						AGGACGACGAGGACTCCAAAC	0.552													g|||	26	0.00519169	0.0	0.0115	5008	,	,		19923	0.0		0.0159	False		,,,				2504	0.002				p.E222E		Atlas-SNP	.											.	SPDYE1	29	.	0			c.G666A						PASS	.	G		18,4388		0,18,2185	110	109	110		666		0.4	7	dbSNP_134	110	148,8442		1,146,4148	no	coding-synonymous	SPDYE1	NM_175064.2		1,164,6333	AA,AG,GG		1.7229,0.4085,1.2773		222/337	44046900	166,12830	2203	4295	6498	SO:0001819	synonymous_variant	285955	exon5			CGACGAGGACTCC	AF412027	CCDS5475.1	7q11.23	2013-05-08	2013-05-08	2009-02-17	ENSG00000136206	ENSG00000136206		"Speedy homologs"	16408	protein-coding gene	gene with protein product	"Speedy E"		"Williams Beuren syndrome chromosome region 19", "speedy homolog E1 (Xenopus laevis)"	WBSCR19		12073013	Standard	NM_175064		Approved	Ringo1, SPDYE	uc003tjf.3	Q8NFV5	OTTHUMG00000128985	ENST00000258704.3:c.666G>A	7.37:g.44046900G>A		144	0	0		235	55	0.234043	NM_175064	Q9NTH5	Silent	SNP	ENST00000258704.3	37	CCDS5475.1																																																																																			G|0.984;A|0.016	0.016	strong		0.552	SPDYE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250974.1	NM_175064		A	44046900	G	A	44046900	2	1	28	1	0	0	0	0	0	0	0	1	15044	991	35	2		2	SPDYE1	7	44046900	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	9955330	44046900	115091763	288	11791											
OGDH	4967	hgsc.bcm.edu	37	chr7	44715599	44715599	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtgaagtaccacctgggcAtgtatcaccgcaggatcaat	12	9	10	10	1	2	1	2	1	0	0	2	2	2	2	3	2	1	4	3	2	4	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:44715599A>T	ENST00000222673.5	+	9	1099	c.1057A>T	c.(1057-1059)Atg>Ttg	p.M353L	OGDH_ENST00000439616.2_Missense_Mutation_p.M203L|OGDH_ENST00000444676.1_Missense_Mutation_p.M368L|OGDH_ENST00000447398.1_Missense_Mutation_p.M364L|OGDH_ENST00000543843.1_Missense_Mutation_p.M304L|OGDH_ENST00000443864.2_Missense_Mutation_p.M353L|OGDH_ENST00000449767.1_Missense_Mutation_p.M349L	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	353					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)	CCACCTGGGCATGTATCACCG	0.547																																					p.M353L		Atlas-SNP	.											.	OGDH	145	.	0			c.A1057T						PASS	.						111	98	102					7																	44715599		2203	4300	6503	SO:0001583	missense	4967	exon9			CTGGGCATGTATC	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.1057A>T	7.37:g.44715599A>T	ENSP00000222673:p.Met353Leu	78	0	0		130	85	0.653846	NM_002541	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Missense_Mutation	SNP	ENST00000222673.5	37	CCDS34627.1	.	.	.	.	.	.	.	.	.	.	A	17.45	3.392130	0.62066	.	.	ENSG00000105953	ENST00000439616;ENST00000443864;ENST00000449767;ENST00000447398;ENST00000444676;ENST00000222673;ENST00000543843	D;T;D;D;D;D;D	0.95724	-3.79;2.71;-3.79;-3.79;-3.79;-3.79;-3.79	5.14	5.14	0.70334	Dehydrogenase, E1 component (1);	0.000000	0.85682	D	0.000000	D	0.93582	0.7951	L	0.52905	1.665	0.58432	D	0.99999	B;B;B;B;B;B;B	0.18310	0.004;0.004;0.002;0.002;0.002;0.002;0.027	B;B;B;B;B;B;B	0.24006	0.029;0.02;0.029;0.029;0.02;0.029;0.05	D	0.91106	0.4918	10	0.37606	T	0.19	-47.9559	14.9242	0.70862	1.0:0.0:0.0:0.0	.	148;203;349;364;255;353;353	B4E3E9;E9PFG7;E9PBM1;E9PDF2;A2VCT2;Q02218;Q96DD3	.;.;.;.;.;ODO1_HUMAN;.	L	203;353;349;364;368;353;304	ENSP00000398576:M203L;ENSP00000388084:M353L;ENSP00000392878:M349L;ENSP00000388183:M364L;ENSP00000414662:M368L;ENSP00000222673:M353L;ENSP00000443821:M304L	ENSP00000222673:M353L	M	+	1	0	OGDH	44682124	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	9.043000	0.93799	2.063000	0.61619	0.379000	0.24179	ATG	.	.	none		0.547	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1			T	44715599	A	T	44715599	3	4	28	1	0	0	0	0	1	0	0	0	10848	217	8	5	1182	5	OGDH	7	44715599	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	668699	44715599	114423064	289	11792											
COBL	23242	hgsc.bcm.edu	37	chr7	51093049	51093049	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcggaagctctggagctcCtcagaagcagaggatgccac	10	7	12	12	1	3	2	1	0	2	2	5	5	4	5	2	3	4	3	2	3	2	0	rs1129262	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:51093049C>T	ENST00000265136.7	-	12	3690	c.3525G>A	c.(3523-3525)gaG>gaA	p.E1175E	RP4-724E13.2_ENST00000582616.1_RNA|COBL_ENST00000395542.2_Silent_p.E1257E	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	1175					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)					TCTGGAGCTCCTCAGAAGCAG	0.527													C|||	15	0.00299521	0.0045	0.0043	5008	,	,		12853	0.0		0.005	False		,,,				2504	0.001				p.E1175E	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											COBL,NS,haematopoietic_neoplasm,0,1	COBL	167	1	0			c.G3525A						PASS	.	C		14,4390		0,14,2188	35	37	36		3525	1.3	1	7	dbSNP_86	36	88,8508		0,88,4210	no	coding-synonymous	COBL	NM_015198.3		0,102,6398	TT,TC,CC		1.0237,0.3179,0.7846		1175/1262	51093049	102,12898	2202	4298	6500	SO:0001819	synonymous_variant	23242	exon12			GAGCTCCTCAGAA	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.3525G>A	7.37:g.51093049C>T		87	0	0		138	31	0.224638	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Silent	SNP	ENST00000265136.7	37	CCDS34637.1																																																																																			C|0.993;T|0.007	0.007	strong		0.527	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198		T	51093049	C	T	51093049	2	4	28	1	0	0	0	0	0	0	0	1	3655	680	24	2		2	COBL	7	51093049	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	6377450	51093049	108045614	290	11793											
POM121L12	285877	hgsc.bcm.edu	37	chr7	53103370	53103370	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacggtcccccagccatgggCgctgcagctccggccgagtc	6	5	13	17	4	0	0	0	0	0	0	3	1	2	0	5	3	4	3	5	3	1	0			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:53103370C>T	ENST00000408890.4	+	1	22	c.6C>T	c.(4-6)ggC>ggT	p.G2G		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	2										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						CAGCCATGGGCGCTGCAGCTC	0.701																																					p.G2G		Atlas-SNP	.											.	POM121L12	146	.	0			c.C6T						PASS	.																																			SO:0001819	synonymous_variant	285877	exon1			CATGGGCGCTGCA		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.6C>T	7.37:g.53103370C>T		59	0	0		72	53	0.736111	NM_182595	Q8NDI9	Silent	SNP	ENST00000408890.4	37	CCDS43584.1																																																																																			.	.	none		0.701	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595		T	53103370	C	T	53103370	2	4	28	1	0	0	0	0	0	0	0	1	12250	755	27	1		1	POM121L12	7	53103370	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2010321	53103370	106035293	291	11794											
WBSCR17	64409	hgsc.bcm.edu	37	chr7	70800578	70800578	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cattgaaggttatggtgggcGgggtaaagggggccttccgg	7	9	19	6	2	0	1	0	1	0	0	1	1	1	1	2	8	0	2	2	8	4	4	rs145721199	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:70800578G>T	ENST00000333538.5	+	2	915	c.281G>T	c.(280-282)cGg>cTg	p.R94L	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	94					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)				TATGGTGGGCGGGGTAAAGGG	0.453																																					p.R94L		Atlas-SNP	.											WBSCR17,mouth,carcinoma,+1,1	WBSCR17	208	1	0			c.G281T						scavenged	.						32	38	36					7																	70800578		2203	4300	6503	SO:0001583	missense	64409	exon2			GTGGGCGGGGTAA	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.281G>T	7.37:g.70800578G>T	ENSP00000329654:p.Arg94Leu	29	0	0		37	2	0.0540541	NM_022479	Q8NFV9|Q9NTA8	Missense_Mutation	SNP	ENST00000333538.5	37	CCDS5540.1	.	.	.	.	.	.	.	.	.	.	G	9.064	0.995119	0.19043	.	.	ENSG00000185274	ENST00000333538;ENST00000447516	T;T	0.52983	0.64;1.93	4.89	4.89	0.63831	.	0.000000	0.85682	D	0.000000	T	0.23572	0.0570	N	0.02539	-0.55	0.80722	D	1	B	0.13145	0.007	B	0.12837	0.008	T	0.13150	-1.0520	10	0.10902	T	0.67	.	17.1948	0.86890	0.0:0.0:1.0:0.0	.	94	Q6IS24	GLTL3_HUMAN	L	94;72	ENSP00000329654:R94L;ENSP00000392019:R72L	ENSP00000329654:R94L	R	+	2	0	WBSCR17	70438514	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.307000	0.78920	2.530000	0.85305	0.491000	0.48974	CGG	G|0.999;A|0.001	.	alt		0.453	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479		T	70800578	G	T	70800578	3	4	28	1	0	0	0	0	1	0	0	0	17279	1116	39	4	287	4	WBSCR17	7	70800578	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	17697208	70800578	88338085	292	11795											
NSUN5	55695	hgsc.bcm.edu	37	chr7	72721583	72721583	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aactccttccagcttacctgGaccaggcctggatcccactt	8	10	7	16	0	0	0	0	0	0	0	3	2	3	2	6	3	3	1	6	3	2	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:72721583G>T	ENST00000252594.6	-	3	403	c.388C>A	c.(388-390)Cca>Aca	p.P130T	NSUN5_ENST00000428206.1_Missense_Mutation_p.P92T|NSUN5_ENST00000310326.8_Missense_Mutation_p.P130T|NSUN5_ENST00000438747.2_Missense_Mutation_p.P130T			Q96P11	NSUN5_HUMAN	NOP2/Sun domain family, member 5	130					rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	8		Lung NSC(55;0.163)				AGCTTACCTGGACCAGGCCTG	0.627																																					p.P130T		Atlas-SNP	.											.	NSUN5	47	.	0			c.C388A						PASS	.						65	54	58					7																	72721583		2203	4300	6503	SO:0001583	missense	55695	exon3			TACCTGGACCAGG	AF420249	CCDS5546.1, CCDS5547.1, CCDS55118.1, CCDS55119.1	7q11.23	2010-04-08	2009-11-23	2005-01-14	ENSG00000130305	ENSG00000130305		"NOP2/Sun domain containing"	16385	protein-coding gene	gene with protein product	"NOP2/Sun domain family, member 5A"	615732	"Williams Beuren syndrome chromosome region 20A", "NOL1/NOP2/Sun domain family, member 5"	WBSCR20, WBSCR20A		11978965, 12073013	Standard	NM_148956		Approved	NOL1R, p120, (NOL1), FLJ10267, NSUN5A, Ynl022cL	uc011kev.2	Q96P11	OTTHUMG00000129869	ENST00000252594.6:c.388C>A	7.37:g.72721583G>T	ENSP00000252594:p.Pro130Thr	41	0	0		62	4	0.0645161	NM_148956	B3KX04|B4DP79|G3V0G9|Q6ZUI8|Q96HT9|Q9NW70	Missense_Mutation	SNP	ENST00000252594.6	37	CCDS5547.1	.	.	.	.	.	.	.	.	.	.	G	0.150	-1.092733	0.01858	.	.	ENSG00000130305	ENST00000428206;ENST00000252594;ENST00000438747;ENST00000310326	T;T;T;T	0.13901	2.55;2.57;2.78;2.77	4.18	-3.05	0.05396	.	1.150850	0.06151	N	0.674063	T	0.08802	0.0218	L	0.39397	1.21	0.09310	N	1	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.002;0.0;0.002	T	0.40869	-0.9540	10	0.12430	T	0.62	.	3.4709	0.07567	0.2185:0.4119:0.2641:0.1055	.	130;92;130;130	B4DP79;G3V0G9;Q96P11;Q96P11-2	.;.;NSUN5_HUMAN;.	T	92;130;130;130	ENSP00000393081:P92T;ENSP00000252594:P130T;ENSP00000388464:P130T;ENSP00000309126:P130T	ENSP00000252594:P130T	P	-	1	0	NSUN5	72359519	0.000000	0.05858	0.036000	0.18154	0.102000	0.19082	-0.935000	0.03950	-0.472000	0.06881	-0.350000	0.07774	CCA	.	.	none		0.627	NSUN5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252113.1	NM_148956		T	72721583	G	T	72721583	3	4	28	1	0	0	0	0	1	0	0	0	10690	1174	41	4	1065	4	NSUN5	7	72721583	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1921005	72721583	86417080	293	11796											
TRIM50	135892	hgsc.bcm.edu	37	chr7	72738638	72738638	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcacacggggcagcgcagctCggcatccaggtggcaggaca	9	3	16	13	3	0	0	0	0	0	0	2	1	1	1	1	6	2	6	1	6	0	0	rs138877207	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:72738638C>T	ENST00000333149.2	-	2	348	c.148G>A	c.(148-150)Gag>Aag	p.E50K	TRIM50_ENST00000453152.1_Missense_Mutation_p.E50K|TRIM50_ENST00000493498.1_5'UTR	NM_178125.2	NP_835226.2	Q86XT4	TRI50_HUMAN	tripartite motif containing 50	50						cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)|skin(2)	20						CAGCGCAGCTCGGCATCCAGG	0.667											OREG0018105	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2	0.000399361	0.0015	0.0	5008	,	,		15859	0.0		0.0	False		,,,				2504	0.0				p.E50K		Atlas-SNP	.											.	TRIM50	78	.	0			c.G148A						PASS	.						52	52	52					7																	72738638		2203	4300	6503	SO:0001583	missense	135892	exon2			GCAGCTCGGCATC	AY081948	CCDS34654.1	7q11.23	2013-01-09	2011-01-25	2006-03-31	ENSG00000146755	ENSG00000146755		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19017	protein-coding gene	gene with protein product		612548	"tripartite motif-containing 50A", "tripartite motif-containing 50"	TRIM50A			Standard	NM_001281450		Approved	FLJ32804	uc003txy.1	Q86XT4	OTTHUMG00000156805	ENST00000333149.2:c.148G>A	7.37:g.72738638C>T	ENSP00000327994:p.Glu50Lys	156	0	0	1139	150	82	0.546667	NM_178125	Q86XT3	Missense_Mutation	SNP	ENST00000333149.2	37	CCDS34654.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	0.430	-0.903959	0.02453	.	.	ENSG00000146755	ENST00000333149;ENST00000453152	T;T	0.08546	3.08;3.08	3.94	-0.221	0.13126	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.408805	0.22937	N	0.053826	T	0.04003	0.0112	N	0.19112	0.55	0.18873	N	0.999982	B;B	0.20780	0.038;0.048	B;B	0.16289	0.009;0.015	T	0.39375	-0.9617	10	0.25106	T	0.35	.	4.0294	0.09701	0.0:0.4312:0.2394:0.3294	.	50;50	Q86XT4-2;Q86XT4	.;TRI50_HUMAN	K	50	ENSP00000327994:E50K;ENSP00000413875:E50K	ENSP00000327994:E50K	E	-	1	0	TRIM50	72376574	0.702000	0.27816	0.244000	0.24202	0.021000	0.10359	1.858000	0.39408	0.127000	0.18452	-1.166000	0.01754	GAG	A|0.000;C|1.000;T|0.000	0.000	strong		0.667	TRIM50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345925.1	NM_178125		T	72738638	C	T	72738638	3	4	28	1	0	0	0	0	1	0	0	0	16541	893	31	1	1339	1	TRIM50	7	72738638	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	17055	72738638	86400025	294	11797											
MDH2	4191	hgsc.bcm.edu	37	chr7	75687382	75687382	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccggaagccatgatctgcGtcattgccaatccggtgagt	8	9	12	12	3	2	2	1	2	1	0	3	3	3	3	4	2	3	0	4	2	2	1	rs111879470	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:75687382G>A	ENST00000315758.5	+	4	509	c.415G>A	c.(415-417)Gtc>Atc	p.V139I	MDH2_ENST00000432020.2_Missense_Mutation_p.V139I|MDH2_ENST00000443006.1_Missense_Mutation_p.V32I	NM_005918.2	NP_005909.2	P40926	MDHM_HUMAN	malate dehydrogenase 2, NAD (mitochondrial)	139					carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|internal protein amino acid acetylation (GO:0006475)|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)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	L-malate dehydrogenase activity (GO:0030060)|malate dehydrogenase (NADP+) activity (GO:0046554)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(2)	14						CATGATCTGCGTCATTGCCAA	0.592													a|||	4	0.000798722	0.0	0.0	5008	,	,		19731	0.0		0.004	False		,,,				2504	0.0				p.V139I		Atlas-SNP	.											.	MDH2	35	.	0			c.G415A						PASS	.	A	ILE/VAL	3,4403	6.2+/-15.9	0,3,2200	57	47	51		415	-4.4	0.9	7	dbSNP_132	51	31,8569	21.0+/-64.5	0,31,4269	yes	missense	MDH2	NM_005918.2	29	0,34,6469	AA,AG,GG		0.3605,0.0681,0.2614	benign	139/339	75687382	34,12972	2203	4300	6503	SO:0001583	missense	4191	exon4			ATCTGCGTCATTG		CCDS5581.1, CCDS64691.1, CCDS75622.1	7q11.23	2013-09-20			ENSG00000146701	ENSG00000146701	1.1.1.37		6971	protein-coding gene	gene with protein product		154100					Standard	NM_005918		Approved		uc003ueo.3	P40926	OTTHUMG00000023827	ENST00000315758.5:c.415G>A	7.37:g.75687382G>A	ENSP00000327070:p.Val139Ile	31	0	0		53	20	0.377358	NM_005918	A8K414|B2RE78|B4DE44|E9PDB2|O43682	Missense_Mutation	SNP	ENST00000315758.5	37	CCDS5581.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	g	1.743	-0.491096	0.04322	6.81E-4	0.003605	ENSG00000146701	ENST00000315758;ENST00000443006;ENST00000432020	D;D;D	0.90676	-2.71;-2.71;-2.71	5.56	-4.41	0.03590	Lactate/malate dehydrogenase, N-terminal (1);NAD(P)-binding domain (1);	0.347793	0.35903	N	0.002909	T	0.63058	0.2479	N	0.02876	-0.465	0.09310	N	0.999998	B;B	0.09022	0.002;0.0	B;B	0.11329	0.006;0.002	T	0.61456	-0.7059	10	0.02654	T	1	-12.2486	12.6346	0.56677	0.6019:0.0:0.3981:0.0	.	139;139	E9PDB2;P40926	.;MDHM_HUMAN	I	139;32;139	ENSP00000327070:V139I;ENSP00000416929:V32I;ENSP00000408649:V139I	ENSP00000327070:V139I	V	+	1	0	MDH2	75525318	0.934000	0.31675	0.889000	0.34880	0.512000	0.34134	0.266000	0.18534	-0.966000	0.03587	-2.037000	0.00419	GTC	G|0.998;A|0.002	0.002	strong		0.592	MDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252851.1			A	75687382	G	A	75687382	3	1	28	1	0	0	0	0	1	0	0	0	9419	1145	40	1	429	1	MDH2	7	75687382	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2948744	75687382	83451281	295	11798											
DLX5	1749	hgsc.bcm.edu	37	chr7	96653684	96653684	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctttggctgggtagctcccGgcggagccgttcacgccgtg	3	9	16	13	5	1	0	1	0	0	0	2	1	2	1	3	4	2	5	3	4	1	3	rs61753628	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:96653684G>C	ENST00000222598.4	-	1	725	c.252C>G	c.(250-252)gcC>gcG	p.A84A	DLX5_ENST00000493764.1_5'UTR|DLX5_ENST00000486603.2_Silent_p.A84A	NM_005221.5	NP_005212.1	P56178	DLX5_HUMAN	distal-less homeobox 5	84					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)					GGTAGCTCCCGGCGGAGCCGT	0.627													G|||	4	0.000798722	0.0	0.0014	5008	,	,		14915	0.0		0.002	False		,,,				2504	0.001				p.A84A		Atlas-SNP	.											DLX5,caecum,carcinoma,0,1	DLX5	52	1	0			c.C252G						scavenged	.	G		1,4405	2.1+/-5.4	0,1,2202	51	52	52		252	3.1	1	7	dbSNP_129	52	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	DLX5	NM_005221.5		0,8,6495	CC,CG,GG		0.0814,0.0227,0.0615		84/290	96653684	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	1749	exon1			GCTCCCGGCGGAG		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.252C>G	7.37:g.96653684G>C		120	1	0.00833333		119	61	0.512605	NM_005221	B7Z4P3|Q9UPL1	Silent	SNP	ENST00000222598.4	37	CCDS5647.1																																																																																			G|0.994;C|0.006	0.006	strong		0.627	DLX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334371.2			C	96653684	G	C	96653684	2	2	28	1	0	0	0	0	0	0	0	1	4576	1103	39	4		4	DLX5	7	96653684	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	20966302	96653684	62484979	296	11799											
ZKSCAN5	23660	hgsc.bcm.edu	37	chr7	99129744	99129744	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atcagagaatccatactggtGagaaaccttttcaatgtaaa	16	11	7	7	0	2	2	2	1	0	2	3	4	3	2	2	1	2	1	2	1	6	4	rs150395462	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:99129744G>C	ENST00000394170.2	+	7	2643	c.2392G>C	c.(2392-2394)Gag>Cag	p.E798Q	ZKSCAN5_ENST00000326775.5_Missense_Mutation_p.E798Q|ZKSCAN5_ENST00000451158.1_Missense_Mutation_p.E798Q	NM_014569.3	NP_055384.1	Q9Y2L8	ZKSC5_HUMAN	zinc finger with KRAB and SCAN domains 5	798					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(3)|endometrium(1)|kidney(1)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	21	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)					CCATACTGGTGAGAAACCTTT	0.398													G|||	4	0.000798722	0.0	0.0014	5008	,	,		20675	0.0		0.003	False		,,,				2504	0.0				p.E798Q		Atlas-SNP	.											.	ZKSCAN5	63	.	0			c.G2392C						PASS	.	G	GLN/GLU,GLN/GLU	5,4401	11.4+/-27.6	0,5,2198	85	91	89		2392,2392	5	1	7	dbSNP_134	89	61,8539	38.8+/-94.9	1,59,4240	yes	missense,missense	ZKSCAN5	NM_014569.3,NM_145102.2	29,29	1,64,6438	CC,CG,GG		0.7093,0.1135,0.5075	probably-damaging,probably-damaging	798/840,798/840	99129744	66,12940	2203	4300	6503	SO:0001583	missense	23660	exon7			ACTGGTGAGAAAC	AF170025	CCDS5667.1	7q22	2013-01-09	2007-02-20	2007-02-20	ENSG00000196652	ENSG00000196652		"Zinc fingers, C2H2-type", "-", "-", "-"	12867	protein-coding gene	gene with protein product		611272	"zinc finger protein homologous to Zfp95 in mouse", "zinc finger protein 95 homolog (mouse)"	ZFP95		10585779	Standard	NM_014569		Approved	ZNF914, ZSCAN37	uc003uqv.3	Q9Y2L8	OTTHUMG00000156749	ENST00000394170.2:c.2392G>C	7.37:g.99129744G>C	ENSP00000377725:p.Glu798Gln	54	0	0		45	21	0.466667	NM_145102	A4D280|D6W5S9	Missense_Mutation	SNP	ENST00000394170.2	37	CCDS5667.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	23.4	4.411517	0.83340	0.001135	0.007093	ENSG00000196652	ENST00000326775;ENST00000451158;ENST00000394170	T;T;T	0.25912	1.77;1.77;1.77	5.03	5.03	0.67393	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.116325	0.38720	N	0.001586	T	0.42177	0.1191	M	0.70595	2.14	0.50171	D	0.99985	D;D	0.76494	0.999;0.999	D;D	0.70935	0.971;0.971	T	0.45556	-0.9253	10	0.72032	D	0.01	.	16.2692	0.82607	0.0:0.0:1.0:0.0	.	798;798	Q8N718;Q9Y2L8	.;ZKSC5_HUMAN	Q	798	ENSP00000322872:E798Q;ENSP00000392104:E798Q;ENSP00000377725:E798Q	ENSP00000322872:E798Q	E	+	1	0	ZKSCAN5	98967680	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.485000	0.66850	2.782000	0.95742	0.655000	0.94253	GAG	G|0.996;C|0.004	0.004	strong		0.398	ZKSCAN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345597.1	NM_014569		C	99129744	G	C	99129744	3	2	28	1	0	0	0	0	1	0	0	0	17705	1291	45	4	2414	4	ZKSCAN5	7	99129744	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2476060	99129744	60008919	297	11800											
AP4M1	9179	hgsc.bcm.edu	37	chr7	99704104	99704104	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgctgggacctgcctcgggtGcaaggaggctctcaactctc	6	8	13	14	2	2	0	1	0	2	0	5	2	2	2	2	4	3	3	2	4	2	0			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:99704104G>A	ENST00000359593.4	+	14	1262	c.1104G>A	c.(1102-1104)gtG>gtA	p.V368V	AP4M1_ENST00000421755.1_Silent_p.V368V|AP4M1_ENST00000422582.1_Silent_p.V240V|AP4M1_ENST00000429084.1_Silent_p.V375V	NM_004722.3	NP_004713.2	O00189	AP4M1_HUMAN	adaptor-related protein complex 4, mu 1 subunit	368	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)					TGCCTCGGGTGCAAGGAGGCT	0.632																																					p.V368V	Pancreas(174;1182 2812 29595 49511)	Atlas-SNP	.											.	AP4M1	39	.	0			c.G1104A						PASS	.						42	45	44					7																	99704104		2203	4300	6503	SO:0001819	synonymous_variant	9179	exon14			TCGGGTGCAAGGA	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.1104G>A	7.37:g.99704104G>A		46	0	0		47	22	0.468085	NM_004722	D6W5U1|Q8WV65|Q9UHK9	Silent	SNP	ENST00000359593.4	37	CCDS5685.1	.	.	.	.	.	.	.	.	.	.	G	9.825	1.186877	0.21870	.	.	ENSG00000221838	ENST00000445295	.	.	.	4.81	-3.93	0.04143	.	.	.	.	.	T	0.36248	0.0960	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33343	-0.9872	4	.	.	.	-22.5569	0.9269	0.01327	0.4879:0.1198:0.1523:0.2401	.	.	.	.	Y	94	.	.	C	+	2	0	AP4M1	99542040	0.957000	0.32711	0.976000	0.42696	0.997000	0.91878	0.023000	0.13533	-0.749000	0.04747	0.561000	0.74099	TGC	.	.	none		0.632	AP4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336772.4	NM_004722		A	99704104	G	A	99704104	2	1	28	1	0	0	0	0	0	0	0	1	753	1306	46	2		2	AP4M1	7	99704104	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	574360	99704104	59434559	298	11801											
TAF6	6878	hgsc.bcm.edu	37	chr7	99711386	99711386	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcctgggcgtggaagccatAgagtggctgtggcaggagag	8	7	18	8	1	0	2	0	0	0	2	1	4	1	3	2	5	1	2	2	5	2	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:99711386A>C	ENST00000344095.4	-	4	775	c.250T>G	c.(250-252)Tat>Gat	p.Y84D	TAF6_ENST00000497233.1_5'Flank|TAF6_ENST00000452041.1_Missense_Mutation_p.Y84D|RP11-506M12.1_ENST00000494221.1_RNA|TAF6_ENST00000418432.2_Missense_Mutation_p.Y27D|TAF6_ENST00000437822.2_Missense_Mutation_p.Y121D|TAF6_ENST00000472509.1_Missense_Mutation_p.Y141D|TAF6_ENST00000453269.2_Missense_Mutation_p.Y84D	NM_005641.3	NP_005632.1	P49848	TAF6_HUMAN	TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80kDa	84					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)					TGGAAGCCATAGAGTGGCTGT	0.607																																					p.Y121D		Atlas-SNP	.											.	TAF6	55	.	0			c.T361G						PASS	.						33	35	35					7																	99711386		2203	4300	6503	SO:0001583	missense	6878	exon4			AGCCATAGAGTGG		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.250T>G	7.37:g.99711386A>C	ENSP00000344537:p.Tyr84Asp	52	0	0		52	8	0.153846	NM_001190415	A4D2B2|A4D2B3|B4DT11|D6W5U2|Q6AI29	Missense_Mutation	SNP	ENST00000344095.4	37	CCDS5686.1	.	.	.	.	.	.	.	.	.	.	A	19.08	3.758276	0.69763	.	.	ENSG00000106290	ENST00000453269;ENST00000472509;ENST00000452041;ENST00000344095;ENST00000418432;ENST00000437822;ENST00000493322;ENST00000440225;ENST00000452438;ENST00000523306;ENST00000449571;ENST00000520135;ENST00000451699	T;T;T;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;0.78;0.78;0.78	5.5	4.35	0.52113	Histone-fold (1);	0.057225	0.64402	D	0.000001	T	0.69006	0.3063	M	0.92219	3.285	0.58432	D	0.99999	P;P;P;P;D;P	0.58970	0.865;0.753;0.639;0.491;0.984;0.919	P;P;P;P;P;P	0.58520	0.642;0.71;0.516;0.54;0.84;0.516	T	0.73493	-0.3965	10	0.62326	D	0.03	-2.7986	9.3794	0.38304	0.9156:0.0:0.0844:0.0	.	121;84;74;84;84;27	B4DT11;P49848-2;A4D299;P49848;C9JTY6;B3KUR4	.;.;.;TAF6_HUMAN;.;.	D	84;141;84;84;27;121;84;84;84;74;84;74;84	ENSP00000389575:Y84D;ENSP00000419760:Y141D;ENSP00000416396:Y84D;ENSP00000344537:Y84D;ENSP00000399982:Y121D;ENSP00000419555:Y84D;ENSP00000410012:Y84D;ENSP00000412346:Y84D;ENSP00000428639:Y74D;ENSP00000390073:Y84D;ENSP00000428071:Y74D;ENSP00000406315:Y84D	ENSP00000344537:Y84D	Y	-	1	0	TAF6	99549322	1.000000	0.71417	0.821000	0.32701	0.907000	0.53573	8.627000	0.90974	0.939000	0.37446	0.456000	0.33151	TAT	.	.	none		0.607	TAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337024.2	NM_005641		C	99711386	A	C	99711386	3	2	28	1	0	0	0	0	1	0	0	0	15545	420	15	5	1831	5	TAF6	7	99711386	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	7282	99711386	59427277	299	11802											
FBXO24	26261	hgsc.bcm.edu	37	chr7	100197690	100197690	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcccatcaccctgtggtgcGgcctcaaccactccctggtg	5	8	11	17	1	2	0	2	0	0	0	3	0	3	0	5	4	2	0	5	4	1	0			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:100197690G>A	ENST00000241071.6	+	9	1565	c.1243G>A	c.(1243-1245)Ggc>Agc	p.G415S	PCOLCE_ENST00000223061.5_5'Flank|PCOLCE-AS1_ENST00000446022.1_RNA|FBXO24_ENST00000468962.1_Missense_Mutation_p.G403S|FBXO24_ENST00000427939.2_Missense_Mutation_p.G453S|PCOLCE-AS1_ENST00000544873.1_RNA|FBXO24_ENST00000360609.2_3'UTR|PCOLCE-AS1_ENST00000442166.2_RNA	NM_033506.2	NP_277041.1	O75426	FBX24_HUMAN	F-box protein 24	415					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)					CCTGTGGTGCGGCCTCAACCA	0.692																																					p.G453S		Atlas-SNP	.											.	FBXO24	125	.	0			c.G1357A						PASS	.						27	29	28					7																	100197690		2203	4300	6503	SO:0001583	missense	26261	exon9			TGGTGCGGCCTCA	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.1243G>A	7.37:g.100197690G>A	ENSP00000241071:p.Gly415Ser	225	0	0		185	49	0.264865	NM_012172	A4D2D4|B4DX91|B4DY42|Q9H0G1	Missense_Mutation	SNP	ENST00000241071.6	37	CCDS5698.1	.	.	.	.	.	.	.	.	.	.	G	17.80	3.477965	0.63849	.	.	ENSG00000106336	ENST00000241071;ENST00000468962;ENST00000427939	D;D;D	0.98028	-4.67;-4.67;-4.67	4.76	4.76	0.60689	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.52532	D	0.000065	D	0.98317	0.9442	M	0.71036	2.16	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.76575	0.982;0.988;0.982	D	0.98525	1.0625	10	0.44086	T	0.13	-19.8922	15.2622	0.73634	0.0:0.0:1.0:0.0	.	403;453;415	B4DY42;B4DX91;O75426	.;.;FBX24_HUMAN	S	415;403;453	ENSP00000241071:G415S;ENSP00000420239:G403S;ENSP00000416558:G453S	ENSP00000241071:G415S	G	+	1	0	FBXO24	100035626	1.000000	0.71417	0.988000	0.46212	0.549000	0.35272	5.078000	0.64425	2.199000	0.70637	0.442000	0.29010	GGC	.	.	none		0.692	FBXO24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356104.1			A	100197690	G	A	100197690	3	1	28	1	0	0	0	0	1	0	0	0	5743	1116	39	1	1434	1	FBXO24	7	100197690	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	486304	100197690	58940973	300	11803											
SLC12A9	56996	hgsc.bcm.edu	37	chr7	100454796	100454796	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	taccctgaaggacaacttggGcggtgagctgggtgctgccg	7	8	16	10	2	0	2	0	2	0	0	0	3	0	3	2	4	5	2	2	4	3	2	rs143666254	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:100454796G>A	ENST00000354161.3	+	5	880	c.755G>A	c.(754-756)gGc>gAc	p.G252D	SLC12A9_ENST00000540482.1_Missense_Mutation_p.G252D|SLC12A9_ENST00000275729.3_Missense_Mutation_p.G163D|SLC12A9_ENST00000428758.1_Missense_Mutation_p.G252D|SLC12A9_ENST00000415287.1_Missense_Mutation_p.G163D	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9	252					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)					GACAACTTGGGCGGTGAGCTG	0.652													G|||	7	0.00139776	0.0008	0.0029	5008	,	,		15798	0.0		0.004	False		,,,				2504	0.0				p.G252D		Atlas-SNP	.											.	SLC12A9	81	.	0			c.G755A						PASS	.	G	ASP/GLY	6,4398		0,6,2196	43	48	46		755	0.7	0.2	7	dbSNP_134	46	59,8537		0,59,4239	yes	missense	SLC12A9	NM_020246.2	94	0,65,6435	AA,AG,GG		0.6864,0.1362,0.5	probably-damaging	252/915	100454796	65,12935	2202	4298	6500	SO:0001583	missense	56996	exon5			ACTTGGGCGGTGA	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.755G>A	7.37:g.100454796G>A	ENSP00000275730:p.Gly252Asp	36	0	0		44	21	0.477273	NM_001267812	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Missense_Mutation	SNP	ENST00000354161.3	37	CCDS5707.1	7	0.003205128205128205	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	2.002	-0.429266	0.04701	0.001362	0.006864	ENSG00000146828	ENST00000540482;ENST00000428758;ENST00000275729;ENST00000415287;ENST00000354161	D;D;D;D;D	0.98862	-5.19;-5.19;-5.19;-5.19;-5.19	4.65	0.708	0.18144	Amino acid permease domain (1);	0.458827	0.21438	N	0.074528	D	0.94470	0.8220	L	0.41710	1.295	0.19775	N	0.99995	B;B	0.24132	0.098;0.002	B;B	0.32149	0.141;0.024	D	0.89635	0.3858	10	0.36615	T	0.2	.	5.9914	0.19465	0.2529:0.3003:0.4469:0.0	.	163;252	Q9BXP2-2;Q9BXP2	.;S12A9_HUMAN	D	252;252;163;163;252	ENSP00000443702:G252D;ENSP00000408301:G252D;ENSP00000275729:G163D;ENSP00000413796:G163D;ENSP00000275730:G252D	ENSP00000275729:G163D	G	+	2	0	SLC12A9	100292732	0.059000	0.20769	0.160000	0.22671	0.005000	0.04900	0.363000	0.20301	-0.175000	0.10725	-1.943000	0.00494	GGC	G|0.996;A|0.004	0.004	strong		0.652	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246		A	100454796	G	A	100454796	3	1	28	1	0	0	0	0	1	0	0	0	14405	1203	42	2	769	2	SLC12A9	7	100454796	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	257106	100454796	58683867	301	11804											
SLC12A9	56996	hgsc.bcm.edu	37	chr7	100463492	100463492	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	accctgttccctcctccccgGgctcctgggagcccccgggc	2	7	11	21	2	0	0	0	0	0	0	4	1	4	1	8	3	1	2	8	3	0	1	rs34433055	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:100463492G>A	ENST00000354161.3	+	14	2135	c.2010G>A	c.(2008-2010)cgG>cgA	p.R670R	TRIP6_ENST00000200457.4_5'Flank	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9	670					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)					CTCCTCCCCGGGCTCCTGGGA	0.667													G|||	26	0.00519169	0.0008	0.0043	5008	,	,		14655	0.0		0.0159	False		,,,				2504	0.0061				p.R670R		Atlas-SNP	.											.	SLC12A9	81	.	0			c.G2010A						PASS	.	G		13,4393	20.2+/-43.8	0,13,2190	30	36	34		2010	3.3	1	7	dbSNP_126	34	132,8466	64.9+/-127.2	1,130,4168	no	coding-synonymous	SLC12A9	NM_020246.2		1,143,6358	AA,AG,GG		1.5352,0.2951,1.115		670/915	100463492	145,12859	2203	4299	6502	SO:0001819	synonymous_variant	56996	exon14			TCCCCGGGCTCCT	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.2010G>A	7.37:g.100463492G>A		100	0	0		98	41	0.418367	NM_020246	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Silent	SNP	ENST00000354161.3	37	CCDS5707.1																																																																																			G|0.991;A|0.009	0.009	strong		0.667	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246		A	100463492	G	A	100463492	2	1	28	1	0	0	0	0	0	0	0	1	14405	1219	43	2		2	SLC12A9	7	100463492	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	8696	100463492	58675171	302	11805											
SPDYE6	0	hgsc.bcm.edu	37	chr7	101988929	101988930	+	IGR	DEL	TG	TG	-																															ggttcgtggaacggtataacTggaaccgacgcttacggagc																										TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:101988929_101988930delTG								Y_RNA (11547 upstream) : PRKRIP1 (15413 downstream)																							ACGGTATAACTGGAACCGACGC	0.569																																					p.315_315del		Atlas-Indel	.											.	SPDYE6	1	.	0			c.944_945del						PASS	.			2,1230		1,0,615							0			1	3,2919		1,1,1459	no	frameshift	SPDYE6	NM_001146210.1		2,1,2074	A1A1,A1R,RR		0.1027,0.1623,0.1204				5,4149				SO:0001628	intergenic_variant	729597	exon6			.																													7.37:g.101988929_101988930delTG		347	0	0		686	48	0.0699708	NM_001146210		Frame_Shift_Del	DEL		37																																																																																				.	.	none	0	0.569									-	101988930	TG	-	101988929	6	5	28	0	1	1	0	1	0	0	0	0	15048	1580	55	0		0	SPDYE6	7	101988929	IGR	DEL	TG	TCGA-G8-6914-01A-11D-2210-10	1525437	101988929	57149734	303	11806											
LRWD1	222229	hgsc.bcm.edu	37	chr7	102112914	102112914	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cccacagcctccaaggggagCggcctgggcaccatctgcct	7	5	12	17	1	1	0	0	0	1	0	2	1	2	1	6	4	3	1	6	4	1	0	rs184787600	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:102112914C>T	ENST00000292616.5	+	13	1700	c.1548C>T	c.(1546-1548)agC>agT	p.S516S	MIR4467_ENST00000578629.1_RNA	NM_152892.1	NP_690852.1	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain containing 1	516					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						CCAAGGGGAGCGGCCTGGGCA	0.682													C|||	16	0.00319489	0.0008	0.0029	5008	,	,		14662	0.0		0.008	False		,,,				2504	0.0051				p.S516S		Atlas-SNP	.											LRWD1,colon,carcinoma,0,1	LRWD1	41	1	0			c.C1548T						PASS	.	C		10,4230		0,10,2110	11	12	12		1548	-4.2	0	7		12	86,8236		0,86,4075	no	coding-synonymous	LRWD1	NM_152892.1		0,96,6185	TT,TC,CC		1.0334,0.2358,0.7642		516/648	102112914	96,12466	2120	4161	6281	SO:0001819	synonymous_variant	222229	exon13			GGGGAGCGGCCTG	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.1548C>T	7.37:g.102112914C>T		22	0	0		23	10	0.434783	NM_152892	A8K4K2|B2R9G2|Q8N0T9|Q8WV43|Q96GJ2	Silent	SNP	ENST00000292616.5	37	CCDS34715.1	10	0.004578754578754579	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	C	5.586	0.292913	0.10567	0.002358	0.010334	ENSG00000161036	ENST00000488689;ENST00000468175	.	.	.	5.1	-4.25	0.03766	.	.	.	.	.	T	0.21962	0.0529	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.34254	-0.9836	4	.	.	.	-19.7101	8.7692	0.34722	0.0949:0.4915:0.0:0.4135	.	.	.	.	V	127;102	.	.	A	+	2	0	LRWD1	101899919	0.000000	0.05858	0.001000	0.08648	0.712000	0.41017	-1.540000	0.02200	-0.725000	0.04901	0.655000	0.94253	GCG	C|0.995;T|0.005	0.005	strong		0.682	LRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349493.1	NM_152892		T	102112914	C	T	102112914	2	4	28	1	0	0	0	0	0	0	0	1	9056	767	27	1		1	LRWD1	7	102112914	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	123985	102112914	57025749	304	11807											
HBP1	26959	hgsc.bcm.edu	37	chr7	106836344	106836344	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagtatggctcgccagcgtcGtgcatctttgtcttgtggag	5	14	13	9	3	2	0	0	0	2	0	4	1	2	1	1	2	2	3	1	2	2	4			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:106836344G>A	ENST00000222574.4	+	9	1319	c.1133G>A	c.(1132-1134)cGt>cAt	p.R378H	HBP1_ENST00000468410.1_Missense_Mutation_p.R378H|HBP1_ENST00000485846.1_Missense_Mutation_p.R378H|HBP1_ENST00000461963.1_3'UTR|CTA-363E19.2_ENST00000607036.1_RNA	NM_012257.3	NP_036389.2	O60381	HBP1_HUMAN	HMG-box transcription factor 1	378					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						CGCCAGCGTCGTGCATCTTTG	0.388																																					p.R388H		Atlas-SNP	.											.	HBP1	31	.	0			c.G1163A						PASS	.						87	85	86					7																	106836344		2203	4300	6503	SO:0001583	missense	26959	exon9			AGCGTCGTGCATC	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.1133G>A	7.37:g.106836344G>A	ENSP00000222574:p.Arg378His	102	0	0		109	55	0.504587	NM_001244262	B3KVB7|Q8TBM1|Q8TE93|Q96AJ2	Missense_Mutation	SNP	ENST00000222574.4	37	CCDS5741.1	.	.	.	.	.	.	.	.	.	.	G	34	5.355207	0.95854	.	.	ENSG00000105856	ENST00000468410;ENST00000222574;ENST00000485846;ENST00000498408	D;D;D	0.99369	-5.78;-5.78;-5.78	5.96	5.96	0.96718	.	0.044632	0.85682	D	0.000000	D	0.98896	0.9626	L	0.29908	0.895	0.58432	D	0.999999	D;D;D	0.89917	0.999;1.0;0.999	D;D;P	0.65773	0.913;0.938;0.869	D	0.99925	1.1280	10	0.72032	D	0.01	-14.0183	20.4084	0.99013	0.0:0.0:1.0:0.0	.	388;378;378	B4DJ36;O60381-3;O60381	.;.;HBP1_HUMAN	H	378;378;378;370	ENSP00000420500:R378H;ENSP00000222574:R378H;ENSP00000418738:R378H	ENSP00000222574:R378H	R	+	2	0	HBP1	106623580	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.950000	0.87804	2.833000	0.97629	0.650000	0.86243	CGT	.	.	none		0.388	HBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349297.1	NM_012257		A	106836344	G	A	106836344	3	1	28	1	0	0	0	0	1	0	0	0	6994	1145	40	1	1163	1	HBP1	7	106836344	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	4723430	106836344	52302319	305	11808											
MET	4233	hgsc.bcm.edu	37	chr7	116435768	116435768	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagccccaccttatcctgaCgtaaacacctttgatataac	12	10	6	13	1	0	2	0	2	0	0	1	3	1	3	5	1	3	1	5	1	5	5	rs41736	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:116435768C>T	ENST00000318493.6	+	20	4099	c.3912C>T	c.(3910-3912)gaC>gaT	p.D1304D	MET_ENST00000397752.3_Silent_p.D1286D|MET_ENST00000539704.1_Silent_p.D156D			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)	p.D1304D(1)		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)			CTTATCCTGACGTAAACACCT	0.473			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)		OREG0003446	type=REGULATORY REGION|Gene=MET|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	c|||	1764	0.352236	0.034	0.464	5008	,	,		18610	0.4673		0.4414	False		,,,				2504	0.4928				p.D1304D		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,carcinoma,0,1	MET	412	1	1	Substitution - coding silent(1)	stomach(1)	c.C3912T						PASS	.	T	,	393,3383		15,363,1510	245	238	240		3858,3912	-10.9	0	7	dbSNP_76	240	3487,4731		756,1975,1378	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	771,2338,2888	TT,TC,CC		42.4312,10.4078,32.3495	,	1286/1391,1304/1409	116435768	3880,8114	1888	4109	5997	SO:0001819	synonymous_variant	4233	exon20	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	TCCTGACGTAAAC	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.3912C>T	7.37:g.116435768C>T		123	1	0.00813008	1473	123	122	0.99187	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			C|0.624;T|0.376	0.376	strong		0.473	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			T	116435768	C	T	116435768	2	4	28	1	0	0	0	0	0	0	0	1	9494	535	19	1		1	MET	7	116435768	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	9599424	116435768	42702895	306	11809			3	50		3	3	330	N	G_C	2.968693e-05
MET	4233	hgsc.bcm.edu	37	chr7	116436022	116436022	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctggtgtcccggatatcagcGatcttctctactttcattgg	6	15	9	11	2	4	0	2	0	2	0	6	2	5	1	1	3	2	0	1	3	2	5	rs2023748	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:116436022G>A	ENST00000318493.6	+	21	4258	c.4071G>A	c.(4069-4071)gcG>gcA	p.A1357A	MET_ENST00000397752.3_Silent_p.A1339A|MET_ENST00000539704.1_Silent_p.A209A			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)	p.A1357A(1)		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)			GGATATCAGCGATCTTCTCTA	0.443			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				G|||	1772	0.353834	0.034	0.4697	5008	,	,		21305	0.4673		0.4433	False		,,,				2504	0.4949				p.A1357A		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,carcinoma,0,1	MET	412	1	1	Substitution - coding silent(1)	stomach(1)	c.G4071A						PASS	.	G	,	405,3531		16,373,1579	140	130	133		4017,4071	-11.4	0	7	dbSNP_94	133	3536,4748		773,1990,1379	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	789,2363,2958	AA,AG,GG		42.6847,10.2896,32.2504	,	1339/1391,1357/1409	116436022	3941,8279	1968	4142	6110	SO:0001819	synonymous_variant	4233	exon21	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	ATCAGCGATCTTC	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.4071G>A	7.37:g.116436022G>A		179	0	0		174	174	1	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			G|0.618;A|0.382	0.382	strong		0.443	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			A	116436022	G	A	116436022	2	1	28	1	0	0	0	0	0	0	0	1	9494	1045	37	1		1	MET	7	116436022	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	254	116436022	42702641	307	11810			3	50		3	3	330	N	G_C	2.968693e-05
MET	4233	hgsc.bcm.edu	37	chr7	116436097	116436097	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aacgtaaaatgtgtcgctccGtatccttctctgttgtcatc	8	15	7	11	3	2	0	1	0	1	0	7	0	4	0	2	0	1	4	2	0	4	4	rs41737	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:116436097G>A	ENST00000318493.6	+	21	4333	c.4146G>A	c.(4144-4146)ccG>ccA	p.P1382P	MET_ENST00000397752.3_Silent_p.P1364P|MET_ENST00000539704.1_Silent_p.P234P			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)	p.P1382P(1)		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)			GTGTCGCTCCGTATCCTTCTC	0.468			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				A|||	1776	0.354633	0.0356	0.4726	5008	,	,		19834	0.4673		0.4433	False		,,,				2504	0.4949				p.P1382P		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,carcinoma,0,1	MET	412	1	1	Substitution - coding silent(1)	stomach(1)	c.G4146A						PASS	.	A	,	418,3602		15,388,1607	193	176	181		4092,4146	-3.1	1	7	dbSNP_76	181	3563,4817		777,2009,1404	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	792,2397,3011	AA,AG,GG		42.5179,10.398,32.1048	,	1364/1391,1382/1409	116436097	3981,8419	2010	4190	6200	SO:0001819	synonymous_variant	4233	exon21	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	CGCTCCGTATCCT	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.4146G>A	7.37:g.116436097G>A		126	0	0		148	148	1	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			G|0.615;A|0.385	0.385	strong		0.468	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			A	116436097	G	A	116436097	2	1	28	1	0	0	0	0	0	0	0	1	9494	1132	40	1		1	MET	7	116436097	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	75	116436097	42702566	308	11811			3	50		3	3	330	N	G_C	2.968693e-05
WNT16	51384	hgsc.bcm.edu	37	chr7	120969825	120969825	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atcaccgccgccgccactacCgccccgatgggcgccagccc	6	3	10	22	6	1	0	1	0	0	0	1	1	1	0	9	1	2	0	9	1	1	1	rs17143291	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:120969825C>A	ENST00000222462.2	+	2	590	c.300C>A	c.(298-300)acC>acA	p.T100T	WNT16_ENST00000361301.2_Silent_p.T90T	NM_057168.1	NP_476509.1	Q9UBV4	WNT16_HUMAN	wingless-type MMTV integration site family, member 16	100					bone remodeling (GO:0046849)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell fate commitment (GO:0045165)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|negative regulation of cell death (GO:0060548)|neuron differentiation (GO:0030182)|optic cup formation involved in camera-type eye development (GO:0003408)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of gene expression (GO:0010628)|positive regulation of JNK cascade (GO:0046330)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|replicative senescence (GO:0090399)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)	18	all_neural(327;0.117)					CCGCCACTACCGCCCCGATGG	0.662													C|||	53	0.0105831	0.0212	0.0216	5008	,	,		13952	0.0		0.0089	False		,,,				2504	0.001				p.T100T		Atlas-SNP	.											.	WNT16	97	.	0			c.C300A						PASS	.	C	,	79,4315		0,79,2118	22	25	24		270,300	2.1	0.2	7	dbSNP_123	24	48,8512		0,48,4232	no	coding-synonymous,coding-synonymous	WNT16	NM_016087.2,NM_057168.1	,	0,127,6350	AA,AC,CC		0.5607,1.7979,0.9804	,	90/356,100/366	120969825	127,12827	2197	4280	6477	SO:0001819	synonymous_variant	51384	exon2			CACTACCGCCCCG	AF152584	CCDS5780.1, CCDS5781.1	7q31	2008-07-18			ENSG00000002745	ENSG00000002745		"Wingless-type MMTV integration sites"	16267	protein-coding gene	gene with protein product		606267				10500199	Standard	NM_016087		Approved		uc003vjw.3	Q9UBV4	OTTHUMG00000156963	ENST00000222462.2:c.300C>A	7.37:g.120969825C>A		14	0	0		15	9	0.6	NM_057168	Q2M3G1|Q9Y5C0	Silent	SNP	ENST00000222462.2	37	CCDS5781.1																																																																																			C|0.988;A|0.012	0.012	strong		0.662	WNT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346843.1	NM_057168		A	120969825	C	A	120969825	2	1	28	1	0	0	0	0	0	0	0	1	17400	639	23	4		4	WNT16	7	120969825	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	4533728	120969825	38168838	309	11812											
KIAA1549	57670	hgsc.bcm.edu	37	chr7	138602865	138602865	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagaaatgccaacactcgTctctgagatttccatggatc	11	10	9	11	1	1	2	0	1	1	2	5	4	2	3	2	2	2	1	2	2	2	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:138602865T>G	ENST00000422774.1	-	2	1555	c.1507A>C	c.(1507-1509)Acg>Ccg	p.T503P	KIAA1549_ENST00000242365.4_Missense_Mutation_p.T453P|KIAA1549_ENST00000440172.1_Missense_Mutation_p.T503P			Q9HCM3	K1549_HUMAN	KIAA1549	503	Ser-rich.					integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						CCAACACTCGTCTCTGAGATT	0.502			O	BRAF	pilocytic astrocytoma																																p.T503P	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549	314	.	0			c.A1507C						PASS	.						34	34	34					7																	138602865		1944	4154	6098	SO:0001583	missense	57670	exon2			CACTCGTCTCTGA		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.1507A>C	7.37:g.138602865T>G	ENSP00000416040:p.Thr503Pro	31	0	0		58	32	0.551724	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	37	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	T	10.13	1.264426	0.23136	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.25912	1.77;1.77;1.77	4.24	-8.13	0.01073	.	2.614330	0.01241	N	0.008611	T	0.11110	0.0271	N	0.12182	0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.14587	-1.0467	10	0.18276	T	0.48	.	5.0234	0.14372	0.2255:0.5515:0.1044:0.1186	.	503;503	Q9HCM3;Q9HCM3-2	K1549_HUMAN;.	P	503;453;503	ENSP00000406661:T503P;ENSP00000242365:T453P;ENSP00000416040:T503P	ENSP00000242365:T453P	T	-	1	0	KIAA1549	138253405	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.452000	0.06787	-1.529000	0.01754	-0.290000	0.09829	ACG	.	.	none		0.502	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1			G	138602865	T	G	138602865	3	3	28	1	0	0	0	0	1	0	0	0	8253	1667	58	5	4421	5	KIAA1549	7	138602865	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	17633040	138602865	20535798	310	11813											
BRAF	673	hgsc.bcm.edu	37	chr7	140449150	140449150	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcaattcatacagaacaatTccaaatgcatatacatctga	18	11	3	9	0	3	2	2	1	1	1	4	2	4	2	1	0	4	1	1	0	7	5	rs9648696	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:140449150T>C	ENST00000288602.6	-	16	1989	c.1929A>G	c.(1927-1929)ggA>ggG	p.G643G		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	643	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|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 stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	ACAGAACAATTCCAAATGCAT	0.348		61	"Mis, T, O"	"AKAP9, KIAA1549"	"melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome				C|||	1758	0.351038	0.7451	0.1585	5008	,	,		17576	0.1825		0.1531	False		,,,				2504	0.3323				p.G643G	Colon(40;35 892 2973 5743 27438)	Atlas-SNP	.		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	.	BRAF	36346	.	0			c.A1929G						PASS	.	C		2904,1502	476.8+/-357.7	963,978,262	105	108	107		1929	2.1	1	7	dbSNP_119	107	1258,7342	758.6+/-407.5	114,1030,3156	no	coding-synonymous	BRAF	NM_004333.4		1077,2008,3418	CC,CT,TT		14.6279,34.0899,32.0006		643/767	140449150	4162,8844	2203	4300	6503	SO:0001819	synonymous_variant	673	exon16	Familial Cancer Database	CFC, CFCS	AACAATTCCAAAT	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1929A>G	7.37:g.140449150T>C		121	0	0		141	84	0.595745	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Silent	SNP	ENST00000288602.6	37	CCDS5863.1	611	0.27976190476190477	355	0.7215447154471545	58	0.16022099447513813	91	0.1590909090909091	107	0.14116094986807387	C	9.723	1.160251	0.21454	0.659101	0.146279	ENSG00000157764	ENST00000496384	.	.	.	5.02	2.11	0.27256	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.33317	-0.9873	3	.	.	.	.	5.8585	0.18732	0.0:0.5864:0.1264:0.2872	rs9648696;rs10238189;rs60896634	.	.	.	G	251	.	.	E	-	2	0	BRAF	140095619	1.000000	0.71417	0.998000	0.56505	0.947000	0.59692	1.503000	0.35715	-0.010000	0.14271	-0.355000	0.07637	GAA	T|0.696;C|0.304	0.304	strong		0.348	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		C	140449150	T	C	140449150	2	2	28	1	0	0	0	0	0	0	0	1	1498	1770	62	3		3	BRAF	7	140449150	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	1846285	140449150	18689513	311	11814											
BRAF	673	hgsc.bcm.edu	37	chr7	140453155	140453155	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cactgtagctagaccaaaatCacctatttttactgtgaggt	12	13	7	9	0	1	2	1	1	0	1	1	2	1	2	2	1	2	2	2	1	6	6	rs397516896		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:140453155C>T	ENST00000288602.6	-	15	1840	c.1780G>A	c.(1780-1782)Gat>Aat	p.D594N		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	594	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		D -> G (in NHL). {ECO:0000269|PubMed:14612909}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|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 stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.D594N(9)|p.D594H(2)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	AGACCAAAATCACCTATTTTT	0.378		61	"Mis, T, O"	"AKAP9, KIAA1549"	"melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												p.D594N	Colon(40;35 892 2973 5743 27438)	Atlas-SNP	.		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	BRAF,rectum,carcinoma,0,77	BRAF	36346	77	11	Substitution - Missense(11)	skin(6)|large_intestine(2)|lung(2)|haematopoietic_and_lymphoid_tissue(1)	c.G1780A						PASS	.						106	100	102					7																	140453155		2203	4300	6503	SO:0001583	missense	673	exon15	Familial Cancer Database	CFC, CFCS	CAAAATCACCTAT	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"v-raf murine sarcoma viral oncogene homolog B"			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1780G>A	7.37:g.140453155C>T	ENSP00000288602:p.Asp594Asn	74	0	0		71	20	0.28169	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.	.	.	.	.	.	.	.	.	.	C	36	5.616687	0.96649	.	.	ENSG00000157764	ENST00000288602	D	0.99849	-7.15	5.65	5.65	0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.99883	0.9944	M	0.94021	3.485	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96728	0.9537	10	0.87932	D	0	.	19.7917	0.96461	0.0:1.0:0.0:0.0	.	594	P15056	BRAF_HUMAN	N	594	ENSP00000288602:D594N	ENSP00000288602:D594N	D	-	1	0	BRAF	140099624	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.702000	0.84576	2.686000	0.91538	0.650000	0.86243	GAT	.	.	none		0.378	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		T	140453155	C	T	140453155	3	4	28	1	0	0	0	0	1	0	0	0	1498	826	29	2	536	2	BRAF	7	140453155	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	4005	140453155	18685508	312	11815											
ARHGEF35	445328	hgsc.bcm.edu	37	chr7	143884216	143884216	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atatgaggcacctggaaacaGgtcacagtgaggagagtcct	13	7	13	8	0	1	3	1	2	0	1	2	5	2	4	2	4	1	1	2	4	2	1	rs200777966	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:143884216G>C	ENST00000378115.2	-	2	1390	c.1261C>G	c.(1261-1263)Ctg>Gtg	p.L421V	ARHGEF35_ENST00000543357.1_Missense_Mutation_p.L421V	NM_001003702.2	NP_001003702.2	A5YM69	ARG35_HUMAN	Rho guanine nucleotide exchange factor (GEF) 35	421										kidney(1)|large_intestine(1)|lung(3)|stomach(1)	6						CCTGGAAACAGGTCACAGTGA	0.587													-|||	6	0.00119808	0.0	0.0014	5008	,	,		17229	0.0		0.005	False		,,,				2504	0.0				p.L421V		Atlas-SNP	.											.	ARHGEF35	11	.	0			c.C1261G						PASS	.	G	VAL/LEU	4,4156		0,4,2076	8	9	8		1261	-4.7	0	7		8	33,8021		1,31,3995	no	missense	ARHGEF35	NM_001003702.2	32	1,35,6071	CC,CG,GG		0.4097,0.0962,0.3029	benign	421/485	143884216	37,12177	2080	4027	6107	SO:0001583	missense	445328	exon2			GAAACAGGTCACA	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.1261C>G	7.37:g.143884216G>C	ENSP00000367355:p.Leu421Val	294	0	0		458	88	0.19214	NM_001003702	Q6ZUI2	Missense_Mutation	SNP	ENST00000378115.2	37	CCDS34770.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	.	4.049	0.006734	0.07866	9.62E-4	0.004097	ENSG00000213214	ENST00000378115;ENST00000543357	.	.	.	2.34	-4.67	0.03319	.	.	.	.	.	T	0.23688	0.0573	L	0.32530	0.975	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.19063	-1.0317	8	0.24483	T	0.36	.	4.1258	0.10126	0.3886:0.2006:0.4109:0.0	.	421	A5YM69	ARG35_HUMAN	V	421	.	ENSP00000367355:L421V	L	-	1	2	ARHGEF35	143515149	0.000000	0.05858	0.000000	0.03702	0.110000	0.19582	-1.471000	0.02344	-1.282000	0.02396	-1.271000	0.01417	CTG	G|0.999;C|0.001	0.001	strong		0.587	ARHGEF35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349997.1	NM_001003702		C	143884216	G	C	143884216	3	2	28	1	0	0	0	0	1	0	0	0	905	991	35	4	197	4	ARHGEF35	7	143884216	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	3431061	143884216	15254447	313	11816											
ACTR3C	653857	hgsc.bcm.edu	37	chr7	149981856	149981856	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcataccttatacagcggacGccgcacatcgatggggcagt	10	8	11	12	4	1	0	1	0	0	0	2	2	1	1	2	3	3	2	2	3	3	3	rs117425825	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:149981856G>A	ENST00000539352.1	-	6	801	c.550C>T	c.(550-552)Cgt>Tgt	p.R184C	ACTR3C_ENST00000252071.4_Missense_Mutation_p.R184C	NM_001164458.1	NP_001157930.1	Q9C0K3	ARP3C_HUMAN	ARP3 actin-related protein 3 homolog C (yeast)	184						extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)										TACAGCGGACGCCGCACATCG	0.403													G|||	105	0.0209665	0.003	0.0187	5008	,	,		13887	0.0		0.0457	False		,,,				2504	0.0429				p.R184C		Atlas-SNP	.											.	.	.	.	0			c.C550T						PASS	.	G	CYS/ARG,CYS/ARG	13,1371		0,13,679	85	73	77		550,550	2.2	0.9	7	dbSNP_132	77	125,3057		1,123,1467	yes	missense,missense	ACTR3C	NM_001164458.1,NM_001164459.1	180,180	1,136,2146	AA,AG,GG		3.9283,0.9393,3.0223	probably-damaging,probably-damaging	184/211,184/211	149981856	138,4428	692	1591	2283	SO:0001583	missense	653857	exon6			GCGGACGCCGCAC		CCDS47744.1	7q36.1	2009-09-23			ENSG00000106526	ENSG00000106526			37282	protein-coding gene	gene with protein product						11162478, 14651955	Standard	NM_001164458		Approved	ARP11	uc022aps.1	Q9C0K3	OTTHUMG00000158323	ENST00000539352.1:c.550C>T	7.37:g.149981856G>A	ENSP00000440990:p.Arg184Cys	58	0	0		61	35	0.57377	NM_001164459	Q5CZI4	Missense_Mutation	SNP	ENST00000539352.1	37	CCDS47744.1	43	0.019688644688644688	0	0.0	10	0.027624309392265192	1	0.0017482517482517483	32	0.04221635883905013	G	13.83	2.352944	0.41700	0.009393	0.039283	ENSG00000106526	ENST00000478393;ENST00000252071;ENST00000539352	T;T;T	0.09350	2.99;2.99;2.99	2.16	2.16	0.27623	.	0.221425	0.28151	N	0.016416	T	0.14141	0.0342	H	0.97587	4.035	0.39214	D	0.963377	D	0.89917	1.0	D	0.68943	0.961	T	0.52961	-0.8505	9	.	.	.	.	10.4552	0.44546	0.0:0.0:1.0:0.0	.	184	Q9C0K3	ARP3C_HUMAN	C	182;184;184	ENSP00000417426:R182C;ENSP00000252071:R184C;ENSP00000440990:R184C	.	R	-	1	0	ACTR3C	149612789	1.000000	0.71417	0.896000	0.35187	0.654000	0.38779	4.696000	0.61774	1.511000	0.48818	0.398000	0.26397	CGT	G|0.976;A|0.024	0.024	strong		0.403	ACTR3C-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350676.2			A	149981856	G	A	149981856	3	1	28	1	0	0	0	0	1	0	0	0	214	1087	38	1	90	1	ACTR3C	7	149981856	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	6097640	149981856	9156807	314	11817											
ABCF2	10061	hgsc.bcm.edu	37	chr7	150920891	150920891	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctctgccttgtcggcatccaGctcctccaggcgctcgtaga	5	10	10	16	3	1	1	0	0	1	1	6	1	4	1	4	2	2	4	4	2	1	2	rs41273648	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:150920891G>A	ENST00000287844.2	-	5	704	c.595C>T	c.(595-597)Ctg>Ttg	p.L199L	ABCF2_ENST00000473874.1_5'Flank|ABCF2_ENST00000222388.2_Silent_p.L199L	NM_007189.1	NP_009120.1	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 2	199	ABC transporter 1. {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)		TCGGCATCCAGCTCCTCCAGG	0.602													G|||	37	0.00738818	0.0015	0.0115	5008	,	,		19099	0.0		0.0209	False		,,,				2504	0.0061				p.L199L		Atlas-SNP	.											.	ABCF2	54	.	0			c.C595T						PASS	.	G	,	21,4385	28.1+/-56.4	0,21,2182	41	36	38		595,595	2.2	1	7	dbSNP_127	38	238,8362	96.8+/-158.5	6,226,4068	no	coding-synonymous,coding-synonymous	ABCF2	NM_005692.3,NM_007189.1	,	6,247,6250	AA,AG,GG		2.7674,0.4766,1.9914	,	199/635,199/624	150920891	259,12747	2203	4300	6503	SO:0001819	synonymous_variant	10061	exon5			CATCCAGCTCCTC	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.595C>T	7.37:g.150920891G>A		67	0	0		54	25	0.462963	NM_007189	O60864|Q75MJ0|Q75MJ1|Q96TE8	Silent	SNP	ENST00000287844.2	37	CCDS5923.1																																																																																			G|0.985;A|0.015	0.015	strong		0.602	ABCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336086.1	NM_005692		A	150920891	G	A	150920891	2	1	28	1	0	0	0	0	0	0	0	1	66	962	34	2		2	ABCF2	7	150920891	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	939035	150920891	8217772	315	11818											
DNAJB6	10049	hgsc.bcm.edu	37	chr7	157202683	157202683	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgggccctgggaccccctcGcgtccgcagcaggtgtgcaa	5	5	14	17	4	0	0	0	0	0	0	2	1	1	1	5	3	2	3	5	3	1	0			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:157202683G>A	ENST00000262177.4	+	9	1091	c.886G>A	c.(886-888)Gcg>Acg	p.A296T	DNAJB6_ENST00000443280.1_Missense_Mutation_p.A181T|DNAJB6_ENST00000452797.2_Missense_Mutation_p.A247T	NM_058246.3	NP_490647.1	O75190	DNJB6_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 6	296					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)		GGACCCCCTCGCGTCCGCAGC	0.701																																					p.A296T	Esophageal Squamous(46;195 967 1350 20350 43814)	Atlas-SNP	.											.	DNAJB6	39	.	0			c.G886A						PASS	.						6	5	5					7																	157202683		2018	3994	6012	SO:0001583	missense	10049	exon9			CCCCTCGCGTCCG	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.886G>A	7.37:g.157202683G>A	ENSP00000262177:p.Ala296Thr	17	0	0		28	13	0.464286	NM_058246	A4D232|A8K7D8|A8KAG0|B4DN73|E9PCZ2|O95806|Q53EN8|Q59EF2|Q6FIC8|Q75MA2|Q9UIK6	Missense_Mutation	SNP	ENST00000262177.4	37	CCDS5946.1	.	.	.	.	.	.	.	.	.	.	G	16.81	3.226791	0.58668	.	.	ENSG00000105993	ENST00000262177;ENST00000452797;ENST00000443280	T;T;T	0.63255	0.39;-0.03;-0.02	4.5	-5.97	0.02227	.	3.940110	0.01650	N	0.024503	T	0.36054	0.0953	N	0.08118	0	0.09310	N	1	B;B;B;B	0.33494	0.0;0.414;0.001;0.001	B;B;B;B	0.24006	0.0;0.05;0.001;0.001	T	0.32107	-0.9919	10	0.45353	T	0.12	.	8.0691	0.30678	0.668:0.2188:0.1132:0.0	.	181;247;296;296	E9PH18;B4DN73;A8KAG0;O75190	.;.;.;DNJB6_HUMAN	T	296;247;181	ENSP00000262177:A296T;ENSP00000402270:A247T;ENSP00000396267:A181T	ENSP00000262177:A296T	A	+	1	0	DNAJB6	156895444	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.031000	0.03578	-1.112000	0.02984	-0.140000	0.14226	GCG	.	.	none		0.701	DNAJB6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000348119.2			A	157202683	G	A	157202683	3	1	28	1	0	0	0	0	1	0	0	0	4626	1087	38	1	951	1	DNAJB6	7	157202683	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	6281792	157202683	1935980	316	11819											
DEFA5	1670	hgsc.bcm.edu	37	chr8	6914169	6914169	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tcctggagtgactcagcctgGgcctgcagggccaccaggag	7	6	15	13	0	1	1	1	1	0	0	2	3	2	3	5	4	2	1	5	4	0	0	rs147432781	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:6914169G>A	ENST00000330590.2	-	1	87	c.51C>T	c.(49-51)gcC>gcT	p.A17A		NM_021010.1	NP_066290.1	Q01523	DEF5_HUMAN	defensin, alpha 5, Paneth cell-specific	17					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)|secretory granule lumen (GO:0034774)				NS(1)|lung(4)|skin(1)|stomach(1)	7				COAD - Colon adenocarcinoma(149;0.0572)|READ - Rectum adenocarcinoma(644;0.121)		ACTCAGCCTGGGCCTGCAGGG	0.582													.|||	10	0.00199681	0.0	0.0	5008	,	,		18658	0.0		0.008	False		,,,				2504	0.002				p.A17A		Atlas-SNP	.											.	DEFA5	17	.	0			c.C51T						PASS	.	G		13,4393		0,13,2190	109	99	102		51	0.8	0.1	8	dbSNP_134	102	108,8492		0,108,4192	no	coding-synonymous	DEFA5	NM_021010.1		0,121,6382	AA,AG,GG		1.2558,0.2951,0.9303		17/95	6914169	121,12885	2203	4300	6503	SO:0001819	synonymous_variant	1670	exon1			AGCCTGGGCCTGC	BC069690	CCDS5963.1	8p23.1	2007-02-20			ENSG00000164816	ENSG00000164816		"Defensins, alpha"	2764	protein-coding gene	gene with protein product		600472		DEF5		1429669	Standard	NM_021010		Approved	HD-5	uc003wra.1	Q01523	OTTHUMG00000090383	ENST00000330590.2:c.51C>T	8.37:g.6914169G>A		110	0	0		99	45	0.454545	NM_021010	A0JDY6|Q3KNV2	Silent	SNP	ENST00000330590.2	37	CCDS5963.1																																																																																			G|0.993;A|0.007	0.007	strong		0.582	DEFA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206755.1	NM_021010		A	6914169	G	A	6914169	2	1	28	1	0	0	0	0	0	0	0	1	4394	1219	43	2		2	DEFA5	8	6914169	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10		6914169	139449853	317	11820											
SGK223	157285	hgsc.bcm.edu	37	chr8	8234526	8234526	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtggctgacacctggggagTtgggtctgggctgtcccggc	3	9	19	10	1	1	1	0	1	1	0	2	2	2	2	2	7	0	3	2	7	0	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:8234526T>A	ENST00000520004.1	-	3	1657	c.1393A>T	c.(1393-1395)Act>Tct	p.T465S	SGK223_ENST00000330777.4_Missense_Mutation_p.T465S			Q86YV5	SG223_HUMAN		467							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										ACCTGGGGAGTTGGGTCTGGG	0.637																																					p.T465S	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.A1393T						PASS	.						43	50	48					8																	8234526		2092	4227	6319	SO:0001583	missense	0	exon2			GGGGAGTTGGGTC																												ENST00000520004.1:c.1393A>T	8.37:g.8234526T>A	ENSP00000428054:p.Thr465Ser	80	0	0		91	30	0.32967	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	.	.	.	.	.	.	.	.	.	.	T	11.67	1.707584	0.30322	.	.	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.58940	0.3;0.3	5.02	1.03	0.20045	.	2.041710	0.02601	N	0.101061	T	0.43612	0.1255	N	0.19112	0.55	0.09310	N	1	B	0.14012	0.009	B	0.16289	0.015	T	0.25152	-1.0140	10	0.34782	T	0.22	.	7.1243	0.25463	0.0:0.4468:0.0:0.5532	.	465	Q86YV5	SG223_HUMAN	S	465	ENSP00000330930:T465S;ENSP00000428054:T465S	ENSP00000330930:T465S	T	-	1	0	AC068353.1	8271936	0.000000	0.05858	0.000000	0.03702	0.894000	0.52154	-0.045000	0.12003	0.249000	0.21456	-0.177000	0.13119	ACT	.	.	none		0.637	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1			A	8234526	T	A	8234526	3	1	28	1	0	0	0	0	1	0	0	0	14225	1725	60	5	2831	5	SGK223	8	8234526	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	1320357	8234526	138129496	318	11821											
TNKS	8658	hgsc.bcm.edu	37	chr8	9584176	9584176	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acacctatacgtacttctgaTgttgattatcgactcttaga	11	15	6	9	2	2	3	0	2	2	1	3	4	2	3	1	0	2	2	1	0	5	7			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:9584176T>C	ENST00000310430.6	+	13	1973	c.1947T>C	c.(1945-1947)gaT>gaC	p.D649D	TNKS_ENST00000518281.1_Silent_p.D412D	NM_003747.2	NP_003738.2	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	649					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)		GTACTTCTGATGTTGATTATC	0.373																																					p.D649D		Atlas-SNP	.											.	TNKS	198	.	0			c.T1947C						PASS	.						257	262	260					8																	9584176		2203	4300	6503	SO:0001819	synonymous_variant	8658	exon13			TTCTGATGTTGAT	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.1947T>C	8.37:g.9584176T>C		71	0	0		84	41	0.488095	NM_003747	O95272|Q4G0F2	Silent	SNP	ENST00000310430.6	37	CCDS5974.1																																																																																			.	.	none		0.373	TNKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206935.1	NM_003747		C	9584176	T	C	9584176	2	2	28	1	0	0	0	0	0	0	0	1	16334	1461	51	3		3	TNKS	8	9584176	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	1349650	9584176	136779846	319	11822											
FDFT1	2222	hgsc.bcm.edu	37	chr8	11667253	11667253	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catgaccatcagtgtggaaaAgaaggtcccgctgttacaca	13	8	10	10	1	1	2	1	1	0	1	2	3	2	3	2	2	1	2	2	2	4	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:11667253A>G	ENST00000220584.4	+	3	497	c.275A>G	c.(274-276)aAg>aGg	p.K92R	FDFT1_ENST00000530664.1_Missense_Mutation_p.K28R|FDFT1_ENST00000525777.1_Missense_Mutation_p.K7R|FDFT1_ENST00000446331.2_Intron|FDFT1_ENST00000528643.1_Missense_Mutation_p.K7R|FDFT1_ENST00000538689.1_5'UTR|FDFT1_ENST00000528812.1_Missense_Mutation_p.K28R|FDFT1_ENST00000443614.2_Missense_Mutation_p.K92R|FDFT1_ENST00000525900.1_Missense_Mutation_p.K85R	NM_004462.3	NP_004453.3	P37268	FDFT_HUMAN	farnesyl-diphosphate farnesyltransferase 1	92					cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	farnesyl-diphosphate farnesyltransferase activity (GO:0004310)|oxidoreductase activity (GO:0016491)|squalene synthase activity (GO:0051996)			breast(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)	12	all_epithelial(15;0.234)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.18)		AGTGTGGAAAAGAAGGTCCCG	0.473																																					p.K92R		Atlas-SNP	.											.	FDFT1	25	.	0			c.A275G						PASS	.						138	115	123					8																	11667253		2203	4300	6503	SO:0001583	missense	2222	exon3			TGGAAAAGAAGGT	X69141	CCDS5985.1, CCDS75696.1, CCDS75697.1	8p23.1-p22	2005-03-07			ENSG00000079459	ENSG00000079459	2.5.1.21		3629	protein-coding gene	gene with protein product	"squalene synthase"	184420					Standard	NM_001287742		Approved		uc003wui.3	P37268	OTTHUMG00000090801	ENST00000220584.4:c.275A>G	8.37:g.11667253A>G	ENSP00000220584:p.Lys92Arg	99	0	0		123	55	0.447154	NM_004462	B3KQ95|B4DJE5|B4DT56|B7Z1J3|Q96GT0	Missense_Mutation	SNP	ENST00000220584.4	37	CCDS5985.1	.	.	.	.	.	.	.	.	.	.	A	10.89	1.479017	0.26511	.	.	ENSG00000079459	ENST00000530337;ENST00000220584;ENST00000443614;ENST00000525900;ENST00000528812;ENST00000530664;ENST00000528643;ENST00000525777	D;D;D;D;D;D;T;T	0.81996	-1.56;-1.56;-1.56;-1.56;-1.56;-1.56;-0.57;-0.57	4.91	-1.99	0.07457	Terpenoid synthase (2);	0.360845	0.31760	N	0.007118	T	0.66436	0.2789	L	0.42245	1.32	0.09310	N	0.999998	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.06405	0.002;0.002;0.001;0.001	T	0.47100	-0.9143	10	0.25106	T	0.35	-7.7419	0.1655	0.00108	0.2664:0.2386:0.2384:0.2566	.	92;149;85;92	B4DJE5;B4DND3;E9PNM1;P37268	.;.;.;FDFT_HUMAN	R	92;92;92;85;28;28;7;7	ENSP00000431852:K92R;ENSP00000220584:K92R;ENSP00000390367:K92R;ENSP00000434714:K85R;ENSP00000431749:K28R;ENSP00000432331:K28R;ENSP00000431649:K7R;ENSP00000436069:K7R	ENSP00000220584:K92R	K	+	2	0	FDFT1	11704662	0.008000	0.16893	0.000000	0.03702	0.943000	0.58893	0.527000	0.22987	-0.398000	0.07679	0.402000	0.26972	AAG	.	.	none		0.473	FDFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207588.2			G	11667253	A	G	11667253	3	3	28	1	0	0	0	0	1	0	0	0	5810	72	3	3	285	3	FDFT1	8	11667253	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	2083077	11667253	134696769	320	11823											
DOCK5	80005	hgsc.bcm.edu	37	chr8	25149612	25149612	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgagtggcggtcccagatcCtgtctgggacgctccccaag	6	8	13	14	3	1	1	0	0	1	1	5	3	4	2	4	3	0	1	4	3	1	0			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:25149612C>T	ENST00000276440.7	+	6	438	c.394C>T	c.(394-396)Ctg>Ttg	p.L132L	DOCK5_ENST00000481100.1_Silent_p.L132L	NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	132					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)		GTCCCAGATCCTGTCTGGGAC	0.493																																					p.L132L	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											.	DOCK5	167	.	0			c.C394T						PASS	.						37	34	35					8																	25149612		2203	4298	6501	SO:0001819	synonymous_variant	80005	exon6			CAGATCCTGTCTG		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.394C>T	8.37:g.25149612C>T		51	0	0		69	16	0.231884	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Silent	SNP	ENST00000276440.7	37	CCDS6047.1																																																																																			.	.	none		0.493	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940		T	25149612	C	T	25149612	2	4	28	1	0	0	0	0	0	0	0	1	4692	680	24	2		2	DOCK5	8	25149612	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	13482359	25149612	121214410	321	11824											
KCNU1	157855	hgsc.bcm.edu	37	chr8	36692303	36692303	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgtccgatcttgaagggtaGgtggaatctgcagaggcatg	9	10	15	7	1	2	2	0	1	2	1	3	4	3	3	1	4	1	3	1	4	3	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:36692303G>T	ENST00000399881.3	+	12	1249		c.e12-1			NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1						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)		TTGAAGGGTAGGTGGAATCTG	0.408																																					.		Atlas-SNP	.											KCNU1_ENST00000399881,colon,carcinoma,0,2	KCNU1	359	2	0			c.1213-1G>T						PASS	.						103	100	101					8																	36692303		1871	4112	5983	SO:0001630	splice_region_variant	157855	exon12			AGGGTAGGTGGAA	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.1213-1G>T	8.37:g.36692303G>T		141	0	0		116	61	0.525862	NM_001031836		Splice_Site	SNP	ENST00000399881.3	37	CCDS55220.1	.	.	.	.	.	.	.	.	.	.	G	12.20	1.865287	0.32977	.	.	ENSG00000215262	ENST00000399881	.	.	.	5.9	5.02	0.67125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.9023	0.63812	0.0733:0.0:0.9266:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KCNU1	36811461	1.000000	0.71417	0.998000	0.56505	0.080000	0.17528	8.882000	0.92420	1.499000	0.48617	0.650000	0.86243	.	.	.	none		0.408	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836	Intron	T	36692303	G	T	36692303	5	4	28	1	0	0	0	0	0	0	1	0	8102	1014	35	4	1258	4	KCNU1	8	36692303	Splice_Site	SNP	G	TCGA-G8-6914-01A-11D-2210-10	11542691	36692303	109671719	322	11825											
RB1CC1	9821	hgsc.bcm.edu	37	chr8	53558307	53558307	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaacattttgcatttcttcAttctttcttttttcttgctc	5	23	3	10	1	5	0	1	0	4	0	6	1	5	0	0	0	3	2	0	0	1	10	rs34701924	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:53558307A>T	ENST00000025008.5	-	16	4465	c.3942T>A	c.(3940-3942)aaT>aaA	p.N1314K	RB1CC1_ENST00000435644.2_Missense_Mutation_p.N1314K|RB1CC1_ENST00000539297.1_Missense_Mutation_p.N1314K|RB1CC1_ENST00000521611.1_Intron	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	1314			N -> K (in dbSNP:rs34701924).		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)				GCATTTCTTCATTCTTTCTTT	0.343													A|||	22	0.00439297	0.0015	0.0	5008	,	,		16444	0.002		0.0129	False		,,,				2504	0.0051				p.N1314K	GBM(180;1701 2102 13475 42023 52570)	Atlas-SNP	.											.	RB1CC1	163	.	0			c.T3942A						PASS	.	A	LYS/ASN,LYS/ASN	6,4400	12.9+/-30.5	0,6,2197	85	80	82		3942,3942	4.3	1	8	dbSNP_126	82	87,8513	49.8+/-109.6	1,85,4214	yes	missense,missense	RB1CC1	NM_001083617.1,NM_014781.4	94,94	1,91,6411	TT,TA,AA		1.0116,0.1362,0.7151	probably-damaging,probably-damaging	1314/1592,1314/1595	53558307	93,12913	2203	4300	6503	SO:0001583	missense	9821	exon16			TTCTTCATTCTTT	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.3942T>A	8.37:g.53558307A>T	ENSP00000025008:p.Asn1314Lys	63	0	0		88	45	0.511364	NM_001083617	Q86YR4|Q8WVU9|Q92601	Missense_Mutation	SNP	ENST00000025008.5	37	CCDS34892.1	12	0.005494505494505495	1	0.0020325203252032522	0	0.0	2	0.0034965034965034965	9	0.011873350923482849	A	16.47	3.132726	0.56828	0.001362	0.010116	ENSG00000023287	ENST00000025008;ENST00000435644;ENST00000539297	T;T;T	0.16743	2.32;2.32;2.32	5.43	4.26	0.50523	.	0.000000	0.85682	D	0.000000	T	0.18087	0.0434	L	0.36672	1.1	0.58432	D	0.999998	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.994	T	0.08493	-1.0719	10	0.06757	T	0.87	-23.2034	10.0886	0.42434	0.8596:0.0:0.1404:0.0	rs34701924;rs52802517	1314;1314	Q8TDY2-2;Q8TDY2	.;RBCC1_HUMAN	K	1314	ENSP00000025008:N1314K;ENSP00000396067:N1314K;ENSP00000445960:N1314K	ENSP00000025008:N1314K	N	-	3	2	RB1CC1	53720860	0.997000	0.39634	1.000000	0.80357	0.998000	0.95712	0.523000	0.22925	0.896000	0.36366	0.533000	0.62120	AAT	A|0.993;T|0.007	0.007	strong		0.343	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781		T	53558307	A	T	53558307	3	4	28	1	0	0	0	0	1	0	0	0	13114	214	8	5	878	5	RB1CC1	8	53558307	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	16866004	53558307	92805715	323	11826											
RP1	6101	hgsc.bcm.edu	37	chr8	55533805	55533805	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggggcaggcacagcatcacGcgcctggaggagctggagga	9	3	18	11	3	1	0	1	0	0	0	1	4	1	4	1	7	2	4	1	7	0	0	rs144293929	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:55533805G>T	ENST00000220676.1	+	2	427	c.279G>T	c.(277-279)acG>acT	p.T93T		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	93	Doublecortin 1. {ECO:0000255|PROSITE- ProRule:PRU00072}.				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)			ACAGCATCACGCGCCTGGAGG	0.617													G|||	7	0.00139776	0.0008	0.0014	5008	,	,		13894	0.0		0.001	False		,,,				2504	0.0041				p.T93T	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.G279T						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	83	71	75		279	-6.7	0.1	8	dbSNP_134	75	21,8579	15.3+/-51.7	0,21,4279	no	coding-synonymous	RP1	NM_006269.1		0,23,6480	TT,TG,GG		0.2442,0.0454,0.1768		93/2157	55533805	23,12983	2203	4300	6503	SO:0001819	synonymous_variant	6101	exon2			CATCACGCGCCTG	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.279G>T	8.37:g.55533805G>T		56	0	0		43	27	0.627907	NM_006269		Silent	SNP	ENST00000220676.1	37	CCDS6160.1																																																																																			G|0.998;T|0.002	0.002	strong		0.617	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		T	55533805	G	T	55533805	2	4	28	1	0	0	0	0	0	0	0	1	13547	1074	38	4		4	RP1	8	55533805	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1975498	55533805	90830217	324	11827											
UBXN2B	137886	hgsc.bcm.edu	37	chr8	59329407	59329407	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taacaagcctgttattatgtAgttggccttggcagaattgt	10	15	10	6	0	0	1	0	0	0	1	0	1	0	1	2	2	2	4	2	2	6	7			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:59329407A>T	ENST00000399598.2	+	2	206		c.e2-1		UBXN2B_ENST00000522978.1_Splice_Site	NM_001077619.1	NP_001071087.1	Q14CS0	UBX2B_HUMAN	UBX domain protein 2B							endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	13						GTTATTATGTAGTTGGCCTTG	0.378																																					.		Atlas-SNP	.											.	UBXN2B	36	.	0			c.85-2A>T						PASS	.						87	79	81					8																	59329407		1877	4089	5966	SO:0001630	splice_region_variant	137886	exon2			TTATGTAGTTGGC	AK054658	CCDS43741.1	8q12.1	2008-08-08			ENSG00000215114	ENSG00000215114		"UBX domain containing"	27035	protein-coding gene	gene with protein product		610686				8619474, 9110174	Standard	NM_001077619		Approved	p37	uc003xtl.3	Q14CS0	OTTHUMG00000164300	ENST00000399598.2:c.85-1A>T	8.37:g.59329407A>T		54	0	0		33	10	0.30303	NM_001077619	B3KWZ3	Splice_Site	SNP	ENST00000399598.2	37	CCDS43741.1	.	.	.	.	.	.	.	.	.	.	A	16.23	3.063813	0.55432	.	.	ENSG00000215114	ENST00000399598	.	.	.	5.89	5.89	0.94794	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.7027	0.57043	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UBXN2B	59491961	1.000000	0.71417	0.920000	0.36463	0.789000	0.44602	4.736000	0.62059	2.257000	0.74773	0.460000	0.39030	.	.	.	none		0.378	UBXN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378184.1	NM_001077619	Intron	T	59329407	A	T	59329407	5	4	28	1	0	0	0	0	0	0	1	0	16930	434	15	5	89	5	UBXN2B	8	59329407	Splice_Site	SNP	A	TCGA-G8-6914-01A-11D-2210-10	3795602	59329407	87034615	325	11828											
ARFGEF1	10565	hgsc.bcm.edu	37	chr8	68130065	68130065	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccagtgtgcagttgcaagttTtatcccagatttctagggta	9	14	10	8	0	1	1	0	0	1	1	2	1	2	1	2	1	2	5	2	1	4	6	rs200528352		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:68130065T>C	ENST00000262215.3	-	32	4954	c.4565A>G	c.(4564-4566)aAa>aGa	p.K1522R	ARFGEF1_ENST00000518230.1_Missense_Mutation_p.K360R|ARFGEF1_ENST00000520381.1_Missense_Mutation_p.K976R	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	1522					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)			GTTGCAAGTTTTATCCCAGAT	0.343																																					p.K1522R		Atlas-SNP	.											.	ARFGEF1	196	.	0			c.A4565G						PASS	.						105	104	104					8																	68130065		2203	4300	6503	SO:0001583	missense	10565	exon32			CAAGTTTTATCCC	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.4565A>G	8.37:g.68130065T>C	ENSP00000262215:p.Lys1522Arg	114	0	0		133	65	0.488722	NM_006421	Q9NV46|Q9UFV2|Q9UNL0	Missense_Mutation	SNP	ENST00000262215.3	37	CCDS6199.1	.	.	.	.	.	.	.	.	.	.	T	17.24	3.339243	0.60963	.	.	ENSG00000066777	ENST00000520381;ENST00000262215;ENST00000518230	T;T;T	0.48522	0.81;0.81;0.81	5.48	5.48	0.80851	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.41558	0.1164	L	0.40543	1.245	0.58432	D	0.999994	B;B;B	0.19706	0.038;0.002;0.002	B;B;B	0.18561	0.022;0.003;0.003	T	0.19712	-1.0297	10	0.35671	T	0.21	.	15.8539	0.78960	0.0:0.0:0.0:1.0	.	1522;1000;976	Q9Y6D6;Q59FY5;E5RIF2	BIG1_HUMAN;.;.	R	976;1522;360	ENSP00000428429:K976R;ENSP00000262215:K1522R;ENSP00000430891:K360R	ENSP00000262215:K1522R	K	-	2	0	ARFGEF1	68292619	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.153000	0.71819	2.199000	0.70637	0.533000	0.62120	AAA	.	.	weak		0.343	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421		C	68130065	T	C	68130065	3	2	28	1	0	0	0	0	1	0	0	0	852	1841	64	3	1016	3	ARFGEF1	8	68130065	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	8800658	68130065	78233957	326	11829											
CSMD3	114788	hgsc.bcm.edu	37	chr8	113349030	113349030	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagaataaatggtgccattCattgcagttatattcccacc	12	12	8	9	0	1	1	1	0	0	1	2	2	2	1	3	2	2	2	3	2	5	6			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:113349030C>A	ENST00000297405.5	-	44	7114	c.6870G>T	c.(6868-6870)atG>atT	p.M2290I	CSMD3_ENST00000352409.3_Missense_Mutation_p.M2220I|CSMD3_ENST00000343508.3_Missense_Mutation_p.M2250I|CSMD3_ENST00000455883.2_Missense_Mutation_p.M2186I	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2290	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						TGGTGCCATTCATTGCAGTTA	0.363										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.M2290I		Atlas-SNP	.											.	CSMD3	2325	.	0			c.G6870T						PASS	.						79	73	75					8																	113349030		2203	4300	6503	SO:0001583	missense	114788	exon44			GCCATTCATTGCA	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.6870G>T	8.37:g.113349030C>A	ENSP00000297405:p.Met2290Ile	61	0	0		60	10	0.166667	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	13.24	2.177692	0.38413	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.17691	2.26;2.26;2.26;2.26;2.26	5.64	5.64	0.86602	CUB (5);	0.057323	0.64402	D	0.000003	T	0.25121	0.0610	L	0.39326	1.205	0.45097	D	0.998113	B;B;P	0.37688	0.171;0.257;0.605	B;B;P	0.46076	0.193;0.216;0.503	T	0.00417	-1.1752	10	0.30078	T	0.28	.	19.8946	0.96949	0.0:1.0:0.0:0.0	.	2186;2290;2250	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	I	2250;2290;1560;2186;2220	ENSP00000345799:M2250I;ENSP00000297405:M2290I;ENSP00000341558:M1560I;ENSP00000412263:M2186I;ENSP00000343124:M2220I	ENSP00000297405:M2290I	M	-	3	0	CSMD3	113418206	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.429000	0.44758	2.937000	0.99478	0.650000	0.86243	ATG	.	.	none		0.363	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113349030	C	A	113349030	3	1	28	1	0	0	0	0	1	0	0	0	3948	826	29	4	4365	4	CSMD3	8	113349030	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	45218965	113349030	33014992	327	11830											
ZHX2	22882	hgsc.bcm.edu	37	chr8	123964819	123964819	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cccagttggcccccacaaagGtgacgcagcccatcctccag	9	5	9	18	1	0	1	0	1	0	0	2	1	2	1	6	2	1	2	6	2	1	1	rs9649951	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:123964819G>A	ENST00000314393.4	+	3	1904	c.1069G>A	c.(1069-1071)Gtg>Atg	p.V357M		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	357	Required for homodimerization.|Required for interaction with NFYA.|Required for nuclear localization.|Required for repressor activity.		V -> M (in dbSNP:rs9649951).		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)			CCCCACAAAGGTGACGCAGCC	0.617													G|||	50	0.00998403	0.0015	0.0144	5008	,	,		17314	0.001		0.0258	False		,,,				2504	0.0112				p.V357M	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											.	ZHX2	106	.	0			c.G1069A						PASS	.	G	MET/VAL	41,4365	45.3+/-79.5	0,41,2162	77	64	69		1069	1.4	0.4	8	dbSNP_119	69	373,8227	123.1+/-182.0	6,361,3933	yes	missense	ZHX2	NM_014943.3	21	6,402,6095	AA,AG,GG		4.3372,0.9305,3.1831	benign	357/838	123964819	414,12592	2203	4300	6503	SO:0001583	missense	22882	exon3			ACAAAGGTGACGC	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.1069G>A	8.37:g.123964819G>A	ENSP00000314709:p.Val357Met	69	0	0		83	36	0.433735	NM_014943		Missense_Mutation	SNP	ENST00000314393.4	37	CCDS6336.1	29	0.013278388278388278	1	0.0020325203252032522	10	0.027624309392265192	1	0.0017482517482517483	17	0.022427440633245383	G	6.657	0.489767	0.12702	0.009305	0.043372	ENSG00000178764	ENST00000314393	T	0.17370	2.28	5.62	1.42	0.22433	.	0.551628	0.20995	N	0.081968	T	0.02119	0.0066	N	0.22421	0.69	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.24404	-1.0161	10	0.40728	T	0.16	-6.6533	8.5687	0.33556	0.636:0.0:0.364:0.0	rs9649951;rs9649951	357	Q9Y6X8	ZHX2_HUMAN	M	357	ENSP00000314709:V357M	ENSP00000314709:V357M	V	+	1	0	ZHX2	124034000	1.000000	0.71417	0.392000	0.26245	0.782000	0.44232	1.466000	0.35310	0.008000	0.14787	-0.361000	0.07541	GTG	G|0.974;A|0.026	0.026	strong		0.617	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943		A	123964819	G	A	123964819	3	1	28	1	0	0	0	0	1	0	0	0	17691	1261	44	2	1071	2	ZHX2	8	123964819	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	10615789	123964819	22399203	328	11831											
COL22A1	169044	hgsc.bcm.edu	37	chr8	139609156	139609156	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagatactcactttcaagctGcttccccagctcttcttgaa	9	13	5	14	0	4	2	2	1	2	1	5	2	5	2	2	0	4	3	2	0	3	5			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:139609156G>A	ENST00000303045.6	-	62	4869	c.4423C>T	c.(4423-4425)Cag>Tag	p.Q1475*	COL22A1_ENST00000435777.1_Nonsense_Mutation_p.Q1455*|COL22A1_ENST00000341807.4_5'UTR	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1475	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)		p.Q1475K(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)			CTTTCAAGCTGCTTCCCCAGC	0.507										HNSCC(7;0.00092)																											p.Q1475X		Atlas-SNP	.											COL22A1,NS,carcinoma,0,1	COL22A1	390	1	1	Substitution - Missense(1)	lung(1)	c.C4423T						PASS	.						182	182	182					8																	139609156		2203	4300	6503	SO:0001587	stop_gained	169044	exon62			CAAGCTGCTTCCC	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.4423C>T	8.37:g.139609156G>A	ENSP00000303153:p.Gln1475*	113	0	0		92	20	0.217391	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Nonsense_Mutation	SNP	ENST00000303045.6	37	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	G	47	13.734218	0.99760	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	.	.	.	5.06	5.06	0.68205	.	0.000000	0.44688	U	0.000425	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	.	17.4049	0.87470	0.0:0.0:1.0:0.0	.	.	.	.	X	1475;1455;1168	.	ENSP00000303153:Q1475X	Q	-	1	0	COL22A1	139678338	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	8.323000	0.90002	2.349000	0.79799	0.563000	0.77884	CAG	.	.	none		0.507	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257		A	139609156	G	A	139609156	4	1	28	1	0	0	0	0	0	1	0	0	3683	1328	46	2	473	2	COL22A1	8	139609156	Nonsense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	15644337	139609156	6754866	329	11832											
TRAPPC9	83696	hgsc.bcm.edu	37	chr8	141461017	141461017	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agcacgatgaacagtgactcGatgaagtcctcgattctctt	11	11	9	10	3	1	3	0	3	1	0	5	6	2	3	1	0	2	1	1	0	2	2	rs61740786	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:141461017G>A	ENST00000438773.2	-	2	589	c.456C>T	c.(454-456)atC>atT	p.I152I	TRAPPC9_ENST00000389327.3_Silent_p.I152I|TRAPPC9_ENST00000389328.4_Silent_p.I250I	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	152					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						ACAGTGACTCGATGAAGTCCT	0.572													G|||	26	0.00519169	0.0015	0.0101	5008	,	,		19773	0.0		0.0169	False		,,,				2504	0.0				p.I250I		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.C750T						PASS	.	G	,	14,4392	21.2+/-45.6	0,14,2189	66	56	59		456,750	-2.4	1	8	dbSNP_129	59	130,8470	66.3+/-128.7	1,128,4171	no	coding-synonymous,coding-synonymous	TRAPPC9	NM_001160372.1,NM_031466.5	,	1,142,6360	AA,AG,GG		1.5116,0.3177,1.1072	,	152/1149,250/1247	141461017	144,12862	2203	4300	6503	SO:0001819	synonymous_variant	83696	exon2			TGACTCGATGAAG	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.456C>T	8.37:g.141461017G>A		45	0	0		51	27	0.529412	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Silent	SNP	ENST00000438773.2	37	CCDS55278.1	21	0.009615384615384616	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	13	0.017150395778364115	G	8.082	0.772536	0.16051	0.003177	0.015116	ENSG00000167632	ENST00000520857	.	.	.	5.61	-2.44	0.06502	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.0785	0.36536	0.538:0.1001:0.3619:0.0	.	.	.	.	X	5	.	.	R	-	1	2	TRAPPC9	141530199	0.083000	0.21467	0.973000	0.42090	0.755000	0.42902	-0.396000	0.07278	-0.397000	0.07691	-0.812000	0.03155	CGA	G|0.989;A|0.011	0.011	strong		0.572	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466		A	141461017	G	A	141461017	2	1	28	1	0	0	0	0	0	0	0	1	16480	1048	37	1		1	TRAPPC9	8	141461017	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1851861	141461017	4903005	330	11833											
PTK2	5747	hgsc.bcm.edu	37	chr8	141840574	141840574	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaggagactctaattaccttGacagaatccagtaaactctt	15	11	6	9	0	2	3	0	1	2	2	3	4	3	3	2	1	2	1	2	1	6	5	rs148611560	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:141840574G>A	ENST00000522684.1	-	8	874	c.645C>T	c.(643-645)gtC>gtT	p.V215V	PTK2_ENST00000519419.1_Silent_p.V259V|PTK2_ENST00000340930.3_Silent_p.V215V|PTK2_ENST00000535192.1_Silent_p.V215V|PTK2_ENST00000521059.1_Silent_p.V215V|PTK2_ENST00000395218.2_Silent_p.V215V|PTK2_ENST00000517887.1_Silent_p.V259V	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	215	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)			TAATTACCTTGACAGAATCCA	0.303													G|||	4	0.000798722	0.0	0.0029	5008	,	,		15534	0.0		0.002	False		,,,				2504	0.0				p.V237V		Atlas-SNP	.											.	PTK2	311	.	0			c.C711T						PASS	.	G	,,	3,4361		0,3,2179	30	31	30		645,711,645	5.2	1	8	dbSNP_134	30	18,8528		0,18,4255	no	coding-synonymous,coding-synonymous,coding-synonymous	PTK2	NM_001199649.1,NM_005607.4,NM_153831.3	,,	0,21,6434	AA,AG,GG		0.2106,0.0687,0.1627	,,	215/1066,237/1075,215/1053	141840574	21,12889	2182	4273	6455	SO:0001819	synonymous_variant	5747	exon8			TACCTTGACAGAA	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.645C>T	8.37:g.141840574G>A		160	0	0		165	82	0.49697	NM_005607	B4E2N6|F5H4S4|Q14291|Q9UD85	Silent	SNP	ENST00000522684.1	37	CCDS6381.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	9.907	1.208441	0.22205	6.87E-4	0.002106	ENSG00000169398	ENST00000519654	.	.	.	5.25	5.25	0.73442	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4863	0.55874	0.0:0.1681:0.8319:0.0	.	.	.	.	X	226	.	.	Q	-	1	0	PTK2	141909756	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.739000	0.38217	2.618000	0.88619	0.655000	0.94253	CAA	G|0.998;A|0.002	0.002	strong		0.303	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607		A	141840574	G	A	141840574	2	1	28	1	0	0	0	0	0	0	0	1	12775	1277	45	2		2	PTK2	8	141840574	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	379557	141840574	4523448	331	11834											
FAM83H	286077	hgsc.bcm.edu	37	chr8	144810346	144810346	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gaggaacgtctgccgcgacaCctgccgcgcggccgcgaagt	7	4	15	15	8	1	0	0	0	1	0	1	4	1	1	4	2	3	0	4	2	2	0	rs144418186	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:144810346C>A	ENST00000388913.3	-	5	1410	c.1285G>T	c.(1285-1287)Gtg>Ttg	p.V429L		NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	429					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)			TGCCGCGACACCTGCCGCGCG	0.682													C|||	21	0.00419329	0.0	0.013	5008	,	,		6410	0.0		0.008	False		,,,				2504	0.0041				p.V429L		Atlas-SNP	.											.	FAM83H	68	.	0			c.G1285T						PASS	.	C	LEU/VAL	8,4120		0,8,2056	15	24	21		1285	4	1	8	dbSNP_134	21	137,8219		2,133,4043	yes	missense	FAM83H	NM_198488.3	32	2,141,6099	AA,AC,CC		1.6395,0.1938,1.1615	possibly-damaging	429/1180	144810346	145,12339	2064	4178	6242	SO:0001583	missense	286077	exon5			GCGACACCTGCCG	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.1285G>T	8.37:g.144810346C>A	ENSP00000373565:p.Val429Leu	11	0	0		24	13	0.541667	NM_198488	A0JLS2|Q8N4W0	Missense_Mutation	SNP	ENST00000388913.3	37	CCDS6410.2	9	0.004120879120879121	0	0.0	3	0.008287292817679558	0	0.0	6	0.0079155672823219	c	8.338	0.828008	0.16749	0.001938	0.016395	ENSG00000180921	ENST00000388913	T	0.15017	2.46	4.96	4.02	0.46733	.	0.947136	0.08665	N	0.911838	T	0.05731	0.0150	L	0.27053	0.805	0.25299	N	0.9893	B	0.31581	0.329	B	0.25987	0.065	T	0.11372	-1.0590	10	0.21014	T	0.42	.	10.4754	0.44661	0.361:0.639:0.0:0.0	.	429	Q6ZRV2	FA83H_HUMAN	L	429	ENSP00000373565:V429L	ENSP00000373565:V429L	V	-	1	0	FAM83H	144882334	0.976000	0.34144	0.995000	0.50966	0.035000	0.12851	2.070000	0.41491	2.277000	0.76020	0.555000	0.69702	GTG	C|0.991;A|0.009	0.009	strong		0.682	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488		A	144810346	C	A	144810346	3	1	28	1	0	0	0	0	1	0	0	0	5648	507	18	4	2258	4	FAM83H	8	144810346	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2969772	144810346	1553676	332	11835											
CPSF1	29894	hgsc.bcm.edu	37	chr8	145634452	145634452	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctgcgaggtcccggccactaCcaggttgcgctcgctgttgt	4	10	13	14	4	0	0	0	0	0	0	2	1	1	0	3	3	3	4	3	3	1	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:145634452C>T	ENST00000349769.3	-	2	185	c.91G>A	c.(91-93)Gta>Ata	p.V31I	GS1-393G12.14_ENST00000607491.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	31					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)			CCGGCCACTACCAGGTTGCGC	0.652																																					p.V31I	NSCLC(133;1088 1848 27708 34777 35269)	Atlas-SNP	.											.	CPSF1	92	.	0			c.G91A						PASS	.						132	126	128					8																	145634452		2203	4300	6503	SO:0001583	missense	29894	exon2			CCACTACCAGGTT	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.91G>A	8.37:g.145634452C>T	ENSP00000339353:p.Val31Ile	92	0	0		107	51	0.476636	NM_013291	Q96AF0	Missense_Mutation	SNP	ENST00000349769.3	37	CCDS34966.1	.	.	.	.	.	.	.	.	.	.	C	37	6.015090	0.97205	.	.	ENSG00000071894	ENST00000349769;ENST00000531042	T	0.55760	0.5	5.18	5.18	0.71444	.	0.000000	0.64402	D	0.000003	T	0.60856	0.2301	L	0.57536	1.79	0.80722	D	1	P;P	0.47545	0.675;0.897	B;P	0.51945	0.254;0.685	T	0.57894	-0.7732	10	0.31617	T	0.26	-0.1634	16.1609	0.81704	0.0:1.0:0.0:0.0	.	31;31	B4DEF4;Q10570	.;CPSF1_HUMAN	I	31	ENSP00000339353:V31I	ENSP00000339353:V31I	V	-	1	0	CPSF1	145605260	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.070000	0.76763	2.415000	0.81967	0.561000	0.74099	GTA	.	.	none		0.652	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291		T	145634452	C	T	145634452	3	4	28	1	0	0	0	0	1	0	0	0	3826	507	18	2	4388	2	CPSF1	8	145634452	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	824106	145634452	729570	333	11836											
KANK1	23189	hgsc.bcm.edu	37	chr9	712052	712052	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaggatgcagctgtagggaCacttgttgagatgagaaatt	13	11	13	4	0	0	2	0	2	0	2	0	6	0	4	0	2	2	4	0	2	3	5			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:712052C>T	ENST00000382303.1	+	7	1938	c.1286C>T	c.(1285-1287)aCa>aTa	p.T429I	KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382297.2_Missense_Mutation_p.T429I|KANK1_ENST00000382293.3_Missense_Mutation_p.T271I	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	429	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)		GCTGTAGGGACACTTGTTGAG	0.532																																					p.T429I		Atlas-SNP	.											.	KANK1	231	.	0			c.C1286T						PASS	.						118	101	107					9																	712052		2203	4300	6503	SO:0001583	missense	23189	exon7			TAGGGACACTTGT	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.1286C>T	9.37:g.712052C>T	ENSP00000371740:p.Thr429Ile	105	0	0		92	44	0.478261	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	37	CCDS34976.1	.	.	.	.	.	.	.	.	.	.	C	12.68	2.010448	0.35511	.	.	ENSG00000107104	ENST00000382303;ENST00000354485;ENST00000382297;ENST00000382293	T;T;T	0.43294	0.95;0.95;0.96	5.73	3.89	0.44902	.	0.112785	0.40728	N	0.001035	T	0.56277	0.1974	M	0.74258	2.255	0.80722	D	1	P;P	0.51147	0.942;0.865	P;P	0.56563	0.801;0.71	T	0.55976	-0.8055	10	0.44086	T	0.13	-15.3443	11.3529	0.49598	0.0:0.8043:0.127:0.0687	.	429;429	Q5W0W1;Q14678	.;KANK1_HUMAN	I	429;429;429;271	ENSP00000371740:T429I;ENSP00000371734:T429I;ENSP00000371730:T271I	ENSP00000346479:T429I	T	+	2	0	KANK1	702052	0.995000	0.38212	0.133000	0.22050	0.124000	0.20399	3.732000	0.55021	0.781000	0.33589	0.655000	0.94253	ACA	.	.	none		0.532	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158		T	712052	C	T	712052	3	4	28	1	0	0	0	0	1	0	0	0	7985	478	17	2	1292	2	KANK1	9	712052	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10		712052	140501379	334	11837											
JAK2	3717	hgsc.bcm.edu	37	chr9	5050706	5050706	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcggcatgattttgtgcaCggatggataaaagtacctgt	10	12	13	6	2	0	1	0	1	0	0	0	3	0	3	1	4	2	3	1	4	3	4	rs2230722	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:5050706C>T	ENST00000381652.3	+	6	983	c.489C>T	c.(487-489)caC>caT	p.H163H	JAK2_ENST00000544510.1_Silent_p.H14H|JAK2_ENST00000539801.1_Silent_p.H163H	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	163	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)	ATTTTGTGCACGGATGGATAA	0.343		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial				T|||	1794	0.358227	0.4887	0.3905	5008	,	,		15245	0.2708		0.3002	False		,,,				2504	0.3088				p.H163H		Atlas-SNP	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	35466	.	0			c.C489T						PASS	.	T		2047,2359	609.9+/-391.4	488,1071,644	110	123	118		489	-0.9	0.9	9	dbSNP_119	118	2589,6011	689.4+/-404.4	366,1857,2077	no	coding-synonymous	JAK2	NM_004972.3		854,2928,2721	TT,TC,CC		30.1047,46.4594,35.6451		163/1133	5050706	4636,8370	2203	4300	6503	SO:0001819	synonymous_variant	3717	exon6	Familial Cancer Database		TGTGCACGGATGG		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.489C>T	9.37:g.5050706C>T		64	0	0		64	34	0.53125	NM_004972	O14636|O75297	Silent	SNP	ENST00000381652.3	37	CCDS6457.1																																																																																			C|0.647;T|0.353	0.353	strong		0.343	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			T	5050706	C	T	5050706	2	4	28	1	0	0	0	0	0	0	0	1	7947	535	19	1		1	JAK2	9	5050706	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	4338654	5050706	136162725	335	11838											
JAK2	3717	hgsc.bcm.edu	37	chr9	5081780	5081780	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aatatgaggataggtgccctGgggttttctggtgcctttga	7	14	14	6	0	1	2	0	2	1	0	1	3	1	3	2	5	2	1	2	5	3	5	rs2230724	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:5081780G>A	ENST00000381652.3	+	19	2984	c.2490G>A	c.(2488-2490)ctG>ctA	p.L830L	JAK2_ENST00000544510.1_Silent_p.L681L|JAK2_ENST00000539801.1_Silent_p.L830L|AL161450.1_ENST00000601793.1_Intron	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	830					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)	TAGGTGCCCTGGGGTTTTCTG	0.348		1	"T, Mis, O"	"ETV6, PCM1, BCR"	"ALL, AML, MPD,  CML"				Polycythemia Vera, Familial				A|||	3089	0.616813	0.9312	0.5879	5008	,	,		17517	0.4395		0.5239	False		,,,				2504	0.4908				p.L830L		Atlas-SNP	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	35466	.	0			c.G2490A						PASS	.	A		3825,581	258.0+/-262.2	1671,483,49	109	110	110		2490	-3	0.1	9	dbSNP_98	110	4294,4306	577.7+/-390.6	1073,2148,1079	no	coding-synonymous	JAK2	NM_004972.3		2744,2631,1128	AA,AG,GG		49.9302,13.1866,37.575		830/1133	5081780	8119,4887	2203	4300	6503	SO:0001819	synonymous_variant	3717	exon19	Familial Cancer Database		TGCCCTGGGGTTT		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.2490G>A	9.37:g.5081780G>A		75	0	0		103	40	0.38835	NM_004972	O14636|O75297	Silent	SNP	ENST00000381652.3	37	CCDS6457.1																																																																																			G|0.386;A|0.614	0.614	strong		0.348	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1			A	5081780	G	A	5081780	2	1	28	1	0	0	0	0	0	0	0	1	7947	1335	47	2		2	JAK2	9	5081780	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	31074	5081780	136131651	336	11839											
IL33	90865	hgsc.bcm.edu	37	chr9	6254467	6254467	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttcttaattgtaaggtgacGgtgttgatggtaagatgtta	10	17	12	2	1	1	3	0	2	1	1	1	3	1	3	0	3	0	4	0	3	4	7	rs148943384		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:6254467G>A	ENST00000381434.3	+	6	539	c.526G>A	c.(526-528)Ggt>Agt	p.G176S	IL33_ENST00000417746.2_Missense_Mutation_p.G50S|IL33_ENST00000456383.2_Missense_Mutation_p.G134S	NM_033439.3	NP_254274.1	O95760	IL33_HUMAN	interleukin 33	176					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)		GTAAGGTGACGGTGTTGATGG	0.333																																					p.G176S		Atlas-SNP	.											.	IL33	27	.	0			c.G526A						PASS	.	G	SER/GLY,SER/GLY,SER/GLY	0,4406		0,0,2203	73	69	71		400,148,526	1.6	0	9	dbSNP_134	71	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	IL33	NM_001199640.1,NM_001199641.1,NM_033439.3	56,56,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	134/229,50/145,176/271	6254467	1,13005	2203	4300	6503	SO:0001583	missense	90865	exon7			GGTGACGGTGTTG	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.526G>A	9.37:g.6254467G>A	ENSP00000370842:p.Gly176Ser	73	0	0		89	4	0.0449438	NM_033439	B2R8L1|B4DJ35|B4E1Q9|D3DRI5|E7EAX4|Q2YEJ5	Missense_Mutation	SNP	ENST00000381434.3	37	CCDS6468.1	.	.	.	.	.	.	.	.	.	.	G	15.73	2.919265	0.52546	0.0	1.16E-4	ENSG00000137033	ENST00000417746;ENST00000456383;ENST00000381434	T;T;T	0.51817	0.69;0.69;0.69	4.47	1.57	0.23409	.	2.047450	0.01906	N	0.039500	T	0.35653	0.0939	L	0.29908	0.895	0.80722	D	1	B;B;B	0.26602	0.06;0.154;0.06	B;B;B	0.13407	0.005;0.009;0.009	T	0.33727	-0.9857	10	0.72032	D	0.01	0.2295	3.6079	0.08049	0.2088:0.0:0.5934:0.1978	.	50;134;176	B4DJ35;B4E1Q9;O95760	.;.;IL33_HUMAN	S	50;134;176	ENSP00000394039:G50S;ENSP00000414238:G134S;ENSP00000370842:G176S	ENSP00000370842:G176S	G	+	1	0	IL33	6244467	0.020000	0.18652	0.000000	0.03702	0.032000	0.12392	0.634000	0.24614	0.227000	0.20999	0.655000	0.94253	GGT	G|1.000;A|0.000	0.000	weak		0.333	IL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051655.1	NM_033439		A	6254467	G	A	6254467	3	1	28	1	0	0	0	0	1	0	0	0	7702	1116	39	1	548	1	IL33	9	6254467	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1172687	6254467	134958964	337	11840											
KDM4C	23081	hgsc.bcm.edu	37	chr9	7011719	7011719	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attgcctgaggttctgtccaTtgaggaggaagtggaagaaa	12	10	14	5	0	1	3	0	2	1	1	2	6	2	6	2	4	1	1	2	4	3	3	rs34369202		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:7011719T>C	ENST00000381309.3	+	13	2373	c.1808T>C	c.(1807-1809)aTt>aCt	p.I603T	KDM4C_ENST00000428870.2_Missense_Mutation_p.I290T|KDM4C_ENST00000543771.1_Missense_Mutation_p.I603T|KDM4C_ENST00000442236.2_Missense_Mutation_p.I348T|KDM4C_ENST00000381306.3_Missense_Mutation_p.I603T|KDM4C_ENST00000536108.1_Missense_Mutation_p.I422T|KDM4C_ENST00000535193.1_Missense_Mutation_p.I625T	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	603					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						GTTCTGTCCATTGAGGAGGAA	0.463													T|||	1	0.000199681	0.0	0.0	5008	,	,		21962	0.0		0.0	False		,,,				2504	0.001				p.I625T		Atlas-SNP	.											.	KDM4C	186	.	0			c.T1874C						PASS	.	T	THR/ILE,THR/ILE,THR/ILE,THR/ILE	0,4406		0,0,2203	99	97	98		1808,1808,1874,1808	0.8	0	9	dbSNP_126	98	10,8590	7.7+/-29.5	0,10,4290	yes	missense,missense,missense,missense	KDM4C	NM_001146694.1,NM_001146695.1,NM_001146696.1,NM_015061.3	89,89,89,89	0,10,6493	CC,CT,TT		0.1163,0.0,0.0769	benign,benign,benign,benign	603/1048,603/814,625/836,603/1057	7011719	10,12996	2203	4300	6503	SO:0001583	missense	23081	exon13			TGTCCATTGAGGA	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.1808T>C	9.37:g.7011719T>C	ENSP00000370710:p.Ile603Thr	109	0	0		101	39	0.386139	NM_001146696	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	37	CCDS6471.1	.	.	.	.	.	.	.	.	.	.	T	1.169	-0.641475	0.03531	0.0	0.001163	ENSG00000107077	ENST00000535193;ENST00000543771;ENST00000381309;ENST00000381306;ENST00000442236;ENST00000536108;ENST00000428870	T;T;T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58;0.58;0.58	5.76	0.841	0.18918	.	0.988395	0.08268	N	0.971876	T	0.40791	0.1131	L	0.47716	1.5	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	0.08055	0.001;0.003;0.002;0.001;0.001	T	0.27468	-1.0073	10	0.20046	T	0.44	.	5.1095	0.14802	0.1283:0.3276:0.0:0.544	rs34369202	348;603;625;603;603	E7EV17;F5H347;F5H7P0;Q9H3R0;Q9H3R0-2	.;.;.;KDM4C_HUMAN;.	T	625;603;603;603;348;422;290	ENSP00000442382:I625T;ENSP00000445427:I603T;ENSP00000370710:I603T;ENSP00000370707:I603T;ENSP00000409353:I348T;ENSP00000440656:I422T;ENSP00000405739:I290T	ENSP00000370707:I603T	I	+	2	0	KDM4C	7001719	0.000000	0.05858	0.027000	0.17364	0.458000	0.32498	0.834000	0.27518	-0.091000	0.12440	-0.333000	0.08304	ATT	T|0.999;C|0.001	0.001	strong		0.463	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061		C	7011719	T	C	7011719	3	2	28	1	0	0	0	0	1	0	0	0	8139	1493	52	3	1924	3	KDM4C	9	7011719	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	757252	7011719	134201712	338	11841											
BNC2	54796	hgsc.bcm.edu	37	chr9	16419519	16419519	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cgagccccatggggtgctggGcaccatatatcttcaccaaa	10	8	10	13	1	2	0	1	0	1	0	2	1	2	0	4	3	2	2	4	3	3	3	rs117452684	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:16419519G>A	ENST00000380672.4	-	7	2825	c.2768C>T	c.(2767-2769)gCc>gTc	p.A923V	BNC2_ENST00000545497.1_Missense_Mutation_p.A828V|BNC2_ENST00000380667.2_Missense_Mutation_p.A856V	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)		GGGGTGCTGGGCACCATATAT	0.572													G|||	45	0.00898562	0.0008	0.0086	5008	,	,		16876	0.0		0.0288	False		,,,				2504	0.0092				p.A923V		Atlas-SNP	.											.	BNC2	166	.	0			c.C2768T						PASS	.	G	VAL/ALA	30,4376	36.0+/-67.5	0,30,2173	83	87	86		2768	5.5	1	9	dbSNP_132	86	293,8307	107.0+/-167.8	3,287,4010	yes	missense	BNC2	NM_017637.5	64	3,317,6183	AA,AG,GG		3.407,0.6809,2.4835	benign	923/1100	16419519	323,12683	2203	4300	6503	SO:0001583	missense	54796	exon7			TGCTGGGCACCAT	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.2768C>T	9.37:g.16419519G>A	ENSP00000370047:p.Ala923Val	71	0	0		77	38	0.493506	NM_017637		Missense_Mutation	SNP	ENST00000380672.4	37	CCDS6482.2	26	0.011904761904761904	0	0.0	3	0.008287292817679558	0	0.0	23	0.030343007915567283	G	13.60	2.286262	0.40494	0.006809	0.03407	ENSG00000173068	ENST00000380672;ENST00000380667;ENST00000545497	T;T;T	0.31510	1.49;1.5;1.5	5.5	5.5	0.81552	.	0.166180	0.51477	D	0.000083	T	0.07954	0.0199	N	0.22421	0.69	0.80722	D	1	P;P;B	0.41673	0.578;0.759;0.18	B;B;B	0.39027	0.158;0.288;0.051	T	0.01844	-1.1262	10	0.27082	T	0.32	-9.5452	14.94	0.70986	0.0:0.1426:0.8574:0.0	.	828;923;688	F5H586;Q6ZN30;D3DRJ1	.;BNC2_HUMAN;.	V	923;856;828	ENSP00000370047:A923V;ENSP00000370042:A856V;ENSP00000444640:A828V	ENSP00000370042:A856V	A	-	2	0	BNC2	16409519	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.336000	0.52113	2.586000	0.87340	0.591000	0.81541	GCC	G|0.979;A|0.021	0.021	strong		0.572	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637		A	16419519	G	A	16419519	3	1	28	1	0	0	0	0	1	0	0	0	1475	1203	42	2	535	2	BNC2	9	16419519	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	9407800	16419519	124793912	339	11842											
DENND4C	55667	hgsc.bcm.edu	37	chr9	19352096	19352096	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gttccatttccaagaggcatGaaagggcaagactttgaaaa	15	9	10	7	0	0	4	0	2	0	2	2	4	2	4	2	2	0	3	2	2	5	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:19352096G>A	ENST00000380432.2	+	20	3699	c.3666G>A	c.(3664-3666)atG>atA	p.M1222I	DENND4C_ENST00000434457.2_Missense_Mutation_p.M1507I|DENND4C_ENST00000602925.1_Missense_Mutation_p.M1458I			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	1222					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						CAAGAGGCATGAAAGGGCAAG	0.348																																					p.M1458I		Atlas-SNP	.											.	DENND4C	120	.	0			c.G4374A						PASS	.						148	138	141					9																	19352096		2203	4300	6503	SO:0001583	missense	55667	exon24			AGGCATGAAAGGG	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.3666G>A	9.37:g.19352096G>A	ENSP00000369797:p.Met1222Ile	79	0	0		94	19	0.202128	NM_017925	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	37		.	.	.	.	.	.	.	.	.	.	G	5.514	0.279774	0.10458	.	.	ENSG00000137145	ENST00000380437;ENST00000307015;ENST00000453857;ENST00000540671;ENST00000380432;ENST00000380427;ENST00000361024;ENST00000380424	T;T	0.20881	2.05;2.04	5.27	-2.51	0.06365	.	1.303380	0.04496	N	0.380371	T	0.09818	0.0241	N	0.11560	0.145	0.28170	N	0.928596	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	0.28902	-1.0029	10	0.34782	T	0.22	-0.4352	2.7946	0.05397	0.1982:0.2628:0.4155:0.1235	.	552;1222;404;1222	B7Z660;Q5VZ89-5;Q5VZ89-3;Q5VZ89	.;.;.;DEN4C_HUMAN	I	1222;695;404;552;695;404;219;93	ENSP00000305795:M695I;ENSP00000443804:M552I	ENSP00000305795:M695I	M	+	3	0	DENND4C	19342096	0.685000	0.27652	0.809000	0.32408	0.994000	0.84299	0.215000	0.17562	-0.207000	0.10187	0.655000	0.94253	ATG	.	.	none		0.348	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925		A	19352096	G	A	19352096	3	1	28	1	0	0	0	0	1	0	0	0	4437	1290	45	2	3744	2	DENND4C	9	19352096	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2932577	19352096	121861335	340	11843											
ACO1	48	hgsc.bcm.edu	37	chr9	32433803	32433803	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aattccaaatctacgtatatCaaatcaccaccattctttga	15	13	2	11	1	4	1	2	1	2	0	5	1	5	1	3	0	1	1	3	0	6	6	rs61752944	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:32433803C>A	ENST00000309951.6	+	16	2067	c.1929C>A	c.(1927-1929)atC>atA	p.I643I	ACO1_ENST00000379923.1_Silent_p.I643I|ACO1_ENST00000541043.1_Silent_p.I544I	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	643					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)		CTACGTATATCAAATCACCAC	0.328													C|||	2	0.000399361	0.0	0.0	5008	,	,		17515	0.0		0.002	False		,,,				2504	0.0				p.I643I		Atlas-SNP	.											.	ACO1	149	.	0			c.C1929A						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	107	107	107		1929	1.2	0.8	9	dbSNP_129	107	15,8585	11.2+/-40.8	0,15,4285	no	coding-synonymous	ACO1	NM_002197.2		0,17,6486	AA,AC,CC		0.1744,0.0454,0.1307		643/890	32433803	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	48	exon16			GTATATCAAATCA	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.1929C>A	9.37:g.32433803C>A		68	0	0		61	26	0.42623	NM_002197	D3DRK7|Q14652|Q5VZA7	Silent	SNP	ENST00000309951.6	37	CCDS6525.1																																																																																			C|0.999;A|0.001	0.001	strong		0.328	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3	NM_002197		A	32433803	C	A	32433803	2	1	28	1	0	0	0	0	0	0	0	1	146	816	29	4		4	ACO1	9	32433803	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	13081707	32433803	108779628	341	11844											
DDX58	23586	hgsc.bcm.edu	37	chr9	32457307	32457308	+	Frame_Shift_Ins	INS	-	-	AGAA																															gctgcagttctgtcgggcacINSagaatatctttgctcttttt																								rs573952640	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:32457307_32457308insAGAA	ENST00000379883.2	-	18	2747_2748	c.2590_2591insTTCT	c.(2590-2592)tgtfs	p.C864fs	DDX58_ENST00000379882.1_Frame_Shift_Ins_p.C819fs|DDX58_ENST00000542096.1_Frame_Shift_Ins_p.C793fs|DDX58_ENST00000379868.1_Frame_Shift_Ins_p.C661fs	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	864	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)		CTGTCGGGCACAGAATATCTTT	0.396														3	0.000599042	0.0	0.0014	5008	,	,		16937	0.0		0.0	False		,,,				2504	0.002				p.C864fs		Pindel,Atlas-Indel	.											.	DDX58	82	.	0			c.2591_2592insTTCT						PASS	.			0,4262		0,0,2131						5.8	1			112	13,8241		0,13,4114	no	frameshift	DDX58	NM_014314.3		0,13,6245	A1A1,A1R,RR		0.1575,0.0,0.1039				13,12503				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.2587_2590dupTTCT	9.37:g.32457308_32457311dupAGAA	ENSP00000369213:p.Cys864fs	108	0	.		103	33	0.32	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Frame_Shift_Ins	INS	ENST00000379883.2	37	CCDS6526.1																																																																																			.	.	none		0.396	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314		AGAA	32457308	-	AGAA	32457307	7	5	28	1	0	1	1	0	0	0	0	0	4377	478	17	0	190	0	DDX58	9	32457307	Frame_Shift_Ins	INS	-	TCGA-G8-6914-01A-11D-2210-10	23504	32457307	108756124	342	11845											
DDX58	23586	hgsc.bcm.edu	37	chr9	32481339	32481339	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttaaaaagaggaacgtaccCgcaaatgtgaagtgtataaa	18	8	9	6	2	0	2	0	1	0	1	0	3	0	3	1	1	2	3	1	1	10	4	rs61752945	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:32481339C>T	ENST00000379883.2	-	11	1794	c.1637G>A	c.(1636-1638)cGg>cAg	p.R546Q	DDX58_ENST00000379882.1_Splice_Site_p.R501Q|DDX58_ENST00000545044.1_Splice_Site_p.R343Q|DDX58_ENST00000542096.1_Splice_Site_p.R475Q|DDX58_ENST00000379868.1_Splice_Site_p.R343Q	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	546	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)		GGAACGTACCCGCAAATGTGA	0.443													C|||	57	0.0113818	0.0204	0.0101	5008	,	,		17585	0.0		0.0089	False		,,,				2504	0.0143				p.R546Q		Atlas-SNP	.											DDX58,colon,carcinoma,-1,1	DDX58	82	1	0			c.G1637A						scavenged	.	C	GLN/ARG	83,4323	70.3+/-108.2	1,81,2121	139	117	124		1637	3.9	1	9	dbSNP_129	124	113,8487	59.8+/-121.6	1,111,4188	yes	missense-near-splice	DDX58	NM_014314.3	43	2,192,6309	TT,TC,CC		1.314,1.8838,1.507	probably-damaging	546/926	32481339	196,12810	2203	4300	6503	SO:0001630	splice_region_variant	23586	exon11			CGTACCCGCAAAT	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.1638+1G>A	9.37:g.32481339C>T		88	1	0.0113636		78	38	0.487179	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Missense_Mutation	SNP	ENST00000379883.2	37	CCDS6526.1	21	0.009615384615384616	11	0.022357723577235773	4	0.011049723756906077	0	0.0	6	0.0079155672823219	C	24.3	4.511527	0.85389	0.018838	0.01314	ENSG00000107201	ENST00000379882;ENST00000379883;ENST00000379868;ENST00000542096;ENST00000545044	T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6	4.77	3.87	0.44632	.	0.000000	0.64402	D	0.000002	T	0.59810	0.2221	M	0.88775	2.98	0.45284	D	0.998289	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.995;0.952;0.985	T	0.70561	-0.4838	10	0.30078	T	0.28	-5.8222	12.4045	0.55432	0.0:0.915:0.0:0.085	rs61752945	343;501;475;546	F5H5W6;O95786-2;B3KWW1;O95786	.;.;.;DDX58_HUMAN	Q	501;546;343;475;343	ENSP00000369212:R501Q;ENSP00000369213:R546Q;ENSP00000369197:R343Q;ENSP00000442160:R475Q;ENSP00000443055:R343Q	ENSP00000369197:R343Q	R	-	2	0	DDX58	32471339	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	2.447000	0.44917	1.308000	0.44962	0.655000	0.94253	CGG	C|0.987;T|0.013	0.013	strong		0.443	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314	Missense_Mutation	T	32481339	C	T	32481339	5	4	28	1	0	0	0	0	0	0	1	0	4377	666	23	1	1172	1	DDX58	9	32481339	Splice_Site	SNP	C	TCGA-G8-6914-01A-11D-2210-10	24032	32481339	108732092	343	11846											
TOPORS	10210	hgsc.bcm.edu	37	chr9	32542793	32542793	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atactctgtctcctcttacaGatgagttcaggtttctggga	8	15	9	9	0	5	2	1	1	4	1	6	3	5	3	1	2	2	2	1	2	2	4	rs79708790	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:32542793G>T	ENST00000360538.2	-	3	1846	c.1730C>A	c.(1729-1731)tCt>tAt	p.S577Y	TOPORS_ENST00000379858.1_Missense_Mutation_p.S512Y	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	577	Interaction with SUMO1.|Interaction with TOP1.|Interaction with p53/TP53.				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)		TCCTCTTACAGATGAGTTCAG	0.378													G|||	2	0.000399361	0.0	0.0014	5008	,	,		22549	0.0		0.001	False		,,,				2504	0.0				p.S577Y		Atlas-SNP	.											.	TOPORS	127	.	0			c.C1730A						PASS	.	G	TYR/SER,TYR/SER	0,4406		0,0,2203	176	175	175		1535,1730	5.7	0.8	9	dbSNP_131	175	30,8570	20.4+/-63.3	0,30,4270	yes	missense,missense	TOPORS	NM_001195622.1,NM_005802.4	144,144	0,30,6473	TT,TG,GG		0.3488,0.0,0.2307	possibly-damaging,possibly-damaging	512/981,577/1046	32542793	30,12976	2203	4300	6503	SO:0001583	missense	10210	exon3			CTTACAGATGAGT	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.1730C>A	9.37:g.32542793G>T	ENSP00000353735:p.Ser577Tyr	137	0	0		168	77	0.458333	NM_005802	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	37	CCDS6527.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	4.776	0.144262	0.09134	0.0	0.003488	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.17528	2.3;2.27	5.65	5.65	0.86999	.	0.000000	0.39615	N	0.001311	T	0.18718	0.0449	N	0.24115	0.695	0.40496	D	0.980597	P	0.48407	0.91	P	0.45946	0.498	T	0.01212	-1.1417	10	0.72032	D	0.01	-10.5062	18.4994	0.90876	0.0:0.0:1.0:0.0	.	577	Q9NS56	TOPRS_HUMAN	Y	577;512	ENSP00000353735:S577Y;ENSP00000369187:S512Y	ENSP00000353735:S577Y	S	-	2	0	TOPORS	32532793	1.000000	0.71417	0.754000	0.31244	0.181000	0.23173	6.680000	0.74518	2.655000	0.90218	0.557000	0.71058	TCT	G|0.998;T|0.002	0.002	strong		0.378	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802		T	32542793	G	T	32542793	3	4	28	1	0	0	0	0	1	0	0	0	16385	942	33	4	1411	4	TOPORS	9	32542793	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	61454	32542793	108670638	344	11847											
TOPORS	10210	hgsc.bcm.edu	37	chr9	32543801	32543801	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcaaagatctttcatctgccGtagttggcctccttactgca	8	13	8	12	1	3	1	1	0	2	1	4	1	4	1	3	1	3	4	3	1	3	4	rs41272913	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:32543801G>A	ENST00000360538.2	-	3	838	c.722C>T	c.(721-723)aCg>aTg	p.T241M	TOPORS_ENST00000379858.1_Missense_Mutation_p.T176M	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	241	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)		TTCATCTGCCGTAGTTGGCCT	0.378													G|||	2	0.000399361	0.0008	0.0	5008	,	,		21477	0.0		0.001	False		,,,				2504	0.0				p.T241M		Atlas-SNP	.											.	TOPORS	127	.	0			c.C722T						PASS	.	G	MET/THR,MET/THR	6,4400	11.4+/-27.6	0,6,2197	112	116	115		527,722	3.2	0	9	dbSNP_127	115	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	TOPORS	NM_001195622.1,NM_005802.4	81,81	0,9,6494	AA,AG,GG		0.0349,0.1362,0.0692	probably-damaging,probably-damaging	176/981,241/1046	32543801	9,12997	2203	4300	6503	SO:0001583	missense	10210	exon3			TCTGCCGTAGTTG	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.722C>T	9.37:g.32543801G>A	ENSP00000353735:p.Thr241Met	63	0	0		57	27	0.473684	NM_005802	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	37	CCDS6527.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	G	13.72	2.322059	0.41096	0.001362	3.49E-4	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.15256	2.44;2.45	5.2	3.18	0.36537	.	0.543306	0.16954	N	0.192770	T	0.07188	0.0182	N	0.08118	0	0.09310	N	1	P	0.42010	0.768	B	0.33521	0.165	T	0.18085	-1.0348	10	0.52906	T	0.07	-1.9948	8.0253	0.30434	0.0:0.1386:0.467:0.3944	rs41272913	241	Q9NS56	TOPRS_HUMAN	M	241;176	ENSP00000353735:T241M;ENSP00000369187:T176M	ENSP00000353735:T241M	T	-	2	0	TOPORS	32533801	0.003000	0.15002	0.009000	0.14445	0.458000	0.32498	1.039000	0.30266	1.478000	0.48253	0.655000	0.94253	ACG	G|0.999;A|0.001	0.001	strong		0.378	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802		A	32543801	G	A	32543801	3	1	28	1	0	0	0	0	1	0	0	0	16385	1145	40	1	2419	1	TOPORS	9	32543801	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1008	32543801	108669630	345	11848											
C9orf25	203259	hgsc.bcm.edu	37	chr9	34401049	34401049	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggggatgaggtctaggtcCtcgtcgtcggggatctcatc	5	10	17	9	3	2	1	1	1	2	0	8	3	3	3	1	7	0	0	1	7	1	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:34401049C>T	ENST00000445726.1	-	6	777	c.471G>A	c.(469-471)gaG>gaA	p.E157E	FAM219A_ENST00000379081.1_Silent_p.E128E|FAM219A_ENST00000379080.1_Silent_p.E144E|FAM219A_ENST00000297620.4_Silent_p.E140E|FAM219A_ENST00000379087.1_Silent_p.E138E|FAM219A_ENST00000379084.1_Silent_p.E139E|FAM219A_ENST00000379089.1_Silent_p.E155E	NM_001184940.1|NM_001184941.1	NP_001171869.1|NP_001171870.1	Q8IW50	F219A_HUMAN	family with sequence similarity 219, member A	157																	GGTCTAGGTCCTCGTCGTCGG	0.617																																					p.E157E		Atlas-SNP	.											.	FAM219A	3	.	0			c.G471A						PASS	.						119	105	110					9																	34401049		2203	4300	6503	SO:0001819	synonymous_variant	203259	exon6			TAGGTCCTCGTCG	AK096350	CCDS6556.1, CCDS55304.1	9p11.2	2012-03-06	2012-03-06	2012-03-06	ENSG00000164970	ENSG00000164970			19920	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 25"	C9orf25		9110174, 8619474	Standard	NM_147202		Approved	bA573M23.5, FLJ39031	uc011lok.2	Q8IW50	OTTHUMG00000019822	ENST00000445726.1:c.471G>A	9.37:g.34401049C>T		37	0	0		48	4	0.0833333	NM_001184940	A2A364|B4DFE1|B4DSR8|Q5T590|Q5T591|Q5T592|Q5T594|Q5T595|Q8TAZ8	Silent	SNP	ENST00000445726.1	37	CCDS55304.1																																																																																			.	.	none		0.617	FAM219A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001184940		T	34401049	C	T	34401049	2	4	28	1	0	0	0	0	0	0	0	1	2478	680	24	2		2	C9orf25	9	34401049	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1857248	34401049	106812382	346	11849											
FLJ46321	389763	hgsc.bcm.edu	37	chr9	84607492	84607492	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tccagcgcagatggggcctgCcccgcagaatccatgagtct	8	7	12	14	2	1	3	0	1	1	2	3	3	3	3	5	2	2	2	5	2	1	0	rs190878253		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:84607492C>T	ENST00000344803.2	+	4	2154	c.2107C>T	c.(2107-2109)Ccc>Tcc	p.P703S		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	703					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											ATGGGGCCTGCCCCGCAGAAT	0.473																																					p.P703S		Atlas-SNP	.											.	.	.	.	0			c.C2107T						PASS	.						59	57	58					9																	84607492		1839	4077	5916	SO:0001583	missense	389763	exon4			GGCCTGCCCCGCA		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.2107C>T	9.37:g.84607492C>T	ENSP00000341988:p.Pro703Ser	227	0	0		272	62	0.227941	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	14.61	2.587655	0.46110	.	.	ENSG00000214929	ENST00000344803	T	0.24151	1.87	3.51	2.51	0.30379	.	0.258257	0.27946	N	0.017208	T	0.48624	0.1510	M	0.85462	2.755	0.19945	N	0.999942	D	0.64830	0.994	D	0.71184	0.972	T	0.22173	-1.0224	10	0.66056	D	0.02	-8.1379	8.1735	0.31268	0.0:0.7513:0.2486:0.0	.	703	Q6ZQQ2	F75D1_HUMAN	S	703	ENSP00000341988:P703S	ENSP00000341988:P703S	P	+	1	0	FAM75D1	83797312	0.161000	0.22892	0.349000	0.25694	0.013000	0.08279	1.044000	0.30329	1.978000	0.57642	0.561000	0.74099	CCC	C|0.999;T|0.001	0.001	strong		0.473	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		T	84607492	C	T	84607492	3	4	28	1	0	0	0	0	1	0	0	0	5940	739	26	2	2121	2	FLJ46321	9	84607492	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	50206443	84607492	56605939	347	11850											
FLJ46321	389763	hgsc.bcm.edu	37	chr9	84608900	84608900	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcaggaagctgctcactgaCaaatgtgaaagcaagcactt	14	8	10	9	0	2	2	2	2	0	0	2	3	2	3	0	1	4	4	0	1	4	1	rs75742550	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:84608900C>T	ENST00000344803.2	+	4	3562	c.3515C>T	c.(3514-3516)aCa>aTa	p.T1172I		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	1172					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TGCTCACTGACAAATGTGAAA	0.408													C|||	30	0.00599042	0.0	0.0043	5008	,	,		21271	0.005		0.0149	False		,,,				2504	0.0072				p.T1172I		Atlas-SNP	.											.	.	.	.	0			c.C3515T						PASS	.	C	ILE/THR	15,3741		0,15,1863	53	51	51		3515	-6.1	0	9	dbSNP_132	51	76,8174		1,74,4050	yes	missense	FAM75D1	NM_001001670.2	89	1,89,5913	TT,TC,CC		0.9212,0.3994,0.758	possibly-damaging	1172/1577	84608900	91,11915	1878	4125	6003	SO:0001583	missense	389763	exon4			CACTGACAAATGT		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.3515C>T	9.37:g.84608900C>T	ENSP00000341988:p.Thr1172Ile	80	0	0		72	32	0.444444	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	17	0.007783882783882784	0	0.0	1	0.0027624309392265192	2	0.0034965034965034965	14	0.018469656992084433	C	0.004	-2.302874	0.00240	0.003994	0.009212	ENSG00000214929	ENST00000344803	T	0.04015	3.73	3.05	-6.11	0.02131	.	.	.	.	.	T	0.00784	0.0026	N	0.04508	-0.205	0.09310	N	1	B	0.14438	0.01	B	0.15052	0.012	T	0.43245	-0.9403	9	0.27082	T	0.32	.	0.1448	0.00087	0.2811:0.1577:0.2358:0.3254	.	1172	Q6ZQQ2	F75D1_HUMAN	I	1172	ENSP00000341988:T1172I	ENSP00000341988:T1172I	T	+	2	0	FAM75D1	83798720	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.244000	0.00542	-2.594000	0.00455	-1.379000	0.01178	ACA	C|0.993;T|0.007	0.007	strong		0.408	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		T	84608900	C	T	84608900	3	4	28	1	0	0	0	0	1	0	0	0	5940	478	17	2	3529	2	FLJ46321	9	84608900	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1408	84608900	56604531	348	11851											
FLJ46321	389763	hgsc.bcm.edu	37	chr9	84609249	84609249	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcaagttacgaatttcccAccagctgtaaacagagtgag	13	10	9	9	1	1	2	1	1	0	1	2	3	2	2	2	0	3	3	2	0	5	3	rs116948895	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:84609249A>T	ENST00000344803.2	+	4	3911	c.3864A>T	c.(3862-3864)ccA>ccT	p.P1288P		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	1288					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CGAATTTCCCACCAGCTGTAA	0.557													A|||	30	0.00599042	0.0	0.0043	5008	,	,		18184	0.005		0.0149	False		,,,				2504	0.0072				p.P1288P		Atlas-SNP	.											.	.	.	.	0			c.A3864T						PASS	.	A		15,3903		0,15,1944	44	45	44		3864	-3.8	0	9	dbSNP_132	44	76,8228		1,74,4077	no	coding-synonymous	FAM75D1	NM_001001670.2		1,89,6021	TT,TA,AA		0.9152,0.3828,0.7446		1288/1577	84609249	91,12131	1959	4152	6111	SO:0001819	synonymous_variant	389763	exon4			TTTCCCACCAGCT		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.3864A>T	9.37:g.84609249A>T		65	0	0		70	29	0.414286	NM_001001670		Silent	SNP	ENST00000344803.2	37	CCDS47986.1																																																																																			A|0.993;T|0.007	0.007	strong		0.557	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		T	84609249	A	T	84609249	2	4	28	1	0	0	0	0	0	0	0	1	5940	146	6	5		5	FLJ46321	9	84609249	Silent	SNP	A	TCGA-G8-6914-01A-11D-2210-10	349	84609249	56604182	349	11852											
KIF27	55582	hgsc.bcm.edu	37	chr9	86518566	86518566	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatccctatatggaatatgTgaactcttcctgcgtgggtc	8	13	10	10	1	1	1	0	1	1	0	4	2	3	2	2	2	2	1	2	2	5	4			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:86518566T>C	ENST00000297814.2	-	4	1010	c.867A>G	c.(865-867)tcA>tcG	p.S289S	KIF27_ENST00000413982.1_Silent_p.S289S|KIF27_ENST00000334204.2_Silent_p.S289S	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	289	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				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						ATGGAATATGTGAACTCTTCC	0.453																																					p.S289S		Atlas-SNP	.											.	KIF27	103	.	0			c.A867G						PASS	.						74	79	77					9																	86518566		2203	4300	6503	SO:0001819	synonymous_variant	55582	exon4			AATATGTGAACTC	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.867A>G	9.37:g.86518566T>C		196	0	0		219	96	0.438356	NM_017576	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Silent	SNP	ENST00000297814.2	37	CCDS6665.1																																																																																			.	.	none		0.453	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576		C	86518566	T	C	86518566	2	2	28	1	0	0	0	0	0	0	0	1	8305	1683	59	3		3	KIF27	9	86518566	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	1909317	86518566	54694865	350	11853											
DAPK1	1612	hgsc.bcm.edu	37	chr9	90321293	90321293	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcgggaccatggtggacGtcccagccctgatcaagaca	10	5	13	13	2	1	2	1	1	0	1	2	4	2	4	3	3	2	1	3	3	1	0	rs200627640		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:90321293G>A	ENST00000408954.3	+	26	3642	c.3307G>A	c.(3307-3309)Gtc>Atc	p.V1103I	DAPK1_ENST00000358077.5_Missense_Mutation_p.V1103I|DAPK1_ENST00000469640.2_Missense_Mutation_p.V1128I|DAPK1_ENST00000472284.1_Missense_Mutation_p.V1103I|DAPK1_ENST00000491893.1_Missense_Mutation_p.V1037I	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	1103					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						CATGGTGGACGTCCCAGCCCT	0.647									Chronic Lymphocytic Leukemia, Familial Clustering of				G|||	1	0.000199681	0.0	0.0	5008	,	,		18449	0.0		0.001	False		,,,				2504	0.0				p.V1103I		Atlas-SNP	.											.	DAPK1	329	.	0			c.G3307A						PASS	.	G	ILE/VAL	0,4382		0,0,2191	76	87	84		3307	3.4	1	9		84	2,8538		0,2,4268	yes	missense	DAPK1	NM_004938.2	29	0,2,6459	AA,AG,GG		0.0234,0.0,0.0155	benign	1103/1431	90321293	2,12920	2191	4270	6461	SO:0001583	missense	1612	exon26	Familial Cancer Database	Familial CLL	GTGGACGTCCCAG	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.3307G>A	9.37:g.90321293G>A	ENSP00000386135:p.Val1103Ile	175	0	0		221	99	0.447964	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	37	CCDS43842.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	1.630	-0.519121	0.04171	0.0	2.34E-4	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	T;T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04;-0.03	5.59	3.42	0.39159	.	0.243390	0.26366	N	0.024792	T	0.25717	0.0626	N	0.01267	-0.92	0.31840	N	0.623597	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.34900	-0.9810	10	0.02654	T	1	.	8.3592	0.32348	0.8799:0.0:0.1201:0.0	.	1037;1103;1103	B7ZLE7;P53355-3;P53355	.;.;DAPK1_HUMAN	I	1103;1103;1128;1103;1037	ENSP00000350785:V1103I;ENSP00000417076:V1103I;ENSP00000418885:V1128I;ENSP00000386135:V1103I;ENSP00000419026:V1037I	ENSP00000350785:V1103I	V	+	1	0	DAPK1	89511113	0.992000	0.36948	0.994000	0.49952	0.932000	0.56968	2.244000	0.43124	0.540000	0.28808	0.561000	0.74099	GTC	G|0.999;A|0.001	0.001	strong		0.647	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938		A	90321293	G	A	90321293	3	1	28	1	0	0	0	0	1	0	0	0	4237	1145	40	1	3405	1	DAPK1	9	90321293	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	3802727	90321293	50892138	351	11854											
LPPR1	54886	hgsc.bcm.edu	37	chr9	104032338	104032338	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tattgtgtgctggctgccacCccaactgctattgtaagtac	8	13	9	11	0	0	0	0	0	0	0	0	0	0	0	3	1	5	5	3	1	5	6	rs7847596	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:104032338C>T	ENST00000374874.3	+	3	679	c.240C>T	c.(238-240)acC>acT	p.T80T	LPPR1_ENST00000395056.2_Silent_p.T80T	NM_207299.1	NP_997182.1	Q8TBJ4	LPPR1_HUMAN		80					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)										TGGCTGCCACCCCAACTGCTA	0.443													C|||	86	0.0171725	0.003	0.0187	5008	,	,		19611	0.001		0.0417	False		,,,				2504	0.0266				p.T80T		Atlas-SNP	.											.	.	.	.	0			c.C240T						PASS	.	C	,	32,4374	34.3+/-65.2	0,32,2171	83	81	82		240,240	-1.7	1	9	dbSNP_116	82	342,8258	112.7+/-172.9	5,332,3963	no	coding-synonymous,coding-synonymous	LPPR1	NM_017753.2,NM_207299.1	,	5,364,6134	TT,TC,CC		3.9767,0.7263,2.8756	,	80/326,80/326	104032338	374,12632	2203	4300	6503	SO:0001819	synonymous_variant	0	exon3			TGCCACCCCAACT																												ENST00000374874.3:c.240C>T	9.37:g.104032338C>T		116	0	0		110	61	0.554545	NM_207299	Q5VX23|Q9NXE2	Silent	SNP	ENST00000374874.3	37	CCDS6751.1																																																																																			C|0.973;T|0.027	0.027	strong		0.443	LPPR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053425.1			T	104032338	C	T	104032338	2	4	28	1	0	0	0	0	0	0	0	1	8933	610	22	2		2	LPPR1	9	104032338	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	13711045	104032338	37181093	352	11855											
KIAA1958	158405	hgsc.bcm.edu	37	chr9	115337154	115337154	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccatcagcacggagctagAcccacacggtatgtctgcat	10	8	10	13	2	2	1	1	0	1	1	2	2	2	2	2	2	4	4	2	2	2	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:115337154A>G	ENST00000337530.6	+	2	1090	c.794A>G	c.(793-795)gAc>gGc	p.D265G	KIAA1958_ENST00000536272.1_Missense_Mutation_p.D265G|KIAA1958_ENST00000374244.3_Missense_Mutation_p.D265G	NM_133465.2	NP_597722.1	Q8N8K9	K1958_HUMAN	KIAA1958	265										endometrium(1)|large_intestine(9)|lung(10)|prostate(2)|skin(3)	25						ACGGAGCTAGACCCACACGGT	0.547																																					p.D265G		Atlas-SNP	.											KIAA1958_ENST00000374244,NS,carcinoma,+1,3	KIAA1958	52	3	0			c.A794G						PASS	.						239	211	221					9																	115337154		2203	4300	6503	SO:0001583	missense	158405	exon2			AGCTAGACCCACA	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.794A>G	9.37:g.115337154A>G	ENSP00000336940:p.Asp265Gly	99	0	0		102	5	0.0490196	NM_133465	B7ZKW6|Q2M336|Q5T252|Q8TF43|Q96N02	Missense_Mutation	SNP	ENST00000337530.6	37	CCDS35108.1	.	.	.	.	.	.	.	.	.	.	A	16.00	2.999186	0.54147	.	.	ENSG00000165185	ENST00000337530;ENST00000374244;ENST00000536272	T;T;T	0.41758	0.99;0.99;0.99	6.07	6.07	0.98685	.	0.067648	0.64402	D	0.000011	T	0.33059	0.0850	N	0.14661	0.345	0.58432	D	0.999991	P;P	0.46395	0.877;0.734	B;B	0.43194	0.411;0.321	T	0.24297	-1.0164	10	0.66056	D	0.02	-10.9977	16.6288	0.85011	1.0:0.0:0.0:0.0	.	265;265	B7ZKW6;Q8N8K9	.;K1958_HUMAN	G	265	ENSP00000336940:D265G;ENSP00000363362:D265G;ENSP00000440504:D265G	ENSP00000336940:D265G	D	+	2	0	KIAA1958	114376975	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.696000	0.74598	2.326000	0.78906	0.533000	0.62120	GAC	.	.	none		0.547	KIAA1958-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053690.1	NM_133465		G	115337154	A	G	115337154	3	3	28	1	0	0	0	0	1	0	0	0	8273	275	10	3	796	3	KIAA1958	9	115337154	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	11304816	115337154	25876277	353	11856											
CEP110	11064	hgsc.bcm.edu	37	chr9	123917045	123917045	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtcttatgactgaactagaaAtagaaaaatcactcaaacat	19	10	5	7	0	3	4	2	2	1	2	3	4	3	4	0	0	2	0	0	0	8	3	rs149632088	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:123917045A>G	ENST00000373855.1	+	27	4479	c.4219A>G	c.(4219-4221)Ata>Gta	p.I1407V	CNTRL_ENST00000238341.5_Missense_Mutation_p.I1407V|CNTRL_ENST00000373845.2_3'UTR|CNTRL_ENST00000373847.1_Missense_Mutation_p.I855V|CNTRL_ENST00000373850.1_Missense_Mutation_p.I855V			Q7Z7A1	CNTRL_HUMAN	centriolin	1407					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						TGAACTAGAAATAGAAAAATC	0.343													A|||	2	0.000399361	0.0	0.0	5008	,	,		19659	0.0		0.002	False		,,,				2504	0.0				p.I1407V		Atlas-SNP	.											.	CNTRL	161	.	0			c.A4219G						PASS	.	A	VAL/ILE	2,4404	2.1+/-5.4	0,2,2201	65	62	63		4219	1.9	1	9	dbSNP_134	63	3,8597	3.0+/-9.4	0,3,4297	yes	missense	CNTRL	NM_007018.4	29	0,5,6498	GG,GA,AA		0.0349,0.0454,0.0384	benign	1407/2326	123917045	5,13001	2203	4300	6503	SO:0001583	missense	11064	exon25			CTAGAAATAGAAA	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.4219A>G	9.37:g.123917045A>G	ENSP00000362962:p.Ile1407Val	56	0	0		65	39	0.6	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	37	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	A	9.257	1.042151	0.19748	4.54E-4	3.49E-4	ENSG00000119397	ENST00000373855;ENST00000238341;ENST00000454238;ENST00000439778;ENST00000373850;ENST00000373847;ENST00000431571;ENST00000373845	T;T;T;T;T	0.77489	2.57;2.57;2.57;2.57;-1.1	5.58	1.93	0.25924	.	.	.	.	.	T	0.64023	0.2561	L	0.47716	1.5	0.24107	N	0.995855	B	0.20780	0.048	B	0.16289	0.015	T	0.50303	-0.8844	9	0.30078	T	0.28	.	0.594	0.00733	0.3991:0.2274:0.1411:0.2325	.	1407	Q7Z7A1	CNTRL_HUMAN	V	1407;1407;1407;163;855;855;76;76	ENSP00000362962:I1407V;ENSP00000238341:I1407V;ENSP00000362956:I855V;ENSP00000362953:I855V;ENSP00000413014:I76V	ENSP00000238341:I1407V	I	+	1	0	CNTRL	122956866	0.975000	0.34042	0.997000	0.53966	0.931000	0.56810	0.100000	0.15231	0.135000	0.18707	-0.250000	0.11733	ATA	A|0.999;G|0.001	0.001	strong		0.343	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018		G	123917045	A	G	123917045	3	3	28	1	0	0	0	0	1	0	0	0	3247	101	4	3	4317	3	CEP110	9	123917045	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	8579891	123917045	17296386	354	11857											
RABGAP1	23637	hgsc.bcm.edu	37	chr9	125748669	125748669	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcactagatgttaccctttcAgtgccgaatgtgtctgaagg	9	13	10	9	1	3	2	2	1	1	1	3	3	3	2	2	1	2	1	2	1	4	3	rs376096787		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:125748669A>G	ENST00000373647.4	+	4	695	c.561A>G	c.(559-561)tcA>tcG	p.S187S		NM_012197.3	NP_036329.3	Q9Y3P9	RBGP1_HUMAN	RAB GTPase activating protein 1	187	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				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						TTACCCTTTCAGTGCCGAATG	0.438																																					p.S187S		Atlas-SNP	.											.	RABGAP1	164	.	0			c.A561G						PASS	.	A		0,4406		0,0,2203	185	179	181		561	-10.1	0.1	9		181	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RABGAP1	NM_012197.3		0,1,6502	GG,GA,AA		0.0116,0.0,0.0077		187/1070	125748669	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23637	exon4			CCTTTCAGTGCCG	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.561A>G	9.37:g.125748669A>G		199	0	0		205	107	0.521951	NM_012197	B9A6L2|Q05CW2|Q6ZMY1|Q9HA28|Q9P0E2|Q9UG67	Silent	SNP	ENST00000373647.4	37	CCDS6848.2																																																																																			.	.	weak		0.438	RABGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053976.3	NM_012197		G	125748669	A	G	125748669	2	3	28	1	0	0	0	0	0	0	0	1	12979	175	7	3		3	RABGAP1	9	125748669	Silent	SNP	A	TCGA-G8-6914-01A-11D-2210-10	1831624	125748669	15464762	355	11858											
DOLK	22845	hgsc.bcm.edu	37	chr9	131708710	131708710	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atgcgggtgtctgtctggaaGagaaactgaagaagccagag	13	7	15	6	1	2	4	0	1	2	3	2	6	2	5	1	2	3	0	1	2	4	0	rs148646968	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:131708710G>A	ENST00000372586.3	-	1	1188	c.873C>T	c.(871-873)ctC>ctT	p.L291L	NUP188_ENST00000372577.2_5'Flank|RP11-101E3.5_ENST00000482796.1_Intron	NM_014908.3	NP_055723.1	Q9UPQ8	DOLK_HUMAN	dolichol kinase	291					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|dolichyl monophosphate biosynthetic process (GO:0043048)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	dolichol kinase activity (GO:0004168)			breast(1)|large_intestine(5)|lung(3)|ovary(1)|urinary_tract(1)	11						CTGTCTGGAAGAGAAACTGAA	0.577													G|||	2	0.000399361	0.0	0.0	5008	,	,		18331	0.0		0.002	False		,,,				2504	0.0				p.L291L		Atlas-SNP	.											DOLK,colon,carcinoma,-2,1	DOLK	39	1	0			c.C873T						PASS	.	G		0,4406		0,0,2203	71	77	75		873	0.7	1	9	dbSNP_134	75	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	DOLK	NM_014908.3		0,4,6499	AA,AG,GG		0.0465,0.0,0.0308		291/539	131708710	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	22845	exon1			CTGGAAGAGAAAC	AB029017	CCDS6915.1	9q34.13	2014-09-17	2007-02-09	2007-02-09	ENSG00000175283	ENSG00000175283			23406	protein-coding gene	gene with protein product	"dolichol kinase 1"	610746	"transmembrane protein 15"	TMEM15		12975309, 16923818	Standard	NM_014908		Approved	KIAA1094, DK1	uc004bwr.3	Q9UPQ8	OTTHUMG00000020765	ENST00000372586.3:c.873C>T	9.37:g.131708710G>A		70	0	0		74	36	0.486486	NM_014908	Q5SRE6	Silent	SNP	ENST00000372586.3	37	CCDS6915.1																																																																																			G|1.000;A|0.000	0.000	strong		0.577	DOLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054515.1	NM_014908		A	131708710	G	A	131708710	2	1	28	1	0	0	0	0	0	0	0	1	4705	929	33	2		2	DOLK	9	131708710	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	5960041	131708710	9504721	356	11859											
NUP188	23511	hgsc.bcm.edu	37	chr9	131768786	131768786	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctttttttcttgtagagcacGctgctgtccagcctctcgcg	4	15	9	13	3	2	1	0	0	2	1	4	1	3	1	2	0	3	4	2	0	1	5	rs150379581	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:131768786G>A	ENST00000372577.2	+	44	5100	c.5079G>A	c.(5077-5079)acG>acA	p.T1693T	RP11-167N5.5_ENST00000594418.1_lincRNA	NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	1693					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						TGTAGAGCACGCTGCTGTCCA	0.642											OREG0019528	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	24	0.00479233	0.0008	0.0072	5008	,	,		15926	0.0		0.0169	False		,,,				2504	0.001				p.T1693T		Atlas-SNP	.											.	NUP188	140	.	0			c.G5079A						PASS	.	G		13,4393	21.2+/-45.6	0,13,2190	59	66	64		5079	-10.4	0.6	9	dbSNP_134	64	136,8464	67.7+/-130.1	0,136,4164	no	coding-synonymous	NUP188	NM_015354.1		0,149,6354	AA,AG,GG		1.5814,0.2951,1.1456		1693/1750	131768786	149,12857	2203	4300	6503	SO:0001819	synonymous_variant	23511	exon44			GAGCACGCTGCTG	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.5079G>A	9.37:g.131768786G>A		108	0	0	1590	109	53	0.486239	NM_015354	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Silent	SNP	ENST00000372577.2	37	CCDS35156.1																																																																																			G|0.990;A|0.010	0.010	strong		0.642	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2			A	131768786	G	A	131768786	2	1	28	1	0	0	0	0	0	0	0	1	10767	1074	38	1		1	NUP188	9	131768786	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	60076	131768786	9444645	357	11860											
ABL1	25	hgsc.bcm.edu	37	chr9	133755528	133755528	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttgaaacaatgttccaggaAtccagtatctcagacggtaa	14	11	8	8	1	1	2	1	1	1	1	4	3	3	3	2	2	1	3	2	2	5	4	rs2227985	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:133755528A>G	ENST00000318560.5	+	9	1878	c.1497A>G	c.(1495-1497)gaA>gaG	p.E499E		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	499					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)	TGTTCCAGGAATCCAGTATCT	0.542			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"								A|||	429	0.0856629	0.2057	0.0836	5008	,	,		18557	0.001		0.0696	False		,,,				2504	0.0286				p.E518E		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.A1554G						PASS	.	A	,	757,3649	309.7+/-291.2	52,653,1498	106	106	106		1497,1554	-2.8	1	9	dbSNP_98	106	641,7959	164.3+/-216.7	27,587,3686	no	coding-synonymous,coding-synonymous	ABL1	NM_005157.4,NM_007313.2	,	79,1240,5184	GG,GA,AA		7.4535,17.1811,10.7489	,	499/1131,518/1150	133755528	1398,11608	2203	4300	6503	SO:0001819	synonymous_variant	25	exon9			CCAGGAATCCAGT	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.1497A>G	9.37:g.133755528A>G		79	0	0		66	29	0.439394	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																			A|0.898;G|0.102	0.102	strong		0.542	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		G	133755528	A	G	133755528	2	3	28	1	0	0	0	0	0	0	0	1	92	98	4	3		3	ABL1	9	133755528	Silent	SNP	A	TCGA-G8-6914-01A-11D-2210-10	1986742	133755528	7457903	358	11861											
ABL1	25	hgsc.bcm.edu	37	chr9	133760029	133760029	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcacagtaacgcctcccccCaggctggtgaaaaagaatga	13	5	11	12	1	0	3	0	2	0	1	1	3	1	3	4	3	1	3	4	3	4	1	rs2229070	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:133760029C>G	ENST00000318560.5	+	11	2733	c.2352C>G	c.(2350-2352)ccC>ccG	p.P784P		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	784	Pro-rich.				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)	CGCCTCCCCCCAGGCTGGTGA	0.592			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"								C|||	534	0.106629	0.2821	0.0865	5008	,	,		18610	0.001		0.0696	False		,,,				2504	0.0307				p.P803P		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.C2409G						PASS	.	C	,	985,3415		107,771,1322	26	30	28		2352,2409	1.6	0.2	9	dbSNP_98	28	622,7976		27,568,3704	no	coding-synonymous,coding-synonymous	ABL1	NM_005157.4,NM_007313.2	,	134,1339,5026	GG,GC,CC		7.2342,22.3864,12.3634	,	784/1131,803/1150	133760029	1607,11391	2200	4299	6499	SO:0001819	synonymous_variant	25	exon11			TCCCCCCAGGCTG	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.2352C>G	9.37:g.133760029C>G		21	0	0		27	14	0.518519	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																			C|0.885;G|0.115	0.115	strong		0.592	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		G	133760029	C	G	133760029	2	3	28	1	0	0	0	0	0	0	0	1	92	581	21	4		4	ABL1	9	133760029	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	4501	133760029	7453402	359	11862											
ABL1	25	hgsc.bcm.edu	37	chr9	133761001	133761001	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgacagcaggcagtggtccAgcggccactcaggacttcag	9	5	14	13	2	2	0	2	0	0	0	3	2	3	1	2	4	2	2	2	4	0	1	rs1056171	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:133761001A>G	ENST00000318560.5	+	11	3705	c.3324A>G	c.(3322-3324)ccA>ccG	p.P1108P		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	1108	F-actin-binding.				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)	GCAGTGGTCCAGCGGCCACTC	0.557			"T, Mis"	"BCR, ETV6, NUP214"	"CML, ALL, T-ALL"								G|||	3276	0.654153	0.882	0.6974	5008	,	,		18771	0.5952		0.4881	False		,,,				2504	0.547				p.P1127P		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	ABL1,scalp,carcinoma,+2,1	ABL1	1632	1	0			c.A3381G						scavenged	.	G	,	3592,814	300.1+/-286.2	1470,652,81	29	34	32		3324,3381	-10.5	0.2	9	dbSNP_86	32	4015,4585	586.5+/-392.0	924,2167,1209	no	coding-synonymous,coding-synonymous	ABL1	NM_005157.4,NM_007313.2	,	2394,2819,1290	GG,GA,AA		46.686,18.4748,41.5116	,	1108/1131,1127/1150	133761001	7607,5399	2203	4300	6503	SO:0001819	synonymous_variant	25	exon11			TGGTCCAGCGGCC	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.3324A>G	9.37:g.133761001A>G		108	2	0.0185185		112	58	0.517857	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																			A|0.391;G|0.609	0.609	strong		0.557	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		G	133761001	A	G	133761001	2	3	28	1	0	0	0	0	0	0	0	1	92	175	7	3		3	ABL1	9	133761001	Silent	SNP	A	TCGA-G8-6914-01A-11D-2210-10	972	133761001	7452430	360	11863											
BAT2L1	84726	hgsc.bcm.edu	37	chr9	134340444	134340444	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaaggcatctccccaggaaAacggccctgctgtccacaaa	13	5	9	14	1	1	1	0	0	1	1	3	2	2	2	4	3	2	2	4	3	4	0	rs201633009	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:134340444A>G	ENST00000357304.4	+	11	1754	c.1699A>G	c.(1699-1701)Aac>Gac	p.N567D	PRRC2B_ENST00000458550.1_Missense_Mutation_p.N567D|PRRC2B_ENST00000405995.1_Missense_Mutation_p.N567D|PRRC2B_ENST00000372249.1_5'UTR	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	567							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						TCCCCAGGAAAACGGCCCTGC	0.572													A|||	2	0.000399361	0.0	0.0029	5008	,	,		17186	0.0		0.0	False		,,,				2504	0.0				p.N567D		Atlas-SNP	.											.	PRRC2B	266	.	0			c.A1699G						PASS	.	A	ASP/ASN	0,3984		0,0,1992	41	47	45		1699	5.5	1	9		45	13,8289		1,11,4139	yes	missense	PRRC2B	NM_013318.3	23	1,11,6131	GG,GA,AA		0.1566,0.0,0.1058	probably-damaging	567/2230	134340444	13,12273	1992	4151	6143	SO:0001583	missense	84726	exon11			CAGGAAAACGGCC	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.1699A>G	9.37:g.134340444A>G	ENSP00000349856:p.Asn567Asp	63	0	0		70	37	0.528571	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	37	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	A	16.66	3.185233	0.57909	0.0	0.001566	ENSG00000130723	ENST00000405995;ENST00000357304;ENST00000458550;ENST00000422467	T;T;T;T	0.12672	2.66;2.66;2.66;2.66	5.48	5.48	0.80851	.	0.000000	0.44483	U	0.000450	T	0.31827	0.0809	L	0.57536	1.79	0.80722	D	1	D	0.69078	0.997	D	0.73380	0.98	T	0.01914	-1.1248	10	0.26408	T	0.33	-2.5709	14.7458	0.69490	1.0:0.0:0.0:0.0	.	567	Q5JSZ5	PRC2B_HUMAN	D	567;567;567;107	ENSP00000384606:N567D;ENSP00000349856:N567D;ENSP00000398853:N567D;ENSP00000391063:N107D	ENSP00000349856:N567D	N	+	1	0	PRRC2B	133330265	1.000000	0.71417	0.998000	0.56505	0.221000	0.24807	4.399000	0.59703	2.075000	0.62263	0.459000	0.35465	AAC	A|0.994;G|0.006	0.006	strong		0.572	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	134340444	A	G	134340444	3	3	28	1	0	0	0	0	1	0	0	0	1320	14	1	3	1741	3	BAT2L1	9	134340444	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	579443	134340444	6872987	361	11864											
RAPGEF1	2889	hgsc.bcm.edu	37	chr9	134501410	134501410	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	attcgacaggggctgaggaaCctccatgctgaaagggcaga	12	6	14	9	1	0	3	0	2	0	1	2	5	1	4	2	4	2	3	2	4	2	1	rs200547421		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:134501410C>T	ENST00000372189.3	-	10	1673	c.1550G>A	c.(1549-1551)gGt>gAt	p.G517D	RAPGEF1_ENST00000372195.1_Missense_Mutation_p.G534D|RAPGEF1_ENST00000481260.1_5'Flank|RAPGEF1_ENST00000372190.3_Missense_Mutation_p.G535D	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1	517					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)		GGCTGAGGAACCTCCATGCTG	0.537													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18229	0.0		0.0	False		,,,				2504	0.0				p.G535D		Atlas-SNP	.											.	RAPGEF1	126	.	0			c.G1604A						PASS	.	C	ASP/GLY,ASP/GLY	0,4064		0,0,2032	79	84	82		1550,1604	1.9	0.5	9		82	12,8340		1,10,4165	yes	missense,missense	RAPGEF1	NM_005312.2,NM_198679.1	94,94	1,10,6197	TT,TC,CC		0.1437,0.0,0.0966	benign,benign	517/1078,535/1096	134501410	12,12404	2032	4176	6208	SO:0001583	missense	2889	exon10			GAGGAACCTCCAT	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.1550G>A	9.37:g.134501410C>T	ENSP00000361263:p.Gly517Asp	118	0	0		111	48	0.432432	NM_198679	Q5JUE4|Q8IV73	Missense_Mutation	SNP	ENST00000372189.3	37	CCDS48047.1	.	.	.	.	.	.	.	.	.	.	C	13.98	2.397773	0.42512	0.0	0.001437	ENSG00000107263	ENST00000266110;ENST00000372195;ENST00000429421;ENST00000372189;ENST00000372190;ENST00000411834;ENST00000337036;ENST00000372191;ENST00000357686	T;T;T	0.25749	1.78;1.78;1.78	5.07	1.9	0.25705	.	0.158578	0.56097	D	0.000029	T	0.10937	0.0267	N	0.03608	-0.345	0.22675	N	0.998864	B;B;B	0.25235	0.121;0.072;0.118	B;B;B	0.32980	0.031;0.046;0.156	T	0.39057	-0.9632	10	0.13853	T	0.58	.	9.0597	0.36427	0.0:0.4277:0.4828:0.0895	.	534;517;535	Q68DL3;Q13905;Q13905-3	.;RPGF1_HUMAN;.	D	517;534;411;517;535;497;443;212;534	ENSP00000361269:G534D;ENSP00000361263:G517D;ENSP00000361264:G535D	ENSP00000266110:G517D	G	-	2	0	RAPGEF1	133491231	0.026000	0.19158	0.521000	0.27850	0.981000	0.71138	0.914000	0.28624	0.488000	0.27723	0.655000	0.94253	GGT	C|0.993;T|0.007	0.007	strong		0.537	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312		T	134501410	C	T	134501410	3	4	28	1	0	0	0	0	1	0	0	0	13058	507	18	2	1743	2	RAPGEF1	9	134501410	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	160966	134501410	6712021	362	11865											
TSC1	7248	hgsc.bcm.edu	37	chr9	135771682	135771682	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtagctgtccaacactgtcCggggtcgggggagacgggtg	6	8	18	9	3	0	1	0	0	0	1	3	2	2	1	2	5	2	2	2	5	2	1	rs140352085	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:135771682C>T	ENST00000298552.3	-	23	3656	c.3435G>A	c.(3433-3435)ccG>ccA	p.P1145P	TSC1_ENST00000440111.2_Silent_p.P1145P|TSC1_ENST00000545250.1_Silent_p.P1094P	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	1145					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)		CAACACTGTCCGGGGTCGGGG	0.498			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis				C|||	4	0.000798722	0.0	0.0029	5008	,	,		20397	0.0		0.0	False		,,,				2504	0.002				p.P1145P		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"E, O"	.	TSC1	167	.	1	Unknown(1)	bone(1)	c.G3435A						PASS	.	C	,,	0,4406		0,0,2203	177	153	161		3435,3432,3282	-5.2	0	9	dbSNP_134	161	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	TSC1	NM_000368.4,NM_001162426.1,NM_001162427.1	,,	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	,,	1145/1165,1144/1164,1094/1114	135771682	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	7248	exon23	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	ACTGTCCGGGGTC	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.3435G>A	9.37:g.135771682C>T		151	0	0		152	63	0.414474	NM_000368	B7Z897|Q5VVN5	Silent	SNP	ENST00000298552.3	37	CCDS6956.1																																																																																			C|1.000;T|0.000	0.000	strong		0.498	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1			T	135771682	C	T	135771682	2	4	28	1	0	0	0	0	0	0	0	1	16620	639	23	1		1	TSC1	9	135771682	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1270272	135771682	5441749	363	11866											
TSC1	7248	hgsc.bcm.edu	37	chr9	135804239	135804239	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agcatggcaagaagctccccGacatttgcttgttgggccat	9	10	11	11	1	0	1	0	0	0	1	1	2	1	1	3	2	3	5	3	2	2	3	rs145987906		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:135804239G>A	ENST00000298552.3	-	3	242	c.21C>T	c.(19-21)gtC>gtT	p.V7V	TSC1_ENST00000440111.2_Silent_p.V7V|TSC1_ENST00000475903.1_5'UTR|TSC1_ENST00000545250.1_Silent_p.V7V|TSC1_ENST00000403810.1_Silent_p.V7V	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	7					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)			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)		GAAGCTCCCCGACATTTGCTT	0.527			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.V7V		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"E, O"	.	TSC1	167	.	0			c.C21T						PASS	.						104	84	91					9																	135804239		2203	4300	6503	SO:0001819	synonymous_variant	7248	exon3	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	CTCCCCGACATTT	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.21C>T	9.37:g.135804239G>A		84	0	0		82	52	0.634146	NM_000368	B7Z897|Q5VVN5	Silent	SNP	ENST00000298552.3	37	CCDS6956.1																																																																																			G|1.000;C|0.000	.	alt		0.527	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1			A	135804239	G	A	135804239	2	1	28	1	0	0	0	0	0	0	0	1	16620	1045	37	1		1	TSC1	9	135804239	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	32557	135804239	5409192	364	11867											
MED22	6837	hgsc.bcm.edu	37	chr9	136208442	136208442	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagcactgggctccggggaCgccagcagaggggccgagag	8	2	18	13	3	0	2	0	0	0	2	1	4	1	3	4	5	2	3	4	5	0	0	rs78711238	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:136208442C>T	ENST00000491289.1	-	5	1097	c.516G>A	c.(514-516)gcG>gcA	p.A172A	MED22_ENST00000343730.5_Silent_p.A172A|MED22_ENST00000344469.5_3'UTR|MED22_ENST00000471524.1_5'Flank|MED22_ENST00000476080.1_3'UTR			Q15528	MED22_HUMAN	mediator complex subunit 22	172						cytoplasm (GO:0005737)|mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			endometrium(1)|large_intestine(1)|ovary(1)|urinary_tract(1)	4				OV - Ovarian serous cystadenocarcinoma(145;1.14e-06)|Epithelial(140;8.2e-06)|all cancers(34;6.94e-05)		GCTCCGGGGACGCCAGCAGAG	0.677													C|||	37	0.00738818	0.0038	0.0043	5008	,	,		15768	0.0		0.0258	False		,,,				2504	0.0031				p.A172A		Atlas-SNP	.											.	MED22	13	.	0			c.G516A						PASS	.	C	,	25,4381	31.7+/-61.6	0,25,2178	32	35	34		516,	-5.3	0.4	9	dbSNP_133	34	122,8478	62.1+/-124.0	1,120,4179	no	coding-synonymous,utr-3	MED22	NM_133640.3,NM_181491.1	,	1,145,6357	TT,TC,CC		1.4186,0.5674,1.1302	,	172/201,	136208442	147,12859	2203	4300	6503	SO:0001819	synonymous_variant	6837	exon5			CGGGGACGCCAGC		CCDS6963.1, CCDS6964.1	9q34.1	2008-02-05	2007-07-30	2007-07-30	ENSG00000148297	ENSG00000148297			11477	protein-coding gene	gene with protein product		185641	"surfeit 5"	SURF5		8499913, 15175163	Standard	NM_133640		Approved	Med24	uc004cdc.3	Q15528	OTTHUMG00000020869	ENST00000491289.1:c.516G>A	9.37:g.136208442C>T		120	0	0		133	62	0.466165	NM_133640	B3KW83|B3KWX4|O76072|Q5T8U0	Silent	SNP	ENST00000491289.1	37	CCDS6963.1																																																																																			C|0.988;T|0.012	0.012	strong		0.677	MED22-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054898.2	NM_133640		T	136208442	C	T	136208442	2	4	28	1	0	0	0	0	0	0	0	1	9449	523	19	1		1	MED22	9	136208442	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	404203	136208442	5004989	365	11868											
AGPAT2	10555	hgsc.bcm.edu	37	chr9	139571430	139571430	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacgttctccctgaccatgcGctcgcccaggtcggccatca	6	8	9	18	4	2	1	1	1	1	0	5	1	2	1	4	2	1	2	4	2	0	1	rs142993240	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:139571430G>A	ENST00000371696.2	-	3	540	c.475C>T	c.(475-477)Cgc>Tgc	p.R159C	AGPAT2_ENST00000538402.1_Missense_Mutation_p.R159C|AGPAT2_ENST00000371694.3_Missense_Mutation_p.R159C	NM_006412.3	NP_006403.2	O15120	PLCB_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 2	159					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)		CTGACCATGCGCTCGCCCAGG	0.672													g|||	15	0.00299521	0.0008	0.0014	5008	,	,		12176	0.0		0.008	False		,,,				2504	0.0051				p.R159C		Atlas-SNP	.											.	AGPAT2	17	.	0			c.C475T						PASS	.	G	CYS/ARG,CYS/ARG	6,4400	11.4+/-27.6	0,6,2197	55	58	57		475,475	2.7	1	9	dbSNP_134	57	48,8552	31.2+/-83.2	0,48,4252	yes	missense,missense	AGPAT2	NM_001012727.1,NM_006412.3	180,180	0,54,6449	AA,AG,GG		0.5581,0.1362,0.4152	possibly-damaging,possibly-damaging	159/247,159/279	139571430	54,12952	2203	4300	6503	SO:0001583	missense	10555	exon3			CCATGCGCTCGCC	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.475C>T	9.37:g.139571430G>A	ENSP00000360761:p.Arg159Cys	81	0	0		91	40	0.43956	NM_001012727	O00516|O15106|Q5VUD3|Q5VUD4|Q9BSV7|Q9BWR7	Missense_Mutation	SNP	ENST00000371696.2	37	CCDS7003.1	6	0.0027472527472527475	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	G	15.73	2.920536	0.52653	0.001362	0.005581	ENSG00000169692	ENST00000371694;ENST00000371696;ENST00000538402	D;D;D	0.93604	-3.25;-3.25;-3.25	4.75	2.66	0.31614	Phospholipid/glycerol acyltransferase (2);1-acyl-sn-glycerol-3-phosphate acyltransferase (1);	0.654070	0.14876	N	0.293250	D	0.93552	0.7942	M	0.83692	2.655	0.40657	D	0.98209	D;D	0.65815	0.994;0.995	P;P	0.59595	0.827;0.86	D	0.92032	0.5634	10	0.54805	T	0.06	-9.0385	6.8996	0.24275	0.0:0.1308:0.3813:0.488	.	159;159	O15120-2;O15120	.;PLCB_HUMAN	C	159	ENSP00000360759:R159C;ENSP00000360761:R159C;ENSP00000438919:R159C	ENSP00000360759:R159C	R	-	1	0	AGPAT2	138691251	0.999000	0.42202	0.977000	0.42913	0.479000	0.33129	2.180000	0.42537	0.978000	0.38470	0.655000	0.94253	CGC	G|0.997;A|0.003	0.003	strong		0.672	AGPAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055090.1	NM_006412		A	139571430	G	A	139571430	3	1	28	1	0	0	0	0	1	0	0	0	387	1087	38	1	377	1	AGPAT2	9	139571430	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	3362988	139571430	1642001	366	11869											
FBXW5	54461	hgsc.bcm.edu	37	chr9	139835558	139835558	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agttgaccacatcctcgtgcCgcagcctggccagacagatg	9	7	11	14	2	0	3	0	1	0	2	2	3	1	3	5	1	2	2	5	1	0	1	rs45559439	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:139835558C>T	ENST00000325285.3	-	9	1602	c.1523G>A	c.(1522-1524)cGg>cAg	p.R508Q	FBXW5_ENST00000483559.1_5'UTR	NM_018998.3	NP_061871.1	Q969U6	FBXW5_HUMAN	F-box and WD repeat domain containing 5	508				R -> Q (in Ref. 5; BAD92963). {ECO:0000305}.	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)		ATCCTCGTGCCGCAGCCTGGC	0.677													C|||	49	0.00978435	0.0	0.0245	5008	,	,		15182	0.0		0.0298	False		,,,				2504	0.002				p.R508Q		Atlas-SNP	.											.	FBXW5	36	.	0			c.G1523A						PASS	.	C	GLN/ARG	22,4320		0,22,2149	66	61	62		1523	2.2	1	9	dbSNP_127	62	215,8361		3,209,4076	yes	missense	FBXW5	NM_018998.2	43	3,231,6225	TT,TC,CC		2.507,0.5067,1.8346	benign	508/567	139835558	237,12681	2171	4288	6459	SO:0001583	missense	54461	exon9			TCGTGCCGCAGCC	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.1523G>A	9.37:g.139835558C>T	ENSP00000313034:p.Arg508Gln	73	0	0		81	39	0.481481	NM_018998	B2RDZ6|Q59ET5|Q5SPZ8|Q5SPZ9|Q5SQ00|Q5SQ02|Q5SQ03|Q5SQ04|Q8WY79|Q96GJ6|Q9BSU8|Q9H6A8|Q9HBQ6|Q9NSZ3	Missense_Mutation	SNP	ENST00000325285.3	37	CCDS7014.1	33	0.01510989010989011	0	0.0	10	0.027624309392265192	0	0.0	23	0.030343007915567283	C	10.25	1.298726	0.23650	0.005067	0.02507	ENSG00000159069	ENST00000325285	T	0.65549	-0.16	4.05	2.21	0.28008	WD40/YVTN repeat-like-containing domain (1);Soluble quinoprotein glucose/sorbosone dehydrogenase (1);WD40-repeat-containing domain (1);	0.432182	0.22954	N	0.053633	T	0.11922	0.0290	N	0.04705	-0.18	0.35200	D	0.774171	B	0.06786	0.001	B	0.04013	0.001	T	0.09122	-1.0689	10	0.09338	T	0.73	-16.5307	4.2639	0.10754	0.0:0.5978:0.19:0.2122	rs45559439	508	Q969U6	FBXW5_HUMAN	Q	508	ENSP00000313034:R508Q	ENSP00000313034:R508Q	R	-	2	0	FBXW5	138955379	0.994000	0.37717	1.000000	0.80357	0.857000	0.48899	1.227000	0.32576	0.403000	0.25479	-0.265000	0.10407	CGG	C|0.985;T|0.015	0.015	strong		0.677	FBXW5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055227.1	NM_018998		T	139835558	C	T	139835558	3	4	28	1	0	0	0	0	1	0	0	0	5776	652	23	1	181	1	FBXW5	9	139835558	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	264128	139835558	1377873	367	11870											
PNPLA7	375775	hgsc.bcm.edu	37	chr9	140444627	140444628	+	Frame_Shift_Ins	INS	-	-	T																															cgagttacatacctgtgggcINStgtcatctttctcttcctcc																								rs372921391|rs372038516	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:140444627_140444628insT	ENST00000277531.4	-	1	208_209	c.22_23insA	c.(22-24)agcfs	p.S8fs	MRPL41_ENST00000371443.5_5'Flank|PNPLA7_ENST00000406427.1_Frame_Shift_Ins_p.S8fs	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	8					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)		TACCTGTGGGCTGTCATCTTTC	0.559													C|T|TT|complex_insertion	13	0.00259585	0.0	0.0043	5008	,	,		18178	0.0		0.0099	False		,,,				2504	0.0				p.S8fs		Pindel,Atlas-Indel	.											.	PNPLA7	124	.	0			c.23_24insA						PASS	.		,	12,4252		0,12,2120					,	0.2	0			114	100,8154		0,100,4027	no	frameshift,frameshift	PNPLA7	NM_152286.3,NM_001098537.1	,	0,112,6147	A1A1,A1R,RR		1.2115,0.2814,0.8947	,	,		112,12406				SO:0001589	frameshift_variant	375775	exon1			.	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.23dupA	9.37:g.140444628_140444628dupT	ENSP00000277531:p.Ser8fs	42	0	.		36	19	0.528	NM_152286	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Frame_Shift_Ins	INS	ENST00000277531.4	37	CCDS7045.1																																																																																			.	.	weak		0.559	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286		T	140444628	-	T	140444627	7	5	28	1	0	1	1	0	0	0	0	0	12179	797	28	0	4145	0	PNPLA7	9	140444627	Frame_Shift_Ins	INS	-	TCGA-G8-6914-01A-11D-2210-10	609069	140444627	768804	368	11871											
AKR1C1	1645	hgsc.bcm.edu	37	chr10	5011027	5011027	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttcccaggccgtggagaagtGtaaagatgcaggattggcca	11	8	14	8	1	0	2	0	0	0	2	1	4	1	3	3	4	1	2	3	4	3	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:5011027G>A	ENST00000380872.4	+	5	653	c.461G>A	c.(460-462)tGt>tAt	p.C154Y	AKR1C1_ENST00000380859.1_Missense_Mutation_p.C156Y|AKR1C1_ENST00000434459.2_Missense_Mutation_p.C154Y|AKR1C1_ENST00000477661.1_3'UTR	NM_001353.5	NP_001344.2	Q04828	AK1C1_HUMAN	aldo-keto reductase family 1, member C1	154					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)	GTGGAGAAGTGTAAAGATGCA	0.473																																					p.C154Y	Colon(130;2054 2316 13360 15380)	Atlas-SNP	.											.	AKR1C1	39	.	0			c.G461A						PASS	.						131	115	121					10																	5011027		2203	4300	6503	SO:0001583	missense	1645	exon5			AGAAGTGTAAAGA	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.461G>A	10.37:g.5011027G>A	ENSP00000370254:p.Cys154Tyr	171	0	0		136	34	0.25	NM_001353	P52896|Q5SR15|Q7M4N2|Q9UCX2	Missense_Mutation	SNP	ENST00000380872.4	37	CCDS7061.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	4.273|4.273	0.049878|0.049878	0.08243|0.08243	.|.	.|.	ENSG00000187134|ENSG00000187134	ENST00000434459;ENST00000380872;ENST00000380859|ENST00000442997	T;T;T|.	0.23552|.	1.9;1.9;1.9|.	2.1|2.1	2.1|2.1	0.27182|0.27182	Aldo/keto reductase, conserved site (1);NADP-dependent oxidoreductase domain (3);|.	0.170003|.	0.42053|.	D|.	0.000762|.	T|T	0.41488|0.41488	0.1161|0.1161	L|L	0.46670|0.46670	1.46|1.46	0.28041|0.28041	N|N	0.933763|0.933763	D|.	0.62365|.	0.991|.	D|.	0.67103|.	0.949|.	T|T	0.31138|0.31138	-0.9954|-0.9954	10|5	0.87932|.	D|.	0|.	.|.	10.2386|10.2386	0.43299|0.43299	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	154|.	Q04828|.	AK1C1_HUMAN|.	Y|I	154;154;156|121	ENSP00000412248:C154Y;ENSP00000370254:C154Y;ENSP00000370240:C156Y|.	ENSP00000370240:C156Y|.	C|V	+|+	2|1	0|0	AKR1C1|AKR1C1	5001027|5001027	1.000000|1.000000	0.71417|0.71417	0.820000|0.820000	0.32676|0.32676	0.054000|0.054000	0.15201|0.15201	3.786000|3.786000	0.55431|0.55431	1.475000|1.475000	0.48197|0.48197	0.305000|0.305000	0.20034|0.20034	TGT|GTA	.	.	none		0.473	AKR1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046523.2	NM_001353		A	5011027	G	A	5011027	3	1	28	1	0	0	0	0	1	0	0	0	469	1377	48	2	479	2	AKR1C1	10	5011027	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10		5011027	130523720	369	11872											
ITIH2	3698	hgsc.bcm.edu	37	chr10	7774397	7774397	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagatcccgatttcaccaggAaactgtgggcctatctaacc	11	9	8	13	1	2	1	1	0	1	1	3	3	3	2	4	2	2	0	4	2	3	3	rs141156651		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:7774397A>G	ENST00000358415.4	+	14	1910	c.1744A>G	c.(1744-1746)Aaa>Gaa	p.K582E	ITIH2_ENST00000379587.4_Missense_Mutation_p.K571E	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	582					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						TTTCACCAGGAAACTGTGGGC	0.493																																					p.K582E		Atlas-SNP	.											.	ITIH2	144	.	0			c.A1744G						PASS	.	A	GLU/LYS	0,4406		0,0,2203	101	91	95		1744	5.3	0.8	10	dbSNP_134	95	6,8594	5.7+/-21.5	0,6,4294	yes	missense	ITIH2	NM_002216.2	56	0,6,6497	GG,GA,AA		0.0698,0.0,0.0461	possibly-damaging	582/947	7774397	6,13000	2203	4300	6503	SO:0001583	missense	3698	exon14			ACCAGGAAACTGT	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.1744A>G	10.37:g.7774397A>G	ENSP00000351190:p.Lys582Glu	84	0	0		76	39	0.513158	NM_002216	Q14659|Q15484|Q5T986	Missense_Mutation	SNP	ENST00000358415.4	37	CCDS31141.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.202257	0.79127	0.0	6.98E-4	ENSG00000151655	ENST00000358415;ENST00000379587	T;T	0.30714	1.52;1.52	5.32	5.32	0.75619	.	0.054094	0.85682	D	0.000000	T	0.40619	0.1124	M	0.76838	2.35	0.41456	D	0.988014	P	0.45902	0.868	P	0.45167	0.472	T	0.47724	-0.9095	10	0.87932	D	0	-28.5342	11.323	0.49433	0.848:0.152:0.0:0.0	.	582	P19823	ITIH2_HUMAN	E	582;571	ENSP00000351190:K582E;ENSP00000368906:K571E	ENSP00000351190:K582E	K	+	1	0	ITIH2	7814403	1.000000	0.71417	0.827000	0.32855	0.967000	0.64934	6.049000	0.71053	2.022000	0.59522	0.523000	0.50628	AAA	A|1.000;G|0.000	0.000	weak		0.493	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216		G	7774397	A	G	7774397	3	3	28	1	0	0	0	0	1	0	0	0	7913	247	9	3	1798	3	ITIH2	10	7774397	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	2763370	7774397	127760350	370	11873											
CCDC3	83643	hgsc.bcm.edu	37	chr10	12940631	12940631	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctgctgcagtttcttgaCgtggtcctcctcctcaaaca	6	15	7	13	1	3	1	1	1	2	0	6	1	6	1	3	1	3	3	3	1	1	3	rs145872952		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:12940631C>T	ENST00000378825.3	-	3	724	c.598G>A	c.(598-600)Gtc>Atc	p.V200I	CCDC3_ENST00000378839.1_Missense_Mutation_p.V75I	NM_031455.3	NP_113643.1	Q9BQI4	CCDC3_HUMAN	coiled-coil domain containing 3	200						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)			AGTTTCTTGACGTGGTCCTCC	0.602													C|||	1	0.000199681	0.0	0.0	5008	,	,		16856	0.0		0.001	False		,,,				2504	0.0				p.V200I		Atlas-SNP	.											.	CCDC3	27	.	0			c.G598A						PASS	.	C	ILE/VAL	0,4406		0,0,2203	72	62	65		598	5.4	1	10	dbSNP_134	65	4,8596	3.7+/-12.6	0,4,4296	yes	missense	CCDC3	NM_031455.3	29	0,4,6499	TT,TC,CC		0.0465,0.0,0.0308	benign	200/271	12940631	4,13002	2203	4300	6503	SO:0001583	missense	83643	exon3			TCTTGACGTGGTC	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.598G>A	10.37:g.12940631C>T	ENSP00000368102:p.Val200Ile	83	0	0		109	51	0.46789	NM_031455	Q5VYV8|Q5VYV9	Missense_Mutation	SNP	ENST00000378825.3	37	CCDS7093.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	23.8	4.455433	0.84209	0.0	4.65E-4	ENSG00000151468	ENST00000378839;ENST00000378825	T	0.17691	2.26	5.42	5.42	0.78866	.	0.330512	0.26106	N	0.026308	T	0.18257	0.0438	M	0.64997	1.995	0.40106	D	0.976437	P	0.44946	0.846	B	0.30251	0.113	T	0.10245	-1.0638	10	0.56958	D	0.05	-25.0542	18.1996	0.89833	0.0:1.0:0.0:0.0	.	200	Q9BQI4	CCDC3_HUMAN	I	75;200	ENSP00000368116:V75I	ENSP00000368102:V200I	V	-	1	0	CCDC3	12980637	0.999000	0.42202	0.998000	0.56505	0.880000	0.50808	4.526000	0.60566	2.550000	0.86006	0.561000	0.74099	GTC	C|1.000;T|0.000	0.000	strong		0.602	CCDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046829.1	NM_031455		T	12940631	C	T	12940631	3	4	28	1	0	0	0	0	1	0	0	0	2806	536	19	1	218	1	CCDC3	10	12940631	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	5166234	12940631	122594116	371	11874											
BEND7	222389	hgsc.bcm.edu	37	chr10	13481466	13481466	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcaccgctgcactcccaccCggcagaacagtgcagggccc	8	4	11	18	2	1	1	1	0	0	1	2	1	2	1	4	2	3	4	4	2	1	0	rs76298779	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:13481466C>T	ENST00000396900.2	-	9	1265	c.1266G>A	c.(1264-1266)ccG>ccA	p.P422P	BEND7_ENST00000486542.1_5'UTR|BEND7_ENST00000341083.3_Silent_p.P371P			Q8N7W2	BEND7_HUMAN	BEN domain containing 7	422						extracellular vesicular exosome (GO:0070062)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|stomach(1)	17						CACTCCCACCCGGCAGAACAG	0.527													C|||	142	0.0283546	0.1036	0.0072	5008	,	,		21405	0.0		0.0	False		,,,				2504	0.0				p.P371P		Atlas-SNP	.											.	BEND7	85	.	0			c.G1113A						PASS	.	C		389,4017	193.6+/-218.7	15,359,1829	56	50	52		1113	1.2	0	10	dbSNP_131	52	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	BEND7	NM_152751.2		15,361,6127	TT,TC,CC		0.0233,8.8289,3.0063		371/469	13481466	391,12615	2203	4300	6503	SO:0001819	synonymous_variant	222389	exon9			CCCACCCGGCAGA	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.1266G>A	10.37:g.13481466C>T		60	0	0		66	30	0.454545	NM_152751	Q5SYY7|Q5SYY8|Q5SYY9|Q8N5T7	Silent	SNP	ENST00000396900.2	37																																																																																				C|0.965;T|0.035	0.035	strong		0.527	BEND7-202	KNOWN	basic	protein_coding	protein_coding		NM_152751		T	13481466	C	T	13481466	2	4	28	1	0	0	0	0	0	0	0	1	1403	639	23	1		1	BEND7	10	13481466	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	540835	13481466	122053281	372	11875											
PRPF18	8559	hgsc.bcm.edu	37	chr10	13639490	13639490	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tatttcaagcgtagtgagctCgccaaaaaagaagaggaagc	16	7	11	7	2	1	3	1	1	0	2	2	4	1	4	1	1	3	2	1	1	8	3	rs2502213	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:13639490C>T	ENST00000378572.3	+	2	259	c.99C>T	c.(97-99)ctC>ctT	p.L33L		NM_003675.3	NP_003666.1	Q99633	PRP18_HUMAN	pre-mRNA processing factor 18	33					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	potassium channel inhibitor activity (GO:0019870)			central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(5)|prostate(1)	17						GTAGTGAGCTCGCCAAAAAAG	0.284													C|||	136	0.0271565	0.0968	0.0072	5008	,	,		16174	0.001		0.0	False		,,,				2504	0.002				p.L33L		Atlas-SNP	.											.	PRPF18	32	.	0			c.C99T						PASS	.	C		399,4007	198.7+/-222.5	17,365,1821	92	93	93		99	-1.6	0.9	10	dbSNP_100	93	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	PRPF18	NM_003675.3		17,371,6115	TT,TC,CC		0.0698,9.0558,3.1139		33/343	13639490	405,12601	2203	4300	6503	SO:0001819	synonymous_variant	8559	exon2			TGAGCTCGCCAAA	U51990	CCDS7100.1	10p12.33	2013-06-10	2013-06-10		ENSG00000165630	ENSG00000165630			17351	protein-coding gene	gene with protein product		604993	"PRP18 pre-mRNA processing factor 18 homolog (yeast)", "PRP18 pre-mRNA processing factor 18 homolog (S. cerevisiae)"			9000057	Standard	XM_005252634		Approved	hPrp18	uc001imp.3	Q99633	OTTHUMG00000017702	ENST00000378572.3:c.99C>T	10.37:g.13639490C>T		40	0	0		43	22	0.511628	NM_003675	Q5T9P9|Q9BUI9	Silent	SNP	ENST00000378572.3	37	CCDS7100.1																																																																																			C|0.972;T|0.028	0.028	strong		0.284	PRPF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046879.1			T	13639490	C	T	13639490	2	4	28	1	0	0	0	0	0	0	0	1	12575	871	31	1		1	PRPF18	10	13639490	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	158024	13639490	121895257	373	11876											
KIAA1217	56243	hgsc.bcm.edu	37	chr10	24833407	24833407	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcgataccttcagcttcacgTaaggtatcttggtctgctgg	7	14	10	10	2	4	0	2	0	2	0	5	1	4	0	1	3	3	4	1	3	3	6			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:24833407T>C	ENST00000376454.3	+	19	5238	c.5208T>C	c.(5206-5208)cgT>cgC	p.R1736R	KIAA1217_ENST00000396446.1_Intron|KIAA1217_ENST00000307544.6_Intron|KIAA1217_ENST00000376462.1_Intron|KIAA1217_ENST00000396445.1_Intron|KIAA1217_ENST00000458595.1_Intron|KIAA1217_ENST00000376452.3_Intron|KIAA1217_ENST00000376451.2_Silent_p.R1419R	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	1736					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						CAGCTTCACGTAAGGTATCTT	0.493																																					p.R1736R		Atlas-SNP	.											KIAA1217,colon,carcinoma,+1,1	KIAA1217	235	1	0			c.T5208C						scavenged	.						45	45	45					10																	24833407		2203	4300	6503	SO:0001819	synonymous_variant	56243	exon19			TTCACGTAAGGTA	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.5208T>C	10.37:g.24833407T>C		48	0	0		65	3	0.0461538	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Silent	SNP	ENST00000376454.3	37	CCDS31165.1																																																																																			.	.	none		0.493	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590		C	24833407	T	C	24833407	2	2	28	1	0	0	0	0	0	0	0	1	8225	1625	57	3		3	KIAA1217	10	24833407	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	11193917	24833407	110701340	374	11877											
MYO3A	53904	hgsc.bcm.edu	37	chr10	26455090	26455090	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aagctggtctcgataactggGctcttggaaaaacaaaagta	15	9	10	7	1	2	0	0	0	2	0	3	2	2	1	0	3	3	3	0	3	7	3	rs34918608	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:26455090G>A	ENST00000265944.5	+	27	3260	c.3094G>A	c.(3094-3096)Gct>Act	p.A1032T	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1032	Myosin motor.		A -> T (in dbSNP:rs34918608). {ECO:0000269|PubMed:17344846}.		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						CGATAACTGGGCTCTTGGAAA	0.408													G|||	18	0.00359425	0.0008	0.0072	5008	,	,		18704	0.0		0.0119	False		,,,				2504	0.0				p.A1032T		Atlas-SNP	.											MYO3A,NS,carcinoma,-1,1	MYO3A	371	1	0			c.G3094A						PASS	.	G	THR/ALA	8,4398	12.9+/-30.5	0,8,2195	96	103	101		3094	5.2	1	10	dbSNP_126	101	73,8527	44.0+/-102.2	1,71,4228	yes	missense	MYO3A	NM_017433.4	58	1,79,6423	AA,AG,GG		0.8488,0.1816,0.6228	possibly-damaging	1032/1617	26455090	81,12925	2203	4300	6503	SO:0001583	missense	53904	exon27			AACTGGGCTCTTG	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.3094G>A	10.37:g.26455090G>A	ENSP00000265944:p.Ala1032Thr	45	0	0		35	18	0.514286	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	12	0.005494505494505495	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	8	0.010554089709762533	G	20.1	3.938089	0.73557	0.001816	0.008488	ENSG00000095777	ENST00000265944	D	0.87256	-2.23	6.07	5.17	0.71159	Myosin head, motor domain (2);	0.231325	0.47455	N	0.000222	D	0.84338	0.5450	M	0.63428	1.95	0.80722	D	1	P	0.43412	0.806	P	0.47705	0.555	D	0.84836	0.0805	10	0.39692	T	0.17	.	12.1062	0.53813	0.1365:0.0:0.8635:0.0	rs34918608;rs61729832	1032	Q8NEV4	MYO3A_HUMAN	T	1032	ENSP00000265944:A1032T	ENSP00000265944:A1032T	A	+	1	0	MYO3A	26495096	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.247000	0.65416	1.586000	0.49944	0.650000	0.86243	GCT	G|0.994;A|0.006	0.006	strong		0.408	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		A	26455090	G	A	26455090	3	1	28	1	0	0	0	0	1	0	0	0	10085	1203	42	2	3192	2	MYO3A	10	26455090	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1621683	26455090	109079657	375	11878											
MASTL	84930	hgsc.bcm.edu	37	chr10	27458886	27458886	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctcttaggaaagtgatgaagCattgggcccaacaatgatga	14	9	11	7	0	1	4	0	4	1	0	1	5	1	5	1	2	2	1	1	2	5	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:27458886C>T	ENST00000375940.4	+	8	1055	c.998C>T	c.(997-999)gCa>gTa	p.A333V	MASTL_ENST00000342386.6_Missense_Mutation_p.A333V|MASTL_ENST00000375946.4_Missense_Mutation_p.A333V|MASTL_ENST00000477034.1_3'UTR			Q96GX5	GWL_HUMAN	microtubule associated serine/threonine kinase-like	333	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						AGTGATGAAGCATTGGGCCCA	0.358																																					p.A333V		Atlas-SNP	.											.	MASTL	81	.	0			c.C998T						PASS	.						66	65	65					10																	27458886		2203	4300	6503	SO:0001583	missense	84930	exon8			ATGAAGCATTGGG	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.998C>T	10.37:g.27458886C>T	ENSP00000365107:p.Ala333Val	73	0	0		59	20	0.338983	NM_032844	Q5T8D5|Q5T8D7|Q8NCD6|Q96SJ5	Missense_Mutation	SNP	ENST00000375940.4	37	CCDS53502.1	.	.	.	.	.	.	.	.	.	.	C	0.061	-1.224400	0.01530	.	.	ENSG00000120539	ENST00000375946;ENST00000342386;ENST00000375940	T;T;T	0.65549	-0.02;-0.16;-0.02	5.28	2.44	0.29823	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.881451	0.10156	N	0.708985	T	0.46814	0.1412	L	0.38531	1.155	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.09377	0.004;0.001;0.002	T	0.31194	-0.9952	10	0.25751	T	0.34	-2.2806	4.3382	0.11097	0.1893:0.5647:0.0:0.246	.	333;333;333	Q96GX5-2;Q96GX5;Q96GX5-3	.;GWL_HUMAN;.	V	333	ENSP00000365113:A333V;ENSP00000343446:A333V;ENSP00000365107:A333V	ENSP00000343446:A333V	A	+	2	0	MASTL	27498892	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	0.005000	0.13129	0.370000	0.24538	-0.133000	0.14855	GCA	.	.	none		0.358	MASTL-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047320.1	NM_032844		T	27458886	C	T	27458886	3	4	28	1	0	0	0	0	1	0	0	0	9337	710	25	2	1028	2	MASTL	10	27458886	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1003796	27458886	108075861	376	11879											
CCDC7	79741	hgsc.bcm.edu	37	chr10	32780886	32780886	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gactaatcgatttaatgccaTgttgaaagtatttgaaaacc	15	13	7	6	1	0	2	0	2	0	0	1	4	0	2	2	0	2	2	2	0	6	6	rs145255525	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:32780886T>C	ENST00000362006.5	+	10	1376	c.833T>C	c.(832-834)aTg>aCg	p.M278T	CCDC7_ENST00000535327.1_Intron|CCDC7_ENST00000489718.1_3'UTR|CCDC7_ENST00000537047.1_3'UTR|CCDC7_ENST00000539197.1_Intron|CCDC7_ENST00000277657.6_Missense_Mutation_p.M278T|CCDC7_ENST00000545067.1_Intron	NM_145023.4	NP_659460.3	Q96M83	CCDC7_HUMAN	coiled-coil domain containing 7	278										NS(1)|breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(2)	14		Breast(68;0.000207)|Prostate(175;0.0107)				TTTAATGCCATGTTGAAAGTA	0.249																																					p.M278T		Atlas-SNP	.											.	CCDC7	47	.	0			c.T833C						PASS	.	T	THR/MET,THR/MET	0,4406		0,0,2203	76	85	82		833,833	4.1	0.5	10	dbSNP_134	82	4,8586	3.7+/-12.6	0,4,4291	yes	missense,missense	CCDC7	NM_001026383.1,NM_145023.4	81,81	0,4,6494	CC,CT,TT		0.0466,0.0,0.0308	possibly-damaging,possibly-damaging	278/487,278/487	32780886	4,12992	2203	4295	6498	SO:0001583	missense	221016	exon10			ATGCCATGTTGAA	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.833T>C	10.37:g.32780886T>C	ENSP00000355078:p.Met278Thr	86	0	0		68	36	0.529412	NM_145023	Q5VW55|Q8IVQ0|Q8NEQ0	Missense_Mutation	SNP	ENST00000362006.5	37	CCDS7173.1	.	.	.	.	.	.	.	.	.	.	T	13.47	2.248137	0.39697	0.0	4.66E-4	ENSG00000216937	ENST00000277657;ENST00000362006	T;T	0.38077	1.16;1.16	4.13	4.13	0.48395	.	.	.	.	.	T	0.40322	0.1112	L	0.36672	1.1	0.80722	D	1	D	0.54964	0.969	P	0.55087	0.768	T	0.28202	-1.0051	9	0.72032	D	0.01	-22.3335	9.8398	0.40991	0.0:0.0:0.0:1.0	.	278	Q96M83	CCDC7_HUMAN	T	278	ENSP00000277657:M278T;ENSP00000355078:M278T	ENSP00000277657:M278T	M	+	2	0	CCDC7	32820892	0.994000	0.37717	0.468000	0.27192	0.520000	0.34377	2.364000	0.44187	2.098000	0.63641	0.459000	0.35465	ATG	T|1.000;C|0.000	0.000	strong		0.249	CCDC7-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047490.1	NM_145023		C	32780886	T	C	32780886	3	2	28	1	0	0	0	0	1	0	0	0	2844	1464	51	3	867	3	CCDC7	10	32780886	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	5322000	32780886	102753861	377	11880											
SYT15	83849	hgsc.bcm.edu	37	chr10	46965017	46965017	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ctcactgacaatgcctctgtCctcctggagccggaggccct	6	9	10	16	1	2	1	1	1	1	0	4	3	4	3	5	3	2	0	5	3	1	0	rs200586361	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:46965017C>T	ENST00000374321.4	-	6	994	c.928G>A	c.(928-930)Gac>Aac	p.D310N	SYT15_ENST00000374325.3_Missense_Mutation_p.D310N|RP11-38L15.3_ENST00000506914.1_RNA|SYT15_ENST00000374323.4_Missense_Mutation_p.D363N|SYT15_ENST00000503753.1_Missense_Mutation_p.D310N	NM_031912.4	NP_114118.2	Q9BQS2	SYT15_HUMAN	synaptotagmin XV	310	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						ATGCCTCTGTCCTCCTGGAGC	0.612													C|||	11	0.00219649	0.0	0.0043	5008	,	,		40565	0.0		0.008	False		,,,				2504	0.0				p.D310N	Ovarian(57;1152 1428 19651 37745)	Atlas-SNP	.											SYT15_ENST00000374328,NS,carcinoma,-1,1	SYT15	165	1	0			c.G928A						PASS	.	C	ASN/ASP,ASN/ASP	6,4270		0,6,2132	53	61	58		928,928	3.2	0	10		58	47,8463		0,47,4208	yes	missense,missense	SYT15	NM_031912.4,NM_181519.2	23,23	0,53,6340	TT,TC,CC		0.5523,0.1403,0.4145	benign,benign	310/422,310/391	46965017	53,12733	2138	4255	6393	SO:0001583	missense	83849	exon6			CTCTGTCCTCCTG	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.928G>A	10.37:g.46965017C>T	ENSP00000363441:p.Asp310Asn	107	0	0		115	26	0.226087	NM_031912	A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	Missense_Mutation	SNP	ENST00000374321.4	37	CCDS44376.1	.	.	.	.	.	.	.	.	.	.	.	12.54	1.967239	0.34754	0.001403	0.005523	ENSG00000204176	ENST00000416127;ENST00000374328;ENST00000374325;ENST00000503753;ENST00000374330;ENST00000374323;ENST00000374321	T;T;T;T;T	0.68765	-0.35;-0.35;-0.35;-0.35;-0.35	5.06	3.16	0.36331	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.144113	0.64402	N	0.000009	T	0.45115	0.1326	L	0.35793	1.09	0.21290	N	0.999734	B;B	0.11235	0.004;0.004	B;B	0.13407	0.009;0.005	T	0.39563	-0.9608	10	0.38643	T	0.18	.	9.1541	0.36983	0.0:0.7682:0.1482:0.0836	.	310;310	Q9BQS2;Q9BQS2-2	SYT15_HUMAN;.	N	310;100;310;310;149;363;310	ENSP00000363448:D100N;ENSP00000363445:D310N;ENSP00000427607:D310N;ENSP00000363443:D363N;ENSP00000363441:D310N	ENSP00000363441:D310N	D	-	1	0	SYT15	46385023	0.254000	0.23992	0.011000	0.14972	0.936000	0.57629	1.068000	0.30629	0.763000	0.33175	0.561000	0.74099	GAC	C|0.998;T|0.002	0.002	weak		0.612	SYT15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367008.1	NM_031912		T	46965017	C	T	46965017	3	4	28	1	0	0	0	0	1	0	0	0	15486	855	30	2	403	2	SYT15	10	46965017	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	14184131	46965017	88569730	378	11881											
PHYHIPL	84457	hgsc.bcm.edu	37	chr10	61005204	61005204	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	taccaccatgcccaggatgtCattttagaagtcatttacac	12	12	6	11	0	2	1	2	0	0	1	2	2	2	2	3	1	3	0	3	1	4	5	rs138490289	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:61005204C>T	ENST00000373880.4	+	5	1248	c.984C>T	c.(982-984)gtC>gtT	p.V328V	PHYHIPL_ENST00000373878.3_Silent_p.V302V	NM_032439.3	NP_115815.2	Q96FC7	PHIPL_HUMAN	phytanoyl-CoA 2-hydroxylase interacting protein-like	328						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						CCCAGGATGTCATTTTAGAAG	0.433													C|||	2	0.000399361	0.0	0.0029	5008	,	,		18642	0.0		0.0	False		,,,				2504	0.0				p.V328V		Atlas-SNP	.											.	PHYHIPL	44	.	0			c.C984T						PASS	.	C	,	2,4404	4.2+/-10.8	0,2,2201	75	70	72		906,984	2.7	1	10	dbSNP_134	72	18,8582	14.6+/-50.1	0,18,4282	no	coding-synonymous,coding-synonymous	PHYHIPL	NM_001143774.1,NM_032439.3	,	0,20,6483	TT,TC,CC		0.2093,0.0454,0.1538	,	302/351,328/377	61005204	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	84457	exon5			GGATGTCATTTTA	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.984C>T	10.37:g.61005204C>T		99	0	0		109	44	0.40367	NM_032439	B7WP61|Q68DF3|Q6UXY3|Q8N3W3|Q96JM9|Q96NP7	Silent	SNP	ENST00000373880.4	37	CCDS7254.1																																																																																			C|0.998;T|0.002	0.002	strong		0.433	PHYHIPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048156.1	NM_032439		T	61005204	C	T	61005204	2	4	28	1	0	0	0	0	0	0	0	1	11876	813	29	2		2	PHYHIPL	10	61005204	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	14040187	61005204	74529543	379	11882											
SIRT1	23411	hgsc.bcm.edu	37	chr10	69644820	69644820	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagggcccatctcgggagcCaccgctggccgacaacttgt	7	6	13	15	3	1	0	0	0	1	0	2	2	1	1	4	3	2	2	4	3	1	1	rs182199697	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:69644820C>A	ENST00000212015.6	+	1	394	c.341C>A	c.(340-342)cCa>cAa	p.P114Q	SIRT1_ENST00000432464.1_5'Flank	NM_012238.4	NP_036370.2	Q96EB6	SIR1_HUMAN	sirtuin 1	114	Interaction with CLOCK. {ECO:0000250|UniProtKB:Q923E4}.|Interaction with HIST1H1E.				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						TCTCGGGAGCCACCGCTGGCC	0.721													C|||	8	0.00159744	0.0	0.0043	5008	,	,		9467	0.0		0.005	False		,,,				2504	0.0				p.P114Q		Atlas-SNP	.											.	SIRT1	38	.	0			c.C341A						PASS	.	C	GLN/PRO	3,3319		0,3,1658	3	4	4		341	3	0.9	10		4	24,6694		0,24,3335	yes	missense	SIRT1	NM_012238.4	76	0,27,4993	AA,AC,CC		0.3572,0.0903,0.2689	benign	114/748	69644820	27,10013	1661	3359	5020	SO:0001583	missense	23411	exon1			GGGAGCCACCGCT	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.341C>A	10.37:g.69644820C>A	ENSP00000212015:p.Pro114Gln	32	0	0		43	27	0.627907	NM_012238	Q2XNF6|Q5JVQ0|Q9GZR9|Q9Y6F0	Missense_Mutation	SNP	ENST00000212015.6	37	CCDS7273.1	23	0.010531135531135532	11	0.022357723577235773	4	0.011049723756906077	0	0.0	8	0.010554089709762533	c	9.153	1.016794	0.19355	9.03E-4	0.003572	ENSG00000096717	ENST00000212015	T	0.36157	1.27	3.91	3.0	0.34707	.	1.246700	0.05789	N	0.609970	T	0.18718	0.0449	L	0.44542	1.39	0.80722	D	1	P	0.36733	0.567	B	0.37387	0.248	T	0.03000	-1.1084	10	0.35671	T	0.21	0.1106	7.5885	0.28006	0.0:0.8736:0.0:0.1264	.	114	Q96EB6	SIRT1_HUMAN	Q	114	ENSP00000212015:P114Q	ENSP00000212015:P114Q	P	+	2	0	SIRT1	69314826	0.994000	0.37717	0.940000	0.37924	0.069000	0.16628	0.498000	0.22530	0.746000	0.32786	0.556000	0.70494	CCA	C|0.989;A|0.011	0.011	strong		0.721	SIRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048296.1			A	69644820	C	A	69644820	3	1	28	1	0	0	0	0	1	0	0	0	14352	594	21	4	343	4	SIRT1	10	69644820	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	8639616	69644820	65889927	380	11883											
MYPN	84665	hgsc.bcm.edu	37	chr10	69902800	69902800	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggaagcctttgaagaggacAcaggacgctattcctgcttt	10	10	11	10	2	0	2	0	1	0	1	1	5	1	5	2	3	2	2	2	3	3	4			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:69902800A>T	ENST00000358913.5	+	3	1494	c.1006A>T	c.(1006-1008)Aca>Tca	p.T336S	MYPN_ENST00000354393.2_Missense_Mutation_p.T61S|MYPN_ENST00000373675.3_Missense_Mutation_p.T336S|MYPN_ENST00000540630.1_Missense_Mutation_p.T336S	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	336	Ig-like 1.|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						TGAAGAGGACACAGGACGCTA	0.443																																					p.T336S		Atlas-SNP	.											.	MYPN	189	.	0			c.A1006T						PASS	.						118	107	111					10																	69902800		2203	4300	6503	SO:0001583	missense	84665	exon3			GAGGACACAGGAC	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.1006A>T	10.37:g.69902800A>T	ENSP00000351790:p.Thr336Ser	58	0	0		64	33	0.515625	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	37	CCDS7275.1	.	.	.	.	.	.	.	.	.	.	A	32	5.115153	0.94339	.	.	ENSG00000138347	ENST00000354393;ENST00000542332;ENST00000358913;ENST00000540630;ENST00000373675	T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1	5.59	5.59	0.84812	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.53286	0.1787	N	0.01188	-0.97	0.80722	D	1	D;D;D;D	0.89917	0.998;1.0;0.999;0.999	D;D;D;D	0.87578	0.987;0.996;0.998;0.996	T	0.64706	-0.6344	9	.	.	.	.	15.7811	0.78260	1.0:0.0:0.0:0.0	.	336;336;61;336	F5GWA6;Q86TC9-3;Q86TC9-2;Q86TC9	.;.;.;MYPN_HUMAN	S	61;61;336;336;336	ENSP00000346369:T61S;ENSP00000351790:T336S;ENSP00000441668:T336S;ENSP00000362779:T336S	.	T	+	1	0	MYPN	69572806	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.253000	0.95501	2.123000	0.65237	0.533000	0.62120	ACA	.	.	none		0.443	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578		T	69902800	A	T	69902800	3	4	28	1	0	0	0	0	1	0	0	0	10107	159	6	5	1012	5	MYPN	10	69902800	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	257980	69902800	65631947	381	11884											
HK1	3098	hgsc.bcm.edu	37	chr10	71142492	71142492	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgaggaagcagacgcacaaCaatgccgtggttaagatgct	13	7	12	9	2	0	3	0	1	0	2	0	4	0	4	1	2	4	4	1	2	4	1	rs140498607	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:71142492C>T	ENST00000359426.6	+	10	1619	c.1515C>T	c.(1513-1515)aaC>aaT	p.N505N	HK1_ENST00000494253.1_3'UTR|HK1_ENST00000298649.3_Silent_p.N504N|HK1_ENST00000448642.2_Silent_p.N540N|HK1_ENST00000360289.2_Silent_p.N493N|HK1_ENST00000404387.2_Silent_p.N509N	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	505	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						AGACGCACAACAATGCCGTGG	0.622													C|||	12	0.00239617	0.0008	0.0014	5008	,	,		19064	0.001		0.008	False		,,,				2504	0.001				p.N509N		Atlas-SNP	.											.	HK1	170	.	0			c.C1527T						PASS	.	C	,,,,	2,4404	4.2+/-10.8	0,2,2201	103	77	86		1515,1512,1527,1527,1479	-9.8	0	10	dbSNP_134	86	54,8546	34.3+/-88.2	0,54,4246	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HK1	NM_000188.2,NM_033496.2,NM_033497.2,NM_033498.2,NM_033500.2	,,,,	0,56,6447	TT,TC,CC		0.6279,0.0454,0.4306	,,,,	505/918,504/917,509/922,509/922,493/906	71142492	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	3098	exon13			GCACAACAATGCC	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.1515C>T	10.37:g.71142492C>T		51	0	0		49	17	0.346939	NM_033498	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Silent	SNP	ENST00000359426.6	37	CCDS7292.1																																																																																			C|0.997;T|0.003	0.003	strong		0.622	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048429.2	NM_000188		T	71142492	C	T	71142492	2	4	28	1	0	0	0	0	0	0	0	1	7199	477	17	2		2	HK1	10	71142492	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1239692	71142492	64392255	382	11885											
CDHR1	92211	hgsc.bcm.edu	37	chr10	85958847	85958847	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gatgaggcgcccaggttcatCcaggagccttatgttgccct	7	10	12	12	1	1	1	1	1	0	0	2	3	2	2	4	3	2	2	4	3	1	3	rs148125234	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:85958847C>T	ENST00000372117.3	+	5	511	c.408C>T	c.(406-408)atC>atT	p.I136I	CDHR1_ENST00000332904.3_Silent_p.I136I|CDHR1_ENST00000440770.2_5'Flank	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	136	Cadherin 2. {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						CCAGGTTCATCCAGGAGCCTT	0.597													C|||	5	0.000998403	0.0008	0.0	5008	,	,		17525	0.0		0.004	False		,,,				2504	0.0				p.I136I		Atlas-SNP	.											.	CDHR1	122	.	0			c.C408T						PASS	.	C	,	1,4047		0,1,2023	95	77	83		408,408	3.3	0.9	10	dbSNP_134	83	15,7755		0,15,3870	no	coding-synonymous,coding-synonymous	CDHR1	NM_001171971.1,NM_033100.2	,	0,16,5893	TT,TC,CC		0.1931,0.0247,0.1354	,	136/746,136/860	85958847	16,11802	2024	3885	5909	SO:0001819	synonymous_variant	92211	exon5			GTTCATCCAGGAG	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.408C>T	10.37:g.85958847C>T		98	0	0		94	39	0.414894	NM_001171971	Q69YZ8|Q8IXY5	Silent	SNP	ENST00000372117.3	37	CCDS7372.1																																																																																			C|0.999;T|0.001	0.001	strong		0.597	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100		T	85958847	C	T	85958847	2	4	28	1	0	0	0	0	0	0	0	1	3120	845	30	2		2	CDHR1	10	85958847	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	14816355	85958847	49575900	383	11886											
LRIT1	26103	hgsc.bcm.edu	37	chr10	85992255	85992255	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgtcccccaccaccttcaCagacctcaccattcgtgcct	8	9	5	19	1	2	1	2	0	0	1	4	1	3	1	7	0	1	0	7	0	0	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:85992255C>T	ENST00000372105.3	-	4	1321	c.1300G>A	c.(1300-1302)Gtg>Atg	p.V434M		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	434	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.					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						ACCACCTTCACAGACCTCACC	0.587																																					p.V434M		Atlas-SNP	.											.	LRIT1	73	.	0			c.G1300A						PASS	.						107	83	91					10																	85992255		2203	4300	6503	SO:0001583	missense	26103	exon4			CCTTCACAGACCT	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.1300G>A	10.37:g.85992255C>T	ENSP00000361177:p.Val434Met	100	0	0		82	19	0.231707	NM_015613	Q0QD41|Q9Y4N7	Missense_Mutation	SNP	ENST00000372105.3	37	CCDS7373.1	.	.	.	.	.	.	.	.	.	.	C	17.10	3.303962	0.60305	.	.	ENSG00000148602	ENST00000372105	T	0.60797	0.16	5.58	3.68	0.42216	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.124327	0.53938	D	0.000047	T	0.52533	0.1740	L	0.43923	1.385	0.51012	D	0.999902	P	0.37276	0.589	B	0.39935	0.314	T	0.58668	-0.7596	10	0.62326	D	0.03	.	13.8294	0.63370	0.0:0.5725:0.4275:0.0	.	434	Q9P2V4	LRIT1_HUMAN	M	434	ENSP00000361177:V434M	ENSP00000361177:V434M	V	-	1	0	LRIT1	85982235	0.996000	0.38824	0.897000	0.35233	0.451000	0.32288	2.950000	0.49081	1.347000	0.45714	-0.165000	0.13383	GTG	.	.	none		0.587	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613		T	85992255	C	T	85992255	3	4	28	1	0	0	0	0	1	0	0	0	8956	478	17	2	575	2	LRIT1	10	85992255	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	33408	85992255	49542492	384	11887											
LDB3	11155	hgsc.bcm.edu	37	chr10	88466465	88466465	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccctgcttcaagtcctgcCgacagcccaaggtaactggg	8	7	11	15	1	1	0	1	0	0	0	2	1	2	0	5	2	4	2	5	2	3	2	rs45459491	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:88466465C>T	ENST00000361373.4	+	7	1095	c.1074C>T	c.(1072-1074)gcC>gcT	p.A358A	LDB3_ENST00000352360.5_Intron|LDB3_ENST00000458213.2_Intron|LDB3_ENST00000429277.2_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						CAAGTCCTGCCGACAGCCCAA	0.672													C|||	101	0.0201677	0.0008	0.0159	5008	,	,		18021	0.0		0.0368	False		,,,				2504	0.0532				p.A358A		Atlas-SNP	.											.	LDB3	164	.	0			c.C1074T						PASS	.	C	,,	34,4366		1,32,2167	29	22	25		,,1074	-0.1	0	10	dbSNP_127	25	317,8279		5,307,3986	no	intron,intron,coding-synonymous	LDB3	NM_001080114.1,NM_001171610.1,NM_007078.2	,,	6,339,6153	TT,TC,CC		3.6878,0.7727,2.7008	,,	,,358/728	88466465	351,12645	2200	4298	6498	SO:0001819	synonymous_variant	11155	exon7			TCCTGCCGACAGC	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.1074C>T	10.37:g.88466465C>T		139	0	0		164	71	0.432927	NM_007078		Silent	SNP	ENST00000361373.4	37	CCDS7377.1																																																																																			C|0.976;T|0.024	0.024	strong		0.672	LDB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049160.2			T	88466465	C	T	88466465	2	4	28	1	0	0	0	0	0	0	0	1	8706	639	23	1		1	LDB3	10	88466465	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2474210	88466465	47068282	385	11888											
RRP12	23223	hgsc.bcm.edu	37	chr10	99126513	99126513	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcacctgtcacctttgccCtgggcgggctcctcctcctc	2	12	8	19	1	2	0	2	0	1	0	7	0	5	0	6	2	1	1	6	2	0	1	rs45527941	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:99126513C>T	ENST00000370992.4	-	27	3312	c.3201G>A	c.(3199-3201)caG>caA	p.Q1067Q	RRP12_ENST00000315563.6_Silent_p.Q967Q|RRP12_ENST00000536831.1_Silent_p.Q785Q|RRP12_ENST00000414986.1_Silent_p.Q1006Q|RRP12_ENST00000479481.1_5'UTR	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	1067	Glu-rich.					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)		CACCTTTGCCCTGGGCGGGct	0.672													C|||	128	0.0255591	0.0038	0.0548	5008	,	,		15272	0.0		0.0716	False		,,,				2504	0.0133				p.Q1067Q		Atlas-SNP	.											.	RRP12	97	.	0			c.G3201A						PASS	.	C	,	58,4348	56.2+/-92.4	0,58,2145	70	82	78		3018,3201	4.8	1	10	dbSNP_127	78	501,8099	143.6+/-199.6	17,467,3816	no	coding-synonymous,coding-synonymous	RRP12	NM_001145114.1,NM_015179.3	,	17,525,5961	TT,TC,CC		5.8256,1.3164,4.298	,	1006/1237,1067/1298	99126513	559,12447	2203	4300	6503	SO:0001819	synonymous_variant	23223	exon27			TTTGCCCTGGGCG		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.3201G>A	10.37:g.99126513C>T		43	0	0		37	18	0.486486	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																			C|0.962;T|0.038	0.038	strong		0.672	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179		T	99126513	C	T	99126513	2	4	28	1	0	0	0	0	0	0	0	1	13701	680	24	2		2	RRP12	10	99126513	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	10660048	99126513	36408234	386	11889											
RRP12	23223	hgsc.bcm.edu	37	chr10	99150237	99150237	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggtacacctgaagggtcacGgggtagccccaggcctccag	8	6	14	13	1	1	1	1	1	0	0	2	1	2	1	5	5	2	2	5	5	3	2	rs41300219	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:99150237G>A	ENST00000370992.4	-	6	807	c.696C>T	c.(694-696)ccC>ccT	p.P232P	RRP12_ENST00000315563.6_Intron|RRP12_ENST00000536831.1_Silent_p.P38P|RRP12_ENST00000414986.1_Silent_p.P171P	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	232						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)		GAAGGGTCACGGGGTAGCCCC	0.612													G|||	201	0.0401358	0.0598	0.0533	5008	,	,		19526	0.0		0.0716	False		,,,				2504	0.0133				p.P232P		Atlas-SNP	.											.	RRP12	97	.	0			c.C696T						PASS	.	G	,	254,4152	148.0+/-182.4	9,236,1958	58	56	57		513,696	-11	0	10	dbSNP_127	57	501,8099	144.5+/-200.4	17,467,3816	no	coding-synonymous,coding-synonymous	RRP12	NM_001145114.1,NM_015179.3	,	26,703,5774	AA,AG,GG		5.8256,5.7649,5.805	,	171/1237,232/1298	99150237	755,12251	2203	4300	6503	SO:0001819	synonymous_variant	23223	exon6			GGTCACGGGGTAG		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.696C>T	10.37:g.99150237G>A		20	0	0		31	18	0.580645	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																			G|0.949;A|0.051	0.051	strong		0.612	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179		A	99150237	G	A	99150237	2	1	28	1	0	0	0	0	0	0	0	1	13701	1103	39	1		1	RRP12	10	99150237	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	23724	99150237	36384510	387	11890											
HPS1	3257	hgsc.bcm.edu	37	chr10	100185638	100185638	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagtacatggtgtggggcacTagggggcagtagctttcctt	7	11	15	8	0	0	0	0	0	0	0	1	0	1	0	1	5	2	5	1	5	3	5			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:100185638T>C	ENST00000325103.6	-	12	1325	c.1092A>G	c.(1090-1092)ctA>ctG	p.L364L	HPS1_ENST00000361490.4_Silent_p.L364L|HPS1_ENST00000467246.1_5'UTR	NM_000195.3	NP_000186.2	Q92902	HPS1_HUMAN	Hermansky-Pudlak syndrome 1	364					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)		TGTGGGGCACTAGGGGGCAGT	0.612									Hermansky-Pudlak syndrome		OREG0020430	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L364L		Atlas-SNP	.											.	HPS1	65	.	0			c.A1092G						PASS	.						105	108	107					10																	100185638		2203	4300	6503	SO:0001819	synonymous_variant	3257	exon12	Familial Cancer Database	HPS, HPS1-8	GGGCACTAGGGGG	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.1092A>G	10.37:g.100185638T>C		112	0	0	1349	108	59	0.546296	NM_000195	A8MRT2|O15402|O15502|Q5TAA3|Q8WXE5	Silent	SNP	ENST00000325103.6	37	CCDS7475.1																																																																																			.	.	none		0.612	HPS1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049776.1	NM_000195, NM_182637, NM_182638, NM_182639		C	100185638	T	C	100185638	2	2	28	1	0	0	0	0	0	0	0	1	7348	1509	53	3		3	HPS1	10	100185638	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	1035401	100185638	35349109	388	11891											
CNNM1	26507	hgsc.bcm.edu	37	chr10	101090246	101090246	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgacccggcttctgatggcaGccgccttccccgtgtgctac	4	10	11	16	3	1	2	0	2	1	0	2	2	2	2	5	2	3	3	5	2	1	3	rs144944413	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:101090246G>A	ENST00000356713.4	+	1	1391	c.1102G>A	c.(1102-1104)Gcc>Acc	p.A368T	CNNM1_ENST00000370534.4_Missense_Mutation_p.A3T|CNNM1_ENST00000446890.1_Missense_Mutation_p.A297T|CNNM1_ENST00000370528.3_Missense_Mutation_p.A297T	NM_020348.2	NP_065081.2	Q9NRU3	CNNM1_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 1	368	DUF21.				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)		TCTGATGGCAGCCGCCTTCCC	0.657													G|||	6	0.00119808	0.0	0.0058	5008	,	,		15163	0.0		0.002	False		,,,				2504	0.0				p.A368T		Atlas-SNP	.											.	CNNM1	101	.	0			c.G1102A						PASS	.	G	THR/ALA	2,4362		0,2,2180	8	9	8		1102	4.7	1	10	dbSNP_134	8	7,8501		0,7,4247	yes	missense	CNNM1	NM_020348.2	58	0,9,6427	AA,AG,GG		0.0823,0.0458,0.0699	benign	368/952	101090246	9,12863	2182	4254	6436	SO:0001583	missense	26507	exon1			ATGGCAGCCGCCT	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.1102G>A	10.37:g.101090246G>A	ENSP00000349147:p.Ala368Thr	45	0	0		55	36	0.654545	NM_020348	Q4QQG7|Q4QQH8|Q4QQP9|Q9NT45	Missense_Mutation	SNP	ENST00000356713.4	37	CCDS7478.2	4	0.0018315018315018315	0	0.0	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	G	14.74	2.624272	0.46840	4.58E-4	8.23E-4	ENSG00000119946	ENST00000356713;ENST00000446890;ENST00000370528;ENST00000370534	D;D;D;T	0.88431	-2.38;-2.38;-2.38;-0.66	4.67	4.67	0.58626	Domain of unknown function DUF21 (1);	0.155169	0.45361	D	0.000368	T	0.78033	0.4220	N	0.19112	0.55	0.36254	D	0.854107	P;B;B;B	0.35033	0.481;0.209;0.133;0.268	B;B;B;B	0.34536	0.164;0.185;0.045;0.143	D	0.85941	0.1458	10	0.72032	D	0.01	-5.7061	17.3611	0.87350	0.0:0.0:1.0:0.0	.	3;368;3;368	F5H5J0;Q9NRU3-2;B7Z5S3;Q9NRU3	.;.;.;CNNM1_HUMAN	T	368;297;297;3	ENSP00000349147:A368T;ENSP00000406492:A297T;ENSP00000359559:A297T;ENSP00000359565:A3T	ENSP00000349147:A368T	A	+	1	0	CNNM1	101080236	0.002000	0.14202	1.000000	0.80357	0.908000	0.53690	0.819000	0.27308	2.425000	0.82216	0.462000	0.41574	GCC	G|0.999;A|0.001	0.001	strong		0.657	CNNM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049792.2	NM_020348		A	101090246	G	A	101090246	3	1	28	1	0	0	0	0	1	0	0	0	3614	971	34	2	1104	2	CNNM1	10	101090246	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	904608	101090246	34444501	389	11892											
CPN1	1369	hgsc.bcm.edu	37	chr10	101823428	101823428	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccatctgggaagtaatctcCgcagttccaaccttggaaca	11	9	9	12	1	2	0	0	0	2	0	4	2	3	2	4	2	2	3	4	2	4	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:101823428C>T	ENST00000370418.3	-	5	1065	c.814G>A	c.(814-816)Gga>Aga	p.G272R		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	272	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)		AAGTAATCTCCGCAGTTCCAA	0.502																																					p.G272R		Atlas-SNP	.											.	CPN1	62	.	0			c.G814A						PASS	.						120	109	113					10																	101823428		2203	4300	6503	SO:0001583	missense	1369	exon5			AATCTCCGCAGTT	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.814G>A	10.37:g.101823428C>T	ENSP00000359446:p.Gly272Arg	92	0	0		84	47	0.559524	NM_001308	B1AP59	Missense_Mutation	SNP	ENST00000370418.3	37	CCDS7486.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.143860	0.77888	.	.	ENSG00000120054	ENST00000370418;ENST00000441382	T;T	0.32023	2.15;1.47	5.61	4.7	0.59300	Peptidase M14, carboxypeptidase A (2);	0.098868	0.64402	D	0.000001	T	0.46249	0.1383	L	0.48174	1.505	0.58432	D	0.999995	D	0.71674	0.998	D	0.64144	0.922	T	0.33240	-0.9876	10	0.36615	T	0.2	-13.7978	15.9713	0.80024	0.1358:0.8642:0.0:0.0	.	272	P15169	CBPN_HUMAN	R	272;69	ENSP00000359446:G272R;ENSP00000410895:G69R	ENSP00000359446:G272R	G	-	1	0	CPN1	101813418	1.000000	0.71417	1.000000	0.80357	0.800000	0.45204	7.341000	0.79300	1.355000	0.45865	0.555000	0.69702	GGA	.	.	none		0.502	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049828.1	NM_001308		T	101823428	C	T	101823428	3	4	28	1	0	0	0	0	1	0	0	0	3811	661	23	1	582	1	CPN1	10	101823428	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	733182	101823428	33711319	390	11893											
NOLC1	9221	hgsc.bcm.edu	37	chr10	103912218	103912218	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccagcgacctgtatcccctCgtgctcggcttcctgcgcga	4	9	10	18	5	0	0	0	0	0	0	4	2	2	0	5	1	3	3	5	1	1	2	rs117993238	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:103912218C>A	ENST00000605788.1	+	1	286	c.51C>A	c.(49-51)ctC>ctA	p.L17L	NOLC1_ENST00000488254.2_Silent_p.L17L|NOLC1_ENST00000405356.1_Silent_p.L17L|NOLC1_ENST00000603742.1_De_novo_Start_OutOfFrame	NM_001284389.1|NM_004741.3	NP_001271318.1|NP_004732.2	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	17	LisH. {ECO:0000255|PROSITE- ProRule:PRU00126}.				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)		TGTATCCCCTCGTGCTCGGCT	0.637													C|||	4	0.000798722	0.0	0.0014	5008	,	,		18450	0.0		0.003	False		,,,				2504	0.0				p.L17L		Atlas-SNP	.											.	NOLC1	61	.	0			c.C51A						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	81	77	78		51	-4.4	1	10	dbSNP_132	78	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous	NOLC1	NM_004741.3		0,12,6491	AA,AC,CC		0.1279,0.0227,0.0923		17/700	103912218	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	9221	exon1			TCCCCTCGTGCTC	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.51C>A	10.37:g.103912218C>A		55	0	0		47	19	0.404255	NM_004741	Q15030|Q5VV70|Q9BUV3	Silent	SNP	ENST00000605788.1	37	CCDS7530.1																																																																																			C|0.999;A|0.001	0.001	strong		0.637	NOLC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050012.2	NM_004741		A	103912218	C	A	103912218	2	1	28	1	0	0	0	0	0	0	0	1	10538	871	31	4		4	NOLC1	10	103912218	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2088790	103912218	31622529	391	11894											
SORCS1	114815	hgsc.bcm.edu	37	chr10	108339209	108339209	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catggcagatccactgtgggTtggagtgaggtccaccaggg	8	8	16	9	0	0	2	0	1	0	1	2	3	2	3	3	5	0	2	3	5	0	1	rs187136160	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:108339209T>C	ENST00000263054.6	-	25	3296	c.3289A>G	c.(3289-3291)Acc>Gcc	p.T1097A	SORCS1_ENST00000369698.1_Missense_Mutation_p.T632A|SORCS1_ENST00000344440.6_Missense_Mutation_p.T1097A	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	1097					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)		CCACTGTGGGTTGGAGTGAGG	0.527													T|||	2	0.000399361	0.0	0.0	5008	,	,		16881	0.0		0.002	False		,,,				2504	0.0				p.T1097A		Atlas-SNP	.											SORCS1_ENST00000344440,NS,carcinoma,+2,4	SORCS1	534	4	0			c.A3289G						PASS	.	T	ALA/THR,ALA/THR,ALA/THR,ALA/THR,ALA/THR,ALA/THR	0,4406		0,0,2203	94	74	81		3289,3289,3289,3289,3289,3289	3.6	0.9	10		81	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense,missense,missense	SORCS1	NM_001013031.2,NM_001206569.1,NM_001206570.1,NM_001206571.1,NM_001206572.1,NM_052918.4	58,58,58,58,58,58	0,3,6500	CC,CT,TT		0.0349,0.0,0.0231	benign,benign,benign,benign,benign,benign	1097/1199,1097/1180,1097/1131,1097/1160,1097/1180,1097/1169	108339209	3,13003	2203	4300	6503	SO:0001583	missense	114815	exon25			TGTGGGTTGGAGT	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.3289A>G	10.37:g.108339209T>C	ENSP00000263054:p.Thr1097Ala	62	0	0		33	16	0.484848	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	37	CCDS7559.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	9.840	1.190688	0.21954	0.0	3.49E-4	ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440	T;T;T	0.20881	2.04;2.57;2.6	5.92	3.59	0.41128	.	0.242564	0.40222	N	0.001147	T	0.09291	0.0229	N	0.08118	0	0.32196	N	0.578402	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;0.001;0.001;0.001	T	0.22661	-1.0210	9	.	.	.	-10.911	7.9891	0.30229	0.0:0.232:0.0:0.768	.	1097;1097;1097;1097;1097	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	A	632;1097;1097	ENSP00000358712:T632A;ENSP00000263054:T1097A;ENSP00000345964:T1097A	.	T	-	1	0	SORCS1	108329199	0.989000	0.36119	0.910000	0.35882	0.943000	0.58893	2.132000	0.42083	0.495000	0.27882	-0.385000	0.06624	ACC	T|0.999;C|0.001	0.001	strong		0.527	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		C	108339209	T	C	108339209	3	2	28	1	0	0	0	0	1	0	0	0	14945	1725	60	3	459	3	SORCS1	10	108339209	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	4426991	108339209	27195538	392	11895											
SORCS1	114815	hgsc.bcm.edu	37	chr10	108432670	108432670	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagtcctcttcggcacaccGtctatcaaaaatggacttgt	10	12	8	11	2	3	0	1	0	2	0	5	1	4	1	2	2	0	2	2	2	4	4	rs143914023		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:108432670G>A	ENST00000263054.6	-	15	2021	c.2014C>T	c.(2014-2016)Cgg>Tgg	p.R672W	SORCS1_ENST00000369698.1_Missense_Mutation_p.R207W|SORCS1_ENST00000344440.6_Missense_Mutation_p.R672W	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	672					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)		TCGGCACACCGTCTATCAAAA	0.488																																					p.R672W		Atlas-SNP	.											.	SORCS1	534	.	0			c.C2014T						PASS	.	G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	84	70	75		2014,2014,2014,2014,2014,2014	-0.1	0.8	10	dbSNP_134	75	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense	SORCS1	NM_001013031.2,NM_001206569.1,NM_001206570.1,NM_001206571.1,NM_001206572.1,NM_052918.4	101,101,101,101,101,101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	672/1199,672/1180,672/1131,672/1160,672/1180,672/1169	108432670	1,13005	2203	4300	6503	SO:0001583	missense	114815	exon15			CACACCGTCTATC	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.2014C>T	10.37:g.108432670G>A	ENSP00000263054:p.Arg672Trp	67	0	0		72	26	0.361111	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	37	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	G	18.71	3.681592	0.68042	0.0	1.16E-4	ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440	T;T;T	0.29917	1.55;1.55;1.55	5.47	-0.143	0.13444	VPS10 (1);	0.132411	0.49305	N	0.000151	T	0.47691	0.1459	M	0.67953	2.075	0.40136	D	0.976777	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.75484	0.968;0.978;0.986;0.968;0.986	T	0.42137	-0.9469	9	.	.	.	-6.2946	11.4184	0.49967	0.064:0.0:0.2926:0.6433	.	672;672;672;672;672	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	W	207;672;672	ENSP00000358712:R207W;ENSP00000263054:R672W;ENSP00000345964:R672W	.	R	-	1	2	SORCS1	108422660	0.134000	0.22483	0.849000	0.33467	0.991000	0.79684	0.199000	0.17237	-0.009000	0.14296	0.563000	0.77884	CGG	G|1.000;A|0.000	0.000	weak		0.488	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		A	108432670	G	A	108432670	3	1	28	1	0	0	0	0	1	0	0	0	14945	1144	40	1	1774	1	SORCS1	10	108432670	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	93461	108432670	27102077	393	11896											
PDCD4	27250	hgsc.bcm.edu	37	chr10	112654238	112654238	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	attttggatttattaaagtcCctttggaagtcttctaccat	10	18	6	7	0	2	0	0	0	2	0	3	2	3	2	2	2	1	0	2	2	5	8	rs41292602	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:112654238C>T	ENST00000280154.7	+	10	1441	c.1167C>T	c.(1165-1167)tcC>tcT	p.S389S	PDCD4_ENST00000393104.2_Silent_p.S378S	NM_001199492.1|NM_014456.4	NP_001186421.1|NP_055271.2	Q53EL6	PDCD4_HUMAN	programmed cell death 4 (neoplastic transformation inhibitor)	389	MI 2. {ECO:0000255|PROSITE- ProRule:PRU00698}.				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)		TATTAAAGTCCCTTTGGAAGT	0.284													C|||	9	0.00179712	0.0008	0.0014	5008	,	,		17286	0.0		0.007	False		,,,				2504	0.0				p.S389S	Ovarian(115;1498 1603 9363 40056 40885)	Atlas-SNP	.											.	PDCD4	39	.	0			c.C1167T						PASS	.	C	,,	3,4399	2.1+/-5.4	0,3,2198	87	97	93		1125,1167,1134	-7.2	0.5	10	dbSNP_127	93	45,8529	27.9+/-77.7	0,45,4242	no	coding-synonymous,coding-synonymous,coding-synonymous	PDCD4	NM_001199492.1,NM_014456.4,NM_145341.3	,,	0,48,6440	TT,TC,CC		0.5248,0.0682,0.3699	,,	375/456,389/470,378/459	112654238	48,12928	2201	4287	6488	SO:0001819	synonymous_variant	27250	exon10			AAAGTCCCTTTGG	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.1167C>T	10.37:g.112654238C>T		31	0	0		30	15	0.5	NM_014456	B2RCV4|B5ME91|O15501|Q5VZS6|Q6PJI5|Q8TAR5|Q99834	Silent	SNP	ENST00000280154.7	37	CCDS7567.1																																																																																			C|0.997;T|0.003	0.003	strong		0.284	PDCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050361.1	NM_014456		T	112654238	C	T	112654238	2	4	28	1	0	0	0	0	0	0	0	1	11630	610	22	2		2	PDCD4	10	112654238	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	4221568	112654238	22880509	394	11897											
AFAP1L2	84632	hgsc.bcm.edu	37	chr10	116064528	116064528	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggatgcggaaggagtagaGgtggtcggggctggggtctg	7	7	23	4	2	1	1	0	0	1	1	2	5	1	4	0	9	1	2	0	9	2	1	rs73365341	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:116064528G>A	ENST00000304129.4	-	11	1263	c.1234C>T	c.(1234-1236)Ctc>Ttc	p.L412F	AFAP1L2_ENST00000491814.1_5'Flank|AFAP1L2_ENST00000545353.1_Missense_Mutation_p.L465F|AFAP1L2_ENST00000369271.3_Missense_Mutation_p.L412F			Q8N4X5	AF1L2_HUMAN	actin filament associated protein 1-like 2	412	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)		AAGGAGTAGAGGTGGTCGGGG	0.682													G|||	531	0.10603	0.354	0.0375	5008	,	,		12908	0.0		0.0199	False		,,,				2504	0.0174				p.L412F		Atlas-SNP	.											.	AFAP1L2	90	.	0			c.C1234T						PASS	.	G	PHE/LEU,PHE/LEU	1464,2940	461.5+/-352.9	257,950,995	39	38	38		1234,1234	5.3	1	10	dbSNP_130	38	165,8435	76.3+/-139.0	3,159,4138	yes	missense,missense	AFAP1L2	NM_001001936.1,NM_032550.2	22,22	260,1109,5133	AA,AG,GG		1.9186,33.2425,12.5269	probably-damaging,probably-damaging	412/819,412/815	116064528	1629,11375	2202	4300	6502	SO:0001583	missense	84632	exon11			AGTAGAGGTGGTC	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.1234C>T	10.37:g.116064528G>A	ENSP00000303042:p.Leu412Phe	36	0	0		24	14	0.583333	NM_032550	A8K6P7|B3KVQ8|Q2UZW3|Q8TB54|Q96PX4|Q96SY5	Missense_Mutation	SNP	ENST00000304129.4	37	CCDS31286.1	224	0.10256410256410256	195	0.39634146341463417	15	0.04143646408839779	0	0.0	14	0.018469656992084433	G	26.3	4.722438	0.89298	0.332425	0.019186	ENSG00000169129	ENST00000369271;ENST00000304129;ENST00000392974;ENST00000545353	T;T;T	0.75589	-0.95;-0.95;-0.95	5.3	5.3	0.74995	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.62723	1.935	0.09310	P	0.999999814385	D;D;D;D;D	0.89917	1.0;1.0;0.997;1.0;1.0	D;D;D;D;D	0.97110	0.998;0.999;0.984;0.998;1.0	T	0.02104	-1.1213	9	0.45353	T	0.12	-16.927	18.9486	0.92632	0.0:0.0:1.0:0.0	.	465;466;440;412;412	F5GZE1;B7Z2Q0;Q8N4X5-4;Q8N4X5-2;Q8N4X5	.;.;.;.;AF1L2_HUMAN	F	412;412;439;465	ENSP00000358276:L412F;ENSP00000303042:L412F;ENSP00000444511:L465F	ENSP00000303042:L412F	L	-	1	0	AFAP1L2	116054518	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	7.973000	0.88032	2.470000	0.83445	0.563000	0.77884	CTC	G|0.884;A|0.116	0.116	strong		0.682	AFAP1L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050462.1	NM_032550		A	116064528	G	A	116064528	3	1	28	1	0	0	0	0	1	0	0	0	355	1000	35	2	1258	2	AFAP1L2	10	116064528	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	3410290	116064528	19470219	395	11898											
KIAA1598	57698	hgsc.bcm.edu	37	chr10	118713596	118713596	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	actgagacacaagtctcggcGgcaccgtctgtgtctgtagt	8	10	12	11	3	3	1	0	1	3	1	4	2	3	1	1	2	0	2	1	2	2	1	rs117277365	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:118713596G>A	ENST00000355371.4	-	5	890	c.393C>T	c.(391-393)gcC>gcT	p.A131A	KIAA1598_ENST00000392901.4_Silent_p.A71A|KIAA1598_ENST00000392903.2_Silent_p.A131A|KIAA1598_ENST00000497044.1_5'UTR|KIAA1598_ENST00000260777.10_Silent_p.A131A	NM_001127211.2|NM_001258298.1|NM_001258299.1	NP_001120683.1|NP_001245227.1|NP_001245228.1	A0MZ66	SHOT1_HUMAN	KIAA1598	131					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)		AAGTCTCGGCGGCACCGTCTG	0.403													G|||	3	0.000599042	0.0	0.0	5008	,	,		17591	0.0		0.003	False		,,,				2504	0.0				p.A131A		Atlas-SNP	.											.	KIAA1598	74	.	0			c.C393T						PASS	.	G	,	4,4402	8.1+/-20.4	0,4,2199	136	118	124		393,393	-8.1	0	10	dbSNP_133	124	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous,coding-synonymous	KIAA1598	NM_001127211.1,NM_018330.5	,	0,12,6491	AA,AG,GG		0.093,0.0908,0.0923	,	131/632,131/457	118713596	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	57698	exon5			CTCGGCGGCACCG	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.393C>T	10.37:g.118713596G>A		80	0	0		76	21	0.276316	NM_001258299	A8MYU7|B3KRD3|B3KRH2|B3KTE0|B3KTJ7|B3KTJ8|B4E3U1|B7Z7Z9|Q68DG1|Q6PIM5|Q9HCH4|Q9NUV0	Silent	SNP	ENST00000355371.4	37	CCDS44482.1																																																																																			G|0.999;A|0.001	0.001	strong		0.403	KIAA1598-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018330		A	118713596	G	A	118713596	2	1	28	1	0	0	0	0	0	0	0	1	8255	1103	39	1		1	KIAA1598	10	118713596	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2649068	118713596	16821151	396	11899											
BTBD16	118663	hgsc.bcm.edu	37	chr10	124096014	124096014	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcactctctttgcagagaatAaagcacacagacctggaatc	14	9	7	11	0	2	2	1	0	1	2	4	4	2	3	1	1	2	2	1	1	4	2	rs150944464	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:124096014A>G	ENST00000260723.4	+	15	1520	c.1269A>G	c.(1267-1269)atA>atG	p.I423M	BTBD16_ENST00000368994.2_Missense_Mutation_p.I424M|BTBD16_ENST00000495370.2_3'UTR	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	423										breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(3)|skin(2)|stomach(1)|urinary_tract(1)	15		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)				TGCAGAGAATAAAGCACACAG	0.542													A|||	25	0.00499201	0.0	0.0043	5008	,	,		18397	0.0		0.0209	False		,,,				2504	0.001				p.I423M		Atlas-SNP	.											.	BTBD16	44	.	0			c.A1269G						PASS	.	A	MET/ILE	13,4393	21.2+/-45.6	0,13,2190	52	45	47		1269	-8.5	0	10	dbSNP_134	47	129,8471	58.7+/-120.3	0,129,4171	yes	missense	BTBD16	NM_144587.2	10	0,142,6361	GG,GA,AA		1.5,0.2951,1.0918	benign	423/507	124096014	142,12864	2203	4300	6503	SO:0001583	missense	118663	exon15			GAGAATAAAGCAC	AK058088	CCDS31301.1	10q26.13	2013-01-24	2006-07-04	2006-07-04	ENSG00000138152	ENSG00000138152		"BTB/POZ domain containing"	26340	protein-coding gene	gene with protein product			"chromosome 10 open reading frame 87"	C10orf87			Standard	NM_144587		Approved	FLJ25359, Em:AC061711.1	uc001lgc.1	Q32M84	OTTHUMG00000019182	ENST00000260723.4:c.1269A>G	10.37:g.124096014A>G	ENSP00000260723:p.Ile423Met	76	0	0		63	17	0.269841	NM_144587	A6NM63|Q4VXL1|Q96LN0	Missense_Mutation	SNP	ENST00000260723.4	37	CCDS31301.1	23	0.010531135531135532	0	0.0	4	0.011049723756906077	0	0.0	19	0.025065963060686015	A	15.45	2.838596	0.51057	0.002951	0.015	ENSG00000138152	ENST00000260723;ENST00000368994	T;T	0.22134	1.97;1.97	5.68	-8.52	0.00920	.	0.900138	0.09479	N	0.796551	T	0.02807	0.0084	N	0.19112	0.55	0.09310	N	1	P;P	0.37207	0.587;0.587	B;B	0.32465	0.146;0.146	T	0.17107	-1.0380	10	0.44086	T	0.13	-1.7584	9.6517	0.39902	0.1783:0.3913:0.4304:0.0	.	424;423	Q32M84-2;Q32M84	.;BTBDG_HUMAN	M	423;424	ENSP00000260723:I423M;ENSP00000357990:I424M	ENSP00000260723:I423M	I	+	3	3	BTBD16	124086004	0.338000	0.24775	0.016000	0.15963	0.381000	0.30169	-0.278000	0.08490	-1.358000	0.02177	-0.290000	0.09829	ATA	A|0.990;G|0.010	0.010	strong		0.542	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587		G	124096014	A	G	124096014	3	3	28	1	0	0	0	0	1	0	0	0	1543	352	13	3	1323	3	BTBD16	10	124096014	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	5382418	124096014	11438733	397	11900											
UROS	7390	hgsc.bcm.edu	37	chr10	127484721	127484721	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttggattcctgggtgtgcaActgtctgatacacagttatg	8	14	11	8	0	1	1	0	1	1	0	2	2	2	2	1	2	3	2	1	2	3	4	rs17173752	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:127484721A>G	ENST00000368797.4	-	8	736	c.512T>C	c.(511-513)gTt>gCt	p.V171A	UROS_ENST00000368786.1_Missense_Mutation_p.V171A|UROS_ENST00000462490.1_5'UTR	NM_000375.2	NP_000366.1	P10746	HEM4_HUMAN	uroporphyrinogen III synthase	171			V -> G (in dbSNP:rs17173752).		cellular response to amine stimulus (GO:0071418)|cellular response to arsenic-containing substance (GO:0071243)|heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to antibiotic (GO:0046677)|small molecule metabolic process (GO:0044281)|uroporphyrinogen III biosynthetic process (GO:0006780)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	cofactor binding (GO:0048037)|uroporphyrinogen-III synthase activity (GO:0004852)			endometrium(2)|large_intestine(2)|lung(2)|skin(1)	7		all_lung(145;0.00756)|Lung NSC(174;0.0116)|Colorectal(57;0.0855)|all_neural(114;0.0937)|Breast(234;0.203)				TGGGTGTGCAACTGTCTGATA	0.557																																					p.V171A		Atlas-SNP	.											.	UROS	20	.	0			c.T512C						PASS	.						298	255	269					10																	127484721		2203	4300	6503	SO:0001583	missense	7390	exon8			TGTGCAACTGTCT	J03824	CCDS7648.1	10q25.2-q26.3	2008-07-31	2008-07-31		ENSG00000188690	ENSG00000188690	4.2.1.75		12592	protein-coding gene	gene with protein product	"congenital erythropoietic porphyria"	606938				2037278	Standard	NM_000375		Approved		uc001lix.4	P10746	OTTHUMG00000019236	ENST00000368797.4:c.512T>C	10.37:g.127484721A>G	ENSP00000357787:p.Val171Ala	145	0	0		131	62	0.473282	NM_000375	B2RC13|D3DRF7|Q9H2T1	Missense_Mutation	SNP	ENST00000368797.4	37	CCDS7648.1	.	.	.	.	.	.	.	.	.	.	A	0.013	-1.608054	0.00842	.	.	ENSG00000188690	ENST00000368797;ENST00000368786;ENST00000420761	D;D;D	0.93604	-3.25;-3.25;-3.25	4.98	2.59	0.31030	Tetrapyrrole biosynthesis, uroporphyrinogen III synthase (2);	0.587899	0.17904	N	0.158084	T	0.78039	0.4221	N	0.02391	-0.57	0.58432	P	1.0000000000287557E-6	B;B	0.09022	0.002;0.002	B;B	0.16722	0.005;0.016	T	0.70163	-0.4947	9	0.08599	T	0.76	-0.1402	5.5774	0.17231	0.7614:0.0:0.2386:0.0	.	171;143	P10746;E9PG85	HEM4_HUMAN;.	A	171;171;143	ENSP00000357787:V171A;ENSP00000357775:V171A;ENSP00000414833:V143A	ENSP00000357775:V171A	V	-	2	0	UROS	127474711	0.005000	0.15991	0.006000	0.13384	0.004000	0.04260	1.536000	0.36072	0.703000	0.31848	-0.417000	0.06048	GTT	A|0.994;C|0.006	.	alt		0.557	UROS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050929.1	NM_000375		G	127484721	A	G	127484721	3	3	28	1	0	0	0	0	1	0	0	0	17045	43	2	3	297	3	UROS	10	127484721	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	3388707	127484721	8050026	398	11901											
EFCAB4A	283229	hgsc.bcm.edu	37	chr11	831552	831553	+	Frame_Shift_Ins	INS	-	-	GC																															agggagctgaatacacggctINSgcgggatgacagggacgcct																										TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:831552_831553insGC	ENST00000525077.1	+	9	1144_1145	c.1043_1044insGC	c.(1042-1047)ctgcggfs	p.LR348fs	CD151_ENST00000322008.4_5'Flank|EFCAB4A_ENST00000528542.2_Frame_Shift_Ins_p.A293fs|CD151_ENST00000397420.3_5'Flank|CD151_ENST00000397421.1_5'Flank|EFCAB4A_ENST00000450448.1_Frame_Shift_Ins_p.A293fs|AP006621.8_ENST00000532946.1_RNA			Q8N4Y2	EFC4A_HUMAN		348					cellular protein localization (GO:0034613)|regulation of store-operated calcium entry (GO:2001256)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(1)|lung(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;1.45e-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)		AATACACGGCTGCGGGATGACA	0.673																																					p.A292fs		Pindel,Atlas-Indel	.											.	EFCAB4A	16	.	0			c.876_877insGC						PASS	.			0,3832		0,0,1916						4.1	0.5			34	2,7932		0,2,3965	no	frameshift	EFCAB4A	NM_173584.3		0,2,5881	A1A1,A1R,RR		0.0252,0.0,0.017				2,11764				SO:0001589	frameshift_variant	283229	exon9			.																												ENST00000525077.1:c.1044_1045dupGC	11.37:g.831553_831554dupGC	ENSP00000435299:p.Leu348fs	60	0	.		71	20	0.282	NM_173584	D5LPR2|Q8NBW8	Frame_Shift_Ins	INS	ENST00000525077.1	37																																																																																				.	.	none		0.673	EFCAB4A-007	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000383097.1			GC	831553	-	GC	831552	7	5	28	1	0	1	1	0	0	0	0	0	4938	1567	55	0	906	0	EFCAB4A	11	831552	Frame_Shift_Ins	INS	-	TCGA-G8-6914-01A-11D-2210-10		831552	134174964	399	11902											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1274209	1274209	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacttccactatgagtgcgaGtgtgagtgcgtcggtggccg	6	10	16	9	4	0	2	0	2	0	0	2	4	1	2	2	2	2	0	2	2	1	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1274209G>T	ENST00000529681.1	+	33	15274	c.15216G>T	c.(15214-15216)gaG>gaT	p.E5072D	MUC5B_ENST00000447027.1_Splice_Site_p.E5075D	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5072					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)		ATGAGTGCGAGTGTGAGTGCG	0.642																																					p.E5072D		Atlas-SNP	.											.	MUC5B	473	.	0			c.G15216T						PASS	.						53	59	57					11																	1274209		2132	4227	6359	SO:0001630	splice_region_variant	727897	exon33			GTGCGAGTGTGAG	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.15217+1G>T	11.37:g.1274209G>T		70	0	0		100	44	0.44	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	G	10.24	1.295134	0.23564	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.15487	2.42;2.61	4.64	-4.49	0.03504	.	.	.	.	.	T	0.09949	0.0244	L	0.28274	0.84	0.20873	N	0.999838	P;P	0.43094	0.799;0.799	B;B	0.36845	0.234;0.234	T	0.20672	-1.0268	9	0.87932	D	0	.	9.6818	0.40074	0.7156:0.0:0.1642:0.1202	.	5394;5075	A7Y9J9;E9PBJ0	.;.	D	5072;5075;5016;4771	ENSP00000436812:E5072D;ENSP00000415793:E5075D	ENSP00000343037:E5016D	E	+	3	2	MUC5B	1230785	0.001000	0.12720	0.574000	0.28523	0.561000	0.35649	-2.094000	0.01351	-0.851000	0.04147	-0.258000	0.10820	GAG	.	.	none		0.642	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	Missense_Mutation	T	1274209	G	T	1274209	5	4	28	1	0	0	0	0	0	0	1	0	9988	1043	36	4	15355	4	MUC5B	11	1274209	Splice_Site	SNP	G	TCGA-G8-6914-01A-11D-2210-10	442657	1274209	133732307	400	11903											
TRPM5	29850	hgsc.bcm.edu	37	chr11	2436464	2436464	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagaaggccggtggccccgCgggtggctcccgggcctgct	3	5	19	14	4	0	1	0	0	0	1	1	2	1	1	5	7	1	2	5	7	1	0	rs34551253	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:2436464C>T	ENST00000155858.6	-	9	1374	c.1366G>A	c.(1366-1368)Gcg>Acg	p.A456T	TRPM5_ENST00000528453.1_Missense_Mutation_p.A456T|TRPM5_ENST00000533060.1_Missense_Mutation_p.A456T|TRPM5_ENST00000452833.1_Missense_Mutation_p.A458T	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)		GGTGGCCCCGCGGGTGGCTCC	0.716													C|||	54	0.0107827	0.0023	0.0245	5008	,	,		13476	0.001		0.0308	False		,,,				2504	0.002				p.A456T	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.G1366A						PASS	.	C	THR/ALA	35,4235		1,33,2101	7	9	9		1366	-6.4	0	11	dbSNP_126	9	273,8141		6,261,3940	yes	missense	TRPM5	NM_014555.3	58	7,294,6041	TT,TC,CC		3.2446,0.8197,2.4283	benign	456/1166	2436464	308,12376	2135	4207	6342	SO:0001583	missense	29850	exon9			GCCCCGCGGGTGG	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.1366G>A	11.37:g.2436464C>T	ENSP00000155858:p.Ala456Thr	3	0	0		10	5	0.5	NM_014555		Missense_Mutation	SNP	ENST00000155858.6	37	CCDS31340.1	35	0.016025641025641024	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	22	0.029023746701846966	C	0.009	-1.820965	0.00595	0.008197	0.032446	ENSG00000070985	ENST00000533881;ENST00000155858;ENST00000452833;ENST00000533060;ENST00000528453;ENST00000437542	T;T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31;-0.31	3.19	-6.37	0.01963	.	1.134030	0.06672	N	0.766349	T	0.14227	0.0344	N	0.08118	0	0.09310	N	1	B;B;B	0.13594	0.005;0.005;0.008	B;B;B	0.09377	0.002;0.001;0.004	T	0.05517	-1.0880	10	0.14252	T	0.57	0.2166	1.5474	0.02568	0.2706:0.3676:0.1989:0.1629	rs34551253	456;458;456	E9PRW0;Q9NZQ8-2;Q9NZQ8	.;.;TRPM5_HUMAN	T	450;456;458;456;456;456	ENSP00000434383:A450T;ENSP00000155858:A456T;ENSP00000387965:A458T;ENSP00000434121:A456T;ENSP00000436809:A456T	ENSP00000155858:A456T	A	-	1	0	TRPM5	2393040	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-2.025000	0.01435	-3.859000	0.00098	-1.579000	0.00862	GCG	C|0.983;T|0.017	0.017	strong		0.716	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555		T	2436464	C	T	2436464	3	4	28	1	0	0	0	0	1	0	0	0	16604	768	27	1	2195	1	TRPM5	11	2436464	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1162255	2436464	132570052	401	11904											
SLC22A18	5002	hgsc.bcm.edu	37	chr11	2929502	2929502	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcctggattccattgccttcGgctacctgcaaaccaccttc	7	11	7	16	1	0	0	0	0	0	0	3	1	1	1	6	2	4	2	6	2	2	5	rs143044180	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:2929502G>A	ENST00000380574.1	+	3	615	c.184G>A	c.(184-186)Ggc>Agc	p.G62S	SLC22A18_ENST00000449793.2_Missense_Mutation_p.G62S|SLC22A18_ENST00000347936.2_Missense_Mutation_p.G62S|SLC22A18_ENST00000312221.5_Missense_Mutation_p.G62S			Q96BI1	S22AI_HUMAN	solute carrier family 22, member 18	62					drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|excretion (GO:0007588)|organic cation transport (GO:0015695)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|symporter activity (GO:0015293)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	8		all_epithelial(84;0.000124)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)|all_lung(207;0.198)		BRCA - Breast invasive adenocarcinoma(625;0.00256)|LUSC - Lung squamous cell carcinoma(625;0.192)		CATTGCCTTCGGCTACCTGCA	0.617																																					p.G62S		Atlas-SNP	.											SLC22A18,NS,carcinoma,0,1	SLC22A18	20	1	0			c.G184A						PASS	.						86	82	84					11																	2929502		2202	4299	6501	SO:0001583	missense	5002	exon3			GCCTTCGGCTACC	AF028738	CCDS7740.1	11p15.5	2013-05-22	2008-01-11	2004-01-21	ENSG00000110628	ENSG00000110628		"Solute carriers"	10964	protein-coding gene	gene with protein product		602631	"solute carrier family 22 (organic cation transporter), member 1-like"	ORCTL2, BWSCR1A, IMPT1, SLC22A1L		9499412, 9520460	Standard	NM_183233		Approved	BWR1A, TSSC5, ITM	uc001lwx.3	Q96BI1	OTTHUMG00000010037	ENST00000380574.1:c.184G>A	11.37:g.2929502G>A	ENSP00000369948:p.Gly62Ser	59	0	0		54	21	0.388889	NM_002555	O14906|O43562|O60485|O60680|Q7LDS5|Q7LGF7	Missense_Mutation	SNP	ENST00000380574.1	37	CCDS7740.1	.	.	.	.	.	.	.	.	.	.	G	15.78	2.935071	0.52866	.	.	ENSG00000110628	ENST00000347936;ENST00000312221;ENST00000449793;ENST00000380574;ENST00000485423	T;T;T;T;D	0.84442	0.1;0.1;-0.06;0.1;-1.85	4.27	3.34	0.38264	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.64402	D	0.000001	D	0.87128	0.6100	L	0.56340	1.77	0.52501	D	0.999959	D;D	0.71674	0.991;0.998	P;P	0.62740	0.461;0.906	D	0.86466	0.1782	10	0.59425	D	0.04	-1.8758	7.3817	0.26859	0.1199:0.0:0.8801:0.0	.	62;62	E9PRM7;Q96BI1	.;S22AI_HUMAN	S	62	ENSP00000307859:G62S;ENSP00000311139:G62S;ENSP00000392072:G62S;ENSP00000369948:G62S;ENSP00000433019:G62S	ENSP00000311139:G62S	G	+	1	0	SLC22A18	2886078	1.000000	0.71417	0.933000	0.37362	0.037000	0.13140	2.882000	0.48546	2.105000	0.64084	0.491000	0.48974	GGC	G|0.998;T|0.002	.	alt		0.617	SLC22A18-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027770.1	NM_183233		A	2929502	G	A	2929502	3	1	28	1	0	0	0	0	1	0	0	0	14464	1116	39	1	190	1	SLC22A18	11	2929502	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	493038	2929502	132077014	402	11905											
OR51B5	282763	hgsc.bcm.edu	37	chr11	5364295	5364295	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggcctgattgggggaacaaCggatacaaatcccctcatca	12	7	11	11	1	2	1	2	1	0	0	3	3	3	3	3	4	3	0	3	4	4	2	rs12273630	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5364295C>T	ENST00000300773.2	-	1	514	c.460G>A	c.(460-462)Gtt>Att	p.V154I	HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	154			V -> I (in dbSNP:rs12273630).		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)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGGGGAACAACGGATACAAAT	0.438													C|||	487	0.0972444	0.3026	0.0476	5008	,	,		19117	0.0		0.0467	False		,,,				2504	0.0072				p.V154I		Atlas-SNP	.											.	OR51B5	60	.	0			c.G460A						PASS	.	C	ILE/VAL	1218,3184	414.4+/-336.8	162,894,1145	53	59	57		460	-1.3	0	11	dbSNP_120	57	453,8141	135.1+/-192.4	13,427,3857	yes	missense	OR51B5	NM_001005567.2	29	175,1321,5002	TT,TC,CC		5.2711,27.6692,12.8578	benign	154/313	5364295	1671,11325	2201	4297	6498	SO:0001583	missense	282763	exon5			GAACAACGGATAC	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"GPCR / Class A : Olfactory receptors"	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.460G>A	11.37:g.5364295C>T	ENSP00000300773:p.Val154Ile	49	0	0		43	25	0.581395	NM_001005567	B2RN59	Missense_Mutation	SNP	ENST00000300773.2	37	CCDS31378.1	188	0.08608058608058608	134	0.27235772357723576	20	0.055248618784530384	0	0.0	34	0.044854881266490766	C	0.678	-0.799441	0.02841	0.276692	0.052711	ENSG00000242180	ENST00000300773	T	0.37411	1.2	4.76	-1.28	0.09318	GPCR, rhodopsin-like superfamily (1);	0.194438	0.24818	N	0.035344	T	0.00012	0.0000	N	0.01789	-0.72	0.80722	P	0.0	B	0.16166	0.016	B	0.15870	0.014	T	0.32402	-0.9908	9	0.02654	T	1	.	5.2403	0.15467	0.0:0.4688:0.239:0.2922	rs12273630;rs52831752;rs59964283;rs12273630	154	Q9H339	O51B5_HUMAN	I	154	ENSP00000300773:V154I	ENSP00000300773:V154I	V	-	1	0	OR51B5	5320871	0.000000	0.05858	0.002000	0.10522	0.868000	0.49771	-3.516000	0.00445	-0.111000	0.12001	0.650000	0.86243	GTT	C|0.888;T|0.112	0.112	strong		0.438	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567		T	5364295	C	T	5364295	3	4	28	1	0	0	0	0	1	0	0	0	11100	536	19	1	482	1	OR51B5	11	5364295	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2434793	5364295	129642221	403	11906			4	51		3	3	182	N	G_C	8.983672e-06
OR51B5	282763	hgsc.bcm.edu	37	chr11	5364431	5364431	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcaagcagaatgccagactcGagaaaggaaagtgagtgtat	16	6	13	6	1	0	4	0	1	0	3	1	6	0	5	1	1	2	3	1	1	5	1	rs58233587	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5364431G>A	ENST00000300773.2	-	1	378	c.324C>T	c.(322-324)ctC>ctT	p.L108L	HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	108					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)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGCCAGACTCGAGAAAGGAAA	0.493													G|||	486	0.0970447	0.3041	0.0476	5008	,	,		20358	0.0		0.0457	False		,,,				2504	0.0051				p.L108L		Atlas-SNP	.											OR51B5,NS,carcinoma,-1,1	OR51B5	60	1	0			c.C324T						PASS	.	G		1214,3188	413.5+/-336.5	164,886,1151	46	45	46		324	-8.8	0.1	11	dbSNP_129	46	454,8140	135.6+/-192.8	13,428,3856	no	coding-synonymous	OR51B5	NM_001005567.2		177,1314,5007	AA,AG,GG		5.2828,27.5784,12.8347		108/313	5364431	1668,11328	2201	4297	6498	SO:0001819	synonymous_variant	282763	exon5			AGACTCGAGAAAG	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"GPCR / Class A : Olfactory receptors"	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.324C>T	11.37:g.5364431G>A		27	0	0		23	9	0.391304	NM_001005567	B2RN59	Silent	SNP	ENST00000300773.2	37	CCDS31378.1																																																																																			G|0.886;A|0.114	0.114	strong		0.493	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567		A	5364431	G	A	5364431	2	1	28	1	0	0	0	0	0	0	0	1	11100	1045	37	1		1	OR51B5	11	5364431	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	136	5364431	129642085	404	11907			4	51		3	3	182	N	G_C	8.983672e-06
OR51B5	282763	hgsc.bcm.edu	37	chr11	5364476	5364476	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	taggcctgggaaaagcaggcCgcacttccaatctccctgtg	9	8	11	13	1	1	0	0	0	1	0	3	1	2	1	4	3	1	2	4	3	4	2	rs61738485	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5364476C>T	ENST00000300773.2	-	1	333	c.279G>A	c.(277-279)gcG>gcA	p.A93A	HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	93					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)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AAAAGCAGGCCGCACTTCCAA	0.562													T|||	491	0.0980431	0.3071	0.049	5008	,	,		18817	0.0		0.0457	False		,,,				2504	0.0051				p.A93A		Atlas-SNP	.											OR51B5,NS,carcinoma,-1,1	OR51B5	60	1	0			c.G279A						PASS	.	T		1240,3162	701.9+/-406.8	168,904,1129	43	42	42		279	-8.9	0	11	dbSNP_129	42	455,8139	796.1+/-407.5	13,429,3855	no	coding-synonymous	OR51B5	NM_001005567.2		181,1333,4984	TT,TC,CC		5.2944,28.169,13.0425		93/313	5364476	1695,11301	2201	4297	6498	SO:0001819	synonymous_variant	282763	exon5			GCAGGCCGCACTT	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"GPCR / Class A : Olfactory receptors"	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.279G>A	11.37:g.5364476C>T		32	0	0		25	9	0.36	NM_001005567	B2RN59	Silent	SNP	ENST00000300773.2	37	CCDS31378.1																																																																																			C|0.885;T|0.115	0.115	strong		0.562	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567		T	5364476	C	T	5364476	2	4	28	1	0	0	0	0	0	0	0	1	11100	639	23	1		1	OR51B5	11	5364476	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	45	5364476	129642040	405	11908			4	51		3	3	182	N	G_C	8.983672e-06
TRIM22	10346	hgsc.bcm.edu	37	chr11	5730343	5730343	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgctatttctgtggatcagaGacaagtgaaaactgtacgca	13	11	10	7	1	2	2	1	1	1	1	2	4	2	3	0	1	3	3	0	1	5	3	rs12364019	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5730343G>A	ENST00000379965.3	+	8	1239	c.962G>A	c.(961-963)aGa>aAa	p.R321K	TRIM5_ENST00000380027.1_Intron	NM_001199573.1|NM_006074.4	NP_001186502.1|NP_006065.2	Q8IYM9	TRI22_HUMAN	tripartite motif containing 22	321	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		R -> K (in dbSNP:rs12364019).		defense response to virus (GO:0051607)|immune response (GO:0006955)|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 trimerization (GO:0070206)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			kidney(3)|large_intestine(8)|lung(9)|prostate(1)|stomach(2)	23		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;7.54e-09)|BRCA - Breast invasive adenocarcinoma(625;0.14)		GTGGATCAGAGACAAGTGAAA	0.418													G|||	58	0.0115815	0.0008	0.0144	5008	,	,		20306	0.0		0.0308	False		,,,				2504	0.0164				p.R321K	GBM(104;491 2336 5222)	Atlas-SNP	.											.	TRIM22	66	.	0			c.G962A						PASS	.	G	LYS/ARG,LYS/ARG	16,3874		0,16,1929	148	139	142		950,962	2.8	0.7	11	dbSNP_120	142	338,7968		9,320,3824	yes	missense,missense	TRIM22	NM_001199573.1,NM_006074.4	26,26	9,336,5753	AA,AG,GG		4.0693,0.4113,2.9026	probably-damaging,probably-damaging	317/495,321/499	5730343	354,11842	1945	4153	6098	SO:0001583	missense	10346	exon8			ATCAGAGACAAGT	X82200	CCDS41612.1	11p15	2013-01-09	2011-01-25		ENSG00000132274	ENSG00000132274		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16379	protein-coding gene	gene with protein product		606559	"tripartite motif-containing 22"			11331580, 11096452	Standard	NM_006074		Approved	STAF50, GPSTAF50, RNF94	uc001mbr.3	Q8IYM9	OTTHUMG00000066904	ENST00000379965.3:c.962G>A	11.37:g.5730343G>A	ENSP00000369299:p.Arg321Lys	75	0	0		98	40	0.408163	NM_006074	Q05CQ0|Q15521	Missense_Mutation	SNP	ENST00000379965.3	37	CCDS41612.1	32	0.014652014652014652	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	24	0.0316622691292876	G	20.4	3.976912	0.74360	0.004113	0.040693	ENSG00000132274	ENST00000379965;ENST00000545338;ENST00000454828;ENST00000455293	T;T	0.59638	2.71;0.25	3.72	2.77	0.32553	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.34658	0.0905	L	0.43152	1.355	0.23411	N	0.997739	D;D;D	0.89917	0.99;1.0;0.999	D;D;D	0.83275	0.979;0.991;0.996	T	0.38178	-0.9673	9	0.87932	D	0	.	9.9749	0.41777	0.1096:0.0:0.8904:0.0	rs12364019;rs52821696;rs12364019	243;317;321	F8WAP8;Q8IYM9-2;Q8IYM9	.;.;TRI22_HUMAN	K	321;132;289;243	ENSP00000369299:R321K;ENSP00000393250:R289K	ENSP00000369299:R321K	R	+	2	0	TRIM22	5686919	0.118000	0.22208	0.678000	0.29963	0.381000	0.30169	0.558000	0.23469	0.825000	0.34637	0.460000	0.39030	AGA	G|0.976;A|0.024	0.024	strong		0.418	TRIM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143387.2	NM_006074		A	5730343	G	A	5730343	3	1	28	1	0	0	0	0	1	0	0	0	16511	942	33	2	988	2	TRIM22	11	5730343	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	365867	5730343	129276173	406	11909											
DNHD1	144132	hgsc.bcm.edu	37	chr11	6559961	6559961	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgcatgcgcatcctgggggaGtttcgcagctacctgcccct	5	10	12	14	2	0	0	0	0	0	0	2	1	1	1	4	2	5	5	4	2	1	2	rs118078642	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:6559961G>A	ENST00000527990.2	+	14	3246	c.3246G>A	c.(3244-3246)gaG>gaA	p.E1082E	DNHD1_ENST00000254579.6_Silent_p.E1082E			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	1082					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)		TCCTGGGGGAGTTTCGCAGCT	0.602													G|||	13	0.00259585	0.0	0.0072	5008	,	,		17960	0.0		0.007	False		,,,				2504	0.001				p.E1082E		Atlas-SNP	.											.	DNHD1	198	.	0			c.G3246A						PASS	.	G		6,1376		0,6,685	13	13	13		3246	3.2	1	11	dbSNP_132	13	31,3151		0,31,1560	no	coding-synonymous	DNHD1	NM_144666.2		0,37,2245	AA,AG,GG		0.9742,0.4342,0.8107		1082/4754	6559961	37,4527	691	1591	2282	SO:0001819	synonymous_variant	144132	exon16			GGGGGAGTTTCGC	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.3246G>A	11.37:g.6559961G>A		71	0	0		67	44	0.656716	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Silent	SNP	ENST00000527990.2	37	CCDS44532.1																																																																																			G|0.997;A|0.003	0.003	strong		0.602	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		A	6559961	G	A	6559961	2	1	28	1	0	0	0	0	0	0	0	1	4670	1020	36	2		2	DNHD1	11	6559961	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	829618	6559961	128446555	407	11910											
ST5	6764	hgsc.bcm.edu	37	chr11	8724191	8724191	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agattcggatgagctggcgcAcactgaggcaggtaaaaagg	13	6	15	7	2	0	3	0	2	0	1	1	4	0	4	0	5	1	4	0	5	3	2	rs113126215	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:8724191A>G	ENST00000534127.1	-	17	3033	c.2648T>C	c.(2647-2649)gTg>gCg	p.V883A	ST5_ENST00000534278.1_Missense_Mutation_p.V74A|ST5_ENST00000313726.6_Missense_Mutation_p.V883A|ST5_ENST00000530991.1_Missense_Mutation_p.V355A|ST5_ENST00000530438.1_Missense_Mutation_p.V463A|ST5_ENST00000357665.1_Missense_Mutation_p.V883A|RPL27A_ENST00000531102.1_Intron|ST5_ENST00000526757.1_Missense_Mutation_p.V463A|ST5_ENST00000526099.1_Missense_Mutation_p.V396A	NM_005418.3	NP_005409.3	P78524	ST5_HUMAN	suppression of tumorigenicity 5	883	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				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)		GAGCTGGCGCACACTGAGGCA	0.582													a|||	8	0.00159744	0.0008	0.0014	5008	,	,		19188	0.0		0.005	False		,,,				2504	0.001				p.V883A		Atlas-SNP	.											.	ST5	85	.	0			c.T2648C						PASS	.	A	ALA/VAL,ALA/VAL,ALA/VAL	9,4393	15.5+/-35.6	0,9,2192	86	79	81		2648,1388,2648	4.7	1	11	dbSNP_132	81	48,8544	31.2+/-83.2	0,48,4248	yes	missense,missense,missense	ST5	NM_005418.3,NM_139157.2,NM_213618.1	64,64,64	0,57,6440	GG,GA,AA		0.5587,0.2045,0.4387	benign,benign,benign	883/1138,463/718,883/1138	8724191	57,12937	2201	4296	6497	SO:0001583	missense	6764	exon17			TGGCGCACACTGA	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.2648T>C	11.37:g.8724191A>G	ENSP00000433528:p.Val883Ala	37	0	0		35	17	0.485714	NM_005418	B2R6X7|B3KXQ6|P78523|Q16492|Q7KYY2|Q7KZ12|Q8NE12|Q9BQQ6	Missense_Mutation	SNP	ENST00000534127.1	37	CCDS7791.1	4	0.0018315018315018315	1	0.0020325203252032522	0	0.0	0	0.0	3	0.00395778364116095	a	16.30	3.083512	0.55861	0.002045	0.005587	ENSG00000166444	ENST00000526757;ENST00000534127;ENST00000313726;ENST00000530991;ENST00000357665;ENST00000526099;ENST00000534278;ENST00000530438;ENST00000533081	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	4.72	4.72	0.59763	DENN (3);	0.000000	0.85682	D	0.000000	T	0.19406	0.0466	M	0.78801	2.425	0.53005	D	0.999961	B;B;B	0.28026	0.023;0.012;0.198	B;B;B	0.38755	0.202;0.038;0.281	T	0.05699	-1.0869	10	0.87932	D	0	-10.884	14.2346	0.65916	1.0:0.0:0.0:0.0	.	396;463;883	B4DDL8;P78524-2;P78524	.;.;ST5_HUMAN	A	463;883;883;355;883;396;74;463;73	ENSP00000435097:V463A;ENSP00000433528:V883A;ENSP00000319678:V883A;ENSP00000432887:V355A;ENSP00000350294:V883A;ENSP00000436808:V396A;ENSP00000433349:V74A;ENSP00000436802:V463A;ENSP00000436067:V73A	ENSP00000319678:V883A	V	-	2	0	ST5	8680767	0.990000	0.36364	1.000000	0.80357	0.992000	0.81027	7.573000	0.82421	1.760000	0.52011	0.398000	0.26397	GTG	A|0.996;G|0.004	0.004	strong		0.582	ST5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386518.1	NM_005418		G	8724191	A	G	8724191	3	3	28	1	0	0	0	0	1	0	0	0	15235	159	6	3	793	3	ST5	11	8724191	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	2164230	8724191	126282325	408	11911											
SCUBE2	57758	hgsc.bcm.edu	37	chr11	9082068	9082068	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctccattgttgacagcacacGtttctggcaaggaggtaaga	11	10	11	9	1	1	2	0	1	1	1	2	3	2	3	1	3	1	5	1	3	2	4	rs35703942|rs72547298	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:9082068G>A	ENST00000309263.3	-	8	926	c.854C>T	c.(853-855)aCg>aTg	p.T285M	SCUBE2_ENST00000450649.2_Missense_Mutation_p.T285M|SCUBE2_ENST00000520467.1_Missense_Mutation_p.T285M|RP11-467K18.2_ENST00000521394.2_RNA|SCUBE2_ENST00000457346.2_Missense_Mutation_p.T285M			Q9NQ36	SCUB2_HUMAN	signal peptide, CUB domain, EGF-like 2	285						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)		GACAGCACACGTTTCTGGCAA	0.498													G|||	14	0.00279553	0.0	0.0029	5008	,	,		23726	0.0		0.0089	False		,,,				2504	0.0031				p.T285M		Atlas-SNP	.											.	SCUBE2	102	.	0			c.C854T						PASS	.	G	MET/THR,MET/THR	12,4390	19.1+/-41.9	0,12,2189	143	133	136		854,854	5.9	1	11	dbSNP_130	136	92,8500	51.9+/-112.3	3,86,4207	yes	missense,missense	SCUBE2	NM_001170690.1,NM_020974.2	81,81	3,98,6396	AA,AG,GG		1.0708,0.2726,0.8004	probably-damaging,probably-damaging	285/808,285/972	9082068	104,12890	2201	4296	6497	SO:0001583	missense	57758	exon8			GCACACGTTTCTG	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.854C>T	11.37:g.9082068G>A	ENSP00000310658:p.Thr285Met	41	0	0		52	26	0.5	NM_001170690	Q2NKQ8|Q6ZWI1	Missense_Mutation	SNP	ENST00000309263.3	37		7|7	0.003205128205128205|0.003205128205128205	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	7|7	0.009234828496042216|0.009234828496042216	G|G	23.8|23.8	4.462764|4.462764	0.84425|0.84425	0.002726|0.002726	0.010708|0.010708	ENSG00000175356|ENSG00000175356	ENST00000519788;ENST00000531429|ENST00000457346;ENST00000309263;ENST00000450649;ENST00000520467	.|T;T;D;D	.|0.84589	.|-1.34;-1.41;-1.87;-1.53	5.94|5.94	5.94|5.94	0.96194|0.96194	.|Epidermal growth factor-like (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.91885|0.91885	0.7431|0.7431	M|M	0.86953|0.86953	2.85|2.85	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.97110	.|0.999;1.0;0.999	D|D	0.92305|0.92305	0.5853|0.5853	5|10	.|0.72032	.|D	.|0.01	.|.	20.3736|20.3736	0.98901|0.98901	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|285;285;285	.|Q9NQ36-3;Q9NQ36-2;Q9NQ36	.|.;.;SCUB2_HUMAN	C|M	9;50|285	.|ENSP00000390481:T285M;ENSP00000310658:T285M;ENSP00000415187:T285M;ENSP00000429969:T285M	.|ENSP00000310658:T285M	R|T	-|-	1|2	0|0	SCUBE2|SCUBE2	9038644|9038644	1.000000|1.000000	0.71417|0.71417	0.968000|0.968000	0.41197|0.41197	0.916000|0.916000	0.54674|0.54674	9.869000|9.869000	0.99810|0.99810	2.820000|2.820000	0.97059|0.97059	0.650000|0.650000	0.86243|0.86243	CGT|ACG	G|0.994;A|0.006	0.006	strong		0.498	SCUBE2-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000385812.2	NM_020974		A	9082068	G	A	9082068	3	1	28	1	0	0	0	0	1	0	0	0	13960	1145	40	1	2296	1	SCUBE2	11	9082068	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	357877	9082068	125924448	409	11912											
PIK3C2A	5286	hgsc.bcm.edu	37	chr11	17118730	17118730	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctcatcattagaaggaagAccagaaaaacgaagctgagc	17	5	11	8	1	2	4	2	1	0	3	2	6	2	5	1	2	3	2	1	2	6	1	rs113662142	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:17118730A>G	ENST00000265970.7	-	26	4199	c.4200T>C	c.(4198-4200)ggT>ggC	p.G1400G	PIK3C2A_ENST00000531428.1_5'UTR|PIK3C2A_ENST00000540361.1_Silent_p.G1020G	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	1400					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						TAGAAGGAAGACCAGAAAAAC	0.358													A|||	27	0.00539137	0.0023	0.0	5008	,	,		19765	0.0		0.0089	False		,,,				2504	0.0153				p.G1400G		Atlas-SNP	.											.	PIK3C2A	148	.	0			c.T4200C						PASS	.	A		12,4388	19.1+/-41.9	0,12,2188	116	111	113		4200	0.9	1	11	dbSNP_132	113	80,8506	45.8+/-104.6	1,78,4214	no	coding-synonymous	PIK3C2A	NM_002645.2		1,90,6402	GG,GA,AA		0.9317,0.2727,0.7085		1400/1687	17118730	92,12894	2200	4293	6493	SO:0001819	synonymous_variant	5286	exon26			AGGAAGACCAGAA	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.4200T>C	11.37:g.17118730A>G		58	0	0		55	19	0.345455	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Silent	SNP	ENST00000265970.7	37	CCDS7824.1																																																																																			A|0.992;G|0.008	0.008	strong		0.358	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		G	17118730	A	G	17118730	2	3	28	1	0	0	0	0	0	0	0	1	11918	262	10	3		3	PIK3C2A	11	17118730	Silent	SNP	A	TCGA-G8-6914-01A-11D-2210-10	8036662	17118730	117887786	410	11913											
HPS5	11234	hgsc.bcm.edu	37	chr11	18318354	18318354	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acattcatcaccttcatttcCgtgtgagccacaacactgat	11	12	5	13	1	3	2	3	2	0	0	4	2	4	2	3	0	2	0	3	0	1	3	rs143784823	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:18318354C>T	ENST00000349215.3	-	12	1778	c.1501G>A	c.(1501-1503)Gga>Aga	p.G501R	HPS5_ENST00000531848.1_Missense_Mutation_p.G387R|HPS5_ENST00000438420.2_Missense_Mutation_p.G387R|HPS5_ENST00000396253.3_Missense_Mutation_p.G387R|HPS5_ENST00000352460.3_5'Flank	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	501					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						CCTTCATTTCCGTGTGAGCCA	0.458									Hermansky-Pudlak syndrome				C|||	9	0.00179712	0.0	0.0	5008	,	,		17393	0.0		0.0089	False		,,,				2504	0.0				p.G501R		Atlas-SNP	.											.	HPS5	70	.	0			c.G1501A						PASS	.	C	ARG/GLY,ARG/GLY,ARG/GLY	4,4394	8.1+/-20.4	0,4,2195	260	249	253		1159,1501,1159	2.8	0	11	dbSNP_134	253	32,8554	21.6+/-65.8	1,30,4262	yes	missense,missense,missense	HPS5	NM_007216.3,NM_181507.1,NM_181508.1	125,125,125	1,34,6457	TT,TC,CC		0.3727,0.091,0.2773	benign,benign,benign	387/1016,501/1130,387/1016	18318354	36,12948	2199	4293	6492	SO:0001583	missense	11234	exon12	Familial Cancer Database	HPS, HPS1-8	CATTTCCGTGTGA	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.1501G>A	11.37:g.18318354C>T	ENSP00000265967:p.Gly501Arg	145	0	0		178	81	0.455056	NM_181507	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Missense_Mutation	SNP	ENST00000349215.3	37	CCDS7836.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	C	0.033	-1.322402	0.01320	9.1E-4	0.003727	ENSG00000110756	ENST00000396253;ENST00000438420;ENST00000349215;ENST00000531848	T;T;T;T	0.53423	0.63;0.63;0.62;1.6	5.71	2.83	0.33086	.	1.416520	0.04002	N	0.296561	T	0.18425	0.0442	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.20107	-1.0285	10	0.08179	T	0.78	.	7.3826	0.26864	0.0:0.6515:0.0:0.3485	.	501	Q9UPZ3	HPS5_HUMAN	R	387;387;501;387	ENSP00000379552:G387R;ENSP00000399590:G387R;ENSP00000265967:G501R;ENSP00000431758:G387R	ENSP00000265967:G501R	G	-	1	0	HPS5	18274930	0.000000	0.05858	0.002000	0.10522	0.108000	0.19459	0.521000	0.22893	0.347000	0.23924	-0.214000	0.12660	GGA	C|0.997;T|0.003	0.003	strong		0.458	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1	NM_181507		T	18318354	C	T	18318354	3	4	28	1	0	0	0	0	1	0	0	0	7351	661	23	1	1936	1	HPS5	11	18318354	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1199624	18318354	116688162	411	11914											
LDHA	3939	hgsc.bcm.edu	37	chr11	18427072	18427072	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tagcagatttggcagagagtAtaatgaagaatcttaggcgg	14	10	13	4	1	1	4	0	1	1	3	1	5	1	4	0	3	1	3	0	3	6	5			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:18427072A>G	ENST00000422447.3	+	7	1060	c.787A>G	c.(787-789)Ata>Gta	p.I263V	LDHA_ENST00000227157.4_Intron|LDHA_ENST00000379412.5_Missense_Mutation_p.I263V|AC084117.3_ENST00000496975.2_RNA|LDHA_ENST00000540430.1_Missense_Mutation_p.I292V|LDHA_ENST00000542179.1_Missense_Mutation_p.I263V|LDHA_ENST00000396222.2_Intron|LDHA_ENST00000430553.2_Missense_Mutation_p.I205V	NM_001135239.1|NM_005566.3	NP_001128711.1|NP_005557.1	P00338	LDHA_HUMAN	lactate dehydrogenase A	263					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						GGCAGAGAGTATAATGAAGAA	0.423																																					p.I292V		Atlas-SNP	.											.	LDHA	118	.	0			c.A874G						PASS	.						111	113	112					11																	18427072		2199	4293	6492	SO:0001583	missense	3939	exon7			GAGAGTATAATGA	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.787A>G	11.37:g.18427072A>G	ENSP00000395337:p.Ile263Val	71	0	0		91	4	0.043956	NM_001165414	B4DKQ2|B7Z5E3|D3DQY3|F8W819|Q53G53|Q6IBM7|Q6ZNV1|Q9UDE8|Q9UDE9	Missense_Mutation	SNP	ENST00000422447.3	37	CCDS7839.1	.	.	.	.	.	.	.	.	.	.	A	14.33	2.502896	0.44558	.	.	ENSG00000134333	ENST00000422447;ENST00000430553;ENST00000541620;ENST00000445376;ENST00000540430;ENST00000379412;ENST00000542179	T;T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24;-0.24	5.12	5.12	0.69794	Lactate/malate dehydrogenase, C-terminal (1);Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal (2);	0.103731	0.64402	D	0.000003	T	0.66197	0.2765	L	0.55834	1.745	0.80722	D	1	B;B;B;B	0.16166	0.016;0.001;0.001;0.013	B;B;B;B	0.30251	0.113;0.025;0.026;0.056	T	0.65886	-0.6059	10	0.62326	D	0.03	-3.2056	15.205	0.73173	1.0:0.0:0.0:0.0	.	292;205;236;263	B7Z5E3;B4DKQ2;B4DJI1;P00338	.;.;.;LDHA_HUMAN	V	263;205;235;236;292;263;263	ENSP00000395337:I263V;ENSP00000406172:I205V;ENSP00000445175:I292V;ENSP00000368722:I263V;ENSP00000445331:I263V	ENSP00000368722:I263V	I	+	1	0	LDHA	18383648	1.000000	0.71417	1.000000	0.80357	0.642000	0.38348	4.095000	0.57728	2.056000	0.61249	0.374000	0.22700	ATA	.	.	none		0.423	LDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258172.2	NM_005566		G	18427072	A	G	18427072	3	3	28	1	0	0	0	0	1	0	0	0	8707	449	16	3	900	3	LDHA	11	18427072	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	108718	18427072	116579444	412	11915											
MRGPRX1	259249	hgsc.bcm.edu	37	chr11	18955515	18955515	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctaaaggagcccacgaagaAgtaaatgatggggttggcac	14	6	13	8	1	0	2	0	1	0	1	0	4	0	3	2	4	1	3	2	4	6	3	rs138263314	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:18955515A>G	ENST00000302797.3	-	1	1041	c.817T>C	c.(817-819)Ttc>Ctc	p.F273L	MRGPRX1_ENST00000526914.1_5'Flank|RP11-583F24.8_ENST00000528646.1_RNA	NM_147199.3	NP_671732.3	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	273					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						CCCACGAAGAAGTAAATGATG	0.493													A|||	102	0.0203674	0.0015	0.0605	5008	,	,		27612	0.0		0.0318	False		,,,				2504	0.0266				p.F273L		Atlas-SNP	.											MRGPRX1,NS,carcinoma,+1,1	MRGPRX1	84	1	0			c.T817C						scavenged	.	A	LEU/PHE	23,4365		0,23,2171	78	76	77		817	1.1	0.4	11	dbSNP_134	77	203,8367		0,203,4082	no	missense	MRGPRX1	NM_147199.3	22	0,226,6253	GG,GA,AA		2.3687,0.5242,1.7441	possibly-damaging	273/323	18955515	226,12732	2194	4285	6479	SO:0001583	missense	259249	exon1			CGAAGAAGTAAAT		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.817T>C	11.37:g.18955515A>G	ENSP00000305766:p.Phe273Leu	61	1	0.0163934		85	29	0.341176	NM_147199	Q4V9L2|Q8TDD8|Q8TDD9	Missense_Mutation	SNP	ENST00000302797.3	37	CCDS7846.1	49	0.022435897435897436	2	0.0040650406504065045	23	0.06353591160220995	0	0.0	24	0.0316622691292876	.	17.20	3.328525	0.60743	0.005242	0.023687	ENSG00000170255	ENST00000302797	T	0.35421	1.31	2.28	1.06	0.20224	.	0.210366	0.32753	N	0.005690	T	0.08179	0.0204	M	0.83692	2.655	0.25544	N	0.987152	D	0.59357	0.985	P	0.53518	0.728	T	0.04178	-1.0971	10	0.32370	T	0.25	.	6.7944	0.23717	0.7627:0.2373:0.0:0.0	.	273	Q96LB2	MRGX1_HUMAN	L	273	ENSP00000305766:F273L	ENSP00000305766:F273L	F	-	1	0	MRGPRX1	18912091	0.218000	0.23608	0.370000	0.25965	0.402000	0.30811	0.633000	0.24598	0.270000	0.21984	0.402000	0.26972	TTC	A|0.980;G|0.020	0.020	strong		0.493	MRGPRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369913.1	NM_147199		G	18955515	A	G	18955515	3	3	28	1	0	0	0	0	1	0	0	0	9775	72	3	3	155	3	MRGPRX1	11	18955515	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	528443	18955515	116051001	413	11916											
BBOX1	8424	hgsc.bcm.edu	37	chr11	27148847	27148847	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atcttttctttaggtgatgtGattacttttgataactggcg	8	19	9	5	1	2	3	0	3	2	0	2	3	2	3	0	2	2	0	0	2	3	8	rs77035197	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:27148847G>A	ENST00000529202.1	+	8	1350	c.1011G>A	c.(1009-1011)gtG>gtA	p.V337V	BBOX1_ENST00000528583.1_Silent_p.V337V|BBOX1_ENST00000525090.1_Silent_p.V337V|BBOX1_ENST00000263182.3_Silent_p.V337V|RP11-1L12.3_ENST00000526061.1_RNA|RP11-1L12.3_ENST00000530430.1_RNA|RP11-1L12.3_ENST00000525302.1_RNA			O75936	BODG_HUMAN	butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 1	337					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)	TAGGTGATGTGATTACTTTTG	0.398													G|||	104	0.0207668	0.0008	0.0375	5008	,	,		18591	0.0		0.0507	False		,,,				2504	0.0266				p.V337V		Atlas-SNP	.											.	BBOX1	46	.	0			c.G1011A						PASS	.	G		26,4378	32.6+/-62.9	0,26,2176	104	93	96		1011	4	1	11	dbSNP_132	96	366,8232	121.1+/-180.3	9,348,3942	no	coding-synonymous	BBOX1	NM_003986.2		9,374,6118	AA,AG,GG		4.2568,0.5904,3.0149		337/388	27148847	392,12610	2202	4299	6501	SO:0001819	synonymous_variant	8424	exon9			TGATGTGATTACT	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.1011G>A	11.37:g.27148847G>A		67	0	0		55	30	0.545455	NM_003986	B2R8L7|D3DQZ1|Q6IBJ2	Silent	SNP	ENST00000529202.1	37	CCDS7862.1																																																																																			G|0.968;A|0.032	0.032	strong		0.398	BBOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387946.1	NM_003986		A	27148847	G	A	27148847	2	1	28	1	0	0	0	0	0	0	0	1	1334	1277	45	2		2	BBOX1	11	27148847	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	8193332	27148847	107857669	414	11917											
IMMP1L	196294	hgsc.bcm.edu	37	chr11	31482246	31482246	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attttgaattgtaggctccaTtgatggtccagaacactgaa	12	13	9	7	0	0	4	0	3	0	1	2	4	2	4	2	2	1	2	2	2	4	5	rs370083551		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:31482246T>C	ENST00000278200.1	-	4	316	c.121A>G	c.(121-123)Atg>Gtg	p.M41V	IMMP1L_ENST00000533642.1_Intron|IMMP1L_ENST00000532287.1_Missense_Mutation_p.M41V|IMMP1L_ENST00000534812.1_Intron|IMMP1L_ENST00000526776.1_Intron|IMMP1L_ENST00000528161.1_Intron	NM_144981.1	NP_659418.1	Q96LU5	IMP1L_HUMAN	IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae)	41					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)					GTAGGCTCCATTGATGGTCCA	0.279																																					p.M41V		Atlas-SNP	.											.	IMMP1L	16	.	0			c.A121G						PASS	.	T	VAL/MET	0,4404		0,0,2202	69	72	71		121	5.6	1	11		71	1,8585	1.2+/-3.3	0,1,4292	no	missense	IMMP1L	NM_144981.1	21	0,1,6494	CC,CT,TT		0.0116,0.0,0.0077	possibly-damaging	41/167	31482246	1,12989	2202	4293	6495	SO:0001583	missense	196294	exon4			GCTCCATTGATGG		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.121A>G	11.37:g.31482246T>C	ENSP00000278200:p.Met41Val	220	0	0		228	111	0.486842	NM_144981	D3DQZ7|Q96SH9	Missense_Mutation	SNP	ENST00000278200.1	37	CCDS7874.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.083575	0.76642	0.0	1.16E-4	ENSG00000148950	ENST00000532287;ENST00000278200;ENST00000529749;ENST00000530023	.	.	.	5.58	5.58	0.84498	Peptidase S24/S26A/S26B/S26C (1);Peptidase S24/S26A/S26B/S26C, beta-ribbon domain (1);Peptidase S24/S26A/S26B (1);	0.000000	0.85682	D	0.000000	D	0.86997	0.6068	H	0.95043	3.615	0.80722	D	1	D;P	0.53885	0.963;0.873	D;P	0.69824	0.966;0.687	D	0.90553	0.4510	9	0.66056	D	0.02	-8.7493	16.0334	0.80603	0.0:0.0:0.0:1.0	.	41;41	E9PIG6;Q96LU5	.;IMP1L_HUMAN	V	41	.	ENSP00000278200:M41V	M	-	1	0	IMMP1L	31438822	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.023000	0.76437	2.243000	0.73865	0.533000	0.62120	ATG	.	.	weak		0.279	IMMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388496.1	NM_144981		C	31482246	T	C	31482246	3	2	28	1	0	0	0	0	1	0	0	0	7725	1493	52	3	395	3	IMMP1L	11	31482246	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	4333399	31482246	103524270	415	11918											
TMEM132A	54972	hgsc.bcm.edu	37	chr11	60701176	60701176	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agctcaccgacaccaccctcGagcaggtccgcggctggagg	8	4	13	16	4	1	0	1	0	0	0	3	3	2	1	4	4	2	3	4	4	0	0			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:60701176G>A	ENST00000453848.2	+	8	1677	c.1519G>A	c.(1519-1521)Gag>Aag	p.E507K	TMEM132A_ENST00000005286.4_Missense_Mutation_p.E508K			Q24JP5	T132A_HUMAN	transmembrane protein 132A	507						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						CACCACCCTCGAGCAGGTCCG	0.701																																					p.E508K		Atlas-SNP	.											.	TMEM132A	135	.	0			c.G1522A						PASS	.						13	12	12					11																	60701176		2189	4283	6472	SO:0001583	missense	54972	exon8			ACCCTCGAGCAGG	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.1519G>A	11.37:g.60701176G>A	ENSP00000405823:p.Glu507Lys	44	0	0		51	21	0.411765	NM_017870	Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Missense_Mutation	SNP	ENST00000453848.2	37	CCDS44618.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.6|20.6	4.013820|4.013820	0.75161|0.75161	.|.	.|.	ENSG00000006118|ENSG00000006118	ENST00000444690;ENST00000453848;ENST00000005286|ENST00000536409	T;T|.	0.13538|.	2.58;2.58|.	4.25|4.25	4.25|4.25	0.50352|0.50352	.|.	0.338551|.	0.26387|.	N|.	0.024675|.	T|T	0.61553|0.61553	0.2356|0.2356	L|L	0.47716|0.47716	1.5|1.5	0.34210|0.34210	D|D	0.674176|0.674176	D;D;D|.	0.62365|.	0.989;0.991;0.991|.	P;P;P|.	0.54270|.	0.743;0.677;0.747|.	T|T	0.69416|0.69416	-0.5151|-0.5151	10|5	0.87932|.	D|.	0|.	.|.	15.3168|15.3168	0.74085|0.74085	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	258;507;508|.	Q24JP5-4;Q24JP5;Q24JP5-2|.	.;T132A_HUMAN;.|.	K|Q	258;507;508|98	ENSP00000405823:E507K;ENSP00000005286:E508K|.	ENSP00000005286:E508K|.	E|R	+|+	1|2	0|0	TMEM132A|TMEM132A	60457752|60457752	0.987000|0.987000	0.35691|0.35691	0.975000|0.975000	0.42487|0.42487	0.817000|0.817000	0.46193|0.46193	1.938000|1.938000	0.40203|0.40203	2.285000|2.285000	0.76669|0.76669	0.555000|0.555000	0.69702|0.69702	GAG|CGA	.	.	none		0.701	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870		A	60701176	G	A	60701176	3	1	28	1	0	0	0	0	1	0	0	0	16060	1059	37	1	1552	1	TMEM132A	11	60701176	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	29218930	60701176	74305340	416	11919											
SLC22A24	283238	hgsc.bcm.edu	37	chr11	62902146	62902146	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgacactcacctgtctgaaAgatggccatatattagacct	13	11	7	10	0	2	4	1	2	1	2	2	4	2	4	3	1	0	0	3	1	4	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:62902146A>G	ENST00000417740.1	-	2	938	c.497T>C	c.(496-498)cTt>cCt	p.L166P	SLC22A24_ENST00000326192.5_Missense_Mutation_p.L166P	NM_001136506.2	NP_001129978.2	Q8N4F4	S22AO_HUMAN	solute carrier family 22, member 24	166					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				kidney(1)|stomach(1)	2						CCTGTCTGAAAGATGGCCATA	0.383																																					p.L166P		Atlas-SNP	.											.	SLC22A24	31	.	0			c.T497C						PASS	.						93	72	79					11																	62902146		692	1591	2283	SO:0001583	missense	283238	exon2			TCTGAAAGATGGC		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.497T>C	11.37:g.62902146A>G	ENSP00000396586:p.Leu166Pro	120	0	0		160	49	0.30625	NM_001136506		Missense_Mutation	SNP	ENST00000417740.1	37		.	.	.	.	.	.	.	.	.	.	A	18.12	3.553416	0.65425	.	.	ENSG00000197658	ENST00000417740;ENST00000531535;ENST00000326192	D;T	0.85013	-1.93;-0.36	3.52	3.52	0.40303	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.237783	0.35615	U	0.003083	D	0.93631	0.7966	H	0.95043	3.615	0.35699	D	0.815434	D;D	0.89917	0.999;1.0	D;D	0.80764	0.994;0.994	D	0.95896	0.8911	10	0.87932	D	0	.	10.166	0.42879	1.0:0.0:0.0:0.0	.	166;166	Q8N4F4;C9JC66	S22AO_HUMAN;.	P	166	ENSP00000396586:L166P;ENSP00000321549:L166P	ENSP00000321549:L166P	L	-	2	0	SLC22A24	62658722	0.140000	0.22579	0.047000	0.18901	0.691000	0.40173	5.090000	0.64498	1.474000	0.48178	0.321000	0.21382	CTT	.	.	none		0.383	SLC22A24-003	PUTATIVE	non_canonical_polymorphism|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000383747.1	NM_173586		G	62902146	A	G	62902146	3	3	28	1	0	0	0	0	1	0	0	0	14468	72	3	3	1192	3	SLC22A24	11	62902146	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	2200970	62902146	72104370	417	11920											
SYVN1	84447	hgsc.bcm.edu	37	chr11	64897292	64897292	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	acgcaggctctgcagccgggCctccaggtgctgccgctcat	5	7	13	16	3	2	0	1	0	1	0	3	0	3	0	4	3	4	5	4	3	0	0	rs141712194	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:64897292C>T	ENST00000377190.3	-	14	1598	c.1504G>A	c.(1504-1506)Gcc>Acc	p.A502T	SYVN1_ENST00000526060.1_Missense_Mutation_p.A501T|SYVN1_ENST00000526121.1_5'Flank|SYVN1_ENST00000294256.8_Missense_Mutation_p.A501T|SYVN1_ENST00000307289.6_Missense_Mutation_p.A450T	NM_172230.2	NP_757385.1	Q86TM6	SYVN1_HUMAN	synovial apoptosis inhibitor 1, synoviolin	502					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						TGCAGCCGGGCCTCCAGGTGC	0.657													c|||	2	0.000399361	0.0	0.0	5008	,	,		17978	0.0		0.002	False		,,,				2504	0.0				p.A502T		Atlas-SNP	.											.	SYVN1	55	.	0			c.G1504A						PASS	.	C	THR/ALA,THR/ALA	1,4401	2.1+/-5.4	0,1,2200	40	45	43		1504,1501	3.8	1	11	dbSNP_134	43	4,8590	3.7+/-12.6	0,4,4293	yes	missense,missense	SYVN1	NM_172230.2,NM_032431.2	58,58	0,5,6493	TT,TC,CC		0.0465,0.0227,0.0385	benign,benign	502/618,501/617	64897292	5,12991	2201	4297	6498	SO:0001583	missense	84447	exon14			GCCGGGCCTCCAG	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.1504G>A	11.37:g.64897292C>T	ENSP00000366395:p.Ala502Thr	87	0	0		102	47	0.460784	NM_172230	Q8N3K3|Q8N6E8|Q96JL5|Q96PK3	Missense_Mutation	SNP	ENST00000377190.3	37	CCDS31605.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	18.41	3.616870	0.66672	2.27E-4	4.65E-4	ENSG00000162298	ENST00000377190;ENST00000294256;ENST00000434219;ENST00000307289;ENST00000526060	T;T;T;T	0.15718	2.43;2.4;2.52;2.4	4.75	3.82	0.43975	.	0.062439	0.64402	D	0.000006	T	0.40719	0.1128	M	0.78049	2.395	0.80722	D	1	D;B;B	0.67145	0.996;0.361;0.247	D;B;B	0.77557	0.99;0.293;0.153	T	0.32052	-0.9921	10	0.54805	T	0.06	-14.4894	12.007	0.53265	0.1742:0.8258:0.0:0.0	.	450;501;502	Q86TM6-2;Q86TM6-3;Q86TM6	.;.;SYVN1_HUMAN	T	502;501;502;450;501	ENSP00000366395:A502T;ENSP00000294256:A501T;ENSP00000302035:A450T;ENSP00000436984:A501T	ENSP00000294256:A501T	A	-	1	0	SYVN1	64653868	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.189000	0.77747	1.213000	0.43380	0.561000	0.74099	GCC	C|0.999;T|0.001	0.001	strong		0.657	SYVN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385274.1	NM_032431		T	64897292	C	T	64897292	3	4	28	1	0	0	0	0	1	0	0	0	15502	739	26	2	361	2	SYVN1	11	64897292	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1995146	64897292	70109224	418	11921											
SLC25A45	283130	hgsc.bcm.edu	37	chr11	65144331	65144331	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtactggcgacagagcccttCataggtgatgaagtagatcc	11	9	12	9	1	1	4	1	2	0	2	2	5	2	4	2	2	2	2	2	2	4	4	rs371949191		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:65144331C>T	ENST00000527174.1	-	5	611	c.556G>A	c.(556-558)Gaa>Aaa	p.E186K	SLC25A45_ENST00000534028.1_Missense_Mutation_p.E162K|SLC25A45_ENST00000417511.2_Missense_Mutation_p.E144K|SLC25A45_ENST00000398802.1_Missense_Mutation_p.E186K|SLC25A45_ENST00000526432.1_Missense_Mutation_p.E124K|SLC25A45_ENST00000377152.2_Missense_Mutation_p.E82K|SLC25A45_ENST00000360662.3_Missense_Mutation_p.E162K|SLC25A45_ENST00000294187.6_Missense_Mutation_p.E144K|RP11-867O8.5_ENST00000533886.1_RNA			Q8N413	S2545_HUMAN	solute carrier family 25, member 45	186					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						CAGAGCCCTTCATAGGTGATG	0.627																																					p.E186K		Atlas-SNP	.											.	SLC25A45	23	.	0			c.G556A						PASS	.	C	LYS/GLU,LYS/GLU	0,4070		0,0,2035	138	145	143		556,430	4.3	0.2	11		143	1,8389		0,1,4194	no	missense,missense	SLC25A45	NM_182556.2,NM_001077241.1	56,56	0,1,6229	TT,TC,CC		0.0119,0.0,0.0080	benign,benign	186/289,144/247	65144331	1,12459	2035	4195	6230	SO:0001583	missense	283130	exon6			GCCCTTCATAGGT	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.556G>A	11.37:g.65144331C>T	ENSP00000435489:p.Glu186Lys	203	0	0		211	89	0.421801	NM_182556	Q6PL49|Q8IW29	Missense_Mutation	SNP	ENST00000527174.1	37	CCDS41670.1	.	.	.	.	.	.	.	.	.	.	C	15.95	2.983275	0.53827	0.0	1.19E-4	ENSG00000162241	ENST00000527174;ENST00000534028;ENST00000398802;ENST00000360662;ENST00000377152;ENST00000294187;ENST00000417511;ENST00000526432	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	5.23	4.26	0.50523	Mitochondrial carrier domain (2);	0.116851	0.53938	D	0.000048	D	0.89336	0.6686	M	0.86343	2.81	0.39497	D	0.968142	D;B;B	0.54964	0.969;0.203;0.242	P;B;B	0.58077	0.832;0.099;0.159	D	0.88486	0.3072	10	0.27785	T	0.31	-0.3137	13.3171	0.60413	0.0:0.8399:0.1601:0.0	.	124;162;186	E9PJQ3;Q8N413-4;Q8N413	.;.;S2545_HUMAN	K	186;162;186;162;82;144;144;124	ENSP00000435489:E186K;ENSP00000431769:E162K;ENSP00000381782:E186K;ENSP00000353879:E162K;ENSP00000366357:E82K;ENSP00000294187:E144K;ENSP00000407530:E144K;ENSP00000435547:E124K	ENSP00000294187:E144K	E	-	1	0	SLC25A45	64900907	0.000000	0.05858	0.240000	0.24138	0.281000	0.26958	0.738000	0.26158	2.617000	0.88574	0.561000	0.74099	GAA	.	.	weak		0.627	SLC25A45-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388744.3	NM_182556		T	65144331	C	T	65144331	3	4	28	1	0	0	0	0	1	0	0	0	14525	835	29	2	318	2	SLC25A45	11	65144331	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	247039	65144331	69862185	419	11922											
CATSPER1	117144	hgsc.bcm.edu	37	chr11	65789004	65789004	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccggattgccctcagggcccGcaggctcttgaagaccttga	7	8	12	14	2	2	3	1	2	1	1	2	4	2	4	4	3	1	2	4	3	1	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:65789004G>A	ENST00000312106.5	-	4	1791	c.1654C>T	c.(1654-1656)Cgg>Tgg	p.R552W		NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1	552					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						CTCAGGGCCCGCAGGCTCTTG	0.627																																					p.R552W		Atlas-SNP	.											.	CATSPER1	101	.	0			c.C1654T						PASS	.						60	64	63					11																	65789004		2201	4296	6497	SO:0001583	missense	117144	exon4			GGGCCCGCAGGCT	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.1654C>T	11.37:g.65789004G>A	ENSP00000309052:p.Arg552Trp	36	0	0		72	31	0.430556	NM_053054	Q96P76	Missense_Mutation	SNP	ENST00000312106.5	37	CCDS8127.1	.	.	.	.	.	.	.	.	.	.	G	13.91	2.378231	0.42207	.	.	ENSG00000175294	ENST00000312106	D	0.98633	-5.04	4.99	3.08	0.35506	Ion transport (1);	0.000000	0.30565	U	0.009357	D	0.99211	0.9726	H	0.95917	3.74	0.23331	N	0.997892	D	0.89917	1.0	D	0.97110	1.0	D	0.96270	0.9198	10	0.87932	D	0	-21.6854	6.1104	0.20097	0.0968:0.0:0.7178:0.1855	.	552	Q8NEC5	CTSR1_HUMAN	W	552	ENSP00000309052:R552W	ENSP00000309052:R552W	R	-	1	2	CATSPER1	65545580	1.000000	0.71417	0.893000	0.35052	0.020000	0.10135	1.757000	0.38400	0.495000	0.27882	0.561000	0.74099	CGG	.	.	none		0.627	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054		A	65789004	G	A	65789004	3	1	28	1	0	0	0	0	1	0	0	0	2689	1086	38	1	724	1	CATSPER1	11	65789004	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	644673	65789004	69217512	420	11923											
TBX10	347853	hgsc.bcm.edu	37	chr11	67399173	67399173	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccttgatccctatcagccCggatgttggggagggggtat	6	11	14	10	1	1	1	1	1	0	0	3	3	3	3	3	5	1	2	3	5	2	4	rs146672518	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:67399173C>T	ENST00000335385.3	-	8	1148	c.1061G>A	c.(1060-1062)cGg>cAg	p.R354Q	NUDT8_ENST00000376693.2_5'Flank|NUDT8_ENST00000301490.4_5'Flank	NM_005995.4	NP_005986.2	O75333	TBX10_HUMAN	T-box 10	354					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						CCTATCAGCCCGGATGTTGGG	0.652													C|||	18	0.00359425	0.0015	0.0058	5008	,	,		15763	0.0		0.0089	False		,,,				2504	0.0031				p.R354Q		Atlas-SNP	.											.	TBX10	25	.	0			c.G1061A	GRCh37	CM055547	TBX10	M	rs146672518	PASS	.	C	GLN/ARG	6,4394		0,6,2194	22	20	21		1061	-6.5	0	11	dbSNP_134	21	99,8487		1,97,4195	yes	missense	TBX10	NM_005995.4	43	1,103,6389	TT,TC,CC		1.153,0.1364,0.8086	benign	354/386	67399173	105,12881	2200	4293	6493	SO:0001583	missense	347853	exon8			TCAGCCCGGATGT	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.1061G>A	11.37:g.67399173C>T	ENSP00000335191:p.Arg354Gln	43	0	0		46	26	0.565217	NM_005995	Q14D64|Q86XS3	Missense_Mutation	SNP	ENST00000335385.3	37	CCDS31621.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	C	4.834	0.155029	0.09236	0.001364	0.01153	ENSG00000167800	ENST00000335385	D	0.85955	-2.05	3.79	-6.47	0.01902	.	5.537720	0.00166	N	0.000011	T	0.55242	0.1908	N	0.04508	-0.205	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.53788	-0.8389	10	0.25106	T	0.35	.	2.5625	0.04775	0.1339:0.1628:0.1338:0.5696	.	354	O75333	TBX10_HUMAN	Q	354	ENSP00000335191:R354Q	ENSP00000335191:R354Q	R	-	2	0	TBX10	67155749	0.000000	0.05858	0.001000	0.08648	0.063000	0.16089	-0.708000	0.05035	-0.878000	0.04007	-0.258000	0.10820	CGG	C|0.994;T|0.006	0.006	strong		0.652	TBX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394034.1	NM_005995		T	67399173	C	T	67399173	3	4	28	1	0	0	0	0	1	0	0	0	15666	652	23	1	100	1	TBX10	11	67399173	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1610169	67399173	67607343	421	11924											
CCND1	595	hgsc.bcm.edu	37	chr11	69462802	69462802	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccgccctccatggtggcagcGgggagcgtggtggccgcagt	4	6	18	13	4	0	0	0	0	0	0	1	1	1	1	4	6	2	2	4	6	0	0			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:69462802G>A	ENST00000227507.2	+	4	842	c.615G>A	c.(613-615)gcG>gcA	p.A205A	CCND1_ENST00000536559.1_3'UTR	NM_053056.2	NP_444284.1	P24385	CCND1_HUMAN	cyclin D1	205					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)	TGGTGGCAGCGGGGAGCGTGG	0.607			T	"IGH@, FSTL3"	"CLL, B-ALL, breast"					Multiple Myeloma(6;0.086)																											p.A205A	Pancreas(65;393 884 2788 21700 24360 27795 36895)	Atlas-SNP	.		Dom	yes		11	11q13	595	cyclin D1		"L, E"	CCND1,NS,carcinoma,0,1	CCND1	107	1	0			c.G615A						PASS	.						112	111	112					11																	69462802		2200	4294	6494	SO:0001819	synonymous_variant	595	exon4			GGCAGCGGGGAGC	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.615G>A	11.37:g.69462802G>A		73	0	0		72	35	0.486111	NM_053056	Q6LEF0	Silent	SNP	ENST00000227507.2	37	CCDS8191.1																																																																																			.	.	none		0.607	CCND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396775.2	NM_053056		A	69462802	G	A	69462802	2	1	28	1	0	0	0	0	0	0	0	1	2918	1103	39	1		1	CCND1	11	69462802	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2063629	69462802	65543714	422	11925											
PPFIA1	8500	hgsc.bcm.edu	37	chr11	70189892	70189892	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atggtgaagatgacagggacActctcctcagctcagttgac	11	9	11	10	0	3	4	2	3	1	1	4	5	3	5	1	2	1	2	1	2	1	1	rs146858711	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:70189892A>G	ENST00000253925.7	+	15	2040	c.1825A>G	c.(1825-1827)Act>Gct	p.T609A	AP000487.6_ENST00000528607.1_RNA|PPFIA1_ENST00000389547.3_Missense_Mutation_p.T609A	NM_003626.3	NP_003617.1	Q13136	LIPA1_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	609					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)			TGACAGGGACACTCTCCTCAG	0.557													A|||	7	0.00139776	0.0	0.0	5008	,	,		17819	0.0		0.007	False		,,,				2504	0.0				p.T609A		Atlas-SNP	.											.	PPFIA1	114	.	0			c.A1825G						PASS	.	A	ALA/THR,ALA/THR	1,4399	2.1+/-5.4	0,1,2199	139	95	110		1825,1825	1.7	0.7	11	dbSNP_134	110	13,8575	9.8+/-36.6	0,13,4281	yes	missense,missense	PPFIA1	NM_003626.2,NM_177423.1	58,58	0,14,6480	GG,GA,AA		0.1514,0.0227,0.1078	benign,benign	609/1203,609/1186	70189892	14,12974	2200	4294	6494	SO:0001583	missense	8500	exon15			AGGGACACTCTCC	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.1825A>G	11.37:g.70189892A>G	ENSP00000253925:p.Thr609Ala	76	0	0		72	36	0.5	NM_177423	A6NLE3|Q13135|Q14567|Q8N4I2	Missense_Mutation	SNP	ENST00000253925.7	37	CCDS31627.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	A	9.790	1.177733	0.21787	2.27E-4	0.001514	ENSG00000131626	ENST00000253925;ENST00000389547;ENST00000544950	T;T	0.23950	1.88;1.88	5.3	1.66	0.24008	.	0.134893	0.49305	N	0.000153	T	0.17789	0.0427	M	0.72118	2.19	0.42471	D	0.992829	B;B	0.15473	0.001;0.013	B;B	0.17979	0.009;0.02	T	0.04041	-1.0982	10	0.37606	T	0.19	.	6.1866	0.20500	0.7209:0.1362:0.1429:0.0	.	609;609	Q13136;Q13136-2	LIPA1_HUMAN;.	A	609;609;96	ENSP00000253925:T609A;ENSP00000374198:T609A	ENSP00000253925:T609A	T	+	1	0	PPFIA1	69867540	1.000000	0.71417	0.739000	0.30968	0.957000	0.61999	2.204000	0.42761	0.033000	0.15463	0.459000	0.35465	ACT	A|0.998;G|0.002	0.002	strong		0.557	PPFIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393905.1	NM_003626		G	70189892	A	G	70189892	3	3	28	1	0	0	0	0	1	0	0	0	12318	159	6	3	1879	3	PPFIA1	11	70189892	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	727090	70189892	64816624	423	11926											
ARAP1	116985	hgsc.bcm.edu	37	chr11	72421569	72421569	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagataagcgctagagagcCgggcccgggcacgctgctca	9	4	15	13	4	1	2	1	0	0	2	1	3	1	2	2	2	3	5	2	2	2	2	rs369752678	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:72421569C>T	ENST00000393609.3	-	10	1479	c.1277G>A	c.(1276-1278)cGg>cAg	p.R426Q	ARAP1_ENST00000393605.3_Missense_Mutation_p.R186Q|ARAP1_ENST00000455638.2_Missense_Mutation_p.R426Q|ARAP1_ENST00000429686.1_Missense_Mutation_p.R181Q|ARAP1_ENST00000426523.1_Missense_Mutation_p.R181Q|ARAP1_ENST00000359373.5_Missense_Mutation_p.R426Q|ARAP1_ENST00000334211.8_Missense_Mutation_p.R181Q	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	426					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						GCTAGAGAGCCGGGCCCGGGC	0.632													C|||	2	0.000399361	0.0015	0.0	5008	,	,		16560	0.0		0.0	False		,,,				2504	0.0				p.R426Q	Ovarian(102;1198 1520 13195 17913 37529)	Atlas-SNP	.											.	ARAP1	168	.	0			c.G1277A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	0,4400		0,0,2200	34	36	35		1277,542,542	1.5	0	11		35	1,8585	1.2+/-3.3	0,1,4292	no	missense,missense,missense	ARAP1	NM_001040118.2,NM_001135190.1,NM_015242.4	43,43,43	0,1,6492	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	426/1451,181/1134,181/1206	72421569	1,12985	2200	4293	6493	SO:0001583	missense	116985	exon10			GAGAGCCGGGCCC	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.1277G>A	11.37:g.72421569C>T	ENSP00000377233:p.Arg426Gln	57	0	0		48	22	0.458333	NM_001040118	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Missense_Mutation	SNP	ENST00000393609.3	37	CCDS41687.1	.	.	.	.	.	.	.	.	.	.	C	2.665	-0.278826	0.05642	0.0	1.16E-4	ENSG00000186635	ENST00000359373;ENST00000455638;ENST00000393605;ENST00000334211;ENST00000393609;ENST00000426523;ENST00000429686;ENST00000340247	T;T;T;T;T;T;T	0.06371	3.34;3.34;3.33;3.38;3.36;3.37;3.31	5.55	1.46	0.22682	.	0.843042	0.10345	N	0.685879	T	0.04543	0.0124	L	0.36672	1.1	0.09310	N	1	B;B;B;B;B	0.06786	0.0;0.0;0.001;0.001;0.0	B;B;B;B;B	0.06405	0.001;0.0;0.001;0.0;0.002	T	0.49113	-0.8973	10	0.08381	T	0.77	.	4.7688	0.13146	0.0:0.5092:0.148:0.3428	.	181;181;426;426;186	E7EU13;B2RTS2;Q96P48-3;Q96P48;Q96P48-1	.;.;.;ARAP1_HUMAN;.	Q	426;426;186;181;426;181;181;215	ENSP00000352332:R426Q;ENSP00000390461:R426Q;ENSP00000377230:R186Q;ENSP00000335506:R181Q;ENSP00000377233:R426Q;ENSP00000392264:R181Q;ENSP00000403127:R181Q	ENSP00000335506:R181Q	R	-	2	0	ARAP1	72099217	0.000000	0.05858	0.013000	0.15412	0.255000	0.26057	0.317000	0.19487	0.014000	0.14944	0.655000	0.94253	CGG	.	.	weak		0.632	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118		T	72421569	C	T	72421569	3	4	28	1	0	0	0	0	1	0	0	0	838	652	23	1	3179	1	ARAP1	11	72421569	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2231677	72421569	62584947	424	11927											
KLHL35	283212	hgsc.bcm.edu	37	chr11	75134832	75134832	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccccatgacatagatggtGtcctcaagggagacagcctc	10	7	10	14	0	1	3	1	1	0	2	3	4	2	3	5	2	1	0	5	2	2	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:75134832G>T	ENST00000539798.1	-	5	1466	c.1467C>A	c.(1465-1467)gaC>gaA	p.D489E	KLHL35_ENST00000376292.4_Missense_Mutation_p.D269E	NM_001039548.2	NP_001034637.2	Q6PF15	KLH35_HUMAN	kelch-like family member 35	489										lung(2)|stomach(1)	3						CATAGATGGTGTCCTCAAGGG	0.597																																					p.D489E	Colon(77;683 1691 18820 23811)	Atlas-SNP	.											.	KLHL35	15	.	0			c.C1467A						PASS	.						99	109	105					11																	75134832		2031	4177	6208	SO:0001583	missense	283212	exon5			GATGGTGTCCTCA		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.1467C>A	11.37:g.75134832G>T	ENSP00000438526:p.Asp489Glu	82	0	0		81	4	0.0493827	NM_001039548	A2RU06|F5H412|Q86XM7|Q8NBB1	Missense_Mutation	SNP	ENST00000539798.1	37	CCDS44685.2	.	.	.	.	.	.	.	.	.	.	G	10.26	1.300475	0.23650	.	.	ENSG00000149243	ENST00000376292;ENST00000539798	T;T	0.68903	-0.36;-0.36	5.12	3.23	0.37069	Kelch-type beta propeller (1);	0.216802	0.37304	N	0.002158	T	0.52075	0.1712	L	0.35793	1.09	0.24569	N	0.993936	B	0.19200	0.034	B	0.23150	0.044	T	0.49244	-0.8960	10	0.66056	D	0.02	.	4.9596	0.14059	0.1754:0.0:0.658:0.1666	.	269	Q6PF15	KLH35_HUMAN	E	269;489	ENSP00000365469:D269E;ENSP00000438526:D489E	ENSP00000365469:D269E	D	-	3	2	KLHL35	74812480	1.000000	0.71417	0.986000	0.45419	0.202000	0.24057	0.617000	0.24359	0.726000	0.32339	0.650000	0.86243	GAC	.	.	none		0.597	KLHL35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173583		T	75134832	G	T	75134832	3	4	28	1	0	0	0	0	1	0	0	0	8397	1368	48	4	292	4	KLHL35	11	75134832	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2713263	75134832	59871684	425	11928											
GDPD4	220032	hgsc.bcm.edu	37	chr11	76944178	76944178	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaaagccaaggctcattgacGgtgtatacgttgatatggat	13	11	11	6	2	1	2	1	2	0	0	1	3	1	3	1	3	2	3	1	3	6	5	rs17751194	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:76944178G>A	ENST00000376217.2	-	13	1531	c.1281C>T	c.(1279-1281)acC>acT	p.T427T	GDPD4_ENST00000315938.4_Silent_p.T427T			Q6W3E5	GDPD4_HUMAN	glycerophosphodiester phosphodiesterase domain containing 4	427	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						GCTCATTGACGGTGTATACGT	0.443													G|||	30	0.00599042	0.0	0.0058	5008	,	,		20824	0.0		0.0179	False		,,,				2504	0.0082				p.T427T		Atlas-SNP	.											.	GDPD4	49	.	0			c.C1281T						PASS	.	G		15,4385	22.3+/-47.3	1,13,2186	176	154	162		1281	-5.5	0	11	dbSNP_123	162	136,8448	68.4+/-130.8	2,132,4158	no	coding-synonymous	GDPD4	NM_182833.1		3,145,6344	AA,AG,GG		1.5843,0.3409,1.163		427/521	76944178	151,12833	2200	4292	6492	SO:0001819	synonymous_variant	220032	exon13			ATTGACGGTGTAT	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.1281C>T	11.37:g.76944178G>A		69	0	0		62	36	0.580645	NM_182833	Q7Z5B0	Silent	SNP	ENST00000376217.2	37																																																																																				G|0.988;A|0.012	0.012	strong		0.443	GDPD4-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382075.1	NM_182833		A	76944178	G	A	76944178	2	1	28	1	0	0	0	0	0	0	0	1	6334	1103	39	1		1	GDPD4	11	76944178	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1809346	76944178	58062338	426	11929											
GAB2	9846	hgsc.bcm.edu	37	chr11	77930447	77930447	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accttctcatcagaggtgacGgatgaagtagatggctgagg	11	9	14	7	1	2	5	2	3	1	2	3	6	2	6	1	4	0	2	1	4	2	2	rs61749244	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:77930447G>A	ENST00000361507.4	-	10	1987	c.1902C>T	c.(1900-1902)tcC>tcT	p.S634S	GAB2_ENST00000340149.2_Silent_p.S596S	NM_080491.2	NP_536739.1	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2	634					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)	p.S634S(1)	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)			CAGAGGTGACGGATGAAGTAG	0.567													g|||	31	0.0061901	0.0023	0.013	5008	,	,		22020	0.0		0.0149	False		,,,				2504	0.0041				p.S634S		Atlas-SNP	.											GAB2,rectum,carcinoma,-2,4	GAB2	63	4	1	Substitution - coding silent(1)	ovary(1)	c.C1902T						PASS	.	G	,	25,4375	31.7+/-61.6	0,25,2175	121	98	106		1788,1902	-10.7	0	11	dbSNP_129	106	236,8348	96.3+/-158.1	3,230,4059	no	coding-synonymous,coding-synonymous	GAB2	NM_012296.3,NM_080491.2	,	3,255,6234	AA,AG,GG		2.7493,0.5682,2.0102	,	596/639,634/677	77930447	261,12723	2200	4292	6492	SO:0001819	synonymous_variant	9846	exon10			GGTGACGGATGAA	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.1902C>T	11.37:g.77930447G>A		107	0	0		95	52	0.547368	NM_080491	A2RRM2|A6NEW9|A7MD36|O60317	Silent	SNP	ENST00000361507.4	37	CCDS8259.1																																																																																			G|0.983;A|0.017	0.017	strong		0.567	GAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391085.1	NM_080491		A	77930447	G	A	77930447	2	1	28	1	0	0	0	0	0	0	0	1	6157	1103	39	1		1	GAB2	11	77930447	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	986269	77930447	57076069	427	11930											
SYTL2	54843	hgsc.bcm.edu	37	chr11	85445365	85445365	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gaagctcatccttcactgcaGagaatctcacatgctttaat	12	12	6	11	0	3	1	3	0	1	1	5	3	4	1	1	0	3	3	1	0	3	3	rs74718633	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:85445365G>C	ENST00000528231.1	-	6	1281	c.1004C>G	c.(1003-1005)tCt>tGt	p.S335C	SYTL2_ENST00000527523.1_Missense_Mutation_p.S287C|SYTL2_ENST00000389960.4_Missense_Mutation_p.S335C|SYTL2_ENST00000316356.4_Missense_Mutation_p.S336C|SYTL2_ENST00000524452.1_Missense_Mutation_p.S335C	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	335					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)		CTTCACTGCAGAGAATCTCAC	0.443													G|||	19	0.00379393	0.0008	0.0058	5008	,	,		19642	0.0		0.0139	False		,,,				2504	0.0				p.S336C		Atlas-SNP	.											.	SYTL2	231	.	0			c.C1007G						PASS	.	G	CYS/SER,CYS/SER,CYS/SER	10,4396	16.8+/-37.8	0,10,2193	104	107	106		1004,1007,1004	5.2	1	11	dbSNP_131	106	113,8485	61.0+/-122.8	1,111,4187	yes	missense,missense,missense	SYTL2	NM_001162951.1,NM_001162953.1,NM_032943.3	112,112,112	1,121,6380	CC,CG,GG		1.3143,0.227,0.9459	,,	335/935,336/936,335/911	85445365	123,12881	2203	4299	6502	SO:0001583	missense	54843	exon6			ACTGCAGAGAATC	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.1004C>G	11.37:g.85445365G>C	ENSP00000431701:p.Ser335Cys	116	0	0		102	51	0.5	NM_001162953	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	37	CCDS53688.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	G	20.5	4.002879	0.74932	0.00227	0.013143	ENSG00000137501	ENST00000389960;ENST00000316356;ENST00000528231;ENST00000527523;ENST00000524452	T;T;T;T;T	0.59083	0.29;0.69;0.62;0.49;0.29	6.06	5.15	0.70609	.	.	.	.	.	T	0.67011	0.2848	M	0.66939	2.045	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	0.997;0.999;0.999;0.994;1.0	T	0.71836	-0.4472	8	.	.	.	.	14.79	0.69833	0.0694:0.0:0.9306:0.0	.	287;335;335;336;193	Q9HCH5-14;Q9HCH5-6;Q9HCH5;Q9HCH5-13;Q9HCH5-15	.;.;SYTL2_HUMAN;.;.	C	335;336;335;287;335	ENSP00000374610:S335C;ENSP00000318803:S336C;ENSP00000431701:S335C;ENSP00000434010:S287C;ENSP00000435238:S335C	.	S	-	2	0	SYTL2	85123013	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.541000	0.73865	1.567000	0.49668	0.650000	0.86243	TCT	G|0.993;C|0.007	0.007	strong		0.443	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927		C	85445365	G	C	85445365	3	2	28	1	0	0	0	0	1	0	0	0	15498	942	33	4	4333	4	SYTL2	11	85445365	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	7514918	85445365	49561151	428	11931											
TYR	7299	hgsc.bcm.edu	37	chr11	88911575	88911575	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tcagctcagactatgtcatcCccatagggacctatggccaa	11	9	8	13	0	3	1	3	0	0	1	4	2	4	2	4	2	1	1	4	2	4	3	rs145513733	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:88911575C>T	ENST00000263321.5	+	1	956	c.454C>T	c.(454-456)Ccc>Tcc	p.P152S	TYR_ENST00000526139.1_3'UTR	NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	152			P -> S (in OCA1B). {ECO:0000269|PubMed:8128955}.		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)	CTATGTCATCCCCATAGGGAC	0.403																																					p.P152S		Atlas-SNP	.											.	TYR	130	.	0			c.C454T	GRCh37	CM941344	TYR	M	rs145513733	PASS	.	C	SER/PRO	0,4402		0,0,2201	152	144	147		454	5	1	11	dbSNP_134	147	3,8595	3.0+/-9.4	0,3,4296	yes	missense	TYR	NM_000372.4	74	0,3,6497	TT,TC,CC		0.0349,0.0,0.0231	possibly-damaging	152/530	88911575	3,12997	2201	4299	6500	SO:0001583	missense	7299	exon1			GTCATCCCCATAG	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.454C>T	11.37:g.88911575C>T	ENSP00000263321:p.Pro152Ser	61	0	0		75	38	0.506667	NM_000372	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Missense_Mutation	SNP	ENST00000263321.5	37	CCDS8284.1	.	.	.	.	.	.	.	.	.	.	C	17.83	3.485562	0.63962	0.0	3.49E-4	ENSG00000077498	ENST00000263321	D	0.83591	-1.74	5.97	5.01	0.66863	Uncharacterised domain, di-copper centre (2);	0.157178	0.56097	D	0.000032	T	0.80042	0.4551	L	0.41573	1.285	0.36372	D	0.861346	P	0.45078	0.85	P	0.46208	0.507	T	0.81814	-0.0760	9	.	.	.	.	14.0119	0.64503	0.0:0.6866:0.3134:0.0	.	152	P14679	TYRO_HUMAN	S	152	ENSP00000263321:P152S	.	P	+	1	0	TYR	88551223	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	4.338000	0.59316	2.828000	0.97474	0.655000	0.94253	CCC	C|0.999;T|0.001	0.001	strong		0.403	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	NM_000372		T	88911575	C	T	88911575	3	4	28	1	0	0	0	0	1	0	0	0	16828	623	22	2	456	2	TYR	11	88911575	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	3466210	88911575	46094941	429	11932											
PGR	5241	hgsc.bcm.edu	37	chr11	100933407	100933407	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttggctttcatttggaacGcccactggctgtgggagagc	6	11	14	10	1	1	1	1	0	0	1	1	3	1	2	1	4	2	3	1	4	1	3	rs139646398		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:100933407G>A	ENST00000325455.5	-	4	3436	c.1983C>T	c.(1981-1983)ggC>ggT	p.G661G	PGR_ENST00000263463.5_Intron|PGR_ENST00000534013.1_Silent_p.G67G	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	661					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)	CATTTGGAACGCCCACTGGCT	0.418													G|||	1	0.000199681	0.0008	0.0	5008	,	,		15046	0.0		0.0	False		,,,				2504	0.0				p.G661G	Pancreas(124;2271 2354 21954 22882)	Atlas-SNP	.											.	PGR	115	.	0			c.C1983T						PASS	.	G	,	2,4404	4.2+/-10.8	0,2,2201	129	112	118		1983,1491	4.5	0.9	11	dbSNP_134	118	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous,coding-synonymous	PGR	NM_000926.4,NM_001202474.1	,	0,12,6491	AA,AG,GG		0.1163,0.0454,0.0923	,	661/934,497/770	100933407	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	5241	exon4			TGGAACGCCCACT	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.1983C>T	11.37:g.100933407G>A		89	0	0		72	31	0.430556	NM_000926	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Silent	SNP	ENST00000325455.5	37	CCDS8310.1																																																																																			G|0.999;A|0.001	0.001	strong		0.418	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1			A	100933407	G	A	100933407	2	1	28	1	0	0	0	0	0	0	0	1	11814	1074	38	1		1	PGR	11	100933407	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	12021832	100933407	34073109	430	11933											
MMP27	64066	hgsc.bcm.edu	37	chr11	102567522	102567522	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attggagtgagagagccccaGtgcatgaccaaattcatgag	13	8	12	8	0	1	4	1	3	0	1	1	6	1	5	3	1	2	1	3	1	1	2	rs201248506	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:102567522G>A	ENST00000260229.4	-	5	755	c.664C>T	c.(664-666)Ctg>Ttg	p.L222L		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	222					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)	GAGAGCCCCAGTGCATGACCA	0.423													G|||	2	0.000399361	0.0	0.0	5008	,	,		18938	0.0		0.002	False		,,,				2504	0.0				p.L222L		Atlas-SNP	.											.	MMP27	84	.	0			c.C664T						PASS	.	G		0,4406		0,0,2203	81	69	73		664	3.9	0.9	11		73	3,8595	3.0+/-9.4	0,3,4296	no	coding-synonymous	MMP27	NM_022122.2		0,3,6499	AA,AG,GG		0.0349,0.0,0.0231		222/514	102567522	3,13001	2203	4299	6502	SO:0001819	synonymous_variant	64066	exon5			GCCCCAGTGCATG	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.664C>T	11.37:g.102567522G>A		55	0	0		72	36	0.5	NM_022122	Q6UWK6	Silent	SNP	ENST00000260229.4	37	CCDS8319.1																																																																																			G|0.999;A|0.001	0.001	strong		0.423	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122		A	102567522	G	A	102567522	2	1	28	1	0	0	0	0	0	0	0	1	9673	1020	36	2		2	MMP27	11	102567522	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1634115	102567522	32438994	431	11934											
AASDHPPT	60496	hgsc.bcm.edu	37	chr11	105962172	105962172	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aagaaacacgtttattcctgGatggagaggaagaaaaagaa	19	7	11	4	1	0	4	0	0	0	4	1	7	1	6	1	3	1	1	1	3	7	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:105962172G>A	ENST00000278618.4	+	4	883	c.661G>A	c.(661-663)Gat>Aat	p.D221N	RP11-677I18.3_ENST00000532422.1_RNA	NM_015423.2	NP_056238.2	Q9NRN7	ADPPT_HUMAN	aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase	221					macromolecule biosynthetic process (GO:0009059)|pantothenate metabolic process (GO:0015939)|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)	holo-[acyl-carrier-protein] synthase activity (GO:0008897)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)	17		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.78e-05)|Epithelial(105;0.00622)|all cancers(92;0.041)		TTTATTCCTGGATGGAGAGGA	0.323																																					p.D221N		Atlas-SNP	.											.	AASDHPPT	40	.	0			c.G661A						PASS	.						72	79	77					11																	105962172		2200	4299	6499	SO:0001583	missense	60496	exon4			TTCCTGGATGGAG	AF302110	CCDS31664.1	11q22	2010-12-09			ENSG00000149313	ENSG00000149313	1.2.1.31		14235	protein-coding gene	gene with protein product		607756				12815048, 11286508	Standard	NM_015423		Approved	LYS5, CGI-80, AASD-PPT	uc001pjc.1	Q9NRN7	OTTHUMG00000166253	ENST00000278618.4:c.661G>A	11.37:g.105962172G>A	ENSP00000278618:p.Asp221Asn	101	0	0		91	29	0.318681	NM_015423	B2R6D1|B4DDW7|Q9C068|Q9P0Q3|Q9UG80|Q9Y389	Missense_Mutation	SNP	ENST00000278618.4	37	CCDS31664.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.447623	0.84101	.	.	ENSG00000149313	ENST00000533423;ENST00000524411;ENST00000278618	.	.	.	5.77	5.77	0.91146	4&apos (2);-phosphopantetheinyl transferase (2);	0.000000	0.85682	D	0.000000	T	0.53690	0.1812	L	0.33753	1.03	0.58432	D	0.999998	P	0.51057	0.941	P	0.44647	0.456	T	0.49969	-0.8882	9	0.33141	T	0.24	.	19.981	0.97324	0.0:0.0:1.0:0.0	.	221	Q9NRN7	ADPPT_HUMAN	N	156;156;221	.	ENSP00000278618:D221N	D	+	1	0	AASDHPPT	105467382	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	8.453000	0.90349	2.729000	0.93468	0.585000	0.79938	GAT	.	.	none		0.323	AASDHPPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388734.1	NM_015423		A	105962172	G	A	105962172	3	1	28	1	0	0	0	0	1	0	0	0	23	1174	41	2	675	2	AASDHPPT	11	105962172	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	3394650	105962172	29044344	432	11935											
ATM	472	hgsc.bcm.edu	37	chr11	108163487	108163487	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	attgttggtacacttataccCcttgtgtatgagcaggtgga	9	14	11	7	0	0	1	0	1	0	0	0	2	0	2	2	3	3	4	2	3	4	7	rs1800889	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:108163487C>T	ENST00000452508.2	+	31	4767	c.4578C>T	c.(4576-4578)ccC>ccT	p.P1526P	ATM_ENST00000278616.4_Silent_p.P1526P			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1526					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)	CACTTATACCCCTTGTGTATG	0.358			"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)			C|||	77	0.0153754	0.003	0.0288	5008	,	,		18654	0.0		0.0398	False		,,,				2504	0.0133				p.P1526P		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	.	ATM	1657	.	0			c.C4578T						PASS	.	C		43,4359	44.6+/-78.6	0,43,2158	197	173	181		4578	-0.5	0.9	11	dbSNP_89	181	438,8158	133.0+/-190.5	21,396,3881	no	coding-synonymous	ATM	NM_000051.3		21,439,6039	TT,TC,CC		5.0954,0.9768,3.7006		1526/3057	108163487	481,12517	2201	4298	6499	SO:0001819	synonymous_variant	472	exon30	Familial Cancer Database	AT, Louis-Bar syndrome	TATACCCCTTGTG	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.4578C>T	11.37:g.108163487C>T		122	0	0		139	69	0.496403	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Silent	SNP	ENST00000452508.2	37	CCDS31669.1																																																																																			C|0.972;T|0.028	0.028	strong		0.358	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		T	108163487	C	T	108163487	2	4	28	1	0	0	0	0	0	0	0	1	1109	610	22	2		2	ATM	11	108163487	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2201315	108163487	26843029	433	11936											
ZBTB16	7704	hgsc.bcm.edu	37	chr11	114121182	114121182	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagtactgccccagcctcTcctccatgcagaagcacatg	10	7	8	16	0	1	2	0	0	1	2	3	2	2	2	5	0	5	3	5	0	2	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:114121182T>A	ENST00000335953.4	+	7	2307	c.1927T>A	c.(1927-1929)Tcc>Acc	p.S643T	RP11-64D24.2_ENST00000544925.1_RNA|ZBTB16_ENST00000535379.1_3'UTR|ZBTB16_ENST00000392996.2_Missense_Mutation_p.S643T	NM_006006.4	NP_005997.2	Q05516	ZBT16_HUMAN	zinc finger and BTB domain containing 16	643					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)		CCCCAGCCTCTCCTCCATGCA	0.602																																					p.S643T		Atlas-SNP	.											ZBTB16_ENST00000335953,NS,carcinoma,0,1	ZBTB16	101	1	0			c.T1927A						scavenged	.						76	68	71					11																	114121182		2201	4296	6497	SO:0001583	missense	7704	exon7			AGCCTCTCCTCCA	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.1927T>A	11.37:g.114121182T>A	ENSP00000338157:p.Ser643Thr	59	0	0		38	2	0.0526316	NM_006006	Q8TAL4	Missense_Mutation	SNP	ENST00000335953.4	37	CCDS8367.1	.	.	.	.	.	.	.	.	.	.	t	18.33	3.599781	0.66332	.	.	ENSG00000109906	ENST00000335953;ENST00000392996;ENST00000310883	T;T	0.62232	0.04;0.04	5.39	5.39	0.77823	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.066981	0.64402	D	0.000008	T	0.47040	0.1424	N	0.14661	0.345	0.45272	D	0.998277	P	0.38767	0.646	B	0.36464	0.225	T	0.54925	-0.8220	10	0.59425	D	0.04	-13.3009	15.4492	0.75259	0.0:0.0:0.0:1.0	.	643	Q05516	ZBT16_HUMAN	T	643;643;520	ENSP00000338157:S643T;ENSP00000376721:S643T	ENSP00000309507:S520T	S	+	1	0	ZBTB16	113626392	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.924000	0.63418	2.047000	0.60756	0.358000	0.22013	TCC	.	.	none		0.602	ZBTB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398940.1	NM_006006		A	114121182	T	A	114121182	3	1	28	1	0	0	0	0	1	0	0	0	17541	1551	54	5	1949	5	ZBTB16	11	114121182	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	5957695	114121182	20885334	434	11937											
BACE1	23621	hgsc.bcm.edu	37	chr11	117186506	117186506	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aggagccagggcagggcttgGgccatggtgggccccggcct	5	5	19	12	1	0	0	0	0	0	0	0	1	0	1	5	7	1	2	5	7	0	1	rs28917234	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:117186506G>A	ENST00000313005.6	-	1	466	c.6C>T	c.(4-6)gcC>gcT	p.A2A	BACE1_ENST00000428381.2_Silent_p.A2A|BACE1_ENST00000514464.1_5'UTR|BACE1_ENST00000528053.1_Silent_p.A2A|BACE1_ENST00000513780.1_Silent_p.A2A|BACE1_ENST00000445823.2_Silent_p.A2A|AP000892.4_ENST00000504906.1_RNA	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	2					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)		GCAGGGCTTGGGCCATGGTGG	0.746													G|||	92	0.0183706	0.0023	0.0159	5008	,	,		10280	0.0		0.0378	False		,,,				2504	0.0409				p.A2A		Atlas-SNP	.											.	BACE1	33	.	0			c.C6T						PASS	.	G	,,,	14,2658		0,14,1322	2	3	3		6,6,6,6	0.6	0.9	11	dbSNP_125	3	131,5129		1,129,2500	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BACE1	NM_012104.4,NM_138971.3,NM_138972.3,NM_138973.3	,,,	1,143,3822	AA,AG,GG		2.4905,0.524,1.828	,,,	2/502,2/458,2/477,2/433	117186506	145,7787	1336	2630	3966	SO:0001819	synonymous_variant	23621	exon1			GGCTTGGGCCATG	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.6C>T	11.37:g.117186506G>A		0	0	.		20	12	0.6	NM_138972	A0M8W7|B0YIU9|E9PE65|H7BXJ9|Q9BYB9|Q9BYC0|Q9BYC1|Q9UJT5|Q9ULS1	Silent	SNP	ENST00000313005.6	37	CCDS8383.1																																																																																			G|0.979;A|0.021	0.021	strong		0.746	BACE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361505.1			A	117186506	G	A	117186506	2	1	28	1	0	0	0	0	0	0	0	1	1281	1219	43	2		2	BACE1	11	117186506	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	3065324	117186506	17820010	435	11938											
MPZL2	10205	hgsc.bcm.edu	37	chr11	118134830	118134830	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cctgtgagctgtatgccaagGagaagaagcaccgcacgagt	12	6	13	10	2	0	3	0	1	0	2	0	5	0	3	3	1	3	4	3	1	4	1	rs36040758	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:118134830G>A	ENST00000278937.2	-	1	167	c.39C>T	c.(37-39)ctC>ctT	p.L13L	MPZL2_ENST00000438295.2_Silent_p.L13L|MPZL2_ENST00000525647.1_5'UTR	NM_005797.3	NP_005788.1	O60487	MPZL2_HUMAN	myelin protein zero-like 2	13					anatomical structure morphogenesis (GO:0009653)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)|T cell differentiation in thymus (GO:0033077)	cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|skin(1)	11	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;3.04e-05)		GTATGCCAAGGAGAAGAAGCA	0.547													G|||	8	0.00159744	0.0008	0.0014	5008	,	,		17565	0.0		0.005	False		,,,				2504	0.001				p.L13L		Atlas-SNP	.											.	MPZL2	20	.	0			c.C39T						PASS	.	G	,	9,4391	15.5+/-35.6	0,9,2191	81	75	77		39,39	-1.1	0.1	11	dbSNP_126	77	74,8518	44.0+/-102.2	0,74,4222	no	coding-synonymous,coding-synonymous	MPZL2	NM_005797.3,NM_144765.2	,	0,83,6413	AA,AG,GG		0.8613,0.2045,0.6389	,	13/216,13/216	118134830	83,12909	2200	4296	6496	SO:0001819	synonymous_variant	10205	exon1			GCCAAGGAGAAGA	AF275945	CCDS8393.1	11q24	2013-01-11	2007-08-01	2007-08-01		ENSG00000149573		"Immunoglobulin superfamily / V-set domain containing"	3496	protein-coding gene	gene with protein product		604873	"epithelial V-like antigen 1"	EVA1		9585423	Standard	NM_005797		Approved	EVA	uc001psn.3	O60487		ENST00000278937.2:c.39C>T	11.37:g.118134830G>A		38	0	0		72	33	0.458333	NM_005797	A8K2R1	Silent	SNP	ENST00000278937.2	37	CCDS8393.1																																																																																			G|0.993;A|0.007	0.007	strong		0.547	MPZL2-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392113.1	NM_005797		A	118134830	G	A	118134830	2	1	28	1	0	0	0	0	0	0	0	1	9759	1161	41	2		2	MPZL2	11	118134830	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	948324	118134830	16871686	436	11939											
CBL	867	hgsc.bcm.edu	37	chr11	119168130	119168130	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagcagattgatagctgtacGtatgaagcaatgtataatat	15	12	9	5	1	0	3	0	2	0	1	0	3	0	3	0	0	4	6	0	0	8	7	rs143840974	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:119168130G>C	ENST00000264033.4	+	14	2566	c.2190G>C	c.(2188-2190)acG>acC	p.T730T		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	730	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)	p.T730T(1)		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)		ATAGCTGTACGTATGAAGCAA	0.393			"T, Mis S, O"	MLL	"AML, JMML, MDS"				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies				G|||	2	0.000399361	0.0	0.0	5008	,	,		20497	0.0		0.002	False		,,,				2504	0.0				p.T730T		Atlas-SNP	.		"Dom, Rec"	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	CBL,NS,haematopoietic_neoplasm,0,1	CBL	408	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2190C						PASS	.	G		2,4396	4.2+/-10.8	0,2,2197	117	106	110		2190	-10.6	0.2	11	dbSNP_134	110	28,8562	19.8+/-62.0	0,28,4267	no	coding-synonymous	CBL	NM_005188.2		0,30,6464	CC,CG,GG		0.326,0.0455,0.231		730/907	119168130	30,12958	2199	4295	6494	SO:0001819	synonymous_variant	867	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;CBL-associated JMML	CTGTACGTATGAA	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.2190G>C	11.37:g.119168130G>C		95	0	0		84	39	0.464286	NM_005188	A3KMP8	Silent	SNP	ENST00000264033.4	37	CCDS8418.1																																																																																			G|0.997;C|0.003	0.003	strong		0.393	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188		C	119168130	G	C	119168130	2	2	28	1	0	0	0	0	0	0	0	1	2702	1132	40	4		4	CBL	11	119168130	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1033300	119168130	15838386	437	11940											
SORL1	6653	hgsc.bcm.edu	37	chr11	121498410	121498410	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgcagagcagcttcaccGccttcgccaacagccactac	9	6	9	17	2	1	1	1	0	0	1	2	1	1	1	4	1	6	4	4	1	2	3	rs146742626		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:121498410G>A	ENST00000260197.7	+	47	6640	c.6511G>A	c.(6511-6513)Gcc>Acc	p.A2171T	SORL1_ENST00000534286.1_Missense_Mutation_p.A1081T|SORL1_ENST00000532694.1_Missense_Mutation_p.A1017T|SORL1_ENST00000527934.1_Missense_Mutation_p.A786T|SORL1_ENST00000525532.1_Missense_Mutation_p.A1115T	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	2171					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)		CAGCTTCACCGCCTTCGCCAA	0.607																																					p.A2171T		Atlas-SNP	.											.	SORL1	218	.	0			c.G6511A						PASS	.	G	THR/ALA	0,4404		0,0,2202	59	52	54		6511	6	0.2	11	dbSNP_134	54	1,8597	1.2+/-3.3	0,1,4298	no	missense	SORL1	NM_003105.5	58	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	2171/2215	121498410	1,13001	2202	4299	6501	SO:0001583	missense	6653	exon47			TTCACCGCCTTCG	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.6511G>A	11.37:g.121498410G>A	ENSP00000260197:p.Ala2171Thr	70	0	0		90	40	0.444444	NM_003105	B2RNX7|Q92856	Missense_Mutation	SNP	ENST00000260197.7	37	CCDS8436.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.610245	0.87258	0.0	1.16E-4	ENSG00000137642	ENST00000260197;ENST00000525532;ENST00000532694;ENST00000534286;ENST00000527934	D;D;D;D;D	0.91464	-2.85;-2.59;-2.23;-2.26;-2.13	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	D	0.93058	0.7790	L	0.59436	1.845	0.58432	D	0.99999	D;D	0.62365	0.983;0.991	B;P	0.54629	0.397;0.757	D	0.91897	0.5528	10	0.44086	T	0.13	.	20.4008	0.98991	0.0:0.0:1.0:0.0	.	786;2171	E9PKB0;Q92673	.;SORL_HUMAN	T	2171;1115;1017;1081;786	ENSP00000260197:A2171T;ENSP00000434634:A1115T;ENSP00000432131:A1017T;ENSP00000436447:A1081T;ENSP00000435405:A786T	ENSP00000260197:A2171T	A	+	1	0	SORL1	121003620	1.000000	0.71417	0.204000	0.23530	0.947000	0.59692	5.412000	0.66392	2.826000	0.97356	0.655000	0.94253	GCC	G|1.000;A|0.000	0.000	weak		0.607	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105		A	121498410	G	A	121498410	3	1	28	1	0	0	0	0	1	0	0	0	14949	1087	38	1	6697	1	SORL1	11	121498410	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2330280	121498410	13508106	438	11941											
OR8B4	283162	hgsc.bcm.edu	37	chr11	124294213	124294213	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgggtgctggtgcaggagagCtgcaagagggggagaacgtc	9	6	20	6	1	0	3	0	0	0	3	1	5	0	3	0	5	5	4	0	5	2	0	rs61736181	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:124294213C>A	ENST00000356130.3	-	1	576	c.555G>T	c.(553-555)caG>caT	p.Q185H		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	185						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)		TGCAGGAGAGCTGCAAGAGGG	0.502													C|||	41	0.0081869	0.0023	0.013	5008	,	,		22316	0.0		0.0249	False		,,,				2504	0.0041				p.Q185H		Atlas-SNP	.											.	OR8B4	60	.	0			c.G555T						PASS	.	C	HIS/GLN	23,4379	29.9+/-59.1	0,23,2178	82	58	66		555	3.1	1	11	dbSNP_129	66	220,8378	92.3+/-154.4	3,214,4082	yes	missense	OR8B4	NM_001005196.1	24	3,237,6260	AA,AC,CC		2.5587,0.5225,1.8692	possibly-damaging	185/310	124294213	243,12757	2201	4299	6500	SO:0001583	missense	283162	exon1			GGAGAGCTGCAAG	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.555G>T	11.37:g.124294213C>A	ENSP00000348449:p.Gln185His	117	0	0		121	58	0.479339	NM_001005196	B2RNF8|Q6IFQ7	Missense_Mutation	SNP	ENST00000356130.3	37	CCDS31710.1	28	0.01282051282051282	3	0.006097560975609756	6	0.016574585635359115	0	0.0	19	0.025065963060686015	c	14.77	2.635013	0.47049	0.005225	0.025587	ENSG00000198657	ENST00000356130	T	0.00137	8.68	4.02	3.06	0.35304	GPCR, rhodopsin-like superfamily (1);	0.495221	0.17506	N	0.171789	T	0.00109	0.0003	L	0.43757	1.38	0.32996	D	0.525657	D	0.57899	0.981	D	0.64877	0.93	T	0.68322	-0.5439	10	0.87932	D	0	.	6.7728	0.23602	0.0:0.6864:0.0:0.3136	.	185	Q96RC9	OR8B4_HUMAN	H	185	ENSP00000348449:Q185H	ENSP00000348449:Q185H	Q	-	3	2	OR8B4	123799423	0.000000	0.05858	0.994000	0.49952	0.955000	0.61496	-1.016000	0.03633	1.219000	0.43474	0.650000	0.86243	CAG	C|0.982;A|0.018	0.018	strong		0.502	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196		A	124294213	C	A	124294213	3	1	28	1	0	0	0	0	1	0	0	0	11238	796	28	4	376	4	OR8B4	11	124294213	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2795803	124294213	10712303	439	11942											
SPA17	53340	hgsc.bcm.edu	37	chr11	124564252	124564252	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttgctgctgtcaaaatccaAgctgccttccggggacacat	9	10	10	12	1	1	0	1	0	0	0	3	1	3	1	3	2	4	4	3	2	3	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:124564252A>G	ENST00000532692.1	+	4	1787	c.366A>G	c.(364-366)caA>caG	p.Q122Q	SPA17_ENST00000524614.1_3'UTR|SIAE_ENST00000525730.1_5'UTR|SPA17_ENST00000227135.2_Silent_p.Q122Q			Q15506	SP17_HUMAN	sperm autoantigenic protein 17	122	IQ. {ECO:0000255|PROSITE- ProRule:PRU00116}.				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)		TCAAAATCCAAGCTGCCTTCC	0.413																																					p.Q122Q		Atlas-SNP	.											SPA17,NS,malignant_melanoma,+2,1	SPA17	16	1	0			c.A366G						PASS	.						94	96	96					11																	124564252		2201	4299	6500	SO:0001819	synonymous_variant	53340	exon5			AATCCAAGCTGCC	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.366A>G	11.37:g.124564252A>G		112	0	0		99	46	0.464646	NM_017425	B2R4F2|Q9BXF7	Silent	SNP	ENST00000532692.1	37	CCDS8450.1																																																																																			.	.	none		0.413	SPA17-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387075.1	NM_017425		G	124564252	A	G	124564252	2	3	28	1	0	0	0	0	0	0	0	1	14986	69	3	3		3	SPA17	11	124564252	Silent	SNP	A	TCGA-G8-6914-01A-11D-2210-10	270039	124564252	10442264	440	11943											
DCPS	28960	hgsc.bcm.edu	37	chr11	126213242	126213242	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cgccatctgccatcgccgggGcatcagatccctacgcgacc	7	6	10	18	5	2	1	1	0	1	1	4	2	3	1	5	2	2	1	5	2	1	1	rs35836343	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:126213242G>A	ENST00000263579.4	+	5	1006	c.677G>A	c.(676-678)gGc>gAc	p.G226D	DCPS_ENST00000530860.1_3'UTR	NM_014026.3	NP_054745.1	Q96C86	DCPS_HUMAN	decapping enzyme, scavenger	226					cellular response to menadione (GO:0036245)|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 cis splicing, via spliceosome (GO:0045292)|mRNA metabolic process (GO:0016071)|negative regulation of programmed cell death (GO:0043069)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	m7G(5')pppN diphosphatase activity (GO:0050072)|RNA 7-methylguanosine cap binding (GO:0000340)			endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00949)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.08)		CATCGCCGGGGCATCAGATCC	0.607													G|||	5	0.000998403	0.0	0.0043	5008	,	,		18355	0.0		0.002	False		,,,				2504	0.0				p.G226D		Atlas-SNP	.											.	DCPS	33	.	0			c.G677A						PASS	.	G	ASP/GLY	5,4397	11.4+/-27.6	0,5,2196	84	62	69		677	0.2	1	11	dbSNP_126	69	66,8530	38.8+/-94.9	0,66,4232	yes	missense	DCPS	NM_014026.3	94	0,71,6428	AA,AG,GG		0.7678,0.1136,0.5462	possibly-damaging	226/338	126213242	71,12927	2201	4298	6499	SO:0001583	missense	28960	exon5			GCCGGGGCATCAG	AF077201	CCDS8473.1	11q24	2008-02-05			ENSG00000110063	ENSG00000110063			29812	protein-coding gene	gene with protein product		610534				12198172, 14523240	Standard	NM_014026		Approved	HSPC015, HINT-5, HSL1	uc001qdp.3	Q96C86	OTTHUMG00000165829	ENST00000263579.4:c.677G>A	11.37:g.126213242G>A	ENSP00000263579:p.Gly226Asp	36	0	0		37	19	0.513514	NM_014026	Q8NHL8|Q9Y2S5	Missense_Mutation	SNP	ENST00000263579.4	37	CCDS8473.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	G	11.16	1.556018	0.27827	0.001136	0.007678	ENSG00000110063	ENST00000263579	D	0.94966	-3.57	5.31	0.2	0.15181	Histidine triad-like motif (1);	0.269864	0.42548	N	0.000697	T	0.78272	0.4257	N	0.04820	-0.15	0.50171	D	0.999857	B	0.16603	0.018	B	0.30316	0.114	T	0.68667	-0.5348	10	0.02654	T	1	-8.8663	7.34	0.26632	0.3137:0.1113:0.5751:0.0	rs35836343	226	Q96C86	DCPS_HUMAN	D	226	ENSP00000263579:G226D	ENSP00000263579:G226D	G	+	2	0	DCPS	125718452	0.981000	0.34729	0.986000	0.45419	0.713000	0.41058	1.462000	0.35266	-0.091000	0.12440	-0.123000	0.14984	GGC	G|0.995;A|0.005	0.005	strong		0.607	DCPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386455.1	NM_014026		A	126213242	G	A	126213242	3	1	28	1	0	0	0	0	1	0	0	0	4303	1203	42	2	695	2	DCPS	11	126213242	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1648990	126213242	8793274	441	11944											
DCPS	28960	hgsc.bcm.edu	37	chr11	126215507	126215507	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcaggaggctcagcaaagctGaattaactcaggcagaagag	15	5	13	8	0	2	3	2	1	0	2	2	4	2	4	0	3	3	5	0	3	4	1	rs139354381	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:126215507G>A	ENST00000263579.4	+	6	1342	c.1013G>A	c.(1012-1014)tGa>tAa	p.*338*	DCPS_ENST00000530860.1_3'UTR	NM_014026.3	NP_054745.1	Q96C86	DCPS_HUMAN	decapping enzyme, scavenger	0					cellular response to menadione (GO:0036245)|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 cis splicing, via spliceosome (GO:0045292)|mRNA metabolic process (GO:0016071)|negative regulation of programmed cell death (GO:0043069)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	m7G(5')pppN diphosphatase activity (GO:0050072)|RNA 7-methylguanosine cap binding (GO:0000340)			endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00949)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.08)		CAGCAAAGCTGAATTAACTCA	0.502													G|||	5	0.000998403	0.0	0.0043	5008	,	,		18179	0.0		0.002	False		,,,				2504	0.0				p.X338X		Atlas-SNP	.											.	DCPS	33	.	0			c.G1013A						PASS	.	G		5,4397	8.1+/-20.4	0,5,2196	73	78	76		1013	5.2	1	11	dbSNP_134	76	73,8523	39.8+/-96.3	0,73,4225	no	coding-synonymous	DCPS	NM_014026.3		0,78,6421	AA,AG,GG		0.8492,0.1136,0.6001		338/338	126215507	78,12920	2201	4298	6499	SO:0001819	synonymous_variant	28960	exon6			AAAGCTGAATTAA	AF077201	CCDS8473.1	11q24	2008-02-05			ENSG00000110063	ENSG00000110063			29812	protein-coding gene	gene with protein product		610534				12198172, 14523240	Standard	NM_014026		Approved	HSPC015, HINT-5, HSL1	uc001qdp.3	Q96C86	OTTHUMG00000165829	ENST00000263579.4:c.1013G>A	11.37:g.126215507G>A		23	0	0		21	10	0.47619	NM_014026	Q8NHL8|Q9Y2S5	Silent	SNP	ENST00000263579.4	37	CCDS8473.1																																																																																			G|0.995;A|0.005	0.005	strong		0.502	DCPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386455.1	NM_014026		A	126215507	G	A	126215507	2	1	28	1	0	0	0	0	0	0	0	1	4303	1285	45	2		2	DCPS	11	126215507	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2265	126215507	8791009	442	11945											
SLC6A13	6540	hgsc.bcm.edu	37	chr12	333267	333267	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagggtacatgtccaccagcGctgtcaccaggctttctaca	9	9	10	13	1	2	0	1	0	1	0	3	1	3	0	3	2	3	3	3	2	2	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:333267G>A	ENST00000343164.4	-	11	1254	c.1202C>T	c.(1201-1203)gCg>gTg	p.A401V	SLC6A13_ENST00000539668.1_5'UTR|SLC6A13_ENST00000445055.2_Missense_Mutation_p.A309V	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	401					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)			GTCCACCAGCGCTGTCACCAG	0.557																																					p.A401V		Atlas-SNP	.											.	SLC6A13	62	.	0			c.C1202T						PASS	.						106	89	95					12																	333267		2203	4300	6503	SO:0001583	missense	6540	exon11			ACCAGCGCTGTCA	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.1202C>T	12.37:g.333267G>A	ENSP00000339260:p.Ala401Val	79	0	0		84	42	0.5	NM_016615	B4DJL1|Q8TCC2|Q8WW56	Missense_Mutation	SNP	ENST00000343164.4	37	CCDS8502.1	.	.	.	.	.	.	.	.	.	.	G	31	5.059781	0.93846	.	.	ENSG00000010379	ENST00000445055;ENST00000313154;ENST00000343164	T;T	0.78003	-1.14;-1.14	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	D	0.88724	0.6514	M	0.77103	2.36	0.80722	D	1	D;D;D	0.89917	1.0;0.997;0.997	D;P;D	0.76071	0.987;0.893;0.941	D	0.89618	0.3846	10	0.87932	D	0	.	19.3766	0.94512	0.0:0.0:1.0:0.0	.	309;380;401	B4DJL1;B4DJS3;Q9NSD5	.;.;S6A13_HUMAN	V	309;380;401	ENSP00000407104:A309V;ENSP00000339260:A401V	ENSP00000318097:A380V	A	-	2	0	SLC6A13	203528	1.000000	0.71417	0.994000	0.49952	0.952000	0.60782	7.876000	0.87215	2.596000	0.87737	0.491000	0.48974	GCG	.	.	none		0.557	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615		A	333267	G	A	333267	3	1	28	1	0	0	0	0	1	0	0	0	14691	1087	38	1	626	1	SLC6A13	12	333267	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10		333267	133518628	443	11946											
WNK1	65125	hgsc.bcm.edu	37	chr12	936230	936230	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctgaaaaggtttaaagtgAtgaagatcaaagttctaaga	18	11	9	3	0	3	5	1	3	2	2	3	5	3	5	0	1	0	2	0	1	7	4			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:936230A>T	ENST00000315939.6	+	3	1598	c.955A>T	c.(955-957)Atg>Ttg	p.M319L	WNK1_ENST00000447667.2_Missense_Mutation_p.M319L|WNK1_ENST00000535572.1_Missense_Mutation_p.M319L|WNK1_ENST00000530271.2_Missense_Mutation_p.M319L|WNK1_ENST00000537687.1_Missense_Mutation_p.M319L	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	319	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)			GTTTAAAGTGATGAAGATCAA	0.358																																					p.M319L	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.A955T						PASS	.						102	99	100					12																	936230		2203	4300	6503	SO:0001583	missense	65125	exon3			AAAGTGATGAAGA	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.955A>T	12.37:g.936230A>T	ENSP00000313059:p.Met319Leu	87	0	0		93	17	0.182796	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	A	34	5.350017	0.95830	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000447667;ENST00000530271	T;T;T;T;T	0.59638	0.25;0.25;0.25;0.25;0.25	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	0.64402	D	0.000001	T	0.44644	0.1303	N	0.00337	-1.62	0.80722	D	1	P;P;B	0.52692	0.944;0.955;0.252	P;D;B	0.68353	0.866;0.957;0.157	T	0.73385	-0.3999	10	0.66056	D	0.02	-15.3692	15.6803	0.77364	1.0:0.0:0.0:0.0	.	319;319;319	F5GWT4;Q9H4A3;F6UYG0	.;WNK1_HUMAN;.	L	319	ENSP00000441972:M319L;ENSP00000313059:M319L;ENSP00000444465:M319L;ENSP00000392542:M319L;ENSP00000433548:M319L	ENSP00000313059:M319L	M	+	1	0	WNK1	806491	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.339000	0.96797	2.115000	0.64714	0.482000	0.46254	ATG	.	.	none		0.358	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		T	936230	A	T	936230	3	4	28	1	0	0	0	0	1	0	0	0	17392	333	12	5	965	5	WNK1	12	936230	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	602963	936230	132915665	444	11947											
WNK1	65125	hgsc.bcm.edu	37	chr12	998378	998378	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagatgatcacagtgactTctgcggttggtgtaagtttt	9	14	12	6	1	2	3	1	2	1	1	2	4	2	3	0	2	1	3	0	2	1	5			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:998378T>A	ENST00000315939.6	+	21	6080	c.5437T>A	c.(5437-5439)Tct>Act	p.S1813T	WNK1_ENST00000340908.4_Missense_Mutation_p.S1406T|WNK1_ENST00000535572.1_Missense_Mutation_p.S1566T|WNK1_ENST00000530271.2_Missense_Mutation_p.S2311T|WNK1_ENST00000537687.1_Missense_Mutation_p.S2073T	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1813					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)			CACAGTGACTTCTGCGGTTGG	0.363																																					p.S2073T	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.T6217A						PASS	.						166	161	163					12																	998378		2203	4300	6503	SO:0001583	missense	65125	exon21			GTGACTTCTGCGG	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.5437T>A	12.37:g.998378T>A	ENSP00000313059:p.Ser1813Thr	108	0	0		112	54	0.482143	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	T	11.90	1.778019	0.31502	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000252477;ENST00000530271;ENST00000340908	T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88	5.77	2.15	0.27550	.	0.284463	0.31092	N	0.008273	T	0.29783	0.0744	L	0.40543	1.245	0.25832	N	0.984158	B;B;B	0.13594	0.003;0.003;0.008	B;B;B	0.13407	0.006;0.009;0.004	T	0.23940	-1.0174	10	0.66056	D	0.02	-5.5426	5.5835	0.17262	0.128:0.1412:0.0:0.7307	.	1566;1566;1813	Q9H4A3-2;F5GWT4;Q9H4A3	.;.;WNK1_HUMAN	T	1566;1813;2073;986;2311;1406	ENSP00000441972:S1566T;ENSP00000313059:S1813T;ENSP00000444465:S2073T;ENSP00000433548:S2311T;ENSP00000341292:S1406T	ENSP00000252477:S986T	S	+	1	0	WNK1	868639	0.866000	0.29940	0.306000	0.25113	0.265000	0.26407	1.118000	0.31246	0.528000	0.28580	-0.336000	0.08194	TCT	.	.	none		0.363	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		A	998378	T	A	998378	3	1	28	1	0	0	0	0	1	0	0	0	17392	1783	62	5	7021	5	WNK1	12	998378	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	62148	998378	132853517	445	11948											
ERC1	23085	hgsc.bcm.edu	37	chr12	1137145	1137145	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgttcacccaggcttccaCgttcccctcgcttgggtcac	4	10	10	17	3	2	0	2	0	0	0	5	0	4	0	4	3	0	4	4	3	0	4			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:1137145C>T	ENST00000397203.2	+	2	482	c.76C>T	c.(76-78)Cgt>Tgt	p.R26C	ERC1_ENST00000546231.2_Missense_Mutation_p.R26C|ERC1_ENST00000355446.5_Missense_Mutation_p.R26C|ERC1_ENST00000360905.4_Missense_Mutation_p.R26C|ERC1_ENST00000543086.3_Missense_Mutation_p.R26C|ERC1_ENST00000589028.1_Missense_Mutation_p.R26C			Q8IUD2	RB6I2_HUMAN	ELKS/RAB6-interacting/CAST family member 1	26					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)			CAGGCTTCCACGTTCCCCTCG	0.572																																					p.R26C		Atlas-SNP	.											.	ERC1	95	.	0			c.C76T						PASS	.						96	95	95					12																	1137145		2203	4300	6503	SO:0001583	missense	23085	exon2			CTTCCACGTTCCC	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.76C>T	12.37:g.1137145C>T	ENSP00000380386:p.Arg26Cys	41	0	0		34	12	0.352941	NM_178039	A2RU77|A7E295|D3DUP7|D3DUP8|Q6NVK2|Q8IUD3|Q8IUD4|Q8IUD5|Q8NAS1|Q9NXN5|Q9UIK7|Q9UPS1	Missense_Mutation	SNP	ENST00000397203.2	37	CCDS8508.1	.	.	.	.	.	.	.	.	.	.	C	18.69	3.678245	0.68042	.	.	ENSG00000082805	ENST00000347735;ENST00000397203;ENST00000454194;ENST00000537890;ENST00000299183;ENST00000543086;ENST00000542302;ENST00000545948;ENST00000546231;ENST00000355446;ENST00000360905;ENST00000440394	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	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	D	0.91267	0.7247	L	0.34521	1.04	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.994;0.952	D	0.92057	0.5653	10	0.87932	D	0	-10.8759	15.2513	0.73549	0.141:0.859:0.0:0.0	.	26;26;26	Q8IUD2-2;Q8IUD2-3;Q8IUD2	.;.;RB6I2_HUMAN	C	26	ENSP00000340054:R26C;ENSP00000380386:R26C;ENSP00000438546:R26C;ENSP00000445336:R26C;ENSP00000442976:R26C;ENSP00000442739:R26C;ENSP00000347621:R26C;ENSP00000354158:R26C;ENSP00000410064:R26C	ENSP00000299183:R26C	R	+	1	0	ERC1	1007406	1.000000	0.71417	0.993000	0.49108	0.996000	0.88848	4.827000	0.62723	2.644000	0.89710	0.655000	0.94253	CGT	.	.	none		0.572	ERC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398380.2	NM_015064		T	1137145	C	T	1137145	3	4	28	1	0	0	0	0	1	0	0	0	5212	536	19	1	78	1	ERC1	12	1137145	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	138767	1137145	132714750	446	11949											
SLC2A14	144195	hgsc.bcm.edu	37	chr12	7985318	7985318	+	Splice_Site	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttgtggcctggcactcacCgtctcaggagcattgatgac	7	11	11	12	1	3	2	2	2	2	0	4	3	3	3	2	3	1	2	2	3	0	2	rs10846018	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:7985318C>A	ENST00000543909.1	-	8	939	c.180G>T	c.(178-180)acG>acT	p.T60T	SLC2A14_ENST00000431042.2_Splice_Site_p.T37T|SLC2A14_ENST00000542505.1_Intron|SLC2A14_ENST00000542546.1_Splice_Site_p.R5L|SLC2A14_ENST00000535295.1_Splice_Site_p.R5L|SLC2A14_ENST00000539924.1_Splice_Site_p.T75T|SLC2A14_ENST00000340749.5_Splice_Site_p.T37T|SLC2A14_ENST00000396589.2_Splice_Site_p.T60T			Q8TDB8	GTR14_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 14	60					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)		TGGCACTCACCGTCTCAGGAG	0.478											OREG0021654	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	c|||	55	0.0109824	0.0015	0.0144	5008	,	,		-128	0.0		0.0398	False		,,,				2504	0.0031				p.T60T		Atlas-SNP	.											.	SLC2A14	78	.	0			c.G180T						PASS	.	C		40,4366	43.8+/-77.6	0,40,2163	96	92	93		180	0.5	0.4	12	dbSNP_120	93	276,8324	104.6+/-165.6	4,268,4028	yes	coding-synonymous-near-splice	SLC2A14	NM_153449.2		4,308,6191	AA,AC,CC		3.2093,0.9079,2.4296		60/521	7985318	316,12690	2203	4300	6503	SO:0001630	splice_region_variant	144195	exon4			ACTCACCGTCTCA	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.180+1G>T	12.37:g.7985318C>A		97	0	0	645	93	50	0.537634	NM_153449	B3KVB5|B3KWW7|B7Z844|B7ZAC3|Q6UY84|Q8TDB9	Silent	SNP	ENST00000543909.1	37	CCDS8585.1	42	0.019230769230769232	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	34	0.044854881266490766	C	14.99	2.701667	0.48307	0.009079	0.032093	ENSG00000173262	ENST00000535295;ENST00000542546	D;D	0.83837	-1.77;-1.77	2.59	0.538	0.17150	.	.	.	.	.	T	0.69187	0.3083	.	.	.	0.53688	D	0.999972	D	0.64830	0.994	D	0.68943	0.961	T	0.77040	-0.2735	7	.	.	.	.	8.4863	0.33074	0.0:0.7381:0.0:0.2619	rs10846018;rs10846018	5	B7Z844	.	L	5	ENSP00000440492:R5L;ENSP00000443903:R5L	.	R	-	2	0	SLC2A14	7876585	0.256000	0.24012	0.446000	0.26920	0.094000	0.18550	0.809000	0.27168	-0.343000	0.08351	-1.641000	0.00772	CGG	C|0.979;A|0.021	0.021	strong		0.478	SLC2A14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399836.2	NM_153449	Silent	A	7985318	C	A	7985318	5	1	28	1	0	0	0	0	0	0	1	0	14558	666	23	4	1418	4	SLC2A14	12	7985318	Splice_Site	SNP	C	TCGA-G8-6914-01A-11D-2210-10	6848173	7985318	125866577	447	11950											
CAPZA3	93661	hgsc.bcm.edu	37	chr12	18891966	18891966	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caatgaagccctgagaaaaaTtctacgaagggatcttccag	15	8	9	9	1	2	2	0	2	2	1	3	5	3	3	2	1	2	0	2	1	6	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:18891966T>C	ENST00000317658.3	+	1	922	c.764T>C	c.(763-765)aTt>aCt	p.I255T	PLCZ1_ENST00000447925.2_5'Flank|RP11-361I14.2_ENST00000536931.1_RNA|PLCZ1_ENST00000435379.1_5'Flank|PLCZ1_ENST00000266505.7_5'Flank|PLCZ1_ENST00000539875.1_5'Flank	NM_033328.2	NP_201585.1	Q96KX2	CAZA3_HUMAN	capping protein (actin filament) muscle Z-line, alpha 3	255					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cortical cytoskeleton (GO:0030863)|F-actin capping protein complex (GO:0008290)|membrane (GO:0016020)|nucleus (GO:0005634)|WASH complex (GO:0071203)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|prostate(1)	19	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)	Hepatocellular(102;0.194)				CTGAGAAAAATTCTACGAAGG	0.418																																					p.I255T		Atlas-SNP	.											.	CAPZA3	51	.	0			c.T764C						PASS	.						48	51	50					12																	18891966		2203	4299	6502	SO:0001583	missense	93661	exon1			GAAAAATTCTACG	AB053259	CCDS8681.1	12p12.3	2008-02-05			ENSG00000177938	ENSG00000177938			24205	protein-coding gene	gene with protein product		608722				12029070	Standard	NM_033328		Approved	Gsg3, CAPPA3	uc001rdy.3	Q96KX2	OTTHUMG00000169001	ENST00000317658.3:c.764T>C	12.37:g.18891966T>C	ENSP00000326238:p.Ile255Thr	23	0	0		31	9	0.290323	NM_033328	Q969J0	Missense_Mutation	SNP	ENST00000317658.3	37	CCDS8681.1	.	.	.	.	.	.	.	.	.	.	T	8.214	0.801016	0.16397	.	.	ENSG00000177938	ENST00000317658	.	.	.	4.63	2.16	0.27623	F-actin capping protein, alpha subunit, conserved site (1);	0.428352	0.23132	N	0.051565	T	0.21841	0.0526	N	0.16478	0.41	0.31847	N	0.622758	B	0.10296	0.003	B	0.11329	0.006	T	0.08722	-1.0708	9	0.39692	T	0.17	-16.7227	3.7138	0.08430	0.3352:0.0947:0.0:0.5702	.	255	Q96KX2	CAZA3_HUMAN	T	255	.	ENSP00000326238:I255T	I	+	2	0	CAPZA3	18783233	0.896000	0.30565	0.969000	0.41365	0.943000	0.58893	0.619000	0.24388	0.781000	0.33589	0.379000	0.24179	ATT	.	.	none		0.418	CAPZA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401902.1	NM_033328		C	18891966	T	C	18891966	3	2	28	1	0	0	0	0	1	0	0	0	2644	1493	52	3	766	3	CAPZA3	12	18891966	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	10906648	18891966	114959929	448	11951											
OVCH1	341350	hgsc.bcm.edu	37	chr12	29649191	29649191	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttcctccacagaagtggtgCtcatctgattttagggagac	9	12	10	10	0	2	3	1	1	1	2	4	4	4	3	2	2	1	1	2	2	2	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:29649191C>T	ENST00000318184.5	-	3	203	c.204G>A	c.(202-204)gaG>gaA	p.E68E		NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	68	Peptidase S1 1. {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)					AGAAGTGGTGCTCATCTGATT	0.448																																					p.E68E		Atlas-SNP	.											.	OVCH1	195	.	0			c.G204A						PASS	.						67	67	67					12																	29649191		1951	4150	6101	SO:0001819	synonymous_variant	341350	exon3			GTGGTGCTCATCT	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.204G>A	12.37:g.29649191C>T		35	0	0		37	7	0.189189	NM_183378		Silent	SNP	ENST00000318184.5	37																																																																																				.	.	none		0.448	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378		T	29649191	C	T	29649191	2	4	28	1	0	0	0	0	0	0	0	1	11332	796	28	2		2	OVCH1	12	29649191	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	10757225	29649191	104202704	449	11952											
ADCY6	112	hgsc.bcm.edu	37	chr12	49162439	49162439	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cttgcccttcaccttgaccaCccctcgacactccagctggt	6	10	6	19	1	1	1	1	1	0	0	3	2	2	1	6	1	2	1	6	1	0	3	rs200204618		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:49162439C>G	ENST00000307885.4	-	21	4136	c.3442G>C	c.(3442-3444)Gtg>Ctg	p.V1148L	RP11-579D7.2_ENST00000548742.1_RNA|ADCY6_ENST00000357869.3_Missense_Mutation_p.V1095L|ADCY6_ENST00000550422.1_Missense_Mutation_p.V1095L	NM_015270.3	NP_056085.1	O43306	ADCY6_HUMAN	adenylate cyclase 6	1148					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						ACCTTGACCACCCCTCGACAC	0.607																																					p.V1148L		Atlas-SNP	.											.	ADCY6	81	.	0			c.G3442C						PASS	.	C	LEU/VAL,LEU/VAL	0,4406		0,0,2203	104	88	93		3442,3283	4.2	1	12		93	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	ADCY6	NM_015270.3,NM_020983.2	32,32	0,2,6501	GG,GC,CC		0.0233,0.0,0.0154	benign,benign	1148/1169,1095/1116	49162439	2,13004	2203	4300	6503	SO:0001583	missense	112	exon21			TGACCACCCCTCG		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.3442G>C	12.37:g.49162439C>G	ENSP00000311405:p.Val1148Leu	92	0	0		96	51	0.53125	NM_015270	Q9NR75|Q9UDB0	Missense_Mutation	SNP	ENST00000307885.4	37	CCDS8767.1	.	.	.	.	.	.	.	.	.	.	C	11.76	1.735662	0.30774	0.0	2.33E-4	ENSG00000174233	ENST00000357869;ENST00000550422;ENST00000307885	T;T;T	0.80738	-1.41;-1.41;-1.41	5.12	4.23	0.50019	Adenylyl cyclase class-3/4/guanylyl cyclase (3);	0.246243	0.32563	N	0.005938	T	0.56834	0.2012	N	0.01679	-0.765	0.47778	D	0.999511	B;B	0.13594	0.007;0.008	B;B	0.15484	0.012;0.013	T	0.53165	-0.8477	10	0.19590	T	0.45	.	15.4765	0.75485	0.0:0.86:0.14:0.0	.	1095;1148	O43306-2;O43306	.;ADCY6_HUMAN	L	1095;1095;1148	ENSP00000350536:V1095L;ENSP00000446730:V1095L;ENSP00000311405:V1148L	ENSP00000311405:V1148L	V	-	1	0	ADCY6	47448706	0.944000	0.32072	1.000000	0.80357	0.994000	0.84299	1.300000	0.33436	1.491000	0.48482	-0.223000	0.12442	GTG	.	.	weak		0.607	ADCY6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408863.1	NM_020983		G	49162439	C	G	49162439	3	3	28	1	0	0	0	0	1	0	0	0	298	507	18	4	68	4	ADCY6	12	49162439	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	19513248	49162439	84689456	450	11953											
MLL2	8085	hgsc.bcm.edu	37	chr12	49426818	49426818	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaagagcccatgggctgagcGctcagtttgggctgcccact	8	8	13	12	1	1	2	1	1	0	1	1	2	1	2	2	2	3	4	2	2	1	1	rs376471354		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:49426818G>A	ENST00000301067.7	-	39	11669	c.11670C>T	c.(11668-11670)agC>agT	p.S3890S	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3890	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)										TGGGCTGAGCGCTCAGTTTGG	0.572													G|||	1	0.000199681	0.0	0.0014	5008	,	,		19150	0.0		0.0	False		,,,				2504	0.0				p.S3890S		Atlas-SNP	.											.	MLL2	1173	.	0			c.C11670T						PASS	.	G		0,3580		0,0,1790	22	27	25		11670	-9.3	0	12		25	3,6691		0,3,3344	no	coding-synonymous	MLL2	NM_003482.3		0,3,5134	AA,AG,GG		0.0448,0.0,0.0292		3890/5538	49426818	3,10271	1790	3347	5137	SO:0001819	synonymous_variant	8085	exon39			CTGAGCGCTCAGT	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.11670C>T	12.37:g.49426818G>A		58	0	0		64	29	0.453125	NM_003482	O14687	Silent	SNP	ENST00000301067.7	37	CCDS44873.1																																																																																			.	.	weak		0.572	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49426818	G	A	49426818	2	1	28	1	0	0	0	0	0	0	0	1	9630	1078	38	1		1	MLL2	12	49426818	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	264379	49426818	84425077	451	11954											
MLL2	8085	hgsc.bcm.edu	37	chr12	49445949	49445949	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaaaaggtgatgattcaggtGggggagacagaggagactcc	14	6	16	5	0	1	5	1	2	0	3	2	7	2	5	1	5	0	0	1	5	2	1	rs367925817		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:49445949G>T	ENST00000301067.7	-	10	1516	c.1517C>A	c.(1516-1518)cCa>cAa	p.P506Q		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	506	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)										TGATTCAGGTGGGGGAGACAG	0.612																																					p.P506Q		Atlas-SNP	.											.	MLL2	1173	.	0			c.C1517A						PASS	.	G	GLN/PRO	0,4072		0,0,2036	48	55	52		1517	0	1	12		52	1,8375		0,1,4187	no	missense	MLL2	NM_003482.3	76	0,1,6223	TT,TG,GG		0.0119,0.0,0.0080	possibly-damaging	506/5538	49445949	1,12447	2036	4188	6224	SO:0001583	missense	8085	exon10			TCAGGTGGGGGAG	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.1517C>A	12.37:g.49445949G>T	ENSP00000301067:p.Pro506Gln	86	0	0		97	49	0.505155	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	6.497	0.459924	0.12342	0.0	1.19E-4	ENSG00000167548	ENST00000301067	T	0.79653	-1.29	4.2	-0.0106	0.13996	.	.	.	.	.	T	0.57301	0.2044	N	0.08118	0	0.09310	N	1	P	0.34462	0.454	B	0.34722	0.188	T	0.53851	-0.8380	9	0.87932	D	0	.	0.6454	0.00817	0.2995:0.1688:0.3582:0.1735	.	506	O14686	MLL2_HUMAN	Q	506	ENSP00000301067:P506Q	ENSP00000301067:P506Q	P	-	2	0	MLL2	47732216	0.015000	0.18098	0.993000	0.49108	0.853000	0.48598	0.189000	0.17037	0.178000	0.19917	-0.678000	0.03780	CCA	.	.	weak		0.612	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			T	49445949	G	T	49445949	3	4	28	1	0	0	0	0	1	0	0	0	9630	1348	47	4	15276	4	MLL2	12	49445949	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	19131	49445949	84405946	452	11955											
NCKAP5L	57701	hgsc.bcm.edu	37	chr12	50186585	50186585	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggcacctcccgctccagTgtgtgggcgcggcgggggac	3	6	17	15	4	0	0	0	0	0	0	2	1	2	1	4	5	0	2	4	5	0	0	rs138292278	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:50186585T>C	ENST00000335999.6	-	11	3726	c.3525A>G	c.(3523-3525)acA>acG	p.T1175T		NM_001037806.3	NP_001032895.2	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	1171	Pro-rich.									central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(8)|prostate(2)	18						CCCGCTCCAGTGTGTGGGCGC	0.687													T|||	54	0.0107827	0.0023	0.0029	5008	,	,		11936	0.0		0.0109	False		,,,				2504	0.0389				p.T1175T		Atlas-SNP	.											.	NCKAP5L	142	.	0			c.A3525G						PASS	.	T		10,3996		0,10,1993	9	12	11		3525	-7.7	0.6	12	dbSNP_134	11	76,8136		0,76,4030	no	coding-synonymous	NCKAP5L	NM_001037806.3		0,86,6023	CC,CT,TT		0.9255,0.2496,0.7039		1175/1335	50186585	86,12132	2003	4106	6109	SO:0001819	synonymous_variant	57701	exon11			CTCCAGTGTGTGG	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.3525A>G	12.37:g.50186585T>C		54	0	0		78	34	0.435897	NM_001037806	Q2TB26|Q71RH1|Q8N4W1|Q96HX2	Silent	SNP	ENST00000335999.6	37	CCDS41781.2	16	0.007326007326007326	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	11	0.014511873350923483	T	7.331	0.618991	0.14129	0.002496	0.009255	ENSG00000167566	ENST00000433948	.	.	.	4.3	-7.72	0.01250	.	0.000000	0.45126	D	0.000393	T	0.43831	0.1265	.	.	.	0.48040	D	0.999577	.	.	.	.	.	.	T	0.57201	-0.7852	6	0.72032	D	0.01	-11.3794	4.1532	0.10247	0.1022:0.264:0.1016:0.5322	.	.	.	.	A	890	.	ENSP00000402619:T890A	T	-	1	0	NCKAP5L	48472852	0.000000	0.05858	0.623000	0.29173	0.865000	0.49528	-6.231000	0.00075	-1.638000	0.01529	-1.226000	0.01582	ACT	T|0.993;C|0.007	0.007	strong		0.687	NCKAP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346884.2	XM_035497		C	50186585	T	C	50186585	2	2	28	1	0	0	0	0	0	0	0	1	10233	1683	59	3		3	NCKAP5L	12	50186585	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	740636	50186585	83665310	453	11956											
TFCP2	7024	hgsc.bcm.edu	37	chr12	51500329	51500329	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttccccaagagaaaaactgCtatgggaactgttgaagcca	14	8	9	10	0	0	2	0	1	0	1	1	4	1	3	3	1	4	2	3	1	6	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:51500329C>T	ENST00000257915.5	-	8	1354	c.896G>A	c.(895-897)aGc>aAc	p.S299N	TFCP2_ENST00000549867.1_Missense_Mutation_p.S299N|TFCP2_ENST00000307660.4_Missense_Mutation_p.S248N|TFCP2_ENST00000548115.1_Missense_Mutation_p.S248N	NM_001173452.1|NM_005653.4	NP_001166923.1|NP_005644.2	Q12800	TFCP2_HUMAN	transcription factor CP2	299	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						AGAAAAACTGCTATGGGAACT	0.368																																					p.S299N		Atlas-SNP	.											.	TFCP2	49	.	0			c.G896A						PASS	.						81	79	80					12																	51500329		2203	4300	6503	SO:0001583	missense	7024	exon8			AAACTGCTATGGG	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.896G>A	12.37:g.51500329C>T	ENSP00000257915:p.Ser299Asn	62	0	0		59	4	0.0677966	NM_001173452	A8K5E9|Q12801|Q9UD75|Q9UD77	Missense_Mutation	SNP	ENST00000257915.5	37	CCDS8808.1	.	.	.	.	.	.	.	.	.	.	C	12.71	2.019071	0.35606	.	.	ENSG00000135457	ENST00000257915;ENST00000307660;ENST00000549867;ENST00000548115;ENST00000548108	T;T;T;T;T	0.45276	2.22;0.91;2.24;0.9;2.24	5.53	4.64	0.57946	Sterile alpha motif/pointed domain (1);	0.047786	0.85682	D	0.000000	T	0.19765	0.0475	N	0.03194	-0.395	0.40060	D	0.975885	B;B;B;B	0.23990	0.0;0.095;0.0;0.0	B;B;B;B	0.26416	0.002;0.069;0.001;0.001	T	0.09840	-1.0656	10	0.19147	T	0.46	-8.47	10.179	0.42957	0.0:0.8443:0.0:0.1557	.	248;299;299;299	Q12800-2;F8VX55;Q12800;Q12800-4	.;.;TFCP2_HUMAN;.	N	299;248;299;248;201	ENSP00000257915:S299N;ENSP00000304411:S248N;ENSP00000449742:S299N;ENSP00000447991:S248N;ENSP00000449280:S201N	ENSP00000257915:S299N	S	-	2	0	TFCP2	49786596	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.788000	0.26872	1.482000	0.48325	0.655000	0.94253	AGC	.	.	none		0.368	TFCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405119.1	NM_005653		T	51500329	C	T	51500329	3	4	28	1	0	0	0	0	1	0	0	0	15810	797	28	2	644	2	TFCP2	12	51500329	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1313744	51500329	82351566	454	11957											
OR9K2	441639	hgsc.bcm.edu	37	chr12	55523833	55523833	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctaggcaatctctccttcaTtgatcttttctattcatctg	7	18	4	12	0	6	1	2	1	4	0	8	1	7	1	2	1	0	1	2	1	3	7			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:55523833T>C	ENST00000305377.5	+	1	369	c.281T>C	c.(280-282)aTt>aCt	p.I94T		NM_001005243.1	NP_001005243.1	Q8NGE7	OR9K2_HUMAN	olfactory receptor, family 9, subfamily K, member 2	94						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						CTCTCCTTCATTGATCTTTTC	0.423																																					p.I94T		Atlas-SNP	.											.	OR9K2	63	.	0			c.T281C						PASS	.						181	179	180					12																	55523833		2203	4300	6503	SO:0001583	missense	441639	exon1			CCTTCATTGATCT	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.281T>C	12.37:g.55523833T>C	ENSP00000307598:p.Ile94Thr	65	0	0		53	25	0.471698	NM_001005243	B9EH19|Q6IFD6	Missense_Mutation	SNP	ENST00000305377.5	37	CCDS31814.1	.	.	.	.	.	.	.	.	.	.	T	12.88	2.071507	0.36566	.	.	ENSG00000170605	ENST00000305377	T	0.03181	4.02	4.98	4.98	0.66077	GPCR, rhodopsin-like superfamily (1);	0.256644	0.27384	N	0.019611	T	0.07234	0.0183	L	0.37561	1.115	0.09310	N	1	P	0.49358	0.923	P	0.49597	0.616	T	0.09885	-1.0654	10	0.72032	D	0.01	-15.6178	14.8097	0.69985	0.0:0.0:0.0:1.0	.	94	Q8NGE7	OR9K2_HUMAN	T	94	ENSP00000307598:I94T	ENSP00000307598:I94T	I	+	2	0	OR9K2	53810100	0.007000	0.16637	0.673000	0.29887	0.816000	0.46133	1.733000	0.38156	2.223000	0.72356	0.528000	0.53228	ATT	.	.	none		0.423	OR9K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406105.1			C	55523833	T	C	55523833	3	2	28	1	0	0	0	0	1	0	0	0	11263	1493	52	3	283	3	OR9K2	12	55523833	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	4023504	55523833	78328062	455	11958											
BAZ2A	11176	hgsc.bcm.edu	37	chr12	56995907	56995907	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ccatcttcatagagaagaggGcagggttgagtgacgcatgg	11	8	15	7	1	2	4	1	2	1	2	2	5	2	4	1	3	0	3	1	3	2	3	rs202169462		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:56995907G>A	ENST00000551812.1	-	20	3693	c.3500C>T	c.(3499-3501)gCc>gTc	p.A1167V	BAZ2A_ENST00000549884.1_Missense_Mutation_p.A1165V|BAZ2A_ENST00000379441.3_Missense_Mutation_p.A1137V|BAZ2A_ENST00000553222.1_5'Flank|BAZ2A_ENST00000179765.5_Missense_Mutation_p.A1135V	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	1167					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						AGAGAAGAGGGCAGGGTTGAG	0.512													G|||	1	0.000199681	0.0	0.0014	5008	,	,		18914	0.0		0.0	False		,,,				2504	0.0				p.A1167V		Atlas-SNP	.											.	BAZ2A	263	.	0			c.C3500T						PASS	.	G	VAL/ALA	0,3988		0,0,1994	18	19	18		3500	1.7	0	12		18	3,8319		0,3,4158	yes	missense	BAZ2A	NM_013449.3	64	0,3,6152	AA,AG,GG		0.036,0.0,0.0244	benign	1167/1906	56995907	3,12307	1994	4161	6155	SO:0001583	missense	11176	exon20			AAGAGGGCAGGGT	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.3500C>T	12.37:g.56995907G>A	ENSP00000446880:p.Ala1167Val	87	0	0		87	45	0.517241	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Missense_Mutation	SNP	ENST00000551812.1	37	CCDS44924.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	2.919	-0.223686	0.06061	0.0	3.6E-4	ENSG00000076108	ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549787;ENST00000549884	T;T;T;T;T	0.70164	-0.15;-0.15;-0.15;-0.46;-0.15	5.6	1.72	0.24424	.	0.512331	0.20956	N	0.082651	T	0.49133	0.1539	L	0.38531	1.155	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	0.29212	-1.0019	10	0.30854	T	0.27	.	4.9226	0.13878	0.239:0.0:0.6142:0.1468	.	1165;1167;1167	F8VU39;Q9UIF9-3;Q9UIF9	.;.;BAZ2A_HUMAN	V	1137;1135;1167;103;1165	ENSP00000368754:A1137V;ENSP00000179765:A1135V;ENSP00000446880:A1167V;ENSP00000448760:A103V;ENSP00000447941:A1165V	ENSP00000179765:A1135V	A	-	2	0	BAZ2A	55282174	0.008000	0.16893	0.000000	0.03702	0.010000	0.07245	1.643000	0.37217	0.123000	0.18342	-0.229000	0.12294	GCC	G|0.999;A|0.001	0.001	strong		0.512	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449		A	56995907	G	A	56995907	3	1	28	1	0	0	0	0	1	0	0	0	1331	1203	42	2	2257	2	BAZ2A	12	56995907	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1472074	56995907	76855988	456	11959											
ZBTB39	9880	hgsc.bcm.edu	37	chr12	57397250	57397250	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttaaggtgacgctggtcgcaGacactgcaggcctggccctt	7	9	13	12	2	0	2	0	1	0	1	1	2	0	2	2	4	1	3	2	4	1	2	rs145214115		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:57397250G>C	ENST00000300101.2	-	2	1537	c.1452C>G	c.(1450-1452)gtC>gtG	p.V484V		NM_014830.2	NP_055645.1	O15060	ZBT39_HUMAN	zinc finger and BTB domain containing 39	484					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						GCTGGTCGCAGACACTGCAGG	0.547													G|||	1	0.000199681	0.0	0.0014	5008	,	,		21109	0.0		0.0	False		,,,				2504	0.0				p.V484V		Atlas-SNP	.											.	ZBTB39	58	.	0			c.C1452G						PASS	.	G		0,4406		0,0,2203	58	52	54		1452	0.1	0.9	12	dbSNP_134	54	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ZBTB39	NM_014830.2		0,2,6501	CC,CG,GG		0.0233,0.0,0.0154		484/713	57397250	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	9880	exon2			GTCGCAGACACTG	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.1452C>G	12.37:g.57397250G>C		104	0	0		93	44	0.473118	NM_014830	A7MD38|Q9UD98	Silent	SNP	ENST00000300101.2	37	CCDS31839.1																																																																																			G|0.999;C|0.001	0.001	strong		0.547	ZBTB39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411214.1	NM_014830		C	57397250	G	C	57397250	2	2	28	1	0	0	0	0	0	0	0	1	17555	929	33	4		4	ZBTB39	12	57397250	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	401343	57397250	76454645	457	11960											
LRP1	4035	hgsc.bcm.edu	37	chr12	57579390	57579390	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggccgtgggcagcgggcctgCgcctgtgcccacgggatgct	3	6	18	14	4	0	0	0	0	0	0	0	1	0	1	4	4	4	2	4	4	0	0	rs149556819	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:57579390C>T	ENST00000243077.3	+	41	7006	c.6540C>T	c.(6538-6540)tgC>tgT	p.C2180C		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	2180	EGF-like 9. {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)	AGCGGGCCTGCGCCTGTGCCC	0.672																																					p.C2180C		Atlas-SNP	.											.	LRP1	428	.	0			c.C6540T						PASS	.	C		2,4402	4.2+/-10.8	0,2,2200	31	28	29		6540	-4.2	1	12	dbSNP_134	29	0,8594		0,0,4297	no	coding-synonymous	LRP1	NM_002332.2		0,2,6497	TT,TC,CC		0.0,0.0454,0.0154		2180/4545	57579390	2,12996	2202	4297	6499	SO:0001819	synonymous_variant	4035	exon41			GGCCTGCGCCTGT	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.6540C>T	12.37:g.57579390C>T		24	0	0		50	30	0.6	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			C|0.999;T|0.001	0.001	strong		0.672	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		T	57579390	C	T	57579390	2	4	28	1	0	0	0	0	0	0	0	1	8960	776	27	1		1	LRP1	12	57579390	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	182140	57579390	76272505	458	11961											
LRP1	4035	hgsc.bcm.edu	37	chr12	57592067	57592067	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcaatggggcctatcggacGgtgctggtcagctctggcct	5	10	14	12	2	3	0	2	0	1	0	4	1	3	1	2	6	2	2	2	6	2	1	rs143423493	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:57592067G>A	ENST00000243077.3	+	59	9877	c.9411G>A	c.(9409-9411)acG>acA	p.T3137T		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	3137					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)	CCTATCGGACGGTGCTGGTCA	0.637													G|||	11	0.00219649	0.0008	0.0014	5008	,	,		21534	0.0		0.006	False		,,,				2504	0.0031				p.T3137T		Atlas-SNP	.											LRP1,colon,carcinoma,+2,1	LRP1	428	1	0			c.G9411A						scavenged	.	G		1,4405	2.1+/-5.4	0,1,2202	78	79	78		9411	-6.1	0.7	12	dbSNP_134	78	36,8564	25.1+/-72.6	0,36,4264	no	coding-synonymous	LRP1	NM_002332.2		0,37,6466	AA,AG,GG		0.4186,0.0227,0.2845		3137/4545	57592067	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	4035	exon59			TCGGACGGTGCTG	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.9411G>A	12.37:g.57592067G>A		47	1	0.0212766		55	26	0.472727	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			G|0.996;A|0.004	0.004	strong		0.637	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		A	57592067	G	A	57592067	2	1	28	1	0	0	0	0	0	0	0	1	8960	1103	39	1		1	LRP1	12	57592067	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	12677	57592067	76259828	459	11962											
NUP107	57122	hgsc.bcm.edu	37	chr12	69113184	69113184	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caacacttgaaggctggaaaCtgtaccatgaccctaatgtt	13	10	8	10	0	0	2	0	2	0	0	0	3	0	3	2	2	3	3	2	2	5	4	rs35209116	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:69113184C>T	ENST00000229179.4	+	13	1479	c.1147C>T	c.(1147-1149)Ctg>Ttg	p.L383L	NUP107_ENST00000539906.1_Silent_p.L354L|NUP107_ENST00000378905.2_Silent_p.L232L	NM_020401.2	NP_065134.1	P57740	NU107_HUMAN	nucleoporin 107kDa	383					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 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)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|structural constituent of nuclear pore (GO:0017056)		NUP107/LGR5(2)	breast(3)|endometrium(4)|kidney(4)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(2)	39	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)			AGGCTGGAAACTGTACCATGA	0.413													C|||	22	0.00439297	0.0	0.0072	5008	,	,		18922	0.0		0.007	False		,,,				2504	0.0102				p.L383L		Atlas-SNP	.											.	NUP107	88	.	0			c.C1147T						PASS	.	C		7,4399	11.4+/-27.6	0,7,2196	122	112	115		1147	1.2	0	12	dbSNP_126	115	47,8553	32.8+/-85.7	1,45,4254	no	coding-synonymous	NUP107	NM_020401.2		1,52,6450	TT,TC,CC		0.5465,0.1589,0.4152		383/926	69113184	54,12952	2203	4300	6503	SO:0001819	synonymous_variant	57122	exon13			TGGAAACTGTACC	AK055629	CCDS8985.1	12q14	2004-03-19			ENSG00000111581	ENSG00000111581			29914	protein-coding gene	gene with protein product		607617				12552102, 12705868	Standard	XM_005269037		Approved	NUP84	uc001suf.3	P57740	OTTHUMG00000169265	ENST00000229179.4:c.1147C>T	12.37:g.69113184C>T		146	0	0		144	77	0.534722	NM_020401	B4DZ67|Q6PJE1	Silent	SNP	ENST00000229179.4	37	CCDS8985.1																																																																																			C|0.996;T|0.004	0.004	strong		0.413	NUP107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403195.1	NM_020401		T	69113184	C	T	69113184	2	4	28	1	0	0	0	0	0	0	0	1	10762	564	20	2		2	NUP107	12	69113184	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	11521117	69113184	64738711	460	11963											
OSBPL8	114882	hgsc.bcm.edu	37	chr12	76844711	76844711	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gataagcttcttttccttggCgctgactcatctttcctggt	5	17	8	11	1	3	1	1	1	2	0	5	2	5	1	2	2	1	2	2	2	1	6			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:76844711C>T	ENST00000261183.3	-	4	616	c.137G>A	c.(136-138)cGc>cAc	p.R46H	OSBPL8_ENST00000393250.4_Missense_Mutation_p.R4H|OSBPL8_ENST00000393249.2_Missense_Mutation_p.R4H	NM_020841.4	NP_065892.1	Q9BZF1	OSBL8_HUMAN	oxysterol binding protein-like 8	46					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						TTTTCCTTGGCGCTGACTCAT	0.443																																					p.R46H		Atlas-SNP	.											.	OSBPL8	86	.	0			c.G137A						PASS	.						160	139	146					12																	76844711		2203	4300	6503	SO:0001583	missense	114882	exon4			CCTTGGCGCTGAC	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.137G>A	12.37:g.76844711C>T	ENSP00000261183:p.Arg46His	113	0	0		118	5	0.0423729	NM_020841	A8K1T2|E9PE66|E9PE68|Q52LQ3|Q68D75|Q8WXP8|Q9P277	Missense_Mutation	SNP	ENST00000261183.3	37	CCDS31862.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.943872	0.73672	.	.	ENSG00000091039	ENST00000393249;ENST00000261183;ENST00000446075;ENST00000393250;ENST00000438913;ENST00000547540;ENST00000548341;ENST00000553139;ENST00000549570;ENST00000551927;ENST00000547544	T;T;T;T;T;T	0.53423	1.34;2.64;1.34;2.64;2.64;0.62	5.66	5.66	0.87406	.	0.368655	0.29752	N	0.011290	T	0.37320	0.0999	N	0.19112	0.55	0.42098	D	0.991322	D	0.61080	0.989	B	0.42087	0.375	T	0.26573	-1.0099	10	0.42905	T	0.14	-3.9225	18.3033	0.90171	0.0:1.0:0.0:0.0	.	46	Q9BZF1	OSBL8_HUMAN	H	4;46;31;4;46;46;33;4;4;46;43	ENSP00000376939:R4H;ENSP00000261183:R46H;ENSP00000376940:R4H;ENSP00000450238:R46H;ENSP00000446886:R33H;ENSP00000449618:R4H	ENSP00000261183:R46H	R	-	2	0	OSBPL8	75368842	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.348000	0.52209	2.669000	0.90835	0.655000	0.94253	CGC	.	.	none		0.443	OSBPL8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406357.1	NM_020841		T	76844711	C	T	76844711	3	4	28	1	0	0	0	0	1	0	0	0	11292	768	27	1	2616	1	OSBPL8	12	76844711	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	7731527	76844711	57007184	461	11964											
UTP20	27340	hgsc.bcm.edu	37	chr12	101767224	101767224	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaccttggaaatgatcgcCtatctctttgacacgttccc	8	13	6	14	2	1	2	0	2	1	0	5	3	3	3	4	1	0	1	4	1	2	4	rs112278934	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:101767224C>T	ENST00000261637.4	+	53	7098	c.6924C>T	c.(6922-6924)gcC>gcT	p.A2308A		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	2308					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						AAATGATCGCCTATCTCTTTG	0.463													C|||	4	0.000798722	0.0	0.0014	5008	,	,		17679	0.0		0.002	False		,,,				2504	0.001				p.A2308A		Atlas-SNP	.											.	UTP20	222	.	0			c.C6924T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	88	88	88		6924	-3.3	0.6	12	dbSNP_132	88	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	UTP20	NM_014503.2		0,9,6494	TT,TC,CC		0.093,0.0227,0.0692		2308/2786	101767224	9,12997	2203	4300	6503	SO:0001819	synonymous_variant	27340	exon53			GATCGCCTATCTC	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.6924C>T	12.37:g.101767224C>T		84	0	0		76	35	0.460526	NM_014503	Q9H3H4	Silent	SNP	ENST00000261637.4	37	CCDS9081.1																																																																																			C|0.998;T|0.002	0.002	strong		0.463	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		T	101767224	C	T	101767224	2	4	28	1	0	0	0	0	0	0	0	1	17114	668	24	2		2	UTP20	12	101767224	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	24922513	101767224	32084671	462	11965											
NUP37	79023	hgsc.bcm.edu	37	chr12	102494849	102494849	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagatctgaagtaaataaTctaattttcatatcagcagc	16	13	6	6	0	4	3	2	2	2	1	4	3	4	3	0	0	2	2	0	0	7	6	rs17438178	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:102494849T>C	ENST00000552283.1	-	4	454	c.315A>G	c.(313-315)agA>agG	p.R105R	NUP37_ENST00000251074.1_Silent_p.R105R|NUP37_ENST00000543021.1_5'UTR			Q8NFH4	NUP37_HUMAN	nucleoporin 37kDa	105					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						AAGTAAATAATCTAATTTTCA	0.308													T|||	110	0.0219649	0.0401	0.0058	5008	,	,		16106	0.0		0.0308	False		,,,				2504	0.0225				p.R105R		Atlas-SNP	.											.	NUP37	26	.	0			c.A315G						PASS	.	T		130,4262		4,122,2070	29	31	31		315	0.3	1	12	dbSNP_123	31	211,8361		2,207,4077	no	coding-synonymous	NUP37	NM_024057.2		6,329,6147	CC,CT,TT		2.4615,2.9599,2.6304		105/327	102494849	341,12623	2196	4286	6482	SO:0001819	synonymous_variant	79023	exon3			AAATAATCTAATT	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.315A>G	12.37:g.102494849T>C		164	0	0		130	66	0.507692	NM_024057	Q9H644	Silent	SNP	ENST00000552283.1	37	CCDS9089.1																																																																																			T|0.976;C|0.024	0.024	strong		0.308	NUP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409330.1	NM_024057		C	102494849	T	C	102494849	2	2	28	1	0	0	0	0	0	0	0	1	10773	1432	50	3		3	NUP37	12	102494849	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	727625	102494849	31357046	463	11966											
STAB2	55576	hgsc.bcm.edu	37	chr12	104025446	104025446	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acctgtgagtgctactctgcGtacactggccccaagtgtga	8	10	11	12	1	1	2	0	2	1	0	1	2	1	2	3	1	4	2	3	1	3	2	rs147053330	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:104025446G>A	ENST00000388887.2	+	6	762	c.558G>A	c.(556-558)gcG>gcA	p.A186A		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						GCTACTCTGCGTACACTGGCC	0.468													g|||	13	0.00259585	0.0	0.0	5008	,	,		19013	0.001		0.0119	False		,,,				2504	0.0				p.A186A		Atlas-SNP	.											.	STAB2	370	.	0			c.G558A						PASS	.	A		4,4402	8.1+/-20.4	0,4,2199	229	174	193		558	-9.4	0	12	dbSNP_134	193	68,8532	40.8+/-97.7	0,68,4232	no	coding-synonymous	STAB2	NM_017564.9		0,72,6431	AA,AG,GG		0.7907,0.0908,0.5536		186/2552	104025446	72,12934	2203	4300	6503	SO:0001819	synonymous_variant	55576	exon6			CTCTGCGTACACT	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.558G>A	12.37:g.104025446G>A		137	0	0		126	58	0.460317	NM_017564		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																			G|0.994;A|0.006	0.006	strong		0.468	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			A	104025446	G	A	104025446	2	1	28	1	0	0	0	0	0	0	0	1	15253	1132	40	1		1	STAB2	12	104025446	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1530597	104025446	29826449	464	11967											
ACACB	32	hgsc.bcm.edu	37	chr12	109665242	109665242	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcaccggcagctcccggacGgcacctgcgtggtagaattc	8	6	13	14	4	0	1	0	0	0	1	2	2	1	2	3	4	3	5	3	4	2	2	rs60293430	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:109665242G>A	ENST00000338432.7	+	28	4068	c.3949G>A	c.(3949-3951)Ggc>Agc	p.G1317S	ACACB_ENST00000377854.5_Missense_Mutation_p.G1247S|ACACB_ENST00000377848.3_Missense_Mutation_p.G1317S			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	1317					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)	GCTCCCGGACGGCACCTGCGT	0.577													G|||	259	0.0517173	0.1074	0.0548	5008	,	,		17197	0.002		0.0586	False		,,,				2504	0.0184				p.G1317S		Atlas-SNP	.											.	ACACB	330	.	0			c.G3949A						PASS	.	G	SER/GLY	456,3950	214.8+/-234.0	23,410,1770	53	45	47		3949	5.4	1	12	dbSNP_129	47	522,8078	144.3+/-200.2	19,484,3797	yes	missense	ACACB	NM_001093.3	56	42,894,5567	AA,AG,GG		6.0698,10.3495,7.5196	benign	1317/2459	109665242	978,12028	2203	4300	6503	SO:0001583	missense	32	exon27			CCGGACGGCACCT	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.3949G>A	12.37:g.109665242G>A	ENSP00000341044:p.Gly1317Ser	67	0	0		73	38	0.520548	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	105	0.04807692307692308	45	0.09146341463414634	22	0.06077348066298342	0	0.0	38	0.05013192612137203	G	16.13	3.034855	0.54896	0.103495	0.060698	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854;ENST00000390027	T;T;T	0.44881	0.91;0.91;0.91	5.38	5.38	0.77491	Acetyl-CoA carboxylase, central domain (1);	0.053759	0.85682	D	0.000000	T	0.02342	0.0072	L	0.55213	1.73	0.09310	P	1.0	D	0.65815	0.995	P	0.62813	0.907	T	0.04128	-1.0975	9	0.17832	T	0.49	.	14.364	0.66792	0.0:0.0:0.852:0.148	rs60293430;rs61752506	1317	O00763	ACACB_HUMAN	S	1317;1317;1247;548	ENSP00000341044:G1317S;ENSP00000367079:G1317S;ENSP00000367085:G1247S	ENSP00000341044:G1317S	G	+	1	0	ACACB	108149625	1.000000	0.71417	0.985000	0.45067	0.984000	0.73092	4.727000	0.61993	2.679000	0.91253	0.655000	0.94253	GGC	G|0.932;A|0.068	0.068	strong		0.577	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		A	109665242	G	A	109665242	3	1	28	1	0	0	0	0	1	0	0	0	107	1116	39	1	4055	1	ACACB	12	109665242	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	5639796	109665242	24186653	465	11968											
NAA25	80018	hgsc.bcm.edu	37	chr12	112486213	112486213	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgggatcttctcaaatgcaCcatatttgtaagcttgaata	12	14	7	8	0	2	1	1	1	2	0	3	2	2	2	1	1	2	3	1	1	5	6			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:112486213C>T	ENST00000261745.4	-	16	2011	c.1763G>A	c.(1762-1764)gGt>gAt	p.G588D		NM_024953.3	NP_079229.2	Q14CX7	NAA25_HUMAN	N(alpha)-acetyltransferase 25, NatB auxiliary subunit	588						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						CTCAAATGCACCATATTTGTA	0.388																																					p.G588D		Atlas-SNP	.											.	NAA25	105	.	0			c.G1763A						PASS	.						111	106	108					12																	112486213		2203	4300	6503	SO:0001583	missense	80018	exon16			AATGCACCATATT	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.1763G>A	12.37:g.112486213C>T	ENSP00000261745:p.Gly588Asp	49	0	0		57	4	0.0701754	NM_024953	A0JLU7|Q6MZH1|Q7Z4N6|Q9H911	Missense_Mutation	SNP	ENST00000261745.4	37	CCDS9159.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.545698	0.86022	.	.	ENSG00000111300	ENST00000261745	T	0.53857	0.6	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.75722	0.3888	M	0.82323	2.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.989	T	0.75442	-0.3316	10	0.40728	T	0.16	-12.8941	19.5841	0.95484	0.0:1.0:0.0:0.0	.	588;588	A8K8X0;Q14CX7	.;NAA25_HUMAN	D	588	ENSP00000261745:G588D	ENSP00000261745:G588D	G	-	2	0	NAA25	110970596	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.604000	0.88044	0.655000	0.94253	GGT	.	.	none		0.388	NAA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405205.1	NM_024953		T	112486213	C	T	112486213	3	4	28	1	0	0	0	0	1	0	0	0	10130	507	18	2	1191	2	NAA25	12	112486213	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2820971	112486213	21365682	466	11969											
C12orf51	283450	hgsc.bcm.edu	37	chr12	112622244	112622244	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccggcaggcagcggatccAcagagaggtcgctgacggtt	8	5	17	11	4	0	2	0	1	0	1	2	4	1	3	2	6	1	4	2	6	0	1	rs369692553		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:112622244A>G	ENST00000430131.2	-	60	10405	c.9260T>C	c.(9259-9261)gTg>gCg	p.V3087A	HECTD4_ENST00000550722.1_Missense_Mutation_p.V3363A|HECTD4_ENST00000377560.5_Missense_Mutation_p.V3337A			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3087					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)										CAGCGGATCCACAGAGAGGTC	0.677																																					p.V3375A		Atlas-SNP	.											.	.	.	.	0			c.T10124C						PASS	.	A	ALA/VAL	0,4366		0,0,2183	20	26	24		10010	2.1	0.7	12		24	1,8559		0,1,4279	no	missense	C12orf51	NM_001109662.2	64	0,1,6462	GG,GA,AA		0.0117,0.0,0.0077	benign	3337/4247	112622244	1,12925	2183	4280	6463	SO:0001583	missense	283450	exon61			GGATCCACAGAGA	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.9260T>C	12.37:g.112622244A>G	ENSP00000404379:p.Val3087Ala	30	0	0		36	18	0.5	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	37		.	.	.	.	.	.	.	.	.	.	A	9.809	1.182707	0.21870	0.0	1.17E-4	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722	T;T;T	0.51325	0.71;0.71;0.71	5.82	2.06	0.26882	.	.	.	.	.	T	0.27866	0.0686	N	0.14661	0.345	0.29651	N	0.843934	B	0.02656	0.0	B	0.01281	0.0	T	0.18429	-1.0337	9	0.42905	T	0.14	.	6.5643	0.22503	0.7294:0.1299:0.1406:0.0	.	3087	Q9Y4D8	K0614_HUMAN	A	3337;3087;3363	ENSP00000366783:V3337A;ENSP00000404379:V3087A;ENSP00000449784:V3363A	ENSP00000366783:V3337A	V	-	2	0	C12orf51	111106627	0.368000	0.25031	0.678000	0.29963	0.067000	0.16453	3.175000	0.50855	0.479000	0.27511	0.533000	0.62120	GTG	.	.	weak		0.677	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813		G	112622244	A	G	112622244	3	3	28	1	0	0	0	0	1	0	0	0	1698	159	6	3	2794	3	C12orf51	12	112622244	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	136031	112622244	21229651	467	11970											
SRRM4	84530	hgsc.bcm.edu	37	chr12	119568596	119568596	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagtccagtcgcccgcccaGtcaacccctccagatgcttg	7	7	8	19	2	1	1	1	0	0	1	4	1	3	1	7	0	2	1	7	0	1	1	rs7297606	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:119568596G>A	ENST00000267260.4	+	8	1116	c.728G>A	c.(727-729)aGt>aAt	p.S243N	SRRM4_ENST00000537597.1_3'UTR	NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	243	Ser-rich.		S -> N (in dbSNP:rs7297606).		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						CGCCCGCCCAGTCAACCCCTC	0.627													G|||	500	0.0998403	0.2042	0.1124	5008	,	,		15715	0.0268		0.0547	False		,,,				2504	0.0716				p.S243N		Atlas-SNP	.											.	SRRM4	131	.	0			c.G728A						PASS	.	G	ASN/SER	638,3266		55,528,1369	25	31	29		728	3.3	1	12	dbSNP_116	29	626,7648		17,592,3528	yes	missense	SRRM4	NM_194286.3	46	72,1120,4897	AA,AG,GG		7.5659,16.3422,10.3794	benign	243/612	119568596	1264,10914	1952	4137	6089	SO:0001583	missense	84530	exon8			CGCCCAGTCAACC	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.728G>A	12.37:g.119568596G>A	ENSP00000267260:p.Ser243Asn	18	0	0		26	14	0.538462	NM_194286	A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	Missense_Mutation	SNP	ENST00000267260.4	37	CCDS44994.1	191	0.08745421245421245	94	0.1910569105691057	36	0.09944751381215469	20	0.03496503496503497	41	0.05408970976253298	G	7.164	0.586356	0.13749	0.163422	0.075659	ENSG00000139767	ENST00000267260	T	0.24538	1.85	5.21	3.34	0.38264	.	0.747332	0.13340	N	0.395235	T	0.00039	0.0001	L	0.44542	1.39	0.41880	P	0.009688999999999948	B	0.30281	0.275	B	0.29942	0.109	T	0.23440	-1.0188	9	0.12430	T	0.62	-8.2941	11.354	0.49605	0.0752:0.1274:0.7974:0.0	rs7297606;rs52809663;rs58175205;rs7297606	243	A7MD48	SRRM4_HUMAN	N	243	ENSP00000267260:S243N	ENSP00000267260:S243N	S	+	2	0	SRRM4	118052979	1.000000	0.71417	0.992000	0.48379	0.053000	0.15095	1.326000	0.33735	0.207000	0.20607	-1.688000	0.00730	AGT	G|0.908;A|0.092	0.092	strong		0.627	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	NM_194286		A	119568596	G	A	119568596	3	1	28	1	0	0	0	0	1	0	0	0	15186	1029	36	2	758	2	SRRM4	12	119568596	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	6946352	119568596	14283299	468	11971											
CCDC60	160777	hgsc.bcm.edu	37	chr12	119961587	119961587	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cagcgtagcccaggaggctgGcttctgcctgcaggacaaga	9	6	14	12	1	1	1	0	0	1	1	1	3	1	3	2	4	4	4	2	4	2	2	rs78218795	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:119961587G>A	ENST00000327554.2	+	11	1658	c.1193G>A	c.(1192-1194)gGc>gAc	p.G398D	RP11-768F21.1_ENST00000509470.2_lincRNA	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	398										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)		CAGGAGGCTGGCTTCTGCCTG	0.483													G|||	156	0.0311502	0.0862	0.0274	5008	,	,		20637	0.001		0.0129	False		,,,				2504	0.0092				p.G398D		Atlas-SNP	.											.	CCDC60	84	.	0			c.G1193A						PASS	.	G	ASP/GLY	319,4087	170.1+/-200.6	11,297,1895	100	82	88		1193	4.2	1	12	dbSNP_131	88	148,8452	72.6+/-135.2	0,148,4152	yes	missense	CCDC60	NM_178499.3	94	11,445,6047	AA,AG,GG		1.7209,7.2401,3.5907	probably-damaging	398/551	119961587	467,12539	2203	4300	6503	SO:0001583	missense	160777	exon11			AGGCTGGCTTCTG	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.1193G>A	12.37:g.119961587G>A	ENSP00000333374:p.Gly398Asp	68	0	0		60	32	0.533333	NM_178499		Missense_Mutation	SNP	ENST00000327554.2	37	CCDS9190.1	60	0.027472527472527472	43	0.08739837398373984	7	0.019337016574585635	1	0.0017482517482517483	9	0.011873350923482849	G	16.22	3.061173	0.55432	0.072401	0.017209	ENSG00000183273	ENST00000327554	T	0.22743	1.94	4.16	4.16	0.48862	.	0.128128	0.35407	N	0.003225	T	0.01558	0.0050	L	0.55481	1.735	0.80722	D	1	D	0.71674	0.998	D	0.68039	0.955	T	0.00032	-1.2278	9	.	.	.	-20.1692	11.8272	0.52273	0.0:0.0:1.0:0.0	.	398	Q8IWA6	CCD60_HUMAN	D	398	ENSP00000333374:G398D	.	G	+	2	0	CCDC60	118445970	1.000000	0.71417	0.999000	0.59377	0.921000	0.55340	2.598000	0.46223	2.156000	0.67533	0.655000	0.94253	GGC	G|0.968;A|0.032	0.032	strong		0.483	CCDC60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401680.1	NM_178499		A	119961587	G	A	119961587	3	1	28	1	0	0	0	0	1	0	0	0	2833	1203	42	2	1235	2	CCDC60	12	119961587	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	392991	119961587	13890308	469	11972											
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120593190	120593190	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tcacgtcgtcaatcagcaagGagcagaggtctggctgcagg	10	7	14	10	2	4	1	3	0	1	1	5	2	4	2	0	4	3	4	0	4	2	0	rs183298599	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:120593190G>A	ENST00000300648.6	-	30	3497	c.3485C>T	c.(3484-3486)tCc>tTc	p.S1162F	MIR4498_ENST00000577599.1_RNA	NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1162					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)					AATCAGCAAGGAGCAGAGGTC	0.607													G|||	3	0.000599042	0.0	0.0	5008	,	,		19268	0.0		0.003	False		,,,				2504	0.0				p.S1162F		Atlas-SNP	.											GCN1L1,NS,lymphoid_neoplasm,0,1	GCN1L1	207	1	0			c.C3485T						PASS	.	G	PHE/SER	0,4058		0,0,2029	69	74	72		3485	4.7	1	12		72	9,8377		0,9,4184	yes	missense	GCN1L1	NM_006836.1	155	0,9,6213	AA,AG,GG		0.1073,0.0,0.0723	possibly-damaging	1162/2672	120593190	9,12435	2029	4193	6222	SO:0001583	missense	10985	exon30			AGCAAGGAGCAGA	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.3485C>T	12.37:g.120593190G>A	ENSP00000300648:p.Ser1162Phe	41	0	0		36	36	1	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	37	CCDS41847.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	24.2	4.503043	0.85176	0.0	0.001073	ENSG00000089154	ENST00000300648	T	0.38560	1.13	5.56	4.67	0.58626	Armadillo-like helical (1);Armadillo-type fold (1);	0.111386	0.64402	N	0.000005	T	0.44222	0.1283	M	0.63843	1.955	0.80722	D	1	D	0.54397	0.966	B	0.43536	0.423	T	0.50127	-0.8864	10	0.59425	D	0.04	.	14.1912	0.65639	0.0713:0.0:0.9287:0.0	.	1162	Q92616	GCN1L_HUMAN	F	1162	ENSP00000300648:S1162F	ENSP00000300648:S1162F	S	-	2	0	GCN1L1	119077573	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	6.119000	0.71590	1.358000	0.45922	0.655000	0.94253	TCC	G|0.998;A|0.002	0.002	strong		0.607	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			A	120593190	G	A	120593190	3	1	28	1	0	0	0	0	1	0	0	0	6307	1174	41	2	4646	2	GCN1L1	12	120593190	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	631603	120593190	13258705	470	11973											
HNF1A	6927	hgsc.bcm.edu	37	chr12	121416622	121416622	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gagctcctggcggccctgctCgagtcagggctgagcaaaga	8	6	15	12	2	1	2	1	1	0	1	3	4	2	2	2	3	3	4	2	3	1	0	rs1169289	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:121416622C>G	ENST00000257555.6	+	1	277	c.51C>G	c.(49-51)ctC>ctG	p.L17L	HNF1A_ENST00000544413.1_Silent_p.L17L|HNF1A_ENST00000543427.1_Intron|HNF1A_ENST00000541395.1_Silent_p.L17L|HNF1A-AS1_ENST00000535301.1_RNA|HNF1A_ENST00000538626.1_Silent_p.L17L|HNF1A-AS1_ENST00000433033.2_RNA|HNF1A_ENST00000402929.1_Silent_p.L17L|HNF1A_ENST00000400024.2_Silent_p.L17L|HNF1A-AS1_ENST00000537361.1_RNA			P20823	HNF1A_HUMAN	HNF1 homeobox A	17	Dimerization.				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)					CGGCCCTGCTCGAGTCAGGGC	0.687									Hepatic Adenoma, Familial Clustering of				C|||	2146	0.428514	0.3169	0.438	5008	,	,		11818	0.3819		0.4692	False		,,,				2504	0.5787				p.L17L		Atlas-SNP	.											HNF1A,NS,carcinoma,0,1	HNF1A	302	1	1	Unknown(1)	endometrium(1)	c.C51G						scavenged	.	C		1508,2894		278,952,971	24	29	27		51	-3.7	0.9	12	dbSNP_87	27	3915,4673		915,2085,1294	no	coding-synonymous	HNF1A	NM_000545.5		1193,3037,2265	GG,GC,CC		45.5869,34.2572,41.7475		17/632	121416622	5423,7567	2201	4294	6495	SO:0001819	synonymous_variant	6927	exon1	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CCTGCTCGAGTCA	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.51C>G	12.37:g.121416622C>G		134	1	0.00746269		135	72	0.533333	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Silent	SNP	ENST00000257555.6	37	CCDS9209.1																																																																																			G|0.405;C|0.595	0.405	strong		0.687	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		G	121416622	C	G	121416622	2	3	28	1	0	0	0	0	0	0	0	1	7260	871	31	4		4	HNF1A	12	121416622	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	823432	121416622	12435273	471	11974											
KDM2B	84678	hgsc.bcm.edu	37	chr12	121877738	121877738	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgatagactggtcggtgaCgtggttacagtaactgaggt	9	12	15	5	2	0	4	0	3	0	1	1	4	0	4	0	4	2	3	0	4	3	4	rs200642027		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:121877738C>T	ENST00000377071.4	-	22	3823	c.3751G>A	c.(3751-3753)Gtc>Atc	p.V1251I	KDM2B_ENST00000542973.1_Missense_Mutation_p.V619I|KDM2B_ENST00000536437.1_Intron|KDM2B_ENST00000377069.4_Missense_Mutation_p.V1182I	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	1251					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						TGGTCGGTGACGTGGTTACAG	0.607																																					p.V1251I		Atlas-SNP	.											.	KDM2B	218	.	0			c.G3751A						PASS	.	C	ILE/VAL,ILE/VAL	0,4368		0,0,2184	125	148	140		3544,3751	3.9	0.6	12		140	4,8542		0,4,4269	yes	missense,missense	KDM2B	NM_001005366.1,NM_032590.4	29,29	0,4,6453	TT,TC,CC		0.0468,0.0,0.031	benign,benign	1182/1266,1251/1337	121877738	4,12910	2184	4273	6457	SO:0001583	missense	84678	exon22			CGGTGACGTGGTT	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.3751G>A	12.37:g.121877738C>T	ENSP00000366271:p.Val1251Ile	67	0	0		73	33	0.452055	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Missense_Mutation	SNP	ENST00000377071.4	37	CCDS41850.1	.	.	.	.	.	.	.	.	.	.	C	13.16	2.154362	0.38021	0.0	4.68E-4	ENSG00000089094	ENST00000397480;ENST00000542973;ENST00000377069;ENST00000377071;ENST00000540043;ENST00000261824	T;T;T	0.01172	5.23;5.23;5.23	5.73	3.88	0.44766	.	0.145937	0.30575	N	0.009338	T	0.00468	0.0015	N	0.01624	-0.795	0.80722	D	1	B;B;B;B	0.30114	0.103;0.001;0.269;0.037	B;B;B;B	0.15484	0.008;0.001;0.013;0.008	T	0.52343	-0.8588	10	0.02654	T	1	-15.9978	10.6917	0.45875	0.0:0.7916:0.0:0.2084	.	691;1251;1182;694	B7ZB05;Q8NHM5;A8MRS1;B4DSN4	.;KDM2B_HUMAN;.;.	I	1241;619;1182;1251;694;1254	ENSP00000437821:V619I;ENSP00000366269:V1182I;ENSP00000366271:V1251I	ENSP00000261824:V1254I	V	-	1	0	KDM2B	120362121	1.000000	0.71417	0.613000	0.29037	0.983000	0.72400	1.995000	0.40767	0.742000	0.32697	0.655000	0.94253	GTC	.	.	weak		0.607	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590		T	121877738	C	T	121877738	3	4	28	1	0	0	0	0	1	0	0	0	8134	536	19	1	319	1	KDM2B	12	121877738	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	461116	121877738	11974157	472	11975											
WDR66	144406	hgsc.bcm.edu	37	chr12	122361711	122361711	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcttgaggagaaaaccgacCggatgccccaagatgaactg	14	5	12	10	2	0	4	0	2	0	2	0	7	0	5	4	2	4	1	4	2	4	1	rs34703321	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:122361711C>T	ENST00000288912.4	+	3	1416	c.562C>T	c.(562-564)Cgg>Tgg	p.R188W	WDR66_ENST00000397454.2_Missense_Mutation_p.R188W	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	188							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)		GAAAACCGACCGGATGCCCCA	0.478													C|||	11	0.00219649	0.0	0.0029	5008	,	,		16696	0.0		0.007	False		,,,				2504	0.002				p.R188W	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											.	WDR66	143	.	0			c.C562T						PASS	.	C	TRP/ARG,TRP/ARG	8,3728		0,8,1860	104	100	101		562,562	2.5	0	12	dbSNP_126	101	68,8122		1,66,4028	yes	missense,missense	WDR66	NM_001178003.1,NM_144668.5	101,101	1,74,5888	TT,TC,CC		0.8303,0.2141,0.6373	benign,benign	188/942,188/1150	122361711	76,11850	1868	4095	5963	SO:0001583	missense	144406	exon3			ACCGACCGGATGC	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.562C>T	12.37:g.122361711C>T	ENSP00000288912:p.Arg188Trp	62	0	0		75	36	0.48	NM_001178003	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	37	CCDS41853.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	C	6.949	0.544851	0.13312	0.002141	0.008303	ENSG00000158023	ENST00000288912;ENST00000397454	T;T	0.17854	2.25;2.25	4.43	2.53	0.30540	.	3.743330	0.00887	N	0.002196	T	0.08358	0.0208	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.31110	-0.9955	10	0.51188	T	0.08	.	9.2319	0.37441	0.0:0.7611:0.1476:0.0914	rs34703321	188	Q8TBY9	WDR66_HUMAN	W	188	ENSP00000288912:R188W;ENSP00000380595:R188W	ENSP00000288912:R188W	R	+	1	2	WDR66	120846094	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.848000	0.27710	0.188000	0.20168	-1.641000	0.00772	CGG	C|0.995;T|0.005	0.005	strong		0.478	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668		T	122361711	C	T	122361711	3	4	28	1	0	0	0	0	1	0	0	0	17332	643	23	1	568	1	WDR66	12	122361711	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	483973	122361711	11490184	473	11976											
WDR66	144406	hgsc.bcm.edu	37	chr12	122404946	122404946	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcatggcggagctacagaaaCgctacttggtgtttattaac	11	11	11	8	2	0	1	0	0	0	1	0	2	0	2	0	3	5	4	0	3	5	6	rs146415200	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:122404946C>T	ENST00000288912.4	+	16	3432	c.2578C>T	c.(2578-2580)Cgc>Tgc	p.R860C	WDR66_ENST00000545752.1_3'UTR|WDR66_ENST00000397454.2_Missense_Mutation_p.R860C	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	860							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)		GCTACAGAAACGCTACTTGGT	0.483													C|||	13	0.00259585	0.0	0.0043	5008	,	,		14206	0.001		0.007	False		,,,				2504	0.002				p.R860C	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											WDR66,NS,carcinoma,-1,1	WDR66	143	1	0			c.C2578T						PASS	.	C	CYS/ARG,CYS/ARG	8,3860		0,8,1926	110	111	111		2578,2578	4.6	1	12	dbSNP_134	111	69,8201		1,67,4067	yes	missense,missense	WDR66	NM_001178003.1,NM_144668.5	180,180	1,75,5993	TT,TC,CC		0.8343,0.2068,0.6344	possibly-damaging,possibly-damaging	860/942,860/1150	122404946	77,12061	1934	4135	6069	SO:0001583	missense	144406	exon16			CAGAAACGCTACT	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.2578C>T	12.37:g.122404946C>T	ENSP00000288912:p.Arg860Cys	82	0	0		83	42	0.506024	NM_001178003	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	37	CCDS41853.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	C	14.97	2.695530	0.48202	0.002068	0.008343	ENSG00000158023	ENST00000288912;ENST00000397454	T;T	0.56776	0.44;1.19	4.61	4.61	0.57282	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.385177	0.27415	N	0.019473	T	0.49304	0.1549	M	0.78916	2.43	0.42205	D	0.991785	P	0.52316	0.952	P	0.44561	0.453	T	0.64592	-0.6371	10	0.66056	D	0.02	.	13.2823	0.60222	0.0:0.8409:0.1591:0.0	.	860	Q8TBY9	WDR66_HUMAN	C	860	ENSP00000288912:R860C;ENSP00000380595:R860C	ENSP00000288912:R860C	R	+	1	0	WDR66	120889329	0.923000	0.31300	0.999000	0.59377	0.216000	0.24613	1.620000	0.36976	2.124000	0.65301	0.551000	0.68910	CGC	C|0.995;T|0.005	0.005	strong		0.483	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668		T	122404946	C	T	122404946	3	4	28	1	0	0	0	0	1	0	0	0	17332	536	19	1	2636	1	WDR66	12	122404946	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	43235	122404946	11446949	474	11977											
CLIP1	6249	hgsc.bcm.edu	37	chr12	122825398	122825398	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cttcatttccgatttaccttCggaactggctttccgaagtg	7	15	8	11	3	1	0	1	0	0	0	4	3	3	1	3	2	2	1	3	2	3	6	rs61954403	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:122825398C>T	ENST00000540338.1	-	10	2394	c.2353G>A	c.(2353-2355)Gaa>Aaa	p.E785K	CLIP1_ENST00000302528.7_Missense_Mutation_p.E774K|CLIP1_ENST00000537178.1_Missense_Mutation_p.E739K|CLIP1_ENST00000545889.1_Intron|CLIP1_ENST00000361654.4_Intron|CLIP1_ENST00000358808.2_Missense_Mutation_p.E774K			P30622	CLIP1_HUMAN	CAP-GLY domain containing linker protein 1	785					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)		GATTTACCTTCGGAACTGGCT	0.388													C|||	33	0.00658946	0.0015	0.0144	5008	,	,		21925	0.0		0.0199	False		,,,				2504	0.001				p.E785K		Atlas-SNP	.											.	CLIP1	126	.	0			c.G2353A						PASS	.	C	LYS/GLU,LYS/GLU	15,4391	22.3+/-47.3	0,15,2188	141	139	140		2320,2215	5.7	1	12	dbSNP_129	140	130,8470	66.3+/-128.7	0,130,4170	yes	missense,missense	CLIP1	NM_002956.2,NM_198240.1	56,56	0,145,6358	TT,TC,CC		1.5116,0.3404,1.1149	possibly-damaging,possibly-damaging	774/1428,739/1393	122825398	145,12861	2203	4300	6503	SO:0001583	missense	6249	exon11			TACCTTCGGAACT		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.2353G>A	12.37:g.122825398C>T	ENSP00000439093:p.Glu785Lys	175	0	0		174	93	0.534483	NM_001247997	A0AVD3|Q17RS4|Q29RG0	Missense_Mutation	SNP	ENST00000540338.1	37	CCDS58285.1	16	0.007326007326007326	0	0.0	1	0.0027624309392265192	0	0.0	15	0.01978891820580475	C	26.0	4.699526	0.88830	0.003404	0.015116	ENSG00000130779	ENST00000302528;ENST00000358808;ENST00000537178;ENST00000540338	T;T;T;T	0.56275	0.56;0.56;0.57;0.47	5.73	5.73	0.89815	.	0.052582	0.85682	D	0.000000	T	0.48466	0.1501	M	0.64997	1.995	0.53005	D	0.999968	D;D;D	0.64830	0.994;0.994;0.977	P;P;P	0.53649	0.731;0.731;0.487	T	0.52094	-0.8621	10	0.29301	T	0.29	-19.7607	20.2602	0.98440	0.0:1.0:0.0:0.0	rs61954403	739;774;785	P30622-2;P30622-1;P30622	.;.;CLIP1_HUMAN	K	774;774;739;785	ENSP00000303585:E774K;ENSP00000351665:E774K;ENSP00000445531:E739K;ENSP00000439093:E785K	ENSP00000303585:E774K	E	-	1	0	CLIP1	121391351	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.025000	0.57225	2.861000	0.98227	0.655000	0.94253	GAA	C|0.990;T|0.010	0.010	strong		0.388	CLIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401625.1	NM_002956		T	122825398	C	T	122825398	3	4	28	1	0	0	0	0	1	0	0	0	3534	893	31	1	2027	1	CLIP1	12	122825398	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	420452	122825398	11026497	475	11978											
DDX55	57696	hgsc.bcm.edu	37	chr12	124086736	124086736	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcctgggagtcgctgcctgTgccgctgcacccgcaggtgc	3	8	14	16	3	0	0	0	0	0	0	2	1	1	1	4	2	4	4	4	2	0	0	rs141195308	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:124086736T>G	ENST00000238146.4	+	1	91	c.41T>G	c.(40-42)gTg>gGg	p.V14G	DDX55_ENST00000538744.1_Missense_Mutation_p.V14G	NM_020936.1	NP_065987.1	Q8NHQ9	DDX55_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55	14						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)		TCGCTGCCTGTGCCGCTGCAC	0.706													T|||	6	0.00119808	0.0	0.0029	5008	,	,		15400	0.0		0.004	False		,,,				2504	0.0				p.V14G		Atlas-SNP	.											DDX55,NS,lymphoid_neoplasm,0,1	DDX55	51	1	0			c.T41G						scavenged	.	T	GLY/VAL	3,4375		0,3,2186	12	13	13		41	3.9	0.3	12	dbSNP_134	13	25,8541		0,25,4258	yes	missense	DDX55	NM_020936.1	109	0,28,6444	GG,GT,TT		0.2919,0.0685,0.2163	benign	14/601	124086736	28,12916	2189	4283	6472	SO:0001583	missense	57696	exon1			TGCCTGTGCCGCT	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.41T>G	12.37:g.124086736T>G	ENSP00000238146:p.Val14Gly	45	1	0.0222222		48	21	0.4375	NM_020936	Q658L6|Q8IYH0|Q9HCH7	Missense_Mutation	SNP	ENST00000238146.4	37	CCDS9251.1	8	0.003663003663003663	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	3	0.00395778364116095	T	8.130	0.782942	0.16189	6.85E-4	0.002919	ENSG00000111364	ENST00000238146;ENST00000538449;ENST00000538744	T;T	0.04234	3.95;3.67	5.03	3.89	0.44902	RNA helicase, DEAD-box type, Q motif (1);	0.578293	0.17416	N	0.175019	T	0.04679	0.0127	M	0.72894	2.215	0.80722	D	1	B	0.25850	0.136	B	0.19391	0.025	T	0.16600	-1.0397	10	0.22109	T	0.4	-20.8964	9.5249	0.39158	0.0:0.0796:0.0:0.9204	.	14	Q8NHQ9	DDX55_HUMAN	G	14	ENSP00000238146:V14G;ENSP00000443114:V14G	ENSP00000238146:V14G	V	+	2	0	DDX55	122652689	0.995000	0.38212	0.349000	0.25694	0.004000	0.04260	2.926000	0.48892	0.941000	0.37499	0.533000	0.62120	GTG	T|0.998;G|0.002	0.002	strong		0.706	DDX55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400616.2			G	124086736	T	G	124086736	3	3	28	1	0	0	0	0	1	0	0	0	4375	1696	59	5	43	5	DDX55	12	124086736	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	1261338	124086736	9765159	476	11979											
DNAH10	196385	hgsc.bcm.edu	37	chr12	124355003	124355003	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agttccagagtatattcatgCccccgagaggaaattcatca	13	10	8	10	1	3	2	3	0	0	2	4	4	4	3	3	1	1	2	3	1	3	5			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:124355003C>T	ENST00000409039.3	+	43	7281	c.7256C>T	c.(7255-7257)gCc>gTc	p.A2419V		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2419	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(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)		TATATTCATGCCCCCGAGAGG	0.433																																					p.A2419V		Atlas-SNP	.											.	DNAH10	888	.	0			c.C7256T						PASS	.						81	77	78					12																	124355003		1865	4114	5979	SO:0001583	missense	196385	exon43			TTCATGCCCCCGA	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.7256C>T	12.37:g.124355003C>T	ENSP00000386770:p.Ala2419Val	63	0	0		91	40	0.43956	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	C	12.19	1.863422	0.32884	.	.	ENSG00000197653	ENST00000409039	T	0.22134	1.97	5.06	-6.26	0.02033	.	5.622030	0.00939	U	0.002819	T	0.08935	0.0221	N	0.11364	0.135	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.16512	-1.0400	10	0.39692	T	0.17	.	0.4362	0.00479	0.3524:0.2407:0.1472:0.2597	.	2419	Q8IVF4	DYH10_HUMAN	V	2419	ENSP00000386770:A2419V	ENSP00000386770:A2419V	A	+	2	0	DNAH10	122920956	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.150000	0.10189	-0.924000	0.03780	-0.137000	0.14449	GCC	.	.	none		0.433	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124355003	C	T	124355003	3	4	28	1	0	0	0	0	1	0	0	0	4600	739	26	2	7426	2	DNAH10	12	124355003	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	268267	124355003	9496892	477	11980											
NCOR2	9612	hgsc.bcm.edu	37	chr12	124856830	124856830	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgtgtccactgccagctcctCagccgcggggggcttctgct	3	10	13	15	2	2	0	1	0	1	0	4	0	4	0	4	3	4	3	4	3	0	1	rs142292731	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:124856830C>T	ENST00000405201.1	-	20	2545	c.2545G>A	c.(2545-2547)Gag>Aag	p.E849K	NCOR2_ENST00000397355.1_Missense_Mutation_p.E832K|NCOR2_ENST00000356219.3_Missense_Mutation_p.E849K|NCOR2_ENST00000404121.2_Missense_Mutation_p.E402K|NCOR2_ENST00000429285.2_Missense_Mutation_p.E831K|NCOR2_ENST00000404621.1_Missense_Mutation_p.E831K			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	849					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)		GCCAGCTCCTCAGCCGCGGGG	0.701													C|||	21	0.00419329	0.0	0.0101	5008	,	,		10880	0.0		0.0129	False		,,,				2504	0.001				p.E849K		Atlas-SNP	.											.	NCOR2	475	.	0			c.G2545A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU	15,3945		0,15,1965	19	23	22		2491,2491,2545	0.7	0	12	dbSNP_134	22	226,8042		3,220,3911	yes	missense,missense,missense	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	56,56,56	3,235,5876	TT,TC,CC		2.7334,0.3788,1.9709	benign,benign,benign	831/2459,831/2505,849/2515	124856830	241,11987	1980	4134	6114	SO:0001583	missense	9612	exon22			GCTCCTCAGCCGC	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.2545G>A	12.37:g.124856830C>T	ENSP00000384018:p.Glu849Lys	32	0	0		62	23	0.370968	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	37	CCDS41858.2	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	C	10.89	1.477039	0.26511	0.003788	0.027334	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285;ENST00000458234	T;T;T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48;1.48;1.48	4.77	0.655	0.17839	.	0.491076	0.15915	N	0.238404	T	0.05273	0.0140	N	0.22421	0.69	0.09310	N	0.99999	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.001;0.002	T	0.17868	-1.0355	10	0.27785	T	0.31	-1.4997	4.0561	0.09818	0.2308:0.4004:0.2913:0.0776	.	831;832;849	C9J0Q5;C9J239;C9JFD3	.;.;.	K	849;831;849;832;848;402;831;849	ENSP00000384018:E849K;ENSP00000384202:E831K;ENSP00000348551:E849K;ENSP00000380513:E832K;ENSP00000385618:E402K;ENSP00000400281:E831K;ENSP00000402808:E849K	ENSP00000348551:E849K	E	-	1	0	NCOR2	123422783	0.527000	0.26306	0.001000	0.08648	0.004000	0.04260	2.329000	0.43876	-0.171000	0.10797	-0.310000	0.09108	GAG	C|0.988;T|0.012	0.012	strong		0.701	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		T	124856830	C	T	124856830	3	4	28	1	0	0	0	0	1	0	0	0	10245	835	29	2	5135	2	NCOR2	12	124856830	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	501827	124856830	8995065	478	11981											
LATS2	26524	hgsc.bcm.edu	37	chr13	21563311	21563311	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgcggcatctcctccagcGccgtggggccgtcagcgccg	3	5	15	18	7	2	0	1	0	1	0	4	0	3	0	6	3	2	1	6	3	0	0	rs77919685	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:21563311G>A	ENST00000382592.4	-	4	1013	c.608C>T	c.(607-609)gCg>gTg	p.A203V	LATS2_ENST00000472754.1_5'UTR|LATS2_ENST00000542899.1_Missense_Mutation_p.A203V	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)		CTCCTCCAGCGCCGTGGGGCC	0.692													G|||	103	0.0205671	0.0	0.0216	5008	,	,		14848	0.0248		0.0249	False		,,,				2504	0.0389				p.A203V		Atlas-SNP	.											.	LATS2	176	.	0			c.C608T						PASS	.	G	VAL/ALA	19,4387	25.3+/-52.1	0,19,2184	50	45	46		608	3	0	13	dbSNP_131	46	149,8449	71.0+/-133.6	4,141,4154	yes	missense	LATS2	NM_014572.2	64	4,160,6338	AA,AG,GG		1.733,0.4312,1.2919	benign	203/1089	21563311	168,12836	2203	4299	6502	SO:0001583	missense	26524	exon4			TCCAGCGCCGTGG	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.608C>T	13.37:g.21563311G>A	ENSP00000372035:p.Ala203Val	28	0	0		44	23	0.522727	NM_014572		Missense_Mutation	SNP	ENST00000382592.4	37	CCDS9294.1	43	0.019688644688644688	0	0.0	6	0.016574585635359115	18	0.03146853146853147	19	0.025065963060686015	G	7.001	0.554851	0.13436	0.004312	0.01733	ENSG00000150457	ENST00000382592;ENST00000542899	T;T	0.26957	1.7;1.7	5.05	3.04	0.35103	.	1.593970	0.03426	N	0.207082	T	0.03739	0.0106	N	0.02011	-0.69	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.16928	-1.0386	10	0.52906	T	0.07	.	5.4494	0.16554	0.7351:0.0:0.2649:0.0	.	203	Q9NRM7	LATS2_HUMAN	V	203	ENSP00000372035:A203V;ENSP00000441817:A203V	ENSP00000372035:A203V	A	-	2	0	LATS2	20461311	0.002000	0.14202	0.000000	0.03702	0.015000	0.08874	1.484000	0.35508	0.425000	0.26087	0.485000	0.47835	GCG	G|0.986;A|0.014	0.014	strong		0.692	LATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044102.1			A	21563311	G	A	21563311	3	1	28	1	0	0	0	0	1	0	0	0	8656	1087	38	1	2678	1	LATS2	13	21563311	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10		21563311	93606567	479	11982											
MIPEP	4285	hgsc.bcm.edu	37	chr13	24443512	24443512	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttgccagaagatctctgcTgctgagcaattcttctaaac	10	13	7	11	0	3	3	0	1	3	2	4	3	3	3	1	0	5	3	1	0	4	4	rs149856612	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:24443512T>G	ENST00000382172.3	-	7	960	c.862A>C	c.(862-864)Agc>Cgc	p.S288R		NM_005932.3	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase	288					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)		AGATCTCTGCTGCTGAGCAAT	0.403													T|||	5	0.000998403	0.0	0.0014	5008	,	,		17922	0.0		0.002	False		,,,				2504	0.002				p.S288R		Atlas-SNP	.											.	MIPEP	53	.	0			c.A862C						PASS	.	T	ARG/SER	1,4405	2.1+/-5.4	0,1,2202	88	89	89		862	3.4	0	13	dbSNP_134	89	3,8597	3.0+/-9.4	0,3,4297	yes	missense	MIPEP	NM_005932.3	110	0,4,6499	GG,GT,TT		0.0349,0.0227,0.0308	possibly-damaging	288/714	24443512	4,13002	2203	4300	6503	SO:0001583	missense	4285	exon7			CTCTGCTGCTGAG		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.862A>C	13.37:g.24443512T>G	ENSP00000371607:p.Ser288Arg	83	0	0		55	37	0.672727	NM_005932	Q5JV15|Q5T9Q9|Q96G65	Missense_Mutation	SNP	ENST00000382172.3	37	CCDS9303.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	11.52	1.662789	0.29515	2.27E-4	3.49E-4	ENSG00000027001	ENST00000382172	T	0.07688	3.17	5.9	3.38	0.38709	Neurolysin/Thimet oligopeptidase, domain 2 (1);	0.354147	0.38605	N	0.001630	T	0.13329	0.0323	L	0.54323	1.7	0.09310	N	0.999996	P	0.41498	0.752	P	0.45794	0.493	T	0.03473	-1.1033	10	0.44086	T	0.13	.	12.8495	0.57850	0.0:0.0:0.2573:0.7427	.	288	Q99797	MIPEP_HUMAN	R	288	ENSP00000371607:S288R	ENSP00000371607:S288R	S	-	1	0	MIPEP	23341512	0.998000	0.40836	0.010000	0.14722	0.350000	0.29205	3.528000	0.53524	0.442000	0.26555	0.459000	0.35465	AGC	T|1.000;G|0.000	0.000	strong		0.403	MIPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044169.1			G	24443512	T	G	24443512	3	3	28	1	0	0	0	0	1	0	0	0	9601	1580	55	5	1331	5	MIPEP	13	24443512	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	2880201	24443512	90726366	480	11983											
TRPC4	7223	hgsc.bcm.edu	37	chr13	38225406	38225406	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catgctgtgttcttacccctAttgttccaaaactttctggc	7	16	6	12	0	2	0	0	0	2	0	3	0	3	0	3	1	3	3	3	1	4	6			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:38225406A>G	ENST00000379705.3	-	8	2932	c.2075T>C	c.(2074-2076)aTa>aCa	p.I692T	TRPC4_ENST00000338947.5_Missense_Mutation_p.I519T|TRPC4_ENST00000426868.2_3'UTR|TRPC4_ENST00000379681.3_Missense_Mutation_p.I692T|TRPC4_ENST00000355779.2_Missense_Mutation_p.I692T|TRPC4_ENST00000379673.2_Intron|TRPC4_ENST00000358477.2_Missense_Mutation_p.I692T|TRPC4_ENST00000379679.1_Missense_Mutation_p.I519T|TRPC4_ENST00000447043.1_Missense_Mutation_p.I692T			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	692	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)		TCTTACCCCTATTGTTCCAAA	0.363																																					p.I692T		Atlas-SNP	.											.	TRPC4	389	.	0			c.T2075C						PASS	.						130	127	128					13																	38225406		2203	4300	6503	SO:0001583	missense	7223	exon8			ACCCCTATTGTTC	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.2075T>C	13.37:g.38225406A>G	ENSP00000369027:p.Ile692Thr	254	1	0.00393701		237	112	0.472574	NM_003306	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Missense_Mutation	SNP	ENST00000379705.3	37	CCDS9365.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.097773	0.76870	.	.	ENSG00000133107	ENST00000379705;ENST00000379681;ENST00000338947;ENST00000379679;ENST00000355779;ENST00000358477;ENST00000447043	D;D;D;D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63;-1.63;-1.63;-1.63	5.7	5.7	0.88788	.	0.094472	0.64402	D	0.000001	D	0.83862	0.5346	L	0.42245	1.32	0.80722	D	1	B;P;P;P;P	0.51057	0.336;0.718;0.941;0.506;0.59	B;B;P;B;B	0.51777	0.253;0.215;0.679;0.333;0.25	D	0.83644	0.0152	10	0.40728	T	0.16	-26.2199	15.9668	0.79979	1.0:0.0:0.0:0.0	.	692;692;519;692;692	Q9UBN4-3;Q9UBN4-5;Q9UBN4-6;Q9UBN4-2;Q9UBN4	.;.;.;.;TRPC4_HUMAN	T	692;692;519;519;692;692;692	ENSP00000369027:I692T;ENSP00000369003:I692T;ENSP00000342580:I519T;ENSP00000369001:I519T;ENSP00000348025:I692T;ENSP00000351264:I692T;ENSP00000414316:I692T	ENSP00000342580:I519T	I	-	2	0	TRPC4	37123406	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.310000	0.96267	2.182000	0.69389	0.459000	0.35465	ATA	.	.	none		0.363	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306		G	38225406	A	G	38225406	3	3	28	1	0	0	0	0	1	0	0	0	16595	449	16	3	889	3	TRPC4	13	38225406	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	13781894	38225406	76944472	481	11984											
C13orf23	80209	hgsc.bcm.edu	37	chr13	39588144	39588146	+	In_Frame_Del	DEL	AGC	AGC	-																															gaatttgggttgctggtagaAgcagcagaagagctggtgga																								rs568365521		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	AGC	AGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:39588144_39588146delAGC	ENST00000352251.3	-	11	2076_2078	c.1243_1245delGCT	c.(1243-1245)gctdel	p.A415del	PROSER1_ENST00000484434.3_Intron|PROSER1_ENST00000350125.3_In_Frame_Del_p.A393del	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	415	Ser-rich.																TGCTGGTAGAAGCAGCAGAAGAG	0.522																																					p.415_416del		Pindel,Atlas-Indel	.											.	.	.	.	0			c.1244_1246del						PASS	.																																			SO:0001651	inframe_deletion	80209	exon11			.	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.1243_1245delGCT	13.37:g.39588147_39588149delAGC	ENSP00000332034:p.Ala415del	108	0	.		113	37	0.327	NM_025138	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	In_Frame_Del	DEL	ENST00000352251.3	37	CCDS9368.2																																																																																			.	.	none		0.522	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138		-	39588146	AGC	-	39588144	7	5	28	1	0	1	0	1	0	0	0	0	1723	59	3	0	1601	0	C13orf23	13	39588144	In_Frame_Del	DEL	AGC	TCGA-G8-6914-01A-11D-2210-10	1362738	39588144	75581734	482	11985											
NEK3	4752	hgsc.bcm.edu	37	chr13	52707924	52707924	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgcttctgtttcttcagacAgggggcctttcaagaaccct	8	13	9	11	0	4	2	2	0	2	2	4	2	4	2	2	2	2	2	2	2	2	4	rs200805375		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:52707924A>C	ENST00000400357.2	-	13	2579	c.1286T>G	c.(1285-1287)cTg>cGg	p.L429R	NEK3_ENST00000378101.2_Missense_Mutation_p.L446R|NEK3_ENST00000452082.2_Missense_Mutation_p.L450R|NEK3_ENST00000339406.3_Missense_Mutation_p.L446R			P51956	NEK3_HUMAN	NIMA-related kinase 3	446					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)		TTCTTCAGACAGGGGGCCTTT	0.418																																					p.L446R		Atlas-SNP	.											.	NEK3	41	.	0			c.T1337G						PASS	.	A	ARG/LEU,ARG/LEU	0,3778		0,0,1889	43	40	41		1286,1336	3.8	1	13		41	2,8224		0,2,4111	yes	missense,missense	NEK3	NM_001146099.1,NM_152720.2	102,102	0,2,6000	CC,CA,AA		0.0243,0.0,0.0167	probably-damaging,probably-damaging	429/490,446/507	52707924	2,12002	1889	4113	6002	SO:0001583	missense	4752	exon15			TCAGACAGGGGGC	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.1286T>G	13.37:g.52707924A>C	ENSP00000383210:p.Leu429Arg	104	0	0		72	30	0.416667	NM_002498	A8K2J4|Q5TAP2|Q8J023|Q8WUN5	Missense_Mutation	SNP	ENST00000400357.2	37	CCDS53871.1	.	.	.	.	.	.	.	.	.	.	A	16.05	3.012638	0.54468	0.0	2.43E-4	ENSG00000136098	ENST00000339406;ENST00000378101;ENST00000400357;ENST00000452082;ENST00000547422	T;T;T;T;T	0.78816	-1.03;-1.03;-1.21;-1.11;-1.04	4.99	3.78	0.43462	.	0.141261	0.48767	D	0.000177	D	0.85796	0.5780	M	0.74258	2.255	0.34463	D	0.702004	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.89208	0.3562	10	0.87932	D	0	.	9.7246	0.40324	0.8455:0.0:0.0:0.1545	.	446;450;423	P51956;Q6ZN64;F8VS47	NEK3_HUMAN;.;.	R	446;446;429;450;423	ENSP00000339429:L446R;ENSP00000367341:L446R;ENSP00000383210:L429R;ENSP00000404197:L450R;ENSP00000448716:L423R	ENSP00000339429:L446R	L	-	2	0	NEK3	51605925	1.000000	0.71417	0.998000	0.56505	0.625000	0.37756	5.553000	0.67287	0.807000	0.34208	0.383000	0.25322	CTG	A|0.999;C|0.001	0.001	weak		0.418	NEK3-002	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045047.3			C	52707924	A	C	52707924	3	2	28	1	0	0	0	0	1	0	0	0	10334	188	7	5	191	5	NEK3	13	52707924	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	13119780	52707924	62461954	483	11986											
VPS36	51028	hgsc.bcm.edu	37	chr13	52997751	52997751	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	actaagcagtacacctccgtGagtgacattattccccctcg	10	10	7	14	2	0	2	0	2	0	0	3	2	2	2	4	0	2	2	4	0	3	4	rs148697614	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:52997751G>A	ENST00000378060.4	-	10	825	c.798C>T	c.(796-798)ctC>ctT	p.L266L		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)	266					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)		ACACCTCCGTGAGTGACATTA	0.308													G|||	10	0.00199681	0.0	0.0058	5008	,	,		15634	0.0		0.006	False		,,,				2504	0.0				p.L266L		Atlas-SNP	.											.	VPS36	38	.	0			c.C798T						PASS	.	G		8,4398		0,8,2195	113	116	115		798	-2.3	0.9	13	dbSNP_134	115	29,8571		0,29,4271	no	coding-synonymous	VPS36	NM_016075.2		0,37,6466	AA,AG,GG		0.3372,0.1816,0.2845		266/387	52997751	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	51028	exon10			CTCCGTGAGTGAC	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.798C>T	13.37:g.52997751G>A		10	0	0		16	6	0.375	NM_016075	A8K125|Q3ZCV7|Q5H9S1|Q5VXB6|Q9H8Z5|Q9Y3E3	Silent	SNP	ENST00000378060.4	37	CCDS9434.1																																																																																			G|0.997;A|0.003	0.003	strong		0.308	VPS36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045059.3			A	52997751	G	A	52997751	2	1	28	1	0	0	0	0	0	0	0	1	17219	1277	45	2		2	VPS36	13	52997751	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	289827	52997751	62172127	484	11987											
SLITRK1	114798	hgsc.bcm.edu	37	chr13	84454391	84454391	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccaaaaggttcttgaaagTgttgttctctacagtagcga	11	13	10	7	1	2	1	0	1	2	0	4	2	3	1	1	1	2	4	1	1	5	6	rs150504822		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:84454391T>A	ENST00000377084.2	-	1	2137	c.1252A>T	c.(1252-1254)Act>Tct	p.T418S		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	418				T -> S (in Ref. 4; AAH51738). {ECO:0000305}.	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)		TTCTTGAAAGTGTTGTTCTCT	0.458													T|||	1	0.000199681	0.0	0.0	5008	,	,		21199	0.0		0.001	False		,,,				2504	0.0				p.T418S		Atlas-SNP	.											.	SLITRK1	196	.	0			c.A1252T						PASS	.	T	SER/THR	0,4406		0,0,2203	225	217	220		1252	5.2	1	13	dbSNP_134	220	12,8588	9.1+/-34.3	0,12,4288	yes	missense	SLITRK1	NM_052910.1	58	0,12,6491	AA,AT,TT		0.1395,0.0,0.0923	benign	418/697	84454391	12,12994	2203	4300	6503	SO:0001583	missense	114798	exon1			TGAAAGTGTTGTT	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.1252A>T	13.37:g.84454391T>A	ENSP00000366288:p.Thr418Ser	110	0	0		141	73	0.51773	NM_052910	Q5U5I6|Q96SF9	Missense_Mutation	SNP	ENST00000377084.2	37	CCDS9464.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	13.37	2.215492	0.39102	0.0	0.001395	ENSG00000178235	ENST00000377084	T	0.48201	0.82	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.36799	0.0980	N	0.05177	-0.1	0.51482	D	0.999926	B	0.24963	0.115	B	0.41174	0.349	T	0.36939	-0.9727	10	0.30854	T	0.27	-8.2603	13.9445	0.64075	0.0:0.0:0.0:1.0	.	418	Q96PX8	SLIK1_HUMAN	S	418	ENSP00000366288:T418S	ENSP00000366288:T418S	T	-	1	0	SLITRK1	83352392	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.270000	0.58896	1.985000	0.57927	0.459000	0.35465	ACT	T|0.999;A|0.001	0.001	strong		0.458	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910		A	84454391	T	A	84454391	3	1	28	1	0	0	0	0	1	0	0	0	14757	1696	59	5	842	5	SLITRK1	13	84454391	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	31456640	84454391	30715487	485	11988											
TNFSF13B	10673	hgsc.bcm.edu	37	chr13	108955609	108955609	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttcattgcaggatcttacAcatttgttccatggcttctc	7	17	6	11	0	4	0	1	0	3	0	6	1	5	1	1	2	2	3	1	2	1	6			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:108955609A>G	ENST00000375887.4	+	4	668	c.490A>G	c.(490-492)Aca>Gca	p.T164A	TNFSF13B_ENST00000479435.1_3'UTR|TNFSF13B_ENST00000542136.1_Intron|TNFSF13B_ENST00000430559.1_Missense_Mutation_p.T145A|RNA5SP39_ENST00000411245.1_RNA	NM_006573.4	NP_006564.1	Q9Y275	TN13B_HUMAN	tumor necrosis factor (ligand) superfamily, member 13b	164					B cell costimulation (GO:0031296)|B cell homeostasis (GO:0001782)|cell proliferation (GO:0008283)|immune response (GO:0006955)|immunoglobulin secretion (GO:0048305)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell proliferation (GO:0008284)|positive regulation of germinal center formation (GO:0002636)|positive regulation of T cell proliferation (GO:0042102)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			large_intestine(1)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(23;0.000396)|all_neural(89;0.00256)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00902)|Lung SC(71;0.104)		all cancers(43;0.184)|BRCA - Breast invasive adenocarcinoma(86;0.19)		Belimumab(DB08879)	AGGATCTTACACATTTGTTCC	0.343																																					p.T164A		Atlas-SNP	.											.	TNFSF13B	25	.	0			c.A490G						PASS	.						52	54	53					13																	108955609		2199	4298	6497	SO:0001583	missense	10673	exon4			TCTTACACATTTG	AF136293	CCDS9509.1, CCDS45067.1	13q32-q34	2008-05-14			ENSG00000102524	ENSG00000102524		"Tumor necrosis factor (ligand) superfamily", "CD molecules"	11929	protein-coding gene	gene with protein product		603969		TNFSF20		10331498, 10359578	Standard	NM_006573		Approved	BAFF, THANK, BLYS, TALL-1, TALL1, CD257	uc001vqr.3	Q9Y275	OTTHUMG00000017329	ENST00000375887.4:c.490A>G	13.37:g.108955609A>G	ENSP00000365048:p.Thr164Ala	74	0	0		46	11	0.23913	NM_006573	E0ADT7|Q6FHD6|Q7Z5J2	Missense_Mutation	SNP	ENST00000375887.4	37	CCDS9509.1	.	.	.	.	.	.	.	.	.	.	A	16.50	3.141866	0.57044	.	.	ENSG00000102524	ENST00000430559;ENST00000375887	T;T	0.31769	1.48;1.48	5.95	5.95	0.96441	Tumour necrosis factor (2);Tumour necrosis factor-like (2);	0.101283	0.64402	D	0.000003	T	0.27629	0.0679	L	0.39898	1.24	0.80722	D	1	B;B	0.34399	0.452;0.299	B;B	0.36719	0.231;0.164	T	0.09079	-1.0691	10	0.62326	D	0.03	-22.6206	9.8726	0.41185	0.9173:0.0:0.0827:0.0	.	145;164	Q9Y275-2;Q9Y275	.;TN13B_HUMAN	A	145;164	ENSP00000389540:T145A;ENSP00000365048:T164A	ENSP00000365048:T164A	T	+	1	0	TNFSF13B	107753610	1.000000	0.71417	0.987000	0.45799	0.977000	0.68977	7.198000	0.77823	2.281000	0.76405	0.528000	0.53228	ACA	.	.	none		0.343	TNFSF13B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045739.3			G	108955609	A	G	108955609	3	3	28	1	0	0	0	0	1	0	0	0	16321	159	6	3	504	3	TNFSF13B	13	108955609	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	24501218	108955609	6214269	486	11989											
CDC16	8881	hgsc.bcm.edu	37	chr13	115002275	115002275	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtgaatttttccctccagaAgaaccccaggacatctattg	11	12	7	11	0	1	3	0	1	1	2	3	4	3	4	4	1	1	0	4	1	4	4			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:115002275A>G	ENST00000356221.3	+	3	213	c.105A>G	c.(103-105)gaA>gaG	p.E35E	CDC16_ENST00000252458.6_Splice_Site|CDC16_ENST00000375308.1_Splice_Site|CDC16_ENST00000360383.3_Splice_Site_p.E35E|CDC16_ENST00000375310.1_Splice_Site|CDC16_ENST00000252457.5_Splice_Site|CDC16_ENST00000375312.3_5'UTR			Q13042	CDC16_HUMAN	cell division cycle 16	35					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|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 mitosis (GO:0007088)|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)|spindle (GO:0005819)				endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22	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)			TCCCTCCAGAAGAACCCCAGG	0.413																																					p.E35E		Atlas-SNP	.											.	CDC16	50	.	0			c.A105G						PASS	.						135	135	135					13																	115002275		2203	4300	6503	SO:0001630	splice_region_variant	8881	exon3			TCCAGAAGAACCC	U18291	CCDS9542.2	13q34	2013-01-17	2013-01-17		ENSG00000130177	ENSG00000130177		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1720	protein-coding gene	gene with protein product	"anaphase-promoting complex, subunit 6"	603461	"CDC16 (cell division cycle 16, S. cerevisiae, homolog)", "CDC16 cell division cycle 16 homolog (S. cerevisiae)", "cell division cycle 16 homolog (S. cerevisiae)"			7736578	Standard	NM_001078645		Approved	APC6, ANAPC6, CUT9	uc001vul.1	Q13042	OTTHUMG00000017402	ENST00000356221.3:c.104-1A>G	13.37:g.115002275A>G		91	0	0		84	4	0.047619	NM_003903	A2A365|Q5T8C8|Q96AE6|Q9Y564	Silent	SNP	ENST00000356221.3	37	CCDS9542.2	.	.	.	.	.	.	.	.	.	.	A	9.067	0.995900	0.19043	.	.	ENSG00000130177	ENST00000252457	.	.	.	5.43	2.58	0.30949	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.6961	0.40158	0.2981:0.0:0.7019:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CDC16	114020377	1.000000	0.71417	0.999000	0.59377	0.274000	0.26718	1.778000	0.38614	0.864000	0.35578	-0.146000	0.13790	.	.	.	none		0.413	CDC16-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276737.1	NM_003903	Silent	G	115002275	A	G	115002275	5	3	28	1	0	0	0	0	0	0	1	0	3060	86	3	3	115	3	CDC16	13	115002275	Splice_Site	SNP	A	TCGA-G8-6914-01A-11D-2210-10	6046666	115002275	167603	487	11990											
TEP1	7011	hgsc.bcm.edu	37	chr14	20871901	20871901	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggagagcggggtggccggCgggggtgtctcttggcccgg	2	7	22	10	4	1	1	0	0	1	1	2	2	1	1	2	9	1	0	2	9	0	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:20871901C>T	ENST00000262715.5	-	6	1215	c.1175G>A	c.(1174-1176)cGc>cAc	p.R392H	TEP1_ENST00000556935.1_Intron	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	392	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)		GGGTGGCCGGCGGGGGTGTCT	0.627																																					p.R392H		Atlas-SNP	.											TEP1,NS,carcinoma,-1,1	TEP1	224	1	0			c.G1175A						PASS	.						57	69	65					14																	20871901		2203	4300	6503	SO:0001583	missense	7011	exon6			GGCCGGCGGGGGT		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.1175G>A	14.37:g.20871901C>T	ENSP00000262715:p.Arg392His	64	0	0		55	34	0.618182	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	c	12.44	1.939881	0.34189	.	.	ENSG00000129566	ENST00000262715;ENST00000359243	T	0.19250	2.16	5.54	-2.45	0.06481	TROVE (2);	0.558259	0.18672	N	0.134420	T	0.19446	0.0467	M	0.74258	2.255	0.09310	N	1	B	0.13145	0.007	B	0.10450	0.005	T	0.19811	-1.0294	10	0.51188	T	0.08	-0.5193	5.7588	0.18188	0.0:0.4309:0.2237:0.3453	.	392	Q99973	TEP1_HUMAN	H	392	ENSP00000262715:R392H	ENSP00000262715:R392H	R	-	2	0	TEP1	19941741	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.167000	0.03126	-0.499000	0.06623	-0.119000	0.15052	CGC	.	.	none		0.627	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110		T	20871901	C	T	20871901	3	4	28	1	0	0	0	0	1	0	0	0	15774	768	27	1	6908	1	TEP1	14	20871901	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10		20871901	86477639	488	11991											
DHRS4	10901	hgsc.bcm.edu	37	chr14	24435542	24435542	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccttgctgggcctgaccaaGaccctggccatagagctggc	7	7	13	14	0	0	3	0	1	0	2	0	3	0	3	5	3	2	2	5	3	2	2	rs11556285		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24435542G>T	ENST00000313250.5	+	6	785	c.582G>T	c.(580-582)aaG>aaT	p.K194N	DHRS4_ENST00000558263.1_Intron|DHRS4_ENST00000397075.3_Intron|DHRS4_ENST00000397073.2_Intron|DHRS4_ENST00000558581.1_Missense_Mutation_p.K160N|DHRS4_ENST00000421831.1_Missense_Mutation_p.K142N|DHRS4_ENST00000382761.3_Intron|DHRS4_ENST00000559632.1_Intron|DHRS4_ENST00000543741.2_Intron|DHRS4_ENST00000308178.8_Intron|DHRS4_ENST00000397074.3_Intron	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	194					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)	GCCTGACCAAGACCCTGGCCA	0.502																																					p.K194N		Atlas-SNP	.											.	DHRS4	22	.	0			c.G582T						PASS	.																																			SO:0001583	missense	10901	exon6			GACCAAGACCCTG	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.582G>T	14.37:g.24435542G>T	ENSP00000326219:p.Lys194Asn	685	0	0		751	38	0.0505992	NM_021004	B2RB10|B7WNS9|D3YTB8|E2QRL8|O95162|Q20CR0|Q2LC19|Q2LE81|Q58IU4|Q6E0Y1|Q6UWU3|Q71UQ6|Q8TD03|Q9H3N5|Q9NV08	Missense_Mutation	SNP	ENST00000313250.5	37	CCDS9605.1	.	.	.	.	.	.	.	.	.	.	G	11.78	1.739826	0.30865	.	.	ENSG00000157326	ENST00000313250;ENST00000421831	T;T	0.46063	0.88;0.88	3.53	2.63	0.31362	Short-chain dehydrogenase/reductase, conserved site (1);NAD(P)-binding domain (1);	0.294117	0.30639	N	0.009188	T	0.54838	0.1883	M	0.82056	2.57	0.80722	D	1	B;P	0.39862	0.326;0.692	B;P	0.52823	0.238;0.71	T	0.54609	-0.8268	10	0.72032	D	0.01	.	5.9644	0.19316	0.251:0.0:0.749:0.0	rs11556285;rs11556285	160;194	Q9BTZ2-4;Q9BTZ2	.;DHRS4_HUMAN	N	194;142	ENSP00000326219:K194N;ENSP00000404147:K142N	ENSP00000326219:K194N	K	+	3	2	DHRS4	23505382	1.000000	0.71417	0.998000	0.56505	0.689000	0.40095	1.961000	0.40432	0.599000	0.29845	0.580000	0.79431	AAG	G|0.998;T|0.002	0.002	weak		0.502	DHRS4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071857.3			T	24435542	G	T	24435542	3	4	28	1	0	0	0	0	1	0	0	0	4494	933	33	4	604	4	DHRS4	14	24435542	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	3563641	24435542	82913998	489	11992											
LRRC16B	90668	hgsc.bcm.edu	37	chr14	24534270	24534270	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtttcactttcgccggcccCggagcttcaagggggacagg	6	9	14	12	3	2	0	2	0	0	0	3	2	2	2	3	5	1	2	3	5	1	3	rs117833529	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24534270C>T	ENST00000342740.5	+	33	3338	c.3184C>T	c.(3184-3186)Cgg>Tgg	p.R1062W	LRRC16B_ENST00000334420.7_Missense_Mutation_p.R158W	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	1062				R -> W (in Ref. 2; CAD38886). {ECO:0000305}.		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)		TCGCCGGCCCCGGAGCTTCAA	0.716													C|||	108	0.0215655	0.0015	0.0418	5008	,	,		8025	0.0		0.0368	False		,,,				2504	0.0409				p.R1062W		Atlas-SNP	.											.	LRRC16B	120	.	0			c.C3184T						PASS	.	C	TRP/ARG	23,3751		0,23,1864	19	24	22		3184	2.8	1	14	dbSNP_132	22	255,7637		2,251,3693	yes	missense	LRRC16B	NM_138360.3	101	2,274,5557	TT,TC,CC		3.2311,0.6094,2.383	probably-damaging	1062/1373	24534270	278,11388	1887	3946	5833	SO:0001583	missense	90668	exon33			CGGCCCCGGAGCT	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.3184C>T	14.37:g.24534270C>T	ENSP00000340467:p.Arg1062Trp	21	0	0		41	19	0.463415	NM_138360	Q8TEF7|Q96HS9	Missense_Mutation	SNP	ENST00000342740.5	37	CCDS32054.1	46	0.021062271062271064	2	0.0040650406504065045	19	0.052486187845303865	0	0.0	25	0.032981530343007916	C	12.56	1.973870	0.34848	0.006094	0.032311	ENSG00000186648	ENST00000342740;ENST00000334420	T;T	0.60797	1.2;0.16	4.66	2.77	0.32553	.	0.254810	0.20948	N	0.082818	T	0.29389	0.0732	L	0.59436	1.845	0.28233	N	0.926034	D;D	0.89917	1.0;0.999	D;P	0.80764	0.994;0.876	T	0.48725	-0.9010	10	0.87932	D	0	-13.2657	9.764	0.40550	0.3756:0.6244:0.0:0.0	.	158;1062	Q8ND23-2;Q8ND23	.;LR16B_HUMAN	W	1062;158	ENSP00000340467:R1062W;ENSP00000334701:R158W	ENSP00000334701:R158W	R	+	1	2	LRRC16B	23604110	0.999000	0.42202	1.000000	0.80357	0.602000	0.36980	1.625000	0.37029	0.375000	0.24679	-0.348000	0.07805	CGG	C|0.976;T|0.024	0.024	strong		0.716	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360		T	24534270	C	T	24534270	3	4	28	1	0	0	0	0	1	0	0	0	8981	643	23	1	3314	1	LRRC16B	14	24534270	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	98728	24534270	82815270	490	11993											
FITM1	161247	hgsc.bcm.edu	37	chr14	24600828	24600828	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccggggcccgaatccaggCactgctgggctgcctgctca	5	6	15	15	2	1	0	1	0	0	0	2	1	2	0	4	5	3	4	4	5	1	0	rs147792464		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24600828C>T	ENST00000267426.5	+	1	345	c.56C>T	c.(55-57)gCa>gTa	p.A19V	FITM1_ENST00000559294.1_5'Flank|RP11-468E2.6_ENST00000558325.1_Silent_p.G206G	NM_203402.2	NP_981947.1	A5D6W6	FITM1_HUMAN	fat storage-inducing transmembrane protein 1	19					lipid particle organization (GO:0034389)|positive regulation of sequestering of triglyceride (GO:0010890)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	11						CGAATCCAGGCACTGCTGGGC	0.672																																					p.A19V		Atlas-SNP	.											.	FITM1	25	.	0			c.C56T						PASS	.	C	VAL/ALA	0,4406		0,0,2203	18	23	21		56	1.6	0.9	14	dbSNP_134	21	6,8592		0,6,4293	yes	missense	FITM1	NM_203402.2	64	0,6,6496	TT,TC,CC		0.0698,0.0,0.0461	benign	19/293	24600828	6,12998	2203	4299	6502	SO:0001583	missense	161247	exon1			TCCAGGCACTGCT		CCDS9611.1	14q12	2009-07-09			ENSG00000139914	ENSG00000139914			33714	protein-coding gene	gene with protein product	"fat-inducing transcript 1"	612028				18160536	Standard	NM_203402		Approved	FIT1	uc001wmf.2	A5D6W6	OTTHUMG00000133476	ENST00000267426.5:c.56C>T	14.37:g.24600828C>T	ENSP00000267426:p.Ala19Val	123	0	0		101	46	0.455446	NM_203402	Q8IUQ7	Missense_Mutation	SNP	ENST00000267426.5	37	CCDS9611.1	.	.	.	.	.	.	.	.	.	.	c	7.996	0.754445	0.15778	0.0	6.98E-4	ENSG00000139914	ENST00000267426	.	.	.	4.6	1.58	0.23477	.	0.188323	0.32655	N	0.005818	T	0.13030	0.0316	N	0.03608	-0.345	0.25699	N	0.985606	B	0.02656	0.0	B	0.01281	0.0	T	0.20240	-1.0281	9	0.21540	T	0.41	-7.9479	5.6671	0.17700	0.0:0.6485:0.0:0.3515	.	19	A5D6W6	FITM1_HUMAN	V	19	.	ENSP00000267426:A19V	A	+	2	0	FITM1	23670668	0.001000	0.12720	0.860000	0.33809	0.460000	0.32559	0.514000	0.22786	0.567000	0.29293	-0.369000	0.07265	GCA	C|1.000;T|0.000	0.000	weak		0.672	FITM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257366.1	NM_203402		T	24600828	C	T	24600828	3	4	28	1	0	0	0	0	1	0	0	0	5906	710	25	2	58	2	FITM1	14	24600828	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	66558	24600828	82748712	491	11994											
MBIP	51562	hgsc.bcm.edu	37	chr14	36784062	36784062	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cccatttctgttcttcctatCtcttcaacagcagttgtatt	7	18	4	12	0	4	0	1	0	3	0	6	0	5	0	2	0	2	4	2	0	3	8			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:36784062C>G	ENST00000416007.4	-	3	396	c.309G>C	c.(307-309)gaG>gaC	p.E103D	MBIP_ENST00000318473.7_Missense_Mutation_p.E103D|MBIP_ENST00000359527.7_Missense_Mutation_p.E103D|MBIP_ENST00000603913.1_5'Flank	NM_001144891.1|NM_016586.2	NP_001138363.1|NP_057670.2	Q9NS73	MBIP1_HUMAN	MAP3K12 binding inhibitory protein 1	103					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|inactivation of MAPK activity involved in osmosensory signaling pathway (GO:0000173)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|protein kinase inhibitor activity (GO:0004860)			breast(2)|large_intestine(1)|lung(5)	8	all_cancers(3;1.55e-52)|all_epithelial(1;2.69e-62)|Breast(36;0.0505)|Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)		Lung(8;1.28e-07)|LUAD - Lung adenocarcinoma(9;3e-07)|Epithelial(34;0.0303)|all cancers(34;0.0781)	GBM - Glioblastoma multiforme(112;0.0191)		TTCTTCCTATCTCTTCAACAG	0.378																																					p.E103D		Atlas-SNP	.											.	MBIP	25	.	0			c.G309C						PASS	.						131	120	124					14																	36784062		2201	4300	6501	SO:0001583	missense	51562	exon3			TCCTATCTCTTCA	BC016821	CCDS9658.1, CCDS45096.1	14q13.2	2005-01-10			ENSG00000151332	ENSG00000151332			20427	protein-coding gene	gene with protein product		609431				10801814	Standard	NM_016586		Approved		uc001wtm.2	Q9NS73	OTTHUMG00000140222	ENST00000416007.4:c.309G>C	14.37:g.36784062C>G	ENSP00000399718:p.Glu103Asp	119	0	0		148	57	0.385135	NM_016586	Q86TZ2|Q96AS5|Q9BS93|Q9NZE1	Missense_Mutation	SNP	ENST00000416007.4	37	CCDS9658.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	6.648|6.648	0.488059|0.488059	0.12641|0.12641	.|.	.|.	ENSG00000151332|ENSG00000151332	ENST00000553977|ENST00000416007;ENST00000318473;ENST00000359527;ENST00000396329;ENST00000553298;ENST00000553549;ENST00000556427	.|T;T;T	.|0.46063	.|0.88;0.88;0.88	6.17|6.17	0.564|0.564	0.17302|0.17302	.|.	.|0.715788	.|0.14682	.|N	.|0.304691	T|T	0.24275|0.24275	0.0588|0.0588	L|L	0.36672|0.36672	1.1|1.1	0.25366|0.25366	N|N	0.988744|0.988744	.|B;B;B	.|0.06786	.|0.001;0.001;0.001	.|B;B;B	.|0.04013	.|0.001;0.001;0.001	T|T	0.15752|0.15752	-1.0426|-1.0426	5|10	.|0.21014	.|T	.|0.42	-2.0398|-2.0398	1.586|1.586	0.02644|0.02644	0.2059:0.402:0.2295:0.1626|0.2059:0.402:0.2295:0.1626	.|.	.|103;103;103	.|Q9NS73-5;Q9NS73-3;Q9NS73	.|.;.;MBIP1_HUMAN	H|D	100|103;103;103;110;63;82;61	.|ENSP00000399718:E103D;ENSP00000324444:E103D;ENSP00000352517:E103D	.|ENSP00000324444:E103D	D|E	-|-	1|3	0|2	MBIP|MBIP	35853813|35853813	0.597000|0.597000	0.26874|0.26874	0.995000|0.995000	0.50966|0.50966	0.821000|0.821000	0.46438|0.46438	0.313000|0.313000	0.19415|0.19415	0.089000|0.089000	0.17243|0.17243	-0.211000|-0.211000	0.12701|0.12701	GAT|GAG	.	.	none		0.378	MBIP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276685.2	NM_016586		G	36784062	C	G	36784062	3	3	28	1	0	0	0	0	1	0	0	0	9358	912	32	4	753	4	MBIP	14	36784062	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	12183234	36784062	70565478	492	11995											
NID2	22795	hgsc.bcm.edu	37	chr14	52509063	52509063	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tttcccattcactcggtgagGtgcccctaaaagacagcaaa	12	9	8	12	1	1	2	1	1	0	1	3	2	2	2	3	2	2	1	3	2	3	3	rs17831525	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:52509063G>A	ENST00000216286.5	-	7	1584	c.1585C>T	c.(1585-1587)Cct>Tct	p.P529S	NID2_ENST00000541773.1_Missense_Mutation_p.P476S	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	529	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.		P -> S (in dbSNP:rs17831525).		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)					ACTCGGTGAGGTGCCCCTAAA	0.512													g|||	53	0.0105831	0.0008	0.0173	5008	,	,		21125	0.0		0.0398	False		,,,				2504	0.0				p.P529S		Atlas-SNP	.											.	NID2	201	.	0			c.C1585T						PASS	.	G	SER/PRO	34,4372	38.4+/-70.7	0,34,2169	104	105	105		1585	6.2	1	14	dbSNP_123	105	269,8331	103.1+/-164.3	7,255,4038	yes	missense	NID2	NM_007361.3	74	7,289,6207	AA,AG,GG		3.1279,0.7717,2.3297	probably-damaging	529/1376	52509063	303,12703	2203	4300	6503	SO:0001583	missense	22795	exon7			GGTGAGGTGCCCC	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.1585C>T	14.37:g.52509063G>A	ENSP00000216286:p.Pro529Ser	64	0	0		46	27	0.586957	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	37	CCDS9706.1	38	0.0173992673992674	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	28	0.036939313984168866	G	19.57	3.851885	0.71719	0.007717	0.031279	ENSG00000087303	ENST00000216286;ENST00000541773;ENST00000395707	T;T	0.53640	0.61;0.61	6.16	6.16	0.99307	G2 nidogen/fibulin G2F (3);Green fluorescent protein-like (1);	0.147145	0.64402	D	0.000007	T	0.37945	0.1022	M	0.79123	2.44	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	P;D;D	0.69479	0.893;0.964;0.934	T	0.60424	-0.7266	10	0.72032	D	0.01	.	16.2426	0.82423	0.0:0.1689:0.8311:0.0	rs17831525;rs52794399;rs17831525	476;531;529	Q14112-2;Q5CZI2;Q14112	.;.;NID2_HUMAN	S	529;476;531	ENSP00000216286:P529S;ENSP00000443730:P476S	ENSP00000216286:P529S	P	-	1	0	NID2	51578813	1.000000	0.71417	0.970000	0.41538	0.553000	0.35397	5.969000	0.70422	2.937000	0.99478	0.650000	0.86243	CCT	G|0.978;A|0.022	0.022	strong		0.512	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1			A	52509063	G	A	52509063	3	1	28	1	0	0	0	0	1	0	0	0	10424	1261	44	2	2606	2	NID2	14	52509063	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	15725001	52509063	54840477	493	11996											
PAPLN	89932	hgsc.bcm.edu	37	chr14	73726151	73726151	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggtcgggctcagggccccAcgactgcagacacagtcctc	7	5	13	16	3	1	1	1	0	0	1	4	2	2	1	3	3	1	2	3	3	0	0	rs17182244	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:73726151A>G	ENST00000554301.1	+	15	2046	c.1883A>G	c.(1882-1884)cAc>cGc	p.H628R	PAPLN_ENST00000555445.1_Missense_Mutation_p.H628R|PAPLN_ENST00000427855.1_Missense_Mutation_p.H628R|PAPLN_ENST00000381166.3_Missense_Mutation_p.H628R|PAPLN_ENST00000340738.5_Missense_Mutation_p.H601R			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	628			H -> R (in dbSNP:rs17182244).			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)		TCAGGGCCCCACGACTGCAGA	0.711													A|||	55	0.0109824	0.0015	0.0115	5008	,	,		15850	0.0		0.0408	False		,,,				2504	0.0041				p.H601R		Atlas-SNP	.											.	PAPLN	180	.	0			c.A1802G						PASS	.	A	ARG/HIS	33,4373		0,33,2170	20	24	23		1802	-5.5	0	14	dbSNP_123	23	320,8268		4,312,3978	yes	missense	PAPLN	NM_173462.3	29	4,345,6148	GG,GA,AA		3.7261,0.749,2.7166	benign	601/1252	73726151	353,12641	2203	4294	6497	SO:0001583	missense	89932	exon15			GGCCCCACGACTG	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.1883A>G	14.37:g.73726151A>G	ENSP00000451803:p.His628Arg	135	0	0		124	60	0.483871	NM_173462	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Missense_Mutation	SNP	ENST00000554301.1	37		41	0.018772893772893772	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	33	0.04353562005277045	A	4.734	0.136524	0.09032	0.00749	0.037261	ENSG00000100767	ENST00000340738;ENST00000427855;ENST00000381166;ENST00000554301;ENST00000555445	T;T;T;T;T	0.61627	0.09;0.09;0.39;0.09;0.23	4.23	-5.49	0.02584	.	.	.	.	.	T	0.03871	0.0109	N	0.00436	-1.5	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.31081	-0.9956	9	0.11182	T	0.66	.	8.8397	0.35135	0.6381:0.1121:0.2498:0.0	rs17182244;rs17182244	628;628;601	O95428-5;O95428;O95428-6	.;PPN_HUMAN;.	R	601;628;628;628;628	ENSP00000345395:H601R;ENSP00000403403:H628R;ENSP00000370558:H628R;ENSP00000451803:H628R;ENSP00000451729:H628R	ENSP00000216658:H628R	H	+	2	0	PAPLN	72795904	0.000000	0.05858	0.000000	0.03702	0.737000	0.42083	-1.238000	0.02919	-0.688000	0.05155	0.379000	0.24179	CAC	A|0.976;G|0.024	0.024	strong		0.711	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462		G	73726151	A	G	73726151	3	3	28	1	0	0	0	0	1	0	0	0	11437	159	6	3	1856	3	PAPLN	14	73726151	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	21217088	73726151	33623389	494	11997											
ENTPD5	957	hgsc.bcm.edu	37	chr14	74444009	74444009	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acacctctcccaccttcgtcGgatccatccatgatgctaac	9	10	5	17	2	1	1	0	1	1	0	6	2	3	2	5	1	2	1	5	1	1	2	rs143835358	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:74444009G>A	ENST00000334696.6	-	7	829	c.510C>T	c.(508-510)tcC>tcT	p.S170S	ENTPD5_ENST00000557325.1_Silent_p.S170S	NM_001249.2	NP_001240.1	O75356	ENTP5_HUMAN	ectonucleoside triphosphate diphosphohydrolase 5	170					'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)		CACCTTCGTCGGATCCATCCA	0.453													G|||	5	0.000998403	0.0	0.0	5008	,	,		17509	0.0		0.005	False		,,,				2504	0.0				p.S170S		Atlas-SNP	.											.	ENTPD5	26	.	0			c.C510T						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	113	99	103		510	2.5	1	14	dbSNP_134	103	17,8583	11.9+/-42.8	1,15,4284	no	coding-synonymous	ENTPD5	NM_001249.2		1,17,6485	AA,AG,GG		0.1977,0.0454,0.1461		170/429	74444009	19,12987	2203	4300	6503	SO:0001819	synonymous_variant	957	exon7			TTCGTCGGATCCA	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.510C>T	14.37:g.74444009G>A		25	0	0		43	20	0.465116	NM_001249	A1L4C5|Q96RX0	Silent	SNP	ENST00000334696.6	37	CCDS9825.1																																																																																			G|0.998;A|0.002	0.002	strong		0.453	ENTPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412637.1	NM_001249		A	74444009	G	A	74444009	2	1	28	1	0	0	0	0	0	0	0	1	5144	1103	39	1		1	ENTPD5	14	74444009	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	717858	74444009	32905531	495	11998											
TTLL5	23093	hgsc.bcm.edu	37	chr14	76232469	76232469	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agtgaagaggaggaagaagtCgcattagataatgaagatga	18	7	14	2	1	0	7	0	3	0	4	1	9	0	9	0	2	0	1	0	2	6	2	rs61741261	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:76232469C>T	ENST00000298832.9	+	20	1978	c.1773C>T	c.(1771-1773)gtC>gtT	p.V591V	TTLL5_ENST00000556893.1_Silent_p.V142V|TTLL5_ENST00000554510.1_Silent_p.V100V|TTLL5_ENST00000557636.1_Silent_p.V605V|TTLL5_ENST00000555422.1_3'UTR	NM_015072.4	NP_055887.3	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	591					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)		AGGAAGAAGTCGCATTAGATA	0.398													c|||	6	0.00119808	0.0	0.0	5008	,	,		16548	0.0		0.006	False		,,,				2504	0.0				p.V591V		Atlas-SNP	.											.	TTLL5	102	.	0			c.C1773T						PASS	.			0,4406		0,0,2203	86	82	83		1773	-3.9	0.1	14	dbSNP_129	83	17,8583	13.3+/-46.6	0,17,4283	no	coding-synonymous	TTLL5	NM_015072.4		0,17,6486	TT,TC,CC		0.1977,0.0,0.1307		591/1282	76232469	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	23093	exon20			AGAAGTCGCATTA	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.1773C>T	14.37:g.76232469C>T		61	0	0		47	22	0.468085	NM_015072	B9EGH8|B9EGH9|Q9BUB0|Q9H0G4|Q9H7W2|Q9P1V5|Q9UPZ4	Silent	SNP	ENST00000298832.9	37	CCDS32124.1																																																																																			C|0.998;T|0.002	0.002	strong		0.398	TTLL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414453.1	NM_015072		T	76232469	C	T	76232469	2	4	28	1	0	0	0	0	0	0	0	1	16745	871	31	1		1	TTLL5	14	76232469	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1788460	76232469	31117071	496	11999											
GSTZ1	2954	hgsc.bcm.edu	37	chr14	77793237	77793237	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccatcaatctcataaaggatGggggccaacaggtaagaagg	15	6	12	8	0	2	1	2	0	1	1	3	2	2	2	2	5	1	1	2	5	6	2	rs7972	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:77793237G>A	ENST00000556627.1	+	3	255	c.124G>A	c.(124-126)Ggg>Agg	p.G42R	GSTZ1_ENST00000554279.1_Missense_Mutation_p.G42R|GSTZ1_ENST00000557053.1_5'UTR|GSTZ1_ENST00000349555.3_Missense_Mutation_p.G42R|GSTZ1_ENST00000216465.5_Missense_Mutation_p.G42R|GSTZ1_ENST00000393734.1_5'UTR|GSTZ1_ENST00000361389.4_5'UTR|GSTZ1_ENST00000557639.1_5'UTR|GSTZ1_ENST00000553586.1_Missense_Mutation_p.G43R			O43708	MAAI_HUMAN	glutathione S-transferase zeta 1	42	GST N-terminal.		R -> G (in allele GSTZ1*B and allele GSTZ1*C; dbSNP:rs7972). {ECO:0000269|PubMed:10373324, ECO:0000269|PubMed:10739172, ECO:0000269|PubMed:12508121, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9417084, ECO:0000269|PubMed:9925947, ECO:0000269|Ref.6, ECO:0000269|Ref.7, ECO:0000269|Ref.9}.		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)	CATAAAGGATGGGGGCCAACA	0.567													G|||	153	0.0305511	0.0038	0.0274	5008	,	,		21279	0.0		0.1113	False		,,,				2504	0.0174				p.G42R		Atlas-SNP	.											.	GSTZ1	35	.	0			c.G124A						PASS	.	G	,ARG/GLY,ARG/GLY	78,4326	62.9+/-100.1	0,78,2124	43	35	37		,124,124	5.6	1	14	dbSNP_52	37	707,7893	164.3+/-216.7	41,625,3634	yes	utr-5,missense,missense	GSTZ1	NM_001513.3,NM_145870.2,NM_145871.2	,125,125	41,703,5758	AA,AG,GG		8.2209,1.7711,6.0366	,benign,benign	,42/217,42/175	77793237	785,12219	2202	4300	6502	SO:0001583	missense	2954	exon3			AAGGATGGGGGCC	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.124G>A	14.37:g.77793237G>A	ENSP00000450487:p.Gly42Arg	38	0	0		54	22	0.407407	NM_145871	A6NED0|A6NNB8|A8MWD7|B2RCK3|O15308|O75430|Q6IB17|Q7Z610|Q9BV63	Missense_Mutation	SNP	ENST00000556627.1	37		109	0.04990842490842491	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	96	0.1266490765171504	G	28.3	4.909294	0.92107	0.017711	0.082209	ENSG00000100577	ENST00000216465;ENST00000554279;ENST00000349555;ENST00000556627;ENST00000553586	T;T;T;T;T	0.18810	4.45;3.14;2.19;2.36;4.44	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.00637	0.0021	.	.	.	0.09310	P	1.0	D	0.89917	1.0	D	0.83275	0.996	T	0.00335	-1.1808	8	0.72032	D	0.01	-6.8373	16.4581	0.84029	0.0:0.0:1.0:0.0	rs7972;rs1128968;rs2266617;rs3177429;rs3186383;rs11551317;rs17353483;rs17750846;rs52835763;rs58270987;rs7972	42	A6NED0	.	R	42;42;42;42;43	ENSP00000216465:G42R;ENSP00000452498:G42R;ENSP00000314404:G42R;ENSP00000450487:G42R;ENSP00000451976:G43R	ENSP00000216465:G42R	G	+	1	0	GSTZ1	76862990	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	5.705000	0.68355	2.614000	0.88457	0.655000	0.94253	GGG	G|0.949;A|0.051	0.051	strong		0.567	GSTZ1-012	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000414090.1	NM_145870		A	77793237	G	A	77793237	3	1	28	1	0	0	0	0	1	0	0	0	6857	1348	47	2	134	2	GSTZ1	14	77793237	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1560768	77793237	29556303	497	12000											
TMED8	283578	hgsc.bcm.edu	37	chr14	77810133	77810133	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	agactggatcataacgatgtCcccagacctctgtggaactt	11	10	9	11	1	2	2	1	0	1	2	3	5	3	4	3	2	2	0	3	2	2	2	rs142882254	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:77810133C>T	ENST00000216468.7	-	4	416	c.361G>A	c.(361-363)Gac>Aac	p.D121N		NM_213601.1	NP_998766.1	Q6PL24	TMED8_HUMAN	transmembrane emp24 protein transport domain containing 8	121					transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)	15			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)		ATAACGATGTCCCCAGACCTC	0.438													C|||	5	0.000998403	0.0	0.0	5008	,	,		19285	0.0		0.005	False		,,,				2504	0.0				p.D121N		Atlas-SNP	.											.	TMED8	27	.	0			c.G361A						PASS	.	C	ASN/ASP	2,4404	4.2+/-10.8	0,2,2201	143	136	138		361	6	1	14	dbSNP_134	138	33,8567	22.2+/-67.0	0,33,4267	yes	missense	TMED8	NM_213601.1	23	0,35,6468	TT,TC,CC		0.3837,0.0454,0.2691	probably-damaging	121/326	77810133	35,12971	2203	4300	6503	SO:0001583	missense	283578	exon4			CGATGTCCCCAGA	AK095650	CCDS32125.1	14q24.3	2005-08-26	2005-08-26	2005-01-07		ENSG00000100580			18633	protein-coding gene	gene with protein product			"family with sequence similarity 15, member B", "transmembrane emp24 domain containing 8"	FAM15B			Standard	NM_213601		Approved		uc001xto.1	Q6PL24		ENST00000216468.7:c.361G>A	14.37:g.77810133C>T	ENSP00000216468:p.Asp121Asn	101	0	0		85	37	0.435294	NM_213601	B3KTI6|Q3MJB0|Q9P1V9	Missense_Mutation	SNP	ENST00000216468.7	37	CCDS32125.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	29.0	4.971209	0.92919	4.54E-4	0.003837	ENSG00000100580	ENST00000216468	T	0.29142	1.58	5.98	5.98	0.97165	.	0.051631	0.85682	D	0.000000	T	0.39682	0.1087	L	0.34521	1.04	0.52099	D	0.999945	D	0.89917	1.0	D	0.83275	0.996	T	0.10359	-1.0633	10	0.36615	T	0.2	-2.0029	20.4293	0.99080	0.0:1.0:0.0:0.0	.	121	Q6PL24	TMED8_HUMAN	N	121	ENSP00000216468:D121N	ENSP00000216468:D121N	D	-	1	0	TMED8	76879886	0.999000	0.42202	1.000000	0.80357	0.988000	0.76386	5.026000	0.64103	2.833000	0.97629	0.655000	0.94253	GAC	C|0.996;T|0.004	0.004	strong		0.438	TMED8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414100.1	NM_213601		T	77810133	C	T	77810133	3	4	28	1	0	0	0	0	1	0	0	0	16026	855	30	2	627	2	TMED8	14	77810133	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	16896	77810133	29539407	498	12001											
C14orf159	80017	hgsc.bcm.edu	37	chr14	91666131	91666131	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggtggccatagagcgtgcCggaagagctgctgatggcaa	9	7	16	9	2	0	3	0	1	0	2	0	4	0	4	2	4	4	3	2	4	3	1	rs28481732	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:91666131C>T	ENST00000523771.1	+	11	1914	c.1311C>T	c.(1309-1311)gcC>gcT	p.A437A	C14orf159_ENST00000521077.2_Silent_p.A442A|C14orf159_ENST00000428926.2_Silent_p.A437A|C14orf159_ENST00000522322.1_Silent_p.A437A|C14orf159_ENST00000520328.1_Silent_p.A425A|C14orf159_ENST00000412671.2_Silent_p.A442A|C14orf159_ENST00000518868.1_Silent_p.A442A|C14orf159_ENST00000256324.10_Silent_p.A442A|C14orf159_ENST00000525393.2_Silent_p.A313A|C14orf159_ENST00000523816.1_Silent_p.A437A			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	437						mitochondrion (GO:0005739)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		TAGAGCGTGCCGGAAGAGCTG	0.512													C|||	121	0.0241613	0.0658	0.0303	5008	,	,		19104	0.0		0.0089	False		,,,				2504	0.0041				p.A442A		Atlas-SNP	.											.	C14orf159	57	.	0			c.C1326T						PASS	.	C	,,,,	223,4183	134.9+/-171.1	8,207,1988	125	119	121		1311,1311,1326,1275,1311	-9.8	0	14	dbSNP_125	121	112,8488	59.5+/-121.1	0,112,4188	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	C14orf159	NM_001102366.1,NM_001102367.1,NM_001102368.1,NM_001102369.1,NM_024952.6	,,,,	8,319,6176	TT,TC,CC		1.3023,5.0613,2.5757	,,,,	437/617,437/617,442/622,425/565,437/617	91666131	335,12671	2203	4300	6503	SO:0001819	synonymous_variant	80017	exon11			GCGTGCCGGAAGA	AK097294	CCDS32141.1, CCDS41979.1, CCDS45150.1, CCDS66693.1, CCDS73677.1	14q32.11	2012-09-26			ENSG00000133943	ENSG00000133943			20498	protein-coding gene	gene with protein product							Standard	NM_001102367		Approved	FLJ39975	uc001xze.2	Q7Z3D6	OTTHUMG00000164980	ENST00000523771.1:c.1311C>T	14.37:g.91666131C>T		122	0	0		138	69	0.5	NM_001102368	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Silent	SNP	ENST00000523771.1	37	CCDS32141.1	41	0.018772893772893772	24	0.04878048780487805	11	0.03038674033149171	0	0.0	6	0.0079155672823219	C	0.268	-0.994827	0.02145	0.050613	0.013023	ENSG00000133943	ENST00000522816	.	.	.	5.05	-9.84	0.00479	.	.	.	.	.	T	0.05686	0.0149	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33979	-0.9847	4	.	.	.	.	0.4736	0.00536	0.1844:0.1765:0.3025:0.3367	rs28481732	.	.	.	L	38	.	.	P	+	2	0	C14orf159	90735884	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.872000	0.01639	-2.087000	0.00862	-2.357000	0.00240	CCG	C|0.977;T|0.023	0.023	strong		0.512	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952		T	91666131	C	T	91666131	2	4	28	1	0	0	0	0	0	0	0	1	1757	639	23	1		1	C14orf159	14	91666131	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	13855998	91666131	15683409	499	12002											
C14orf159	80017	hgsc.bcm.edu	37	chr14	91666248	91666248	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attcctggaatctcatcaacTggtaagtatggagtactggg	11	12	11	7	0	2	0	2	0	1	0	4	2	3	2	1	4	2	3	1	4	5	4	rs28715808	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:91666248T>C	ENST00000523771.1	+	11	2031	c.1428T>C	c.(1426-1428)acT>acC	p.T476T	C14orf159_ENST00000521077.2_Splice_Site_p.T481T|C14orf159_ENST00000428926.2_Splice_Site_p.T476T|C14orf159_ENST00000522322.1_Splice_Site_p.T476T|C14orf159_ENST00000520328.1_Splice_Site_p.T464T|C14orf159_ENST00000412671.2_Splice_Site_p.T481T|C14orf159_ENST00000518868.1_Splice_Site_p.T481T|C14orf159_ENST00000256324.10_Splice_Site_p.T481T|C14orf159_ENST00000525393.2_Splice_Site_p.T352T|C14orf159_ENST00000523816.1_Splice_Site_p.T476T			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	476						mitochondrion (GO:0005739)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		TCTCATCAACTGGTAAGTATG	0.458													T|||	181	0.0361422	0.1067	0.0346	5008	,	,		22154	0.0		0.0109	False		,,,				2504	0.0051				p.T481T		Atlas-SNP	.											.	C14orf159	57	.	0			c.T1443C						PASS	.	T	,,,,	337,4069	176.9+/-206.0	16,305,1882	151	142	145		1428,1428,1443,1392,1428	-2.7	0.1	14	dbSNP_125	145	117,8483	61.0+/-122.8	0,117,4183	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	C14orf159	NM_001102366.1,NM_001102367.1,NM_001102368.1,NM_001102369.1,NM_024952.6	,,,,	16,422,6065	CC,CT,TT		1.3605,7.6487,3.4907	,,,,	476/617,476/617,481/622,464/565,476/617	91666248	454,12552	2203	4300	6503	SO:0001630	splice_region_variant	80017	exon11			ATCAACTGGTAAG	AK097294	CCDS32141.1, CCDS41979.1, CCDS45150.1, CCDS66693.1, CCDS73677.1	14q32.11	2012-09-26			ENSG00000133943	ENSG00000133943			20498	protein-coding gene	gene with protein product							Standard	NM_001102367		Approved	FLJ39975	uc001xze.2	Q7Z3D6	OTTHUMG00000164980	ENST00000523771.1:c.1429+1T>C	14.37:g.91666248T>C		125	0	0		120	60	0.5	NM_001102368	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Silent	SNP	ENST00000523771.1	37	CCDS32141.1	60	0.027472527472527472	41	0.08333333333333333	12	0.03314917127071823	0	0.0	7	0.009234828496042216	T	0.894	-0.724442	0.03158	0.076487	0.013605	ENSG00000133943	ENST00000522816	.	.	.	5.1	-2.71	0.05986	.	.	.	.	.	T	0.00967	0.0032	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.22173	-1.0224	3	.	.	.	.	2.29	0.04136	0.3649:0.0777:0.3565:0.2009	rs28715808	.	.	.	P	77	.	.	L	+	2	0	C14orf159	90736001	0.990000	0.36364	0.051000	0.19133	0.053000	0.15095	0.237000	0.17985	-0.360000	0.08138	-0.461000	0.05368	CTG	T|0.967;C|0.033	0.033	strong		0.458	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952	Silent	C	91666248	T	C	91666248	5	2	28	1	0	0	0	0	0	0	1	0	1757	1594	55	3	1477	3	C14orf159	14	91666248	Splice_Site	SNP	T	TCGA-G8-6914-01A-11D-2210-10	117	91666248	15683292	500	12003											
C14orf159	80017	hgsc.bcm.edu	37	chr14	91681784	91681784	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaggctatgccctggcctgcGcactctacatcctgtactca	7	10	9	15	1	2	0	1	0	1	0	3	1	3	0	3	2	4	3	3	2	3	3	rs115874122	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:91681784G>A	ENST00000523771.1	+	13	2188	c.1585G>A	c.(1585-1587)Gca>Aca	p.A529T	C14orf159_ENST00000521077.2_Missense_Mutation_p.A494T|C14orf159_ENST00000428926.2_Missense_Mutation_p.A529T|C14orf159_ENST00000522322.1_Missense_Mutation_p.A529T|C14orf159_ENST00000520328.1_Missense_Mutation_p.A477T|C14orf159_ENST00000412671.2_Missense_Mutation_p.A534T|C14orf159_ENST00000518868.1_Missense_Mutation_p.A534T|C14orf159_ENST00000256324.10_Missense_Mutation_p.A534T|C14orf159_ENST00000525393.2_Missense_Mutation_p.A405T|C14orf159_ENST00000523816.1_Missense_Mutation_p.A529T			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	529						mitochondrion (GO:0005739)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		CCTGGCCTGCGCACTCTACAT	0.542													G|||	20	0.00399361	0.0	0.0245	5008	,	,		17334	0.001		0.001	False		,,,				2504	0.001				p.A534T		Atlas-SNP	.											.	C14orf159	57	.	0			c.G1600A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	2,4404	4.2+/-10.8	0,2,2201	132	118	123		1585,1585,1600,1429,1585	1.3	0	14	dbSNP_132	123	11,8589	8.4+/-32.0	0,11,4289	yes	missense,missense,missense,missense,missense	C14orf159	NM_001102366.1,NM_001102367.1,NM_001102368.1,NM_001102369.1,NM_024952.6	58,58,58,58,58	0,13,6490	AA,AG,GG		0.1279,0.0454,0.1	benign,benign,benign,benign,benign	529/617,529/617,534/622,477/565,529/617	91681784	13,12993	2203	4300	6503	SO:0001583	missense	80017	exon13			GCCTGCGCACTCT	AK097294	CCDS32141.1, CCDS41979.1, CCDS45150.1, CCDS66693.1, CCDS73677.1	14q32.11	2012-09-26			ENSG00000133943	ENSG00000133943			20498	protein-coding gene	gene with protein product							Standard	NM_001102367		Approved	FLJ39975	uc001xze.2	Q7Z3D6	OTTHUMG00000164980	ENST00000523771.1:c.1585G>A	14.37:g.91681784G>A	ENSP00000429655:p.Ala529Thr	61	0	0		56	27	0.482143	NM_001102368	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Missense_Mutation	SNP	ENST00000523771.1	37	CCDS32141.1	10	0.004578754578754579	0	0.0	9	0.024861878453038673	1	0.0017482517482517483	0	0.0	G	9.610	1.130943	0.21041	4.54E-4	0.001279	ENSG00000133943	ENST00000520328;ENST00000256324;ENST00000521077;ENST00000518868;ENST00000523816;ENST00000525393;ENST00000428926;ENST00000522322;ENST00000523771;ENST00000412671	T;T;T;T;T;T;T;T;T;T	0.20598	2.06;2.06;2.06;2.06;2.06;2.06;2.06;2.06;2.06;2.06	5.34	1.28	0.21552	.	0.240499	0.41097	N	0.000955	T	0.07728	0.0194	M	0.62088	1.915	0.09310	N	1	B;P;B;B;B	0.43662	0.202;0.814;0.168;0.41;0.168	B;B;B;B;B	0.34931	0.034;0.192;0.02;0.033;0.02	T	0.14615	-1.0466	10	0.54805	T	0.06	.	4.7277	0.12948	0.2495:0.0:0.5999:0.1506	.	529;405;477;534;494	Q7Z3D6;Q8NB88;Q7Z3D6-5;Q7Z3D6-2;Q7Z3D6-3	CN159_HUMAN;.;.;.;.	T	477;534;494;534;529;405;529;529;529;534	ENSP00000429453:A477T;ENSP00000256324:A534T;ENSP00000430137:A494T;ENSP00000428263:A534T;ENSP00000428974:A529T;ENSP00000435459:A405T;ENSP00000404343:A529T;ENSP00000427953:A529T;ENSP00000429655:A529T;ENSP00000404196:A534T	ENSP00000256324:A534T	A	+	1	0	C14orf159	90751537	0.408000	0.25360	0.014000	0.15608	0.002000	0.02628	2.292000	0.43549	0.265000	0.21872	-0.136000	0.14681	GCA	G|0.998;A|0.002	0.002	strong		0.542	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952		A	91681784	G	A	91681784	3	1	28	1	0	0	0	0	1	0	0	0	1757	1087	38	1	1642	1	C14orf159	14	91681784	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	15536	91681784	15667756	501	12004											
TECPR2	9895	hgsc.bcm.edu	37	chr14	102916966	102916966	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgggcctttgtgttggcttCtgcagctcccacgaaggaag	7	11	13	10	1	1	0	0	0	1	0	2	2	2	1	2	3	2	4	2	3	2	3	rs139247564		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:102916966C>A	ENST00000359520.7	+	15	3612	c.3386C>A	c.(3385-3387)tCt>tAt	p.S1129Y	TECPR2_ENST00000558678.1_Missense_Mutation_p.S1129Y	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	1129					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						GTGTTGGCTTCTGCAGCTCCC	0.498																																					p.S1129Y		Atlas-SNP	.											.	TECPR2	114	.	0			c.C3386A						PASS	.						104	83	90					14																	102916966		2203	4300	6503	SO:0001583	missense	9895	exon15			TGGCTTCTGCAGC	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.3386C>A	14.37:g.102916966C>A	ENSP00000352510:p.Ser1129Tyr	169	0	0		170	72	0.423529	NM_001172631	A5PKY3|A6NFY9|A7E2X3|H0YMM9|Q9UEG6	Missense_Mutation	SNP	ENST00000359520.7	37	CCDS32162.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.493237	0.84962	.	.	ENSG00000196663	ENST00000359520	T	0.20598	2.06	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.37019	0.0988	L	0.27053	0.805	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.87578	0.997;0.997;0.998	T	0.20207	-1.0282	10	0.87932	D	0	.	19.3784	0.94521	0.0:1.0:0.0:0.0	.	312;1129;1129	B4DSD3;A5PKY3;O15040	.;.;TCPR2_HUMAN	Y	1129	ENSP00000352510:S1129Y	ENSP00000352510:S1129Y	S	+	2	0	TECPR2	101986719	1.000000	0.71417	0.172000	0.22920	0.842000	0.47809	6.757000	0.74924	2.585000	0.87301	0.655000	0.94253	TCT	C|0.999;A|0.001	0.001	weak		0.498	TECPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415056.2	NM_014844		A	102916966	C	A	102916966	3	1	28	1	0	0	0	0	1	0	0	0	15759	913	32	4	3440	4	TECPR2	14	102916966	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	11235182	102916966	4432574	502	12005											
MARK3	4140	hgsc.bcm.edu	37	chr14	103941454	103941454	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcagtgctgttggaggaaaGggaattgctccagccagtcc	9	8	15	9	0	0	0	0	0	0	0	2	3	2	3	3	4	3	4	3	4	2	2	rs56126530	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:103941454G>A	ENST00000429436.2	+	13	1899	c.1389G>A	c.(1387-1389)aaG>aaA	p.K463K	MARK3_ENST00000440884.3_Silent_p.K384K|MARK3_ENST00000416682.2_Silent_p.K486K|MARK3_ENST00000335102.5_Silent_p.K486K|MARK3_ENST00000561071.1_Intron|MARK3_ENST00000553942.1_Silent_p.K463K|MARK3_ENST00000303622.9_Silent_p.K463K|MARK3_ENST00000216288.7_Silent_p.K447K	NM_001128918.1|NM_001128919.1	NP_001122390.1|NP_001122391.1	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	463						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)			TTGGAGGAAAGGGAATTGCTC	0.488													G|||	20	0.00399361	0.0	0.0029	5008	,	,		18604	0.001		0.0169	False		,,,				2504	0.0				p.K463K		Atlas-SNP	.											.	MARK3	86	.	0			c.G1389A						PASS	.	G	,,,,	3,3887		0,3,1942	78	77	77		1389,1389,1341,1152,1389	3.9	1	14	dbSNP_129	77	95,8197		2,91,4053	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MARK3	NM_001128918.1,NM_001128919.1,NM_001128920.1,NM_001128921.1,NM_002376.5	,,,,	2,94,5995	AA,AG,GG		1.1457,0.0771,0.8045	,,,,	463/754,463/745,447/714,384/660,463/730	103941454	98,12084	1945	4146	6091	SO:0001819	synonymous_variant	4140	exon13			AGGAAAGGGAATT	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.1389G>A	14.37:g.103941454G>A		95	0	0		105	51	0.485714	NM_001128919	O60219|Q86TT8|Q8TB41|Q8WX83|Q96RG1|Q9UMY9|Q9UN34	Silent	SNP	ENST00000429436.2	37	CCDS45165.1	18	0.008241758241758242	0	0.0	0	0.0	1	0.0017482517482517483	17	0.022427440633245383	G	9.682	1.149478	0.21288	7.71E-4	0.011457	ENSG00000075413	ENST00000554627	.	.	.	5.78	3.91	0.45181	.	.	.	.	.	T	0.31040	0.0784	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.25882	-1.0119	4	.	.	.	.	3.6647	0.08252	0.2736:0.0:0.5486:0.1777	rs56126530	.	.	.	K	215	.	.	R	+	2	0	MARK3	103011207	1.000000	0.71417	0.960000	0.40013	0.953000	0.61014	1.561000	0.36342	0.744000	0.32741	0.655000	0.94253	AGG	G|0.989;A|0.011	0.011	strong		0.488	MARK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415144.1	NM_001128918		A	103941454	G	A	103941454	2	1	28	1	0	0	0	0	0	0	0	1	9323	991	35	2		2	MARK3	14	103941454	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1024488	103941454	3408086	503	12006											
KIF26A	26153	hgsc.bcm.edu	37	chr14	104640098	104640098	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgggcagctgtgaggcggcGgctggcagggccggggaggc	4	4	23	10	3	0	1	0	1	0	0	0	2	0	2	1	9	1	4	1	9	0	0	rs61745565	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:104640098G>A	ENST00000423312.2	+	10	1923	c.1923G>A	c.(1921-1923)gcG>gcA	p.A641A	KIF26A_ENST00000315264.7_Silent_p.A502A	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	641	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				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)		GTGAGGCGGCGGCTGGCAGGG	0.687													G|||	83	0.0165735	0.0015	0.0288	5008	,	,		15832	0.0		0.0388	False		,,,				2504	0.0225				p.A641A		Atlas-SNP	.											.	KIF26A	84	.	0			c.G1923A						PASS	.	G		24,3842		0,24,1909	17	24	22		1923	-2.2	0	14	dbSNP_129	22	289,7937		9,271,3833	no	coding-synonymous	KIF26A	NM_015656.1		9,295,5742	AA,AG,GG		3.5133,0.6208,2.5885		641/1883	104640098	313,11779	1933	4113	6046	SO:0001819	synonymous_variant	26153	exon10			GGCGGCGGCTGGC	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.1923G>A	14.37:g.104640098G>A		31	0	0		56	31	0.553571	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Silent	SNP	ENST00000423312.2	37	CCDS45171.1																																																																																			G|0.981;A|0.019	0.019	strong		0.687	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1			A	104640098	G	A	104640098	2	1	28	1	0	0	0	0	0	0	0	1	8303	1103	39	1		1	KIF26A	14	104640098	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	698644	104640098	2709442	504	12007											
AKT1	207	hgsc.bcm.edu	37	chr14	105239894	105239894	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggtcctcggagaacacacgCtcccgggacaggtggaagaa	11	4	14	12	4	0	2	0	0	0	2	3	5	2	4	2	5	1	1	2	5	3	0	rs1130233	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:105239894C>T	ENST00000554581.1	-	8	2206	c.726G>A	c.(724-726)gaG>gaA	p.E242E	AKT1_ENST00000349310.3_Silent_p.E242E|AKT1_ENST00000555458.1_5'Flank|AKT1_ENST00000544168.1_Silent_p.E180E|AKT1_ENST00000402615.2_Silent_p.E242E|AKT1_ENST00000554848.1_Silent_p.E242E|AKT1_ENST00000407796.2_Silent_p.E242E|AKT1_ENST00000555528.1_Silent_p.E242E|AKT1_ENST00000554585.1_5'Flank|AKT1_ENST00000554192.1_5'Flank			P31749	AKT1_HUMAN	v-akt murine thymoma viral oncogene homolog 1	242	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)	AGAACACACGCTCCCGGGACA	0.652		1	Mis		"breast, colorectal, ovarian, NSCLC"								C|||	1615	0.322484	0.0787	0.4222	5008	,	,		14497	0.6002		0.2425	False		,,,				2504	0.3773				p.E242E		Atlas-SNP	.		Dom	yes		14	14q32.32	207	v-akt murine thymoma viral oncogene homolog 1		E	.	AKT1	379	.	0			c.G726A	GRCh37	CM081515	AKT1	M	rs1130233	PASS	.	C	,,	507,3897	216.1+/-234.9	33,441,1728	31	26	28		726,726,726	4.8	0.9	14	dbSNP_86	28	2115,6485	334.9+/-321.2	269,1577,2454	no	coding-synonymous,coding-synonymous,coding-synonymous	AKT1	NM_001014431.1,NM_001014432.1,NM_005163.2	,,	302,2018,4182	TT,TC,CC		24.593,11.5123,20.163	,,	242/481,242/481,242/481	105239894	2622,10382	2202	4300	6502	SO:0001819	synonymous_variant	207	exon9			CACACGCTCCCGG	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.726G>A	14.37:g.105239894C>T		114	0	0		90	89	0.988889	NM_005163	B2RAM5|B7Z5R1|Q9BWB6	Silent	SNP	ENST00000554581.1	37	CCDS9994.1																																																																																			C|0.769;T|0.231	0.231	strong		0.652	AKT1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410418.1	NM_005163		T	105239894	C	T	105239894	2	4	28	1	0	0	0	0	0	0	0	1	478	796	28	2		2	AKT1	14	105239894	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	599796	105239894	2109646	505	12008											
KIAA0284	283638	hgsc.bcm.edu	37	chr14	105352910	105352910	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcccccaggaggggcccacGtggagcaggggtcggcgctc	6	3	18	14	3	0	0	0	0	0	0	2	2	0	2	3	7	2	2	3	7	0	0	rs373896765		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:105352910G>A	ENST00000414716.3	+	12	2562	c.2334G>A	c.(2332-2334)acG>acA	p.T778T	CEP170B_ENST00000453495.1_Silent_p.T779T|CEP170B_ENST00000556508.1_Silent_p.T708T|CEP170B_ENST00000418279.1_Silent_p.T708T	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	778						cytoplasm (GO:0005737)|microtubule (GO:0005874)											AGGGGCCCACGTGGAGCAGGG	0.682																																					p.T778T		Atlas-SNP	.											.	.	.	.	0			c.G2334A						PASS	.	G	,	0,3656		0,0,1828	9	11	10		2334,2124	-6.8	0	14		10	3,8099		0,3,4048	no	coding-synonymous,coding-synonymous	KIAA0284	NM_001112726.2,NM_015005.2	,	0,3,5876	AA,AG,GG		0.037,0.0,0.0255	,	778/1555,708/1520	105352910	3,11755	1828	4051	5879	SO:0001819	synonymous_variant	283638	exon12			GCCCACGTGGAGC	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.2334G>A	14.37:g.105352910G>A		19	0	0		41	16	0.390244	NM_001112726	Q2KHR7|Q86TI7	Silent	SNP	ENST00000414716.3	37	CCDS45175.1																																																																																			.	.	weak		0.682	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726		A	105352910	G	A	105352910	2	1	28	1	0	0	0	0	0	0	0	1	8175	1132	40	1		1	KIAA0284	14	105352910	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	113016	105352910	1996630	506	12009											
JAG2	3714	hgsc.bcm.edu	37	chr14	105615514	105615514	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccgcacccagcacctctgcaGgccccgccagggcacggctc	6	3	11	21	3	1	0	0	0	1	0	2	0	1	0	6	3	2	5	6	3	0	0	rs368778866		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:105615514G>A	ENST00000331782.3	-	13	2149	c.1746C>T	c.(1744-1746)gcC>gcT	p.A582A	JAG2_ENST00000347004.2_Silent_p.A544A	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	582	EGF-like 10; 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)		CACCTCTGCAGGCCCCGCCAG	0.657																																					p.A582A		Atlas-SNP	.											.	JAG2	69	.	0			c.C1746T						PASS	.	G	,	0,4400		0,0,2200	43	50	47		1746,1632	1	1	14		47	2,8578		0,2,4288	no	coding-synonymous,coding-synonymous	JAG2	NM_002226.3,NM_145159.1	,	0,2,6488	AA,AG,GG		0.0233,0.0,0.0154	,	582/1239,544/1201	105615514	2,12978	2200	4290	6490	SO:0001819	synonymous_variant	3714	exon13			TCTGCAGGCCCCG	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.1746C>T	14.37:g.105615514G>A		52	0	0		103	53	0.514563	NM_002226	Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Silent	SNP	ENST00000331782.3	37	CCDS9998.1																																																																																			.	.	weak		0.657	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2			A	105615514	G	A	105615514	2	1	28	1	0	0	0	0	0	0	0	1	7944	987	35	2		2	JAG2	14	105615514	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	262604	105615514	1734026	507	12010											
BRF1	2972	hgsc.bcm.edu	37	chr14	105707747	105707747	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcgtggaatatacaggcaCgggtctgcggcagacacagc	12	5	14	10	3	1	1	0	0	1	1	1	2	1	2	0	4	4	2	0	4	4	2	rs144658695	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:105707747C>T	ENST00000546474.1	-	6	15508	c.549G>A	c.(547-549)ccG>ccA	p.P183P	BRF1_ENST00000440513.3_Silent_p.P68P|BRF1_ENST00000446501.2_Intron|BRF1_ENST00000379937.2_Silent_p.P156P|BRF1_ENST00000392557.4_De_novo_Start_OutOfFrame|BRF1_ENST00000327359.3_Silent_p.P68P|BRF1_ENST00000551787.1_De_novo_Start_OutOfFrame|BRF1_ENST00000379932.4_De_novo_Start_OutOfFrame	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	183					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)		TATACAGGCACGGGTCTGCGG	0.627													C|||	13	0.00259585	0.0015	0.0	5008	,	,		18733	0.0		0.006	False		,,,				2504	0.0051				p.P183P		Atlas-SNP	.											.	BRF1	102	.	0			c.G549A						PASS	.	C	,,,,,	2,4396	6.2+/-15.9	0,2,2197	82	67	72		204,204,468,,549,	-9	0.8	14	dbSNP_134	72	41,8559	27.9+/-77.7	0,41,4259	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous,utr-5	BRF1	NM_001242786.1,NM_001242787.1,NM_001242788.1,NM_001242789.1,NM_001519.3,NM_145685.2	,,,,,	0,43,6456	TT,TC,CC		0.4767,0.0455,0.3308	,,,,,	68/585,68/563,156/651,,183/678,	105707747	43,12955	2199	4300	6499	SO:0001819	synonymous_variant	2972	exon6			CAGGCACGGGTCT	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.549G>A	14.37:g.105707747C>T		50	0	0		22	10	0.454545	NM_001519	B3KU36|B4DIG5|B7Z2N3|F5H5Z7|F8WA46|Q13223|Q3SYD9|Q5PR24|Q6IQ02|Q96KX3|Q9HCW6|Q9HCW7|Q9HCW8	Silent	SNP	ENST00000546474.1	37	CCDS10001.1	5	0.0022893772893772895	1	0.0020325203252032522	0	0.0	0	0.0	4	0.005277044854881266	C	3.854	-0.031251	0.07543	4.55E-4	0.004767	ENSG00000185024	ENST00000546417	.	.	.	4.51	-9.01	0.00744	.	.	.	.	.	T	0.27967	0.0689	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41324	-0.9515	4	.	.	.	.	3.9767	0.09478	0.0832:0.3485:0.3231:0.2452	.	.	.	.	M	37	.	.	V	-	1	0	BRF1	104778792	0.000000	0.05858	0.826000	0.32828	0.338000	0.28826	-4.034000	0.00309	-1.654000	0.01499	-0.191000	0.12829	GTG	C|0.997;T|0.003	0.003	strong		0.627	BRF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074548.4	NM_001519		T	105707747	C	T	105707747	2	4	28	1	0	0	0	0	0	0	0	1	1512	523	19	1		1	BRF1	14	105707747	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	92233	105707747	1641793	508	12011											
GABRG3	2567	hgsc.bcm.edu	37	chr15	27772697	27772697	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtgcttcctgtttgtcttCgccgcgctgatggagtatgc	3	15	13	10	3	1	1	0	1	1	0	3	2	2	2	2	1	2	4	2	1	1	4			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:27772697C>A	ENST00000333743.6	+	8	1238	c.984C>A	c.(982-984)ttC>ttA	p.F328L	RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	328					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)	TGTTTGTCTTCGCCGCGCTGA	0.542																																					p.F328L	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											GABRG3,NS,carcinoma,0,2	GABRG3	115	2	0			c.C984A						PASS	.						124	112	116					15																	27772697		2161	4270	6431	SO:0001583	missense	2567	exon8			TGTCTTCGCCGCG		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.984C>A	15.37:g.27772697C>A	ENSP00000331912:p.Phe328Leu	126	0	0		105	37	0.352381	NM_033223	G3V594|Q9HD46|Q9NYT2	Missense_Mutation	SNP	ENST00000333743.6	37	CCDS45195.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.45|18.45	3.626426|3.626426	0.66901|0.66901	.|.	.|.	ENSG00000182256|ENSG00000182256	ENST00000333743|ENST00000451330	D|.	0.87029|.	-2.2|.	5.48|5.48	-0.806|-0.806	0.10875|0.10875	Neurotransmitter-gated ion-channel transmembrane domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.71375|.	0.3332|.	M|M	0.82323|0.82323	2.585|2.585	0.80722|0.80722	D|D	1|1	D|.	0.67145|.	0.996|.	D|.	0.79108|.	0.992|.	T|.	0.71290|.	-0.4637|.	10|.	0.87932|.	D|.	0|.	.|.	10.0297|10.0297	0.42092|0.42092	0.0:0.3808:0.0:0.6192|0.0:0.3808:0.0:0.6192	.|.	328|.	Q99928|.	GBRG3_HUMAN|.	L|X	328|91	ENSP00000331912:F328L|.	ENSP00000331912:F328L|.	F|S	+|+	3|2	2|0	GABRG3|GABRG3	25446292|25446292	0.994000|0.994000	0.37717|0.37717	0.988000|0.988000	0.46212|0.46212	0.588000|0.588000	0.36517|0.36517	0.247000|0.247000	0.18179|0.18179	0.045000|0.045000	0.15804|0.15804	-0.251000|-0.251000	0.11542|0.11542	TTC|TCG	.	.	none		0.542	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2			A	27772697	C	A	27772697	3	1	28	1	0	0	0	0	1	0	0	0	6181	883	31	4	1014	4	GABRG3	15	27772697	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10		27772697	74758695	509	12012											
OCA2	4948	hgsc.bcm.edu	37	chr15	28117060	28117060	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tattctattaagtggagatgTgccaatgcctagaagaaagg	14	11	11	5	0	1	3	0	0	1	3	1	4	1	3	2	2	2	0	2	2	7	5			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:28117060T>A	ENST00000354638.3	-	20	2243	c.2088A>T	c.(2086-2088)gcA>gcT	p.A696A	OCA2_ENST00000353809.5_Silent_p.A672A	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II	696					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)			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)		AGTGGAGATGTGCCAATGCCT	0.338									Oculocutaneous Albinism																												p.A696A		Atlas-SNP	.											.	OCA2	173	.	0			c.A2088T						PASS	.						112	116	115					15																	28117060		2203	4300	6503	SO:0001819	synonymous_variant	4948	exon20	Familial Cancer Database		GAGATGTGCCAAT		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.2088A>T	15.37:g.28117060T>A		52	0	0		36	6	0.166667	NM_000275	Q15211|Q15212|Q96EN1|Q9UMI5	Silent	SNP	ENST00000354638.3	37	CCDS10020.1																																																																																			.	.	none		0.338	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	NM_000275		A	28117060	T	A	28117060	2	1	28	1	0	0	0	0	0	0	0	1	10824	1683	59	5		5	OCA2	15	28117060	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	344363	28117060	74414332	510	12013											
OTUD7A	161725	hgsc.bcm.edu	37	chr15	31776837	31776837	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gctgttagaattgctgcacaCcgaatcgcggtccgagtcca	9	9	11	12	4	0	1	0	0	0	1	3	3	2	1	3	1	2	4	3	1	3	2	rs76704217	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:31776837C>G	ENST00000307050.4	-	11	1533	c.1441G>C	c.(1441-1443)Gtg>Ctg	p.V481L	OTUD7A_ENST00000382902.1_Missense_Mutation_p.V488L	NM_130901.1	NP_570971.1	Q8TE49	OTU7A_HUMAN	OTU deubiquitinase 7A	481					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)		TTGCTGCACACCGAATCGCGG	0.642													C|||	57	0.0113818	0.0015	0.0173	5008	,	,		19876	0.001		0.0378	False		,,,				2504	0.0041				p.V481L		Atlas-SNP	.											.	OTUD7A	89	.	0			c.G1441C						PASS	.	C	LEU/VAL	30,4354		0,30,2162	80	57	64		1441	2.4	1	15	dbSNP_131	64	415,8183		14,387,3898	yes	missense	OTUD7A	NM_130901.1	32	14,417,6060	GG,GC,CC		4.8267,0.6843,3.4278	benign	481/927	31776837	445,12537	2192	4299	6491	SO:0001583	missense	161725	exon11			TGCACACCGAATC	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.1441G>C	15.37:g.31776837C>G	ENSP00000305926:p.Val481Leu	81	0	0		84	46	0.547619	NM_130901	Q8IWK5	Missense_Mutation	SNP	ENST00000307050.4	37	CCDS10026.1	45	0.020604395604395604	2	0.0040650406504065045	7	0.019337016574585635	1	0.0017482517482517483	35	0.04617414248021108	C	14.83	2.652700	0.47362	0.006843	0.048267	ENSG00000169918	ENST00000307050;ENST00000382902	T;T	0.34472	1.37;1.36	4.35	2.4	0.29515	.	0.175056	0.50627	D	0.000102	T	0.06005	0.0156	M	0.69823	2.125	0.28750	N	0.90147	B;B	0.12013	0.005;0.003	B;B	0.13407	0.009;0.004	T	0.12656	-1.0539	10	0.51188	T	0.08	-32.5726	3.9645	0.09424	0.0:0.5203:0.2199:0.2599	.	488;481	Q8TE49-2;Q8TE49	.;OTU7A_HUMAN	L	481;488	ENSP00000305926:V481L;ENSP00000372358:V488L	ENSP00000305926:V481L	V	-	1	0	OTUD7A	29564129	1.000000	0.71417	0.994000	0.49952	0.995000	0.86356	2.060000	0.41394	0.936000	0.37367	0.655000	0.94253	GTG	C|0.970;G|0.030	0.030	strong		0.642	OTUD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251393.2	NM_130901		G	31776837	C	G	31776837	3	3	28	1	0	0	0	0	1	0	0	0	11327	507	18	4	1343	4	OTUD7A	15	31776837	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	3659777	31776837	70754555	511	12014											
FMN1	342184	hgsc.bcm.edu	37	chr15	33359950	33359950	+	Intron	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctcttctggattcacagattCtaatttactcgtaaacccaa	12	14	4	11	1	4	1	1	0	3	1	5	2	4	2	1	1	2	1	1	1	5	7	rs141655944	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:33359950C>G	ENST00000559047.1	-	3	2043				FMN1_ENST00000334528.9_Missense_Mutation_p.E46Q|FMN1_ENST00000559150.1_Intron|FMN1_ENST00000561249.1_Intron|FMN1_ENST00000558197.1_Missense_Mutation_p.E46Q			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)		TTCACAGATTCTAATTTACTC	0.443													C|||	17	0.00339457	0.0	0.0014	5008	,	,		21879	0.0		0.0149	False		,,,				2504	0.001				p.E46Q		Atlas-SNP	.											.	FMN1	174	.	0			c.G136C						PASS	.	C	GLN/GLU	12,3768		0,12,1878	71	68	69		136	4.9	1	15	dbSNP_134	69	111,8147		2,107,4020	yes	missense	FMN1	NM_001103184.2	29	2,119,5898	GG,GC,CC		1.3442,0.3175,1.0218	probably-damaging	46/1197	33359950	123,11915	1890	4129	6019	SO:0001627	intron_variant	342184	exon1			CAGATTCTAATTT	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.2044-2675G>C	15.37:g.33359950C>G		109	0	0		84	43	0.511905	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	37		13	0.005952380952380952	0	0.0	1	0.0027624309392265192	0	0.0	12	0.0158311345646438	C	11.34	1.608899	0.28623	0.003175	0.013442	ENSG00000248905	ENST00000334528	T	0.52983	0.64	4.92	4.92	0.64577	.	.	.	.	.	T	0.50616	0.1626	.	.	.	.	.	.	D;D	0.67145	0.996;0.989	P;P	0.59357	0.856;0.714	T	0.66333	-0.5950	7	0.66056	D	0.02	.	18.2894	0.90124	0.0:1.0:0.0:0.0	.	46;46	Q68DA7-3;Q68DA7-5	.;.	Q	46	ENSP00000333950:E46Q	ENSP00000333950:E46Q	E	-	1	0	FMN1	31147242	0.996000	0.38824	0.977000	0.42913	0.071000	0.16799	5.064000	0.64338	2.556000	0.86216	0.655000	0.94253	GAA	C|0.993;G|0.007	0.007	strong		0.443	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184		G	33359950	C	G	33359950	1	3	28	0	1	0	0	0	0	0	0	0	5957	922	32	4		4	FMN1	15	33359950	Intron	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1583113	33359950	69171442	512	12015											
RYR3	6263	hgsc.bcm.edu	37	chr15	34137131	34137131	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggaattcctttaatgacgaGgaagaggaagaagcgatggt	14	9	14	4	2	0	3	0	1	0	2	1	8	1	6	1	4	1	0	1	4	5	3	rs118177681	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:34137131G>A	ENST00000389232.4	+	93	13435	c.13365G>A	c.(13363-13365)gaG>gaA	p.E4455E	RYR3_ENST00000415757.3_Silent_p.E4450E	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	4455					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)		TTAATGACGAGGAAGAGGAAG	0.463													G|||	42	0.00838658	0.0	0.013	5008	,	,		19806	0.0		0.006	False		,,,				2504	0.0276				p.E4455E		Atlas-SNP	.											.	RYR3	760	.	0			c.G13365A						PASS	.	G		11,3879		0,11,1934	135	126	129		13365	-0.3	1	15	dbSNP_132	129	88,8196		0,88,4054	no	coding-synonymous	RYR3	NM_001036.3		0,99,5988	AA,AG,GG		1.0623,0.2828,0.8132		4455/4871	34137131	99,12075	1945	4142	6087	SO:0001819	synonymous_variant	6263	exon93			TGACGAGGAAGAG		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.13365G>A	15.37:g.34137131G>A		112	0	0		102	56	0.54902	NM_001036	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			G|0.993;A|0.007	0.007	strong		0.463	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			A	34137131	G	A	34137131	2	1	28	1	0	0	0	0	0	0	0	1	13785	991	35	2		2	RYR3	15	34137131	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	777181	34137131	68394261	513	12016											
PAK6	56924	hgsc.bcm.edu	37	chr15	40564441	40564441	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcagcccaactcctctttccGaccgccgcagaaagacaacc	11	5	7	18	3	1	2	0	0	1	2	3	3	3	2	6	0	3	2	6	0	3	1	rs150100570	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:40564441G>A	ENST00000542403.2	+	4	986	c.875G>A	c.(874-876)cGa>cAa	p.R292Q	PAK6_ENST00000455577.2_Missense_Mutation_p.R292Q|PAK6_ENST00000453867.1_Missense_Mutation_p.R292Q|PAK6_ENST00000441369.1_Missense_Mutation_p.R292Q|RP11-133K1.2_ENST00000558658.1_3'UTR|PAK6_ENST00000560346.1_Missense_Mutation_p.R292Q|PAK6_ENST00000260404.4_Missense_Mutation_p.R292Q	NM_001276717.1	NP_001263646.1	Q9NQU5	PAK6_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 6	292	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)		TCCTCTTTCCGACCGCCGCAG	0.637																																					p.R292Q		Atlas-SNP	.											PAK6,NS,adenocarcinoma,+1,1	PAK6	49	1	0			c.G875A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	68	84	79		875,875,875	3.1	0.9	15	dbSNP_134	79	16,8584	10.5+/-38.8	0,16,4284	yes	missense,missense,missense	PAK6	NM_001128628.1,NM_001128629.1,NM_020168.4	43,43,43	0,16,6487	AA,AG,GG		0.186,0.0,0.123	possibly-damaging,possibly-damaging,possibly-damaging	292/682,292/682,292/682	40564441	16,12990	2203	4300	6503	SO:0001583	missense	56924	exon5			CTTTCCGACCGCC	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.875G>A	15.37:g.40564441G>A	ENSP00000439597:p.Arg292Gln	64	0	0		81	39	0.481481	NM_001128629	A8K2G2|B3KYB0|G5E9R2	Missense_Mutation	SNP	ENST00000542403.2	37	CCDS10054.1	.	.	.	.	.	.	.	.	.	.	G	11.06	1.529004	0.27387	0.0	0.00186	ENSG00000137843	ENST00000441369;ENST00000453867;ENST00000455577;ENST00000260404;ENST00000542403	T;T;T;T;T	0.74842	-0.81;-0.81;-0.88;-0.81;-0.81	5.02	3.14	0.36123	.	0.683340	0.13547	N	0.379732	T	0.57799	0.2078	L	0.27053	0.805	0.37769	D	0.926619	B;B	0.21905	0.037;0.062	B;B	0.10450	0.002;0.005	T	0.47947	-0.9077	10	0.15499	T	0.54	.	9.1394	0.36894	0.2362:0.0:0.7638:0.0	.	292;292	Q9NQU5;G5E9R2	PAK6_HUMAN;.	Q	292	ENSP00000406873:R292Q;ENSP00000401153:R292Q;ENSP00000409465:R292Q;ENSP00000260404:R292Q;ENSP00000439597:R292Q	ENSP00000260404:R292Q	R	+	2	0	PAK6	38351733	0.340000	0.24792	0.917000	0.36280	0.835000	0.47333	0.975000	0.29449	0.632000	0.30432	0.555000	0.69702	CGA	G|0.999;A|0.001	0.001	strong		0.637	PAK6-004	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000418355.1			A	40564441	G	A	40564441	3	1	28	1	0	0	0	0	1	0	0	0	11413	1058	37	1	885	1	PAK6	15	40564441	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	6427310	40564441	61966951	514	12017											
DISP2	85455	hgsc.bcm.edu	37	chr15	40656724	40656724	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgttgggggcccggctgccCgacttctccaagcctttgct	3	11	12	15	2	1	0	0	0	1	0	2	1	1	0	4	3	3	3	4	3	1	3	rs72733418	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:40656724C>T	ENST00000267889.3	+	4	669	c.582C>T	c.(580-582)ccC>ccT	p.P194P		NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	194					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)		CCCGGCTGCCCGACTTCTCCA	0.637													C|||	38	0.00758786	0.0212	0.0014	5008	,	,		18401	0.0		0.008	False		,,,				2504	0.001				p.P194P		Atlas-SNP	.											.	DISP2	86	.	0			c.C582T						PASS	.	C		120,4286	88.2+/-126.9	0,120,2083	56	59	58		582	-9.8	0	15	dbSNP_130	58	66,8534	40.8+/-97.7	0,66,4234	no	coding-synonymous	DISP2	NM_033510.1		0,186,6317	TT,TC,CC		0.7674,2.7236,1.4301		194/1402	40656724	186,12820	2203	4300	6503	SO:0001819	synonymous_variant	85455	exon4			GCTGCCCGACTTC	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.582C>T	15.37:g.40656724C>T		40	0	0		70	43	0.614286	NM_033510	Q6AHW3|Q9C0C1	Silent	SNP	ENST00000267889.3	37	CCDS10056.1																																																																																			C|0.987;T|0.013	0.013	strong		0.637	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510		T	40656724	C	T	40656724	2	4	28	1	0	0	0	0	0	0	0	1	4542	639	23	1		1	DISP2	15	40656724	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	92283	40656724	61874668	515	12018											
VPS18	57617	hgsc.bcm.edu	37	chr15	41192540	41192540	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcttggggctctgcagggCgacccagaggccctgactct	5	7	15	14	2	2	2	0	1	2	1	2	3	2	2	2	5	1	3	2	5	0	1	rs79536497	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:41192540C>T	ENST00000220509.5	+	4	1863	c.1524C>T	c.(1522-1524)ggC>ggT	p.G508G	VPS18_ENST00000558474.1_Intron	NM_020857.2	NP_065908.1	Q9P253	VPS18_HUMAN	vacuolar protein sorting 18 homolog (S. cerevisiae)	508					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)		CTCTGCAGGGCGACCCAGAGG	0.612													C|||	7	0.00139776	0.0008	0.0	5008	,	,		17114	0.0		0.006	False		,,,				2504	0.0				p.G508G		Atlas-SNP	.											.	VPS18	67	.	0			c.C1524T						PASS	.	C		5,4401	9.9+/-24.2	0,5,2198	76	86	82		1524	-5.3	0.7	15	dbSNP_131	82	65,8535	38.8+/-94.9	0,65,4235	no	coding-synonymous	VPS18	NM_020857.2		0,70,6433	TT,TC,CC		0.7558,0.1135,0.5382		508/974	41192540	70,12936	2203	4300	6503	SO:0001819	synonymous_variant	57617	exon4			GCAGGGCGACCCA	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.1524C>T	15.37:g.41192540C>T		61	0	0		54	23	0.425926	NM_020857	Q8TCG0|Q96DI3|Q9H268	Silent	SNP	ENST00000220509.5	37	CCDS10069.1																																																																																			C|0.996;T|0.004	0.004	strong		0.612	VPS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252443.2			T	41192540	C	T	41192540	2	4	28	1	0	0	0	0	0	0	0	1	17209	755	27	1		1	VPS18	15	41192540	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	535816	41192540	61338852	516	12019											
TYRO3	7301	hgsc.bcm.edu	37	chr15	41857307	41857307	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctggatgccaggtgctgatGgccgagctctgctacagtcc	6	9	13	13	1	1	1	0	1	1	0	2	3	2	2	4	3	5	3	4	3	1	1	rs141641556	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:41857307G>A	ENST00000263798.3	+	6	975	c.751G>A	c.(751-753)Ggc>Agc	p.G251S	TYRO3_ENST00000559066.1_Missense_Mutation_p.G206S	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase	251	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		AGGTGCTGATGGCCGAGCTCT	0.592													G|||	42	0.00838658	0.0	0.0202	5008	,	,		20484	0.0		0.0268	False		,,,				2504	0.001				p.G251S		Atlas-SNP	.											TYRO3_ENST00000263798,NS,haematopoietic_neoplasm,0,2	TYRO3	169	2	0			c.G751A						scavenged	.	G	SER/GLY	8,4398	15.5+/-35.6	0,8,2195	94	84	87		751	4.9	0.6	15	dbSNP_134	87	128,8472	63.5+/-125.6	0,128,4172	yes	missense	TYRO3	NM_006293.3	56	0,136,6367	AA,AG,GG		1.4884,0.1816,1.0457	probably-damaging	251/891	41857307	136,12870	2203	4300	6503	SO:0001583	missense	7301	exon6			GCTGATGGCCGAG	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.751G>A	15.37:g.41857307G>A	ENSP00000263798:p.Gly251Ser	52	0	0		44	6	0.136364	NM_006293	O14953|Q86VR3	Missense_Mutation	SNP	ENST00000263798.3	37	CCDS10080.1	14	0.00641025641025641	0	0.0	4	0.011049723756906077	0	0.0	10	0.013192612137203167	G	31	5.104713	0.94245	0.001816	0.014884	ENSG00000092445	ENST00000540218;ENST00000263798	T	0.60920	0.15	4.95	4.95	0.65309	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.41712	D	0.000828	T	0.59266	0.2181	L	0.55103	1.725	0.58432	D	0.999997	D	0.64830	0.994	P	0.58970	0.849	T	0.64689	-0.6348	10	0.51188	T	0.08	-23.6363	13.5493	0.61723	0.0:0.0:1.0:0.0	.	251	Q06418	TYRO3_HUMAN	S	183;251	ENSP00000263798:G251S	ENSP00000263798:G251S	G	+	1	0	TYRO3	39644599	1.000000	0.71417	0.626000	0.29213	0.989000	0.77384	6.282000	0.72639	2.581000	0.87130	0.563000	0.77884	GGC	G|0.992;A|0.008	0.008	strong		0.592	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2			A	41857307	G	A	41857307	3	1	28	1	0	0	0	0	1	0	0	0	16829	1348	47	2	773	2	TYRO3	15	41857307	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	664767	41857307	60674085	517	12020											
PLA2G4D	283748	hgsc.bcm.edu	37	chr15	42363433	42363433	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgtcaggaagcctttaaaTgcctgggccagcgccgtgcc	7	8	12	14	2	1	0	1	0	0	0	1	1	1	1	6	2	4	0	6	2	3	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:42363433T>A	ENST00000290472.3	-	17	1858	c.1764A>T	c.(1762-1764)gcA>gcT	p.A588A		NM_178034.3	NP_828848.3	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD (cytosolic)	588	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				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)|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)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		AGCCTTTAAATGCCTGGGCCA	0.642																																					p.A588A		Atlas-SNP	.											.	PLA2G4D	72	.	0			c.A1764T						PASS	.						28	32	30					15																	42363433		2202	4297	6499	SO:0001819	synonymous_variant	283748	exon17			TTTAAATGCCTGG	AB090876	CCDS32203.1	15q14	2008-09-19				ENSG00000159337	3.1.1.4		30038	protein-coding gene	gene with protein product		612864				14709560	Standard	NM_178034		Approved	cPLA2delta	uc001zox.3	Q86XP0		ENST00000290472.3:c.1764A>T	15.37:g.42363433T>A		36	0	0		44	28	0.636364	NM_178034	Q8N176	Silent	SNP	ENST00000290472.3	37	CCDS32203.1																																																																																			.	.	none		0.642	PLA2G4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419317.1	NM_178034		A	42363433	T	A	42363433	2	1	28	1	0	0	0	0	0	0	0	1	12013	1451	51	5		5	PLA2G4D	15	42363433	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	506126	42363433	60167959	518	12021											
CDAN1	146059	hgsc.bcm.edu	37	chr15	43020456	43020457	+	Frame_Shift_Ins	INS	-	-	TGAC																															cagccccagggctcttccttINStgacagaacctaaaagggga																										TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:43020456_43020457insTGAC	ENST00000356231.3	-	21	2836_2837	c.2813_2814insGTCA	c.(2812-2814)caafs	p.-938fs		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1						chromatin assembly (GO:0031497)|chromatin organization (GO:0006325)|negative regulation of DNA replication (GO:0008156)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	24		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		GGCTCTTCCTTTGACAGAACCT	0.619																																					p.Q938fs		Pindel,Atlas-Indel	.											.	CDAN1	70	.	0			c.2814_2815insGTCA						PASS	.																																			SO:0001589	frameshift_variant	146059	exon21			.	AF525398	CCDS32209.1	15q15.2	2012-04-25	2012-04-25			ENSG00000140326			1713	protein-coding gene	gene with protein product		607465	"congenital dyserythropoietic anemia, type I"			8634422, 12434312	Standard	XM_005254177		Approved	CDA-I, CDAI	uc001zql.3	Q8IWY9		ENST00000356231.3:c.2810_2813dupGTCA	15.37:g.43020457_43020460dupTGAC	ENSP00000348564:p.Gln938fs	63	0	.		60	19	0.317	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Frame_Shift_Ins	INS	ENST00000356231.3	37	CCDS32209.1																																																																																			.	.	none		0.619	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300		TGAC	43020457	-	TGAC	43020456	7	5	28	1	0	1	1	0	0	0	0	0	3056	1838	64	0	901	0	CDAN1	15	43020456	Frame_Shift_Ins	INS	-	TCGA-G8-6914-01A-11D-2210-10	657023	43020456	59510936	519	12022											
PDIA3	2923	hgsc.bcm.edu	37	chr15	44038850	44038850	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggacgacaacttcgagagtcGcatctccgacacgggctctg	9	7	12	13	5	2	1	0	0	2	1	5	5	2	2	1	2	1	2	1	2	1	1	rs61734331	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:44038850G>T	ENST00000300289.5	+	1	261	c.113G>T	c.(112-114)cGc>cTc	p.R38L	CATSPER2P1_ENST00000381680.2_RNA|PDIA3_ENST00000538521.1_5'UTR|PDIA3_ENST00000469684.1_3'UTR	NM_005313.4	NP_005304.3	P30101	PDIA3_HUMAN	protein disulfide isomerase family A, member 3	38	Thioredoxin 1. {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)		TTCGAGAGTCGCATCTCCGAC	0.682													G|||	8	0.00159744	0.0	0.0	5008	,	,		12466	0.001		0.003	False		,,,				2504	0.0041				p.R38L		Atlas-SNP	.											.	PDIA3	40	.	0			c.G113T						PASS	.	G	LEU/ARG	0,4334		0,0,2167	33	33	33		113	4.5	1	15	dbSNP_129	33	3,8511		0,3,4254	yes	missense	PDIA3	NM_005313.4	102	0,3,6421	TT,TG,GG		0.0352,0.0,0.0233	benign	38/506	44038850	3,12845	2167	4257	6424	SO:0001583	missense	2923	exon1			AGAGTCGCATCTC		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.113G>T	15.37:g.44038850G>T	ENSP00000300289:p.Arg38Leu	59	0	0		57	29	0.508772	NM_005313	Q13453|Q14255|Q8IYF8|Q9UMU7	Missense_Mutation	SNP	ENST00000300289.5	37	CCDS10101.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	12.28	1.890128	0.33348	0.0	3.52E-4	ENSG00000167004	ENST00000300289	T	0.34667	1.35	5.46	4.53	0.55603	Thioredoxin domain (1);Thioredoxin-like fold (3);Disulphide isomerase (1);	0.293323	0.39834	N	0.001245	T	0.18173	0.0436	N	0.03324	-0.35	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.03773	-1.1005	10	0.27082	T	0.32	.	14.1256	0.65217	0.0:0.1506:0.8494:0.0	rs61734331	38	P30101	PDIA3_HUMAN	L	38	ENSP00000300289:R38L	ENSP00000300289:R38L	R	+	2	0	PDIA3	41826142	1.000000	0.71417	0.997000	0.53966	0.228000	0.25075	2.749000	0.47492	1.273000	0.44346	0.313000	0.20887	CGC	G|0.999;T|0.001	0.001	strong		0.682	PDIA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103532.3	NM_005313		T	44038850	G	T	44038850	3	4	28	1	0	0	0	0	1	0	0	0	11678	1087	38	4	115	4	PDIA3	15	44038850	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1018394	44038850	58492542	520	12023											
SPG11	80208	hgsc.bcm.edu	37	chr15	44890486	44890486	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tttatttcctgttgctgaatGctgttccatgtaccttcttc	5	20	6	10	0	1	1	0	1	1	0	4	1	3	1	3	0	3	5	3	0	3	8			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:44890486G>C	ENST00000261866.7	-	23	3994	c.3978C>G	c.(3976-3978)agC>agG	p.S1326R	SPG11_ENST00000558319.1_Missense_Mutation_p.S1326R|SPG11_ENST00000427534.2_Missense_Mutation_p.S1326R|SPG11_ENST00000535302.2_Missense_Mutation_p.S1326R	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	1326					cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		GTTGCTGAATGCTGTTCCATG	0.378																																					p.S1326R		Atlas-SNP	.											.	SPG11	207	.	0			c.C3978G						PASS	.						152	131	138					15																	44890486		2198	4298	6496	SO:0001583	missense	80208	exon23			CTGAATGCTGTTC		CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"spatacsin"	610844	"KIAA1840"	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.3978C>G	15.37:g.44890486G>C	ENSP00000261866:p.Ser1326Arg	123	0	0		152	68	0.447368	NM_025137	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Missense_Mutation	SNP	ENST00000261866.7	37	CCDS10112.1	.	.	.	.	.	.	.	.	.	.	G	15.07	2.725352	0.48833	.	.	ENSG00000104133	ENST00000261866;ENST00000535302;ENST00000427534	T;T;T	0.80304	-1.36;-1.36;-1.36	5.77	1.3	0.21679	.	0.489617	0.24520	N	0.037813	T	0.74550	0.3731	L	0.51422	1.61	0.80722	D	1	P;P;P	0.50443	0.773;0.935;0.773	B;P;B	0.48815	0.414;0.591;0.332	T	0.67288	-0.5708	10	0.19590	T	0.45	.	6.1682	0.20402	0.315:0.0:0.5586:0.1264	.	1326;1326;1326	C4B7M2;F5H3N6;Q96JI7	.;.;SPTCS_HUMAN	R	1326	ENSP00000261866:S1326R;ENSP00000445278:S1326R;ENSP00000396110:S1326R	ENSP00000261866:S1326R	S	-	3	2	SPG11	42677778	0.423000	0.25482	0.999000	0.59377	0.899000	0.52679	0.278000	0.18753	0.373000	0.24621	0.655000	0.94253	AGC	.	.	none		0.378	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1			C	44890486	G	C	44890486	3	2	28	1	0	0	0	0	1	0	0	0	15056	1310	46	4	3425	4	SPG11	15	44890486	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	851636	44890486	57640906	521	12024											
SLC30A4	7782	hgsc.bcm.edu	37	chr15	45778828	45778828	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttagctgtatgtgaactatGgcagtagattttcctgaagt	10	15	10	6	0	0	3	0	2	0	1	1	3	1	3	1	1	2	4	1	1	6	6	rs145466606	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:45778828G>A	ENST00000261867.4	-	7	1430	c.1116C>T	c.(1114-1116)gcC>gcT	p.A372A	RP11-519G16.3_ENST00000558536.1_RNA|RP11-519G16.3_ENST00000560647.1_RNA	NM_013309.4	NP_037441.2	O14863	ZNT4_HUMAN	solute carrier family 30 (zinc transporter), member 4	372					regulation of sequestering of zinc ion (GO:0061088)|response to toxic substance (GO:0009636)|zinc ion homeostasis (GO:0055069)|zinc ion transmembrane transport (GO:0071577)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(3)|large_intestine(2)|lung(8)|prostate(1)|stomach(1)	15		Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.58e-16)|GBM - Glioblastoma multiforme(94;2.15e-06)		TGTGAACTATGGCAGTAGATT	0.373																																					p.A372A		Atlas-SNP	.											.	SLC30A4	25	.	0			c.C1116T						PASS	.	G		1,4395		0,1,2197	131	135	134		1116	4.6	1	15	dbSNP_134	134	8,8588	6.4+/-24.3	0,8,4290	no	coding-synonymous	SLC30A4	NM_013309.4		0,9,6487	AA,AG,GG		0.0931,0.0227,0.0693		372/430	45778828	9,12983	2198	4298	6496	SO:0001819	synonymous_variant	7782	exon7			AACTATGGCAGTA		CCDS10125.1	15q21.1	2013-05-22			ENSG00000104154	ENSG00000104154		"Solute carriers"	11015	protein-coding gene	gene with protein product		602095		ZNT4			Standard	NM_013309		Approved		uc001zvj.3	O14863	OTTHUMG00000131439	ENST00000261867.4:c.1116C>T	15.37:g.45778828G>A		58	0	0		55	25	0.454545	NM_013309	Q8TC39	Silent	SNP	ENST00000261867.4	37	CCDS10125.1																																																																																			G|0.999;A|0.001	0.001	strong		0.373	SLC30A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254236.1			A	45778828	G	A	45778828	2	1	28	1	0	0	0	0	0	0	0	1	14572	1335	47	2		2	SLC30A4	15	45778828	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	888342	45778828	56752564	522	12025											
SPPL2A	84888	hgsc.bcm.edu	37	chr15	51041909	51041909	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	agtccttggttgtgccatttCcagacgcatgcaagattgct	8	13	10	10	1	0	2	0	0	0	2	2	2	2	2	3	1	3	4	3	1	1	4	rs145832874	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:51041909C>T	ENST00000261854.5	-	2	375	c.101G>A	c.(100-102)gGa>gAa	p.G34E	RP11-507J18.2_ENST00000558317.1_RNA	NM_032802.3	NP_116191.2	Q8TCT8	SPP2A_HUMAN	signal peptide peptidase like 2A	34					membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|regulation of immune response (GO:0050776)	extracellular vesicular exosome (GO:0070062)|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)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15				all cancers(107;0.000712)|GBM - Glioblastoma multiforme(94;0.00314)		TGTGCCATTTCCAGACGCATG	0.403													C|||	13	0.00259585	0.0	0.0043	5008	,	,		20240	0.0		0.002	False		,,,				2504	0.0082				p.G34E	Melanoma(50;790 1209 4069 22965 33125)	Atlas-SNP	.											.	SPPL2A	26	.	0			c.G101A						PASS	.	C	GLU/GLY	0,4392		0,0,2196	137	129	132		101	3.8	1	15	dbSNP_134	132	14,8574	11.2+/-40.8	0,14,4280	yes	missense	SPPL2A	NM_032802.3	98	0,14,6476	TT,TC,CC		0.163,0.0,0.1079	benign	34/521	51041909	14,12966	2196	4294	6490	SO:0001583	missense	84888	exon2			CCATTTCCAGACG		CCDS10138.1	15q21.2	2012-02-21			ENSG00000138600	ENSG00000138600			30227	protein-coding gene	gene with protein product	"intramembrane protease 3", "presenilin-like protein 2"	608238				12077416, 12139484	Standard	NM_032802		Approved	IMP3, PSL2	uc001zyv.3	Q8TCT8	OTTHUMG00000131647	ENST00000261854.5:c.101G>A	15.37:g.51041909C>T	ENSP00000261854:p.Gly34Glu	73	0	0		88	46	0.522727	NM_032802	B2RDS0|Q8TAW1|Q96SZ8	Missense_Mutation	SNP	ENST00000261854.5	37	CCDS10138.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	15.84	2.951845	0.53293	0.0	0.00163	ENSG00000138600	ENST00000261854	T	0.10960	2.82	5.72	3.8	0.43715	.	0.291695	0.39909	N	0.001238	T	0.06050	0.0157	L	0.36672	1.1	0.32630	N	0.522116	B	0.17038	0.02	B	0.16289	0.015	T	0.04413	-1.0953	10	0.45353	T	0.12	-4.7508	8.2699	0.31838	0.0:0.7246:0.1402:0.1353	.	34	Q8TCT8	PSL2_HUMAN	E	34	ENSP00000261854:G34E	ENSP00000261854:G34E	G	-	2	0	AC012100.1	48829201	0.998000	0.40836	0.995000	0.50966	0.954000	0.61252	1.261000	0.32980	1.384000	0.46424	0.650000	0.86243	GGA	C|0.998;T|0.002	0.002	strong		0.403	SPPL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254543.3	NM_032802		T	51041909	C	T	51041909	3	4	28	1	0	0	0	0	1	0	0	0	15103	855	30	2	1517	2	SPPL2A	15	51041909	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	5263081	51041909	51489483	523	12026											
MYO5A	4644	hgsc.bcm.edu	37	chr15	52635394	52635394	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtaatccagagcagatgaTcttccatgcaaaaggaacaa	16	8	9	8	0	1	3	0	1	1	2	3	4	3	4	2	2	3	3	2	2	5	2	rs61731219	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:52635394T>A	ENST00000399231.3	-	31	4203	c.3960A>T	c.(3958-3960)agA>agT	p.R1320S	MYO5A_ENST00000356338.6_Intron|MYO5A_ENST00000553916.1_Intron|MYO5A_ENST00000358212.6_Splice_Site_p.R1320S|MYO5A_ENST00000399233.2_Splice_Site_p.R1317S	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	1320					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)		GAGCAGATGATCTTCCATGCA	0.408													T|||	58	0.0115815	0.0023	0.0072	5008	,	,		19797	0.0		0.0437	False		,,,				2504	0.0061				p.R1320S		Atlas-SNP	.											.	MYO5A	145	.	0			c.A3960T						PASS	.	T	SER/ARG,	24,3884		0,24,1930	92	85	87		3960,	5.9	1	15	dbSNP_129	87	339,7997		6,327,3835	yes	missense-near-splice,intron	MYO5A	NM_000259.3,NM_001142495.1	110,	6,351,5765	AA,AT,TT		4.0667,0.6141,2.9647	benign,	1320/1856,	52635394	363,11881	1954	4168	6122	SO:0001630	splice_region_variant	4644	exon31			AGATGATCTTCCA		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.3960-1A>T	15.37:g.52635394T>A		67	0	0		70	36	0.514286	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	37	CCDS42037.1	37	0.01694139194139194	0	0.0	4	0.011049723756906077	0	0.0	33	0.04353562005277045	T	15.01	2.706322	0.48412	0.006141	0.040667	ENSG00000197535	ENST00000399231;ENST00000399233;ENST00000358212;ENST00000399228	T;T;T;T	0.04454	3.62;3.62;3.62;3.62	5.87	5.87	0.94306	.	0.059846	0.64402	D	0.000003	T	0.02807	0.0084	L	0.43152	1.355	0.80722	D	1	D;D;P	0.61080	0.989;0.989;0.495	D;D;B	0.75020	0.985;0.985;0.034	T	0.05566	-1.0877	10	0.38643	T	0.18	.	10.8931	0.47006	0.0:0.0783:0.0:0.9217	rs61731219	110;113;1320	Q9UES5;O95317;Q9Y4I1	.;.;MYO5A_HUMAN	S	1320;1317;1320;110	ENSP00000382177:R1320S;ENSP00000382179:R1317S;ENSP00000350945:R1320S;ENSP00000382174:R110S	ENSP00000350945:R1320S	R	-	3	2	MYO5A	50422686	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.751000	0.55165	2.236000	0.73375	0.528000	0.53228	AGA	T|0.955;A|0.045	0.045	strong		0.408	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259	Missense_Mutation	A	52635394	T	A	52635394	5	1	28	1	0	0	0	0	0	0	1	0	10087	1449	50	5	1651	5	MYO5A	15	52635394	Splice_Site	SNP	T	TCGA-G8-6914-01A-11D-2210-10	1593485	52635394	49895998	524	12027											
PRTG	283659	hgsc.bcm.edu	37	chr15	55965666	55965666	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaatccgaaccaggtagacActgtcaggtttcaggccttc	10	10	10	11	1	2	1	2	0	0	1	4	2	3	1	3	3	1	3	3	3	3	4	rs75403514	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:55965666A>G	ENST00000389286.4	-	10	1802	c.1755T>C	c.(1753-1755)agT>agC	p.S585S		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)		CCAGGTAGACACTGTCAGGTT	0.522													A|||	13	0.00259585	0.0	0.0014	5008	,	,		14634	0.0		0.0109	False		,,,				2504	0.001				p.S585S		Atlas-SNP	.											.	PRTG	110	.	0			c.T1755C						PASS	.	A		11,3823		0,11,1906	87	88	87		1755	-0.2	1	15	dbSNP_131	87	119,8139		4,111,4014	no	coding-synonymous	PRTG	NM_173814.4		4,122,5920	GG,GA,AA		1.441,0.2869,1.0751		585/1151	55965666	130,11962	1917	4129	6046	SO:0001819	synonymous_variant	283659	exon10			GTAGACACTGTCA	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.1755T>C	15.37:g.55965666A>G		176	0	0		154	72	0.467532	NM_173814		Silent	SNP	ENST00000389286.4	37	CCDS42040.1																																																																																			A|0.994;G|0.006	0.006	strong		0.522	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814		G	55965666	A	G	55965666	2	3	28	1	0	0	0	0	0	0	0	1	12650	156	6	3		3	PRTG	15	55965666	Silent	SNP	A	TCGA-G8-6914-01A-11D-2210-10	3330272	55965666	46565726	525	12028											
IGDCC4	57722	hgsc.bcm.edu	37	chr15	65688088	65688088	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cccgccccaggccgacgtacCccgtgccttctggtagtgga	5	7	12	17	4	1	0	0	0	1	0	1	2	1	1	7	3	2	2	7	3	2	3	rs201037111		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:65688088C>A	ENST00000352385.2	-	7	1620	c.1411G>T	c.(1411-1413)Ggc>Tgc	p.G471C		NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	471	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.					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						GCCGACGTACCCCGTGCCTTC	0.662																																					p.G471C		Atlas-SNP	.											.	IGDCC4	95	.	0			c.G1411T						PASS	.	C	CYS/GLY	1,4241		0,1,2120	7	7	7		1411	4.4	1	15		7	2,8360		0,2,4179	yes	missense-near-splice	IGDCC4	NM_020962.1	159	0,3,6299	AA,AC,CC		0.0239,0.0236,0.0238	probably-damaging	471/1251	65688088	3,12601	2121	4181	6302	SO:0001630	splice_region_variant	57722	exon7			ACGTACCCCGTGC		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.1411+1G>T	15.37:g.65688088C>A		26	0	0		35	17	0.485714	NM_020962	Q9HCE4	Missense_Mutation	SNP	ENST00000352385.2	37	CCDS10206.1	.	.	.	.	.	.	.	.	.	.	C	17.16	3.319127	0.60524	2.36E-4	2.39E-4	ENSG00000103742	ENST00000352385;ENST00000356152	T	0.59638	0.25	4.45	4.45	0.53987	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.055509	0.64402	D	0.000001	T	0.62636	0.2444	M	0.73217	2.22	0.80722	D	1	P	0.48764	0.915	P	0.45343	0.477	T	0.67499	-0.5655	9	.	.	.	-21.5089	17.4669	0.87635	0.0:1.0:0.0:0.0	.	471	Q8TDY8	IGDC4_HUMAN	C	471;200	ENSP00000319623:G471C	.	G	-	1	0	IGDCC4	63475141	1.000000	0.71417	0.981000	0.43875	0.079000	0.17450	6.706000	0.74649	2.187000	0.69744	0.462000	0.41574	GGC	.	.	weak		0.662	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962	Missense_Mutation	A	65688088	C	A	65688088	5	1	28	1	0	0	0	0	0	0	1	0	7578	637	22	4	2397	4	IGDCC4	15	65688088	Splice_Site	SNP	C	TCGA-G8-6914-01A-11D-2210-10	9722422	65688088	36843304	526	12029											
MEGF11	84465	hgsc.bcm.edu	37	chr15	66206303	66206303	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggattcagctcctccatcaTgagggcagctgcgggcagag	8	7	15	11	1	2	2	2	1	0	1	4	3	4	3	2	3	3	4	2	3	0	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:66206303T>C	ENST00000409699.2	-	20	2654	c.2482A>G	c.(2482-2484)Atg>Gtg	p.M828V	MEGF11_ENST00000395625.2_Missense_Mutation_p.M753V|MEGF11_ENST00000395614.1_Start_Codon_SNP_p.M1V|MEGF11_ENST00000288745.3_Missense_Mutation_p.M753V|MEGF11_ENST00000478721.1_5'UTR|MEGF11_ENST00000422354.1_Missense_Mutation_p.M828V|MEGF11_ENST00000360698.4_3'UTR			A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11	828					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						TCCTCCATCATGAGGGCAGCT	0.607																																					p.M828V		Atlas-SNP	.											.	MEGF11	70	.	0			c.A2482G						PASS	.						39	37	38					15																	66206303		2201	4299	6500	SO:0001583	missense	84465	exon20			CCATCATGAGGGC	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.2482A>G	15.37:g.66206303T>C	ENSP00000386908:p.Met828Val	64	0	0		56	25	0.446429	NM_032445	Q17R86|Q6UXS5|Q8ND91|Q96KG6	Missense_Mutation	SNP	ENST00000409699.2	37	CCDS10213.2	.	.	.	.	.	.	.	.	.	.	T	18.50	3.636511	0.67130	.	.	ENSG00000157890	ENST00000409699;ENST00000288745;ENST00000422354;ENST00000395625;ENST00000395614	T;T;T;T;T	0.34472	2.4;2.4;2.4;2.4;1.36	4.65	4.65	0.58169	.	0.000000	0.51477	U	0.000100	T	0.16342	0.0393	N	0.04508	-0.205	0.80722	D	1	B;B	0.25441	0.092;0.126	B;B	0.25987	0.065;0.039	T	0.10042	-1.0647	10	0.02654	T	1	.	14.2339	0.65911	0.0:0.0:0.0:1.0	.	828;753	A6BM72;A6BM72-2	MEG11_HUMAN;.	V	828;753;828;753;1	ENSP00000386908:M828V;ENSP00000288745:M753V;ENSP00000414475:M828V;ENSP00000378987:M753V;ENSP00000378976:M1V	ENSP00000288745:M753V	M	-	1	0	MEGF11	63993357	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.659000	0.61504	1.948000	0.56530	0.454000	0.30748	ATG	.	.	none		0.607	MEGF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329307.2	NM_032445		C	66206303	T	C	66206303	3	2	28	1	0	0	0	0	1	0	0	0	9470	1464	51	3	668	3	MEGF11	15	66206303	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	518215	66206303	36325089	527	12030											
MYO9A	4649	hgsc.bcm.edu	37	chr15	72170400	72170400	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctttgtggctgtgcaatctGaagtcttgaattcattcata	9	16	8	8	0	4	2	2	2	2	0	4	2	4	2	1	1	1	2	1	1	4	5	rs148435644	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:72170400G>A	ENST00000356056.5	-	31	6384	c.5912C>T	c.(5911-5913)tCa>tTa	p.S1971L	MYO9A_ENST00000444904.1_Missense_Mutation_p.S1952L|MYO9A_ENST00000564571.1_Missense_Mutation_p.S1971L|MYO9A_ENST00000424560.1_Missense_Mutation_p.S2042L	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1971	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						TGTGCAATCTGAAGTCTTGAA	0.343													G|||	56	0.0111821	0.0	0.0317	5008	,	,		16355	0.0		0.0338	False		,,,				2504	0.0				p.S1971L		Atlas-SNP	.											.	MYO9A	203	.	0			c.C5912T						PASS	.	G	LEU/SER	24,4374	29.9+/-59.1	1,22,2176	62	64	63		5912	0.1	0.5	15	dbSNP_134	63	287,8307	105.6+/-166.5	6,275,4016	yes	missense	MYO9A	NM_006901.2	145	7,297,6192	AA,AG,GG		3.3395,0.5457,2.3938	benign	1971/2549	72170400	311,12681	2199	4297	6496	SO:0001583	missense	4649	exon31			CAATCTGAAGTCT	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.5912C>T	15.37:g.72170400G>A	ENSP00000348349:p.Ser1971Leu	141	0	0		118	47	0.398305	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	37	CCDS10239.1	36	0.016483516483516484	0	0.0	11	0.03038674033149171	0	0.0	25	0.032981530343007916	G	1.667	-0.509968	0.04231	0.005457	0.033395	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	D;D;D	0.83591	-1.74;-1.73;-1.74	5.21	0.132	0.14762	.	.	.	.	.	T	0.31544	0.0800	N	0.01297	-0.9	0.20926	N	0.999826	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33979	-0.9847	9	0.22706	T	0.39	.	9.0444	0.36338	0.8015:0.0:0.1985:0.0	.	2042;1971	B2RTY4-4;B2RTY4	.;MYO9A_HUMAN	L	1971;2042;1952	ENSP00000348349:S1971L;ENSP00000399162:S2042L;ENSP00000398250:S1952L	ENSP00000348349:S1971L	S	-	2	0	MYO9A	69957454	0.999000	0.42202	0.470000	0.27216	0.826000	0.46750	2.312000	0.43726	0.174000	0.19809	0.591000	0.81541	TCA	G|0.977;A|0.023	0.023	strong		0.343	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		A	72170400	G	A	72170400	3	1	28	1	0	0	0	0	1	0	0	0	10093	1294	45	2	1782	2	MYO9A	15	72170400	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	5964097	72170400	30360992	528	12031											
SENP8	123228	hgsc.bcm.edu	37	chr15	72432140	72432140	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tttcatcagccctgaagtcaCccagttcatcaagtgcacta	11	11	6	13	0	5	1	5	1	0	0	5	1	5	1	2	0	2	2	2	0	3	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:72432140C>T	ENST00000542035.2	+	2	509	c.176C>T	c.(175-177)aCc>aTc	p.T59I	SENP8_ENST00000544411.1_Missense_Mutation_p.T59I|SENP8_ENST00000340912.4_Missense_Mutation_p.T59I|SENP8_ENST00000544171.1_Missense_Mutation_p.T59I|RP11-2I17.4_ENST00000568984.1_RNA	NM_001166340.1	NP_001159812.1	Q96LD8	SENP8_HUMAN	SUMO/sentrin specific peptidase family member 8	59	Protease.						cysteine-type peptidase activity (GO:0008234)			breast(1)|kidney(2)|lung(1)|ovary(1)|skin(1)	6						CCTGAAGTCACCCAGTTCATC	0.453																																					p.T59I		Atlas-SNP	.											.	SENP8	18	.	0			c.C176T						PASS	.						156	135	142					15																	72432140		2199	4297	6496	SO:0001583	missense	123228	exon2			AAGTCACCCAGTT	BC031411	CCDS10240.1	15q22.33	2005-08-17	2005-08-17	2004-01-30	ENSG00000166192	ENSG00000166192			22992	protein-coding gene	gene with protein product	"NEDD8-specific protease 1", "sentrin/SUMO-specific protease SENP8", "deneddylase 1"	608659	"protease, cysteine, 2 (NEDD8 specific)", "SUMO/sentrin specific protease family member 8"	PRSC2		12730221, 12759362	Standard	NM_145204		Approved	NEDP1, DEN1, HsT17512	uc021spt.1	Q96LD8	OTTHUMG00000133441	ENST00000542035.2:c.176C>T	15.37:g.72432140C>T	ENSP00000446057:p.Thr59Ile	106	0	0		125	5	0.04	NM_001166340	Q96QA4	Missense_Mutation	SNP	ENST00000542035.2	37	CCDS10240.1	.	.	.	.	.	.	.	.	.	.	C	19.03	3.747790	0.69533	.	.	ENSG00000166192	ENST00000542035;ENST00000544411;ENST00000340912;ENST00000544171	T;T;T;T	0.30448	1.53;1.53;1.53;1.53	5.62	4.71	0.59529	.	0.167236	0.52532	D	0.000072	T	0.40347	0.1113	M	0.70903	2.155	0.58432	D	0.999993	P	0.40332	0.713	P	0.45577	0.486	T	0.27606	-1.0069	10	0.42905	T	0.14	-21.7606	11.9463	0.52930	0.137:0.7313:0.1317:0.0	.	59	Q96LD8	SENP8_HUMAN	I	59	ENSP00000446057:T59I;ENSP00000441753:T59I;ENSP00000340505:T59I;ENSP00000439415:T59I	ENSP00000340505:T59I	T	+	2	0	SENP8	70219194	1.000000	0.71417	1.000000	0.80357	0.759000	0.43091	5.879000	0.69690	1.517000	0.48917	0.655000	0.94253	ACC	.	.	none		0.453	SENP8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420036.1	NM_145204		T	72432140	C	T	72432140	3	4	28	1	0	0	0	0	1	0	0	0	14067	507	18	2	178	2	SENP8	15	72432140	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	261740	72432140	30099252	529	12032											
NEIL1	79661	hgsc.bcm.edu	37	chr15	75646194	75646194	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gcaggaccggcatggccgtaCcatctggttccaggttgggc	6	8	15	12	2	1	0	0	0	1	0	2	1	2	1	4	6	1	5	4	6	1	3	rs142213781	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:75646194C>T	ENST00000564784.1	+	7	1462	c.833C>T	c.(832-834)aCc>aTc	p.T278I	NEIL1_ENST00000569035.1_Missense_Mutation_p.T278I|NEIL1_ENST00000355059.4_Missense_Mutation_p.T278I|RP11-817O13.6_ENST00000563660.1_lincRNA|MIR631_ENST00000384904.1_RNA			Q96FI4	NEIL1_HUMAN	nei endonuclease VIII-like 1 (E. coli)	278					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						CATGGCCGTACCATCTGGTTC	0.617								Base excision repair (BER), DNA glycosylases					C|||	3	0.000599042	0.0	0.0	5008	,	,		21794	0.0		0.001	False		,,,				2504	0.002				p.T364I		Atlas-SNP	.											.	NEIL1	36	.	0			c.C1091T						PASS	.	C	ILE/THR	0,4394		0,0,2197	79	83	81		833	5.1	1	15	dbSNP_134	81	6,8582	4.3+/-15.6	0,6,4288	yes	missense	NEIL1	NM_024608.2	89	0,6,6485	TT,TC,CC		0.0699,0.0,0.0462	probably-damaging	278/391	75646194	6,12976	2197	4294	6491	SO:0001583	missense	79661	exon6			GCCGTACCATCTG	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.833C>T	15.37:g.75646194C>T	ENSP00000457352:p.Thr278Ile	36	0	0		47	22	0.468085	NM_001256552	D3DW75|Q6ZRA7|Q86XW7|Q9H6C3	Missense_Mutation	SNP	ENST00000564784.1	37	CCDS10278.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	26.0	4.695071	0.88830	0.0	6.99E-4	ENSG00000140398	ENST00000355059	T	0.65916	-0.18	5.09	5.09	0.68999	Endonuclease VIII-like 1, DNA binding (1);	0.000000	0.85682	D	0.000000	T	0.77525	0.4143	L	0.61218	1.895	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.79836	-0.1635	10	0.72032	D	0.01	-31.8003	17.4649	0.87629	0.0:1.0:0.0:0.0	.	278	Q96FI4	NEIL1_HUMAN	I	278	ENSP00000347170:T278I	ENSP00000347170:T278I	T	+	2	0	NEIL1	73433247	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.710000	0.74670	2.375000	0.81037	0.561000	0.74099	ACC	C|0.999;T|0.001	0.001	strong		0.617	NEIL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419885.1	NM_024608		T	75646194	C	T	75646194	3	4	28	1	0	0	0	0	1	0	0	0	10327	507	18	2	851	2	NEIL1	15	75646194	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	3214054	75646194	26885198	530	12033											
CSPG4	1464	hgsc.bcm.edu	37	chr15	75981765	75981765	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tggggtgggtcattgacaggGttgacctggatgggcaggag	7	9	20	5	0	1	2	1	2	0	0	1	4	1	4	1	7	0	2	1	7	0	2	rs149356457	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:75981765G>T	ENST00000308508.5	-	3	1733	c.1641C>A	c.(1639-1641)aaC>aaA	p.N547K		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	547	Globular or compact configuration stabilized by disulfide bonds.|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						CATTGACAGGGTTGACCTGGA	0.622													G|||	5	0.000998403	0.0	0.0	5008	,	,		20725	0.0		0.001	False		,,,				2504	0.0041				p.N547K		Atlas-SNP	.											.	CSPG4	175	.	0			c.C1641A						PASS	.	G	LYS/ASN	1,4393		0,1,2196	35	31	32		1641	3.2	0.1	15	dbSNP_134	32	13,8563		0,13,4275	no	missense	CSPG4	NM_001897.4	94	0,14,6471	TT,TG,GG		0.1516,0.0228,0.1079	benign	547/2323	75981765	14,12956	2197	4288	6485	SO:0001583	missense	1464	exon3			GACAGGGTTGACC	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.1641C>A	15.37:g.75981765G>T	ENSP00000312506:p.Asn547Lys	69	0	0		100	41	0.41	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	2.454	-0.325794	0.05350	2.28E-4	0.001516	ENSG00000173546	ENST00000308508	T	0.45668	0.89	5.21	3.23	0.37069	.	0.608532	0.16274	N	0.221645	T	0.29288	0.0729	L	0.60455	1.87	0.41510	D	0.988332	B	0.32302	0.363	B	0.26969	0.075	T	0.08785	-1.0705	10	0.06236	T	0.91	.	5.9733	0.19365	0.1589:0.0:0.6881:0.153	.	547	Q6UVK1	CSPG4_HUMAN	K	547	ENSP00000312506:N547K	ENSP00000312506:N547K	N	-	3	2	CSPG4	73768820	0.381000	0.25140	0.100000	0.21137	0.055000	0.15305	0.522000	0.22909	0.507000	0.28148	0.555000	0.69702	AAC	G|0.998;T|0.002	0.002	strong		0.622	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		T	75981765	G	T	75981765	3	4	28	1	0	0	0	0	1	0	0	0	3962	1252	44	4	5359	4	CSPG4	15	75981765	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	335571	75981765	26549627	531	12034											
CTSH	1512	hgsc.bcm.edu	37	chr15	79224732	79224732	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accaaggacagcatctttccGgttgcgatggcgatcgcaga	10	8	12	11	4	1	1	0	0	1	1	3	4	2	2	2	3	2	3	2	3	1	2	rs149231812	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:79224732G>A	ENST00000220166.5	-	6	583	c.474C>T	c.(472-474)acC>acT	p.T158T	CTSH_ENST00000534533.1_5'UTR	NM_004390.3	NP_004381.2	P09668	CATH_HUMAN	cathepsin H	158					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						GCATCTTTCCGGTTGCGATGG	0.622																																					p.T158T		Atlas-SNP	.											.	CTSH	23	.	0			c.C474T						PASS	.	G		0,4392		0,0,2196	73	72	73		474	-9.4	0	15	dbSNP_134	73	7,8579	5.0+/-18.6	0,7,4286	no	coding-synonymous	CTSH	NM_004390.3		0,7,6482	AA,AG,GG		0.0815,0.0,0.0539		158/336	79224732	7,12971	2196	4293	6489	SO:0001819	synonymous_variant	1512	exon6			CTTTCCGGTTGCG	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.474C>T	15.37:g.79224732G>A		54	0	0		75	42	0.56	NM_004390	B2RBK0|Q96NY6|Q9BUM7	Silent	SNP	ENST00000220166.5	37	CCDS10308.1																																																																																			G|0.999;A|0.001	0.001	strong		0.622	CTSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291370.1	NM_004390		A	79224732	G	A	79224732	2	1	28	1	0	0	0	0	0	0	0	1	4038	1103	39	1		1	CTSH	15	79224732	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	3242967	79224732	23306660	532	12035											
RLBP1	6017	hgsc.bcm.edu	37	chr15	89753546	89753546	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gtgttctcagcttgggcctgGgggccaaagagctgctcagc	6	9	15	11	0	2	1	2	0	1	1	3	1	2	1	2	3	4	4	2	3	1	2	rs144615495	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:89753546G>C	ENST00000268125.5	-	9	1363	c.924C>G	c.(922-924)ccC>ccG	p.P308P		NM_000326.4	NP_000317.1	P12271	RLBP1_HUMAN	retinaldehyde binding protein 1	308					phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	cell body (GO:0044297)|cytosol (GO:0005829)	11-cis retinal binding (GO:0005502)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(1)|prostate(1)|skin(1)	18	Lung NSC(78;0.0472)|all_lung(78;0.089)				Vitamin A(DB00162)	CTTGGGCCTGGGGGCCAAAGA	0.562													G|||	2	0.000399361	0.0	0.0	5008	,	,		20947	0.0		0.002	False		,,,				2504	0.0				p.P308P		Atlas-SNP	.											.	RLBP1	34	.	0			c.C924G						PASS	.	G		1,4399	2.1+/-5.4	0,1,2199	94	92	93		924	-0.9	0.1	15	dbSNP_134	93	15,8583	11.2+/-40.8	0,15,4284	no	coding-synonymous	RLBP1	NM_000326.4		0,16,6483	CC,CG,GG		0.1745,0.0227,0.1231		308/318	89753546	16,12982	2200	4299	6499	SO:0001819	synonymous_variant	6017	exon9			GGCCTGGGGGCCA	BC004199	CCDS32324.1	15q26.1	2007-07-16	2001-11-28			ENSG00000140522			10024	protein-coding gene	gene with protein product		180090	"retinaldehyde-binding protein 1"			1733864, 9326942	Standard	NM_000326		Approved	CRALBP	uc002bnl.3	P12271		ENST00000268125.5:c.924C>G	15.37:g.89753546G>C		44	0	0		35	19	0.542857	NM_000326	B2R667	Silent	SNP	ENST00000268125.5	37	CCDS32324.1																																																																																			G|0.999;C|0.001	0.001	strong		0.562	RLBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421135.1	NM_000326		C	89753546	G	C	89753546	2	2	28	1	0	0	0	0	0	0	0	1	13403	1219	43	4		4	RLBP1	15	89753546	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	10528814	89753546	12777846	533	12036											
CHD2	1106	hgsc.bcm.edu	37	chr15	93557954	93557954	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gaagaaagacgacgtgactgGgggtaagaaaccatttcgtc	14	7	13	7	3	0	4	0	1	0	3	2	6	0	4	1	2	1	1	1	2	4	2	rs56227200	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:93557954G>C	ENST00000394196.4	+	37	5789	c.4721G>C	c.(4720-4722)gGg>gCg	p.G1574A	CHD2_ENST00000557381.1_Missense_Mutation_p.G1574A	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1574			G -> A (in dbSNP:rs56227200).		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)			GACGTGACTGGGGGTAAGAAA	0.483													G|||	53	0.0105831	0.0015	0.0173	5008	,	,		16711	0.0		0.0378	False		,,,				2504	0.001				p.G1574A		Atlas-SNP	.											.	CHD2	280	.	0			c.G4721C						PASS	.	G	ALA/GLY	22,4372	28.1+/-56.4	0,22,2175	96	101	99		4721	5.8	1	15	dbSNP_129	99	246,8350	97.2+/-158.9	1,244,4053	yes	missense	CHD2	NM_001271.3	60	1,266,6228	CC,CG,GG		2.8618,0.5007,2.0631	benign	1574/1829	93557954	268,12722	2197	4298	6495	SO:0001583	missense	1106	exon37			TGACTGGGGGTAA	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.4721G>C	15.37:g.93557954G>C	ENSP00000377747:p.Gly1574Ala	79	0	0		105	43	0.409524	NM_001271	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	37	CCDS10374.2	38	0.0173992673992674	0	0.0	8	0.022099447513812154	0	0.0	30	0.0395778364116095	G	4.134	0.023158	0.08006	0.005007	0.028618	ENSG00000173575	ENST00000394196;ENST00000557381;ENST00000557759	D;D;T	0.89343	-2.5;-2.49;0.98	5.76	5.76	0.90799	.	0.239796	0.21044	U	0.081118	T	0.51958	0.1705	N	0.19112	0.55	0.80722	D	1	B;B	0.26147	0.088;0.143	B;B	0.28465	0.025;0.09	T	0.66960	-0.5791	10	0.06236	T	0.91	-18.5026	13.4137	0.60956	0.0745:0.0:0.9255:0.0	rs56227200;rs61735574	1574;1574	O14647;O14647-2	CHD2_HUMAN;.	A	1574;1574;99	ENSP00000377747:G1574A;ENSP00000451366:G1574A;ENSP00000451539:G99A	ENSP00000377747:G1574A	G	+	2	0	CHD2	91358958	1.000000	0.71417	0.994000	0.49952	0.542000	0.35054	6.743000	0.74848	2.730000	0.93505	0.591000	0.81541	GGG	G|0.981;C|0.019	0.019	strong		0.483	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271		C	93557954	G	C	93557954	3	2	28	1	0	0	0	0	1	0	0	0	3327	1232	43	4	4867	4	CHD2	15	93557954	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	3804408	93557954	8973438	534	12037											
WDR90	197335	hgsc.bcm.edu	37	chr16	703648	703648	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtgcctgttccggagcccaAtgcacgttgtctgctctctc	4	13	10	14	2	2	0	0	0	2	0	5	1	3	1	3	1	4	4	3	1	1	2	rs143047488	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:703648A>G	ENST00000293879.4	+	12	1357	c.1357A>G	c.(1357-1359)Atg>Gtg	p.M453V	WDR90_ENST00000549091.1_Missense_Mutation_p.M453V|LA16c-349E10.1_ENST00000573609.1_RNA			Q96KV7	WDR90_HUMAN	WD repeat domain 90	453										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CCGGAGCCCAATGCACGTTGT	0.637													A|||	7	0.00139776	0.0	0.0014	5008	,	,		18008	0.001		0.004	False		,,,				2504	0.001				p.M453V		Atlas-SNP	.											.	WDR90	107	.	0			c.A1357G						PASS	.	A	VAL/MET	1,4113		0,1,2056	55	61	59		1357	-5.9	0	16	dbSNP_134	59	14,8368		0,14,4177	yes	missense	WDR90	NM_145294.4	21	0,15,6233	GG,GA,AA		0.167,0.0243,0.12	benign	453/1749	703648	15,12481	2057	4191	6248	SO:0001583	missense	197335	exon12			AGCCCAATGCACG	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.1357A>G	16.37:g.703648A>G	ENSP00000293879:p.Met453Val	94	0	0		61	34	0.557377	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	37	CCDS42092.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	0	-2.592739	0.00126	2.43E-4	0.00167	ENSG00000161996	ENST00000549091;ENST00000293879	T;T	0.01265	5.08;5.08	4.74	-5.88	0.02290	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	0.312485	0.23962	N	0.042850	T	0.00440	0.0014	N	0.00560	-1.38	0.19300	N	0.999974	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.44997	-0.9291	10	0.20519	T	0.43	.	7.8237	0.29303	0.3658:0.2096:0.4247:0.0	.	453;454;453	Q96KV7;C9JMK1;Q96KV7-3	WDR90_HUMAN;.;.	V	453	ENSP00000448122:M453V;ENSP00000293879:M453V	ENSP00000293879:M453V	M	+	1	0	WDR90	643649	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.485000	0.06520	-1.101000	0.03027	-1.545000	0.00906	ATG	A|0.997;G|0.003	0.003	strong		0.637	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294		G	703648	A	G	703648	3	3	28	1	0	0	0	0	1	0	0	0	17352	101	4	3	1403	3	WDR90	16	703648	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10		703648	89651105	535	12038											
WDR90	197335	hgsc.bcm.edu	37	chr16	716971	716971	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcccccgggacccacctcCtggctgttggctttgctggt	2	12	12	15	1	0	0	0	0	0	0	2	1	2	1	5	4	1	4	5	4	0	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:716971C>T	ENST00000293879.4	+	40	5071	c.5071C>T	c.(5071-5073)Ctg>Ttg	p.L1691L	WDR90_ENST00000549091.1_Silent_p.L1693L|WDR90_ENST00000547944.1_Silent_p.L290L|WDR90_ENST00000315764.4_Silent_p.L242L|RHOT2_ENST00000315082.4_5'Flank			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1691										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				GACCCACCTCCTGGCTGTTGG	0.617																																					p.L1691L		Atlas-SNP	.											.	WDR90	107	.	0			c.C5071T						PASS	.						69	73	72					16																	716971		2108	4232	6340	SO:0001819	synonymous_variant	197335	exon40			CACCTCCTGGCTG	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.5071C>T	16.37:g.716971C>T		113	0	0		100	51	0.51	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Silent	SNP	ENST00000293879.4	37	CCDS42092.1																																																																																			.	.	none		0.617	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294		T	716971	C	T	716971	2	4	28	1	0	0	0	0	0	0	0	1	17352	680	24	2		2	WDR90	16	716971	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	13323	716971	89637782	536	12039											
CCDC78	124093	hgsc.bcm.edu	37	chr16	775236	775236	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctaggtggctgcacactcaCgccgctccccagcctgtgct	5	8	11	17	2	1	0	1	0	0	0	2	0	2	0	4	2	3	5	4	2	1	1	rs138669350	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:775236C>T	ENST00000293889.6	-	5	598		c.e5+1		HAGHL_ENST00000341413.4_5'Flank|HAGHL_ENST00000389703.3_5'Flank|HAGHL_ENST00000561546.1_5'Flank|HAGHL_ENST00000564537.1_5'Flank|HAGHL_ENST00000564545.1_5'Flank|HAGHL_ENST00000549114.1_5'Flank	NM_001031737.2	NP_001026907.2	A2IDD5	CCD78_HUMAN	coiled-coil domain containing 78						cell projection organization (GO:0030030)|de novo centriole assembly (GO:0098535)|skeletal muscle contraction (GO:0003009)	centriole (GO:0005814)|deuterosome (GO:0098536)|perinuclear region of cytoplasm (GO:0048471)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|lung(2)|skin(3)	9		Hepatocellular(780;0.0218)				TGCACACTCACGCCGCTCCCC	0.642													C|||	7	0.00139776	0.0008	0.0029	5008	,	,		17690	0.0		0.003	False		,,,				2504	0.001				.		Atlas-SNP	.											.	CCDC78	26	.	0			c.492+1G>A						PASS	.	C		7,4383	11.4+/-27.6	0,7,2188	63	74	70			-0.3	0	16	dbSNP_134	70	13,8577	9.8+/-36.6	0,13,4282	yes	splice-5	CCDC78	NM_001031737.2		0,20,6470	TT,TC,CC		0.1513,0.1595,0.1541			775236	20,12960	2195	4295	6490	SO:0001630	splice_region_variant	124093	exon6			CACTCACGCCGCT	BC042110	CCDS32353.1	16p13.3	2014-07-15		2006-02-20	ENSG00000162004	ENSG00000162004			14153	protein-coding gene	gene with protein product		614666		C16orf25		24075808	Standard	NM_001031737		Approved	FLJ34512	uc002cjg.3	A2IDD5	OTTHUMG00000121176	ENST00000293889.6:c.492+1G>A	16.37:g.775236C>T		59	0	0		65	34	0.523077	NM_001031737	B4DNY4|B4E1U6|Q05BY7|Q05CA0|Q6T2V5|Q6ZR33|Q8IUR3|Q8NAY7|Q96S12	Splice_Site	SNP	ENST00000293889.6	37	CCDS32353.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	4.939	0.174544	0.09391	0.001595	0.001513	ENSG00000162004	ENST00000345165;ENST00000293889	.	.	.	3.84	-0.34	0.12643	.	.	.	.	.	.	.	.	.	.	.	0.21325	N	0.999729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.3859	0.21559	0.0:0.5601:0.0:0.4399	.	.	.	.	.	-1	.	.	.	-	.	.	CCDC78	715237	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.394000	0.07296	-0.010000	0.14271	0.561000	0.74099	.	C|0.998;T|0.002	0.002	strong		0.642	CCDC78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241665.3	NM_173476	Intron	T	775236	C	T	775236	5	4	28	1	0	0	0	0	0	0	1	0	2854	550	19	1	863	1	CCDC78	16	775236	Splice_Site	SNP	C	TCGA-G8-6914-01A-11D-2210-10	58265	775236	89579517	537	12040											
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1256127	1256127	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggagatcgtggggcaggCggacggtggcttgtctgtgc	4	9	20	8	3	1	1	0	0	1	1	2	3	1	2	0	7	1	2	0	7	0	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1256127C>T	ENST00000348261.5	+	12	2875	c.2627C>T	c.(2626-2628)gCg>gTg	p.A876V	CACNA1H_ENST00000358590.4_Missense_Mutation_p.A876V|CACNA1H_ENST00000565831.1_Missense_Mutation_p.A876V|RP11-616M22.3_ENST00000564700.1_RNA	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	876					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)	GTGGGGCAGGCGGACGGTGGC	0.701																																					p.A876V		Atlas-SNP	.											.	CACNA1H	317	.	0			c.C2627T						PASS	.																																			SO:0001583	missense	8912	exon12			GGCAGGCGGACGG	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.2627C>T	16.37:g.1256127C>T	ENSP00000334198:p.Ala876Val	54	0	0		49	12	0.244898	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	C	18.36	3.607711	0.66558	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.98419	-4.92;-4.92	3.96	3.96	0.45880	Ion transport (1);	0.416444	0.21210	N	0.078324	D	0.97782	0.9272	L	0.39467	1.215	0.37503	D	0.91685	D;D	0.69078	0.997;0.989	P;P	0.61658	0.892;0.805	D	0.99229	1.0881	10	0.46703	T	0.11	.	15.1886	0.73025	0.0:1.0:0.0:0.0	.	876;876	O95180-2;O95180	.;CAC1H_HUMAN	V	876	ENSP00000334198:A876V;ENSP00000351401:A876V	ENSP00000334198:A876V	A	+	2	0	CACNA1H	1196128	1.000000	0.71417	0.943000	0.38184	0.404000	0.30871	4.442000	0.59988	2.050000	0.60909	0.561000	0.74099	GCG	.	.	none		0.701	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		T	1256127	C	T	1256127	3	4	28	1	0	0	0	0	1	0	0	0	2547	768	27	1	2669	1	CACNA1H	16	1256127	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	480891	1256127	89098626	538	12041											
PTX4	390667	hgsc.bcm.edu	37	chr16	1537956	1537956	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	caggtgtgtccaggtcacctCctggaatctccggaactgta	8	10	11	12	1	2	0	1	0	1	0	5	2	4	2	4	4	1	1	4	4	3	1	rs144904207	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1537956C>G	ENST00000447419.2	-	2	182	c.157G>C	c.(157-159)Gag>Cag	p.E53Q	PTX4_ENST00000440447.2_Missense_Mutation_p.E53Q|PTX4_ENST00000293922.1_Missense_Mutation_p.E48Q			Q96A99	PTX4_HUMAN	pentraxin 4, long	53						extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						CAGGTCACCTCCTGGAATCTC	0.632													C|||	3	0.000599042	0.0	0.0	5008	,	,		16358	0.0		0.003	False		,,,				2504	0.0				p.E48Q		Atlas-SNP	.											.	PTX4	46	.	0			c.G142C						PASS	.	C	GLN/GLU	0,4236		0,0,2118	81	81	81		142	4.7	0.1	16	dbSNP_134	81	10,8270		0,10,4130	yes	missense	PTX4	NM_001013658.1	29	0,10,6248	GG,GC,CC		0.1208,0.0,0.0799	benign	48/474	1537956	10,12506	2118	4140	6258	SO:0001583	missense	390667	exon2			TCACCTCCTGGAA		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"chromosome 16 open reading frame 38"	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.157G>C	16.37:g.1537956C>G	ENSP00000445277:p.Glu53Gln	43	0	0		48	25	0.520833	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		.	.	.	.	.	.	.	.	.	.	C	6.632	0.485074	0.12641	0.0	0.001208	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.06768	3.39;3.26	5.68	4.71	0.59529	.	0.500926	0.20061	N	0.100088	T	0.07728	0.0194	L	0.34521	1.04	0.20196	N	0.999925	B	0.30033	0.266	B	0.30401	0.115	T	0.31475	-0.9942	10	0.23302	T	0.38	.	12.3329	0.55049	0.0:0.8226:0.1774:0.0	.	48	Q96A99-2	.	Q	53;48	ENSP00000445277:E53Q;ENSP00000293922:E48Q	ENSP00000293922:E48Q	E	-	1	0	PTX4	1477957	1.000000	0.71417	0.060000	0.19600	0.002000	0.02628	2.545000	0.45769	1.368000	0.46115	0.563000	0.77884	GAG	C|0.998;G|0.002	0.002	strong		0.632	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658		G	1537956	C	G	1537956	3	3	28	1	0	0	0	0	1	0	0	0	12838	864	30	4	1286	4	PTX4	16	1537956	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	281829	1537956	88816797	539	12042											
MAPK8IP3	23162	hgsc.bcm.edu	37	chr16	1817855	1817855	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cgcatcacggccctgcttgtCgcgggcagccggctctgggt	3	8	15	15	5	2	0	1	0	1	0	3	0	2	0	2	4	2	4	2	4	0	1	rs118038816	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1817855C>T	ENST00000250894.4	+	28	3613	c.3456C>T	c.(3454-3456)gtC>gtT	p.V1152V	MAPK8IP3_ENST00000356010.5_Silent_p.V1146V	NM_015133.3	NP_055948.2	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting protein 3	1152					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						CCCTGCTTGTCGCGGGCAGCC	0.667													C|||	46	0.0091853	0.0189	0.0014	5008	,	,		18035	0.0		0.005	False		,,,				2504	0.0153				p.V1152V		Atlas-SNP	.											.	MAPK8IP3	164	.	0			c.C3456T						PASS	.	C	,	63,4141		0,63,2039	61	73	69		3438,3456	-5.8	0.1	16	dbSNP_132	69	31,8405		0,31,4187	no	coding-synonymous,coding-synonymous	MAPK8IP3	NM_001040439.1,NM_015133.3	,	0,94,6226	TT,TC,CC		0.3675,1.4986,0.7437	,	1146/1331,1152/1337	1817855	94,12546	2102	4218	6320	SO:0001819	synonymous_variant	23162	exon28			GCTTGTCGCGGGC	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.3456C>T	16.37:g.1817855C>T		65	0	0		84	47	0.559524	NM_015133	A2A2B3|A7E2B3|Q96RY4|Q9H4I4|Q9H7P1|Q9NUG0	Silent	SNP	ENST00000250894.4	37	CCDS10442.2																																																																																			C|0.995;T|0.005	0.005	strong		0.667	MAPK8IP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250508.2	NM_001040439		T	1817855	C	T	1817855	2	4	28	1	0	0	0	0	0	0	0	1	9295	871	31	1		1	MAPK8IP3	16	1817855	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	279899	1817855	88536898	540	12043											
NTN3	4917	hgsc.bcm.edu	37	chr16	2522536	2522536	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgatctgcgactgtcggcaTggcaccgagggccctgactg	6	8	14	13	3	1	2	0	2	1	0	2	4	1	2	2	3	1	2	2	3	0	0	rs148996457		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:2522536T>C	ENST00000293973.1	+	1	1037	c.834T>C	c.(832-834)caT>caC	p.H278H	TBC1D24_ENST00000293970.5_5'Flank|TBC1D24_ENST00000567020.1_5'Flank	NM_006181.2	NP_006172.1	O00634	NET3_HUMAN	netrin 3	278	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)	Golgi apparatus (GO:0005794)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|central_nervous_system(2)|lung(3)|prostate(1)	7						ACTGTCGGCATGGCACCGAGG	0.687																																					p.H278H		Atlas-SNP	.											.	NTN3	28	.	0			c.T834C						PASS	.	T		0,4370		0,0,2185	26	26	26		834	-6.5	0.7	16	dbSNP_134	26	3,8559		0,3,4278	no	coding-synonymous	NTN3	NM_006181.2		0,3,6463	CC,CT,TT		0.035,0.0,0.0232		278/581	2522536	3,12929	2185	4281	6466	SO:0001819	synonymous_variant	4917	exon1			TCGGCATGGCACC	U86759	CCDS10469.1	16p13.3	2013-03-01	2008-10-29	2008-10-29	ENSG00000162068	ENSG00000162068		"Netrins"	8030	protein-coding gene	gene with protein product	"Netrin-3"	602349	"netrin 2 (chicken)-like", "netrin 2-like (chicken)"	NTN2L		9143507, 10366627	Standard	NM_006181		Approved		uc002cqj.3	O00634	OTTHUMG00000128867	ENST00000293973.1:c.834T>C	16.37:g.2522536T>C		31	0	0		33	17	0.515152	NM_006181		Silent	SNP	ENST00000293973.1	37	CCDS10469.1																																																																																			T|1.000;C|0.000	0.000	weak		0.687	NTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250812.1	NM_006181		C	2522536	T	C	2522536	2	2	28	1	0	0	0	0	0	0	0	1	10710	1461	51	3		3	NTN3	16	2522536	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	704681	2522536	87832217	541	12044											
ALG1	56052	hgsc.bcm.edu	37	chr16	5123201	5123201	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcaaagttgtacttcaggctAtgtacttgctgtggaagttg	9	15	11	6	0	2	0	2	0	0	0	2	1	2	1	0	2	3	6	0	2	5	7	rs113219939	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:5123201A>C	ENST00000262374.5	+	3	365	c.334A>C	c.(334-336)Atg>Ctg	p.M112L	ALG1_ENST00000588623.1_Start_Codon_SNP_p.M1L|ALG1_ENST00000544428.1_Start_Codon_SNP_p.M1L	NM_019109.4	NP_061982.3	Q9BT22	ALG1_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase	112					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)				ACTTCAGGCTATGTACTTGCT	0.512													A|||	66	0.0131789	0.0492	0.0014	5008	,	,		19810	0.0		0.0	False		,,,				2504	0.0				p.M112L		Atlas-SNP	.											.	ALG1	35	.	0			c.A334C						PASS	.	A	LEU/MET	169,4225	112.5+/-150.6	4,161,2032	251	230	237		334	-2.3	0	16	dbSNP_132	237	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ALG1	NM_019109.4	15	4,162,6331	CC,CA,AA		0.0116,3.8462,1.3083	benign	112/465	5123201	170,12824	2197	4300	6497	SO:0001583	missense	56052	exon3			CAGGCTATGTACT	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.334A>C	16.37:g.5123201A>C	ENSP00000262374:p.Met112Leu	224	0	0		220	96	0.436364	NM_019109	B4DP08|Q6UVZ9|Q8N5Y4|Q9P2Y2	Missense_Mutation	SNP	ENST00000262374.5	37	CCDS10528.1	22	0.010073260073260074	21	0.042682926829268296	1	0.0027624309392265192	0	0.0	0	0.0	A	0.289	-0.981205	0.02197	0.038462	1.16E-4	ENSG00000033011	ENST00000262374;ENST00000544428	T;T	0.80994	-1.44;-0.88	4.82	-2.31	0.06765	.	0.580414	0.18457	N	0.140653	T	0.08626	0.0214	N	0.00221	-1.82	0.45046	D	0.99806	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44236	-0.9341	10	0.02654	T	1	-10.1101	0.992	0.01459	0.1831:0.3173:0.2475:0.2521	.	1;112	B4DP08;Q9BT22	.;ALG1_HUMAN	L	112;1	ENSP00000262374:M112L;ENSP00000440019:M1L	ENSP00000262374:M112L	M	+	1	0	ALG1	5063202	0.004000	0.15560	0.022000	0.16811	0.284000	0.27059	-0.033000	0.12246	-0.059000	0.13154	-0.337000	0.08149	ATG	A|0.984;C|0.016	0.016	strong		0.512	ALG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251716.2	NM_019109		C	5123201	A	C	5123201	3	2	28	1	0	0	0	0	1	0	0	0	510	449	16	5	344	5	ALG1	16	5123201	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	2600665	5123201	85231552	542	12045											
ALG1	56052	hgsc.bcm.edu	37	chr16	5127460	5127460	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttcaggtacgagaagttctTtgggcgcctgtcccacctga	7	12	11	11	2	2	2	1	1	1	1	3	3	3	2	3	2	1	2	3	2	2	4	rs112668461	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:5127460T>G	ENST00000262374.5	+	5	585	c.554T>G	c.(553-555)tTt>tGt	p.F185C	ALG1_ENST00000588623.1_Missense_Mutation_p.F74C|ALG1_ENST00000544428.1_Missense_Mutation_p.F74C	NM_019109.4	NP_061982.3	Q9BT22	ALG1_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase	185					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)				GAGAAGTTCTTTGGGCGCCTG	0.557													T|||	73	0.0145767	0.0545	0.0014	5008	,	,		15459	0.0		0.0	False		,,,				2504	0.0				p.F185C		Atlas-SNP	.											.	ALG1	35	.	0			c.T554G						PASS	.	T	CYS/PHE	179,4215	115.9+/-153.8	4,171,2022	102	92	96		554	-0.3	0.1	16	dbSNP_132	96	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ALG1	NM_019109.4	205	4,172,6321	GG,GT,TT		0.0116,4.0737,1.3853	benign	185/465	5127460	180,12814	2197	4300	6497	SO:0001583	missense	56052	exon5			AGTTCTTTGGGCG	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.554T>G	16.37:g.5127460T>G	ENSP00000262374:p.Phe185Cys	62	0	0		61	27	0.442623	NM_019109	B4DP08|Q6UVZ9|Q8N5Y4|Q9P2Y2	Missense_Mutation	SNP	ENST00000262374.5	37	CCDS10528.1	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	T	10.06	1.246611	0.22796	0.040737	1.16E-4	ENSG00000033011	ENST00000262374;ENST00000544428	D;D	0.86297	-2.1;-2.1	5.79	-0.341	0.12639	.	0.364426	0.34223	N	0.004141	T	0.55529	0.1926	L	0.45422	1.42	0.54753	D	0.999989	B;B	0.22746	0.011;0.074	B;B	0.22152	0.009;0.038	T	0.64166	-0.6471	10	0.49607	T	0.09	-2.3162	14.4032	0.67063	0.0:0.0:0.338:0.662	.	74;185	B4DP08;Q9BT22	.;ALG1_HUMAN	C	185;74	ENSP00000262374:F185C;ENSP00000440019:F74C	ENSP00000262374:F185C	F	+	2	0	ALG1	5067461	0.953000	0.32496	0.133000	0.22050	0.575000	0.36095	1.537000	0.36083	-0.348000	0.08286	0.459000	0.35465	TTT	T|0.982;G|0.018	0.018	strong		0.557	ALG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251716.2	NM_019109		G	5127460	T	G	5127460	3	3	28	1	0	0	0	0	1	0	0	0	510	1841	64	5	572	5	ALG1	16	5127460	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	4259	5127460	85227293	543	12046											
CLEC16A	23274	hgsc.bcm.edu	37	chr16	11272479	11272479	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccgctgtccacgccggctGccgcctgcacagagcccgtg	4	5	12	20	5	0	1	0	0	0	1	1	1	1	1	7	1	3	3	7	1	0	0	rs74163631		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:11272479G>A	ENST00000409790.1	+	24	3324	c.3094G>A	c.(3094-3096)Gcc>Acc	p.A1032T	CLEC16A_ENST00000381822.2_Missense_Mutation_p.A119T	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						CACGCCGGCTGCCGCCTGCAC	0.687																																					p.A1032T		Atlas-SNP	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.G3094A						PASS	.	G	THR/ALA	0,4094		0,0,2047	10	13	12		3094	-7.3	0	16	dbSNP_130	12	2,8338		0,2,4168	no	missense	CLEC16A	NM_015226.2	58	0,2,6215	AA,AG,GG		0.024,0.0,0.0161	benign	1032/1054	11272479	2,12432	2047	4170	6217	SO:0001583	missense	23274	exon23			CCGGCTGCCGCCT	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.3094G>A	16.37:g.11272479G>A	ENSP00000387122:p.Ala1032Thr	10	0	0		26	13	0.5	NM_015226		Missense_Mutation	SNP	ENST00000409790.1	37	CCDS45409.1	.	.	.	.	.	.	.	.	.	.	G	13.01	2.109842	0.37242	0.0	2.4E-4	ENSG00000038532	ENST00000409790;ENST00000542102;ENST00000381822	T	0.44083	0.93	4.4	-7.33	0.01431	.	1.036120	0.07675	N	0.936064	T	0.15089	0.0364	N	0.08118	0	0.09310	N	1	B;B	0.28350	0.208;0.002	B;B	0.22152	0.038;0.004	T	0.15723	-1.0427	10	0.49607	T	0.09	0.8435	1.4953	0.02465	0.3763:0.2341:0.2704:0.1192	.	119;1032	Q2KHT3-3;Q2KHT3	.;CL16A_HUMAN	T	1032;1032;119	ENSP00000387122:A1032T	ENSP00000371244:A119T	A	+	1	0	CLEC16A	11179980	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.117000	0.10708	-1.280000	0.02402	-0.140000	0.14226	GCC	.	.	weak		0.687	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226		A	11272479	G	A	11272479	3	1	28	1	0	0	0	0	1	0	0	0	3502	1319	46	2	3184	2	CLEC16A	16	11272479	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	6145019	11272479	79082274	544	12047											
RSL1D1	26156	hgsc.bcm.edu	37	chr16	11935639	11935639	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgggaagtgcagccgatttCtcagttttcacaaacaggag	12	10	11	8	1	2	0	2	0	1	0	3	3	2	2	1	2	3	2	1	2	2	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:11935639C>A	ENST00000571133.1	-	7	840	c.768G>T	c.(766-768)gaG>gaT	p.E256D	RSL1D1_ENST00000542106.1_Missense_Mutation_p.E36D	NM_015659.2	NP_056474.2	O76021	RL1D1_HUMAN	ribosomal L1 domain containing 1	256					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						CAGCCGATTTCTCAGTTTTCA	0.358																																					p.E256D		Atlas-SNP	.											.	RSL1D1	40	.	0			c.G768T						PASS	.						71	72	72					16																	11935639		2197	4300	6497	SO:0001583	missense	26156	exon7			CGATTTCTCAGTT	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.768G>T	16.37:g.11935639C>A	ENSP00000460871:p.Glu256Asp	74	0	0		92	44	0.478261	NM_015659	B4DJ58|D3DUG7|Q2M1T7|Q6PL22|Q8IWS7|Q8WUZ1|Q9HDA9|Q9Y3Z9	Missense_Mutation	SNP	ENST00000571133.1	37	CCDS10551.1	.	.	.	.	.	.	.	.	.	.	C	11.36	1.615664	0.28801	.	.	ENSG00000171490	ENST00000355674;ENST00000396503;ENST00000542106	T	0.42513	0.97	4.91	2.53	0.30540	Ribosomal protein L1, 2-layer alpha/beta-sandwich (1);Ribosomal protein L1, superfamily (1);	0.556020	0.17525	N	0.171095	T	0.50718	0.1632	M	0.72479	2.2	0.19300	N	0.999975	D;P	0.55800	0.973;0.952	P;P	0.58928	0.848;0.785	T	0.35699	-0.9778	10	0.21014	T	0.42	-11.795	5.6426	0.17572	0.3284:0.5515:0.0:0.12	.	256;256	Q32Q62;O76021	.;RL1D1_HUMAN	D	255;256;36	ENSP00000347897:E255D	ENSP00000347897:E255D	E	-	3	2	RSL1D1	11843140	0.118000	0.22208	0.556000	0.28293	0.161000	0.22273	-0.318000	0.08050	0.599000	0.29845	-2.175000	0.00321	GAG	.	.	none		0.358	RSL1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252059.2	NM_015659		A	11935639	C	A	11935639	3	1	28	1	0	0	0	0	1	0	0	0	13715	912	32	4	716	4	RSL1D1	16	11935639	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	663160	11935639	78419114	545	12048											
PDXDC1	23042	hgsc.bcm.edu	37	chr16	15127249	15127249	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcccgggagatagaggagaActcgagggtccgtagcaccc	11	4	15	11	3	0	3	0	0	0	3	2	6	1	3	3	3	3	2	3	3	3	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:15127249A>G	ENST00000396410.4	+	19	1902	c.1805A>G	c.(1804-1806)aAc>aGc	p.N602S	PDXDC1_ENST00000447912.2_Missense_Mutation_p.N511S|PDXDC1_ENST00000569715.1_Missense_Mutation_p.N575S|PDXDC1_ENST00000325823.7_Missense_Mutation_p.N587S|PDXDC1_ENST00000563679.1_Missense_Mutation_p.N620S|PDXDC1_ENST00000535621.2_Intron|PDXDC1_ENST00000450288.2_Missense_Mutation_p.N574S	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	602					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						ATAGAGGAGAACTCGAGGGTC	0.572																																					p.N602S		Atlas-SNP	.											.	PDXDC1	59	.	0			c.A1805G						PASS	.						120	112	115					16																	15127249		2197	4300	6497	SO:0001583	missense	23042	exon19			AGGAGAACTCGAG	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.1805A>G	16.37:g.15127249A>G	ENSP00000379691:p.Asn602Ser	62	0	0		72	46	0.638889	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Missense_Mutation	SNP	ENST00000396410.4	37	CCDS32393.1	.	.	.	.	.	.	.	.	.	.	A	9.764	1.170997	0.21621	.	.	ENSG00000179889	ENST00000325823;ENST00000447912;ENST00000396410;ENST00000450288	T;T;T;T	0.71698	-0.59;-0.59;-0.59;-0.59	5.83	5.83	0.93111	.	0.077261	0.85682	D	0.000000	T	0.54806	0.1881	N	0.17631	0.505	0.80722	D	1	B;B;B;B	0.26400	0.021;0.148;0.021;0.037	B;B;B;B	0.23574	0.029;0.047;0.029;0.029	T	0.52902	-0.8513	10	0.12103	T	0.63	-25.0955	15.3837	0.74681	1.0:0.0:0.0:0.0	.	574;511;574;602	E7EPL4;E7EMH5;B4DR55;Q6P996	.;.;.;PDXD1_HUMAN	S	587;511;602;574	ENSP00000322807:N587S;ENSP00000400310:N511S;ENSP00000379691:N602S;ENSP00000391147:N574S	ENSP00000322807:N587S	N	+	2	0	PDXDC1	15034750	1.000000	0.71417	0.994000	0.49952	0.218000	0.24690	4.530000	0.60595	2.231000	0.72958	0.459000	0.35465	AAC	.	.	none		0.572	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027		G	15127249	A	G	15127249	3	3	28	1	0	0	0	0	1	0	0	0	11705	43	2	3	1879	3	PDXDC1	16	15127249	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	3191610	15127249	75227504	546	12049											
RRN3	54700	hgsc.bcm.edu	37	chr16	15188018	15188018	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ttacccagtcctcgacgcgcCcagcttcttaactgcagagg	8	9	9	15	3	1	1	0	0	1	1	3	2	2	1	3	1	4	2	3	1	2	3	rs141593500	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:15188018C>T	ENST00000198767.6	-	1	156	c.73G>A	c.(73-75)Ggc>Agc	p.G25S	RRN3_ENST00000429751.2_Missense_Mutation_p.G25S|RRN3_ENST00000564131.1_Missense_Mutation_p.G25S|RRN3_ENST00000563559.1_Missense_Mutation_p.G25S|RP11-72I8.1_ENST00000569858.1_RNA|PDXDC1_ENST00000535621.2_Intron|RRN3_ENST00000327307.7_5'Flank	NM_018427.3	NP_060897.3	Q9NYV6	RRN3_HUMAN	RRN3 RNA polymerase I transcription factor homolog (S. cerevisiae)	25					cell proliferation (GO:0008283)|cytoplasm organization (GO:0007028)|gene expression (GO:0010467)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902254)|nucleolus organization (GO:0007000)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, initiation (GO:2000142)|ribosome biogenesis (GO:0042254)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(2)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)	20						CTCGACGCGCCCAGCTTCTTA	0.617													.|||	5	0.000998403	0.0	0.0	5008	,	,		9426	0.0		0.0	False		,,,				2504	0.0051				p.G25S		Atlas-SNP	.											.	RRN3	36	.	0			c.G73A						PASS	.	C	SER/GLY	0,4394		0,0,2197	26	23	24		73	1.1	0	16	dbSNP_134	24	4,8596		0,4,4296	yes	missense	RRN3	NM_018427.3	56	0,4,6493	TT,TC,CC		0.0465,0.0,0.0308	benign	25/652	15188018	4,12990	2197	4300	6497	SO:0001583	missense	54700	exon1			ACGCGCCCAGCTT	AF227156	CCDS10559.1, CCDS73833.1	16p13.11	2009-10-26	2006-04-04		ENSG00000085721	ENSG00000085721			30346	protein-coding gene	gene with protein product		605121	"RRN3 RNA polymerase I transcription factor homolog (yeast)"			10758157, 11250903	Standard	XM_005255375		Approved	DKFZp566E104	uc002dde.3	Q9NYV6	OTTHUMG00000129847	ENST00000198767.6:c.73G>A	16.37:g.15188018C>T	ENSP00000198767:p.Gly25Ser	124	0	0		120	60	0.5	NM_018427	A2RTY9|B4E0J7|B4E3T2|Q3MHU9|Q6IPL4|Q9H4F0	Missense_Mutation	SNP	ENST00000198767.6	37	CCDS10559.1	.	.	.	.	.	.	.	.	.	.	.	12.30	1.897935	0.33535	0.0	4.65E-4	ENSG00000085721	ENST00000198767;ENST00000429751	T;T	0.44881	1.0;0.91	3.13	1.07	0.20283	.	.	.	.	.	T	0.17195	0.0413	N	0.08118	0	0.26447	N	0.975673	B;B;B	0.13145	0.0;0.007;0.001	B;B;B	0.12156	0.003;0.007;0.003	T	0.30327	-0.9982	9	0.07813	T	0.8	.	4.8484	0.13524	0.0:0.6849:0.0:0.3151	.	25;25;25	F5H148;Q3MHU9;Q9NYV6	.;.;RRN3_HUMAN	S	25	ENSP00000198767:G25S;ENSP00000402027:G25S	ENSP00000198767:G25S	G	-	1	0	RRN3	15095519	0.000000	0.05858	0.029000	0.17559	0.160000	0.22226	-0.057000	0.11768	0.155000	0.19261	0.305000	0.20034	GGC	C|1.000;T|0.000	0.000	weak		0.617	RRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252087.2	NM_018427		T	15188018	C	T	15188018	3	4	28	1	0	0	0	0	1	0	0	0	13699	623	22	2	1954	2	RRN3	16	15188018	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	60769	15188018	75166735	547	12050											
ABCC6	368	hgsc.bcm.edu	37	chr16	16259742	16259742	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaagagcaacctggatgccCgggccccacctaggagcacc	10	3	13	15	1	0	1	0	0	0	1	0	4	0	4	6	4	4	2	6	4	3	1	rs373863345		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:16259742C>T	ENST00000205557.7	-	23	3073	c.3044G>A	c.(3043-3045)cGg>cAg	p.R1015Q		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1015	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)	CCTGGATGCCCGGGCCCCACC	0.617																																					p.R1015Q		Atlas-SNP	.											.	ABCC6	110	.	0			c.G3044A						PASS	.	C	GLN/ARG	0,4394		0,0,2197	36	37	36		3044	2.1	1	16		36	1,8599	1.2+/-3.3	0,1,4299	no	missense	ABCC6	NM_001171.5	43	0,1,6496	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	1015/1504	16259742	1,12993	2197	4300	6497	SO:0001583	missense	368	exon23			GATGCCCGGGCCC	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.3044G>A	16.37:g.16259742C>T	ENSP00000205557:p.Arg1015Gln	69	0	0		73	40	0.547945	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	CCDS10568.1	.	.	.	.	.	.	.	.	.	.	C	11.82	1.751682	0.31046	0.0	1.16E-4	ENSG00000091262	ENST00000205557;ENST00000205558	D	0.91351	-2.83	5.52	2.07	0.26955	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.724655	0.11525	U	0.555272	T	0.80768	0.4686	L	0.31476	0.935	0.09310	N	0.999997	B	0.30211	0.273	B	0.19946	0.027	T	0.66736	-0.5848	10	0.26408	T	0.33	.	4.8069	0.13325	0.2447:0.4906:0.0:0.2647	.	1015	O95255	MRP6_HUMAN	Q	1015;20	ENSP00000205557:R1015Q	ENSP00000205557:R1015Q	R	-	2	0	ABCC6	16167243	0.036000	0.19791	0.983000	0.44433	0.808000	0.45660	1.233000	0.32648	0.701000	0.31803	0.561000	0.74099	CGG	.	.	weak		0.617	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2			T	16259742	C	T	16259742	3	4	28	1	0	0	0	0	1	0	0	0	57	652	23	1	1503	1	ABCC6	16	16259742	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1071724	16259742	74095011	548	12051											
TMC7	79905	hgsc.bcm.edu	37	chr16	19056695	19056695	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caagttgggcaggaaatgtaCaagctgatgatcttcgactt	12	11	11	7	1	1	2	0	2	1	0	2	4	1	3	0	2	2	4	0	2	4	4	rs137989665	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:19056695C>T	ENST00000304381.5	+	11	1618	c.1488C>T	c.(1486-1488)taC>taT	p.Y496Y	TMC7_ENST00000569532.1_Silent_p.Y496Y|TMC7_ENST00000421369.3_Silent_p.Y386Y	NM_024847.3	NP_079123.3	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7	496					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						AGGAAATGTACAAGCTGATGA	0.493																																					p.Y496Y		Atlas-SNP	.											.	TMC7	75	.	0			c.C1488T						PASS	.	C	,	0,4394		0,0,2197	163	131	142		1158,1488	2.9	1	16	dbSNP_134	142	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	TMC7	NM_001160364.1,NM_024847.3	,	0,1,6496	TT,TC,CC		0.0116,0.0,0.0077	,	386/614,496/724	19056695	1,12993	2197	4300	6497	SO:0001819	synonymous_variant	79905	exon11			AATGTACAAGCTG	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.1488C>T	16.37:g.19056695C>T		172	0	0		156	69	0.442308	NM_024847	E7ERB6|Q5H9Q8|Q7Z5M4|Q86WX0|Q9H766	Silent	SNP	ENST00000304381.5	37	CCDS10573.1																																																																																			C|1.000;T|0.000	0.000	strong		0.493	TMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254276.3	NM_024847		T	19056695	C	T	19056695	2	4	28	1	0	0	0	0	0	0	0	1	16005	489	17	2		2	TMC7	16	19056695	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2796953	19056695	71298058	549	12052											
ZP2	7783	hgsc.bcm.edu	37	chr16	21213101	21213101	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaggagtaaggctttcaacgTtgatgtttagtagcatgtca	11	13	12	5	1	2	1	2	1	0	0	2	3	2	2	0	2	2	6	0	2	4	6	rs201054139		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:21213101T>C	ENST00000574002.1	-	14	1912	c.1430A>G	c.(1429-1431)aAc>aGc	p.N477S	ZP2_ENST00000219593.4_Missense_Mutation_p.N477S|ZP2_ENST00000574091.1_Missense_Mutation_p.N468S|AF001550.7_ENST00000572747.1_RNA			Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 (sperm receptor)	477	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)		GCTTTCAACGTTGATGTTTAG	0.418													T|||	1	0.000199681	0.0	0.0014	5008	,	,		20965	0.0		0.0	False		,,,				2504	0.0				p.N477S		Atlas-SNP	.											.	ZP2	92	.	0			c.A1430G						PASS	.						166	151	156					16																	21213101		2200	4300	6500	SO:0001583	missense	7783	exon13			TCAACGTTGATGT	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.1430A>G	16.37:g.21213101T>C	ENSP00000460971:p.Asn477Ser	210	0	0		208	104	0.5	NM_003460	B2R7J2|Q4VAN9|Q4VAP0|Q4VAP1	Missense_Mutation	SNP	ENST00000574002.1	37	CCDS10596.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	T	4.765	0.142318	0.09083	.	.	ENSG00000103310	ENST00000219593	D	0.81499	-1.5	5.64	-0.5	0.12012	Zona pellucida sperm-binding protein (3);	0.414857	0.24343	N	0.039351	T	0.68970	0.3059	L	0.33245	0.995	0.09310	N	1	B;B	0.25105	0.118;0.1	B;B	0.32090	0.14;0.088	T	0.54768	-0.8244	10	0.21540	T	0.41	-4.7459	11.0072	0.47641	0.0:0.3295:0.0:0.6705	.	468;477	Q4VAP1;Q05996	.;ZP2_HUMAN	S	477	ENSP00000219593:N477S	ENSP00000219593:N477S	N	-	2	0	ZP2	21120602	0.000000	0.05858	0.000000	0.03702	0.125000	0.20455	0.162000	0.16501	-0.387000	0.07809	-0.326000	0.08463	AAC	T|1.000;C|0.000	0.000	strong		0.418	ZP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207365.2			C	21213101	T	C	21213101	3	2	28	1	0	0	0	0	1	0	0	0	18231	1725	60	3	835	3	ZP2	16	21213101	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	2156406	21213101	69141652	550	12053											
ANKS4B	257629	hgsc.bcm.edu	37	chr16	21261302	21261302	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tcaccaggctgaaggagcagGctcagaagaatgccaggagg	13	4	15	9	0	2	3	2	1	0	2	2	5	2	5	2	5	2	3	2	5	3	0	rs539999603		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:21261302G>A	ENST00000311620.5	+	2	488	c.415G>A	c.(415-417)Gct>Act	p.A139T		NM_145865.2	NP_665872.2	Q8N8V4	ANS4B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 4B	139					response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|lung(11)|ovary(2)	20				GBM - Glioblastoma multiforme(48;0.0565)		GAAGGAGCAGGCTCAGAAGAA	0.542													G|||	1	0.000199681	0.0	0.0	5008	,	,		21059	0.0		0.0	False		,,,				2504	0.001				p.A139T		Atlas-SNP	.											.	ANKS4B	43	.	0			c.G415A						PASS	.						49	50	50					16																	21261302		2088	4223	6311	SO:0001583	missense	257629	exon2			GAGCAGGCTCAGA	AK096138	CCDS42130.1	16p12.2	2013-01-10				ENSG00000175311		"Sterile alpha motif (SAM) domain containing", "Ankyrin repeat domain containing"	26795	protein-coding gene	gene with protein product		609901					Standard	NM_145865		Approved	FLJ38819, HARP	uc010bwp.1	Q8N8V4		ENST00000311620.5:c.415G>A	16.37:g.21261302G>A	ENSP00000308772:p.Ala139Thr	80	0	0		91	49	0.538462	NM_145865		Missense_Mutation	SNP	ENST00000311620.5	37	CCDS42130.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.609379	0.87258	.	.	ENSG00000175311	ENST00000311620	T	0.51071	0.72	5.77	4.81	0.61882	Ankyrin repeat-containing domain (2);	0.000000	0.85682	D	0.000000	T	0.69169	0.3081	M	0.78801	2.425	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.73946	-0.3822	10	0.66056	D	0.02	-10.602	15.2442	0.73493	0.0:0.0:0.8584:0.1416	.	139	Q8N8V4	ANS4B_HUMAN	T	139	ENSP00000308772:A139T	ENSP00000308772:A139T	A	+	1	0	ANKS4B	21168803	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.776000	0.99001	1.422000	0.47177	-0.282000	0.10007	GCT	.	.	none		0.542	ANKS4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436535.1	NM_145865		A	21261302	G	A	21261302	3	1	28	1	0	0	0	0	1	0	0	0	691	1203	42	2	421	2	ANKS4B	16	21261302	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	48201	21261302	69093451	551	12054											
PRKCB	5579	hgsc.bcm.edu	37	chr16	24046861	24046861	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcgacagggacgtcctcatTgtcctcggtaggtggccctg	6	10	13	12	3	1	0	1	0	0	0	5	2	3	1	3	4	0	1	3	4	1	2	rs116345778	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:24046861T>C	ENST00000321728.7	+	5	697	c.522T>C	c.(520-522)atT>atC	p.I174I	PRKCB_ENST00000303531.7_Silent_p.I174I	NM_212535.2	NP_997700.1	P05771	KPCB_HUMAN	protein kinase C, beta	174	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)	ACGTCCTCATTGTCCTCGGTA	0.647													T|||	48	0.00958466	0.0174	0.0029	5008	,	,		13772	0.0		0.005	False		,,,				2504	0.0184				p.I174I		Atlas-SNP	.											.	PRKCB	383	.	0			c.T522C						PASS	.	T	,	68,4326	63.5+/-100.7	1,66,2130	74	69	71		522,522	-4.3	0.6	16	dbSNP_132	71	16,8584	11.2+/-40.8	0,16,4284	no	coding-synonymous,coding-synonymous	PRKCB	NM_002738.6,NM_212535.2	,	1,82,6414	CC,CT,TT		0.186,1.5476,0.6465	,	174/674,174/672	24046861	84,12910	2197	4300	6497	SO:0001819	synonymous_variant	5579	exon5			CCTCATTGTCCTC	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.522T>C	16.37:g.24046861T>C		94	0	0		121	47	0.38843	NM_212535	C5IFJ8|D3DWF5|O43744|P05127|Q15138|Q93060|Q9UE49|Q9UE50|Q9UEH8|Q9UJ30|Q9UJ33	Silent	SNP	ENST00000321728.7	37	CCDS10618.1																																																																																			T|0.993;C|0.007	0.007	strong		0.647	PRKCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254504.2	NM_212535		C	24046861	T	C	24046861	2	2	28	1	0	0	0	0	0	0	0	1	12520	1800	63	3		3	PRKCB	16	24046861	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	2785559	24046861	66307892	552	12055											
TBX6	6911	hgsc.bcm.edu	37	chr16	30100401	30100401	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caggcggggctctgccttgcCgctgggctcccagcgccggc	2	6	16	17	4	1	0	0	0	1	0	2	0	2	0	4	5	3	3	4	5	0	1	rs56098093	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:30100401C>T	ENST00000395224.2	-	4	543	c.484G>A	c.(484-486)Ggc>Agc	p.G162S	TBX6_ENST00000279386.2_Missense_Mutation_p.G162S|TBX6_ENST00000553607.1_Missense_Mutation_p.G162S	NM_004608.3	NP_004599.2	O95947	TBX6_HUMAN	T-box 6	162			G -> S (in dbSNP:rs56098093).		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						TCTGCCTTGCCGCTGGGCTCC	0.647													C|||	4	0.000798722	0.0	0.0	5008	,	,		13926	0.0		0.004	False		,,,				2504	0.0				p.G162S		Atlas-SNP	.											.	TBX6	29	.	0			c.G484A						PASS	.	C	SER/GLY	5,4389	9.9+/-24.2	0,5,2192	47	52	50		484	5.8	1	16	dbSNP_129	50	52,8546	32.3+/-84.9	0,52,4247	yes	missense	TBX6	NM_004608.3	56	0,57,6439	TT,TC,CC		0.6048,0.1138,0.4387	probably-damaging	162/437	30100401	57,12935	2197	4299	6496	SO:0001583	missense	6911	exon4			CCTTGCCGCTGGG	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.484G>A	16.37:g.30100401C>T	ENSP00000378650:p.Gly162Ser	48	0	0		79	46	0.582278	NM_004608	Q8TAS4|Q9HA44	Missense_Mutation	SNP	ENST00000395224.2	37	CCDS10670.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	36	5.633723	0.96682	0.001138	0.006048	ENSG00000149922	ENST00000395224;ENST00000279386;ENST00000553607	D;D;D	0.91237	-2.81;-2.81;-2.81	5.8	5.8	0.92144	p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.95287	0.8471	M	0.90977	3.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.95019	0.8159	10	0.87932	D	0	.	18.8306	0.92137	0.0:1.0:0.0:0.0	rs56098093	162;162	O95947;Q9HA44	TBX6_HUMAN;.	S	162	ENSP00000378650:G162S;ENSP00000279386:G162S;ENSP00000461223:G162S	ENSP00000279386:G162S	G	-	1	0	TBX6	30007902	0.998000	0.40836	0.997000	0.53966	0.971000	0.66376	4.819000	0.62664	2.747000	0.94245	0.462000	0.41574	GGC	C|0.997;T|0.003	0.003	strong		0.647	TBX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255157.2	NM_004608, NM_080758		T	30100401	C	T	30100401	3	4	28	1	0	0	0	0	1	0	0	0	15677	652	23	1	850	1	TBX6	16	30100401	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	6053540	30100401	60254352	553	12056											
ITGAX	3687	hgsc.bcm.edu	37	chr16	31382470	31382470	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caggcactgagcgggggtcaAgacctcacccaggatggact	10	5	14	12	1	2	2	2	1	0	1	2	4	2	4	2	5	1	1	2	5	1	0	rs138137251	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:31382470A>G	ENST00000268296.4	+	15	1897	c.1776A>G	c.(1774-1776)caA>caG	p.Q592Q	ITGAX_ENST00000562522.1_Silent_p.Q592Q	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	592					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						GCGGGGGTCAAGACCTCACCC	0.642													A|||	32	0.00638978	0.0015	0.0173	5008	,	,		17052	0.0		0.0169	False		,,,				2504	0.001				p.Q592Q		Atlas-SNP	.											.	ITGAX	198	.	0			c.A1776G						PASS	.	A		4,4390	8.1+/-20.4	0,4,2193	56	63	61		1776	3.3	1	16	dbSNP_134	61	112,8488	57.9+/-119.4	0,112,4188	no	coding-synonymous	ITGAX	NM_000887.3		0,116,6381	GG,GA,AA		1.3023,0.091,0.8927		592/1164	31382470	116,12878	2197	4300	6497	SO:0001819	synonymous_variant	3687	exon15			GGGTCAAGACCTC	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.1776A>G	16.37:g.31382470A>G		55	0	0		48	25	0.520833	NM_000887	Q8IVA6	Silent	SNP	ENST00000268296.4	37	CCDS10711.1																																																																																			A|0.991;G|0.009	0.009	strong		0.642	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887		G	31382470	A	G	31382470	2	3	28	1	0	0	0	0	0	0	0	1	7898	69	3	3		3	ITGAX	16	31382470	Silent	SNP	A	TCGA-G8-6914-01A-11D-2210-10	1282069	31382470	58972283	554	12057											
NOD2	64127	hgsc.bcm.edu	37	chr16	50753892	50753892	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agtgctggccgaggggctccGaggcaacacctccttgcagt	7	7	14	13	2	0	0	0	0	0	0	2	2	2	0	4	4	3	4	4	4	1	1	rs201831159		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:50753892G>A	ENST00000300589.2	+	7	2792	c.2687G>A	c.(2686-2688)cGa>cAa	p.R896Q		NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	896					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)				GAGGGGCTCCGAGGCAACACC	0.597													G|||	1	0.000199681	0.0	0.0	5008	,	,		18894	0.0		0.001	False		,,,				2504	0.0				p.R896Q		Atlas-SNP	.											.	NOD2	118	.	0			c.G2687A						PASS	.						75	80	78					16																	50753892		2198	4300	6498	SO:0001583	missense	64127	exon7			GGCTCCGAGGCAA	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.2687G>A	16.37:g.50753892G>A	ENSP00000300589:p.Arg896Gln	51	0	0		67	41	0.61194	NM_022162	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Missense_Mutation	SNP	ENST00000300589.2	37	CCDS10746.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	8.658	0.899935	0.17686	.	.	ENSG00000167207	ENST00000526417;ENST00000300589;ENST00000431240	T	0.52983	0.64	5.91	3.31	0.37934	.	0.369818	0.23142	N	0.051460	T	0.30479	0.0766	L	0.47716	1.5	0.09310	N	1	P;P	0.50066	0.788;0.931	B;B	0.37267	0.245;0.091	T	0.13282	-1.0515	10	0.18710	T	0.47	.	5.1538	0.15025	0.367:0.0:0.633:0.0	.	869;896	Q9HC29-2;Q9HC29	.;NOD2_HUMAN	Q	869;896;36	ENSP00000300589:R896Q	ENSP00000300589:R896Q	R	+	2	0	NOD2	49311393	0.115000	0.22152	0.283000	0.24790	0.014000	0.08584	0.496000	0.22499	1.161000	0.42604	0.655000	0.94253	CGA	G|1.000;A|0.000	0.000	strong		0.597	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162		A	50753892	G	A	50753892	3	1	28	1	0	0	0	0	1	0	0	0	10526	1058	37	1	2713	1	NOD2	16	50753892	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	19371422	50753892	39600861	555	12058											
FTO	79068	hgsc.bcm.edu	37	chr16	53860253	53860253	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agagcagagcagcatacaacGtaactttgctgaatttcatg	14	10	9	8	1	1	3	1	1	0	2	1	3	1	3	0	0	7	5	0	0	4	4	rs150450891	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:53860253G>A	ENST00000471389.1	+	3	823	c.601G>A	c.(601-603)Gta>Ata	p.V201I	FTO_ENST00000394647.3_Intron	NM_001080432.2	NP_001073901.1	Q9C0B1	FTO_HUMAN	fat mass and obesity associated	201	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						AGCATACAACGTAACTTTGCT	0.453																																					p.V201I		Atlas-SNP	.											.	FTO	51	.	0			c.G601A						PASS	.	G	ILE/VAL	0,4396		0,0,2198	158	139	145		601	3.1	0.9	16	dbSNP_134	145	7,8593	5.7+/-21.5	0,7,4293	yes	missense	FTO	NM_001080432.2	29	0,7,6491	AA,AG,GG		0.0814,0.0,0.0539	benign	201/506	53860253	7,12989	2198	4300	6498	SO:0001583	missense	79068	exon3			TACAACGTAACTT	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.601G>A	16.37:g.53860253G>A	ENSP00000418823:p.Val201Ile	115	0	0		103	56	0.543689	NM_001080432	A2RUH1|B2RNS0|Q0P676|Q7Z785	Missense_Mutation	SNP	ENST00000471389.1	37	CCDS32448.1	.	.	.	.	.	.	.	.	.	.	G	15.53	2.861372	0.51482	0.0	8.14E-4	ENSG00000140718	ENST00000471389	T	0.80994	-1.44	5.32	3.09	0.35607	Alpha-ketoglutarate-dependent dioxygenase FTO, catalytic domain (1);	0.170382	0.49916	D	0.000131	T	0.74981	0.3788	M	0.64404	1.975	0.80722	D	1	P	0.39576	0.679	B	0.35114	0.196	T	0.76868	-0.2800	10	0.62326	D	0.03	-8.3027	10.9439	0.47289	0.0:0.1016:0.6004:0.298	.	201	Q9C0B1	FTO_HUMAN	I	201	ENSP00000418823:V201I	ENSP00000418823:V201I	V	+	1	0	FTO	52417754	0.751000	0.28327	0.911000	0.35937	0.981000	0.71138	0.893000	0.28336	1.196000	0.43129	0.655000	0.94253	GTA	G|0.999;A|0.001	0.001	strong		0.453	FTO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352196.1	NM_001080432		A	53860253	G	A	53860253	3	1	28	1	0	0	0	0	1	0	0	0	6094	1145	40	1	611	1	FTO	16	53860253	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	3106361	53860253	36494500	556	12059											
SLC6A2	6530	hgsc.bcm.edu	37	chr16	55690874	55690874	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctacctctgctacaagaacGgcggcggtgagcgtggggtc	7	7	15	12	4	1	2	0	1	1	1	2	2	1	2	2	5	5	1	2	5	4	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:55690874G>A	ENST00000379906.2	+	1	523	c.268G>A	c.(268-270)Ggc>Agc	p.G90S	SLC6A2_ENST00000568943.1_Missense_Mutation_p.G90S|SLC6A2_ENST00000414754.3_Missense_Mutation_p.G90S|SLC6A2_ENST00000566163.1_Missense_Mutation_p.G90S|SLC6A2_ENST00000219833.8_Missense_Mutation_p.G90S|SLC6A2_ENST00000561820.1_Missense_Mutation_p.G90S	NM_001043.3	NP_001034.1	P23975	SC6A2_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 2	90					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)	CTACAAGAACGGCGGCGGTGA	0.622																																					p.G90S		Atlas-SNP	.											SLC6A2_ENST00000219833,colon,carcinoma,0,2	SLC6A2	189	2	0			c.G268A						PASS	.						69	74	72					16																	55690874		2198	4300	6498	SO:0001583	missense	6530	exon2			AAGAACGGCGGCG		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.268G>A	16.37:g.55690874G>A	ENSP00000369237:p.Gly90Ser	67	0	0		42	20	0.47619	NM_001172501	B2R707|B4DX48|Q96KH8	Missense_Mutation	SNP	ENST00000379906.2	37	CCDS10754.1	.	.	.	.	.	.	.	.	.	.	G	19.72	3.879435	0.72294	.	.	ENSG00000103546	ENST00000414754;ENST00000379906;ENST00000219833	D;D;D	0.87491	-2.26;-2.26;-2.26	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.96775	0.8947	H	0.99169	4.455	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98465	1.0598	10	0.87932	D	0	.	19.2658	0.93984	0.0:0.0:1.0:0.0	.	90;90	Q96KH8;P23975	.;SC6A2_HUMAN	S	90	ENSP00000394956:G90S;ENSP00000369237:G90S;ENSP00000219833:G90S	ENSP00000219833:G90S	G	+	1	0	SLC6A2	54248375	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.728000	0.98792	2.620000	0.88729	0.563000	0.77884	GGC	.	.	none		0.622	SLC6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256922.2			A	55690874	G	A	55690874	3	1	28	1	0	0	0	0	1	0	0	0	14698	1116	39	1	270	1	SLC6A2	16	55690874	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1830621	55690874	34663879	557	12060											
CMTM2	146225	hgsc.bcm.edu	37	chr16	66613725	66613725	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagggggtgtcgccgctaccGgtgggaattaaaagacagca	11	6	16	8	3	0	1	0	0	0	1	1	3	0	2	2	4	2	2	2	4	4	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:66613725G>A	ENST00000268595.2	+	1	366	c.215G>A	c.(214-216)cGg>cAg	p.R72Q	CMTM2_ENST00000379486.2_Missense_Mutation_p.R72Q|RP11-403P17.2_ENST00000568430.1_RNA	NM_144673.2	NP_653274.1	Q8TAZ6	CKLF2_HUMAN	CKLF-like MARVEL transmembrane domain containing 2	72					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)		CGCCGCTACCGGTGGGAATTA	0.562																																					p.R72Q		Atlas-SNP	.											.	CMTM2	33	.	0			c.G215A						PASS	.						48	52	51					16																	66613725		2201	4300	6501	SO:0001583	missense	146225	exon1			GCTACCGGTGGGA	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.215G>A	16.37:g.66613725G>A	ENSP00000268595:p.Arg72Gln	69	0	0		80	40	0.5	NM_001199317	Q5I2A4|Q8N7E5	Missense_Mutation	SNP	ENST00000268595.2	37	CCDS10814.1	.	.	.	.	.	.	.	.	.	.	G	19.20	3.781718	0.70222	.	.	ENSG00000140932	ENST00000379486;ENST00000268595	T;T	0.49139	0.79;1.37	4.51	-7.19	0.01500	.	1.889910	0.02580	N	0.098726	T	0.26955	0.0660	L	0.36672	1.1	0.09310	N	1	P;B	0.38167	0.621;0.447	B;B	0.27608	0.081;0.045	T	0.21415	-1.0246	10	0.28530	T	0.3	1.8102	4.3444	0.11126	0.2588:0.0:0.2537:0.4874	.	72;72	Q5I2A4;Q8TAZ6	.;CKLF2_HUMAN	Q	72	ENSP00000368800:R72Q;ENSP00000268595:R72Q	ENSP00000268595:R72Q	R	+	2	0	CMTM2	65171226	0.001000	0.12720	0.000000	0.03702	0.848000	0.48234	-1.284000	0.02793	-1.329000	0.02258	0.561000	0.74099	CGG	.	.	none		0.562	CMTM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268808.1			A	66613725	G	A	66613725	3	1	28	1	0	0	0	0	1	0	0	0	3585	1116	39	1	217	1	CMTM2	16	66613725	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	10922851	66613725	23741028	558	12061											
IL34	146433	hgsc.bcm.edu	37	chr16	70693991	70693991	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tcattgcagtatgcggccacCcagctgtaccctccgccccc	6	8	8	19	2	1	0	1	0	0	0	2	0	2	0	6	1	4	4	6	1	2	3	rs138439611		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:70693991C>T	ENST00000288098.2	+	6	1013	c.630C>T	c.(628-630)acC>acT	p.T210T	IL34_ENST00000429149.2_Silent_p.T210T|FLJ00418_ENST00000597002.1_5'Flank|IL34_ENST00000566361.1_Silent_p.T185T	NM_001172772.1	NP_001166243.1	Q6ZMJ4	IL34_HUMAN	interleukin 34	210					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						ATGCGGCCACCCAGCTGTACC	0.652																																					p.T210T		Atlas-SNP	.											.	IL34	26	.	0			c.C630T						PASS	.	C	,,	0,4396		0,0,2198	84	94	91		627,630,630	-1.8	0	16	dbSNP_134	91	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	IL34	NM_001172771.1,NM_001172772.1,NM_152456.2	,,	0,2,6496	TT,TC,CC		0.0233,0.0,0.0154	,,	209/242,210/243,210/243	70693991	2,12994	2198	4300	6498	SO:0001819	synonymous_variant	146433	exon7			GGCCACCCAGCTG	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.630C>T	16.37:g.70693991C>T		153	0	0		189	65	0.343915	NM_152456	B2RC28|B2Z4A8|B2ZC70|Q8N6L2	Silent	SNP	ENST00000288098.2	37	CCDS10895.1																																																																																			C|1.000;T|0.000	0.000	weak		0.652	IL34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268971.3	NM_152456		T	70693991	C	T	70693991	2	4	28	1	0	0	0	0	0	0	0	1	7703	610	22	2		2	IL34	16	70693991	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	4080266	70693991	19660762	559	12062											
DHX38	9785	hgsc.bcm.edu	37	chr16	72132832	72132832	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gctgctgttcccaggtctgtGaggggcaagtactcggatga	7	10	15	9	1	1	2	0	2	1	0	3	3	2	3	1	4	2	5	1	4	2	2	rs150221434	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:72132832G>A	ENST00000268482.3	+	6	1280	c.771G>A	c.(769-771)gtG>gtA	p.V257V	DHX38_ENST00000536867.1_Intron	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	257					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)				CCAGGTCTGTGAGGGGCAAGT	0.582													G|||	4	0.000798722	0.0	0.0029	5008	,	,		19641	0.0		0.002	False		,,,				2504	0.0				p.V257V	Melanoma(97;711 1442 7855 13832 28836)	Atlas-SNP	.											.	DHX38	91	.	0			c.G771A						PASS	.	G		1,4395	2.1+/-5.4	0,1,2197	53	53	53		771	2.8	1	16	dbSNP_134	53	17,8583	12.6+/-44.7	0,17,4283	no	coding-synonymous	DHX38	NM_014003.3		0,18,6480	AA,AG,GG		0.1977,0.0227,0.1385		257/1228	72132832	18,12978	2198	4300	6498	SO:0001819	synonymous_variant	9785	exon6			GTCTGTGAGGGGC	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.771G>A	16.37:g.72132832G>A		113	0	0		128	61	0.476562	NM_014003	B4DVG8|D3DWS7|O75212|Q96HN7	Silent	SNP	ENST00000268482.3	37	CCDS10907.1																																																																																			G|0.999;A|0.001	0.001	strong		0.582	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003		A	72132832	G	A	72132832	2	1	28	1	0	0	0	0	0	0	0	1	4513	1277	45	2		2	DHX38	16	72132832	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1438841	72132832	18221921	560	12063											
PSMD7	5713	hgsc.bcm.edu	37	chr16	74334016	74334016	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tctgttttctcattcagaatCggcaaggttggaaaccagaa	12	12	9	8	1	3	2	2	0	2	2	5	3	3	3	1	3	1	3	1	3	4	4	rs140080000	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:74334016C>T	ENST00000219313.4	+	2	218	c.78C>T	c.(76-78)atC>atT	p.I26I	PSMD7_ENST00000540379.1_5'UTR|PSMD7_ENST00000568615.2_Silent_p.I26I|PSMD7_ENST00000567958.1_Silent_p.I26I	NM_002811.4	NP_002802.2	P51665	PSMD7_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 7	26	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)|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)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	protein homodimerization activity (GO:0042803)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)	15						CATTCAGAATCGGCAAGGTTG	0.418													C|||	3	0.000599042	0.0	0.0	5008	,	,		19257	0.0		0.002	False		,,,				2504	0.001				p.I26I		Atlas-SNP	.											.	PSMD7	29	.	0			c.C78T						PASS	.	C		1,4395	2.1+/-5.4	0,1,2197	129	108	115		78	-0.2	1	16	dbSNP_134	115	14,8586	11.2+/-40.8	0,14,4286	no	coding-synonymous	PSMD7	NM_002811.4		0,15,6483	TT,TC,CC		0.1628,0.0227,0.1154		26/325	74334016	15,12981	2198	4300	6498	SO:0001819	synonymous_variant	5713	exon2			CAGAATCGGCAAG	D50063	CCDS10910.1	16q22.3	2010-10-15	2007-07-06		ENSG00000103035	ENSG00000103035		"Proteasome (prosome, macropain) subunits"	9565	protein-coding gene	gene with protein product	"Mov34 homolog"	157970	"proteasome (prosome, macropain) 26S subunit, non-ATPase, 7 (Mov34 homolog)"			7755639	Standard	NM_002811		Approved	S12, P40, MOV34, Rpn8	uc002fcq.3	P51665	OTTHUMG00000137601	ENST00000219313.4:c.78C>T	16.37:g.74334016C>T		84	0	0		81	37	0.45679	NM_002811	D3DWS9|Q6PKI2|Q96E97	Silent	SNP	ENST00000219313.4	37	CCDS10910.1																																																																																			C|0.999;T|0.001	0.001	strong		0.418	PSMD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269010.2	NM_002811		T	74334016	C	T	74334016	2	4	28	1	0	0	0	0	0	0	0	1	12715	874	31	1		1	PSMD7	16	74334016	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2201184	74334016	16020737	561	12064											
PKD1L2	114780	hgsc.bcm.edu	37	chr16	81209325	81209325	+	RNA	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gcagatacactgatgggaggGcaggttcagggccacagtgt	10	7	16	8	0	1	2	1	1	0	1	1	3	1	3	1	4	1	3	1	4	1	2	rs145948343	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:81209325G>A	ENST00000527937.1	-	0	349				PKD1L2_ENST00000531391.1_RNA|PKD1L2_ENST00000533478.1_RNA|PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000337114.4_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						TGATGGGAGGGCAGGTTCAGG	0.547													G|||	2	0.000399361	0.0	0.0	5008	,	,		18881	0.0		0.002	False		,,,				2504	0.0				p.A823V		Atlas-SNP	.											.	PKD1L2	361	.	0			c.C2468T						PASS	.	G	VAL/ALA,VAL/ALA	1,4073		0,1,2036	85	87	86		2468,2468	-0.1	0.9	16	dbSNP_134	86	4,8360		0,4,4178	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	64,64	0,5,6214	AA,AG,GG		0.0478,0.0245,0.0402	benign,benign	823/992,823/2460	81209325	5,12433	2037	4182	6219			114780	exon15			GGGAGGGCAGGTT	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		16.37:g.81209325G>A		89	0	0		73	36	0.493151	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000527937.1	37		2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	10.51	1.369906	0.24771	2.45E-4	4.78E-4	ENSG00000166473	ENST00000531391;ENST00000337114;ENST00000527937	T;T;T	0.70631	-0.5;-0.5;2.14	4.82	-0.11	0.13580	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	0.500926	0.19769	N	0.106485	T	0.44307	0.1287	.	.	.	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	0.08973	-1.0696	9	0.18710	T	0.47	-8.2539	2.0758	0.03623	0.225:0.1363:0.4838:0.1549	.	79;823;823	Q7Z442-6;Q7Z442-3;Q7Z442	.;.;PK1L2_HUMAN	V	138;823;79	ENSP00000436309:A138V;ENSP00000337397:A823V;ENSP00000432818:A79V	ENSP00000337397:A823V	A	-	2	0	PKD1L2	79766826	0.386000	0.25180	0.907000	0.35723	0.962000	0.63368	-0.022000	0.12480	0.331000	0.23511	-0.611000	0.04053	GCC	G|0.999;A|0.001	0.001	strong		0.547	PKD1L2-007	KNOWN	basic|exp_conf	protein_coding	polymorphic_pseudogene	OTTHUMT00000387978.1			A	81209325	G	A	81209325	1	1	28	0	1	0	0	0	0	0	0	0	11974	1203	42	2		2	PKD1L2	16	81209325	RNA	SNP	G	TCGA-G8-6914-01A-11D-2210-10	6875309	81209325	9145428	562	12065											
SDR42E1	93517	hgsc.bcm.edu	37	chr16	82033022	82033022	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtgaaccatctctgttagAaaagcaaagcagtagaccaa	18	7	8	8	0	1	3	0	1	1	2	2	3	1	3	2	0	3	4	2	0	8	2	rs11861598	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:82033022A>G	ENST00000328945.5	-	3	1003	c.876T>C	c.(874-876)ttT>ttC	p.F292F	SDR42E1_ENST00000534209.1_5'Flank	NM_145168.2	NP_660151.2	Q8WUS8	D42E1_HUMAN	short chain dehydrogenase/reductase family 42E, member 1	292					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						TCTCTGTTAGAAAAGCAAAGC	0.483													A|||	243	0.0485224	0.1596	0.0173	5008	,	,		20516	0.001		0.0129	False		,,,				2504	0.0061				p.F292F		Atlas-SNP	.											.	SDR42E1	26	.	0			c.T876C						PASS	.	A		538,3326		32,474,1426	70	68	69		876	4.3	1	16	dbSNP_120	69	77,8211		0,77,4067	no	coding-synonymous	SDR42E1	NM_145168.2		32,551,5493	GG,GA,AA		0.9291,13.9234,5.0609		292/394	82033022	615,11537	1932	4144	6076	SO:0001819	synonymous_variant	93517	exon3			TGTTAGAAAAGCA	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.876T>C	16.37:g.82033022A>G		56	0	0		51	31	0.607843	NM_145168	B2RDS1|Q9P0D1	Silent	SNP	ENST00000328945.5	37	CCDS42205.1																																																																																			A|0.956;G|0.044	0.044	strong		0.483	SDR42E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388081.2	NM_145168		G	82033022	A	G	82033022	2	3	28	1	0	0	0	0	0	0	0	1	13988	243	9	3		3	SDR42E1	16	82033022	Silent	SNP	A	TCGA-G8-6914-01A-11D-2210-10	823697	82033022	8321731	563	12066											
CDH13	1012	hgsc.bcm.edu	37	chr16	83636136	83636136	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatgttggattaacaggcacGgccacagccacgatcatgat	12	8	11	10	2	1	1	1	1	0	0	1	4	1	2	2	3	2	2	2	3	1	2	rs371581191	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:83636136G>A	ENST00000566620.1	+	8	1328	c.1038G>A	c.(1036-1038)acG>acA	p.T346T	CDH13_ENST00000268613.10_Silent_p.T393T|CDH13_ENST00000428848.3_Silent_p.T307T	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	346	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)		TAACAGGCACGGCCACAGCCA	0.458													G|||	4	0.000798722	0.0	0.0	5008	,	,		15867	0.0		0.003	False		,,,				2504	0.001				p.T393T		Atlas-SNP	.											.	CDH13	97	.	0			c.G1179A						PASS	.	G	,,,	1,3891		0,1,1945	182	184	183		1179,921,276,1038	-12	0	16		183	20,8320		0,20,4150	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CDH13	NM_001220488.1,NM_001220489.1,NM_001220490.1,NM_001257.4	,,,	0,21,6095	AA,AG,GG		0.2398,0.0257,0.1717	,,,	393/761,307/675,92/460,346/714	83636136	21,12211	1946	4170	6116	SO:0001819	synonymous_variant	1012	exon9			AGGCACGGCCACA	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.1038G>A	16.37:g.83636136G>A		101	0	0		78	42	0.538462	NM_001220488	A8W476|A8W477|B7Z590|C9JRI6|J3KN62|Q6GTW4|Q8TBX3	Silent	SNP	ENST00000566620.1	37	CCDS58486.1																																																																																			.	.	weak		0.458	CDH13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432917.1	NM_001257		A	83636136	G	A	83636136	2	1	28	1	0	0	0	0	0	0	0	1	3101	1103	39	1		1	CDH13	16	83636136	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1603114	83636136	6718617	564	12067											
SLC7A5	8140	hgsc.bcm.edu	37	chr16	87885369	87885369	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gcccagcaggatgatcagggCcagggccaggagcttggcgg	8	4	18	11	1	1	1	1	1	0	0	1	3	1	3	3	6	2	2	3	6	0	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:87885369C>T	ENST00000261622.4	-	2	690	c.625G>A	c.(625-627)Gcc>Acc	p.A209T	SLC7A5_ENST00000565644.1_5'UTR	NM_003486.5	NP_003477.4	Q01650	LAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 5	209					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|neutral amino acid transport (GO:0015804)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|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)|peptide antigen binding (GO:0042605)			endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(80;0.049)	Dextrothyroxine(DB00509)|L-DOPA(DB01235)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Melphalan(DB01042)	ATGATCAGGGCCAGGGCCAGG	0.667																																					p.A209T		Atlas-SNP	.											.	SLC7A5	28	.	0			c.G625A						PASS	.						40	38	38					16																	87885369		2197	4300	6497	SO:0001583	missense	8140	exon2			TCAGGGCCAGGGC	AF077866	CCDS10964.1	16q24.3	2013-05-22	2011-07-12		ENSG00000103257	ENSG00000103257		"CD molecules", "Solute carriers"	11063	protein-coding gene	gene with protein product		600182				9751058, 7829099	Standard	XM_006721286		Approved	LAT1, E16, D16S469E, MPE16, CD98	uc002fkm.3	Q01650	OTTHUMG00000137658	ENST00000261622.4:c.625G>A	16.37:g.87885369C>T	ENSP00000261622:p.Ala209Thr	175	0	0		171	48	0.280702	NM_003486	Q8IV97|Q9UBN8|Q9UP15|Q9UQC0	Missense_Mutation	SNP	ENST00000261622.4	37	CCDS10964.1	.	.	.	.	.	.	.	.	.	.	C	17.40	3.378913	0.61735	.	.	ENSG00000103257	ENST00000261622	D	0.90620	-2.7	5.17	5.17	0.71159	Amino acid permease domain (1);	0.499292	0.20200	N	0.097117	D	0.88157	0.6361	L	0.56280	1.765	0.23361	N	0.997833	B	0.22003	0.063	B	0.19666	0.026	T	0.81609	-0.0855	10	0.72032	D	0.01	.	12.7141	0.57105	0.1645:0.8355:0.0:0.0	.	209	Q01650	LAT1_HUMAN	T	209	ENSP00000261622:A209T	ENSP00000261622:A209T	A	-	1	0	SLC7A5	86442870	0.088000	0.21588	0.710000	0.30468	0.944000	0.59088	1.045000	0.30341	2.386000	0.81285	0.655000	0.94253	GCC	.	.	none		0.667	SLC7A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269110.2	NM_003486		T	87885369	C	T	87885369	3	4	28	1	0	0	0	0	1	0	0	0	14715	739	26	2	934	2	SLC7A5	16	87885369	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	4249233	87885369	2469384	565	12068											
CBFA2T3	863	hgsc.bcm.edu	37	chr16	88951466	88951466	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgctcaccaagcggccgatGgcgctctcgtagctcccggg	5	7	13	16	5	2	0	1	0	1	0	4	1	3	0	3	3	3	4	3	3	2	1	rs143614023	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:88951466G>A	ENST00000268679.4	-	7	1501	c.1105C>T	c.(1105-1107)Cat>Tat	p.H369Y	RP11-830F9.5_ENST00000569249.1_RNA|RP11-830F9.5_ENST00000562574.1_RNA|CBFA2T3_ENST00000327483.5_Missense_Mutation_p.H283Y|RP11-830F9.5_ENST00000562405.1_RNA|CBFA2T3_ENST00000360302.2_Missense_Mutation_p.H283Y|RP11-830F9.5_ENST00000565053.1_RNA|CBFA2T3_ENST00000436887.2_Missense_Mutation_p.H331Y|CBFA2T3_ENST00000448839.1_Missense_Mutation_p.H293Y	NM_005187.5	NP_005178.4	O75081	MTG16_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 3	369	Mediates interaction with PDE7A (in isoform 2).|Mediates localization to the nucleus. {ECO:0000250}.				cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	17				BRCA - Breast invasive adenocarcinoma(80;0.0275)		AGCGGCCGATGGCGCTCTCGT	0.682			T	RUNX1	AML																																p.H369Y		Atlas-SNP	.		Dom	yes		16	16q24	863	"core-binding factor, runt domain, alpha subunit 2; translocated to, 3 (MTG-16)"		L	.	CBFA2T3	47	.	0			c.C1105T						PASS	.	G	TYR/HIS,TYR/HIS	0,4376		0,0,2188	50	47	48		1105,847	4.3	1	16	dbSNP_134	48	5,8579	4.3+/-15.6	0,5,4287	yes	missense,missense	CBFA2T3	NM_005187.5,NM_175931.2	83,83	0,5,6475	AA,AG,GG		0.0582,0.0,0.0386	benign,benign	369/654,283/568	88951466	5,12955	2188	4292	6480	SO:0001583	missense	863	exon7			GCCGATGGCGCTC	AF052213	CCDS10972.1, CCDS10973.1	16q24	2013-10-16			ENSG00000129993	ENSG00000129993		"Zinc fingers, MYND-type", "A-kinase anchor proteins"	1537	protein-coding gene	gene with protein product	"myeloid translocation gene 8 and 16b"	603870				9790752, 20150326	Standard	NM_005187		Approved	MTGR2, ZMYND4, MTG16	uc002fmm.2	O75081	OTTHUMG00000137864	ENST00000268679.4:c.1105C>T	16.37:g.88951466G>A	ENSP00000268679:p.His369Tyr	10	0	0		27	13	0.481481	NM_005187	D3DX78|O60615|O60616|O60617|O75082|O75107|O75108|Q0P5Z6|Q6P5W6	Missense_Mutation	SNP	ENST00000268679.4	37	CCDS10972.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.627420	0.46944	0.0	5.82E-4	ENSG00000129993	ENST00000327483;ENST00000268679;ENST00000436887;ENST00000448839;ENST00000360302	T;T;T;T;T	0.48201	1.41;0.82;0.85;1.41;1.41	4.32	4.32	0.51571	.	0.293527	0.31335	N	0.007833	T	0.52354	0.1729	M	0.61703	1.905	0.58432	D	0.999993	P;P;B;B	0.49185	0.92;0.586;0.186;0.134	P;B;B;B	0.46419	0.516;0.125;0.141;0.183	T	0.55903	-0.8067	10	0.39692	T	0.17	-1.3703	16.93	0.86188	0.0:0.0:1.0:0.0	.	331;369;369;283	E7EU24;B2RBQ7;O75081;O75081-2	.;.;MTG16_HUMAN;.	Y	283;369;331;293;283	ENSP00000332122:H283Y;ENSP00000268679:H369Y;ENSP00000395739:H331Y;ENSP00000401254:H293Y;ENSP00000353449:H283Y	ENSP00000268679:H369Y	H	-	1	0	CBFA2T3	87478967	1.000000	0.71417	1.000000	0.80357	0.305000	0.27757	7.062000	0.76706	2.386000	0.81285	0.561000	0.74099	CAT	G|1.000;A|0.000	0.000	strong		0.682	CBFA2T3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269545.2	NM_005187		A	88951466	G	A	88951466	3	1	28	1	0	0	0	0	1	0	0	0	2700	1348	47	2	880	2	CBFA2T3	16	88951466	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1066097	88951466	1403287	566	12069											
C16orf55	124045	hgsc.bcm.edu	37	chr16	89724755	89724755	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caggcaggcagacagggagtCggagaagcctgtggacagcc	11	3	17	10	1	0	2	0	0	0	2	1	5	0	4	2	5	2	2	2	5	1	0	rs13329897	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:89724755C>T	ENST00000301031.4	+	2	134	c.134C>T	c.(133-135)tCg>tTg	p.S45L	SPATA33_ENST00000568929.1_Missense_Mutation_p.S15L|CHMP1A_ENST00000397901.3_5'Flank|SPATA33_ENST00000579310.1_Missense_Mutation_p.S46L|CHMP1A_ENST00000550102.1_5'Flank|CHMP1A_ENST00000547614.1_5'Flank|CHMP1A_ENST00000535997.2_5'Flank|CHMP1A_ENST00000253475.5_5'Flank	NM_001271908.1|NM_153025.1	NP_001258837.1|NP_694570.1	Q96N06	SPT33_HUMAN	spermatogenesis associated 33	45			S -> L (in dbSNP:rs13329897).			cytoplasm (GO:0005737)|nucleus (GO:0005634)											GACAGGGAGTCGGAGAAGCCT	0.612													C|||	37	0.00738818	0.0	0.013	5008	,	,		13663	0.0		0.0249	False		,,,				2504	0.0031				p.S46L		Atlas-SNP	.											.	C16orf55	6	.	0			c.C137T						PASS	.		LEU/SER	24,4370	29.9+/-59.1	0,24,2173	34	38	37		134	-1.5	0	16	dbSNP_121	37	174,8426	79.5+/-142.1	2,170,4128	yes	missense	C16orf55	NM_153025.1	145	2,194,6301	TT,TC,CC		2.0233,0.5462,1.5238	possibly-damaging	45/140	89724755	198,12796	2197	4300	6497	SO:0001583	missense	124045	exon2			GGGAGTCGGAGAA	AK056168	CCDS10983.1, CCDS62012.1, CCDS73929.1	16q24.3	2013-07-16	2013-07-05	2013-07-05	ENSG00000167523	ENSG00000167523			26463	protein-coding gene	gene with protein product		615409	"chromosome 16 open reading frame 55"	C16orf55		23844118	Standard	NM_153025		Approved	FLJ31606	uc010vpk.2	Q96N06	OTTHUMG00000138048	ENST00000301031.4:c.134C>T	16.37:g.89724755C>T	ENSP00000301031:p.Ser45Leu	64	0	0		69	28	0.405797	NM_001271910	A8WFL2|B4DZN8	Missense_Mutation	SNP	ENST00000301031.4	37	CCDS10983.1	23	0.010531135531135532	0	0.0	6	0.016574585635359115	0	0.0	17	0.022427440633245383	C	6.839	0.524082	0.13066	0.005462	0.020233	ENSG00000167523	ENST00000301031;ENST00000457689	T	0.40225	1.04	1.95	-1.52	0.08637	.	.	.	.	.	T	0.11665	0.0284	L	0.27053	0.805	0.09310	N	1	B;B;B	0.22851	0.004;0.076;0.008	B;B;B	0.08055	0.001;0.003;0.001	T	0.12426	-1.0548	9	0.36615	T	0.2	.	2.8748	0.05628	0.0:0.4326:0.2424:0.325	rs13329897;rs52799200;rs13329897	46;59;45	B4DZN8;Q86XC3;Q96N06	.;.;CP055_HUMAN	L	45;46	ENSP00000301031:S45L	ENSP00000301031:S45L	S	+	2	0	C16orf55	88252256	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.868000	0.04236	-0.356000	0.08187	-2.290000	0.00267	TCG	C|0.987;T|0.013	0.013	strong		0.612	SPATA33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269924.2	NM_153025		T	89724755	C	T	89724755	3	4	28	1	0	0	0	0	1	0	0	0	1822	893	31	1	140	1	C16orf55	16	89724755	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	773289	89724755	629998	567	12070											
C16orf7	9605	hgsc.bcm.edu	37	chr16	89774870	89774870	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctccagggccgcgcactcCgacaccagctgagggaggcc	7	4	13	17	3	0	1	0	1	0	0	3	3	3	2	6	3	1	2	6	3	0	0	rs369209003		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:89774870C>T	ENST00000389386.3	-	14	1891	c.1767G>A	c.(1765-1767)tcG>tcA	p.S589S	VPS9D1_ENST00000565452.1_5'Flank|VPS9D1_ENST00000561976.1_Silent_p.S519S	NM_004913.2	NP_004904.2	Q9Y2B5	VP9D1_HUMAN	VPS9 domain containing 1	589	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				ATP synthesis coupled proton transport (GO:0015986)		GTPase activator activity (GO:0005096)|transporter activity (GO:0005215)										CCGCGCACTCCGACACCAGCT	0.657																																					p.S589S		Atlas-SNP	.											C16orf7,colon,carcinoma,-1,1	.	.	1	0			c.G1767A						PASS	.	C		0,4254		0,0,2127	27	34	31		1767	-10.3	0.5	16		31	1,8465		0,1,4232	no	coding-synonymous	C16orf7	NM_004913.2		0,1,6359	TT,TC,CC		0.0118,0.0,0.0079		589/632	89774870	1,12719	2127	4233	6360	SO:0001819	synonymous_variant	9605	exon14			GCACTCCGACACC	AB018551	CCDS42220.1	16q24.3	2012-10-09	2012-10-09	2012-10-09	ENSG00000075399	ENSG00000075399			13526	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 7"	C16orf7		10231027	Standard	NM_004913		Approved	ATP-BL	uc002fom.1	Q9Y2B5	OTTHUMG00000173219	ENST00000389386.3:c.1767G>A	16.37:g.89774870C>T		177	0	0		205	104	0.507317	NM_004913		Silent	SNP	ENST00000389386.3	37	CCDS42220.1																																																																																			.	.	weak		0.657	VPS9D1-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422508.1	NM_004913		T	89774870	C	T	89774870	2	4	28	1	0	0	0	0	0	0	0	1	1830	639	23	1		1	C16orf7	16	89774870	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	50115	89774870	579883	568	12071											
RTN4RL1	146760	hgsc.bcm.edu	37	chr17	1840677	1840677	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtactgcaggctgtgcaggcCgccaaagacgccggccggca	8	4	15	14	4	0	1	0	0	0	1	0	1	0	1	4	4	3	5	4	4	2	1	rs181444163	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:1840677C>T	ENST00000331238.6	-	2	918	c.439G>A	c.(439-441)Ggc>Agc	p.G147S		NM_178568.2	NP_848663.1			reticulon 4 receptor-like 1									p.G147S(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|prostate(2)|skin(1)	11						CTGTGCAGGCCGCCAAAGACG	0.622													C|||	24	0.00479233	0.0091	0.0058	5008	,	,		18221	0.002		0.006	False		,,,				2504	0.0				p.G147S	GBM(68;949 1139 14865 32798 38342)	Atlas-SNP	.											RTN4RL1,NS,carcinoma,0,1	RTN4RL1	21	1	1	Substitution - Missense(1)	prostate(1)	c.G439A						PASS	.	C	SER/GLY	30,4296		0,30,2133	40	46	44		439	5.7	1	17		44	113,8417		1,111,4153	yes	missense	RTN4RL1	NM_178568.2	56	1,141,6286	TT,TC,CC		1.3247,0.6935,1.1123	probably-damaging	147/442	1840677	143,12713	2163	4265	6428	SO:0001583	missense	146760	exon2			GCAGGCCGCCAAA	AF532859	CCDS45569.1	17p13.3	2008-02-05				ENSG00000185924			21329	protein-coding gene	gene with protein product	"nogo-66 receptor homolog 2"	610461					Standard	NM_178568		Approved	NGRH2, NgR3, DKFZp547J144	uc002ftp.3	Q86UN2		ENST00000331238.6:c.439G>A	17.37:g.1840677C>T	ENSP00000330631:p.Gly147Ser	70	0	0		63	35	0.555556	NM_178568		Missense_Mutation	SNP	ENST00000331238.6	37	CCDS45569.1	7	0.003205128205128205	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	27.1	4.803980	0.90623	0.006935	0.013247	ENSG00000185924	ENST00000331238	T	0.61510	0.1	5.72	5.72	0.89469	.	0.000000	0.40064	N	0.001187	T	0.66684	0.2814	L	0.56280	1.765	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	T	0.68213	-0.5468	10	0.44086	T	0.13	.	19.9443	0.97176	0.0:1.0:0.0:0.0	.	147	Q86UN2	R4RL1_HUMAN	S	147	ENSP00000330631:G147S	ENSP00000330631:G147S	G	-	1	0	RTN4RL1	1787427	1.000000	0.71417	0.964000	0.40570	0.955000	0.61496	7.484000	0.81180	2.717000	0.92951	0.644000	0.83932	GGC	C|0.995;T|0.005	0.005	strong		0.622	RTN4RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450155.2	NM_178568		T	1840677	C	T	1840677	3	4	28	1	0	0	0	0	1	0	0	0	13746	652	23	1	890	1	RTN4RL1	17	1840677	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10		1840677	79354533	569	12072											
GSG2	83903	hgsc.bcm.edu	37	chr17	3628759	3628759	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatcacacacccgtagccatAaaaatcattgctattgaagg	15	9	7	10	1	2	1	2	1	0	0	2	2	2	1	2	1	2	2	2	1	6	5	rs146480185		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:3628759A>G	ENST00000325418.4	+	1	1549	c.1530A>G	c.(1528-1530)atA>atG	p.I510M	ITGAE_ENST00000571185.1_Intron|CTD-3195I5.3_ENST00000571741.1_RNA|ITGAE_ENST00000263087.4_Intron	NM_031965.2	NP_114171.2	Q8TF76	HASP_HUMAN	germ cell associated 2 (haspin)	510	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.				histone H3-T3 phosphorylation involved in chromosome passenger complex localization to kinetochore (GO:2000751)|intracellular signal transduction (GO:0035556)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|protein localization to chromosome, centromeric region (GO:0071459)|protein phosphorylation (GO:0006468)|regulation of spindle checkpoint (GO:0090231)	centrosome (GO:0005813)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|histone kinase activity (H3-T3 specific) (GO:0072354)|protein kinase activity (GO:0004672)										CCGTAGCCATAAAAATCATTG	0.443																																					p.I510M		Atlas-SNP	.											.	GSG2	48	.	0			c.A1530G						PASS	.	A	,MET/ILE	0,4406		0,0,2203	68	66	67		,1530	2.6	1	17	dbSNP_134	67	1,8599	1.2+/-3.3	0,1,4299	no	intron,missense	ITGAE,GSG2	NM_002208.4,NM_031965.2	,10	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	,benign	,510/799	3628759	1,13005	2203	4300	6503	SO:0001583	missense	83903	exon1			AGCCATAAAAATC	AB039834	CCDS11036.1	17p13	2005-01-19			ENSG00000177602	ENSG00000177602			19682	protein-coding gene	gene with protein product		609240					Standard	NM_031965		Approved	haspin	uc002fwp.3	Q8TF76	OTTHUMG00000090703	ENST00000325418.4:c.1530A>G	17.37:g.3628759A>G	ENSP00000325290:p.Ile510Met	90	0	0		137	65	0.474453	NM_031965	Q5U5K3|Q96MN1|Q9BXS7	Missense_Mutation	SNP	ENST00000325418.4	37	CCDS11036.1	.	.	.	.	.	.	.	.	.	.	A	9.753	1.167938	0.21621	0.0	1.16E-4	ENSG00000177602	ENST00000325418	T	0.68624	-0.34	4.87	2.62	0.31277	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.249150	0.20240	N	0.096308	T	0.56202	0.1969	L	0.33093	0.98	0.30357	N	0.784223	B	0.13145	0.007	B	0.31946	0.138	T	0.57625	-0.7779	10	0.87932	D	0	-37.732	7.5752	0.27931	0.8258:0.0:0.1742:0.0	.	510	Q8TF76	HASP_HUMAN	M	510	ENSP00000325290:I510M	ENSP00000325290:I510M	I	+	3	3	GSG2	3575508	1.000000	0.71417	0.997000	0.53966	0.594000	0.36715	0.746000	0.26275	0.420000	0.25954	0.533000	0.62120	ATA	A|1.000;G|0.000	0.000	weak		0.443	GSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207391.1	NM_031965		G	3628759	A	G	3628759	3	3	28	1	0	0	0	0	1	0	0	0	6831	352	13	3	1532	3	GSG2	17	3628759	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	1788082	3628759	77566451	570	12073											
ITGAE	3682	hgsc.bcm.edu	37	chr17	3664361	3664361	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgtcttcctcctcctcctTctccagagcccggcgctgcc	2	12	7	20	2	2	1	0	0	2	1	7	1	6	1	7	1	2	1	7	1	0	3	rs140947594	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:3664361T>C	ENST00000263087.4	-	6	642	c.544A>G	c.(544-546)Aag>Gag	p.K182E		NM_002208.4	NP_002199.3	P38570	ITAE_HUMAN	integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)	182	Glu-rich (acidic).|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)		tcctcctccttctccAGAGCC	0.567													T|||	16	0.00319489	0.0008	0.0029	5008	,	,		19977	0.0		0.0119	False		,,,				2504	0.001				p.K182E	NSCLC(182;635 2928 8995 38788)	Atlas-SNP	.											.	ITGAE	96	.	0			c.A544G						PASS	.	T	GLU/LYS	3,4403	6.2+/-15.9	0,3,2200	127	131	130		544	-6	0	17	dbSNP_134	130	49,8551	28.5+/-78.6	0,49,4251	yes	missense	ITGAE	NM_002208.4	56	0,52,6451	CC,CT,TT		0.5698,0.0681,0.3998	benign	182/1180	3664361	52,12954	2203	4300	6503	SO:0001583	missense	3682	exon6			CCTCCTTCTCCAG	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.544A>G	17.37:g.3664361T>C	ENSP00000263087:p.Lys182Glu	26	0	0		26	13	0.5	NM_002208	Q17RS6|Q9NZU9	Missense_Mutation	SNP	ENST00000263087.4	37	CCDS32531.1	11	0.005036630036630037	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	T	3.041	-0.197461	0.06259	6.81E-4	0.005698	ENSG00000083457	ENST00000263087	T	0.59772	0.24	3.57	-6.0	0.02206	.	.	.	.	.	T	0.18425	0.0442	N	0.11427	0.14	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31724	-0.9933	9	0.02654	T	1	.	5.5585	0.17129	0.0:0.215:0.2778:0.5073	.	182	P38570	ITAE_HUMAN	E	182	ENSP00000263087:K182E	ENSP00000263087:K182E	K	-	1	0	ITGAE	3611110	0.000000	0.05858	0.001000	0.08648	0.157000	0.22087	-1.083000	0.03397	-1.253000	0.02488	-0.534000	0.04291	AAG	T|0.996;C|0.004	0.004	strong		0.567	ITGAE-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438169.1	NM_002208		C	3664361	T	C	3664361	3	2	28	1	0	0	0	0	1	0	0	0	7894	1792	62	3	3099	3	ITGAE	17	3664361	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	35602	3664361	77530849	571	12074											
WSCD1	23302	hgsc.bcm.edu	37	chr17	6012955	6012955	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttggccattctcaggggctGggaatgctactgtgcttacc	6	12	12	11	0	1	0	1	0	1	0	2	1	1	1	2	4	4	3	2	4	3	4	rs267604993		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:6012955G>A	ENST00000574946.1	+	6	1268	c.878G>A	c.(877-879)tGg>tAg	p.W293*	WSCD1_ENST00000539421.1_Nonsense_Mutation_p.W293*|WSCD1_ENST00000574232.1_Nonsense_Mutation_p.W293*|WSCD1_ENST00000573634.1_Nonsense_Mutation_p.W177*|WSCD1_ENST00000317744.5_Nonsense_Mutation_p.W293*			Q658N2	WSCD1_HUMAN	WSC domain containing 1	293	WSC 2. {ECO:0000255|PROSITE- ProRule:PRU00558}.					integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)	35						CTCAGGGGCTGGGAATGCTAC	0.572																																					p.W293X		Atlas-SNP	.											.	WSCD1	84	.	0			c.G878A						PASS	.						241	225	231					17																	6012955		2203	4300	6503	SO:0001587	stop_gained	23302	exon6			GGGGCTGGGAATG		CCDS32538.1	17p13.2	2008-02-05				ENSG00000179314			29060	protein-coding gene	gene with protein product							Standard	XM_005256572		Approved	KIAA0523	uc002gcn.3	Q658N2		ENST00000574946.1:c.878G>A	17.37:g.6012955G>A	ENSP00000460825:p.Trp293*	65	0	0		63	19	0.301587	NM_015253	A8K0N8|D3DTM3|O60276|Q96G45	Nonsense_Mutation	SNP	ENST00000574946.1	37	CCDS32538.1	.	.	.	.	.	.	.	.	.	.	G	37	6.412301	0.97546	.	.	ENSG00000179314	ENST00000317744;ENST00000539421	.	.	.	5.91	3.83	0.44106	.	0.417502	0.27122	N	0.020825	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-23.0413	13.247	0.60028	0.0:0.4832:0.5167:0.0	.	.	.	.	X	293	.	ENSP00000323087:W293X	W	+	2	0	WSCD1	5953679	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.973000	0.29422	1.464000	0.47987	0.650000	0.86243	TGG	.	.	none		0.572	WSCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438965.4	NM_015253		A	6012955	G	A	6012955	4	1	28	1	0	0	0	0	0	1	0	0	17421	1357	47	2	896	2	WSCD1	17	6012955	Nonsense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2348594	6012955	75182255	572	12075											
SLC2A4	6517	hgsc.bcm.edu	37	chr17	7188459	7188459	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctccatctcctgggcctggCgggcatgtgtggctgtgcca	3	10	15	13	1	1	0	0	0	1	0	3	0	2	0	4	4	1	3	4	4	0	0	rs8192702	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7188459C>T	ENST00000317370.8	+	9	1341	c.1073C>T	c.(1072-1074)gCg>gTg	p.A358V	RP1-4G17.2_ENST00000576271.1_RNA|SLC2A4_ENST00000424875.2_Missense_Mutation_p.A348V|SLC2A4_ENST00000571308.1_Missense_Mutation_p.A358V	NM_001042.2	NP_001033.1	P14672	GTR4_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 4	358			A -> V (in dbSNP:rs8192702).		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						CTGGGCCTGGCGGGCATGTGT	0.662													C|||	8	0.00159744	0.0	0.0	5008	,	,		17560	0.0		0.007	False		,,,				2504	0.001				p.A358V		Atlas-SNP	.											.	SLC2A4	44	.	0			c.C1073T						PASS	.	C	VAL/ALA	5,4401		1,3,2199	34	36	35		1073	5.9	1	17	dbSNP_117	35	61,8539		0,61,4239	yes	missense	SLC2A4	NM_001042.2	64	1,64,6438	TT,TC,CC		0.7093,0.1135,0.5075	benign	358/510	7188459	66,12940	2203	4300	6503	SO:0001583	missense	6517	exon9			GCCTGGCGGGCAT	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.1073C>T	17.37:g.7188459C>T	ENSP00000320935:p.Ala358Val	36	0	0		57	31	0.54386	NM_001042	Q05BQ3|Q14CX2	Missense_Mutation	SNP	ENST00000317370.8	37	CCDS11097.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	15.10	2.733429	0.48939	0.001135	0.007093	ENSG00000181856	ENST00000317370;ENST00000424875	T;T	0.80480	0.35;-1.38	5.92	5.92	0.95590	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.209191	0.41712	D	0.000827	T	0.65709	0.2717	L	0.37800	1.135	0.36892	D	0.889926	B;B	0.31351	0.175;0.32	B;B	0.29524	0.103;0.024	T	0.72437	-0.4294	10	0.41790	T	0.15	.	13.4065	0.60915	0.0:0.8425:0.1575:0.0	rs8192702	358;348	P14672;F5H081	GTR4_HUMAN;.	V	358;348	ENSP00000320935:A358V;ENSP00000396887:A348V	ENSP00000320935:A358V	A	+	2	0	SLC2A4	7129183	0.040000	0.19996	0.983000	0.44433	0.909000	0.53808	0.267000	0.18552	2.813000	0.96785	0.561000	0.74099	GCG	C|0.996;T|0.004	0.004	strong		0.662	SLC2A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220031.3			T	7188459	C	T	7188459	3	4	28	1	0	0	0	0	1	0	0	0	14561	768	27	1	1107	1	SLC2A4	17	7188459	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1175504	7188459	74006751	573	12076											
FXR2	9513	hgsc.bcm.edu	37	chr17	7496411	7496411	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctttcttcccctcgggttggGggatccctgtcgccaggccc	2	11	12	16	2	1	0	0	0	1	0	5	1	3	1	5	4	0	1	5	4	0	3	rs61730843	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7496411G>A	ENST00000250113.7	-	13	1753	c.1419C>T	c.(1417-1419)ccC>ccT	p.P473P	SOX15_ENST00000250055.2_5'Flank|FXR2_ENST00000573057.1_5'Flank	NM_004860.3	NP_004851.2	P51116	FXR2_HUMAN	fragile X mental retardation, autosomal homolog 2	473						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)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)	26				READ - Rectum adenocarcinoma(115;0.17)		CTCGGGTTGGGGGATCCCTGT	0.627													G|||	29	0.00579073	0.0	0.0101	5008	,	,		13144	0.0		0.0119	False		,,,				2504	0.0102				p.P473P		Atlas-SNP	.											.	FXR2	44	.	0			c.C1419T						PASS	.	G		6,3684		0,6,1839	19	19	19		1419	1.9	1	17	dbSNP_129	19	66,8118		0,66,4026	no	coding-synonymous	FXR2	NM_004860.3		0,72,5865	AA,AG,GG		0.8065,0.1626,0.6064		473/674	7496411	72,11802	1845	4092	5937	SO:0001819	synonymous_variant	9513	exon13			GGTTGGGGGATCC	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.1419C>T	17.37:g.7496411G>A		71	0	0		74	41	0.554054	NM_004860	B2R9M2|D3DTQ1|Q86V09|Q8WUM2	Silent	SNP	ENST00000250113.7	37	CCDS45604.1																																																																																			G|0.995;A|0.005	0.005	strong		0.627	FXR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441084.1			A	7496411	G	A	7496411	2	1	28	1	0	0	0	0	0	0	0	1	6124	1219	43	2		2	FXR2	17	7496411	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	307952	7496411	73698799	574	12077											
DNAH2	146754	hgsc.bcm.edu	37	chr17	7701922	7701922	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggtggagctcaagaccacGtccttcatttttgtggacac	8	11	12	10	1	2	1	2	0	0	1	3	3	3	3	2	4	1	1	2	4	1	3	rs146210717	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7701922G>A	ENST00000572933.1	+	55	9905	c.8445G>A	c.(8443-8445)acG>acA	p.T2815T	DNAH2_ENST00000389173.2_Silent_p.T2815T			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	2815	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)				TCAAGACCACGTCCTTCATTT	0.547													G|||	4	0.000798722	0.0	0.0	5008	,	,		18237	0.0		0.004	False		,,,				2504	0.0				p.T2815T		Atlas-SNP	.											.	DNAH2	498	.	0			c.G8445A						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	111	102	105		8445	-9.6	0.9	17	dbSNP_134	105	24,8576	17.9+/-57.8	0,24,4276	no	coding-synonymous	DNAH2	NM_020877.2		0,26,6477	AA,AG,GG		0.2791,0.0454,0.1999		2815/4428	7701922	26,12980	2203	4300	6503	SO:0001819	synonymous_variant	146754	exon54			GACCACGTCCTTC	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.8445G>A	17.37:g.7701922G>A		48	0	0		61	33	0.540984	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	37	CCDS32551.1																																																																																			G|0.999;A|0.001	0.001	strong		0.547	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		A	7701922	G	A	7701922	2	1	28	1	0	0	0	0	0	0	0	1	4604	1132	40	1		1	DNAH2	17	7701922	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	205511	7701922	73493288	575	12078											
KDM6B	23135	hgsc.bcm.edu	37	chr17	7749972	7749972	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacccccagtggtgcagcctGtgcctcctgcagcactctca	7	8	9	17	0	1	0	1	0	1	0	3	0	2	0	5	1	6	3	5	1	1	0	rs148641957	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7749972G>T	ENST00000448097.2	+	8	956	c.625G>T	c.(625-627)Gtg>Ttg	p.V209L	KDM6B_ENST00000254846.5_Missense_Mutation_p.V209L			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	209	Pro-rich.				cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						GGTGCAGCCTGTGCCTCCTGC	0.607													G|||	10	0.00199681	0.0	0.0058	5008	,	,		9853	0.0		0.006	False		,,,				2504	0.0				p.V209L		Atlas-SNP	.											.	KDM6B	95	.	0			c.G625T						PASS	.	G	LEU/VAL	6,4400	11.4+/-27.6	0,6,2197	53	60	58		625	1.4	1	17	dbSNP_134	58	34,8566	23.4+/-69.3	0,34,4266	yes	missense	KDM6B	NM_001080424.1	32	0,40,6463	TT,TG,GG		0.3953,0.1362,0.3076	benign	209/1683	7749972	40,12966	2203	4300	6503	SO:0001583	missense	23135	exon8			CAGCCTGTGCCTC	AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"Chromatin-modifying enzymes / K-demethylases"	29012	protein-coding gene	gene with protein product		611577	"jumonji domain containing 3", "jumonji domain containing 3, histone lysine demethylase"	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.625G>T	17.37:g.7749972G>T	ENSP00000412513:p.Val209Leu	62	0	0		68	28	0.411765	NM_001080424	C9IZ40|Q96G33	Missense_Mutation	SNP	ENST00000448097.2	37		5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	G	10.41	1.342148	0.24339	0.001362	0.003953	ENSG00000132510	ENST00000254846;ENST00000448097	T;T	0.06933	3.24;3.24	5.14	1.42	0.22433	.	0.725657	0.12197	N	0.490623	T	0.02380	0.0073	N	0.08118	0	0.23440	N	0.997671	B	0.06786	0.001	B	0.06405	0.002	T	0.47275	-0.9130	10	0.19147	T	0.46	-1.9231	4.5059	0.11887	0.3322:0.1581:0.5097:0.0	.	209	O15054-1	.	L	209	ENSP00000254846:V209L;ENSP00000412513:V209L	ENSP00000254846:V209L	V	+	1	0	KDM6B	7690697	0.994000	0.37717	0.996000	0.52242	0.991000	0.79684	0.849000	0.27723	0.108000	0.17862	0.561000	0.74099	GTG	G|0.997;T|0.003	0.003	strong		0.607	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272		T	7749972	G	T	7749972	3	4	28	1	0	0	0	0	1	0	0	0	8147	1377	48	4	643	4	KDM6B	17	7749972	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	48050	7749972	73445238	576	12079											
CHD3	1107	hgsc.bcm.edu	37	chr17	7796805	7796805	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccacccccatagcaccctcCggaccccccgcccttccacc	6	4	5	26	2	0	0	0	0	0	0	2	1	2	1	11	1	1	1	11	1	1	2	rs199898244	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7796805C>G	ENST00000330494.7	+	5	861	c.711C>G	c.(709-711)tcC>tcG	p.S237S	CHD3_ENST00000358181.4_Silent_p.S237S|CHD3_ENST00000380358.4_Silent_p.S296S	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	237					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)				TAGCACCCTCCGGACCCCCCG	0.647													C|||	7	0.00139776	0.0	0.0058	5008	,	,		7723	0.0		0.003	False		,,,				2504	0.0				p.S296S		Atlas-SNP	.											.	CHD3	169	.	0			c.C888G						PASS	.	C	,,	1,4397		0,1,2198	16	17	17		888,711,711	-6.8	0.9	17		17	21,8559		0,21,4269	yes	coding-synonymous,coding-synonymous,coding-synonymous	CHD3	NM_001005271.2,NM_001005273.2,NM_005852.3	,,	0,22,6467	GG,GC,CC		0.2448,0.0227,0.1695	,,	296/2060,237/2001,237/1967	7796805	22,12956	2199	4290	6489	SO:0001819	synonymous_variant	1107	exon5			ACCCTCCGGACCC	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.711C>G	17.37:g.7796805C>G		130	0	0		105	46	0.438095	NM_001005271	D3DTQ9|E9PG89|Q9Y4I0	Silent	SNP	ENST00000330494.7	37	CCDS32554.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	5.459	0.269736	0.10349	2.27E-4	0.002448	ENSG00000170004	ENST00000452447	.	.	.	4.82	-6.78	0.01721	.	.	.	.	.	T	0.45377	0.1339	.	.	.	0.46901	D	0.999246	.	.	.	.	.	.	T	0.49725	-0.8909	4	.	.	.	-19.0971	6.1106	0.20097	0.195:0.3477:0.0:0.4573	.	.	.	.	G	112	.	.	R	+	1	2	CHD3	7737530	0.596000	0.26866	0.933000	0.37362	0.882000	0.50991	-0.099000	0.11007	-0.867000	0.04063	-1.391000	0.01154	CGG	C|0.999;G|0.001	0.001	strong		0.647	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273		G	7796805	C	G	7796805	2	3	28	1	0	0	0	0	0	0	0	1	3328	639	23	4		4	CHD3	17	7796805	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	46833	7796805	73398405	577	12080											
PFAS	5198	hgsc.bcm.edu	37	chr17	8172506	8172506	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggcatggcgaccccctccatTtgatactctgaccacctccc	7	9	7	18	1	1	2	0	2	1	0	3	3	3	2	6	2	1	1	6	2	1	2	rs62637606	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:8172506T>G	ENST00000314666.6	+	28	4074	c.3941T>G	c.(3940-3942)tTt>tGt	p.F1314C	PFAS_ENST00000545834.1_Missense_Mutation_p.F890C	NM_012393.2	NP_036525.1	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	1314					'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)	CCCCCTCCATTTGATACTCTG	0.637													T|||	130	0.0259585	0.0023	0.0591	5008	,	,		14648	0.0		0.0467	False		,,,				2504	0.0399				p.F1314C		Atlas-SNP	.											.	PFAS	91	.	0			c.T3941G						PASS	.	T	CYS/PHE	60,4346	57.4+/-93.9	1,58,2144	45	45	45		3941	5.5	1	17	dbSNP_129	45	549,8051	150.1+/-205.1	19,511,3770	yes	missense	PFAS	NM_012393.2	205	20,569,5914	GG,GT,TT		6.3837,1.3618,4.6825	benign	1314/1339	8172506	609,12397	2203	4300	6503	SO:0001583	missense	5198	exon28			CTCCATTTGATAC	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.3941T>G	17.37:g.8172506T>G	ENSP00000313490:p.Phe1314Cys	92	0	0		93	45	0.483871	NM_012393	A6H8V8	Missense_Mutation	SNP	ENST00000314666.6	37	CCDS11136.1	69	0.03159340659340659	1	0.0020325203252032522	32	0.08839779005524862	0	0.0	36	0.047493403693931395	T	14.30	2.494705	0.44352	0.013618	0.063837	ENSG00000178921	ENST00000545834;ENST00000314666;ENST00000546020	T;T	0.30981	1.51;2.25	5.46	5.46	0.80206	Glutamine amidotransferase type 1 (1);	0.179053	0.46145	D	0.000302	T	0.01287	0.0042	L	0.55017	1.72	0.38160	D	0.939011	B	0.28998	0.23	B	0.32211	0.142	T	0.02698	-1.1122	10	0.87932	D	0	-5.1281	13.4903	0.61390	0.0:0.0:0.0:1.0	rs62637606	1314	O15067	PUR4_HUMAN	C	890;1314;723	ENSP00000441706:F890C;ENSP00000313490:F1314C	ENSP00000313490:F1314C	F	+	2	0	PFAS	8113231	0.941000	0.31946	0.969000	0.41365	0.996000	0.88848	1.167000	0.31847	2.057000	0.61298	0.533000	0.62120	TTT	T|0.957;G|0.043	0.043	strong		0.637	PFAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226994.2			G	8172506	T	G	8172506	3	3	28	1	0	0	0	0	1	0	0	0	11763	1841	64	5	4047	5	PFAS	17	8172506	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	375701	8172506	73022704	578	12081											
MYH10	4628	hgsc.bcm.edu	37	chr17	8413247	8413247	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccgagccccttcctcctcGtctagctgttcttccaggtc	3	13	8	17	2	2	0	0	0	2	0	7	1	5	0	6	1	3	2	6	1	1	4	rs139264814		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:8413247G>A	ENST00000269243.4	-	23	3018	c.2880C>T	c.(2878-2880)gaC>gaT	p.D960D	RNU7-43P_ENST00000516554.1_RNA|MYH10_ENST00000360416.3_Silent_p.D991D|MYH10_ENST00000396239.1_Silent_p.D981D|MYH10_ENST00000379980.4_Silent_p.D976D	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	960					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						CTTCCTCCTCGTCTAGCTGTT	0.493																																					p.D991D		Atlas-SNP	.											.	MYH10	148	.	0			c.C2973T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	88	81	83		2880	-8.3	0.7	17	dbSNP_134	83	0,8600		0,0,4300	no	coding-synonymous	MYH10	NM_005964.1		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		960/1977	8413247	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	4628	exon25			CTCCTCGTCTAGC	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.2880C>T	17.37:g.8413247G>A		67	0	0		57	13	0.22807	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	37	CCDS11144.1																																																																																			G|1.000;A|0.000	0.000	weak		0.493	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			A	8413247	G	A	8413247	2	1	28	1	0	0	0	0	0	0	0	1	10039	1136	40	1		1	MYH10	17	8413247	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	240741	8413247	72781963	579	12082											
PIGL	9487	hgsc.bcm.edu	37	chr17	16203290	16203290	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagaagtgaatggcatcaatCtggtaagggggcagctccct	11	9	13	8	0	2	2	1	1	1	1	3	2	3	2	1	4	1	4	1	4	5	2	rs115958467	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:16203290C>A	ENST00000225609.5	+	3	441	c.424C>A	c.(424-426)Ctg>Atg	p.L142M	PIGL_ENST00000498772.2_Missense_Mutation_p.L142M|PIGL_ENST00000581006.1_Missense_Mutation_p.L142M|PIGL_ENST00000395844.4_Missense_Mutation_p.L142M	NM_004278.3	NP_004269.1	Q9Y2B2	PIGL_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class L	142					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)	N-acetylglucosaminylphosphatidylinositol deacetylase activity (GO:0000225)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|skin(1)	11				UCEC - Uterine corpus endometrioid carcinoma (92;0.0934)		TGGCATCAATCTGGTAAGGGG	0.522													C|||	11	0.00219649	0.0	0.0086	5008	,	,		20273	0.0		0.005	False		,,,				2504	0.0				p.L142M		Atlas-SNP	.											.	PIGL	16	.	0			c.C424A						PASS	.	C	MET/LEU	10,4396	16.8+/-37.8	0,10,2193	133	115	121		424	1.3	1	17	dbSNP_132	121	61,8539	38.3+/-94.2	1,59,4240	yes	missense	PIGL	NM_004278.3	15	1,69,6433	AA,AC,CC		0.7093,0.227,0.5459	probably-damaging	142/253	16203290	71,12935	2203	4300	6503	SO:0001583	missense	9487	exon3			ATCAATCTGGTAA	AB017165	CCDS11176.1	17p12-p11.2	2013-02-26	2006-06-28		ENSG00000108474	ENSG00000108474	3.5.1.89	"Phosphatidylinositol glycan anchor biosynthesis"	8966	protein-coding gene	gene with protein product	"N-acetylglucosaminylphosphatidylinositol deacetylase"	605947	"phosphatidylinositol glycan, class L"			10085243	Standard	NM_004278		Approved		uc002gpv.3	Q9Y2B2	OTTHUMG00000059346	ENST00000225609.5:c.424C>A	17.37:g.16203290C>A	ENSP00000225609:p.Leu142Met	58	0	0		73	40	0.547945	NM_004278	A8KA67|B4DYN4	Missense_Mutation	SNP	ENST00000225609.5	37	CCDS11176.1	8	0.003663003663003663	0	0.0	4	0.011049723756906077	0	0.0	4	0.005277044854881266	C	12.67	2.008068	0.35415	0.00227	0.007093	ENSG00000108474	ENST00000225609;ENST00000395844	T;T	0.78707	-1.2;-1.2	4.47	1.28	0.21552	Putative deacetylase LmbE-like domain (2);	0.000000	0.64402	D	0.000001	T	0.73426	0.3585	M	0.66378	2.025	0.35873	D	0.828373	D;D	0.56968	0.978;0.978	P;P	0.54499	0.754;0.754	T	0.77930	-0.2403	10	0.54805	T	0.06	-14.4259	6.9712	0.24650	0.0:0.7108:0.0:0.2892	.	142;142	B4DYN4;Q9Y2B2	.;PIGL_HUMAN	M	142	ENSP00000225609:L142M;ENSP00000379185:L142M	ENSP00000225609:L142M	L	+	1	2	PIGL	16144015	0.733000	0.28132	0.962000	0.40283	0.273000	0.26683	0.159000	0.16442	0.221000	0.20879	0.460000	0.39030	CTG	C|0.996;A|0.004	0.004	strong		0.522	PIGL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131881.1			A	16203290	C	A	16203290	3	1	28	1	0	0	0	0	1	0	0	0	11900	912	32	4	434	4	PIGL	17	16203290	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	7790043	16203290	64991920	580	12083											
PEMT	10400	hgsc.bcm.edu	37	chr17	17409140	17409140	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggacccggaggctttctgccGgtagatctcagcggtgaagg	7	8	16	10	3	2	2	1	1	2	1	3	4	2	4	2	6	2	2	2	6	2	2	rs140621950		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:17409140G>A	ENST00000395783.1	-	7	744	c.565C>T	c.(565-567)Cgg>Tgg	p.R189W	PEMT_ENST00000255389.5_Missense_Mutation_p.R226W|PEMT_ENST00000395782.1_Missense_Mutation_p.R189W|PEMT_ENST00000435340.2_3'UTR|PEMT_ENST00000395781.2_3'UTR|PEMT_ENST00000484838.2_5'UTR|RP11-524F11.1_ENST00000582325.1_RNA	NM_007169.2	NP_009100.2	Q9UBM1	PEMT_HUMAN	phosphatidylethanolamine N-methyltransferase	189					cell proliferation (GO:0008283)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	phosphatidyl-N-dimethylethanolamine N-methyltransferase activity (GO:0080101)|phosphatidyl-N-methylethanolamine N-methyltransferase activity (GO:0000773)|phosphatidylethanolamine N-methyltransferase activity (GO:0004608)			endometrium(1)|kidney(1)|large_intestine(2)|prostate(3)	7				Colorectal(2;0.0157)|READ - Rectum adenocarcinoma(2;0.0891)		GCTTTCTGCCGGTAGATCTCA	0.662													G|||	1	0.000199681	0.0	0.0	5008	,	,		16588	0.0		0.001	False		,,,				2504	0.0				p.R226W		Atlas-SNP	.											.	PEMT	12	.	0			c.C676T						PASS	.	G	TRP/ARG,TRP/ARG,TRP/ARG	2,4404	4.2+/-10.8	0,2,2201	63	57	59		565,676,565	2.3	1	17	dbSNP_134	59	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense,missense	PEMT	NM_007169.2,NM_148172.1,NM_148173.1	101,101,101	0,8,6495	AA,AG,GG		0.0698,0.0454,0.0615	probably-damaging,probably-damaging,probably-damaging	189/200,226/237,189/200	17409140	8,12998	2203	4300	6503	SO:0001583	missense	10400	exon7			TCTGCCGGTAGAT	AF176806	CCDS11186.1, CCDS11187.1, CCDS58520.1	17p11.2	2008-02-05			ENSG00000133027	ENSG00000133027	2.1.1.17		8830	protein-coding gene	gene with protein product		602391				9989271, 17881348	Standard	NM_148173		Approved	PEMPT, PEMT2	uc002grl.4	Q9UBM1	OTTHUMG00000059290	ENST00000395783.1:c.565C>T	17.37:g.17409140G>A	ENSP00000379129:p.Arg189Trp	152	0	0		151	64	0.423841	NM_148172	A8MZ66|B4DY41|D3DXC3|Q6IAQ5|Q86VL3|Q9BW86|Q9UHY6|Q9Y6V9	Missense_Mutation	SNP	ENST00000395783.1	37	CCDS11187.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.460614	0.43736	4.54E-4	6.98E-4	ENSG00000133027	ENST00000255389;ENST00000395783;ENST00000395782	T;T;T	0.44482	0.92;0.92;0.92	3.29	2.3	0.28687	.	0.487586	0.21644	N	0.071298	T	0.61185	0.2327	M	0.79805	2.47	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.68192	0.927;0.956	T	0.64322	-0.6435	10	0.66056	D	0.02	-31.4459	9.9715	0.41757	0.0:0.0:0.7954:0.2046	.	226;189	Q9UBM1-2;Q9UBM1	.;PEMT_HUMAN	W	226;189;189	ENSP00000255389:R226W;ENSP00000379129:R189W;ENSP00000379128:R189W	ENSP00000255389:R226W	R	-	1	2	PEMT	17349865	1.000000	0.71417	0.989000	0.46669	0.268000	0.26511	2.878000	0.48515	0.946000	0.37632	0.561000	0.74099	CGG	G|0.999;A|0.001	0.001	strong		0.662	PEMT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131657.1	NM_007169		A	17409140	G	A	17409140	3	1	28	1	0	0	0	0	1	0	0	0	11735	1115	39	1	38	1	PEMT	17	17409140	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1205850	17409140	63786070	581	12084											
FAM83G	644815	hgsc.bcm.edu	37	chr17	18907198	18907198	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gaggaagtctcggatgttctCccgcttgagcacctcgtaga	8	10	12	11	3	2	2	0	1	2	1	5	5	2	4	2	2	1	4	2	2	2	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:18907198C>T	ENST00000388995.6	-	2	380	c.157G>A	c.(157-159)Gag>Aag	p.E53K	SLC5A10_ENST00000395643.2_Intron|SLC5A10_ENST00000395647.2_Intron|FAM83G_ENST00000585154.2_Missense_Mutation_p.E53K|FAM83G_ENST00000345041.4_Missense_Mutation_p.E53K|SLC5A10_ENST00000395642.1_Intron|SLC5A10_ENST00000317977.6_Intron|SLC5A10_ENST00000417251.2_Intron|SLC5A10_ENST00000395645.3_Intron			A6ND36	FA83G_HUMAN	family with sequence similarity 83, member G	53					BMP signaling pathway (GO:0030509)	cytosol (GO:0005829)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(3)|stomach(1)	22						CGGATGTTCTCCCGCTTGAGC	0.672																																					p.E53K		Atlas-SNP	.											.	FAM83G	51	.	0			c.G157A						PASS	.						35	41	39					17																	18907198		2015	4183	6198	SO:0001583	missense	644815	exon2			TGTTCTCCCGCTT	AK123558	CCDS42276.1	17p11.2	2014-05-01	2006-03-22		ENSG00000188522	ENSG00000188522			32554	protein-coding gene	gene with protein product	"protein associated with SMAD1"	615886				24554596	Standard	NM_001039999		Approved	FLJ41564, PAWS1	uc002guw.3	A6ND36	OTTHUMG00000059411	ENST00000388995.6:c.157G>A	17.37:g.18907198C>T	ENSP00000373647:p.Glu53Lys	110	0	0		116	60	0.517241	NM_001039999	Q3KQZ4|Q6ZW60	Missense_Mutation	SNP	ENST00000388995.6	37	CCDS42276.1	.	.	.	.	.	.	.	.	.	.	C	14.85	2.658749	0.47467	.	.	ENSG00000188522	ENST00000388995;ENST00000345041;ENST00000399096	T;T	0.15487	2.42;2.42	5.01	5.01	0.66863	.	0.392245	0.26746	N	0.022701	T	0.31040	0.0784	M	0.84511	2.7	0.34765	D	0.733098	P	0.34934	0.476	B	0.36186	0.219	T	0.53732	-0.8397	10	0.87932	D	0	-36.4032	18.3131	0.90207	0.0:1.0:0.0:0.0	.	53	A6ND36	FA83G_HUMAN	K	53	ENSP00000373647:E53K;ENSP00000343279:E53K	ENSP00000343279:E53K	E	-	1	0	FAM83G	18847923	0.905000	0.30787	1.000000	0.80357	0.987000	0.75469	1.035000	0.30216	2.332000	0.79248	0.491000	0.48974	GAG	.	.	none		0.672	FAM83G-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253108.4			T	18907198	C	T	18907198	3	4	28	1	0	0	0	0	1	0	0	0	5647	864	30	2	2334	2	FAM83G	17	18907198	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1498058	18907198	62288012	582	12085											
KCNJ12	3768	hgsc.bcm.edu	37	chr17	21318826	21318826	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagtgcaacattgagttcGccaacatggacgagaagtca	13	7	11	10	2	1	2	1	1	0	1	2	4	1	3	2	1	3	2	2	1	3	2	rs142399667	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:21318826G>A	ENST00000583088.1	+	3	1067	c.172G>A	c.(172-174)Gcc>Acc	p.A58T	KCNJ12_ENST00000331718.5_Missense_Mutation_p.A58T	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	58					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)	CATTGAGTTCGCCAACATGGA	0.597										Prostate(3;0.18)																											p.A58T		Atlas-SNP	.											KCNJ12,NS,carcinoma,0,1	.	.	1	0			c.G172A						PASS	.	G	THR/ALA	69,4337	52.3+/-87.9	0,69,2134	197	131	153		172	5.3	1	17	dbSNP_134	153	62,8538	26.8+/-75.7	0,62,4238	yes	missense	KCNJ12	NM_021012.4	58	0,131,6372	AA,AG,GG		0.7209,1.566,1.0072	benign	58/434	21318826	131,12875	2203	4300	6503	SO:0001583	missense	100134444	exon3			GAGTTCGCCAACA	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.172G>A	17.37:g.21318826G>A	ENSP00000463778:p.Ala58Thr	160	0	0		192	26	0.135417	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	37	CCDS11219.1	.	.	.	.	.	.	.	.	.	.	G	11.62	1.692589	0.30052	0.01566	0.007209	ENSG00000184185	ENST00000331718	D	0.93859	-3.3	5.33	5.33	0.75918	Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);	0.248894	0.40908	D	0.000997	T	0.77631	0.4159	N	0.16233	0.39	0.36661	D	0.877951	B	0.12630	0.006	B	0.18263	0.021	T	0.80009	-0.1562	10	0.32370	T	0.25	.	10.2342	0.43273	0.1224:0.0:0.8776:0.0	.	58	Q14500	IRK12_HUMAN	T	58	ENSP00000328150:A58T	ENSP00000328150:A58T	A	+	1	0	KCNJ12	21259419	0.993000	0.37304	1.000000	0.80357	0.988000	0.76386	2.230000	0.42999	2.506000	0.84524	0.591000	0.81541	GCC	G|0.993;A|0.007	0.007	strong		0.597	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012		A	21318826	G	A	21318826	3	1	28	1	0	0	0	0	1	0	0	0	8055	1087	38	1	174	1	KCNJ12	17	21318826	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2411628	21318826	59876384	583	12086											
PIGS	94005	hgsc.bcm.edu	37	chr17	26888506	26888506	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctctggaaggtggtcagccaGagcagcagcaagcacatcct	11	6	12	12	0	2	1	1	0	1	1	3	2	3	2	2	3	5	4	2	3	2	0	rs140545278	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:26888506G>C	ENST00000308360.7	-	6	985	c.610C>G	c.(610-612)Ctg>Gtg	p.L204V	PIGS_ENST00000395346.2_Missense_Mutation_p.L196V|PIGS_ENST00000543734.1_Missense_Mutation_p.L143V|PIGS_ENST00000465444.1_5'UTR	NM_033198.3	NP_149975.1	Q96S52	PIGS_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class S	204					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)					TGGTCAGCCAGAGCAGCAGCA	0.602																																					p.L204V		Atlas-SNP	.											.	PIGS	42	.	0			c.C610G						PASS	.	G	VAL/LEU	0,4406		0,0,2203	83	66	72		610	2.2	0.9	17	dbSNP_134	72	4,8596	3.7+/-12.6	0,4,4296	yes	missense	PIGS	NM_033198.3	32	0,4,6499	CC,CG,GG		0.0465,0.0,0.0308	probably-damaging	204/556	26888506	4,13002	2203	4300	6503	SO:0001583	missense	94005	exon6			CAGCCAGAGCAGC		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.610C>G	17.37:g.26888506G>C	ENSP00000309430:p.Leu204Val	106	0	0		111	55	0.495495	NM_033198	Q6UVX6	Missense_Mutation	SNP	ENST00000308360.7	37	CCDS11235.1	.	.	.	.	.	.	.	.	.	.	G	17.70	3.454766	0.63290	0.0	4.65E-4	ENSG00000087111	ENST00000395346;ENST00000308360;ENST00000543734	T;T;T	0.49139	0.86;0.86;0.79	5.68	2.21	0.28008	.	0.000000	0.85682	D	0.000000	T	0.59390	0.2190	M	0.72479	2.2	0.52099	D	0.99994	D;D	0.63880	0.993;0.991	D;P	0.66084	0.941;0.862	T	0.55218	-0.8175	10	0.17832	T	0.49	-12.9026	10.0958	0.42475	0.2491:0.0:0.7509:0.0	.	204;196	Q96S52;Q96S52-2	PIGS_HUMAN;.	V	196;204;143	ENSP00000378755:L196V;ENSP00000309430:L204V;ENSP00000438447:L143V	ENSP00000309430:L204V	L	-	1	2	PIGS	23912633	1.000000	0.71417	0.939000	0.37840	0.997000	0.91878	2.033000	0.41136	0.191000	0.20236	0.655000	0.94253	CTG	G|0.999;C|0.001	0.001	strong		0.602	PIGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255833.3	NM_033198		C	26888506	G	C	26888506	3	2	28	1	0	0	0	0	1	0	0	0	11907	933	33	4	1085	4	PIGS	17	26888506	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	5569680	26888506	54306704	584	12087											
KIAA0100	9703	hgsc.bcm.edu	37	chr17	26961735	26961735	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagtgcccggcgcatgggtGtgttgccatagagacgacgg	7	7	17	10	4	0	1	0	0	0	1	0	3	0	1	2	3	2	3	2	3	1	2	rs118181996		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:26961735G>A	ENST00000528896.2	-	16	2944	c.2870C>T	c.(2869-2871)aCa>aTa	p.T957I	KIAA0100_ENST00000544884.1_Missense_Mutation_p.T814I|KIAA0100_ENST00000389003.3_Missense_Mutation_p.T814I|RP11-192H23.7_ENST00000577814.1_RNA|RP11-192H23.7_ENST00000583787.1_RNA	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	957						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)					GCGCATGGGTGTGTTGCCATA	0.527													G|||	1	0.000199681	0.0	0.0	5008	,	,		19628	0.0		0.001	False		,,,				2504	0.0				p.T957I		Atlas-SNP	.											.	KIAA0100	175	.	0			c.C2870T						PASS	.	G	ILE/THR	0,4406		0,0,2203	113	112	113		2870	5.9	1	17	dbSNP_132	113	3,8597	3.0+/-9.4	0,3,4297	yes	missense	KIAA0100	NM_014680.3	89	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging	957/2236	26961735	3,13003	2203	4300	6503	SO:0001583	missense	9703	exon16			ATGGGTGTGTTGC	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.2870C>T	17.37:g.26961735G>A	ENSP00000436773:p.Thr957Ile	66	0	0		72	22	0.305556	NM_014680	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	37	CCDS32595.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	21.4	4.139429	0.77775	0.0	3.49E-4	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	T;T	0.25085	1.83;1.82	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.46347	0.1388	L	0.47716	1.5	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.04537	-1.0944	10	0.25106	T	0.35	.	20.2651	0.98459	0.0:0.0:1.0:0.0	.	957	Q14667	K0100_HUMAN	I	957;927;957;814	ENSP00000436773:T957I;ENSP00000446443:T814I	ENSP00000005905:T957I	T	-	2	0	KIAA0100	23985862	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.328000	0.79160	2.796000	0.96246	0.563000	0.77884	ACA	G|0.999;A|0.001	0.001	strong		0.527	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680		A	26961735	G	A	26961735	3	1	28	1	0	0	0	0	1	0	0	0	8163	1377	48	2	3933	2	KIAA0100	17	26961735	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	73229	26961735	54233475	585	12088											
TIAF1	9220	hgsc.bcm.edu	37	chr17	27401176	27401176	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ccagcgtctccagctgcacaGagaaaggactgctctctgaa	11	7	10	13	1	2	2	0	1	2	1	4	4	2	3	2	1	4	3	2	1	2	0	rs1049848	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:27401176G>C	ENST00000359450.6	-	1	4699	c.42C>G	c.(40-42)ctC>ctG	p.L14L	MYO18A_ENST00000533112.1_3'UTR|TIAF1_ENST00000408971.2_Silent_p.L14L|MYO18A_ENST00000527372.1_3'UTR|MYO18A_ENST00000354329.4_3'UTR|MYO18A_ENST00000531253.1_3'UTR|MYO18A_ENST00000529578.1_5'UTR	NM_004740.3	NP_004731.2	O95411	TIAF1_HUMAN	TGFB1-induced anti-apoptotic factor 1	14					apoptotic process (GO:0006915)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of apoptotic process (GO:0043066)	nucleus (GO:0005634)				kidney(1)|lung(1)|urinary_tract(1)	3	Lung NSC(42;0.015)		Epithelial(11;1.19e-05)|all cancers(11;6.57e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000153)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			CAGCTGCACAGAGAAAGGACT	0.597													G|||	24	0.00479233	0.0	0.0	5008	,	,		16628	0.001		0.0209	False		,,,				2504	0.002				p.L14L		Atlas-SNP	.											.	TIAF1	9	.	0			c.C42G						PASS	.	G	,,	18,4388	25.3+/-52.1	0,18,2185	50	51	51		42,,	1.7	0	17	dbSNP_86	51	135,8465	68.7+/-131.2	1,133,4166	no	coding-synonymous,utr-3,utr-3	TIAF1,MYO18A	NM_004740.3,NM_078471.3,NM_203318.1	,,	1,151,6351	CC,CG,GG		1.5698,0.4085,1.1764	,,	14/116,,	27401176	153,12853	2203	4300	6503	SO:0001819	synonymous_variant	9220	exon1			TGCACAGAGAAAG	AF105277	CCDS32599.1	17q11.2	2006-08-07				ENSG00000221995			11803	protein-coding gene	gene with protein product		609517				9918798	Standard	NM_004740		Approved		uc002hdv.1	O95411		ENST00000359450.6:c.42C>G	17.37:g.27401176G>C		48	0	0		55	27	0.490909	NM_004740	A2RRE2|Q6PEG2	Silent	SNP	ENST00000359450.6	37	CCDS32599.1																																																																																			G|0.988;C|0.012	0.012	strong		0.597	TIAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372394.2	NM_004740		C	27401176	G	C	27401176	2	2	28	1	0	0	0	0	0	0	0	1	15903	929	33	4		4	TIAF1	17	27401176	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	439441	27401176	53794034	586	12089											
SPACA3	124912	hgsc.bcm.edu	37	chr17	31323886	31323886	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgccttgcttatttcacaagCggtttcaacgcagctgcttt	7	15	8	11	2	2	0	2	0	0	0	2	0	2	0	1	1	6	5	1	1	3	5	rs200596990	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:31323886C>T	ENST00000269053.3	+	3	439	c.369C>T	c.(367-369)agC>agT	p.S123S	SPACA3_ENST00000394637.2_3'UTR|SPACA3_ENST00000580599.1_Silent_p.S54S|SPACA3_ENST00000394638.1_Silent_p.S20S	NM_173847.3	NP_776246.1	Q8IXA5	SACA3_HUMAN	sperm acrosome associated 3	123					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)			ATTTCACAAGCGGTTTCAACG	0.582																																					p.S123S		Atlas-SNP	.											SPACA3,NS,carcinoma,+1,1	SPACA3	35	1	0			c.C369T						PASS	.	C		0,4406		0,0,2203	104	92	96		369	0.9	1	17		96	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	SPACA3	NM_173847.3		0,4,6499	TT,TC,CC		0.0465,0.0,0.0308		123/216	31323886	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	124912	exon3			CACAAGCGGTTTC	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.369C>T	17.37:g.31323886C>T		56	0	0		59	37	0.627119	NM_173847	Q7Z4Y5	Silent	SNP	ENST00000269053.3	37	CCDS11275.1																																																																																			C|0.998;T|0.002	0.002	strong		0.582	SPACA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256380.1	NM_173847		T	31323886	C	T	31323886	2	4	28	1	0	0	0	0	0	0	0	1	14988	767	27	1		1	SPACA3	17	31323886	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	3922710	31323886	49871324	587	12090											
MYO19	80179	hgsc.bcm.edu	37	chr17	34854121	34854121	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaacgtacctgaggcagcgCtcggatggacgtgacaccag	11	5	13	12	4	0	2	0	2	0	0	1	4	0	4	2	3	3	3	2	3	2	1	rs139565052	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:34854121C>T	ENST00000431794.3	-	25	3268	c.2746G>A	c.(2746-2748)Gcg>Acg	p.A916T	ZNHIT3_ENST00000588253.1_3'UTR|ZNHIT3_ENST00000590858.1_3'UTR|MYO19_ENST00000268852.9_Missense_Mutation_p.A716T	NM_001163735.1	NP_001157207.1	Q96H55	MYO19_HUMAN	myosin XIX	916	Mitochondrial targeting.					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)		TGAGGCAGCGCTCGGATGGAC	0.572													C|||	3	0.000599042	0.0	0.0014	5008	,	,		17680	0.0		0.002	False		,,,				2504	0.0				p.A916T		Atlas-SNP	.											.	MYO19	130	.	0			c.G2746A						PASS	.	C	THR/ALA,THR/ALA	1,4313		0,1,2156	74	76	75		2746,2146	5.9	1	17	dbSNP_134	75	18,8512		0,18,4247	yes	missense,missense	MYO19	NM_001163735.1,NM_025109.5	58,58	0,19,6403	TT,TC,CC		0.211,0.0232,0.1479	probably-damaging,probably-damaging	916/971,716/771	34854121	19,12825	2157	4265	6422	SO:0001583	missense	80179	exon26			GCAGCGCTCGGAT	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.2746G>A	17.37:g.34854121C>T	ENSP00000409936:p.Ala916Thr	20	0	0		28	10	0.357143	NM_001163735	Q59GS4|Q9H5X2	Missense_Mutation	SNP	ENST00000431794.3	37	CCDS54112.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	27.1	4.800048	0.90538	2.32E-4	0.00211	ENSG00000141140	ENST00000415126;ENST00000431794;ENST00000268852	T;T	0.74002	-0.8;-0.8	5.91	5.91	0.95273	.	0.000000	0.42294	D	0.000730	D	0.85353	0.5677	M	0.65498	2.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.85959	0.1469	10	0.87932	D	0	.	17.0716	0.86576	0.0:1.0:0.0:0.0	.	916;716	Q96H55;Q96H55-4	MYO19_HUMAN;.	T	374;916;716	ENSP00000409936:A916T;ENSP00000268852:A716T	ENSP00000268852:A716T	A	-	1	0	MYO19	31928234	1.000000	0.71417	0.999000	0.59377	0.831000	0.47069	4.579000	0.60936	2.821000	0.97095	0.485000	0.47835	GCG	C|0.999;T|0.001	0.001	strong		0.572	MYO19-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451074.1	NM_025109		T	34854121	C	T	34854121	3	4	28	1	0	0	0	0	1	0	0	0	10076	797	28	2	174	2	MYO19	17	34854121	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	3530235	34854121	46341089	588	12091											
MED24	9862	hgsc.bcm.edu	37	chr17	38178679	38178679	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcggtgtctcttcttctggcGggtggacgcctgtcccttgt	1	14	14	12	3	3	0	0	0	3	0	5	1	4	1	2	4	0	0	2	4	0	3	rs149459087	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:38178679G>A	ENST00000394128.2	-	22	2572	c.2491C>T	c.(2491-2493)Cgc>Tgc	p.R831C	MED24_ENST00000394127.2_Missense_Mutation_p.R818C|MED24_ENST00000394126.1_Missense_Mutation_p.R856C|MED24_ENST00000356271.3_Missense_Mutation_p.R818C|MED24_ENST00000501516.3_Missense_Mutation_p.R850C	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	831					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)					TTCTTCTGGCGGGTGGACGCC	0.587													G|||	3	0.000599042	0.0	0.0	5008	,	,		18089	0.0		0.003	False		,,,				2504	0.0				p.R831C		Atlas-SNP	.											.	MED24	89	.	0			c.C2491T						PASS	.	G	CYS/ARG,CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	43	40	41		2452,2491	5.5	1	17	dbSNP_134	41	27,8573	19.2+/-60.6	0,27,4273	yes	missense,missense	MED24	NM_001079518.1,NM_014815.3	180,180	0,29,6474	AA,AG,GG		0.314,0.0454,0.223	probably-damaging,probably-damaging	818/977,831/990	38178679	29,12977	2203	4300	6503	SO:0001583	missense	9862	exon22			TCTGGCGGGTGGA	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.2491C>T	17.37:g.38178679G>A	ENSP00000377686:p.Arg831Cys	97	0	0		109	60	0.550459	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Missense_Mutation	SNP	ENST00000394128.2	37	CCDS11359.1	2|2	9.157509157509158E-4|9.157509157509158E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	G|G	13.32|13.32	2.201336|2.201336	0.38905|0.38905	4.54E-4|4.54E-4	0.00314|0.00314	ENSG00000008838|ENSG00000008838	ENST00000422942|ENST00000394126;ENST00000356271;ENST00000394128;ENST00000535071;ENST00000394127;ENST00000536318;ENST00000431269	.|T;T;T	.|0.48836	.|0.8;0.8;0.8	5.48|5.48	5.48|5.48	0.80851|0.80851	.|Mediator complex, subunit Med24, N-terminal (1);	.|0.054745	.|0.85682	.|D	.|0.000000	T|T	0.58481|0.58481	0.2125|0.2125	L|L	0.57536|0.57536	1.79|1.79	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.76494	.|0.98;0.995;0.998;0.999;0.98	.|P;P;P;P;P	.|0.60345	.|0.606;0.817;0.799;0.873;0.606	T|T	0.60321|0.60321	-0.7286|-0.7286	5|10	.|0.59425	.|D	.|0.04	-17.5546|-17.5546	10.1133|10.1133	0.42576|0.42576	0.0719:0.0:0.7899:0.1382|0.0719:0.0:0.7899:0.1382	.|.	.|741;741;818;831;773	.|F8W9R9;B4E1A5;O75448-2;O75448;F5H0K1	.|.;.;.;MED24_HUMAN;.	L|C	85|831;831;831;781;818;773;741	.|ENSP00000377686:R831C;ENSP00000443344:R781C;ENSP00000377685:R818C	.|ENSP00000348610:R831C	P|R	-|-	2|1	0|0	MED24|MED24	35432205|35432205	1.000000|1.000000	0.71417|0.71417	0.986000|0.986000	0.45419|0.45419	0.566000|0.566000	0.35808|0.35808	3.807000|3.807000	0.55591|0.55591	2.572000|2.572000	0.86782|0.86782	0.655000|0.655000	0.94253|0.94253	CCG|CGC	G|0.998;A|0.002	0.002	strong		0.587	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815		A	38178679	G	A	38178679	3	1	28	1	0	0	0	0	1	0	0	0	9451	1116	39	1	498	1	MED24	17	38178679	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	3324558	38178679	43016531	589	12092											
KRT38	8687	hgsc.bcm.edu	37	chr17	39595537	39595537	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggtcggccttggccagggtcGcatcatccaggagcttctgt	5	10	14	12	2	2	0	1	0	1	0	5	1	3	1	3	5	1	2	3	5	0	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39595537G>A	ENST00000246646.3	-	3	649	c.650C>T	c.(649-651)gCg>gTg	p.A217V		NM_006771.3	NP_006762.3	O76015	KRT38_HUMAN	keratin 38	217	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)				GGCCAGGGTCGCATCATCCAG	0.637																																					p.A217V		Atlas-SNP	.											.	KRT38	63	.	0			c.C650T						PASS	.						83	75	78					17																	39595537		2203	4300	6503	SO:0001583	missense	8687	exon3			AGGGTCGCATCAT	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.650C>T	17.37:g.39595537G>A	ENSP00000246646:p.Ala217Val	63	0	0		89	5	0.0561798	NM_006771	A2RRM5|Q6A164	Missense_Mutation	SNP	ENST00000246646.3	37	CCDS11392.1	.	.	.	.	.	.	.	.	.	.	G	12.41	1.928753	0.34002	.	.	ENSG00000171360	ENST00000246646	D	0.90004	-2.6	4.31	3.11	0.35812	Filament (1);	1.672080	0.04241	N	0.336988	D	0.85961	0.5819	L	0.45051	1.395	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.71217	-0.4658	10	0.72032	D	0.01	.	7.6159	0.28158	0.8792:0.0:0.1208:0.0	.	217	O76015	KRT38_HUMAN	V	217	ENSP00000246646:A217V	ENSP00000246646:A217V	A	-	2	0	KRT38	36849063	0.044000	0.20184	0.710000	0.30468	0.780000	0.44128	3.320000	0.51991	0.590000	0.29694	0.484000	0.47621	GCG	.	.	none		0.637	KRT38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257307.2	NM_006771		A	39595537	G	A	39595537	3	1	28	1	0	0	0	0	1	0	0	0	8484	1087	38	1	740	1	KRT38	17	39595537	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1416858	39595537	41599673	590	12093											
KRT16	3868	hgsc.bcm.edu	37	chr17	39767731	39767731	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcggcctccacagtctgccGcagggccagttcatgctcat	6	9	11	15	2	3	0	2	0	1	0	5	0	4	0	4	2	2	3	4	2	0	1	rs148173278	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39767731G>A	ENST00000301653.4	-	3	701	c.637C>T	c.(637-639)Cgg>Tgg	p.R213W		NM_005557.3	NP_005548.2	P08779	K1C16_HUMAN	keratin 16	213	Coil 1B.|Rod.				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)				ACAGTCTGCCGCAGGGCCAGT	0.637													g|||	10	0.00199681	0.0076	0.0	5008	,	,		19186	0.0		0.0	False		,,,				2504	0.0				p.R213W		Atlas-SNP	.											.	KRT16	45	.	0			c.C637T						PASS	.	G	TRP/ARG	34,4372	38.4+/-70.7	0,34,2169	47	48	48		637	0.3	1	17	dbSNP_134	48	1,8599	1.2+/-3.3	0,1,4299	yes	missense	KRT16	NM_005557.3	101	0,35,6468	AA,AG,GG		0.0116,0.7717,0.2691	probably-damaging	213/474	39767731	35,12971	2203	4300	6503	SO:0001583	missense	3868	exon3			TCTGCCGCAGGGC	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.637C>T	17.37:g.39767731G>A	ENSP00000301653:p.Arg213Trp	128	0	0		147	70	0.47619	NM_005557	A8K488|P30654|Q16402|Q9UBG8	Missense_Mutation	SNP	ENST00000301653.4	37	CCDS11401.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	17.20	3.329471	0.60743	0.007717	1.16E-4	ENSG00000186832	ENST00000301653	D	0.92099	-2.97	4.84	0.345	0.16011	Filament (1);	0.000000	0.47852	D	0.000203	D	0.95567	0.8559	H	0.98199	4.17	0.50171	D	0.999858	D	0.89917	1.0	D	0.85130	0.997	D	0.93019	0.6438	10	0.87932	D	0	.	6.7407	0.23435	0.141:0.0:0.6081:0.251	.	213	P08779	K1C16_HUMAN	W	213	ENSP00000301653:R213W	ENSP00000301653:R213W	R	-	1	2	KRT16	37021257	1.000000	0.71417	0.999000	0.59377	0.584000	0.36387	2.574000	0.46016	0.338000	0.23692	0.561000	0.74099	CGG	G|0.997;A|0.003	0.003	strong		0.637	KRT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257408.1	NM_005557		A	39767731	G	A	39767731	3	1	28	1	0	0	0	0	1	0	0	0	8462	1086	38	1	808	1	KRT16	17	39767731	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	172194	39767731	41427479	591	12094											
JUP	3728	hgsc.bcm.edu	37	chr17	39925713	39925713	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtgagctcgggcagggcgCgagtggccagctcggcatcg	5	6	19	11	5	0	1	0	1	0	0	3	2	0	1	1	5	2	4	1	5	0	0	rs41283425	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39925713C>T	ENST00000393931.3	-	3	543	c.425G>A	c.(424-426)cGc>cAc	p.R142H	JUP_ENST00000540235.1_Missense_Mutation_p.R142H|JUP_ENST00000310706.5_Missense_Mutation_p.R142H|JUP_ENST00000393930.1_Missense_Mutation_p.R142H	NM_002230.2	NP_002221.1	P14923	PLAK_HUMAN	junction plakoglobin	142	Interaction with DSC1 and DSG1.		R -> H (in dbSNP:rs41283425). {ECO:0000269|PubMed:19863551, ECO:0000269|PubMed:20031617}.		adherens junction organization (GO:0034332)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell-cell junction organization (GO:0045216)|cellular response to indole-3-methanol (GO:0071681)|cytoskeletal anchoring at plasma membrane (GO:0007016)|desmosome assembly (GO:0002159)|detection of mechanical stimulus (GO:0050982)|ectoderm development (GO:0007398)|endothelial cell-cell adhesion (GO:0071603)|establishment of protein localization to plasma membrane (GO:0090002)|gastrulation (GO:0007369)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of Wnt signaling pathway involved in heart development (GO:0003308)|nervous system development (GO:0007399)|oocyte development (GO:0048599)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein heterooligomerization (GO:0051291)|regulation of cell proliferation (GO:0042127)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)|ventricular cardiac muscle cell action potential (GO:0086005)	actin cytoskeleton (GO:0015629)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|gamma-catenin-TCF7L2 complex (GO:0071665)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|cadherin binding (GO:0045296)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|structural constituent of cell wall (GO:0005199)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	23		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)		GGGCAGGGCGCGAGTGGCCAG	0.652													C|||	120	0.0239617	0.0023	0.0331	5008	,	,		18035	0.0		0.0567	False		,,,				2504	0.0378				p.R142H	Colon(16;42 520 6044 17852 28530)	Atlas-SNP	.											.	JUP	64	.	0			c.G425A						PASS	.	C	HIS/ARG,HIS/ARG	49,4357	45.3+/-79.5	1,47,2155	26	25	26		425,425	5.5	1	17	dbSNP_127	26	500,8100	137.9+/-194.8	10,480,3810	yes	missense,missense	JUP	NM_002230.2,NM_021991.2	29,29	11,527,5965	TT,TC,CC		5.814,1.1121,4.2211	possibly-damaging,possibly-damaging	142/746,142/746	39925713	549,12457	2203	4300	6503	SO:0001583	missense	3728	exon3			AGGGCGCGAGTGG	AF233882	CCDS11407.1	17q21	2014-09-17	2004-08-09		ENSG00000173801	ENSG00000173801		"Armadillo repeat containing"	6207	protein-coding gene	gene with protein product		173325	"catenin (cadherin-associated protein), gamma 80kDa"	CTNNG		1889810, 7604000	Standard	NM_021991		Approved	DP3, PDGB, PKGB, DPIII	uc002hxs.2	P14923	OTTHUMG00000133494	ENST00000393931.3:c.425G>A	17.37:g.39925713C>T	ENSP00000377508:p.Arg142His	95	0	0		110	48	0.436364	NM_021991	Q15093|Q15151|Q7L3S5|Q86W21|Q9BWC4|Q9HCX9	Missense_Mutation	SNP	ENST00000393931.3	37	CCDS11407.1	61	0.027930402930402932	0	0.0	15	0.04143646408839779	0	0.0	46	0.06068601583113457	c	34	5.375802	0.95923	0.011121	0.05814	ENSG00000173801	ENST00000540235;ENST00000393930;ENST00000310706;ENST00000393931;ENST00000449889;ENST00000437187;ENST00000420370;ENST00000424457	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	5.52	5.52	0.82312	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.35913	0.0948	M	0.73430	2.235	0.54753	D	0.999984	D;D	0.89917	1.0;1.0	D;P	0.79784	0.993;0.901	T	0.67628	-0.5622	10	0.72032	D	0.01	-47.1096	18.4331	0.90633	0.0:1.0:0.0:0.0	rs41283425	142;142	B4DE59;P14923	.;PLAK_HUMAN	H	142	ENSP00000441751:R142H;ENSP00000377507:R142H;ENSP00000311113:R142H;ENSP00000377508:R142H;ENSP00000389886:R142H;ENSP00000394146:R142H;ENSP00000411449:R142H;ENSP00000401034:R142H	ENSP00000311113:R142H	R	-	2	0	JUP	37179239	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	7.809000	0.86057	2.593000	0.87608	0.556000	0.70494	CGC	C|0.962;T|0.038	0.038	strong		0.652	JUP-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257406.1			T	39925713	C	T	39925713	3	4	28	1	0	0	0	0	1	0	0	0	7981	768	27	1	1860	1	JUP	17	39925713	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	157982	39925713	41269497	592	12095											
STAT3	6774	hgsc.bcm.edu	37	chr17	40498635	40498635	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttgtgctgatagagaacattCgactcttgcaggaagcggct	10	11	12	8	2	1	2	0	1	1	1	2	5	1	3	0	2	4	3	0	2	3	4	rs146184566	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:40498635C>T	ENST00000264657.5	-	3	537	c.225G>A	c.(223-225)tcG>tcA	p.S75S	STAT3_ENST00000404395.3_Silent_p.S75S|STAT3_ENST00000389272.3_5'UTR|STAT3_ENST00000588969.1_Silent_p.S75S|STAT3_ENST00000585517.1_Silent_p.S75S	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)	75					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)		AGAGAACATTCGACTCTTGCA	0.478									Hyperimmunoglobulin E Recurrent Infection Syndrome				C|||	10	0.00199681	0.0076	0.0	5008	,	,		19275	0.0		0.0	False		,,,				2504	0.0				p.S75S		Atlas-SNP	.											STAT3,NS,carcinoma,0,1	STAT3	268	1	0			c.G225A						PASS	.	C	,,	7,4399	11.4+/-27.6	0,7,2196	225	220	222		225,225,225	-11	0.7	17	dbSNP_134	222	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	STAT3	NM_003150.3,NM_139276.2,NM_213662.1	,,	0,7,6496	TT,TC,CC		0.0,0.1589,0.0538	,,	75/770,75/771,75/723	40498635	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	6774	exon3	Familial Cancer Database	HIES, Hyper IgE syndrome, autosomal dominant (Job syndrome) / recessive	AACATTCGACTCT	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.225G>A	17.37:g.40498635C>T		128	0	0		100	42	0.42	NM_003150	A8K7B8|K7ENL3|O14916|Q9BW54	Silent	SNP	ENST00000264657.5	37	CCDS32656.1																																																																																			C|0.999;T|0.001	0.001	strong		0.478	STAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319353.3	NM_139276, NM_003150		T	40498635	C	T	40498635	2	4	28	1	0	0	0	0	0	0	0	1	15281	871	31	1		1	STAT3	17	40498635	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	572922	40498635	40696575	593	12096											
HSD17B1	3292	hgsc.bcm.edu	37	chr17	40706596	40706596	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagaaccctgaggaggtggCggaggtgagcgccgggctgg	7	4	21	9	3	0	3	0	2	0	1	0	5	0	5	2	7	2	2	2	7	1	0	rs147402365	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:40706596C>T	ENST00000585807.1	+	5	4433	c.713C>T	c.(712-714)gCg>gTg	p.A238V	HSD17B1_ENST00000225929.5_Missense_Mutation_p.A239V|RP11-400F19.6_ENST00000590513.1_RNA|RP11-400F19.8_ENST00000585572.1_RNA	NM_000413.2	NP_000404.2	P14061	DHB1_HUMAN	hydroxysteroid (17-beta) dehydrogenase 1	238			A -> V. {ECO:0000269|PubMed:8389226}.		bone development (GO:0060348)|cellular response to metal ion (GO:0071248)|estrogen biosynthetic process (GO:0006703)|estrogen metabolic process (GO:0008210)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|estradiol 17-beta-dehydrogenase activity (GO:0004303)			NS(1)|endometrium(1)|kidney(1)|lung(2)	5		all_cancers(22;5.59e-08)|all_epithelial(22;7e-07)|Ovarian(249;0.0261)		BRCA - Breast invasive adenocarcinoma(366;0.129)	Equilin(DB02187)	GAGGAGGTGGCGGAGGTGAGC	0.687													C|||	14	0.00279553	0.0008	0.0	5008	,	,		12600	0.0		0.0129	False		,,,				2504	0.0				p.A238V		Atlas-SNP	.											.	HSD17B1	24	.	0			c.C713T						PASS	.	C	VAL/ALA	9,4395	15.5+/-35.6	0,9,2193	39	31	34		713	-0.4	0	17	dbSNP_134	34	70,8530	42.2+/-99.7	0,70,4230	yes	missense	HSD17B1	NM_000413.2	64	0,79,6423	TT,TC,CC		0.814,0.2044,0.6075	benign	238/329	40706596	79,12925	2202	4300	6502	SO:0001583	missense	3292	exon5			AGGTGGCGGAGGT		CCDS11428.1	17q11-q21	2011-09-14					1.1.1.62	"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	5210	protein-coding gene	gene with protein product	"Estradiol 17-beta-dehydrogenase-1", "short chain dehydrogenase/reductase family 28CE, member 1"	109684		EDHB17, EDH17B2		2330005, 19027726	Standard	NM_000413		Approved	HSD17, MGC138140, SDR28C1	uc002hzw.3	P14061		ENST00000585807.1:c.713C>T	17.37:g.40706596C>T	ENSP00000466799:p.Ala238Val	24	0	0		43	28	0.651163	NM_000413	B3KXS1|Q2M2L8	Missense_Mutation	SNP	ENST00000585807.1	37	CCDS11428.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	C	8.655	0.899159	0.17686	0.002044	0.00814	ENSG00000108786	ENST00000225929	.	.	.	4.16	-0.383	0.12477	NAD(P)-binding domain (1);	1.163550	0.06218	N	0.686122	T	0.07503	0.0189	N	0.04636	-0.2	0.09310	N	1	B;P	0.41102	0.002;0.738	B;B	0.28553	0.002;0.091	T	0.15065	-1.0450	9	0.30854	T	0.27	.	6.1916	0.20528	0.0:0.5144:0.0:0.4856	.	269;238	B3RFR9;P14061	.;DHB1_HUMAN	V	238	.	ENSP00000225929:A238V	A	+	2	0	HSD17B1	37960122	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	0.067000	0.14510	0.095000	0.17434	-0.658000	0.03865	GCG	C|0.996;T|0.004	0.004	strong		0.687	HSD17B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450392.1	NM_000413		T	40706596	C	T	40706596	3	4	28	1	0	0	0	0	1	0	0	0	7387	768	27	1	731	1	HSD17B1	17	40706596	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	207961	40706596	40488614	594	12097											
CNTNAP1	8506	hgsc.bcm.edu	37	chr17	40839829	40839829	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaagtgcccggtttcccacGccgtggccgcctggcagtct	4	9	12	16	4	2	0	1	0	1	0	3	0	3	0	5	3	1	2	5	3	1	1	rs375309204		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:40839829G>A	ENST00000264638.4	+	8	1353	c.1136G>A	c.(1135-1137)cGc>cAc	p.R379H	CTD-3193K9.3_ENST00000592440.1_RNA	NM_003632.2	NP_003623.1	P78357	CNTP1_HUMAN	contactin associated protein 1	379					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)		GGTTTCCCACGCCGTGGCCGC	0.637																																					p.R379H		Atlas-SNP	.											.	CNTNAP1	116	.	0			c.G1136A						PASS	.	G	HIS/ARG	0,4406		0,0,2203	96	88	90		1136	5	0.2	17		90	1,8599	1.2+/-3.3	0,1,4299	no	missense	CNTNAP1	NM_003632.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	379/1385	40839829	1,13005	2203	4300	6503	SO:0001583	missense	8506	exon8			TCCCACGCCGTGG	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.1136G>A	17.37:g.40839829G>A	ENSP00000264638:p.Arg379His	101	0	0		86	23	0.267442	NM_003632		Missense_Mutation	SNP	ENST00000264638.4	37	CCDS11436.1	.	.	.	.	.	.	.	.	.	.	G	14.77	2.634266	0.47049	0.0	1.16E-4	ENSG00000108797	ENST00000264638	T	0.79247	-1.25	5.02	5.02	0.67125	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.187385	0.37955	N	0.001877	T	0.80773	0.4687	L	0.43152	1.355	0.44927	D	0.997946	D	0.76494	0.999	P	0.59643	0.861	T	0.80410	-0.1394	10	0.42905	T	0.14	.	13.3172	0.60413	0.0:0.0:0.8419:0.1581	.	379	P78357	CNTP1_HUMAN	H	379	ENSP00000264638:R379H	ENSP00000264638:R379H	R	+	2	0	CNTNAP1	38093355	1.000000	0.71417	0.248000	0.24265	0.483000	0.33249	7.263000	0.78421	2.302000	0.77476	0.655000	0.94253	CGC	.	.	weak		0.637	CNTNAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452342.1	NM_003632		A	40839829	G	A	40839829	3	1	28	1	0	0	0	0	1	0	0	0	3648	1087	38	1	1166	1	CNTNAP1	17	40839829	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	133233	40839829	40355381	595	12098											
CD300LG	146894	hgsc.bcm.edu	37	chr17	41926023	41926023	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gaagagctgagggaccaccgGaagtactggtgcaggaaggg	12	4	18	7	1	0	2	0	1	0	1	0	6	0	5	2	5	3	3	2	5	4	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:41926023G>A	ENST00000317310.4	+	2	182	c.141G>A	c.(139-141)cgG>cgA	p.R47R	CD300LG_ENST00000377203.4_Silent_p.R47R|CD300LG_ENST00000293396.8_Silent_p.R47R|CD300LG_ENST00000586233.1_Silent_p.R47R|CD300LG_ENST00000539718.1_Silent_p.R47R|CD300LG_ENST00000588884.1_Silent_p.R47R	NM_145273.3	NP_660316.2	Q6UXG3	CLM9_HUMAN	CD300 molecule-like family member g	47	Ig-like V-type.				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)		GGGACCACCGGAAGTACTGGT	0.577																																					p.R47R		Atlas-SNP	.											.	CD300LG	46	.	0			c.G141A						PASS	.						85	72	77					17																	41926023		2203	4300	6503	SO:0001819	synonymous_variant	146894	exon2			CCACCGGAAGTAC	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.141G>A	17.37:g.41926023G>A		88	0	0		106	60	0.566038	NM_001168323	B4DNY5|F5H7P9|F8W9M3|Q8IX38|Q8IX39|Q8TA95	Silent	SNP	ENST00000317310.4	37	CCDS11470.1																																																																																			.	.	none		0.577	CD300LG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457646.1	NM_145273		A	41926023	G	A	41926023	2	1	28	1	0	0	0	0	0	0	0	1	3004	1161	41	2		2	CD300LG	17	41926023	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1086194	41926023	39269187	596	12099											
SCRN2	90507	hgsc.bcm.edu	37	chr17	45917703	45917703	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cggctcagaatcacagcgtgCgtcttcgacacctgttccac	8	9	9	15	4	3	1	2	0	1	1	5	2	4	1	2	1	2	2	2	1	1	2	rs11652952	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:45917703C>T	ENST00000290216.9	-	3	335	c.210G>A	c.(208-210)acG>acA	p.T70T	SCRN2_ENST00000584123.1_Silent_p.T78T|SCRN2_ENST00000407215.3_Silent_p.T70T	NM_001145023.1|NM_138355.3	NP_001138495.1|NP_612364.2	Q96FV2	SCRN2_HUMAN	secernin 2	70						extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)			cervix(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	14						TCACAGCGTGCGTCTTCGACA	0.592													C|||	147	0.029353	0.0658	0.0231	5008	,	,		20332	0.0		0.0358	False		,,,				2504	0.0082				p.T70T		Atlas-SNP	.											.	SCRN2	35	.	0			c.G210A						PASS	.	C	,	237,4169	139.2+/-174.8	7,223,1973	103	77	86		210,210	-10.2	0.3	17	dbSNP_120	86	295,8305	108.8+/-169.4	6,283,4011	no	coding-synonymous,coding-synonymous	SCRN2	NM_001145023.1,NM_138355.3	,	13,506,5984	TT,TC,CC		3.4302,5.379,4.0904	,	70/379,70/426	45917703	532,12474	2203	4300	6503	SO:0001819	synonymous_variant	90507	exon3			AGCGTGCGTCTTC	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.210G>A	17.37:g.45917703C>T		97	0	0		116	66	0.568965	NM_138355	A8K3N1|B7Z8S7|E9PBV5|Q96AC3|Q9BU04	Silent	SNP	ENST00000290216.9	37	CCDS11519.1																																																																																			C|0.963;T|0.037	0.037	strong		0.592	SCRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441383.1	NM_138355		T	45917703	C	T	45917703	2	4	28	1	0	0	0	0	0	0	0	1	13954	755	27	1		1	SCRN2	17	45917703	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	3991680	45917703	35277507	597	12100											
NGFR	4804	hgsc.bcm.edu	37	chr17	47579567	47579567	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtgagccctgcctggacaGtgagtagagggtggcgggca	7	7	19	8	1	0	3	0	2	0	1	0	4	0	4	2	4	2	2	2	4	1	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:47579567G>A	ENST00000172229.3	+	2	333		c.e2+1		NGFR_ENST00000504201.1_Splice_Site	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)					TGCCTGGACAGTGAGTAGAGG	0.637																																					.		Atlas-SNP	.											.	NGFR	46	.	0			c.208+1G>A						PASS	.						47	42	44					17																	47579567		2203	4300	6503	SO:0001630	splice_region_variant	4804	exon2			TGGACAGTGAGTA	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.208+1G>A	17.37:g.47579567G>A		26	0	0		35	9	0.257143	NM_002507	B2R961|B4E096	Splice_Site	SNP	ENST00000172229.3	37	CCDS11549.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.132712	0.77662	.	.	ENSG00000064300	ENST00000172229	.	.	.	5.33	5.33	0.75918	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.8004	0.88585	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NGFR	44934566	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	9.150000	0.94667	2.513000	0.84729	0.561000	0.74099	.	.	.	none		0.637	NGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365150.1		Intron	A	47579567	G	A	47579567	5	1	28	1	0	0	0	0	0	0	1	0	10405	1043	36	2	215	2	NGFR	17	47579567	Splice_Site	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1661864	47579567	33615643	598	12101											
DLX4	1748	hgsc.bcm.edu	37	chr17	48050500	48050501	+	Frame_Shift_Ins	INS	-	-	C																															cctcaggcccccgccaaaaaINSgctccgcaagccgaggacca																										TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:48050500_48050501insC	ENST00000240306.3	+	2	642_643	c.347_348insC	c.(346-351)aagctcfs	p.KL116fs	DLX4_ENST00000503410.1_3'UTR|DLX4_ENST00000411890.2_Frame_Shift_Ins_p.KL44fs	NM_138281.2	NP_612138.1	Q92988	DLX4_HUMAN	distal-less homeobox 4	116					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						CCCGCCAAAAAGCTCCGCAAGC	0.678																																					p.K116fs		Atlas-Indel	.											.	DLX4	25	.	0			c.347_348insC						PASS	.																																			SO:0001589	frameshift_variant	1748	exon2			.		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	Exception_encountered	17.37:g.48050500_48050501insC	ENSP00000240306:p.Lys116fs	140	0	0		138	10	0.0724638	NM_138281	D3DTX2|D3DTX3|O60480|Q13265|Q6PJK0|Q9HBE0	Frame_Shift_Ins	INS	ENST00000240306.3	37	CCDS11555.1																																																																																			.	.	none		0.678	DLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366214.1			C	48050501	-	C	48050500	7	5	28	1	0	1	1	0	0	0	0	0	4575	72	3	0	420	0	DLX4	17	48050500	Frame_Shift_Ins	INS	-	TCGA-G8-6914-01A-11D-2210-10	470933	48050500	33144710	599	12102											
TBX2	6909	hgsc.bcm.edu	37	chr17	59480547	59480547	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gagaccgacttcatcgccgtCactgcctaccagaatgacaa	12	7	8	14	3	2	3	2	1	0	2	3	5	2	3	4	0	2	0	4	0	3	2	rs140013823		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:59480547C>T	ENST00000240328.3	+	3	1070	c.789C>T	c.(787-789)gtC>gtT	p.V263V	RP11-332H18.4_ENST00000592009.1_RNA|RP11-332H18.5_ENST00000585765.1_RNA	NM_005994.3	NP_005985.3	Q13207	TBX2_HUMAN	T-box 2	263					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						TCATCGCCGTCACTGCCTACC	0.637													C|||	1	0.000199681	0.0	0.0014	5008	,	,		14472	0.0		0.0	False		,,,				2504	0.0				p.V263V	GBM(3;187 253 11467 14965 23079)	Atlas-SNP	.											.	TBX2	30	.	0			c.C789T						PASS	.	C		0,4406		0,0,2203	90	76	81		789	4.8	1	17	dbSNP_134	81	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous	TBX2	NM_005994.3		0,13,6490	TT,TC,CC		0.1512,0.0,0.1		263/713	59480547	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	6909	exon3			CGCCGTCACTGCC	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.789C>T	17.37:g.59480547C>T		38	0	0		44	24	0.545455	NM_005994	Q16424|Q7Z647	Silent	SNP	ENST00000240328.3	37	CCDS11627.2																																																																																			C|0.999;T|0.001	0.001	strong		0.637	TBX2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346977.2	NM_005994		T	59480547	C	T	59480547	2	4	28	1	0	0	0	0	0	0	0	1	15670	813	29	2		2	TBX2	17	59480547	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	11430047	59480547	21714663	600	12103											
TBX4	9496	hgsc.bcm.edu	37	chr17	59560751	59560751	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccaagggtgtgagaggaaGccaccctcgccacatctaaa	12	5	10	14	1	1	1	0	1	1	1	2	3	1	2	5	2	1	0	5	2	4	1	rs117324438	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:59560751G>A	ENST00000240335.1	+	8	1557	c.1512G>A	c.(1510-1512)aaG>aaA	p.K504K	TBX4_ENST00000393853.4_Silent_p.K505K	NM_018488.2	NP_060958.2	P57082	TBX4_HUMAN	T-box 4	504					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						GTGAGAGGAAGCCACCCTCGC	0.552													G|||	4	0.000798722	0.0	0.0	5008	,	,		17921	0.0		0.003	False		,,,				2504	0.001				p.K504K		Atlas-SNP	.											.	TBX4	69	.	0			c.G1512A						PASS	.	G		9,4397	15.5+/-35.6	0,9,2194	69	69	69		1512	2.4	1	17	dbSNP_133	69	26,8574	17.9+/-57.8	0,26,4274	no	coding-synonymous	TBX4	NM_018488.2		0,35,6468	AA,AG,GG		0.3023,0.2043,0.2691		504/546	59560751	35,12971	2203	4300	6503	SO:0001819	synonymous_variant	9496	exon8			GAGGAAGCCACCC	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.1512G>A	17.37:g.59560751G>A		94	0	0		103	53	0.514563	NM_018488	A5PKU7|B2RMT1|B7ZLV3	Silent	SNP	ENST00000240335.1	37	CCDS11629.1																																																																																			G|0.999;A|0.001	0.001	strong		0.552	TBX4-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449649.1	NM_018488		A	59560751	G	A	59560751	2	1	28	1	0	0	0	0	0	0	0	1	15675	962	34	2		2	TBX4	17	59560751	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	80204	59560751	21634459	601	12104											
SCN4A	6329	hgsc.bcm.edu	37	chr17	62049749	62049749	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gatggccccgcgcctgactaCgctgaaggggctcagcaggt	7	6	15	13	3	1	2	1	2	0	0	1	3	1	2	3	4	2	3	3	4	2	1	rs41280110	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:62049749C>T	ENST00000435607.1	-	2	431	c.355G>A	c.(355-357)Gta>Ata	p.V119I	SCN4A_ENST00000578147.1_Missense_Mutation_p.V119I|CTC-264K15.6_ENST00000577329.1_lincRNA	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	119					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)	CGCCTGACTACGCTGAAGGGG	0.607													C|||	6	0.00119808	0.0	0.0	5008	,	,		21598	0.0		0.004	False		,,,				2504	0.002				p.V119I		Atlas-SNP	.											SCN4A,NS,carcinoma,+1,1	SCN4A	205	1	0			c.G355A						PASS	.	C	ILE/VAL	2,4316		0,2,2157	66	72	70		355	-1	0.1	17	dbSNP_127	70	36,8498		0,36,4231	yes	missense	SCN4A	NM_000334.4	29	0,38,6388	TT,TC,CC		0.4218,0.0463,0.2957	benign	119/1837	62049749	38,12814	2159	4267	6426	SO:0001583	missense	6329	exon2			TGACTACGCTGAA	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.355G>A	17.37:g.62049749C>T	ENSP00000396320:p.Val119Ile	119	0	0		146	85	0.582192	NM_000334	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	37	CCDS45761.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	3.276	-0.148162	0.06627	4.63E-4	0.004218	ENSG00000007314	ENST00000435607	D	0.95918	-3.85	4.23	-0.98	0.10272	.	1.351180	0.04536	N	0.387199	D	0.82296	0.5006	N	0.00801	-1.175	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.74624	-0.3603	10	0.33141	T	0.24	.	2.0281	0.03523	0.1273:0.1785:0.4109:0.2833	rs41280110	119	P35499	SCN4A_HUMAN	I	119	ENSP00000396320:V119I	ENSP00000396320:V119I	V	-	1	0	SCN4A	59403481	0.000000	0.05858	0.116000	0.21606	0.196000	0.23810	-0.152000	0.10159	-0.405000	0.07599	-2.222000	0.00295	GTA	C|0.998;T|0.002	0.002	strong		0.607	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334		T	62049749	C	T	62049749	3	4	28	1	0	0	0	0	1	0	0	0	13935	536	19	1	5247	1	SCN4A	17	62049749	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2488998	62049749	19145461	602	12105											
RECQL5	9400	hgsc.bcm.edu	37	chr17	73624466	73624466	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgcccttgacctcagctacGacggagggcttggctgaggg	6	8	15	12	2	1	2	1	2	0	0	1	4	1	3	2	4	3	3	2	4	1	3	rs140010427	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:73624466G>A	ENST00000317905.5	-	18	2796	c.2637C>T	c.(2635-2637)gtC>gtT	p.V879V	RECQL5_ENST00000443199.2_5'UTR|RECQL5_ENST00000423245.2_Silent_p.V852V	NM_004259.6	NP_004250.4	O94762	RECQ5_HUMAN	RecQ protein-like 5	879					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)			CCTCAGCTACGACGGAGGGCT	0.637								Other identified genes with known or suspected DNA repair function					G|||	16	0.00319489	0.0008	0.0	5008	,	,		17331	0.0149		0.0	False		,,,				2504	0.0				p.V879V		Atlas-SNP	.											.	RECQL5	77	.	0			c.C2637T						PASS	.	G		0,4128		0,0,2064	60	71	67		2637	3	0	17	dbSNP_134	67	6,8362		0,6,4178	no	coding-synonymous	RECQL5	NM_004259.6		0,6,6242	AA,AG,GG		0.0717,0.0,0.048		879/992	73624466	6,12490	2064	4184	6248	SO:0001819	synonymous_variant	9400	exon18			AGCTACGACGGAG	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.2637C>T	17.37:g.73624466G>A		87	0	0		67	30	0.447761	NM_004259	Q9H0B1|Q9P1W7|Q9UNC8	Silent	SNP	ENST00000317905.5	37	CCDS42380.1																																																																																			G|0.997;A|0.003	0.003	strong		0.637	RECQL5-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448207.1	NM_004259		A	73624466	G	A	73624466	2	1	28	1	0	0	0	0	0	0	0	1	13218	1045	37	1		1	RECQL5	17	73624466	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	11574717	73624466	7570744	603	12106											
ITGB4	2584	hgsc.bcm.edu	37	chr17	73751175	73751175	+	Intron	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acacgggaggagcaggcttcCgctgtcctgggccctggggt	5	7	17	12	2	0	0	0	0	0	0	2	2	2	2	3	6	1	3	3	6	0	1	rs140501692		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:73751175C>T	ENST00000225614.2	-	8	1301				ITGB4_ENST00000200181.3_Intron|ITGB4_ENST00000450894.3_Intron|ITGB4_ENST00000339591.3_Missense_Mutation_p.P1463L|ITGB4_ENST00000579662.1_Intron|ITGB4_ENST00000449880.2_Missense_Mutation_p.P1463L			P51570	GALK1_HUMAN	galactokinase 1						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)			AGCAGGCTTCCGCTGTCCTGG	0.622													C|||	1	0.000199681	0.0	0.0	5008	,	,		17871	0.001		0.0	False		,,,				2504	0.0				p.P1463L		Atlas-SNP	.											ITGB4_ENST00000339591,colon,carcinoma,+1,1	ITGB4	165	1	0			c.C4388T						PASS	.	C	,LEU/PRO,	0,4406		0,0,2203	47	49	48		,4388,	5.3	1	17	dbSNP_134	48	5,8589		0,5,4292	yes	intron,missense,intron	ITGB4	NM_000213.3,NM_001005619.1,NM_001005731.1	,98,	0,5,6495	TT,TC,CC		0.0582,0.0,0.0385	,,	,1463/1806,	73751175	5,12995	2203	4297	6500	SO:0001627	intron_variant	3691	exon33			GGCTTCCGCTGTC		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	ENST00000225614.2:c.1176+2939G>A	17.37:g.73751175C>T		50	0	0		43	22	0.511628	NM_001005619	B2RC07|B4E1G6	Missense_Mutation	SNP	ENST00000225614.2	37	CCDS11728.1	.	.	.	.	.	.	.	.	.	.	C	16.09	3.025433	0.54683	0.0	5.82E-4	ENSG00000132470	ENST00000339591;ENST00000449880	T;T	0.73152	-0.72;-0.72	5.26	5.26	0.73747	.	.	.	.	.	T	0.58323	0.2114	.	.	.	0.80722	D	1	B	0.20459	0.045	B	0.13407	0.009	T	0.53920	-0.8370	8	0.30078	T	0.28	.	11.5095	0.50486	0.0:0.9144:0.0:0.0856	.	1463	P16144-3	.	L	1463	ENSP00000344079:P1463L;ENSP00000400217:P1463L	ENSP00000344079:P1463L	P	+	2	0	ITGB4	71262770	0.989000	0.36119	1.000000	0.80357	0.996000	0.88848	1.319000	0.33655	2.455000	0.83008	0.561000	0.74099	CCG	C|1.000;T|0.000	0.000	weak		0.622	GALK1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448427.1			T	73751175	C	T	73751175	1	4	28	0	1	0	0	0	0	0	0	0	7906	652	23	1		1	ITGB4	17	73751175	Intron	SNP	C	TCGA-G8-6914-01A-11D-2210-10	126709	73751175	7444035	604	12107											
RNF213	57674	hgsc.bcm.edu	37	chr17	78363033	78363033	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgcagtcctacagcgatGcctgtgaagtgctgtctgtc	7	11	12	11	1	1	1	0	1	1	0	3	2	2	1	2	0	6	3	2	0	2	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:78363033G>A	ENST00000582970.1	+	65	15204	c.15061G>A	c.(15061-15063)Gcc>Acc	p.A5021T	CTD-2047H16.4_ENST00000572151.1_RNA|CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000508628.2_Missense_Mutation_p.A5070T|RNF213_ENST00000427003.3_3'UTR|RNF213_ENST00000336301.6_Missense_Mutation_p.A3094T|CTD-2047H16.4_ENST00000573394.1_RNA	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	5021			A -> V (variant detected in cases of Moyamoya disease in East Asian populations; dbSNP:rs138130613). {ECO:0000269|PubMed:21799892}.		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)			CTACAGCGATGCCTGTGAAGT	0.537																																					p.A5021T		Atlas-SNP	.											.	RNF213	766	.	0			c.G15061A						PASS	.						141	123	129					17																	78363033		2203	4300	6503	SO:0001583	missense	57674	exon65			AGCGATGCCTGTG	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.15061G>A	17.37:g.78363033G>A	ENSP00000464087:p.Ala5021Thr	151	0	0		179	89	0.497207	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	G	12.70	2.015431	0.35511	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301;ENST00000427003	T	0.23950	1.88	5.39	1.87	0.25490	.	0.435749	0.22236	N	0.062742	T	0.26340	0.0643	M	0.72479	2.2	0.25084	N	0.990904	B;B	0.22146	0.031;0.065	B;B	0.14578	0.011;0.01	T	0.19877	-1.0292	10	0.56958	D	0.05	.	9.3461	0.38109	0.3281:0.0:0.6719:0.0	.	5021;3094	D6RI12;Q63HN8	.;RN213_HUMAN	T	5021;5070;3094;371	ENSP00000338218:A3094T	ENSP00000338218:A3094T	A	+	1	0	RNF213	75977628	1.000000	0.71417	0.244000	0.24202	0.451000	0.32288	2.945000	0.49043	0.124000	0.18369	-0.345000	0.07892	GCC	.	.	none		0.537	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914		A	78363033	G	A	78363033	3	1	28	1	0	0	0	0	1	0	0	0	13492	1319	46	2	15634	2	RNF213	17	78363033	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	4611858	78363033	2832177	605	12108											
C17orf90	339229	hgsc.bcm.edu	37	chr17	79632327	79632327	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagggcagccagggcccgCtccccaccgtcctggaagtg	6	5	13	17	2	0	0	0	0	0	0	3	1	3	1	7	3	1	2	7	3	1	0	rs137928765		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:79632327C>T	ENST00000374741.3	-	2	358	c.348G>A	c.(346-348)gaG>gaA	p.E116E	PDE6G_ENST00000571224.1_5'Flank|OXLD1_ENST00000571503.1_3'UTR|PDE6G_ENST00000574777.1_5'Flank|OXLD1_ENST00000573786.1_5'UTR|CCDC137_ENST00000329214.8_5'Flank	NM_001039842.1	NP_001034931.1	Q5BKU9	OXLD1_HUMAN	oxidoreductase-like domain containing 1	116						mitochondrion (GO:0005739)											CCAGGGCCCGCTCCCCACCGT	0.657																																					p.E116E		Atlas-SNP	.											.	.	.	.	0			c.G348A						PASS	.	C		0,4406		0,0,2203	40	39	39		348	2.7	1	17	dbSNP_134	39	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	C17orf90	NM_001039842.1		0,5,6498	TT,TC,CC		0.0581,0.0,0.0384		116/148	79632327	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	339229	exon2			GGCCCGCTCCCCA		CCDS32766.1	17q25.3	2012-07-20	2012-07-20	2012-07-20	ENSG00000204237	ENSG00000204237			27901	protein-coding gene	gene with protein product			"chromosome 17 open reading frame 90"	C17orf90			Standard	NM_001039842		Approved	MGC104712	uc002kba.3	Q5BKU9	OTTHUMG00000178063	ENST00000374741.3:c.348G>A	17.37:g.79632327C>T		101	0	0		96	40	0.416667	NM_001039842	A6ND24	Silent	SNP	ENST00000374741.3	37	CCDS32766.1																																																																																			C|1.000;T|0.000	0.000	strong		0.657	OXLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440380.1	NM_001039842		T	79632327	C	T	79632327	2	4	28	1	0	0	0	0	0	0	0	1	1893	796	28	2		2	C17orf90	17	79632327	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1269294	79632327	1562883	606	12109											
FASN	2194	hgsc.bcm.edu	37	chr17	80044214	80044214	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccggggagtccaggaggccGctgagcagagggtcctctgg	6	5	19	11	2	1	2	0	1	1	1	3	4	3	4	4	6	1	2	4	6	0	0	rs530379505		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:80044214G>A	ENST00000306749.2	-	22	3866	c.3648C>T	c.(3646-3648)agC>agT	p.S1216S		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	1216					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)	CCAGGAGGCCGCTGAGCAGAG	0.672																																					p.S1216S	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.C3648T						PASS	.						26	23	24					17																	80044214		2184	4293	6477	SO:0001819	synonymous_variant	2194	exon22			GAGGCCGCTGAGC	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.3648C>T	17.37:g.80044214G>A		71	0	0		79	4	0.0506329	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Silent	SNP	ENST00000306749.2	37	CCDS11801.1																																																																																			.	.	none		0.672	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		A	80044214	G	A	80044214	2	1	28	1	0	0	0	0	0	0	0	1	5691	1078	38	1		1	FASN	17	80044214	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	411887	80044214	1150996	607	12110											
CCDC57	284001	hgsc.bcm.edu	37	chr17	80146154	80146154	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tgtctccactctgccctgcgGagctgcgcctcgagggtctc	3	10	12	16	3	3	0	0	0	3	0	6	2	3	1	3	2	4	1	3	2	0	0	rs201504809	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:80146154G>C	ENST00000389641.4	-	7	1029	c.993C>G	c.(991-993)ctC>ctG	p.L331L	CCDC57_ENST00000392347.1_Silent_p.L331L|CCDC57_ENST00000392343.3_Silent_p.L331L			Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	331										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)			CTGCCCTGCGGAGCTGCGCCT	0.667													G|||	5	0.000998403	0.0	0.0	5008	,	,		16916	0.0		0.005	False		,,,				2504	0.0				p.L331L		Atlas-SNP	.											.	CCDC57	102	.	0			c.C993G						PASS	.	G		0,4394		0,0,2197	22	25	24		993	-1.5	0.9	17		24	28,8552		0,28,4262	no	coding-synonymous	CCDC57	NM_198082.2		0,28,6459	CC,CG,GG		0.3263,0.0,0.2158		331/916	80146154	28,12946	2197	4290	6487	SO:0001819	synonymous_variant	284001	exon7			CCTGCGGAGCTGC	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.993C>G	17.37:g.80146154G>C		50	0	0		55	23	0.418182	NM_198082	A6NP51|A8MQC7|Q8IWG2|Q8TER3	Silent	SNP	ENST00000389641.4	37																																																																																				G|0.994;C|0.006	0.006	weak		0.667	CCDC57-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000277182.3	NM_198082		C	80146154	G	C	80146154	2	2	28	1	0	0	0	0	0	0	0	1	2829	1161	41	4		4	CCDC57	17	80146154	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	101940	80146154	1049056	608	12111											
HEXDC	284004	hgsc.bcm.edu	37	chr17	80393704	80393704	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccagcgtgacacccctggTgtgggacgacatgctccgag	7	6	13	15	3	0	1	0	1	0	0	1	4	1	2	5	2	2	1	5	2	0	0			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:80393704T>C	ENST00000327949.9	+	5	598	c.587T>C	c.(586-588)gTg>gCg	p.V196A	HEXDC_ENST00000577944.1_Missense_Mutation_p.V196A|HEXDC_ENST00000337014.6_Missense_Mutation_p.V196A			Q8WVB3	HEXDC_HUMAN	hexosaminidase (glycosyl hydrolase family 20, catalytic domain) containing	196					carbohydrate metabolic process (GO:0005975)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	beta-N-acetylhexosaminidase activity (GO:0004563)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			ACACCCCTGGTGTGGGACGAC	0.682																																					p.V196A		Atlas-SNP	.											.	HEXDC	43	.	0			c.T587C						PASS	.						50	60	57					17																	80393704		2060	4155	6215	SO:0001583	missense	284004	exon6			CCCTGGTGTGGGA	AK074405	CCDS42402.1	17q25.3	2011-12-19			ENSG00000169660	ENSG00000169660			26307	protein-coding gene	gene with protein product						12477932	Standard	NM_173620		Approved	FLJ23825	uc002kev.4	Q8WVB3		ENST00000327949.9:c.587T>C	17.37:g.80393704T>C	ENSP00000332634:p.Val196Ala	30	0	0		42	15	0.357143	NM_173620	B7UUP6|Q8IYN4|Q8TE81	Missense_Mutation	SNP	ENST00000327949.9	37		.	.	.	.	.	.	.	.	.	.	T	10.28	1.306572	0.23736	.	.	ENSG00000169660	ENST00000337014;ENST00000327949	D;D	0.95821	-3.82;-3.82	5.72	4.65	0.58169	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycoside hydrolase, family 20, catalytic core (1);	0.286925	0.43110	N	0.000601	D	0.87474	0.6186	N	0.05592	-0.015	0.36187	D	0.849809	B;B	0.22276	0.027;0.067	B;B	0.20955	0.026;0.032	D	0.83518	0.0084	10	0.30854	T	0.27	-18.7938	8.2399	0.31654	0.0:0.152:0.0:0.848	.	196;196	Q8WVB3;Q8WVB3-2	HEXDC_HUMAN;.	A	196	ENSP00000337854:V196A;ENSP00000332634:V196A	ENSP00000332634:V196A	V	+	2	0	HEXDC	77986993	1.000000	0.71417	1.000000	0.80357	0.289000	0.27227	4.183000	0.58317	0.995000	0.38917	-0.376000	0.06991	GTG	.	.	none		0.682	HEXDC-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000443513.1	NM_173620		C	80393704	T	C	80393704	3	2	28	1	0	0	0	0	1	0	0	0	7084	1696	59	3	605	3	HEXDC	17	80393704	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	247550	80393704	801506	609	12112											
TBCD	6904	hgsc.bcm.edu	37	chr17	80899349	80899349	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcgtacccaggccccagcTggtgccccaggtaaccctgt	6	6	13	16	1	0	0	0	0	0	0	0	0	0	0	6	4	4	3	6	4	2	2	rs2292969	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:80899349T>C	ENST00000355528.4	+	38	3684	c.3554T>C	c.(3553-3555)cTg>cCg	p.L1185P	TBCD_ENST00000576691.1_3'UTR|TBCD_ENST00000539345.2_Missense_Mutation_p.L1223P	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	1185			L -> P (in dbSNP:rs2292969).		'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)			AGGCCCCAGCTGGTGCCCCAG	0.622													T|||	23	0.00459265	0.0	0.0058	5008	,	,		18723	0.002		0.0089	False		,,,				2504	0.0082				p.L1185P		Atlas-SNP	.											.	TBCD	94	.	0			c.T3554C						PASS	.	T	PRO/LEU	6,4162		0,6,2078	44	58	53		3554	5	1	17	dbSNP_100	53	48,8376		1,46,4165	yes	missense	TBCD	NM_005993.4	98	1,52,6243	CC,CT,TT		0.5698,0.144,0.4288	probably-damaging	1185/1193	80899349	54,12538	2084	4212	6296	SO:0001583	missense	6904	exon38			CCCAGCTGGTGCC	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.3554T>C	17.37:g.80899349T>C	ENSP00000347719:p.Leu1185Pro	31	0	0		25	12	0.48	NM_005993	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Missense_Mutation	SNP	ENST00000355528.4	37	CCDS45818.1	10|10	0.004578754578754579|0.004578754578754579	0|0	0.0|0.0	3|3	0.008287292817679558|0.008287292817679558	2|2	0.0034965034965034965|0.0034965034965034965	5|5	0.006596306068601583|0.006596306068601583	T|T	13.78|13.78	2.340685|2.340685	0.41498|0.41498	0.00144|0.00144	0.005698|0.005698	ENSG00000141556|ENSG00000141556	ENST00000355528;ENST00000539345|ENST00000334614	T|.	0.22336|.	1.96|.	4.96|4.96	4.96|4.96	0.65561|0.65561	.|.	.|0.369474	.|0.21711	.|N	.|0.070272	T|T	0.65481|0.65481	0.2695|0.2695	M|M	0.75777|0.75777	2.31|2.31	0.80722|0.80722	D|D	1|1	B|.	0.26744|.	0.158|.	B|.	0.26202|.	0.067|.	T|T	0.70096|0.70096	-0.4966|-0.4966	8|6	.|.	.|.	.|.	.|.	11.3315|11.3315	0.49479|0.49479	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs2292969;rs2292969|rs2292969;rs2292969	1185|.	Q9BTW9|.	TBCD_HUMAN|.	P|R	1185;177|973	ENSP00000347719:L1185P|.	.|.	L|W	+|+	2|1	0|0	TBCD|TBCD	78492638|78492638	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.664000|0.664000	0.39144|0.39144	3.885000|3.885000	0.56182|0.56182	2.015000|2.015000	0.59207|0.59207	0.460000|0.460000	0.39030|0.39030	CTG|TGG	T|0.994;C|0.006	0.006	strong		0.622	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993		C	80899349	T	C	80899349	3	2	28	1	0	0	0	0	1	0	0	0	15648	1580	55	3	3704	3	TBCD	17	80899349	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	505645	80899349	295861	610	12113											
THOC1	9984	hgsc.bcm.edu	37	chr18	264030	264030	+	Silent	SNP	A	A	G																															acggaaccatacttaccttcAgttactcccccaatagcaag																								rs371643145		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:264030A>G	ENST00000261600.6	-	4	259	c.252T>C	c.(250-252)acT>acC	p.T84T	THOC1_ENST00000582313.1_5'UTR	NM_005131.2	NP_005122.2	Q96FV9	THOC1_HUMAN	THO complex 1	84					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)				ACTTACCTTCAGTTACTCCCC	0.353																																					p.T84T		Atlas-SNP	.											.	THOC1	43	.	0			c.T252C						PASS	.	A		0,3698		0,0,1849	86	73	77		252	1	1	18		77	5,8177		0,5,4086	no	coding-synonymous	THOC1	NM_005131.2		0,5,5935	GG,GA,AA		0.0611,0.0,0.0421		84/658	264030	5,11875	1849	4091	5940	SO:0001819	synonymous_variant	9984	exon4			ACCTTCAGTTACT	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.252T>C	18.37:g.264030A>G		162	0	0		182	61	0.335165	NM_005131	B2RBP6|Q15219|Q64I72|Q64I73	Silent	SNP	ENST00000261600.6	37	CCDS45820.1																																																																																			.	.	weak		0.353	THOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440348.5	NM_005131		G	264030	A	G	264030	2	3	28	1	0	0	0	0	0	0	0	1	15879	175	7	3		3	THOC1	18	264030	Silent	SNP	A	TCGA-G8-6914-01A-11D-2210-10		264030	77813218	611	12114	148	2									
THOC1	9984	hgsc.bcm.edu	37	chr18	264039	264039	+	Silent	SNP	C	C	A																															tacttaccttcagttactccCccaatagcaagagaaataat																								rs376944925		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:264039C>A	ENST00000261600.6	-	4	250	c.243G>T	c.(241-243)ggG>ggT	p.G81G	THOC1_ENST00000582313.1_5'UTR	NM_005131.2	NP_005122.2	Q96FV9	THOC1_HUMAN	THO complex 1	81					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)				CAGTTACTCCCCCAATAGCAA	0.358																																					p.G81G		Atlas-SNP	.											.	THOC1	43	.	0			c.G243T						PASS	.	C		0,3690		0,0,1845	86	74	78		243	4.3	1	18		78	5,8171		0,5,4083	no	coding-synonymous	THOC1	NM_005131.2		0,5,5928	AA,AC,CC		0.0612,0.0,0.0421		81/658	264039	5,11861	1845	4088	5933	SO:0001819	synonymous_variant	9984	exon4			TACTCCCCCAATA	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.243G>T	18.37:g.264039C>A		162	0	0		179	62	0.346369	NM_005131	B2RBP6|Q15219|Q64I72|Q64I73	Silent	SNP	ENST00000261600.6	37	CCDS45820.1																																																																																			.	.	weak		0.358	THOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440348.5	NM_005131		A	264039	C	A	264039	2	1	28	1	0	0	0	0	0	0	0	1	15879	610	22	4		4	THOC1	18	264039	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	9	264039	77813209	612	12115	148	2									
LPIN2	9663	hgsc.bcm.edu	37	chr18	2929103	2929103	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggttaggattgtctataaGtccagggttttctgcaaatt	11	15	10	5	0	2	0	0	0	2	0	3	1	3	1	1	3	1	3	1	3	5	7	rs104895500	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:2929103G>A	ENST00000261596.4	-	10	1748	c.1510C>T	c.(1510-1512)Ctt>Ttt	p.L504F		NM_014646.2	NP_055461.1	Q92539	LPIN2_HUMAN	lipin 2	504					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)		TTGTCTATAAGTCCAGGGTTT	0.294													G|||	10	0.00199681	0.0008	0.0043	5008	,	,		16858	0.0		0.005	False		,,,				2504	0.001				p.L504F		Atlas-SNP	.											.	LPIN2	75	.	0			c.C1510T	GRCh37	CM082924	LPIN2	M	rs104895500	PASS	.	G	PHE/LEU	5,4399	11.4+/-27.6	0,5,2197	126	139	135	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1510	6	1	18	dbSNP_132	135	39,8555	25.7+/-73.6	0,39,4258	yes	missense	LPIN2	NM_014646.2	22	0,44,6455	AA,AG,GG		0.4538,0.1135,0.3385	benign	504/897	2929103	44,12954	2202	4297	6499	SO:0001583	missense	9663	exon10			CTATAAGTCCAGG	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.1510C>T	18.37:g.2929103G>A	ENSP00000261596:p.Leu504Phe	48	0	0		100	28	0.28	NM_014646	A7MD25|D3DUH3	Missense_Mutation	SNP	ENST00000261596.4	37	CCDS11829.1	8	0.003663003663003663	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	G	24.1	4.489970	0.84962	0.001135	0.004538	ENSG00000101577	ENST00000261596	D	0.83419	-1.72	6.03	6.03	0.97812	.	0.051415	0.85682	D	0.000000	D	0.83175	0.5197	M	0.75615	2.305	0.52099	D	0.99994	P	0.52842	0.956	P	0.50049	0.629	D	0.86195	0.1615	10	0.72032	D	0.01	.	15.2928	0.73879	0.0:0.0:0.86:0.14	.	504	Q92539	LPIN2_HUMAN	F	504	ENSP00000261596:L504F	ENSP00000261596:L504F	L	-	1	0	LPIN2	2919103	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	6.723000	0.74742	2.861000	0.98227	0.655000	0.94253	CTT	G|0.998;A|0.002	0.002	strong		0.294	LPIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254363.2	NM_014646		A	2929103	G	A	2929103	3	1	28	1	0	0	0	0	1	0	0	0	8928	1029	36	2	1224	2	LPIN2	18	2929103	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2665064	2929103	75148145	613	12116											
EPB41L3	23136	hgsc.bcm.edu	37	chr18	5478295	5478295	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtatcactttgcactgcatgCttttaggctttttgacaatc	8	17	7	9	0	1	1	1	1	0	0	2	1	1	1	0	1	3	5	0	1	3	6	rs117900256	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:5478295C>A	ENST00000341928.2	-	3	666	c.326G>T	c.(325-327)aGc>aTc	p.S109I	EPB41L3_ENST00000342933.3_Missense_Mutation_p.S109I|EPB41L3_ENST00000544123.1_Missense_Mutation_p.S109I|RP11-286N3.1_ENST00000577527.1_RNA|EPB41L3_ENST00000540638.2_Missense_Mutation_p.S109I|EPB41L3_ENST00000400111.3_Missense_Mutation_p.S109I	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	109					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						GCACTGCATGCTTTTAGGCTT	0.383													C|||	61	0.0121805	0.003	0.0101	5008	,	,		17612	0.0		0.0119	False		,,,				2504	0.0389				p.S109I		Atlas-SNP	.											.	EPB41L3	222	.	0			c.G326T						PASS	.	C	ILE/SER	12,4394	20.2+/-43.8	0,12,2191	180	162	168		326	4.3	1	18	dbSNP_132	168	107,8493	57.5+/-118.9	0,107,4193	yes	missense	EPB41L3	NM_012307.2	142	0,119,6384	AA,AC,CC		1.2442,0.2724,0.915	benign	109/1088	5478295	119,12887	2203	4300	6503	SO:0001583	missense	23136	exon3			TGCATGCTTTTAG	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.326G>T	18.37:g.5478295C>A	ENSP00000343158:p.Ser109Ile	199	0	0		310	175	0.564516	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	37	CCDS11838.1	18	0.008241758241758242	3	0.006097560975609756	4	0.011049723756906077	0	0.0	11	0.014511873350923483	C	13.03	2.115698	0.37339	0.002724	0.012442	ENSG00000082397	ENST00000341928;ENST00000544123;ENST00000342933;ENST00000400111;ENST00000542652	T;D;T;D	0.83075	-1.46;-1.64;-1.46;-1.68	5.16	4.27	0.50696	Band 4.1 domain (1);	0.241444	0.40385	N	0.001115	T	0.74268	0.3694	L	0.51422	1.61	0.80722	D	1	D;B;P;B	0.56746	0.977;0.002;0.858;0.002	P;B;B;B	0.47470	0.548;0.003;0.255;0.004	T	0.76814	-0.2820	10	0.42905	T	0.14	.	8.9723	0.35915	0.0:0.7703:0.0:0.2297	.	109;109;109;109	F5GX05;Q9Y2J2-3;Q9Y2J2-2;Q9Y2J2	.;.;.;E41L3_HUMAN	I	109;109;109;109;190	ENSP00000343158:S109I;ENSP00000441174:S109I;ENSP00000341138:S109I;ENSP00000382981:S109I	ENSP00000343158:S109I	S	-	2	0	EPB41L3	5468295	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.834000	0.27518	2.378000	0.81104	0.579000	0.79373	AGC	C|0.990;A|0.010	0.010	strong		0.383	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307		A	5478295	C	A	5478295	3	1	28	1	0	0	0	0	1	0	0	0	5156	797	28	4	3017	4	EPB41L3	18	5478295	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2549192	5478295	72598953	614	12117											
LAMA1	284217	hgsc.bcm.edu	37	chr18	7010233	7010233	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cttcttgttcctgtctcactCcattctctggggctggtgca	3	16	9	13	0	3	0	1	0	3	0	7	0	5	0	2	3	1	3	2	3	0	4			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:7010233C>T	ENST00000389658.3	-	26	3932	c.3839G>A	c.(3838-3840)gGa>gAa	p.G1280E		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1280	Laminin IV type A 2. {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)				CTGTCTCACTCCATTCTCTGG	0.443																																					p.G1280E		Atlas-SNP	.											.	LAMA1	458	.	0			c.G3839A						PASS	.						193	164	174					18																	7010233		2203	4300	6503	SO:0001583	missense	284217	exon26			CTCACTCCATTCT	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.3839G>A	18.37:g.7010233C>T	ENSP00000374309:p.Gly1280Glu	211	0	0		254	52	0.204724	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	C	17.96	3.516908	0.64634	.	.	ENSG00000101680	ENST00000389658	T	0.31247	1.5	5.57	5.57	0.84162	Laminin B type IV (2);Laminin B, subgroup (1);	0.059894	0.64402	D	0.000003	T	0.55561	0.1928	M	0.64080	1.96	0.58432	D	0.999993	D	0.89917	1.0	D	0.85130	0.997	T	0.51926	-0.8643	10	0.48119	T	0.1	.	19.5479	0.95307	0.0:1.0:0.0:0.0	.	1280	P25391	LAMA1_HUMAN	E	1280	ENSP00000374309:G1280E	ENSP00000374309:G1280E	G	-	2	0	LAMA1	7000233	0.987000	0.35691	0.982000	0.44146	0.385000	0.30292	5.643000	0.67895	2.632000	0.89209	0.579000	0.79373	GGA	.	.	none		0.443	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		T	7010233	C	T	7010233	3	4	28	1	0	0	0	0	1	0	0	0	8614	855	30	2	5540	2	LAMA1	18	7010233	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1531938	7010233	71067015	615	12118											
GATA6	2627	hgsc.bcm.edu	37	chr18	19762989	19762989	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatacttcccccacaacacaAcctacagcctcaggggtaag	14	6	6	15	0	1	0	1	0	0	0	2	0	2	0	4	2	5	1	4	2	6	4	rs117646477	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:19762989A>G	ENST00000269216.3	+	6	1882	c.1605A>G	c.(1603-1605)caA>caG	p.Q535Q	GATA6_ENST00000581694.1_Silent_p.Q535Q|RNU6-702P_ENST00000364982.1_RNA	NM_005257.4	NP_005248.2	Q92908	GATA6_HUMAN	GATA binding protein 6	535					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)			CCACAACACAACCTACAGCCT	0.393													A|||	3	0.000599042	0.0	0.0	5008	,	,		15678	0.0		0.002	False		,,,				2504	0.001				p.Q535Q	Colon(8;48 282 46199 46856)|Melanoma(177;170 2725 12489 26999)	Atlas-SNP	.											.	GATA6	35	.	0			c.A1605G						PASS	.	A		0,4406		0,0,2203	104	92	96		1605	2.4	1	18	dbSNP_133	96	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	GATA6	NM_005257.3		0,4,6499	GG,GA,AA		0.0465,0.0,0.0308		535/596	19762989	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	2627	exon6			AACACAACCTACA	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.1605A>G	18.37:g.19762989A>G		134	0	0		160	97	0.60625	NM_005257	B0YJ17|P78327	Silent	SNP	ENST00000269216.3	37	CCDS11872.1																																																																																			A|0.999;G|0.001	0.001	strong		0.393	GATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254696.1	NM_005257		G	19762989	A	G	19762989	2	3	28	1	0	0	0	0	0	0	0	1	6266	40	2	3		3	GATA6	18	19762989	Silent	SNP	A	TCGA-G8-6914-01A-11D-2210-10	12752756	19762989	58314259	616	12119											
LAMA3	3909	hgsc.bcm.edu	37	chr18	21496533	21496533	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaggaaggaagagtcagaCaaaaattattttgaaggtac	18	8	12	3	0	1	3	1	1	0	2	1	6	1	6	0	4	1	1	0	4	7	4	rs61751706	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:21496533C>T	ENST00000313654.9	+	60	8038	c.7797C>T	c.(7795-7797)gaC>gaT	p.D2599D	LAMA3_ENST00000399516.3_Silent_p.D2543D|LAMA3_ENST00000587184.1_Silent_p.D934D|LAMA3_ENST00000269217.6_Silent_p.D990D|LAMA3_ENST00000588770.1_3'UTR	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2599	Laminin G-like 2. {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)					AAGAGTCAGACAAAAATTATT	0.423													C|||	5	0.000998403	0.0	0.0014	5008	,	,		18308	0.0		0.004	False		,,,				2504	0.0				p.D2599D		Atlas-SNP	.											.	LAMA3	397	.	0			c.C7797T						PASS	.	C	,,,	5,4401	9.9+/-24.2	0,5,2198	161	149	153		2970,7629,2802,7797	5.2	1	18	dbSNP_129	153	60,8540	37.8+/-93.5	1,58,4241	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LAMA3	NM_000227.3,NM_001127717.1,NM_001127718.1,NM_198129.1	,,,	1,63,6439	TT,TC,CC		0.6977,0.1135,0.4998	,,,	990/1725,2543/3278,934/1669,2599/3334	21496533	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	3909	exon60			GTCAGACAAAAAT	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.7797C>T	18.37:g.21496533C>T		63	0	0		103	59	0.572816	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	37	CCDS42419.1																																																																																			C|0.995;T|0.005	0.005	strong		0.423	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		T	21496533	C	T	21496533	2	4	28	1	0	0	0	0	0	0	0	1	8616	477	17	2		2	LAMA3	18	21496533	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1733544	21496533	56580715	617	12120											
TTC39C	125488	hgsc.bcm.edu	37	chr18	21662974	21662974	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgaagctaaggaaattctcCttaaaaaagaagctgcttat	17	11	7	6	0	1	2	0	1	1	1	2	3	1	3	1	1	3	3	1	1	8	4			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:21662974C>T	ENST00000317571.3	+	6	1149	c.913C>T	c.(913-915)Ctt>Ttt	p.L305F	TTC39C_ENST00000304621.6_Missense_Mutation_p.L244F|RP11-403A21.3_ENST00000578443.1_RNA	NM_001135993.1	NP_001129465.1	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C	305										breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	19						GGAAATTCTCCTTAAAAAAGA	0.413																																					p.L305F		Atlas-SNP	.											.	TTC39C	83	.	0			c.C913T						PASS	.						135	138	137					18																	21662974		2203	4300	6503	SO:0001583	missense	125488	exon6			ATTCTCCTTAAAA	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.913C>T	18.37:g.21662974C>T	ENSP00000323645:p.Leu305Phe	135	0	0		163	34	0.208589	NM_001135993	B7WP63|J3QRR1|Q0VAJ2|Q8N284	Missense_Mutation	SNP	ENST00000317571.3	37	CCDS45839.1	.	.	.	.	.	.	.	.	.	.	C	15.43	2.831199	0.50845	.	.	ENSG00000168234	ENST00000304621;ENST00000317571	T;T	0.76578	-1.03;-1.03	5.7	5.7	0.88788	.	0.377714	0.30556	N	0.009377	T	0.58708	0.2141	N	0.08118	0	0.80722	D	1	B	0.26002	0.139	B	0.18263	0.021	T	0.59857	-0.7375	10	0.56958	D	0.05	-23.3579	11.3611	0.49644	0.1316:0.725:0.1435:0.0	.	305	Q8N584	TT39C_HUMAN	F	244;305	ENSP00000306598:L244F;ENSP00000323645:L305F	ENSP00000306598:L244F	L	+	1	0	TTC39C	19916972	0.889000	0.30405	0.998000	0.56505	0.994000	0.84299	1.412000	0.34714	2.681000	0.91329	0.557000	0.71058	CTT	.	.	none		0.413	TTC39C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446107.1	NM_153211		T	21662974	C	T	21662974	3	4	28	1	0	0	0	0	1	0	0	0	16724	681	24	2	935	2	TTC39C	18	21662974	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	166441	21662974	56414274	618	12121											
ZNF521	25925	hgsc.bcm.edu	37	chr18	22804942	22804942	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtatcaagactcttactatgCgtgactttgtgttcagtaag	10	15	9	7	1	3	2	2	1	1	1	3	2	3	2	0	0	2	3	0	0	5	6	rs187705938	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:22804942C>T	ENST00000361524.3	-	4	3088	c.2940G>A	c.(2938-2940)acG>acA	p.T980T	ZNF521_ENST00000538137.2_Silent_p.T980T|ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000584787.1_Silent_p.T760T	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	980					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)					TCTTACTATGCGTGACTTTGT	0.468			T	PAX5	ALL								C|||	2	0.000399361	0.0	0.0	5008	,	,		21326	0.0		0.002	False		,,,				2504	0.0				p.T980T		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	ZNF521,NS,carcinoma,-1,1	ZNF521	269	1	0			c.G2940A						PASS	.	C		0,4406		0,0,2203	69	67	68		2940	-11.9	0.2	18		68	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	ZNF521	NM_015461.2		0,4,6499	TT,TC,CC		0.0465,0.0,0.0308		980/1312	22804942	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	25925	exon4			ACTATGCGTGACT	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.2940G>A	18.37:g.22804942C>T		68	0	0		81	28	0.345679	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Silent	SNP	ENST00000361524.3	37	CCDS32806.1																																																																																			C|0.999;T|0.001	0.001	strong		0.468	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461		T	22804942	C	T	22804942	2	4	28	1	0	0	0	0	0	0	0	1	17980	755	27	1		1	ZNF521	18	22804942	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1141968	22804942	55272306	619	12122											
DSG1	1828	hgsc.bcm.edu	37	chr18	28934274	28934274	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	attcagaaagcatatgcttaCgcagatgaagatgaaggacg	16	8	11	6	2	1	5	1	2	0	3	1	6	1	6	0	1	3	3	0	1	5	3	rs146192657	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:28934274C>T	ENST00000257192.4	+	15	2327	c.2115C>T	c.(2113-2115)taC>taT	p.Y705Y	RP11-534N16.1_ENST00000578477.1_RNA|RP11-534N16.1_ENST00000581452.1_RNA|DSG1_ENST00000462981.2_Silent_p.Y64Y|RP11-534N16.1_ENST00000578119.1_RNA|RP11-534N16.1_ENST00000581856.1_RNA	NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	705					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)	p.Y705*(2)		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)			CATATGCTTACGCAGATGAAG	0.373													T|||	15	0.00299521	0.0008	0.0072	5008	,	,		17640	0.0		0.0089	False		,,,				2504	0.0				p.Y705Y		Atlas-SNP	.											.	DSG1	176	.	2	Substitution - Nonsense(2)	lung(2)	c.C2115T						PASS	.	T		7,4399	825.6+/-416.5	0,7,2196	91	90	90		2115	3.6	1	18	dbSNP_134	90	77,8523	815.9+/-406.9	0,77,4223	no	coding-synonymous	DSG1	NM_001942.2		0,84,6419	TT,TC,CC		0.8953,0.1589,0.6459		705/1050	28934274	84,12922	2203	4300	6503	SO:0001819	synonymous_variant	1828	exon15			TGCTTACGCAGAT	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.2115C>T	18.37:g.28934274C>T		112	0	0		135	87	0.644444	NM_001942	B7Z845	Silent	SNP	ENST00000257192.4	37	CCDS11896.1																																																																																			C|0.994;T|0.006	0.006	strong		0.373	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942		T	28934274	C	T	28934274	2	4	28	1	0	0	0	0	0	0	0	1	4778	547	19	1		1	DSG1	18	28934274	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	6129332	28934274	49142974	620	12123											
SLC14A2	8170	hgsc.bcm.edu	37	chr18	43204739	43204739	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gccctcgacatccccggataCtcacccagctctgcccctcc	6	7	6	22	2	2	0	1	0	1	0	5	2	4	1	7	1	3	1	7	1	1	1	rs34461862	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:43204739C>T	ENST00000255226.6	+	2	926	c.110C>T	c.(109-111)aCt>aTt	p.T37I	SLC14A2_ENST00000586448.1_Missense_Mutation_p.T37I	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	37			T -> I (in dbSNP:rs34461862).		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						TCCCCGGATACTCACCCAGCT	0.582													C|||	72	0.014377	0.0015	0.0346	5008	,	,		19755	0.0		0.0417	False		,,,				2504	0.0041				p.T37I		Atlas-SNP	.											.	SLC14A2	121	.	0			c.C110T						PASS	.	C	ILE/THR,ILE/THR	26,4380	31.7+/-61.6	0,26,2177	82	78	80		110,110	4.5	1	18	dbSNP_126	80	383,8217	124.3+/-183.0	9,365,3926	yes	missense,missense	SLC14A2	NM_001242692.1,NM_007163.3	89,89	9,391,6103	TT,TC,CC		4.4535,0.5901,3.1447	benign,benign	37/921,37/921	43204739	409,12597	2203	4300	6503	SO:0001583	missense	8170	exon3			CGGATACTCACCC	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.110C>T	18.37:g.43204739C>T	ENSP00000255226:p.Thr37Ile	57	0	0		82	46	0.560976	NM_001242692	A8K8Q7|Q2TBD6|Q96PH5	Missense_Mutation	SNP	ENST00000255226.6	37	CCDS11924.1	41	0.018772893772893772	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	29	0.03825857519788918	C	12.62	1.992557	0.35131	0.005901	0.044535	ENSG00000132874	ENST00000255226;ENST00000323329	T;T	0.57752	1.09;0.38	5.38	4.47	0.54385	.	0.382979	0.24666	N	0.036585	T	0.27697	0.0681	L	0.54323	1.7	0.32498	N	0.539278	D;D	0.65815	0.995;0.969	P;P	0.56278	0.795;0.585	T	0.58381	-0.7646	10	0.45353	T	0.12	-9.3842	12.1733	0.54172	0.0:0.829:0.171:0.0	rs34461862	37;37	Q15849;E7EPU1	UT2_HUMAN;.	I	37	ENSP00000255226:T37I;ENSP00000320689:T37I	ENSP00000255226:T37I	T	+	2	0	SLC14A2	41458737	0.988000	0.35896	0.998000	0.56505	0.260000	0.26232	1.538000	0.36094	2.517000	0.84864	0.462000	0.41574	ACT	C|0.973;T|0.027	0.027	strong		0.582	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1			T	43204739	C	T	43204739	3	4	28	1	0	0	0	0	1	0	0	0	14412	565	20	2	112	2	SLC14A2	18	43204739	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	14270465	43204739	34872509	621	12124											
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43523997	43523997	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttaaacccaagaagatgcTgaaagagttcatgaaagggg	16	8	11	6	0	1	5	1	2	0	3	1	5	1	5	1	2	2	2	1	2	6	3	rs61734402	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:43523997T>C	ENST00000282041.5	-	8	1800	c.1766A>G	c.(1765-1767)cAg>cGg	p.Q589R		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	589					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						AAGAAGATGCTGAAAGAGTTC	0.398													T|||	16	0.00319489	0.0008	0.0029	5008	,	,		20382	0.0		0.0129	False		,,,				2504	0.0				p.Q589R		Atlas-SNP	.											.	EPG5	199	.	0			c.A1766G						PASS	.	T	ARG/GLN	10,3706		0,10,1848	150	134	139		1766	5.2	0.9	18	dbSNP_129	139	147,8069		1,145,3962	yes	missense	EPG5	NM_020964.2	43	1,155,5810	CC,CT,TT		1.7892,0.2691,1.3158	benign	589/2580	43523997	157,11775	1858	4108	5966	SO:0001583	missense	57724	exon8			AGATGCTGAAAGA	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.1766A>G	18.37:g.43523997T>C	ENSP00000282041:p.Gln589Arg	75	0	0		90	42	0.466667	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	13	0.005952380952380952	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	T	9.853	1.194070	0.22037	0.002691	0.017892	ENSG00000152223	ENST00000282041	T	0.09817	2.94	5.25	5.25	0.73442	.	0.170822	0.38720	N	0.001587	T	0.04998	0.0134	L	0.40543	1.245	0.29097	N	0.881736	P;B	0.34724	0.465;0.4	B;B	0.34242	0.178;0.085	T	0.08868	-1.0701	10	0.22109	T	0.4	-10.7121	15.1999	0.73126	0.0:0.0:0.0:1.0	.	589;589	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	R	589	ENSP00000282041:Q589R	ENSP00000282041:Q589R	Q	-	2	0	EPG5	41777995	1.000000	0.71417	0.894000	0.35097	0.212000	0.24457	4.972000	0.63756	1.991000	0.58162	0.374000	0.22700	CAG	T|0.994;C|0.006	0.006	strong		0.398	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		C	43523997	T	C	43523997	3	2	28	1	0	0	0	0	1	0	0	0	8258	1580	55	3	6121	3	KIAA1632	18	43523997	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	319258	43523997	34553251	622	12125											
CDH20	28316	hgsc.bcm.edu	37	chr18	59195294	59195294	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgaacttgggcccatttcAggacacaacaacagtgcaca	13	8	8	12	0	2	1	1	1	1	0	2	2	2	2	1	2	4	1	1	2	3	2	rs35923922	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:59195294A>G	ENST00000262717.4	+	7	1510	c.1112A>G	c.(1111-1113)cAg>cGg	p.Q371R	CDH20_ENST00000538374.1_Missense_Mutation_p.Q371R|CDH20_ENST00000536675.2_Missense_Mutation_p.Q371R			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	371	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		Q -> R (in dbSNP:rs35923922).		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)				GGCCCATTTCAGGACACAACA	0.498													A|||	43	0.00858626	0.0287	0.0058	5008	,	,		18645	0.0		0.001	False		,,,				2504	0.0				p.Q371R		Atlas-SNP	.											CDH20,NS,carcinoma,+1,1	CDH20	117	1	0			c.A1112G						PASS	.	A	ARG/GLN	88,4318	74.1+/-112.3	2,84,2117	132	124	127		1112	5.9	1	18	dbSNP_126	127	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CDH20	NM_031891.2	43	2,86,6415	GG,GA,AA		0.0233,1.9973,0.692	benign	371/802	59195294	90,12916	2203	4300	6503	SO:0001583	missense	28316	exon6			CATTTCAGGACAC	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.1112A>G	18.37:g.59195294A>G	ENSP00000262717:p.Gln371Arg	181	0	0		185	113	0.610811	NM_031891	Q495S3	Missense_Mutation	SNP	ENST00000262717.4	37	CCDS11977.1	16	0.007326007326007326	12	0.024390243902439025	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	A	11.09	1.535027	0.27475	0.019973	2.33E-4	ENSG00000101542	ENST00000536675;ENST00000538374;ENST00000262717	T;T;T	0.51325	0.71;0.71;0.71	5.88	5.88	0.94601	Cadherin (4);Cadherin-like (1);	0.452719	0.25270	N	0.031885	T	0.12475	0.0303	N	0.04805	-0.155	0.27597	N	0.94909	B	0.02656	0.0	B	0.06405	0.002	T	0.04400	-1.0954	10	0.33940	T	0.23	.	6.32	0.21213	0.8101:0.0:0.1899:0.0	rs35923922	371	Q9HBT6	CAD20_HUMAN	R	371	ENSP00000444767:Q371R;ENSP00000442226:Q371R;ENSP00000262717:Q371R	ENSP00000262717:Q371R	Q	+	2	0	CDH20	57346274	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	3.994000	0.56994	2.252000	0.74401	0.529000	0.55759	CAG	A|0.992;G|0.008	0.008	strong		0.498	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891		G	59195294	A	G	59195294	3	3	28	1	0	0	0	0	1	0	0	0	3108	188	7	3	1134	3	CDH20	18	59195294	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	15671297	59195294	18881954	623	12126											
TNFRSF11A	8792	hgsc.bcm.edu	37	chr18	60027236	60027236	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	catcatgggacagagaaatcCgatgcggtttgcagttcttc	10	11	11	9	2	2	1	1	0	1	1	4	4	3	2	1	2	2	3	1	2	1	3	rs12721430	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:60027236C>T	ENST00000586569.1	+	6	608	c.570C>T	c.(568-570)tcC>tcT	p.S190S	TNFRSF11A_ENST00000269485.7_Silent_p.S190S	NM_001270949.1|NM_003839.3	NP_001257878.1|NP_003830.1	Q9Y6Q6	TNR11_HUMAN	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	190					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)				CAGAGAAATCCGATGCGGTTT	0.448													C|||	8	0.00159744	0.0	0.0029	5008	,	,		19769	0.0		0.004	False		,,,				2504	0.002				p.S190S		Atlas-SNP	.											.	TNFRSF11A	51	.	0			c.C570T						PASS	.	C		4,4402	8.1+/-20.4	0,4,2199	116	105	109		570	-2.3	1	18	dbSNP_121	109	40,8560	25.7+/-73.6	0,40,4260	no	coding-synonymous	TNFRSF11A	NM_003839.2		0,44,6459	TT,TC,CC		0.4651,0.0908,0.3383		190/617	60027236	44,12962	2203	4300	6503	SO:0001819	synonymous_variant	8792	exon6			GAAATCCGATGCG	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.570C>T	18.37:g.60027236C>T		145	0	0		160	114	0.7125	NM_001270951	I4EC36|I4EC38|I4EC39|I7JE63|N0GVH0|Q59EP9	Silent	SNP	ENST00000586569.1	37	CCDS11980.1																																																																																			C|0.997;T|0.003	0.003	strong		0.448	TNFRSF11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256186.2			T	60027236	C	T	60027236	2	4	28	1	0	0	0	0	0	0	0	1	16299	639	23	1		1	TNFRSF11A	18	60027236	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	831942	60027236	18050012	624	12127											
SERPINB10	5273	hgsc.bcm.edu	37	chr18	61584726	61584726	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagaccagggagtcaaatgtGaccctgaaagtgaaaaaaaa	19	5	11	6	0	1	4	1	3	0	1	1	6	1	5	2	1	0	0	2	1	6	0	rs143009235	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:61584726G>T	ENST00000238508.3	+	3	264	c.205G>T	c.(205-207)Gac>Tac	p.D69Y		NM_005024.1	NP_005015.1	P48595	SPB10_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 10	69					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)				AGTCAAATGTGACCCTGAAAG	0.274													G|||	18	0.00359425	0.003	0.0058	5008	,	,		15269	0.0		0.0099	False		,,,				2504	0.0				p.D69Y		Atlas-SNP	.											.	SERPINB10	53	.	0			c.G205T						PASS	.	G	TYR/ASP	4,4382		0,4,2189	33	33	33		205	-4.8	0	18	dbSNP_134	33	64,8478		0,64,4207	yes	missense	SERPINB10	NM_005024.1	160	0,68,6396	TT,TG,GG		0.7492,0.0912,0.526		69/398	61584726	68,12860	2193	4271	6464	SO:0001583	missense	5273	exon2			AAATGTGACCCTG	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.205G>T	18.37:g.61584726G>T	ENSP00000238508:p.Asp69Tyr	77	0	0		103	34	0.330097	NM_005024	Q4VAX4|Q4VAX7	Missense_Mutation	SNP	ENST00000238508.3	37	CCDS11990.1	15	0.006868131868131868	3	0.006097560975609756	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	G	4.514	0.095366	0.08681	9.12E-4	0.007492	ENSG00000242550	ENST00000238508	D	0.85088	-1.94	5.1	-4.8	0.03190	Serpin domain (3);	1.218670	0.05583	N	0.573270	T	0.55305	0.1912	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	0.50466	-0.8825	9	.	.	.	.	7.1303	0.25497	0.3286:0.0:0.4743:0.1971	.	69;69	P48595;B2RC45	SPB10_HUMAN;.	Y	69	ENSP00000238508:D69Y	.	D	+	1	0	SERPINB10	59735706	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.633000	0.05483	-0.892000	0.03935	-0.813000	0.03139	GAC	G|0.993;T|0.007	0.007	strong		0.274	SERPINB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134012.3	NM_005024		T	61584726	G	T	61584726	3	4	28	1	0	0	0	0	1	0	0	0	14112	1290	45	4	211	4	SERPINB10	18	61584726	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1557490	61584726	16492522	625	12128											
CNDP1	84735	hgsc.bcm.edu	37	chr18	72228154	72228154	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgaactggggagcgatcccAcgaaaggcaccgtgtgcttc	9	6	13	13	4	0	0	0	0	0	0	2	4	1	1	3	3	3	2	3	3	2	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:72228154A>C	ENST00000358821.3	+	4	595	c.367A>C	c.(367-369)Acg>Ccg	p.T123P	CNDP1_ENST00000585136.1_Intron|CNDP1_ENST00000582365.1_Missense_Mutation_p.T80P|RP11-231E4.3_ENST00000583702.1_RNA	NM_032649.5	NP_116038	Q96KN2	CNDP1_HUMAN	carnosine dipeptidase 1 (metallopeptidase M20 family)	123						extracellular region (GO:0005576)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27		Esophageal squamous(42;0.129)|Prostate(75;0.157)|Melanoma(33;0.211)		BRCA - Breast invasive adenocarcinoma(31;0.109)		GAGCGATCCCACGAAAGGCAC	0.577																																					p.T123P	Melanoma(32;1029 1042 25286 38395 44237)	Atlas-SNP	.											CNDP1,NS,carcinoma,-1,1	CNDP1	98	1	0			c.A367C						PASS	.						124	121	122					18																	72228154		2203	4300	6503	SO:0001583	missense	84735	exon4			GATCCCACGAAAG		CCDS12007.1	18q22.3	2014-07-14			ENSG00000150656	ENSG00000150656	3.4.13.20		20675	protein-coding gene	gene with protein product	"carnosinase 1", "glutamate carboxypeptidase-like protein 2"	609064				12473676	Standard	NM_032649		Approved	MGC10825, CN1, CPGL2, HsT2308	uc002llq.3	Q96KN2	OTTHUMG00000132852	ENST00000358821.3:c.367A>C	18.37:g.72228154A>C	ENSP00000351682:p.Thr123Pro	87	0	0		113	34	0.300885	NM_032649	Q14D40|Q17S05|Q2TBG0|Q6UWK2|Q9BT98	Missense_Mutation	SNP	ENST00000358821.3	37	CCDS12007.1	.	.	.	.	.	.	.	.	.	.	A	8.474	0.858173	0.17178	.	.	ENSG00000150656	ENST00000358821	T	0.14893	2.47	4.93	-2.86	0.05717	.	0.808128	0.11858	N	0.522700	T	0.07908	0.0198	N	0.08118	0	0.09310	N	1	B	0.18610	0.029	B	0.23716	0.048	T	0.33727	-0.9857	10	0.51188	T	0.08	-4.9001	7.9888	0.30229	0.3867:0.4619:0.1513:0.0	.	123	Q96KN2	CNDP1_HUMAN	P	123	ENSP00000351682:T123P	ENSP00000351682:T123P	T	+	1	0	CNDP1	70379134	0.000000	0.05858	0.002000	0.10522	0.128000	0.20619	-0.201000	0.09464	-0.375000	0.07955	0.533000	0.62120	ACG	.	.	none		0.577	CNDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256326.1	NM_032649		C	72228154	A	C	72228154	3	2	28	1	0	0	0	0	1	0	0	0	3595	159	6	5	381	5	CNDP1	18	72228154	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	10643428	72228154	5849094	626	12129											
ZADH2	284273	hgsc.bcm.edu	37	chr18	72913920	72913920	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaattacatggcactttgcCttctttgaaagctgcatggc	9	13	8	11	0	1	1	0	1	1	0	1	1	1	1	2	2	4	3	2	2	3	4	rs61910717	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:72913920C>T	ENST00000322342.3	-	2	874	c.585G>A	c.(583-585)aaG>aaA	p.K195K	ZADH2_ENST00000537114.2_Silent_p.K72K	NM_175907.4	NP_787103.1	Q8N4Q0	ZADH2_HUMAN	zinc binding alcohol dehydrogenase domain containing 2	195						mitochondrion (GO:0005739)|peroxisome (GO:0005777)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(3)|lung(8)|skin(1)	15		Esophageal squamous(42;0.131)|Prostate(75;0.155)		READ - Rectum adenocarcinoma(2;0.0276)|BRCA - Breast invasive adenocarcinoma(31;0.216)		GGCACTTTGCCTTCTTTGAAA	0.478													C|||	127	0.0253594	0.003	0.0202	5008	,	,		21275	0.0		0.0358	False		,,,				2504	0.0746				p.K195K		Atlas-SNP	.											.	ZADH2	25	.	0			c.G585A						PASS	.	C		38,4368	41.6+/-74.8	0,38,2165	177	189	185		585	2.3	0.6	18	dbSNP_129	185	317,8283	111.0+/-171.3	5,307,3988	no	coding-synonymous	ZADH2	NM_175907.4		5,345,6153	TT,TC,CC		3.686,0.8625,2.7295		195/378	72913920	355,12651	2203	4300	6503	SO:0001819	synonymous_variant	284273	exon2			CTTTGCCTTCTTT	BC033780	CCDS12008.1	18q22.3	2008-05-29	2008-05-29		ENSG00000180011	ENSG00000180011			28697	protein-coding gene	gene with protein product						12477932	Standard	NM_175907		Approved	MGC45594	uc002llx.3	Q8N4Q0	OTTHUMG00000132858	ENST00000322342.3:c.585G>A	18.37:g.72913920C>T		76	0	0		84	59	0.702381	NM_175907	A8KA15|B4DZ91	Silent	SNP	ENST00000322342.3	37	CCDS12008.1																																																																																			C|0.973;T|0.027	0.027	strong		0.478	ZADH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256332.1	NM_175907		T	72913920	C	T	72913920	2	4	28	1	0	0	0	0	0	0	0	1	17526	680	24	2		2	ZADH2	18	72913920	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	685766	72913920	5163328	627	12130											
TMPRSS9	360200	hgsc.bcm.edu	37	chr19	2421857	2421857	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccttcctttctagggtgaCtctgggggccccctggcctg	2	13	12	14	0	2	1	0	1	2	0	4	1	4	1	5	4	0	0	5	4	1	4	rs72971482	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:2421857C>T	ENST00000332578.3	+	13	2058	c.2058C>T	c.(2056-2058)gaC>gaT	p.D686D		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	686	Peptidase S1 2. {ECO:0000255|PROSITE- ProRule:PRU00274}.				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)		TCTAGGGTGACTCTGGGGGCC	0.627													C|||	10	0.00199681	0.0	0.0014	5008	,	,		15313	0.0		0.008	False		,,,				2504	0.001				p.D686D		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.C2058T						PASS	.	C		14,4390	20.2+/-43.8	0,14,2188	43	50	48		2058	-0.4	1	19	dbSNP_130	48	102,8496	52.3+/-112.8	1,100,4198	no	coding-synonymous	TMPRSS9	NM_182973.1		1,114,6386	TT,TC,CC		1.1863,0.3179,0.8922		686/1060	2421857	116,12886	2202	4299	6501	SO:0001819	synonymous_variant	360200	exon13			GGGTGACTCTGGG	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.2058C>T	19.37:g.2421857C>T		64	0	0		81	38	0.469136	NM_182973	Q6ZND6|Q7Z411	Silent	SNP	ENST00000332578.3	37	CCDS12088.1																																																																																			C|0.993;T|0.007	0.007	strong		0.627	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973		T	2421857	C	T	2421857	2	4	28	1	0	0	0	0	0	0	0	1	16268	564	20	2		2	TMPRSS9	19	2421857	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10		2421857	56707126	628	12131											
ZNF77	58492	hgsc.bcm.edu	37	chr19	2934249	2934249	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttacattcatacggtttctcTccagtgtgtgttctgacatg	7	17	8	9	1	3	1	1	1	2	0	5	1	4	1	1	1	2	2	1	1	2	5			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:2934249T>C	ENST00000314531.4	-	4	968	c.876A>G	c.(874-876)ggA>ggG	p.G292G		NM_021217.2	NP_067040.1	Q15935	ZNF77_HUMAN	zinc finger protein 77	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)			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)		ACGGTTTCTCTCCAGTGTGTG	0.458																																					p.G292G		Atlas-SNP	.											.	ZNF77	47	.	0			c.A876G						PASS	.						167	152	157					19																	2934249		2203	4300	6503	SO:0001819	synonymous_variant	58492	exon4			TTTCTCTCCAGTG	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.876A>G	19.37:g.2934249T>C		76	0	0		100	39	0.39	NM_021217	Q86XJ3|Q9NPP0	Silent	SNP	ENST00000314531.4	37	CCDS12099.1																																																																																			.	.	none		0.458	ZNF77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451924.1	NM_021217		C	2934249	T	C	2934249	2	2	28	1	0	0	0	0	0	0	0	1	18157	1538	54	3		3	ZNF77	19	2934249	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	512392	2934249	56194734	629	12132											
TJP3	27134	hgsc.bcm.edu	37	chr19	3747891	3747891	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gccgcgttaacagcgactacGagacggacggcgagggcggc	9	3	17	12	8	0	1	0	0	0	1	0	5	0	2	1	4	3	1	1	4	2	2	rs144472063	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:3747891G>A	ENST00000541714.2	+	19	2884	c.2422G>A	c.(2422-2424)Gag>Aag	p.E808K	TJP3_ENST00000587686.1_Missense_Mutation_p.E827K|TJP3_ENST00000589378.1_Missense_Mutation_p.E817K|TJP3_ENST00000382008.3_Missense_Mutation_p.E822K|TJP3_ENST00000539908.2_Missense_Mutation_p.E772K|TJP3_ENST00000262968.9_Missense_Mutation_p.E841K	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	808					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)		CAGCGACTACGAGACGGACGG	0.677													G|||	2	0.000399361	0.0008	0.0014	5008	,	,		16795	0.0		0.0	False		,,,				2504	0.0				p.E817K		Atlas-SNP	.											.	TJP3	79	.	0			c.G2449A						PASS	.	G	LYS/GLU	1,4403	2.1+/-5.4	0,1,2201	35	30	32		2521	4.5	0.8	19	dbSNP_134	32	0,8596		0,0,4298	no	missense	TJP3	NM_014428.1	56	0,1,6499	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	841/953	3747891	1,12999	2202	4298	6500	SO:0001583	missense	27134	exon19			GACTACGAGACGG	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.2422G>A	19.37:g.3747891G>A	ENSP00000439278:p.Glu808Lys	72	0	0		92	50	0.543478	NM_001267561	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Missense_Mutation	SNP	ENST00000541714.2	37	CCDS32873.2	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	21.2	4.114574	0.77210	2.27E-4	0.0	ENSG00000105289	ENST00000541714;ENST00000539908;ENST00000382008;ENST00000262968	T;T;T;T	0.11821	2.76;2.93;2.74;2.81	4.54	4.54	0.55810	.	0.112463	0.64402	D	0.000016	T	0.39410	0.1077	M	0.77820	2.39	0.51482	D	0.999924	D;D;D;D	0.89917	1.0;1.0;0.998;1.0	D;D;P;D	0.76575	0.946;0.988;0.771;0.946	T	0.40850	-0.9541	10	0.87932	D	0	.	16.2624	0.82553	0.0:0.0:1.0:0.0	.	827;841;822;808	O95049-3;O95049-2;O95049;F5H2X0	.;.;ZO3_HUMAN;.	K	808;772;822;841	ENSP00000439278:E808K;ENSP00000439991:E772K;ENSP00000371438:E822K;ENSP00000262968:E841K	ENSP00000262968:E841K	E	+	1	0	TJP3	3698891	1.000000	0.71417	0.841000	0.33234	0.048000	0.14542	7.375000	0.79646	2.062000	0.61559	0.561000	0.74099	GAG	G|1.000;A|0.000	0.000	strong		0.677	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1			A	3747891	G	A	3747891	3	1	28	1	0	0	0	0	1	0	0	0	15946	1059	37	1	2591	1	TJP3	19	3747891	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	813642	3747891	55381092	630	12133											
SEMA6B	10501	hgsc.bcm.edu	37	chr19	4550183	4550183	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catggcccagcgagggcaccGcctcgtccatcagagggtgg	7	5	15	14	3	1	1	1	0	0	1	3	2	2	1	4	4	1	1	4	4	0	0	rs142864702	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:4550183G>A	ENST00000586582.1	-	12	1533	c.1223C>T	c.(1222-1224)gCg>gTg	p.A408V	SEMA6B_ENST00000301293.3_Missense_Mutation_p.A408V|SEMA6B_ENST00000586965.1_Missense_Mutation_p.A408V	NM_032108.3	NP_115484.2	Q9H3T3	SEM6B_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	408	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)		CGAGGGCACCGCCTCGTCCAT	0.657													G|||	12	0.00239617	0.0	0.0101	5008	,	,		18713	0.002		0.003	False		,,,				2504	0.0				p.A408V		Atlas-SNP	.											SEMA6B,NS,carcinoma,+1,1	SEMA6B	51	1	0			c.C1223T						PASS	.	G	VAL/ALA	0,4406		0,0,2203	70	56	61		1223	2.2	1	19	dbSNP_134	61	20,8580		0,20,4280	yes	missense	SEMA6B	NM_032108.3	64	0,20,6483	AA,AG,GG		0.2326,0.0,0.1538	possibly-damaging	408/889	4550183	20,12986	2203	4300	6503	SO:0001583	missense	10501	exon12			GGCACCGCCTCGT	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.1223C>T	19.37:g.4550183G>A	ENSP00000467290:p.Ala408Val	117	0	0		131	66	0.503817	NM_032108	A5PKU4|F6IB19|Q9NRK9	Missense_Mutation	SNP	ENST00000586582.1	37	CCDS12131.1	6	0.0027472527472527475	0	0.0	4	0.011049723756906077	1	0.0017482517482517483	1	0.0013192612137203166	.	21.8	4.204157	0.79127	0.0	0.002326	ENSG00000167680	ENST00000301293;ENST00000301292	T	0.10573	2.86	2.17	2.17	0.27698	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.196139	0.42964	U	0.000634	T	0.17492	0.0420	L	0.58925	1.835	0.42906	D	0.994242	D;D	0.89917	0.997;1.0	P;D	0.64321	0.484;0.924	T	0.03384	-1.1042	10	0.87932	D	0	.	12.0039	0.53248	0.0:0.0:1.0:0.0	.	408;408	B4DT36;Q9H3T3	.;SEM6B_HUMAN	V	408	ENSP00000301293:A408V	ENSP00000301292:A408V	A	-	2	0	SEMA6B	4501183	0.999000	0.42202	0.996000	0.52242	0.933000	0.57130	9.245000	0.95431	1.580000	0.49851	0.478000	0.44815	GCG	G|0.999;A|0.001	0.001	strong		0.657	SEMA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458656.2	NM_032108		A	4550183	G	A	4550183	3	1	28	1	0	0	0	0	1	0	0	0	14055	1087	38	1	1467	1	SEMA6B	19	4550183	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	802292	4550183	54578800	631	12134											
SAFB2	9667	hgsc.bcm.edu	37	chr19	5590291	5590291	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggggctcacccactaacctGgggggagggggcagcccccg	6	4	17	14	1	1	0	1	0	0	0	1	1	1	1	4	7	2	2	4	7	1	1	rs117896034	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:5590291G>T	ENST00000252542.4	-	18	2787	c.2523C>A	c.(2521-2523)ccC>ccA	p.P841P		NM_014649.2	NP_055464.1	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	841	Gly-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)		CCACTAACCTGGGGGGAGGGG	0.677													G|||	44	0.00878594	0.0	0.0144	5008	,	,		15349	0.0089		0.0199	False		,,,				2504	0.0051				p.P841P	Ovarian(127;888 1728 23957 44128 52668)	Atlas-SNP	.											.	SAFB2	90	.	0			c.C2523A						PASS	.	G		8,4326		0,8,2159	7	10	9		2523	3.3	1	19	dbSNP_132	9	122,8386		1,120,4133	no	coding-synonymous	SAFB2	NM_014649.2		1,128,6292	TT,TG,GG		1.4339,0.1846,1.0123		841/954	5590291	130,12712	2167	4254	6421	SO:0001819	synonymous_variant	9667	exon18			TAACCTGGGGGGA	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.2523C>A	19.37:g.5590291G>T		71	0	0		60	28	0.466667	NM_014649	B4DKG3|Q8TB13	Silent	SNP	ENST00000252542.4	37	CCDS32879.1																																																																																			G|0.984;T|0.016	0.016	strong		0.677	SAFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451016.1	NM_014649		T	5590291	G	T	5590291	2	4	28	1	0	0	0	0	0	0	0	1	13822	1335	47	4		4	SAFB2	19	5590291	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1040108	5590291	53538692	632	12135											
GTF2F1	2962	hgsc.bcm.edu	37	chr19	6392906	6392906	+	Missense_Mutation	SNP	G	G	T																															tattcagtgacattctggctGctagggccctgcggaaagag																								rs151336104		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:6392906G>T	ENST00000394456.5	-	2	485	c.21C>A	c.(19-21)agC>agA	p.S7R	GTF2F1_ENST00000429701.2_5'Flank|CTB-180A7.6_ENST00000599584.1_RNA	NM_002096.2	NP_002087.2	P35269	T2FA_HUMAN	general transcription factor IIF, polypeptide 1, 74kDa	7					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						CATTCTGGCTGCTAGGGCCCT	0.592											OREG0025199	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0.0	0.0	5008	,	,		16554	0.0		0.001	False		,,,				2504	0.0				p.S7R		Atlas-SNP	.											.	GTF2F1	39	.	0			c.C21A						PASS	.	G	ARG/SER	0,4406		0,0,2203	138	139	139		21	2.9	1	19	dbSNP_134	139	3,8597	2.2+/-6.3	0,3,4297	yes	missense	GTF2F1	NM_002096.2	110	0,3,6500	TT,TG,GG		0.0349,0.0,0.0231	benign	7/518	6392906	3,13003	2203	4300	6503	SO:0001583	missense	2962	exon2			CTGGCTGCTAGGG		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.21C>A	19.37:g.6392906G>T	ENSP00000377969:p.Ser7Arg	70	0	0	633	80	35	0.4375	NM_002096	B2RCS0|Q9BWN0	Missense_Mutation	SNP	ENST00000394456.5	37	CCDS12165.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	16.51	3.143568	0.57044	0.0	3.49E-4	ENSG00000125651	ENST00000394456;ENST00000541263	T	0.50001	0.76	5.07	2.86	0.33363	Transcription Factor IIF, Rap30/Rap74, interaction (1);	0.314292	0.37483	N	0.002061	T	0.35566	0.0936	L	0.34521	1.04	0.80722	D	1	B	0.31040	0.305	B	0.33890	0.172	T	0.29941	-0.9995	10	0.59425	D	0.04	-8.1482	8.3825	0.32479	0.086:0.156:0.758:0.0	.	7	P35269	T2FA_HUMAN	R	7	ENSP00000377969:S7R	ENSP00000377969:S7R	S	-	3	2	GTF2F1	6343906	1.000000	0.71417	0.997000	0.53966	0.686000	0.39977	2.995000	0.49441	1.334000	0.45468	-0.282000	0.10007	AGC	G|0.999;T|0.001	0.001	strong		0.592	GTF2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398033.1	NM_002096		T	6392906	G	T	6392906	3	4	28	1	0	0	0	0	1	0	0	0	6867	1310	46	4	1580	4	GTF2F1	19	6392906	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	802615	6392906	52736077	633	12136	149	3									
GTF2F1	2962	hgsc.bcm.edu	37	chr19	6392908	6392908	+	Missense_Mutation	SNP	T	T	C																															ttcagtgacattctggctgcTagggccctgcggaaagagga																								rs140541374		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:6392908T>C	ENST00000394456.5	-	2	483	c.19A>G	c.(19-21)Agc>Ggc	p.S7G	GTF2F1_ENST00000429701.2_5'Flank|CTB-180A7.6_ENST00000599584.1_RNA	NM_002096.2	NP_002087.2	P35269	T2FA_HUMAN	general transcription factor IIF, polypeptide 1, 74kDa	7					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						TTCTGGCTGCTAGGGCCCTGC	0.597											OREG0025199	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	1	0.000199681	0.0	0.0	5008	,	,		16539	0.0		0.001	False		,,,				2504	0.0				p.S7G		Atlas-SNP	.											.	GTF2F1	39	.	0			c.A19G						PASS	.						135	136	136					19																	6392908		2203	4300	6503	SO:0001583	missense	2962	exon2			GGCTGCTAGGGCC		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.19A>G	19.37:g.6392908T>C	ENSP00000377969:p.Ser7Gly	70	0	0	633	80	37	0.4625	NM_002096	B2RCS0|Q9BWN0	Missense_Mutation	SNP	ENST00000394456.5	37	CCDS12165.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	11.77	1.737992	0.30774	.	.	ENSG00000125651	ENST00000394456;ENST00000541263	T	0.49720	0.77	5.07	-2.96	0.05547	Transcription Factor IIF, Rap30/Rap74, interaction (1);	0.314292	0.37483	N	0.002061	T	0.26593	0.0650	N	0.14661	0.345	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.02512	-1.1148	10	0.46703	T	0.11	-8.1482	12.3718	0.55260	0.0:0.1636:0.0:0.8364	.	7	P35269	T2FA_HUMAN	G	7	ENSP00000377969:S7G	ENSP00000377969:S7G	S	-	1	0	GTF2F1	6343908	0.999000	0.42202	0.929000	0.37066	0.680000	0.39746	0.351000	0.20096	-0.625000	0.05604	-0.353000	0.07706	AGC	T|0.999;C|0.001	0.001	strong		0.597	GTF2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398033.1	NM_002096		C	6392908	T	C	6392908	3	2	28	1	0	0	0	0	1	0	0	0	6867	1522	53	3	1582	3	GTF2F1	19	6392908	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	2	6392908	52736075	634	12137	149	3									
GTF2F1	2962	hgsc.bcm.edu	37	chr19	6392910	6392910	+	Missense_Mutation	SNP	G	G	A																															cagtgacattctggctgctaGggccctgcggaaagaggaag																								rs150462935		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:6392910G>A	ENST00000394456.5	-	2	481	c.17C>T	c.(16-18)cCt>cTt	p.P6L	GTF2F1_ENST00000429701.2_5'Flank|CTB-180A7.6_ENST00000599584.1_RNA	NM_002096.2	NP_002087.2	P35269	T2FA_HUMAN	general transcription factor IIF, polypeptide 1, 74kDa	6					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						CTGGCTGCTAGGGCCCTGCGG	0.602											OREG0025199	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0.0	0.0	5008	,	,		16382	0.0		0.001	False		,,,				2504	0.0				p.P6L		Atlas-SNP	.											.	GTF2F1	39	.	0			c.C17T						PASS	.	G	LEU/PRO	0,4406		0,0,2203	134	135	134		17	5.1	1	19	dbSNP_134	134	4,8596	1.2+/-3.3	0,4,4296	yes	missense	GTF2F1	NM_002096.2	98	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	benign	6/518	6392910	4,13002	2203	4300	6503	SO:0001583	missense	2962	exon2			CTGCTAGGGCCCT		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.17C>T	19.37:g.6392910G>A	ENSP00000377969:p.Pro6Leu	71	0	0	633	79	35	0.443038	NM_002096	B2RCS0|Q9BWN0	Missense_Mutation	SNP	ENST00000394456.5	37	CCDS12165.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	16.23	3.063678	0.55432	0.0	4.65E-4	ENSG00000125651	ENST00000394456;ENST00000541263	T	0.46451	0.87	5.07	5.07	0.68467	.	0.397846	0.25529	N	0.030059	T	0.26521	0.0648	N	0.08118	0	0.80722	D	1	B	0.21225	0.053	B	0.16289	0.015	T	0.10177	-1.0641	10	0.72032	D	0.01	-21.0264	15.4688	0.75426	0.0:0.0:1.0:0.0	.	6	P35269	T2FA_HUMAN	L	6	ENSP00000377969:P6L	ENSP00000377969:P6L	P	-	2	0	GTF2F1	6343910	1.000000	0.71417	0.997000	0.53966	0.751000	0.42716	2.686000	0.46968	2.629000	0.89072	0.591000	0.81541	CCT	G|0.999;A|0.001	0.001	strong		0.602	GTF2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398033.1	NM_002096		A	6392910	G	A	6392910	3	1	28	1	0	0	0	0	1	0	0	0	6867	1000	35	2	1584	2	GTF2F1	19	6392910	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2	6392910	52736073	635	12138	149	3									
ANGPTL4	51129	hgsc.bcm.edu	37	chr19	8431131	8431131	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tagaccatgaggtggccaagCctgcccgaagaaagaggctg	12	5	14	10	1	0	4	0	1	0	3	0	5	0	4	4	3	2	1	4	3	4	1	rs547981454		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:8431131C>G	ENST00000301455.2	+	3	646	c.475C>G	c.(475-477)Cct>Gct	p.P159A	ANGPTL4_ENST00000393962.2_Missense_Mutation_p.P159A|ANGPTL4_ENST00000541807.1_5'UTR	NM_139314.1	NP_647475.1	Q9BY76	ANGL4_HUMAN	angiopoietin-like 4	159					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						GGTGGCCAAGCCTGCCCGAAG	0.652																																					p.P159A		Atlas-SNP	.											.	ANGPTL4	21	.	0			c.C475G						PASS	.						83	85	84					19																	8431131		2203	4300	6503	SO:0001583	missense	51129	exon3			GCCAAGCCTGCCC	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.475C>G	19.37:g.8431131C>G	ENSP00000301455:p.Pro159Ala	77	0	0		64	25	0.390625	NM_001039667	A8MY84|B4E089|D6W670|F5H0I2|Q53HQ6|Q53HU1|Q6UXN0|Q9HBV4|Q9NZU4|Q9Y5B3	Missense_Mutation	SNP	ENST00000301455.2	37	CCDS12200.1	.	.	.	.	.	.	.	.	.	.	C	8.367	0.834379	0.16820	.	.	ENSG00000167772	ENST00000301455;ENST00000393962	T;T	0.54866	0.71;0.55	4.09	-1.04	0.10068	.	613.611000	0.00166	N	0.000000	T	0.28167	0.0695	N	0.08118	0	0.09310	N	0.999992	B;B	0.06786	0.001;0.001	B;B	0.09377	0.001;0.004	T	0.06463	-1.0825	10	0.25106	T	0.35	.	0.667	0.00852	0.1966:0.3829:0.1774:0.2431	.	159;159	A8MY84;Q9BY76	.;ANGL4_HUMAN	A	159	ENSP00000301455:P159A;ENSP00000377534:P159A	ENSP00000301455:P159A	P	+	1	0	ANGPTL4	8337131	0.001000	0.12720	0.004000	0.12327	0.796000	0.44982	-0.456000	0.06754	-0.190000	0.10465	0.655000	0.94253	CCT	.	.	none		0.652	ANGPTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460322.1	NM_139314		G	8431131	C	G	8431131	3	3	28	1	0	0	0	0	1	0	0	0	616	739	26	4	485	4	ANGPTL4	19	8431131	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2038221	8431131	50697852	636	12139											
MUC16	94025	hgsc.bcm.edu	37	chr19	8995959	8995959	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tagtagaatactcactgctgGtggtggacacagagctccga	11	9	12	9	1	1	2	1	0	0	2	2	4	2	3	1	3	3	3	1	3	4	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:8995959G>T	ENST00000397910.4	-	62	41485	c.41282C>A	c.(41281-41283)aCc>aAc	p.T13761N	MUC16_ENST00000380951.5_Missense_Mutation_p.T402N	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13763				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						CTCACTGCTGGTGGTGGACAC	0.527																																					p.T13761N		Atlas-SNP	.											.	MUC16	4315	.	0			c.C41282A						PASS	.						89	78	81					19																	8995959		1947	4143	6090	SO:0001583	missense	94025	exon62			CTGCTGGTGGTGG	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.41282C>A	19.37:g.8995959G>T	ENSP00000381008:p.Thr13761Asn	51	0	0		45	14	0.311111	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	6.099|6.099	0.386626|0.386626	0.11524|0.11524	.|.	.|.	ENSG00000181143|ENSG00000181143	ENST00000542240|ENST00000397910;ENST00000380951	.|T;T	.|0.35973	.|1.28;1.28	1.84|1.84	0.727|0.727	0.18254|0.18254	.|.	.|.	.|.	.|.	.|.	T|T	0.53254|0.53254	0.1785|0.1785	M|M	0.81239|0.81239	2.535|2.535	.|.	.|.	.|.	.|B;D	.|0.53745	.|0.099;0.962	.|B;D	.|0.66716	.|0.007;0.946	T|T	0.58142|0.58142	-0.7688|-0.7688	4|8	.|0.44086	.|T	.|0.13	-3.0332|-3.0332	5.3761|5.3761	0.16166|0.16166	0.0:0.0:0.6654:0.3346|0.0:0.0:0.6654:0.3346	.|.	.|21406;13761	.|Q8WXI7;B5ME49	.|MUC16_HUMAN;.	T|N	601|13761;402	.|ENSP00000381008:T13761N;ENSP00000370338:T402N	.|ENSP00000370338:T402N	P|T	-|-	1|2	0|0	MUC16|MUC16	8856959|8856959	0.002000|0.002000	0.14202|0.14202	0.034000|0.034000	0.17996|0.17996	0.195000|0.195000	0.23768|0.23768	0.094000|0.094000	0.15107|0.15107	0.320000|0.320000	0.23234|0.23234	0.455000|0.455000	0.32223|0.32223	CCA|ACC	.	.	none		0.527	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	8995959	G	T	8995959	3	4	28	1	0	0	0	0	1	0	0	0	9982	1261	44	4	2333	4	MUC16	19	8995959	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	564828	8995959	50133024	637	12140											
MUC16	94025	hgsc.bcm.edu	37	chr19	9015351	9015351	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtctgcagccagagtacagaGggccaacactggtgttcttg	9	9	13	10	0	2	2	0	0	2	2	2	2	2	2	2	2	4	3	2	2	2	3	rs201449501	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9015351G>A	ENST00000397910.4	-	30	38440	c.38237C>T	c.(38236-38238)cCt>cTt	p.P12746L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12748	SEA 5. {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						AGAGTACAGAGGGCCAACACT	0.512													-|||	7	0.00139776	0.0008	0.0	5008	,	,		20370	0.003		0.001	False		,,,				2504	0.002				p.P12746L		Atlas-SNP	.											.	MUC16	4315	.	0			c.C38237T						PASS	.	G	LEU/PRO	0,4000		0,0,2000	153	130	137		38237	-1.6	0	19	dbSNP_134	137	4,8338		0,4,4167	no	missense	MUC16	NM_024690.2	98	0,4,6167	AA,AG,GG		0.048,0.0,0.0324	possibly-damaging	12746/14508	9015351	4,12338	2000	4171	6171	SO:0001583	missense	94025	exon30			TACAGAGGGCCAA	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.38237C>T	19.37:g.9015351G>A	ENSP00000381008:p.Pro12746Leu	119	0	0		112	18	0.160714	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	10.49	1.365631	0.24684	0.0	4.8E-4	ENSG00000181143	ENST00000397910	T	0.38077	1.16	2.82	-1.58	0.08479	.	.	.	.	.	T	0.39759	0.1090	.	.	.	.	.	.	P	0.50710	0.938	P	0.50270	0.636	T	0.52419	-0.8578	7	0.87932	D	0	.	8.0693	0.30680	0.0:0.0:0.3447:0.6553	.	12746	B5ME49	.	L	12746	ENSP00000381008:P12746L	ENSP00000381008:P12746L	P	-	2	0	MUC16	8876351	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	0.413000	0.21148	-0.376000	0.07943	0.305000	0.20034	CCT	G|0.998;A|0.002	0.002	weak		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9015351	G	A	9015351	3	1	28	1	0	0	0	0	1	0	0	0	9982	1000	35	2	5506	2	MUC16	19	9015351	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	19392	9015351	50113632	638	12141											
DNM2	1785	hgsc.bcm.edu	37	chr19	10939884	10939884	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgacatcagcaccagcactgTgtccacgcctgtacccccgc	8	7	8	18	2	1	1	1	1	0	0	2	1	2	1	5	0	3	3	5	0	1	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:10939884T>C	ENST00000355667.6	+	19	2311	c.2231T>C	c.(2230-2232)gTg>gCg	p.V744A	DNM2_ENST00000389253.4_Missense_Mutation_p.V744A|DNM2_ENST00000359692.6_Missense_Mutation_p.V740A|DNM2_ENST00000408974.4_Missense_Mutation_p.V740A|DNM2_ENST00000314646.5_Missense_Mutation_p.V744A|DNM2_ENST00000585892.1_Missense_Mutation_p.V744A	NM_001005360.2|NM_001190716.1	NP_001005360.1|NP_001177645.1	P50570	DYN2_HUMAN	dynamin 2	744	GED. {ECO:0000255|PROSITE- ProRule:PRU00720}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|endocytosis (GO:0006897)|G2/M transition of mitotic cell cycle (GO:0000086)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|nitric oxide metabolic process (GO:0046209)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic vesicle transport (GO:0048489)|transferrin transport (GO:0033572)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	enzyme binding (GO:0019899)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|microtubule binding (GO:0008017)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	42			Epithelial(33;4.17e-05)|all cancers(31;8.48e-05)			ACCAGCACTGTGTCCACGCCT	0.637			"F, N, Splice, Mis, O"		ETP ALL																																p.V744A		Atlas-SNP	.		Rec	yes		19	19p13.2	1785	dynamin 2		L	.	DNM2	175	.	0			c.T2231C						PASS	.						86	64	71					19																	10939884		2203	4300	6503	SO:0001583	missense	1785	exon19			GCACTGTGTCCAC		CCDS32907.1, CCDS32908.1, CCDS45968.1, CCDS45969.1, CCDS59351.1	19p	2014-09-17						"Pleckstrin homology (PH) domain containing"	2974	protein-coding gene	gene with protein product	"dynamin II", "cytoskeletal protein"	602378				7590285, 9143510	Standard	NM_001190716		Approved	DYNII, DYN2, CMTDIB, CMTDI1, DI-CMTB	uc002mps.2	P50570		ENST00000355667.6:c.2231T>C	19.37:g.10939884T>C	ENSP00000347890:p.Val744Ala	76	0	0		79	44	0.556962	NM_001005361	A8K1B6|E7EV30|E9PEQ4|K7ESI9|Q5I0Y0|Q7Z5S3|Q9UPH4	Missense_Mutation	SNP	ENST00000355667.6	37	CCDS45968.1	.	.	.	.	.	.	.	.	.	.	T	10.09	1.254187	0.22965	.	.	ENSG00000079805	ENST00000408974;ENST00000355667;ENST00000359692;ENST00000389253;ENST00000314646;ENST00000545324	D;D;D;D	0.92911	-3.13;-3.06;-3.12;-3.12	4.83	4.83	0.62350	GTPase effector domain, GED (1);	0.361801	0.25241	N	0.032084	D	0.87485	0.6189	L	0.42245	1.32	0.37324	D	0.909672	B;B;B;B;B;B;B	0.14012	0.009;0.004;0.005;0.002;0.002;0.0;0.002	B;B;B;B;B;B;B	0.15052	0.005;0.012;0.009;0.005;0.008;0.005;0.003	D	0.85541	0.1215	10	0.59425	D	0.04	.	8.187	0.31346	0.0:0.0927:0.0:0.9073	.	338;744;473;740;740;744;744	Q8N1K8;F5H4R9;B4DJ53;A8K1B6;P50570-2;P50570;E9PEQ4	.;.;.;.;.;DYN2_HUMAN;.	A	740;740;744;744;744;351	ENSP00000386192:V740A;ENSP00000352721:V744A;ENSP00000373905:V744A;ENSP00000313164:V744A	ENSP00000313164:V744A	V	+	2	0	DNM2	10800884	0.996000	0.38824	0.990000	0.47175	0.005000	0.04900	5.022000	0.64078	1.808000	0.52836	0.377000	0.23210	GTG	.	.	none		0.637	DNM2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452592.1	NM_004945		C	10939884	T	C	10939884	3	2	28	1	0	0	0	0	1	0	0	0	4674	1696	59	3	2448	3	DNM2	19	10939884	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	1924533	10939884	48189099	639	12142											
ZNF653	115950	hgsc.bcm.edu	37	chr19	11598288	11598288	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aggtgaatgccctcggccgtGagagcgtcgtaaccagggcc	8	6	15	12	4	0	2	0	2	0	1	2	3	0	2	4	3	3	1	4	3	2	1	rs145806085	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:11598288G>C	ENST00000293771.5	-	4	1126	c.990C>G	c.(988-990)ctC>ctG	p.L330L	CTC-398G3.6_ENST00000585656.1_Intron	NM_138783.3	NP_620138.2	Q96CK0	ZN653_HUMAN	zinc finger protein 653	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)			endometrium(2)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	17						CCTCGGCCGTGAGAGCGTCGT	0.672													G|||	7	0.00139776	0.0	0.0	5008	,	,		17152	0.0		0.007	False		,,,				2504	0.0				p.L330L	Pancreas(83;980 1446 4542 6441 43352)	Atlas-SNP	.											.	ZNF653	48	.	0			c.C990G						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	65	60	61		990	1.8	0.9	19	dbSNP_134	61	12,8588	9.8+/-36.6	0,12,4288	no	coding-synonymous	ZNF653	NM_138783.3		0,13,6490	CC,CG,GG		0.1395,0.0227,0.1		330/616	11598288	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	115950	exon4			GGCCGTGAGAGCG	AY072704	CCDS12261.1	19p13.2	2013-01-08						"Zinc fingers, C2H2-type"	25196	protein-coding gene	gene with protein product		611371				12477932	Standard	NM_138783		Approved	Zip67	uc002mrz.2	Q96CK0		ENST00000293771.5:c.990C>G	19.37:g.11598288G>C		53	0	0		43	23	0.534884	NM_138783	Q96AS7	Silent	SNP	ENST00000293771.5	37	CCDS12261.1																																																																																			G|0.998;C|0.002	0.002	strong		0.672	ZNF653-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458836.2	NM_138783		C	11598288	G	C	11598288	2	2	28	1	0	0	0	0	0	0	0	1	18081	1277	45	4		4	ZNF653	19	11598288	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	658404	11598288	47530695	640	12143											
TRMT1	55621	hgsc.bcm.edu	37	chr19	13218417	13218417	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acactgagaatgcggaacgcTgggctagtctctgatagtcg	10	9	13	9	3	1	2	0	2	1	1	3	4	1	3	0	2	2	2	0	2	4	2	rs148858467	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:13218417T>C	ENST00000592062.1	-	15	2124	c.1554A>G	c.(1552-1554)ccA>ccG	p.P518P	TRMT1_ENST00000221504.8_Silent_p.P489P|TRMT1_ENST00000437766.1_Silent_p.P518P|TRMT1_ENST00000357720.4_Silent_p.P518P			Q9NXH9	TRM1_HUMAN	tRNA methyltransferase 1 homolog (S. cerevisiae)	518							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)		TGCGGAACGCTGGGCTAGTCT	0.592													T|||	9	0.00179712	0.0	0.0043	5008	,	,		20409	0.0		0.006	False		,,,				2504	0.0				p.P518P		Atlas-SNP	.											.	TRMT1	31	.	0			c.A1554G						PASS	.	T	,,	4,4402	8.1+/-20.4	0,4,2199	64	39	48		1554,1467,1554	-8	0	19	dbSNP_134	48	75,8523	41.2+/-98.3	0,75,4224	no	coding-synonymous,coding-synonymous,coding-synonymous	TRMT1	NM_001136035.2,NM_001142554.1,NM_017722.3	,,	0,79,6423	CC,CT,TT		0.8723,0.0908,0.6075	,,	518/660,489/631,518/660	13218417	79,12925	2203	4299	6502	SO:0001819	synonymous_variant	55621	exon14			GAACGCTGGGCTA	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.1554A>G	19.37:g.13218417T>C		75	0	0		64	21	0.328125	NM_001136035	O76103|Q548Y5|Q8WVA6	Silent	SNP	ENST00000592062.1	37	CCDS12293.1																																																																																			T|0.995;C|0.005	0.005	strong		0.592	TRMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452780.2	NM_017722		C	13218417	T	C	13218417	2	2	28	1	0	0	0	0	0	0	0	1	16576	1567	55	3		3	TRMT1	19	13218417	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	1620129	13218417	45910566	641	12144											
EMR2	30817	hgsc.bcm.edu	37	chr19	14854338	14854338	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accatttcccatattgctccCggacctgcagaggcaaagtg	10	9	9	13	1	0	1	0	0	0	1	2	2	2	2	4	2	2	3	4	2	2	3	rs117617387	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:14854338C>T	ENST00000315576.3	-	20	2808	c.2357G>A	c.(2356-2358)cGg>cAg	p.R786Q	EMR2_ENST00000353005.1_Missense_Mutation_p.R644Q|EMR2_ENST00000392965.3_Missense_Mutation_p.R728Q|EMR2_ENST00000594294.1_Missense_Mutation_p.R737Q|EMR2_ENST00000596991.2_Missense_Mutation_p.R775Q|EMR2_ENST00000601345.1_Missense_Mutation_p.R775Q|EMR2_ENST00000392967.2_Missense_Mutation_p.R775Q|EMR2_ENST00000353876.1_Missense_Mutation_p.R693Q|EMR2_ENST00000594076.1_Missense_Mutation_p.R693Q|EMR2_ENST00000346057.1_Missense_Mutation_p.R737Q|EMR2_ENST00000595839.1_Missense_Mutation_p.R644Q	NM_013447.3	NP_038475.2	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 2	786					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						ATATTGCTCCCGGACCTGCAG	0.547													c|||	36	0.0071885	0.0015	0.0086	5008	,	,		20652	0.0		0.0089	False		,,,				2504	0.0194				p.R786Q		Atlas-SNP	.											EMR2,NS,carcinoma,+1,1	EMR2	99	1	0			c.G2357A						scavenged	.		GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	17,4389	22.3+/-47.3	0,17,2186	304	290	295		2357,2210,2078,1931,2324,2177,2045	-3.3	0	19	dbSNP_132	295	155,8445	74.2+/-136.8	2,151,4147	yes	missense,missense,missense,missense,missense,missense,missense	EMR2	NM_013447.2,NM_152916.1,NM_152917.1,NM_152918.1,NM_152919.1,NM_152920.1,NM_152921.1	43,43,43,43,43,43,43	2,168,6333	TT,TC,CC		1.8023,0.3858,1.3225	benign,benign,benign,benign,benign,benign,benign	786/824,737/775,693/731,644/682,775/813,726/764,682/720	14854338	172,12834	2203	4300	6503	SO:0001583	missense	30817	exon20			TGCTCCCGGACCT	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.2357G>A	19.37:g.14854338C>T	ENSP00000319883:p.Arg786Gln	169	1	0.00591716		190	99	0.521053	NM_013447	B4DQ96|E7ESD7|E9PBR1|E9PEL6|E9PFQ5|E9PG91|Q8NG96|Q9Y4B1	Missense_Mutation	SNP	ENST00000315576.3	37	CCDS32935.1	11	0.005036630036630037	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	6	0.0079155672823219	c	15.15	2.747296	0.49257	0.003858	0.018023	ENSG00000127507	ENST00000315576;ENST00000392967;ENST00000346057;ENST00000353876;ENST00000353005;ENST00000392965	T;T;T;T;T;T	0.57273	0.41;0.41;0.41;0.41;0.41;0.41	5.02	-3.26	0.05064	.	.	.	.	.	T	0.27313	0.0670	L	0.43923	1.385	0.09310	N	0.999996	B;B;B;P;B;B;B;B	0.46952	0.026;0.107;0.014;0.887;0.289;0.238;0.054;0.045	B;B;B;P;B;B;B;B	0.45794	0.006;0.08;0.011;0.493;0.141;0.103;0.022;0.099	T	0.35599	-0.9782	9	0.23891	T	0.37	.	9.6794	0.40061	0.0:0.4651:0.0:0.5349	.	728;693;786;644;737;786;786;775	E7ESD7;Q9UHX3-4;A0JNV7;Q9UHX3-5;Q9UHX3-3;A8K6W1;Q9UHX3;Q9UHX3-2	.;.;.;.;.;.;EMR2_HUMAN;.	Q	786;775;737;693;644;728	ENSP00000319883:R786Q;ENSP00000376694:R775Q;ENSP00000263380:R737Q;ENSP00000319454:R693Q;ENSP00000319838:R644Q;ENSP00000376692:R728Q	ENSP00000319883:R786Q	R	-	2	0	EMR2	14715338	0.007000	0.16637	0.033000	0.17914	0.247000	0.25773	0.266000	0.18534	-0.410000	0.07542	-0.205000	0.12727	CGG	C|0.989;T|0.011	0.011	strong		0.547	EMR2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466502.2			T	14854338	C	T	14854338	3	4	28	1	0	0	0	0	1	0	0	0	5107	652	23	1	122	1	EMR2	19	14854338	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1635921	14854338	44274645	642	12145											
SIN3B	23309	hgsc.bcm.edu	37	chr19	16973724	16973724	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggacacttctccagggttcGtggacagacgattactgcat	9	11	11	10	2	1	1	0	0	1	1	3	4	1	3	1	3	2	2	1	3	1	3	rs143287291	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:16973724G>A	ENST00000379803.1	+	10	1310	c.1296G>A	c.(1294-1296)tcG>tcA	p.S432S	SIN3B_ENST00000595541.1_5'Flank|SIN3B_ENST00000248054.5_Intron	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						TCCAGGGTTCGTGGACAGACG	0.527													.|||	22	0.00439297	0.0	0.0072	5008	,	,		19490	0.0		0.0119	False		,,,				2504	0.0051				p.S432S		Atlas-SNP	.											SIN3B,NS,malignant_melanoma,+1,1	SIN3B	90	1	0			c.G1296A						PASS	.	G		9,4397	16.8+/-37.8	0,9,2194	254	236	242		1296	-0.3	0	19	dbSNP_134	242	86,8514	49.8+/-109.6	1,84,4215	no	coding-synonymous	SIN3B	NM_015260.2		1,93,6409	AA,AG,GG		1.0,0.2043,0.7304		432/1163	16973724	95,12911	2203	4300	6503	SO:0001819	synonymous_variant	23309	exon10			GGGTTCGTGGACA	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.1296G>A	19.37:g.16973724G>A		157	0	0		188	87	0.462766	NM_015260		Silent	SNP	ENST00000379803.1	37	CCDS32946.1																																																																																			G|0.992;A|0.008	0.008	strong		0.527	SIN3B-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462848.1	NM_015260		A	16973724	G	A	16973724	2	1	28	1	0	0	0	0	0	0	0	1	14341	1132	40	1		1	SIN3B	19	16973724	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2119386	16973724	42155259	643	12146											
MYO9B	4650	hgsc.bcm.edu	37	chr19	17212925	17212925	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcgcaggccacagccacccGgcgcctagtggagcgtggcc	6	3	16	16	4	0	0	0	0	0	0	0	1	0	1	5	5	2	1	5	5	1	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:17212925G>A	ENST00000594824.1	+	2	545	c.398G>A	c.(397-399)cGg>cAg	p.R133Q	MYO9B_ENST00000397274.2_Missense_Mutation_p.R133Q|MYO9B_ENST00000595618.1_Missense_Mutation_p.R133Q|CTD-2528A14.5_ENST00000597045.1_RNA			Q13459	MYO9B_HUMAN	myosin IXB	133					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						ACAGCCACCCGGCGCCTAGTG	0.617																																					p.R133Q		Atlas-SNP	.											.	MYO9B	264	.	0			c.G398A						PASS	.						33	35	35					19																	17212925		2002	4174	6176	SO:0001583	missense	4650	exon2			CCACCCGGCGCCT		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.398G>A	19.37:g.17212925G>A	ENSP00000471367:p.Arg133Gln	40	0	0		33	14	0.424242	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Missense_Mutation	SNP	ENST00000594824.1	37		.	.	.	.	.	.	.	.	.	.	G	11.59	1.683444	0.29872	.	.	ENSG00000099331	ENST00000397274	D	0.84730	-1.89	5.62	3.5	0.40072	.	0.178051	0.27891	N	0.017422	T	0.79713	0.4493	L	0.52126	1.63	0.30811	N	0.738814	B;B;B	0.24651	0.108;0.108;0.064	B;B;B	0.17979	0.01;0.01;0.02	T	0.74475	-0.3653	10	0.37606	T	0.19	.	11.4579	0.50193	0.1454:0.0:0.8546:0.0	.	133;133;139	Q13459;B0I1T6;Q4LE74	MYO9B_HUMAN;.;.	Q	133	ENSP00000380444:R133Q	ENSP00000380444:R133Q	R	+	2	0	MYO9B	17073925	1.000000	0.71417	0.977000	0.42913	0.326000	0.28443	3.417000	0.52714	0.747000	0.32809	-0.119000	0.15052	CGG	.	.	none		0.617	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1			A	17212925	G	A	17212925	3	1	28	1	0	0	0	0	1	0	0	0	10094	1116	39	1	400	1	MYO9B	19	17212925	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	239201	17212925	41916058	644	12147											
JAK3	3718	hgsc.bcm.edu	37	chr19	17945696	17945696	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcactgatgggcatggtgaCgccactaaacacttcccaga	11	7	11	12	1	0	3	0	2	0	1	1	3	1	3	2	3	1	2	2	3	2	2	rs3213409	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:17945696C>T	ENST00000527670.1	-	15	2193	c.2164G>A	c.(2164-2166)Gtc>Atc	p.V722I	JAK3_ENST00000534444.1_Missense_Mutation_p.V722I|JAK3_ENST00000458235.1_Missense_Mutation_p.V722I			P52333	JAK3_HUMAN	Janus kinase 3	722	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> I (in dbSNP:rs3213409). {ECO:0000269|PubMed:10982185, ECO:0000269|PubMed:14615376, ECO:0000269|PubMed:17344846, ECO:0000269|Ref.4}.		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)	p.V722I(2)		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)	GGCATGGTGACGCCACTAAAC	0.627		2	Mis		"acute megakaryocytic leukemia, ETP ALL"								C|||	18	0.00359425	0.0023	0.0014	5008	,	,		16598	0.0		0.007	False		,,,				2504	0.0072				p.V722I		Atlas-SNP	.		Dom	yes		19	19p13.1	3718	Janus kinase 3		L	JAK3,NS,haematopoietic_neoplasm,0,2	JAK3	341	2	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.G2164A	GRCh37	CM000172	JAK3	M	rs3213409	PASS	.	C	ILE/VAL	9,4397	14.3+/-33.2	1,7,2195	82	88	86	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2164	0.2	0	19	dbSNP_106	86	114,8486	61.0+/-122.8	2,110,4188	yes	missense	JAK3	NM_000215.3	29	3,117,6383	TT,TC,CC		1.3256,0.2043,0.9457	benign	722/1125	17945696	123,12883	2203	4300	6503	SO:0001583	missense	3718	exon16			TGGTGACGCCACT	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.2164G>A	19.37:g.17945696C>T	ENSP00000432511:p.Val722Ile	72	0	0		90	51	0.566667	NM_000215	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Missense_Mutation	SNP	ENST00000527670.1	37	CCDS12366.1	8	0.003663003663003663	3	0.006097560975609756	0	0.0	0	0.0	5	0.006596306068601583	C	8.473	0.857929	0.17178	0.002043	0.013256	ENSG00000105639	ENST00000458235;ENST00000527670;ENST00000534444	T;T;T	0.61980	0.06;0.06;0.06	4.89	0.248	0.15526	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.618726	0.15813	N	0.243360	T	0.33147	0.0853	N	0.17082	0.46	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.09377	0.003;0.004	T	0.24977	-1.0145	10	0.62326	D	0.03	-7.2327	7.7407	0.28839	0.0:0.6163:0.0:0.3837	rs3213409;rs52813014;rs3213409	722;722	P52333-2;P52333	.;JAK3_HUMAN	I	722	ENSP00000391676:V722I;ENSP00000432511:V722I;ENSP00000436421:V722I	ENSP00000391676:V722I	V	-	1	0	JAK3	17806696	0.011000	0.17503	0.000000	0.03702	0.008000	0.06430	1.524000	0.35942	-0.126000	0.11682	0.555000	0.69702	GTC	C|0.991;T|0.009	0.009	strong		0.627	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215		T	17945696	C	T	17945696	3	4	28	1	0	0	0	0	1	0	0	0	7948	536	19	1	1246	1	JAK3	19	17945696	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	732771	17945696	41183287	645	12148											
ELL	8178	hgsc.bcm.edu	37	chr19	18583657	18583657	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaacttaccccttggcttccTtgaaatcggatagatggcct	10	12	8	11	1	0	2	0	1	0	1	2	3	1	3	4	3	2	1	4	3	4	5			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:18583657T>C	ENST00000262809.4	-	2	242	c.171A>G	c.(169-171)caA>caG	p.Q57Q	ELL_ENST00000596124.3_5'UTR	NM_006532.3	NP_006523.1	P55199	ELL_HUMAN	elongation factor RNA polymerase II	57					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)		CTTGGCTTCCTTGAAATCGGA	0.398			T	MLL	AL																																p.Q57Q		Atlas-SNP	.		Dom	yes		19	19p13.1	8178	ELL gene (11-19 lysine-rich leukemia gene)		L	.	ELL	52	.	0			c.A171G						PASS	.						108	99	102					19																	18583657		2203	4300	6503	SO:0001819	synonymous_variant	8178	exon2			GCTTCCTTGAAAT	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.171A>G	19.37:g.18583657T>C		22	0	0		28	12	0.428571	NM_006532		Silent	SNP	ENST00000262809.4	37	CCDS12380.1																																																																																			.	.	none		0.398	ELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466362.1	NM_006532		C	18583657	T	C	18583657	2	2	28	1	0	0	0	0	0	0	0	1	5064	1606	56	3		3	ELL	19	18583657	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10	637961	18583657	40545326	646	12149											
CRLF1	9244	hgsc.bcm.edu	37	chr19	18710496	18710496	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccagagccaaggtggaggcGttgagtacacgggagagctc	10	5	17	9	2	0	3	0	1	0	2	1	5	0	4	2	4	3	3	2	4	2	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:18710496G>A	ENST00000392386.3	-	2	469	c.276C>T	c.(274-276)aaC>aaT	p.N92N		NM_004750.4	NP_004741.1	O75462	CRLF1_HUMAN	cytokine receptor-like factor 1	92	Ig-like C2-type.				negative regulation of motor neuron apoptotic process (GO:2000672)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of cell proliferation (GO:0008284)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|ureteric bud development (GO:0001657)	CRLF-CLCF1 complex (GO:0097058)|extracellular space (GO:0005615)	cytokine binding (GO:0019955)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)	9						AGGTGGAGGCGTTGAGTACAC	0.692																																					p.N92N		Atlas-SNP	.											.	CRLF1	32	.	0			c.C276T						PASS	.						24	23	23					19																	18710496		2200	4298	6498	SO:0001819	synonymous_variant	9244	exon2			GGAGGCGTTGAGT	AF059293	CCDS32962.1	19p12	2013-02-11				ENSG00000006016		"Fibronectin type III domain containing"	2364	protein-coding gene	gene with protein product	"cold-induced sweating syndrome"	604237				9686600	Standard	NM_004750		Approved	CLF-1, CLF, CISS, CISS1	uc010ebt.2	O75462		ENST00000392386.3:c.276C>T	19.37:g.18710496G>A		105	0	0		135	69	0.511111	NM_004750	Q9UHH5	Silent	SNP	ENST00000392386.3	37	CCDS32962.1																																																																																			.	.	none		0.692	CRLF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465129.1			A	18710496	G	A	18710496	2	1	28	1	0	0	0	0	0	0	0	1	3888	1136	40	1		1	CRLF1	19	18710496	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	126839	18710496	40418487	647	12150											
PBX4	80714	hgsc.bcm.edu	37	chr19	19680276	19680276	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctgggagatggtgaggccGcccttcctggccagctcttc	5	9	13	14	1	1	2	0	1	1	1	3	3	2	2	5	4	1	1	5	4	0	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:19680276G>A	ENST00000251203.9	-	5	1036	c.750C>T	c.(748-750)ggC>ggT	p.G250G		NM_025245.2	NP_079521.1	Q9BYU1	PBX4_HUMAN	pre-B-cell leukemia homeobox 4	250					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						TGGTGAGGCCGCCCTTCCTGG	0.567																																					p.G250G		Atlas-SNP	.											.	PBX4	34	.	0			c.C750T						PASS	.						187	159	168					19																	19680276		2203	4300	6503	SO:0001819	synonymous_variant	80714	exon5			GAGGCCGCCCTTC	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.750C>T	19.37:g.19680276G>A		104	0	0		115	49	0.426087	NM_025245	A5D8Y0|B3KUK9	Silent	SNP	ENST00000251203.9	37	CCDS12406.1																																																																																			.	.	none		0.567	PBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417784.6			A	19680276	G	A	19680276	2	1	28	1	0	0	0	0	0	0	0	1	11504	1074	38	1		1	PBX4	19	19680276	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	969780	19680276	39448707	648	12151											
ZNF486	90649	hgsc.bcm.edu	37	chr19	20308207	20308207	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacaccttactacacataagAtaactcatactagagagaaa	19	8	4	10	0	1	3	1	0	0	3	1	4	1	3	1	0	4	0	1	0	7	6	rs148497901	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:20308207A>T	ENST00000335117.8	+	4	745	c.688A>T	c.(688-690)Ata>Tta	p.I230L	CTC-260E6.6_ENST00000585498.1_RNA|CTC-260E6.6_ENST00000586657.1_RNA|CTC-260E6.6_ENST00000593655.1_RNA	NM_052852.3	NP_443084.2	Q96H40	ZN486_HUMAN	zinc finger protein 486	230					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						TACACATAAGATAACTCATAC	0.363													A|||	31	0.0061901	0.0008	0.0058	5008	,	,		19318	0.0		0.0249	False		,,,				2504	0.001				p.I230L		Atlas-SNP	.											.	ZNF486	74	.	0			c.A688T						PASS	.	A	LEU/ILE	16,4292		0,16,2138	40	43	42		688	0.8	0	19	dbSNP_134	42	187,8375		6,175,4100	no	missense	ZNF486	NM_052852.2	5	6,191,6238	TT,TA,AA		2.1841,0.3714,1.5773	benign	230/464	20308207	203,12667	2154	4281	6435	SO:0001583	missense	90649	exon4			CATAAGATAACTC	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.688A>T	19.37:g.20308207A>T	ENSP00000335042:p.Ile230Leu	25	0	0		36	27	0.75	NM_052852	Q0VG00	Missense_Mutation	SNP	ENST00000335117.8	37	CCDS46029.1	24	0.01098901098901099	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	19	0.025065963060686015	a	9.789	1.177288	0.21787	0.003714	0.021841	ENSG00000256229	ENST00000545779;ENST00000335117	T	0.18016	2.24	0.814	0.814	0.18756	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02267	0.0070	N	0.01076	-1.035	0.19575	N	0.999961	B	0.32467	0.372	B	0.42959	0.403	T	0.36311	-0.9753	9	0.66056	D	0.02	.	5.4337	0.16469	1.0:0.0:0.0:0.0	.	230	Q96H40	ZN486_HUMAN	L	269;230	ENSP00000335042:I230L	ENSP00000335042:I230L	I	+	1	0	ZNF486	20169207	0.000000	0.05858	0.037000	0.18230	0.036000	0.12997	-0.471000	0.06631	0.158000	0.19367	0.156000	0.16432	ATA	A|0.986;T|0.014	0.014	strong		0.363	ZNF486-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447843.2	NM_052852		T	20308207	A	T	20308207	3	4	28	1	0	0	0	0	1	0	0	0	17954	333	12	5	702	5	ZNF486	19	20308207	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	627931	20308207	38820776	649	12152											
ZNF100	163227	hgsc.bcm.edu	37	chr19	21910621	21910621	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agttatcaaacactggtttaAtttgttatcatgttctttgt	10	20	6	5	0	3	0	2	0	1	0	3	0	3	0	0	1	1	4	0	1	4	7	rs11556742	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:21910621A>G	ENST00000358296.6	-	5	691	c.493T>C	c.(493-495)Tta>Cta	p.L165L	ZNF100_ENST00000305570.6_Silent_p.L101L	NM_173531.3	NP_775802.2	Q8IYN0	ZN100_HUMAN	zinc finger protein 100	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)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)	21						CACTGGTTTAATTTGTTATCA	0.313													N|||	92	0.0183706	0.0023	0.0576	5008	,	,		16971	0.0		0.0249	False		,,,				2504	0.0245				p.L165L		Atlas-SNP	.											.	ZNF100	62	.	0			c.T493C						PASS	.	A		16,4080		0,16,2032	168	169	169		493	1.4	0	19	dbSNP_120	169	178,8286		1,176,4055	no	coding-synonymous	ZNF100	NM_173531.3		1,192,6087	GG,GA,AA		2.103,0.3906,1.5446		165/543	21910621	194,12366	2048	4232	6280	SO:0001819	synonymous_variant	163227	exon5			GGTTTAATTTGTT	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.493T>C	19.37:g.21910621A>G		95	0	0		111	48	0.432432	NM_173531	Q7M4M0	Silent	SNP	ENST00000358296.6	37	CCDS42538.1																																																																																			A|0.980;G|0.020	0.020	strong		0.313	ZNF100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464087.1	NM_173531		G	21910621	A	G	21910621	2	3	28	1	0	0	0	0	0	0	0	1	17728	98	4	3		3	ZNF100	19	21910621	Silent	SNP	A	TCGA-G8-6914-01A-11D-2210-10	1602414	21910621	37218362	650	12153											
ZNF681	148213	hgsc.bcm.edu	37	chr19	23927604	23927604	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acgtttgtagagtttgtctcTagtataaattatcttatgtg	10	19	8	4	1	2	1	0	0	2	1	3	1	2	1	0	0	0	4	0	0	7	8	rs147282314	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:23927604T>C	ENST00000402377.3	-	4	889	c.748A>G	c.(748-750)Aga>Gga	p.R250G	ZNF681_ENST00000395385.3_Missense_Mutation_p.R181G	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	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)			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)				AGTTTGTCTCTAGTATAAATT	0.348													T|||	4	0.000798722	0.003	0.0	5008	,	,		18422	0.0		0.0	False		,,,				2504	0.0				p.R250G		Atlas-SNP	.											.	ZNF681	76	.	0			c.A748G						PASS	.	T	GLY/ARG	10,4396		0,10,2193	97	96	97		748	-3.2	0	19	dbSNP_134	97	0,8600		0,0,4300	no	missense	ZNF681	NM_138286.2	125	0,10,6493	CC,CT,TT		0.0,0.227,0.0769	benign	250/646	23927604	10,12996	2203	4300	6503	SO:0001583	missense	148213	exon4			TGTCTCTAGTATA	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.748A>G	19.37:g.23927604T>C	ENSP00000384000:p.Arg250Gly	61	0	0		75	38	0.506667	NM_138286	B3KVF7	Missense_Mutation	SNP	ENST00000402377.3	37	CCDS12414.2	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	.	0.010	-1.745110	0.00675	0.00227	0.0	ENSG00000196172	ENST00000402377;ENST00000395385	T;T	0.07908	3.29;3.15	1.6	-3.2	0.05156	Zinc finger, C2H2 (1);	.	.	.	.	T	0.01156	0.0038	N	0.00387	-1.565	0.20703	N	0.999865	B	0.02656	0.0	B	0.01281	0.0	T	0.38607	-0.9653	9	0.02654	T	1	.	9.6115	0.39665	0.0:0.7478:0.0:0.2522	.	250	Q96N22	ZN681_HUMAN	G	250;181	ENSP00000384000:R250G;ENSP00000378783:R181G	ENSP00000378783:R181G	R	-	1	2	ZNF681	23719444	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.592000	0.23984	-1.681000	0.01448	-1.783000	0.00646	AGA	T|0.999;C|0.001	0.001	strong		0.348	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286		C	23927604	T	C	23927604	3	2	28	1	0	0	0	0	1	0	0	0	18103	1530	53	3	1193	3	ZNF681	19	23927604	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	2016983	23927604	35201379	651	12154											
ZNF536	9745	hgsc.bcm.edu	37	chr19	31039256	31039256	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tatcaaagcattgtgagcaaCggtgtgaatttccaagggtc	12	11	11	7	1	1	2	1	2	0	0	3	2	2	2	1	2	3	2	1	2	5	3	rs111707808	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:31039256C>T	ENST00000355537.3	+	4	2877	c.2730C>T	c.(2728-2730)aaC>aaT	p.N910N		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	910					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)					TTGTGAGCAACGGTGTGAATT	0.498													C|||	229	0.0457268	0.0348	0.0173	5008	,	,		21120	0.005		0.0338	False		,,,				2504	0.135				p.N910N		Atlas-SNP	.											ZNF536,colon,carcinoma,+1,1	ZNF536	424	1	0			c.C2730T						scavenged	.	C		161,4245	108.6+/-147.0	2,157,2044	178	183	181		2730	-0.6	1	19	dbSNP_132	181	287,8313	106.8+/-167.6	5,277,4018	no	coding-synonymous	ZNF536	NM_014717.1		7,434,6062	TT,TC,CC		3.3372,3.6541,3.4446		910/1301	31039256	448,12558	2203	4300	6503	SO:0001819	synonymous_variant	9745	exon4			GAGCAACGGTGTG		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.2730C>T	19.37:g.31039256C>T		43	1	0.0232558		44	28	0.636364	NM_014717	A2RU18	Silent	SNP	ENST00000355537.3	37	CCDS32984.1																																																																																			C|0.970;T|0.030	0.030	strong		0.498	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		T	31039256	C	T	31039256	2	4	28	1	0	0	0	0	0	0	0	1	17989	535	19	1		1	ZNF536	19	31039256	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	7111652	31039256	28089727	652	12155											
ZNF536	9745	hgsc.bcm.edu	37	chr19	31039669	31039669	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaagaccaagcccgggaggCgagtaagatggccctgctgc	11	4	14	12	2	0	2	0	0	0	2	0	4	0	3	3	3	3	2	3	3	3	1	rs77238711	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:31039669C>T	ENST00000355537.3	+	4	3290	c.3143C>T	c.(3142-3144)gCg>gTg	p.A1048V		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	1048					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)					GCCCGGGAGGCGAGTAAGATG	0.537													C|||	229	0.0457268	0.0348	0.0173	5008	,	,		19387	0.005		0.0338	False		,,,				2504	0.135				p.A1048V		Atlas-SNP	.											.	ZNF536	424	.	0			c.C3143T						PASS	.	C	VAL/ALA	161,4245	108.6+/-147.0	2,157,2044	79	73	75		3143	0.6	0.1	19	dbSNP_131	75	288,8312	107.0+/-167.8	5,278,4017	yes	missense	ZNF536	NM_014717.1	64	7,435,6061	TT,TC,CC		3.3488,3.6541,3.4523	benign	1048/1301	31039669	449,12557	2203	4300	6503	SO:0001583	missense	9745	exon4			GGGAGGCGAGTAA		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.3143C>T	19.37:g.31039669C>T	ENSP00000347730:p.Ala1048Val	28	0	0		35	22	0.628571	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	37	CCDS32984.1	50	0.022893772893772892	15	0.03048780487804878	8	0.022099447513812154	0	0.0	27	0.03562005277044855	C	0.303	-0.972510	0.02215	0.036541	0.033488	ENSG00000198597	ENST00000355537	T	0.09538	2.97	5.74	0.614	0.17603	.	0.308174	0.30383	N	0.009750	T	0.01156	0.0038	N	0.14661	0.345	0.23492	N	0.99756	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.002	T	0.37619	-0.9698	10	0.36615	T	0.2	-16.6787	8.9777	0.35946	0.0:0.6367:0.1064:0.2569	.	1048;1048	A7E228;O15090	.;ZN536_HUMAN	V	1048	ENSP00000347730:A1048V	ENSP00000347730:A1048V	A	+	2	0	ZNF536	35731509	0.146000	0.22672	0.080000	0.20451	0.020000	0.10135	0.203000	0.17315	0.337000	0.23665	-0.768000	0.03414	GCG	C|0.970;T|0.030	0.030	strong		0.537	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		T	31039669	C	T	31039669	3	4	28	1	0	0	0	0	1	0	0	0	17989	768	27	1	3153	1	ZNF536	19	31039669	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	413	31039669	28089314	653	12156											
MLL4	9757	hgsc.bcm.edu	37	chr19	36223699	36223699	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcctcggggccagggcacGcctccttcggggccaggagt	5	5	16	15	3	0	0	0	0	0	0	3	1	1	1	5	6	1	1	5	6	0	1	rs375564425	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:36223699G>T	ENST00000222270.7	+	28	6249	c.6249G>T	c.(6247-6249)acG>acT	p.T2083T	KMT2B_ENST00000420124.1_Silent_p.T2083T|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	2083					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)										GCCAGGGCACGCCTCCTTCGG	0.687													T|||	2	0.000399361	0.0008	0.0	5008	,	,		12848	0.0		0.001	False		,,,				2504	0.0				p.T2083T		Atlas-SNP	.											.	MLL4	229	.	0			c.G6249T						PASS	.	T		1,3869		0,1,1934	11	13	12		6249	0.5	1	19		12	18,8212		0,18,4097	no	coding-synonymous	MLL4	NM_014727.1		0,19,6031	TT,TG,GG		0.2187,0.0258,0.157		2083/2716	36223699	19,12081	1935	4115	6050	SO:0001819	synonymous_variant	8085	exon28			GGGCACGCCTCCT	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.6249G>T	19.37:g.36223699G>T		41	0	0		80	41	0.5125	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Silent	SNP	ENST00000222270.7	37	CCDS46055.1																																																																																			.	.	weak		0.687	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		T	36223699	G	T	36223699	2	4	28	1	0	0	0	0	0	0	0	1	9632	1074	38	4		4	MLL4	19	36223699	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	5184030	36223699	22905284	654	12157											
APLP1	333	hgsc.bcm.edu	37	chr19	36370092	36370092	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgcgcaggaagaagccctaCggggctatcagccatggcgt	9	6	14	12	3	1	1	1	0	0	1	1	2	1	2	2	4	4	2	2	4	4	2	rs138562956		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:36370092C>T	ENST00000221891.4	+	16	2022	c.1830C>T	c.(1828-1830)taC>taT	p.Y610Y	RN7SL402P_ENST00000465059.1_RNA|APLP1_ENST00000537454.2_Silent_p.Y570Y|APLP1_ENST00000586861.1_Silent_p.Y603Y	NM_001024807.1|NM_005166.3	NP_001019978.1|NP_005157.1	P51693	APLP1_HUMAN	amyloid beta (A4) precursor-like protein 1	609					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)			AGAAGCCCTACGGGGCTATCA	0.652													C|||	1	0.000199681	0.0	0.0	5008	,	,		17200	0.0		0.001	False		,,,				2504	0.0				p.Y610Y		Atlas-SNP	.											.	APLP1	77	.	0			c.C1830T						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	55	58	57		1830,1827	-1.7	1	19	dbSNP_134	57	20,8580	14.6+/-50.1	0,20,4280	no	coding-synonymous,coding-synonymous	APLP1	NM_001024807.1,NM_005166.3	,	0,21,6482	TT,TC,CC		0.2326,0.0227,0.1615	,	610/652,609/651	36370092	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	333	exon16			GCCCTACGGGGCT	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.1830C>T	19.37:g.36370092C>T		35	0	0		37	16	0.432432	NM_001024807	O00113|Q96A92	Silent	SNP	ENST00000221891.4	37	CCDS32997.1																																																																																			C|0.999;T|0.001	0.001	strong		0.652	APLP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452564.1	NM_001024807		T	36370092	C	T	36370092	2	4	28	1	0	0	0	0	0	0	0	1	778	547	19	1		1	APLP1	19	36370092	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	146393	36370092	22758891	655	12158											
PAK4	10298	hgsc.bcm.edu	37	chr19	39668381	39668381	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gagagcccccctacttcaacGagccacccctcaaagccatg	11	5	7	18	1	2	1	2	0	0	1	2	3	2	1	7	0	5	0	7	0	3	2	rs372098486		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:39668381G>A	ENST00000593690.1	+	10	1979	c.1552G>A	c.(1552-1554)Gag>Aag	p.E518K	PAK4_ENST00000599470.1_Missense_Mutation_p.E365K|PAK4_ENST00000435673.2_Missense_Mutation_p.E518K|PAK4_ENST00000599386.1_Missense_Mutation_p.E365K|PAK4_ENST00000358301.3_Missense_Mutation_p.E518K|PAK4_ENST00000321944.4_Missense_Mutation_p.E428K|PAK4_ENST00000360442.3_Missense_Mutation_p.E518K	NM_001014831.2	NP_001014831.1	O96013	PAK4_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 4	518	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)			CTACTTCAACGAGCCACCCCT	0.602																																					p.E518K		Atlas-SNP	.											.	PAK4	40	.	0			c.G1552A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	0,4406		0,0,2203	166	134	145		1552,1552,1093,1093,1552	5.1	1	19		145	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	PAK4	NM_001014831.2,NM_001014832.1,NM_001014834.2,NM_001014835.1,NM_005884.3	56,56,56,56,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	518/592,518/592,365/439,365/439,518/592	39668381	1,13005	2203	4300	6503	SO:0001583	missense	10298	exon8			TTCAACGAGCCAC	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.1552G>A	19.37:g.39668381G>A	ENSP00000469413:p.Glu518Lys	75	0	0		98	4	0.0408163	NM_001014832	B4DGG6|Q8N4E1|Q8NCH5|Q8NDE3|Q9BU33|Q9ULS8	Missense_Mutation	SNP	ENST00000593690.1	37	CCDS12528.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.248588	0.80024	0.0	1.16E-4	ENSG00000130669	ENST00000358301;ENST00000321944;ENST00000358801;ENST00000542377;ENST00000435673;ENST00000360442	T;T;T	0.65364	-0.15;-0.15;-0.15	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	0.64204	0.2577	N	0.12471	0.22	0.80722	D	1	D;P;P	0.76494	0.999;0.782;0.817	D;B;B	0.70716	0.97;0.115;0.276	T	0.71083	-0.4695	10	0.87932	D	0	.	15.9831	0.80127	0.0:0.0:1.0:0.0	.	428;365;518	O96013-4;O96013-3;O96013	.;.;PAK4_HUMAN	K	518;365;322;274;518;518	ENSP00000351049:E518K;ENSP00000392753:E518K;ENSP00000353625:E518K	ENSP00000326864:E365K	E	+	1	0	PAK4	44360221	1.000000	0.71417	0.979000	0.43373	0.795000	0.44927	9.657000	0.98554	2.629000	0.89072	0.555000	0.69702	GAG	.	.	weak		0.602	PAK4-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463823.1			A	39668381	G	A	39668381	3	1	28	1	0	0	0	0	1	0	0	0	11412	1059	37	1	1578	1	PAK4	19	39668381	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	3298289	39668381	19460602	656	12159											
PSG8	440533	hgsc.bcm.edu	37	chr19	43268388	43268388	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggttggctgggcttcaatcGtgacttgggcagtcgtgggt	4	13	17	7	2	1	1	1	1	0	0	3	1	1	1	0	5	0	4	0	5	1	3	rs142689447		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:43268388G>A	ENST00000306511.4	-	2	207	c.110C>T	c.(109-111)aCg>aTg	p.T37M	PSG8_ENST00000401467.2_Missense_Mutation_p.T37M|PSG8_ENST00000404209.4_Missense_Mutation_p.T37M|PSG8_ENST00000406636.3_Intron	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	37	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)				GGCTTCAATCGTGACTTGGGC	0.463													.|||	1	0.000199681	0.0	0.0	5008	,	,		21250	0.0		0.001	False		,,,				2504	0.0				p.T37M		Atlas-SNP	.											.	PSG8	101	.	0			c.C110T						PASS	.	G	MET/THR,,MET/THR	0,4406		0,0,2203	173	170	171		110,,110	1.4	0	19	dbSNP_134	171	8,8590	6.4+/-24.3	0,8,4291	no	missense,intron,missense	PSG8	NM_001130167.1,NM_001130168.1,NM_182707.2	81,,81	0,8,6494	AA,AG,GG		0.093,0.0,0.0615	benign,,benign	37/420,,37/427	43268388	8,12996	2203	4299	6502	SO:0001583	missense	440533	exon2			TCAATCGTGACTT	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.110C>T	19.37:g.43268388G>A	ENSP00000305005:p.Thr37Met	135	0	0		105	50	0.47619	NM_001130167	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Missense_Mutation	SNP	ENST00000306511.4	37	CCDS33037.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	g	5.019	0.189287	0.09547	0.0	9.3E-4	ENSG00000124467	ENST00000404209;ENST00000401467;ENST00000407488;ENST00000306511	T;T;T	0.68331	-0.32;-0.32;-0.32	1.35	1.35	0.21983	Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.72415	0.3457	M	0.77712	2.385	0.09310	N	1	P;B;P;B;B	0.44690	0.841;0.062;0.538;0.174;0.208	P;B;B;B;B	0.52646	0.705;0.063;0.204;0.066;0.109	T	0.60662	-0.7219	9	0.49607	T	0.09	.	6.1568	0.20342	0.0:0.0:1.0:0.0	.	37;37;37;37;37	B5MCQ0;Q9UQ74;E7ENH0;Q9UQ74-3;A5PKV3	.;PSG8_HUMAN;.;.;.	M	37	ENSP00000385869:T37M;ENSP00000386090:T37M;ENSP00000305005:T37M	ENSP00000305005:T37M	T	-	2	0	PSG8	47960228	0.007000	0.16637	0.011000	0.14972	0.031000	0.12232	2.204000	0.42761	1.063000	0.40649	0.184000	0.17185	ACG	G|1.000;A|0.000	0.000	strong		0.463	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1			A	43268388	G	A	43268388	3	1	28	1	0	0	0	0	1	0	0	0	12673	1145	40	1	1207	1	PSG8	19	43268388	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	3600007	43268388	15860595	657	12160											
ZNF230	7773	hgsc.bcm.edu	37	chr19	44515492	44515492	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggcttgtacaccggtcttTctgtaaagaccaacaaggag	12	9	11	9	1	2	1	0	0	2	1	2	3	2	2	2	3	2	3	2	3	5	4	rs6413542	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:44515492T>A	ENST00000429154.2	+	5	1529	c.1301T>A	c.(1300-1302)tTc>tAc	p.F434Y		NM_006300.3	NP_006291.2	Q9UIE0	ZN230_HUMAN	zinc finger protein 230	434			F -> Y (in dbSNP:rs6413542).		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)				CACCGGTCTTTCTGTAAAGAC	0.428													T|||	27	0.00539137	0.0	0.0014	5008	,	,		16061	0.0		0.0239	False		,,,				2504	0.002				p.F434Y	GBM(175;914 2069 22996 47111 52600)	Atlas-SNP	.											.	ZNF230	44	.	0			c.T1301A						PASS	.	T	TYR/PHE	4,4402	8.1+/-20.4	0,4,2199	53	58	56		1301	-1.1	0	19	dbSNP_116	56	95,8505	49.8+/-109.6	0,95,4205	yes	missense	ZNF230	NM_006300.3	22	0,99,6404	AA,AT,TT		1.1047,0.0908,0.7612	benign	434/475	44515492	99,12907	2203	4300	6503	SO:0001583	missense	7773	exon5			GGTCTTTCTGTAA	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.1301T>A	19.37:g.44515492T>A	ENSP00000409318:p.Phe434Tyr	41	0	0		55	31	0.563636	NM_006300	O15322|Q504X7|Q86W84|Q9P1U6	Missense_Mutation	SNP	ENST00000429154.2	37	CCDS33044.1	23	0.010531135531135532	0	0.0	0	0.0	0	0.0	23	0.030343007915567283	T	0.541	-0.853455	0.02630	9.08E-4	0.011047	ENSG00000159882	ENST00000429154	T	0.14640	2.49	2.55	-1.12	0.09808	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01156	0.0038	N	0.02751	-0.505	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42799	-0.9430	9	0.09590	T	0.72	.	2.3511	0.04283	0.2475:0.0:0.2858:0.4666	rs6413542;rs52791695;rs6413542	434	Q9UIE0	ZN230_HUMAN	Y	434	ENSP00000409318:F434Y	ENSP00000409318:F434Y	F	+	2	0	ZNF230	49207332	0.000000	0.05858	0.000000	0.03702	0.423000	0.31445	-0.228000	0.09114	-0.182000	0.10602	-1.285000	0.01374	TTC	T|0.992;A|0.008	0.008	strong		0.428	ZNF230-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460456.1			A	44515492	T	A	44515492	3	1	28	1	0	0	0	0	1	0	0	0	17799	1783	62	5	1315	5	ZNF230	19	44515492	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	1247104	44515492	14613491	658	12161											
ZNF229	7772	hgsc.bcm.edu	37	chr19	44932704	44932704	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccttgaagatgtgagctcTgactatagcccttcccacac	10	10	8	13	0	1	4	0	3	1	1	2	5	2	4	3	0	2	1	3	0	3	4	rs375182987	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:44932704T>C	ENST00000588931.1	-	6	2685	c.2252A>G	c.(2251-2253)cAg>cGg	p.Q751R	CTC-512J12.4_ENST00000588655.1_RNA|ZNF229_ENST00000591289.1_Intron|ZNF229_ENST00000291187.4_Missense_Mutation_p.Q745R	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	751					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)				ATGTGAGCTCTGACTATAGCC	0.512																																					p.Q751R		Atlas-SNP	.											.	ZNF229	123	.	0			c.A2252G						PASS	.	T	ARG/GLN	0,4404		0,0,2202	73	81	79		2252	0.6	0	19		79	2,8598	2.2+/-6.3	0,2,4298	no	missense	ZNF229	NM_014518.2	43	0,2,6500	CC,CT,TT		0.0233,0.0,0.0154	benign	751/826	44932704	2,13002	2202	4300	6502	SO:0001583	missense	7772	exon6			GAGCTCTGACTAT	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.2252A>G	19.37:g.44932704T>C	ENSP00000466519:p.Gln751Arg	135	0	0		173	88	0.508671	NM_014518	B2RWN3|Q59FV2|Q86WL9	Missense_Mutation	SNP	ENST00000588931.1	37	CCDS42574.1	.	.	.	.	.	.	.	.	.	.	T	14.31	2.497781	0.44455	0.0	2.33E-4	ENSG00000167383	ENST00000291187	.	.	.	4.04	0.594	0.17485	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11196	0.0273	N	0.03294	-0.36	0.09310	N	1	P	0.39216	0.664	B	0.37267	0.245	T	0.25152	-1.0140	8	0.10902	T	0.67	.	7.7713	0.29010	0.0:0.2711:0.0:0.7289	.	751	Q9UJW7	ZN229_HUMAN	R	751	.	ENSP00000291187:Q751R	Q	-	2	0	ZNF229	49624544	0.000000	0.05858	0.000000	0.03702	0.755000	0.42902	-2.022000	0.01439	-0.284000	0.09102	0.496000	0.49642	CAG	.	.	weak		0.512	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518		C	44932704	T	C	44932704	3	2	28	1	0	0	0	0	1	0	0	0	17797	1580	55	3	229	3	ZNF229	19	44932704	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	417212	44932704	14196279	659	12162											
PVRL2	5819	hgsc.bcm.edu	37	chr19	45381649	45381649	+	Intron	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggaggagccagtggcgaCgggggattctacgatccgaa	10	5	18	8	4	1	0	0	0	1	0	2	7	2	4	2	6	2	0	2	6	2	2	rs373022885		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:45381649C>T	ENST00000252483.5	+	6	1042				PVRL2_ENST00000252485.4_Silent_p.D404D	NM_001042724.1	NP_001036189.1	Q92692	PVRL2_HUMAN	poliovirus receptor-related 2 (herpesvirus entry mediator B)						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)		CCAGTGGCGACGGGGGATTCT	0.612																																					p.D404D		Atlas-SNP	.											.	PVRL2	58	.	0			c.C1212T						PASS	.	C	,	0,4336		0,0,2168	60	42	48		,1212	-2.3	0	19		48	1,8497		0,1,4248	no	intron,coding-synonymous	PVRL2	NM_001042724.1,NM_002856.2	,	0,1,6416	TT,TC,CC		0.0118,0.0,0.0078	,	,404/480	45381649	1,12833	2168	4249	6417	SO:0001627	intron_variant	5819	exon6			TGGCGACGGGGGA	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.1043-3819C>T	19.37:g.45381649C>T		75	0	0		69	36	0.521739	NM_002856	A8K5L5|O75455|Q6IBI6|Q96J29	Silent	SNP	ENST00000252483.5	37	CCDS42576.1																																																																																			.	.	weak		0.612	PVRL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453231.1	NM_002856		T	45381649	C	T	45381649	1	4	28	0	1	0	0	0	0	0	0	0	12855	535	19	1		1	PVRL2	19	45381649	Intron	SNP	C	TCGA-G8-6914-01A-11D-2210-10	448945	45381649	13747334	660	12163											
ERCC1	2067	hgsc.bcm.edu	37	chr19	45923598	45923598	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacctgaggaacagggcacAggtgctctggcccagcacat	10	6	12	13	0	2	1	1	1	1	0	2	2	2	2	2	4	3	3	2	4	1	0			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:45923598A>G	ENST00000300853.3	-	4	1000	c.409T>C	c.(409-411)Tgt>Cgt	p.C137R	ERCC1_ENST00000423698.2_Missense_Mutation_p.C65R|ERCC1_ENST00000013807.5_Missense_Mutation_p.C137R|ERCC1_ENST00000589165.1_Missense_Mutation_p.C137R|ERCC1_ENST00000340192.7_Missense_Mutation_p.C137R|ERCC1_ENST00000591636.1_Missense_Mutation_p.C137R	NM_001983.3	NP_001974.1	P07992	ERCC1_HUMAN	excision repair cross-complementation group 1	137					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)		AACAGGGCACAGGTGCTCTGG	0.617								Nucleotide excision repair (NER)																													p.C137R		Atlas-SNP	.											.	ERCC1	46	.	0			c.T409C						PASS	.						87	68	74					19																	45923598		2203	4300	6503	SO:0001583	missense	2067	exon4			GGGCACAGGTGCT		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.409T>C	19.37:g.45923598A>G	ENSP00000300853:p.Cys137Arg	68	0	0		59	38	0.644068	NM_001983	B2RC01|B3KRR0|Q7Z7F5|Q96S40	Missense_Mutation	SNP	ENST00000300853.3	37	CCDS12662.1	.	.	.	.	.	.	.	.	.	.	A	18.20	3.572338	0.65765	.	.	ENSG00000012061	ENST00000300853;ENST00000340192;ENST00000423698;ENST00000013807	T;T;T;T	0.52526	0.76;0.66;0.87;0.71	5.28	5.28	0.74379	Restriction endonuclease, type II-like (1);	0.000000	0.85682	D	0.000000	T	0.62319	0.2418	M	0.91561	3.22	0.80722	D	1	P;B;P;P	0.43973	0.731;0.054;0.681;0.823	P;B;B;B	0.45913	0.497;0.064;0.32;0.399	T	0.71210	-0.4660	10	0.66056	D	0.02	-2.2056	11.5895	0.50938	1.0:0.0:0.0:0.0	.	137;65;137;137	Q7Z7F5;B3KRR0;Q96S40;P07992	.;.;.;ERCC1_HUMAN	R	137;137;65;137	ENSP00000300853:C137R;ENSP00000345203:C137R;ENSP00000394875:C65R;ENSP00000013807:C137R	ENSP00000013807:C137R	C	-	1	0	ERCC1	50615438	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.739000	0.84976	2.013000	0.59113	0.374000	0.22700	TGT	.	.	none		0.617	ERCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459542.1	NM_001983		G	45923598	A	G	45923598	3	3	28	1	0	0	0	0	1	0	0	0	5214	188	7	3	641	3	ERCC1	19	45923598	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	541949	45923598	13205385	661	12164											
SLC1A5	6510	hgsc.bcm.edu	37	chr19	47280587	47280587	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	acggtggcgccgatgggcagGatgaaacggctgatgtgctt	8	8	17	8	4	0	2	0	2	0	0	0	4	0	3	1	5	2	3	1	5	1	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:47280587G>A	ENST00000542575.2	-	6	1762	c.1134C>T	c.(1132-1134)atC>atT	p.I378I	SLC1A5_ENST00000412532.2_Silent_p.I150I|SLC1A5_ENST00000594991.1_Silent_p.I202I|SLC1A5_ENST00000434726.2_Silent_p.I176I	NM_005628.2	NP_005619.1	Q15758	AAAT_HUMAN	solute carrier family 1 (neutral amino acid transporter), member 5	378					amino acid transport (GO:0006865)|extracellular amino acid transport (GO:0006860)|glutamine transport (GO:0006868)|ion transport (GO:0006811)|neutral amino acid transport (GO:0015804)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-glutamine transmembrane transporter activity (GO:0015186)|L-serine transmembrane transporter activity (GO:0015194)|neutral amino acid transmembrane transporter activity (GO:0015175)|receptor activity (GO:0004872)|sodium:dicarboxylate symporter activity (GO:0017153)|virus receptor activity (GO:0001618)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(2)|stomach(1)	13		all_epithelial(76;0.00314)|Ovarian(192;0.0798)|all_neural(266;0.107)		OV - Ovarian serous cystadenocarcinoma(262;0.000338)|all cancers(93;0.000882)|Epithelial(262;0.0211)|GBM - Glioblastoma multiforme(486;0.0341)	L-Asparagine(DB00174)|L-Glutamine(DB00130)	CGATGGGCAGGATGAAACGGC	0.607																																					p.I378I		Atlas-SNP	.											.	SLC1A5	31	.	0			c.C1134T						PASS	.						67	56	60					19																	47280587		2203	4300	6503	SO:0001819	synonymous_variant	6510	exon6			GGGCAGGATGAAA	U53347	CCDS12692.1, CCDS46125.1, CCDS46126.1	19q13.32	2013-07-15			ENSG00000105281	ENSG00000105281		"Solute carriers"	10943	protein-coding gene	gene with protein product		109190		RDRC, M7V1		8702519, 10051606	Standard	NM_005628		Approved	AAAT, ASCT2	uc002pfs.3	Q15758	OTTHUMG00000183434	ENST00000542575.2:c.1134C>T	19.37:g.47280587G>A		80	0	0		90	34	0.377778	NM_005628	A8K9H5|B4DR77|B4DWS4|B7ZB81|D0EYG6|E9PC01|O95720|Q96RL9|Q9BWQ3|Q9UNP2	Silent	SNP	ENST00000542575.2	37	CCDS12692.1																																																																																			.	.	none		0.607	SLC1A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466630.1			A	47280587	G	A	47280587	2	1	28	1	0	0	0	0	0	0	0	1	14450	1164	41	2		2	SLC1A5	19	47280587	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1356989	47280587	11848396	662	12165											
GPR77	27202	hgsc.bcm.edu	37	chr19	47844383	47844383	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggtgcagtgggctgtcgggcGctgccctccatcatcctgct	3	10	14	14	2	1	0	1	0	0	0	4	0	3	0	3	3	3	4	3	3	0	0	rs373920189		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:47844383G>T	ENST00000595464.1	+	2	545	c.327G>T	c.(325-327)gcG>gcT	p.A109A	C5AR2_ENST00000257267.2_Silent_p.A109A|C5AR2_ENST00000600626.1_Silent_p.A109A	NM_001271749.1	NP_001258678.1	Q9P296	C5AR2_HUMAN	complement component 5a receptor 2	109					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)										GCTGTCGGGCGCTGCCCTCCA	0.647																																					p.A109A		Atlas-SNP	.											.	.	.	.	0			c.G327T						PASS	.						96	91	93					19																	47844383		2203	4300	6503	SO:0001819	synonymous_variant	27202	exon2			TCGGGCGCTGCCC	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.327G>T	19.37:g.47844383G>T		26	0	0		33	17	0.515152	NM_001271750	B2RA09	Silent	SNP	ENST00000595464.1	37	CCDS12699.1																																																																																			.	.	alt		0.647	C5AR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466926.1	NM_018485		T	47844383	G	T	47844383	2	4	28	1	0	0	0	0	0	0	0	1	6717	1074	38	4		4	GPR77	19	47844383	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	563796	47844383	11284600	663	12166											
GLTSCR1	29998	hgsc.bcm.edu	37	chr19	48183748	48183748	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggccccgccgcagccccccGgggccctgagcaaacccatg	6	2	12	21	4	0	1	0	1	0	0	0	1	0	1	8	3	3	2	8	3	1	0			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:48183748G>A	ENST00000396720.3	+	6	1515	c.1321G>A	c.(1321-1323)Ggg>Agg	p.G441R	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	441										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)		gcagccccccggggcccTGAG	0.687																																					p.G441R		Atlas-SNP	.											.	GLTSCR1	79	.	0			c.G1321A						PASS	.						12	17	16					19																	48183748		1779	3787	5566	SO:0001583	missense	29998	exon6			CCCCCCGGGGCCC	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.1321G>A	19.37:g.48183748G>A	ENSP00000379946:p.Gly441Arg	14	0	0		22	12	0.545455	NM_015711	A8MW01	Missense_Mutation	SNP	ENST00000396720.3	37	CCDS46134.1	.	.	.	.	.	.	.	.	.	.	G	6.411	0.443896	0.12164	.	.	ENSG00000063169	ENST00000396720	T	0.33216	1.42	3.93	3.93	0.45458	.	.	.	.	.	T	0.25419	0.0618	N	0.14661	0.345	0.32728	N	0.50933	D	0.62365	0.991	P	0.52856	0.711	T	0.05989	-1.0852	9	0.16420	T	0.52	.	11.3225	0.49430	0.0:0.0:1.0:0.0	.	441	Q9NZM4	GSCR1_HUMAN	R	441	ENSP00000379946:G441R	ENSP00000379946:G441R	G	+	1	0	GLTSCR1	52875560	0.914000	0.31030	0.859000	0.33776	0.345000	0.29048	2.650000	0.46665	2.018000	0.59344	0.491000	0.48974	GGG	.	.	none		0.687	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711		A	48183748	G	A	48183748	3	1	28	1	0	0	0	0	1	0	0	0	6482	1116	39	1	1335	1	GLTSCR1	19	48183748	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	339365	48183748	10945235	664	12167											
LIG1	3978	hgsc.bcm.edu	37	chr19	48664687	48664687	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccttcgctgcccaggaccCgggccgccttcctccctggc	2	7	10	22	3	0	0	0	0	0	0	3	1	2	1	8	3	1	1	8	3	0	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:48664687C>T	ENST00000263274.7	-	4	604	c.185G>A	c.(184-186)cGg>cAg	p.R62Q	LIG1_ENST00000536218.1_Missense_Mutation_p.R62Q|LIG1_ENST00000427526.2_Missense_Mutation_p.R32Q|LIG1_ENST00000599165.1_Intron	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	62			R -> W (in dbSNP:rs3730863). {ECO:0000269|Ref.2}.		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)	GCCCAGGACCCGGGCCGCCTT	0.602								Nucleotide excision repair (NER)																													p.R62Q		Atlas-SNP	.											.	LIG1	151	.	0			c.G185A						PASS	.						124	120	121					19																	48664687		2203	4300	6503	SO:0001583	missense	3978	exon4			AGGACCCGGGCCG		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.185G>A	19.37:g.48664687C>T	ENSP00000263274:p.Arg62Gln	55	0	0		38	24	0.631579	NM_000234	B2RAI8|Q2TB12|Q32P23	Missense_Mutation	SNP	ENST00000263274.7	37	CCDS12711.1	.	.	.	.	.	.	.	.	.	.	C	12.86	2.063708	0.36373	.	.	ENSG00000105486	ENST00000263274;ENST00000544761;ENST00000427526;ENST00000536218;ENST00000542460	T;T;T;T	0.58652	0.45;0.32;0.46;1.98	4.62	-1.03	0.10102	.	0.681137	0.14004	N	0.347948	T	0.39545	0.1082	L	0.39397	1.21	0.20975	N	0.999815	B;B;B	0.18013	0.008;0.025;0.008	B;B;B	0.09377	0.001;0.004;0.001	T	0.25710	-1.0124	10	0.12766	T	0.61	-5.9785	7.7073	0.28657	0.0:0.5183:0.0:0.4817	.	32;62;62	B4DTU4;F5GZ28;P18858	.;.;DNLI1_HUMAN	Q	62;94;32;62;62	ENSP00000263274:R62Q;ENSP00000442841:R32Q;ENSP00000441531:R62Q;ENSP00000445928:R62Q	ENSP00000263274:R62Q	R	-	2	0	LIG1	53356499	0.489000	0.26004	0.781000	0.31783	0.827000	0.46813	-0.049000	0.11924	-0.188000	0.10499	-0.369000	0.07265	CGG	.	.	none		0.602	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1	NM_000234		T	48664687	C	T	48664687	3	4	28	1	0	0	0	0	1	0	0	0	8790	652	23	1	2674	1	LIG1	19	48664687	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	480939	48664687	10464296	665	12168											
PRRG2	5639	hgsc.bcm.edu	37	chr19	50091763	50091763	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctttcctgcagggcgtggacGagtggatgtggccagcctgg	5	9	17	10	2	0	0	0	0	0	0	1	3	1	2	3	5	2	1	3	5	0	1	rs117225796	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:50091763G>A	ENST00000246794.5	+	5	480	c.311G>A	c.(310-312)cGa>cAa	p.R104Q	PRRG2_ENST00000596700.1_Intron	NM_000951.2	NP_000942.1	O14669	TMG2_HUMAN	proline rich Gla (G-carboxyglutamic acid) 2	104						extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			lung(1)|skin(1)|soft_tissue(1)	3		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00295)|GBM - Glioblastoma multiforme(134;0.0121)		GGGCGTGGACGAGTGGATGTG	0.607													G|||	16	0.00319489	0.0	0.0029	5008	,	,		17535	0.0		0.0089	False		,,,				2504	0.0051				p.R104Q		Atlas-SNP	.											.	PRRG2	13	.	0			c.G311A						PASS	.	G	GLN/ARG	4,4398		0,4,2197	35	29	31		311	2.4	0.2	19	dbSNP_132	31	68,8532		0,68,4232	yes	missense	PRRG2	NM_000951.2	43	0,72,6429	AA,AG,GG		0.7907,0.0909,0.5538	benign	104/203	50091763	72,12930	2201	4300	6501	SO:0001583	missense	5639	exon5			GTGGACGAGTGGA		CCDS12773.1	19q13.33	2008-02-05	2004-05-27						9470	protein-coding gene	gene with protein product		604429	"proline-rich Gla (G-carboxyglutamic acid) polypeptide 2"			9256434	Standard	NM_000951		Approved	PRGP2	uc002pon.3	O14669		ENST00000246794.5:c.311G>A	19.37:g.50091763G>A	ENSP00000246794:p.Arg104Gln	58	0	0		62	37	0.596774	NM_000951	Q6IBF8	Missense_Mutation	SNP	ENST00000246794.5	37	CCDS12773.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	G	10.82	1.459638	0.26248	9.09E-4	0.007907	ENSG00000126460	ENST00000246794;ENST00000543867	D	0.99773	-6.72	5.62	2.36	0.29203	Gamma-carboxyglutamic acid-rich (GLA) domain (1);	0.544550	0.17501	N	0.171991	D	0.98061	0.9361	L	0.50333	1.59	0.09310	N	1	B;B	0.20052	0.028;0.041	B;B	0.13407	0.009;0.002	D	0.97650	1.0154	10	0.23302	T	0.38	-7.5056	6.9565	0.24574	0.276:0.0:0.724:0.0	.	81;104	F5GZ13;O14669	.;TMG2_HUMAN	Q	104;81	ENSP00000246794:R104Q	ENSP00000246794:R104Q	R	+	2	0	PRRG2	54783575	0.740000	0.28207	0.163000	0.22734	0.416000	0.31233	1.066000	0.30604	0.738000	0.32606	0.563000	0.77884	CGA	G|0.995;A|0.005	0.005	strong		0.607	PRRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465257.1	NM_000951		A	50091763	G	A	50091763	3	1	28	1	0	0	0	0	1	0	0	0	12618	1058	37	1	325	1	PRRG2	19	50091763	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1427076	50091763	9037220	666	12169											
ETFB	2109	hgsc.bcm.edu	37	chr19	51856469	51856469	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacctgcaggggacccaagcGttctgcttctgctgggggca	6	8	14	13	1	2	0	0	0	2	0	2	1	2	1	2	4	4	5	2	4	1	2	rs147353781	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:51856469G>A	ENST00000309244.4	-	3	383	c.292C>T	c.(292-294)Cgc>Tgc	p.R98C	CTD-2616J11.9_ENST00000600974.1_RNA|ETFB_ENST00000354232.4_Missense_Mutation_p.R189C|CTD-2616J11.11_ENST00000600067.1_3'UTR	NM_001985.2	NP_001976.1	P38117	ETFB_HUMAN	electron-transfer-flavoprotein, beta polypeptide	98					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)		GGACCCAAGCGTTCTGCTTCT	0.637													g|||	2	0.000399361	0.0	0.0014	5008	,	,		16497	0.0		0.001	False		,,,				2504	0.0				p.R189C		Atlas-SNP	.											ETFB_ENST00000309244,NS,carcinoma,0,2	ETFB	46	2	0			c.C565T						PASS	.		CYS/ARG,CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	112	99	104		565,292	3	0.1	19	dbSNP_134	104	13,8587	9.8+/-36.6	0,13,4287	yes	missense,missense	ETFB	NM_001014763.1,NM_001985.2	180,180	0,15,6488	AA,AG,GG		0.1512,0.0454,0.1153	probably-damaging,probably-damaging	189/347,98/256	51856469	15,12991	2203	4300	6503	SO:0001583	missense	2109	exon2			CCAAGCGTTCTGC	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.292C>T	19.37:g.51856469G>A	ENSP00000311930:p.Arg98Cys	44	0	0		49	28	0.571429	NM_001014763	A8K766|B3KNY2|Q6IBH7|Q71RF6|Q9Y3S7	Missense_Mutation	SNP	ENST00000309244.4	37	CCDS12828.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	g	13.39	2.223595	0.39300	4.54E-4	0.001512	ENSG00000105379	ENST00000309244;ENST00000354232	D;D	0.82803	-1.65;-1.65	5.18	3.0	0.34707	Electron transfer flavoprotein, alpha/beta-subunit, N-terminal (2);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.416981	0.27315	N	0.019921	T	0.81389	0.4812	L	0.39898	1.24	0.09310	N	0.999997	B;D	0.58620	0.218;0.983	B;P	0.55667	0.369;0.781	T	0.71774	-0.4491	10	0.72032	D	0.01	.	6.2267	0.20711	0.088:0.0:0.5739:0.3381	.	98;189	P38117;P38117-2	ETFB_HUMAN;.	C	98;189	ENSP00000311930:R98C;ENSP00000346173:R189C	ENSP00000311930:R98C	R	-	1	0	ETFB	56548281	0.020000	0.18652	0.107000	0.21349	0.673000	0.39480	1.050000	0.30404	0.561000	0.29186	-0.233000	0.12211	CGC	G|0.999;A|0.001	0.001	strong		0.637	ETFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464273.1			A	51856469	G	A	51856469	3	1	28	1	0	0	0	0	1	0	0	0	5272	1145	40	1	491	1	ETFB	19	51856469	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1764706	51856469	7272514	667	12170											
SIGLEC8	27181	hgsc.bcm.edu	37	chr19	51961519	51961519	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcagggcacatggacacaCaggccctcctgcaccgtcac	10	4	11	16	1	1	0	1	0	0	0	2	2	2	1	3	3	2	3	3	3	0	0	rs140904107	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:51961519C>A	ENST00000321424.3	-	1	189	c.123G>T	c.(121-123)ctG>ctT	p.L41L	SIGLEC8_ENST00000597352.1_5'Flank|SIGLEC8_ENST00000340550.5_Silent_p.L41L|SIGLEC8_ENST00000430817.1_Silent_p.L41L	NM_014442.2	NP_055257.2	Q9NYZ4	SIGL8_HUMAN	sialic acid binding Ig-like lectin 8	41	Ig-like V-type.				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)		CATGGACACACAGGCCCTCCT	0.597																																					p.L41L		Atlas-SNP	.											SIGLEC8,NS,carcinoma,-2,1	SIGLEC8	130	1	0			c.G123T						PASS	.	C		2,4404		0,2,2201	141	124	130		123	-0.2	0.8	19	dbSNP_134	130	6,8594		0,6,4294	no	coding-synonymous	SIGLEC8	NM_014442.2		0,8,6495	AA,AC,CC		0.0698,0.0454,0.0615		41/500	51961519	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	27181	exon1			GACACACAGGCCC	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.123G>T	19.37:g.51961519C>A		178	0	0		196	89	0.454082	NM_014442	Q7Z728	Silent	SNP	ENST00000321424.3	37	CCDS33086.1																																																																																			C|0.999;A|0.001	0.001	strong		0.597	SIGLEC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463648.2	NM_014442		A	51961519	C	A	51961519	2	1	28	1	0	0	0	0	0	0	0	1	14329	465	17	4		4	SIGLEC8	19	51961519	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	105050	51961519	7167464	668	12171											
SIGLEC12	89858	hgsc.bcm.edu	37	chr19	52000192	52000192	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcctgtatcccccacgcccActgctggccttgccgatttc	4	11	8	18	2	0	0	0	0	0	0	2	1	1	0	6	1	3	2	6	1	1	3	rs144032115	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:52000192A>G	ENST00000291707.3	-	7	1596	c.1541T>C	c.(1540-1542)gTg>gCg	p.V514A	SIGLEC12_ENST00000598614.1_Missense_Mutation_p.V396A	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	514					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)		CCCCACGCCCACTGCTGGCCT	0.582													N|||	5	0.000998403	0.0015	0.0	5008	,	,		19279	0.0		0.001	False		,,,				2504	0.002				p.V514A		Atlas-SNP	.											SIGLEC12,NS,haematopoietic_neoplasm,0,1	SIGLEC12	243	1	0			c.T1541C						PASS	.	G	ALA/VAL,ALA/VAL	0,4406		0,0,2203	164	127	140		1187,1541	-2.7	0	19	dbSNP_134	140	5,8595		0,5,4295	no	missense,missense	SIGLEC12	NM_033329.1,NM_053003.2	64,64	0,5,6498	GG,GA,AA		0.0581,0.0,0.0384	benign,benign	396/478,514/596	52000192	5,13001	2203	4300	6503	SO:0001583	missense	89858	exon7			ACGCCCACTGCTG	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.1541T>C	19.37:g.52000192A>G	ENSP00000291707:p.Val514Ala	95	0	0		132	15	0.113636	NM_053003	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	37	CCDS12833.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	.	0.001	-3.340068	0.00017	0.0	5.81E-4	ENSG00000254521	ENST00000291707	T	0.35789	1.29	1.34	-2.69	0.06022	.	.	.	.	.	T	0.10981	0.0268	N	0.03194	-0.395	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.10894	-1.0610	9	0.11485	T	0.65	.	0.7864	0.01049	0.2935:0.3354:0.2021:0.169	.	514;396	Q96PQ1;Q96PQ1-2	SIG12_HUMAN;.	A	514	ENSP00000291707:V514A	ENSP00000291707:V514A	V	-	2	0	SIGLEC12	56692004	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-5.050000	0.00156	-3.045000	0.00262	-1.416000	0.01114	GTG	A|1.000;G|0.000	0.000	strong		0.582	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003		G	52000192	A	G	52000192	3	3	28	1	0	0	0	0	1	0	0	0	14323	159	6	3	254	3	SIGLEC12	19	52000192	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	38673	52000192	7128791	669	12172											
NLRP7	199713	hgsc.bcm.edu	37	chr19	55451256	55451256	+	Missense_Mutation	SNP	G	G	T																															gatcggctgctgcgccaggaGctggaggtccctcagtgccc																								rs79513034	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55451256G>T	ENST00000590030.1	-	3	971	c.931C>A	c.(931-933)Ctc>Atc	p.L311I	NLRP7_ENST00000448121.2_Missense_Mutation_p.L311I|NLRP7_ENST00000340844.2_Missense_Mutation_p.L311I|NLRP7_ENST00000328092.5_Missense_Mutation_p.L311I|NLRP7_ENST00000446217.1_Missense_Mutation_p.L339I|NLRP7_ENST00000588756.1_Missense_Mutation_p.L311I|NLRP7_ENST00000592784.1_Missense_Mutation_p.L311I			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	311	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.			QL -> RI (in Ref. 4; AAI09126). {ECO:0000305}.			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)		TGCGCCAGGAGCTGGAGGTCC	0.627													.|||	26	0.00519169	0.0015	0.0029	5008	,	,		16625	0.0		0.0219	False		,,,				2504	0.0				p.L311I		Atlas-SNP	.											.	NLRP7	411	.	0			c.C931A						PASS	.	G	ILE/LEU,ILE/LEU,ILE/LEU	3,4403	6.2+/-15.9	0,3,2200	38	38	38		931,931,931	-1.9	0	19	dbSNP_131	38	135,8465	60.2+/-122.0	1,133,4166	no	missense,missense,missense	NLRP7	NM_001127255.1,NM_139176.3,NM_206828.3	5,5,5	1,136,6366	TT,TG,GG		1.5698,0.0681,1.061	benign,benign,benign	311/1038,311/1010,311/981	55451256	138,12868	2203	4300	6503	SO:0001583	missense	199713	exon4			CCAGGAGCTGGAG	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.931C>A	19.37:g.55451256G>T	ENSP00000465520:p.Leu311Ile	92	0	0		92	37	0.402174	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	37	CCDS33109.1	19	0.0086996336996337	0	0.0	3	0.008287292817679558	0	0.0	16	0.021108179419525065	G	4.165	0.029214	0.08054	6.81E-4	0.015698	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217	T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16	1.77	-1.85	0.07784	NACHT nucleoside triphosphatase (1);	.	.	.	.	T	0.46678	0.1405	L	0.39397	1.21	0.09310	N	1	P;P;P	0.39601	0.68;0.68;0.63	B;B;B	0.40066	0.318;0.318;0.212	T	0.47045	-0.9147	9	0.17369	T	0.5	.	3.7385	0.08520	0.2934:0.4095:0.2972:0.0	.	339;311;311	E7EPM2;Q8WX94;Q8WX94-2	.;NALP7_HUMAN;.	I	311;311;311;339	ENSP00000329568:L311I;ENSP00000409137:L311I;ENSP00000339491:L311I;ENSP00000414273:L339I	ENSP00000329568:L311I	L	-	1	0	NLRP7	60143068	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.029000	0.12329	-0.432000	0.07297	-0.368000	0.07277	CTC	G|0.989;T|0.011	0.011	strong		0.627	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		T	55451256	G	T	55451256	3	4	28	1	0	0	0	0	1	0	0	0	10491	971	34	4	2214	4	NLRP7	19	55451256	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	3451064	55451256	3677727	670	12173	150	2									
NLRP7	199713	hgsc.bcm.edu	37	chr19	55451258	55451258	+	Missense_Mutation	SNP	T	T	C																															tcggctgctgcgccaggagcTggaggtccctcagtgccctg																								rs77812009	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55451258T>C	ENST00000590030.1	-	3	969	c.929A>G	c.(928-930)cAg>cGg	p.Q310R	NLRP7_ENST00000448121.2_Missense_Mutation_p.Q310R|NLRP7_ENST00000340844.2_Missense_Mutation_p.Q310R|NLRP7_ENST00000328092.5_Missense_Mutation_p.Q310R|NLRP7_ENST00000446217.1_Missense_Mutation_p.Q338R|NLRP7_ENST00000588756.1_Missense_Mutation_p.Q310R|NLRP7_ENST00000592784.1_Missense_Mutation_p.Q310R			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	310	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.			QL -> RI (in Ref. 4; AAI09126). {ECO:0000305}.			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)		CGCCAGGAGCTGGAGGTCCCT	0.627													.|||	26	0.00519169	0.0015	0.0029	5008	,	,		16817	0.0		0.0219	False		,,,				2504	0.0				p.Q310R		Atlas-SNP	.											NLRP7_ENST00000328092,NS,lymphoid_neoplasm,+1,2	NLRP7	411	2	0			c.A929G						PASS	.	T	ARG/GLN,ARG/GLN,ARG/GLN	3,4403	6.2+/-15.9	0,3,2200	38	38	38		929,929,929	-3.5	0	19	dbSNP_131	38	136,8464	59.8+/-121.6	1,134,4165	no	missense,missense,missense	NLRP7	NM_001127255.1,NM_139176.3,NM_206828.3	43,43,43	1,137,6365	CC,CT,TT		1.5814,0.0681,1.0687	benign,benign,benign	310/1038,310/1010,310/981	55451258	139,12867	2203	4300	6503	SO:0001583	missense	199713	exon4			AGGAGCTGGAGGT	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.929A>G	19.37:g.55451258T>C	ENSP00000465520:p.Gln310Arg	92	0	0		92	38	0.413043	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	37	CCDS33109.1	19	0.0086996336996337	0	0.0	3	0.008287292817679558	0	0.0	16	0.021108179419525065	T	0.005	-2.144416	0.00332	6.81E-4	0.015814	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217	T;T;T;T	0.80824	-1.42;-1.42;-1.42;-1.42	1.77	-3.54	0.04653	NACHT nucleoside triphosphatase (1);	.	.	.	.	T	0.30293	0.0760	N	0.02539	-0.55	0.09310	N	1	B;B;B	0.09022	0.002;0.002;0.002	B;B;B	0.12156	0.007;0.007;0.002	T	0.37596	-0.9699	9	0.06099	T	0.92	.	3.6467	0.08187	0.1766:0.364:0.0:0.4594	.	338;310;310	E7EPM2;Q8WX94;Q8WX94-2	.;NALP7_HUMAN;.	R	310;310;310;338	ENSP00000329568:Q310R;ENSP00000409137:Q310R;ENSP00000339491:Q310R;ENSP00000414273:Q338R	ENSP00000329568:Q310R	Q	-	2	0	NLRP7	60143070	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.617000	0.24359	-1.039000	0.03275	-1.457000	0.01029	CAG	T|0.989;C|0.011	0.011	strong		0.627	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		C	55451258	T	C	55451258	3	2	28	1	0	0	0	0	1	0	0	0	10491	1580	55	3	2216	3	NLRP7	19	55451258	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	2	55451258	3677725	671	12174	150	2									
NLRP7	199713	hgsc.bcm.edu	37	chr19	55451613	55451613	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcagtctgtccagtccagcaTacactttttggccagcgtgg	7	11	11	12	1	1	0	0	0	1	0	3	0	3	0	3	2	3	2	3	2	1	3	rs104895529	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55451613T>G	ENST00000590030.1	-	3	614	c.574A>C	c.(574-576)Atg>Ctg	p.M192L	NLRP7_ENST00000448121.2_Missense_Mutation_p.M192L|NLRP7_ENST00000340844.2_Missense_Mutation_p.M192L|NLRP7_ENST00000328092.5_Missense_Mutation_p.M192L|NLRP7_ENST00000446217.1_Missense_Mutation_p.M220L|NLRP7_ENST00000588756.1_Missense_Mutation_p.M192L|NLRP7_ENST00000592784.1_Missense_Mutation_p.M192L			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	192	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)		CAGTCCAGCATACACTTTTTG	0.582													.|||	4	0.000798722	0.0	0.0	5008	,	,		19202	0.0		0.003	False		,,,				2504	0.001				p.M192L		Atlas-SNP	.											.	NLRP7	411	.	0			c.A574C						PASS	.	T	LEU/MET,LEU/MET,LEU/MET	3,4403	6.2+/-15.9	0,3,2200	124	122	122	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	574,574,574	-0.6	0	19	dbSNP_132	122	36,8564	25.1+/-72.6	1,34,4265	yes	missense,missense,missense	NLRP7	NM_001127255.1,NM_139176.3,NM_206828.3	15,15,15	1,37,6465	GG,GT,TT		0.4186,0.0681,0.2999	benign,benign,benign	192/1038,192/1010,192/981	55451613	39,12967	2203	4300	6503	SO:0001583	missense	199713	exon4			CCAGCATACACTT	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.574A>C	19.37:g.55451613T>G	ENSP00000465520:p.Met192Leu	125	0	0		108	56	0.518519	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	37	CCDS33109.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	9.712	1.157458	0.21454	6.81E-4	0.004186	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217	T;T;T;T	0.80033	-1.33;-1.33;-1.33;-1.33	1.88	-0.548	0.11833	NACHT nucleoside triphosphatase (1);	0.000000	0.38837	N	0.001543	T	0.68393	0.2996	L	0.41632	1.29	0.09310	N	1	B;B;B;B	0.34147	0.438;0.438;0.438;0.384	B;B;B;B	0.40782	0.34;0.34;0.34;0.23	T	0.59423	-0.7457	10	0.49607	T	0.09	.	0.1778	0.00120	0.2414:0.1591:0.2466:0.3529	.	220;192;192;192	E7EPM2;Q32MH9;Q8WX94;Q8WX94-2	.;.;NALP7_HUMAN;.	L	192;192;192;220	ENSP00000329568:M192L;ENSP00000409137:M192L;ENSP00000339491:M192L;ENSP00000414273:M220L	ENSP00000329568:M192L	M	-	1	0	NLRP7	60143425	0.008000	0.16893	0.016000	0.15963	0.144000	0.21451	0.142000	0.16096	-0.222000	0.09958	0.379000	0.24179	ATG	T|0.998;G|0.002	0.002	strong		0.582	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176		G	55451613	T	G	55451613	3	3	28	1	0	0	0	0	1	0	0	0	10491	1406	49	5	2571	5	NLRP7	19	55451613	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	355	55451613	3677370	672	12175											
ZNF418	147686	hgsc.bcm.edu	37	chr19	58437767	58437767	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gtaaatgtttttccacattcCctgcattcataaggcctttc	9	16	5	11	0	1	0	1	0	0	0	4	0	3	0	3	1	1	3	3	1	3	7	rs199612939	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:58437767C>A	ENST00000396147.1	-	4	2073	c.1782G>T	c.(1780-1782)agG>agT	p.R594S	ZNF418_ENST00000600989.1_Intron|ZNF418_ENST00000595830.1_Missense_Mutation_p.R594S|ZNF418_ENST00000599852.1_Missense_Mutation_p.R509S|ZNF418_ENST00000599086.1_5'Flank|ZNF418_ENST00000425570.3_Missense_Mutation_p.R615S	NM_133460.1	NP_597717.1	Q8TF45	ZN418_HUMAN	zinc finger protein 418	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)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	31		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;0.0158)		TTCCACATTCCCTGCATTCAT	0.448																																					p.R594S		Atlas-SNP	.											.	ZNF418	76	.	0			c.G1782T						PASS	.	C	SER/ARG	8,4390		0,8,2191	86	89	88		1782	-5.5	0	19		88	87,8513		1,85,4214	yes	missense	ZNF418	NM_133460.1	110	1,93,6405	AA,AC,CC		1.0116,0.1819,0.7309	benign	594/677	58437767	95,12903	2199	4300	6499	SO:0001583	missense	147686	exon4			ACATTCCCTGCAT	AB075836, AY695825	CCDS42642.1	19q13.43	2013-01-08				ENSG00000196724		"Zinc fingers, C2H2-type", "-"	20647	protein-coding gene	gene with protein product						11853319	Standard	NM_133460		Approved	KIAA1956, FLJ31551	uc002qqs.1	Q8TF45		ENST00000396147.1:c.1782G>T	19.37:g.58437767C>A	ENSP00000379451:p.Arg594Ser	87	0	0		53	8	0.150943	NM_133460	Q2M1S2|Q670L5|Q96N18	Missense_Mutation	SNP	ENST00000396147.1	37	CCDS42642.1	12	0.005494505494505495	0	0.0	3	0.008287292817679558	0	0.0	9	0.011873350923482849	.	0	-2.840553	0.00068	0.001819	0.010116	ENSG00000196724	ENST00000396147;ENST00000425570;ENST00000545403	T;T	0.16457	2.34;2.34	2.76	-5.51	0.02568	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02193	0.0068	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.11203	-1.0597	9	0.07813	T	0.8	.	1.0134	0.01502	0.1849:0.1646:0.3013:0.3492	.	594	Q8TF45	ZN418_HUMAN	S	594;615;560	ENSP00000379451:R594S;ENSP00000407039:R615S	ENSP00000379451:R594S	R	-	3	2	ZNF418	63129579	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-10.328000	0.00007	-4.068000	0.00076	-1.399000	0.01144	AGG	C|0.989;A|0.011	0.011	strong		0.448	ZNF418-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466693.1	NM_133460		A	58437767	C	A	58437767	3	1	28	1	0	0	0	0	1	0	0	0	17910	622	22	4	252	4	ZNF418	19	58437767	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2986154	58437767	691216	673	12176											
ZSCAN22	342945	hgsc.bcm.edu	37	chr19	58850357	58850357	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acacgggggagcggccctacGagtgtgacgcgtgtgggaaa	9	5	18	9	5	0	1	0	1	0	0	0	4	0	3	1	4	2	0	1	4	2	1	rs138944686	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:58850357G>A	ENST00000329665.4	+	3	1288	c.1141G>A	c.(1141-1143)Gag>Aag	p.E381K		NM_181846.2	NP_862829.1	P10073	ZSC22_HUMAN	zinc finger and SCAN domain containing 22	381					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)		GCGGCCCTACGAGTGTGACGC	0.607													G|||	69	0.013778	0.025	0.0202	5008	,	,		19277	0.0		0.0209	False		,,,				2504	0.001				p.E381K		Atlas-SNP	.											.	ZSCAN22	47	.	0			c.G1141A						PASS	.	G	LYS/GLU	69,4337	63.5+/-100.7	1,67,2135	68	64	65		1141	0.3	0.2	19	dbSNP_134	65	87,8513	51.1+/-111.2	1,85,4214	no	missense	ZSCAN22	NM_181846.2	56	2,152,6349	AA,AG,GG		1.0116,1.566,1.1994	possibly-damaging	381/492	58850357	156,12850	2203	4300	6503	SO:0001583	missense	342945	exon3			CCCTACGAGTGTG	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.1141G>A	19.37:g.58850357G>A	ENSP00000332433:p.Glu381Lys	28	0	0		47	20	0.425532	NM_181846	Q15922|Q7Z3L8	Missense_Mutation	SNP	ENST00000329665.4	37	CCDS12975.1	39	0.017857142857142856	14	0.028455284552845527	8	0.022099447513812154	0	0.0	17	0.022427440633245383	G	8.214	0.801043	0.16397	0.01566	0.010116	ENSG00000182318	ENST00000329665	T	0.06608	3.28	3.72	0.353	0.16058	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00580	0.0019	N	0.01284	-0.91	0.09310	N	1	B	0.27117	0.168	B	0.15052	0.012	T	0.44375	-0.9332	9	0.27082	T	0.32	.	0.7237	0.00945	0.2251:0.1908:0.3878:0.1963	.	381	P10073	ZSC22_HUMAN	K	381	ENSP00000332433:E381K	ENSP00000332433:E381K	E	+	1	0	ZSCAN22	63542169	0.000000	0.05858	0.163000	0.22734	0.372000	0.29890	-2.584000	0.00904	0.344000	0.23847	-0.300000	0.09419	GAG	G|0.986;A|0.014	0.014	strong		0.607	ZSCAN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466765.1	NM_181846		A	58850357	G	A	58850357	3	1	28	1	0	0	0	0	1	0	0	0	18249	1059	37	1	1147	1	ZSCAN22	19	58850357	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	412590	58850357	278626	674	12177											
ZNF324	25799	hgsc.bcm.edu	37	chr19	58983321	58983321	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgtgtgtacgcagtgtggcCgcgccttccgtgagcgcccg	3	9	15	14	7	0	1	0	1	0	0	2	1	1	1	4	1	2	2	4	1	1	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:58983321C>T	ENST00000536459.2	+	4	2171	c.1462C>T	c.(1462-1464)Cgc>Tgc	p.R488C	ZNF324_ENST00000196482.3_Missense_Mutation_p.R488C|ZNF324_ENST00000535298.1_Missense_Mutation_p.R265C|ZNF446_ENST00000596341.1_5'Flank			O75467	Z324A_HUMAN	zinc finger protein 324	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)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(2)|prostate(2)|urinary_tract(2)	16		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)		GCAGTGTGGCCGCGCCTTCCG	0.692																																					p.R488C		Atlas-SNP	.											ZNF324,NS,carcinoma,-2,1	ZNF324	46	1	0			c.C1462T						PASS	.						32	34	34					19																	58983321		2201	4299	6500	SO:0001583	missense	25799	exon4			TGTGGCCGCGCCT	AF060503	CCDS12981.1	19q13.43	2013-01-08				ENSG00000083812		"Zinc fingers, C2H2-type", "-"	14096	protein-coding gene	gene with protein product							Standard	NM_014347		Approved	ZF5128, ZNF324A	uc002qsw.2	O75467		ENST00000536459.2:c.1462C>T	19.37:g.58983321C>T	ENSP00000444812:p.Arg488Cys	27	0	0		36	14	0.388889	NM_014347	B3KRX1	Missense_Mutation	SNP	ENST00000536459.2	37	CCDS12981.1	.	.	.	.	.	.	.	.	.	.	C	13.54	2.268427	0.40095	.	.	ENSG00000083812	ENST00000196482;ENST00000536459;ENST00000539101;ENST00000535298	T;T;T	0.19806	2.12;2.12;2.12	3.84	3.84	0.44239	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.39475	N	0.001353	T	0.46386	0.1390	M	0.87547	2.89	0.45108	D	0.998126	D	0.69078	0.997	P	0.62740	0.906	T	0.53933	-0.8368	10	0.87932	D	0	.	11.5508	0.50719	0.0:1.0:0.0:0.0	.	488	O75467	Z324A_HUMAN	C	488;488;478;265	ENSP00000196482:R488C;ENSP00000444812:R488C;ENSP00000439588:R265C	ENSP00000196482:R488C	R	+	1	0	ZNF324	63675133	0.016000	0.18221	0.998000	0.56505	0.157000	0.22087	0.719000	0.25881	2.433000	0.82419	0.400000	0.26472	CGC	.	.	none		0.692	ZNF324-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467044.1	NM_014347		T	58983321	C	T	58983321	3	4	28	1	0	0	0	0	1	0	0	0	17859	652	23	1	1472	1	ZNF324	19	58983321	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	132964	58983321	145662	675	12178											
SDCBP2	27111	hgsc.bcm.edu	37	chr20	1301053	1301053	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cctctagagatgggtacaggGatgacatggctgattctcag	10	10	13	8	0	2	3	1	2	2	1	3	5	2	4	1	3	1	2	1	3	2	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:1301053G>A	ENST00000360779.3	-	2	181	c.8C>T	c.(7-9)tCc>tTc	p.S3F	SDCBP2_ENST00000339987.3_Missense_Mutation_p.S3F|SDCBP2_ENST00000381812.1_Missense_Mutation_p.S3F	NM_080489.4	NP_536737.3	Q9H190	SDCB2_HUMAN	syndecan binding protein (syntenin) 2	3					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						TGGGTACAGGGATGACATGGC	0.552																																					p.S3F		Atlas-SNP	.											.	SDCBP2	78	.	0			c.C8T						PASS	.						142	138	139					20																	1301053		1976	4166	6142	SO:0001583	missense	27111	exon2			TACAGGGATGACA	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.8C>T	20.37:g.1301053G>A	ENSP00000354013:p.Ser3Phe	85	0	0		89	22	0.247191	NM_080489	O95892|Q5W0X1|Q9BZ42|Q9H567|Q9NRY8	Missense_Mutation	SNP	ENST00000360779.3	37	CCDS42848.1	.	.	.	.	.	.	.	.	.	.	G	10.74	1.434411	0.25813	.	.	ENSG00000125775	ENST00000381812;ENST00000360779;ENST00000339987	T;T;T	0.44881	0.91;0.91;0.91	4.83	0.43	0.16515	.	1.007080	0.07972	N	0.984107	T	0.54711	0.1875	L	0.55481	1.735	0.23204	N	0.998129	P;D	0.67145	0.911;0.996	B;D	0.63033	0.382;0.91	T	0.47156	-0.9139	10	0.87932	D	0	-5.793	9.2402	0.37491	0.3788:0.0:0.6212:0.0	.	3;3	B4DKI5;Q9H190	.;SDCB2_HUMAN	F	3	ENSP00000371233:S3F;ENSP00000354013:S3F;ENSP00000342935:S3F	ENSP00000342935:S3F	S	-	2	0	SDCBP2	1249053	0.635000	0.27199	0.232000	0.24009	0.011000	0.07611	3.304000	0.51866	0.243000	0.21327	-0.258000	0.10820	TCC	.	.	none		0.552	SDCBP2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077513.2	NM_080489		A	1301053	G	A	1301053	3	1	28	1	0	0	0	0	1	0	0	0	13971	1174	41	2	902	2	SDCBP2	20	1301053	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10		1301053	61724467	676	12179											
RASSF2	9770	hgsc.bcm.edu	37	chr20	4768282	4768282	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acccaaagggaactcacgtcGtaggtgacttcctccacctg	10	8	9	14	2	1	1	1	1	0	0	4	2	3	2	4	2	1	1	4	2	3	2	rs6052876	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:4768282G>A	ENST00000379400.3	-	10	1005	c.810C>T	c.(808-810)taC>taT	p.Y270Y	RASSF2_ENST00000478553.1_5'UTR|RASSF2_ENST00000379376.2_Silent_p.Y270Y	NM_014737.2	NP_055552.1	P50749	RASF2_HUMAN	Ras association (RalGDS/AF-6) domain family member 2	270					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						AACTCACGTCGTAGGTGACTT	0.537													A|||	236	0.0471246	0.171	0.0115	5008	,	,		19617	0.0		0.0	False		,,,				2504	0.002				p.Y270Y	Melanoma(158;1891 3343 50738)	Atlas-SNP	.											.	RASSF2	75	.	0			c.C810T						PASS	.	A	,	679,3727	763.0+/-413.2	61,557,1585	117	94	102		810,810	1.8	1	20	dbSNP_114	102	9,8591	818.9+/-406.8	0,9,4291	no	coding-synonymous,coding-synonymous	RASSF2	NM_014737.2,NM_170774.1	,	61,566,5876	AA,AG,GG		0.1047,15.4108,5.2899	,	270/327,270/327	4768282	688,12318	2203	4300	6503	SO:0001819	synonymous_variant	9770	exon10			CACGTCGTAGGTG	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.810C>T	20.37:g.4768282G>A		114	0	0		98	36	0.367347	NM_014737	A6NIX9|A8K5Z3|Q17S06|Q53HD0|Q6AHZ2|Q8IZA5	Silent	SNP	ENST00000379400.3	37	CCDS13083.1																																																																																			G|0.954;A|0.046	0.046	strong		0.537	RASSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077828.1	NM_014737		A	4768282	G	A	4768282	2	1	28	1	0	0	0	0	0	0	0	1	13101	1140	40	1		1	RASSF2	20	4768282	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	3467229	4768282	58257238	677	12180											
SLC23A2	9962	hgsc.bcm.edu	37	chr20	4855309	4855309	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggaaatttaacatttctggcGtattgagaaaacagtaatac	16	12	8	5	1	1	1	0	1	1	1	1	3	1	2	0	2	3	2	0	2	7	7	rs41282100	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:4855309G>A	ENST00000379333.1	-	10	1250	c.858C>T	c.(856-858)taC>taT	p.Y286Y	SLC23A2_ENST00000424750.2_Silent_p.Y172Y|SLC23A2_ENST00000338244.1_Silent_p.Y286Y|SLC23A2_ENST00000468355.1_5'UTR	NM_203327.1	NP_976072.1	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 2	286					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						CATTTCTGGCGTATTGAGAAA	0.368													A|||	32	0.00638978	0.0129	0.0101	5008	,	,		20889	0.0		0.008	False		,,,				2504	0.0				p.Y286Y		Atlas-SNP	.											.	SLC23A2	62	.	0			c.C858T						PASS	.	A	,	55,4351	821.2+/-416.4	0,55,2148	119	122	121		858,858	3.7	1	20	dbSNP_127	121	107,8493	814.5+/-407.0	1,105,4194	no	coding-synonymous,coding-synonymous	SLC23A2	NM_005116.5,NM_203327.1	,	1,160,6342	AA,AG,GG		1.2442,1.2483,1.2456	,	286/651,286/651	4855309	162,12844	2203	4300	6503	SO:0001819	synonymous_variant	9962	exon10			TCTGGCGTATTGA	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.858C>T	20.37:g.4855309G>A		79	0	0		60	29	0.483333	NM_203327	B4DJZ1|Q8WWR4|Q92512|Q96D54|Q9UNU1|Q9UP85	Silent	SNP	ENST00000379333.1	37	CCDS13085.1	11	0.005036630036630037	3	0.006097560975609756	5	0.013812154696132596	0	0.0	3	0.00395778364116095	A	0.141	-1.102585	0.01828	0.012483	0.012442	ENSG00000089057	ENST00000423430	.	.	.	5.9	3.67	0.42095	.	.	.	.	.	T	0.50000	0.1590	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44772	-0.9306	4	.	.	.	-10.7793	8.3011	0.32014	0.7051:0.0:0.2949:0.0	rs41282100	.	.	.	C	43	.	.	R	-	1	0	SLC23A2	4803309	1.000000	0.71417	0.982000	0.44146	0.006000	0.05464	2.001000	0.40825	0.161000	0.19458	-0.982000	0.02568	CGC	G|0.990;A|0.010	0.010	strong		0.368	SLC23A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077832.1			A	4855309	G	A	4855309	2	1	28	1	0	0	0	0	0	0	0	1	14478	1140	40	1		1	SLC23A2	20	4855309	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	87027	4855309	58170211	678	12181											
C20orf30	29058	hgsc.bcm.edu	37	chr20	5086918	5086918	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aacagcacagtggcaagtgcGatggccttataagggatctt	12	9	12	8	1	1	0	0	0	1	0	1	2	1	1	1	3	3	2	1	3	4	3	rs147693982	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:5086918G>A	ENST00000379286.2	-	4	558	c.138C>T	c.(136-138)atC>atT	p.I46I	TMEM230_ENST00000202834.7_Silent_p.I46I|TMEM230_ENST00000492419.1_5'UTR|TMEM230_ENST00000379279.2_Silent_p.I46I|TMEM230_ENST00000379277.2_Silent_p.I46I|TMEM230_ENST00000342308.5_Silent_p.I109I|TMEM230_ENST00000379283.2_Silent_p.I46I	NM_001009924.1	NP_001009924.1	Q96A57	TM230_HUMAN	transmembrane protein 230	46						integral component of membrane (GO:0016021)											TGGCAAGTGCGATGGCCTTAT	0.443													G|||	21	0.00419329	0.0	0.0058	5008	,	,		15312	0.0		0.0169	False		,,,				2504	0.0				p.I109I		Atlas-SNP	.											.	.	.	.	0			c.C327T						PASS	.	G	,,,	26,4380	32.6+/-62.9	0,26,2177	63	62	62		327,138,138,138	-5.4	0.7	20	dbSNP_134	62	156,8444	74.5+/-137.1	2,152,4146	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	C20orf30	NM_001009923.1,NM_001009924.1,NM_001009925.1,NM_014145.4	,,,	2,178,6323	AA,AG,GG		1.814,0.5901,1.3994	,,,	109/184,46/121,46/121,46/121	5086918	182,12824	2203	4300	6503	SO:0001819	synonymous_variant	29058	exon4			AAGTGCGATGGCC	AF161392	CCDS13086.1, CCDS33438.1	20p13	2012-03-16	2012-03-16	2012-03-16	ENSG00000089063	ENSG00000089063			15876	protein-coding gene	gene with protein product			"chromosome 20 open reading frame 30"	C20orf30			Standard	XM_005260713		Approved	HSPC274	uc002wlk.3	Q96A57	OTTHUMG00000031796	ENST00000379286.2:c.138C>T	20.37:g.5086918G>A		88	0	0		81	43	0.530864	NM_001009923	B2RDM8|D3DVZ9|Q0VGC8|Q5TDS5|Q96ES2|Q9P0A7	Silent	SNP	ENST00000379286.2	37	CCDS13086.1																																																																																			G|0.990;A|0.010	0.010	strong		0.443	TMEM230-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077846.1			A	5086918	G	A	5086918	2	1	28	1	0	0	0	0	0	0	0	1	2112	1048	37	1		1	C20orf30	20	5086918	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	231609	5086918	57938602	679	12182											
CSRP2BP	57325	hgsc.bcm.edu	37	chr20	18143261	18143261	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagagaaaagaggaagcctcAgctggagaaggacacaaagc	18	3	13	7	0	1	3	1	0	0	3	1	7	1	5	1	3	3	1	1	3	6	1			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:18143261A>G	ENST00000435364.3	+	6	1684	c.1343A>G	c.(1342-1344)cAg>cGg	p.Q448R	CSRP2BP_ENST00000377681.3_Missense_Mutation_p.Q447R|CSRP2BP_ENST00000489634.2_Missense_Mutation_p.Q320R	NM_020536.4	NP_065397	Q9H8E8	CSR2B_HUMAN	CSRP2 binding protein	448					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						AGGAAGCCTCAGCTGGAGAAG	0.502																																					p.Q448R		Atlas-SNP	.											.	CSRP2BP	80	.	0			c.A1343G						PASS	.						71	74	73					20																	18143261		2203	4300	6503	SO:0001583	missense	57325	exon6			AGCCTCAGCTGGA	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.1343A>G	20.37:g.18143261A>G	ENSP00000392318:p.Gln448Arg	72	0	0		63	30	0.47619	NM_020536	A2A2I5|Q96GW6|Q96IH3|Q9HBF0|Q9UIY5	Missense_Mutation	SNP	ENST00000435364.3	37	CCDS13133.1	.	.	.	.	.	.	.	.	.	.	A	4.422	0.078067	0.08485	.	.	ENSG00000149474	ENST00000278816;ENST00000377681;ENST00000435364;ENST00000489634	T;T;T;T	0.15017	2.46;2.46;2.46;2.47	6.17	0.00674	0.14068	.	0.384216	0.28859	N	0.013905	T	0.07503	0.0189	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.38628	-0.9652	10	0.16420	T	0.52	-20.6595	7.114	0.25407	0.3473:0.3538:0.0:0.2988	.	320;448	Q9H8E8-2;Q9H8E8	.;CSR2B_HUMAN	R	448;447;448;320	ENSP00000278816:Q448R;ENSP00000366909:Q447R;ENSP00000392318:Q448R;ENSP00000425909:Q320R	ENSP00000278816:Q448R	Q	+	2	0	CSRP2BP	18091261	0.192000	0.23301	0.001000	0.08648	0.983000	0.72400	0.681000	0.25320	-0.235000	0.09767	0.533000	0.62120	CAG	.	.	none		0.502	CSRP2BP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078152.5	NM_020536		G	18143261	A	G	18143261	3	3	28	1	0	0	0	0	1	0	0	0	3970	188	7	3	1365	3	CSRP2BP	20	18143261	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	13056343	18143261	44882259	680	12183											
GZF1	64412	hgsc.bcm.edu	37	chr20	23350290	23350290	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacgccctccagcgccaccGccgcatccacacaggggaga	10	2	10	19	4	0	1	0	0	0	1	2	2	2	1	6	2	2	1	6	2	1	0	rs144872945	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:23350290G>A	ENST00000338121.5	+	5	1774	c.1697G>A	c.(1696-1698)cGc>cAc	p.R566H	GZF1_ENST00000377051.2_Missense_Mutation_p.R566H|GZF1_ENST00000542987.1_Missense_Mutation_p.R75H|GZF1_ENST00000544236.1_Missense_Mutation_p.R90H			Q9H116	GZF1_HUMAN	GDNF-inducible zinc finger protein 1	566					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)					CAGCGCCACCGCCGCATCCAC	0.632													G|||	5	0.000998403	0.0	0.0014	5008	,	,		18962	0.0		0.004	False		,,,				2504	0.0				p.R566H		Atlas-SNP	.											GZF1,NS,adenocarcinoma,0,1	GZF1	61	1	0			c.G1697A						PASS	.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	94	85	88		1697	3.7	1	20	dbSNP_134	88	12,8588	9.1+/-34.3	0,12,4288	yes	missense	GZF1	NM_022482.3	29	0,13,6490	AA,AG,GG		0.1395,0.0227,0.1	benign	566/712	23350290	13,12993	2203	4300	6503	SO:0001583	missense	64412	exon4			GCCACCGCCGCAT	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.1697G>A	20.37:g.23350290G>A	ENSP00000338290:p.Arg566His	80	0	0		78	33	0.423077	NM_022482	A8K199|B2RBC3|B3KPL4|B4DF58|D3DW39|Q54A22|Q96N08|Q9BQK9|Q9H117|Q9H6W6	Missense_Mutation	SNP	ENST00000338121.5	37	CCDS13151.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	9.792	1.178312	0.21787	2.27E-4	0.001395	ENSG00000125812	ENST00000544236;ENST00000338121;ENST00000542987;ENST00000377051	T;T;T;T	0.37584	3.17;1.19;3.17;1.19	5.95	3.74	0.42951	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.205916	0.32055	N	0.006644	T	0.15739	0.0379	N	0.26092	0.79	0.35685	D	0.814363	B	0.06786	0.001	B	0.06405	0.002	T	0.16129	-1.0413	10	0.16896	T	0.51	.	7.9996	0.30288	0.8298:0.0:0.1702:0.0	.	566	Q9H116	GZF1_HUMAN	H	90;566;75;566	ENSP00000445458:R90H;ENSP00000338290:R566H;ENSP00000445118:R75H;ENSP00000366250:R566H	ENSP00000338290:R566H	R	+	2	0	GZF1	23298290	1.000000	0.71417	0.993000	0.49108	0.987000	0.75469	6.157000	0.71846	0.545000	0.28902	0.655000	0.94253	CGC	G|0.999;A|0.001	0.001	strong		0.632	GZF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078333.1	NM_022482		A	23350290	G	A	23350290	3	1	28	1	0	0	0	0	1	0	0	0	6923	1087	38	1	1711	1	GZF1	20	23350290	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	5207029	23350290	39675230	681	12184											
ACSS1	84532	hgsc.bcm.edu	37	chr20	25003705	25003705	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccatgctctctggggcgcaAacagggtcctccttggccat	6	9	11	15	1	1	0	0	0	1	0	4	0	3	0	4	4	2	2	4	4	1	1	rs41308619	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:25003705A>C	ENST00000323482.4	-	5	910	c.831T>G	c.(829-831)gtT>gtG	p.V277V	ACSS1_ENST00000537502.1_Silent_p.V194V|ACSS1_ENST00000542618.1_Silent_p.V156V|ACSS1_ENST00000432802.2_Silent_p.V277V	NM_001252675.1|NM_032501.3	NP_001239604.1|NP_115890.2	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	277				V -> M (in Ref. 4; AAH39261). {ECO:0000305}.	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)	CTGGGGCGCAAACAGGGTCCT	0.612													C|||	176	0.0351438	0.0968	0.0274	5008	,	,		20418	0.0		0.0278	False		,,,				2504	0.001				p.V277V		Atlas-SNP	.											.	ACSS1	46	.	0			c.T831G						PASS	.	C		412,3994	787.6+/-414.9	19,374,1810	63	52	55		831	-1.6	0	20	dbSNP_127	55	188,8412	810.6+/-407.1	1,186,4113	no	coding-synonymous	ACSS1	NM_032501.2		20,560,5923	CC,CA,AA		2.186,9.3509,4.6133		277/690	25003705	600,12406	2203	4300	6503	SO:0001819	synonymous_variant	84532	exon5			GGCGCAAACAGGG		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.831T>G	20.37:g.25003705A>C		46	0	0		45	16	0.355556	NM_001252677	B3KXL2|B4DJZ3|D3DW48|F5H6F4|F8W7Y1|Q5TF42|Q8IV99|Q8N234|Q96JI1|Q96JX6|Q9NU28	Silent	SNP	ENST00000323482.4	37	CCDS13167.1																																																																																			A|0.960;C|0.040	0.040	strong		0.612	ACSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078386.2	NM_032501		C	25003705	A	C	25003705	2	2	28	1	0	0	0	0	0	0	0	1	188	1	1	5		5	ACSS1	20	25003705	Silent	SNP	A	TCGA-G8-6914-01A-11D-2210-10	1653415	25003705	38021815	682	12185											
VSX1	30813	hgsc.bcm.edu	37	chr20	25060143	25060143	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcctgtcttcagactggctGtcctcatctgatggcacaga	7	13	9	12	0	4	3	2	1	2	2	6	3	6	3	2	2	0	2	2	2	0	2	rs140122268	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:25060143G>C	ENST00000376709.4	-	2	695	c.432C>G	c.(430-432)gaC>gaG	p.D144E	VSX1_ENST00000424574.1_Missense_Mutation_p.D144E|VSX1_ENST00000451258.1_Missense_Mutation_p.D144E|VSX1_ENST00000444511.2_Missense_Mutation_p.D144E|VSX1_ENST00000429762.3_Missense_Mutation_p.D144E|VSX1_ENST00000376707.3_Missense_Mutation_p.D144E	NM_014588.5	NP_055403.2	Q9NZR4	VSX1_HUMAN	visual system homeobox 1	144	Asp/Glu-rich (acidic).		D -> E (in PPCD1 and KTCN1; dbSNP:rs140122268). {ECO:0000269|PubMed:11978762, ECO:0000269|PubMed:15623752}.		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						CAGACTGGCTGTCCTCATCTG	0.502													G|||	11	0.00219649	0.0	0.0029	5008	,	,		19019	0.001		0.005	False		,,,				2504	0.0031				p.D144E		Atlas-SNP	.											.	VSX1	20	.	0			c.C432G	GRCh37	CM020983	VSX1	M	rs140122268	PASS	.	G	GLU/ASP,GLU/ASP	4,4402	8.1+/-20.4	0,4,2199	59	46	50		432,432	1.8	0.9	20	dbSNP_134	50	31,8569	21.6+/-65.8	0,31,4269	yes	missense,missense	VSX1	NM_014588.4,NM_199425.1	45,45	0,35,6468	CC,CG,GG		0.3605,0.0908,0.2691	possibly-damaging,possibly-damaging	144/366,144/240	25060143	35,12971	2203	4300	6503	SO:0001583	missense	30813	exon2			CTGGCTGTCCTCA	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.432C>G	20.37:g.25060143G>C	ENSP00000365899:p.Asp144Glu	29	0	0		39	20	0.512821	NM_014588	B9EGJ4|D1MF28|Q0GM60|Q0GM61|Q0GM62|Q0GM63|Q0GM64|Q0GM65|Q5TF40|Q5TF41|Q9HCU3|Q9NU27	Missense_Mutation	SNP	ENST00000376709.4	37	CCDS13168.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	G	11.20	1.568006	0.28003	9.08E-4	0.003605	ENSG00000100987	ENST00000429762;ENST00000444511;ENST00000424574;ENST00000451258;ENST00000376709;ENST00000376707	D;D;D;D;D;D	0.92965	-2.89;-3.14;-2.88;-2.99;-2.99;-3.05	5.01	1.75	0.24633	.	0.158273	0.56097	N	0.000035	D	0.85124	0.5625	L	0.47716	1.5	0.80722	D	1	B;B;B;B	0.29136	0.234;0.027;0.122;0.023	B;B;B;B	0.35859	0.212;0.013;0.16;0.016	T	0.80099	-0.1524	10	0.44086	T	0.13	.	9.0206	0.36198	0.0:0.1814:0.5437:0.2748	.	144;144;144;144	Q9NZR4-7;Q9NZR4-8;Q9NZR4-2;Q9NZR4	.;.;.;VSX1_HUMAN	E	144	ENSP00000401690:D144E;ENSP00000387720:D144E;ENSP00000399496:D144E;ENSP00000389654:D144E;ENSP00000365899:D144E;ENSP00000365897:D144E	ENSP00000365897:D144E	D	-	3	2	VSX1	25008143	1.000000	0.71417	0.933000	0.37362	0.545000	0.35147	0.397000	0.20883	0.188000	0.20168	0.462000	0.41574	GAC	G|0.997;C|0.003	0.003	strong		0.502	VSX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078384.3			C	25060143	G	C	25060143	3	2	28	1	0	0	0	0	1	0	0	0	17246	1368	48	4	774	4	VSX1	20	25060143	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	56438	25060143	37965377	683	12186											
TGM2	7052	hgsc.bcm.edu	37	chr20	36766591	36766591	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagatcccattgtagctgacGgtgcgggcacagagcaggag	11	6	15	9	2	0	3	0	1	0	2	1	4	1	4	1	3	3	4	1	3	2	2	rs140171902	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:36766591G>A	ENST00000361475.2	-	10	1712	c.1539C>T	c.(1537-1539)acC>acT	p.T513T	TGM2_ENST00000536701.1_Silent_p.T432T|TGM2_ENST00000536724.1_Silent_p.T453T	NM_004613.2|NM_198951.1	NP_004604.2|NP_945189.1	P21980	TGM2_HUMAN	transglutaminase 2	513					apoptotic cell clearance (GO:0043277)|blood vessel remodeling (GO:0001974)|branching involved in salivary gland morphogenesis (GO:0060445)|isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein homooligomerization (GO:0051260)|salivary gland cavitation (GO:0060662)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			endometrium(2)|large_intestine(11)|liver(1)|lung(7)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Myeloproliferative disorder(115;0.00878)			L-Glutamine(DB00130)	TGTAGCTGACGGTGCGGGCAC	0.577													G|||	3	0.000599042	0.0	0.0029	5008	,	,		17458	0.0		0.001	False		,,,				2504	0.0				p.T513T		Atlas-SNP	.											.	TGM2	88	.	0			c.C1539T						PASS	.	G	,	0,4406		0,0,2203	93	70	78		1539,1539	-7.9	0.8	20	dbSNP_134	78	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	TGM2	NM_004613.2,NM_198951.1	,	0,5,6498	AA,AG,GG		0.0581,0.0,0.0384	,	513/688,513/549	36766591	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	7052	exon10			GCTGACGGTGCGG	M98478	CCDS13302.1	20q12	2013-05-02	2013-05-02		ENSG00000198959	ENSG00000198959	2.3.2.13	"Transglutaminases"	11778	protein-coding gene	gene with protein product	"C polypeptide, protein-glutamine-gamma-glutamyltransferase"	190196	"transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase)"			7912692, 11390390	Standard	NM_004613		Approved	TGC	uc002xhr.3	P21980	OTTHUMG00000032437	ENST00000361475.2:c.1539C>T	20.37:g.36766591G>A		127	0	0		154	75	0.487013	NM_198951	E1P5V9|Q16436|Q6B838|Q9BTN7|Q9UH35	Silent	SNP	ENST00000361475.2	37	CCDS13302.1																																																																																			G|1.000;A|0.000	0.000	strong		0.577	TGM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079151.2	NM_198951		A	36766591	G	A	36766591	2	1	28	1	0	0	0	0	0	0	0	1	15845	1103	39	1		1	TGM2	20	36766591	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	11706448	36766591	26258929	684	12187											
C20orf165	128497	hgsc.bcm.edu	37	chr20	44515244	44515244	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcatgtgcctgctcccacCgcgccccctccacagcaccc	5	5	9	22	2	0	0	0	0	0	0	2	0	2	0	7	1	3	3	7	1	0	0	rs146744825	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:44515244C>T	ENST00000372519.3	-	2	640	c.596G>A	c.(595-597)cGg>cAg	p.R199Q		NM_080608.3	NP_542175.1	Q9BR10	SPT25_HUMAN	spermatogenesis associated 25	199					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CTGCTCCCACCGCGCCCCCTC	0.612													c|||	57	0.0113818	0.0015	0.0764	5008	,	,		16944	0.0		0.002	False		,,,				2504	0.0				p.R199Q		Atlas-SNP	.											.	.	.	.	0			c.G596A						PASS	.	T	GLN/ARG	13,4393	20.2+/-43.8	0,13,2190	65	70	68		596	-5.7	0	20	dbSNP_134	68	22,8578	16.6+/-54.9	0,22,4278	yes	missense	C20orf165	NM_080608.3	43	0,35,6468	TT,TC,CC		0.2558,0.2951,0.2691	benign	199/228	44515244	35,12971	2203	4300	6503	SO:0001583	missense	128497	exon2			TCCCACCGCGCCC	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.596G>A	20.37:g.44515244C>T	ENSP00000361597:p.Arg199Gln	72	0	0		84	41	0.488095	NM_080608		Missense_Mutation	SNP	ENST00000372519.3	37	CCDS13383.1	34	0.015567765567765568	1	0.0020325203252032522	32	0.08839779005524862	0	0.0	1	0.0013192612137203166	c	0.495	-0.873413	0.02570	0.002951	0.002558	ENSG00000149634	ENST00000372519	T	0.40756	1.02	5.55	-5.74	0.02391	.	1.042410	0.07602	N	0.923760	T	0.00754	0.0025	N	0.11560	0.145	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.33085	-0.9882	10	0.09338	T	0.73	-0.1318	15.7642	0.78114	0.0:0.2044:0.0:0.7956	.	199	Q9BR10	CT165_HUMAN	Q	199	ENSP00000361597:R199Q	ENSP00000361597:R199Q	R	-	2	0	C20orf165	43948651	0.000000	0.05858	0.002000	0.10522	0.099000	0.18886	-1.573000	0.02134	-1.357000	0.02180	-1.552000	0.00895	CGG	C|0.994;T|0.006	0.006	strong		0.612	SPATA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079541.1			T	44515244	C	T	44515244	3	4	28	1	0	0	0	0	1	0	0	0	2096	652	23	1	91	1	C20orf165	20	44515244	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	7748653	44515244	18510276	685	12188											
C20orf165	128497	hgsc.bcm.edu	37	chr20	44515322	44515322	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccagatcaggtcctcttccCgaactcctgggacgggcacg	7	7	11	16	3	2	1	1	0	1	1	5	3	5	2	4	3	1	1	4	3	1	1	rs76638086	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:44515322C>T	ENST00000372519.3	-	2	562	c.518G>A	c.(517-519)cGg>cAg	p.R173Q		NM_080608.3	NP_542175.1	Q9BR10	SPT25_HUMAN	spermatogenesis associated 25	173					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GTCCTCTTCCCGAACTCCTGG	0.652													C|||	12	0.00239617	0.0008	0.0072	5008	,	,		18142	0.0		0.005	False		,,,				2504	0.001				p.R173Q		Atlas-SNP	.											.	.	.	.	0			c.G518A						PASS	.	C	GLN/ARG	7,4399	11.4+/-27.6	0,7,2196	62	64	64		518	3.6	1	20	dbSNP_132	64	36,8564	25.1+/-72.6	0,36,4264	yes	missense	C20orf165	NM_080608.3	43	0,43,6460	TT,TC,CC		0.4186,0.1589,0.3306	probably-damaging	173/228	44515322	43,12963	2203	4300	6503	SO:0001583	missense	128497	exon2			TCTTCCCGAACTC	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.518G>A	20.37:g.44515322C>T	ENSP00000361597:p.Arg173Gln	110	0	0		93	42	0.451613	NM_080608		Missense_Mutation	SNP	ENST00000372519.3	37	CCDS13383.1	8	0.003663003663003663	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	4	0.005277044854881266	C	20.8	4.042836	0.75732	0.001589	0.004186	ENSG00000149634	ENST00000372519	T	0.56941	0.43	5.55	3.63	0.41609	.	0.134112	0.33515	N	0.004823	T	0.28797	0.0714	L	0.34521	1.04	0.31251	N	0.693996	B	0.30021	0.265	B	0.23852	0.049	T	0.42050	-0.9474	10	0.87932	D	0	-13.3192	6.8348	0.23931	0.0:0.6984:0.1454:0.1562	.	173	Q9BR10	CT165_HUMAN	Q	173	ENSP00000361597:R173Q	ENSP00000361597:R173Q	R	-	2	0	C20orf165	43948729	0.718000	0.27976	1.000000	0.80357	0.974000	0.67602	0.589000	0.23939	0.908000	0.36671	0.655000	0.94253	CGG	C|0.997;T|0.003	0.003	strong		0.652	SPATA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079541.1			T	44515322	C	T	44515322	3	4	28	1	0	0	0	0	1	0	0	0	2096	652	23	1	169	1	C20orf165	20	44515322	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	78	44515322	18510198	686	12189											
NFATC2	4773	hgsc.bcm.edu	37	chr20	50092193	50092193	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttgttttccatgtagccaTggagctggtgggggagaaaa	9	11	15	6	0	0	1	0	0	0	1	1	3	1	2	2	4	2	4	2	4	3	4	rs12479626	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:50092193T>C	ENST00000396009.3	-	4	1556	c.1337A>G	c.(1336-1338)cAt>cGt	p.H446R	NFATC2_ENST00000414705.1_Missense_Mutation_p.H426R|NFATC2_ENST00000371564.3_Missense_Mutation_p.H446R|NFATC2_ENST00000609943.1_Missense_Mutation_p.H426R|NFATC2_ENST00000610033.1_Missense_Mutation_p.H227R|NFATC2_ENST00000609507.1_Missense_Mutation_p.H227R	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	446	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.		H -> R (in dbSNP:rs12479626).		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)	p.H446R(1)	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)					CATGTAGCCATGGAGCTGGTG	0.502													T|||	65	0.0129792	0.0023	0.0274	5008	,	,		17874	0.0387		0.0	False		,,,				2504	0.0041				p.H446R		Atlas-SNP	.											NFATC2,NS,carcinoma,0,1	NFATC2	112	1	1	Substitution - Missense(1)	stomach(1)	c.A1337G						scavenged	.	T	ARG/HIS,ARG/HIS,ARG/HIS	5,4401	8.1+/-20.4	0,5,2198	65	60	61		1277,1337,1337	5.4	1	20	dbSNP_120	61	8,8592	7.1+/-27.0	0,8,4292	yes	missense,missense,missense	NFATC2	NM_001136021.1,NM_012340.3,NM_173091.2	29,29,29	0,13,6490	CC,CT,TT		0.093,0.1135,0.1	benign,benign,benign	426/902,446/922,446/926	50092193	13,12993	2203	4300	6503	SO:0001583	missense	4773	exon4			TAGCCATGGAGCT	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.1337A>G	20.37:g.50092193T>C	ENSP00000379330:p.His446Arg	129	1	0.00775194		124	53	0.427419	NM_012340	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Missense_Mutation	SNP	ENST00000396009.3	37	CCDS13437.1	34	0.015567765567765568	3	0.006097560975609756	3	0.008287292817679558	28	0.04895104895104895	0	0.0	T	23.5	4.419816	0.83559	0.001135	9.3E-4	ENSG00000101096	ENST00000371564;ENST00000396009;ENST00000371567;ENST00000414705	T;T;T	0.42900	0.96;0.96;0.96	5.44	5.44	0.79542	Rel homology (3);p53-like transcription factor, DNA-binding (1);	0.048788	0.85682	D	0.000000	T	0.04907	0.0132	N	0.08118	0	0.58432	D	0.999991	B;P;B;B	0.51351	0.114;0.944;0.068;0.068	B;P;B;B	0.44394	0.032;0.448;0.058;0.032	T	0.02691	-1.1123	10	0.29301	T	0.29	-19.6058	15.5154	0.75818	0.0:0.0:0.0:1.0	rs12479626;rs52802474;rs12479626	426;426;446;446	B5B2N9;B5B2P2;Q13469;B5B2N8	.;.;NFAC2_HUMAN;.	R	446;446;227;426	ENSP00000360619:H446R;ENSP00000379330:H446R;ENSP00000396471:H426R	ENSP00000360619:H446R	H	-	2	0	NFATC2	49525600	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	6.153000	0.71819	2.063000	0.61619	0.528000	0.53228	CAT	T|0.992;C|0.008	0.008	strong		0.502	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340		C	50092193	T	C	50092193	3	2	28	1	0	0	0	0	1	0	0	0	10371	1464	51	3	1516	3	NFATC2	20	50092193	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	5576871	50092193	12933327	687	12190											
ZBP1	81030	hgsc.bcm.edu	37	chr20	56191475	56191475	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accagctgggcaagtttcacCggggagccagcctctgtcag	8	7	13	13	1	3	0	2	0	1	0	3	1	3	1	4	3	3	3	4	3	1	1	rs16981188	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:56191475C>T	ENST00000371173.3	-	2	261	c.84G>A	c.(82-84)ccG>ccA	p.P28P	ZBP1_ENST00000538947.1_5'UTR|ZBP1_ENST00000395822.3_Intron|ZBP1_ENST00000541799.1_Silent_p.P28P|ZBP1_ENST00000340462.4_Silent_p.P28P|ZBP1_ENST00000343535.4_Silent_p.P28P	NM_001160417.1|NM_030776.2	NP_001153889.1|NP_110403.2	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1	28					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)			CAAGTTTCACCGGGGAGCCAG	0.577													C|||	98	0.0195687	0.028	0.0317	5008	,	,		18817	0.0		0.0308	False		,,,				2504	0.0082				p.P28P		Atlas-SNP	.											.	ZBP1	65	.	0			c.G84A						PASS	.	C	,,,	158,4248	108.2+/-146.6	0,158,2045	95	94	94		84,,84,84	-7.3	0	20	dbSNP_123	94	318,8282	112.9+/-173.0	5,308,3987	no	coding-synonymous,intron,coding-synonymous,coding-synonymous	ZBP1	NM_001160417.1,NM_001160418.1,NM_001160419.1,NM_030776.2	,,,	5,466,6032	TT,TC,CC		3.6977,3.586,3.6598	,,,	28/429,,28/249,28/430	56191475	476,12530	2203	4300	6503	SO:0001819	synonymous_variant	81030	exon2			TTTCACCGGGGAG	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.84G>A	20.37:g.56191475C>T		82	0	0		118	54	0.457627	NM_001160419	A2A2F7|B3KVA1|F5GYT1|Q5JY39|Q9BYW4	Silent	SNP	ENST00000371173.3	37	CCDS13461.1																																																																																			C|0.967;T|0.033	0.033	strong		0.577	ZBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079849.1	NM_030776		T	56191475	C	T	56191475	2	4	28	1	0	0	0	0	0	0	0	1	17536	639	23	1		1	ZBP1	20	56191475	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	6099282	56191475	6834045	688	12191											
GNAS	2778	hgsc.bcm.edu	37	chr20	57478807	57478807	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cagttcagagtggactacatCctgagtgtgatgaacgtgcc	10	10	12	9	1	1	4	1	3	0	1	2	5	2	5	2	1	3	1	2	1	2	2	rs7121	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:57478807C>T	ENST00000371085.3	+	5	817	c.393C>T	c.(391-393)atC>atT	p.I131I	GNAS_ENST00000371100.4_Silent_p.I774I|GNAS_ENST00000313949.7_3'UTR|GNAS_ENST00000371102.4_Silent_p.I760I|GNAS_ENST00000371075.3_3'UTR|GNAS_ENST00000354359.7_Silent_p.I132I|GNAS_ENST00000371095.3_Silent_p.I117I|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000306090.10_Silent_p.I117I|GNAS_ENST00000265620.7_Silent_p.I116I	NM_000516.4	NP_000507.1	P63092	GNAS2_HUMAN	GNAS complex locus	131					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)			TGGACTACATCCTGAGTGTGA	0.557			Mis		pituitary adenoma		"McCune-Albright syndrome; pseudohypoparathyroidism, type IA"			TSP Lung(22;0.16)			T|||	3227	0.644369	0.8139	0.6124	5008	,	,		18620	0.6716		0.4742	False		,,,				2504	0.5849				p.I774I	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.C2322T	GRCh37	CM023931	GNAS	M	rs7121	PASS	.	T	,,,,,,	3298,1108	398.3+/-330.8	1234,830,139	247	224	232		393,396,348,,,2322,351	-9.2	0.2	20	dbSNP_52	232	4238,4362	582.0+/-391.3	1060,2118,1122	no	coding-synonymous,coding-synonymous,coding-synonymous,utr-3,utr-3,coding-synonymous,coding-synonymous	GNAS	NM_000516.4,NM_001077488.2,NM_001077489.2,NM_001077490.1,NM_016592.2,NM_080425.2,NM_080426.2	,,,,,,	2294,2948,1261	TT,TC,CC		49.2791,25.1475,42.0575	,,,,,,	131/395,132/396,116/380,,,774/1038,117/381	57478807	7536,5470	2203	4300	6503	SO:0001819	synonymous_variant	2778	exon5			CTACATCCTGAGT	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.393C>T	20.37:g.57478807C>T		194	0	0		209	94	0.449761	NM_080425	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Silent	SNP	ENST00000371085.3	37	CCDS13472.1	1341	0.614010989010989	407	0.8272357723577236	227	0.6270718232044199	366	0.6398601398601399	341	0.449868073878628	T	10.08	1.252619	0.22880	0.748525	0.492791	ENSG00000087460	ENST00000450130	.	.	.	5.81	-9.18	0.00688	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999101873	.	.	.	.	.	.	T	0.04400	-1.0954	3	.	.	.	.	21.0308	0.99944	0.0914:0.759:0.0:0.1496	rs7121;rs1053389;rs3171206;rs3730167;rs17829840;rs61041002;rs7121	.	.	.	S	146	.	.	P	+	1	0	GNAS	56912202	0.382000	0.25148	0.173000	0.22940	0.924000	0.55760	-0.313000	0.08103	-2.651000	0.00424	-1.760000	0.00671	CCT	C|0.395;T|0.605	0.605	strong		0.557	GNAS-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080431.2	NM_000516		T	57478807	C	T	57478807	2	4	28	1	0	0	0	0	0	0	0	1	6518	845	30	2		2	GNAS	20	57478807	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1287332	57478807	5546713	689	12192											
LAMA5	3911	hgsc.bcm.edu	37	chr20	60899513	60899513	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tcaccacacagacgccagagCcagggaggcagcggtctgag	11	3	14	13	2	2	3	1	1	1	2	2	4	2	4	3	3	2	1	3	3	0	0	rs148177752	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:60899513C>A	ENST00000252999.3	-	42	5693	c.5627G>T	c.(5626-5628)gGc>gTc	p.G1876V		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1876	Laminin EGF-like 17. {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)			GACGCCAGAGCCAGGGAGGCA	0.622													.|||	5	0.000998403	0.0008	0.0	5008	,	,		18736	0.0		0.004	False		,,,				2504	0.0				p.G1876V		Atlas-SNP	.											.	LAMA5	268	.	0			c.G5627T						PASS	.	C	VAL/GLY	10,4384	15.5+/-35.6	1,8,2188	42	36	38		5627	4.2	1	20	dbSNP_134	38	54,8532	31.2+/-83.2	1,52,4240	yes	missense	LAMA5	NM_005560.3	109	2,60,6428	AA,AC,CC		0.6289,0.2276,0.4931	probably-damaging	1876/3696	60899513	64,12916	2197	4293	6490	SO:0001583	missense	3911	exon42			CCAGAGCCAGGGA	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.5627G>T	20.37:g.60899513C>A	ENSP00000252999:p.Gly1876Val	89	0	0		90	48	0.533333	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	6	0.0027472527472527475	1	0.0020325203252032522	0	0.0	0	0.0	5	0.006596306068601583	C	18.61	3.660047	0.67586	0.002276	0.006289	ENSG00000130702	ENST00000252999	T	0.60424	0.19	4.25	4.25	0.50352	TNFR/CD27/30/40/95 cysteine-rich region (1);EGF-like, laminin (3);	0.000000	0.85682	U	0.000000	T	0.62636	0.2444	L	0.46567	1.45	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.66638	-0.5873	10	0.36615	T	0.2	.	16.9991	0.86377	0.0:1.0:0.0:0.0	.	1876	O15230	LAMA5_HUMAN	V	1876	ENSP00000252999:G1876V	ENSP00000252999:G1876V	G	-	2	0	LAMA5	60332908	1.000000	0.71417	0.995000	0.50966	0.568000	0.35870	4.553000	0.60753	2.074000	0.62210	0.579000	0.79373	GGC	C|0.996;A|0.004	0.004	strong		0.622	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		A	60899513	C	A	60899513	3	1	28	1	0	0	0	0	1	0	0	0	8618	739	26	4	5616	4	LAMA5	20	60899513	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	3420706	60899513	2126007	690	12193											
PRIC285	85441	hgsc.bcm.edu	37	chr20	62193733	62193733	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cacgcacggcttcctccttgCggctgggggtgaaggcagac	6	7	15	13	3	0	2	0	1	0	1	2	2	2	2	2	5	1	4	2	5	1	2	rs370768380		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:62193733C>T	ENST00000467148.1	-	9	6374	c.6305G>A	c.(6304-6306)cGc>cAc	p.R2102H	HELZ2_ENST00000427522.2_Missense_Mutation_p.R1533H	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	2102					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)										TTCCTCCTTGCGGCTGGGGGT	0.682																																					p.R2102H		Atlas-SNP	.											PRIC285,colon,carcinoma,0,1	.	.	1	0			c.G6305A						PASS	.	C	HIS/ARG,HIS/ARG	0,4222		0,0,2111	8	9	9		6305,4598	4.2	1	20		9	1,8395		0,1,4197	no	missense,missense	PRIC285	NM_001037335.2,NM_033405.3	29,29	0,1,6308	TT,TC,CC		0.0119,0.0,0.0079	probably-damaging,probably-damaging	2102/2650,1533/2081	62193733	1,12617	2111	4198	6309	SO:0001583	missense	85441	exon10			TCCTTGCGGCTGG	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.6305G>A	20.37:g.62193733C>T	ENSP00000417401:p.Arg2102His	53	0	0		48	23	0.479167	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	37	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.227358	0.79576	0.0	1.19E-4	ENSG00000130589	ENST00000427522;ENST00000467148	D;D	0.84800	-1.9;-1.72	4.15	4.15	0.48705	.	0.311695	0.30043	N	0.010556	D	0.91233	0.7237	M	0.74258	2.255	0.53688	D	0.999977	D;D	0.89917	1.0;1.0	D;D	0.74348	0.961;0.983	D	0.92378	0.5911	10	0.87932	D	0	-31.3164	13.9239	0.63950	0.0:1.0:0.0:0.0	.	2102;1533	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	H	1533;2102	ENSP00000393257:R1533H;ENSP00000417401:R2102H	ENSP00000393257:R1533H	R	-	2	0	RP4-697K14.7	61664177	1.000000	0.71417	1.000000	0.80357	0.750000	0.42670	2.523000	0.45580	1.867000	0.54127	0.313000	0.20887	CGC	.	.	weak		0.682	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		T	62193733	C	T	62193733	3	4	28	1	0	0	0	0	1	0	0	0	12497	768	27	1	1688	1	PRIC285	20	62193733	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1294220	62193733	831787	691	12194											
ARFRP1	10139	hgsc.bcm.edu	37	chr20	62333231	62333231	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agacggggacaccgcacagcGcctcgctggtcaccaccttc	8	5	11	17	4	1	1	1	0	0	1	3	2	1	2	4	3	1	2	4	3	0	1	rs139547982	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:62333231G>A	ENST00000359715.5	-	5	934	c.368C>T	c.(367-369)gCg>gTg	p.A123V	ARFRP1_ENST00000607873.1_Missense_Mutation_p.A76V|ARFRP1_ENST00000324228.2_Missense_Mutation_p.A123V|ARFRP1_ENST00000485858.1_5'Flank|ARFRP1_ENST00000440854.1_Missense_Mutation_p.A123V|ARFRP1_ENST00000609142.1_Missense_Mutation_p.A123V			Q13795	ARFRP_HUMAN	ADP-ribosylation factor related protein 1	123					gastrulation (GO:0007369)|Golgi to plasma membrane protein transport (GO:0043001)|GTP catabolic process (GO:0006184)|protein localization to Golgi apparatus (GO:0034067)|retrograde transport, endosome to Golgi (GO:0042147)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	7	all_cancers(38;9.53e-13)|all_epithelial(29;2.64e-14)|Lung NSC(23;7e-10)|all_lung(23;2.53e-09)		Epithelial(9;4.09e-08)|all cancers(9;1.7e-07)|OV - Ovarian serous cystadenocarcinoma(5;0.0102)			ACCGCACAGCGCCTCGCTGGT	0.687													G|||	2	0.000399361	0.0	0.0014	5008	,	,		15284	0.001		0.0	False		,,,				2504	0.0				p.A123V		Atlas-SNP	.											ARFRP1,colon,carcinoma,+1,1	ARFRP1	17	1	0			c.C368T						PASS	.	G	VAL/ALA,VAL/ALA	1,4167		0,1,2083	48	28	35		368,368	4.6	0.6	20	dbSNP_134	35	10,8152		0,10,4071	yes	missense,missense	ARFRP1	NM_001134758.1,NM_003224.3	64,64	0,11,6154	AA,AG,GG		0.1225,0.024,0.0892	benign,benign	123/174,123/202	62333231	11,12319	2084	4081	6165	SO:0001583	missense	10139	exon6			CACAGCGCCTCGC	X91504	CCDS13533.1, CCDS46630.1, CCDS68172.1, CCDS68173.1	20q13.3	2014-05-09			ENSG00000101246	ENSG00000101246		"ADP-ribosylation factors"	662	protein-coding gene	gene with protein product		604699				8530503	Standard	NM_003224		Approved	ARP, Arp1, ARL18	uc031rup.1	Q13795	OTTHUMG00000032993	ENST00000359715.5:c.368C>T	20.37:g.62333231G>A	ENSP00000352746:p.Ala123Val	120	0	0		123	59	0.479675	NM_001134758	B7ZKX7|E1P5J9|Q6IBQ0	Missense_Mutation	SNP	ENST00000359715.5	37	CCDS13533.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	2	0.0034965034965034965	1	0.0013192612137203166	G	11.15	1.552881	0.27739	2.4E-4	0.001225	ENSG00000101246	ENST00000440854;ENST00000359715;ENST00000324228	T;T;T	0.63913	-0.07;-0.07;-0.07	5.53	4.57	0.56435	Small GTP-binding protein domain (1);	0.234257	0.42053	D	0.000776	T	0.41351	0.1155	L	0.33624	1.015	0.50467	D	0.999877	B	0.12630	0.006	B	0.12156	0.007	T	0.44757	-0.9307	10	0.51188	T	0.08	-29.5252	10.3719	0.44060	0.1489:0.0:0.8511:0.0	.	123	Q13795	ARFRP_HUMAN	V	123	ENSP00000403942:A123V;ENSP00000352746:A123V;ENSP00000326884:A123V	ENSP00000326884:A123V	A	-	2	0	ARFRP1	61803675	0.992000	0.36948	0.594000	0.28785	0.597000	0.36814	2.904000	0.48719	2.590000	0.87494	0.462000	0.41574	GCG	G|0.999;A|0.001	0.001	strong		0.687	ARFRP1-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472024.1			A	62333231	G	A	62333231	3	1	28	1	0	0	0	0	1	0	0	0	856	1087	38	1	253	1	ARFRP1	20	62333231	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	139498	62333231	692289	692	12195											
BAGE2	85319	hgsc.bcm.edu	37	chr21	11058322	11058322	+	RNA	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agtgcttacaaaatgcacatCgctgaaaggggtaaaggaga	16	7	12	6	1	0	2	0	1	0	1	1	3	0	2	0	3	3	4	0	3	6	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:11058322C>T	ENST00000470054.1	-	0	325							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)		AAATGCACATCGCTGAAAGGG	0.383																																					p.D40N		Atlas-SNP	.											.	.	.	.	0			c.G118A						PASS	.						92	70	77					21																	11058322		692	1591	2283			85318	exon3			GCACATCGCTGAA	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		21.37:g.11058322C>T		200	0	0		238	14	0.0588235	NM_182481	A8K925|Q08ER0	Missense_Mutation	SNP	ENST00000470054.1	37																																																																																				C|0.750;T|0.250	0.250	strong		0.383	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482		T	11058322	C	T	11058322	1	4	28	0	1	0	0	0	0	0	0	0	1292	898	31	1		1	BAGE2	21	11058322	RNA	SNP	C	TCGA-G8-6914-01A-11D-2210-10		11058322	37071573	693	12196											
GCFC1	94104	hgsc.bcm.edu	37	chr21	34132288	34132288	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tagtacatattcacttctgcGggttgactggcttgaaccta	9	14	9	9	1	2	2	1	2	1	0	2	2	2	2	1	2	3	3	1	2	5	8	rs149224793	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:34132288G>A	ENST00000331923.4	-	6	1182	c.993C>T	c.(991-993)ccC>ccT	p.P331P	PAXBP1_ENST00000472588.1_5'UTR|PAXBP1_ENST00000290178.4_Silent_p.P331P	NM_016631.3	NP_057715.2	Q9Y5B6	PAXB1_HUMAN	PAX3 and PAX7 binding protein 1	331					muscle organ development (GO:0007517)|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 satellite cell proliferation (GO:0014842)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TCACTTCTGCGGGTTGACTGG	0.373													G|||	3	0.000599042	0.0	0.0014	5008	,	,		18563	0.0		0.002	False		,,,				2504	0.0				p.P331P		Atlas-SNP	.											.	.	.	.	0			c.C993T						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	100	103	102		993,993	0.4	0.2	21	dbSNP_134	102	25,8575	17.3+/-56.4	0,25,4275	no	coding-synonymous,coding-synonymous	GCFC1	NM_013329.3,NM_016631.3	,	0,26,6477	AA,AG,GG		0.2907,0.0227,0.1999	,	331/816,331/918	34132288	26,12980	2203	4300	6503	SO:0001819	synonymous_variant	94104	exon6			TTCTGCGGGTTGA	AF231920	CCDS13619.1, CCDS33541.1	21q22.11	2014-01-23	2013-01-08	2013-01-08	ENSG00000159086	ENSG00000159086			13579	protein-coding gene	gene with protein product	"functional spliceosome-associated protein 105", "GC-rich sequence DNA-binding factor candidate"		"chromosome 21 open reading frame 66", "GC-rich sequence DNA-binding factor 1"	C21orf66, GCFC1		11707072, 22862948	Standard	NM_016631		Approved	GCFC, fSAP105	uc002yqn.3	Q9Y5B6	OTTHUMG00000064980	ENST00000331923.4:c.993C>T	21.37:g.34132288G>A		104	0	0		96	43	0.447917	NM_013329	D3DSE7|Q96DU8|Q9NYQ0	Silent	SNP	ENST00000331923.4	37	CCDS13619.1																																																																																			G|0.999;A|0.001	0.001	strong		0.373	PAXBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139563.1	NM_013329		A	34132288	G	A	34132288	2	1	28	1	0	0	0	0	0	0	0	1	6297	1103	39	1		1	GCFC1	21	34132288	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	23073966	34132288	13997607	694	12197											
MORC3	23515	hgsc.bcm.edu	37	chr21	37710067	37710067	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtcaccatgaatggtcatGtcccagttggattatatggg	11	12	11	7	0	2	1	2	1	0	0	3	2	3	2	2	3	0	1	2	3	4	3	rs370616843		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:37710067G>A	ENST00000400485.1	+	4	359	c.283G>A	c.(283-285)Gtc>Atc	p.V95I	MORC3_ENST00000487909.1_3'UTR	NM_015358.2	NP_056173.1	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	95					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						GAATGGTCATGTCCCAGTTGG	0.348																																					p.V95I		Atlas-SNP	.											.	MORC3	78	.	0			c.G283A						PASS	.	G	ILE/VAL	0,3660		0,0,1830	90	79	82		283	4.3	1	21		82	1,8161		0,1,4080	no	missense	MORC3	NM_015358.2	29	0,1,5910	AA,AG,GG		0.0123,0.0,0.0085	possibly-damaging	95/940	37710067	1,11821	1830	4081	5911	SO:0001583	missense	23515	exon4			GGTCATGTCCCAG	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.283G>A	21.37:g.37710067G>A	ENSP00000383333:p.Val95Ile	108	0	0		86	38	0.44186	NM_015358	A8KA92|Q9UEZ2	Missense_Mutation	SNP	ENST00000400485.1	37	CCDS42924.1	.	.	.	.	.	.	.	.	.	.	G	19.88	3.908699	0.72868	0.0	1.23E-4	ENSG00000159256	ENST00000400485	D	0.94862	-3.54	5.21	4.33	0.51752	ATPase-like, ATP-binding domain (2);	0.187242	0.45361	D	0.000366	D	0.91533	0.7326	L	0.31664	0.95	0.47698	D	0.999497	B	0.34241	0.444	B	0.42062	0.374	D	0.88791	0.3278	10	0.24483	T	0.36	-11.2373	14.267	0.66126	0.0727:0.0:0.9273:0.0	.	95	Q14149	MORC3_HUMAN	I	95	ENSP00000383333:V95I	ENSP00000383333:V95I	V	+	1	0	MORC3	36631937	1.000000	0.71417	0.998000	0.56505	0.863000	0.49368	6.480000	0.73604	1.323000	0.45263	0.591000	0.81541	GTC	.	.	weak		0.348	MORC3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000194640.1	NM_015358		A	37710067	G	A	37710067	3	1	28	1	0	0	0	0	1	0	0	0	9712	1377	48	2	297	2	MORC3	21	37710067	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	3577779	37710067	10419828	695	12198											
ETS2	2114	hgsc.bcm.edu	37	chr21	40190408	40190408	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agaattaccccaaaggcggcCtcctggacagcatgtgtccg	10	7	11	13	2	0	1	0	0	0	1	2	2	2	2	5	3	2	1	5	3	3	1	rs61735785	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:40190408C>A	ENST00000360214.3	+	8	1109	c.649C>A	c.(649-651)Ctc>Atc	p.L217I	ETS2_ENST00000360938.3_Missense_Mutation_p.L217I	NM_001256295.1	NP_001243224.1	P15036	ETS2_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 2	217					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)				CAAAGGCGGCCTCCTGGACAG	0.567													C|||	17	0.00339457	0.0	0.0086	5008	,	,		17462	0.0		0.0089	False		,,,				2504	0.002				p.L357I		Atlas-SNP	.											.	ETS2	87	.	0			c.C1069A						PASS	.	C	ILE/LEU	4,4402	8.1+/-20.4	0,4,2199	149	155	153		649	5.3	0.9	21	dbSNP_129	153	103,8497	56.4+/-117.6	1,101,4198	yes	missense	ETS2	NM_005239.4	5	1,105,6397	AA,AC,CC		1.1977,0.0908,0.8227	probably-damaging	217/470	40190408	107,12899	2203	4300	6503	SO:0001583	missense	2114	exon8			GGCGGCCTCCTGG		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.649C>A	21.37:g.40190408C>A	ENSP00000353344:p.Leu217Ile	61	0	0		69	32	0.463768	NM_001256295	A6NM68|D3DSH6|Q53Y89	Missense_Mutation	SNP	ENST00000360214.3	37	CCDS13659.1	12	0.005494505494505495	0	0.0	5	0.013812154696132596	0	0.0	7	0.009234828496042216	C	13.05	2.120236	0.37436	9.08E-4	0.011977	ENSG00000157557	ENST00000360214;ENST00000360938;ENST00000456966	T;T;T	0.41400	2.48;2.48;1.0	6.16	5.28	0.74379	.	2.205300	0.02436	N	0.084067	T	0.42832	0.1220	M	0.69823	2.125	0.42985	D	0.994471	P;D	0.54397	0.908;0.966	B;P	0.46144	0.277;0.505	T	0.54649	-0.8262	10	0.07990	T	0.79	.	12.2106	0.54377	0.1305:0.7322:0.1373:0.0	rs61735785	217;217	P15036;C9JAG2	ETS2_HUMAN;.	I	217	ENSP00000353344:L217I;ENSP00000354194:L217I;ENSP00000411086:L217I	ENSP00000353344:L217I	L	+	1	0	ETS2	39112278	0.976000	0.34144	0.916000	0.36221	0.114000	0.19823	2.340000	0.43974	1.609000	0.50190	0.650000	0.86243	CTC	C|0.993;A|0.007	0.007	strong		0.567	ETS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207544.1			A	40190408	C	A	40190408	3	1	28	1	0	0	0	0	1	0	0	0	5278	681	24	4	671	4	ETS2	21	40190408	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2480341	40190408	7939487	696	12199											
DSCAM	1826	hgsc.bcm.edu	37	chr21	42064785	42064785	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	catgagacgacagtgatgtaCgcctccaccgaggaggggat	11	6	14	10	3	0	2	0	2	0	1	1	7	1	4	3	3	1	1	3	3	1	1	rs79669041	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:42064785C>T	ENST00000400454.1	-	3	936	c.459G>A	c.(457-459)gcG>gcA	p.A153A		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	153	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)				CAGTGATGTACGCCTCCACCG	0.527													c|||	23	0.00459265	0.0	0.0072	5008	,	,		20320	0.0		0.0159	False		,,,				2504	0.002				p.A153A	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.G459A						PASS	.	T		9,4065		0,9,2028	136	134	134		459	-1.4	1	21	dbSNP_132	134	88,8274		0,88,4093	no	coding-synonymous	DSCAM	NM_001389.3		0,97,6121	TT,TC,CC		1.0524,0.2209,0.78		153/2013	42064785	97,12339	2037	4181	6218	SO:0001819	synonymous_variant	1826	exon3			GATGTACGCCTCC	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.459G>A	21.37:g.42064785C>T		49	0	0		62	33	0.532258	NM_001271534	O60468	Silent	SNP	ENST00000400454.1	37	CCDS42929.1																																																																																			C|0.993;T|0.007	0.007	strong		0.527	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		T	42064785	C	T	42064785	2	4	28	1	0	0	0	0	0	0	0	1	4770	523	19	1		1	DSCAM	21	42064785	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1874377	42064785	6065110	697	12200											
PRDM15	63977	hgsc.bcm.edu	37	chr21	43230669	43230669	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcttgtcgcacacggagcaCgtccactgcttgcccacttt	6	12	8	15	3	1	0	0	0	1	0	3	1	2	1	2	1	3	3	2	1	0	4	rs146699277	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:43230669C>T	ENST00000269844.3	-	28	3701	c.3591G>A	c.(3589-3591)acG>acA	p.T1197T	PRDM15_ENST00000398548.1_Silent_p.T868T|PRDM15_ENST00000422911.1_Silent_p.T888T|PRDM15_ENST00000538201.1_Silent_p.T851T|PRDM15_ENST00000470586.1_5'UTR|PRDM15_ENST00000447207.2_Silent_p.T831T	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	1197					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						ACACGGAGCACGTCCACTGCT	0.582													c|||	9	0.00179712	0.0008	0.0043	5008	,	,		20936	0.0		0.003	False		,,,				2504	0.002				p.T1197T		Atlas-SNP	.											.	PRDM15	110	.	0			c.G3591A						PASS	.		,	0,4406		0,0,2203	134	78	97		2604,3591	-4.3	1	21	dbSNP_134	97	12,8588	9.1+/-34.3	0,12,4288	no	coding-synonymous,coding-synonymous	PRDM15	NM_001040424.1,NM_022115.3	,	0,12,6491	TT,TC,CC		0.1395,0.0,0.0923	,	868/1179,1197/1508	43230669	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	63977	exon28			GGAGCACGTCCAC	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.3591G>A	21.37:g.43230669C>T		41	0	0		52	19	0.365385	NM_022115	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Silent	SNP	ENST00000269844.3	37	CCDS13676.1																																																																																			C|0.999;T|0.001	0.001	strong		0.582	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115		T	43230669	C	T	43230669	2	4	28	1	0	0	0	0	0	0	0	1	12468	523	19	1		1	PRDM15	21	43230669	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1165884	43230669	4899226	698	12201											
KRTAP10-9	386676	hgsc.bcm.edu	37	chr21	46047105	46047105	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcatggccgcgtccaccaTgtccatccgctccagcgctt	6	8	9	18	4	0	0	0	0	0	0	4	0	4	0	6	1	2	3	6	1	0	1	rs200504844		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:46047105T>C	ENST00000397911.3	+	1	66	c.17T>C	c.(16-18)aTg>aCg	p.M6T	KRTAP10-9_ENST00000484861.1_3'UTR|TSPEAR_ENST00000323084.4_Intron	NM_198690.2	NP_941963.2	P60411	KR109_HUMAN	keratin associated protein 10-9	6						keratin filament (GO:0045095)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9						GCGTCCACCATGTCCATCCGC	0.642													T|||	1	0.000199681	0.0	0.0	5008	,	,		16835	0.0		0.001	False		,,,				2504	0.0				p.M6T		Atlas-SNP	.											.	KRTAP10-9	24	.	0			c.T17C						PASS	.	T	,THR/MET	0,4406		0,0,2203	73	85	81		,17	-1	0.9	21		81	8,8592	5.7+/-21.5	0,8,4292	no	intron,missense	TSPEAR,KRTAP10-9	NM_144991.2,NM_198690.2	,81	0,8,6495	CC,CT,TT		0.093,0.0,0.0615	,benign	,6/293	46047105	8,12998	2203	4300	6503	SO:0001583	missense	386676	exon1			CCACCATGTCCAT	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.17T>C	21.37:g.46047105T>C	ENSP00000381009:p.Met6Thr	91	0	0		90	47	0.522222	NM_198690	A2RRG1|A6NIR9|Q70LJ1	Missense_Mutation	SNP	ENST00000397911.3	37	CCDS42961.1	.	.	.	.	.	.	.	.	.	.	t	3.359	-0.130818	0.06753	0.0	9.3E-4	ENSG00000221837	ENST00000397911	T	0.13196	2.61	3.67	-0.997	0.10215	.	.	.	.	.	T	0.09158	0.0226	L	0.41573	1.285	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.39440	-0.9614	9	0.66056	D	0.02	.	0.7715	0.01024	0.16:0.2466:0.1626:0.4307	.	6	P60411	KR109_HUMAN	T	6	ENSP00000381009:M6T	ENSP00000381009:M6T	M	+	2	0	KRTAP10-9	44871533	0.058000	0.20735	0.903000	0.35520	0.008000	0.06430	0.077000	0.14738	0.001000	0.14605	-0.408000	0.06270	ATG	T|0.999;C|0.001	0.001	weak		0.642	KRTAP10-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128040.1			C	46047105	T	C	46047105	3	2	28	1	0	0	0	0	1	0	0	0	8525	1464	51	3	19	3	KRTAP10-9	21	46047105	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	2816436	46047105	2082790	699	12202											
COL6A2	1292	hgsc.bcm.edu	37	chr21	47537804	47537804	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagggccccgacggttaccCgggggaagcagggagtccag	8	4	17	12	3	1	0	1	0	0	0	2	3	2	2	4	5	2	2	4	5	2	1	rs199929757	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:47537804C>G	ENST00000300527.4	+	12	1174	c.1070C>G	c.(1069-1071)cCg>cGg	p.P357R	COL6A2_ENST00000397763.1_Missense_Mutation_p.P357R|COL6A2_ENST00000310645.5_Missense_Mutation_p.P357R|COL6A2_ENST00000357838.4_Missense_Mutation_p.P357R|COL6A2_ENST00000409416.1_Missense_Mutation_p.P357R	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	357	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)		GACGGTTACCCGGGGGAAGCA	0.682													C|||	3	0.000599042	0.0	0.0014	5008	,	,		16264	0.0		0.002	False		,,,				2504	0.0				p.P357R		Atlas-SNP	.											.	COL6A2	351	.	0			c.C1070G						PASS	.	C	ARG/PRO,ARG/PRO,ARG/PRO	2,4388	2.1+/-5.4	0,2,2193	50	48	48		1070,1070,1070	2.6	0.1	21		48	14,8574	9.1+/-34.3	0,14,4280	yes	missense,missense,missense	COL6A2	NM_001849.3,NM_058174.2,NM_058175.2	103,103,103	0,16,6473	GG,GC,CC		0.163,0.0456,0.1233	benign,benign,benign	357/1020,357/919,357/829	47537804	16,12962	2195	4294	6489	SO:0001583	missense	1292	exon12			GTTACCCGGGGGA	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.1070C>G	21.37:g.47537804C>G	ENSP00000300527:p.Pro357Arg	48	0	0		45	31	0.688889	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Missense_Mutation	SNP	ENST00000300527.4	37	CCDS13728.1	.	.	.	.	.	.	.	.	.	.	C	2.941	-0.218840	0.06101	4.56E-4	0.00163	ENSG00000142173	ENST00000300527;ENST00000357838;ENST00000310645;ENST00000409416;ENST00000397763	D;D;D;D;D	0.96885	-4.16;-4.16;-4.16;-4.16;-4.16	4.46	2.59	0.31030	.	0.302904	0.36303	N	0.002665	D	0.94463	0.8218	L	0.46741	1.465	0.49915	D	0.999832	P;P;B	0.44877	0.81;0.845;0.111	P;P;B	0.47626	0.552;0.504;0.103	D	0.91557	0.5261	10	0.44086	T	0.13	-0.2304	9.7478	0.40457	0.0:0.8421:0.0:0.1579	.	357;357;357	P12110;P12110-2;P12110-3	CO6A2_HUMAN;.;.	R	357	ENSP00000300527:P357R;ENSP00000350497:P357R;ENSP00000312529:P357R;ENSP00000387115:P357R;ENSP00000380870:P357R	ENSP00000300527:P357R	P	+	2	0	COL6A2	46362232	0.902000	0.30710	0.087000	0.20705	0.104000	0.19210	2.090000	0.41682	0.411000	0.25702	0.305000	0.20034	CCG	C|0.996;G|0.005	0.005	strong		0.682	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1			G	47537804	C	G	47537804	3	3	28	1	0	0	0	0	1	0	0	0	3702	652	23	4	1112	4	COL6A2	21	47537804	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1490699	47537804	592091	700	12203											
LSS	4047	hgsc.bcm.edu	37	chr21	47642626	47642626	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccggctggcagagggatgcGtgccacgtggcaagtgatca	8	7	16	10	3	1	2	1	1	0	1	2	3	2	3	2	4	2	3	2	4	1	0	rs139003098	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:47642626G>A	ENST00000397728.3	-	4	424	c.346C>T	c.(346-348)Cgc>Tgc	p.R116C	AP001469.5_ENST00000418029.1_RNA|LSS_ENST00000464357.1_5'UTR|LSS_ENST00000522411.1_Missense_Mutation_p.R116C|LSS_ENST00000457828.2_Missense_Mutation_p.R36C|LSS_ENST00000356396.4_Missense_Mutation_p.R116C	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	116					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)					AGAGGGATGCGTGCCACGTGG	0.617													G|||	4	0.000798722	0.0	0.0014	5008	,	,		20008	0.0		0.002	False		,,,				2504	0.001				p.R116C	Pancreas(114;955 2313 34923 50507)	Atlas-SNP	.											.	LSS	50	.	0			c.C346T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	5,4401	9.9+/-24.2	0,5,2198	115	91	99		346,346,106,346	0.2	0	21	dbSNP_134	99	16,8584	11.9+/-42.8	0,16,4284	yes	missense,missense,missense,missense	LSS	NM_001001438.2,NM_001145436.1,NM_001145437.1,NM_002340.5	180,180,180,180	0,21,6482	AA,AG,GG		0.186,0.1135,0.1615	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	116/733,116/722,36/653,116/733	47642626	21,12985	2203	4300	6503	SO:0001583	missense	4047	exon4			GGATGCGTGCCAC	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.346C>T	21.37:g.47642626G>A	ENSP00000380837:p.Arg116Cys	56	0	0		45	24	0.533333	NM_001145436	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Missense_Mutation	SNP	ENST00000397728.3	37	CCDS13733.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	13.36	2.214719	0.39102	0.001135	0.00186	ENSG00000160285	ENST00000356396;ENST00000457828;ENST00000397728;ENST00000522411;ENST00000450351	T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93	5.17	0.224	0.15297	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	1.046430	0.07412	N	0.892629	T	0.35799	0.0944	L	0.34521	1.04	0.09310	N	1	D;D	0.60160	0.987;0.978	B;B	0.41412	0.356;0.194	T	0.47560	-0.9108	10	0.87932	D	0	.	14.9473	0.71042	0.0:0.0:0.3631:0.6369	.	116;116	E9PEI9;P48449	.;ERG7_HUMAN	C	116;36;116;116;117	ENSP00000348762:R116C;ENSP00000409191:R36C;ENSP00000380837:R116C;ENSP00000429133:R116C;ENSP00000391368:R117C	ENSP00000348762:R116C	R	-	1	0	LSS	46467054	0.001000	0.12720	0.000000	0.03702	0.690000	0.40134	0.702000	0.25631	0.228000	0.21019	0.609000	0.83330	CGC	G|0.998;A|0.002	0.002	strong		0.617	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2			A	47642626	G	A	47642626	3	1	28	1	0	0	0	0	1	0	0	0	9074	1145	40	1	1928	1	LSS	21	47642626	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	104822	47642626	487269	701	12204											
MCM3AP	8888	hgsc.bcm.edu	37	chr21	47664746	47664746	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggggtggaaggtccatctgCggaagctggaacccgagcac	10	5	16	10	2	1	0	0	0	1	0	2	4	2	3	2	6	4	2	2	6	3	0	rs17183255	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:47664746C>A	ENST00000397708.1	-	24	5267	c.5013G>T	c.(5011-5013)ccG>ccT	p.P1671P	MCM3AP-AS1_ENST00000591223.1_RNA|MCM3AP-AS1_ENST00000588753.1_RNA|MCM3AP-AS1_ENST00000432735.1_RNA|MCM3AP-AS1_ENST00000455567.1_RNA|MCM3AP_ENST00000467026.1_5'UTR|MCM3AP-AS1_ENST00000590829.1_RNA|MCM3AP_ENST00000291688.1_Silent_p.P1671P|MCM3AP-AS1_ENST00000421927.1_RNA|MCM3AP-AS1_ENST00000444998.1_RNA|MCM3AP-AS1_ENST00000414659.1_RNA|AP001469.7_ENST00000444966.1_RNA			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1671	Acetyltransferase.				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)					GGTCCATCTGCGGAAGCTGGA	0.637																																					p.P1671P		Atlas-SNP	.											.	MCM3AP	146	.	0			c.G5013T						PASS	.						34	35	35					21																	47664746		2203	4300	6503	SO:0001819	synonymous_variant	8888	exon23			CATCTGCGGAAGC	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.5013G>T	21.37:g.47664746C>A		46	0	0		54	20	0.37037	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Silent	SNP	ENST00000397708.1	37	CCDS13734.1																																																																																			C|0.997;T|0.003	.	alt		0.637	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906		A	47664746	C	A	47664746	2	1	28	1	0	0	0	0	0	0	0	1	9397	755	27	4		4	MCM3AP	21	47664746	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	22120	47664746	465149	702	12205											
POTEH	23784	hgsc.bcm.edu	37	chr22	16287538	16287538	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggtctccagaagtgcccacGttgctcttgccgctccccct	4	11	9	17	2	2	1	0	0	2	1	4	1	3	1	5	1	3	3	5	1	1	2	rs200179046	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:16287538G>A	ENST00000343518.6	-	1	399	c.348C>T	c.(346-348)aaC>aaT	p.N116N		NM_001136213.1	NP_001129685.1	Q6S545	POTEH_HUMAN	POTE ankyrin domain family, member H	116										NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(20)|ovary(1)|skin(7)|urinary_tract(2)	37						AAGTGCCCACGTTGCTCTTGC	0.602													G|||	29	0.00579073	0.0113	0.0	5008	,	,		24150	0.001		0.002	False		,,,				2504	0.0112				p.N116N		Atlas-SNP	.											POTEH,colon,carcinoma,0,1	POTEH	114	1	0			c.C348T						scavenged	.						95	108	103					22																	16287538		2058	3900	5958	SO:0001819	synonymous_variant	23784	exon1			GCCCACGTTGCTC	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.348C>T	22.37:g.16287538G>A		128	1	0.0078125		270	22	0.0814815	NM_001136213	A2CEK4|A6NCI1|A9Z1W0	Silent	SNP	ENST00000343518.6	37	CCDS46658.1																																																																																			A|0.008;C|0.006;G|0.986	0.008	strong		0.602	POTEH-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276918.4	NM_001136213		A	16287538	G	A	16287538	2	1	28	1	0	0	0	0	0	0	0	1	12276	1136	40	1		1	POTEH	22	16287538	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10		16287538	35017028	703	12206											
CDC45	8318	hgsc.bcm.edu	37	chr22	19482035	19482035	+	Intron	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gaacctttgggccagtggctCtgggagtgaacctgtggccg	6	9	16	10	1	1	1	0	1	1	0	1	3	1	2	4	4	2	1	4	4	2	1	rs151216373	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:19482035C>G	ENST00000407835.1	+	7	798				CDC45_ENST00000483431.1_3'UTR|CDC45_ENST00000437685.2_Missense_Mutation_p.S183C|CDC45_ENST00000404724.3_Intron|CDC45_ENST00000263201.1_Intron			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						GCCAGTGGCTCTGGGAGTGAA	0.562													C|||	19	0.00379393	0.0	0.0159	5008	,	,		14122	0.0		0.008	False		,,,				2504	0.0				p.S183C		Atlas-SNP	.											.	CDC45	48	.	0			c.C548G						PASS	.																																			SO:0001627	intron_variant	8318	exon7			GTGGCTCTGGGAG	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+130C>G	22.37:g.19482035C>G		49	0	0		32	10	0.3125	NM_001178010	B4DDB4|B4DDU3|E9PDH7|O60856|Q20WK8|Q6UW54|Q9UP68	Missense_Mutation	SNP	ENST00000407835.1	37	CCDS13762.1	16	0.007326007326007326	0	0.0	8	0.022099447513812154	0	0.0	8	0.010554089709762533	C	10.30	1.312792	0.23908	.	.	ENSG00000093009	ENST00000437685	T	0.23754	1.89	4.21	-2.11	0.07187	.	.	.	.	.	T	0.07908	0.0198	L	0.32530	0.975	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.25363	-1.0134	9	0.59425	D	0.04	.	4.7364	0.12989	0.0:0.4021:0.3216:0.2763	.	183	E9PDH7	.	C	183	ENSP00000405726:S183C	ENSP00000405726:S183C	S	+	2	0	CDC45	17862035	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.293000	0.08320	-0.352000	0.08237	-0.136000	0.14681	TCT	C|0.993;G|0.007	0.007	strong		0.562	CDC45-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317903.1	NM_003504		G	19482035	C	G	19482035	1	3	28	0	1	0	0	0	0	0	0	0	3083	913	32	4		4	CDC45	22	19482035	Intron	SNP	C	TCGA-G8-6914-01A-11D-2210-10	3194497	19482035	31822531	704	12207											
TRMT2A	27037	hgsc.bcm.edu	37	chr22	20103263	20103263	+	Missense_Mutation	SNP	G	G	T																															gtgcttgtgcctctgctcgaGcagccagggcagcaaggcac																								rs9605067|rs71317167	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:20103263G>T	ENST00000252136.7	-	3	1028	c.640C>A	c.(640-642)Ctc>Atc	p.L214I	RANBP1_ENST00000402752.1_5'Flank|TRMT2A_ENST00000492988.1_5'Flank|TRMT2A_ENST00000403707.3_Missense_Mutation_p.L214I|TRMT2A_ENST00000439169.2_Missense_Mutation_p.L214I|RANBP1_ENST00000430524.1_5'Flank|TRMT2A_ENST00000404751.3_Missense_Mutation_p.L214I|RANBP1_ENST00000331821.3_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)	214					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						CTCTGCTCGAGCAGCCAGGGC	0.637													G|||	59	0.0117812	0.0023	0.013	5008	,	,		17914	0.0		0.0378	False		,,,				2504	0.0092				p.L214I		Atlas-SNP	.											.	TRMT2A	34	.	0			c.C640A						PASS	.	G	ILE/LEU,ILE/LEU	27,4377	33.5+/-64.1	1,25,2176	45	42	43		640,640	-1	0.3	22	dbSNP_119	43	326,8274	113.7+/-173.7	12,302,3986	yes	missense,missense	TRMT2A	NM_022727.4,NM_182984.3	5,5	13,327,6162	TT,TG,GG		3.7907,0.6131,2.7145	benign,benign	214/626,214/626	20103263	353,12651	2202	4300	6502	SO:0001583	missense	27037	exon3			GCTCGAGCAGCCA	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.640C>A	22.37:g.20103263G>T	ENSP00000252136:p.Leu214Ile	189	0	0		201	97	0.482587	NM_001257994	D3DX25|Q32P57|Q96ME6|Q9H732	Missense_Mutation	SNP	ENST00000252136.7	37	CCDS13774.1	32	0.014652014652014652	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	25	0.032981530343007916	G	9.951	1.220275	0.22457	0.006131	0.037907	ENSG00000099899	ENST00000252136;ENST00000403707;ENST00000404751;ENST00000439169	T;T;T	0.44482	0.92;0.92;0.92	5.37	-1.03	0.10102	.	0.284900	0.40385	N	0.001117	T	0.05868	0.0153	L	0.43923	1.385	0.22796	N	0.998726	B;B;B;B	0.10296	0.003;0.001;0.0;0.0	B;B;B;B	0.09377	0.004;0.002;0.002;0.001	T	0.04621	-1.0938	10	0.25106	T	0.35	-17.0401	0.75	0.00989	0.4301:0.1753:0.2184:0.1762	rs9605067	214;214;214;214	B4E213;F2Z2W7;Q8IZ69-2;Q8IZ69	.;.;.;TRM2A_HUMAN	I	214	ENSP00000252136:L214I;ENSP00000385807:L214I;ENSP00000395738:L214I	ENSP00000252136:L214I	L	-	1	0	TRMT2A	18483263	1.000000	0.71417	0.273000	0.24645	0.285000	0.27093	2.279000	0.43435	0.010000	0.14839	-0.273000	0.10243	CTC	G|0.978;T|0.022	0.022	strong		0.637	TRMT2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318168.3	NM_022727		T	20103263	G	T	20103263	3	4	28	1	0	0	0	0	1	0	0	0	16580	971	34	4	1277	4	TRMT2A	22	20103263	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	621228	20103263	31201303	705	12208	151	2									
TRMT2A	27037	hgsc.bcm.edu	37	chr22	20103264	20103264	+	Silent	SNP	C	C	T																															tgcttgtgcctctgctcgagCagccagggcagcaaggcacg																								rs9605068|rs71317167	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:20103264C>T	ENST00000252136.7	-	3	1027	c.639G>A	c.(637-639)ctG>ctA	p.L213L	RANBP1_ENST00000402752.1_5'Flank|TRMT2A_ENST00000492988.1_5'Flank|TRMT2A_ENST00000403707.3_Silent_p.L213L|TRMT2A_ENST00000439169.2_Silent_p.L213L|RANBP1_ENST00000430524.1_5'Flank|TRMT2A_ENST00000404751.3_Silent_p.L213L|RANBP1_ENST00000331821.3_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)	213					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						TCTGCTCGAGCAGCCAGGGCA	0.637													C|||	59	0.0117812	0.0023	0.013	5008	,	,		18163	0.0		0.0378	False		,,,				2504	0.0092				p.L213L		Atlas-SNP	.											.	TRMT2A	34	.	0			c.G639A						PASS	.	C	,	27,4377	33.5+/-64.1	1,25,2176	45	42	43		639,639	1.8	0.7	22	dbSNP_119	43	327,8273	114.0+/-174.0	12,303,3985	no	coding-synonymous,coding-synonymous	TRMT2A	NM_022727.4,NM_182984.3	,	13,328,6161	TT,TC,CC		3.8023,0.6131,2.7222	,	213/626,213/626	20103264	354,12650	2202	4300	6502	SO:0001819	synonymous_variant	27037	exon3			CTCGAGCAGCCAG	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.639G>A	22.37:g.20103264C>T		191	0	0		203	98	0.482759	NM_001257994	D3DX25|Q32P57|Q96ME6|Q9H732	Silent	SNP	ENST00000252136.7	37	CCDS13774.1																																																																																			C|0.978;T|0.022	0.022	strong		0.637	TRMT2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318168.3	NM_022727		T	20103264	C	T	20103264	2	4	28	1	0	0	0	0	0	0	0	1	16580	697	25	2		2	TRMT2A	22	20103264	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1	20103264	31201302	706	12209	151	2									
PI4KA	5297	hgsc.bcm.edu	37	chr22	21064270	21064270	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agagtgaccagggagacgacCgcgtccatgtagggcctggg	9	5	17	10	3	0	3	0	1	0	2	1	5	1	3	4	3	0	1	4	3	1	1	rs151214632		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:21064270C>T	ENST00000572273.1	-	53	6155	c.5925G>A	c.(5923-5925)gcG>gcA	p.A1975A	PI4KA_ENST00000414196.3_Silent_p.A785A|PI4KA_ENST00000255882.6_Silent_p.A2033A			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	1975	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)			GGGAGACGACCGCGTCCATGT	0.617													N|||	1	0.000199681	0.0	0.0	5008	,	,		20530	0.0		0.001	False		,,,				2504	0.0				p.A2033A	GBM(136;1332 1831 3115 23601 50806)	Atlas-SNP	.											.	PI4KA	313	.	0			c.G6099A						PASS	.	C	,	3,4403	6.2+/-15.9	0,3,2200	113	89	97		2355,5925	-10.5	0.2	22	dbSNP_134	97	26,8574	18.5+/-59.3	0,26,4274	no	coding-synonymous,coding-synonymous	PI4KA	NM_002650.2,NM_058004.3	,	0,29,6474	TT,TC,CC		0.3023,0.0681,0.223	,	785/855,1975/2045	21064270	29,12977	2203	4300	6503	SO:0001819	synonymous_variant	5297	exon53			GACGACCGCGTCC	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.5925G>A	22.37:g.21064270C>T		429	0	0		465	234	0.503226	NM_058004	Q7Z625|Q9UPG2	Silent	SNP	ENST00000572273.1	37																																																																																				C|0.998;T|0.002	0.002	strong		0.617	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004		T	21064270	C	T	21064270	2	4	28	1	0	0	0	0	0	0	0	1	11882	639	23	1		1	PI4KA	22	21064270	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	961006	21064270	30240296	707	12210											
LZTR1	8216	hgsc.bcm.edu	37	chr22	21347142	21347142	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcggacgccatgtacatcttCgggggcacggtggacaacaa	10	7	13	11	4	1	0	0	0	1	0	3	2	1	2	1	5	2	2	1	5	3	2	rs145833752	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:21347142C>T	ENST00000215739.8	+	11	1568	c.1209C>T	c.(1207-1209)ttC>ttT	p.F403F	LZTR1_ENST00000479606.1_3'UTR|LZTR1_ENST00000389355.3_Silent_p.F384F	NM_006767.3	NP_006758.2	Q8N653	LZTR1_HUMAN	leucine-zipper-like transcription regulator 1	403					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)			TGTACATCTTCGGGGGCACGG	0.652													C|||	24	0.00479233	0.0023	0.0029	5008	,	,		19667	0.001		0.0109	False		,,,				2504	0.0072				p.F403F		Atlas-SNP	.											.	LZTR1	99	.	0			c.C1209T						PASS	.	C		7,4393	12.9+/-30.5	0,7,2193	55	45	48		1209	-5.1	1	22	dbSNP_134	48	78,8522	43.6+/-101.6	0,78,4222	no	coding-synonymous	LZTR1	NM_006767.3		0,85,6415	TT,TC,CC		0.907,0.1591,0.6538		403/841	21347142	85,12915	2200	4300	6500	SO:0001819	synonymous_variant	8216	exon11			CATCTTCGGGGGC	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.1209C>T	22.37:g.21347142C>T		93	0	0		116	64	0.551724	NM_006767	Q14776|Q20WK0	Silent	SNP	ENST00000215739.8	37	CCDS33606.1																																																																																			C|0.994;T|0.006	0.006	strong		0.652	LZTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320387.1	NM_006767		T	21347142	C	T	21347142	2	4	28	1	0	0	0	0	0	0	0	1	9146	883	31	1		1	LZTR1	22	21347142	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	282872	21347142	29957424	708	12211											
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230312	23230312	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccaggcagcgctggcccctgCtgctgctgggtctggccatg	3	8	15	15	1	1	0	0	0	1	0	1	0	1	0	4	4	4	5	4	4	0	0			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:23230312C>T	ENST00000526893.1	+	1	353	c.79C>T	c.(79-81)Ctg>Ttg	p.L27L	IGLL5_ENST00000532223.2_Silent_p.L27L|IGLL5_ENST00000531372.1_Silent_p.L27L|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	27						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CTGGCCCCTGCTGCTGCTGGG	0.667																																					p.L27L		Atlas-SNP	.											IGLL5,NS,lymphoid_neoplasm,-2,1	IGLL5	26	1	0			c.C79T						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			CCCCTGCTGCTGC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.79C>T	22.37:g.23230312C>T		111	0	0		125	43	0.344	NM_001178126		Silent	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.667	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		T	23230312	C	T	23230312	2	4	28	1	0	0	0	0	0	0	0	1	7603	796	28	2		2	IGLL5	22	23230312	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1883170	23230312	28074254	709	12212			5	52		3	3	129	N	G_C	4.486186e-06
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230399	23230399	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acccagaccctggagcctcaGttggaagcagccgatccagc	10	5	11	15	1	1	1	1	0	0	1	2	4	2	3	5	2	4	2	5	2	1	1	rs531309531	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:23230399G>C	ENST00000526893.1	+	1	440	c.166G>C	c.(166-168)Gtt>Ctt	p.V56L	IGLL5_ENST00000532223.2_Missense_Mutation_p.V56L|IGLL5_ENST00000531372.1_Missense_Mutation_p.V56L|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	56						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						TGGAGCCTCAGTTGGAAGCAG	0.667													G|||	2	0.000399361	0.0008	0.0	5008	,	,		10555	0.0		0.001	False		,,,				2504	0.0				p.V56L		Atlas-SNP	.											.	IGLL5	26	.	0			c.G166C						PASS	.																																			SO:0001583	missense	100423062	exon1			GCCTCAGTTGGAA	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.166G>C	22.37:g.23230399G>C	ENSP00000431254:p.Val56Leu	124	0	0		108	35	0.324074	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	10.19	1.282876	0.23392	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00573	6.48;6.48	3.92	-7.84	0.01196	.	.	.	.	.	T	0.00412	0.0013	L	0.27053	0.805	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.47058	-0.9146	9	0.87932	D	0	.	3.3385	0.07110	0.5698:0.1407:0.1627:0.1268	.	56	B9A064	IGLL5_HUMAN	L	56	ENSP00000436353:V56L;ENSP00000431254:V56L	ENSP00000431254:V56L	V	+	1	0	IGLL5	21560399	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.883000	0.04170	-1.783000	0.01274	-0.152000	0.13540	GTT	.	.	none		0.667	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		C	23230399	G	C	23230399	3	2	28	1	0	0	0	0	1	0	0	0	7603	1029	36	4	168	4	IGLL5	22	23230399	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	87	23230399	28074167	710	12213			5	52		3	3	129	N	G_C	4.486186e-06
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230440	23230440	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctgcggagcctgtggggcagGtaaggggcaagagattccag	9	6	18	8	1	0	1	0	0	0	1	1	3	1	2	2	6	2	3	2	6	2	2			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:23230440G>A	ENST00000526893.1	+	1	480		c.e1+1		IGLL5_ENST00000532223.2_Splice_Site|IGLL5_ENST00000531372.1_Splice_Site|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5							extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						TGTGGGGCAGGTAAGGGGCAA	0.627																																					.		Atlas-SNP	.											.	IGLL5	26	.	0			c.100+1G>A						PASS	.																																			SO:0001630	splice_region_variant	100423062	exon1			GGGCAGGTAAGGG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.206+1G>A	22.37:g.23230440G>A		97	0	0		86	29	0.337209	NM_001256296		Splice_Site	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	10.15	1.271539	0.23221	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	.	.	.	3.92	3.92	0.45320	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.74	0.51788	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	IGLL5	21560440	1.000000	0.71417	1.000000	0.80357	0.199000	0.23934	1.700000	0.37815	2.481000	0.83766	0.643000	0.83706	.	.	.	none		0.627	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	Intron	A	23230440	G	A	23230440	5	1	28	1	0	0	0	0	0	0	1	0	7603	1275	44	2	209	2	IGLL5	22	23230440	Splice_Site	SNP	G	TCGA-G8-6914-01A-11D-2210-10	41	23230440	28074126	711	12214			5	52		3	3	129	N	G_C	4.486186e-06
TFIP11	24144	hgsc.bcm.edu	37	chr22	26899695	26899695	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atggactgagtggtgcgctcGgatccataagcccccacagc	9	7	12	13	2	0	1	0	1	0	0	2	3	1	3	3	3	3	1	3	3	1	1	rs74334826	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:26899695G>A	ENST00000407690.1	-	7	868	c.585C>T	c.(583-585)tcC>tcT	p.S195S	TFIP11_ENST00000496523.1_5'UTR|TFIP11_ENST00000407431.1_Silent_p.S195S|TFIP11_ENST00000407148.1_Silent_p.S195S|TFIP11_ENST00000405938.1_Silent_p.S195S	NM_012143.2	NP_036275.1	Q9UBB9	TFP11_HUMAN	tuftelin interacting protein 11	195	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.				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						TGGTGCGCTCGGATCCATAAG	0.483													G|||	22	0.00439297	0.0008	0.0072	5008	,	,		19610	0.0		0.0149	False		,,,				2504	0.001				p.S195S		Atlas-SNP	.											.	TFIP11	72	.	0			c.C585T						PASS	.	G	,	12,4394	17.9+/-39.9	0,12,2191	154	135	141		585,585	-11.4	0	22	dbSNP_132	141	143,8457	71.3+/-133.9	0,143,4157	no	coding-synonymous,coding-synonymous	TFIP11	NM_001008697.1,NM_012143.2	,	0,155,6348	AA,AG,GG		1.6628,0.2724,1.1918	,	195/838,195/838	26899695	155,12851	2203	4300	6503	SO:0001819	synonymous_variant	24144	exon8			GCGCTCGGATCCA	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.585C>T	22.37:g.26899695G>A		74	0	0		88	44	0.5	NM_001008697	O95908|Q20WL0|Q5H8V8|Q9UGV7|Q9Y2Q8	Silent	SNP	ENST00000407690.1	37	CCDS13838.1	12	0.005494505494505495	0	0.0	3	0.008287292817679558	0	0.0	9	0.011873350923482849	G	0.332	-0.955568	0.02267	0.002724	0.016628	ENSG00000100109	ENST00000450493	.	.	.	5.68	-11.4	0.00090	.	.	.	.	.	T	0.17789	0.0427	.	.	.	0.51012	D	0.999905	.	.	.	.	.	.	T	0.45542	-0.9254	4	.	.	.	-16.0333	1.8375	0.03143	0.1951:0.1397:0.2425:0.4227	.	.	.	.	L	32	.	.	P	-	2	0	TFIP11	25229695	0.000000	0.05858	0.008000	0.14137	0.031000	0.12232	-7.970000	0.00027	-3.591000	0.00136	-0.867000	0.03001	CCG	G|0.991;A|0.009	0.009	strong		0.483	TFIP11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320750.1	NM_001008697		A	26899695	G	A	26899695	2	1	28	1	0	0	0	0	0	0	0	1	15822	1103	39	1		1	TFIP11	22	26899695	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	3669255	26899695	24404871	712	12215											
SLC5A4	6527	hgsc.bcm.edu	37	chr22	32647802	32647802	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	actcctgaagctgctcctgtCccagccagccccacatagtg	8	8	8	17	0	0	1	0	1	0	0	3	1	3	1	6	0	4	2	6	0	2	1	rs144495809	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:32647802C>T	ENST00000266086.4	-	3	278	c.267G>A	c.(265-267)ggG>ggA	p.G89G	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	89					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						CTGCTCCTGTCCCAGCCAGCC	0.478													c|||	11	0.00219649	0.0008	0.0072	5008	,	,		17002	0.004		0.001	False		,,,				2504	0.0				p.G89G		Atlas-SNP	.											.	SLC5A4	82	.	0			c.G267A						PASS	.	C		4,4402	8.1+/-20.4	0,4,2199	96	95	95		267	-2.2	0.4	22	dbSNP_134	95	29,8571	20.4+/-63.3	0,29,4271	no	coding-synonymous	SLC5A4	NM_014227.2		0,33,6470	TT,TC,CC		0.3372,0.0908,0.2537		89/660	32647802	33,12973	2203	4300	6503	SO:0001819	synonymous_variant	6527	exon3			TCCTGTCCCAGCC	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.267G>A	22.37:g.32647802C>T		42	0	0		46	22	0.478261	NM_014227	O15279	Silent	SNP	ENST00000266086.4	37	CCDS13903.1																																																																																			C|0.997;T|0.003	0.003	strong		0.478	SLC5A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315724.1	NM_014227		T	32647802	C	T	32647802	2	4	28	1	0	0	0	0	0	0	0	1	14682	842	30	2		2	SLC5A4	22	32647802	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	5748107	32647802	18656764	713	12216											
MYH9	4627	hgsc.bcm.edu	37	chr22	36681272	36681272	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgccctccatctcctgcagcTtgaccttaagctccttgttc	5	14	6	16	0	1	1	0	1	1	0	5	1	3	1	5	0	4	4	5	0	1	4	rs141440715	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:36681272T>C	ENST00000216181.5	-	38	5608	c.5378A>G	c.(5377-5379)aAg>aGg	p.K1793R	MYH9_ENST00000475726.1_5'UTR	NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1793					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						CTCCTGCAGCTTGACCTTAAG	0.587			T	ALK	ALCL		"Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"		Hereditary Macrothrombocytopenia, MYH9-associated																												p.K1793R		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"myosin, heavy polypeptide 9, non-muscle"	yes	L	.	MYH9	225	.	0			c.A5378G						PASS	.	T	ARG/LYS	1,4405	2.1+/-5.4	0,1,2202	144	115	125		5378	5	1	22	dbSNP_134	125	3,8597	3.7+/-12.6	0,3,4297	yes	missense	MYH9	NM_002473.4	26	0,4,6499	CC,CT,TT		0.0349,0.0227,0.0308	benign	1793/1961	36681272	4,13002	2203	4300	6503	SO:0001583	missense	4627	exon38	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	TGCAGCTTGACCT		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.5378A>G	22.37:g.36681272T>C	ENSP00000216181:p.Lys1793Arg	97	0	0		122	60	0.491803	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Missense_Mutation	SNP	ENST00000216181.5	37	CCDS13927.1	.	.	.	.	.	.	.	.	.	.	T	16.04	3.011097	0.54361	2.27E-4	3.49E-4	ENSG00000100345	ENST00000337818;ENST00000397231;ENST00000216181	T	0.75154	-0.91	5.03	5.03	0.67393	Myosin tail (1);Regulator of G protein signalling superfamily (1);	0.000000	0.85682	D	0.000000	T	0.60779	0.2295	N	0.25647	0.755	0.80722	D	1	B	0.24651	0.108	B	0.31016	0.123	T	0.56001	-0.8051	10	0.02654	T	1	.	14.7562	0.69567	0.0:0.0:0.0:1.0	.	1793	P35579	MYH9_HUMAN	R	1215;395;1793	ENSP00000216181:K1793R	ENSP00000216181:K1793R	K	-	2	0	MYH9	35011218	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.692000	0.84203	1.879000	0.54435	0.455000	0.32223	AAG	T|1.000;C|0.000	0.000	strong		0.587	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473		C	36681272	T	C	36681272	3	2	28	1	0	0	0	0	1	0	0	0	10051	1609	56	3	520	3	MYH9	22	36681272	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	4033470	36681272	14623294	714	12217											
FOXRED2	80020	hgsc.bcm.edu	37	chr22	36886112	36886112	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	agaggccctggagccaggggGgaacctagtggctcttggtc	7	7	17	10	0	1	1	0	0	1	1	2	3	1	3	3	7	2	1	3	7	2	2	rs34949308	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:36886112G>A	ENST00000397224.4	-	9	2091	c.1998C>T	c.(1996-1998)tcC>tcT	p.S666S	FOXRED2_ENST00000216187.6_Silent_p.S666S|FOXRED2_ENST00000397223.4_Silent_p.S666S|FOXRED2_ENST00000366463.3_Silent_p.S218S	NM_001102371.1	NP_001095841.1	Q8IWF2	FXRD2_HUMAN	FAD-dependent oxidoreductase domain containing 2	666					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						GAGCCAGGGGGGAACCTAGTG	0.642													G|||	40	0.00798722	0.0	0.0	5008	,	,		18397	0.0		0.0099	False		,,,				2504	0.0307				p.S666S		Atlas-SNP	.											.	FOXRED2	48	.	0			c.C1998T						PASS	.	G	,	12,4394	17.9+/-39.9	0,12,2191	33	37	36		1998,1998	-4.8	0	22	dbSNP_126	36	123,8477	61.0+/-122.8	1,121,4178	no	coding-synonymous,coding-synonymous	FOXRED2	NM_001102371.1,NM_024955.5	,	1,133,6369	AA,AG,GG		1.4302,0.2724,1.038	,	666/685,666/685	36886112	135,12871	2203	4300	6503	SO:0001819	synonymous_variant	80020	exon9			CAGGGGGGAACCT	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.1998C>T	22.37:g.36886112G>A		63	0	0		64	24	0.375	NM_001102371	B2RDI4|Q8N378|Q96BD1|Q9H5L5|Q9H6M8	Silent	SNP	ENST00000397224.4	37	CCDS13929.1																																																																																			G|0.991;A|0.009	0.009	strong		0.642	FOXRED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104098.2	NM_024955		A	36886112	G	A	36886112	2	1	28	1	0	0	0	0	0	0	0	1	6042	1219	43	2		2	FOXRED2	22	36886112	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	204840	36886112	14418454	715	12218											
GCAT	23464	hgsc.bcm.edu	37	chr22	38211287	38211287	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttcctggggcccacaggacGgtgggaccatgtggcacctg	6	7	15	13	1	0	0	0	0	0	0	1	2	1	2	4	6	0	1	4	6	0	1	rs200392738	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:38211287G>A	ENST00000248924.6	+	5	787	c.731G>A	c.(730-732)cGg>cAg	p.R244Q	GCAT_ENST00000323205.6_Splice_Site_p.R270Q	NM_014291.3	NP_055106.1	O75600	KBL_HUMAN	glycine C-acetyltransferase	244					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)	CCCACAGGACGGTGGGACCAT	0.622													G|||	2	0.000399361	0.0	0.0	5008	,	,		18933	0.002		0.0	False		,,,				2504	0.0				p.R270Q		Atlas-SNP	.											.	GCAT	27	.	0			c.G809A						PASS	.	G	GLN/ARG,GLN/ARG	0,4404		0,0,2202	30	27	28		809,731	2.5	1	22		28	1,8599	1.2+/-3.3	0,1,4299	yes	missense-near-splice,missense-near-splice	GCAT	NM_001171690.1,NM_014291.3	43,43	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	270/446,244/420	38211287	1,13003	2202	4300	6502	SO:0001630	splice_region_variant	23464	exon5			CAGGACGGTGGGA	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.731+1G>A	22.37:g.38211287G>A		94	0	0		91	62	0.681319	NM_001171690	E2QC23|Q6ZWF1|Q96CA9	Missense_Mutation	SNP	ENST00000248924.6	37	CCDS13957.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.426184	0.83667	0.0	1.16E-4	ENSG00000100116	ENST00000323205;ENST00000248924	D;D	0.90504	-2.68;-2.68	4.68	2.53	0.30540	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.109395	0.64402	D	0.000014	D	0.95831	0.8643	M	0.91038	3.17	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.75020	0.985;0.922	D	0.96264	0.9193	10	0.87932	D	0	-6.0188	14.7411	0.69455	0.0:0.2752:0.7248:0.0	.	270;244	E2QC23;O75600	.;KBL_HUMAN	Q	270;244	ENSP00000371110:R270Q;ENSP00000248924:R244Q	ENSP00000248924:R244Q	R	+	2	0	GCAT	36541233	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	6.642000	0.74329	0.563000	0.29222	-0.305000	0.09177	CGG	.	.	weak		0.622	GCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319506.1	NM_014291.2	Missense_Mutation	A	38211287	G	A	38211287	5	1	28	1	0	0	0	0	0	0	1	0	6292	1130	39	1	827	1	GCAT	22	38211287	Splice_Site	SNP	G	TCGA-G8-6914-01A-11D-2210-10	1325175	38211287	13093279	716	12219											
SYNGR1	9145	hgsc.bcm.edu	37	chr22	39777880	39777880	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cagcagccggccaacaccttCgacaccgagccccagggcta	10	3	10	18	3	0	0	0	0	0	0	1	2	0	0	6	2	4	2	6	2	2	2	rs74681509	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:39777880C>T	ENST00000328933.5	+	4	678	c.663C>T	c.(661-663)ttC>ttT	p.F221F		NM_004711.4	NP_004702.2	O43759	SNG1_HUMAN	synaptogyrin 1	221					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)					CCAACACCTTCGACACCGAGC	0.701													C|||	2	0.000399361	0.0	0.0	5008	,	,		13145	0.001		0.0	False		,,,				2504	0.001				p.F221F		Atlas-SNP	.											SYNGR1,colon,carcinoma,0,1	SYNGR1	19	1	0			c.C663T						PASS	.	C		1,4405		0,1,2202	25	26	25		663	-6.1	0.3	22	dbSNP_131	25	0,8594		0,0,4297	no	coding-synonymous	SYNGR1	NM_004711.4		0,1,6499	TT,TC,CC		0.0,0.0227,0.0077		221/234	39777880	1,12999	2203	4297	6500	SO:0001819	synonymous_variant	9145	exon4			CACCTTCGACACC	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.663C>T	22.37:g.39777880C>T		96	0	0		90	34	0.377778	NM_004711	A6NP69|A8K0E2|O43757|O43758|Q53Y02|Q96J56|Q9UGZ4	Silent	SNP	ENST00000328933.5	37	CCDS13989.1																																																																																			C|1.000;T|0.000	0.000	strong		0.701	SYNGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075866.2	NM_004711		T	39777880	C	T	39777880	2	4	28	1	0	0	0	0	0	0	0	1	15463	883	31	1		1	SYNGR1	22	39777880	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	1566593	39777880	11526686	717	12220											
GRAP2	9402	hgsc.bcm.edu	37	chr22	40366924	40366924	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aacagcgagtgcggtgggccCgggcgctgtatgactttgag	7	8	17	9	4	0	2	0	2	0	0	0	3	0	2	1	3	3	2	1	3	2	2	rs149718626	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:40366924C>T	ENST00000344138.4	+	8	1092	c.829C>T	c.(829-831)Cgg>Tgg	p.R277W	GRAP2_ENST00000540310.1_Missense_Mutation_p.R211W|GRAP2_ENST00000544756.1_Missense_Mutation_p.R205W|GRAP2_ENST00000543252.1_Missense_Mutation_p.R237W|GRAP2_ENST00000407075.3_Missense_Mutation_p.R277W|GRAP2_ENST00000399090.2_Missense_Mutation_p.R164W	NM_004810.2	NP_004801.1	O75791	GRAP2_HUMAN	GRB2-related adaptor protein 2	277	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						GCGGTGGGCCCGGGCGCTGTA	0.657																																					p.R277W		Atlas-SNP	.											.	GRAP2	29	.	0			c.C829T						PASS	.	C	TRP/ARG	0,4406		0,0,2203	42	44	43		829	0.6	0.9	22	dbSNP_134	43	2,8598	2.2+/-6.3	0,2,4298	yes	missense	GRAP2	NM_004810.2	101	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	277/331	40366924	2,13004	2203	4300	6503	SO:0001583	missense	9402	exon8			TGGGCCCGGGCGC	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.829C>T	22.37:g.40366924C>T	ENSP00000339186:p.Arg277Trp	61	0	0		39	18	0.461538	NM_004810	B7Z8I3|O43726|Q9NRB7	Missense_Mutation	SNP	ENST00000344138.4	37	CCDS13999.1	.	.	.	.	.	.	.	.	.	.	C	19.22	3.786068	0.70337	0.0	2.33E-4	ENSG00000100351	ENST00000344138;ENST00000543252;ENST00000544006;ENST00000540310;ENST00000544756;ENST00000399090;ENST00000407075	T;T;T;T;T;T	0.52983	0.64;1.37;0.64;0.64;0.64;0.64	5.45	0.607	0.17564	Src homology-3 domain (5);	0.508670	0.20690	N	0.087471	T	0.69513	0.3119	M	0.92649	3.33	0.40772	D	0.983098	D;D;D;D;D	0.89917	1.0;0.998;0.999;0.999;0.998	D;P;D;P;P	0.68765	0.96;0.817;0.921;0.877;0.817	T	0.73257	-0.4040	10	0.66056	D	0.02	-14.6978	8.7497	0.34609	0.5226:0.4077:0.0:0.0697	.	164;277;211;251;277	B7Z8I3;Q6FI14;F5H548;B7Z8F8;O75791	.;.;.;.;GRAP2_HUMAN	W	277;237;251;211;205;164;277	ENSP00000339186:R277W;ENSP00000446350:R237W;ENSP00000444734:R211W;ENSP00000442195:R205W;ENSP00000382040:R164W;ENSP00000385607:R277W	ENSP00000339186:R277W	R	+	1	2	GRAP2	38696870	0.999000	0.42202	0.932000	0.37286	0.880000	0.50808	0.823000	0.27366	0.593000	0.29745	0.557000	0.71058	CGG	C|1.000;T|0.000	0.000	strong		0.657	GRAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321295.1	NM_004810		T	40366924	C	T	40366924	3	4	28	1	0	0	0	0	1	0	0	0	6763	643	23	1	855	1	GRAP2	22	40366924	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	589044	40366924	10937642	718	12221											
EP300	2033	hgsc.bcm.edu	37	chr22	41574383	41574383	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttggctacccaccacagcAgcagcagcggatgcagcatc	11	5	11	14	1	0	0	0	0	0	0	1	1	0	1	2	2	7	7	2	2	1	2	rs1046088	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:41574383A>C	ENST00000263253.7	+	31	7887	c.6668A>C	c.(6667-6669)cAg>cCg	p.Q2223P	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	2223	Interaction with NCOA2.		Q -> P (in dbSNP:rs1046088). {ECO:0000269|PubMed:7523245}.		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						CCACCACAGCAGCAGCAGCGG	0.577			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome				A|||	57	0.0113818	0.0015	0.0173	5008	,	,		21238	0.0		0.0388	False		,,,				2504	0.0041				p.Q2223P		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300	367	.	0			c.A6668C						PASS	.	A	PRO/GLN	25,4381	32.6+/-62.9	0,25,2178	60	60	60		6668	3.3	1	22	dbSNP_86	60	312,8288	111.4+/-171.7	5,302,3993	yes	missense	EP300	NM_001429.3	76	5,327,6171	CC,CA,AA		3.6279,0.5674,2.5911	benign	2223/2415	41574383	337,12669	2203	4300	6503	SO:0001583	missense	2033	exon31	Familial Cancer Database	Broad Thumb-Hallux syndrome	CACAGCAGCAGCA	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.6668A>C	22.37:g.41574383A>C	ENSP00000263253:p.Gln2223Pro	91	0	0		108	43	0.398148	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	42	0.019230769230769232	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	33	0.04353562005277045	A	7.129	0.579572	0.13686	0.005674	0.036279	ENSG00000100393	ENST00000263253	D	0.84944	-1.92	5.5	3.27	0.37495	.	0.532986	0.15322	N	0.268513	T	0.45337	0.1337	N	0.22421	0.69	0.39836	D	0.973045	B	0.02656	0.0	B	0.01281	0.0	T	0.58561	-0.7615	10	0.27082	T	0.32	.	12.1846	0.54231	0.7172:0.2828:0.0:0.0	rs1046088;rs60456996;rs1046088	2223	Q09472	EP300_HUMAN	P	2223	ENSP00000263253:Q2223P	ENSP00000263253:Q2223P	Q	+	2	0	EP300	39904329	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.250000	0.58772	0.920000	0.36970	0.533000	0.62120	CAG	A|0.977;C|0.023	0.023	strong		0.577	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		C	41574383	A	C	41574383	3	2	28	1	0	0	0	0	1	0	0	0	5150	188	7	5	6790	5	EP300	22	41574383	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	1207459	41574383	9730183	719	12222											
A4GALT	53947	hgsc.bcm.edu	37	chr22	43089833	43089833	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctccttgggctctcccacaAcgtgccagtagatcatgatg	8	11	9	13	1	3	2	1	1	2	1	5	2	3	2	3	1	2	2	3	1	2	2	rs148881382		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:43089833A>G	ENST00000401850.1	-	2	614	c.125T>C	c.(124-126)gTt>gCt	p.V42A	A4GALT_ENST00000465765.2_5'Flank|A4GALT_ENST00000249005.2_Missense_Mutation_p.V42A|A4GALT_ENST00000381278.3_Missense_Mutation_p.V42A			Q9NPC4	A4GAT_HUMAN	alpha 1,4-galactosyltransferase	42					globoside biosynthetic process (GO:0001576)|glycosphingolipid biosynthetic process (GO:0006688)|plasma membrane organization (GO:0007009)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	galactosyltransferase activity (GO:0008378)|lactosylceramide 4-alpha-galactosyltransferase activity (GO:0050512)|toxic substance binding (GO:0015643)			NS(1)|central_nervous_system(2)|large_intestine(6)|skin(1)|urinary_tract(1)	11						CTCTCCCACAACGTGCCAGTA	0.622																																					p.V42A		Atlas-SNP	.											.	A4GALT	35	.	0			c.T125C						PASS	.	A	ALA/VAL	0,4404		0,0,2202	28	20	23		125	2.3	0	22	dbSNP_134	23	4,8592		0,4,4294	yes	missense	A4GALT	NM_017436.4	64	0,4,6496	GG,GA,AA		0.0465,0.0,0.0308	benign	42/354	43089833	4,12996	2202	4298	6500	SO:0001583	missense	53947	exon3			CCCACAACGTGCC		CCDS14041.1	22q13.2	2014-07-18	2008-07-31		ENSG00000128274	ENSG00000128274	2.4.1.228		18149	protein-coding gene	gene with protein product	"Gb3 synthase", "CD77 synthase", "globotriaosylceramide synthase", "lactosylceramide 4-alpha-galactosyltransferase"	607922	"alpha 1,4-galactosyltransferase (globotriaosylceramide synthase, P blood group)"			10854428	Standard	XM_005261643		Approved	A14GALT, Gb3S, P(k)	uc003bdb.3	Q9NPC4	OTTHUMG00000150744	ENST00000401850.1:c.125T>C	22.37:g.43089833A>G	ENSP00000384794:p.Val42Ala	71	0	0		90	44	0.488889	NM_017436	B2R7C4|Q9P1X5	Missense_Mutation	SNP	ENST00000401850.1	37	CCDS14041.1	.	.	.	.	.	.	.	.	.	.	A	9.301	1.053038	0.19907	0.0	4.65E-4	ENSG00000128274	ENST00000401850;ENST00000249005;ENST00000381278;ENST00000535654	T;T;T	0.80393	-1.37;-1.37;-1.37	4.49	2.33	0.28932	.	0.613294	0.12950	U	0.425919	T	0.60932	0.2307	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.12156	0.007	T	0.47611	-0.9104	10	0.29301	T	0.29	-9.9823	8.3249	0.32151	0.8269:0.0:0.1731:0.0	.	42	Q9NPC4	A4GAT_HUMAN	A	42	ENSP00000384794:V42A;ENSP00000249005:V42A;ENSP00000370678:V42A	ENSP00000249005:V42A	V	-	2	0	A4GALT	41419777	0.020000	0.18652	0.000000	0.03702	0.056000	0.15407	2.025000	0.41059	0.324000	0.23333	-0.464000	0.05259	GTT	A|1.000;G|0.000	0.000	weak		0.622	A4GALT-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319917.1	NM_017436		G	43089833	A	G	43089833	3	3	28	1	0	0	0	0	1	0	0	0	6	43	2	3	940	3	A4GALT	22	43089833	Missense_Mutation	SNP	A	TCGA-G8-6914-01A-11D-2210-10	1515450	43089833	8214733	720	12223											
SMC1B	27127	hgsc.bcm.edu	37	chr22	45750920	45750920	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggggctgctgttttcagtaAgatatcttcctgggatgcta	7	15	12	7	0	2	1	1	0	1	1	3	2	3	2	1	3	2	5	1	3	3	6	rs61748560	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:45750920A>G	ENST00000357450.4	-	20	3036	c.3037T>C	c.(3037-3039)Tta>Cta	p.L1013L	SMC1B_ENST00000404354.3_Silent_p.L1013L	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	1013					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)		GTTTTCAGTAAGATATCTTCC	0.443													A|||	17	0.00339457	0.0	0.0043	5008	,	,		18176	0.0		0.0129	False		,,,				2504	0.001				p.L1013L		Atlas-SNP	.											.	SMC1B	215	.	0			c.T3037C						PASS	.	A		6,3840		0,6,1917	206	194	197		3037	-0.4	0	22	dbSNP_129	197	87,8191		0,87,4052	no	coding-synonymous	SMC1B	NM_148674.3		0,93,5969	GG,GA,AA		1.051,0.156,0.7671		1013/1236	45750920	93,12031	1923	4139	6062	SO:0001819	synonymous_variant	27127	exon20			TCAGTAAGATATC	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.3037T>C	22.37:g.45750920A>G		180	0	0		170	85	0.5	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Silent	SNP	ENST00000357450.4	37	CCDS43027.1																																																																																			A|0.989;G|0.011	0.011	strong		0.443	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674		G	45750920	A	G	45750920	2	3	28	1	0	0	0	0	0	0	0	1	14797	69	3	3		3	SMC1B	22	45750920	Silent	SNP	A	TCGA-G8-6914-01A-11D-2210-10	2661087	45750920	5553646	721	12224											
BRD1	23774	hgsc.bcm.edu	37	chr22	50187853	50187853	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggagccgctggacttcatagCgcaggtgaggtcgagcatgt	8	8	16	9	3	1	1	1	1	0	0	2	4	1	3	1	4	3	3	1	4	1	2	rs35331092	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:50187853C>T	ENST00000216267.8	-	6	2674	c.2188G>A	c.(2188-2190)Gct>Act	p.A730T	BRD1_ENST00000342989.5_Missense_Mutation_p.A325T|BRD1_ENST00000404034.1_Missense_Mutation_p.A730T|BRD1_ENST00000542442.1_Missense_Mutation_p.A418T|BRD1_ENST00000404760.1_Missense_Mutation_p.A730T|BRD1_ENST00000457780.2_Missense_Mutation_p.A730T	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	730			A -> T (in dbSNP:rs35331092).		histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			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)		GACTTCATAGCGCAGGTGAGG	0.607													C|||	342	0.0682907	0.0825	0.0317	5008	,	,		18559	0.003		0.0596	False		,,,				2504	0.1513				p.A730T		Atlas-SNP	.											.	BRD1	144	.	0			c.G2188A						PASS	.	C	THR/ALA	422,3984	206.5+/-228.1	21,380,1802	59	63	62		2188	-0.9	0.4	22	dbSNP_126	62	590,8010	156.4+/-210.3	24,542,3734	yes	missense	BRD1	NM_014577.1	58	45,922,5536	TT,TC,CC		6.8605,9.5778,7.781	benign	730/1059	50187853	1012,11994	2203	4300	6503	SO:0001583	missense	23774	exon6			TCATAGCGCAGGT	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.2188G>A	22.37:g.50187853C>T	ENSP00000216267:p.Ala730Thr	61	0	0		76	38	0.5	NM_014577	A6ZJA4	Missense_Mutation	SNP	ENST00000216267.8	37	CCDS14080.1	96	0.04395604395604396	41	0.08333333333333333	12	0.03314917127071823	0	0.0	43	0.05672823218997362	C	14.17	2.456934	0.43634	0.095778	0.068605	ENSG00000100425	ENST00000216267;ENST00000404034;ENST00000404760;ENST00000457780;ENST00000542442;ENST00000342989;ENST00000419212	T;T;T;T;T;T	0.28255	2.57;2.57;2.58;2.44;1.62;2.01	5.4	-0.94	0.10405	.	0.418477	0.26248	N	0.025479	T	0.00754	0.0025	L	0.39898	1.24	0.28355	P	0.9207138	P;P;P;D	0.54964	0.948;0.63;0.788;0.969	B;B;B;B	0.43728	0.247;0.12;0.169;0.429	T	0.07654	-1.0761	9	0.31617	T	0.26	.	21.7236	0.99959	0.1644:0.8356:0.0:0.0	rs35331092	730;325;730;730	Q86X06;B7Z926;O95696;O95696-2	.;.;BRD1_HUMAN;.	T	730;730;730;730;418;325;190	ENSP00000216267:A730T;ENSP00000384076:A730T;ENSP00000385858:A730T;ENSP00000410042:A730T;ENSP00000437514:A418T;ENSP00000345886:A325T	ENSP00000216267:A730T	A	-	1	0	BRD1	48573857	0.065000	0.20965	0.369000	0.25952	0.980000	0.70556	0.428000	0.21395	-0.460000	0.07003	0.655000	0.94253	GCT	C|0.936;T|0.064	0.064	strong		0.607	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577		T	50187853	C	T	50187853	3	4	28	1	0	0	0	0	1	0	0	0	1503	768	27	1	1016	1	BRD1	22	50187853	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	4436933	50187853	1116713	722	12225											
BRD1	23774	hgsc.bcm.edu	37	chr22	50217300	50217300	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgctgttctgacactccccGtccatgcagatgcagcacac	8	10	8	15	1	1	2	0	1	1	1	3	2	3	2	3	0	4	5	3	0	0	2	rs374070979		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:50217300G>A	ENST00000216267.8	-	1	1152	c.666C>T	c.(664-666)gaC>gaT	p.D222D	BRD1_ENST00000342989.5_5'Flank|BRD1_ENST00000459821.1_5'Flank|BRD1_ENST00000404034.1_Silent_p.D222D|BRD1_ENST00000542442.1_5'Flank|BRD1_ENST00000404760.1_Silent_p.D222D|BRD1_ENST00000457780.2_Silent_p.D222D	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	222					histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			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)		GACACTCCCCGTCCATGCAGA	0.612																																					p.D222D		Atlas-SNP	.											.	BRD1	144	.	0			c.C666T						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	62	49	53		666	-4.3	1	22		53	0,8600		0,0,4300	no	coding-synonymous	BRD1	NM_014577.1		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		222/1059	50217300	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	23774	exon1			CTCCCCGTCCATG	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.666C>T	22.37:g.50217300G>A		46	0	0		57	33	0.578947	NM_014577	A6ZJA4	Silent	SNP	ENST00000216267.8	37	CCDS14080.1																																																																																			.	.	weak		0.612	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577		A	50217300	G	A	50217300	2	1	28	1	0	0	0	0	0	0	0	1	1503	1136	40	1		1	BRD1	22	50217300	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	29447	50217300	1087266	723	12226											
BRD1	23774	hgsc.bcm.edu	37	chr22	50217387	50217387	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcgcagtgcgactccttctcGaagcggtccatcaggaactc	8	9	10	14	4	2	0	1	0	1	0	7	3	4	1	2	2	3	1	2	2	2	1	rs11912787	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:50217387G>A	ENST00000216267.8	-	1	1065	c.579C>T	c.(577-579)ttC>ttT	p.F193F	BRD1_ENST00000342989.5_5'Flank|BRD1_ENST00000459821.1_5'Flank|BRD1_ENST00000404034.1_Silent_p.F193F|BRD1_ENST00000542442.1_5'Flank|BRD1_ENST00000404760.1_Silent_p.F193F|BRD1_ENST00000457780.2_Silent_p.F193F	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	193					histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			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)		ACTCCTTCTCGAAGCGGTCCA	0.602													G|||	508	0.101438	0.1664	0.0432	5008	,	,		21111	0.003		0.0746	False		,,,				2504	0.184				p.F193F		Atlas-SNP	.											.	BRD1	144	.	0			c.C579T						PASS	.	G		801,3605	322.9+/-297.8	69,663,1471	72	61	65		579	-5.2	1	22	dbSNP_120	65	702,7898	172.6+/-223.3	31,640,3629	no	coding-synonymous	BRD1	NM_014577.1		100,1303,5100	AA,AG,GG		8.1628,18.1798,11.5562		193/1059	50217387	1503,11503	2203	4300	6503	SO:0001819	synonymous_variant	23774	exon1			CTTCTCGAAGCGG	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.579C>T	22.37:g.50217387G>A		94	0	0		93	42	0.451613	NM_014577	A6ZJA4	Silent	SNP	ENST00000216267.8	37	CCDS14080.1																																																																																			G|0.899;A|0.101	0.101	strong		0.602	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577		A	50217387	G	A	50217387	2	1	28	1	0	0	0	0	0	0	0	1	1503	1049	37	1		1	BRD1	22	50217387	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	87	50217387	1087179	724	12227											
CRELD2	79174	hgsc.bcm.edu	37	chr22	50315382	50315382	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acggctacttcagctcgctcCggaacgagacccacagcatc	10	6	9	16	4	1	1	1	0	0	1	4	3	2	2	2	2	4	4	2	2	2	2	rs74510325	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:50315382C>G	ENST00000328268.4	+	5	639	c.565C>G	c.(565-567)Cgg>Ggg	p.R189G	CRELD2_ENST00000404488.3_Missense_Mutation_p.R189G|CRELD2_ENST00000444954.1_3'UTR|CRELD2_ENST00000407217.3_Missense_Mutation_p.R189G|CRELD2_ENST00000403427.3_Missense_Mutation_p.R189G	NM_024324.3	NP_077300.3	Q6UXH1	CREL2_HUMAN	cysteine-rich with EGF-like domains 2	189						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)		CAGCTCGCTCCGGAACGAGAC	0.672													C|||	43	0.00858626	0.0015	0.0115	5008	,	,		18650	0.0		0.0288	False		,,,				2504	0.0041				p.R189G		Atlas-SNP	.											.	CRELD2	57	.	0			c.C565G						PASS	.	C	GLY/ARG,GLY/ARG	40,4366	43.1+/-76.7	0,40,2163	81	82	82		565,565	-1.7	0.4	22	dbSNP_132	82	341,8259	116.3+/-176.0	8,325,3967	yes	missense,missense	CRELD2	NM_001135101.1,NM_024324.3	125,125	8,365,6130	GG,GC,CC		3.9651,0.9079,2.9294	probably-damaging,probably-damaging	189/403,189/354	50315382	381,12625	2203	4300	6503	SO:0001583	missense	79174	exon5			TCGCTCCGGAACG	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.565C>G	22.37:g.50315382C>G	ENSP00000332223:p.Arg189Gly	71	0	0		96	45	0.46875	NM_024324	A5GZA2|A5GZA3|A5GZA4|A5GZA5|A5GZA6|Q4W0V0|Q86UC0|Q9BU47	Missense_Mutation	SNP	ENST00000328268.4	37	CCDS14082.1	25	0.011446886446886446	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	21	0.027704485488126648	C	12.01	1.808463	0.31961	0.009079	0.039651	ENSG00000184164	ENST00000450207;ENST00000404488;ENST00000328268;ENST00000407217;ENST00000403427	T;T;T;T;T	0.58358	2.46;0.51;0.38;0.56;0.34	4.12	-1.66	0.08265	EGF-like, laminin (1);Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	T	0.21307	0.0513	N	0.20483	0.58	0.37318	D	0.90941	D;D;D;P;D;D	0.71674	0.997;0.998;0.997;0.91;0.99;0.98	D;D;D;P;P;P	0.69307	0.915;0.963;0.915;0.492;0.825;0.857	T	0.47522	-0.9111	10	0.59425	D	0.04	.	14.2293	0.65879	0.302:0.698:0.0:0.0	.	189;189;189;189;189;189	Q6UXH1-2;Q6UXH1-5;Q6UXH1-4;A5GZA6;Q6UXH1;Q6UXH1-3	.;.;.;.;CREL2_HUMAN;.	G	189	ENSP00000387769:R189G;ENSP00000383938:R189G;ENSP00000332223:R189G;ENSP00000386034:R189G;ENSP00000384111:R189G	ENSP00000332223:R189G	R	+	1	2	CRELD2	48701386	0.963000	0.33076	0.423000	0.26634	0.819000	0.46315	0.917000	0.28665	-0.606000	0.05746	-0.274000	0.10170	CGG	C|0.978;G|0.022	0.022	strong		0.672	CRELD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317409.1	NM_024324		G	50315382	C	G	50315382	3	3	28	1	0	0	0	0	1	0	0	0	3869	643	23	4	583	4	CRELD2	22	50315382	Missense_Mutation	SNP	C	TCGA-G8-6914-01A-11D-2210-10	97995	50315382	989184	725	12228											
SHANK3	85358	hgsc.bcm.edu	37	chr22	51160581	51160581	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgaagcagtcctcggacagCgagctcatggcccagcagca	10	5	12	14	2	1	1	1	1	0	0	3	3	2	2	2	2	5	4	2	2	1	0			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:51160581C>T	ENST00000414786.2	+	21	4505	c.4278C>T	c.(4276-4278)agC>agT	p.S1426S	SHANK3_ENST00000262795.3_Silent_p.S1456S|SHANK3_ENST00000445220.2_Silent_p.S1442S			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	1440					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)		CCTCGGACAGCGAGCTCATGG	0.682																																					p.S1426S		Atlas-SNP	.											.	SHANK3	96	.	0			c.C4278T						PASS	.						14	19	17					22																	51160581		2085	4202	6287	SO:0001819	synonymous_variant	85358	exon21			GGACAGCGAGCTC	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.4278C>T	22.37:g.51160581C>T		9	0	0		14	9	0.642857	NM_033517	D7UT47|Q8TET3	Silent	SNP	ENST00000414786.2	37																																																																																				.	.	none		0.682	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420		T	51160581	C	T	51160581	2	4	28	1	0	0	0	0	0	0	0	1	14281	767	27	1		1	SHANK3	22	51160581	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	845199	51160581	143985	726	12229											
WWC3	55841	hgsc.bcm.edu	37	chrX	10085227	10085227	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtccctagcctccagccgTgggtctctggcctccagccg	3	8	13	17	2	1	0	0	0	1	0	5	0	4	0	7	3	3	0	7	3	1	1	rs7058143	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:10085227T>C	ENST00000380861.4	+	11	1519	c.1128T>C	c.(1126-1128)cgT>cgC	p.R376R	WWC3_ENST00000454666.1_Silent_p.R376R	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	376	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						CCTCCAGCCGTGGGTCTCTGG	0.672													C|||	774	0.205033	0.5401	0.0648	3775	,	,		12301	0.0		0.0149	False		,,,				2504	0.0				p.R376R		Atlas-SNP	.											.	WWC3	142	.	0			c.T1128C						PASS	.	C		2272,1558		575,780,342,277,224	36	44	41		1128	-3.3	0.3	X	dbSNP_116	41	142,6583		0,105,37,2323,1832	no	coding-synonymous	WWC3	NM_015691.3		575,885,379,2600,2056	CC,CT,C,TT,T		2.1115,40.6789,22.8707		376/1093	10085227	2414,8141	2198	4297	6495	SO:0001819	synonymous_variant	55841	exon11			CAGCCGTGGGTCT	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.1128T>C	X.37:g.10085227T>C		49	0	0		39	39	1	NM_015691	A8KA96|Q659C1|Q9BTQ1	Silent	SNP	ENST00000380861.4	37	CCDS14136.1																																																																																			0|0.004;C|0.221	0.221	strong		0.672	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691		C	10085227	T	C	10085227	2	2	28	1	0	0	0	0	0	0	0	1	17428	1683	59	3		3	WWC3	23	10085227	Silent	SNP	T	TCGA-G8-6914-01A-11D-2210-10		10085227	145185333	727	12230											
WWC3	55841	hgsc.bcm.edu	37	chrX	10085602	10085602	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccctagacagactgcgggcAcacgcctcggctatggggga	8	5	15	13	3	0	2	0	0	0	2	1	3	0	3	2	4	1	2	2	4	2	2	rs56130457		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:10085602A>C	ENST00000380861.4	+	11	1894	c.1503A>C	c.(1501-1503)gcA>gcC	p.A501A	WWC3_ENST00000454666.1_Silent_p.A501A	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	501					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						GACTGCGGGCACACGCCTCGG	0.716													A|||	8	0.00211921	0.0008	0.0014	3775	,	,		11380	0.0		0.006	False		,,,				2504	0.0				p.A501A		Atlas-SNP	.											.	WWC3	142	.	0			c.A1503C						PASS	.	A		8,3752		0,6,2,1607,532	7	7	7		1503	-10.9	0	X	dbSNP_129	7	85,6535		0,60,25,2350,1775	no	coding-synonymous	WWC3	NM_015691.3		0,66,27,3957,2307	CC,CA,C,AA,A		1.284,0.2128,0.896		501/1093	10085602	93,10287	2147	4210	6357	SO:0001819	synonymous_variant	55841	exon11			GCGGGCACACGCC	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.1503A>C	X.37:g.10085602A>C		25	0	0		27	27	1	NM_015691	A8KA96|Q659C1|Q9BTQ1	Silent	SNP	ENST00000380861.4	37	CCDS14136.1																																																																																			A|0.995;C|0.005	0.005	strong		0.716	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691		C	10085602	A	C	10085602	2	2	28	1	0	0	0	0	0	0	0	1	17428	146	6	5		5	WWC3	23	10085602	Silent	SNP	A	TCGA-G8-6914-01A-11D-2210-10	375	10085602	145184958	728	12231											
ZNF645	158506	hgsc.bcm.edu	37	chrX	22291942	22291942	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctcatcatattatacctcaGaaacagcattatgcgccacc	13	10	4	14	1	3	1	3	0	0	1	3	1	3	1	4	0	4	1	4	0	5	4	rs138094158	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:22291942G>A	ENST00000323684.1	+	1	878	c.834G>A	c.(832-834)caG>caA	p.Q278Q		NM_152577.3	NP_689790.1	Q8N7E2	ZN645_HUMAN	zinc finger protein 645	278	Pro-rich.				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						TTATACCTCAGAAACAGCATT	0.463													G|||	1	0.000264901	0.0	0.0	3775	,	,		16433	0.0		0.001	False		,,,				2504	0.0				p.Q278Q		Atlas-SNP	.											.	ZNF645	67	.	0			c.G834A						PASS	.	G		2,3833		0,2,0,1630,571	149	119	129		834	-5.1	0	X	dbSNP_134	129	28,6700		0,19,9,2409,1863	no	coding-synonymous	ZNF645	NM_152577.3		0,21,9,4039,2434	AA,AG,A,GG,G		0.4162,0.0522,0.284		278/426	22291942	30,10533	2203	4300	6503	SO:0001819	synonymous_variant	158506	exon1			ACCTCAGAAACAG	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.834G>A	X.37:g.22291942G>A		156	0	0		161	160	0.993789	NM_152577	A0AV29|A0AV31|E3SBK4|Q6DJY9	Silent	SNP	ENST00000323684.1	37	CCDS14205.1																																																																																			G|0.997;A|0.003	0.003	strong		0.463	ZNF645-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056037.1	NM_152577		A	22291942	G	A	22291942	2	1	28	1	0	0	0	0	0	0	0	1	18076	933	33	2		2	ZNF645	23	22291942	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	12206340	22291942	132978618	729	12232											
POLA1	5422	hgsc.bcm.edu	37	chrX	25014016	25014016	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcttgtcccgaagtggctaCtccgaagtgaatctgagcaa	10	11	10	10	2	2	2	0	2	2	0	4	4	4	2	2	1	2	2	2	1	5	3	rs11573531	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:25014016C>T	ENST00000379059.3	+	37	4353	c.4338C>T	c.(4336-4338)taC>taT	p.Y1446Y	POLA1_ENST00000379068.3_Silent_p.Y1452Y	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	1446					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)	GAAGTGGCTACTCCGAAGTGA	0.443													C|||	8	0.00211921	0.0	0.0014	3775	,	,		12343	0.0		0.007	False		,,,				2504	0.0				p.Y1446Y		Atlas-SNP	.											.	POLA1	117	.	0			c.C4338T						PASS	.	C		9,3824		0,7,2,1624,569	73	60	64		4338	3.3	1	X	dbSNP_120	64	101,6627		0,79,22,2349,1850	no	coding-synonymous	POLA1	NM_016937.3		0,86,24,3973,2419	TT,TC,T,CC,C		1.5012,0.2348,1.0416		1446/1463	25014016	110,10451	2202	4300	6502	SO:0001819	synonymous_variant	5422	exon37			TGGCTACTCCGAA		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.4338C>T	X.37:g.25014016C>T		150	0	0		139	139	1	NM_016937	Q86UQ7	Silent	SNP	ENST00000379059.3	37	CCDS14214.1																																																																																			C|0.990;T|0.010	0.010	strong		0.443	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937		T	25014016	C	T	25014016	2	4	28	1	0	0	0	0	0	0	0	1	12196	576	20	2		2	POLA1	23	25014016	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	2722074	25014016	130256544	730	12233											
SMC1A	8243	hgsc.bcm.edu	37	chrX	53407996	53407996	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tcatccaggacgaagaagggGgctggcttgtagctgggagg	9	7	18	7	1	1	1	1	0	0	1	2	4	2	3	1	6	1	4	1	6	3	2	rs142611198	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:53407996G>A	ENST00000322213.4	-	23	3577	c.3450C>T	c.(3448-3450)gcC>gcT	p.A1150A	SMC1A_ENST00000469129.1_5'Flank	NM_006306.2	NP_006297.2	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	1150	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						CGAAGAAGGGGGCTGGCTTGT	0.617													G|||	2	0.000529801	0.0	0.0014	3775	,	,		10861	0.0		0.001	False		,,,				2504	0.0				p.A1150A		Atlas-SNP	.											.	SMC1A	112	.	0			c.C3450T						PASS	.	G		0,3835		0,0,0,1632,571	67	58	61		3450	3.5	1	X	dbSNP_134	61	10,6718		0,8,2,2420,1870	no	coding-synonymous	SMC1A	NM_006306.2		0,8,2,4052,2441	AA,AG,A,GG,G		0.1486,0.0,0.0947		1150/1234	53407996	10,10553	2203	4300	6503	SO:0001819	synonymous_variant	8243	exon23			GAAGGGGGCTGGC	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.3450C>T	X.37:g.53407996G>A		75	0	0		106	103	0.971698	NM_006306	O14995|Q16351|Q2M228	Silent	SNP	ENST00000322213.4	37	CCDS14352.1																																																																																			G|0.999;A|0.001	0.001	strong		0.617	SMC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056756.2	NM_006306		A	53407996	G	A	53407996	2	1	28	1	0	0	0	0	0	0	0	1	14796	1219	43	2		2	SMC1A	23	53407996	Silent	SNP	G	TCGA-G8-6914-01A-11D-2210-10	28393980	53407996	101862564	731	12234											
CHIC1	53344	hgsc.bcm.edu	37	chrX	72797296	72797296	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccctccgttctaacagggaAggtaagtgagaatttgcttt	10	13	10	8	1	1	1	0	1	1	1	3	3	3	2	2	2	2	3	2	2	4	5			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:72797296A>T	ENST00000373502.5	+	2	427	c.350A>T	c.(349-351)aAg>aTg	p.K117M	CHIC1_ENST00000373504.6_Splice_Site_p.K117M	NM_001039840.2	NP_001034929.2	Q5VXU3	CHIC1_HUMAN	cysteine-rich hydrophobic domain 1	117						cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)|lung(2)	4	Renal(35;0.156)					CTAACAGGGAAGGTAAGTGAG	0.343																																					p.K117M		Atlas-SNP	.											.	CHIC1	13	.	0			c.A350T						PASS	.						225	188	201					X																	72797296		2203	4300	6503	SO:0001630	splice_region_variant	53344	exon2			CAGGGAAGGTAAG	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.351+1A>T	X.37:g.72797296A>T		41	0	0		45	25	0.555556	NM_001039840	A0PJZ2|B0QZ87|B9EGS5|Q5CZ84	Missense_Mutation	SNP	ENST00000373502.5	37	CCDS35335.2	.	.	.	.	.	.	.	.	.	.	A	19.40	3.820831	0.71028	.	.	ENSG00000204116	ENST00000373502;ENST00000373504	.	.	.	4.4	4.4	0.53042	Golgin subfamily A member 7/ERF4 (1);	0.000000	0.85682	D	0.000000	T	0.76644	0.4016	M	0.76574	2.34	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.995;0.999;1.0	T	0.79132	-0.1929	9	0.72032	D	0.01	-22.424	11.0475	0.47867	1.0:0.0:0.0:0.0	.	117;117;117	B7Z3I1;Q5VXU3-2;Q5VXU3	.;.;CHIC1_HUMAN	M	117	.	ENSP00000362601:K117M	K	+	2	0	CHIC1	72714021	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.715000	0.91416	1.682000	0.51000	0.437000	0.28790	AAG	.	.	none		0.343	CHIC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057233.3		Missense_Mutation	T	72797296	A	T	72797296	5	4	28	1	0	0	0	0	0	0	1	0	3345	86	3	5	356	5	CHIC1	23	72797296	Splice_Site	SNP	A	TCGA-G8-6914-01A-11D-2210-10	19389300	72797296	82473264	732	12235											
AMOT	154796	hgsc.bcm.edu	37	chrX	112053138	112053138	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttactttttgcaaagagctgCgagatggtttttctggtgtc	7	17	11	6	1	1	2	0	0	1	2	2	3	1	2	0	2	4	3	0	2	2	5	rs57201849	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:112053138C>T	ENST00000524145.1	-	5	1688	c.1614G>A	c.(1612-1614)tcG>tcA	p.S538S	AMOT_ENST00000371962.1_Silent_p.S306S|AMOT_ENST00000304758.1_Silent_p.S129S|AMOT_ENST00000371958.1_Silent_p.S306S|AMOT_ENST00000371959.3_Silent_p.S538S			Q4VCS5	AMOT_HUMAN	angiomotin	538					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						CAAAGAGCTGCGAGATGGTTT	0.458													C|||	85	0.0225166	0.062	0.0043	3775	,	,		14472	0.0		0.0	False		,,,				2504	0.0				p.S538S		Atlas-SNP	.											.	AMOT	204	.	0			c.G1614A						PASS	.	C	,	221,3614		4,173,40,1455,531	254	220	231		1614,387	-0.6	1	X	dbSNP_129	231	4,6724		0,4,0,2424,1872	no	coding-synonymous,coding-synonymous	AMOT	NM_001113490.1,NM_133265.2	,	4,177,40,3879,2403	TT,TC,T,CC,C		0.0595,5.7627,2.1301	,	538/1085,129/676	112053138	225,10338	2203	4300	6503	SO:0001819	synonymous_variant	154796	exon4			GAGCTGCGAGATG	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.1614G>A	X.37:g.112053138C>T		36	0	0		31	31	1	NM_001113490	Q504X5|Q9HD27|Q9UPT1	Silent	SNP	ENST00000524145.1	37	CCDS48154.1																																																																																			C|0.980;T|0.020	0.020	strong		0.458	AMOT-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378570.1	NM_133265		T	112053138	C	T	112053138	2	4	28	1	0	0	0	0	0	0	0	1	582	755	27	1		1	AMOT	23	112053138	Silent	SNP	C	TCGA-G8-6914-01A-11D-2210-10	39255842	112053138	43217422	733	12236											
LAMP2	3920	hgsc.bcm.edu	37	chrX	119576455	119576455	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggccagtgctttgcttaccGgagccattaaccaaatacat	12	10	8	11	1	0	0	0	0	0	0	0	1	0	1	4	2	6	2	4	2	4	4	rs73219144	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:119576455G>A	ENST00000200639.4	-	7	1063	c.927C>T	c.(925-927)tcC>tcT	p.S309S	LAMP2_ENST00000434600.2_Splice_Site_p.S309S|LAMP2_ENST00000540603.1_Splice_Site_p.S262S|LAMP2_ENST00000538785.1_Splice_Site_p.S198S|LAMP2_ENST00000371335.4_Splice_Site_p.S309S			P13473	LAMP2_HUMAN	lysosomal-associated membrane protein 2	309	Second lumenal domain.				blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	enzyme binding (GO:0019899)			endometrium(4)|large_intestine(2)|lung(5)|ovary(2)|urinary_tract(2)	15						TTTGCTTACCGGAGCCATTAA	0.358													G|||	50	0.013245	0.0	0.0072	3775	,	,		13506	0.0		0.0398	False		,,,				2504	0.0051				p.S309S		Atlas-SNP	.											.	LAMP2	101	.	0			c.C927T						PASS	.	G	,,	29,3806		0,24,5,1608,566	254	242	246		927,927,927	0.9	1	X	dbSNP_130	246	274,6454		6,187,75,2235,1797	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	LAMP2	NM_001122606.1,NM_002294.2,NM_013995.2	,,	6,211,80,3843,2363	AA,AG,A,GG,G		4.0725,0.7562,2.8685	,,	309/412,309/411,309/411	119576455	303,10260	2203	4300	6503	SO:0001630	splice_region_variant	3920	exon7			CTTACCGGAGCCA	X77196	CCDS14599.1, CCDS14600.1, CCDS48159.1	Xq24-q25	2014-09-17			ENSG00000005893	ENSG00000005893		"CD molecules"	6501	protein-coding gene	gene with protein product		309060					Standard	NM_002294		Approved	CD107b	uc004ess.4	P13473	OTTHUMG00000022301	ENST00000200639.4:c.928+1C>T	X.37:g.119576455G>A		46	0	0		38	36	0.947368	NM_013995	A8K4X5|D3DTF0|Q16641|Q6Q3G8|Q96J30|Q99534|Q9UD93	Silent	SNP	ENST00000200639.4	37	CCDS14599.1																																																																																			G|0.975;A|0.025	0.025	strong		0.358	LAMP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058099.1		Silent	A	119576455	G	A	119576455	5	1	28	1	0	0	0	0	0	0	1	0	8627	1130	39	1	608	1	LAMP2	23	119576455	Splice_Site	SNP	G	TCGA-G8-6914-01A-11D-2210-10	7523317	119576455	35694105	734	12237											
ODZ1	10178	hgsc.bcm.edu	37	chrX	123514900	123514900	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttccaggtaatgggcattaTtgagaatggcagcaagccgc	11	10	12	8	1	0	1	0	1	0	1	1	2	1	1	2	3	2	4	2	3	4	4			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:123514900T>C	ENST00000371130.3	-	31	7727	c.7664A>G	c.(7663-7665)aAt>aGt	p.N2555S	STAG2_ENST00000469481.1_Intron|TENM1_ENST00000422452.2_Missense_Mutation_p.N2562S	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	2555					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)										ATGGGCATTATTGAGAATGGC	0.443																																					p.N2562S		Atlas-SNP	.											.	.	.	.	0			c.A7685G						PASS	.						88	79	82					X																	123514900		2203	4300	6503	SO:0001583	missense	10178	exon32			GCATTATTGAGAA	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.7664A>G	X.37:g.123514900T>C	ENSP00000360171:p.Asn2555Ser	52	0	0		55	55	1	NM_001163278	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	T	18.76	3.692756	0.68271	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.87491	-2.26;-2.23	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	D	0.91754	0.7392	M	0.63843	1.955	0.80722	D	1	D;D;D	0.89917	0.997;0.997;1.0	D;D;D	0.83275	0.97;0.985;0.996	D	0.90007	0.4118	10	0.24483	T	0.36	.	15.1686	0.72850	0.0:0.0:0.0:1.0	.	2561;2562;2555	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	S	2555;2562	ENSP00000360171:N2555S;ENSP00000403954:N2562S	ENSP00000360171:N2555S	N	-	2	0	ODZ1	123342581	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.040000	0.89188	1.965000	0.57142	0.486000	0.48141	AAT	.	.	none		0.443	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		C	123514900	T	C	123514900	3	2	28	1	0	0	0	0	1	0	0	0	10843	1493	52	3	517	3	ODZ1	23	123514900	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	3938445	123514900	31755660	735	12238											
CNGA2	1260	hgsc.bcm.edu	37	chrX	150908168	150908168	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gaccacacaggagggggatgGcaaaggcgacaaggatggcg	13	2	18	8	2	0	0	0	0	0	0	0	5	0	3	1	7	0	1	1	7	2	0	rs144366408	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:150908168G>T	ENST00000329903.4	+	3	371	c.338G>T	c.(337-339)gGc>gTc	p.G113V		NM_005140.1	NP_005131.1	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	113					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)					GAGGGGGATGGCAAAGGCGAC	0.542													G|||	13	0.00344371	0.0015	0.0029	3775	,	,		14551	0.0		0.005	False		,,,				2504	0.0041				p.G113V		Atlas-SNP	.											.	CNGA2	136	.	0			c.G338T						PASS	.	G	VAL/GLY	2,3833		0,2,0,1630,571	128	96	107		338	2.8	1	X	dbSNP_134	107	55,6673		0,36,19,2392,1853	yes	missense	CNGA2	NM_005140.1	109	0,38,19,4022,2424	TT,TG,T,GG,G		0.8175,0.0522,0.5396	benign	113/665	150908168	57,10506	2203	4300	6503	SO:0001583	missense	1260	exon4			GGGATGGCAAAGG	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.338G>T	X.37:g.150908168G>T	ENSP00000328478:p.Gly113Val	39	0	0		44	44	1	NM_005140	A0AVD0	Missense_Mutation	SNP	ENST00000329903.4	37	CCDS14701.1	7	0.004219409282700422	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	3	0.003968253968253968	G	9.795	1.178974	0.21787	5.22E-4	0.008175	ENSG00000183862	ENST00000329903	D	0.97328	-4.34	5.58	2.75	0.32379	.	0.401066	0.26948	N	0.021695	D	0.88991	0.6588	L	0.31926	0.97	0.58432	D	0.999997	B	0.15473	0.013	B	0.16289	0.015	T	0.79567	-0.1750	10	0.20519	T	0.43	.	2.2593	0.04063	0.1718:0.1496:0.5206:0.1579	.	113	Q16280	CNGA2_HUMAN	V	113	ENSP00000328478:G113V	ENSP00000328478:G113V	G	+	2	0	CNGA2	150658824	0.971000	0.33674	0.998000	0.56505	0.632000	0.37999	0.882000	0.28186	0.138000	0.18790	-0.343000	0.07986	GGC	G|0.994;T|0.006	0.006	strong		0.542	CNGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060888.1	NM_005140		T	150908168	G	T	150908168	3	4	28	1	0	0	0	0	1	0	0	0	3599	1203	42	4	348	4	CNGA2	23	150908168	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	27393268	150908168	4362392	736	12239											
GABRA3	2556	hgsc.bcm.edu	37	chrX	151358333	151358333	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacggctatgaaccagtccaTggccgtcgcatatgccactt	9	9	10	13	3	0	1	0	1	0	0	2	2	1	1	4	2	2	2	4	2	3	3			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:151358333T>C	ENST00000370314.4	-	9	1250	c.1012A>G	c.(1012-1014)Atg>Gtg	p.M338V	GABRA3_ENST00000535043.1_Missense_Mutation_p.M338V|GABRA3_ENST00000497894.1_5'UTR	NM_000808.3	NP_000799.1	P34903	GBRA3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 3	338					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)	AACCAGTCCATGGCCGTCGCA	0.478																																					p.M338V	NSCLC(142;2578 2613 10251 16743)	Atlas-SNP	.											.	GABRA3	97	.	0			c.A1012G						PASS	.						86	81	83					X																	151358333		2203	4300	6503	SO:0001583	missense	2556	exon9			AGTCCATGGCCGT		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.1012A>G	X.37:g.151358333T>C	ENSP00000359337:p.Met338Val	33	0	0		45	13	0.288889	NM_000808	Q8TAF9	Missense_Mutation	SNP	ENST00000370314.4	37	CCDS14706.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.089013	0.76756	.	.	ENSG00000011677	ENST00000370314;ENST00000370311;ENST00000535043	D;D;D	0.85955	-2.05;-2.05;-2.05	5.56	5.56	0.83823	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	T	0.76737	0.4029	N	0.19112	0.55	0.58432	D	0.999993	B	0.18166	0.026	B	0.22880	0.042	T	0.73972	-0.3814	10	0.87932	D	0	.	12.5432	0.56184	0.0:0.0:0.0:1.0	.	338	P34903	GBRA3_HUMAN	V	338	ENSP00000359337:M338V;ENSP00000359334:M338V;ENSP00000443527:M338V	ENSP00000359334:M338V	M	-	1	0	GABRA3	151108989	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.989000	0.88205	1.868000	0.54150	0.483000	0.47432	ATG	.	.	none		0.478	GABRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060921.1	NM_000808		C	151358333	T	C	151358333	3	2	28	1	0	0	0	0	1	0	0	0	6170	1464	51	3	474	3	GABRA3	23	151358333	Missense_Mutation	SNP	T	TCGA-G8-6914-01A-11D-2210-10	450165	151358333	3912227	737	12240											
FLNA	2316	hgsc.bcm.edu	37	chrX	153594535	153594535	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctccagctgaggctctaccGtgcccttctgtcccatgggg	4	10	11	16	1	2	1	0	1	2	0	4	1	4	1	5	3	3	2	5	3	1	2	rs36051194		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:153594535G>A	ENST00000369850.3	-	9	1522	c.1286C>T	c.(1285-1287)aCg>aTg	p.T429M	FLNA_ENST00000360319.4_Missense_Mutation_p.T429M|FLNA_ENST00000344736.4_Missense_Mutation_p.T429M|FLNA_ENST00000422373.1_Missense_Mutation_p.T429M	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	429			T -> M. {ECO:0000269|PubMed:12612583}.		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)					AGGCTCTACCGTGCCCTTCTG	0.682													G|||	16	0.00423841	0.0	0.0058	3775	,	,		12254	0.0		0.0119	False		,,,				2504	0.0				p.T429M		Atlas-SNP	.											.	FLNA	373	.	0			c.C1286T	GRCh37	CM065185	FLNA	M	rs36051194	PASS	.		MET/THR,MET/THR	9,3653		0,7,2,1539,568	48	53	51		1286,1286	3.8	0.3	X	dbSNP_126	51	107,6462		0,74,33,2305,1778	yes	missense,missense	FLNA	NM_001110556.1,NM_001456.3	81,81	0,81,35,3844,2346	AA,AG,A,GG,G		1.6289,0.2458,1.1338	probably-damaging,probably-damaging	429/2648,429/2640	153594535	116,10115	2116	4190	6306	SO:0001583	missense	2316	exon9			TCTACCGTGCCCT	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.1286C>T	X.37:g.153594535G>A	ENSP00000358866:p.Thr429Met	52	0	0		56	52	0.928571	NM_001456	E9KL45|Q5HY53|Q5HY55|Q8NF52	Missense_Mutation	SNP	ENST00000369850.3	37	CCDS48194.1	8	0.004822182037371911	0	0.0	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	G	4.764	0.142126	0.09083	0.002458	0.016289	ENSG00000196924	ENST00000360319;ENST00000369852;ENST00000422373;ENST00000369850;ENST00000344736	D;D;D;D	0.84800	-1.9;-1.9;-1.9;-1.9	4.68	3.81	0.43845	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.83626	0.5295	M	0.78285	2.405	0.80722	D	1	P;D	0.69078	0.839;0.997	B;D	0.62955	0.281;0.909	D	0.84840	0.0807	10	0.40728	T	0.16	.	11.1083	0.48216	0.096:0.0:0.904:0.0	rs36051194	429;429	P21333-2;P21333	.;FLNA_HUMAN	M	429;402;429;429;429	ENSP00000353467:T429M;ENSP00000416926:T429M;ENSP00000358866:T429M;ENSP00000358863:T429M	ENSP00000358863:T429M	T	-	2	0	FLNA	153247729	1.000000	0.71417	0.266000	0.24541	0.038000	0.13279	3.356000	0.52269	0.763000	0.33175	0.464000	0.42555	ACG	G|0.995;A|0.005	0.005	strong		0.682	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3			A	153594535	G	A	153594535	3	1	28	1	0	0	0	0	1	0	0	0	5941	1145	40	1	6817	1	FLNA	23	153594535	Missense_Mutation	SNP	G	TCGA-G8-6914-01A-11D-2210-10	2236202	153594535	1676025	738	12241											
ATAD3C	219293	hgsc.bcm.edu	37	chr1	1403848	1403848	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	actttgtccagcagcaccagCagatgatgcgctggctgaag	10	8	12	11	1	0	3	0	2	0	1	1	3	1	3	2	1	4	5	2	1	1	1	rs370109447		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:1403848C>G	ENST00000378785.2	+	12	2169	c.1174C>G	c.(1174-1176)Cag>Gag	p.Q392E		NM_001039211.2	NP_001034300.2	Q5T2N8	ATD3C_HUMAN	ATPase family, AAA domain containing 3C	392							ATP binding (GO:0005524)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|lung(4)	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;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)		GCAGCACCAGCAGATGATGCG	0.657																																					p.Q392E		Atlas-SNP	.											.	ATAD3C	23	.	0			c.C1174G						PASS	.	C	GLU/GLN	0,4406		0,0,2203	32	35	34		1174	1.5	1	1		34	2,8588		0,2,4293	no	missense	ATAD3C	NM_001039211.2	29	0,2,6496	GG,GC,CC		0.0233,0.0,0.0154	possibly-damaging	392/412	1403848	2,12994	2203	4295	6498	SO:0001583	missense	219293	exon12			CACCAGCAGATGA	AK091918	CCDS44039.1	1p36.33	2010-04-21		2007-02-08	ENSG00000215915	ENSG00000215915		"ATPases / AAA-type"	32151	protein-coding gene	gene with protein product							Standard	NM_001039211		Approved	FLJ34599	uc001aft.2	Q5T2N8	OTTHUMG00000000531	ENST00000378785.2:c.1174C>G	1.37:g.1403848C>G	ENSP00000368062:p.Gln392Glu	196	0	0		172	80	0.465116	NM_001039211	Q8N1Z5	Missense_Mutation	SNP	ENST00000378785.2	37	CCDS44039.1	.	.	.	.	.	.	.	.	.	.	.	9.977	1.227126	0.22542	0.0	2.33E-4	ENSG00000215915	ENST00000378785	D	0.94576	-3.46	1.47	1.47	0.22746	.	.	.	.	.	D	0.92883	0.7736	M	0.81341	2.54	0.54753	D	0.999986	B	0.34015	0.435	B	0.32149	0.141	D	0.92131	0.5712	9	0.56958	D	0.05	.	10.4293	0.44398	0.0:1.0:0.0:0.0	.	392	Q5T2N8	ATD3C_HUMAN	E	392	ENSP00000368062:Q392E	ENSP00000368062:Q392E	Q	+	1	0	ATAD3C	1393711	1.000000	0.71417	0.997000	0.53966	0.055000	0.15305	5.266000	0.65525	1.135000	0.42183	0.194000	0.17425	CAG	.	.	none		0.657	ATAD3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001279.3	NM_001039211		G	1403848	C	G	1403848	3	3	29	1	0	0	0	0	1	0	0	0	1075	711	25	4	1220	4	ATAD3C	1	1403848	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10		1403848	247846773	1	12242											
ATAD3B	83858	hgsc.bcm.edu	37	chr1	1425644	1425644	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccctgtcctacagattcatgCtggtcctggccagcaatctg	7	11	9	14	0	2	1	1	0	1	1	4	1	4	1	4	2	3	2	4	2	2	2	rs373123252		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:1425644C>G	ENST00000308647.7	+	14	1461	c.1345C>G	c.(1345-1347)Ctg>Gtg	p.L449V		NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	449						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)		CAGATTCATGCTGGTCCTGGC	0.627																																					p.L449V		Atlas-SNP	.											.	ATAD3B	68	.	0			c.C1345G						PASS	.	C	VAL/LEU	0,4402		0,0,2201	62	59	60		1345	2.1	1	1		60	2,8596		0,2,4297	no	missense	ATAD3B	NM_031921.4	32	0,2,6498	GG,GC,CC		0.0233,0.0,0.0154	possibly-damaging	449/649	1425644	2,12998	2201	4299	6500	SO:0001583	missense	83858	exon14			TTCATGCTGGTCC	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.1345C>G	1.37:g.1425644C>G	ENSP00000311766:p.Leu449Val	92	0	0		101	50	0.49505	NM_031921	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Missense_Mutation	SNP	ENST00000308647.7	37	CCDS30.1	.	.	.	.	.	.	.	.	.	.	.	10.95	1.495279	0.26774	0.0	2.33E-4	ENSG00000160072	ENST00000378737;ENST00000308647	D	0.94497	-3.44	2.07	2.07	0.26955	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.64402	D	0.000001	D	0.91250	0.7242	N	0.10782	0.045	0.80722	D	1	D;P	0.54397	0.966;0.946	P;P	0.58130	0.833;0.822	D	0.90536	0.4499	10	0.49607	T	0.09	.	11.3902	0.49809	0.0:1.0:0.0:0.0	.	403;449	Q5T9A4-3;Q5T9A4	.;ATD3B_HUMAN	V	252;449	ENSP00000311766:L449V	ENSP00000311766:L449V	L	+	1	2	ATAD3B	1415507	1.000000	0.71417	1.000000	0.80357	0.043000	0.13939	2.740000	0.47418	1.139000	0.42245	0.205000	0.17691	CTG	.	.	none		0.627	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921		G	1425644	C	G	1425644	3	3	29	1	0	0	0	0	1	0	0	0	1074	796	28	4	1399	4	ATAD3B	1	1425644	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	21796	1425644	247824977	2	12243											
NPHP4	261734	hgsc.bcm.edu	37	chr1	6012866	6012866	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccaagtgccccgtgatgggcTtctggaggcgaggctttcgg	5	9	16	11	3	1	1	0	1	1	0	2	3	1	2	3	5	1	2	3	5	1	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:6012866T>G	ENST00000378156.4	-	7	969	c.704A>C	c.(703-705)aAg>aCg	p.K235T	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	235					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)		CGTGATGGGCTTCTGGAGGCG	0.577																																					p.K235T		Atlas-SNP	.											.	NPHP4	119	.	0			c.A704C						PASS	.						25	28	27					1																	6012866		1883	4106	5989	SO:0001583	missense	261734	exon7			ATGGGCTTCTGGA	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.704A>C	1.37:g.6012866T>G	ENSP00000367398:p.Lys235Thr	42	0	0		42	11	0.261905	NM_015102	Q8IWC0	Missense_Mutation	SNP	ENST00000378156.4	37	CCDS44052.1	.	.	.	.	.	.	.	.	.	.	t	17.28	3.350455	0.61183	.	.	ENSG00000131697	ENST00000378156	D	0.88975	-2.45	5.04	5.04	0.67666	.	0.137440	0.47455	D	0.000235	D	0.92776	0.7703	M	0.75264	2.295	0.37280	D	0.907778	D	0.76494	0.999	D	0.71656	0.974	D	0.93997	0.7272	10	0.62326	D	0.03	.	8.8131	0.34978	0.0:0.0886:0.0:0.9114	.	235	O75161	NPHP4_HUMAN	T	235	ENSP00000367398:K235T	ENSP00000367398:K235T	K	-	2	0	NPHP4	5935453	0.995000	0.38212	0.977000	0.42913	0.809000	0.45718	2.595000	0.46197	1.892000	0.54788	0.459000	0.35465	AAG	.	.	none		0.577	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2			G	6012866	T	G	6012866	3	3	29	1	0	0	0	0	1	0	0	0	10590	1609	56	5	3672	5	NPHP4	1	6012866	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	4587222	6012866	243237755	3	12244											
CASZ1	54897	hgsc.bcm.edu	37	chr1	10705018	10705018	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggtgaagtatttgaagccaTtggctgcccgccgctccgcc	6	10	12	13	3	0	2	0	2	0	0	1	2	1	2	5	2	2	3	5	2	3	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:10705018T>C	ENST00000377022.3	-	18	4141	c.3824A>G	c.(3823-3825)aAt>aGt	p.N1275S	RP4-734G22.3_ENST00000606802.1_RNA	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	1275					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)		TTTGAAGCCATTGGCTGCCCG	0.607																																					p.N1275S		Atlas-SNP	.											.	CASZ1	150	.	0			c.A3824G						PASS	.						63	74	70					1																	10705018		2042	4191	6233	SO:0001583	missense	54897	exon18			AAGCCATTGGCTG	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.3824A>G	1.37:g.10705018T>C	ENSP00000366221:p.Asn1275Ser	103	0	0		81	40	0.493827	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	37	CCDS41246.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.536822	0.85812	.	.	ENSG00000130940	ENST00000377022	.	.	.	5.15	5.15	0.70609	.	0.000000	0.48286	U	0.000188	T	0.62295	0.2416	N	0.19112	0.55	0.80722	D	1	D	0.71674	0.998	D	0.80764	0.994	T	0.64411	-0.6414	9	0.41790	T	0.15	-21.2576	14.9882	0.71365	0.0:0.0:0.0:1.0	.	1275	Q86V15	CASZ1_HUMAN	S	1275	.	ENSP00000366221:N1275S	N	-	2	0	CASZ1	10627605	1.000000	0.71417	0.934000	0.37439	0.979000	0.70002	8.040000	0.89188	1.943000	0.56356	0.459000	0.35465	AAT	.	.	none		0.607	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766		C	10705018	T	C	10705018	3	2	29	1	0	0	0	0	1	0	0	0	2687	1493	52	3	1471	3	CASZ1	1	10705018	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	4692152	10705018	238545603	4	12245											
C1orf127	148345	hgsc.bcm.edu	37	chr1	11008102	11008102	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	taggaagaactgccaggggcGctgccagcctcaccctgggc	8	5	14	14	1	1	1	1	0	0	1	1	2	1	2	4	4	4	1	4	4	3	1	rs1281018	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:11008102G>A	ENST00000377008.4	-	11	2035	c.1589C>T	c.(1588-1590)gCg>gTg	p.A530V	C1orf127_ENST00000377004.4_Missense_Mutation_p.A697V			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	530			A -> V (in dbSNP:rs1281018).							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)		TGCCAGGGGCGCTGCCAGCCT	0.622													G|||	442	0.0882588	0.2542	0.0245	5008	,	,		18073	0.0069		0.0447	False		,,,				2504	0.0378				p.A697V		Atlas-SNP	.											.	C1orf127	134	.	0			c.C2090T						PASS	.	G	VAL/ALA	809,3597	299.6+/-285.9	81,647,1475	36	38	37		2090	-2	0	1	dbSNP_87	37	346,8254	112.3+/-172.5	4,338,3958	yes	missense	C1orf127	NM_001170754.1	64	85,985,5433	AA,AG,GG		4.0233,18.3613,8.8805	possibly-damaging	697/824	11008102	1155,11851	2203	4300	6503	SO:0001583	missense	148345	exon12			AGGGGCGCTGCCA	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.1589C>T	1.37:g.11008102G>A	ENSP00000366207:p.Ala530Val	64	0	0		71	37	0.521127	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Missense_Mutation	SNP	ENST00000377008.4	37		165|165	0.07554945054945054|0.07554945054945054	115|115	0.23373983739837398|0.23373983739837398	8|8	0.022099447513812154|0.022099447513812154	2|2	0.0034965034965034965|0.0034965034965034965	40|40	0.052770448548812667|0.052770448548812667	G|G	7.224|7.224	0.597877|0.597877	0.13939|0.13939	0.183613|0.183613	0.040233|0.040233	ENSG00000175262|ENSG00000175262	ENST00000377004;ENST00000377008|ENST00000418570;ENST00000520253	T;T|.	0.33865|.	1.39;1.39|.	3.9|3.9	-2.05|-2.05	0.07321|0.07321	.|.	0.523531|.	0.14669|.	N|.	0.305451|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.14661|0.14661	0.345|0.345	0.80722|0.80722	P|P	0.0|0.0	P;P;P|.	0.42961|.	0.795;0.795;0.795|.	B;B;B|.	0.31390|.	0.129;0.129;0.081|.	T|T	0.35051|0.35051	-0.9804|-0.9804	9|4	0.18276|.	T|.	0.48|.	-0.422|-0.422	0.9467|0.9467	0.01367|0.01367	0.2137:0.3268:0.2711:0.1885|0.2137:0.3268:0.2711:0.1885	rs1281018;rs1281018|rs1281018;rs1281018	548;522;530|.	B7ZLG7;Q8N9H9-2;Q8N9H9|.	.;.;CA127_HUMAN|.	V|C	697;530|532;649	ENSP00000366203:A697V;ENSP00000366207:A530V|.	ENSP00000366203:A697V|.	A|R	-|-	2|1	0|0	C1orf127|C1orf127	10930689|10930689	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.030000|0.030000	0.12068|0.12068	-2.362000|-2.362000	0.01082|0.01082	-0.266000|-0.266000	0.09339|0.09339	-0.474000|-0.474000	0.04947|0.04947	GCG|CGC	G|0.914;A|0.086	0.086	strong		0.622	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507		A	11008102	G	A	11008102	3	1	29	1	0	0	0	0	1	0	0	0	1996	1087	38	1	385	1	C1orf127	1	11008102	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	303084	11008102	238242519	5	12246			1	53		4	4	1602	N	G_C_A	1.583063e-05
C1orf127	148345	hgsc.bcm.edu	37	chr1	11008594	11008594	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtgacagatggtcctgagAccagaagtgattcaggtcgt	10	9	15	7	1	1	5	1	3	0	3	3	6	2	5	2	3	0	0	2	3	1	1	rs1281016	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:11008594A>T	ENST00000377008.4	-	11	1543	c.1097T>A	c.(1096-1098)gTc>gAc	p.V366D	C1orf127_ENST00000377004.4_Missense_Mutation_p.V533D			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	366			V -> D (in dbSNP:rs1281016).							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)		TGGTCCTGAGACCAGAAGTGA	0.612													A|||	346	0.0690895	0.2035	0.0144	5008	,	,		19200	0.004		0.0427	False		,,,				2504	0.0204				p.V533D		Atlas-SNP	.											.	C1orf127	134	.	0			c.T1598A						PASS	.	A	ASP/VAL	735,3671	303.5+/-288.0	65,605,1533	56	53	54		1598	0.5	0	1	dbSNP_87	54	343,8257	116.3+/-176.0	4,335,3961	yes	missense	C1orf127	NM_001170754.1	152	69,940,5494	TT,TA,AA		3.9884,16.6818,8.2885	probably-damaging	533/824	11008594	1078,11928	2203	4300	6503	SO:0001583	missense	148345	exon12			CCTGAGACCAGAA	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.1097T>A	1.37:g.11008594A>T	ENSP00000366207:p.Val366Asp	126	0	0		159	83	0.522013	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Missense_Mutation	SNP	ENST00000377008.4	37		167|167	0.07646520146520147|0.07646520146520147	123|123	0.25|0.25	4|4	0.011049723756906077|0.011049723756906077	1|1	0.0017482517482517483|0.0017482517482517483	39|39	0.051451187335092345|0.051451187335092345	A|A	13.05|13.05	2.122259|2.122259	0.37436|0.37436	0.166818|0.166818	0.039884|0.039884	ENSG00000175262|ENSG00000175262	ENST00000418570;ENST00000520253|ENST00000377004;ENST00000377008	.|T;T	.|0.26518	.|1.73;1.73	4.15|4.15	0.48|0.48	0.16804|0.16804	.|.	.|0.956786	.|0.08574	.|N	.|0.925628	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.24115|0.24115	0.695|0.695	0.80722|0.80722	P|P	0.0|0.0	.|P;P;P	.|0.46512	.|0.879;0.879;0.879	.|B;B;B	.|0.42163	.|0.378;0.378;0.378	T|T	0.19484|0.19484	-1.0304|-1.0304	4|9	.|0.15952	.|T	.|0.53	-5.9143|-5.9143	0.8883|0.8883	0.01249|0.01249	0.3866:0.3152:0.136:0.1622|0.3866:0.3152:0.136:0.1622	rs1281016;rs52819154;rs1281016|rs1281016;rs52819154;rs1281016	.|384;358;366	.|B7ZLG7;Q8N9H9-2;Q8N9H9	.|.;.;CA127_HUMAN	T|D	368;485|533;366	.|ENSP00000366203:V533D;ENSP00000366207:V366D	.|ENSP00000366203:V533D	S|V	-|-	1|2	0|0	C1orf127|C1orf127	10931181|10931181	0.000000|0.000000	0.05858|0.05858	0.008000|0.008000	0.14137|0.14137	0.057000|0.057000	0.15508|0.15508	-0.110000|-0.110000	0.10824|0.10824	0.317000|0.317000	0.23160|0.23160	0.402000|0.402000	0.26972|0.26972	TCT|GTC	A|0.922;T|0.078	0.078	strong		0.612	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507		T	11008594	A	T	11008594	3	4	29	1	0	0	0	0	1	0	0	0	1996	275	10	5	877	5	C1orf127	1	11008594	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	492	11008594	238242027	6	12247			1	53		4	4	1602	N	G_C_A	1.583063e-05
C1orf127	148345	hgsc.bcm.edu	37	chr1	11009679	11009679	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaggatgcagccatagacgtGctttggccagtgcgtcggaa	9	8	15	9	3	0	1	0	0	0	1	1	4	0	3	2	3	4	2	2	3	2	2	rs1281013	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:11009679G>A	ENST00000377008.4	-	10	1236		c.e10+1		C1orf127_ENST00000377004.4_Splice_Site			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127											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)		CCATAGACGTGCTTTGGCCAG	0.612													G|||	346	0.0690895	0.2035	0.0144	5008	,	,		17717	0.004		0.0427	False		,,,				2504	0.0204				.		Atlas-SNP	.											.	C1orf127	134	.	0			c.1290+2C>T						PASS	.	G		719,3679		64,591,1544	34	29	31			-0.6	0	1	dbSNP_87	31	331,8269		4,323,3973	yes	splice-5	C1orf127	NM_001170754.1		68,914,5517	AA,AG,GG		3.8488,16.3483,8.0782			11009679	1050,11948	2199	4300	6499	SO:0001630	splice_region_variant	148345	exon12			AGACGTGCTTTGG	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.789+1C>T	1.37:g.11009679G>A		56	0	0		51	29	0.568627	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Splice_Site	SNP	ENST00000377008.4	37		166	0.076007326007326	122	0.24796747967479674	4	0.011049723756906077	1	0.0017482517482517483	39	0.051451187335092345	G	2.596	-0.293985	0.05568	0.163483	0.038488	ENSG00000175262	ENST00000418570;ENST00000377004;ENST00000377008	.	.	.	3.68	-0.578	0.11724	.	.	.	.	.	.	.	.	.	.	.	0.51012	P	9.899999999996023E-5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1.2328	0.01946	0.2149:0.1807:0.4347:0.1697	rs1281013;rs1281013	.	.	.	.	-1	.	.	.	-	.	.	C1orf127	10932266	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.106000	0.15354	-0.247000	0.09597	-0.354000	0.07668	.	G|0.907;A|0.093	0.093	strong		0.612	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	Intron	A	11009679	G	A	11009679	5	1	29	1	0	0	0	0	0	0	1	0	1996	1333	46	2	1187	2	C1orf127	1	11009679	Splice_Site	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1085	11009679	238240942	7	12248			1	53		4	4	1602	N	G_C_A	1.583063e-05
C1orf127	148345	hgsc.bcm.edu	37	chr1	11009703	11009703	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggccagtgcgtcggaaggcCggtgcaggaggtcccgagaa	8	5	18	10	4	0	1	0	0	0	1	2	4	1	3	3	6	2	1	3	6	2	0	rs1281012	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:11009703C>T	ENST00000377008.4	-	10	1213	c.767G>A	c.(766-768)cGg>cAg	p.R256Q	C1orf127_ENST00000377004.4_Missense_Mutation_p.R423Q			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	256	Pro-rich.		R -> Q (in dbSNP:rs1281012).							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)		GTCGGAAGGCCGGTGCAGGAG	0.622													C|||	347	0.0692891	0.2042	0.0144	5008	,	,		17273	0.004		0.0427	False		,,,				2504	0.0204				p.R423Q		Atlas-SNP	.											.	C1orf127	134	.	0			c.G1268A						PASS	.	C	GLN/ARG	725,3675		66,593,1541	40	34	36		1268	-6.4	0	1	dbSNP_87	36	333,8267		4,325,3971	yes	missense	C1orf127	NM_001170754.1	43	70,918,5512	TT,TC,CC		3.8721,16.4773,8.1385	benign	423/824	11009703	1058,11942	2200	4300	6500	SO:0001583	missense	148345	exon11			GAAGGCCGGTGCA	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.767G>A	1.37:g.11009703C>T	ENSP00000366207:p.Arg256Gln	61	0	0		54	29	0.537037	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Missense_Mutation	SNP	ENST00000377008.4	37		167|167	0.07646520146520147|0.07646520146520147	123|123	0.25|0.25	4|4	0.011049723756906077|0.011049723756906077	1|1	0.0017482517482517483|0.0017482517482517483	39|39	0.051451187335092345|0.051451187335092345	C|C	1.843|1.843	-0.467033|-0.467033	0.04476|0.04476	0.164773|0.164773	0.038721|0.038721	ENSG00000175262|ENSG00000175262	ENST00000418570|ENST00000377004;ENST00000377008	.|T;T	.|0.29142	.|1.58;1.58	3.98|3.98	-6.39|-6.39	0.01951|0.01951	.|.	.|6.202500	.|0.00166	.|N	.|0.000011	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02539|0.02539	-0.55|-0.55	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.09022	.|0.002;0.002	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.18999|0.18999	-1.0319|-1.0319	4|9	.|0.23891	.|T	.|0.37	.|.	2.3424|2.3424	0.04263|0.04263	0.1182:0.3558:0.1181:0.4079|0.1182:0.3558:0.1181:0.4079	rs1281012;rs1281012|rs1281012;rs1281012	.|274;256	.|B7ZLG7;Q8N9H9	.|.;CA127_HUMAN	S|Q	258|423;256	.|ENSP00000366203:R423Q;ENSP00000366207:R256Q	.|ENSP00000366203:R423Q	G|R	-|-	1|2	0|0	C1orf127|C1orf127	10932290|10932290	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-1.451000|-1.451000	0.02387|0.02387	-1.615000|-1.615000	0.01573|0.01573	-1.314000|-1.314000	0.01303|0.01303	GGC|CGG	C|0.907;T|0.093	0.093	strong		0.622	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507		T	11009703	C	T	11009703	3	4	29	1	0	0	0	0	1	0	0	0	1996	652	23	1	1211	1	C1orf127	1	11009703	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	24	11009703	238240918	8	12249			1	53		4	4	1602	N	G_C_A	1.583063e-05
HNRNPCL1	343069	hgsc.bcm.edu	37	chr1	12907263	12907263	+	Nonstop_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcaaccccactatgtgcttAagagtcatcctggccattgg	9	11	8	13	0	2	1	2	0	0	1	3	1	3	1	4	2	2	1	4	2	3	3	rs370005849		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:12907263A>T	ENST00000317869.6	-	2	1105	c.880T>A	c.(880-882)Taa>Aaa	p.*294K		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	0						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						CTATGTGCTTAAGAGTCATCC	0.448																																					p.X294K		Atlas-SNP	.											.	HNRNPCL1	68	.	0			c.T880A						PASS	.	A	LYS/stop	0,4406		0,0,2203	113	124	120		880	-0.2	0	1		120	2,8596		0,2,4297	no	stop-lost	HNRNPCL1	NM_001013631.1		0,2,6500	TT,TA,AA		0.0233,0.0,0.0154		294/294	12907263	2,13002	2203	4299	6502	SO:0001578	stop_lost	343069	exon2			GTGCTTAAGAGTC	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.880T>A	1.37:g.12907263A>T		126	0	0		130	30	0.230769	NM_001013631	B2RP44	Missense_Mutation	SNP	ENST00000317869.6	37	CCDS30591.1	.	.	.	.	.	.	.	.	.	.	.	0.569	-0.841782	0.02671	0.0	2.33E-4	ENSG00000179172	ENST00000317869	.	.	.	1.09	-0.244	0.13031	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.6398	0.17557	0.7289:0.271:0.0:0.0	.	.	.	.	K	294	.	.	X	-	1	0	HNRNPCL1	12829850	1.000000	0.71417	0.023000	0.16930	0.082000	0.17680	1.836000	0.39191	-0.137000	0.11455	-1.850000	0.00570	TAA	.	.	none		0.448	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	NM_001013631		T	12907263	A	T	12907263	4	4	29	1	0	0	0	0	0	0	0	0	7272	376	13	5	3	5	HNRNPCL1	1	12907263	Nonstop_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	1897560	12907263	236343358	9	12250											
CLCNKA	1187	hgsc.bcm.edu	37	chr1	16355287	16355287	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	actccgctctggccaccttgCttctcgcctccatcacctac	5	11	5	20	2	3	0	1	0	2	0	6	0	5	0	6	1	2	2	6	1	1	3	rs45588635	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:16355287C>G	ENST00000331433.4	+	11	1019	c.1000C>G	c.(1000-1002)Ctt>Gtt	p.L334V	CLCNKA_ENST00000375692.1_Missense_Mutation_p.L334V|CLCNKA_ENST00000464764.1_3'UTR|CLCNKA_ENST00000420078.1_Missense_Mutation_p.L334V|CLCNKA_ENST00000439316.2_Missense_Mutation_p.L291V			P51800	CLCKA_HUMAN	chloride channel, voltage-sensitive Ka	334					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)	GGCCACCTTGCTTCTCGCCTC	0.632													C|||	51	0.0101837	0.0023	0.0101	5008	,	,		15106	0.002		0.0249	False		,,,				2504	0.0143				p.L334V		Atlas-SNP	.											.	CLCNKA	56	.	0			c.C1000G						PASS	.	C	VAL/LEU,VAL/LEU	22,4384	29.0+/-57.7	0,22,2181	197	142	161		1000,1000	-1.2	0	1	dbSNP_127	161	258,8342	100.6+/-161.9	7,244,4049	yes	missense,missense	CLCNKA	NM_001042704.1,NM_004070.3	32,32	7,266,6230	GG,GC,CC		3.0,0.4993,2.1529	benign,benign	334/687,334/688	16355287	280,12726	2203	4300	6503	SO:0001583	missense	1187	exon11			ACCTTGCTTCTCG		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.1000C>G	1.37:g.16355287C>G	ENSP00000332771:p.Leu334Val	79	0	0		61	60	0.983607	NM_004070	B4DPD3|E7EPH6|Q5T5P8|Q5T5Q4|Q7Z6D1|Q86VT1	Missense_Mutation	SNP	ENST00000331433.4	37	CCDS167.1	28	0.01282051282051282	2	0.0040650406504065045	3	0.008287292817679558	2	0.0034965034965034965	21	0.027704485488126648	C	2.898	-0.228251	0.06022	0.004993	0.03	ENSG00000186510	ENST00000375692;ENST00000420078;ENST00000439316;ENST00000331433	D;D;D;D	0.94232	-3.38;-3.38;-3.38;-3.38	3.37	-1.2	0.09554	Chloride channel, core (2);	0.571234	0.18352	N	0.143854	T	0.62612	0.2442	N	0.12471	0.22	0.30637	N	0.756893	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.16289	0.015;0.015;0.015	T	0.64296	-0.6441	10	0.07644	T	0.81	.	7.6981	0.28606	0.1941:0.5514:0.2544:0.0	rs45588635	291;334;334	E7EPH6;Q5T5Q4;P51800	.;.;CLCKA_HUMAN	V	334;334;291;334	ENSP00000364844:L334V;ENSP00000410353:L334V;ENSP00000414445:L291V;ENSP00000332771:L334V	ENSP00000332771:L334V	L	+	1	0	CLCNKA	16227874	0.000000	0.05858	0.003000	0.11579	0.252000	0.25951	-0.757000	0.04772	-0.350000	0.08262	-0.702000	0.03669	CTT	C|0.981;G|0.019	0.019	strong		0.632	CLCNKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026326.1			G	16355287	C	G	16355287	3	3	29	1	0	0	0	0	1	0	0	0	3471	797	28	4	1038	4	CLCNKA	1	16355287	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	3448024	16355287	232895334	10	12251											
TAS1R2	80834	hgsc.bcm.edu	37	chr1	19175944	19175944	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctggctccggtcccattgcCactggacaatctccaagtgc	7	10	9	15	1	2	0	0	0	2	0	5	1	4	1	4	3	2	1	4	3	2	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:19175944C>T	ENST00000375371.3	-	4	1379	c.1358G>A	c.(1357-1359)tGg>tAg	p.W453*	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	453					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)	GTCCCATTGCCACTGGACAAT	0.567																																					p.W453X		Atlas-SNP	.											.	TAS1R2	134	.	0			c.G1358A						PASS	.						101	88	92					1																	19175944		2203	4300	6503	SO:0001587	stop_gained	80834	exon4			CATTGCCACTGGA		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.1358G>A	1.37:g.19175944C>T	ENSP00000364520:p.Trp453*	86	0	0		92	4	0.0434783	NM_152232	Q5TZ19	Nonsense_Mutation	SNP	ENST00000375371.3	37	CCDS187.1	.	.	.	.	.	.	.	.	.	.	C	16.82	3.228655	0.58777	.	.	ENSG00000179002	ENST00000375371	.	.	.	4.49	3.57	0.40892	.	0.561733	0.15487	N	0.259793	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.754	0.40492	0.2057:0.7943:0.0:0.0	.	.	.	.	X	453	.	ENSP00000364520:W453X	W	-	2	0	TAS1R2	19048531	1.000000	0.71417	1.000000	0.80357	0.231000	0.25187	5.144000	0.64832	1.091000	0.41335	0.561000	0.74099	TGG	.	.	none		0.567	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1			T	19175944	C	T	19175944	4	4	29	1	0	0	0	0	0	1	0	0	15578	595	21	2	1173	2	TAS1R2	1	19175944	Nonsense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2820657	19175944	230074677	11	12252											
TAS1R2	80834	hgsc.bcm.edu	37	chr1	19181279	19181279	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcgatgcagatgtcgcgccGggccacgcgctcgccaagca	7	4	15	15	7	0	1	0	0	0	1	2	2	0	1	3	2	2	3	3	2	1	0	rs140330444		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:19181279G>A	ENST00000375371.3	-	3	706	c.685C>T	c.(685-687)Cgg>Tgg	p.R229W	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	229					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)	ATGTCGCGCCGGGCCACGCGC	0.632													G|||	1	0.000199681	0.0	0.0014	5008	,	,		18910	0.0		0.0	False		,,,				2504	0.0				p.R229W		Atlas-SNP	.											.	TAS1R2	134	.	0			c.C685T						PASS	.	G	TRP/ARG	0,4404		0,0,2202	41	38	39		685	-10	0	1	dbSNP_134	39	8,8590	5.7+/-21.5	0,8,4291	yes	missense	TAS1R2	NM_152232.2	101	0,8,6493	AA,AG,GG		0.093,0.0,0.0615	probably-damaging	229/840	19181279	8,12994	2202	4299	6501	SO:0001583	missense	80834	exon3			CGCGCCGGGCCAC		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.685C>T	1.37:g.19181279G>A	ENSP00000364520:p.Arg229Trp	53	0	0		39	14	0.358974	NM_152232	Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	37	CCDS187.1	.	.	.	.	.	.	.	.	.	.	G	12.01	1.809991	0.31961	0.0	9.3E-4	ENSG00000179002	ENST00000375371	D	0.82984	-1.67	4.99	-9.98	0.00438	Extracellular ligand-binding receptor (1);	1.875720	0.02649	N	0.106245	T	0.77883	0.4197	L	0.39898	1.24	0.09310	N	1	D	0.61697	0.99	P	0.47376	0.545	T	0.76974	-0.2760	10	0.72032	D	0.01	.	11.3667	0.49677	0.0637:0.6431:0.1293:0.1639	.	229	Q8TE23	TS1R2_HUMAN	W	229	ENSP00000364520:R229W	ENSP00000364520:R229W	R	-	1	2	TAS1R2	19053866	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.329000	0.01111	-1.436000	0.01970	-0.270000	0.10280	CGG	G|1.000;A|0.000	0.000	weak		0.632	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1			A	19181279	G	A	19181279	3	1	29	1	0	0	0	0	1	0	0	0	15578	1115	39	1	1850	1	TAS1R2	1	19181279	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	5335	19181279	230069342	12	12253											
UBR4	23352	hgsc.bcm.edu	37	chr1	19500088	19500088	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taggatcctccacagtatcaAgaagtaatattgaagggcac	15	9	9	8	0	1	2	1	1	0	1	3	3	3	3	2	2	0	3	2	2	7	5	rs41273197	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:19500088A>G	ENST00000375254.3	-	23	3037	c.3010T>C	c.(3010-3012)Ttg>Ctg	p.L1004L	UBR4_ENST00000375217.2_Silent_p.L1004L|UBR4_ENST00000375267.2_Silent_p.L1004L|UBR4_ENST00000375226.2_Silent_p.L1004L	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	1004					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)		CACAGTATCAAGAAGTAATAT	0.448													A|||	9	0.00179712	0.0	0.0043	5008	,	,		19762	0.0		0.003	False		,,,				2504	0.0031				p.L1004L		Atlas-SNP	.											.	UBR4	415	.	0			c.T3010C						PASS	.	A		12,4394	17.9+/-39.9	0,12,2191	83	78	80		3010	-0.9	1	1	dbSNP_127	80	76,8524	43.6+/-101.6	2,72,4226	no	coding-synonymous	UBR4	NM_020765.2		2,84,6417	GG,GA,AA		0.8837,0.2724,0.6766		1004/5184	19500088	88,12918	2203	4300	6503	SO:0001819	synonymous_variant	23352	exon23			GTATCAAGAAGTA	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.3010T>C	1.37:g.19500088A>G		78	0	0		112	59	0.526786	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	37	CCDS189.1																																																																																			A|0.995;G|0.005	0.005	strong		0.448	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		G	19500088	A	G	19500088	2	3	29	1	0	0	0	0	0	0	0	1	16919	69	3	3		3	UBR4	1	19500088	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	318809	19500088	229750533	13	12254											
MAN1C1	57134	hgsc.bcm.edu	37	chr1	26110236	26110236	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccgaggcccacccactcccgGtgaaccactcagacagctcc	9	4	8	20	2	1	2	1	1	0	1	3	3	3	2	6	2	2	1	6	2	1	0	rs79507311	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:26110236G>A	ENST00000374332.4	+	12	2179	c.1849G>A	c.(1849-1851)Gtg>Atg	p.V617M	MAN1C1_ENST00000263979.3_Missense_Mutation_p.V437M|MAN1C1_ENST00000374329.1_Missense_Mutation_p.V388M	NM_020379.2	NP_065112.1	Q9NR34	MA1C1_HUMAN	mannosidase, alpha, class 1C, member 1	617					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)		CCCACTCCCGGTGAACCACTC	0.627													G|||	31	0.0061901	0.0008	0.0043	5008	,	,		17272	0.001		0.0239	False		,,,				2504	0.002				p.V617M		Atlas-SNP	.											.	MAN1C1	48	.	0			c.G1849A						PASS	.	G	MET/VAL	6,4400	11.4+/-27.6	0,6,2197	54	53	53		1849	2.3	0	1	dbSNP_131	53	119,8481	62.4+/-124.4	1,117,4182	yes	missense	MAN1C1	NM_020379.2	21	1,123,6379	AA,AG,GG		1.3837,0.1362,0.9611	possibly-damaging	617/631	26110236	125,12881	2203	4300	6503	SO:0001583	missense	57134	exon12			CTCCCGGTGAACC	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.1849G>A	1.37:g.26110236G>A	ENSP00000363452:p.Val617Met	31	0	0		40	27	0.675	NM_020379	A6NNE2|B2RNP2|Q9Y545	Missense_Mutation	SNP	ENST00000374332.4	37	CCDS265.1	22	0.010073260073260074	1	0.0020325203252032522	2	0.0055248618784530384	1	0.0017482517482517483	18	0.023746701846965697	G	17.85	3.489365	0.64074	0.001362	0.013837	ENSG00000117643	ENST00000374332;ENST00000263979;ENST00000374329	T;T;T	0.73363	-0.74;-0.74;-0.74	5.25	2.26	0.28386	.	0.244180	0.34484	N	0.003930	T	0.74489	0.3723	M	0.84219	2.685	0.29541	N	0.852042	D	0.76494	0.999	D	0.76575	0.988	T	0.75013	-0.3467	10	0.59425	D	0.04	.	8.8057	0.34936	0.4815:0.0:0.5185:0.0	.	617	Q9NR34	MA1C1_HUMAN	M	617;437;388	ENSP00000363452:V617M;ENSP00000263979:V437M;ENSP00000363449:V388M	ENSP00000263979:V437M	V	+	1	0	MAN1C1	25982823	0.892000	0.30473	0.027000	0.17364	0.975000	0.68041	1.342000	0.33919	0.182000	0.20032	0.561000	0.74099	GTG	G|0.990;A|0.010	0.010	strong		0.627	MAN1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012828.3	NM_020379		A	26110236	G	A	26110236	3	1	29	1	0	0	0	0	1	0	0	0	9222	1261	44	2	1895	2	MAN1C1	1	26110236	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	6610148	26110236	223140385	14	12255											
PAQR7	164091	hgsc.bcm.edu	37	chr1	26189517	26189517	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaaagttggtggccctgccCgaagacatggcagctgccag	10	6	14	11	1	0	1	0	0	0	1	0	3	0	1	3	3	3	3	3	3	3	1	rs6689014	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:26189517C>T	ENST00000374296.3	-	2	1480	c.814G>A	c.(814-816)Ggg>Agg	p.G272R	RP1-125I3.2_ENST00000455431.1_RNA	NM_178422.5	NP_848509.1	Q86WK9	MPRA_HUMAN	progestin and adipoQ receptor family member VII	272			G -> R (in dbSNP:rs6689014).		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)		TGGCCCTGCCCGAAGACATGG	0.587													C|||	19	0.00379393	0.0	0.0029	5008	,	,		20920	0.0		0.0169	False		,,,				2504	0.0				p.G272R	Esophageal Squamous(111;1206 1556 18433 19151 38418)	Atlas-SNP	.											.	PAQR7	23	.	0			c.G814A						PASS	.	C	ARG/GLY	7,4399	12.9+/-30.5	0,7,2196	51	51	51		814	4.3	1	1	dbSNP_116	51	76,8524	43.6+/-101.6	0,76,4224	yes	missense	PAQR7	NM_178422.5	125	0,83,6420	TT,TC,CC		0.8837,0.1589,0.6382	probably-damaging	272/347	26189517	83,12923	2203	4300	6503	SO:0001583	missense	164091	exon2			CCTGCCCGAAGAC		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.814G>A	1.37:g.26189517C>T	ENSP00000363414:p.Gly272Arg	101	0	0		113	57	0.504425	NM_178422	A2A2D3|Q5XKF9|Q86VE4	Missense_Mutation	SNP	ENST00000374296.3	37	CCDS267.1	9	0.004120879120879121	0	0.0	0	0.0	0	0.0	9	0.011873350923482849	C	21.1	4.099077	0.76983	0.001589	0.008837	ENSG00000182749	ENST00000374296	T	0.37752	1.18	5.2	4.28	0.50868	.	0.000000	0.85682	D	0.000000	T	0.57021	0.2025	M	0.87971	2.92	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.70572	-0.4835	10	0.72032	D	0.01	-19.195	14.8991	0.70664	0.1446:0.8554:0.0:0.0	rs6689014;rs52808965;rs6689014	272	Q86WK9	MPRA_HUMAN	R	272	ENSP00000363414:G272R	ENSP00000363414:G272R	G	-	1	0	PAQR7	26062104	1.000000	0.71417	0.993000	0.49108	0.775000	0.43874	5.912000	0.69948	1.390000	0.46547	-0.182000	0.12963	GGG	C|0.995;T|0.005	0.005	strong		0.587	PAQR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019312.1	NM_178422		T	26189517	C	T	26189517	3	4	29	1	0	0	0	0	1	0	0	0	11449	652	23	1	230	1	PAQR7	1	26189517	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	79281	26189517	223061104	15	12256											
NUDC	10726	hgsc.bcm.edu	37	chr1	27268110	27268110	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggccccagatcaaggagctaActgatgaagaggcagagagg	14	4	15	8	0	1	5	1	2	0	3	1	7	1	6	2	4	2	2	2	4	3	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:27268110A>C	ENST00000321265.5	+	3	445	c.322A>C	c.(322-324)Act>Cct	p.T108P		NM_006600.3	NP_006591.1	Q9Y266	NUDC_HUMAN	nudC nuclear distribution protein	108					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)		CAAGGAGCTAACTGATGAAGA	0.647																																					p.T108P		Atlas-SNP	.											.	NUDC	15	.	0			c.A322C						PASS	.						36	38	37					1																	27268110		2203	4299	6502	SO:0001583	missense	10726	exon3			GAGCTAACTGATG		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.322A>C	1.37:g.27268110A>C	ENSP00000319664:p.Thr108Pro	84	0	0		105	6	0.0571429	NM_006600	Q5QP31|Q5QP35|Q9H0N2|Q9Y2B6	Missense_Mutation	SNP	ENST00000321265.5	37	CCDS292.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.512255	0.85389	.	.	ENSG00000090273	ENST00000435827;ENST00000321265;ENST00000452707	T	0.42900	0.96	5.52	4.4	0.53042	.	0.045787	0.85682	D	0.000000	T	0.61986	0.2391	M	0.78637	2.42	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.80764	0.994;0.986	T	0.63980	-0.6514	10	0.48119	T	0.1	7.7528	10.843	0.46726	0.9265:0.0:0.0735:0.0	.	59;108	Q9H2R7;Q9Y266	.;NUDC_HUMAN	P	112;108;59	ENSP00000319664:T108P	ENSP00000319664:T108P	T	+	1	0	NUDC	27140697	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.283000	0.78640	2.111000	0.64477	0.533000	0.62120	ACT	.	.	none		0.647	NUDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012172.2			C	27268110	A	C	27268110	3	2	29	1	0	0	0	0	1	0	0	0	10730	43	2	5	332	5	NUDC	1	27268110	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	1078593	27268110	221982511	16	12257											
WDTC1	23038	hgsc.bcm.edu	37	chr1	27631526	27631526	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcgtcagtggctctgacgatGgctccttcttcatctgggaa	6	13	11	11	2	5	1	2	1	3	0	7	3	6	2	1	3	0	2	1	3	1	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:27631526G>A	ENST00000319394.3	+	15	2213	c.1678G>A	c.(1678-1680)Ggc>Agc	p.G560S	WDTC1_ENST00000361771.3_Missense_Mutation_p.G559S	NM_001276252.1|NM_015023.3	NP_001263181.1|NP_055838.2	Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1	560					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)		CTCTGACGATGGCTCCTTCTT	0.592																																					p.G560S		Atlas-SNP	.											.	WDTC1	69	.	0			c.G1678A						PASS	.						75	61	65					1																	27631526		2203	4300	6503	SO:0001583	missense	23038	exon15			GACGATGGCTCCT	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.1678G>A	1.37:g.27631526G>A	ENSP00000317971:p.Gly560Ser	42	0	0		58	33	0.568965	NM_001276252	D3DPL5|Q5SSC5|Q9NV87|Q9UPW4	Missense_Mutation	SNP	ENST00000319394.3	37		.	.	.	.	.	.	.	.	.	.	G	34	5.344179	0.95807	.	.	ENSG00000142784	ENST00000319394;ENST00000361771	D;D	0.84146	-1.81;-1.81	4.82	4.82	0.62117	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	0.93429	0.7904	M	0.89163	3.01	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.94408	0.7629	10	0.66056	D	0.02	.	17.0684	0.86565	0.0:0.0:1.0:0.0	.	560;559	Q8N5D0;Q8N5D0-4	WDTC1_HUMAN;.	S	560;559	ENSP00000317971:G560S;ENSP00000355317:G559S	ENSP00000317971:G560S	G	+	1	0	WDTC1	27504113	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.460000	0.80816	2.500000	0.84329	0.455000	0.32223	GGC	.	.	none		0.592	WDTC1-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015023		A	27631526	G	A	27631526	3	1	29	1	0	0	0	0	1	0	0	0	17357	1348	47	2	1729	2	WDTC1	1	27631526	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	363416	27631526	221619095	17	12258											
KHDRBS1	10657	hgsc.bcm.edu	37	chr1	32479924	32479924	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acctgcccgaactcatggccGagaaggactcgctcgacccg	9	5	11	16	5	1	1	1	0	0	1	3	5	1	2	4	2	2	1	4	2	2	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:32479924G>A	ENST00000327300.7	+	1	495	c.328G>A	c.(328-330)Gag>Aag	p.E110K	KHDRBS1_ENST00000492989.1_Missense_Mutation_p.E110K|KHDRBS1_ENST00000307714.8_3'UTR	NM_006559.1	NP_006550.1			KH domain containing, RNA binding, signal transduction associated 1											endometrium(4)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	14		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				ACTCATGGCCGAGAAGGACTC	0.692																																					p.E110K	Ovarian(173;401 1982 12359 31110 42403)	Atlas-SNP	.											.	KHDRBS1	34	.	0			c.G328A						PASS	.						22	19	20					1																	32479924		2199	4294	6493	SO:0001583	missense	10657	exon1			ATGGCCGAGAAGG	U78971	CCDS350.1, CCDS60067.1	1p32	2008-07-18			ENSG00000121774	ENSG00000121774			18116	protein-coding gene	gene with protein product	"GAP-associated tyrosine phosphoprotein p62 (Sam68)"	602489				1374686, 10564820	Standard	NM_006559		Approved	Sam68, p62, FLJ34027	uc001bub.4	Q07666	OTTHUMG00000003921	ENST00000327300.7:c.328G>A	1.37:g.32479924G>A	ENSP00000313829:p.Glu110Lys	73	0	0		84	28	0.333333	NM_006559		Missense_Mutation	SNP	ENST00000327300.7	37	CCDS350.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.637903	0.87760	.	.	ENSG00000121774	ENST00000327300;ENST00000492989;ENST00000355201	T;T	0.61510	0.48;0.1	4.18	3.26	0.37387	.	0.101044	0.64402	D	0.000002	T	0.73313	0.3571	M	0.77820	2.39	0.58432	D	0.999995	D;D	0.89917	0.997;1.0	P;D	0.67382	0.842;0.951	T	0.77965	-0.2389	10	0.87932	D	0	.	12.9521	0.58407	0.0:0.1634:0.8365:0.0	.	110;110	Q07666;Q07666-3	KHDR1_HUMAN;.	K	110;110;86	ENSP00000313829:E110K;ENSP00000417731:E110K	ENSP00000313829:E110K	E	+	1	0	KHDRBS1	32252511	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	5.345000	0.65987	1.339000	0.45563	0.655000	0.94253	GAG	.	.	none		0.692	KHDRBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011199.4	NM_006559		A	32479924	G	A	32479924	3	1	29	1	0	0	0	0	1	0	0	0	8155	1059	37	1	330	1	KHDRBS1	1	32479924	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	4848398	32479924	216770697	18	12259											
TMEM54	113452	hgsc.bcm.edu	37	chr1	33361552	33361552	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcgtgacaacacgatggctgCgatgcctgaagtgatgacct	10	8	13	10	3	0	4	0	4	0	0	0	6	0	4	2	1	3	1	2	1	2	0	rs139394643	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:33361552C>T	ENST00000373463.3	-	3	348	c.229G>A	c.(229-231)Gca>Aca	p.A77T	TMEM54_ENST00000475208.1_Intron|TMEM54_ENST00000329151.5_Intron	NM_033504.2	NP_277039.1	Q969K7	TMM54_HUMAN	transmembrane protein 54	77						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)				ACGATGGCTGCGATGCCTGAA	0.627													C|||	2	0.000399361	0.0008	0.0	5008	,	,		21423	0.0		0.001	False		,,,				2504	0.0				p.A77T		Atlas-SNP	.											.	TMEM54	12	.	0			c.G229A						PASS	.	C	THR/ALA	2,4404	4.2+/-10.8	0,2,2201	70	62	65		229	0.3	0.7	1	dbSNP_134	65	32,8568	21.6+/-65.8	0,32,4268	yes	missense	TMEM54	NM_033504.2	58	0,34,6469	TT,TC,CC		0.3721,0.0454,0.2614	benign	77/223	33361552	34,12972	2203	4300	6503	SO:0001583	missense	113452	exon3			TGGCTGCGATGCC		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.229G>A	1.37:g.33361552C>T	ENSP00000362562:p.Ala77Thr	32	0	0		37	15	0.405405	NM_033504	Q6UV18|Q8IVD0|Q9UM12	Missense_Mutation	SNP	ENST00000373463.3	37	CCDS371.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	12.06	1.824482	0.32237	4.54E-4	0.003721	ENSG00000121900	ENST00000373463	T	0.41400	1.0	4.51	0.262	0.15597	.	0.776453	0.12444	N	0.468393	T	0.11024	0.0269	N	0.00538	-1.39	0.80722	D	1	B	0.11235	0.004	B	0.06405	0.002	T	0.10154	-1.0642	10	0.25751	T	0.34	.	4.3725	0.11255	0.3239:0.4944:0.0:0.1818	.	77	Q969K7	TMM54_HUMAN	T	77	ENSP00000362562:A77T	ENSP00000362562:A77T	A	-	1	0	TMEM54	33134139	0.000000	0.05858	0.743000	0.31040	0.866000	0.49608	0.316000	0.19469	0.170000	0.19704	0.462000	0.41574	GCA	C|0.998;T|0.002	0.002	strong		0.627	TMEM54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011474.1	NM_033504		T	33361552	C	T	33361552	3	4	29	1	0	0	0	0	1	0	0	0	16195	768	27	1	455	1	TMEM54	1	33361552	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	881628	33361552	215889069	19	12260											
INPP5B	3633	hgsc.bcm.edu	37	chr1	38343863	38343863	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	taccagctgccacctaccccGatgtcaaacactgagctgac	11	7	7	16	1	1	2	1	2	0	0	1	3	1	2	5	0	6	2	5	0	3	2	rs141357169	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:38343863G>A	ENST00000373026.1	-	15	1914	c.1914C>T	c.(1912-1914)atC>atT	p.I638I	INPP5B_ENST00000373024.3_Silent_p.I558I|INPP5B_ENST00000373023.2_Silent_p.I638I|INPP5B_ENST00000458109.2_3'UTR|INPP5B_ENST00000373027.1_Silent_p.I394I			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	638	5-phosphatase. {ECO:0000250}.				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)				CACCTACCCCGATGTCAAACA	0.483													G|||	3	0.000599042	0.0	0.0	5008	,	,		20679	0.0		0.003	False		,,,				2504	0.0				p.I558I		Atlas-SNP	.											.	INPP5B	76	.	0			c.C1674T						PASS	.	G		0,4002		0,0,2001	98	100	99		1674	-2.4	1	1	dbSNP_134	99	21,8325		0,21,4152	no	coding-synonymous	INPP5B	NM_005540.2		0,21,6153	AA,AG,GG		0.2516,0.0,0.1701		558/914	38343863	21,12327	2001	4173	6174	SO:0001819	synonymous_variant	3633	exon16			TACCCCGATGTCA	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.1914C>T	1.37:g.38343863G>A		118	0	0		92	37	0.402174	NM_005540	C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	Silent	SNP	ENST00000373026.1	37																																																																																				G|0.997;A|0.003	0.003	strong		0.483	INPP5B-003	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000012968.1	NM_005540		A	38343863	G	A	38343863	2	1	29	1	0	0	0	0	0	0	0	1	7764	1048	37	1		1	INPP5B	1	38343863	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	4982311	38343863	210906758	20	12261											
YBX1	4904	hgsc.bcm.edu	37	chr1	43149084	43149084	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttttccagcaacgaaggtTttgggaacagtaaaatggtt	12	13	10	6	1	1	0	0	0	1	0	2	2	2	1	1	3	3	4	1	3	5	6			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:43149084T>C	ENST00000321358.7	+	2	316	c.177T>C	c.(175-177)gtT>gtC	p.V59V	YBX1_ENST00000467957.1_3'UTR|RP5-994D16.3_ENST00000414339.1_lincRNA	NM_004559.3	NP_004550.2	P67809	YBOX1_HUMAN	Y box binding protein 1	59	Interaction with ss-DNA.				CRD-mediated mRNA stabilization (GO:0070934)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|histone pre-mRNA 3'end processing complex (GO:0071204)|intracellular membrane-bounded organelle (GO:0043231)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|U12-type spliceosomal complex (GO:0005689)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)			large_intestine(2)|lung(4)|ovary(4)|prostate(4)|upper_aerodigestive_tract(2)	16	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				CAACGAAGGTTTTGGGAACAG	0.502																																					p.V59V		Atlas-SNP	.											.	YBX1	49	.	0			c.T177C						PASS	.						92	95	94					1																	43149084		2203	4300	6503	SO:0001819	synonymous_variant	4904	exon2			GAAGGTTTTGGGA	BC013838	CCDS470.1	1p34	2008-02-05	2005-08-11	2005-08-11	ENSG00000065978	ENSG00000065978			8014	protein-coding gene	gene with protein product		154030	"nuclease sensitive element binding protein 1"	NSEP1		1891370, 3174636	Standard	NM_004559		Approved	YB-1, YB1, DBPB, NSEP-1, MDR-NF1, BP-8, CSDB, CSDA2	uc001chs.3	P67809	OTTHUMG00000007523	ENST00000321358.7:c.177T>C	1.37:g.43149084T>C		104	0	0		104	28	0.269231	NM_004559	P16990|P16991|Q14972|Q15325|Q5FVF0	Silent	SNP	ENST00000321358.7	37	CCDS470.1																																																																																			.	.	none		0.502	YBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019786.2	NM_004559		C	43149084	T	C	43149084	2	2	29	1	0	0	0	0	0	0	0	1	17484	1828	64	3		3	YBX1	1	43149084	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	4805221	43149084	206101537	21	12262											
C1orf210	149466	hgsc.bcm.edu	37	chr1	43748923	43748923	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atcctcccactgtcactcacTtttgtttgtctcattcatgg	6	17	5	13	0	4	0	4	0	1	0	7	0	6	0	2	1	0	1	2	1	0	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:43748923T>G	ENST00000523677.1	-	2	252	c.19A>C	c.(19-21)Aca>Cca	p.T7P	C1orf210_ENST00000423420.1_Splice_Site_p.T7P	NM_001164829.1|NM_182517.2	NP_001158301.1|NP_872323.1	Q8IVY1	CA210_HUMAN	chromosome 1 open reading frame 210	7						integral component of membrane (GO:0016021)				breast(1)	1	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				TGTCACTCACTTTTGTTTGTC	0.587																																					p.T7P		Atlas-SNP	.											.	C1orf210	9	.	0			c.A19C						PASS	.						87	85	86					1																	43748923		2203	4300	6503	SO:0001630	splice_region_variant	149466	exon2			ACTCACTTTTGTT	BC041633	CCDS481.1	1p34.2	2006-03-22			ENSG00000253313	ENSG00000253313			28755	protein-coding gene	gene with protein product						12477932	Standard	NM_182517		Approved	MGC52423	uc001cit.4	Q8IVY1	OTTHUMG00000007289	ENST00000523677.1:c.19+1A>C	1.37:g.43748923T>G		350	0	0		392	16	0.0408163	NM_182517	D3DPX2	Missense_Mutation	SNP	ENST00000523677.1	37	CCDS481.1	.	.	.	.	.	.	.	.	.	.	T	10.30	1.311803	0.23821	.	.	ENSG00000253313	ENST00000523677;ENST00000423420	T;T	0.50001	0.76;0.76	3.99	3.99	0.46301	.	0.985827	0.08284	N	0.969437	T	0.65196	0.2668	M	0.63428	1.95	0.25968	N	0.982537	D	0.76494	0.999	D	0.83275	0.996	T	0.50381	-0.8835	9	.	.	.	.	9.554	0.39328	0.0:0.0:0.0:1.0	.	7	Q8IVY1	CA210_HUMAN	P	7	ENSP00000430918:T7P;ENSP00000429399:T7P	.	T	-	1	0	C1orf210	43521510	0.996000	0.38824	0.298000	0.25002	0.223000	0.24884	3.457000	0.53007	2.038000	0.60285	0.459000	0.35465	ACA	.	.	none		0.587	C1orf210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019035.2	NM_182517	Missense_Mutation	G	43748923	T	G	43748923	5	3	29	1	0	0	0	0	0	0	1	0	2031	1623	56	5	330	5	C1orf210	1	43748923	Splice_Site	SNP	T	TCGA-GR-7351-01A-11D-2210-10	599839	43748923	205501698	22	12263											
TMEM69	51249	hgsc.bcm.edu	37	chr1	46159157	46159157	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctggcaggactaatccccttCgttgctccaccactggtcat	7	11	8	15	1	1	0	1	0	0	0	4	1	3	1	4	3	1	3	4	3	1	3	rs61735666	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:46159157C>T	ENST00000372025.4	+	3	1481	c.324C>T	c.(322-324)ttC>ttT	p.F108F	TMEM69_ENST00000496366.1_3'UTR|RP11-767N6.7_ENST00000430643.1_RNA	NM_016486.3	NP_057570.2	Q5SWH9	TMM69_HUMAN	transmembrane protein 69	108						integral component of membrane (GO:0016021)				kidney(3)|lung(4)|ovary(1)	8	Acute lymphoblastic leukemia(166;0.155)					TAATCCCCTTCGTTGCTCCAC	0.458													C|||	26	0.00519169	0.0015	0.0	5008	,	,		21035	0.0		0.005	False		,,,				2504	0.0194				p.F108F		Atlas-SNP	.											.	TMEM69	20	.	0			c.C324T						PASS	.	C		5,3905		0,5,1950	167	164	165		324	-7.3	0	1	dbSNP_129	165	54,8254		1,52,4101	no	coding-synonymous	TMEM69	NM_016486.3		1,57,6051	TT,TC,CC		0.65,0.1279,0.4829		108/248	46159157	59,12159	1955	4154	6109	SO:0001819	synonymous_variant	51249	exon3			CCCCTTCGTTGCT	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.324C>T	1.37:g.46159157C>T		84	0	0		92	38	0.413043	NM_016486	Q3SWW5|Q7Z2G0|Q9P0P9	Silent	SNP	ENST00000372025.4	37	CCDS41325.1																																																																																			C|0.996;T|0.004	0.004	strong		0.458	TMEM69-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098390.1	NM_016486		T	46159157	C	T	46159157	2	4	29	1	0	0	0	0	0	0	0	1	16213	883	31	1		1	TMEM69	1	46159157	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2410234	46159157	203091464	23	12264											
OMA1	115209	hgsc.bcm.edu	37	chr1	58999896	58999896	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	acccaattgatctgagagatCcctggaacatctttattgca	12	12	7	10	0	2	3	0	2	2	1	3	5	3	4	2	1	2	1	2	1	3	4	rs41287650		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:58999896C>A	ENST00000371226.3	-	4	950	c.837G>T	c.(835-837)ggG>ggT	p.G279G	DAB1_ENST00000485760.1_Intron|OMA1_ENST00000358603.2_Silent_p.G279G|OMA1_ENST00000467063.1_5'UTR	NM_145243.3	NP_660286.1	Q96E52	OMA1_HUMAN	OMA1 zinc metallopeptidase	279					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)					TCTGAGAGATCCCTGGAACAT	0.358													C|||	1	0.000199681	0.0	0.0	5008	,	,		16906	0.0		0.001	False		,,,				2504	0.0				p.G279G		Atlas-SNP	.											.	OMA1	50	.	0			c.G837T						PASS	.	C		0,4406		0,0,2203	78	77	77		837	-1.8	0.1	1	dbSNP_127	77	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	OMA1	NM_145243.3		0,7,6496	AA,AC,CC		0.0814,0.0,0.0538		279/525	58999896	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	115209	exon4			AGAGATCCCTGGA	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.837G>T	1.37:g.58999896C>A		281	0	0		231	89	0.385281	NM_145243	D3DQ54|Q5T3G6|Q5T3G7|Q5T3G8|Q5T3G9|Q5T3H0|Q8NBB3	Silent	SNP	ENST00000371226.3	37	CCDS608.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	5.604	0.296110	0.10622	0.0	8.14E-4	ENSG00000162600	ENST00000421528	.	.	.	4.9	-1.81	0.07882	.	.	.	.	.	T	0.28928	0.0718	.	.	.	0.18873	N	0.999985	.	.	.	.	.	.	T	0.32613	-0.9900	4	.	.	.	-8.8864	6.6045	0.22718	0.0:0.3943:0.2766:0.329	rs41287650	.	.	.	Y	121	.	.	D	-	1	0	OMA1	58772484	0.193000	0.23313	0.076000	0.20297	0.911000	0.54048	0.160000	0.16462	-0.139000	0.11414	0.563000	0.77884	GAT	C|1.000;A|0.000	0.000	strong		0.358	OMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027819.1	NM_145243		A	58999896	C	A	58999896	2	1	29	1	0	0	0	0	0	0	0	1	10873	842	30	4		4	OMA1	1	58999896	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	12840739	58999896	190250725	24	12265											
EFCAB7	84455	hgsc.bcm.edu	37	chr1	64011657	64011657	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgaaatcattagtcatcagtAcaggatgcaaatagctcaga	16	10	8	7	0	4	2	4	1	0	1	4	3	4	3	0	1	3	3	0	1	5	3	rs41313264	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:64011657A>G	ENST00000371088.4	+	7	1121	c.875A>G	c.(874-876)tAc>tGc	p.Y292C	DLEU2L_ENST00000371086.2_5'Flank|DLEU2L_ENST00000340052.3_5'Flank	NM_032437.2	NP_115813.2	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	292							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						AGTCATCAGTACAGGATGCAA	0.333													A|||	9	0.00179712	0.0008	0.0043	5008	,	,		17625	0.0		0.004	False		,,,				2504	0.001				p.Y292C		Atlas-SNP	.											.	EFCAB7	45	.	0			c.A875G						PASS	.	A	CYS/TYR	8,4398	14.3+/-33.2	0,8,2195	96	96	96		875	5.8	1	1	dbSNP_127	96	93,8507	52.3+/-112.8	0,93,4207	yes	missense	EFCAB7	NM_032437.2	194	0,101,6402	GG,GA,AA		1.0814,0.1816,0.7766	probably-damaging	292/630	64011657	101,12905	2203	4300	6503	SO:0001583	missense	84455	exon7			ATCAGTACAGGAT	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.875A>G	1.37:g.64011657A>G	ENSP00000360129:p.Tyr292Cys	164	0	0		170	75	0.441176	NM_032437	Q658P0|Q96B95|Q96JM6	Missense_Mutation	SNP	ENST00000371088.4	37	CCDS30737.1	8	0.003663003663003663	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	A	21.5	4.164949	0.78339	0.001816	0.010814	ENSG00000203965	ENST00000371088	T	0.56444	0.46	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.66548	0.2800	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.71570	-0.4553	10	0.87932	D	0	-9.1975	16.0742	0.80958	1.0:0.0:0.0:0.0	rs41313264;rs61744578	292	A8K855	EFCB7_HUMAN	C	292	ENSP00000360129:Y292C	ENSP00000360129:Y292C	Y	+	2	0	EFCAB7	63784245	1.000000	0.71417	0.994000	0.49952	0.993000	0.82548	6.808000	0.75206	2.204000	0.70986	0.482000	0.46254	TAC	A|0.993;G|0.007	0.007	strong		0.333	EFCAB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024910.1	NM_032437		G	64011657	A	G	64011657	3	3	29	1	0	0	0	0	1	0	0	0	4942	391	14	3	897	3	EFCAB7	1	64011657	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	5011761	64011657	185238964	25	12266											
JAK1	3716	hgsc.bcm.edu	37	chr1	65312343	65312343	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacacttactctccacgtcgCggacacagacgccatagagg	11	6	9	15	4	1	2	0	0	1	2	3	3	1	3	2	2	1	0	2	2	2	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:65312343C>T	ENST00000342505.4	-	14	2224	c.1976G>A	c.(1975-1977)cGc>cAc	p.R659H	JAK1_ENST00000465376.1_5'UTR	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	659	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)	CTCCACGTCGCGGACACAGAC	0.582			Mis		ALL																																p.R659H		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	JAK1,NS,malignant_melanoma,0,1	JAK1	209	1	0			c.G1976A						PASS	.						83	90	88					1																	65312343		2141	4271	6412	SO:0001583	missense	3716	exon14			ACGTCGCGGACAC	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.1976G>A	1.37:g.65312343C>T	ENSP00000343204:p.Arg659His	94	0	0		73	20	0.273973	NM_002227	Q59GQ2|Q9UD26	Missense_Mutation	SNP	ENST00000342505.4	37	CCDS41346.1	.	.	.	.	.	.	.	.	.	.	C	8.986	0.976479	0.18736	.	.	ENSG00000162434	ENST00000342505	D	0.82803	-1.65	4.3	3.39	0.38822	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.60011	0.2236	L	0.45422	1.42	0.43457	D	0.995651	B	0.30973	0.302	B	0.24006	0.05	T	0.59925	-0.7362	9	0.13470	T	0.59	-3.1424	12.914	0.58195	0.0:0.9197:0.0:0.0803	.	659	P23458	JAK1_HUMAN	H	659	ENSP00000343204:R659H	ENSP00000343204:R659H	R	-	2	0	JAK1	65084931	0.996000	0.38824	0.930000	0.37139	0.236000	0.25371	3.316000	0.51960	1.395000	0.46643	0.561000	0.74099	CGC	.	.	none		0.582	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		T	65312343	C	T	65312343	3	4	29	1	0	0	0	0	1	0	0	0	7946	768	27	1	1536	1	JAK1	1	65312343	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1300686	65312343	183938278	26	12267											
JAK1	3716	hgsc.bcm.edu	37	chr1	65313232	65313232	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgccagggaaatatccctgtGgctggggtctaagactttga	9	11	13	8	0	1	2	0	1	1	1	2	3	2	3	2	4	1	1	2	4	3	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:65313232G>A	ENST00000342505.4	-	13	2130	c.1882C>T	c.(1882-1884)Cac>Tac	p.H628Y	JAK1_ENST00000465376.1_5'UTR	NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	628	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.L624_R629>W(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)	ATATCCCTGTGGCTGGGGTCT	0.488			Mis		ALL																																p.H628Y		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	1	Complex - deletion inframe(1)	haematopoietic_and_lymphoid_tissue(1)	c.C1882T						PASS	.						213	222	219					1																	65313232		1890	4105	5995	SO:0001583	missense	3716	exon13			CCCTGTGGCTGGG	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.1882C>T	1.37:g.65313232G>A	ENSP00000343204:p.His628Tyr	135	0	0		126	39	0.309524	NM_002227	Q59GQ2|Q9UD26	Missense_Mutation	SNP	ENST00000342505.4	37	CCDS41346.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.662143	0.88251	.	.	ENSG00000162434	ENST00000342505	D	0.82344	-1.6	5.01	5.01	0.66863	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.89897	0.6848	M	0.75884	2.315	0.58432	D	0.999998	D	0.76494	0.999	D	0.83275	0.996	D	0.89400	0.3695	9	0.54805	T	0.06	-8.2173	18.8858	0.92376	0.0:0.0:1.0:0.0	.	628	P23458	JAK1_HUMAN	Y	628	ENSP00000343204:H628Y	ENSP00000343204:H628Y	H	-	1	0	JAK1	65085820	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.295000	0.78780	2.775000	0.95449	0.655000	0.94253	CAC	.	.	none		0.488	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227		A	65313232	G	A	65313232	3	1	29	1	0	0	0	0	1	0	0	0	7946	1348	47	2	1634	2	JAK1	1	65313232	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	889	65313232	183937389	27	12268											
LEPR	3953	hgsc.bcm.edu	37	chr1	66102617	66102617	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctagtaagaagacttttgcAtcttacatgcctcaattcca	12	14	5	10	0	3	2	1	0	2	2	4	2	4	2	2	0	3	2	2	0	5	6	rs61781316	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:66102617A>G	ENST00000349533.6	+	20	3602	c.3417A>G	c.(3415-3417)gcA>gcG	p.A1139A	LEPR_ENST00000406510.3_Silent_p.A206A	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)		AGACTTTTGCATCTTACATGC	0.383													A|||	3	0.000599042	0.0	0.0	5008	,	,		17998	0.0		0.003	False		,,,				2504	0.0				p.A1139A		Atlas-SNP	.											.	LEPR	284	.	0			c.A3417G						PASS	.	A		2,4404	4.2+/-10.8	0,2,2201	73	74	74		3417	-8.3	0.3	1	dbSNP_129	74	47,8553	29.6+/-80.5	0,47,4253	no	coding-synonymous	LEPR	NM_002303.5		0,49,6454	GG,GA,AA		0.5465,0.0454,0.3767		1139/1166	66102617	49,12957	2203	4300	6503	SO:0001819	synonymous_variant	3953	exon20			TTTTGCATCTTAC	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.3417A>G	1.37:g.66102617A>G		71	0	0		44	17	0.386364	NM_002303	Q6FHL5	Silent	SNP	ENST00000349533.6	37	CCDS631.1																																																																																			A|0.997;G|0.003	0.003	strong		0.383	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303		G	66102617	A	G	66102617	2	3	29	1	0	0	0	0	0	0	0	1	8737	204	8	3		3	LEPR	1	66102617	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	789385	66102617	183148004	28	12269											
SGIP1	84251	hgsc.bcm.edu	37	chr1	67148009	67148009	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctacaggactgtggtttcGtcccccggacctggctcggg	5	9	13	14	3	0	0	0	0	0	0	3	2	1	2	4	5	1	2	4	5	1	2	rs61798708	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:67148009G>A	ENST00000371037.4	+	15	1349	c.1272G>A	c.(1270-1272)tcG>tcA	p.S424S	SGIP1_ENST00000371035.3_Intron|SGIP1_ENST00000371036.3_Intron|SGIP1_ENST00000237247.6_Silent_p.S428S|SGIP1_ENST00000371039.1_Intron	NM_032291.2	NP_115667.2	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting protein 1	424	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						CTGTGGTTTCGTCCCCCGGAC	0.552													G|||	16	0.00319489	0.0015	0.0014	5008	,	,		18121	0.005		0.007	False		,,,				2504	0.001				p.S424S		Atlas-SNP	.											.	SGIP1	272	.	0			c.G1272A						PASS	.	G		7,4399		0,7,2196	106	120	115		1272	-0.2	1	1	dbSNP_129	115	73,8527		0,73,4227	no	coding-synonymous	SGIP1	NM_032291.2		0,80,6423	AA,AG,GG		0.8488,0.1589,0.6151		424/829	67148009	80,12926	2203	4300	6503	SO:0001819	synonymous_variant	84251	exon15			GGTTTCGTCCCCC	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.1272G>A	1.37:g.67148009G>A		109	0	0		106	45	0.424528	NM_032291	A6NL81|A6NLD1|Q4LE32|Q5VYE2|Q5VYE3|Q5VYE4|Q68D76|Q6MZY6|Q8IWC2	Silent	SNP	ENST00000371037.4	37	CCDS30744.1																																																																																			G|0.994;A|0.006	0.006	strong		0.552	SGIP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025395.4	NM_032291		A	67148009	G	A	67148009	2	1	29	1	0	0	0	0	0	0	0	1	14221	1132	40	1		1	SGIP1	1	67148009	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1045392	67148009	182102612	29	12270											
SERBP1	26135	hgsc.bcm.edu	37	chr1	67895758	67895758	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcgggttcttgcggtcttTctgggactccttgcgcagct	3	13	13	12	3	3	0	0	0	3	0	4	1	4	1	1	3	4	3	1	3	0	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:67895758T>G	ENST00000370995.2	-	1	311	c.226A>C	c.(226-228)Aaa>Caa	p.K76Q	SERBP1_ENST00000361219.6_Missense_Mutation_p.K76Q|SERBP1_ENST00000370990.5_Missense_Mutation_p.K76Q|SERBP1_ENST00000370994.4_Missense_Mutation_p.K76Q			Q8NC51	PAIRB_HUMAN	SERPINE1 mRNA binding protein 1	76					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						TTGCGGTCTTTCTGGGACTCC	0.667																																					p.K76Q		Atlas-SNP	.											.	SERBP1	31	.	0			c.A226C						PASS	.						45	55	52					1																	67895758		2195	4283	6478	SO:0001583	missense	26135	exon1			GGTCTTTCTGGGA	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.226A>C	1.37:g.67895758T>G	ENSP00000360034:p.Lys76Gln	169	0	0		149	50	0.33557	NM_001018067	Q5VU19|Q5VU20|Q5VU22|Q8WUH0|Q96SE2|Q9BTY3|Q9BUM4|Q9Y367|Q9Y4S3	Missense_Mutation	SNP	ENST00000370995.2	37	CCDS30746.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.614731	0.87359	.	.	ENSG00000142864	ENST00000370994;ENST00000370995;ENST00000361219;ENST00000370990	.	.	.	4.99	3.78	0.43462	.	0.000000	0.85682	D	0.000000	T	0.70124	0.3188	M	0.74389	2.26	0.50632	D	0.999889	P;D;D;D	0.89917	0.818;1.0;1.0;1.0	B;D;D;D	0.85130	0.198;0.996;0.997;0.997	T	0.72633	-0.4234	9	0.52906	T	0.07	.	10.7053	0.45952	0.1426:0.0:0.0:0.8574	.	139;139;76;76	D3DQ69;D3DQ70;Q8NC51-3;Q8NC51	.;.;.;PAIRB_HUMAN	Q	76	.	ENSP00000354591:K76Q	K	-	1	0	SERBP1	67668346	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.400000	0.59709	2.000000	0.58554	0.379000	0.24179	AAA	.	.	none		0.667	SERBP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025984.2	NM_001018067		G	67895758	T	G	67895758	3	3	29	1	0	0	0	0	1	0	0	0	14090	1792	62	5	1032	5	SERBP1	1	67895758	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	747749	67895758	181354863	30	12271											
SERBP1	26135	hgsc.bcm.edu	37	chr1	67895779	67895779	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgggactccttgcgcagctGtttgcctgccgcgttggagt	3	12	14	12	3	0	0	0	0	0	0	1	2	1	2	3	2	4	4	3	2	0	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:67895779G>A	ENST00000370995.2	-	1	290	c.205C>T	c.(205-207)Cag>Tag	p.Q69*	SERBP1_ENST00000361219.6_Nonsense_Mutation_p.Q69*|SERBP1_ENST00000370990.5_Nonsense_Mutation_p.Q69*|SERBP1_ENST00000370994.4_Nonsense_Mutation_p.Q69*			Q8NC51	PAIRB_HUMAN	SERPINE1 mRNA binding protein 1	69					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						TTGCGCAGCTGTTTGCCTGCC	0.657																																					p.Q69X		Atlas-SNP	.											.	SERBP1	31	.	0			c.C205T						PASS	.						37	46	43					1																	67895779		2197	4289	6486	SO:0001587	stop_gained	26135	exon1			GCAGCTGTTTGCC	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.205C>T	1.37:g.67895779G>A	ENSP00000360034:p.Gln69*	127	0	0		110	39	0.354545	NM_001018067	Q5VU19|Q5VU20|Q5VU22|Q8WUH0|Q96SE2|Q9BTY3|Q9BUM4|Q9Y367|Q9Y4S3	Nonsense_Mutation	SNP	ENST00000370995.2	37	CCDS30746.1	.	.	.	.	.	.	.	.	.	.	G	38	7.040941	0.98021	.	.	ENSG00000142864	ENST00000370994;ENST00000370995;ENST00000361219;ENST00000370990	.	.	.	4.99	4.99	0.66335	.	0.056967	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	-3.4359	17.4097	0.87482	0.0:0.0:1.0:0.0	.	.	.	.	X	69	.	ENSP00000354591:Q69X	Q	-	1	0	SERBP1	67668367	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.730000	0.91510	2.471000	0.83476	0.462000	0.41574	CAG	.	.	none		0.657	SERBP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025984.2	NM_001018067		A	67895779	G	A	67895779	4	1	29	1	0	0	0	0	0	1	0	0	14090	1386	48	2	1053	2	SERBP1	1	67895779	Nonsense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	21	67895779	181354842	31	12272											
LRRIQ3	127255	hgsc.bcm.edu	37	chr1	74648375	74648375	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgttaacaagaacatgtctAtatccttttttaaggcttac	12	16	5	8	0	1	1	0	0	1	1	2	1	2	1	1	1	3	2	1	1	7	7			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:74648375A>G	ENST00000395089.1	-	2	419	c.420T>C	c.(418-420)taT>taC	p.Y140Y	LRRIQ3_ENST00000370911.3_Silent_p.Y140Y|LRRIQ3_ENST00000370909.2_Intron|LRRIQ3_ENST00000354431.4_Silent_p.Y140Y			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	140	LRRCT.									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						GAACATGTCTATATCCTTTTT	0.373																																					p.Y140Y		Atlas-SNP	.											.	LRRIQ3	146	.	0			c.T420C						PASS	.						115	111	112					1																	74648375		2203	4298	6501	SO:0001819	synonymous_variant	127255	exon3			ATGTCTATATCCT	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.420T>C	1.37:g.74648375A>G		68	0	0		83	26	0.313253	NM_001105659	A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Silent	SNP	ENST00000395089.1	37	CCDS41350.1																																																																																			.	.	none		0.373	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258		G	74648375	A	G	74648375	2	3	29	1	0	0	0	0	0	0	0	1	9039	456	16	3		3	LRRIQ3	1	74648375	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	6752596	74648375	174602246	32	12273											
RABGGTB	5876	hgsc.bcm.edu	37	chr1	76260248	76260248	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggattgtcacttttgggagaAgaacagattaaacctgttaa	14	12	10	5	0	1	3	1	0	0	3	1	5	1	4	1	2	2	1	1	2	5	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:76260248A>C	ENST00000319942.3	+	9	980	c.909A>C	c.(907-909)gaA>gaC	p.E303D	RABGGTB_ENST00000496055.1_3'UTR|MSH4_ENST00000263187.3_5'Flank|RABGGTB_ENST00000535300.1_Missense_Mutation_p.E129D	NM_004582.3	NP_004573.2	P53611	PGTB2_HUMAN	Rab geranylgeranyltransferase, beta subunit	303					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(2)|large_intestine(6)|lung(7)|ovary(1)	19						TTTTGGGAGAAGAACAGATTA	0.353																																					p.E303D		Atlas-SNP	.											.	RABGGTB	37	.	0			c.A909C						PASS	.						111	114	113					1																	76260248		2203	4300	6503	SO:0001583	missense	5876	exon9			GGGAGAAGAACAG	U49245	CCDS669.1	1p31	2008-02-05			ENSG00000137955	ENSG00000137955			9796	protein-coding gene	gene with protein product		179080				8706741, 8954794	Standard	NM_004582		Approved		uc001dgy.2	P53611	OTTHUMG00000009786	ENST00000319942.3:c.909A>C	1.37:g.76260248A>C	ENSP00000317473:p.Glu303Asp	72	0	0		78	20	0.25641	NM_004582	Q92697	Missense_Mutation	SNP	ENST00000319942.3	37	CCDS669.1	.	.	.	.	.	.	.	.	.	.	A	13.56	2.272993	0.40194	.	.	ENSG00000137955	ENST00000535300;ENST00000319942	T;T	0.42900	0.96;0.96	5.55	1.78	0.24846	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.242531	0.47852	N	0.000216	T	0.09774	0.0240	N	0.20766	0.605	0.42372	D	0.992459	B	0.02656	0.0	B	0.01281	0.0	T	0.06607	-1.0817	10	0.35671	T	0.21	-14.8082	3.3956	0.07304	0.6396:0.1221:0.1201:0.1182	.	303	P53611	PGTB2_HUMAN	D	129;303	ENSP00000440452:E129D;ENSP00000317473:E303D	ENSP00000317473:E303D	E	+	3	2	RABGGTB	76032836	0.998000	0.40836	1.000000	0.80357	0.971000	0.66376	0.621000	0.24418	1.005000	0.39183	0.460000	0.39030	GAA	.	.	none		0.353	RABGGTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026972.1	NM_004582		C	76260248	A	C	76260248	3	2	29	1	0	0	0	0	1	0	0	0	12983	69	3	5	943	5	RABGGTB	1	76260248	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	1611873	76260248	172990373	33	12274											
COL24A1	255631	hgsc.bcm.edu	37	chr1	86488270	86488270	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctctcctgctgtgccttgtTcaccctggaaagcacaattt	7	13	8	13	0	2	0	1	0	1	0	3	1	2	1	3	1	3	4	3	1	2	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:86488270T>G	ENST00000370571.2	-	17	2519	c.2153A>C	c.(2152-2154)gAa>gCa	p.E718A	COL24A1_ENST00000436319.1_Missense_Mutation_p.E718A	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	718	Collagen-like 3.				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)		TGTGCCTTGTTCACCCTGGAA	0.333																																					p.E718A		Atlas-SNP	.											.	COL24A1	202	.	0			c.A2153C						PASS	.						62	62	62					1																	86488270		1866	4098	5964	SO:0001583	missense	255631	exon17			CCTTGTTCACCCT	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.2153A>C	1.37:g.86488270T>G	ENSP00000359603:p.Glu718Ala	148	0	0		166	16	0.0963855	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Missense_Mutation	SNP	ENST00000370571.2	37	CCDS41353.1	.	.	.	.	.	.	.	.	.	.	T	13.91	2.376743	0.42105	.	.	ENSG00000171502	ENST00000370571;ENST00000436319	D;D	0.93488	-3.23;-3.23	5.62	5.62	0.85841	.	0.000000	0.37348	N	0.002132	D	0.91546	0.7330	L	0.33189	0.99	0.49687	D	0.999816	D	0.63880	0.993	D	0.65140	0.932	D	0.90183	0.4244	10	0.22109	T	0.4	.	14.0686	0.64847	0.0:0.0:0.0:1.0	.	718	Q17RW2	COOA1_HUMAN	A	718	ENSP00000359603:E718A;ENSP00000392531:E718A	ENSP00000359603:E718A	E	-	2	0	COL24A1	86260858	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.078000	0.57606	2.129000	0.65627	0.533000	0.62120	GAA	.	.	none		0.333	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890		G	86488270	T	G	86488270	3	3	29	1	0	0	0	0	1	0	0	0	3685	1783	62	5	3167	5	COL24A1	1	86488270	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	10228022	86488270	162762351	34	12275											
COL24A1	255631	hgsc.bcm.edu	37	chr1	86591014	86591014	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttcctcagtgatcatttcTttggcctgaatcccatggtt	6	17	7	11	0	4	2	2	2	2	0	6	2	6	2	3	2	0	1	3	2	1	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:86591014T>C	ENST00000370571.2	-	3	1371	c.1005A>G	c.(1003-1005)aaA>aaG	p.K335K	COL24A1_ENST00000436319.1_Silent_p.K335K	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	335					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)		TGATCATTTCTTTGGCCTGAA	0.403																																					p.K335K		Atlas-SNP	.											.	COL24A1	202	.	0			c.A1005G						PASS	.						112	98	102					1																	86591014		1905	4128	6033	SO:0001819	synonymous_variant	255631	exon3			CATTTCTTTGGCC	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.1005A>G	1.37:g.86591014T>C		207	0	0		183	12	0.0655738	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Silent	SNP	ENST00000370571.2	37	CCDS41353.1																																																																																			.	.	none		0.403	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890		C	86591014	T	C	86591014	2	2	29	1	0	0	0	0	0	0	0	1	3685	1606	56	3		3	COL24A1	1	86591014	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	102744	86591014	162659607	35	12276											
CLCA2	9635	hgsc.bcm.edu	37	chr1	86913384	86913384	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acagggattttatcccattcTtaatgccactgtcactgcca	10	13	6	12	0	2	0	1	0	1	0	3	1	3	1	3	1	2	0	3	1	2	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:86913384T>A	ENST00000370565.4	+	11	2069	c.1907T>A	c.(1906-1908)cTt>cAt	p.L636H		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	636					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)		TATCCCATTCTTAATGCCACT	0.473																																					p.L636H	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											.	CLCA2	102	.	0			c.T1907A						PASS	.						107	103	104					1																	86913384		2203	4300	6503	SO:0001583	missense	9635	exon11			CCATTCTTAATGC		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.1907T>A	1.37:g.86913384T>A	ENSP00000359596:p.Leu636His	76	0	0		89	20	0.224719	NM_006536	A8K2T3|Q9Y6N2	Missense_Mutation	SNP	ENST00000370565.4	37	CCDS708.1	.	.	.	.	.	.	.	.	.	.	T	13.55	2.271256	0.40194	.	.	ENSG00000137975	ENST00000370565	T	0.40476	1.03	5.82	2.13	0.27403	Domain of unknown function DUF1973 (1);	0.262170	0.31010	N	0.008430	T	0.38878	0.1057	M	0.87617	2.895	0.19300	N	0.99997	D	0.59767	0.986	P	0.53988	0.739	T	0.35847	-0.9772	10	0.62326	D	0.03	-5.1849	4.7281	0.12950	0.1189:0.0655:0.1245:0.691	.	636	Q9UQC9	CLCA2_HUMAN	H	636	ENSP00000359596:L636H	ENSP00000359596:L636H	L	+	2	0	CLCA2	86685972	0.998000	0.40836	0.817000	0.32601	0.287000	0.27160	2.049000	0.41288	0.100000	0.17581	-0.316000	0.08728	CTT	.	.	none		0.473	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536		A	86913384	T	A	86913384	3	1	29	1	0	0	0	0	1	0	0	0	3460	1609	56	5	1949	5	CLCA2	1	86913384	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	322370	86913384	162337237	36	12277											
GBP1	2633	hgsc.bcm.edu	37	chr1	89523844	89523844	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acgggccgatcaaagacaaaGcattttttctttgggaagaa	14	10	10	7	2	2	2	1	0	1	2	2	4	2	3	1	2	1	1	1	2	4	4	rs141095851	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:89523844G>A	ENST00000370473.4	-	6	924	c.705C>T	c.(703-705)tgC>tgT	p.C235C	GBP1_ENST00000484970.1_5'Flank	NM_002053.2	NP_002044.2	P32455	GBP1_HUMAN	guanylate binding protein 1, interferon-inducible	235	GB1/RHD3-type G.|GTPase domain (Globular).				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)	cytosol (GO:0005829)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			endometrium(7)|kidney(4)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	30		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)		CAAAGACAAAGCATTTTTTCT	0.413													.|||	3	0.000599042	0.0	0.0	5008	,	,		16439	0.0		0.003	False		,,,				2504	0.0				p.C235C		Atlas-SNP	.											.	GBP1	68	.	0			c.C705T						PASS	.	G		5,4401	8.1+/-20.4	0,5,2198	150	165	160		705	2.6	1	1	dbSNP_134	160	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	GBP1	NM_002053.2		0,19,6484	AA,AG,GG		0.1628,0.1135,0.1461		235/593	89523844	19,12987	2203	4300	6503	SO:0001819	synonymous_variant	2633	exon6			GACAAAGCATTTT	BC002666	CCDS718.1	1p22.2	2011-03-09	2011-03-09		ENSG00000117228	ENSG00000117228			4182	protein-coding gene	gene with protein product		600411	"guanylate binding protein 1, interferon-inducible, 67kDa"			7518790	Standard	NM_002053		Approved		uc001dmx.2	P32455	OTTHUMG00000010614	ENST00000370473.4:c.705C>T	1.37:g.89523844G>A		106	0	0		125	62	0.496	NM_002053	D3DT26|Q5T8M1	Silent	SNP	ENST00000370473.4	37	CCDS718.1																																																																																			G|0.999;A|0.001	0.001	strong		0.413	GBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029289.3	NM_002053		A	89523844	G	A	89523844	2	1	29	1	0	0	0	0	0	0	0	1	6281	963	34	2		2	GBP1	1	89523844	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2610460	89523844	159726777	37	12278											
SLC44A3	126969	hgsc.bcm.edu	37	chr1	95330440	95330440	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	attgtcatgtacatgcaaaaCgcactgaaagaacaggtaag	17	8	9	7	1	1	2	1	1	0	1	1	2	1	2	0	1	4	4	0	1	6	3	rs142406496	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:95330440C>T	ENST00000271227.6	+	11	1482	c.1380C>T	c.(1378-1380)aaC>aaT	p.N460N	SLC44A3_ENST00000467909.1_Silent_p.N412N|SLC44A3_ENST00000446120.2_Silent_p.N424N|SLC44A3_ENST00000529450.1_Silent_p.N428N|SLC44A3_ENST00000532427.1_Silent_p.N380N|SLC44A3_ENST00000530397.1_3'UTR|SLC44A3_ENST00000527077.1_Silent_p.N392N	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	460					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)	ACATGCAAAACGCACTGAAAG	0.438													C|||	10	0.00199681	0.0	0.0014	5008	,	,		19243	0.001		0.008	False		,,,				2504	0.0				p.N460N		Atlas-SNP	.											.	SLC44A3	109	.	0			c.C1380T						PASS	.	C	,	4,4402	8.1+/-20.4	0,4,2199	201	187	192		1380,1236	4.9	0	1	dbSNP_134	192	47,8553	31.7+/-84.0	0,47,4253	no	coding-synonymous,coding-synonymous	SLC44A3	NM_001114106.1,NM_152369.3	,	0,51,6452	TT,TC,CC		0.5465,0.0908,0.3921	,	460/654,412/606	95330440	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	126969	exon11			GCAAAACGCACTG	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.1380C>T	1.37:g.95330440C>T		83	0	0		99	51	0.515152	NM_001114106	B4DVY4|B4E1M4|B7ZA08|E9PJH2|E9PJY8|Q6UWT1|Q7Z6C5|Q9BWY7	Silent	SNP	ENST00000271227.6	37	CCDS44176.1																																																																																			C|0.996;T|0.004	0.004	strong		0.438	SLC44A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029544.3	NM_152369		T	95330440	C	T	95330440	2	4	29	1	0	0	0	0	0	0	0	1	14652	535	19	1		1	SLC44A3	1	95330440	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	5806596	95330440	153920181	38	12279											
ALG14	199857	hgsc.bcm.edu	37	chr1	95538342	95538342	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acccagccactaccaagataCtgagagactcccggggcgta	12	5	10	14	2	0	3	0	1	0	2	1	4	1	3	4	2	3	1	4	2	4	3	rs139521179	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:95538342C>A	ENST00000370205.5	-	1	159	c.113G>T	c.(112-114)aGt>aTt	p.S38I	ALG14_ENST00000495856.1_5'UTR	NM_144988.3	NP_659425.1	Q96F25	ALG14_HUMAN	ALG14, UDP-N-acetylglucosaminyltransferase subunit	38					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)		TACCAAGATACTGAGAGACTC	0.582													C|||	5	0.000998403	0.0	0.0014	5008	,	,		17973	0.0		0.004	False		,,,				2504	0.0				p.S38I		Atlas-SNP	.											.	ALG14	13	.	0			c.G113T						PASS	.	C	ILE/SER	3,4403	6.2+/-15.9	0,3,2200	128	116	121		113	5	1	1	dbSNP_134	121	40,8560	27.4+/-76.7	0,40,4260	yes	missense	ALG14	NM_144988.3	142	0,43,6460	AA,AC,CC		0.4651,0.0681,0.3306	benign	38/217	95538342	43,12963	2203	4300	6503	SO:0001583	missense	199857	exon1			AAGATACTGAGAG		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.113G>T	1.37:g.95538342C>A	ENSP00000359224:p.Ser38Ile	58	0	0		61	29	0.47541	NM_144988	A8K030	Missense_Mutation	SNP	ENST00000370205.5	37	CCDS752.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	13.48	2.248804	0.39797	6.81E-4	0.004651	ENSG00000172339	ENST00000370205	T	0.46819	0.86	4.99	4.99	0.66335	.	0.528179	0.21965	N	0.066526	T	0.17959	0.0431	N	0.08118	0	0.38423	D	0.946221	P	0.36909	0.573	B	0.34824	0.19	T	0.15809	-1.0424	10	0.54805	T	0.06	-3.7389	15.8023	0.78463	0.0:1.0:0.0:0.0	.	38	Q96F25	ALG14_HUMAN	I	38	ENSP00000359224:S38I	ENSP00000359224:S38I	S	-	2	0	ALG14	95310930	0.853000	0.29707	0.993000	0.49108	0.346000	0.29079	1.131000	0.31406	2.591000	0.87537	0.591000	0.81541	AGT	C|0.997;A|0.003	0.003	strong		0.582	ALG14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029699.2	NM_144988		A	95538342	C	A	95538342	3	1	29	1	0	0	0	0	1	0	0	0	516	565	20	4	553	4	ALG14	1	95538342	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	207902	95538342	153712279	39	12280											
PTBP2	58155	hgsc.bcm.edu	37	chr1	97235290	97235290	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatagtaaaaaatttaaaggAgaagataaaatggatggtgc	20	9	11	1	0	0	2	0	0	0	2	0	5	0	3	0	3	1	1	0	3	9	5	rs139414147	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:97235290A>G	ENST00000426398.2	+	4	190	c.147A>G	c.(145-147)ggA>ggG	p.G49G	PTBP2_ENST00000482253.1_3'UTR|PTBP2_ENST00000370197.1_Silent_p.G49G|PTBP2_ENST00000370198.1_Silent_p.G49G|PTBP2_ENST00000541987.1_Silent_p.G18G|PTBP2_ENST00000394184.3_Silent_p.G60G|PTBP2_ENST00000609116.1_Silent_p.G49G	NM_021190.2	NP_067013.1	Q9UKA9	PTBP2_HUMAN	polypyrimidine tract binding protein 2	49					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)		AATTTAAAGGAGAAGATAAAA	0.313													A|||	8	0.00159744	0.0	0.0014	5008	,	,		15902	0.0		0.0	False		,,,				2504	0.0072				p.G49G		Atlas-SNP	.											.	PTBP2	62	.	0			c.A147G						PASS	.	A		1,4405	2.1+/-5.4	0,1,2202	87	96	93		147	3	1	1	dbSNP_134	93	25,8575	16.6+/-54.9	0,25,4275	no	coding-synonymous	PTBP2	NM_021190.2		0,26,6477	GG,GA,AA		0.2907,0.0227,0.1999		49/532	97235290	26,12980	2203	4300	6503	SO:0001819	synonymous_variant	58155	exon4			TAAAGGAGAAGAT	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.147A>G	1.37:g.97235290A>G		100	0	0		89	33	0.370787	NM_021190	Q8N0Z1|Q8N160|Q8NFB0|Q8NFB1|Q969N9|Q96Q76	Silent	SNP	ENST00000426398.2	37	CCDS754.1																																																																																			A|0.998;G|0.002	0.002	strong		0.313	PTBP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029453.1			G	97235290	A	G	97235290	2	3	29	1	0	0	0	0	0	0	0	1	12738	291	11	3		3	PTBP2	1	97235290	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	1696948	97235290	152015331	40	12281											
CLCC1	23155	hgsc.bcm.edu	37	chr1	109477406	109477406	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttcagacttgagctgggcCttttccgctgcgggtgaacc	5	11	13	12	2	1	3	1	2	0	1	2	3	2	3	3	2	3	3	3	2	1	4	rs150029224	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:109477406C>T	ENST00000369971.2	-	11	1671	c.1542G>A	c.(1540-1542)aaG>aaA	p.K514K	CLCC1_ENST00000369968.2_Silent_p.K329K|CLCC1_ENST00000482889.1_Intron|CLCC1_ENST00000369969.2_Silent_p.K393K|CLCC1_ENST00000356970.2_Silent_p.K514K|CLCC1_ENST00000302500.4_Silent_p.K393K|CLCC1_ENST00000415331.1_Silent_p.K464K|CLCC1_ENST00000348264.2_Silent_p.K329K|CLCC1_ENST00000369970.3_Silent_p.K464K|AKNAD1_ENST00000357393.4_Intron|CLCC1_ENST00000369976.1_Intron	NM_001048210.1	NP_001041675.1	Q96S66	CLCC1_HUMAN	chloride channel CLIC-like 1	514						chloride channel complex (GO:0034707)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	chloride channel activity (GO:0005254)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|liver(1)|skin(1)	14		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.231)		TGAGCTGGGCCTTTTCCGCTG	0.592																																					p.K514K		Atlas-SNP	.											.	CLCC1	55	.	0			c.G1542A						PASS	.	C	,	0,4406		0,0,2203	145	130	135		1542,1392	5.9	0.2	1	dbSNP_134	135	12,8588	9.8+/-36.6	0,12,4288	no	coding-synonymous,coding-synonymous	CLCC1	NM_001048210.1,NM_015127.3	,	0,12,6491	TT,TC,CC		0.1395,0.0,0.0923	,	514/552,464/502	109477406	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	23155	exon11			CTGGGCCTTTTCC	AB018304	CCDS793.1, CCDS41362.1, CCDS60214.1, CCDS60215.1	1p13.3	2008-02-05			ENSG00000121940	ENSG00000121940			29675	protein-coding gene	gene with protein product	"Mid1-related chloride channel (yeast)"					9872452, 11279057	Standard	NM_001048210		Approved	MCLC	uc001dwf.2	Q96S66	OTTHUMG00000011732	ENST00000369971.2:c.1542G>A	1.37:g.109477406C>T		228	1	0.00438596		203	102	0.502463	NM_001048210	O94861|Q8WYP8|Q8WYP9|Q9BU25	Silent	SNP	ENST00000369971.2	37	CCDS41362.1																																																																																			C|1.000;T|0.000	0.000	strong		0.592	CLCC1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032405.1	NM_015127		T	109477406	C	T	109477406	2	4	29	1	0	0	0	0	0	0	0	1	3462	680	24	2		2	CLCC1	1	109477406	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	12242116	109477406	139773215	41	12282											
KCNC4	3749	hgsc.bcm.edu	37	chr1	110766185	110766185	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcaagaacatccccattggCttctggtgggctgtggtcac	7	12	11	11	0	3	1	2	0	1	1	4	1	4	1	2	4	1	2	2	4	2	3	rs368399763		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:110766185C>T	ENST00000369787.3	+	2	1305	c.1278C>T	c.(1276-1278)ggC>ggT	p.G426G	KCNC4_ENST00000438661.2_Silent_p.G426G|KCNC4_ENST00000413138.3_Silent_p.G426G|KCNC4_ENST00000412512.2_Intron	NM_004978.4	NP_004969.2	Q03721	KCNC4_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 4	426					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)		TCCCCATTGGCTTCTGGTGGG	0.587																																					p.G426G		Atlas-SNP	.											.	KCNC4	113	.	0			c.C1278T						PASS	.	C	,	0,4406		0,0,2203	117	106	110		1278,1278	3.8	1	1		110	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	KCNC4	NM_001039574.2,NM_004978.4	,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,	426/627,426/636	110766185	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	3749	exon2			CATTGGCTTCTGG	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.1278C>T	1.37:g.110766185C>T		110	0	0		81	42	0.518519	NM_001039574	Q3MIM4|Q5TBI6	Silent	SNP	ENST00000369787.3	37	CCDS821.1																																																																																			.	.	none		0.587	KCNC4-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052146.2	NM_001039574		T	110766185	C	T	110766185	2	4	29	1	0	0	0	0	0	0	0	1	8026	784	28	2		2	KCNC4	1	110766185	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1288779	110766185	138484436	42	12283											
LRIG2	9860	hgsc.bcm.edu	37	chr1	113637308	113637308	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgactccttaagatctttgaAaatgcagcggaatggaatta	14	12	9	6	1	1	3	0	2	1	1	2	5	2	5	1	2	2	1	1	2	6	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:113637308A>G	ENST00000361127.5	+	6	932	c.734A>G	c.(733-735)aAa>aGa	p.K245R		NM_014813.1	NP_055628.1	O94898	LRIG2_HUMAN	leucine-rich repeats and immunoglobulin-like domains 2	245					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)		AGATCTTTGAAAATGCAGCGG	0.353																																					p.K245R		Atlas-SNP	.											.	LRIG2	67	.	0			c.A734G						PASS	.						123	127	126					1																	113637308		2203	4300	6503	SO:0001583	missense	9860	exon6			CTTTGAAAATGCA	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.734A>G	1.37:g.113637308A>G	ENSP00000355396:p.Lys245Arg	239	0	0		209	94	0.449761	NM_014813	Q9NSN2	Missense_Mutation	SNP	ENST00000361127.5	37	CCDS30808.1	.	.	.	.	.	.	.	.	.	.	A	17.48	3.399000	0.62177	.	.	ENSG00000198799	ENST00000361127	T	0.56941	0.43	5.94	5.94	0.96194	.	0.000000	0.85682	D	0.000000	T	0.27933	0.0688	N	0.25094	0.71	0.49798	D	0.999822	B	0.27910	0.193	B	0.32533	0.147	T	0.14337	-1.0476	10	0.25106	T	0.35	.	16.3985	0.83631	1.0:0.0:0.0:0.0	.	245	O94898	LRIG2_HUMAN	R	245	ENSP00000355396:K245R	ENSP00000355396:K245R	K	+	2	0	LRIG2	113438831	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.520000	0.81821	2.274000	0.75844	0.519000	0.50382	AAA	.	.	none		0.353	LRIG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033549.2	NM_014813		G	113637308	A	G	113637308	3	3	29	1	0	0	0	0	1	0	0	0	8954	14	1	3	756	3	LRIG2	1	113637308	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	2871123	113637308	135613313	43	12284											
CSDE1	7812	hgsc.bcm.edu	37	chr1	115272916	115272916	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgggctagtggttttaggaTtggaaaaagtggcttctttt	8	17	13	3	0	1	0	0	0	1	0	1	2	1	2	0	5	0	3	0	5	4	8	rs149300730		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:115272916T>C	ENST00000358528.4	-	12	1745	c.1319A>G	c.(1318-1320)aAt>aGt	p.N440S	CSDE1_ENST00000530886.1_Missense_Mutation_p.N310S|Y_RNA_ENST00000365030.1_RNA|CSDE1_ENST00000369530.1_Missense_Mutation_p.N455S|CSDE1_ENST00000261443.5_Missense_Mutation_p.N409S|CSDE1_ENST00000438362.2_Missense_Mutation_p.N486S|CSDE1_ENST00000339438.6_Missense_Mutation_p.N409S|CSDE1_ENST00000534699.1_Missense_Mutation_p.N440S	NM_001007553.2	NP_001007554.1	O75534	CSDE1_HUMAN	cold shock domain containing E1, RNA-binding	440					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)		GGTTTTAGGATTGGAAAAAGT	0.388																																					p.N486S		Atlas-SNP	.											.	CSDE1	145	.	0			c.A1457G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN	0,4406		0,0,2203	130	137	135		1319,1364,1457,1319,1226,1226	4.5	1	1	dbSNP_134	135	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense,missense,missense,missense	CSDE1	NM_001007553.2,NM_001130523.2,NM_001242891.1,NM_001242892.1,NM_001242893.1,NM_007158.5	46,46,46,46,46,46	0,2,6501	CC,CT,TT		0.0233,0.0,0.0154	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	440/799,455/814,486/845,440/799,409/768,409/768	115272916	2,13004	2203	4300	6503	SO:0001583	missense	7812	exon13			TTAGGATTGGAAA		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.1319A>G	1.37:g.115272916T>C	ENSP00000351329:p.Asn440Ser	100	0	0		108	39	0.361111	NM_001242891	A8K281|E9PGZ0|G5E9Q2|O94961|Q5TF04|Q5TF05|Q68DF1|Q68DI9|Q9Y2S4	Missense_Mutation	SNP	ENST00000358528.4	37	CCDS30812.1	.	.	.	.	.	.	.	.	.	.	T	12.12	1.843379	0.32606	0.0	2.33E-4	ENSG00000009307	ENST00000339438;ENST00000438362;ENST00000358528;ENST00000261443;ENST00000530886;ENST00000369530;ENST00000534699	.	.	.	5.61	4.48	0.54585	.	0.393339	0.26072	N	0.026508	T	0.41119	0.1145	L	0.36672	1.1	0.35973	D	0.835437	B;B;D	0.56035	0.243;0.007;0.974	B;B;D	0.67725	0.079;0.011;0.953	T	0.36504	-0.9745	9	0.09084	T	0.74	-10.7066	11.1387	0.48390	0.0:0.0:0.1548:0.8452	.	455;440;486	E9PGZ0;O75534;G5E9Q2	.;CSDE1_HUMAN;.	S	409;486;440;409;310;455;440	.	ENSP00000261443:N409S	N	-	2	0	CSDE1	115074439	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	2.729000	0.47327	0.949000	0.37715	-0.313000	0.08912	AAT	T|1.000;C|0.000	0.000	weak		0.388	CSDE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033397.1	NM_007158		C	115272916	T	C	115272916	3	2	29	1	0	0	0	0	1	0	0	0	3931	1493	52	3	1113	3	CSDE1	1	115272916	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	1635608	115272916	133977705	44	12285											
VANGL1	81839	hgsc.bcm.edu	37	chr1	116206871	116206871	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgatggcgagtcccgcttctAcagcctgggacacctgaggt	7	8	13	13	3	1	1	0	1	1	0	2	4	2	2	3	3	2	1	3	3	1	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:116206871A>G	ENST00000355485.2	+	4	1065	c.794A>G	c.(793-795)tAc>tGc	p.Y265C	VANGL1_ENST00000310260.3_Missense_Mutation_p.Y265C|VANGL1_ENST00000369510.4_Missense_Mutation_p.Y263C|VANGL1_ENST00000369509.1_Missense_Mutation_p.Y265C	NM_001172411.1|NM_138959.2	NP_001165882.1|NP_620409.1	Q8TAA9	VANG1_HUMAN	VANGL planar cell polarity protein 1	265					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)		TCCCGCTTCTACAGCCTGGGA	0.597																																					p.Y265C		Atlas-SNP	.											.	VANGL1	65	.	0			c.A794G						PASS	.						30	29	30					1																	116206871		2203	4299	6502	SO:0001583	missense	81839	exon4			GCTTCTACAGCCT	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.794A>G	1.37:g.116206871A>G	ENSP00000347672:p.Tyr265Cys	60	0	0		46	25	0.543478	NM_138959	Q5T1D3|Q5T1D4|Q86WG8|Q8N559	Missense_Mutation	SNP	ENST00000355485.2	37	CCDS883.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.167639	0.78339	.	.	ENSG00000173218	ENST00000355485;ENST00000369510;ENST00000310260;ENST00000369509	D;D;D;D	0.87571	-2.27;-2.27;-2.27;-2.27	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.94039	0.8090	M	0.89601	3.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.95115	0.8241	10	0.87932	D	0	0.8661	16.3383	0.83074	1.0:0.0:0.0:0.0	.	263;265	Q8TAA9-2;Q8TAA9	.;VANG1_HUMAN	C	265;263;265;265	ENSP00000347672:Y265C;ENSP00000358523:Y263C;ENSP00000310800:Y265C;ENSP00000358522:Y265C	ENSP00000310800:Y265C	Y	+	2	0	VANGL1	116008394	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.962000	0.93254	2.322000	0.78497	0.528000	0.53228	TAC	.	.	none		0.597	VANGL1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033096.1			G	116206871	A	G	116206871	3	3	29	1	0	0	0	0	1	0	0	0	17134	391	14	3	804	3	VANGL1	1	116206871	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	933955	116206871	133043750	45	12286											
SLC22A15	55356	hgsc.bcm.edu	37	chr1	116577849	116577849	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttatggcctaactctgagtgCgggtgatctaggtggaagta	9	12	14	6	1	2	2	0	2	2	0	2	3	2	3	1	4	2	1	1	4	5	4	rs201564754		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:116577849C>T	ENST00000369503.4	+	7	1116	c.986C>T	c.(985-987)gCg>gTg	p.A329V	SLC22A15_ENST00000481127.1_3'UTR	NM_018420.2	NP_060890.2	Q8IZD6	S22AF_HUMAN	solute carrier family 22, member 15	329					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)		ACTCTGAGTGCGGGTGATCTA	0.453													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18324	0.0		0.0	False		,,,				2504	0.0				p.A329V		Atlas-SNP	.											.	SLC22A15	65	.	0			c.C986T						PASS	.						190	180	183					1																	116577849		1941	4155	6096	SO:0001583	missense	55356	exon7			TGAGTGCGGGTGA	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.986C>T	1.37:g.116577849C>T	ENSP00000358515:p.Ala329Val	245	0	0		247	64	0.259109	NM_018420	A8MUR3|Q6UXP5|Q8TAL9|Q9NSH5	Missense_Mutation	SNP	ENST00000369503.4	37	CCDS44198.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	18.02	3.529828	0.64860	.	.	ENSG00000163393	ENST00000369503	T	0.59083	0.29	5.76	5.76	0.90799	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.109676	0.64402	D	0.000009	T	0.21267	0.0512	N	0.25890	0.77	0.80722	D	1	B	0.16166	0.016	B	0.21360	0.034	T	0.07158	-1.0787	10	0.02654	T	1	.	10.9622	0.47391	0.0:0.8876:0.0:0.1124	.	329	Q8IZD6	S22AF_HUMAN	V	329	ENSP00000358515:A329V	ENSP00000358515:A329V	A	+	2	0	SLC22A15	116379372	0.992000	0.36948	1.000000	0.80357	0.995000	0.86356	2.889000	0.48601	2.722000	0.93159	0.650000	0.86243	GCG	C|1.000;T|0.000	0.000	strong		0.453	SLC22A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033220.2	NM_018420		T	116577849	C	T	116577849	3	4	29	1	0	0	0	0	1	0	0	0	14461	768	27	1	1012	1	SLC22A15	1	116577849	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	370978	116577849	132672772	46	12287											
TRIM45	80263	hgsc.bcm.edu	37	chr1	117659283	117659283	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cggcaacttgaacgttgtctCctcccctgcccatgatttct	6	13	7	15	2	2	2	0	2	2	0	4	2	3	2	4	1	3	2	4	1	2	3	rs61758105	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:117659283C>T	ENST00000256649.4	-	3	1833	c.1307G>A	c.(1306-1308)gGa>gAa	p.G436E	TRIM45_ENST00000369464.3_Missense_Mutation_p.G418E|TRIM45_ENST00000369461.3_Missense_Mutation_p.G379E	NM_025188.3	NP_079464.2	Q9H8W5	TRI45_HUMAN	tripartite motif containing 45	436					bone development (GO:0060348)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|prostate(1)	23	Lung SC(450;0.225)	all_cancers(81;0.000979)|all_lung(203;7.65e-05)|all_epithelial(167;0.000134)|Lung NSC(69;0.000389)		Lung(183;0.0537)|Colorectal(144;0.172)|LUSC - Lung squamous cell carcinoma(189;0.187)		AACGTTGTCTCCTCCCCTGCC	0.473													C|||	56	0.0111821	0.0	0.0663	5008	,	,		18984	0.0		0.006	False		,,,				2504	0.0041				p.G436E		Atlas-SNP	.											.	TRIM45	55	.	0			c.G1307A						PASS	.	C	GLU/GLY,GLU/GLY	18,4388	25.3+/-52.1	0,18,2185	92	86	88		1253,1307	5.1	1	1	dbSNP_129	88	137,8463	68.7+/-131.2	2,133,4165	yes	missense,missense	TRIM45	NM_001145635.1,NM_025188.3	98,98	2,151,6350	TT,TC,CC		1.593,0.4085,1.1918	probably-damaging,probably-damaging	418/563,436/581	117659283	155,12851	2203	4300	6503	SO:0001583	missense	80263	exon3			TTGTCTCCTCCCC		CCDS893.1, CCDS44200.1	1p13.1	2011-04-20	2011-01-25		ENSG00000134253	ENSG00000134253		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	19018	protein-coding gene	gene with protein product		609318	"tripartite motif-containing 45"			15351693	Standard	NM_025188		Approved	FLJ13181, RNF99	uc001egz.2	Q9H8W5	OTTHUMG00000012119	ENST00000256649.4:c.1307G>A	1.37:g.117659283C>T	ENSP00000256649:p.Gly436Glu	80	0	0		73	40	0.547945	NM_025188	Q53GN0|Q5T2K4|Q5T2K5|Q8IYV6	Missense_Mutation	SNP	ENST00000256649.4	37	CCDS893.1	21	0.009615384615384616	0	0.0	16	0.04419889502762431	0	0.0	5	0.006596306068601583	C	25.2	4.612106	0.87258	0.004085	0.01593	ENSG00000134253	ENST00000256649;ENST00000369464;ENST00000369461	D;D;D	0.85171	-1.95;-1.95;-1.95	5.09	5.09	0.68999	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.92021	0.7472	M	0.87180	2.865	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.91709	0.5380	10	0.46703	T	0.11	-17.7023	15.8106	0.78561	0.0:1.0:0.0:0.0	rs61758105	418;436	Q9H8W5-2;Q9H8W5	.;TRI45_HUMAN	E	436;418;379	ENSP00000256649:G436E;ENSP00000358476:G418E;ENSP00000358473:G379E	ENSP00000256649:G436E	G	-	2	0	TRIM45	117460806	1.000000	0.71417	1.000000	0.80357	0.782000	0.44232	6.277000	0.72608	2.646000	0.89796	0.563000	0.77884	GGA	C|0.989;T|0.011	0.011	strong		0.473	TRIM45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033503.1	NM_025188		T	117659283	C	T	117659283	3	4	29	1	0	0	0	0	1	0	0	0	16535	855	30	2	451	2	TRIM45	1	117659283	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1081434	117659283	131591338	47	12288											
NUDT17	200035	hgsc.bcm.edu	37	chr1	145586672	145586679	+	Frame_Shift_Del	DEL	TTTTACAC	TTTTACAC	-																															tgggtccaggtaagctgcacTtttacacggtgggggtgttc																								rs201063949|rs199513201|rs199927874|rs150364859	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TTTTACAC	TTTTACAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:145586672_145586679delTTTTACAC	ENST00000334513.5	-	8	908_915	c.897_904delGTGTAAAA	c.(895-906)ccgtgtaaaagtfs	p.CKS300fs	NUDT17_ENST00000444015.2_5'Flank	NM_001012758.2	NP_001012776.1	P0C025	NUD17_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 17	300							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)					TAAGCTGCACTTTTACACGGTGGGGGTG	0.534																																					p.300_302del		Pindel	.											.	NUDT17	25	.	0			c.898_905del						PASS	.																																			SO:0001589	frameshift_variant	200035	exon8			.	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.897_904delGTGTAAAA	1.37:g.145586672_145586679delTTTTACAC	ENSP00000334437:p.Cys300fs	116	0	.		84	21	0.25	NM_001012758		Frame_Shift_Del	DEL	ENST00000334513.5	37	CCDS30830.1																																																																																			-|0.017;TTTTA|0.983	0.017	alt		0.534	NUDT17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038541.3	XM_496395		-	145586679	TTTTACAC	-	145586672	7	5	29	1	0	1	0	1	0	0	0	0	10743	1609	56	0	86	0	NUDT17	1	145586672	Frame_Shift_Del	DEL	TTTTACAC	TCGA-GR-7351-01A-11D-2210-10	27927389	145586672	103663949	48	12289											
BCL9	607	hgsc.bcm.edu	37	chr1	147090956	147090956	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcagatcccaaagcccctcCgcctccaccagtgtccagtg	9	6	8	18	1	0	1	0	0	0	1	4	1	4	1	8	0	2	1	8	0	1	0	rs61751616	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:147090956C>T	ENST00000234739.3	+	8	1735	c.995C>T	c.(994-996)cCg>cTg	p.P332L		NM_004326.2	NP_004317.2	O00512	BCL9_HUMAN	B-cell CLL/lymphoma 9	332	Poly-Pro.|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)					AAAGCCCCTCCGCCTCCACCA	0.612			T	"IGH@, IGL@"	B-ALL								C|||	25	0.00499201	0.0008	0.0043	5008	,	,		15292	0.0		0.0209	False		,,,				2504	0.0				p.P332L		Atlas-SNP	.		Dom	yes		1	1q21	607	B-cell CLL/lymphoma 9		L	.	BCL9	150	.	0			c.C995T						PASS	.	C	LEU/PRO	12,4394	19.1+/-41.9	0,12,2191	58	64	62		995	4.6	0.9	1	dbSNP_129	62	119,8481	61.3+/-123.2	1,117,4182	yes	missense	BCL9	NM_004326.2	98	1,129,6373	TT,TC,CC		1.3837,0.2724,1.0072	benign	332/1427	147090956	131,12875	2203	4300	6503	SO:0001583	missense	607	exon8			CCCCTCCGCCTCC	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.995C>T	1.37:g.147090956C>T	ENSP00000234739:p.Pro332Leu	25	0	0		46	23	0.5	NM_004326	Q5T489	Missense_Mutation	SNP	ENST00000234739.3	37	CCDS30833.1	20	0.009157509157509158	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	17	0.022427440633245383	C	7.697	0.692207	0.15039	0.002724	0.013837	ENSG00000116128	ENST00000234739	T	0.55052	0.54	5.61	4.63	0.57726	.	0.293568	0.38326	N	0.001739	T	0.17746	0.0426	N	0.12182	0.205	0.35771	D	0.820903	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.03717	-1.1010	10	0.25106	T	0.35	-4.5305	11.3271	0.49454	0.0:0.907:0.0:0.093	rs61751616	332;332	Q1JQ81;O00512	.;BCL9_HUMAN	L	332	ENSP00000234739:P332L	ENSP00000234739:P332L	P	+	2	0	BCL9	145557580	0.702000	0.27816	0.858000	0.33744	0.685000	0.39939	2.819000	0.48049	2.937000	0.99478	0.650000	0.86243	CCG	C|0.990;T|0.010	0.010	strong		0.612	BCL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039468.1	NM_004326		T	147090956	C	T	147090956	3	4	29	1	0	0	0	0	1	0	0	0	1381	652	23	1	1013	1	BCL9	1	147090956	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1504284	147090956	102159665	49	12290											
ACP6	51205	hgsc.bcm.edu	37	chr1	147131611	147131611	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aaacatttgctgcatgcccaCcttggtcagctgcccagcaa	10	9	8	14	0	1	0	1	0	0	0	1	0	1	0	3	1	7	4	3	1	2	2	rs144959805	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:147131611C>T	ENST00000369238.6	-	3	826	c.379G>A	c.(379-381)Gtg>Atg	p.V127M	ACP6_ENST00000392988.2_Missense_Mutation_p.V127M	NM_016361.3	NP_057445.4	Q9NPH0	PPA6_HUMAN	acid phosphatase 6, lysophosphatidic	127	Substrate binding. {ECO:0000250}.				dephosphorylation (GO:0016311)|lysobisphosphatidic acid metabolic process (GO:2001311)|phospholipid metabolic process (GO:0006644)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	acid phosphatase activity (GO:0003993)|lysophosphatidic acid phosphatase activity (GO:0052642)			breast(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(4)|prostate(1)	16	all_hematologic(923;0.0276)					TGCATGCCCACCTTGGTCAGC	0.488													C|||	2	0.000399361	0.0	0.0	5008	,	,		22613	0.0		0.002	False		,,,				2504	0.0				p.V127M		Atlas-SNP	.											.	ACP6	36	.	0			c.G379A						PASS	.	C	MET/VAL	2,4404	4.2+/-10.8	0,2,2201	97	90	92		379	4.7	1	1	dbSNP_134	92	9,8591	7.1+/-27.0	0,9,4291	yes	missense	ACP6	NM_016361.3	21	0,11,6492	TT,TC,CC		0.1047,0.0454,0.0846	probably-damaging	127/429	147131611	11,12995	2203	4300	6503	SO:0001583	missense	51205	exon3			TGCCCACCTTGGT	BC009965	CCDS928.1	1q21	2008-02-05			ENSG00000162836	ENSG00000162836			29609	protein-coding gene	gene with protein product		611471				12010880, 10506173	Standard	NM_016361		Approved	LPAP, ACPL1	uc001epr.2	Q9NPH0	OTTHUMG00000014019	ENST00000369238.6:c.379G>A	1.37:g.147131611C>T	ENSP00000358241:p.Val127Met	69	0	0		124	61	0.491935	NM_016361	Q59G61|Q5T490|Q6IAQ3|Q7LG81|Q9UIG6	Missense_Mutation	SNP	ENST00000369238.6	37	CCDS928.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	19.37	3.814172	0.70912	4.54E-4	0.001047	ENSG00000162836	ENST00000369238;ENST00000392988	T;T	0.30182	1.54;1.54	5.66	4.72	0.59763	.	0.253086	0.41605	D	0.000858	T	0.45558	0.1348	M	0.72479	2.2	0.45806	D	0.998685	D;D	0.62365	0.989;0.991	P;D	0.67103	0.768;0.949	T	0.34079	-0.9843	10	0.48119	T	0.1	.	15.9939	0.80228	0.1351:0.8649:0.0:0.0	.	127;127	Q9NPH0-2;Q9NPH0	.;PPA6_HUMAN	M	127	ENSP00000358241:V127M;ENSP00000376714:V127M	ENSP00000358241:V127M	V	-	1	0	ACP6	145598235	0.599000	0.26891	0.965000	0.40720	0.996000	0.88848	1.076000	0.30729	2.656000	0.90262	0.655000	0.94253	GTG	C|0.999;T|0.001	0.001	strong		0.488	ACP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039420.2	NM_016361		T	147131611	C	T	147131611	3	4	29	1	0	0	0	0	1	0	0	0	165	507	18	2	939	2	ACP6	1	147131611	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	40655	147131611	102119010	50	12291											
HIST2H3D	653604	hgsc.bcm.edu	37	chr1	149784843	149784843	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccttaggcccgctccccgcGgatgcggcgggccaactgga	5	5	15	16	5	0	0	0	0	0	0	1	2	1	2	5	5	2	1	5	5	2	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:149784843G>A	ENST00000331491.1	-	1	393	c.394C>T	c.(394-396)Cgc>Tgc	p.R132C	HIST2H2BF_ENST00000469483.1_5'Flank|HIST2H2BF_ENST00000369167.1_5'Flank|RP11-196G18.21_ENST00000420462.1_RNA|HIST2H2BF_ENST00000545683.1_5'Flank|HIST2H2BF_ENST00000427880.2_5'Flank	NM_001123375.2	NP_001116847.1	Q71DI3	H32_HUMAN	histone cluster 2, H3d	132					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)			biliary_tract(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(3)	7						CGCTCCCCGCGGATGCGGCGG	0.577																																					p.R132C		Atlas-SNP	.											.	HIST2H3D	15	.	0			c.C394T						PASS	.						57	60	59					1																	149784843		1567	3581	5148	SO:0001583	missense	653604	exon1			CCCCGCGGATGCG	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.394C>T	1.37:g.149784843G>A	ENSP00000333277:p.Arg132Cys	239	0	0		238	15	0.0630252	NM_001123375	A2BDF6|A6NFS4|Q6B053	Missense_Mutation	SNP	ENST00000331491.1	37	CCDS41388.1	.	.	.	.	.	.	.	.	.	.	G	18.28	3.590096	0.66105	.	.	ENSG00000183598	ENST00000331491	T	0.70164	-0.46	4.04	4.04	0.47022	.	0.000000	0.53938	U	0.000041	T	0.71187	0.3310	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.74278	-0.3717	7	0.52906	T	0.07	.	15.2971	0.73916	0.0:0.0:1.0:0.0	.	.	.	.	C	132	ENSP00000333277:R132C	ENSP00000333277:R132C	R	-	1	0	HIST2H3D	148051467	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.027000	0.76463	2.262000	0.75019	0.436000	0.28706	CGC	.	.	none		0.577	HIST2H3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033452.1	NM_001123375		A	149784843	G	A	149784843	3	1	29	1	0	0	0	0	1	0	0	0	7190	1116	39	1	18	1	HIST2H3D	1	149784843	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2653232	149784843	99465778	51	12292											
HIST2H2AC	8338	hgsc.bcm.edu	37	chr1	149858806	149858806	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atccgcaacgacgaggaactGaacaagctgctgggcaaagt	14	5	12	10	3	0	1	0	1	0	0	1	4	1	2	1	2	5	4	1	2	5	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:149858806G>A	ENST00000331380.2	+	1	282	c.282G>A	c.(280-282)ctG>ctA	p.L94L	BOLA1_ENST00000369153.2_5'Flank|HIST2H2BE_ENST00000369155.2_5'Flank	NM_003517.2	NP_003508.1	Q16777	H2A2C_HUMAN	histone cluster 2, H2ac	94						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.L94L(2)		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)			ACGAGGAACTGAACAAGCTGC	0.582																																					p.L94L		Atlas-SNP	.											HIST2H2AC,NS,carcinoma,0,3	HIST2H2AC	75	3	2	Substitution - coding silent(2)	lung(2)	c.G282A						PASS	.						71	71	71					1																	149858806		2203	4298	6501	SO:0001819	synonymous_variant	8338	exon1			GGAACTGAACAAG	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.282G>A	1.37:g.149858806G>A		211	0	0		209	11	0.0526316	NM_003517	Q6DRA7|Q8IUE5	Silent	SNP	ENST00000331380.2	37	CCDS937.1																																																																																			.	.	none		0.582	HIST2H2AC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087128.1	NM_003517		A	149858806	G	A	149858806	2	1	29	1	0	0	0	0	0	0	0	1	7187	1277	45	2		2	HIST2H2AC	1	149858806	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	73963	149858806	99391815	52	12293											
FLG	2312	hgsc.bcm.edu	37	chr1	152275921	152275921	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctcctgactgttcctcattaCgtgtttctctgcttgcactt	4	18	6	13	1	2	1	1	1	1	0	5	1	4	1	2	0	3	4	2	0	1	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:152275921C>T	ENST00000368799.1	-	3	11476	c.11441G>A	c.(11440-11442)cGt>cAt	p.R3814H	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3814	Ser-rich.		R -> C (in dbSNP:rs2184953).		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.R3814H(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)			TTCCTCATTACGTGTTTCTCT	0.577									Ichthyosis																												p.R3814H		Atlas-SNP	.											FLG,NS,carcinoma,0,1	FLG	900	1	1	Substitution - Missense(1)	lung(1)	c.G11441A						PASS	.						377	368	371					1																	152275921		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TCATTACGTGTTT	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.11441G>A	1.37:g.152275921C>T	ENSP00000357789:p.Arg3814His	161	0	0		156	57	0.365385	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	9.179	1.023218	0.19433	.	.	ENSG00000143631	ENST00000368799	T	0.01705	4.68	2.47	0.363	0.16118	.	.	.	.	.	T	0.01454	0.0047	L	0.31207	0.915	0.09310	N	1	D	0.71674	0.998	D	0.69479	0.964	T	0.53027	-0.8496	9	0.35671	T	0.21	.	8.2839	0.31917	0.0:0.5204:0.4796:0.0	.	3814	P20930	FILA_HUMAN	H	3814	ENSP00000357789:R3814H	ENSP00000357789:R3814H	R	-	2	0	FLG	150542545	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.512000	0.00446	-0.036000	0.13669	-0.369000	0.07265	CGT	.	.	none		0.577	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		T	152275921	C	T	152275921	3	4	29	1	0	0	0	0	1	0	0	0	5930	536	19	1	748	1	FLG	1	152275921	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2417115	152275921	96974700	53	12294											
IVL	3713	hgsc.bcm.edu	37	chr1	152882648	152882648	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctaaacaaacagctggaagaAgagaagaagctcttagacca	19	5	9	8	0	1	4	0	0	1	4	1	6	1	5	1	1	4	2	1	1	8	2	rs572279454	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:152882648A>C	ENST00000368764.3	+	2	439	c.375A>C	c.(373-375)gaA>gaC	p.E125D	IVL_ENST00000392667.2_5'UTR			P07476	INVO_HUMAN	involucrin	125					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)			AGCTGGAAGAAGAGAAGAAGC	0.473																																					p.E125D		Atlas-SNP	.											.	IVL	100	.	0			c.A375C						PASS	.						61	66	64					1																	152882648		2203	4300	6503	SO:0001583	missense	3713	exon2			GGAAGAAGAGAAG	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.375A>C	1.37:g.152882648A>C	ENSP00000357753:p.Glu125Asp	82	0	0		79	11	0.139241	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	37	CCDS1030.1	.	.	.	.	.	.	.	.	.	.	A	14.19	2.461146	0.43736	.	.	ENSG00000163207	ENST00000368764	T	0.09073	3.02	4.61	-0.221	0.13126	.	.	.	.	.	T	0.02119	0.0066	L	0.40543	1.245	0.30851	N	0.734551	P	0.47409	0.895	B	0.41236	0.351	T	0.47381	-0.9122	9	0.36615	T	0.2	0.146	3.861	0.08996	0.4357:0.0:0.4003:0.164	.	125	P07476	INVO_HUMAN	D	125	ENSP00000357753:E125D	ENSP00000357753:E125D	E	+	3	2	IVL	151149272	0.000000	0.05858	0.010000	0.14722	0.344000	0.29017	0.286000	0.18902	0.134000	0.18681	0.358000	0.22013	GAA	.	.	none		0.473	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547		C	152882648	A	C	152882648	3	2	29	1	0	0	0	0	1	0	0	0	7938	69	3	5	377	5	IVL	1	152882648	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	606727	152882648	96367973	54	12295											
S100A7A	338324	hgsc.bcm.edu	37	chr1	153390649	153390649	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atggcaagattgagaagccaAgcctgctgacgatgatgaag	14	7	13	7	1	0	5	0	4	0	2	0	7	0	5	2	1	3	2	2	1	4	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:153390649A>G	ENST00000368729.4	+	2	148	c.91A>G	c.(91-93)Agc>Ggc	p.S31G	S100A7A_ENST00000329256.2_Missense_Mutation_p.S31G|S100A7A_ENST00000368728.2_Missense_Mutation_p.S31G	NM_176823.3	NP_789793.1	Q86SG5	S1A7A_HUMAN	S100 calcium binding protein A7A	31	EF-hand 1. {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)			TGAGAAGCCAAGCCTGCTGAC	0.488																																					p.S31G		Atlas-SNP	.											.	S100A7A	24	.	0			c.A91G						PASS	.						223	193	203					1																	153390649		2203	4300	6503	SO:0001583	missense	338324	exon2			AAGCCAAGCCTGC	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.91A>G	1.37:g.153390649A>G	ENSP00000357718:p.Ser31Gly	155	0	0		184	47	0.255435	NM_176823	D3DV38|Q5SY69	Missense_Mutation	SNP	ENST00000368729.4	37	CCDS30872.1	.	.	.	.	.	.	.	.	.	.	.	0.006	-2.021565	0.00414	.	.	ENSG00000184330	ENST00000368729;ENST00000368728;ENST00000329256	T;T;T	0.09255	3.0;3.0;3.0	2.27	0.278	0.15673	S100/CaBP-9k-type, calcium binding, subdomain (1);EF-hand-like domain (1);	.	.	.	.	T	0.00815	0.0027	N	0.00729	-1.24	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.47156	-0.9139	9	0.45353	T	0.12	.	4.5895	0.12299	0.3303:0.0:0.6697:0.0	.	31	Q86SG5	S1A7A_HUMAN	G	31	ENSP00000357718:S31G;ENSP00000357717:S31G;ENSP00000329008:S31G	ENSP00000329008:S31G	S	+	1	0	S100A7A	151657273	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	0.315000	0.19451	0.051000	0.15978	-0.353000	0.07706	AGC	.	.	none		0.488	S100A7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036786.2	NM_176823		G	153390649	A	G	153390649	3	3	29	1	0	0	0	0	1	0	0	0	13799	72	3	3	93	3	S100A7A	1	153390649	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	508001	153390649	95859972	55	12296											
S100A7	6278	hgsc.bcm.edu	37	chr1	153431435	153431435	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcatcacgtctggtgtattTgtgaaacatgtcgatcatgc	9	14	10	8	2	4	1	3	1	1	0	5	2	4	1	0	1	2	1	0	1	2	2	rs72708760	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:153431435T>G	ENST00000368723.3	-	2	165	c.55A>C	c.(55-57)Aaa>Caa	p.K19Q	S100A7_ENST00000368722.1_Missense_Mutation_p.K19Q	NM_002963.3	NP_002954.2	P31151	S10A7_HUMAN	S100 calcium binding protein A7	19	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				angiogenesis (GO:0001525)|defense response to Gram-negative bacterium (GO:0050829)|epidermis development (GO:0008544)|innate immune response (GO:0045087)|keratinocyte differentiation (GO:0030216)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of granulocyte chemotaxis (GO:0071624)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of T cell chemotaxis (GO:0010820)|response to lipopolysaccharide (GO:0032496)|response to reactive oxygen species (GO:0000302)|sequestering of metal ion (GO:0051238)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|RAGE receptor binding (GO:0050786)|zinc ion binding (GO:0008270)			breast(1)|large_intestine(2)|lung(5)|skin(2)	10	all_lung(78;2.4e-33)|Lung NSC(65;8.13e-32)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			CTGGTGTATTTGTGAAACATG	0.428													T|||	8	0.00159744	0.0	0.0014	5008	,	,		20640	0.0		0.007	False		,,,				2504	0.0				p.K19Q		Atlas-SNP	.											.	S100A7	23	.	0			c.A55C						PASS	.	T	GLN/LYS	4,4402		0,4,2199	271	231	244		55	-0.5	0	1	dbSNP_130	244	52,8548		0,52,4248	yes	missense	S100A7	NM_002963.3	53	0,56,6447	GG,GT,TT		0.6047,0.0908,0.4306	benign	19/102	153431435	56,12950	2203	4300	6503	SO:0001583	missense	6278	exon2			TGTATTTGTGAAA	BC034687	CCDS1039.1	1q21	2013-01-10	2006-09-11		ENSG00000143556	ENSG00000143556		"S100 calcium binding proteins", "EF-hand domain containing"	10497	protein-coding gene	gene with protein product		600353	"S100 calcium-binding protein A7 (psoriasin 1)", "S100 calcium binding protein A7 (psoriasin 1)"	PSOR1		1940442	Standard	NM_002963		Approved	S100A7c	uc001fbv.1	P31151	OTTHUMG00000013123	ENST00000368723.3:c.55A>C	1.37:g.153431435T>G	ENSP00000357712:p.Lys19Gln	177	0	0		160	77	0.48125	NM_002963	Q5SY67|Q6FGE3|Q9H1E2	Missense_Mutation	SNP	ENST00000368723.3	37	CCDS1039.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	.	6.578	0.475062	0.12521	9.08E-4	0.006047	ENSG00000143556	ENST00000368723;ENST00000368722	T;T	0.08896	3.04;3.04	2.1	-0.492	0.12041	S100/CaBP-9k-type, calcium binding, subdomain (1);EF-hand-like domain (1);	.	.	.	.	T	0.01222	0.0040	L	0.33485	1.01	0.09310	N	1	B	0.22683	0.073	B	0.24394	0.053	T	0.48234	-0.9053	9	0.08381	T	0.77	.	2.3716	0.04331	0.0:0.2008:0.3031:0.4961	.	19	P31151	S10A7_HUMAN	Q	19	ENSP00000357712:K19Q;ENSP00000357711:K19Q	ENSP00000357711:K19Q	K	-	1	0	S100A7	151698059	0.004000	0.15560	0.001000	0.08648	0.747000	0.42532	0.196000	0.17176	-0.097000	0.12307	0.163000	0.16589	AAA	T|0.997;G|0.003	0.003	strong		0.428	S100A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036789.1	NM_002963		G	153431435	T	G	153431435	3	3	29	1	0	0	0	0	1	0	0	0	13798	1821	63	5	258	5	S100A7	1	153431435	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	40786	153431435	95819186	56	12297											
CREB3L4	148327	hgsc.bcm.edu	37	chr1	153941842	153941842	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcatttatggtgcctgatTcctgcatggtcagtgagctg	7	13	12	9	0	1	2	1	2	0	0	2	2	2	2	2	2	4	3	2	2	1	3	rs186432230		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:153941842T>G	ENST00000368607.3	+	4	720	c.454T>G	c.(454-456)Tcc>Gcc	p.S152A	CREB3L4_ENST00000368603.1_Missense_Mutation_p.S152A|CREB3L4_ENST00000271889.4_Missense_Mutation_p.S152A|CREB3L4_ENST00000405694.3_Missense_Mutation_p.S5A|SLC39A1_ENST00000310483.6_5'Flank|CREB3L4_ENST00000368600.3_Missense_Mutation_p.S132A|CREB3L4_ENST00000368601.1_Missense_Mutation_p.S152A|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	152					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)			GGTGCCTGATTCCTGCATGGT	0.577													T|||	1	0.000199681	0.0	0.0	5008	,	,		21087	0.0		0.001	False		,,,				2504	0.0				p.S152A		Atlas-SNP	.											.	CREB3L4	36	.	0			c.T454G						PASS	.						134	122	126					1																	153941842		2203	4300	6503	SO:0001583	missense	148327	exon4			CCTGATTCCTGCA	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.454T>G	1.37:g.153941842T>G	ENSP00000357596:p.Ser152Ala	125	0	0		119	62	0.521008	NM_001255978	D3DV62|Q5T4L0|Q86YW6	Missense_Mutation	SNP	ENST00000368607.3	37	CCDS1056.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	1.414	-0.574595	0.03882	.	.	ENSG00000143578	ENST00000405694;ENST00000449724;ENST00000368607;ENST00000271889;ENST00000368601;ENST00000368603;ENST00000368600;ENST00000431292	T;T;T;T;T;T;T;T	0.74106	-0.81;-0.05;-0.04;-0.04;1.02;-0.04;-0.04;1.0	4.64	1.64	0.23874	.	0.952104	0.08771	N	0.896201	T	0.13841	0.0335	N	0.01209	-0.955	0.23406	N	0.997746	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.32322	-0.9911	10	0.02654	T	1	.	3.111	0.06359	0.0976:0.1705:0.5475:0.1844	.	132;152	Q5T4L0;Q8TEY5	.;CR3L4_HUMAN	A	5;132;152;152;152;152;132;152	ENSP00000385104:S5A;ENSP00000391847:S132A;ENSP00000357596:S152A;ENSP00000271889:S152A;ENSP00000357590:S152A;ENSP00000357592:S152A;ENSP00000357589:S132A;ENSP00000402308:S152A	ENSP00000271889:S152A	S	+	1	0	CREB3L4	152208466	0.269000	0.24143	0.782000	0.31804	0.760000	0.43138	0.381000	0.20619	0.179000	0.19938	-0.302000	0.09304	TCC	T|1.000;G|0.000	0.000	strong		0.577	CREB3L4-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000090291.1	NM_130898		G	153941842	T	G	153941842	3	3	29	1	0	0	0	0	1	0	0	0	3861	1783	62	5	464	5	CREB3L4	1	153941842	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	510407	153941842	95308779	57	12298											
FLAD1	80308	hgsc.bcm.edu	37	chr1	154956487	154956487	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctagggcctctgaactttCtccggggcgcagcgtgacgg	6	9	14	12	4	3	2	0	2	3	0	4	2	3	2	2	4	2	1	2	4	2	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:154956487C>A	ENST00000292180.3	+	1	639	c.317C>A	c.(316-318)tCt>tAt	p.S106Y	FLAD1_ENST00000368432.1_Missense_Mutation_p.S9Y|FLAD1_ENST00000368433.1_Missense_Mutation_p.S106Y|FLAD1_ENST00000487371.1_3'UTR|FLAD1_ENST00000315144.10_Missense_Mutation_p.S9Y|FLAD1_ENST00000368431.3_5'UTR	NM_025207.4	NP_079483.3	Q8NFF5	FAD1_HUMAN	flavin adenine dinucleotide synthetase 1	106					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)			TCTGAACTTTCTCCGGGGCGC	0.597																																					p.S106Y		Atlas-SNP	.											.	FLAD1	52	.	0			c.C317A						PASS	.						29	28	28					1																	154956487		2203	4300	6503	SO:0001583	missense	80308	exon1			AACTTTCTCCGGG		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.317C>A	1.37:g.154956487C>A	ENSP00000292180:p.Ser106Tyr	102	0	0		103	31	0.300971	NM_025207	Q8N5J1|Q8N686|Q8WU93|Q8WUJ4|Q96CR8|Q99764|Q9HBN6	Missense_Mutation	SNP	ENST00000292180.3	37	CCDS1078.1	.	.	.	.	.	.	.	.	.	.	C	13.48	2.248705	0.39797	.	.	ENSG00000160688	ENST00000368433;ENST00000315144;ENST00000368432;ENST00000292180	.	.	.	5.3	5.3	0.74995	Molybdopterin binding (1);	0.385773	0.26016	N	0.026854	T	0.38295	0.1035	N	0.20986	0.625	0.80722	D	1	B	0.22080	0.064	B	0.19391	0.025	T	0.33701	-0.9858	9	0.54805	T	0.06	-14.8505	17.1337	0.86733	0.0:1.0:0.0:0.0	.	106	Q8NFF5	FAD1_HUMAN	Y	106;9;9;106	.	ENSP00000292180:S106Y	S	+	2	0	FLAD1	153223111	0.035000	0.19736	0.576000	0.28549	0.262000	0.26303	1.899000	0.39818	2.655000	0.90218	0.555000	0.69702	TCT	.	.	none		0.597	FLAD1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091089.1	NM_025207		A	154956487	C	A	154956487	3	1	29	1	0	0	0	0	1	0	0	0	5928	913	32	4	319	4	FLAD1	1	154956487	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1014645	154956487	94294134	58	12299											
DCST2	127579	hgsc.bcm.edu	37	chr1	155004092	155004092	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtttgaagggcatgagcaCgtaacacaggtggtaggctt	11	9	14	7	1	0	2	0	2	0	0	0	2	0	2	0	4	2	6	0	4	3	4	rs373275652		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:155004092C>T	ENST00000368424.3	-	4	755	c.697G>A	c.(697-699)Gtg>Atg	p.V233M	DCST1_ENST00000368419.2_5'Flank|DCST1_ENST00000295542.1_5'Flank|DCST1_ENST00000392480.1_5'Flank|DCST1_ENST00000423025.2_5'Flank|DCST2_ENST00000295536.5_Missense_Mutation_p.V233M	NM_144622.2	NP_653223.2	Q5T1A1	DCST2_HUMAN	DC-STAMP domain containing 2	233						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)			GGCATGAGCACGTAACACAGG	0.592																																					p.V233M		Atlas-SNP	.											.	DCST2	80	.	0			c.G697A						PASS	.	C	MET/VAL	0,4406		0,0,2203	147	115	126		697	2.2	0.9	1		126	1,8599	1.2+/-3.3	0,1,4299	no	missense	DCST2	NM_144622.2	21	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	233/774	155004092	1,13005	2203	4300	6503	SO:0001583	missense	127579	exon4			TGAGCACGTAACA	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.697G>A	1.37:g.155004092C>T	ENSP00000357409:p.Val233Met	161	0	0		165	78	0.472727	NM_144622	Q2M2R2|Q8N810|Q96M03	Missense_Mutation	SNP	ENST00000368424.3	37	CCDS1082.2	.	.	.	.	.	.	.	.	.	.	C	14.72	2.620203	0.46736	0.0	1.16E-4	ENSG00000163354	ENST00000368424;ENST00000295536	T;T	0.26373	1.74;1.78	5.57	2.18	0.27775	.	0.652606	0.13132	N	0.411331	T	0.06234	0.0161	L	0.29908	0.895	0.09310	N	0.999991	D	0.54601	0.967	B	0.39660	0.306	T	0.18681	-1.0329	10	0.30078	T	0.28	-10.1195	7.9825	0.30192	0.0:0.6559:0.0:0.3441	.	233	Q5T1A1	DCST2_HUMAN	M	233	ENSP00000357409:V233M;ENSP00000295536:V233M	ENSP00000295536:V233M	V	-	1	0	DCST2	153270716	0.149000	0.22717	0.913000	0.36048	0.967000	0.64934	0.384000	0.20668	0.702000	0.31825	0.655000	0.94253	GTG	.	.	none		0.592	DCST2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090953.3	NM_144622		T	155004092	C	T	155004092	3	4	29	1	0	0	0	0	1	0	0	0	4305	536	19	1	1672	1	DCST2	1	155004092	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	47605	155004092	94246529	59	12300											
BCAN	63827	hgsc.bcm.edu	37	chr1	156616814	156616814	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaaggtgaacgaggcctacCggttccgcgtggcactgcct	7	8	13	13	4	1	1	1	1	0	0	2	2	2	1	4	4	3	2	4	4	3	2	rs115373136	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:156616814C>G	ENST00000329117.5	+	3	649	c.313C>G	c.(313-315)Cgg>Ggg	p.R105G	BCAN_ENST00000361588.5_Missense_Mutation_p.R105G|RP11-284F21.10_ENST00000605886.1_RNA|RP11-284F21.7_ENST00000448869.1_RNA	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	105	Ig-like V-type.				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)					CGAGGCCTACCGGTTCCGCGT	0.682													C|||	28	0.00559105	0.0	0.0043	5008	,	,		14357	0.0		0.0199	False		,,,				2504	0.0051				p.R105G		Atlas-SNP	.											.	BCAN	174	.	0			c.C313G						PASS	.	C	GLY/ARG,GLY/ARG	8,4398	14.3+/-33.2	0,8,2195	47	35	39		313,313	2.5	1	1	dbSNP_132	39	116,8480	57.5+/-118.9	0,116,4182	yes	missense,missense	BCAN	NM_021948.4,NM_198427.1	125,125	0,124,6377	GG,GC,CC		1.3495,0.1816,0.9537	possibly-damaging,possibly-damaging	105/912,105/672	156616814	124,12878	2203	4298	6501	SO:0001583	missense	63827	exon3			GCCTACCGGTTCC	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.313C>G	1.37:g.156616814C>G	ENSP00000331210:p.Arg105Gly	62	0	0		47	22	0.468085	NM_198427	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Missense_Mutation	SNP	ENST00000329117.5	37	CCDS1149.1	20	0.009157509157509158	0	0.0	2	0.0055248618784530384	0	0.0	18	0.023746701846965697	C	14.87	2.664022	0.47572	0.001816	0.013495	ENSG00000132692	ENST00000441358;ENST00000255029;ENST00000329117;ENST00000457777;ENST00000361588	T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14	4.61	2.47	0.30058	Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin V-set, subgroup (1);Immunoglobulin-like fold (1);	0.000000	0.52532	D	0.000061	T	0.64238	0.2580	L	0.53671	1.685	0.36444	D	0.865697	D;P	0.65815	0.995;0.856	D;B	0.67382	0.951;0.285	T	0.70353	-0.4895	10	0.87932	D	0	-20.2388	12.8011	0.57586	0.3062:0.6938:0.0:0.0	.	105;105	Q96GW7;Q96GW7-2	PGCB_HUMAN;.	G	105	ENSP00000392731:R105G;ENSP00000331210:R105G;ENSP00000389898:R105G;ENSP00000354925:R105G	ENSP00000255029:R105G	R	+	1	2	BCAN	154883438	0.000000	0.05858	1.000000	0.80357	0.530000	0.34684	-0.350000	0.07721	1.088000	0.41272	0.455000	0.32223	CGG	C|0.989;G|0.011	0.011	strong		0.682	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948		G	156616814	C	G	156616814	3	3	29	1	0	0	0	0	1	0	0	0	1345	643	23	4	319	4	BCAN	1	156616814	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1612722	156616814	92633807	60	12301											
ARHGEF11	9826	hgsc.bcm.edu	37	chr1	156928576	156928576	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgcttctcagccacttggCgctctcggagagggtcccca	5	9	12	15	2	2	1	1	0	2	1	5	2	3	1	3	3	2	3	3	3	0	2	rs142957547	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:156928576C>T	ENST00000361409.2	-	16	2082	c.1340G>A	c.(1339-1341)cGc>cAc	p.R447H	ARHGEF11_ENST00000368194.3_Missense_Mutation_p.R487H	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	447	RGSL. {ECO:0000255|PROSITE- ProRule:PRU00171}.				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)					AGCCACTTGGCGCTCTCGGAG	0.537													C|||	8	0.00159744	0.0	0.0014	5008	,	,		19364	0.0		0.004	False		,,,				2504	0.0031				p.R487H		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.G1460A						PASS	.	C	HIS/ARG,HIS/ARG	2,4404	4.2+/-10.8	0,2,2201	49	45	46		1340,1460	4.1	1	1	dbSNP_134	46	42,8558	27.4+/-76.7	0,42,4258	yes	missense,missense	ARHGEF11	NM_014784.2,NM_198236.1	29,29	0,44,6459	TT,TC,CC		0.4884,0.0454,0.3383	benign,benign	447/1523,487/1563	156928576	44,12962	2203	4300	6503	SO:0001583	missense	9826	exon17			ACTTGGCGCTCTC	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.1340G>A	1.37:g.156928576C>T	ENSP00000354644:p.Arg447His	131	0	0		134	58	0.432836	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Missense_Mutation	SNP	ENST00000361409.2	37	CCDS1162.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	18.83	3.706799	0.68615	4.54E-4	0.004884	ENSG00000132694	ENST00000368194;ENST00000361409	D;D	0.86627	-2.15;-2.15	4.98	4.06	0.47325	Regulator of G protein signalling superfamily (1);Regulator of G protein signalling-like fold (1);	0.222251	0.32055	N	0.006652	T	0.80454	0.4626	M	0.73962	2.25	0.80722	D	1	B;B	0.27013	0.162;0.166	B;B	0.22152	0.022;0.038	T	0.82137	-0.0606	10	0.66056	D	0.02	-8.7914	13.0194	0.58777	0.0:0.9212:0.0:0.0788	.	447;487	O15085;O15085-2	ARHGB_HUMAN;.	H	487;447	ENSP00000357177:R487H;ENSP00000354644:R447H	ENSP00000354644:R447H	R	-	2	0	ARHGEF11	155195200	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	2.468000	0.45102	1.334000	0.45468	0.491000	0.48974	CGC	C|0.996;T|0.004	0.004	strong		0.537	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236		T	156928576	C	T	156928576	3	4	29	1	0	0	0	0	1	0	0	0	896	768	27	1	3328	1	ARHGEF11	1	156928576	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	311762	156928576	92322045	61	12302											
FCRL3	115352	hgsc.bcm.edu	37	chr1	157670258	157670258	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catctactcactcaggatcaGcagcagcagccacagaagca	14	5	8	14	0	4	1	3	0	1	1	4	2	4	2	1	1	6	4	1	1	2	1	rs201961888		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:157670258G>C	ENST00000368184.3	-	2	313	c.22C>G	c.(22-24)Ctg>Gtg	p.L8V	FCRL3_ENST00000473231.1_5'Flank|FCRL3_ENST00000368186.5_Missense_Mutation_p.L8V	NM_052939.3	NP_443171.2	Q96P31	FCRL3_HUMAN	Fc receptor-like 3	8						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(1)|large_intestine(13)|lung(31)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)	69	all_hematologic(112;0.0378)					CTCAGGATCAGCAGCAGCAGC	0.547													G|||	1	0.000199681	0.0	0.0	5008	,	,		16345	0.0		0.001	False		,,,				2504	0.0				p.L8V		Atlas-SNP	.											.	FCRL3	163	.	0			c.C22G						PASS	.						46	49	48					1																	157670258		2203	4300	6503	SO:0001583	missense	115352	exon2			GGATCAGCAGCAG	AF459027	CCDS1167.1	1q21-q22	2013-01-11			ENSG00000160856	ENSG00000160856		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18506	protein-coding gene	gene with protein product		606510				11493702, 12014205	Standard	XR_241065		Approved	FCRH3, IRTA3, IFGP3, SPAP2a, SPAP2, SPAP2b, SPAP2c, SPAP2d, SPAP2e, CD307c	uc001frb.3	Q96P31	OTTHUMG00000019400	ENST00000368184.3:c.22C>G	1.37:g.157670258G>C	ENSP00000357167:p.Leu8Val	163	0	0		132	43	0.325758	NM_052939	A0N0M4|A8MTH7|D3DVD2|Q5VXZ8|Q8N6S2|Q96LA4|Q96P27|Q96P28|Q96P29|Q96P30	Missense_Mutation	SNP	ENST00000368184.3	37	CCDS1167.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	6.556	0.470796	0.12461	.	.	ENSG00000160856	ENST00000368186;ENST00000368184;ENST00000292392	T;T	0.66638	-0.22;-0.22	3.6	2.69	0.31865	.	0.702293	0.10648	U	0.650160	T	0.69913	0.3164	M	0.70842	2.15	0.40781	D	0.98317	D;D	0.76494	0.999;0.999	D;D	0.80764	0.986;0.994	T	0.67503	-0.5654	10	0.45353	T	0.12	.	6.8585	0.24054	0.1278:0.0:0.8722:0.0	.	8;8	Q96P31;Q96P31-6	FCRL3_HUMAN;.	V	8	ENSP00000357169:L8V;ENSP00000357167:L8V	ENSP00000292392:L8V	L	-	1	2	FCRL3	155936882	0.995000	0.38212	0.996000	0.52242	0.930000	0.56654	1.824000	0.39072	1.095000	0.41419	0.467000	0.42956	CTG	G|1.000;C|0.000	0.000	strong		0.547	FCRL3-006	NOVEL	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051419.2	NM_052939		C	157670258	G	C	157670258	3	2	29	1	0	0	0	0	1	0	0	0	5804	962	34	4	2238	4	FCRL3	1	157670258	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	741682	157670258	91580363	62	12303											
OR10J1	26476	hgsc.bcm.edu	37	chr1	159410258	159410258	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cattatctctacaatcctcaAgattgcttcagttgagggcc	10	13	7	11	0	3	2	2	1	1	1	5	2	4	2	2	1	2	2	2	1	4	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:159410258A>C	ENST00000423932.3	+	1	747	c.710A>C	c.(709-711)aAg>aCg	p.K237T	RP11-550P17.5_ENST00000431862.1_RNA	NM_012351.2	NP_036483.2	P30954	O10J1_HUMAN	olfactory receptor, family 10, subfamily J, member 1	237					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)					ACAATCCTCAAGATTGCTTCA	0.463																																					p.K237T		Atlas-SNP	.											OR10J1,NS,carcinoma,0,1	OR10J1	118	1	0			c.A710C						PASS	.						202	192	196					1																	159410258		2203	4300	6503	SO:0001583	missense	26476	exon1			TCCTCAAGATTGC	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.710A>C	1.37:g.159410258A>C	ENSP00000399078:p.Lys237Thr	229	0	0		226	69	0.30531	NM_012351	Q2M1M8|Q5VSV1|Q6IET5|Q96R56	Missense_Mutation	SNP	ENST00000423932.3	37	CCDS1185.1	.	.	.	.	.	.	.	.	.	.	A	15.55	2.867724	0.51588	.	.	ENSG00000196184	ENST00000423932	T	0.00169	8.63	4.29	0.577	0.17385	GPCR, rhodopsin-like superfamily (1);	0.159875	0.29239	N	0.012721	T	0.00144	0.0004	M	0.78637	2.42	0.09310	N	1	P	0.48503	0.911	P	0.56216	0.794	T	0.30238	-0.9985	10	0.87932	D	0	.	7.3103	0.26471	0.7181:0.0:0.2819:0.0	.	237	P30954	O10J1_HUMAN	T	237	ENSP00000399078:K237T	ENSP00000399078:K237T	K	+	2	0	OR10J1	157676882	0.000000	0.05858	0.216000	0.23742	0.957000	0.61999	0.008000	0.13197	-0.011000	0.14247	0.454000	0.30748	AAG	.	.	none		0.463	OR10J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059020.1	NM_012351		C	159410258	A	C	159410258	3	2	29	1	0	0	0	0	1	0	0	0	10919	72	3	5	712	5	OR10J1	1	159410258	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	1740000	159410258	89840363	63	12304											
CD48	962	hgsc.bcm.edu	37	chr1	160681535	160681535	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ttccagagccagacacgaatCccaacctctggagcacatgc	12	6	8	15	1	1	2	0	0	1	2	3	4	3	3	4	1	4	1	4	1	2	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:160681535C>T	ENST00000368046.3	-	1	106	c.19G>A	c.(19-21)Gat>Aat	p.D7N	CD48_ENST00000368045.3_Missense_Mutation_p.D7N	NM_001778.3	NP_001769.2	P09326	CD48_HUMAN	CD48 molecule	7					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)			AGACACGAATCCCAACCTCTG	0.512																																					p.D7N		Atlas-SNP	.											.	CD48	31	.	0			c.G19A						PASS	.						116	94	102					1																	160681535		2203	4300	6503	SO:0001583	missense	962	exon1			ACGAATCCCAACC	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.19G>A	1.37:g.160681535C>T	ENSP00000357025:p.Asp7Asn	275	0	0		265	53	0.2	NM_001256030	Q5U055|Q8MGR0	Missense_Mutation	SNP	ENST00000368046.3	37	CCDS1208.1	.	.	.	.	.	.	.	.	.	.	C	3.053	-0.194989	0.06259	.	.	ENSG00000117091	ENST00000368046;ENST00000368045	T;T	0.50001	3.91;0.76	4.06	-8.12	0.01078	.	4.906520	0.00166	N	0.000004	T	0.06050	0.0157	N	0.03608	-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	0.05699	-1.0869	10	0.30854	T	0.27	-16.7883	5.9139	0.19043	0.0895:0.2615:0.0886:0.5604	.	7;7;7	Q8MGR0;Q6IAZ2;P09326	.;.;CD48_HUMAN	N	7	ENSP00000357025:D7N;ENSP00000357024:D7N	ENSP00000357024:D7N	D	-	1	0	CD48	158948159	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.228000	0.01209	-3.054000	0.00259	-2.852000	0.00102	GAT	.	.	none		0.512	CD48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060471.1	NM_001778		T	160681535	C	T	160681535	3	4	29	1	0	0	0	0	1	0	0	0	3022	855	30	2	728	2	CD48	1	160681535	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1271277	160681535	88569086	64	12305											
DDR2	4921	hgsc.bcm.edu	37	chr1	162729613	162729613	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagggctaggccaattgacCgatggtgtgtctggcctgga	8	9	16	8	1	1	1	0	1	1	0	1	4	1	2	3	5	0	1	3	5	3	2	rs56351141	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:162729613C>T	ENST00000367922.3	+	9	1137	c.699C>T	c.(697-699)acC>acT	p.T233T	DDR2_ENST00000367921.3_Silent_p.T233T	NM_001014796.1	NP_001014796.1	Q16832	DDR2_HUMAN	discoidin domain receptor tyrosine kinase 2	233					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)	GCCAATTGACCGATGGTGTGT	0.537													C|||	27	0.00539137	0.0015	0.0115	5008	,	,		17195	0.0		0.0119	False		,,,				2504	0.0051				p.T233T	NSCLC(161;314 2006 8283 19651 23192)	Atlas-SNP	.											DDR2_ENST00000367922,right_upper_lobe,carcinoma,0,2	DDR2	228	2	0			c.C699T						PASS	.	C	,	9,4397	16.8+/-37.8	0,9,2194	102	89	94		699,699	-8.8	0.7	1	dbSNP_129	94	119,8481	62.1+/-124.0	1,117,4182	no	coding-synonymous,coding-synonymous	DDR2	NM_001014796.1,NM_006182.2	,	1,126,6376	TT,TC,CC		1.3837,0.2043,0.9842	,	233/856,233/856	162729613	128,12878	2203	4300	6503	SO:0001819	synonymous_variant	4921	exon9			ATTGACCGATGGT	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.699C>T	1.37:g.162729613C>T		107	0	0		82	29	0.353659	NM_001014796	Q7Z730	Silent	SNP	ENST00000367922.3	37	CCDS1241.1																																																																																			C|0.991;T|0.009	0.009	strong		0.537	DDR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083213.2	NM_006182		T	162729613	C	T	162729613	2	4	29	1	0	0	0	0	0	0	0	1	4339	639	23	1		1	DDR2	1	162729613	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2048078	162729613	86521008	65	12306											
PBX1	5087	hgsc.bcm.edu	37	chr1	164761924	164761924	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cattcagattacagagccaaActctcacagatcagacaaat	17	8	5	11	0	3	4	3	0	1	4	4	4	3	4	1	0	3	0	1	0	3	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:164761924A>C	ENST00000420696.2	+	3	647	c.459A>C	c.(457-459)aaA>aaC	p.K153N	PBX1_ENST00000560641.1_Missense_Mutation_p.K48N|PBX1_ENST00000367897.1_Missense_Mutation_p.K153N|PBX1_ENST00000401534.1_Missense_Mutation_p.K153N|PBX1_ENST00000540246.1_Missense_Mutation_p.K48N|PBX1_ENST00000559240.1_Missense_Mutation_p.K153N|PBX1_ENST00000540236.1_Missense_Mutation_p.K153N	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	153					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						ACAGAGCCAAACTCTCACAGA	0.592			T	"TCF3, EWSR1"	"pre B-ALL, myoepithelioma"																																p.K153N		Atlas-SNP	.		Dom	yes		1	1q23	5087	pre-B-cell leukemia transcription factor 1		"L, M"	.	PBX1	60	.	0			c.A459C						PASS	.						32	38	36					1																	164761924		2202	4300	6502	SO:0001583	missense	5087	exon3			AGCCAAACTCTCA	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.459A>C	1.37:g.164761924A>C	ENSP00000405890:p.Lys153Asn	58	0	0		51	13	0.254902	NM_001204963	B4DSC1|F5H4U9|Q5T488	Missense_Mutation	SNP	ENST00000420696.2	37	CCDS1246.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.030748	0.75504	.	.	ENSG00000185630	ENST00000340699;ENST00000420696;ENST00000367897;ENST00000540236;ENST00000401534;ENST00000540246	T;T;T;T;T;T	0.38560	1.13;1.13;1.13;1.13;1.13;1.13	5.23	1.65	0.23941	PBX (1);	0.000000	0.85682	D	0.000000	T	0.52821	0.1758	M	0.86651	2.83	0.09310	N	0.999999	D;D;D;D;D	0.71674	0.998;0.998;0.995;0.998;0.996	D;D;D;D;D	0.76575	0.982;0.982;0.962;0.988;0.978	T	0.59182	-0.7502	9	0.87932	D	0	-9.1405	8.5144	0.33237	0.6736:0.0:0.3264:0.0	.	48;153;153;153;153	B7Z774;A8K5V0;F5H4U9;P40424;Q53YC7	.;.;.;PBX1_HUMAN;.	N	153;153;153;153;153;48	ENSP00000341455:K153N;ENSP00000405890:K153N;ENSP00000356872:K153N;ENSP00000439943:K153N;ENSP00000384856:K153N;ENSP00000440869:K48N	ENSP00000341455:K153N	K	+	3	2	PBX1	163028548	0.981000	0.34729	1.000000	0.80357	0.998000	0.95712	0.288000	0.18939	0.297000	0.22615	0.460000	0.39030	AAA	.	.	none		0.592	PBX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082864.4	NM_002585		C	164761924	A	C	164761924	3	2	29	1	0	0	0	0	1	0	0	0	11501	40	2	5	469	5	PBX1	1	164761924	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	2032311	164761924	84488697	66	12307											
LMX1A	4009	hgsc.bcm.edu	37	chr1	165322487	165322487	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcgcagacagacttggggCtcaccgctctgcctgtagcc	6	8	11	16	2	2	2	1	0	1	2	3	2	2	2	4	2	2	4	4	2	1	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:165322487C>A	ENST00000342310.3	-	3	471	c.89G>T	c.(88-90)aGc>aTc	p.S30I	LMX1A_ENST00000294816.2_Missense_Mutation_p.S30I|LMX1A_ENST00000367893.4_Missense_Mutation_p.S30I	NM_177398.3	NP_796372.1	Q8TE12	LMX1A_HUMAN	LIM homeobox transcription factor 1, alpha	30					axon guidance (GO:0007411)|central nervous system neuron differentiation (GO:0021953)|cerebellum development (GO:0021549)|dentate gyrus development (GO:0021542)|dopaminergic neuron differentiation (GO:0071542)|midbrain development (GO:0030901)|negative regulation of neuron differentiation (GO:0045665)|regulation of cell growth (GO:0001558)|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(2)|biliary_tract(1)|central_nervous_system(3)|cervix(2)|endometrium(4)|large_intestine(6)|lung(10)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(4)	35	all_hematologic(923;0.248)					AGACTTGGGGCTCACCGCTCT	0.637																																					p.S30I		Atlas-SNP	.											.	LMX1A	87	.	0			c.G89T						PASS	.						30	30	30					1																	165322487		2203	4299	6502	SO:0001583	missense	4009	exon3			TTGGGGCTCACCG	AY078391	CCDS1247.1	1q24.1	2011-06-20			ENSG00000162761	ENSG00000162761		"Homeoboxes / LIM class"	6653	protein-coding gene	gene with protein product		600298		LMX1		7698771	Standard	NM_177398		Approved	LMX1.1	uc001gcz.2	Q8TE12	OTTHUMG00000034575	ENST00000342310.3:c.89G>T	1.37:g.165322487C>A	ENSP00000340226:p.Ser30Ile	36	0	0		38	11	0.289474	NM_001174069	B3KXP6|Q0VDB5|Q5VWG4|Q8TE11	Missense_Mutation	SNP	ENST00000342310.3	37	CCDS1247.1	.	.	.	.	.	.	.	.	.	.	C	13.29	2.192981	0.38707	.	.	ENSG00000162761	ENST00000342310;ENST00000294816;ENST00000367893	D;D;D	0.87029	-2.2;-2.2;-2.2	5.56	4.55	0.56014	.	0.485820	0.24426	N	0.038640	T	0.58163	0.2103	N	0.08118	0	0.28227	N	0.92627	B	0.10296	0.003	B	0.04013	0.001	T	0.53464	-0.8435	9	0.40728	T	0.16	.	6.8856	0.24197	0.0:0.6971:0.1832:0.1197	.	30	Q8TE12	LMX1A_HUMAN	I	30	ENSP00000340226:S30I;ENSP00000294816:S30I;ENSP00000356868:S30I	ENSP00000294816:S30I	S	-	2	0	LMX1A	163589111	0.989000	0.36119	1.000000	0.80357	0.995000	0.86356	0.505000	0.22642	2.606000	0.88127	0.561000	0.74099	AGC	.	.	none		0.637	LMX1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083668.2	NM_177398		A	165322487	C	A	165322487	3	1	29	1	0	0	0	0	1	0	0	0	8870	797	28	4	1087	4	LMX1A	1	165322487	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	560563	165322487	83928134	67	12308											
ALDH9A1	223	hgsc.bcm.edu	37	chr1	165638577	165638577	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtggacccatccttgtatcTtccagaaggggatctccaat	10	11	9	11	0	2	1	0	0	2	1	5	3	4	3	4	3	0	1	4	3	3	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:165638577T>G	ENST00000354775.4	-	7	1345	c.1041A>C	c.(1039-1041)gaA>gaC	p.E347D	ALDH9A1_ENST00000538148.1_Missense_Mutation_p.E253D	NM_000696.3	NP_000687.3	P49189	AL9A1_HUMAN	aldehyde dehydrogenase 9 family, member A1	323					carnitine biosynthetic process (GO:0045329)|cellular aldehyde metabolic process (GO:0006081)|cellular nitrogen compound metabolic process (GO:0034641)|hormone metabolic process (GO:0042445)|kidney development (GO:0001822)|liver development (GO:0001889)|neurotransmitter biosynthetic process (GO:0042136)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	1-pyrroline dehydrogenase activity (GO:0033737)|3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|4-trimethylammoniobutyraldehyde dehydrogenase activity (GO:0047105)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|amine binding (GO:0043176)|aminobutyraldehyde dehydrogenase activity (GO:0019145)|NAD binding (GO:0051287)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	21	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)					TCCTTGTATCTTCCAGAAGGG	0.438																																					p.E347D	Ovarian(179;1583 2014 18106 33801 42447)	Atlas-SNP	.											.	ALDH9A1	75	.	0			c.A1041C						PASS	.						147	139	142					1																	165638577		2203	4300	6503	SO:0001583	missense	223	exon7			TGTATCTTCCAGA	U34252	CCDS1250.2	1q22-q23	2008-02-05			ENSG00000143149	ENSG00000143149		"Aldehyde dehydrogenases"	412	protein-coding gene	gene with protein product		602733		ALDH7, ALDH4, ALDH9		8112751, 8786138	Standard	NM_000696		Approved	E3	uc001gdh.1	P49189	OTTHUMG00000034677	ENST00000354775.4:c.1041A>C	1.37:g.165638577T>G	ENSP00000346827:p.Glu347Asp	200	0	0		201	69	0.343284	NM_000696	B2R6X1|B4DXY7|Q5VV90|Q6LCL1|Q9NZT7	Missense_Mutation	SNP	ENST00000354775.4	37	CCDS1250.2	.	.	.	.	.	.	.	.	.	.	T	10.86	1.468997	0.26335	.	.	ENSG00000143149	ENST00000354775;ENST00000538148	T;T	0.77750	-1.12;-1.12	5.05	2.67	0.31697	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.095319	0.64402	N	0.000001	T	0.37320	0.0999	N	0.20986	0.625	0.44843	D	0.997857	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.002;0.001;0.002	T	0.04495	-1.0947	9	0.23302	T	0.38	.	4.2403	0.10645	0.0:0.1805:0.1747:0.6448	.	253;337;323;347	B4DYY1;B4DX14;P49189;B9EKV4	.;.;AL9A1_HUMAN;.	D	347;253	ENSP00000346827:E347D;ENSP00000440026:E253D	ENSP00000346827:E347D	E	-	3	2	ALDH9A1	163905201	0.998000	0.40836	0.998000	0.56505	0.890000	0.51754	0.281000	0.18810	0.252000	0.21531	-0.446000	0.05623	GAA	.	.	none		0.438	ALDH9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083899.1			G	165638577	T	G	165638577	3	3	29	1	0	0	0	0	1	0	0	0	506	1606	56	5	535	5	ALDH9A1	1	165638577	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	316090	165638577	83612044	68	12309											
BAT2L2	23215	hgsc.bcm.edu	37	chr1	171509275	171509275	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttagacctcaccatactgaTgcaaataatcagtctgcttg	12	12	7	10	0	3	2	2	1	1	1	3	2	3	2	2	0	3	3	2	0	4	4	rs75723046	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:171509275T>C	ENST00000338920.4	+	16	2901	c.2664T>C	c.(2662-2664)gaT>gaC	p.D888D	PRRC2C_ENST00000426496.2_Silent_p.D888D|PRRC2C_ENST00000392078.3_Silent_p.D890D|PRRC2C_ENST00000367742.3_Silent_p.D890D	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	888					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										ACCATACTGATGCAAATAATC	0.443													T|||	13	0.00259585	0.0008	0.0043	5008	,	,		20079	0.0		0.0089	False		,,,				2504	0.0				p.D888D		Atlas-SNP	.											.	.	.	.	0			c.T2664C						PASS	.	T		1,4405	2.1+/-5.4	0,1,2202	115	115	115		2664	-6.5	0	1	dbSNP_132	115	64,8536	39.3+/-95.6	0,64,4236	no	coding-synonymous	PRRC2C	NM_015172.3		0,65,6438	CC,CT,TT		0.7442,0.0227,0.4998		888/2818	171509275	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	23215	exon16			TACTGATGCAAAT	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.2664T>C	1.37:g.171509275T>C		112	0	0		100	44	0.44	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Silent	SNP	ENST00000338920.4	37	CCDS1296.2																																																																																			T|0.997;C|0.003	0.003	strong		0.443	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172		C	171509275	T	C	171509275	2	2	29	1	0	0	0	0	0	0	0	1	1321	1461	51	3		3	BAT2L2	1	171509275	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	5870698	171509275	77741346	69	12310											
HMCN1	83872	hgsc.bcm.edu	37	chr1	186121995	186121995	+	Missense_Mutation	SNP	A	A	T																															ttcagtcacctgctgaagtcActgtaaaggtaaaatgccag																								rs114364265	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:186121995A>T	ENST00000271588.4	+	96	15239	c.15010A>T	c.(15010-15012)Act>Tct	p.T5004S	HMCN1_ENST00000367492.2_Missense_Mutation_p.T5004S	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	5004	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						TGCTGAAGTCACTGTAAAGGT	0.438													A|||	9	0.00179712	0.0	0.0	5008	,	,		18499	0.0		0.008	False		,,,				2504	0.001				p.T5004S		Atlas-SNP	.											.	HMCN1	797	.	0			c.A15010T						PASS	.	A	SER/THR	3,4403	4.2+/-10.8	0,3,2200	196	170	179		15010	0.8	0.1	1	dbSNP_133	179	28,8572	9.1+/-34.3	1,26,4273	yes	missense	HMCN1	NM_031935.2	58	1,29,6473	TT,TA,AA		0.3256,0.0681,0.2384	benign	5004/5636	186121995	31,12975	2203	4300	6503	SO:0001583	missense	83872	exon96			GAAGTCACTGTAA	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.15010A>T	1.37:g.186121995A>T	ENSP00000271588:p.Thr5004Ser	158	0	0		169	72	0.426035	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	A	2.871	-0.233991	0.05983	6.81E-4	0.003256	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.32988	1.43;1.43	5.9	0.836	0.18891	G2 nidogen/fibulin G2F (2);Green fluorescent protein-like (1);	0.929918	0.09308	N	0.819936	T	0.08582	0.0213	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.32161	-0.9917	10	0.05833	T	0.94	.	6.2405	0.20787	0.6238:0.1195:0.2567:0.0	.	5004	Q96RW7	HMCN1_HUMAN	S	5004	ENSP00000271588:T5004S;ENSP00000356462:T5004S	ENSP00000271588:T5004S	T	+	1	0	HMCN1	184388618	0.001000	0.12720	0.065000	0.19835	0.779000	0.44077	0.806000	0.27126	-0.101000	0.12219	-0.263000	0.10527	ACT	A|0.996;T|0.004	0.004	strong		0.438	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		T	186121995	A	T	186121995	3	4	29	1	0	0	0	0	1	0	0	0	7229	159	6	5	15392	5	HMCN1	1	186121995	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	14612720	186121995	63128626	70	12311	152	2									
HMCN1	83872	hgsc.bcm.edu	37	chr1	186121996	186121996	+	Missense_Mutation	SNP	C	C	T																															tcagtcacctgctgaagtcaCtgtaaaggtaaaatgccagg																								rs114629728	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:186121996C>T	ENST00000271588.4	+	96	15240	c.15011C>T	c.(15010-15012)aCt>aTt	p.T5004I	HMCN1_ENST00000367492.2_Missense_Mutation_p.T5004I	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	5004	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						GCTGAAGTCACTGTAAAGGTA	0.433													C|||	10	0.00199681	0.0	0.0014	5008	,	,		18553	0.0		0.008	False		,,,				2504	0.001				p.T5004I		Atlas-SNP	.											.	HMCN1	797	.	0			c.C15011T						PASS	.	C	ILE/THR	4,4402	2.1+/-5.4	0,4,2199	196	170	179		15011	2.9	0	1	dbSNP_133	179	29,8571	9.1+/-34.3	1,27,4272	yes	missense	HMCN1	NM_031935.2	89	1,31,6471	TT,TC,CC		0.3372,0.0908,0.2537	benign	5004/5636	186121996	33,12973	2203	4300	6503	SO:0001583	missense	83872	exon96			AAGTCACTGTAAA	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.15011C>T	1.37:g.186121996C>T	ENSP00000271588:p.Thr5004Ile	156	0	0		168	72	0.428571	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	8.698	0.909113	0.17833	9.08E-4	0.003372	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.31510	1.49;1.49	5.9	2.9	0.33743	G2 nidogen/fibulin G2F (2);Green fluorescent protein-like (1);	0.929918	0.09308	N	0.819936	T	0.12603	0.0306	N	0.08118	0	0.09310	N	1	B	0.27316	0.175	B	0.30855	0.121	T	0.34601	-0.9822	10	0.29301	T	0.29	.	9.0753	0.36517	0.4557:0.2514:0.2928:0.0	.	5004	Q96RW7	HMCN1_HUMAN	I	5004	ENSP00000271588:T5004I;ENSP00000356462:T5004I	ENSP00000271588:T5004I	T	+	2	0	HMCN1	184388619	0.000000	0.05858	0.026000	0.17262	0.758000	0.43043	0.220000	0.17660	0.314000	0.23086	0.650000	0.86243	ACT	C|0.996;T|0.004	0.004	strong		0.433	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		T	186121996	C	T	186121996	3	4	29	1	0	0	0	0	1	0	0	0	7229	565	20	2	15393	2	HMCN1	1	186121996	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1	186121996	63128625	71	12312	152	2									
FAM5C	339479	hgsc.bcm.edu	37	chr1	190067970	190067970	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agatatttcatctcgagatcTtgcaggtcagtttcaaagcc	11	13	8	9	1	5	2	3	0	2	2	6	3	5	2	1	1	2	2	1	1	2	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:190067970T>G	ENST00000367462.3	-	8	1710	c.1479A>C	c.(1477-1479)caA>caC	p.Q493H	BRINP3_ENST00000534846.1_Missense_Mutation_p.Q391H	NM_199051.1	NP_950252.1	Q76B58	BRNP3_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 3	493					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)											TCTCGAGATCTTGCAGGTCAG	0.502																																					p.Q493H		Atlas-SNP	.											FAM5C,colon,carcinoma,-2,1	FAM5C	343	1	0			c.A1479C						PASS	.						163	160	161					1																	190067970		2203	4300	6503	SO:0001583	missense	339479	exon8			GAGATCTTGCAGG	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.1479A>C	1.37:g.190067970T>G	ENSP00000356432:p.Gln493His	96	0	0		135	35	0.259259	NM_199051	B3KVP1|B7Z260|O95726|Q2M330	Missense_Mutation	SNP	ENST00000367462.3	37	CCDS1373.1	.	.	.	.	.	.	.	.	.	.	T	15.38	2.814998	0.50527	.	.	ENSG00000162670	ENST00000367462;ENST00000534846	T;T	0.53423	0.62;0.62	5.75	-1.39	0.08997	.	0.000000	0.85682	D	0.000000	T	0.43567	0.1253	M	0.72894	2.215	0.49483	D	0.999797	B;B	0.28713	0.22;0.064	B;B	0.29267	0.1;0.018	T	0.44314	-0.9336	10	0.87932	D	0	.	10.6986	0.45913	0.0:0.5576:0.0:0.4424	.	391;493	B7Z260;Q76B58	.;FAM5C_HUMAN	H	493;391	ENSP00000356432:Q493H;ENSP00000438022:Q391H	ENSP00000356432:Q493H	Q	-	3	2	FAM5C	188334593	0.721000	0.28007	0.997000	0.53966	0.996000	0.88848	-0.076000	0.11412	-0.178000	0.10672	0.482000	0.46254	CAA	.	.	none		0.502	BRINP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086278.1	NM_199051		G	190067970	T	G	190067970	3	3	29	1	0	0	0	0	1	0	0	0	5602	1606	56	5	825	5	FAM5C	1	190067970	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	3945974	190067970	59182651	72	12313											
RGS1	5996	hgsc.bcm.edu	37	chr1	192545417	192545417	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cttttatgtcttttgtagtgGaatggatatgaaagcatacc	11	16	9	5	0	1	1	0	1	1	0	1	3	1	3	1	2	2	2	1	2	6	7			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:192545417G>A	ENST00000367459.3	+	2	206	c.140G>A	c.(139-141)gGa>gAa	p.G47E	RGS1_ENST00000469578.2_Missense_Mutation_p.G47E	NM_002922.3	NP_002913.3	Q08116	RGS1_HUMAN	regulator of G-protein signaling 1	47					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|immune response (GO:0006955)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|GTPase activator activity (GO:0005096)			kidney(8)|large_intestine(1)|lung(13)	22		Breast(1374;0.188)				TTTTGTAGTGGAATGGATATG	0.308																																					p.G47E		Atlas-SNP	.											.	RGS1	75	.	0			c.G140A						PASS	.						70	72	71					1																	192545417		2203	4297	6500	SO:0001583	missense	5996	exon2			GTAGTGGAATGGA	AF493925	CCDS1375.2	1q31	2008-02-05	2007-08-14		ENSG00000090104	ENSG00000090104		"Regulators of G-protein signaling"	9991	protein-coding gene	gene with protein product		600323	"regulator of G-protein signalling 1"	IER1		8241276, 8602223	Standard	NM_002922		Approved	1R20, IR20, BL34	uc001gsi.1	Q08116	OTTHUMG00000035598	ENST00000367459.3:c.140G>A	1.37:g.192545417G>A	ENSP00000356429:p.Gly47Glu	182	0	0		178	43	0.241573	NM_002922	B2RDM9|B4DZY0|Q07918|Q9H1W2	Missense_Mutation	SNP	ENST00000367459.3	37	CCDS1375.2	.	.	.	.	.	.	.	.	.	.	G	13.06	2.124692	0.37533	.	.	ENSG00000090104	ENST00000367459	T	0.37584	1.19	6.17	6.17	0.99709	.	0.241459	0.36002	N	0.002853	T	0.47525	0.1450	L	0.29908	0.895	0.43084	D	0.994743	D;B	0.76494	0.999;0.149	D;B	0.72075	0.976;0.032	T	0.26985	-1.0087	10	0.38643	T	0.18	.	14.9828	0.71324	0.0:0.1422:0.8578:0.0	.	47;47	Q08116-2;Q08116	.;RGS1_HUMAN	E	47	ENSP00000356429:G47E	ENSP00000356429:G47E	G	+	2	0	RGS1	190812040	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	3.974000	0.56852	2.941000	0.99782	0.655000	0.94253	GGA	.	.	none		0.308	RGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086391.1	NM_002922		A	192545417	G	A	192545417	3	1	29	1	0	0	0	0	1	0	0	0	13307	1174	41	2	146	2	RGS1	1	192545417	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2477447	192545417	56705204	73	12314											
CFHR2	3080	hgsc.bcm.edu	37	chr1	196918724	196918724	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgtctccttcaaaatccttTtggactcgcataacgtgcgc	8	13	8	12	3	2	0	1	0	1	0	5	1	3	1	2	1	2	1	2	1	3	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:196918724T>A	ENST00000367415.5	+	2	298	c.198T>A	c.(196-198)ttT>ttA	p.F66L	CFHR2_ENST00000496448.1_Intron|CFHR2_ENST00000476712.2_Missense_Mutation_p.F66L|CFHR2_ENST00000367421.3_Missense_Mutation_p.F66L	NM_005666.2	NP_005657.1	P36980	FHR2_HUMAN	complement factor H-related 2	66	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.					extracellular region (GO:0005576)				large_intestine(2)|ovary(1)|skin(3)	6						CAAAATCCTTTTGGACTCGCA	0.378																																					p.F66L		Atlas-SNP	.											.	CFHR2	73	.	0			c.T198A						PASS	.						89	83	85					1																	196918724		2203	4300	6503	SO:0001583	missense	3080	exon2			ATCCTTTTGGACT	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	ENST00000367415.5:c.198T>A	1.37:g.196918724T>A	ENSP00000356385:p.Phe66Leu	235	0	0		219	14	0.0639269	NM_005666	Q14310|Q5T9T1	Missense_Mutation	SNP	ENST00000367415.5	37	CCDS30959.1	.	.	.	.	.	.	.	.	.	.	T	2.806	-0.247958	0.05867	.	.	ENSG00000080910	ENST00000367421;ENST00000367415	T;T	0.40756	1.02;1.02	2.77	-0.909	0.10514	Complement control module (2);Sushi/SCR/CCP (2);	1.185540	0.06609	N	0.755236	T	0.27027	0.0662	L	0.33485	1.01	0.09310	N	1	B	0.12013	0.005	B	0.15484	0.013	T	0.24261	-1.0165	10	0.11485	T	0.65	.	5.6889	0.17819	0.0:0.4428:0.0:0.5572	.	66	P36980	FHR2_HUMAN	L	66	ENSP00000356391:F66L;ENSP00000356385:F66L	ENSP00000356385:F66L	F	+	3	2	CFHR2	195185347	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-2.610000	0.00885	-0.221000	0.09973	-0.478000	0.04885	TTT	.	.	none		0.378	CFHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088815.2	NM_005666		A	196918724	T	A	196918724	3	1	29	1	0	0	0	0	1	0	0	0	3287	1838	64	5	204	5	CFHR2	1	196918724	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	4373307	196918724	52331897	74	12315											
BTG2	7832	hgsc.bcm.edu	37	chr1	203274835	203274835	+	Missense_Mutation	SNP	G	G	A																															gggctgcgtgagcgagcagaGgcttaaggtcttcagcgggg																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:203274835G>A	ENST00000290551.4	+	1	172	c.101G>A	c.(100-102)aGg>aAg	p.R34K	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	34					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			AGCGAGCAGAGGCTTAAGGTC	0.711																																					p.R34K		Atlas-SNP	.											.	BTG2	16	.	0			c.G101A						PASS	.						15	16	16					1																	203274835		2146	4205	6351	SO:0001583	missense	7832	exon1			AGCAGAGGCTTAA		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.101G>A	1.37:g.203274835G>A	ENSP00000290551:p.Arg34Lys	124	0	0		110	31	0.281818	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	G	16.86	3.239008	0.58995	.	.	ENSG00000159388	ENST00000290551	T	0.21543	2.0	4.66	2.79	0.32731	Anti-proliferative protein (3);	0.165673	0.37761	N	0.001941	T	0.11067	0.0270	N	0.13299	0.325	0.31292	N	0.689358	B	0.14012	0.009	B	0.20577	0.03	T	0.08066	-1.0740	10	0.41790	T	0.15	-8.3253	6.0943	0.20010	0.386:0.0:0.614:0.0	.	34	P78543	BTG2_HUMAN	K	34	ENSP00000290551:R34K	ENSP00000290551:R34K	R	+	2	0	BTG2	201541458	1.000000	0.71417	0.012000	0.15200	0.830000	0.47004	5.105000	0.64591	0.589000	0.29677	0.478000	0.44815	AGG	.	.	none		0.711	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		A	203274835	G	A	203274835	3	1	29	1	0	0	0	0	1	0	0	0	1556	1000	35	2	103	2	BTG2	1	203274835	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	6356111	203274835	45975786	75	12316	153	2									
BTG2	7832	hgsc.bcm.edu	37	chr1	203274836	203274836	+	Silent	SNP	G	G	A																															ggctgcgtgagcgagcagagGcttaaggtcttcagcggggc																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:203274836G>A	ENST00000290551.4	+	1	173	c.102G>A	c.(100-102)agG>agA	p.R34R	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	34					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			GCGAGCAGAGGCTTAAGGTCT	0.716																																					p.R34R		Atlas-SNP	.											.	BTG2	16	.	0			c.G102A						PASS	.						15	16	15					1																	203274836		2144	4202	6346	SO:0001819	synonymous_variant	7832	exon1			GCAGAGGCTTAAG		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.102G>A	1.37:g.203274836G>A		125	0	0		110	30	0.272727	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Silent	SNP	ENST00000290551.4	37	CCDS1437.1																																																																																			.	.	none		0.716	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		A	203274836	G	A	203274836	2	1	29	1	0	0	0	0	0	0	0	1	1556	1194	42	2		2	BTG2	1	203274836	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1	203274836	45975785	76	12317	153	2									
BTG2	7832	hgsc.bcm.edu	37	chr1	203274867	203274867	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tcagcggggcgctccaggagGcactcacaggtgagcgcatg	8	5	16	12	3	2	1	2	1	0	0	3	2	3	2	1	5	2	3	1	5	0	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:203274867G>C	ENST00000290551.4	+	1	204	c.133G>C	c.(133-135)Gca>Cca	p.A45P	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	45					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.A45T(1)		haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			GCTCCAGGAGGCACTCACAGG	0.706																																					p.A45P		Atlas-SNP	.											BTG2,lymph_node,lymphoid_neoplasm,-1,2	BTG2	16	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G133C						PASS	.						11	13	13					1																	203274867		2020	3950	5970	SO:0001583	missense	7832	exon1			CAGGAGGCACTCA		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.133G>C	1.37:g.203274867G>C	ENSP00000290551:p.Ala45Pro	90	0	0		81	30	0.37037	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.163593	0.78226	.	.	ENSG00000159388	ENST00000290551	T	0.25085	1.82	4.4	4.4	0.53042	Anti-proliferative protein (3);	0.078518	0.49916	D	0.000121	T	0.52008	0.1708	M	0.82630	2.6	0.47374	D	0.999406	D	0.62365	0.991	D	0.64687	0.928	T	0.58222	-0.7674	10	0.51188	T	0.08	-33.413	15.7078	0.77598	0.0:0.0:1.0:0.0	.	45	P78543	BTG2_HUMAN	P	45	ENSP00000290551:A45P	ENSP00000290551:A45P	A	+	1	0	BTG2	201541490	1.000000	0.71417	0.991000	0.47740	0.943000	0.58893	4.326000	0.59241	2.282000	0.76494	0.471000	0.43371	GCA	.	.	none		0.706	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		C	203274867	G	C	203274867	3	2	29	1	0	0	0	0	1	0	0	0	1556	1203	42	4	135	4	BTG2	1	203274867	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	31	203274867	45975754	77	12318											
CTSE	1510	hgsc.bcm.edu	37	chr1	206319201	206319201	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgggtcccctctgtgtactGcactagcccagcctgcagta	6	10	10	15	0	1	0	0	0	1	0	2	0	2	0	4	1	5	4	4	1	3	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:206319201G>A	ENST00000358184.2	+	3	444	c.326G>A	c.(325-327)tGc>tAc	p.C109Y	CTSE_ENST00000432969.2_Missense_Mutation_p.C34Y|CTSE_ENST00000360218.2_Missense_Mutation_p.C109Y|CTSE_ENST00000361052.3_Missense_Mutation_p.C109Y	NM_001910.3	NP_001901.1	P14091	CATE_HUMAN	cathepsin E	109					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)			TCTGTGTACTGCACTAGCCCA	0.592																																					p.C109Y		Atlas-SNP	.											.	CTSE	72	.	0			c.G326A						PASS	.						83	73	76					1																	206319201		2203	4300	6503	SO:0001583	missense	1510	exon3			TGTACTGCACTAG	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.326G>A	1.37:g.206319201G>A	ENSP00000350911:p.Cys109Tyr	102	0	0		88	13	0.147727	NM_001910	Q5TZ01|Q5TZ02|Q9NY58|Q9UCE3|Q9UCE4	Missense_Mutation	SNP	ENST00000358184.2	37	CCDS1462.1	.	.	.	.	.	.	.	.	.	.	G	17.47	3.397470	0.62177	.	.	ENSG00000196188	ENST00000358184;ENST00000361052;ENST00000360218;ENST00000432969	T;T;T;T	0.65916	-0.18;-0.18;0.0;-0.06	4.78	4.78	0.61160	.	0.142191	0.49916	D	0.000133	D	0.86843	0.6030	H	0.98155	4.16	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.998	D;D;D	0.70016	0.967;0.96;0.919	D	0.91790	0.5443	10	0.87932	D	0	.	17.9775	0.89131	0.0:0.0:1.0:0.0	.	34;109;109	B4DNU8;P14091-2;P14091-1	.;.;.	Y	109;109;109;34	ENSP00000350911:C109Y;ENSP00000354337:C109Y;ENSP00000353350:C109Y;ENSP00000394607:C34Y	ENSP00000350911:C109Y	C	+	2	0	CTSE	204485824	1.000000	0.71417	1.000000	0.80357	0.432000	0.31715	8.910000	0.92685	2.655000	0.90218	0.655000	0.94253	TGC	.	.	none		0.592	CTSE-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000087998.1	NM_001910		A	206319201	G	A	206319201	3	1	29	1	0	0	0	0	1	0	0	0	4035	1319	46	2	336	2	CTSE	1	206319201	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	3044334	206319201	42931420	78	12319											
FAIM3	9214	hgsc.bcm.edu	37	chr1	207078467	207078467	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agctggtcttcagagatgggGcatggagccagggagattca	10	8	16	7	0	3	2	2	0	1	2	3	5	3	3	1	5	2	2	1	5	0	2	rs41304091	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:207078467G>A	ENST00000367091.3	-	8	1213	c.1070C>T	c.(1069-1071)gCc>gTc	p.A357V	FAIM3_ENST00000442471.2_Missense_Mutation_p.A245V|FAIM3_ENST00000420007.2_3'UTR|FAIM3_ENST00000528654.1_5'UTR	NM_005449.4	NP_005440.1	O60667	FAIM3_HUMAN	Fas apoptotic inhibitory molecule 3	357					cellular defense response (GO:0006968)|immune system process (GO:0002376)|negative regulation of apoptotic process (GO:0043066)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	15	Breast(84;0.201)					CAGAGATGGGGCATGGAGCCA	0.502													G|||	8	0.00159744	0.0	0.0	5008	,	,		19983	0.0		0.008	False		,,,				2504	0.0				p.A357V		Atlas-SNP	.											.	FAIM3	36	.	0			c.C1070T						PASS	.	G	VAL/ALA,,VAL/ALA	16,4390	23.3+/-48.9	0,16,2187	114	108	110		734,,1070	2	0	1	dbSNP_127	110	128,8472	65.3+/-127.6	0,128,4172	yes	missense,utr-3,missense	FAIM3	NM_001142473.1,NM_001193338.1,NM_005449.4	64,,64	0,144,6359	AA,AG,GG		1.4884,0.3631,1.1072	benign,,benign	245/279,,357/391	207078467	144,12862	2203	4300	6503	SO:0001583	missense	9214	exon8			GATGGGGCATGGA	AF057557	CCDS1473.1, CCDS44304.1	1q32.1	2013-01-11			ENSG00000162894	ENSG00000162894		"Immunoglobulin superfamily / Immunoglobulin-like domain containing"	14315	protein-coding gene	gene with protein product		606015				9586636, 1563211	Standard	NM_005449		Approved	TOSO	uc001hey.3	O60667	OTTHUMG00000036457	ENST00000367091.3:c.1070C>T	1.37:g.207078467G>A	ENSP00000356058:p.Ala357Val	65	0	0		64	23	0.359375	NM_005449	A8K7J2|B7Z6Z0|D9MWM3	Missense_Mutation	SNP	ENST00000367091.3	37	CCDS1473.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	G	2.553	-0.303557	0.05495	0.003631	0.014884	ENSG00000162894	ENST00000367091;ENST00000442471	T	0.24151	1.87	5.14	2.02	0.26589	.	0.514876	0.16940	N	0.193320	T	0.09598	0.0236	N	0.19112	0.55	0.09310	N	1	B;B;B	0.22746	0.074;0.074;0.044	B;B;B	0.20955	0.032;0.032;0.014	T	0.21280	-1.0250	10	0.34782	T	0.22	-5.9354	4.7727	0.13164	0.2118:0.1724:0.6158:0.0	rs41304091	266;245;357	B7Z497;B7Z6Z0;O60667	.;.;FAIM3_HUMAN	V	357;245	ENSP00000356058:A357V	ENSP00000356058:A357V	A	-	2	0	FAIM3	205145090	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.162000	0.16501	0.126000	0.18424	0.655000	0.94253	GCC	G|0.992;A|0.008	0.008	strong		0.502	FAIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088677.1	NM_005449		A	207078467	G	A	207078467	3	1	29	1	0	0	0	0	1	0	0	0	5382	1203	42	2	106	2	FAIM3	1	207078467	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	759266	207078467	42172154	79	12320											
HLX	3142	hgsc.bcm.edu	37	chr1	221057573	221057573	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaccggcggatgaagtggCggcactccaaggaggcccag	11	3	16	11	3	0	2	0	1	0	1	1	4	1	4	3	6	1	1	3	6	3	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:221057573C>T	ENST00000366903.6	+	4	2495	c.994C>T	c.(994-996)Cgg>Tgg	p.R332W	HLX_ENST00000549319.1_Missense_Mutation_p.R118W	NM_021958.3	NP_068777.1	Q14774	HLX_HUMAN	H2.0-like homeobox	332					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)	p.R332W(1)		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)		GATGAAGTGGCGGCACTCCAA	0.632																																					p.R332W		Atlas-SNP	.											HLX,NS,carcinoma,0,1	HLX	67	1	1	Substitution - Missense(1)	endometrium(1)	c.C994T						scavenged	.						36	41	39					1																	221057573		2202	4300	6502	SO:0001583	missense	3142	exon4			AAGTGGCGGCACT	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.994C>T	1.37:g.221057573C>T	ENSP00000355870:p.Arg332Trp	114	1	0.00877193		136	40	0.294118	NM_021958	B2R8A8|Q15988|Q59HE7|Q9NZ75	Missense_Mutation	SNP	ENST00000366903.6	37	CCDS1527.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.037543	0.75617	.	.	ENSG00000136630	ENST00000366903;ENST00000427693;ENST00000549319	D;D;D	0.97665	-4.48;-4.48;-4.48	5.17	0.831	0.18860	Homeobox, eukaryotic (1);Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.52532	D	0.000061	D	0.98798	0.9595	H	0.96518	3.835	0.48632	D	0.999682	D	0.89917	1.0	D	0.97110	1.0	D	0.99632	1.0986	10	0.87932	D	0	-29.0787	14.4728	0.67529	0.6337:0.3663:0.0:0.0	.	332	Q14774	HLX_HUMAN	W	332;65;118	ENSP00000355870:R332W;ENSP00000408248:R65W;ENSP00000449882:R118W	ENSP00000355870:R332W	R	+	1	2	HLX	219124196	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	1.035000	0.30216	-0.022000	0.13986	-0.310000	0.09108	CGG	.	.	none		0.632	HLX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090902.3	NM_021958		T	221057573	C	T	221057573	3	4	29	1	0	0	0	0	1	0	0	0	7225	759	27	1	1008	1	HLX	1	221057573	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	13979106	221057573	28193048	80	12321											
KIAA1804	84451	hgsc.bcm.edu	37	chr1	233511675	233511675	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttttagtgacttcagatgaAagcaataaaacttggggaag	15	12	10	4	0	1	3	1	2	0	1	1	4	1	4	0	2	2	1	0	2	6	6	rs35758282	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:233511675A>C	ENST00000366624.3	+	7	1950	c.1689A>C	c.(1687-1689)gaA>gaC	p.E563D	MLK4_ENST00000366622.1_Missense_Mutation_p.E9D	NM_032435.2	NP_115811.2																					CTTCAGATGAAAGCAATAAAA	0.308													A|||	8	0.00159744	0.0	0.0029	5008	,	,		17798	0.0		0.006	False		,,,				2504	0.0				p.E563D		Atlas-SNP	.											.	KIAA1804	129	.	0			c.A1689C						PASS	.	A	ASP/GLU	1,4405	2.1+/-5.4	0,1,2202	82	84	84		1689	-0.7	1	1	dbSNP_126	84	21,8577	16.0+/-53.3	0,21,4278	yes	missense	KIAA1804	NM_032435.2	45	0,22,6480	CC,CA,AA		0.2442,0.0227,0.1692	benign	563/1037	233511675	22,12982	2203	4299	6502	SO:0001583	missense	0	exon7			AGATGAAAGCAAT																												ENST00000366624.3:c.1689A>C	1.37:g.233511675A>C	ENSP00000355583:p.Glu563Asp	112	0	0		116	53	0.456897	NM_032435		Missense_Mutation	SNP	ENST00000366624.3	37	CCDS1598.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	A	12.19	1.862541	0.32884	2.27E-4	0.002442	ENSG00000143674	ENST00000366624;ENST00000366622	T;T	0.10960	2.82;2.82	5.44	-0.691	0.11305	.	0.000000	0.85682	D	0.000000	T	0.10121	0.0248	L	0.31476	0.935	0.36608	D	0.875022	D;B	0.56521	0.976;0.191	D;B	0.62955	0.909;0.084	T	0.08848	-1.0702	10	0.87932	D	0	.	6.7874	0.23682	0.4566:0.0:0.4213:0.1221	rs35758282	10;563	Q5TCX8-3;Q5TCX8	.;M3KL4_HUMAN	D	563;9	ENSP00000355583:E563D;ENSP00000355581:E9D	ENSP00000355581:E9D	E	+	3	2	RP5-862P8.2	231578298	0.799000	0.28903	0.998000	0.56505	0.984000	0.73092	0.024000	0.13555	-0.026000	0.13895	0.533000	0.62120	GAA	A|0.998;C|0.002	0.002	strong		0.308	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1			C	233511675	A	C	233511675	3	2	29	1	0	0	0	0	1	0	0	0	8268	11	1	5	1715	5	KIAA1804	1	233511675	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	12454102	233511675	15738946	81	12322											
LYST	1130	hgsc.bcm.edu	37	chr1	235887393	235887393	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaagatttctacagcattatCtctcaattgccaccaacgct	13	12	4	12	1	3	1	1	0	2	1	4	1	3	1	2	0	4	2	2	0	5	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:235887393C>T	ENST00000389794.3	-	39	9424	c.9250G>A	c.(9250-9252)Gat>Aat	p.D3084N	LYST_ENST00000389793.2_Missense_Mutation_p.D3084N|LYST_ENST00000473037.1_5'UTR			Q99698	LYST_HUMAN	lysosomal trafficking regulator	3084					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)			ACAGCATTATCTCTCAATTGC	0.363																																					p.D3084N		Atlas-SNP	.											.	LYST	370	.	0			c.G9250A						PASS	.						113	111	112					1																	235887393		2203	4300	6503	SO:0001583	missense	1130	exon39			CATTATCTCTCAA	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.9250G>A	1.37:g.235887393C>T	ENSP00000374444:p.Asp3084Asn	150	0	0		128	14	0.109375	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	37	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	C	34	5.344370	0.95807	.	.	ENSG00000143669	ENST00000389794;ENST00000389793	T;T	0.61980	0.06;0.06	5.23	5.23	0.72850	PH-BEACH domain (1);	0.046332	0.85682	N	0.000000	T	0.74145	0.3678	L	0.43646	1.37	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73104	-0.4088	10	0.44086	T	0.13	.	19.1565	0.93511	0.0:1.0:0.0:0.0	.	3084	Q99698	LYST_HUMAN	N	3084	ENSP00000374444:D3084N;ENSP00000374443:D3084N	ENSP00000374443:D3084N	D	-	1	0	LYST	233954016	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.776000	0.85560	2.597000	0.87782	0.460000	0.39030	GAT	.	.	none		0.363	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			T	235887393	C	T	235887393	3	4	29	1	0	0	0	0	1	0	0	0	9137	913	32	2	2215	2	LYST	1	235887393	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2375718	235887393	13363228	82	12323											
LYST	1130	hgsc.bcm.edu	37	chr1	235918870	235918870	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgaagatacaactggttggcTagcaaggaaaatccacgatt	15	9	10	7	1	0	2	0	1	0	1	1	4	1	3	1	3	3	3	1	3	7	4	rs61738992	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:235918870T>G	ENST00000389794.3	-	25	7311	c.7137A>C	c.(7135-7137)ctA>ctC	p.L2379L	LYST_ENST00000389793.2_Silent_p.L2379L			Q99698	LYST_HUMAN	lysosomal trafficking regulator	2379					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)			ACTGGTTGGCTAGCAAGGAAA	0.343													T|||	105	0.0209665	0.0015	0.085	5008	,	,		16726	0.0		0.0298	False		,,,				2504	0.0143				p.L2379L		Atlas-SNP	.											.	LYST	370	.	0			c.A7137C						PASS	.	T		31,4375	37.6+/-69.7	0,31,2172	174	176	176		7137	-1.4	1	1	dbSNP_129	176	295,8305	107.4+/-168.2	3,289,4008	no	coding-synonymous	LYST	NM_000081.2		3,320,6180	GG,GT,TT		3.4302,0.7036,2.5065		2379/3802	235918870	326,12680	2203	4300	6503	SO:0001819	synonymous_variant	1130	exon25			GTTGGCTAGCAAG	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.7137A>C	1.37:g.235918870T>G		96	0	0		88	41	0.465909	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	37	CCDS31062.1																																																																																			T|0.976;G|0.024	0.024	strong		0.343	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			G	235918870	T	G	235918870	2	3	29	1	0	0	0	0	0	0	0	1	9137	1509	53	5		5	LYST	1	235918870	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	31477	235918870	13331751	83	12324											
CHML	1122	hgsc.bcm.edu	37	chr1	241797585	241797585	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgcatgtcatggttgaagaaCataattctgtgacccgtaca	12	12	9	8	1	2	3	1	2	1	1	2	3	2	3	1	1	3	3	1	1	4	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:241797585C>G	ENST00000366553.1	-	1	1647	c.1484G>C	c.(1483-1485)tGt>tCt	p.C495S	OPN3_ENST00000366554.2_Intron|OPN3_ENST00000331838.5_Intron|OPN3_ENST00000469376.1_Intron	NM_001821.3	NP_001812.2	P26374	RAE2_HUMAN	choroideremia-like (Rab escort protein 2)	495					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)			GGTTGAAGAACATAATTCTGT	0.413																																					p.C495S		Atlas-SNP	.											.	CHML	82	.	0			c.G1484C						PASS	.						92	87	89					1																	241797585		2203	4299	6502	SO:0001583	missense	1122	exon1			GAAGAACATAATT	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.1484G>C	1.37:g.241797585C>G	ENSP00000355511:p.Cys495Ser	86	0	0		90	47	0.522222	NM_001821	B2RAB9|Q17RE0|Q9H1Y4	Missense_Mutation	SNP	ENST00000366553.1	37	CCDS31073.1	.	.	.	.	.	.	.	.	.	.	C	11.85	1.762053	0.31228	.	.	ENSG00000203668	ENST00000366553	T	0.76448	-1.02	5.08	5.08	0.68730	.	0.047679	0.85682	U	0.000000	T	0.62221	0.2410	.	.	.	0.58432	D	0.99999	B	0.25667	0.131	B	0.31751	0.135	T	0.57487	-0.7803	9	0.02654	T	1	-4.293	16.3808	0.83460	0.0:1.0:0.0:0.0	.	495	P26374	RAE2_HUMAN	S	495	ENSP00000355511:C495S	ENSP00000355511:C495S	C	-	2	0	CHML	239864208	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.326000	0.52037	2.826000	0.97356	0.655000	0.94253	TGT	.	.	none		0.413	CHML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095712.1	NM_001821		G	241797585	C	G	241797585	3	3	29	1	0	0	0	0	1	0	0	0	3353	478	17	4	490	4	CHML	1	241797585	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	5878715	241797585	7453036	84	12325											
C1orf101	257044	hgsc.bcm.edu	37	chr1	244715882	244715882	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctttcacacaactgattcAttcaaatcttggaccagaat	14	12	4	11	0	4	2	3	1	1	1	4	3	4	3	2	1	1	0	2	1	3	4	rs34510134	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:244715882A>G	ENST00000366534.4	+	9	849	c.795A>G	c.(793-795)tcA>tcG	p.S265S	C1orf101_ENST00000366533.4_Silent_p.S265S|C1orf101_ENST00000366531.3_Silent_p.S114S|C1orf101_ENST00000473875.1_Intron	NM_001130957.1	NP_001124429.1	Q5SY80	CA101_HUMAN	chromosome 1 open reading frame 101	265						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)			CAACTGATTCATTCAAATCTT	0.458													A|||	307	0.0613019	0.2231	0.0159	5008	,	,		15160	0.0		0.001	False		,,,				2504	0.0				p.S265S		Atlas-SNP	.											.	C1orf101	158	.	0			c.A795G						PASS	.	A	,,	846,3560	334.9+/-303.7	85,676,1442	149	135	140		795,342,795	-0.5	1	1	dbSNP_126	140	10,8590	7.1+/-27.0	0,10,4290	no	coding-synonymous,coding-synonymous,coding-synonymous	C1orf101	NM_001130957.1,NM_001242340.1,NM_173807.4	,,	85,686,5732	GG,GA,AA		0.1163,19.2011,6.5816	,,	265/952,114/801,265/833	244715882	856,12150	2203	4300	6503	SO:0001819	synonymous_variant	257044	exon9			TGATTCATTCAAA	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.795A>G	1.37:g.244715882A>G		227	0	0		194	86	0.443299	NM_173807	B4DZR4|B7Z7X5|E9PEA3|Q8IYZ6	Silent	SNP	ENST00000366534.4	37	CCDS44340.1																																																																																			A|0.933;G|0.067	0.067	strong		0.458	C1orf101-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096701.1	NM_173807		G	244715882	A	G	244715882	2	3	29	1	0	0	0	0	0	0	0	1	1978	204	8	3		3	C1orf101	1	244715882	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	2918297	244715882	4534739	85	12326											
OR2W5	441932	hgsc.bcm.edu	37	chr1	247655102	247655102	+	RNA	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tatggcgtgattgcagccgcGgtgctgaggatgaagtcagc	8	9	16	8	3	1	3	1	3	0	0	1	4	1	4	1	3	4	2	1	3	2	2	rs143904230	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:247655102G>A	ENST00000522351.1	+	0	733							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)			TTGCAGCCGCGGTGCTGAGGA	0.567													G|||	29	0.00579073	0.0023	0.0144	5008	,	,		18573	0.0		0.0129	False		,,,				2504	0.0031				p.G225S		Atlas-SNP	.											.	OR2W5	97	.	0			c.G673A						PASS	.	G	SER/GLY	11,4395	17.9+/-39.9	0,11,2192	120	114	116		673	-4.1	0.1	1	dbSNP_134	116	137,8463	69.7+/-132.2	1,135,4164	yes	missense	OR2W5	NM_001004698.2	56	1,146,6356	AA,AG,GG		1.593,0.2497,1.1379	benign	225/321	247655102	148,12858	2203	4300	6503			441932	exon1			AGCCGCGGTGCTG			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.247655102G>A		76	0	0		94	60	0.638298	NM_001004698	B9EH85	Missense_Mutation	SNP	ENST00000522351.1	37																																																																																				G|0.989;A|0.011	0.011	strong		0.567	OR2W5-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000375789.1	NM_001004698		A	247655102	G	A	247655102	1	1	29	0	1	0	0	0	0	0	0	0	11043	1116	39	1		1	OR2W5	1	247655102	RNA	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2939220	247655102	1595519	86	12327											
OR2L3	391192	hgsc.bcm.edu	37	chr1	248224227	248224227	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccattgttcctaagatggcaTctgattttctgtctggtaac	8	16	8	9	0	3	2	0	1	3	1	4	2	4	2	2	2	1	3	2	2	2	6	rs146249174	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248224227T>C	ENST00000359959.3	+	1	244	c.244T>C	c.(244-246)Tct>Cct	p.S82P	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, member 3	82						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)			TAAGATGGCATCTGATTTTCT	0.453													t|||	13	0.00259585	0.0	0.0043	5008	,	,		22569	0.0		0.0099	False		,,,				2504	0.0				p.S82P		Atlas-SNP	.											.	OR2L3	97	.	0			c.T244C						PASS	.	T	PRO/SER,	13,4393		0,13,2190	296	271	279		244,	0.6	0	1	dbSNP_134	279	122,8478		1,120,4179	no	missense,intron	OR2L13,OR2L3	NM_001004687.1,NM_175911.2	74,	1,133,6369	CC,CT,TT		1.4186,0.2951,1.038	benign,	82/313,	248224227	135,12871	2203	4300	6503	SO:0001583	missense	391192	exon1			ATGGCATCTGATT	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.244T>C	1.37:g.248224227T>C	ENSP00000353044:p.Ser82Pro	234	0	0		223	107	0.479821	NM_001004687	B9EH44	Missense_Mutation	SNP	ENST00000359959.3	37	CCDS31104.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	.	6.953	0.545676	0.13312	0.002951	0.014186	ENSG00000198128	ENST00000359959	T	0.00402	7.56	2.05	0.632	0.17705	GPCR, rhodopsin-like superfamily (1);	0.970417	0.08347	U	0.959841	T	0.00300	0.0009	L	0.45470	1.425	0.09310	N	1	B	0.33379	0.41	B	0.42692	0.395	T	0.40270	-0.9572	10	0.37606	T	0.19	.	3.912	0.09207	0.1729:0.0:0.2867:0.5404	.	82	Q8NG85	OR2L3_HUMAN	P	82	ENSP00000353044:S82P	ENSP00000353044:S82P	S	+	1	0	OR2L3	246290850	0.000000	0.05858	0.004000	0.12327	0.072000	0.16883	-2.738000	0.00800	0.928000	0.37168	0.379000	0.24179	TCT	T|0.992;C|0.008	0.008	strong		0.453	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1	NM_001004687		C	248224227	T	C	248224227	3	2	29	1	0	0	0	0	1	0	0	0	11017	1435	50	3	246	3	OR2L3	1	248224227	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	569125	248224227	1026394	87	12328											
OR2T1	26696	hgsc.bcm.edu	37	chr1	248570057	248570057	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgatgtatgtgtgctgtgtTttgatgctgctgattccttt	4	20	12	5	0	0	3	0	3	0	0	1	3	1	3	1	0	3	5	1	0	1	5	rs138375160	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248570057T>C	ENST00000366474.1	+	1	762	c.762T>C	c.(760-762)gtT>gtC	p.V254V		NM_030904.1	NP_112166.1	O43869	OR2T1_HUMAN	olfactory receptor, family 2, subfamily T, member 1	254						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)			TGTGCTGTGTTTTGATGCTGC	0.512													.|||	12	0.00239617	0.0	0.0014	5008	,	,		24031	0.0		0.0099	False		,,,				2504	0.001				p.V254V		Atlas-SNP	.											.	OR2T1	89	.	0			c.T762C						PASS	.	T		10,4396	16.8+/-37.8	0,10,2193	275	231	246		762	-9.5	0	1	dbSNP_134	246	80,8520	45.8+/-104.6	1,78,4221	no	coding-synonymous	OR2T1	NM_030904.1		1,88,6414	CC,CT,TT		0.9302,0.227,0.692		254/370	248570057	90,12916	2203	4300	6503	SO:0001819	synonymous_variant	26696	exon1			CTGTGTTTTGATG	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.762T>C	1.37:g.248570057T>C		181	0	0		157	73	0.464968	NM_030904	Q6IEZ9	Silent	SNP	ENST00000366474.1	37	CCDS31115.1																																																																																			T|0.994;C|0.006	0.006	strong		0.512	OR2T1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097346.2			C	248570057	T	C	248570057	2	2	29	1	0	0	0	0	0	0	0	1	11025	1828	64	3		3	OR2T1	1	248570057	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	345830	248570057	680564	88	12329											
OR2T27	403239	hgsc.bcm.edu	37	chr1	248813470	248813470	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccatgtgtgaggagcaggtgGccacagcctttcccctcccc	6	8	11	16	0	0	1	0	1	0	0	2	2	2	2	7	3	2	1	7	3	0	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr1:248813470G>A	ENST00000344889.3	-	1	715	c.716C>T	c.(715-717)gCc>gTc	p.A239V		NM_001001824.1	NP_001001824.1	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T, member 27	239						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)			GGAGCAGGTGGCCACAGCCTT	0.522																																					p.A239V		Atlas-SNP	.											.	OR2T27	52	.	0			c.C716T						PASS	.						48	32	38					1																	248813470		2184	4257	6441	SO:0001583	missense	403239	exon1			CAGGTGGCCACAG		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.716C>T	1.37:g.248813470G>A	ENSP00000342008:p.Ala239Val	84	0	0		91	27	0.296703	NM_001001824		Missense_Mutation	SNP	ENST00000344889.3	37	CCDS31124.1	.	.	.	.	.	.	.	.	.	.	.	12.87	2.068166	0.36470	.	.	ENSG00000187701	ENST00000344889	T	0.00115	8.71	3.42	3.42	0.39159	GPCR, rhodopsin-like superfamily (1);	0.186819	0.26099	N	0.026342	T	0.00241	0.0007	L	0.34521	1.04	0.21579	N	0.999634	P	0.49696	0.927	P	0.59825	0.864	T	0.65043	-0.6264	10	0.48119	T	0.1	.	14.1834	0.65588	0.0:0.0:1.0:0.0	.	239	Q8NH04	O2T27_HUMAN	V	239	ENSP00000342008:A239V	ENSP00000342008:A239V	A	-	2	0	OR2T27	246880093	0.863000	0.29885	0.984000	0.44739	0.113000	0.19764	1.636000	0.37144	1.921000	0.55644	0.400000	0.26472	GCC	.	.	none		0.522	OR2T27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097124.1	NM_001001824		A	248813470	G	A	248813470	3	1	29	1	0	0	0	0	1	0	0	0	11030	1203	42	2	240	2	OR2T27	1	248813470	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	243413	248813470	437151	89	12330											
TTC15	51112	hgsc.bcm.edu	37	chr2	3391458	3391458	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccgcacccccctcagctcGcgcctccggaggagcagggg	5	3	13	20	4	1	0	1	0	0	0	3	2	2	2	7	4	2	3	7	4	0	0	rs200941005	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:3391458G>A	ENST00000324266.5	+	2	259	c.64G>A	c.(64-66)Gcg>Acg	p.A22T	TRAPPC12_ENST00000382110.2_Missense_Mutation_p.A22T	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	22					vesicle-mediated transport (GO:0016192)												CCCTCAGCTCGCGCCTCCGGA	0.652													G|||	7	0.00139776	0.0008	0.0	5008	,	,		8905	0.0		0.004	False		,,,				2504	0.002				p.A22T		Atlas-SNP	.											.	.	.	.	0			c.G64A						PASS	.	G	THR/ALA	2,4368		0,2,2183	16	16	16		64	2.5	0	2		16	25,8533		0,25,4254	yes	missense	TTC15	NM_016030.5	58	0,27,6437	AA,AG,GG		0.2921,0.0458,0.2088	benign	22/736	3391458	27,12901	2185	4279	6464	SO:0001583	missense	51112	exon2			CAGCTCGCGCCTC	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.64G>A	2.37:g.3391458G>A	ENSP00000324318:p.Ala22Thr	43	0	0		46	34	0.73913	NM_016030	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Missense_Mutation	SNP	ENST00000324266.5	37	CCDS1652.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	8.692	0.907612	0.17833	4.58E-4	0.002921	ENSG00000171853	ENST00000382110;ENST00000324266	T;T	0.68025	-0.3;-0.3	4.34	2.46	0.29980	.	1.827870	0.02663	N	0.107730	T	0.41627	0.1167	L	0.29908	0.895	0.09310	N	1	B;P	0.42692	0.429;0.787	B;B	0.34418	0.019;0.182	T	0.38693	-0.9649	10	0.14656	T	0.56	.	5.7337	0.18055	0.1029:0.0:0.7068:0.1903	.	22;22	Q8WVT3;Q53S18	TPC12_HUMAN;.	T	22	ENSP00000371544:A22T;ENSP00000324318:A22T	ENSP00000324318:A22T	A	+	1	0	TTC15	3370465	0.027000	0.19231	0.000000	0.03702	0.001000	0.01503	1.104000	0.31074	0.524000	0.28502	0.563000	0.77884	GCG	G|0.998;A|0.002	0.002	strong		0.652	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030		A	3391458	G	A	3391458	3	1	29	1	0	0	0	0	1	0	0	0	16697	1087	38	1	66	1	TTC15	2	3391458	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10		3391458	239807915	90	12331											
IAH1	285148	hgsc.bcm.edu	37	chr2	9616161	9616161	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagcatcgctggctgacaggCtggtcaggtgagaatggttt	8	10	16	7	1	1	2	1	2	0	1	2	4	1	2	0	5	1	5	0	5	1	1	rs61732203	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:9616161C>G	ENST00000497473.1	+	2	164	c.127C>G	c.(127-129)Ctg>Gtg	p.L43V	IAH1_ENST00000545602.1_Intron|IAH1_ENST00000482918.1_5'UTR|IAH1_ENST00000489468.1_3'UTR|IAH1_ENST00000470914.1_Intron	NM_001039613.1	NP_001034702.1	Q2TAA2	IAH1_HUMAN	isoamyl acetate-hydrolyzing esterase 1 homolog (S. cerevisiae)	43					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)					GGCTGACAGGCTGGTCAGGTG	0.468													C|||	43	0.00858626	0.0015	0.0043	5008	,	,		19592	0.0		0.0348	False		,,,				2504	0.0031				p.L43V		Atlas-SNP	.											.	IAH1	12	.	0			c.C127G						PASS	.	C	VAL/LEU	11,3921		0,11,1955	104	105	104		127	5.8	1	2	dbSNP_129	104	218,8110		6,206,3952	yes	missense	IAH1	NM_001039613.1	32	6,217,5907	GG,GC,CC		2.6177,0.2798,1.8679	probably-damaging	43/249	9616161	229,12031	1966	4164	6130	SO:0001583	missense	285148	exon2			GACAGGCTGGTCA	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.127C>G	2.37:g.9616161C>G	ENSP00000417580:p.Leu43Val	170	0	0		179	178	0.994413	NM_001039613	B4DMV3	Missense_Mutation	SNP	ENST00000497473.1	37	CCDS42651.1	31	0.014194139194139194	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	27	0.03562005277044855	C	21.8	4.203472	0.79127	0.002798	0.026177	ENSG00000134330	ENST00000497473;ENST00000481688	T;T	0.25085	1.82;1.82	5.78	5.78	0.91487	Esterase, SGNH hydrolase-type (1);Esterase, SGNH hydrolase-type, subgroup (1);Lipase, GDSL (1);	0.000000	0.64402	U	0.000002	T	0.16214	0.0390	L	0.58428	1.81	0.80722	D	1	D	0.67145	0.996	D	0.66847	0.947	T	0.01786	-1.1274	10	0.72032	D	0.01	-0.4573	14.5371	0.67969	0.0:0.9301:0.0:0.0699	rs61732203	43	Q2TAA2	IAH1_HUMAN	V	43;18	ENSP00000417580:L43V;ENSP00000420532:L18V	ENSP00000420532:L18V	L	+	1	2	IAH1	9533612	0.993000	0.37304	0.981000	0.43875	0.980000	0.70556	3.057000	0.49931	2.894000	0.99253	0.591000	0.81541	CTG	C|0.982;G|0.018	0.018	strong		0.468	IAH1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353192.1	NM_001039613		G	9616161	C	G	9616161	3	3	29	1	0	0	0	0	1	0	0	0	7480	796	28	4	133	4	IAH1	2	9616161	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	6224703	9616161	233583212	91	12332											
MSGN1	343930	hgsc.bcm.edu	37	chr2	17998001	17998001	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggctgccctgtgagcacggCggggccagcagtgggggcag	5	4	21	11	2	0	1	0	1	0	0	0	1	0	1	2	6	3	4	2	6	0	0	rs201149255	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:17998001C>T	ENST00000281047.3	+	1	239	c.216C>T	c.(214-216)ggC>ggT	p.G72G		NM_001105569.1	NP_001099039.1	A6NI15	MSGN1_HUMAN	mesogenin 1	72					cell differentiation (GO:0030154)|segment specification (GO:0007379)|somitogenesis (GO:0001756)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			NS(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	11	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					GTGAGCACGGCGGGGCCAGCA	0.627													C|||	3	0.000599042	0.0	0.0	5008	,	,		17091	0.0		0.002	False		,,,				2504	0.001				p.G72G	Melanoma(127;325 1712 14802 40657 49130)	Atlas-SNP	.											MSGN1,NS,carcinoma,+1,1	MSGN1	39	1	0			c.C216T						PASS	.	C		4,3852		0,4,1924	39	46	44		216	-10.2	0	2		44	21,8207		0,21,4093	no	coding-synonymous	MSGN1	NM_001105569.1		0,25,6017	TT,TC,CC		0.2552,0.1037,0.2069		72/194	17998001	25,12059	1928	4114	6042	SO:0001819	synonymous_variant	343930	exon1			GCACGGCGGGGCC		CCDS42657.1	2p24.2	2007-07-23			ENSG00000151379	ENSG00000151379			14907	protein-coding gene	gene with protein product	"paraxial mesogenin"	612209				10837126	Standard	NM_001105569		Approved	pMesogenin1	uc010yjt.2	A6NI15	OTTHUMG00000159089	ENST00000281047.3:c.216C>T	2.37:g.17998001C>T		67	0	0		77	33	0.428571	NM_001105569		Silent	SNP	ENST00000281047.3	37	CCDS42657.1																																																																																			C|0.999;T|0.001	0.001	strong		0.627	MSGN1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353253.1	XM_292850		T	17998001	C	T	17998001	2	4	29	1	0	0	0	0	0	0	0	1	9878	755	27	1		1	MSGN1	2	17998001	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	8381840	17998001	225201372	92	12333											
NT5C1B	93034	hgsc.bcm.edu	37	chr2	18767638	18767638	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcgagagtctgtcttccgcAgtgatgattcttgtgatccc	6	14	10	11	2	3	4	0	3	3	1	6	5	5	4	2	0	0	1	2	0	0	3	rs147855918	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:18767638A>G	ENST00000359846.2	-	4	397	c.320T>C	c.(319-321)cTg>cCg	p.L107P	NT5C1B_ENST00000460052.1_5'UTR|NT5C1B-RDH14_ENST00000532967.1_Missense_Mutation_p.L107P|RNU6-1215P_ENST00000384441.1_RNA|NT5C1B_ENST00000304081.4_Missense_Mutation_p.L47P|NT5C1B_ENST00000600945.1_Missense_Mutation_p.L107P	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	107	Ser-rich.				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)				TGTCTTCCGCAGTGATGATTC	0.498													a|||	10	0.00199681	0.0008	0.0086	5008	,	,		19665	0.0		0.003	False		,,,				2504	0.0				p.L124P		Atlas-SNP	.											.	NT5C1B	72	.	0			c.T371C						PASS	.	G	PRO/LEU,PRO/LEU,PRO/LEU,PRO/LEU,PRO/LEU,PRO/LEU,PRO/LEU	6,4400	11.4+/-27.6	0,6,2197	109	96	100		320,269,371,320,140,320,140	1.9	0	2	dbSNP_134	100	54,8546	34.3+/-88.2	0,54,4246	yes	missense,missense,missense,missense,missense,missense,missense	NT5C1B,NT5C1B-RDH14	NM_001002006.2,NM_001199086.1,NM_001199087.1,NM_001199088.1,NM_001199103.1,NM_001199104.1,NM_033253.3	98,98,98,98,98,98,98	0,60,6443	GG,GA,AA		0.6279,0.1362,0.4613	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	107/611,90/594,124/628,107/613,47/651,107/603,47/551	18767638	60,12946	2203	4300	6503	SO:0001583	missense	93034	exon4			TTCCGCAGTGATG	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.320T>C	2.37:g.18767638A>G	ENSP00000352904:p.Leu107Pro	113	0	0		130	59	0.453846	NM_001199087	B5MCR0|B7ZVX7|Q53RX2|Q8N9W3|Q8NA26|Q96DU5|Q96KE6|Q96M25|Q96SA3	Missense_Mutation	SNP	ENST00000359846.2	37	CCDS33150.1	7	0.003205128205128205	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	2	0.002638522427440633	a	8.645	0.896775	0.17686	0.001362	0.006279	ENSG00000250741;ENSG00000250741;ENSG00000185013;ENSG00000185013;ENSG00000185013	ENST00000532967;ENST00000444297;ENST00000304081;ENST00000359846;ENST00000416783	D	0.91631	-2.88	4.23	1.86	0.25419	.	2.009920	0.02795	N	0.122481	D	0.86952	0.6057	L	0.27053	0.805	0.09310	N	0.999997	B;B;P;B;P;P;P;P	0.52692	0.001;0.0;0.828;0.001;0.736;0.892;0.924;0.955	B;B;B;B;B;P;B;P	0.50537	0.0;0.0;0.44;0.002;0.282;0.643;0.44;0.643	T	0.78656	-0.2119	10	0.49607	T	0.09	-11.0741	5.9108	0.19027	0.7916:0.0:0.2084:0.0	.	90;124;47;90;47;47;107;107	E7EXB7;B4DZ86;B4DXQ9;B4DXZ9;C9J2C7;Q96P26-2;Q96P26;Q96P26-4	.;.;.;.;.;.;5NT1B_HUMAN;.	P	107;47;47;107;124	ENSP00000412639:L47P	ENSP00000305979:L47P	L	-	2	0	NT5C1B-RDH14;NT5C1B	18631119	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.628000	0.24522	0.431000	0.26258	-0.253000	0.11424	CTG	A|0.997;G|0.003	0.003	strong		0.498	NT5C1B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323822.1			G	18767638	A	G	18767638	3	3	29	1	0	0	0	0	1	0	0	0	10695	188	7	3	1540	3	NT5C1B	2	18767638	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	769637	18767638	224431735	93	12334											
SF3B14	51639	hgsc.bcm.edu	37	chr2	24291323	24291323	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gttcctctagtttcaggtgtGttccccctggagaggtaagt	6	14	12	9	0	2	1	1	0	1	1	4	2	4	1	3	3	0	4	3	3	2	5	rs41281479	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:24291323G>A	ENST00000233468.4	-	3	369	c.156C>T	c.(154-156)aaC>aaT	p.N52N		NM_016047.3	NP_057131.1														NS(1)|kidney(1)|large_intestine(1)|lung(1)	4	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTTCAGGTGTGTTCCCCCTGG	0.378													G|||	3	0.000599042	0.0	0.0	5008	,	,		16944	0.0		0.003	False		,,,				2504	0.0				p.N52N		Atlas-SNP	.											.	SF3B14	6	.	0			c.C156T						PASS	.	G		9,4397	15.5+/-35.6	0,9,2194	135	124	128		156	3.2	1	2	dbSNP_127	128	64,8536	39.3+/-95.6	1,62,4237	no	coding-synonymous	SF3B14	NM_016047.3		1,71,6431	AA,AG,GG		0.7442,0.2043,0.5613		52/126	24291323	73,12933	2203	4300	6503	SO:0001819	synonymous_variant	0	exon3			AGGTGTGTTCCCC																												ENST00000233468.4:c.156C>T	2.37:g.24291323G>A		110	0	0		100	49	0.49	NM_016047		Silent	SNP	ENST00000233468.4	37	CCDS1707.1																																																																																			G|0.997;A|0.003	0.003	strong		0.378	SF3B14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246826.1			A	24291323	G	A	24291323	2	1	29	1	0	0	0	0	0	0	0	1	14165	1368	48	2		2	SF3B14	2	24291323	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	5523685	24291323	218908050	94	12335											
DTNB	1838	hgsc.bcm.edu	37	chr2	25611102	25611102	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcctcctgcacgtctcccccGactccgctcagcgagtcctg	4	8	9	20	4	2	0	1	0	1	0	6	2	5	0	6	0	2	2	6	0	0	0	rs200383554	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:25611102G>A	ENST00000406818.3	-	17	1953	c.1704C>T	c.(1702-1704)gtC>gtT	p.V568V	DTNB_ENST00000496972.2_Silent_p.V504V|DTNB_ENST00000405222.1_Silent_p.V531V|DTNB_ENST00000404103.3_Silent_p.V568V|DTNB_ENST00000545439.1_Silent_p.V357V|DTNB_ENST00000407186.1_Silent_p.V531V|DTNB_ENST00000407661.3_Silent_p.V568V|DTNB_ENST00000407038.3_Silent_p.V538V|DTNB_ENST00000288642.8_Silent_p.V568V	NM_001256303.1|NM_021907.4	NP_001243232.1|NP_068707.1	O60941	DTNB_HUMAN	dystrobrevin, beta	568						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)					CGTCTCCCCCGACTCCGCTCA	0.652													G|||	4	0.000798722	0.0008	0.0	5008	,	,		16368	0.0		0.002	False		,,,				2504	0.001				p.V568V		Atlas-SNP	.											.	DTNB	43	.	0			c.C1704T						PASS	.	G	,,,,	5,3975		0,5,1985	18	22	21		1704,1704,1614,1704,1593	-3.3	0.5	2		21	42,8304		0,42,4131	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DTNB	NM_021907.3,NM_033147.2,NM_033148.2,NM_183360.1,NM_183361.1	,,,,	0,47,6116	AA,AG,GG		0.5032,0.1256,0.3813	,,,,	568/628,568/598,538/568,568/610,531/561	25611102	47,12279	1990	4173	6163	SO:0001819	synonymous_variant	1838	exon17			TCCCCCGACTCCG	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.1704C>T	2.37:g.25611102G>A		45	0	0		36	22	0.611111	NM_021907	B7Z733|F5GZG4|G5E9F6|O43782|O60881|O75538|Q86VR4|Q96AW0|Q9UE14|Q9UE15|Q9UE16	Silent	SNP	ENST00000406818.3	37	CCDS46237.1																																																																																			G|1.000;A|0.000	0.000	strong		0.652	DTNB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325361.1	NM_033147		A	25611102	G	A	25611102	2	1	29	1	0	0	0	0	0	0	0	1	4791	1045	37	1		1	DTNB	2	25611102	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1319779	25611102	217588271	95	12336											
DPYSL5	56896	hgsc.bcm.edu	37	chr2	27121394	27121394	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gccaactcagccagcgtgagGatcctcatcaagggaggcaa	12	5	12	12	1	3	1	3	1	0	0	4	3	4	3	3	3	3	1	3	3	3	0	rs79644076	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:27121394G>A	ENST00000288699.6	+	2	185	c.27G>A	c.(25-27)agG>agA	p.R9R	DPYSL5_ENST00000401478.1_Silent_p.R9R	NM_001253724.1|NM_020134.3	NP_001240653.1|NP_064519.2	Q9BPU6	DPYL5_HUMAN	dihydropyrimidinase-like 5	9					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)					CCAGCGTGAGGATCCTCATCA	0.547													G|||	7	0.00139776	0.0	0.0014	5008	,	,		23911	0.0		0.005	False		,,,				2504	0.001				p.R9R		Atlas-SNP	.											.	DPYSL5	69	.	0			c.G27A						PASS	.	G		10,4396	16.8+/-37.8	0,10,2193	218	196	203		27	4.6	1	2	dbSNP_132	203	75,8525	44.9+/-103.4	0,75,4225	no	coding-synonymous	DPYSL5	NM_020134.3		0,85,6418	AA,AG,GG		0.8721,0.227,0.6535		9/565	27121394	85,12921	2203	4300	6503	SO:0001819	synonymous_variant	56896	exon2			CGTGAGGATCCTC	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.27G>A	2.37:g.27121394G>A		213	1	0.00469484		223	110	0.493274	NM_001253724	Q8TCL6|Q9NQC4|Q9NRY9	Silent	SNP	ENST00000288699.6	37	CCDS1730.1																																																																																			G|0.995;A|0.005	0.005	strong		0.547	DPYSL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214187.2	NM_020134		A	27121394	G	A	27121394	2	1	29	1	0	0	0	0	0	0	0	1	4752	1165	41	2		2	DPYSL5	2	27121394	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1510292	27121394	216077979	96	12337											
C2orf53	339779	hgsc.bcm.edu	37	chr2	27360773	27360773	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggtgggaaggggactggcaaGgtgagtggggaagggaggag	10	4	25	2	0	0	1	0	1	0	0	0	6	0	6	0	10	0	1	0	10	3	0	rs61741796	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:27360773G>A	ENST00000335524.3	-	3	950	c.425C>T	c.(424-426)cCt>cTt	p.P142L		NM_178553.3	NP_848648.2	Q53SZ7	PRR30_HUMAN		142	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)					ggactggcaaggtgagtgggg	0.612													g|||	11	0.00219649	0.0	0.0014	5008	,	,		15255	0.0		0.0089	False		,,,				2504	0.001				p.P142L		Atlas-SNP	.											.	C2orf53	45	.	0			c.C425T						PASS	.		LEU/PRO	13,4393	17.9+/-39.9	0,13,2190	37	39	38		425	-9.5	0	2	dbSNP_129	38	92,8508	49.8+/-109.6	0,92,4208	yes	missense	C2orf53	NM_178553.3	98	0,105,6398	AA,AG,GG		1.0698,0.2951,0.8073	benign	142/413	27360773	105,12901	2203	4300	6503	SO:0001583	missense	339779	exon3			TGGCAAGGTGAGT																												ENST00000335524.3:c.425C>T	2.37:g.27360773G>A	ENSP00000335017:p.Pro142Leu	47	0	0		43	20	0.465116	NM_178553	Q86UE2	Missense_Mutation	SNP	ENST00000335524.3	37	CCDS1739.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	g	8.874	0.949947	0.18431	0.002951	0.010698	ENSG00000186143	ENST00000335524	T	0.30182	1.54	4.75	-9.51	0.00581	.	2.854260	0.01695	N	0.026858	T	0.10852	0.0265	N	0.14661	0.345	0.09310	N	1	B	0.29037	0.231	B	0.25405	0.06	T	0.08700	-1.0709	10	0.36615	T	0.2	3.6732	8.0189	0.30398	0.0677:0.1111:0.5291:0.2922	.	142	Q53SZ7	CB053_HUMAN	L	142	ENSP00000335017:P142L	ENSP00000335017:P142L	P	-	2	0	C2orf53	27214277	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-2.954000	0.00676	-2.979000	0.00283	-0.271000	0.10264	CCT	G|0.993;A|0.007	0.007	strong		0.612	C2orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250188.1			A	27360773	G	A	27360773	3	1	29	1	0	0	0	0	1	0	0	0	2176	1000	35	2	817	2	C2orf53	2	27360773	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	239379	27360773	215838600	97	12338											
ALK	238	hgsc.bcm.edu	37	chr2	29449819	29449819	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acgccatcctcagccagcacCgtcccgtggtcacagaagca	10	5	9	17	3	2	1	2	0	0	1	4	1	4	1	5	1	3	2	5	1	1	0	rs2293563	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:29449819C>T	ENST00000389048.3	-	18	3942	c.3036G>A	c.(3034-3036)acG>acA	p.T1012T	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1012			T -> M (in dbSNP:rs35073634). {ECO:0000269|PubMed:17344846}.		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)	p.T1012T(1)	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)	CAGCCAGCACCGTCCCGTGGT	0.542			"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				C|||	851	0.169928	0.2277	0.147	5008	,	,		21422	0.119		0.1928	False		,,,				2504	0.137				p.T1012T		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	ALK,NS,carcinoma,0,1	ALK	533	1	1	Substitution - coding silent(1)	stomach(1)	c.G3036A						PASS	.	C		974,3432	366.4+/-317.8	105,764,1334	202	180	187		3036	-10.8	0.1	2	dbSNP_100	187	1492,7108	283.2+/-296.0	137,1218,2945	no	coding-synonymous	ALK	NM_004304.4		242,1982,4279	TT,TC,CC		17.3488,22.1062,18.9605		1012/1621	29449819	2466,10540	2203	4300	6503	SO:0001819	synonymous_variant	238	exon18	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	CAGCACCGTCCCG	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.3036G>A	2.37:g.29449819C>T		126	0	0		119	60	0.504202	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			C|0.816;T|0.184	0.184	strong		0.542	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		T	29449819	C	T	29449819	2	4	29	1	0	0	0	0	0	0	0	1	525	639	23	1		1	ALK	2	29449819	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2089046	29449819	213749554	98	12339											
ALK	238	hgsc.bcm.edu	37	chr2	29543736	29543736	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaagttgcagtaaaaacccAcaggcagtttccctatggag	14	8	9	10	0	0	0	0	0	0	0	1	1	1	1	2	2	2	5	2	2	5	4	rs35093491	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:29543736A>G	ENST00000389048.3	-	7	2333	c.1427T>C	c.(1426-1428)gTg>gCg	p.V476A	ALK_ENST00000498037.1_5'Flank|ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	476			V -> A (in dbSNP:rs35093491). {ECO:0000269|PubMed:17344846}.		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)	GTAAAAACCCACAGGCAGTTT	0.512			"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				A|||	80	0.0159744	0.0008	0.0216	5008	,	,		20583	0.0		0.0427	False		,,,				2504	0.0215				p.V476A		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	.	ALK	533	.	0			c.T1427C						PASS	.	A	ALA/VAL	30,4376	35.2+/-66.4	0,30,2173	165	152	156		1427	3	0.9	2	dbSNP_126	156	326,8274	114.6+/-174.5	4,318,3978	yes	missense	ALK	NM_004304.4	64	4,348,6151	GG,GA,AA		3.7907,0.6809,2.7372	benign	476/1621	29543736	356,12650	2203	4300	6503	SO:0001583	missense	238	exon7	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	AAACCCACAGGCA	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.1427T>C	2.37:g.29543736A>G	ENSP00000373700:p.Val476Ala	80	0	0		97	48	0.494845	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	ENST00000389048.3	37	CCDS33172.1	35	0.016025641025641024	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	28	0.036939313984168866	A	1.964	-0.438159	0.04636	0.006809	0.037907	ENSG00000171094	ENST00000389048	T	0.01933	4.55	5.87	2.96	0.34315	Concanavalin A-like lectin/glucanase (1);	0.461885	0.18118	N	0.151131	T	0.00356	0.0011	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.57573	-0.7788	9	.	.	.	.	6.3805	0.21531	0.1514:0.0:0.7015:0.1471	rs35093491;rs61744478	476	Q9UM73	ALK_HUMAN	A	476	ENSP00000373700:V476A	.	V	-	2	0	ALK	29397240	0.990000	0.36364	0.947000	0.38551	0.008000	0.06430	0.866000	0.27954	0.451000	0.26802	-0.177000	0.13119	GTG	A|0.973;G|0.027	0.027	strong		0.512	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		G	29543736	A	G	29543736	3	3	29	1	0	0	0	0	1	0	0	0	525	159	6	3	3527	3	ALK	2	29543736	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	93917	29543736	213655637	99	12340											
BIRC6	57448	hgsc.bcm.edu	37	chr2	32774473	32774473	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ggcagaacagtaatgcccttCcttctgtacttctcgagctt	8	13	8	12	1	2	1	0	0	2	1	4	2	3	1	2	1	4	4	2	1	3	6			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:32774473C>T	ENST00000421745.2	+	65	13203	c.13069C>T	c.(13069-13071)Cct>Tct	p.P4357S		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	4357					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)					TAATGCCCTTCCTTCTGTACT	0.438																																					p.P4357S	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.C13069T						PASS	.						165	148	154					2																	32774473		2203	4300	6503	SO:0001583	missense	57448	exon65			GCCCTTCCTTCTG	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.13069C>T	2.37:g.32774473C>T	ENSP00000393596:p.Pro4357Ser	237	0	0		258	72	0.27907	NM_016252	Q9ULD1	Missense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	C	16.37	3.105423	0.56291	.	.	ENSG00000115760	ENST00000421745	T	0.75821	-0.97	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	D	0.84986	0.5594	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.85486	0.1182	10	0.72032	D	0.01	.	19.7806	0.96414	0.0:1.0:0.0:0.0	.	4357	Q9NR09	BIRC6_HUMAN	S	4357	ENSP00000393596:P4357S	ENSP00000393596:P4357S	P	+	1	0	BIRC6	32627977	1.000000	0.71417	0.982000	0.44146	0.060000	0.15804	7.818000	0.86416	2.669000	0.90835	0.650000	0.86243	CCT	.	.	none		0.438	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		T	32774473	C	T	32774473	3	4	29	1	0	0	0	0	1	0	0	0	1438	855	30	2	13327	2	BIRC6	2	32774473	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	3230737	32774473	210424900	100	12341											
LTBP1	4052	hgsc.bcm.edu	37	chr2	33172827	33172827	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgcgctccaaggtgccgcagGagacccagagcggcggaggc	8	3	17	13	4	0	2	0	0	0	2	1	4	1	3	3	5	3	2	3	5	1	0	rs147166401	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:33172827G>A	ENST00000404816.2	+	1	789	c.436G>A	c.(436-438)Gag>Aag	p.E146K	Y_RNA_ENST00000384224.1_RNA|LTBP1_ENST00000354476.3_Missense_Mutation_p.E146K			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	146					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)				GGTGCCGCAGGAGACCCAGAG	0.721													G|||	19	0.00379393	0.0	0.0058	5008	,	,		8786	0.0		0.0089	False		,,,				2504	0.0061				p.E146K		Atlas-SNP	.											.	LTBP1	317	.	0			c.G436A						PASS	.	G	LYS/GLU	11,3139		0,11,1564	9	9	9		436	2.6	0.1	2	dbSNP_134	9	94,5748		1,92,2828	yes	missense	LTBP1	NM_206943.2	56	1,103,4392	AA,AG,GG		1.609,0.3492,1.1677	benign	146/1722	33172827	105,8887	1575	2921	4496	SO:0001583	missense	4052	exon1			CCGCAGGAGACCC		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.436G>A	2.37:g.33172827G>A	ENSP00000386043:p.Glu146Lys	84	0	0		67	39	0.58209	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	37	CCDS33177.2	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	13.22	2.172646	0.38413	0.003492	0.01609	ENSG00000049323	ENST00000404816;ENST00000354476	T;T	0.80909	-1.43;-1.41	4.59	2.64	0.31445	.	.	.	.	.	T	0.47728	0.1461	N	0.14661	0.345	0.19575	N	0.999965	B	0.15473	0.013	B	0.19391	0.025	T	0.43032	-0.9416	9	0.25106	T	0.35	.	7.6966	0.28598	0.089:0.2885:0.6225:0.0	.	146	Q14766-4	.	K	146	ENSP00000386043:E146K;ENSP00000346467:E146K	ENSP00000346467:E146K	E	+	1	0	LTBP1	33026331	0.999000	0.42202	0.068000	0.19968	0.979000	0.70002	2.030000	0.41108	0.919000	0.36945	0.561000	0.74099	GAG	G|0.992;A|0.008	0.008	strong		0.721	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943		A	33172827	G	A	33172827	3	1	29	1	0	0	0	0	1	0	0	0	9082	1175	41	2	438	2	LTBP1	2	33172827	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	398354	33172827	210026546	101	12342											
FEZ2	9637	hgsc.bcm.edu	37	chr2	36818109	36818109	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtatgcgatgacttccagtcTacaggcatcacattcccata	11	11	7	12	1	2	1	1	1	1	0	4	2	4	1	2	1	2	2	2	1	3	5	rs117617575	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:36818109T>C	ENST00000405912.3	-	2	311	c.312A>G	c.(310-312)gtA>gtG	p.V104V	FEZ2_ENST00000305852.7_5'UTR|FEZ2_ENST00000379245.4_Silent_p.V104V	NM_005102.2	NP_005093.2	Q9UHY8	FEZ2_HUMAN	fasciculation and elongation protein zeta 2 (zygin II)	104					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)				ACTTCCAGTCTACAGGCATCA	0.368													T|||	3	0.000599042	0.0008	0.0	5008	,	,		21313	0.001		0.001	False		,,,				2504	0.0				p.V104V		Atlas-SNP	.											.	FEZ2	13	.	0			c.A312G						PASS	.	T	,	3,3759		0,3,1878	125	113	117		312,312	-9.1	1	2	dbSNP_132	117	41,8165		0,41,4062	no	coding-synonymous,coding-synonymous	FEZ2	NM_001042548.1,NM_005102.2	,	0,44,5940	CC,CT,TT		0.4996,0.0797,0.3676	,	104/381,104/354	36818109	44,11924	1881	4103	5984	SO:0001819	synonymous_variant	9637	exon2			CCAGTCTACAGGC	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.312A>G	2.37:g.36818109T>C		176	0	0		197	92	0.467005	NM_001042548	Q5EBN3|Q76LN0|Q99690	Silent	SNP	ENST00000405912.3	37	CCDS46257.1																																																																																			T|0.998;C|0.002	0.002	strong		0.368	FEZ2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325432.1			C	36818109	T	C	36818109	2	2	29	1	0	0	0	0	0	0	0	1	5832	1509	53	3		3	FEZ2	2	36818109	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	3645282	36818109	206381264	102	12343											
ATL2	64225	hgsc.bcm.edu	37	chr2	38537579	38537579	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctgaagctcttcatgttgaTtttgttttacctgagggcgg	6	17	11	7	1	3	3	1	3	2	0	3	3	3	3	1	2	2	3	1	2	2	6	rs34873284	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:38537579T>C	ENST00000378954.4	-	8	816	c.815A>G	c.(814-816)aAt>aGt	p.N272S	ATL2_ENST00000419554.2_Missense_Mutation_p.N272S|ATL2_ENST00000539122.1_Missense_Mutation_p.N101S|ATL2_ENST00000402054.1_Missense_Mutation_p.N101S|ATL2_ENST00000452935.2_Missense_Mutation_p.N254S|ATL2_ENST00000406122.1_Missense_Mutation_p.N101S|ATL2_ENST00000546051.1_Missense_Mutation_p.N101S|ATL2_ENST00000332337.4_Missense_Mutation_p.N254S	NM_001135673.1|NM_022374.2	NP_001129145.1|NP_071769.2	Q8NHH9	ATLA2_HUMAN	atlastin GTPase 2	272	GB1/RHD3-type G.		N -> S (in dbSNP:rs34873284).		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						TTCATGTTGATTTTGTTTTAC	0.383													T|||	72	0.014377	0.0045	0.0216	5008	,	,		17843	0.0		0.0398	False		,,,				2504	0.0112				p.N272S		Atlas-SNP	.											.	ATL2	49	.	0			c.A815G						PASS	.	T	SER/ASN,SER/ASN	48,4358	48.9+/-83.8	1,46,2156	133	118	123		815,815	5.1	1	2	dbSNP_126	123	420,8180	130.8+/-188.7	10,400,3890	yes	missense,missense	ATL2	NM_001135673.1,NM_022374.2	46,46	11,446,6046	CC,CT,TT		4.8837,1.0894,3.5983	benign,benign	272/584,272/580	38537579	468,12538	2203	4300	6503	SO:0001583	missense	64225	exon8			TGTTGATTTTGTT		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.815A>G	2.37:g.38537579T>C	ENSP00000368237:p.Asn272Ser	107	0	0		97	58	0.597938	NM_001135673	B7Z1X2|B7Z7X8|Q4ZG30|Q7Z630|Q8NHH8|Q9H5M7	Missense_Mutation	SNP	ENST00000378954.4	37	CCDS46260.1	40|40	0.018315018315018316|0.018315018315018316	4|4	0.008130081300813009|0.008130081300813009	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	31|31	0.040897097625329816|0.040897097625329816	T|T	15.82|15.82	2.945674|2.945674	0.53079|0.53079	0.010894|0.010894	0.048837|0.048837	ENSG00000119787|ENSG00000119787	ENST00000443098|ENST00000378954;ENST00000406122;ENST00000402054;ENST00000539122;ENST00000332337;ENST00000419554;ENST00000452935;ENST00000546051;ENST00000449130	.|T;T;T;T;T;T;T;T;T	.|0.74421	.|-0.84;-0.84;-0.84;-0.84;-0.84;-0.84;-0.84;-0.84;-0.84	5.11|5.11	5.11|5.11	0.69529|0.69529	.|Guanylate-binding protein, N-terminal (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.28764|0.28764	0.0713|0.0713	L|L	0.47078|0.47078	1.49|1.49	0.80722|0.80722	D|D	1|1	.|B;B;B;B;B	.|0.17268	.|0.021;0.001;0.003;0.005;0.001	.|B;B;B;B;B	.|0.11329	.|0.006;0.001;0.001;0.002;0.002	T|T	0.53542|0.53542	-0.8424|-0.8424	5|10	.|0.44086	.|T	.|0.13	-21.5939|-21.5939	14.0983|14.0983	0.65037|0.65037	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs34873284;rs61754250|rs34873284;rs61754250	.|101;254;254;272;272	.|B5MCN0;B7Z7X8;Q8NHH9-4;Q8NHH9-2;Q8NHH9	.|.;.;.;.;ATLA2_HUMAN	V|S	191|272;101;101;101;254;272;254;101;90	.|ENSP00000368237:N272S;ENSP00000385446:N101S;ENSP00000384062:N101S;ENSP00000446192:N101S;ENSP00000333393:N254S;ENSP00000415336:N272S;ENSP00000390743:N254S;ENSP00000438938:N101S;ENSP00000409811:N90S	.|ENSP00000333393:N254S	I|N	-|-	1|2	0|0	ATL2|ATL2	38391083|38391083	1.000000|1.000000	0.71417|0.71417	0.973000|0.973000	0.42090|0.42090	0.982000|0.982000	0.71751|0.71751	6.134000|6.134000	0.71689|0.71689	1.917000|1.917000	0.55516|0.55516	0.455000|0.455000	0.32223|0.32223	ATC|AAT	T|0.967;C|0.033	0.033	strong		0.383	ATL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219886.2	NM_022374		C	38537579	T	C	38537579	3	2	29	1	0	0	0	0	1	0	0	0	1107	1493	52	3	1072	3	ATL2	2	38537579	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	1719470	38537579	204661794	103	12344											
DHX57	90957	hgsc.bcm.edu	37	chr2	39090515	39090515	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caatttactcagatccagcaTcagcatcttgttcttgcagg	10	13	7	11	0	4	1	2	0	2	1	5	1	5	1	1	1	4	4	1	1	2	5	rs199537184		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:39090515T>G	ENST00000295373.6	-	3	497	c.371A>C	c.(370-372)gAt>gCt	p.D124A	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	124							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)				AGATCCAGCATCAGCATCTTG	0.398																																					p.D124A	Melanoma(191;1090 2095 4375 23729 47341)	Atlas-SNP	.											.	DHX57	127	.	0			c.A371C						PASS	.	T	ALA/ASP	0,4406		0,0,2203	119	116	117		371	5.7	1	2		117	2,8598	2.2+/-6.3	0,2,4298	yes	missense	DHX57	NM_198963.1	126	0,2,6501	GG,GT,TT		0.0233,0.0,0.0154	benign	124/1387	39090515	2,13004	2203	4300	6503	SO:0001583	missense	90957	exon3			CCAGCATCAGCAT	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.371A>C	2.37:g.39090515T>G	ENSP00000295373:p.Asp124Ala	46	0	0		58	30	0.517241	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Missense_Mutation	SNP	ENST00000295373.6	37	CCDS1800.1	.	.	.	.	.	.	.	.	.	.	T	14.13	2.443869	0.43429	0.0	2.33E-4	ENSG00000163214	ENST00000295373;ENST00000355320;ENST00000417233	T	0.02812	4.15	5.68	5.68	0.88126	.	0.107041	0.41294	D	0.000916	T	0.02380	0.0073	N	0.19112	0.55	0.41499	D	0.988279	B;B	0.28350	0.208;0.012	B;B	0.22152	0.038;0.006	T	0.60786	-0.7194	10	0.22706	T	0.39	.	12.2022	0.54333	0.0:0.0:0.1822:0.8178	.	124;124	Q6P158-2;Q6P158	.;DHX57_HUMAN	A	124;22;22	ENSP00000295373:D124A	ENSP00000295373:D124A	D	-	2	0	DHX57	38944019	1.000000	0.71417	0.994000	0.49952	0.990000	0.78478	5.043000	0.64208	2.156000	0.67533	0.459000	0.35465	GAT	.	.	weak		0.398	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646		G	39090515	T	G	39090515	3	3	29	1	0	0	0	0	1	0	0	0	4515	1435	50	5	3877	5	DHX57	2	39090515	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	552936	39090515	204108858	104	12345											
ABCG8	64241	hgsc.bcm.edu	37	chr2	44073405	44073405	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgggcatccagaacctaagcTtcaaagtgagaagtgggcag	13	7	13	8	0	1	2	1	1	0	2	2	3	2	2	2	2	2	3	2	2	4	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:44073405T>C	ENST00000272286.2	+	3	367	c.277T>C	c.(277-279)Ttc>Ctc	p.F93L		NM_022437.2	NP_071882.1	Q9H221	ABCG8_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 8	93	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)|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)	GAACCTAAGCTTCAAAGTGAG	0.532																																					p.F93L		Atlas-SNP	.											.	ABCG8	98	.	0			c.T277C						PASS	.						72	68	69					2																	44073405		2203	4300	6503	SO:0001583	missense	64241	exon3			CTAAGCTTCAAAG	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.277T>C	2.37:g.44073405T>C	ENSP00000272286:p.Phe93Leu	115	0	0		109	26	0.238532	NM_022437	Q53QN8	Missense_Mutation	SNP	ENST00000272286.2	37	CCDS1815.1	.	.	.	.	.	.	.	.	.	.	T	0.949	-0.707002	0.03230	.	.	ENSG00000143921	ENST00000272286	D	0.92805	-3.11	5.69	4.34	0.51931	ABC transporter-like (1);	0.256767	0.41712	N	0.000831	T	0.80586	0.4651	N	0.16602	0.42	0.37015	D	0.895938	B;B	0.09022	0.002;0.001	B;B	0.11329	0.006;0.003	T	0.72381	-0.4311	10	0.02654	T	1	.	7.4098	0.27011	0.0:0.1238:0.134:0.7422	.	93;93	Q9H221-2;Q9H221	.;ABCG8_HUMAN	L	93	ENSP00000272286:F93L	ENSP00000272286:F93L	F	+	1	0	ABCG8	43926909	1.000000	0.71417	1.000000	0.80357	0.228000	0.25075	2.243000	0.43115	2.168000	0.68352	0.528000	0.53228	TTC	.	.	none		0.532	ABCG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250671.1	NM_022437		C	44073405	T	C	44073405	3	2	29	1	0	0	0	0	1	0	0	0	72	1609	56	3	287	3	ABCG8	2	44073405	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	4982890	44073405	199125968	105	12346											
NRXN1	9378	hgsc.bcm.edu	37	chr2	51255307	51255307	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcgtccattggccctcggcGcccggaaactccagcccgct	5	6	11	19	6	0	0	0	0	0	0	3	1	2	1	5	3	2	1	5	3	1	1	rs55640811		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:51255307G>T	ENST00000406316.2	-	2	1581	c.105C>A	c.(103-105)ggC>ggA	p.G35G	NRXN1_ENST00000405581.1_Silent_p.G35G|NRXN1_ENST00000405472.3_Silent_p.G35G|NRXN1_ENST00000406859.3_Silent_p.G35G|NRXN1_ENST00000404971.1_Silent_p.G35G|NRXN1_ENST00000402717.3_Silent_p.G35G|NRXN1_ENST00000401669.2_Silent_p.G35G	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	35	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)			GGCCCTCGGCGCCCGGAAACT	0.692																																					p.G35G		Atlas-SNP	.											.	NRXN1	1118	.	0			c.C105A						PASS	.	G	,	2,3844		0,2,1921	5	7	7		105,105	-1	1	2	dbSNP_129	7	8,8162		0,8,4077	no	coding-synonymous,coding-synonymous	NRXN1	NM_001135659.1,NM_004801.4	,	0,10,5998	TT,TG,GG		0.0979,0.052,0.0832	,	35/1548,35/1478	51255307	10,12006	1923	4085	6008	SO:0001819	synonymous_variant	9378	exon2			CTCGGCGCCCGGA	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.105C>A	2.37:g.51255307G>T		37	0	0		38	22	0.578947	NM_004801	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	37	CCDS54360.1																																																																																			.	.	weak		0.692	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			T	51255307	G	T	51255307	2	4	29	1	0	0	0	0	0	0	0	1	10674	1074	38	4		4	NRXN1	2	51255307	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	7181902	51255307	191944066	106	12347											
PSME4	23198	hgsc.bcm.edu	37	chr2	54161756	54161756	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaaaccatcatggcggtgaTccatattacagcatgtccta	13	10	7	11	1	1	1	1	1	0	0	3	1	3	1	3	2	3	1	3	2	4	3	rs146618010		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:54161756T>C	ENST00000404125.1	-	8	998	c.943A>G	c.(943-945)Atc>Gtc	p.I315V	PSME4_ENST00000421748.2_Intron	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	315					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)			ATGGCGGTGATCCATATTACA	0.363																																					p.I315V		Atlas-SNP	.											.	PSME4	247	.	0			c.A943G						PASS	.	T	VAL/ILE	0,4406		0,0,2203	101	101	101		943	4.5	1	2	dbSNP_134	101	1,8599	1.2+/-3.3	0,1,4299	yes	missense	PSME4	NM_014614.2	29	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	benign	315/1844	54161756	1,13005	2203	4300	6503	SO:0001583	missense	23198	exon8			CGGTGATCCATAT	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.943A>G	2.37:g.54161756T>C	ENSP00000384211:p.Ile315Val	65	0	0		53	22	0.415094	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Missense_Mutation	SNP	ENST00000404125.1	37	CCDS33197.2	.	.	.	.	.	.	.	.	.	.	T	13.72	2.322036	0.41096	0.0	1.16E-4	ENSG00000068878	ENST00000404125	T	0.06294	3.32	5.64	4.49	0.54785	.	0.051963	0.85682	D	0.000000	T	0.09686	0.0238	M	0.73217	2.22	0.80722	D	1	B	0.30542	0.284	B	0.31290	0.127	T	0.08432	-1.0722	10	0.24483	T	0.36	.	11.5732	0.50845	0.0:0.0697:0.0:0.9303	.	315	Q14997	PSME4_HUMAN	V	315	ENSP00000384211:I315V	ENSP00000374643:I315V	I	-	1	0	PSME4	54015260	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	2.789000	0.47813	1.078000	0.41014	0.482000	0.46254	ATC	T|1.000;C|0.000	0.000	weak		0.363	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		C	54161756	T	C	54161756	3	2	29	1	0	0	0	0	1	0	0	0	12721	1435	50	3	4744	3	PSME4	2	54161756	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	2906449	54161756	189037617	107	12348											
PSME4	23198	hgsc.bcm.edu	37	chr2	54176359	54176359	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aattgataccagctcatacaAtaacttaataaaaagaacat	21	10	3	7	0	1	2	1	1	0	1	1	2	1	2	1	0	5	1	1	0	10	6			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:54176359A>G	ENST00000404125.1	-	2	359	c.304T>C	c.(304-306)Ttg>Ctg	p.L102L	PSME4_ENST00000421748.2_Intron	NM_014614.2	NP_055429.2	Q14997	PSME4_HUMAN	proteasome (prosome, macropain) activator subunit 4	102					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)			AGCTCATACAATAACTTAATA	0.328																																					p.L102L		Atlas-SNP	.											.	PSME4	247	.	0			c.T304C						PASS	.						67	68	67					2																	54176359		2203	4300	6503	SO:0001819	synonymous_variant	23198	exon2			CATACAATAACTT	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.304T>C	2.37:g.54176359A>G		59	0	0		74	23	0.310811	NM_014614	Q1XBG4|Q1XBG5|Q1XBG6|Q2M1Z0|Q6IPR2|Q86XF8	Silent	SNP	ENST00000404125.1	37	CCDS33197.2																																																																																			.	.	none		0.328	PSME4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324163.1	XM_040158		G	54176359	A	G	54176359	2	3	29	1	0	0	0	0	0	0	0	1	12721	98	4	3		3	PSME4	2	54176359	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	14603	54176359	189023014	108	12349											
CCDC85A	114800	hgsc.bcm.edu	37	chr2	56603044	56603044	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	atgccacaccttcccagcagCctgaacctgtggtacattct	9	10	7	15	0	1	1	0	1	1	0	2	1	2	1	5	1	5	2	5	1	2	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:56603044C>T	ENST00000407595.2	+	5	2048	c.1546C>T	c.(1546-1548)Cct>Tct	p.P516S	RP11-482H16.1_ENST00000607540.1_RNA	NM_001080433.1	NP_001073902.1	Q96PX6	CC85A_HUMAN	coiled-coil domain containing 85A	516										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)			TTCCCAGCAGCCTGAACCTGT	0.488																																					p.P516S		Atlas-SNP	.											.	CCDC85A	70	.	0			c.C1546T						PASS	.						85	85	85					2																	56603044		2041	4187	6228	SO:0001583	missense	114800	exon5			CAGCAGCCTGAAC	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.1546C>T	2.37:g.56603044C>T	ENSP00000384040:p.Pro516Ser	177	0	0		189	45	0.238095	NM_001080433		Missense_Mutation	SNP	ENST00000407595.2	37	CCDS46290.1	.	.	.	.	.	.	.	.	.	.	C	13.34	2.207790	0.39003	.	.	ENSG00000055813	ENST00000407595;ENST00000407862	.	.	.	5.15	5.15	0.70609	.	0.143817	0.32093	N	0.006595	T	0.35038	0.0918	N	0.14661	0.345	0.34306	D	0.684947	B	0.21452	0.056	B	0.19666	0.026	T	0.45600	-0.9250	9	0.52906	T	0.07	-32.921	10.7187	0.46028	0.0:0.9059:0.0:0.0941	.	516	Q96PX6	CC85A_HUMAN	S	516;105	.	ENSP00000384040:P516S	P	+	1	0	CCDC85A	56456548	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.253000	0.43205	2.673000	0.90976	0.467000	0.42956	CCT	.	.	none		0.488	CCDC85A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324993.1			T	56603044	C	T	56603044	3	4	29	1	0	0	0	0	1	0	0	0	2861	739	26	2	1564	2	CCDC85A	2	56603044	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2426685	56603044	186596329	109	12350											
APLF	200558	hgsc.bcm.edu	37	chr2	68765205	68765205	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgagtgcccagggcgactcaCttcaggatgagtctcaaggg	9	7	14	11	2	3	1	3	1	1	0	4	4	3	2	1	3	1	0	1	3	1	1	rs13404469	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:68765205C>T	ENST00000303795.4	+	7	1177	c.1006C>T	c.(1006-1008)Ctt>Ttt	p.L336F	APLF_ENST00000471727.1_3'UTR	NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	336			L -> F (in dbSNP:rs13404469).		cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of DNA ligation (GO:0051106)|regulation of isotype switching (GO:0045191)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|endodeoxyribonuclease activity (GO:0004520)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	25						GGGCGACTCACTTCAGGATGA	0.423													T|||	395	0.0788738	0.1483	0.0735	5008	,	,		18007	0.005		0.0726	False		,,,				2504	0.0716				p.L336F		Atlas-SNP	.											.	APLF	69	.	0			c.C1006T						PASS	.	T	PHE/LEU	637,3769		51,535,1617	92	86	88		1006	4	0	2	dbSNP_121	88	695,7905		33,629,3638	yes	missense	APLF	NM_173545.2	22	84,1164,5255	TT,TC,CC		8.0814,14.4576,10.2414	benign	336/512	68765205	1332,11674	2203	4300	6503	SO:0001583	missense	200558	exon7			GACTCACTTCAGG	BC030711	CCDS1888.1	2p14	2014-02-20	2008-10-01	2008-10-01	ENSG00000169621	ENSG00000169621			28724	protein-coding gene	gene with protein product	"XRCC1-interacting protein 1", "zinc finger, CX5CX6HX5H motif containing 1"	611035	"chromosome 2 open reading frame 13"	C2orf13		18474613, 18077224, 17353262	Standard	NM_173545		Approved	MGC47799, Xip1, ZCCHH1	uc002sep.3	Q8IW19	OTTHUMG00000129566	ENST00000303795.4:c.1006C>T	2.37:g.68765205C>T	ENSP00000307004:p.Leu336Phe	173	0	0		123	91	0.739837	NM_173545	A8K476|Q53P47|Q53PB9|Q53QU0	Missense_Mutation	SNP	ENST00000303795.4	37	CCDS1888.1	151	0.06913919413919414	62	0.12601626016260162	28	0.07734806629834254	4	0.006993006993006993	57	0.07519788918205805	.	0.181	-1.061812	0.01950	0.144576	0.080814	ENSG00000169621	ENST00000303795	T	0.23950	1.88	5.19	4.0	0.46444	.	1.310930	0.04804	N	0.434102	T	0.00073	0.0002	N	0.00289	-1.7	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.30475	-0.9977	9	0.26408	T	0.33	.	8.0877	0.30782	0.0:0.1667:0.0:0.8333	rs13404469;rs52799369;rs13404469	336	Q8IW19	APLF_HUMAN	F	336	ENSP00000307004:L336F	ENSP00000307004:L336F	L	+	1	0	APLF	68618709	0.006000	0.16342	0.002000	0.10522	0.063000	0.16089	0.651000	0.24873	0.274000	0.22072	-0.381000	0.06696	CTT	C|0.910;T|0.090	0.090	strong		0.423	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545		T	68765205	C	T	68765205	3	4	29	1	0	0	0	0	1	0	0	0	776	565	20	2	1032	2	APLF	2	68765205	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	12162161	68765205	174434168	110	12351											
PROKR1	10887	hgsc.bcm.edu	37	chr2	68882661	68882661	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagacctggacctcaagacaAttgggatgcctgccaccgaa	12	6	10	13	1	1	2	1	0	0	2	1	5	1	4	5	2	2	0	5	2	3	1	rs34715748	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:68882661A>G	ENST00000303786.3	+	3	1555	c.1135A>G	c.(1135-1137)Att>Gtt	p.I379V	PROKR1_ENST00000394342.2_Missense_Mutation_p.I379V			Q8TCW9	PKR1_HUMAN	prokineticin receptor 1	379					negative regulation of apoptotic process (GO:0043066)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)	p.I379V(1)		endometrium(3)|kidney(2)|large_intestine(14)|lung(9)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						CCTCAAGACAATTGGGATGCC	0.488													A|||	234	0.0467252	0.0038	0.036	5008	,	,		21534	0.1111		0.0388	False		,,,				2504	0.0542				p.I379V		Atlas-SNP	.											PROKR1,NS,carcinoma,0,1	PROKR1	69	1	1	Substitution - Missense(1)	stomach(1)	c.A1135G						PASS	.	A	VAL/ILE	36,4370	40.0+/-72.8	0,36,2167	66	62	63		1135	1.9	0	2	dbSNP_126	63	401,8199	128.3+/-186.6	10,381,3909	yes	missense	PROKR1	NM_138964.2	29	10,417,6076	GG,GA,AA		4.6628,0.8171,3.36	benign	379/394	68882661	437,12569	2203	4300	6503	SO:0001583	missense	10887	exon2			AAGACAATTGGGA	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.1135A>G	2.37:g.68882661A>G	ENSP00000303775:p.Ile379Val	79	0	0		41	25	0.609756	NM_138964	A5JUU2|Q53QT9|Q8NFJ7	Missense_Mutation	SNP	ENST00000303786.3	37	CCDS1889.1	103	0.04716117216117216	2	0.0040650406504065045	10	0.027624309392265192	55	0.09615384615384616	36	0.047493403693931395	A	1.463	-0.562016	0.03939	0.008171	0.046628	ENSG00000169618	ENST00000303786;ENST00000394342	T;T	0.70869	-0.52;-0.52	4.22	1.88	0.25563	.	0.587506	0.18660	N	0.134753	T	0.01558	0.0050	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.01652	-1.1303	10	0.32370	T	0.25	.	7.1531	0.25622	0.8081:0.0:0.1919:0.0	rs34715748;rs61732947	379	Q8TCW9	PKR1_HUMAN	V	379	ENSP00000303775:I379V;ENSP00000377874:I379V	ENSP00000303775:I379V	I	+	1	0	PROKR1	68736165	0.001000	0.12720	0.005000	0.12908	0.004000	0.04260	1.677000	0.37576	0.426000	0.26116	0.533000	0.62120	ATT	A|0.960;G|0.040	0.040	strong		0.488	PROKR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251760.2			G	68882661	A	G	68882661	3	3	29	1	0	0	0	0	1	0	0	0	12564	101	4	3	1141	3	PROKR1	2	68882661	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	117456	68882661	174316712	111	12352											
BMP10	27302	hgsc.bcm.edu	37	chr2	69093413	69093413	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcctgacttttgccaacGtctgatggcatctgtgacat	8	13	10	10	1	2	4	0	4	2	0	2	4	2	4	2	1	3	1	2	1	1	2	rs34008398	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:69093413G>A	ENST00000295379.1	-	2	783	c.625C>T	c.(625-627)Cgt>Tgt	p.R209C		NM_014482.1	NP_055297.1	O95393	BMP10_HUMAN	bone morphogenetic protein 10	209					activin receptor signaling pathway (GO:0032924)|adult heart development (GO:0007512)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heart trabecula formation (GO:0060347)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell migration (GO:0010596)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction (GO:0055117)|sarcomere organization (GO:0045214)|ventricular cardiac muscle cell development (GO:0055015)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Z disc (GO:0030018)	hormone activity (GO:0005179)|receptor serine/threonine kinase binding (GO:0033612)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(15)|ovary(2)	27						TTTTGCCAACGTCTGATGGCA	0.498													G|||	19	0.00379393	0.0008	0.0014	5008	,	,		20267	0.0		0.0169	False		,,,				2504	0.0				p.R209C		Atlas-SNP	.											.	BMP10	70	.	0			c.C625T						PASS	.	G	CYS/ARG	13,4393	20.2+/-43.8	0,13,2190	141	120	128		625	4.6	1	2	dbSNP_126	128	100,8500	56.8+/-118.0	0,100,4200	yes	missense	BMP10	NM_014482.1	180	0,113,6390	AA,AG,GG		1.1628,0.2951,0.8688	possibly-damaging	209/425	69093413	113,12893	2203	4300	6503	SO:0001583	missense	27302	exon2			GCCAACGTCTGAT	AF101441	CCDS1890.1	2p13.2	2014-09-17			ENSG00000163217	ENSG00000163217		"Bone morphogenetic proteins", "Endogenous ligands"	20869	protein-coding gene	gene with protein product		608748				10072785	Standard	NM_014482		Approved		uc002sez.1	O95393	OTTHUMG00000129573	ENST00000295379.1:c.625C>T	2.37:g.69093413G>A	ENSP00000295379:p.Arg209Cys	285	0	0		209	151	0.722488	NM_014482	Q53R17|Q6NTE0	Missense_Mutation	SNP	ENST00000295379.1	37	CCDS1890.1	9	0.004120879120879121	1	0.0020325203252032522	0	0.0	0	0.0	8	0.010554089709762533	G	15.35	2.808940	0.50421	0.002951	0.011628	ENSG00000163217	ENST00000295379	T	0.69040	-0.37	5.44	4.57	0.56435	Transforming growth factor-beta, N-terminal (1);	0.338806	0.37095	N	0.002250	T	0.66684	0.2814	M	0.72353	2.195	0.58432	D	0.999999	D	0.55605	0.972	P	0.49597	0.616	T	0.76219	-0.3039	10	0.87932	D	0	.	15.5959	0.76578	0.0:0.1377:0.8622:0.0	rs34008398	209	O95393	BMP10_HUMAN	C	209	ENSP00000295379:R209C	ENSP00000295379:R209C	R	-	1	0	BMP10	68946917	0.998000	0.40836	0.997000	0.53966	0.334000	0.28698	5.487000	0.66863	1.527000	0.49086	-0.150000	0.13652	CGT	G|0.991;A|0.009	0.009	strong		0.498	BMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251768.1	NM_014482		A	69093413	G	A	69093413	3	1	29	1	0	0	0	0	1	0	0	0	1457	1145	40	1	653	1	BMP10	2	69093413	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	210752	69093413	174105960	112	12353											
PAIP2B	400961	hgsc.bcm.edu	37	chr2	71415619	71415619	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttctcggctcagtacttcTctcctggaataaactccttg	7	15	6	13	1	3	0	1	0	2	0	7	1	5	1	2	2	2	2	2	2	4	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:71415619T>C	ENST00000244221.8	-	4	528	c.362A>G	c.(361-363)gAg>gGg	p.E121G		NM_020459.1	NP_065192.1	Q9ULR5	PAI2B_HUMAN	poly(A) binding protein interacting protein 2B	121					negative regulation of translational initiation (GO:0045947)	cytoplasm (GO:0005737)	translation repressor activity, nucleic acid binding (GO:0000900)			large_intestine(1)|lung(1)	2						TCAGTACTTCTCTCCTGGAAT	0.458																																					p.E121G		Atlas-SNP	.											.	PAIP2B	7	.	0			c.A362G						PASS	.						90	84	86					2																	71415619		1870	4114	5984	SO:0001583	missense	400961	exon4			TACTTCTCTCCTG		CCDS46322.1	2p13.3	2007-07-16			ENSG00000124374	ENSG00000124374			29200	protein-coding gene	gene with protein product		611018				16804161	Standard	NM_020459		Approved	KIAA1155	uc002shu.2	Q9ULR5	OTTHUMG00000153284	ENST00000244221.8:c.362A>G	2.37:g.71415619T>C	ENSP00000244221:p.Glu121Gly	143	0	0		80	54	0.675	NM_020459		Missense_Mutation	SNP	ENST00000244221.8	37	CCDS46322.1	.	.	.	.	.	.	.	.	.	.	T	14.47	2.545159	0.45280	.	.	ENSG00000124374	ENST00000244221	.	.	.	5.4	4.23	0.50019	.	0.224838	0.38381	N	0.001705	T	0.34978	0.0916	N	0.14661	0.345	0.33638	D	0.606887	B	0.10296	0.003	B	0.12837	0.008	T	0.41324	-0.9515	9	0.72032	D	0.01	-12.7367	9.9702	0.41749	0.8459:0.0:0.0:0.1541	.	121	Q9ULR5	PAI2B_HUMAN	G	121	.	ENSP00000244221:E121G	E	-	2	0	PAIP2B	71269127	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	5.295000	0.65692	0.869000	0.35703	-0.917000	0.02746	GAG	.	.	none		0.458	PAIP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330547.2	XM_376062		C	71415619	T	C	71415619	3	2	29	1	0	0	0	0	1	0	0	0	11407	1551	54	3	13	3	PAIP2B	2	71415619	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	2322206	71415619	171783754	113	12354											
ALMS1	7840	hgsc.bcm.edu	37	chr2	73676965	73676965	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctcacaaagagagaagcctgGtattttctaccaacagacct	14	9	7	11	0	2	3	1	0	1	3	2	4	2	3	3	1	3	1	3	1	5	4	rs201074268	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:73676965G>A	ENST00000264448.6	+	8	3419	c.3308G>A	c.(3307-3309)gGt>gAt	p.G1103D	ALMS1_ENST00000409009.1_Missense_Mutation_p.G1061D|ALMS1_ENST00000377715.1_Missense_Mutation_p.G1103D	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	1103	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						GAGAAGCCTGGTATTTTCTAC	0.488													G|||	5	0.000998403	0.0	0.0029	5008	,	,		19306	0.0		0.003	False		,,,				2504	0.0				p.G1103D		Atlas-SNP	.											.	ALMS1	384	.	0			c.G3308A						PASS	.	G	ASP/GLY	0,3726		0,0,1863	101	103	102		3308	-8.9	0	2		102	21,8177		0,21,4078	yes	missense	ALMS1	NM_015120.4	94	0,21,5941	AA,AG,GG		0.2562,0.0,0.1761	benign	1103/4168	73676965	21,11903	1863	4099	5962	SO:0001583	missense	7840	exon8			AGCCTGGTATTTT	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.3308G>A	2.37:g.73676965G>A	ENSP00000264448:p.Gly1103Asp	64	0	0		61	42	0.688525	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	G	2.987	-0.208957	0.06140	0.0	0.002562	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.14893	3.35;3.35;2.47	4.46	-8.91	0.00778	.	3.168410	0.00654	N	0.000568	T	0.06508	0.0167	L	0.34521	1.04	0.09310	N	1	B;B;P	0.40602	0.015;0.034;0.723	B;B;B	0.41510	0.015;0.015;0.359	T	0.41233	-0.9520	10	0.06099	T	0.92	.	2.1614	0.03826	0.3512:0.0833:0.1306:0.4348	.	1103;1061;1103	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	D	1061;1103;1103	ENSP00000386627:G1061D;ENSP00000264448:G1103D;ENSP00000366944:G1103D	ENSP00000264448:G1103D	G	+	2	0	ALMS1	73530473	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-5.200000	0.00142	-3.469000	0.00157	-1.083000	0.02208	GGT	G|0.998;A|0.002	0.002	strong		0.488	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		A	73676965	G	A	73676965	3	1	29	1	0	0	0	0	1	0	0	0	535	1261	44	2	3338	2	ALMS1	2	73676965	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2261346	73676965	169522408	114	12355											
TET3	200424	hgsc.bcm.edu	37	chr2	74320089	74320089	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagtcgctcccctgtacaagCgactggcccctcaggcctat	8	8	9	16	2	1	0	1	0	0	0	3	1	2	0	5	2	2	2	5	2	4	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:74320089C>T	ENST00000409262.3	+	6	2695	c.2695C>T	c.(2695-2697)Cga>Tga	p.R899*		NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3	899					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						CCTGTACAAGCGACTGGCCCC	0.612																																					p.R899X		Atlas-SNP	.											.	TET3	101	.	0			c.C2695T						PASS	.						19	20	20					2																	74320089		1934	4130	6064	SO:0001587	stop_gained	200424	exon6			TACAAGCGACTGG		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.2695C>T	2.37:g.74320089C>T	ENSP00000386869:p.Arg899*	202	0	0		144	74	0.513889	NM_144993	A6NEI3|Q86Z24|Q8TBM9	Nonsense_Mutation	SNP	ENST00000409262.3	37	CCDS46339.1	.	.	.	.	.	.	.	.	.	.	C	39	7.569305	0.98365	.	.	ENSG00000187605	ENST00000409262;ENST00000233310	.	.	.	4.61	2.62	0.31277	.	0.543822	0.18552	N	0.137888	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.7839	0.52030	0.4338:0.5662:0.0:0.0	.	.	.	.	X	899	.	ENSP00000233310:R899X	R	+	1	2	TET3	74173597	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.062000	0.41413	1.240000	0.43803	0.655000	0.94253	CGA	.	.	none		0.612	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328141.4			T	74320089	C	T	74320089	4	4	29	1	0	0	0	0	0	1	0	0	15786	760	27	1	2717	1	TET3	2	74320089	Nonsense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	643124	74320089	168879284	115	12356											
SLC4A5	57835	hgsc.bcm.edu	37	chr2	74450058	74450058	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttccatgggaatctttataaCcgagggaggagggaactggg	11	9	15	6	1	1	0	0	0	1	0	2	5	2	4	2	5	2	0	2	5	4	4	rs36081793	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:74450058C>T	ENST00000377634.4	-	30	3715	c.3316G>A	c.(3316-3318)Gtt>Att	p.V1106I	SLC4A5_ENST00000358683.4_Missense_Mutation_p.V988I|SLC4A5_ENST00000483195.1_5'UTR|SLC4A5_ENST00000423644.1_3'UTR|SLC4A5_ENST00000346834.4_Missense_Mutation_p.V1009I|SLC4A5_ENST00000359484.4_Missense_Mutation_p.V988I|SLC4A5_ENST00000394019.2_Missense_Mutation_p.V1090I|SLC4A5_ENST00000377632.1_Missense_Mutation_p.V1009I|SLC4A5_ENST00000357822.5_Missense_Mutation_p.V1106I|RP11-287D1.3_ENST00000451608.2_3'UTR					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						ATCTTTATAACCGAGGGAGGA	0.418													C|||	61	0.0121805	0.0023	0.0288	5008	,	,		20198	0.0		0.0308	False		,,,				2504	0.0072				p.V1106I		Atlas-SNP	.											.	SLC4A5	215	.	0			c.G3316A						PASS	.	C	ILE/VAL,ILE/VAL	33,4373	39.2+/-71.8	1,31,2171	121	119	120		3316,3268	5.1	1	2	dbSNP_126	120	291,8309	107.0+/-167.8	4,283,4013	yes	missense,missense	SLC4A5	NM_021196.3,NM_133478.2	29,29	5,314,6184	TT,TC,CC		3.3837,0.749,2.4912	possibly-damaging,possibly-damaging	1106/1138,1090/1122	74450058	324,12682	2203	4300	6503	SO:0001583	missense	57835	exon25			TTATAACCGAGGG	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.3316G>A	2.37:g.74450058C>T	ENSP00000366861:p.Val1106Ile	104	0	0		82	47	0.573171	NM_021196		Missense_Mutation	SNP	ENST00000377634.4	37	CCDS1936.1	39	0.017857142857142856	2	0.0040650406504065045	12	0.03314917127071823	0	0.0	25	0.032981530343007916	C	14.19	2.460025	0.43736	0.00749	0.033837	ENSG00000188687	ENST00000394019;ENST00000451608;ENST00000346834;ENST00000359484;ENST00000358683;ENST00000357822;ENST00000377632;ENST00000377634	T;T;T;T;T;T;T	0.76968	-1.05;-0.91;-1.06;-1.06;-1.06;-0.91;-1.06	5.92	5.05	0.67936	.	0.542606	0.16548	N	0.209601	T	0.46190	0.1380	L	0.46157	1.445	0.80722	D	1	B;B;B;B	0.14805	0.011;0.004;0.003;0.001	B;B;B;B	0.14023	0.01;0.004;0.002;0.002	T	0.55211	-0.8176	10	0.15066	T	0.55	.	11.2264	0.48886	0.0:0.9158:0.0:0.0842	rs36081793	1009;988;1106;1090	Q9BY07-4;Q9BY07-7;Q9BY07;Q9BY07-3	.;.;S4A5_HUMAN;.	I	1090;1111;1009;988;988;1106;1009;1106	ENSP00000377587:V1090I;ENSP00000251768:V1009I;ENSP00000352461:V988I;ENSP00000351513:V988I;ENSP00000350475:V1106I;ENSP00000366859:V1009I;ENSP00000366861:V1106I	ENSP00000251768:V1009I	V	-	1	0	SLC4A5	74303566	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	0.684000	0.25364	1.515000	0.48885	-0.150000	0.13652	GTT	C|0.977;T|0.023	0.023	strong		0.418	SLC4A5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206583.3			T	74450058	C	T	74450058	3	4	29	1	0	0	0	0	1	0	0	0	14672	507	18	2	105	2	SLC4A5	2	74450058	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	129969	74450058	168749315	116	12357											
POLR1A	25885	hgsc.bcm.edu	37	chr2	86317012	86317012	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtattgttctaattcctccCgaatttcagaggcagaggga	10	13	10	8	1	2	2	1	0	1	2	4	4	4	3	2	2	0	3	2	2	3	6	rs146078741	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:86317012C>G	ENST00000263857.6	-	4	851	c.473G>C	c.(472-474)cGg>cCg	p.R158P	POLR1A_ENST00000409681.1_Missense_Mutation_p.R158P			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	158					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						TAATTCCTCCCGAATTTCAGA	0.453													C|||	24	0.00479233	0.0	0.0173	5008	,	,		20367	0.0		0.0119	False		,,,				2504	0.0				p.R158P		Atlas-SNP	.											.	POLR1A	137	.	0			c.G473C						PASS	.	C	PRO/ARG	7,3743		0,7,1868	164	152	156		473	4	1	2	dbSNP_134	156	74,8140		1,72,4034	yes	missense	POLR1A	NM_015425.3	103	1,79,5902	GG,GC,CC		0.9009,0.1867,0.677	benign	158/1721	86317012	81,11883	1875	4107	5982	SO:0001583	missense	25885	exon4			TCCTCCCGAATTT	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.473G>C	2.37:g.86317012C>G	ENSP00000263857:p.Arg158Pro	152	0	0		69	18	0.26087	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	ENST00000263857.6	37	CCDS42706.1	14	0.00641025641025641	0	0.0	6	0.016574585635359115	0	0.0	8	0.010554089709762533	C	4.071	0.011112	0.07912	0.001867	0.009009	ENSG00000068654	ENST00000263857;ENST00000409681	T;T	0.22539	1.95;1.95	5.2	4.04	0.47022	RNA polymerase Rpb1, domain 1 (1);	0.483471	0.23437	N	0.048199	T	0.08980	0.0222	N	0.24115	0.695	0.28088	N	0.93191	P;B	0.43287	0.802;0.293	P;B	0.48488	0.579;0.204	T	0.03875	-1.0996	10	0.30854	T	0.27	-17.9919	7.1854	0.25797	0.0:0.1768:0.0:0.8232	.	158;158	B9ZVN9;O95602	.;RPA1_HUMAN	P	158	ENSP00000263857:R158P;ENSP00000386300:R158P	ENSP00000263857:R158P	R	-	2	0	POLR1A	86170523	1.000000	0.71417	1.000000	0.80357	0.076000	0.17211	1.894000	0.39768	0.911000	0.36747	-0.294000	0.09567	CGG	C|0.991;G|0.009	0.009	strong		0.453	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425		G	86317012	C	G	86317012	3	3	29	1	0	0	0	0	1	0	0	0	12218	652	23	4	4813	4	POLR1A	2	86317012	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	11866954	86317012	156882361	117	12358											
SMYD1	150572	hgsc.bcm.edu	37	chr2	88387508	88387508	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggaggagcagaaggacctgCgggtggacgtggacacattc	11	5	17	8	2	0	1	0	0	0	1	1	6	0	6	1	6	2	1	1	6	1	1	rs113636517	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:88387508C>A	ENST00000419482.2	+	3	527	c.442C>A	c.(442-444)Cgg>Agg	p.R148R	SMYD1_ENST00000468008.1_3'UTR|SMYD1_ENST00000438570.1_Intron|SMYD1_ENST00000444564.2_Silent_p.R148R	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	148	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				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						GAAGGACCTGCGGGTGGACGT	0.627													C|||	6	0.00119808	0.0	0.0	5008	,	,		18746	0.0		0.003	False		,,,				2504	0.0031				p.R148R		Atlas-SNP	.											.	SMYD1	95	.	0			c.C442A						PASS	.	C		9,4397	15.5+/-35.6	0,9,2194	123	92	103		442	4.8	0.9	2	dbSNP_132	103	68,8532	40.8+/-97.7	0,68,4232	no	coding-synonymous	SMYD1	NM_198274.3		0,77,6426	AA,AC,CC		0.7907,0.2043,0.592		148/491	88387508	77,12929	2203	4300	6503	SO:0001819	synonymous_variant	150572	exon3			GACCTGCGGGTGG	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.442C>A	2.37:g.88387508C>A		239	1	0.0041841		191	132	0.691099	NM_198274	A0AV30|A6NE13	Silent	SNP	ENST00000419482.2	37	CCDS33240.1																																																																																			C|0.995;A|0.005	0.005	strong		0.627	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915		A	88387508	C	A	88387508	2	1	29	1	0	0	0	0	0	0	0	1	14836	759	27	4		4	SMYD1	2	88387508	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2070496	88387508	154811865	118	12359											
DUSP2	1844	hgsc.bcm.edu	37	chr2	96810556	96810556	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggttttgtcccctgttggcgGcagcgcaggggcgggggcct	2	9	19	11	3	0	0	0	0	0	0	1	0	1	0	3	7	1	4	3	7	0	3	rs537374232		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:96810556G>A	ENST00000288943.4	-	2	539	c.454C>T	c.(454-456)Ccg>Tcg	p.P152S	AC012307.2_ENST00000449242.1_lincRNA	NM_004418.3	NP_004409.1	Q05923	DUS2_HUMAN	dual specificity phosphatase 2	152					endoderm formation (GO:0001706)|inactivation of MAPK activity (GO:0000188)|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)|protein tyrosine/threonine phosphatase activity (GO:0008330)			NS(1)|breast(1)|lung(2)|skin(1)	5		Ovarian(717;0.0228)				CCTGTTGGCGGCAGCGCAGGG	0.662													g|||	1	0.000199681	0.0008	0.0	5008	,	,		11061	0.0		0.0	False		,,,				2504	0.0				p.P152S		Atlas-SNP	.											DUSP2,NS,carcinoma,+2,1	DUSP2	20	1	0			c.C454T						PASS	.						11	16	14					2																	96810556		2150	4241	6391	SO:0001583	missense	1844	exon2			TTGGCGGCAGCGC	L11329	CCDS2016.1	2q11	2011-06-09			ENSG00000158050	ENSG00000158050		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3068	protein-coding gene	gene with protein product		603068				7806236, 7590752, 12673251	Standard	NM_004418		Approved	PAC-1	uc002svk.4	Q05923	OTTHUMG00000130456	ENST00000288943.4:c.454C>T	2.37:g.96810556G>A	ENSP00000288943:p.Pro152Ser	92	0	0		76	9	0.118421	NM_004418	Q53T45	Missense_Mutation	SNP	ENST00000288943.4	37	CCDS2016.1	.	.	.	.	.	.	.	.	.	.	g	8.217	0.801609	0.16397	.	.	ENSG00000158050	ENST00000288943	T	0.02446	4.29	4.3	-1.0	0.10196	.	0.865607	0.10283	N	0.693284	T	0.01421	0.0046	N	0.12443	0.215	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.49331	-0.8951	10	0.11794	T	0.64	.	2.8978	0.05696	0.2993:0.0:0.373:0.3277	.	152	Q05923	DUS2_HUMAN	S	152	ENSP00000288943:P152S	ENSP00000288943:P152S	P	-	1	0	DUSP2	96174283	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.181000	0.03085	-0.453000	0.07076	-0.509000	0.04479	CCG	.	.	none		0.662	DUSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252847.1	NM_004418		A	96810556	G	A	96810556	3	1	29	1	0	0	0	0	1	0	0	0	4821	1203	42	2	502	2	DUSP2	2	96810556	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	8423048	96810556	146388817	119	12360											
DUSP2	1844	hgsc.bcm.edu	37	chr2	96810609	96810609	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cgggacagcagccctggaagCcgtcgaagcctcctgcaagg	9	4	14	14	3	0	0	0	0	0	0	2	3	1	2	4	3	5	2	4	3	3	0	rs572028879		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:96810609C>T	ENST00000288943.4	-	2	486	c.401G>A	c.(400-402)gGc>gAc	p.G134D	AC012307.2_ENST00000449242.1_lincRNA	NM_004418.3	NP_004409.1	Q05923	DUS2_HUMAN	dual specificity phosphatase 2	134	Rhodanese. {ECO:0000255|PROSITE- ProRule:PRU00173}.				endoderm formation (GO:0001706)|inactivation of MAPK activity (GO:0000188)|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)|protein tyrosine/threonine phosphatase activity (GO:0008330)			NS(1)|breast(1)|lung(2)|skin(1)	5		Ovarian(717;0.0228)				GCCCTGGAAGCCGTCGAAGCC	0.697													C|||	1	0.000199681	0.0008	0.0	5008	,	,		11195	0.0		0.0	False		,,,				2504	0.0				p.G134D		Atlas-SNP	.											.	DUSP2	20	.	0			c.G401A						PASS	.						15	20	18					2																	96810609		2094	4175	6269	SO:0001583	missense	1844	exon2			TGGAAGCCGTCGA	L11329	CCDS2016.1	2q11	2011-06-09			ENSG00000158050	ENSG00000158050		"Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"	3068	protein-coding gene	gene with protein product		603068				7806236, 7590752, 12673251	Standard	NM_004418		Approved	PAC-1	uc002svk.4	Q05923	OTTHUMG00000130456	ENST00000288943.4:c.401G>A	2.37:g.96810609C>T	ENSP00000288943:p.Gly134Asp	75	0	0		60	20	0.333333	NM_004418	Q53T45	Missense_Mutation	SNP	ENST00000288943.4	37	CCDS2016.1	.	.	.	.	.	.	.	.	.	.	C	3.560	-0.089892	0.07053	.	.	ENSG00000158050	ENST00000288943	T	0.26373	1.74	4.31	2.38	0.29361	Rhodanese-like (5);	0.285507	0.32736	N	0.005712	T	0.26774	0.0655	L	0.58101	1.795	0.25586	N	0.986743	B	0.31459	0.324	B	0.37091	0.241	T	0.14504	-1.0470	10	0.28530	T	0.3	.	10.6808	0.45813	0.0:0.5226:0.4774:0.0	.	134	Q05923	DUS2_HUMAN	D	134	ENSP00000288943:G134D	ENSP00000288943:G134D	G	-	2	0	DUSP2	96174336	0.037000	0.19845	0.471000	0.27229	0.207000	0.24258	0.181000	0.16880	0.349000	0.23975	0.456000	0.33151	GGC	.	.	none		0.697	DUSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252847.1	NM_004418		T	96810609	C	T	96810609	3	4	29	1	0	0	0	0	1	0	0	0	4821	739	26	2	555	2	DUSP2	2	96810609	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	53	96810609	146388764	120	12361											
ANKRD36	375248	hgsc.bcm.edu	37	chr2	97790211	97790211	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttagatcagccctcatacAtgctgttactcttggagaaa	11	14	7	9	0	3	2	2	0	1	2	3	3	3	2	1	1	4	2	1	1	4	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:97790211A>T	ENST00000461153.2	+	5	852	c.608A>T	c.(607-609)cAt>cTt	p.H203L	ANKRD36_ENST00000420699.2_Missense_Mutation_p.H203L			A6QL64	AN36A_HUMAN	ankyrin repeat domain 36	203								p.H203L(2)		endometrium(9)|kidney(5)|liver(1)|lung(3)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	23						GCCCTCATACATGCTGTTACT	0.323																																					p.H203L		Atlas-SNP	.											ANKRD36_ENST00000420699,extremity,malignant_melanoma,0,2	ANKRD36	170	2	2	Substitution - Missense(2)	NS(1)|skin(1)	c.A608T						scavenged	.						79	60	65					2																	97790211		692	1589	2281	SO:0001583	missense	375248	exon5			TCATACATGCTGT	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.608A>T	2.37:g.97790211A>T	ENSP00000419530:p.His203Leu	153	1	0.00653595		178	9	0.0505618	NM_001164315	B4E3I8|Q6UX02|Q86X62|Q9HCD1	Missense_Mutation	SNP	ENST00000461153.2	37	CCDS54379.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.781271	0.00634	.	.	ENSG00000135976	ENST00000461153;ENST00000420699;ENST00000393513;ENST00000455519	T;T	0.60920	0.15;0.15	0.946	-0.341	0.12639	Ankyrin repeat-containing domain (4);	.	.	.	.	T	0.16642	0.0400	N	0.00855	-1.145	0.47511	D	0.999447	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.37384	-0.9708	9	0.02654	T	1	.	3.0347	0.06118	0.3942:0.0:0.0:0.6058	.	203;203	A6QL64;F2Z332	AN36A_HUMAN;.	L	203	ENSP00000419530:H203L;ENSP00000391950:H203L	ENSP00000377149:H203L	H	+	2	0	ANKRD36	97153938	0.990000	0.36364	0.731000	0.30826	0.427000	0.31564	0.125000	0.15749	-0.131000	0.11578	-1.495000	0.00966	CAT	.	.	none		0.323	ANKRD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339154.5			T	97790211	A	T	97790211	3	4	29	1	0	0	0	0	1	0	0	0	665	217	8	5	626	5	ANKRD36	2	97790211	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	979602	97790211	145409162	121	12362											
NPAS2	4862	hgsc.bcm.edu	37	chr2	101606810	101606810	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttcagcagcgccacagctgcGctcccgccaagtctgaatct	8	8	9	16	3	3	1	1	1	2	0	4	1	4	1	3	0	4	3	3	0	2	1	rs1053091	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:101606810G>A	ENST00000335681.5	+	18	2205	c.1920G>A	c.(1918-1920)gcG>gcA	p.A640A	NPAS2_ENST00000542504.1_Silent_p.A705A	NM_002518.3	NP_002509.2	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2	640					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						CCACAGCTGCGCTCCCGCCAA	0.617													G|||	52	0.0103834	0.0	0.0029	5008	,	,		14253	0.0		0.0278	False		,,,				2504	0.0225				p.A640A		Atlas-SNP	.											.	NPAS2	88	.	0			c.G1920A						PASS	.	G		16,4390	23.3+/-48.9	0,16,2187	50	53	52		1920	0	0.3	2	dbSNP_86	52	143,8457	71.3+/-133.9	1,141,4158	no	coding-synonymous	NPAS2	NM_002518.3		1,157,6345	AA,AG,GG		1.6628,0.3631,1.2225		640/825	101606810	159,12847	2203	4300	6503	SO:0001819	synonymous_variant	4862	exon18			AGCTGCGCTCCCG	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.1920G>A	2.37:g.101606810G>A		105	0	0		108	43	0.398148	NM_002518	Q4ZFV9|Q53SQ3|Q86V96|Q99629	Silent	SNP	ENST00000335681.5	37	CCDS2048.1	27	0.012362637362637362	0	0.0	1	0.0027624309392265192	0	0.0	26	0.03430079155672823	G	6.049	0.377437	0.11466	0.003631	0.016628	ENSG00000170485	ENST00000433408	T	0.42900	0.96	4.68	0.0241	0.14140	.	2.104730	0.02762	N	0.118661	T	0.14657	0.0354	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.24190	-1.0167	7	0.44086	T	0.13	.	5.2335	0.15434	0.2565:0.2928:0.4506:0.0	rs1053091;rs3193576;rs1053091	.	.	.	T	139	ENSP00000393396:A139T	ENSP00000393396:A139T	A	+	1	0	NPAS2	100973242	0.014000	0.17966	0.293000	0.24932	0.101000	0.19017	0.173000	0.16724	0.368000	0.24481	-0.463000	0.05309	GCT	G|0.989;A|0.011	0.011	strong		0.617	NPAS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253168.3			A	101606810	G	A	101606810	2	1	29	1	0	0	0	0	0	0	0	1	10572	1074	38	1		1	NPAS2	2	101606810	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	3816599	101606810	141592563	122	12363											
GCC2	9648	hgsc.bcm.edu	37	chr2	109087929	109087931	+	In_Frame_Del	DEL	AAG	AAG	-																															ggaggtttttttgtctcaaaAagaagatgttatccttaaag																								rs553103180		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:109087929_109087931delAAG	ENST00000309863.6	+	6	2858_2860	c.2144_2146delAAG	c.(2143-2148)aaagaa>aaa	p.E716del		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	716					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						TTGTCTCAAAAAGAAGATGTTAT	0.305																																					p.715_715del		Pindel,Atlas-Indel	.											.	GCC2	129	.	0			c.2143_2145del						PASS	.			4,4246		1,2,2122						4.2	1			133	12,8222		2,8,4107	no	coding	GCC2	NM_181453.3		3,10,6229	A1A1,A1R,RR		0.1457,0.0941,0.1282				16,12468				SO:0001651	inframe_deletion	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.2144_2146delAAG	2.37:g.109087932_109087934delAAG	ENSP00000307939:p.Glu716del	109	0	.		83	24	0.289	NM_181453	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	In_Frame_Del	DEL	ENST00000309863.6	37	CCDS33268.1																																																																																			.	.	none		0.305	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635		-	109087931	AAG	-	109087929	7	5	29	1	0	1	0	1	0	0	0	0	6294	14	1	0	2166	0	GCC2	2	109087929	In_Frame_Del	DEL	AAG	TCGA-GR-7351-01A-11D-2210-10	7481119	109087929	134111444	123	12364											
SH3RF3	344558	hgsc.bcm.edu	37	chr2	110065896	110065896	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	catcggtgttctgtccacatCcagccccaccaacacgggat	9	8	8	16	2	1	0	0	0	1	0	4	1	3	1	5	2	2	1	5	2	1	1	rs192679474	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:110065896C>T	ENST00000309415.6	+	8	2099	c.2099C>T	c.(2098-2100)tCc>tTc	p.S700F		NM_001099289.1	NP_001092759.1	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3	700							zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(5)|ovary(2)	18						CTGTCCACATCCAGCCCCACC	0.597													C|||	4	0.000798722	0.0	0.0	5008	,	,		18161	0.0		0.004	False		,,,				2504	0.0				p.S700F		Atlas-SNP	.											.	SH3RF3	62	.	0			c.C2099T						PASS	.	C	PHE/SER	8,4010		0,8,2001	38	43	41		2099	3.1	0.5	2		41	48,8272		0,48,4112	yes	missense	SH3RF3	NM_001099289.1	155	0,56,6113	TT,TC,CC		0.5769,0.1991,0.4539	possibly-damaging	700/883	110065896	56,12282	2009	4160	6169	SO:0001583	missense	344558	exon8			CCACATCCAGCCC	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.2099C>T	2.37:g.110065896C>T	ENSP00000309186:p.Ser700Phe	114	0	0		97	42	0.43299	NM_001099289	A0SDZ7|A8MPR1|Q8NDU1	Missense_Mutation	SNP	ENST00000309415.6	37		3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	14.04	2.416624	0.42918	0.001991	0.005769	ENSG00000172985	ENST00000418513;ENST00000309415	T;T	0.58652	0.32;2.12	4.9	3.06	0.35304	.	1.159960	0.06021	N	0.651244	T	0.49338	0.1551	.	.	.	0.23827	N	0.996736	D	0.54397	0.966	P	0.47430	0.547	T	0.39440	-0.9614	9	0.49607	T	0.09	-5.2094	8.14	0.31078	0.0:0.4772:0.4348:0.0879	.	700	Q8TEJ3	SH3R3_HUMAN	F	700	ENSP00000414997:S700F;ENSP00000309186:S700F	ENSP00000309186:S700F	S	+	2	0	SH3RF3	109432328	0.053000	0.20554	0.513000	0.27749	0.645000	0.38454	0.930000	0.28858	0.630000	0.30394	0.655000	0.94253	TCC	C|0.998;T|0.002	0.002	strong		0.597	SH3RF3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001099289		T	110065896	C	T	110065896	3	4	29	1	0	0	0	0	1	0	0	0	14275	855	30	2	2129	2	SH3RF3	2	110065896	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	977967	110065896	133133477	124	12365											
PROC	5624	hgsc.bcm.edu	37	chr2	128178900	128178900	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcgtgcccaccaggtgctgCggatccgcaaacgtgccaac	9	5	12	15	4	0	0	0	0	0	0	1	1	1	1	4	2	7	2	4	2	2	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:128178900C>T	ENST00000234071.3	+	3	199	c.112C>T	c.(112-114)Cgg>Tgg	p.R38W	PROC_ENST00000453608.2_Missense_Mutation_p.R59W|MIR4783_ENST00000580343.1_RNA|PROC_ENST00000422777.3_Missense_Mutation_p.R38W|PROC_ENST00000409048.1_Missense_Mutation_p.R38W	NM_000312.3	NP_000303.1	P04070	PROC_HUMAN	protein C (inactivator of coagulation factors Va and VIIIa)	38			R -> W (in patients with PROC deficiency). {ECO:0000269|PubMed:8324221}.		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)	CCAGGTGCTGCGGATCCGCAA	0.632																																					p.R38W		Atlas-SNP	.											PROC,colon,carcinoma,-1,1	PROC	31	1	0			c.C112T	GRCh37	CM930605	PROC	M		PASS	.						81	73	76					2																	128178900		2203	4300	6503	SO:0001583	missense	5624	exon3			GTGCTGCGGATCC	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.112C>T	2.37:g.128178900C>T	ENSP00000234071:p.Arg38Trp	202	0	0		127	47	0.370079	NM_000312	B4DPQ7|Q15189|Q15190|Q16001|Q53S74|Q9UC55	Missense_Mutation	SNP	ENST00000234071.3	37	CCDS2145.1	.	.	.	.	.	.	.	.	.	.	C	17.94	3.511314	0.64522	.	.	ENSG00000115718	ENST00000234071;ENST00000429925;ENST00000442644;ENST00000453608;ENST00000427769;ENST00000409048;ENST00000422777	D;D;D;D;D;D;D	0.99709	-3.09;-5.96;-6.48;-3.17;-5.65;-3.14;-3.09	5.2	3.17	0.36434	Gamma-carboxyglutamic acid-rich (GLA) domain (1);	0.000000	0.38436	N	0.001686	D	0.99429	0.9798	L	0.54323	1.7	0.40797	D	0.983301	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.81914	0.988;0.995;0.988;0.988	D	0.98660	1.0683	10	0.87932	D	0	.	11.6367	0.51209	0.6041:0.3959:0.0:0.0	.	59;59;38;38	B4DPQ7;B4DPQ3;E7END6;P04070	.;.;.;PROC_HUMAN	W	38;38;38;59;38;38;38	ENSP00000234071:R38W;ENSP00000412697:R38W;ENSP00000411241:R38W;ENSP00000404030:R59W;ENSP00000406295:R38W;ENSP00000386679:R38W;ENSP00000409543:R38W	ENSP00000234071:R38W	R	+	1	2	PROC	127895370	0.992000	0.36948	0.598000	0.28837	0.506000	0.33950	2.484000	0.45242	1.156000	0.42514	0.561000	0.74099	CGG	.	.	none		0.632	PROC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254385.2	NM_000312		T	128178900	C	T	128178900	3	4	29	1	0	0	0	0	1	0	0	0	12557	759	27	1	118	1	PROC	2	128178900	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	18113004	128178900	115020473	125	12366											
MYO7B	4648	hgsc.bcm.edu	37	chr2	128367451	128367451	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtcatatggaacgtcatcCtgaggttcatgggtgatctc	8	13	12	8	1	4	2	3	2	1	0	6	3	5	3	1	4	1	1	1	4	2	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:128367451C>T	ENST00000409816.2	+	23	3084	c.3052C>T	c.(3052-3054)Ctg>Ttg	p.L1018L	MYO7B_ENST00000428314.1_Silent_p.L1018L|MYO7B_ENST00000389524.4_Silent_p.L1018L			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1018	MyTH4 1. {ECO:0000255|PROSITE- ProRule:PRU00359}.					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)		GAACGTCATCCTGAGGTTCAT	0.597																																					p.L1018L		Atlas-SNP	.											.	MYO7B	359	.	0			c.C3052T						PASS	.						45	49	48					2																	128367451		2091	4242	6333	SO:0001819	synonymous_variant	4648	exon24			GTCATCCTGAGGT		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.3052C>T	2.37:g.128367451C>T		177	0	0		116	13	0.112069	NM_001080527	Q14786|Q8TEE1	Silent	SNP	ENST00000409816.2	37	CCDS46405.1																																																																																			.	.	none		0.597	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001		T	128367451	C	T	128367451	2	4	29	1	0	0	0	0	0	0	0	1	10092	680	24	2		2	MYO7B	2	128367451	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	188551	128367451	114831922	126	12367											
R3HDM1	23518	hgsc.bcm.edu	37	chr2	136467080	136467080	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacttcaccatgcagttcccAgcagcttcaaggccaccaat	11	8	6	16	0	2	0	2	0	0	0	3	0	3	0	4	1	3	4	4	1	2	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:136467080A>T	ENST00000264160.4	+	21	2802	c.2432A>T	c.(2431-2433)cAg>cTg	p.Q811L	R3HDM1_ENST00000409478.1_Missense_Mutation_p.Q683L|R3HDM1_ENST00000409606.1_Missense_Mutation_p.Q812L|R3HDM1_ENST00000410054.1_Missense_Mutation_p.Q756L|R3HDM1_ENST00000329971.3_Missense_Mutation_p.Q682L	NM_001282798.1|NM_015361.2	NP_001269727.1|NP_056176.2	Q15032	R3HD1_HUMAN	R3H domain containing 1	811							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)		TGCAGTTCCCAGCAGCTTCAA	0.388																																					p.Q811L		Atlas-SNP	.											.	R3HDM1	84	.	0			c.A2432T						PASS	.						126	110	115					2																	136467080		2203	4300	6503	SO:0001583	missense	23518	exon21			GTTCCCAGCAGCT	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.2432A>T	2.37:g.136467080A>T	ENSP00000264160:p.Gln811Leu	253	0	0		206	87	0.42233	NM_015361	A8K1V0|B3KXQ9|E9PBB4|E9PG42|G5E9G8|Q8IW32	Missense_Mutation	SNP	ENST00000264160.4	37	CCDS2177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.31|12.31	1.899556|1.899556	0.33535|0.33535	.|.	.|.	ENSG00000048991|ENSG00000048991	ENST00000409478;ENST00000264160;ENST00000329971;ENST00000410054;ENST00000409606|ENST00000445855	T;T;T;T;T|.	0.33654|.	1.41;1.4;1.41;1.4;1.4|.	5.61|5.61	5.61|5.61	0.85477|0.85477	.|.	0.136231|.	0.51477|.	N|.	0.000087|.	T|T	0.71533|0.71533	0.3351|0.3351	M|M	0.61703|0.61703	1.905|1.905	0.48288|0.48288	D|D	0.999627|0.999627	D;B;B;B|.	0.53745|.	0.962;0.156;0.057;0.057|.	D;B;B;B|.	0.66716|.	0.946;0.034;0.023;0.023|.	T|T	0.70637|0.70637	-0.4817|-0.4817	10|5	0.34782|.	T|.	0.22|.	-0.8796|-0.8796	15.5092|15.5092	0.75766|0.75766	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	683;812;756;811|.	G5E9G8;E9PBB4;E9PG42;Q15032|.	.;.;.;R3HD1_HUMAN|.	L|C	683;811;682;756;812|107	ENSP00000386457:Q683L;ENSP00000264160:Q811L;ENSP00000331396:Q682L;ENSP00000386877:Q756L;ENSP00000387010:Q812L|.	ENSP00000264160:Q811L|.	Q|S	+|+	2|1	0|0	R3HDM1|R3HDM1	136183550|136183550	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.969000|0.969000	0.65631|0.65631	7.042000|7.042000	0.76565|0.76565	2.138000|2.138000	0.66242|0.66242	0.524000|0.524000	0.50904|0.50904	CAG|AGC	.	.	none		0.388	R3HDM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254659.1	NM_015361		T	136467080	A	T	136467080	3	4	29	1	0	0	0	0	1	0	0	0	12902	188	7	5	2506	5	R3HDM1	2	136467080	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	8099629	136467080	106732293	127	12368											
MCM6	4175	hgsc.bcm.edu	37	chr2	136602196	136602196	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcagagtctatctctgattcGatttccttcaagtaccagtt	9	16	6	10	1	4	2	2	1	2	1	7	3	5	2	2	0	1	2	2	0	3	6	rs4988270	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:136602196G>A	ENST00000264156.2	-	16	2328	c.2268C>T	c.(2266-2268)atC>atT	p.I756I	MCM6_ENST00000492091.1_5'UTR	NM_005915.5	NP_005906.2	Q14566	MCM6_HUMAN	minichromosome maintenance complex component 6	756					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)		TCTCTGATTCGATTTCCTTCA	0.378													G|||	9	0.00179712	0.0	0.0	5008	,	,		20306	0.0		0.007	False		,,,				2504	0.002				p.I756I	Ovarian(196;141 2104 8848 24991 25939)	Atlas-SNP	.											.	MCM6	64	.	0			c.C2268T						PASS	.	G		3,4403	6.2+/-15.9	0,3,2200	140	135	137		2268	-8.5	0.8	2	dbSNP_113	137	40,8560	26.8+/-75.7	0,40,4260	no	coding-synonymous	MCM6	NM_005915.4		0,43,6460	AA,AG,GG		0.4651,0.0681,0.3306		756/822	136602196	43,12963	2203	4300	6503	SO:0001819	synonymous_variant	4175	exon16			TGATTCGATTTCC		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.2268C>T	2.37:g.136602196G>A		48	0	0		54	10	0.185185	NM_005915	B2R6H2|Q13504|Q99859	Silent	SNP	ENST00000264156.2	37	CCDS2179.1																																																																																			G|0.997;A|0.003	0.003	strong		0.378	MCM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254658.1	NM_005915		A	136602196	G	A	136602196	2	1	29	1	0	0	0	0	0	0	0	1	9400	1048	37	1		1	MCM6	2	136602196	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	135116	136602196	106597177	128	12369											
ZEB2	9839	hgsc.bcm.edu	37	chr2	145274844	145274844	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttggttcgggctgcttcttaCcgtttttcctcctgggattg	2	18	11	10	2	1	0	0	0	1	0	4	1	3	1	3	3	2	4	3	3	1	7			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:145274844C>T	ENST00000558170.2	-	2	1258		c.e2+1		ZEB2-AS1_ENST00000421083.1_RNA|ZEB2-AS1_ENST00000602006.1_RNA|ZEB2-AS1_ENST00000609376.1_RNA|ZEB2-AS1_ENST00000595109.1_RNA|ZEB2_ENST00000465070.1_Splice_Site|ZEB2_ENST00000493689.1_Splice_Site|ZEB2-AS1_ENST00000609842.1_RNA|ZEB2-AS1_ENST00000427278.3_RNA|ZEB2_ENST00000462355.1_Splice_Site|ZEB2-AS1_ENST00000609819.1_RNA|ZEB2_ENST00000539609.3_Splice_Site|ZEB2-AS1_ENST00000610265.1_RNA|ZEB2_ENST00000303660.4_Splice_Site|ZEB2-AS1_ENST00000608361.1_RNA|ZEB2_ENST00000470879.1_Splice_Site|ZEB2_ENST00000409487.3_Splice_Site|ZEB2-AS1_ENST00000428623.1_RNA	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN	zinc finger E-box binding homeobox 2						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)		CTGCTTCTTACCGTTTTTCCT	0.602																																					.	Melanoma(33;1235 1264 5755 16332)	Atlas-SNP	.											ZEB2,NS,NS,0,1	ZEB2	218	1	0			c.73+1G>A	GRCh37	CS031468	ZEB2	S		PASS	.						175	182	180					2																	145274844		2203	4300	6503	SO:0001630	splice_region_variant	9839	exon3			TTCTTACCGTTTT	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.73+1G>A	2.37:g.145274844C>T		56	0	0		50	27	0.54	NM_001171653	A0JP09|B7Z2P2|F5H814|Q9UED1	Splice_Site	SNP	ENST00000558170.2	37	CCDS2186.1	.	.	.	.	.	.	.	.	.	.	C	16.50	3.140744	0.56936	.	.	ENSG00000169554	ENST00000392860;ENST00000539609;ENST00000303660;ENST00000409487;ENST00000427902;ENST00000392861;ENST00000431672;ENST00000409211;ENST00000435831;ENST00000444559	.	.	.	3.3	3.3	0.37823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.7876	0.46413	0.2422:0.7578:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ZEB2	144991314	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	6.742000	0.74843	1.789000	0.52484	0.442000	0.29010	.	.	.	none		0.602	ZEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254778.5	NM_014795	Intron	T	145274844	C	T	145274844	5	4	29	1	0	0	0	0	0	0	1	0	17639	521	18	2	3606	2	ZEB2	2	145274844	Splice_Site	SNP	C	TCGA-GR-7351-01A-11D-2210-10	8672648	145274844	97924529	129	12370											
GPD2	2820	hgsc.bcm.edu	37	chr2	157367399	157367399	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catggtggtgtgagatatctGcagaaggccatcatgaagtt	11	11	13	6	0	2	3	1	2	1	2	2	4	2	3	1	3	1	2	1	3	3	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:157367399G>T	ENST00000310454.6	+	4	738	c.366G>T	c.(364-366)ctG>ctT	p.L122L	GPD2_ENST00000409674.1_Silent_p.L122L|GPD2_ENST00000438166.2_Silent_p.L122L|GPD2_ENST00000409125.4_Intron|GPD2_ENST00000540309.1_Silent_p.L122L	NM_001083112.2	NP_001076581.2	P43304	GPDM_HUMAN	glycerol-3-phosphate dehydrogenase 2 (mitochondrial)	122					camera-type eye development (GO:0043010)|cellular lipid metabolic process (GO:0044255)|gluconeogenesis (GO:0006094)|glycerol catabolic process (GO:0019563)|glycerol-3-phosphate metabolic process (GO:0006072)|multicellular organism growth (GO:0035264)|small molecule metabolic process (GO:0044281)	glycerol-3-phosphate dehydrogenase complex (GO:0009331)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|glycerol-3-phosphate dehydrogenase activity (GO:0004368)|sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity (GO:0052591)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(1)|stomach(1)	22						TGAGATATCTGCAGAAGGCCA	0.403																																					p.L122L		Atlas-SNP	.											.	GPD2	59	.	0			c.G366T						PASS	.						179	177	178					2																	157367399		2203	4300	6503	SO:0001819	synonymous_variant	2820	exon4			ATATCTGCAGAAG		CCDS2202.1	2q24.1	2013-01-10			ENSG00000115159	ENSG00000115159	1.1.1.8	"EF-hand domain containing"	4456	protein-coding gene	gene with protein product		138430					Standard	NM_001083112		Approved		uc002tzd.4	P43304	OTTHUMG00000131951	ENST00000310454.6:c.366G>T	2.37:g.157367399G>T		199	1	0.00502513		144	107	0.743056	NM_001083112	A8K4V0|B3KSA9|Q59FR1|Q9HAP9	Silent	SNP	ENST00000310454.6	37	CCDS2202.1																																																																																			.	.	none		0.403	GPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254910.3			T	157367399	G	T	157367399	2	4	29	1	0	0	0	0	0	0	0	1	6614	1306	46	4		4	GPD2	2	157367399	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	12092555	157367399	85831974	130	12371											
ACVR1C	130399	hgsc.bcm.edu	37	chr2	158412701	158412701	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agagagtggttcctccacatTtggtctctttttcttcctgt	5	18	8	10	0	2	1	0	0	2	1	6	2	5	1	3	2	0	1	3	2	0	5	rs55920843	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:158412701T>G	ENST00000243349.8	-	3	808	c.448A>C	c.(448-450)Aat>Cat	p.N150H	ACVR1C_ENST00000335450.7_Intron|ACVR1C_ENST00000409680.3_Missense_Mutation_p.N100H|ACVR1C_ENST00000348328.5_Intron	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						TCCTCCACATTTGGTCTCTTT	0.478													T|||	18	0.00359425	0.0008	0.0	5008	,	,		16524	0.001		0.0149	False		,,,				2504	0.001				p.N150H		Atlas-SNP	.											.	ACVR1C	85	.	0			c.A448C						PASS	.	T	HIS/ASN,,,HIS/ASN	12,4394	19.1+/-41.9	0,12,2191	101	89	93		298,,,448	5.7	0.3	2	dbSNP_129	93	92,8508	51.9+/-112.3	0,92,4208	yes	missense,intron,intron,missense	ACVR1C	NM_001111031.1,NM_001111032.1,NM_001111033.1,NM_145259.2	68,,,68	0,104,6399	GG,GT,TT		1.0698,0.2724,0.7996	benign,,,benign	100/444,,,150/494	158412701	104,12902	2203	4300	6503	SO:0001583	missense	130399	exon3			CCACATTTGGTCT	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.448A>C	2.37:g.158412701T>G	ENSP00000243349:p.Asn150His	146	0	0		134	33	0.246269	NM_145259		Missense_Mutation	SNP	ENST00000243349.8	37	CCDS2205.1	13	0.005952380952380952	0	0.0	0	0.0	1	0.0017482517482517483	12	0.0158311345646438	T	11.40	1.627039	0.28978	0.002724	0.010698	ENSG00000123612	ENST00000243349;ENST00000409680	D;D	0.88124	-2.34;-2.24	5.73	5.73	0.89815	.	0.000000	0.56097	D	0.000021	T	0.71829	0.3386	L	0.55481	1.735	0.80722	D	1	B	0.10296	0.003	B	0.15870	0.014	T	0.72384	-0.4310	10	0.16420	T	0.52	.	10.8735	0.46899	0.1405:0.0:0.0:0.8595	rs55920843	150	Q8NER5	ACV1C_HUMAN	H	150;100	ENSP00000243349:N150H;ENSP00000387168:N100H	ENSP00000243349:N150H	N	-	1	0	ACVR1C	158120947	0.422000	0.25473	0.256000	0.24389	0.757000	0.42996	2.177000	0.42509	2.189000	0.69895	0.528000	0.53228	AAT	T|0.993;G|0.007	0.007	strong		0.478	ACVR1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254924.2	NM_145259		G	158412701	T	G	158412701	3	3	29	1	0	0	0	0	1	0	0	0	222	1841	64	5	1061	5	ACVR1C	2	158412701	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	1045302	158412701	84786672	131	12372											
UPP2	151531	hgsc.bcm.edu	37	chr2	158991346	158991346	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcctggtggagtaccagcaaCggcctcagctcctaatctcc	8	9	9	15	1	2	0	1	0	1	0	5	1	4	1	5	3	4	3	5	3	3	2	rs144945330	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:158991346C>T	ENST00000005756.4	+	7	1092	c.898C>T	c.(898-900)Cgg>Tgg	p.R300W	UPP2_ENST00000460456.1_3'UTR|UPP2_ENST00000409859.4_Missense_Mutation_p.R357W|UPP2_ENST00000605860.1_Missense_Mutation_p.R357W|UPP2-IT1_ENST00000439185.1_RNA	NM_173355.3	NP_775491.1	O95045	UPP2_HUMAN	uridine phosphorylase 2	300					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)	GTACCAGCAACGGCCTCAGCT	0.527																																					p.R357W		Atlas-SNP	.											.	UPP2	60	.	0			c.C1069T						PASS	.	C	TRP/ARG,TRP/ARG	2,4404	4.2+/-10.8	0,2,2201	170	149	156		1069,898	1.1	0.2	2	dbSNP_134	156	8,8592	6.4+/-24.3	0,8,4292	yes	missense,missense	UPP2	NM_001135098.1,NM_173355.3	101,101	0,10,6493	TT,TC,CC		0.093,0.0454,0.0769	probably-damaging,probably-damaging	357/375,300/318	158991346	10,12996	2203	4300	6503	SO:0001583	missense	151531	exon9			CAGCAACGGCCTC	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.898C>T	2.37:g.158991346C>T	ENSP00000005756:p.Arg300Trp	138	0	0		91	20	0.21978	NM_001135098	B3KV87	Missense_Mutation	SNP	ENST00000005756.4	37	CCDS2207.1	.	.	.	.	.	.	.	.	.	.	C	13.02	2.111302	0.37242	4.54E-4	9.3E-4	ENSG00000007001	ENST00000409859;ENST00000005756	D;D	0.88277	-2.36;-2.36	4.94	1.14	0.20703	Nucleoside phosphorylase domain (1);	0.237699	0.41938	N	0.000790	D	0.93383	0.7890	M	0.90019	3.08	0.52099	D	0.999941	D	0.89917	1.0	D	0.97110	1.0	D	0.89713	0.3913	10	0.72032	D	0.01	.	3.7355	0.08508	0.1699:0.5569:0.0:0.2731	.	300	O95045	UPP2_HUMAN	W	357;300	ENSP00000387230:R357W;ENSP00000005756:R300W	ENSP00000005756:R300W	R	+	1	2	UPP2	158699592	0.971000	0.33674	0.241000	0.24154	0.212000	0.24457	0.214000	0.17541	0.029000	0.15352	-1.100000	0.02121	CGG	C|0.999;T|0.001	0.001	strong		0.527	UPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254929.2	NM_173355		T	158991346	C	T	158991346	3	4	29	1	0	0	0	0	1	0	0	0	17028	527	19	1	1103	1	UPP2	2	158991346	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	578645	158991346	84208027	132	12373											
BAZ2B	29994	hgsc.bcm.edu	37	chr2	160182374	160182374	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttgcctttctttgactcaTtagtcttttttcctttgaca	5	22	4	10	0	4	2	1	2	3	0	5	2	5	2	2	0	1	0	2	0	1	8	rs148382881	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:160182374T>C	ENST00000392783.2	-	35	6494	c.5999A>G	c.(5998-6000)aAt>aGt	p.N2000S	BAZ2B_ENST00000355831.2_Missense_Mutation_p.N1966S|BAZ2B_ENST00000392782.1_Missense_Mutation_p.N1964S|BAZ2B_ENST00000343439.5_Missense_Mutation_p.N1900S	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	2000					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						CTTTGACTCATTAGTCTTTTT	0.328													T|||	30	0.00599042	0.0015	0.0173	5008	,	,		16283	0.001		0.0149	False		,,,				2504	0.0				p.N2000S		Atlas-SNP	.											.	BAZ2B	196	.	0			c.A5999G						PASS	.	T	SER/ASN	13,3637		0,13,1812	99	90	93		5999	3.7	0.9	2	dbSNP_134	93	136,8022		3,130,3946	yes	missense	BAZ2B	NM_013450.2	46	3,143,5758	CC,CT,TT		1.6671,0.3562,1.2619	benign	2000/2169	160182374	149,11659	1825	4079	5904	SO:0001583	missense	29994	exon35			GACTCATTAGTCT	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.5999A>G	2.37:g.160182374T>C	ENSP00000376534:p.Asn2000Ser	132	0	0		103	20	0.194175	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	37	CCDS2209.2	15	0.006868131868131868	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	5	0.006596306068601583	T	9.716	1.158442	0.21454	0.003562	0.016671	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831;ENST00000343439	T;T;T;T	0.56611	0.45;0.45;0.45;0.45	4.83	3.66	0.41972	.	0.000000	0.36972	U	0.002312	T	0.18257	0.0438	L	0.27053	0.805	0.28931	N	0.891542	B;B	0.24768	0.111;0.016	B;B	0.23574	0.047;0.006	T	0.12553	-1.0543	10	0.15952	T	0.53	-12.5921	5.4583	0.16602	0.0:0.1583:0.1464:0.6953	.	1964;2000	Q9UIF8-5;Q9UIF8	.;BAZ2B_HUMAN	S	1964;2000;1966;1900	ENSP00000376533:N1964S;ENSP00000376534:N2000S;ENSP00000348087:N1966S;ENSP00000339670:N1900S	ENSP00000339670:N1900S	N	-	2	0	BAZ2B	159890620	0.976000	0.34144	0.938000	0.37757	0.998000	0.95712	0.748000	0.26305	0.696000	0.31696	0.454000	0.30748	AAT	T|0.987;C|0.013	0.013	strong		0.328	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2			C	160182374	T	C	160182374	3	2	29	1	0	0	0	0	1	0	0	0	1332	1493	52	3	519	3	BAZ2B	2	160182374	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	1191028	160182374	83016999	133	12374											
TANK	10010	hgsc.bcm.edu	37	chr2	162036195	162036195	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggataaaaacattggcgagCaactcaataaagcgtatgaa	18	8	9	6	2	1	1	1	1	0	0	1	3	1	2	0	2	4	2	0	2	9	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:162036195C>T	ENST00000392749.2	+	2	261	c.22C>T	c.(22-24)Caa>Taa	p.Q8*	TANK_ENST00000406287.1_Nonsense_Mutation_p.Q66*|TANK_ENST00000402568.1_Nonsense_Mutation_p.Q66*|TANK_ENST00000405852.1_Nonsense_Mutation_p.Q8*|TANK_ENST00000457476.1_Nonsense_Mutation_p.Q8*|TANK_ENST00000259075.2_Nonsense_Mutation_p.Q8*|TANK_ENST00000403609.1_Nonsense_Mutation_p.Q8*	NM_001199135.1	NP_001186064.1	Q92844	TANK_HUMAN	TRAF family member-associated NFKB activator	8					I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)	21						CATTGGCGAGCAACTCAATAA	0.393																																					p.Q8X		Atlas-SNP	.											.	TANK	35	.	0			c.C22T						PASS	.						123	113	117					2																	162036195		2203	4300	6503	SO:0001587	stop_gained	10010	exon2			GGCGAGCAACTCA	U59863	CCDS2215.1, CCDS46436.1	2q24-q31	2008-02-05			ENSG00000136560	ENSG00000136560			11562	protein-coding gene	gene with protein product		603893		TRAF2		8710854, 8855313	Standard	NM_004180		Approved	I-TRAF	uc002ubr.2	Q92844	OTTHUMG00000132037	ENST00000392749.2:c.22C>T	2.37:g.162036195C>T	ENSP00000376505:p.Gln8*	136	0	0		100	41	0.41	NM_004180	D3DPB5|Q7Z4J6|Q92885	Nonsense_Mutation	SNP	ENST00000392749.2	37	CCDS2215.1	.	.	.	.	.	.	.	.	.	.	C	38	6.652831	0.97734	.	.	ENSG00000136560	ENST00000259075;ENST00000432002;ENST00000457476;ENST00000392749;ENST00000440506;ENST00000429217;ENST00000406287;ENST00000402568;ENST00000405852;ENST00000456358;ENST00000403609	.	.	.	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-11.5692	20.1743	0.98175	0.0:1.0:0.0:0.0	.	.	.	.	X	8;8;8;8;8;8;66;66;8;34;8	.	ENSP00000259075:Q8X	Q	+	1	0	TANK	161744441	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.913000	0.69957	2.873000	0.98535	0.561000	0.74099	CAA	.	.	none		0.393	TANK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324232.1	NM_133484		T	162036195	C	T	162036195	4	4	29	1	0	0	0	0	0	1	0	0	15561	711	25	2	24	2	TANK	2	162036195	Nonsense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1853821	162036195	81163178	134	12375											
KCNH7	90134	hgsc.bcm.edu	37	chr2	163228507	163228507	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgtcttgttttaaaagtgaAgtcaagttgtcttctgaagc	10	16	9	6	0	4	2	1	2	3	0	4	2	4	2	0	0	1	2	0	0	5	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:163228507A>C	ENST00000332142.5	-	16	3522	c.3423T>G	c.(3421-3423)acT>acG	p.T1141T		NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	1141					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)	TTAAAAGTGAAGTCAAGTTGT	0.388																																					p.T1141T	GBM(196;1492 2208 17507 24132 45496)	Atlas-SNP	.											KCNH7,NS,carcinoma,0,1	KCNH7	378	1	0			c.T3423G						PASS	.						86	84	85					2																	163228507		2203	4300	6503	SO:0001819	synonymous_variant	90134	exon16			AAGTGAAGTCAAG	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.3423T>G	2.37:g.163228507A>C		117	0	0		77	33	0.428571	NM_033272	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Silent	SNP	ENST00000332142.5	37	CCDS2219.1																																																																																			.	.	none		0.388	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255093.1	NM_033272		C	163228507	A	C	163228507	2	2	29	1	0	0	0	0	0	0	0	1	8046	59	3	5		5	KCNH7	2	163228507	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	1192312	163228507	79970866	135	12376											
LASS6	253782	hgsc.bcm.edu	37	chr2	169312974	169312974	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaagatggcagggatcttaGcctggttctggaacgagagg	10	8	16	7	1	2	2	0	0	2	2	2	5	2	4	1	5	2	3	1	5	3	2	rs4496303	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:169312974G>A	ENST00000305747.6	+	1	603	c.16G>A	c.(16-18)Gcc>Acc	p.A6T	CERS6_ENST00000392687.4_Missense_Mutation_p.A6T	NM_203463.2	NP_982288.1	Q6ZMG9	CERS6_HUMAN	ceramide synthase 6	6					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)										AGGGATCTTAGCCTGGTTCTG	0.657													G|||	39	0.00778754	0.0061	0.0101	5008	,	,		8564	0.0		0.0209	False		,,,				2504	0.0031				p.A6T		Atlas-SNP	.											.	.	.	.	0			c.G16A						PASS	.	G	THR/ALA	35,4371	40.0+/-72.8	2,31,2170	162	130	141		16	4.3	1	2	dbSNP_111	141	101,8499	56.4+/-117.6	0,101,4199	yes	missense	CERS6	NM_203463.1	58	2,132,6369	AA,AG,GG		1.1744,0.7944,1.0457	benign	6/385	169312974	136,12870	2203	4300	6503	SO:0001583	missense	253782	exon1			ATCTTAGCCTGGT	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.16G>A	2.37:g.169312974G>A	ENSP00000306579:p.Ala6Thr	75	0	0		72	36	0.5	NM_001256126	Q32M63|Q8N617	Missense_Mutation	SNP	ENST00000305747.6	37	CCDS2228.1	24	0.01098901098901099	4	0.008130081300813009	4	0.011049723756906077	0	0.0	16	0.021108179419525065	G	21.6	4.173118	0.78452	0.007944	0.011744	ENSG00000172292	ENST00000305747;ENST00000392687	T;T	0.21734	1.99;1.99	5.22	4.34	0.51931	.	0.105238	0.64402	N	0.000004	T	0.08358	0.0208	L	0.40543	1.245	0.58432	D	0.999999	B;B	0.32203	0.209;0.36	B;B	0.28465	0.045;0.09	T	0.04165	-1.0972	10	0.22706	T	0.39	-18.0462	13.4206	0.60996	0.0755:0.0:0.9245:0.0	.	6;6	Q32M63;Q6ZMG9	.;CERS6_HUMAN	T	6	ENSP00000306579:A6T;ENSP00000376453:A6T	ENSP00000306579:A6T	A	+	1	0	CERS6	169021220	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	9.346000	0.97056	1.188000	0.43014	0.467000	0.42956	GCC	A|0.008;G|0.990;T|0.002	0.008	strong		0.657	CERS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255235.2	NM_203463		A	169312974	G	A	169312974	3	1	29	1	0	0	0	0	1	0	0	0	8652	971	34	2	18	2	LASS6	2	169312974	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	6084467	169312974	73886399	136	12377											
LRP2	4036	hgsc.bcm.edu	37	chr2	170063380	170063380	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatagaattttcaaaaacagTgatgccataaggagttgggt	15	11	11	4	0	1	2	1	1	0	1	1	4	1	3	1	2	2	1	1	2	5	5	rs35413340	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:170063380T>C	ENST00000263816.3	-	39	7135	c.6850A>G	c.(6850-6852)Act>Gct	p.T2284A		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2284					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)"	TCAAAAACAGTGATGCCATAA	0.398													T|||	3	0.000599042	0.0	0.0014	5008	,	,		21566	0.0		0.002	False		,,,				2504	0.0				p.T2284A		Atlas-SNP	.											.	LRP2	751	.	0			c.A6850G						PASS	.	T	ALA/THR	2,4404	4.2+/-10.8	0,2,2201	126	129	128		6850	5.9	1	2	dbSNP_126	128	21,8579	16.0+/-53.3	0,21,4279	yes	missense	LRP2	NM_004525.2	58	0,23,6480	CC,CT,TT		0.2442,0.0454,0.1768	possibly-damaging	2284/4656	170063380	23,12983	2203	4300	6503	SO:0001583	missense	4036	exon39			AAACAGTGATGCC		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.6850A>G	2.37:g.170063380T>C	ENSP00000263816:p.Thr2284Ala	85	0	0		79	36	0.455696	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	T	4.072	0.011210	0.07912	4.54E-4	0.002442	ENSG00000081479	ENST00000263816	D	0.89681	-2.55	5.89	5.89	0.94794	Six-bladed beta-propeller, TolB-like (1);	0.045886	0.85682	D	0.000000	T	0.77432	0.4129	N	0.20328	0.56	0.80722	D	1	P	0.35192	0.489	B	0.26310	0.068	T	0.77696	-0.2491	10	0.02654	T	1	.	16.3127	0.82898	0.0:0.0:0.0:1.0	rs35413340	2284	P98164	LRP2_HUMAN	A	2284	ENSP00000263816:T2284A	ENSP00000263816:T2284A	T	-	1	0	LRP2	169771626	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.885000	0.48570	2.246000	0.74042	0.533000	0.62120	ACT	T|0.999;C|0.001	0.001	strong		0.398	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		C	170063380	T	C	170063380	3	2	29	1	0	0	0	0	1	0	0	0	8965	1696	59	3	7281	3	LRP2	2	170063380	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	750406	170063380	73135993	137	12378											
FASTKD1	79675	hgsc.bcm.edu	37	chr2	170387132	170387133	+	Frame_Shift_Ins	INS	-	-	T																															cccagaatttccaaatgtcgINSttttttcatagcagattttc																								rs148187838|rs566862006	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:170387132_170387133insT	ENST00000453153.2	-	14	2752_2753	c.2406_2407insA	c.(2404-2409)aaacgafs	p.R803fs	FASTKD1_ENST00000453929.2_Frame_Shift_Ins_p.R760fs|FASTKD1_ENST00000495505.1_5'UTR	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	803	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						TCCAAATGTCGTTTTTTCATAG	0.342													TTTTTT|TTTTTT|TTTTTTT|insertion	18	0.00359425	0.0008	0.0029	5008	,	,		15503	0.0		0.007	False		,,,				2504	0.0082				p.R803fs		Pindel,Atlas-Indel	.											.	FASTKD1	86	.	0			c.2407_2408insA						PASS	.			8,4258		0,8,2125						3.3	1			159	99,8155		1,97,4029	no	frameshift	FASTKD1	NM_024622.3		1,105,6154	A1A1,A1R,RR		1.1994,0.1875,0.8546				107,12413				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.2407dupA	2.37:g.170387138_170387138dupT	ENSP00000400513:p.Arg803fs	190	0	.		222	69	0.311	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Frame_Shift_Ins	INS	ENST00000453153.2	37	CCDS33318.1																																																																																			.	.	none		0.342	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622		T	170387133	-	T	170387132	7	5	29	1	0	1	1	0	0	0	0	0	5693	1153	40	0	144	0	FASTKD1	2	170387132	Frame_Shift_Ins	INS	-	TCGA-GR-7351-01A-11D-2210-10	323752	170387132	72812241	138	12379											
TTC30A	92104	hgsc.bcm.edu	37	chr2	178482246	178482246	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtcttgcttcctgtacttgcTtggtgagtctccgaagctgc	4	15	11	11	1	2	1	0	1	2	0	4	2	3	1	2	1	5	4	2	1	2	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:178482246T>G	ENST00000355689.5	-	1	1448	c.1184A>C	c.(1183-1185)aAg>aCg	p.K395T	AC073834.3_ENST00000357045.4_RNA	NM_152275.3	NP_689488.3	Q86WT1	TT30A_HUMAN	tetratricopeptide repeat domain 30A	395					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)			CTGTACTTGCTTGGTGAGTCT	0.453																																					p.K395T		Atlas-SNP	.											.	TTC30A	60	.	0			c.A1184C						PASS	.						238	237	237					2																	178482246		2203	4300	6503	SO:0001583	missense	92104	exon1			ACTTGCTTGGTGA	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.1184A>C	2.37:g.178482246T>G	ENSP00000347915:p.Lys395Thr	241	0	0		246	31	0.126016	NM_152275	A8K8N0|Q8IVP2	Missense_Mutation	SNP	ENST00000355689.5	37	CCDS2276.1	.	.	.	.	.	.	.	.	.	.	T	3.347	-0.133430	0.06711	.	.	ENSG00000197557	ENST00000355689	T	0.21734	1.99	5.91	-6.04	0.02178	.	0.330531	0.38959	N	0.001515	T	0.29524	0.0736	M	0.85945	2.785	0.49798	D	0.999822	B	0.32918	0.39	B	0.39617	0.305	T	0.29761	-1.0001	10	0.46703	T	0.11	.	15.5572	0.76203	0.6891:0.0:0.0:0.3109	.	395	Q86WT1	TT30A_HUMAN	T	395	ENSP00000347915:K395T	ENSP00000347915:K395T	K	-	2	0	TTC30A	178190492	0.212000	0.23540	0.397000	0.26308	0.105000	0.19272	0.477000	0.22196	-1.344000	0.02216	-1.497000	0.00963	AAG	.	.	none		0.453	TTC30A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255728.2	NM_152275		G	178482246	T	G	178482246	3	3	29	1	0	0	0	0	1	0	0	0	16713	1609	56	5	817	5	TTC30A	2	178482246	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	8095114	178482246	64717127	139	12380											
DNAH7	56171	hgsc.bcm.edu	37	chr2	196825256	196825256	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttcatgtctaaaaaagaggaGactgtggagtcatctgatgg	13	11	12	5	0	4	3	2	1	2	2	4	5	4	4	0	3	0	0	0	3	3	2	rs115124743	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:196825256G>C	ENST00000312428.6	-	18	2719	c.2619C>G	c.(2617-2619)gtC>gtG	p.V873V		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	873	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						AAAAAGAGGAGACTGTGGAGT	0.448													G|||	94	0.01877	0.0045	0.0389	5008	,	,		19851	0.0		0.0507	False		,,,				2504	0.0102				p.V873V		Atlas-SNP	.											.	DNAH7	512	.	0			c.C2619G						PASS	.	G		30,3736		0,30,1853	105	103	104		2619	2.4	0.8	2	dbSNP_132	104	347,7895		8,331,3782	no	coding-synonymous	DNAH7	NM_018897.2		8,361,5635	CC,CG,GG		4.2101,0.7966,3.1396		873/4025	196825256	377,11631	1883	4121	6004	SO:0001819	synonymous_variant	56171	exon18			AGAGGAGACTGTG	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.2619C>G	2.37:g.196825256G>C		106	0	0		128	80	0.625	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	37	CCDS42794.1																																																																																			G|0.969;C|0.031	0.031	strong		0.448	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		C	196825256	G	C	196825256	2	2	29	1	0	0	0	0	0	0	0	1	4608	929	33	4		4	DNAH7	2	196825256	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	18343010	196825256	46374117	140	12381											
STK17B	9262	hgsc.bcm.edu	37	chr2	197004468	197004575	+	Splice_Site	DEL	CTCCCACAAATGGTGATGTGTGAGTTAACAACATATATGCTATTATACCAATATTCCTGAAAAACAAGGGAGGGGAACTTAAAATGTATGTTAATTTTTAAACATTTA	CTCCCACAAATGGTGATGTGTGAGTTAACAACATATATGCTATTATACCAATATTCCTGAAAAACAAGGGAGGGGAACTTAAAATGTATGTTAATTTTTAAACATTTA	-																															gtatgtttcttgattatcttCtcccacaaatggtgatgtgt																								rs567859155|rs140646128|rs374561119		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CTCCCACAAATGGTGATGTGTGAGTTAACAACATATATGCTATTATACCAATATTCCTGAAAAACAAGGGAGGGGAACTTAAAATGTATGTTAATTTTTAAACATTTA	CTCCCACAAATGGTGATGTGTGAGTTAACAACATATATGCTATTATACCAATATTCCTGAAAAACAAGGGAGGGGAACTTAAAATGTATGTTAATTTTTAAACATTTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:197004468_197004575delCTCCCACAAATGGTGATGTGTGAGTTAACAACATATATGCTATTATACCAATATTCCTGAAAAACAAGGGAGGGGAACTTAAAATGTATGTTAATTTTTAAACATTTA	ENST00000263955.4	-	7	943_998	c.657_712delTAAATGTTTAAAAATTAACATACATTTTAAGTTCCCCTCCCTTGTTTTTCAGGAATATTGGTATAATAGCATATATGTTGTTAACTCACACATCACCATTTGTGGGAG	c.(655-714)tgtaaatgtttaaaaattaacatacattttaagttcccctcccttgtttttcaggaatat>tgat	p.219_238CKCLKINIHFKFPSLVFQEY>*	STK17B_ENST00000409228.1_Splice_Site_p.219_238CKCLKINIHFKFPSLVFQEY>*	NM_004226.3	NP_004217.1	O94768	ST17B_HUMAN	serine/threonine kinase 17b	219	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)			TGATTATCTTCTCCCACAAATGGTGATGTGTGAGTTAACAACATATATGCTATTATACCAATATTCCTGAAAAACAAGGGAGGGGAACTTAAAATGTATGTTAATTTTTAAACATTTATACAAAGTAC	0.315																																					p.219_238del		Pindel	.											.	STK17B	28	.	0			c.657_713del						PASS	.																																			SO:0001630	splice_region_variant	9262	exon7			.	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.657-1TAAATGTTTAAAAATTAACATACATTTTAAGTTCCCCTCCCTTGTTTTTCAGGAATATTGGTATAATAGCATATATGTTGTTAACTCACACATCACCATTTGTGGGAG>-	2.37:g.197004468_197004575delCTCCCACAAATGGTGATGTGTGAGTTAACAACATATATGCTATTATACCAATATTCCTGAAAAACAAGGGAGGGGAACTTAAAATGTATGTTAATTTTTAAACATTTA		84	0	.		68	15	0.221	NM_004226		In_Frame_Del	DEL	ENST00000263955.4	37	CCDS2315.1																																																																																			.	.	none		0.315	STK17B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256092.2		In_Frame_Del	-	197004575	CTCCCACAAATGGTGATGTGTGAGTTAACAACATATATGCTATTATACCAATATTCCTGAAAAACAAGGGAGGGGAACTTAAAATGTATGTTAATTTTTAAACATTTA	-	197004468	8	5	29	1	0	1	0	1	0	0	1	0	15306	922	32	0	414	0	STK17B	2	197004468	Splice_Site	DEL	CTCCCACAAATGGTGATGTGTGAGTTAACAACATATATGCTATTATACCAATATTCCTGAAAAACAAGGGAGGGGAACTTAAAATGTATGTTAATTTTTAAACATTTA	TCGA-GR-7351-01A-11D-2210-10	179212	197004468	46194905	141	12382											
SF3B1	23451	hgsc.bcm.edu	37	chr2	198270136	198270136	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accacccaaaggtgttggagTagctgtcagctttcgagctg	9	10	12	10	1	1	0	1	0	0	0	2	2	1	1	2	2	3	5	2	2	2	3	rs367701030		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:198270136T>C	ENST00000335508.6	-	10	1391	c.1300A>G	c.(1300-1302)Act>Gct	p.T434A	SF3B1_ENST00000462613.1_5'Flank|SNORA4_ENST00000365564.1_RNA	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	434	Interaction with PPP1R8.				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)			GGTGTTGGAGTAGCTGTCAGC	0.398			Mis		myelodysplastic syndrome																																p.T434A		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"splicing factor 3b, subunit 1, 155kDa"		L	.	SF3B1	1038	.	0			c.A1300G						PASS	.						50	50	50					2																	198270136		2203	4300	6503	SO:0001583	missense	23451	exon10			TTGGAGTAGCTGT	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.1300A>G	2.37:g.198270136T>C	ENSP00000335321:p.Thr434Ala	177	0	0		156	44	0.282051	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	37	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	T	18.10	3.549172	0.65311	.	.	ENSG00000115524	ENST00000335508	.	.	.	5.66	5.66	0.87406	Splicing factor 3B subunit 1 (1);	0.000000	0.85682	D	0.000000	T	0.73087	0.3542	M	0.80746	2.51	0.80722	D	1	B	0.31752	0.338	B	0.38194	0.267	T	0.73597	-0.3932	9	0.45353	T	0.12	.	16.1922	0.82000	0.0:0.0:0.0:1.0	.	434	O75533	SF3B1_HUMAN	A	434	.	ENSP00000335321:T434A	T	-	1	0	SF3B1	197978381	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.883000	0.87264	2.280000	0.76307	0.533000	0.62120	ACT	.	.	alt		0.398	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2			C	198270136	T	C	198270136	3	2	29	1	0	0	0	0	1	0	0	0	14164	1638	57	3	2678	3	SF3B1	2	198270136	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	1265668	198270136	44929237	142	12383											
NOP58	51602	hgsc.bcm.edu	37	chr2	203157538	203157538	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tatcgaacccagctctatgaAtatctacaaaatcgaatgat	16	11	5	9	2	2	2	0	2	2	0	4	4	2	2	1	0	3	1	1	0	9	4	rs16839032	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:203157538A>G	ENST00000264279.5	+	9	1045	c.819A>G	c.(817-819)gaA>gaG	p.E273E	SNORD11B_ENST00000607707.1_RNA|SNORD11_ENST00000459124.1_RNA	NM_015934.3	NP_057018.1	Q9Y2X3	NOP58_HUMAN	NOP58 ribonucleoprotein	273					cell growth (GO:0016049)|rRNA processing (GO:0006364)|snRNP protein import into nucleus (GO:0006608)	box C/D snoRNP complex (GO:0031428)|Cajal body (GO:0015030)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)	p.E273E(1)		breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|lung(4)|prostate(2)	16						AGCTCTATGAATATCTACAAA	0.368													A|||	31	0.0061901	0.0	0.0187	5008	,	,		18977	0.0		0.0159	False		,,,				2504	0.002				p.E273E		Atlas-SNP	.											NOP58,NS,carcinoma,0,1	NOP58	41	1	1	Substitution - coding silent(1)	prostate(1)	c.A819G						PASS	.	A		12,4394	19.1+/-41.9	0,12,2191	159	160	160		819	0.3	1	2	dbSNP_123	160	133,8467	67.0+/-129.4	3,127,4170	no	coding-synonymous	NOP58	NM_015934.3		3,139,6361	GG,GA,AA		1.5465,0.2724,1.1149		273/530	203157538	145,12861	2203	4300	6503	SO:0001819	synonymous_variant	51602	exon9			CTATGAATATCTA		CCDS2353.1	2q33.1	2012-12-10	2012-12-10		ENSG00000055044	ENSG00000055044			29926	protein-coding gene	gene with protein product			"NOP58 ribonucleoprotein homolog (yeast)"			10606270, 10925205	Standard	NM_015934		Approved	NOP5, HSPC120	uc002uzb.3	Q9Y2X3	OTTHUMG00000132840	ENST00000264279.5:c.819A>G	2.37:g.203157538A>G		116	0	0		132	66	0.5	NM_015934	Q53SA4|Q6PK08|Q9P036|Q9UFN3	Silent	SNP	ENST00000264279.5	37	CCDS2353.1																																																																																			A|0.989;G|0.011	0.011	strong		0.368	NOP58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256313.2	NM_015934		G	203157538	A	G	203157538	2	3	29	1	0	0	0	0	0	0	0	1	10549	98	4	3		3	NOP58	2	203157538	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	4887402	203157538	40041835	143	12384											
ALS2CR8	79800	hgsc.bcm.edu	37	chr2	203847044	203847044	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aaaatctagttgcaatggacGagctggtagaagttggagat	14	10	13	4	1	1	2	0	0	1	2	1	5	1	3	0	3	2	5	0	3	6	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:203847044G>A	ENST00000402905.3	+	15	2260	c.1939G>A	c.(1939-1941)Gag>Aag	p.E647K	CARF_ENST00000320443.8_Missense_Mutation_p.E647K|CARF_ENST00000414439.1_Missense_Mutation_p.E545K|CARF_ENST00000438828.2_Missense_Mutation_p.E647K|CARF_ENST00000545253.1_Missense_Mutation_p.E559K|WDR12_ENST00000477723.1_Intron|CARF_ENST00000545262.1_Missense_Mutation_p.E571K|CARF_ENST00000428585.1_Missense_Mutation_p.E571K	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	647					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)										TGCAATGGACGAGCTGGTAGA	0.428																																					p.E647K		Atlas-SNP	.											.	ALS2CR8	56	.	0			c.G1939A						PASS	.						89	85	86					2																	203847044		1918	4142	6060	SO:0001583	missense	79800	exon16			ATGGACGAGCTGG	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.1939G>A	2.37:g.203847044G>A	ENSP00000384006:p.Glu647Lys	139	0	0		170	52	0.305882	NM_024744	B4E1W7|G3V1K7|Q8ND29|Q8WXC0|Q96J78|Q96Q38|Q96Q39|Q9H712	Missense_Mutation	SNP	ENST00000402905.3	37	CCDS42801.1	.	.	.	.	.	.	.	.	.	.	G	17.61	3.431639	0.62844	.	.	ENSG00000138380	ENST00000402905;ENST00000414439;ENST00000428585;ENST00000545253;ENST00000545262;ENST00000320443;ENST00000438828	.	.	.	5.83	4.96	0.65561	.	0.075586	0.53938	D	0.000052	T	0.26521	0.0648	N	0.08118	0	0.25176	N	0.990241	B;B;B	0.09022	0.002;0.002;0.002	B;B;B	0.10450	0.005;0.005;0.005	T	0.26467	-1.0102	9	0.66056	D	0.02	-2.4529	14.485	0.67611	0.0:0.8521:0.1479:0.0	.	559;571;647	B4DIA7;G3V1K7;Q8N187	.;.;AL2S8_HUMAN	K	647;545;571;559;571;647;647	.	ENSP00000316224:E647K	E	+	1	0	ALS2CR8	203555289	1.000000	0.71417	0.999000	0.59377	0.741000	0.42261	3.706000	0.54830	1.487000	0.48415	-0.133000	0.14855	GAG	.	.	none		0.428	CARF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335768.5	NM_001104586		A	203847044	G	A	203847044	3	1	29	1	0	0	0	0	1	0	0	0	555	1059	37	1	1989	1	ALS2CR8	2	203847044	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	689506	203847044	39352329	144	12385											
INO80D	54891	hgsc.bcm.edu	37	chr2	206872126	206872126	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atctcattggcaatgtcatcCggcaactcatcagcactcag	11	10	7	13	1	5	0	5	0	1	0	7	0	6	0	1	2	2	3	1	2	2	1	rs116331438	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:206872126C>T	ENST00000403263.1	-	10	2204	c.1800G>A	c.(1798-1800)ccG>ccA	p.P600P	Vault_ENST00000516676.1_RNA	NM_017759.4	NP_060229.3	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	600					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.P600P(1)|p.P495P(1)		NS(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	26						CAATGTCATCCGGCAACTCAT	0.498													C|||	2	0.000399361	0.0	0.0	5008	,	,		19913	0.0		0.001	False		,,,				2504	0.001				p.P600P		Atlas-SNP	.											INO80D_ENST00000403263,NS,carcinoma,0,2	INO80D	134	2	2	Substitution - coding silent(2)	kidney(2)	c.G1800A						PASS	.	C		3,4115		0,3,2056	130	130	130		1800	2.8	1	2	dbSNP_132	130	22,8406		0,22,4192	no	coding-synonymous	INO80D	NM_017759.4		0,25,6248	TT,TC,CC		0.261,0.0729,0.1993		600/1028	206872126	25,12521	2059	4214	6273	SO:0001819	synonymous_variant	54891	exon10			GTCATCCGGCAAC		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.1800G>A	2.37:g.206872126C>T		202	0	0		241	118	0.489627	NM_017759	B3KU68|B9EG77|Q6PJC6|Q6PJU1|Q6PKA1|Q9NXD5	Silent	SNP	ENST00000403263.1	37	CCDS46500.1																																																																																			C|0.999;T|0.001	0.001	strong		0.498	INO80D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336459.1	NM_017759		T	206872126	C	T	206872126	2	4	29	1	0	0	0	0	0	0	0	1	7758	639	23	1		1	INO80D	2	206872126	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	3025082	206872126	36327247	145	12386											
FASTKD2	22868	hgsc.bcm.edu	37	chr2	207632128	207632128	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacctactgttcagtcttcaCgccatagtgaagcttggaat	10	13	8	10	1	3	1	2	1	1	0	3	2	3	2	2	1	3	2	2	1	5	6	rs150195745		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:207632128C>T	ENST00000236980.6	+	2	1059	c.711C>T	c.(709-711)caC>caT	p.H237H	MDH1B_ENST00000392214.2_5'Flank|FASTKD2_ENST00000402774.3_Silent_p.H237H|MDH1B_ENST00000454776.2_5'Flank|MDH1B_ENST00000374412.3_5'Flank|MDH1B_ENST00000449792.1_5'Flank|FASTKD2_ENST00000403094.3_Silent_p.H237H	NM_014929.3	NP_055744.2	Q9NYY8	FAKD2_HUMAN	FAST kinase domains 2	237					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)		TCAGTCTTCACGCCATAGTGA	0.413																																					p.H237H		Atlas-SNP	.											.	FASTKD2	49	.	0			c.C711T						PASS	.	C	,,	1,4315		0,1,2157	84	82	83		711,711,711	-0.4	0.1	2	dbSNP_134	83	0,8568		0,0,4284	no	coding-synonymous,coding-synonymous,coding-synonymous	FASTKD2	NM_001136193.1,NM_001136194.1,NM_014929.3	,,	0,1,6441	TT,TC,CC		0.0,0.0232,0.0078	,,	237/711,237/711,237/711	207632128	1,12883	2158	4284	6442	SO:0001819	synonymous_variant	22868	exon2			TCTTCACGCCATA	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.711C>T	2.37:g.207632128C>T		55	0	0		49	25	0.510204	NM_001136193	Q9NVX6|Q9Y2H7	Silent	SNP	ENST00000236980.6	37	CCDS2371.1																																																																																			C|1.000;T|0.000	0.000	weak		0.413	FASTKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256428.2	NM_014929		T	207632128	C	T	207632128	2	4	29	1	0	0	0	0	0	0	0	1	5694	535	19	1		1	FASTKD2	2	207632128	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	760002	207632128	35567245	146	12387											
ERBB4	2066	hgsc.bcm.edu	37	chr2	212251864	212251864	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcaaaacctccatctcggtaTacaaactggttctgttaata	13	12	6	10	1	2	0	0	0	2	0	4	0	3	0	2	2	3	4	2	2	7	5	rs3748962	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:212251864T>C	ENST00000342788.4	-	27	3505	c.3195A>G	c.(3193-3195)gtA>gtG	p.V1065V	ERBB4_ENST00000402597.1_Silent_p.V1055V|ERBB4_ENST00000436443.1_Silent_p.V1049V	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	1065					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)	CATCTCGGTATACAAACTGGT	0.433										TSP Lung(8;0.080)			T|||	1117	0.223043	0.0756	0.2983	5008	,	,		18765	0.2887		0.2992	False		,,,				2504	0.2229				p.V1065V		Atlas-SNP	.											.	ERBB4	480	.	0			c.A3195G						PASS	.	T	,	444,3962	214.5+/-233.7	29,386,1788	110	113	112		3147,3195	-8.9	0.3	2	dbSNP_107	112	2843,5757	447.9+/-361.7	499,1845,1956	no	coding-synonymous,coding-synonymous	ERBB4	NM_001042599.1,NM_005235.2	,	528,2231,3744	CC,CT,TT		33.0581,10.0772,25.273	,	1049/1293,1065/1309	212251864	3287,9719	2203	4300	6503	SO:0001819	synonymous_variant	2066	exon27			TCGGTATACAAAC	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.3195A>G	2.37:g.212251864T>C		165	0	0		189	92	0.486772	NM_005235	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Silent	SNP	ENST00000342788.4	37	CCDS2394.1																																																																																			T|0.756;C|0.244	0.244	strong		0.433	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		C	212251864	T	C	212251864	2	2	29	1	0	0	0	0	0	0	0	1	5211	1393	49	3		3	ERBB4	2	212251864	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	4619736	212251864	30947509	147	12388											
VIL1	7429	hgsc.bcm.edu	37	chr2	219313993	219313993	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggcctttgggatgactccAgctgccttctctgctctgcc	4	12	10	15	0	2	1	0	1	2	0	4	2	3	2	4	2	4	2	4	2	0	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:219313993A>C	ENST00000248444.5	+	20	2506	c.2418A>C	c.(2416-2418)ccA>ccC	p.P806P	VIL1_ENST00000392114.2_Silent_p.P495P	NM_007127.2	NP_009058.2	P09327	VILI_HUMAN	villin 1	806	HP. {ECO:0000255|PROSITE- ProRule:PRU00595}.|Headpiece.				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)		GGATGACTCCAGCTGCCTTCT	0.478																																					p.P806P		Atlas-SNP	.											.	VIL1	65	.	0			c.A2418C						PASS	.						229	230	230					2																	219313993		2203	4300	6503	SO:0001819	synonymous_variant	7429	exon20			GACTCCAGCTGCC	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.2418A>C	2.37:g.219313993A>C		119	0	0		101	48	0.475248	NM_007127	B2R9A7|Q53S11|Q96AC8	Silent	SNP	ENST00000248444.5	37	CCDS2417.1																																																																																			.	.	none		0.478	VIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256778.3	NM_007127		C	219313993	A	C	219313993	2	2	29	1	0	0	0	0	0	0	0	1	17179	175	7	5		5	VIL1	2	219313993	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	7062129	219313993	23885380	148	12389											
USP37	57695	hgsc.bcm.edu	37	chr2	219360656	219360656	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agctggtccaaacactgactTaaaaattcatgagcatccta	15	10	6	10	0	1	2	1	2	0	0	3	2	3	2	2	1	3	2	2	1	5	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:219360656T>C	ENST00000258399.3	-	14	1711	c.1299A>G	c.(1297-1299)ttA>ttG	p.L433L	USP37_ENST00000454775.1_Silent_p.L433L|USP37_ENST00000415516.1_Silent_p.L361L|USP37_ENST00000418019.1_Silent_p.L433L	NM_020935.2	NP_065986	Q86T82	UBP37_HUMAN	ubiquitin specific peptidase 37	433	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)		AACACTGACTTAAAAATTCAT	0.348																																					p.L433L		Atlas-SNP	.											.	USP37	76	.	0			c.A1299G						PASS	.						64	67	66					2																	219360656		2203	4300	6503	SO:0001819	synonymous_variant	57695	exon14			CTGACTTAAAAAT	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.1299A>G	2.37:g.219360656T>C		77	0	0		59	21	0.355932	NM_020935	A2RUQ8|B7ZM38|B7ZM41|E9PHL3|Q2KHT2|Q53S10|Q7Z3A5|Q9HCH8	Silent	SNP	ENST00000258399.3	37	CCDS2418.1																																																																																			.	.	none		0.348	USP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256779.3	NM_020935		C	219360656	T	C	219360656	2	2	29	1	0	0	0	0	0	0	0	1	17083	1751	61	3		3	USP37	2	219360656	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	46663	219360656	23838717	149	12390											
CDK5R2	8941	hgsc.bcm.edu	37	chr2	219824731	219824731	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccgtccgtgctcatctcggcGctcacctggaagcgcctggt	4	9	12	16	5	3	0	2	0	1	0	5	1	4	1	4	3	2	2	4	3	1	0	rs78141300	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:219824731G>C	ENST00000302625.4	+	1	355	c.189G>C	c.(187-189)gcG>gcC	p.A63A	AC097468.7_ENST00000429343.1_RNA	NM_003936.4	NP_003927.1	Q13319	CD5R2_HUMAN	cyclin-dependent kinase 5, regulatory subunit 2 (p39)	63					cerebellum development (GO:0021549)|hippocampus development (GO:0021766)|layer formation in cerebral cortex (GO:0021819)|neuron migration (GO:0001764)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|superior olivary nucleus maturation (GO:0021722)	cyclin-dependent protein kinase 5 holoenzyme complex (GO:0016533)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	cyclin-dependent protein kinase 5 activator activity (GO:0016534)|lipid binding (GO:0008289)			central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(1)|ovary(1)	8		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)		TCATCTCGGCGCTCACCTGGA	0.716													G|||	163	0.0325479	0.0061	0.0375	5008	,	,		7620	0.0179		0.0398	False		,,,				2504	0.0726				p.A63A		Atlas-SNP	.											.	CDK5R2	17	.	0			c.G189C						PASS	.	G		22,4302		2,18,2142	10	14	13		189	2.5	1	2	dbSNP_131	13	213,8313		1,211,4051	no	coding-synonymous	CDK5R2	NM_003936.3		3,229,6193	CC,CG,GG		2.4982,0.5088,1.8288		63/368	219824731	235,12615	2162	4263	6425	SO:0001819	synonymous_variant	8941	exon1			CTCGGCGCTCACC	U34051	CCDS2427.1	2q35	2008-05-22			ENSG00000171450	ENSG00000171450			1776	protein-coding gene	gene with protein product	"neuronal CDK5 activator isoform"	603764				7592934	Standard	NM_003936		Approved	p39nck5ai, P39, NCK5AI	uc002vjf.4	Q13319	OTTHUMG00000133083	ENST00000302625.4:c.189G>C	2.37:g.219824731G>C		26	0	0		22	12	0.545455	NM_003936	Q4ZFW6	Silent	SNP	ENST00000302625.4	37	CCDS2427.1																																																																																			G|0.972;C|0.028	0.028	strong		0.716	CDK5R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256728.1	NM_003936		C	219824731	G	C	219824731	2	2	29	1	0	0	0	0	0	0	0	1	3146	1074	38	4		4	CDK5R2	2	219824731	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	464075	219824731	23374642	150	12391											
ZFAND2B	130617	hgsc.bcm.edu	37	chr2	220072382	220072382	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gactacaggatatccaggtaCctgtgtgccctctctgtaat	9	12	9	11	0	1	0	0	0	1	0	3	2	2	1	3	2	3	2	3	2	4	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:220072382C>T	ENST00000289528.5	+	3	358	c.163C>T	c.(163-165)Cct>Tct	p.P55S	ZFAND2B_ENST00000409206.1_Missense_Mutation_p.P55S|ZFAND2B_ENST00000409594.1_Missense_Mutation_p.P55S|ZFAND2B_ENST00000409336.1_Missense_Mutation_p.P55S|ZFAND2B_ENST00000409412.1_Missense_Mutation_p.P55S|ZFAND2B_ENST00000409097.1_Missense_Mutation_p.P55S|ZFAND2B_ENST00000409319.1_Missense_Mutation_p.P55S|ZFAND2B_ENST00000409217.1_Missense_Mutation_p.P55S|ZFAND2B_ENST00000468301.1_3'UTR|ZFAND2B_ENST00000444522.2_Missense_Mutation_p.P55S	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	55						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)		TATCCAGGTACCTGTGTGCCC	0.557																																					p.P55S		Atlas-SNP	.											ZFAND2B_ENST00000444522,NS,carcinoma,-1,2	ZFAND2B	28	2	0			c.C163T						PASS	.						97	86	90					2																	220072382		2203	4300	6503	SO:0001583	missense	130617	exon3			CAGGTACCTGTGT	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.163C>T	2.37:g.220072382C>T	ENSP00000289528:p.Pro55Ser	80	0	0		82	28	0.341463	NM_138802	Q8NB98	Missense_Mutation	SNP	ENST00000289528.5	37	CCDS2435.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.033810	0.93575	.	.	ENSG00000158552	ENST00000409206;ENST00000409594;ENST00000289528;ENST00000422255;ENST00000409412;ENST00000409097;ENST00000409336;ENST00000409217;ENST00000409319;ENST00000444522	T;T;T;T;T;T;T;T;T;T	0.49432	0.88;0.88;0.78;0.83;0.93;0.81;0.78;0.81;0.93;0.81	5.17	5.17	0.71159	Zinc finger, AN1-type (1);	0.000000	0.85682	D	0.000000	T	0.76644	0.4016	M	0.92604	3.325	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.80764	0.96;0.994	T	0.82063	-0.0643	10	0.62326	D	0.03	-17.9994	18.4617	0.90741	0.0:1.0:0.0:0.0	.	55;55	Q8WV99;B4DEN4	ZFN2B_HUMAN;.	S	55	ENSP00000386824:P55S;ENSP00000386399:P55S;ENSP00000289528:P55S;ENSP00000409931:P55S;ENSP00000386847:P55S;ENSP00000387179:P55S;ENSP00000386898:P55S;ENSP00000386370:P55S;ENSP00000387312:P55S;ENSP00000411334:P55S	ENSP00000289528:P55S	P	+	1	0	ZFAND2B	219780626	1.000000	0.71417	0.982000	0.44146	0.998000	0.95712	7.080000	0.76837	2.691000	0.91804	0.655000	0.94253	CCT	.	.	none		0.557	ZFAND2B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256824.2	NM_138802		T	220072382	C	T	220072382	3	4	29	1	0	0	0	0	1	0	0	0	17643	507	18	2	173	2	ZFAND2B	2	220072382	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	247651	220072382	23126991	151	12392											
NCL	4691	hgsc.bcm.edu	37	chr2	232325406	232325408	+	In_Frame_Del	DEL	TCA	TCA	-																															cctcctcttcttcctcctccTcatcatcttcatcatcatca																								rs556842200|rs200406507	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TCA	TCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:232325406_232325408delTCA	ENST00000322723.4	-	4	1023_1025	c.783_785delTGA	c.(781-786)gatgag>gag	p.D261del	SNORD82_ENST00000365530.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	261	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)		TTCCTCCTCCtcatcatcttcat	0.433														27	0.00539137	0.0023	0.0043	5008	,	,		27425	0.006		0.004	False		,,,				2504	0.0112				p.262_262del		Pindel,Atlas-Indel	.											.	NCL	80	.	0			c.784_786del						PASS	.			103,4161		0,103,2029						-8.8	0		dbSNP_130	203	81,8169		0,81,4044	no	coding	NCL	NM_005381.2		0,184,6073	A1A1,A1R,RR		0.9818,2.4156,1.4704				184,12330				SO:0001651	inframe_deletion	4691	exon4			.		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.783_785delTGA	2.37:g.232325409_232325411delTCA	ENSP00000318195:p.Asp261del	154	0	.		153	34	0.222	NM_005381	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	In_Frame_Del	DEL	ENST00000322723.4	37	CCDS33397.1																																																																																			.	.	none		0.433	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381		-	232325408	TCA	-	232325406	7	5	29	1	0	1	0	1	0	0	0	0	10235	1551	54	0	1391	0	NCL	2	232325406	In_Frame_Del	DEL	TCA	TCGA-GR-7351-01A-11D-2210-10	12253024	232325406	10873967	152	12393											
RBM44	375316	hgsc.bcm.edu	37	chr2	238725962	238725962	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctcctttaagttcagaattaGatcctgaagtgcagaaaaaa	16	11	7	7	0	1	4	1	1	0	3	3	4	3	4	2	0	1	2	2	0	7	4	rs182474506		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:238725962G>A	ENST00000409864.1	+	3	657	c.403G>A	c.(403-405)Gat>Aat	p.D135N	RBM44_ENST00000444524.2_Intron|RBM44_ENST00000316997.4_Missense_Mutation_p.D135N			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	134						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)		TTCAGAATTAGATCCTGAAGT	0.313													G|||	1	0.000199681	0.0	0.0014	5008	,	,		20081	0.0		0.0	False		,,,				2504	0.0				p.D135N		Atlas-SNP	.											.	RBM44	167	.	0			c.G403A						PASS	.	G	ASN/ASP	1,3595		0,1,1797	25	24	24		403	1.4	0.2	2		24	13,8105		0,13,4046	yes	missense	RBM44	NM_001080504.2	23	0,14,5843	AA,AG,GG		0.1601,0.0278,0.1195	benign	135/1053	238725962	14,11700	1798	4059	5857	SO:0001583	missense	375316	exon3			GAATTAGATCCTG	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.403G>A	2.37:g.238725962G>A	ENSP00000386727:p.Asp135Asn	103	0	0		99	44	0.444444	NM_001080504	A0AUW3	Missense_Mutation	SNP	ENST00000409864.1	37	CCDS46554.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	12.37	1.916209	0.33815	2.78E-4	0.001601	ENSG00000177483	ENST00000316997;ENST00000409864	T;T	0.30182	1.54;1.54	5.47	1.35	0.21983	.	0.605422	0.15459	N	0.261208	T	0.23688	0.0573	L	0.54323	1.7	0.09310	N	1	B	0.28760	0.221	B	0.19148	0.024	T	0.15607	-1.0431	10	0.54805	T	0.06	-3.5583	5.6878	0.17813	0.1812:0.2994:0.5194:0.0	.	134	Q6ZP01	RBM44_HUMAN	N	135	ENSP00000321179:D135N;ENSP00000386727:D135N	ENSP00000321179:D135N	D	+	1	0	RBM44	238390701	0.795000	0.28851	0.183000	0.23137	0.182000	0.23217	0.220000	0.17660	-0.018000	0.14079	0.558000	0.71614	GAT	G|0.999;A|0.001	0.001	strong		0.313	RBM44-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328733.2	NM_001080504		A	238725962	G	A	238725962	3	1	29	1	0	0	0	0	1	0	0	0	13153	942	33	2	409	2	RBM44	2	238725962	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	6400556	238725962	4473411	153	12394											
KIF1A	547	hgsc.bcm.edu	37	chr2	241710437	241710437	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggggcaaacaagatgcgcTcgtggaggctggacacggag	10	4	17	10	4	0	1	0	0	0	1	1	4	0	4	1	6	2	3	1	6	2	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:241710437T>C	ENST00000320389.7	-	14	1423	c.1265A>G	c.(1264-1266)gAg>gGg	p.E422G	KIF1A_ENST00000498729.2_Missense_Mutation_p.E431G	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	422					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)		CAAGATGCGCTCGTGGAGGCT	0.647																																					p.E431G		Atlas-SNP	.											.	KIF1A	152	.	0			c.A1292G						PASS	.						44	56	52					2																	241710437		2080	4234	6314	SO:0001583	missense	547	exon15			ATGCGCTCGTGGA	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.1265A>G	2.37:g.241710437T>C	ENSP00000322791:p.Glu422Gly	45	0	0		63	15	0.238095	NM_001244008	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Missense_Mutation	SNP	ENST00000320389.7	37	CCDS46561.1	.	.	.	.	.	.	.	.	.	.	T	18.52	3.641091	0.67244	.	.	ENSG00000130294	ENST00000320389;ENST00000498729;ENST00000373308;ENST00000404283	T;T;T	0.73897	-0.66;-0.72;-0.79	4.11	4.11	0.48088	.	0.122605	0.53938	N	0.000052	T	0.60274	0.2256	L	0.27053	0.805	0.58432	D	0.999997	B;P;P	0.40909	0.002;0.688;0.732	B;B;B	0.37601	0.008;0.235;0.254	T	0.59768	-0.7392	10	0.29301	T	0.29	.	13.1308	0.59380	0.0:0.0:0.0:1.0	.	431;431;422	F5H045;Q12756-2;Q12756	.;.;KIF1A_HUMAN	G	422;431;431;431	ENSP00000322791:E422G;ENSP00000438388:E431G;ENSP00000384231:E431G	ENSP00000322791:E422G	E	-	2	0	KIF1A	241359110	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.804000	0.85993	1.508000	0.48769	0.454000	0.30748	GAG	.	.	none		0.647	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483		C	241710437	T	C	241710437	3	2	29	1	0	0	0	0	1	0	0	0	8292	1551	54	3	3943	3	KIF1A	2	241710437	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	2984475	241710437	1488936	154	12395											
MTERFD2	130916	hgsc.bcm.edu	37	chr2	242039210	242039210	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggaggctgtagtcagtttgcGcaacaaagaagctgtcgtcc	10	9	13	9	2	1	1	1	0	0	1	3	2	2	2	1	2	3	5	1	2	4	2	rs143756138	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:242039210G>A	ENST00000391980.2	-	2	179	c.121C>T	c.(121-123)Cgc>Tgc	p.R41C	MTERFD2_ENST00000495694.1_Missense_Mutation_p.R41C|MTERFD2_ENST00000406593.1_Intron|MTERFD2_ENST00000464344.2_Intron|MTERFD2_ENST00000407095.3_Missense_Mutation_p.R41C	NM_182501.3	NP_872307.2	Q7Z6M4	MTEF4_HUMAN		41					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)		GTCAGTTTGCGCAACAAAGAA	0.512													G|||	2	0.000399361	0.0	0.0014	5008	,	,		19876	0.0		0.001	False		,,,				2504	0.0				p.R41C		Atlas-SNP	.											.	MTERFD2	33	.	0			c.C121T						PASS	.	G	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	63	62	62		121	1.7	0	2	dbSNP_134	62	4,8596	3.7+/-12.6	0,4,4296	yes	missense	MTERFD2	NM_182501.3	180	0,5,6498	AA,AG,GG		0.0465,0.0227,0.0384	probably-damaging	41/382	242039210	5,13001	2203	4300	6503	SO:0001583	missense	130916	exon2			GTTTGCGCAACAA																												ENST00000391980.2:c.121C>T	2.37:g.242039210G>A	ENSP00000375840:p.Arg41Cys	79	0	0		93	42	0.451613	NM_182501	A8K6K0|Q9P0E0	Missense_Mutation	SNP	ENST00000391980.2	37	CCDS2544.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	11.21	1.570481	0.28003	2.27E-4	4.65E-4	ENSG00000122085	ENST00000495694;ENST00000401626;ENST00000391980;ENST00000424798;ENST00000407095;ENST00000434791	T;T;T;T;T;T	0.54479	0.57;0.66;2.42;1.26;1.28;0.72	4.57	1.73	0.24493	.	0.943497	0.08723	N	0.903139	T	0.28896	0.0717	N	0.08118	0	0.09310	N	1	B;B	0.26577	0.029;0.153	B;B	0.15052	0.005;0.012	T	0.16394	-1.0404	10	0.37606	T	0.19	-22.0841	6.2517	0.20850	0.337:0.0:0.663:0.0	.	41;41	B4DKD5;Q7Z6M4	.;MTER2_HUMAN	C	41;41;41;34;41;20	ENSP00000419315:R41C;ENSP00000385183:R41C;ENSP00000375840:R41C;ENSP00000409023:R34C;ENSP00000385630:R41C;ENSP00000393063:R20C	ENSP00000241527:R41C	R	-	1	0	MTERFD2	241687883	0.001000	0.12720	0.001000	0.08648	0.429000	0.31625	0.448000	0.21726	0.047000	0.15862	0.591000	0.81541	CGC	G|0.999;A|0.001	0.001	strong		0.512	MTERFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323798.4			A	242039210	G	A	242039210	3	1	29	1	0	0	0	0	1	0	0	0	9929	1087	38	1	1036	1	MTERFD2	2	242039210	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	328773	242039210	1160163	155	12396											
FARP2	9855	hgsc.bcm.edu	37	chr2	242407679	242407680	+	Frame_Shift_Del	DEL	CT	CT	-																															gcagaaggtctgctacttgcCtctcaacacgttcctgctga																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr2:242407679_242407680delCT	ENST00000264042.3	+	18	2188_2189	c.2018_2019delCT	c.(2017-2019)cctfs	p.P673fs		NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	673	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				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)		TGCTACTTGCCTCTCAACACGT	0.564																																					p.673_673del		Pindel,Atlas-Indel	.											.	FARP2	92	.	0			c.2017_2018del						PASS	.			18,4248		9,0,2124						5	1			109	40,8212		19,2,4105	no	frameshift	FARP2	NM_014808.2		28,2,6229	A1A1,A1R,RR		0.4847,0.4219,0.4633				58,12460				SO:0001589	frameshift_variant	9855	exon18			.	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.2018_2019delCT	2.37:g.242407681_242407682delCT	ENSP00000264042:p.Pro673fs	82	0	.		62	17	0.274	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Frame_Shift_Del	DEL	ENST00000264042.3	37	CCDS33424.1																																																																																			.	.	none		0.564	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1			-	242407680	CT	-	242407679	7	5	29	1	0	1	0	1	0	0	0	0	5685	681	24	0	2084	0	FARP2	2	242407679	Frame_Shift_Del	DEL	CT	TCGA-GR-7351-01A-11D-2210-10	368469	242407679	791694	156	12397											
SETD5	55209	hgsc.bcm.edu	37	chr3	9483818	9483818	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aattgtatccctagaccataCccctttgtgctcttctactc	8	15	4	14	0	2	1	0	0	2	1	4	1	3	1	4	0	3	2	4	0	5	7			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:9483818C>G	ENST00000406341.1	+	9	1156	c.966C>G	c.(964-966)taC>taG	p.Y322*	SETD5_ENST00000407969.1_Nonsense_Mutation_p.Y341*|SETD5_ENST00000402198.1_Nonsense_Mutation_p.Y322*|SETD5_ENST00000402466.1_Nonsense_Mutation_p.Y224*|SETD5_ENST00000302463.6_Nonsense_Mutation_p.Y224*			Q9C0A6	SETD5_HUMAN	SET domain containing 5	322	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)		CTAGACCATACCCCTTTGTGC	0.418																																					p.Y322X		Atlas-SNP	.											.	SETD5	210	.	0			c.C966G						PASS	.						131	115	120					3																	9483818		1900	4124	6024	SO:0001587	stop_gained	55209	exon10			ACCATACCCCTTT	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.966C>G	3.37:g.9483818C>G	ENSP00000383939:p.Tyr322*	31	0	0		47	17	0.361702	NM_001080517	Q6AI17|Q8WUB6|Q9H3X4|Q9H6V7|Q9H7S3|Q9NVI9	Nonsense_Mutation	SNP	ENST00000406341.1	37	CCDS46741.1	.	.	.	.	.	.	.	.	.	.	C	43	10.335419	0.99385	.	.	ENSG00000168137	ENST00000402198;ENST00000402466;ENST00000406341;ENST00000407969;ENST00000302463	.	.	.	5.49	1.36	0.22044	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.8775	8.1691	0.31243	0.0:0.3117:0.0:0.6883	.	.	.	.	X	322;224;322;341;224	.	ENSP00000302028:Y224X	Y	+	3	2	SETD5	9458818	0.972000	0.33761	1.000000	0.80357	0.992000	0.81027	0.196000	0.17176	0.188000	0.20168	-0.137000	0.14449	TAC	.	.	none		0.418	SETD5-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318425.1	XM_371614		G	9483818	C	G	9483818	4	3	29	1	0	0	0	0	0	1	0	0	14149	518	18	4	996	4	SETD5	3	9483818	Nonsense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10		9483818	188538612	157	12398											
TTLL3	26140	hgsc.bcm.edu	37	chr3	9874914	9874914	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagtccctctgctgacccagCgaggctctggggaaggcaag	8	6	14	13	1	2	1	0	1	2	0	3	3	3	2	2	4	2	3	2	4	2	0	rs115917139	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:9874914C>T	ENST00000547186.1	+	11	1897	c.1681C>T	c.(1681-1683)Cga>Tga	p.R561*	TTLL3_ENST00000430793.1_Nonsense_Mutation_p.R349*|TTLL3_ENST00000383827.1_Intron|TTLL3_ENST00000455274.1_Intron|TTLL3_ENST00000426895.4_Nonsense_Mutation_p.R704*|ARPC4-TTLL3_ENST00000397256.1_Intron|TTLL3_ENST00000427853.3_Intron|TTLL3_ENST00000397241.1_Intron	NM_001025930.3	NP_001021100.3	Q9Y4R7	TTLL3_HUMAN	tubulin tyrosine ligase-like family, member 3	561					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)					GCTGACCCAGCGAGGCTCTGG	0.647													C|||	115	0.0229633	0.0	0.0231	5008	,	,		16546	0.001		0.0408	False		,,,				2504	0.0583				p.R704X		Atlas-SNP	.											.	TTLL3	51	.	0			c.C2110T						PASS	.	C	stop/ARG,	28,3784		0,28,1878	29	31	30		2110,	3.6	0.3	3	dbSNP_132	30	360,7860		10,340,3760	yes	stop-gained,intron	TTLL3,ARPC4-TTLL3	NM_001025930.3,NM_001198793.1	,	10,368,5638	TT,TC,CC		4.3796,0.7345,3.2247	,	704/916,	9874914	388,11644	1906	4110	6016	SO:0001587	stop_gained	26140	exon11			ACCCAGCGAGGCT		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.1681C>T	3.37:g.9874914C>T	ENSP00000446659:p.Arg561*	82	0	0		61	37	0.606557	NM_001025930	Q4KMS8|Q6AWA3|Q6ZU95|Q8NDN8|Q96GG8|Q9H876|Q9UI99	Nonsense_Mutation	SNP	ENST00000547186.1	37		43	0.019688644688644688	0	0.0	11	0.03038674033149171	0	0.0	32	0.04221635883905013	C	38	6.974468	0.97975	0.007345	0.043796	ENSG00000214021	ENST00000426895;ENST00000547186;ENST00000443148;ENST00000430793	.	.	.	5.39	3.58	0.41010	.	0.000000	0.27782	U	0.017874	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.6056	0.33771	0.3092:0.5413:0.1495:0.0	rs3208837;rs17407417	.	.	.	X	704;561;499;349	.	ENSP00000392549:R704X	R	+	1	2	TTLL3	9849914	0.009000	0.17119	0.270000	0.24601	0.659000	0.38960	0.677000	0.25262	0.639000	0.30564	-0.152000	0.13540	CGA	C|0.975;T|0.025	0.025	strong		0.647	TTLL3-203	KNOWN	basic	protein_coding	protein_coding		NM_001025930.2		T	9874914	C	T	9874914	4	4	29	1	0	0	0	0	0	1	0	0	16743	760	27	1	1719	1	TTLL3	3	9874914	Nonsense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	391096	9874914	188147516	158	12399											
PRRT3	285368	hgsc.bcm.edu	37	chr3	9989028	9989028	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgtgcccagagccacggccGcgccccaggcgcacgacaag	8	1	14	18	6	0	1	0	0	0	1	0	2	0	1	5	2	2	1	5	2	1	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:9989028G>A	ENST00000412055.1	-	4	1958	c.1829C>T	c.(1828-1830)gCg>gTg	p.A610V	PRRT3-AS1_ENST00000431558.1_RNA	NM_207351.3	NP_997234.3	Q5FWE3	PRRT3_HUMAN	proline-rich transmembrane protein 3	610						integral component of membrane (GO:0016021)				NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(1)|skin(1)|stomach(2)	13						AGCCACGGCCGCGCCCCAGGC	0.711																																					p.A610V		Atlas-SNP	.											.	PRRT3	35	.	0			c.C1829T						PASS	.						9	11	11					3																	9989028		1927	3904	5831	SO:0001583	missense	285368	exon4			ACGGCCGCGCCCC	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.1829C>T	3.37:g.9989028G>A	ENSP00000392511:p.Ala610Val	6	0	0		17	5	0.294118	NM_207351	Q49AD0|Q6UXY6|Q8NBC9	Missense_Mutation	SNP	ENST00000412055.1	37	CCDS43049.1	.	.	.	.	.	.	.	.	.	.	G	14.12	2.440426	0.43326	.	.	ENSG00000163704	ENST00000412055	T	0.14640	2.49	4.43	4.43	0.53597	.	0.183502	0.37623	N	0.002019	T	0.10252	0.0251	N	0.14661	0.345	0.80722	D	1	D	0.61080	0.989	P	0.49085	0.6	T	0.12372	-1.0550	9	.	.	.	-20.0165	8.2211	0.31541	0.106:0.0:0.894:0.0	.	610	Q5FWE3	PRRT3_HUMAN	V	610	ENSP00000392511:A610V	.	A	-	2	0	PRRT3	9964028	0.999000	0.42202	0.934000	0.37439	0.981000	0.71138	4.195000	0.58400	2.298000	0.77334	0.462000	0.41574	GCG	.	.	none		0.711	PRRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339322.1	NM_207351		A	9989028	G	A	9989028	3	1	29	1	0	0	0	0	1	0	0	0	12623	1087	38	1	1120	1	PRRT3	3	9989028	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	114114	9989028	188033402	159	12400											
SLC6A11	6538	hgsc.bcm.edu	37	chr3	10960057	10960057	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaacagcggcaccagcttcGtggctgggtttgccatcttc	6	11	12	12	2	1	1	0	1	1	0	3	1	1	1	2	3	4	4	2	3	1	3	rs376135284		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:10960057G>A	ENST00000254488.2	+	8	1105	c.1039G>A	c.(1039-1041)Gtg>Atg	p.V347M		NM_014229.1	NP_055044.1	P48066	S6A11_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 11	347					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)	CACCAGCTTCGTGGCTGGGTT	0.597																																					p.V347M		Atlas-SNP	.											.	SLC6A11	87	.	0			c.G1039A						PASS	.	G	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	120	95	103		1039	3.4	1	3		103	0,8600		0,0,4300	no	missense	SLC6A11	NM_014229.1	21	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	347/633	10960057	1,13005	2203	4300	6503	SO:0001583	missense	6538	exon8			AGCTTCGTGGCTG	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.1039G>A	3.37:g.10960057G>A	ENSP00000254488:p.Val347Met	111	0	0		100	42	0.42	NM_014229	B2R6U6|Q8IYC9	Missense_Mutation	SNP	ENST00000254488.2	37	CCDS2602.1	.	.	.	.	.	.	.	.	.	.	G	17.77	3.470463	0.63625	2.27E-4	0.0	ENSG00000132164	ENST00000254488	T	0.74632	-0.86	4.29	3.41	0.39046	.	0.070049	0.56097	D	0.000028	T	0.75258	0.3825	M	0.66506	2.035	0.80722	D	1	P	0.42518	0.782	P	0.45195	0.473	T	0.77019	-0.2743	10	0.62326	D	0.03	.	12.3978	0.55395	0.0849:0.0:0.9151:0.0	.	347	P48066	S6A11_HUMAN	M	347	ENSP00000254488:V347M	ENSP00000254488:V347M	V	+	1	0	SLC6A11	10935057	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	4.372000	0.59530	0.926000	0.37118	0.484000	0.47621	GTG	.	.	weak		0.597	SLC6A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251927.1	NM_014229		A	10960057	G	A	10960057	3	1	29	1	0	0	0	0	1	0	0	0	14689	1145	40	1	1069	1	SLC6A11	3	10960057	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	971029	10960057	187062373	160	12401											
FGD5	152273	hgsc.bcm.edu	37	chr3	14862049	14862049	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccactctgggaaggtggccGgctatgtcccagaaaccgtc	8	7	12	14	2	1	1	0	0	1	1	3	2	2	2	4	4	1	1	4	4	3	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:14862049G>A	ENST00000285046.5	+	1	1581	c.1471G>A	c.(1471-1473)Ggc>Agc	p.G491S	FGD5_ENST00000543601.1_Missense_Mutation_p.G250S	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	491					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						GAAGGTGGCCGGCTATGTCCC	0.617																																					p.G491S		Atlas-SNP	.											FGD5_ENST00000285046,NS,carcinoma,0,2	FGD5	248	2	0			c.G1471A						PASS	.						39	43	42					3																	14862049		1938	4118	6056	SO:0001583	missense	152273	exon1			GTGGCCGGCTATG	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.1471G>A	3.37:g.14862049G>A	ENSP00000285046:p.Gly491Ser	84	0	0		84	32	0.380952	NM_152536	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Missense_Mutation	SNP	ENST00000285046.5	37	CCDS46767.1	.	.	.	.	.	.	.	.	.	.	G	18.03	3.532256	0.64972	.	.	ENSG00000154783	ENST00000285046;ENST00000543601	D;D	0.89552	-2.53;-2.27	4.76	4.76	0.60689	.	0.000000	0.53938	D	0.000044	D	0.94202	0.8139	M	0.73598	2.24	0.47153	D	0.999332	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.94924	0.8076	10	0.72032	D	0.01	-34.9884	17.8006	0.88586	0.0:0.0:1.0:0.0	.	250;491	B7ZM68;Q6ZNL6	.;FGD5_HUMAN	S	491;250	ENSP00000285046:G491S;ENSP00000445949:G250S	ENSP00000285046:G491S	G	+	1	0	FGD5	14837053	1.000000	0.71417	0.525000	0.27900	0.087000	0.18053	5.876000	0.69667	2.206000	0.71126	0.585000	0.79938	GGC	.	.	none		0.617	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536		A	14862049	G	A	14862049	3	1	29	1	0	0	0	0	1	0	0	0	5844	1116	39	1	1473	1	FGD5	3	14862049	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	3901992	14862049	183160381	161	12402											
ZFYVE20	64145	hgsc.bcm.edu	37	chr3	15126313	15126313	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcagaggcggcagtggtggCggcggttccggatgctgaac	6	6	19	10	5	0	2	0	1	0	1	1	3	1	3	1	7	2	4	1	7	1	1	rs578256587		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:15126313C>T	ENST00000253699.3	-	8	1140	c.527G>A	c.(526-528)cGc>cAc	p.R176H	ZFYVE20_ENST00000449964.2_5'UTR|ZFYVE20_ENST00000476527.2_Missense_Mutation_p.R176H|ZFYVE20_ENST00000435849.3_Missense_Mutation_p.R176H	NM_022340.2	NP_071735.2	Q9H1K0	RBNS5_HUMAN	zinc finger, FYVE domain containing 20	176	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						GCAGTGGTGGCGGCGGTTCCG	0.552													C|||	1	0.000199681	0.0008	0.0	5008	,	,		15809	0.0		0.0	False		,,,				2504	0.0				p.R176H		Atlas-SNP	.											.	ZFYVE20	61	.	0			c.G527A						PASS	.						54	63	60					3																	15126313		2203	4300	6503	SO:0001583	missense	64145	exon8			TGGTGGCGGCGGT	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.527G>A	3.37:g.15126313C>T	ENSP00000253699:p.Arg176His	119	0	0		123	58	0.471545	NM_022340	B4DWY8|C9J4P5|Q3KP30|Q59EY8|Q8NAQ1	Missense_Mutation	SNP	ENST00000253699.3	37	CCDS2623.1	.	.	.	.	.	.	.	.	.	.	C	33	5.277929	0.95459	.	.	ENSG00000131381	ENST00000253699;ENST00000476527;ENST00000435849	T;T;T	0.77877	-1.13;-1.13;-1.13	5.33	4.46	0.54185	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	0.91050	0.7184	H	0.95611	3.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	D	0.93160	0.6557	10	0.87932	D	0	-14.4964	13.5262	0.61597	0.0:0.9252:0.0:0.0748	.	176;176	B4DWY8;Q9H1K0	.;RBNS5_HUMAN	H	176	ENSP00000253699:R176H;ENSP00000422551:R176H;ENSP00000391039:R176H	ENSP00000253699:R176H	R	-	2	0	ZFYVE20	15101317	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.813000	0.86123	1.248000	0.43934	0.484000	0.47621	CGC	.	.	none		0.552	ZFYVE20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252102.2	NM_022340		T	15126313	C	T	15126313	3	4	29	1	0	0	0	0	1	0	0	0	17681	768	27	1	1855	1	ZFYVE20	3	15126313	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	264264	15126313	182896117	162	12403											
BTD	686	hgsc.bcm.edu	37	chr3	15686611	15686611	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaaaggaaggctatctccaCgtctgttccaatggcctctg	9	10	11	11	1	3	0	0	0	3	0	5	2	4	2	3	4	0	2	3	4	4	2	rs397514404|rs397514435|rs372039874	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:15686611C>T	ENST00000303498.5	+	4	1357	c.1248C>T	c.(1246-1248)caC>caT	p.H416H	BTD_ENST00000437172.1_Silent_p.H418H|BTD_ENST00000449107.1_Silent_p.H418H|BTD_ENST00000383778.4_Silent_p.H396H	NM_000060.2|NM_001281723.1	NP_000051.1|NP_001268652.1	P43251	BTD_HUMAN	biotinidase	416					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						GCTATCTCCACGTCTGTTCCA	0.502													C|||	2	0.000399361	0.0008	0.0014	5008	,	,		20372	0.0		0.0	False		,,,				2504	0.0				p.H416H		Atlas-SNP	.											.	BTD	49	.	0			c.C1248T						PASS	.	C		0,4406		0,0,2203	158	152	154		1248	-11.2	0	3		154	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	BTD	NM_000060.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		416/544	15686611	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	686	exon4			TCTCCACGTCTGT	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.1248C>T	3.37:g.15686611C>T		117	0	0		131	64	0.48855	NM_000060	A6NHF2|B2R865|B4DFX1|B4DLJ9|B7Z7C9|F8W1Q3|Q96EM9	Silent	SNP	ENST00000303498.5	37	CCDS2628.1																																																																																			.	.	weak		0.502	BTD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252103.2	NM_000060		T	15686611	C	T	15686611	2	4	29	1	0	0	0	0	0	0	0	1	1552	535	19	1		1	BTD	3	15686611	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	560298	15686611	182335819	163	12404											
TRANK1	9881	hgsc.bcm.edu	37	chr3	36873866	36873866	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagccggatgaagcacaggTgggtcttgtccatattttca	10	11	12	8	1	2	1	1	1	1	0	3	3	3	2	2	3	2	1	2	3	3	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:36873866T>A	ENST00000429976.2	-	21	7323	c.7076A>T	c.(7075-7077)cAc>cTc	p.H2359L	TRANK1_ENST00000428977.2_Missense_Mutation_p.H1809L|TRANK1_ENST00000301807.6_Missense_Mutation_p.H1809L	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	2359							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						GAAGCACAGGTGGGTCTTGTC	0.473																																					p.H2359L		Atlas-SNP	.											.	TRANK1	398	.	0			c.A7076T						PASS	.						97	102	100					3																	36873866		1954	4144	6098	SO:0001583	missense	9881	exon21			CACAGGTGGGTCT	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.7076A>T	3.37:g.36873866T>A	ENSP00000416168:p.His2359Leu	273	0	0		270	153	0.566667	NM_014831	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	37	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	T	10.14	1.267837	0.23136	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.34472	1.36;1.77;1.36	5.16	3.97	0.46021	.	0.108511	0.40469	N	0.001086	T	0.27967	0.0689	L	0.32530	0.975	0.32062	N	0.595608	B	0.31680	0.335	B	0.30401	0.115	T	0.30621	-0.9972	10	0.44086	T	0.13	.	12.5047	0.55975	0.0:0.0:0.1394:0.8606	.	2359	O15050	TRNK1_HUMAN	L	1809;2359;1809	ENSP00000416826:H1809L;ENSP00000416168:H2359L;ENSP00000301807:H1809L	ENSP00000301807:H1809L	H	-	2	0	TRANK1	36848870	1.000000	0.71417	0.995000	0.50966	0.400000	0.30750	4.152000	0.58111	0.878000	0.35920	0.459000	0.35465	CAC	.	.	none		0.473	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		A	36873866	T	A	36873866	3	1	29	1	0	0	0	0	1	0	0	0	16469	1696	59	5	1713	5	TRANK1	3	36873866	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	21187255	36873866	161148564	164	12405											
MLH1	4292	hgsc.bcm.edu	37	chr3	37053568	37053568	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtggacaatattcgctccAtctttggaaatgctgttagt	9	14	9	9	2	1	0	0	0	1	0	3	2	2	2	2	2	1	3	2	2	4	4	rs1799977	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:37053568A>G	ENST00000231790.2	+	8	871	c.655A>G	c.(655-657)Atc>Gtc	p.I219V	MLH1_ENST00000539477.1_5'UTR|MLH1_ENST00000435176.1_Missense_Mutation_p.I121V|MLH1_ENST00000455445.2_5'UTR|MLH1_ENST00000536378.1_5'UTR|MLH1_ENST00000458205.2_5'UTR	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	219			I -> V (common polymorphism; found in 37% of alleles; dbSNP:rs1799977). {ECO:0000269|PubMed:10375096, ECO:0000269|PubMed:10777691, ECO:0000269|PubMed:11754112, ECO:0000269|PubMed:12115348, ECO:0000269|PubMed:12200596, ECO:0000269|PubMed:12362047, ECO:0000269|PubMed:9032648, ECO:0000269|PubMed:9067757, ECO:0000269|PubMed:9087566, ECO:0000269|PubMed:9218993, ECO:0000269|PubMed:9833759, ECO:0000269|Ref.5}.		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.I219V(1)|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						TATTCGCTCCATCTTTGGAAA	0.368		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				A|||	649	0.129593	0.0386	0.1686	5008	,	,		18149	0.0258		0.325	False		,,,				2504	0.1309				p.I219V		Atlas-SNP	.	yes	Rec	yes	"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	3	3p21.3	4292	E.coli MutL homolog gene		"E, O"	MLH1,NS,carcinoma,0,1	MLH1	226	1	2	Substitution - Missense(1)|Whole gene deletion(1)	ovary(1)|prostate(1)	c.A655G	GRCh37	CM970958	MLH1	M	rs1799977	PASS	.	A	VAL/ILE,VAL/ILE,,	406,4000	199.4+/-223.0	27,352,1824	145	129	135	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	655,361,,	4.6	1	3	dbSNP_89	135	2754,5846	438.0+/-358.8	442,1870,1988	yes	missense,missense,utr-5,utr-5	MLH1	NM_000249.3,NM_001167617.1,NM_001167618.1,NM_001167619.1	29,29,,	469,2222,3812	GG,GA,AA		32.0233,9.2147,24.2965	benign,benign,,	219/757,121/659,,	37053568	3160,9846	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	CGCTCCATCTTTG	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.655A>G	3.37:g.37053568A>G	ENSP00000231790:p.Ile219Val	81	0	0		73	38	0.520548	NM_000249	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	37	CCDS2663.1	374	0.17124542124542125	28	0.056910569105691054	72	0.19889502762430938	16	0.027972027972027972	258	0.3403693931398417	A	14.01	2.408011	0.42715	0.092147	0.320233	ENSG00000076242	ENST00000231790;ENST00000436867;ENST00000537937;ENST00000383761;ENST00000435176	D;D	0.83591	-1.74;-1.74	5.76	4.61	0.57282	Ribosomal protein S5 domain 2-type fold (1);DNA mismatch repair protein, N-terminal (1);ATPase-like, ATP-binding domain (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);DNA mismatch repair protein, C-terminal (1);	0.113678	0.64402	D	0.000010	T	0.00012	0.0000	N	0.25992	0.78	0.09310	P	1.0	B;B;B	0.16603	0.018;0.018;0.018	B;B;B	0.26864	0.028;0.074;0.06	T	0.07424	-1.0773	9	0.12430	T	0.62	-17.9526	7.4844	0.27423	0.7886:0.0:0.2114:0.0	rs1799977;rs2229023;rs11541861;rs17809298;rs52803721;rs56722302;rs1799977	121;219;219	E9PCU2;Q53GX1;P40692	.;.;MLH1_HUMAN	V	219;185;185;83;121	ENSP00000231790:I219V;ENSP00000402564:I121V	ENSP00000231790:I219V	I	+	1	0	MLH1	37028572	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.446000	0.44908	2.209000	0.71365	0.533000	0.62120	ATC	A|0.799;G|0.201	0.201	strong		0.368	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249		G	37053568	A	G	37053568	3	3	29	1	0	0	0	0	1	0	0	0	9626	217	8	3	685	3	MLH1	3	37053568	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	179702	37053568	160968862	165	12406											
ACAA1	30	hgsc.bcm.edu	37	chr3	38167095	38167095	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcattgagcagcgtgatgAcctgtcgtgccccagtgcag	7	9	13	12	2	1	3	1	3	0	0	2	3	1	3	3	0	4	3	3	0	0	1	rs2229528	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:38167095A>G	ENST00000333167.8	-	11	1332	c.1160T>C	c.(1159-1161)gTc>gCc	p.V387A	Y_RNA_ENST00000365095.1_RNA|ACAA1_ENST00000450296.1_Missense_Mutation_p.V346A|ACAA1_ENST00000301810.7_Missense_Mutation_p.V294A|ACAA1_ENST00000480865.1_5'UTR	NM_001607.3	NP_001598.1	P09110	THIK_HUMAN	acetyl-CoA acyltransferase 1	387			V -> A (in dbSNP:rs2229528). {ECO:0000269|PubMed:15489334}.		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)		CAGCGTGATGACCTGTCGTGC	0.612													A|||	60	0.0119808	0.0023	0.0144	5008	,	,		18767	0.0		0.0427	False		,,,				2504	0.0041				p.V387A		Atlas-SNP	.											.	ACAA1	32	.	0			c.T1160C						PASS	.	A	ALA/VAL,ALA/VAL	27,4379	33.5+/-64.1	0,27,2176	66	62	63		881,1160	5.6	1	3	dbSNP_131	63	350,8250	118.5+/-177.9	6,338,3956	yes	missense,missense	ACAA1	NM_001130410.1,NM_001607.3	64,64	6,365,6132	GG,GA,AA		4.0698,0.6128,2.8987	benign,benign	294/332,387/425	38167095	377,12629	2203	4300	6503	SO:0001583	missense	30	exon11			GTGATGACCTGTC	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.1160T>C	3.37:g.38167095A>G	ENSP00000333664:p.Val387Ala	105	0	0		100	46	0.46	NM_001607	G5E935|Q96CA6	Missense_Mutation	SNP	ENST00000333167.8	37	CCDS2673.1	43|43	0.019688644688644688|0.019688644688644688	3|3	0.006097560975609756|0.006097560975609756	9|9	0.024861878453038673|0.024861878453038673	0|0	0.0|0.0	31|31	0.040897097625329816|0.040897097625329816	A|A	18.59|18.59	3.657401|3.657401	0.67586|0.67586	0.006128|0.006128	0.040698|0.040698	ENSG00000060971|ENSG00000060971	ENST00000452171;ENST00000421218|ENST00000333167;ENST00000301810;ENST00000450296;ENST00000358122	.|D;D;D	.|0.83075	.|-1.68;-1.68;-1.68	5.62|5.62	5.62|5.62	0.85841|0.85841	.|Thiolase-like, subgroup (1);Thiolase-like (1);Thiolase, C-terminal (1);	.|0.114891	.|0.64402	.|D	.|0.000015	T|T	0.59183|0.59183	0.2175|0.2175	L|L	0.53249|0.53249	1.67|1.67	0.80722|0.80722	D|D	1|1	.|B;P;P	.|0.48162	.|0.383;0.906;0.615	.|B;P;P	.|0.50440	.|0.208;0.641;0.544	T|T	0.74705|0.74705	-0.3575|-0.3575	5|10	.|0.49607	.|T	.|0.09	-44.228|-44.228	10.2096|10.2096	0.43132|0.43132	0.926:0.0:0.074:0.0|0.926:0.0:0.074:0.0	rs2229528;rs17845420;rs17858286;rs17845420|rs2229528;rs17845420;rs17858286;rs17845420	.|346;294;387	.|C9JDE9;G5E935;P09110	.|.;.;THIK_HUMAN	P|A	200;277|387;294;346;319	.|ENSP00000333664:V387A;ENSP00000301810:V294A;ENSP00000395183:V346A	.|ENSP00000301810:V294A	S|V	-|-	1|2	0|0	ACAA1|ACAA1	38142099|38142099	1.000000|1.000000	0.71417|0.71417	0.992000|0.992000	0.48379|0.48379	0.991000|0.991000	0.79684|0.79684	6.176000|6.176000	0.71955|0.71955	2.144000|2.144000	0.66660|0.66660	0.533000|0.533000	0.62120|0.62120	TCA|GTC	T|0.067;G|0.026	0.026	strong		0.612	ACAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342980.1	NM_001607		G	38167095	A	G	38167095	3	3	29	1	0	0	0	0	1	0	0	0	104	275	10	3	122	3	ACAA1	3	38167095	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	1113527	38167095	159855335	166	12407											
GORASP1	64689	hgsc.bcm.edu	37	chr3	39140352	39140352	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cacactggcattgctgttgtCcaagagagaaattcccgaca	12	9	9	11	1	0	2	0	0	0	2	2	4	2	2	2	1	1	3	2	1	2	3	rs138864486	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:39140352C>A	ENST00000319283.3	-	8	1770	c.949G>T	c.(949-951)Gac>Tac	p.D317Y	GORASP1_ENST00000479927.1_Missense_Mutation_p.D222Y|GORASP1_ENST00000422110.2_Missense_Mutation_p.D162Y|GORASP1_ENST00000476334.1_5'UTR	NM_031899.2	NP_114105.1	Q9BQQ3	GORS1_HUMAN	golgi reassembly stacking protein 1, 65kDa	317					Golgi organization (GO:0007030)|mitotic cell cycle (GO:0000278)|negative regulation of dendrite morphogenesis (GO:0050774)|protein transport (GO:0015031)	Golgi membrane (GO:0000139)				central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(1)|ovary(3)|urinary_tract(1)	14				KIRC - Kidney renal clear cell carcinoma(284;0.0519)|Kidney(284;0.0653)		TTGCTGTTGTCCAAGAGAGAA	0.582													C|||	46	0.0091853	0.0	0.013	5008	,	,		19642	0.0		0.0089	False		,,,				2504	0.0286				p.D317Y		Atlas-SNP	.											.	GORASP1	42	.	0			c.G949T						PASS	.	C	TYR/ASP	7,4399	12.9+/-30.5	0,7,2196	100	91	94		949	4.7	1	3	dbSNP_134	94	83,8517	48.5+/-108.0	0,83,4217	yes	missense	GORASP1	NM_031899.2	160	0,90,6413	AA,AC,CC		0.9651,0.1589,0.692	probably-damaging	317/441	39140352	90,12916	2203	4300	6503	SO:0001583	missense	64689	exon8			TGTTGTCCAAGAG	AJ409349	CCDS2681.1, CCDS63596.1, CCDS63597.1	3p22-p21.33	2008-04-23	2002-08-29	2002-05-24	ENSG00000114745	ENSG00000114745			16769	protein-coding gene	gene with protein product		606867	"golgi phosphoprotein 5"	GOLPH5			Standard	NM_001278789		Approved	GRASP65, P65, FLJ23443	uc003ciw.1	Q9BQQ3	OTTHUMG00000131292	ENST00000319283.3:c.949G>T	3.37:g.39140352C>A	ENSP00000313869:p.Asp317Tyr	107	0	0		131	58	0.442748	NM_031899	B3KWC8|Q3SYG7|Q8N272|Q96H42	Missense_Mutation	SNP	ENST00000319283.3	37	CCDS2681.1	12	0.005494505494505495	0	0.0	6	0.016574585635359115	0	0.0	6	0.0079155672823219	C	19.94	3.920111	0.73098	0.001589	0.009651	ENSG00000114745	ENST00000319283;ENST00000422110;ENST00000479927	T;T;T	0.56275	0.66;0.47;0.56	4.68	4.68	0.58851	.	0.587157	0.18456	N	0.140696	T	0.53706	0.1813	M	0.65975	2.015	0.39515	D	0.96841	D;D;D	0.89917	0.996;1.0;0.989	P;D;P	0.71870	0.819;0.975;0.781	T	0.67229	-0.5723	10	0.72032	D	0.01	-29.4781	13.3563	0.60629	0.0:1.0:0.0:0.0	.	222;162;317	B4E1H8;B3KPY8;Q9BQQ3	.;.;GORS1_HUMAN	Y	317;162;222	ENSP00000313869:D317Y;ENSP00000395709:D162Y;ENSP00000419123:D222Y	ENSP00000313869:D317Y	D	-	1	0	GORASP1	39115356	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	3.606000	0.54095	2.608000	0.88229	0.650000	0.86243	GAC	C|0.993;A|0.007	0.007	strong		0.582	GORASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254060.1			A	39140352	C	A	39140352	3	1	29	1	0	0	0	0	1	0	0	0	6583	855	30	4	381	4	GORASP1	3	39140352	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	973257	39140352	158882078	167	12408											
TRAK1	22906	hgsc.bcm.edu	37	chr3	42251321	42251321	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	accttgggggcatcctggacCcccggcccggtgtggtcacc	4	7	14	16	2	1	0	1	0	0	0	2	1	2	1	6	6	0	1	6	6	0	1	rs375255978		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:42251321C>T	ENST00000327628.5	+	14	2207	c.1807C>T	c.(1807-1809)Ccc>Tcc	p.P603S	TRAK1_ENST00000487159.1_3'UTR|TRAK1_ENST00000396175.1_Missense_Mutation_p.P545S|TRAK1_ENST00000341421.3_Missense_Mutation_p.P545S	NM_001042646.2	NP_001036111.1	Q9UPV9	TRAK1_HUMAN	trafficking protein, kinesin binding 1	603					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						CATCCTGGACCCCCGGCCCGG	0.587																																					p.P603S	GBM(44;195 884 22595 31865 41850)	Atlas-SNP	.											.	TRAK1	188	.	0			c.C1807T						PASS	.	C	SER/PRO,SER/PRO	0,4406		0,0,2203	75	76	76		1807,1633	5.5	1	3		76	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	TRAK1	NM_001042646.1,NM_014965.3	74,74	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	603/954,545/687	42251321	1,13005	2203	4300	6503	SO:0001583	missense	22906	exon14			CTGGACCCCCGGC		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.1807C>T	3.37:g.42251321C>T	ENSP00000328998:p.Pro603Ser	55	0	0		60	24	0.4	NM_001265608	E9PDS2|J3KNT7|Q63HR0|Q659B5|Q96B69	Missense_Mutation	SNP	ENST00000327628.5	37	CCDS43072.1	.	.	.	.	.	.	.	.	.	.	C	15.44	2.833399	0.50951	0.0	1.16E-4	ENSG00000182606	ENST00000327628;ENST00000543338;ENST00000396175;ENST00000341421	T;T;T	0.09073	3.05;3.06;3.02	5.49	5.49	0.81192	.	0.062197	0.64402	D	0.000005	T	0.11580	0.0282	L	0.39898	1.24	0.38529	D	0.948939	P;P;P;P;B	0.52316	0.524;0.728;0.851;0.952;0.105	B;B;B;B;B	0.43916	0.095;0.196;0.253;0.436;0.038	T	0.03221	-1.1059	10	0.46703	T	0.11	.	18.3674	0.90396	0.0:1.0:0.0:0.0	.	529;545;603;545;603	B7Z218;C9JC32;B7Z347;Q9UPV9-2;Q9UPV9	.;.;.;.;TRAK1_HUMAN	S	603;603;545;545	ENSP00000328998:P603S;ENSP00000379478:P545S;ENSP00000340702:P545S	ENSP00000328998:P603S	P	+	1	0	TRAK1	42226325	0.999000	0.42202	1.000000	0.80357	0.998000	0.95712	1.457000	0.35212	2.571000	0.86741	0.655000	0.94253	CCC	.	.	weak		0.587	TRAK1-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343413.1	NM_014965		T	42251321	C	T	42251321	3	4	29	1	0	0	0	0	1	0	0	0	16464	623	22	2	1977	2	TRAK1	3	42251321	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	3110969	42251321	155771109	168	12409											
NKTR	4820	hgsc.bcm.edu	37	chr3	42662976	42662976	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttttatcaatggcaaatcgAgggaaacataccaatggttc	14	11	8	8	1	1	0	1	0	0	0	3	2	1	1	1	3	2	2	1	3	6	4	rs35419602	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:42662976A>C	ENST00000232978.8	+	6	530	c.342A>C	c.(340-342)cgA>cgC	p.R114R	RP4-613B23.1_ENST00000445452.1_RNA|RP4-613B23.1_ENST00000438017.1_RNA	NM_005385.3	NP_005376.2	P30414	NKTR_HUMAN	natural killer cell triggering receptor	114	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				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)		TGGCAAATCGAGGGAAACATA	0.358													A|||	35	0.00698882	0.0083	0.0072	5008	,	,		15576	0.0		0.0179	False		,,,				2504	0.001				p.R114R		Atlas-SNP	.											.	NKTR	116	.	0			c.A342C						PASS	.	A		32,4374	39.2+/-71.8	0,32,2171	76	73	74		342	-1.8	1	3	dbSNP_126	74	128,8470	65.6+/-127.9	1,126,4172	no	coding-synonymous	NKTR	NM_005385.3		1,158,6343	CC,CA,AA		1.4887,0.7263,1.2304		114/1463	42662976	160,12844	2203	4299	6502	SO:0001819	synonymous_variant	4820	exon6			AAATCGAGGGAAA		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.342A>C	3.37:g.42662976A>C		67	0	0		78	29	0.371795	NM_005385		Silent	SNP	ENST00000232978.8	37	CCDS2702.1																																																																																			A|0.988;C|0.012	0.012	strong		0.358	NKTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256642.2	NM_005385		C	42662976	A	C	42662976	2	2	29	1	0	0	0	0	0	0	0	1	10457	291	11	5		5	NKTR	3	42662976	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	411655	42662976	155359454	169	12410											
ABHD5	51099	hgsc.bcm.edu	37	chr3	43743773	43743773	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaataaaatatggacactgaAgttctctcataatatttcaa	18	13	4	6	0	3	1	2	1	1	0	4	2	3	2	0	1	0	1	0	1	8	6			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:43743773A>C	ENST00000458276.2	+	3	323	c.200A>C	c.(199-201)aAg>aCg	p.K67T		NM_016006.4	NP_057090.2	Q8WTS1	ABHD5_HUMAN	abhydrolase domain containing 5	67					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)		TGGACACTGAAGTTCTCTCAT	0.373																																					p.K67T		Atlas-SNP	.											ABHD5,NS,carcinoma,-1,1	ABHD5	33	1	0			c.A200C						PASS	.						96	99	98					3																	43743773		2203	4300	6503	SO:0001583	missense	51099	exon3			CACTGAAGTTCTC	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.200A>C	3.37:g.43743773A>C	ENSP00000390849:p.Lys67Thr	81	0	0		63	20	0.31746	NM_016006	B2R9K0|Q9Y369	Missense_Mutation	SNP	ENST00000458276.2	37	CCDS2711.1	.	.	.	.	.	.	.	.	.	.	A	2.866	-0.235130	0.05983	.	.	ENSG00000011198	ENST00000456453;ENST00000458276;ENST00000454293	T;D;T	0.82344	-0.96;-1.6;-0.57	5.96	4.78	0.61160	.	0.270286	0.39834	N	0.001247	T	0.66848	0.2831	L	0.31476	0.935	0.25387	N	0.988565	B	0.02656	0.0	B	0.08055	0.003	T	0.51505	-0.8697	10	0.02654	T	1	-23.1746	6.1406	0.20257	0.5209:0.2363:0.0:0.2428	.	67	Q8WTS1	ABHD5_HUMAN	T	26;67;26	ENSP00000391582:K26T;ENSP00000390849:K67T;ENSP00000412014:K26T	ENSP00000412014:K26T	K	+	2	0	ABHD5	43718777	0.761000	0.28439	1.000000	0.80357	0.997000	0.91878	1.463000	0.35277	1.038000	0.40049	0.528000	0.53228	AAG	.	.	none		0.373	ABHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256644.2	NM_016006		C	43743773	A	C	43743773	3	2	29	1	0	0	0	0	1	0	0	0	85	72	3	5	210	5	ABHD5	3	43743773	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	1080797	43743773	154278657	170	12411											
ZNF660	285349	hgsc.bcm.edu	37	chr3	44636279	44636280	+	Frame_Shift_Del	DEL	AT	AT	-																															tgtaaggagtgtgggaaaacAtgtggttctaatacaaagat																								rs552732245	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:44636279_44636280delAT	ENST00000322734.2	+	3	927_928	c.594_595delAT	c.(592-597)acatgtfs	p.C199fs	RP11-944L7.4_ENST00000457331.1_RNA	NM_173658.2	NP_775929.2	Q6AZW8	ZN660_HUMAN	zinc finger protein 660	199					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(2)|lung(4)	6				KIRC - Kidney renal clear cell carcinoma(197;0.0468)|Kidney(197;0.0585)		GTGGGAAAACATGTGGTTCTAA	0.386														5	0.000998403	0.0	0.0	5008	,	,		21714	0.0		0.005	False		,,,				2504	0.0				p.198_198del		Pindel,Atlas-Indel	.											.	ZNF660	28	.	0			c.593_594del						PASS	.			4,4262		0,4,2129						4.3	1			87	60,8192		0,60,4066	no	frameshift	ZNF660	NM_173658.2		0,64,6195	A1A1,A1R,RR		0.7271,0.0938,0.5113				64,12454				SO:0001589	frameshift_variant	285349	exon3			.	AK094189	CCDS2716.1	3p21.32	2013-01-08			ENSG00000144792	ENSG00000144792		"Zinc fingers, C2H2-type"	26720	protein-coding gene	gene with protein product							Standard	NM_173658		Approved	FLJ36870	uc003cnl.1	Q6AZW8	OTTHUMG00000133097	ENST00000322734.2:c.594_595delAT	3.37:g.44636279_44636280delAT	ENSP00000324605:p.Cys199fs	41	0	.		38	13	0.342	NM_173658	Q7Z331|Q8N9M8	Frame_Shift_Del	DEL	ENST00000322734.2	37	CCDS2716.1																																																																																			.	.	none		0.386	ZNF660-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256756.4	NM_173658		-	44636280	AT	-	44636279	7	5	29	1	0	1	0	1	0	0	0	0	18085	204	8	0	596	0	ZNF660	3	44636279	Frame_Shift_Del	DEL	AT	TCGA-GR-7351-01A-11D-2210-10	892506	44636279	153386151	171	12412											
KIAA1143	57456	hgsc.bcm.edu	37	chr3	44794955	44794955	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggcttcttcttttttgagcTtgctgttaaacctgaatatt	7	20	7	7	0	2	2	0	2	2	0	2	2	2	2	1	1	3	4	1	1	4	9	rs138479225	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:44794955T>C	ENST00000296121.4	-	3	402	c.343A>G	c.(343-345)Agc>Ggc	p.S115G	KIAA1143_ENST00000484437.1_5'UTR	NM_020696.3	NP_065747.1	Q96AT1	K1143_HUMAN	KIAA1143	115										NS(1)|breast(1)|central_nervous_system(1)|large_intestine(1)|stomach(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.00847)|KIRC - Kidney renal clear cell carcinoma(197;0.0465)|Kidney(197;0.0582)		TTTTTTGAGCTTGCTGTTAAA	0.358													T|||	7	0.00139776	0.0	0.0014	5008	,	,		16388	0.0		0.006	False		,,,				2504	0.0				p.S115G		Atlas-SNP	.											.	KIAA1143	10	.	0			c.A343G						PASS	.	T	GLY/SER	8,4398	14.3+/-33.2	0,8,2195	81	84	83		343	5.2	1	3	dbSNP_134	83	32,8562	22.8+/-68.1	0,32,4265	yes	missense	KIAA1143	NM_020696.3	56	0,40,6460	CC,CT,TT		0.3724,0.1816,0.3077	benign	115/155	44794955	40,12960	2203	4297	6500	SO:0001583	missense	57456	exon3			TTGAGCTTGCTGT	AB032969	CCDS2721.1	3p21.31	2005-08-15			ENSG00000163807	ENSG00000163807			29198	protein-coding gene	gene with protein product						10574461	Standard	NM_020696		Approved		uc011bac.2	Q96AT1	OTTHUMG00000133088	ENST00000296121.4:c.343A>G	3.37:g.44794955T>C	ENSP00000296121:p.Ser115Gly	110	0	0		140	72	0.514286	NM_020696	A8K0I4|Q96HJ8|Q9ULS7	Missense_Mutation	SNP	ENST00000296121.4	37	CCDS2721.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	T	18.36	3.606381	0.66445	0.001816	0.003724	ENSG00000163807	ENST00000296121	T	0.51325	0.71	5.17	5.17	0.71159	.	0.125552	0.64402	D	0.000001	T	0.38161	0.1030	M	0.68593	2.085	0.54753	D	0.999989	P	0.36909	0.573	B	0.33454	0.164	T	0.45948	-0.9226	10	0.44086	T	0.13	-11.295	14.9851	0.71342	0.0:0.0:0.0:1.0	.	115	Q96AT1	K1143_HUMAN	G	115	ENSP00000296121:S115G	ENSP00000296121:S115G	S	-	1	0	KIAA1143	44769959	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.531000	0.67148	2.074000	0.62210	0.377000	0.23210	AGC	T|0.997;C|0.003	0.003	strong		0.358	KIAA1143-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256746.1	NM_020696		C	44794955	T	C	44794955	3	2	29	1	0	0	0	0	1	0	0	0	8218	1609	56	3	125	3	KIAA1143	3	44794955	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	158676	44794955	153227475	172	12413											
FYCO1	79443	hgsc.bcm.edu	37	chr3	46008011	46008011	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctctcgctcccttgaggctgCctctttggcgtcctggagct	2	13	11	15	2	2	1	0	1	2	0	5	2	4	2	3	3	2	3	3	3	0	2	rs531750827		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:46008011C>G	ENST00000296137.2	-	8	3020	c.2815G>C	c.(2815-2817)Gca>Cca	p.A939P	FYCO1_ENST00000535325.1_Missense_Mutation_p.A939P	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	939					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)		CTTGAGGCTGCCTCTTTGGCG	0.632																																					p.A939P		Atlas-SNP	.											.	FYCO1	115	.	0			c.G2815C						PASS	.						60	59	59					3																	46008011		2203	4300	6503	SO:0001583	missense	79443	exon8			AGGCTGCCTCTTT	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.2815G>C	3.37:g.46008011C>G	ENSP00000296137:p.Ala939Pro	147	0	0		135	71	0.525926	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Missense_Mutation	SNP	ENST00000296137.2	37	CCDS2734.1	.	.	.	.	.	.	.	.	.	.	C	6.021	0.372341	0.11409	.	.	ENSG00000163820	ENST00000296137;ENST00000535325	T;T	0.79352	-1.26;-1.26	5.39	3.35	0.38373	.	1.014420	0.07877	N	0.968878	T	0.71962	0.3402	L	0.51422	1.61	0.25832	N	0.984155	P;P	0.47604	0.883;0.898	B;P	0.44477	0.346;0.451	T	0.61466	-0.7057	10	0.37606	T	0.19	-1.0259	3.3906	0.07287	0.0:0.455:0.2375:0.3074	.	939;939	B7ZKT7;Q9BQS8	.;FYCO1_HUMAN	P	939	ENSP00000296137:A939P;ENSP00000441178:A939P	ENSP00000296137:A939P	A	-	1	0	FYCO1	45983015	0.139000	0.22563	0.594000	0.28785	0.047000	0.14425	0.695000	0.25527	1.289000	0.44618	-0.136000	0.14681	GCA	.	.	none		0.632	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513		G	46008011	C	G	46008011	3	3	29	1	0	0	0	0	1	0	0	0	6133	739	26	4	1665	4	FYCO1	3	46008011	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1213056	46008011	152014419	173	12414											
CCR2	729230	hgsc.bcm.edu	37	chr3	46399581	46399581	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccagaaagaagattctgtttAtgtctgtggcccttattttc	9	16	8	8	0	2	3	0	0	2	3	3	3	2	3	2	1	0	1	2	1	4	6			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:46399581A>C	ENST00000400888.2	+	1	602	c.563A>C	c.(562-564)tAt>tCt	p.Y188S	CCR2_ENST00000292301.4_Missense_Mutation_p.Y188S|CCR2_ENST00000465202.1_Intron|CCR2_ENST00000445132.2_Missense_Mutation_p.Y188S			P41597	CCR2_HUMAN	chemokine (C-C motif) receptor 2	188					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)		GATTCTGTTTATGTCTGTGGC	0.463																																					p.Y188S		Atlas-SNP	.											.	CCR2	103	.	0			c.A563C						PASS	.						282	271	274					3																	46399581		1568	3582	5150	SO:0001583	missense	729230	exon2			CTGTTTATGTCTG		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.563A>C	3.37:g.46399581A>C	ENSP00000383681:p.Tyr188Ser	168	0	0		143	51	0.356643	NM_001123041	A0AVQ3|B2RMT0|Q4VBL2	Missense_Mutation	SNP	ENST00000400888.2	37	CCDS43078.1	.	.	.	.	.	.	.	.	.	.	A	4.000	-0.002637	0.07819	.	.	ENSG00000121807	ENST00000445132;ENST00000292301;ENST00000400888	T;T;T	0.36878	1.23;1.23;1.23	5.04	-1.23	0.09465	GPCR, rhodopsin-like superfamily (1);	1.456690	0.04308	N	0.348450	T	0.36663	0.0975	M	0.70108	2.13	0.09310	N	1	B;B	0.23128	0.08;0.012	B;B	0.32022	0.139;0.014	T	0.36114	-0.9761	10	0.48119	T	0.1	.	0.2076	0.00152	0.3403:0.2277:0.1565:0.2756	.	188;188	P41597;Q4VBL2	CCR2_HUMAN;.	S	188	ENSP00000399285:Y188S;ENSP00000292301:Y188S;ENSP00000383681:Y188S	ENSP00000292301:Y188S	Y	+	2	0	CCR2	46374585	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.595000	0.05727	-0.382000	0.07870	0.528000	0.53228	TAT	.	.	none		0.463	CCR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344292.1	NM_000647		C	46399581	A	C	46399581	3	2	29	1	0	0	0	0	1	0	0	0	2943	449	16	5	565	5	CCR2	3	46399581	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	391570	46399581	151622849	174	12415											
NBEAL2	23218	hgsc.bcm.edu	37	chr3	47046485	47046485	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccctgggtcctgcaggactaCgtgtccccaaccctggacct	6	8	10	17	1	0	0	0	0	0	0	2	2	2	2	6	3	3	1	6	3	2	1	rs141569354	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:47046485C>T	ENST00000450053.3	+	39	6497	c.6318C>T	c.(6316-6318)taC>taT	p.Y2106Y	NBEAL2_ENST00000383740.2_Silent_p.Y385Y|NBEAL2_ENST00000292309.5_Silent_p.Y1922Y	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	2106	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)		TGCAGGACTACGTGTCCCCAA	0.662													C|||	15	0.00299521	0.0	0.0043	5008	,	,		17699	0.0		0.0119	False		,,,				2504	0.0				p.Y2106Y		Atlas-SNP	.											.	NBEAL2	267	.	0			c.C6318T						PASS	.	C		9,4051		0,9,2021	41	47	45		6318	-1.1	1	3	dbSNP_134	45	100,8250		0,100,4075	no	coding-synonymous	NBEAL2	NM_015175.1		0,109,6096	TT,TC,CC		1.1976,0.2217,0.8783		2106/2755	47046485	109,12301	2030	4175	6205	SO:0001819	synonymous_variant	23218	exon39			GGACTACGTGTCC	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.6318C>T	3.37:g.47046485C>T		84	0	0		86	39	0.453488	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Silent	SNP	ENST00000450053.3	37	CCDS46817.1	11|11	0.005036630036630037|0.005036630036630037	1|1	0.0020325203252032522|0.0020325203252032522	0|0	0.0|0.0	0|0	0.0|0.0	10|10	0.013192612137203167|0.013192612137203167	C|C	7.555|7.555	0.663419|0.663419	0.14710|0.14710	0.002217|0.002217	0.011976|0.011976	ENSG00000160796|ENSG00000160796	ENST00000443829|ENST00000416683	.|.	.|.	.|.	4.65|4.65	-1.12|-1.12	0.09808|0.09808	.|.	.|.	.|.	.|.	.|.	T|T	0.47322|0.47322	0.1439|0.1439	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.47861|0.47861	-0.9084|-0.9084	4|4	.|.	.|.	.|.	.|.	9.8379|9.8379	0.40980|0.40980	0.0:0.4626:0.0:0.5374|0.0:0.4626:0.0:0.5374	.|.	.|.	.|.	.|.	C|M	475|1394	.|.	.|.	R|T	+|+	1|2	0|0	NBEAL2|NBEAL2	47021489|47021489	0.978000|0.978000	0.34361|0.34361	0.997000|0.997000	0.53966|0.53966	0.989000|0.989000	0.77384|0.77384	0.260000|0.260000	0.18424|0.18424	-0.088000|-0.088000	0.12506|0.12506	0.561000|0.561000	0.74099|0.74099	CGT|ACG	C|0.995;T|0.005	0.005	strong		0.662	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064		T	47046485	C	T	47046485	2	4	29	1	0	0	0	0	0	0	0	1	10198	547	19	1		1	NBEAL2	3	47046485	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	646904	47046485	150975945	175	12416											
RNF123	63891	hgsc.bcm.edu	37	chr3	49749979	49749979	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattgagcacggtgatcgcaCagggtctctctttgccttca	7	12	10	12	2	3	2	1	2	2	0	5	2	3	2	1	2	2	2	1	2	0	3	rs201817210		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:49749979C>T	ENST00000327697.6	+	27	2708	c.2564C>T	c.(2563-2565)aCa>aTa	p.T855I	RNF123_ENST00000432042.1_Missense_Mutation_p.T709I|RNF123_ENST00000433785.1_5'Flank	NM_022064.3	NP_071347.2	Q5XPI4	RN123_HUMAN	ring finger protein 123	855					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)		GGTGATCGCACAGGGTCTCTC	0.582																																					p.T855I		Atlas-SNP	.											.	RNF123	100	.	0			c.C2564T						PASS	.						166	126	140					3																	49749979		2203	4300	6503	SO:0001583	missense	63891	exon27			ATCGCACAGGGTC	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.2564C>T	3.37:g.49749979C>T	ENSP00000328287:p.Thr855Ile	126	0	0		110	45	0.409091	NM_022064	A1L4Q3|A6NLS5|Q5I022|Q6PFW4|Q71RH0|Q8IW18|Q9H0M8|Q9H5L8|Q9H9T2	Missense_Mutation	SNP	ENST00000327697.6	37	CCDS33758.1	.	.	.	.	.	.	.	.	.	.	C	16.14	3.038965	0.55003	.	.	ENSG00000164068	ENST00000327697;ENST00000389066;ENST00000432042	T;T	0.76968	-0.74;-1.06	5.91	5.91	0.95273	.	0.088191	0.85682	D	0.000000	D	0.84570	0.5501	L	0.55481	1.735	0.80722	D	1	D;D	0.69078	0.997;0.997	P;P	0.60789	0.879;0.879	T	0.82831	-0.0263	10	0.41790	T	0.15	-16.3403	19.2739	0.94023	0.0:1.0:0.0:0.0	.	709;855	C9J266;Q5XPI4	.;RN123_HUMAN	I	855;855;709	ENSP00000328287:T855I;ENSP00000392443:T709I	ENSP00000328287:T855I	T	+	2	0	RNF123	49724983	1.000000	0.71417	0.966000	0.40874	0.279000	0.26890	4.573000	0.60893	2.803000	0.96430	0.650000	0.86243	ACA	C|0.999;T|0.001	0.001	weak		0.582	RNF123-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346475.2	NM_022064		T	49749979	C	T	49749979	3	4	29	1	0	0	0	0	1	0	0	0	13448	478	17	2	2666	2	RNF123	3	49749979	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2703494	49749979	148272451	176	12417											
STAB1	23166	hgsc.bcm.edu	37	chr3	52557136	52557136	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggctgccactgccaacttcTccaccttctatggggtgtgt	5	13	10	13	0	2	0	0	0	2	0	3	0	2	0	4	3	3	1	4	3	2	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:52557136T>G	ENST00000321725.6	+	63	7082	c.7006T>G	c.(7006-7008)Tcc>Gcc	p.S2336A		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	2336	FAS1 7. {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)		TGCCAACTTCTCCACCTTCTA	0.627																																					p.S2336A		Atlas-SNP	.											.	STAB1	178	.	0			c.T7006G						PASS	.						70	74	73					3																	52557136		2202	4299	6501	SO:0001583	missense	23166	exon63			AACTTCTCCACCT	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.7006T>G	3.37:g.52557136T>G	ENSP00000312946:p.Ser2336Ala	61	0	0		54	5	0.0925926	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	37	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.535227	0.85812	.	.	ENSG00000010327	ENST00000321725	D	0.93604	-3.25	5.74	5.74	0.90152	FAS1 domain (3);	0.000000	0.85682	D	0.000000	D	0.95711	0.8605	M	0.62016	1.91	0.47547	D	0.999452	D;D	0.76494	0.999;0.994	D;P	0.68192	0.956;0.893	D	0.95543	0.8614	10	0.49607	T	0.09	.	15.7088	0.77609	0.0:0.0:0.0:1.0	.	223;2336	B3KSK0;Q9NY15	.;STAB1_HUMAN	A	2336	ENSP00000312946:S2336A	ENSP00000312946:S2336A	S	+	1	0	STAB1	52532176	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.595000	0.61048	2.190000	0.69967	0.459000	0.35465	TCC	.	.	none		0.627	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136		G	52557136	T	G	52557136	3	3	29	1	0	0	0	0	1	0	0	0	15252	1551	54	5	7256	5	STAB1	3	52557136	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	2807157	52557136	145465294	177	12418											
C3orf63	23272	hgsc.bcm.edu	37	chr3	56667896	56667896	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaatggagaggatggaaactGgtaatcagaacttctctgtc	14	10	11	6	0	2	2	1	0	1	2	4	5	2	4	0	4	2	1	0	4	4	2	rs200904014	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:56667896G>T	ENST00000493960.2	-	18	2933	c.2923C>A	c.(2923-2925)Cag>Aag	p.Q975K	FAM208A_ENST00000355628.5_Intron|FAM208A_ENST00000431842.2_Intron	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	975							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						GATGGAAACTGGTAATCAGAA	0.507													G|||	27	0.00539137	0.0	0.0014	5008	,	,		16957	0.0		0.003	False		,,,				2504	0.0235				p.Q975K		Atlas-SNP	.											.	FAM208A	113	.	0			c.C2923A						PASS	.	G	LYS/GLN,	1,4405	2.1+/-5.4	0,1,2202	26	24	25		2923,	4.7	1	3		25	15,8585	9.8+/-36.6	0,15,4285	yes	missense,intron	FAM208A	NM_001112736.1,NM_015224.3	53,	0,16,6487	TT,TG,GG		0.1744,0.0227,0.123	benign,	975/1513,	56667896	16,12990	2203	4300	6503	SO:0001583	missense	23272	exon18			GAAACTGGTAATC	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.2923C>A	3.37:g.56667896G>T	ENSP00000417509:p.Gln975Lys	97	0	0		67	36	0.537313	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Missense_Mutation	SNP	ENST00000493960.2	37	CCDS46853.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	15.13	2.743511	0.49151	2.27E-4	0.001744	ENSG00000163946	ENST00000493960	T	0.11604	2.76	5.62	4.69	0.59074	.	.	.	.	.	T	0.08403	0.0209	L	0.36672	1.1	0.80722	D	1	B;B	0.28082	0.2;0.067	B;B	0.24155	0.051;0.012	T	0.04593	-1.0940	9	0.02654	T	1	.	15.6619	0.77193	0.0:0.0:0.8623:0.1377	.	975;975	Q9UK61-3;Q9UK61	.;F208A_HUMAN	K	975	ENSP00000417509:Q975K	ENSP00000417509:Q975K	Q	-	1	0	C3orf63	56642936	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.602000	0.61098	2.801000	0.96364	0.650000	0.86243	CAG	G|0.999;T|0.001	0.001	strong		0.507	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224		T	56667896	G	T	56667896	3	4	29	1	0	0	0	0	1	0	0	0	2241	1357	47	4	2177	4	C3orf63	3	56667896	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	4110760	56667896	141354534	178	12419											
FHIT	2272	hgsc.bcm.edu	37	chr3	60522657	60522657	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgttttgagaaacactacAgagggcttgatgagatgttg	11	13	12	5	0	1	4	0	3	1	3	1	6	1	4	0	1	2	3	0	1	2	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:60522657A>C	ENST00000468189.1	-	5	409	c.39T>G	c.(37-39)tcT>tcG	p.S13S	FHIT_ENST00000341848.4_Silent_p.S13S|FHIT_ENST00000492590.1_Silent_p.S13S|FHIT_ENST00000476844.1_Silent_p.S13S			P49789	FHIT_HUMAN	fragile histidine triad	13	HIT. {ECO:0000255|PROSITE- ProRule:PRU00464}.				DNA replication (GO:0006260)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|nucleotide metabolic process (GO:0009117)|purine nucleotide metabolic process (GO:0006163)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	bis(5'-adenosyl)-triphosphatase activity (GO:0047710)|catalytic activity (GO:0003824)|hydrolase activity (GO:0016787)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)|prostate(1)|stomach(1)	12		all_cancers(2;2.37e-314)|all_epithelial(2;5.17e-286)|Colorectal(2;1.24e-68)|all_lung(2;1.31e-45)|Lung NSC(2;1.79e-44)|all_hematologic(2;1.59e-23)|Renal(2;1.03e-13)|Breast(2;1.06e-10)|Esophageal squamous(2;6.31e-09)|Melanoma(2;1.83e-07)|Acute lymphoblastic leukemia(2;5.46e-05)|all_neural(2;0.00118)|Medulloblastoma(2;0.00263)|Hepatocellular(2;0.0245)|Ovarian(2;0.0408)		UCEC - Uterine corpus endometrioid carcinoma (45;0.0887)|Epithelial(1;9.28e-70)|all cancers(1;3.07e-60)|Colorectal(1;2.33e-53)|STAD - Stomach adenocarcinoma(1;7.22e-48)|COAD - Colon adenocarcinoma(3;1.05e-44)|READ - Rectum adenocarcinoma(3;2.41e-08)|KIRC - Kidney renal clear cell carcinoma(10;0.000109)|Kidney(10;0.000125)|Lung(1;0.000161)|LUSC - Lung squamous cell carcinoma(1;0.000742)|OV - Ovarian serous cystadenocarcinoma(275;0.00372)|BRCA - Breast invasive adenocarcinoma(55;0.00448)		GAAACACTACAGAGGGCTTGA	0.373			T	HMGA2	pleomorphic salivary gland adenoma				Renal Cell Cancer associated with constitutional translocation of chromosome 3																												p.S13S		Atlas-SNP	.		Dom	yes		3	3p14.2	2272	fragile histidine triad gene		E	.	FHIT	44	.	0			c.T39G						PASS	.						96	89	92					3																	60522657		2203	4300	6503	SO:0001819	synonymous_variant	2272	exon5	Familial Cancer Database		CACTACAGAGGGC	BC032336	CCDS2894.1	3p14.2	2012-02-27	2012-02-27		ENSG00000189283	ENSG00000189283			3701	protein-coding gene	gene with protein product		601153	"fragile histidine triad gene"			8598045, 9671749	Standard	NM_002012		Approved	FRA3B, AP3Aase	uc003dky.3	P49789	OTTHUMG00000158591	ENST00000468189.1:c.39T>G	3.37:g.60522657A>C		42	0	0		59	13	0.220339	NM_002012	A2IAS9|A2IAT0|A2IAT6|A8K1A9|Q45QG9|Q6IU12	Silent	SNP	ENST00000468189.1	37	CCDS2894.1																																																																																			.	.	none		0.373	FHIT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351648.1	NM_002012		C	60522657	A	C	60522657	2	2	29	1	0	0	0	0	0	0	0	1	5885	175	7	5		5	FHIT	3	60522657	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	3854761	60522657	137499773	179	12420											
LMOD3	56203	hgsc.bcm.edu	37	chr3	69168747	69168747	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggttgagttccttcatgtcAggatcatttttcctaactct	8	17	7	9	0	4	1	3	1	1	0	6	2	6	2	2	2	1	2	2	2	1	6	rs115972674	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:69168747A>G	ENST00000420581.2	-	2	938	c.759T>C	c.(757-759)ccT>ccC	p.P253P	LMOD3_ENST00000489031.1_Silent_p.P253P|LMOD3_ENST00000475434.1_Silent_p.P253P	NM_198271.3	NP_938012.2	Q0VAK6	LMOD3_HUMAN	leiomodin 3 (fetal)	253						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)		CCTTCATGTCAGGATCATTTT	0.408													A|||	63	0.0125799	0.0023	0.0231	5008	,	,		22033	0.0		0.0348	False		,,,				2504	0.0092				p.P253P		Atlas-SNP	.											.	LMOD3	92	.	0			c.T759C						PASS	.	A		21,3747		0,21,1863	182	167	172		759	-9.6	0.9	3	dbSNP_132	172	377,7853		10,357,3748	no	coding-synonymous	LMOD3	NM_198271.3		10,378,5611	GG,GA,AA		4.5808,0.5573,3.3172		253/561	69168747	398,11600	1884	4115	5999	SO:0001819	synonymous_variant	56203	exon2			CATGTCAGGATCA	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.759T>C	3.37:g.69168747A>G		72	0	0		57	31	0.54386	NM_198271	B4DT85|Q0JTT2|Q5JPG6|Q8IUK4|Q96LS4	Silent	SNP	ENST00000420581.2	37	CCDS46862.1																																																																																			A|0.979;G|0.021	0.021	strong		0.408	LMOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352138.1	XM_067529		G	69168747	A	G	69168747	2	3	29	1	0	0	0	0	0	0	0	1	8867	175	7	3		3	LMOD3	3	69168747	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	8646090	69168747	128853683	180	12421											
OR5K3	403277	hgsc.bcm.edu	37	chr3	98110414	98110414	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aataaatattatgaaaaaaaTtatgaagaagagaaaatttt	24	12	5	0	0	0	4	0	2	0	2	0	5	0	4	0	0	0	0	0	0	13	6	rs199575537		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:98110414T>A	ENST00000383695.1	+	1	905	c.905T>A	c.(904-906)aTt>aAt	p.I302N	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005516.1	NP_001005516.1	A6NET4	OR5K3_HUMAN	olfactory receptor, family 5, subfamily K, member 3	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)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|prostate(1)|skin(1)|urinary_tract(1)	27						ATGAAAAAAATTATGAAGAAG	0.264																																					p.I302N		Atlas-SNP	.											OR5K3,NS,carcinoma,0,2	OR5K3	60	2	0			c.T905A						scavenged	.						28	31	30					3																	98110414		2102	4200	6302	SO:0001583	missense	403277	exon1			AAAAAATTATGAA		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.905T>A	3.37:g.98110414T>A	ENSP00000373194:p.Ile302Asn	23	0	0		27	2	0.0740741	NM_001005516		Missense_Mutation	SNP	ENST00000383695.1	37	CCDS33803.1	.	.	.	.	.	.	.	.	.	.	T	11.32	1.604568	0.28623	.	.	ENSG00000206536	ENST00000383695	T	0.39592	1.07	4.88	-2.06	0.07298	.	2.020920	0.02943	N	0.140719	T	0.35682	0.0940	L	0.52126	1.63	0.09310	N	1	B	0.13594	0.008	B	0.11329	0.006	T	0.32693	-0.9897	10	0.66056	D	0.02	-0.152	3.649	0.08196	0.2583:0.2504:0.0:0.4913	.	302	A6NET4	OR5K3_HUMAN	N	302	ENSP00000373194:I302N	ENSP00000373194:I302N	I	+	2	0	OR5K3	99593104	0.000000	0.05858	0.000000	0.03702	0.104000	0.19210	-0.590000	0.05760	-0.275000	0.09219	-0.416000	0.06073	ATT	.	.	weak		0.264	OR5K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359110.1			A	98110414	T	A	98110414	3	1	29	1	0	0	0	0	1	0	0	0	11177	1493	52	5	907	5	OR5K3	3	98110414	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	28941667	98110414	99912016	181	12422											
COL8A1	1295	hgsc.bcm.edu	37	chr3	99513830	99513830	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cccaggacccaaaggtgaccGgggcatgggaggtgttcctg	8	6	16	11	1	0	1	0	1	0	0	1	3	1	3	4	6	0	2	4	6	1	1	rs139380413		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:99513830G>A	ENST00000261037.3	+	5	1465	c.1085G>A	c.(1084-1086)cGg>cAg	p.R362Q	COL8A1_ENST00000273342.4_Missense_Mutation_p.R362Q	NM_001850.4	NP_001841.2	P27658	CO8A1_HUMAN	collagen, type VIII, alpha 1	362	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						AAAGGTGACCGGGGCATGGGA	0.627													G|||	1	0.000199681	0.0	0.0	5008	,	,		17087	0.0		0.001	False		,,,				2504	0.0				p.R362Q		Atlas-SNP	.											.	COL8A1	68	.	0			c.G1085A						PASS	.	G	GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	25	31	29		1085,1085	2.8	1	3	dbSNP_134	29	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	COL8A1	NM_020351.2,NM_001850.3	43,43	0,4,6499	AA,AG,GG		0.0349,0.0227,0.0308	benign,benign	362/745,362/745	99513830	4,13002	2203	4300	6503	SO:0001583	missense	1295	exon5			GTGACCGGGGCAT	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.1085G>A	3.37:g.99513830G>A	ENSP00000261037:p.Arg362Gln	50	0	0		39	20	0.512821	NM_001850	D3DN42|Q53XI6|Q96D07	Missense_Mutation	SNP	ENST00000261037.3	37	CCDS2934.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	11.23	1.577317	0.28092	2.27E-4	3.49E-4	ENSG00000144810	ENST00000261037;ENST00000273342	D;D	0.90788	-2.73;-2.73	5.93	2.8	0.32819	.	0.294580	0.37669	N	0.001998	D	0.82861	0.5129	L	0.38733	1.17	0.34343	D	0.68898	B;B	0.22541	0.071;0.071	B;B	0.15052	0.012;0.012	T	0.75536	-0.3283	10	0.17832	T	0.49	.	9.3612	0.38197	0.1574:0.0:0.8426:0.0	.	363;362	E7EPK9;P27658	.;CO8A1_HUMAN	Q	362	ENSP00000261037:R362Q;ENSP00000273342:R362Q	ENSP00000261037:R362Q	R	+	2	0	COL8A1	100996520	0.573000	0.26676	0.966000	0.40874	0.962000	0.63368	3.041000	0.49807	0.239000	0.21243	0.563000	0.77884	CGG	G|0.999;A|0.001	0.001	strong		0.627	COL8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309001.1	NM_001850		A	99513830	G	A	99513830	3	1	29	1	0	0	0	0	1	0	0	0	3707	1116	39	1	1091	1	COL8A1	3	99513830	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1403416	99513830	98508600	182	12423											
GPR128	84873	hgsc.bcm.edu	37	chr3	100328750	100328750	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgctggtggctgtcgtgtGtggactactgactggcatca	5	12	16	8	1	1	1	1	1	0	0	2	2	1	2	0	5	2	3	0	5	1	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:100328750G>A	ENST00000273352.3	+	1	318	c.50G>A	c.(49-51)tGt>tAt	p.C17Y		NM_032787.2	NP_116176.2	Q96K78	GP128_HUMAN	G protein-coupled receptor 128	17					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						GCTGTCGTGTGTGGACTACTG	0.493																																					p.C17Y	Pancreas(87;185 1975 7223 18722)	Atlas-SNP	.											.	GPR128	126	.	0			c.G50A						PASS	.						214	175	188					3																	100328750		2203	4300	6503	SO:0001583	missense	84873	exon1			TCGTGTGTGGACT	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.50G>A	3.37:g.100328750G>A	ENSP00000273352:p.Cys17Tyr	225	0	0		254	113	0.444882	NM_032787	Q14D94|Q86SQ2	Missense_Mutation	SNP	ENST00000273352.3	37	CCDS2938.1	.	.	.	.	.	.	.	.	.	.	G	18.95	3.730751	0.69074	.	.	ENSG00000144820	ENST00000273352	T	0.41400	1.0	5.69	1.54	0.23209	.	0.095269	0.46442	D	0.000299	T	0.36441	0.0967	M	0.65975	2.015	0.21020	N	0.999803	B	0.24721	0.11	B	0.24541	0.054	T	0.32052	-0.9921	10	0.51188	T	0.08	.	6.5832	0.22607	0.0853:0.0:0.4113:0.5034	.	17	Q96K78	GP128_HUMAN	Y	17	ENSP00000273352:C17Y	ENSP00000273352:C17Y	C	+	2	0	GPR128	101811440	0.916000	0.31088	0.744000	0.31058	0.497000	0.33675	0.814000	0.27239	0.678000	0.31325	0.563000	0.77884	TGT	.	.	none		0.493	GPR128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353236.1			A	100328750	G	A	100328750	3	1	29	1	0	0	0	0	1	0	0	0	6649	1377	48	2	52	2	GPR128	3	100328750	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	814920	100328750	97693680	183	12424											
ZPLD1	131368	hgsc.bcm.edu	37	chr3	102171858	102171858	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggttattcggaaacagatCtggcactgaatggaaggcat	12	9	13	7	2	1	2	0	1	1	1	2	4	1	4	0	5	1	3	0	5	4	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:102171858C>A	ENST00000491959.1	+	10	1084	c.202C>A	c.(202-204)Ctg>Atg	p.L68M	ZPLD1_ENST00000466937.1_Missense_Mutation_p.L68M|ZPLD1_ENST00000306176.1_Missense_Mutation_p.L84M			Q8TCW7	ZPLD1_HUMAN	zona pellucida-like domain containing 1	68	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.					integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(18)|ovary(2)|skin(3)	35						GGAAACAGATCTGGCACTGAA	0.438																																					p.L84M		Atlas-SNP	.											.	ZPLD1	82	.	0			c.C250A						PASS	.						101	97	98					3																	102171858		2203	4300	6503	SO:0001583	missense	131368	exon3			ACAGATCTGGCAC	AY090780	CCDS2947.1	3q12.3	2009-03-25			ENSG00000170044	ENSG00000170044			27022	protein-coding gene	gene with protein product		615915				18632209	Standard	NM_175056		Approved		uc003dvt.1	Q8TCW7	OTTHUMG00000159229	ENST00000491959.1:c.202C>A	3.37:g.102171858C>A	ENSP00000420265:p.Leu68Met	143	0	0		118	44	0.372881	NM_175056	Q49AS1|Q8WU36	Missense_Mutation	SNP	ENST00000491959.1	37		.	.	.	.	.	.	.	.	.	.	C	16.88	3.244144	0.59103	.	.	ENSG00000170044	ENST00000491959;ENST00000306176;ENST00000466937	D;D;D	0.84589	-1.87;-1.87;-1.87	5.99	4.18	0.49190	Zona pellucida sperm-binding protein (3);	0.065284	0.64402	D	0.000006	T	0.81408	0.4816	L	0.39020	1.185	0.58432	D	0.999992	P;P	0.48694	0.875;0.914	B;P	0.47206	0.241;0.541	T	0.81656	-0.0834	10	0.52906	T	0.07	-1.7625	11.6233	0.51130	0.0:0.8362:0.0:0.1638	.	84;68	Q8TCW7-2;Q8TCW7	.;ZPLD1_HUMAN	M	68;84;68	ENSP00000420265:L68M;ENSP00000307801:L84M;ENSP00000418253:L68M	ENSP00000307801:L84M	L	+	1	2	ZPLD1	103654548	0.947000	0.32204	1.000000	0.80357	0.994000	0.84299	0.155000	0.16362	2.840000	0.97914	0.655000	0.94253	CTG	.	.	none		0.438	ZPLD1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000353984.1	NM_175056		A	102171858	C	A	102171858	3	1	29	1	0	0	0	0	1	0	0	0	18236	912	32	4	260	4	ZPLD1	3	102171858	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1843108	102171858	95850572	184	12425											
CCDC54	84692	hgsc.bcm.edu	37	chr3	107096926	107096926	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctggagggagaaaggggtaaAgaaatcacagaactgcttta	16	7	13	5	0	1	3	1	0	0	3	1	5	1	4	0	4	2	2	0	4	6	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:107096926A>C	ENST00000261058.1	+	1	739	c.492A>C	c.(490-492)aaA>aaC	p.K164N		NM_032600.2	NP_115989.1	Q8NEL0	CCD54_HUMAN	coiled-coil domain containing 54	164										NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	19						AAAGGGGTAAAGAAATCACAG	0.418																																					p.K164N		Atlas-SNP	.											.	CCDC54	56	.	0			c.A492C						PASS	.						77	68	71					3																	107096926		2203	4300	6503	SO:0001583	missense	84692	exon1			GGGTAAAGAAATC	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.492A>C	3.37:g.107096926A>C	ENSP00000261058:p.Lys164Asn	207	0	0		215	50	0.232558	NM_032600	Q96A43	Missense_Mutation	SNP	ENST00000261058.1	37	CCDS2949.1	.	.	.	.	.	.	.	.	.	.	A	6.335	0.429836	0.11987	.	.	ENSG00000138483	ENST00000261058	T	0.55930	0.49	5.23	2.88	0.33553	.	0.487140	0.18842	N	0.129644	T	0.48960	0.1529	M	0.62723	1.935	0.09310	N	1	B	0.32051	0.354	B	0.37047	0.24	T	0.49351	-0.8949	10	0.66056	D	0.02	-0.8298	6.0356	0.19706	0.7984:0.0:0.2016:0.0	.	164	Q8NEL0	CCD54_HUMAN	N	164	ENSP00000261058:K164N	ENSP00000261058:K164N	K	+	3	2	CCDC54	108579616	0.978000	0.34361	0.080000	0.20451	0.012000	0.07955	2.718000	0.47236	0.841000	0.35020	0.377000	0.23210	AAA	.	.	none		0.418	CCDC54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353651.1	NM_032600		C	107096926	A	C	107096926	3	2	29	1	0	0	0	0	1	0	0	0	2826	69	3	5	494	5	CCDC54	3	107096926	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	4925068	107096926	90925504	185	12426											
CCDC80	151887	hgsc.bcm.edu	37	chr3	112356977	112356977	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtttctgatagccatcctgTtctgttttacctcctttttt	4	21	6	10	0	2	1	0	1	2	0	4	1	4	1	4	1	2	3	4	1	2	8	rs35149092	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:112356977T>C	ENST00000206423.3	-	2	2729	c.1776A>G	c.(1774-1776)gaA>gaG	p.E592E	CCDC80_ENST00000439685.2_Silent_p.E592E|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	592	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						AGCCATCCTGTTCTGTTTTAC	0.448													T|||	10	0.00199681	0.0	0.0101	5008	,	,		19219	0.0		0.003	False		,,,				2504	0.0				p.E592E		Atlas-SNP	.											.	CCDC80	100	.	0			c.A1776G						PASS	.	T	,	3,4403	6.2+/-15.9	0,3,2200	260	241	247		1776,1776	4.1	1	3	dbSNP_126	247	28,8572	20.4+/-63.3	0,28,4272	no	coding-synonymous,coding-synonymous	CCDC80	NM_199511.1,NM_199512.1	,	0,31,6472	CC,CT,TT		0.3256,0.0681,0.2384	,	592/951,592/951	112356977	31,12975	2203	4300	6503	SO:0001819	synonymous_variant	151887	exon2			ATCCTGTTCTGTT	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.1776A>G	3.37:g.112356977T>C		239	0	0		233	116	0.497854	NM_199511	D3DN67|Q5PR20|Q6GPG9|Q8IVT6|Q8NBV1|Q8NHY8	Silent	SNP	ENST00000206423.3	37	CCDS2968.1																																																																																			T|0.996;C|0.004	0.004	strong		0.448	CCDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354219.1	NM_199511		C	112356977	T	C	112356977	2	2	29	1	0	0	0	0	0	0	0	1	2856	1722	60	3		3	CCDC80	3	112356977	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	5260051	112356977	85665453	186	12427											
GTPBP8	29083	hgsc.bcm.edu	37	chr3	112718352	112718352	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttttaaaacaagtgcttcaGatccagaaatttgttaacat	15	14	5	7	0	1	2	1	0	0	2	2	2	2	2	1	0	3	2	1	0	5	5	rs1054263	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:112718352G>T	ENST00000383678.2	+	5	808	c.726G>T	c.(724-726)caG>caT	p.Q242H	GTPBP8_ENST00000467752.1_Missense_Mutation_p.Q131H|GTPBP8_ENST00000383677.3_Missense_Mutation_p.Q209H|GTPBP8_ENST00000473129.1_Missense_Mutation_p.Q92H	NM_014170.2	NP_054889.2	Q8N3Z3	GTPB8_HUMAN	GTP-binding protein 8 (putative)	242	EngB-type G.		Q -> H (in dbSNP:rs1054263).		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						AAGTGCTTCAGATCCAGAAAT	0.279													G|||	235	0.0469249	0.1218	0.0245	5008	,	,		17422	0.003		0.0308	False		,,,				2504	0.0235				p.Q242H		Atlas-SNP	.											GTPBP8,lymph_node,lymphoid_neoplasm,0,1	GTPBP8	22	1	0			c.G726T						PASS	.	G	HIS/GLN,HIS/GLN	487,3917	228.1+/-243.1	31,425,1746	94	95	94		726,627	4.9	1	3	dbSNP_86	94	296,8298	107.4+/-168.2	5,286,4006	yes	missense,missense	GTPBP8	NM_014170.2,NM_138485.1	24,24	36,711,5752	TT,TG,GG		3.4443,11.0581,6.024	possibly-damaging,possibly-damaging	242/285,209/252	112718352	783,12215	2202	4297	6499	SO:0001583	missense	29083	exon5			GCTTCAGATCCAG	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.726G>T	3.37:g.112718352G>T	ENSP00000373176:p.Gln242His	247	0	0		180	73	0.405556	NM_014170	A6NE99|A6NN11|A8K0P6|Q5I0Y4	Missense_Mutation	SNP	ENST00000383678.2	37	CCDS33820.1	85	0.03891941391941392	47	0.09552845528455285	13	0.03591160220994475	0	0.0	25	0.032981530343007916	G	13.81	2.347604	0.41599	0.110581	0.034443	ENSG00000163607	ENST00000383678;ENST00000383677;ENST00000305485;ENST00000467752;ENST00000473129	T;T;T;T	0.71817	2.5;-0.6;2.5;-0.6	5.81	4.93	0.64822	.	0.368391	0.29715	N	0.011388	T	0.03739	0.0106	L	0.57536	1.79	0.33973	D	0.646991	P;B	0.42123	0.771;0.391	B;B	0.43251	0.413;0.235	T	0.55425	-0.8143	10	0.52906	T	0.07	-9.4679	13.5676	0.61828	0.0756:0.0:0.9244:0.0	rs1054263;rs3194778;rs1054263	209;242	Q8N3Z3-2;Q8N3Z3	.;GTPB8_HUMAN	H	242;209;265;131;92	ENSP00000373176:Q242H;ENSP00000373175:Q209H;ENSP00000417632:Q131H;ENSP00000418514:Q92H	ENSP00000303802:Q265H	Q	+	3	2	GTPBP8	114201042	1.000000	0.71417	0.997000	0.53966	0.950000	0.60333	2.759000	0.47573	1.461000	0.47929	0.655000	0.94253	CAG	G|0.948;T|0.052	0.052	strong		0.279	GTPBP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354260.2	NM_014170		T	112718352	G	T	112718352	3	4	29	1	0	0	0	0	1	0	0	0	6893	933	33	4	744	4	GTPBP8	3	112718352	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	361375	112718352	85304078	187	12428											
C3orf17	25871	hgsc.bcm.edu	37	chr3	112724619	112724619	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctatgcacagtacagtgtgAgagtctccacttagcactgg	10	11	10	10	0	2	1	0	1	2	1	3	2	2	1	1	1	3	3	1	1	3	3	rs7628368	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:112724619A>G	ENST00000314400.5	-	9	1659	c.1468T>C	c.(1468-1470)Tca>Cca	p.S490P	C3orf17_ENST00000472762.1_5'Flank|C3orf17_ENST00000393857.2_Missense_Mutation_p.S354P|C3orf17_ENST00000383675.2_Missense_Mutation_p.S420P	NM_015412.3	NP_056227.2	Q6NW34	CC017_HUMAN	chromosome 3 open reading frame 17	490			S -> P (in dbSNP:rs7628368). {ECO:0000269|PubMed:17974005}.		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						GTACAGTGTGAGAGTCTCCAC	0.433													A|||	232	0.0463259	0.1218	0.0231	5008	,	,		20084	0.003		0.0308	False		,,,				2504	0.0215				p.S490P		Atlas-SNP	.											C3orf17,lymph_node,lymphoid_neoplasm,0,1	C3orf17	37	1	0			c.T1468C						PASS	.	A	PRO/SER	487,3919	228.1+/-243.1	31,425,1747	120	110	114		1468	0.4	0	3	dbSNP_116	114	298,8302	108.8+/-169.4	5,288,4007	yes	missense	C3orf17	NM_015412.3	74	36,713,5754	GG,GA,AA		3.4651,11.0531,6.0357	possibly-damaging	490/568	112724619	785,12221	2203	4300	6503	SO:0001583	missense	25871	exon9			AGTGTGAGAGTCT	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.1468T>C	3.37:g.112724619A>G	ENSP00000320251:p.Ser490Pro	129	0	0		116	65	0.560345	NM_015412	D3DN69|Q68DM6|Q9H7U0|Q9UFM4	Missense_Mutation	SNP	ENST00000314400.5	37	CCDS33824.1	85	0.03891941391941392	47	0.09552845528455285	13	0.03591160220994475	0	0.0	25	0.032981530343007916	A	18.01	3.528189	0.64860	0.110531	0.034651	ENSG00000163608	ENST00000314400;ENST00000383675;ENST00000412848;ENST00000393857	T;T;T	0.40756	1.02;1.02;1.02	5.9	0.438	0.16560	.	0.700302	0.13762	N	0.364499	T	0.01558	0.0050	L	0.59436	1.845	0.09310	N	1	P;P;D;D	0.61080	0.911;0.948;0.989;0.989	P;P;P;P	0.58454	0.63;0.718;0.839;0.776	T	0.04178	-1.0971	10	0.66056	D	0.02	-3.5088	13.1573	0.59524	0.3745:0.6255:0.0:0.0	rs7628368;rs52792426;rs7628368	379;287;420;490	E7EN80;E7EQH6;Q6NW34-2;Q6NW34	.;.;.;CC017_HUMAN	P	490;420;137;354	ENSP00000320251:S490P;ENSP00000373173:S420P;ENSP00000377438:S354P	ENSP00000320251:S490P	S	-	1	0	C3orf17	114207309	0.003000	0.15002	0.001000	0.08648	0.131000	0.20780	0.157000	0.16402	0.120000	0.18254	-0.291000	0.09656	TCA	A|0.949;G|0.051	0.051	strong		0.433	C3orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354405.3	NM_015412		G	112724619	A	G	112724619	3	3	29	1	0	0	0	0	1	0	0	0	2212	304	11	3	239	3	C3orf17	3	112724619	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	6267	112724619	85297811	188	12429											
ZBTB20	26137	hgsc.bcm.edu	37	chr3	114058008	114058008	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gggggtgtgcctgcagggggGgtcccattgctggcactgtg	3	9	20	9	0	0	0	0	0	0	0	1	0	1	0	2	6	3	3	2	6	0	1	rs139619357	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:114058008G>T	ENST00000474710.1	-	5	2248	c.2070C>A	c.(2068-2070)acC>acA	p.T690T	ZBTB20_ENST00000464560.1_Silent_p.T617T|ZBTB20_ENST00000462705.1_Silent_p.T617T|ZBTB20_ENST00000481632.1_Silent_p.T617T|ZBTB20_ENST00000393785.2_Silent_p.T617T|ZBTB20_ENST00000357258.3_Silent_p.T617T|ZBTB20_ENST00000471418.1_Silent_p.T617T	NM_001164342.1	NP_001157814.1	Q9HC78	ZBT20_HUMAN	zinc finger and BTB domain containing 20	690						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(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)		CTGCAGGGGGGGTCCCATTGC	0.642													G|||	2	0.000399361	0.0	0.0	5008	,	,		15690	0.0		0.0	False		,,,				2504	0.002				p.T690T	NSCLC(69;748 1344 9802 11203 30933)	Atlas-SNP	.											.	ZBTB20	157	.	0			c.C2070A						PASS	.	G	,,,,,,	3,4403	6.2+/-15.9	0,3,2200	64	62	63		2070,1851,1851,1851,1851,1851,1851	5.3	1	3	dbSNP_134	63	15,8585	11.9+/-42.8	0,15,4285	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZBTB20	NM_001164342.1,NM_001164343.1,NM_001164344.1,NM_001164345.1,NM_001164346.1,NM_001164347.1,NM_015642.4	,,,,,,	0,18,6485	TT,TG,GG		0.1744,0.0681,0.1384	,,,,,,	690/742,617/669,617/669,617/669,617/669,617/669,617/669	114058008	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	26137	exon5			AGGGGGGGTCCCA	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.2070C>A	3.37:g.114058008G>T		126	0	0		104	45	0.432692	NM_001164342	Q63HP6|Q8N6R5|Q9Y410	Silent	SNP	ENST00000474710.1	37	CCDS54626.1																																																																																			G|0.999;T|0.001	0.001	strong		0.642	ZBTB20-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354951.1	NM_015642		T	114058008	G	T	114058008	2	4	29	1	0	0	0	0	0	0	0	1	17544	1219	43	4		4	ZBTB20	3	114058008	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1333389	114058008	83964422	189	12430											
C3orf30	152405	hgsc.bcm.edu	37	chr3	118865647	118865647	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aatgtctggcgaggctgagcGaagaacttctgagcagatta	12	9	13	7	2	2	4	0	2	2	2	2	6	2	4	0	2	3	2	0	2	4	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:118865647G>A	ENST00000295622.1	+	1	651	c.611G>A	c.(610-612)cGa>cAa	p.R204Q	IGSF11_ENST00000425327.2_5'Flank|RP11-484M3.5_ENST00000490594.1_5'Flank|IGSF11_ENST00000441144.2_5'Flank|IGSF11_ENST00000354673.2_5'Flank	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	204										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)		GAGGCTGAGCGAAGAACTTCT	0.517																																					p.R204Q		Atlas-SNP	.											C3orf30,NS,carcinoma,0,1	C3orf30	64	1	0			c.G611A						PASS	.						110	114	112					3																	118865647		2203	4300	6503	SO:0001583	missense	152405	exon1			CTGAGCGAAGAAC	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.611G>A	3.37:g.118865647G>A	ENSP00000295622:p.Arg204Gln	68	0	0		47	22	0.468085	NM_152539	A1L4B7	Missense_Mutation	SNP	ENST00000295622.1	37	CCDS2984.1	.	.	.	.	.	.	.	.	.	.	G	9.048	0.991375	0.18966	.	.	ENSG00000163424	ENST00000295622;ENST00000470341	T	0.23950	1.88	3.6	-3.75	0.04372	.	1.346930	0.05074	N	0.482208	T	0.16128	0.0388	N	0.24115	0.695	0.09310	N	1	B;B	0.22909	0.077;0.038	B;B	0.14578	0.006;0.011	T	0.29671	-1.0004	10	0.16896	T	0.51	-0.1891	11.8007	0.52124	0.7483:0.0:0.2517:0.0	.	204;204	E9PFE5;Q96M34	.;CC030_HUMAN	Q	204	ENSP00000295622:R204Q	ENSP00000295622:R204Q	R	+	2	0	C3orf30	120348337	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.508000	0.06344	-1.001000	0.03434	-0.351000	0.07748	CGA	.	.	none		0.517	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539		A	118865647	G	A	118865647	3	1	29	1	0	0	0	0	1	0	0	0	2222	1058	37	1	613	1	C3orf30	3	118865647	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	4807639	118865647	79156783	190	12431											
POLQ	10721	hgsc.bcm.edu	37	chr3	121208294	121208294	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tattttttctgcctcaacagCtactcctctgcccttttcac	6	17	3	15	0	4	0	2	0	2	0	5	0	5	0	3	0	5	1	3	0	3	7			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:121208294C>T	ENST00000264233.5	-	16	3612	c.3484G>A	c.(3484-3486)Gct>Act	p.A1162T		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1162					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)		GCCTCAACAGCTACTCCTCTG	0.368								DNA polymerases (catalytic subunits)																													p.A1162T	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.G3484A						PASS	.						186	185	185					3																	121208294		2203	4300	6503	SO:0001583	missense	10721	exon16			CAACAGCTACTCC	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.3484G>A	3.37:g.121208294C>T	ENSP00000264233:p.Ala1162Thr	178	0	0		150	38	0.253333	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	C	7.638	0.680344	0.14907	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.52983	0.64	5.25	4.36	0.52297	.	2.127980	0.01493	N	0.017160	T	0.41305	0.1153	L	0.27053	0.805	0.09310	N	1	B;B	0.29301	0.156;0.241	B;B	0.25140	0.026;0.058	T	0.36768	-0.9734	10	0.28530	T	0.3	.	13.2429	0.60008	0.0:0.8408:0.1592:0.0	.	1162;334	O75417;O75417-2	DPOLQ_HUMAN;.	T	785;1162;1298	ENSP00000264233:A1162T	ENSP00000264233:A1162T	A	-	1	0	POLQ	122690984	0.015000	0.18098	0.011000	0.14972	0.099000	0.18886	1.197000	0.32211	1.408000	0.46895	0.563000	0.77884	GCT	.	.	none		0.368	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		T	121208294	C	T	121208294	3	4	29	1	0	0	0	0	1	0	0	0	12217	797	28	2	4348	2	POLQ	3	121208294	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2342647	121208294	76814136	191	12432											
POLQ	10721	hgsc.bcm.edu	37	chr3	121251922	121251922	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caacttttactgactccaaaAgcggtacagggcgaaagtcg	13	8	10	10	3	0	1	0	1	0	0	2	2	1	1	1	2	4	1	1	2	6	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:121251922A>G	ENST00000264233.5	-	6	1003	c.875T>C	c.(874-876)cTt>cCt	p.L292P	POLQ_ENST00000488282.1_5'UTR	NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	292					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)		TGACTCCAAAAGCGGTACAGG	0.428								DNA polymerases (catalytic subunits)																													p.L292P	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.T875C						PASS	.						93	92	92					3																	121251922		2203	4300	6503	SO:0001583	missense	10721	exon6			TCCAAAAGCGGTA	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.875T>C	3.37:g.121251922A>G	ENSP00000264233:p.Leu292Pro	228	0	0		237	66	0.278481	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.089579	0.76756	.	.	ENSG00000051341	ENST00000264233;ENST00000393672	T	0.67698	-0.28	5.29	5.29	0.74685	DEAD-like helicase (1);	0.063724	0.64402	D	0.000005	D	0.87026	0.6075	H	0.95745	3.715	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91012	0.4850	10	0.87932	D	0	.	15.5172	0.75833	1.0:0.0:0.0:0.0	.	292	O75417	DPOLQ_HUMAN	P	292;427	ENSP00000264233:L292P	ENSP00000264233:L292P	L	-	2	0	POLQ	122734612	1.000000	0.71417	1.000000	0.80357	0.752000	0.42762	8.851000	0.92205	2.126000	0.65437	0.377000	0.23210	CTT	.	.	none		0.428	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420		G	121251922	A	G	121251922	3	3	29	1	0	0	0	0	1	0	0	0	12217	72	3	3	6997	3	POLQ	3	121251922	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	43628	121251922	76770508	192	12433											
SEC61A1	29927	hgsc.bcm.edu	37	chr3	127774411	127774411	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatcaccctctttatcttctTagtgtgctgccaggtaagct	7	16	7	11	0	4	0	1	0	3	0	4	0	4	0	2	1	3	3	2	1	4	6			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:127774411T>C	ENST00000243253.3	+	3	312	c.128T>C	c.(127-129)tTa>tCa	p.L43S	SEC61A1_ENST00000464451.1_Missense_Mutation_p.L49S|SEC61A1_ENST00000424880.2_Intron	NM_013336.3	NP_037468.1	P61619	S61A1_HUMAN	Sec61 alpha 1 subunit (S. cerevisiae)	43					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						TTTATCTTCTTAGTGTGCTGC	0.458																																					p.L43S		Atlas-SNP	.											.	SEC61A1	39	.	0			c.T128C						PASS	.						185	176	179					3																	127774411		2203	4300	6503	SO:0001583	missense	29927	exon3			TCTTCTTAGTGTG	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.128T>C	3.37:g.127774411T>C	ENSP00000243253:p.Leu43Ser	155	0	0		158	64	0.405063	NM_013336	P38378|P57726|Q5JPF8|Q8N0Z4|Q8N3U3|Q8NC71|Q9BU16|Q9Y2R3	Missense_Mutation	SNP	ENST00000243253.3	37	CCDS3046.1	.	.	.	.	.	.	.	.	.	.	T	26.9	4.777511	0.90195	.	.	ENSG00000058262	ENST00000464451;ENST00000243253	.	.	.	5.69	5.69	0.88448	Translocon Sec61/SecY, plug domain (1);SecY subunit domain (2);	0.000000	0.85682	D	0.000000	D	0.83788	0.5330	M	0.86573	2.825	0.80722	D	1	D	0.65815	0.995	D	0.70016	0.967	D	0.86848	0.2021	9	0.87932	D	0	.	15.9604	0.79926	0.0:0.0:0.0:1.0	.	43	P61619	S61A1_HUMAN	S	49;43	.	ENSP00000243253:L43S	L	+	2	0	SEC61A1	129257101	1.000000	0.71417	0.993000	0.49108	0.883000	0.51084	8.035000	0.88872	2.168000	0.68352	0.528000	0.53228	TTA	.	.	none		0.458	SEC61A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356541.2	NM_013336		C	127774411	T	C	127774411	3	2	29	1	0	0	0	0	1	0	0	0	14015	1764	61	3	138	3	SEC61A1	3	127774411	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	6522489	127774411	70248019	193	12434											
EEFSEC	60678	hgsc.bcm.edu	37	chr3	128060346	128060346	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gccggttgatgttcttcagtCctgctccagataactttgac	7	14	9	11	1	2	3	1	2	1	1	4	3	4	3	3	1	2	3	3	1	1	5	rs374389896		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:128060346C>T	ENST00000254730.6	+	5	1111	c.1057C>T	c.(1057-1059)Cct>Tct	p.P353S	EEFSEC_ENST00000483457.1_Missense_Mutation_p.P298S|EEFSEC_ENST00000483569.1_3'UTR	NM_021937.3	NP_068756.2	P57772	SELB_HUMAN	eukaryotic elongation factor, selenocysteine-tRNA-specific	353					selenocysteine incorporation (GO:0001514)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ribonucleoprotein complex binding (GO:0043021)|selenocysteine insertion sequence binding (GO:0035368)|translation elongation factor activity (GO:0003746)|tRNA binding (GO:0000049)			NS(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(10)|ovary(1)	25						GTTCTTCAGTCCTGCTCCAGA	0.493													C|||	1	0.000199681	0.0	0.0	5008	,	,		20430	0.0		0.0	False		,,,				2504	0.001				p.P353S		Atlas-SNP	.											.	EEFSEC	53	.	0			c.C1057T						PASS	.	C	SER/PRO	0,4406		0,0,2203	67	65	66		1057	5.4	1	3		66	1,8599	1.2+/-3.3	0,1,4299	no	missense	EEFSEC	NM_021937.3	74	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	353/597	128060346	1,13005	2203	4300	6503	SO:0001583	missense	60678	exon5			TTCAGTCCTGCTC		CCDS33849.1	3q21.3	2007-05-25			ENSG00000132394	ENSG00000132394			24614	protein-coding gene	gene with protein product	"elongation factor for selenoprotein translation"	607695				10970870, 15229221	Standard	XM_005247696		Approved	SELB, EFSEC	uc003eki.3	P57772	OTTHUMG00000159659	ENST00000254730.6:c.1057C>T	3.37:g.128060346C>T	ENSP00000254730:p.Pro353Ser	122	0	0		95	52	0.547368	NM_021937	Q96HZ6	Missense_Mutation	SNP	ENST00000254730.6	37	CCDS33849.1	.	.	.	.	.	.	.	.	.	.	C	9.164	1.019497	0.19355	0.0	1.16E-4	ENSG00000132394	ENST00000254730;ENST00000483457	T;T	0.53206	1.04;0.63	5.44	5.44	0.79542	.	0.098967	0.64402	D	0.000001	T	0.37732	0.1014	L	0.38531	1.155	0.45554	D	0.998502	B;B	0.23442	0.085;0.002	B;B	0.14023	0.01;0.003	T	0.28713	-1.0035	10	0.07325	T	0.83	-17.2308	19.2453	0.93899	0.0:1.0:0.0:0.0	.	298;353	C9J8T0;P57772	.;SELB_HUMAN	S	353;298	ENSP00000254730:P353S;ENSP00000417660:P298S	ENSP00000254730:P353S	P	+	1	0	EEFSEC	129543036	1.000000	0.71417	0.994000	0.49952	0.548000	0.35241	3.159000	0.50731	2.536000	0.85505	0.591000	0.81541	CCT	.	.	weak		0.493	EEFSEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356738.2	NM_021937		T	128060346	C	T	128060346	3	4	29	1	0	0	0	0	1	0	0	0	4933	855	30	2	1075	2	EEFSEC	3	128060346	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	285935	128060346	69962084	194	12435											
GATA2	2624	hgsc.bcm.edu	37	chr3	128204641	128204641	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gtccccccaggaagcctccgGggtggaagagtccgctgctg	6	6	15	14	2	0	1	0	0	0	1	3	3	3	3	6	4	2	2	6	4	2	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:128204641G>T	ENST00000341105.2	-	3	1131	c.800C>A	c.(799-801)cCc>cAc	p.P267H	GATA2_ENST00000430265.2_Missense_Mutation_p.P267H|GATA2_ENST00000487848.1_Missense_Mutation_p.P267H	NM_032638.4	NP_116027.2	P23769	GATA2_HUMAN	GATA binding protein 2	267					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)		GAAGCCTCCGGGGTGGAAGAG	0.647			Mis		AML(CML blast transformation)																																p.P267H		Atlas-SNP	.		Dom	yes		3	3q21.3	2624	GATA binding protein 2		L	.	GATA2	122	.	0			c.C800A						PASS	.						38	43	41					3																	128204641		2203	4300	6503	SO:0001583	missense	2624	exon3			CCTCCGGGGTGGA	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.800C>A	3.37:g.128204641G>T	ENSP00000345681:p.Pro267His	94	0	0		102	31	0.303922	NM_001145662	D3DNB3|Q53YE0|Q96BH0|Q96BH8|Q9BUJ6	Missense_Mutation	SNP	ENST00000341105.2	37	CCDS3049.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.431859	0.83776	.	.	ENSG00000179348	ENST00000341105;ENST00000430265;ENST00000487848	D;D;D	0.97642	-4.46;-4.47;-4.46	4.62	4.62	0.57501	.	0.000000	0.85682	D	0.000000	D	0.98040	0.9354	M	0.69463	2.115	0.80722	D	1	D;D	0.89917	1.0;0.999	D;P	0.91635	0.999;0.894	D	0.98494	1.0611	10	0.48119	T	0.1	-13.2977	17.4411	0.87565	0.0:0.0:1.0:0.0	.	267;267	P23769-2;P23769	.;GATA2_HUMAN	H	267	ENSP00000345681:P267H;ENSP00000400259:P267H;ENSP00000417074:P267H	ENSP00000345681:P267H	P	-	2	0	GATA2	129687331	1.000000	0.71417	0.924000	0.36721	0.808000	0.45660	7.843000	0.86859	2.099000	0.63709	0.491000	0.48974	CCC	.	.	none		0.647	GATA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356925.1	NM_032638		T	128204641	G	T	128204641	3	4	29	1	0	0	0	0	1	0	0	0	6262	1232	43	4	658	4	GATA2	3	128204641	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	144295	128204641	69817789	195	12436											
COL6A5	256076	hgsc.bcm.edu	37	chr3	130104153	130104153	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttagctttgggcagaactttGatgctttgaaaagcataaaa	14	13	9	5	0	0	3	0	2	0	1	0	3	0	3	0	1	4	4	0	1	6	5	rs149308947		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:130104153G>A	ENST00000432398.2	+	5	2301	c.1807G>A	c.(1807-1809)Gat>Aat	p.D603N	COL6A5_ENST00000265379.6_Missense_Mutation_p.D603N	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	603	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						GCAGAACTTTGATGCTTTGAA	0.388													G|||	1	0.000199681	0.0	0.0	5008	,	,		21518	0.0		0.001	False		,,,				2504	0.0				p.D603N		Atlas-SNP	.											.	COL6A5	205	.	0			c.G1807A						PASS	.						34	30	31					3																	130104153		692	1590	2282	SO:0001583	missense	256076	exon5			AACTTTGATGCTT	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.1807G>A	3.37:g.130104153G>A	ENSP00000390895:p.Asp603Asn	75	0	0		56	23	0.410714	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	16.84	3.232744	0.58777	.	.	ENSG00000172752	ENST00000432398;ENST00000265379	T;T	0.79554	-1.28;-1.28	5.28	5.28	0.74379	.	.	.	.	.	D	0.85362	0.5679	L	0.35793	1.09	0.46725	D	0.99917	D	0.89917	1.0	D	0.83275	0.996	D	0.84806	0.0787	9	0.40728	T	0.16	.	17.7195	0.88347	0.0:0.0:1.0:0.0	.	603	A8TX70-2	.	N	603	ENSP00000390895:D603N;ENSP00000265379:D603N	ENSP00000265379:D603N	D	+	1	0	COL6A5	131586843	1.000000	0.71417	0.997000	0.53966	0.395000	0.30598	6.422000	0.73357	2.469000	0.83416	0.557000	0.71058	GAT	G|1.000;A|0.000	0.000	strong		0.388	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		A	130104153	G	A	130104153	3	1	29	1	0	0	0	0	1	0	0	0	3704	1290	45	2	1821	2	COL6A5	3	130104153	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1899512	130104153	67918277	196	12437											
COL6A6	131873	hgsc.bcm.edu	37	chr3	130311551	130311551	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tattttcagggaaacagaggActaaatggacaggaggtatg	15	9	13	4	0	1	1	1	0	0	1	1	5	1	5	0	5	1	1	0	5	5	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:130311551A>T	ENST00000358511.6	+	14	4387	c.4356A>T	c.(4354-4356)ggA>ggT	p.G1452G	COL6A6_ENST00000453409.2_Silent_p.G1452G	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	1452	Triple-helical 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						GAAACAGAGGACTAAATGGAC	0.313																																					p.G1452G		Atlas-SNP	.											COL6A6_ENST00000358511,bladder,carcinoma,+1,2	COL6A6	497	2	0			c.A4356T						PASS	.						162	153	156					3																	130311551		1844	4080	5924	SO:0001819	synonymous_variant	131873	exon14			CAGAGGACTAAAT	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.4356A>T	3.37:g.130311551A>T		131	0	0		108	28	0.259259	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Silent	SNP	ENST00000358511.6	37	CCDS46911.1	.	.	.	.	.	.	.	.	.	.	A	1.893	-0.455057	0.04540	.	.	ENSG00000206384	ENST00000511332	.	.	.	5.83	3.41	0.39046	.	.	.	.	.	T	0.55178	0.1904	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50180	-0.8858	4	.	.	.	.	6.402	0.21644	0.7606:0.1572:0.0822:0.0	.	.	.	.	V	231	.	.	D	+	2	0	COL6A6	131794241	0.998000	0.40836	0.987000	0.45799	0.114000	0.19823	1.173000	0.31920	1.021000	0.39600	0.460000	0.39030	GAC	.	.	none		0.313	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		T	130311551	A	T	130311551	2	4	29	1	0	0	0	0	0	0	0	1	3705	262	10	5		5	COL6A6	3	130311551	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	207398	130311551	67710879	197	12438											
DNAJC13	23317	hgsc.bcm.edu	37	chr3	132221139	132221139	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ttttattctctcagagtattCcccgcgtagctgctcttggg	5	16	9	11	2	3	1	1	0	2	1	5	1	4	1	2	1	2	4	2	1	3	7	rs55825559	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:132221139C>T	ENST00000260818.6	+	40	4791	c.4543C>T	c.(4543-4545)Ccc>Tcc	p.P1515S		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	1515			P -> S (in dbSNP:rs55825559).		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						TCAGAGTATTCCCCGCGTAGC	0.413													C|||	60	0.0119808	0.0	0.0245	5008	,	,		15388	0.0		0.0368	False		,,,				2504	0.0061				p.P1515S		Atlas-SNP	.											.	DNAJC13	253	.	0			c.C4543T						PASS	.	C	SER/PRO	26,4380	32.6+/-62.9	0,26,2177	117	113	115		4543	5.8	1	3	dbSNP_129	115	239,8361	94.5+/-156.4	5,229,4066	yes	missense	DNAJC13	NM_015268.3	74	5,255,6243	TT,TC,CC		2.7791,0.5901,2.0375	benign	1515/2244	132221139	265,12741	2203	4300	6503	SO:0001583	missense	23317	exon40			AGTATTCCCCGCG	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.4543C>T	3.37:g.132221139C>T	ENSP00000260818:p.Pro1515Ser	125	0	0		115	59	0.513043	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	37	CCDS33857.1	34	0.015567765567765568	0	0.0	9	0.024861878453038673	0	0.0	25	0.032981530343007916	C	14.92	2.678748	0.47886	0.005901	0.027791	ENSG00000138246	ENST00000260818;ENST00000538066	T	0.52057	0.68	5.81	5.81	0.92471	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.24812	0.0602	M	0.69185	2.1	0.54753	D	0.999985	B	0.20368	0.044	B	0.15870	0.014	T	0.17653	-1.0362	10	0.40728	T	0.16	.	16.3288	0.82997	0.0:0.868:0.132:0.0	rs55825559;rs61748104	1515	O75165	DJC13_HUMAN	S	1515;162	ENSP00000260818:P1515S	ENSP00000260818:P1515S	P	+	1	0	DNAJC13	133703829	1.000000	0.71417	0.998000	0.56505	0.614000	0.37383	4.644000	0.61397	2.734000	0.93682	0.650000	0.86243	CCC	C|0.981;T|0.019	0.019	strong		0.413	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268		T	132221139	C	T	132221139	3	4	29	1	0	0	0	0	1	0	0	0	4634	855	30	2	4697	2	DNAJC13	3	132221139	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1909588	132221139	65801291	198	12439											
TMEM108	66000	hgsc.bcm.edu	37	chr3	133098806	133098806	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcagctcccatggcaacacCgacaccccgtgcagaggggc	9	4	12	16	2	0	1	0	0	0	1	1	2	1	1	4	3	4	4	4	3	1	0	rs34111099	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:133098806C>T	ENST00000321871.6	+	4	461	c.251C>T	c.(250-252)cCg>cTg	p.P84L	TMEM108_ENST00000515826.1_Missense_Mutation_p.P84L|TMEM108_ENST00000508711.1_Intron|TMEM108_ENST00000393130.3_Missense_Mutation_p.P84L	NM_001136469.1|NM_023943.2	NP_001129941.1|NP_076432.1	Q6UXF1	TM108_HUMAN	transmembrane protein 108	84	Pro-rich.		P -> L (in dbSNP:rs34111099). {ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:12975309}.			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						ATGGCAACACCGACACCCCGT	0.627													c|||	145	0.0289537	0.0136	0.0173	5008	,	,		15503	0.0		0.0616	False		,,,				2504	0.0542				p.P84L		Atlas-SNP	.											TMEM108,rectum,carcinoma,0,1	TMEM108	67	1	0			c.C251T						PASS	.		LEU/PRO,LEU/PRO	82,4324	68.7+/-106.4	2,78,2123	97	89	92		251,251	0.9	0	3	dbSNP_126	92	597,8003	157.7+/-211.4	23,551,3726	yes	missense,missense	TMEM108	NM_001136469.1,NM_023943.2	98,98	25,629,5849	TT,TC,CC		6.9419,1.8611,5.2207	benign,benign	84/576,84/576	133098806	679,12327	2203	4300	6503	SO:0001583	missense	66000	exon4			CAACACCGACACC	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.251C>T	3.37:g.133098806C>T	ENSP00000324651:p.Pro84Leu	125	0	0		109	55	0.504587	NM_023943	D3DNC9|Q9BQH1|Q9BW81|Q9C0H3	Missense_Mutation	SNP	ENST00000321871.6	37	CCDS33858.1	61	0.027930402930402932	12	0.024390243902439025	4	0.011049723756906077	0	0.0	45	0.059366754617414245	c	2.305	-0.359279	0.05138	0.018611	0.069419	ENSG00000144868	ENST00000321871;ENST00000393130;ENST00000514894;ENST00000512662;ENST00000512137;ENST00000515826;ENST00000510183	T;T;T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88;0.88;0.88	2.76	0.893	0.19236	.	0.467395	0.15982	N	0.235273	T	0.01189	0.0039	N	0.08118	0	0.09310	N	1	B;B	0.29862	0.259;0.007	B;B	0.20384	0.029;0.004	T	0.08269	-1.0730	10	0.52906	T	0.07	0.0198	3.2014	0.06651	0.2607:0.5932:0.0:0.1461	rs34111099	84;84	E9PB58;Q6UXF1	.;TM108_HUMAN	L	84;84;35;35;84;84;84	ENSP00000324651:P84L;ENSP00000376838:P84L;ENSP00000422072:P35L;ENSP00000427447:P35L;ENSP00000426301:P84L;ENSP00000423338:P84L;ENSP00000421486:P84L	ENSP00000324651:P84L	P	+	2	0	TMEM108	134581496	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	0.106000	0.15354	0.219000	0.20840	0.457000	0.33378	CCG	C|0.952;T|0.048	0.048	strong		0.627	TMEM108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356907.2	NM_023943		T	133098806	C	T	133098806	3	4	29	1	0	0	0	0	1	0	0	0	16039	652	23	1	257	1	TMEM108	3	133098806	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	877667	133098806	64923624	199	12440											
HLTF	6596	hgsc.bcm.edu	37	chr3	148756993	148756993	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggccatggaaccatccaaaCgagtaaacacaaatccagag	17	4	9	11	1	0	1	0	0	0	1	2	3	2	2	4	2	3	1	4	2	5	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:148756993C>T	ENST00000310053.5	-	23	2832	c.2639G>A	c.(2638-2640)cGt>cAt	p.R880H	HLTF_ENST00000465259.1_Missense_Mutation_p.R879H|HLTF_ENST00000392912.2_Missense_Mutation_p.R880H|HLTF_ENST00000494055.1_Missense_Mutation_p.R880H	NM_003071.3|NM_139048.2	NP_003062.2|NP_620636.1	Q14527	HLTF_HUMAN	helicase-like transcription factor	880	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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)			ACCATCCAAACGAGTAAACAC	0.343																																					p.R880H		Atlas-SNP	.											.	HLTF	87	.	0			c.G2639A						PASS	.						51	51	51					3																	148756993		2203	4300	6503	SO:0001583	missense	6596	exon23			TCCAAACGAGTAA	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.2639G>A	3.37:g.148756993C>T	ENSP00000308944:p.Arg880His	69	0	0		73	22	0.30137	NM_139048	D3DNH3|Q14536|Q16051|Q7KYJ6|Q86YA5|Q92652|Q96KM9	Missense_Mutation	SNP	ENST00000310053.5	37	CCDS33875.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.872131	0.91587	.	.	ENSG00000071794	ENST00000465259;ENST00000310053;ENST00000392912;ENST00000494055;ENST00000467858	T;T;T;T;T	0.77229	-1.08;-1.08;-1.08;-1.08;-1.08	5.98	5.98	0.97165	Helicase, C-terminal (3);	.	.	.	.	D	0.90820	0.7117	M	0.94021	3.485	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	0.92423	0.5947	9	0.87932	D	0	-17.5805	14.5887	0.68347	0.0:0.929:0.0:0.071	.	880;880;880	Q59GQ7;A8K5B6;Q14527	.;.;HLTF_HUMAN	H	879;880;880;880;348	ENSP00000420745:R879H;ENSP00000308944:R880H;ENSP00000376644:R880H;ENSP00000420429:R880H;ENSP00000420106:R348H	ENSP00000308944:R880H	R	-	2	0	HLTF	150239683	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.529000	0.67135	2.835000	0.97688	0.650000	0.86243	CGT	.	.	none		0.343	HLTF-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356064.1			T	148756993	C	T	148756993	3	4	29	1	0	0	0	0	1	0	0	0	7224	536	19	1	402	1	HLTF	3	148756993	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	15658187	148756993	49265437	200	12441											
IGSF10	285313	hgsc.bcm.edu	37	chr3	151165641	151165641	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acttgtgcttgaggtgtgttTtccaacctcagcctccatca	7	14	8	12	0	2	1	2	1	0	0	4	1	4	1	4	1	3	2	4	1	1	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:151165641T>G	ENST00000282466.3	-	4	2127	c.2128A>C	c.(2128-2130)Aaa>Caa	p.K710Q		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	710					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)			GAGGTGTGTTTTCCAACCTCA	0.488																																					p.K710Q		Atlas-SNP	.											.	IGSF10	279	.	0			c.A2128C						PASS	.						80	67	71					3																	151165641		2203	4300	6503	SO:0001583	missense	285313	exon4			TGTGTTTTCCAAC	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.2128A>C	3.37:g.151165641T>G	ENSP00000282466:p.Lys710Gln	197	0	0		201	11	0.0547264	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	37	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	T	10.59	1.394224	0.25205	.	.	ENSG00000152580	ENST00000282466	T	0.69040	-0.37	4.66	4.66	0.58398	.	0.474372	0.17291	N	0.179644	T	0.50769	0.1635	L	0.29908	0.895	0.09310	N	1	B	0.21905	0.062	B	0.16289	0.015	T	0.31641	-0.9936	10	0.22109	T	0.4	.	9.5824	0.39495	0.0:0.0:0.2373:0.7627	.	710	Q6WRI0	IGS10_HUMAN	Q	710	ENSP00000282466:K710Q	ENSP00000282466:K710Q	K	-	1	0	IGSF10	152648331	0.002000	0.14202	0.024000	0.17045	0.020000	0.10135	0.929000	0.28844	1.876000	0.54355	0.482000	0.46254	AAA	.	.	none		0.488	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822		G	151165641	T	G	151165641	3	3	29	1	0	0	0	0	1	0	0	0	7606	1850	64	5	5803	5	IGSF10	3	151165641	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	2408648	151165641	46856789	201	12442											
GMPS	8833	hgsc.bcm.edu	37	chr3	155633817	155633817	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgattatagattgccaatGaagtaattggagaaatgaac	16	12	10	3	0	0	5	0	3	0	2	0	6	0	5	1	1	2	2	1	1	7	6	rs201869567		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:155633817G>T	ENST00000496455.2	+	9	1383	c.1048G>T	c.(1048-1050)Gaa>Taa	p.E350*	GMPS_ENST00000295920.7_Nonsense_Mutation_p.E251*	NM_003875.2	NP_003866.1	P49915	GUAA_HUMAN	guanine monphosphate synthase	350	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)	GATTGCCAATGAAGTAATTGG	0.368			T	MLL	AML																																p.E350X	Ovarian(153;896 1876 4149 15499 28134)	Atlas-SNP	.		Dom	yes		3	3q24	8833	guanine monphosphate synthetase		L	.	GMPS	70	.	0			c.G1048T						PASS	.						66	61	62					3																	155633817		1824	4087	5911	SO:0001587	stop_gained	8833	exon9			GCCAATGAAGTAA	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.1048G>T	3.37:g.155633817G>T	ENSP00000419851:p.Glu350*	70	0	0		53	4	0.0754717	NM_003875	A8K639|B4DXV7|F8W720	Nonsense_Mutation	SNP	ENST00000496455.2	37	CCDS46941.1	.	.	.	.	.	.	.	.	.	.	G	40	8.493974	0.98836	.	.	ENSG00000163655	ENST00000496455;ENST00000295920;ENST00000537975;ENST00000541628	.	.	.	5.36	5.36	0.76844	.	0.261311	0.38605	N	0.001621	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	-21.8965	19.0809	0.93180	0.0:0.0:1.0:0.0	.	.	.	.	X	350;251;299;350	.	ENSP00000295920:E251X	E	+	1	0	GMPS	157116511	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	9.149000	0.94659	2.505000	0.84491	0.549000	0.68633	GAA	G|0.999;A|0.001	.	alt		0.368	GMPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351260.2			T	155633817	G	T	155633817	4	4	29	1	0	0	0	0	0	1	0	0	6506	1291	45	4	1082	4	GMPS	3	155633817	Nonsense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	4468176	155633817	42388613	202	12443											
ZBBX	79740	hgsc.bcm.edu	37	chr3	167023485	167023485	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttggcctcttatacagattGctcaattccaaggattcttt	9	16	6	10	0	3	1	1	0	2	1	4	2	4	2	2	2	2	1	2	2	4	7			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:167023485G>T	ENST00000392766.2	-	17	2011	c.1671C>A	c.(1669-1671)agC>agA	p.S557R	ZBBX_ENST00000307529.5_Missense_Mutation_p.S557R|ZBBX_ENST00000455345.2_Missense_Mutation_p.S557R|ZBBX_ENST00000392767.2_Missense_Mutation_p.S557R|ZBBX_ENST00000392764.1_Missense_Mutation_p.S528R	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	557						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						TATACAGATTGCTCAATTCCA	0.318																																					p.S557R		Atlas-SNP	.											.	ZBBX	299	.	0			c.C1671A						PASS	.						73	65	67					3																	167023485		1805	4064	5869	SO:0001583	missense	79740	exon17			CAGATTGCTCAAT	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.1671C>A	3.37:g.167023485G>T	ENSP00000376519:p.Ser557Arg	202	0	0		169	37	0.218935	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	37	CCDS3199.2	.	.	.	.	.	.	.	.	.	.	G	9.950	1.219989	0.22373	.	.	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764	T;T;T;T;T	0.12672	2.83;2.83;2.84;2.84;2.66	5.3	0.467	0.16721	.	0.470940	0.24740	N	0.035987	T	0.17959	0.0431	L	0.59436	1.845	0.09310	N	1	D;D	0.59357	0.985;0.975	P;P	0.52217	0.693;0.497	T	0.07139	-1.0788	10	0.66056	D	0.02	-1.3445	4.9275	0.13901	0.344:0.1509:0.5051:0.0	.	557;557	A8MT70-2;A8MT70	.;ZBBX_HUMAN	R	557;557;557;557;528	ENSP00000376519:S557R;ENSP00000376520:S557R;ENSP00000390232:S557R;ENSP00000305065:S557R;ENSP00000376517:S528R	ENSP00000305065:S557R	S	-	3	2	ZBBX	168506179	0.266000	0.24112	0.013000	0.15412	0.012000	0.07955	-0.013000	0.12678	0.142000	0.18901	0.650000	0.86243	AGC	.	.	none		0.318	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687		T	167023485	G	T	167023485	3	4	29	1	0	0	0	0	1	0	0	0	17531	1310	46	4	751	4	ZBBX	3	167023485	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	11389668	167023485	30998945	203	12444											
WDR49	151790	hgsc.bcm.edu	37	chr3	167240215	167240215	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttttgaatctcactttccaCtaaattagtatctcttttag	10	19	3	9	0	2	1	1	1	2	0	5	1	3	1	1	0	0	1	1	0	6	8	rs202225646		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:167240215C>T	ENST00000308378.3	-	12	1911	c.1606G>A	c.(1606-1608)Gtg>Atg	p.V536M	WDR49_ENST00000453925.2_Intron|WDR49_ENST00000479765.1_Intron|WDR49_ENST00000476376.1_Missense_Mutation_p.V361M	NM_178824.3	NP_849146.1	Q8IV35	WDR49_HUMAN	WD repeat domain 49	536										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						TCACTTTCCACTAAATTAGTA	0.294																																					p.V536M		Atlas-SNP	.											.	WDR49	188	.	0			c.G1606A						PASS	.	C	MET/VAL	0,4406		0,0,2203	66	70	68		1606	-1.5	0	3		68	2,8596	2.2+/-6.3	0,2,4297	yes	missense	WDR49	NM_178824.3	21	0,2,6500	TT,TC,CC		0.0233,0.0,0.0154	benign	536/698	167240215	2,13002	2203	4299	6502	SO:0001583	missense	151790	exon12			TTTCCACTAAATT	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.1606G>A	3.37:g.167240215C>T	ENSP00000311343:p.Val536Met	47	0	0		72	39	0.541667	NM_178824	Q8N297	Missense_Mutation	SNP	ENST00000308378.3	37	CCDS3201.1	.	.	.	.	.	.	.	.	.	.	C	2.789	-0.251853	0.05829	0.0	2.33E-4	ENSG00000174776	ENST00000308378;ENST00000476376	T;T	0.53423	0.62;1.92	5.23	-1.55	0.08558	WD40 repeat-like-containing domain (1);	0.994051	0.08174	N	0.986607	T	0.24236	0.0587	N	0.04203	-0.255	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.20773	-1.0265	10	0.37606	T	0.19	.	9.614	0.39681	0.0:0.4515:0.0:0.5485	.	536	Q8IV35	WDR49_HUMAN	M	536;361	ENSP00000311343:V536M;ENSP00000420508:V361M	ENSP00000311343:V536M	V	-	1	0	WDR49	168722909	0.000000	0.05858	0.001000	0.08648	0.064000	0.16182	0.104000	0.15313	-0.173000	0.10761	-0.312000	0.09012	GTG	.	.	weak		0.294	WDR49-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000350592.3	NM_178824		T	167240215	C	T	167240215	3	4	29	1	0	0	0	0	1	0	0	0	17317	565	20	2	503	2	WDR49	3	167240215	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	216730	167240215	30782215	204	12445											
SPATA16	83893	hgsc.bcm.edu	37	chr3	172835469	172835469	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctttggaacaagctgatcaTgatagatcctattcactgca	12	13	7	9	0	3	3	2	2	1	1	4	4	4	4	1	1	3	2	1	1	4	4	rs115897458	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:172835469T>C	ENST00000351008.3	-	2	236	c.53A>G	c.(52-54)cAt>cGt	p.H18R		NM_031955.5	NP_114161.3	Q9BXB7	SPT16_HUMAN	spermatogenesis associated 16	18					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)			AAGCTGATCATGATAGATCCT	0.428													T|||	7	0.00139776	0.0	0.0014	5008	,	,		19584	0.0		0.006	False		,,,				2504	0.0				p.H18R		Atlas-SNP	.											.	SPATA16	111	.	0			c.A53G						PASS	.	T	ARG/HIS	7,4399	14.3+/-33.2	0,7,2196	181	168	173		53	-1.2	0	3	dbSNP_132	173	65,8535	40.3+/-97.0	1,63,4236	yes	missense	SPATA16	NM_031955.5	29	1,70,6432	CC,CT,TT		0.7558,0.1589,0.5536	benign	18/570	172835469	72,12934	2203	4300	6503	SO:0001583	missense	83893	exon2			TGATCATGATAGA	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.53A>G	3.37:g.172835469T>C	ENSP00000341765:p.His18Arg	231	1	0.004329		210	92	0.438095	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	37	CCDS3221.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	T	0.017	-1.490377	0.01018	0.001589	0.007558	ENSG00000144962	ENST00000351008	T	0.14022	2.54	5.23	-1.2	0.09554	.	0.934285	0.08915	N	0.875252	T	0.03263	0.0095	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.43048	-0.9415	10	0.06757	T	0.87	-2.7449	5.2779	0.15659	0.0:0.2885:0.3529:0.3586	.	18	Q9BXB7	SPT16_HUMAN	R	18	ENSP00000341765:H18R	ENSP00000341765:H18R	H	-	2	0	SPATA16	174318163	0.041000	0.20044	0.020000	0.16555	0.075000	0.17131	0.281000	0.18810	-0.144000	0.11314	0.528000	0.53228	CAT	T|0.996;C|0.004	0.004	strong		0.428	SPATA16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346322.1	NM_031955		C	172835469	T	C	172835469	3	2	29	1	0	0	0	0	1	0	0	0	15016	1464	51	3	1696	3	SPATA16	3	172835469	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	5595254	172835469	25186961	205	12446											
NAALADL2	254827	hgsc.bcm.edu	37	chr3	174974265	174974265	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggattaggaaaataaaaaaCgtaacaaatcagatcgcact	21	7	7	6	2	1	1	1	0	0	1	2	3	1	3	0	2	2	2	0	2	8	3	rs192980349	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:174974265C>T	ENST00000454872.1	+	4	1013	c.885C>T	c.(883-885)aaC>aaT	p.N295N	NAALADL2_ENST00000473253.1_3'UTR|NAALADL2-AS2_ENST00000424690.1_RNA	NM_207015.2	NP_996898.2	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 2	295						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)		AAATAAAAAACGTAACAAATC	0.353													T|||	2	0.000399361	0.0	0.0	5008	,	,		18334	0.0		0.002	False		,,,				2504	0.0				p.N295N		Atlas-SNP	.											.	NAALADL2	86	.	0			c.C885T						PASS	.	T		2,3672		0,2,1835	91	85	87		885	2.2	0.1	3		87	13,8173		0,13,4080	no	coding-synonymous	NAALADL2	NM_207015.2		0,15,5915	TT,TC,CC		0.1588,0.0544,0.1265		295/796	174974265	15,11845	1837	4093	5930	SO:0001819	synonymous_variant	254827	exon4			AAAAAACGTAACA		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.885C>T	3.37:g.174974265C>T		118	0	0		102	48	0.470588	NM_207015	Q658X9|Q6H9J8|Q6H9J9|Q6PG38	Silent	SNP	ENST00000454872.1	37	CCDS46960.1																																																																																			C|0.999;T|0.001	0.001	strong		0.353	NAALADL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347390.2	NM_207015		T	174974265	C	T	174974265	2	4	29	1	0	0	0	0	0	0	0	1	10139	535	19	1		1	NAALADL2	3	174974265	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2138796	174974265	23048165	206	12447											
USP13	8975	hgsc.bcm.edu	37	chr3	179424788	179424788	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaagcaggacccagacacgTgggaaaatgaattgccagta	16	5	12	8	1	0	2	0	1	0	1	0	5	0	4	2	2	2	2	2	2	5	2	rs141550831	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:179424788T>C	ENST00000263966.3	+	5	1015	c.544T>C	c.(544-546)Tgg>Cgg	p.W182R	USP13_ENST00000482333.1_3'UTR|USP13_ENST00000496897.1_Missense_Mutation_p.W117R	NM_003940.2	NP_003931.2	Q92995	UBP13_HUMAN	ubiquitin specific peptidase 13 (isopeptidase T-3)	182					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)			CCCAGACACGTGGGAAAATGA	0.423																																					p.W182R		Atlas-SNP	.											USP13,NS,carcinoma,-1,1	USP13	117	1	0			c.T544C						PASS	.	T	ARG/TRP	2,4404	4.2+/-10.8	0,2,2201	102	92	95		544	6	1	3	dbSNP_134	95	4,8596	3.7+/-12.6	0,4,4296	yes	missense	USP13	NM_003940.2	101	0,6,6497	CC,CT,TT		0.0465,0.0454,0.0461	probably-damaging	182/864	179424788	6,13000	2203	4300	6503	SO:0001583	missense	8975	exon5			GACACGTGGGAAA	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.544T>C	3.37:g.179424788T>C	ENSP00000263966:p.Trp182Arg	157	0	0		150	89	0.593333	NM_003940	A8K2S3|B4DYF3|D3DNS2|Q96B25	Missense_Mutation	SNP	ENST00000263966.3	37	CCDS3235.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.717237	0.89205	4.54E-4	4.65E-4	ENSG00000058056	ENST00000263966;ENST00000496897	T;T	0.35789	1.31;1.29	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.64034	0.2562	M	0.80183	2.485	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.68515	-0.5388	10	0.87932	D	0	-10.5405	16.5494	0.84464	0.0:0.0:0.0:1.0	.	182;182	Q92995;A8K2S3	UBP13_HUMAN;.	R	182;117	ENSP00000263966:W182R;ENSP00000417146:W117R	ENSP00000263966:W182R	W	+	1	0	USP13	180907482	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	7.698000	0.84413	2.299000	0.77371	0.528000	0.53228	TGG	T|0.999;C|0.001	0.001	strong		0.423	USP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349617.1			C	179424788	T	C	179424788	3	2	29	1	0	0	0	0	1	0	0	0	17059	1696	59	3	562	3	USP13	3	179424788	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	4450523	179424788	18597642	207	12448											
MCCC1	56922	hgsc.bcm.edu	37	chr3	182755074	182755074	+	Frame_Shift_Del	DEL	C	C	-																															tgagacccagggctgcctggCataaagactctttggctgca																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:182755074delC	ENST00000265594.4	-	13	1672	c.1526delG	c.(1525-1527)tgcfs	p.C509fs	MCCC1_ENST00000489909.1_5'UTR|MCCC1_ENST00000492597.1_Frame_Shift_Del_p.C400fs|MCCC1_ENST00000539926.1_Frame_Shift_Del_p.C374fs	NM_020166.3	NP_064551.3	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-CoA carboxylase 1 (alpha)	509					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)	GGCTGCCTGGCATAAAGACTC	0.507																																					p.C509fs		Pindel,Atlas-Indel	.											.	MCCC1	87	.	0			c.1527delC	GRCh37	CD053583	MCCC1	D		PASS	.						122	106	112					3																	182755074		2203	4300	6503	SO:0001589	frameshift_variant	56922	exon13			.	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.1526delG	3.37:g.182755074delC	ENSP00000265594:p.Cys509fs	122	0	.		131	39	0.298	NM_020166	Q59ES4|Q9H959|Q9NS97	Frame_Shift_Del	DEL	ENST00000265594.4	37	CCDS3241.1																																																																																			.	.	none		0.507	MCCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350775.1	NM_020166		-	182755074	C	-	182755074	7	5	29	1	0	1	0	1	0	0	0	0	9383	710	25	0	679	0	MCCC1	3	182755074	Frame_Shift_Del	DEL	C	TCGA-GR-7351-01A-11D-2210-10	3330286	182755074	15267356	208	12449											
MCCC1	56922	hgsc.bcm.edu	37	chr3	182804555	182804555	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctgggagggagcggggcCgatggaatatgcttcatctg	7	9	17	8	2	2	0	1	0	1	0	2	4	2	3	1	5	3	2	1	5	2	2	rs375244642		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:182804555C>T	ENST00000265594.4	-	4	441	c.295G>A	c.(295-297)Ggc>Agc	p.G99S	MCCC1_ENST00000492597.1_5'UTR|MCCC1_ENST00000539926.1_Intron	NM_020166.3	NP_064551.3	Q96RQ3	MCCA_HUMAN	methylcrotonoyl-CoA carboxylase 1 (alpha)	99	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)	GGAGCGGGGCCGATGGAATAT	0.463																																					p.G99S		Atlas-SNP	.											.	MCCC1	87	.	0			c.G295A						PASS	.	C	SER/GLY	0,4406		0,0,2203	82	69	73		295	5.5	0.3	3		73	1,8599	1.2+/-3.3	0,1,4299	no	missense	MCCC1	NM_020166.3	56	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	99/726	182804555	1,13005	2203	4300	6503	SO:0001583	missense	56922	exon4			CGGGGCCGATGGA	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.295G>A	3.37:g.182804555C>T	ENSP00000265594:p.Gly99Ser	80	0	0		60	28	0.466667	NM_020166	Q59ES4|Q9H959|Q9NS97	Missense_Mutation	SNP	ENST00000265594.4	37	CCDS3241.1	.	.	.	.	.	.	.	.	.	.	C	21.6	4.180502	0.78677	0.0	1.16E-4	ENSG00000078070	ENST00000265594;ENST00000476176;ENST00000448585	D;D	0.97811	-4.55;-4.55	5.5	5.5	0.81552	Pre-ATP-grasp fold (1);PreATP-grasp-like fold (1);Biotin carboxylation domain (1);Carbamoyl-phosphate synthase, large subunit, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99149	0.9706	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	0.99289	1.0898	10	0.87932	D	0	.	18.991	0.92793	0.0:1.0:0.0:0.0	.	52;99	E9PG35;Q96RQ3	.;MCCA_HUMAN	S	99;52;52	ENSP00000265594:G99S;ENSP00000420433:G52S	ENSP00000265594:G99S	G	-	1	0	MCCC1	184287249	1.000000	0.71417	0.319000	0.25293	0.163000	0.22366	7.160000	0.77495	2.601000	0.87937	0.563000	0.77884	GGC	.	.	weak		0.463	MCCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350775.1	NM_020166		T	182804555	C	T	182804555	3	4	29	1	0	0	0	0	1	0	0	0	9383	652	23	1	1946	1	MCCC1	3	182804555	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	49481	182804555	15217875	209	12450											
MCF2L2	23101	hgsc.bcm.edu	37	chr3	182941927	182941927	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acactcttgccagattgcccTagctcggggcagattcttat	8	12	9	12	1	2	2	0	0	2	2	3	2	2	2	2	2	3	2	2	2	2	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:182941927T>C	ENST00000328913.3	-	19	2464	c.2167A>G	c.(2167-2169)Agg>Ggg	p.R723G	MCF2L2_ENST00000473233.1_Missense_Mutation_p.R723G	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	723	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)			CAGATTGCCCTAGCTCGGGGC	0.368																																					p.R723G		Atlas-SNP	.											.	MCF2L2	164	.	0			c.A2167G						PASS	.						151	156	154					3																	182941927		2203	4300	6503	SO:0001583	missense	23101	exon19			TTGCCCTAGCTCG	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.2167A>G	3.37:g.182941927T>C	ENSP00000328118:p.Arg723Gly	96	0	0		77	4	0.0519481	NM_015078	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Missense_Mutation	SNP	ENST00000328913.3	37	CCDS3243.1	.	.	.	.	.	.	.	.	.	.	T	15.12	2.739040	0.49045	.	.	ENSG00000053524	ENST00000328913;ENST00000473233	T;T	0.63096	-0.02;-0.02	4.61	2.23	0.28157	Dbl homology (DH) domain (5);	0.487586	0.22204	N	0.063187	T	0.42200	0.1192	L	0.27053	0.805	0.09310	N	1	B	0.33413	0.411	B	0.31495	0.131	T	0.38001	-0.9681	10	0.87932	D	0	.	4.2628	0.10749	0.0:0.1046:0.2079:0.6876	.	723	Q86YR7	MF2L2_HUMAN	G	723	ENSP00000328118:R723G;ENSP00000420070:R723G	ENSP00000328118:R723G	R	-	1	2	MCF2L2	184424621	0.001000	0.12720	0.019000	0.16419	0.998000	0.95712	0.880000	0.28159	0.875000	0.35847	0.460000	0.39030	AGG	.	.	none		0.368	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078		C	182941927	T	C	182941927	3	2	29	1	0	0	0	0	1	0	0	0	9389	1521	53	3	1225	3	MCF2L2	3	182941927	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	137372	182941927	15080503	210	12451											
B3GNT5	84002	hgsc.bcm.edu	37	chr3	182987591	182987591	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acagacttgagtggatatgaGaatgttggttagtggcagaa	13	11	14	3	0	0	4	0	2	0	3	0	6	0	5	0	3	0	3	0	3	4	4	rs115825683	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:182987591G>A	ENST00000326505.3	+	2	535	c.5G>A	c.(4-6)aGa>aAa	p.R2K	MCF2L2_ENST00000447025.2_Intron|MCF2L2_ENST00000328913.3_Intron|B3GNT5_ENST00000465010.1_Missense_Mutation_p.R2K|B3GNT5_ENST00000460419.1_Missense_Mutation_p.R2K|MCF2L2_ENST00000473233.1_Intron	NM_032047.4	NP_114436.1	Q9BYG0	B3GN5_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	2					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)			GTGGATATGAGAATGTTGGTT	0.388													g|||	17	0.00339457	0.0	0.0029	5008	,	,		19069	0.0		0.0099	False		,,,				2504	0.0051				p.R2K		Atlas-SNP	.											.	B3GNT5	26	.	0			c.G5A						PASS	.		,LYS/ARG	7,4399	12.9+/-30.5	0,7,2196	113	113	113		,5	5.6	1	3	dbSNP_132	113	118,8482	61.7+/-123.6	2,114,4184	yes	intron,missense	MCF2L2,B3GNT5	NM_015078.2,NM_032047.4	,26	2,121,6380	AA,AG,GG		1.3721,0.1589,0.9611	,benign	,2/379	182987591	125,12881	2203	4300	6503	SO:0001583	missense	84002	exon2			ATATGAGAATGTT	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.5G>A	3.37:g.182987591G>A	ENSP00000316173:p.Arg2Lys	69	0	0		63	26	0.412698	NM_032047	D3DNS5|Q59FE3|Q7L9Z5|Q8WWP9	Missense_Mutation	SNP	ENST00000326505.3	37	CCDS3244.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	g	15.44	2.833998	0.50951	0.001589	0.013721	ENSG00000176597	ENST00000326505;ENST00000464191;ENST00000460419;ENST00000464923;ENST00000465010;ENST00000481531	T;T;T	0.37915	1.17;1.17;1.17	5.62	5.62	0.85841	.	0.575937	0.18329	N	0.144543	T	0.43411	0.1246	L	0.57536	1.79	0.33902	D	0.638687	D	0.60575	0.988	P	0.52343	0.696	T	0.60209	-0.7308	10	0.87932	D	0	.	20.0252	0.97521	0.0:0.0:1.0:0.0	.	2	Q9BYG0	B3GN5_HUMAN	K	2	ENSP00000316173:R2K;ENSP00000420778:R2K;ENSP00000417868:R2K	ENSP00000316173:R2K	R	+	2	0	B3GNT5	184470285	1.000000	0.71417	1.000000	0.80357	0.775000	0.43874	2.861000	0.48380	2.801000	0.96364	0.651000	0.88453	AGA	G|0.994;A|0.006	0.006	strong		0.388	B3GNT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351009.1	NM_032047		A	182987591	G	A	182987591	3	1	29	1	0	0	0	0	1	0	0	0	1260	942	33	2	7	2	B3GNT5	3	182987591	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	45664	182987591	15034839	211	12452											
B3GNT5	84002	hgsc.bcm.edu	37	chr3	182988131	182988131	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gttcagttgggcaaatacctAttgtccacatgccaaatttc	11	13	7	10	0	1	0	1	0	0	0	3	0	2	0	3	1	2	3	3	1	4	6			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:182988131A>G	ENST00000326505.3	+	2	1075	c.545A>G	c.(544-546)tAt>tGt	p.Y182C	MCF2L2_ENST00000447025.2_Intron|MCF2L2_ENST00000328913.3_Intron|B3GNT5_ENST00000465010.1_Missense_Mutation_p.Y182C|B3GNT5_ENST00000460419.1_Missense_Mutation_p.Y182C|MCF2L2_ENST00000473233.1_Intron	NM_032047.4	NP_114436.1	Q9BYG0	B3GN5_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 5	182					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)			GCAAATACCTATTGTCCACAT	0.333																																					p.Y182C		Atlas-SNP	.											.	B3GNT5	26	.	0			c.A545G						PASS	.						94	93	94					3																	182988131		2203	4300	6503	SO:0001583	missense	84002	exon2			ATACCTATTGTCC	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.545A>G	3.37:g.182988131A>G	ENSP00000316173:p.Tyr182Cys	168	0	0		156	69	0.442308	NM_032047	D3DNS5|Q59FE3|Q7L9Z5|Q8WWP9	Missense_Mutation	SNP	ENST00000326505.3	37	CCDS3244.1	.	.	.	.	.	.	.	.	.	.	A	14.65	2.598341	0.46318	.	.	ENSG00000176597	ENST00000326505;ENST00000460419;ENST00000465010	T;T;T	0.44083	0.93;0.93;0.93	5.91	1.73	0.24493	.	0.273852	0.36665	N	0.002479	T	0.59715	0.2214	M	0.89658	3.05	0.39485	D	0.96795	D	0.56968	0.978	P	0.53722	0.733	T	0.68364	-0.5428	10	0.56958	D	0.05	.	11.4792	0.50316	0.578:0.0:0.0:0.422	.	182	Q9BYG0	B3GN5_HUMAN	C	182	ENSP00000316173:Y182C;ENSP00000420778:Y182C;ENSP00000417868:Y182C	ENSP00000316173:Y182C	Y	+	2	0	B3GNT5	184470825	1.000000	0.71417	0.858000	0.33744	0.985000	0.73830	2.639000	0.46570	0.399000	0.25367	-0.451000	0.05528	TAT	.	.	none		0.333	B3GNT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351009.1	NM_032047		G	182988131	A	G	182988131	3	3	29	1	0	0	0	0	1	0	0	0	1260	449	16	3	547	3	B3GNT5	3	182988131	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	540	182988131	15034299	212	12453											
RFC4	5984	hgsc.bcm.edu	37	chr3	186508121	186508122	+	Frame_Shift_Del	DEL	CA	CA	-																															taagctgactttaccttgacCacagcttctagtttgtcaaa																								rs2066497	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:186508121_186508122delCA	ENST00000392481.2	-	9	1156_1157	c.875_876delTG	c.(874-876)gtgfs	p.V293fs	SNORA63_ENST00000363450.1_RNA|SNORA4_ENST00000584302.1_RNA|RFC4_ENST00000296273.2_Frame_Shift_Del_p.V293fs|RFC4_ENST00000433496.1_Intron	NM_181573.2	NP_853551.1	P35249	RFC4_HUMAN	replication factor C (activator 1) 4, 37kDa	293					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)		TTACCTTGACCACAGCTTCTAG	0.356																																					p.292_293del		Pindel,Atlas-Indel	.											RFC4,NS,carcinoma,+2,2	RFC4	54	2	0			c.876_877del						PASS	.																																			SO:0001589	frameshift_variant	5984	exon9			.		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.875_876delTG	3.37:g.186508123_186508124delCA	ENSP00000376272:p.Val293fs	134	0	.		112	24	0.214	NM_002916	B4DM41|D3DNV2|Q6FHX7	Frame_Shift_Del	DEL	ENST00000392481.2	37	CCDS3283.1																																																																																			.	.	none		0.356	RFC4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344471.1	NM_002916		-	186508122	CA	-	186508121	7	5	29	1	0	1	0	1	0	0	0	0	13262	581	21	0	227	0	RFC4	3	186508121	Frame_Shift_Del	DEL	CA	TCGA-GR-7351-01A-11D-2210-10	3519990	186508121	11514309	213	12454											
ADIPOQ	9370	hgsc.bcm.edu	37	chr3	186572089	186572089	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctggagaaggtgcctatgtaTaccgctcagcattcagtgtg	9	11	12	9	1	2	1	2	0	0	1	2	2	2	1	2	2	3	3	2	2	4	4	rs17366743	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:186572089T>C	ENST00000412955.2	+	3	472	c.331T>C	c.(331-333)Tac>Cac	p.Y111H	ADIPOQ_ENST00000320741.2_Missense_Mutation_p.Y111H|ADIPOQ-AS1_ENST00000422718.1_RNA|ADIPOQ_ENST00000444204.2_Missense_Mutation_p.Y111H			Q15848	ADIPO_HUMAN	adiponectin, C1Q and collagen domain containing	111	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.		Y -> H (in dbSNP:rs17366743). {ECO:0000269|PubMed:12354786}.		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)		TGCCTATGTATACCGCTCAGC	0.517													T|||	57	0.0113818	0.0015	0.0072	5008	,	,		19832	0.0		0.0378	False		,,,				2504	0.0123				p.Y111H		Atlas-SNP	.											.	ADIPOQ	35	.	0			c.T331C	GRCh37	CM056934	ADIPOQ	M	rs17366743	PASS	.	T	HIS/TYR,HIS/TYR	34,4372	39.2+/-71.8	0,34,2169	162	145	151	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	331,331	3.1	0.9	3	dbSNP_123	151	275,8325	104.0+/-165.0	7,261,4032	yes	missense,missense	ADIPOQ	NM_001177800.1,NM_004797.3	83,83	7,295,6201	CC,CT,TT		3.1977,0.7717,2.3758	benign,benign	111/245,111/245	186572089	309,12697	2203	4300	6503	SO:0001583	missense	9370	exon4			TATGTATACCGCT	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.331T>C	3.37:g.186572089T>C	ENSP00000405611:p.Tyr111His	159	0	0		173	69	0.398844	NM_001177800	Q58EX9	Missense_Mutation	SNP	ENST00000412955.2	37	CCDS3284.1	38	0.0173992673992674	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	32	0.04221635883905013	T	12.88	2.071182	0.36566	0.007717	0.031977	ENSG00000181092	ENST00000412955;ENST00000320741;ENST00000444204	D;D;D	0.83506	-1.73;-1.73;-1.73	5.45	3.07	0.35406	Tumour necrosis factor-like (1);Complement C1q protein (2);	0.316112	0.30630	N	0.009220	T	0.38321	0.1036	L	0.33245	0.995	0.22620	N	0.99893	B	0.12630	0.006	B	0.15052	0.012	T	0.32771	-0.9894	10	0.15066	T	0.55	.	7.1499	0.25604	0.0:0.2542:0.0:0.7458	rs17366743;rs52807560;rs17366743	111	Q15848	ADIPO_HUMAN	H	111	ENSP00000405611:Y111H;ENSP00000320709:Y111H;ENSP00000389814:Y111H	ENSP00000320709:Y111H	Y	+	1	0	ADIPOQ	188054783	0.750000	0.28316	0.905000	0.35620	0.821000	0.46438	1.011000	0.29911	0.467000	0.27218	0.459000	0.35465	TAC	T|0.981;C|0.019	0.019	strong		0.517	ADIPOQ-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344490.2	NM_004797		C	186572089	T	C	186572089	3	2	29	1	0	0	0	0	1	0	0	0	317	1406	49	3	337	3	ADIPOQ	3	186572089	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	63968	186572089	11450341	214	12455											
ATP13A4	84239	hgsc.bcm.edu	37	chr3	193272556	193272556	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttctcttctccttcattgagCagagcgtgctggcccttctc	4	15	8	14	1	4	2	1	1	3	1	7	2	4	2	2	1	3	2	2	1	0	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:193272556C>T	ENST00000342695.4	-	1	355	c.33G>A	c.(31-33)ctG>ctA	p.L11L	ATP13A4-AS1_ENST00000426459.1_RNA|ATP13A4_ENST00000295548.3_Silent_p.L11L|ATP13A4-AS1_ENST00000431512.1_RNA|ATP13A4_ENST00000392443.3_Silent_p.L11L	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	11						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)		CTTCATTGAGCAGAGCGTGCT	0.507																																					p.L11L		Atlas-SNP	.											.	ATP13A4	154	.	0			c.G33A						PASS	.						304	267	280					3																	193272556		2203	4300	6503	SO:0001819	synonymous_variant	84239	exon1			ATTGAGCAGAGCG	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.33G>A	3.37:g.193272556C>T		124	0	0		118	12	0.101695	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Silent	SNP	ENST00000342695.4	37	CCDS3304.2																																																																																			.	.	none		0.507	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279		T	193272556	C	T	193272556	2	4	29	1	0	0	0	0	0	0	0	1	1126	697	25	2		2	ATP13A4	3	193272556	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	6700467	193272556	4749874	215	12456											
OPA1	4976	hgsc.bcm.edu	37	chr3	193332566	193332566	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaataaaaggaagtttaccActacaaaaactacatctggt	18	9	7	7	0	1	0	0	0	1	0	1	2	1	2	1	3	4	1	1	3	9	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:193332566A>G	ENST00000392438.3	+	2	321	c.87A>G	c.(85-87)ccA>ccG	p.P29P	OPA1_ENST00000361150.2_Silent_p.P29P|OPA1_ENST00000361510.2_Silent_p.P29P|OPA1_ENST00000361715.2_Silent_p.P29P|OPA1_ENST00000361908.3_Silent_p.P29P|OPA1_ENST00000361828.2_Silent_p.P29P	NM_015560.2	NP_056375.2	O60313	OPA1_HUMAN	optic atrophy 1 (autosomal dominant)	29					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)		GAAGTTTACCACTACAAAAAC	0.388																																					p.P29P		Atlas-SNP	.											.	OPA1	79	.	0			c.A87G						PASS	.						119	109	112					3																	193332566		2203	4300	6503	SO:0001819	synonymous_variant	4976	exon2			TTTACCACTACAA	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.87A>G	3.37:g.193332566A>G		155	0	0		158	8	0.0506329	NM_130832	D3DNW4	Silent	SNP	ENST00000392438.3	37	CCDS43186.1																																																																																			.	.	none		0.388	OPA1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313812.2	NM_130837		G	193332566	A	G	193332566	2	3	29	1	0	0	0	0	0	0	0	1	10880	146	6	3		3	OPA1	3	193332566	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	60010	193332566	4689864	216	12457											
TNK2	10188	hgsc.bcm.edu	37	chr3	195594931	195594931	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggcttgtcgtcacccccCgggctgggagagggggccgg	3	6	20	12	3	1	1	1	0	0	1	2	2	1	1	4	7	0	2	4	7	0	1	rs200272067	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:195594931C>T	ENST00000333602.6	-	12	2810	c.2193G>A	c.(2191-2193)ccG>ccA	p.P731P	TNK2_ENST00000381916.2_Silent_p.P809P|TNK2_ENST00000428187.1_Silent_p.P763P|TNK2_ENST00000392400.1_Silent_p.P731P	NM_005781.4	NP_005772.3	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2	731	Pro-rich.			Missing (in Ref. 4; AAH08884). {ECO:0000305}.	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)	CGTCACCCCCCGGGCTGGGAG	0.726													c|||	34	0.00678914	0.0151	0.0014	5008	,	,		12349	0.0		0.003	False		,,,				2504	0.0102				p.P809P		Atlas-SNP	.											.	TNK2	246	.	0			c.G2427A						PASS	.		,	18,4172		0,18,2077	6	9	8		2427,2193	-8.3	0	3		8	16,8346		0,16,4165	no	coding-synonymous,coding-synonymous	TNK2	NM_001010938.1,NM_005781.4	,	0,34,6242	TT,TC,CC		0.1913,0.4296,0.2709	,	809/1087,731/1039	195594931	34,12518	2095	4181	6276	SO:0001819	synonymous_variant	10188	exon13			ACCCCCCGGGCTG	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.2193G>A	3.37:g.195594931C>T		50	0	0		45	21	0.466667	NM_001010938	Q6ZMQ0|Q8N6U7|Q96H59	Silent	SNP	ENST00000333602.6	37	CCDS33928.1																																																																																			C|0.997;T|0.003	0.003	strong		0.726	TNK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341437.3	NM_005781		T	195594931	C	T	195594931	2	4	29	1	0	0	0	0	0	0	0	1	16333	639	23	1		1	TNK2	3	195594931	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2262365	195594931	2427499	217	12458											
KIAA0226	9711	hgsc.bcm.edu	37	chr3	197427584	197427584	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtctgcccctctgagaagctGgacctgcggaggacactgga	8	7	14	12	1	2	1	0	1	2	1	2	6	2	5	3	4	3	1	3	4	1	0	rs368476866		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr3:197427584G>A	ENST00000296343.5	-	7	1160	c.1161C>T	c.(1159-1161)tcC>tcT	p.S387S	KIAA0226_ENST00000389665.5_Silent_p.S387S|KIAA0226_ENST00000467303.1_5'Flank|KIAA0226_ENST00000273582.5_Silent_p.S327S|KIAA0226_ENST00000449205.1_Silent_p.S387S	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	387	Ser-rich.				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)		CTGAGAAGCTGGACCTGCGGA	0.597																																					p.S387S	Esophageal Squamous(3;167 355 3763 15924)	Atlas-SNP	.											.	KIAA0226	136	.	0			c.C1161T						PASS	.	G	,	0,4100		0,0,2050	68	72	71		981,1161	4.1	1	3		71	6,8382		0,6,4188	no	coding-synonymous,coding-synonymous	KIAA0226	NM_001145642.2,NM_014687.1	,	0,6,6238	AA,AG,GG		0.0715,0.0,0.048	,	327/928,387/973	197427584	6,12482	2050	4194	6244	SO:0001819	synonymous_variant	9711	exon7			GAAGCTGGACCTG	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.1161C>T	3.37:g.197427584G>A		97	0	0		132	63	0.477273	NM_014687	Q96CK5	Silent	SNP	ENST00000296343.5	37	CCDS43195.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.751|9.751	1.167581|1.167581	0.21621|0.21621	0.0|0.0	7.15E-4|7.15E-4	ENSG00000145016|ENSG00000145016	ENST00000415452|ENST00000413360	.|.	.|.	.|.	5.85|5.85	4.05|4.05	0.47172|0.47172	.|.	.|.	.|.	.|.	.|.	T|.	0.60907|.	0.2305|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.56727|.	-0.7931|.	4|.	.|.	.|.	.|.	.|.	9.9492|9.9492	0.41628|0.41628	0.1594:0.0:0.8406:0.0|0.1594:0.0:0.8406:0.0	.|.	.|.	.|.	.|.	L|X	146|366	.|.	.|.	P|Q	-|-	2|1	0|0	KIAA0226|KIAA0226	198911981|198911981	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	2.081000|2.081000	0.41596|0.41596	0.791000|0.791000	0.33826|0.33826	0.655000|0.655000	0.94253|0.94253	CCA|CAG	.	.	weak		0.597	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901		A	197427584	G	A	197427584	2	1	29	1	0	0	0	0	0	0	0	1	8171	1335	47	2		2	KIAA0226	3	197427584	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1832653	197427584	594846	218	12459											
PIGG	54872	hgsc.bcm.edu	37	chr4	509850	509850	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttaccgattccaaaagacagTgtagggagcctcctattccc	11	10	8	12	1	0	1	0	0	0	1	3	3	3	2	5	1	2	1	5	1	5	5	rs11726338	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:509850T>C	ENST00000453061.2	+	6	1096	c.990T>C	c.(988-990)agT>agC	p.S330S	PIGG_ENST00000536264.1_Silent_p.S208S|PIGG_ENST00000504346.1_Silent_p.S241S|PIGG_ENST00000310340.5_Silent_p.S330S|PIGG_ENST00000509768.1_Silent_p.S241S|PIGG_ENST00000503111.1_Silent_p.S241S|PIGG_ENST00000296306.7_Silent_p.S241S|PIGG_ENST00000383028.4_Silent_p.S197S	NM_001127178.1	NP_001120650.1	Q5H8A4	PIGG_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class G	330					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 (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CP2 mannose-ethanolamine phosphotransferase activity (GO:0051267)|phosphotransferase activity, for other substituted phosphate groups (GO:0016780)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	39						CAAAAGACAGTGTAGGGAGCC	0.463													C|||	103	0.0205671	0.0363	0.0187	5008	,	,		20071	0.0		0.0288	False		,,,				2504	0.0133				p.S330S		Atlas-SNP	.											.	PIGG	86	.	0			c.T990C						PASS	.	C	,	122,4284	815.1+/-416.2	3,116,2084	125	122	123		990,990	-6.1	0	4	dbSNP_120	123	232,8368	809.0+/-407.2	7,218,4075	no	coding-synonymous,coding-synonymous	PIGG	NM_001127178.1,NM_017733.3	,	10,334,6159	CC,CT,TT		2.6977,2.769,2.7218	,	330/984,330/976	509850	354,12652	2203	4300	6503	SO:0001819	synonymous_variant	54872	exon6			AGACAGTGTAGGG		CCDS3336.1, CCDS46992.1, CCDS75080.1, CCDS75081.1, CCDS75082.1, CCDS75083.1	4p16.3	2013-02-26	2006-06-28		ENSG00000174227	ENSG00000174227		"Phosphatidylinositol glycan anchor biosynthesis"	25985	protein-coding gene	gene with protein product			"phosphatidylinositol glycan, class G"			15632136	Standard	XM_005272287		Approved	FLJ20265, GPI7, LAS21	uc003gak.4	Q5H8A4	OTTHUMG00000112457	ENST00000453061.2:c.990T>C	4.37:g.509850T>C		86	0	0		80	27	0.3375	NM_017733	B4DKC7|Q2TAK5|Q6UX31|Q7L5Y4|Q8N866|Q8NCC9|Q96SY9|Q9BVT7|Q9NXG5	Silent	SNP	ENST00000453061.2	37	CCDS46992.1																																																																																			T|0.972;C|0.028	0.028	strong		0.463	PIGG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357494.1	NM_017733		C	509850	T	C	509850	2	2	29	1	0	0	0	0	0	0	0	1	11897	1693	59	3		3	PIGG	4	509850	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10		509850	190644426	219	12460											
DGKQ	1609	hgsc.bcm.edu	37	chr4	956309	956309	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtccagcggtccatgagcaCggcgtcggcctcgtccacag	6	6	14	15	5	0	1	0	1	0	0	5	1	3	1	4	4	2	1	4	4	0	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:956309C>T	ENST00000273814.3	-	18	2201	c.2128G>A	c.(2128-2130)Gtg>Atg	p.V710M	DGKQ_ENST00000502309.1_5'Flank	NM_001347.3	NP_001338.2	P52824	DGKQ_HUMAN	diacylglycerol kinase, theta 110kDa	710	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				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)			TCCATGAGCACGGCGTCGGCC	0.672																																					p.V710M	Esophageal Squamous(17;537 645 4447 26373)	Atlas-SNP	.											.	DGKQ	29	.	0			c.G2128A						PASS	.						49	50	50					4																	956309		2200	4299	6499	SO:0001583	missense	1609	exon18			TGAGCACGGCGTC	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.2128G>A	4.37:g.956309C>T	ENSP00000273814:p.Val710Met	72	0	0		57	6	0.105263	NM_001347	Q6P3W4	Missense_Mutation	SNP	ENST00000273814.3	37	CCDS3342.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.520695	0.85495	.	.	ENSG00000145214	ENST00000273814	T	0.46451	0.87	4.8	4.8	0.61643	Diacylglycerol kinase, catalytic domain (3);	0.116434	0.56097	D	0.000022	T	0.62122	0.2402	M	0.62266	1.93	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.976;0.999	T	0.65969	-0.6039	10	0.87932	D	0	.	15.6931	0.77469	0.0:1.0:0.0:0.0	.	710;710	E9KL49;P52824	.;DGKQ_HUMAN	M	710	ENSP00000273814:V710M	ENSP00000273814:V710M	V	-	1	0	DGKQ	946309	0.963000	0.33076	0.945000	0.38365	0.517000	0.34286	2.895000	0.48648	2.338000	0.79540	0.655000	0.94253	GTG	.	.	none		0.672	DGKQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000200888.1			T	956309	C	T	956309	3	4	29	1	0	0	0	0	1	0	0	0	4475	536	19	1	724	1	DGKQ	4	956309	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	446459	956309	190197967	220	12461											
WHSC1	7468	hgsc.bcm.edu	37	chr4	1957774	1957774	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atattcagaaaatgaagcacGagattggagaattccctgtg	15	10	10	6	1	1	4	1	1	0	3	2	6	2	4	1	1	1	1	1	1	5	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:1957774G>A	ENST00000382895.3	+	17	3171	c.2740G>A	c.(2740-2742)Gag>Aag	p.E914K	WHSC1_ENST00000508803.1_Missense_Mutation_p.E914K|WHSC1_ENST00000382888.3_Missense_Mutation_p.E262K|WHSC1_ENST00000382892.2_Missense_Mutation_p.E914K|WHSC1_ENST00000382891.5_Missense_Mutation_p.E914K|WHSC1_ENST00000482415.2_3'UTR	NM_133330.2	NP_579877.1	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1	914	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)		AATGAAGCACGAGATTGGAGA	0.463			T	IGH@	MM																																p.E914K		Atlas-SNP	.		Dom	yes		4	4p16.3	7468	Wolf-Hirschhorn syndrome candidate 1(MMSET)		L	.	WHSC1	180	.	0			c.G2740A						PASS	.						144	171	162					4																	1957774		2203	4300	6503	SO:0001583	missense	7468	exon15			AAGCACGAGATTG	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.2740G>A	4.37:g.1957774G>A	ENSP00000372351:p.Glu914Lys	109	0	0		93	4	0.0430108	NM_133335	A2A2T2|A2A2T3|A2A2T4|A7MCZ1|D3DVQ2|O96031|Q4VBY8|Q672J1|Q6IS00|Q86V01|Q9BZB4|Q9UI92|Q9UPR2	Missense_Mutation	SNP	ENST00000382895.3	37	CCDS33940.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	32|32	5.141559|5.141559	0.94560|0.94560	.|.	.|.	ENSG00000109685|ENSG00000109685	ENST00000508803;ENST00000382891;ENST00000382892;ENST00000382895;ENST00000382888|ENST00000514329	T;T;T;T;T|.	0.69306|.	-0.39;-0.39;-0.39;-0.39;-0.39|.	5.97|5.97	5.97|5.97	0.96955|0.96955	PWWP (3);|.	0.000000|.	0.64402|.	D|.	0.000016|.	T|T	0.51702|0.51702	0.1690|0.1690	N|N	0.12887|0.12887	0.27|0.27	0.80722|0.80722	D|D	1|1	P;D|.	0.76494|.	0.615;0.999|.	B;P|.	0.56700|.	0.227;0.804|.	T|T	0.44097|0.44097	-0.9350|-0.9350	10|5	0.22109|.	T|.	0.4|.	.|.	20.4387|20.4387	0.99107|0.99107	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	262;914|.	A2A2T2;O96028|.	.;NSD2_HUMAN|.	K|Q	914;914;914;914;262|237	ENSP00000423972:E914K;ENSP00000372347:E914K;ENSP00000372348:E914K;ENSP00000372351:E914K;ENSP00000372344:E262K|.	ENSP00000372344:E262K|.	E|R	+|+	1|2	0|0	WHSC1|WHSC1	1927572|1927572	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	6.562000|6.562000	0.73960|0.73960	2.836000|2.836000	0.97738|0.97738	0.655000|0.655000	0.94253|0.94253	GAG|CGA	.	.	none		0.463	WHSC1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366269.2	NM_133330		A	1957774	G	A	1957774	3	1	29	1	0	0	0	0	1	0	0	0	17377	1059	37	1	2870	1	WHSC1	4	1957774	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1001465	1957774	189196502	221	12462											
JAKMIP1	152789	hgsc.bcm.edu	37	chr4	6062160	6062160	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctcctgctcacctgtcccttCtcaaccagtaacttctccaa	8	12	3	18	0	3	0	2	0	2	0	7	0	5	0	5	0	3	2	5	0	3	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:6062160C>T	ENST00000282924.5	-	11	2120	c.1635G>A	c.(1633-1635)gaG>gaA	p.E545E	JAKMIP1_ENST00000457227.2_5'Flank|JAKMIP1_ENST00000409021.3_Silent_p.E545E|JAKMIP1_ENST00000410077.2_Silent_p.E380E|JAKMIP1_ENST00000409371.3_Silent_p.E360E|JAKMIP1_ENST00000409831.1_Silent_p.E545E	NM_144720.3	NP_653321.1	Q96N16	JKIP1_HUMAN	janus kinase and microtubule interacting protein 1	545	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						CCTGTCCCTTCTCAACCAGTA	0.537																																					p.E545E		Atlas-SNP	.											.	JAKMIP1	250	.	0			c.G1635A						PASS	.						214	201	206					4																	6062160		2203	4300	6503	SO:0001819	synonymous_variant	152789	exon11			TCCCTTCTCAACC	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.1635G>A	4.37:g.6062160C>T		92	0	0		83	29	0.349398	NM_001099433	A6H2J2|A6H2J3|A6H2J4|A6H2J5|A8MTK6|B4DHZ8|B8ZZR7|D3DVT0|Q86Y69|Q8N7G3	Silent	SNP	ENST00000282924.5	37	CCDS3385.1																																																																																			.	.	none		0.537	JAKMIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246816.2	NM_144720		T	6062160	C	T	6062160	2	4	29	1	0	0	0	0	0	0	0	1	7949	912	32	2		2	JAKMIP1	4	6062160	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	4104386	6062160	185092116	222	12463											
KIAA0232	9778	hgsc.bcm.edu	37	chr4	6843852	6843852	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taagaaatggggaaagagtaAgaaaaaatgttcagatctaa	21	8	10	2	0	2	4	1	0	1	4	2	5	2	5	0	2	0	2	0	2	8	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:6843852A>G	ENST00000307659.5	+	4	745	c.290A>G	c.(289-291)aAg>aGg	p.K97R	KIAA0232_ENST00000425103.1_Missense_Mutation_p.K97R	NM_014743.2	NP_055558.2	Q92628	K0232_HUMAN	KIAA0232	97							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						GGAAAGAGTAAGAAAAAATGT	0.388																																					p.K97R		Atlas-SNP	.											KIAA0232,bladder,carcinoma,-1,1	KIAA0232	102	1	0			c.A290G						scavenged	.						121	124	123					4																	6843852		1827	4084	5911	SO:0001583	missense	9778	exon4			AGAGTAAGAAAAA	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.290A>G	4.37:g.6843852A>G	ENSP00000303928:p.Lys97Arg	37	0	0		34	3	0.0882353	NM_014743	A7E2D2	Missense_Mutation	SNP	ENST00000307659.5	37	CCDS43209.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.957945	0.73902	.	.	ENSG00000170871	ENST00000425103;ENST00000307659	.	.	.	4.9	4.9	0.64082	.	0.166625	0.52532	D	0.000068	T	0.68815	0.3042	L	0.42245	1.32	0.58432	D	0.999998	D	0.89917	1.0	D	0.85130	0.997	T	0.71344	-0.4621	9	0.59425	D	0.04	-25.162	14.5021	0.67729	1.0:0.0:0.0:0.0	.	97	Q92628	K0232_HUMAN	R	97	.	ENSP00000303928:K97R	K	+	2	0	KIAA0232	6894753	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.522000	0.60539	1.817000	0.53016	0.533000	0.62120	AAG	.	.	none		0.388	KIAA0232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359102.2	NM_014743		G	6843852	A	G	6843852	3	3	29	1	0	0	0	0	1	0	0	0	8172	72	3	3	296	3	KIAA0232	4	6843852	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	781692	6843852	184310424	223	12464											
SLC2A9	56606	hgsc.bcm.edu	37	chr4	9998476	9998476	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgatggcgaatatggacacAgtcacagaccagagcaaagt	15	5	11	10	2	1	2	1	0	0	2	1	5	1	3	2	2	1	1	2	2	3	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:9998476A>G	ENST00000264784.3	-	3	392	c.339T>C	c.(337-339)acT>acC	p.T113T	SLC2A9_ENST00000506583.1_Silent_p.T84T|SLC2A9_ENST00000309065.3_Silent_p.T84T	NM_020041.2	NP_064425.2	Q9NRM0	GTR9_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 9	113					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)	ATATGGACACAGTCACAGACC	0.473																																					p.T113T		Atlas-SNP	.											.	SLC2A9	158	.	0			c.T339C						PASS	.						144	124	131					4																	9998476		2203	4300	6503	SO:0001819	synonymous_variant	56606	exon3			GGACACAGTCACA	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.339T>C	4.37:g.9998476A>G		216	0	0		203	60	0.295566	NM_020041	Q0VGC4|Q4W5D1|Q8WV30|Q96P00	Silent	SNP	ENST00000264784.3	37	CCDS3407.1																																																																																			.	.	none		0.473	SLC2A9-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207055.1			G	9998476	A	G	9998476	2	3	29	1	0	0	0	0	0	0	0	1	14567	175	7	3		3	SLC2A9	4	9998476	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	3154624	9998476	181155800	224	12465											
BST1	683	hgsc.bcm.edu	37	chr4	15720553	15720553	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcctgcggggaaggcagcaTgaaagtcctggaaaagaggc	13	5	15	8	1	0	2	0	1	0	1	2	4	2	4	2	5	2	2	2	5	4	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:15720553T>C	ENST00000265016.4	+	7	923	c.728T>C	c.(727-729)aTg>aCg	p.M243T	BST1_ENST00000382346.3_Missense_Mutation_p.M258T	NM_004334.2	NP_004325.2	Q10588	BST1_HUMAN	bone marrow stromal cell antigen 1	243					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						GAAGGCAGCATGAAAGTCCTG	0.403																																					p.M243T		Atlas-SNP	.											.	BST1	30	.	0			c.T728C						PASS	.						113	108	110					4																	15720553		2203	4300	6503	SO:0001583	missense	683	exon7			GCAGCATGAAAGT	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.728T>C	4.37:g.15720553T>C	ENSP00000265016:p.Met243Thr	82	0	0		79	38	0.481013	NM_004334	B2R6A2|Q1XII0|Q5U0K0|Q96EN3	Missense_Mutation	SNP	ENST00000265016.4	37	CCDS3416.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.727|8.727	0.915766|0.915766	0.17907|0.17907	.|.	.|.	ENSG00000109743|ENSG00000109743	ENST00000265016;ENST00000382346;ENST00000514445|ENST00000505785;ENST00000514989	T;T;T|.	0.17213|.	2.29;2.29;2.29|.	4.75|4.75	4.75|4.75	0.60458|0.60458	NAD(P)-binding domain (1);|.	0.412136|.	0.23912|.	N|.	0.043325|.	T|.	0.38983|.	0.1061|.	L|L	0.36672|0.36672	1.1|1.1	0.26095|0.26095	N|N	0.980894|0.980894	B;B|.	0.31125|.	0.309;0.309|.	B;B|.	0.33568|.	0.166;0.166|.	T|.	0.24119|.	-1.0169|.	10|.	0.72032|.	D|.	0.01|.	-15.8415|-15.8415	10.8134|10.8134	0.46559|0.46559	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	258;243|.	A6NC48;Q10588|.	.;BST1_HUMAN|.	T|R	243;258;93|139;51	ENSP00000265016:M243T;ENSP00000371783:M258T;ENSP00000420925:M93T|.	ENSP00000265016:M243T|.	M|X	+|+	2|1	0|0	BST1|BST1	15329651|15329651	1.000000|1.000000	0.71417|0.71417	0.946000|0.946000	0.38457|0.38457	0.127000|0.127000	0.20565|0.20565	4.043000|4.043000	0.57354|0.57354	2.128000|2.128000	0.65567|0.65567	0.528000|0.528000	0.53228|0.53228	ATG|TGA	.	.	none		0.403	BST1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214968.2	NM_004334		C	15720553	T	C	15720553	3	2	29	1	0	0	0	0	1	0	0	0	1535	1464	51	3	754	3	BST1	4	15720553	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	5722077	15720553	175433723	225	12466											
ALB	213	hgsc.bcm.edu	37	chr4	74280774	74280774	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttttgtatgaatatgcaagaAggcatcctgattactctgtc	11	15	8	7	0	1	3	0	2	1	1	3	3	2	3	1	1	2	3	1	1	6	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:74280774A>C	ENST00000503124.1	+	7	838	c.631A>C	c.(631-633)Agg>Cgg	p.R211R	ALB_ENST00000505649.1_3'UTR|ALB_ENST00000401494.3_Silent_p.R246R|ALB_ENST00000415165.2_Silent_p.R169R|ALB_ENST00000509063.1_Silent_p.R361R|ALB_ENST00000295897.4_Silent_p.R361R			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)			ATATGCAAGAAGGCATCCTGA	0.378																																					p.R361R		Atlas-SNP	.											.	ALB	132	.	0			c.A1081C						PASS	.						149	149	149					4																	74280774		2203	4300	6503	SO:0001819	synonymous_variant	213	exon9			GCAAGAAGGCATC	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.631A>C	4.37:g.74280774A>C		98	0	0		125	30	0.24	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000503124.1	37		.	.	.	.	.	.	.	.	.	.	A	8.900	0.956161	0.18507	.	.	ENSG00000163631	ENST00000511370	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	T	0.71375	0.3332	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.70502	-0.4854	4	.	.	.	-18.0923	15.0348	0.71738	1.0:0.0:0.0:0.0	.	.	.	.	T	205	.	.	K	+	2	0	ALB	74499638	1.000000	0.71417	1.000000	0.80357	0.793000	0.44817	4.402000	0.59722	2.232000	0.73038	0.533000	0.62120	AAG	.	.	none		0.378	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477		C	74280774	A	C	74280774	2	2	29	1	0	0	0	0	0	0	0	1	486	63	3	5		5	ALB	4	74280774	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	58560221	74280774	116873502	226	12467											
CCDC158	339965	hgsc.bcm.edu	37	chr4	77255210	77255210	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gttcttccatcttcctctgtCttgctcagagacacagctgg	6	14	8	13	0	5	1	1	0	4	1	7	2	7	1	2	1	2	3	2	1	0	4	rs113022439	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:77255210C>T	ENST00000388914.3	-	18	2927	c.2775G>A	c.(2773-2775)aaG>aaA	p.K925K		NM_001042784.1	NP_001036249.1	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	925										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						CTTCCTCTGTCTTGCTCAGAG	0.483													C|||	32	0.00638978	0.0015	0.0072	5008	,	,		17210	0.0		0.0239	False		,,,				2504	0.001				p.K925K		Atlas-SNP	.											.	CCDC158	114	.	0			c.G2775A						PASS	.	C		15,4101		0,15,2043	158	159	159		2775	3.8	0.6	4	dbSNP_132	159	300,8128		4,292,3918	no	coding-synonymous	CCDC158	NM_001042784.1		4,307,5961	TT,TC,CC		3.5596,0.3644,2.5112		925/1114	77255210	315,12229	2058	4214	6272	SO:0001819	synonymous_variant	339965	exon18			CTCTGTCTTGCTC	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.2775G>A	4.37:g.77255210C>T		138	0	0		140	140	1	NM_001042784	Q8IYQ1|Q8N7D4|Q8N7E3	Silent	SNP	ENST00000388914.3	37	CCDS43242.1																																																																																			C|0.984;T|0.016	0.016	strong		0.483	CCDC158-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362694.2	NM_001042784		T	77255210	C	T	77255210	2	4	29	1	0	0	0	0	0	0	0	1	2792	912	32	2		2	CCDC158	4	77255210	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2974436	77255210	113899066	227	12468											
FGF5	2250	hgsc.bcm.edu	37	chr4	81188221	81188221	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gagcagagcagtttccagtgGagcccctcggggcgccggac	7	5	16	13	3	0	1	0	0	0	1	2	4	1	3	4	4	3	3	4	4	0	1	rs112475347		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:81188221G>T	ENST00000312465.7	+	1	469	c.243G>T	c.(241-243)tgG>tgT	p.W81C	FGF5_ENST00000456523.3_Missense_Mutation_p.W81C	NM_004464.3	NP_004455.2	P12034	FGF5_HUMAN	fibroblast growth factor 5	81					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						GTTTCCAGTGGAGCCCCTCGG	0.607													G|||	1	0.000199681	0.0	0.0	5008	,	,		14528	0.0		0.001	False		,,,				2504	0.0				p.W81C		Atlas-SNP	.											.	FGF5	49	.	0			c.G243T						PASS	.	G	CYS/TRP,CYS/TRP	1,4405	2.1+/-5.4	0,1,2202	50	57	55		243,243	5.4	1	4	dbSNP_132	55	20,8580	14.6+/-50.1	0,20,4280	yes	missense,missense	FGF5	NM_004464.3,NM_033143.2	215,215	0,21,6482	TT,TG,GG		0.2326,0.0227,0.1615	probably-damaging,probably-damaging	81/269,81/124	81188221	21,12985	2203	4300	6503	SO:0001583	missense	2250	exon1			CCAGTGGAGCCCC	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.243G>T	4.37:g.81188221G>T	ENSP00000311697:p.Trp81Cys	121	0	0		111	57	0.513514	NM_004464	B2R554|O75846|Q3Y8M3|Q8NF90	Missense_Mutation	SNP	ENST00000312465.7	37	CCDS34021.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.410863	0.83340	2.27E-4	0.002326	ENSG00000138675	ENST00000312465;ENST00000456523	T;T	0.08102	3.13;3.13	5.41	5.41	0.78517	.	0.695962	0.12612	N	0.453741	T	0.22003	0.0530	L	0.36672	1.1	0.80722	D	1	D;D	0.76494	0.999;0.993	D;P	0.65874	0.939;0.72	T	0.00837	-1.1546	10	0.46703	T	0.11	.	19.0018	0.92837	0.0:0.0:1.0:0.0	.	81;81	P12034-2;P12034	.;FGF5_HUMAN	C	81	ENSP00000311697:W81C;ENSP00000398353:W81C	ENSP00000311697:W81C	W	+	3	0	FGF5	81407245	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	6.324000	0.72896	2.816000	0.96949	0.561000	0.74099	TGG	G|0.998;T|0.002	0.002	strong		0.607	FGF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252627.2			T	81188221	G	T	81188221	3	4	29	1	0	0	0	0	1	0	0	0	5863	1183	41	4	245	4	FGF5	4	81188221	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	3933011	81188221	109966055	228	12469											
TIGD2	166815	hgsc.bcm.edu	37	chr4	90034450	90034450	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgcaaaacaagccaagttcTtttttgatgctttgggaatg	11	14	10	6	0	1	1	0	1	1	0	1	2	1	2	1	1	4	3	1	1	5	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:90034450T>C	ENST00000317005.2	+	1	483	c.325T>C	c.(325-327)Ttt>Ctt	p.F109L	FAM13A_ENST00000502459.1_5'Flank|RP11-84C13.1_ENST00000603357.1_lincRNA	NM_145715.2	NP_663761.1	Q4W5G0	TIGD2_HUMAN	tigger transposable element derived 2	109	HTH CENPB-type. {ECO:0000255|PROSITE- ProRule:PRU00583}.					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)		AGCCAAGTTCTTTTTTGATGC	0.433																																					p.F109L		Atlas-SNP	.											.	TIGD2	36	.	0			c.T325C						PASS	.						116	116	116					4																	90034450		2201	4298	6499	SO:0001583	missense	166815	exon1			AAGTTCTTTTTTG	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.325T>C	4.37:g.90034450T>C	ENSP00000317170:p.Phe109Leu	63	0	0		76	7	0.0921053	NM_145715		Missense_Mutation	SNP	ENST00000317005.2	37	CCDS3633.1	.	.	.	.	.	.	.	.	.	.	t	15.10	2.732150	0.48939	.	.	ENSG00000180346	ENST00000317005	T	0.20598	2.06	4.02	4.02	0.46733	Homeodomain-related (1);Pogo transposase / Cenp-B / PDC2, DNA-binding HTH domain (3);Homeodomain-like (1);	0.000000	0.42172	U	0.000748	T	0.12732	0.0309	N	0.11892	0.195	0.35836	D	0.825657	B	0.30326	0.276	B	0.37833	0.259	T	0.20438	-1.0275	10	0.10636	T	0.68	-5.0561	10.9959	0.47575	0.0:0.0:0.0:1.0	.	109	Q4W5G0	TIGD2_HUMAN	L	109	ENSP00000317170:F109L	ENSP00000317170:F109L	F	+	1	0	TIGD2	90253473	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.865000	0.39479	1.703000	0.51240	0.446000	0.29264	TTT	.	.	none		0.433	TIGD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253545.2	NM_145715		C	90034450	T	C	90034450	3	2	29	1	0	0	0	0	1	0	0	0	15911	1609	56	3	327	3	TIGD2	4	90034450	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	8846229	90034450	101119826	229	12470											
C4orf37	285555	hgsc.bcm.edu	37	chr4	98902403	98902403	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatgttttcttcaaagactTgagagcagttcgaggttcat	10	15	10	6	1	3	3	2	2	1	2	4	5	3	3	0	1	1	4	0	1	1	6	rs76740552	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:98902403T>C	ENST00000295268.3	-	6	768	c.679A>G	c.(679-681)Aag>Gag	p.K227E		NM_174952.2	NP_777612.1	Q8N412	STPG2_HUMAN	sperm-tail PG-rich repeat containing 2	227																	TTCAAAGACTTGAGAGCAGTT	0.403													T|||	34	0.00678914	0.025	0.0014	5008	,	,		16243	0.0		0.0	False		,,,				2504	0.0				p.K227E		Atlas-SNP	.											.	.	.	.	0			c.A679G						PASS	.	T	GLU/LYS	70,4336	63.5+/-100.7	0,70,2133	152	149	150		679	1.6	0	4	dbSNP_131	150	2,8598	2.2+/-6.3	0,2,4298	yes	missense	C4orf37	NM_174952.2	56	0,72,6431	CC,CT,TT		0.0233,1.5887,0.5536	benign	227/460	98902403	72,12934	2203	4300	6503	SO:0001583	missense	285555	exon6			AAGACTTGAGAGC	BC036870	CCDS3645.1	4q22.3-q23	2013-10-11	2012-07-30	2012-07-30	ENSG00000163116	ENSG00000163116			28712	protein-coding gene	gene with protein product			"chromosome 4 open reading frame 37"	C4orf37		23031811	Standard	NM_174952		Approved	MGC46496	uc003htt.2	Q8N412	OTTHUMG00000131009	ENST00000295268.3:c.679A>G	4.37:g.98902403T>C	ENSP00000295268:p.Lys227Glu	134	0	0		92	56	0.608696	NM_174952		Missense_Mutation	SNP	ENST00000295268.3	37	CCDS3645.1	15	0.006868131868131868	14	0.028455284552845527	1	0.0027624309392265192	0	0.0	0	0.0	T	0.042	-1.280208	0.01398	0.015887	2.33E-4	ENSG00000163116	ENST00000295268	T	0.11169	2.8	5.41	1.6	0.23607	.	0.284305	0.30401	N	0.009707	T	0.00906	0.0030	N	0.03154	-0.405	0.19575	N	0.999964	B	0.11235	0.004	B	0.16289	0.015	T	0.41592	-0.9500	10	0.02654	T	1	-29.499	2.4269	0.04461	0.2322:0.378:0.0:0.3898	.	227	Q8N412	CD037_HUMAN	E	227	ENSP00000295268:K227E	ENSP00000295268:K227E	K	-	1	0	C4orf37	99121426	0.446000	0.25665	0.001000	0.08648	0.381000	0.30169	0.483000	0.22292	0.332000	0.23536	0.460000	0.39030	AAG	T|0.994;C|0.006	0.006	strong		0.403	STPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253642.1	NM_174952		C	98902403	T	C	98902403	3	2	29	1	0	0	0	0	1	0	0	0	2269	1821	63	3	724	3	C4orf37	4	98902403	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	8867953	98902403	92251873	230	12471											
TET2	54790	hgsc.bcm.edu	37	chr4	106158509	106158510	+	Splice_Site	INS	-	-	T																															ccatcttgcagatgtgtaggINStaagtgccagaaatgtactg																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:106158509_106158510insT	ENST00000540549.1	+	3	4269		c.e3+1		TET2_ENST00000380013.4_Splice_Site|TET2_ENST00000305737.2_Frame_Shift_Ins_p.K1138fs|TET2_ENST00000394764.1_Frame_Shift_Ins_p.K1138fs|TET2_ENST00000513237.1_Splice_Site|TET2_ENST00000413648.2_Splice_Site|TET2_ENST00000545826.1_Splice_Site			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2						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)	p.?(1)		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)		AGATGTGTAGGTAAGTGCCAGA	0.342			"Mis N, F"		MDS																																p.G1137fs		Pindel,Atlas-Indel	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	TET2,NS,haematopoietic_neoplasm,0,1	TET2	1762	1	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.3410_3411insT						PASS	.																																			SO:0001630	splice_region_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	ENST00000540549.1:c.3409+1->T	4.37:g.106158510_106158510dupT		250	0	.		272	55	0.202	NM_017628	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Frame_Shift_Ins	INS	ENST00000540549.1	37	CCDS47120.1																																																																																			.	.	none		0.342	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628	Intron	T	106158510	-	T	106158509	8	5	29	1	0	1	1	0	0	0	1	0	15785	1275	44	0	3412	0	TET2	4	106158509	Splice_Site	INS	-	TCGA-GR-7351-01A-11D-2210-10	7256106	106158509	84995767	231	12472											
TET2	54790	hgsc.bcm.edu	37	chr4	106196525	106196525	+	Frame_Shift_Del	DEL	G	G	-																															atcccatgaacccttaccctGggcttttgaatcagaatacc																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:106196525delG	ENST00000540549.1	+	11	5718	c.4858delG	c.(4858-4860)gggfs	p.G1620fs	TET2_ENST00000380013.4_Frame_Shift_Del_p.G1620fs|TET2_ENST00000513237.1_Frame_Shift_Del_p.G1641fs|TET2_ENST00000545826.1_3'UTR			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1620					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)		CCCTTACCCTGGGCTTTTGAA	0.433			"Mis N, F"		MDS																																p.P1619fs		Pindel,Atlas-Indel	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	0			c.4857delT						PASS	.						47	40	42					4																	106196525		692	1591	2283	SO:0001589	frameshift_variant	54790	exon11			.	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.4858delG	4.37:g.106196525delG	ENSP00000442788:p.Gly1620fs	96	0	.		76	13	0.171	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Frame_Shift_Del	DEL	ENST00000540549.1	37	CCDS47120.1																																																																																			.	.	none		0.433	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		-	106196525	G	-	106196525	7	5	29	1	0	1	0	1	0	0	0	0	15785	1348	47	0	4981	0	TET2	4	106196525	Frame_Shift_Del	DEL	G	TCGA-GR-7351-01A-11D-2210-10	38016	106196525	84957751	232	12473											
FAT4	79633	hgsc.bcm.edu	37	chr4	126329944	126329944	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttaatgttactgatgcagAtgatggtatgtattttattt	10	20	9	2	0	0	3	0	2	0	1	0	3	0	3	0	1	2	5	0	1	5	8			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:126329944A>T	ENST00000394329.3	+	4	5928	c.5915A>T	c.(5914-5916)gAt>gTt	p.D1972V	FAT4_ENST00000335110.5_Missense_Mutation_p.D270V	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1972	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						ACTGATGCAGATGATGGTATG	0.289																																					p.D1972V		Atlas-SNP	.											.	FAT4	1752	.	0			c.A5915T						PASS	.						95	96	96					4																	126329944		2203	4299	6502	SO:0001583	missense	79633	exon4			ATGCAGATGATGG	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.5915A>T	4.37:g.126329944A>T	ENSP00000377862:p.Asp1972Val	78	0	0		62	4	0.0645161	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	A	21.0	4.077181	0.76415	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.74737	-0.87;-0.87	5.22	5.22	0.72569	Cadherin (4);Cadherin-like (1);	0.000000	0.35378	U	0.003259	D	0.91294	0.7255	H	0.98005	4.125	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.999;0.999	D	0.94437	0.7655	10	0.87932	D	0	.	15.12	0.72434	1.0:0.0:0.0:0.0	.	270;1972	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	V	1972;270	ENSP00000377862:D1972V;ENSP00000335169:D270V	ENSP00000335169:D270V	D	+	2	0	FAT4	126549394	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.770000	0.91746	1.971000	0.57363	0.528000	0.53228	GAT	.	.	none		0.289	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126329944	A	T	126329944	3	4	29	1	0	0	0	0	1	0	0	0	5700	333	12	5	5929	5	FAT4	4	126329944	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	20133419	126329944	64824332	233	12474											
PCDH10	57575	hgsc.bcm.edu	37	chr4	134072185	134072185	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagccacatttcgccccgggCgcgggagcttttcggactct	5	9	12	15	5	1	0	0	0	1	0	3	2	1	2	3	3	2	1	3	3	0	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:134072185C>T	ENST00000264360.5	+	1	1716	c.890C>T	c.(889-891)gCg>gTg	p.A297V	RP11-9G1.3_ENST00000505289.1_lincRNA	NM_032961.1	NP_116586.1	Q9P2E7	PCD10_HUMAN	protocadherin 10	297	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(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)		TCGCCCCGGGCGCGGGAGCTT	0.632																																					p.A297V		Atlas-SNP	.											.	PCDH10	290	.	0			c.C890T						PASS	.						41	45	43					4																	134072185		2203	4300	6503	SO:0001583	missense	57575	exon1			CCCGGGCGCGGGA	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.890C>T	4.37:g.134072185C>T	ENSP00000264360:p.Ala297Val	48	0	0		39	9	0.230769	NM_032961	Q4W5F6|Q96SF0	Missense_Mutation	SNP	ENST00000264360.5	37	CCDS34063.1	.	.	.	.	.	.	.	.	.	.	C	0.017	-1.492356	0.01009	.	.	ENSG00000138650	ENST00000264360;ENST00000394248	T	0.37058	1.22	4.33	3.47	0.39725	Cadherin (4);Cadherin-like (1);	0.000000	0.44902	D	0.000402	T	0.11537	0.0281	N	0.02658	-0.545	0.36301	D	0.857014	B;B	0.11235	0.004;0.002	B;B	0.06405	0.002;0.002	T	0.24404	-1.0161	10	0.02654	T	1	.	7.7575	0.28933	0.0:0.7463:0.166:0.0877	.	297;297	Q9P2E7;Q96SF0	PCD10_HUMAN;.	V	297	ENSP00000264360:A297V	ENSP00000264360:A297V	A	+	2	0	PCDH10	134291635	0.980000	0.34600	0.451000	0.26982	0.421000	0.31385	2.230000	0.42999	0.991000	0.38814	-0.416000	0.06073	GCG	.	.	none		0.632	PCDH10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000364457.2	NM_032961		T	134072185	C	T	134072185	3	4	29	1	0	0	0	0	1	0	0	0	11516	768	27	1	892	1	PCDH10	4	134072185	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	7742241	134072185	57082091	234	12475											
PCDH10	57575	hgsc.bcm.edu	37	chr4	134072208	134072208	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gggagcttttcggactctcgCcgcgcactggcagactggag	6	8	15	12	4	1	1	0	0	1	1	3	4	1	4	1	4	1	3	1	4	0	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:134072208C>G	ENST00000264360.5	+	1	1739	c.913C>G	c.(913-915)Ccg>Gcg	p.P305A	RP11-9G1.3_ENST00000505289.1_lincRNA	NM_032961.1	NP_116586.1	Q9P2E7	PCD10_HUMAN	protocadherin 10	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)			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)		CGGACTCTCGCCGCGCACTGG	0.637																																					p.P305A		Atlas-SNP	.											PCDH10,NS,carcinoma,-2,2	PCDH10	290	2	0			c.C913G						PASS	.						46	47	47					4																	134072208		2203	4300	6503	SO:0001583	missense	57575	exon1			CTCTCGCCGCGCA	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.913C>G	4.37:g.134072208C>G	ENSP00000264360:p.Pro305Ala	58	0	0		43	10	0.232558	NM_032961	Q4W5F6|Q96SF0	Missense_Mutation	SNP	ENST00000264360.5	37	CCDS34063.1	.	.	.	.	.	.	.	.	.	.	C	10.33	1.320381	0.23994	.	.	ENSG00000138650	ENST00000264360;ENST00000394248	T	0.53423	0.62	4.2	4.2	0.49525	Cadherin (4);Cadherin-like (1);	0.000000	0.44902	D	0.000415	T	0.43366	0.1244	L	0.46741	1.465	0.46260	D	0.998954	B;B	0.12013	0.002;0.005	B;B	0.17979	0.003;0.02	T	0.36672	-0.9738	10	0.37606	T	0.19	.	16.3343	0.83052	0.0:1.0:0.0:0.0	.	305;305	Q9P2E7;Q96SF0	PCD10_HUMAN;.	A	305	ENSP00000264360:P305A	ENSP00000264360:P305A	P	+	1	0	PCDH10	134291658	0.889000	0.30405	0.998000	0.56505	0.974000	0.67602	1.861000	0.39438	2.137000	0.66172	0.407000	0.27541	CCG	.	.	none		0.637	PCDH10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000364457.2	NM_032961		G	134072208	C	G	134072208	3	3	29	1	0	0	0	0	1	0	0	0	11516	739	26	4	915	4	PCDH10	4	134072208	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	23	134072208	57082068	235	12476											
NAA15	80155	hgsc.bcm.edu	37	chr4	140264020	140264020	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcagcttcgacctgcgcagaGagcatcatggattggttatg	9	11	12	9	2	2	1	2	0	0	1	3	4	2	2	1	2	3	4	1	2	1	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:140264020G>A	ENST00000296543.5	+	5	766	c.443G>A	c.(442-444)aGa>aAa	p.R148K	NAA15_ENST00000398947.1_Missense_Mutation_p.R148K|NAA15_ENST00000480277.2_3'UTR	NM_057175.3	NP_476516.1	Q9BXJ9	NAA15_HUMAN	N(alpha)-acetyltransferase 15, NatA auxiliary subunit	148					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						CCTGCGCAGAGAGCATCATGG	0.348																																					p.R148K		Atlas-SNP	.											.	NAA15	88	.	0			c.G443A						PASS	.						137	127	130					4																	140264020		1857	4118	5975	SO:0001583	missense	80155	exon5			CGCAGAGAGCATC	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.443G>A	4.37:g.140264020G>A	ENSP00000296543:p.Arg148Lys	137	0	0		128	40	0.3125	NM_057175	D3DNY6|Q52LG9|Q8IWH4|Q8NEV2|Q9H8P6	Missense_Mutation	SNP	ENST00000296543.5	37	CCDS43270.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.334046	0.81801	.	.	ENSG00000164134	ENST00000296543;ENST00000544077;ENST00000398947	T;T	0.52526	0.66;0.66	5.25	5.25	0.73442	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.066107	0.64402	D	0.000018	T	0.53061	0.1773	M	0.76170	2.325	0.80722	D	1	P	0.38922	0.651	B	0.38194	0.267	T	0.55945	-0.8060	10	0.41790	T	0.15	-13.5405	19.4069	0.94651	0.0:0.0:1.0:0.0	.	148	Q9BXJ9	NAA15_HUMAN	K	148;22;148	ENSP00000296543:R148K;ENSP00000381920:R148K	ENSP00000296543:R148K	R	+	2	0	NAA15	140483470	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.075000	0.94004	2.894000	0.99253	0.591000	0.81541	AGA	.	.	none		0.348	NAA15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000267839.2	NM_057175		A	140264020	G	A	140264020	3	1	29	1	0	0	0	0	1	0	0	0	10127	942	33	2	461	2	NAA15	4	140264020	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	6191812	140264020	50890256	236	12477											
OTUD4	54726	hgsc.bcm.edu	37	chr4	146063471	146063471	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctggatttgacaaagacaCatgttctgctggcttcttca	10	13	9	9	0	3	2	1	1	2	1	3	3	3	3	0	2	2	4	0	2	1	4	rs151020153	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:146063471C>T	ENST00000447906.2	-	18	1886	c.1699G>A	c.(1699-1701)Gtg>Atg	p.V567M	OTUD4_ENST00000455611.2_5'UTR|OTUD4_ENST00000454497.2_Missense_Mutation_p.V502M			Q01804	OTUD4_HUMAN	OTU deubiquitinase 4	567					protein K48-linked deubiquitination (GO:0071108)		poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(180;0.151)					GACAAAGACACATGTTCTGCT	0.468													C|||	4	0.000798722	0.0	0.0	5008	,	,		19395	0.0		0.004	False		,,,				2504	0.0				p.V502M		Atlas-SNP	.											.	OTUD4	120	.	0			c.G1504A						PASS	.	C	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	111	120	117		1504	5.3	1	4	dbSNP_134	117	35,8565	24.0+/-70.4	0,35,4265	yes	missense	OTUD4	NM_001102653.1	21	0,36,6467	TT,TC,CC		0.407,0.0227,0.2768	possibly-damaging	502/1050	146063471	36,12970	2203	4300	6503	SO:0001583	missense	54726	exon18			AAGACACATGTTC		CCDS3764.1, CCDS47139.1	4q31.21	2014-02-24	2014-02-24		ENSG00000164164	ENSG00000164164		"OTU domain containing"	24949	protein-coding gene	gene with protein product		611744	"OTU domain containing 4"			1475186, 12727813, 19996094	Standard	NM_001102653		Approved	HSHIN1, KIAA1046, DUBA6	uc003ika.4	Q01804	OTTHUMG00000161480	ENST00000447906.2:c.1699G>A	4.37:g.146063471C>T	ENSP00000395487:p.Val567Met	50	0	0		65	35	0.538462	NM_001102653	B4DYS4|Q147U2|Q1ZYK1|Q6PG39|Q96MQ5|Q9NT94|Q9UPV6	Missense_Mutation	SNP	ENST00000447906.2	37		5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	18.08	3.544424	0.65198	2.27E-4	0.00407	ENSG00000164164	ENST00000454497;ENST00000447906	T;T	0.34072	1.39;1.38	6.16	5.31	0.75309	.	0.224719	0.32055	N	0.006652	T	0.24928	0.0605	N	0.24115	0.695	0.80722	D	1	P;P	0.42203	0.773;0.664	P;B	0.48840	0.592;0.388	T	0.10683	-1.0619	10	0.62326	D	0.03	-7.2241	7.8627	0.29520	0.2599:0.6608:0.0:0.0793	.	567;566	G3V0I6;Q01804	.;OTUD4_HUMAN	M	502;567	ENSP00000409279:V502M;ENSP00000395487:V567M	ENSP00000395487:V567M	V	-	1	0	OTUD4	146282921	0.877000	0.30153	1.000000	0.80357	0.974000	0.67602	0.769000	0.26604	1.594000	0.50039	0.650000	0.86243	GTG	C|0.998;T|0.002	0.002	strong		0.468	OTUD4-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000365117.2	NM_017493		T	146063471	C	T	146063471	3	4	29	1	0	0	0	0	1	0	0	0	11323	478	17	2	1661	2	OTUD4	4	146063471	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	5799451	146063471	45090805	237	12478											
KIAA0922	23240	hgsc.bcm.edu	37	chr4	154519764	154519764	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataacttgactgttattgacAtgattggcgtggaaggattt	11	15	11	4	1	0	3	0	3	0	0	0	5	0	5	0	3	1	1	0	3	3	6	rs72729691	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:154519764A>G	ENST00000409663.3	+	21	2195	c.2143A>G	c.(2143-2145)Atg>Gtg	p.M715V	KIAA0922_ENST00000409959.3_Missense_Mutation_p.M716V|KIAA0922_ENST00000440693.1_Missense_Mutation_p.M632V	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	715						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)				TGTTATTGACATGATTGGCGT	0.408													A|||	21	0.00419329	0.0008	0.0086	5008	,	,		14654	0.0		0.0109	False		,,,				2504	0.0031				p.M716V		Atlas-SNP	.											.	KIAA0922	214	.	0			c.A2146G						PASS	.	A	VAL/MET,VAL/MET	10,4396	15.5+/-35.6	0,10,2193	138	140	139		2146,2143	1.9	0.9	4	dbSNP_130	139	71,8529	43.6+/-101.6	0,71,4229	yes	missense,missense	KIAA0922	NM_001131007.1,NM_015196.3	21,21	0,81,6422	GG,GA,AA		0.8256,0.227,0.6228	benign,benign	716/1611,715/1610	154519764	81,12925	2203	4300	6503	SO:0001583	missense	23240	exon21			ATTGACATGATTG	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.2143A>G	4.37:g.154519764A>G	ENSP00000386574:p.Met715Val	77	0	0		75	34	0.453333	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	37	CCDS3783.2	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	A	6.379	0.438031	0.12104	0.00227	0.008256	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487	T;T;T;T	0.16196	2.63;2.36;2.63;2.36	5.79	1.94	0.25998	.	0.199425	0.64402	N	0.000012	T	0.06554	0.0168	L	0.35793	1.09	0.46279	D	0.998961	B;B;B	0.16802	0.019;0.004;0.001	B;B;B	0.22880	0.042;0.006;0.001	T	0.29212	-1.0019	10	0.02654	T	1	-4.0838	5.0559	0.14533	0.5505:0.1489:0.3006:0.0	.	632;716;715	A2VDJ0-3;A2VDJ0-5;A2VDJ0	.;.;T131L_HUMAN	V	715;632;716;493	ENSP00000386574:M715V;ENSP00000409663:M632V;ENSP00000386787:M716V;ENSP00000240487:M493V	ENSP00000240487:M493V	M	+	1	0	KIAA0922	154739214	1.000000	0.71417	0.904000	0.35570	0.459000	0.32528	1.972000	0.40540	0.091000	0.17302	0.533000	0.62120	ATG	A|0.994;G|0.006	0.006	strong		0.408	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196		G	154519764	A	G	154519764	3	3	29	1	0	0	0	0	1	0	0	0	8210	217	8	3	2228	3	KIAA0922	4	154519764	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	8456293	154519764	36634512	238	12479											
TMEM144	55314	hgsc.bcm.edu	37	chr4	159161513	159161513	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	caagtactgtctactttctgGcctactgcatagccatgaaa	11	12	7	11	0	2	1	0	1	2	0	2	1	2	1	2	1	5	2	2	1	6	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:159161513G>A	ENST00000296529.6	+	10	1265	c.745G>A	c.(745-747)Gcc>Acc	p.A249T	TMEM144_ENST00000503404.1_3'UTR	NM_018342.4	NP_060812.2	Q7Z5S9	TM144_HUMAN	transmembrane protein 144	249						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)		CTACTTTCTGGCCTACTGCAT	0.358																																					p.A249T		Atlas-SNP	.											.	TMEM144	34	.	0			c.G745A						PASS	.						123	112	116					4																	159161513		2203	4300	6503	SO:0001583	missense	55314	exon10			TTTCTGGCCTACT	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.745G>A	4.37:g.159161513G>A	ENSP00000296529:p.Ala249Thr	117	0	0		89	46	0.516854	NM_018342	D3DP24|Q49A05|Q9NUT3	Missense_Mutation	SNP	ENST00000296529.6	37	CCDS3799.1	.	.	.	.	.	.	.	.	.	.	G	15.23	2.771943	0.49680	.	.	ENSG00000164124	ENST00000296529	T	0.70164	-0.46	5.35	4.49	0.54785	.	0.484301	0.22175	N	0.063597	T	0.59074	0.2167	M	0.63843	1.955	0.46167	D	0.998902	B	0.33318	0.408	B	0.37601	0.254	T	0.51148	-0.8742	10	0.12430	T	0.62	-29.0069	5.6699	0.17717	0.1618:0.1716:0.6666:0.0	.	249	Q7Z5S9	TM144_HUMAN	T	249	ENSP00000296529:A249T	ENSP00000296529:A249T	A	+	1	0	TMEM144	159380963	1.000000	0.71417	0.981000	0.43875	0.967000	0.64934	3.462000	0.53042	1.216000	0.43427	0.467000	0.42956	GCC	.	.	none		0.358	TMEM144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365597.1	NM_018342		A	159161513	G	A	159161513	3	1	29	1	0	0	0	0	1	0	0	0	16073	1203	42	2	775	2	TMEM144	4	159161513	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	4641749	159161513	31992763	239	12480											
GALNTL6	442117	hgsc.bcm.edu	37	chr4	173269737	173269737	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcattatcccatttcataaTgaaggttggacttcactcct	11	15	5	10	0	3	1	3	1	0	0	5	2	5	2	2	2	0	1	2	2	3	5	rs114177519	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:173269737T>C	ENST00000506823.1	+	5	1107	c.450T>C	c.(448-450)aaT>aaC	p.N150N	GALNTL6_ENST00000457021.1_3'UTR|GALNTL6_ENST00000508122.1_Silent_p.N133N	NM_001034845.2	NP_001030017.2	Q49A17	GLTL6_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 6	150	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						CATTTCATAATGAAGGTTGGA	0.423													T|||	21	0.00419329	0.0008	0.0086	5008	,	,		19203	0.0		0.0139	False		,,,				2504	0.0				p.N150N		Atlas-SNP	.											.	GALNTL6	102	.	0			c.T450C						PASS	.	T		3,4403	6.2+/-15.9	0,3,2200	144	135	138		450	-1.7	1	4	dbSNP_132	138	62,8538	37.8+/-93.5	0,62,4238	no	coding-synonymous	GALNTL6	NM_001034845.2		0,65,6438	CC,CT,TT		0.7209,0.0681,0.4998		150/602	173269737	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	442117	exon5			TCATAATGAAGGT		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.450T>C	4.37:g.173269737T>C		111	0	0		148	78	0.527027	NM_001034845	Q2L4S6	Silent	SNP	ENST00000506823.1	37	CCDS34104.1																																																																																			T|0.994;C|0.006	0.006	strong		0.423	GALNTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362395.1	NM_001034845		C	173269737	T	C	173269737	2	2	29	1	0	0	0	0	0	0	0	1	6233	1461	51	3		3	GALNTL6	4	173269737	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	14108224	173269737	17884539	240	12481											
TLR3	7098	hgsc.bcm.edu	37	chr4	187004078	187004078	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttctcccttacacatactcaAcctaaccaagaataaaatct	16	11	1	13	0	3	1	1	0	2	1	4	1	3	1	3	0	4	0	3	0	8	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:187004078A>C	ENST00000296795.3	+	4	1342	c.1238A>C	c.(1237-1239)aAc>aCc	p.N413T	TLR3_ENST00000504367.1_Missense_Mutation_p.N136T	NM_003265.2	NP_003256.1	O15455	TLR3_HUMAN	toll-like receptor 3	413					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)		CACATACTCAACCTAACCAAG	0.378																																					p.N413T		Atlas-SNP	.											.	TLR3	83	.	0			c.A1238C						PASS	.						61	57	58					4																	187004078		2203	4300	6503	SO:0001583	missense	7098	exon4			TACTCAACCTAAC	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.1238A>C	4.37:g.187004078A>C	ENSP00000296795:p.Asn413Thr	101	0	0		86	26	0.302326	NM_003265	B2RAI7|B7Z7K0|E6Y0F0|E6Y0F1|E9PGH4|Q4VAL2|Q504W0	Missense_Mutation	SNP	ENST00000296795.3	37	CCDS3846.1	.	.	.	.	.	.	.	.	.	.	A	14.16	2.452831	0.43531	.	.	ENSG00000164342	ENST00000296795;ENST00000513189;ENST00000542020;ENST00000504367	T;T;T	0.39997	1.75;1.05;1.75	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.53061	0.1773	M	0.72118	2.19	0.80722	D	1	P	0.41569	0.755	P	0.46144	0.505	T	0.57917	-0.7728	10	0.72032	D	0.01	.	16.1132	0.81278	1.0:0.0:0.0:0.0	.	413	O15455	TLR3_HUMAN	T	413;349;413;136	ENSP00000296795:N413T;ENSP00000423386:N349T;ENSP00000423684:N136T	ENSP00000296795:N413T	N	+	2	0	TLR3	187241072	1.000000	0.71417	1.000000	0.80357	0.508000	0.34012	9.339000	0.96797	2.208000	0.71279	0.455000	0.32223	AAC	.	.	none		0.378	TLR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360313.4			C	187004078	A	C	187004078	3	2	29	1	0	0	0	0	1	0	0	0	15967	43	2	5	1248	5	TLR3	4	187004078	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	13734341	187004078	4150198	241	12482											
MTNR1A	4543	hgsc.bcm.edu	37	chr4	187455399	187455399	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tcgggtcgtactggagagtcCctgcacggaggttgggcagg	6	8	18	9	3	0	1	0	0	0	1	3	3	1	2	1	6	2	4	1	6	1	2	rs28383653	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:187455399C>T	ENST00000307161.5	-	2	698	c.497G>A	c.(496-498)gGg>gAg	p.G166E	RP11-215A19.2_ENST00000509111.1_Intron	NM_005958.3	NP_005949.1	P48039	MTR1A_HUMAN	melatonin receptor 1A	166					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)	CTGGAGAGTCCCTGCACGGAG	0.607													C|||	17	0.00339457	0.0015	0.0086	5008	,	,		18017	0.0		0.0089	False		,,,				2504	0.0				p.G166E		Atlas-SNP	.											.	MTNR1A	46	.	0			c.G497A						PASS	.	C	GLU/GLY	13,4393	20.2+/-43.8	0,13,2190	127	103	111		497	4.1	0.1	4	dbSNP_125	111	139,8461	69.7+/-132.2	1,137,4162	yes	missense	MTNR1A	NM_005958.3	98	1,150,6352	TT,TC,CC		1.6163,0.2951,1.1687	possibly-damaging	166/351	187455399	152,12854	2203	4300	6503	SO:0001583	missense	4543	exon2			AGAGTCCCTGCAC		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.497G>A	4.37:g.187455399C>T	ENSP00000302811:p.Gly166Glu	71	0	0		69	33	0.478261	NM_005958	A0AVC5|B0M0L2	Missense_Mutation	SNP	ENST00000307161.5	37	CCDS3848.1	22	0.010073260073260074	3	0.006097560975609756	7	0.019337016574585635	2	0.0034965034965034965	10	0.013192612137203167	C	14.72	2.619115	0.46736	0.002951	0.016163	ENSG00000168412	ENST00000307161	T	0.39592	1.07	4.96	4.08	0.47627	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.43478	0.1249	M	0.82630	2.6	0.80722	D	1	D	0.55172	0.97	P	0.59012	0.85	T	0.56214	-0.8016	10	0.13108	T	0.6	-14.904	15.3219	0.74129	0.0:0.8602:0.1398:0.0	rs28383653	166	P48039	MTR1A_HUMAN	E	166	ENSP00000302811:G166E	ENSP00000302811:G166E	G	-	2	0	MTNR1A	187692393	0.993000	0.37304	0.053000	0.19242	0.019000	0.09904	3.190000	0.50973	2.295000	0.77249	0.655000	0.94253	GGG	C|0.988;T|0.012	0.012	strong		0.607	MTNR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360189.1			T	187455399	C	T	187455399	3	4	29	1	0	0	0	0	1	0	0	0	9960	623	22	2	559	2	MTNR1A	4	187455399	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	451321	187455399	3698877	242	12483											
FAT1	2195	hgsc.bcm.edu	37	chr4	187541971	187541971	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tccatagaaaacttctccccGatgttgccttcggtgatgga	9	12	9	11	2	1	2	0	1	1	1	4	4	2	3	4	2	2	1	4	2	3	4	rs372720339	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:187541971G>A	ENST00000441802.2	-	10	5978	c.5769C>T	c.(5767-5769)atC>atT	p.I1923I		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1923	Cadherin 17. {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						ACTTCTCCCCGATGTTGCCTT	0.438										HNSCC(5;0.00058)			G|||	2	0.000399361	0.0008	0.0	5008	,	,		20290	0.0		0.0	False		,,,				2504	0.001				p.I1923I	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C5769T						PASS	.						92	94	93					4																	187541971		1917	4141	6058	SO:0001819	synonymous_variant	2195	exon10			CTCCCCGATGTTG	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.5769C>T	4.37:g.187541971G>A		135	0	0		119	62	0.521008	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			.	.	alt		0.438	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		A	187541971	G	A	187541971	2	1	29	1	0	0	0	0	0	0	0	1	5697	1048	37	1		1	FAT1	4	187541971	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	86572	187541971	3612305	243	12484											
FAT1	2195	hgsc.bcm.edu	37	chr4	187629137	187629137	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccgagttggggtttaaactAaagaaatccagttcatttcc	12	12	8	9	1	1	1	1	0	0	1	3	2	3	1	3	2	1	3	3	2	5	6	rs4862726	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr4:187629137A>G	ENST00000441802.2	-	2	2054	c.1845T>C	c.(1843-1845)ttT>ttC	p.F615F		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	615	Cadherin 5. {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						GGTTTAAACTAAAGAAATCCA	0.433										HNSCC(5;0.00058)			A|||	78	0.0155751	0.0	0.0101	5008	,	,		20191	0.0258		0.0368	False		,,,				2504	0.0082				p.F615F	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T1845C						PASS	.	A		23,3713		0,23,1845	68	63	64		1845	-1.3	0.6	4	dbSNP_111	64	305,7891		4,297,3797	no	coding-synonymous	FAT1	NM_005245.3		4,320,5642	GG,GA,AA		3.7213,0.6156,2.7489		615/4589	187629137	328,11604	1868	4098	5966	SO:0001819	synonymous_variant	2195	exon2			TAAACTAAAGAAA	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.1845T>C	4.37:g.187629137A>G		54	0	0		41	17	0.414634	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			A|0.975;G|0.025	0.025	strong		0.433	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		G	187629137	A	G	187629137	2	3	29	1	0	0	0	0	0	0	0	1	5697	359	13	3		3	FAT1	4	187629137	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	87166	187629137	3525139	244	12485											
KIAA0947	23379	hgsc.bcm.edu	37	chr5	5441314	5441314	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggaagaactgggatctttaaAagcagagctagaagagaaaa	19	6	12	4	0	1	4	0	0	1	4	1	7	1	6	0	2	3	2	0	2	8	3	rs72646675	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:5441314A>G	ENST00000296564.7	+	5	509	c.287A>G	c.(286-288)aAa>aGa	p.K96R	KIAA0947_ENST00000512608.1_3'UTR	NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		96					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						GGATCTTTAAAAGCAGAGCTA	0.358													A|||	3	0.000599042	0.0	0.0	5008	,	,		15735	0.0		0.003	False		,,,				2504	0.0				p.K96R		Atlas-SNP	.											.	KIAA0947	301	.	0			c.A287G						PASS	.	A	ARG/LYS	1,3585		0,1,1792	26	25	25		287	4.6	1	5	dbSNP_130	25	12,8084		0,12,4036	yes	missense	KIAA0947	NM_015325.1	26	0,13,5828	GG,GA,AA		0.1482,0.0279,0.1113	possibly-damaging	96/2267	5441314	13,11669	1793	4048	5841	SO:0001583	missense	23379	exon5			CTTTAAAAGCAGA																												ENST00000296564.7:c.287A>G	5.37:g.5441314A>G	ENSP00000296564:p.Lys96Arg	201	0	0		203	93	0.458128	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	ENST00000296564.7	37	CCDS47187.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	20.5	3.995633	0.74703	2.79E-4	0.001482	ENSG00000164151	ENST00000296564	T	0.14266	2.52	5.78	4.61	0.57282	.	0.070003	0.56097	D	0.000040	T	0.20170	0.0485	L	0.29908	0.895	0.25024	N	0.991316	D	0.64830	0.994	D	0.65010	0.931	T	0.05338	-1.0891	10	0.35671	T	0.21	-37.5493	8.4511	0.32871	0.9118:0.0:0.0882:0.0	.	96	Q9Y2F5	K0947_HUMAN	R	96	ENSP00000296564:K96R	ENSP00000296564:K96R	K	+	2	0	KIAA0947	5494314	1.000000	0.71417	0.992000	0.48379	0.992000	0.81027	2.791000	0.47829	1.014000	0.39417	0.477000	0.44152	AAA	A|0.999;G|0.001	0.001	strong		0.358	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			G	5441314	A	G	5441314	3	3	29	1	0	0	0	0	1	0	0	0	8211	14	1	3	305	3	KIAA0947	5	5441314	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10		5441314	175473946	245	12486											
MTRR	4552	hgsc.bcm.edu	37	chr5	7873566	7873566	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacccacccgacacagcccgCaagtttgttaaggaaataca	14	6	8	13	2	0	0	0	0	0	0	0	3	0	1	3	1	2	3	3	1	4	3	rs41282641	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:7873566C>G	ENST00000264668.2	+	3	321	c.291C>G	c.(289-291)cgC>cgG	p.R97R	MTRR_ENST00000502509.1_Intron|MTRR_ENST00000341013.6_Intron|MTRR_ENST00000440940.2_Silent_p.R70R	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	97	Flavodoxin-like. {ECO:0000255|PROSITE- ProRule:PRU00088}.				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)	ACACAGCCCGCAAGTTTGTTA	0.468													C|||	4	0.000798722	0.0	0.0	5008	,	,		15728	0.0		0.003	False		,,,				2504	0.001				p.R97R		Atlas-SNP	.											.	MTRR	74	.	0			c.C291G						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	148	154	152		210,291	1.5	1	5	dbSNP_127	152	55,8545	35.3+/-89.8	0,55,4245	no	coding-synonymous,coding-synonymous	MTRR	NM_002454.2,NM_024010.2	,	0,56,6447	GG,GC,CC		0.6395,0.0227,0.4306	,	70/699,97/726	7873566	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	4552	exon3			AGCCCGCAAGTTT	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.291C>G	5.37:g.7873566C>G		94	0	0		80	37	0.4625	NM_024010	O60471|Q32MA9|Q7Z4M8	Silent	SNP	ENST00000264668.2	37	CCDS3874.1																																																																																			C|0.997;G|0.003	0.003	strong		0.468	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1			G	7873566	C	G	7873566	2	3	29	1	0	0	0	0	0	0	0	1	9970	697	25	4		4	MTRR	5	7873566	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2432252	7873566	173041694	246	12487											
DNAH5	1767	hgsc.bcm.edu	37	chr5	13788927	13788927	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaactcctcctctaccaaacTtactaaagccttatcaaacc	15	10	1	15	0	2	0	1	0	1	0	4	0	4	0	5	0	6	0	5	0	8	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:13788927T>G	ENST00000265104.4	-	51	8649	c.8545A>C	c.(8545-8547)Agt>Cgt	p.S2849R		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2849					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)					TCTACCAAACTTACTAAAGCC	0.423									Kartagener syndrome																												p.S2849R		Atlas-SNP	.											.	DNAH5	868	.	0			c.A8545C						PASS	.						124	118	120					5																	13788927		2203	4300	6503	SO:0001583	missense	1767	exon51	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CCAAACTTACTAA	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.8545A>C	5.37:g.13788927T>G	ENSP00000265104:p.Ser2849Arg	207	0	0		199	37	0.18593	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	T	6.870	0.529813	0.13127	.	.	ENSG00000039139	ENST00000265104	T	0.23348	1.91	6.06	2.34	0.29019	.	0.290888	0.41823	N	0.000811	T	0.11965	0.0291	N	0.16266	0.395	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35674	-0.9779	10	0.09843	T	0.71	.	7.2973	0.26401	0.0:0.1272:0.1225:0.7503	.	2849	Q8TE73	DYH5_HUMAN	R	2849	ENSP00000265104:S2849R	ENSP00000265104:S2849R	S	-	1	0	DNAH5	13841927	0.173000	0.23056	0.000000	0.03702	0.990000	0.78478	1.723000	0.38053	0.169000	0.19679	0.533000	0.62120	AGT	.	.	none		0.423	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369		G	13788927	T	G	13788927	3	3	29	1	0	0	0	0	1	0	0	0	4606	1609	56	5	5445	5	DNAH5	5	13788927	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	5915361	13788927	167126333	247	12488											
PRDM9	56979	hgsc.bcm.edu	37	chr5	23510038	23510038	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cttcttttcaggtctcagagCcactcgaccagctttcatgt	7	14	7	13	1	4	1	3	0	2	1	6	2	4	1	2	1	2	1	2	1	0	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:23510038C>A	ENST00000296682.3	+	4	385	c.203C>A	c.(202-204)gCc>gAc	p.A68D		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	68	KRAB-related. {ECO:0000255|PROSITE- ProRule:PRU00120}.				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						GGTCTCAGAGCCACTCGACCA	0.488										HNSCC(3;0.000094)																											p.A68D		Atlas-SNP	.											.	PRDM9	344	.	0			c.C203A						PASS	.						72	69	70					5																	23510038		1879	4115	5994	SO:0001583	missense	56979	exon4			TCAGAGCCACTCG	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.203C>A	5.37:g.23510038C>A	ENSP00000296682:p.Ala68Asp	215	0	0		172	50	0.290698	NM_020227	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	C	17.41	3.381532	0.61845	.	.	ENSG00000164256	ENST00000502755;ENST00000296682	T;T	0.00848	5.62;5.62	3.79	3.79	0.43588	Krueppel-associated box (2);Krueppel-associated box-related (1);	.	.	.	.	T	0.03178	0.0093	L	0.45051	1.395	0.29855	N	0.828075	D	0.71674	0.998	D	0.77557	0.99	T	0.26087	-1.0113	9	0.87932	D	0	-2.7458	11.3346	0.49496	0.0:1.0:0.0:0.0	.	68	Q9NQV7	PRDM9_HUMAN	D	68	ENSP00000425471:A68D;ENSP00000296682:A68D	ENSP00000296682:A68D	A	+	2	0	PRDM9	23545795	0.973000	0.33851	1.000000	0.80357	0.801000	0.45260	0.979000	0.29500	2.130000	0.65690	0.609000	0.83330	GCC	.	.	none		0.488	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		A	23510038	C	A	23510038	3	1	29	1	0	0	0	0	1	0	0	0	12475	739	26	4	213	4	PRDM9	5	23510038	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	9721111	23510038	157405222	248	12489											
ADAMTS12	81792	hgsc.bcm.edu	37	chr5	33614391	33614391	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccagtggccgtactgccagaAgtacatctgctgctcaacat	10	9	9	13	1	2	1	1	0	1	1	2	1	2	1	3	1	6	4	3	1	4	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:33614391A>T	ENST00000504830.1	-	16	2814	c.2479T>A	c.(2479-2481)Ttc>Atc	p.F827I	ADAMTS12_ENST00000504582.1_5'UTR|ADAMTS12_ENST00000352040.3_Missense_Mutation_p.F742I	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	827	Spacer 1.|TSP type-1 2. {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						TACTGCCAGAAGTACATCTGC	0.502										HNSCC(64;0.19)																											p.F827I		Atlas-SNP	.											.	ADAMTS12	464	.	0			c.T2479A						PASS	.						209	147	168					5																	33614391		2203	4300	6503	SO:0001583	missense	81792	exon16			GCCAGAAGTACAT	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.2479T>A	5.37:g.33614391A>T	ENSP00000422554:p.Phe827Ile	111	0	0		104	10	0.0961538	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	A	12.45	1.940819	0.34283	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.60424	0.19;0.19	5.73	5.73	0.89815	.	0.413754	0.28927	N	0.013686	T	0.59865	0.2225	L	0.34521	1.04	0.80722	D	1	D;B	0.67145	0.996;0.077	P;B	0.62184	0.899;0.052	T	0.55328	-0.8158	10	0.20519	T	0.43	.	10.865	0.46849	0.8593:0.0:0.0:0.1407	.	742;827	P58397-3;P58397	.;ATS12_HUMAN	I	827;742	ENSP00000422554:F827I;ENSP00000344847:F742I	ENSP00000344847:F742I	F	-	1	0	ADAMTS12	33650148	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	2.846000	0.48262	2.179000	0.69175	0.459000	0.35465	TTC	.	.	none		0.502	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955		T	33614391	A	T	33614391	3	4	29	1	0	0	0	0	1	0	0	0	257	72	3	5	2341	5	ADAMTS12	5	33614391	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	10104353	33614391	147300869	249	12490											
EGFLAM	133584	hgsc.bcm.edu	37	chr5	38438505	38438505	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agctgccggcccaggaaggaGggctatgactgtgactgccc	8	6	15	12	1	0	2	0	2	0	0	0	4	0	4	3	4	3	2	3	4	2	1	rs35767836	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:38438505G>C	ENST00000354891.3	+	17	2758	c.2412G>C	c.(2410-2412)gaG>gaC	p.E804D	EGFLAM_ENST00000397202.2_Missense_Mutation_p.E170D|EGFLAM_ENST00000322350.5_Missense_Mutation_p.E804D|EGFLAM_ENST00000336740.6_Missense_Mutation_p.E570D	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	804	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)					CCAGGAAGGAGGGCTATGACT	0.617													G|||	40	0.00798722	0.0015	0.0144	5008	,	,		14121	0.0		0.0239	False		,,,				2504	0.0041				p.E804D	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											.	EGFLAM	302	.	0			c.G2412C						PASS	.	G	ASP/GLU,ASP/GLU,ASP/GLU	23,4383	30.8+/-60.4	0,23,2180	39	39	39		2412,2412,1710	1.5	0.9	5	dbSNP_126	39	200,8400	86.6+/-149.0	4,192,4104	yes	missense,missense,missense	EGFLAM	NM_001205301.1,NM_152403.3,NM_182798.2	45,45,45	4,215,6284	CC,CG,GG		2.3256,0.522,1.7146	benign,benign,benign	804/1018,804/1010,570/776	38438505	223,12783	2203	4300	6503	SO:0001583	missense	133584	exon17			GAAGGAGGGCTAT	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.2412G>C	5.37:g.38438505G>C	ENSP00000346964:p.Glu804Asp	107	0	0		123	54	0.439024	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Missense_Mutation	SNP	ENST00000354891.3	37	CCDS56363.1	25	0.011446886446886446	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	19	0.025065963060686015	G	9.330	1.060369	0.19987	0.00522	0.023256	ENSG00000164318	ENST00000354891;ENST00000322350;ENST00000336740;ENST00000397202;ENST00000339580	T;T;T;D	0.92446	-1.19;-1.19;-1.19;-3.04	5.73	1.47	0.22746	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.143839	0.64402	N	0.000010	T	0.47210	0.1433	N	0.01209	-0.955	0.80722	D	1	B;B;B	0.12013	0.003;0.005;0.001	B;B;B	0.14023	0.008;0.01;0.008	T	0.52290	-0.8595	10	0.08837	T	0.75	-3.2598	3.303	0.06989	0.0786:0.2203:0.2607:0.4403	rs35767836	570;804;804	Q63HQ2-4;Q63HQ2;Q63HQ2-2	.;EGFLA_HUMAN;.	D	804;804;570;170;570	ENSP00000346964:E804D;ENSP00000313084:E804D;ENSP00000337607:E570D;ENSP00000380385:E170D	ENSP00000313084:E804D	E	+	3	2	EGFLAM	38474262	0.905000	0.30787	0.927000	0.36925	0.957000	0.61999	0.065000	0.14466	0.332000	0.23536	0.655000	0.94253	GAG	G|0.987;C|0.013	0.013	strong		0.617	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403		C	38438505	G	C	38438505	3	2	29	1	0	0	0	0	1	0	0	0	4968	991	35	4	2492	4	EGFLAM	5	38438505	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	4824114	38438505	142476755	250	12491											
RICTOR	253260	hgsc.bcm.edu	37	chr5	38944635	38944635	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttctttgcgaaggagtataCggcacattggtgtatcatct	9	14	10	8	2	3	0	1	0	2	0	3	2	3	1	0	3	2	3	0	3	4	6			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:38944635C>T	ENST00000357387.3	-	36	4856	c.4826G>A	c.(4825-4827)cGt>cAt	p.R1609H	RICTOR_ENST00000296782.5_Missense_Mutation_p.R1633H	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)					AAGGAGTATACGGCACATTGG	0.323																																					p.R1609H		Atlas-SNP	.											RICTOR,colon,carcinoma,0,1	RICTOR	182	1	0			c.G4826A						PASS	.						101	98	99					5																	38944635		2203	4300	6503	SO:0001583	missense	253260	exon36			AGTATACGGCACA		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.4826G>A	5.37:g.38944635C>T	ENSP00000349959:p.Arg1609His	60	0	0		73	4	0.0547945	NM_152756		Missense_Mutation	SNP	ENST00000357387.3	37	CCDS34148.1	.	.	.	.	.	.	.	.	.	.	C	34	5.397706	0.96009	.	.	ENSG00000164327	ENST00000357387;ENST00000296782	T;T	0.53857	0.62;0.6	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.66616	0.2807	L	0.56769	1.78	0.80722	D	1	D;D	0.69078	0.997;0.997	P;P	0.57152	0.747;0.814	T	0.69262	-0.5191	10	0.87932	D	0	-14.5494	19.4767	0.94992	0.0:1.0:0.0:0.0	.	1609;1633	Q6R327;Q6R327-3	RICTR_HUMAN;.	H	1609;1633	ENSP00000349959:R1609H;ENSP00000296782:R1633H	ENSP00000296782:R1633H	R	-	2	0	RICTOR	38980392	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.366000	0.59492	2.601000	0.87937	0.563000	0.77884	CGT	.	.	none		0.323	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756		T	38944635	C	T	38944635	3	4	29	1	0	0	0	0	1	0	0	0	13373	536	19	1	312	1	RICTOR	5	38944635	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	506130	38944635	141970625	251	12492											
PRKAA1	5562	hgsc.bcm.edu	37	chr5	40798278	40798278	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcgccatctttctccaggaaCtgagtctgcgcatggcgctg	6	11	11	13	3	3	1	0	1	3	0	5	2	3	2	2	2	2	2	2	2	1	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:40798278C>T	ENST00000397128.2	-	1	22	c.14G>A	c.(13-15)aGt>aAt	p.S5N	PRKAA1_ENST00000296800.4_5'Flank|PRKAA1_ENST00000354209.3_Missense_Mutation_p.S5N	NM_006251.5|NM_206907.3	NP_006242.5|NP_996790.3	Q13131	AAPK1_HUMAN	protein kinase, AMP-activated, alpha 1 catalytic subunit	5				S -> C (in Ref. 4; BAG35788). {ECO:0000305}.	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)	TCTCCAGGAACTGAGTCTGCG	0.721																																					p.S5N		Atlas-SNP	.											.	PRKAA1	27	.	0			c.G14A						PASS	.						43	50	48					5																	40798278		2175	4295	6470	SO:0001583	missense	5562	exon1			CAGGAACTGAGTC		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.14G>A	5.37:g.40798278C>T	ENSP00000380317:p.Ser5Asn	83	0	0		117	22	0.188034	NM_006251	A8MTQ6|B2R7E1|O00286|Q5D0E1|Q86VS1|Q9UNQ4	Missense_Mutation	SNP	ENST00000397128.2	37	CCDS3932.2	.	.	.	.	.	.	.	.	.	.	C	15.74	2.922306	0.52653	.	.	ENSG00000132356	ENST00000397128;ENST00000354209	T;T	0.73152	-0.66;-0.72	3.56	2.69	0.31865	.	0.555807	0.15939	U	0.237270	T	0.55816	0.1944	N	0.22421	0.69	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.53394	-0.8445	10	0.62326	D	0.03	-0.1809	10.7188	0.46028	0.0:0.903:0.0:0.097	.	5;5	Q13131;Q13131-2	AAPK1_HUMAN;.	N	5	ENSP00000380317:S5N;ENSP00000346148:S5N	ENSP00000346148:S5N	S	-	2	0	AC008810.1	40834035	1.000000	0.71417	1.000000	0.80357	0.772000	0.43724	0.840000	0.27600	0.822000	0.34565	0.205000	0.17691	AGT	.	.	none		0.721	PRKAA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253833.2	NM_006251		T	40798278	C	T	40798278	3	4	29	1	0	0	0	0	1	0	0	0	12505	565	20	2	1750	2	PRKAA1	5	40798278	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1853643	40798278	140116982	252	12493											
HEATR7B2	133558	hgsc.bcm.edu	37	chr5	41064591	41064598	+	Frame_Shift_Del	DEL	TTCATCCT	TTCATCCT	-																															caccaatacagaaagtccccTtcatcctttcatcctcggcc																								rs377494374|rs533532784		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TTCATCCT	TTCATCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:41064591_41064598delTTCATCCT	ENST00000399564.4	-	5	886_893	c.436_443delAGGATGAA	c.(436-444)aggatgaagfs	p.RMK146fs		NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	146																	GAAAGTCCCCTTCATCCTTTCATCCTCG	0.462																																					p.146_148del		Pindel,Atlas-Indel	.											.	.	.	.	0			c.437_444del						PASS	.			32,3684		15,2,1841						0.8	0.6			86	127,7795		50,27,3884	no	frameshift	HEATR7B2	NM_173489.4		65,29,5725	A1A1,A1R,RR		1.6031,0.8611,1.3662				159,11479				SO:0001589	frameshift_variant	133558	exon5			.		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.436_443delAGGATGAA	5.37:g.41064599_41064606delTTCATCCT	ENSP00000382476:p.Arg146fs	46	0	.		36	13	0.361	NM_173489	Q68DM1|Q7Z4U4|Q8N7X3	Frame_Shift_Del	DEL	ENST00000399564.4	37	CCDS47202.1																																																																																			.	.	none		0.462	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489		-	41064598	TTCATCCT	-	41064591	7	5	29	1	0	1	0	1	0	0	0	0	7044	1609	56	0	4466	0	HEATR7B2	5	41064591	Frame_Shift_Del	DEL	TTCATCCT	TCGA-GR-7351-01A-11D-2210-10	266313	41064591	139850669	253	12494											
ZNF131	7690	hgsc.bcm.edu	37	chr5	43173541	43173541	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaaggaaggaagaagctctaCgaatgccaggtatgtgcaga	16	6	13	6	1	1	2	0	0	1	2	1	5	1	4	1	3	4	3	1	3	7	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:43173541C>T	ENST00000399534.1	+	6	1220	c.1176C>T	c.(1174-1176)taC>taT	p.Y392Y	ZNF131_ENST00000505606.2_Silent_p.Y358Y|ZNF131_ENST00000509156.1_Silent_p.Y392Y|ZNF131_ENST00000509931.1_Intron|ZNF131_ENST00000306938.4_Silent_p.Y358Y|ZNF131_ENST00000509634.1_Silent_p.Y358Y			P52739	ZN131_HUMAN	zinc finger protein 131	392					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						AGAAGCTCTACGAATGCCAGG	0.418																																					p.Y358Y		Atlas-SNP	.											.	ZNF131	51	.	0			c.C1074T						PASS	.						70	67	68					5																	43173541		1917	4148	6065	SO:0001819	synonymous_variant	7690	exon7			GCTCTACGAATGC	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.1176C>T	5.37:g.43173541C>T		87	0	0		85	38	0.447059	NM_003432	B4DRL3|Q6PIF0	Silent	SNP	ENST00000399534.1	37																																																																																				.	.	none		0.418	ZNF131-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000367982.1	NM_003432		T	43173541	C	T	43173541	2	4	29	1	0	0	0	0	0	0	0	1	17736	547	19	1		1	ZNF131	5	43173541	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2108950	43173541	137741719	254	12495											
HCN1	348980	hgsc.bcm.edu	37	chr5	45396654	45396654	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	attaaagcggtggcatggccGacaaacatggcatagcaggt	13	7	13	8	2	0	0	0	0	0	0	0	1	0	0	1	5	3	3	1	5	4	2	rs369683016		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:45396654G>A	ENST00000303230.4	-	4	1227	c.1170C>T	c.(1168-1170)gtC>gtT	p.V390V		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	390					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						TGGCATGGCCGACAAACATGG	0.498																																					p.V390V		Atlas-SNP	.											.	HCN1	298	.	0			c.C1170T						PASS	.	A		0,4406		0,0,2203	78	68	72		1170	-10.8	0	5		72	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	HCN1	NM_021072.3		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		390/891	45396654	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	348980	exon4			ATGGCCGACAAAC	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.1170C>T	5.37:g.45396654G>A		157	0	0		157	43	0.273885	NM_021072		Silent	SNP	ENST00000303230.4	37	CCDS3952.1																																																																																			.	.	weak		0.498	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072		A	45396654	G	A	45396654	2	1	29	1	0	0	0	0	0	0	0	1	7005	1045	37	1		1	HCN1	5	45396654	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2223113	45396654	135518606	255	12496											
MAP3K1	4214	hgsc.bcm.edu	37	chr5	56178615	56178615	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaattgccatggcaatgtcAgcgtctcaggatgccctccc	8	9	10	14	1	2	0	2	0	1	0	4	1	3	1	3	2	3	2	3	2	2	1	rs55912465	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:56178615A>C	ENST00000399503.3	+	14	3588	c.3588A>C	c.(3586-3588)tcA>tcC	p.S1196S		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	1196					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)		TGGCAATGTCAGCGTCTCAGG	0.393													A|||	3	0.000599042	0.0	0.0014	5008	,	,		22938	0.0		0.002	False		,,,				2504	0.0				p.S1196S		Atlas-SNP	.											.	MAP3K1	355	.	0			c.A3588C						PASS	.	A		3,4211		0,3,2104	83	85	84		3588	0.2	1	5	dbSNP_129	84	39,8457		0,39,4209	no	coding-synonymous	MAP3K1	NM_005921.1		0,42,6313	CC,CA,AA		0.459,0.0712,0.3304		1196/1513	56178615	42,12668	2107	4248	6355	SO:0001819	synonymous_variant	4214	exon14			AATGTCAGCGTCT	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.3588A>C	5.37:g.56178615A>C		55	0	0		47	28	0.595745	NM_005921		Silent	SNP	ENST00000399503.3	37	CCDS43318.1																																																																																			A|0.993;C|0.007	0.007	strong		0.393	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066		C	56178615	A	C	56178615	2	2	29	1	0	0	0	0	0	0	0	1	9252	175	7	5		5	MAP3K1	5	56178615	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	10781961	56178615	124736645	256	12497											
CD180	4064	hgsc.bcm.edu	37	chr5	66492387	66492387	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtttggactcacctcaatgCacatctgatcccaggaggtg	10	10	10	11	0	3	1	2	1	1	0	4	3	4	3	2	3	1	2	2	3	1	1	rs377501004		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:66492387C>T	ENST00000256447.4	-	1	240	c.83G>A	c.(82-84)tGc>tAc	p.C28Y		NM_005582.2	NP_005573.2	Q99467	CD180_HUMAN	CD180 molecule	28					B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(2)|kidney(7)|large_intestine(12)|liver(1)|lung(8)|ovary(1)|stomach(2)	34		Lung NSC(167;4.94e-05)|Prostate(74;0.00601)|Ovarian(174;0.0654)|Breast(144;0.198)|Colorectal(97;0.234)		Lung(70;0.0046)		CACCTCAATGCACATCTGATC	0.458																																					p.C28Y		Atlas-SNP	.											.	CD180	78	.	0			c.G83A						PASS	.	C	TYR/CYS	2,4404	4.2+/-10.8	0,2,2201	168	167	167		83	5	1	5		167	0,8600		0,0,4300	no	missense	CD180	NM_005582.2	194	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging	28/662	66492387	2,13004	2203	4300	6503	SO:0001583	missense	4064	exon1			TCAATGCACATCT	D83597	CCDS3992.1	5q12	2008-02-05	2006-03-28	2005-06-07	ENSG00000134061	ENSG00000134061		"CD molecules"	6726	protein-coding gene	gene with protein product		602226	"lymphocyte antigen 64 (mouse) homolog, radioprotective, 105kD", "CD180 antigen"	LY64		9763566, 8975706	Standard	NM_005582		Approved	RP105, Ly78	uc003juy.2	Q99467	OTTHUMG00000131229	ENST00000256447.4:c.83G>A	5.37:g.66492387C>T	ENSP00000256447:p.Cys28Tyr	64	0	0		88	6	0.0681818	NM_005582	B2R7Z7|Q32MM5	Missense_Mutation	SNP	ENST00000256447.4	37	CCDS3992.1	.	.	.	.	.	.	.	.	.	.	C	16.34	3.094491	0.56075	4.54E-4	0.0	ENSG00000134061	ENST00000256447	T	0.60040	0.22	4.99	4.99	0.66335	.	0.148429	0.47455	D	0.000228	T	0.78742	0.4331	M	0.85462	2.755	0.49213	D	0.999768	D	0.89917	1.0	D	0.85130	0.997	T	0.82020	-0.0664	10	0.87932	D	0	.	16.5748	0.84633	0.0:1.0:0.0:0.0	.	28	Q99467	CD180_HUMAN	Y	28	ENSP00000256447:C28Y	ENSP00000256447:C28Y	C	-	2	0	CD180	66528143	1.000000	0.71417	0.991000	0.47740	0.479000	0.33129	3.847000	0.55895	2.754000	0.94517	0.591000	0.81541	TGC	.	.	weak		0.458	CD180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253973.2	NM_005582		T	66492387	C	T	66492387	3	4	29	1	0	0	0	0	1	0	0	0	2974	710	25	2	1914	2	CD180	5	66492387	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	10313772	66492387	114422873	257	12498											
MAP1B	4131	hgsc.bcm.edu	37	chr5	71491950	71491950	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaagcagggagtagacgacaTtgaaaaatttgaagatgaag	18	7	13	3	1	0	5	0	3	0	2	0	8	0	6	0	1	1	2	0	1	6	3	rs143194383	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:71491950T>C	ENST00000296755.7	+	5	3066	c.2768T>C	c.(2767-2769)aTt>aCt	p.I923T		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	923					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)		GTAGACGACATTGAAAAATTT	0.512													T|||	2	0.000399361	0.0	0.0014	5008	,	,		20663	0.0		0.001	False		,,,				2504	0.0				p.I923T	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.T2768C						PASS	.	T	THR/ILE	5,4401	9.9+/-24.2	0,5,2198	56	62	60		2768	-5.8	0	5	dbSNP_134	60	14,8586	10.5+/-38.8	0,14,4286	yes	missense	MAP1B	NM_005909.3	89	0,19,6484	CC,CT,TT		0.1628,0.1135,0.1461	benign	923/2469	71491950	19,12987	2203	4300	6503	SO:0001583	missense	4131	exon5			ACGACATTGAAAA	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.2768T>C	5.37:g.71491950T>C	ENSP00000296755:p.Ile923Thr	74	0	0		83	49	0.590361	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	0.011	-1.725172	0.00694	0.001135	0.001628	ENSG00000131711	ENST00000296755	T	0.03004	4.08	5.6	-5.81	0.02340	.	0.728470	0.12932	N	0.427289	T	0.02012	0.0063	N	0.22421	0.69	0.20489	N	0.999891	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47959	-0.9076	10	0.12430	T	0.62	-0.4578	8.5315	0.33337	0.1813:0.4869:0.0:0.3318	.	797;923	A2BDK6;P46821	.;MAP1B_HUMAN	T	923	ENSP00000296755:I923T	ENSP00000296755:I923T	I	+	2	0	MAP1B	71527706	0.055000	0.20627	0.010000	0.14722	0.054000	0.15201	-0.302000	0.08221	-0.724000	0.04908	-0.353000	0.07706	ATT	T|1.000;C|0.000	0.000	strong		0.512	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		C	71491950	T	C	71491950	3	2	29	1	0	0	0	0	1	0	0	0	9237	1493	52	3	2786	3	MAP1B	5	71491950	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	4999563	71491950	109423310	258	12499											
AGGF1	55109	hgsc.bcm.edu	37	chr5	76331449	76331449	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atcaacaagatcaagctatcGaaacttctattttgaattct	15	14	4	8	1	4	2	2	1	2	1	5	3	4	2	0	0	3	1	0	0	7	6	rs34203073	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:76331449G>A	ENST00000312916.7	+	3	779	c.397G>A	c.(397-399)Gaa>Aaa	p.E133K	AGGF1_ENST00000506806.1_Missense_Mutation_p.E133K|AGGF1_ENST00000503538.1_3'UTR	NM_018046.4	NP_060516.2	Q8N302	AGGF1_HUMAN	angiogenic factor with G patch and FHA domains 1	133			E -> K (in KTS; in 5 patients; displays a stronger angiogenic activity; dbSNP:rs34203073). {ECO:0000269|PubMed:14961121}.		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)		TCAAGCTATCGAAACTTCTAT	0.328													G|||	39	0.00778754	0.0045	0.0058	5008	,	,		18392	0.001		0.0219	False		,,,				2504	0.0061				p.E133K		Atlas-SNP	.											AGGF1,colon,carcinoma,0,1	AGGF1	71	1	0			c.G397A	GRCh37	CM040277	AGGF1	M	rs34203073	scavenged	.	G	LYS/GLU	17,4389	24.3+/-50.5	0,17,2186	75	78	77		397	1.1	0	5	dbSNP_126	77	168,8430	77.2+/-139.8	2,164,4133	yes	missense	AGGF1	NM_018046.4	56	2,181,6319	AA,AG,GG		1.9539,0.3858,1.4226	benign	133/715	76331449	185,12819	2203	4299	6502	SO:0001583	missense	55109	exon3			GCTATCGAAACTT	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.397G>A	5.37:g.76331449G>A	ENSP00000316109:p.Glu133Lys	208	2	0.00961538		244	105	0.430328	NM_018046	O00581|Q53YS3|Q9BU84|Q9NW66	Missense_Mutation	SNP	ENST00000312916.7	37	CCDS4035.1	19	0.0086996336996337	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	14	0.018469656992084433	G	7.640	0.680759	0.14907	0.003858	0.019539	ENSG00000164252	ENST00000312916;ENST00000506806	T;T	0.79653	1.14;-1.29	5.96	1.13	0.20643	.	0.387612	0.28510	N	0.015088	T	0.49762	0.1576	L	0.43152	1.355	0.09310	N	1	B;B	0.13145	0.002;0.007	B;B	0.09377	0.001;0.004	T	0.40156	-0.9578	10	0.25106	T	0.35	-19.1001	2.2151	0.03957	0.2699:0.1226:0.4876:0.1198	rs34203073	133;133	Q8N302;Q8N302-3	AGGF1_HUMAN;.	K	133	ENSP00000316109:E133K;ENSP00000424733:E133K	ENSP00000316109:E133K	E	+	1	0	AGGF1	76367205	0.047000	0.20315	0.000000	0.03702	0.004000	0.04260	0.750000	0.26334	-0.075000	0.12798	-0.143000	0.13931	GAA	G|0.986;A|0.014	0.014	strong		0.328	AGGF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219971.2	NM_018046		A	76331449	G	A	76331449	3	1	29	1	0	0	0	0	1	0	0	0	382	1059	37	1	407	1	AGGF1	5	76331449	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	4839499	76331449	104583811	259	12500											
CHD1	1105	hgsc.bcm.edu	37	chr5	98216991	98216991	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttttttttacctggggctCttgttcttctccttcaggtt	2	23	7	9	0	4	0	1	0	3	0	5	0	4	0	2	3	1	3	2	3	1	10			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:98216991C>A	ENST00000284049.3	-	20	3105	c.2956G>T	c.(2956-2958)Gag>Tag	p.E986*		NM_001270.2	NP_001261.2	O14646	CHD1_HUMAN	chromodomain helicase DNA binding protein 1	986					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)	ACCTGGGGCTCTTGTTCTTCT	0.318																																					p.E986X		Atlas-SNP	.											.	CHD1	137	.	0			c.G2956T						PASS	.						15	14	14					5																	98216991		2172	4267	6439	SO:0001587	stop_gained	1105	exon20			GGGGCTCTTGTTC	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.2956G>T	5.37:g.98216991C>A	ENSP00000284049:p.Glu986*	197	0	0		183	40	0.218579	NM_001270	Q17RZ3	Nonsense_Mutation	SNP	ENST00000284049.3	37	CCDS34204.1	.	.	.	.	.	.	.	.	.	.	C	41	8.840979	0.98974	.	.	ENSG00000153922	ENST00000284049	.	.	.	5.23	5.23	0.72850	.	0.000000	0.33916	U	0.004434	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	19.1612	0.93533	0.0:1.0:0.0:0.0	.	.	.	.	X	986	.	ENSP00000284049:E986X	E	-	1	0	CHD1	98244891	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	7.818000	0.86416	2.600000	0.87896	0.585000	0.79938	GAG	.	.	none		0.318	CHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370295.1	NM_001270		A	98216991	C	A	98216991	4	1	29	1	0	0	0	0	0	1	0	0	3325	922	32	4	2240	4	CHD1	5	98216991	Nonsense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	21885542	98216991	82698269	260	12501											
SLCO6A1	133482	hgsc.bcm.edu	37	chr5	101834386	101834386	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gaaccttatcaaggcctctgGaagtagtctcagataccggt	11	10	10	10	1	3	1	2	0	2	1	4	3	3	2	3	3	2	1	3	3	6	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:101834386G>A	ENST00000506729.1	-	1	334	c.163C>T	c.(163-165)Cca>Tca	p.P55S	SLCO6A1_ENST00000379807.3_Missense_Mutation_p.P55S|SLCO6A1_ENST00000513675.1_Missense_Mutation_p.P55S|SLCO6A1_ENST00000389019.3_Missense_Mutation_p.P55S|SLCO6A1_ENST00000514551.1_5'Flank|RP11-58B2.1_ENST00000502494.1_RNA|SLCO6A1_ENST00000379810.1_Missense_Mutation_p.P55S			Q86UG4	SO6A1_HUMAN	solute carrier organic anion transporter family, member 6A1	55						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)		AAGGCCTCTGGAAGTAGTCTC	0.572																																					p.P55S		Atlas-SNP	.											.	SLCO6A1	153	.	0			c.C163T						PASS	.						154	170	165					5																	101834386		2203	4300	6503	SO:0001583	missense	133482	exon1			CCTCTGGAAGTAG	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.163C>T	5.37:g.101834386G>A	ENSP00000421339:p.Pro55Ser	103	0	0		122	5	0.0409836	NM_173488	A6NHC1|Q6ZMY5|Q86UV2|Q8IYU5	Missense_Mutation	SNP	ENST00000506729.1	37	CCDS34206.1	.	.	.	.	.	.	.	.	.	.	G	13.70	2.315767	0.40996	.	.	ENSG00000205359	ENST00000506729;ENST00000379807;ENST00000389019;ENST00000513675;ENST00000379810	T;T;T;T;T	0.62498	0.57;0.57;0.24;0.02;0.02	3.52	-0.367	0.12541	.	16.882000	0.00166	N	0.000000	T	0.47600	0.1454	L	0.29908	0.895	0.09310	N	1	P;P;P	0.46142	0.873;0.799;0.799	B;B;B	0.40066	0.318;0.256;0.169	T	0.37478	-0.9704	10	0.39692	T	0.17	.	2.8587	0.05579	0.3443:0.0:0.4559:0.1998	.	55;55;55	Q86UG4-2;C9J020;Q86UG4	.;.;SO6A1_HUMAN	S	55	ENSP00000421339:P55S;ENSP00000369135:P55S;ENSP00000373671:P55S;ENSP00000421990:P55S;ENSP00000369138:P55S	ENSP00000369135:P55S	P	-	1	0	SLCO6A1	101862285	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.165000	0.09968	-0.098000	0.12285	0.484000	0.47621	CCA	.	.	none		0.572	SLCO6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370335.1	NM_173488		A	101834386	G	A	101834386	3	1	29	1	0	0	0	0	1	0	0	0	14747	1174	41	2	2048	2	SLCO6A1	5	101834386	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	3617395	101834386	79080874	261	12502											
EPB41L4A	64097	hgsc.bcm.edu	37	chr5	111531387	111531387	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcttaagatctgaatcttcAccactgttatgggctttcct	8	16	7	10	0	3	2	1	1	2	1	4	2	4	2	2	1	1	3	2	1	3	4	rs149373122	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:111531387A>T	ENST00000261486.5	-	16	1671	c.1395T>A	c.(1393-1395)ggT>ggA	p.G465G	CTC-459M5.2_ENST00000515563.1_RNA|EPB41L4A_ENST00000507810.1_5'UTR|CTC-459M5.2_ENST00000506875.1_RNA	NM_022140.3	NP_071423	Q9HCS5	E41LA_HUMAN	erythrocyte membrane protein band 4.1 like 4A	465						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)		CTGAATCTTCACCACTGTTAT	0.373													A|||	10	0.00199681	0.0	0.0058	5008	,	,		18453	0.0		0.005	False		,,,				2504	0.001				p.G465G		Atlas-SNP	.											.	EPB41L4A	130	.	0			c.T1395A						PASS	.	A		8,3658		0,8,1825	113	103	106		1395	-2.2	1	5	dbSNP_134	106	77,8093		1,75,4009	no	coding-synonymous	EPB41L4A	NM_022140.3		1,83,5834	TT,TA,AA		0.9425,0.2182,0.7181		465/687	111531387	85,11751	1833	4085	5918	SO:0001819	synonymous_variant	64097	exon16			ATCTTCACCACTG	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.1395T>A	5.37:g.111531387A>T		86	0	0		77	37	0.480519	NM_022140	A4FUI6	Silent	SNP	ENST00000261486.5	37	CCDS43350.1																																																																																			A|0.993;T|0.007	0.007	strong		0.373	EPB41L4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370969.1			T	111531387	A	T	111531387	2	4	29	1	0	0	0	0	0	0	0	1	5157	146	6	5		5	EPB41L4A	5	111531387	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	9697001	111531387	69383873	262	12503											
ALDH7A1	501	hgsc.bcm.edu	37	chr5	125928395	125928395	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttctcttgctttctttacAgtttcttcatagtctgccac	5	19	5	12	0	5	0	1	0	4	0	6	0	5	0	1	0	3	3	1	0	2	8	rs60720055	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:125928395A>G	ENST00000409134.3	-	3	492	c.273T>C	c.(271-273)acT>acC	p.T91T	ALDH7A1_ENST00000553117.1_Silent_p.T91T|ALDH7A1_ENST00000413020.1_5'UTR|ALDH7A1_ENST00000447989.2_Silent_p.T118T	NM_001182.4|NM_001201377.1	NP_001173.2|NP_001188306.1	P49419	AL7A1_HUMAN	aldehyde dehydrogenase 7 family, member A1	91					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)		CTTTCTTTACAGTTTCTTCAT	0.368													A|||	302	0.0603035	0.1717	0.0274	5008	,	,		18399	0.0		0.0288	False		,,,				2504	0.0276				p.T118T		Atlas-SNP	.											.	ALDH7A1	57	.	0			c.T354C						PASS	.	A	,,	657,3749	278.1+/-274.1	42,573,1588	111	105	107		273,189,354	-9.2	0.1	5	dbSNP_129	107	214,8386	88.9+/-151.2	2,210,4088	no	coding-synonymous,coding-synonymous,coding-synonymous	ALDH7A1	NM_001182.4,NM_001201377.1,NM_001202404.1	,,	44,783,5676	GG,GA,AA		2.4884,14.9115,6.6969	,,	91/540,63/512,118/503	125928395	871,12135	2203	4300	6503	SO:0001819	synonymous_variant	501	exon3			CTTTACAGTTTCT	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.273T>C	5.37:g.125928395A>G		106	0	0		96	51	0.53125	NM_001202404	B2R669|B4DIC7|B4DMA0|E7EPT3|O14619|Q6IPU8|Q9BUL4	Silent	SNP	ENST00000409134.3	37	CCDS4137.2																																																																																			A|0.941;G|0.059	0.059	strong		0.368	ALDH7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250921.2	NM_001182		G	125928395	A	G	125928395	2	3	29	1	0	0	0	0	0	0	0	1	504	175	7	3		3	ALDH7A1	5	125928395	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	14397008	125928395	54986865	263	12504											
LYRM7	90624	hgsc.bcm.edu	37	chr5	130515811	130515811	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttacagctctttaaaacactGcacaggaccagacaacaagt	16	8	6	11	0	1	1	0	0	1	1	1	2	1	2	1	1	5	2	1	1	5	3	rs113642581	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:130515811G>A	ENST00000379380.4	+	2	253	c.42G>A	c.(40-42)ctG>ctA	p.L14L	LYRM7_ENST00000507584.1_Silent_p.L14L|LYRM7_ENST00000510516.1_Silent_p.L14L	NM_181705.2	NP_859056.2	Q5U5X0	LYRM7_HUMAN	LYR motif containing 7	14						mitochondrion (GO:0005739)				upper_aerodigestive_tract(1)	1		all_cancers(142;0.0377)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TTAAAACACTGCACAGGACCA	0.403													G|||	72	0.014377	0.0	0.0202	5008	,	,		16607	0.0		0.0457	False		,,,				2504	0.0123				p.L14L		Atlas-SNP	.											.	LYRM7	7	.	0			c.G42A						PASS	.	G		36,4370	41.6+/-74.8	1,34,2168	120	116	117		42	4.3	1	5	dbSNP_132	117	374,8226	123.2+/-182.1	12,350,3938	no	coding-synonymous	LYRM7	NM_181705.2		13,384,6106	AA,AG,GG		4.3488,0.8171,3.1524		14/105	130515811	410,12596	2203	4300	6503	SO:0001819	synonymous_variant	90624	exon2			AACACTGCACAGG	BC047079	CCDS4148.1	5q31.1	2013-05-24	2012-10-23	2006-10-17	ENSG00000186687	ENSG00000186687		"LYR motif containing"	28072	protein-coding gene	gene with protein product		615831	"chromosome 5 open reading frame 31", "Lyrm7 homolog (mouse)"	C5orf31		23168492	Standard	NM_181705		Approved	FLJ20796, MZM1L	uc003kvg.1	Q5U5X0	OTTHUMG00000128994	ENST00000379380.4:c.42G>A	5.37:g.130515811G>A		54	0	0		48	23	0.479167	NM_181705	A8MPQ9|Q86Y68	Silent	SNP	ENST00000379380.4	37	CCDS4148.1																																																																																			A|0.027;C|0.000;G|0.973	0.027	strong		0.403	LYRM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250983.1	NM_181705		A	130515811	G	A	130515811	2	1	29	1	0	0	0	0	0	0	0	1	9132	1306	46	2		2	LYRM7	5	130515811	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	4587416	130515811	50399449	264	12505											
P4HA2	8974	hgsc.bcm.edu	37	chr5	131539462	131539462	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtaacaattctgcagtcttTactgttaaccctgtgatatg	10	16	7	8	0	2	1	0	1	2	0	2	1	2	1	1	0	4	3	1	0	5	6	rs144253110	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:131539462T>C	ENST00000401867.1	-	11	1798	c.1230A>G	c.(1228-1230)gtA>gtG	p.V410V	P4HA2_ENST00000360568.3_Silent_p.V410V|P4HA2_ENST00000379104.2_Silent_p.V410V|P4HA2_ENST00000166534.4_Silent_p.V410V|P4HA2_ENST00000379100.2_Silent_p.V410V|P4HA2_ENST00000379086.1_Silent_p.V410V			O15460	P4HA2_HUMAN	prolyl 4-hydroxylase, alpha polypeptide II	410					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)	CTGCAGTCTTTACTGTTAACC	0.493																																					p.V410V	Esophageal Squamous(68;117 1135 17362 19256 34242)	Atlas-SNP	.											.	P4HA2	72	.	0			c.A1230G						PASS	.	T	,,,,	0,4406		0,0,2203	88	75	80		1230,1230,1230,1230,1230	-8.1	0.6	5	dbSNP_134	80	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	P4HA2	NM_001017973.1,NM_001017974.1,NM_001142598.1,NM_001142599.1,NM_004199.2	,,,,	0,11,6492	CC,CT,TT		0.1279,0.0,0.0846	,,,,	410/534,410/534,410/534,410/536,410/536	131539462	11,12995	2203	4300	6503	SO:0001819	synonymous_variant	8974	exon10			AGTCTTTACTGTT	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.1230A>G	5.37:g.131539462T>C		118	0	0		136	64	0.470588	NM_001017974	D3DQ85|D3DQ86|Q8WWN0	Silent	SNP	ENST00000401867.1	37	CCDS4151.1																																																																																			T|0.999;C|0.001	0.001	strong		0.493	P4HA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000132653.4	NM_004199		C	131539462	T	C	131539462	2	2	29	1	0	0	0	0	0	0	0	1	11366	1741	61	3		3	P4HA2	5	131539462	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	1023651	131539462	49375798	265	12506											
IRF1	3659	hgsc.bcm.edu	37	chr5	131825083	131825083	+	Splice_Site	SNP	C	C	A																															aacccaaagagttacactcaCtttattaatccagatgagcc																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:131825083C>A	ENST00000245414.4	-	2	346		c.e2+1		IRF1_ENST00000463784.1_Intron|IRF1_ENST00000405885.2_Splice_Site	NM_002198.2	NP_002189.1	P10914	IRF1_HUMAN	interferon regulatory factor 1						apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell cycle arrest (GO:0007050)|cellular response to interferon-beta (GO:0035458)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cell proliferation (GO:0008285)|negative regulation of regulatory T cell differentiation (GO:0045590)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|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 adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta T cell proliferation (GO:2000564)|regulation of cell cycle (GO:0051726)|regulation of innate immune response (GO:0045088)|regulation of MyD88-dependent toll-like receptor signaling pathway (GO:0034124)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(2)|prostate(2)|skin(1)|urinary_tract(1)	11		all_cancers(142;0.026)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	LUAD - Lung adenocarcinoma(142;0.247)		GTTACACTCACTTTATTAATC	0.473																																					.		Atlas-SNP	.											.	IRF1	26	.	0			c.87+1G>T						PASS	.						83	85	85					5																	131825083		2202	4300	6502	SO:0001630	splice_region_variant	3659	exon3			CACTCACTTTATT		CCDS4155.1	5q23-q31	2008-07-18			ENSG00000125347	ENSG00000125347			6116	protein-coding gene	gene with protein product	"interferon regulatory factor-1"	147575				2726461, 1680796	Standard	NM_002198		Approved	MAR	uc003kxa.2	P10914	OTTHUMG00000059497	ENST00000245414.4:c.87+1G>T	5.37:g.131825083C>A		66	0	0		49	21	0.428571	NM_002198	Q96GG7	Splice_Site	SNP	ENST00000245414.4	37	CCDS4155.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.794920	0.90453	.	.	ENSG00000125347	ENST00000245414;ENST00000405885;ENST00000437654;ENST00000458069	.	.	.	5.59	5.59	0.84812	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.96	0.97242	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	IRF1	131852982	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.373000	0.79623	2.793000	0.96121	0.561000	0.74099	.	.	.	none		0.473	IRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132340.1	NM_002198	Intron	A	131825083	C	A	131825083	5	1	29	1	0	0	0	0	0	0	1	0	7836	579	20	4	925	4	IRF1	5	131825083	Splice_Site	SNP	C	TCGA-GR-7351-01A-11D-2210-10	285621	131825083	49090177	266	12507	154	2									
IRF1	3659	hgsc.bcm.edu	37	chr5	131825088	131825088	+	Missense_Mutation	SNP	T	T	G																															aaagagttacactcactttaTtaatccagatgagccccggg																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:131825088T>G	ENST00000245414.4	-	2	341	c.83A>C	c.(82-84)aAt>aCt	p.N28T	IRF1_ENST00000463784.1_Intron|IRF1_ENST00000405885.2_Missense_Mutation_p.N28T	NM_002198.2	NP_002189.1	P10914	IRF1_HUMAN	interferon regulatory factor 1	28					apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell cycle arrest (GO:0007050)|cellular response to interferon-beta (GO:0035458)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cell proliferation (GO:0008285)|negative regulation of regulatory T cell differentiation (GO:0045590)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|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 adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta T cell proliferation (GO:2000564)|regulation of cell cycle (GO:0051726)|regulation of innate immune response (GO:0045088)|regulation of MyD88-dependent toll-like receptor signaling pathway (GO:0034124)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(2)|prostate(2)|skin(1)|urinary_tract(1)	11		all_cancers(142;0.026)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	LUAD - Lung adenocarcinoma(142;0.247)		ACTCACTTTATTAATCCAGAT	0.463																																					p.N28T		Atlas-SNP	.											.	IRF1	26	.	0			c.A83C						PASS	.						86	88	87					5																	131825088		2203	4300	6503	SO:0001583	missense	3659	exon2			ACTTTATTAATCC		CCDS4155.1	5q23-q31	2008-07-18			ENSG00000125347	ENSG00000125347			6116	protein-coding gene	gene with protein product	"interferon regulatory factor-1"	147575				2726461, 1680796	Standard	NM_002198		Approved	MAR	uc003kxa.2	P10914	OTTHUMG00000059497	ENST00000245414.4:c.83A>C	5.37:g.131825088T>G	ENSP00000245414:p.Asn28Thr	69	0	0		48	19	0.395833	NM_002198	Q96GG7	Missense_Mutation	SNP	ENST00000245414.4	37	CCDS4155.1	.	.	.	.	.	.	.	.	.	.	T	28.7	4.943292	0.92593	.	.	ENSG00000125347	ENST00000245414;ENST00000405885;ENST00000437654;ENST00000458069	D;D;D;D	0.98264	-4.83;-4.83;-4.83;-4.83	5.59	5.59	0.84812	Interferon regulatory factor, conserved site (1);Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (3);	0.081526	0.85682	D	0.000000	D	0.98918	0.9633	M	0.83223	2.63	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.77557	0.99;0.953	D	0.99840	1.1061	10	0.87932	D	0	-31.594	16.0664	0.80878	0.0:0.0:0.0:1.0	.	28;28	Q5FBX3;P10914	.;IRF1_HUMAN	T	28	ENSP00000245414:N28T;ENSP00000384406:N28T;ENSP00000405655:N28T;ENSP00000396318:N28T	ENSP00000245414:N28T	N	-	2	0	IRF1	131852987	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.905000	0.87416	2.254000	0.74563	0.459000	0.35465	AAT	.	.	none		0.463	IRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132340.1	NM_002198		G	131825088	T	G	131825088	3	3	29	1	0	0	0	0	1	0	0	0	7836	1493	52	5	930	5	IRF1	5	131825088	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	5	131825088	49090172	267	12508	154	2									
GDF9	2661	hgsc.bcm.edu	37	chr5	132200000	132200000	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctggctgcagcctaggtgAcccacctcgcccaacagata	9	7	10	15	1	1	2	0	1	1	1	2	2	1	2	4	2	3	2	4	2	3	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:132200000A>C	ENST00000378673.2	-	2	1092	c.226T>G	c.(226-228)Tca>Gca	p.S76A	UQCRQ_ENST00000378670.3_5'Flank|GDF9_ENST00000296875.2_Missense_Mutation_p.S76A|UQCRQ_ENST00000378667.1_5'Flank|UQCRQ_ENST00000378665.1_5'Flank|GDF9_ENST00000464378.1_5'UTR			O60383	GDF9_HUMAN	growth differentiation factor 9	76					female gamete generation (GO:0007292)|negative regulation of cell growth (GO:0030308)|oocyte growth (GO:0001555)|positive regulation of cell proliferation (GO:0008284)|regulation of progesterone secretion (GO:2000870)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	growth factor activity (GO:0008083)			NS(1)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	22		all_cancers(142;0.105)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGCCTAGGTGACCCACCTCGC	0.498																																					p.S76A		Atlas-SNP	.											.	GDF9	50	.	0			c.T226G						PASS	.						110	117	115					5																	132200000		2203	4300	6503	SO:0001583	missense	2661	exon1			TAGGTGACCCACC		CCDS4162.1, CCDS75299.1	5q31.1	2014-01-30			ENSG00000164404	ENSG00000164404		"Endogenous ligands"	4224	protein-coding gene	gene with protein product		601918				7760846	Standard	NM_005260		Approved		uc003kxz.1	O60383	OTTHUMG00000059842	ENST00000378673.2:c.226T>G	5.37:g.132200000A>C	ENSP00000367942:p.Ser76Ala	95	0	0		100	13	0.13	NM_005260	Q4VAW5	Missense_Mutation	SNP	ENST00000378673.2	37	CCDS4162.1	.	.	.	.	.	.	.	.	.	.	A	4.388	0.071601	0.08436	.	.	ENSG00000164404	ENST00000378673;ENST00000296875	T;T	0.58506	0.33;0.33	5.92	-11.5	0.00074	.	1.261530	0.04922	N	0.455213	T	0.10680	0.0261	N	0.00138	-2.015	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.07271	-1.0781	10	0.05436	T	0.98	.	2.0974	0.03671	0.2333:0.151:0.1436:0.472	.	76	O60383	GDF9_HUMAN	A	76	ENSP00000367942:S76A;ENSP00000296875:S76A	ENSP00000296875:S76A	S	-	1	0	GDF9	132227899	0.000000	0.05858	0.000000	0.03702	0.523000	0.34469	-1.884000	0.01622	-2.824000	0.00342	-0.132000	0.14878	TCA	.	.	none		0.498	GDF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133060.2	NM_005260		C	132200000	A	C	132200000	3	2	29	1	0	0	0	0	1	0	0	0	6327	275	10	5	1146	5	GDF9	5	132200000	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	374912	132200000	48715260	268	12509											
PHF15	23338	hgsc.bcm.edu	37	chr5	133901934	133901934	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctgccaggagcacagtgaCgggggcccacgtaatgagcc	9	6	14	12	2	1	2	0	2	1	0	1	3	1	3	3	3	3	2	3	3	1	2	rs148155246	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:133901934C>T	ENST00000402835.1	+	9	1353	c.1098C>T	c.(1096-1098)gaC>gaT	p.D366D	PHF15_ENST00000282605.4_Silent_p.D366D|PHF15_ENST00000361895.2_Silent_p.D366D|PHF15_ENST00000395003.1_Silent_p.D366D																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)			AGCACAGTGACGGGGGCCCAC	0.587													C|||	4	0.000798722	0.0	0.0	5008	,	,		20135	0.0		0.004	False		,,,				2504	0.0				p.D366D		Atlas-SNP	.											.	PHF15	60	.	0			c.C1098T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	93	83	86		1098	-11.1	0	5	dbSNP_134	86	32,8568	21.6+/-65.8	0,32,4268	no	coding-synonymous	PHF15	NM_015288.4		0,34,6469	TT,TC,CC		0.3721,0.0454,0.2614		366/791	133901934	34,12972	2203	4300	6503	SO:0001819	synonymous_variant	23338	exon9			CAGTGACGGGGGC																												ENST00000402835.1:c.1098C>T	5.37:g.133901934C>T		114	0	0		84	43	0.511905	NM_015288		Silent	SNP	ENST00000402835.1	37																																																																																				C|0.997;T|0.003	0.003	strong		0.587	PHF15-007	PUTATIVE	alternative_5_UTR|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000318543.1			T	133901934	C	T	133901934	2	4	29	1	0	0	0	0	0	0	0	1	11835	535	19	1		1	PHF15	5	133901934	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1701934	133901934	47013326	269	12510											
C5orf20	140947	hgsc.bcm.edu	37	chr5	134782396	134782396	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaacgggtagagtctgaaacTacaaaccagatgtttccggg	13	8	12	8	2	1	3	0	1	1	2	2	4	2	3	2	2	4	2	2	2	5	3	rs67187482	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:134782396T>A	ENST00000503143.2	-	1	642	c.403A>T	c.(403-405)Agt>Tgt	p.S135C	TIFAB_ENST00000537858.1_3'UTR	NM_130848.2	NP_570900.1	Q8TF63	DCNP1_HUMAN		135						nucleus (GO:0005634)				endometrium(1)|lung(1)|prostate(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGTCTGAAACTACAAACCAGA	0.547													T|||	430	0.0858626	0.2867	0.0418	5008	,	,		19738	0.0		0.0179	False		,,,				2504	0.0041				p.S135C		Atlas-SNP	.											.	C5orf20	16	.	0			c.A403T						PASS	.	T	CYS/SER	1116,3290	402.4+/-332.3	149,818,1236	132	143	139		403	-1.8	0	5	dbSNP_130	139	119,8481	61.7+/-123.6	1,117,4182	yes	missense	C5orf20	NM_130848.2	112	150,935,5418	AA,AT,TT		1.3837,25.3291,9.4956	benign	135/245	134782396	1235,11771	2203	4300	6503	SO:0001583	missense	140947	exon1			TGAAACTACAAAC																												ENST00000503143.2:c.403A>T	5.37:g.134782396T>A	ENSP00000421871:p.Ser135Cys	76	0	0		79	31	0.392405	NM_130848		Missense_Mutation	SNP	ENST00000503143.2	37	CCDS4186.1	163	0.07463369963369963	132	0.2682926829268293	14	0.03867403314917127	0	0.0	17	0.022427440633245383	T	4.521	0.096694	0.08681	0.253291	0.013837	ENSG00000251380	ENST00000503143	T	0.39056	1.1	2.85	-1.79	0.07932	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.32508	-0.9904	8	0.87932	D	0	.	4.0496	0.09790	0.3788:0.41:0.0:0.2112	.	135	Q8TF63	DCNP1_HUMAN	C	135	ENSP00000421871:S135C	ENSP00000421871:S135C	S	-	1	0	C5orf20	134810295	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.310000	0.19356	-0.278000	0.09180	-0.892000	0.02923	AGT	T|0.905;A|0.095	0.095	strong		0.547	C5orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372531.1			A	134782396	T	A	134782396	3	1	29	1	0	0	0	0	1	0	0	0	2286	1522	53	5	335	5	C5orf20	5	134782396	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	880462	134782396	46132864	270	12511											
C5orf20	140947	hgsc.bcm.edu	37	chr5	134782443	134782443	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cccgcctggtctggcctgtcTtccttctgctgctatgcagt	2	14	10	15	1	3	0	0	0	3	0	4	0	4	0	4	2	3	3	4	2	1	3	rs113429044	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:134782443T>C	ENST00000503143.2	-	1	595	c.356A>G	c.(355-357)aAg>aGg	p.K119R	TIFAB_ENST00000537858.1_3'UTR	NM_130848.2	NP_570900.1	Q8TF63	DCNP1_HUMAN		119						nucleus (GO:0005634)				endometrium(1)|lung(1)|prostate(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CTGGCCTGTCTTCCTTCTGCT	0.547													T|||	452	0.0902556	0.3033	0.0418	5008	,	,		19866	0.0		0.0179	False		,,,				2504	0.0041				p.K119R		Atlas-SNP	.											.	C5orf20	16	.	0			c.A356G						PASS	.	T	ARG/LYS	1160,3246	410.9+/-335.5	154,852,1197	112	120	117		356	0.2	0	5	dbSNP_132	117	119,8481	61.7+/-123.6	1,117,4182	yes	missense	C5orf20	NM_130848.2	26	155,969,5379	CC,CT,TT		1.3837,26.3277,9.8339	benign	119/245	134782443	1279,11727	2203	4300	6503	SO:0001583	missense	140947	exon1			CCTGTCTTCCTTC																												ENST00000503143.2:c.356A>G	5.37:g.134782443T>C	ENSP00000421871:p.Lys119Arg	65	0	0		58	24	0.413793	NM_130848		Missense_Mutation	SNP	ENST00000503143.2	37	CCDS4186.1	170	0.07783882783882784	139	0.28252032520325204	14	0.03867403314917127	0	0.0	17	0.022427440633245383	T	5.813	0.334340	0.11013	0.263277	0.013837	ENSG00000251380	ENST00000503143	T	0.37915	1.17	2.78	0.236	0.15471	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	5.000000000032756E-6	B	0.16603	0.018	B	0.08055	0.003	T	0.36089	-0.9762	8	0.87932	D	0	.	3.1238	0.06400	0.5045:0.2511:0.0:0.2444	.	119	Q8TF63	DCNP1_HUMAN	R	119	ENSP00000421871:K119R	ENSP00000421871:K119R	K	-	2	0	C5orf20	134810342	0.000000	0.05858	0.013000	0.15412	0.047000	0.14425	-0.373000	0.07494	0.043000	0.15746	-0.669000	0.03829	AAG	T|0.902;C|0.098	0.098	strong		0.547	C5orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372531.1			C	134782443	T	C	134782443	3	2	29	1	0	0	0	0	1	0	0	0	2286	1609	56	3	382	3	C5orf20	5	134782443	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	47	134782443	46132817	271	12512											
CXCL14	9547	hgsc.bcm.edu	37	chr5	134914455	134914455	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcaggagcagcgcggccGccaggagcctcatgctgacc	8	3	15	15	3	1	1	1	1	0	0	1	3	1	3	4	3	5	4	4	3	0	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:134914455G>A	ENST00000337225.5	-	1	514	c.50C>T	c.(49-51)gCg>gTg	p.A17V	CTC-321K16.1_ENST00000509372.1_RNA|CXCL14_ENST00000512158.1_Missense_Mutation_p.A5V|CTC-321K16.1_ENST00000514446.1_RNA	NM_004887.4	NP_004878.2	O95715	CXL14_HUMAN	chemokine (C-X-C motif) ligand 14	17					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)			CAGCGCGGCCGCCAGGAGCCT	0.736																																					p.A17V		Atlas-SNP	.											.	CXCL14	13	.	0			c.C50T						PASS	.						7	7	7					5																	134914455		1872	3636	5508	SO:0001583	missense	9547	exon1			GCGGCCGCCAGGA	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.50C>T	5.37:g.134914455G>A	ENSP00000337065:p.Ala17Val	52	0	0		23	7	0.304348	NM_004887	B3KQU8|Q6UW97|Q86U69|Q9BTR1|Q9NS21	Missense_Mutation	SNP	ENST00000337225.5	37	CCDS4188.1	.	.	.	.	.	.	.	.	.	.	G	15.04	2.715059	0.48622	.	.	ENSG00000145824	ENST00000337225;ENST00000512158	.	.	.	4.67	2.87	0.33458	.	0.397487	0.29355	N	0.012388	T	0.17534	0.0421	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.06405	0.002	T	0.15752	-1.0426	9	0.42905	T	0.14	12.4482	7.9254	0.29872	0.0825:0.0:0.7596:0.1579	.	17	O95715	CXL14_HUMAN	V	17;5	.	ENSP00000337065:A17V	A	-	2	0	CXCL14	134942354	0.997000	0.39634	0.016000	0.15963	0.994000	0.84299	3.004000	0.49513	0.404000	0.25506	0.563000	0.77884	GCG	.	.	none		0.736	CXCL14-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_004887		A	134914455	G	A	134914455	3	1	29	1	0	0	0	0	1	0	0	0	4084	1087	38	1	301	1	CXCL14	5	134914455	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	132012	134914455	46000805	272	12513											
SPOCK1	6695	hgsc.bcm.edu	37	chr5	136834138	136834138	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actggtcattgtctaggaaaTtgccgtggttggggcccgcg	6	11	15	9	3	2	0	1	0	1	0	2	1	2	1	2	5	1	1	2	5	2	4	rs111393448	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:136834138T>C	ENST00000394945.1	-	2	279	c.110A>G	c.(109-111)aAt>aGt	p.N37S	SPOCK1_ENST00000282223.7_Missense_Mutation_p.N37S	NM_004598.3	NP_004589.1	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1	37					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)			GTCTAGGAAATTGCCGTGGTT	0.682													T|||	19	0.00379393	0.0	0.0058	5008	,	,		9286	0.0		0.0129	False		,,,				2504	0.002				p.N37S		Atlas-SNP	.											.	SPOCK1	58	.	0			c.A110G						PASS	.	T	SER/ASN	9,4397		0,9,2194	22	21	22		110	3.7	1	5	dbSNP_132	22	106,8492		3,100,4196	yes	missense	SPOCK1	NM_004598.3	46	3,109,6390	CC,CT,TT		1.2328,0.2043,0.8843	benign	37/440	136834138	115,12889	2203	4299	6502	SO:0001583	missense	6695	exon2			AGGAAATTGCCGT	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.110A>G	5.37:g.136834138T>C	ENSP00000378401:p.Asn37Ser	44	0	0		41	20	0.487805	NM_004598	B3KSW3|Q59EW0|Q8N630|Q9UCL8	Missense_Mutation	SNP	ENST00000394945.1	37	CCDS4191.1	14	0.00641025641025641	0	0.0	2	0.0055248618784530384	0	0.0	12	0.0158311345646438	T	24.2	4.510460	0.85389	0.002043	0.012328	ENSG00000152377	ENST00000394945;ENST00000282223;ENST00000505690	T;T;T	0.58940	0.3;0.3;0.34	3.66	3.66	0.41972	.	0.344437	0.23803	N	0.044419	T	0.33498	0.0865	L	0.51914	1.62	0.27215	N	0.959807	B	0.15930	0.015	B	0.14578	0.011	T	0.44112	-0.9349	10	0.56958	D	0.05	.	10.3639	0.44012	0.0:0.0:0.0:1.0	.	37	Q08629	TICN1_HUMAN	S	37	ENSP00000378401:N37S;ENSP00000282223:N37S;ENSP00000424517:N37S	ENSP00000282223:N37S	N	-	2	0	SPOCK1	136862037	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.481000	0.53179	1.439000	0.47511	0.379000	0.24179	AAT	T|0.991;C|0.009	0.009	strong		0.682	SPOCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251222.1	NM_004598		C	136834138	T	C	136834138	3	2	29	1	0	0	0	0	1	0	0	0	15094	1493	52	3	1249	3	SPOCK1	5	136834138	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	1919683	136834138	44081122	273	12514											
CDC25C	995	hgsc.bcm.edu	37	chr5	137627769	137627769	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tggcctgttcaagttctctgGcatcgacggggagcgatata	8	11	13	9	3	2	0	1	0	1	0	4	3	2	1	1	4	1	3	1	4	3	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:137627769G>C	ENST00000323760.6	-	8	930	c.652C>G	c.(652-654)Cca>Gca	p.P218A	CDC25C_ENST00000348983.3_Missense_Mutation_p.P145A|CDC25C_ENST00000356505.3_Missense_Mutation_p.P188A|CDC25C_ENST00000513970.1_Missense_Mutation_p.P218A|CDC25C_ENST00000514555.1_Missense_Mutation_p.P188A|CDC25C_ENST00000415130.2_Missense_Mutation_p.P145A|CDC25C_ENST00000357274.3_Missense_Mutation_p.P175A	NM_001790.3	NP_001781.2	P30307	MPIP3_HUMAN	cell division cycle 25C	218					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)			AAGTTCTCTGGCATCGACGGG	0.443																																					p.P218A		Atlas-SNP	.											.	CDC25C	37	.	0			c.C652G						PASS	.						145	150	148					5																	137627769		2203	4300	6503	SO:0001583	missense	995	exon8			TCTCTGGCATCGA	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.652C>G	5.37:g.137627769G>C	ENSP00000321656:p.Pro218Ala	97	0	0		91	32	0.351648	NM_001790	D3DQB8|Q96PL3|Q9H168|Q9H2E8|Q9H2E9|Q9H2F1	Missense_Mutation	SNP	ENST00000323760.6	37	CCDS4202.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.68|15.68	2.905323|2.905323	0.52333|0.52333	.|.	.|.	ENSG00000158402|ENSG00000158402	ENST00000514017|ENST00000323760;ENST00000356505;ENST00000357274;ENST00000348983;ENST00000415130;ENST00000513970;ENST00000534892;ENST00000514555;ENST00000503022	.|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	3.09|3.09	3.09|3.09	0.35607|0.35607	.|.	.|0.258164	.|0.31461	.|N	.|0.007614	T|T	0.54695|0.54695	0.1874|0.1874	M|M	0.62723|0.62723	1.935|1.935	0.33220|0.33220	D|D	0.554573|0.554573	.|D;D;D;D	.|0.76494	.|0.974;0.987;0.999;0.979	.|P;P;D;P	.|0.80764	.|0.747;0.747;0.994;0.836	T|T	0.67150|0.67150	-0.5743|-0.5743	5|10	.|0.51188	.|T	.|0.08	-7.2435|-7.2435	14.0879|14.0879	0.64971|0.64971	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|235;188;145;218	.|G3V1P6;P30307-2;P30307-4;P30307	.|.;.;.;MPIP3_HUMAN	G|A	12|218;188;175;145;145;218;235;188;218	.|ENSP00000321656:P218A;ENSP00000348898:P188A;ENSP00000349821:P175A;ENSP00000345205:P145A;ENSP00000392631:P145A;ENSP00000424795:P218A;ENSP00000425470:P188A;ENSP00000427251:P218A	.|ENSP00000321656:P218A	A|P	-|-	2|1	0|0	CDC25C|CDC25C	137655668|137655668	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.412000|0.412000	0.31113|0.31113	4.268000|4.268000	0.58883|0.58883	2.012000|2.012000	0.59069|0.59069	0.557000|0.557000	0.71058|0.71058	GCC|CCA	.	.	none		0.443	CDC25C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251280.1			C	137627769	G	C	137627769	3	2	29	1	0	0	0	0	1	0	0	0	3066	1203	42	4	797	4	CDC25C	5	137627769	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	793631	137627769	43287491	274	12515											
SLC23A1	9963	hgsc.bcm.edu	37	chr5	138715033	138715034	+	Frame_Shift_Ins	INS	-	-	C																															ccgcagtcaccgtgggcaggINSccccactgacctgtgctcgg																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:138715033_138715034insC	ENST00000348729.3	-	9	981_982	c.935_936insG	c.(934-936)ggcfs	p.G312fs	SLC23A1_ENST00000353963.3_Frame_Shift_Ins_p.G316fs|SLC23A1_ENST00000503919.1_5'Flank	NM_005847.4	NP_005838	Q9UHI7	S23A1_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 1	312					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)	CCGTGGGCAGGCCCCACTGACC	0.599																																					p.G316fs		Pindel,Atlas-Indel	.											.	SLC23A1	51	.	0			c.948_949insG						PASS	.																																			SO:0001589	frameshift_variant	9963	exon9			.	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.936dupG	5.37:g.138715037_138715037dupC	ENSP00000302701:p.Gly312fs	85	0	.		99	16	0.162	NM_152685	O95191|Q8WWB6|Q9UGH4|Q9UI39	Frame_Shift_Ins	INS	ENST00000348729.3	37	CCDS4212.1																																																																																			.	.	none		0.599	SLC23A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374185.1	NM_152685		C	138715034	-	C	138715033	7	5	29	1	0	1	1	0	0	0	0	0	14477	1190	42	0	884	0	SLC23A1	5	138715033	Frame_Shift_Ins	INS	-	TCGA-GR-7351-01A-11D-2210-10	1087264	138715033	42200227	275	12516											
PCDHA1	56147	hgsc.bcm.edu	37	chr5	140167033	140167033	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggtgccaacgggcaggtgacTtgctccttaatgccccacgt	7	9	12	13	2	0	1	0	1	0	0	1	1	1	1	4	3	4	2	4	3	2	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140167033T>G	ENST00000504120.2	+	1	1158	c.1158T>G	c.(1156-1158)acT>acG	p.T386T	PCDHA1_ENST00000394633.3_Silent_p.T386T|PCDHA1_ENST00000378133.3_Silent_p.T386T	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	386	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)			GGCAGGTGACTTGCTCCTTAA	0.567																																					p.T386T		Atlas-SNP	.											.	PCDHA1	387	.	0			c.T1158G						PASS	.						125	109	114					5																	140167033		2203	4300	6503	SO:0001819	synonymous_variant	56147	exon1			GGTGACTTGCTCC	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.1158T>G	5.37:g.140167033T>G		116	0	0		100	18	0.18	NM_031411	O75288|Q9NRT7	Silent	SNP	ENST00000504120.2	37	CCDS54913.1																																																																																			.	.	none		0.567	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900		G	140167033	T	G	140167033	2	3	29	1	0	0	0	0	0	0	0	1	11528	1596	56	5		5	PCDHA1	5	140167033	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	1452000	140167033	40748227	276	12517											
PCDHA13	56136	hgsc.bcm.edu	37	chr5	140263210	140263210	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccgacgtgaacgacaacgcgCcggcgttcgcgcagcccgag	8	3	14	16	10	0	1	0	1	0	0	1	4	0	1	3	1	3	2	3	1	2	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140263210C>G	ENST00000289272.2	+	1	1357	c.1357C>G	c.(1357-1359)Ccg>Gcg	p.P453A	PCDHA6_ENST00000529310.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA13_ENST00000409494.1_Missense_Mutation_p.P453A|PCDHA2_ENST00000526136.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	453	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)|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)			CGACAACGCGCCGGCGTTCGC	0.672																																					p.P453A	Melanoma(147;1739 1852 5500 27947 37288)	Atlas-SNP	.											PCDHA13,NS,carcinoma,-2,1	PCDHA13	213	1	0			c.C1357G						PASS	.						69	73	72					5																	140263210		2203	4299	6502	SO:0001583	missense	56136	exon1			AACGCGCCGGCGT	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.1357C>G	5.37:g.140263210C>G	ENSP00000289272:p.Pro453Ala	75	0	0		72	6	0.0833333	NM_031865	O75277	Missense_Mutation	SNP	ENST00000289272.2	37	CCDS4240.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.388941	0.82902	.	.	ENSG00000239389	ENST00000409494;ENST00000289272	D;D	0.84660	-1.88;-1.88	5.15	5.15	0.70609	Cadherin (5);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	D	0.96046	0.8712	H	0.99299	4.505	0.49051	D	0.999749	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.81914	0.994;0.989;0.995	D	0.98200	1.0467	9	0.87932	D	0	.	18.2655	0.90051	0.0:1.0:0.0:0.0	.	453;453;453	Q9Y5I0;C9JA99;Q9Y5I0-2	PCDAD_HUMAN;.;.	A	453	ENSP00000386821:P453A;ENSP00000289272:P453A	ENSP00000289272:P453A	P	+	1	0	PCDHA13	140243394	1.000000	0.71417	0.995000	0.50966	0.967000	0.64934	5.813000	0.69201	2.386000	0.81285	0.556000	0.70494	CCG	.	.	none		0.672	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		G	140263210	C	G	140263210	3	3	29	1	0	0	0	0	1	0	0	0	11532	739	26	4	1359	4	PCDHA13	5	140263210	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	96177	140263210	40652050	277	12518											
PCDHAC1	56135	hgsc.bcm.edu	37	chr5	140306924	140306924	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttactctcccgaatgcccaAgatgacgacgagggaagcaa	13	7	10	11	3	1	2	0	1	1	1	2	6	1	3	2	1	3	1	2	1	5	2	rs532353795		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140306924A>T	ENST00000253807.2	+	1	447	c.447A>T	c.(445-447)caA>caT	p.Q149H	PCDHA6_ENST00000529310.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHAC1_ENST00000409700.3_Missense_Mutation_p.Q149H|PCDHA8_ENST00000531613.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1	149	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)			CGAATGCCCAAGATGACGACG	0.587																																					p.Q149H		Atlas-SNP	.											.	PCDHAC1	141	.	0			c.A447T						PASS	.						76	79	78					5																	140306924		2203	4300	6503	SO:0001583	missense	56135	exon1			TGCCCAAGATGAC	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.447A>T	5.37:g.140306924A>T	ENSP00000253807:p.Gln149His	95	0	0		71	15	0.211268	NM_031882	Q9Y5F5|Q9Y5I5	Missense_Mutation	SNP	ENST00000253807.2	37	CCDS4241.1	.	.	.	.	.	.	.	.	.	.	A	10.51	1.371097	0.24771	.	.	ENSG00000248383	ENST00000409700;ENST00000253807	T;T	0.51325	0.71;0.71	5.7	1.15	0.20763	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.34861	0.0912	L	0.42686	1.345	0.27250	N	0.95892	B;B	0.20164	0.042;0.004	B;B	0.25405	0.06;0.015	T	0.30621	-0.9972	9	0.18710	T	0.47	.	5.7204	0.17985	0.3761:0.0:0.4813:0.1425	.	149;149	Q9H158;Q9H158-2	PCDC1_HUMAN;.	H	149	ENSP00000386356:Q149H;ENSP00000253807:Q149H	ENSP00000253807:Q149H	Q	+	3	2	PCDHAC1	140287108	0.000000	0.05858	0.999000	0.59377	0.965000	0.64279	-2.304000	0.01134	0.110000	0.17919	0.459000	0.35465	CAA	.	.	none		0.587	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	NM_018898		T	140306924	A	T	140306924	3	4	29	1	0	0	0	0	1	0	0	0	11541	69	3	5	449	5	PCDHAC1	5	140306924	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	43714	140306924	40608336	278	12519											
PCDHB16	57717	hgsc.bcm.edu	37	chr5	140564454	140564454	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgaagccgattatccccaacTtctctccttagggcactagg	9	11	8	13	1	1	1	0	1	1	0	4	2	3	1	4	2	2	1	4	2	5	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140564454T>G	ENST00000361016.2	+	1	3475	c.2320T>G	c.(2320-2322)Ttc>Gtc	p.F774V		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	774					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)			TATCCCCAACTTCTCTCCTTA	0.438																																					p.F774V		Atlas-SNP	.											.	PCDHB16	159	.	0			c.T2320G						PASS	.						84	84	84					5																	140564454		2203	4300	6503	SO:0001583	missense	57717	exon1			CCCAACTTCTCTC	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.2320T>G	5.37:g.140564454T>G	ENSP00000354293:p.Phe774Val	133	0	0		152	50	0.328947	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	37	CCDS4251.1	.	.	.	.	.	.	.	.	.	.	t	10.13	1.265980	0.23136	.	.	ENSG00000196963	ENST00000361016	T	0.50548	0.74	3.79	-0.32	0.12721	.	1.460060	0.04979	N	0.465254	T	0.35970	0.0950	L	0.38531	1.155	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.22730	-1.0208	10	0.44086	T	0.13	.	4.5606	0.12158	0.147:0.379:0.0:0.4741	.	774	Q9NRJ7	PCDBG_HUMAN	V	774	ENSP00000354293:F774V	ENSP00000354293:F774V	F	+	1	0	PCDHB16	140544638	0.000000	0.05858	0.000000	0.03702	0.066000	0.16364	-2.526000	0.00947	-0.228000	0.09869	-0.425000	0.05940	TTC	.	.	none		0.438	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957		G	140564454	T	G	140564454	3	3	29	1	0	0	0	0	1	0	0	0	11550	1609	56	5	2322	5	PCDHB16	5	140564454	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	257530	140564454	40350806	279	12520											
PCDHB11	56125	hgsc.bcm.edu	37	chr5	140580963	140580963	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccacagaccgcggctcccCggctttgagcagcgaggcgc	6	4	14	17	6	0	2	0	1	0	1	1	3	1	2	4	3	2	3	4	3	0	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140580963C>T	ENST00000354757.3	+	1	1616	c.1616C>T	c.(1615-1617)cCg>cTg	p.P539L	PCDHB11_ENST00000536699.1_Missense_Mutation_p.P174L	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	539	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)			CGCGGCTCCCCGGCTTTGAGC	0.677																																					p.P539L		Atlas-SNP	.											.	PCDHB11	162	.	0			c.C1616T						PASS	.						35	48	44					5																	140580963		2202	4297	6499	SO:0001583	missense	56125	exon1			GCTCCCCGGCTTT	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.1616C>T	5.37:g.140580963C>T	ENSP00000346802:p.Pro539Leu	203	0	0		150	59	0.393333	NM_018931	B4DSF7|Q2M223	Missense_Mutation	SNP	ENST00000354757.3	37	CCDS4253.1	.	.	.	.	.	.	.	.	.	.	c	17.38	3.375882	0.61735	.	.	ENSG00000197479	ENST00000536699;ENST00000354757	T;T	0.01647	4.71;4.71	2.51	2.51	0.30379	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.09905	0.0243	M	0.80616	2.505	0.50467	D	0.999876	D	0.89917	1.0	D	0.97110	1.0	T	0.03354	-1.1045	9	0.87932	D	0	.	13.0572	0.58988	0.0:1.0:0.0:0.0	.	539	Q9Y5F2	PCDBB_HUMAN	L	174;539	ENSP00000440344:P174L;ENSP00000346802:P539L	ENSP00000346802:P539L	P	+	2	0	PCDHB11	140561147	0.996000	0.38824	0.014000	0.15608	0.076000	0.17211	3.578000	0.53892	1.412000	0.46977	0.298000	0.19748	CCG	.	.	none		0.677	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931		T	140580963	C	T	140580963	3	4	29	1	0	0	0	0	1	0	0	0	11545	652	23	1	1618	1	PCDHB11	5	140580963	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	16509	140580963	40334297	280	12521											
PCDHGA4	56111	hgsc.bcm.edu	37	chr5	140735361	140735361	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagagctggtgctggaacgCgctctagatcgcgaggaaga	10	6	15	10	4	1	3	0	0	1	3	2	6	1	5	1	3	3	3	1	3	3	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140735361C>T	ENST00000571252.1	+	1	594	c.594C>T	c.(592-594)cgC>cgT	p.R198R	PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	198	Cadherin 2. {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)			TGCTGGAACGCGCTCTAGATC	0.567																																					p.R198R		Atlas-SNP	.											.	PCDHGA4	150	.	0			c.C594T						PASS	.						27	30	29					5																	140735361		2160	4285	6445	SO:0001819	synonymous_variant	56111	exon1			GGAACGCGCTCTA	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.594C>T	5.37:g.140735361C>T		80	0	0		72	31	0.430556	NM_018917	Q9Y5D3	Silent	SNP	ENST00000571252.1	37	CCDS58979.1																																																																																			.	.	none		0.567	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917		T	140735361	C	T	140735361	2	4	29	1	0	0	0	0	0	0	0	1	11565	755	27	1		1	PCDHGA4	5	140735361	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	154398	140735361	40179899	281	12522											
PCDHGA5	56110	hgsc.bcm.edu	37	chr5	140745959	140745959	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ccattgaccctgaggatctgGacctcacactctatcttgtg	8	12	8	13	0	4	2	1	2	3	0	4	4	4	4	3	2	0	0	3	2	1	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140745959G>A	ENST00000518069.1	+	1	2062	c.2062G>A	c.(2062-2064)Gac>Aac	p.D688N	PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron	NM_018918.2|NM_032054.1	NP_061741.1|NP_114443.1	Q9Y5G8	PCDG5_HUMAN	protocadherin gamma subfamily A, 5	688					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)			TGAGGATCTGGACCTCACACT	0.597																																					p.D688N		Atlas-SNP	.											.	PCDHGA5	215	.	0			c.G2062A						PASS	.						286	302	297					5																	140745959		2203	4299	6502	SO:0001583	missense	56110	exon1			GATCTGGACCTCA	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.2062G>A	5.37:g.140745959G>A	ENSP00000429834:p.Asp688Asn	128	0	0		101	48	0.475248	NM_032054	Q2M3F5|Q9Y5D2	Missense_Mutation	SNP	ENST00000518069.1	37	CCDS54925.1	.	.	.	.	.	.	.	.	.	.	.	9.353	1.066093	0.20067	.	.	ENSG00000253485	ENST00000518069	T	0.50001	0.76	4.84	-0.0131	0.13985	.	.	.	.	.	T	0.37652	0.1011	L	0.45422	1.42	0.09310	N	1	B;B	0.12013	0.005;0.001	B;B	0.20384	0.029;0.02	T	0.31138	-0.9954	9	0.25106	T	0.35	.	10.8617	0.46831	0.2605:0.0:0.7395:0.0	.	688;688	Q9Y5G8-2;Q9Y5G8	.;PCDG5_HUMAN	N	688	ENSP00000429834:D688N	ENSP00000429834:D688N	D	+	1	0	PCDHGA5	140726143	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.324000	0.19610	0.125000	0.18397	0.563000	0.77884	GAC	.	.	none		0.597	PCDHGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374742.1	NM_018918		A	140745959	G	A	140745959	3	1	29	1	0	0	0	0	1	0	0	0	11566	1174	41	2	2064	2	PCDHGA5	5	140745959	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	10598	140745959	40169301	282	12523											
PCDHGB3	56102	hgsc.bcm.edu	37	chr5	140751891	140751891	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccgcccgccagcgcctgctgGtcactgtgcgtgatggagga	5	7	15	14	4	1	1	1	1	0	0	1	3	1	3	4	3	3	1	4	3	0	0	rs559633972		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140751891G>A	ENST00000576222.1	+	1	2061	c.1930G>A	c.(1930-1932)Gtc>Atc	p.V644I	PCDHGB1_ENST00000523390.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_5'Flank|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron	NM_018924.2|NM_032097.1	NP_061747.1|NP_115268.1	Q9Y5G1	PCDGF_HUMAN	protocadherin gamma subfamily B, 3	644	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)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGCCTGCTGGTCACTGTGCG	0.647													.|||	1	0.000199681	0.0	0.0	5008	,	,		18457	0.001		0.0	False		,,,				2504	0.0				p.V644I		Atlas-SNP	.											.	PCDHGB3	168	.	0			c.G1930A						PASS	.						44	49	48					5																	140751891		2110	4238	6348	SO:0001583	missense	56102	exon1			CTGCTGGTCACTG	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.1930G>A	5.37:g.140751891G>A	ENSP00000461862:p.Val644Ile	35	0	0		27	9	0.333333	NM_018924	A7E229|Q9Y5C7	Missense_Mutation	SNP	ENST00000576222.1	37	CCDS58980.1																																																																																			.	.	none		0.647	PCDHGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437094.1	NM_018924		A	140751891	G	A	140751891	3	1	29	1	0	0	0	0	1	0	0	0	11573	1261	44	2	1932	2	PCDHGB3	5	140751891	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	5932	140751891	40163369	283	12524											
PCDHGA9	56107	hgsc.bcm.edu	37	chr5	140783628	140783628	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aacagtaattcttcttttcaAtgctcatgaccgagactccg	11	13	6	11	2	4	2	2	1	2	1	5	3	5	2	2	0	2	2	2	0	3	5	rs375910829		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:140783628A>G	ENST00000573521.1	+	1	1109	c.1109A>G	c.(1108-1110)aAt>aGt	p.N370S	PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron	NM_018921.2|NM_032089.1	NP_061744.1|NP_114478.1	Q9Y5G4	PCDG9_HUMAN	protocadherin gamma subfamily A, 9	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)|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)			CTTCTTTTCAATGCTCATGAC	0.398													.|||	1	0.000199681	0.0008	0.0	5008	,	,		19094	0.0		0.0	False		,,,				2504	0.0				p.N370S		Atlas-SNP	.											.	PCDHGA9	110	.	0			c.A1109G						PASS	.	A	,,,,,,,,SER/ASN,,,,,,SER/ASN	1,3923		0,1,1961	51	52	52		,,,,,,,,1109,,,,,,1109	5.3	1	5		52	0,8306		0,0,4153	no	intron,intron,intron,intron,intron,intron,intron,intron,missense,intron,intron,intron,intron,intron,missense	PCDHGB4,PCDHGA8,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_032088.1,NM_032089.1	,,,,,,,,46,,,,,,46	0,1,6114	GG,GA,AA		0.0,0.0255,0.0082	,,,,,,,,,,,,,,	,,,,,,,,370/933,,,,,,370/829	140783628	1,12229	1962	4153	6115	SO:0001583	missense	56107	exon1			TTTTCAATGCTCA	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.1109A>G	5.37:g.140783628A>G	ENSP00000460274:p.Asn370Ser	124	0	0		139	71	0.510791	NM_032089	A2RU65|Q9Y5C9	Missense_Mutation	SNP	ENST00000573521.1	37	CCDS58981.1																																																																																			.	.	weak		0.398	PCDHGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437105.1	NM_018921		G	140783628	A	G	140783628	3	3	29	1	0	0	0	0	1	0	0	0	11570	101	4	3	1111	3	PCDHGA9	5	140783628	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	31737	140783628	40131632	284	12525											
ARAP3	64411	hgsc.bcm.edu	37	chr5	141052986	141052986	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accttgtcactgccaaagtaCatcagactcctcccattgaa	12	10	5	14	0	2	2	2	1	0	1	4	2	4	2	4	0	2	1	4	0	3	3	rs150744263	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:141052986C>T	ENST00000239440.4	-	6	1019	c.954G>A	c.(952-954)atG>atA	p.M318I	ARAP3_ENST00000513878.1_5'Flank|ARAP3_ENST00000508305.1_Missense_Mutation_p.M240I	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	318	PH 1. {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						TGCCAAAGTACATCAGACTCC	0.527													C|||	12	0.00239617	0.0015	0.0014	5008	,	,		17660	0.0		0.0089	False		,,,				2504	0.0				p.M318I		Atlas-SNP	.											.	ARAP3	139	.	0			c.G954A						PASS	.	C	ILE/MET	1,4405	2.1+/-5.4	0,1,2202	114	110	112		954	4.3	1	5	dbSNP_134	112	38,8562	26.3+/-74.7	0,38,4262	yes	missense	ARAP3	NM_022481.5	10	0,39,6464	TT,TC,CC		0.4419,0.0227,0.2999	possibly-damaging	318/1545	141052986	39,12967	2203	4300	6503	SO:0001583	missense	64411	exon6			AAAGTACATCAGA	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.954G>A	5.37:g.141052986C>T	ENSP00000239440:p.Met318Ile	259	1	0.003861		224	104	0.464286	NM_022481	B4DIT1|D3DQE3	Missense_Mutation	SNP	ENST00000239440.4	37	CCDS4266.1	11	0.005036630036630037	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	C	16.27	3.074584	0.55646	2.27E-4	0.004419	ENSG00000120318	ENST00000522690;ENST00000508305;ENST00000239440;ENST00000504448	T;T;T	0.74737	-0.87;-0.87;-0.87	5.21	4.34	0.51931	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.144833	0.64402	D	0.000014	T	0.63757	0.2538	L	0.49640	1.575	0.80722	D	1	B;P	0.34934	0.42;0.476	B;B	0.38921	0.099;0.285	T	0.67252	-0.5717	10	0.44086	T	0.13	.	12.7252	0.57166	0.0:0.9185:0.0:0.0815	.	240;318	G5E9Y3;Q8WWN8	.;ARAP3_HUMAN	I	237;240;318;318	ENSP00000421826:M240I;ENSP00000239440:M318I;ENSP00000421148:M318I	ENSP00000239440:M318I	M	-	3	0	ARAP3	141033170	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.256000	0.51492	1.192000	0.43071	0.557000	0.71058	ATG	C|0.997;T|0.003	0.003	strong		0.527	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481		T	141052986	C	T	141052986	3	4	29	1	0	0	0	0	1	0	0	0	840	478	17	2	3792	2	ARAP3	5	141052986	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	269358	141052986	39862274	285	12526											
LARS	51520	hgsc.bcm.edu	37	chr5	145522992	145522992	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacctaatgcccagcggagaCtctgcctgtccatgcaagtt	10	9	9	13	1	1	1	0	0	1	1	2	2	2	1	4	1	5	2	4	1	3	2	rs146906828	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:145522992C>T	ENST00000394434.2	-	19	2026	c.1860G>A	c.(1858-1860)gaG>gaA	p.E620E	LARS_ENST00000545646.1_Silent_p.E574E|LARS_ENST00000510191.1_Silent_p.E566E|LARS_ENST00000274562.9_Silent_p.E593E	NM_020117.9	NP_064502.9	Q9P2J5	SYLC_HUMAN	leucyl-tRNA synthetase	620					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)	CCAGCGGAGACTCTGCCTGTC	0.393													C|||	2	0.000399361	0.0	0.0	5008	,	,		13876	0.002		0.0	False		,,,				2504	0.0				p.E620E		Atlas-SNP	.											.	LARS	100	.	0			c.G1860A						PASS	.	C		0,4406		0,0,2203	196	195	195		1860	-2.7	1	5	dbSNP_134	195	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	LARS	NM_020117.9		0,4,6499	TT,TC,CC		0.0465,0.0,0.0308		620/1177	145522992	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	51520	exon19			CGGAGACTCTGCC	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.1860G>A	5.37:g.145522992C>T		79	0	0		88	45	0.511364	NM_020117	A2RRR4|A7E266|B4DJ10|Q2TU79|Q9NSE1	Silent	SNP	ENST00000394434.2	37	CCDS34265.1																																																																																			C|0.997;T|0.003	0.003	strong		0.393	LARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000373367.1	NM_020117		T	145522992	C	T	145522992	2	4	29	1	0	0	0	0	0	0	0	1	8643	564	20	2		2	LARS	5	145522992	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	4470006	145522992	35392268	286	12527											
ABLIM3	22885	hgsc.bcm.edu	37	chr5	148618836	148618836	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gggaacattatctccctactCccaggtaattcagctgatag	11	11	8	11	0	2	1	1	1	1	0	4	2	3	2	2	2	3	2	2	2	5	5	rs201076202		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:148618836C>T	ENST00000506113.1	+	11	1552	c.1070C>T	c.(1069-1071)tCc>tTc	p.S357F	RP11-331K21.1_ENST00000522685.1_RNA|ABLIM3_ENST00000504238.1_Intron|ABLIM3_ENST00000326685.7_Intron|RP11-331K21.1_ENST00000512647.2_RNA|ABLIM3_ENST00000519549.1_3'UTR|ABLIM3_ENST00000309868.7_Missense_Mutation_p.S357F|ABLIM3_ENST00000508983.1_Missense_Mutation_p.S357F|AC012613.2_ENST00000523176.1_RNA|ABLIM3_ENST00000356541.3_Intron			O94929	ABLM3_HUMAN	actin binding LIM protein family, member 3	357					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|cilium assembly (GO:0042384)|lamellipodium assembly (GO:0030032)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTCCCTACTCCCAGGTAATT	0.488																																					p.S357F		Atlas-SNP	.											.	ABLIM3	91	.	0			c.C1070T						PASS	.	C	PHE/SER	1,4405	2.1+/-5.4	0,1,2202	162	154	156		1070	5	1	5		156	2,8598	2.2+/-6.3	0,2,4298	yes	missense	ABLIM3	NM_014945.2	155	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	benign	357/684	148618836	3,13003	2203	4300	6503	SO:0001583	missense	22885	exon12			CCTACTCCCAGGT	AB020650	CCDS4294.1	5q33.1	2008-02-05			ENSG00000173210	ENSG00000173210			29132	protein-coding gene	gene with protein product		611305					Standard	XM_005268392		Approved	KIAA0843	uc003lpy.2	O94929	OTTHUMG00000129932	ENST00000506113.1:c.1070C>T	5.37:g.148618836C>T	ENSP00000425394:p.Ser357Phe	189	0	0		179	85	0.47486	NM_014945	A8K121|Q19VH3|Q658S1|Q68CI5|Q9BV32	Missense_Mutation	SNP	ENST00000506113.1	37	CCDS4294.1	.	.	.	.	.	.	.	.	.	.	C	15.65	2.896731	0.52121	2.27E-4	2.33E-4	ENSG00000173210	ENST00000309868;ENST00000506113;ENST00000508983	T;T;T	0.56103	0.54;0.54;0.48	5.01	5.01	0.66863	.	0.121045	0.56097	D	0.000022	T	0.39835	0.1093	L	0.28400	0.85	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.23797	-1.0178	10	0.10377	T	0.69	.	16.4609	0.84044	0.0:1.0:0.0:0.0	.	357	O94929	ABLM3_HUMAN	F	357	ENSP00000310309:S357F;ENSP00000425394:S357F;ENSP00000420855:S357F	ENSP00000310309:S357F	S	+	2	0	ABLIM3	148599029	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	5.565000	0.67365	2.481000	0.83766	0.462000	0.41574	TCC	.	.	weak		0.488	ABLIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373435.1	NM_014945		T	148618836	C	T	148618836	3	4	29	1	0	0	0	0	1	0	0	0	96	855	30	2	1112	2	ABLIM3	5	148618836	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	3095844	148618836	32296424	287	12528											
AFAP1L1	134265	hgsc.bcm.edu	37	chr5	148695859	148695859	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaccgaggaggaggttccCtgctgtggtgggtccagggc	5	8	17	11	1	0	0	0	0	0	0	3	3	3	2	4	6	1	2	4	6	0	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:148695859C>T	ENST00000296721.4	+	11	1358	c.1260C>T	c.(1258-1260)ccC>ccT	p.P420P	AFAP1L1_ENST00000515000.1_Silent_p.P420P	NM_001146337.1|NM_152406.2	NP_001139809.1|NP_689619.1	Q8TED9	AF1L1_HUMAN	actin filament associated protein 1-like 1	420	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.					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)			AGGAGGTTCCCTGCTGTGGTG	0.647																																					p.P420P		Atlas-SNP	.											.	AFAP1L1	86	.	0			c.C1260T						PASS	.						57	59	58					5																	148695859		2203	4300	6503	SO:0001819	synonymous_variant	134265	exon11			GGTTCCCTGCTGT	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.1260C>T	5.37:g.148695859C>T		91	0	0		124	13	0.104839	NM_001146337	Q08AN4|Q08AN5|Q8IW82|Q8N8Z5|Q8N9Q4	Silent	SNP	ENST00000296721.4	37	CCDS34274.1																																																																																			.	.	none		0.647	AFAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373443.1	NM_152406		T	148695859	C	T	148695859	2	4	29	1	0	0	0	0	0	0	0	1	354	668	24	2		2	AFAP1L1	5	148695859	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	77023	148695859	32219401	288	12529											
CSNK1A1	1452	hgsc.bcm.edu	37	chr5	148904609	148904609	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taatcaaaatttcacataccTggtcagctaacataagtaca	17	11	4	9	0	3	0	3	0	0	0	3	0	3	0	1	1	4	2	1	1	7	6			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:148904609T>A	ENST00000377843.2	-	3	835	c.356A>T	c.(355-357)cAg>cTg	p.Q119L	CSNK1A1_ENST00000504676.1_Splice_Site_p.Q30L|CSNK1A1_ENST00000261798.5_Splice_Site_p.Q119L|CSNK1A1_ENST00000515435.1_Splice_Site_p.Q30L|CSNK1A1_ENST00000515768.1_Splice_Site_p.Q119L	NM_001025105.1|NM_001892.4	NP_001020276.1|NP_001883.4	P48729	KC1A_HUMAN	casein kinase 1, alpha 1	119	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)		TTCACATACCTGGTCAGCTAA	0.348																																					p.Q119L	Colon(5;64 69 1309 10383)	Atlas-SNP	.											.	CSNK1A1	63	.	0			c.A356T						PASS	.						63	61	62					5																	148904609		2080	4245	6325	SO:0001630	splice_region_variant	1452	exon3			CATACCTGGTCAG	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.357+1A>T	5.37:g.148904609T>A		212	0	0		261	18	0.0689655	NM_001025105	D3DQG0|D3DQG1|Q4JJA0|Q5U046|Q5U047|Q6FGA2|Q71TU5|Q96HD2|Q9UDK3	Missense_Mutation	SNP	ENST00000377843.2	37	CCDS47303.1	.	.	.	.	.	.	.	.	.	.	T	31	5.103355	0.94245	.	.	ENSG00000113712	ENST00000261798;ENST00000377843;ENST00000504676;ENST00000515435;ENST00000322237;ENST00000515768	T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58	5.69	5.69	0.88448	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	U	0.000000	T	0.73024	0.3534	H	0.99058	4.415	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;0.999;0.999;1.0	D;D;D;D;D	0.83275	0.996;0.995;0.983;0.976;0.992	D	0.85007	0.0903	10	0.87932	D	0	.	15.9537	0.79865	0.0:0.0:0.0:1.0	.	30;119;119;119;30	B4DER9;Q71TU5;P48729;P48729-2;D6REM4	.;.;KC1A_HUMAN;.;.	L	119;119;30;30;119;119	ENSP00000261798:Q119L;ENSP00000367074:Q119L;ENSP00000426747:Q30L;ENSP00000427031:Q30L;ENSP00000421689:Q119L	ENSP00000261798:Q119L	Q	-	2	0	CSNK1A1	148884802	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.040000	0.89188	2.179000	0.69175	0.528000	0.53228	CAG	.	.	none		0.348	CSNK1A1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001892	Missense_Mutation	A	148904609	T	A	148904609	5	1	29	1	0	0	0	0	0	0	1	0	3952	1594	55	5	777	5	CSNK1A1	5	148904609	Splice_Site	SNP	T	TCGA-GR-7351-01A-11D-2210-10	208750	148904609	32010651	289	12530											
CSF1R	1436	hgsc.bcm.edu	37	chr5	149460355	149460355	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acatagaggtggatggcggcGctgcctcccagggggtctcc	6	7	16	12	2	1	1	0	0	1	1	3	2	2	2	3	6	1	1	3	6	1	1	rs41287102	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:149460355G>A	ENST00000286301.3	-	3	573	c.282C>T	c.(280-282)agC>agT	p.S94S	CSF1R_ENST00000543093.1_Silent_p.S94S	NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	94	Ig-like C2-type 1.				cell proliferation (GO:0008283)|cell-cell junction maintenance (GO:0045217)|cellular response to cytokine stimulus (GO:0071345)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cytokine-mediated signaling pathway (GO:0019221)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary gland duct morphogenesis (GO:0060603)|monocyte differentiation (GO:0030224)|multicellular organismal development (GO:0007275)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of bone resorption (GO:0045124)|regulation of cell shape (GO:0008360)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|macrophage colony-stimulating factor receptor activity (GO:0005011)|protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(38)|kidney(2)|large_intestine(6)|liver(3)|lung(23)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	93			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	GGATGGCGGCGCTGCCTCCCA	0.587																																					p.S94S		Atlas-SNP	.											.	CSF1R	250	.	0			c.C282T						PASS	.	G		4,4402	6.2+/-15.9	0,4,2199	73	55	61		282	-9.1	0	5	dbSNP_127	61	67,8533	40.8+/-97.7	0,67,4233	no	coding-synonymous	CSF1R	NM_005211.3		0,71,6432	AA,AG,GG		0.7791,0.0908,0.5459		94/973	149460355	71,12935	2203	4300	6503	SO:0001819	synonymous_variant	1436	exon3			GGCGGCGCTGCCT	U63963	CCDS4302.1	5q32	2013-01-11	2008-08-01		ENSG00000182578	ENSG00000182578		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	2433	protein-coding gene	gene with protein product		164770	"McDonough feline sarcoma viral (v-fms) oncogene homolog"	FMS		1611909	Standard	NM_005211		Approved	C-FMS, CSFR, CD115	uc003lrm.3	P07333	OTTHUMG00000130050	ENST00000286301.3:c.282C>T	5.37:g.149460355G>A		149	0	0		151	70	0.463576	NM_005211	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Silent	SNP	ENST00000286301.3	37	CCDS4302.1																																																																																			G|0.994;A|0.006	0.006	strong		0.587	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2	NM_005211		A	149460355	G	A	149460355	2	1	29	1	0	0	0	0	0	0	0	1	3934	1078	38	1		1	CSF1R	5	149460355	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	555746	149460355	31454905	290	12531											
ARSI	340075	hgsc.bcm.edu	37	chr5	149677635	149677635	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acactgttgttgtagaaaccGtagcgcttgagggcccaggt	9	10	13	9	2	0	2	0	1	0	1	0	2	0	2	2	2	2	5	2	2	3	5	rs139203947	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:149677635G>A	ENST00000328668.7	-	2	1431	c.852C>T	c.(850-852)taC>taT	p.Y284Y		NM_001012301.2	NP_001012301.1	Q5FYB1	ARSI_HUMAN	arylsulfatase family, member I	284					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)			TGTAGAAACCGTAGCGCTTGA	0.602													G|||	5	0.000998403	0.0	0.0	5008	,	,		22146	0.0		0.005	False		,,,				2504	0.0				p.Y284Y		Atlas-SNP	.											.	ARSI	65	.	0			c.C852T						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	39	33	35		852	-7.8	0.6	5	dbSNP_134	35	15,8585	11.2+/-40.8	0,15,4285	no	coding-synonymous	ARSI	NM_001012301.2		0,17,6486	AA,AG,GG		0.1744,0.0454,0.1307		284/570	149677635	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	340075	exon2			GAAACCGTAGCGC	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.852C>T	5.37:g.149677635G>A		44	0	0		47	23	0.489362	NM_001012301	A1L3B0|B3KV22|B7XD03	Silent	SNP	ENST00000328668.7	37	CCDS34275.1																																																																																			G|0.999;A|0.001	0.001	strong		0.602	ARSI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373681.1	NM_001012301		A	149677635	G	A	149677635	2	1	29	1	0	0	0	0	0	0	0	1	994	1140	40	1		1	ARSI	5	149677635	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	217280	149677635	31237625	291	12532											
NMUR2	56923	hgsc.bcm.edu	37	chr5	151777633	151777633	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacttacacagcatcttgtTgactgattttctgcagggtc	8	14	9	10	0	2	2	0	2	2	0	3	2	2	2	0	1	3	4	0	1	1	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:151777633T>G	ENST00000255262.3	-	2	964	c.799A>C	c.(799-801)Aac>Cac	p.N267H	NMUR2_ENST00000518933.1_5'UTR	NM_020167.4	NP_064552.3	Q9GZQ4	NMUR2_HUMAN	neuromedin U receptor 2	267					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)	p.N267H(1)		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)			AGCATCTTGTTGACTGATTTT	0.398																																					p.N267H		Atlas-SNP	.											NMUR2,NS,carcinoma,0,1	NMUR2	111	1	1	Substitution - Missense(1)	lung(1)	c.A799C						PASS	.						138	131	133					5																	151777633		2203	4300	6503	SO:0001583	missense	56923	exon2			TCTTGTTGACTGA	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.799A>C	5.37:g.151777633T>G	ENSP00000255262:p.Asn267His	64	0	0		83	5	0.060241	NM_020167	Q7LC54|Q96AM5|Q9NRA6	Missense_Mutation	SNP	ENST00000255262.3	37	CCDS4321.1	.	.	.	.	.	.	.	.	.	.	T	14.62	2.588339	0.46110	.	.	ENSG00000132911	ENST00000255262	T	0.72051	-0.62	5.8	4.62	0.57501	GPCR, rhodopsin-like superfamily (1);	0.218017	0.40469	N	0.001094	T	0.67720	0.2923	L	0.48642	1.525	0.25169	N	0.990293	P	0.43938	0.822	P	0.44623	0.455	T	0.62134	-0.6918	10	0.56958	D	0.05	-12.0026	12.2618	0.54655	0.0:0.0:0.1421:0.8579	.	267	Q9GZQ4	NMUR2_HUMAN	H	267	ENSP00000255262:N267H	ENSP00000255262:N267H	N	-	1	0	NMUR2	151757826	1.000000	0.71417	0.985000	0.45067	0.451000	0.32288	2.866000	0.48420	0.990000	0.38787	0.477000	0.44152	AAC	.	.	none		0.398	NMUR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252439.1	NM_020167		G	151777633	T	G	151777633	3	3	29	1	0	0	0	0	1	0	0	0	10516	1812	63	5	460	5	NMUR2	5	151777633	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	2099998	151777633	29137627	292	12533											
HAVCR1	26762	hgsc.bcm.edu	37	chr5	156482296	156482296	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gcaacaatatacgccactgtCagacacagctgtattttcta	13	11	6	11	1	2	1	1	0	1	1	2	1	2	1	1	0	3	3	1	0	6	6	rs56084311	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:156482296C>G	ENST00000339252.3	-	2	827	c.295G>C	c.(295-297)Gac>Cac	p.D99H	HAVCR1_ENST00000522693.1_Missense_Mutation_p.D99H|HAVCR1_ENST00000425854.1_Missense_Mutation_p.D99H|HAVCR1_ENST00000523175.1_Missense_Mutation_p.D99H|HAVCR1_ENST00000544197.1_Missense_Mutation_p.D99H	NM_012206.2	NP_036338.2	Q96D42	HAVR1_HUMAN	hepatitis A virus cellular receptor 1	0	Ig-like V-type.				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)			ACGCCACTGTCAGACACAGCT	0.458													C|||	17	0.00339457	0.0008	0.0029	5008	,	,		20324	0.0		0.0129	False		,,,				2504	0.001				p.D99H		Atlas-SNP	.											HAVCR1,NS,carcinoma,+1,1	HAVCR1	84	1	0			c.G295C						PASS	.	C	HIS/ASP,HIS/ASP,HIS/ASP	9,4029		0,9,2010	93	82	85		295,295,295	5.8	1	5	dbSNP_129	85	97,8309		0,97,4106	yes	missense,missense,missense	HAVCR1	NM_001099414.1,NM_001173393.1,NM_012206.2	81,81,81	0,106,6116	GG,GC,CC		1.1539,0.2229,0.8518	probably-damaging,probably-damaging,probably-damaging	99/365,99/365,99/365	156482296	106,12338	2019	4203	6222	SO:0001583	missense	26762	exon3			CACTGTCAGACAC	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.295G>C	5.37:g.156482296C>G	ENSP00000344844:p.Asp99His	112	0	0		133	71	0.533835	NM_001099414	O43656	Missense_Mutation	SNP	ENST00000339252.3	37	CCDS43392.1	12	0.005494505494505495	0	0.0	0	0.0	0	0.0	12	0.0158311345646438	C	13.39	2.222182	0.39300	0.002229	0.011539	ENSG00000113249	ENST00000522693;ENST00000523175;ENST00000339252;ENST00000425854;ENST00000544197;ENST00000518745	D;D;D;D;D;D	0.87729	-2.29;-2.29;-2.29;-2.29;-2.29;-2.29	5.78	5.78	0.91487	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.92227	0.7535	H	0.94771	3.58	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93034	0.6451	10	0.87932	D	0	-45.3525	18.7919	0.91976	0.0:1.0:0.0:0.0	rs56084311	99;99	F1CME6;Q96D42	.;HAVR1_HUMAN	H	99	ENSP00000428524:D99H;ENSP00000427898:D99H;ENSP00000344844:D99H;ENSP00000403333:D99H;ENSP00000440258:D99H;ENSP00000428422:D99H	ENSP00000344844:D99H	D	-	1	0	HAVCR1	156414874	0.995000	0.38212	0.961000	0.40146	0.046000	0.14306	4.840000	0.62817	2.729000	0.93468	0.650000	0.86243	GAC	C|0.992;G|0.008	0.008	strong		0.458	HAVCR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373698.1			G	156482296	C	G	156482296	3	3	29	1	0	0	0	0	1	0	0	0	6982	826	29	4	827	4	HAVCR1	5	156482296	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	4704663	156482296	24432964	293	12534											
RANBP17	64901	hgsc.bcm.edu	37	chr5	170338066	170338066	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttaactgccttaactttgacTtcattggcagttcagcagat	10	15	7	9	0	2	2	2	1	0	1	2	2	2	2	1	1	4	3	1	1	2	6			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:170338066T>G	ENST00000523189.1	+	7	852	c.688T>G	c.(688-690)Ttc>Gtc	p.F230V		NM_022897.3	NP_075048.1	Q9H2T7	RBP17_HUMAN	RAN binding protein 17	230					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)			TAACTTTGACTTCATTGGCAG	0.403			T	TRD@	ALL																																p.F230V		Atlas-SNP	.		Dom	yes		5	5q34	64901	RAN binding protein 17		L	.	RANBP17	108	.	0			c.T688G						PASS	.						87	81	83					5																	170338066		2203	4298	6501	SO:0001583	missense	64901	exon7			TTTGACTTCATTG	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.688T>G	5.37:g.170338066T>G	ENSP00000427975:p.Phe230Val	143	0	0		171	41	0.239766	NM_022897	Q8IU74	Missense_Mutation	SNP	ENST00000523189.1	37	CCDS34287.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	29.1|29.1	4.975804|4.975804	0.92982|0.92982	.|.	.|.	ENSG00000204764|ENSG00000204764	ENST00000523189;ENST00000545246|ENST00000522734	T|.	0.68025|.	-0.3|.	5.43|5.43	5.43|5.43	0.79202|0.79202	Armadillo-type fold (1);|.	0.000000|.	0.64402|.	D|.	0.000008|.	D|D	0.85366|0.85366	0.5680|0.5680	M|M	0.93106|0.93106	3.38|3.38	0.58432|0.58432	D|D	0.999995|0.999995	D|.	0.71674|.	0.998|.	D|.	0.69307|.	0.963|.	D|D	0.89121|0.89121	0.3503|0.3503	10|5	0.87932|.	D|.	0|.	-18.1852|-18.1852	15.4379|15.4379	0.75160|0.75160	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	230|.	Q9H2T7|.	RBP17_HUMAN|.	V|R	230;126|12	ENSP00000427975:F230V|.	ENSP00000373770:F230V|.	F|L	+|+	1|2	0|0	RANBP17|RANBP17	170270644|170270644	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.898000|7.898000	0.87363|0.87363	2.174000|2.174000	0.68829|0.68829	0.533000|0.533000	0.62120|0.62120	TTC|CTT	.	.	none		0.403	RANBP17-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000372036.1	NM_022897		G	170338066	T	G	170338066	3	3	29	1	0	0	0	0	1	0	0	0	13042	1609	56	5	714	5	RANBP17	5	170338066	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	13855770	170338066	10577194	294	12535											
SH3PXD2B	285590	hgsc.bcm.edu	37	chr5	171766135	171766135	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgcagatgtcgacttggtcTtcgccctgaggtggctccgt	4	13	13	11	3	1	2	0	1	1	1	4	3	2	2	2	3	1	2	2	3	0	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:171766135T>G	ENST00000311601.5	-	13	2144	c.1974A>C	c.(1972-1974)gaA>gaC	p.E658D	SH3PXD2B_ENST00000519643.1_Intron	NM_001017995.2	NP_001017995.1	A1X283	SPD2B_HUMAN	SH3 and PX domains 2B	658					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)			CGACTTGGTCTTCGCCCTGAG	0.587																																					p.E658D		Atlas-SNP	.											.	SH3PXD2B	91	.	0			c.A1974C						PASS	.						105	100	102					5																	171766135		2203	4300	6503	SO:0001583	missense	285590	exon13			TTGGTCTTCGCCC	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.1974A>C	5.37:g.171766135T>G	ENSP00000309714:p.Glu658Asp	100	0	0		113	28	0.247788	NM_001017995	B6F0V2|Q9P2Q1	Missense_Mutation	SNP	ENST00000311601.5	37	CCDS34291.1	.	.	.	.	.	.	.	.	.	.	T	6.943	0.543719	0.13250	.	.	ENSG00000174705	ENST00000311601	T	0.61627	0.09	4.94	1.31	0.21738	.	0.309439	0.34223	N	0.004160	T	0.29423	0.0733	N	0.12746	0.255	0.32639	N	0.520891	B	0.15141	0.012	B	0.14023	0.01	T	0.09862	-1.0655	9	.	.	.	-9.4913	2.9632	0.05899	0.1917:0.3214:0.0:0.487	.	658	A1X283	SPD2B_HUMAN	D	658	ENSP00000309714:E658D	.	E	-	3	2	SH3PXD2B	171698740	0.991000	0.36638	0.995000	0.50966	0.525000	0.34531	0.257000	0.18369	0.396000	0.25283	0.454000	0.30748	GAA	.	.	none		0.587	SH3PXD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372449.1	NM_017963		G	171766135	T	G	171766135	3	3	29	1	0	0	0	0	1	0	0	0	14272	1606	56	5	765	5	SH3PXD2B	5	171766135	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	1428069	171766135	9149125	295	12536											
FAF2	23197	hgsc.bcm.edu	37	chr5	175926010	175926010	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggagaaagaaagaaagaaacGggaggagcgggagcgtaagc	18	1	18	4	3	0	4	0	0	0	4	0	8	0	7	0	4	4	1	0	4	5	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:175926010G>A	ENST00000261942.6	+	9	988	c.935G>A	c.(934-936)cGg>cAg	p.R312Q		NM_014613.2	NP_055428.1	Q96CS3	FAF2_HUMAN	Fas associated factor family member 2	312					lipid particle organization (GO:0034389)|negative regulation of catalytic activity (GO:0043086)|response to unfolded protein (GO:0006986)	Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)	lipase binding (GO:0035473)|lipase inhibitor activity (GO:0055102)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	10						AGAAAGAAACGGGAGGAGCGG	0.562																																					p.R312Q		Atlas-SNP	.											.	FAF2	38	.	0			c.G935A						PASS	.						89	93	91					5																	175926010		2203	4300	6503	SO:0001583	missense	23197	exon9			AGAAACGGGAGGA	BC015791	CCDS34296.1	5q35.2	2011-06-28	2008-07-25	2008-07-25	ENSG00000113194	ENSG00000113194		"UBX domain containing"	24666	protein-coding gene	gene with protein product	"expressed in T cells and eosinophils in atopic dermatitis", "UBX domain protein 3B"		"UBX domain containing 8"	UBXD8		10048485, 12372427	Standard	NM_014613		Approved	ETEA, KIAA0887, UBXN3B	uc003mej.4	Q96CS3	OTTHUMG00000163228	ENST00000261942.6:c.935G>A	5.37:g.175926010G>A	ENSP00000261942:p.Arg312Gln	43	0	0		55	22	0.4	NM_014613	O94963|Q8IUF2|Q9BRP2|Q9BVM7	Missense_Mutation	SNP	ENST00000261942.6	37	CCDS34296.1	.	.	.	.	.	.	.	.	.	.	G	8.857	0.946084	0.18356	.	.	ENSG00000113194	ENST00000261942	T	0.63096	-0.02	4.82	2.86	0.33363	.	0.193233	0.52532	D	0.000075	T	0.38692	0.1050	L	0.27975	0.815	0.37360	D	0.911177	B	0.15141	0.012	B	0.08055	0.003	T	0.18023	-1.0350	10	0.09338	T	0.73	-8.2648	4.4655	0.11687	0.4314:0.0:0.5686:0.0	.	312	Q96CS3	FAF2_HUMAN	Q	312	ENSP00000261942:R312Q	ENSP00000261942:R312Q	R	+	2	0	FAF2	175858616	1.000000	0.71417	0.986000	0.45419	0.998000	0.95712	3.577000	0.53885	1.249000	0.43950	0.561000	0.74099	CGG	.	.	none		0.562	FAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372194.1	NM_014613		A	175926010	G	A	175926010	3	1	29	1	0	0	0	0	1	0	0	0	5375	1116	39	1	969	1	FAF2	5	175926010	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	4159875	175926010	4989250	296	12537											
ZFP2	80108	hgsc.bcm.edu	37	chr5	178359075	178359075	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggaaaagccttcagtcaaaGcatgcatcttattgtacatc	13	12	7	9	0	3	0	2	0	1	0	4	1	3	1	1	1	4	3	1	1	5	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:178359075G>C	ENST00000361362.2	+	5	1291	c.761G>C	c.(760-762)aGc>aCc	p.S254T	ZFP2_ENST00000503510.2_Missense_Mutation_p.S254T|ZFP2_ENST00000523286.1_Missense_Mutation_p.S254T|ZFP2_ENST00000520301.1_Missense_Mutation_p.S254T	NM_030613.2	NP_085116.2	Q6ZN57	ZFP2_HUMAN	ZFP2 zinc finger protein	254					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)		TTCAGTCAAAGCATGCATCTT	0.383																																					p.S254T		Atlas-SNP	.											.	ZFP2	70	.	0			c.G761C						PASS	.						68	71	70					5																	178359075		2203	4300	6503	SO:0001583	missense	80108	exon5			GTCAAAGCATGCA	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.761G>C	5.37:g.178359075G>C	ENSP00000354453:p.Ser254Thr	27	0	0		44	17	0.386364	NM_030613	A5PLN5|B7ZM23|Q9H6Z6	Missense_Mutation	SNP	ENST00000361362.2	37	CCDS4440.1	.	.	.	.	.	.	.	.	.	.	g	6.700	0.497745	0.12762	.	.	ENSG00000198939	ENST00000361362;ENST00000520301;ENST00000523286;ENST00000503510	T;T;T;T	0.07567	3.18;3.18;3.18;3.18	4.67	4.67	0.58626	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.38111	N	0.001818	T	0.11024	0.0269	M	0.74389	2.26	0.09310	N	1	B	0.17667	0.023	B	0.08055	0.003	T	0.10132	-1.0643	10	0.33141	T	0.24	-5.845	8.6489	0.34022	0.1014:0.0:0.8986:0.0	.	254	Q6ZN57	ZFP2_HUMAN	T	254	ENSP00000354453:S254T;ENSP00000430980:S254T;ENSP00000430531:S254T;ENSP00000438114:S254T	ENSP00000354453:S254T	S	+	2	0	ZFP2	178291681	0.000000	0.05858	0.998000	0.56505	0.997000	0.91878	0.566000	0.23593	2.408000	0.81797	0.650000	0.86243	AGC	.	.	none		0.383	ZFP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253470.2	NM_030613		C	178359075	G	C	178359075	3	2	29	1	0	0	0	0	1	0	0	0	17656	971	34	4	763	4	ZFP2	5	178359075	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2433065	178359075	2556185	297	12538											
GRM6	2916	hgsc.bcm.edu	37	chr5	178415983	178415983	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagaagcatccgcccatcaGtgggttccatcgccgggcac	8	6	12	15	3	1	1	1	0	0	1	4	1	3	1	4	2	1	4	4	2	1	1	rs5019554	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:178415983G>A	ENST00000517717.1	-	7	1345	c.1307C>T	c.(1306-1308)aCt>aTt	p.T436I	GRM6_ENST00000231188.5_Missense_Mutation_p.T436I|RP11-281O15.4_ENST00000519491.1_RNA			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	436					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)		CCGCCCATCAGTGGGTTCCAT	0.627													G|||	13	0.00259585	0.0	0.0086	5008	,	,		12866	0.0		0.007	False		,,,				2504	0.0				p.T436I		Atlas-SNP	.											.	GRM6	149	.	0			c.C1307T						PASS	.						72	69	70					5																	178415983		2203	4300	6503	SO:0001583	missense	2916	exon6			CCATCAGTGGGTT	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.1307C>T	5.37:g.178415983G>A	ENSP00000430767:p.Thr436Ile	163	0	0		122	49	0.401639	NM_000843		Missense_Mutation	SNP	ENST00000517717.1	37	CCDS4442.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	0.962	-0.702814	0.03255	.	.	ENSG00000113262	ENST00000319065;ENST00000231188;ENST00000517717	D;D	0.86562	-2.14;-2.14	5.28	5.28	0.74379	Extracellular ligand-binding receptor (1);	.	.	.	.	T	0.56963	0.2021	N	0.01197	-0.965	0.34940	D	0.750266	B;B	0.31383	0.321;0.001	B;B	0.32724	0.151;0.006	T	0.68277	-0.5451	9	0.06757	T	0.87	.	10.2758	0.43510	0.09:0.0:0.91:0.0	rs5019554;rs5019555;rs17839800	476;436	E7EX65;O15303	.;GRM6_HUMAN	I	476;436;436	ENSP00000231188:T436I;ENSP00000430767:T436I	ENSP00000231188:T436I	T	-	2	0	GRM6	178348589	0.983000	0.35010	0.958000	0.39756	0.161000	0.22273	6.201000	0.72124	2.643000	0.89663	0.555000	0.69702	ACT	A|0.008;G|0.992	0.008	strong		0.627	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2			A	178415983	G	A	178415983	3	1	29	1	0	0	0	0	1	0	0	0	6810	1029	36	2	1346	2	GRM6	5	178415983	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	56908	178415983	2499277	298	12539											
SQSTM1	8878	hgsc.bcm.edu	37	chr5	179263542	179263542	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cagaccaagaactatgacatCggagcggctctggacaccat	13	6	10	12	2	1	3	0	1	1	2	2	5	1	5	2	3	2	1	2	3	3	1	rs374985304		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr5:179263542C>T	ENST00000389805.4	+	8	1450	c.1272C>T	c.(1270-1272)atC>atT	p.I424I	SQSTM1_ENST00000360718.5_Silent_p.I340I|SQSTM1_ENST00000510187.1_Missense_Mutation_p.S341L|SQSTM1_ENST00000376929.3_Silent_p.I340I|C5orf45_ENST00000523267.1_5'Flank|C5orf45_ENST00000403396.2_3'UTR|SQSTM1_ENST00000402874.3_Silent_p.I340I	NM_003900.4	NP_003891.1	Q13501	SQSTM_HUMAN	sequestosome 1	424	Interaction with NTRK1. {ECO:0000250}.|UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				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)	p.I424I(1)	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)			ACTATGACATCGGAGCGGCTC	0.572																																					p.I424I		Atlas-SNP	.											SQSTM1,NS,carcinoma,0,1	SQSTM1	30	1	1	Substitution - coding silent(1)	endometrium(1)	c.C1272T						PASS	.	C	,,	0,4406		0,0,2203	145	138	141		1020,1020,1272	-4.3	0.9	5		141	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	SQSTM1	NM_001142298.1,NM_001142299.1,NM_003900.4	,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,	340/357,340/357,424/441	179263542	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8878	exon8			TGACATCGGAGCG	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.1272C>T	5.37:g.179263542C>T		81	0	0		70	30	0.428571	NM_003900	A6NFN7|B2R661|B3KUW5|Q13446|Q9BUV7|Q9BVS6|Q9UEU1	Silent	SNP	ENST00000389805.4	37	CCDS34317.1	.	.	.	.	.	.	.	.	.	.	C	4.985	0.182894	0.09495	0.0	1.16E-4	ENSG00000161011	ENST00000510187	T	0.15372	2.43	4.53	-4.32	0.03688	.	.	.	.	.	T	0.14485	0.0350	.	.	.	0.80722	D	1	B	0.10296	0.003	B	0.06405	0.002	T	0.04400	-1.0954	8	0.72032	D	0.01	-13.2762	13.8049	0.63225	0.0:0.3694:0.0:0.6306	.	341	E7EMC7	.	L	341	ENSP00000424477:S341L	ENSP00000424477:S341L	S	+	2	0	SQSTM1	179196148	0.000000	0.05858	0.912000	0.35992	0.106000	0.19336	-1.795000	0.01752	-1.138000	0.02884	-1.263000	0.01449	TCG	.	.	weak		0.572	SQSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319344.1			T	179263542	C	T	179263542	2	4	29	1	0	0	0	0	0	0	0	1	15145	874	31	1		1	SQSTM1	5	179263542	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	847559	179263542	1651718	299	12540											
BPHL	670	hgsc.bcm.edu	37	chr6	3129402	3129402	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctggggcgccaacgcctacGtcactgacgaagacagcatg	10	6	12	13	4	2	2	1	1	1	1	2	3	2	2	2	2	3	1	2	2	3	1	rs199698749	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:3129402G>A	ENST00000380379.5	+	4	551	c.502G>A	c.(502-504)Gtc>Atc	p.V168I	BPHL_ENST00000380375.3_Missense_Mutation_p.V151I|BPHL_ENST00000434640.1_Missense_Mutation_p.V151I|BPHL_ENST00000380368.2_Missense_Mutation_p.V151I	NM_004332.2	NP_004323.2	Q86WA6	BPHL_HUMAN	biphenyl hydrolase-like (serine hydrolase)	168					cellular amino acid metabolic process (GO:0006520)|response to toxic substance (GO:0009636)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			endometrium(4)|kidney(1)|large_intestine(2)|lung(6)	13	Ovarian(93;0.0386)	all_hematologic(90;0.108)				CAACGCCTACGTCACTGACGA	0.537													G|||	2	0.000399361	0.0	0.0014	5008	,	,		12023	0.0		0.001	False		,,,				2504	0.0				p.V168I		Atlas-SNP	.											.	BPHL	32	.	0			c.G502A						PASS	.	G	ILE/VAL	0,4406		0,0,2203	109	84	93		502	4.4	0.7	6	dbSNP_132	93	2,8598	2.2+/-6.3	0,2,4298	yes	missense	BPHL	NM_004332.2	29	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	168/292	3129402	2,13004	2203	4300	6503	SO:0001583	missense	670	exon4			GCCTACGTCACTG	X81372	CCDS4483.2	6p25	2008-08-29	2008-08-29		ENSG00000137274	ENSG00000137274			1094	protein-coding gene	gene with protein product	"breast epithelial mucin-associated antigen"	603156		MCNAA		7759552, 9721218, 15832508	Standard	NM_004332		Approved	Bph-rp	uc003mva.3	Q86WA6	OTTHUMG00000014140	ENST00000380379.5:c.502G>A	6.37:g.3129402G>A	ENSP00000369739:p.Val168Ile	55	0	0		71	25	0.352113	NM_004332	Q00306|Q13855|Q3KP51	Missense_Mutation	SNP	ENST00000380379.5	37	CCDS4483.2	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	8.973	0.973452	0.18736	0.0	2.33E-4	ENSG00000137274	ENST00000434640;ENST00000380375;ENST00000380368;ENST00000380379	T;T;T;T	0.75704	-0.96;-0.96;-0.25;-0.96	5.23	4.36	0.52297	.	0.000000	0.85682	D	0.000000	T	0.38746	0.1052	N	0.25094	0.71	0.80722	D	1	B;B	0.13145	0.007;0.006	B;B	0.21917	0.037;0.022	T	0.30327	-0.9982	10	0.08837	T	0.75	-24.7051	10.9534	0.47343	0.1506:0.0:0.8494:0.0	.	168;151	Q86WA6;Q86WA6-2	BPHL_HUMAN;.	I	151;151;151;168	ENSP00000390472:V151I;ENSP00000369734:V151I;ENSP00000369726:V151I;ENSP00000369739:V168I	ENSP00000369726:V151I	V	+	1	0	BPHL	3074401	1.000000	0.71417	0.747000	0.31113	0.384000	0.30261	6.156000	0.71840	1.206000	0.43276	0.561000	0.74099	GTC	G|1.000;A|0.000	0.000	strong		0.537	BPHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039670.5			A	3129402	G	A	3129402	3	1	29	1	0	0	0	0	1	0	0	0	1491	1145	40	1	516	1	BPHL	6	3129402	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10		3129402	167985665	300	12541											
CD83	9308	hgsc.bcm.edu	37	chr6	14118297	14118297	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	acacggtctcctgggtcaagGtaggtgctgcgatacccacg	8	8	13	12	3	2	0	1	0	1	0	3	1	2	0	2	4	3	2	2	4	3	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:14118297G>A	ENST00000379153.3	+	2	324		c.e2+1			NM_001040280.1|NM_001251901.1|NM_004233.3	NP_001035370.1|NP_001238830.1|NP_004224.1	Q01151	CD83_HUMAN	CD83 molecule						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)				CTGGGTCAAGGTAGGTGCTGC	0.642																																					.		Atlas-SNP	.											.	CD83	23	.	0			c.153+1G>A						PASS	.						22	22	22					6																	14118297		2203	4300	6503	SO:0001630	splice_region_variant	9308	exon2			GTCAAGGTAGGTG	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.153+1G>A	6.37:g.14118297G>A		29	0	0		32	10	0.3125	NM_001040280	Q5THX9	Splice_Site	SNP	ENST00000379153.3	37	CCDS4532.1	.	.	.	.	.	.	.	.	.	.	G	11.75	1.732915	0.30684	.	.	ENSG00000112149	ENST00000379153	.	.	.	4.49	4.49	0.54785	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.6741	0.56884	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CD83	14226276	1.000000	0.71417	0.998000	0.56505	0.141000	0.21300	4.759000	0.62227	2.031000	0.59945	0.491000	0.48974	.	.	.	none		0.642	CD83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039916.1		Intron	A	14118297	G	A	14118297	5	1	29	1	0	0	0	0	0	0	1	0	3043	1275	44	2	160	2	CD83	6	14118297	Splice_Site	SNP	G	TCGA-GR-7351-01A-11D-2210-10	10988895	14118297	156996770	301	12542											
MBOAT1	154141	hgsc.bcm.edu	37	chr6	20124710	20124710	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ataagtagcagagtcgagccGgaaagcttgctttatggaca	13	9	12	7	2	0	1	0	0	0	1	1	4	0	3	1	2	4	4	1	2	4	5	rs146228602		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:20124710G>A	ENST00000324607.7	-	8	1000	c.836C>T	c.(835-837)cCg>cTg	p.P279L	MBOAT1_ENST00000541730.1_Missense_Mutation_p.P130L	NM_001080480.1	NP_001073949.1	Q6ZNC8	MBOA1_HUMAN	membrane bound O-acyltransferase domain containing 1	279					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)			GAGTCGAGCCGGAAAGCTTGC	0.448													G|||	1	0.000199681	0.0	0.0	5008	,	,		24093	0.0		0.001	False		,,,				2504	0.0				p.P279L		Atlas-SNP	.											MBOAT1,NS,carcinoma,+1,1	MBOAT1	48	1	0			c.C836T						PASS	.	G	LEU/PRO	0,4406		0,0,2203	162	140	147		836	0.6	0.4	6	dbSNP_134	147	11,8589	8.4+/-32.0	0,11,4289	yes	missense	MBOAT1	NM_001080480.1	98	0,11,6492	AA,AG,GG		0.1279,0.0,0.0846	benign	279/496	20124710	11,12995	2203	4300	6503	SO:0001583	missense	154141	exon8			CGAGCCGGAAAGC	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.836C>T	6.37:g.20124710G>A	ENSP00000324944:p.Pro279Leu	92	0	0		85	14	0.164706	NM_001080480	A9EDQ5|B4DL59|B4E3J4|Q86XC2|Q8N9R5	Missense_Mutation	SNP	ENST00000324607.7	37	CCDS34346.1	.	.	.	.	.	.	.	.	.	.	G	1.658	-0.512287	0.04200	0.0	0.001279	ENSG00000172197	ENST00000541730;ENST00000324607	T;T	0.23950	1.88;1.88	5.61	0.549	0.17213	.	0.225123	0.38381	N	0.001710	T	0.01976	0.0062	N	0.02120	-0.675	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.0	T	0.48055	-0.9068	10	0.02654	T	1	-14.5864	9.466	0.38813	0.7298:0.0:0.2702:0.0	.	130;279	Q6ZNC8-2;Q6ZNC8	.;MBOA1_HUMAN	L	130;279	ENSP00000441568:P130L;ENSP00000324944:P279L	ENSP00000324944:P279L	P	-	2	0	MBOAT1	20232689	0.973000	0.33851	0.426000	0.26672	0.068000	0.16541	2.103000	0.41806	-0.061000	0.13110	-0.302000	0.09304	CCG	G|0.999;A|0.001	0.001	strong		0.448	MBOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039980.1			A	20124710	G	A	20124710	3	1	29	1	0	0	0	0	1	0	0	0	9365	1116	39	1	675	1	MBOAT1	6	20124710	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	6006413	20124710	150990357	302	12543											
DCDC2	51473	hgsc.bcm.edu	37	chr6	24302049	24302049	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaggaggcgagaagctgggtTtatgaggtctccatttgcaa	11	10	14	6	1	1	2	0	1	1	1	2	4	1	3	1	4	2	3	1	4	4	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:24302049T>G	ENST00000378454.3	-	4	752	c.451A>C	c.(451-453)Aac>Cac	p.N151H		NM_001195610.1|NM_016356.3	NP_001182539.1|NP_057440.2	Q9UHG0	DCDC2_HUMAN	doublecortin domain containing 2	151	Doublecortin 2. {ECO:0000255|PROSITE- ProRule:PRU00072}.				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)				GAAGCTGGGTTTATGAGGTCT	0.438																																					p.N151H		Atlas-SNP	.											.	DCDC2	53	.	0			c.A451C						PASS	.						115	112	113					6																	24302049		2203	4300	6503	SO:0001583	missense	51473	exon5			CTGGGTTTATGAG	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.451A>C	6.37:g.24302049T>G	ENSP00000367715:p.Asn151His	131	0	0		131	10	0.0763359	NM_001195610	Q5VTR8|Q5VTR9|Q86W35|Q9UFD1|Q9UHG1|Q9ULR6	Missense_Mutation	SNP	ENST00000378454.3	37	CCDS4550.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.957842	0.73902	.	.	ENSG00000146038	ENST00000378454	D	0.93019	-3.15	5.87	4.68	0.58851	Doublecortin domain (4);	0.605738	0.19684	N	0.108433	T	0.81422	0.4819	N	0.24115	0.695	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.75648	-0.3245	10	0.33940	T	0.23	-2.7516	13.3134	0.60393	0.0:0.0:0.1321:0.8679	.	151	Q9UHG0	DCDC2_HUMAN	H	151	ENSP00000367715:N151H	ENSP00000367715:N151H	N	-	1	0	DCDC2	24410028	1.000000	0.71417	0.655000	0.29622	0.997000	0.91878	4.518000	0.60510	1.119000	0.41883	0.533000	0.62120	AAC	.	.	none		0.438	DCDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043604.1	NM_016356		G	24302049	T	G	24302049	3	3	29	1	0	0	0	0	1	0	0	0	4287	1841	64	5	1007	5	DCDC2	6	24302049	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	4177339	24302049	146813018	303	12544											
TDP2	51567	hgsc.bcm.edu	37	chr6	24653283	24653283	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggagcctcttgcattttcttTaaaaccatttttaactgatt	10	18	5	8	0	2	1	0	1	2	0	2	2	2	2	2	1	4	1	2	1	3	9	rs11559067	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:24653283T>C	ENST00000378198.4	-	6	905	c.735A>G	c.(733-735)ttA>ttG	p.L245L	TDP2_ENST00000545995.1_Silent_p.L275L|TDP2_ENST00000341060.3_Silent_p.L187L|TDP2_ENST00000478285.1_5'Flank			O95551	TYDP2_HUMAN	tyrosyl-DNA phosphodiesterase 2	245					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						GCATTTTCTTTAAAACCATTT	0.428								Direct reversal of damage					T|||	60	0.0119808	0.003	0.0202	5008	,	,		17943	0.001		0.0318	False		,,,				2504	0.0092				p.L245L		Atlas-SNP	.											.	TDP2	29	.	0			c.A735G						PASS	.	T		39,4367	43.1+/-76.7	0,39,2164	212	222	219		735	-1.5	0	6	dbSNP_120	219	322,8278	113.5+/-173.5	7,308,3985	no	coding-synonymous	TDP2	NM_016614.2		7,347,6149	CC,CT,TT		3.7442,0.8852,2.7756		245/363	24653283	361,12645	2203	4300	6503	SO:0001819	synonymous_variant	51567	exon6			TTTCTTTAAAACC	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.735A>G	6.37:g.24653283T>C		74	0	0		86	74	0.860465	NM_016614	B4DKL8|B4DQ95|Q2TBE2|Q5JYM0|Q7Z6U5|Q9NUK5|Q9NYY9	Silent	SNP	ENST00000378198.4	37	CCDS4557.1																																																																																			T|0.977;C|0.023	0.023	strong		0.428	TDP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000040012.1			C	24653283	T	C	24653283	2	2	29	1	0	0	0	0	0	0	0	1	15744	1751	61	3		3	TDP2	6	24653283	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	351234	24653283	146461784	304	12545											
FAM65B	9750	hgsc.bcm.edu	37	chr6	24839461	24839461	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcactttcaactgtgagacTtaaactggaagacctgctgc	12	10	9	10	0	1	2	1	1	0	2	1	4	1	3	1	1	5	2	1	1	4	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:24839461T>G	ENST00000259698.4	-	15	2135	c.1960A>C	c.(1960-1962)Agt>Cgt	p.S654R	AL512428.1_ENST00000583229.1_RNA|FAM65B_ENST00000538035.1_Missense_Mutation_p.S633R|FAM65B_ENST00000473070.1_5'Flank	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	654					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						ACTGTGAGACTTAAACTGGAA	0.473																																					p.S654R		Atlas-SNP	.											.	FAM65B	134	.	0			c.A1960C						PASS	.						77	68	71					6																	24839461		692	1591	2283	SO:0001583	missense	9750	exon15			TGAGACTTAAACT	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.1960A>C	6.37:g.24839461T>G	ENSP00000259698:p.Ser654Arg	120	0	0		118	38	0.322034	NM_014722	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Missense_Mutation	SNP	ENST00000259698.4	37	CCDS47383.1	.	.	.	.	.	.	.	.	.	.	T	28.6	4.931738	0.92389	.	.	ENSG00000111913	ENST00000259698;ENST00000538035	T;T	0.50813	0.73;0.73	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	T	0.63534	0.2519	M	0.73598	2.24	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.68526	-0.5385	10	0.72032	D	0.01	-20.4236	16.2879	0.82732	0.0:0.0:0.0:1.0	.	633;654	F5GX51;Q9Y4F9	.;FA65B_HUMAN	R	654;633	ENSP00000259698:S654R;ENSP00000441138:S633R	ENSP00000259698:S654R	S	-	1	0	FAM65B	24947440	1.000000	0.71417	0.970000	0.41538	0.998000	0.95712	7.353000	0.79414	2.242000	0.73789	0.533000	0.62120	AGT	.	.	none		0.473	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2			G	24839461	T	G	24839461	3	3	29	1	0	0	0	0	1	0	0	0	5608	1609	56	5	1282	5	FAM65B	6	24839461	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	186178	24839461	146275606	305	12546											
FAM65B	9750	hgsc.bcm.edu	37	chr6	24843183	24843183	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctaatgcaagtaaaagcccAttaaaagcatcctctaagct	16	10	5	10	0	2	0	0	0	2	0	3	0	3	0	2	0	4	4	2	0	7	4	rs145837095	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:24843183A>G	ENST00000259698.4	-	14	2002	c.1827T>C	c.(1825-1827)aaT>aaC	p.N609N	AL512428.1_ENST00000583229.1_RNA|FAM65B_ENST00000510784.2_Silent_p.N593N|FAM65B_ENST00000540914.1_Silent_p.N559N|FAM65B_ENST00000538035.1_Silent_p.N588N|FAM65B_ENST00000378023.4_Silent_p.N559N|FAM65B_ENST00000473070.1_5'UTR	NM_014722.2	NP_055537.2	Q9Y4F9	FA65B_HUMAN	family with sequence similarity 65, member B	609					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						GTAAAAGCCCATTAAAAGCAT	0.413													A|||	8	0.00159744	0.0	0.0058	5008	,	,		18595	0.001		0.003	False		,,,				2504	0.0				p.N609N		Atlas-SNP	.											FAM65B_ENST00000259698,NS,carcinoma,-1,2	FAM65B	134	2	0			c.T1827C						PASS	.	A	,	2,3798		0,2,1898	115	115	115		1827,1677	-11.3	0	6	dbSNP_134	115	47,8187		0,47,4070	yes	coding-synonymous,coding-synonymous	FAM65B	NM_014722.2,NM_015864.2	,	0,49,5968	GG,GA,AA		0.5708,0.0526,0.4072	,	609/1069,559/592	24843183	49,11985	1900	4117	6017	SO:0001819	synonymous_variant	9750	exon14			AAGCCCATTAAAA	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.1827T>C	6.37:g.24843183A>G		72	0	0		87	68	0.781609	NM_014722	A6NHP2|Q13529|Q5VV37|Q5VV38|Q9BQ28	Silent	SNP	ENST00000259698.4	37	CCDS47383.1																																																																																			A|0.998;G|0.002	0.002	strong		0.413	FAM65B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040024.2			G	24843183	A	G	24843183	2	3	29	1	0	0	0	0	0	0	0	1	5608	214	8	3		3	FAM65B	6	24843183	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	3722	24843183	146271884	306	12547											
HIST1H2AC	8334	hgsc.bcm.edu	37	chr6	26124610	26124610	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gttggggcaggcgcgccggtGtacctggcggcggtgttaga	4	8	20	9	5	0	1	0	0	0	1	0	1	0	1	2	7	1	4	2	7	2	3	rs139293879		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:26124610G>A	ENST00000602637.1	+	1	180	c.150G>A	c.(148-150)gtG>gtA	p.V50V	HIST1H2AC_ENST00000377791.2_Silent_p.V50V|HIST1H2BC_ENST00000314332.5_5'Flank|HIST1H2BC_ENST00000396984.1_5'Flank			Q93077	H2A1C_HUMAN	histone cluster 1, H2ac	50						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(5)	12						GCGCGCCGGTGTACCTGGCGG	0.672																																					p.V50V		Atlas-SNP	.											.	HIST1H2AC	29	.	0			c.G150A						PASS	.						44	46	45					6																	26124610		2203	4299	6502	SO:0001819	synonymous_variant	8334	exon1			GCCGGTGTACCTG	Z80778	CCDS4585.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000180573	ENSG00000180573		"Histones / Replication-dependent"	4733	protein-coding gene	gene with protein product		602794	"H2A histone family, member L", "histone 1, H2ac"	H2AFL		9119399, 12408966	Standard	NM_003512		Approved		uc003ngm.3	Q93077	OTTHUMG00000014428	ENST00000602637.1:c.150G>A	6.37:g.26124610G>A		100	0	0		92	24	0.26087	NM_003512	B2R4F7|O00775|O00776|O00777|O00778|Q540R1	Silent	SNP	ENST00000602637.1	37	CCDS4585.1																																																																																			G|1.000;C|0.000	.	alt		0.672	HIST1H2AC-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468023.1	NM_003512		A	26124610	G	A	26124610	2	1	29	1	0	0	0	0	0	0	0	1	7139	1364	48	2		2	HIST1H2AC	6	26124610	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1281427	26124610	144990457	307	12548											
HIST1H2AD	3013	hgsc.bcm.edu	37	chr6	26199193	26199193	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttacccagcaacttgtttagCtcctcgtcgttgcggatggc	6	13	10	12	3	0	0	0	0	0	0	3	1	1	1	2	2	5	4	2	2	3	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:26199193C>T	ENST00000341023.1	-	1	278	c.279G>A	c.(277-279)gaG>gaA	p.E93E	HIST1H3D_ENST00000377831.5_5'UTR|HIST1H3D_ENST00000356476.2_5'Flank|HIST1H2BF_ENST00000359985.1_5'Flank	NM_021065.2	NP_066409.1	P20671	H2A1D_HUMAN	histone cluster 1, H2ad	93						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E93D(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6		all_hematologic(11;0.196)				ACTTGTTTAGCTCCTCGTCGT	0.602																																					p.E93E		Atlas-SNP	.											HIST1H2AD,NS,lymphoid_neoplasm,0,1	HIST1H2AD	20	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G279A						PASS	.						128	121	123					6																	26199193		2203	4300	6503	SO:0001819	synonymous_variant	3013	exon1			GTTTAGCTCCTCG	Z80776	CCDS4591.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000196866	ENSG00000196866		"Histones / Replication-dependent"	4729	protein-coding gene	gene with protein product		602792	"H2A histone family, member G", "histone 1, H2ad"	H2AFG		9119399, 12408966	Standard	NM_021065		Approved	H2A/g, H2A.3	uc003ngw.4	P20671	OTTHUMG00000014437	ENST00000341023.1:c.279G>A	6.37:g.26199193C>T		182	0	0		164	31	0.189024	NM_021065	A0PK91|P57754|Q6FGY6	Silent	SNP	ENST00000341023.1	37	CCDS4591.1																																																																																			.	.	none		0.602	HIST1H2AD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040100.1	NM_021065		T	26199193	C	T	26199193	2	4	29	1	0	0	0	0	0	0	0	1	7140	796	28	2		2	HIST1H2AD	6	26199193	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	74583	26199193	144915874	308	12549											
HIST1H2AE	3012	hgsc.bcm.edu	37	chr6	26217245	26217245	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcggcaaagctcgggcaaaaGctaaaacgcgttcttccagg	12	6	12	11	4	1	0	0	0	1	0	3	0	2	0	1	3	3	5	1	3	5	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:26217245G>A	ENST00000303910.2	+	1	81	c.43G>A	c.(43-45)Gct>Act	p.A15T	HIST1H2BG_ENST00000244601.3_5'Flank	NM_021052.2	NP_066390.1	P04908	H2A1B_HUMAN	histone cluster 1, H2ae	15						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)				TCGGGCAAAAGCTAAAACGCG	0.547																																					p.A15T		Atlas-SNP	.											.	HIST1H2AE	25	.	0			c.G43A						PASS	.						66	57	60					6																	26217245		2203	4300	6503	SO:0001583	missense	3012	exon1			GCAAAAGCTAAAA	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.43G>A	6.37:g.26217245G>A	ENSP00000303373:p.Ala15Thr	89	0	0		81	25	0.308642	NM_021052	P28001|Q76P63	Missense_Mutation	SNP	ENST00000303910.2	37	CCDS4595.1	.	.	.	.	.	.	.	.	.	.	.	11.85	1.762076	0.31228	.	.	ENSG00000168274	ENST00000303910	T	0.40756	1.02	3.99	3.99	0.46301	.	0.000000	0.33753	U	0.004582	T	0.49389	0.1554	M	0.69185	2.1	0.48452	D	0.999659	.	.	.	.	.	.	T	0.56257	-0.8009	8	0.87932	D	0	.	15.5885	0.76506	0.0:0.0:1.0:0.0	.	.	.	.	T	15	ENSP00000303373:A15T	ENSP00000303373:A15T	A	+	1	0	HIST1H2AE	26325224	1.000000	0.71417	0.930000	0.37139	0.125000	0.20455	7.595000	0.82710	2.219000	0.72066	0.591000	0.81541	GCT	.	.	none		0.547	HIST1H2AE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040103.1	NM_021052		A	26217245	G	A	26217245	3	1	29	1	0	0	0	0	1	0	0	0	7141	971	34	2	45	2	HIST1H2AE	6	26217245	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	18052	26217245	144897822	309	12550											
HIST1H4I	8294	hgsc.bcm.edu	37	chr6	27107302	27107302	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cgtgatccgggacgccgtgaCctacacggagcacgccaagc	9	4	13	15	6	0	2	0	2	0	0	1	4	1	4	4	2	3	1	4	2	2	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:27107302C>G	ENST00000354348.2	+	1	227	c.215C>G	c.(214-216)aCc>aGc	p.T72S	HIST1H2BK_ENST00000396891.4_Intron	NM_003495.2	NP_003486.1	P62805	H4_HUMAN	histone cluster 1, H4i	72					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						GACGCCGTGACCTACACGGAG	0.642			T	BCL6	NHL																																p.T72S		Atlas-SNP	.		Dom	yes		6	6p21.3	8294	"histone 1, H4i (H4FM)"		L	.	HIST1H4I	26	.	0			c.C215G						PASS	.						77	69	72					6																	27107302		2203	4300	6503	SO:0001583	missense	8294	exon1			CCGTGACCTACAC	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.215C>G	6.37:g.27107302C>G	ENSP00000346316:p.Thr72Ser	116	0	0		141	93	0.659574	NM_003495	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000354348.2	37	CCDS4620.1	.	.	.	.	.	.	.	.	.	.	.	22.7	4.318985	0.81469	.	.	ENSG00000198339	ENST00000354348	T	0.67523	-0.27	3.8	3.8	0.43715	.	0.000000	0.41605	U	0.000849	T	0.75221	0.3820	M	0.82823	2.61	0.50313	D	0.999864	.	.	.	.	.	.	T	0.80155	-0.1500	8	0.72032	D	0.01	.	13.9996	0.64424	0.0:1.0:0.0:0.0	.	.	.	.	S	72	ENSP00000346316:T72S	ENSP00000346316:T72S	T	+	2	0	HIST1H4I	27215281	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.052000	0.76634	2.068000	0.61886	0.655000	0.94253	ACC	.	.	none		0.642	HIST1H4I-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040139.1	NM_003495		G	27107302	C	G	27107302	3	3	29	1	0	0	0	0	1	0	0	0	7182	507	18	4	217	4	HIST1H4I	6	27107302	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	890057	27107302	144007765	310	12551											
HIST1H2BL	8340	hgsc.bcm.edu	37	chr6	27775367	27775367	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gacaccgcgtgcttggccagCtcccccggaagcagcaggcg	7	4	14	16	4	0	0	0	0	0	0	1	2	1	1	4	3	4	4	4	3	1	1	rs563781327		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:27775367C>T	ENST00000377401.2	-	1	342	c.318G>A	c.(316-318)gaG>gaA	p.E106E	HIST1H2AI_ENST00000358739.3_5'Flank|HIST1H3H_ENST00000369163.2_5'Flank	NM_003519.3	NP_003510.1	Q99880	H2B1L_HUMAN	histone cluster 1, H2bl	106					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						GCTTGGCCAGCTCCCCCGGAA	0.612													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17875	0.0		0.0	False		,,,				2504	0.0				p.E106E		Atlas-SNP	.											.	HIST1H2BL	48	.	0			c.G318A						PASS	.						74	77	76					6																	27775367		2203	4300	6503	SO:0001819	synonymous_variant	8340	exon1			GGCCAGCTCCCCC	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.318G>A	6.37:g.27775367C>T		115	0	0		94	29	0.308511	NM_003519	B2R5A3|Q52LW9	Silent	SNP	ENST00000377401.2	37	CCDS4625.1																																																																																			.	.	none		0.612	HIST1H2BL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040153.1	NM_003519		T	27775367	C	T	27775367	2	4	29	1	0	0	0	0	0	0	0	1	7160	796	28	2		2	HIST1H2BL	6	27775367	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	668065	27775367	143339700	311	12552											
HIST1H2AK	8330	hgsc.bcm.edu	37	chr6	27805865	27805865	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcgttgcggatggccagctGcaagtggcgcgggatgatgc	6	8	18	9	4	0	1	0	1	0	0	1	3	0	3	1	4	4	3	1	4	1	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:27805865G>A	ENST00000330180.2	-	1	252	c.253C>T	c.(253-255)Cag>Tag	p.Q85*	HIST1H2BN_ENST00000606613.1_5'Flank|HIST1H2BN_ENST00000396980.3_5'Flank	NM_003510.2	NP_003501.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2ak	85						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						ATGGCCAGCTGCAAGTGGCGC	0.632																																					p.Q85X		Atlas-SNP	.											.	HIST1H2AK	28	.	0			c.C253T						PASS	.						116	117	116					6																	27805865		2203	4298	6501	SO:0001587	stop_gained	8330	exon1			CCAGCTGCAAGTG	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.253C>T	6.37:g.27805865G>A	ENSP00000330307:p.Gln85*	121	0	0		128	50	0.390625	NM_003510	P02261|Q2M1R2|Q76PA6	Nonsense_Mutation	SNP	ENST00000330180.2	37	CCDS4632.1	.	.	.	.	.	.	.	.	.	.	.	28.7	4.945640	0.92593	.	.	ENSG00000184348	ENST00000330180	.	.	.	4.28	4.28	0.50868	.	0.000000	0.30168	U	0.010251	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.5671	0.84601	0.0:0.0:1.0:0.0	.	.	.	.	X	85	.	ENSP00000330307:Q85X	Q	-	1	0	HIST1H2AK	27913844	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.459000	0.97638	2.295000	0.77249	0.555000	0.69702	CAG	.	.	none		0.632	HIST1H2AK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043814.1	NM_003510		A	27805865	G	A	27805865	4	1	29	1	0	0	0	0	0	1	0	0	7146	1328	46	2	143	2	HIST1H2AK	6	27805865	Nonsense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	30498	27805865	143309202	312	12553											
HIST1H3J	8356	hgsc.bcm.edu	37	chr6	27858310	27858310	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgcagcgccatcaccgccgaGctctggaaacgaaggtcggt	9	6	13	13	5	2	0	1	0	1	0	3	3	2	1	3	3	4	2	3	3	2	0	rs543379280		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:27858310G>A	ENST00000359303.2	-	1	260	c.261C>T	c.(259-261)agC>agT	p.S87S	HIST1H3J_ENST00000479986.1_5'Flank|HIST1H2BO_ENST00000303806.4_5'Flank	NM_003535.2	NP_003526.1	P68431	H31_HUMAN	histone cluster 1, H3j	87					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						TCACCGCCGAGCTCTGGAAAC	0.542																																					p.S87S		Atlas-SNP	.											.	HIST1H3J	16	.	0			c.C261T						PASS	.						56	56	56					6																	27858310		2203	4300	6503	SO:0001819	synonymous_variant	8356	exon1			CGCCGAGCTCTGG	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.261C>T	6.37:g.27858310G>A		93	0	0		81	8	0.0987654	NM_003535	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000359303.2	37	CCDS4638.1																																																																																			.	.	none		0.542	HIST1H3J-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043453.2	NM_003535		A	27858310	G	A	27858310	2	1	29	1	0	0	0	0	0	0	0	1	7173	962	34	2		2	HIST1H3J	6	27858310	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	52445	27858310	143256757	313	12554											
ZNF311	282890	hgsc.bcm.edu	37	chr6	28963861	28963861	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ttgaaagccttcccacactgGgtgcaattaaaaggtttctc	11	12	8	10	0	1	1	0	1	1	0	3	1	2	1	2	2	2	2	2	2	4	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:28963861G>C	ENST00000377179.3	-	7	1430	c.918C>G	c.(916-918)acC>acG	p.T306T	ZNF311_ENST00000483450.1_5'UTR	NM_001010877.2	NP_001010877.2	Q5JNZ3	ZN311_HUMAN	zinc finger protein 311	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)			NS(1)|breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|skin(3)|upper_aerodigestive_tract(2)	28						TCCCACACTGGGTGCAATTAA	0.488																																					p.T306T		Atlas-SNP	.											.	ZNF311	59	.	0			c.C918G						PASS	.						81	82	82					6																	28963861		1510	2708	4218	SO:0001819	synonymous_variant	282890	exon7			ACACTGGGTGCAA	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.918C>G	6.37:g.28963861G>C		91	0	0		107	79	0.738318	NM_001010877	A2BFK5|B0S7Y4|Q92971	Silent	SNP	ENST00000377179.3	37	CCDS34357.1																																																																																			.	.	none		0.488	ZNF311-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076631.3	XM_212581		C	28963861	G	C	28963861	2	2	29	1	0	0	0	0	0	0	0	1	17849	1219	43	4		4	ZNF311	6	28963861	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1105551	28963861	142151206	314	12555											
OR2J3	442186	hgsc.bcm.edu	37	chr6	29080267	29080267	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gatacccatgtcaatgagctGaccctcatgatcacaagctc	12	9	7	13	0	3	3	3	3	0	0	4	4	3	3	2	0	3	2	2	0	3	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:29080267G>A	ENST00000377169.1	+	1	600	c.600G>A	c.(598-600)ctG>ctA	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.G600A						PASS	.						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>A	6.37:g.29080267G>A		318	0	0		295	17	0.0576271	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Silent	SNP	ENST00000377169.1	37	CCDS43433.1																																																																																			.	.	none		0.463	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2			A	29080267	G	A	29080267	2	1	29	1	0	0	0	0	0	0	0	1	11013	1277	45	2		2	OR2J3	6	29080267	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	116406	29080267	142034800	315	12556											
OR12D3	81797	hgsc.bcm.edu	37	chr6	29342271	29342271	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tccggtcctgaatcatggagGtggctgaagcaggacgaata	11	8	14	8	2	1	2	1	2	0	0	3	5	3	4	2	5	1	2	2	5	4	1	rs369042428		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:29342271G>A	ENST00000396806.3	-	1	797	c.794C>T	c.(793-795)aCc>aTc	p.T265I	OR5V1_ENST00000377154.1_Intron	NM_030959.2	NP_112221.1	Q9UGF7	O12D3_HUMAN	olfactory receptor, family 12, subfamily D, member 3	265						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						AATCATGGAGGTGGCTGAAGC	0.473																																					p.T265I		Atlas-SNP	.											.	OR12D3	55	.	0			c.C794T						PASS	.	G	ILE/THR	0,3018		0,0,1509	91	84	86		794	1	0	6		86	1,5413		0,1,2706	no	missense	OR12D3	NM_030959.2	89	0,1,4215	AA,AG,GG		0.0185,0.0,0.0119	possibly-damaging	265/317	29342271	1,8431	1509	2707	4216	SO:0001583	missense	81797	exon1			ATGGAGGTGGCTG		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.794C>T	6.37:g.29342271G>A	ENSP00000380023:p.Thr265Ile	124	0	0		106	29	0.273585	NM_030959	A2BDZ1|Q5SQI8|Q6IF23	Missense_Mutation	SNP	ENST00000396806.3	37	CCDS4658.1	.	.	.	.	.	.	.	.	.	.	G	10.12	1.263638	0.23136	0.0	1.85E-4	ENSG00000112462	ENST00000377143;ENST00000396806	T	0.00107	8.72	4.19	1.0	0.19881	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00039	0.0001	N	0.17674	0.51	0.09310	N	1	P	0.48834	0.916	P	0.51550	0.673	T	0.00809	-1.1557	9	0.33141	T	0.24	-7.0619	8.4505	0.32869	0.0:0.1285:0.4082:0.4634	.	265	Q9UGF7	O12D3_HUMAN	I	265	ENSP00000380023:T265I	ENSP00000366348:T265I	T	-	2	0	OR12D3	29450250	0.000000	0.05858	0.000000	0.03702	0.297000	0.27493	0.837000	0.27558	0.342000	0.23796	0.205000	0.17691	ACC	.	.	weak		0.473	OR12D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076056.3			A	29342271	G	A	29342271	3	1	29	1	0	0	0	0	1	0	0	0	10941	1261	44	2	160	2	OR12D3	6	29342271	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	262004	29342271	141772796	316	12557											
DPCR1	135656	hgsc.bcm.edu	37	chr6	30919798	30919798	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaccacaagaaccccagaaaAgcctacgctatactcagaga	18	4	6	13	1	1	3	1	0	0	3	1	4	1	3	4	0	5	1	4	0	8	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:30919798A>C	ENST00000462446.1	+	2	3585	c.3557A>C	c.(3556-3558)aAg>aCg	p.K1186T	HCG21_ENST00000419481.1_RNA|DPCR1_ENST00000304311.2_Missense_Mutation_p.K28T			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	314						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						ACCCCAGAAAAGCCTACGCTA	0.473																																					p.K1186T		Atlas-SNP	.											.	DPCR1	99	.	0			c.A3557C						PASS	.						161	160	161					6																	30919798		2203	4300	6503	SO:0001583	missense	135656	exon2			CAGAAAAGCCTAC	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.3557A>C	6.37:g.30919798A>C	ENSP00000417182:p.Lys1186Thr	25	0	0		45	16	0.355556	NM_080870	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	37	CCDS4692.2	.	.	.	.	.	.	.	.	.	.	A	9.633	1.137016	0.21123	.	.	ENSG00000168631	ENST00000462446;ENST00000304311	T;T	0.26518	1.73;1.75	1.6	0.339	0.15979	.	.	.	.	.	T	0.15176	0.0366	L	0.59436	1.845	0.09310	N	1	D	0.62365	0.991	P	0.53401	0.725	T	0.07616	-1.0763	9	0.31617	T	0.26	.	5.0167	0.14339	0.7344:0.0:0.0:0.2656	.	1186	E9PEI6	.	T	1186;28	ENSP00000417182:K1186T;ENSP00000305948:K28T	ENSP00000305948:K28T	K	+	2	0	DPCR1	31027777	0.000000	0.05858	0.002000	0.10522	0.149000	0.21700	-1.215000	0.02985	0.066000	0.16515	-0.737000	0.03537	AAG	.	.	none		0.473	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870		C	30919798	A	C	30919798	3	2	29	1	0	0	0	0	1	0	0	0	4714	72	3	5	3563	5	DPCR1	6	30919798	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	1577527	30919798	140195269	317	12558											
TNF	7124	hgsc.bcm.edu	37	chr6	31543607	31543607	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccccagggctccaggcggtGcttgttcctcagcctcttct	3	11	11	16	1	3	0	1	0	2	0	5	0	5	0	5	3	2	3	5	3	0	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31543607G>A	ENST00000449264.2	+	1	264	c.89G>A	c.(88-90)tGc>tAc	p.C30Y		NM_000594.3	NP_000585.2	P01375	TNFA_HUMAN	tumor necrosis factor	30					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|calcium-mediated signaling (GO:0019722)|cell activation (GO:0001775)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nicotine (GO:0071316)|cellular response to organic cyclic compound (GO:0071407)|chronic inflammatory response to antigenic stimulus (GO:0002439)|defense response to Gram-positive bacterium (GO:0050830)|embryonic digestive tract development (GO:0048566)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|glucose metabolic process (GO:0006006)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|JNK cascade (GO:0007254)|leukocyte tethering or rolling (GO:0050901)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|necroptotic signaling pathway (GO:0097527)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of branching involved in lung morphogenesis (GO:0061048)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of glucose import (GO:0046325)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of L-glutamate transport (GO:0002037)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of lipid storage (GO:0010888)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein complex disassembly (GO:0043242)|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)|organ morphogenesis (GO:0009887)|osteoclast differentiation (GO:0030316)|positive regulation of apoptotic process (GO:0043065)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of chronic inflammatory response to antigenic stimulus (GO:0002876)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fever generation (GO:0031622)|positive regulation of gene expression (GO:0010628)|positive regulation of hair follicle development (GO:0051798)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|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 interferon-gamma production (GO:0032729)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mitosis (GO:0045840)|positive regulation of mononuclear cell migration (GO:0071677)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of podosome assembly (GO:0071803)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein transport (GO:0051222)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of synaptic transmission (GO:0050806)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translational initiation by iron (GO:0045994)|positive regulation of vitamin D biosynthetic process (GO:0060557)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|receptor biosynthetic process (GO:0032800)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of immunoglobulin secretion (GO:0051023)|regulation of insulin secretion (GO:0050796)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to salt stress (GO:0009651)|response to virus (GO:0009615)|sequestering of triglyceride (GO:0030730)|skeletal muscle contraction (GO:0003009)|transformed cell apoptotic process (GO:0006927)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	cytokine activity (GO:0005125)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|transcription regulatory region DNA binding (GO:0044212)|tumor necrosis factor receptor binding (GO:0005164)			large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|skin(3)	8		Ovarian(999;0.00556)			Adalimumab(DB00051)|Amrinone(DB01427)|Certolizumab pegol(DB08904)|Chloroquine(DB00608)|Clenbuterol(DB01407)|Epinephrine(DB00668)|Etanercept(DB00005)|Glucosamine(DB01296)|golimumab(DB06674)|Infliximab(DB00065)|Pomalidomide(DB08910)|Pranlukast(DB01411)|Pseudoephedrine(DB00852)|Thalidomide(DB01041)	TCCAGGCGGTGCTTGTTCCTC	0.637									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of																												p.C30Y		Atlas-SNP	.											.	TNF	15	.	0			c.G89A						PASS	.						74	75	75					6																	31543607		2203	4300	6503	SO:0001583	missense	7124	exon1	Familial Cancer Database	incl.: Familial Head and Neck Cancer	GGCGGTGCTTGTT	X02910	CCDS4702.1	6p21.3	2013-05-22	2010-05-04		ENSG00000232810	ENSG00000232810		"Tumor necrosis factor (ligand) superfamily"	11892	protein-coding gene	gene with protein product	"TNF superfamily, member 2"	191160	"tumor necrosis factor (TNF superfamily, member 2)"	TNFA		2413547, 6392892	Standard	NM_000594		Approved	TNFSF2, DIF, TNF-alpha	uc003nui.4	P01375	OTTHUMG00000031194	ENST00000449264.2:c.89G>A	6.37:g.31543607G>A	ENSP00000398698:p.Cys30Tyr	71	0	0		43	7	0.162791	NM_000594	O43647|Q9P1Q2|Q9UIV3	Missense_Mutation	SNP	ENST00000449264.2	37	CCDS4702.1	.	.	.	.	.	.	.	.	.	.	G	9.575	1.122136	0.20877	.	.	ENSG00000232810	ENST00000449264	T	0.75589	-0.95	5.77	3.97	0.46021	.	0.369263	0.30252	N	0.010055	T	0.67599	0.2910	M	0.85945	2.785	0.09310	N	0.99999	P	0.38729	0.644	B	0.43658	0.426	T	0.64279	-0.6445	10	0.54805	T	0.06	.	8.8854	0.35400	0.0782:0.0:0.7725:0.1493	.	30	P01375	TNFA_HUMAN	Y	30	ENSP00000398698:C30Y	ENSP00000398698:C30Y	C	+	2	0	TNF	31651586	0.988000	0.35896	0.006000	0.13384	0.138000	0.21146	3.044000	0.49830	0.769000	0.33313	0.655000	0.94253	TGC	.	.	none		0.637	TNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076390.2			A	31543607	G	A	31543607	3	1	29	1	0	0	0	0	1	0	0	0	16286	1319	46	2	91	2	TNF	6	31543607	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	623809	31543607	139571460	318	12559											
LTB	4050	hgsc.bcm.edu	37	chr6	31549599	31549599	+	Missense_Mutation	SNP	T	T	C																															gtctgctcttacccagtcctTgctgggcctgtgccccgggg																								rs532757438		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31549599T>C	ENST00000429299.2	-	2	207	c.200A>G	c.(199-201)cAa>cGa	p.Q67R	LTB_ENST00000446745.2_Intron|LTB_ENST00000483972.1_Intron	NM_002341.1	NP_002332.1	Q06643	TNFC_HUMAN	lymphotoxin beta (TNF superfamily, member 3)	67				DPGAQAQQGL -> GLSAPGSGRT (in Ref. 2; AAB37342). {ECO:0000305}.	cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|signal transduction (GO:0007165)|skin development (GO:0043588)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	9						ACCCAGTCCTTGCTGGGCCTG	0.622																																					p.Q67R		Atlas-SNP	.											.	LTB	19	.	0			c.A200G						PASS	.						92	102	98					6																	31549599		1510	2708	4218	SO:0001583	missense	4050	exon2			AGTCCTTGCTGGG	L11015	CCDS4703.1, CCDS4704.1	6p21.3	2013-05-22			ENSG00000227507	ENSG00000227507		"Tumor necrosis factor (ligand) superfamily"	6711	protein-coding gene	gene with protein product		600978		TNFC		7916655, 1714477	Standard	NM_002341		Approved	p33, TNFSF3	uc003nuk.3	Q06643	OTTHUMG00000031136	ENST00000429299.2:c.200A>G	6.37:g.31549599T>C	ENSP00000410481:p.Gln67Arg	70	0	0		84	46	0.547619	NM_002341	P78370|Q52LU8|Q99761	Missense_Mutation	SNP	ENST00000429299.2	37	CCDS4703.1	.	.	.	.	.	.	.	.	.	.	T	4.177	0.031512	0.08101	.	.	ENSG00000227507	ENST00000429299	T	0.20738	2.05	5.45	-0.106	0.13596	.	1.357640	0.04844	N	0.441054	T	0.05823	0.0152	M	0.64997	1.995	0.09310	N	0.999996	B	0.02656	0.0	B	0.04013	0.001	T	0.32561	-0.9902	10	0.16420	T	0.52	0.0039	1.252	0.01984	0.3122:0.0874:0.1618:0.4386	.	67	Q06643	TNFC_HUMAN	R	67	ENSP00000410481:Q67R	ENSP00000410481:Q67R	Q	-	2	0	LTB	31657578	0.024000	0.19004	0.068000	0.19968	0.859000	0.49053	0.201000	0.17276	0.044000	0.15775	0.533000	0.62120	CAA	.	.	none		0.622	LTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076239.3			C	31549599	T	C	31549599	3	2	29	1	0	0	0	0	1	0	0	0	9079	1812	63	3	546	3	LTB	6	31549599	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	5992	31549599	139565468	319	12560	155	2									
LTB	4050	hgsc.bcm.edu	37	chr6	31549604	31549604	+	Silent	SNP	G	G	A																															ctcttacccagtccttgctgGgcctgtgccccggggtcggc																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31549604G>A	ENST00000429299.2	-	2	202	c.195C>T	c.(193-195)gcC>gcT	p.A65A	LTB_ENST00000446745.2_Intron|LTB_ENST00000483972.1_Intron	NM_002341.1	NP_002332.1	Q06643	TNFC_HUMAN	lymphotoxin beta (TNF superfamily, member 3)	65				DPGAQAQQGL -> GLSAPGSGRT (in Ref. 2; AAB37342). {ECO:0000305}.	cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|signal transduction (GO:0007165)|skin development (GO:0043588)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	9						GTCCTTGCTGGGCCTGTGCCC	0.617																																					p.A65A		Atlas-SNP	.											.	LTB	19	.	0			c.C195T						PASS	.						91	100	97					6																	31549604		1510	2708	4218	SO:0001819	synonymous_variant	4050	exon2			TTGCTGGGCCTGT	L11015	CCDS4703.1, CCDS4704.1	6p21.3	2013-05-22			ENSG00000227507	ENSG00000227507		"Tumor necrosis factor (ligand) superfamily"	6711	protein-coding gene	gene with protein product		600978		TNFC		7916655, 1714477	Standard	NM_002341		Approved	p33, TNFSF3	uc003nuk.3	Q06643	OTTHUMG00000031136	ENST00000429299.2:c.195C>T	6.37:g.31549604G>A		69	0	0		80	27	0.3375	NM_002341	P78370|Q52LU8|Q99761	Silent	SNP	ENST00000429299.2	37	CCDS4703.1																																																																																			.	.	none		0.617	LTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076239.3			A	31549604	G	A	31549604	2	1	29	1	0	0	0	0	0	0	0	1	9079	1219	43	2		2	LTB	6	31549604	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	5	31549604	139565463	320	12561	155	2									
BAT2	7916	hgsc.bcm.edu	37	chr6	31603046	31603046	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccagtttggcactagtgaCaaggtctgtgtgggctggat	7	12	15	7	0	1	1	0	1	1	0	2	2	2	2	1	4	0	3	1	4	2	2	rs139053368	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31603046C>T	ENST00000376033.2	+	22	5532	c.5298C>T	c.(5296-5298)gaC>gaT	p.D1766D	PRRC2A_ENST00000376007.4_Silent_p.D1766D	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1766	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						GCACTAGTGACAAGGTCTGTG	0.567													C|||	2	0.000399361	0.0	0.0	5008	,	,		19020	0.0		0.0	False		,,,				2504	0.002				p.D1766D		Atlas-SNP	.											.	PRRC2A	152	.	0			c.C5298T						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	86	77	80		5298,5298	3.8	1	6	dbSNP_134	80	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous	PRRC2A	NM_004638.3,NM_080686.2	,	0,5,6498	TT,TC,CC		0.0465,0.0227,0.0384	,	1766/2158,1766/2158	31603046	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	7916	exon22			TAGTGACAAGGTC	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.5298C>T	6.37:g.31603046C>T		114	0	0		105	19	0.180952	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Silent	SNP	ENST00000376033.2	37	CCDS4708.1																																																																																			C|0.999;T|0.001	0.001	strong		0.567	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686		T	31603046	C	T	31603046	2	4	29	1	0	0	0	0	0	0	0	1	1319	477	17	2		2	BAT2	6	31603046	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	53442	31603046	139512021	321	12562											
LY6G5C	80741	hgsc.bcm.edu	37	chr6	31647044	31647044	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caattgacaggaacaaacttAcctagaacacagagaagtgc	18	6	8	9	0	0	3	0	1	0	2	0	5	0	4	1	1	5	0	1	1	7	3	rs143778717	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:31647044A>G	ENST00000383237.4	-	2	126	c.123T>C	c.(121-123)ggT>ggC	p.G41G	LY6G5C_ENST00000375858.3_Splice_Site_p.G38G|LY6G5C_ENST00000474395.1_5'UTR|LY6G5C_ENST00000375860.2_Splice_Site_p.G39G			Q5SRR4	LY65C_HUMAN	lymphocyte antigen 6 complex, locus G5C	41						extracellular region (GO:0005576)				endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	7						GAACAAACTTACCTAGAACAC	0.557													A|||	2	0.000399361	0.0	0.0	5008	,	,		19799	0.0		0.0	False		,,,				2504	0.002				p.G41G		Atlas-SNP	.											.	LY6G5C	8	.	0			c.T123C						PASS	.	A		1,3019		0,1,1509	151	130	137		123	-1.2	0.1	6	dbSNP_134	137	3,5415		0,3,2706	yes	coding-synonymous-near-splice	LY6G5C	NM_025262.3		0,4,4215	GG,GA,AA		0.0554,0.0331,0.0474		41/151	31647044	4,8434	1510	2709	4219	SO:0001630	splice_region_variant	80741	exon2			AAACTTACCTAGA		CCDS34401.1, CCDS34401.2	6p21	2010-02-17	2002-07-29	2002-08-01	ENSG00000204428	ENSG00000204428			13932	protein-coding gene	gene with protein product		610434	"chromosome 6 open reading frame 20"	C6orf20		12079290	Standard	NM_025262		Approved	G5c, NG33	uc003nvu.2	Q5SRR4	OTTHUMG00000031228	ENST00000383237.4:c.122-1T>C	6.37:g.31647044A>G		80	0	0		69	18	0.26087	NM_025262	A6NCW4|B0UXB3|B0UXB4|B0UZ69|B0UZQ0|B1B0L9|O95871|Q5SQ59|Q8NDY0|Q8NDY1	Silent	SNP	ENST00000383237.4	37	CCDS34401.2	.	.	.	.	.	.	.	.	.	.	A	9.297	1.052217	0.19827	3.31E-4	5.54E-4	ENSG00000204428	ENST00000375863	.	.	.	2.93	-1.22	0.09494	.	.	.	.	.	T	0.24624	0.0597	.	.	.	0.44587	D	0.997556	.	.	.	.	.	.	T	0.25012	-1.0144	4	.	.	.	-3.476	2.375	0.04339	0.5268:0.0:0.2584:0.2149	.	.	.	.	A	116	.	.	V	-	2	0	LY6G5C	31755023	0.024000	0.19004	0.095000	0.20976	0.925000	0.55904	-0.071000	0.11505	-0.233000	0.09797	0.379000	0.24179	GTA	A|0.999;G|0.001	0.001	strong		0.557	LY6G5C-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076473.4		Silent	G	31647044	A	G	31647044	5	3	29	1	0	0	0	0	0	0	1	0	9102	405	14	3	337	3	LY6G5C	6	31647044	Splice_Site	SNP	A	TCGA-GR-7351-01A-11D-2210-10	43998	31647044	139468023	322	12563											
CUTA	51596	hgsc.bcm.edu	37	chr6	33384473	33384473	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaactgactctgtgacctggCgcacccactgcaggtacgga	10	7	11	13	2	1	2	0	2	1	0	1	3	1	3	2	3	3	3	2	3	2	1	rs41267649	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:33384473C>T	ENST00000488034.1	-	6	615	c.494G>A	c.(493-495)cGc>cAc	p.R165H	CUTA_ENST00000607266.1_Missense_Mutation_p.R142H|CUTA_ENST00000492510.1_5'Flank|CUTA_ENST00000494751.1_Intron|CUTA_ENST00000374500.5_Missense_Mutation_p.R184H|CUTA_ENST00000374496.3_Missense_Mutation_p.R142H|CUTA_ENST00000488478.1_Silent_p.A148A|CUTA_ENST00000440279.3_Missense_Mutation_p.R142H	NM_001014837.1|NM_001014838.1|NM_001014840.1|NM_015921.2	NP_001014837.1|NP_001014838.1|NP_001014840.1|NP_057005.1	O60888	CUTA_HUMAN	cutA divalent cation tolerance homolog (E. coli)	165					protein localization (GO:0008104)|response to metal ion (GO:0010038)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	enzyme binding (GO:0019899)		SLC22A1/CUTA(2)	kidney(1)|lung(3)|urinary_tract(1)	5						TGTGACCTGGCGCACCCACTG	0.532													C|||	28	0.00559105	0.0008	0.0101	5008	,	,		17858	0.0		0.0189	False		,,,				2504	0.001				p.R184H		Atlas-SNP	.											.	CUTA	5	.	0			c.G551A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	30,4376	36.0+/-67.5	0,30,2173	107	91	96		551,425,425,494,425	-5.2	0.2	6	dbSNP_127	96	191,8409	84.0+/-146.5	3,185,4112	yes	missense,missense,missense,missense,missense	CUTA	NM_001014433.2,NM_001014837.1,NM_001014838.1,NM_001014840.1,NM_015921.2	29,29,29,29,29	3,215,6285	TT,TC,CC		2.2209,0.6809,1.6992	benign,benign,benign,benign,benign	184/199,142/157,142/157,165/180,142/157	33384473	221,12785	2203	4300	6503	SO:0001583	missense	51596	exon6			ACCTGGCGCACCC	AF106943	CCDS4779.1, CCDS34432.1, CCDS34433.1	6p21.32	2008-02-04	2006-02-15	2006-02-15	ENSG00000112514	ENSG00000112514			21101	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 82", "acetylcholinesterase-associated protein"	C6orf82, ACHAP			Standard	XM_006715108		Approved		uc003oen.1	O60888	OTTHUMG00000031254	ENST00000488034.1:c.494G>A	6.37:g.33384473C>T	ENSP00000417544:p.Arg165His	183	0	0		173	142	0.820809	NM_001014433	A2AB26|A2BEL4|Q3B784|Q5JXM9|Q5SU05|Q9NYQ9	Missense_Mutation	SNP	ENST00000488034.1	37	CCDS34433.1	21	0.009615384615384616	0	0.0	6	0.016574585635359115	0	0.0	15	0.01978891820580475	C	7.391	0.630765	0.14322	0.006809	0.022209	ENSG00000112514	ENST00000374500;ENST00000440279;ENST00000488034;ENST00000374496	.	.	.	4.68	-5.17	0.02849	Nitrogen regulatory PII-like, alpha/beta (1);	0.671906	0.15234	N	0.273279	T	0.08980	0.0222	N	0.16130	0.375	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.18777	-1.0326	9	0.38643	T	0.18	-10.3034	13.7621	0.62973	0.0:0.2317:0.0:0.7683	rs41267649	184;165	O60888-2;O60888	.;CUTA_HUMAN	H	184;142;165;142	.	ENSP00000363620:R142H	R	-	2	0	CUTA	33492451	0.003000	0.15002	0.167000	0.22817	0.437000	0.31866	-1.933000	0.01553	-1.162000	0.02797	-0.766000	0.03442	CGC	C|0.986;T|0.014	0.014	strong		0.532	CUTA-008	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076541.3	NM_015921		T	33384473	C	T	33384473	3	4	29	1	0	0	0	0	1	0	0	0	4064	768	27	1	49	1	CUTA	6	33384473	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1737429	33384473	137730594	323	12564											
SYNGAP1	8831	hgsc.bcm.edu	37	chr6	33409006	33409006	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgagtttctggagctggaatGgggttccatgcagcagtttt	7	14	14	6	0	1	1	0	1	1	0	2	3	2	3	1	4	3	6	1	4	1	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:33409006G>A	ENST00000418600.2	+	12	2071	c.1970G>A	c.(1969-1971)tGg>tAg	p.W657*	SYNGAP1_ENST00000293748.5_Nonsense_Mutation_p.W657*|SYNGAP1_ENST00000428982.2_Nonsense_Mutation_p.W598*|SYNGAP1_ENST00000496374.1_3'UTR|MIR5004_ENST00000579078.1_RNA	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	657					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						GAGCTGGAATGGGGTTCCATG	0.478																																					p.W657X		Atlas-SNP	.											.	SYNGAP1	202	.	0			c.G1970A						PASS	.						152	131	138					6																	33409006		2203	4300	6503	SO:0001587	stop_gained	8831	exon12			TGGAATGGGGTTC	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.1970G>A	6.37:g.33409006G>A	ENSP00000403636:p.Trp657*	70	0	0		118	11	0.0932203	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Nonsense_Mutation	SNP	ENST00000418600.2	37	CCDS34434.2	.	.	.	.	.	.	.	.	.	.	G	39	7.288432	0.98189	.	.	ENSG00000197283	ENST00000293748;ENST00000418600;ENST00000449372;ENST00000428982	.	.	.	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.7055	0.45952	0.0:0.0:0.8099:0.1901	.	.	.	.	X	657;657;657;598	.	ENSP00000293748:W657X	W	+	2	0	SYNGAP1	33516984	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.669000	0.83911	2.573000	0.86826	0.655000	0.94253	TGG	.	.	none		0.478	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407		A	33409006	G	A	33409006	4	1	29	1	0	0	0	0	0	1	0	0	15462	1357	47	2	2016	2	SYNGAP1	6	33409006	Nonsense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	24533	33409006	137706061	324	12565											
SPDEF	25803	hgsc.bcm.edu	37	chr6	34507305	34507305	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggctcaccacagtagtgaatCgccccaggtgaagtccgctc	9	7	11	14	2	1	2	1	2	0	0	4	2	2	2	4	2	0	3	4	2	3	1	rs374584207		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:34507305C>T	ENST00000374037.3	-	4	1083	c.669G>A	c.(667-669)gcG>gcA	p.A223A	SPDEF_ENST00000544425.1_Intron	NM_012391.2	NP_036523.1	O95238	SPDEF_HUMAN	SAM pointed domain containing ETS transcription factor	223					cell differentiation (GO:0030154)|intestinal epithelial cell development (GO:0060576)|lung goblet cell differentiation (GO:0060480)|multicellular organismal development (GO:0007275)|negative regulation of cell fate commitment (GO:0010454)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell fate commitment (GO:0010455)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|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)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|skin(3)	15						AGTAGTGAATCGCCCCAGGTG	0.687																																					p.A223A		Atlas-SNP	.											.	SPDEF	34	.	0			c.G669A						PASS	.	C		0,4328		0,0,2164	10	11	11		669	-10.4	0	6		11	4,8518		0,4,4257	no	coding-synonymous	SPDEF	NM_012391.1		0,4,6421	TT,TC,CC		0.0469,0.0,0.0311		223/336	34507305	4,12846	2164	4261	6425	SO:0001819	synonymous_variant	25803	exon4			GTGAATCGCCCCA	AF071538	CCDS4794.1, CCDS59013.1	6p21.3	2013-08-07	2013-08-07		ENSG00000124664	ENSG00000124664			17257	protein-coding gene	gene with protein product		608144	"SAM pointed domain containing ets transcription factor"			10625666, 6857767	Standard	NM_012391		Approved	PDEF, bA375E1.3	uc003ojq.2	O95238	OTTHUMG00000014548	ENST00000374037.3:c.669G>A	6.37:g.34507305C>T		217	0	0		190	34	0.178947	NM_012391	B4DWH8|F5H778	Silent	SNP	ENST00000374037.3	37	CCDS4794.1																																																																																			.	.	weak		0.687	SPDEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040246.1	NM_012391		T	34507305	C	T	34507305	2	4	29	1	0	0	0	0	0	0	0	1	15041	871	31	1		1	SPDEF	6	34507305	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1098299	34507305	136607762	325	12566											
UHRF1BP1	54887	hgsc.bcm.edu	37	chr6	34789443	34789443	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttttcaggttcactaagaatCtttccccagacaaaatcaac	14	12	4	11	0	4	2	3	0	1	2	5	2	5	2	2	1	1	1	2	1	5	5	rs369670668		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:34789443C>G	ENST00000192788.5	+	2	229	c.58C>G	c.(58-60)Ctt>Gtt	p.L20V	UHRF1BP1_ENST00000452449.2_Missense_Mutation_p.L20V|Y_RNA_ENST00000383990.1_RNA	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	20							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						CACTAAGAATCTTTCCCCAGA	0.438																																					p.L20V		Atlas-SNP	.											.	UHRF1BP1	102	.	0			c.C58G						PASS	.	C	VAL/LEU	0,3714		0,0,1857	42	42	42		58	3.9	1	6		42	1,8213		0,1,4106	no	missense	UHRF1BP1	NM_017754.3	32	0,1,5963	GG,GC,CC		0.0122,0.0,0.0084	probably-damaging	20/1441	34789443	1,11927	1857	4107	5964	SO:0001583	missense	54887	exon2			AAGAATCTTTCCC	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.58C>G	6.37:g.34789443C>G	ENSP00000192788:p.Leu20Val	115	0	0		114	14	0.122807	NM_017754	Q9NXE0	Missense_Mutation	SNP	ENST00000192788.5	37	CCDS43455.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.184160	0.78677	0.0	1.22E-4	ENSG00000065060	ENST00000192788;ENST00000452449	D;D	0.85171	-1.95;-1.95	5.79	3.93	0.45458	.	0.000000	0.64402	D	0.000001	D	0.89015	0.6595	M	0.72479	2.2	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.88591	0.3143	10	0.59425	D	0.04	-15.3813	11.3038	0.49323	0.0:0.8033:0.1278:0.0689	.	20	Q6BDS2	URFB1_HUMAN	V	20	ENSP00000192788:L20V;ENSP00000400628:L20V	ENSP00000192788:L20V	L	+	1	0	UHRF1BP1	34897421	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.312000	0.51927	2.732000	0.93576	0.557000	0.71058	CTT	.	.	weak		0.438	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754		G	34789443	C	G	34789443	3	3	29	1	0	0	0	0	1	0	0	0	16983	913	32	4	64	4	UHRF1BP1	6	34789443	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	282138	34789443	136325624	326	12567											
PNPLA1	285848	hgsc.bcm.edu	37	chr6	36269675	36269675	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttcctccaagagagtgatTttcccccgggtggaagtgta	8	12	11	10	1	1	2	0	1	1	1	4	4	4	3	4	2	0	1	4	2	3	4	rs201231660		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:36269675T>A	ENST00000394571.2	+	6	813	c.813T>A	c.(811-813)atT>atA	p.I271I	PNPLA1_ENST00000388715.3_Silent_p.I176I|PNPLA1_ENST00000312917.5_Silent_p.I185I	NM_001145717.1	NP_001139189.2	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	271					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						AGAGAGTGATTTTCCCCCGGG	0.512											OREG0017382	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	1	0.000199681	0.0	0.0	5008	,	,		20927	0.0		0.001	False		,,,				2504	0.0				p.I271I		Atlas-SNP	.											.	PNPLA1	92	.	0			c.T813A						PASS	.	T	,,	1,4405	2.1+/-5.4	0,1,2202	79	82	81		555,813,528	-5.1	0.9	6		81	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	PNPLA1	NM_001145716.1,NM_001145717.1,NM_173676.2	,,	0,1,6502	AA,AT,TT		0.0,0.0227,0.0077	,,	185/447,271/533,176/438	36269675	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	285848	exon6			AGTGATTTTCCCC		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.813T>A	6.37:g.36269675T>A		108	0	0	861	87	61	0.701149	NM_001145717	A3RMU3|J3JS20|Q2A6N1|Q3SY95|Q3SY96|Q5R3L2	Silent	SNP	ENST00000394571.2	37	CCDS54997.1																																																																																			T|1.000;A|0.000	0.000	strong		0.512	PNPLA1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_173676		A	36269675	T	A	36269675	2	1	29	1	0	0	0	0	0	0	0	1	12173	1829	64	5		5	PNPLA1	6	36269675	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	1480232	36269675	134845392	327	12568											
PIM1	5292	hgsc.bcm.edu	37	chr6	37138946	37138946	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aagtggtcctgctgaagaagGtgagctcgggtttctccggc	7	10	15	9	2	1	3	0	2	1	1	4	3	2	3	2	4	2	3	2	4	3	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:37138946G>A	ENST00000373509.5	+	4	659	c.286G>A	c.(286-288)Gtg>Atg	p.V96M		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	187					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)	GCTGAAGAAGGTGAGCTCGGG	0.652			T	BCL6	NHL																																p.V187M		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.G559A						PASS	.						80	89	86					6																	37138946		2203	4300	6503	SO:0001583	missense	5292	exon4			AAGAAGGTGAGCT		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.286G>A	6.37:g.37138946G>A	ENSP00000362608:p.Val96Met	53	0	0		55	8	0.145455	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.518058	0.85495	.	.	ENSG00000137193	ENST00000373509	T	0.66638	-0.22	4.14	4.14	0.48551	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.077156	0.51477	D	0.000084	T	0.54191	0.1843	N	0.25426	0.745	0.54753	D	0.999985	P	0.37015	0.578	P	0.46076	0.503	T	0.65327	-0.6195	10	0.87932	D	0	.	16.5618	0.84568	0.0:0.0:1.0:0.0	.	187	P11309	PIM1_HUMAN	M	96	ENSP00000362608:V96M	ENSP00000362608:V96M	V	+	1	0	PIM1	37246924	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.549000	0.98106	2.283000	0.76528	0.549000	0.68633	GTG	.	.	none		0.652	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			A	37138946	G	A	37138946	3	1	29	1	0	0	0	0	1	0	0	0	11936	1261	44	2	300	2	PIM1	6	37138946	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	869271	37138946	133976121	328	12569											
MDGA1	266727	hgsc.bcm.edu	37	chr6	37605158	37605158	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctctcatcatctctgcaacgCcaagaggaagatggccatgg	11	8	10	12	1	3	2	2	0	2	2	5	3	3	3	2	3	2	1	2	3	3	0	rs201115181	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:37605158C>T	ENST00000434837.3	-	17	4032	c.2854G>A	c.(2854-2856)Gcg>Acg	p.A952T	MDGA1_ENST00000297153.7_Missense_Mutation_p.A956T	NM_153487.3	NP_705691.1	Q8NFP4	MDGA1_HUMAN	MAM domain containing glycosylphosphatidylinositol anchor 1	952					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						CTCTGCAACGCCAAGAGGAAG	0.632													C|||	4	0.000798722	0.0008	0.0029	5008	,	,		18342	0.0		0.001	False		,,,				2504	0.0				p.A952T		Atlas-SNP	.											MDGA1,NS,carcinoma,+2,1	MDGA1	104	1	0			c.G2854A						PASS	.	C	THR/ALA	1,4071		0,1,2035	41	46	45		2854	3.8	1	6		45	12,8338		0,12,4163	yes	missense	MDGA1	NM_153487.3	58	0,13,6198	TT,TC,CC		0.1437,0.0246,0.1047	benign	952/956	37605158	13,12409	2036	4175	6211	SO:0001583	missense	266727	exon17			GCAACGCCAAGAG	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.2854G>A	6.37:g.37605158C>T	ENSP00000402584:p.Ala952Thr	127	0	0		101	20	0.19802	NM_153487	A6NHG0|Q8NBE3	Missense_Mutation	SNP	ENST00000434837.3	37	CCDS47417.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	17.24	3.339139	0.60963	2.46E-4	0.001437	ENSG00000112139	ENST00000434837;ENST00000297153	T;T	0.55588	0.51;0.65	4.77	3.83	0.44106	.	22.481800	0.00424	N	0.000065	T	0.18002	0.0432	N	0.08118	0	0.24923	N	0.991966	B	0.34103	0.437	B	0.24541	0.054	T	0.11275	-1.0594	10	0.62326	D	0.03	.	11.7524	0.51855	0.1766:0.8233:0.0:0.0	.	952	Q8NFP4	MDGA1_HUMAN	T	952;956	ENSP00000402584:A952T;ENSP00000297153:A956T	ENSP00000297153:A956T	A	-	1	0	MDGA1	37713136	1.000000	0.71417	0.995000	0.50966	0.965000	0.64279	3.082000	0.50128	2.353000	0.79882	0.555000	0.69702	GCG	C|0.999;T|0.001	0.001	strong		0.632	MDGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040419.3			T	37605158	C	T	37605158	3	4	29	1	0	0	0	0	1	0	0	0	9415	739	26	2	17	2	MDGA1	6	37605158	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	466212	37605158	133509909	329	12570											
DNAH8	1769	hgsc.bcm.edu	37	chr6	38883000	38883000	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttagcagaagtcacagtaagCgctcaggcttcagccaaaat	14	8	9	10	1	3	1	3	0	0	1	3	1	3	1	1	1	3	4	1	1	5	3	rs150857304	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:38883000C>T	ENST00000359357.3	+	66	9590	c.9336C>T	c.(9334-9336)agC>agT	p.S3112S	DNAH8_ENST00000449981.2_Silent_p.S3329S|DNAH8_ENST00000441566.1_Silent_p.S3076S			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	3112	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						TCACAGTAAGCGCTCAGGCTT	0.353													C|||	4	0.000798722	0.0	0.0	5008	,	,		15337	0.001		0.002	False		,,,				2504	0.001				p.S3329S		Atlas-SNP	.											.	DNAH8	1239	.	0			c.C9987T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	60	60	60		9987	3	1	6	dbSNP_134	60	31,8569	21.6+/-65.8	0,31,4269	no	coding-synonymous	DNAH8	NM_001206927.1		0,33,6470	TT,TC,CC		0.3605,0.0454,0.2537		3329/4708	38883000	33,12973	2203	4300	6503	SO:0001819	synonymous_variant	1769	exon68			AGTAAGCGCTCAG	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.9336C>T	6.37:g.38883000C>T		89	0	0		103	79	0.76699	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	37																																																																																				C|0.998;T|0.002	0.002	strong		0.353	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927		T	38883000	C	T	38883000	2	4	29	1	0	0	0	0	0	0	0	1	4609	767	27	1		1	DNAH8	6	38883000	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1277842	38883000	132232067	330	12571											
TREML2	79865	hgsc.bcm.edu	37	chr6	41166063	41166063	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cttcctgattttgcaccaaaCcttgccctccacgcggtttt	6	14	6	15	2	0	1	0	1	0	0	2	1	2	1	5	1	3	2	5	1	1	6	rs147506354	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:41166063C>A	ENST00000483722.1	-	2	345	c.160G>T	c.(160-162)Gtt>Ttt	p.V54F		NM_024807.2	NP_079083.2	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid cells-like 2	54	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)					TTGCACCAAACCTTGCCCTCC	0.547																																					p.V54F		Atlas-SNP	.											.	TREML2	41	.	0			c.G160T						PASS	.	C	PHE/VAL	0,4406		0,0,2203	171	179	176		160	3.8	1	6	dbSNP_134	176	14,8586		0,14,4286	yes	missense	TREML2	NM_024807.2	50	0,14,6489	AA,AC,CC		0.1628,0.0,0.1076	probably-damaging	54/322	41166063	14,12992	2203	4300	6503	SO:0001583	missense	79865	exon2			ACCAAACCTTGCC	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.160G>T	6.37:g.41166063C>A	ENSP00000418767:p.Val54Phe	75	0	0		72	59	0.819444	NM_024807	Q08AP8|Q08AP9|Q8IWY0|Q9H8E9	Missense_Mutation	SNP	ENST00000483722.1	37	CCDS4853.2	.	.	.	.	.	.	.	.	.	.	.	15.93	2.976798	0.53720	0.0	0.001628	ENSG00000112195	ENST00000483722	T	0.64991	-0.13	4.75	3.84	0.44239	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.430853	0.19331	N	0.116887	T	0.54367	0.1854	L	0.47716	1.5	0.27559	N	0.950258	D	0.76494	0.999	D	0.75020	0.985	T	0.45977	-0.9224	10	0.17832	T	0.49	-4.2985	10.1612	0.42853	0.2078:0.7922:0.0:0.0	.	54	Q5T2D2	TRML2_HUMAN	F	54	ENSP00000418767:V54F	ENSP00000418767:V54F	V	-	1	0	TREML2	41274041	0.996000	0.38824	0.968000	0.41197	0.601000	0.36947	0.775000	0.26689	1.054000	0.40438	0.563000	0.77884	GTT	C|0.998;A|0.002	0.002	strong		0.547	TREML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043756.3	NM_024807		A	41166063	C	A	41166063	3	1	29	1	0	0	0	0	1	0	0	0	16488	507	18	4	821	4	TREML2	6	41166063	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2283063	41166063	129949004	331	12572											
CCND3	896	hgsc.bcm.edu	37	chr6	41909273	41909273	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaagtaggaggcgcggggtaCgtagcgctcctccaggcgga	8	5	18	10	5	0	0	0	0	0	0	2	3	2	2	2	6	2	4	2	6	4	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:41909273C>T	ENST00000372991.4	-	1	313	c.115G>A	c.(115-117)Gta>Ata	p.V39I	CCND3_ENST00000511642.1_Intron|CCND3_ENST00000415497.2_Intron|CCND3_ENST00000511686.1_Intron|CCND3_ENST00000372988.4_Intron|CCND3_ENST00000414200.2_Missense_Mutation_p.V39I|CCND3_ENST00000372987.4_5'Flank|CCND3_ENST00000510503.1_Intron	NM_001760.3	NP_001751.1	P30281	CCND3_HUMAN	cyclin D3	39	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)|signal transduction (GO:0007165)|T cell proliferation (GO:0042098)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase binding (GO:0019901)			endometrium(2)|haematopoietic_and_lymphoid_tissue(13)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	20	Colorectal(47;0.121)		Epithelial(12;0.000178)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			GCGCGGGGTACGTAGCGCTCC	0.706			T	IGH@	MM																																p.V39I		Atlas-SNP	.		Dom	yes		6	6p21	896	cyclin D3		L	.	CCND3	40	.	0			c.G115A						PASS	.						18	19	19					6																	41909273		2202	4297	6499	SO:0001583	missense	896	exon1			GGGGTACGTAGCG		CCDS4863.1, CCDS47425.1, CCDS47426.1, CCDS47427.1, CCDS75452.1	6p21	2008-08-26			ENSG00000112576	ENSG00000112576			1585	protein-coding gene	gene with protein product		123834				1386335	Standard	NM_001136125		Approved		uc003orn.3	P30281	OTTHUMG00000014690	ENST00000372991.4:c.115G>A	6.37:g.41909273C>T	ENSP00000362082:p.Val39Ile	104	0	0		72	22	0.305556	NM_001760	B2RD63|B3KQ22|E9PAS4|E9PB36|Q5T8J0|Q6FG62|Q96F49	Missense_Mutation	SNP	ENST00000372991.4	37	CCDS4863.1	.	.	.	.	.	.	.	.	.	.	c	13.50	2.255643	0.39896	.	.	ENSG00000112576	ENST00000372991;ENST00000414200	T;T	0.41758	2.82;0.99	3.15	2.2	0.27929	Cyclin, N-terminal (1);Cyclin-like (1);	0.986976	0.08207	U	0.981311	T	0.22859	0.0552	N	0.24115	0.695	0.80722	D	1	D;B;B	0.57899	0.981;0.079;0.006	P;B;B	0.62184	0.899;0.018;0.007	T	0.51116	-0.8746	10	0.19147	T	0.46	.	1.6151	0.02701	0.2449:0.4433:0.1833:0.1285	.	39;39;39	B4DRB9;E9PAS4;P30281	.;.;CCND3_HUMAN	I	39	ENSP00000362082:V39I;ENSP00000397545:V39I	ENSP00000362082:V39I	V	-	1	0	CCND3	42017251	0.000000	0.05858	1.000000	0.80357	0.772000	0.43724	0.043000	0.13971	0.568000	0.29311	0.313000	0.20887	GTA	.	.	none		0.706	CCND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040540.2	NM_001760		T	41909273	C	T	41909273	3	4	29	1	0	0	0	0	1	0	0	0	2920	536	19	1	783	1	CCND3	6	41909273	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	743210	41909273	129205794	332	12573											
TRERF1	55809	hgsc.bcm.edu	37	chr6	42236973	42236973	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gggagtaggtgtattggtagCcatcagtgggctcagcctgg	7	10	17	7	0	2	0	2	0	0	0	2	1	2	1	2	5	2	4	2	5	3	4	rs61756353	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:42236973C>T	ENST00000372922.4	-	5	918	c.356G>A	c.(355-357)gGc>gAc	p.G119D	TRERF1_ENST00000541110.1_Missense_Mutation_p.G119D|TRERF1_ENST00000354325.2_Missense_Mutation_p.G119D|TRERF1_ENST00000340840.2_Missense_Mutation_p.G119D|TRERF1_ENST00000372917.4_Missense_Mutation_p.G119D	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	119					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)			GTATTGGTAGCCATCAGTGGG	0.572													C|||	15	0.00299521	0.0	0.0	5008	,	,		19457	0.0		0.002	False		,,,				2504	0.0133				p.G119D		Atlas-SNP	.											.	TRERF1	124	.	0			c.G356A						PASS	.	C	ASP/GLY	3,4403	6.2+/-15.9	0,3,2200	165	167	166		356	4.6	1	6	dbSNP_129	166	29,8571	20.4+/-63.3	0,29,4271	yes	missense	TRERF1	NM_033502.2	94	0,32,6471	TT,TC,CC		0.3372,0.0681,0.246	probably-damaging	119/1201	42236973	32,12974	2203	4300	6503	SO:0001583	missense	55809	exon5			TGGTAGCCATCAG	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.356G>A	6.37:g.42236973C>T	ENSP00000362013:p.Gly119Asp	59	0	0		90	19	0.211111	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Missense_Mutation	SNP	ENST00000372922.4	37	CCDS4867.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	15.88	2.964211	0.53507	6.81E-4	0.003372	ENSG00000124496	ENST00000541110;ENST00000372917;ENST00000372922;ENST00000340840;ENST00000354325	T;T;T;T;T	0.18960	2.43;2.18;2.37;2.18;2.19	5.5	4.61	0.57282	.	0.096885	0.45361	D	0.000363	T	0.23886	0.0578	L	0.32530	0.975	0.37383	D	0.912135	D;D;D	0.76494	0.999;0.995;0.995	D;P;P	0.71414	0.973;0.878;0.878	T	0.07908	-1.0748	10	0.87932	D	0	-9.923	14.61	0.68510	0.0:0.7229:0.2771:0.0	rs61756353	119;119;119	Q96PN7-4;Q05GC8;Q96PN7	.;.;TREF1_HUMAN	D	119	ENSP00000439689:G119D;ENSP00000362008:G119D;ENSP00000362013:G119D;ENSP00000339438:G119D;ENSP00000346285:G119D	ENSP00000339438:G119D	G	-	2	0	TRERF1	42344951	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	3.339000	0.52135	1.291000	0.44653	0.462000	0.41574	GGC	C|0.997;T|0.003	0.003	strong		0.572	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502		T	42236973	C	T	42236973	3	4	29	1	0	0	0	0	1	0	0	0	16490	739	26	2	3302	2	TRERF1	6	42236973	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	327700	42236973	128878094	333	12574											
UBR2	23304	hgsc.bcm.edu	37	chr6	42613298	42613298	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtatcaagcctatggctcaTagtgaattggtaaagtcttt	12	14	9	6	0	3	1	2	1	1	0	3	1	3	1	1	2	1	3	1	2	7	6			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:42613298T>C	ENST00000372899.1	+	21	2637	c.2379T>C	c.(2377-2379)caT>caC	p.H793H	UBR2_ENST00000372883.3_Silent_p.H297H|UBR2_ENST00000372901.1_Silent_p.H793H	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	793					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)			CTATGGCTCATAGTGAATTGG	0.378																																					p.H793H		Atlas-SNP	.											.	UBR2	134	.	0			c.T2379C						PASS	.						114	109	111					6																	42613298		2203	4300	6503	SO:0001819	synonymous_variant	23304	exon21			GGCTCATAGTGAA	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.2379T>C	6.37:g.42613298T>C		45	0	0		47	20	0.425532	NM_015255	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Silent	SNP	ENST00000372899.1	37	CCDS4870.1																																																																																			.	.	none		0.378	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255		C	42613298	T	C	42613298	2	2	29	1	0	0	0	0	0	0	0	1	16917	1403	49	3		3	UBR2	6	42613298	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	376325	42613298	128501769	334	12575											
ZNF318	24149	hgsc.bcm.edu	37	chr6	43305991	43305991	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctagcccctcctcactaacAactgaaactccttgctcttg	9	12	4	16	0	3	1	1	1	2	0	5	1	5	1	4	0	5	1	4	0	4	4	rs374528550		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:43305991A>T	ENST00000361428.2	-	10	5822	c.5745T>A	c.(5743-5745)gtT>gtA	p.V1915V	ZNF318_ENST00000318149.3_Intron	NM_014345.2	NP_055160.2	Q5VUA4	ZN318_HUMAN	zinc finger protein 318	1915					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)			CCTCACTAACAACTGAAACTC	0.438																																					p.V1915V		Atlas-SNP	.											.	ZNF318	175	.	0			c.T5745A						PASS	.	A		0,4406		0,0,2203	98	98	98		5745	4	0.1	6		98	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ZNF318	NM_014345.2		0,1,6502	TT,TA,AA		0.0116,0.0,0.0077		1915/2280	43305991	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	24149	exon10			ACTAACAACTGAA	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.5745T>A	6.37:g.43305991A>T		96	0	0		102	58	0.568627	NM_014345	O94796|Q4G0E4|Q8NEM6|Q9UNU8|Q9Y2W9	Silent	SNP	ENST00000361428.2	37	CCDS4895.2																																																																																			.	.	weak		0.438	ZNF318-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040601.2	NM_014345		T	43305991	A	T	43305991	2	4	29	1	0	0	0	0	0	0	0	1	17851	117	5	5		5	ZNF318	6	43305991	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	692693	43305991	127809076	335	12576											
ENPP5	59084	hgsc.bcm.edu	37	chr6	46135795	46135795	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gttagggtaggtttttgtaaTaaaaacattagtaacttgct	13	16	9	3	0	0	0	0	0	0	0	0	0	0	0	0	2	3	6	0	2	8	9	rs34432940	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:46135795T>C	ENST00000371383.2	-	3	465	c.205A>G	c.(205-207)Att>Gtt	p.I69V	ENPP5_ENST00000230565.3_Missense_Mutation_p.I69V|ENPP5_ENST00000492313.1_5'Flank					ectonucleotide pyrophosphatase/phosphodiesterase 5 (putative)											endometrium(3)|kidney(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	12						GTTTTTGTAATAAAAACATTA	0.348													T|||	10	0.00199681	0.0	0.0043	5008	,	,		19208	0.0		0.007	False		,,,				2504	0.0				p.I69V		Atlas-SNP	.											.	ENPP5	44	.	0			c.A205G						PASS	.	T	VAL/ILE	11,4395	17.9+/-39.9	0,11,2192	53	50	51		205	3.1	1	6	dbSNP_126	51	76,8524	44.0+/-102.2	0,76,4224	yes	missense	ENPP5	NM_021572.4	29	0,87,6416	CC,CT,TT		0.8837,0.2497,0.6689	benign	69/478	46135795	87,12919	2203	4300	6503	SO:0001583	missense	59084	exon2			TTGTAATAAAAAC	AL035701	CCDS4915.1	6p21.1-p11.2	2010-06-24	2010-06-24		ENSG00000112796	ENSG00000112796			13717	protein-coding gene	gene with protein product						11027689	Standard	XM_005249259		Approved		uc003oxz.1	Q9UJA9	OTTHUMG00000014781	ENST00000371383.2:c.205A>G	6.37:g.46135795T>C	ENSP00000360436:p.Ile69Val	60	0	0		81	40	0.493827	NM_021572		Missense_Mutation	SNP	ENST00000371383.2	37	CCDS4915.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	T	11.84	1.757670	0.31137	0.002497	0.008837	ENSG00000112796	ENST00000371383;ENST00000230565	T;T	0.72167	-0.63;-0.63	5.51	3.07	0.35406	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.050250	0.85682	D	0.000000	T	0.32882	0.0844	N	0.20685	0.6	0.36437	D	0.865251	B;B	0.19331	0.035;0.035	B;B	0.24006	0.05;0.05	T	0.08743	-1.0707	10	0.21014	T	0.42	-24.9657	8.0281	0.30448	0.0:0.1187:0.1209:0.7604	rs34432940	69;69	A8K9X7;Q9UJA9	.;ENPP5_HUMAN	V	69	ENSP00000360436:I69V;ENSP00000230565:I69V	ENSP00000230565:I69V	I	-	1	0	ENPP5	46243754	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.504000	0.45416	1.010000	0.39314	0.482000	0.46254	ATT	T|0.993;C|0.007	0.007	strong		0.348	ENPP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040779.2			C	46135795	T	C	46135795	3	2	29	1	0	0	0	0	1	0	0	0	5135	1406	49	3	1240	3	ENPP5	6	46135795	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	2829804	46135795	124979272	336	12577											
DEFB110	245913	hgsc.bcm.edu	37	chr6	49986738	49986738	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ggtcttatgcagtaagcaatCctaatttcattttcatgaca	12	15	6	8	0	3	1	2	1	1	0	4	1	4	1	1	1	2	3	1	1	4	6	rs115648436	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:49986738C>T	ENST00000371148.2	-	2	201	c.156G>A	c.(154-156)agG>agA	p.R52R	DEFB110_ENST00000393660.2_Intron	NM_001037497.1	NP_001032586.1	Q30KQ9	DB110_HUMAN	defensin, beta 110 locus	52					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(1)|lung(1)|ovary(1)	3	Lung NSC(77;0.042)					AGTAAGCAATCCTAATTTCAT	0.403													C|||	30	0.00599042	0.0008	0.0115	5008	,	,		21326	0.0		0.0209	False		,,,				2504	0.0				p.R52R		Atlas-SNP	.											.	DEFB110	5	.	0			c.G156A						PASS	.	C	,	14,4392	19.1+/-41.9	0,14,2189	164	139	147		156,	-4.2	0.9	6	dbSNP_132	147	129,8471	66.3+/-128.7	0,129,4171	no	coding-synonymous,intron	DEFB110	NM_001037497.1,NM_001037728.2	,	0,143,6360	TT,TC,CC		1.5,0.3177,1.0995	,	52/68,	49986738	143,12863	2203	4300	6503	SO:0001819	synonymous_variant	245913	exon2			AGCAATCCTAATT	DQ012014, BC148541	CCDS43473.1, CCDS34475.1	6p12.3	2010-11-26	2010-11-26		ENSG00000203970	ENSG00000203970		"Defensins, beta"	18091	protein-coding gene	gene with protein product			"defensin, beta 110"			11854508, 16033865	Standard	NM_001037728		Approved	DEFB-10, DEFB-11, DEFB111	uc003pac.3	Q30KQ9	OTTHUMG00000160208	ENST00000371148.2:c.156G>A	6.37:g.49986738C>T		159	0	0		132	65	0.492424	NM_001037497	Q30KR0	Silent	SNP	ENST00000371148.2	37	CCDS34475.1																																																																																			C|0.991;T|0.009	0.009	strong		0.403	DEFB110-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359664.1	NM_001037728		T	49986738	C	T	49986738	2	4	29	1	0	0	0	0	0	0	0	1	4402	854	30	2		2	DEFB110	6	49986738	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	3850943	49986738	121128329	337	12578											
DST	667	hgsc.bcm.edu	37	chr6	56505175	56505175	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcaggcgggaagtcatcccTgatgacaggccagaagtcat	11	7	13	10	1	3	3	3	2	0	1	4	4	4	4	2	3	0	0	2	3	2	0	rs113432929	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:56505175T>A	ENST00000361203.3	-	14	1630	c.1623A>T	c.(1621-1623)tcA>tcT	p.S541S	DST_ENST00000370769.4_Silent_p.S541S|DST_ENST00000518935.1_Silent_p.S215S|DST_ENST00000421834.2_Silent_p.S541S|DST_ENST00000370788.2_Silent_p.S541S|DST_ENST00000312431.6_Silent_p.S541S|DST_ENST00000370765.6_Silent_p.S215S|DST_ENST00000370754.5_Silent_p.S719S|DST_ENST00000244364.6_Silent_p.S215S|DST_ENST00000446842.2_Silent_p.S215S			Q03001	DYST_HUMAN	dystonin	541					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)			AAGTCATCCCTGATGACAGGC	0.483													T|||	11	0.00219649	0.0	0.0	5008	,	,		18999	0.0		0.005	False		,,,				2504	0.0061				p.S215S		Atlas-SNP	.											.	DST	1427	.	0			c.A645T						PASS	.	T	,	4,4402	8.1+/-20.4	0,4,2199	139	141	141		645,645	-4.8	0.6	6	dbSNP_132	141	36,8564	25.1+/-72.6	0,36,4264	yes	coding-synonymous,coding-synonymous	DST	NM_001723.5,NM_015548.4	,	0,40,6463	AA,AT,TT		0.4186,0.0908,0.3076	,	215/2650,215/5172	56505175	40,12966	2203	4300	6503	SO:0001819	synonymous_variant	667	exon4			CATCCCTGATGAC	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.1623A>T	6.37:g.56505175T>A		136	0	0		132	70	0.530303	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	37																																																																																				T|0.997;A|0.003	0.003	strong		0.483	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		A	56505175	T	A	56505175	2	1	29	1	0	0	0	0	0	0	0	1	4785	1567	55	5		5	DST	6	56505175	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	6518437	56505175	114609892	338	12579											
KIAA1586	57691	hgsc.bcm.edu	37	chr6	56918304	56918304	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctagtgatttatctccagtGcacaattcagtcagctcctg	9	13	7	12	0	3	1	2	1	1	0	5	1	4	1	3	0	2	2	3	0	3	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:56918304G>A	ENST00000370733.4	+	4	1214	c.1007G>A	c.(1006-1008)tGc>tAc	p.C336Y	KIAA1586_ENST00000545356.1_Missense_Mutation_p.C309Y	NM_020931.2	NP_065982.1	Q9HCI6	K1586_HUMAN	KIAA1586	336							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)			TATCTCCAGTGCACAATTCAG	0.338																																					p.C336Y		Atlas-SNP	.											.	KIAA1586	59	.	0			c.G1007A						PASS	.						118	118	118					6																	56918304		2203	4298	6501	SO:0001583	missense	57691	exon4			TCCAGTGCACAAT	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.1007G>A	6.37:g.56918304G>A	ENSP00000359768:p.Cys336Tyr	74	0	0		83	31	0.373494	NM_020931	A8K4M3|Q8IW25	Missense_Mutation	SNP	ENST00000370733.4	37	CCDS34480.1	.	.	.	.	.	.	.	.	.	.	g	0.157	-1.085057	0.01888	.	.	ENSG00000168116	ENST00000370733;ENST00000545356	T;T	0.14893	2.47;2.47	2.93	0.941	0.19519	Ribonuclease H-like (1);	.	.	.	.	T	0.01353	0.0044	N	0.08118	0	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.002	T	0.47275	-0.9130	9	0.02654	T	1	1.9773	3.2772	0.06902	0.1485:0.0:0.5958:0.2557	.	309;336	F5H2N6;Q9HCI6	.;K1586_HUMAN	Y	336;309	ENSP00000359768:C336Y;ENSP00000445507:C309Y	ENSP00000359768:C336Y	C	+	2	0	KIAA1586	57026263	0.107000	0.21998	0.032000	0.17829	0.981000	0.71138	0.017000	0.13399	0.070000	0.16634	0.467000	0.42956	TGC	.	.	none		0.338	KIAA1586-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041033.1	NM_020931		A	56918304	G	A	56918304	3	1	29	1	0	0	0	0	1	0	0	0	8254	1319	46	2	1021	2	KIAA1586	6	56918304	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	413129	56918304	114196763	339	12580											
BAI3	577	hgsc.bcm.edu	37	chr6	69348966	69348966	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttattcaaatacgtcgagtAtttccaactaatttcccagg	12	15	5	9	2	1	0	1	0	0	0	4	1	3	0	2	1	2	1	2	1	6	8			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:69348966A>C	ENST00000370598.1	+	3	1220	c.399A>C	c.(397-399)gtA>gtC	p.V133V		NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	133	CUB. {ECO:0000255|PROSITE- ProRule:PRU00059}.				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)				TACGTCGAGTATTTCCAACTA	0.323																																					p.V133V		Atlas-SNP	.											BAI3,NS,carcinoma,+1,1	BAI3	451	1	0			c.A399C						scavenged	.						39	42	41					6																	69348966		2202	4300	6502	SO:0001819	synonymous_variant	577	exon3			TCGAGTATTTCCA	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.399A>C	6.37:g.69348966A>C		36	0	0		43	9	0.209302	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Silent	SNP	ENST00000370598.1	37	CCDS4968.1																																																																																			.	.	none		0.323	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			C	69348966	A	C	69348966	2	2	29	1	0	0	0	0	0	0	0	1	1300	436	16	5		5	BAI3	6	69348966	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	12430662	69348966	101766101	340	12581											
CD109	135228	hgsc.bcm.edu	37	chr6	74481186	74481186	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtaaagtgaaagctgaacCatctgagaaagtctctctta	15	10	9	7	0	3	3	0	3	3	1	4	5	3	3	1	0	2	2	1	0	6	2	rs41266745	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:74481186C>T	ENST00000287097.5	+	15	1821	c.1709C>T	c.(1708-1710)cCa>cTa	p.P570L	CD109_ENST00000437994.2_Missense_Mutation_p.P570L|CD109_ENST00000422508.2_Missense_Mutation_p.P493L			Q6YHK3	CD109_HUMAN	CD109 molecule	570					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						AAAGCTGAACCATCTGAGAAA	0.368													C|||	3	0.000599042	0.0	0.0014	5008	,	,		18121	0.0		0.001	False		,,,				2504	0.001				p.P570L		Atlas-SNP	.											.	CD109	170	.	0			c.C1709T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO	9,4397	15.5+/-35.6	1,7,2195	94	90	92		1709,1478,1709	4.6	0.9	6	dbSNP_127	92	35,8565	24.6+/-71.5	0,35,4265	yes	missense,missense,missense	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	98,98,98	1,42,6460	TT,TC,CC		0.407,0.2043,0.3383	probably-damaging,probably-damaging,probably-damaging	570/1429,493/1369,570/1446	74481186	44,12962	2203	4300	6503	SO:0001583	missense	135228	exon15			CTGAACCATCTGA	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.1709C>T	6.37:g.74481186C>T	ENSP00000287097:p.Pro570Leu	57	0	0		43	23	0.534884	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	37	CCDS4982.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	15.80	2.940037	0.52972	0.002043	0.00407	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.79554	-1.28;-1.28;-1.28	5.5	4.64	0.57946	Alpha-2-macroglobulin, N-terminal 2 (1);	0.000000	0.85682	D	0.000000	D	0.88851	0.6549	M	0.88570	2.965	0.58432	D	0.999999	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.91635	0.935;0.999;0.999;0.998	D	0.91181	0.4976	10	0.87932	D	0	.	13.4261	0.61026	0.0:0.9239:0.0:0.0761	rs41266745	493;570;570;570	Q6YHK3-2;Q6YHK3-3;Q6YHK3-4;Q6YHK3	.;.;.;CD109_HUMAN	L	570;493;570	ENSP00000388062:P570L;ENSP00000404475:P493L;ENSP00000287097:P570L	ENSP00000287097:P570L	P	+	2	0	CD109	74537907	1.000000	0.71417	0.884000	0.34674	0.286000	0.27126	4.749000	0.62155	1.567000	0.49668	0.655000	0.94253	CCA	C|0.998;T|0.002	0.002	strong		0.368	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493		T	74481186	C	T	74481186	3	4	29	1	0	0	0	0	1	0	0	0	2965	594	21	2	1767	2	CD109	6	74481186	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	5132220	74481186	96633881	341	12582											
COL12A1	1303	hgsc.bcm.edu	37	chr6	75827165	75827165	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctcaaaagattcaaagtcGtccacaatgaacacgtgccg	14	9	7	11	3	2	2	2	1	1	1	5	2	3	2	2	0	2	0	2	0	5	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:75827165G>A	ENST00000322507.8	-	47	7761	c.7452C>T	c.(7450-7452)gaC>gaT	p.D2484D	COL12A1_ENST00000483888.2_Silent_p.D2484D|COL12A1_ENST00000416123.2_Silent_p.D2484D|COL12A1_ENST00000345356.6_Silent_p.D1320D	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	2484	Nonhelical region (NC3).|VWFA 4. {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)	p.D2484E(1)		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						ATTCAAAGTCGTCCACAATGA	0.423																																					p.D2484D		Atlas-SNP	.											COL12A1,NS,carcinoma,0,1	COL12A1	385	1	1	Substitution - Missense(1)	lung(1)	c.C7452T						PASS	.						120	118	119					6																	75827165		1968	4174	6142	SO:0001819	synonymous_variant	1303	exon47			AAAGTCGTCCACA	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.7452C>T	6.37:g.75827165G>A		98	0	0		67	22	0.328358	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	37	CCDS43482.1																																																																																			.	.	none		0.423	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		A	75827165	G	A	75827165	2	1	29	1	0	0	0	0	0	0	0	1	3671	1136	40	1		1	COL12A1	6	75827165	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1345979	75827165	95287902	342	12583											
MYO6	4646	hgsc.bcm.edu	37	chr6	76572352	76572352	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgggaatactggatatttTggatgaagaaaatcgccttc	13	12	11	5	1	0	2	0	1	0	1	2	5	0	5	1	3	1	0	1	3	6	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:76572352T>G	ENST00000369977.3	+	16	1725	c.1586T>G	c.(1585-1587)tTg>tGg	p.L529W	MYO6_ENST00000369981.3_Missense_Mutation_p.L529W|RNA5SP209_ENST00000411237.1_RNA|MYO6_ENST00000369985.4_Missense_Mutation_p.L529W|MYO6_ENST00000369975.1_Missense_Mutation_p.L529W	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	529	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)		CTGGATATTTTGGATGAAGAA	0.348																																					p.L529W		Atlas-SNP	.											.	MYO6	124	.	0			c.T1586G						PASS	.						103	94	97					6																	76572352		2203	4300	6503	SO:0001583	missense	4646	exon16			ATATTTTGGATGA	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.1586T>G	6.37:g.76572352T>G	ENSP00000358994:p.Leu529Trp	133	0	0		124	6	0.0483871	NM_004999	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Missense_Mutation	SNP	ENST00000369977.3	37	CCDS34487.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.123528	0.77436	.	.	ENSG00000196586	ENST00000428345;ENST00000369981;ENST00000369985;ENST00000369977;ENST00000369975	D;D;D;D	0.86097	-2.07;-2.07;-2.07;-2.07	5.9	3.46	0.39613	.	0.000000	0.64402	D	0.000001	D	0.94820	0.8327	H	0.99719	4.725	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.94846	0.8009	10	0.87932	D	0	.	11.41	0.49921	0.2412:0.0:0.0:0.7588	.	529;529	Q9UM54-2;Q9UM54-1	.;.	W	529	ENSP00000358998:L529W;ENSP00000359002:L529W;ENSP00000358994:L529W;ENSP00000358992:L529W	ENSP00000358992:L529W	L	+	2	0	MYO6	76629072	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.698000	0.84413	0.458000	0.26988	0.528000	0.53228	TTG	.	.	none		0.348	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999		G	76572352	T	G	76572352	3	3	29	1	0	0	0	0	1	0	0	0	10090	1821	63	5	1644	5	MYO6	6	76572352	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	745187	76572352	94542715	343	12584											
SYNCRIP	10492	hgsc.bcm.edu	37	chr6	86332210	86332210	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctatcattacctttgccataAcctcaggatcaggatcttct	10	14	5	12	0	5	0	3	0	2	0	5	2	5	2	3	2	3	0	3	2	3	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:86332210A>C	ENST00000369622.3	-	8	1498	c.998T>G	c.(997-999)gTt>gGt	p.V333G	SYNCRIP_ENST00000355238.6_Missense_Mutation_p.V333G	NM_001159675.1|NM_006372.4	NP_001153147.1|NP_006363.4	O60506	HNRPQ_HUMAN	synaptotagmin binding, cytoplasmic RNA interacting protein	333					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)		CTTTGCCATAACCTCAGGATC	0.448																																					p.V333G		Atlas-SNP	.											.	SYNCRIP	80	.	0			c.T998G						PASS	.						221	215	217					6																	86332210		2203	4300	6503	SO:0001583	missense	10492	exon8			GCCATAACCTCAG	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.998T>G	6.37:g.86332210A>C	ENSP00000358635:p.Val333Gly	93	0	0		113	6	0.0530973	NM_006372	E1P501|E1P502|Q53H05|Q5TCG2|Q5TCG3|Q8IW78|Q8N599|Q96LC1|Q96LC2|Q9Y583	Missense_Mutation	SNP	ENST00000369622.3	37	CCDS5005.1	.	.	.	.	.	.	.	.	.	.	A	18.50	3.636864	0.67130	.	.	ENSG00000135316	ENST00000355238;ENST00000369622	T;T	0.74526	-0.85;-0.85	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.59376	0.2189	L	0.41079	1.255	0.80722	D	1	B;B;B;B;B	0.28667	0.219;0.122;0.089;0.193;0.219	B;B;B;B;B	0.31442	0.054;0.078;0.13;0.066;0.054	T	0.65800	-0.6080	10	0.87932	D	0	.	16.0711	0.80936	1.0:0.0:0.0:0.0	.	333;235;181;333;333	O60506;B7Z645;O60506-5;O60506-3;B2R8Z8	HNRPQ_HUMAN;.;.;.;.	G	333	ENSP00000347380:V333G;ENSP00000358635:V333G	ENSP00000347380:V333G	V	-	2	0	SYNCRIP	86388929	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.287000	0.95975	2.197000	0.70478	0.482000	0.46254	GTT	.	.	none		0.448	SYNCRIP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041396.1	NM_006372		C	86332210	A	C	86332210	3	2	29	1	0	0	0	0	1	0	0	0	15459	43	2	5	935	5	SYNCRIP	6	86332210	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	9759858	86332210	84782857	344	12585											
GRIK2	2898	hgsc.bcm.edu	37	chr6	102074485	102074485	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtttttcaagtggaaaaccGtcacggttgtgtatgatgac	11	13	11	6	2	2	2	2	2	0	0	2	3	2	3	1	2	1	3	1	2	4	4	rs201893729		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:102074485G>A	ENST00000421544.1	+	3	1004	c.514G>A	c.(514-516)Gtc>Atc	p.V172I	GRIK2_ENST00000358361.3_Missense_Mutation_p.V172I|GRIK2_ENST00000369138.1_Missense_Mutation_p.V172I|GRIK2_ENST00000413795.1_Missense_Mutation_p.V172I|GRIK2_ENST00000369137.3_Missense_Mutation_p.V172I|GRIK2_ENST00000369134.4_Missense_Mutation_p.V123I|GRIK2_ENST00000318991.6_Missense_Mutation_p.V172I	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	172					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)	GTGGAAAACCGTCACGGTTGT	0.408																																					p.V172I		Atlas-SNP	.											GRIK2_ENST00000421544,NS,carcinoma,0,2	GRIK2	487	2	0			c.G514A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL	0,4406		0,0,2203	73	77	76		514,514,514	5.8	1	6		76	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	GRIK2	NM_001166247.1,NM_021956.4,NM_175768.3	29,29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign	172/893,172/909,172/870	102074485	1,13005	2203	4300	6503	SO:0001583	missense	2898	exon3			AAAACCGTCACGG		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.514G>A	6.37:g.102074485G>A	ENSP00000397026:p.Val172Ile	96	0	0		107	60	0.560748	NM_021956	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Missense_Mutation	SNP	ENST00000421544.1	37	CCDS5048.1	.	.	.	.	.	.	.	.	.	.	G	17.01	3.278793	0.59758	0.0	1.16E-4	ENSG00000164418	ENST00000421544;ENST00000413795;ENST00000369138;ENST00000358361;ENST00000369137;ENST00000318991;ENST00000403289;ENST00000369134;ENST00000540076	D;D;D;D;D;D;D	0.86497	-2.13;-2.13;-2.13;-2.13;-2.13;-2.13;-2.13	5.79	5.79	0.91817	Extracellular ligand-binding receptor (1);	0.135274	0.49305	D	0.000153	T	0.80788	0.4690	L	0.46670	1.46	0.51767	D	0.999939	B;B;B	0.09022	0.002;0.002;0.002	B;B;B	0.21151	0.033;0.022;0.019	T	0.74928	-0.3497	10	0.45353	T	0.12	.	20.024	0.97514	0.0:0.0:1.0:0.0	.	172;172;172	Q13002-5;Q13002;Q13002-2	.;GRIK2_HUMAN;.	I	172;172;172;172;172;172;172;123;134	ENSP00000397026:V172I;ENSP00000405596:V172I;ENSP00000358134:V172I;ENSP00000351128:V172I;ENSP00000358133:V172I;ENSP00000313276:V172I;ENSP00000358130:V123I	ENSP00000313276:V172I	V	+	1	0	GRIK2	102181178	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	7.647000	0.83462	2.718000	0.92993	0.655000	0.94253	GTC	G|0.999;A|0.001	0.001	weak		0.408	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1			A	102074485	G	A	102074485	3	1	29	1	0	0	0	0	1	0	0	0	6783	1145	40	1	524	1	GRIK2	6	102074485	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	15742275	102074485	69040582	345	12586											
SCML4	256380	hgsc.bcm.edu	37	chr6	108067907	108067907	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccttacctgacaccatctcaCcaccatagccctgcttgacc	9	9	4	19	0	1	2	1	2	1	0	2	2	1	2	7	0	3	1	7	0	2	3	rs142985964	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:108067907C>T	ENST00000369020.3	-	4	718	c.473G>A	c.(472-474)gGt>gAt	p.G158D	SCML4_ENST00000479803.1_5'Flank|SCML4_ENST00000369021.3_Missense_Mutation_p.G129D|SCML4_ENST00000369022.2_Missense_Mutation_p.G100D	NM_198081.3	NP_932347.2	Q8N228	SCML4_HUMAN	sex comb on midleg-like 4 (Drosophila)	158					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(1)	25		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)		CACCATCTCACCACCATAGCC	0.622													C|||	2	0.000399361	0.0	0.0	5008	,	,		17701	0.0		0.002	False		,,,				2504	0.0				p.G158D		Atlas-SNP	.											.	SCML4	65	.	0			c.G473A						PASS	.	C	ASP/GLY	4,4402	6.2+/-15.9	0,4,2199	101	99	100		473	5	0.8	6	dbSNP_134	100	16,8584	11.2+/-40.8	0,16,4284	yes	missense	SCML4	NM_198081.3	94	0,20,6483	TT,TC,CC		0.186,0.0908,0.1538	probably-damaging	158/415	108067907	20,12986	2203	4300	6503	SO:0001583	missense	256380	exon4			ATCTCACCACCAT		CCDS5060.2, CCDS69163.1, CCDS75500.1	6q21	2013-01-10			ENSG00000146285	ENSG00000146285		"Sterile alpha motif (SAM) domain containing"	21397	protein-coding gene	gene with protein product							Standard	NM_001286409		Approved	dJ47M23.1	uc010kdf.3	Q8N228	OTTHUMG00000015313	ENST00000369020.3:c.473G>A	6.37:g.108067907C>T	ENSP00000358016:p.Gly158Asp	85	0	0		63	35	0.555556	NM_198081	B0QZ10|B0QZ11|B7ZBX3|Q5JXD0|Q5T0T6|Q8IYY6	Missense_Mutation	SNP	ENST00000369020.3	37	CCDS5060.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	21.6	4.172295	0.78452	9.08E-4	0.00186	ENSG00000146285	ENST00000369022;ENST00000369020;ENST00000369021;ENST00000440927	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	4.98	4.98	0.66077	.	0.787668	0.12505	N	0.462982	T	0.68449	0.3002	M	0.84326	2.69	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.97110	1.0;0.987;0.991	T	0.69011	-0.5258	10	0.54805	T	0.06	.	18.4486	0.90695	0.0:1.0:0.0:0.0	.	158;158;129	B4E0X3;Q8N228;Q8N228-3	.;SCML4_HUMAN;.	D	100;158;129;129	ENSP00000358018:G100D;ENSP00000358016:G158D;ENSP00000358017:G129D;ENSP00000404688:G129D	ENSP00000358016:G158D	G	-	2	0	SCML4	108174600	0.999000	0.42202	0.798000	0.32154	0.803000	0.45373	4.444000	0.60001	2.589000	0.87451	0.563000	0.77884	GGT	C|0.999;T|0.001	0.001	strong		0.622	SCML4-005	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000041700.3	XM_171128		T	108067907	C	T	108067907	3	4	29	1	0	0	0	0	1	0	0	0	13926	507	18	2	791	2	SCML4	6	108067907	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	5993422	108067907	63047160	346	12587											
ZBTB24	9841	hgsc.bcm.edu	37	chr6	109796673	109796673	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatggcagtctttgcattccGgtaatgagtggccttgtcgc	6	13	13	9	2	1	1	0	1	1	0	3	2	2	1	2	3	1	3	2	3	1	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:109796673G>A	ENST00000230122.3	-	5	1384	c.1217C>T	c.(1216-1218)cCg>cTg	p.P406L		NM_001164313.1|NM_014797.2	NP_001157785.1|NP_055612.2	O43167	ZBT24_HUMAN	zinc finger and BTB domain containing 24	406					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)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	22		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;0.0154)|all cancers(137;0.0216)|OV - Ovarian serous cystadenocarcinoma(136;0.0242)|BRCA - Breast invasive adenocarcinoma(108;0.059)		TTTGCATTCCGGTAATGAGTG	0.448																																					p.P406L		Atlas-SNP	.											.	ZBTB24	64	.	0			c.C1217T						PASS	.						184	153	163					6																	109796673		2203	4300	6503	SO:0001583	missense	9841	exon5			CATTCCGGTAATG	AB007901	CCDS34509.1	6q21	2014-09-17	2004-04-15	2004-04-16	ENSG00000112365	ENSG00000112365		"-", "Zinc fingers, C2H2-type", "BTB/POZ domain containing"	21143	protein-coding gene	gene with protein product	"POZ (BTB) and AT hook containing zinc finger 2"	614064	"zinc finger protein 450"	ZNF450		9455477	Standard	NM_014797		Approved	KIAA0441, BIF1, PATZ2	uc003ptl.1	O43167	OTTHUMG00000015349	ENST00000230122.3:c.1217C>T	6.37:g.109796673G>A	ENSP00000230122:p.Pro406Leu	82	0	0		74	4	0.0540541	NM_014797	Q17RC6|Q5TED5|Q8N455	Missense_Mutation	SNP	ENST00000230122.3	37	CCDS34509.1	.	.	.	.	.	.	.	.	.	.	G	17.53	3.412005	0.62511	.	.	ENSG00000112365	ENST00000230122	T	0.35605	1.3	6.17	6.17	0.99709	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	0.000000	0.85682	D	0.000000	T	0.26557	0.0649	N	0.01493	-0.835	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.54879	-0.8227	10	0.36615	T	0.2	-25.2969	20.8794	0.99867	0.0:0.0:1.0:0.0	.	406	O43167	ZBT24_HUMAN	L	406	ENSP00000230122:P406L	ENSP00000230122:P406L	P	-	2	0	ZBTB24	109903366	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	7.334000	0.79224	2.941000	0.99782	0.655000	0.94253	CCG	.	.	none		0.448	ZBTB24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041758.1	NM_014797		A	109796673	G	A	109796673	3	1	29	1	0	0	0	0	1	0	0	0	17546	1116	39	1	888	1	ZBTB24	6	109796673	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1728766	109796673	61318394	347	12588											
LAMA4	3910	hgsc.bcm.edu	37	chr6	112493894	112493894	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttaagggcctggtcaagtgcTtcctggagatctgacaactt	9	12	11	9	0	2	2	1	1	1	1	3	3	3	2	2	3	2	1	2	3	3	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:112493894T>A	ENST00000230538.7	-	12	1867	c.1470A>T	c.(1468-1470)gaA>gaT	p.E490D	LAMA4_ENST00000389463.4_Missense_Mutation_p.E483D|LAMA4_ENST00000522006.1_Missense_Mutation_p.E483D|LAMA4_ENST00000424408.2_Missense_Mutation_p.E483D	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	490	Domain II and I.				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)		GGTCAAGTGCTTCCTGGAGAT	0.567																																					p.E490D		Atlas-SNP	.											.	LAMA4	227	.	0			c.A1470T						PASS	.						112	92	99					6																	112493894		2203	4300	6503	SO:0001583	missense	3910	exon12			AAGTGCTTCCTGG		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.1470A>T	6.37:g.112493894T>A	ENSP00000230538:p.Glu490Asp	109	0	0		100	41	0.41	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Missense_Mutation	SNP	ENST00000230538.7	37	CCDS43491.1	.	.	.	.	.	.	.	.	.	.	T	5.231	0.228154	0.09916	.	.	ENSG00000112769	ENST00000230538;ENST00000522006;ENST00000389463;ENST00000424408	T;T;T;T	0.10960	2.82;2.82;2.82;2.82	5.51	-2.99	0.05497	Laminin I (1);	0.481995	0.24449	N	0.038440	T	0.06096	0.0158	L	0.50333	1.59	0.80722	D	1	P;P	0.51057	0.941;0.928	P;P	0.51516	0.672;0.597	T	0.24012	-1.0172	10	0.16420	T	0.52	.	12.0218	0.53348	0.0:0.6685:0.0:0.3315	.	490;483	Q16363;Q16363-2	LAMA4_HUMAN;.	D	490;483;483;483	ENSP00000230538:E490D;ENSP00000429488:E483D;ENSP00000374114:E483D;ENSP00000416470:E483D	ENSP00000230538:E490D	E	-	3	2	LAMA4	112600587	0.999000	0.42202	0.971000	0.41717	0.337000	0.28794	0.376000	0.20535	-0.328000	0.08539	-0.371000	0.07208	GAA	.	.	none		0.567	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206		A	112493894	T	A	112493894	3	1	29	1	0	0	0	0	1	0	0	0	8617	1606	56	5	4113	5	LAMA4	6	112493894	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	2697221	112493894	58621173	348	12589											
VGLL2	245806	hgsc.bcm.edu	37	chr6	117586990	117586990	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agccctacttcgcagccgccTacaccccctaccaccaggta	9	6	6	20	2	0	0	0	0	0	0	1	0	0	0	7	1	5	2	7	1	4	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:117586990T>G	ENST00000326274.5	+	1	254	c.64T>G	c.(64-66)Tac>Gac	p.Y22D	VGLL2_ENST00000352536.3_Missense_Mutation_p.Y22D	NM_182645.3	NP_872586.1	Q8N8G2	VGLL2_HUMAN	vestigial-like family member 2	22					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)		CGCAGCCGCCTACACCCCCTA	0.587																																					p.Y22D		Atlas-SNP	.											.	VGLL2	18	.	0			c.T64G						PASS	.						104	83	90					6																	117586990		2203	4300	6503	SO:0001583	missense	245806	exon1			GCCGCCTACACCC	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.64T>G	6.37:g.117586990T>G	ENSP00000320957:p.Tyr22Asp	53	0	0		68	24	0.352941	NM_182645	Q8WWX1	Missense_Mutation	SNP	ENST00000326274.5	37	CCDS5115.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.336151	0.81801	.	.	ENSG00000170162	ENST00000352536;ENST00000326274	T	0.49720	0.77	5.17	5.17	0.71159	.	0.165964	0.41712	D	0.000824	T	0.49253	0.1546	L	0.34521	1.04	0.58432	D	0.999998	D;D	0.71674	0.997;0.998	D;D	0.78314	0.991;0.991	T	0.56637	-0.7946	10	0.72032	D	0.01	-6.5683	15.0077	0.71524	0.0:0.0:0.0:1.0	.	22;22	Q8N8G2-2;Q8N8G2	.;VGLL2_HUMAN	D	22	ENSP00000320957:Y22D	ENSP00000320957:Y22D	Y	+	1	0	VGLL2	117693683	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.294000	0.65687	1.961000	0.56991	0.460000	0.39030	TAC	.	.	none		0.587	VGLL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041975.2	NM_153453		G	117586990	T	G	117586990	3	3	29	1	0	0	0	0	1	0	0	0	17174	1522	53	5	66	5	VGLL2	6	117586990	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	5093096	117586990	53528077	349	12590											
FABP7	2173	hgsc.bcm.edu	37	chr6	123104889	123104889	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttttggtgatgtggttgctGttcgccactatgagaaggca	7	14	13	7	1	0	2	0	2	0	1	1	3	0	2	1	3	1	4	1	3	2	5	rs77153426	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:123104889G>A	ENST00000368444.3	+	4	696	c.376G>A	c.(376-378)Gtt>Att	p.V126I		NM_001446.3	NP_001437.1	O15540	FABP7_HUMAN	fatty acid binding protein 7, brain	126					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)	TGTGGTTGCTGTTCGCCACTA	0.393													G|||	2	0.000399361	0.0	0.0	5008	,	,		15417	0.0		0.001	False		,,,				2504	0.001				p.V126I		Atlas-SNP	.											.	FABP7	10	.	0			c.G376A						PASS	.						175	166	169					6																	123104889		2203	4300	6503	SO:0001583	missense	2173	exon4			GTTGCTGTTCGCC	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.376G>A	6.37:g.123104889G>A	ENSP00000357429:p.Val126Ile	120	0	0		137	65	0.474453	NM_001446	B2R4L1|O14951|Q6IAU7|Q9H047	Missense_Mutation	SNP	ENST00000368444.3	37	CCDS5127.1	.	.	.	.	.	.	.	.	.	.	G	16.45	3.128112	0.56721	.	.	ENSG00000164434	ENST00000368444	T	0.08720	3.06	5.4	3.59	0.41128	Calycin-like (1);Cytosolic fatty-acid binding (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	.	.	.	.	T	0.03695	0.0105	L	0.45285	1.41	0.80722	D	1	B	0.06786	0.001	B	0.11329	0.006	T	0.16100	-1.0414	9	0.49607	T	0.09	.	11.852	0.52417	0.143:0.0:0.857:0.0	.	126	O15540	FABP7_HUMAN	I	126	ENSP00000357429:V126I	ENSP00000357429:V126I	V	+	1	0	FABP7	123146588	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.409000	0.59768	1.414000	0.47017	0.462000	0.41574	GTT	.	.	alt		0.393	FABP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042037.1	NM_001446		A	123104889	G	A	123104889	3	1	29	1	0	0	0	0	1	0	0	0	5367	1377	48	2	390	2	FABP7	6	123104889	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	5517899	123104889	48010178	350	12591											
LAMA2	3908	hgsc.bcm.edu	37	chr6	129813567	129813567	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcagctccagctgaaatagTtatccagcctgagccagttc	11	9	9	12	0	0	2	0	2	0	0	3	2	2	2	4	0	5	5	4	0	3	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:129813567T>A	ENST00000421865.2	+	58	8232	c.8183T>A	c.(8182-8184)gTt>gAt	p.V2728D	LAMA2_ENST00000498257.1_3'UTR	NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2728					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)		GCTGAAATAGTTATCCAGCCT	0.473																																					p.V2728D		Atlas-SNP	.											.	LAMA2	481	.	0			c.T8183A						PASS	.						92	95	94					6																	129813567		2203	4300	6503	SO:0001583	missense	3908	exon58			AAATAGTTATCCA	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.8183T>A	6.37:g.129813567T>A	ENSP00000400365:p.Val2728Asp	90	0	0		73	39	0.534247	NM_000426	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	.	.	.	.	.	.	.	.	.	.	T	12.75	2.031933	0.35893	.	.	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865;ENST00000443169	T	0.34072	1.38	5.62	4.43	0.53597	.	0.789321	0.11925	N	0.516246	T	0.08802	0.0218	N	0.22421	0.69	0.09310	N	0.999995	B;B	0.28552	0.215;0.121	B;B	0.26517	0.07;0.051	T	0.29336	-1.0015	9	.	.	.	.	6.9619	0.24601	0.1322:0.071:0.0:0.7969	.	2729;2728	A6NF00;P24043	.;LAMA2_HUMAN	D	2728;2727;2728;746	ENSP00000400365:V2728D	.	V	+	2	0	LAMA2	129855260	0.038000	0.19896	0.001000	0.08648	0.077000	0.17291	2.630000	0.46494	0.921000	0.36994	0.460000	0.39030	GTT	.	.	none		0.473	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1			A	129813567	T	A	129813567	3	1	29	1	0	0	0	0	1	0	0	0	8615	1725	60	5	8413	5	LAMA2	6	129813567	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	6708678	129813567	41301500	351	12592											
ARHGAP18	93663	hgsc.bcm.edu	37	chr6	129929191	129929191	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttgcttctagttcttggcAaagattctgataggcacgaa	10	14	9	8	1	3	2	0	1	3	1	3	3	3	2	0	2	1	4	0	2	4	7			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:129929191A>C	ENST00000368149.2	-	9	1217	c.1129T>G	c.(1129-1131)Tgc>Ggc	p.C377G		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)		AGTTCTTGGCAAAGATTCTGA	0.373																																					p.C377G		Atlas-SNP	.											.	ARHGAP18	52	.	0			c.T1129G						PASS	.						46	47	47					6																	129929191		2203	4300	6503	SO:0001583	missense	93663	exon9			CTTGGCAAAGATT	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.1129T>G	6.37:g.129929191A>C	ENSP00000357131:p.Cys377Gly	25	0	0		38	9	0.236842	NM_033515		Missense_Mutation	SNP	ENST00000368149.2	37	CCDS34535.1	.	.	.	.	.	.	.	.	.	.	A	17.56	3.419687	0.62622	.	.	ENSG00000146376	ENST00000368149;ENST00000275189	.	.	.	5.84	4.67	0.58626	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.090614	0.85682	D	0.000000	T	0.58595	0.2133	M	0.72353	2.195	0.58432	D	0.999995	D;P	0.65815	0.995;0.823	P;P	0.54544	0.755;0.565	T	0.62263	-0.6891	8	.	.	.	.	12.1678	0.54139	0.9322:0.0:0.0678:0.0	.	377;377	A9UK01;Q8N392	.;RHG18_HUMAN	G	332;377	.	.	C	-	1	0	ARHGAP18	129970884	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.300000	0.72776	2.228000	0.72767	0.533000	0.62120	TGC	.	.	none		0.373	ARHGAP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042185.2	NM_033515		C	129929191	A	C	129929191	3	2	29	1	0	0	0	0	1	0	0	0	868	130	5	5	890	5	ARHGAP18	6	129929191	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	115624	129929191	41185876	352	12593											
SGK1	6446	hgsc.bcm.edu	37	chr6	134494280	134494280	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagaacattccgctccgacaTaatatgcttctcctaggaaa	13	10	6	12	2	1	1	0	0	1	1	4	3	3	2	3	1	2	2	3	1	5	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:134494280T>A	ENST00000237305.7	-	6	518	c.430A>T	c.(430-432)Atg>Ttg	p.M144L	SGK1_ENST00000528577.1_Missense_Mutation_p.M172L|SGK1_ENST00000413996.3_Missense_Mutation_p.M158L|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000367857.5_Missense_Mutation_p.M134L|SGK1_ENST00000475719.2_Intron|SGK1_ENST00000367858.5_Missense_Mutation_p.M239L	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	144	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)		CGCTCCGACATAATATGCTTC	0.433																																					p.M239L		Atlas-SNP	.											.	SGK1	387	.	0			c.A715T						PASS	.						101	105	103					6																	134494280		2203	4300	6503	SO:0001583	missense	6446	exon8			CCGACATAATATG	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.430A>T	6.37:g.134494280T>A	ENSP00000237305:p.Met144Leu	96	0	0		96	20	0.208333	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	T	16.46	3.130515	0.56828	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577	T;T;T;T;T	0.62941	-0.01;-0.01;-0.01;-0.01;-0.01	6.04	6.04	0.98038	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	0.46425	0.1392	N	0.04297	-0.235	0.80722	D	1	D;D;P;D;D	0.56287	0.969;0.973;0.939;0.969;0.975	P;D;P;P;D	0.76575	0.891;0.988;0.721;0.891;0.934	T	0.53933	-0.8368	10	0.11182	T	0.66	.	16.5885	0.84745	0.0:0.0:0.0:1.0	.	172;158;134;239;144	O00141-5;O00141-3;O00141-4;O00141-2;O00141	.;.;.;.;SGK1_HUMAN	L	239;158;144;134;172	ENSP00000356832:M239L;ENSP00000396242:M158L;ENSP00000237305:M144L;ENSP00000356831:M134L;ENSP00000434450:M172L	ENSP00000237305:M144L	M	-	1	0	SGK1	134535973	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	6.264000	0.72527	2.317000	0.78254	0.460000	0.39030	ATG	.	.	none		0.433	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			A	134494280	T	A	134494280	3	1	29	1	0	0	0	0	1	0	0	0	14222	1406	49	5	893	5	SGK1	6	134494280	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	4565089	134494280	36620787	353	12594			2	54		12	9	1446	N	T_G_C	2.136778e-16
SGK1	6446	hgsc.bcm.edu	37	chr6	134494655	134494655	+	Missense_Mutation	SNP	G	G	A																															agtgaaagtcagatggtttaGcatgaggattggacgacggg																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:134494655G>A	ENST00000237305.7	-	4	366	c.278C>T	c.(277-279)gCt>gTt	p.A93V	SGK1_ENST00000528577.1_Missense_Mutation_p.A121V|SGK1_ENST00000413996.3_Missense_Mutation_p.A107V|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000367857.5_Missense_Mutation_p.A83V|SGK1_ENST00000475719.2_Missense_Mutation_p.A93V|SGK1_ENST00000367858.5_Missense_Mutation_p.A188V	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	93					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)		AGATGGTTTAGCATGAGGATT	0.383																																					p.A188V		Atlas-SNP	.											.	SGK1	387	.	0			c.C563T						PASS	.						70	75	73					6																	134494655		2203	4300	6503	SO:0001583	missense	6446	exon6			GGTTTAGCATGAG	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.278C>T	6.37:g.134494655G>A	ENSP00000237305:p.Ala93Val	81	0	0		85	16	0.188235	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	19.43	3.826296	0.71143	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719	T;T;T;T;T;T	0.71934	3.23;3.23;3.23;3.23;3.23;-0.61	6.02	6.02	0.97574	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.66665	0.2812	M	0.74881	2.28	0.80722	D	1	P;D;B;B;P;B	0.56968	0.686;0.978;0.318;0.434;0.816;0.307	B;B;B;B;P;B	0.47915	0.272;0.39;0.176;0.175;0.561;0.085	T	0.66937	-0.5797	10	0.07813	T	0.8	.	20.5407	0.99260	0.0:0.0:1.0:0.0	.	121;107;93;83;188;93	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	V	188;107;93;83;121;93	ENSP00000356832:A188V;ENSP00000396242:A107V;ENSP00000237305:A93V;ENSP00000356831:A83V;ENSP00000434450:A121V;ENSP00000434302:A93V	ENSP00000237305:A93V	A	-	2	0	SGK1	134536348	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.790000	0.99075	2.865000	0.98341	0.655000	0.94253	GCT	.	.	none		0.383	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			A	134494655	G	A	134494655	3	1	29	1	0	0	0	0	1	0	0	0	14222	971	34	2	1053	2	SGK1	6	134494655	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	375	134494655	36620412	354	12595	156	2	2	54		12	9	1446	N	T_G_C	2.136778e-16
SGK1	6446	hgsc.bcm.edu	37	chr6	134494661	134494661	+	Missense_Mutation	SNP	G	G	A																															agtcagatggtttagcatgaGgattggacgacgggccaagg																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:134494661G>A	ENST00000237305.7	-	4	360	c.272C>T	c.(271-273)cCt>cTt	p.P91L	SGK1_ENST00000528577.1_Missense_Mutation_p.P119L|SGK1_ENST00000413996.3_Missense_Mutation_p.P105L|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000367857.5_Missense_Mutation_p.P81L|SGK1_ENST00000475719.2_Missense_Mutation_p.P91L|SGK1_ENST00000367858.5_Missense_Mutation_p.P186L	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	91					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)	p.P186L(1)|p.P81L(1)|p.P91L(1)		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)		TTTAGCATGAGGATTGGACGA	0.378																																					p.P186L		Atlas-SNP	.											SGK1_ENST00000367858,lymph_node,lymphoid_neoplasm,0,3	SGK1	387	3	3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	c.C557T						PASS	.						73	77	76					6																	134494661		2203	4300	6503	SO:0001583	missense	6446	exon6			GCATGAGGATTGG	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.272C>T	6.37:g.134494661G>A	ENSP00000237305:p.Pro91Leu	82	0	0		81	23	0.283951	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.349626	0.82132	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719	T;T;T;T;T;T	0.73897	3.3;3.3;3.3;3.3;3.3;-0.79	6.02	6.02	0.97574	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.78266	0.4256	M	0.74881	2.28	0.80722	D	1	P;P;P;P;P;P	0.52170	0.89;0.951;0.715;0.739;0.942;0.774	P;P;B;P;P;B	0.49192	0.448;0.495;0.35;0.497;0.602;0.301	T	0.80410	-0.1394	10	0.72032	D	0.01	.	20.5407	0.99260	0.0:0.0:1.0:0.0	.	119;105;91;81;186;91	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	L	186;105;91;81;119;91	ENSP00000356832:P186L;ENSP00000396242:P105L;ENSP00000237305:P91L;ENSP00000356831:P81L;ENSP00000434450:P119L;ENSP00000434302:P91L	ENSP00000237305:P91L	P	-	2	0	SGK1	134536354	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	9.790000	0.99075	2.865000	0.98341	0.655000	0.94253	CCT	.	.	none		0.378	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			A	134494661	G	A	134494661	3	1	29	1	0	0	0	0	1	0	0	0	14222	1000	35	2	1059	2	SGK1	6	134494661	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	6	134494661	36620406	355	12596	156	2	2	54		12	9	1446	N	T_G_C	2.136778e-16
SGK1	6446	hgsc.bcm.edu	37	chr6	134495154	134495154	+	Missense_Mutation	SNP	G	G	A																															aaaacttactggaggagaagGgttggcattcataagctcag																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:134495154G>A	ENST00000237305.7	-	3	305	c.217C>T	c.(217-219)Cct>Tct	p.P73S	SGK1_ENST00000528577.1_Missense_Mutation_p.P101S|SGK1_ENST00000413996.3_Missense_Mutation_p.P87S|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000367857.5_Missense_Mutation_p.P63S|SGK1_ENST00000475719.2_Missense_Mutation_p.P73S|SGK1_ENST00000367858.5_Missense_Mutation_p.P168S	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	73					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)	p.P73S(2)|p.P168S(2)|p.P63S(1)|p.P101S(1)		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)		GGAGGAGAAGGGTTGGCATTC	0.438																																					p.P168S		Atlas-SNP	.											SGK1_ENST00000367858,NS,carcinoma,0,5	SGK1	387	5	6	Substitution - Missense(6)	lung(4)|haematopoietic_and_lymphoid_tissue(2)	c.C502T						PASS	.						150	145	147					6																	134495154		2203	4300	6503	SO:0001583	missense	6446	exon5			GAGAAGGGTTGGC	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.217C>T	6.37:g.134495154G>A	ENSP00000237305:p.Pro73Ser	75	0	0		60	12	0.2	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	15.32	2.799278	0.50208	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T	0.73258	-0.73;-0.7;-0.68;-0.65;-0.7;-0.66	5.99	5.99	0.97316	Protein kinase-like domain (1);	0.047776	0.85682	D	0.000000	T	0.35566	0.0936	N	0.14661	0.345	0.80722	D	1	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	0.11329	0.002;0.001;0.001;0.002;0.006;0.0	T	0.28170	-1.0052	10	0.11485	T	0.65	.	13.6422	0.62257	0.0702:0.0:0.9298:0.0	.	101;87;73;63;168;73	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	S	168;87;73;63;101;73;137	ENSP00000356832:P168S;ENSP00000396242:P87S;ENSP00000237305:P73S;ENSP00000356831:P63S;ENSP00000434450:P101S;ENSP00000434302:P73S	ENSP00000237305:P73S	P	-	1	0	SGK1	134536847	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.350000	0.73017	2.840000	0.97914	0.655000	0.94253	CCT	.	.	none		0.438	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			A	134495154	G	A	134495154	3	1	29	1	0	0	0	0	1	0	0	0	14222	1232	43	2	1118	2	SGK1	6	134495154	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	493	134495154	36619913	356	12597	157	2	2	54		12	9	1446	N	T_G_C	2.136778e-16
SGK1	6446	hgsc.bcm.edu	37	chr6	134495155	134495155	+	Silent	SNP	G	G	A																															aaacttactggaggagaaggGttggcattcataagctcagg																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:134495155G>A	ENST00000237305.7	-	3	304	c.216C>T	c.(214-216)aaC>aaT	p.N72N	SGK1_ENST00000528577.1_Silent_p.N100N|SGK1_ENST00000413996.3_Silent_p.N86N|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000367857.5_Silent_p.N62N|SGK1_ENST00000475719.2_Silent_p.N72N|SGK1_ENST00000367858.5_Silent_p.N167N	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	72					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)		GAGGAGAAGGGTTGGCATTCA	0.443																																					p.N167N		Atlas-SNP	.											SGK1_ENST00000528577,NS,lymphoid_neoplasm,-2,5	SGK1	387	5	0			c.C501T						scavenged	.						151	146	148					6																	134495155		2203	4300	6503	SO:0001819	synonymous_variant	6446	exon5			AGAAGGGTTGGCA	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.216C>T	6.37:g.134495155G>A		76	1	0.0131579		61	12	0.196721	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Silent	SNP	ENST00000237305.7	37	CCDS5170.1																																																																																			.	.	none		0.443	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			A	134495155	G	A	134495155	2	1	29	1	0	0	0	0	0	0	0	1	14222	1252	44	2		2	SGK1	6	134495155	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1	134495155	36619912	357	12598	157	2	2	54		12	9	1446	N	T_G_C	2.136778e-16
SGK1	6446	hgsc.bcm.edu	37	chr6	134495169	134495169	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agaagggttggcattcataaGctcaggctcctgaggttggg	9	10	15	7	0	2	2	2	1	0	1	3	2	3	2	1	5	1	5	1	5	2	4	rs141028225		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:134495169G>A	ENST00000237305.7	-	3	290	c.202C>T	c.(202-204)Ctt>Ttt	p.L68F	SGK1_ENST00000528577.1_Missense_Mutation_p.L96F|SGK1_ENST00000413996.3_Missense_Mutation_p.L82F|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000367857.5_Missense_Mutation_p.L58F|SGK1_ENST00000475719.2_Missense_Mutation_p.L68F|SGK1_ENST00000367858.5_Missense_Mutation_p.L163F	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	68					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)		GCATTCATAAGCTCAGGCTCC	0.478																																					p.L163F		Atlas-SNP	.											.	SGK1	387	.	0			c.C487T						PASS	.						151	144	146					6																	134495169		2203	4300	6503	SO:0001583	missense	6446	exon5			TCATAAGCTCAGG	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.202C>T	6.37:g.134495169G>A	ENSP00000237305:p.Leu68Phe	80	0	0		72	21	0.291667	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	13.62	2.292643	0.40594	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T	0.72942	-0.69;-0.7;-0.67;-0.68;-0.67;-0.67	5.99	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.57489	0.2057	L	0.54323	1.7	0.80722	D	1	P;P;B;P;P;P	0.44380	0.825;0.834;0.0;0.571;0.573;0.595	B;B;B;B;B;B	0.44163	0.443;0.234;0.001;0.252;0.325;0.142	T	0.64019	-0.6505	10	0.56958	D	0.05	.	11.0283	0.47757	0.1506:0.0:0.8494:0.0	.	96;82;68;58;163;68	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	F	163;82;68;58;96;68;132	ENSP00000356832:L163F;ENSP00000396242:L82F;ENSP00000237305:L68F;ENSP00000356831:L58F;ENSP00000434450:L96F;ENSP00000434302:L68F	ENSP00000237305:L68F	L	-	1	0	SGK1	134536862	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.307000	0.51888	1.377000	0.46286	0.655000	0.94253	CTT	G|1.000;C|0.000	.	alt		0.478	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			A	134495169	G	A	134495169	3	1	29	1	0	0	0	0	1	0	0	0	14222	971	34	2	1133	2	SGK1	6	134495169	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	14	134495169	36619898	358	12599			2	54		12	9	1446	N	T_G_C	2.136778e-16
SGK1	6446	hgsc.bcm.edu	37	chr6	134495200	134495200	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgaggttgggagatcttcaaGatggactgaacttcagggct	10	11	14	6	0	3	4	2	2	1	2	3	6	3	5	0	4	1	2	0	4	2	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:134495200G>C	ENST00000237305.7	-	3	259	c.171C>G	c.(169-171)atC>atG	p.I57M	SGK1_ENST00000528577.1_Missense_Mutation_p.I85M|SGK1_ENST00000413996.3_Missense_Mutation_p.I71M|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000367857.5_Missense_Mutation_p.I47M|SGK1_ENST00000475719.2_Missense_Mutation_p.I57M|SGK1_ENST00000367858.5_Missense_Mutation_p.I152M	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	57	Necessary for localization to the mitochondria.				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)		AGATCTTCAAGATGGACTGAA	0.493																																					p.I152M		Atlas-SNP	.											.	SGK1	387	.	0			c.C456G						PASS	.						133	125	128					6																	134495200		2203	4300	6503	SO:0001583	missense	6446	exon5			CTTCAAGATGGAC	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.171C>G	6.37:g.134495200G>C	ENSP00000237305:p.Ile57Met	72	0	0		76	5	0.0657895	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	12.83	2.056994	0.36277	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T;T	0.38887	1.58;1.58;1.58;1.58;1.58;1.58;1.11	5.99	4.87	0.63330	.	0.090924	0.85682	D	0.000000	T	0.12944	0.0314	N	0.22421	0.69	0.80722	D	1	B;B;B;B;B;B	0.27192	0.171;0.053;0.004;0.021;0.006;0.022	B;B;B;B;B;B	0.25291	0.059;0.013;0.005;0.041;0.016;0.018	T	0.06075	-1.0847	10	0.41790	T	0.15	.	6.963	0.24608	0.7211:0.0:0.2789:0.0	.	85;71;57;47;152;57	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	M	152;71;57;47;85;57;121	ENSP00000356832:I152M;ENSP00000396242:I71M;ENSP00000237305:I57M;ENSP00000356831:I47M;ENSP00000434450:I85M;ENSP00000434302:I57M;ENSP00000435577:I121M	ENSP00000237305:I57M	I	-	3	3	SGK1	134536893	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.721000	0.38032	1.147000	0.42369	0.655000	0.94253	ATC	.	.	none		0.493	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			C	134495200	G	C	134495200	3	2	29	1	0	0	0	0	1	0	0	0	14222	932	33	4	1164	4	SGK1	6	134495200	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	31	134495200	36619867	359	12600			2	54		12	9	1446	N	T_G_C	2.136778e-16
SGK1	6446	hgsc.bcm.edu	37	chr6	134495218	134495218	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aagatggactgaacttcaggGctgcagggaataaagggcac	14	6	14	7	0	1	2	1	1	0	1	1	4	1	4	0	4	2	3	0	4	5	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:134495218G>A	ENST00000237305.7	-	3	241	c.153C>T	c.(151-153)caC>caT	p.H51H	SGK1_ENST00000528577.1_Splice_Site_p.H79H|SGK1_ENST00000413996.3_Splice_Site_p.H65H|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000367857.5_Splice_Site_p.H41H|SGK1_ENST00000475719.2_Splice_Site_p.H51H|SGK1_ENST00000367858.5_Splice_Site_p.H146H	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	51	Necessary for localization to the mitochondria.				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)		GAACTTCAGGGCTGCAGGGAA	0.498																																					p.H146H		Atlas-SNP	.											SGK1_ENST00000528577,NS,lymphoid_neoplasm,0,4	SGK1	387	4	0			c.C438T						PASS	.						111	104	107					6																	134495218		2203	4300	6503	SO:0001630	splice_region_variant	6446	exon5			TTCAGGGCTGCAG	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.153-1C>T	6.37:g.134495218G>A		62	0	0		70	21	0.3	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Silent	SNP	ENST00000237305.7	37	CCDS5170.1																																																																																			.	.	none		0.498	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		Silent	A	134495218	G	A	134495218	5	1	29	1	0	0	0	0	0	0	1	0	14222	1217	42	2	1182	2	SGK1	6	134495218	Splice_Site	SNP	G	TCGA-GR-7351-01A-11D-2210-10	18	134495218	36619849	360	12601			2	54		12	9	1446	N	T_G_C	2.136778e-16
SGK1	6446	hgsc.bcm.edu	37	chr6	134495674	134495674	+	Missense_Mutation	SNP	C	C	T																															gcatgcataggagttattggCaatcttctgaataaagtcgt																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:134495674C>T	ENST00000237305.7	-	2	215	c.127G>A	c.(127-129)Gcc>Acc	p.A43T	SGK1_ENST00000528577.1_Missense_Mutation_p.A71T|SGK1_ENST00000413996.3_Missense_Mutation_p.A57T|SGK1_ENST00000489458.2_5'Flank|SGK1_ENST00000367857.5_Missense_Mutation_p.A33T|SGK1_ENST00000475719.2_Missense_Mutation_p.A43T|SGK1_ENST00000367858.5_Missense_Mutation_p.A138T	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	43	Necessary for localization to the mitochondria.				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)		GAGTTATTGGCAATCTTCTGA	0.413											OREG0017675	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A138T		Atlas-SNP	.											.	SGK1	387	.	0			c.G412A						PASS	.						91	89	90					6																	134495674		2203	4300	6503	SO:0001583	missense	6446	exon4			TATTGGCAATCTT	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.127G>A	6.37:g.134495674C>T	ENSP00000237305:p.Ala43Thr	71	0	0	1611	45	7	0.155556	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.296537	0.81025	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T;T	0.42900	1.51;1.51;1.51;1.51;1.51;1.51;0.96	5.89	5.89	0.94794	.	0.047350	0.85682	D	0.000000	T	0.33177	0.0854	L	0.51422	1.61	0.80722	D	1	B;B;B;B;B;B	0.29988	0.217;0.264;0.046;0.077;0.217;0.046	B;B;B;B;B;B	0.31946	0.098;0.124;0.045;0.098;0.138;0.028	T	0.17349	-1.0372	10	0.62326	D	0.03	.	20.2576	0.98430	0.0:1.0:0.0:0.0	.	71;57;43;33;138;43	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	T	138;57;43;33;71;43;107	ENSP00000356832:A138T;ENSP00000396242:A57T;ENSP00000237305:A43T;ENSP00000356831:A33T;ENSP00000434450:A71T;ENSP00000434302:A43T;ENSP00000435577:A107T	ENSP00000237305:A43T	A	-	1	0	SGK1	134537367	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.766000	0.62279	2.783000	0.95769	0.655000	0.94253	GCC	.	.	none		0.413	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			T	134495674	C	T	134495674	3	4	29	1	0	0	0	0	1	0	0	0	14222	710	25	2	1212	2	SGK1	6	134495674	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	456	134495674	36619393	361	12602	158	2	2	54		12	9	1446	N	T_G_C	2.136778e-16
SGK1	6446	hgsc.bcm.edu	37	chr6	134495683	134495683	+	Missense_Mutation	SNP	G	G	C																															ggagttattggcaatcttctGaataaagtcgttcagaccca																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:134495683G>C	ENST00000237305.7	-	2	206	c.118C>G	c.(118-120)Cag>Gag	p.Q40E	SGK1_ENST00000528577.1_Missense_Mutation_p.Q68E|SGK1_ENST00000413996.3_Missense_Mutation_p.Q54E|SGK1_ENST00000489458.2_5'Flank|SGK1_ENST00000367857.5_Missense_Mutation_p.Q30E|SGK1_ENST00000475719.2_Missense_Mutation_p.Q40E|SGK1_ENST00000367858.5_Missense_Mutation_p.Q135E	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	40	Necessary for localization to the mitochondria.				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)	p.Q40*(1)|p.Q135*(1)		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)		GCAATCTTCTGAATAAAGTCG	0.423											OREG0017675	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q135E		Atlas-SNP	.											SGK1_ENST00000367858,NS,lymphoid_neoplasm,0,2	SGK1	387	2	2	Substitution - Nonsense(2)	haematopoietic_and_lymphoid_tissue(2)	c.C403G						PASS	.						90	88	89					6																	134495683		2203	4300	6503	SO:0001583	missense	6446	exon4			TCTTCTGAATAAA	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.118C>G	6.37:g.134495683G>C	ENSP00000237305:p.Gln40Glu	70	0	0	1611	46	16	0.347826	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.645700	0.87958	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T;T	0.42513	1.47;1.47;1.47;1.47;1.47;1.47;0.97	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.48624	0.1510	M	0.73962	2.25	0.80722	D	1	P;P;P;P;D;P	0.54772	0.936;0.792;0.895;0.721;0.968;0.81	P;B;B;B;P;B	0.51170	0.511;0.337;0.41;0.373;0.661;0.23	T	0.39354	-0.9618	10	0.34782	T	0.22	.	20.2576	0.98430	0.0:0.0:1.0:0.0	.	68;54;40;30;135;40	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	E	135;54;40;30;68;40;104	ENSP00000356832:Q135E;ENSP00000396242:Q54E;ENSP00000237305:Q40E;ENSP00000356831:Q30E;ENSP00000434450:Q68E;ENSP00000434302:Q40E;ENSP00000435577:Q104E	ENSP00000237305:Q40E	Q	-	1	0	SGK1	134537376	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.783000	0.95769	0.655000	0.94253	CAG	.	.	none		0.423	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			C	134495683	G	C	134495683	3	2	29	1	0	0	0	0	1	0	0	0	14222	1299	45	4	1221	4	SGK1	6	134495683	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	9	134495683	36619384	362	12603	158	2	2	54		12	9	1446	N	T_G_C	2.136778e-16
SGK1	6446	hgsc.bcm.edu	37	chr6	134495709	134495709	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agtcgttcagacccatcctcCtctgcttcatgaaagctgtg	8	12	8	13	1	3	2	2	1	1	1	6	2	5	2	3	0	2	3	3	0	1	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:134495709C>T	ENST00000237305.7	-	2	180	c.92G>A	c.(91-93)aGg>aAg	p.R31K	SGK1_ENST00000528577.1_Missense_Mutation_p.R59K|SGK1_ENST00000413996.3_Missense_Mutation_p.R45K|SGK1_ENST00000489458.2_5'Flank|SGK1_ENST00000367857.5_Missense_Mutation_p.R21K|SGK1_ENST00000475719.2_Missense_Mutation_p.R31K|SGK1_ENST00000367858.5_Missense_Mutation_p.R126K	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	31	Necessary for localization to the mitochondria.				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)		ACCCATCCTCCTCTGCTTCAT	0.428											OREG0017675	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R126K		Atlas-SNP	.											SGK1_ENST00000367858,NS,lymphoid_neoplasm,-1,2	SGK1	387	2	0			c.G377A						PASS	.						78	78	78					6																	134495709		2203	4300	6503	SO:0001583	missense	6446	exon4			ATCCTCCTCTGCT	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.92G>A	6.37:g.134495709C>T	ENSP00000237305:p.Arg31Lys	70	0	0	1611	40	8	0.2	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.971432	0.92919	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T;T	0.60040	0.22;0.22;0.22;0.22;0.22;0.22;0.22	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.48874	0.1524	L	0.49455	1.56	0.80722	D	1	B;B;B;B;B;B	0.33694	0.282;0.009;0.05;0.106;0.421;0.05	B;B;B;B;B;B	0.37346	0.205;0.009;0.115;0.149;0.247;0.043	T	0.50457	-0.8826	10	0.48119	T	0.1	.	20.2576	0.98430	0.0:1.0:0.0:0.0	.	59;45;31;21;126;31	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	K	126;45;31;21;59;31;95	ENSP00000356832:R126K;ENSP00000396242:R45K;ENSP00000237305:R31K;ENSP00000356831:R21K;ENSP00000434450:R59K;ENSP00000434302:R31K;ENSP00000435577:R95K	ENSP00000237305:R31K	R	-	2	0	SGK1	134537402	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.818000	0.86416	2.783000	0.95769	0.655000	0.94253	AGG	.	.	none		0.428	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2			T	134495709	C	T	134495709	3	4	29	1	0	0	0	0	1	0	0	0	14222	681	24	2	1247	2	SGK1	6	134495709	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	26	134495709	36619358	363	12604			2	54		12	9	1446	N	T_G_C	2.136778e-16
SGK1	6446	hgsc.bcm.edu	37	chr6	134495725	134495725	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctcctctgcttcatgaaagCtgtggatgaaggaggagaaa	12	9	12	8	0	2	3	1	2	1	1	3	6	3	5	2	3	2	2	2	3	3	1	rs186450029		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:134495725C>G	ENST00000237305.7	-	2	165		c.e2-1		SGK1_ENST00000528577.1_Splice_Site|SGK1_ENST00000413996.3_Splice_Site|SGK1_ENST00000489458.2_5'Flank|SGK1_ENST00000367857.5_Missense_Mutation_p.A16P|SGK1_ENST00000475719.2_Splice_Site|SGK1_ENST00000367858.5_Splice_Site	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)		TTCATGAAAGCTGTGGATGAA	0.433											OREG0017675	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Atlas-SNP	.											SGK1_ENST00000528577,NS,lymphoid_neoplasm,0,4	SGK1	387	4	0			c.77-1G>C						PASS	.						73	73	73					6																	134495725		2203	4300	6503	SO:0001630	splice_region_variant	6446	exon3			TGAAAGCTGTGGA	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.77-1G>C	6.37:g.134495725C>G		67	0	0	1611	41	11	0.268293	NM_005627	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Splice_Site	SNP	ENST00000237305.7	37	CCDS5170.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.8|27.8	4.862399|4.862399	0.91511|0.91511	.|.	.|.	ENSG00000118515|ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000528577;ENST00000475719;ENST00000461976|ENST00000367857	.|T	.|0.30981	.|1.51	5.89|5.89	5.89|5.89	0.94794|0.94794	.|.	.|.	.|.	.|.	.|.	.|T	.|0.30355	.|0.0762	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|P	.|0.52170	.|0.951	.|P	.|0.47827	.|0.558	.|T	.|0.01027	.|-1.1476	.|7	.|.	.|.	.|.	.|.	20.2576|20.2576	0.98430|0.98430	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|16	.|O00141-4	.|.	.|P	-1|16	.|ENSP00000356831:A16P	.|.	.|A	-|-	.|1	.|0	SGK1|SGK1	134537418|134537418	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.926000|0.926000	0.56050|0.56050	7.818000|7.818000	0.86416|0.86416	2.783000|2.783000	0.95769|0.95769	0.655000|0.655000	0.94253|0.94253	.|GCT	C|1.000;T|0.000	.	alt		0.433	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		Intron	G	134495725	C	G	134495725	5	3	29	1	0	0	0	0	0	0	1	0	14222	811	28	4	1263	4	SGK1	6	134495725	Splice_Site	SNP	C	TCGA-GR-7351-01A-11D-2210-10	16	134495725	36619342	364	12605			2	54		12	9	1446	N	T_G_C	2.136778e-16
SASH1	23328	hgsc.bcm.edu	37	chr6	148840980	148840980	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ggcccagaaagtgtcccgctCcctcaccgagggggagatga	9	5	14	13	2	1	3	1	1	0	2	3	5	3	3	4	3	0	1	4	3	1	0	rs116958992	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:148840980C>T	ENST00000367467.3	+	10	1635	c.1160C>T	c.(1159-1161)tCc>tTc	p.S387F		NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	387					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)		GTGTCCCGCTCCCTCACCGAG	0.567													C|||	15	0.00299521	0.0008	0.0014	5008	,	,		17240	0.001		0.0089	False		,,,				2504	0.0031				p.S387F		Atlas-SNP	.											.	SASH1	123	.	0			c.C1160T						PASS	.	C	PHE/SER	6,4398		0,6,2196	17	19	18		1160	4.7	1	6	dbSNP_132	18	86,8512		1,84,4214	yes	missense	SASH1	NM_015278.3	155	1,90,6410	TT,TC,CC		1.0002,0.1362,0.7076	probably-damaging	387/1248	148840980	92,12910	2202	4299	6501	SO:0001583	missense	23328	exon10			CCCGCTCCCTCAC	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.1160C>T	6.37:g.148840980C>T	ENSP00000356437:p.Ser387Phe	21	0	0		16	6	0.375	NM_015278	Q5TGN5|Q8TAI0|Q9H7R7	Missense_Mutation	SNP	ENST00000367467.3	37	CCDS5212.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	C	21.4	4.136970	0.77775	0.001362	0.010002	ENSG00000111961	ENST00000367467;ENST00000535767	T	0.49720	0.77	5.6	4.74	0.60224	.	0.048773	0.85682	N	0.000000	T	0.25044	0.0608	L	0.34521	1.04	0.53005	D	0.99996	P;P	0.47106	0.89;0.89	B;B	0.39840	0.311;0.197	T	0.12400	-1.0549	10	0.72032	D	0.01	-22.8395	14.3413	0.66627	0.0:0.929:0.0:0.071	.	368;387	Q6P4R9;O94885	.;SASH1_HUMAN	F	387;148	ENSP00000356437:S387F	ENSP00000356437:S387F	S	+	2	0	SASH1	148882673	1.000000	0.71417	0.994000	0.49952	0.998000	0.95712	7.247000	0.78257	1.380000	0.46344	0.650000	0.86243	TCC	C|0.994;T|0.006	0.006	strong		0.567	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278		T	148840980	C	T	148840980	3	4	29	1	0	0	0	0	1	0	0	0	13863	855	30	2	1198	2	SASH1	6	148840980	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	14345255	148840980	22274087	365	12606											
RAET1L	154064	hgsc.bcm.edu	37	chr6	150342155	150342155	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ggccacatccttgtcattctCccacttttctttcatctttc	5	18	3	15	0	5	0	2	0	3	0	8	0	6	0	3	1	0	0	3	1	0	6	rs148198102	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:150342155C>T	ENST00000367341.1	-	3	516	c.517G>A	c.(517-519)Gag>Aag	p.E173K	RAET1L_ENST00000286380.2_Missense_Mutation_p.E173K			Q5VY80	RET1L_HUMAN	retinoic acid early transcript 1L	173	MHC class I alpha-2 like. {ECO:0000250}.				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)		TTGTCATTCTCCCACTTTTCT	0.483													C|||	16	0.00319489	0.0008	0.0029	5008	,	,		21805	0.0		0.008	False		,,,				2504	0.0051				p.E173K		Atlas-SNP	.											.	RAET1L	21	.	0			c.G517A						PASS	.	C	LYS/GLU	10,4396	16.8+/-37.8	0,10,2193	296	259	272		517	0	0	6	dbSNP_134	272	84,8516	47.6+/-106.9	0,84,4216	no	missense	RAET1L	NM_130900.2	56	0,94,6409	TT,TC,CC		0.9767,0.227,0.7227	possibly-damaging	173/247	150342155	94,12912	2203	4300	6503	SO:0001583	missense	154064	exon3			CATTCTCCCACTT	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.517G>A	6.37:g.150342155C>T	ENSP00000356310:p.Glu173Lys	307	1	0.00325733		297	144	0.484848	NM_130900	A3KME4|Q8TE74	Missense_Mutation	SNP	ENST00000367341.1	37	CCDS5224.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	c	12.88	2.069672	0.36470	0.00227	0.009767	ENSG00000155918	ENST00000367341;ENST00000286380	T;T	0.09445	2.98;2.98	1.91	-0.0121	0.13989	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	0.10594	0.0259	M	0.72576	2.205	0.09310	N	1	D	0.58620	0.983	P	0.59424	0.857	T	0.08743	-1.0707	9	0.87932	D	0	.	4.1768	0.10356	0.0:0.6012:0.0:0.3988	.	173	Q5VY80	RET1L_HUMAN	K	173	ENSP00000356310:E173K;ENSP00000286380:E173K	ENSP00000286380:E173K	E	-	1	0	RAET1L	150383848	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	-0.064000	0.11636	-0.026000	0.13895	0.491000	0.48974	GAG	C|0.994;T|0.006	0.006	strong		0.483	RAET1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042676.1	NM_130900		T	150342155	C	T	150342155	3	4	29	1	0	0	0	0	1	0	0	0	13016	864	30	2	230	2	RAET1L	6	150342155	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1501175	150342155	20772912	366	12607											
PLEKHG1	57480	hgsc.bcm.edu	37	chr6	151152250	151152250	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgataacatcagttatgaggActtaaaactaatggttgcta	15	13	8	5	0	1	2	1	2	0	0	1	3	1	3	0	2	3	3	0	2	6	6	rs148178393	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:151152250A>G	ENST00000358517.2	+	15	2214	c.2003A>G	c.(2002-2004)gAc>gGc	p.D668G	PLEKHG1_ENST00000367328.1_Missense_Mutation_p.D668G			Q9ULL1	PKHG1_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 1	668							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)		AGTTATGAGGACTTAAAACTA	0.478													A|||	26	0.00519169	0.0015	0.0144	5008	,	,		21879	0.0		0.0129	False		,,,				2504	0.001				p.D668G		Atlas-SNP	.											.	PLEKHG1	97	.	0			c.A2003G						PASS	.	A	GLY/ASP	13,4393	17.9+/-39.9	0,13,2190	45	45	45		2003	5.3	1	6	dbSNP_134	45	92,8508	51.1+/-111.2	0,92,4208	yes	missense	PLEKHG1	NM_001029884.1	94	0,105,6398	GG,GA,AA		1.0698,0.2951,0.8073	probably-damaging	668/1386	151152250	105,12901	2203	4300	6503	SO:0001583	missense	57480	exon16			ATGAGGACTTAAA	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.2003A>G	6.37:g.151152250A>G	ENSP00000351318:p.Asp668Gly	55	0	0		71	35	0.492958	NM_001029884	Q5T1F2	Missense_Mutation	SNP	ENST00000358517.2	37	CCDS34552.1	21	0.009615384615384616	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	12	0.0158311345646438	A	22.1	4.244378	0.79912	0.002951	0.010698	ENSG00000120278	ENST00000367328;ENST00000535018;ENST00000358517	T;T	0.70516	-0.49;-0.49	5.31	5.31	0.75309	.	0.089123	0.85682	D	0.000000	T	0.78742	0.4331	M	0.68952	2.095	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74674	0.984;0.976;0.976	T	0.82212	-0.0569	10	0.87932	D	0	.	15.3102	0.74026	1.0:0.0:0.0:0.0	.	475;668;668	Q5EBL9;Q5JYA6;Q9ULL1	.;.;PKHG1_HUMAN	G	668	ENSP00000356297:D668G;ENSP00000351318:D668G	ENSP00000351318:D668G	D	+	2	0	PLEKHG1	151193943	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	8.962000	0.93254	2.024000	0.59613	0.454000	0.30748	GAC	A|0.991;G|0.009	0.009	strong		0.478	PLEKHG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042691.1			G	151152250	A	G	151152250	3	3	29	1	0	0	0	0	1	0	0	0	12077	275	10	3	2057	3	PLEKHG1	6	151152250	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	810095	151152250	19962817	367	12608											
ESR1	2099	hgsc.bcm.edu	37	chr6	152201863	152201863	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaggaagagctgccaggcCtgccggctccgtaaatgcta	10	6	14	11	2	0	1	0	0	0	1	1	3	1	3	4	4	4	4	4	4	4	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:152201863C>T	ENST00000206249.3	+	3	1079	c.717C>T	c.(715-717)gcC>gcT	p.A239A	ESR1_ENST00000440973.1_Silent_p.A239A|ESR1_ENST00000338799.5_Silent_p.A239A|ESR1_ENST00000406599.1_Intron|ESR1_ENST00000427531.2_Silent_p.A66A|ESR1_ENST00000456483.2_Silent_p.A239A|ESR1_ENST00000443427.1_Silent_p.A239A	NM_000125.3	NP_000116.2	P03372	ESR1_HUMAN	estrogen receptor 1	239	Mediates interaction with DNTTIP2.				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)	GCTGCCAGGCCTGCCGGCTCC	0.527																																					p.A239A		Atlas-SNP	.											.	ESR1	94	.	0			c.C717T						PASS	.						54	55	54					6																	152201863		2203	4300	6503	SO:0001819	synonymous_variant	2099	exon3			CCAGGCCTGCCGG	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.717C>T	6.37:g.152201863C>T		59	0	0		50	4	0.08	NM_000125	Q13511|Q14276|Q5T5H7|Q6MZQ9|Q9NU51|Q9UDZ7|Q9UIS7	Silent	SNP	ENST00000206249.3	37	CCDS5234.1	.	.	.	.	.	.	.	.	.	.	C	11.50	1.657168	0.29425	.	.	ENSG00000091831	ENST00000427531	.	.	.	5.42	4.54	0.55810	.	.	.	.	.	T	0.52273	0.1724	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50725	-0.8794	4	.	.	.	.	11.7374	0.51773	0.0:0.8597:0.0:0.1403	.	.	.	.	L	144	.	.	P	+	2	0	ESR1	152243556	0.957000	0.32711	1.000000	0.80357	0.997000	0.91878	0.119000	0.15626	2.563000	0.86464	0.655000	0.94253	CCT	.	.	none		0.527	ESR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043308.1			T	152201863	C	T	152201863	2	4	29	1	0	0	0	0	0	0	0	1	5258	668	24	2		2	ESR1	6	152201863	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1049613	152201863	18913204	368	12609											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152532702	152532702	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcaaaatctgctgacgacTgaacatctcggcttgaaaca	13	9	9	10	2	2	3	0	3	2	0	3	4	2	3	0	1	4	3	0	1	4	1	rs35763277	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:152532702T>C	ENST00000367255.5	-	124	23117	c.22516A>G	c.(22516-22518)Agt>Ggt	p.S7506G	SYNE1_ENST00000356820.4_Missense_Mutation_p.S2030G|SYNE1_ENST00000423061.1_Missense_Mutation_p.S7435G|SYNE1_ENST00000448038.1_Missense_Mutation_p.S7435G|SYNE1_ENST00000341594.5_Missense_Mutation_p.S7118G|SYNE1_ENST00000265368.4_Missense_Mutation_p.S7506G	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	7506			S -> G (in dbSNP:rs35763277).		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)		TGCTGACGACTGAACATCTCG	0.328										HNSCC(10;0.0054)			T|||	23	0.00459265	0.0008	0.0072	5008	,	,		17739	0.0		0.0169	False		,,,				2504	0.0				p.S7506G		Atlas-SNP	.											.	SYNE1	3227	.	0			c.A22516G						PASS	.	T	GLY/SER,GLY/SER	18,4388	26.2+/-53.5	0,18,2185	83	82	82		22303,22516	5.6	1	6	dbSNP_126	82	147,8453	71.3+/-133.9	2,143,4155	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	56,56	2,161,6340	CC,CT,TT		1.7093,0.4085,1.2686	probably-damaging,probably-damaging	7435/8750,7506/8798	152532702	165,12841	2203	4300	6503	SO:0001583	missense	23345	exon124			GACGACTGAACAT	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.22516A>G	6.37:g.152532702T>C	ENSP00000356224:p.Ser7506Gly	64	0	0		55	34	0.618182	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	37	CCDS5236.2	17	0.007783882783882784	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	13	0.017150395778364115	T	25.9	4.689644	0.88735	0.004085	0.017093	ENSG00000131018	ENST00000367255;ENST00000367257;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594;ENST00000356820;ENST00000367251	T;T;T;T;T;T;T;T	0.50813	1.3;0.73;1.3;1.3;1.3;1.3;0.73;0.73	5.62	5.62	0.85841	.	0.000000	0.64402	D	0.000001	T	0.61726	0.2370	M	0.70595	2.14	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	0.997;0.997;0.999;0.997	T	0.64863	-0.6307	10	0.54805	T	0.06	.	16.1197	0.81342	0.0:0.0:0.0:1.0	rs35763277;rs36215571	7506;7506;7435;7435	Q8NF91;E7EQI5;Q8NF91-4;E9PEL9	SYNE1_HUMAN;.;.;.	G	7506;152;7435;7506;7435;7118;2030;428	ENSP00000356224:S7506G;ENSP00000356226:S152G;ENSP00000396024:S7435G;ENSP00000265368:S7506G;ENSP00000390975:S7435G;ENSP00000341887:S7118G;ENSP00000349276:S2030G;ENSP00000356220:S428G	ENSP00000265368:S7506G	S	-	1	0	SYNE1	152574395	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.941000	0.87700	2.257000	0.74773	0.455000	0.32223	AGT	T|0.988;C|0.012	0.012	strong		0.328	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		C	152532702	T	C	152532702	3	2	29	1	0	0	0	0	1	0	0	0	15460	1580	55	3	4042	3	SYNE1	6	152532702	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	330839	152532702	18582365	369	12610											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152668211	152668211	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccctctgagctgtgctgcAgatcgctgagtagctgtcct	6	11	11	13	1	1	3	0	2	1	1	3	3	2	3	2	0	4	6	2	0	1	1	rs111449472	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:152668211A>G	ENST00000367255.5	-	73	12662	c.12061T>C	c.(12061-12063)Tgc>Cgc	p.C4021R	SYNE1_ENST00000423061.1_Missense_Mutation_p.C3950R|SYNE1_ENST00000448038.1_Missense_Mutation_p.C3950R|SYNE1_ENST00000341594.5_Intron|SYNE1_ENST00000265368.4_Missense_Mutation_p.C4021R	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4021					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)		GCTGTGCTGCAGATCGCTGAG	0.483										HNSCC(10;0.0054)			A|||	27	0.00539137	0.003	0.0086	5008	,	,		18057	0.0		0.0119	False		,,,				2504	0.0051				p.C4021R		Atlas-SNP	.											.	SYNE1	3227	.	0			c.T12061C						PASS	.	A	ARG/CYS,ARG/CYS	16,4390	22.3+/-47.3	0,16,2187	159	131	141		11848,12061	5.7	1	6	dbSNP_132	141	130,8470	66.0+/-128.3	1,128,4171	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	180,180	1,144,6358	GG,GA,AA		1.5116,0.3631,1.1226	probably-damaging,probably-damaging	3950/8750,4021/8798	152668211	146,12860	2203	4300	6503	SO:0001583	missense	23345	exon73			TGCTGCAGATCGC	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.12061T>C	6.37:g.152668211A>G	ENSP00000356224:p.Cys4021Arg	116	0	0		104	42	0.403846	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	37	CCDS5236.2	19	0.0086996336996337	3	0.006097560975609756	3	0.008287292817679558	0	0.0	13	0.017150395778364115	A	13.58	2.279409	0.40294	0.003631	0.015116	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038	T;T;T;T	0.32988	1.43;1.43;1.43;1.43	5.71	5.71	0.89125	.	0.000000	0.64402	D	0.000005	T	0.46425	0.1392	M	0.66939	2.045	0.80722	D	1	D;D;D;B	0.89917	1.0;1.0;1.0;0.0	D;D;D;B	0.91635	0.999;0.999;0.999;0.0	T	0.46816	-0.9164	10	0.54805	T	0.06	.	15.9869	0.80160	1.0:0.0:0.0:0.0	.	4021;4021;4021;3950	B7ZBC3;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	R	4021;3950;4021;3950	ENSP00000356224:C4021R;ENSP00000396024:C3950R;ENSP00000265368:C4021R;ENSP00000390975:C3950R	ENSP00000265368:C4021R	C	-	1	0	SYNE1	152709904	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	8.905000	0.92613	2.171000	0.68590	0.533000	0.62120	TGC	A|0.990;G|0.010	0.010	strong		0.483	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		G	152668211	A	G	152668211	3	3	29	1	0	0	0	0	1	0	0	0	15460	188	7	3	14701	3	SYNE1	6	152668211	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	135509	152668211	18446856	370	12611											
RBM16	22828	hgsc.bcm.edu	37	chr6	155114112	155114112	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctatgagcaatactccaggTatgttgctttaatatagatt	12	15	8	6	0	0	2	0	1	0	1	1	2	1	2	1	1	3	5	1	1	7	9			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:155114112T>A	ENST00000367178.3	+	5	1051		c.e5+2		SCAF8_ENST00000367186.4_Splice_Site|SCAF8_ENST00000417268.1_Splice_Site	NM_014892.3	NP_055707.3	Q9UPN6	SCAF8_HUMAN	SR-related CTD-associated factor 8						mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase core enzyme binding (GO:0043175)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(15)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	46						ATACTCCAGGTATGTTGCTTT	0.398																																					.		Atlas-SNP	.											.	SCAF8	122	.	0			c.475+2T>A						PASS	.						60	59	60					6																	155114112		2203	4300	6503	SO:0001630	splice_region_variant	22828	exon5			TCCAGGTATGTTG	AB029039	CCDS5247.1, CCDS69226.1, CCDS75541.1	6q25.1-q25.3	2013-02-12	2011-01-10	2011-01-10	ENSG00000213079	ENSG00000213079		"RNA binding motif (RRM) containing"	20959	protein-coding gene	gene with protein product			"RNA binding motif protein 16"	RBM16		10470851	Standard	NM_001286189		Approved	KIAA1116	uc003qpz.3	Q9UPN6	OTTHUMG00000015877	ENST00000367178.3:c.475+2T>A	6.37:g.155114112T>A		84	0	0		61	26	0.42623	NM_014892	B7Z888|Q5TBU6|Q6NSK3|Q9BQN8|Q9BX43	Splice_Site	SNP	ENST00000367178.3	37	CCDS5247.1	.	.	.	.	.	.	.	.	.	.	T	16.45	3.126604	0.56721	.	.	ENSG00000213079	ENST00000367178;ENST00000417268;ENST00000367186	.	.	.	4.47	3.25	0.37280	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.2621	0.43434	0.1485:0.0:0.0:0.8515	.	.	.	.	.	-1	.	.	.	+	.	.	SCAF8	155155804	1.000000	0.71417	0.994000	0.49952	0.766000	0.43426	6.932000	0.75869	0.629000	0.30376	0.379000	0.24179	.	.	.	none		0.398	SCAF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042798.1	NM_014892	Intron	A	155114112	T	A	155114112	5	1	29	1	0	0	0	0	0	0	1	0	13133	1652	57	5	495	5	RBM16	6	155114112	Splice_Site	SNP	T	TCGA-GR-7351-01A-11D-2210-10	2445901	155114112	16000955	371	12612											
TIAM2	26230	hgsc.bcm.edu	37	chr6	155458562	155458562	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atagaaacatctacagaaacCgccgagtccagcagcgagtc	15	5	9	12	3	1	2	0	0	1	2	3	4	2	2	3	0	5	1	3	0	4	2	rs374521659		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:155458562C>T	ENST00000461783.3	+	7	2719	c.1446C>T	c.(1444-1446)acC>acT	p.T482T	TIAM2_ENST00000360366.4_Silent_p.T482T|TIAM2_ENST00000318981.5_Silent_p.T482T|TIAM2_ENST00000529824.2_Silent_p.T482T|TIAM2_ENST00000456144.1_Silent_p.T482T|TIAM2_ENST00000367174.2_5'UTR			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	482					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)		CTACAGAAACCGCCGAGTCCA	0.527																																					p.T482T		Atlas-SNP	.											.	TIAM2	161	.	0			c.C1446T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	89	97	94		1446	-12.2	0	6		94	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TIAM2	NM_012454.3		0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154		482/1702	155458562	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	26230	exon4			AGAAACCGCCGAG		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.1446C>T	6.37:g.155458562C>T		89	0	0		86	33	0.383721	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Silent	SNP	ENST00000461783.3	37	CCDS34558.1																																																																																			.	.	weak		0.527	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454		T	155458562	C	T	155458562	2	4	29	1	0	0	0	0	0	0	0	1	15906	639	23	1		1	TIAM2	6	155458562	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	344450	155458562	15656505	372	12613											
TIAM2	26230	hgsc.bcm.edu	37	chr6	155575639	155575639	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacataaagtgtgaattacCactggagaaaacgtgtaagg	16	9	10	6	1	1	2	1	1	0	1	1	3	1	2	1	2	2	1	1	2	7	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:155575639C>T	ENST00000461783.3	+	28	5673	c.4400C>T	c.(4399-4401)cCa>cTa	p.P1467L	TIAM2_ENST00000360366.4_Missense_Mutation_p.P1491L|TIAM2_ENST00000275246.7_Missense_Mutation_p.P392L|TIAM2_ENST00000318981.5_Missense_Mutation_p.P1467L|TIAM2_ENST00000529824.2_Missense_Mutation_p.P1496L|TIAM2_ENST00000456144.1_Missense_Mutation_p.P1496L|TIAM2_ENST00000367174.2_Missense_Mutation_p.P843L|TIAM2_ENST00000456877.2_Missense_Mutation_p.P779L|RP11-477D19.2_ENST00000435295.1_RNA|TIAM2_ENST00000528391.2_Missense_Mutation_p.P803L			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	1467	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)		TGTGAATTACCACTGGAGAAA	0.448																																					p.P1467L		Atlas-SNP	.											TIAM2,NS,carcinoma,+1,1	TIAM2	161	1	0			c.C4400T						PASS	.						163	143	150					6																	155575639		2203	4300	6503	SO:0001583	missense	26230	exon25			AATTACCACTGGA		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.4400C>T	6.37:g.155575639C>T	ENSP00000437188:p.Pro1467Leu	144	0	0		175	94	0.537143	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Missense_Mutation	SNP	ENST00000461783.3	37	CCDS34558.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.415307	0.83449	.	.	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000456144;ENST00000318981;ENST00000367174;ENST00000360366;ENST00000529824;ENST00000456877;ENST00000528391;ENST00000275246	T;T;T;T;T;T;T;T;T	0.09445	3.44;3.18;3.44;3.21;3.38;3.18;3.23;3.31;2.98	5.66	5.66	0.87406	.	0.121042	0.56097	D	0.000030	T	0.11965	0.0291	L	0.36672	1.1	0.50632	D	0.999885	P;D;D;D	0.57899	0.885;0.981;0.981;0.967	P;P;P;P	0.54629	0.546;0.757;0.757;0.576	T	0.02339	-1.1174	10	0.41790	T	0.15	.	17.934	0.89007	0.0:1.0:0.0:0.0	.	803;1496;1491;1467	E9PKT1;Q8IVF5-2;Q8IVF5-5;Q8IVF5	.;.;.;TIAM2_HUMAN	L	1467;1713;1496;1467;843;1491;1496;779;803;392	ENSP00000437188:P1467L;ENSP00000407746:P1496L;ENSP00000327315:P1467L;ENSP00000356142:P843L;ENSP00000353528:P1491L;ENSP00000433348:P1496L;ENSP00000407183:P779L;ENSP00000435335:P803L;ENSP00000275246:P392L	ENSP00000275246:P392L	P	+	2	0	TIAM2	155617331	0.980000	0.34600	0.351000	0.25721	0.997000	0.91878	5.249000	0.65427	2.673000	0.90976	0.650000	0.86243	CCA	.	.	none		0.448	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454		T	155575639	C	T	155575639	3	4	29	1	0	0	0	0	1	0	0	0	15906	594	21	2	4490	2	TIAM2	6	155575639	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	117077	155575639	15539428	373	12614											
TULP4	56995	hgsc.bcm.edu	37	chr6	158923378	158923378	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcaccaccttcgacagcagtGgcaacgtggaggaggtgtgc	9	7	14	11	2	1	0	1	0	0	0	2	3	1	2	2	4	3	2	2	4	1	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:158923378G>A	ENST00000367097.3	+	13	4040	c.2683G>A	c.(2683-2685)Ggc>Agc	p.G895S	TULP4_ENST00000367094.2_Intron	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	895					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)		CGACAGCAGTGGCAACGTGGA	0.637																																					p.G895S		Atlas-SNP	.											.	TULP4	137	.	0			c.G2683A						PASS	.						68	72	71					6																	158923378		2203	4300	6503	SO:0001583	missense	56995	exon13			AGCAGTGGCAACG		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.2683G>A	6.37:g.158923378G>A	ENSP00000356064:p.Gly895Ser	87	0	0		82	4	0.0487805	NM_020245	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Missense_Mutation	SNP	ENST00000367097.3	37	CCDS34561.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.940588	0.92526	.	.	ENSG00000130338	ENST00000367097	T	0.75589	-0.95	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	D	0.83202	0.5203	M	0.65498	2.005	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85241	0.1038	10	0.87932	D	0	-33.3275	18.5327	0.90999	0.0:0.0:1.0:0.0	.	895	Q9NRJ4	TULP4_HUMAN	S	895	ENSP00000356064:G895S	ENSP00000356064:G895S	G	+	1	0	TULP4	158843366	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	8.894000	0.92506	2.379000	0.81126	0.561000	0.74099	GGC	.	.	none		0.637	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245		A	158923378	G	A	158923378	3	1	29	1	0	0	0	0	1	0	0	0	16791	1348	47	2	2733	2	TULP4	6	158923378	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	3347739	158923378	12191689	374	12615											
C6orf118	168090	hgsc.bcm.edu	37	chr6	165715405	165715405	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgaagtgtgggaaagagaggCctgggggttcaggtacctga	10	8	18	5	0	1	3	1	2	0	1	1	5	1	4	2	5	1	2	2	5	3	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:165715405C>T	ENST00000230301.8	-	2	426	c.406G>A	c.(406-408)Gcc>Acc	p.A136T	C6orf118_ENST00000543069.1_Missense_Mutation_p.A32T	NM_144980.3	NP_659417.2	Q5T5N4	CF118_HUMAN	chromosome 6 open reading frame 118	136										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)		GAAAGAGAGGCCTGGGGGTTC	0.627																																					p.A136T		Atlas-SNP	.											.	C6orf118	116	.	0			c.G406A						PASS	.						66	74	71					6																	165715405		2203	4299	6502	SO:0001583	missense	168090	exon2			GAGAGGCCTGGGG		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.406G>A	6.37:g.165715405C>T	ENSP00000230301:p.Ala136Thr	28	0	0		29	9	0.310345	NM_144980	Q8TC11	Missense_Mutation	SNP	ENST00000230301.8	37	CCDS5288.1	.	.	.	.	.	.	.	.	.	.	C	12.33	1.904170	0.33628	.	.	ENSG00000112539	ENST00000230301;ENST00000543069	T;T	0.15017	2.68;2.46	4.9	-3.28	0.05033	.	0.915788	0.09168	N	0.839280	T	0.02767	0.0083	L	0.34521	1.04	0.09310	N	1	B	0.24721	0.11	B	0.21151	0.033	T	0.44097	-0.9350	10	0.28530	T	0.3	.	2.3892	0.04374	0.1184:0.163:0.4086:0.3101	.	136	Q5T5N4	CF118_HUMAN	T	136;32	ENSP00000230301:A136T;ENSP00000439288:A32T	ENSP00000230301:A136T	A	-	1	0	C6orf118	165635395	0.000000	0.05858	0.000000	0.03702	0.105000	0.19272	-3.014000	0.00646	-0.308000	0.08792	0.655000	0.94253	GCC	.	.	none		0.627	C6orf118-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043026.1	NM_144980		T	165715405	C	T	165715405	3	4	29	1	0	0	0	0	1	0	0	0	2325	739	26	2	1035	2	C6orf118	6	165715405	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	6792027	165715405	5399662	375	12616											
FRMD1	79981	hgsc.bcm.edu	37	chr6	168458002	168458002	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgctgctcctcactgaccccGgctgtcatttcctggatctg	4	13	9	15	1	3	1	2	1	1	0	5	2	5	2	4	2	2	3	4	2	0	1	rs55991596	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr6:168458002G>A	ENST00000283309.6	-	11	1489	c.1425C>T	c.(1423-1425)gcC>gcT	p.A475A	FRMD1_ENST00000440994.2_Silent_p.A407A|FRMD1_ENST00000537786.1_Silent_p.A246A|FRMD1_ENST00000432403.1_5'UTR	NM_024919.3	NP_079195.3	Q8N878	FRMD1_HUMAN	FERM domain containing 1	475						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)		CACTGACCCCGGCTGTCATTT	0.657													G|||	107	0.0213658	0.003	0.0403	5008	,	,		17366	0.0		0.0666	False		,,,				2504	0.0082				p.A475A	GBM(50;8 1094 9538 34399)|Ovarian(80;676 1857 8675 49015)	Atlas-SNP	.											.	FRMD1	52	.	0			c.C1425T						PASS	.	G	,	55,4351	52.9+/-88.7	0,55,2148	30	29	29		1221,1425	-0.1	0	6	dbSNP_129	29	548,8052	142.0+/-198.3	14,520,3766	no	coding-synonymous,coding-synonymous	FRMD1	NM_001122841.1,NM_024919.3	,	14,575,5914	AA,AG,GG		6.3721,1.2483,4.6363	,	407/482,475/550	168458002	603,12403	2203	4300	6503	SO:0001819	synonymous_variant	79981	exon11			GACCCCGGCTGTC		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.1425C>T	6.37:g.168458002G>A		77	0	0		72	37	0.513889	NM_024919	B2RNV8|B3KUM6|Q5SZU7|Q9UFB0	Silent	SNP	ENST00000283309.6	37	CCDS5306.1																																																																																			G|0.958;A|0.042	0.042	strong		0.657	FRMD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362513.2	NM_024919		A	168458002	G	A	168458002	2	1	29	1	0	0	0	0	0	0	0	1	6057	1103	39	1		1	FRMD1	6	168458002	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2742597	168458002	2657065	376	12617											
C7orf27	221927	hgsc.bcm.edu	37	chr7	2578924	2578924	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	taactctcagggtcctggagGagctgcagggccagctgagg	8	7	16	10	0	1	1	1	1	1	0	3	3	2	3	2	5	4	3	2	5	1	1	rs61746940	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:2578924G>A	ENST00000340611.4	-	13	1915	c.1659C>T	c.(1657-1659)ctC>ctT	p.L553L	BRAT1_ENST00000473879.1_Intron	NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	553					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						GGTCCTGGAGGAGCTGCAGGG	0.647													G|||	2	0.000399361	0.0	0.0	5008	,	,		18093	0.0		0.001	False		,,,				2504	0.001				p.L553L		Atlas-SNP	.											.	BRAT1	57	.	0			c.C1659T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	31	31	31		1659	-5.8	0.8	7	dbSNP_129	31	29,8571	19.8+/-62.0	0,29,4271	no	coding-synonymous	BRAT1	NM_152743.3		0,30,6473	AA,AG,GG		0.3372,0.0227,0.2307		553/822	2578924	30,12976	2203	4300	6503	SO:0001819	synonymous_variant	221927	exon13			CTGGAGGAGCTGC	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.1659C>T	7.37:g.2578924G>A		122	0	0		162	70	0.432099	NM_152743	A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	Silent	SNP	ENST00000340611.4	37	CCDS5334.1																																																																																			G|0.998;A|0.002	0.002	strong		0.647	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239305.2	NM_152743		A	2578924	G	A	2578924	2	1	29	1	0	0	0	0	0	0	0	1	2384	1161	41	2		2	C7orf27	7	2578924	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10		2578924	156559739	377	12618											
CARD11	84433	hgsc.bcm.edu	37	chr7	2983886	2983886	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcctcatgaccgccatgttcTtctcctcactgagctgtgcg	5	13	8	15	2	4	2	2	2	2	0	6	2	5	2	4	0	2	2	4	0	0	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:2983886T>A	ENST00000396946.4	-	5	1047	c.644A>T	c.(643-645)aAg>aTg	p.K215M	AC004906.3_ENST00000423194.1_RNA	NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	215					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)		CGCCATGTTCTTCTCCTCACT	0.572			Mis		DLBCL																																p.K215M		Atlas-SNP	.		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	CARD11,colon,carcinoma,-1,6	CARD11	339	6	0			c.A644T						PASS	.						187	114	139					7																	2983886		2203	4300	6503	SO:0001583	missense	84433	exon5			ATGTTCTTCTCCT	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.644A>T	7.37:g.2983886T>A	ENSP00000380150:p.Lys215Met	174	0	0		199	88	0.442211	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	T	18.62	3.662813	0.67700	.	.	ENSG00000198286	ENST00000396946	T	0.38722	1.12	4.16	4.16	0.48862	.	0.000000	0.85682	D	0.000000	T	0.59582	0.2204	L	0.57536	1.79	0.58432	D	0.999998	D	0.89917	1.0	D	0.85130	0.997	T	0.63664	-0.6586	10	0.72032	D	0.01	-28.1579	13.4982	0.61438	0.0:0.0:0.0:1.0	.	215	Q9BXL7	CAR11_HUMAN	M	215	ENSP00000380150:K215M	ENSP00000380150:K215M	K	-	2	0	CARD11	2950412	1.000000	0.71417	0.991000	0.47740	0.982000	0.71751	5.720000	0.68470	1.650000	0.50662	0.459000	0.35465	AAG	.	.	none		0.572	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		A	2983886	T	A	2983886	3	1	29	1	0	0	0	0	1	0	0	0	2647	1609	56	5	2904	5	CARD11	7	2983886	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	404962	2983886	156154777	378	12619											
CARD11	84433	hgsc.bcm.edu	37	chr7	2984153	2984153	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcatcaggaagtgcgtgaggCcctcgtggccttcctccact	6	10	11	14	2	2	1	2	1	0	0	5	2	4	2	4	3	1	0	4	3	1	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:2984153C>T	ENST00000396946.4	-	5	780	c.377G>A	c.(376-378)gGc>gAc	p.G126D	AC004906.3_ENST00000423194.1_RNA	NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	126					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.G119D(2)		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)		GTGCGTGAGGCCCTCGTGGCC	0.617			Mis		DLBCL																																p.G126D		Atlas-SNP	.		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	CARD11,colon,carcinoma,+1,4	CARD11	339	4	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.G377A						PASS	.						57	54	55					7																	2984153		2203	4300	6503	SO:0001583	missense	84433	exon5			GTGAGGCCCTCGT	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.377G>A	7.37:g.2984153C>T	ENSP00000380150:p.Gly126Asp	45	0	0		63	25	0.396825	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	C	25.1	4.601697	0.87055	.	.	ENSG00000198286	ENST00000396946	T	0.38077	1.16	4.24	4.24	0.50183	.	0.053038	0.85682	D	0.000000	T	0.58991	0.2161	M	0.72353	2.195	0.80722	D	1	D	0.71674	0.998	D	0.70487	0.969	T	0.64041	-0.6500	10	0.54805	T	0.06	-41.4985	17.0013	0.86382	0.0:1.0:0.0:0.0	.	126	Q9BXL7	CAR11_HUMAN	D	126	ENSP00000380150:G126D	ENSP00000380150:G126D	G	-	2	0	CARD11	2950679	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.273000	0.78527	2.071000	0.62044	0.655000	0.94253	GGC	.	.	none		0.617	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		T	2984153	C	T	2984153	3	4	29	1	0	0	0	0	1	0	0	0	2647	739	26	2	3171	2	CARD11	7	2984153	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	267	2984153	156154510	379	12620											
PMS2	5395	hgsc.bcm.edu	37	chr7	6018231	6018231	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctaattaataacttaccattTtcatcgataacaaaatcaaa	19	13	1	8	1	2	0	2	0	0	0	3	1	2	0	1	0	3	0	1	0	8	7			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:6018231T>C	ENST00000265849.7	-	13	2376	c.2271A>G	c.(2269-2271)gaA>gaG	p.E757E	PMS2_ENST00000406569.3_Intron|PMS2_ENST00000382321.4_Silent_p.E356E|PMS2_ENST00000441476.2_Silent_p.E651E	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	757					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|single base insertion or deletion binding (GO:0032138)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		ACTTACCATTTTCATCGATAA	0.433			"Mis, N, F"			"colorectal, endometrial, ovarian, medulloblastoma, glioma"		Direct reversal of damage;Mismatch excision repair (MMR)	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome																												p.E757E		Atlas-SNP	.	yes	Rec		"Hereditary non-polyposis colorectal cancer, Turcot syndrome"	7	7p22	5395	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)		E	.	PMS2	88	.	0			c.A2271G						PASS	.						78	64	69					7																	6018231		2194	4281	6475	SO:0001819	synonymous_variant	5395	exon13	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	ACCATTTTCATCG		CCDS5343.1	7p22.1	2014-09-17	2001-11-28		ENSG00000122512	ENSG00000122512			9122	protein-coding gene	gene with protein product		600259	"postmeiotic segregation increased (S. cerevisiae) 2"	PMSL2		8072530	Standard	NM_000535		Approved	H_DJ0042M02.9, HNPCC4	uc003spl.3	P54278	OTTHUMG00000023135	ENST00000265849.7:c.2271A>G	7.37:g.6018231T>C		325	0	0		396	212	0.535354	NM_000535	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Silent	SNP	ENST00000265849.7	37	CCDS5343.1																																																																																			.	.	none		0.433	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535		C	6018231	T	C	6018231	2	2	29	1	0	0	0	0	0	0	0	1	12152	1838	64	3		3	PMS2	7	6018231	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	3034078	6018231	153120432	380	12621											
ABCA13	154664	hgsc.bcm.edu	37	chr7	48312084	48312084	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgaaccacaaaaacaagaaGttgataaaattttgactcac	19	9	5	8	0	1	4	1	3	0	1	1	4	1	4	1	0	2	1	1	0	7	4	rs78575608	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:48312084G>C	ENST00000435803.1	+	17	2845	c.2821G>C	c.(2821-2823)Gtt>Ctt	p.V941L		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	941					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						AAAACAAGAAGTTGATAAAAT	0.368													G|||	126	0.0251597	0.003	0.0202	5008	,	,		17420	0.0		0.0557	False		,,,				2504	0.0532				p.V941L		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G2821C						PASS	.	G	LEU/VAL	45,3611		0,45,1783	58	56	56		2821	-6.4	0	7	dbSNP_131	56	532,7648		14,504,3572	yes	missense	ABCA13	NM_152701.3	32	14,549,5355	CC,CG,GG		6.5037,1.2309,4.875	benign	941/5059	48312084	577,11259	1828	4090	5918	SO:0001583	missense	154664	exon17			CAAGAAGTTGATA	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.2821G>C	7.37:g.48312084G>C	ENSP00000411096:p.Val941Leu	164	0	0		120	26	0.216667	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	47	0.02152014652014652	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	37	0.048812664907651716	G	4.662	0.123148	0.08931	0.012309	0.065037	ENSG00000179869	ENST00000435803	D	0.82984	-1.67	5.81	-6.43	0.01926	.	1.110050	0.06993	N	0.821921	T	0.09202	0.0227	N	0.16368	0.405	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.45775	-0.9238	10	0.05525	T	0.97	.	1.2609	0.02001	0.3788:0.2867:0.186:0.1485	.	941	Q86UQ4	ABCAD_HUMAN	L	941	ENSP00000411096:V941L	ENSP00000411096:V941L	V	+	1	0	ABCA13	48282630	0.000000	0.05858	0.000000	0.03702	0.986000	0.74619	-1.314000	0.02715	-0.919000	0.03803	0.655000	0.94253	GTT	G|0.974;C|0.026	0.026	strong		0.368	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		C	48312084	G	C	48312084	3	2	29	1	0	0	0	0	1	0	0	0	31	1029	36	4	2716	4	ABCA13	7	48312084	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	42293853	48312084	110826579	381	12622											
EGFR	1956	hgsc.bcm.edu	37	chr7	55229255	55229255	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgctggggcccggagcccaGggactgcgtctcttgccgga	4	7	16	14	3	1	0	0	0	1	0	2	3	1	3	3	5	4	1	3	5	0	1	rs2227983	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:55229255G>A	ENST00000275493.2	+	13	1739	c.1562G>A	c.(1561-1563)aGg>aAg	p.R521K	EGFR_ENST00000454757.2_Missense_Mutation_p.R468K|EGFR_ENST00000342916.3_Missense_Mutation_p.R521K|EGFR_ENST00000455089.1_Missense_Mutation_p.R476K|EGFR_ENST00000442591.1_Missense_Mutation_p.R521K|EGFR_ENST00000344576.2_Missense_Mutation_p.R521K	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	521			R -> K (in dbSNP:rs2227983). {ECO:0000269|PubMed:17344846, ECO:0000269|Ref.7}.		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)	CCGGAGCCCAGGGACTGCGTC	0.617		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			G|||	1463	0.292133	0.0643	0.33	5008	,	,		17432	0.5238		0.2763	False		,,,				2504	0.3507				p.R521K		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.G1562A	GRCh37	CM942312	EGFR	M	rs2227983	PASS	.	G	LYS/ARG,LYS/ARG,LYS/ARG	391,4015	196.0+/-220.5	12,367,1824	111	114	113		1562,1562,1562	-5.8	0	7	dbSNP_98	113	2245,6355	380.6+/-339.7	317,1611,2372	yes	missense,missense,missense	EGFR	NM_005228.3,NM_201282.1,NM_201284.1	26,26,26	329,1978,4196	AA,AG,GG		26.1047,8.8743,20.2676	benign,benign,benign	521/1211,521/629,521/706	55229255	2636,10370	2203	4300	6503	SO:0001583	missense	1956	exon13	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	AGCCCAGGGACTG		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.1562G>A	7.37:g.55229255G>A	ENSP00000275493:p.Arg521Lys	52	0	0		44	25	0.568182	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	CCDS5514.1	652	0.29853479853479853	29	0.05894308943089431	108	0.2983425414364641	302	0.527972027972028	213	0.28100263852242746	G	1.353	-0.590998	0.03799	0.088743	0.261047	ENSG00000146648	ENST00000455089;ENST00000342916;ENST00000395504;ENST00000344576;ENST00000275493;ENST00000442591;ENST00000454757;ENST00000533450	T;T;T;T;T;T	0.28069	1.63;1.63;1.63;1.63;1.63;1.63	6.07	-5.79	0.02354	Growth factor, receptor (1);	1.067450	0.06989	N	0.821201	T	0.00012	0.0000	N	0.16368	0.405	0.80722	P	0.0	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	0.48043	-0.9069	9	0.10377	T	0.69	.	2.4933	0.04615	0.5094:0.1722:0.17:0.1484	rs2227983;rs3752650;rs11543848;rs12234746;rs17336807;rs11543848	476;521;521;521	Q504U8;P00533;P00533-3;P00533-4	.;EGFR_HUMAN;.;.	K	476;521;391;521;521;521;468;315	ENSP00000415559:R476K;ENSP00000342376:R521K;ENSP00000345973:R521K;ENSP00000275493:R521K;ENSP00000410031:R521K;ENSP00000395243:R468K	ENSP00000275493:R521K	R	+	2	0	EGFR	55196749	0.000000	0.05858	0.000000	0.03702	0.265000	0.26407	-0.793000	0.04589	-1.106000	0.03008	-0.165000	0.13383	AGG	A|0.243;C|0.000;G|0.757;T|0.000	0.243	strong		0.617	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		A	55229255	G	A	55229255	3	1	29	1	0	0	0	0	1	0	0	0	4969	1000	35	2	1623	2	EGFR	7	55229255	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	6917171	55229255	103909408	382	12623											
EGFR	1956	hgsc.bcm.edu	37	chr7	55238874	55238874	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcacttcctacagatgcacTgggccaggtcttgaaggctg	8	11	11	11	0	2	2	1	1	1	1	3	2	3	2	2	3	2	2	2	3	2	4	rs2227984	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:55238874T>A	ENST00000275493.2	+	16	2064	c.1887T>A	c.(1885-1887)acT>acA	p.T629T	EGFR_ENST00000454757.2_Silent_p.T576T|EGFR_ENST00000455089.1_Silent_p.T584T|EGFR_ENST00000442591.1_Silent_p.T629T	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	629					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)	ACAGATGCACTGGGCCAGGTC	0.398		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			T|||	1955	0.390375	0.2678	0.3977	5008	,	,		21298	0.5347		0.3559	False		,,,				2504	0.4376				p.T629T		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.T1887A						PASS	.	T		1213,3193	422.3+/-339.7	168,877,1158	135	120	125		1887	-5.9	0	7	dbSNP_123	125	2981,5619	461.9+/-365.5	537,1907,1856	no	coding-synonymous	EGFR	NM_005228.3		705,2784,3014	AA,AT,TT		34.6628,27.5306,32.2467		629/1211	55238874	4194,8812	2203	4300	6503	SO:0001819	synonymous_variant	1956	exon16	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	ATGCACTGGGCCA		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.1887T>A	7.37:g.55238874T>A		59	0	0		40	14	0.35	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																			T|0.645;A|0.355	0.355	strong		0.398	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		A	55238874	T	A	55238874	2	1	29	1	0	0	0	0	0	0	0	1	4969	1567	55	5		5	EGFR	7	55238874	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	9619	55238874	103899789	383	12624											
WBSCR17	64409	hgsc.bcm.edu	37	chr7	71142240	71142240	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtctgcttggaccaggggccGctggagaaccacacagcaat	10	6	13	12	1	1	1	0	0	1	1	1	3	1	2	3	4	3	3	3	4	2	1	rs77485397	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:71142240G>A	ENST00000333538.5	+	9	2083	c.1449G>A	c.(1447-1449)ccG>ccA	p.P483P	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	483	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)				ACCAGGGGCCGCTGGAGAACC	0.532													G|||	74	0.0147764	0.0151	0.0245	5008	,	,		17185	0.006		0.0	False		,,,				2504	0.0317				p.P483P		Atlas-SNP	.											WBSCR17,NS,carcinoma,+1,2	WBSCR17	208	2	0			c.G1449A						PASS	.	G		56,4350	54.9+/-90.9	0,56,2147	225	224	224		1449	-10.4	0	7	dbSNP_131	224	0,8600		0,0,4300	no	coding-synonymous	WBSCR17	NM_022479.1		0,56,6447	AA,AG,GG		0.0,1.271,0.4306		483/599	71142240	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	64409	exon9			GGGGCCGCTGGAG	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.1449G>A	7.37:g.71142240G>A		45	0	0		49	25	0.510204	NM_022479	Q8NFV9|Q9NTA8	Silent	SNP	ENST00000333538.5	37	CCDS5540.1																																																																																			G|0.995;A|0.005	0.005	strong		0.532	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479		A	71142240	G	A	71142240	2	1	29	1	0	0	0	0	0	0	0	1	17279	1074	38	1		1	WBSCR17	7	71142240	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	15903366	71142240	87996423	384	12625											
WBSCR17	64409	hgsc.bcm.edu	37	chr7	71177023	71177023	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aatggagccatcatgaacaaGggcacgggacgctgcctgga	12	5	14	10	2	1	1	1	1	0	0	1	4	1	4	2	4	3	2	2	4	3	0	rs75947590	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:71177023G>A	ENST00000333538.5	+	11	2323	c.1689G>A	c.(1687-1689)aaG>aaA	p.K563K	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	563	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)				TCATGAACAAGGGCACGGGAC	0.567													G|||	33	0.00658946	0.0	0.0231	5008	,	,		16311	0.006		0.0	False		,,,				2504	0.0112				p.K563K		Atlas-SNP	.											.	WBSCR17	208	.	0			c.G1689A						PASS	.	G		3,4403	6.2+/-15.9	0,3,2200	72	78	76		1689	-2.2	0.9	7	dbSNP_131	76	0,8600		0,0,4300	no	coding-synonymous	WBSCR17	NM_022479.1		0,3,6500	AA,AG,GG		0.0,0.0681,0.0231		563/599	71177023	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	64409	exon11			GAACAAGGGCACG	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.1689G>A	7.37:g.71177023G>A		57	0	0		58	28	0.482759	NM_022479	Q8NFV9|Q9NTA8	Silent	SNP	ENST00000333538.5	37	CCDS5540.1																																																																																			G|0.998;A|0.002	0.002	strong		0.567	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479		A	71177023	G	A	71177023	2	1	29	1	0	0	0	0	0	0	0	1	17279	991	35	2		2	WBSCR17	7	71177023	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	34783	71177023	87961640	385	12626											
BAZ1B	9031	hgsc.bcm.edu	37	chr7	72883898	72883898	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtgtggtctttgcagtgatGgttgaatcggtagtcaatgc	7	15	14	5	1	2	2	1	2	1	0	3	2	2	2	0	3	2	3	0	3	3	3	rs145043036	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:72883898G>A	ENST00000339594.4	-	9	3153	c.2815C>T	c.(2815-2817)Cat>Tat	p.H939Y	BAZ1B_ENST00000404251.1_Missense_Mutation_p.H939Y	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	939					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)				TTGCAGTGATGGTTGAATCGG	0.433													G|||	5	0.000998403	0.0	0.0029	5008	,	,		21118	0.0		0.003	False		,,,				2504	0.0				p.H939Y	Esophageal Squamous(112;1167 1561 21085 43672 48228)	Atlas-SNP	.											.	BAZ1B	147	.	0			c.C2815T						PASS	.	G	TYR/HIS	2,4404	6.2+/-15.9	0,2,2201	238	193	208		2815	3.8	0.8	7	dbSNP_134	208	10,8590	7.7+/-29.5	0,10,4290	yes	missense	BAZ1B	NM_032408.3	83	0,12,6491	AA,AG,GG		0.1163,0.0454,0.0923	benign	939/1484	72883898	12,12994	2203	4300	6503	SO:0001583	missense	9031	exon9			AGTGATGGTTGAA	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.2815C>T	7.37:g.72883898G>A	ENSP00000342434:p.His939Tyr	136	0	0		117	59	0.504274	NM_032408	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Missense_Mutation	SNP	ENST00000339594.4	37	CCDS5549.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	G	3.549	-0.092107	0.07053	4.54E-4	0.001163	ENSG00000009954	ENST00000339594;ENST00000404251	T;T	0.58060	0.36;0.36	5.59	3.78	0.43462	.	0.277384	0.41001	D	0.000975	T	0.23133	0.0559	N	0.08118	0	0.32807	D	0.500921	B	0.24483	0.104	B	0.19946	0.027	T	0.25047	-1.0143	10	0.27785	T	0.31	-8.3342	11.8585	0.52453	0.1431:0.0:0.8569:0.0	.	939	Q9UIG0	BAZ1B_HUMAN	Y	939	ENSP00000342434:H939Y;ENSP00000385442:H939Y	ENSP00000342434:H939Y	H	-	1	0	BAZ1B	72521834	1.000000	0.71417	0.761000	0.31378	0.591000	0.36615	4.342000	0.59341	0.722000	0.32252	-0.137000	0.14449	CAT	G|0.999;A|0.001	0.001	strong		0.433	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408		A	72883898	G	A	72883898	3	1	29	1	0	0	0	0	1	0	0	0	1330	1348	47	2	1680	2	BAZ1B	7	72883898	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1706875	72883898	86254765	386	12627											
MLXIPL	51085	hgsc.bcm.edu	37	chr7	73010191	73010191	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cttaatggcggcattgagctCctcaatctcatcccgcagct	8	11	8	14	2	2	1	2	1	1	0	5	1	4	1	2	2	2	4	2	2	2	2	rs149244334	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:73010191C>T	ENST00000313375.3	-	14	2214	c.2167G>A	c.(2167-2169)Gag>Aag	p.E723K	MLXIPL_ENST00000414749.2_Missense_Mutation_p.E721K|MLXIPL_ENST00000434326.1_Missense_Mutation_p.E629K|MLXIPL_ENST00000354613.1_Missense_Mutation_p.E702K|MLXIPL_ENST00000429400.2_Missense_Mutation_p.E704K|MLXIPL_ENST00000395189.1_Missense_Mutation_p.E630K	NM_032951.2|NM_032953.2	NP_116569.1|NP_116571.1	Q9NP71	MLXPL_HUMAN	MLX interacting protein-like	723	Leucine-zipper.				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)				GCATTGAGCTCCTCAATCTCA	0.647													C|||	5	0.000998403	0.0008	0.0029	5008	,	,		14413	0.0		0.002	False		,,,				2504	0.0				p.E723K		Atlas-SNP	.											.	MLXIPL	54	.	0			c.G2167A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	1,4403		0,1,2201	34	30	31		2167,2110,2161,2104	5	1	7	dbSNP_134	31	9,8591		0,9,4291	yes	missense,missense,missense,missense	MLXIPL	NM_032951.2,NM_032952.2,NM_032953.2,NM_032954.2	56,56,56,56	0,10,6492	TT,TC,CC		0.1047,0.0227,0.0769	probably-damaging,probably-damaging,probably-damaging,probably-damaging	723/853,704/834,721/851,702/832	73010191	10,12994	2202	4300	6502	SO:0001583	missense	51085	exon14			TGAGCTCCTCAAT	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.2167G>A	7.37:g.73010191C>T	ENSP00000320886:p.Glu723Lys	52	0	0		35	16	0.457143	NM_032951	C5HU02|C5HU03|C5HU04|Q96E48|Q9BY03|Q9BY04|Q9BY05|Q9BY06|Q9Y2P3	Missense_Mutation	SNP	ENST00000313375.3	37	CCDS5553.1	5	0.0022893772893772895	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	C	21.5	4.162639	0.78226	2.27E-4	0.001047	ENSG00000009950	ENST00000414749;ENST00000429400;ENST00000313375;ENST00000354613;ENST00000395189;ENST00000434326	D;D;D;D;D;D	0.98493	-4.95;-4.96;-4.95;-4.96;-4.95;-4.95	5.04	5.04	0.67666	.	0.372017	0.26362	N	0.024805	D	0.98283	0.9431	M	0.78916	2.43	0.37356	D	0.911005	D;D;D;D;D	0.63880	0.993;0.979;0.99;0.971;0.971	D;P;D;P;P	0.72982	0.922;0.549;0.979;0.754;0.832	D	0.97181	0.9851	10	0.72032	D	0.01	-16.78	15.9196	0.79552	0.0:1.0:0.0:0.0	.	630;723;704;721;702	Q9NP71-6;Q9NP71;Q9NP71-2;Q9NP71-3;Q9NP71-4	.;MLXPL_HUMAN;.;.;.	K	721;704;723;702;630;629	ENSP00000412330:E721K;ENSP00000406296:E704K;ENSP00000320886:E723K;ENSP00000346629:E702K;ENSP00000378616:E630K;ENSP00000392636:E629K	ENSP00000320886:E723K	E	-	1	0	MLXIPL	72648127	0.981000	0.34729	1.000000	0.80357	0.993000	0.82548	2.179000	0.42528	2.350000	0.79820	0.558000	0.71614	GAG	C|0.999;T|0.001	0.001	strong		0.647	MLXIPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252262.1	NM_032951		T	73010191	C	T	73010191	3	4	29	1	0	0	0	0	1	0	0	0	9646	864	30	2	407	2	MLXIPL	7	73010191	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	126293	73010191	86128472	387	12628											
ZP3	7784	hgsc.bcm.edu	37	chr7	76062798	76062798	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtctttcagagaactggaacGctgagaagaggtcccccacc	11	7	11	12	1	2	3	1	1	1	3	3	6	3	4	3	2	2	1	3	2	3	1	rs74676082	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:76062798G>A	ENST00000394857.3	+	4	605	c.547G>A	c.(547-549)Gct>Act	p.A183T	ZP3_ENST00000336517.4_Missense_Mutation_p.A132T|ZP3_ENST00000416245.1_Missense_Mutation_p.A7T	NM_001110354.1	NP_001103824.1	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 (sperm receptor)	183	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						GAACTGGAACGCTGAGAAGAG	0.592													G|||	33	0.00658946	0.0008	0.0418	5008	,	,		18285	0.0		0.003	False		,,,				2504	0.0				p.A183T		Atlas-SNP	.											.	ZP3	32	.	0			c.G547A						PASS	.	G	THR/ALA,THR/ALA	2,4404	4.2+/-10.8	0,2,2201	72	69	70		547,394	-10.8	0	7	dbSNP_131	70	49,8551	31.2+/-83.2	0,49,4251	yes	missense,missense	ZP3	NM_001110354.1,NM_007155.5	58,58	0,51,6452	AA,AG,GG		0.5698,0.0454,0.3921	benign,benign	183/425,132/374	76062798	51,12955	2203	4300	6503	SO:0001583	missense	7784	exon4			TGGAACGCTGAGA	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.547G>A	7.37:g.76062798G>A	ENSP00000378326:p.Ala183Thr	39	0	0		21	13	0.619048	NM_001110354	Q06633|Q29RW0	Missense_Mutation	SNP	ENST00000394857.3	37	CCDS47618.1	13	0.005952380952380952	0	0.0	10	0.027624309392265192	0	0.0	3	0.00395778364116095	G	0.623	-0.820170	0.02755	4.54E-4	0.005698	ENSG00000188372	ENST00000336517;ENST00000394857;ENST00000544121;ENST00000416245	T;T;T	0.81247	-1.47;-1.47;-1.47	5.4	-10.8	0.00216	Zona pellucida sperm-binding protein (3);	1.021960	0.07766	N	0.950871	T	0.23289	0.0563	N	0.05177	-0.1	0.09310	N	1	B;B	0.09022	0.002;0.0	B;B	0.08055	0.003;0.002	T	0.21245	-1.0251	10	0.07030	T	0.85	0.1179	3.818	0.08824	0.5092:0.0732:0.1109:0.3067	.	132;183	P21754-3;P21754	.;ZP3_HUMAN	T	132;183;183;7	ENSP00000337310:A132T;ENSP00000378326:A183T;ENSP00000411955:A7T	ENSP00000337310:A132T	A	+	1	0	ZP3	75900734	0.000000	0.05858	0.000000	0.03702	0.108000	0.19459	-2.663000	0.00849	-3.205000	0.00216	-1.069000	0.02264	GCT	G|0.996;A|0.004	0.004	strong		0.592	ZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253004.1			A	76062798	G	A	76062798	3	1	29	1	0	0	0	0	1	0	0	0	18232	1087	38	1	561	1	ZP3	7	76062798	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	3052607	76062798	83075865	388	12629											
ZP3	7784	hgsc.bcm.edu	37	chr7	76062913	76062913	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaccactgcgtggccacacCgacaccagaccagaatgcct	11	4	10	16	2	0	2	0	0	0	2	0	4	0	3	6	2	2	0	6	2	1	0	rs139729790	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:76062913C>G	ENST00000394857.3	+	4	720	c.662C>G	c.(661-663)cCg>cGg	p.P221R	ZP3_ENST00000336517.4_Missense_Mutation_p.P170R|ZP3_ENST00000416245.1_Missense_Mutation_p.P45R	NM_001110354.1	NP_001103824.1	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 (sperm receptor)	221	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						GTGGCCACACCGACACCAGAC	0.592													C|||	22	0.00439297	0.0015	0.0058	5008	,	,		19217	0.0		0.0119	False		,,,				2504	0.0041				p.P221R		Atlas-SNP	.											ZP3_ENST00000394857,NS,lymphoid_neoplasm,0,2	ZP3	32	2	0			c.C662G						PASS	.	C	ARG/PRO,ARG/PRO	18,4388	25.3+/-52.1	0,18,2185	132	113	119		662,509	-2.1	0	7	dbSNP_134	119	119,8481	62.4+/-124.4	0,119,4181	yes	missense,missense	ZP3	NM_001110354.1,NM_007155.5	103,103	0,137,6366	GG,GC,CC		1.3837,0.4085,1.0534	probably-damaging,probably-damaging	221/425,170/374	76062913	137,12869	2203	4300	6503	SO:0001583	missense	7784	exon4			CCACACCGACACC	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.662C>G	7.37:g.76062913C>G	ENSP00000378326:p.Pro221Arg	74	0	0		59	26	0.440678	NM_001110354	Q06633|Q29RW0	Missense_Mutation	SNP	ENST00000394857.3	37	CCDS47618.1	13|13	0.005952380952380952|0.005952380952380952	0|0	0.0|0.0	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	10|10	0.013192612137203167|0.013192612137203167	C|C	9.849|9.849	1.193169|1.193169	0.22037|0.22037	0.004085|0.004085	0.013837|0.013837	ENSG00000188372|ENSG00000188372	ENST00000336517;ENST00000394857;ENST00000544121;ENST00000416245|ENST00000394860	D;D;D|.	0.83837|.	-1.77;-1.77;-1.77|.	5.42|5.42	-2.08|-2.08	0.07254|0.07254	Endoglin/CD105 antigen conserved site (1);Endoglin/CD105 antigen subgroup (1);Zona pellucida sperm-binding protein (3);|.	1.140650|.	0.06482|.	N|.	0.733073|.	T|T	0.32133|0.32133	0.0819|0.0819	L|L	0.60455|0.60455	1.87|1.87	0.09310|0.09310	N|N	1|1	D;D|.	0.69078|.	0.997;0.991|.	D;D|.	0.70487|.	0.969;0.951|.	T|T	0.39522|0.39522	-0.9610|-0.9610	10|5	0.39692|.	T|.	0.17|.	-8.2099|-8.2099	6.7596|6.7596	0.23532|0.23532	0.1157:0.4103:0.0:0.474|0.1157:0.4103:0.0:0.474	.|.	170;221|.	P21754-3;P21754|.	.;ZP3_HUMAN|.	R|G	170;221;221;45|43	ENSP00000337310:P170R;ENSP00000378326:P221R;ENSP00000411955:P45R|.	ENSP00000337310:P170R|.	P|R	+|+	2|1	0|2	ZP3|ZP3	75900849|75900849	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.011000|0.011000	0.07611|0.07611	0.066000|0.066000	0.14489|0.14489	-0.288000|-0.288000	0.09051|0.09051	-0.768000|-0.768000	0.03414|0.03414	CCG|CGA	C|0.991;G|0.009	0.009	strong		0.592	ZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253004.1			G	76062913	C	G	76062913	3	3	29	1	0	0	0	0	1	0	0	0	18232	652	23	4	676	4	ZP3	7	76062913	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	115	76062913	83075750	389	12630											
CCDC146	57639	hgsc.bcm.edu	37	chr7	76866265	76866265	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttatgttctctttgctagtTacatgctatgggaaaacttc	9	17	7	8	0	1	0	0	0	1	0	3	1	1	1	0	1	4	4	0	1	6	7			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:76866265T>C	ENST00000285871.4	+	3	285	c.158T>C	c.(157-159)tTa>tCa	p.L53S	CCDC146_ENST00000431197.1_5'UTR	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	53										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)				CTTTGCTAGTTACATGCTATG	0.398																																					p.L53S		Atlas-SNP	.											.	CCDC146	87	.	0			c.T158C						PASS	.						170	130	144					7																	76866265		2203	4300	6503	SO:0001630	splice_region_variant	57639	exon3			GCTAGTTACATGC	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.157-1T>C	7.37:g.76866265T>C		81	0	0		69	30	0.434783	NM_020879	A8K8X6|Q9P223	Missense_Mutation	SNP	ENST00000285871.4	37	CCDS34671.1	.	.	.	.	.	.	.	.	.	.	T	17.55	3.418000	0.62622	.	.	ENSG00000135205	ENST00000415750;ENST00000285871	D;D	0.84660	-1.88;-1.88	5.55	5.55	0.83447	.	0.000000	0.64402	D	0.000006	D	0.91872	0.7427	M	0.75447	2.3	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.92425	0.5949	10	0.59425	D	0.04	-0.1732	15.6441	0.77033	0.0:0.0:0.0:1.0	.	53;53	Q8IYE0;C9JRR4	CC146_HUMAN;.	S	53	ENSP00000388649:L53S;ENSP00000285871:L53S	ENSP00000285871:L53S	L	+	2	0	AC007000.1	76704201	0.998000	0.40836	0.895000	0.35142	0.514000	0.34195	5.404000	0.66344	2.238000	0.73509	0.477000	0.44152	TTA	.	.	none		0.398	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879	Missense_Mutation	C	76866265	T	C	76866265	5	2	29	1	0	0	0	0	0	0	1	0	2782	1768	61	3	164	3	CCDC146	7	76866265	Splice_Site	SNP	T	TCGA-GR-7351-01A-11D-2210-10	803352	76866265	82272398	390	12631											
PTPN12	5782	hgsc.bcm.edu	37	chr7	77267956	77267956	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cttagatcatccagcgggagGtattcactatgaaatgtgca	12	11	10	8	1	2	2	2	1	0	1	3	3	3	3	1	2	2	2	1	2	4	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:77267956G>A	ENST00000248594.6	+	17	2461	c.2189G>A	c.(2188-2190)gGt>gAt	p.G730D	PTPN12_ENST00000435495.2_Missense_Mutation_p.G600D|PTPN12_ENST00000415482.2_Missense_Mutation_p.G611D	NM_002835.3	NP_002826.3	Q05209	PTN12_HUMAN	protein tyrosine phosphatase, non-receptor type 12	730					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						CCAGCGGGAGGTATTCACTAT	0.348																																					p.G730D		Atlas-SNP	.											.	PTPN12	83	.	0			c.G2189A						PASS	.						108	110	109					7																	77267956		2203	4300	6503	SO:0001583	missense	5782	exon17			CGGGAGGTATTCA		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.2189G>A	7.37:g.77267956G>A	ENSP00000248594:p.Gly730Asp	128	0	0		101	47	0.465347	NM_002835	A4D1C5|B4DKY2|E9PBR5|E9PEH9|Q16130|Q59FD6|Q75MN8|Q86XU4	Missense_Mutation	SNP	ENST00000248594.6	37	CCDS5592.1	.	.	.	.	.	.	.	.	.	.	G	4.258	0.046837	0.08243	.	.	ENSG00000127947	ENST00000248594;ENST00000415482;ENST00000435495;ENST00000407343	T;T;T;T	0.32753	3.88;3.29;3.29;1.44	5.5	1.15	0.20763	.	1.074940	0.07016	N	0.825987	T	0.24392	0.0591	L	0.44542	1.39	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.28681	-1.0036	10	0.38643	T	0.18	.	4.3593	0.11194	0.2806:0.0:0.5685:0.1509	.	730	Q05209	PTN12_HUMAN	D	730;611;600;212	ENSP00000248594:G730D;ENSP00000392429:G611D;ENSP00000397991:G600D;ENSP00000385079:G212D	ENSP00000248594:G730D	G	+	2	0	PTPN12	77105892	0.000000	0.05858	0.002000	0.10522	0.046000	0.14306	0.138000	0.16016	-0.011000	0.14247	0.551000	0.68910	GGT	.	.	none		0.348	PTPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253183.3			A	77267956	G	A	77267956	3	1	29	1	0	0	0	0	1	0	0	0	12794	1261	44	2	2255	2	PTPN12	7	77267956	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	401691	77267956	81870707	391	12632											
MAGI2	9863	hgsc.bcm.edu	37	chr7	78636484	78636484	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaacccttttgaaatcgtaAgttgaggtagtgacgaaggt	13	11	12	5	2	0	4	0	3	0	1	1	5	0	4	1	2	1	3	1	2	5	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:78636484A>C	ENST00000354212.4	-	2	593	c.340T>G	c.(340-342)Tta>Gta	p.L114V	MAGI2_ENST00000419488.1_Missense_Mutation_p.L114V|MAGI2_ENST00000522391.1_Missense_Mutation_p.L114V|MAGI2-AS2_ENST00000411616.1_RNA	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	114	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				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)	p.L114V(1)		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)				TGAAATCGTAAGTTGAGGTAG	0.388																																					p.L114V		Atlas-SNP	.											MAGI2,caecum,carcinoma,0,1	MAGI2	246	1	1	Substitution - Missense(1)	large_intestine(1)	c.T340G						PASS	.						147	126	133					7																	78636484		2203	4300	6503	SO:0001583	missense	9863	exon2			ATCGTAAGTTGAG	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.340T>G	7.37:g.78636484A>C	ENSP00000346151:p.Leu114Val	100	0	0		74	25	0.337838	NM_012301	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Missense_Mutation	SNP	ENST00000354212.4	37	CCDS5594.1	.	.	.	.	.	.	.	.	.	.	A	20.5	3.994850	0.74703	.	.	ENSG00000187391	ENST00000419488;ENST00000354212;ENST00000536298;ENST00000522391	T;T;T	0.11277	2.89;2.89;2.79	5.29	4.1	0.47936	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (1);	.	.	.	.	T	0.23492	0.0568	L	0.52573	1.65	0.80722	D	1	D;D	0.89917	1.0;0.996	D;P	0.91635	0.999;0.82	T	0.00647	-1.1628	9	0.35671	T	0.21	.	9.4432	0.38681	0.8477:0.0:0.1523:0.0	.	114;114	Q86UL8-2;Q86UL8	.;MAGI2_HUMAN	V	114	ENSP00000405766:L114V;ENSP00000346151:L114V;ENSP00000428389:L114V	ENSP00000346151:L114V	L	-	1	2	MAGI2	78474420	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.746000	0.55127	0.802000	0.34089	0.519000	0.50382	TTA	.	.	none		0.388	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		C	78636484	A	C	78636484	3	2	29	1	0	0	0	0	1	0	0	0	9200	69	3	5	4111	5	MAGI2	7	78636484	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	1368528	78636484	80502179	392	12633											
SAMD9L	219285	hgsc.bcm.edu	37	chr7	92761064	92761064	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagacctctcggagttgtttTtttagcgtggtaagtggttg	7	16	13	5	2	1	1	0	0	1	1	2	2	1	2	1	3	1	4	1	3	3	7			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:92761064T>G	ENST00000318238.4	-	5	5437	c.4221A>C	c.(4219-4221)aaA>aaC	p.K1407N	SAMD9L_ENST00000411955.1_Missense_Mutation_p.K1407N|SAMD9L_ENST00000437805.1_Missense_Mutation_p.K1407N	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	1407					common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)				central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			GGAGTTGTTTTTTTAGCGTGG	0.413																																					p.K1407N		Atlas-SNP	.											.	SAMD9L	227	.	0			c.A4221C						PASS	.						156	157	157					7																	92761064		2203	4300	6503	SO:0001583	missense	219285	exon5			TTGTTTTTTTAGC	AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"Sterile alpha motif (SAM) domain containing"	1349	protein-coding gene	gene with protein product		611170	"chromosome 7 open reading frame 6"	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.4221A>C	7.37:g.92761064T>G	ENSP00000326247:p.Lys1407Asn	63	0	0		75	17	0.226667	NM_152703	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Missense_Mutation	SNP	ENST00000318238.4	37	CCDS34681.1	.	.	.	.	.	.	.	.	.	.	T	9.547	1.114998	0.20795	.	.	ENSG00000177409	ENST00000318238;ENST00000411955;ENST00000437805;ENST00000394472	T;T;T	0.24350	1.86;1.86;1.86	5.22	1.58	0.23477	.	0.272209	0.30781	N	0.008884	T	0.36963	0.0986	L	0.47716	1.5	0.20307	N	0.999919	D	0.71674	0.998	D	0.66351	0.943	T	0.08617	-1.0713	10	0.62326	D	0.03	-22.1012	9.3808	0.38313	0.0:0.2436:0.0:0.7564	.	1407	Q8IVG5	SAM9L_HUMAN	N	1407;1407;1407;229	ENSP00000326247:K1407N;ENSP00000405760:K1407N;ENSP00000408796:K1407N	ENSP00000326247:K1407N	K	-	3	2	SAMD9L	92599000	0.000000	0.05858	0.971000	0.41717	0.037000	0.13140	0.116000	0.15561	0.458000	0.26988	0.383000	0.25322	AAA	.	.	none		0.413	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703		G	92761064	T	G	92761064	3	3	29	1	0	0	0	0	1	0	0	0	13842	1838	64	5	537	5	SAMD9L	7	92761064	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	14124580	92761064	66377599	393	12634											
GNGT1	2792	hgsc.bcm.edu	37	chr7	93540153	93540153	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acgttgaagaacgatctggcGaggatccactggtaaagggc	12	7	14	8	3	1	2	0	1	1	1	2	5	2	3	1	4	1	2	1	4	4	2	rs17243826	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:93540153G>A	ENST00000248572.5	+	3	296	c.148G>A	c.(148-150)Gag>Aag	p.E50K	GNGT1_ENST00000455502.1_3'UTR|GNGT1_ENST00000429473.1_Missense_Mutation_p.E50K	NM_021955.3	NP_068774.1	P63211	GBG1_HUMAN	guanine nucleotide binding protein (G protein), gamma transducing activity polypeptide 1	50			E -> K (in dbSNP:rs17243826).		cardiac muscle cell apoptotic process (GO:0010659)|cellular response to hypoxia (GO:0071456)|eye photoreceptor cell development (GO:0042462)|GTP catabolic process (GO:0006184)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	heterotrimeric G-protein complex (GO:0005834)|photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|plasma membrane (GO:0005886)	GTPase activity (GO:0003924)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(1)|lung(3)|prostate(1)	6	all_cancers(62;2.39e-10)|all_epithelial(64;1.54e-09)|Lung NSC(181;0.218)		STAD - Stomach adenocarcinoma(171;0.000967)			ACGATCTGGCGAGGATCCACT	0.388													G|||	143	0.0285543	0.0166	0.0519	5008	,	,		15953	0.0		0.0487	False		,,,				2504	0.0368				p.E50K		Atlas-SNP	.											.	GNGT1	12	.	0			c.G148A						PASS	.	G	LYS/GLU	112,4294	80.9+/-119.3	8,96,2099	86	84	85		148	5.6	0.6	7	dbSNP_123	85	442,8158	133.0+/-190.5	27,388,3885	yes	missense	GNGT1	NM_021955.3	56	35,484,5984	AA,AG,GG		5.1395,2.542,4.2596	possibly-damaging	50/75	93540153	554,12452	2203	4300	6503	SO:0001583	missense	2792	exon3			TCTGGCGAGGATC		CCDS5633.1	7q21.3	2008-07-18			ENSG00000127928	ENSG00000127928			4411	protein-coding gene	gene with protein product		189970				8661128	Standard	NM_021955		Approved	GNG1	uc003unc.1	P63211	OTTHUMG00000022908	ENST00000248572.5:c.148G>A	7.37:g.93540153G>A	ENSP00000248572:p.Glu50Lys	97	0	0		101	39	0.386139	NM_021955	A4D1H2|O43835|Q08447|Q16026|Q6LCP6	Missense_Mutation	SNP	ENST00000248572.5	37	CCDS5633.1	63	0.028846153846153848	12	0.024390243902439025	21	0.058011049723756904	0	0.0	30	0.0395778364116095	G	16.90	3.248745	0.59103	0.02542	0.051395	ENSG00000127928	ENST00000248572;ENST00000429473	T;T	0.19394	2.15;2.15	5.6	5.6	0.85130	G-protein gamma domain (5);	0.052380	0.64402	D	0.000001	T	0.01730	0.0055	.	.	.	0.80722	D	1	P	0.43094	0.799	B	0.36244	0.22	T	0.05225	-1.0898	9	0.24483	T	0.36	-18.2019	18.7588	0.91842	0.0:0.0:1.0:0.0	rs17243826;rs17243826	50	P63211	GBG1_HUMAN	K	50	ENSP00000248572:E50K;ENSP00000388777:E50K	ENSP00000248572:E50K	E	+	1	0	GNGT1	93378089	1.000000	0.71417	0.597000	0.28824	0.172000	0.22775	6.792000	0.75125	2.809000	0.96659	0.655000	0.94253	GAG	A|0.023;C|0.029;G|0.948	0.023	strong		0.388	GNGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254718.2	NM_021955		A	93540153	G	A	93540153	3	1	29	1	0	0	0	0	1	0	0	0	6541	1059	37	1	154	1	GNGT1	7	93540153	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	779089	93540153	65598510	394	12635											
PON1	5444	hgsc.bcm.edu	37	chr7	94953765	94953765	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccagtcccatccccaagaggGtgagcgcaatcagcttcgcc	9	6	10	16	2	1	2	1	1	0	1	4	2	3	2	5	1	2	2	5	1	2	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:94953765G>C	ENST00000222381.3	-	1	254	c.23C>G	c.(22-24)aCc>aGc	p.T8S	PON1_ENST00000542556.1_Intron	NM_000446.5	NP_000437.3	P27169	PON1_HUMAN	paraoxonase 1	8					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)	CCCCAAGAGGGTGAGCGCAAT	0.612																																					p.T8S	GBM(119;715 1622 17358 22490 33240)	Atlas-SNP	.											.	PON1	55	.	0			c.C23G						PASS	.						137	100	113					7																	94953765		2203	4300	6503	SO:0001583	missense	5444	exon1			AAGAGGGTGAGCG	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.23C>G	7.37:g.94953765G>C	ENSP00000222381:p.Thr8Ser	36	0	0		48	14	0.291667	NM_000446	B2RA40|Q16052|Q6B0J6|Q9UCB1	Missense_Mutation	SNP	ENST00000222381.3	37	CCDS5638.1	.	.	.	.	.	.	.	.	.	.	G	0.082	-1.181847	0.01633	.	.	ENSG00000005421	ENST00000222381	T	0.34859	1.34	4.31	3.43	0.39272	Six-bladed beta-propeller, TolB-like (1);	0.403795	0.27000	N	0.021422	T	0.20780	0.0500	L	0.28014	0.82	0.40848	D	0.983722	B	0.02656	0.0	B	0.04013	0.001	T	0.06075	-1.0847	10	0.10902	T	0.67	-2.7887	8.2699	0.31838	0.106:0.0:0.894:0.0	.	8	P27169	PON1_HUMAN	S	8	ENSP00000222381:T8S	ENSP00000222381:T8S	T	-	2	0	PON1	94791701	0.991000	0.36638	0.488000	0.27440	0.038000	0.13279	2.607000	0.46300	1.414000	0.47017	0.555000	0.69702	ACC	.	.	none		0.612	PON1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000332865.2	NM_000446		C	94953765	G	C	94953765	3	2	29	1	0	0	0	0	1	0	0	0	12257	1261	44	4	1080	4	PON1	7	94953765	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1413612	94953765	64184898	395	12636											
DYNC1I1	1780	hgsc.bcm.edu	37	chr7	95442624	95442624	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgaagctggaagccaagacTcaggcgatctggggccatta	11	7	14	9	1	2	2	1	1	1	1	2	4	2	3	2	4	2	1	2	4	4	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:95442624T>A	ENST00000324972.6	+	4	533	c.340T>A	c.(340-342)Tca>Aca	p.S114T	DYNC1I1_ENST00000413338.1_Missense_Mutation_p.S97T|DYNC1I1_ENST00000437599.1_Missense_Mutation_p.S114T|DYNC1I1_ENST00000457059.1_Missense_Mutation_p.S97T|DYNC1I1_ENST00000537881.1_Missense_Mutation_p.S97T|DYNC1I1_ENST00000447467.2_Missense_Mutation_p.S97T|DYNC1I1_ENST00000359388.4_Missense_Mutation_p.S97T	NM_004411.4	NP_004402.1	O14576	DC1I1_HUMAN	dynein, cytoplasmic 1, intermediate chain 1	114	Interaction with DCTN1. {ECO:0000250}.				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)			AAGCCAAGACTCAGGCGATCT	0.418																																					p.S114T		Atlas-SNP	.											.	DYNC1I1	111	.	0			c.T340A						PASS	.						76	74	74					7																	95442624		2203	4300	6503	SO:0001583	missense	1780	exon4			CAAGACTCAGGCG	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.340T>A	7.37:g.95442624T>A	ENSP00000320130:p.Ser114Thr	62	0	0		63	7	0.111111	NM_004411	B4DME3|F5H050|G5E9K1|Q8TBF7|Q9Y2X1	Missense_Mutation	SNP	ENST00000324972.6	37	CCDS5644.1	.	.	.	.	.	.	.	.	.	.	T	15.85	2.954071	0.53293	.	.	ENSG00000158560	ENST00000447467;ENST00000324972;ENST00000537881;ENST00000437599;ENST00000359388;ENST00000413338;ENST00000518089;ENST00000457059	T;T;T;T;T;T	0.76186	-0.67;-0.77;-1.0;-0.73;-0.79;-0.67	4.55	4.55	0.56014	.	0.146929	0.47093	D	0.000259	T	0.62829	0.2460	L	0.28649	0.875	0.58432	D	0.999992	B;B;P;B;P	0.36789	0.25;0.097;0.57;0.25;0.57	B;B;B;B;B	0.35413	0.041;0.09;0.142;0.041;0.202	T	0.63497	-0.6624	10	0.31617	T	0.26	-6.2365	14.9476	0.71044	0.0:0.0:0.0:1.0	.	97;114;97;114;97	Q7Z6M0;G5E9K1;O14576-2;O14576;O14576-3	.;.;.;DC1I1_HUMAN;.	T	97;114;97;114;97;97;97;97	ENSP00000392337:S97T;ENSP00000320130:S114T;ENSP00000438377:S97T;ENSP00000398118:S114T;ENSP00000352348:S97T;ENSP00000412444:S97T	ENSP00000320130:S114T	S	+	1	0	DYNC1I1	95280560	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.769000	0.85360	2.267000	0.75376	0.533000	0.62120	TCA	.	.	none		0.418	DYNC1I1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333432.1	NM_004411		A	95442624	T	A	95442624	3	1	29	1	0	0	0	0	1	0	0	0	4844	1551	54	5	350	5	DYNC1I1	7	95442624	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	488859	95442624	63696039	396	12637											
CYP3A4	1576	hgsc.bcm.edu	37	chr7	99358595	99358595	+	Silent	SNP	C	C	T																															tctatgttgtccttgttcttCttgctgaatctggttccacg																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:99358595C>T	ENST00000336411.2	-	12	1446	c.1263G>A	c.(1261-1263)aaG>aaA	p.K421K	CYP3A4_ENST00000354593.2_Silent_p.K271K	NM_001202855.2|NM_017460.5	NP_001189784.1|NP_059488.2	P08684	CP3A4_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 4	421					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)	CCTTGTTCTTCTTGCTGAATC	0.413																																					p.K421K		Atlas-SNP	.											.	CYP3A4	56	.	0			c.G1263A						PASS	.						384	334	351					7																	99358595		2203	4300	6503	SO:0001819	synonymous_variant	1576	exon12			GTTCTTCTTGCTG	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.1263G>A	7.37:g.99358595C>T		287	1	0.00348432		261	110	0.421456	NM_017460	P05184|Q16757|Q9UK50	Silent	SNP	ENST00000336411.2	37	CCDS5674.1																																																																																			.	.	none		0.413	CYP3A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345059.1			T	99358595	C	T	99358595	2	4	29	1	0	0	0	0	0	0	0	1	4180	912	32	2		2	CYP3A4	7	99358595	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	3915971	99358595	59780068	397	12638	159	3									
CYP3A4	1576	hgsc.bcm.edu	37	chr7	99358598	99358598	+	Silent	SNP	G	G	A																															atgttgtccttgttcttcttGctgaatctggttccacgttg																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:99358598G>A	ENST00000336411.2	-	12	1443	c.1260C>T	c.(1258-1260)agC>agT	p.S420S	CYP3A4_ENST00000354593.2_Silent_p.S270S	NM_001202855.2|NM_017460.5	NP_001189784.1|NP_059488.2	P08684	CP3A4_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 4	420					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)	TGTTCTTCTTGCTGAATCTGG	0.413																																					p.S420S		Atlas-SNP	.											.	CYP3A4	56	.	0			c.C1260T						PASS	.						375	327	343					7																	99358598		2203	4300	6503	SO:0001819	synonymous_variant	1576	exon12			CTTCTTGCTGAAT	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.1260C>T	7.37:g.99358598G>A		276	0	0		252	105	0.416667	NM_017460	P05184|Q16757|Q9UK50	Silent	SNP	ENST00000336411.2	37	CCDS5674.1																																																																																			.	.	none		0.413	CYP3A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345059.1			A	99358598	G	A	99358598	2	1	29	1	0	0	0	0	0	0	0	1	4180	1310	46	2		2	CYP3A4	7	99358598	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	3	99358598	59780065	398	12639	159	3									
CYP3A4	1576	hgsc.bcm.edu	37	chr7	99358604	99358604	+	Splice_Site	SNP	T	T	C																															tccttgttcttcttgctgaaTctggttccacgttggtagat																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:99358604T>C	ENST00000336411.2	-	12	1437	c.1254A>G	c.(1252-1254)agA>agG	p.R418R	CYP3A4_ENST00000354593.2_Splice_Site_p.R268R	NM_001202855.2|NM_017460.5	NP_001189784.1|NP_059488.2	P08684	CP3A4_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 4	418					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)	TCTTGCTGAATCTGGTTCCAC	0.413																																					p.R418R		Atlas-SNP	.											.	CYP3A4	56	.	0			c.A1254G						PASS	.						372	324	341					7																	99358604		2203	4300	6503	SO:0001630	splice_region_variant	1576	exon12			GCTGAATCTGGTT	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.1254-1A>G	7.37:g.99358604T>C		270	1	0.0037037		240	102	0.425	NM_017460	P05184|Q16757|Q9UK50	Silent	SNP	ENST00000336411.2	37	CCDS5674.1																																																																																			.	.	none		0.413	CYP3A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345059.1		Silent	C	99358604	T	C	99358604	5	2	29	1	0	0	0	0	0	0	1	0	4180	1449	50	3	265	3	CYP3A4	7	99358604	Splice_Site	SNP	T	TCGA-GR-7351-01A-11D-2210-10	6	99358604	59780059	399	12640	159	3									
GNB2	2783	hgsc.bcm.edu	37	chr7	100273936	100273936	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gaggccgagcagctccggaaCcagatccgggtgagggcctg	8	4	17	12	3	0	2	0	1	0	1	2	5	2	3	5	4	3	2	5	4	1	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:100273936C>T	ENST00000303210.4	+	2	530	c.48C>T	c.(46-48)aaC>aaT	p.N16N	GNB2_ENST00000436220.1_Intron|GNB2_ENST00000424361.1_Intron|GNB2_ENST00000393924.1_Silent_p.N16N|GNB2_ENST00000427895.1_Intron|GNB2_ENST00000393926.1_Silent_p.N16N|GNB2_ENST00000419828.1_Intron	NM_005273.3	NP_005264.2	P62879	GBB2_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 2	16					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)				AGCTCCGGAACCAGATCCGGG	0.726																																					p.N16N		Atlas-SNP	.											.	GNB2	29	.	0			c.C48T						PASS	.						20	19	19					7																	100273936		2185	4291	6476	SO:0001819	synonymous_variant	2783	exon2			CCGGAACCAGATC	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.48C>T	7.37:g.100273936C>T		109	0	0		98	10	0.102041	NM_005273	B3KPU1|P11016|P54312	Silent	SNP	ENST00000303210.4	37	CCDS5703.1																																																																																			.	.	none		0.726	GNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268391.2	NM_005273		T	100273936	C	T	100273936	2	4	29	1	0	0	0	0	0	0	0	1	6525	506	18	2		2	GNB2	7	100273936	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	915332	100273936	58864727	400	12641											
EPHB4	2050	hgsc.bcm.edu	37	chr7	100417879	100417879	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgggcatggctggcaggacCcttctcctgacaggggcttg	5	9	15	12	0	1	1	0	1	1	0	2	2	1	2	2	6	0	4	2	6	0	2	rs201531252		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:100417879C>T	ENST00000358173.3	-	5	1316	c.848G>A	c.(847-849)gGg>gAg	p.G283E	EPHB4_ENST00000477446.1_5'UTR|EPHB4_ENST00000360620.3_Missense_Mutation_p.G283E|RN7SL750P_ENST00000582814.1_RNA	NM_004444.4	NP_004435.3	P54760	EPHB4_HUMAN	EPH receptor B4	283	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)					CTGGCAGGACCCTTCTCCTGA	0.592																																					p.G283E	GBM(200;2113 3072 25865 52728)	Atlas-SNP	.											.	EPHB4	106	.	0			c.G848A						PASS	.						105	120	115					7																	100417879		2203	4300	6503	SO:0001583	missense	2050	exon5			CAGGACCCTTCTC	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.848G>A	7.37:g.100417879C>T	ENSP00000350896:p.Gly283Glu	49	0	0		46	24	0.521739	NM_004444	B5A970|B5A971|B5A972|Q7Z635|Q9BTA5|Q9BXP0	Missense_Mutation	SNP	ENST00000358173.3	37	CCDS5706.1	.	.	.	.	.	.	.	.	.	.	C	8.451	0.853099	0.17106	.	.	ENSG00000196411	ENST00000360620;ENST00000358173	T;T	0.15256	2.44;2.44	5.35	4.47	0.54385	Tyrosine-protein kinase ephrin type A/B receptor-like (1);	0.120033	0.37437	N	0.002098	T	0.10937	0.0267	L	0.31476	0.935	0.32118	N	0.588384	B;B;B;B	0.16603	0.018;0.018;0.001;0.009	B;B;B;B	0.20184	0.025;0.028;0.003;0.014	T	0.19321	-1.0309	10	0.02654	T	1	.	11.4994	0.50428	0.0:0.912:0.0:0.088	.	283;283;283;283	B5A972;B5A970;Q96L35;P54760	.;.;.;EPHB4_HUMAN	E	283	ENSP00000353833:G283E;ENSP00000350896:G283E	ENSP00000350896:G283E	G	-	2	0	EPHB4	100255815	0.995000	0.38212	1.000000	0.80357	0.997000	0.91878	3.317000	0.51968	1.240000	0.43803	0.655000	0.94253	GGG	C|0.999;T|0.001	0.001	weak		0.592	EPHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347222.1	NM_004444		T	100417879	C	T	100417879	3	4	29	1	0	0	0	0	1	0	0	0	5179	623	22	2	2167	2	EPHB4	7	100417879	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	143943	100417879	58720784	401	12642											
SLC12A9	56996	hgsc.bcm.edu	37	chr7	100464136	100464136	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgatcccgcccgatacccccGctacctggcgctactggaga	7	6	10	18	5	0	1	0	0	0	1	1	4	1	1	5	2	3	2	5	2	3	3	rs374047787		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:100464136G>A	ENST00000354161.3	+	14	2779	c.2654G>A	c.(2653-2655)cGc>cAc	p.R885H	TRIP6_ENST00000200457.4_5'Flank	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9	885					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)					CGATACCCCCGCTACCTGGCG	0.677																																					p.R885H		Atlas-SNP	.											.	SLC12A9	81	.	0			c.G2654A						PASS	.	G	HIS/ARG	0,4368		0,0,2184	14	11	12		2654	0.4	0	7		12	1,8575		0,1,4287	no	missense	SLC12A9	NM_020246.2	29	0,1,6471	AA,AG,GG		0.0117,0.0,0.0077	benign	885/915	100464136	1,12943	2184	4288	6472	SO:0001583	missense	56996	exon14			ACCCCCGCTACCT	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.2654G>A	7.37:g.100464136G>A	ENSP00000275730:p.Arg885His	26	0	0		52	20	0.384615	NM_020246	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Missense_Mutation	SNP	ENST00000354161.3	37	CCDS5707.1	.	.	.	.	.	.	.	.	.	.	G	3.991	-0.004508	0.07773	0.0	1.17E-4	ENSG00000146828	ENST00000354161	D	0.91124	-2.79	4.7	0.364	0.16124	.	0.285942	0.33591	N	0.004743	T	0.81814	0.4902	L	0.29908	0.895	0.24237	N	0.995379	B	0.09022	0.002	B	0.04013	0.001	T	0.68580	-0.5371	10	0.41790	T	0.15	.	7.9231	0.29859	0.4236:0.0:0.5764:0.0	.	885	Q9BXP2	S12A9_HUMAN	H	885	ENSP00000275730:R885H	ENSP00000275730:R885H	R	+	2	0	SLC12A9	100302072	0.000000	0.05858	0.003000	0.11579	0.014000	0.08584	0.153000	0.16323	-0.128000	0.11641	-0.378000	0.06908	CGC	.	.	weak		0.677	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246		A	100464136	G	A	100464136	3	1	29	1	0	0	0	0	1	0	0	0	14405	1087	38	1	2704	1	SLC12A9	7	100464136	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	46257	100464136	58674527	402	12643											
TFEC	22797	hgsc.bcm.edu	37	chr7	115580893	115580893	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	actgaattctgctcaggatgGctctgctgtttggtgacatg	7	14	12	8	0	3	2	1	2	2	0	3	3	3	3	0	3	2	4	0	3	1	2	rs34298819	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:115580893G>A	ENST00000265440.7	-	8	936	c.756C>T	c.(754-756)agC>agT	p.S252S	TFEC_ENST00000320239.7_Silent_p.S223S|TFEC_ENST00000393485.1_3'UTR|TFEC_ENST00000457268.1_Silent_p.S185S	NM_012252.3	NP_036384.1	O14948	TFEC_HUMAN	transcription factor EC	252					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)			GCTCAGGATGGCTCTGCTGTT	0.483													G|||	26	0.00519169	0.0015	0.0086	5008	,	,		18076	0.0		0.0179	False		,,,				2504	0.0				p.S252S		Atlas-SNP	.											.	TFEC	51	.	0			c.C756T						PASS	.	G	,	14,4392	21.2+/-45.6	0,14,2189	139	139	139		669,756	-1.6	0.9	7	dbSNP_126	139	134,8466	66.3+/-128.7	2,130,4168	no	coding-synonymous,coding-synonymous	TFEC	NM_001018058.2,NM_012252.3	,	2,144,6357	AA,AG,GG		1.5581,0.3177,1.1379	,	223/319,252/348	115580893	148,12858	2203	4300	6503	SO:0001819	synonymous_variant	22797	exon8			AGGATGGCTCTGC	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.756C>T	7.37:g.115580893G>A		153	0	0		147	70	0.47619	NM_012252	B2R8X5|Q5H9U8|Q709A4|Q8N6J9	Silent	SNP	ENST00000265440.7	37	CCDS5762.1																																																																																			G|0.988;A|0.012	0.012	strong		0.483	TFEC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000059839.4	NM_012252		A	115580893	G	A	115580893	2	1	29	1	0	0	0	0	0	0	0	1	15817	1194	42	2		2	TFEC	7	115580893	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	15116757	115580893	43557770	403	12644											
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121659234	121659234	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tagctgaggggttggaatccGagaagaaggcagttataccc	12	8	14	7	1	0	3	0	1	0	2	1	5	1	4	2	4	2	4	2	4	6	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:121659234G>A	ENST00000393386.2	+	13	5311	c.4900G>A	c.(4900-4902)Gag>Aag	p.E1634K	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.E774K	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1634					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						GTTGGAATCCGAGAAGAAGGC	0.438																																					p.E1634K		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.G4900A						PASS	.						213	190	198					7																	121659234		2203	4300	6503	SO:0001583	missense	5803	exon13			GAATCCGAGAAGA	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.4900G>A	7.37:g.121659234G>A	ENSP00000377047:p.Glu1634Lys	172	0	0		173	9	0.0520231	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.930084	0.92389	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	T;T	0.76968	0.84;-1.06	5.37	5.37	0.77165	.	0.000000	0.64402	D	0.000001	D	0.86640	0.5981	M	0.64997	1.995	0.54753	D	0.999989	D;P;D	0.89917	0.996;0.946;1.0	P;B;D	0.68765	0.714;0.31;0.96	D	0.87100	0.2178	10	0.59425	D	0.04	.	19.1031	0.93282	0.0:0.0:1.0:0.0	.	773;774;1634	P23471-2;C9JFM0;P23471	.;.;PTPRZ_HUMAN	K	1634;774	ENSP00000377047:E1634K;ENSP00000410000:E774K	ENSP00000377047:E1634K	E	+	1	0	PTPRZ1	121446470	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.670000	0.54569	2.539000	0.85634	0.585000	0.79938	GAG	.	.	none		0.438	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		A	121659234	G	A	121659234	3	1	29	1	0	0	0	0	1	0	0	0	12829	1059	37	1	4950	1	PTPRZ1	7	121659234	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	6078341	121659234	37479429	404	12645											
TRYX3	136541	hgsc.bcm.edu	37	chr7	141955390	141955390	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcagctgtgatcacccaaagCgggtggatcaggactccagc	10	6	13	12	1	2	1	2	1	0	0	3	3	3	3	2	3	3	2	2	3	1	0	rs145731516	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:141955390C>T	ENST00000552471.1	-	2	463	c.144G>A	c.(142-144)ccG>ccA	p.P48P	PRSS58_ENST00000547058.2_Silent_p.P48P			Q8IYP2	PRS58_HUMAN	protease, serine, 58	48	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						TCACCCAAAGCGGGTGGATCA	0.502													C|||	16	0.00319489	0.0	0.0029	5008	,	,		17941	0.0		0.0119	False		,,,				2504	0.002				p.P48P		Atlas-SNP	.											.	PRSS58	41	.	0			c.G144A						PASS	.	C		8,4398	14.3+/-33.2	0,8,2195	79	77	77		144	-10	0	7	dbSNP_134	77	75,8525	44.5+/-102.8	0,75,4225	no	coding-synonymous	PRSS58	NM_001001317.3		0,83,6420	TT,TC,CC		0.8721,0.1816,0.6382		48/242	141955390	83,12923	2203	4300	6503	SO:0001819	synonymous_variant	136541	exon3			CCAAAGCGGGTGG		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.144G>A	7.37:g.141955390C>T		101	0	0		109	47	0.431193	NM_001001317	B3KVJ6|D3DXD2	Silent	SNP	ENST00000552471.1	37	CCDS5871.1																																																																																			C|0.994;T|0.006	0.006	strong		0.502	PRSS58-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351328.2	NM_001001317		T	141955390	C	T	141955390	2	4	29	1	0	0	0	0	0	0	0	1	16619	755	27	1		1	TRYX3	7	141955390	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	20296156	141955390	17183273	405	12646											
EPHB6	2051	hgsc.bcm.edu	37	chr7	142561786	142561786	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggacctttgaggcatgtcaTgtggcaggggcccctccagg	6	8	15	12	1	1	1	1	1	0	0	2	2	2	2	4	6	0	2	4	6	0	1	rs56300555	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:142561786T>C	ENST00000392957.2	+	7	1015	c.228T>C	c.(226-228)caT>caC	p.H76H	EPHB6_ENST00000442129.1_Silent_p.H76H|EPHB6_ENST00000411471.2_Intron	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	76	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.					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)					AGGCATGTCATGTGGCAGGGG	0.637													T|||	32	0.00638978	0.0015	0.0058	5008	,	,		16121	0.0		0.0219	False		,,,				2504	0.0041				p.H76H		Atlas-SNP	.											.	EPHB6	168	.	0			c.T228C						PASS	.	T		15,4389	21.2+/-45.6	0,15,2187	125	134	131		228	2.3	1	7	dbSNP_129	131	138,8458	66.0+/-128.3	1,136,4161	no	coding-synonymous	EPHB6	NM_004445.3		1,151,6348	CC,CT,TT		1.6054,0.3406,1.1769		76/1022	142561786	153,12847	2202	4298	6500	SO:0001819	synonymous_variant	2051	exon7			ATGTCATGTGGCA	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.228T>C	7.37:g.142561786T>C		171	0	0		143	73	0.51049	NM_004445	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Silent	SNP	ENST00000392957.2	37	CCDS5873.2																																																																																			T|0.990;C|0.010	0.010	strong		0.637	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			C	142561786	T	C	142561786	2	2	29	1	0	0	0	0	0	0	0	1	5180	1461	51	3		3	EPHB6	7	142561786	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	606396	142561786	16576877	406	12647											
EPHA1	2041	hgsc.bcm.edu	37	chr7	143088584	143088584	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctgaatactgcaaagaatgCgcttctggtgcccgggcagt	9	9	12	11	2	1	2	0	1	1	1	1	2	1	2	2	2	4	3	2	2	4	2	rs139482378	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:143088584C>T	ENST00000275815.3	-	18	2983	c.2897G>A	c.(2896-2898)cGc>cAc	p.R966H	EPHA1_ENST00000458129.1_5'Flank	NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	966	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)				GCAAAGAATGCGCTTCTGGTG	0.622													C|||	3	0.000599042	0.0008	0.0	5008	,	,		17063	0.0		0.002	False		,,,				2504	0.0				p.R966H		Atlas-SNP	.											EPHA1,NS,carcinoma,-1,1	EPHA1	193	1	0			c.G2897A						PASS	.	C	HIS/ARG	0,4406		0,0,2203	95	61	72		2897	5.2	1	7	dbSNP_134	72	10,8590	8.4+/-32.0	0,10,4290	yes	missense	EPHA1	NM_005232.4	29	0,10,6493	TT,TC,CC		0.1163,0.0,0.0769	probably-damaging	966/977	143088584	10,12996	2203	4300	6503	SO:0001583	missense	2041	exon18			AGAATGCGCTTCT	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.2897G>A	7.37:g.143088584C>T	ENSP00000275815:p.Arg966His	121	0	0		104	52	0.5	NM_005232	A1L3V3|B5A966|B5A967|Q15405	Missense_Mutation	SNP	ENST00000275815.3	37	CCDS5884.1	3	0.0013736263736263737	1	0.0020325203252032522	0	0.0	0	0.0	2	0.002638522427440633	C	25.0	4.594043	0.86953	0.0	0.001163	ENSG00000146904	ENST00000275815	T	0.55052	0.54	5.24	5.24	0.73138	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 1 (1);	0.000000	0.56097	D	0.000029	T	0.77274	0.4106	M	0.92555	3.32	0.53005	D	0.999961	D	0.89917	1.0	D	0.79784	0.993	T	0.82014	-0.0667	10	0.87932	D	0	.	12.3566	0.55178	0.0:0.9237:0.0:0.0763	.	966	P21709	EPHA1_HUMAN	H	966	ENSP00000275815:R966H	ENSP00000275815:R966H	R	-	2	0	EPHA1	142798706	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.577000	0.46042	2.724000	0.93272	0.561000	0.74099	CGC	C|0.999;T|0.001	0.001	strong		0.622	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1			T	143088584	C	T	143088584	3	4	29	1	0	0	0	0	1	0	0	0	5167	768	27	1	37	1	EPHA1	7	143088584	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	526798	143088584	16050079	407	12648											
SSPO	23145	hgsc.bcm.edu	37	chr7	149492640	149492640	+	RNA	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccccaggcatcctagtgccGgagactggctcctccaacgc	7	7	10	17	2	0	1	0	0	0	1	4	2	4	1	6	3	2	2	6	3	2	1	rs372238122		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:149492640G>A	ENST00000378016.2	+	0	6420							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)			TCCTAGTGCCGGAGACTGGCT	0.617																																					p.P2140P		Atlas-SNP	.											.	.	.	.	0			c.G6420A						PASS	.	G		0,4254		0,0,2127	57	65	63		6424	2.8	0	7		63	1,8491		0,1,4245	no	coding-notMod3	SSPO	NM_198455.2		0,1,6372	AA,AG,GG		0.0118,0.0,0.0078			149492640	1,12745	2127	4246	6373			23145	exon43			AGTGCCGGAGACT	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.149492640G>A		115	0	0		109	58	0.53211	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				.	.	weak		0.617	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				A	149492640	G	A	149492640	1	1	29	0	1	0	0	0	0	0	0	0	15204	1103	39	1		1	SSPO	7	149492640	RNA	SNP	G	TCGA-GR-7351-01A-11D-2210-10	6404056	149492640	9646023	408	12649											
MLL3	58508	hgsc.bcm.edu	37	chr7	151962183	151962183	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctgcacgttttaatggagtaAccgctatatccaggcacatt	11	12	8	10	2	0	0	0	0	0	0	1	1	1	1	2	2	2	5	2	2	4	6			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr7:151962183A>C	ENST00000262189.6	-	8	1342	c.1124T>G	c.(1123-1125)gTt>gGt	p.V375G	KMT2C_ENST00000355193.2_Missense_Mutation_p.V375G	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	375					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)										TAATGGAGTAACCGCTATATC	0.448																																					p.V375G		Atlas-SNP	.											MLL3_ENST00000355193,right_upper_lobe,carcinoma,0,2	MLL3	1564	2	0			c.T1124G						scavenged	.						497	442	460					7																	151962183		2203	4300	6503	SO:0001583	missense	58508	exon8			GGAGTAACCGCTA	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.1124T>G	7.37:g.151962183A>C	ENSP00000262189:p.Val375Gly	245	0	0		288	20	0.0694444	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	A	9.892	1.204596	0.22205	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.98958	-5.27;-5.27	4.65	4.65	0.58169	Zinc finger, PHD-finger (1);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, PHD-type (1);Protein kinase C-like, phorbol ester/diacylglycerol binding (1);Zinc finger, FYVE/PHD-type (1);	0.203382	0.23918	U	0.043277	D	0.98349	0.9452	M	0.76170	2.325	0.80722	D	1	D	0.64830	0.994	P	0.52109	0.69	D	0.98139	1.0435	10	0.40728	T	0.16	.	14.395	0.67005	1.0:0.0:0.0:0.0	.	375	Q8NEZ4	MLL3_HUMAN	G	375	ENSP00000262189:V375G;ENSP00000347325:V375G	ENSP00000262189:V375G	V	-	2	0	MLL3	151593116	1.000000	0.71417	0.992000	0.48379	0.034000	0.12701	4.542000	0.60677	1.843000	0.53566	0.455000	0.32223	GTT	.	.	none		0.448	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			C	151962183	A	C	151962183	3	2	29	1	0	0	0	0	1	0	0	0	9631	43	2	5	13819	5	MLL3	7	151962183	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	2469543	151962183	7176480	409	12650											
CLN8	2055	hgsc.bcm.edu	37	chr8	1719450	1719450	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgcagtctttggtgttcagaGcacagccgcaggcctgtggg	6	10	15	10	1	2	1	1	0	1	1	2	1	2	1	2	3	3	4	2	3	0	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:1719450G>C	ENST00000331222.4	+	2	477	c.230G>C	c.(229-231)aGc>aCc	p.S77T		NM_018941.3	NP_061764.2	Q9UBY8	CLN8_HUMAN	ceroid-lipofuscinosis, neuronal 8 (epilepsy, progressive with mental retardation)	77	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				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)		GGTGTTCAGAGCACAGCCGCA	0.612																																					p.S77T	Pancreas(155;338 1942 6138 10888 50612)	Atlas-SNP	.											.	CLN8	64	.	0			c.G230C						PASS	.						73	68	70					8																	1719450		2203	4300	6503	SO:0001583	missense	2055	exon2			TTCAGAGCACAGC	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.230G>C	8.37:g.1719450G>C	ENSP00000328182:p.Ser77Thr	140	0	0		160	18	0.1125	NM_018941	Q86U71|Q96I95	Missense_Mutation	SNP	ENST00000331222.4	37	CCDS5956.1	.	.	.	.	.	.	.	.	.	.	G	15.79	2.936506	0.52972	.	.	ENSG00000182372	ENST00000331222	D	0.87491	-2.26	5.06	5.06	0.68205	TRAM/LAG1/CLN8 homology domain (3);	0.131081	0.49305	U	0.000147	D	0.88183	0.6368	L	0.54323	1.7	0.54753	D	0.999987	P	0.51537	0.946	P	0.53146	0.719	D	0.84829	0.0801	10	0.07482	T	0.82	-1.7549	18.4221	0.90594	0.0:0.0:1.0:0.0	.	77	Q9UBY8	CLN8_HUMAN	T	77	ENSP00000328182:S77T	ENSP00000328182:S77T	S	+	2	0	CLN8	1706857	1.000000	0.71417	0.992000	0.48379	0.140000	0.21249	8.757000	0.91657	2.329000	0.79093	0.455000	0.32223	AGC	.	.	none		0.612	CLN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206715.2	NM_018941		C	1719450	G	C	1719450	3	2	29	1	0	0	0	0	1	0	0	0	3548	971	34	4	232	4	CLN8	8	1719450	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10		1719450	144644572	410	12651											
CSMD1	64478	hgsc.bcm.edu	37	chr8	3019696	3019696	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatacctgcagggtgtacccGggctcgcactggaaggagag	9	6	16	10	2	0	1	0	0	0	1	1	4	0	2	2	4	3	4	2	4	3	2	rs145598896	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:3019696G>A	ENST00000520002.1	-	39	6387	c.5832C>T	c.(5830-5832)ccC>ccT	p.P1944P	CSMD1_ENST00000537824.1_Silent_p.P1943P|CSMD1_ENST00000400186.3_Silent_p.P1944P|CSMD1_ENST00000542608.1_Silent_p.P1943P|CSMD1_ENST00000539096.1_Silent_p.P1943P|CSMD1_ENST00000602557.1_Silent_p.P1944P|CSMD1_ENST00000523387.1_5'UTR|CSMD1_ENST00000602723.1_Silent_p.P1944P			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1944	Sushi 11. {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)		GGGTGTACCCGGGCTCGCACT	0.517													G|||	11	0.00219649	0.0053	0.0	5008	,	,		16675	0.002		0.002	False		,,,				2504	0.0				p.P1943P		Atlas-SNP	.											.	CSMD1	1469	.	0			c.C5829T						PASS	.	G		8,3932		0,8,1962	71	75	73		5829	-10.8	0	8	dbSNP_134	73	12,8308		0,12,4148	no	coding-synonymous	CSMD1	NM_033225.5		0,20,6110	AA,AG,GG		0.1442,0.203,0.1631		1943/3565	3019696	20,12240	1970	4160	6130	SO:0001819	synonymous_variant	64478	exon38			GTACCCGGGCTCG			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.5832C>T	8.37:g.3019696G>A		40	0	0		45	18	0.4	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37		2	9.157509157509158E-4	0	0.0	0	0.0	1	0.0017482517482517483	1	0.0013192612137203166	G	0.119	-1.128140	0.01770	0.00203	0.001442	ENSG00000183117	ENST00000335551	.	.	.	5.38	-10.8	0.00216	.	.	.	.	.	T	0.33731	0.0873	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58036	-0.7707	4	.	.	.	.	2.5509	0.04749	0.3963:0.2923:0.0797:0.2317	.	.	.	.	W	1424	.	.	R	-	1	2	CSMD1	3007103	0.000000	0.05858	0.005000	0.12908	0.154000	0.21943	-4.988000	0.00162	-5.089000	0.00022	-2.954000	0.00084	CGG	G|0.999;A|0.001	0.001	strong		0.517	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	3019696	G	A	3019696	2	1	29	1	0	0	0	0	0	0	0	1	3946	1103	39	1		1	CSMD1	8	3019696	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1300246	3019696	143344326	411	12652											
CSMD1	64478	hgsc.bcm.edu	37	chr8	3253868	3253868	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aactggctggcccatctctgAcctccaaggtgtcataattg	9	11	9	12	0	2	1	1	1	1	0	4	1	3	1	3	3	1	1	3	3	3	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:3253868A>T	ENST00000520002.1	-	18	2999	c.2444T>A	c.(2443-2445)gTc>gAc	p.V815D	CSMD1_ENST00000537824.1_Missense_Mutation_p.V814D|CSMD1_ENST00000400186.3_Missense_Mutation_p.V815D|CSMD1_ENST00000542608.1_Missense_Mutation_p.V814D|CSMD1_ENST00000539096.1_Missense_Mutation_p.V814D|CSMD1_ENST00000602557.1_Missense_Mutation_p.V815D|CSMD1_ENST00000602723.1_Missense_Mutation_p.V815D			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	815	CUB 5. {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)		CCCATCTCTGACCTCCAAGGT	0.527																																					p.V814D		Atlas-SNP	.											.	CSMD1	1469	.	0			c.T2441A						PASS	.						49	63	58					8																	3253868		2163	4270	6433	SO:0001583	missense	64478	exon17			TCTCTGACCTCCA			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.2444T>A	8.37:g.3253868A>T	ENSP00000430733:p.Val815Asp	61	0	0		97	28	0.28866	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.	.	.	.	.	.	.	.	.	.	A	15.68	2.905140	0.52333	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29	5.3	5.3	0.74995	CUB (5);	0.073354	0.53938	D	0.000046	D	0.88142	0.6357	H	0.97611	4.04	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.91635	0.999;0.982	D	0.92260	0.5816	10	0.72032	D	0.01	.	15.2632	0.73640	1.0:0.0:0.0:0.0	.	815;815	E5RIG2;Q96PZ7	.;CSMD1_HUMAN	D	815;815;677;814;814;814	ENSP00000383047:V815D;ENSP00000430733:V815D;ENSP00000441462:V814D;ENSP00000446243:V814D;ENSP00000441675:V814D	ENSP00000320445:V677D	V	-	2	0	CSMD1	3241275	1.000000	0.71417	0.116000	0.21606	0.009000	0.06853	9.112000	0.94314	1.981000	0.57761	0.533000	0.62120	GTC	.	.	none		0.527	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		T	3253868	A	T	3253868	3	4	29	1	0	0	0	0	1	0	0	0	3946	275	10	5	8469	5	CSMD1	8	3253868	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	234172	3253868	143110154	412	12653											
MTUS1	57509	hgsc.bcm.edu	37	chr8	17532715	17532715	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctagctctccccggaggttaAcaagttcttgagatagggtt	9	12	11	9	1	2	1	0	1	2	1	3	3	2	2	2	3	2	4	2	3	4	6			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:17532715A>C	ENST00000262102.6	-	8	3109	c.2885T>G	c.(2884-2886)gTt>gGt	p.V962G	MTUS1_ENST00000519263.1_Missense_Mutation_p.V908G|MTUS1_ENST00000518713.1_5'UTR|MTUS1_ENST00000297488.6_Missense_Mutation_p.V128G|MTUS1_ENST00000544260.1_Missense_Mutation_p.V107G|MTUS1_ENST00000381869.3_Missense_Mutation_p.V908G|MTUS1_ENST00000381861.3_Missense_Mutation_p.V209G|MTUS1_ENST00000400046.1_Missense_Mutation_p.V34G	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	962					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)		CCGGAGGTTAACAAGTTCTTG	0.443																																					p.V962G		Atlas-SNP	.											.	MTUS1	144	.	0			c.T2885G						PASS	.						205	188	194					8																	17532715		1932	4128	6060	SO:0001583	missense	57509	exon8			AGGTTAACAAGTT	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.2885T>G	8.37:g.17532715A>C	ENSP00000262102:p.Val962Gly	92	0	0		128	27	0.210938	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	.	.	.	.	.	.	.	.	.	.	A	15.93	2.976972	0.53720	.	.	ENSG00000129422	ENST00000381869;ENST00000544260;ENST00000400046;ENST00000297488;ENST00000381861;ENST00000262102;ENST00000519263	T;T;T;T;T;T;T	0.36699	1.24;1.24;2.14;1.24;1.24;1.24;1.24	4.61	4.61	0.57282	.	0.674999	0.14765	N	0.299724	T	0.37517	0.1006	L	0.35487	1.065	0.58432	D	0.999997	B;B;B;B	0.29646	0.043;0.253;0.141;0.231	B;B;B;B	0.41202	0.191;0.35;0.191;0.1	T	0.18053	-1.0349	10	0.32370	T	0.25	-7.869	14.5445	0.68017	1.0:0.0:0.0:0.0	.	908;962;209;128	Q9ULD2-2;Q9ULD2;Q9ULD2-6;Q9ULD2-3	.;MTUS1_HUMAN;.;.	G	908;107;34;128;209;962;908	ENSP00000371293:V908G;ENSP00000445738:V107G;ENSP00000382921:V34G;ENSP00000297488:V128G;ENSP00000371285:V209G;ENSP00000262102:V962G;ENSP00000430167:V908G	ENSP00000262102:V962G	V	-	2	0	MTUS1	17576995	0.133000	0.22466	0.969000	0.41365	0.996000	0.88848	3.829000	0.55760	2.083000	0.62718	0.378000	0.23410	GTT	.	.	none		0.443	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031		C	17532715	A	C	17532715	3	2	29	1	0	0	0	0	1	0	0	0	9974	43	2	5	959	5	MTUS1	8	17532715	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	14278847	17532715	128831307	413	12654											
FGL1	2267	hgsc.bcm.edu	37	chr8	17731876	17731876	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcataattagcacacctgttAaagttttcactgccatcaga	13	13	5	10	0	3	1	3	0	0	1	3	1	3	1	2	0	2	3	2	0	4	5	rs34871936	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:17731876A>G	ENST00000398056.2	-	6	1214	c.399T>C	c.(397-399)ttT>ttC	p.F133F	FGL1_ENST00000381841.2_Silent_p.F133F|FGL1_ENST00000427924.1_Silent_p.F133F|FGL1_ENST00000398054.1_Silent_p.F133F|FGL1_ENST00000522444.1_Silent_p.F133F|FGL1_ENST00000518650.1_Silent_p.F133F|FGL1_ENST00000381840.2_Silent_p.F133F			Q08830	FGL1_HUMAN	fibrinogen-like 1	133	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				adipose tissue development (GO:0060612)|cholesterol metabolic process (GO:0008203)|regulation of glucose metabolic process (GO:0010906)|response to stilbenoid (GO:0035634)	extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)	13				Colorectal(111;0.0573)|COAD - Colon adenocarcinoma(73;0.215)		CACACCTGTTAAAGTTTTCAC	0.368													A|||	25	0.00499201	0.0015	0.0072	5008	,	,		17596	0.0		0.0119	False		,,,				2504	0.0061				p.F133F		Atlas-SNP	.											.	FGL1	31	.	0			c.T399C						PASS	.	A	,,,	13,4393	20.2+/-43.8	0,13,2190	116	108	111		399,399,399,399	1.4	1	8	dbSNP_126	111	117,8483	63.1+/-125.2	2,113,4185	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FGL1	NM_004467.3,NM_147203.2,NM_201552.1,NM_201553.1	,,,	2,126,6375	GG,GA,AA		1.3605,0.2951,0.9995	,,,	133/313,133/313,133/313,133/313	17731876	130,12876	2203	4300	6503	SO:0001819	synonymous_variant	2267	exon5			CCTGTTAAAGTTT	D14446	CCDS6004.1	8p22	2013-02-06			ENSG00000104760	ENSG00000104760		"Fibrinogen C domain containing"	3695	protein-coding gene	gene with protein product		605776				8390249	Standard	NM_004467		Approved	HFREP-1	uc003wyb.3	Q08830	OTTHUMG00000096989	ENST00000398056.2:c.399T>C	8.37:g.17731876A>G		115	0	0		102	45	0.441176	NM_201553	A6NKU4|Q4PJH9|Q53YF1|Q8NG32|Q96KW6|Q96QM6	Silent	SNP	ENST00000398056.2	37	CCDS6004.1																																																																																			A|0.990;G|0.010	0.010	strong		0.368	FGL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375254.1	NM_004467		G	17731876	A	G	17731876	2	3	29	1	0	0	0	0	0	0	0	1	5880	359	13	3		3	FGL1	8	17731876	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	199161	17731876	128632146	414	12655											
NEFM	4741	hgsc.bcm.edu	37	chr8	24774646	24774646	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	actgggccactgtatacacaCcgacccccaatcacaatatc	13	7	5	16	1	1	0	1	0	0	0	2	1	1	0	4	1	1	1	4	1	5	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:24774646C>G	ENST00000221166.5	+	3	2060	c.1278C>G	c.(1276-1278)caC>caG	p.H426Q	GS1-72M22.1_ENST00000607058.1_RNA|NEFM_ENST00000437366.2_Missense_Mutation_p.H426Q|NEFM_ENST00000521540.1_3'UTR|NEFM_ENST00000518131.1_Missense_Mutation_p.H426Q|NEFM_ENST00000433454.2_Missense_Mutation_p.H50Q			P07197	NFM_HUMAN	neurofilament, medium polypeptide	426	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)		TGTATACACACCGACCCCCAA	0.443																																					p.H426Q		Atlas-SNP	.											.	NEFM	115	.	0			c.C1278G						PASS	.						65	64	65					8																	24774646		2203	4300	6503	SO:0001583	missense	4741	exon3			TACACACCGACCC	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.1278C>G	8.37:g.24774646C>G	ENSP00000221166:p.His426Gln	148	0	0		140	79	0.564286	NM_005382	B4DGN2|E9PBF7|Q4QRK6	Missense_Mutation	SNP	ENST00000221166.5	37	CCDS6046.1	.	.	.	.	.	.	.	.	.	.	C	14.52	2.559906	0.45590	.	.	ENSG00000104722	ENST00000221166;ENST00000518131;ENST00000437366;ENST00000433454	D;D;D;D	0.93659	-1.61;-1.62;-1.64;-3.26	4.92	4.92	0.64577	.	0.128053	0.34531	N	0.003893	D	0.92932	0.7751	L	0.56124	1.755	0.58432	D	0.99999	D;P	0.54047	0.964;0.947	P;B	0.46275	0.51;0.355	D	0.93719	0.7031	10	0.62326	D	0.03	.	18.4956	0.90864	0.0:1.0:0.0:0.0	.	426;426	E7EMV2;P07197	.;NFM_HUMAN	Q	426;426;426;50	ENSP00000221166:H426Q;ENSP00000427872:H426Q;ENSP00000410137:H426Q;ENSP00000412295:H50Q	ENSP00000221166:H426Q	H	+	3	2	NEFM	24830551	1.000000	0.71417	1.000000	0.80357	0.757000	0.42996	2.443000	0.44881	2.421000	0.82119	0.563000	0.77884	CAC	.	.	none		0.443	NEFM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254954.2	NM_005382		G	24774646	C	G	24774646	3	3	29	1	0	0	0	0	1	0	0	0	10325	506	18	4	1288	4	NEFM	8	24774646	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	7042770	24774646	121589376	415	12656											
ELP3	55140	hgsc.bcm.edu	37	chr8	27957438	27957438	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctcctcagtatcgcaaggtCttgatgcccaagttaaaggc	10	10	9	12	1	2	1	1	1	1	0	4	1	3	1	3	2	1	3	3	2	5	3	rs200001470	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:27957438C>T	ENST00000256398.8	+	3	590	c.213C>T	c.(211-213)gtC>gtT	p.V71V	ELP3_ENST00000380353.4_Intron|ELP3_ENST00000524103.1_5'UTR|ELP3_ENST00000521015.1_Silent_p.V57V|ELP3_ENST00000542181.1_Intron|ELP3_ENST00000523760.1_3'UTR|ELP3_ENST00000537665.1_5'UTR	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	71					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)		ATCGCAAGGTCTTGATGCCCA	0.522													C|||	2	0.000399361	0.0015	0.0	5008	,	,		20896	0.0		0.0	False		,,,				2504	0.0				p.V71V		Atlas-SNP	.											.	ELP3	36	.	0			c.C213T						PASS	.	C		0,4406		0,0,2203	144	119	127		213	3.5	1	8		127	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ELP3	NM_018091.5		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		71/548	27957438	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	55140	exon3			CAAGGTCTTGATG		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.213C>T	8.37:g.27957438C>T		60	0	0		65	27	0.415385	NM_018091	B4DE19|B4DIG1|E2QRI5|Q53G84|Q6AWB0|Q9BVF7|Q9NVZ1	Silent	SNP	ENST00000256398.8	37	CCDS6065.1																																																																																			C|1.000;T|0.000	0.000	strong		0.522	ELP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219963.2	NM_018091		T	27957438	C	T	27957438	2	4	29	1	0	0	0	0	0	0	0	1	5083	900	32	2		2	ELP3	8	27957438	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	3182792	27957438	118406584	416	12657											
HMBOX1	79618	hgsc.bcm.edu	37	chr8	28827928	28827928	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attatctacatccaatggaaAgatgtcaccaactcgctacc	14	10	5	12	1	2	1	1	0	1	1	4	2	3	2	3	1	3	1	3	1	6	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:28827928A>T	ENST00000397358.3	+	4	1096	c.392A>T	c.(391-393)aAg>aTg	p.K131M	HMBOX1_ENST00000355231.5_Missense_Mutation_p.K131M|HMBOX1_ENST00000524238.1_Missense_Mutation_p.K131M|HMBOX1_ENST00000403668.2_Missense_Mutation_p.K131M|HMBOX1_ENST00000519047.1_Missense_Mutation_p.K131M|HMBOX1_ENST00000523613.1_Missense_Mutation_p.K131M|HMBOX1_ENST00000287701.10_Missense_Mutation_p.K131M|HMBOX1_ENST00000444075.1_Missense_Mutation_p.K131M|HMBOX1_ENST00000558662.1_Missense_Mutation_p.K131M	NM_024567.3	NP_078843.2	Q6NT76	HMBX1_HUMAN	homeobox containing 1	131					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)		TCCAATGGAAAGATGTCACCA	0.448																																					p.K131M		Atlas-SNP	.											.	HMBOX1	34	.	0			c.A392T						PASS	.						78	76	77					8																	28827928		2203	4300	6503	SO:0001583	missense	79618	exon4			ATGGAAAGATGTC	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.392A>T	8.37:g.28827928A>T	ENSP00000380516:p.Lys131Met	52	0	0		87	4	0.045977	NM_024567	A4K385|A8K3R8|B4DHY5|D3DSU0|Q3Y6P1|Q96GS5|Q9H701	Missense_Mutation	SNP	ENST00000397358.3	37	CCDS6071.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.453485	0.84209	.	.	ENSG00000147421	ENST00000287701;ENST00000444075;ENST00000403668;ENST00000519047;ENST00000397358;ENST00000524238;ENST00000517340;ENST00000355231	D;D;D;D;D;D	0.98474	-4.95;-4.95;-4.95;-4.95;-4.95;-4.95	5.88	5.88	0.94601	Hepatocyte nuclear factor 1, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98435	0.9479	L	0.51422	1.61	0.58432	D	0.999999	D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.87578	0.998;0.997;0.997;0.997;0.998;0.998	D	0.99764	1.1022	10	0.54805	T	0.06	-12.0241	16.2965	0.82776	1.0:0.0:0.0:0.0	.	131;131;131;131;131;131	Q6NT76-5;D3DSU2;Q6NT76-2;Q6NT76-3;Q6NT76;E5RGZ2	.;.;.;.;HMBX1_HUMAN;.	M	131	ENSP00000287701:K131M;ENSP00000401769:K131M;ENSP00000384261:K131M;ENSP00000430059:K131M;ENSP00000380516:K131M;ENSP00000430110:K131M	ENSP00000287701:K131M	K	+	2	0	HMBOX1	28883847	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.818000	0.91991	2.243000	0.73865	0.528000	0.53228	AAG	.	.	none		0.448	HMBOX1-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255267.4	NM_024567		T	28827928	A	T	28827928	3	4	29	1	0	0	0	0	1	0	0	0	7227	72	3	5	398	5	HMBOX1	8	28827928	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	870490	28827928	117536094	417	12658											
KIF13B	23303	hgsc.bcm.edu	37	chr8	29033628	29033628	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtcacgatatggaacaaatTtattcttgtttttgccagca	12	15	7	7	1	2	0	1	0	1	0	2	2	2	1	1	1	3	2	1	1	4	7			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:29033628T>G	ENST00000524189.1	-	10	940	c.902A>C	c.(901-903)aAa>aCa	p.K301T	KIF13B_ENST00000521515.1_Missense_Mutation_p.K301T	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	301	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)		TGGAACAAATTTATTCTTGTT	0.423																																					p.K301T		Atlas-SNP	.											KIF13B_ENST00000524189,colon,carcinoma,+1,2	KIF13B	192	2	0			c.A902C						scavenged	.						79	74	76					8																	29033628		1895	4111	6006	SO:0001583	missense	23303	exon10			ACAAATTTATTCT	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.902A>C	8.37:g.29033628T>G	ENSP00000427900:p.Lys301Thr	81	0	0		61	3	0.0491803	NM_015254	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Missense_Mutation	SNP	ENST00000524189.1	37	CCDS55217.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.642317	0.87859	.	.	ENSG00000197892	ENST00000524189;ENST00000521515	T;T	0.75589	-0.95;-0.95	5.31	5.31	0.75309	Kinesin, motor domain (3);	0.000000	0.85682	D	0.000000	T	0.79924	0.4530	L	0.37507	1.11	0.80722	D	1	D;D;B	0.89917	0.999;1.0;0.33	D;D;B	0.85130	0.997;0.994;0.257	T	0.77613	-0.2522	10	0.30078	T	0.28	.	15.4324	0.75112	0.0:0.0:0.0:1.0	.	287;301;301	C9JK41;Q9NQT8;F8VPJ2	.;KI13B_HUMAN;.	T	301	ENSP00000427900:K301T;ENSP00000429201:K301T	ENSP00000429201:K301T	K	-	2	0	KIF13B	29089547	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	7.803000	0.85983	2.231000	0.72958	0.460000	0.39030	AAA	.	.	none		0.423	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1			G	29033628	T	G	29033628	3	3	29	1	0	0	0	0	1	0	0	0	8284	1841	64	5	4702	5	KIF13B	8	29033628	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	205700	29033628	117330394	418	12659											
KCNU1	157855	hgsc.bcm.edu	37	chr8	36664917	36664917	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggttcctaagagccttgcGcctgctagaactccctcaaa	11	9	8	13	1	1	2	1	0	0	2	3	2	3	2	4	1	4	2	4	1	5	4	rs180964986		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:36664917G>A	ENST00000399881.3	+	6	642	c.605G>A	c.(604-606)cGc>cAc	p.R202H		NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	202					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)	p.R202H(2)		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)		AGAGCCTTGCGCCTGCTAGAA	0.443													G|||	1	0.000199681	0.0	0.0	5008	,	,		17222	0.001		0.0	False		,,,				2504	0.0				p.R202H		Atlas-SNP	.											KCNU1,NS,carcinoma,0,1	KCNU1	359	1	2	Substitution - Missense(2)	endometrium(2)	c.G605A						PASS	.						145	144	144					8																	36664917		1860	4104	5964	SO:0001583	missense	157855	exon6			CCTTGCGCCTGCT	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.605G>A	8.37:g.36664917G>A	ENSP00000382770:p.Arg202His	100	0	0		73	18	0.246575	NM_001031836		Missense_Mutation	SNP	ENST00000399881.3	37	CCDS55220.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	16.97	3.268650	0.59540	.	.	ENSG00000215262	ENST00000523973;ENST00000399881	D;D	0.99591	-6.24;-6.24	5.22	3.37	0.38596	Ion transport (1);	0.000000	0.34555	U	0.003866	D	0.99333	0.9766	M	0.67625	2.065	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	D	0.99320	1.0906	10	0.87932	D	0	-0.2079	8.4945	0.33119	0.0852:0.153:0.7618:0.0	.	202	A8MYU2	KCNU1_HUMAN	H	202	ENSP00000429951:R202H;ENSP00000382770:R202H	ENSP00000382770:R202H	R	+	2	0	KCNU1	36784075	0.998000	0.40836	0.285000	0.24819	0.224000	0.24922	4.805000	0.62561	1.174000	0.42811	0.650000	0.86243	CGC	G|1.000;A|0.000	0.000	strong		0.443	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836		A	36664917	G	A	36664917	3	1	29	1	0	0	0	0	1	0	0	0	8102	1087	38	1	627	1	KCNU1	8	36664917	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	7631289	36664917	109699105	419	12660											
SGK196	84197	hgsc.bcm.edu	37	chr8	42977591	42977591	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtgcgactccaacgacctGccgaagacactgtcccagta	11	7	9	14	3	0	1	0	0	0	1	2	4	2	1	4	0	3	1	4	0	3	1	rs34040483	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:42977591G>C	ENST00000331373.5	+	5	879	c.624G>C	c.(622-624)ctG>ctC	p.L208L		NM_001277971.1|NM_032237.3	NP_001264900.1|NP_115613.1	Q9H5K3	SG196_HUMAN	protein-O-mannose kinase	208	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				brain development (GO:0007420)|carbohydrate phosphorylation (GO:0046835)|learning or memory (GO:0007611)|neuromuscular process (GO:0050905)|neuron migration (GO:0001764)|protein O-linked glycosylation (GO:0006493)|sensory perception of pain (GO:0019233)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|carbohydrate kinase activity (GO:0019200)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)|protein kinase activity (GO:0004672)										CCAACGACCTGCCGAAGACAC	0.557													G|||	23	0.00459265	0.0008	0.013	5008	,	,		22021	0.0		0.0129	False		,,,				2504	0.0				p.L208L		Atlas-SNP	.											.	.	.	.	0			c.G624C						PASS	.	G		8,4398	14.3+/-33.2	0,8,2195	66	52	57		624	3.3	1	8	dbSNP_126	57	110,8490	58.3+/-119.8	1,108,4191	no	coding-synonymous	SGK196	NM_032237.3		1,116,6386	CC,CG,GG		1.2791,0.1816,0.9073		208/351	42977591	118,12888	2203	4300	6503	SO:0001819	synonymous_variant	0	exon5			CGACCTGCCGAAG		CCDS6141.1	8p11.21	2013-08-22			ENSG00000185900	ENSG00000185900			26267	protein-coding gene	gene with protein product		615247				16879967, 23519211	Standard	NM_001277971		Approved	FLJ23356, SgK196		Q9H5K3	OTTHUMG00000164100	ENST00000331373.5:c.624G>C	8.37:g.42977591G>C		90	0	0		85	38	0.447059	NM_032237		Silent	SNP	ENST00000331373.5	37	CCDS6141.1																																																																																			G|0.992;C|0.008	0.008	strong		0.557	POMK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377291.2	NM_032237		C	42977591	G	C	42977591	2	2	29	1	0	0	0	0	0	0	0	1	14223	1306	46	4		4	SGK196	8	42977591	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	6312674	42977591	103386431	420	12661											
HGSNAT	138050	hgsc.bcm.edu	37	chr8	43053062	43053062	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	acccagttgtggatgtgaagGggctgtggacaggaacccca	10	7	15	9	0	0	1	0	1	0	0	0	4	0	4	3	5	1	2	3	5	2	1	rs148632988	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:43053062G>C	ENST00000458501.2	+	17	1777	c.1777G>C	c.(1777-1779)Ggg>Cgg	p.G593R	HGSNAT_ENST00000521576.1_Missense_Mutation_p.G282R|HGSNAT_ENST00000379644.4_Missense_Mutation_p.G565R|HGSNAT_ENST00000297798.7_Missense_Mutation_p.G297R			Q68CP4	HGNAT_HUMAN	heparan-alpha-glucosaminide N-acetyltransferase	593					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)			GGATGTGAAGGGGCTGTGGAC	0.557													G|||	21	0.00419329	0.0008	0.0029	5008	,	,		17354	0.0		0.0089	False		,,,				2504	0.0092				p.G565R		Atlas-SNP	.											.	HGSNAT	85	.	0			c.G1693C						PASS	.	G	ARG/GLY	7,3871		0,7,1932	125	121	122		1693	5.1	1	8	dbSNP_134	122	87,8207		1,85,4061	yes	missense	HGSNAT	NM_152419.2	125	1,92,5993	CC,CG,GG		1.049,0.1805,0.7723	benign	565/636	43053062	94,12078	1939	4147	6086	SO:0001583	missense	138050	exon17			GTGAAGGGGCTGT		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.1777G>C	8.37:g.43053062G>C	ENSP00000389524:p.Gly593Arg	209	0	0		236	123	0.521186	NM_152419	B4E2V0	Missense_Mutation	SNP	ENST00000458501.2	37		11	0.005036630036630037	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	G	9.728	1.161382	0.21538	0.001805	0.01049	ENSG00000165102	ENST00000458501;ENST00000379644;ENST00000521576;ENST00000297798	D;D;D;D	0.86694	-2.16;-2.16;-2.16;-2.16	6.07	5.1	0.69264	.	0.372260	0.31438	N	0.007646	T	0.66015	0.2747	N	0.12443	0.215	0.45777	D	0.998663	B	0.12013	0.005	B	0.06405	0.002	T	0.64711	-0.6343	10	0.38643	T	0.18	-14.3505	5.7907	0.18359	0.2131:0.0:0.7869:0.0	.	593	Q68CP4	HGNAT_HUMAN	R	593;565;282;297	ENSP00000389524:G593R;ENSP00000368965:G565R;ENSP00000429029:G282R;ENSP00000297798:G297R	ENSP00000297798:G297R	G	+	1	0	HGSNAT	43172219	0.552000	0.26505	0.974000	0.42286	0.849000	0.48306	2.331000	0.43894	2.885000	0.99019	0.655000	0.94253	GGG	G|0.995;C|0.005	0.005	strong		0.557	HGSNAT-202	KNOWN	basic	protein_coding	protein_coding		XM_372038		C	43053062	G	C	43053062	3	2	29	1	0	0	0	0	1	0	0	0	7097	1232	43	4	1759	4	HGSNAT	8	43053062	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	75471	43053062	103310960	421	12662											
KIAA0146	23514	hgsc.bcm.edu	37	chr8	48612997	48612997	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcagtttgattgacacccTgtggcccccagcgatacctc	7	12	8	14	1	1	2	1	2	0	0	2	3	1	2	4	1	2	1	4	1	1	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:48612997T>A	ENST00000297423.4	+	12	2102	c.1718T>A	c.(1717-1719)cTg>cAg	p.L573Q	SPIDR_ENST00000517693.1_Missense_Mutation_p.L48Q|SPIDR_ENST00000521214.1_3'UTR|SPIDR_ENST00000541342.1_Missense_Mutation_p.L503Q|SPIDR_ENST00000518074.1_Missense_Mutation_p.L513Q	NM_001080394.2|NM_001282916.1	NP_001073863.1|NP_001269845.1	Q14159	SPIDR_HUMAN	scaffolding protein involved in DNA repair	573					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)											ATTGACACCCTGTGGCCCCCA	0.522																																					p.L573Q		Atlas-SNP	.											.	KIAA0146	64	.	0			c.T1718A						PASS	.						185	178	180					8																	48612997		1913	4115	6028	SO:0001583	missense	23514	exon12			ACACCCTGTGGCC	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.1718T>A	8.37:g.48612997T>A	ENSP00000297423:p.Leu573Gln	119	0	0		103	10	0.0970874	NM_001080394	B4DFV2|B4E0Y6|Q96BI5	Missense_Mutation	SNP	ENST00000297423.4	37	CCDS43737.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.90|14.90	2.672941|2.672941	0.47781|0.47781	.|.	.|.	ENSG00000164808|ENSG00000164808	ENST00000519401|ENST00000297423;ENST00000518074;ENST00000541342;ENST00000519141;ENST00000517693;ENST00000519362	.|.	.|.	.|.	5.41|5.41	4.25|4.25	0.50352|0.50352	.|.	.|0.646742	.|0.16164	.|N	.|0.226637	T|T	0.60907|0.60907	0.2305|0.2305	L|L	0.58101|0.58101	1.795|1.795	0.30107|0.30107	N|N	0.806873|0.806873	.|D;D;D;P;D;P;D;P	.|0.67145	.|0.989;0.989;0.996;0.95;0.989;0.95;0.996;0.95	.|D;D;D;P;D;P;D;P	.|0.66351	.|0.912;0.912;0.931;0.776;0.912;0.776;0.943;0.776	T|T	0.60316|0.60316	-0.7287|-0.7287	5|9	.|0.87932	.|D	.|0	.|.	9.5224|9.5224	0.39143|0.39143	0.0:0.0811:0.0:0.9189|0.0:0.0811:0.0:0.9189	.|.	.|63;78;513;503;573;262;48;573	.|B4DZY2;B4DWT8;B4E0Y6;B4DFV2;B4DEV5;B4DFT3;B3KP42;Q14159	.|.;.;.;.;.;.;.;K0146_HUMAN	S|Q	255|573;513;503;78;48;48	.|.	.|ENSP00000297423:L573Q	C|L	+|+	1|2	0|0	KIAA0146|KIAA0146	48775550|48775550	0.964000|0.964000	0.33143|0.33143	0.065000|0.065000	0.19835|0.19835	0.150000|0.150000	0.21749|0.21749	2.139000|2.139000	0.42149|0.42149	0.889000|0.889000	0.36185|0.36185	0.533000|0.533000	0.62120|0.62120	TGT|CTG	.	.	none		0.522	SPIDR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377611.1	NM_001080394		A	48612997	T	A	48612997	3	1	29	1	0	0	0	0	1	0	0	0	8166	1580	55	5	1764	5	KIAA0146	8	48612997	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	5559935	48612997	97751025	422	12663											
RP1	6101	hgsc.bcm.edu	37	chr8	55538741	55538741	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ataaattaaatactactcaaAattccaaggttcaaggactt	18	12	4	7	0	2	0	2	0	0	0	3	1	3	1	1	2	2	1	1	2	10	7			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:55538741A>G	ENST00000220676.1	+	4	2447	c.2299A>G	c.(2299-2301)Aat>Gat	p.N767D		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	767					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)			TACTACTCAAAATTCCAAGGT	0.284																																					p.N767D	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.A2299G						PASS	.						23	27	25					8																	55538741		2155	4271	6426	SO:0001583	missense	6101	exon4			ACTCAAAATTCCA	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.2299A>G	8.37:g.55538741A>G	ENSP00000220676:p.Asn767Asp	53	0	0		44	17	0.386364	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	A	11.03	1.520141	0.27211	.	.	ENSG00000104237	ENST00000220676	T	0.25250	1.81	5.93	5.93	0.95920	.	0.438446	0.21621	N	0.071658	T	0.27900	0.0687	L	0.56769	1.78	0.09310	N	1	B	0.21381	0.055	B	0.20955	0.032	T	0.22173	-1.0224	10	0.72032	D	0.01	.	11.4794	0.50316	0.9282:0.0:0.0717:0.0	.	767	P56715	RP1_HUMAN	D	767	ENSP00000220676:N767D	ENSP00000220676:N767D	N	+	1	0	RP1	55701294	0.638000	0.27225	0.018000	0.16275	0.594000	0.36715	4.922000	0.63404	2.270000	0.75569	0.482000	0.46254	AAT	.	.	none		0.284	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		G	55538741	A	G	55538741	3	3	29	1	0	0	0	0	1	0	0	0	13547	14	1	3	2309	3	RP1	8	55538741	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	6925744	55538741	90825281	423	12664											
MYBL1	4603	hgsc.bcm.edu	37	chr8	67478431	67478431	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgcacctattgtcatgtatTtccaataatggtatcattaa	12	17	5	7	0	2	0	2	0	0	0	3	0	3	0	2	1	1	3	2	1	6	8	rs61729530	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:67478431T>G	ENST00000522677.3	-	15	2408	c.1998A>C	c.(1996-1998)gaA>gaC	p.E666D	MYBL1_ENST00000522419.1_Intron|MYBL1_ENST00000517885.1_Missense_Mutation_p.E324D|MYBL1_ENST00000524176.2_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	666					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)			TGTCATGTATTTCCAATAATG	0.279													T|||	27	0.00539137	0.0015	0.0058	5008	,	,		16344	0.002		0.0139	False		,,,				2504	0.0051				p.E666D		Atlas-SNP	.											.	MYBL1	73	.	0			c.A1998C						PASS	.	T	ASP/GLU,	16,3544		0,16,1764	130	107	114		1998,	4.7	1	8	dbSNP_129	114	118,7958		1,116,3921	yes	missense,intron	MYBL1	NM_001080416.2,NM_001144755.1	45,	1,132,5685	GG,GT,TT		1.4611,0.4494,1.1516	probably-damaging,	666/753,	67478431	134,11502	1780	4038	5818	SO:0001583	missense	4603	exon15			ATGTATTTCCAAT	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.1998A>C	8.37:g.67478431T>G	ENSP00000429633:p.Glu666Asp	102	0	0		123	70	0.569106	NM_001080416	E7EW29|Q495F9	Missense_Mutation	SNP	ENST00000522677.3	37	CCDS47867.1	18	0.008241758241758242	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	12	0.0158311345646438	T	18.91	3.724456	0.68959	0.004494	0.014611	ENSG00000185697	ENST00000522677;ENST00000517885	T;T	0.20069	2.58;2.1	5.87	4.73	0.59995	.	0.049569	0.85682	D	0.000000	T	0.24198	0.0586	M	0.71036	2.16	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.04294	-1.0962	10	0.30078	T	0.28	-19.2094	8.646	0.34005	0.0:0.1422:0.0:0.8578	.	666	P10243	MYBA_HUMAN	D	666;324	ENSP00000429633:E666D;ENSP00000428265:E324D	ENSP00000428265:E324D	E	-	3	2	MYBL1	67640985	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	2.954000	0.49113	2.236000	0.73375	0.528000	0.53228	GAA	T|0.991;G|0.009	0.009	strong		0.279	MYBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379221.3	XM_034274		G	67478431	T	G	67478431	3	3	29	1	0	0	0	0	1	0	0	0	10018	1838	64	5	268	5	MYBL1	8	67478431	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	11939690	67478431	78885591	424	12665											
C8orf45	157777	hgsc.bcm.edu	37	chr8	67786817	67786817	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggacaattgcagactgaaaCgcaagtaagttttagttaca	15	11	9	6	1	0	2	0	1	0	1	0	3	0	3	0	1	3	5	0	1	6	5	rs116671744	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:67786817C>T	ENST00000422365.2	+	4	452	c.281C>T	c.(280-282)aCg>aTg	p.T94M	MCMDC2_ENST00000541540.1_Missense_Mutation_p.T31M|MCMDC2_ENST00000469823.1_3'UTR|MCMDC2_ENST00000313616.5_Missense_Mutation_p.T94M|MCMDC2_ENST00000396592.3_Missense_Mutation_p.T94M|MCMDC2_ENST00000492775.1_Missense_Mutation_p.T94M	NM_173518.4	NP_775789.3	Q4G0Z9	MCMD2_HUMAN	minichromosome maintenance domain containing 2	94				T -> M (in Ref. 1; BAG63905). {ECO:0000305}.	DNA replication (GO:0006260)		ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(2)|kidney(2)|lung(5)	9						CAGACTGAAACGCAAGTAAGT	0.289													C|||	188	0.0375399	0.0469	0.0576	5008	,	,		14741	0.0079		0.0288	False		,,,				2504	0.0501				p.T94M		Atlas-SNP	.											.	MCMDC2	84	.	0			c.C281T						PASS	.	C	MET/THR,MET/THR,MET/THR	170,4234	109.9+/-148.2	1,168,2033	70	63	65		281,281,281	2	1	8	dbSNP_132	65	271,8323	102.3+/-163.5	4,263,4030	yes	missense,missense,missense	C8orf45	NM_001136160.1,NM_001136161.1,NM_173518.4	81,81,81	5,431,6063	TT,TC,CC		3.1534,3.8601,3.3928	probably-damaging,probably-damaging,probably-damaging	94/633,94/591,94/682	67786817	441,12557	2202	4297	6499	SO:0001583	missense	157777	exon4			CTGAAACGCAAGT	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.281C>T	8.37:g.67786817C>T	ENSP00000413632:p.Thr94Met	120	0	0		117	50	0.42735	NM_173518	B4DYZ3|B4DZM4|B4E293|Q6P533|Q7Z3P4	Missense_Mutation	SNP	ENST00000422365.2	37	CCDS6197.2	69	0.03159340659340659	18	0.036585365853658534	18	0.049723756906077346	6	0.01048951048951049	27	0.03562005277044855	C	12.79	2.043193	0.36085	0.038601	0.031534	ENSG00000178460	ENST00000396592;ENST00000422365;ENST00000492775;ENST00000313616;ENST00000541540	T;T;T;T;T	0.32753	1.44;1.44;1.44;1.44;1.44	4.87	2.04	0.26737	.	0.229019	0.45361	D	0.000376	T	0.03739	0.0106	L	0.44542	1.39	0.27205	N	0.960063	B;B;B;B	0.18610	0.029;0.017;0.017;0.029	B;B;B;B	0.13407	0.009;0.004;0.004;0.009	T	0.08207	-1.0733	10	0.41790	T	0.15	-2.164	8.4645	0.32947	0.3907:0.5391:0.0:0.0702	.	31;94;94;94	Q4G0Z9-4;Q4G0Z9;B4DXX4;G3XAN3	.;CH045_HUMAN;.;.	M	94;94;94;94;31	ENSP00000379837:T94M;ENSP00000413632:T94M;ENSP00000428037:T94M;ENSP00000317234:T94M;ENSP00000445629:T31M	ENSP00000317234:T94M	T	+	2	0	C8orf45	67949371	0.790000	0.28787	0.965000	0.40720	0.533000	0.34776	0.902000	0.28459	0.194000	0.20326	-0.142000	0.14014	ACG	C|0.970;T|0.030	0.030	strong		0.289	MCMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347350.1	NM_173518		T	67786817	C	T	67786817	3	4	29	1	0	0	0	0	1	0	0	0	2432	536	19	1	291	1	C8orf45	8	67786817	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	308386	67786817	78577205	425	12666											
C8orf45	157777	hgsc.bcm.edu	37	chr8	67813482	67813482	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttgaatgtagaattcagcttGgaagcagaaagaatgaccca	16	9	10	6	0	1	5	1	2	0	3	1	6	1	6	1	1	2	3	1	1	6	4	rs139959817	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:67813482G>A	ENST00000422365.2	+	13	1839	c.1668G>A	c.(1666-1668)ttG>ttA	p.L556L	MCMDC2_ENST00000541540.1_Silent_p.L493L|MCMDC2_ENST00000313616.5_Silent_p.L556L|MCMDC2_ENST00000396592.3_Silent_p.L556L	NM_173518.4	NP_775789.3	Q4G0Z9	MCMD2_HUMAN	minichromosome maintenance domain containing 2	556	MCM.				DNA replication (GO:0006260)		ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(2)|kidney(2)|lung(5)	9						AATTCAGCTTGGAAGCAGAAA	0.353													G|||	129	0.0257588	0.0038	0.0576	5008	,	,		17119	0.0079		0.0268	False		,,,				2504	0.0501				p.L556L		Atlas-SNP	.											.	MCMDC2	84	.	0			c.G1668A						PASS	.	G	,,	42,4364	45.3+/-79.5	0,42,2161	79	79	79		1668,1668,1668	4.6	1	8	dbSNP_134	79	268,8332	102.7+/-163.9	5,258,4037	no	coding-synonymous,coding-synonymous,coding-synonymous	C8orf45	NM_001136160.1,NM_001136161.1,NM_173518.4	,,	5,300,6198	AA,AG,GG		3.1163,0.9532,2.3835	,,	556/633,556/591,556/682	67813482	310,12696	2203	4300	6503	SO:0001819	synonymous_variant	157777	exon13			CAGCTTGGAAGCA	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.1668G>A	8.37:g.67813482G>A		180	0	0		171	65	0.380117	NM_173518	B4DYZ3|B4DZM4|B4E293|Q6P533|Q7Z3P4	Silent	SNP	ENST00000422365.2	37	CCDS6197.2																																																																																			G|0.979;A|0.021	0.021	strong		0.353	MCMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347350.1	NM_173518		A	67813482	G	A	67813482	2	1	29	1	0	0	0	0	0	0	0	1	2432	1339	47	2		2	C8orf45	8	67813482	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	26665	67813482	78550540	426	12667											
SLC26A7	115111	hgsc.bcm.edu	37	chr8	92330561	92330561	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttcacaagtcaaatatctcTtgggaatgaaaatgccatat	15	12	6	8	0	3	1	2	1	1	0	4	2	3	2	1	1	1	0	1	1	7	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:92330561T>C	ENST00000276609.3	+	5	834	c.595T>C	c.(595-597)Ttg>Ctg	p.L199L	SLC26A7_ENST00000523719.1_Silent_p.L199L|SLC26A7_ENST00000309536.2_Silent_p.L199L	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)			CAAATATCTCTTGGGAATGAA	0.438																																					p.L199L		Atlas-SNP	.											.	SLC26A7	207	.	0			c.T595C						PASS	.						128	128	128					8																	92330561		2203	4300	6503	SO:0001819	synonymous_variant	115111	exon5			TATCTCTTGGGAA	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.595T>C	8.37:g.92330561T>C		101	0	0		86	10	0.116279	NM_134266		Silent	SNP	ENST00000276609.3	37	CCDS6254.1																																																																																			.	.	none		0.438	SLC26A7-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377011.1			C	92330561	T	C	92330561	2	2	29	1	0	0	0	0	0	0	0	1	14537	1606	56	3		3	SLC26A7	8	92330561	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	24517079	92330561	54033461	427	12668											
GRHL2	79977	hgsc.bcm.edu	37	chr8	102570830	102570830	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atcccggtgtcgggaatcacGgtggtgaaagctgaagattt	10	10	14	7	3	1	3	1	2	0	1	3	4	2	4	1	4	1	1	1	4	3	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:102570830G>A	ENST00000251808.3	+	4	806	c.468G>A	c.(466-468)acG>acA	p.T156T	GRHL2_ENST00000395927.1_Silent_p.T140T	NM_024915.3	NP_079191.2	Q6ISB3	GRHL2_HUMAN	grainyhead-like 2 (Drosophila)	156					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)			CGGGAATCACGGTGGTGAAAG	0.522																																					p.T156T		Atlas-SNP	.											GRHL2,right_lower_lobe,carcinoma,0,1	GRHL2	68	1	0			c.G468A						PASS	.						107	100	103					8																	102570830		2203	4300	6503	SO:0001819	synonymous_variant	79977	exon4			AATCACGGTGGTG	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.468G>A	8.37:g.102570830G>A		101	0	0		119	33	0.277311	NM_024915	A1L303|Q6NT03|Q9H8B8	Silent	SNP	ENST00000251808.3	37	CCDS34931.1																																																																																			.	.	none		0.522	GRHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313882.1	NM_024915		A	102570830	G	A	102570830	2	1	29	1	0	0	0	0	0	0	0	1	6773	1103	39	1		1	GRHL2	8	102570830	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	10240269	102570830	43793192	428	12669											
ENPP2	5168	hgsc.bcm.edu	37	chr8	120569823	120569823	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caggatttctgggtagctgcGgctggtctttcggaagaagt	7	12	15	7	2	2	1	0	0	2	1	3	3	2	3	0	5	2	3	0	5	3	3	rs61738778	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:120569823G>A	ENST00000075322.6	-	25	2588	c.2530C>T	c.(2530-2532)Cgc>Tgc	p.R844C	ENPP2_ENST00000427067.2_Missense_Mutation_p.R865C|ENPP2_ENST00000259486.6_Missense_Mutation_p.R896C|ENPP2_ENST00000522167.1_Missense_Mutation_p.R479C|ENPP2_ENST00000522826.1_Missense_Mutation_p.R869C	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	844	Required for secretion. {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)			GGGTAGCTGCGGCTGGTCTTT	0.463													G|||	5	0.000998403	0.0	0.0	5008	,	,		17365	0.0		0.004	False		,,,				2504	0.001				p.R896C	Melanoma(20;305 879 2501 4818 31020)	Atlas-SNP	.											.	ENPP2	254	.	0			c.C2686T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG	5,4401	9.9+/-24.2	0,5,2198	187	174	179		2530,2605,2686	6	1	8	dbSNP_129	179	56,8544	36.4+/-91.3	0,56,4244	yes	missense,missense,missense	ENPP2	NM_001040092.1,NM_001130863.1,NM_006209.3	180,180,180	0,61,6442	AA,AG,GG		0.6512,0.1135,0.469	probably-damaging,probably-damaging,probably-damaging	844/864,869/889,896/916	120569823	61,12945	2203	4300	6503	SO:0001583	missense	5168	exon26			AGCTGCGGCTGGT	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.2530C>T	8.37:g.120569823G>A	ENSP00000075322:p.Arg844Cys	120	0	0		106	51	0.481132	NM_006209	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Missense_Mutation	SNP	ENST00000075322.6	37	CCDS34936.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	G	22.7	4.328424	0.81690	0.001135	0.006512	ENSG00000136960	ENST00000259486;ENST00000427067;ENST00000522167;ENST00000522826;ENST00000075322	T;T;T;T;T	0.68765	-0.35;-0.35;-0.35;-0.35;-0.35	6.02	6.02	0.97574	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.049096	0.85682	D	0.000000	T	0.74884	0.3775	L	0.54323	1.7	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	0.76071	0.987;0.976;0.939;0.978;0.984	T	0.77373	-0.2612	10	0.62326	D	0.03	.	20.5407	0.99260	0.0:0.0:1.0:0.0	.	382;869;844;896;479	B4DJD3;E9PHP7;Q13822;Q13822-2;E5RIA2	.;.;ENPP2_HUMAN;.;.	C	896;865;479;869;844	ENSP00000259486:R896C;ENSP00000403315:R865C;ENSP00000429476:R479C;ENSP00000428291:R869C;ENSP00000075322:R844C	ENSP00000075322:R844C	R	-	1	0	ENPP2	120639004	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	5.287000	0.65645	2.865000	0.98341	0.655000	0.94253	CGC	G|0.996;A|0.004	0.004	strong		0.463	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1			A	120569823	G	A	120569823	3	1	29	1	0	0	0	0	1	0	0	0	5132	1116	39	1	65	1	ENPP2	8	120569823	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	17998993	120569823	25794199	429	12670											
ENPP2	5168	hgsc.bcm.edu	37	chr8	120569870	120569870	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtgagatgttcaatgtcaCgcaccctagctgtgtgcatc	8	12	11	10	1	2	1	2	1	0	1	3	2	2	1	1	1	2	4	1	1	2	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:120569870C>T	ENST00000075322.6	-	25	2541	c.2483G>A	c.(2482-2484)cGt>cAt	p.R828H	ENPP2_ENST00000427067.2_Missense_Mutation_p.R849H|ENPP2_ENST00000259486.6_Missense_Mutation_p.R880H|ENPP2_ENST00000522167.1_Missense_Mutation_p.R463H|ENPP2_ENST00000522826.1_Missense_Mutation_p.R853H	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	828					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)			TTCAATGTCACGCACCCTAGC	0.458																																					p.R880H	Melanoma(20;305 879 2501 4818 31020)	Atlas-SNP	.											.	ENPP2	254	.	0			c.G2639A						PASS	.						240	213	222					8																	120569870		2203	4300	6503	SO:0001583	missense	5168	exon26			ATGTCACGCACCC	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.2483G>A	8.37:g.120569870C>T	ENSP00000075322:p.Arg828His	108	0	0		106	5	0.0471698	NM_006209	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Missense_Mutation	SNP	ENST00000075322.6	37	CCDS34936.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.737032	0.89482	.	.	ENSG00000136960	ENST00000259486;ENST00000427067;ENST00000522167;ENST00000522826;ENST00000075322	T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51	5.91	5.91	0.95273	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.051359	0.85682	D	0.000000	T	0.60818	0.2298	M	0.78637	2.42	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	1.0;1.0;1.0;0.999;1.0	T	0.62105	-0.6924	10	0.87932	D	0	.	20.3053	0.98627	0.0:1.0:0.0:0.0	.	366;853;828;880;463	B4DJD3;E9PHP7;Q13822;Q13822-2;E5RIA2	.;.;ENPP2_HUMAN;.;.	H	880;849;463;853;828	ENSP00000259486:R880H;ENSP00000403315:R849H;ENSP00000429476:R463H;ENSP00000428291:R853H;ENSP00000075322:R828H	ENSP00000075322:R828H	R	-	2	0	ENPP2	120639051	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.989000	0.70587	2.808000	0.96608	0.655000	0.94253	CGT	.	.	none		0.458	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1			T	120569870	C	T	120569870	3	4	29	1	0	0	0	0	1	0	0	0	5132	536	19	1	112	1	ENPP2	8	120569870	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	47	120569870	25794152	430	12671											
ATAD2	29028	hgsc.bcm.edu	37	chr8	124357253	124357253	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaactatttcccaccacacGtggatatgaggaacatacac	14	8	6	13	1	0	1	0	1	0	0	1	3	1	3	3	2	3	0	3	2	5	4	rs16898247	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:124357253G>A	ENST00000287394.5	-	19	2696	c.2589C>T	c.(2587-2589)caC>caT	p.H863H	RNU6-875P_ENST00000516488.1_RNA|ATAD2_ENST00000521903.1_Silent_p.H181H	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	863					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)			CCCACCACACGTGGATATGAG	0.398													G|||	741	0.147963	0.5053	0.0663	5008	,	,		16240	0.001		0.0189	False		,,,				2504	0.0072				p.H863H		Atlas-SNP	.											ATAD2,NS,carcinoma,-2,1	ATAD2	160	1	0			c.C2589T						PASS	.	G		1923,2483	548.7+/-377.6	424,1075,704	236	207	216		2589	2.7	1	8	dbSNP_123	216	186,8414	82.6+/-145.2	2,182,4116	no	coding-synonymous	ATAD2	NM_014109.3		426,1257,4820	AA,AG,GG		2.1628,43.645,16.2156		863/1391	124357253	2109,10897	2203	4300	6503	SO:0001819	synonymous_variant	29028	exon19			CCACACGTGGATA	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.2589C>T	8.37:g.124357253G>A		69	0	0		91	40	0.43956	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Silent	SNP	ENST00000287394.5	37	CCDS6343.1																																																																																			G|0.843;A|0.157	0.157	strong		0.398	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109		A	124357253	G	A	124357253	2	1	29	1	0	0	0	0	0	0	0	1	1071	1136	40	1		1	ATAD2	8	124357253	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	3787383	124357253	22006769	431	12672											
ATAD2	29028	hgsc.bcm.edu	37	chr8	124360487	124360487	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgggattccaatccctggtGtgaatctttagaatctcttt	8	17	8	8	0	2	2	0	1	2	1	5	3	4	3	2	2	0	0	2	2	4	5	rs77106954	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:124360487G>A	ENST00000287394.5	-	15	1940	c.1833C>T	c.(1831-1833)caC>caT	p.H611H	ATAD2_ENST00000521903.1_5'UTR|MIR548AA1_ENST00000384971.2_RNA	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	611					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)			AATCCCTGGTGTGAATCTTTA	0.284													G|||	105	0.0209665	0.0499	0.0187	5008	,	,		14148	0.001		0.0179	False		,,,				2504	0.0072				p.H611H		Atlas-SNP	.											.	ATAD2	160	.	0			c.C1833T						PASS	.	G		172,4232	103.8+/-142.4	3,166,2033	36	38	37		1833	1.5	1	8	dbSNP_132	37	174,8424	78.9+/-141.6	1,172,4126	no	coding-synonymous	ATAD2	NM_014109.3		4,338,6159	AA,AG,GG		2.0237,3.9055,2.6611		611/1391	124360487	346,12656	2202	4299	6501	SO:0001819	synonymous_variant	29028	exon15			CCTGGTGTGAATC	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.1833C>T	8.37:g.124360487G>A		124	0	0		73	26	0.356164	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Silent	SNP	ENST00000287394.5	37	CCDS6343.1																																																																																			G|0.979;A|0.021	0.021	strong		0.284	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109		A	124360487	G	A	124360487	2	1	29	1	0	0	0	0	0	0	0	1	1071	1368	48	2		2	ATAD2	8	124360487	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	3234	124360487	22003535	432	12673											
KIAA0196	9897	hgsc.bcm.edu	37	chr8	126056088	126056088	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcattatagcctcgagataCgcagtccaaatcttctgtgt	10	14	7	10	2	3	1	1	0	2	1	5	2	4	1	2	0	2	1	2	0	4	5	rs369339497		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:126056088C>T	ENST00000318410.7	-	23	3178	c.2829G>A	c.(2827-2829)gcG>gcA	p.A943A	KIAA0196_ENST00000517845.1_Silent_p.A795A|KIAA0196-AS1_ENST00000519140.1_RNA	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	943					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)			CCTCGAGATACGCAGTCCAAA	0.303													C|||	1	0.000199681	0.0	0.0	5008	,	,		17952	0.001		0.0	False		,,,				2504	0.0				p.A943A		Atlas-SNP	.											KIAA0196,NS,carcinoma,0,1	KIAA0196	90	1	0			c.G2829A						PASS	.	C		0,4406		0,0,2203	84	78	80		2829	0	0.9	8		80	1,8599	2.2+/-6.3	0,1,4299	no	coding-synonymous	KIAA0196	NM_014846.3		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		943/1160	126056088	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9897	exon23			GAGATACGCAGTC		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.2829G>A	8.37:g.126056088C>T		112	0	0		137	70	0.510949	NM_014846	A8K4R7|Q3KQX5|Q8TBQ2	Silent	SNP	ENST00000318410.7	37	CCDS6355.1	.	.	.	.	.	.	.	.	.	.	C	1.691	-0.503992	0.04261	0.0	1.16E-4	ENSG00000164961	ENST00000523273	.	.	.	5.28	-0.0402	0.13872	.	.	.	.	.	T	0.52451	0.1735	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44375	-0.9332	4	.	.	.	-2.3241	7.0005	0.24807	0.486:0.2384:0.0:0.2756	.	.	.	.	H	560	.	.	R	-	2	0	KIAA0196	126125270	0.951000	0.32395	0.914000	0.36105	0.259000	0.26198	0.151000	0.16283	0.347000	0.23924	-1.268000	0.01426	CGT	.	.	weak		0.303	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846		T	126056088	C	T	126056088	2	4	29	1	0	0	0	0	0	0	0	1	8170	523	19	1		1	KIAA0196	8	126056088	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1695601	126056088	20307934	433	12674											
FAM135B	51059	hgsc.bcm.edu	37	chr8	139160926	139160926	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatttttctttggcctgataAaaactggagaatacactaat	15	14	6	6	0	1	2	0	1	1	1	1	3	1	2	1	2	2	0	1	2	7	6			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:139160926A>G	ENST00000395297.1	-	14	3455	c.3285T>C	c.(3283-3285)ttT>ttC	p.F1095F		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	1095										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)			TGGCCTGATAAAAACTGGAGA	0.388										HNSCC(54;0.14)																											p.F1095F		Atlas-SNP	.											.	FAM135B	423	.	0			c.T3285C						PASS	.						30	30	30					8																	139160926		2203	4300	6503	SO:0001819	synonymous_variant	51059	exon14			CTGATAAAAACTG	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.3285T>C	8.37:g.139160926A>G		41	0	0		49	13	0.265306	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Silent	SNP	ENST00000395297.1	37	CCDS6375.2																																																																																			.	.	none		0.388	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		G	139160926	A	G	139160926	2	3	29	1	0	0	0	0	0	0	0	1	5454	11	1	3		3	FAM135B	8	139160926	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	13104838	139160926	7203096	434	12675											
PTK2	5747	hgsc.bcm.edu	37	chr8	141711117	141711117	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctcgcaggtccaatactgtaGagtcctggaagaagggttga	11	9	13	8	1	0	3	0	1	0	2	3	4	2	4	2	3	1	3	2	3	5	3	rs185796736		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:141711117G>C	ENST00000522684.1	-	26	2601	c.2372C>G	c.(2371-2373)tCt>tGt	p.S791C	PTK2_ENST00000519465.1_Missense_Mutation_p.S419C|PTK2_ENST00000517887.1_Missense_Mutation_p.S835C|PTK2_ENST00000340930.3_Missense_Mutation_p.S791C|PTK2_ENST00000430260.2_Missense_Mutation_p.S101C|PTK2_ENST00000535192.1_Missense_Mutation_p.S745C|PTK2_ENST00000519419.1_Missense_Mutation_p.S835C|PTK2_ENST00000395218.2_Missense_Mutation_p.S791C|PTK2_ENST00000538769.1_Missense_Mutation_p.S459C|PTK2_ENST00000521059.1_Missense_Mutation_p.S791C	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	791	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)			CAATACTGTAGAGTCCTGGAA	0.433													G|||	1	0.000199681	0.0	0.0	5008	,	,		18321	0.0		0.001	False		,,,				2504	0.0				p.S813C		Atlas-SNP	.											.	PTK2	311	.	0			c.C2438G						PASS	.						68	61	63					8																	141711117		2203	4300	6503	SO:0001583	missense	5747	exon26			ACTGTAGAGTCCT	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.2372C>G	8.37:g.141711117G>C	ENSP00000429911:p.Ser791Cys	131	0	0		140	67	0.478571	NM_005607	B4E2N6|F5H4S4|Q14291|Q9UD85	Missense_Mutation	SNP	ENST00000522684.1	37	CCDS6381.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	19.73	3.881225	0.72294	.	.	ENSG00000169398	ENST00000522684;ENST00000535192;ENST00000519465;ENST00000517887;ENST00000521059;ENST00000395214;ENST00000395218;ENST00000354438;ENST00000395221;ENST00000523539;ENST00000340930;ENST00000538769;ENST00000519419;ENST00000430260;ENST00000521986;ENST00000522424;ENST00000521562	T;T;T;T;T;T;T;T;T;T;T;T	0.76968	-1.02;-1.06;-1.02;-1.02;-1.02;-1.03;-1.0;-1.02;-1.0;-1.02;1.42;-1.02	5.91	5.91	0.95273	.	0.450679	0.27856	N	0.017569	T	0.76018	0.3929	L	0.36672	1.1	0.40191	D	0.977405	P;P;P;D;P;P;P;P;P;P	0.57257	0.938;0.517;0.899;0.979;0.94;0.953;0.517;0.488;0.938;0.833	P;B;P;B;B;B;P;P;P;P	0.46718	0.502;0.325;0.502;0.394;0.428;0.319;0.447;0.525;0.502;0.502	T	0.75563	-0.3274	10	0.38643	T	0.18	.	19.9156	0.97061	0.0:0.0:1.0:0.0	.	791;486;711;791;813;745;743;639;459;419	B4E2N6;B4DH13;Q59GN8;Q05397;Q658W2;Q8IYN9;Q59GM6;Q05397-2;Q8N9D7;E9PEI4	.;.;.;FAK1_HUMAN;.;.;.;.;.;.	C	791;745;419;835;791;743;791;712;486;463;791;459;835;101;489;101;101	ENSP00000429911:S791C;ENSP00000438009:S745C;ENSP00000429170:S419C;ENSP00000429082:S835C;ENSP00000429474:S791C;ENSP00000378644:S791C;ENSP00000428492:S463C;ENSP00000341189:S791C;ENSP00000445742:S459C;ENSP00000429129:S835C;ENSP00000403416:S101C;ENSP00000430603:S489C	ENSP00000341189:S791C	S	-	2	0	PTK2	141780299	1.000000	0.71417	0.873000	0.34254	0.911000	0.54048	4.259000	0.58828	2.808000	0.96608	0.655000	0.94253	TCT	G|0.999;C|0.001	0.001	strong		0.433	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607		C	141711117	G	C	141711117	3	2	29	1	0	0	0	0	1	0	0	0	12775	942	33	4	814	4	PTK2	8	141711117	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2550191	141711117	4652905	435	12676											
GPR20	2843	hgsc.bcm.edu	37	chr8	142367087	142367087	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcacgctctccgtgctggcCgaagaggcctcggacggtgg	5	7	15	14	5	2	1	1	0	1	1	4	3	2	2	3	5	1	2	3	5	1	0	rs34591516	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:142367087C>T	ENST00000377741.3	-	2	1027	c.937G>A	c.(937-939)Ggc>Agc	p.G313S	CTD-3064M3.3_ENST00000562459.1_RNA	NM_005293.2	NP_005284.2	Q99678	GPR20_HUMAN	G protein-coupled receptor 20	313			G -> S (in dbSNP:rs34591516).		G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(3)|lung(4)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	15	all_cancers(97;4.32e-16)|all_epithelial(106;6.61e-14)|Lung NSC(106;9.4e-06)|all_lung(105;1.35e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0415)			CCGTGCTGGCCGAAGAGGCCT	0.652													C|||	243	0.0485224	0.1051	0.062	5008	,	,		19947	0.0		0.0517	False		,,,				2504	0.0092				p.G313S		Atlas-SNP	.											.	GPR20	43	.	0			c.G937A						PASS	.	C	SER/GLY	422,3984	204.1+/-226.4	18,386,1799	73	63	67		937	1.2	0.1	8	dbSNP_126	67	491,8109	142.3+/-198.5	15,461,3824	yes	missense	GPR20	NM_005293.2	56	33,847,5623	TT,TC,CC		5.7093,9.5778,7.0198	benign	313/359	142367087	913,12093	2203	4300	6503	SO:0001583	missense	2843	exon2			GCTGGCCGAAGAG	U66579	CCDS34949.1	8q24.3	2012-08-21				ENSG00000204882		"GPCR / Class A : Orphans"	4475	protein-coding gene	gene with protein product		601908				18347022	Standard	NM_005293		Approved		uc003ywf.3	Q99678		ENST00000377741.3:c.937G>A	8.37:g.142367087C>T	ENSP00000366970:p.Gly313Ser	103	0	0		80	36	0.45	NM_005293	Q17R96	Missense_Mutation	SNP	ENST00000377741.3	37	CCDS34949.1	119	0.05448717948717949	60	0.12195121951219512	27	0.07458563535911603	0	0.0	32	0.04221635883905013	C	1.474	-0.559060	0.03967	0.095778	0.057093	ENSG00000204882	ENST00000377741	T	0.37235	1.21	5.21	1.16	0.20824	.	1.376680	0.05461	U	0.551317	T	0.00241	0.0007	N	0.14661	0.345	0.09310	N	0.999998	B	0.29671	0.254	B	0.16289	0.015	T	0.08597	-1.0714	10	0.09084	T	0.74	-5.6003	3.7924	0.08726	0.0829:0.3719:0.3049:0.2403	rs34591516	313	Q99678	GPR20_HUMAN	S	313	ENSP00000366970:G313S	ENSP00000366970:G313S	G	-	1	0	GPR20	142436269	0.202000	0.23423	0.092000	0.20876	0.040000	0.13550	0.335000	0.19806	-0.079000	0.12707	-0.311000	0.09066	GGC	C|0.934;T|0.066	0.066	strong		0.652	GPR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378968.1	NM_005293		T	142367087	C	T	142367087	3	4	29	1	0	0	0	0	1	0	0	0	6688	652	23	1	143	1	GPR20	8	142367087	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	655970	142367087	3996935	436	12677											
EEF1D	1936	hgsc.bcm.edu	37	chr8	144671955	144671955	+	Intron	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcccaggagggccaggtcCgcggggccgagcccgctctt	5	4	17	15	4	1	0	0	0	1	0	2	2	2	1	5	6	1	1	5	6	0	1	rs61757370	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144671955C>T	ENST00000529272.1	-	2	397				EEF1D_ENST00000442189.2_Silent_p.A99A|EEF1D_ENST00000423316.2_Silent_p.A99A|EEF1D_ENST00000528610.1_Intron|EEF1D_ENST00000531621.1_Intron|EEF1D_ENST00000395119.3_Intron|EEF1D_ENST00000526838.1_Intron|EEF1D_ENST00000531770.1_5'Flank|EEF1D_ENST00000419152.2_Intron|EEF1D_ENST00000532400.1_Intron|EEF1D_ENST00000532741.1_Silent_p.A149A|EEF1D_ENST00000317198.6_Intron|EEF1D_ENST00000524624.1_Intron			P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)						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)			GGGCCAGGTCCGCGGGGCCGA	0.662													C|||	63	0.0125799	0.0454	0.0043	5008	,	,		14599	0.0		0.0	False		,,,				2504	0.0				p.A99A		Atlas-SNP	.											.	EEF1D	48	.	0			c.G297A						PASS	.	C	,,,,,,	197,4199		3,191,2004	20	22	21		297,,,,,,297	-7	0	8	dbSNP_129	21	8,8590		0,8,4291	no	coding-synonymous,intron,intron,intron,intron,intron,coding-synonymous	EEF1D	NM_001130053.2,NM_001130055.2,NM_001130056.2,NM_001130057.2,NM_001195203.1,NM_001960.4,NM_032378.4	,,,,,,	3,199,6295	TT,TC,CC		0.093,4.4813,1.5777	,,,,,,	99/648,,,,,,99/648	144671955	205,12789	2198	4299	6497	SO:0001627	intron_variant	1936	exon3			CAGGTCCGCGGGG	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.4-2936G>A	8.37:g.144671955C>T		53	0	0		55	29	0.527273	NM_001130053	B4DDU4|D3DWK3|E9PBQ9|Q4VBZ6|Q969J1|Q96I38	Silent	SNP	ENST00000529272.1	37	CCDS6405.1																																																																																			C|0.987;T|0.013	0.013	strong		0.662	EEF1D-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382592.2	NM_032378		T	144671955	C	T	144671955	1	4	29	0	1	0	0	0	0	0	0	0	4928	639	23	1		1	EEF1D	8	144671955	Intron	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2304868	144671955	1692067	437	12678											
ZNF623	9831	hgsc.bcm.edu	37	chr8	144733650	144733654	+	Stop_Codon_Del	DEL	ATAAA	ATAAA	-																															ggggaacacacaggtaacttAtaaaataattactttcccgc																								rs202122969|rs376588040		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	ATAAA	ATAAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144733650_144733654delATAAA	ENST00000501748.2	+	0	1697_1701				ZNF623_ENST00000458270.2_Stop_Codon_Del|ZNF623_ENST00000526926.1_Stop_Codon_Del	NM_014789.3	NP_055604	O75123	ZN623_HUMAN	zinc finger protein 623						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(3)|large_intestine(6)|lung(11)|prostate(1)|stomach(1)|urinary_tract(3)	27	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;2.46e-41)|Epithelial(56;5.28e-40)|all cancers(56;5.23e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			CAGGTAACTTATAAAATAATTACTT	0.415																																					p.536_537del		Pindel,Atlas-Indel	.											.	ZNF623	63	.	0			c.1607_1611del						PASS	.		,	67,4197		0,67,2065					,	-1.8	0			55	7,8247		0,7,4120	no	frameshift,frameshift	ZNF623	NM_014789.3,NM_001082480.1	,	0,74,6185	A1A1,A1R,RR		0.0848,1.5713,0.5911	,	,		74,12444				SO:0001567	stop_retained_variant	9831	exon1			.	AB014528	CCDS34957.1, CCDS47931.1	8q24.3	2013-01-08				ENSG00000183309		"Zinc fingers, C2H2-type"	29084	protein-coding gene	gene with protein product						9734811	Standard	NM_014789		Approved	KIAA0628	uc003yzd.2	O75123		Exception_encountered	8.37:g.144733650_144733654delATAAA		145	0	.		143	57	0.399	NM_014789	A4FU80|B4DGP3|E7ENV5	Frame_Shift_Del	DEL	ENST00000501748.2	37	CCDS34957.1																																																																																			ATAAA|0.993;-|0.007	0.007	strong		0.415	ZNF623-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382522.3	NM_014789		-	144733654	ATAAA	-	144733650	7	5	29	1	0	1	0	1	0	0	0	0	18062	446	16	0	1610	0	ZNF623	8	144733650	Stop_Codon_Del	DEL	ATAAA	TCGA-GR-7351-01A-11D-2210-10	61695	144733650	1630372	438	12679											
FAM83H	286077	hgsc.bcm.edu	37	chr8	144808953	144808953	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctcgataaatcctgtagttGgacttcctcttcgagtggaa	9	13	10	9	2	1	0	0	0	1	0	5	4	3	2	2	2	0	3	2	2	4	5	rs200179667	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144808953G>T	ENST00000388913.3	-	5	2803	c.2678C>A	c.(2677-2679)cCa>cAa	p.P893Q		NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	893					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)			TCCTGTAGTTGGACTTCCTCT	0.637													g|||	11	0.00219649	0.0083	0.0	5008	,	,		13854	0.0		0.0	False		,,,				2504	0.0				p.P893Q		Atlas-SNP	.											.	FAM83H	68	.	0			c.C2678A						PASS	.		GLN/PRO	11,3803		0,11,1896	22	23	23		2678	4.4	0.5	8		23	4,8216		0,4,4106	yes	missense	FAM83H	NM_198488.3	76	0,15,6002	TT,TG,GG		0.0487,0.2884,0.1246	probably-damaging	893/1180	144808953	15,12019	1907	4110	6017	SO:0001583	missense	286077	exon5			GTAGTTGGACTTC	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.2678C>A	8.37:g.144808953G>T	ENSP00000373565:p.Pro893Gln	62	0	0		47	22	0.468085	NM_198488	A0JLS2|Q8N4W0	Missense_Mutation	SNP	ENST00000388913.3	37	CCDS6410.2	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	g	5.326	0.245407	0.10077	0.002884	4.87E-4	ENSG00000180921	ENST00000388913	T	0.51574	0.7	4.4	4.4	0.53042	.	1.318910	0.05373	N	0.535775	T	0.33177	0.0854	N	0.17082	0.46	0.09310	N	1	B	0.30584	0.286	B	0.25884	0.064	T	0.12319	-1.0552	10	0.34782	T	0.22	.	9.1646	0.37043	0.0:0.1571:0.681:0.1619	.	893	Q6ZRV2	FA83H_HUMAN	Q	893	ENSP00000373565:P893Q	ENSP00000373565:P893Q	P	-	2	0	FAM83H	144880941	1.000000	0.71417	0.511000	0.27724	0.126000	0.20510	3.435000	0.52849	2.165000	0.68154	0.556000	0.70494	CCA	G|0.999;T|0.001	0.001	strong		0.637	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488		T	144808953	G	T	144808953	3	4	29	1	0	0	0	0	1	0	0	0	5648	1348	47	4	865	4	FAM83H	8	144808953	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	75303	144808953	1555069	439	12680											
EPPK1	83481	hgsc.bcm.edu	37	chr8	144941940	144941940	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtcgtggtgatgatttccaGcaatttctccaggcccccac	7	12	9	13	1	1	2	0	2	1	0	4	2	2	2	4	2	1	1	4	2	1	2	rs73715514	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144941940G>A	ENST00000525985.1	-	2	5553	c.5482C>T	c.(5482-5484)Ctg>Ttg	p.L1828L				P58107	EPIPL_HUMAN	epiplakin 1	1828						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)			ATGATTTCCAGCAATTTCTCC	0.537													G|||	314	0.0626997	0.2239	0.0202	5008	,	,		18564	0.0		0.004	False		,,,				2504	0.0				p.L1828L		Atlas-SNP	.											.	EPPK1	199	.	0			c.C5482T						PASS	.	G		691,3381		58,575,1403	233	230	231		5482	-6.8	0	8	dbSNP_130	231	18,8370		0,18,4176	no	coding-synonymous	EPPK1	NM_031308.1		58,593,5579	AA,AG,GG		0.2146,16.9695,5.6902		1828/2420	144941940	709,11751	2036	4194	6230	SO:0001819	synonymous_variant	83481	exon1			TTTCCAGCAATTT	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.5482C>T	8.37:g.144941940G>A		112	0	0		117	58	0.495726	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				G|0.951;A|0.049	0.049	strong		0.537	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		A	144941940	G	A	144941940	2	1	29	1	0	0	0	0	0	0	0	1	5192	962	34	2		2	EPPK1	8	144941940	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	132987	144941940	1422082	440	12681			3	55		6	6	5123	N	T_G_C	5.179884e-07
EPPK1	83481	hgsc.bcm.edu	37	chr8	144942794	144942794	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggctcagctcgtccagcGtcttcctgctgatcagctgc	4	11	10	16	2	3	1	2	1	1	0	6	1	5	1	3	1	5	4	3	1	0	1	rs373737061	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144942794G>A	ENST00000525985.1	-	2	4699	c.4628C>T	c.(4627-4629)aCg>aTg	p.T1543M				P58107	EPIPL_HUMAN	epiplakin 1	1543						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)			CTCGTCCAGCGTCTTCCTGCT	0.647													G|||	5	0.000998403	0.0008	0.0014	5008	,	,		20163	0.001		0.002	False		,,,				2504	0.0				p.T1543M		Atlas-SNP	.											EPPK1,NS,carcinoma,0,1	EPPK1	199	1	0			c.C4628T						PASS	.	G	MET/THR	0,4186		0,0,2093	20	22	22		4628	2.6	0.1	8		22	3,8413		0,3,4205	no	missense	EPPK1	NM_031308.1	81	0,3,6298	AA,AG,GG		0.0356,0.0,0.0238	probably-damaging	1543/2420	144942794	3,12599	2093	4208	6301	SO:0001583	missense	83481	exon1			TCCAGCGTCTTCC	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.4628C>T	8.37:g.144942794G>A	ENSP00000436337:p.Thr1543Met	66	0	0		82	44	0.536585	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		.	.	.	.	.	.	.	.	.	.	G	10.52	1.373843	0.24857	0.0	3.56E-4	ENSG00000227184	ENST00000525985	T	0.70986	-0.53	4.41	2.62	0.31277	.	.	.	.	.	T	0.77844	0.4191	L	0.49455	1.56	0.19945	N	0.999945	D	0.89917	1.0	D	0.91635	0.999	T	0.64706	-0.6344	9	0.72032	D	0.01	.	8.5002	0.33152	0.192:0.0:0.808:0.0	.	1543	E9PPU0	.	M	1543	ENSP00000436337:T1543M	ENSP00000436337:T1543M	T	-	2	0	EPPK1	145014782	0.117000	0.22190	0.131000	0.22000	0.300000	0.27592	1.414000	0.34736	0.497000	0.27926	-0.218000	0.12543	ACG	.	.	weak		0.647	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		A	144942794	G	A	144942794	3	1	29	1	0	0	0	0	1	0	0	0	5192	1145	40	1	2638	1	EPPK1	8	144942794	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	854	144942794	1421228	441	12682			3	55		6	6	5123	N	T_G_C	5.179884e-07
EPPK1	83481	hgsc.bcm.edu	37	chr8	144943223	144943223	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggggtcaaagaagaacttgTtgtccttgtcaactgcagtc	10	12	11	8	0	2	2	2	0	0	2	4	2	3	2	1	2	3	2	1	2	4	3	rs139952490	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144943223T>C	ENST00000525985.1	-	2	4270	c.4199A>G	c.(4198-4200)aAc>aGc	p.N1400S				P58107	EPIPL_HUMAN	epiplakin 1	1400						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)			GAAGAACTTGTTGTCCTTGTC	0.627													T|||	41	0.0081869	0.0272	0.0043	5008	,	,		21219	0.0		0.002	False		,,,				2504	0.0				p.N1400S		Atlas-SNP	.											.	EPPK1	199	.	0			c.A4199G						PASS	.	T	SER/ASN	50,4324		0,50,2137	29	34	32		4199	0.7	0	8	dbSNP_134	32	8,8560		0,8,4276	yes	missense	EPPK1	NM_031308.1	46	0,58,6413	CC,CT,TT		0.0934,1.1431,0.4482	benign	1400/2420	144943223	58,12884	2187	4284	6471	SO:0001583	missense	83481	exon1			AACTTGTTGTCCT	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.4199A>G	8.37:g.144943223T>C	ENSP00000436337:p.Asn1400Ser	36	0	0		50	20	0.4	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		11	0.005036630036630037	8	0.016260162601626018	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	T	9.127	1.010504	0.19277	0.011431	9.34E-4	ENSG00000227184	ENST00000525985	T	0.66280	-0.2	4.66	0.728	0.18260	.	.	.	.	.	T	0.15955	0.0384	N	0.08118	0	0.20764	N	0.999852	B	0.12013	0.005	B	0.04013	0.001	T	0.12682	-1.0538	9	0.07175	T	0.84	.	0.4678	0.00527	0.2139:0.3149:0.1697:0.3015	.	1400	E9PPU0	.	S	1400	ENSP00000436337:N1400S	ENSP00000436337:N1400S	N	-	2	0	EPPK1	145015211	0.000000	0.05858	0.008000	0.14137	0.598000	0.36846	-0.047000	0.11963	0.046000	0.15833	0.533000	0.62120	AAC	T|0.995;C|0.005	0.005	strong		0.627	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		C	144943223	T	C	144943223	3	2	29	1	0	0	0	0	1	0	0	0	5192	1725	60	3	3067	3	EPPK1	8	144943223	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	429	144943223	1420799	442	12683			3	55		6	6	5123	N	T_G_C	5.179884e-07
EPPK1	83481	hgsc.bcm.edu	37	chr8	144943384	144943384	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aagccctcgttctgtggcacGagccccttctccatggcctg	5	10	10	16	2	2	0	0	0	2	0	4	1	2	0	5	2	2	2	5	2	1	2	rs189024404	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144943384G>A	ENST00000525985.1	-	2	4109	c.4038C>T	c.(4036-4038)ctC>ctT	p.L1346L				P58107	EPIPL_HUMAN	epiplakin 1	1346						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)			TCTGTGGCACGAGCCCCTTCT	0.697													G|||	99	0.0197684	0.0681	0.0101	5008	,	,		16771	0.0		0.002	False		,,,				2504	0.0				p.L1346L		Atlas-SNP	.											.	EPPK1	199	.	0			c.C4038T						PASS	.	G		125,3773		1,123,1825	18	22	21		4038	-8.7	0	8		21	7,8235		0,7,4114	no	coding-synonymous	EPPK1	NM_031308.1		1,130,5939	AA,AG,GG		0.0849,3.2068,1.0873		1346/2420	144943384	132,12008	1949	4121	6070	SO:0001819	synonymous_variant	83481	exon1			TGGCACGAGCCCC	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.4038C>T	8.37:g.144943384G>A		37	0	0		48	30	0.625	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				G|0.988;A|0.012	0.012	strong		0.697	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		A	144943384	G	A	144943384	2	1	29	1	0	0	0	0	0	0	0	1	5192	1045	37	1		1	EPPK1	8	144943384	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	161	144943384	1420638	443	12684			3	55		6	6	5123	N	T_G_C	5.179884e-07
EPPK1	83481	hgsc.bcm.edu	37	chr8	144945535	144945535	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cggaggagccccttgcatcgGgcctcatagatgctcaggcg	7	7	14	13	3	2	1	2	0	0	1	3	3	2	3	3	4	3	2	3	4	1	2	rs73715515	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144945535G>A	ENST00000525985.1	-	2	1958	c.1887C>T	c.(1885-1887)gcC>gcT	p.A629A				P58107	EPIPL_HUMAN	epiplakin 1	629						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)			CCTTGCATCGGGCCTCATAGA	0.637													G|||	154	0.0307508	0.1097	0.0101	5008	,	,		18770	0.0		0.002	False		,,,				2504	0.0				p.A629A		Atlas-SNP	.											.	EPPK1	199	.	0			c.C1887T						PASS	.	G		306,3848		12,282,1783	28	30	29		1887	-1.8	0	8	dbSNP_130	29	12,8424		0,12,4206	no	coding-synonymous	EPPK1	NM_031308.1		12,294,5989	AA,AG,GG		0.1422,7.3664,2.5258		629/2420	144945535	318,12272	2077	4218	6295	SO:0001819	synonymous_variant	83481	exon1			GCATCGGGCCTCA	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.1887C>T	8.37:g.144945535G>A		62	0	0		60	22	0.366667	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				G|0.977;A|0.023	0.023	strong		0.637	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		A	144945535	G	A	144945535	2	1	29	1	0	0	0	0	0	0	0	1	5192	1219	43	2		2	EPPK1	8	144945535	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2151	144945535	1418487	444	12685			3	55		6	6	5123	N	T_G_C	5.179884e-07
EPPK1	83481	hgsc.bcm.edu	37	chr8	144947062	144947062	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtaggggtcaggatagccCgtagtggcacgctcagcggc	7	6	16	12	4	2	0	2	0	0	0	2	1	2	1	2	5	2	4	2	5	3	3	rs7819087	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:144947062C>T	ENST00000525985.1	-	2	431	c.360G>A	c.(358-360)acG>acA	p.T120T				P58107	EPIPL_HUMAN	epiplakin 1	120						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)			CAGGATAGCCCGTAGTGGCAC	0.677													C|||	150	0.0299521	0.1067	0.0101	5008	,	,		19734	0.0		0.002	False		,,,				2504	0.0				p.T120T		Atlas-SNP	.											.	EPPK1	199	.	0			c.G360A						PASS	.	C		277,3819		11,255,1782	27	33	31		360	-2.5	0.6	8	dbSNP_116	31	10,8366		0,10,4178	no	coding-synonymous	EPPK1	NM_031308.1		11,265,5960	TT,TC,CC		0.1194,6.7627,2.3012		120/2420	144947062	287,12185	2048	4188	6236	SO:0001819	synonymous_variant	83481	exon1			ATAGCCCGTAGTG	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.360G>A	8.37:g.144947062C>T		123	0	0		113	70	0.619469	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				C|0.955;T|0.045	0.045	strong		0.677	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		T	144947062	C	T	144947062	2	4	29	1	0	0	0	0	0	0	0	1	5192	639	23	1		1	EPPK1	8	144947062	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1527	144947062	1416960	445	12686			3	55		6	6	5123	N	T_G_C	5.179884e-07
SPATC1	375686	hgsc.bcm.edu	37	chr8	145095768	145095768	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acacaccctcaagcaccaccCacatcgcccagggtgccccc	10	3	6	22	1	1	0	1	0	0	0	2	0	1	0	6	1	2	1	6	1	1	0	rs150277218	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:145095768C>T	ENST00000377470.3	+	3	1168	c.1066C>T	c.(1066-1068)Cac>Tac	p.H356Y	SPATC1_ENST00000447830.2_Missense_Mutation_p.H356Y	NM_198572.2	NP_940974.2	Q76KD6	SPERI_HUMAN	spermatogenesis and centriole associated 1	356						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)			AAGCACCACCCACATCGCCCA	0.677																																					p.H356Y		Atlas-SNP	.											.	SPATC1	77	.	0			c.C1066T						PASS	.	C	TYR/HIS,TYR/HIS	3,4391		0,3,2194	150	53	86		1066,1066	2	0.1	8	dbSNP_134	86	1,8593		0,1,4296	yes	missense,missense	SPATC1	NM_001134374.1,NM_198572.2	83,83	0,4,6490	TT,TC,CC		0.0116,0.0683,0.0308	possibly-damaging,possibly-damaging	356/442,356/592	145095768	4,12984	2197	4297	6494	SO:0001583	missense	375686	exon3			ACCACCCACATCG	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.1066C>T	8.37:g.145095768C>T	ENSP00000366690:p.His356Tyr	58	0	0		64	30	0.46875	NM_001134374	B4DWW9|Q5U5I8|Q7Z6L7	Missense_Mutation	SNP	ENST00000377470.3	37	CCDS6413.2	.	.	.	.	.	.	.	.	.	.	C	10.60	1.395949	0.25205	6.83E-4	1.16E-4	ENSG00000186583	ENST00000377470;ENST00000447830	T	0.49139	0.79	3.94	1.99	0.26369	.	.	.	.	.	T	0.45135	0.1327	L	0.51422	1.61	0.09310	N	1	D;D	0.61697	0.99;0.99	P;P	0.57324	0.818;0.818	T	0.39165	-0.9627	9	0.02654	T	1	.	4.0862	0.09948	0.2339:0.6394:0.0:0.1267	.	356;356	B4DWW9;Q76KD6	.;SPERI_HUMAN	Y	356	ENSP00000366690:H356Y	ENSP00000366690:H356Y	H	+	1	0	SPATC1	145167756	0.001000	0.12720	0.051000	0.19133	0.200000	0.23975	0.160000	0.16462	0.717000	0.32145	0.561000	0.74099	CAC	C|0.999;T|0.001	0.001	strong		0.677	SPATC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346926.1	NM_198572		T	145095768	C	T	145095768	3	4	29	1	0	0	0	0	1	0	0	0	15032	594	21	2	1076	2	SPATC1	8	145095768	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	148706	145095768	1268254	446	12687											
HEATR7A	727957	hgsc.bcm.edu	37	chr8	145223239	145223239	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	acgccatcaccgataaggacCccctggtgcaggagcaggtc	10	5	12	14	2	1	0	1	0	0	0	2	3	1	2	4	4	2	2	4	4	1	1	rs374952645		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr8:145223239C>T	ENST00000528919.1	+	3	185	c.64C>T	c.(64-66)Ccc>Tcc	p.P22S	MROH1_ENST00000326134.5_Missense_Mutation_p.P22S|MROH1_ENST00000423230.2_Missense_Mutation_p.P22S|MROH1_ENST00000534366.1_Missense_Mutation_p.P22S|MROH1_ENST00000398656.4_Missense_Mutation_p.P22S	NM_032450.2	NP_115826	Q8NDA8	MROH1_HUMAN	maestro heat-like repeat family member 1	22																	CGATAAGGACCCCCTGGTGCA	0.657																																					p.P22S		Atlas-SNP	.											.	.	.	.	0			c.C64T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO	1,4221		0,1,2110	29	33	32		64,64,64	5.2	1	8		32	0,8440		0,0,4220	no	missense,missense,missense	HEATR7A	NM_001099280.1,NM_001099281.1,NM_032450.2	74,74,74	0,1,6330	TT,TC,CC		0.0,0.0237,0.0079	benign,benign,benign	22/423,22/423,22/1642	145223239	1,12661	2111	4220	6331	SO:0001583	missense	727957	exon4			AAGGACCCCCTGG		CCDS47938.1, CCDS47939.1, CCDS75803.1	8q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000179832	ENSG00000179832		"maestro heat-like repeat containing"	26958	protein-coding gene	gene with protein product			"HEAT repeat containing 7A"	HEATR7A		11347906	Standard	NM_032450		Approved	KIAA1833	uc003zbk.4	Q8NDA8	OTTHUMG00000165781	ENST00000528919.1:c.64C>T	8.37:g.145223239C>T	ENSP00000435565:p.Pro22Ser	31	0	0		36	9	0.25	NM_001099280	C9JWM5|D3DWL5|Q0P612|Q569G6|Q6NVW4|Q8N230|Q8NAD1|Q8ND95|Q96JJ4	Missense_Mutation	SNP	ENST00000528919.1	37	CCDS47938.1	.	.	.	.	.	.	.	.	.	.	C	13.01	2.108333	0.37242	2.37E-4	0.0	ENSG00000179832	ENST00000423230;ENST00000398656;ENST00000534366;ENST00000528919;ENST00000326134	T;T;T;T;T	0.68624	-0.27;-0.34;-0.34;-0.34;-0.34	5.18	5.18	0.71444	Armadillo-like helical (1);Armadillo-type fold (1);	0.420102	0.19324	U	0.117043	T	0.68869	0.3048	M	0.61703	1.905	0.80722	D	1	B;D;D;B;B	0.54047	0.098;0.964;0.964;0.199;0.2	B;P;P;B;B	0.49140	0.031;0.601;0.601;0.067;0.047	T	0.64715	-0.6342	10	0.10636	T	0.68	.	16.5435	0.84408	0.0:1.0:0.0:0.0	.	22;22;22;22;22	Q8NDA8-2;E9PHY8;Q8NDA8;Q8NDA8-4;Q8NDA8-5	.;.;HTR7A_HUMAN;.;.	S	22	ENSP00000388174:P22S;ENSP00000381649:P22S;ENSP00000436636:P22S;ENSP00000435565:P22S;ENSP00000321737:P22S	ENSP00000321737:P22S	P	+	1	0	HEATR7A	145295227	0.186000	0.23225	0.981000	0.43875	0.443000	0.32047	2.161000	0.42358	2.582000	0.87167	0.563000	0.77884	CCC	.	.	weak		0.657	MROH1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386183.1	NM_032450		T	145223239	C	T	145223239	3	4	29	1	0	0	0	0	1	0	0	0	7043	623	22	2	70	2	HEATR7A	8	145223239	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	127471	145223239	1140783	447	12688											
DOCK8	81704	hgsc.bcm.edu	37	chr9	399255	399255	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcatcagacattattgcaGccaggtgagtgtccccccca	9	9	8	15	0	2	2	2	1	0	1	3	2	3	2	5	1	2	1	5	1	1	2	rs34627722	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:399255G>A	ENST00000453981.1	+	26	3342	c.3230G>A	c.(3229-3231)aGc>aAc	p.S1077N	DOCK8_ENST00000382329.1_Missense_Mutation_p.S544N|DOCK8_ENST00000432829.2_Missense_Mutation_p.S1009N|DOCK8_ENST00000382331.1_Missense_Mutation_p.S379N|DOCK8_ENST00000469391.1_Missense_Mutation_p.S977N			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1077					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)		CATTATTGCAGCCAGGTGAGT	0.512													A|||	306	0.0611022	0.1415	0.0865	5008	,	,		14936	0.0		0.0338	False		,,,				2504	0.0256				p.S1077N		Atlas-SNP	.											.	DOCK8	401	.	0			c.G3230A						PASS	.	A	ASN/SER,ASN/SER,ASN/SER	473,3933	779.0+/-414.3	27,419,1757	139	127	131		2930,3026,3230	3.7	1	9	dbSNP_126	131	281,8319	805.8+/-407.3	4,273,4023	yes	missense,missense,missense	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	46,46,46	31,692,5780	AA,AG,GG		3.2674,10.7354,5.7973	benign,benign,benign	977/2000,1009/2032,1077/2100	399255	754,12252	2203	4300	6503	SO:0001583	missense	81704	exon26			ATTGCAGCCAGGT	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.3230G>A	9.37:g.399255G>A	ENSP00000408464:p.Ser1077Asn	138	0	0		96	40	0.416667	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	37	CCDS6440.2	126	0.057692307692307696	69	0.1402439024390244	28	0.07734806629834254	0	0.0	29	0.03825857519788918	A	12.92	2.081509	0.36758	0.107354	0.032674	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000469391;ENST00000382331;ENST00000382329	T;T;T;T;T	0.19806	2.12;2.12;2.12;2.12;2.12	6.04	3.69	0.42338	.	0.254353	0.44483	N	0.000448	T	0.00073	0.0002	N	0.04994	-0.135	0.20563	N	0.999885	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	0.41662	-0.9496	10	0.18276	T	0.48	.	7.2832	0.26322	0.7505:0.1227:0.1269:0.0	rs34627722;rs57242371	379;977;544;1077	A2A370;E9PH09;A2A369;Q8NF50	.;.;.;DOCK8_HUMAN	N	1077;1045;1009;977;379;544	ENSP00000408464:S1077N;ENSP00000394888:S1009N;ENSP00000419438:S977N;ENSP00000371768:S379N;ENSP00000371766:S544N	ENSP00000287364:S1045N	S	+	2	0	DOCK8	389255	1.000000	0.71417	0.993000	0.49108	0.891000	0.51852	4.343000	0.59348	0.173000	0.19788	-0.360000	0.07572	AGC	G|0.945;A|0.055	0.055	strong		0.512	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307		A	399255	G	A	399255	3	1	29	1	0	0	0	0	1	0	0	0	4695	971	34	2	3332	2	DOCK8	9	399255	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10		399255	140814176	448	12689											
DMRT3	58524	hgsc.bcm.edu	37	chr9	990235	990235	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acggaggcaaccccgagagcCgccctgacagccccaagtgt	10	3	12	16	3	0	2	0	1	0	1	0	4	0	3	6	2	3	1	6	2	2	0	rs61737966	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:990235C>T	ENST00000190165.2	+	2	687	c.649C>T	c.(649-651)Cgc>Tgc	p.R217C		NM_021240.2	NP_067063.1	Q9NQL9	DMRT3_HUMAN	doublesex and mab-3 related transcription factor 3	217					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)		CCCCGAGAGCCGCCCTGACAG	0.597													C|||	10	0.00199681	0.0	0.0101	5008	,	,		16117	0.0		0.003	False		,,,				2504	0.0				p.R217C		Atlas-SNP	.											.	DMRT3	83	.	0			c.C649T						PASS	.	C	CYS/ARG	5,4401	9.9+/-24.2	0,5,2198	50	59	56		649	1.5	0.8	9	dbSNP_129	56	56,8544	35.9+/-90.5	0,56,4244	yes	missense	DMRT3	NM_021240.2	180	0,61,6442	TT,TC,CC		0.6512,0.1135,0.469	benign	217/473	990235	61,12945	2203	4300	6503	SO:0001583	missense	58524	exon2			GAGAGCCGCCCTG	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.649C>T	9.37:g.990235C>T	ENSP00000190165:p.Arg217Cys	35	0	0		29	16	0.551724	NM_021240	Q7LA03|Q7LCH8|Q96SC7|Q9NRQ9	Missense_Mutation	SNP	ENST00000190165.2	37	CCDS6443.1	6	0.0027472527472527475	0	0.0	3	0.008287292817679558	0	0.0	3	0.00395778364116095	C	5.112	0.206206	0.09704	0.001135	0.006512	ENSG00000064218	ENST00000190165;ENST00000417254	T;T	0.32515	1.45;1.45	4.8	1.49	0.22878	.	0.471170	0.18808	N	0.130585	T	0.19046	0.0457	L	0.54323	1.7	0.33463	D	0.58522	B	0.09022	0.002	B	0.04013	0.001	T	0.25398	-1.0133	10	0.52906	T	0.07	-11.9879	7.7357	0.28812	0.3549:0.5579:0.0:0.0872	rs61737966	217	Q9NQL9	DMRT3_HUMAN	C	217;80	ENSP00000190165:R217C;ENSP00000387472:R80C	ENSP00000190165:R217C	R	+	1	0	DMRT3	980235	1.000000	0.71417	0.788000	0.31933	0.031000	0.12232	2.448000	0.44926	0.991000	0.38814	0.455000	0.32223	CGC	C|0.995;T|0.005	0.005	strong		0.597	DMRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051490.1	NM_021240		T	990235	C	T	990235	3	4	29	1	0	0	0	0	1	0	0	0	4589	652	23	1	655	1	DMRT3	9	990235	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	590980	990235	140223196	449	12690											
RANBP6	26953	hgsc.bcm.edu	37	chr9	6012347	6012347	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgttcatcatcaagttgtgaTacacattccaaccataaatc	14	13	4	10	0	3	1	3	1	0	0	5	1	4	1	2	0	2	2	2	0	5	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:6012347T>A	ENST00000259569.5	-	1	3271	c.3261A>T	c.(3259-3261)gtA>gtT	p.V1087V	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	1087					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				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)		CAAGTTGTGATACACATTCCA	0.353																																					p.V1087V		Atlas-SNP	.											.	RANBP6	127	.	0			c.A3261T						PASS	.						78	73	74					9																	6012347		2203	4300	6503	SO:0001819	synonymous_variant	26953	exon1			TTGTGATACACAT	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.3261A>T	9.37:g.6012347T>A		81	0	0		79	29	0.367089	NM_012416	Q5T7X4|Q7Z3V2|Q96E78	Silent	SNP	ENST00000259569.5	37	CCDS6467.1																																																																																			.	.	none		0.353	RANBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051650.1	NM_012416		A	6012347	T	A	6012347	2	1	29	1	0	0	0	0	0	0	0	1	13046	1393	49	5		5	RANBP6	9	6012347	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	5022112	6012347	135201084	450	12691											
UHRF2	115426	hgsc.bcm.edu	37	chr9	6413498	6413498	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctaggcgccaagatgtggaTacaggttcgcaccattgatg	10	10	12	9	2	1	2	0	1	1	1	2	3	1	3	2	3	1	2	2	3	3	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:6413498T>A	ENST00000276893.5	+	1	176	c.8T>A	c.(7-9)aTa>aAa	p.I3K	UHRF2_ENST00000381373.3_Missense_Mutation_p.I3K|RP11-307L3.4_ENST00000411561.1_RNA	NM_152896.2	NP_690856.1	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase	3	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				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)		AAGATGTGGATACAGGTTCGC	0.662																																					p.I3K		Atlas-SNP	.											.	UHRF2	50	.	0			c.T8A						PASS	.						57	58	57					9																	6413498		2203	4300	6503	SO:0001583	missense	115426	exon1			TGTGGATACAGGT	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.8T>A	9.37:g.6413498T>A	ENSP00000276893:p.Ile3Lys	73	0	0		70	13	0.185714	NM_152896	Q5VYR1|Q5VYR3|Q659C8|Q8TAG7	Missense_Mutation	SNP	ENST00000276893.5	37	CCDS6469.1	.	.	.	.	.	.	.	.	.	.	T	34	5.300914	0.95601	.	.	ENSG00000147854	ENST00000276893;ENST00000381373	T;T	0.57907	0.37;0.37	4.87	4.87	0.63330	Ubiquitin supergroup (1);Ubiquitin (1);	0.000000	0.85682	D	0.000000	T	0.80544	0.4643	H	0.96111	3.77	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	D	0.86923	0.2068	10	0.87932	D	0	-7.8255	14.2948	0.66304	0.0:0.0:0.0:1.0	.	3	Q96PU4	UHRF2_HUMAN	K	3	ENSP00000276893:I3K;ENSP00000370778:I3K	ENSP00000276893:I3K	I	+	2	0	UHRF2	6403498	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.099000	0.76981	2.043000	0.60533	0.459000	0.35465	ATA	.	.	none		0.662	UHRF2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051665.3	NM_152306		A	6413498	T	A	6413498	3	1	29	1	0	0	0	0	1	0	0	0	16985	1406	49	5	10	5	UHRF2	9	6413498	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	401151	6413498	134799933	451	12692			4	56		5	3	146	N	T_G	8.66359e-06
UHRF2	115426	hgsc.bcm.edu	37	chr9	6413513	6413513	+	Frame_Shift_Del	DEL	T	T	-																															gtggatacaggttcgcaccaTtgatggctccaagacgtgca																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:6413513delT	ENST00000276893.5	+	1	191	c.23delT	c.(22-24)attfs	p.I8fs	UHRF2_ENST00000381373.3_Frame_Shift_Del_p.I8fs|RP11-307L3.4_ENST00000411561.1_RNA	NM_152896.2	NP_690856.1	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase	8	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				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)		GTTCGCACCATTGATGGCTCC	0.667																																					p.I8fs		Atlas-Indel	.											.	UHRF2	50	.	0			c.22delA						PASS	.						60	60	60					9																	6413513		2203	4300	6503	SO:0001589	frameshift_variant	115426	exon1			.	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.23delT	9.37:g.6413513delT	ENSP00000276893:p.Ile8fs	87	0	0		75	14	0.186667	NM_152896	Q5VYR1|Q5VYR3|Q659C8|Q8TAG7	Frame_Shift_Del	DEL	ENST00000276893.5	37	CCDS6469.1																																																																																			.	.	none		0.667	UHRF2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051665.3	NM_152306		-	6413513	T	-	6413513	7	5	29	1	0	1	0	1	0	0	0	0	16985	1493	52	0	25	0	UHRF2	9	6413513	Frame_Shift_Del	DEL	T	TCGA-GR-7351-01A-11D-2210-10	15	6413513	134799918	452	12693	160	2	4	56		5	3	146	N	T_G	8.66359e-06
UHRF2	115426	hgsc.bcm.edu	37	chr9	6413515	6413515	+	Missense_Mutation	SNP	G	G	C																															ggatacaggttcgcaccattGatggctccaagacgtgcacc																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:6413515G>C	ENST00000276893.5	+	1	193	c.25G>C	c.(25-27)Gat>Cat	p.D9H	UHRF2_ENST00000381373.3_Missense_Mutation_p.D9H|RP11-307L3.4_ENST00000411561.1_RNA	NM_152896.2	NP_690856.1	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase	9	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				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)		TCGCACCATTGATGGCTCCAA	0.662																																					p.D9H		Atlas-SNP	.											UHRF2,NS,carcinoma,-1,1	UHRF2	50	1	0			c.G25C						PASS	.						60	60	60					9																	6413515		2203	4300	6503	SO:0001583	missense	115426	exon1			ACCATTGATGGCT	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.25G>C	9.37:g.6413515G>C	ENSP00000276893:p.Asp9His	87	0	0		77	14	0.181818	NM_152896	Q5VYR1|Q5VYR3|Q659C8|Q8TAG7	Missense_Mutation	SNP	ENST00000276893.5	37	CCDS6469.1	.	.	.	.	.	.	.	.	.	.	G	33	5.248236	0.95305	.	.	ENSG00000147854	ENST00000276893;ENST00000381373	T;T	0.12361	2.69;2.69	4.87	4.87	0.63330	Ubiquitin supergroup (1);Ubiquitin (2);	0.056041	0.64402	D	0.000002	T	0.45836	0.1362	M	0.88906	2.99	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.55786	-0.8086	10	0.87932	D	0	-12.9077	17.7967	0.88574	0.0:0.0:1.0:0.0	.	9	Q96PU4	UHRF2_HUMAN	H	9	ENSP00000276893:D9H;ENSP00000370778:D9H	ENSP00000276893:D9H	D	+	1	0	UHRF2	6403515	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	8.728000	0.91484	2.526000	0.85167	0.561000	0.74099	GAT	.	.	none		0.662	UHRF2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051665.3	NM_152306		C	6413515	G	C	6413515	3	2	29	1	0	0	0	0	1	0	0	0	16985	1290	45	4	27	4	UHRF2	9	6413515	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2	6413515	134799916	453	12694	160	2	4	56		5	3	146	N	T_G	8.66359e-06
UHRF2	115426	hgsc.bcm.edu	37	chr9	6413640	6413640	+	Silent	SNP	G	G	A																															cgcctcttctaccggggcaaGcaggtgaggcgcgcccgccg																								rs540145571		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:6413640G>A	ENST00000276893.5	+	1	318	c.150G>A	c.(148-150)aaG>aaA	p.K50K	UHRF2_ENST00000381373.3_Silent_p.K50K|RP11-307L3.4_ENST00000411561.1_RNA	NM_152896.2	NP_690856.1	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase	50	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				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)		ACCGGGGCAAGCAGGTGAGGC	0.726													G|||	1	0.000199681	0.0008	0.0	5008	,	,		8973	0.0		0.0	False		,,,				2504	0.0				p.K50K		Atlas-SNP	.											.	UHRF2	50	.	0			c.G150A						PASS	.						12	15	14					9																	6413640		2199	4298	6497	SO:0001819	synonymous_variant	115426	exon1			GGGCAAGCAGGTG	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.150G>A	9.37:g.6413640G>A		24	0	0		16	7	0.4375	NM_152896	Q5VYR1|Q5VYR3|Q659C8|Q8TAG7	Silent	SNP	ENST00000276893.5	37	CCDS6469.1																																																																																			.	.	none		0.726	UHRF2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051665.3	NM_152306		A	6413640	G	A	6413640	2	1	29	1	0	0	0	0	0	0	0	1	16985	962	34	2		2	UHRF2	9	6413640	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	125	6413640	134799791	454	12695	161	2	4	56		5	3	146	N	T_G	8.66359e-06
UHRF2	115426	hgsc.bcm.edu	37	chr9	6413643	6413643	+	Splice_Site	SNP	G	G	A																															ctcttctaccggggcaagcaGgtgaggcgcgcccgccgcgc																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:6413643G>A	ENST00000276893.5	+	1	321	c.153G>A	c.(151-153)caG>caA	p.Q51Q	UHRF2_ENST00000381373.3_Splice_Site_p.Q51Q|RP11-307L3.4_ENST00000411561.1_RNA	NM_152896.2	NP_690856.1	Q96PU4	UHRF2_HUMAN	ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase	51	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				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)		GGGGCAAGCAGGTGAGGCGCG	0.726																																					p.Q51Q		Atlas-SNP	.											.	UHRF2	50	.	0			c.G153A						PASS	.						11	14	13					9																	6413643		2197	4297	6494	SO:0001630	splice_region_variant	115426	exon1			CAAGCAGGTGAGG	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.153+1G>A	9.37:g.6413643G>A		22	0	0		14	5	0.357143	NM_152896	Q5VYR1|Q5VYR3|Q659C8|Q8TAG7	Silent	SNP	ENST00000276893.5	37	CCDS6469.1																																																																																			.	.	none		0.726	UHRF2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051665.3	NM_152306	Silent	A	6413643	G	A	6413643	5	1	29	1	0	0	0	0	0	0	1	0	16985	1014	35	2	155	2	UHRF2	9	6413643	Splice_Site	SNP	G	TCGA-GR-7351-01A-11D-2210-10	3	6413643	134799788	455	12696	161	2	4	56		5	3	146	N	T_G	8.66359e-06
PTPRD	5789	hgsc.bcm.edu	37	chr9	8376067	8376067	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgaactggaattgtctcacTtctctcttctcacttgaacc	8	15	6	12	0	4	2	2	2	4	0	7	3	4	3	1	1	2	0	1	1	3	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:8376067T>G	ENST00000381196.4	-	36	5073	c.4530A>C	c.(4528-4530)gaA>gaC	p.E1510D	PTPRD_ENST00000540109.1_Missense_Mutation_p.E1510D|PTPRD_ENST00000356435.5_Missense_Mutation_p.E1510D|PTPRD_ENST00000486161.1_Missense_Mutation_p.E1103D|PTPRD_ENST00000358503.5_Missense_Mutation_p.E1488D|PTPRD_ENST00000355233.5_Missense_Mutation_p.E1104D|PTPRD_ENST00000397606.3_Missense_Mutation_p.E1103D|PTPRD_ENST00000360074.4_Missense_Mutation_p.E1497D|PTPRD_ENST00000397617.3_Missense_Mutation_p.E1103D|PTPRD_ENST00000397611.3_Missense_Mutation_p.E1100D|PTPRD_ENST00000537002.1_Missense_Mutation_p.E1100D	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1510	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)		ATTGTCTCACTTCTCTCTTCT	0.433										TSP Lung(15;0.13)																											p.E1510D		Atlas-SNP	.											.	PTPRD	1348	.	0			c.A4530C						PASS	.						104	92	96					9																	8376067		2203	4299	6502	SO:0001583	missense	5789	exon39			TCTCACTTCTCTC	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.4530A>C	9.37:g.8376067T>G	ENSP00000370593:p.Glu1510Asp	75	0	0		56	5	0.0892857	NM_002839	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	37	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	T	15.05	2.719582	0.48728	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606	T;T;T;T;T;T;T;T;T;T;T	0.32023	1.47;1.47;1.47;1.47;1.47;1.47;1.47;1.47;1.47;1.47;1.47	5.71	4.56	0.56223	Protein-tyrosine phosphatase, receptor/non-receptor type (4);	0.000000	0.85682	D	0.000000	T	0.48150	0.1484	M	0.76433	2.335	0.80722	D	1	B;P;P;P;B;P;B;P;B	0.43826	0.071;0.73;0.73;0.73;0.014;0.721;0.063;0.818;0.013	B;P;P;P;B;B;B;B;B	0.55087	0.036;0.768;0.768;0.768;0.03;0.203;0.035;0.255;0.024	T	0.45366	-0.9266	9	.	.	.	.	11.8465	0.52387	0.0:0.0696:0.0:0.9303	.	1103;1094;1103;1104;1100;1100;1497;1510;1510	Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;PTPRD_HUMAN	D	1510;1510;1497;1488;1104;1103;1100;1100;981;1510;1103;1103	ENSP00000370593:E1510D;ENSP00000348812:E1510D;ENSP00000353187:E1497D;ENSP00000351293:E1488D;ENSP00000347373:E1104D;ENSP00000380741:E1103D;ENSP00000380735:E1100D;ENSP00000440515:E1100D;ENSP00000438164:E1510D;ENSP00000417093:E1103D;ENSP00000380731:E1103D	.	E	-	3	2	PTPRD	8366067	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.262000	0.51538	2.178000	0.69098	0.477000	0.44152	GAA	.	.	none		0.433	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			G	8376067	T	G	8376067	3	3	29	1	0	0	0	0	1	0	0	0	12814	1606	56	5	1240	5	PTPRD	9	8376067	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	1962424	8376067	132837364	456	12697											
PTPRD	5789	hgsc.bcm.edu	37	chr9	8449782	8449782	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gtctgttgggtggtgtgaagGgatctccttattgttcggta	5	16	15	5	1	2	1	0	1	2	0	4	2	2	2	1	4	0	3	1	4	3	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:8449782G>A	ENST00000381196.4	-	31	4474	c.3931C>T	c.(3931-3933)Cct>Tct	p.P1311S	PTPRD_ENST00000540109.1_Missense_Mutation_p.P1311S|PTPRD_ENST00000356435.5_Missense_Mutation_p.P1311S|PTPRD_ENST00000486161.1_Missense_Mutation_p.P904S|PTPRD_ENST00000358503.5_Missense_Mutation_p.P1289S|PTPRD_ENST00000355233.5_Missense_Mutation_p.P905S|PTPRD_ENST00000397606.3_Missense_Mutation_p.P890S|PTPRD_ENST00000360074.4_Missense_Mutation_p.P1298S|PTPRD_ENST00000397617.3_Missense_Mutation_p.P890S|PTPRD_ENST00000397611.3_Missense_Mutation_p.P901S|PTPRD_ENST00000537002.1_Missense_Mutation_p.P901S	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1311					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)		TGGTGTGAAGGGATCTCCTTA	0.433										TSP Lung(15;0.13)																											p.P1311S		Atlas-SNP	.											.	PTPRD	1348	.	0			c.C3931T						PASS	.						373	343	353					9																	8449782		2203	4300	6503	SO:0001583	missense	5789	exon34			GTGAAGGGATCTC	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.3931C>T	9.37:g.8449782G>A	ENSP00000370593:p.Pro1311Ser	228	0	0		189	57	0.301587	NM_002839	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	37	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	G	13.20	2.167160	0.38217	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606	T;T;T;T;T;T;T;T;T;T;T	0.52295	0.71;0.71;0.74;0.79;0.89;0.99;0.79;0.67;0.71;0.9;0.99	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.28599	0.0708	N	0.04203	-0.255	0.80722	D	1	B;B;B;B;B;B;B;B;B	0.33612	0.295;0.295;0.295;0.295;0.003;0.419;0.002;0.001;0.001	B;B;B;B;B;B;B;B;B	0.32342	0.068;0.068;0.068;0.068;0.01;0.144;0.007;0.002;0.002	T	0.12477	-1.0546	9	.	.	.	.	19.9455	0.97180	0.0:0.0:1.0:0.0	.	890;895;904;905;901;901;1298;1311;1311	Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;PTPRD_HUMAN	S	1311;1311;1298;1289;905;890;901;901;782;1311;904;890	ENSP00000370593:P1311S;ENSP00000348812:P1311S;ENSP00000353187:P1298S;ENSP00000351293:P1289S;ENSP00000347373:P905S;ENSP00000380741:P890S;ENSP00000380735:P901S;ENSP00000440515:P901S;ENSP00000438164:P1311S;ENSP00000417093:P904S;ENSP00000380731:P890S	.	P	-	1	0	PTPRD	8439782	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.143000	0.71756	2.788000	0.95919	0.650000	0.86243	CCT	.	.	none		0.433	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			A	8449782	G	A	8449782	3	1	29	1	0	0	0	0	1	0	0	0	12814	1232	43	2	1905	2	PTPRD	9	8449782	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	73715	8449782	132763649	457	12698											
FREM1	158326	hgsc.bcm.edu	37	chr9	14740229	14740229	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	acagttacaaggttgcccagGtatctaaatgcaaatgaaaa	17	9	8	7	0	1	1	0	1	1	0	1	1	1	1	1	2	3	4	1	2	8	4	rs187325866		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:14740229G>A	ENST00000380880.3	-	36	7041	c.6258C>T	c.(6256-6258)taC>taT	p.Y2086Y	FREM1_ENST00000380894.1_Silent_p.Y622Y|FREM1_ENST00000422223.2_Silent_p.Y2086Y|FREM1_ENST00000380881.4_Silent_p.Y2087Y			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	2086	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)		GGTTGCCCAGGTATCTAAATG	0.413																																					p.Y2086Y		Atlas-SNP	.											.	FREM1	261	.	0			c.C6258T						PASS	.	G	,	6,3836		0,6,1915	87	85	85		1866,6258	3.5	0.5	9		85	14,8270		0,14,4128	no	coding-synonymous,coding-synonymous	FREM1	NM_001177704.1,NM_144966.5	,	0,20,6043	AA,AG,GG		0.169,0.1562,0.1649	,	622/716,2086/2180	14740229	20,12106	1921	4142	6063	SO:0001819	synonymous_variant	158326	exon37			GCCCAGGTATCTA	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.6258C>T	9.37:g.14740229G>A		42	0	0		64	32	0.5	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	37	CCDS47952.1																																																																																			G|0.999;A|0.001	0.001	strong		0.413	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		A	14740229	G	A	14740229	2	1	29	1	0	0	0	0	0	0	0	1	6052	1256	44	2		2	FREM1	9	14740229	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	6290447	14740229	126473202	458	12699											
CHMP5	51510	hgsc.bcm.edu	37	chr9	33266075	33266075	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgctgagctagtgaagtataAggatcagatcaagaagatga	16	9	12	4	0	2	6	2	3	0	3	2	7	2	7	0	1	2	3	0	1	6	3	rs146626883	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:33266075A>C	ENST00000223500.8	+	2	274	c.137A>C	c.(136-138)aAg>aCg	p.K46T	BAG1_ENST00000379704.2_5'Flank|CHMP5_ENST00000419016.2_Missense_Mutation_p.K46T|BAG1_ENST00000472232.3_5'Flank	NM_016410.5	NP_057494.3	Q9NZZ3	CHMP5_HUMAN	charged multivesicular body protein 5	46					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)			GTGAAGTATAAGGATCAGATC	0.448																																					p.K46T		Atlas-SNP	.											CHMP5,rectum,carcinoma,-1,1	CHMP5	15	1	0			c.A137C						PASS	.	A	THR/LYS,THR/LYS	0,4406		0,0,2203	84	77	79		137,137	5.6	1	9	dbSNP_134	79	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	CHMP5	NM_001195536.1,NM_016410.5	78,78	0,3,6500	CC,CA,AA		0.0349,0.0,0.0231	probably-damaging,probably-damaging	46/172,46/220	33266075	3,13003	2203	4300	6503	SO:0001583	missense	51510	exon2			AGTATAAGGATCA	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.137A>C	9.37:g.33266075A>C	ENSP00000223500:p.Lys46Thr	72	0	0		73	29	0.39726	NM_016410	B2RD95|B4DIR6|Q5VXW2|Q96AV2|Q9HB68|Q9NYS4|Q9Y323	Missense_Mutation	SNP	ENST00000223500.8	37	CCDS6537.1	.	.	.	.	.	.	.	.	.	.	A	29.3	4.994287	0.93167	0.0	3.49E-4	ENSG00000086065	ENST00000223500;ENST00000419016	T;T	0.72725	-0.68;-0.68	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	D	0.86318	0.5904	M	0.90922	3.16	0.58432	D	0.999996	D;P	0.67145	0.996;0.933	D;P	0.68353	0.957;0.891	D	0.89316	0.3636	10	0.87932	D	0	-2.8598	13.6556	0.62336	1.0:0.0:0.0:0.0	.	46;46	B4DIR6;Q9NZZ3	.;CHMP5_HUMAN	T	46	ENSP00000223500:K46T;ENSP00000442725:K46T	ENSP00000223500:K46T	K	+	2	0	CHMP5	33256075	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.852000	0.92215	2.109000	0.64355	0.379000	0.24179	AAG	A|0.999;C|0.001	0.001	strong		0.448	CHMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052040.3	NM_016410		C	33266075	A	C	33266075	3	2	29	1	0	0	0	0	1	0	0	0	3361	72	3	5	143	5	CHMP5	9	33266075	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	18525846	33266075	107947356	459	12700											
PRSS3	5646	hgsc.bcm.edu	37	chr9	33799103	33799103	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggccatggctgtgcctggaaGaacaggcctggagtctacac	9	7	14	11	0	1	1	0	0	1	1	1	3	1	3	3	5	3	1	3	5	3	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:33799103G>A	ENST00000361005.5	+	5	840	c.840G>A	c.(838-840)aaG>aaA	p.K280K	PRSS3_ENST00000342836.4_Silent_p.K237K|PRSS3_ENST00000429677.3_Silent_p.K216K|RP11-133O22.6_ENST00000454429.2_RNA|PRSS3_ENST00000495682.1_3'UTR|PRSS3_ENST00000379405.3_Silent_p.K223K	NM_007343.3	NP_031369	P35030	TRY3_HUMAN	protease, serine, 3	280	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)			GTGCCTGGAAGAACAGGCCTG	0.572																																					p.K280K		Atlas-SNP	.											.	PRSS3	79	.	0			c.G840A						PASS	.						95	91	92					9																	33799103		2203	4300	6503	SO:0001819	synonymous_variant	5646	exon5			CTGGAAGAACAGG		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.840G>A	9.37:g.33799103G>A		176	0	0		210	9	0.0428571	NM_007343	A8CED1|A8CED3|A9Z1Y4|E7ES07|F8W7P3|P15951|Q15665|Q5VXV0|Q6ISJ4|Q9UQV3	Silent	SNP	ENST00000361005.5	37	CCDS47958.1																																																																																			.	.	none		0.572	PRSS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052121.1	NM_002771		A	33799103	G	A	33799103	2	1	29	1	0	0	0	0	0	0	0	1	12634	933	33	2		2	PRSS3	9	33799103	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	533028	33799103	107414328	460	12701											
UBAP2	55833	hgsc.bcm.edu	37	chr9	33998847	33998847	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatcacttgagcgagacgcaTctgttcagctgttgcctgga	8	11	12	10	2	3	2	2	1	1	1	3	5	3	3	1	1	3	4	1	1	0	3	rs149441020	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:33998847T>C	ENST00000379238.1	-	3	232	c.115A>G	c.(115-117)Atg>Gtg	p.M39V	UBAP2_ENST00000539807.1_Start_Codon_SNP_p.M1V|UBAP2_ENST00000379239.4_5'UTR|UBAP2_ENST00000449054.1_Missense_Mutation_p.M39V|UBAP2_ENST00000480885.1_5'UTR|UBAP2_ENST00000418786.2_Missense_Mutation_p.M39V|UBAP2_ENST00000360802.1_Missense_Mutation_p.M39V					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)		GCGAGACGCATCTGTTCAGCT	0.358													T|||	3	0.000599042	0.0	0.0	5008	,	,		19492	0.0		0.003	False		,,,				2504	0.0				p.M39V		Atlas-SNP	.											.	UBAP2	82	.	0			c.A115G						PASS	.	T	VAL/MET	0,4406		0,0,2203	104	99	101		115	6.2	1	9	dbSNP_134	101	2,8598	2.2+/-6.3	0,2,4298	yes	missense	UBAP2	NM_018449.2	21	0,2,6501	CC,CT,TT		0.0233,0.0,0.0154	benign	39/1120	33998847	2,13004	2203	4300	6503	SO:0001583	missense	55833	exon3			GACGCATCTGTTC	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.115A>G	9.37:g.33998847T>C	ENSP00000368540:p.Met39Val	25	0	0		16	11	0.6875	NM_018449		Missense_Mutation	SNP	ENST00000379238.1	37	CCDS6547.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	19.13	3.767752	0.69878	0.0	2.33E-4	ENSG00000137073	ENST00000379238;ENST00000449054;ENST00000360802;ENST00000431417;ENST00000539807;ENST00000351580;ENST00000418786;ENST00000412543	T;T;T;T;T;T	0.27720	1.65;1.65;1.65;2.58;1.65;1.65	6.17	6.17	0.99709	UBA-like (1);	0.082223	0.85682	D	0.000000	T	0.32763	0.0840	L	0.40543	1.245	0.48696	D	0.999693	P;B;B;B;B;B	0.37731	0.607;0.291;0.225;0.053;0.192;0.125	B;B;B;B;B;B	0.40602	0.334;0.145;0.032;0.019;0.069;0.082	T	0.05053	-1.0909	10	0.54805	T	0.06	-8.1025	16.8222	0.85835	0.0:0.0:0.0:1.0	.	39;1;1;1;1;39	E7EWG4;F5H4D5;F5H2U4;F5H2C8;B4DH66;Q5T6F2	.;.;.;.;.;UBAP2_HUMAN	V	39;39;39;1;1;39;39;39	ENSP00000368540:M39V;ENSP00000416932:M39V;ENSP00000354039:M39V;ENSP00000439329:M1V;ENSP00000404436:M39V;ENSP00000414800:M39V	ENSP00000259602:M39V	M	-	1	0	UBAP2	33988847	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.845000	0.69437	2.371000	0.80710	0.533000	0.62120	ATG	T|0.999;C|0.001	0.001	strong		0.358	UBAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001071.1	NM_018449		C	33998847	T	C	33998847	3	2	29	1	0	0	0	0	1	0	0	0	16852	1435	50	3	3352	3	UBAP2	9	33998847	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	199744	33998847	107214584	461	12702											
UNC13B	10497	hgsc.bcm.edu	37	chr9	35399243	35399243	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gcgtggtgatgaacacaatgGagaggatgattgttctgccc	10	10	14	7	1	1	4	0	3	1	1	1	6	1	5	1	3	2	1	1	3	2	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:35399243G>A	ENST00000378495.3	+	33	4135	c.3913G>A	c.(3913-3915)Gag>Aag	p.E1305K	UNC13B_ENST00000396787.1_Missense_Mutation_p.E1317K|UNC13B_ENST00000378496.4_Missense_Mutation_p.E1305K	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	1305	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)			GAACACAATGGAGAGGATGAT	0.562																																					p.E1305K		Atlas-SNP	.											.	UNC13B	153	.	0			c.G3913A						PASS	.						210	182	192					9																	35399243		2203	4300	6503	SO:0001583	missense	10497	exon33			ACAATGGAGAGGA	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.3913G>A	9.37:g.35399243G>A	ENSP00000367756:p.Glu1305Lys	223	0	0		186	8	0.0430108	NM_006377	Q5VYM8	Missense_Mutation	SNP	ENST00000378495.3	37	CCDS6579.1	.	.	.	.	.	.	.	.	.	.	G	36	5.688200	0.96784	.	.	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496;ENST00000535471	T;T;T	0.75704	-0.96;-0.96;-0.96	6.08	6.08	0.98989	Mammalian uncoordinated homology 13, domain 2 (1);Mammalian uncoordinated homology 13, subgroup, domain 2 (1);	0.000000	0.85682	D	0.000000	D	0.89136	0.6629	M	0.89095	3.005	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.995;0.998	D	0.89952	0.4080	10	0.87932	D	0	-22.8301	19.4349	0.94788	0.0:0.0:1.0:0.0	.	1305;1305	F8W8M9;O14795	.;UN13B_HUMAN	K	1317;1305;1305;892	ENSP00000380006:E1317K;ENSP00000367756:E1305K;ENSP00000367757:E1305K	ENSP00000367756:E1305K	E	+	1	0	UNC13B	35389243	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.338000	0.96553	2.894000	0.99253	0.655000	0.94253	GAG	.	.	none		0.562	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377		A	35399243	G	A	35399243	3	1	29	1	0	0	0	0	1	0	0	0	17000	1175	41	2	4043	2	UNC13B	9	35399243	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1400396	35399243	105814188	462	12703											
CREB3	7094	hgsc.bcm.edu	37	chr9	35733116	35733116	+	5'Flank	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accacacctactccctcccaCgggaaactgtctctatggat	10	9	6	16	1	1	0	0	0	1	0	4	2	3	2	4	2	2	0	4	2	3	2	rs200166825		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:35733116C>T	ENST00000314888.9	-	0	0				CREB3_ENST00000353704.2_Missense_Mutation_p.R85W|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)			CTCCCTCCCACGGGAAACTGT	0.532																																					p.R85W		Atlas-SNP	.											.	CREB3	24	.	0			c.C253T						PASS	.		TRP/ARG	0,4406		0,0,2203	103	100	101		253	4.8	0.2	9		101	3,8597	3.0+/-9.4	0,3,4297	no	missense	CREB3	NM_006368.4	101	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging	85/372	35733116	3,13003	2203	4300	6503	SO:0001631	upstream_gene_variant	10488	exon2			CTCCCACGGGAAA	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		9.37:g.35733116C>T	Exception_encountered	263	0	0		250	135	0.54	NM_006368	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	37	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	c	16.81	3.226051	0.58668	0.0	3.49E-4	ENSG00000107175	ENST00000353704	T	0.64991	-0.13	4.77	4.77	0.60923	.	0.983520	0.08280	N	0.970123	T	0.49795	0.1578	N	0.14661	0.345	0.24140	N	0.995734	D	0.63880	0.993	B	0.43916	0.436	T	0.43278	-0.9401	10	0.87932	D	0	.	10.7772	0.46356	0.0:0.9013:0.0:0.0987	.	85	O43889-2	.	W	85	ENSP00000342136:R85W	ENSP00000342136:R85W	R	+	1	2	CREB3	35723116	0.403000	0.25319	0.245000	0.24217	0.122000	0.20287	1.449000	0.35123	2.381000	0.81170	0.580000	0.79431	CGG	C|0.999;T|0.001	0.001	weak		0.532	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		T	35733116	C	T	35733116	1	4	29	0	1	0	0	0	0	0	0	0	3857	527	19	1		1	CREB3	9	35733116	5'Flank	SNP	C	TCGA-GR-7351-01A-11D-2210-10	333873	35733116	105480315	463	12704											
PAX5	5079	hgsc.bcm.edu	37	chr9	37033992	37033992	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcggtcctacctgtcctgcTggtccgaggagtcggataat	6	10	13	12	4	0	0	0	0	0	0	4	3	3	2	4	4	2	1	4	4	2	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:37033992T>C	ENST00000358127.4	-	1	111	c.37A>G	c.(37-39)Agc>Ggc	p.S13G	PAX5_ENST00000520281.1_Missense_Mutation_p.S13G|PAX5_ENST00000523241.1_Missense_Mutation_p.S13G|PAX5_ENST00000522003.1_5'UTR|PAX5_ENST00000377847.2_Missense_Mutation_p.S13G|PAX5_ENST00000520154.1_Missense_Mutation_p.S13G|PAX5_ENST00000414447.1_Missense_Mutation_p.S13G|PAX5_ENST00000446742.1_Missense_Mutation_p.S13G|PAX5_ENST00000523145.1_5'UTR|PAX5_ENST00000377853.2_Missense_Mutation_p.S13G|PAX5_ENST00000377852.2_Missense_Mutation_p.S13G	NM_001280554.1|NM_001280556.1|NM_016734.1	NP_001267483.1|NP_001267485.1|NP_057953.1	Q02548	PAX5_HUMAN	paired box 5	13					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.?(10)	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)		CCTGTCCTGCTGGTCCGAGGA	0.522			"T, Mis, D, F, S"	"IGH@, ETV6, PML, FOXP1, ZNF521, ELN"	"NHL, ALL, B-ALL"																																p.S13G		Atlas-SNP	.		Dom	yes		9	9p13	5079	paired box gene 5 (B-cell lineage specific activator protein)		L	.	PAX5	250	.	10	Unknown(10)	haematopoietic_and_lymphoid_tissue(10)	c.A37G						PASS	.						67	63	64					9																	37033992		2203	4300	6503	SO:0001583	missense	5079	exon1			TCCTGCTGGTCCG		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.37A>G	9.37:g.37033992T>C	ENSP00000350844:p.Ser13Gly	61	0	0		89	41	0.460674	NM_016734	A3QVP6|A3QVP7|A3QVP8|C0KTF6|C0KTF7|C0KTF8|C0KTF9|C0KTG0|O75933|Q5SFM2|Q6S728|Q6S729|Q6S730|Q6S731|Q6S732	Missense_Mutation	SNP	ENST00000358127.4	37	CCDS6607.1	.	.	.	.	.	.	.	.	.	.	T	13.57	2.276510	0.40294	.	.	ENSG00000196092	ENST00000358127;ENST00000377853;ENST00000377852;ENST00000523241;ENST00000520154;ENST00000520281;ENST00000446742;ENST00000414447;ENST00000377847	D;D;D;D;D;D;D;D;D	0.97924	-4.13;-4.13;-4.12;-4.61;-4.61;-4.54;-3.77;-4.54;-4.61	6.08	0.879	0.19155	.	0.627134	0.17080	N	0.187840	D	0.92133	0.7506	N	0.16862	0.45	0.27406	N	0.954724	B;B;B;B;B;B;B;B;B	0.09022	0.0;0.0;0.0;0.0;0.001;0.002;0.0;0.0;0.0	B;B;B;B;B;B;B;B;B	0.08055	0.0;0.0;0.0;0.0;0.003;0.001;0.0;0.0;0.0	D	0.84947	0.0869	10	0.42905	T	0.14	.	5.7732	0.18265	0.1214:0.5281:0.0:0.3505	.	13;13;13;13;13;13;13;13;13	C0KTF8;C0KTF7;C0KTF9;C0KTF6;E7ERW5;E7EQT0;Q6S730;Q6S731;Q02548	.;.;.;.;.;.;.;.;PAX5_HUMAN	G	13	ENSP00000350844:S13G;ENSP00000367084:S13G;ENSP00000367083:S13G;ENSP00000429637:S13G;ENSP00000429291:S13G;ENSP00000430773:S13G;ENSP00000404687:S13G;ENSP00000412188:S13G;ENSP00000367078:S13G	ENSP00000350844:S13G	S	-	1	0	PAX5	37023992	1.000000	0.71417	0.996000	0.52242	0.999000	0.98932	1.043000	0.30316	-0.099000	0.12263	0.533000	0.62120	AGC	.	.	none		0.522	PAX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052433.1			C	37033992	T	C	37033992	3	2	29	1	0	0	0	0	1	0	0	0	11491	1580	55	3	1178	3	PAX5	9	37033992	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	1300876	37033992	104179439	464	12705											
MAMDC2	256691	hgsc.bcm.edu	37	chr9	72723204	72723204	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	taagtcctgacttacaggctGaggaatggagctgcctccgt	9	10	12	10	1	0	2	0	2	0	0	2	4	2	4	3	3	3	2	3	3	3	2	rs139498917	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:72723204G>A	ENST00000377182.4	+	3	843	c.226G>A	c.(226-228)Gag>Aag	p.E76K	MAMDC2-AS1_ENST00000591368.1_RNA|MAMDC2-AS1_ENST00000414515.3_RNA	NM_153267.4	NP_694999.3	Q7Z304	MAMC2_HUMAN	MAM domain containing 2	76	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						CTTACAGGCTGAGGAATGGAG	0.488													G|||	5	0.000998403	0.0008	0.0014	5008	,	,		17888	0.0		0.003	False		,,,				2504	0.0				p.E76K		Atlas-SNP	.											.	MAMDC2	55	.	0			c.G226A						PASS	.	G	LYS/GLU	4,4402	8.1+/-20.4	0,4,2199	116	108	111		226	5.9	1	9	dbSNP_134	111	26,8574	19.2+/-60.6	0,26,4274	yes	missense	MAMDC2	NM_153267.4	56	0,30,6473	AA,AG,GG		0.3023,0.0908,0.2307	possibly-damaging	76/687	72723204	30,12976	2203	4300	6503	SO:0001583	missense	256691	exon3			CAGGCTGAGGAAT	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.226G>A	9.37:g.72723204G>A	ENSP00000366387:p.Glu76Lys	149	0	0		125	63	0.504	NM_153267	Q5VW47|Q8WX43|Q96BM4	Missense_Mutation	SNP	ENST00000377182.4	37	CCDS6631.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	13.73	2.323034	0.41096	9.08E-4	0.003023	ENSG00000165072	ENST00000377182	T	0.01981	4.52	5.93	5.93	0.95920	Concanavalin A-like lectin/glucanase (1);MAM domain (3);	0.391658	0.29916	N	0.010874	T	0.04588	0.0125	L	0.59436	1.845	0.39469	D	0.967694	P	0.41345	0.746	B	0.41988	0.372	T	0.52866	-0.8518	10	0.07813	T	0.8	-29.7414	20.3324	0.98724	0.0:0.0:1.0:0.0	.	76	Q7Z304	MAMC2_HUMAN	K	76	ENSP00000366387:E76K	ENSP00000366387:E76K	E	+	1	0	MAMDC2	71913024	1.000000	0.71417	0.999000	0.59377	0.757000	0.42996	4.560000	0.60802	2.799000	0.96334	0.650000	0.86243	GAG	G|0.999;A|0.001	0.001	strong		0.488	MAMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052600.1	NM_153267		A	72723204	G	A	72723204	3	1	29	1	0	0	0	0	1	0	0	0	9212	1291	45	2	236	2	MAMDC2	9	72723204	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	35689212	72723204	68490227	465	12706											
PCSK5	5125	hgsc.bcm.edu	37	chr9	78789900	78789900	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatttcattattatttctcaAggtaaattgaaagaatggtc	14	16	7	4	0	2	2	2	1	1	1	4	3	2	2	0	2	0	1	0	2	7	6			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:78789900A>C	ENST00000545128.1	+	14	2294		c.e14-1		PCSK5_ENST00000376767.3_Splice_Site|PCSK5_ENST00000376752.4_Splice_Site	NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5						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						TTATTTCTCAAGGTAAATTGA	0.413																																					.		Atlas-SNP	.											PCSK5_ENST00000545128,NS,carcinoma,0,3	PCSK5	329	3	0			c.1757-2A>C						PASS	.						118	114	116					9																	78789900		2203	4300	6503	SO:0001630	splice_region_variant	5125	exon14			TTCTCAAGGTAAA		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.1757-1A>C	9.37:g.78789900A>C		164	0	0		153	10	0.0653595	NM_001190482	F5H2G7|Q13527|Q96EP4	Splice_Site	SNP	ENST00000545128.1	37	CCDS55320.1	.	.	.	.	.	.	.	.	.	.	A	24.0	4.486799	0.84854	.	.	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000376767;ENST00000396108;ENST00000376752;ENST00000424854	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0502	0.80755	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PCSK5	77979720	1.000000	0.71417	0.931000	0.37212	0.991000	0.79684	8.652000	0.91083	2.197000	0.70478	0.528000	0.53228	.	.	.	none		0.413	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			Intron	C	78789900	A	C	78789900	5	2	29	1	0	0	0	0	0	0	1	0	11612	86	3	5	1809	5	PCSK5	9	78789900	Splice_Site	SNP	A	TCGA-GR-7351-01A-11D-2210-10	6066696	78789900	62423531	466	12707											
FLJ46321	389763	hgsc.bcm.edu	37	chr9	84605777	84605777	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgcccagaccccgtctgtcGggtgtgtaagagagcaactg	9	8	13	11	2	1	2	0	0	1	2	2	3	1	2	3	1	3	2	3	1	2	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:84605777G>A	ENST00000344803.2	+	4	439	c.392G>A	c.(391-393)cGg>cAg	p.R131Q		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	131					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CCCGTCTGTCGGGTGTGTAAG	0.552																																					p.R131Q		Atlas-SNP	.											.	.	.	.	0			c.G392A						PASS	.						107	102	104					9																	84605777		1984	4157	6141	SO:0001583	missense	389763	exon4			TCTGTCGGGTGTG		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.392G>A	9.37:g.84605777G>A	ENSP00000341988:p.Arg131Gln	152	0	0		170	84	0.494118	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	g	8.742	0.919112	0.17982	.	.	ENSG00000214929	ENST00000344803	T	0.04360	3.64	2.98	0.49	0.16861	.	1.929580	0.02564	N	0.097117	T	0.02688	0.0081	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40365	-0.9567	10	0.56958	D	0.05	-1.5821	3.4169	0.07378	0.6335:0.2342:0.1323:0.0	.	131	Q6ZQQ2	F75D1_HUMAN	Q	131	ENSP00000341988:R131Q	ENSP00000341988:R131Q	R	+	2	0	FAM75D1	83795597	0.976000	0.34144	0.135000	0.22099	0.000000	0.00434	0.412000	0.21131	0.092000	0.17331	-1.291000	0.01355	CGG	.	.	none		0.552	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		A	84605777	G	A	84605777	3	1	29	1	0	0	0	0	1	0	0	0	5940	1116	39	1	406	1	FLJ46321	9	84605777	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	5815877	84605777	56607654	467	12708											
SHC3	53358	hgsc.bcm.edu	37	chr9	91652977	91652977	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgcccgtgaggacaaaggaGcccgggttggtggtgctctt	7	9	16	9	2	1	1	0	1	1	0	1	3	1	3	2	5	3	2	2	5	1	2	rs56005403	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:91652977G>A	ENST00000375835.4	-	11	1893	c.1587C>T	c.(1585-1587)ggC>ggT	p.G529G	SHC3_ENST00000375831.1_Silent_p.G77G|SHC3_ENST00000375830.1_Silent_p.G77G	NM_016848.5	NP_058544.3	Q92529	SHC3_HUMAN	SHC (Src homology 2 domain containing) transforming protein 3	529	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				central nervous system development (GO:0007417)|epidermal growth factor receptor signaling pathway (GO:0007173)|insulin receptor signaling pathway (GO:0008286)|learning or memory (GO:0007611)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|synaptic transmission, glutamatergic (GO:0035249)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)	signal transducer activity (GO:0004871)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|skin(3)	28						GGACAAAGGAGCCCGGGTTGG	0.632													G|||	19	0.00379393	0.0	0.0029	5008	,	,		16704	0.0		0.0139	False		,,,				2504	0.0031				p.G529G		Atlas-SNP	.											.	SHC3	66	.	0			c.C1587T						PASS	.	G		13,4393	20.2+/-43.8	0,13,2190	132	134	134		1587	-0.9	1	9	dbSNP_129	134	157,8443	74.8+/-137.4	0,157,4143	no	coding-synonymous	SHC3	NM_016848.5		0,170,6333	AA,AG,GG		1.8256,0.2951,1.3071		529/595	91652977	170,12836	2203	4300	6503	SO:0001819	synonymous_variant	53358	exon11			AAAGGAGCCCGGG	D84361	CCDS6681.1	9q22.1	2013-02-14	2005-05-24		ENSG00000148082	ENSG00000148082		"SH2 domain containing"	18181	protein-coding gene	gene with protein product		605263	"src homology 2 domain containing transforming protein C3"			8808684	Standard	NM_016848		Approved	N-Shc, NSHC, SHCC	uc004aqf.2	Q92529	OTTHUMG00000020179	ENST00000375835.4:c.1587C>T	9.37:g.91652977G>A		29	0	0		40	20	0.5	NM_016848	Q5T7I7|Q8TAP2|Q9UCX5	Silent	SNP	ENST00000375835.4	37	CCDS6681.1																																																																																			G|0.990;A|0.010	0.010	strong		0.632	SHC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052986.1	NM_016848		A	91652977	G	A	91652977	2	1	29	1	0	0	0	0	0	0	0	1	14287	958	34	2		2	SHC3	9	91652977	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	7047200	91652977	49560454	468	12709											
SECISBP2	79048	hgsc.bcm.edu	37	chr9	91954848	91954848	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gaatagagacaccgaaatttCaatctaagcagcagccacag	17	6	8	10	1	2	1	1	0	1	1	2	4	2	1	2	0	3	2	2	0	5	3	rs45452691	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:91954848C>G	ENST00000375807.3	+	9	1353	c.1282C>G	c.(1282-1284)Caa>Gaa	p.Q428E	SECISBP2_ENST00000339901.4_Missense_Mutation_p.Q355E|SECISBP2_ENST00000534113.2_Missense_Mutation_p.Q360E	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	428			Q -> E (in dbSNP:rs45452691).		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)			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						ACCGAAATTTCAATCTAAGCA	0.408													C|||	90	0.0179712	0.0023	0.0202	5008	,	,		13904	0.0		0.0596	False		,,,				2504	0.0133				p.Q428E		Atlas-SNP	.											.	SECISBP2	64	.	0			c.C1282G						PASS	.	C	GLU/GLN	46,4360	47.5+/-82.1	0,46,2157	85	86	85		1282	3.7	0.7	9	dbSNP_127	85	507,8093	143.9+/-199.8	11,485,3804	no	missense	SECISBP2	NM_024077.3	29	11,531,5961	GG,GC,CC		5.8953,1.044,4.2519	benign	428/855	91954848	553,12453	2203	4300	6503	SO:0001583	missense	79048	exon9			AAATTTCAATCTA	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.1282C>G	9.37:g.91954848C>G	ENSP00000364965:p.Gln428Glu	61	0	0		43	19	0.44186	NM_024077	F8W892|Q5HYY1|Q8IYC0|Q9H0A1	Missense_Mutation	SNP	ENST00000375807.3	37	CCDS6683.1	61	0.027930402930402932	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	49	0.06464379947229551	C	13.48	2.248565	0.39797	0.01044	0.058953	ENSG00000187742	ENST00000375807;ENST00000395669;ENST00000339901;ENST00000534113;ENST00000425851	T;T;T;T	0.72942	-0.68;-0.7;-0.69;0.94	4.64	3.73	0.42828	.	0.820878	0.10928	N	0.618701	T	0.13114	0.0318	L	0.51422	1.61	0.22571	N	0.998972	B;B;B	0.32467	0.255;0.372;0.255	B;B;B	0.33392	0.078;0.163;0.057	T	0.47328	-0.9126	10	0.02654	T	1	-0.1047	6.3816	0.21538	0.0:0.8236:0.0:0.1764	rs45452691;rs61744906	435;355;428	Q59H19;Q96T21-2;Q96T21	.;.;SEBP2_HUMAN	E	428;434;355;360;225	ENSP00000364965:Q428E;ENSP00000364959:Q355E;ENSP00000436650:Q360E;ENSP00000414288:Q225E	ENSP00000364959:Q355E	Q	+	1	0	SECISBP2	91144668	0.384000	0.25164	0.714000	0.30535	0.944000	0.59088	-0.422000	0.07043	2.583000	0.87209	0.655000	0.94253	CAA	C|0.961;G|0.039	0.039	strong		0.408	SECISBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052990.3	NM_024077		G	91954848	C	G	91954848	3	3	29	1	0	0	0	0	1	0	0	0	14021	827	29	4	1316	4	SECISBP2	9	91954848	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	301871	91954848	49258583	469	12710											
ROR2	4920	hgsc.bcm.edu	37	chr9	94495595	94495595	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcgtcgcggcacagctcaCgcggcttgggtgtccgggag	5	7	16	13	6	1	0	1	0	0	0	4	1	2	1	1	4	1	3	1	4	0	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:94495595C>T	ENST00000375708.3	-	6	944	c.746G>A	c.(745-747)cGt>cAt	p.R249H	ROR2_ENST00000375715.1_Missense_Mutation_p.R109H|ROR2_ENST00000550066.1_5'UTR	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	249	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						GCACAGCTCACGCGGCTTGGG	0.647																																					p.R249H		Atlas-SNP	.											.	ROR2	167	.	0			c.G746A						PASS	.						44	41	42					9																	94495595		2203	4299	6502	SO:0001583	missense	4920	exon6			AGCTCACGCGGCT	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.746G>A	9.37:g.94495595C>T	ENSP00000364860:p.Arg249His	96	0	0		101	8	0.0792079	NM_004560	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Missense_Mutation	SNP	ENST00000375708.3	37	CCDS6691.1	.	.	.	.	.	.	.	.	.	.	C	35	5.489687	0.96323	.	.	ENSG00000169071	ENST00000375715;ENST00000375708	T;T	0.76060	0.54;-0.99	4.37	4.37	0.52481	Frizzled domain (2);Kringle (1);	0.000000	0.39146	N	0.001446	D	0.83830	0.5339	L	0.59436	1.845	0.80722	D	1	D;D;D	0.89917	0.977;1.0;0.973	P;D;P	0.87578	0.581;0.998;0.763	D	0.85333	0.1091	10	0.56958	D	0.05	.	17.1327	0.86730	0.0:1.0:0.0:0.0	.	249;249;109	A1L4F5;Q01974;B1APY4	.;ROR2_HUMAN;.	H	109;249	ENSP00000364867:R109H;ENSP00000364860:R249H	ENSP00000364860:R249H	R	-	2	0	ROR2	93535416	1.000000	0.71417	0.978000	0.43139	0.949000	0.60115	7.560000	0.82277	2.271000	0.75665	0.511000	0.50034	CGT	.	.	none		0.647	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1			T	94495595	C	T	94495595	3	4	29	1	0	0	0	0	1	0	0	0	13542	536	19	1	2101	1	ROR2	9	94495595	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2540747	94495595	46717836	470	12711											
ROR2	4920	hgsc.bcm.edu	37	chr9	94499797	94499797	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacccatcctcgtggtaatcAtccctggtaagaaacacaca	14	8	6	13	1	1	1	1	0	0	1	4	1	3	1	3	2	2	2	3	2	4	2	rs16907720	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:94499797A>G	ENST00000375708.3	-	5	696	c.498T>C	c.(496-498)gaT>gaC	p.D166D	ROR2_ENST00000375715.1_Silent_p.D26D|ROR2_ENST00000550066.1_5'UTR	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	166					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						CGTGGTAATCATCCCTGGTAA	0.512													A|||	361	0.0720847	0.1959	0.0504	5008	,	,		16550	0.0		0.0537	False		,,,				2504	0.0133				p.D166D		Atlas-SNP	.											.	ROR2	167	.	0			c.T498C						PASS	.	A		757,3649	309.1+/-290.9	63,631,1509	80	73	75		498	-4.9	0.8	9	dbSNP_123	75	573,8027	153.7+/-208.1	19,535,3746	no	coding-synonymous	ROR2	NM_004560.3		82,1166,5255	GG,GA,AA		6.6628,17.1811,10.226		166/944	94499797	1330,11676	2203	4300	6503	SO:0001819	synonymous_variant	4920	exon5			GTAATCATCCCTG	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.498T>C	9.37:g.94499797A>G		36	0	0		30	14	0.466667	NM_004560	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Silent	SNP	ENST00000375708.3	37	CCDS6691.1																																																																																			A|0.902;G|0.098	0.098	strong		0.512	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1			G	94499797	A	G	94499797	2	3	29	1	0	0	0	0	0	0	0	1	13542	214	8	3		3	ROR2	9	94499797	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	4202	94499797	46713634	471	12712											
WNK2	65268	hgsc.bcm.edu	37	chr9	96030957	96030957	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catctgtccggtggctgagcAccccgcccccgaggcccctg	4	6	12	19	3	1	1	0	1	1	0	2	2	2	1	7	3	1	2	7	3	0	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:96030957A>G	ENST00000297954.4	+	18	3962	c.3962A>G	c.(3961-3963)cAc>cGc	p.H1321R	WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000427277.2_Missense_Mutation_p.H933R|WNK2_ENST00000349097.3_Missense_Mutation_p.H933R|WNK2_ENST00000395477.2_Missense_Mutation_p.H1321R|WNK2_ENST00000395475.2_3'UTR	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1321					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						GTGGCTGAGCACCCCGCCCCC	0.632																																					p.H1321R		Atlas-SNP	.											.	WNK2	277	.	0			c.A3962G						PASS	.						56	47	50					9																	96030957		2203	4300	6503	SO:0001583	missense	65268	exon18			CTGAGCACCCCGC	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.3962A>G	9.37:g.96030957A>G	ENSP00000297954:p.His1321Arg	116	0	0		95	27	0.284211	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Missense_Mutation	SNP	ENST00000297954.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.28|18.28	3.588088|3.588088	0.66105|0.66105	.|.	.|.	ENSG00000165238|ENSG00000165238	ENST00000297954;ENST00000395477;ENST00000349097;ENST00000427277|ENST00000432730;ENST00000448251	T;T;T;T|.	0.33865|.	1.39;1.39;1.39;1.39|.	5.95|5.95	5.95|5.95	0.96441|0.96441	.|.	0.185244|.	0.47455|.	D|.	0.000234|.	T|T	0.36908|0.36908	0.0984|0.0984	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	D;B;B;D|.	0.63880|.	0.99;0.183;0.418;0.993|.	P;B;B;D|.	0.72338|.	0.882;0.026;0.058;0.977|.	T|T	0.33137|0.33137	-0.9880|-0.9880	10|5	0.27785|.	T|.	0.31|.	.|.	12.2871|12.2871	0.54797|0.54797	0.8587:0.1413:0.0:0.0|0.8587:0.1413:0.0:0.0	.|.	1321;924;1321;1321|.	Q9Y3S1-2;A6PVR4;F8W9F9;Q9Y3S1|.	.;.;.;WNK2_HUMAN|.	R|A	1321;1321;933;933|1317;118	ENSP00000297954:H1321R;ENSP00000378860:H1321R;ENSP00000297876:H933R;ENSP00000411181:H933R|.	ENSP00000297954:H1321R|.	H|T	+|+	2|1	0|0	WNK2|WNK2	95070778|95070778	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.675000|0.675000	0.39556|0.39556	3.831000|3.831000	0.55776|0.55776	2.279000|2.279000	0.76181|0.76181	0.533000|0.533000	0.62120|0.62120	CAC|ACC	.	.	none		0.632	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648		G	96030957	A	G	96030957	3	3	29	1	0	0	0	0	1	0	0	0	17393	159	6	3	4032	3	WNK2	9	96030957	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	1531160	96030957	45182474	472	12713											
WNK2	65268	hgsc.bcm.edu	37	chr9	96030979	96030979	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccgcccccgaggcccctgaAtcttcgcccccacttcctct	4	8	6	23	3	2	1	0	1	2	0	4	2	3	1	8	1	0	0	8	1	1	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:96030979A>T	ENST00000297954.4	+	18	3984	c.3984A>T	c.(3982-3984)gaA>gaT	p.E1328D	WNK2_ENST00000356055.3_5'UTR|WNK2_ENST00000427277.2_Missense_Mutation_p.E940D|WNK2_ENST00000349097.3_Missense_Mutation_p.E940D|WNK2_ENST00000395477.2_Missense_Mutation_p.E1328D|WNK2_ENST00000395475.2_3'UTR	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1328					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						AGGCCCCTGAATCTTCGCCCC	0.622																																					p.E1328D		Atlas-SNP	.											.	WNK2	277	.	0			c.A3984T						PASS	.						36	34	34					9																	96030979		2203	4300	6503	SO:0001583	missense	65268	exon18			CCCTGAATCTTCG	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.3984A>T	9.37:g.96030979A>T	ENSP00000297954:p.Glu1328Asp	109	0	0		91	28	0.307692	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Missense_Mutation	SNP	ENST00000297954.4	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	17.42|17.42|17.42	3.384909|3.384909|3.384909	0.61956|0.61956|0.61956	.|.|.	.|.|.	ENSG00000165238|ENSG00000165238|ENSG00000165238	ENST00000297954;ENST00000395477;ENST00000349097;ENST00000427277|ENST00000411624|ENST00000432730;ENST00000448251	T;T;T;T|.|.	0.41400|.|.	1.0;1.0;1.0;1.0|.|.	5.95|5.95|5.95	-9.28|-9.28|-9.28	0.00656|0.00656|0.00656	.|.|.	0.600559|.|.	0.17654|.|.	N|.|.	0.166571|.|.	T|T|T	0.60287|0.60287|0.60287	0.2257|0.2257|0.2257	L|L|L	0.51422|0.51422|0.51422	1.61|1.61|1.61	0.49687|0.49687|0.49687	D|D|D	0.999815|0.999815|0.999815	D;B;B;D|.|.	0.67145|.|.	0.996;0.028;0.047;0.991|.|.	P;B;B;P|.|.	0.60117|.|.	0.869;0.012;0.027;0.675|.|.	T|T|T	0.68872|0.68872|0.68872	-0.5294|-0.5294|-0.5294	10|5|5	0.13470|.|.	T|.|.	0.59|.|.	.|.|.	15.7974|15.7974|15.7974	0.78423|0.78423|0.78423	0.3327:0.0843:0.583:0.0|0.3327:0.0843:0.583:0.0|0.3327:0.0843:0.583:0.0	.|.|.	1328;931;1328;1328|.|.	Q9Y3S1-2;A6PVR4;F8W9F9;Q9Y3S1|.|.	.;.;.;WNK2_HUMAN|.|.	D|F|I	1328;1328;940;940|932|1324;125	ENSP00000297954:E1328D;ENSP00000378860:E1328D;ENSP00000297876:E940D;ENSP00000411181:E940D|.|.	ENSP00000297954:E1328D|.|.	E|I|N	+|+|+	3|1|2	2|0|0	WNK2|WNK2|WNK2	95070800|95070800|95070800	0.000000|0.000000|0.000000	0.05858|0.05858|0.05858	0.000000|0.000000|0.000000	0.03702|0.03702|0.03702	0.388000|0.388000|0.388000	0.30384|0.30384|0.30384	-1.194000|-1.194000|-1.194000	0.03046|0.03046|0.03046	-1.603000|-1.603000|-1.603000	0.01597|0.01597|0.01597	-0.250000|-0.250000|-0.250000	0.11733|0.11733|0.11733	GAA|ATC|AAT	.	.	none		0.622	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648		T	96030979	A	T	96030979	3	4	29	1	0	0	0	0	1	0	0	0	17393	98	4	5	4054	5	WNK2	9	96030979	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	22	96030979	45182452	473	12714											
FAM22G	441457	hgsc.bcm.edu	37	chr9	99701002	99701002	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	accaaggacgccttgggtctCcctggagagtctcctgtcaa	8	9	11	13	1	3	1	1	0	2	1	5	3	3	2	4	3	0	0	4	3	2	1	rs199656301	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:99701002C>T	ENST00000372322.3	+	7	1818	c.1797C>T	c.(1795-1797)ctC>ctT	p.L599L	HIATL2_ENST00000506067.1_Intron|NUTM2G_ENST00000354649.3_Intron	NM_001170741.1	NP_001164212.1	Q5VZR2	NTM2G_HUMAN	NUT family member 2G	599																	CCTTGGGTCTCCCTGGAGAGT	0.637																																					p.L599L		Atlas-SNP	.											.	FAM22G	66	.	0			c.C1797T						PASS	.						9	14	12					9																	99701002		685	1576	2261	SO:0001819	synonymous_variant	441457	exon7			GGGTCTCCCTGGA		CCDS43854.1, CCDS55329.1	9q22.33	2013-05-02	2013-03-14	2013-05-02	ENSG00000188152	ENSG00000188152			23449	protein-coding gene	gene with protein product			"family with sequence similarity 22, member G"	FAM22G			Standard	NM_001045477		Approved			Q5VZR2	OTTHUMG00000020305	ENST00000372322.3:c.1797C>T	9.37:g.99701002C>T		315	0	0		360	124	0.344444	NM_001170741	A6NNI5|Q5VZR3	Silent	SNP	ENST00000372322.3	37	CCDS55329.1																																																																																			T|1.000;|0.000	1.000	weak		0.637	NUTM2G-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053291.2	NM_001170741		T	99701002	C	T	99701002	2	4	29	1	0	0	0	0	0	0	0	1	5551	842	30	2		2	FAM22G	9	99701002	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	3670023	99701002	41512429	474	12715											
TMOD1	7111	hgsc.bcm.edu	37	chr9	100331188	100331188	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttcaaggcccttgctgagAtgctcaaggagaacaaggtg	11	8	13	9	0	2	2	2	1	0	2	2	4	2	2	1	3	3	3	1	3	4	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:100331188A>T	ENST00000259365.4	+	8	952	c.739A>T	c.(739-741)Atg>Ttg	p.M247L	TMOD1_ENST00000375175.1_Missense_Mutation_p.M120L|TMOD1_ENST00000395211.2_Missense_Mutation_p.M247L	NM_003275.3	NP_003266.1	P28289	TMOD1_HUMAN	tropomodulin 1	247					adult locomotory behavior (GO:0008344)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)	cortical cytoskeleton (GO:0030863)|cytosol (GO:0005829)|membrane (GO:0016020)|myofibril (GO:0030016)				breast(1)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(2)|urinary_tract(1)	11		Acute lymphoblastic leukemia(62;0.154)		STAD - Stomach adenocarcinoma(157;0.105)		CCTTGCTGAGATGCTCAAGGA	0.527																																					p.M247L		Atlas-SNP	.											.	TMOD1	29	.	0			c.A739T						PASS	.						118	110	113					9																	100331188		2203	4300	6503	SO:0001583	missense	7111	exon8			GCTGAGATGCTCA		CCDS6726.1	9q22	2008-07-21		2003-03-21	ENSG00000136842	ENSG00000136842			11871	protein-coding gene	gene with protein product		190930		D9S57E, TMOD		1370827, 8661028	Standard	NM_003275		Approved	ETMOD	uc004axl.2	P28289	OTTHUMG00000020325	ENST00000259365.4:c.739A>T	9.37:g.100331188A>T	ENSP00000259365:p.Met247Leu	102	0	0		97	50	0.515464	NM_001166116	B2RB77|Q5T7W3|Q9BUF1	Missense_Mutation	SNP	ENST00000259365.4	37	CCDS6726.1	.	.	.	.	.	.	.	.	.	.	A	22.1	4.250806	0.80135	.	.	ENSG00000136842	ENST00000395211;ENST00000259365;ENST00000375175	D;D;D	0.92805	-3.11;-3.11;-3.11	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.93638	0.7968	M	0.64630	1.985	0.58432	D	0.999994	D	0.53885	0.963	P	0.56042	0.79	D	0.93032	0.6449	10	0.39692	T	0.17	-30.4856	14.4885	0.67634	1.0:0.0:0.0:0.0	.	247	P28289	TMOD1_HUMAN	L	247;247;120	ENSP00000378637:M247L;ENSP00000259365:M247L;ENSP00000364318:M120L	ENSP00000259365:M247L	M	+	1	0	TMOD1	99371009	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	7.109000	0.77062	2.135000	0.66039	0.460000	0.39030	ATG	.	.	none		0.527	TMOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053320.2	NM_003275		T	100331188	A	T	100331188	3	4	29	1	0	0	0	0	1	0	0	0	16248	333	12	5	765	5	TMOD1	9	100331188	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	630186	100331188	40882243	475	12716											
COL15A1	1306	hgsc.bcm.edu	37	chr9	101804366	101804366	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgacactggtttacctggcTttccaggactaaaaggagaa	12	10	11	8	0	0	2	0	1	0	1	1	4	1	3	2	4	1	2	2	4	4	4	rs35901514	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:101804366T>C	ENST00000375001.3	+	24	2974	c.2551T>C	c.(2551-2553)Ttt>Ctt	p.F851L		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	851	Collagen-like 3.|Triple-helical region 4 (COL4).				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)				TTTACCTGGCTTTCCAGGACT	0.423													T|||	16	0.00319489	0.0015	0.0058	5008	,	,		17702	0.0		0.008	False		,,,				2504	0.002				p.F851L		Atlas-SNP	.											.	COL15A1	211	.	0			c.T2551C						PASS	.	T	LEU/PHE	11,4395	17.9+/-39.9	0,11,2192	95	103	100		2551	5.9	1	9	dbSNP_126	100	108,8492	57.2+/-118.5	0,108,4192	yes	missense	COL15A1	NM_001855.3	22	0,119,6384	CC,CT,TT		1.2558,0.2497,0.915	probably-damaging	851/1389	101804366	119,12887	2203	4300	6503	SO:0001583	missense	1306	exon24			CCTGGCTTTCCAG	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.2551T>C	9.37:g.101804366T>C	ENSP00000364140:p.Phe851Leu	54	0	0		67	37	0.552239	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	37	CCDS35081.1	11	0.005036630036630037	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	T	19.54	3.846980	0.71603	0.002497	0.012558	ENSG00000204291	ENST00000375001	D	0.93133	-3.17	5.92	5.92	0.95590	.	0.251977	0.40818	N	0.001007	D	0.88815	0.6539	N	0.10760	0.04	0.40583	D	0.981411	D	0.69078	0.997	D	0.77004	0.989	D	0.88409	0.3020	10	0.20046	T	0.44	-12.7642	12.7552	0.57331	0.0:0.0:0.0:1.0	rs35901514	851	P39059	COFA1_HUMAN	L	851	ENSP00000364140:F851L	ENSP00000364140:F851L	F	+	1	0	COL15A1	100844187	0.997000	0.39634	1.000000	0.80357	0.986000	0.74619	2.145000	0.42207	2.270000	0.75569	0.459000	0.35465	TTT	T|0.993;C|0.007	0.007	strong		0.423	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855		C	101804366	T	C	101804366	3	2	29	1	0	0	0	0	1	0	0	0	3674	1609	56	3	2645	3	COL15A1	9	101804366	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	1473178	101804366	39409065	476	12717											
PTPN3	5774	hgsc.bcm.edu	37	chr9	112145817	112145817	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcggggggatctggccagtaCtggtgacatttggtctgtaa	7	12	15	7	1	2	1	0	1	2	0	3	2	2	2	1	6	1	2	1	6	2	3	rs146869100		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:112145817C>T	ENST00000374541.2	-	23	2372	c.2268G>A	c.(2266-2268)caG>caA	p.Q756Q	PTPN3_ENST00000446349.1_Silent_p.Q580Q|PTPN3_ENST00000412145.1_Silent_p.Q625Q|PTPN3_ENST00000262539.3_Silent_p.Q602Q|PTPN3_ENST00000394827.3_Silent_p.Q224Q	NM_001145368.1|NM_002829.3	NP_001138840.1|NP_002820.3	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type 3	756	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						CTGGCCAGTACTGGTGACATT	0.572													C|||	1	0.000199681	0.0	0.0	5008	,	,		17585	0.0		0.001	False		,,,				2504	0.0				p.Q756Q		Atlas-SNP	.											.	PTPN3	106	.	0			c.G2268A						PASS	.	C	,,,,,	3,4403	6.2+/-15.9	0,3,2200	121	113	116		2133,1875,1740,1407,1272,2268	4.8	1	9	dbSNP_134	116	18,8582	12.6+/-44.7	0,18,4282	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPN3	NM_001145368.1,NM_001145369.1,NM_001145370.1,NM_001145371.1,NM_001145372.1,NM_002829.3	,,,,,	0,21,6482	TT,TC,CC		0.2093,0.0681,0.1615	,,,,,	711/869,625/783,580/738,469/627,424/582,756/914	112145817	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	5774	exon23			CCAGTACTGGTGA		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.2268G>A	9.37:g.112145817C>T		82	0	0		79	41	0.518987	NM_002829	A0AUW9|E7EN99|E9PGU7	Silent	SNP	ENST00000374541.2	37	CCDS6776.1																																																																																			C|0.998;T|0.002	0.002	strong		0.572	PTPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053598.4			T	112145817	C	T	112145817	2	4	29	1	0	0	0	0	0	0	0	1	12804	564	20	2		2	PTPN3	9	112145817	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	10341451	112145817	29067614	477	12718											
ALAD	210	hgsc.bcm.edu	37	chr9	116152915	116152915	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacctcagccagccgctggcGgctctcctcagcccggaatg	6	6	11	18	3	3	0	2	0	1	0	4	1	3	1	5	3	3	2	5	3	1	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:116152915G>A	ENST00000409155.3	-	6	635	c.439C>T	c.(439-441)Cgc>Tgc	p.R147C	ALAD_ENST00000277315.5_Missense_Mutation_p.R130C|ALAD_ENST00000482001.1_5'Flank	NM_000031.5	NP_000022.3	P13716	HEM2_HUMAN	aminolevulinate dehydratase	147					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)	AGCCGCTGGCGGCTCTCCTCA	0.632																																					p.R147C		Atlas-SNP	.											.	ALAD	36	.	0			c.C439T						PASS	.						31	33	32					9																	116152915		2203	4300	6503	SO:0001583	missense	210	exon6			GCTGGCGGCTCTC	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.439C>T	9.37:g.116152915G>A	ENSP00000386284:p.Arg147Cys	40	0	0		29	16	0.551724	NM_000031	A8K375|B2R6F2|Q16870|Q16871|Q9BVQ9	Missense_Mutation	SNP	ENST00000409155.3	37	CCDS6794.2	.	.	.	.	.	.	.	.	.	.	G	12.42	1.933839	0.34096	.	.	ENSG00000148218	ENST00000409155;ENST00000277315	D;D	0.86865	-2.18;-2.18	5.8	3.72	0.42706	Aldolase-type TIM barrel (1);	0.131674	0.64402	N	0.000001	T	0.63438	0.2511	N	0.01277	-0.915	0.47476	D	0.999439	B;B;B	0.09022	0.001;0.001;0.002	B;B;B	0.09377	0.001;0.003;0.004	T	0.59490	-0.7445	10	0.56958	D	0.05	-6.8616	3.4528	0.07505	0.2886:0.0:0.487:0.2244	.	147;130;176	P13716;B7Z3I9;P13716-2	HEM2_HUMAN;.;.	C	147;130	ENSP00000386284:R147C;ENSP00000277315:R130C	ENSP00000277315:R130C	R	-	1	0	ALAD	115192736	1.000000	0.71417	1.000000	0.80357	0.728000	0.41692	4.589000	0.61006	1.358000	0.45922	-0.345000	0.07892	CGC	.	.	none		0.632	ALAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053724.3	NM_001003945		A	116152915	G	A	116152915	3	1	29	1	0	0	0	0	1	0	0	0	483	1116	39	1	581	1	ALAD	9	116152915	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	4007098	116152915	25060516	478	12719											
COL27A1	85301	hgsc.bcm.edu	37	chr9	117029826	117029826	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaccgggccttcctggggaaGccgggatgaaggtgaggtgg	8	6	19	8	2	0	2	0	2	0	0	1	4	1	4	4	7	2	0	4	7	3	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:117029826G>A	ENST00000356083.3	+	34	3881	c.3490G>A	c.(3490-3492)Gcc>Acc	p.A1164T		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1164	Collagen-like 9.|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						TCCTGGGGAAGCCGGGATGAA	0.562																																					p.A1164T		Atlas-SNP	.											.	COL27A1	200	.	0			c.G3490A						PASS	.						78	90	86					9																	117029826		2203	4300	6503	SO:0001583	missense	85301	exon34			GGGGAAGCCGGGA	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.3490G>A	9.37:g.117029826G>A	ENSP00000348385:p.Ala1164Thr	53	0	0		61	4	0.0655738	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	37	CCDS6802.1	.	.	.	.	.	.	.	.	.	.	G	15.23	2.771909	0.49680	.	.	ENSG00000196739	ENST00000356083;ENST00000357257	D	0.93426	-3.22	5.22	3.18	0.36537	.	.	.	.	.	D	0.83608	0.5291	N	0.11673	0.155	0.22292	N	0.999229	B	0.30793	0.295	B	0.29267	0.1	T	0.73379	-0.4001	9	0.26408	T	0.33	.	7.4249	0.27094	0.0:0.1776:0.6234:0.199	.	1164	Q8IZC6	CORA1_HUMAN	T	1164	ENSP00000348385:A1164T	ENSP00000348385:A1164T	A	+	1	0	COL27A1	116069647	1.000000	0.71417	0.991000	0.47740	0.948000	0.59901	1.803000	0.38863	1.141000	0.42275	0.462000	0.41574	GCC	.	.	none		0.562	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888		A	117029826	G	A	117029826	3	1	29	1	0	0	0	0	1	0	0	0	3687	971	34	2	3624	2	COL27A1	9	117029826	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	876911	117029826	24183605	479	12720											
TLR4	7099	hgsc.bcm.edu	37	chr9	120476365	120476365	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtagcagttctggtctataaGttctattttcacctgatgct	8	17	8	8	0	4	1	1	1	3	0	4	1	4	1	1	1	2	5	1	1	4	8	rs5030721	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:120476365G>A	ENST00000355622.6	+	3	2060	c.1959G>A	c.(1957-1959)aaG>aaA	p.K653K	TLR4_ENST00000394487.4_Silent_p.K613K|TLR4_ENST00000472304.1_3'UTR	NM_138554.4|NM_138557.2	NP_612564.1|NP_612567.1	O00206	TLR4_HUMAN	toll-like receptor 4	653					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)	TGGTCTATAAGTTCTATTTTC	0.418													G|||	24	0.00479233	0.0008	0.0014	5008	,	,		20759	0.001		0.0099	False		,,,				2504	0.0112				p.K653K		Atlas-SNP	.											.	TLR4	220	.	0			c.G1959A						PASS	.	G		8,4398	14.3+/-33.2	0,8,2195	158	139	145		1959	1	1	9	dbSNP_113	145	99,8501	54.0+/-114.7	0,99,4201	no	coding-synonymous	TLR4	NM_138554.3		0,107,6396	AA,AG,GG		1.1512,0.1816,0.8227		653/840	120476365	107,12899	2203	4300	6503	SO:0001819	synonymous_variant	7099	exon3			CTATAAGTTCTAT	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.1959G>A	9.37:g.120476365G>A		57	0	0		61	24	0.393443	NM_138554	A8K1Y8|A9XLP9|A9XLQ0|A9XLQ1|B4E194|D1CS52|D1CS53|Q5VZI8|Q5VZI9|Q9UK78|Q9UM57	Silent	SNP	ENST00000355622.6	37	CCDS6818.1																																																																																			G|0.993;A|0.007	0.007	strong		0.418	TLR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055549.3	NM_138554		A	120476365	G	A	120476365	2	1	29	1	0	0	0	0	0	0	0	1	15968	1020	36	2		2	TLR4	9	120476365	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	3446539	120476365	20737066	480	12721											
OR1L3	26735	hgsc.bcm.edu	37	chr9	125437664	125437664	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caaagatgctcgtgaacttcTtatcagagaaaaagaccatt	16	10	7	8	1	2	4	1	1	1	3	3	5	2	4	1	0	2	1	1	0	5	3	rs56304399	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:125437664T>G	ENST00000304820.2	+	1	350	c.256T>G	c.(256-258)Tta>Gta	p.L86V		NM_001005234.1	NP_001005234.1	Q8NH93	OR1L3_HUMAN	olfactory receptor, family 1, subfamily L, member 3	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)|kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	16						CGTGAACTTCTTATCAGAGAA	0.403													T|||	19	0.00379393	0.0015	0.0072	5008	,	,		24153	0.0		0.0119	False		,,,				2504	0.0				p.L86V		Atlas-SNP	.											.	OR1L3	51	.	0			c.T256G						PASS	.	T	VAL/LEU	6,4400	11.4+/-27.6	0,6,2197	161	159	160		256	-2.4	0.4	9	dbSNP_129	160	82,8518	48.1+/-107.5	2,78,4220	yes	missense	OR1L3	NM_001005234.1	32	2,84,6417	GG,GT,TT		0.9535,0.1362,0.6766	probably-damaging	86/325	125437664	88,12918	2203	4300	6503	SO:0001583	missense	26735	exon1			AACTTCTTATCAG		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.256T>G	9.37:g.125437664T>G	ENSP00000302863:p.Leu86Val	124	0	0		132	72	0.545455	NM_001005234	B2RNF4|Q6IFN1	Missense_Mutation	SNP	ENST00000304820.2	37	CCDS35128.1	14	0.00641025641025641	0	0.0	4	0.011049723756906077	0	0.0	10	0.013192612137203167	T	13.22	2.171475	0.38315	0.001362	0.009535	ENSG00000171481	ENST00000304820	T	0.10288	2.89	4.54	-2.43	0.06522	GPCR, rhodopsin-like superfamily (1);	0.286366	0.17522	U	0.171239	T	0.08802	0.0218	L	0.39898	1.24	0.09310	N	1	D	0.61697	0.99	D	0.63381	0.914	T	0.19647	-1.0299	10	0.22109	T	0.4	-5.4795	1.9974	0.03459	0.1313:0.3675:0.2093:0.2919	rs56304399	86	Q8NH93	OR1L3_HUMAN	V	86	ENSP00000302863:L86V	ENSP00000302863:L86V	L	+	1	2	OR1L3	124477485	0.000000	0.05858	0.360000	0.25837	0.990000	0.78478	-0.099000	0.11007	-0.170000	0.10816	0.524000	0.50904	TTA	T|0.993;G|0.007	0.007	strong		0.403	OR1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053950.1			G	125437664	T	G	125437664	3	3	29	1	0	0	0	0	1	0	0	0	10973	1606	56	5	258	5	OR1L3	9	125437664	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	4961299	125437664	15775767	481	12722											
FAM129B	64855	hgsc.bcm.edu	37	chr9	130270782	130270782	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ttccccagctcctggtgcagGagggtctcgaacgtatacac	8	9	11	13	2	1	0	0	0	1	0	4	2	3	1	3	3	4	3	3	3	3	3	rs11545937	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:130270782G>A	ENST00000373312.3	-	11	1566	c.1353C>T	c.(1351-1353)ctC>ctT	p.L451L	FAM129B_ENST00000468379.1_Intron|FAM129B_ENST00000373314.3_Silent_p.L438L	NM_022833.2	NP_073744.2	Q96TA1	NIBL1_HUMAN	family with sequence similarity 129, member B	451					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						CCTGGTGCAGGAGGGTCTCGA	0.652													G|||	118	0.0235623	0.0045	0.0389	5008	,	,		17611	0.0		0.0596	False		,,,				2504	0.0256				p.L451L		Atlas-SNP	.											.	FAM129B	84	.	0			c.C1353T						PASS	.	G	,	56,4350	55.5+/-91.7	0,56,2147	137	133	135		1314,1353	-1.5	1	9	dbSNP_120	135	570,8030	153.9+/-208.2	20,530,3750	no	coding-synonymous,coding-synonymous	FAM129B	NM_001035534.1,NM_022833.2	,	20,586,5897	AA,AG,GG		6.6279,1.271,4.8132	,	438/734,451/747	130270782	626,12380	2203	4300	6503	SO:0001819	synonymous_variant	64855	exon11			GTGCAGGAGGGTC	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.1353C>T	9.37:g.130270782G>A		47	0	0		41	17	0.414634	NM_022833	Q4LE55|Q5VVW6|Q5VVW7|Q9BUS2|Q9NT35	Silent	SNP	ENST00000373312.3	37	CCDS35145.1																																																																																			G|0.957;C|0.000;A|0.043	0.043	strong		0.652	FAM129B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054196.1	NM_022833		A	130270782	G	A	130270782	2	1	29	1	0	0	0	0	0	0	0	1	5442	1161	41	2		2	FAM129B	9	130270782	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	4833118	130270782	10942649	482	12723											
FAM102A	399665	hgsc.bcm.edu	37	chr9	130742413	130742413	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cttcttcttcatcaagaaagCcatgagcgagttccctgagt	10	12	8	11	1	4	3	2	2	2	1	5	4	5	3	2	0	2	1	2	0	2	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:130742413C>T	ENST00000373095.1	-	1	379	c.4G>A	c.(4-6)Gct>Act	p.A2T		NM_001035254.2	NP_001030331.1	Q5T9C2	F102A_HUMAN	family with sequence similarity 102, member A	2										breast(1)|cervix(1)|large_intestine(3)|lung(1)|ovary(4)	10						ATCAAGAAAGCCATGAGCGAG	0.517																																					p.A2T		Atlas-SNP	.											.	FAM102A	32	.	0			c.G4A						PASS	.						89	103	98					9																	130742413		2203	4300	6503	SO:0001583	missense	399665	exon1			AGAAAGCCATGAG		CCDS6888.1, CCDS35150.1	9q34.11	2012-11-05	2005-11-17	2005-11-17	ENSG00000167106	ENSG00000167106			31419	protein-coding gene	gene with protein product	"sym-3 homolog A (C. elegans)"	610891	"chromosome 9 open reading frame 132"	C9orf132			Standard	NM_001035254		Approved	Eeig1, bA203J24.7, SYM-3A	uc004bsx.2	Q5T9C2	OTTHUMG00000020720	ENST00000373095.1:c.4G>A	9.37:g.130742413C>T	ENSP00000362187:p.Ala2Thr	65	0	0		66	15	0.227273	NM_001035254	A2A329|Q8TEL4	Missense_Mutation	SNP	ENST00000373095.1	37	CCDS35150.1	.	.	.	.	.	.	.	.	.	.	C	16.50	3.141355	0.57044	.	.	ENSG00000167106	ENST00000373095	.	.	.	4.76	4.76	0.60689	.	0.117104	0.56097	D	0.000025	T	0.54013	0.1832	L	0.43152	1.355	0.80722	D	1	B	0.29162	0.235	B	0.17098	0.017	T	0.55023	-0.8205	9	0.42905	T	0.14	-9.6451	16.7632	0.85517	0.0:1.0:0.0:0.0	.	2	Q5T9C2	F102A_HUMAN	T	2	.	ENSP00000362187:A2T	A	-	1	0	FAM102A	129782234	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.711000	0.54868	2.185000	0.69588	0.462000	0.41574	GCT	.	.	none		0.517	FAM102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054298.2			T	130742413	C	T	130742413	3	4	29	1	0	0	0	0	1	0	0	0	5387	739	26	2	1194	2	FAM102A	9	130742413	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	471631	130742413	10471018	483	12724											
PKN3	29941	hgsc.bcm.edu	37	chr9	131469190	131469190	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacagggcctgagctgctggCggaggagctacagcatcgac	9	5	15	12	2	0	1	0	1	0	0	1	4	0	3	1	4	5	4	1	4	1	1	rs56251280	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:131469190C>A	ENST00000291906.4	+	5	932	c.539C>A	c.(538-540)gCg>gAg	p.A180E	RN7SL560P_ENST00000577943.1_RNA	NM_013355.3	NP_037487.2	Q6P5Z2	PKN3_HUMAN	protein kinase N3	180			A -> E (in dbSNP:rs56251280). {ECO:0000269|PubMed:17344846}.		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						GAGCTGCTGGCGGAGGAGCTA	0.647													C|||	9	0.00179712	0.0	0.0043	5008	,	,		20063	0.0		0.004	False		,,,				2504	0.002				p.A180E		Atlas-SNP	.											.	PKN3	62	.	0			c.C539A						PASS	.	C	GLU/ALA	3,4401	8.1+/-20.4	0,3,2199	49	53	51		539	0.7	0.2	9	dbSNP_129	51	53,8547	33.3+/-86.6	0,53,4247	yes	missense	PKN3	NM_013355.3	107	0,56,6446	AA,AC,CC		0.6163,0.0681,0.4306	benign	180/890	131469190	56,12948	2202	4300	6502	SO:0001583	missense	29941	exon5			TGCTGGCGGAGGA	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.539C>A	9.37:g.131469190C>A	ENSP00000291906:p.Ala180Glu	49	0	0		60	33	0.55	NM_013355	Q9UM03	Missense_Mutation	SNP	ENST00000291906.4	37	CCDS6908.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	C	14.24	2.475101	0.43942	6.81E-4	0.006163	ENSG00000160447	ENST00000291906	T	0.30714	1.52	5.18	0.681	0.17986	.	.	.	.	.	T	0.28928	0.0718	L	0.36672	1.1	0.25043	N	0.991189	P;D	0.55172	0.917;0.97	P;P	0.60236	0.834;0.871	T	0.14671	-1.0464	9	0.66056	D	0.02	.	7.5493	0.27786	0.0:0.4389:0.0:0.5611	rs56251280	180;180	Q05BU1;Q6P5Z2	.;PKN3_HUMAN	E	180	ENSP00000291906:A180E	ENSP00000291906:A180E	A	+	2	0	PKN3	130509011	0.983000	0.35010	0.242000	0.24170	0.746000	0.42486	2.163000	0.42377	0.060000	0.16281	0.561000	0.74099	GCG	C|0.996;A|0.004	0.004	strong		0.647	PKN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054487.1	NM_013355		A	131469190	C	A	131469190	3	1	29	1	0	0	0	0	1	0	0	0	11990	768	27	4	557	4	PKN3	9	131469190	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	726777	131469190	9744241	484	12725											
C9orf114	51490	hgsc.bcm.edu	37	chr9	131585086	131585086	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tggatgaggccaggctgcagGgcggccagggagatgaggat	9	5	20	7	1	0	3	0	2	0	1	0	6	0	5	2	7	1	2	2	7	0	0	rs35677895	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:131585086G>C	ENST00000361256.5	-	12	1129	c.1089C>G	c.(1087-1089)gcC>gcG	p.A363A		NM_016390.3	NP_057474.2	Q5T280	CI114_HUMAN	chromosome 9 open reading frame 114	363							poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(4)|ovary(1)	7						CAGGCTGCAGGGCGGCCAGGG	0.662													G|||	25	0.00499201	0.0015	0.0058	5008	,	,		16485	0.0		0.0179	False		,,,				2504	0.001				p.A363A		Atlas-SNP	.											.	C9orf114	28	.	0			c.C1089G						PASS	.	G		13,4367		0,13,2177	33	33	33		1089	2	1	9	dbSNP_126	33	157,8421		0,157,4132	no	coding-synonymous	C9orf114	NM_016390.2		0,170,6309	CC,CG,GG		1.8303,0.2968,1.3119		363/377	131585086	170,12788	2190	4289	6479	SO:0001819	synonymous_variant	51490	exon12			CTGCAGGGCGGCC		CCDS6913.1	9q34.11	2014-05-29			ENSG00000198917	ENSG00000198917			26933	protein-coding gene	gene with protein product	"centromere protein 32"					20813266	Standard	NM_016390		Approved	HSPC109, CENP-32	uc004bwd.3	Q5T280	OTTHUMG00000020762	ENST00000361256.5:c.1089C>G	9.37:g.131585086G>C		97	0	0		119	63	0.529412	NM_016390	Q0D2P6|Q6P469|Q6PGP9|Q6PIJ1|Q6PJV9	Silent	SNP	ENST00000361256.5	37	CCDS6913.1	18	0.008241758241758242	0	0.0	2	0.0055248618784530384	0	0.0	16	0.021108179419525065	G	11.45	1.642891	0.29246	0.002968	0.018303	ENSG00000198917	ENST00000372618	.	.	.	4.91	1.98	0.26296	.	0.844601	0.10689	N	0.645425	T	0.18173	0.0436	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.24012	-1.0172	8	0.28530	T	0.3	-7.5275	1.3407	0.02154	0.2665:0.1449:0.44:0.1486	rs35677895	362	E7ESY7	.	R	362	.	ENSP00000361701:P362R	P	-	2	0	C9orf114	130624907	0.753000	0.28349	0.989000	0.46669	0.966000	0.64601	-0.116000	0.10724	0.644000	0.30656	0.455000	0.32223	CCC	G|0.990;C|0.010	0.010	strong		0.662	C9orf114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054500.1	NM_016390		C	131585086	G	C	131585086	2	2	29	1	0	0	0	0	0	0	0	1	2451	1219	43	4		4	C9orf114	9	131585086	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	115896	131585086	9628345	485	12726											
C9orf98	158067	hgsc.bcm.edu	37	chr9	135703450	135703450	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtttctctcgatcaggaccGtgtctggagcactcagcaca	9	10	10	12	2	4	0	2	0	2	0	6	3	4	2	1	2	2	3	1	2	0	1	rs114347984	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:135703450G>T	ENST00000298545.3	-	7	1027	c.506C>A	c.(505-507)aCg>aAg	p.T169K	AK8_ENST00000477396.1_5'UTR	NM_152572.2	NP_689785.1	Q96MA6	KAD8_HUMAN	adenylate kinase 8	169	Adenylate kinase 1.				nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			NS(1)|kidney(2)|large_intestine(4)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(2)	23						GATCAGGACCGTGTCTGGAGC	0.547													G|||	10	0.00199681	0.0076	0.0	5008	,	,		19731	0.0		0.0	False		,,,				2504	0.0				p.T169K		Atlas-SNP	.											.	AK8	45	.	0			c.C506A						PASS	.	G	LYS/THR	38,4368		0,38,2165	74	53	60		506	1.8	0	9	dbSNP_132	60	6,8592		0,6,4293	yes	missense	AK8	NM_152572.2	78	0,44,6458	TT,TG,GG		0.0698,0.8625,0.3384	benign	169/480	135703450	44,12960	2203	4299	6502	SO:0001583	missense	158067	exon7			AGGACCGTGTCTG	AK093446	CCDS6954.1	9q34.13	2013-04-29	2010-12-07	2010-12-07	ENSG00000165695	ENSG00000165695	2.7.4.3	"Adenylate kinases"	26526	protein-coding gene	gene with protein product		615365	"chromosome 9 open reading frame 98"	C9orf98		21080915	Standard	NM_152572		Approved	FLJ32704	uc004cbu.1	Q96MA6	OTTHUMG00000021009	ENST00000298545.3:c.506C>A	9.37:g.135703450G>T	ENSP00000298545:p.Thr169Lys	55	0	0		49	18	0.367347	NM_152572	A8K821|Q8N9W9	Missense_Mutation	SNP	ENST00000298545.3	37	CCDS6954.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	9.781	1.175339	0.21704	0.008625	6.98E-4	ENSG00000165695	ENST00000298545	T	0.39997	1.05	5.78	1.84	0.25277	.	0.528145	0.21938	N	0.066940	T	0.28433	0.0703	L	0.53249	1.67	0.19775	N	0.999957	B	0.32939	0.391	B	0.38655	0.278	T	0.19257	-1.0311	10	0.17832	T	0.49	-9.7495	8.0442	0.30540	0.403:0.0:0.597:0.0	.	169	Q96MA6	KAD8_HUMAN	K	169	ENSP00000298545:T169K	ENSP00000298545:T169K	T	-	2	0	AK8	134693271	0.041000	0.20044	0.007000	0.13788	0.018000	0.09664	0.259000	0.18405	0.065000	0.16485	-0.244000	0.11960	ACG	G|0.997;T|0.003	0.003	strong		0.547	AK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055413.1	NM_152572		T	135703450	G	T	135703450	3	4	29	1	0	0	0	0	1	0	0	0	2511	1145	40	4	961	4	C9orf98	9	135703450	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	4118364	135703450	5509981	486	12727											
CEL	1056	hgsc.bcm.edu	37	chr9	135942008	135942008	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaccccaacaacatcacgctCttcggggagtctgctggagg	9	7	12	13	2	3	0	1	0	2	0	4	3	3	2	2	4	3	2	2	4	2	1	rs529444912		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:135942008C>T	ENST00000372080.4	+	5	655	c.639C>T	c.(637-639)ctC>ctT	p.L213L	CEL_ENST00000351304.7_Silent_p.L210L	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	210					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)		ACATCACGCTCTTCGGGGAGT	0.617													C|||	1	0.000199681	0.0008	0.0	5008	,	,		14997	0.0		0.0	False		,,,				2504	0.0				p.L213L		Atlas-SNP	.											.	CEL	71	.	0			c.C639T						PASS	.						86	96	93					9																	135942008		1964	4160	6124	SO:0001819	synonymous_variant	1056	exon5			CACGCTCTTCGGG	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.639C>T	9.37:g.135942008C>T		33	0	0		52	26	0.5	NM_001807	Q16398|Q5T7U7|Q9UCH1|Q9UP41	Silent	SNP	ENST00000372080.4	37	CCDS43896.1																																																																																			.	.	none		0.617	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054823.1			T	135942008	C	T	135942008	2	4	29	1	0	0	0	0	0	0	0	1	3211	900	32	2		2	CEL	9	135942008	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	238558	135942008	5271423	487	12728											
ADAMTS13	11093	hgsc.bcm.edu	37	chr9	136320665	136320665	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcccggggcctgctcttcTccccggctccccagcctcgg	2	7	12	20	3	2	0	0	0	2	0	5	0	3	0	7	5	2	2	7	5	0	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:136320665T>C	ENST00000371929.3	+	25	3952	c.3508T>C	c.(3508-3510)Tcc>Ccc	p.S1170P	ADAMTS13_ENST00000485925.1_Intron|ADAMTS13_ENST00000371916.1_3'UTR|ADAMTS13_ENST00000355699.2_Intron|ADAMTS13_ENST00000356589.2_Intron|ADAMTS13_ENST00000371910.1_5'Flank	NM_139025.3|NM_139027.3	NP_620594.1|NP_620596.2	Q76LX8	ATS13_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 13	1170					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)		CCTGCTCTTCTCCCCGGCTCC	0.687																																					p.S1170P		Atlas-SNP	.											.	ADAMTS13	113	.	0			c.T3508C						PASS	.						29	37	34					9																	136320665		2187	4277	6464	SO:0001583	missense	11093	exon25			CTCTTCTCCCCGG	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.3508T>C	9.37:g.136320665T>C	ENSP00000360997:p.Ser1170Pro	47	0	0		35	19	0.542857	NM_139025	Q6UY16|Q710F6|Q711T8|Q96L37|Q9H0G3|Q9UGQ1	Missense_Mutation	SNP	ENST00000371929.3	37	CCDS6970.1	.	.	.	.	.	.	.	.	.	.	T	8.768	0.925251	0.18056	.	.	ENSG00000160323	ENST00000371929	D	0.81996	-1.56	5.21	1.62	0.23740	.	.	.	.	.	T	0.69949	0.3168	L	0.31294	0.92	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.53143	-0.8480	8	.	.	.	.	6.5444	0.22398	0.0:0.4072:0.0:0.5928	.	1170	Q76LX8	ATS13_HUMAN	P	1170	ENSP00000360997:S1170P	.	S	+	1	0	ADAMTS13	135310486	0.000000	0.05858	0.023000	0.16930	0.035000	0.12851	-0.151000	0.10175	0.310000	0.22990	0.459000	0.35465	TCC	.	.	none		0.687	ADAMTS13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054920.1	NM_139025		C	136320665	T	C	136320665	3	2	29	1	0	0	0	0	1	0	0	0	258	1551	54	3	3606	3	ADAMTS13	9	136320665	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	378657	136320665	4892766	488	12729											
ABCA2	20	hgsc.bcm.edu	37	chr9	139904722	139904722	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgaaggtgctggtcttgccCgcaccgttgacgcccaggag	6	9	14	12	3	1	2	0	2	1	0	1	3	1	3	3	3	2	3	3	3	1	3	rs34125425	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139904722C>T	ENST00000371605.3	-	40	6420	c.6273G>A	c.(6271-6273)gcG>gcA	p.A2091A	ABCA2_ENST00000341511.6_Silent_p.A2092A|ABCA2_ENST00000265662.5_Silent_p.A2092A			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	2091	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)		TGGTCTTGCCCGCACCGTTGA	0.667													C|||	66	0.0131789	0.0008	0.0288	5008	,	,		11162	0.0		0.0278	False		,,,				2504	0.0174				p.A2122A		Atlas-SNP	.											.	ABCA2	113	.	0			c.G6366A						PASS	.	C	,	18,4210		0,18,2096	12	15	14		6276,6366	-6.7	0.4	9	dbSNP_126	14	212,8236		1,210,4013	yes	coding-synonymous,coding-synonymous	ABCA2	NM_001606.4,NM_212533.2	,	1,228,6109	TT,TC,CC		2.5095,0.4257,1.8145	,	2092/2437,2122/2467	139904722	230,12446	2114	4224	6338	SO:0001819	synonymous_variant	20	exon41			CTTGCCCGCACCG	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.6273G>A	9.37:g.139904722C>T		60	0	0		63	30	0.47619	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Silent	SNP	ENST00000371605.3	37																																																																																				C|0.984;T|0.016	0.016	strong		0.667	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606		T	139904722	C	T	139904722	2	4	29	1	0	0	0	0	0	0	0	1	32	639	23	1		1	ABCA2	9	139904722	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	3584057	139904722	1308709	489	12730											
C9orf140	89958	hgsc.bcm.edu	37	chr9	139959231	139959231	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgatgcgctcactcttctcGgtcacctcctgggcaggtgc	4	11	12	14	2	4	1	2	1	2	0	6	1	5	1	2	3	2	2	2	3	0	1	rs140919217	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr9:139959231G>A	ENST00000409687.3	-	6	1192	c.1065C>T	c.(1063-1065)acC>acT	p.T355T	RP11-229P13.22_ENST00000435463.2_RNA|RP11-229P13.23_ENST00000456356.2_RNA	NM_178448.3	NP_848543.2	Q86UD0	SAPC2_HUMAN	suppressor APC domain containing 2	355						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)											CACTCTTCTCGGTCACCTCCT	0.677											OREG0019628	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	15	0.00299521	0.0023	0.0043	5008	,	,		15193	0.0		0.008	False		,,,				2504	0.001				p.T355T		Atlas-SNP	.											.	.	.	.	0			c.C1065T						PASS	.	G		9,4377		0,9,2184	40	36	37		1065	-7.7	0.6	9	dbSNP_134	37	59,8523		0,59,4232	no	coding-synonymous	C9orf140	NM_178448.3		0,68,6416	AA,AG,GG		0.6875,0.2052,0.5244		355/395	139959231	68,12900	2193	4291	6484	SO:0001819	synonymous_variant	89958	exon6			CTTCTCGGTCACC	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.1065C>T	9.37:g.139959231G>A		114	0	0	1652	112	59	0.526786	NM_178448		Silent	SNP	ENST00000409687.3	37	CCDS7027.2																																																																																			G|0.995;A|0.005	0.005	strong		0.677	SAPCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055215.2	NM_178448		A	139959231	G	A	139959231	2	1	29	1	0	0	0	0	0	0	0	1	2462	1103	39	1		1	C9orf140	9	139959231	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	54509	139959231	1254200	490	12731											
ADARB2	105	hgsc.bcm.edu	37	chr10	1246060	1246060	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tccacgaagtgggacaggagCgcgccctgcagccccaggac	9	3	14	15	3	0	0	0	0	0	0	1	4	1	3	4	3	3	1	4	3	1	0	rs138375235	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:1246060C>T	ENST00000381312.1	-	8	2035	c.1710G>A	c.(1708-1710)gcG>gcA	p.A570A	ADARB2_ENST00000381305.1_5'UTR|ADARB2_ENST00000381310.3_Silent_p.A79A	NM_018702.3	NP_061172.1	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2 (non-functional)	570	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				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)		GGGACAGGAGCGCGCCCTGCA	0.692													C|||	4	0.000798722	0.0	0.0029	5008	,	,		16229	0.0		0.002	False		,,,				2504	0.0				p.A570A		Atlas-SNP	.											.	ADARB2	95	.	0			c.G1710A						PASS	.	C		3,4293		0,3,2145	23	21	22		1710	-11.5	0	10	dbSNP_134	22	11,8469		0,11,4229	no	coding-synonymous	ADARB2	NM_018702.3		0,14,6374	TT,TC,CC		0.1297,0.0698,0.1096		570/740	1246060	14,12762	2148	4240	6388	SO:0001819	synonymous_variant	105	exon8			CAGGAGCGCGCCC	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.1710G>A	10.37:g.1246060C>T		47	0	0		44	31	0.704545	NM_018702	B2RPJ5|Q5VUT6|Q5VW42	Silent	SNP	ENST00000381312.1	37	CCDS7058.1																																																																																			C|0.997;T|0.003	0.003	strong		0.692	ADARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046426.1	NM_018702		T	1246060	C	T	1246060	2	4	29	1	0	0	0	0	0	0	0	1	283	755	27	1		1	ADARB2	10	1246060	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10		1246060	134288687	491	12732											
SFMBT2	57713	hgsc.bcm.edu	37	chr10	7412243	7412243	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acacaagctgctttacatacGtgtttgaatgatgtgtgggg	10	13	12	6	1	0	2	0	2	0	0	0	2	0	2	0	2	4	3	0	2	4	4	rs142871492	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:7412243G>A	ENST00000361972.4	-	3	285	c.195C>T	c.(193-195)caC>caT	p.H65H	SFMBT2_ENST00000397167.1_Splice_Site_p.H65H|SFMBT2_ENST00000379711.2_Splice_Site_p.H65H|SFMBT2_ENST00000397160.3_Splice_Site_p.H65H|SFMBT2_ENST00000379713.3_Splice_Site_p.H65H	NM_001018039.1	NP_001018049.1	Q5VUG0	SMBT2_HUMAN	Scm-like with four mbt domains 2	65					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						CTTTACATACGTGTTTGAATG	0.473													G|||	3	0.000599042	0.0015	0.0	5008	,	,		20525	0.0		0.001	False		,,,				2504	0.0				p.H65H		Atlas-SNP	.											.	SFMBT2	209	.	0			c.C195T						PASS	.	G	,	6,4400	11.4+/-27.6	0,6,2197	118	107	111		195,195	-6.2	0.8	10	dbSNP_134	111	38,8562	26.3+/-74.7	0,38,4262	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	SFMBT2	NM_001018039.1,NM_001029880.2	,	0,44,6459	AA,AG,GG		0.4419,0.1362,0.3383	,	65/895,65/895	7412243	44,12962	2203	4300	6503	SO:0001630	splice_region_variant	57713	exon3			ACATACGTGTTTG	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.195+1C>T	10.37:g.7412243G>A		119	0	0		73	32	0.438356	NM_001029880	A7MD09|Q9HCF5	Silent	SNP	ENST00000361972.4	37	CCDS31138.1																																																																																			G|0.997;A|0.003	0.003	strong		0.473	SFMBT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046673.1	NM_001029880	Silent	A	7412243	G	A	7412243	5	1	29	1	0	0	0	0	0	0	1	0	14173	1159	40	1	2565	1	SFMBT2	10	7412243	Splice_Site	SNP	G	TCGA-GR-7351-01A-11D-2210-10	6166183	7412243	128122504	492	12733											
MASTL	84930	hgsc.bcm.edu	37	chr10	27462061	27462061	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aattagcagaccccaaatcaGatcaagtcgggaactccata	16	7	7	11	1	2	2	2	0	0	2	4	3	3	3	3	1	2	1	3	1	6	2	rs41282228	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:27462061G>A	ENST00000375940.4	+	9	2196	c.2139G>A	c.(2137-2139)caG>caA	p.Q713Q	MASTL_ENST00000342386.6_Silent_p.Q712Q|MASTL_ENST00000375946.4_Silent_p.Q712Q|MASTL_ENST00000477034.1_3'UTR			Q96GX5	GWL_HUMAN	microtubule associated serine/threonine kinase-like	713	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						CCCCAAATCAGATCAAGTCGG	0.438													G|||	50	0.00998403	0.0008	0.0029	5008	,	,		17354	0.0		0.0199	False		,,,				2504	0.0276				p.Q713Q		Atlas-SNP	.											.	MASTL	81	.	0			c.G2139A						PASS	.	G	,,	12,4394	19.1+/-41.9	0,12,2191	158	166	163		2139,2136,2136	1.3	0	10	dbSNP_127	163	151,8449	72.9+/-135.5	2,147,4151	no	coding-synonymous,coding-synonymous,coding-synonymous	MASTL	NM_001172303.1,NM_001172304.1,NM_032844.3	,,	2,159,6342	AA,AG,GG		1.7558,0.2724,1.2533	,,	713/880,712/841,712/879	27462061	163,12843	2203	4300	6503	SO:0001819	synonymous_variant	84930	exon9			AAATCAGATCAAG	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.2139G>A	10.37:g.27462061G>A		52	0	0		66	31	0.469697	NM_001172303	Q5T8D5|Q5T8D7|Q8NCD6|Q96SJ5	Silent	SNP	ENST00000375940.4	37	CCDS53502.1																																																																																			G|0.989;A|0.011	0.011	strong		0.438	MASTL-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047320.1	NM_032844		A	27462061	G	A	27462061	2	1	29	1	0	0	0	0	0	0	0	1	9337	933	33	2		2	MASTL	10	27462061	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	20049818	27462061	108072686	493	12734											
ARHGAP12	94134	hgsc.bcm.edu	37	chr10	32097650	32097650	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgtctgattaggtccttaaCagcagcgactcgctgtcttg	7	13	10	11	2	2	1	0	1	2	0	4	2	3	1	1	1	3	2	1	1	2	3	rs34750454		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:32097650C>T	ENST00000344936.2	-	19	2527	c.2293G>A	c.(2293-2295)Gtt>Att	p.V765I	ARHGAP12_ENST00000396144.4_Missense_Mutation_p.V760I|ARHGAP12_ENST00000375250.5_Missense_Mutation_p.V735I|ARHGAP12_ENST00000375245.4_Missense_Mutation_p.V713I|ARHGAP12_ENST00000492028.1_5'UTR|ARHGAP12_ENST00000311380.4_Missense_Mutation_p.V713I	NM_001270697.1|NM_018287.6	NP_001257626.1|NP_060757.4	Q8IWW6	RHG12_HUMAN	Rho GTPase activating protein 12	765	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				morphogenesis of an epithelial sheet (GO:0002011)|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(3)|endometrium(2)|kidney(1)|large_intestine(11)|lung(10)|skin(1)|urinary_tract(2)	31		Prostate(175;0.0199)				AGGTCCTTAACAGCAGCGACT	0.423																																					p.V765I		Atlas-SNP	.											.	ARHGAP12	79	.	0			c.G2293A						PASS	.						301	261	274					10																	32097650		2203	4300	6503	SO:0001583	missense	94134	exon19			CCTTAACAGCAGC	AY033594	CCDS7170.1, CCDS59214.1, CCDS59215.1, CCDS59216.1, CCDS73082.1	10p11.22	2013-01-10			ENSG00000165322	ENSG00000165322		"Rho GTPase activating proteins", "Pleckstrin homology (PH) domain containing"	16348	protein-coding gene	gene with protein product		610577				11854031	Standard	NM_001270695		Approved	FLJ20737, FLJ10971, FLJ21785	uc001ivz.2	Q8IWW6	OTTHUMG00000017911	ENST00000344936.2:c.2293G>A	10.37:g.32097650C>T	ENSP00000345808:p.Val765Ile	102	0	0		102	31	0.303922	NM_018287	B1ANY0|B1ANY1|B1ANY2|Q504X1|Q86UB3|Q8IWW7|Q8N3L1|Q9NT76	Missense_Mutation	SNP	ENST00000344936.2	37	CCDS7170.1	.	.	.	.	.	.	.	.	.	.	C	12.52	1.961807	0.34659	.	.	ENSG00000165322	ENST00000311380;ENST00000375250;ENST00000344936;ENST00000396144;ENST00000375245	T;T;T;T;T	0.18657	2.2;2.2;2.2;2.2;2.2	5.36	5.36	0.76844	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.119448	0.56097	D	0.000029	T	0.11836	0.0288	N	0.04275	-0.24	0.42256	D	0.991994	B;B;B;B;B;B	0.09022	0.001;0.002;0.002;0.002;0.002;0.0	B;B;B;B;B;B	0.29077	0.088;0.059;0.098;0.098;0.059;0.007	T	0.23154	-1.0196	10	0.26408	T	0.33	.	12.7667	0.57396	0.0:0.9245:0.0:0.0755	rs34750454	718;735;760;765;713;64	Q1RLN5;Q8IWW6-2;Q504X1;Q8IWW6;Q8IWW6-3;Q9NV28	.;.;.;RHG12_HUMAN;.;.	I	713;735;765;760;713	ENSP00000310984:V713I;ENSP00000364399:V735I;ENSP00000345808:V765I;ENSP00000379448:V760I;ENSP00000364394:V713I	ENSP00000310984:V713I	V	-	1	0	ARHGAP12	32137656	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	3.129000	0.50500	2.667000	0.90743	0.650000	0.86243	GTT	C|0.987;T|0.013	0.013	weak		0.423	ARHGAP12-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000047465.1			T	32097650	C	T	32097650	3	4	29	1	0	0	0	0	1	0	0	0	865	478	17	2	255	2	ARHGAP12	10	32097650	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	4635589	32097650	103437097	494	12735											
KIF5B	3799	hgsc.bcm.edu	37	chr10	32320002	32320002	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aaataaaactatatcctaccGatttctgattcaattcatca	16	14	2	9	1	4	1	3	1	1	0	5	2	5	1	2	0	2	0	2	0	7	7	rs35441986	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:32320002G>A	ENST00000302418.4	-	14	2037	c.1580C>T	c.(1579-1581)tCg>tTg	p.S527L		NM_004521.2	NP_004512.1	P33176	KINH_HUMAN	kinesin family member 5B	527					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)				ATATCCTACCGATTTCTGATT	0.294			T	"RET, ALK"	NSCLC								G|||	2	0.000399361	0.0	0.0	5008	,	,		18252	0.0		0.002	False		,,,				2504	0.0				p.S527L		Atlas-SNP	.		Dom	yes		10	10p11.22	3799	kinesin family member 5B		E	.	KIF5B	81	.	0			c.C1580T						PASS	.	G	LEU/SER	3,4403	4.2+/-10.8	0,3,2200	72	71	71		1580	6	1	10	dbSNP_126	71	31,8569	21.0+/-64.5	0,31,4269	yes	missense-near-splice	KIF5B	NM_004521.2	145	0,34,6469	AA,AG,GG		0.3605,0.0681,0.2614	benign	527/964	32320002	34,12972	2203	4300	6503	SO:0001630	splice_region_variant	3799	exon14			CCTACCGATTTCT	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.1581+1C>T	10.37:g.32320002G>A		83	0	0		79	44	0.556962	NM_004521	A0AVB2|Q5VZ85	Missense_Mutation	SNP	ENST00000302418.4	37	CCDS7171.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	19.33	3.807250	0.70797	6.81E-4	0.003605	ENSG00000170759	ENST00000302418	D	0.86694	-2.16	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.81370	0.4808	N	0.20685	0.6	0.80722	D	1	B	0.13145	0.007	B	0.08055	0.003	T	0.73329	-0.4017	10	0.40728	T	0.16	.	20.5948	0.99439	0.0:0.0:1.0:0.0	rs35441986	527	P33176	KINH_HUMAN	L	527	ENSP00000307078:S527L	ENSP00000307078:S527L	S	-	2	0	KIF5B	32360008	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.018000	0.88722	2.873000	0.98535	0.563000	0.77884	TCG	G|0.998;A|0.002	0.002	strong		0.294	KIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047467.1	NM_004521	Missense_Mutation	A	32320002	G	A	32320002	5	1	29	1	0	0	0	0	0	0	1	0	8315	1072	37	1	1359	1	KIF5B	10	32320002	Splice_Site	SNP	G	TCGA-GR-7351-01A-11D-2210-10	222352	32320002	103214745	495	12736											
RET	5979	hgsc.bcm.edu	37	chr10	43610119	43610119	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggtcagctactcctcttccGgtgcccgccggccctcgctg	2	9	11	19	5	2	0	1	0	1	0	5	0	4	0	5	3	3	2	5	3	1	2	rs1799939	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:43610119G>A	ENST00000355710.3	+	11	2303	c.2071G>A	c.(2071-2073)Ggt>Agt	p.G691S	RET_ENST00000340058.5_Missense_Mutation_p.G691S	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	691			G -> S (in dbSNP:rs1799939). {ECO:0000269|PubMed:14566559, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9223675, ECO:0000269|PubMed:9497256}.		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)	CTCCTCTTCCGGTGCCCGCCG	0.647		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				G|||	847	0.169129	0.0923	0.2565	5008	,	,		18422	0.121		0.1889	False		,,,				2504	0.2403				p.G691S	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_ENST00000340058,adrenal_gland,pheochromocytoma,0,2	RET	916	2	0			c.G2071A	GRCh37	CM023821	RET	M	rs1799939	PASS	.	G	SER/GLY,SER/GLY	455,3951	216.4+/-235.1	19,417,1767	61	55	57	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2071,2071	-1.1	0	10	dbSNP_89	57	1587,7013	295.7+/-302.5	155,1277,2868	yes	missense,missense	RET	NM_020630.4,NM_020975.4	56,56	174,1694,4635	AA,AG,GG		18.4535,10.3268,15.7004	possibly-damaging,possibly-damaging	691/1073,691/1115	43610119	2042,10964	2203	4300	6503	SO:0001583	missense	5979	exon11	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	TCTTCCGGTGCCC	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.2071G>A	10.37:g.43610119G>A	ENSP00000347942:p.Gly691Ser	60	0	0		46	25	0.543478	NM_020630	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Missense_Mutation	SNP	ENST00000355710.3	37	CCDS7200.1	338	0.15476190476190477	45	0.09146341463414634	82	0.2265193370165746	60	0.1048951048951049	151	0.19920844327176782	G	8.525	0.869582	0.17322	0.103268	0.184535	ENSG00000165731	ENST00000355710;ENST00000340058	T;T	0.78246	-1.05;-1.16	4.75	-1.08	0.09936	.	0.349618	0.34603	N	0.003826	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.24426	0.062;0.062;0.103	B;B;B	0.16722	0.004;0.007;0.016	T	0.04128	-1.0975	9	0.07990	T	0.79	.	9.2584	0.37597	0.7374:0.0:0.2626:0.0	rs1799939;rs3781260;rs17362555;rs17845010;rs17857772;rs1799939	437;691;691	B4DGX8;P07949;P07949-2	.;RET_HUMAN;.	S	691	ENSP00000347942:G691S;ENSP00000344798:G691S	ENSP00000344798:G691S	G	+	1	0	RET	42930125	1.000000	0.71417	0.000000	0.03702	0.411000	0.31082	4.395000	0.59678	-0.060000	0.13132	0.462000	0.41574	GGT	G|0.839;A|0.161	0.161	strong		0.647	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975		A	43610119	G	A	43610119	3	1	29	1	0	0	0	0	1	0	0	0	13250	1116	39	1	2113	1	RET	10	43610119	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	11290117	43610119	91924628	496	12737											
OGDHL	55753	hgsc.bcm.edu	37	chr10	50944528	50944528	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgctcaggggcccgtgctgCggccccatcttcaggaatca	6	8	12	15	2	4	0	3	0	1	0	4	1	4	1	3	4	3	2	3	4	1	1	rs140281439	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:50944528C>A	ENST00000374103.4	-	21	2714	c.2629G>T	c.(2629-2631)Gca>Tca	p.A877S	OGDHL_ENST00000432695.1_Missense_Mutation_p.A668S|OGDHL_ENST00000490844.1_5'UTR|OGDHL_ENST00000419399.1_Missense_Mutation_p.A820S	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	877					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)	p.A877T(1)		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						GCCCGTGCTGCGGCCCCATCT	0.632													C|||	2	0.000399361	0.0	0.0	5008	,	,		19100	0.0		0.002	False		,,,				2504	0.0				p.A877S		Atlas-SNP	.											OGDHL,NS,carcinoma,0,1	OGDHL	149	1	1	Substitution - Missense(1)	lung(1)	c.G2629T						PASS	.	C	SER/ALA,SER/ALA,SER/ALA	2,4404	4.2+/-10.8	0,2,2201	55	61	59		2458,2002,2629	5.4	0.1	10	dbSNP_134	59	24,8576	17.3+/-56.4	0,24,4276	yes	missense,missense,missense	OGDHL	NM_001143996.1,NM_001143997.1,NM_018245.2	99,99,99	0,26,6477	AA,AC,CC		0.2791,0.0454,0.1999	benign,benign,benign	820/954,668/802,877/1011	50944528	26,12980	2203	4300	6503	SO:0001583	missense	55753	exon21			GTGCTGCGGCCCC	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.2629G>T	10.37:g.50944528C>A	ENSP00000363216:p.Ala877Ser	58	0	0		63	28	0.444444	NM_018245	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Missense_Mutation	SNP	ENST00000374103.4	37	CCDS7234.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	12.90	2.076304	0.36662	4.54E-4	0.002791	ENSG00000197444	ENST00000374103;ENST00000419399;ENST00000432695	T;T;T	0.10382	2.88;2.88;2.88	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.23210	0.0561	M	0.64404	1.975	0.80722	D	1	P;P;P	0.44281	0.831;0.726;0.74	P;P;B	0.50049	0.629;0.535;0.426	T	0.00443	-1.1736	10	0.30078	T	0.28	.	19.1605	0.93529	0.0:1.0:0.0:0.0	.	820;668;877	Q9ULD0-2;Q9ULD0-3;Q9ULD0	.;.;OGDHL_HUMAN	S	877;820;668	ENSP00000363216:A877S;ENSP00000401356:A820S;ENSP00000390240:A668S	ENSP00000363216:A877S	A	-	1	0	OGDHL	50614534	1.000000	0.71417	0.113000	0.21522	0.092000	0.18411	7.818000	0.86416	2.538000	0.85594	0.484000	0.47621	GCA	C|0.998;A|0.002	0.002	strong		0.632	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245		A	50944528	C	A	50944528	3	1	29	1	0	0	0	0	1	0	0	0	10849	768	27	4	415	4	OGDHL	10	50944528	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	7334409	50944528	84590219	497	12738											
AGAP6	414189	hgsc.bcm.edu	37	chr10	51769058	51769058	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accagccccaagctcaacccGcccccctctcctcatgctaa	9	6	4	22	1	3	0	2	0	1	0	4	0	3	0	8	0	4	2	8	0	3	1	rs200123722	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:51769058G>A	ENST00000374056.4	+	7	1502	c.1104G>A	c.(1102-1104)ccG>ccA	p.P368P	AGAP6_ENST00000412531.3_Silent_p.P391P			Q5VW22	AGAP6_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 6	368	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(1)|lung(8)|prostate(3)|skin(1)|stomach(2)	29						AGCTCAACCCGCCCCCCTCTC	0.507																																					p.P391P		Atlas-SNP	.											AGAP6,NS,carcinoma,+1,1	AGAP6	53	1	0			c.G1173A						scavenged	.																																			SO:0001819	synonymous_variant	414189	exon8			CAACCCGCCCCCC		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.1104G>A	10.37:g.51769058G>A		156	0	0		112	40	0.357143	NM_001077665		Silent	SNP	ENST00000374056.4	37																																																																																				G|0.985;A|0.015	0.015	strong		0.507	AGAP6-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_001077665		A	51769058	G	A	51769058	2	1	29	1	0	0	0	0	0	0	0	1	372	1074	38	1		1	AGAP6	10	51769058	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	824530	51769058	83765689	498	12739											
CCAR1	55749	hgsc.bcm.edu	37	chr10	70513614	70513614	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgtctgtttttcagtcccaGttgtgacatgatggaactaa	10	15	9	7	0	2	2	1	2	1	0	3	3	3	3	1	1	1	2	1	1	2	4	rs368721550		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:70513614G>T	ENST00000265872.6	+	11	1243	c.1124G>T	c.(1123-1125)aGt>aTt	p.S375I	SNORD98_ENST00000408255.1_RNA|CCAR1_ENST00000535016.1_Missense_Mutation_p.S360I|CCAR1_ENST00000543719.1_Missense_Mutation_p.S360I	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	375					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						TTCAGTCCCAGTTGTGACATG	0.328																																					p.S375I		Atlas-SNP	.											.	CCAR1	118	.	0			c.G1124T						PASS	.	G	ILE/SER	0,4406		0,0,2203	141	144	143		1124	5.9	1	10		143	1,8599	1.2+/-3.3	0,1,4299	no	missense	CCAR1	NM_018237.2	142	0,1,6502	TT,TG,GG		0.0116,0.0,0.0077	probably-damaging	375/1151	70513614	1,13005	2203	4300	6503	SO:0001583	missense	55749	exon11			GTCCCAGTTGTGA	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.1124G>T	10.37:g.70513614G>T	ENSP00000265872:p.Ser375Ile	122	0	0		109	55	0.504587	NM_018237	A0JLT7|A1L4P7|A8K9D4|B4DNP8|B4DRK8|Q32NE3|Q5EBM3|Q5VUP6|Q6PIZ0|Q6X935|Q9H8N4|Q9NVA7|Q9NVQ0|Q9NWM6	Missense_Mutation	SNP	ENST00000265872.6	37	CCDS7282.1	.	.	.	.	.	.	.	.	.	.	G	16.94	3.261009	0.59431	0.0	1.16E-4	ENSG00000060339	ENST00000265872;ENST00000535016;ENST00000543719;ENST00000539539;ENST00000543225;ENST00000536012	T;T;T;T;T;T	0.23950	1.89;1.88;1.88;1.88;1.89;1.89	5.95	5.95	0.96441	.	0.076157	0.85682	D	0.000000	T	0.23133	0.0559	L	0.28192	0.835	0.43133	D	0.994878	P;D;B	0.56521	0.729;0.976;0.1	B;B;B	0.41988	0.372;0.361;0.043	T	0.01021	-1.1478	10	0.38643	T	0.18	-14.4237	20.3886	0.98946	0.0:0.0:1.0:0.0	.	360;375;349	Q8IX12-2;Q8IX12;F5H2E6	.;CCAR1_HUMAN;.	I	375;360;360;360;349;180	ENSP00000265872:S375I;ENSP00000441820:S360I;ENSP00000445254:S360I;ENSP00000439252:S360I;ENSP00000438610:S349I;ENSP00000439642:S180I	ENSP00000265872:S375I	S	+	2	0	CCAR1	70183620	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.053000	0.57427	2.810000	0.96702	0.650000	0.86243	AGT	.	.	none		0.328	CCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048356.2	NM_018237		T	70513614	G	T	70513614	3	4	29	1	0	0	0	0	1	0	0	0	2732	1029	36	4	1162	4	CCAR1	10	70513614	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	18744556	70513614	65021133	499	12740											
KIAA1274	27143	hgsc.bcm.edu	37	chr10	72298745	72298745	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgcatgcccatctacggcaCggcccagcccagcgccaagg	8	3	11	19	4	1	0	0	0	1	0	1	0	1	0	5	3	4	2	5	3	2	1	rs117244352	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:72298745C>T	ENST00000263563.6	+	13	1818	c.1550C>T	c.(1549-1551)aCg>aTg	p.T517M		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	517						cytosol (GO:0005829)											ATCTACGGCACGGCCCAGCCC	0.701													C|||	33	0.00658946	0.0015	0.0058	5008	,	,		16036	0.0		0.0249	False		,,,				2504	0.002				p.T517M		Atlas-SNP	.											.	.	.	.	0			c.C1550T						PASS	.	C	MET/THR	9,4397	15.5+/-35.6	0,9,2194	46	51	49		1550	-5.5	0	10	dbSNP_132	49	125,8473	63.5+/-125.6	1,123,4175	yes	missense	KIAA1274	NM_014431.2	81	1,132,6369	TT,TC,CC		1.4538,0.2043,1.0305	benign	517/857	72298745	134,12870	2203	4299	6502	SO:0001583	missense	27143	exon13			ACGGCACGGCCCA	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.1550C>T	10.37:g.72298745C>T	ENSP00000263563:p.Thr517Met	115	0	0		99	49	0.494949	NM_014431	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Missense_Mutation	SNP	ENST00000263563.6	37	CCDS31215.1	21	0.009615384615384616	1	0.0020325203252032522	0	0.0	0	0.0	20	0.026385224274406333	c	0.509	-0.867379	0.02590	0.002043	0.014538	ENSG00000107719	ENST00000263563;ENST00000373214	T	0.30182	1.54	5.01	-5.46	0.02608	.	0.342769	0.36066	N	0.002808	T	0.04770	0.0129	N	0.12422	0.21	0.23266	N	0.998011	B	0.20550	0.046	B	0.20184	0.028	T	0.06023	-1.0850	10	0.31617	T	0.26	-2.6083	14.93	0.70908	0.0:0.4702:0.0:0.5298	.	517	Q9ULE6	PALD_HUMAN	M	517	ENSP00000263563:T517M	ENSP00000263563:T517M	T	+	2	0	KIAA1274	71968751	0.084000	0.21492	0.013000	0.15412	0.480000	0.33159	0.407000	0.21049	-1.036000	0.03287	-1.137000	0.01932	ACG	C|0.990;T|0.010	0.010	strong		0.701	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431		T	72298745	C	T	72298745	3	4	29	1	0	0	0	0	1	0	0	0	8229	536	19	1	1596	1	KIAA1274	10	72298745	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1785131	72298745	63236002	500	12741											
SFTPA1	653509	hgsc.bcm.edu	37	chr10	81373562	81373562	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcaatgggcagtccatcaCttttgatgccattcaggagg	10	10	11	10	0	2	1	2	1	0	0	3	2	3	2	2	3	2	2	2	3	1	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:81373562C>G	ENST00000398636.3	+	6	578	c.440C>G	c.(439-441)aCt>aGt	p.T147S	SFTPA1_ENST00000372313.5_Missense_Mutation_p.T88S|SFTPA1_ENST00000372308.3_Missense_Mutation_p.T147S|SFTPA1_ENST00000419470.2_Missense_Mutation_p.T162S|SFTPA1_ENST00000428376.2_Missense_Mutation_p.T147S	NM_001164644.1|NM_001164646.1|NM_005411.4	NP_001158116.1|NP_001158118.1|NP_005402.3	Q8IWL2	SFTA1_HUMAN	surfactant protein A1	147	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				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)			CAGTCCATCACTTTTGATGCC	0.552																																					p.T162S		Atlas-SNP	.											.	SFTPA1	23	.	0			c.C485G						PASS	.						57	61	59					10																	81373562		2191	4249	6440	SO:0001583	missense	653509	exon6			CCATCACTTTTGA	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		ENST00000398636.3:c.440C>G	10.37:g.81373562C>G	ENSP00000381633:p.Thr147Ser	306	0	0		299	115	0.384615	NM_001093770	A8K3T8|B7ZW50|E3VLD8|E3VLD9|E3VLE0|E3VLE1|G5E9J3|P07714|Q14DV4|Q5RIR5|Q5RIR7|Q6PIT0|Q8TC19	Missense_Mutation	SNP	ENST00000398636.3	37	CCDS44445.1	.	.	.	.	.	.	.	.	.	.	.	0.102	-1.150419	0.01700	.	.	ENSG00000122852	ENST00000372308;ENST00000398636;ENST00000428376;ENST00000372313;ENST00000419470;ENST00000394569;ENST00000429958;ENST00000439264	T;T;T;T;T;D;D	0.88201	0.31;0.31;0.31;0.31;0.31;-2.35;-2.35	2.6	0.155	0.14906	C-type lectin fold (2);C-type lectin-like (2);C-type lectin (6);	0.446637	0.24189	N	0.040729	T	0.76898	0.4052	L	0.28776	0.89	0.09310	N	0.999992	B;B;B	0.31153	0.202;0.168;0.31	B;B;B	0.33846	0.171;0.069;0.171	T	0.62120	-0.6921	10	0.12103	T	0.63	-0.5574	4.1587	0.10273	0.6468:0.2212:0.1321:0.0	.	147;162;147	Q8IWL1;G5E9J3;Q8IWL2	SFPA2_HUMAN;.;SFTA1_HUMAN	S	147;147;147;88;162;147;147;147	ENSP00000361382:T147S;ENSP00000381633:T147S;ENSP00000411102:T147S;ENSP00000361387:T88S;ENSP00000397082:T162S;ENSP00000395527:T147S;ENSP00000401649:T147S	ENSP00000361382:T147S	T	+	2	0	SFTPA1	81043568	0.363000	0.24989	0.207000	0.23584	0.043000	0.13939	1.187000	0.32090	0.016000	0.14998	0.297000	0.19635	ACT	.	.	none		0.552	SFTPA1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_005411		G	81373562	C	G	81373562	3	3	29	1	0	0	0	0	1	0	0	0	14204	565	20	4	503	4	SFTPA1	10	81373562	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	9074817	81373562	54161185	501	12742											
ANKRD1	27063	hgsc.bcm.edu	37	chr10	92679979	92679979	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ttgctcccccagggtcacagGgtgggctagaagtgtcttca	7	10	13	11	0	3	1	2	0	1	1	4	1	4	1	2	3	1	2	2	3	2	3	rs397517248		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:92679979G>C	ENST00000371697.3	-	2	402	c.154C>G	c.(154-156)Cct>Gct	p.P52A	RNU6-740P_ENST00000364734.1_RNA	NM_014391.2	NP_055206.2	Q15327	ANKR1_HUMAN	ankyrin repeat domain 1 (cardiac muscle)	52					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)				AGGGTCACAGGGTGGGCTAGA	0.527																																					p.P52A		Atlas-SNP	.											.	ANKRD1	50	.	0			c.C154G						PASS	.						217	207	210					10																	92679979		2203	4300	6503	SO:0001583	missense	27063	exon2			TCACAGGGTGGGC	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.154C>G	10.37:g.92679979G>C	ENSP00000360762:p.Pro52Ala	144	0	0		147	71	0.482993	NM_014391	Q96LE7	Missense_Mutation	SNP	ENST00000371697.3	37	CCDS7412.1	.	.	.	.	.	.	.	.	.	.	G	0.736	-0.778119	0.02929	.	.	ENSG00000148677	ENST00000371697	T	0.65178	-0.14	5.76	0.17	0.15021	.	1.015060	0.07860	N	0.966081	T	0.39172	0.1068	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.25047	-1.0143	10	0.44086	T	0.13	.	6.7379	0.23419	0.4033:0.0:0.4791:0.1176	.	52	Q15327	ANKR1_HUMAN	A	52	ENSP00000360762:P52A	ENSP00000360762:P52A	P	-	1	0	ANKRD1	92669959	0.003000	0.15002	0.025000	0.17156	0.275000	0.26752	0.012000	0.13287	0.053000	0.16036	0.650000	0.86243	CCT	.	.	none		0.527	ANKRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049357.1	NM_014391		C	92679979	G	C	92679979	3	2	29	1	0	0	0	0	1	0	0	0	637	1232	43	4	837	4	ANKRD1	10	92679979	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	11306417	92679979	42854768	502	12743											
CYP26A1	1592	hgsc.bcm.edu	37	chr10	94835624	94835624	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaactcctctttggaggacaCgaaaccacggccagtgcagc	11	6	11	13	2	1	0	0	0	1	0	2	4	2	2	3	3	4	1	3	3	2	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:94835624C>T	ENST00000224356.4	+	5	951	c.906C>T	c.(904-906)caC>caT	p.H302H	CYP26A1_ENST00000371531.1_Silent_p.H233H|CYP26A1_ENST00000394139.1_Silent_p.H233H	NM_000783.3	NP_000774.2	O43174	CP26A_HUMAN	cytochrome P450, family 26, subfamily A, polypeptide 1	302					anterior/posterior pattern specification (GO:0009952)|cellular response to retinoic acid (GO:0071300)|central nervous system development (GO:0007417)|metabolic process (GO:0008152)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|neural crest cell development (GO:0014032)|retinoic acid catabolic process (GO:0034653)|retinoic acid receptor signaling pathway (GO:0048384)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|retinoic acid 4-hydroxylase activity (GO:0008401)|retinoic acid binding (GO:0001972)			breast(1)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	16		Colorectal(252;0.122)			Acitretin(DB00459)|Ketoconazole(DB01026)|Vitamin A(DB00162)	TTGGAGGACACGAAACCACGG	0.498																																					p.H302H		Atlas-SNP	.											.	CYP26A1	59	.	0			c.C906T						PASS	.						80	76	78					10																	94835624		2203	4300	6503	SO:0001819	synonymous_variant	1592	exon5			AGGACACGAAACC	AF005418	CCDS7426.1, CCDS7427.1	10q23-q24	2003-10-06	2003-01-14		ENSG00000095596	ENSG00000095596		"Cytochrome P450s"	2603	protein-coding gene	gene with protein product		602239	"cytochrome P450, subfamily XXVIA, polypeptide 1"			9228017, 9521883	Standard	NM_000783		Approved	P450RAI, CP26, CYP26, P450RAI1	uc001kil.2	O43174	OTTHUMG00000018765	ENST00000224356.4:c.906C>T	10.37:g.94835624C>T		75	0	0		94	4	0.0425532	NM_000783	B3KNI4|Q5VXH9|Q5VXI0	Silent	SNP	ENST00000224356.4	37	CCDS7426.1																																																																																			.	.	none		0.498	CYP26A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049408.3			T	94835624	C	T	94835624	2	4	29	1	0	0	0	0	0	0	0	1	4157	535	19	1		1	CYP26A1	10	94835624	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2155645	94835624	40699123	503	12744											
ENTPD1	953	hgsc.bcm.edu	37	chr10	97471746	97471746	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaggacctgacaagccagcaGaagggtaagaaattcttacc	16	6	10	9	0	1	3	0	1	1	2	1	4	1	4	3	2	3	2	3	2	6	3	rs200247284	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:97471746G>A	ENST00000453258.2	+	1	211	c.33G>A	c.(31-33)caG>caA	p.Q11Q		NM_001098175.1	NP_001091645.1	P49961	ENTP1_HUMAN	ectonucleoside triphosphate diphosphohydrolase 1	0					ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell death (GO:0008219)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|purine ribonucleoside diphosphate catabolic process (GO:0009181)	basal lamina (GO:0005605)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			cervix(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(3)|prostate(1)|skin(1)	16		Colorectal(252;0.0821)		Epithelial(162;1.31e-07)|all cancers(201;5.33e-06)		caagccagcagaagggtaaga	0.498													G|||	6	0.00119808	0.0	0.0	5008	,	,		17840	0.0		0.006	False		,,,				2504	0.0				p.Q11Q		Atlas-SNP	.											.	ENTPD1	44	.	0			c.G33A						PASS	.	G		2,3754		0,2,1876	59	65	63		33	0.5	0.6	10		63	40,8154		0,40,4057	no	coding-synonymous	ENTPD1	NM_001098175.1		0,42,5933	AA,AG,GG		0.4882,0.0532,0.3515		11/518	97471746	42,11908	1878	4097	5975	SO:0001819	synonymous_variant	953	exon1			CCAGCAGAAGGGT	S73813	CCDS7444.1, CCDS53556.1, CCDS53557.1, CCDS53558.1, CCDS41554.1	10q24.1	2014-03-03			ENSG00000138185	ENSG00000138185		"CD molecules"	3363	protein-coding gene	gene with protein product		601752		CD39		9226376, 24482476	Standard	NM_001098175		Approved	NTPDase-1, ATPDase, SPG64	uc010qoj.2	P49961	OTTHUMG00000018818	ENST00000453258.2:c.33G>A	10.37:g.97471746G>A		64	0	0		76	33	0.434211	NM_001098175	A9Z1X8|B4DWB9|B4E1X1|B7Z599|G3XAF6|Q5T561|Q5T562|Q86VV3|Q9UQQ9|Q9Y3Q9	Silent	SNP	ENST00000453258.2	37	CCDS41554.1																																																																																			G|0.994;A|0.006	0.006	strong		0.498	ENTPD1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049563.1	NM_001776		A	97471746	G	A	97471746	2	1	29	1	0	0	0	0	0	0	0	1	5140	933	33	2		2	ENTPD1	10	97471746	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2636122	97471746	38063001	504	12745											
HPSE2	60495	hgsc.bcm.edu	37	chr10	100481475	100481475	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attagggccatataagctggCtctggaataaatccggatgg	12	10	12	7	1	1	0	0	0	1	0	2	2	2	2	2	5	1	2	2	5	6	4	rs142102360	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:100481475C>T	ENST00000370552.3	-	5	954	c.895G>A	c.(895-897)Gcc>Acc	p.A299T	HPSE2_ENST00000404542.1_Missense_Mutation_p.A187T|HPSE2_ENST00000370549.1_Missense_Mutation_p.A241T|HPSE2_ENST00000370546.1_Missense_Mutation_p.A299T	NM_021828.4	NP_068600.4	Q8WWQ2	HPSE2_HUMAN	heparanase 2 (inactive)	299					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)		TATAAGCTGGCTCTGGAATAA	0.493													C|||	6	0.00119808	0.0	0.0014	5008	,	,		14180	0.0		0.004	False		,,,				2504	0.001				p.A299T		Atlas-SNP	.											.	HPSE2	203	.	0			c.G895A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA	4,4402	8.1+/-20.4	0,4,2199	66	63	64		721,559,895,895	5.4	1	10	dbSNP_134	64	36,8564	25.1+/-72.6	0,36,4264	yes	missense,missense,missense,missense	HPSE2	NM_001166244.1,NM_001166245.1,NM_001166246.1,NM_021828.4	58,58,58,58	0,40,6463	TT,TC,CC		0.4186,0.0908,0.3076	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	241/535,187/481,299/549,299/593	100481475	40,12966	2203	4300	6503	SO:0001583	missense	60495	exon5			AGCTGGCTCTGGA	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.895G>A	10.37:g.100481475C>T	ENSP00000359583:p.Ala299Thr	61	0	0		52	21	0.403846	NM_001166246	Q5VUH4|Q5VUH5|Q5VUH6|Q8WWQ1|Q9HB37|Q9HB38|Q9HB39	Missense_Mutation	SNP	ENST00000370552.3	37	CCDS7477.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	22.5	4.298050	0.81025	9.08E-4	0.004186	ENSG00000172987	ENST00000370552;ENST00000370549;ENST00000370546;ENST00000404542	T;T;T;T	0.34859	1.34;1.34;1.34;1.34	5.44	5.44	0.79542	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.062834	0.64402	D	0.000006	T	0.32010	0.0815	L	0.47016	1.485	0.58432	D	0.999996	P;P;P;P	0.51351	0.869;0.775;0.944;0.892	B;B;P;P	0.49421	0.38;0.356;0.572;0.61	T	0.02345	-1.1173	10	0.26408	T	0.33	-10.1813	14.4756	0.67544	0.147:0.853:0.0:0.0	.	187;299;241;299	Q8WWQ2-4;Q8WWQ2-2;Q8WWQ2-3;Q8WWQ2	.;.;.;HPSE2_HUMAN	T	299;241;299;187	ENSP00000359583:A299T;ENSP00000359580:A241T;ENSP00000359577:A299T;ENSP00000384384:A187T	ENSP00000359577:A299T	A	-	1	0	HPSE2	100471465	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.129000	0.57957	2.706000	0.92434	0.551000	0.68910	GCC	C|0.997;T|0.003	0.003	strong		0.493	HPSE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049789.1	NM_021828		T	100481475	C	T	100481475	3	4	29	1	0	0	0	0	1	0	0	0	7354	797	28	2	953	2	HPSE2	10	100481475	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	3009729	100481475	35053272	505	12746											
PDCD11	22984	hgsc.bcm.edu	37	chr10	105160184	105160184	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagagggatccaccaaaagaAaaaagagccagaaggggcca	20	1	12	8	0	0	4	0	0	0	4	1	5	1	5	4	3	1	0	4	3	7	0	rs150893869	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:105160184A>G	ENST00000369797.3	+	3	227	c.133A>G	c.(133-135)Aaa>Gaa	p.K45E		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	45					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)		CACCAAAAGAAAAAAGAGCCA	0.423													A|||	103	0.0205671	0.0	0.0086	5008	,	,		13928	0.002		0.006	False		,,,				2504	0.091				p.K45E		Atlas-SNP	.											.	PDCD11	160	.	0			c.A133G						PASS	.	A	GLU/LYS	3,4403	9.9+/-24.2	0,3,2200	57	66	63		133	5.8	1	10	dbSNP_134	63	54,8546	32.3+/-84.9	0,54,4246	yes	missense	PDCD11	NM_014976.1	56	0,57,6446	GG,GA,AA		0.6279,0.0681,0.4383	probably-damaging	45/1872	105160184	57,12949	2203	4300	6503	SO:0001583	missense	22984	exon3			AAAAGAAAAAAGA	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.133A>G	10.37:g.105160184A>G	ENSP00000358812:p.Lys45Glu	23	0	0		17	10	0.588235	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Missense_Mutation	SNP	ENST00000369797.3	37	CCDS31276.1	8	0.003663003663003663	0	0.0	4	0.011049723756906077	0	0.0	4	0.005277044854881266	A	27.6	4.844336	0.91197	6.81E-4	0.006279	ENSG00000148843	ENST00000369797;ENST00000543503	T	0.14391	2.51	5.84	5.84	0.93424	.	0.235564	0.45606	D	0.000344	T	0.21307	0.0513	M	0.64404	1.975	0.51012	D	0.999903	D	0.58620	0.983	P	0.54815	0.761	T	0.00621	-1.1640	10	0.87932	D	0	-6.4297	14.4461	0.67349	1.0:0.0:0.0:0.0	.	45	Q14690	RRP5_HUMAN	E	45	ENSP00000358812:K45E	ENSP00000358812:K45E	K	+	1	0	PDCD11	105150174	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	5.140000	0.64807	2.235000	0.73313	0.459000	0.35465	AAA	A|0.995;G|0.005	0.005	strong		0.423	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1			G	105160184	A	G	105160184	3	3	29	1	0	0	0	0	1	0	0	0	11626	15	1	3	139	3	PDCD11	10	105160184	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	4678709	105160184	30374563	506	12747											
SORCS1	114815	hgsc.bcm.edu	37	chr10	108434858	108434858	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccagaaccccatccacaaaaAgtggaatagatgtgaaactg	17	6	8	10	0	0	3	0	1	0	2	1	4	1	4	4	1	2	0	4	1	6	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:108434858A>C	ENST00000263054.6	-	14	1896	c.1889T>G	c.(1888-1890)cTt>cGt	p.L630R	SORCS1_ENST00000369698.1_Missense_Mutation_p.L165R|SORCS1_ENST00000344440.6_Missense_Mutation_p.L630R	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	630					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)		ATCCACAAAAAGTGGAATAGA	0.388																																					p.L630R		Atlas-SNP	.											.	SORCS1	534	.	0			c.T1889G						PASS	.						124	118	120					10																	108434858		2203	4300	6503	SO:0001583	missense	114815	exon14			ACAAAAAGTGGAA	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.1889T>G	10.37:g.108434858A>C	ENSP00000263054:p.Leu630Arg	66	0	0		74	25	0.337838	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	37	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.488184	0.84854	.	.	ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440	T;T;T	0.33438	1.41;1.41;1.41	5.92	5.92	0.95590	VPS10 (1);	0.000000	0.85682	D	0.000000	T	0.61198	0.2328	M	0.86178	2.8	0.51767	D	0.999937	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	T	0.65833	-0.6072	9	.	.	.	-15.917	16.3631	0.83280	1.0:0.0:0.0:0.0	.	630;630;630;630;630	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	R	165;630;630	ENSP00000358712:L165R;ENSP00000263054:L630R;ENSP00000345964:L630R	.	L	-	2	0	SORCS1	108424848	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.266000	0.75297	0.533000	0.62120	CTT	.	.	none		0.388	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		C	108434858	A	C	108434858	3	2	29	1	0	0	0	0	1	0	0	0	14945	72	3	5	1903	5	SORCS1	10	108434858	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	3274674	108434858	27099889	507	12748											
ATRNL1	26033	hgsc.bcm.edu	37	chr10	117061434	117061434	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gacatcatgttccaactgtaCaagcaatggcatggagtgta	13	10	10	8	0	1	0	1	0	0	0	2	2	2	1	1	2	3	5	1	2	5	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:117061434C>T	ENST00000355044.3	+	17	2825	c.2699C>T	c.(2698-2700)aCa>aTa	p.T900I	ATRNL1_ENST00000423111.2_5'UTR|ATRNL1_ENST00000303745.7_5'Flank	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	900	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)		TCCAACTGTACAAGCAATGGC	0.403																																					p.T900I		Atlas-SNP	.											.	ATRNL1	219	.	0			c.C2699T						PASS	.						246	175	199					10																	117061434		2203	4300	6503	SO:0001583	missense	26033	exon17			ACTGTACAAGCAA	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.2699C>T	10.37:g.117061434C>T	ENSP00000347152:p.Thr900Ile	97	0	0		107	24	0.224299	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Missense_Mutation	SNP	ENST00000355044.3	37	CCDS7592.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.423342	0.83559	.	.	ENSG00000107518	ENST00000355044	T	0.15256	2.44	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.42108	0.1188	M	0.63428	1.95	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.19128	-1.0315	10	0.56958	D	0.05	-15.0727	19.0195	0.92908	0.0:1.0:0.0:0.0	.	900	Q5VV63	ATRN1_HUMAN	I	900	ENSP00000347152:T900I	ENSP00000347152:T900I	T	+	2	0	ATRNL1	117051424	1.000000	0.71417	0.688000	0.30117	0.983000	0.72400	7.730000	0.84881	2.491000	0.84063	0.591000	0.81541	ACA	.	.	none		0.403	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349		T	117061434	C	T	117061434	3	4	29	1	0	0	0	0	1	0	0	0	1207	478	17	2	2765	2	ATRNL1	10	117061434	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	8626576	117061434	18473313	508	12749											
DMBT1	1755	hgsc.bcm.edu	37	chr10	124330421	124330421	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	tgcaggttctccatttccctCggagtcgaccctggagtcaa	7	11	10	13	2	2	0	1	0	1	0	6	3	3	2	3	3	1	2	3	3	1	2	rs75209396	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:124330421C>G	ENST00000338354.3	+	4	261	c.155C>G	c.(154-156)tCg>tGg	p.S52W	DMBT1_ENST00000368909.3_Missense_Mutation_p.S52W|DMBT1_ENST00000359586.6_Missense_Mutation_p.S52W|DMBT1_ENST00000368955.3_Missense_Mutation_p.S52W|DMBT1_ENST00000330163.4_Missense_Mutation_p.S52W|DMBT1_ENST00000368956.2_Missense_Mutation_p.S52W|DMBT1_ENST00000344338.3_Missense_Mutation_p.S52W			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	52			S -> W (in dbSNP:rs75209396). {ECO:0000269|PubMed:12185598, ECO:0000269|PubMed:12353266}.		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)				CCATTTCCCTCGGAGTCGACC	0.537													c|||	329	0.0656949	0.23	0.0231	5008	,	,		22102	0.001		0.007	False		,,,				2504	0.001				p.S52W	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.C155G						PASS	.	C	TRP/SER,TRP/SER,TRP/SER	658,3106		51,556,1275	168	167	167		155,155,155	1	0	10	dbSNP_132	167	51,8185		0,51,4067	yes	missense,missense,missense	DMBT1	NM_004406.2,NM_007329.2,NM_017579.2	177,177,177	51,607,5342	GG,GC,CC		0.6192,17.4814,5.9083	probably-damaging,probably-damaging,probably-damaging	52/1786,52/2414,52/2404	124330421	709,11291	1882	4118	6000	SO:0001583	missense	1755	exon4			TTCCCTCGGAGTC		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.155C>G	10.37:g.124330421C>G	ENSP00000342210:p.Ser52Trp	161	0	0		192	94	0.489583	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	37		130	0.05952380952380952	118	0.23983739837398374	9	0.024861878453038673	0	0.0	3	0.00395778364116095	C	10.71	1.426167	0.25726	0.174814	0.006192	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956;ENST00000359586	T;T;T;T;T;T;T	0.26223	1.85;1.84;1.78;1.85;1.84;1.78;1.75	1.9	0.968	0.19680	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D;P;P;P;D	0.76494	0.997;0.572;0.922;0.529;0.999	D;B;B;B;P	0.65443	0.935;0.152;0.206;0.202;0.902	T	0.24476	-1.0159	8	0.66056	D	0.02	.	4.3987	0.11376	0.0:0.7908:0.0:0.2092	.	52;52;52;52;52	F8WEF7;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;DMBT1_HUMAN	W	52	ENSP00000342210:S52W;ENSP00000343175:S52W;ENSP00000327747:S52W;ENSP00000357905:S52W;ENSP00000357951:S52W;ENSP00000357952:S52W;ENSP00000352593:S52W	ENSP00000331522:S52W	S	+	2	0	DMBT1	124320411	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.122000	0.15687	0.337000	0.23665	0.205000	0.17691	TCG	C|0.950;G|0.050	0.050	strong		0.537	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		G	124330421	C	G	124330421	3	3	29	1	0	0	0	0	1	0	0	0	4579	893	31	4	169	4	DMBT1	10	124330421	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	7268987	124330421	11204326	509	12750											
DMBT1	1755	hgsc.bcm.edu	37	chr10	124345721	124345721	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aatgtggtctgcaggcagctGggctgtggctgggccatgtt	5	11	17	8	0	1	0	0	0	1	0	1	0	1	0	1	5	2	6	1	5	1	1	rs539603965		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:124345721G>T	ENST00000338354.3	+	16	1711	c.1605G>T	c.(1603-1605)ctG>ctT	p.L535L	DMBT1_ENST00000368909.3_Silent_p.L535L|DMBT1_ENST00000359586.6_Intron|DMBT1_ENST00000368955.3_Silent_p.L525L|DMBT1_ENST00000330163.4_Intron|DMBT1_ENST00000368956.2_Intron|DMBT1_ENST00000344338.3_Silent_p.L525L			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	535	SRCR 4. {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)				GCAGGCAGCTGGGCTGTGGCT	0.617																																					p.L535L	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.G1605T						PASS	.						238	184	202					10																	124345721		2038	4168	6206	SO:0001819	synonymous_variant	1755	exon16			GCAGCTGGGCTGT		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.1605G>T	10.37:g.124345721G>T		76	0	0		93	49	0.526882	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Silent	SNP	ENST00000338354.3	37																																																																																				.	.	none		0.617	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		T	124345721	G	T	124345721	2	4	29	1	0	0	0	0	0	0	0	1	4579	1335	47	4		4	DMBT1	10	124345721	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	15300	124345721	11189026	510	12751											
FAM53B	9679	hgsc.bcm.edu	37	chr10	126370517	126370517	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcagggctgccctccaaatcGgtggtggagtcctgcctggt	5	9	15	12	1	0	0	0	0	0	0	3	1	2	1	4	5	2	2	4	5	1	0	rs147832040		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:126370517G>C	ENST00000337318.3	-	4	776	c.565C>G	c.(565-567)Cga>Gga	p.R189G	RP11-12J10.3_ENST00000494792.1_3'UTR|FAM53B_ENST00000280780.6_Missense_Mutation_p.R189G|FAM53B_ENST00000392754.3_Missense_Mutation_p.R189G	NM_014661.3	NP_055476.3	Q14153	FA53B_HUMAN	family with sequence similarity 53, member B	189										cervix(1)|lung(5)|ovary(2)|pancreas(1)	9		all_lung(145;0.0191)|Lung NSC(174;0.0301)|Colorectal(57;0.106)|all_neural(114;0.117)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.15)		CCTCCAAATCGGTGGTGGAGT	0.667													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17444	0.0		0.0	False		,,,				2504	0.0				p.R189G		Atlas-SNP	.											.	FAM53B	22	.	0			c.C565G						PASS	.	G	GLY/ARG	1,4405	2.1+/-5.4	0,1,2202	34	37	36		565	2.5	0	10	dbSNP_134	36	23,8577	15.3+/-51.7	0,23,4277	yes	missense	FAM53B	NM_014661.3	125	0,24,6479	CC,CG,GG		0.2674,0.0227,0.1845	probably-damaging	189/423	126370517	24,12982	2203	4300	6503	SO:0001583	missense	9679	exon4			CAAATCGGTGGTG	D50930	CCDS7641.1	10q26.13	2004-11-24	2004-11-24	2004-11-24	ENSG00000189319	ENSG00000189319			28968	protein-coding gene	gene with protein product			"KIAA0140"	KIAA0140		8590280	Standard	NM_014661		Approved	bA12J10.2	uc001lhv.1	Q14153	OTTHUMG00000019215	ENST00000337318.3:c.565C>G	10.37:g.126370517G>C	ENSP00000338532:p.Arg189Gly	76	0	0		71	40	0.56338	NM_014661	D3DRF1|Q5VUW1|Q5VUW2|Q8N5S6	Missense_Mutation	SNP	ENST00000337318.3	37	CCDS7641.1	3	0.0013736263736263737	1	0.0020325203252032522	0	0.0	0	0.0	2	0.002638522427440633	G	4.500	0.092832	0.08632	2.27E-4	0.002674	ENSG00000189319	ENST00000337318;ENST00000392754;ENST00000280780	T;T;T	0.45668	0.89;0.89;0.89	4.5	2.54	0.30619	.	0.743246	0.11858	N	0.522691	T	0.39733	0.1089	L	0.58101	1.795	0.09310	N	1	P;P;P	0.42620	0.6;0.785;0.6	B;B;B	0.43754	0.247;0.43;0.247	T	0.16217	-1.0410	10	0.13108	T	0.6	-3.0764	9.3857	0.38340	0.0:0.1397:0.5718:0.2884	.	189;189;189	Q14153-2;Q14153;B3KMZ2	.;FA53B_HUMAN;.	G	189	ENSP00000338532:R189G;ENSP00000376509:R189G;ENSP00000280780:R189G	ENSP00000280780:R189G	R	-	1	2	FAM53B	126360507	0.022000	0.18835	0.000000	0.03702	0.029000	0.11900	1.867000	0.39499	0.580000	0.29522	0.655000	0.94253	CGA	G|0.998;C|0.002	0.002	strong		0.667	FAM53B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050879.1	NM_014661		C	126370517	G	C	126370517	3	2	29	1	0	0	0	0	1	0	0	0	5588	1124	39	4	711	4	FAM53B	10	126370517	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2024796	126370517	9164230	511	12752											
C10orf137	26098	hgsc.bcm.edu	37	chr10	127412393	127412393	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttaagaacataaaaaaacTcctgaaaattccctacagca	19	10	3	9	0	0	2	0	1	0	1	2	2	2	2	2	0	4	1	2	0	9	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:127412393T>C	ENST00000356792.4	+	4	630	c.398T>C	c.(397-399)cTc>cCc	p.L133P	C10orf137_ENST00000337623.3_Missense_Mutation_p.L133P	NM_001202438.1	NP_001189367.1	Q3B7T1	EDRF1_HUMAN		133					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)				ATAAAAAAACTCCTGAAAATT	0.323																																					p.L133P		Atlas-SNP	.											.	C10orf137	153	.	0			c.T398C						PASS	.						74	84	80					10																	127412393		2203	4299	6502	SO:0001583	missense	26098	exon4			AAAAACTCCTGAA																												ENST00000356792.4:c.398T>C	10.37:g.127412393T>C	ENSP00000349244:p.Leu133Pro	113	0	0		102	17	0.166667	NM_015608	B2RC65|Q3KR40|Q4G190|Q5VZQ4|Q8IZ74|Q9Y3W4	Missense_Mutation	SNP	ENST00000356792.4	37	CCDS55733.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.347429	0.82022	.	.	ENSG00000107938	ENST00000356792;ENST00000392732;ENST00000337623	.	.	.	5.72	5.72	0.89469	.	0.128515	0.53938	D	0.000045	T	0.78084	0.4228	M	0.72479	2.2	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	0.80638	-0.1293	9	0.87932	D	0	.	14.5722	0.68218	0.0:0.0:0.0:1.0	.	133;133;133	Q3B7T1;Q3B7T1-5;Q3B7T1-3	EDRF1_HUMAN;.;.	P	133	.	ENSP00000336727:L133P	L	+	2	0	C10orf137	127402383	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.698000	0.84413	2.177000	0.69029	0.528000	0.53228	CTC	.	.	none		0.323	C10orf137-007	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388539.1			C	127412393	T	C	127412393	3	2	29	1	0	0	0	0	1	0	0	0	1596	1551	54	3	412	3	C10orf137	10	127412393	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	1041876	127412393	8122354	512	12753											
BCCIP	55760	hgsc.bcm.edu	37	chr10	127541743	127541743	+	Intron	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtttctctgaaggctggactAattcaatcaagatcaactct	12	13	7	9	0	5	2	3	1	2	1	6	3	5	3	0	2	1	2	0	2	5	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:127541743A>G	ENST00000284690.3	-	5	1583				DHX32_ENST00000284688.6_Intron|BCCIP_ENST00000368759.5_Silent_p.L300L|DHX32_ENST00000368721.1_Intron	NM_018180.2	NP_060650.2	Q7L7V1	DHX32_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 32							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)				AGGCTGGACTAATTCAATCAA	0.433																																					p.L300L		Atlas-SNP	.											.	BCCIP	48	.	0			c.A900G						PASS	.						130	127	128					10																	127541743		2203	4300	6503	SO:0001627	intron_variant	56647	exon8			TGGACTAATTCAA		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.1093-532T>C	10.37:g.127541743A>G		79	0	0		61	28	0.459016	NM_016567	A8MSV2|D3DRF9|Q49AG5|Q5T3L0|Q5T3L5|Q96NY1|Q9BUN0|Q9H769|Q9NSL5|Q9NV74|Q9NVJ7	Silent	SNP	ENST00000284690.3	37	CCDS7652.1																																																																																			.	.	none		0.433	DHX32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050945.2	NM_018180		G	127541743	A	G	127541743	1	3	29	0	1	0	0	0	0	0	0	0	1356	349	13	3		3	BCCIP	10	127541743	Intron	SNP	A	TCGA-GR-7351-01A-11D-2210-10	129350	127541743	7993004	513	12754											
DHX32	55760	hgsc.bcm.edu	37	chr10	127548215	127548215	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caatgtcacctttctcacccGagtggtgaatttcaaagata	12	12	7	10	1	3	2	3	1	1	1	4	3	3	2	2	1	0	0	2	1	4	3	rs201005566		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:127548215G>A	ENST00000284690.3	-	3	1296	c.806C>T	c.(805-807)tCg>tTg	p.S269L	DHX32_ENST00000284688.6_Missense_Mutation_p.S269L	NM_018180.2	NP_060650.2	Q7L7V1	DHX32_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 32	269						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)				TTTCTCACCCGAGTGGTGAAT	0.383																																					p.S269L		Atlas-SNP	.											.	DHX32	67	.	0			c.C806T						PASS	.	G	LEU/SER	0,4406		0,0,2203	63	67	65		806	4.8	1	10		65	2,8598	3.0+/-9.4	0,2,4298	yes	missense	DHX32	NM_018180.2	145	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	269/744	127548215	2,13004	2203	4300	6503	SO:0001583	missense	55760	exon3			TCACCCGAGTGGT		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.806C>T	10.37:g.127548215G>A	ENSP00000284690:p.Ser269Leu	84	0	0		66	34	0.515152	NM_018180	A8MSV2|D3DRF9|Q49AG5|Q5T3L0|Q5T3L5|Q96NY1|Q9BUN0|Q9H769|Q9NSL5|Q9NV74|Q9NVJ7	Missense_Mutation	SNP	ENST00000284690.3	37	CCDS7652.1	.	.	.	.	.	.	.	.	.	.	G	16.91	3.253871	0.59212	0.0	2.33E-4	ENSG00000089876	ENST00000284690;ENST00000284688	T;T	0.08634	3.07;3.07	4.84	4.84	0.62591	.	0.122763	0.53938	D	0.000053	T	0.10035	0.0246	L	0.42744	1.35	0.24376	N	0.994816	P;P	0.52170	0.951;0.84	B;B	0.40134	0.32;0.17	T	0.10613	-1.0622	10	0.87932	D	0	-16.7608	17.1401	0.86750	0.0:0.0:1.0:0.0	.	269;269	Q7L7V1-2;Q7L7V1	.;DHX32_HUMAN	L	269	ENSP00000284690:S269L;ENSP00000284688:S269L	ENSP00000284688:S269L	S	-	2	0	DHX32	127538205	0.997000	0.39634	0.989000	0.46669	0.996000	0.88848	8.758000	0.91663	2.512000	0.84698	0.655000	0.94253	TCG	.	.	weak		0.383	DHX32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050945.2	NM_018180		A	127548215	G	A	127548215	3	1	29	1	0	0	0	0	1	0	0	0	4507	1059	37	1	1461	1	DHX32	10	127548215	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	6472	127548215	7986532	514	12755											
CLRN3	119467	hgsc.bcm.edu	37	chr10	129690837	129690837	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tacctgcaaactttttctttGgttctgcaagtccgtgactc	7	16	7	11	1	2	1	0	1	2	0	4	1	3	1	2	1	4	3	2	1	3	5	rs35890579	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:129690837G>T	ENST00000368671.3	-	1	374	c.212C>A	c.(211-213)cCa>cAa	p.P71Q		NM_152311.3	NP_689524.1	Q8NCR9	CLRN3_HUMAN	clarin 3	71						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	6		all_epithelial(44;0.00168)|all_lung(145;0.0586)|Lung NSC(174;0.0765)|all_neural(114;0.201)|Glioma(114;0.222)|Colorectal(57;0.235)				CTTTTTCTTTGGTTCTGCAAG	0.358													G|||	75	0.014976	0.0023	0.0159	5008	,	,		18682	0.0		0.0467	False		,,,				2504	0.0143				p.P71Q		Atlas-SNP	.											.	CLRN3	27	.	0			c.C212A						PASS	.	G	GLN/PRO	37,4369	41.6+/-74.8	0,37,2166	84	81	82		212	3	0	10	dbSNP_126	82	441,8159	132.3+/-190.0	15,411,3874	yes	missense	CLRN3	NM_152311.3	76	15,448,6040	TT,TG,GG		5.1279,0.8398,3.6752	benign	71/227	129690837	478,12528	2203	4300	6503	SO:0001583	missense	119467	exon1			TTCTTTGGTTCTG	BC029478	CCDS7656.1	10q26.2	2006-11-24	2006-11-23	2006-11-23	ENSG00000180745	ENSG00000180745			20795	protein-coding gene	gene with protein product			"transmembrane protein 12"	TMEM12		12145752, 12080385	Standard	NM_152311		Approved	MGC32871, USH3AL1	uc001lka.1	Q8NCR9	OTTHUMG00000019253	ENST00000368671.3:c.212C>A	10.37:g.129690837G>T	ENSP00000357660:p.Pro71Gln	50	0	0		79	38	0.481013	NM_152311	Q6MZX8	Missense_Mutation	SNP	ENST00000368671.3	37	CCDS7656.1	45	0.020604395604395604	3	0.006097560975609756	8	0.022099447513812154	0	0.0	34	0.044854881266490766	G	9.541	1.113346	0.20795	0.008398	0.051279	ENSG00000180745	ENST00000368671	T	0.75589	-0.95	5.52	2.96	0.34315	.	1.135500	0.06413	N	0.721034	T	0.27967	0.0689	L	0.36672	1.1	0.09310	N	1	P	0.43542	0.81	P	0.45998	0.5	T	0.31696	-0.9934	10	0.12430	T	0.62	.	6.9764	0.24677	0.2997:0.0:0.7003:0.0	rs35890579	71	Q8NCR9	CLRN3_HUMAN	Q	71	ENSP00000357660:P71Q	ENSP00000357660:P71Q	P	-	2	0	CLRN3	129580827	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.299000	0.19138	0.460000	0.27045	0.655000	0.94253	CCA	G|0.966;T|0.034	0.034	strong		0.358	CLRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050987.1	NM_152311		T	129690837	G	T	129690837	3	4	29	1	0	0	0	0	1	0	0	0	3561	1348	47	4	480	4	CLRN3	10	129690837	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2142622	129690837	5843910	515	12756											
KNDC1	85442	hgsc.bcm.edu	37	chr10	135027195	135027195	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccacttcctgaactcacgggCcctgggcgtcatggacaaga	9	7	11	14	2	2	2	2	1	0	1	3	3	3	3	3	3	1	0	3	3	2	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr10:135027195C>T	ENST00000304613.3	+	25	4511	c.4490C>T	c.(4489-4491)gCc>gTc	p.A1497V	KNDC1_ENST00000368572.2_Missense_Mutation_p.A1499V			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	1497	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)		AACTCACGGGCCCTGGGCGTC	0.602																																					p.A1497V		Atlas-SNP	.											.	KNDC1	155	.	0			c.C4490T						PASS	.						94	77	83					10																	135027195		2203	4300	6503	SO:0001583	missense	85442	exon25			CACGGGCCCTGGG	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.4490C>T	10.37:g.135027195C>T	ENSP00000304437:p.Ala1497Val	61	0	0		52	10	0.192308	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	37	CCDS7674.1	.	.	.	.	.	.	.	.	.	.	C	16.97	3.267975	0.59540	.	.	ENSG00000171798	ENST00000304613;ENST00000368572	T;T	0.29142	1.58;1.58	4.26	4.26	0.50523	Guanine-nucleotide dissociation stimulator CDC25 (3);Ras guanine nucleotide exchange factor, domain (1);	0.241819	0.34932	N	0.003571	T	0.46054	0.1373	L	0.47716	1.5	0.45330	D	0.998325	D	0.64830	0.994	D	0.67103	0.949	T	0.35276	-0.9795	10	0.41790	T	0.15	-25.7247	14.5448	0.68020	0.0:1.0:0.0:0.0	.	1497	Q76NI1	VKIND_HUMAN	V	1497;1499	ENSP00000304437:A1497V;ENSP00000357561:A1499V	ENSP00000304437:A1497V	A	+	2	0	KNDC1	134877185	1.000000	0.71417	0.998000	0.56505	0.282000	0.26991	2.812000	0.47994	2.093000	0.63338	0.313000	0.20887	GCC	.	.	none		0.602	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643		T	135027195	C	T	135027195	3	4	29	1	0	0	0	0	1	0	0	0	8435	739	26	2	4588	2	KNDC1	10	135027195	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	5336358	135027195	507552	516	12757											
B4GALNT4	338707	hgsc.bcm.edu	37	chr11	380395	380395	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagggcaggctggccttcgCgcccgtggtcatgcgcctga	4	7	17	13	4	1	1	1	1	0	0	2	2	1	2	3	5	1	2	3	5	0	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:380395C>T	ENST00000329962.6	+	18	2819	c.2819C>T	c.(2818-2820)gCg>gTg	p.A940V		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	940					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)		CTGGCCTTCGCGCCCGTGGTC	0.687																																					p.A940V		Atlas-SNP	.											B4GALNT4,NS,carcinoma,+1,1	B4GALNT4	83	1	0			c.C2819T						PASS	.						55	40	45					11																	380395		2202	4299	6501	SO:0001583	missense	338707	exon18			CCTTCGCGCCCGT	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.2819C>T	11.37:g.380395C>T	ENSP00000328277:p.Ala940Val	70	0	0		55	4	0.0727273	NM_178537	Q96LV2	Missense_Mutation	SNP	ENST00000329962.6	37	CCDS7694.1	.	.	.	.	.	.	.	.	.	.	c	25.9	4.682412	0.88542	.	.	ENSG00000182272	ENST00000329962	T	0.35236	1.32	3.81	3.81	0.43845	.	0.000000	0.85682	D	0.000000	T	0.41858	0.1177	M	0.67517	2.055	0.58432	D	0.99999	P	0.46512	0.879	P	0.45856	0.495	T	0.36432	-0.9748	10	0.20519	T	0.43	-32.7173	16.2551	0.82510	0.0:1.0:0.0:0.0	.	940	Q76KP1	B4GN4_HUMAN	V	940	ENSP00000328277:A940V	ENSP00000328277:A940V	A	+	2	0	B4GALNT4	370395	1.000000	0.71417	0.977000	0.42913	0.811000	0.45836	7.456000	0.80751	2.118000	0.64928	0.561000	0.74099	GCG	.	.	none		0.687	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537		T	380395	C	T	380395	3	4	29	1	0	0	0	0	1	0	0	0	1269	768	27	1	2889	1	B4GALNT4	11	380395	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10		380395	134626121	517	12758											
PKP3	11187	hgsc.bcm.edu	37	chr11	403658	403658	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cctggccctggagcaggagcGtattctgaaccccctgctag	7	8	12	14	1	1	1	0	1	1	0	1	3	1	3	4	3	4	3	4	3	3	3	rs147657735		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:403658G>C	ENST00000331563.2	+	10	2040	c.1964G>C	c.(1963-1965)cGt>cCt	p.R655P		NM_007183.2	NP_009114.1	Q9Y446	PKP3_HUMAN	plakophilin 3	655					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)		GAGCAGGAGCGTATTCTGAAC	0.667													g|||	1	0.000199681	0.0	0.0	5008	,	,		16683	0.0		0.001	False		,,,				2504	0.0				p.R655P		Atlas-SNP	.											PKP3,NS,lymphoid_neoplasm,0,1	PKP3	36	1	0			c.G1964C						PASS	.		PRO/ARG	5,4357	9.9+/-24.2	0,5,2176	68	60	62		1964	3.8	1	11	dbSNP_134	62	10,8556	7.7+/-29.5	0,10,4273	yes	missense	PKP3	NM_007183.2	103	0,15,6449	CC,CG,GG		0.1167,0.1146,0.116	probably-damaging	655/798	403658	15,12913	2181	4283	6464	SO:0001583	missense	11187	exon10			AGGAGCGTATTCT	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.1964G>C	11.37:g.403658G>C	ENSP00000331678:p.Arg655Pro	26	0	0		28	17	0.607143	NM_007183	F8J390|Q53EX8	Missense_Mutation	SNP	ENST00000331563.2	37	CCDS7695.1	.	.	.	.	.	.	.	.	.	.	g	17.63	3.436167	0.62955	0.001146	0.001167	ENSG00000184363	ENST00000331563	T	0.48201	0.82	3.85	3.85	0.44370	Armadillo-like helical (1);Armadillo-type fold (1);	0.088251	0.50627	D	0.000102	T	0.66781	0.2824	M	0.66939	2.045	0.58432	D	0.999996	D	0.89917	1.0	D	0.87578	0.998	T	0.72567	-0.4254	10	0.87932	D	0	-16.9262	16.3352	0.83056	0.0:0.0:1.0:0.0	.	655	Q9Y446	PKP3_HUMAN	P	655	ENSP00000331678:R655P	ENSP00000331678:R655P	R	+	2	0	PKP3	393658	1.000000	0.71417	0.995000	0.50966	0.471000	0.32888	7.439000	0.80444	2.172000	0.68678	0.306000	0.20318	CGT	G|0.999;C|0.001	0.001	strong		0.667	PKP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239281.1	NM_007183		C	403658	G	C	403658	3	2	29	1	0	0	0	0	1	0	0	0	11995	1145	40	4	2002	4	PKP3	11	403658	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	23263	403658	134602858	518	12759											
MUC2	4583	hgsc.bcm.edu	37	chr11	1097794	1097794	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctggtgaacgacccctccaAgccacactgcccccacagca	10	4	8	19	1	0	1	0	1	0	0	1	2	1	1	6	1	4	2	6	1	2	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1097794A>T	ENST00000441003.2	+	36	6914	c.6887A>T	c.(6886-6888)aAg>aTg	p.K2296M	MUC2_ENST00000361558.6_3'UTR	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4658					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)	GACCCCTCCAAGCCACACTGC	0.657																																					p.K2292M		Atlas-SNP	.											.	MUC2	614	.	0			c.A6875T						PASS	.						30	41	37					11																	1097794		2097	4203	6300	SO:0001583	missense	4583	exon37			CCTCCAAGCCACA	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.6887A>T	11.37:g.1097794A>T	ENSP00000415183:p.Lys2296Met	74	0	0		68	5	0.0735294	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	A	9.090	1.001589	0.19121	.	.	ENSG00000198788	ENST00000441003	T	0.14766	2.48	3.88	2.71	0.32032	.	.	.	.	.	T	0.27933	0.0688	M	0.77313	2.365	0.20563	N	0.999886	D	0.61080	0.989	P	0.53809	0.735	T	0.07616	-1.0763	9	0.59425	D	0.04	.	9.7512	0.40477	0.8264:0.1736:0.0:0.0	.	2296	E7EUV1	.	M	2296	ENSP00000415183:K2296M	ENSP00000415183:K2296M	K	+	2	0	MUC2	1087794	1.000000	0.71417	0.887000	0.34795	0.669000	0.39330	5.420000	0.66441	0.510000	0.28216	0.459000	0.35465	AAG	.	.	none		0.657	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1097794	A	T	1097794	3	4	29	1	0	0	0	0	1	0	0	0	9984	72	3	5	7021	5	MUC2	11	1097794	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	694136	1097794	133908722	519	12760											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1272793	1272793	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cagccactgcctccacggttCccagctcgtccaccgtgggg	5	7	11	18	3	0	0	0	0	0	0	4	0	3	0	6	3	3	2	6	3	0	1	rs56159668	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1272793C>T	ENST00000529681.1	+	31	14741	c.14683C>T	c.(14683-14685)Ccc>Tcc	p.P4895S	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.P4898S	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4895	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)		CTCCACGGTTCCCAGCTCGTC	0.657													C|||	18	0.00359425	0.0	0.0072	5008	,	,		18506	0.0		0.0109	False		,,,				2504	0.002				p.P4895S		Atlas-SNP	.											.	MUC5B	473	.	0			c.C14683T						PASS	.	C	SER/PRO	10,4316		0,10,2153	44	58	53		14683	-3.6	0	11	dbSNP_129	53	80,8408		0,80,4164	yes	missense	MUC5B	NM_002458.2	74	0,90,6317	TT,TC,CC		0.9425,0.2312,0.7024	benign	4895/5763	1272793	90,12724	2163	4244	6407	SO:0001583	missense	727897	exon31			ACGGTTCCCAGCT	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.14683C>T	11.37:g.1272793C>T	ENSP00000436812:p.Pro4895Ser	86	0	0		90	43	0.477778	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	13	0.005952380952380952	0	0.0	5	0.013812154696132596	0	0.0	8	0.010554089709762533	C	3.499	-0.102189	0.06967	0.002312	0.009425	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.15834	2.39;2.57	1.82	-3.64	0.04515	.	.	.	.	.	T	0.07458	0.0188	L	0.40543	1.245	0.09310	N	1	B;B	0.34015	0.435;0.435	B;B	0.24701	0.055;0.055	T	0.10660	-1.0620	9	0.87932	D	0	.	6.4846	0.22081	0.2903:0.2746:0.4351:0.0	rs56159668;rs61745878	5217;4898	A7Y9J9;E9PBJ0	.;.	S	4895;4898;4839;4594	ENSP00000436812:P4895S;ENSP00000415793:P4898S	ENSP00000343037:P4839S	P	+	1	0	MUC5B	1229369	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-6.164000	0.00078	-1.181000	0.02730	0.485000	0.47835	CCC	C|0.992;T|0.008	0.008	strong		0.657	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		T	1272793	C	T	1272793	3	4	29	1	0	0	0	0	1	0	0	0	9988	855	30	2	14814	2	MUC5B	11	1272793	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	174999	1272793	133733723	520	12761											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1281932	1281932	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaggtcaacatcaccttctgCgagggctcctgccccggagc	7	7	12	15	2	3	0	2	0	1	0	4	3	4	1	4	3	4	1	4	3	1	1	rs61734215	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1281932C>T	ENST00000529681.1	+	48	17101	c.17043C>T	c.(17041-17043)tgC>tgT	p.C5681C	MUC5B_ENST00000447027.1_Silent_p.C5684C	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5681	CTCK. {ECO:0000255|PROSITE- ProRule:PRU00039}.				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)		TCACCTTCTGCGAGGGCTCCT	0.652													C|||	19	0.00379393	0.0	0.0072	5008	,	,		18404	0.0		0.0119	False		,,,				2504	0.002				p.C5681C		Atlas-SNP	.											.	MUC5B	473	.	0			c.C17043T						PASS	.	C		13,4251		0,13,2119	50	56	54		17043	-2	1	11	dbSNP_129	54	80,8370		0,80,4145	no	coding-synonymous	MUC5B	NM_002458.2		0,93,6264	TT,TC,CC		0.9467,0.3049,0.7315		5681/5763	1281932	93,12621	2132	4225	6357	SO:0001819	synonymous_variant	727897	exon48			CTTCTGCGAGGGC	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.17043C>T	11.37:g.1281932C>T		137	0	0		106	49	0.462264	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			C|0.992;T|0.008	0.008	strong		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		T	1281932	C	T	1281932	2	4	29	1	0	0	0	0	0	0	0	1	9988	776	27	1		1	MUC5B	11	1281932	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	9139	1281932	133724584	521	12762											
DUSP8	1850	hgsc.bcm.edu	37	chr11	1580172	1580172	+	Missense_Mutation	SNP	T	T	A																															gaggtgaggcaggatgcgggTcaggcccacgctgggcacag																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1580172T>A	ENST00000397374.3	-	4	611	c.484A>T	c.(484-486)Acc>Tcc	p.T162S	DUSP8_ENST00000331588.4_Missense_Mutation_p.T162S|DUSP8_ENST00000528778.1_5'UTR	NM_004420.2	NP_004411.2	Q13202	DUS8_HUMAN	dual specificity phosphatase 8	162	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)		AGGATGCGGGTCAGGCCCACG	0.652																																					p.T162S		Atlas-SNP	.											.	DUSP8	22	.	0			c.A484T						PASS	.						93	78	83					11																	1580172		2202	4299	6501	SO:0001583	missense	1850	exon4			TGCGGGTCAGGCC		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.484A>T	11.37:g.1580172T>A	ENSP00000380530:p.Thr162Ser	119	0	0		121	34	0.280992	NM_004420	Q86SS8	Missense_Mutation	SNP	ENST00000397374.3	37	CCDS7724.1	.	.	.	.	.	.	.	.	.	.	T	17.00	3.276345	0.59649	.	.	ENSG00000184545	ENST00000397374;ENST00000331588	T;T	0.56611	0.45;0.45	4.18	4.18	0.49190	Dual specificity phosphatase, subgroup, catalytic domain (2);	0.000000	0.53938	U	0.000049	T	0.38692	0.1050	N	0.12746	0.255	0.58432	D	0.999999	B	0.31077	0.307	B	0.36092	0.217	T	0.46247	-0.9205	10	0.72032	D	0.01	.	13.4127	0.60952	0.0:0.0:0.0:1.0	.	162	Q13202	DUS8_HUMAN	S	162	ENSP00000380530:T162S;ENSP00000329539:T162S	ENSP00000329539:T162S	T	-	1	0	DUSP8	1536748	1.000000	0.71417	1.000000	0.80357	0.359000	0.29487	7.637000	0.83313	1.762000	0.52044	0.448000	0.29417	ACC	.	.	none		0.652	DUSP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257178.3	NM_004420		A	1580172	T	A	1580172	3	1	29	1	0	0	0	0	1	0	0	0	4833	1667	58	5	1409	5	DUSP8	11	1580172	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	298240	1580172	133426344	522	12763	162	2									
DUSP8	1850	hgsc.bcm.edu	37	chr11	1580173	1580173	+	Silent	SNP	C	C	A																															aggtgaggcaggatgcgggtCaggcccacgctgggcacagg																								rs17854342		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1580173C>A	ENST00000397374.3	-	4	610	c.483G>T	c.(481-483)ctG>ctT	p.L161L	DUSP8_ENST00000331588.4_Silent_p.L161L|DUSP8_ENST00000528778.1_5'UTR	NM_004420.2	NP_004411.2	Q13202	DUS8_HUMAN	dual specificity phosphatase 8	161					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)		GGATGCGGGTCAGGCCCACGC	0.652																																					p.L161L		Atlas-SNP	.											.	DUSP8	22	.	0			c.G483T						PASS	.						91	76	81					11																	1580173		2202	4299	6501	SO:0001819	synonymous_variant	1850	exon4			GCGGGTCAGGCCC		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.483G>T	11.37:g.1580173C>A		119	0	0		119	34	0.285714	NM_004420	Q86SS8	Silent	SNP	ENST00000397374.3	37	CCDS7724.1																																																																																			.	.	alt		0.652	DUSP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257178.3	NM_004420		A	1580173	C	A	1580173	2	1	29	1	0	0	0	0	0	0	0	1	4833	813	29	4		4	DUSP8	11	1580173	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1	1580173	133426343	523	12764	162	2									
KRTAP5-5	439915	hgsc.bcm.edu	37	chr11	1651150	1651150	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctgtgggggctgtggctccgGctgtggaggctgtggctctg	1	11	20	9	1	1	0	0	0	1	0	2	1	2	1	1	7	0	5	1	7	0	0	rs201376522	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:1651150G>A	ENST00000399676.2	+	1	118	c.80G>A	c.(79-81)gGc>gAc	p.G27D		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	27						keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		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)		tgtggctccggctgtggaggc	0.711													-|||	5	0.000998403	0.0	0.0072	5008	,	,		8675	0.0		0.0	False		,,,				2504	0.0				p.G27D		Atlas-SNP	.											KRTAP5-5,right_upper_lobe,carcinoma,-1,2	KRTAP5-5	86	2	0			c.G80A						PASS	.	G	ASP/GLY	1,4273		0,1,2136	29	40	36		80	3	0.1	11		36	4,8460		0,4,4228	no	missense	KRTAP5-5	NM_001001480.2	94	0,5,6364	AA,AG,GG		0.0473,0.0234,0.0393	benign	27/238	1651150	5,12733	2137	4232	6369	SO:0001583	missense	439915	exon1			GCTCCGGCTGTGG	AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"Keratin associated proteins"	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.80G>A	11.37:g.1651150G>A	ENSP00000382584:p.Gly27Asp	56	0	0		55	38	0.690909	NM_001001480	A8MWN2	Missense_Mutation	SNP	ENST00000399676.2	37	CCDS41592.1	.	.	.	.	.	.	.	.	.	.	G	5.003	0.186328	0.09495	2.34E-4	4.73E-4	ENSG00000185940	ENST00000399676;ENST00000422553	T	0.01159	5.25	2.97	2.97	0.34412	.	.	.	.	.	T	0.02012	0.0063	M	0.71036	2.16	0.21802	N	0.999538	B	0.33694	0.421	B	0.30029	0.11	T	0.34976	-0.9807	9	0.44086	T	0.13	.	11.376	0.49728	0.0:0.0:1.0:0.0	.	27	Q701N2	KRA55_HUMAN	D	27;25	ENSP00000382584:G27D	ENSP00000382584:G27D	G	+	2	0	KRTAP5-5	1607726	0.987000	0.35691	0.068000	0.19968	0.043000	0.13939	1.957000	0.40392	1.183000	0.42943	0.442000	0.29010	GGC	.	.	weak		0.711	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1			A	1651150	G	A	1651150	3	1	29	1	0	0	0	0	1	0	0	0	8573	1203	42	2	82	2	KRTAP5-5	11	1651150	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	70977	1651150	133355366	524	12765											
MRGPRE	116534	hgsc.bcm.edu	37	chr11	3249972	3249972	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gatgaggttgaaggccacatCctcctgggcgccgttggcgg	6	8	16	11	3	0	2	0	2	0	0	2	3	2	2	4	5	0	2	4	5	1	2	rs200284450		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:3249972C>A	ENST00000389832.5	-	2	364	c.58G>T	c.(58-60)Gat>Tat	p.D20Y	AC109309.4_ENST00000418995.2_RNA|MRGPRE_ENST00000436689.2_Missense_Mutation_p.D19Y			Q86SM8	MRGRE_HUMAN	MAS-related GPR, member E	20						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)		AAGGCCACATCCTCCTGGGCG	0.667																																					p.D20Y		Atlas-SNP	.											.	MRGPRE	35	.	0			c.G58T						PASS	.	C	TYR/ASP	4,3946		0,4,1971	39	43	42		55	2.8	0.1	11		42	3,8301		0,3,4149	yes	missense	MRGPRE	NM_001039165.2	160	0,7,6120	AA,AC,CC		0.0361,0.1013,0.0571	probably-damaging	19/312	3249972	7,12247	1975	4152	6127	SO:0001583	missense	116534	exon2			CCACATCCTCCTG	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.58G>T	11.37:g.3249972C>A	ENSP00000374482:p.Asp20Tyr	45	0	0		43	21	0.488372	NM_001039165	Q2M1V7	Missense_Mutation	SNP	ENST00000389832.5	37		.	.	.	.	.	.	.	.	.	.	c	14.72	2.620103	0.46736	0.001013	3.61E-4	ENSG00000184350	ENST00000436689;ENST00000389832	.	.	.	2.83	2.83	0.33086	.	1.905200	0.03619	U	0.236065	T	0.17408	0.0418	N	0.08118	0	0.09310	N	1	P	0.49090	0.919	B	0.36989	0.238	T	0.25012	-1.0144	9	0.59425	D	0.04	-2.7001	8.884	0.35392	0.0:1.0:0.0:0.0	.	19	Q86SM8	MRGRE_HUMAN	Y	20;19	.	ENSP00000374482:D19Y	D	-	1	0	MRGPRE	3206548	0.057000	0.20700	0.062000	0.19696	0.065000	0.16274	2.890000	0.48609	1.399000	0.46721	0.484000	0.47621	GAT	.	.	weak		0.667	MRGPRE-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000032346.5	XM_171536		A	3249972	C	A	3249972	3	1	29	1	0	0	0	0	1	0	0	0	9773	855	30	4	884	4	MRGPRE	11	3249972	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1598822	3249972	131756544	525	12766											
ART5	116969	hgsc.bcm.edu	37	chr11	3660238	3660238	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggaagggcaactcacctggcGcagacacacagccccgcctc	10	3	11	17	2	1	1	1	0	0	1	2	2	1	2	4	3	2	2	4	3	2	0	rs142998376	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:3660238G>A	ENST00000397068.3	-	3	1207	c.815C>T	c.(814-816)gCg>gTg	p.A272V	TRPC2_ENST00000526541.1_RNA|ART5_ENST00000397067.3_Missense_Mutation_p.A204V|ART5_ENST00000359918.4_Missense_Mutation_p.A272V	NM_053017.3	NP_443750.2	Q96L15	NAR5_HUMAN	ADP-ribosyltransferase 5	272					protein ADP-ribosylation (GO:0006471)	extracellular region (GO:0005576)|membrane (GO:0016020)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|NAD+ nucleosidase activity (GO:0003953)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(6)|ovary(1)	11		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0336)|LUSC - Lung squamous cell carcinoma(625;0.19)		CTCACCTGGCGCAGACACACA	0.637													G|||	17	0.00339457	0.0091	0.0072	5008	,	,		16924	0.0		0.0	False		,,,				2504	0.0				p.A272V		Atlas-SNP	.											.	ART5	38	.	0			c.C815T						PASS	.	G	VAL/ALA,VAL/ALA	18,4314		0,18,2148	60	52	55		815,815	-8.6	0	11	dbSNP_134	55	16,8478		0,16,4231	yes	missense,missense	ART5	NM_001079536.1,NM_053017.3	64,64	0,34,6379	AA,AG,GG		0.1884,0.4155,0.2651	benign,benign	272/292,272/292	3660238	34,12792	2166	4247	6413	SO:0001583	missense	116969	exon3			CCTGGCGCAGACA	Y16835	CCDS7743.1, CCDS73242.1	11p15.4	2008-02-05			ENSG00000167311	ENSG00000167311			24049	protein-coding gene	gene with protein product		610625				11587854, 10448534	Standard	NM_001079536		Approved		uc001lyb.1	Q96L15	OTTHUMG00000011842	ENST00000397068.3:c.815C>T	11.37:g.3660238G>A	ENSP00000380258:p.Ala272Val	83	0	0		73	33	0.452055	NM_053017	C9IYG7|Q6UX84|Q86W02	Missense_Mutation	SNP	ENST00000397068.3	37	CCDS7743.1	5	0.0022893772893772895	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	0	0.0	G	8.738	0.918215	0.17982	0.004155	0.001884	ENSG00000167311	ENST00000397068;ENST00000397067;ENST00000359918	T;T;T	0.08458	3.09;3.17;3.09	5.87	-8.63	0.00878	.	3.067170	0.00805	N	0.001445	T	0.02494	0.0076	N	0.11927	0.2	0.09310	N	1	B;B	0.25206	0.12;0.0	B;B	0.21917	0.037;0.0	T	0.32428	-0.9907	10	0.27785	T	0.31	7.2848	4.0976	0.09998	0.1934:0.1975:0.5108:0.0983	.	204;272	Q96L15-2;Q96L15	.;NAR5_HUMAN	V	272;204;272	ENSP00000380258:A272V;ENSP00000380257:A204V;ENSP00000352992:A272V	ENSP00000352992:A272V	A	-	2	0	ART5	3616814	0.000000	0.05858	0.000000	0.03702	0.542000	0.35054	-1.166000	0.03129	-1.233000	0.02551	0.655000	0.94253	GCG	G|0.998;A|0.002	0.002	strong		0.637	ART5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032760.2	NM_053017		A	3660238	G	A	3660238	3	1	29	1	0	0	0	0	1	0	0	0	1000	1087	38	1	68	1	ART5	11	3660238	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	410266	3660238	131346278	526	12767											
OR51E1	143503	hgsc.bcm.edu	37	chr11	4674343	4674343	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctggcctgtgatgatatccGggtcaatgtcgtctatggcc	6	12	13	10	2	2	2	1	2	1	0	4	2	3	2	3	3	0	1	3	3	3	2	rs139501861	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:4674343G>A	ENST00000396952.5	+	2	1237	c.587G>A	c.(586-588)cGg>cAg	p.R196Q	OR51E1_ENST00000530215.1_Intron	NM_152430.3	NP_689643.2	Q8TCB6	O51E1_HUMAN	olfactory receptor, family 51, subfamily E, member 1	195						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)		GATGATATCCGGGTCAATGTC	0.488													G|||	9	0.00179712	0.0	0.0043	5008	,	,		24525	0.0		0.005	False		,,,				2504	0.001				p.R196Q		Atlas-SNP	.											OR51E1,caecum,carcinoma,-1,1	OR51E1	67	1	0			c.G587A						scavenged	.	G	GLN/ARG	11,4391	17.9+/-39.9	0,11,2190	237	206	216		587	-2.6	0.3	11	dbSNP_134	216	62,8534	38.8+/-94.9	0,62,4236	yes	missense	OR51E1	NM_152430.3	43	0,73,6426	AA,AG,GG		0.7213,0.2499,0.5616	possibly-damaging	196/319	4674343	73,12925	2201	4298	6499	SO:0001583	missense	143503	exon2			ATATCCGGGTCAA	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.587G>A	11.37:g.4674343G>A	ENSP00000380155:p.Arg196Gln	143	1	0.00699301		138	74	0.536232	NM_152430	A8KAM6|Q5S4P5|Q66X57|Q6IF93	Missense_Mutation	SNP	ENST00000396952.5	37	CCDS31358.2	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	9.562	1.118610	0.20877	0.002499	0.007213	ENSG00000180785	ENST00000396952	T	0.37752	1.18	4.98	-2.56	0.06268	GPCR, rhodopsin-like superfamily (1);	1.290730	0.05102	N	0.487404	T	0.33644	0.0870	L	0.50919	1.6	0.09310	N	1	P	0.43431	0.807	P	0.48270	0.572	T	0.50972	-0.8764	10	0.54805	T	0.06	.	11.1371	0.48381	0.5891:0.0:0.4109:0.0	.	195	Q8TCB6	O51E1_HUMAN	Q	196	ENSP00000380155:R196Q	ENSP00000380155:R196Q	R	+	2	0	OR51E1	4630919	0.000000	0.05858	0.286000	0.24833	0.395000	0.30598	-2.797000	0.00763	-0.557000	0.06126	-0.736000	0.03550	CGG	G|0.996;A|0.004	0.004	strong		0.488	OR51E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347136.2	NM_152430		A	4674343	G	A	4674343	3	1	29	1	0	0	0	0	1	0	0	0	11103	1116	39	1	589	1	OR51E1	11	4674343	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1014105	4674343	130332173	527	12768											
HBE1	3046	hgsc.bcm.edu	37	chr11	5289816	5289816	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccagaataatcaccatcacGttacccaggagctgttaggc	12	8	9	12	1	2	1	2	0	0	1	2	2	2	2	3	2	2	3	3	2	4	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:5289816G>A	ENST00000380237.1	-	5	671	c.327C>T	c.(325-327)aaC>aaT	p.N109N	HBE1_ENST00000292896.2_Silent_p.N109N|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron			P02100	HBE_HUMAN	hemoglobin, epsilon 1	109					blood coagulation (GO:0007596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein heterooligomerization (GO:0051291)	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)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|skin(1)	20		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.34e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCACCATCACGTTACCCAGGA	0.458																																					p.N109N		Atlas-SNP	.											.	HBE1	42	.	0			c.C327T						PASS	.						170	154	159					11																	5289816		2201	4298	6499	SO:0001819	synonymous_variant	3046	exon3			CATCACGTTACCC	BC015537	CCDS7756.1	11p15.5	2012-10-02			ENSG00000213931	ENSG00000213931			4830	protein-coding gene	gene with protein product		142100				2649166	Standard	NM_005330		Approved	HBE	uc001mal.1	P02100	OTTHUMG00000066675	ENST00000380237.1:c.327C>T	11.37:g.5289816G>A		49	0	0		54	6	0.111111	NM_005330	Q6FH44	Silent	SNP	ENST00000380237.1	37	CCDS7756.1																																																																																			.	.	none		0.458	HBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142973.2	NM_005330		A	5289816	G	A	5289816	2	1	29	1	0	0	0	0	0	0	0	1	6989	1136	40	1		1	HBE1	11	5289816	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	615473	5289816	129716700	528	12769											
DNHD1	144132	hgsc.bcm.edu	37	chr11	6578788	6578788	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gtctaacaccatccataggaCcagtaagcagggggatgaag	14	6	12	9	0	1	1	0	1	1	0	2	3	2	3	3	3	2	2	3	3	4	3	rs111982303	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6578788C>T	ENST00000527990.2	+	23	8263	c.8263C>T	c.(8263-8265)Cca>Tca	p.P2755S	DNHD1_ENST00000254579.6_Missense_Mutation_p.P2755S			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	2755					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)		ATCCATAGGACCAGTAAGCAG	0.473													C|||	114	0.0227636	0.0061	0.0245	5008	,	,		22472	0.0099		0.004	False		,,,				2504	0.0767				p.P2755S		Atlas-SNP	.											.	DNHD1	198	.	0			c.C8263T						PASS	.	C	SER/PRO	10,1374		0,10,682	81	81	81		8263	0.2	0	11	dbSNP_132	81	25,3157		0,25,1566	yes	missense	DNHD1	NM_144666.2	74	0,35,2248	TT,TC,CC		0.7857,0.7225,0.7665	benign	2755/4754	6578788	35,4531	692	1591	2283	SO:0001583	missense	144132	exon25			ATAGGACCAGTAA	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.8263C>T	11.37:g.6578788C>T	ENSP00000436180:p.Pro2755Ser	71	0	0		62	38	0.612903	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	26	0.011904761904761904	4	0.008130081300813009	9	0.024861878453038673	10	0.017482517482517484	3	0.00395778364116095	C	0.280	-0.986911	0.02180	0.007225	0.007857	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000534210	T;T	0.25912	1.77;1.77	4.91	0.165	0.14995	.	.	.	.	.	T	0.04272	0.0118	N	0.08118	0	0.09310	N	1	B;B	0.22909	0.01;0.077	B;B	0.20767	0.007;0.031	T	0.34601	-0.9822	9	0.14252	T	0.57	.	2.3474	0.04275	0.1445:0.5153:0.1405:0.1997	.	2755;502	Q96M86;E9PHZ7	DNHD1_HUMAN;.	S	2755;2755;502	ENSP00000254579:P2755S;ENSP00000436180:P2755S	ENSP00000254579:P2755S	P	+	1	0	DNHD1	6535364	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.244000	0.08903	-0.116000	0.11893	-0.266000	0.10368	CCA	C|0.988;T|0.012	0.012	strong		0.473	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		T	6578788	C	T	6578788	3	4	29	1	0	0	0	0	1	0	0	0	4670	507	18	2	8362	2	DNHD1	11	6578788	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1288972	6578788	128427728	529	12770											
RRP8	23378	hgsc.bcm.edu	37	chr11	6622218	6622218	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	caagtcaaagcaatgcacagGgttccggatacttgaagcca	14	7	10	10	1	1	1	1	1	0	0	2	2	2	2	2	2	4	3	2	2	5	3	rs17834692	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6622218G>A	ENST00000254605.6	-	4	1102	c.985C>T	c.(985-987)Cct>Tct	p.P329S	RP11-732A19.8_ENST00000527191.1_RNA|ILK_ENST00000299421.4_5'Flank|ILK_ENST00000528995.1_5'Flank|ILK_ENST00000396751.2_5'Flank|ILK_ENST00000537806.1_5'Flank|ILK_ENST00000420936.2_5'Flank|RRP8_ENST00000534343.1_Intron	NM_015324.3	NP_056139.1	O43159	RRP8_HUMAN	ribosomal RNA processing 8, methyltransferase, homolog (yeast)	329			P -> S (in dbSNP:rs17834692).		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						CAATGCACAGGGTTCCGGATA	0.552													G|||	151	0.0301518	0.0045	0.0836	5008	,	,		20815	0.0109		0.008	False		,,,				2504	0.0695				p.P329S		Atlas-SNP	.											.	RRP8	40	.	0			c.C985T						PASS	.	G	SER/PRO	43,4359	45.3+/-79.5	0,43,2158	104	103	104		985	2.2	1	11	dbSNP_123	104	68,8524	40.8+/-97.7	0,68,4228	yes	missense	RRP8	NM_015324.3	74	0,111,6386	AA,AG,GG		0.7914,0.9768,0.8542	benign	329/457	6622218	111,12883	2201	4296	6497	SO:0001583	missense	23378	exon4			GCACAGGGTTCCG	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.985C>T	11.37:g.6622218G>A	ENSP00000254605:p.Pro329Ser	60	0	0		91	39	0.428571	NM_015324	Q7KZ78|Q9BVM6	Missense_Mutation	SNP	ENST00000254605.6	37	CCDS31411.1	43	0.019688644688644688	1	0.0020325203252032522	24	0.06629834254143646	11	0.019230769230769232	7	0.009234828496042216	G	10.87	1.472472	0.26423	0.009768	0.007914	ENSG00000132275	ENST00000254605	T	0.39229	1.09	5.41	2.22	0.28083	.	0.387563	0.27500	N	0.019093	T	0.01287	0.0042	N	0.01576	-0.805	0.80722	D	1	B	0.18166	0.026	B	0.19666	0.026	T	0.05131	-1.0904	10	0.40728	T	0.16	0.8153	14.0765	0.64893	0.0:0.0:0.4887:0.5113	rs17834692;rs52826857;rs17834692	329	O43159	RRP8_HUMAN	S	329	ENSP00000254605:P329S	ENSP00000254605:P329S	P	-	1	0	RRP8	6578794	0.999000	0.42202	1.000000	0.80357	0.996000	0.88848	1.286000	0.33273	0.796000	0.33947	0.655000	0.94253	CCT	G|0.986;A|0.014	0.014	strong		0.552	RRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384505.1	NM_015324		A	6622218	G	A	6622218	3	1	29	1	0	0	0	0	1	0	0	0	13705	1232	43	2	401	2	RRP8	11	6622218	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	43430	6622218	128384298	530	12771											
OR6A2	8590	hgsc.bcm.edu	37	chr11	6816750	6816751	+	Frame_Shift_Ins	INS	-	-	A																															agaaaggacatattagctagINSaaaaaagtacatgggtttgt																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6816750_6816751insA	ENST00000332601.3	-	1	377_378	c.189_190insT	c.(187-192)tttctafs	p.L64fs		NM_003696.2	NP_003687.2	O95222	OR6A2_HUMAN	olfactory receptor, family 6, subfamily A, member 2	64					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)		ATATTAGCTAGAAAAAAGTACA	0.441																																					p.L64fs		Atlas-Indel	.											.	OR6A2	68	.	0			c.190_191insT						PASS	.																																			SO:0001589	frameshift_variant	8590	exon1			.	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.190dupT	11.37:g.6816756_6816756dupA	ENSP00000330384:p.Leu64fs	149	0	0		157	33	0.210191	NM_003696	Q3MJC7|Q6IF35|Q9H206	Frame_Shift_Ins	INS	ENST00000332601.3	37	CCDS7772.1																																																																																			.	.	none		0.441	OR6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385981.1	NM_003696		A	6816751	-	A	6816750	7	5	29	1	0	1	1	0	0	0	0	0	11195	933	33	0	797	0	OR6A2	11	6816750	Frame_Shift_Ins	INS	-	TCGA-GR-7351-01A-11D-2210-10	194532	6816750	128189766	531	12772											
OR10A5	144124	hgsc.bcm.edu	37	chr11	6867588	6867588	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatactcgcattgctgctgcTatcctcaagatcccatcagc	9	12	6	14	1	2	1	2	0	0	1	5	1	4	1	2	0	5	4	2	0	4	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:6867588T>C	ENST00000299454.4	+	1	706	c.675T>C	c.(673-675)gcT>gcC	p.A225A	OR10A5_ENST00000379831.2_Silent_p.A229A			Q9H207	O10A5_HUMAN	olfactory receptor, family 10, subfamily A, member 5	225					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)		TTGCTGCTGCTATCCTCAAGA	0.473																																					p.A225A	Pancreas(44;21 1072 25662 28041 45559)	Atlas-SNP	.											.	OR10A5	48	.	0			c.T675C						PASS	.						286	234	252					11																	6867588		2201	4296	6497	SO:0001819	synonymous_variant	144124	exon1			TGCTGCTATCCTC	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.675T>C	11.37:g.6867588T>C		243	0	0		224	12	0.0535714	NM_178168	O95223|Q52M66|Q96R21|Q96R22	Silent	SNP	ENST00000299454.4	37	CCDS7773.1																																																																																			.	.	none		0.473	OR10A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385983.1	NM_178168		C	6867588	T	C	6867588	2	2	29	1	0	0	0	0	0	0	0	1	10902	1509	53	3		3	OR10A5	11	6867588	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	50838	6867588	128138928	532	12773											
PPFIBP2	8495	hgsc.bcm.edu	37	chr11	7662851	7662851	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cattaagaagttctggggaaAgtaagttggtgccgttgatc	11	12	13	5	1	1	2	0	1	1	1	2	3	1	3	1	3	1	4	1	3	4	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:7662851A>C	ENST00000299492.4	+	16	1905	c.1517A>C	c.(1516-1518)aAa>aCa	p.K506T	PPFIBP2_ENST00000530181.1_Splice_Site_p.K363T|PPFIBP2_ENST00000533792.1_Splice_Site_p.K348T|PPFIBP2_ENST00000530582.1_3'UTR|PPFIBP2_ENST00000528883.1_Splice_Site_p.K394T	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	506					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)		TTCTGGGGAAAGTAAGTTGGT	0.438																																					p.K506T		Atlas-SNP	.											.	PPFIBP2	87	.	0			c.A1517C						PASS	.						133	120	125					11																	7662851		2201	4296	6497	SO:0001630	splice_region_variant	8495	exon16			GGGGAAAGTAAGT	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.1517+1A>C	11.37:g.7662851A>C		94	0	0		92	24	0.26087	NM_003621	B7Z433|E9PK77|O75337|Q8WW26	Missense_Mutation	SNP	ENST00000299492.4	37	CCDS31419.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.70|18.70	3.680571|3.680571	0.68042|0.68042	.|.	.|.	ENSG00000166387|ENSG00000166387	ENST00000534409|ENST00000299492;ENST00000533792;ENST00000537467;ENST00000541115;ENST00000528883;ENST00000530181;ENST00000530081	.|T;T;T;T	.|0.48836	.|1.23;0.81;1.23;0.8	6.03|6.03	4.91|4.91	0.64330|0.64330	.|.	0.063724|0.063724	0.64402|0.64402	D|D	0.000005|0.000005	T|T	0.60945|0.60945	0.2308|0.2308	L|L	0.59436|0.59436	1.845|1.845	0.58432|0.58432	D|D	0.999991|0.999991	.|D;D;D;D;D;D	.|0.76494	.|0.998;0.995;0.999;0.998;0.998;0.998	.|D;P;D;P;P;D	.|0.78314	.|0.931;0.844;0.991;0.898;0.898;0.98	T|T	0.62623|0.62623	-0.6815|-0.6815	6|10	.|0.87932	.|D	.|0	-15.9732|-15.9732	7.7136|7.7136	0.28692|0.28692	0.8399:0.0:0.1601:0.0|0.8399:0.0:0.1601:0.0	.|.	.|394;394;429;348;363;506	.|E9PK77;B7Z433;F5GWB0;E9PP16;E9PMU1;Q8ND30	.|.;.;.;.;.;LIPB2_HUMAN	N|T	196|506;348;348;429;394;363;167	.|ENSP00000299492:K506T;ENSP00000436498:K348T;ENSP00000435469:K394T;ENSP00000437321:K363T	.|ENSP00000299492:K506T	K|K	+|+	3|2	2|0	PPFIBP2|PPFIBP2	7619427|7619427	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	3.973000|3.973000	0.56845|0.56845	1.102000|1.102000	0.41551|0.41551	0.533000|0.533000	0.62120|0.62120	AAA|AAA	.	.	none		0.438	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621	Missense_Mutation	C	7662851	A	C	7662851	5	2	29	1	0	0	0	0	0	0	1	0	12323	86	3	5	1575	5	PPFIBP2	11	7662851	Splice_Site	SNP	A	TCGA-GR-7351-01A-11D-2210-10	795263	7662851	127343665	533	12774											
TUB	7275	hgsc.bcm.edu	37	chr11	8119298	8119298	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaggaagagaaagaagagtaAaacttccaattacctcatct	19	8	7	7	0	2	3	1	0	1	3	3	5	3	4	2	1	2	1	2	1	8	3	rs55892969	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:8119298A>G	ENST00000299506.2	+	8	1072	c.923A>G	c.(922-924)aAa>aGa	p.K308R	TUB_ENST00000305253.4_Missense_Mutation_p.K363R|TUB_ENST00000534099.1_Missense_Mutation_p.K314R	NM_177972.2	NP_813977.1	P50607	TUB_HUMAN	tubby bipartite transcription factor	308					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)		AAGAAGAGTAAAACTTCCAAT	0.517													A|||	40	0.00798722	0.0008	0.0072	5008	,	,		20036	0.0		0.0298	False		,,,				2504	0.0041				p.K363R		Atlas-SNP	.											.	TUB	71	.	0			c.A1088G						PASS	.	A	ARG/LYS,ARG/LYS	31,4371	36.8+/-68.6	0,31,2170	157	165	162		1088,923	4.7	1	11	dbSNP_129	162	253,8339	99.9+/-161.4	6,241,4049	yes	missense,missense	TUB	NM_003320.4,NM_177972.2	26,26	6,272,6219	GG,GA,AA		2.9446,0.7042,2.1856	benign,benign	363/562,308/507	8119298	284,12710	2201	4296	6497	SO:0001583	missense	7275	exon9			AGAGTAAAACTTC	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.923A>G	11.37:g.8119298A>G	ENSP00000299506:p.Lys308Arg	112	0	0		106	59	0.556604	NM_003320	D3DQU4|O00293|Q6B007	Missense_Mutation	SNP	ENST00000299506.2	37	CCDS7787.1	27	0.012362637362637362	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	23	0.030343007915567283	A	20.5	4.002333	0.74932	0.007042	0.029446	ENSG00000166402	ENST00000534099;ENST00000305253;ENST00000299506	D;D;D	0.96619	-4.07;-4.07;-4.07	4.7	4.7	0.59300	Tubby, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.89206	0.6649	L	0.55743	1.74	0.80722	D	1	B;B;B	0.32245	0.19;0.361;0.326	B;B;B	0.39503	0.11;0.301;0.297	D	0.90008	0.4119	10	0.56958	D	0.05	-22.229	14.4578	0.67428	1.0:0.0:0.0:0.0	rs55892969	314;308;363	E9PQR4;P50607;P50607-2	.;TUB_HUMAN;.	R	314;363;308	ENSP00000434400:K314R;ENSP00000305426:K363R;ENSP00000299506:K308R	ENSP00000299506:K308R	K	+	2	0	TUB	8075874	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.339000	0.96797	1.886000	0.54624	0.477000	0.44152	AAA	A|0.983;G|0.017	0.017	strong		0.517	TUB-003	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385823.1	NM_003320		G	8119298	A	G	8119298	3	3	29	1	0	0	0	0	1	0	0	0	16757	14	1	3	1164	3	TUB	11	8119298	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	456447	8119298	126887218	534	12775											
PARVA	55742	hgsc.bcm.edu	37	chr11	12525965	12525965	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	accatgtttccatccaagtgGttgtggtccaggtaagacag	10	11	11	9	0	0	1	0	0	0	1	3	1	3	1	4	3	0	3	4	3	2	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:12525965G>C	ENST00000550549.1	+	6	695	c.646G>C	c.(646-648)Gtt>Ctt	p.V216L	PARVA_ENST00000334956.8_Missense_Mutation_p.V256L|PARVA_ENST00000539723.1_Missense_Mutation_p.V216L|PARVA_ENST00000538608.1_Missense_Mutation_p.V163L			Q9NVD7	PARVA_HUMAN	parvin, alpha	216					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)		CATCCAAGTGGTTGTGGTCCA	0.498																																					p.V256L		Atlas-SNP	.											.	PARVA	27	.	0			c.G766C						PASS	.						101	96	98					11																	12525965		2036	4169	6205	SO:0001583	missense	55742	exon6			CAAGTGGTTGTGG	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.646G>C	11.37:g.12525965G>C	ENSP00000447198:p.Val216Leu	160	0	0		131	63	0.480916	NM_018222	Q96C85|Q9HA48	Missense_Mutation	SNP	ENST00000550549.1	37		.	.	.	.	.	.	.	.	.	.	G	16.41	3.115564	0.56505	.	.	ENSG00000197702	ENST00000334956;ENST00000539723;ENST00000550549;ENST00000538608;ENST00000528916	T;T;T;T;T	0.70164	-0.46;-0.44;-0.44;0.16;0.16	5.03	5.03	0.67393	Calponin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.74313	0.3700	M	0.61703	1.905	0.80722	D	1	P;B	0.46512	0.879;0.303	P;B	0.52031	0.688;0.05	T	0.71777	-0.4490	10	0.33940	T	0.23	-19.2457	18.5136	0.90926	0.0:0.0:1.0:0.0	.	163;216	B7Z952;Q9NVD7	.;PARVA_HUMAN	L	256;216;216;163;180	ENSP00000334008:V256L;ENSP00000438967:V216L;ENSP00000447198:V216L;ENSP00000442960:V163L;ENSP00000435860:V180L	ENSP00000334008:V256L	V	+	1	0	PARVA	12482541	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.620000	0.83070	2.775000	0.95449	0.655000	0.94253	GTT	.	.	none		0.498	PARVA-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_018222		C	12525965	G	C	12525965	3	2	29	1	0	0	0	0	1	0	0	0	11477	1261	44	4	668	4	PARVA	11	12525965	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	4406667	12525965	122480551	535	12776											
USH1C	10083	hgsc.bcm.edu	37	chr11	17527386	17527386	+	Intron	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggggcttaccagaacttcAgatttcacagctggcctgta	11	10	10	10	0	2	2	2	0	0	2	2	2	2	2	2	3	3	3	2	3	4	4	rs369021714		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:17527386A>G	ENST00000318024.4	-	16	1393				USH1C_ENST00000527720.1_Intron|USH1C_ENST00000529563.1_Intron|USH1C_ENST00000005226.7_Silent_p.S708S|USH1C_ENST00000527020.1_Intron	NM_005709.3	NP_005700.2	Q9Y6N9	USH1C_HUMAN	Usher syndrome 1C (autosomal recessive, severe)						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						CCAGAACTTCAGATTTCACAG	0.592																																					p.S708S		Atlas-SNP	.											.	USH1C	157	.	0			c.T2124C						PASS	.	A	,	0,4400		0,0,2200	59	59	59		,2124	-10.4	0.2	11		59	1,8585	1.2+/-3.3	0,1,4292	no	intron,coding-synonymous	USH1C	NM_005709.3,NM_153676.3	,	0,1,6492	GG,GA,AA		0.0116,0.0,0.0077	,	,708/900	17527386	1,12985	2200	4293	6493	SO:0001627	intron_variant	10083	exon19			AACTTCAGATTTC	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.1285-3859T>C	11.37:g.17527386A>G		74	0	0		80	41	0.5125	NM_153676	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Silent	SNP	ENST00000318024.4	37	CCDS31438.1																																																																																			.	.	weak		0.592	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709		G	17527386	A	G	17527386	1	3	29	0	1	0	0	0	0	0	0	0	17049	175	7	3		3	USH1C	11	17527386	Intron	SNP	A	TCGA-GR-7351-01A-11D-2210-10	5001421	17527386	117479130	536	12777											
USH1C	10083	hgsc.bcm.edu	37	chr11	17552707	17552707	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctctgtttgctcacctggagCccgacgctgtctgcctgacc	4	11	10	16	2	3	1	1	1	2	0	3	3	3	2	4	1	3	3	4	1	0	1	rs41282942	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:17552707C>A	ENST00000318024.4	-	4	489	c.381G>T	c.(379-381)ggG>ggT	p.G127G	USH1C_ENST00000527720.1_Silent_p.G96G|USH1C_ENST00000005226.7_Silent_p.G127G|USH1C_ENST00000527020.1_Silent_p.G127G	NM_005709.3	NP_005700.2	Q9Y6N9	USH1C_HUMAN	Usher syndrome 1C (autosomal recessive, severe)	127	PDZ 1. {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						TCACCTGGAGCCCGACGCTGT	0.642													C|||	7	0.00139776	0.0008	0.0014	5008	,	,		16949	0.001		0.003	False		,,,				2504	0.001				p.G127G		Atlas-SNP	.											.	USH1C	157	.	0			c.G381T						PASS	.	C	,	2,4398	4.2+/-10.8	0,2,2198	33	37	36		381,381	3.5	1	11	dbSNP_127	36	39,8547	25.1+/-72.6	0,39,4254	no	coding-synonymous,coding-synonymous	USH1C	NM_005709.3,NM_153676.3	,	0,41,6452	AA,AC,CC		0.4542,0.0455,0.3157	,	127/553,127/900	17552707	41,12945	2200	4293	6493	SO:0001819	synonymous_variant	10083	exon4			CTGGAGCCCGACG	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.381G>T	11.37:g.17552707C>A		65	0	0		75	36	0.48	NM_005709	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Silent	SNP	ENST00000318024.4	37	CCDS31438.1																																																																																			C|0.998;A|0.002	0.002	strong		0.642	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709		A	17552707	C	A	17552707	2	1	29	1	0	0	0	0	0	0	0	1	17049	726	26	4		4	USH1C	11	17552707	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	25321	17552707	117453809	537	12778											
LDHAL6A	160287	hgsc.bcm.edu	37	chr11	18485611	18485611	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttatgaaaatgccaaataTtgtctccagcaaaggttaat	15	14	6	6	0	1	1	0	1	1	0	2	1	1	1	2	1	2	2	2	1	7	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:18485611T>C	ENST00000280706.2	+	2	1027	c.230T>C	c.(229-231)aTt>aCt	p.I77T	LDHAL6A_ENST00000396213.3_Missense_Mutation_p.I77T	NM_144972.4	NP_659409.2	Q6ZMR3	LDH6A_HUMAN	lactate dehydrogenase A-like 6A	77					cellular carbohydrate metabolic process (GO:0044262)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	L-lactate dehydrogenase activity (GO:0004459)			large_intestine(3)|lung(9)|urinary_tract(1)	13						ATGCCAAATATTGTCTCCAGC	0.343																																					p.I77T		Atlas-SNP	.											.	LDHAL6A	35	.	0			c.T230C						PASS	.						113	99	104					11																	18485611		2199	4293	6492	SO:0001583	missense	160287	exon2			CAAATATTGTCTC	AK131523	CCDS7841.1	11p15.1	2011-01-27			ENSG00000166800	ENSG00000166800			28335	protein-coding gene	gene with protein product						12477932	Standard	NM_001144071		Approved	MGC23940, LDH6A	uc001mop.1	Q6ZMR3	OTTHUMG00000167724	ENST00000280706.2:c.230T>C	11.37:g.18485611T>C	ENSP00000280706:p.Ile77Thr	56	0	0		67	25	0.373134	NM_144972	D3DQY5	Missense_Mutation	SNP	ENST00000280706.2	37	CCDS7841.1	.	.	.	.	.	.	.	.	.	.	T	14.77	2.634138	0.47049	.	.	ENSG00000166800	ENST00000396213;ENST00000280706	D;D	0.90844	-2.74;-2.74	3.95	2.79	0.32731	Lactate/malate dehydrogenase, N-terminal (1);NAD(P)-binding domain (1);	0.000000	0.64402	U	0.000010	D	0.94235	0.8149	M	0.81497	2.545	0.51767	D	0.99993	D	0.76494	0.999	D	0.76071	0.987	D	0.93050	0.6465	10	0.87932	D	0	.	9.3871	0.38349	0.0:0.0:0.1803:0.8196	.	77	Q6ZMR3	LDH6A_HUMAN	T	77	ENSP00000379516:I77T;ENSP00000280706:I77T	ENSP00000280706:I77T	I	+	2	0	LDHAL6A	18442187	1.000000	0.71417	0.327000	0.25402	0.745000	0.42441	4.294000	0.59043	0.400000	0.25396	0.533000	0.62120	ATT	.	.	none		0.343	LDHAL6A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395904.1	NM_144972		C	18485611	T	C	18485611	3	2	29	1	0	0	0	0	1	0	0	0	8708	1493	52	3	236	3	LDHAL6A	11	18485611	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	932904	18485611	116520905	538	12779											
LDHAL6A	160287	hgsc.bcm.edu	37	chr11	18487252	18487253	+	Frame_Shift_Del	DEL	AC	AC	-																															cacgccagaaaaaaggagaaAcacgccttgatttagtccag																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:18487252_18487253delAC	ENST00000280706.2	+	3	1110_1111	c.313_314delAC	c.(313-315)acafs	p.T105fs	LDHAL6A_ENST00000396213.3_Frame_Shift_Del_p.T105fs	NM_144972.4	NP_659409.2	Q6ZMR3	LDH6A_HUMAN	lactate dehydrogenase A-like 6A	105					cellular carbohydrate metabolic process (GO:0044262)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	L-lactate dehydrogenase activity (GO:0004459)			large_intestine(3)|lung(9)|urinary_tract(1)	13						AAAAGGAGAAACACGCCTTGAT	0.376																																					p.104_105del		Pindel,Atlas-Indel	.											.	LDHAL6A	35	.	0			c.312_313del						PASS	.																																			SO:0001589	frameshift_variant	160287	exon3			.	AK131523	CCDS7841.1	11p15.1	2011-01-27			ENSG00000166800	ENSG00000166800			28335	protein-coding gene	gene with protein product						12477932	Standard	NM_001144071		Approved	MGC23940, LDH6A	uc001mop.1	Q6ZMR3	OTTHUMG00000167724	ENST00000280706.2:c.313_314delAC	11.37:g.18487254_18487255delAC	ENSP00000280706:p.Thr105fs	152	0	.		179	56	0.313	NM_144972	D3DQY5	Frame_Shift_Del	DEL	ENST00000280706.2	37	CCDS7841.1																																																																																			.	.	none		0.376	LDHAL6A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395904.1	NM_144972		-	18487253	AC	-	18487252	7	5	29	1	0	1	0	1	0	0	0	0	8708	43	2	0	323	0	LDHAL6A	11	18487252	Frame_Shift_Del	DEL	AC	TCGA-GR-7351-01A-11D-2210-10	1641	18487252	116519264	539	12780											
NELL1	4745	hgsc.bcm.edu	37	chr11	20939776	20939776	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttatgccgaatggatatataAcacagtgtccaaatctaaat	16	12	6	7	1	1	0	0	0	1	0	2	2	2	1	2	1	2	0	2	1	8	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:20939776A>T	ENST00000357134.5	+	6	804	c.652A>T	c.(652-654)Aca>Tca	p.T218S	NELL1_ENST00000298925.5_Missense_Mutation_p.T246S|NELL1_ENST00000325319.5_Missense_Mutation_p.T161S|NELL1_ENST00000532434.1_Missense_Mutation_p.T218S	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	218	Laminin G-like.				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						TGGATATATAACACAGTGTCC	0.353																																					p.T218S		Atlas-SNP	.											.	NELL1	179	.	0			c.A652T						PASS	.						155	148	150					11																	20939776		2203	4299	6502	SO:0001583	missense	4745	exon6			TATATAACACAGT	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.652A>T	11.37:g.20939776A>T	ENSP00000349654:p.Thr218Ser	90	0	0		96	20	0.208333	NM_006157	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Missense_Mutation	SNP	ENST00000357134.5	37	CCDS7855.1	.	.	.	.	.	.	.	.	.	.	A	14.67	2.606104	0.46527	.	.	ENSG00000165973	ENST00000298925;ENST00000357134;ENST00000325319;ENST00000532434	T;T;T;T	0.78924	-1.22;-1.19;-1.06;-1.1	5.93	4.81	0.61882	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.61553	0.2356	N	0.24115	0.695	0.38160	D	0.939013	B;B;B;B	0.31548	0.041;0.024;0.328;0.024	B;B;B;B	0.36186	0.029;0.013;0.219;0.007	T	0.56426	-0.7981	10	0.06757	T	0.87	-3.5175	8.232	0.31603	0.815:0.0:0.0656:0.1194	.	161;246;218;218	F5H6I3;B3KXR2;Q92832-2;Q92832	.;.;.;NELL1_HUMAN	S	246;218;161;218	ENSP00000298925:T246S;ENSP00000349654:T218S;ENSP00000317837:T161S;ENSP00000437170:T218S	ENSP00000298925:T246S	T	+	1	0	NELL1	20896352	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	4.618000	0.61211	1.077000	0.40990	0.533000	0.62120	ACA	.	.	none		0.353	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157		T	20939776	A	T	20939776	3	4	29	1	0	0	0	0	1	0	0	0	10342	43	2	5	674	5	NELL1	11	20939776	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	2452524	20939776	114066740	540	12781											
CHST1	8534	hgsc.bcm.edu	37	chr11	45671241	45671241	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacccgcaccgcccgggtcaCgagaaggggcggaagtcccg	8	2	15	16	6	1	1	1	0	0	1	2	3	2	2	4	4	0	1	4	4	2	0	rs7115779	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:45671241C>G	ENST00000308064.2	-	4	1903	c.1233G>C	c.(1231-1233)tcG>tcC	p.S411S	RP11-495O11.1_ENST00000525563.1_RNA|CHST1_ENST00000533673.1_5'Flank	NM_003654.5	NP_003645.1	O43916	CHST1_HUMAN	carbohydrate (keratan sulfate Gal-6) sulfotransferase 1	411					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)		GCCCGGGTCACGAGAAGGGGC	0.627													C|||	12	0.00239617	0.0	0.0014	5008	,	,		14438	0.0		0.007	False		,,,				2504	0.0041				p.S411S		Atlas-SNP	.											CHST1,colon,adenoma,0,1	CHST1	81	1	0			c.G1233C						PASS	.	C		5,4395		0,5,2195	32	40	38		1233	4.4	1	11	dbSNP_116	38	30,8532		0,30,4251	yes	coding-synonymous	CHST1	NM_003654.5		0,35,6446	GG,GC,CC		0.3504,0.1136,0.27		411/412	45671241	35,12927	2200	4281	6481	SO:0001819	synonymous_variant	8534	exon4			GGGTCACGAGAAG	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.1233G>C	11.37:g.45671241C>G		27	0	0		25	11	0.44	NM_003654	D3DQP2	Silent	SNP	ENST00000308064.2	37	CCDS7913.1																																																																																			C|0.989;G|0.011	0.011	strong		0.627	CHST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390127.1	NM_003654		G	45671241	C	G	45671241	2	3	29	1	0	0	0	0	0	0	0	1	3399	523	19	4		4	CHST1	11	45671241	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	24731465	45671241	89335275	541	12782											
AMBRA1	55626	hgsc.bcm.edu	37	chr11	46456444	46456444	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcccaggttatggggggccaGggagtacactgccaggatgc	8	6	17	10	0	0	0	0	0	0	0	0	2	0	2	3	6	3	2	3	6	2	2	rs61999319	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:46456444G>A	ENST00000458649.2	-	13	3194	c.2776C>T	c.(2776-2778)Ctg>Ttg	p.L926L	AMBRA1_ENST00000426438.1_Silent_p.L897L|AMBRA1_ENST00000314845.3_Silent_p.L836L|AMBRA1_ENST00000534300.1_Silent_p.L866L|AMBRA1_ENST00000528950.1_Silent_p.L897L|AMBRA1_ENST00000298834.3_Silent_p.L866L|AMBRA1_ENST00000533727.1_Silent_p.L807L			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	926					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)		TGGGGGGCCAGGGAGTACACT	0.572													G|||	38	0.00758786	0.003	0.0159	5008	,	,		20047	0.0		0.0229	False		,,,				2504	0.0				p.L929L		Atlas-SNP	.											.	AMBRA1	201	.	0			c.C2785T						PASS	.	G		21,4381	28.1+/-56.4	1,19,2181	79	68	71		2506	3.5	1	11	dbSNP_129	71	209,8389	89.4+/-151.6	1,207,4091	no	coding-synonymous	AMBRA1	NM_017749.2		2,226,6272	AA,AG,GG		2.4308,0.4771,1.7692		836/1209	46456444	230,12770	2201	4299	6500	SO:0001819	synonymous_variant	55626	exon15			GGGCCAGGGAGTA	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.2776C>T	11.37:g.46456444G>A		161	0	0		176	101	0.573864	NM_001267782	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Silent	SNP	ENST00000458649.2	37																																																																																				G|0.985;A|0.015	0.015	strong		0.572	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749		A	46456444	G	A	46456444	2	1	29	1	0	0	0	0	0	0	0	1	565	991	35	2		2	AMBRA1	11	46456444	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	785203	46456444	88550072	542	12783											
F2	2147	hgsc.bcm.edu	37	chr11	46751059	46751059	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgcccattgtggagcggccGgtctgcaaggactccacccg	6	7	13	15	3	1	0	0	0	1	0	2	2	2	2	4	4	3	1	4	4	1	1	rs5900	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:46751059G>A	ENST00000311907.5	+	12	1658	c.1602G>A	c.(1600-1602)ccG>ccA	p.P534P	F2_ENST00000530231.1_Silent_p.P495P	NM_000506.3	NP_000497.1	P00734	THRB_HUMAN	coagulation factor II (thrombin)	534	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				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)	TGGAGCGGCCGGTCTGCAAGG	0.627													G|||	37	0.00738818	0.0015	0.0173	5008	,	,		17598	0.0		0.0229	False		,,,				2504	0.0				p.P534P	Esophageal Squamous(147;1147 1808 2148 38609 51144)	Atlas-SNP	.											.	F2	75	.	0			c.G1602A						PASS	.	G		17,4385	24.3+/-50.5	1,15,2185	100	84	89		1602	-11.5	0	11	dbSNP_52	89	209,8389	89.7+/-151.9	1,207,4091	no	coding-synonymous	F2	NM_000506.3		2,222,6276	AA,AG,GG		2.4308,0.3862,1.7385		534/623	46751059	226,12774	2201	4299	6500	SO:0001819	synonymous_variant	2147	exon12			GCGGCCGGTCTGC	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.1602G>A	11.37:g.46751059G>A		37	0	0		48	27	0.5625	NM_000506	B2R7F7|B4E1A7|Q4QZ40|Q53H04|Q53H06|Q69EZ7|Q7Z7P3|Q9UCA1	Silent	SNP	ENST00000311907.5	37	CCDS31476.1																																																																																			A|0.014;C|0.000;G|0.986	0.014	strong		0.627	F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317706.1			A	46751059	G	A	46751059	2	1	29	1	0	0	0	0	0	0	0	1	5344	1103	39	1		1	F2	11	46751059	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	294615	46751059	88255457	543	12784											
OR4A47	403253	hgsc.bcm.edu	37	chr11	48511105	48511105	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttctttgttccttgtatttTtatgtatgctagacctgcta	6	21	6	8	0	1	1	0	0	1	1	2	1	2	1	2	0	2	5	2	0	5	11			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:48511105T>G	ENST00000446524.1	+	1	837	c.761T>G	c.(760-762)tTt>tGt	p.F254C		NM_001005512.2	NP_001005512.2	Q6IF82	O4A47_HUMAN	olfactory receptor, family 4, subfamily A, member 47	254						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						CCTTGTATTTTTATGTATGCT	0.428																																					p.F254C		Atlas-SNP	.											.	OR4A47	72	.	0			c.T761G						PASS	.						211	204	207					11																	48511105		2201	4298	6499	SO:0001583	missense	403253	exon1			GTATTTTTATGTA	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.761T>G	11.37:g.48511105T>G	ENSP00000412752:p.Phe254Cys	89	0	0		106	8	0.0754717	NM_001005512		Missense_Mutation	SNP	ENST00000446524.1	37	CCDS31490.1	.	.	.	.	.	.	.	.	.	.	N	12.63	1.994217	0.35226	.	.	ENSG00000237388	ENST00000446524	T	0.00287	8.29	4.59	4.59	0.56863	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000026	T	0.00412	0.0013	M	0.84773	2.715	0.39849	D	0.973213	P	0.39157	0.662	B	0.42112	0.376	T	0.71510	-0.4571	10	0.72032	D	0.01	.	11.9052	0.52708	0.0:0.0:0.0:1.0	.	254	Q6IF82	O4A47_HUMAN	C	254	ENSP00000412752:F254C	ENSP00000412752:F254C	F	+	2	0	OR4A47	48467681	0.290000	0.24343	1.000000	0.80357	0.291000	0.27294	2.135000	0.42112	1.692000	0.51112	0.172000	0.16884	TTT	.	.	none		0.428	OR4A47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390559.1	NM_001005512		G	48511105	T	G	48511105	3	3	29	1	0	0	0	0	1	0	0	0	11051	1841	64	5	763	5	OR4A47	11	48511105	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	1760046	48511105	86495411	544	12785											
OR9G1	390174	hgsc.bcm.edu	37	chr11	56468431	56468431	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tggtggagctggcctgtggcGagaagggcggctataaaatt	9	9	17	6	2	0	1	0	0	0	1	0	3	0	2	1	6	1	2	1	6	4	3	rs141836537	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:56468431G>A	ENST00000312153.1	+	1	568	c.568G>A	c.(568-570)Gag>Aag	p.E190K		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	190						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						GGCCTGTGGCGAGAAGGGCGG	0.473													G|||	3	0.000599042	0.0015	0.0	5008	,	,		20715	0.0		0.001	False		,,,				2504	0.0				p.E190K		Atlas-SNP	.											.	.	.	.	0			c.G568A						PASS	.	G	LYS/GLU	0,4402		0,0,2201	114	116	116		568	-1	0.3	11	dbSNP_134	116	3,8589	3.0+/-9.4	0,3,4293	yes	missense	OR9G1	NM_001005213.1	56	0,3,6494	AA,AG,GG		0.0349,0.0,0.0231	benign	190/306	56468431	3,12991	2201	4296	6497	SO:0001583	missense	504191	exon1			TGTGGCGAGAAGG	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.568G>A	11.37:g.56468431G>A	ENSP00000309012:p.Glu190Lys	167	0	0		143	22	0.153846	NM_001013358	Q6IEU9|Q8NGQ0	Missense_Mutation	SNP	ENST00000312153.1	37	CCDS31536.1	.	.	.	.	.	.	.	.	.	.	G	7.676	0.687951	0.14973	0.0	3.49E-4	ENSG00000174914	ENST00000312153	T	0.00115	8.71	4.52	-1.04	0.10068	GPCR, rhodopsin-like superfamily (1);	1.803510	0.02484	N	0.088744	T	0.00144	0.0004	L	0.39085	1.19	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.37174	-0.9717	10	0.66056	D	0.02	-0.9116	6.1547	0.20330	0.4733:0.1374:0.3892:0.0	.	190	Q8NH87	OR9G1_HUMAN	K	190	ENSP00000309012:E190K	ENSP00000309012:E190K	E	+	1	0	OR9G1	56225007	0.000000	0.05858	0.269000	0.24586	0.178000	0.23041	0.239000	0.18023	-0.048000	0.13401	-0.510000	0.04470	GAG	G|1.000;A|0.000	0.000	weak		0.473	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213		A	56468431	G	A	56468431	3	1	29	1	0	0	0	0	1	0	0	0	11259	1059	37	1	570	1	OR9G1	11	56468431	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	7957326	56468431	78538085	545	12786											
SMTNL1	219537	hgsc.bcm.edu	37	chr11	57317522	57317522	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gactccaagtgcgtctacacAtacatccaggaactgtaccg	12	8	8	13	2	1	0	0	0	1	0	3	2	3	1	3	1	5	1	3	1	5	3	rs117673759	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:57317522A>G	ENST00000399154.2	+	8	1311	c.1311A>G	c.(1309-1311)acA>acG	p.T437T	SMTNL1_ENST00000457912.1_Silent_p.T492T|SMTNL1_ENST00000527972.1_Silent_p.T474T			A8MU46	SMTL1_HUMAN	smoothelin-like 1	437	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				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						GCGTCTACACATACATCCAGG	0.557													A|||	4	0.000798722	0.0	0.0	5008	,	,		20156	0.0		0.004	False		,,,				2504	0.0				p.T474T		Atlas-SNP	.											.	SMTNL1	68	.	0			c.A1422G						PASS	.	A		8,4252		0,8,2122	69	71	70		1422	2	1	11	dbSNP_132	70	30,8438		0,30,4204	no	coding-synonymous	SMTNL1	NM_001105565.2		0,38,6326	GG,GA,AA		0.3543,0.1878,0.2986		474/495	57317522	38,12690	2130	4234	6364	SO:0001819	synonymous_variant	219537	exon7			CTACACATACATC	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.1311A>G	11.37:g.57317522A>G		115	0	0		112	50	0.446429	NM_001105565		Silent	SNP	ENST00000399154.2	37																																																																																				A|0.999;G|0.001	0.001	strong		0.557	SMTNL1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_166203		G	57317522	A	G	57317522	2	3	29	1	0	0	0	0	0	0	0	1	14830	204	8	3		3	SMTNL1	11	57317522	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	849091	57317522	77688994	546	12787											
OR9Q1	219956	hgsc.bcm.edu	37	chr11	57947163	57947163	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tcactgtcccccagatgctgGcagtgctgctggagcatggg	6	9	14	12	0	1	1	1	0	0	1	2	2	2	2	2	3	4	5	2	3	0	0	rs111629598	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:57947163G>A	ENST00000335397.3	+	3	563	c.247G>A	c.(247-249)Gca>Aca	p.A83T		NM_001005212.3	NP_001005212.1	Q8NGQ5	OR9Q1_HUMAN	olfactory receptor, family 9, subfamily Q, member 1	83						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)				CCAGATGCTGGCAGTGCTGCT	0.522													G|||	71	0.0141773	0.0015	0.0216	5008	,	,		22598	0.0		0.0348	False		,,,				2504	0.0194				p.A83T		Atlas-SNP	.											.	OR9Q1	60	.	0			c.G247A						PASS	.	G	THR/ALA	28,4374	34.3+/-65.2	0,28,2173	163	139	148		247	4.8	0.8	11	dbSNP_132	148	282,8310	106.2+/-167.1	10,262,4024	yes	missense	OR9Q1	NM_001005212.3	58	10,290,6197	AA,AG,GG		3.2821,0.6361,2.3857	possibly-damaging	83/311	57947163	310,12684	2201	4296	6497	SO:0001583	missense	219956	exon3			ATGCTGGCAGTGC	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.247G>A	11.37:g.57947163G>A	ENSP00000334934:p.Ala83Thr	175	0	0		210	105	0.5	NM_001005212	Q2TAN3|Q96RA7	Missense_Mutation	SNP	ENST00000335397.3	37	CCDS31543.1	41	0.018772893772893772	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	31	0.040897097625329816	G	8.610	0.888822	0.17540	0.006361	0.032821	ENSG00000186509	ENST00000335397	T	0.00397	7.57	4.84	4.84	0.62591	GPCR, rhodopsin-like superfamily (1);	0.435428	0.19416	N	0.114802	T	0.00073	0.0002	L	0.37800	1.135	0.22968	N	0.998493	P	0.44627	0.839	B	0.33750	0.169	T	0.64394	-0.6418	10	0.41790	T	0.15	-8.0467	13.2507	0.60050	0.0:0.1593:0.8407:0.0	.	83	Q8NGQ5	OR9Q1_HUMAN	T	83	ENSP00000334934:A83T	ENSP00000334934:A83T	A	+	1	0	OR9Q1	57703739	0.014000	0.17966	0.758000	0.31321	0.089000	0.18198	0.459000	0.21908	2.680000	0.91292	0.563000	0.77884	GCA	G|0.976;A|0.024	0.024	strong		0.522	OR9Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394538.2	NM_001005212		A	57947163	G	A	57947163	3	1	29	1	0	0	0	0	1	0	0	0	11264	1203	42	2	249	2	OR9Q1	11	57947163	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	629641	57947163	77059353	547	12788											
DAGLA	747	hgsc.bcm.edu	37	chr11	61511794	61511794	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccctcctcgggcatctcaCtctcgccctccttcccgctc	3	10	5	23	3	2	0	1	0	2	0	9	0	5	0	6	1	0	2	6	1	0	1	rs117050893	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:61511794C>G	ENST00000257215.5	+	20	3078	c.2962C>G	c.(2962-2964)Ctc>Gtc	p.L988V	RP11-467L20.10_ENST00000536405.1_lincRNA	NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	988					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)		GGGCATCTCACTCTCGCCCTC	0.667													C|||	33	0.00658946	0.0	0.0331	5008	,	,		16155	0.002		0.006	False		,,,				2504	0.002				p.L988V		Atlas-SNP	.											.	DAGLA	109	.	0			c.C2962G						PASS	.	C	VAL/LEU	18,4386	24.3+/-50.5	0,18,2184	56	62	60		2962	2	0	11	dbSNP_132	60	38,8560	25.7+/-73.6	0,38,4261	yes	missense	DAGLA	NM_006133.2	32	0,56,6445	GG,GC,CC		0.442,0.4087,0.4307	benign	988/1043	61511794	56,12946	2202	4299	6501	SO:0001583	missense	747	exon20			ATCTCACTCTCGC	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.2962C>G	11.37:g.61511794C>G	ENSP00000257215:p.Leu988Val	54	0	0		50	21	0.42	NM_006133	A7E233|Q6WQJ0	Missense_Mutation	SNP	ENST00000257215.5	37	CCDS31578.1	21	0.009615384615384616	0	0.0	15	0.04143646408839779	1	0.0017482517482517483	5	0.006596306068601583	C	5.197	0.221827	0.09863	0.004087	0.00442	ENSG00000134780	ENST00000257215	T	0.25085	1.82	4.03	1.95	0.26073	.	0.158981	0.41097	D	0.000955	T	0.01905	0.0060	N	0.03608	-0.345	0.18873	N	0.999989	B	0.02656	0.0	B	0.04013	0.001	T	0.32268	-0.9913	10	0.17369	T	0.5	-26.7772	8.6434	0.33991	0.0:0.5927:0.3026:0.1048	.	988	Q9Y4D2	DGLA_HUMAN	V	988	ENSP00000257215:L988V	ENSP00000257215:L988V	L	+	1	0	DAGLA	61268370	0.954000	0.32549	0.008000	0.14137	0.636000	0.38137	1.749000	0.38319	0.815000	0.34398	0.462000	0.41574	CTC	C|0.994;G|0.006	0.006	strong		0.667	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133		G	61511794	C	G	61511794	3	3	29	1	0	0	0	0	1	0	0	0	4228	565	20	4	3036	4	DAGLA	11	61511794	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	3564631	61511794	73494722	548	12789											
RTN3	10313	hgsc.bcm.edu	37	chr11	63487033	63487033	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caagtgaaacaacagaccgaTaaatcttctgactgcatcac	16	8	6	11	1	3	3	1	2	2	1	3	4	3	3	1	0	3	1	1	0	5	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:63487033T>C	ENST00000377819.5	+	3	1213	c.1059T>C	c.(1057-1059)gaT>gaC	p.D353D	RTN3_ENST00000354497.4_Intron|RTN3_ENST00000537981.1_Intron|RTN3_ENST00000339997.4_Silent_p.D334D|RTN3_ENST00000540798.1_Silent_p.D241D|RTN3_ENST00000341307.2_Intron|RTN3_ENST00000356000.3_Intron	NM_001265589.1	NP_001252518.1	O95197	RTN3_HUMAN	reticulon 3	353					apoptotic process (GO:0006915)|endoplasmic reticulum tubular network organization (GO:0071786)|response to stress (GO:0006950)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	20						AACAGACCGATAAATCTTCTG	0.383																																					p.D353D		Atlas-SNP	.											.	RTN3	104	.	0			c.T1059C						PASS	.						57	57	57					11																	63487033		2201	4298	6499	SO:0001819	synonymous_variant	10313	exon3			GACCGATAAATCT	AF059524	CCDS8048.1, CCDS8049.1, CCDS8050.1, CCDS41664.1, CCDS58141.1, CCDS58142.1, CCDS58143.1	11q13	2011-01-14			ENSG00000133318	ENSG00000133318			10469	protein-coding gene	gene with protein product	"neuroendocrine-specific protein-like 2", "NSP-like protein II", "isoforme III", "ASY interacting protein", "homolog of ASY protein"	604249				10331947	Standard	NM_006054		Approved	NSPL2, NSPLII, ASYIP, HAP, RTN3-A1	uc001nxq.3	O95197		ENST00000377819.5:c.1059T>C	11.37:g.63487033T>C		87	0	0		86	21	0.244186	NM_001265589	B3KQS2|B7Z308|B7Z4M0|F5H774|Q147U9|Q496K2|Q53GN3|Q59EP0|Q5UEP2|Q6T930|Q7RTM7|Q7RTM8|Q7RTN3	Silent	SNP	ENST00000377819.5	37	CCDS58141.1																																																																																			.	.	none		0.383	RTN3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000397846.1	NM_006054		C	63487033	T	C	63487033	2	2	29	1	0	0	0	0	0	0	0	1	13742	1403	49	3		3	RTN3	11	63487033	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	1975239	63487033	71519483	549	12790											
SLC22A11	55867	hgsc.bcm.edu	37	chr11	64337280	64337280	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gttgtgctgttcttcctcccGgagacccagggacttccgct	4	12	11	14	2	1	1	0	0	1	1	4	3	4	2	4	2	1	4	4	2	0	4	rs34836439	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:64337280G>A	ENST00000301891.4	+	9	1913	c.1539G>A	c.(1537-1539)ccG>ccA	p.P513P	SLC22A11_ENST00000377585.3_Silent_p.P405P|SLC22A11_ENST00000377581.3_Intron	NM_018484.2	NP_060954.1	Q9NSA0	S22AB_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 11	513					organic anion transport (GO:0015711)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|organic anion transmembrane transporter activity (GO:0008514)|sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23					Aminohippurate(DB00345)|Aspartame(DB00168)|Benzylpenicillin(DB01053)|Bumetanide(DB00887)|Cefalotin(DB00456)|Cefamandole(DB01326)|Cefazolin(DB01327)|Cefoperazone(DB01329)|Cefotaxime(DB00493)|Ceftriaxone(DB01212)|Cimetidine(DB00501)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprost Tromethamine(DB01160)|Dinoprostone(DB00917)|Doxycycline(DB00254)|Estradiol(DB00783)|Furosemide(DB00695)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Methotrexate(DB00563)|Minocycline(DB01017)|Novobiocin(DB01051)|Oxytetracycline(DB00595)|Phenylbutazone(DB00812)|Piroxicam(DB00554)|Pravastatin(DB00175)|Probenecid(DB01032)|Salicylic acid(DB00936)|Tetracycline(DB00759)|Zidovudine(DB00495)	TCTTCCTCCCGGAGACCCAGG	0.622													G|||	11	0.00219649	0.0008	0.0144	5008	,	,		18022	0.0		0.0	False		,,,				2504	0.0				p.P513P		Atlas-SNP	.											.	SLC22A11	54	.	0			c.G1539A						PASS	.	G		1,4401	2.1+/-5.4	0,1,2200	113	105	108		1539	-7.1	0.1	11	dbSNP_126	108	4,8590	3.0+/-9.4	0,4,4293	no	coding-synonymous	SLC22A11	NM_018484.2		0,5,6493	AA,AG,GG		0.0465,0.0227,0.0385		513/551	64337280	5,12991	2201	4297	6498	SO:0001819	synonymous_variant	55867	exon9			CCTCCCGGAGACC	AB026116	CCDS8074.1	11q13.3	2013-05-22	2008-01-11		ENSG00000168065	ENSG00000168065		"Solute carriers"	18120	protein-coding gene	gene with protein product		607097				10660625, 15576633, 17229912	Standard	NM_018484		Approved	OAT4	uc001oai.3	Q9NSA0	OTTHUMG00000045142	ENST00000301891.4:c.1539G>A	11.37:g.64337280G>A		38	0	0		44	20	0.454545	NM_018484	A8K426|Q53GR2|Q6ZP72|Q8NBU4	Silent	SNP	ENST00000301891.4	37	CCDS8074.1																																																																																			G|0.996;A|0.004	0.004	strong		0.622	SLC22A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104886.4	NM_018484		A	64337280	G	A	64337280	2	1	29	1	0	0	0	0	0	0	0	1	14457	1103	39	1		1	SLC22A11	11	64337280	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	850247	64337280	70669236	550	12791											
IGHMBP2	3508	hgsc.bcm.edu	37	chr11	68705754	68705754	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgccaagtgcacagccggcGtcacaaccctgggccagttc	8	7	11	15	2	1	0	1	0	0	0	2	0	1	0	4	2	4	2	4	2	2	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:68705754G>A	ENST00000255078.3	+	14	2827	c.2716G>A	c.(2716-2718)Gtc>Atc	p.V906I		NM_002180.2	NP_002171.2	P38935	SMBP2_HUMAN	immunoglobulin mu binding protein 2	906					ATP catabolic process (GO:0006200)|cell death (GO:0008219)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|protein homooligomerization (GO:0051260)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)	axon (GO:0030424)|cytoplasm (GO:0005737)|growth cone (GO:0030426)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|ATP-dependent 5'-3' RNA helicase activity (GO:0032575)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA-dependent ATPase activity (GO:0008094)|ribosome binding (GO:0043022)|RNA binding (GO:0003723)|RNA-dependent ATPase activity (GO:0008186)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)|tRNA binding (GO:0000049)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|liver(1)|lung(15)|ovary(2)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36			STAD - Stomach adenocarcinoma(18;0.0208)|LUAD - Lung adenocarcinoma(13;0.0713)			CACAGCCGGCGTCACAACCCT	0.637																																					p.V906I		Atlas-SNP	.											IGHMBP2,right_upper_lobe,carcinoma,0,1	IGHMBP2	83	1	0			c.G2716A						PASS	.						42	40	41					11																	68705754		2200	4294	6494	SO:0001583	missense	3508	exon14			GCCGGCGTCACAA	L14754	CCDS8187.1	11q13.3	2014-09-17			ENSG00000132740	ENSG00000132740		"Zinc fingers, AN1-type domain containing"	5542	protein-coding gene	gene with protein product	"cardiac transcription factor 1", "zinc finger, AN1-type domain 7"	600502				8349627	Standard	NM_002180		Approved	ZFAND7, SMUBP2, CATF1, SMARD1, HCSA, HMN6	uc001ook.1	P38935	OTTHUMG00000167894	ENST00000255078.3:c.2716G>A	11.37:g.68705754G>A	ENSP00000255078:p.Val906Ile	65	0	0		50	6	0.12	NM_002180	A0PJD2|Q00443|Q14177	Missense_Mutation	SNP	ENST00000255078.3	37	CCDS8187.1	.	.	.	.	.	.	.	.	.	.	G	14.17	2.456863	0.43634	.	.	ENSG00000132740	ENST00000255078	T	0.42131	0.98	5.0	1.51	0.23008	Zinc finger, AN1-type (4);	0.649507	0.15581	N	0.254934	T	0.41789	0.1174	M	0.63428	1.95	0.80722	D	1	D	0.61080	0.989	P	0.46237	0.508	T	0.34925	-0.9809	10	0.59425	D	0.04	-11.9797	7.9942	0.30258	0.3319:0.0:0.6681:0.0	.	906	P38935	SMBP2_HUMAN	I	906	ENSP00000255078:V906I	ENSP00000255078:V906I	V	+	1	0	IGHMBP2	68462330	1.000000	0.71417	0.163000	0.22734	0.003000	0.03518	4.239000	0.58694	0.293000	0.22520	0.462000	0.41574	GTC	.	.	none		0.637	IGHMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396862.1	NM_002180		A	68705754	G	A	68705754	3	1	29	1	0	0	0	0	1	0	0	0	7600	1145	40	1	2770	1	IGHMBP2	11	68705754	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	4368474	68705754	66300762	551	12792											
USP35	57558	hgsc.bcm.edu	37	chr11	77911745	77911745	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctctctggtcaaggaggactCgaactcggggaccagctgcc	8	7	13	13	2	2	0	1	0	1	0	5	4	2	3	2	5	3	1	2	5	2	0	rs147270370	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:77911745C>T	ENST00000529308.1	+	6	1349	c.1088C>T	c.(1087-1089)tCg>tTg	p.S363L	USP35_ENST00000441408.2_5'UTR|USP35_ENST00000530267.1_Intron|USP35_ENST00000526425.1_Missense_Mutation_p.S94L|USP35_ENST00000530535.1_Intron	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	363					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)			AAGGAGGACTCGAACTCGGGG	0.647													C|||	19	0.00379393	0.0015	0.0014	5008	,	,		17401	0.0		0.008	False		,,,				2504	0.0082				p.S363L		Atlas-SNP	.											USP35_ENST00000263311,rectum,carcinoma,-1,2	USP35	179	2	0			c.C1088T						PASS	.	C	LEU/SER	5,3907		0,5,1951	46	52	50		1088	4.7	1	11	dbSNP_134	50	46,8202		0,46,4078	yes	missense	USP35	NM_020798.2	145	0,51,6029	TT,TC,CC		0.5577,0.1278,0.4194	benign	363/1019	77911745	51,12109	1956	4124	6080	SO:0001583	missense	57558	exon6			AGGACTCGAACTC	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.1088C>T	11.37:g.77911745C>T	ENSP00000431876:p.Ser363Leu	95	0	0		119	95	0.798319	NM_020798		Missense_Mutation	SNP	ENST00000529308.1	37	CCDS41693.1	6	0.0027472527472527475	1	0.0020325203252032522	0	0.0	0	0.0	5	0.006596306068601583	C	13.79	2.343705	0.41498	0.001278	0.005577	ENSG00000118369	ENST00000528910;ENST00000529308;ENST00000526425	T;T;T	0.68181	-0.24;-0.31;3.37	4.73	4.73	0.59995	Armadillo-like helical (1);	0.000000	0.52532	D	0.000071	T	0.40448	0.1117	N	0.19112	0.55	0.80722	D	1	B	0.33739	0.422	B	0.22753	0.041	T	0.43925	-0.9361	10	0.18276	T	0.48	-15.0401	17.9135	0.88942	0.0:1.0:0.0:0.0	.	363	Q9P2H5	UBP35_HUMAN	L	119;363;94	ENSP00000436001:S119L;ENSP00000431876:S363L;ENSP00000434942:S94L	ENSP00000434942:S94L	S	+	2	0	USP35	77589393	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.484000	0.66844	2.461000	0.83175	0.561000	0.74099	TCG	C|0.996;T|0.004	0.004	strong		0.647	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	XM_290527		T	77911745	C	T	77911745	3	4	29	1	0	0	0	0	1	0	0	0	17081	893	31	1	1106	1	USP35	11	77911745	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	9205991	77911745	57094771	552	12793											
TMEM135	65084	hgsc.bcm.edu	37	chr11	87020670	87020670	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttctacaataaagaaaacTtccagcttggagcttttctt	12	15	5	9	0	3	1	0	0	3	1	4	2	4	2	1	1	4	2	1	1	6	8			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:87020670T>G	ENST00000305494.5	+	10	931	c.892T>G	c.(892-894)Ttc>Gtc	p.F298V	TMEM135_ENST00000340353.7_Missense_Mutation_p.F276V|TMEM135_ENST00000535167.1_Missense_Mutation_p.F159V|TMEM135_ENST00000532959.1_Missense_Mutation_p.F169V	NM_022918.3	NP_075069.3	Q86UB9	TM135_HUMAN	transmembrane protein 135	298					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)				TAAAGAAAACTTCCAGCTTGG	0.393																																					p.F298V		Atlas-SNP	.											.	TMEM135	40	.	0			c.T892G						PASS	.						85	93	90					11																	87020670		2201	4299	6500	SO:0001583	missense	65084	exon10			GAAAACTTCCAGC	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.892T>G	11.37:g.87020670T>G	ENSP00000306344:p.Phe298Val	65	0	0		70	20	0.285714	NM_022918	Q6AW91|Q8ND01|Q9H6M3	Missense_Mutation	SNP	ENST00000305494.5	37	CCDS8280.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.792969	0.90453	.	.	ENSG00000166575	ENST00000340353;ENST00000544294;ENST00000532959;ENST00000305494;ENST00000535167	T;T;T;T	0.28069	1.63;1.63;1.63;1.63	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.45357	0.1338	L	0.46741	1.465	0.80722	D	1	P;D	0.62365	0.48;0.991	B;P	0.62184	0.143;0.899	T	0.24621	-1.0155	9	.	.	.	-29.3596	14.8495	0.70286	0.0:0.0:0.0:1.0	.	276;298	Q86UB9-2;Q86UB9	.;TM135_HUMAN	V	276;135;169;298;159	ENSP00000345513:F276V;ENSP00000436179:F169V;ENSP00000306344:F298V;ENSP00000439525:F159V	.	F	+	1	0	TMEM135	86698318	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.915000	0.87484	2.160000	0.67779	0.482000	0.46254	TTC	.	.	none		0.393	TMEM135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393875.1	NM_022918		G	87020670	T	G	87020670	3	3	29	1	0	0	0	0	1	0	0	0	16066	1609	56	5	930	5	TMEM135	11	87020670	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	9108925	87020670	47985846	553	12794											
MAML2	84441	hgsc.bcm.edu	37	chr11	95713077	95713077	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	taaaatggtgtgtgttgaaaCtgggtttgccaaagcctggt	10	13	13	5	0	0	1	0	1	0	0	0	1	0	1	2	3	3	2	2	3	4	3	rs34520053	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:95713077C>T	ENST00000524717.1	-	5	3790	c.2506G>A	c.(2506-2508)Gtt>Att	p.V836I		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	836				V -> I (in Ref. 6; CAH10491). {ECO:0000305}.	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)				TGTGTTGAAACTGGGTTTGCC	0.418			T	"MECT1, CRTC3"	salivary gland mucoepidermoid								C|||	31	0.0061901	0.0	0.0014	5008	,	,		20202	0.001		0.0229	False		,,,				2504	0.0061				p.V836I		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2	94	.	0			c.G2506A						PASS	.	C	ILE/VAL	23,3755		0,23,1866	142	134	136		2506	5.3	1	11	dbSNP_126	136	202,8038		2,198,3920	yes	missense	MAML2	NM_032427.1	29	2,221,5786	TT,TC,CC		2.4515,0.6088,1.8722	possibly-damaging	836/1157	95713077	225,11793	1889	4120	6009	SO:0001583	missense	84441	exon5			TTGAAACTGGGTT	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.2506G>A	11.37:g.95713077C>T	ENSP00000434552:p.Val836Ile	149	0	0		191	37	0.193717	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Missense_Mutation	SNP	ENST00000524717.1	37	CCDS44714.1	19	0.0086996336996337	0	0.0	1	0.0027624309392265192	0	0.0	18	0.023746701846965697	C	6.771	0.511215	0.12883	0.006088	0.024515	ENSG00000184384	ENST00000524717;ENST00000440572	T;T	0.44083	0.93;0.93	5.33	5.33	0.75918	.	0.000000	0.64402	D	0.000015	T	0.12732	0.0309	N	0.14661	0.345	0.35651	D	0.811778	B	0.27351	0.176	B	0.26517	0.07	T	0.21314	-1.0249	10	0.21540	T	0.41	-15.338	10.589	0.45298	0.0:0.8812:0.0:0.1188	rs34520053	836	Q8IZL2	MAML2_HUMAN	I	836	ENSP00000434552:V836I;ENSP00000412394:V836I	ENSP00000412394:V836I	V	-	1	0	MAML2	95352725	1.000000	0.71417	1.000000	0.80357	0.016000	0.09150	3.735000	0.55044	2.655000	0.90218	0.650000	0.86243	GTT	C|0.986;T|0.014	0.014	strong		0.418	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1			T	95713077	C	T	95713077	3	4	29	1	0	0	0	0	1	0	0	0	9215	565	20	2	968	2	MAML2	11	95713077	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	8692407	95713077	39293439	554	12795											
CWF19L2	143884	hgsc.bcm.edu	37	chr11	107309826	107309826	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtagaaatacctttagtaatCgatgacacactacagtcttc	14	12	6	9	1	1	2	0	1	1	1	3	3	1	2	1	0	2	2	1	0	6	7	rs201136952		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:107309826C>T	ENST00000282251.5	-	6	681	c.654G>A	c.(652-654)tcG>tcA	p.S218S	CWF19L2_ENST00000433523.1_Silent_p.S218S	NM_152434.2	NP_689647.2	Q2TBE0	C19L2_HUMAN	CWF19-like 2, cell cycle control (S. pombe)	218							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)		CTTTAGTAATCGATGACACAC	0.388													C|||	1	0.000199681	0.0	0.0014	5008	,	,		13512	0.0		0.0	False		,,,				2504	0.0				p.S218S		Atlas-SNP	.											CWF19L2_ENST00000282251,NS,carcinoma,0,2	CWF19L2	135	2	0			c.G654A						PASS	.						78	67	71					11																	107309826		2201	4298	6499	SO:0001819	synonymous_variant	143884	exon6			AGTAATCGATGAC	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.654G>A	11.37:g.107309826C>T		44	0	0		32	8	0.25	NM_152434	A4FU66|A4FU67|A4FU68|Q6PHW1|Q96MI1	Silent	SNP	ENST00000282251.5	37	CCDS8336.2																																																																																			C|1.000;T|0.000	0.000	strong		0.388	CWF19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328825.2	NM_152434		T	107309826	C	T	107309826	2	4	29	1	0	0	0	0	0	0	0	1	4074	871	31	1		1	CWF19L2	11	107309826	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	11596749	107309826	27696690	555	12796											
ATM	472	hgsc.bcm.edu	37	chr11	108124761	108124761	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcttctgaataattactcaTctgaggtgagattttttaaa	13	16	7	5	0	3	3	1	3	2	1	3	4	3	3	0	1	2	1	0	1	5	6	rs4986761	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:108124761T>C	ENST00000452508.2	+	14	2308	c.2119T>C	c.(2119-2121)Tct>Cct	p.S707P	ATM_ENST00000278616.4_Missense_Mutation_p.S707P			Q13315	ATM_HUMAN	ATM serine/threonine kinase	707			S -> P (in dbSNP:rs4986761). {ECO:0000269|PubMed:10534763, ECO:0000269|PubMed:17344846}.|YSS -> FIP (in AT; might be associated with susceptibility to cancer).		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.S707P(2)|p.S707fs*29(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)	TAATTACTCATCTGAGGTGAG	0.393			"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)			T|||	22	0.00439297	0.0	0.0101	5008	,	,		16199	0.0		0.0129	False		,,,				2504	0.002				p.S707P		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	ATM,NS,carcinoma,0,2	ATM	1657	2	3	Substitution - Missense(2)|Deletion - Frameshift(1)	breast(2)|haematopoietic_and_lymphoid_tissue(1)	c.T2119C	GRCh37	CM013692	ATM	M	rs4986761	PASS	.	T	PRO/SER	17,4383	21.2+/-45.6	0,17,2183	55	55	55		2119	3.8	1	11	dbSNP_111	55	94,8502	50.6+/-110.7	1,92,4205	yes	missense	ATM	NM_000051.3	74	1,109,6388	CC,CT,TT		1.0935,0.3864,0.8541	benign	707/3057	108124761	111,12885	2200	4298	6498	SO:0001583	missense	472	exon13	Familial Cancer Database	AT, Louis-Bar syndrome	TACTCATCTGAGG	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.2119T>C	11.37:g.108124761T>C	ENSP00000388058:p.Ser707Pro	53	0	0		41	32	0.780488	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	T	11.63	1.694897	0.30052	0.003864	0.010935	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.78364	-1.17;-1.17;-1.17	6.11	3.81	0.43845	Armadillo-type fold (1);	0.179298	0.50627	N	0.000119	T	0.52141	0.1716	N	0.17872	0.535	0.23076	N	0.998335	B	0.02656	0.0	B	0.01281	0.0	T	0.42565	-0.9444	10	0.31617	T	0.26	.	7.5463	0.27768	0.0:0.2362:0.0:0.7638	rs4986761;rs52832782;rs4986761	707	Q13315	ATM_HUMAN	P	707	ENSP00000435747:S707P;ENSP00000278616:S707P;ENSP00000388058:S707P	ENSP00000278616:S707P	S	+	1	0	ATM	107629971	0.015000	0.18098	0.999000	0.59377	0.911000	0.54048	-0.127000	0.10547	0.553000	0.29044	0.533000	0.62120	TCT	T|0.993;C|0.007	0.007	strong		0.393	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		C	108124761	T	C	108124761	3	2	29	1	0	0	0	0	1	0	0	0	1109	1435	50	3	2165	3	ATM	11	108124761	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	814935	108124761	26881755	556	12797											
PPP2R1B	5519	hgsc.bcm.edu	37	chr11	111637049	111637049	+	Missense_Mutation	SNP	C	C	T																															atctccatctccacccgctgCtcctgggccggtcccgagct																								rs554564263		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:111637049C>T	ENST00000527614.1	-	1	102	c.37G>A	c.(37-39)Gca>Aca	p.A13T	PPP2R1B_ENST00000341980.6_Missense_Mutation_p.A13T|PPP2R1B_ENST00000427203.2_5'UTR|PPP2R1B_ENST00000426998.2_Missense_Mutation_p.A13T|RP11-108O10.2_ENST00000529841.1_lincRNA|PPP2R1B_ENST00000311129.5_Missense_Mutation_p.A13T|PPP2R1B_ENST00000393055.2_Missense_Mutation_p.A13T	NM_001177562.1|NM_002716.4	NP_001171033.1|NP_002707.3	P30154	2AAB_HUMAN	protein phosphatase 2, regulatory subunit A, beta	13					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)		CCACCCGCTGCTCCTGGGCCG	0.672													C|||	1	0.000199681	0.0	0.0	5008	,	,		7436	0.001		0.0	False		,,,				2504	0.0				p.A13T		Atlas-SNP	.											.	PPP2R1B	44	.	0			c.G37A						PASS	.						64	63	63					11																	111637049		2201	4297	6498	SO:0001583	missense	5519	exon1			CCGCTGCTCCTGG	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.37G>A	11.37:g.111637049C>T	ENSP00000437193:p.Ala13Thr	24	0	0		35	17	0.485714	NM_001177562	A8MY67|B0YJ69|B4DGQ6|B4DK91|B4DWW5|F8W8G1|O75620|Q8NHV8	Missense_Mutation	SNP	ENST00000527614.1	37	CCDS8349.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.159377	0.78226	.	.	ENSG00000137713	ENST00000311129;ENST00000412902;ENST00000426998;ENST00000527614;ENST00000341980;ENST00000393055	.	.	.	5.23	4.29	0.51040	.	0.363905	0.30076	N	0.010474	T	0.53400	0.1794	L	0.28192	0.835	0.80722	D	1	B;B;B;P;B	0.49447	0.131;0.357;0.084;0.924;0.137	B;B;B;P;B	0.57776	0.016;0.246;0.034;0.827;0.075	T	0.52756	-0.8533	9	0.46703	T	0.11	-0.7229	10.9852	0.47518	0.1867:0.8133:0.0:0.0	.	13;13;13;13;13	A8MY67;F8W8G1;B4DWW5;P30154;P30154-2	.;.;.;2AAB_HUMAN;.	T	13	.	ENSP00000311344:A13T	A	-	1	0	PPP2R1B	111142259	0.983000	0.35010	0.071000	0.20095	0.022000	0.10575	1.945000	0.40273	1.138000	0.42230	0.557000	0.71058	GCA	.	.	none		0.672	PPP2R1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391298.1	NM_002716		T	111637049	C	T	111637049	3	4	29	1	0	0	0	0	1	0	0	0	12395	797	28	2	2051	2	PPP2R1B	11	111637049	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	3512288	111637049	23369467	557	12798	163	2									
PPP2R1B	5519	hgsc.bcm.edu	37	chr11	111637053	111637053	+	Silent	SNP	T	T	C																															ccatctccacccgctgctccTgggccggtcccgagctctga																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:111637053T>C	ENST00000527614.1	-	1	98	c.33A>G	c.(31-33)ccA>ccG	p.P11P	PPP2R1B_ENST00000341980.6_Silent_p.P11P|PPP2R1B_ENST00000427203.2_5'UTR|PPP2R1B_ENST00000426998.2_Silent_p.P11P|RP11-108O10.2_ENST00000529841.1_lincRNA|PPP2R1B_ENST00000311129.5_Silent_p.P11P|PPP2R1B_ENST00000393055.2_Silent_p.P11P	NM_001177562.1|NM_002716.4	NP_001171033.1|NP_002707.3	P30154	2AAB_HUMAN	protein phosphatase 2, regulatory subunit A, beta	11					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)		CCGCTGCTCCTGGGCCGGTCC	0.672																																					p.P11P		Atlas-SNP	.											.	PPP2R1B	44	.	0			c.A33G						PASS	.						60	59	59					11																	111637053		2201	4297	6498	SO:0001819	synonymous_variant	5519	exon1			TGCTCCTGGGCCG	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.33A>G	11.37:g.111637053T>C		25	0	0		35	17	0.485714	NM_001177562	A8MY67|B0YJ69|B4DGQ6|B4DK91|B4DWW5|F8W8G1|O75620|Q8NHV8	Silent	SNP	ENST00000527614.1	37	CCDS8349.1																																																																																			.	.	none		0.672	PPP2R1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391298.1	NM_002716		C	111637053	T	C	111637053	2	2	29	1	0	0	0	0	0	0	0	1	12395	1567	55	3		3	PPP2R1B	11	111637053	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	4	111637053	23369463	558	12799	163	2									
TTC12	54970	hgsc.bcm.edu	37	chr11	113234603	113234603	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aagatactagctatctgcacGaatagttatcatgaagctcg	14	11	8	8	2	2	2	1	1	1	1	3	3	2	2	0	0	4	4	0	0	8	5	rs34940277	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:113234603G>A	ENST00000529221.1	+	20	1875	c.1770G>A	c.(1768-1770)acG>acA	p.T590T	TTC12_ENST00000314756.3_Silent_p.T590T|TTC12_ENST00000393020.1_Silent_p.T590T|TTC12_ENST00000483239.2_Silent_p.T596T	NM_017868.3	NP_060338.3	Q9H892	TTC12_HUMAN	tetratricopeptide repeat domain 12	590										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)		CTATCTGCACGAATAGTTATC	0.388													G|||	8	0.00159744	0.0	0.0	5008	,	,		22890	0.002		0.002	False		,,,				2504	0.0041				p.T590T		Atlas-SNP	.											.	TTC12	66	.	0			c.G1770A						PASS	.	G		2,4400	4.2+/-10.8	0,2,2199	125	116	119		1770	-11.2	0	11	dbSNP_126	119	9,8583	7.1+/-27.0	0,9,4287	no	coding-synonymous	TTC12	NM_017868.3		0,11,6486	AA,AG,GG		0.1047,0.0454,0.0847		590/706	113234603	11,12983	2201	4296	6497	SO:0001819	synonymous_variant	54970	exon20			CTGCACGAATAGT	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.1770G>A	11.37:g.113234603G>A		89	0	0		94	74	0.787234	NM_017868	Q8N5H9|Q9NWY3	Silent	SNP	ENST00000529221.1	37	CCDS8360.2																																																																																			G|0.999;A|0.001	0.001	strong		0.388	TTC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286455.2	NM_017868		A	113234603	G	A	113234603	2	1	29	1	0	0	0	0	0	0	0	1	16694	1045	37	1		1	TTC12	11	113234603	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1597550	113234603	21771913	559	12800											
ZBTB16	7704	hgsc.bcm.edu	37	chr11	114118019	114118019	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacgggtgagaaaccctacgAgtgcaatggctgtggcaaga	12	6	14	9	2	0	2	0	1	0	2	0	4	0	2	1	3	3	3	1	3	4	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:114118019A>G	ENST00000335953.4	+	6	2104	c.1724A>G	c.(1723-1725)gAg>gGg	p.E575G	ZBTB16_ENST00000392996.2_Missense_Mutation_p.E575G|RP11-64D24.2_ENST00000544925.1_RNA|ZBTB16_ENST00000535379.1_3'UTR	NM_006006.4	NP_005997.2	Q05516	ZBT16_HUMAN	zinc finger and BTB domain containing 16	575					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)		AAACCCTACGAGTGCAATGGC	0.592																																					p.E575G		Atlas-SNP	.											.	ZBTB16	101	.	0			c.A1724G						PASS	.						100	79	86					11																	114118019		2201	4296	6497	SO:0001583	missense	7704	exon6			CCTACGAGTGCAA	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.1724A>G	11.37:g.114118019A>G	ENSP00000338157:p.Glu575Gly	110	0	0		131	25	0.19084	NM_006006	Q8TAL4	Missense_Mutation	SNP	ENST00000335953.4	37	CCDS8367.1	.	.	.	.	.	.	.	.	.	.	A	33	5.276369	0.95459	.	.	ENSG00000109906	ENST00000335953;ENST00000392996;ENST00000310883	T;T	0.22743	1.94;1.94	5.57	5.57	0.84162	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	0.40619	0.1124	L	0.48877	1.53	0.58432	D	0.999995	D	0.76494	0.999	D	0.87578	0.998	T	0.12268	-1.0554	10	0.49607	T	0.09	.	15.7234	0.77732	1.0:0.0:0.0:0.0	.	575	Q05516	ZBT16_HUMAN	G	575;575;452	ENSP00000338157:E575G;ENSP00000376721:E575G	ENSP00000309507:E452G	E	+	2	0	ZBTB16	113623229	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.239000	0.95389	2.113000	0.64589	0.529000	0.55759	GAG	.	.	none		0.592	ZBTB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398940.1	NM_006006		G	114118019	A	G	114118019	3	3	29	1	0	0	0	0	1	0	0	0	17541	304	11	3	1742	3	ZBTB16	11	114118019	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	883416	114118019	20888497	560	12801											
IL10RA	3587	hgsc.bcm.edu	37	chr11	117869878	117869878	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tggggacacacagggtggctCggccttgggccaccacagtc	7	6	15	13	1	0	0	0	0	0	0	2	1	0	1	3	6	0	1	3	6	0	1	rs2229114	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:117869878C>T	ENST00000227752.3	+	7	1379	c.1259C>T	c.(1258-1260)tCg>tTg	p.S420L	IL10RA_ENST00000541785.1_Missense_Mutation_p.S400L|IL10RA_ENST00000545409.1_Missense_Mutation_p.S271L|IL10RA_ENST00000533700.1_3'UTR	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	420			S -> L (in dbSNP:rs2229114). {ECO:0000269|Ref.2}.		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)		CAGGGTGGCTCGGCCTTGGGC	0.622													C|||	84	0.0167732	0.0015	0.0533	5008	,	,		18104	0.0		0.0427	False		,,,				2504	0.002				p.S420L		Atlas-SNP	.											.	IL10RA	46	.	0			c.C1259T						PASS	.	C	LEU/SER	49,4351	50.2+/-85.5	0,49,2151	47	50	49		1259	1.8	0	11	dbSNP_98	49	422,8170	131.5+/-189.3	13,396,3887	yes	missense	IL10RA	NM_001558.3	145	13,445,6038	TT,TC,CC		4.9115,1.1136,3.6253	probably-damaging	420/579	117869878	471,12521	2200	4296	6496	SO:0001583	missense	3587	exon7			GTGGCTCGGCCTT	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.1259C>T	11.37:g.117869878C>T	ENSP00000227752:p.Ser420Leu	96	0	0		116	107	0.922414	NM_001558	A8K6I0|B0YJ27	Missense_Mutation	SNP	ENST00000227752.3	37	CCDS8388.1	62	0.028388278388278388	3	0.006097560975609756	22	0.06077348066298342	0	0.0	37	0.048812664907651716	C	14.11	2.437539	0.43224	0.011136	0.049115	ENSG00000110324	ENST00000227752;ENST00000541785;ENST00000545409;ENST00000536858	T;T;T	0.33654	1.4;1.4;1.4	5.93	1.82	0.25136	.	1.134890	0.06593	N	0.752483	T	0.03783	0.0107	M	0.67953	2.075	0.09310	N	1	P;B	0.37233	0.588;0.317	B;B	0.29524	0.103;0.026	T	0.21348	-1.0248	10	0.66056	D	0.02	-7.4946	2.3827	0.04358	0.1435:0.4211:0.2787:0.1567	rs2229114;rs2229114	400;420	F5GYV8;Q13651	.;I10R1_HUMAN	L	420;400;271;400	ENSP00000227752:S420L;ENSP00000441397:S400L;ENSP00000443019:S271L	ENSP00000227752:S420L	S	+	2	0	IL10RA	117375088	0.001000	0.12720	0.025000	0.17156	0.054000	0.15201	0.608000	0.24223	0.420000	0.25954	0.563000	0.77884	TCG	C|0.969;T|0.031	0.031	strong		0.622	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1			T	117869878	C	T	117869878	3	4	29	1	0	0	0	0	1	0	0	0	7629	893	31	1	1285	1	IL10RA	11	117869878	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	3751859	117869878	17136638	561	12802											
PVRL1	5818	hgsc.bcm.edu	37	chr11	119548402	119548402	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcactgtgccattggggttcCggatctcctggtactctgcc	4	13	11	13	1	3	0	1	0	2	0	5	1	4	1	4	4	3	2	4	4	1	3	rs78809001	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:119548402C>T	ENST00000264025.3	-	3	1126	c.596G>A	c.(595-597)cGg>cAg	p.R199Q	PVRL1_ENST00000340882.2_Missense_Mutation_p.R199Q|PVRL1_ENST00000341398.2_Missense_Mutation_p.R199Q|PVRL1_ENST00000524510.1_5'UTR	NM_002855.4	NP_002846.3	Q15223	PVRL1_HUMAN	poliovirus receptor-related 1 (herpesvirus entry mediator C)	199	Ig-like C2-type 1.				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)		ATTGGGGTTCCGGATCTCCTG	0.597													c|||	17	0.00339457	0.0008	0.0101	5008	,	,		19081	0.0		0.0089	False		,,,				2504	0.0				p.R199Q		Atlas-SNP	.											.	PVRL1	133	.	0			c.G596A						PASS	.		GLN/ARG,GLN/ARG,GLN/ARG	8,4390	12.9+/-30.5	0,8,2191	156	139	145		596,596,596	5.2	1	11	dbSNP_131	145	117,8473	62.1+/-124.0	0,117,4178	yes	missense,missense,missense	PVRL1	NM_002855.4,NM_203285.1,NM_203286.1	43,43,43	0,125,6369	TT,TC,CC		1.362,0.1819,0.9624	probably-damaging,probably-damaging,probably-damaging	199/518,199/459,199/353	119548402	125,12863	2199	4295	6494	SO:0001583	missense	5818	exon3			GGGTTCCGGATCT	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	ENST00000264025.3:c.596G>A	11.37:g.119548402C>T	ENSP00000264025:p.Arg199Gln	192	0	0		208	34	0.163462	NM_002855	O75465|Q2M3D3|Q9HBE6|Q9HBW2	Missense_Mutation	SNP	ENST00000264025.3	37	CCDS8426.1	9	0.004120879120879121	0	0.0	4	0.011049723756906077	0	0.0	5	0.006596306068601583	c	17.34	3.364188	0.61513	0.001819	0.01362	ENSG00000110400	ENST00000341398;ENST00000264025;ENST00000340882	T;T;T	0.76186	-1.0;-1.0;-1.0	5.21	5.21	0.72293	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like fold (1);	0.055119	0.64402	D	0.000001	T	0.72700	0.3493	L	0.53249	1.67	0.43628	D	0.996013	D;D;D	0.89917	0.996;0.997;1.0	B;P;P	0.57911	0.423;0.559;0.829	T	0.75502	-0.3295	9	.	.	.	.	11.2519	0.49031	0.0:0.9162:0.0:0.0838	.	199;199;199	Q15223-3;Q15223;Q15223-2	.;PVRL1_HUMAN;.	Q	199	ENSP00000344974:R199Q;ENSP00000264025:R199Q;ENSP00000345289:R199Q	.	R	-	2	0	PVRL1	119053612	1.000000	0.71417	1.000000	0.80357	0.699000	0.40488	2.997000	0.49457	2.450000	0.82876	0.556000	0.70494	CGG	C|0.991;T|0.009	0.009	strong		0.597	PVRL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388231.1			T	119548402	C	T	119548402	3	4	29	1	0	0	0	0	1	0	0	0	12854	652	23	1	1419	1	PVRL1	11	119548402	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1678524	119548402	15458114	562	12803											
PVRL1	5818	hgsc.bcm.edu	37	chr11	119549473	119549473	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggaccacctgggagtggaCgcctggccaggaggatggca	8	5	17	11	1	0	0	0	0	0	0	0	5	0	5	4	7	0	1	4	7	0	0	rs200377205		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:119549473C>T	ENST00000264025.3	-	2	612	c.82G>A	c.(82-84)Gtc>Atc	p.V28I	PVRL1_ENST00000340882.2_Missense_Mutation_p.V28I|PVRL1_ENST00000341398.2_Missense_Mutation_p.V28I|PVRL1_ENST00000524510.1_5'UTR	NM_002855.4	NP_002846.3	Q15223	PVRL1_HUMAN	poliovirus receptor-related 1 (herpesvirus entry mediator C)	28					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)		TGGGAGTGGACGCCTGGCCAG	0.587																																					p.V28I		Atlas-SNP	.											.	PVRL1	133	.	0			c.G82A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL	0,4398		0,0,2199	52	36	42		82,82,82	-2.6	0	11		42	1,8589	1.2+/-3.3	0,1,4294	no	missense,missense,missense	PVRL1	NM_203286.1,NM_203285.1,NM_002855.4	29,29,29	0,1,6493	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	28/353,28/459,28/518	119549473	1,12987	2199	4295	6494	SO:0001583	missense	5818	exon2			AGTGGACGCCTGG	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	ENST00000264025.3:c.82G>A	11.37:g.119549473C>T	ENSP00000264025:p.Val28Ile	34	0	0		40	9	0.225	NM_002855	O75465|Q2M3D3|Q9HBE6|Q9HBW2	Missense_Mutation	SNP	ENST00000264025.3	37	CCDS8426.1	.	.	.	.	.	.	.	.	.	.	C	12.16	1.853973	0.32791	0.0	1.16E-4	ENSG00000110400	ENST00000341398;ENST00000264025;ENST00000340882	T;T;T	0.75154	-0.84;-0.91;-0.83	5.45	-2.56	0.06268	Immunoglobulin-like (1);	0.453783	0.23048	N	0.052524	T	0.50171	0.1600	N	0.19112	0.55	0.09310	N	1	B;B;B	0.22604	0.023;0.029;0.072	B;B;B	0.11329	0.004;0.001;0.006	T	0.32375	-0.9909	9	.	.	.	.	7.776	0.29037	0.0:0.3707:0.151:0.4783	.	28;28;28	Q15223-3;Q15223;Q15223-2	.;PVRL1_HUMAN;.	I	28	ENSP00000344974:V28I;ENSP00000264025:V28I;ENSP00000345289:V28I	.	V	-	1	0	PVRL1	119054683	0.001000	0.12720	0.013000	0.15412	0.047000	0.14425	0.252000	0.18278	-0.358000	0.08162	-0.373000	0.07131	GTC	C|0.996;T|0.005	0.005	weak		0.587	PVRL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388231.1			T	119549473	C	T	119549473	3	4	29	1	0	0	0	0	1	0	0	0	12854	536	19	1	1937	1	PVRL1	11	119549473	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1071	119549473	15457043	563	12804											
GRIK4	2900	hgsc.bcm.edu	37	chr11	120531044	120531044	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagatgccccgcgtctcggCgcctttggtgctgcttcctg	3	11	13	14	4	1	1	0	0	1	1	3	2	2	1	4	2	3	2	4	2	1	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:120531044C>T	ENST00000527524.2	+	3	304	c.17C>T	c.(16-18)gCg>gTg	p.A6V	GRIK4_ENST00000438375.2_Missense_Mutation_p.A6V	NM_001282470.1	NP_001269399.1	Q16099	GRIK4_HUMAN	glutamate receptor, ionotropic, kainate 4	6					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.A6V(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)		CGCGTCTCGGCGCCTTTGGTG	0.647											OREG0021424	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A6V		Atlas-SNP	.											GRIK4,colon,NS,0,1	GRIK4	149	1	1	Substitution - Missense(1)	large_intestine(1)	c.C17T						PASS	.						70	62	65					11																	120531044		2203	4299	6502	SO:0001583	missense	2900	exon1			TCTCGGCGCCTTT	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.17C>T	11.37:g.120531044C>T	ENSP00000435648:p.Ala6Val	34	0	0	1504	51	20	0.392157	NM_014619	A8K9L1	Missense_Mutation	SNP	ENST00000527524.2	37	CCDS8433.1	.	.	.	.	.	.	.	.	.	.	C	16.91	3.253108	0.59212	.	.	ENSG00000149403	ENST00000527524;ENST00000438375	T;T	0.12465	2.68;2.68	5.55	4.63	0.57726	.	0.000000	0.64402	D	0.000009	T	0.06050	0.0157	N	0.08118	0	0.37509	D	0.917088	P;B	0.34587	0.458;0.102	B;B	0.20184	0.028;0.019	T	0.43589	-0.9382	10	0.20046	T	0.44	.	13.3882	0.60807	0.0:0.9224:0.0:0.0776	.	6;6	A6H8K8;Q16099	.;GRIK4_HUMAN	V	6	ENSP00000435648:A6V;ENSP00000404063:A6V	ENSP00000404063:A6V	A	+	2	0	GRIK4	120036254	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.202000	0.65169	1.467000	0.48044	0.563000	0.77884	GCG	.	.	none		0.647	GRIK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109760.4	NM_014619		T	120531044	C	T	120531044	3	4	29	1	0	0	0	0	1	0	0	0	6785	768	27	1	19	1	GRIK4	11	120531044	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	981571	120531044	14475472	564	12805											
OR10G9	219870	hgsc.bcm.edu	37	chr11	123893757	123893757	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtgacagcgttcatcctcaCgggccttccccatgccccag	6	8	9	18	3	2	1	2	1	0	0	4	1	4	1	6	1	2	1	6	1	0	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:123893757C>T	ENST00000375024.1	+	1	38	c.38C>T	c.(37-39)aCg>aTg	p.T13M		NM_001001953.1	NP_001001953.1	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G, member 9	13						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)		TTCATCCTCACGGGCCTTCCC	0.562																																					p.T13M		Atlas-SNP	.											OR10G9,NS,carcinoma,0,2	OR10G9	80	2	0			c.C38T						scavenged	.						175	170	172					11																	123893757		2201	4299	6500	SO:0001583	missense	219870	exon1			TCCTCACGGGCCT	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.38C>T	11.37:g.123893757C>T	ENSP00000364164:p.Thr13Met	199	0	0		239	25	0.104603	NM_001001953		Missense_Mutation	SNP	ENST00000375024.1	37	CCDS31703.1	.	.	.	.	.	.	.	.	.	.	C	7.277	0.608309	0.14002	.	.	ENSG00000236981	ENST00000375024	T	0.00421	7.46	3.33	-4.34	0.03666	.	1.118960	0.06817	N	0.791372	T	0.00178	0.0005	N	0.04260	-0.245	0.09310	N	0.999992	B	0.06786	0.001	B	0.04013	0.001	T	0.29640	-1.0005	10	0.40728	T	0.16	.	9.7201	0.40297	0.0:0.2623:0.0:0.7377	.	13	Q8NGN4	O10G9_HUMAN	M	13	ENSP00000364164:T13M	ENSP00000364164:T13M	T	+	2	0	OR10G9	123398967	0.000000	0.05858	0.149000	0.22428	0.069000	0.16628	-0.761000	0.04751	-1.009000	0.03400	-0.766000	0.03442	ACG	.	.	none		0.562	OR10G9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387269.1	NM_001001953		T	123893757	C	T	123893757	3	4	29	1	0	0	0	0	1	0	0	0	10913	536	19	1	40	1	OR10G9	11	123893757	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	3362713	123893757	11112759	565	12806											
OR8G2	0	hgsc.bcm.edu	37	chr11	124096271	124096271	+	IGR	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagtgtcctctgtgttttatActattgttgtgcccatgctg	6	18	9	8	0	1	0	0	0	1	0	2	0	2	0	2	0	3	3	2	0	4	6	rs201854907	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:124096271A>G								OR10D3 (39319 upstream) : OR8G1 (24151 downstream)																							TGTGTTTTATACTATTGTTGT	0.448																																					p.T292A		Atlas-SNP	.											.	.	.	.	0			c.A874G						PASS	.	A	ALA/THR	4,3862		0,4,1929	73	68	69		874	1.3	0	11		69	24,8280		0,24,4128	no	missense	OR8G2	NM_001007249.1	58	0,28,6057	GG,GA,AA		0.289,0.1035,0.2301	possibly-damaging	292/305	124096271	28,12142	1933	4152	6085	SO:0001628	intergenic_variant	26492	exon1			TTTTATACTATTG																													11.37:g.124096271A>G		175	0	0		201	16	0.079602	NM_001007249		Missense_Mutation	SNP		37																																																																																				A|0.996;G|0.005	0.005	strong	0	0.448									G	124096271	A	G	124096271	1	3	29	0	1	0	0	0	0	0	0	0	11244	391	14	3		3	OR8G2	11	124096271	IGR	SNP	A	TCGA-GR-7351-01A-11D-2210-10	202514	124096271	10910245	566	12807											
CCDC15	80071	hgsc.bcm.edu	37	chr11	124857192	124857192	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gacaggaatccagagtgttaAgccagatacccaggctgttg	12	8	12	9	0	0	2	0	0	0	2	1	4	1	3	3	2	2	3	3	2	3	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:124857192A>C	ENST00000344762.5	+	8	1329	c.1070A>C	c.(1069-1071)aAg>aCg	p.K357T	CCDC15_ENST00000529051.1_Missense_Mutation_p.K357T	NM_025004.2	NP_079280.2	Q0P6D6	CCD15_HUMAN	coiled-coil domain containing 15	357						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)		CAGAGTGTTAAGCCAGATACC	0.493																																					p.K357T		Atlas-SNP	.											.	CCDC15	134	.	0			c.A1070C						PASS	.						124	119	121					11																	124857192		1838	4093	5931	SO:0001583	missense	80071	exon8			GTGTTAAGCCAGA	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.1070A>C	11.37:g.124857192A>C	ENSP00000341684:p.Lys357Thr	138	0	0		137	20	0.145985	NM_025004	Q9H8U7	Missense_Mutation	SNP	ENST00000344762.5	37	CCDS44756.1	.	.	.	.	.	.	.	.	.	.	A	11.72	1.721457	0.30503	.	.	ENSG00000149548	ENST00000529051;ENST00000344762	T;T	0.32272	1.46;1.46	4.09	1.72	0.24424	.	1.268580	0.05276	N	0.518579	T	0.17280	0.0415	N	0.08118	0	0.09310	N	1	P	0.41848	0.763	B	0.39027	0.288	T	0.17868	-1.0355	10	0.72032	D	0.01	-0.6297	5.4022	0.16303	0.7249:0.1776:0.0975:0.0	.	357	Q0P6D6	CCD15_HUMAN	T	357	ENSP00000435403:K357T;ENSP00000341684:K357T	ENSP00000341684:K357T	K	+	2	0	CCDC15	124362402	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-0.049000	0.11924	0.369000	0.24510	0.379000	0.24179	AAG	.	.	none		0.493	CCDC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387131.1	NM_025004		C	124857192	A	C	124857192	3	2	29	1	0	0	0	0	1	0	0	0	2786	72	3	5	1096	5	CCDC15	11	124857192	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	760921	124857192	10149324	567	12808											
PUS3	83480	hgsc.bcm.edu	37	chr11	125764156	125764156	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcaaacttacagtcatataAgactagaggaaattctacag	17	11	6	7	0	3	2	2	0	1	2	3	3	3	3	0	1	3	0	0	1	7	7			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:125764156A>C	ENST00000530811.1	-	3	1015	c.970T>G	c.(970-972)Tta>Gta	p.L324V	HYLS1_ENST00000425380.2_Intron|PUS3_ENST00000227474.3_Missense_Mutation_p.L324V|HYLS1_ENST00000526028.1_Intron|HYLS1_ENST00000356438.3_Intron			Q9BZE2	PUS3_HUMAN	pseudouridylate synthase 3	324					tRNA pseudouridine synthesis (GO:0031119)	nucleus (GO:0005634)	pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			NS(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	10	all_hematologic(175;0.177)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.131)|all_lung(97;0.139)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.043)		CAGTCATATAAGACTAGAGGA	0.363																																					p.L324V		Atlas-SNP	.											.	PUS3	33	.	0			c.T970G						PASS	.						56	62	60					11																	125764156		2200	4295	6495	SO:0001583	missense	83480	exon4			CATATAAGACTAG	BC004822	CCDS8466.1, CCDS73411.1	11q24.2	2008-02-05							25461	protein-coding gene	gene with protein product						12477932	Standard	NM_031307		Approved	FKSG32	uc001qcy.2	Q9BZE2		ENST00000530811.1:c.970T>G	11.37:g.125764156A>C	ENSP00000432386:p.Leu324Val	33	0	0		62	8	0.129032	NM_031307	B2RAM0|Q96D17|Q96J23|Q96NB4	Missense_Mutation	SNP	ENST00000530811.1	37	CCDS8466.1	.	.	.	.	.	.	.	.	.	.	A	19.02	3.745579	0.69418	.	.	ENSG00000110060	ENST00000227474;ENST00000530811	T;T	0.75050	-0.9;-0.9	5.64	1.72	0.24424	Pseudouridine synthase I, TruA, C-terminal (1);Pseudouridine synthase, catalytic domain (1);Pseudouridine synthase I, TruA, alpha/beta domain (1);	0.000000	0.85682	D	0.000000	D	0.87869	0.6286	H	0.96518	3.835	0.58432	D	0.999996	D	0.89917	1.0	D	0.97110	1.0	D	0.85879	0.1421	10	0.87932	D	0	-8.6407	6.4206	0.21742	0.4951:0.0:0.5049:0.0	.	324	Q9BZE2	PUS3_HUMAN	V	324	ENSP00000227474:L324V;ENSP00000432386:L324V	ENSP00000227474:L324V	L	-	1	2	PUS3	125269366	1.000000	0.71417	0.927000	0.36925	0.980000	0.70556	3.443000	0.52907	0.507000	0.28148	0.482000	0.46254	TTA	.	.	none		0.363	PUS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386783.1	NM_031307		C	125764156	A	C	125764156	3	2	29	1	0	0	0	0	1	0	0	0	12847	69	3	5	479	5	PUS3	11	125764156	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	906964	125764156	9242360	568	12809											
ARHGAP32	9743	hgsc.bcm.edu	37	chr11	128842603	128842603	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgtgctggtattctcttcGggggacccagaaggagggta	7	10	16	8	1	1	1	0	0	1	1	3	3	1	3	1	5	1	4	1	5	3	4	rs376118787		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr11:128842603G>A	ENST00000310343.9	-	21	3755	c.3756C>T	c.(3754-3756)ccC>ccT	p.P1252P	ARHGAP32_ENST00000524655.1_3'UTR|ARHGAP32_ENST00000527272.1_Silent_p.P903P|ARHGAP32_ENST00000392657.3_Silent_p.P903P	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	1252					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						TATTCTCTTCGGGGGACCCAG	0.483																																					p.P1252P		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.C3756T						PASS	.	G	,	1,4401	2.1+/-5.4	0,1,2200	98	103	101		3756,2709	-3.5	0.9	11		101	0,8594		0,0,4297	no	coding-synonymous,coding-synonymous	ARHGAP32	NM_001142685.1,NM_014715.3	,	0,1,6497	AA,AG,GG		0.0,0.0227,0.0077	,	1252/2088,903/1739	128842603	1,12995	2201	4297	6498	SO:0001819	synonymous_variant	9743	exon21			CTCTTCGGGGGAC	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.3756C>T	11.37:g.128842603G>A		128	0	0		137	40	0.291971	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Silent	SNP	ENST00000310343.9	37	CCDS44769.1																																																																																			.	.	weak		0.483	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715		A	128842603	G	A	128842603	2	1	29	1	0	0	0	0	0	0	0	1	881	1103	39	1		1	ARHGAP32	11	128842603	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	3078447	128842603	6163913	569	12810											
SLC6A13	6540	hgsc.bcm.edu	37	chr12	333237	333237	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttccctccggttcttcttgCggaacacgtgagggtacatg	6	12	11	12	3	2	1	0	1	2	0	4	2	4	2	2	3	3	2	2	3	2	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:333237C>T	ENST00000343164.4	-	11	1284	c.1232G>A	c.(1231-1233)cGc>cAc	p.R411H	SLC6A13_ENST00000445055.2_Missense_Mutation_p.R319H|SLC6A13_ENST00000539668.1_5'UTR	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	411					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)			GTTCTTCTTGCGGAACACGTG	0.572																																					p.R411H		Atlas-SNP	.											.	SLC6A13	62	.	0			c.G1232A						PASS	.						122	102	109					12																	333237		2203	4300	6503	SO:0001583	missense	6540	exon11			TTCTTGCGGAACA	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.1232G>A	12.37:g.333237C>T	ENSP00000339260:p.Arg411His	96	0	0		86	5	0.0581395	NM_016615	B4DJL1|Q8TCC2|Q8WW56	Missense_Mutation	SNP	ENST00000343164.4	37	CCDS8502.1	.	.	.	.	.	.	.	.	.	.	C	18.53	3.644952	0.67358	.	.	ENSG00000010379	ENST00000445055;ENST00000313154;ENST00000343164	T;T	0.75938	-0.98;-0.98	5.5	4.6	0.57074	.	0.000000	0.85682	D	0.000000	D	0.85004	0.5598	M	0.88842	2.985	0.80722	D	1	P;P;P	0.47545	0.897;0.778;0.778	P;P;P	0.53224	0.721;0.598;0.598	D	0.88041	0.2781	10	0.72032	D	0.01	.	15.5587	0.76219	0.1392:0.8608:0.0:0.0	.	319;390;411	B4DJL1;B4DJS3;Q9NSD5	.;.;S6A13_HUMAN	H	319;390;411	ENSP00000407104:R319H;ENSP00000339260:R411H	ENSP00000318097:R390H	R	-	2	0	SLC6A13	203498	1.000000	0.71417	1.000000	0.80357	0.269000	0.26545	7.760000	0.85248	1.305000	0.44909	0.491000	0.48974	CGC	.	.	none		0.572	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615		T	333237	C	T	333237	3	4	29	1	0	0	0	0	1	0	0	0	14691	768	27	1	596	1	SLC6A13	12	333237	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10		333237	133518658	570	12811											
WNK1	65125	hgsc.bcm.edu	37	chr12	922913	922913	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gattttatgattcctgggaaTccacagtaaaaggaaagaag	16	10	10	5	0	0	2	0	1	0	1	2	5	2	4	2	2	0	1	2	2	6	4	rs200234585		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:922913T>C	ENST00000315939.6	+	2	1508	c.865T>C	c.(865-867)Tcc>Ccc	p.S289P	WNK1_ENST00000447667.2_Missense_Mutation_p.S289P|WNK1_ENST00000535572.1_Missense_Mutation_p.S289P|WNK1_ENST00000530271.2_Missense_Mutation_p.S289P|WNK1_ENST00000537687.1_Missense_Mutation_p.S289P	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	289	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)			TTCCTGGGAATCCACAGTAAA	0.353																																					p.S289P	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.T865C						PASS	.						110	104	106					12																	922913		2203	4300	6503	SO:0001583	missense	65125	exon2			TGGGAATCCACAG	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.865T>C	12.37:g.922913T>C	ENSP00000313059:p.Ser289Pro	77	0	0		67	31	0.462687	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.297998	0.81025	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000447667;ENST00000530271	T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2	5.83	5.83	0.93111	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000004	T	0.72771	0.3502	L	0.41079	1.255	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.974	D;D;P	0.81914	0.992;0.995;0.899	T	0.75266	-0.3378	10	0.72032	D	0.01	-12.6206	16.1995	0.82060	0.0:0.0:0.0:1.0	.	289;289;289	F5GWT4;Q9H4A3;F6UYG0	.;WNK1_HUMAN;.	P	289	ENSP00000441972:S289P;ENSP00000313059:S289P;ENSP00000444465:S289P;ENSP00000392542:S289P;ENSP00000433548:S289P	ENSP00000313059:S289P	S	+	1	0	WNK1	793174	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.072000	0.64389	2.220000	0.72140	0.459000	0.35465	TCC	.	.	weak		0.353	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979		C	922913	T	C	922913	3	2	29	1	0	0	0	0	1	0	0	0	17392	1435	50	3	871	3	WNK1	12	922913	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	589676	922913	132928982	571	12812											
CACNA2D4	93589	hgsc.bcm.edu	37	chr12	1910786	1910786	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ctgggtcaggacagcaccatCcacctcccccagaaatcttc	10	7	7	17	0	2	1	1	0	1	1	5	2	4	2	5	2	1	1	5	2	1	1	rs62621429	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:1910786C>T	ENST00000382722.5	-	30	3108	c.2746G>A	c.(2746-2748)Gat>Aat	p.D916N	CACNA2D4_ENST00000587995.1_Missense_Mutation_p.D891N|CACNA2D4_ENST00000586184.1_Missense_Mutation_p.D916N|CACNA2D4_ENST00000538027.2_Missense_Mutation_p.D61N|CACNA2D4_ENST00000588077.1_Missense_Mutation_p.D852N|CACNA2D4_ENST00000538450.1_Missense_Mutation_p.D46N|CACNA2D4_ENST00000585708.1_Missense_Mutation_p.D852N	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	916					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)		ACAGCACCATCCACCTCCCCC	0.582													C|||	53	0.0105831	0.0015	0.0187	5008	,	,		18810	0.0		0.0308	False		,,,				2504	0.0072				p.D916N	Colon(2;101 179 21030 23310 28141)	Atlas-SNP	.											.	CACNA2D4	220	.	0			c.G2746A						PASS	.	C	ASN/ASP	21,4043		0,21,2011	57	59	59		2746	4.7	1	12	dbSNP_129	59	221,8131		0,221,3955	yes	missense	CACNA2D4	NM_172364.4	23	0,242,5966	TT,TC,CC		2.6461,0.5167,1.9491	probably-damaging	916/1138	1910786	242,12174	2032	4176	6208	SO:0001583	missense	93589	exon30			CACCATCCACCTC	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.2746G>A	12.37:g.1910786C>T	ENSP00000372169:p.Asp916Asn	49	0	0		61	32	0.52459	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Missense_Mutation	SNP	ENST00000382722.5	37	CCDS44785.1	36	0.016483516483516484	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	23	0.030343007915567283	C	17.44	3.391380	0.62066	0.005167	0.026461	ENSG00000151062	ENST00000456077;ENST00000280663;ENST00000382722;ENST00000538450	D;D	0.82711	-1.64;-1.64	5.58	4.69	0.59074	.	0.127286	0.51477	N	0.000100	T	0.71350	0.3329	L	0.58354	1.805	0.80722	D	1	D;D;P	0.55800	0.973;0.96;0.759	P;P;P	0.58928	0.848;0.556;0.521	T	0.77172	-0.2685	10	0.27785	T	0.31	.	11.5041	0.50454	0.0:0.9163:0.0:0.0837	rs62621429	46;916;852	B4DVU4;Q7Z3S7;Q7Z3S7-4	.;CA2D4_HUMAN;.	N	852;916;916;46	ENSP00000372169:D916N;ENSP00000446341:D46N	ENSP00000280663:D916N	D	-	1	0	CACNA2D4	1781047	1.000000	0.71417	0.992000	0.48379	0.977000	0.68977	5.693000	0.68264	1.358000	0.45922	0.655000	0.94253	GAT	C|0.979;T|0.021	0.021	strong		0.582	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2			T	1910786	C	T	1910786	3	4	29	1	0	0	0	0	1	0	0	0	2553	855	30	2	703	2	CACNA2D4	12	1910786	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	987873	1910786	131941109	572	12813											
CACNA1C	775	hgsc.bcm.edu	37	chr12	2224449	2224449	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tgaatgccaatgcggcagcgGggctggcccctgagcacatc	8	6	14	13	2	0	2	0	2	0	0	1	2	0	2	3	4	4	3	3	4	2	0	rs34534613	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:2224449G>A	ENST00000347598.4	+	2	109	c.109G>A	c.(109-111)Ggg>Agg	p.G37R	CACNA1C_ENST00000399641.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399638.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399601.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399655.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399595.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000406454.3_Missense_Mutation_p.G37R|CACNA1C_ENST00000399621.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000402845.3_Missense_Mutation_p.G37R|CACNA1C_ENST00000399637.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399649.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399606.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399617.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000327702.7_Missense_Mutation_p.G37R|CACNA1C_ENST00000399644.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399629.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000480911.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000335762.5_Missense_Mutation_p.G37R|CACNA1C_ENST00000399634.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399591.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000344100.3_Missense_Mutation_p.G37R|CACNA1C_ENST00000399603.1_Missense_Mutation_p.G37R|CACNA1C_ENST00000399597.1_Missense_Mutation_p.G37R	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	37					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)	TGCGGCAGCGGGGCTGGCCCC	0.627													G|||	2	0.000399361	0.0	0.0014	5008	,	,		16109	0.0		0.0	False		,,,				2504	0.001				p.G37R		Atlas-SNP	.											.	CACNA1C	1023	.	0			c.G109A						PASS	.	G	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	2,3864		0,2,1931	9	11	10		109,109,109,109,109,109,109,109,109,109,109,109,109,109,109,109,109,109,109,109,109,109,109	5.8	0.8	12	dbSNP_126	10	26,8160		0,26,4067	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	CACNA1C	NM_000719.6,NM_001129827.1,NM_001129829.1,NM_001129830.1,NM_001129831.1,NM_001129832.1,NM_001129833.1,NM_001129834.1,NM_001129835.1,NM_001129836.1,NM_001129837.1,NM_001129838.1,NM_001129839.1,NM_001129840.1,NM_001129841.1,NM_001129842.1,NM_001129843.1,NM_001129844.1,NM_001129846.1,NM_001167623.1,NM_001167624.1,NM_001167625.1,NM_199460.2	125,125,125,125,125,125,125,125,125,125,125,125,125,125,125,125,125,125,125,125,125,125,125	0,28,5998	AA,AG,GG		0.3176,0.0517,0.2323	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	37/2139,37/2187,37/2180,37/2174,37/2167,37/2159,37/2158,37/2158,37/2158,37/2156,37/2147,37/2147,37/2145,37/2139,37/2139,37/2139,37/2139,37/2136,37/2128,37/2139,37/2174,37/2199,37/2222	2224449	28,12024	1933	4093	6026	SO:0001583	missense	775	exon2			GCAGCGGGGCTGG	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.109G>A	12.37:g.2224449G>A	ENSP00000266376:p.Gly37Arg	34	0	0		34	17	0.5	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	37	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.085219	0.76642	5.17E-4	0.003176	ENSG00000151067	ENST00000543114;ENST00000335762;ENST00000399655;ENST00000480911;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.96011	-3.84;-3.82;-3.85;-3.87;-3.82;-3.81;-3.83;-3.73;-3.77;-3.88;-3.78;-3.77;-3.88;-3.86;-3.74;-3.66;-3.88;-3.83;-3.81;-3.86;-3.76;-3.85;-3.88	5.77	5.77	0.91146	.	0.513281	0.18641	N	0.135284	D	0.97025	0.9028	L	0.48642	1.525	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;B;D;D;D;D;D;D;D	0.89917	0.999;0.999;1.0;1.0;0.999;0.999;1.0;0.999;0.999;0.999;0.999;1.0;0.138;0.999;0.998;0.999;0.999;0.999;0.999;0.999	D;D;D;D;D;D;D;D;D;D;D;D;B;D;D;D;D;D;D;D	0.91635	0.967;0.967;0.949;0.999;0.967;0.967;0.999;0.967;0.967;0.967;0.967;0.999;0.055;0.967;0.914;0.967;0.967;0.967;0.967;0.967	D	0.97376	0.9979	10	0.87932	D	0	.	19.9785	0.97317	0.0:0.0:1.0:0.0	rs34534613	37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37	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;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	R	67;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37;37	ENSP00000336982:G37R;ENSP00000382563:G37R;ENSP00000437936:G37R;ENSP00000382552:G37R;ENSP00000382547:G37R;ENSP00000382506:G37R;ENSP00000382530:G37R;ENSP00000382546:G37R;ENSP00000382500:G37R;ENSP00000382549:G37R;ENSP00000266376:G37R;ENSP00000382515:G37R;ENSP00000382510:G37R;ENSP00000341092:G37R;ENSP00000382537:G37R;ENSP00000329877:G37R;ENSP00000382557:G37R;ENSP00000385724:G37R;ENSP00000382512:G37R;ENSP00000382542:G37R;ENSP00000382526:G37R;ENSP00000385896:G37R;ENSP00000382504:G37R	ENSP00000329877:G37R	G	+	1	0	CACNA1C	2094710	1.000000	0.71417	0.779000	0.31741	0.079000	0.17450	9.599000	0.98280	2.729000	0.93468	0.555000	0.69702	GGG	G|0.997;A|0.003	0.003	strong		0.627	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719		A	2224449	G	A	2224449	3	1	29	1	0	0	0	0	1	0	0	0	2542	1232	43	2	115	2	CACNA1C	12	2224449	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	313663	2224449	131627446	573	12814											
PARP11	57097	hgsc.bcm.edu	37	chr12	3931308	3931308	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggtggcatagggatggcctcGttttcacagatgtaacttga	9	12	13	7	1	1	2	1	1	0	1	2	3	1	3	1	4	1	3	1	4	2	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:3931308G>A	ENST00000228820.4	-	5	504	c.360C>T	c.(358-360)aaC>aaT	p.N120N	PARP11_ENST00000427057.2_Silent_p.N39N|PARP11_ENST00000397096.2_Silent_p.N113N|PARP11_ENST00000476985.1_5'Flank|PARP11_ENST00000447133.3_Silent_p.N39N	NM_020367.4	NP_065100.2	Q9NR21	PAR11_HUMAN	poly (ADP-ribose) polymerase family, member 11	113	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)			GGATGGCCTCGTTTTCACAGA	0.388																																					p.N120N		Atlas-SNP	.											.	PARP11	39	.	0			c.C360T						PASS	.						106	96	99					12																	3931308		2203	4300	6503	SO:0001819	synonymous_variant	57097	exon5			GGCCTCGTTTTCA	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.360C>T	12.37:g.3931308G>A		87	0	0		93	12	0.129032	NM_020367	B4DRQ0|Q68DS1|Q8N5Y9	Silent	SNP	ENST00000228820.4	37	CCDS8523.2																																																																																			.	.	none		0.388	PARP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344213.1			A	3931308	G	A	3931308	2	1	29	1	0	0	0	0	0	0	0	1	11465	1136	40	1		1	PARP11	12	3931308	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1706859	3931308	129920587	574	12815											
AKAP3	10566	hgsc.bcm.edu	37	chr12	4735922	4735922	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gcccttggctggtaagcactCatataaactatctgggaagg	11	10	11	9	0	2	0	1	0	1	0	2	1	2	1	1	4	2	3	1	4	6	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:4735922C>G	ENST00000545990.2	-	5	2670	c.2146G>C	c.(2146-2148)Gag>Cag	p.E716Q	RP11-500M8.7_ENST00000536588.1_Intron|AKAP3_ENST00000228850.1_Missense_Mutation_p.E716Q	NM_001278309.1	NP_001265238.1	O75969	AKAP3_HUMAN	A kinase (PRKA) anchor protein 3	716					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						GGTAAGCACTCATATAAACTA	0.507																																					p.E716Q		Atlas-SNP	.											.	AKAP3	212	.	0			c.G2146C						PASS	.						67	60	62					12																	4735922		2203	4300	6503	SO:0001583	missense	10566	exon4			AGCACTCATATAA	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.2146G>C	12.37:g.4735922C>G	ENSP00000440994:p.Glu716Gln	98	0	0		112	30	0.267857	NM_006422	O75945|Q86X01|Q9UM61	Missense_Mutation	SNP	ENST00000545990.2	37	CCDS8531.1	.	.	.	.	.	.	.	.	.	.	C	9.085	1.000286	0.19121	.	.	ENSG00000111254	ENST00000228850;ENST00000545990	T;T	0.08282	3.11;3.11	4.91	4.91	0.64330	A-kinase anchor 110kDa, C-terminal (1);	0.111221	0.40144	N	0.001163	T	0.19886	0.0478	M	0.63428	1.95	0.27479	N	0.952633	D	0.56746	0.977	P	0.59357	0.856	T	0.02196	-1.1197	10	0.45353	T	0.12	-22.7839	10.643	0.45604	0.1911:0.8089:0.0:0.0	.	716	O75969	AKAP3_HUMAN	Q	716	ENSP00000228850:E716Q;ENSP00000440994:E716Q	ENSP00000228850:E716Q	E	-	1	0	AKAP3	4606183	0.884000	0.30299	0.652000	0.29579	0.024000	0.10985	2.160000	0.42348	2.544000	0.85801	0.655000	0.94253	GAG	.	.	none		0.507	AKAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398911.2	NM_006422		G	4735922	C	G	4735922	3	3	29	1	0	0	0	0	1	0	0	0	452	835	29	4	423	4	AKAP3	12	4735922	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	804614	4735922	129115973	575	12816											
GALNT8	26290	hgsc.bcm.edu	37	chr12	4835923	4835923	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggcccaggacctcttccggaAgtttggttacaacgcgtacc	8	9	11	13	3	1	0	0	0	1	0	2	2	2	2	4	4	3	3	4	4	4	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:4835923A>C	ENST00000252318.2	+	2	774	c.437A>C	c.(436-438)aAg>aCg	p.K146T	RP11-234B24.6_ENST00000544741.2_3'UTR	NM_017417.1	NP_059113.1	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8	146					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						CTCTTCCGGAAGTTTGGTTAC	0.557																																					p.K146T	Colon(108;631 1558 7270 20097 39846)	Atlas-SNP	.											.	GALNT8	89	.	0			c.A437C						PASS	.						76	70	72					12																	4835923		2203	4300	6503	SO:0001583	missense	26290	exon2			TCCGGAAGTTTGG	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.437A>C	12.37:g.4835923A>C	ENSP00000252318:p.Lys146Thr	53	0	0		52	14	0.269231	NM_017417	B2RU02	Missense_Mutation	SNP	ENST00000252318.2	37	CCDS8533.1	.	.	.	.	.	.	.	.	.	.	A	9.701	1.154514	0.21371	.	.	ENSG00000130035	ENST00000252318	T	0.55413	0.52	4.02	-0.0796	0.13710	.	0.506417	0.15357	N	0.266621	T	0.38161	0.1030	L	0.59436	1.845	0.09310	N	0.999995	P	0.35656	0.514	B	0.30646	0.118	T	0.25847	-1.0120	10	0.46703	T	0.11	.	2.4773	0.04579	0.533:0.0:0.2436:0.2233	.	146	Q9NY28	GALT8_HUMAN	T	146	ENSP00000252318:K146T	ENSP00000252318:K146T	K	+	2	0	GALNT8	4706184	0.066000	0.20996	0.379000	0.26080	0.923000	0.55619	0.165000	0.16564	0.148000	0.19059	-0.274000	0.10170	AAG	.	.	none		0.557	GALNT8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388277.2	NM_017417		C	4835923	A	C	4835923	3	2	29	1	0	0	0	0	1	0	0	0	6227	72	3	5	443	5	GALNT8	12	4835923	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	100001	4835923	129015972	576	12817											
GALNT8	26290	hgsc.bcm.edu	37	chr12	4854722	4854722	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cagttgatgggtttaactggGaactctggtgccgctacgat	8	12	13	8	2	1	1	0	1	1	0	1	3	1	2	1	3	4	3	1	3	3	4	rs201387598		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:4854722G>A	ENST00000252318.2	+	5	1325	c.988G>A	c.(988-990)Gaa>Aaa	p.E330K		NM_017417.1	NP_059113.1	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8	330					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						GTTTAACTGGGAACTCTGGTG	0.488													G|||	1	0.000199681	0.0	0.0	5008	,	,		21588	0.0		0.001	False		,,,				2504	0.0				p.E330K	Colon(108;631 1558 7270 20097 39846)	Atlas-SNP	.											.	GALNT8	89	.	0			c.G988A						PASS	.						117	99	105					12																	4854722		2203	4300	6503	SO:0001583	missense	26290	exon5			AACTGGGAACTCT	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.988G>A	12.37:g.4854722G>A	ENSP00000252318:p.Glu330Lys	111	0	0		94	43	0.457447	NM_017417	B2RU02	Missense_Mutation	SNP	ENST00000252318.2	37	CCDS8533.1	.	.	.	.	.	.	.	.	.	.	G	6.158	0.397270	0.11638	.	.	ENSG00000130035	ENST00000252318	T	0.59638	0.25	4.2	-3.18	0.05186	.	0.312551	0.29699	N	0.011436	T	0.23649	0.0572	N	0.04090	-0.28	0.18873	N	0.999986	B	0.13145	0.007	B	0.16289	0.015	T	0.18713	-1.0328	10	0.15066	T	0.55	.	5.2053	0.15287	0.3905:0.2669:0.3426:0.0	.	330	Q9NY28	GALT8_HUMAN	K	330	ENSP00000252318:E330K	ENSP00000252318:E330K	E	+	1	0	GALNT8	4724983	0.924000	0.31332	0.017000	0.16124	0.784000	0.44337	1.344000	0.33941	-0.510000	0.06523	-0.479000	0.04858	GAA	G|0.999;A|0.001	0.001	weak		0.488	GALNT8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388277.2	NM_017417		A	4854722	G	A	4854722	3	1	29	1	0	0	0	0	1	0	0	0	6227	1175	41	2	1006	2	GALNT8	12	4854722	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	18799	4854722	128997173	577	12818											
NTF3	4908	hgsc.bcm.edu	37	chr12	5604064	5604064	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acctacgtccgagcactgacTtcagagaacaataaactcgt	14	8	7	12	3	1	2	1	1	0	1	3	4	2	2	2	0	4	1	2	0	5	3	rs200399901		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:5604064T>C	ENST00000331010.6	+	1	767	c.684T>C	c.(682-684)acT>acC	p.T228T	NTF3_ENST00000423158.3_Silent_p.T241T|NTF3_ENST00000535299.1_Intron	NM_002527.4	NP_002518.1	P20783	NTF3_HUMAN	neurotrophin 3	228					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						GAGCACTGACTTCAGAGAACA	0.488													T|||	1	0.000199681	0.0	0.0	5008	,	,		15317	0.0		0.001	False		,,,				2504	0.0				p.T241T	GBM(194;1104 2182 8339 9578 18493)	Atlas-SNP	.											.	NTF3	50	.	0			c.T723C						PASS	.	T	,	0,4406		0,0,2203	66	55	59		723,684	2.2	1	12		59	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous,coding-synonymous	NTF3	NM_001102654.1,NM_002527.4	,	0,6,6497	CC,CT,TT		0.0698,0.0,0.0461	,	241/271,228/258	5604064	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	4908	exon2			ACTGACTTCAGAG		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.684T>C	12.37:g.5604064T>C		28	0	0		37	19	0.513514	NM_001102654	B7Z1T5|Q6FH50	Silent	SNP	ENST00000331010.6	37	CCDS8538.1																																																																																			T|0.999;C|0.001	0.001	strong		0.488	NTF3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400486.1			C	5604064	T	C	5604064	2	2	29	1	0	0	0	0	0	0	0	1	10705	1596	56	3		3	NTF3	12	5604064	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	749342	5604064	128247831	578	12819											
NCAPD2	9918	hgsc.bcm.edu	37	chr12	6630996	6630996	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacacaagaaaagaatcccCgggagtctacaggaaacatg	17	4	9	11	1	1	2	0	0	1	2	2	4	2	4	3	2	2	0	3	2	6	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:6630996C>T	ENST00000315579.5	+	15	2546	c.1747C>T	c.(1747-1749)Cgg>Tgg	p.R583W	NCAPD2_ENST00000545962.1_Missense_Mutation_p.R538W	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	583	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						AAAGAATCCCCGGGAGTCTAC	0.468																																					p.R583W		Atlas-SNP	.											NCAPD2,NS,carcinoma,0,1	NCAPD2	99	1	0			c.C1747T						PASS	.						69	72	71					12																	6630996		2203	4300	6503	SO:0001583	missense	9918	exon15			AATCCCCGGGAGT	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.1747C>T	12.37:g.6630996C>T	ENSP00000325017:p.Arg583Trp	70	0	0		66	21	0.318182	NM_014865	D3DUR4|Q8N6U3	Missense_Mutation	SNP	ENST00000315579.5	37	CCDS8548.1	.	.	.	.	.	.	.	.	.	.	C	11.74	1.729860	0.30684	.	.	ENSG00000010292	ENST00000315579;ENST00000382457;ENST00000545962;ENST00000535602	T;T;T	0.31247	2.5;1.5;2.23	5.3	5.3	0.74995	Armadillo-type fold (1);	1.094420	0.06897	N	0.805353	T	0.21674	0.0522	N	0.08118	0	0.09310	N	1	D;P;P	0.56968	0.978;0.733;0.912	B;B;B	0.40101	0.319;0.17;0.17	T	0.42396	-0.9454	10	0.66056	D	0.02	-0.0214	15.8787	0.79185	0.0:1.0:0.0:0.0	.	538;544;583	F5GZJ1;B3KY03;Q15021	.;.;CND1_HUMAN	W	583;455;538;455	ENSP00000325017:R583W;ENSP00000371895:R455W;ENSP00000444417:R538W	ENSP00000325017:R583W	R	+	1	2	NCAPD2	6501257	0.858000	0.29795	0.012000	0.15200	0.004000	0.04260	2.584000	0.46102	2.480000	0.83734	0.467000	0.42956	CGG	.	.	none		0.468	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865		T	6630996	C	T	6630996	3	4	29	1	0	0	0	0	1	0	0	0	10214	643	23	1	1801	1	NCAPD2	12	6630996	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1026932	6630996	127220899	579	12820											
TAS2R14	50840	hgsc.bcm.edu	37	chr12	11091206	11091206	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttccacatggagaagatgaGgagaagaaacattgccaggg	15	7	13	6	0	0	5	0	1	0	4	1	7	1	5	2	3	2	0	2	3	3	2	rs35804287	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:11091206G>A	ENST00000537503.1	-	1	656	c.601C>T	c.(601-603)Ctc>Ttc	p.L201F	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_023922.1	NP_076411.1	Q9NYV8	T2R14_HUMAN	taste receptor, type 2, member 14	201			L -> F (in dbSNP:rs35804287).		detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	8						GAGAAGATGAGGAGAAGAAAC	0.418													G|||	30	0.00599042	0.0	0.0043	5008	,	,		19120	0.0		0.0249	False		,,,				2504	0.002				p.L201F		Atlas-SNP	.											.	TAS2R14	26	.	0			c.C601T						PASS	.	G	PHE/LEU	19,4387	26.2+/-53.5	0,19,2184	86	90	89		601	-0.2	0	12	dbSNP_126	89	157,8443	74.8+/-137.4	4,149,4147	yes	missense	TAS2R14	NM_023922.1	22	4,168,6331	AA,AG,GG		1.8256,0.4312,1.3532	probably-damaging	201/318	11091206	176,12830	2203	4300	6503	SO:0001583	missense	50840	exon1			AGATGAGGAGAAG	AF227138	CCDS8637.1	12p13	2012-08-22			ENSG00000212127	ENSG00000212127		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	14920	protein-coding gene	gene with protein product		604790				10761934, 10766242	Standard	NM_023922		Approved	T2R14, TRB1	uc010shi.2	Q9NYV8	OTTHUMG00000162720	ENST00000537503.1:c.601C>T	12.37:g.11091206G>A	ENSP00000441949:p.Leu201Phe	78	0	0		77	42	0.545455	NM_023922	Q645X3	Missense_Mutation	SNP	ENST00000537503.1	37	CCDS8637.1	29	0.013278388278388278	0	0.0	3	0.008287292817679558	0	0.0	26	0.03430079155672823	G	13.65	2.301826	0.40694	0.004312	0.018256	ENSG00000212127	ENST00000537503	T	0.03272	3.99	3.95	-0.176	0.13311	.	0.112267	0.33534	U	0.004812	T	0.04318	0.0119	M	0.85945	2.785	0.09310	N	1	D	0.89917	1.0	D	0.80764	0.994	T	0.06215	-1.0839	10	0.87932	D	0	.	3.3203	0.07048	0.316:0.0:0.5031:0.1809	rs35804287	201	Q9NYV8	T2R14_HUMAN	F	201	ENSP00000441949:L201F	ENSP00000375094:L201F	L	-	1	0	TAS2R14	10982473	0.000000	0.05858	0.003000	0.11579	0.002000	0.02628	-1.779000	0.01777	-0.144000	0.11314	-0.241000	0.12123	CTC	G|0.989;A|0.011	0.011	strong		0.418	TAS2R14-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370194.4	NM_023922		A	11091206	G	A	11091206	3	1	29	1	0	0	0	0	1	0	0	0	15583	1000	35	2	355	2	TAS2R14	12	11091206	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	4460210	11091206	122760689	580	12821											
TAS2R43	259289	hgsc.bcm.edu	37	chr12	11244199	11244199	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgagatcctttaccatggagCtgcatcttcttgagatgttt	8	16	9	8	0	2	2	0	2	2	2	3	5	3	3	2	1	3	3	2	1	1	5	rs201245949	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:11244199C>G	ENST00000531678.1	-	1	713	c.630G>C	c.(628-630)caG>caC	p.Q210H	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176884.2	NP_795365.2	P59537	T2R43_HUMAN	taste receptor, type 2, member 43	210					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			endometrium(1)|ovary(1)|prostate(2)|urinary_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(49;0.0344)	BRCA - Breast invasive adenocarcinoma(232;0.196)		TACCATGGAGCTGCATCTTCT	0.408																																					p.Q210H		Atlas-SNP	.											.	TAS2R43	19	.	0			c.G630C						PASS	.						121	97	105					12																	11244199		2149	4144	6293	SO:0001583	missense	259289	exon1			ATGGAGCTGCATC	AF494237	CCDS53749.1	12p13.2	2012-08-22				ENSG00000255374		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	18875	protein-coding gene	gene with protein product		612668				12379855	Standard	NM_176884		Approved	T2R52	uc001qzq.1	P59537		ENST00000531678.1:c.630G>C	12.37:g.11244199C>G	ENSP00000431719:p.Gln210His	26	0	0		103	12	0.116505	NM_176884	P59546|Q645X4	Missense_Mutation	SNP	ENST00000531678.1	37	CCDS53749.1	.	.	.	.	.	.	.	.	.	.	-	3.385	-0.125533	0.06795	.	.	ENSG00000255374	ENST00000531678	T	0.00966	5.49	1.45	-0.562	0.11781	.	.	.	.	.	T	0.01976	0.0062	M	0.83852	2.665	0.09310	N	1	B	0.18968	0.032	B	0.32724	0.151	T	0.38672	-0.9650	9	0.54805	T	0.06	.	3.9123	0.09209	0.0:0.53:0.0:0.47	.	210	P59537	T2R43_HUMAN	H	210	ENSP00000431719:Q210H	ENSP00000431719:Q210H	Q	-	3	2	TAS2R43	11135466	0.000000	0.05858	0.088000	0.20740	0.014000	0.08584	-0.691000	0.05133	-0.203000	0.10251	0.195000	0.17529	CAG	C|0.994;G|0.006	0.006	strong		0.408	TAS2R43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383561.1	NM_176884		G	11244199	C	G	11244199	3	3	29	1	0	0	0	0	1	0	0	0	15596	796	28	4	303	4	TAS2R43	12	11244199	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	152993	11244199	122607696	581	12822											
LRP6	4040	hgsc.bcm.edu	37	chr12	12279735	12279735	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttccccatctcccttcataCgtggacacaacatcctctgg	8	12	5	16	1	3	0	1	0	2	0	6	1	5	1	4	2	2	0	4	2	2	3	rs34815107	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:12279735C>T	ENST00000261349.4	-	20	4278	c.4202G>A	c.(4201-4203)cGt>cAt	p.R1401H	LRP6_ENST00000543091.1_Missense_Mutation_p.R1356H|LRP6_ENST00000540415.1_Intron|BCL2L14_ENST00000396369.1_Intron	NM_002336.2	NP_002327.2	O75581	LRP6_HUMAN	low density lipoprotein receptor-related protein 6	1401			R -> H (in dbSNP:rs34815107).		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)				TCCCTTCATACGTGGACACAA	0.448													C|||	15	0.00299521	0.0113	0.0	5008	,	,		20124	0.0		0.0	False		,,,				2504	0.0				p.R1401H		Atlas-SNP	.											.	LRP6	170	.	0			c.G4202A						PASS	.	C	HIS/ARG	72,4334	64.7+/-102.0	0,72,2131	194	161	172		4202	5.6	1	12	dbSNP_126	172	0,8600		0,0,4300	yes	missense	LRP6	NM_002336.2	29	0,72,6431	TT,TC,CC		0.0,1.6341,0.5536	benign	1401/1614	12279735	72,12934	2203	4300	6503	SO:0001583	missense	4040	exon20			TTCATACGTGGAC	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.4202G>A	12.37:g.12279735C>T	ENSP00000261349:p.Arg1401His	110	0	0		93	46	0.494624	NM_002336	Q17RZ2	Missense_Mutation	SNP	ENST00000261349.4	37	CCDS8647.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	C	16.69	3.194168	0.58017	0.016341	0.0	ENSG00000070018	ENST00000261349;ENST00000543091	T;T	0.44482	0.92;0.92	5.64	5.64	0.86602	.	0.000000	0.64402	D	0.000007	T	0.22322	0.0538	L	0.38175	1.15	0.53005	D	0.999968	B;B	0.13145	0.005;0.007	B;B	0.12156	0.002;0.007	T	0.04103	-1.0977	10	0.28530	T	0.3	.	19.6816	0.95965	0.0:1.0:0.0:0.0	rs34815107	1356;1401	F5H7J9;O75581	.;LRP6_HUMAN	H	1401;1356	ENSP00000261349:R1401H;ENSP00000442472:R1356H	ENSP00000261349:R1401H	R	-	2	0	LRP6	12171002	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.510000	0.60455	2.646000	0.89796	0.563000	0.77884	CGT	C|0.994;T|0.006	0.006	strong		0.448	LRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400137.1			T	12279735	C	T	12279735	3	4	29	1	0	0	0	0	1	0	0	0	8971	536	19	1	655	1	LRP6	12	12279735	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1035536	12279735	121572160	582	12823											
APOLD1	81575	hgsc.bcm.edu	37	chr12	12940402	12940402	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	caggcgggcggagggggacaCcaaggttagccaggccgtgc	8	3	19	11	3	0	0	0	0	0	0	0	2	0	2	3	7	2	1	3	7	2	1	rs146348815		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:12940402C>T	ENST00000326765.6	+	2	726	c.656C>T	c.(655-657)aCc>aTc	p.T219I	APOLD1_ENST00000356591.4_Missense_Mutation_p.T188I	NM_001130415.1	NP_001123887.1	Q96LR9	APLD1_HUMAN	apolipoprotein L domain containing 1	219					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|endothelial cell activation (GO:0042118)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|regulation of endothelial cell differentiation (GO:0045601)|response to hypoxia (GO:0001666)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			breast(1)|endometrium(1)|large_intestine(1)|lung(1)|ovary(1)	5		Prostate(47;0.0632)		BRCA - Breast invasive adenocarcinoma(232;0.0338)|GBM - Glioblastoma multiforme(207;0.149)		GAGGGGGACACCAAGGTTAGC	0.612																																					p.T219I		Atlas-SNP	.											.	APOLD1	10	.	0			c.C656T						PASS	.	C	ILE/THR,ILE/THR	0,4406		0,0,2203	63	72	69		656,563	3.4	1	12	dbSNP_134	69	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	APOLD1	NM_001130415.1,NM_030817.2	89,89	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging,probably-damaging	219/280,188/249	12940402	2,13004	2203	4300	6503	SO:0001583	missense	81575	exon2			GGGACACCAAGGT	AL136783	CCDS8654.1, CCDS44833.1	12p13.2	2006-02-03	2006-01-23		ENSG00000178878	ENSG00000178878			25268	protein-coding gene	gene with protein product		612456				11230166	Standard	NM_030817		Approved	FLJ25138, DKFZP434F0318	uc001rau.4	Q96LR9	OTTHUMG00000153561	ENST00000326765.6:c.656C>T	12.37:g.12940402C>T	ENSP00000324277:p.Thr219Ile	87	0	0		80	30	0.375	NM_001130415	Q8IVR2|Q9H0I5	Missense_Mutation	SNP	ENST00000326765.6	37	CCDS44833.1	.	.	.	.	.	.	.	.	.	.	C	15.71	2.913823	0.52439	0.0	2.33E-4	ENSG00000178878	ENST00000326765;ENST00000356591	T;T	0.01379	4.96;4.96	5.35	3.43	0.39272	.	0.204155	0.35378	U	0.003241	T	0.01800	0.0057	L	0.32530	0.975	0.34187	D	0.67166	B;B	0.28055	0.199;0.199	B;B	0.24006	0.031;0.05	T	0.39981	-0.9587	10	0.87932	D	0	-15.4625	15.3834	0.74679	0.0:0.735:0.265:0.0	.	188;219	A0AVN6;Q96LR9	.;APLD1_HUMAN	I	219;188	ENSP00000324277:T219I;ENSP00000348998:T188I	ENSP00000324277:T219I	T	+	2	0	APOLD1	12831669	0.988000	0.35896	0.997000	0.53966	0.271000	0.26615	1.560000	0.36331	0.575000	0.29434	0.579000	0.79373	ACC	C|1.000;T|0.000	0.000	weak		0.612	APOLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000331627.1	NM_030817		T	12940402	C	T	12940402	3	4	29	1	0	0	0	0	1	0	0	0	811	507	18	2	669	2	APOLD1	12	12940402	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	660667	12940402	120911493	583	12824											
HIST4H4	121504	hgsc.bcm.edu	37	chr12	14923887	14923887	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atgagaccagaaatgcgcttGacgcccccacgtcgggcgag	10	5	13	13	5	0	3	0	2	0	2	1	5	0	3	3	1	1	1	3	1	1	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:14923887G>A	ENST00000539745.1	-	1	178	c.132C>T	c.(130-132)gtC>gtT	p.V44V	HIST4H4_ENST00000541592.1_5'Flank	NM_175054.2	NP_778224.1	P62805	H4_HUMAN	histone cluster 4, H4	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)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)	6						AAATGCGCTTGACGCCCCCAC	0.612											OREG0021698	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V44V		Atlas-SNP	.											.	HIST4H4	13	.	0			c.C132T						PASS	.						61	57	59					12																	14923887		2203	4300	6503	SO:0001819	synonymous_variant	121504	exon1			GCGCTTGACGCCC	AY128653	CCDS8665.1	12p12.3	2011-01-27	2006-10-11			ENSG00000197837		"Histones / Replication-dependent"	20510	protein-coding gene	gene with protein product		615069	"histone 4, H4"			12408966	Standard	NM_175054		Approved	MGC24116	uc001rcf.4	P62805		ENST00000539745.1:c.132C>T	12.37:g.14923887G>A		71	0	0	698	83	5	0.060241	NM_175054	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Silent	SNP	ENST00000539745.1	37	CCDS8665.1																																																																																			.	.	none		0.612	HIST4H4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400844.1	NM_175054		A	14923887	G	A	14923887	2	1	29	1	0	0	0	0	0	0	0	1	7194	1277	45	2		2	HIST4H4	12	14923887	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1983485	14923887	118928008	584	12825											
EPS8	2059	hgsc.bcm.edu	37	chr12	15776095	15776095	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggttgacaagtcatacctcCaatgcagctttttgtacagt	11	13	8	9	0	1	1	1	1	0	0	2	1	2	1	2	1	4	4	2	1	4	5	rs1126786	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:15776095C>T	ENST00000281172.5	-	20	2788	c.2352G>A	c.(2350-2352)ttG>ttA	p.L784L	EPS8_ENST00000543523.1_Silent_p.L784L|EPS8_ENST00000543612.1_Silent_p.L784L|EPS8_ENST00000540613.1_Silent_p.L524L|EPS8_ENST00000542903.1_Silent_p.L524L	NM_004447.5	NP_004438.3	Q12929	EPS8_HUMAN	epidermal growth factor receptor pathway substrate 8	784	Effector region. {ECO:0000250}.|Helix bundle 4. {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)		GTCATACCTCCAATGCAGCTT	0.418													T|||	882	0.176118	0.5507	0.0562	5008	,	,		17316	0.0536		0.0209	False		,,,				2504	0.0409				p.L784L		Atlas-SNP	.											.	EPS8	70	.	0			c.G2352A						PASS	.	T		2128,2278	599.1+/-389.2	529,1070,604	131	135	133		2352	-0.9	0.7	12	dbSNP_86	133	204,8396	810.5+/-407.1	2,200,4098	no	coding-synonymous	EPS8	NM_004447.5		531,1270,4702	TT,TC,CC		2.3721,48.2978,17.9302		784/823	15776095	2332,10674	2203	4300	6503	SO:0001819	synonymous_variant	2059	exon20			TACCTCCAATGCA	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.2352G>A	12.37:g.15776095C>T		119	0	0		129	63	0.488372	NM_004447	A6NMC3|A8K6W2|A8KA66|B4DX66|Q8N6J0	Silent	SNP	ENST00000281172.5	37	CCDS31753.1																																																																																			T|0.130;G|0.153;C|0.674;A|0.042	0.130	strong		0.418	EPS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401093.1			T	15776095	C	T	15776095	2	4	29	1	0	0	0	0	0	0	0	1	5196	593	21	2		2	EPS8	12	15776095	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	852208	15776095	118075800	585	12826											
SLCO1B1	10599	hgsc.bcm.edu	37	chr12	21358837	21358837	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atctcatagagatgtaccacTttcttattgcaactcagact	12	14	5	10	0	3	2	2	0	2	2	4	3	3	2	1	0	3	2	1	0	4	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:21358837T>G	ENST00000256958.2	+	11	1463	c.1367T>G	c.(1366-1368)cTt>cGt	p.L456R		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	456	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				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)	GATGTACCACTTTCTTATTGC	0.383																																					p.L456R		Atlas-SNP	.											SLCO1B1,right_lower_lobe,carcinoma,+1,1	SLCO1B1	151	1	0			c.T1367G						PASS	.						116	112	113					12																	21358837		2203	4300	6503	SO:0001583	missense	10599	exon11			TACCACTTTCTTA		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.1367T>G	12.37:g.21358837T>G	ENSP00000256958:p.Leu456Arg	91	0	0		94	22	0.234043	NM_006446	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Missense_Mutation	SNP	ENST00000256958.2	37	CCDS8685.1	.	.	.	.	.	.	.	.	.	.	T	8.595	0.885569	0.17540	.	.	ENSG00000134538	ENST00000256958	T	0.41400	1.0	4.06	2.91	0.33838	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.34828	N	0.003645	T	0.44561	0.1299	M	0.76328	2.33	0.27666	N	0.946908	P	0.35793	0.521	B	0.42163	0.378	T	0.42932	-0.9422	10	0.52906	T	0.07	.	5.5666	0.17175	0.0:0.2326:0.0:0.7674	.	456	Q9Y6L6	SO1B1_HUMAN	R	456	ENSP00000256958:L456R	ENSP00000256958:L456R	L	+	2	0	SLCO1B1	21250104	0.998000	0.40836	0.997000	0.53966	0.557000	0.35523	1.733000	0.38156	0.437000	0.26423	0.397000	0.26171	CTT	.	.	none		0.383	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446		G	21358837	T	G	21358837	3	3	29	1	0	0	0	0	1	0	0	0	14738	1609	56	5	1405	5	SLCO1B1	12	21358837	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	5582742	21358837	112493058	586	12827											
SOX5	6660	hgsc.bcm.edu	37	chr12	23757393	23757393	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggagatacagcagcaccaagGttgccttggggtatgcctgg	9	8	15	9	0	0	1	0	0	0	1	0	2	0	1	3	5	5	4	3	5	3	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:23757393G>T	ENST00000451604.2	-	9	1193	c.1092C>A	c.(1090-1092)aaC>aaA	p.N364K	SOX5_ENST00000381381.2_Missense_Mutation_p.N351K|SOX5_ENST00000541536.1_Missense_Mutation_p.N351K|SOX5_ENST00000537393.1_Missense_Mutation_p.N329K|SOX5_ENST00000309359.1_Missense_Mutation_p.N351K|SOX5_ENST00000546136.1_Missense_Mutation_p.N351K|SOX5_ENST00000545921.1_Missense_Mutation_p.N354K			P35711	SOX5_HUMAN	SRY (sex determining region Y)-box 5	364					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						CAGCACCAAGGTTGCCTTGGG	0.512																																					p.N364K		Atlas-SNP	.											.	SOX5	134	.	0			c.C1092A						PASS	.						149	123	132					12																	23757393		2203	4300	6503	SO:0001583	missense	6660	exon9			ACCAAGGTTGCCT	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.1092C>A	12.37:g.23757393G>T	ENSP00000398273:p.Asn364Lys	137	0	0		124	9	0.0725806	NM_006940	B7Z8V0|F5H5B0|Q86UK8|Q8J017|Q8J018|Q8J019|Q8J020|Q8N1D9|Q8N7E0|Q8TEA4	Missense_Mutation	SNP	ENST00000451604.2	37	CCDS8699.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.589489	0.86851	.	.	ENSG00000134532	ENST00000546136;ENST00000309359;ENST00000381381;ENST00000451604;ENST00000435266;ENST00000537393;ENST00000541536;ENST00000545921	D;D;D;D;D;D;D	0.97279	-4.31;-4.31;-4.2;-4.32;-4.32;-4.2;-4.32	6.16	5.27	0.74061	.	0.443696	0.27831	N	0.017669	D	0.97816	0.9283	M	0.68593	2.085	0.80722	D	1	B;D;B	0.54772	0.321;0.968;0.399	B;D;B	0.70487	0.205;0.969;0.206	D	0.96571	0.9423	10	0.33141	T	0.24	.	14.9931	0.71406	0.0674:0.0:0.9326:0.0	.	329;351;364	F5H0I3;P35711-4;P35711	.;.;SOX5_HUMAN	K	351;351;351;364;316;329;351;354	ENSP00000437487:N351K;ENSP00000308927:N351K;ENSP00000370788:N351K;ENSP00000398273:N364K;ENSP00000439832:N329K;ENSP00000441973:N351K;ENSP00000443520:N354K	ENSP00000308927:N351K	N	-	3	2	SOX5	23648660	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.733000	0.74796	2.937000	0.99478	0.650000	0.86243	AAC	.	.	none		0.512	SOX5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402006.2	NM_006940		T	23757393	G	T	23757393	3	4	29	1	0	0	0	0	1	0	0	0	14969	1252	44	4	1237	4	SOX5	12	23757393	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2398556	23757393	110094502	587	12828											
C12orf77	196415	hgsc.bcm.edu	37	chr12	25148824	25148824	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccctttacactcttttccgtGttcataaacgtgctcagggt	7	15	7	12	2	3	0	2	0	1	0	4	0	4	0	2	1	3	2	2	1	3	6			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:25148824G>T	ENST00000549828.1	-	3	528	c.324C>A	c.(322-324)aaC>aaA	p.N108K	C12orf77_ENST00000549262.1_Missense_Mutation_p.N53K|C12orf77_ENST00000434912.3_Missense_Mutation_p.N53K	NM_001101339.1	NP_001094809.1	C9JDV5	CL097_HUMAN	chromosome 12 open reading frame 77	108										endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)	7						TCTTTTCCGTGTTCATAAACG	0.463																																					p.N108K		Atlas-SNP	.											.	C12orf77	18	.	0			c.C324A						PASS	.						72	74	73					12																	25148824		1919	4117	6036	SO:0001583	missense	196415	exon3			TTCCGTGTTCATA	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.324C>A	12.37:g.25148824G>T	ENSP00000447146:p.Asn108Lys	178	0	0		209	58	0.277512	NM_001101339		Missense_Mutation	SNP	ENST00000549828.1	37	CCDS44846.1	.	.	.	.	.	.	.	.	.	.	G	8.521	0.868659	0.17322	.	.	ENSG00000226397	ENST00000549828;ENST00000549262;ENST00000434912	T;T;T	0.54071	0.64;0.59;0.59	2.79	1.84	0.25277	.	.	.	.	.	T	0.28764	0.0713	N	0.08118	0	0.09310	N	1	P	0.37101	0.582	B	0.33339	0.162	T	0.13872	-1.0493	9	0.87932	D	0	.	7.4561	0.27268	0.0:0.2699:0.7301:0.0	.	108	C9JDV5	CL097_HUMAN	K	108;53;53	ENSP00000447146:N108K;ENSP00000447028:N53K;ENSP00000403451:N53K	ENSP00000403451:N53K	N	-	3	2	C12orf77	25040091	0.000000	0.05858	0.008000	0.14137	0.002000	0.02628	-0.265000	0.08644	0.689000	0.31550	0.655000	0.94253	AAC	.	.	none		0.463	C12orf77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407827.1	NM_001101339		T	25148824	G	T	25148824	3	4	29	1	0	0	0	0	1	0	0	0	1718	1368	48	4	121	4	C12orf77	12	25148824	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1391431	25148824	108703071	588	12829											
C12orf77	196415	hgsc.bcm.edu	37	chr12	25148927	25148927	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgcaggcatccatcgtatgCtgtccagcgtctgcacgttc	6	12	10	13	3	1	0	0	0	1	0	5	0	3	0	2	1	4	6	2	1	1	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:25148927C>T	ENST00000549828.1	-	3	425	c.221G>A	c.(220-222)aGc>aAc	p.S74N	C12orf77_ENST00000549262.1_Missense_Mutation_p.S19N|C12orf77_ENST00000434912.3_Missense_Mutation_p.S19N	NM_001101339.1	NP_001094809.1	C9JDV5	CL097_HUMAN	chromosome 12 open reading frame 77	74										endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)	7						CCATCGTATGCTGTCCAGCGT	0.488																																					p.S74N		Atlas-SNP	.											.	C12orf77	18	.	0			c.G221A						PASS	.						86	90	88					12																	25148927		1985	4159	6144	SO:0001583	missense	196415	exon3			CGTATGCTGTCCA	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.221G>A	12.37:g.25148927C>T	ENSP00000447146:p.Ser74Asn	120	0	0		179	42	0.234637	NM_001101339		Missense_Mutation	SNP	ENST00000549828.1	37	CCDS44846.1	.	.	.	.	.	.	.	.	.	.	C	3.746	-0.052588	0.07362	.	.	ENSG00000226397	ENST00000549828;ENST00000549262;ENST00000434912	T;T;T	0.55588	0.56;0.51;0.51	2.83	-4.99	0.03010	.	.	.	.	.	T	0.26085	0.0636	N	0.08118	0	0.09310	N	1	B	0.20550	0.046	B	0.12837	0.008	T	0.16867	-1.0388	9	0.87932	D	0	.	5.5379	0.17021	0.1635:0.6411:0.0:0.1954	.	74	C9JDV5	CL097_HUMAN	N	74;19;19	ENSP00000447146:S74N;ENSP00000447028:S19N;ENSP00000403451:S19N	ENSP00000403451:S19N	S	-	2	0	C12orf77	25040194	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.337000	0.00507	-1.357000	0.02180	-0.345000	0.07892	AGC	.	.	none		0.488	C12orf77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407827.1	NM_001101339		T	25148927	C	T	25148927	3	4	29	1	0	0	0	0	1	0	0	0	1718	797	28	2	224	2	C12orf77	12	25148927	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	103	25148927	108702968	589	12830											
KRAS	3845	hgsc.bcm.edu	37	chr12	25362777	25362777	+	3'UTR	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctttttcttctttttaccAtctttgctcatcttttcttt	3	27	1	10	0	7	0	1	0	6	0	7	0	7	0	1	0	2	1	1	0	1	11	rs1137282	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:25362777A>G	ENST00000256078.4	-	0	706				KRAS_ENST00000311936.3_Silent_p.D173D|KRAS_ENST00000557334.1_Silent_p.D60D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog						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)			TCTTTTTACCATCTTTGCTCA	0.279		119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			A|||	879	0.175519	0.18	0.1931	5008	,	,		18305	0.0923		0.2187	False		,,,				2504	0.1984				p.D173D	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.T519C						PASS	.	A	,	753,3647	305.5+/-289.0	61,631,1508	68	64	65		519,	3.4	1	12	dbSNP_86	65	1853,6727	328.5+/-318.3	168,1517,2605	no	coding-synonymous,utr-3	KRAS	NM_004985.3,NM_033360.2	,	229,2148,4113	GG,GA,AA		21.5967,17.1136,20.077	,	173/189,	25362777	2606,10374	2200	4290	6490	SO:0001624	3_prime_UTR_variant	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	TTTACCATCTTTG	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.*73T>C	12.37:g.25362777A>G		102	0	0		122	63	0.516393	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Silent	SNP	ENST00000256078.4	37	CCDS8703.1																																																																																			T|0.136;G|0.154;C|0.028;A|0.682	0.154	strong		0.279	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		G	25362777	A	G	25362777	1	3	29	0	1	0	0	0	0	0	0	0	8447	214	8	3		3	KRAS	12	25362777	3'UTR	SNP	A	TCGA-GR-7351-01A-11D-2210-10	213850	25362777	108489118	590	12831											
KLHDC5	57542	hgsc.bcm.edu	37	chr12	27950775	27950775	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	accatctacatcgtggggggGtgtctccacgagctggggcc	6	8	15	12	2	2	0	0	0	2	0	4	1	2	0	3	5	2	1	3	5	1	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:27950775G>A	ENST00000381271.2	+	3	1505	c.1194G>A	c.(1192-1194)ggG>ggA	p.G398G	RP11-860B13.3_ENST00000543527.1_RNA	NM_020782.1	NP_065833.1	Q9P2K6	KLH42_HUMAN	kelch-like family member 42	398					mitotic nuclear division (GO:0007067)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of microtubule-based process (GO:0032886)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											TCGTGGGGGGGTGTCTCCACG	0.597																																					p.G398G		Atlas-SNP	.											.	.	.	.	0			c.G1194A						PASS	.						101	97	99					12																	27950775		2203	4300	6503	SO:0001819	synonymous_variant	57542	exon3			GGGGGGGTGTCTC	AB037761	CCDS31763.1	12p11.22	2013-04-24	2013-02-22	2013-01-30	ENSG00000087448	ENSG00000087448		"Kelch-like"	29252	protein-coding gene	gene with protein product			"kelch domain containing 5"	KLHDC5		19261606	Standard	NM_020782		Approved	KIAA1340, Ctb9	uc001rij.3	Q9P2K6	OTTHUMG00000169217	ENST00000381271.2:c.1194G>A	12.37:g.27950775G>A		60	0	0		52	17	0.326923	NM_020782	Q2VPK1|Q8N334	Silent	SNP	ENST00000381271.2	37	CCDS31763.1																																																																																			.	.	none		0.597	KLHL42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402904.1	NM_020782		A	27950775	G	A	27950775	2	1	29	1	0	0	0	0	0	0	0	1	8368	1248	44	2		2	KLHDC5	12	27950775	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2587998	27950775	105901120	591	12832											
CAPRIN2	65981	hgsc.bcm.edu	37	chr12	30881884	30881884	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctgaactggccacagctttgGtgtctcctgtttcttttgtt	4	18	9	10	0	2	1	0	1	2	0	3	1	2	1	2	2	2	3	2	2	1	5	rs374198235		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:30881884G>A	ENST00000395805.2	-	8	2027	c.1480C>T	c.(1480-1482)Cca>Tca	p.P494S	CAPRIN2_ENST00000298892.5_Missense_Mutation_p.P494S|CAPRIN2_ENST00000417045.1_Missense_Mutation_p.P494S|CAPRIN2_ENST00000538387.1_5'UTR|CAPRIN2_ENST00000308433.5_Missense_Mutation_p.P161S|CAPRIN2_ENST00000251071.5_Missense_Mutation_p.P494S	NM_001206856.1	NP_001193785.1			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)					CACAGCTTTGGTGTCTCCTGT	0.468																																					p.P494S		Atlas-SNP	.											.	CAPRIN2	109	.	0			c.C1480T						PASS	.						169	152	158					12																	30881884		2203	4300	6503	SO:0001583	missense	65981	exon8			GCTTTGGTGTCTC	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	ENST00000395805.2:c.1480C>T	12.37:g.30881884G>A	ENSP00000379150:p.Pro494Ser	161	0	0		155	92	0.593548	NM_023925		Missense_Mutation	SNP	ENST00000395805.2	37	CCDS55816.1	.	.	.	.	.	.	.	.	.	.	G	12.49	1.952458	0.34471	.	.	ENSG00000110888	ENST00000433722;ENST00000298892;ENST00000395805;ENST00000251071;ENST00000308433;ENST00000417045;ENST00000438006;ENST00000537108	T;T;T;T;T;T;T	0.74315	2.51;-0.56;2.92;-0.54;-0.83;2.91;2.53	4.99	4.1	0.47936	.	0.266533	0.37219	N	0.002181	T	0.57066	0.2028	N	0.08118	0	0.33516	D	0.591802	B;P;B;B;B;B;B	0.39216	0.063;0.664;0.335;0.328;0.022;0.005;0.022	B;B;B;B;B;B;B	0.43018	0.013;0.405;0.058;0.085;0.005;0.008;0.005	T	0.66626	-0.5876	10	0.39692	T	0.17	-1.1961	8.8373	0.35119	0.2304:0.0:0.7696:0.0	.	494;220;494;494;494;494;494	Q6IMN6-6;E9PAU5;Q149P6;Q6IMN6-3;Q6IMN6;Q6IMN6-2;E4NKG2	.;.;.;.;CAPR2_HUMAN;.;.	S	240;494;494;494;161;494;220;413	ENSP00000415407:P240S;ENSP00000298892:P494S;ENSP00000379150:P494S;ENSP00000251071:P494S;ENSP00000309785:P161S;ENSP00000391479:P494S;ENSP00000438010:P413S	ENSP00000251071:P494S	P	-	1	0	CAPRIN2	30773151	0.278000	0.24230	1.000000	0.80357	0.979000	0.70002	0.934000	0.28910	1.225000	0.43566	0.561000	0.74099	CCA	.	.	alt		0.468	CAPRIN2-004	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403322.2	NM_023925		A	30881884	G	A	30881884	3	1	29	1	0	0	0	0	1	0	0	0	2638	1261	44	2	1947	2	CAPRIN2	12	30881884	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2931109	30881884	102970011	592	12833											
BICD1	636	hgsc.bcm.edu	37	chr12	32481369	32481369	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gcagcggctcgggagctagcCcccatgattgataaagacaa	12	6	12	11	2	0	3	0	2	0	1	1	4	0	4	2	2	3	3	2	2	4	3	rs34447944	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:32481369C>T	ENST00000281474.5	+	5	2083	c.1980C>T	c.(1978-1980)gcC>gcT	p.A660A	BICD1_ENST00000548411.1_Silent_p.A660A	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	660					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)			GGGAGCTAGCCCCCATGATTG	0.527													C|||	232	0.0463259	0.0023	0.0389	5008	,	,		15395	0.0079		0.0865	False		,,,				2504	0.1094				p.A660A		Atlas-SNP	.											BICD1,colon,carcinoma,0,1	BICD1	89	1	0			c.C1980T						PASS	.	C	,	67,4339	62.9+/-100.1	0,67,2136	66	70	69		1980,1980	0.8	1	12	dbSNP_126	69	743,7857	176.2+/-226.1	30,683,3587	no	coding-synonymous,coding-synonymous	BICD1	NM_001003398.1,NM_001714.2	,	30,750,5723	TT,TC,CC		8.6395,1.5207,6.2279	,	660/836,660/976	32481369	810,12196	2203	4300	6503	SO:0001819	synonymous_variant	636	exon5			GCTAGCCCCCATG	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.1980C>T	12.37:g.32481369C>T		110	0	0		93	32	0.344086	NM_001714	A8K2C3|F8W113|O43892|O43893	Silent	SNP	ENST00000281474.5	37	CCDS8726.1																																																																																			C|0.940;T|0.060	0.060	strong		0.527	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714		T	32481369	C	T	32481369	2	4	29	1	0	0	0	0	0	0	0	1	1428	610	22	2		2	BICD1	12	32481369	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1599485	32481369	101370526	593	12834											
C12orf40	283461	hgsc.bcm.edu	37	chr12	40041723	40041723	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcaaaactaaatttcacaTctggaatagcacctactcct	14	13	3	11	0	3	0	2	0	1	0	4	1	4	1	2	1	3	1	2	1	7	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:40041723T>A	ENST00000324616.5	+	6	668	c.514T>A	c.(514-516)Tct>Act	p.S172T	C12orf40_ENST00000405531.3_Missense_Mutation_p.S172T|C12orf40_ENST00000398716.1_Missense_Mutation_p.S95T	NM_001031748.2	NP_001026918.2	Q86WS4	CL040_HUMAN	chromosome 12 open reading frame 40	172										breast(4)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(6)|prostate(1)|skin(2)	38						AAATTTCACATCTGGAATAGC	0.338																																					p.S172T		Atlas-SNP	.											C12orf40,NS,carcinoma,-1,1	C12orf40	118	1	0			c.T514A						scavenged	.						83	79	80					12																	40041723		1825	4077	5902	SO:0001583	missense	283461	exon6			TTCACATCTGGAA	AK097445	CCDS41770.1	12q12	2008-08-04			ENSG00000180116	ENSG00000180116			26846	protein-coding gene	gene with protein product						12477932	Standard	XM_005268806		Approved	FLJ40126	uc001rmc.3	Q86WS4	OTTHUMG00000133567	ENST00000324616.5:c.514T>A	12.37:g.40041723T>A	ENSP00000317671:p.Ser172Thr	118	1	0.00847458		103	56	0.543689	NM_001031748	B7WNU1|Q8IXY6|Q8N818|V9HW02	Missense_Mutation	SNP	ENST00000324616.5	37	CCDS41770.1	.	.	.	.	.	.	.	.	.	.	T	2.128	-0.399903	0.04865	.	.	ENSG00000180116	ENST00000405531;ENST00000398716;ENST00000324616	T;T	0.43688	0.94;0.95	3.74	1.92	0.25849	.	0.567024	0.14880	N	0.293000	T	0.20981	0.0505	N	0.08118	0	0.09310	N	1	B	0.13145	0.007	B	0.10450	0.005	T	0.17018	-1.0383	10	0.62326	D	0.03	.	6.0078	0.19557	0.0:0.7653:0.0:0.2347	.	172	Q86WS4	CL040_HUMAN	T	172;95;172	ENSP00000383897:S172T;ENSP00000317671:S172T	ENSP00000317671:S172T	S	+	1	0	C12orf40	38327990	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	0.012000	0.13287	0.565000	0.29255	-0.251000	0.11542	TCT	.	.	none		0.338	C12orf40-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257664.2	NM_173599		A	40041723	T	A	40041723	3	1	29	1	0	0	0	0	1	0	0	0	1688	1435	50	5	536	5	C12orf40	12	40041723	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	7560354	40041723	93810172	594	12835											
SFRS2IP	9169	hgsc.bcm.edu	37	chr12	46320944	46320944	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccttttttggggactgagaaCgggattttttccggcctctg	5	15	12	9	2	1	1	0	1	1	1	2	4	2	3	3	4	1	0	3	4	1	6	rs28930670	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:46320944C>T	ENST00000369367.3	-	11	2773	c.2540G>A	c.(2539-2541)cGt>cAt	p.R847H	SCAF11_ENST00000549162.1_Missense_Mutation_p.R655H|SCAF11_ENST00000550629.1_5'Flank|SCAF11_ENST00000419565.2_Missense_Mutation_p.R847H|SCAF11_ENST00000465950.1_Missense_Mutation_p.R532H	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	847	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						GGACTGAGAACGGGATTTTTT	0.468													C|||	38	0.00758786	0.0	0.0159	5008	,	,		16776	0.0		0.0249	False		,,,				2504	0.002				p.R847H		Atlas-SNP	.											.	SCAF11	145	.	0			c.G2540A						PASS	.	C	HIS/ARG	31,4375	36.8+/-68.6	0,31,2172	122	121	122		2540	5	1	12	dbSNP_125	122	316,8284	113.1+/-173.2	8,300,3992	yes	missense	SCAF11	NM_004719.2	29	8,331,6164	TT,TC,CC		3.6744,0.7036,2.668	benign	847/1464	46320944	347,12659	2203	4300	6503	SO:0001583	missense	9169	exon11			TGAGAACGGGATT	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.2540G>A	12.37:g.46320944C>T	ENSP00000358374:p.Arg847His	155	0	0		147	72	0.489796	NM_004719	A6NEU9|A6NLW5|Q8IW59	Missense_Mutation	SNP	ENST00000369367.3	37	CCDS8748.2	25	0.011446886446886446	0	0.0	9	0.024861878453038673	0	0.0	16	0.021108179419525065	C	13.16	2.153957	0.38021	0.007036	0.036744	ENSG00000139218	ENST00000465950;ENST00000369367;ENST00000549162;ENST00000419565;ENST00000547018	T;T;T;T;T	0.49720	1.41;2.13;1.41;2.13;0.77	5.93	5.04	0.67666	.	0.190692	0.36374	N	0.002635	T	0.10208	0.0250	L	0.48362	1.52	0.25928	N	0.983024	P;B	0.41947	0.766;0.14	B;B	0.33121	0.158;0.015	T	0.17837	-1.0356	10	0.48119	T	0.1	-9.1648	8.541	0.33393	0.2631:0.6671:0.0:0.0698	rs28930670	655;847	F8VXG7;Q99590	.;SCAFB_HUMAN	H	532;847;655;847;787	ENSP00000449812:R532H;ENSP00000358374:R847H;ENSP00000448864:R655H;ENSP00000413036:R847H;ENSP00000446746:R787H	ENSP00000358374:R847H	R	-	2	0	SCAF11	44607211	0.379000	0.25123	0.997000	0.53966	0.912000	0.54170	0.485000	0.22324	1.518000	0.48934	0.655000	0.94253	CGT	C|0.978;T|0.022	0.022	strong		0.468	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719		T	46320944	C	T	46320944	3	4	29	1	0	0	0	0	1	0	0	0	14192	536	19	1	1871	1	SFRS2IP	12	46320944	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	6279221	46320944	87530951	595	12836											
RAPGEF3	10411	hgsc.bcm.edu	37	chr12	48143315	48143315	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcatgcagggtggtcaccAgcccctgcagccaggcctca	7	6	11	17	0	3	0	3	0	0	0	3	0	3	0	6	3	4	2	6	3	0	0	rs145878042	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:48143315A>G	ENST00000449771.2	-	10	987	c.899T>C	c.(898-900)cTg>cCg	p.L300P	RAPGEF3_ENST00000549151.1_Missense_Mutation_p.L258P|RAPGEF3_ENST00000389212.3_Missense_Mutation_p.L300P|RAPGEF3_ENST00000171000.4_Missense_Mutation_p.L258P|RAPGEF3_ENST00000405493.2_Missense_Mutation_p.L258P|RAPGEF3_ENST00000395358.3_Missense_Mutation_p.L300P|RAPGEF3_ENST00000548919.1_Missense_Mutation_p.L258P			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	300					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)		GGTGGTCACCAGCCCCTGCAG	0.637													A|||	9	0.00179712	0.0	0.0029	5008	,	,		8210	0.0		0.007	False		,,,				2504	0.0				p.L300P		Atlas-SNP	.											.	RAPGEF3	98	.	0			c.T899C						PASS	.	A	PRO/LEU,PRO/LEU,PRO/LEU	5,4401	9.9+/-24.2	0,5,2198	50	44	46		899,773,773	4.3	1	12	dbSNP_134	46	105,8495	56.4+/-117.6	2,101,4197	yes	missense,missense,missense	RAPGEF3	NM_001098531.2,NM_001098532.2,NM_006105.5	98,98,98	2,106,6395	GG,GA,AA		1.2209,0.1135,0.8458	probably-damaging,probably-damaging,probably-damaging	300/924,258/882,258/882	48143315	110,12896	2203	4300	6503	SO:0001583	missense	10411	exon10			GTCACCAGCCCCT	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.899T>C	12.37:g.48143315A>G	ENSP00000395708:p.Leu300Pro	20	0	0		14	5	0.357143	NM_001098531	A8K2G5|E7EQC8|O95634|Q8WVN0	Missense_Mutation	SNP	ENST00000449771.2	37	CCDS41775.1	10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	A	21.4	4.141017	0.77775	0.001135	0.012209	ENSG00000079337	ENST00000405493;ENST00000449771;ENST00000549151;ENST00000171000;ENST00000389211;ENST00000389212;ENST00000397089;ENST00000548919;ENST00000395358	D;D;D;D;D;D;D	0.92446	-3.04;-3.04;-3.04;-3.04;-3.04;-3.04;-3.04	4.28	4.28	0.50868	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.094510	0.45126	D	0.000383	D	0.89705	0.6792	N	0.21508	0.67	0.80722	D	1	B;D;D	0.76494	0.382;0.999;0.999	P;D;D	0.74674	0.448;0.962;0.984	D	0.91472	0.5197	10	0.87932	D	0	.	12.7023	0.57041	1.0:0.0:0.0:0.0	.	312;300;300	B7Z5J6;O95398-2;O95398	.;.;RPGF3_HUMAN	P	258;300;258;258;258;300;312;258;300	ENSP00000384521:L258P;ENSP00000395708:L300P;ENSP00000448619:L258P;ENSP00000171000:L258P;ENSP00000373864:L300P;ENSP00000448480:L258P;ENSP00000378764:L300P	ENSP00000171000:L258P	L	-	2	0	RAPGEF3	46429582	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.635000	0.91006	1.941000	0.56285	0.528000	0.53228	CTG	A|0.993;G|0.007	0.007	strong		0.637	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257848.1	NM_006105		G	48143315	A	G	48143315	3	3	29	1	0	0	0	0	1	0	0	0	13060	188	7	3	1948	3	RAPGEF3	12	48143315	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	1822371	48143315	85708580	596	12837											
COL2A1	1280	hgsc.bcm.edu	37	chr12	48381394	48381394	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caaagagaagctgcacttacGgaggcaccagcaggcccagg	13	3	13	12	1	0	1	0	0	0	1	0	3	0	2	2	4	4	4	2	4	3	1	rs150865922	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:48381394G>A	ENST00000380518.3	-	19	1385	c.1221C>T	c.(1219-1221)tcC>tcT	p.S407S	COL2A1_ENST00000337299.6_Splice_Site_p.S338S|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	407	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)	CTGCACTTACGGAGGCACCAG	0.617													G|||	12	0.00239617	0.0	0.0029	5008	,	,		18272	0.0		0.0089	False		,,,				2504	0.001				p.S407S		Atlas-SNP	.											.	COL2A1	368	.	0			c.C1221T						PASS	.	G	,	2,4404	4.2+/-10.8	0,2,2201	53	47	49		1221,1014	0.4	1	12	dbSNP_134	49	50,8548	29.6+/-80.5	0,50,4249	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	COL2A1	NM_001844.4,NM_033150.2	,	0,52,6450	AA,AG,GG		0.5815,0.0454,0.3999	,	407/1488,338/1419	48381394	52,12952	2203	4299	6502	SO:0001630	splice_region_variant	1280	exon19			ACTTACGGAGGCA	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.1221+1C>T	12.37:g.48381394G>A		30	0	0		28	12	0.428571	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	37	CCDS41778.1																																																																																			G|0.997;A|0.003	0.003	strong		0.617	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844	Silent	A	48381394	G	A	48381394	5	1	29	1	0	0	0	0	0	0	1	0	3689	1130	39	1	3386	1	COL2A1	12	48381394	Splice_Site	SNP	G	TCGA-GR-7351-01A-11D-2210-10	238079	48381394	85470501	597	12838											
DDX23	9416	hgsc.bcm.edu	37	chr12	49229991	49229991	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgccagtctcagccacaccaAtgatgtcacgattctgtagc	10	10	8	13	1	3	1	2	1	2	0	4	2	3	1	3	0	3	1	3	0	2	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:49229991A>G	ENST00000308025.3	-	11	1374	c.1295T>C	c.(1294-1296)aTt>aCt	p.I432T	DDX23_ENST00000553182.1_5'Flank	NM_004818.2	NP_004809.2	Q9BUQ8	DDX23_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 23	432	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						AGCCACACCAATGATGTCACG	0.512																																					p.I432T		Atlas-SNP	.											.	DDX23	82	.	0			c.T1295C						PASS	.						198	183	188					12																	49229991		2203	4300	6503	SO:0001583	missense	9416	exon11			ACACCAATGATGT	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.1295T>C	12.37:g.49229991A>G	ENSP00000310723:p.Ile432Thr	158	0	0		135	34	0.251852	NM_004818	B2R600|B4DH15|O43188	Missense_Mutation	SNP	ENST00000308025.3	37	CCDS8770.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.708132	0.89018	.	.	ENSG00000174243	ENST00000308025	T	0.16743	2.32	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	0.44664	0.1304	M	0.82056	2.57	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.48258	-0.9051	10	0.87932	D	0	-6.0539	14.5545	0.68091	1.0:0.0:0.0:0.0	.	432	Q9BUQ8	DDX23_HUMAN	T	432	ENSP00000310723:I432T	ENSP00000310723:I432T	I	-	2	0	DDX23	47516258	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.182000	0.94881	2.079000	0.62486	0.459000	0.35465	ATT	.	.	none		0.512	DDX23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408897.2	NM_004818		G	49229991	A	G	49229991	3	3	29	1	0	0	0	0	1	0	0	0	4352	101	4	3	1195	3	DDX23	12	49229991	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	848597	49229991	84621904	598	12839											
DDN	23109	hgsc.bcm.edu	37	chr12	49391394	49391395	+	Frame_Shift_Ins	INS	-	-	C																															ctccagggtctccggtcctgINSccccctctccaagacccaga																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:49391394_49391395insC	ENST00000421952.2	-	2	1285_1286	c.1264_1265insG	c.(1264-1266)gcafs	p.A422fs	RP11-386G11.5_ENST00000547395.1_RNA|RP11-386G11.5_ENST00000547866.1_RNA|RP11-386G11.5_ENST00000552284.1_RNA|RP11-386G11.5_ENST00000552933.1_RNA|RP11-386G11.3_ENST00000549516.1_RNA	NM_015086.1	NP_055901.2	O94850	DEND_HUMAN	dendrin	422	Interaction with ACTN1.|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						CTCCGGTCCTGCCCCCTCTCCA	0.663																																					p.A422fs		Pindel,Atlas-Indel	.											.	DDN	54	.	0			c.1265_1266insG						PASS	.																																			SO:0001589	frameshift_variant	23109	exon2			.	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.1265dupG	12.37:g.49391399_49391399dupC	ENSP00000390590:p.Ala422fs	41	0	.		52	11	0.212	NM_015086		Frame_Shift_Ins	INS	ENST00000421952.2	37	CCDS31791.2																																																																																			.	.	none		0.663	DDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343335.1			C	49391395	-	C	49391394	7	5	29	1	0	1	1	0	0	0	0	0	4335	1319	46	0	874	0	DDN	12	49391394	Frame_Shift_Ins	INS	-	TCGA-GR-7351-01A-11D-2210-10	161403	49391394	84460501	599	12840											
KRT7	3855	hgsc.bcm.edu	37	chr12	52636919	52636919	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agatcgacaacatcaagaacCaggtgggacaagtcctcctg	14	6	10	11	1	1	2	1	0	0	2	4	4	3	3	3	2	2	0	3	2	4	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:52636919C>T	ENST00000331817.5	+	6	1165	c.982C>T	c.(982-984)Cag>Tag	p.Q328*	RP3-416H24.1_ENST00000546686.1_RNA	NM_005556.3	NP_005547.3	P08729	K2C7_HUMAN	keratin 7	328	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)	CATCAAGAACCAGGTGGGACA	0.587																																					p.Q328X		Atlas-SNP	.											.	KRT7	48	.	0			c.C982T						PASS	.						75	63	67					12																	52636919		2203	4300	6503	SO:0001587	stop_gained	3855	exon6			AAGAACCAGGTGG		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.982C>T	12.37:g.52636919C>T	ENSP00000329243:p.Gln328*	37	0	0		40	8	0.2	NM_005556	Q92676|Q9BUD8|Q9Y3R7	Nonsense_Mutation	SNP	ENST00000331817.5	37	CCDS8822.1	.	.	.	.	.	.	.	.	.	.	C	37	6.293061	0.97449	.	.	ENSG00000135480	ENST00000331817;ENST00000422319;ENST00000551537	.	.	.	3.84	3.84	0.44239	.	0.000000	0.35805	N	0.002977	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	16.3259	0.82979	0.0:1.0:0.0:0.0	.	.	.	.	X	328;304;328	.	ENSP00000329243:Q328X	Q	+	1	0	KRT7	50923186	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.609000	0.82925	2.160000	0.67779	0.561000	0.74099	CAG	.	.	none		0.587	KRT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404897.1	NM_005556		T	52636919	C	T	52636919	4	4	29	1	0	0	0	0	0	1	0	0	8492	595	21	2	1004	2	KRT7	12	52636919	Nonsense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	3245525	52636919	81214976	600	12841											
OR6C76	390326	hgsc.bcm.edu	37	chr12	55820685	55820685	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttagtaattctctcctatacTtacatcatcagaactattct	12	17	2	10	0	4	1	2	0	2	1	6	1	5	1	1	0	3	1	1	0	7	8			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:55820685T>G	ENST00000328314.3	+	1	648	c.648T>G	c.(646-648)acT>acG	p.T216T		NM_001005183.1	NP_001005183.1	A6NM76	O6C76_HUMAN	olfactory receptor, family 6, subfamily C, member 76	216						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)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						TCTCCTATACTTACATCATCA	0.368																																					p.T216T		Atlas-SNP	.											.	OR6C76	98	.	0			c.T648G						PASS	.						99	91	93					12																	55820685		2203	4300	6503	SO:0001819	synonymous_variant	390326	exon1			CTATACTTACATC		CCDS31823.1	12q13.2	2013-09-23			ENSG00000185821	ENSG00000185821		"GPCR / Class A : Olfactory receptors"	31305	protein-coding gene	gene with protein product							Standard	NM_001005183		Approved		uc010spm.2	A6NM76	OTTHUMG00000169956	ENST00000328314.3:c.648T>G	12.37:g.55820685T>G		116	0	0		154	50	0.324675	NM_001005183		Silent	SNP	ENST00000328314.3	37	CCDS31823.1																																																																																			.	.	none		0.368	OR6C76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406675.1	NM_001005183		G	55820685	T	G	55820685	2	3	29	1	0	0	0	0	0	0	0	1	11209	1596	56	5		5	OR6C76	12	55820685	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	3183766	55820685	78031210	601	12842											
LRP1	4035	hgsc.bcm.edu	37	chr12	57603636	57603636	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acgtggtcctttaccatcagCacaagcagcccgaaggtggg	10	7	12	12	2	1	0	1	0	0	0	2	1	2	0	3	3	4	2	3	3	3	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:57603636C>T	ENST00000243077.3	+	80	12890	c.12424C>T	c.(12424-12426)Cac>Tac	p.H4142Y		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	4142					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)	TTACCATCAGCACAAGCAGCC	0.607																																					p.H4142Y		Atlas-SNP	.											.	LRP1	428	.	0			c.C12424T						PASS	.						45	46	46					12																	57603636		2203	4300	6503	SO:0001583	missense	4035	exon80			CATCAGCACAAGC	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.12424C>T	12.37:g.57603636C>T	ENSP00000243077:p.His4142Tyr	47	0	0		49	18	0.367347	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	C	5.539	0.284349	0.10513	.	.	ENSG00000123384	ENST00000243077	T	0.24723	1.84	4.45	4.45	0.53987	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.078423	0.52532	D	0.000071	T	0.05410	0.0143	N	0.00483	-1.445	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35798	-0.9774	10	0.02654	T	1	.	6.8782	0.24158	0.0:0.8089:0.0:0.1911	.	4142	Q07954	LRP1_HUMAN	Y	4142	ENSP00000243077:H4142Y	ENSP00000243077:H4142Y	H	+	1	0	LRP1	55889903	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	3.699000	0.54778	2.486000	0.83907	0.557000	0.71058	CAC	.	.	none		0.607	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332		T	57603636	C	T	57603636	3	4	29	1	0	0	0	0	1	0	0	0	8960	710	25	2	12742	2	LRP1	12	57603636	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1782951	57603636	76248259	602	12843											
B4GALNT1	2583	hgsc.bcm.edu	37	chr12	58022555	58022555	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	actaacgcgctctggcttgtCgctgtcgtcagcgatgacca	7	10	11	13	5	2	1	1	1	1	0	4	2	2	1	1	1	2	3	1	1	1	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:58022555C>T	ENST00000341156.4	-	8	1527	c.943G>A	c.(943-945)Gac>Aac	p.D315N	B4GALNT1_ENST00000550943.1_5'Flank|B4GALNT1_ENST00000449184.3_Missense_Mutation_p.D282N|B4GALNT1_ENST00000418555.2_Missense_Mutation_p.D260N	NM_001478.3	NP_001469.1	Q00973	B4GN1_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 1	315					carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|ganglioside biosynthetic process (GO:0001574)|glycosphingolipid metabolic process (GO:0006687)|lipid glycosylation (GO:0030259)|lipid storage (GO:0019915)|protein glycosylation (GO:0006486)|spermatogenesis (GO:0007283)	integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|plasma membrane (GO:0005886)	(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase activity (GO:0003947)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|urinary_tract(1)	20	Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.109)			TCTGGCTTGTCGCTGTCGTCA	0.597																																					p.T315T		Atlas-SNP	.											.	B4GALNT1	53	.	0			c.A943A						PASS	.						81	66	71					12																	58022555		2203	4300	6503	SO:0001583	missense	2583	exon8			GCTTGTCGCTGTC	M83651	CCDS8950.1, CCDS61170.1, CCDS61171.1	12q13.3	2013-09-11	2006-01-08	2006-01-08	ENSG00000135454	ENSG00000135454	2.4.1.92	"Beta 4-glycosyltransferases", "Glycosyltransferase family 2 domain containing"	4117	protein-coding gene	gene with protein product	"GD2 synthase, GM2 synthase"	601873	"UDP-N-acetyl-alpha-D-galactosamine:(N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase (GalNAc-T)", "UDP-Gal:betaGlcNAc beta-1,4-N-acetylgalactosaminyltransferase transferase 1", "spastic paraplegia 26"	GALGT, SPG26		1601877, 23746551	Standard	NM_001478		Approved	beta1-4GalNAc-T	uc001spg.2	Q00973	OTTHUMG00000170190	ENST00000341156.4:c.943G>A	12.37:g.58022555C>T	ENSP00000341562:p.Asp315Asn	91	0	0		69	26	0.376812	NM_001478	B4DE26|Q8N636	Silent	SNP	ENST00000341156.4	37	CCDS8950.1	.	.	.	.	.	.	.	.	.	.	.	18.01	3.527774	0.64860	.	.	ENSG00000135454	ENST00000341156;ENST00000418555	T;T	0.61392	0.11;0.11	4.89	4.89	0.63831	Glycosyl transferase, family 2 (1);	0.175267	0.49916	D	0.000137	T	0.38401	0.1039	N	0.20685	0.6	0.80722	D	1	P;P;P	0.42961	0.683;0.545;0.795	B;B;B	0.34452	0.115;0.055;0.183	T	0.34750	-0.9816	10	0.37606	T	0.19	-4.0522	13.3333	0.60503	0.0:0.8402:0.1598:0.0	.	282;260;315	B4DSP5;B4DE26;Q00973	.;.;B4GN1_HUMAN	N	315;260	ENSP00000341562:D315N;ENSP00000401601:D260N	ENSP00000341562:D315N	D	-	1	0	B4GALNT1	56308822	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	3.646000	0.54396	2.559000	0.86315	0.655000	0.94253	GAC	.	.	none		0.597	B4GALNT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407853.1	NM_001478		T	58022555	C	T	58022555	3	4	29	1	0	0	0	0	1	0	0	0	1266	884	31	1	674	1	B4GALNT1	12	58022555	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	418919	58022555	75829340	603	12844											
AVIL	10677	hgsc.bcm.edu	37	chr12	58204648	58204648	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccattccattggatgatgActttcccaaggtccagcaag	10	10	10	11	0	0	2	0	2	0	0	3	3	3	3	4	3	1	1	4	3	2	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:58204648A>G	ENST00000257861.3	-	5	939	c.509T>C	c.(508-510)gTc>gCc	p.V170A	AVIL_ENST00000537081.1_Missense_Mutation_p.V163A	NM_006576.3	NP_006567.3	O75366	AVIL_HUMAN	advillin	170	Core. {ECO:0000250}.				actin filament capping (GO:0051693)|cilium morphogenesis (GO:0060271)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|positive regulation of neuron projection development (GO:0010976)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)	actin binding (GO:0003779)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(9)|ovary(1)|prostate(6)	32	Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)					TTGGATGATGACTTTCCCAAG	0.488																																					p.V170A		Atlas-SNP	.											.	AVIL	60	.	0			c.T509C						PASS	.						152	150	151					12																	58204648		2203	4300	6503	SO:0001583	missense	10677	exon5			ATGATGACTTTCC	AF041449	CCDS8959.1	12q13.11	2006-03-30				ENSG00000135407			14188	protein-coding gene	gene with protein product		613397				9664034, 12034507	Standard	NM_006576		Approved	p92, FLJ12386, ADVIL, DOC6	uc001sqj.2	O75366	OTTHUMG00000170461	ENST00000257861.3:c.509T>C	12.37:g.58204648A>G	ENSP00000257861:p.Val170Ala	91	0	0		132	6	0.0454545	NM_006576	B2RAU7|Q2NKM9	Missense_Mutation	SNP	ENST00000257861.3	37	CCDS8959.1	.	.	.	.	.	.	.	.	.	.	A	8.559	0.877295	0.17395	.	.	ENSG00000135407	ENST00000537081;ENST00000257861	T;T	0.52983	0.64;0.64	5.35	3.02	0.34903	Gelsolin domain (1);	0.304736	0.36066	N	0.002805	T	0.29684	0.0741	L	0.34521	1.04	0.28434	N	0.917138	B;B	0.02656	0.0;0.0	B;B	0.12156	0.007;0.005	T	0.24404	-1.0161	10	0.08381	T	0.77	-20.9205	7.3653	0.26770	0.7523:0.0:0.2477:0.0	.	163;170	O75366-2;O75366	.;AVIL_HUMAN	A	163;170	ENSP00000443207:V163A;ENSP00000257861:V170A	ENSP00000257861:V170A	V	-	2	0	AVIL	56490915	0.024000	0.19004	1.000000	0.80357	0.953000	0.61014	0.322000	0.19576	0.490000	0.27771	0.533000	0.62120	GTC	.	.	none		0.488	AVIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409276.1	NM_006576		G	58204648	A	G	58204648	3	3	29	1	0	0	0	0	1	0	0	0	1227	275	10	3	2010	3	AVIL	12	58204648	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	182093	58204648	75647247	604	12845											
LEMD3	23592	hgsc.bcm.edu	37	chr12	65563416	65563416	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cggcgcctcagcagctctcgGatgaggagcttttctctcag	6	10	12	13	3	4	1	2	1	2	0	6	3	4	3	1	3	3	3	1	3	0	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:65563416G>A	ENST00000308330.2	+	1	66	c.40G>A	c.(40-42)Gat>Aat	p.D14N	LEMD3_ENST00000541171.1_3'UTR	NM_001167614.1|NM_014319.4	NP_001161086.1|NP_055134.2	Q9Y2U8	MAN1_HUMAN	LEM domain containing 3	14	LEM. {ECO:0000255|PROSITE- ProRule:PRU00313}.				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)		GCAGCTCTCGGATGAGGAGCT	0.627																																					p.D14N		Atlas-SNP	.											.	LEMD3	68	.	0			c.G40A						PASS	.						11	10	10					12																	65563416		2180	4271	6451	SO:0001583	missense	23592	exon1			CTCTCGGATGAGG	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.40G>A	12.37:g.65563416G>A	ENSP00000308369:p.Asp14Asn	66	0	0		63	9	0.142857	NM_001167614	Q9NT47|Q9NYA5	Missense_Mutation	SNP	ENST00000308330.2	37	CCDS8972.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.823509	0.90873	.	.	ENSG00000174106	ENST00000308330	T	0.61274	0.12	3.98	3.98	0.46160	LEM-like domain (2);Lamino-associated polypeptide 2/emerin (3);	0.000000	0.85682	D	0.000000	T	0.59500	0.2198	N	0.20401	0.57	0.52501	D	0.999955	D;D	0.63046	0.992;0.992	D;D	0.64776	0.929;0.929	T	0.58132	-0.7690	9	.	.	.	-14.3277	16.0229	0.80512	0.0:0.0:1.0:0.0	.	14;14	B4E2K7;Q9Y2U8	.;MAN1_HUMAN	N	14	ENSP00000308369:D14N	.	D	+	1	0	LEMD3	63849683	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	8.246000	0.89828	2.501000	0.84356	0.462000	0.41574	GAT	.	.	none		0.627	LEMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401312.2			A	65563416	G	A	65563416	3	1	29	1	0	0	0	0	1	0	0	0	8730	1174	41	2	42	2	LEMD3	12	65563416	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	7358768	65563416	68288479	605	12846											
CAND1	55832	hgsc.bcm.edu	37	chr12	67699536	67699536	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	attgatgcagttctagatgaGctcccacctcttatcagcga	10	12	8	11	1	3	3	1	2	2	1	4	4	4	3	2	0	3	3	2	0	2	4	rs17781675	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:67699536G>A	ENST00000545606.1	+	10	2525	c.2088G>A	c.(2086-2088)gaG>gaA	p.E696E		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	696					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)		TTCTAGATGAGCTCCCACCTC	0.408													G|||	137	0.0273562	0.0159	0.0605	5008	,	,		21008	0.0		0.0586	False		,,,				2504	0.0153				p.E696E		Atlas-SNP	.											.	CAND1	100	.	0			c.G2088A						PASS	.	G		91,4315	76.2+/-114.5	2,87,2114	109	105	106		2088	5.8	1	12	dbSNP_123	106	487,8113	141.7+/-198.0	9,469,3822	no	coding-synonymous	CAND1	NM_018448.3		11,556,5936	AA,AG,GG		5.6628,2.0654,4.4441		696/1231	67699536	578,12428	2203	4300	6503	SO:0001819	synonymous_variant	55832	exon10			AGATGAGCTCCCA		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.2088G>A	12.37:g.67699536G>A		58	0	0		56	22	0.392857	NM_018448	B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Silent	SNP	ENST00000545606.1	37	CCDS8977.1																																																																																			G|0.959;A|0.041	0.041	strong		0.408	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448		A	67699536	G	A	67699536	2	1	29	1	0	0	0	0	0	0	0	1	2617	962	34	2		2	CAND1	12	67699536	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2136120	67699536	66152359	606	12847											
RAB21	23011	hgsc.bcm.edu	37	chr12	72148943	72148943	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gcggcggcggcggcggggcgGcggcggcgggccgagcctac	2	1	24	14	10	0	0	0	0	0	0	0	1	0	0	2	10	2	0	2	10	1	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:72148943G>A	ENST00000261263.3	+	1	290	c.34G>A	c.(34-36)Gcg>Acg	p.A12T		NM_014999.2	NP_055814.1	Q9UL25	RAB21_HUMAN	RAB21, member RAS oncogene family	12					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						cggcggggcggcggcggcggG	0.741																																					p.A12T		Atlas-SNP	.											.	RAB21	17	.	0			c.G34A						PASS	.						8	6	7					12																	72148943		1935	3805	5740	SO:0001583	missense	23011	exon1			GGGGCGGCGGCGG	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.34G>A	12.37:g.72148943G>A	ENSP00000261263:p.Ala12Thr	0	0	.		11	9	0.818182	NM_014999	Q14466|Q569H3	Missense_Mutation	SNP	ENST00000261263.3	37	CCDS9003.1	.	.	.	.	.	.	.	.	.	.	G	8.412	0.844345	0.16963	.	.	ENSG00000080371	ENST00000261263	T	0.67865	-0.29	3.75	3.75	0.43078	.	0.068284	0.64402	D	0.000019	T	0.64681	0.2620	L	0.28504	0.86	0.46654	D	0.999142	D	0.57571	0.98	P	0.57009	0.811	T	0.59026	-0.7531	10	0.15952	T	0.53	-8.1075	13.8606	0.63557	0.0:0.0:1.0:0.0	.	12	Q9UL25	RAB21_HUMAN	T	12	ENSP00000261263:A12T	ENSP00000261263:A12T	A	+	1	0	RAB21	70435210	1.000000	0.71417	0.997000	0.53966	0.253000	0.25986	4.732000	0.62029	2.072000	0.62099	0.557000	0.71058	GCG	.	.	none		0.741	RAB21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404855.1			A	72148943	G	A	72148943	3	1	29	1	0	0	0	0	1	0	0	0	12923	1203	42	2	36	2	RAB21	12	72148943	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	4449407	72148943	61702952	607	12848											
C12orf26	84190	hgsc.bcm.edu	37	chr12	82780676	82780676	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcgaaatactattctgtacaAaacttgggaatatgtactcc	14	12	7	8	1	1	0	0	0	1	0	2	2	2	1	1	1	4	2	1	1	9	7	rs56337649	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:82780676A>G	ENST00000248306.3	+	2	423	c.354A>G	c.(352-354)caA>caG	p.Q118Q	METTL25_ENST00000547357.1_3'UTR	NM_032230.2	NP_115606.2	Q8N6Q8	MET25_HUMAN	methyltransferase like 25	118							methyltransferase activity (GO:0008168)										ATTCTGTACAAAACTTGGGAA	0.383													A|||	75	0.014976	0.0068	0.0288	5008	,	,		15133	0.0		0.0417	False		,,,				2504	0.0041				p.Q118Q		Atlas-SNP	.											.	.	.	.	0			c.A354G						PASS	.	A		60,4346	58.7+/-95.3	0,60,2143	136	136	136		354	2.4	1	12	dbSNP_129	136	370,8230	122.5+/-181.5	6,358,3936	no	coding-synonymous	C12orf26	NM_032230.2		6,418,6079	GG,GA,AA		4.3023,1.3618,3.3062		118/604	82780676	430,12576	2203	4300	6503	SO:0001819	synonymous_variant	84190	exon2			TGTACAAAACTTG	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.354A>G	12.37:g.82780676A>G		69	0	0		89	52	0.58427	NM_032230	Q9H5Y3	Silent	SNP	ENST00000248306.3	37	CCDS9024.1	47	0.02152014652014652	2	0.0040650406504065045	12	0.03314917127071823	0	0.0	33	0.04353562005277045	A	2.978	-0.211051	0.06140	0.013618	0.043023	ENSG00000127720	ENST00000550058	.	.	.	6.14	2.44	0.29823	.	.	.	.	.	T	0.24928	0.0605	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.15607	-1.0431	4	.	.	.	-3.6786	7.9708	0.30126	0.7528:0.0:0.2472:0.0	rs56337649	.	.	.	R	77	.	.	K	+	2	0	C12orf26	81304807	1.000000	0.71417	0.988000	0.46212	0.327000	0.28475	1.215000	0.32431	0.179000	0.19938	0.529000	0.55759	AAA	A|0.969;G|0.031	0.031	strong		0.383	METTL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408192.1	NM_032230		G	82780676	A	G	82780676	2	3	29	1	0	0	0	0	0	0	0	1	1681	11	1	3		3	C12orf26	12	82780676	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	10631733	82780676	51071219	608	12849											
BTG1	694	hgsc.bcm.edu	37	chr12	92539189	92539189	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agcagctcctgcaggctctgGctgaaggtctgcagctgtcg	6	9	14	12	1	2	1	0	1	2	0	4	1	3	1	1	3	5	7	1	3	1	0	rs201780644		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:92539189G>A	ENST00000256015.3	-	1	484	c.123C>T	c.(121-123)agC>agT	p.S41S	RP11-796E2.4_ENST00000499685.2_RNA|RP11-796E2.4_ENST00000501008.2_RNA|C12orf79_ENST00000549802.1_5'Flank|C12orf79_ENST00000546975.1_5'Flank|C12orf79_ENST00000551563.2_5'Flank	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	41					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)			haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				GCAGGCTCTGGCTGAAGGTCT	0.692			T	MYC	BCLL								G|||	1	0.000199681	0.0	0.0014	5008	,	,		11116	0.0		0.0	False		,,,				2504	0.0				p.S41S		Atlas-SNP	.		Dom	yes		12	12q22	694	"B-cell translocation gene 1, anti-proliferative"		L	.	BTG1	30	.	0			c.C123T						PASS	.						34	36	35					12																	92539189		2202	4299	6501	SO:0001819	synonymous_variant	694	exon1			GCTCTGGCTGAAG		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.123C>T	12.37:g.92539189G>A		109	0	0		106	30	0.283019	NM_001731	P31607	Silent	SNP	ENST00000256015.3	37	CCDS9043.1																																																																																			G|1.000;A|0.000	0.000	strong		0.692	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1			A	92539189	G	A	92539189	2	1	29	1	0	0	0	0	0	0	0	1	1555	1194	42	2		2	BTG1	12	92539189	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	9758513	92539189	41312706	609	12850											
BTG1	694	hgsc.bcm.edu	37	chr12	92539223	92539223	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gctgtcgctcgctcgtgagcCccttggtgcggagaaacttg	5	10	14	12	4	0	2	0	1	0	1	3	3	0	2	2	2	3	3	2	2	1	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:92539223C>T	ENST00000256015.3	-	1	450	c.89G>A	c.(88-90)gGg>gAg	p.G30E	RP11-796E2.4_ENST00000499685.2_RNA|RP11-796E2.4_ENST00000501008.2_RNA|C12orf79_ENST00000549802.1_5'Flank|C12orf79_ENST00000546975.1_5'Flank|C12orf79_ENST00000551563.2_5'Flank	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	30					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)			haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				GCTCGTGAGCCCCTTGGTGCG	0.677			T	MYC	BCLL																																p.G30E		Atlas-SNP	.		Dom	yes		12	12q22	694	"B-cell translocation gene 1, anti-proliferative"		L	.	BTG1	30	.	0			c.G89A						PASS	.						43	46	45					12																	92539223		2203	4300	6503	SO:0001583	missense	694	exon1			GTGAGCCCCTTGG		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.89G>A	12.37:g.92539223C>T	ENSP00000256015:p.Gly30Glu	140	0	0		151	48	0.317881	NM_001731	P31607	Missense_Mutation	SNP	ENST00000256015.3	37	CCDS9043.1	.	.	.	.	.	.	.	.	.	.	C	18.69	3.678759	0.68042	.	.	ENSG00000133639	ENST00000256015	T	0.22539	1.95	3.92	3.92	0.45320	Anti-proliferative protein (3);	0.111608	0.64402	D	0.000010	T	0.26122	0.0637	L	0.59436	1.845	0.80722	D	1	P	0.39920	0.695	B	0.39971	0.315	T	0.16305	-1.0407	10	0.59425	D	0.04	-11.2093	16.1014	0.81175	0.0:1.0:0.0:0.0	.	30	P62324	BTG1_HUMAN	E	30	ENSP00000256015:G30E	ENSP00000256015:G30E	G	-	2	0	BTG1	91063354	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	6.620000	0.74224	1.996000	0.58369	0.455000	0.32223	GGG	.	.	none		0.677	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1			T	92539223	C	T	92539223	3	4	29	1	0	0	0	0	1	0	0	0	1555	623	22	2	434	2	BTG1	12	92539223	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	34	92539223	41312672	610	12851											
UTP20	27340	hgsc.bcm.edu	37	chr12	101755803	101755803	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcaccaataagctgcaggtcGgagatttggactcttgttta	10	13	10	8	1	2	1	1	0	1	1	3	3	2	2	1	3	2	3	1	3	3	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:101755803G>A	ENST00000261637.4	+	44	5929	c.5755G>A	c.(5755-5757)Gga>Aga	p.G1919R		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	1919					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						GCTGCAGGTCGGAGATTTGGA	0.388																																					p.G1919R		Atlas-SNP	.											.	UTP20	222	.	0			c.G5755A						PASS	.						179	179	179					12																	101755803		2203	4300	6503	SO:0001583	missense	27340	exon44			CAGGTCGGAGATT	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.5755G>A	12.37:g.101755803G>A	ENSP00000261637:p.Gly1919Arg	79	0	0		76	18	0.236842	NM_014503	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	37	CCDS9081.1	.	.	.	.	.	.	.	.	.	.	G	18.03	3.531664	0.64972	.	.	ENSG00000120800	ENST00000261637	T	0.49139	0.79	6.03	5.15	0.70609	Armadillo-type fold (1);	0.048326	0.85682	N	0.000000	T	0.72447	0.3461	M	0.87758	2.905	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.77688	-0.2494	10	0.56958	D	0.05	-12.7347	15.3525	0.74399	0.0666:0.0:0.9334:0.0	.	1919	O75691	UTP20_HUMAN	R	1919	ENSP00000261637:G1919R	ENSP00000261637:G1919R	G	+	1	0	UTP20	100279934	1.000000	0.71417	0.875000	0.34327	0.271000	0.26615	7.008000	0.76341	1.557000	0.49525	-0.140000	0.14226	GGA	.	.	none		0.388	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		A	101755803	G	A	101755803	3	1	29	1	0	0	0	0	1	0	0	0	17114	1117	39	1	5929	1	UTP20	12	101755803	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	9216580	101755803	32096092	611	12852											
UTP20	27340	hgsc.bcm.edu	37	chr12	101779435	101779435	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgggcttgagagcttctcaTtagcctttgcctctgtacag	6	15	10	10	0	2	1	1	1	2	1	3	2	2	1	2	1	4	3	2	1	2	6	rs149160478		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:101779435T>C	ENST00000261637.4	+	61	8305	c.8131T>C	c.(8131-8133)Tta>Cta	p.L2711L		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	2711					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						GAGCTTCTCATTAGCCTTTGC	0.423																																					p.L2711L		Atlas-SNP	.											.	UTP20	222	.	0			c.T8131C						PASS	.			1,4405	2.1+/-5.4	0,1,2202	88	89	89		8131	-3.6	0	12	dbSNP_134	89	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	UTP20	NM_014503.2		0,3,6500	CC,CT,TT		0.0233,0.0227,0.0231		2711/2786	101779435	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	27340	exon61			TTCTCATTAGCCT	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.8131T>C	12.37:g.101779435T>C		97	0	0		95	49	0.515789	NM_014503	Q9H3H4	Silent	SNP	ENST00000261637.4	37	CCDS9081.1																																																																																			T|1.000;C|0.000	0.000	weak		0.423	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503		C	101779435	T	C	101779435	2	2	29	1	0	0	0	0	0	0	0	1	17114	1490	52	3		3	UTP20	12	101779435	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	23632	101779435	32072460	612	12853											
KIAA1033	23325	hgsc.bcm.edu	37	chr12	105550565	105550565	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcattgtagcagcaatgcCattaggtatggatgcaaaca	13	11	9	8	0	1	0	1	0	0	0	1	1	1	1	1	2	5	5	1	2	5	5	rs35149056	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:105550565C>T	ENST00000332180.5	+	27	2907	c.2820C>T	c.(2818-2820)gcC>gcT	p.A940A		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						GCAGCAATGCCATTAGGTATG	0.308													C|||	217	0.0433307	0.0166	0.0692	5008	,	,		14135	0.001		0.0795	False		,,,				2504	0.0675				p.A940A		Atlas-SNP	.											.	KIAA1033	83	.	0			c.C2820T						PASS	.	C		82,3618		1,80,1769	208	186	193		2820	4.9	1	12	dbSNP_126	193	613,7575		27,559,3508	no	coding-synonymous	KIAA1033	NM_015275.1		28,639,5277	TT,TC,CC		7.4866,2.2162,5.8462		940/1174	105550565	695,11193	1850	4094	5944	SO:0001819	synonymous_variant	23325	exon27			CAATGCCATTAGG	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.2820C>T	12.37:g.105550565C>T		71	0	0		86	38	0.44186	NM_015275		Silent	SNP	ENST00000332180.5	37	CCDS41826.1																																																																																			C|0.946;T|0.054	0.054	strong		0.308	KIAA1033-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406138.4	NM_015275		T	105550565	C	T	105550565	2	4	29	1	0	0	0	0	0	0	0	1	8215	581	21	2		2	KIAA1033	12	105550565	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	3771130	105550565	28301330	613	12854											
DAO	1610	hgsc.bcm.edu	37	chr12	109293183	109293183	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttattggtgaacgaactggcTtccggccagtacgcccccag	8	9	11	13	3	0	1	0	1	0	0	1	2	1	1	4	3	3	2	4	3	4	4	rs113854555		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:109293183T>G	ENST00000228476.3	+	10	1048	c.844T>G	c.(844-846)Ttc>Gtc	p.F282V	DAO_ENST00000551281.1_Missense_Mutation_p.F216V	NM_001917.4	NP_001908.3	P14920	OXDA_HUMAN	D-amino-acid oxidase	282					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)	ACGAACTGGCTTCCGGCCAGT	0.463																																					p.F282V		Atlas-SNP	.											.	DAO	58	.	0			c.T844G						PASS	.						38	34	35					12																	109293183		2203	4300	6503	SO:0001583	missense	1610	exon10			ACTGGCTTCCGGC	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.844T>G	12.37:g.109293183T>G	ENSP00000228476:p.Phe282Val	33	0	0		52	14	0.269231	NM_001917	B2R7I5|Q16758|Q8N6R2	Missense_Mutation	SNP	ENST00000228476.3	37	CCDS9122.1	.	.	.	.	.	.	.	.	.	.	t	9.649	1.141129	0.21205	.	.	ENSG00000110887	ENST00000551281;ENST00000228476;ENST00000547768	T;T;T	0.80393	-1.37;-1.37;-1.37	5.14	2.72	0.32119	FAD dependent oxidoreductase (1);	0.163309	0.56097	D	0.000036	T	0.76615	0.4012	M	0.65975	2.015	0.31918	N	0.613876	B;B	0.14438	0.01;0.004	B;B	0.26202	0.067;0.028	T	0.73861	-0.3849	10	0.66056	D	0.02	-29.9761	6.7285	0.23371	0.0:0.2961:0.0:0.7039	.	282;265	P14920;Q7Z312	OXDA_HUMAN;.	V	216;282;159	ENSP00000446853:F216V;ENSP00000228476:F282V;ENSP00000449967:F159V	ENSP00000228476:F282V	F	+	1	0	DAO	107817312	1.000000	0.71417	0.996000	0.52242	0.011000	0.07611	1.774000	0.38573	0.280000	0.22209	-0.474000	0.04947	TTC	T|0.500;C|0.500	.	alt		0.463	DAO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403682.1			G	109293183	T	G	109293183	3	3	29	1	0	0	0	0	1	0	0	0	4233	1609	56	5	878	5	DAO	12	109293183	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	3742618	109293183	24558712	614	12855											
ACACB	32	hgsc.bcm.edu	37	chr12	109647006	109647006	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agaagctcatgatgaccctcCggcacccgtcactgccgctg	8	7	10	16	3	2	3	2	2	0	1	3	3	3	3	4	1	2	3	4	1	1	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:109647006C>T	ENST00000338432.7	+	21	3216	c.3097C>T	c.(3097-3099)Cgg>Tgg	p.R1033W	ACACB_ENST00000377854.5_Missense_Mutation_p.R1033W|ACACB_ENST00000377848.3_Missense_Mutation_p.R1033W			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	1033					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)	GATGACCCTCCGGCACCCGTC	0.662																																					p.R1033W		Atlas-SNP	.											ACACB,caecum,adenoma,-1,1	ACACB	330	1	0			c.C3097T						PASS	.																																			SO:0001583	missense	32	exon20			ACCCTCCGGCACC	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.3097C>T	12.37:g.109647006C>T	ENSP00000341044:p.Arg1033Trp	109	0	0		115	51	0.443478	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	.	.	.	.	.	.	.	.	.	.	C	22.7	4.325995	0.81580	.	.	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854;ENST00000390027	T;T;T	0.50813	0.73;0.73;0.73	5.5	5.5	0.81552	Acetyl-CoA carboxylase, central domain (1);	0.056446	0.64402	D	0.000001	T	0.75243	0.3823	M	0.89353	3.025	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.80125	-0.1513	10	0.87932	D	0	.	19.425	0.94737	0.0:1.0:0.0:0.0	.	1033	O00763	ACACB_HUMAN	W	1033;1033;1033;264	ENSP00000341044:R1033W;ENSP00000367079:R1033W;ENSP00000367085:R1033W	ENSP00000341044:R1033W	R	+	1	2	ACACB	108131389	1.000000	0.71417	0.996000	0.52242	0.983000	0.72400	4.052000	0.57420	2.584000	0.87258	0.563000	0.77884	CGG	.	.	none		0.662	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		T	109647006	C	T	109647006	3	4	29	1	0	0	0	0	1	0	0	0	107	643	23	1	3175	1	ACACB	12	109647006	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	353823	109647006	24204889	615	12856											
NOS1	4842	hgsc.bcm.edu	37	chr12	117672544	117672544	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctcccgttggtgtggagacGcacgaagatagttgaccgac	9	8	14	10	4	0	3	0	1	0	2	1	6	1	3	2	2	0	4	2	2	2	3	rs375069851		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:117672544G>A	ENST00000338101.4	-	21	3167	c.3163C>T	c.(3163-3165)Cgt>Tgt	p.R1055C	NOS1_ENST00000317775.6_Missense_Mutation_p.R1021C|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)		GTGTGGAGACGCACGAAGATA	0.552																																					p.R1055C	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											NOS1,caecum,carcinoma,0,2	NOS1	240	2	0			c.C3163T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	0,4080		0,0,2040	35	39	38		3061,2053,2053,3163	4.7	1	12		38	2,8402		0,2,4200	no	missense,missense,missense,missense	NOS1	NM_000620.4,NM_001204213.1,NM_001204214.1,NM_001204218.1	180,180,180,180	0,2,6240	AA,AG,GG		0.0238,0.0,0.016	probably-damaging,probably-damaging,probably-damaging,probably-damaging	1021/1435,685/1099,685/1099,1055/1469	117672544	2,12482	2040	4202	6242	SO:0001583	missense	4842	exon22			GGAGACGCACGAA		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.3163C>T	12.37:g.117672544G>A	ENSP00000337459:p.Arg1055Cys	72	0	0		68	26	0.382353	NM_001204218		Missense_Mutation	SNP	ENST00000338101.4	37	CCDS55890.1	.	.	.	.	.	.	.	.	.	.	G	14.67	2.603856	0.46423	0.0	2.38E-4	ENSG00000089250	ENST00000397605;ENST00000317775;ENST00000541241;ENST00000338101	T;T	0.67698	-0.28;-0.28	4.65	4.65	0.58169	Riboflavin synthase-like beta-barrel (1);FAD-binding, type 1 (1);Ferredoxin reductase-type FAD-binding domain (1);	0.056224	0.85682	D	0.000000	T	0.79227	0.4410	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.71414	0.973	T	0.81560	-0.0877	10	0.87932	D	0	-17.9866	18.067	0.89394	0.0:0.0:1.0:0.0	.	1021	P29475	NOS1_HUMAN	C	916;1021;1021;1055	ENSP00000320758:R1021C;ENSP00000337459:R1055C	ENSP00000320758:R1021C	R	-	1	0	NOS1	116156927	1.000000	0.71417	1.000000	0.80357	0.210000	0.24377	4.455000	0.60075	2.568000	0.86640	0.561000	0.74099	CGT	.	.	weak		0.552	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1			A	117672544	G	A	117672544	3	1	29	1	0	0	0	0	1	0	0	0	10550	1087	38	1	1279	1	NOS1	12	117672544	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	8025538	117672544	16179351	616	12857											
CIT	11113	hgsc.bcm.edu	37	chr12	120222830	120222830	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agaagtttcttttccatggaGctagtcttggcaggggagtc	8	13	13	7	0	2	1	0	0	2	1	4	3	3	3	1	4	1	3	1	4	2	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:120222830G>A	ENST00000261833.7	-	11	1387	c.1335C>T	c.(1333-1335)agC>agT	p.S445S	CIT_ENST00000392521.2_Silent_p.S445S|CIT_ENST00000537607.1_5'Flank	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	445					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)		TTTCCATGGAGCTAGTCTTGG	0.507																																					p.S445S		Atlas-SNP	.											.	CIT	535	.	0			c.C1335T						PASS	.						116	101	106					12																	120222830		2203	4300	6503	SO:0001819	synonymous_variant	11113	exon11			CATGGAGCTAGTC	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.1335C>T	12.37:g.120222830G>A		107	0	0		91	25	0.274725	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Silent	SNP	ENST00000261833.7	37	CCDS9192.1	.	.	.	.	.	.	.	.	.	.	G	6.186	0.402510	0.11696	.	.	ENSG00000122966	ENST00000392520	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	T	0.76919	0.4055	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.74228	-0.3733	4	.	.	.	.	20.1379	0.98040	0.0:0.0:1.0:0.0	.	.	.	.	V	73	.	.	A	-	2	0	CIT	118707213	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.810000	0.75216	2.779000	0.95612	0.655000	0.94253	GCT	.	.	none		0.507	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174		A	120222830	G	A	120222830	2	1	29	1	0	0	0	0	0	0	0	1	3440	962	34	2		2	CIT	12	120222830	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2550286	120222830	13629065	617	12858											
HNF1A	6927	hgsc.bcm.edu	37	chr12	121435342	121435342	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggcagcagcctgaccaccCtgcagcccgtccagttctcc	6	7	10	18	1	1	1	0	1	1	0	3	1	2	1	6	1	4	4	6	1	0	1	rs544842497|rs2259820	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:121435342C>T	ENST00000257555.6	+	7	1601	c.1375C>T	c.(1375-1377)Ctg>Ttg	p.L459L	HNF1A_ENST00000538626.1_Silent_p.L41L|RP11-216P16.2_ENST00000606238.1_RNA|HNF1A_ENST00000400024.2_Silent_p.L459L|HNF1A_ENST00000402929.1_3'UTR|HNF1A_ENST00000544413.1_Silent_p.L459L|HNF1A_ENST00000541395.1_Silent_p.L459L			P20823	HNF1A_HUMAN	HNF1 homeobox A	459					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)					CCTGACCACCCTGCAGCCCGT	0.667									Hepatic Adenoma, Familial Clustering of				c|||	1586	0.316693	0.1089	0.3501	5008	,	,		17758	0.4732		0.3161	False		,,,				2504	0.4131				p.L459L		Atlas-SNP	.											.	HNF1A	302	.	0			c.C1375T						PASS	.	C		529,3877	232.0+/-245.7	41,447,1715	33	35	34		1375	4.6	1	12	dbSNP_100	34	2675,5923	412.6+/-350.9	434,1807,2058	no	coding-synonymous	HNF1A	NM_000545.5		475,2254,3773	TT,TC,CC		31.1119,12.0064,24.6386		459/632	121435342	3204,9800	2203	4299	6502	SO:0001819	synonymous_variant	6927	exon7	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	ACCACCCTGCAGC	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.1375C>T	12.37:g.121435342C>T		70	0	0		117	116	0.991453	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Silent	SNP	ENST00000257555.6	37	CCDS9209.1																																																																																			C|0.718;T|0.282	0.282	strong		0.667	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		T	121435342	C	T	121435342	2	4	29	1	0	0	0	0	0	0	0	1	7260	680	24	2		2	HNF1A	12	121435342	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1212512	121435342	12416553	618	12859											
HNF1A	6927	hgsc.bcm.edu	37	chr12	121435427	121435427	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagagccatgtgacccagaGccccttcatggccaccatgg	9	6	11	15	0	1	3	1	1	0	2	1	3	1	3	6	2	2	1	6	2	0	1	rs2464196	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:121435427G>A	ENST00000257555.6	+	7	1686	c.1460G>A	c.(1459-1461)aGc>aAc	p.S487N	HNF1A_ENST00000538626.1_Missense_Mutation_p.S69N|RP11-216P16.2_ENST00000606238.1_RNA|HNF1A_ENST00000400024.2_Missense_Mutation_p.S487N|HNF1A_ENST00000402929.1_3'UTR|HNF1A_ENST00000544413.1_Missense_Mutation_p.S487N|HNF1A_ENST00000541395.1_Missense_Mutation_p.S487N			P20823	HNF1A_HUMAN	HNF1 homeobox A	487			S -> N (in dbSNP:rs2464196). {ECO:0000269|PubMed:9112026, ECO:0000269|PubMed:9133564, ECO:0000269|PubMed:9287055, ECO:0000269|PubMed:9604876, ECO:0000269|PubMed:9621514, ECO:0000269|Ref.6}.		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)					GTGACCCAGAGCCCCTTCATG	0.637									Hepatic Adenoma, Familial Clustering of				g|||	1591	0.317692	0.112	0.3501	5008	,	,		18114	0.4732		0.3161	False		,,,				2504	0.4141				p.S487N		Atlas-SNP	.											.	HNF1A	302	.	0			c.G1460A	GRCh37	CM067474	HNF1A	M	rs2464196	PASS	.	G	ASN/SER	541,3865	230.4+/-244.6	42,457,1704	29	28	29		1460	3.5	1	12	dbSNP_100	29	2676,5924	411.0+/-350.3	431,1814,2055	yes	missense	HNF1A	NM_000545.5	46	473,2271,3759	AA,AG,GG		31.1163,12.2787,24.7347	possibly-damaging	487/632	121435427	3217,9789	2203	4300	6503	SO:0001583	missense	6927	exon7	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CCCAGAGCCCCTT	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.1460G>A	12.37:g.121435427G>A	ENSP00000257555:p.Ser487Asn	114	0	0		127	124	0.976378	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Missense_Mutation	SNP	ENST00000257555.6	37	CCDS9209.1	715	0.3273809523809524	54	0.10975609756097561	132	0.36464088397790057	296	0.5174825174825175	233	0.3073878627968338	G	12.39	1.924644	0.34002	0.122787	0.311163	ENSG00000135100	ENST00000257555;ENST00000535125;ENST00000537424;ENST00000543027;ENST00000541395;ENST00000340577;ENST00000544413	D;D;D	0.97455	-4.39;-4.39;-4.39	4.49	3.53	0.40419	Hepatocyte nuclear factor 1, beta isoform, C-terminal (1);	0.068781	0.64402	N	0.000014	T	0.00012	0.0000	L	0.40543	1.245	0.09310	P	0.99999999123403	B;B;B	0.24576	0.0;0.014;0.106	B;B;B	0.32533	0.005;0.085;0.147	T	0.04153	-1.0973	9	0.42905	T	0.14	-9.2011	10.4952	0.44772	0.104:0.0:0.896:0.0	rs2464196;rs2708085;rs16950667;rs17847503;rs56962510;rs2464196	487;487;487	F5H0K0;P20823;E7EUQ4	.;HNF1A_HUMAN;.	N	487;379;487;308;487;487;487	ENSP00000257555:S487N;ENSP00000443112:S487N;ENSP00000438804:S487N	ENSP00000257555:S487N	S	+	2	0	HNF1A	119919810	0.950000	0.32346	0.992000	0.48379	0.944000	0.59088	1.527000	0.35975	0.976000	0.38417	0.655000	0.94253	AGC	G|0.725;A|0.275	0.275	strong		0.637	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		A	121435427	G	A	121435427	3	1	29	1	0	0	0	0	1	0	0	0	7260	971	34	2	1486	2	HNF1A	12	121435427	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	85	121435427	12416468	619	12860											
GPR81	27198	hgsc.bcm.edu	37	chr12	123214166	123214166	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccgtccagaggaaatagaGtctagcagacacgctgggca	13	5	12	11	2	1	3	0	0	1	3	2	4	2	4	2	2	1	3	2	2	3	2	rs140482291	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:123214166G>A	ENST00000436083.2	-	1	1224	c.721C>T	c.(721-723)Ctc>Ttc	p.L241F	HCAR1_ENST00000356987.2_Missense_Mutation_p.L241F|HCAR1_ENST00000432564.1_Missense_Mutation_p.L241F			Q9BXC0	HCAR1_HUMAN	hydroxycarboxylic acid receptor 1	241					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						AGGAAATAGAGTCTAGCAGAC	0.572													G|||	11	0.00219649	0.0	0.0029	5008	,	,		18469	0.0		0.002	False		,,,				2504	0.0072				p.L241F		Atlas-SNP	.											.	HCAR1	21	.	0			c.C721T						PASS	.	G	PHE/LEU	0,4406		0,0,2203	69	64	66		721	4.6	0.1	12	dbSNP_134	66	13,8587	10.5+/-38.8	0,13,4287	yes	missense	HCAR1	NM_032554.3	22	0,13,6490	AA,AG,GG		0.1512,0.0,0.1	probably-damaging	241/347	123214166	13,12993	2203	4300	6503	SO:0001583	missense	27198	exon1			AATAGAGTCTAGC	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.721C>T	12.37:g.123214166G>A	ENSP00000409980:p.Leu241Phe	48	0	0		70	36	0.514286	NM_032554	B2R9X4|Q3Y5J3|Q4VBN1|Q6NXU5	Missense_Mutation	SNP	ENST00000436083.2	37	CCDS9236.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	13.74	2.327855	0.41197	0.0	0.001512	ENSG00000196917	ENST00000356987;ENST00000432564;ENST00000436083	T;T;T	0.41758	0.99;0.99;0.99	5.51	4.62	0.57501	GPCR, rhodopsin-like superfamily (1);	0.295265	0.24568	N	0.037419	T	0.60366	0.2263	M	0.73372	2.23	0.09310	N	0.999998	D	0.71674	0.998	D	0.74348	0.983	T	0.54248	-0.8322	10	0.66056	D	0.02	-9.9997	10.1712	0.42911	0.0918:0.0:0.9082:0.0	.	241	Q9BXC0	HCAR1_HUMAN	F	241	ENSP00000349478:L241F;ENSP00000389255:L241F;ENSP00000409980:L241F	ENSP00000349478:L241F	L	-	1	0	HCAR1	121780119	0.181000	0.23161	0.126000	0.21872	0.428000	0.31595	1.981000	0.40628	1.326000	0.45319	0.655000	0.94253	CTC	G|0.998;A|0.002	0.002	strong		0.572	HCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401415.1			A	123214166	G	A	123214166	3	1	29	1	0	0	0	0	1	0	0	0	6719	1029	36	2	323	2	GPR81	12	123214166	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1778739	123214166	10637729	620	12861											
HIP1R	9026	hgsc.bcm.edu	37	chr12	123345296	123345296	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcgtctgctcccacgagatcGcagccagcacggcccagctg	7	6	11	17	4	1	1	0	0	1	1	4	2	2	1	3	1	4	4	3	1	0	0	rs141813189	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:123345296G>A	ENST00000253083.4	+	28	2856	c.2731G>A	c.(2731-2733)Gca>Aca	p.A911T		NM_003959.1	NP_003950.1	O75146	HIP1R_HUMAN	huntingtin interacting protein 1 related	911	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.|Important for actin binding.				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)		CCACGAGATCGCAGCCAGCAC	0.672											OREG0022225	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	9	0.00179712	0.0	0.0029	5008	,	,		15132	0.0		0.002	False		,,,				2504	0.0051				p.A911T		Atlas-SNP	.											.	HIP1R	68	.	0			c.G2731A						PASS	.	G	THR/ALA	0,4406		0,0,2203	40	43	42		2731	5.5	1	12	dbSNP_134	42	8,8592	7.1+/-27.0	0,8,4292	yes	missense	HIP1R	NM_003959.1	58	0,8,6495	AA,AG,GG		0.093,0.0,0.0615	probably-damaging	911/1069	123345296	8,12998	2203	4300	6503	SO:0001583	missense	9026	exon28			GAGATCGCAGCCA	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.2731G>A	12.37:g.123345296G>A	ENSP00000253083:p.Ala911Thr	145	0	0	1526	177	82	0.463277	NM_003959	A6NHQ6|Q6NXG8|Q9UED9	Missense_Mutation	SNP	ENST00000253083.4	37	CCDS31922.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	36	5.718378	0.96839	0.0	9.3E-4	ENSG00000130787	ENST00000253083	T	0.50813	0.73	5.49	5.49	0.81192	I/LWEQ (4);	0.000000	0.85682	D	0.000000	T	0.68686	0.3028	M	0.66939	2.045	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.70479	-0.4860	10	0.66056	D	0.02	-17.9631	18.989	0.92783	0.0:0.0:1.0:0.0	.	911	O75146	HIP1R_HUMAN	T	911	ENSP00000253083:A911T	ENSP00000253083:A911T	A	+	1	0	HIP1R	121911249	1.000000	0.71417	0.960000	0.40013	0.905000	0.53344	9.794000	0.99096	2.578000	0.87016	0.655000	0.94253	GCA	G|0.999;A|0.001	0.001	strong		0.672	HIP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400935.1	NM_003959		A	123345296	G	A	123345296	3	1	29	1	0	0	0	0	1	0	0	0	7124	1087	38	1	2841	1	HIP1R	12	123345296	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	131130	123345296	10506599	621	12862											
DNAH10	196385	hgsc.bcm.edu	37	chr12	124417973	124417973	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caggccacctgccggaagaaCggctggccactggaccgctc	8	4	13	16	3	0	1	0	0	0	1	1	3	0	3	5	5	2	2	5	5	2	0	rs56219209	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:124417973C>T	ENST00000409039.3	+	76	13063	c.13038C>T	c.(13036-13038)aaC>aaT	p.N4346N	CCDC92_ENST00000544798.1_Intron|DNAH10OS_ENST00000514254.2_Intron|DNAH10_ENST00000538983.1_3'UTR|RP11-380L11.3_ENST00000602292.1_RNA	NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	4346					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)		GCCGGAAGAACGGCTGGCCAC	0.622													C|||	40	0.00798722	0.0008	0.0072	5008	,	,		19026	0.005		0.0189	False		,,,				2504	0.0102				p.N4346N		Atlas-SNP	.											.	DNAH10	888	.	0			c.C13038T						PASS	.	C		14,3946		0,14,1966	35	38	37		13038	-2.1	1	12	dbSNP_129	37	168,8134		1,166,3984	no	coding-synonymous	DNAH10	NM_207437.3		1,180,5950	TT,TC,CC		2.0236,0.3535,1.4843		4346/4472	124417973	182,12080	1980	4151	6131	SO:0001819	synonymous_variant	196385	exon76			GAAGAACGGCTGG	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.13038C>T	12.37:g.124417973C>T		43	0	0		57	27	0.473684	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																			C|0.985;T|0.015	0.015	strong		0.622	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124417973	C	T	124417973	2	4	29	1	0	0	0	0	0	0	0	1	4600	535	19	1		1	DNAH10	12	124417973	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1072677	124417973	9433922	622	12863											
SFRS8	6433	hgsc.bcm.edu	37	chr12	132239988	132239988	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tattatgagtttaagaagcaGttcttcctccagaaagaagg	14	12	9	6	0	1	4	0	1	1	3	3	4	3	4	2	1	1	3	2	1	6	6	rs139034136	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:132239988G>A	ENST00000261674.4	+	10	1653	c.1512G>A	c.(1510-1512)caG>caA	p.Q504Q	SFSWAP_ENST00000541286.1_Silent_p.Q504Q|RP11-495K9.5_ENST00000537032.1_lincRNA	NM_004592.3	NP_004583.2	Q12872	SFSWA_HUMAN	splicing factor, suppressor of white-apricot family	504					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						TTAAGAAGCAGTTCTTCCTCC	0.468											OREG0022261	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2	0.000399361	0.0	0.0014	5008	,	,		20727	0.0		0.001	False		,,,				2504	0.0				p.Q504Q		Atlas-SNP	.											.	SFSWAP	69	.	0			c.G1512A						PASS	.	G		0,4406	2.1+/-5.4	0,0,2203	94	93	93		1512	2.7	1	12	dbSNP_134	93	18,8582	13.3+/-46.6	0,18,4282	no	coding-synonymous	SFSWAP	NM_004592.2		0,18,6485	AA,AG,GG		0.2093,0.0,0.1384		504/952	132239988	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	6433	exon10			GAAGCAGTTCTTC	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.1512G>A	12.37:g.132239988G>A		33	0	0	1593	28	10	0.357143	NM_001261411	B2RN45|B7ZM97|F5H6B8|Q6PJF7	Silent	SNP	ENST00000261674.4	37	CCDS9273.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	9.086	1.000626	0.19121	0.0	0.002093	ENSG00000061936	ENST00000537164	.	.	.	5.49	2.69	0.31865	.	.	.	.	.	T	0.53834	0.1821	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42649	-0.9439	4	.	.	.	-28.6537	5.5838	0.17264	0.2878:0.1317:0.5806:0.0	.	.	.	.	N	144	.	.	S	+	2	0	SFSWAP	130805941	0.979000	0.34478	1.000000	0.80357	0.983000	0.72400	0.103000	0.15292	0.289000	0.22422	0.561000	0.74099	AGT	G|0.999;A|0.001	0.001	strong		0.468	SFSWAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399276.1	NM_004592		A	132239988	G	A	132239988	2	1	29	1	0	0	0	0	0	0	0	1	14198	1020	36	2		2	SFRS8	12	132239988	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	7822015	132239988	1611907	623	12864											
EP400	57634	hgsc.bcm.edu	37	chr12	132504639	132504639	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaagcccgagggtcgcacCgtggctttccccagcactca	8	6	11	16	3	1	1	1	0	0	1	3	2	2	1	4	2	2	3	4	2	1	1	rs147615479	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:132504639C>T	ENST00000333577.4	+	23	4540	c.4431C>T	c.(4429-4431)acC>acT	p.T1477T	EP400_ENST00000389561.2_Silent_p.T1441T|EP400_ENST00000330386.6_Silent_p.T1441T|EP400_ENST00000332482.4_Silent_p.T1404T|EP400_ENST00000389562.2_Silent_p.T1440T			Q96L91	EP400_HUMAN	E1A binding protein p400	1477					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)		AGGGTCGCACCGTGGCTTTCC	0.647													C|||	12	0.00239617	0.0	0.0058	5008	,	,		14876	0.0		0.007	False		,,,				2504	0.001				p.T1441T		Atlas-SNP	.											.	EP400	370	.	0			c.C4323T						PASS	.	C		9,4397	15.5+/-35.6	0,9,2194	66	63	64		4323	-11.1	0.4	12	dbSNP_134	64	96,8504	54.0+/-114.7	0,96,4204	no	coding-synonymous	EP400	NM_015409.4		0,105,6398	TT,TC,CC		1.1163,0.2043,0.8073		1441/3124	132504639	105,12901	2203	4300	6503	SO:0001819	synonymous_variant	57634	exon22			TCGCACCGTGGCT	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.4431C>T	12.37:g.132504639C>T		57	0	0		48	30	0.625	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37																																																																																				C|0.994;T|0.006	0.006	strong		0.647	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		T	132504639	C	T	132504639	2	4	29	1	0	0	0	0	0	0	0	1	5151	639	23	1		1	EP400	12	132504639	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	264651	132504639	1347256	624	12865											
EP400	57634	hgsc.bcm.edu	37	chr12	132528724	132528724	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctgctctccccgtcaggaCgcagtgatgactgcagtgag	7	9	13	12	2	2	3	1	3	1	0	3	4	2	4	2	1	3	4	2	1	0	0	rs61944617	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:132528724C>T	ENST00000333577.4	+	36	6670	c.6561C>T	c.(6559-6561)gaC>gaT	p.D2187D	EP400_ENST00000389561.2_Silent_p.D2151D|EP400_ENST00000330386.6_Silent_p.D2070D|EP400_ENST00000332482.4_Silent_p.D2114D|EP400_ENST00000389562.2_Silent_p.D2150D			Q96L91	EP400_HUMAN	E1A binding protein p400	2187					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)		CCCGTCAGGACGCAGTGATGA	0.627													c|||	28	0.00559105	0.0	0.0086	5008	,	,		18518	0.0		0.003	False		,,,				2504	0.0194				p.D2151D		Atlas-SNP	.											.	EP400	370	.	0			c.C6453T						PASS	.	T		3,4403	9.9+/-24.2	0,3,2200	55	54	54		6453	-10.6	0	12	dbSNP_129	54	45,8555	29.0+/-79.6	0,45,4255	no	coding-synonymous	EP400	NM_015409.4		0,48,6455	TT,TC,CC		0.5233,0.0681,0.3691		2151/3124	132528724	48,12958	2203	4300	6503	SO:0001819	synonymous_variant	57634	exon35			TCAGGACGCAGTG	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.6561C>T	12.37:g.132528724C>T		70	0	0		74	43	0.581081	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37																																																																																				C|0.996;T|0.004	0.004	strong		0.627	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		T	132528724	C	T	132528724	2	4	29	1	0	0	0	0	0	0	0	1	5151	535	19	1		1	EP400	12	132528724	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	24085	132528724	1323171	625	12866											
DDX51	317781	hgsc.bcm.edu	37	chr12	132625027	132625027	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcctctggccaggcccgtaGcgcgaggagaactcagccac	8	5	12	16	3	2	1	1	0	1	1	3	3	3	1	4	3	3	1	4	3	2	1	rs61942919	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr12:132625027G>A	ENST00000397333.3	-	11	1652	c.1614C>T	c.(1612-1614)cgC>cgT	p.R538R		NM_175066.3	NP_778236.2	Q8N8A6	DDX51_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 51	538	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(1)|lung(5)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.59e-08)|Epithelial(86;3.62e-07)|all cancers(50;2.13e-05)		CAGGCCCGTAGCGCGAGGAGA	0.617													G|||	29	0.00579073	0.0	0.0086	5008	,	,		16503	0.0		0.004	False		,,,				2504	0.0194				p.R538R		Atlas-SNP	.											DDX51,NS,carcinoma,-1,1	DDX51	33	1	0			c.C1614T						PASS	.	G		3,4217		0,3,2107	72	83	79		1614	4.1	0.9	12	dbSNP_129	79	58,8392		0,58,4167	no	coding-synonymous	DDX51	NM_175066.3		0,61,6274	AA,AG,GG		0.6864,0.0711,0.4815		538/667	132625027	61,12609	2110	4225	6335	SO:0001819	synonymous_variant	317781	exon11			CCCGTAGCGCGAG	BC040185	CCDS41865.1	12q24.33	2005-10-12				ENSG00000185163		"DEAD-boxes"	20082	protein-coding gene	gene with protein product							Standard	NM_175066		Approved		uc001ujy.4	Q8N8A6		ENST00000397333.3:c.1614C>T	12.37:g.132625027G>A		87	0	0		84	32	0.380952	NM_175066	A8MPT9|Q5CZ71|Q8IXK5|Q96ED1	Silent	SNP	ENST00000397333.3	37	CCDS41865.1																																																																																			G|0.995;A|0.005	0.005	strong		0.617	DDX51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398978.1	NM_175066		A	132625027	G	A	132625027	2	1	29	1	0	0	0	0	0	0	0	1	4371	958	34	2		2	DDX51	12	132625027	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	96303	132625027	1226868	626	12867											
PABPC3	5042	hgsc.bcm.edu	37	chr13	25670627	25670627	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatcacttcgaaaaagtggAgtgggcaacatattcgttaa	14	10	9	8	2	1	0	1	0	0	0	3	2	1	1	1	2	1	2	1	2	5	4	rs369126872		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:25670627A>G	ENST00000281589.3	+	1	328	c.291A>G	c.(289-291)ggA>ggG	p.G97G		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	97					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)		GAAAAAGTGGAGTGGGCAACA	0.418																																					p.G97G		Atlas-SNP	.											.	PABPC3	129	.	0			c.A291G						PASS	.						96	89	92					13																	25670627		2203	4300	6503	SO:0001819	synonymous_variant	5042	exon1			AAGTGGAGTGGGC	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.291A>G	13.37:g.25670627A>G		137	0	0		151	85	0.562914	NM_030979	Q8NHV0|Q9H086	Silent	SNP	ENST00000281589.3	37	CCDS9311.1																																																																																			.	.	alt		0.418	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979		G	25670627	A	G	25670627	2	3	29	1	0	0	0	0	0	0	0	1	11374	291	11	3		3	PABPC3	13	25670627	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10		25670627	89499251	627	12868											
WASF3	10810	hgsc.bcm.edu	37	chr13	27250805	27250805	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttagacccgacaacaggttGtctcagagtgtgtaccatgg	10	10	11	10	1	1	2	1	0	1	2	2	3	1	2	2	2	2	2	2	2	3	3	rs139779405	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:27250805G>T	ENST00000335327.5	+	7	838	c.660G>T	c.(658-660)ttG>ttT	p.L220F	WASF3_ENST00000361042.4_Intron	NM_006646.5	NP_006637.2	Q9UPY6	WASF3_HUMAN	WAS protein family, member 3	220					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)		ACAACAGGTTGTCTCAGAGTG	0.532													G|||	2	0.000399361	0.0	0.0	5008	,	,		17714	0.0		0.002	False		,,,				2504	0.0				p.L220F		Atlas-SNP	.											.	WASF3	68	.	0			c.G660T						PASS	.	G	PHE/LEU	0,4406		0,0,2203	179	165	170		660	4.1	1	13	dbSNP_134	170	10,8590	7.7+/-29.5	0,10,4290	yes	missense	WASF3	NM_006646.5	22	0,10,6493	TT,TG,GG		0.1163,0.0,0.0769	possibly-damaging	220/503	27250805	10,12996	2203	4300	6503	SO:0001583	missense	10810	exon7			CAGGTTGTCTCAG	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.660G>T	13.37:g.27250805G>T	ENSP00000335055:p.Leu220Phe	72	0	0		69	34	0.492754	NM_006646	O94974|Q86VQ2	Missense_Mutation	SNP	ENST00000335327.5	37	CCDS9318.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	6.363	0.435000	0.12045	0.0	0.001163	ENSG00000132970	ENST00000335327	T	0.43688	0.94	5.77	4.05	0.47172	.	0.150888	0.49916	D	0.000139	T	0.32194	0.0821	L	0.36672	1.1	0.80722	D	1	B	0.20988	0.05	B	0.23716	0.048	T	0.06180	-1.0841	10	0.27082	T	0.32	-16.5533	10.5878	0.45292	0.2073:0.0:0.7927:0.0	.	220	Q9UPY6	WASF3_HUMAN	F	220	ENSP00000335055:L220F	ENSP00000335055:L220F	L	+	3	2	WASF3	26148805	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.331000	0.43894	0.798000	0.33994	0.591000	0.81541	TTG	A|0.000;G|0.999;T|0.001	0.001	strong		0.532	WASF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044258.1			T	27250805	G	T	27250805	3	4	29	1	0	0	0	0	1	0	0	0	17269	1368	48	4	678	4	WASF3	13	27250805	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1580178	27250805	87919073	628	12869											
SLC7A1	6541	hgsc.bcm.edu	37	chr13	30110256	30110256	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	gcgagacagccgcgtctcctCccggctacagtccaccacct	7	6	9	19	4	1	1	0	0	1	1	4	2	3	1	6	1	2	1	6	1	1	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:30110256C>G	ENST00000380752.5	-	3	456	c.70G>C	c.(70-72)Gag>Cag	p.E24Q		NM_003045.4	NP_003036.1	P30825	CTR1_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 1	24					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	arginine transmembrane transporter activity (GO:0015181)			endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|prostate(1)|stomach(1)|urinary_tract(2)	24		Lung SC(185;0.0257)|Breast(139;0.238)		all cancers(112;0.0148)|OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(112;0.0875)|GBM - Glioblastoma multiforme(144;0.179)	L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	CGCGTCTCCTCCCGGCTACAG	0.587																																					p.E24Q		Atlas-SNP	.											.	SLC7A1	64	.	0			c.G70C						PASS	.						57	62	60					13																	30110256		2203	4300	6503	SO:0001583	missense	6541	exon3			TCTCCTCCCGGCT	AF078107	CCDS9333.1	13q12.3	2013-05-22			ENSG00000139514	ENSG00000139514		"Solute carriers"	11057	protein-coding gene	gene with protein product	"ecotropic retroviral receptor", "amino acid transporter, cationic 1"	104615		ERR, ATRC1		1348489	Standard	NM_003045		Approved	CAT-1, HCAT1, REC1L	uc001uso.3	P30825	OTTHUMG00000016658	ENST00000380752.5:c.70G>C	13.37:g.30110256C>G	ENSP00000370128:p.Glu24Gln	78	0	0		71	31	0.43662	NM_003045	Q5JR50	Missense_Mutation	SNP	ENST00000380752.5	37	CCDS9333.1	.	.	.	.	.	.	.	.	.	.	C	12.80	2.046474	0.36085	.	.	ENSG00000139514	ENST00000380752;ENST00000450494	D;D	0.88586	-2.17;-2.4	4.82	4.82	0.62117	.	0.054005	0.64402	D	0.000001	D	0.88500	0.6453	M	0.83012	2.62	0.48452	D	0.999658	B	0.33477	0.413	B	0.35770	0.21	D	0.85308	0.1077	10	0.24483	T	0.36	.	10.6286	0.45523	0.0:0.913:0.0:0.087	.	24	P30825	CTR1_HUMAN	Q	24	ENSP00000370128:E24Q;ENSP00000390092:E24Q	ENSP00000370128:E24Q	E	-	1	0	SLC7A1	29008256	1.000000	0.71417	1.000000	0.80357	0.693000	0.40251	5.803000	0.69129	2.504000	0.84457	0.655000	0.94253	GAG	.	.	none		0.587	SLC7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044337.2	NM_003045		G	30110256	C	G	30110256	3	3	29	1	0	0	0	0	1	0	0	0	14707	864	30	4	1863	4	SLC7A1	13	30110256	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2859451	30110256	85059622	629	12870											
RXFP2	122042	hgsc.bcm.edu	37	chr13	32367033	32367033	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	tcttccccttcagtaacattCgacctggaaaacggcagacc	11	9	7	14	2	2	1	1	0	1	1	4	3	3	2	4	2	2	2	4	2	3	4	rs138951290		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:32367033C>G	ENST00000298386.2	+	16	1665	c.1594C>G	c.(1594-1596)Cga>Gga	p.R532G	RXFP2_ENST00000380314.1_Missense_Mutation_p.R508G	NM_130806.3	NP_570718.1	Q8WXD0	RXFP2_HUMAN	relaxin/insulin-like family peptide receptor 2	532					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oocyte maturation (GO:0001556)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	peptide hormone binding (GO:0017046)|protein-hormone receptor activity (GO:0016500)			cervix(1)|endometrium(2)|large_intestine(15)|lung(13)|prostate(1)|stomach(1)	33		Lung SC(185;0.0262)		all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535)		CAGTAACATTCGACCTGGAAA	0.453													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18297	0.0		0.0	False		,,,				2504	0.0				p.R532G		Atlas-SNP	.											RXFP2,NS,carcinoma,0,1	RXFP2	95	1	0			c.C1594G						PASS	.	C	GLY/ARG,GLY/ARG	1,4405	2.1+/-5.4	0,1,2202	100	90	93		1522,1594	5.7	0.6	13	dbSNP_134	93	9,8591	7.7+/-29.5	0,9,4291	yes	missense,missense	RXFP2	NM_001166058.1,NM_130806.3	125,125	0,10,6493	GG,GC,CC		0.1047,0.0227,0.0769	probably-damaging,probably-damaging	508/731,532/755	32367033	10,12996	2203	4300	6503	SO:0001583	missense	122042	exon16			AACATTCGACCTG	AF403384	CCDS9342.1, CCDS53862.1	13q12.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000133105	ENSG00000133105		"GPCR / Class A : Relaxin family peptide receptors"	17318	protein-coding gene	gene with protein product		606655	"leucine-rich repeat-containing G protein-coupled receptor 8"	LGR8		12217959, 12970298, 15956688, 16507880	Standard	NM_130806		Approved	GREAT, GPR106, INSL3R, RXFPR2	uc001utt.3	Q8WXD0	OTTHUMG00000016690	ENST00000298386.2:c.1594C>G	13.37:g.32367033C>G	ENSP00000298386:p.Arg532Gly	114	0	0		138	67	0.485507	NM_130806	B1ALE9|Q3KU23	Missense_Mutation	SNP	ENST00000298386.2	37	CCDS9342.1	.	.	.	.	.	.	.	.	.	.	C	17.33	3.361723	0.61403	2.27E-4	0.001047	ENSG00000133105	ENST00000380314;ENST00000298386	T;T	0.39592	1.07;1.07	5.73	5.73	0.89815	GPCR, rhodopsin-like superfamily (1);	0.051378	0.85682	D	0.000000	T	0.62612	0.2442	M	0.89534	3.04	0.58432	D	0.999996	B;B	0.26445	0.149;0.149	B;B	0.39185	0.293;0.168	T	0.65915	-0.6052	10	0.72032	D	0.01	.	18.4913	0.90849	0.0:1.0:0.0:0.0	.	508;532	Q3KU23;Q8WXD0	.;RXFP2_HUMAN	G	508;532	ENSP00000369670:R508G;ENSP00000298386:R532G	ENSP00000298386:R532G	R	+	1	2	RXFP2	31265033	0.033000	0.19621	0.590000	0.28732	0.958000	0.62258	0.768000	0.26590	2.721000	0.93114	0.655000	0.94253	CGA	C|0.999;G|0.001	0.001	strong		0.453	RXFP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044399.1	NM_130806		G	32367033	C	G	32367033	3	3	29	1	0	0	0	0	1	0	0	0	13775	876	31	4	1656	4	RXFP2	13	32367033	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2256777	32367033	82802845	630	12871											
FOXO1	2308	hgsc.bcm.edu	37	chr13	41239736	41239736	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcaccttccagcccgccgagCtgttgctgtcacccttatcc	5	11	7	18	2	2	0	2	0	0	0	4	1	4	0	6	0	3	3	6	0	1	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:41239736C>T	ENST00000379561.5	-	1	998	c.614G>A	c.(613-615)aGc>aAc	p.S205N		NM_002015.3	NP_002006.2	Q12778	FOXO1_HUMAN	forkhead box O1	205					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)		GCCCGCCGAGCTGTTGCTGTC	0.657																																					p.S205N		Atlas-SNP	.											.	FOXO1	110	.	0			c.G614A						PASS	.						35	26	29					13																	41239736		2202	4299	6501	SO:0001583	missense	2308	exon1			GCCGAGCTGTTGC		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.614G>A	13.37:g.41239736C>T	ENSP00000368880:p.Ser205Asn	106	0	0		207	46	0.222222	NM_002015	O43523|Q5VYC7|Q6NSK6	Missense_Mutation	SNP	ENST00000379561.5	37	CCDS9371.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.241699	0.79912	.	.	ENSG00000150907	ENST00000379561	D	0.94966	-3.57	3.93	3.93	0.45458	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.086726	0.85682	D	0.000000	D	0.96197	0.8760	L	0.56396	1.775	0.80722	D	1	D	0.69078	0.997	D	0.80764	0.994	D	0.96779	0.9574	10	0.87932	D	0	-13.4585	14.9379	0.70970	0.0:1.0:0.0:0.0	.	205	Q12778	FOXO1_HUMAN	N	205	ENSP00000368880:S205N	ENSP00000368880:S205N	S	-	2	0	FOXO1	40137736	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	7.074000	0.76791	1.732000	0.51606	0.563000	0.77884	AGC	.	.	none		0.657	FOXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044634.3	NM_002015		T	41239736	C	T	41239736	3	4	29	1	0	0	0	0	1	0	0	0	6031	797	28	2	1361	2	FOXO1	13	41239736	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	8872703	41239736	73930142	631	12872											
FOXO1	2308	hgsc.bcm.edu	37	chr13	41240299	41240299	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcacgagcgcggccggggCagcggctcgaagtccgggtc	5	4	19	13	7	0	0	0	0	0	0	3	2	1	0	2	5	3	3	2	5	1	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:41240299C>A	ENST00000379561.5	-	1	435	c.51G>T	c.(49-51)ctG>ctT	p.L17L		NM_002015.3	NP_002006.2	Q12778	FOXO1_HUMAN	forkhead box O1	17					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)		GCGGCCGGGGCAGCGGCTCGA	0.741																																					p.L17L		Atlas-SNP	.											.	FOXO1	110	.	0			c.G51T						PASS	.						1	2	1					13																	41240299		1153	2574	3727	SO:0001819	synonymous_variant	2308	exon1			CCGGGGCAGCGGC		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.51G>T	13.37:g.41240299C>A		3	0	0		11	5	0.454545	NM_002015	O43523|Q5VYC7|Q6NSK6	Silent	SNP	ENST00000379561.5	37	CCDS9371.1																																																																																			.	.	none		0.741	FOXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044634.3	NM_002015		A	41240299	C	A	41240299	2	1	29	1	0	0	0	0	0	0	0	1	6031	697	25	4		4	FOXO1	13	41240299	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	563	41240299	73929579	632	12873											
TSC22D1	8848	hgsc.bcm.edu	37	chr13	45149973	45149973	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gttcaggctttgtggaggcgGaggctgtggtcccgacgtag	5	10	18	8	3	1	0	1	0	0	0	2	3	2	2	1	6	0	4	1	6	1	3	rs140514784		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:45149973G>A	ENST00000458659.2	-	1	728	c.238C>T	c.(238-240)Ccg>Tcg	p.P80S	TSC22D1_ENST00000501704.2_Missense_Mutation_p.P80S|TSC22D1_ENST00000460842.1_5'Flank	NM_183422.3	NP_904358.2	Q15714	T22D1_HUMAN	TSC22 domain family, member 1	80	Pro-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)		TGTGGAGGCGGAGGCTGTGGT	0.592													G|||	1	0.000199681	0.0	0.0	5008	,	,		17451	0.0		0.0	False		,,,				2504	0.001				p.P80S		Atlas-SNP	.											.	TSC22D1	88	.	0			c.C238T						PASS	.	G	SER/PRO	4,4402	8.1+/-20.4	0,4,2199	58	58	58		238	4.2	1	13	dbSNP_134	58	22,8578	15.3+/-51.7	0,22,4278	yes	missense	TSC22D1	NM_183422.3	74	0,26,6477	AA,AG,GG		0.2558,0.0908,0.1999	possibly-damaging	80/1074	45149973	26,12980	2203	4300	6503	SO:0001583	missense	8848	exon1			GAGGCGGAGGCTG	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.238C>T	13.37:g.45149973G>A	ENSP00000397435:p.Pro80Ser	128	0	0		202	151	0.747525	NM_183422	B3KRL7|B9EGI0|O00666|Q6AHX5|Q6IBU1|Q8NCN1|Q96JS5	Missense_Mutation	SNP	ENST00000458659.2	37	CCDS31966.1	.	.	.	.	.	.	.	.	.	.	G	19.45	3.829773	0.71258	9.08E-4	0.002558	ENSG00000102804	ENST00000458659;ENST00000501704;ENST00000493016	T	0.32272	1.46	4.23	4.23	0.50019	.	0.000000	0.48286	D	0.000189	T	0.18087	0.0434	N	0.14661	0.345	0.33605	D	0.602832	P;P	0.39809	0.573;0.689	B;B	0.36666	0.23;0.186	T	0.28396	-1.0045	10	0.52906	T	0.07	.	11.7357	0.51763	0.0:0.0:0.8231:0.1769	.	80;80	B3KRL7;Q15714	.;T22D1_HUMAN	S	80	ENSP00000397435:P80S	ENSP00000397435:P80S	P	-	1	0	TSC22D1	44047973	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	6.180000	0.71981	2.337000	0.79520	0.561000	0.74099	CCG	G|0.999;A|0.001	0.001	strong		0.592	TSC22D1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044743.2	NM_006022		A	45149973	G	A	45149973	3	1	29	1	0	0	0	0	1	0	0	0	16622	1174	41	2	3124	2	TSC22D1	13	45149973	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	3909674	45149973	70019905	633	12874											
INTS6	26512	hgsc.bcm.edu	37	chr13	51950198	51950198	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctaaccttcgtcctgtcctTtcagaaatctgcgagtgctc	7	14	7	13	2	3	1	1	0	2	1	7	2	5	1	3	0	3	1	3	0	2	3	rs144918317	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:51950198T>C	ENST00000311234.4	-	13	2187	c.1715A>G	c.(1714-1716)aAa>aGa	p.K572R	INTS6_ENST00000490542.1_Missense_Mutation_p.K256R|INTS6_ENST00000425000.1_Missense_Mutation_p.K140R|INTS6_ENST00000463928.1_Intron|INTS6_ENST00000497989.1_Missense_Mutation_p.K394R|INTS6_ENST00000398119.2_Missense_Mutation_p.K559R	NM_012141.2	NP_036273.1	Q9UL03	INT6_HUMAN	integrator complex subunit 6	572					signal transduction (GO:0007165)|snRNA processing (GO:0016180)	actin cytoskeleton (GO:0015629)|integrator complex (GO:0032039)|nucleus (GO:0005634)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Breast(56;0.000286)|Lung NSC(96;0.00145)|Prostate(109;0.00403)|Hepatocellular(98;0.065)|Myeloproliferative disorder(33;0.163)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;7.7e-08)		GTCCTGTCCTTTCAGAAATCT	0.323													T|||	3	0.000599042	0.0	0.0	5008	,	,		16958	0.0		0.003	False		,,,				2504	0.0				p.K572R		Atlas-SNP	.											.	INTS6	72	.	0			c.A1715G						PASS	.	T	ARG/LYS,ARG/LYS	1,4405	2.1+/-5.4	0,1,2202	89	87	87		1676,1715	5.5	1	13	dbSNP_134	87	12,8588	8.4+/-32.0	0,12,4288	yes	missense,missense	INTS6	NM_001039937.1,NM_012141.2	26,26	0,13,6490	CC,CT,TT		0.1395,0.0227,0.1	benign,benign	559/875,572/888	51950198	13,12993	2203	4300	6503	SO:0001583	missense	26512	exon13			TGTCCTTTCAGAA	AF097645	CCDS9428.1, CCDS41890.1, CCDS45048.1	13q14.3	2010-08-20	2006-03-15	2006-03-15	ENSG00000102786	ENSG00000102786		"DEAD-boxes"	14879	protein-coding gene	gene with protein product		604331	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 26"	DDX26		10467397, 16239144	Standard	XM_005266340		Approved	DICE1, HDB, Notchl2, DBI-1, DDX26A, INT6	uc001vfk.3	Q9UL03	OTTHUMG00000016945	ENST00000311234.4:c.1715A>G	13.37:g.51950198T>C	ENSP00000310260:p.Lys572Arg	67	0	0		87	26	0.298851	NM_012141	Q0P664|Q6PJP4|Q9UFK0|Q9Y5M9	Missense_Mutation	SNP	ENST00000311234.4	37	CCDS9428.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	9.746	1.166106	0.21621	2.27E-4	0.001395	ENSG00000102786	ENST00000311234;ENST00000398119;ENST00000497989;ENST00000425000;ENST00000490542	T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55	5.48	5.48	0.80851	.	0.049655	0.85682	D	0.000000	T	0.19485	0.0468	N	0.16233	0.39	0.80722	D	1	B	0.06786	0.001	B	0.08055	0.003	T	0.07908	-1.0748	10	0.13853	T	0.58	-20.7448	14.7523	0.69536	0.0:0.0:0.0:1.0	.	572	Q9UL03	INT6_HUMAN	R	572;559;394;140;256	ENSP00000310260:K572R;ENSP00000381187:K559R;ENSP00000419871:K394R;ENSP00000406915:K140R;ENSP00000419984:K256R	ENSP00000310260:K572R	K	-	2	0	INTS6	50848199	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.248000	0.58760	2.085000	0.62840	0.528000	0.53228	AAA	T|0.999;C|0.001	0.001	strong		0.323	INTS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045023.1	NM_012141		C	51950198	T	C	51950198	3	2	29	1	0	0	0	0	1	0	0	0	7791	1841	64	3	972	3	INTS6	13	51950198	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	6800225	51950198	63219680	634	12875											
NEK5	341676	hgsc.bcm.edu	37	chr13	52661569	52661569	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tctctggttgtaatttggctCggcagaagatggacgaagac	10	11	13	7	2	1	3	0	0	1	3	3	5	1	4	0	4	0	4	0	4	3	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:52661569C>T	ENST00000355568.4	-	15	1436	c.1297G>A	c.(1297-1299)Gag>Aag	p.E433K		NM_199289.1	NP_954983.1	Q6P3R8	NEK5_HUMAN	NIMA-related kinase 5	433					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)		TAATTTGGCTCGGCAGAAGAT	0.368																																					p.E433K		Atlas-SNP	.											.	NEK5	189	.	0			c.G1297A						PASS	.						130	121	124					13																	52661569		2203	4300	6503	SO:0001583	missense	341676	exon15			TTGGCTCGGCAGA	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.1297G>A	13.37:g.52661569C>T	ENSP00000347767:p.Glu433Lys	82	0	0		126	65	0.515873	NM_199289	Q5TAP5	Missense_Mutation	SNP	ENST00000355568.4	37	CCDS31979.1	.	.	.	.	.	.	.	.	.	.	C	19.47	3.833151	0.71258	.	.	ENSG00000197168	ENST00000355568	T	0.74421	-0.84	5.45	5.45	0.79879	.	0.090427	0.47455	D	0.000234	T	0.78355	0.4270	L	0.59436	1.845	0.29341	N	0.866027	D	0.71674	0.998	P	0.52793	0.709	T	0.75560	-0.3275	10	0.41790	T	0.15	.	14.7893	0.69827	0.0:1.0:0.0:0.0	.	433	Q6P3R8	NEK5_HUMAN	K	433	ENSP00000347767:E433K	ENSP00000347767:E433K	E	-	1	0	NEK5	51559570	1.000000	0.71417	0.798000	0.32154	0.440000	0.31957	3.947000	0.56652	2.548000	0.85928	0.655000	0.94253	GAG	.	.	none		0.368	NEK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045045.3	NM_199289		T	52661569	C	T	52661569	3	4	29	1	0	0	0	0	1	0	0	0	10336	893	31	1	861	1	NEK5	13	52661569	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	711371	52661569	62508309	635	12876											
PCDH17	27253	hgsc.bcm.edu	37	chr13	58208047	58208047	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcctcccctcaactccaccaAgtcgttcgcgatcaagattc	9	10	5	17	3	2	1	2	0	0	1	8	2	5	1	5	0	1	1	5	0	3	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:58208047A>C	ENST00000377918.3	+	1	1393	c.1367A>C	c.(1366-1368)aAg>aCg	p.K456T		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	456	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)		AACTCCACCAAGTCGTTCGCG	0.607																																					p.K456T	Melanoma(72;952 1291 1619 12849 33676)	Atlas-SNP	.											PCDH17,colon,carcinoma,-1,1	PCDH17	304	1	0			c.A1367C						PASS	.						53	43	46					13																	58208047		2202	4300	6502	SO:0001583	missense	27253	exon1			CCACCAAGTCGTT	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.1367A>C	13.37:g.58208047A>C	ENSP00000367151:p.Lys456Thr	47	0	0		63	10	0.15873	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Missense_Mutation	SNP	ENST00000377918.3	37	CCDS31986.1	.	.	.	.	.	.	.	.	.	.	A	17.13	3.309656	0.60414	.	.	ENSG00000118946	ENST00000377918	T	0.42131	0.98	5.58	5.58	0.84498	Cadherin (5);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.54255	0.1847	L	0.35644	1.08	0.50813	D	0.999899	D;D	0.76494	0.997;0.999	D;D	0.77557	0.959;0.99	T	0.50550	-0.8815	9	.	.	.	.	15.7465	0.77949	1.0:0.0:0.0:0.0	.	456;456	O14917-2;O14917	.;PCD17_HUMAN	T	456	ENSP00000367151:K456T	.	K	+	2	0	PCDH17	57106048	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.962000	0.93254	2.133000	0.65898	0.459000	0.35465	AAG	.	.	none		0.607	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		C	58208047	A	C	58208047	3	2	29	1	0	0	0	0	1	0	0	0	11521	72	3	5	1369	5	PCDH17	13	58208047	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	5546478	58208047	56961831	636	12877											
PCDH9	5101	hgsc.bcm.edu	37	chr13	67802190	67802190	+	Frame_Shift_Del	DEL	A	A	-																															tatccttgacaattatttttAttttgatcagcctgaagaaa																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:67802190delA	ENST00000377865.2	-	1	517	c.383delT	c.(382-384)atafs	p.I128fs	PCDH9_ENST00000328454.5_Frame_Shift_Del_p.I128fs|PCDH9_ENST00000456367.1_Frame_Shift_Del_p.I128fs|PCDH9_ENST00000544246.1_Frame_Shift_Del_p.I128fs|PCDH9_ENST00000377861.3_Frame_Shift_Del_p.I128fs			Q9HC56	PCDH9_HUMAN	protocadherin 9	128	Cadherin 1. {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)		AATTATTTTTATTTTGATCAG	0.408																																					p.I128fs		Atlas-Indel	.											.	PCDH9	252	.	0			c.384delA						PASS	.						87	89	88					13																	67802190		2203	4300	6503	SO:0001589	frameshift_variant	5101	exon2			.	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.383delT	13.37:g.67802190delA	ENSP00000367096:p.Ile128fs	103	0	0		154	12	0.0779221	NM_020403	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Frame_Shift_Del	DEL	ENST00000377865.2	37	CCDS9444.1																																																																																			.	.	none		0.408	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487		-	67802190	A	-	67802190	7	5	29	1	0	1	0	1	0	0	0	0	11527	449	16	0	3346	0	PCDH9	13	67802190	Frame_Shift_Del	DEL	A	TCGA-GR-7351-01A-11D-2210-10	9594143	67802190	47367688	637	12878											
DIS3	22894	hgsc.bcm.edu	37	chr13	73340177	73340177	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	catgtggaatcgaacttcagGagaggatagagtcaaagccc	14	7	12	8	1	2	2	2	0	0	2	3	6	2	4	1	3	2	0	1	3	4	2	rs35017269	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:73340177G>A	ENST00000377767.4	-	15	2003	c.1903C>T	c.(1903-1905)Cct>Tct	p.P635S	DIS3_ENST00000545453.1_Missense_Mutation_p.P473S|DIS3_ENST00000377780.4_Missense_Mutation_p.P605S	NM_014953.3	NP_055768.3	Q9Y2L1	RRP44_HUMAN	DIS3 exosome endoribonuclease and 3'-5' exoribonuclease	635				P -> S (in Ref. 7; CAH56266). {ECO:0000305}.	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)		CGAACTTCAGGAGAGGATAGA	0.328										Multiple Myeloma(4;0.011)			G|||	41	0.0081869	0.003	0.0144	5008	,	,		13716	0.002		0.007	False		,,,				2504	0.0184				p.P635S		Atlas-SNP	.											.	DIS3	103	.	0			c.C1903T						PASS	.	G	SER/PRO,SER/PRO	14,4392	23.3+/-48.9	0,14,2189	43	42	43		1813,1903	6	1	13	dbSNP_126	43	134,8466	64.9+/-127.2	1,132,4167	yes	missense,missense	DIS3	NM_001128226.1,NM_014953.3	74,74	1,146,6356	AA,AG,GG		1.5581,0.3177,1.1379	benign,benign	605/929,635/959	73340177	148,12858	2203	4300	6503	SO:0001583	missense	22894	exon15			CTTCAGGAGAGGA	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.1903C>T	13.37:g.73340177G>A	ENSP00000366997:p.Pro635Ser	23	0	0		25	15	0.6	NM_014953	A6NI21|B2RBL2|Q5W0P7|Q5W0P8|Q658Z7|Q7Z481|Q8WWI2|Q9UG36	Missense_Mutation	SNP	ENST00000377767.4	37	CCDS9447.1	18	0.008241758241758242	4	0.008130081300813009	8	0.022099447513812154	0	0.0	6	0.0079155672823219	G	16.70	3.197149	0.58126	0.003177	0.015581	ENSG00000083520	ENST00000377767;ENST00000377780;ENST00000545453	T;T;T	0.38240	1.15;1.15;1.15	6.04	6.04	0.98038	Ribonuclease II/R (2);	0.054605	0.64402	D	0.000001	T	0.28267	0.0698	L	0.41356	1.27	0.58432	D	0.999999	P;P	0.41947	0.723;0.766	P;P	0.49387	0.474;0.609	T	0.00885	-1.1527	10	0.26408	T	0.33	.	20.5948	0.99439	0.0:0.0:1.0:0.0	rs35017269	605;635	Q9Y2L1-2;Q9Y2L1	.;RRP44_HUMAN	S	635;605;473	ENSP00000366997:P635S;ENSP00000367011:P605S;ENSP00000440058:P473S	ENSP00000366997:P635S	P	-	1	0	DIS3	72238178	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	6.518000	0.73764	2.873000	0.98535	0.563000	0.77884	CCT	G|0.989;A|0.011	0.011	strong		0.328	DIS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045250.2	NM_014953		A	73340177	G	A	73340177	3	1	29	1	0	0	0	0	1	0	0	0	4537	1174	41	2	1001	2	DIS3	13	73340177	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	5537987	73340177	41829701	638	12879											
GPC6	10082	hgsc.bcm.edu	37	chr13	94482567	94482567	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aatgtgaatctggaggaaatGctcaatgacttttgggctcg	11	12	12	6	1	2	2	1	2	1	0	3	4	2	4	0	3	1	2	0	3	4	2	rs369251626		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:94482567G>A	ENST00000377047.4	+	3	1095	c.480G>A	c.(478-480)atG>atA	p.M160I	GPC6-AS2_ENST00000445540.1_RNA	NM_005708.3	NP_005699.1	Q9Y625	GPC6_HUMAN	glypican 6	160					carbohydrate metabolic process (GO:0005975)|cell migration (GO:0016477)|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)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(13)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	38	all_neural(89;0.0684)|Medulloblastoma(90;0.163)	all_cancers(2;5.48e-07)|all_epithelial(2;5.69e-08)|all_lung(2;2.19e-05)|Lung NSC(4;6.09e-05)|Breast(118;0.0395)|Renal(2;0.0568)|Hepatocellular(115;0.217)				TGGAGGAAATGCTCAATGACT	0.463																																					p.M160I		Atlas-SNP	.											.	GPC6	102	.	0			c.G480A						PASS	.	G	ILE/MET	0,4406		0,0,2203	116	114	115		480	5.5	1	13		115	1,8599	1.2+/-3.3	0,1,4299	no	missense	GPC6	NM_005708.3	10	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	160/556	94482567	1,13005	2203	4300	6503	SO:0001583	missense	10082	exon3			GGAAATGCTCAAT	AF111178	CCDS9469.1	13q32	2008-02-05			ENSG00000183098	ENSG00000183098		"Proteoglycans / Cell Surface : Glypicans"	4454	protein-coding gene	gene with protein product	"glypican proteoglycan 6"	604404				10329016	Standard	NM_005708		Approved		uc001vlt.3	Q9Y625	OTTHUMG00000017205	ENST00000377047.4:c.480G>A	13.37:g.94482567G>A	ENSP00000366246:p.Met160Ile	94	0	0		127	77	0.606299	NM_005708	A8K279|Q96SG5|Q96SG8|Q9H1P4	Missense_Mutation	SNP	ENST00000377047.4	37	CCDS9469.1	.	.	.	.	.	.	.	.	.	.	G	14.48	2.547215	0.45383	0.0	1.16E-4	ENSG00000183098	ENST00000377047	T	0.51071	0.72	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.47469	0.1447	M	0.65677	2.01	0.33212	D	0.553497	B;B	0.10296	0.002;0.003	B;B	0.18263	0.021;0.012	T	0.53641	-0.8410	10	0.28530	T	0.3	.	14.6399	0.68717	0.0:0.0:0.8545:0.1455	.	160;160	B4E2M1;Q9Y625	.;GPC6_HUMAN	I	160	ENSP00000366246:M160I	ENSP00000366246:M160I	M	+	3	0	GPC6	93280568	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	7.447000	0.80620	2.775000	0.95449	0.650000	0.86243	ATG	.	.	weak		0.463	GPC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045460.4	NM_005708		A	94482567	G	A	94482567	3	1	29	1	0	0	0	0	1	0	0	0	6610	1319	46	2	490	2	GPC6	13	94482567	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	21142390	94482567	20687311	639	12880											
ABCC4	10257	hgsc.bcm.edu	37	chr13	95696540	95696540	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cttggatccacatttgccgtCgcttcatcaataatcaatat	11	14	5	11	2	3	0	3	0	0	0	5	1	4	1	2	1	1	1	2	1	4	5	rs11568695	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:95696540C>T	ENST00000376887.4	-	28	3723	c.3609G>A	c.(3607-3609)gcG>gcA	p.A1203A	ABCC4_ENST00000412704.1_Silent_p.A1156A	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	1203	ABC transporter 2. {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)	CATTTGCCGTCGCTTCATCAA	0.398													C|||	225	0.0449281	0.1604	0.013	5008	,	,		19815	0.001		0.002	False		,,,				2504	0.001				p.A1203A		Atlas-SNP	.											ABCC4_ENST00000376887,colon,carcinoma,-1,2	ABCC4	248	2	0			c.G3609A						PASS	.	C		644,3762	270.4+/-269.6	52,540,1611	72	64	66		3609	-6.7	0.9	13	dbSNP_126	66	10,8590	7.1+/-27.0	0,10,4290	no	coding-synonymous	ABCC4	NM_005845.3		52,550,5901	TT,TC,CC		0.1163,14.6164,5.0284		1203/1326	95696540	654,12352	2203	4300	6503	SO:0001819	synonymous_variant	10257	exon28			TGCCGTCGCTTCA	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.3609G>A	13.37:g.95696540C>T		95	0	0		126	72	0.571429	NM_005845	A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Silent	SNP	ENST00000376887.4	37	CCDS9474.1																																																																																			C|0.950;T|0.050	0.050	strong		0.398	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045478.2	NM_005845		T	95696540	C	T	95696540	2	4	29	1	0	0	0	0	0	0	0	1	55	871	31	1		1	ABCC4	13	95696540	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1213973	95696540	19473338	640	12881											
ABCC4	10257	hgsc.bcm.edu	37	chr13	95715014	95715014	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagtccaatttcagttgtcaAgatcttatcaatccaaattt	14	15	4	8	0	4	1	3	0	1	1	6	1	6	1	2	0	0	1	2	0	6	4	rs11568655	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:95715014A>G	ENST00000376887.4	-	26	3424	c.3310T>C	c.(3310-3312)Ttg>Ctg	p.L1104L	ABCC4_ENST00000412704.1_Silent_p.L1057L	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	1104	ABC transporter 2. {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)	TCAGTTGTCAAGATCTTATCA	0.423													A|||	130	0.0259585	0.093	0.0086	5008	,	,		16253	0.0		0.001	False		,,,				2504	0.0				p.L1104L		Atlas-SNP	.											.	ABCC4	248	.	0			c.T3310C						PASS	.	A		368,4038	187.8+/-214.3	17,334,1852	130	122	124		3310	6.2	1	13	dbSNP_126	124	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ABCC4	NM_005845.3		17,336,6150	GG,GA,AA		0.0233,8.3522,2.8448		1104/1326	95715014	370,12636	2203	4300	6503	SO:0001819	synonymous_variant	10257	exon26			TTGTCAAGATCTT	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.3310T>C	13.37:g.95715014A>G		71	0	0		81	43	0.530864	NM_005845	A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Silent	SNP	ENST00000376887.4	37	CCDS9474.1																																																																																			A|0.966;G|0.034	0.034	strong		0.423	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045478.2	NM_005845		G	95715014	A	G	95715014	2	3	29	1	0	0	0	0	0	0	0	1	55	69	3	3		3	ABCC4	13	95715014	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	18474	95715014	19454864	641	12882											
BIVM	54841	hgsc.bcm.edu	37	chr13	103460019	103460019	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaaaacttatccaacagcctGggcaagctacctctcgcatg	12	8	8	13	1	1	0	0	0	1	0	3	1	2	0	3	1	5	3	3	1	6	2	rs111947510	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:103460019G>A	ENST00000257336.1	+	3	1081	c.402G>A	c.(400-402)ctG>ctA	p.L134L	BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.G106R|BIVM_ENST00000419638.1_Silent_p.L134L|BIVM_ENST00000448849.2_Intron	NM_017693.3	NP_060163.2	Q86UB2	BIVM_HUMAN	basic, immunoglobulin-like variable motif containing	134						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)					CCAACAGCCTGGGCAAGCTAC	0.403													G|||	29	0.00579073	0.0219	0.0	5008	,	,		20084	0.0		0.0	False		,,,				2504	0.0				p.L134L		Atlas-SNP	.											.	.	.	.	0			c.G402A						PASS	.	G	,,	97,4309	73.6+/-111.7	4,89,2110	41	42	42		,402,402	2.3	1	13	dbSNP_132	42	0,8600		0,0,4300	no	intron,coding-synonymous,coding-synonymous	BIVM,BIVM-ERCC5	NM_001159596.1,NM_001204425.1,NM_017693.3	,,	4,89,6410	AA,AG,GG		0.0,2.2015,0.7458	,,	,134/1641,134/504	103460019	97,12909	2203	4300	6503	SO:0001819	synonymous_variant	0	exon1			CAGCCTGGGCAAG	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.402G>A	13.37:g.103460019G>A		89	0	0		66	21	0.318182	NM_001204425	Q2M1J2|Q9NXM4	Silent	SNP	ENST00000257336.1	37	CCDS9505.1																																																																																			G|0.991;A|0.009	0.009	strong		0.403	BIVM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045704.2			A	103460019	G	A	103460019	2	1	29	1	0	0	0	0	0	0	0	1	1441	1335	47	2		2	BIVM	13	103460019	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	7745005	103460019	11709859	642	12883											
LIG4	3981	hgsc.bcm.edu	37	chr13	108861048	108861048	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tacatgagacactccctcagCtaaacaagaaactacttttg	15	10	5	11	0	1	2	1	1	0	2	2	3	2	2	1	0	5	1	1	0	6	5	rs2232642	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:108861048C>T	ENST00000356922.4	-	2	2841	c.2569G>A	c.(2569-2571)Gct>Act	p.A857T	LIG4_ENST00000442234.1_Missense_Mutation_p.A857T|LIG4_ENST00000405925.1_Missense_Mutation_p.A857T	NM_002312.3|NM_206937.1	NP_002303.2|NP_996820.1	P49917	DNLI4_HUMAN	ligase IV, DNA, ATP-dependent	857	BRCT 2. {ECO:0000255|PROSITE- ProRule:PRU00033}.		A -> T (in dbSNP:rs2232642). {ECO:0000269|Ref.2}.		cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|chromosome organization (GO:0051276)|DNA biosynthetic process (GO:0071897)|DNA ligation (GO:0006266)|DNA ligation involved in DNA recombination (GO:0051102)|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)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|lagging strand elongation (GO:0006273)|negative regulation of neuron apoptotic process (GO:0043524)|neuron apoptotic process (GO:0051402)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|single strand break repair (GO:0000012)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|focal adhesion (GO:0005925)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					ACTCCCTCAGCTAAACAAGAA	0.363								Non-homologous end-joining					C|||	177	0.0353435	0.1263	0.0144	5008	,	,		17213	0.0		0.0	False		,,,				2504	0.0				p.A857T		Atlas-SNP	.											.	LIG4	91	.	0			c.G2569A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	442,3964	211.8+/-231.9	27,388,1788	105	104	105		2569,2569,2569	2.9	1	13	dbSNP_98	105	4,8596	3.0+/-9.4	0,4,4296	yes	missense,missense,missense	LIG4	NM_001098268.1,NM_002312.3,NM_206937.1	58,58,58	27,392,6084	TT,TC,CC		0.0465,10.0318,3.4292	benign,benign,benign	857/912,857/912,857/912	108861048	446,12560	2203	4300	6503	SO:0001583	missense	3981	exon3			CCTCAGCTAAACA	X83441	CCDS9508.1	13q33-q34	2014-09-17			ENSG00000174405	ENSG00000174405	6.5.1.1		6601	protein-coding gene	gene with protein product	"polydeoxyribonucleotide synthase [ATP] 4", "polynucleotide ligase", "sealase", "DNA repair enzyme", "DNA joinase"	601837				7760816	Standard	NM_001098268		Approved		uc001vqo.3	P49917	OTTHUMG00000017328	ENST00000356922.4:c.2569G>A	13.37:g.108861048C>T	ENSP00000349393:p.Ala857Thr	107	0	0		79	21	0.265823	NM_206937	Q8IY66|Q8TEU5	Missense_Mutation	SNP	ENST00000356922.4	37	CCDS9508.1	73	0.033424908424908424	69	0.1402439024390244	4	0.011049723756906077	0	0.0	0	0.0	C	14.05	2.419038	0.42918	0.100318	4.65E-4	ENSG00000174405	ENST00000405925;ENST00000442234;ENST00000356922	T;T;T	0.77489	-1.1;-1.1;-1.1	5.75	2.86	0.33363	BRCT (4);	0.233058	0.43110	N	0.000618	T	0.00845	0.0028	L	0.44542	1.39	0.48040	P	4.2600000000003746E-4	B	0.10296	0.003	B	0.06405	0.002	T	0.12400	-1.0549	9	0.18276	T	0.48	.	6.1326	0.20213	0.1432:0.6532:0.1303:0.0734	rs2232642;rs52801587;rs2232642	857	P49917	DNLI4_HUMAN	T	857	ENSP00000385955:A857T;ENSP00000402030:A857T;ENSP00000349393:A857T	ENSP00000349393:A857T	A	-	1	0	LIG4	107659049	0.983000	0.35010	0.997000	0.53966	0.961000	0.63080	1.621000	0.36986	0.749000	0.32854	0.567000	0.79289	GCT	C|0.958;T|0.042	0.042	strong		0.363	LIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045738.4	NM_002312		T	108861048	C	T	108861048	3	4	29	1	0	0	0	0	1	0	0	0	8792	797	28	2	170	2	LIG4	13	108861048	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	5401029	108861048	6308830	643	12884											
LIG4	3981	hgsc.bcm.edu	37	chr13	108862810	108862810	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccatctagcttggtttctatGtagaaactctgatgtttcat	9	17	7	8	0	4	2	1	1	3	1	4	2	4	2	1	1	2	4	1	1	4	6	rs2232638	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:108862810G>A	ENST00000356922.4	-	2	1079	c.807C>T	c.(805-807)taC>taT	p.Y269Y	LIG4_ENST00000442234.1_Silent_p.Y269Y|LIG4_ENST00000405925.1_Silent_p.Y269Y	NM_002312.3|NM_206937.1	NP_002303.2|NP_996820.1	P49917	DNLI4_HUMAN	ligase IV, DNA, ATP-dependent	269					cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|chromosome organization (GO:0051276)|DNA biosynthetic process (GO:0071897)|DNA ligation (GO:0006266)|DNA ligation involved in DNA recombination (GO:0051102)|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)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|lagging strand elongation (GO:0006273)|negative regulation of neuron apoptotic process (GO:0043524)|neuron apoptotic process (GO:0051402)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|single strand break repair (GO:0000012)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|focal adhesion (GO:0005925)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	42	all_lung(23;0.000238)|all_neural(89;0.00256)|Lung NSC(43;0.0056)|Medulloblastoma(90;0.00596)|Lung SC(71;0.104)					TGGTTTCTATGTAGAAACTCT	0.343								Non-homologous end-joining					G|||	177	0.0353435	0.1263	0.0144	5008	,	,		21707	0.0		0.0	False		,,,				2504	0.0				p.Y269Y		Atlas-SNP	.											.	LIG4	91	.	0			c.C807T						PASS	.	G	,,	443,3963	204.5+/-226.7	28,387,1788	68	66	67		807,807,807	4.7	1	13	dbSNP_98	67	4,8594	3.0+/-9.4	0,4,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	LIG4	NM_001098268.1,NM_002312.3,NM_206937.1	,,	28,391,6083	AA,AG,GG		0.0465,10.0545,3.4374	,,	269/912,269/912,269/912	108862810	447,12557	2203	4299	6502	SO:0001819	synonymous_variant	3981	exon3			TTCTATGTAGAAA	X83441	CCDS9508.1	13q33-q34	2014-09-17			ENSG00000174405	ENSG00000174405	6.5.1.1		6601	protein-coding gene	gene with protein product	"polydeoxyribonucleotide synthase [ATP] 4", "polynucleotide ligase", "sealase", "DNA repair enzyme", "DNA joinase"	601837				7760816	Standard	NM_001098268		Approved		uc001vqo.3	P49917	OTTHUMG00000017328	ENST00000356922.4:c.807C>T	13.37:g.108862810G>A		103	0	0		72	14	0.194444	NM_206937	Q8IY66|Q8TEU5	Silent	SNP	ENST00000356922.4	37	CCDS9508.1																																																																																			G|0.956;A|0.044	0.044	strong		0.343	LIG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045738.4	NM_002312		A	108862810	G	A	108862810	2	1	29	1	0	0	0	0	0	0	0	1	8792	1372	48	2		2	LIG4	13	108862810	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1762	108862810	6307068	644	12885											
COL4A2	1284	hgsc.bcm.edu	37	chr13	111102770	111102770	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aagcgagggcctccaggaccCcccgggctccctggaccacc	7	3	12	19	2	0	0	0	0	0	0	2	3	2	2	8	4	1	1	8	4	1	0	rs78615289	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:111102770C>T	ENST00000360467.5	+	20	1614	c.1308C>T	c.(1306-1308)ccC>ccT	p.P436P		NM_001846.2	NP_001837.2	P08572	CO4A2_HUMAN	collagen, type IV, alpha 2	436	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)			CTCCAGGACCCCCCGGGCTCC	0.642													C|||	62	0.0123802	0.0461	0.0014	5008	,	,		16297	0.0		0.0	False		,,,				2504	0.0				p.P436P		Atlas-SNP	.											.	COL4A2	178	.	0			c.C1308T						PASS	.	C		98,3596		1,96,1750	30	35	34		1308	-1.9	0	13	dbSNP_131	34	4,8174		0,4,4085	yes	coding-synonymous	COL4A2	NM_001846.2		1,100,5835	TT,TC,CC		0.0489,2.653,0.8592		436/1713	111102770	102,11770	1847	4089	5936	SO:0001819	synonymous_variant	1284	exon20			AGGACCCCCCGGG	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.1308C>T	13.37:g.111102770C>T		28	0	0		18	8	0.444444	NM_001846	Q14052|Q548C3|Q5VZA9|Q66K23	Silent	SNP	ENST00000360467.5	37	CCDS41907.1																																																																																			C|0.984;T|0.016	0.016	strong		0.642	COL4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045761.2	NM_001846		T	111102770	C	T	111102770	2	4	29	1	0	0	0	0	0	0	0	1	3692	610	22	2		2	COL4A2	13	111102770	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2239960	111102770	4067108	645	12886											
CARKD	55739	hgsc.bcm.edu	37	chr13	111287893	111287893	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccctgggcaacgtgacggtgGtccagaaaggagagcgcgac	10	4	16	11	4	0	3	0	1	0	2	1	5	1	3	2	4	2	1	2	4	2	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:111287893G>C	ENST00000309957.2	+	8	744	c.730G>C	c.(730-732)Gtc>Ctc	p.V244L	CARKD_ENST00000470164.2_3'UTR|CARKD_ENST00000458711.2_Missense_Mutation_p.V113L|CARKD_ENST00000424185.2_Missense_Mutation_p.V134L	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						CGTGACGGTGGTCCAGAAAGG	0.602																																					p.V244L		Atlas-SNP	.											.	CARKD	36	.	0			c.G730C						PASS	.						152	138	143					13																	111287893		2203	4300	6503	SO:0001583	missense	55739	exon8			ACGGTGGTCCAGA	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.730G>C	13.37:g.111287893G>C	ENSP00000311984:p.Val244Leu	91	0	0		55	40	0.727273	NM_018210		Missense_Mutation	SNP	ENST00000309957.2	37	CCDS9513.1	.	.	.	.	.	.	.	.	.	.	G	13.04	2.118803	0.37436	.	.	ENSG00000213995	ENST00000458711;ENST00000424185;ENST00000439607;ENST00000309957	T;T;T	0.23147	1.92;1.92;1.92	4.86	4.86	0.63082	Uncharacterised domain, carbohydrate kinase-related (3);	0.063290	0.64402	D	0.000006	T	0.21387	0.0515	N	0.20845	0.615	0.80722	D	1	D;P;B;B;B	0.55385	0.971;0.627;0.071;0.34;0.025	P;B;B;B;B	0.51079	0.658;0.329;0.047;0.085;0.047	T	0.02471	-1.1154	10	0.12430	T	0.62	-35.4382	11.1693	0.48563	0.086:0.0:0.914:0.0	.	113;134;226;244;244	B4DQR1;Q8IW45-4;B4DKX7;Q8IW45-2;Q8IW45	.;.;.;.;CARKD_HUMAN	L	113;134;226;244	ENSP00000412789:V113L;ENSP00000413191:V134L;ENSP00000311984:V244L	ENSP00000311984:V244L	V	+	1	0	CARKD	110085894	1.000000	0.71417	0.063000	0.19743	0.245000	0.25701	3.457000	0.53007	2.210000	0.71456	0.462000	0.41574	GTC	.	.	none		0.602	CARKD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045764.1	NM_018210		C	111287893	G	C	111287893	3	2	29	1	0	0	0	0	1	0	0	0	2656	1261	44	4	760	4	CARKD	13	111287893	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	185123	111287893	3881985	646	12887											
TUBGCP3	10426	hgsc.bcm.edu	37	chr13	113140350	113140350	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctggtacccagagacacaCggagcctgggctccctggct	7	6	12	16	1	0	1	0	0	0	1	1	3	1	2	4	4	2	3	4	4	1	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr13:113140350C>T	ENST00000261965.3	-	22	2867	c.2681G>A	c.(2680-2682)cGt>cAt	p.R894H		NM_006322.4	NP_006313.1	Q96CW5	GCP3_HUMAN	tubulin, gamma complex associated protein 3	894					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)					CAGAGACACACGGAGCCTGGG	0.582																																					p.R894H		Atlas-SNP	.											.	TUBGCP3	74	.	0			c.G2681A						PASS	.						35	29	31					13																	113140350		2202	4295	6497	SO:0001583	missense	10426	exon22			GACACACGGAGCC	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.2681G>A	13.37:g.113140350C>T	ENSP00000261965:p.Arg894His	154	0	0		150	101	0.673333	NM_006322	O43631|O60852|O60853|Q5T8L2|Q7Z4K1|Q96I79	Missense_Mutation	SNP	ENST00000261965.3	37	CCDS9525.1	.	.	.	.	.	.	.	.	.	.	C	16.22	3.062569	0.55432	.	.	ENSG00000126216	ENST00000261965	T	0.24908	1.83	4.64	3.74	0.42951	.	0.060412	0.64402	N	0.000002	T	0.35682	0.0940	L	0.47716	1.5	0.80722	D	1	D;D	0.69078	0.997;0.997	P;P	0.56865	0.722;0.808	T	0.05115	-1.0905	10	0.45353	T	0.12	-11.4016	12.0433	0.53464	0.0:0.9099:0.0:0.0901	.	884;894	B4DYP7;Q96CW5	.;GCP3_HUMAN	H	894	ENSP00000261965:R894H	ENSP00000261965:R894H	R	-	2	0	TUBGCP3	112188351	0.999000	0.42202	0.028000	0.17463	0.268000	0.26511	4.824000	0.62701	0.964000	0.38108	-0.345000	0.07892	CGT	.	.	none		0.582	TUBGCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045825.2	NM_006322		T	113140350	C	T	113140350	3	4	29	1	0	0	0	0	1	0	0	0	16782	536	19	1	46	1	TUBGCP3	13	113140350	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1852457	113140350	2029528	647	12888											
OR4K17	390436	hgsc.bcm.edu	37	chr14	20585769	20585769	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttctcggttatctatgtggtCacagttttgggtaaccttct	6	18	9	8	1	4	0	1	0	3	0	5	0	4	0	1	3	1	3	1	3	3	7			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:20585769C>T	ENST00000315543.4	+	1	204	c.204C>T	c.(202-204)gtC>gtT	p.V68V		NM_001004715.1	NP_001004715.1	Q8NGC6	OR4KH_HUMAN	olfactory receptor, family 4, subfamily K, member 17	40						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)		TCTATGTGGTCACAGTTTTGG	0.398																																					p.V68V		Atlas-SNP	.											.	OR4K17	58	.	0			c.C204T						PASS	.						305	290	295					14																	20585769		2203	4300	6503	SO:0001819	synonymous_variant	390436	exon1			TGTGGTCACAGTT		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.204C>T	14.37:g.20585769C>T		267	0	0		205	95	0.463415	NM_001004715	Q6IF12	Silent	SNP	ENST00000315543.4	37	CCDS32030.1																																																																																			.	.	none		0.398	OR4K17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410346.1			T	20585769	C	T	20585769	2	4	29	1	0	0	0	0	0	0	0	1	11080	813	29	2		2	OR4K17	14	20585769	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10		20585769	86763771	648	12889											
OR4E2	26686	hgsc.bcm.edu	37	chr14	22133692	22133692	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	atctgcactccactccactaCcccaatgtgatgaacatgag	12	9	6	14	0	1	3	0	3	1	0	3	3	3	3	4	0	3	1	4	0	3	1	rs553173765		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:22133692C>A	ENST00000408935.1	+	1	396	c.396C>A	c.(394-396)taC>taA	p.Y132*		NM_001001912.1	NP_001001912.1	Q8NGC2	OR4E2_HUMAN	olfactory receptor, family 4, subfamily E, 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)|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)		CACTCCACTACCCCAATGTGA	0.488													C|||	1	0.000199681	0.0008	0.0	5008	,	,		23178	0.0		0.0	False		,,,				2504	0.0				p.Y132X		Atlas-SNP	.											.	OR4E2	44	.	0			c.C396A						PASS	.						190	178	182					14																	22133692		2036	4208	6244	SO:0001587	stop_gained	26686	exon1			CCACTACCCCAAT		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.396C>A	14.37:g.22133692C>A	ENSP00000386195:p.Tyr132*	210	0	0		196	95	0.484694	NM_001001912	Q6IET6|Q96R62	Nonsense_Mutation	SNP	ENST00000408935.1	37	CCDS41916.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.532044	0.85812	.	.	ENSG00000221977	ENST00000408935	.	.	.	5.78	1.91	0.25777	.	0.000000	0.34828	U	0.003654	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.3593	0.32348	0.0:0.6039:0.0:0.3961	.	.	.	.	X	132	.	ENSP00000386195:Y132X	Y	+	3	2	OR4E2	21203532	0.421000	0.25465	0.765000	0.31456	0.943000	0.58893	0.966000	0.29331	0.364000	0.24374	0.585000	0.79938	TAC	.	.	none		0.488	OR4E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401874.1			A	22133692	C	A	22133692	4	1	29	1	0	0	0	0	0	1	0	0	11069	518	18	4	398	4	OR4E2	14	22133692	Nonsense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1547923	22133692	85215848	649	12890											
LRRC16B	90668	hgsc.bcm.edu	37	chr14	24534916	24534916	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tcacggtgttgcccttcccgGgttggaaagagccaagggtt	7	10	14	10	2	1	1	1	0	0	1	2	2	2	2	3	4	2	3	3	4	2	4	rs79328356	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:24534916G>T	ENST00000342740.5	+	34	3636	c.3482G>T	c.(3481-3483)gGg>gTg	p.G1161V	LRRC16B_ENST00000334420.7_Intron	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	1161						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)		GCCCTTCCCGGGTTGGAAAGA	0.617													G|||	98	0.0195687	0.003	0.0245	5008	,	,		17823	0.003		0.0616	False		,,,				2504	0.0123				p.G1161V		Atlas-SNP	.											LRRC16B,NS,carcinoma,+1,1	LRRC16B	120	1	0			c.G3482T						PASS	.	G	VAL/GLY	63,4343	58.7+/-95.3	1,61,2141	123	109	114		3482	4.5	1	14	dbSNP_131	114	574,8026	154.6+/-208.8	26,522,3752	yes	missense	LRRC16B	NM_138360.3	109	27,583,5893	TT,TG,GG		6.6744,1.4299,4.8977	probably-damaging	1161/1373	24534916	637,12369	2203	4300	6503	SO:0001583	missense	90668	exon34			TTCCCGGGTTGGA	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.3482G>T	14.37:g.24534916G>T	ENSP00000340467:p.Gly1161Val	68	0	0		64	33	0.515625	NM_138360	Q8TEF7|Q96HS9	Missense_Mutation	SNP	ENST00000342740.5	37	CCDS32054.1	60	0.027472527472527472	2	0.0040650406504065045	10	0.027624309392265192	1	0.0017482517482517483	47	0.06200527704485488	G	18.54	3.645209	0.67358	0.014299	0.066744	ENSG00000186648	ENST00000342740	T	0.17854	2.25	5.4	4.51	0.55191	.	0.141061	0.33161	N	0.005214	T	0.01835	0.0058	N	0.19112	0.55	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.00950	-1.1503	10	0.72032	D	0.01	-15.7681	9.7564	0.40506	0.0947:0.0:0.9053:0.0	.	1161	Q8ND23	LR16B_HUMAN	V	1161	ENSP00000340467:G1161V	ENSP00000340467:G1161V	G	+	2	0	LRRC16B	23604756	0.964000	0.33143	0.972000	0.41901	0.867000	0.49689	1.806000	0.38892	1.272000	0.44329	0.655000	0.94253	GGG	G|0.958;T|0.042	0.042	strong		0.617	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360		T	24534916	G	T	24534916	3	4	29	1	0	0	0	0	1	0	0	0	8981	1232	43	4	3616	4	LRRC16B	14	24534916	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2401224	24534916	82814624	650	12891											
C14orf21	161424	hgsc.bcm.edu	37	chr14	24771172	24771172	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttctgccctctctccacagtGtttatcactgataagatctc	8	15	5	13	0	4	2	1	1	3	1	7	2	5	2	2	0	1	1	2	0	2	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:24771172G>A	ENST00000267425.3	+	4	903	c.810G>A	c.(808-810)gtG>gtA	p.V270V	NOP9_ENST00000396802.3_Splice_Site_p.V270V|DHRS1_ENST00000396813.1_5'Flank|DHRS1_ENST00000288111.7_5'Flank	NM_174913.1	NP_777573.1	Q86U38	NOP9_HUMAN	NOP9 nucleolar protein	270							poly(A) RNA binding (GO:0044822)										TCTCCACAGTGTTTATCACTG	0.458																																					p.V270V		Atlas-SNP	.											.	.	.	.	0			c.G810A						PASS	.						219	233	228					14																	24771172		2203	4300	6503	SO:0001630	splice_region_variant	161424	exon4			CACAGTGTTTATC		CCDS9624.1, CCDS66616.1	14q12	2012-12-10	2012-12-10	2012-06-06	ENSG00000196943	ENSG00000196943			19826	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 21", "NOP9 nucleolar protein homolog (yeast)"	C14orf21		21653694	Standard	XM_005267385		Approved		uc001wol.1	Q86U38	OTTHUMG00000029342	ENST00000267425.3:c.809-1G>A	14.37:g.24771172G>A		75	0	0		58	11	0.189655	NM_174913	A8MY76|Q8IVF0|Q8TBS6	Silent	SNP	ENST00000267425.3	37	CCDS9624.1																																																																																			.	.	none		0.458	NOP9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073186.2		Silent	A	24771172	G	A	24771172	5	1	29	1	0	0	0	0	0	0	1	0	1771	1391	48	2	824	2	C14orf21	14	24771172	Splice_Site	SNP	G	TCGA-GR-7351-01A-11D-2210-10	236256	24771172	82578368	651	12892											
C14orf21	161424	hgsc.bcm.edu	37	chr14	24772965	24772965	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actgtgcagagccctcatccCggcaagtggcctgtgtgcct	6	9	12	14	1	1	1	1	0	0	1	2	1	2	1	4	2	3	2	4	2	1	0	rs116960868	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:24772965C>A	ENST00000267425.3	+	7	1405	c.1312C>A	c.(1312-1314)Cgg>Agg	p.R438R	NOP9_ENST00000396802.3_Silent_p.R438R	NM_174913.1	NP_777573.1	Q86U38	NOP9_HUMAN	NOP9 nucleolar protein	438							poly(A) RNA binding (GO:0044822)										GCCCTCATCCCGGCAAGTGGC	0.527													C|||	26	0.00519169	0.0	0.0101	5008	,	,		20648	0.0		0.0189	False		,,,				2504	0.0				p.R438R		Atlas-SNP	.											C14orf21,colon,carcinoma,-2,1	.	.	1	0			c.C1312A						PASS	.	C		14,4392	22.3+/-47.3	0,14,2189	78	73	75		1312	4.4	1	14	dbSNP_132	75	125,8475	64.6+/-126.8	0,125,4175	no	coding-synonymous	C14orf21	NM_174913.1		0,139,6364	AA,AC,CC		1.4535,0.3177,1.0687		438/637	24772965	139,12867	2203	4300	6503	SO:0001819	synonymous_variant	161424	exon7			TCATCCCGGCAAG		CCDS9624.1, CCDS66616.1	14q12	2012-12-10	2012-12-10	2012-06-06	ENSG00000196943	ENSG00000196943			19826	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 21", "NOP9 nucleolar protein homolog (yeast)"	C14orf21		21653694	Standard	XM_005267385		Approved		uc001wol.1	Q86U38	OTTHUMG00000029342	ENST00000267425.3:c.1312C>A	14.37:g.24772965C>A		112	0	0		111	56	0.504505	NM_174913	A8MY76|Q8IVF0|Q8TBS6	Silent	SNP	ENST00000267425.3	37	CCDS9624.1																																																																																			C|0.990;A|0.010	0.010	strong		0.527	NOP9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073186.2			A	24772965	C	A	24772965	2	1	29	1	0	0	0	0	0	0	0	1	1771	643	23	4		4	C14orf21	14	24772965	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1793	24772965	82576575	652	12893											
PRKD1	5587	hgsc.bcm.edu	37	chr14	30066797	30066797	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcattaaatgggaatgtgccGcttaggcttacatagatgat	12	13	10	6	1	1	2	1	1	0	1	1	3	1	3	1	2	2	2	1	2	6	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:30066797G>A	ENST00000331968.5	-	16	2563	c.2334C>T	c.(2332-2334)agC>agT	p.S778S	PRKD1_ENST00000415220.2_Silent_p.S786S	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	778	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)		GGAATGTGCCGCTTAGGCTTA	0.463																																					p.S778S		Atlas-SNP	.											.	PRKD1	316	.	0			c.C2334T						PASS	.						156	144	148					14																	30066797		2203	4300	6503	SO:0001819	synonymous_variant	5587	exon16			TGTGCCGCTTAGG		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.2334C>T	14.37:g.30066797G>A		126	0	0		143	29	0.202797	NM_002742	A6NL64|B2RAF6	Silent	SNP	ENST00000331968.5	37	CCDS9637.1																																																																																			.	.	none		0.463	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742		A	30066797	G	A	30066797	2	1	29	1	0	0	0	0	0	0	0	1	12530	1078	38	1		1	PRKD1	14	30066797	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	5293832	30066797	77282743	653	12894											
STRN3	29966	hgsc.bcm.edu	37	chr14	31404490	31404490	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatcgtcagttaggtcagcAgctaaaccttcattacctat	11	12	8	10	1	3	0	3	0	0	0	4	1	3	1	2	2	4	3	2	2	5	5	rs149753992		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:31404490A>C	ENST00000357479.5	-	7	1063	c.867T>G	c.(865-867)gcT>gcG	p.A289A	STRN3_ENST00000355683.5_Silent_p.A289A|STRN3_ENST00000366206.2_5'Flank	NM_001083893.1	NP_001077362.1	Q13033	STRN3_HUMAN	striatin, calmodulin binding protein 3	289					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)		TTAGGTCAGCAGCTAAACCTT	0.363																																					p.A289A		Atlas-SNP	.											.	STRN3	117	.	0			c.T867G						PASS	.	A	,	1,4405	2.1+/-5.4	0,1,2202	94	91	92		867,867	3	1	14	dbSNP_134	92	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	STRN3	NM_001083893.1,NM_014574.3	,	0,3,6500	CC,CA,AA		0.0233,0.0227,0.0231	,	289/798,289/714	31404490	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	29966	exon7			GTCAGCAGCTAAA		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.867T>G	14.37:g.31404490A>C		77	0	0		80	37	0.4625	NM_001083893	A2RTX7|A6NHZ7|Q9NRA5	Silent	SNP	ENST00000357479.5	37	CCDS41938.1	.	.	.	.	.	.	.	.	.	.	A	10.41	1.342669	0.24339	2.27E-4	2.33E-4	ENSG00000196792	ENST00000556577	.	.	.	5.68	2.98	0.34508	.	.	.	.	.	T	0.61553	0.2356	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58769	-0.7578	4	.	.	.	-18.6432	11.3209	0.49421	0.6338:0.0:0.0:0.3662	.	.	.	.	G	50	.	.	C	-	1	0	STRN3	30474241	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.814000	0.27239	0.940000	0.37473	0.459000	0.35465	TGC	A|1.000;C|0.000	0.000	weak		0.363	STRN3-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409713.1	NM_014574		C	31404490	A	C	31404490	2	2	29	1	0	0	0	0	0	0	0	1	15345	175	7	5		5	STRN3	14	31404490	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	1337693	31404490	75945050	654	12895											
SIP1	8487	hgsc.bcm.edu	37	chr14	39587220	39587220	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tagctttcaggatgccaaccCgcccctgaaggttattcccc	8	10	8	15	1	1	1	1	1	0	0	2	2	2	2	6	2	3	2	6	2	4	4	rs150986614	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:39587220C>A	ENST00000308317.6	+	3	356	c.273C>A	c.(271-273)ccC>ccA	p.P91P	GEMIN2_ENST00000250379.8_Silent_p.P91P|GEMIN2_ENST00000396249.2_Silent_p.P91P	NM_003616.2	NP_003607.1	O14893	GEMI2_HUMAN	gem (nuclear organelle) associated protein 2	91					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)											GATGCCAACCCGCCCCTGAAG	0.403													C|||	9	0.00179712	0.0	0.0086	5008	,	,		13289	0.0		0.003	False		,,,				2504	0.0				p.P91P		Atlas-SNP	.											.	.	.	.	0			c.C273A						PASS	.	C	,,	4,4402	8.1+/-20.4	0,4,2199	58	55	56		273,273,273	0.9	1	14	dbSNP_134	56	35,8565	24.0+/-70.4	0,35,4265	no	coding-synonymous,coding-synonymous,coding-synonymous	GEMIN2	NM_001009182.1,NM_001009183.1,NM_003616.2	,,	0,39,6464	AA,AC,CC		0.407,0.0908,0.2999	,,	91/266,91/251,91/281	39587220	39,12967	2203	4300	6503	SO:0001819	synonymous_variant	8487	exon3			CCAACCCGCCCCT	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.273C>A	14.37:g.39587220C>A		40	0	0		51	21	0.411765	NM_003616	B2R9W8|Q2M3B3|Q9H4F5|Q9NS77|Q9NS78|Q9NS79	Silent	SNP	ENST00000308317.6	37	CCDS9669.1	5|5	0.0022893772893772895|0.0022893772893772895	0|0	0.0|0.0	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	C|C	9.553|9.553	1.116509|1.116509	0.20795|0.20795	9.08E-4|9.08E-4	0.00407|0.00407	ENSG00000092208|ENSG00000092208	ENST00000527381|ENST00000534684	.|.	.|.	.|.	6.12|6.12	0.916|0.916	0.19373|0.19373	.|.	0.093555|.	0.85682|.	D|.	0.000000|.	T|T	0.37785|0.37785	0.1016|0.1016	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.18713|0.18713	-1.0328|-1.0328	6|4	0.48119|.	T|.	0.1|.	-14.6395|-14.6395	4.3372|4.3372	0.11092|0.11092	0.2488:0.1419:0.0:0.6094|0.2488:0.1419:0.0:0.6094	.|.	.|.	.|.	.|.	Q|S	80|86	.|.	ENSP00000434048:P80Q|.	P|R	+|+	2|1	0|0	GEMIN2|GEMIN2	38656971|38656971	0.999000|0.999000	0.42202|0.42202	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	0.255000|0.255000	0.18333|0.18333	0.193000|0.193000	0.20303|0.20303	-0.323000|-0.323000	0.08544|0.08544	CCG|CGC	C|0.997;A|0.003	0.003	strong		0.403	GEMIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276730.2			A	39587220	C	A	39587220	2	1	29	1	0	0	0	0	0	0	0	1	14342	639	23	4		4	SIP1	14	39587220	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	8182730	39587220	67762320	655	12896											
CTAGE5	4253	hgsc.bcm.edu	37	chr14	39769122	39769122	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagtgaacttaataaacagAaagtaacatttgaagactcc	18	10	7	6	0	0	5	0	3	0	2	1	5	1	5	1	0	3	1	1	0	7	4	rs34761053	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:39769122A>C	ENST00000280083.3	+	9	1041	c.727A>C	c.(727-729)Aaa>Caa	p.K243Q	CTAGE5_ENST00000396158.2_Missense_Mutation_p.K248Q|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.K778Q|CTAGE5_ENST00000341502.5_Missense_Mutation_p.K243Q|CTAGE5_ENST00000341749.3_Missense_Mutation_p.K231Q|CTAGE5_ENST00000396165.4_Missense_Mutation_p.K214Q|CTAGE5_ENST00000553352.1_Missense_Mutation_p.K214Q|CTAGE5_ENST00000557038.1_Missense_Mutation_p.K163Q|CTAGE5_ENST00000556148.1_Missense_Mutation_p.K168Q|RP11-407N17.3_ENST00000603904.1_Missense_Mutation_p.K214Q|CTAGE5_ENST00000348007.3_Missense_Mutation_p.K243Q			O15320	CTGE5_HUMAN	CTAGE family, member 5	243					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)		TAATAAACAGAAAGTAACATT	0.328													A|||	7	0.00139776	0.0	0.0	5008	,	,		16808	0.0		0.007	False		,,,				2504	0.0				p.K248Q		Atlas-SNP	.											.	CTAGE5	75	.	0			c.A742C						PASS	.	A	GLN/LYS,GLN/LYS,GLN/LYS,GLN/LYS	2,4404	4.2+/-10.8	0,2,2201	132	136	135		727,691,727,640	5.5	1	14	dbSNP_126	135	60,8534	36.4+/-91.3	0,60,4237	no	missense,missense,missense,missense	CTAGE5	NM_005930.3,NM_203354.2,NM_203355.2,NM_203356.2	53,53,53,53	0,62,6438	CC,CA,AA		0.6982,0.0454,0.4769	benign,benign,benign,benign	243/805,231/793,243/762,214/776	39769122	62,12938	2203	4297	6500	SO:0001583	missense	4253	exon9			AAACAGAAAGTAA	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.727A>C	14.37:g.39769122A>C	ENSP00000280083:p.Lys243Gln	85	0	0		60	25	0.416667	NM_001247989	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Missense_Mutation	SNP	ENST00000280083.3	37	CCDS9674.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	A	18.38	3.611043	0.66558	4.54E-4	0.006982	ENSG00000258941;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527	ENST00000553728;ENST00000341749;ENST00000557038;ENST00000382245;ENST00000396165;ENST00000341502;ENST00000396158;ENST00000280083;ENST00000556148;ENST00000348007;ENST00000553352	T;T;T;T;T;T;T;T;T;T	0.77877	1.18;-1.13;1.18;-1.13;-1.13;1.18;-1.13;1.18;-1.13;-1.13	5.49	5.49	0.81192	.	0.241343	0.21531	N	0.073042	T	0.77212	0.4097	M	0.84219	2.685	0.31455	N	0.67022	B;B;B;B;B;B	0.33826	0.427;0.191;0.184;0.112;0.384;0.112	B;B;B;B;B;B	0.40506	0.331;0.183;0.251;0.183;0.251;0.183	T	0.82474	-0.0439	9	.	.	.	.	13.8371	0.63415	1.0:0.0:0.0:0.0	rs34761053	205;248;243;243;214;231	F8W9E1;O15320-5;O15320-2;O15320;O15320-7;G3XAC5	.;.;.;CTGE5_HUMAN;.;.	Q	778;231;163;205;214;243;248;243;168;243;214	ENSP00000452252:K778Q;ENSP00000343897:K231Q;ENSP00000450869:K163Q;ENSP00000379468:K214Q;ENSP00000339286:K243Q;ENSP00000379462:K248Q;ENSP00000280083:K243Q;ENSP00000452562:K168Q;ENSP00000343912:K243Q;ENSP00000450449:K214Q	.	K	+	1	0	CTAGE5;RP11-407N17.3	38838873	1.000000	0.71417	0.997000	0.53966	0.972000	0.66771	5.768000	0.68858	2.075000	0.62263	0.528000	0.53228	AAA	A|0.995;C|0.005	0.005	strong		0.328	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930		C	39769122	A	C	39769122	3	2	29	1	0	0	0	0	1	0	0	0	3996	247	9	5	792	5	CTAGE5	14	39769122	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	181902	39769122	67580418	656	12897											
CTAGE5	4253	hgsc.bcm.edu	37	chr14	39784005	39784008	+	Splice_Site	DEL	TATA	TATA	-																															tcattcttatcaagggcaggTatatatatatgtgtgtgtgt																								rs577313725|rs548723883|rs75318507|rs201697727	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TATA	TATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:39784005_39784008delTATA	ENST00000280083.3	+	15	1670		c.e15+2		CTAGE5_ENST00000396158.2_Splice_Site|RP11-407N17.3_ENST00000553728.1_Splice_Site|CTAGE5_ENST00000341502.5_Splice_Site|CTAGE5_ENST00000341749.3_Splice_Site|CTAGE5_ENST00000396165.4_Splice_Site|CTAGE5_ENST00000553352.1_Splice_Site|CTAGE5_ENST00000557038.1_Splice_Site|CTAGE5_ENST00000556148.1_Splice_Site|RP11-407N17.3_ENST00000603904.1_Splice_Site|CTAGE5_ENST00000348007.3_Splice_Site			O15320	CTGE5_HUMAN	CTAGE family, member 5						positive regulation of catalytic activity (GO:0043085)	membrane (GO:0016020)	enzyme activator activity (GO:0008047)	p.?(1)	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)		CAAGGGCAGGTATATATATAtgtg	0.299														6	0.00119808	0.0	0.0043	5008	,	,		13080	0.001		0.002	False		,,,				2504	0.0				.		Atlas-Indel	.											.	CTAGE5	75	.	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	.						PASS	.																																			SO:0001630	splice_region_variant	4253	.			.	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.1356+2TATA>-	14.37:g.39784009_39784012delTATA		116	0	0		131	79	0.603053	.	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Splice_Site	DEL	ENST00000280083.3	37	CCDS9674.1																																																																																			.	.	alt		0.299	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930	Intron	-	39784008	TATA	-	39784005	8	5	29	1	0	1	0	1	0	0	1	0	3996	1652	57	0	1447	0	CTAGE5	14	39784005	Splice_Site	DEL	TATA	TCGA-GR-7351-01A-11D-2210-10	14883	39784005	67565535	657	12898											
CTAGE5	4253	hgsc.bcm.edu	37	chr14	39790149	39790149	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	cagagcattccccatatggtCcctcaccattgggttggcct	7	11	9	14	0	1	1	1	0	0	1	3	1	3	1	5	3	1	2	5	3	1	4	rs36060072	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:39790149C>G	ENST00000280083.3	+	19	1875	c.1561C>G	c.(1561-1563)Ccc>Gcc	p.P521A	CTAGE5_ENST00000396158.2_Missense_Mutation_p.P526A|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.P1056A|CTAGE5_ENST00000341502.5_Missense_Mutation_p.P521A|CTAGE5_ENST00000341749.3_Missense_Mutation_p.P509A|CTAGE5_ENST00000396165.4_Missense_Mutation_p.P492A|CTAGE5_ENST00000553352.1_Missense_Mutation_p.P492A|CTAGE5_ENST00000557038.1_Missense_Mutation_p.P441A|CTAGE5_ENST00000556148.1_Missense_Mutation_p.P446A|RP11-407N17.3_ENST00000603904.1_Missense_Mutation_p.P492A|CTAGE5_ENST00000348007.3_Intron			O15320	CTGE5_HUMAN	CTAGE family, member 5	521	Pro-rich.				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)		CCCATATGGTCCCTCACCATT	0.433													C|||	7	0.00139776	0.0	0.0	5008	,	,		16160	0.0		0.007	False		,,,				2504	0.0				p.P526A		Atlas-SNP	.											.	CTAGE5	75	.	0			c.C1576G						PASS	.	C	ALA/PRO,ALA/PRO,,ALA/PRO	2,4404	4.2+/-10.8	0,2,2201	130	135	133		1561,1525,,1474	5.1	1	14	dbSNP_126	133	59,8541	35.3+/-89.8	0,59,4241	yes	missense,missense,intron,missense	CTAGE5	NM_005930.3,NM_203354.2,NM_203355.2,NM_203356.2	27,27,,27	0,61,6442	GG,GC,CC		0.686,0.0454,0.469	possibly-damaging,possibly-damaging,,possibly-damaging	521/805,509/793,,492/776	39790149	61,12945	2203	4300	6503	SO:0001583	missense	4253	exon19			TATGGTCCCTCAC	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.1561C>G	14.37:g.39790149C>G	ENSP00000280083:p.Pro521Ala	86	0	0		100	52	0.52	NM_001247989	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Missense_Mutation	SNP	ENST00000280083.3	37	CCDS9674.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	19.63	3.864475	0.71949	4.54E-4	0.00686	ENSG00000258941;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527	ENST00000553728;ENST00000341749;ENST00000557038;ENST00000382245;ENST00000396165;ENST00000341502;ENST00000396158;ENST00000280083;ENST00000556148;ENST00000553352	T;T;T;T;T;T;T;T;T	0.58940	0.3;0.3;0.3;0.3;0.3;0.3;0.3;0.3;0.3	5.95	5.06	0.68205	.	0.494861	0.15184	N	0.275926	T	0.70500	0.3231	M	0.88842	2.985	0.50467	D	0.999875	P;P;P;P	0.50528	0.936;0.936;0.936;0.936	P;P;P;P	0.56127	0.792;0.792;0.792;0.792	T	0.77619	-0.2520	9	.	.	.	.	15.5102	0.75776	0.0:0.8624:0.1376:0.0	rs36060072	483;526;521;509	F8W9E1;O15320-5;O15320;G3XAC5	.;.;CTGE5_HUMAN;.	A	1056;509;441;483;492;521;526;521;446;492	ENSP00000452252:P1056A;ENSP00000343897:P509A;ENSP00000450869:P441A;ENSP00000379468:P492A;ENSP00000339286:P521A;ENSP00000379462:P526A;ENSP00000280083:P521A;ENSP00000452562:P446A;ENSP00000450449:P492A	.	P	+	1	0	CTAGE5;RP11-407N17.3	38859900	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.350000	0.59392	1.503000	0.48686	0.655000	0.94253	CCC	G|0.005;C|0.995	0.005	strong		0.433	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930		G	39790149	C	G	39790149	3	3	29	1	0	0	0	0	1	0	0	0	3996	855	30	4	1666	4	CTAGE5	14	39790149	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	6144	39790149	67559391	658	12899											
CTAGE5	4253	hgsc.bcm.edu	37	chr14	39818076	39818076	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caagaggcccattcttgagaAgaggacctcctttcccccca	10	8	8	15	0	1	3	0	1	1	3	3	5	3	4	6	2	0	0	6	2	2	3	rs61742363	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:39818076A>G	ENST00000280083.3	+	23	2457	c.2143A>G	c.(2143-2145)Aga>Gga	p.R715G	CTAGE5_ENST00000396158.2_Missense_Mutation_p.R720G|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.R1250G|CTAGE5_ENST00000341502.5_Missense_Mutation_p.R715G|CTAGE5_ENST00000553383.1_3'UTR|CTAGE5_ENST00000341749.3_Missense_Mutation_p.R703G|CTAGE5_ENST00000396165.4_Missense_Mutation_p.R686G|CTAGE5_ENST00000553352.1_Missense_Mutation_p.R686G|CTAGE5_ENST00000557038.1_Missense_Mutation_p.R635G|CTAGE5_ENST00000556148.1_Missense_Mutation_p.R640G|RP11-407N17.3_ENST00000603904.1_Missense_Mutation_p.R686G|CTAGE5_ENST00000348007.3_Missense_Mutation_p.R672G			O15320	CTGE5_HUMAN	CTAGE family, member 5	715	Pro-rich.				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)		ATTCTTGAGAAGAGGACCTCC	0.532													A|||	27	0.00539137	0.0	0.0173	5008	,	,		14299	0.0		0.0149	False		,,,				2504	0.0				p.R720G		Atlas-SNP	.											.	CTAGE5	75	.	0			c.A2158G						PASS	.	A	GLY/ARG,GLY/ARG,GLY/ARG,GLY/ARG	16,4390	22.3+/-47.3	0,16,2187	125	130	129		2143,2107,2014,2056	3.1	1	14	dbSNP_129	129	156,8444	73.5+/-136.2	0,156,4144	yes	missense,missense,missense,missense	CTAGE5	NM_005930.3,NM_203354.2,NM_203355.2,NM_203356.2	125,125,125,125	0,172,6331	GG,GA,AA		1.814,0.3631,1.3225	probably-damaging,probably-damaging,probably-damaging,probably-damaging	715/805,703/793,672/762,686/776	39818076	172,12834	2203	4300	6503	SO:0001583	missense	4253	exon23			TTGAGAAGAGGAC	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.2143A>G	14.37:g.39818076A>G	ENSP00000280083:p.Arg715Gly	88	0	0		129	61	0.472868	NM_001247989	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Missense_Mutation	SNP	ENST00000280083.3	37	CCDS9674.1	22	0.010073260073260074	0	0.0	8	0.022099447513812154	0	0.0	14	0.018469656992084433	A	14.78	2.638501	0.47153	0.003631	0.01814	ENSG00000258941;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527	ENST00000553728;ENST00000341749;ENST00000557038;ENST00000396165;ENST00000341502;ENST00000396158;ENST00000280083;ENST00000556148;ENST00000348007;ENST00000553352	T;T;T;T;T;T;T;T;T;T	0.16324	2.35;2.4;2.37;2.36;2.91;2.63;2.64;2.36;3.17;2.36	5.64	3.12	0.35913	.	0.000000	0.37623	N	0.002009	T	0.12178	0.0296	M	0.83312	2.635	0.29744	N	0.83689	B;B;B;B;B	0.28713	0.22;0.181;0.22;0.181;0.22	B;B;B;B;B	0.29267	0.1;0.074;0.1;0.074;0.1	T	0.06588	-1.0818	9	.	.	.	.	11.6343	0.51194	0.6083:0.3917:0.0:0.0	rs61742363	720;672;715;643;703	O15320-5;O15320-2;O15320;O15320-7;G3XAC5	.;.;CTGE5_HUMAN;.;.	G	1250;703;635;686;715;720;715;640;672;686	ENSP00000452252:R1250G;ENSP00000343897:R703G;ENSP00000450869:R635G;ENSP00000379468:R686G;ENSP00000339286:R715G;ENSP00000379462:R720G;ENSP00000280083:R715G;ENSP00000452562:R640G;ENSP00000343912:R672G;ENSP00000450449:R686G	.	R	+	1	2	CTAGE5;RP11-407N17.3	38887827	1.000000	0.71417	0.992000	0.48379	0.895000	0.52256	0.816000	0.27267	0.940000	0.37473	0.533000	0.62120	AGA	A|0.988;G|0.012	0.012	strong		0.532	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930		G	39818076	A	G	39818076	3	3	29	1	0	0	0	0	1	0	0	0	3996	64	3	3	2264	3	CTAGE5	14	39818076	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	27927	39818076	67531464	659	12900											
PYGL	5836	hgsc.bcm.edu	37	chr14	51378517	51378517	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cttgcttccaaccatagggtCattgttcaccacatctgcca	9	12	6	14	0	3	0	2	0	1	0	4	0	4	0	4	1	3	2	4	1	2	5	rs35026927	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:51378517C>G	ENST00000216392.7	-	16	2232	c.1900G>C	c.(1900-1902)Gac>Cac	p.D634H	RP11-218E20.5_ENST00000557343.1_RNA|PYGL_ENST00000532462.1_Missense_Mutation_p.D634H|PYGL_ENST00000544180.2_Missense_Mutation_p.D600H	NM_002863.4	NP_002854.3	P06737	PYGL_HUMAN	phosphorylase, glycogen, liver	634					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)	ACCATAGGGTCATTGTTCACC	0.448													C|||	7	0.00139776	0.0	0.0072	5008	,	,		22205	0.0		0.002	False		,,,				2504	0.0				p.D634H		Atlas-SNP	.											PYGL,colon,carcinoma,+2,1	PYGL	77	1	0			c.G1900C						PASS	.	C	HIS/ASP,HIS/ASP	5,4401	9.9+/-24.2	0,5,2198	111	100	104	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1798,1900	5.6	1	14	dbSNP_126	104	54,8546	34.3+/-88.2	0,54,4246	yes	missense,missense	PYGL	NM_001163940.1,NM_002863.4	81,81	0,59,6444	GG,GC,CC		0.6279,0.1135,0.4536	probably-damaging,probably-damaging	600/814,634/848	51378517	59,12947	2203	4300	6503	SO:0001583	missense	5836	exon16			TAGGGTCATTGTT		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.1900G>C	14.37:g.51378517C>G	ENSP00000216392:p.Asp634His	160	0	0		164	81	0.493902	NM_002863	A6NDQ4|B4DUB7|F5H816|O60567|O60752|O60913|Q501V9|Q641R5|Q96G82	Missense_Mutation	SNP	ENST00000216392.7	37	CCDS32080.1	6	0.0027472527472527475	0	0.0	4	0.011049723756906077	0	0.0	2	0.002638522427440633	C	26.3	4.720583	0.89205	0.001135	0.006279	ENSG00000100504	ENST00000532462;ENST00000544180;ENST00000216392	D;D;D	0.96365	-3.99;-3.99;-3.99	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	D	0.98670	0.9554	H	0.98996	4.395	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.96269	0.9197	10	0.87932	D	0	-31.9632	18.6272	0.91344	0.0:1.0:0.0:0.0	rs35026927	600;600;634	F5H816;B4DUB7;P06737	.;.;PYGL_HUMAN	H	634;600;634	ENSP00000431657:D634H;ENSP00000443787:D600H;ENSP00000216392:D634H	ENSP00000216392:D634H	D	-	1	0	PYGL	50448267	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.792000	0.85828	2.646000	0.89796	0.467000	0.42956	GAC	C|0.996;G|0.004	0.004	strong		0.448	PYGL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390654.3	NM_002863		G	51378517	C	G	51378517	3	3	29	1	0	0	0	0	1	0	0	0	12876	826	29	4	663	4	PYGL	14	51378517	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	11560441	51378517	55971023	660	12901											
GCH1	2643	hgsc.bcm.edu	37	chr14	55369053	55369053	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgacctgagatggtctccTggtagcccttggtgaagaac	9	10	12	10	0	1	4	0	3	1	2	2	5	1	4	3	3	2	1	3	3	3	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:55369053T>C	ENST00000491895.2	-	1	517	c.329A>G	c.(328-330)cAg>cGg	p.Q110R	GCH1_ENST00000543643.2_Missense_Mutation_p.Q110R|GCH1_ENST00000536224.2_Missense_Mutation_p.Q110R|GCH1_ENST00000395514.1_Missense_Mutation_p.Q110R|GCH1_ENST00000254299.4_5'UTR	NM_000161.2	NP_000152.1	P30793	GCH1_HUMAN	GTP cyclohydrolase 1	110					7,8-dihydroneopterin 3'-triphosphate biosynthetic process (GO:0035998)|dopamine biosynthetic process (GO:0042416)|GTP catabolic process (GO:0006184)|metabolic process (GO:0008152)|negative regulation of blood pressure (GO:0045776)|neuromuscular process controlling posture (GO:0050884)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide metabolic process (GO:0046209)|positive regulation of nitric-oxide synthase activity (GO:0051000)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|pteridine-containing compound biosynthetic process (GO:0042559)|regulation of blood pressure (GO:0008217)|regulation of lung blood pressure (GO:0014916)|regulation of nitric-oxide synthase activity (GO:0050999)|response to interferon-gamma (GO:0034341)|response to lipopolysaccharide (GO:0032496)|response to pain (GO:0048265)|response to tumor necrosis factor (GO:0034612)|small molecule metabolic process (GO:0044281)|tetrahydrobiopterin biosynthetic process (GO:0006729)|tetrahydrofolate biosynthetic process (GO:0046654)|vasodilation (GO:0042311)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|coenzyme binding (GO:0050662)|GTP binding (GO:0005525)|GTP cyclohydrolase I activity (GO:0003934)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(2)|lung(7)|skin(2)	11						GATGGTCTCCTGGTAGCCCTT	0.692																																					p.Q110R	Pancreas(198;1245 2204 4807 21567 38372)	Atlas-SNP	.											.	GCH1	16	.	0			c.A329G						PASS	.						21	23	23					14																	55369053		2203	4300	6503	SO:0001583	missense	2643	exon1			GTCTCCTGGTAGC	U19523	CCDS9720.1, CCDS41954.1, CCDS45110.1	14q22.1-q22.2	2014-04-01	2008-08-01		ENSG00000131979	ENSG00000131979	3.5.4.16		4193	protein-coding gene	gene with protein product	"dopa-responsive dystonia"	600225	"dystonia 14"	GCH, DYT5, DYT14		7874165, 8695054	Standard	XM_005267530		Approved	GTPCH1, DYT5a	uc001xbi.1	P30793	OTTHUMG00000029754	ENST00000491895.2:c.329A>G	14.37:g.55369053T>C	ENSP00000419045:p.Gln110Arg	40	0	0		41	15	0.365854	NM_000161	Q6FHY7|Q9Y4I8	Missense_Mutation	SNP	ENST00000491895.2	37	CCDS9720.1	.	.	.	.	.	.	.	.	.	.	T	16.98	3.270301	0.59540	.	.	ENSG00000131979	ENST00000395514;ENST00000543643;ENST00000491895;ENST00000536224;ENST00000395524	D;D;D;D	0.99701	-6.45;-6.45;-6.45;-6.45	4.46	4.46	0.54185	.	0.116646	0.64402	D	0.000012	D	0.97945	0.9324	N	0.16166	0.38	0.80722	D	1	B;B;B;B	0.19445	0.036;0.013;0.018;0.007	B;B;B;B	0.17979	0.02;0.02;0.02;0.005	D	0.97786	1.0235	10	0.42905	T	0.14	.	12.689	0.56964	0.0:0.0:0.0:1.0	.	110;110;110;110	F8W9F6;P30793-2;P30793-4;P30793	.;.;.;GCH1_HUMAN	R	110	ENSP00000378890:Q110R;ENSP00000444011:Q110R;ENSP00000419045:Q110R;ENSP00000445246:Q110R	ENSP00000378890:Q110R	Q	-	2	0	GCH1	54438803	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	4.735000	0.62051	1.858000	0.53909	0.459000	0.35465	CAG	.	.	none		0.692	GCH1-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276895.3			C	55369053	T	C	55369053	3	2	29	1	0	0	0	0	1	0	0	0	6299	1580	55	3	547	3	GCH1	14	55369053	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	3990536	55369053	51980487	661	12902											
KTN1	3895	hgsc.bcm.edu	37	chr14	56119783	56119783	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aagcacatgttcaggaagtaGcacaacataacttgaaagag	18	7	9	7	0	1	2	1	1	0	1	1	3	1	3	0	1	4	4	0	1	6	4	rs139730003		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:56119783G>A	ENST00000395314.3	+	27	2811	c.2743G>A	c.(2743-2745)Gca>Aca	p.A915T	Y_RNA_ENST00000363872.1_RNA|KTN1_ENST00000416613.1_Missense_Mutation_p.A915T|KTN1_ENST00000438792.2_Missense_Mutation_p.A915T|KTN1_ENST00000395309.3_Missense_Mutation_p.A915T|KTN1_ENST00000395308.1_Missense_Mutation_p.A892T|KTN1_ENST00000395311.1_Missense_Mutation_p.A892T|KTN1_ENST00000554507.1_Missense_Mutation_p.A210T|KTN1_ENST00000413890.2_Missense_Mutation_p.A892T	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	915					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						TCAGGAAGTAGCACAACATAA	0.274			T	RET	papillary thryoid																																p.A915T		Atlas-SNP	.		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	KTN1	147	.	0			c.G2743A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA	0,4404		0,0,2202	325	348	340		2743,2674,2743,2743	1.3	0.4	14	dbSNP_134	340	4,8574	3.7+/-12.6	0,4,4285	yes	missense,missense,missense,missense	KTN1	NM_001079521.1,NM_001079522.1,NM_004986.2,NM_182926.2	58,58,58,58	0,4,6487	AA,AG,GG		0.0466,0.0,0.0308	benign,benign,benign,benign	915/1358,892/1307,915/1301,915/1358	56119783	4,12978	2202	4289	6491	SO:0001583	missense	3895	exon27			GAAGTAGCACAAC		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.2743G>A	14.37:g.56119783G>A	ENSP00000378725:p.Ala915Thr	154	0	0		163	75	0.460123	NM_004986	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Missense_Mutation	SNP	ENST00000395314.3	37	CCDS41957.1	.	.	.	.	.	.	.	.	.	.	G	8.195	0.796859	0.16327	0.0	4.66E-4	ENSG00000126777	ENST00000413890;ENST00000395309;ENST00000438792;ENST00000395314;ENST00000395308;ENST00000395311;ENST00000416613;ENST00000554507	T;T;T;T;T;T;T;T	0.43688	1.55;1.53;1.52;1.53;1.55;1.55;1.53;0.94	5.42	1.34	0.21922	.	0.317245	0.22025	N	0.065679	T	0.22044	0.0531	N	0.22421	0.69	0.09310	N	1	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;0.001	T	0.08126	-1.0737	10	0.31617	T	0.26	-3.1377	3.2049	0.06662	0.2076:0.1189:0.5513:0.1222	.	915;210;915;892;915	B4DZ88;G3V4Y7;Q86UP2-2;Q17RZ5;Q86UP2	.;.;.;.;KTN1_HUMAN	T	892;915;915;915;892;892;915;210	ENSP00000394992:A892T;ENSP00000378720:A915T;ENSP00000391964:A915T;ENSP00000378725:A915T;ENSP00000378719:A892T;ENSP00000378722:A892T;ENSP00000388807:A915T;ENSP00000452073:A210T	ENSP00000378719:A892T	A	+	1	0	KTN1	55189536	0.037000	0.19845	0.439000	0.26833	0.742000	0.42306	0.171000	0.16685	0.663000	0.31027	0.585000	0.79938	GCA	G|1.000;A|0.000	0.000	weak		0.274	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2			A	56119783	G	A	56119783	3	1	29	1	0	0	0	0	1	0	0	0	8594	971	34	2	2845	2	KTN1	14	56119783	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	750730	56119783	51229757	662	12903											
ARID4A	5926	hgsc.bcm.edu	37	chr14	58831258	58831258	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatttggccagaatgaagcAggaagtgaacctcatataga	15	9	10	7	0	2	4	2	2	0	2	2	5	2	5	2	2	2	1	2	2	6	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:58831258A>C	ENST00000355431.3	+	20	2824	c.2451A>C	c.(2449-2451)gcA>gcC	p.A817A	ARID4A_ENST00000348476.3_Silent_p.A817A|ARID4A_ENST00000395168.3_Silent_p.A817A|ARID4A_ENST00000431317.2_Silent_p.A817A	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	817					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						AGAATGAAGCAGGAAGTGAAC	0.343																																					p.A817A		Atlas-SNP	.											.	ARID4A	222	.	0			c.A2451C						PASS	.						39	44	42					14																	58831258		2198	4295	6493	SO:0001819	synonymous_variant	5926	exon20			TGAAGCAGGAAGT	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.2451A>C	14.37:g.58831258A>C		87	0	0		85	16	0.188235	NM_002892	Q15991|Q15992|Q15993	Silent	SNP	ENST00000355431.3	37	CCDS9732.1																																																																																			.	.	none		0.343	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001		C	58831258	A	C	58831258	2	2	29	1	0	0	0	0	0	0	0	1	919	175	7	5		5	ARID4A	14	58831258	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	2711475	58831258	48518282	663	12904											
KIAA0586	9786	hgsc.bcm.edu	37	chr14	58899157	58899157	+	Frame_Shift_Del	DEL	G	G	-																															gggacagaaagatgctctaaGaacagttttaaagcaaaagt																								rs534542684	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:58899157delG	ENST00000556134.1	+	5	621	c.347delG	c.(346-348)agafs	p.R116fs	KIAA0586_ENST00000354386.6_Frame_Shift_Del_p.R143fs|KIAA0586_ENST00000261244.5_Frame_Shift_Del_p.R131fs|KIAA0586_ENST00000423743.3_Frame_Shift_Del_p.R46fs	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	Q9BVV6	TALD3_HUMAN	KIAA0586	116					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						GATGCTCTAAGAACAGTTTTA	0.279													G|G|-|deletion	12	0.00239617	0.0	0.0058	5008	,	,		15268	0.0		0.007	False		,,,				2504	0.001				p.R143fs		Pindel,Atlas-Indel	.											.	KIAA0586	180	.	0			c.427delA						PASS	.			3,3511		0,3,1754	44	43	43			5.2	1	14		43	25,7757		0,25,3866	no	frameshift	KIAA0586	NM_014749.3		0,28,5620	A1A1,A1R,RR		0.3213,0.0854,0.2479			58899157	28,11268	1814	4055	5869	SO:0001589	frameshift_variant	9786	exon5			.	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.347delG	14.37:g.58899157delG	ENSP00000452351:p.Arg116fs	170	0	.		152	56	0.368	NM_001244189	B4DZB6|E7EWM8|J3KQH9|O60328|Q6NYC6|Q6UV20	Frame_Shift_Del	DEL	ENST00000556134.1	37	CCDS58321.1																																																																																			.	.	none		0.279	KIAA0586-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411887.1	NM_014749		-	58899157	G	-	58899157	7	5	29	1	0	1	0	1	0	0	0	0	8195	942	33	0	406	0	KIAA0586	14	58899157	Frame_Shift_Del	DEL	G	TCGA-GR-7351-01A-11D-2210-10	67899	58899157	48450383	664	12905											
DACT1	51339	hgsc.bcm.edu	37	chr14	59113721	59113721	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttgtccagactctgcccattCaaacggtaacggccccagac	10	8	8	15	2	2	2	1	0	1	2	3	2	3	2	4	2	3	1	4	2	2	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:59113721C>G	ENST00000335867.4	+	4	2404	c.2380C>G	c.(2380-2382)Caa>Gaa	p.Q794E	DACT1_ENST00000395153.3_Missense_Mutation_p.Q757E|DACT1_ENST00000556859.1_Missense_Mutation_p.Q513E|DACT1_ENST00000541264.2_Missense_Mutation_p.Q513E			Q9NYF0	DACT1_HUMAN	dishevelled-binding antagonist of beta-catenin 1	794					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						TCTGCCCATTCAAACGGTAAC	0.532																																					p.Q794E		Atlas-SNP	.											.	DACT1	119	.	0			c.C2380G						PASS	.						98	102	101					14																	59113721		2203	4300	6503	SO:0001583	missense	51339	exon4			CCCATTCAAACGG	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.2380C>G	14.37:g.59113721C>G	ENSP00000337439:p.Gln794Glu	50	0	0		30	13	0.433333	NM_016651	A8MYJ2|Q86TY0	Missense_Mutation	SNP	ENST00000335867.4	37	CCDS9736.1	.	.	.	.	.	.	.	.	.	.	C	15.09	2.728843	0.48833	.	.	ENSG00000165617	ENST00000556859;ENST00000395151;ENST00000395153;ENST00000335867;ENST00000541264	T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92	5.65	5.65	0.86999	.	0.268108	0.36778	N	0.002414	T	0.46132	0.1377	M	0.62723	1.935	0.50813	D	0.999891	B;B	0.33549	0.417;0.417	B;B	0.35971	0.215;0.215	T	0.27331	-1.0077	10	0.26408	T	0.33	-9.8241	19.9142	0.97043	0.0:1.0:0.0:0.0	.	757;794	A8MYJ2;Q9NYF0	.;DACT1_HUMAN	E	513;513;757;794;513	ENSP00000451598:Q513E;ENSP00000378581:Q513E;ENSP00000378582:Q757E;ENSP00000337439:Q794E;ENSP00000442850:Q513E	ENSP00000337439:Q794E	Q	+	1	0	DACT1	58183474	0.628000	0.27138	0.094000	0.20943	0.591000	0.36615	2.362000	0.44169	2.941000	0.99782	0.655000	0.94253	CAA	.	.	none		0.532	DACT1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325515.1	NM_016651		G	59113721	C	G	59113721	3	3	29	1	0	0	0	0	1	0	0	0	4224	827	29	4	2394	4	DACT1	14	59113721	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	214564	59113721	48235819	665	12906											
ACTN1	87	hgsc.bcm.edu	37	chr14	69341653	69341653	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcacggagtcggggccggTgtagggggccatccgcgcga	5	5	20	11	6	0	0	0	0	0	0	2	2	1	1	3	7	0	2	3	7	1	1	rs11557769	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:69341653T>A	ENST00000193403.6	-	21	2985	c.2602A>T	c.(2602-2604)Acc>Tcc	p.T868S	ACTN1_ENST00000438964.2_Missense_Mutation_p.T863S|ACTN1_ENST00000394419.4_Missense_Mutation_p.T890S|ACTN1_ENST00000538545.2_Missense_Mutation_p.T906S|ACTN1_ENST00000376839.3_Missense_Mutation_p.T798S	NM_001102.3	NP_001093.1	P12814	ACTN1_HUMAN	actinin, alpha 1	868			T -> S (in dbSNP:rs11557769).		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)		TCGGGGCCGGTGTAGGGGGCC	0.662													t|||	31	0.0061901	0.0	0.0159	5008	,	,		14509	0.0		0.0189	False		,,,				2504	0.001				p.T890S		Atlas-SNP	.											ACTN1,NS,carcinoma,+2,1	ACTN1	77	1	0			c.A2668T						PASS	.	T	SER/THR,SER/THR,SER/THR	16,4390	25.3+/-52.1	0,16,2187	42	41	41		2602,2668,2587	-2.7	0.9	14	dbSNP_120	41	142,8458	70.3+/-132.9	0,142,4158	yes	missense,missense,missense	ACTN1	NM_001102.3,NM_001130004.1,NM_001130005.1	58,58,58	0,158,6345	AA,AT,TT		1.6512,0.3631,1.2148	benign,benign,benign	868/893,890/915,863/888	69341653	158,12848	2203	4300	6503	SO:0001583	missense	87	exon22			GGCCGGTGTAGGG	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.2602A>T	14.37:g.69341653T>A	ENSP00000193403:p.Thr868Ser	66	0	0		46	25	0.543478	NM_001130004	B3V8S3|B4DHH3|B7TY16|Q1HE25|Q9BTN1	Missense_Mutation	SNP	ENST00000193403.6	37	CCDS9792.1	18	0.008241758241758242	0	0.0	8	0.022099447513812154	0	0.0	10	0.013192612137203167	T	9.571	1.121108	0.20877	0.003631	0.016512	ENSG00000072110	ENST00000193403;ENST00000394419;ENST00000438964;ENST00000376839;ENST00000538545	T;T;T;T;T	0.39229	1.6;1.09;1.09;1.09;1.09	4.68	-2.72	0.05968	EF-hand, Ca insensitive (1);EF-hand-like domain (1);	0.656003	0.15664	N	0.250756	T	0.09642	0.0237	L	0.28556	0.865	0.22185	N	0.999308	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	0.21690	-1.0238	10	0.08381	T	0.77	.	2.1866	0.03888	0.1289:0.3501:0.1331:0.3879	rs11557769	863;890;868;510	P12814-2;Q1HE25;P12814;B4DFY0	.;.;ACTN1_HUMAN;.	S	868;890;863;798;906	ENSP00000193403:T868S;ENSP00000377941:T890S;ENSP00000414272:T863S;ENSP00000366035:T798S;ENSP00000439828:T906S	ENSP00000193403:T868S	T	-	1	0	ACTN1	68411406	0.003000	0.15002	0.930000	0.37139	0.998000	0.95712	-0.007000	0.12810	-0.578000	0.05959	0.528000	0.53228	ACC	T|0.988;A|0.012	0.012	strong		0.662	ACTN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413233.3	NM_001102		A	69341653	T	A	69341653	3	1	29	1	0	0	0	0	1	0	0	0	204	1696	59	5	80	5	ACTN1	14	69341653	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	10227932	69341653	38007887	666	12907											
PAPLN	89932	hgsc.bcm.edu	37	chr14	73718474	73718474	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	catcctgcattacgagcgggGtgctgagggggacctggccc	6	7	16	12	2	0	1	0	1	0	0	1	3	1	2	3	5	4	2	3	5	1	1	rs141960540	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:73718474G>T	ENST00000554301.1	+	8	936	c.773G>T	c.(772-774)gGt>gTt	p.G258V	PAPLN_ENST00000427855.1_Missense_Mutation_p.G258V|PAPLN_ENST00000381166.3_Missense_Mutation_p.G258V|PAPLN_ENST00000340738.5_Missense_Mutation_p.G231V|PAPLN_ENST00000555445.1_Missense_Mutation_p.G258V			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	258						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)		TACGAGCGGGGTGCTGAGGGG	0.662													G|||	5	0.000998403	0.0008	0.0029	5008	,	,		16188	0.0		0.002	False		,,,				2504	0.0				p.G231V		Atlas-SNP	.											.	PAPLN	180	.	0			c.G692T						PASS	.	G	VAL/GLY	8,4394		0,8,2193	24	30	28		692	4.8	0.7	14	dbSNP_134	28	18,8576		0,18,4279	no	missense	PAPLN	NM_173462.3	109	0,26,6472	TT,TG,GG		0.2094,0.1817,0.2001	probably-damaging	231/1252	73718474	26,12970	2201	4297	6498	SO:0001583	missense	89932	exon8			AGCGGGGTGCTGA	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.773G>T	14.37:g.73718474G>T	ENSP00000451803:p.Gly258Val	122	0	0		146	76	0.520548	NM_173462	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Missense_Mutation	SNP	ENST00000554301.1	37		2	9.157509157509158E-4	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	G	19.70	3.876857	0.72180	0.001817	0.002094	ENSG00000100767	ENST00000340738;ENST00000427855;ENST00000381166;ENST00000554301;ENST00000555445	T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69	4.77	4.77	0.60923	ADAM-TS Spacer 1 (1);	.	.	.	.	T	0.56262	0.1973	L	0.38531	1.155	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.73380	0.967;0.98;0.959	T	0.53012	-0.8498	9	0.34782	T	0.22	.	13.2075	0.59805	0.0:0.1601:0.8398:0.0	.	258;258;231	O95428-5;O95428;O95428-6	.;PPN_HUMAN;.	V	231;258;258;258;258	ENSP00000345395:G231V;ENSP00000403403:G258V;ENSP00000370558:G258V;ENSP00000451803:G258V;ENSP00000451729:G258V	ENSP00000216658:G258V	G	+	2	0	PAPLN	72788227	1.000000	0.71417	0.707000	0.30419	0.682000	0.39822	6.561000	0.73955	2.179000	0.69175	0.561000	0.74099	GGT	G|0.998;T|0.002	0.002	strong		0.662	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462		T	73718474	G	T	73718474	3	4	29	1	0	0	0	0	1	0	0	0	11437	1261	44	4	718	4	PAPLN	14	73718474	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	4376821	73718474	33631066	667	12908											
ACOT4	122970	hgsc.bcm.edu	37	chr14	74061757	74061757	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcttcttttcttccaggtaaAaggcccaggcattgggcttt	7	15	9	10	0	3	0	0	0	3	0	4	0	4	0	2	4	0	3	2	4	2	7	rs141714008		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:74061757A>G	ENST00000326303.4	+	3	919	c.665A>G	c.(664-666)aAa>aGa	p.K222R		NM_152331.3	NP_689544.3	Q8N9L9	ACOT4_HUMAN	acyl-CoA thioesterase 4	222					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)		TTCCAGGTAAAAGGCCCAGGC	0.478																																					p.K222R		Atlas-SNP	.											.	ACOT4	25	.	0			c.A665G						PASS	.	A	ARG/LYS	0,4406		0,0,2203	93	102	99		665	5.4	1	14	dbSNP_134	99	1,8599	1.2+/-3.3	0,1,4299	no	missense	ACOT4	NM_152331.3	26	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign	222/422	74061757	1,13005	2203	4300	6503	SO:0001583	missense	122970	exon3			AGGTAAAAGGCCC	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.665A>G	14.37:g.74061757A>G	ENSP00000323071:p.Lys222Arg	153	0	0		122	59	0.483607	NM_152331	Q17RF4|Q5BKT6|Q86TX0|Q86TX1|Q96N88	Missense_Mutation	SNP	ENST00000326303.4	37	CCDS9817.1	.	.	.	.	.	.	.	.	.	.	A	13.74	2.326631	0.41197	0.0	1.16E-4	ENSG00000177465	ENST00000326303	T	0.42131	0.98	5.41	5.41	0.78517	BAAT/Acyl-CoA thioester hydrolase C-terminal (1);	0.155471	0.56097	D	0.000021	T	0.37073	0.0990	L	0.38838	1.175	0.80722	D	1	B	0.24043	0.096	B	0.33750	0.169	T	0.21621	-1.0240	10	0.39692	T	0.17	-13.6392	11.1594	0.48507	0.8459:0.1541:0.0:0.0	.	222	Q8N9L9	ACOT4_HUMAN	R	222	ENSP00000323071:K222R	ENSP00000323071:K222R	K	+	2	0	ACOT4	73131510	0.449000	0.25689	0.993000	0.49108	0.954000	0.61252	2.093000	0.41710	2.051000	0.60960	0.459000	0.35465	AAA	A|1.000;G|0.000	0.000	weak		0.478	ACOT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404298.2	NM_152331		G	74061757	A	G	74061757	3	3	29	1	0	0	0	0	1	0	0	0	153	14	1	3	675	3	ACOT4	14	74061757	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	343283	74061757	33287783	668	12909											
NPC2	10577	hgsc.bcm.edu	37	chr14	74951269	74951269	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggatgccatgcaccacggccTtgctgcttttagactgaata	9	11	10	11	1	0	2	0	1	0	1	0	3	0	3	3	2	4	3	3	2	3	4	rs142075589		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:74951269T>C	ENST00000555619.1	-	3	449	c.212A>G	c.(211-213)aAg>aGg	p.K71R	NPC2_ENST00000434013.2_Missense_Mutation_p.K71R|NPC2_ENST00000541064.1_Missense_Mutation_p.K71R|NPC2_ENST00000557510.1_Missense_Mutation_p.K71R|NPC2_ENST00000238633.2_Missense_Mutation_p.K71R	NM_006432.3	NP_006423.1	P61916	NPC2_HUMAN	Niemann-Pick disease, type C2	71					cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|glycolipid transport (GO:0046836)|intracellular cholesterol transport (GO:0032367)|intracellular sterol transport (GO:0032366)|phospholipid transport (GO:0015914)|regulation of isoprenoid metabolic process (GO:0019747)|response to virus (GO:0009615)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	cholesterol binding (GO:0015485)|enzyme binding (GO:0019899)			breast(1)|endometrium(2)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(2)	7				BRCA - Breast invasive adenocarcinoma(234;0.00149)		CACCACGGCCTTGCTGCTTTT	0.403													T|||	1	0.000199681	0.0	0.0	5008	,	,		18393	0.0		0.001	False		,,,				2504	0.0				p.K71R	Pancreas(93;260 1497 8575 30964 48133)	Atlas-SNP	.											.	NPC2	9	.	0			c.A212G						PASS	.	T	ARG/LYS	0,4406		0,0,2203	105	101	102		212	4.2	0.9	14	dbSNP_134	102	2,8598		0,2,4298	yes	missense	NPC2	NM_006432.3	26	0,2,6501	CC,CT,TT		0.0233,0.0,0.0154	possibly-damaging	71/152	74951269	2,13004	2203	4300	6503	SO:0001583	missense	10577	exon3			ACGGCCTTGCTGC	X67698	CCDS32121.1	14q24.3	2009-09-12				ENSG00000119655			14537	protein-coding gene	gene with protein product	"epididymal protein 1"	601015				8418812, 11125141	Standard	NM_006432		Approved	HE1, NP-C2, EDDM1	uc001xpy.3	P61916		ENST00000555619.1:c.212A>G	14.37:g.74951269T>C	ENSP00000451112:p.Lys71Arg	46	0	0		47	25	0.531915	NM_006432	B4DQV7|Q15668|Q29413	Missense_Mutation	SNP	ENST00000555619.1	37	CCDS32121.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	T|T	14.54|14.54	2.565104|2.565104	0.45694|0.45694	0.0|0.0	2.33E-4|2.33E-4	ENSG00000119655|ENSG00000119655	ENST00000434013;ENST00000541064;ENST00000555619;ENST00000238633;ENST00000553490;ENST00000557510;ENST00000555592|ENST00000556009	T;T;T;T;T;T;T|.	0.76968|.	-1.06;-1.06;-1.06;-1.06;-1.06;-1.06;-1.06|.	6.07|6.07	4.15|4.15	0.48705|0.48705	MD-2-related lipid-recognition (3);Immunoglobulin E-set (1);|.	0.381390|.	0.31010|.	N|.	0.008424|.	T|T	0.73048|0.73048	0.3537|0.3537	M|M	0.74546|0.74546	2.27|2.27	0.39428|0.39428	D|D	0.96703|0.96703	P;P|.	0.38677|.	0.642;0.642|.	P;B|.	0.46718|.	0.525;0.428|.	T|T	0.74121|0.74121	-0.3767|-0.3767	10|5	0.29301|.	T|.	0.29|.	-11.3591|-11.3591	14.5102|14.5102	0.67780|0.67780	0.0:0.0:0.4367:0.5633|0.0:0.0:0.4367:0.5633	.|.	71;71|.	B4DQV7;P61916|.	.;NPC2_HUMAN|.	R|G	71|93	ENSP00000412103:K71R;ENSP00000442488:K71R;ENSP00000451112:K71R;ENSP00000238633:K71R;ENSP00000451180:K71R;ENSP00000451206:K71R;ENSP00000450887:K71R|.	ENSP00000238633:K71R|.	K|R	-|-	2|1	0|2	NPC2|NPC2	74021022|74021022	0.865000|0.865000	0.29922|0.29922	0.886000|0.886000	0.34754|0.34754	0.099000|0.099000	0.18886|0.18886	1.204000|1.204000	0.32296|0.32296	0.771000|0.771000	0.33359|0.33359	0.533000|0.533000	0.62120|0.62120	AAG|AGG	T|1.000;C|0.000	0.000	strong		0.403	NPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412346.1	NM_006432		C	74951269	T	C	74951269	3	2	29	1	0	0	0	0	1	0	0	0	10581	1609	56	3	255	3	NPC2	14	74951269	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	889512	74951269	32398271	669	12910											
FCF1	51077	hgsc.bcm.edu	37	chr14	75190002	75190002	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtataaccgattgtgtaaTggctgaaattgagaaattgg	14	13	11	3	1	0	2	0	2	0	1	0	4	0	2	1	2	1	3	1	2	5	6	rs41309250	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:75190002T>C	ENST00000341162.4	+	5	374	c.320T>C	c.(319-321)aTg>aCg	p.M107T	FCF1_ENST00000534938.2_Missense_Mutation_p.M95T|FCF1_ENST00000553615.1_Missense_Mutation_p.M92T	NM_015962.4	NP_057046.1	Q9Y324	FCF1_HUMAN	FCF1 rRNA-processing protein	107	PINc.				rRNA processing (GO:0006364)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)	8				BRCA - Breast invasive adenocarcinoma(234;0.0037)		GATTGTGTAATGGCTGAAATT	0.388													T|||	15	0.00299521	0.0	0.0115	5008	,	,		15747	0.0		0.002	False		,,,				2504	0.0051				p.M107T		Atlas-SNP	.											.	FCF1	15	.	0			c.T320C						PASS	.	T	THR/MET	5,4401	9.9+/-24.2	0,5,2198	117	111	113		320	6.1	1	14	dbSNP_127	113	39,8561	26.8+/-75.7	0,39,4261	yes	missense	FCF1	NM_015962.4	81	0,44,6459	CC,CT,TT		0.4535,0.1135,0.3383	possibly-damaging	107/199	75190002	44,12962	2203	4300	6503	SO:0001583	missense	51077	exon5			GTGTAATGGCTGA	AF132969	CCDS9832.1	14q24.2	2013-05-03	2013-05-03	2007-01-30	ENSG00000119616	ENSG00000119616			20220	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 111", "FCF1 small subunit (SSU) processome component homolog (S. cerevisiae)"	C14orf111		16762320	Standard	XR_245690		Approved	CGI-35, Bka, UTP24	uc001xqh.3	Q9Y324		ENST00000341162.4:c.320T>C	14.37:g.75190002T>C	ENSP00000344393:p.Met107Thr	115	0	0		122	67	0.54918	NM_015962	Q86TW8|Q8TBL8	Missense_Mutation	SNP	ENST00000341162.4	37	CCDS9832.1	7	0.003205128205128205	0	0.0	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	T	26.4	4.738739	0.89573	0.001135	0.004535	ENSG00000119616	ENST00000554590;ENST00000341162;ENST00000534938;ENST00000553615	.	.	.	6.06	6.06	0.98353	Nucleotide binding protein, PINc (1);	0.034297	0.85682	D	0.000000	T	0.72914	0.3520	H	0.96175	3.78	0.80722	D	1	P;B	0.37015	0.578;0.159	P;B	0.45712	0.491;0.257	D	0.83359	0.0001	9	0.66056	D	0.02	.	16.6093	0.84858	0.0:0.0:0.0:1.0	rs41309250	107;92	Q9Y324;G3V5S9	FCF1_HUMAN;.	T	18;107;95;92	.	ENSP00000344393:M107T	M	+	2	0	FCF1	74259755	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.760000	0.85248	2.324000	0.78689	0.533000	0.62120	ATG	T|0.995;C|0.005	0.005	strong		0.388	FCF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413622.1	NM_015962		C	75190002	T	C	75190002	3	2	29	1	0	0	0	0	1	0	0	0	5785	1464	51	3	338	3	FCF1	14	75190002	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	238733	75190002	32159538	670	12911											
ESRRB	2103	hgsc.bcm.edu	37	chr14	76966275	76966275	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccatgatggaaaatgccccTtccaatcagctgccttcaca	11	9	7	14	0	2	1	2	1	0	0	3	2	3	2	5	1	3	1	5	1	3	2	rs188462546	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:76966275T>C	ENST00000509242.1	+	9	1464	c.1366T>C	c.(1366-1368)Ttc>Ctc	p.F456L	ESRRB_ENST00000261532.7_3'UTR|RP11-187O7.3_ENST00000554926.1_lincRNA|ESRRB_ENST00000380887.2_Missense_Mutation_p.F456L	NM_004452.3	NP_004443.3	O95718	ERR2_HUMAN	estrogen-related receptor beta	456					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)		AAAATGCCCCTTCCAATCAGC	0.552													T|||	17	0.00339457	0.0008	0.0101	5008	,	,		18910	0.0		0.0089	False		,,,				2504	0.0				p.F456L		Atlas-SNP	.											.	ESRRB	114	.	0			c.T1366C						PASS	.	T	LEU/PHE	6,4400	8.1+/-20.4	0,6,2197	86	74	78		1366	-1.1	0	14		78	42,8558	22.2+/-67.0	0,42,4258	yes	missense	ESRRB	NM_004452.3	22	0,48,6455	CC,CT,TT		0.4884,0.1362,0.3691	benign	456/509	76966275	48,12958	2203	4300	6503	SO:0001583	missense	2103	exon10			TGCCCCTTCCAAT	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.1366T>C	14.37:g.76966275T>C	ENSP00000422488:p.Phe456Leu	97	0	0		91	50	0.549451	NM_004452	A2VDJ2|B6ZGU4|Q5F0P7|Q5F0P8|Q9HCB4	Missense_Mutation	SNP	ENST00000509242.1	37	CCDS9850.2	12	0.005494505494505495	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	8	0.010554089709762533	T	5.424	0.263322	0.10294	0.001362	0.004884	ENSG00000119715	ENST00000512784;ENST00000509242;ENST00000380887	D;D;D	0.92149	-2.97;-2.98;-2.98	3.02	-1.07	0.09968	.	.	.	.	.	T	0.69602	0.3129	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.60915	-0.7168	9	0.11485	T	0.65	.	0.5481	0.00657	0.2112:0.1289:0.2174:0.4425	.	456	Q5F0P7	.	L	461;456;456	ENSP00000424992:F461L;ENSP00000422488:F456L;ENSP00000370270:F456L	ENSP00000370270:F456L	F	+	1	0	ESRRB	76036028	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.131000	0.10482	-0.206000	0.10203	0.528000	0.53228	TTC	T|0.994;C|0.006	0.006	strong		0.552	ESRRB-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360663.1			C	76966275	T	C	76966275	3	2	29	1	0	0	0	0	1	0	0	0	5263	1609	56	3	1392	3	ESRRB	14	76966275	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	1776273	76966275	30383265	671	12912											
PPP4R4	57718	hgsc.bcm.edu	37	chr14	94722815	94722815	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agaatgaaactttgctacctGttgcccaaagtgaaatctac	14	11	7	9	0	1	3	0	2	1	1	1	3	1	3	2	0	5	2	2	0	6	4	rs114970142	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:94722815G>A	ENST00000304338.3	+	17	2038	c.1884G>A	c.(1882-1884)ctG>ctA	p.L628L		NM_058237.1	NP_478144.1	Q6NUP7	PP4R4_HUMAN	protein phosphatase 4, regulatory subunit 4	628					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						TTTGCTACCTGTTGCCCAAAG	0.318													G|||	70	0.0139776	0.0	0.0	5008	,	,		18900	0.0188		0.0	False		,,,				2504	0.0521				p.L628L		Atlas-SNP	.											.	PPP4R4	107	.	0			c.G1884A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	85	89	87		1884	-3.5	0.4	14	dbSNP_132	87	0,8598		0,0,4299	no	coding-synonymous	PPP4R4	NM_058237.1		0,1,6501	AA,AG,GG		0.0,0.0227,0.0077		628/874	94722815	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	57718	exon17			CTACCTGTTGCCC	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.1884G>A	14.37:g.94722815G>A		41	0	0		35	13	0.371429	NM_058237	Q9BUF8|Q9HCF0	Silent	SNP	ENST00000304338.3	37	CCDS9921.1																																																																																			G|0.989;A|0.011	0.011	strong		0.318	PPP4R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413056.1	NM_058237		A	94722815	G	A	94722815	2	1	29	1	0	0	0	0	0	0	0	1	12417	1364	48	2		2	PPP4R4	14	94722815	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	17756540	94722815	12626725	672	12913											
SERPINA10	51156	hgsc.bcm.edu	37	chr14	94750408	94750408	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccactttgatgacaggaggcAtggaataagcagtaatttct	13	11	10	7	0	1	2	0	2	1	0	1	4	1	4	1	3	1	3	1	3	3	4	rs117152910	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:94750408A>C	ENST00000393096.1	-	5	1694	c.1229T>G	c.(1228-1230)aTg>aGg	p.M410R	SERPINA10_ENST00000554723.1_Missense_Mutation_p.M450R|SERPINA10_ENST00000261994.4_Missense_Mutation_p.M410R|SERPINA10_ENST00000554173.1_Missense_Mutation_p.M410R	NM_016186.2	NP_057270.1	Q9UK55	ZPI_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 10	410					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)		GACAGGAGGCATGGAATAAGC	0.443													A|||	70	0.0139776	0.0	0.0	5008	,	,		18909	0.0188		0.0	False		,,,				2504	0.0521				p.M410R		Atlas-SNP	.											SERPINA10,caecum,carcinoma,+1,1	SERPINA10	83	1	0			c.T1229G						PASS	.	A	ARG/MET,ARG/MET	1,4405	2.1+/-5.4	0,1,2202	100	93	95		1229,1229	3.4	0.7	14	dbSNP_132	95	0,8600		0,0,4300	yes	missense,missense	SERPINA10	NM_001100607.1,NM_016186.2	91,91	0,1,6502	CC,CA,AA		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	410/445,410/445	94750408	1,13005	2203	4300	6503	SO:0001583	missense	51156	exon5			GGAGGCATGGAAT	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.1229T>G	14.37:g.94750408A>C	ENSP00000376809:p.Met410Arg	60	0	0		86	42	0.488372	NM_001100607	A5Z2A5|Q6UWX9|Q86U20	Missense_Mutation	SNP	ENST00000393096.1	37	CCDS9923.1	11	0.005036630036630037	0	0.0	0	0.0	11	0.019230769230769232	0	0.0	A	6.486	0.457830	0.12342	2.27E-4	0.0	ENSG00000140093	ENST00000554723;ENST00000393096;ENST00000261994;ENST00000554173	D;D;D;D	0.83837	-1.77;-1.77;-1.77;-1.77	5.7	3.37	0.38596	Serpin domain (3);	0.158112	0.44285	D	0.000475	T	0.68632	0.3022	L	0.41710	1.295	0.32273	N	0.568655	P	0.51537	0.946	P	0.51135	0.66	T	0.76753	-0.2843	10	0.38643	T	0.18	.	9.8433	0.41013	0.8623:0.0:0.1377:0.0	.	410	Q9UK55	ZPI_HUMAN	R	450;410;410;410	ENSP00000450896:M450R;ENSP00000376809:M410R;ENSP00000261994:M410R;ENSP00000450971:M410R	ENSP00000261994:M410R	M	-	2	0	SERPINA10	93820161	0.979000	0.34478	0.707000	0.30419	0.005000	0.04900	1.686000	0.37669	0.448000	0.26722	-0.263000	0.10527	ATG	A|0.993;C|0.007	0.007	strong		0.443	SERPINA10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413061.1	NM_016186		C	94750408	A	C	94750408	3	2	29	1	0	0	0	0	1	0	0	0	14102	217	8	5	109	5	SERPINA10	14	94750408	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	27593	94750408	12599132	673	12914											
C14orf49	161176	hgsc.bcm.edu	37	chr14	95884294	95884294	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaggaggaacagcagcagaaGcagctgcagtgggagcgcca	13	2	17	9	1	0	1	0	0	0	1	0	5	0	4	1	3	7	5	1	3	2	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:95884294G>A	ENST00000334258.5	-	17	2811	c.2797C>T	c.(2797-2799)Ctt>Ttt	p.L933F	SYNE3_ENST00000554873.1_Missense_Mutation_p.L690F|SYNE3_ENST00000557275.1_Missense_Mutation_p.L928F	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	933	KASH. {ECO:0000255|PROSITE- ProRule:PRU00385}.				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						agcagcagaagcagctgcagt	0.642																																					p.L933F		Atlas-SNP	.											.	SYNE3	130	.	0			c.C2797T						PASS	.						78	70	72					14																	95884294		2203	4300	6503	SO:0001583	missense	161176	exon17			GCAGAAGCAGCTG	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.2797C>T	14.37:g.95884294G>A	ENSP00000334308:p.Leu933Phe	98	0	0		81	7	0.0864198	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	37	CCDS9935.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.461520	0.43736	.	.	ENSG00000176438	ENST00000334258;ENST00000554873;ENST00000557275	T;T;T	0.35973	1.28;1.28;1.28	4.67	-0.221	0.13126	Klarsicht/ANC-1/syne-1 homology (2);	0.288824	0.18450	U	0.140875	T	0.33440	0.0863	L	0.51422	1.61	0.80722	D	1	B;B	0.30281	0.232;0.275	B;B	0.35607	0.13;0.206	T	0.22800	-1.0206	10	0.51188	T	0.08	-2.5151	11.5454	0.50690	0.3057:0.0:0.6943:0.0	.	928;933	Q6ZMZ3-2;Q6ZMZ3	.;SYNE3_HUMAN	F	933;690;928	ENSP00000334308:L933F;ENSP00000452154:L690F;ENSP00000450562:L928F	ENSP00000334308:L933F	L	-	1	0	C14orf49	94954047	1.000000	0.71417	0.996000	0.52242	0.906000	0.53458	2.722000	0.47269	0.043000	0.15746	0.289000	0.19496	CTT	.	.	none		0.642	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592		A	95884294	G	A	95884294	3	1	29	1	0	0	0	0	1	0	0	0	1778	971	34	2	134	2	C14orf49	14	95884294	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1133886	95884294	11465246	674	12915											
ATG2B	55102	hgsc.bcm.edu	37	chr14	96800027	96800027	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagtttgagttgcttaccaCggctagaaggtgtacgagct	10	11	12	8	2	0	2	0	1	0	1	0	3	0	2	1	2	4	6	1	2	4	5	rs183527316	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:96800027C>T	ENST00000359933.4	-	8	2098	c.1205G>A	c.(1204-1206)cGt>cAt	p.R402H		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	402					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)		TTGCTTACCACGGCTAGAAGG	0.363													C|||	2	0.000399361	0.0	0.0	5008	,	,		16337	0.0		0.002	False		,,,				2504	0.0				p.R402H		Atlas-SNP	.											.	ATG2B	169	.	0			c.G1205A						PASS	.	C	HIS/ARG	4,3650		0,4,1823	77	70	72		1205	5.6	1	14		72	59,8131		0,59,4036	yes	missense	ATG2B	NM_018036.5	29	0,63,5859	TT,TC,CC		0.7204,0.1095,0.5319	benign	402/2079	96800027	63,11781	1827	4095	5922	SO:0001583	missense	55102	exon8			TTACCACGGCTAG	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.1205G>A	14.37:g.96800027C>T	ENSP00000353010:p.Arg402His	81	0	0		98	50	0.510204	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	37	CCDS9944.2	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	16.68	3.189548	0.57909	0.001095	0.007204	ENSG00000066739	ENST00000359933	T	0.10382	2.88	5.6	5.6	0.85130	.	0.423584	0.20315	U	0.094755	T	0.05640	0.0148	N	0.19112	0.55	0.47341	D	0.999394	B	0.22211	0.066	B	0.14023	0.01	T	0.24657	-1.0154	10	0.41790	T	0.15	.	13.2187	0.59875	0.0:0.9272:0.0:0.0728	.	402	Q96BY7	ATG2B_HUMAN	H	402	ENSP00000353010:R402H	ENSP00000353010:R402H	R	-	2	0	ATG2B	95869780	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.238000	0.65366	2.793000	0.96121	0.591000	0.81541	CGT	C|0.998;T|0.002	0.002	strong		0.363	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036		T	96800027	C	T	96800027	3	4	29	1	0	0	0	0	1	0	0	0	1094	536	19	1	5171	1	ATG2B	14	96800027	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	915733	96800027	10549513	675	12916											
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102482399	102482399	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cccgacttccccatgcagatCgagcagctggagcgctacat	9	7	10	15	3	0	1	0	0	0	1	2	4	1	2	3	1	5	4	3	1	1	2	rs17541158	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:102482399C>T	ENST00000360184.4	+	36	7613	c.7449C>T	c.(7447-7449)atC>atT	p.I2483I		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	2483					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						CCATGCAGATCGAGCAGCTGG	0.622													C|||	76	0.0151757	0.003	0.0231	5008	,	,		20649	0.0		0.0437	False		,,,				2504	0.0123				p.I2483I		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.C7449T						PASS	.	C		33,4373	38.4+/-70.7	0,33,2170	49	37	41		7449	-4.8	0.2	14	dbSNP_123	41	405,8195	125.6+/-184.2	8,389,3903	no	coding-synonymous	DYNC1H1	NM_001376.4		8,422,6073	TT,TC,CC		4.7093,0.749,3.3677		2483/4647	102482399	438,12568	2203	4300	6503	SO:0001819	synonymous_variant	1778	exon36			GCAGATCGAGCAG	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.7449C>T	14.37:g.102482399C>T		36	0	0		47	23	0.489362	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																			C|0.972;T|0.028	0.028	strong		0.622	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		T	102482399	C	T	102482399	2	4	29	1	0	0	0	0	0	0	0	1	4843	874	31	1		1	DYNC1H1	14	102482399	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	5682372	102482399	4867141	676	12917											
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102516487	102516487	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcaaccgcccttcccctgacGcagctgcgctgggtcaagca	7	7	10	17	3	2	1	2	1	0	0	3	1	3	1	4	1	4	4	4	1	2	1	rs35079638	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:102516487G>A	ENST00000360184.4	+	77	13928	c.13764G>A	c.(13762-13764)acG>acA	p.T4588T	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	4588					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						TTCCCCTGACGCAGCTGCGCT	0.567													.|||	5	0.000998403	0.0008	0.0014	5008	,	,		21568	0.0		0.003	False		,,,				2504	0.0				p.T4588T		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.G13764A						PASS	.	G		0,4406		0,0,2203	90	80	83		13764	-9.7	0.7	14	dbSNP_126	83	10,8590	7.1+/-27.0	0,10,4290	no	coding-synonymous	DYNC1H1	NM_001376.4		0,10,6493	AA,AG,GG		0.1163,0.0,0.0769		4588/4647	102516487	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	1778	exon77			CCTGACGCAGCTG	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.13764G>A	14.37:g.102516487G>A		87	0	0		91	52	0.571429	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																			G|0.998;A|0.002	0.002	strong		0.567	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		A	102516487	G	A	102516487	2	1	29	1	0	0	0	0	0	0	0	1	4843	1074	38	1		1	DYNC1H1	14	102516487	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	34088	102516487	4833053	677	12918											
HSP90AA1	3320	hgsc.bcm.edu	37	chr14	102552201	102552201	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actttctcagcaaccaaataAgcagaataaaaaccaacacc	20	6	3	12	0	1	1	1	0	1	1	2	1	1	1	3	0	5	2	3	0	8	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:102552201A>G	ENST00000216281.8	-	3	628	c.423T>C	c.(421-423)gcT>gcC	p.A141A	HSP90AA1_ENST00000334701.7_Silent_p.A263A|HSP90AA1_ENST00000441629.2_Intron	NM_005348.3	NP_005339.3	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 1	141					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)	CAACCAAATAAGCAGAATAAA	0.473																																					p.A263A		Atlas-SNP	.											.	HSP90AA1	65	.	0			c.T789C						PASS	.						86	82	84					14																	102552201		2203	4300	6503	SO:0001819	synonymous_variant	3320	exon4			CAAATAAGCAGAA	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.423T>C	14.37:g.102552201A>G		136	0	0		155	40	0.258065	NM_001017963	A8K500|B3KPJ9|Q2PP14|Q5CAQ6|Q5CAQ7|Q9BVQ5	Silent	SNP	ENST00000216281.8	37	CCDS9967.1																																																																																			.	.	none		0.473	HSP90AA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414952.2	NM_005348		G	102552201	A	G	102552201	2	3	29	1	0	0	0	0	0	0	0	1	7410	59	3	3		3	HSP90AA1	14	102552201	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	35714	102552201	4797339	678	12919											
CDCA4	55038	hgsc.bcm.edu	37	chr14	105478159	105478159	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accagagacatgtccaggagCgactgccgctgcaggctgta	10	6	13	12	2	0	1	0	0	0	1	1	4	1	2	3	2	3	4	3	2	1	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:105478159C>T	ENST00000336219.3	-	2	263	c.108G>A	c.(106-108)tcG>tcA	p.S36S	CDCA4_ENST00000392590.3_Silent_p.S36S	NM_017955.3	NP_060425.2	Q9BXL8	CDCA4_HUMAN	cell division cycle associated 4	36	SERTA. {ECO:0000255|PROSITE- ProRule:PRU00396}.					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)		TGTCCAGGAGCGACTGCCGCT	0.592																																					p.S36S		Atlas-SNP	.											.	CDCA4	18	.	0			c.G108A						PASS	.						71	59	63					14																	105478159		2203	4300	6503	SO:0001819	synonymous_variant	55038	exon2			CAGGAGCGACTGC	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.108G>A	14.37:g.105478159C>T		57	0	0		80	33	0.4125	NM_017955	Q8TB18|Q9NWK7	Silent	SNP	ENST00000336219.3	37	CCDS9996.1																																																																																			.	.	none		0.592	CDCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410311.1	NM_145701		T	105478159	C	T	105478159	2	4	29	1	0	0	0	0	0	0	0	1	3090	755	27	1		1	CDCA4	14	105478159	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2925958	105478159	1871381	679	12920											
CRIP1	1396	hgsc.bcm.edu	37	chr14	105954687	105954687	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcacgaaggcaaaccctactGcaaccacccctgctacgcag	12	4	8	17	2	0	0	0	0	0	0	0	1	0	0	4	1	6	5	4	1	5	2	rs7824	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr14:105954687G>T	ENST00000330233.7	+	3	1098	c.155G>T	c.(154-156)tGc>tTc	p.C52F	C14orf80_ENST00000392523.4_5'Flank|CRIP1_ENST00000392531.3_Missense_Mutation_p.C52F|C14orf80_ENST00000354560.6_5'Flank|C14orf80_ENST00000392522.3_5'Flank|C14orf80_ENST00000334656.7_5'Flank|C14orf80_ENST00000392527.1_5'Flank|CRIP1_ENST00000409393.2_Missense_Mutation_p.C52F|C14orf80_ENST00000329886.7_5'Flank|CRIP1_ENST00000551180.1_Silent_p.L20L			P50238	CRIP1_HUMAN	cysteine-rich protein 1 (intestinal)	52	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell proliferation (GO:0008283)|cellular response to antibiotic (GO:0071236)|cellular response to UV-B (GO:0071493)|heart development (GO:0007507)|immune response (GO:0006955)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|prostate gland stromal morphogenesis (GO:0060741)|regulation of gene expression (GO:0010468)|response to organic substance (GO:0010033)|response to zinc ion (GO:0010043)	cytoplasm (GO:0005737)	AT DNA binding (GO:0003680)|DNA binding, bending (GO:0008301)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)						Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0188)	Epithelial(152;0.235)		AAACCCTACTGCAACCACCCC	0.652													G|||	11	0.00219649	0.0	0.0029	5008	,	,		10618	0.0		0.0089	False		,,,				2504	0.0				p.C52F		Atlas-SNP	.											.	CRIP1	1	.	0			c.G155T						PASS	.	G	PHE/CYS	11,4393	15.5+/-35.6	0,11,2191	46	63	57		155	3.8	1	14	dbSNP_52	57	105,8495	55.6+/-116.7	2,101,4197	yes	missense	CRIP1	NM_001311.4	205	2,112,6388	TT,TG,GG		1.2209,0.2498,0.892	probably-damaging	52/78	105954687	116,12888	2202	4300	6502	SO:0001583	missense	1396	exon4			CCTACTGCAACCA		CCDS10004.1	14q32.33	2004-06-18			ENSG00000213145	ENSG00000213145			2360	protein-coding gene	gene with protein product		123875				9480758	Standard	NM_001311		Approved	CRIP	uc001yri.4	P50238	OTTHUMG00000029908	ENST00000330233.7:c.155G>T	14.37:g.105954687G>T	ENSP00000332449:p.Cys52Phe	123	0	0		110	57	0.518182	NM_001311	H3BPI2|Q13628|Q53XY7|Q96J34	Missense_Mutation	SNP	ENST00000330233.7	37	CCDS10004.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	G	17.03	3.284634	0.59867	0.002498	0.012209	ENSG00000213145	ENST00000330233;ENST00000409393;ENST00000392531	D;D;D	0.99319	-5.74;-5.74;-5.74	4.76	3.8	0.43715	Zinc finger, LIM-type (4);	0.000000	0.56097	U	0.000022	D	0.98868	0.9617	.	.	.	0.58432	D	0.999998	D	0.56287	0.975	D	0.63192	0.912	D	0.95700	0.8748	9	0.87932	D	0	-12.7512	13.1083	0.59259	0.0:0.1623:0.8377:0.0	rs14079;rs11544873	52	P50238	CRIP1_HUMAN	F	52	ENSP00000332449:C52F;ENSP00000386340:C52F;ENSP00000376315:C52F	ENSP00000447493:C52F	C	+	2	0	CRIP1	105025732	1.000000	0.71417	1.000000	0.80357	0.568000	0.35870	8.181000	0.89696	2.186000	0.69663	0.650000	0.86243	TGC	C|0.064;G|0.923;T|0.013	0.013	strong		0.652	CRIP1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335466.2	NM_001311		T	105954687	G	T	105954687	3	4	29	1	0	0	0	0	1	0	0	0	3876	1319	46	4	165	4	CRIP1	14	105954687	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	476528	105954687	1394853	680	12921											
MGA	23269	hgsc.bcm.edu	37	chr15	41988709	41988709	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcgaaaggataaatcttctAtgttggcagaattggaatat	14	13	9	5	1	2	1	0	0	2	1	3	4	2	3	0	3	0	2	0	3	7	6	rs199666635		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:41988709A>G	ENST00000570161.1	+	2	1501	c.1501A>G	c.(1501-1503)Atg>Gtg	p.M501V	MGA_ENST00000566586.1_Missense_Mutation_p.M501V|MGA_ENST00000219905.7_Missense_Mutation_p.M501V|MGA_ENST00000389936.4_Missense_Mutation_p.M501V|MGA_ENST00000568630.1_3'UTR|MGA_ENST00000545763.1_Missense_Mutation_p.M501V			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)	TAAATCTTCTATGTTGGCAGA	0.403																																					p.M501V		Atlas-SNP	.											.	MGA	264	.	0			c.A1501G						PASS	.	A	VAL/MET,VAL/MET	0,3680		0,0,1840	78	73	74		1501,1501	-8.1	0	15		74	5,8175		0,5,4085	yes	missense,missense	MGA	NM_001080541.2,NM_001164273.1	21,21	0,5,5925	GG,GA,AA		0.0611,0.0,0.0422	benign,benign	501/2857,501/3066	41988709	5,11855	1840	4090	5930	SO:0001583	missense	23269	exon3			TCTTCTATGTTGG	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.1501A>G	15.37:g.41988709A>G	ENSP00000457035:p.Met501Val	63	0	0		40	28	0.7	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	37	CCDS55959.1	.	.	.	.	.	.	.	.	.	.	A	3.281	-0.146993	0.06627	0.0	6.11E-4	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	D;D;D	0.82526	-1.61;-1.62;-1.61	4.53	-8.14	0.01069	.	1.679160	0.03077	N	0.157995	T	0.56426	0.1984	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.53049	-0.8493	10	0.21540	T	0.41	.	2.9361	0.05815	0.5423:0.1875:0.1432:0.127	.	501;501	F5H7K2;E7ENI0	.;.	V	501	ENSP00000219905:M501V;ENSP00000374586:M501V;ENSP00000442467:M501V	ENSP00000219905:M501V	M	+	1	0	MGA	39776001	0.002000	0.14202	0.006000	0.13384	0.986000	0.74619	-0.997000	0.03705	-2.196000	0.00751	0.379000	0.24179	ATG	.	.	weak		0.403	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1		G	41988709	A	G	41988709	3	3	29	1	0	0	0	0	1	0	0	0	9549	449	16	3	1507	3	MGA	15	41988709	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10		41988709	60542683	681	12922											
LCMT2	9836	hgsc.bcm.edu	37	chr15	43621483	43621483	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cacaactgcctatttggctgCctttccattcagagtcacaa	10	12	6	13	0	2	1	2	0	0	1	3	1	3	1	3	1	3	1	3	1	3	4	rs144228208		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:43621483C>T	ENST00000305641.5	-	1	1320	c.1205G>A	c.(1204-1206)gGc>gAc	p.G402D	LCMT2_ENST00000544735.1_5'UTR|ADAL_ENST00000422466.2_5'Flank|LCMT2_ENST00000567039.1_3'UTR|ADAL_ENST00000428046.3_5'Flank|ADAL_ENST00000389651.4_5'Flank	NM_014793.4	NP_055608.2	O60294	TYW4_HUMAN	leucine carboxyl methyltransferase 2	402					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)	TATTTGGCTGCCTTTCCATTC	0.532																																					p.G402D		Atlas-SNP	.											LCMT2,NS,carcinoma,-1,1	LCMT2	48	1	0			c.G1205A						PASS	.	C	ASP/GLY	0,4402		0,0,2201	104	109	107		1205	3	1	15	dbSNP_134	107	4,8594	3.7+/-12.6	0,4,4295	yes	missense	LCMT2	NM_014793.4	94	0,4,6496	TT,TC,CC		0.0465,0.0,0.0308	probably-damaging	402/687	43621483	4,12996	2201	4299	6500	SO:0001583	missense	9836	exon1			TGGCTGCCTTTCC	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.1205G>A	15.37:g.43621483C>T	ENSP00000307214:p.Gly402Asp	93	0	0		63	45	0.714286	NM_014793	Q4JFT6|Q96B55|Q9NR10	Missense_Mutation	SNP	ENST00000305641.5	37	CCDS10094.1	.	.	.	.	.	.	.	.	.	.	C	10.62	1.402603	0.25291	0.0	4.65E-4	ENSG00000168806	ENST00000305641	T	0.73897	-0.79	4.99	2.99	0.34606	.	0.852961	0.10614	N	0.654101	T	0.58977	0.2160	L	0.48362	1.52	0.80722	D	1	P	0.50272	0.933	B	0.36719	0.231	T	0.55854	-0.8075	10	0.13108	T	0.6	-26.0582	6.3112	0.21166	0.0:0.7148:0.1871:0.0981	.	402	O60294	LCMT2_HUMAN	D	402	ENSP00000307214:G402D	ENSP00000307214:G402D	G	-	2	0	LCMT2	41408775	0.204000	0.23447	0.985000	0.45067	0.712000	0.41017	1.513000	0.35823	1.479000	0.48272	0.655000	0.94253	GGC	C|1.000;T|0.000	0.000	weak		0.532	LCMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253205.1	NM_014793		T	43621483	C	T	43621483	3	4	29	1	0	0	0	0	1	0	0	0	8688	739	26	2	859	2	LCMT2	15	43621483	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1632774	43621483	58909909	682	12923											
B2M	567	hgsc.bcm.edu	37	chr15	45007888	45007891	+	Frame_Shift_Del	DEL	TAGT	TAGT	-																															gactttgtcacagcccaagaTagttaagtggggtaagtctt																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TAGT	TAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:45007888_45007891delTAGT	ENST00000558401.1	+	2	405_408	c.335_338delTAGT	c.(334-339)atagttfs	p.IV112fs	B2M_ENST00000559220.1_Intron|B2M_ENST00000559916.1_Frame_Shift_Del_p.IV112fs|B2M_ENST00000544417.1_Frame_Shift_Del_p.IV112fs	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	112	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 exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|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 T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|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)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		CAGCCCAAGATAGTTAAGTGGGGT	0.402																																					p.112_113del		Pindel	.											.	B2M	99	.	0			c.334_337del						PASS	.																																			SO:0001589	frameshift_variant	567	exon2			.	AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"Immunoglobulin superfamily / C1-set domain containing"	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.335_338delTAGT	15.37:g.45007888_45007891delTAGT	ENSP00000452780:p.Ile112fs	71	0	.		51	17	0.333	NM_004048	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Frame_Shift_Del	DEL	ENST00000558401.1	37	CCDS10113.1																																																																																			.	.	none		0.402	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048		-	45007891	TAGT	-	45007888	7	5	29	1	0	1	0	1	0	0	0	0	1244	1406	49	0	341	0	B2M	15	45007888	Frame_Shift_Del	DEL	TAGT	TCGA-GR-7351-01A-11D-2210-10	1386405	45007888	57523504	683	12924											
GATM	2628	hgsc.bcm.edu	37	chr15	45660421	45660421	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgataatctcattgcccacAactatcaggatgtctcgagg	11	11	8	11	2	3	0	2	0	2	0	6	3	3	1	1	2	2	0	1	2	3	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:45660421A>G	ENST00000396659.3	-	4	861	c.522T>C	c.(520-522)gtT>gtC	p.V174V	GATM_ENST00000558336.1_Silent_p.V174V	NM_001482.2	NP_001473.1	P50440	GATM_HUMAN	glycine amidinotransferase (L-arginine:glycine amidinotransferase)	174					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)	CATTGCCCACAACTATCAGGA	0.448																																					p.V174V		Atlas-SNP	.											.	GATM	34	.	0			c.T522C						PASS	.						111	95	100					15																	45660421		2198	4298	6496	SO:0001819	synonymous_variant	2628	exon4			GCCCACAACTATC	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.522T>C	15.37:g.45660421A>G		98	0	0		54	23	0.425926	NM_001482	B4DH99|B4DPI3|Q53EQ4	Silent	SNP	ENST00000396659.3	37	CCDS10122.1																																																																																			.	.	none		0.448	GATM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254220.2	NM_001482		G	45660421	A	G	45660421	2	3	29	1	0	0	0	0	0	0	0	1	6271	117	5	3		3	GATM	15	45660421	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	652533	45660421	56870971	684	12925											
WDR72	256764	hgsc.bcm.edu	37	chr15	54007512	54007512	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	taaggacatcttgatattctCcacaacaaagaagccagcct	15	9	6	11	0	2	2	0	1	2	1	3	3	2	3	3	1	3	0	3	1	5	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:54007512C>A	ENST00000396328.1	-	5	631	c.392G>T	c.(391-393)gGa>gTa	p.G131V	WDR72_ENST00000360509.5_Missense_Mutation_p.G131V|WDR72_ENST00000557913.1_Missense_Mutation_p.G131V|WDR72_ENST00000559418.1_Missense_Mutation_p.G131V	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	131										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)		TTGATATTCTCCACAACAAAG	0.378																																					p.G131V		Atlas-SNP	.											.	WDR72	177	.	0			c.G392T						PASS	.						92	89	90					15																	54007512		2194	4293	6487	SO:0001583	missense	256764	exon5			TATTCTCCACAAC	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.392G>T	15.37:g.54007512C>A	ENSP00000379619:p.Gly131Val	223	0	0		223	64	0.286996	NM_182758	Q7Z3I3|Q8N8X2	Missense_Mutation	SNP	ENST00000396328.1	37	CCDS10151.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.410211	0.83340	.	.	ENSG00000166415	ENST00000396328;ENST00000360509	T;T	0.64803	-0.12;-0.12	5.59	5.59	0.84812	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.64402	D	0.000001	T	0.80670	0.4667	M	0.79258	2.445	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.82526	-0.0413	10	0.87932	D	0	.	18.5785	0.91163	0.0:1.0:0.0:0.0	.	131	Q3MJ13	WDR72_HUMAN	V	131	ENSP00000379619:G131V;ENSP00000353699:G131V	ENSP00000353699:G131V	G	-	2	0	WDR72	51794804	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.640000	0.74319	2.629000	0.89072	0.655000	0.94253	GGA	.	.	none		0.378	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758		A	54007512	C	A	54007512	3	1	29	1	0	0	0	0	1	0	0	0	17337	855	30	4	2980	4	WDR72	15	54007512	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	8347091	54007512	48523880	685	12926											
DYX1C1	161582	hgsc.bcm.edu	37	chr15	55789910	55789910	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttttaataaagaacttacCacccgtcacagaaagggtct	14	11	6	10	1	3	2	1	0	2	2	3	2	3	2	2	1	2	0	2	1	6	4	rs17819126	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:55789910C>T	ENST00000321149.3	-	3	638	c.271G>A	c.(271-273)Gtt>Att	p.V91I	DYX1C1_ENST00000457155.2_Splice_Site_p.V91I|DYX1C1_ENST00000448430.2_Splice_Site_p.V91I|DYX1C1_ENST00000380679.1_Splice_Site_p.V91I|DYX1C1-CCPG1_ENST00000565113.1_RNA|DYX1C1_ENST00000348518.3_Splice_Site_p.V91I	NM_130810.3	NP_570722.2	Q8WXU2	DYXC1_HUMAN	dyslexia susceptibility 1 candidate 1	91	Mediates interaction with ESR1 and STUB1.		V -> I (in dbSNP:rs17819126). {ECO:0000269|PubMed:12954984}.		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)		AAGAACTTACCACCCGTCACA	0.393													C|||	110	0.0219649	0.0053	0.0245	5008	,	,		15552	0.0		0.0596	False		,,,				2504	0.0266				p.V91I		Atlas-SNP	.											.	DYX1C1	54	.	0			c.G271A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL	60,4326	56.2+/-92.4	0,60,2133	119	127	125		271,271,271	4.7	1	15	dbSNP_123	125	601,7983	158.6+/-212.1	23,555,3714	yes	missense-near-splice,missense-near-splice,missense-near-splice	DYX1C1	NM_001033559.2,NM_001033560.1,NM_130810.3	29,29,29	23,615,5847	TT,TC,CC		7.0014,1.368,5.0964	benign,benign,benign	91/377,91/382,91/421	55789910	661,12309	2193	4292	6485	SO:0001630	splice_region_variant	161582	exon3			ACTTACCACCCGT		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.271+1G>A	15.37:g.55789910C>T		49	0	0		47	29	0.617021	NM_001033560	Q6P5Y9|Q8N1S6	Missense_Mutation	SNP	ENST00000321149.3	37	CCDS10154.1	49	0.022435897435897436	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	41	0.05408970976253298	C	10.49	1.364727	0.24684	0.01368	0.070014	ENSG00000256061	ENST00000420792;ENST00000448430;ENST00000380679;ENST00000457155;ENST00000321149;ENST00000348518	T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57	4.72	4.72	0.59763	HSP20-like chaperone (1);	0.252489	0.31279	U	0.007926	T	0.01287	0.0042	N	0.19112	0.55	0.34059	D	0.657104	B;B;B	0.15930	0.015;0.002;0.005	B;B;B	0.17433	0.009;0.002;0.018	T	0.11616	-1.0580	9	.	.	.	.	10.0731	0.42345	0.0:0.908:0.0:0.0919	rs17819126;rs52810117;rs17819126	91;91;91	Q8WXU2-3;Q8WXU2;Q8WXU2-2	.;DYXC1_HUMAN;.	I	91	ENSP00000403412:V91I;ENSP00000370054:V91I;ENSP00000402640:V91I;ENSP00000323275:V91I;ENSP00000299561:V91I	.	V	-	1	0	DYX1C1	53577202	0.965000	0.33210	0.999000	0.59377	0.426000	0.31534	1.565000	0.36386	2.450000	0.82876	0.561000	0.74099	GTT	C|0.959;T|0.041	0.041	strong		0.393	DYX1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254976.1	NM_130810	Missense_Mutation	T	55789910	C	T	55789910	5	4	29	1	0	0	0	0	0	0	1	0	4864	608	21	2	1126	2	DYX1C1	15	55789910	Splice_Site	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1782398	55789910	46741482	686	12927											
TCF12	6938	hgsc.bcm.edu	37	chr15	57565432	57565432	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cttcatcaagccgtggcagtCatccttagtctagaacagca	11	10	8	12	1	4	1	3	0	1	1	5	1	5	1	2	1	3	2	2	1	4	3	rs77034126	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:57565432C>T	ENST00000267811.5	+	18	2182	c.1878C>T	c.(1876-1878)gtC>gtT	p.V626V	TCF12_ENST00000559703.1_Silent_p.V283V|TCF12_ENST00000452095.2_Silent_p.V646V|TCF12_ENST00000537840.1_Silent_p.V390V|TCF12_ENST00000557843.1_Silent_p.V626V|TCF12_ENST00000343827.3_Silent_p.V456V|TCF12_ENST00000543579.1_Silent_p.V480V|TCF12_ENST00000559710.1_Silent_p.V260V|TCF12_ENST00000333725.5_Silent_p.V650V|TCF12_ENST00000438423.2_Silent_p.V650V	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN	transcription factor 12	626	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				immune response (GO:0006955)|muscle organ development (GO:0007517)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)		TCF12/NR4A3(2)	breast(2)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	36		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		CCGTGGCAGTCATCCTTAGTC	0.428			T	TEC	extraskeletal myxoid chondrosarcoma								C|||	13	0.00259585	0.0008	0.0086	5008	,	,		20548	0.0		0.006	False		,,,				2504	0.0				p.V650V		Atlas-SNP	.		Dom	yes		15	15q21	6938	"transcription factor 12 (HTF4, helix-loop-helix transcription factors 4)"		M	.	TCF12	242	.	0			c.C1950T						PASS	.	C	,,,,	7,4377	12.9+/-30.5	0,7,2185	88	84	85		1878,1950,1950,1878,1368	4.8	1	15	dbSNP_131	85	52,8532	33.8+/-87.4	0,52,4240	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TCF12	NM_003205.3,NM_207036.1,NM_207037.1,NM_207038.1,NM_207040.1	,,,,	0,59,6425	TT,TC,CC		0.6058,0.1597,0.455	,,,,	626/683,650/707,650/707,626/683,456/513	57565432	59,12909	2192	4292	6484	SO:0001819	synonymous_variant	6938	exon19			GGCAGTCATCCTT	BC050556	CCDS10159.1, CCDS10160.1, CCDS42042.1	15q21	2013-05-21	2008-07-31		ENSG00000140262	ENSG00000140262		"Basic helix-loop-helix proteins"	11623	protein-coding gene	gene with protein product	"helix-loop-helix transcription factor 4"	600480				1886779	Standard	NM_003205		Approved	HEB, HTF4, HsT17266, bHLHb20	uc002aeb.3	Q99081	OTTHUMG00000132047	ENST00000267811.5:c.1878C>T	15.37:g.57565432C>T		127	0	0		121	61	0.504132	NM_207036	Q7Z3D9|Q86TC1|Q86VM2	Silent	SNP	ENST00000267811.5	37	CCDS10159.1																																																																																			C|0.996;T|0.004	0.004	strong		0.428	TCF12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255069.3	NM_003205		T	57565432	C	T	57565432	2	4	29	1	0	0	0	0	0	0	0	1	15702	813	29	2		2	TCF12	15	57565432	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1775522	57565432	44965960	687	12928											
RORA	6095	hgsc.bcm.edu	37	chr15	61521304	61521304	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	accggggcaggcggctcgctCttgcgggcggattcctggtt	3	9	17	12	5	1	0	0	0	1	0	3	1	2	1	2	7	1	4	2	7	0	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:61521304C>T	ENST00000335670.6	-	1	214	c.114G>A	c.(112-114)aaG>aaA	p.K38K		NM_134261.2	NP_599023.1	P35398	RORA_HUMAN	RAR-related orphan receptor A	38					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						GCGGCTCGCTCTTGCGGGCGG	0.766																																					p.K38K		Atlas-SNP	.											.	RORA	114	.	0			c.G114A						PASS	.						5	5	5					15																	61521304		1830	3566	5396	SO:0001819	synonymous_variant	6095	exon1			CTCGCTCTTGCGG	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.114G>A	15.37:g.61521304C>T		49	0	0		45	18	0.4	NM_134261	P35397|P35399|P45445|Q495X4|Q96H83	Silent	SNP	ENST00000335670.6	37	CCDS10177.1																																																																																			.	.	none		0.766	RORA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256142.2			T	61521304	C	T	61521304	2	4	29	1	0	0	0	0	0	0	0	1	13543	912	32	2		2	RORA	15	61521304	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	3955872	61521304	41010088	688	12929											
TLN2	83660	hgsc.bcm.edu	37	chr15	63131091	63131091	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgaaaagagcctcagacaatCttgtccgtgcagcccagaag	13	7	10	11	1	2	4	1	1	1	3	3	4	3	4	3	0	3	1	3	0	4	1	rs140301741	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:63131091C>T	ENST00000561311.1	+	57	7641	c.7411C>T	c.(7411-7413)Ctt>Ttt	p.L2471F	TLN2_ENST00000306829.6_Missense_Mutation_p.L2471F|RP11-1069G10.1_ENST00000558404.1_RNA			Q9Y4G6	TLN2_HUMAN	talin 2	2471	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.				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						CTCAGACAATCTTGTCCGTGC	0.458													C|||	3	0.000599042	0.0	0.0014	5008	,	,		21391	0.0		0.002	False		,,,				2504	0.0				p.L2471F		Atlas-SNP	.											.	TLN2	253	.	0			c.C7411T						PASS	.	C	PHE/LEU	2,4404	6.2+/-15.9	0,2,2201	115	108	110		7411	5.7	1	15	dbSNP_134	110	33,8567	23.4+/-69.3	0,33,4267	yes	missense	TLN2	NM_015059.2	22	0,35,6468	TT,TC,CC		0.3837,0.0454,0.2691	probably-damaging	2471/2543	63131091	35,12971	2203	4300	6503	SO:0001583	missense	83660	exon55			GACAATCTTGTCC	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.7411C>T	15.37:g.63131091C>T	ENSP00000453508:p.Leu2471Phe	62	0	0		58	31	0.534483	NM_015059	A6NLB8	Missense_Mutation	SNP	ENST00000561311.1	37	CCDS32261.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	32	5.128337	0.94473	4.54E-4	0.003837	ENSG00000171914	ENST00000306829	T	0.60548	0.18	5.68	5.68	0.88126	I/LWEQ (4);	0.000000	0.85682	D	0.000000	D	0.83326	0.5230	M	0.93898	3.47	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.97110	0.995;1.0	D	0.87137	0.2200	10	0.87932	D	0	-10.4216	19.786	0.96437	0.0:1.0:0.0:0.0	.	87;2471	B4DGF3;Q9Y4G6	.;TLN2_HUMAN	F	2471	ENSP00000303476:L2471F	ENSP00000303476:L2471F	L	+	1	0	TLN2	60918144	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.776000	0.85560	2.676000	0.91093	0.563000	0.77884	CTT	C|0.998;T|0.002	0.002	strong		0.458	TLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257878.2			T	63131091	C	T	63131091	3	4	29	1	0	0	0	0	1	0	0	0	15963	913	32	2	7629	2	TLN2	15	63131091	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1609787	63131091	39400301	689	12930											
ITGA11	22801	hgsc.bcm.edu	37	chr15	68654003	68654003	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acacatccctgtggtgtagtAggagctcccacactcatgag	10	9	10	12	0	1	1	1	1	0	0	3	2	3	2	2	2	1	3	2	2	2	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:68654003A>G	ENST00000315757.7	-	5	483	c.397T>C	c.(397-399)Tac>Cac	p.Y133H	ITGA11_ENST00000562826.1_5'UTR|ITGA11_ENST00000423218.2_Missense_Mutation_p.Y133H	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	133					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						GTGGTGTAGTAGGAGCTCCCA	0.567																																					p.Y133H		Atlas-SNP	.											.	ITGA11	110	.	0			c.T397C						PASS	.						59	58	58					15																	68654003		1961	4143	6104	SO:0001583	missense	22801	exon5			TGTAGTAGGAGCT	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.397T>C	15.37:g.68654003A>G	ENSP00000327290:p.Tyr133His	37	0	0		57	5	0.0877193	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	37	CCDS45291.1	.	.	.	.	.	.	.	.	.	.	A	12.02	1.812724	0.32053	.	.	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000537153	T;T	0.71934	-0.61;-0.61	4.67	4.67	0.58626	.	0.000000	0.85682	D	0.000000	T	0.76499	0.3996	L	0.47190	1.495	0.41168	D	0.986143	D;D	0.76494	0.997;0.999	D;D	0.72982	0.94;0.979	T	0.72250	-0.4348	10	0.15066	T	0.55	.	13.6022	0.62026	1.0:0.0:0.0:0.0	.	133;133	A8K8T0;Q9UKX5	.;ITA11_HUMAN	H	133	ENSP00000327290:Y133H;ENSP00000403392:Y133H	ENSP00000327290:Y133H	Y	-	1	0	ITGA11	66441057	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.080000	0.57620	1.856000	0.53863	0.459000	0.35465	TAC	.	.	none		0.567	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211		G	68654003	A	G	68654003	3	3	29	1	0	0	0	0	1	0	0	0	7883	420	15	3	3273	3	ITGA11	15	68654003	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	5522912	68654003	33877389	690	12931											
MYO9A	4649	hgsc.bcm.edu	37	chr15	72189925	72189925	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtgttctctttttgaaatgCgattatttgagagtttacag	10	18	9	4	1	1	2	0	2	1	1	2	4	1	2	0	0	2	2	0	0	3	7			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:72189925C>T	ENST00000356056.5	-	25	5391	c.4919G>A	c.(4918-4920)cGc>cAc	p.R1640H	MYO9A_ENST00000566885.1_Missense_Mutation_p.R1260H|MYO9A_ENST00000563542.1_5'UTR|MYO9A_ENST00000444904.1_Missense_Mutation_p.R1621H|MYO9A_ENST00000564571.1_Missense_Mutation_p.R1640H|MYO9A_ENST00000424560.1_Missense_Mutation_p.R1640H	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1640	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						TTTTGAAATGCGATTATTTGA	0.428																																					p.R1640H		Atlas-SNP	.											.	MYO9A	203	.	0			c.G4919A						PASS	.						156	139	145					15																	72189925		2199	4297	6496	SO:0001583	missense	4649	exon25			GAAATGCGATTAT	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.4919G>A	15.37:g.72189925C>T	ENSP00000348349:p.Arg1640His	229	0	0		192	52	0.270833	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	37	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	c	5.821	0.335743	0.11013	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	D;D;D	0.84223	-1.82;-1.82;-1.81	5.19	1.26	0.21427	.	.	.	.	.	T	0.70613	0.3244	N	0.17082	0.46	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.002;0.002;0.0	T	0.58278	-0.7664	9	0.45353	T	0.12	.	4.8546	0.13554	0.0:0.3852:0.2157:0.3991	.	1621;1640;1640	B2RTY4-2;B2RTY4-4;B2RTY4	.;.;MYO9A_HUMAN	H	1640;1640;1621	ENSP00000348349:R1640H;ENSP00000399162:R1640H;ENSP00000398250:R1621H	ENSP00000348349:R1640H	R	-	2	0	MYO9A	69976979	0.000000	0.05858	0.035000	0.18076	0.984000	0.73092	-0.449000	0.06812	0.424000	0.26061	-0.127000	0.14921	CGC	.	.	none		0.428	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		T	72189925	C	T	72189925	3	4	29	1	0	0	0	0	1	0	0	0	10093	768	27	1	2799	1	MYO9A	15	72189925	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	3535922	72189925	30341467	691	12932											
DNAJA4	55466	hgsc.bcm.edu	37	chr15	78565495	78565495	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gatctatataatggagtcacGaagaaattggccctccagaa	15	9	9	8	1	2	2	1	0	1	2	3	5	3	3	2	2	0	0	2	2	6	4	rs74978019	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:78565495G>A	ENST00000394852.3	+	3	562	c.372G>A	c.(370-372)acG>acA	p.T124T	DNAJA4_ENST00000394855.3_Silent_p.T153T|DNAJA4_ENST00000446172.2_Silent_p.T97T|DNAJA4_ENST00000343789.3_Silent_p.T124T	NM_001130182.1	NP_001123654.1	Q8WW22	DNJA4_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 4	124					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						ATGGAGTCACGAAGAAATTGG	0.348													G|||	6	0.00119808	0.0	0.0029	5008	,	,		18129	0.0		0.004	False		,,,				2504	0.0				p.T153T		Atlas-SNP	.											DNAJA4_ENST00000446172,NS,carcinoma,+1,2	DNAJA4	63	2	0			c.G459A						PASS	.	G	,,	3,4389	8.1+/-20.4	0,3,2193	92	97	96		372,291,459	-3.7	0	15	dbSNP_132	96	48,8538	29.6+/-80.5	0,48,4245	no	coding-synonymous,coding-synonymous,coding-synonymous	DNAJA4	NM_001130182.1,NM_001130183.1,NM_018602.3	,,	0,51,6438	AA,AG,GG		0.559,0.0683,0.393	,,	124/398,97/371,153/427	78565495	51,12927	2196	4293	6489	SO:0001819	synonymous_variant	55466	exon4			AGTCACGAAGAAA	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.372G>A	15.37:g.78565495G>A		234	1	0.0042735		255	113	0.443137	NM_018602	E9PDM9|Q6AW87|Q8N5Z4|Q8N7P2	Silent	SNP	ENST00000394852.3	37	CCDS45316.1																																																																																			G|0.997;A|0.003	0.003	strong		0.348	DNAJA4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289801.1	NM_018602		A	78565495	G	A	78565495	2	1	29	1	0	0	0	0	0	0	0	1	4616	1045	37	1		1	DNAJA4	15	78565495	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	6375570	78565495	23965897	692	12933											
BCL2A1	597	hgsc.bcm.edu	37	chr15	80263051	80263051	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcacacatacccagcctccGttttgccttatccattctcc	8	13	3	17	1	2	0	1	0	1	0	5	0	4	0	6	0	3	1	6	0	2	5	rs147879852		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:80263051G>A	ENST00000267953.3	-	1	737	c.411C>T	c.(409-411)aaC>aaT	p.N137N	BCL2A1_ENST00000335661.6_Silent_p.N137N	NM_004049.3	NP_004040.1	Q16548	B2LA1_HUMAN	BCL2-related protein A1	137					extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)	mitochondrial outer membrane (GO:0005741)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.N137N(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	12						CCCAGCCTCCGTTTTGCCTTA	0.368																																					p.N137N		Atlas-SNP	.											BCL2A1,colon,carcinoma,0,1	BCL2A1	28	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C411T						PASS	.	G	,	0,4406		0,0,2203	111	116	114		411,411	-8.2	0.1	15	dbSNP_134	114	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	BCL2A1	NM_001114735.1,NM_004049.3	,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,	137/164,137/176	80263051	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	597	exon1			GCCTCCGTTTTGC		CCDS10312.1, CCDS45322.1	15q24.3	2014-05-20			ENSG00000140379	ENSG00000140379			991	protein-coding gene	gene with protein product		601056		HBPA1		8589678, 12771180	Standard	NM_004049		Approved	GRS, BFL1, BCL2L5, ACC-1, ACC-2	uc002bfc.4	Q16548	OTTHUMG00000144173	ENST00000267953.3:c.411C>T	15.37:g.80263051G>A		160	0	0		187	94	0.502674	NM_001114735	Q6FGZ4|Q6FH19|Q86W13|Q99524	Silent	SNP	ENST00000267953.3	37	CCDS10312.1																																																																																			G|1.000;A|0.000	0.000	weak		0.368	BCL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291372.1	NM_004049		A	80263051	G	A	80263051	2	1	29	1	0	0	0	0	0	0	0	1	1366	1136	40	1		1	BCL2A1	15	80263051	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1697556	80263051	22268341	693	12934											
ISG20	3669	hgsc.bcm.edu	37	chr15	89182736	89182736	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	acaagttcatccggcctgagGgagagatcaccgattacaga	13	7	11	10	2	2	3	2	1	0	2	3	6	3	4	3	2	1	1	3	2	2	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:89182736G>A	ENST00000306072.5	+	2	497	c.139G>A	c.(139-141)Gga>Aga	p.G47R	ISG20_ENST00000560741.1_Missense_Mutation_p.G47R|ISG20_ENST00000379224.5_Missense_Mutation_p.G47R	NM_002201.4	NP_002192.2	Q96AZ6	ISG20_HUMAN	interferon stimulated exonuclease gene 20kDa	47					cell proliferation (GO:0008283)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|DNA catabolic process, exonucleolytic (GO:0000738)|negative regulation of viral genome replication (GO:0045071)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)|type I interferon signaling pathway (GO:0060337)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	3'-5'-exoribonuclease activity (GO:0000175)|exonuclease activity (GO:0004527)|exoribonuclease II activity (GO:0008859)|metal ion binding (GO:0046872)|single-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008310)|U1 snRNA binding (GO:0030619)|U2 snRNA binding (GO:0030620)|U3 snoRNA binding (GO:0034511)			large_intestine(1)|lung(3)|prostate(1)	5	Lung NSC(78;0.0554)|all_lung(78;0.103)		BRCA - Breast invasive adenocarcinoma(143;0.12)			CCGGCCTGAGGGAGAGATCAC	0.642																																					p.G47R		Atlas-SNP	.											.	ISG20	17	.	0			c.G139A						PASS	.						68	68	68					15																	89182736		2200	4299	6499	SO:0001583	missense	3669	exon2			CCTGAGGGAGAGA	X89773	CCDS10345.1	15q26	2006-02-22	2002-08-29		ENSG00000172183	ENSG00000172183			6130	protein-coding gene	gene with protein product		604533	"interferon stimulated gene (20kD)"			9235947, 9605874	Standard	NM_002201		Approved	HEM45, CD25	uc002bmv.1	Q96AZ6	OTTHUMG00000148679	ENST00000306072.5:c.139G>A	15.37:g.89182736G>A	ENSP00000306565:p.Gly47Arg	58	0	0		64	16	0.25	NM_002201	O00441|O00586	Missense_Mutation	SNP	ENST00000306072.5	37	CCDS10345.1	.	.	.	.	.	.	.	.	.	.	G	13.87	2.365645	0.41902	.	.	ENSG00000172183	ENST00000306072;ENST00000379224	T;T	0.19938	2.11;2.11	4.81	3.9	0.45041	Exonuclease (1);Exonuclease, RNase T/DNA polymerase III (1);Ribonuclease H-like (1);	1.105290	0.06796	N	0.787879	T	0.19886	0.0478	L	0.56396	1.775	0.09310	N	1	P	0.34562	0.457	B	0.28011	0.085	T	0.27434	-1.0074	10	0.18276	T	0.48	-10.2487	7.7296	0.28779	0.1947:0.0:0.8053:0.0	.	47	Q96AZ6	ISG20_HUMAN	R	47	ENSP00000306565:G47R;ENSP00000368526:G47R	ENSP00000306565:G47R	G	+	1	0	ISG20	86983740	0.000000	0.05858	0.130000	0.21974	0.967000	0.64934	0.117000	0.15583	1.002000	0.39104	0.561000	0.74099	GGA	.	.	none		0.642	ISG20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309069.2	NM_002201		A	89182736	G	A	89182736	3	1	29	1	0	0	0	0	1	0	0	0	7863	1233	43	2	141	2	ISG20	15	89182736	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	8919685	89182736	13348656	694	12935											
ACAN	176	hgsc.bcm.edu	37	chr15	89402447	89402447	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcacacctcgcagctgggcGttgtcatcagcaccagcatc	8	8	10	15	2	3	0	3	0	0	0	5	0	3	0	2	1	3	5	2	1	0	1	rs533925391		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr15:89402447G>A	ENST00000561243.1	+	11	6631	c.6631G>A	c.(6631-6633)Gtt>Att	p.V2211I	ACAN_ENST00000559004.1_Missense_Mutation_p.V2211I|ACAN_ENST00000352105.7_Missense_Mutation_p.V2211I|ACAN_ENST00000439576.2_Missense_Mutation_p.V2211I			P16112	PGCA_HUMAN	aggrecan	2096	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)			GCAGCTGGGCGTTGTCATCAG	0.597													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18793	0.0		0.0	False		,,,				2504	0.0				p.V2211I		Atlas-SNP	.											.	ACAN	220	.	0			c.G6631A						PASS	.						44	50	48					15																	89402447		2134	4239	6373	SO:0001583	missense	176	exon12			CTGGGCGTTGTCA	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.6631G>A	15.37:g.89402447G>A	ENSP00000453342:p.Val2211Ile	115	0	0		100	47	0.47	NM_001135	Q13650|Q9UCD3|Q9UCP4|Q9UCP5|Q9UDE0	Missense_Mutation	SNP	ENST00000561243.1	37	CCDS53970.1	.	.	.	.	.	.	.	.	.	.	G	0.119	-1.128582	0.01756	.	.	ENSG00000157766	ENST00000439576;ENST00000352105;ENST00000268134	T;T	0.02606	4.36;4.23	5.12	-1.75	0.08031	.	0.642182	0.11888	N	0.519845	T	0.01765	0.0056	N	0.21583	0.68	0.09310	N	1	P;B	0.39311	0.667;0.304	B;B	0.37780	0.258;0.06	T	0.45963	-0.9225	10	0.21540	T	0.41	-2.0E-4	3.0641	0.06209	0.2863:0.11:0.4916:0.1121	.	2211;2211	E7ENV9;E7EX88	.;.	I	2211;2211;2097	ENSP00000387356:V2211I;ENSP00000341615:V2211I	ENSP00000268134:V2097I	V	+	1	0	ACAN	87203451	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-0.782000	0.04643	-0.274000	0.09232	-1.342000	0.01247	GTT	.	.	none		0.597	ACAN-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416267.2	NM_001135		A	89402447	G	A	89402447	3	1	29	1	0	0	0	0	1	0	0	0	117	1145	40	1	6673	1	ACAN	15	89402447	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	219711	89402447	13128945	695	12936											
RAB11FIP3	9727	hgsc.bcm.edu	37	chr16	570737	570737	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gccctacagctcatggaggcGattcagaagcaggaggagat	12	6	14	9	1	2	2	2	0	0	2	2	6	2	4	1	4	3	2	1	4	2	2	rs142673366	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:570737G>A	ENST00000262305.4	+	14	2557	c.2169G>A	c.(2167-2169)gcG>gcA	p.A723A	RAB11FIP3_ENST00000450428.1_Silent_p.A427A|RAB11FIP3_ENST00000457159.1_Silent_p.A768A	NM_014700.3	NP_055515.1	O75154	RFIP3_HUMAN	RAB11 family interacting protein 3 (class II)	723	FIP-RBD. {ECO:0000255|PROSITE- ProRule:PRU00844}.				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)				TCATGGAGGCGATTCAGAAGC	0.582													G|||	3	0.000599042	0.0	0.0	5008	,	,		22162	0.0		0.003	False		,,,				2504	0.0				p.A723A	Melanoma(160;2366 2595 4474 8099)	Atlas-SNP	.											.	RAB11FIP3	31	.	0			c.G2169A						PASS	.	G	,	1,4401	2.1+/-5.4	0,1,2200	128	104	112		1281,2169	-8.7	0	16	dbSNP_134	112	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous,coding-synonymous	RAB11FIP3	NM_001142272.1,NM_014700.3	,	0,15,6486	AA,AG,GG		0.1628,0.0227,0.1154	,	427/461,723/757	570737	15,12987	2201	4300	6501	SO:0001819	synonymous_variant	9727	exon14			GGAGGCGATTCAG	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.2169G>A	16.37:g.570737G>A		91	0	0		93	37	0.397849	NM_014700	B0QYI8|B0QYT8|B1AHQ0|B4DEI7|B4DZR6|Q4VXV7|Q7Z5E9|Q9H155|Q9H1G0|Q9NUI0	Silent	SNP	ENST00000262305.4	37	CCDS32351.1																																																																																			G|0.999;A|0.001	0.001	strong		0.582	RAB11FIP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109066.4	NM_014700		A	570737	G	A	570737	2	1	29	1	0	0	0	0	0	0	0	1	12910	1045	37	1		1	RAB11FIP3	16	570737	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10		570737	89784016	696	12937											
WFIKKN1	117166	hgsc.bcm.edu	37	chr16	683547	683547	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccgcgctgggcctacagcccGctgctgcagcagtgccatcc	5	6	12	18	3	0	0	0	0	0	0	1	0	1	0	5	1	6	5	5	1	1	1	rs148648187	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:683547G>A	ENST00000319070.2	+	2	1459	c.1137G>A	c.(1135-1137)ccG>ccA	p.P379P		NM_053284.2	NP_444514.1	Q96NZ8	WFKN1_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 1	379	BPTI/Kunitz inhibitor 2. {ECO:0000255|PROSITE-ProRule:PRU00031}.				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)	extracellular region (GO:0005576)	metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|prostate(1)|upper_aerodigestive_tract(1)	4		Hepatocellular(780;0.00335)				CCTACAGCCCGCTGCTGCAGC	0.736													g|||	11	0.00219649	0.0	0.0043	5008	,	,		11845	0.0		0.008	False		,,,				2504	0.0				p.P379P		Atlas-SNP	.											.	WFIKKN1	30	.	0			c.G1137A						PASS	.			0,4188		0,0,2094	7	8	8		1137	-3.7	1	16	dbSNP_134	8	36,8240		0,36,4102	no	coding-synonymous	WFIKKN1	NM_053284.2		0,36,6196	AA,AG,GG		0.435,0.0,0.2888		379/549	683547	36,12428	2094	4138	6232	SO:0001819	synonymous_variant	117166	exon2			CAGCCCGCTGCTG	AK075356	CCDS10414.1	16p13	2013-01-21			ENSG00000127578	ENSG00000127578		"Immunoglobulin superfamily / I-set domain containing", "WAP four-disulfide core domain containing"	30912	protein-coding gene	gene with protein product	"WAP four-disulfide core domain 20A"	608021	"chromosome 16 open reading frame 12"	C16orf12		11274388, 11928817	Standard	NM_053284		Approved	RJD2, WFIKKN, WFDC20A	uc002cht.1	Q96NZ8	OTTHUMG00000090359	ENST00000319070.2:c.1137G>A	16.37:g.683547G>A		13	0	0		7	5	0.714286	NM_053284	Q7LDW0|Q8NBQ1|Q96S20	Silent	SNP	ENST00000319070.2	37	CCDS10414.1																																																																																			G|0.994;A|0.006	0.006	strong		0.736	WFIKKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206731.2	NM_053284		A	683547	G	A	683547	2	1	29	1	0	0	0	0	0	0	0	1	17373	1074	38	1		1	WFIKKN1	16	683547	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	112810	683547	89671206	697	12938											
WDR90	197335	hgsc.bcm.edu	37	chr16	705344	705344	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggcagtgtgcggctctggCggctgcgtggcggggtgctg	2	8	22	9	4	1	0	0	0	1	0	1	0	1	0	0	7	3	4	0	7	0	0	rs144704309	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:705344C>A	ENST00000293879.4	+	15	1594	c.1594C>A	c.(1594-1596)Cgg>Agg	p.R532R	WDR90_ENST00000549091.1_Silent_p.R532R|LA16c-349E10.1_ENST00000573609.1_RNA			Q96KV7	WDR90_HUMAN	WD repeat domain 90	532										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				GCGGCTCTGGCGGCTGCGTGG	0.701													C|||	3	0.000599042	0.0008	0.0	5008	,	,		15736	0.0		0.002	False		,,,				2504	0.0				p.R532R		Atlas-SNP	.											.	WDR90	107	.	0			c.C1594A						PASS	.	C		0,4352		0,0,2176	18	28	25		1594	3.6	1	16	dbSNP_134	25	19,8539		0,19,4260	no	coding-synonymous	WDR90	NM_145294.4		0,19,6436	AA,AC,CC		0.222,0.0,0.1472		532/1749	705344	19,12891	2176	4279	6455	SO:0001819	synonymous_variant	197335	exon15			CTCTGGCGGCTGC	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.1594C>A	16.37:g.705344C>A		21	0	0		26	14	0.538462	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Silent	SNP	ENST00000293879.4	37	CCDS42092.1																																																																																			C|0.999;A|0.001	0.001	strong		0.701	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294		A	705344	C	A	705344	2	1	29	1	0	0	0	0	0	0	0	1	17352	759	27	4		4	WDR90	16	705344	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	21797	705344	89649409	698	12939											
HAGHL	84264	hgsc.bcm.edu	37	chr16	777590	777590	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcacgcgcgaggcggtggcCgtggacgtggctgtgcccaa	5	6	17	13	6	1	0	1	0	0	0	1	2	1	1	2	5	1	1	2	5	1	0	rs143758903	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:777590C>T	ENST00000341413.4	+	2	362	c.81C>T	c.(79-81)gcC>gcT	p.A27A	HAGHL_ENST00000549114.1_Silent_p.A27A|NARFL_ENST00000562862.1_5'Flank|HAGHL_ENST00000389703.3_Silent_p.A27A|HAGHL_ENST00000564545.1_Silent_p.A27A|HAGHL_ENST00000561546.1_Silent_p.A27A|HAGHL_ENST00000564537.1_Silent_p.A27A|CCDC78_ENST00000293889.6_5'Flank			Q6PII5	HAGHL_HUMAN	hydroxyacylglutathione hydrolase-like	27							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			lung(3)	3		Hepatocellular(780;0.00335)				AGGCGGTGGCCGTGGACGTGG	0.697													C|||	3	0.000599042	0.0008	0.0	5008	,	,		11895	0.0		0.002	False		,,,				2504	0.0				p.A27A	Pancreas(46;538 1326 12403 32360)	Atlas-SNP	.											.	HAGHL	18	.	0			c.C81T						PASS	.	C		0,4374		0,0,2187	53	39	44		81	-5	0	16	dbSNP_134	44	19,8569	12.6+/-44.7	0,19,4275	no	coding-synonymous	HAGHL	NM_032304.2		0,19,6462	TT,TC,CC		0.2212,0.0,0.1466		27/283	777590	19,12943	2187	4294	6481	SO:0001819	synonymous_variant	84264	exon1			GGTGGCCGTGGAC	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.81C>T	16.37:g.777590C>T		92	0	0		96	45	0.46875	NM_032304	A6NCC4|D3DU64|Q59FX8|Q96BZ3|Q96NR5|Q96S11|Q9BT45	Silent	SNP	ENST00000341413.4	37																																																																																				C|0.999;T|0.001	0.001	strong		0.697	HAGHL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409607.1	NM_032304		T	777590	C	T	777590	2	4	29	1	0	0	0	0	0	0	0	1	6955	639	23	1		1	HAGHL	16	777590	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	72246	777590	89577163	699	12940											
CLCN7	1186	hgsc.bcm.edu	37	chr16	1506130	1506130	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcacccacgggggctccaaaCgccgctgacactccggccgc	7	4	11	19	5	1	1	1	1	0	0	3	1	3	1	5	3	1	2	5	3	1	0	rs41286695	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:1506130C>T	ENST00000382745.4	-	10	1505	c.900G>A	c.(898-900)gcG>gcA	p.A300A	CLCN7_ENST00000262318.8_Silent_p.A276A|CLCN7_ENST00000448525.1_Silent_p.A276A	NM_001287.5	NP_001278.1	P51798	CLCN7_HUMAN	chloride channel, voltage-sensitive 7	300					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)				GGGCTCCAAACGCCGCTGACA	0.642													C|||	79	0.0157748	0.0015	0.0159	5008	,	,		16001	0.0		0.0616	False		,,,				2504	0.0041				p.A300A		Atlas-SNP	.											.	CLCN7	53	.	0			c.G900A						PASS	.	C	,	37,4273		0,37,2118	12	14	14		828,900	-10.2	0	16	dbSNP_127	14	420,8048		4,412,3818	no	coding-synonymous,coding-synonymous	CLCN7	NM_001114331.1,NM_001287.4	,	4,449,5936	TT,TC,CC		4.9598,0.8585,3.5765	,	276/782,300/806	1506130	457,12321	2155	4234	6389	SO:0001819	synonymous_variant	1186	exon10			TCCAAACGCCGCT	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.900G>A	16.37:g.1506130C>T		26	0	0		24	14	0.583333	NM_001287	A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5	Silent	SNP	ENST00000382745.4	37	CCDS32361.1																																																																																			C|0.973;T|0.027	0.027	strong		0.642	CLCN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103598.2	NM_001287		T	1506130	C	T	1506130	2	4	29	1	0	0	0	0	0	0	0	1	3470	523	19	1		1	CLCN7	16	1506130	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	728540	1506130	88848623	700	12941											
PKD1	5310	hgsc.bcm.edu	37	chr16	2164244	2164244	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacagatgggctcctccgccGtcacccgcaggctgaggttg	6	7	13	15	3	1	2	1	1	0	1	3	2	3	2	4	3	0	4	4	3	0	1	rs139963923		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:2164244G>A	ENST00000262304.4	-	11	2988	c.2780C>T	c.(2779-2781)aCg>aTg	p.T927M	PKD1_ENST00000423118.1_Missense_Mutation_p.T927M|RP11-304L19.4_ENST00000568795.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	927	PKD 3. {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						CTCCTCCGCCGTCACCCGCAG	0.677																																					p.T927M		Atlas-SNP	.											.	PKD1	184	.	0			c.C2780T						PASS	.	G	MET/THR,MET/THR	0,4338		0,0,2169	14	14	14		2780,2780	-5.7	0	16	dbSNP_134	14	1,8495		0,1,4247	no	missense,missense	PKD1	NM_000296.3,NM_001009944.2	81,81	0,1,6416	AA,AG,GG		0.0118,0.0,0.0078	possibly-damaging,possibly-damaging	927/4303,927/4304	2164244	1,12833	2169	4248	6417	SO:0001583	missense	5310	exon11			TCCGCCGTCACCC	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.2780C>T	16.37:g.2164244G>A	ENSP00000262304:p.Thr927Met	78	0	0		63	24	0.380952	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	.	.	.	.	.	.	.	.	.	.	g	6.600	0.479161	0.12581	0.0	1.18E-4	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.68903	-0.36;-0.36	4.96	-5.71	0.02413	Polycystin cation channel (1);	0.553584	0.18955	N	0.126571	T	0.32675	0.0837	N	0.12182	0.205	0.09310	N	1	B;B	0.30114	0.269;0.066	B;B	0.17979	0.02;0.008	T	0.10520	-1.0626	10	0.54805	T	0.06	.	1.975	0.03414	0.2493:0.0753:0.3095:0.3658	.	927;927	P98161-3;P98161	.;PKD1_HUMAN	M	927;927;642	ENSP00000262304:T927M;ENSP00000399501:T927M	ENSP00000262304:T927M	T	-	2	0	PKD1	2104245	0.001000	0.12720	0.001000	0.08648	0.192000	0.23643	-0.055000	0.11807	-0.792000	0.04480	-0.476000	0.04901	ACG	G|1.000;A|0.000	0.000	weak		0.677	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			A	2164244	G	A	2164244	3	1	29	1	0	0	0	0	1	0	0	0	11972	1145	40	1	10275	1	PKD1	16	2164244	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	658114	2164244	88190509	701	12942											
OR2C1	4993	hgsc.bcm.edu	37	chr16	3406651	3406651	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcagaggggaggcgaaaggcGttcaatacgtgcctctccca	10	6	14	11	3	2	1	1	0	1	1	3	3	2	2	2	4	2	2	2	4	3	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:3406651G>A	ENST00000304936.2	+	1	763	c.711G>A	c.(709-711)gcG>gcA	p.A237A		NM_012368.2	NP_036500.2	O95371	OR2C1_HUMAN	olfactory receptor, family 2, subfamily C, member 1	237					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						GGCGAAAGGCGTTCAATACGT	0.547																																					p.A237A		Atlas-SNP	.											.	OR2C1	38	.	0			c.G711A						PASS	.						148	122	131					16																	3406651		2197	4300	6497	SO:0001819	synonymous_variant	4993	exon1			AAAGGCGTTCAAT	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.711G>A	16.37:g.3406651G>A		67	0	0		81	34	0.419753	NM_012368	A0AVA4|Q6IF34|Q6IF55	Silent	SNP	ENST00000304936.2	37	CCDS10502.1																																																																																			.	.	none		0.547	OR2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206993.3			A	3406651	G	A	3406651	2	1	29	1	0	0	0	0	0	0	0	1	11001	1132	40	1		1	OR2C1	16	3406651	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1242407	3406651	86948102	702	12943											
ZNF597	146434	hgsc.bcm.edu	37	chr16	3486738	3486738	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	atcgctgcagcgttcagagtCctcgtcgtggctcttctcgg	4	12	12	13	5	3	1	1	0	2	1	8	1	4	1	1	2	2	4	1	2	0	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:3486738C>A	ENST00000301744.4	-	4	1196	c.961G>T	c.(961-963)Gac>Tac	p.D321Y		NM_152457.1	NP_689670.1	Q96LX8	ZN597_HUMAN	zinc finger protein 597	321					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						CGTTCAGAGTCCTCGTCGTGG	0.493																																					p.D321Y		Atlas-SNP	.											.	ZNF597	41	.	0			c.G961T						PASS	.						70	66	67					16																	3486738		2197	4300	6497	SO:0001583	missense	146434	exon4			CAGAGTCCTCGTC	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.961G>T	16.37:g.3486738C>A	ENSP00000301744:p.Asp321Tyr	43	0	0		38	9	0.236842	NM_152457		Missense_Mutation	SNP	ENST00000301744.4	37	CCDS10505.1	.	.	.	.	.	.	.	.	.	.	C	11.56	1.673850	0.29693	.	.	ENSG00000167981	ENST00000301744	T	0.07688	3.17	4.48	0.208	0.15221	.	0.346678	0.20965	N	0.082485	T	0.06005	0.0156	N	0.19112	0.55	0.09310	N	1	D	0.62365	0.991	P	0.47744	0.556	T	0.30268	-0.9984	10	0.87932	D	0	-3.4924	3.4929	0.07644	0.1755:0.4118:0.0:0.4127	.	321	Q96LX8	ZN597_HUMAN	Y	321	ENSP00000301744:D321Y	ENSP00000301744:D321Y	D	-	1	0	ZNF597	3426739	0.000000	0.05858	0.000000	0.03702	0.072000	0.16883	0.646000	0.24797	0.201000	0.20466	0.650000	0.86243	GAC	.	.	none		0.493	ZNF597-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251511.2	NM_152457		A	3486738	C	A	3486738	3	1	29	1	0	0	0	0	1	0	0	0	18042	855	30	4	317	4	ZNF597	16	3486738	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	80087	3486738	86868015	703	12944											
VASN	114990	hgsc.bcm.edu	37	chr16	4431373	4431373	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagctgcgggcactgcccccGctgcgcctgccccgcctgct	2	6	13	20	4	0	0	0	0	0	0	0	1	0	0	6	1	6	4	6	1	0	0	rs740374	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:4431373G>C	ENST00000304735.3	+	2	650	c.495G>C	c.(493-495)ccG>ccC	p.P165P	CORO7_ENST00000537233.2_Intron|CORO7_ENST00000574025.1_Intron|CORO7_ENST00000423908.2_Intron|CORO7_ENST00000251166.4_Intron|CORO7_ENST00000539968.1_Intron|CORO7-PAM16_ENST00000572467.1_Intron	NM_138440.2	NP_612449.2	Q6EMK4	VASN_HUMAN	vasorin	165				Missing (in Ref. 2; AAQ88665). {ECO:0000305}.	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						CACTGCCCCCGCTGCGCCTGC	0.697													G|||	66	0.0131789	0.0008	0.0202	5008	,	,		13608	0.0		0.0358	False		,,,				2504	0.0153				p.P165P		Atlas-SNP	.											.	VASN	21	.	0			c.G495C						PASS	.	G	,,,,	25,4267		0,25,2121	12	9	10		,,,,495	-11.6	0	16	dbSNP_86	10	191,8271		1,189,4041	no	intron,intron,intron,intron,coding-synonymous	CORO7,VASN,CORO7-PAM16	NM_001201472.1,NM_001201473.1,NM_001201479.1,NM_024535.4,NM_138440.2	,,,,	1,214,6162	CC,CG,GG		2.2571,0.5825,1.6936	,,,,	,,,,165/674	4431373	216,12538	2146	4231	6377	SO:0001819	synonymous_variant	114990	exon2			GCCCCCGCTGCGC	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.495G>C	16.37:g.4431373G>C		27	0	0		24	15	0.625	NM_138440	Q6UXL4|Q6UXL5|Q96CX1	Silent	SNP	ENST00000304735.3	37	CCDS10514.1																																																																																			G|0.986;C|0.014	0.014	strong		0.697	VASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251632.1	NM_138440		C	4431373	G	C	4431373	2	2	29	1	0	0	0	0	0	0	0	1	17142	1074	38	4		4	VASN	16	4431373	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	944635	4431373	85923380	704	12945											
CARHSP1	23589	hgsc.bcm.edu	37	chr16	8953030	8953030	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agcctgctccagactcacgcCgagaaggtcctcgtccggcg	7	6	12	16	5	1	2	1	0	0	2	5	3	4	2	5	2	2	1	5	2	1	0	rs2231706	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:8953030C>T	ENST00000396593.2	-	2	515	c.156G>A	c.(154-156)tcG>tcA	p.S52S	CARHSP1_ENST00000567554.1_Silent_p.S52S|CARHSP1_ENST00000311052.5_Silent_p.S52S|CARHSP1_ENST00000561530.1_Silent_p.S52S|RP11-77H9.2_ENST00000565934.1_RNA|CARHSP1_ENST00000567626.1_5'Flank|CARHSP1_ENST00000562843.1_Silent_p.S52S	NM_001042476.1|NM_001278260.1|NM_001278261.1|NM_001278262.1|NM_001278263.1|NM_001278264.1|NM_001278265.1|NM_001278266.1|NM_014316.3	NP_001035941.1|NP_001265189.1|NP_001265190.1|NP_001265191.1|NP_001265192.1|NP_001265193.1|NP_001265194.1|NP_001265195.1|NP_055131.2	Q9Y2V2	CHSP1_HUMAN	calcium regulated heat stable protein 1, 24kDa	52					intracellular signal transduction (GO:0035556)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasmic exosome (RNase complex) (GO:0000177)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|P granule (GO:0043186)	DNA binding (GO:0003677)|mRNA 3'-UTR binding (GO:0003730)|phosphatase binding (GO:0019902)			endometrium(2)|lung(1)	3						AGACTCACGCCGAGAAGGTCC	0.642													C|||	31	0.0061901	0.003	0.0014	5008	,	,		19388	0.0		0.0249	False		,,,				2504	0.001				p.S52S		Atlas-SNP	.											.	CARHSP1	12	.	0			c.G156A						PASS	.	C	,	11,4379		0,11,2184	25	21	22		156,156	-10.7	0.1	16	dbSNP_98	22	158,8440		0,158,4141	no	coding-synonymous,coding-synonymous	CARHSP1	NM_001042476.1,NM_014316.2	,	0,169,6325	TT,TC,CC		1.8376,0.2506,1.3012	,	52/148,52/148	8953030	169,12819	2195	4299	6494	SO:0001819	synonymous_variant	23589	exon2			TCACGCCGAGAAG	AF115345	CCDS10537.1	16p13.2	2008-02-05	2002-08-29		ENSG00000153048	ENSG00000153048			17150	protein-coding gene	gene with protein product			"calcium regulated heat stable protein 1 (24kD)"			9712905	Standard	NM_014316		Approved	CRHSP-24, CSDC1	uc031quz.1	Q9Y2V2	OTTHUMG00000129695	ENST00000396593.2:c.156G>A	16.37:g.8953030C>T		124	0	0		141	63	0.446809	NM_001042476	B2R4C3|D3DUF5|Q2YDX5|Q9BQ53	Silent	SNP	ENST00000396593.2	37	CCDS10537.1																																																																																			C|0.989;T|0.011	0.011	strong		0.642	CARHSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251902.1	NM_014316		T	8953030	C	T	8953030	2	4	29	1	0	0	0	0	0	0	0	1	2655	639	23	1		1	CARHSP1	16	8953030	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	4521657	8953030	81401723	705	12946											
USP7	7874	hgsc.bcm.edu	37	chr16	8989511	8989511	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acagatacctctattcgaaaCgtccggctcgttgcaggaga	11	9	10	11	4	1	2	0	0	1	2	4	4	2	2	2	2	3	3	2	2	3	4	rs61731196	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:8989511C>T	ENST00000344836.4	-	27	3105	c.2907G>A	c.(2905-2907)acG>acA	p.T969T	USP7_ENST00000535863.1_Silent_p.T870T|USP7_ENST00000381886.4_Silent_p.T953T	NM_003470.2	NP_003461.2	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7 (herpes virus-associated)	969					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						CTATTCGAAACGTCCGGCTCG	0.418													C|||	11	0.00219649	0.0	0.0014	5008	,	,		17036	0.0		0.0099	False		,,,				2504	0.0				p.T969T		Atlas-SNP	.											.	USP7	116	.	0			c.G2907A						PASS	.	C		7,4387	12.9+/-30.5	0,7,2190	79	77	77		2907	2.4	1	16	dbSNP_129	77	91,8509	51.1+/-111.2	0,91,4209	no	coding-synonymous	USP7	NM_003470.2		0,98,6399	TT,TC,CC		1.0581,0.1593,0.7542		969/1103	8989511	98,12896	2197	4300	6497	SO:0001819	synonymous_variant	7874	exon27			TCGAAACGTCCGG	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.2907G>A	16.37:g.8989511C>T		94	0	0		84	38	0.452381	NM_003470	A6NMY8|B7Z815|H0Y3G8	Silent	SNP	ENST00000344836.4	37	CCDS32385.1																																																																																			C|0.994;T|0.006	0.006	strong		0.418	USP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434268.2			T	8989511	C	T	8989511	2	4	29	1	0	0	0	0	0	0	0	1	17103	523	19	1		1	USP7	16	8989511	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	36481	8989511	81365242	706	12947											
GRIN2A	2903	hgsc.bcm.edu	37	chr16	9857231	9857231	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcaccgcctgggatggcaaCgagtgtttgtaagggtccga	8	10	14	9	3	1	0	1	0	0	0	2	3	2	1	3	3	1	3	3	3	2	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:9857231C>T	ENST00000396573.2	-	14	4479	c.4170G>A	c.(4168-4170)tcG>tcA	p.S1390S	GRIN2A_ENST00000330684.3_Silent_p.S1390S|GRIN2A_ENST00000396575.2_Silent_p.S1390S|GRIN2A_ENST00000404927.2_Missense_Mutation_p.R1276H|GRIN2A_ENST00000535259.1_Missense_Mutation_p.R1119H|GRIN2A_ENST00000562109.1_Missense_Mutation_p.R1276H	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	1390					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)	GGGATGGCAACGAGTGTTTGT	0.547																																					p.R1276H		Atlas-SNP	.											GRIN2A,colon,carcinoma,0,1	GRIN2A	366	1	0			c.G3827A						PASS	.						118	104	108					16																	9857231		2197	4300	6497	SO:0001819	synonymous_variant	2903	exon14			TGGCAACGAGTGT		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.4170G>A	16.37:g.9857231C>T		99	0	0		86	32	0.372093	NM_001134408	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	37	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	C	11.97	1.796460	0.31777	.	.	ENSG00000183454	ENST00000404927;ENST00000535259	T;T	0.12039	2.72;2.72	5.91	-6.96	0.01622	.	.	.	.	.	T	0.05273	0.0140	.	.	.	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.41805	-0.9488	7	.	.	.	.	4.2924	0.10885	0.0844:0.1963:0.4074:0.312	.	1119;1276	F5GZ52;Q17RZ6	.;.	H	1276;1119	ENSP00000385872:R1276H;ENSP00000441572:R1119H	.	R	-	2	0	GRIN2A	9764732	0.001000	0.12720	0.019000	0.16419	0.954000	0.61252	-0.160000	0.10041	-0.751000	0.04734	0.655000	0.94253	CGT	.	.	none		0.547	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			T	9857231	C	T	9857231	2	4	29	1	0	0	0	0	0	0	0	1	6788	536	19	1		1	GRIN2A	16	9857231	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	867720	9857231	80497522	707	12948											
CIITA	4261	hgsc.bcm.edu	37	chr16	11000862	11000862	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tagacggcttcgaggagctgGaagcgcaagatggcttcctg	9	8	15	9	3	0	2	0	0	0	2	2	5	1	4	1	4	2	4	1	4	3	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:11000862G>T	ENST00000324288.8	+	11	1646	c.1513G>T	c.(1513-1515)Gaa>Taa	p.E505*	CIITA_ENST00000537380.1_Intron|CIITA_ENST00000381835.5_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	505	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						CGAGGAGCTGGAAGCGCAAGA	0.647			T	"FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"	"PMBL, Hodgkin Lymphona, "																																p.E505X		Atlas-SNP	.		Dom	yes		16	16p13	4261	"class II, major histocompatibility complex, transactivator"		L	.	CIITA	92	.	0			c.G1513T						PASS	.						61	65	63					16																	11000862		2197	4300	6497	SO:0001587	stop_gained	4261	exon11			GAGCTGGAAGCGC	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.1513G>T	16.37:g.11000862G>T	ENSP00000316328:p.Glu505*	33	0	0		41	19	0.463415	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Nonsense_Mutation	SNP	ENST00000324288.8	37	CCDS10544.1	.	.	.	.	.	.	.	.	.	.	G	33	5.202661	0.94997	.	.	ENSG00000179583	ENST00000324288;ENST00000388910	.	.	.	5.27	5.27	0.74061	.	0.000000	0.56097	D	0.000027	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	.	12.6857	0.56946	0.0:0.2738:0.7262:0.0	.	.	.	.	X	505;457	.	ENSP00000316328:E505X	E	+	1	0	CIITA	10908363	1.000000	0.71417	0.223000	0.23860	0.234000	0.25298	5.332000	0.65911	2.442000	0.82660	0.561000	0.74099	GAA	.	.	none		0.647	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246		T	11000862	G	T	11000862	4	4	29	1	0	0	0	0	0	1	0	0	3430	1175	41	4	1555	4	CIITA	16	11000862	Nonsense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1143631	11000862	79353891	708	12949											
CIITA	4261	hgsc.bcm.edu	37	chr16	11001256	11001256	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacgccaagctgccctccaCgctcacgggactctatgtcg	7	7	11	16	4	2	0	1	0	1	0	4	2	3	2	3	2	2	2	3	2	2	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:11001256C>T	ENST00000324288.8	+	11	2040	c.1907C>T	c.(1906-1908)aCg>aTg	p.T636M	CIITA_ENST00000537380.1_Intron|CIITA_ENST00000381835.5_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	636	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						CTGCCCTCCACGCTCACGGGA	0.692			T	"FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"	"PMBL, Hodgkin Lymphona, "																																p.T636M		Atlas-SNP	.		Dom	yes		16	16p13	4261	"class II, major histocompatibility complex, transactivator"		L	.	CIITA	92	.	0			c.C1907T						PASS	.						21	21	21					16																	11001256		2197	4295	6492	SO:0001583	missense	4261	exon11			CCTCCACGCTCAC	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.1907C>T	16.37:g.11001256C>T	ENSP00000316328:p.Thr636Met	121	0	0		105	41	0.390476	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Missense_Mutation	SNP	ENST00000324288.8	37	CCDS10544.1	.	.	.	.	.	.	.	.	.	.	C	15.58	2.875438	0.51695	.	.	ENSG00000179583	ENST00000324288;ENST00000388910	D	0.81821	-1.54	5.1	5.1	0.69264	NACHT nucleoside triphosphatase (1);	0.000000	0.56097	D	0.000031	D	0.91264	0.7246	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	0.91635	0.998;0.997;0.999;0.998	D	0.92957	0.6385	10	0.87932	D	0	.	17.076	0.86586	0.0:1.0:0.0:0.0	.	636;636;588;636	A0N0N9;P33076;F2Z2G8;Q96KL4	.;C2TA_HUMAN;.;.	M	636;588	ENSP00000316328:T636M	ENSP00000316328:T636M	T	+	2	0	CIITA	10908757	0.989000	0.36119	0.919000	0.36401	0.068000	0.16541	5.680000	0.68168	2.372000	0.80975	0.655000	0.94253	ACG	.	.	none		0.692	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246		T	11001256	C	T	11001256	3	4	29	1	0	0	0	0	1	0	0	0	3430	536	19	1	1949	1	CIITA	16	11001256	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	394	11001256	79353497	709	12950											
TXNDC11	51061	hgsc.bcm.edu	37	chr16	11785486	11785486	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aagacaccttgttcagagtcGatgaagcctgacacacccct	12	8	8	13	1	1	4	1	2	0	2	2	5	1	4	4	0	1	1	4	0	2	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:11785486G>A	ENST00000356957.3	-	9	1748	c.1641C>T	c.(1639-1641)atC>atT	p.I547I	TXNDC11_ENST00000570917.1_5'Flank|TXNDC11_ENST00000283033.5_Silent_p.I520I			Q6PKC3	TXD11_HUMAN	thioredoxin domain containing 11	547					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						GTTCAGAGTCGATGAAGCCTG	0.473																																					p.I520I		Atlas-SNP	.											.	TXNDC11	75	.	0			c.C1560T						PASS	.						121	112	115					16																	11785486		2197	4300	6497	SO:0001819	synonymous_variant	51061	exon8			AGAGTCGATGAAG	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.1641C>T	16.37:g.11785486G>A		46	0	0		62	33	0.532258	NM_015914	O95887|Q6PJA6|Q8N2Q4|Q96K45|Q96K53	Silent	SNP	ENST00000356957.3	37																																																																																				.	.	none		0.473	TXNDC11-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000437057.1	NM_015914		A	11785486	G	A	11785486	2	1	29	1	0	0	0	0	0	0	0	1	16807	1048	37	1		1	TXNDC11	16	11785486	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	784230	11785486	78569267	710	12951											
C16orf88	400506	hgsc.bcm.edu	37	chr16	19725766	19725767	+	Frame_Shift_Ins	INS	-	-	C																															ctcttccgcttccgtttctgINSccccaaggctgcctgttcct																								rs532893765	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:19725766_19725767insC	ENST00000219837.7	-	2	669_670	c.591_592insG	c.(589-594)gggcagfs	p.Q198fs	AC002550.5_ENST00000565916.1_RNA|KNOP1_ENST00000568230.1_5'Flank|IQCK_ENST00000320394.6_5'Flank	NM_001012991.2	NP_001013009.2	Q1ED39	KNOP1_HUMAN	lysine-rich nucleolar protein 1	198	Lys-rich.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)										TTCCGTTTCTGCCCCAAGGCTG	0.574																																					p.Q198fs		Pindel,Atlas-Indel	.											.	C16orf88	41	.	0			c.592_593insG						PASS	.																																			SO:0001589	frameshift_variant	400506	exon2			.	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.592dupG	16.37:g.19725770_19725770dupC	ENSP00000219837:p.Gln198fs	45	0	.		36	18	0.5	NM_001012991	O43328|Q5FWF3	Frame_Shift_Ins	INS	ENST00000219837.7	37	CCDS42127.1																																																																																			.	.	none		0.574	KNOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435993.2	NM_001012991		C	19725767	-	C	19725766	7	5	29	1	0	1	1	0	0	0	0	0	1843	1328	46	0	800	0	C16orf88	16	19725766	Frame_Shift_Ins	INS	-	TCGA-GR-7351-01A-11D-2210-10	7940280	19725766	70628987	711	12952											
VWA3A	146177	hgsc.bcm.edu	37	chr16	22143031	22143031	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aatctacctcttcactggggGcatccccgaccaggacatgg	9	8	10	14	1	3	0	1	0	2	0	4	2	4	1	4	4	1	1	4	4	2	2	rs199942653		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:22143031G>A	ENST00000389398.5	+	19	1949	c.1853G>A	c.(1852-1854)gGc>gAc	p.G618D	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	618	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.					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)		TTCACTGGGGGCATCCCCGAC	0.567																																					p.G618D		Atlas-SNP	.											.	VWA3A	115	.	0			c.G1853A						PASS	.						52	56	55					16																	22143031		1951	4143	6094	SO:0001583	missense	146177	exon19			CTGGGGGCATCCC	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.1853G>A	16.37:g.22143031G>A	ENSP00000374049:p.Gly618Asp	262	1	0.00381679		220	92	0.418182	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Missense_Mutation	SNP	ENST00000389398.5	37	CCDS45441.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.960192	0.74016	.	.	ENSG00000175267	ENST00000389398;ENST00000299840	T	0.48836	0.8	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.73682	0.3618	M	0.87758	2.905	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.79155	-0.1920	10	0.87932	D	0	.	17.4177	0.87505	0.0:0.0:1.0:0.0	.	618;242	A6NCI4;A6NCI4-2	VWA3A_HUMAN;.	D	618;241	ENSP00000374049:G618D	ENSP00000299840:G241D	G	+	2	0	VWA3A	22050532	1.000000	0.71417	1.000000	0.80357	0.821000	0.46438	6.685000	0.74543	2.438000	0.82558	0.563000	0.77884	GGC	G|0.999;A|0.001	0.001	weak		0.567	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1			A	22143031	G	A	22143031	3	1	29	1	0	0	0	0	1	0	0	0	17255	1203	42	2	1927	2	VWA3A	16	22143031	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2417265	22143031	68211722	712	12953											
ATP2A1	487	hgsc.bcm.edu	37	chr16	28898778	28898778	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagccggcaaggccttgggCatcgtggccaccactggtgt	6	7	15	13	2	0	0	0	0	0	0	1	0	0	0	4	5	1	3	4	5	1	1	rs113803159	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:28898778C>G	ENST00000357084.3	+	8	930	c.663C>G	c.(661-663)ggC>ggG	p.G221G	ATP2A1_ENST00000395503.4_Silent_p.G221G|ATP2A1_ENST00000536376.1_Silent_p.G96G	NM_173201.3	NP_775293.1	O14983	AT2A1_HUMAN	ATPase, Ca++ transporting, cardiac muscle, fast twitch 1	221					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						AGGCCTTGGGCATCGTGGCCA	0.607													C|||	9	0.00179712	0.0	0.0014	5008	,	,		18988	0.0		0.008	False		,,,				2504	0.0				p.G221G		Atlas-SNP	.											.	ATP2A1	116	.	0			c.C663G						PASS	.	C	,	7,4387	12.9+/-30.5	0,7,2190	85	82	83		663,663	3.4	1	16	dbSNP_132	83	72,8528	43.6+/-101.6	1,70,4229	no	coding-synonymous,coding-synonymous	ATP2A1	NM_004320.4,NM_173201.3	,	1,77,6419	GG,GC,CC		0.8372,0.1593,0.608	,	221/995,221/1002	28898778	79,12915	2197	4300	6497	SO:0001819	synonymous_variant	487	exon8			CTTGGGCATCGTG		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.663C>G	16.37:g.28898778C>G		65	0	0		69	39	0.565217	NM_004320	A8K5J9|B3KY17|O14984	Silent	SNP	ENST00000357084.3	37	CCDS10643.1																																																																																			C|0.995;G|0.005	0.005	strong		0.607	ATP2A1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254686.2	NM_004320		G	28898778	C	G	28898778	2	3	29	1	0	0	0	0	0	0	0	1	1136	697	25	4		4	ATP2A1	16	28898778	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	6755747	28898778	61455975	713	12954											
RABEP2	79874	hgsc.bcm.edu	37	chr16	28925694	28925694	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcagggctcaggccctggcGgctttggggcagggaggagc	5	7	19	10	1	2	0	2	0	0	0	2	2	2	2	1	8	1	3	1	8	0	2	rs200278634		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:28925694G>A	ENST00000358201.4	-	5	1345	c.757C>T	c.(757-759)Cgc>Tgc	p.R253C	RABEP2_ENST00000561803.1_5'Flank|RABEP2_ENST00000357573.6_Missense_Mutation_p.R253C|RABEP2_ENST00000544477.1_Missense_Mutation_p.R182C	NM_024816.2	NP_079092.2	Q9H5N1	RABE2_HUMAN	rabaptin, RAB GTPase binding effector protein 2	253					endocytosis (GO:0006897)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	16						AGGCCCTGGCGGCTTTGGGGC	0.667																																					p.R253C	Pancreas(66;639 1284 10093 31061 49099)	Atlas-SNP	.											.	RABEP2	48	.	0			c.C757T						PASS	.																																			SO:0001583	missense	79874	exon5			CCTGGCGGCTTTG	AK026935	CCDS42140.1	16p11.2	2014-09-11			ENSG00000177548	ENSG00000177548			24817	protein-coding gene	gene with protein product		611869				12477932	Standard	NM_024816		Approved	FRA, FLJ23282	uc002drq.3	Q9H5N1	OTTHUMG00000176593	ENST00000358201.4:c.757C>T	16.37:g.28925694G>A	ENSP00000350934:p.Arg253Cys	116	0	0		112	57	0.508929	NM_024816		Missense_Mutation	SNP	ENST00000358201.4	37	CCDS42140.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.836981	0.91117	.	.	ENSG00000177548	ENST00000358201;ENST00000357573;ENST00000544477	T;T;T	0.49139	0.81;0.79;0.83	5.27	5.27	0.74061	.	0.417922	0.25375	N	0.031122	T	0.50905	0.1643	N	0.22421	0.69	0.41436	D	0.987899	D;D;D;D	0.76494	0.998;0.997;0.996;0.999	P;P;P;P	0.57846	0.761;0.648;0.761;0.828	T	0.55774	-0.8088	10	0.66056	D	0.02	-7.4463	15.8139	0.78583	0.0:0.0:1.0:0.0	.	182;253;253;253	B4DHR0;Q9H5N1-2;Q49AT6;Q9H5N1	.;.;.;RABE2_HUMAN	C	253;253;182	ENSP00000350934:R253C;ENSP00000350186:R253C;ENSP00000442798:R182C	ENSP00000350186:R253C	R	-	1	0	RABEP2	28833195	0.267000	0.24122	0.974000	0.42286	0.900000	0.52787	3.127000	0.50484	2.457000	0.83068	0.462000	0.41574	CGC	.	.	weak		0.667	RABEP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432691.1	NM_024816		A	28925694	G	A	28925694	3	1	29	1	0	0	0	0	1	0	0	0	12977	1116	39	1	988	1	RABEP2	16	28925694	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	26916	28925694	61429059	714	12955											
SPNS1	83985	hgsc.bcm.edu	37	chr16	28995211	28995211	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgttggggcactgggcggCgcagccttcctgggcaccgc	3	9	16	13	3	0	0	0	0	0	0	1	0	1	0	3	5	1	4	3	5	0	3	rs113165798	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:28995211C>T	ENST00000311008.11	+	11	1802	c.1425C>T	c.(1423-1425)ggC>ggT	p.G475G	LAT_ENST00000454369.2_5'Flank|RP11-264B17.3_ENST00000569969.1_RNA|SPNS1_ENST00000323081.8_Silent_p.G402G|LAT_ENST00000566177.1_5'Flank|SPNS1_ENST00000334536.8_Silent_p.G423G|SPNS1_ENST00000352260.7_Silent_p.G401G|LAT_ENST00000395456.2_5'Flank|LAT_ENST00000354453.4_5'Flank|SPNS1_ENST00000565975.1_Silent_p.G520G|LAT_ENST00000564277.1_5'Flank|LAT_ENST00000360872.5_5'Flank|LAT_ENST00000395461.3_5'Flank	NM_032038.2	NP_114427.1	Q9H2V7	SPNS1_HUMAN	spinster homolog 1 (Drosophila)	475					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrial inner membrane (GO:0005743)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)|urinary_tract(1)	21						CACTGGGCGGCGCAGCCTTCC	0.672													C|||	9	0.00179712	0.0	0.0014	5008	,	,		18700	0.0		0.008	False		,,,				2504	0.0				p.G475G		Atlas-SNP	.											.	SPNS1	47	.	0			c.C1425T						PASS	.	C	,,,,	7,4387	12.9+/-30.5	0,7,2190	48	51	50		1425,1203,1206,1269,1425	-9.2	0.1	16	dbSNP_132	50	74,8526	44.0+/-102.2	1,72,4227	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPNS1	NM_001142448.1,NM_001142449.1,NM_001142450.1,NM_001142451.1,NM_032038.2	,,,,	1,79,6417	TT,TC,CC		0.8605,0.1593,0.6234	,,,,	475/529,401/455,402/456,423/477,475/529	28995211	81,12913	2197	4300	6497	SO:0001819	synonymous_variant	83985	exon12			GGGCGGCGCAGCC	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.1425C>T	16.37:g.28995211C>T		44	0	0		44	24	0.545455	NM_001142448	B5MDM9|Q6P182|Q71RB5|Q7L541|Q86VU7|Q8N953|Q8TCS5|Q9BRN5	Silent	SNP	ENST00000311008.11	37	CCDS10646.1																																																																																			C|0.995;T|0.005	0.005	strong		0.672	SPNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254690.2	NM_032038		T	28995211	C	T	28995211	2	4	29	1	0	0	0	0	0	0	0	1	15089	755	27	1		1	SPNS1	16	28995211	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	69517	28995211	61359542	715	12956											
TMEM219	124446	hgsc.bcm.edu	37	chr16	29979376	29979376	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggacaactggtccttatcaCagccagggtgaccacagaaa	14	6	10	11	0	1	2	1	1	0	1	2	3	2	3	3	3	2	0	3	3	3	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:29979376C>T	ENST00000566848.1	+	3	853	c.386C>T	c.(385-387)aCa>aTa	p.T129I	TMEM219_ENST00000561899.2_Missense_Mutation_p.T129I|TMEM219_ENST00000414689.2_Missense_Mutation_p.T129I|TMEM219_ENST00000279396.6_Missense_Mutation_p.T129I			Q86XT9	TM219_HUMAN	transmembrane protein 219	129					apoptotic process (GO:0006915)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				large_intestine(1)|lung(1)|prostate(2)	4						GTCCTTATCACAGCCAGGGTG	0.517																																					p.T129I		Atlas-SNP	.											.	TMEM219	10	.	0			c.C386T						PASS	.						99	106	104					16																	29979376		1915	4121	6036	SO:0001583	missense	124446	exon4			TTATCACAGCCAG		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.386C>T	16.37:g.29979376C>T	ENSP00000457492:p.Thr129Ile	99	0	0		95	7	0.0736842	NM_001083613	D5FK14|Q8WVV8	Missense_Mutation	SNP	ENST00000566848.1	37	CCDS42145.1	.	.	.	.	.	.	.	.	.	.	C	19.33	3.806497	0.70682	.	.	ENSG00000149932	ENST00000414689;ENST00000279396	.	.	.	5.66	4.65	0.58169	.	0.000000	0.64402	D	0.000002	T	0.58235	0.2108	L	0.29908	0.895	0.36632	D	0.876375	D	0.76494	0.999	D	0.68192	0.956	T	0.65932	-0.6048	9	0.87932	D	0	-17.3834	11.7475	0.51828	0.0:0.8228:0.1772:0.0	.	129	Q86XT9	TM219_HUMAN	I	129	.	ENSP00000279396:T129I	T	+	2	0	TMEM219	29886877	1.000000	0.71417	0.998000	0.56505	0.926000	0.56050	2.099000	0.41767	2.665000	0.90641	0.561000	0.74099	ACA	.	.	none		0.517	TMEM219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435307.1	NM_001083613		T	29979376	C	T	29979376	3	4	29	1	0	0	0	0	1	0	0	0	16157	478	17	2	396	2	TMEM219	16	29979376	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	984165	29979376	60375377	716	12957											
ZNF646	9726	hgsc.bcm.edu	37	chr16	31090221	31090221	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgcccgaaggagtttgactCtctgcctgccctccgcagcc	5	9	10	17	2	1	1	0	1	1	0	3	3	2	2	5	1	4	2	5	1	1	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:31090221C>T	ENST00000394979.2	+	1	2999	c.2576C>T	c.(2575-2577)tCt>tTt	p.S859F	ZNF646_ENST00000300850.5_Missense_Mutation_p.S859F			O15015	ZN646_HUMAN	zinc finger protein 646	859					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						GAGTTTGACTCTCTGCCTGCC	0.622																																					p.S859F		Atlas-SNP	.											.	ZNF646	133	.	0			c.C2576T						PASS	.						67	73	71					16																	31090221		2197	4300	6497	SO:0001583	missense	9726	exon2			TTGACTCTCTGCC	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.2576C>T	16.37:g.31090221C>T	ENSP00000378429:p.Ser859Phe	83	0	0		91	4	0.043956	NM_014699	Q8IVD8	Missense_Mutation	SNP	ENST00000394979.2	37		.	.	.	.	.	.	.	.	.	.	C	17.73	3.462089	0.63513	.	.	ENSG00000167395	ENST00000300850;ENST00000394979	T;T	0.79247	-1.25;-1.25	5.1	5.1	0.69264	.	.	.	.	.	T	0.79834	0.4514	L	0.38175	1.15	0.32404	N	0.551577	D	0.76494	0.999	D	0.73380	0.98	T	0.78309	-0.2254	9	0.26408	T	0.33	-11.2798	8.9229	0.35623	0.1657:0.6738:0.1604:0.0	.	859	O15015-2	.	F	859	ENSP00000300850:S859F;ENSP00000378429:S859F	ENSP00000300850:S859F	S	+	2	0	ZNF646	30997722	0.882000	0.30256	1.000000	0.80357	0.997000	0.91878	1.968000	0.40500	2.380000	0.81148	0.563000	0.77884	TCT	.	.	none		0.622	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699		T	31090221	C	T	31090221	3	4	29	1	0	0	0	0	1	0	0	0	18077	913	32	2	2578	2	ZNF646	16	31090221	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1110845	31090221	59264532	717	12958											
PRSS36	146547	hgsc.bcm.edu	37	chr16	31152818	31152818	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	acagtgagtggctgccaggaCccagcctggggccaggagga	9	4	17	11	0	0	1	0	1	0	0	0	4	0	4	4	6	2	1	4	6	0	0	rs117442264	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:31152818C>T	ENST00000268281.4	-	12	1931	c.1873G>A	c.(1873-1875)Gtc>Atc	p.V625I	PRSS36_ENST00000569305.1_Missense_Mutation_p.V620I|PRSS36_ENST00000418068.2_Missense_Mutation_p.V625I	NM_001258290.1|NM_173502.4	NP_001245219.1|NP_775773.2	Q5K4E3	POLS2_HUMAN	protease, serine, 36	625	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						GCTGCCAGGACCCAGCCTGGG	0.617													C|||	45	0.00898562	0.0023	0.0303	5008	,	,		15672	0.0		0.0199	False		,,,				2504	0.001				p.V625I		Atlas-SNP	.											.	PRSS36	50	.	0			c.G1873A						PASS	.	C	ILE/VAL	18,4376	23.3+/-48.9	0,18,2179	55	63	61		1873	4.3	1	16	dbSNP_132	61	130,8470	63.9+/-126.0	0,130,4170	yes	missense	PRSS36	NM_173502.3	29	0,148,6349	TT,TC,CC		1.5116,0.4096,1.139	probably-damaging	625/856	31152818	148,12846	2197	4300	6497	SO:0001583	missense	146547	exon12			CCAGGACCCAGCC	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.1873G>A	16.37:g.31152818C>T	ENSP00000268281:p.Val625Ile	25	0	0		32	12	0.375	NM_001258291	A8K2P5|B4DW80|B7ZMK8|E7EX56|Q8NBY4	Missense_Mutation	SNP	ENST00000268281.4	37	CCDS32436.1	26	0.011904761904761904	2	0.0040650406504065045	12	0.03314917127071823	0	0.0	12	0.0158311345646438	C	16.78	3.217405	0.58560	0.004096	0.015116	ENSG00000178226	ENST00000268281;ENST00000418068	T;D	0.87887	-0.48;-2.31	5.29	4.34	0.51931	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.64638	0.2616	L	0.49778	1.585	0.31588	N	0.654304	B;B;B	0.18310	0.027;0.025;0.025	B;B;B	0.20577	0.03;0.028;0.028	T	0.72786	-0.4188	9	0.33141	T	0.24	.	8.0067	0.30329	0.0:0.8159:0.0:0.1841	.	625;620;625	E7EX56;B7ZMK8;Q5K4E3	.;.;POLS2_HUMAN	I	625	ENSP00000268281:V625I;ENSP00000407160:V625I	ENSP00000268281:V625I	V	-	1	0	PRSS36	31060319	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	3.299000	0.51826	1.226000	0.43582	0.455000	0.32223	GTC	C|0.990;T|0.010	0.010	strong		0.617	PRSS36-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433542.1	NM_173502		T	31152818	C	T	31152818	3	4	29	1	0	0	0	0	1	0	0	0	12637	507	18	2	710	2	PRSS36	16	31152818	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	62597	31152818	59201935	718	12959											
DNAJA2	10294	hgsc.bcm.edu	37	chr16	47007480	47007480	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cttcgtgtcagccacgttagCcatggcggccggccgggcag	5	7	15	14	5	1	0	1	0	0	0	2	0	1	0	4	4	2	2	4	4	1	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:47007480C>T	ENST00000317089.5	-	1	219	c.4G>A	c.(4-6)Gct>Act	p.A2T	RP11-169E6.1_ENST00000562536.1_RNA	NM_005880.3	NP_005871.1	O60884	DNJA2_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 2	2					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)				GCCACGTTAGCCATGGCGGCC	0.711																																					p.A2T		Atlas-SNP	.											.	DNAJA2	28	.	0			c.G4A						PASS	.						23	26	25					16																	47007480		2188	4272	6460	SO:0001583	missense	10294	exon1			CGTTAGCCATGGC	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.4G>A	16.37:g.47007480C>T	ENSP00000314030:p.Ala2Thr	39	0	0		40	11	0.275	NM_005880	B2R7L7|O14711	Missense_Mutation	SNP	ENST00000317089.5	37	CCDS10726.1	.	.	.	.	.	.	.	.	.	.	C	19.53	3.845639	0.71603	.	.	ENSG00000069345	ENST00000317089	T	0.38560	1.13	5.07	5.07	0.68467	.	0.124512	0.53938	D	0.000052	T	0.24699	0.0599	N	0.12746	0.255	0.48975	D	0.999737	B	0.18013	0.025	B	0.20767	0.031	T	0.09079	-1.0691	10	0.18276	T	0.48	-7.404	12.3249	0.55005	0.1696:0.8304:0.0:0.0	.	2	O60884	DNJA2_HUMAN	T	2	ENSP00000314030:A2T	ENSP00000314030:A2T	A	-	1	0	DNAJA2	45564981	1.000000	0.71417	1.000000	0.80357	0.580000	0.36256	2.429000	0.44758	2.327000	0.79052	0.491000	0.48974	GCT	.	.	none		0.711	DNAJA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256769.2			T	47007480	C	T	47007480	3	4	29	1	0	0	0	0	1	0	0	0	4614	739	26	2	1270	2	DNAJA2	16	47007480	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	15854662	47007480	43347273	719	12960											
TOX3	27324	hgsc.bcm.edu	37	chr16	52484278	52484278	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tggaggtgaaggagatgtgtGaggcatactggcacctccca	10	8	15	8	0	0	3	0	2	0	1	1	5	1	4	2	5	1	2	2	5	2	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:52484278G>A	ENST00000219746.9	-	4	873	c.589C>T	c.(589-591)Cac>Tac	p.H197Y	TOX3_ENST00000407228.3_Missense_Mutation_p.H192Y	NM_001080430.2	NP_001073899.2	O15405	TOX3_HUMAN	TOX high mobility group box family member 3	197					apoptotic process (GO:0006915)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|estrogen response element binding (GO:0034056)|phosphoprotein binding (GO:0051219)|protein homodimerization activity (GO:0042803)			NS(2)|endometrium(6)|kidney(1)|lung(8)|prostate(3)|stomach(3)|upper_aerodigestive_tract(1)	24						GGAGATGTGTGAGGCATACTG	0.547																																					p.H197Y		Atlas-SNP	.											.	TOX3	121	.	0			c.C589T						PASS	.						147	152	150					16																	52484278		2125	4226	6351	SO:0001583	missense	27324	exon4			ATGTGTGAGGCAT	U80736	CCDS54008.1, CCDS54009.1	16q12.1	2008-02-05	2007-03-20	2007-03-20		ENSG00000103460		"Trinucleotide (CAG) repeat containing"	11972	protein-coding gene	gene with protein product		611416	"trinucleotide repeat containing 9"	TNRC9		9225980	Standard	NM_001080430		Approved	CAGF9	uc002egw.2	O15405		ENST00000219746.9:c.589C>T	16.37:g.52484278G>A	ENSP00000219746:p.His197Tyr	97	0	0		113	33	0.292035	NM_001080430	B4DRD0|B5MCW4	Missense_Mutation	SNP	ENST00000219746.9	37	CCDS54009.1	.	.	.	.	.	.	.	.	.	.	G	16.84	3.234074	0.58886	.	.	ENSG00000103460	ENST00000219746;ENST00000407228	T;T	0.12569	2.68;2.67	5.71	3.66	0.41972	.	0.106561	0.64402	D	0.000006	T	0.18841	0.0452	M	0.73962	2.25	0.54753	D	0.999981	B;B	0.14438	0.01;0.01	B;B	0.11329	0.004;0.006	T	0.04320	-1.0960	10	0.52906	T	0.07	.	12.9391	0.58333	0.0:0.1241:0.7467:0.1292	.	192;197	B4DRD0;O15405	.;TOX3_HUMAN	Y	197;192	ENSP00000219746:H197Y;ENSP00000385705:H192Y	ENSP00000219746:H197Y	H	-	1	0	TOX3	51041779	1.000000	0.71417	1.000000	0.80357	0.399000	0.30720	8.052000	0.89448	1.388000	0.46506	-0.309000	0.09137	CAC	.	.	none		0.547	TOX3-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000422534.1	XM_049037		A	52484278	G	A	52484278	3	1	29	1	0	0	0	0	1	0	0	0	16394	1290	45	2	1157	2	TOX3	16	52484278	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	5476798	52484278	37870475	720	12961											
SLC12A3	6559	hgsc.bcm.edu	37	chr16	56904075	56904075	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggctccatcggcctcattttCgctttcgccaatgccgtggg	4	12	11	14	4	1	0	1	0	0	0	5	0	2	0	4	3	1	2	4	3	1	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:56904075C>T	ENST00000563236.1	+	5	694	c.669C>T	c.(667-669)ttC>ttT	p.F223F	SLC12A3_ENST00000566786.1_Silent_p.F222F|SLC12A3_ENST00000262502.5_Silent_p.F222F|SLC12A3_ENST00000438926.2_Silent_p.F223F			P55017	S12A3_HUMAN	solute carrier family 12 (sodium/chloride transporter), member 3	223					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)	GCCTCATTTTCGCTTTCGCCA	0.642																																					p.F223F		Atlas-SNP	.											.	SLC12A3	99	.	0			c.C669T						PASS	.						69	68	68					16																	56904075		2198	4300	6498	SO:0001819	synonymous_variant	6559	exon5			CATTTTCGCTTTC		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.669C>T	16.37:g.56904075C>T		90	0	0		80	4	0.05	NM_001126108	A8MSJ2|C9JNN9	Silent	SNP	ENST00000563236.1	37	CCDS58464.1																																																																																			.	.	none		0.642	SLC12A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432337.1			T	56904075	C	T	56904075	2	4	29	1	0	0	0	0	0	0	0	1	14399	883	31	1		1	SLC12A3	16	56904075	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	4419797	56904075	33450678	721	12962											
CCDC135	84229	hgsc.bcm.edu	37	chr16	57760115	57760115	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accacatcacggcctccaagCgcgagttcctgcggcgcacc	8	5	10	18	5	1	0	1	0	0	0	3	1	3	0	5	2	2	2	5	2	1	1	rs143054335	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:57760115C>A	ENST00000360716.3	+	14	2115	c.1894C>A	c.(1894-1896)Cgc>Agc	p.R632S	CCDC135_ENST00000394337.4_Missense_Mutation_p.R632S|CCDC135_ENST00000336825.8_Missense_Mutation_p.R567S			Q8IY82	CC135_HUMAN		632					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)		p.R632C(1)		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						GGCCTCCAAGCGCGAGTTCCT	0.662													c|||	3	0.000599042	0.0	0.0	5008	,	,		17076	0.0		0.0	False		,,,				2504	0.0031				p.R632S		Atlas-SNP	.											CCDC135,NS,carcinoma,0,1	CCDC135	97	1	1	Substitution - Missense(1)	cervix(1)	c.C1894A						PASS	.	C	SER/ARG	0,4396		0,0,2198	68	61	63		1894	4	1	16	dbSNP_134	63	1,8595	1.2+/-3.3	0,1,4297	yes	missense	CCDC135	NM_032269.5	110	0,1,6495	AA,AC,CC		0.0116,0.0,0.0077	probably-damaging	632/875	57760115	1,12991	2198	4298	6496	SO:0001583	missense	84229	exon13			TCCAAGCGCGAGT																												ENST00000360716.3:c.1894C>A	16.37:g.57760115C>A	ENSP00000353942:p.Arg632Ser	157	0	0		154	64	0.415584	NM_032269	A8K943|Q8NAA0|Q9H080	Missense_Mutation	SNP	ENST00000360716.3	37	CCDS10787.1	.	.	.	.	.	.	.	.	.	.	c	19.72	3.881029	0.72294	0.0	1.16E-4	ENSG00000159625	ENST00000394337;ENST00000336825;ENST00000360716	T;T;T	0.14266	2.7;2.52;2.7	4.98	3.98	0.46160	.	0.278210	0.32884	N	0.005530	T	0.35008	0.0917	M	0.85630	2.765	0.33459	D	0.584648	D;D	0.76494	0.996;0.999	D;D	0.73380	0.95;0.98	T	0.51108	-0.8747	10	0.62326	D	0.03	-26.7085	6.3029	0.21123	0.3095:0.6029:0.0:0.0876	.	567;632	Q8IY82-2;Q8IY82	.;CC135_HUMAN	S	632;567;632	ENSP00000377869:R632S;ENSP00000338938:R567S;ENSP00000353942:R632S	ENSP00000338938:R567S	R	+	1	0	CCDC135	56317616	0.998000	0.40836	0.988000	0.46212	0.979000	0.70002	0.647000	0.24812	2.325000	0.78763	0.655000	0.94253	CGC	C|1.000;A|0.000	0.000	strong		0.662	CCDC135-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433323.2			A	57760115	C	A	57760115	3	1	29	1	0	0	0	0	1	0	0	0	2771	768	27	4	1940	4	CCDC135	16	57760115	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	856040	57760115	32594638	722	12963											
CNGB1	1258	hgsc.bcm.edu	37	chr16	58001086	58001086	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcggttctggttccacctcCgcctccatctctggctctgg	2	14	9	16	2	3	0	0	0	3	0	8	0	6	0	5	4	0	3	5	4	0	3	rs61997250	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:58001086C>T	ENST00000251102.8	-	2	165	c.105G>A	c.(103-105)gcG>gcA	p.A35A	CNGB1_ENST00000311183.4_Silent_p.A35A|CNGB1_ENST00000564448.1_Silent_p.A35A	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	35	Glu-rich.				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						GTTCCACCTCCGCCTCCATCT	0.647													C|||	41	0.0081869	0.0023	0.0072	5008	,	,		17304	0.0		0.0258	False		,,,				2504	0.0072				p.A35A	Colon(156;1293 1853 16336 28962 38659)	Atlas-SNP	.											.	CNGB1	105	.	0			c.G105A						PASS	.	C	,	32,3990		0,32,1979	96	101	99		105,105	-8.9	0	16	dbSNP_129	99	242,8090		4,234,3928	no	coding-synonymous,coding-synonymous	CNGB1	NM_001135639.1,NM_001297.4	,	4,266,5907	TT,TC,CC		2.9045,0.7956,2.2179	,	35/300,35/1252	58001086	274,12080	2011	4166	6177	SO:0001819	synonymous_variant	1258	exon2			CACCTCCGCCTCC	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.105G>A	16.37:g.58001086C>T		56	0	0		46	20	0.434783	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Silent	SNP	ENST00000251102.8	37	CCDS42169.1																																																																																			C|0.981;T|0.019	0.019	strong		0.647	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297		T	58001086	C	T	58001086	2	4	29	1	0	0	0	0	0	0	0	1	3602	639	23	1		1	CNGB1	16	58001086	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	240971	58001086	32353667	723	12964											
CDH8	1006	hgsc.bcm.edu	37	chr16	61935317	61935317	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tatttgaaatatggtcccagCtccatcacctgataggatat	12	13	7	9	0	1	2	1	2	0	0	3	3	3	3	3	2	1	1	3	2	5	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:61935317C>A	ENST00000577390.1	-	3	1267	c.313G>T	c.(313-315)Gct>Tct	p.A105S	CDH8_ENST00000577730.1_Missense_Mutation_p.A105S|CDH8_ENST00000299345.6_Missense_Mutation_p.A105S|CDH8_ENST00000584337.1_Missense_Mutation_p.A105S	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	105	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)|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)		ATGGTCCCAGCTCCATCACCT	0.408																																					p.A105S		Atlas-SNP	.											CDH8,NS,carcinoma,0,1	CDH8	273	1	0			c.G313T						PASS	.						105	100	102					16																	61935317		2203	4300	6503	SO:0001583	missense	1006	exon3			TCCCAGCTCCATC	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.313G>T	16.37:g.61935317C>A	ENSP00000462701:p.Ala105Ser	87	0	0		98	20	0.204082	NM_001796	B3KWC1|Q14DC6|Q9ULB2	Missense_Mutation	SNP	ENST00000577390.1	37	CCDS10802.1	.	.	.	.	.	.	.	.	.	.	C	31	5.096254	0.94197	.	.	ENSG00000150394	ENST00000299345	T	0.49720	0.77	6.17	6.17	0.99709	Cadherin (4);Cadherin-like (1);	0.097389	0.64402	D	0.000001	T	0.70727	0.3257	M	0.70842	2.15	0.80722	D	1	P	0.43826	0.818	D	0.64144	0.922	T	0.67929	-0.5543	10	0.66056	D	0.02	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	105	P55286	CADH8_HUMAN	S	105	ENSP00000299345:A105S	ENSP00000299345:A105S	A	-	1	0	CDH8	60492818	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.941000	0.99782	0.655000	0.94253	GCT	.	.	none		0.408	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796		A	61935317	C	A	61935317	3	1	29	1	0	0	0	0	1	0	0	0	3118	797	28	4	2126	4	CDH8	16	61935317	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	3934231	61935317	28419436	724	12965											
FHOD1	29109	hgsc.bcm.edu	37	chr16	67281172	67281172	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgcgcgcccaagggcagcgCcccgtccaggctgcaggtgg	5	4	16	16	4	0	0	0	0	0	0	1	0	1	0	4	4	3	3	4	4	1	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:67281172C>T	ENST00000258201.4	-	1	389	c.142G>A	c.(142-144)Gcg>Acg	p.A48T	SLC9A5_ENST00000299798.11_5'Flank	NM_013241.2	NP_037373.2	Q9Y613	FHOD1_HUMAN	formin homology 2 domain containing 1	48					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)		AAGGGCAGCGCCCCGTCCAGG	0.697																																					p.A48T		Atlas-SNP	.											.	FHOD1	86	.	0			c.G142A						PASS	.						20	21	21					16																	67281172		2192	4296	6488	SO:0001583	missense	29109	exon1			GCAGCGCCCCGTC	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.142G>A	16.37:g.67281172C>T	ENSP00000258201:p.Ala48Thr	16	0	0		11	6	0.545455	NM_013241	Q59F76|Q6Y1F2|Q76MS8|Q8N521	Missense_Mutation	SNP	ENST00000258201.4	37	CCDS10834.1	.	.	.	.	.	.	.	.	.	.	C	17.84	3.488654	0.64074	.	.	ENSG00000135723	ENST00000258201	T	0.23754	1.89	5.39	5.39	0.77823	.	0.191112	0.38959	N	0.001503	T	0.17195	0.0413	L	0.27053	0.805	0.80722	D	1	B	0.19706	0.038	B	0.10450	0.005	T	0.08146	-1.0736	10	0.19147	T	0.46	.	11.5832	0.50904	0.0:0.9188:0.0:0.0812	.	48	Q9Y613	FHOD1_HUMAN	T	48	ENSP00000258201:A48T	ENSP00000258201:A48T	A	-	1	0	FHOD1	65838673	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.705000	0.37867	2.536000	0.85505	0.561000	0.74099	GCG	.	.	none		0.697	FHOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268844.2			T	67281172	C	T	67281172	3	4	29	1	0	0	0	0	1	0	0	0	5890	739	26	2	3440	2	FHOD1	16	67281172	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	5345855	67281172	23073581	725	12966											
ZFP90	146198	hgsc.bcm.edu	37	chr16	68598023	68598023	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcaagatgaaagcactcttAccgaagtgaaatcctaccat	15	9	6	11	1	2	3	1	2	1	1	3	4	3	3	3	0	3	1	3	0	6	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:68598023A>G	ENST00000570495.1	+	5	1625	c.1333A>G	c.(1333-1335)Acc>Gcc	p.T445A	ZFP90_ENST00000563169.2_Missense_Mutation_p.T445A|ZFP90_ENST00000398253.2_Missense_Mutation_p.T445A			Q8TF47	ZFP90_HUMAN	ZFP90 zinc finger protein	445					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)		AAGCACTCTTACCGAAGTGAA	0.418																																					p.T445A		Atlas-SNP	.											ZFP90,NS,carcinoma,0,1	ZFP90	67	1	0			c.A1333G						PASS	.						101	97	98					16																	68598023		1996	4184	6180	SO:0001583	missense	146198	exon4			ACTCTTACCGAAG	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.1333A>G	16.37:g.68598023A>G	ENSP00000460547:p.Thr445Ala	79	0	0		70	14	0.2	NM_133458	B2RU00|B3KVE7|Q49AD1|Q96MQ6	Missense_Mutation	SNP	ENST00000570495.1	37	CCDS42183.1	.	.	.	.	.	.	.	.	.	.	A	6.580	0.475358	0.12521	.	.	ENSG00000184939	ENST00000398253	T	0.18810	2.19	5.66	-0.689	0.11313	.	.	.	.	.	T	0.15912	0.0383	L	0.49699	1.58	0.24537	N	0.994082	B	0.06786	0.001	B	0.10450	0.005	T	0.34875	-0.9811	9	0.66056	D	0.02	-3.6822	1.6579	0.02785	0.5267:0.1303:0.2174:0.1255	.	445	Q8TF47	ZFP90_HUMAN	A	445	ENSP00000381304:T445A	ENSP00000381304:T445A	T	+	1	0	ZFP90	67155524	0.000000	0.05858	0.006000	0.13384	0.264000	0.26372	0.966000	0.29331	-0.326000	0.08564	0.533000	0.62120	ACC	.	.	none		0.418	ZFP90-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436217.3	XM_085375		G	68598023	A	G	68598023	3	3	29	1	0	0	0	0	1	0	0	0	17669	391	14	3	1347	3	ZFP90	16	68598023	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	1316851	68598023	21756730	726	12967											
HYDIN	54768	hgsc.bcm.edu	37	chr16	70934989	70934989	+	Frame_Shift_Del	DEL	A	A	-																															cgtactcagcctcaggggggAtggtcccctgcatcagggat																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:70934989delA	ENST00000393567.2	-	53	9116	c.8966delT	c.(8965-8967)atcfs	p.I2989fs		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2989					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)				CTCAGGGGGGATGGTCCCCTG	0.572																																					p.I2989fs		Atlas-Indel	.											.	HYDIN	788	.	0			c.8967delC						PASS	.						164	157	159					16																	70934989		2024	4189	6213	SO:0001589	frameshift_variant	54768	exon53			.	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.8966delT	16.37:g.70934989delA	ENSP00000377197:p.Ile2989fs	45	0	0		110	16	0.145455	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Frame_Shift_Del	DEL	ENST00000393567.2	37	CCDS59269.1																																																																																			.	.	none		0.572	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			-	70934989	A	-	70934989	7	5	29	1	0	1	0	1	0	0	0	0	7476	333	12	0	6535	0	HYDIN	16	70934989	Frame_Shift_Del	DEL	A	TCGA-GR-7351-01A-11D-2210-10	2336966	70934989	19419764	727	12968	164	2									
HYDIN	54768	hgsc.bcm.edu	37	chr16	70934990	70934991	+	In_Frame_Ins	INS	-	-	CCC																															tactcagcctcaggggggatINSggtcccctgcatcagggata																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:70934990_70934991insCCC	ENST00000393567.2	-	53	9114_9115	c.8964_8965insGGG	c.(8962-8967)accatc>accGGGatc	p.2988_2989TI>TGI		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2988					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)				TCAGGGGGGATGGTCCCCTGCA	0.564																																					p.I2989delinsGI		Atlas-Indel	.											.	HYDIN	788	.	0			c.8965_8966insGGG						PASS	.																																			SO:0001652	inframe_insertion	54768	exon53			.	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.8964_8965insGGG	16.37:g.70934990_70934991insCCC	ENSP00000377197:p.Thr2988_Ile2989insGly	47	0	0		108	16	0.148148	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	In_Frame_Ins	INS	ENST00000393567.2	37	CCDS59269.1																																																																																			.	.	none		0.564	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			CCC	70934991	-	CCC	70934990	7	5	29	1	0	1	1	0	0	0	0	0	7476	1464	51	0	6536	0	HYDIN	16	70934990	In_Frame_Ins	INS	-	TCGA-GR-7351-01A-11D-2210-10	1	70934990	19419763	728	12969	164	2									
ADAMTS18	170692	hgsc.bcm.edu	37	chr16	77325285	77325285	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttaatattacggcatcttcGctctgggaaagttatcagct	10	14	8	9	2	3	0	1	0	2	0	4	1	3	1	0	2	2	4	0	2	5	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:77325285G>A	ENST00000282849.5	-	21	3698	c.3280C>T	c.(3280-3282)Cga>Tga	p.R1094*	RP11-538I12.3_ENST00000561672.1_RNA	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	1094	TSP type-1 4. {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						CGGCATCTTCGCTCTGGGAAA	0.517																																					p.R1094X		Atlas-SNP	.											ADAMTS18,NS,carcinoma,+1,2	ADAMTS18	270	2	0			c.C3280T						PASS	.						218	222	221					16																	77325285		2198	4300	6498	SO:0001587	stop_gained	170692	exon21			ATCTTCGCTCTGG	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.3280C>T	16.37:g.77325285G>A	ENSP00000282849:p.Arg1094*	138	0	0		129	31	0.24031	NM_199355	Q6P4R5|Q6ZWJ9	Nonsense_Mutation	SNP	ENST00000282849.5	37	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	G	44	10.621894	0.99439	.	.	ENSG00000140873	ENST00000282849	.	.	.	5.8	4.83	0.62350	.	0.061993	0.64402	D	0.000009	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.5838	0.56406	0.0:0.0:0.5802:0.4198	.	.	.	.	X	1094	.	ENSP00000282849:R1094X	R	-	1	2	ADAMTS18	75882786	1.000000	0.71417	1.000000	0.80357	0.708000	0.40852	3.887000	0.56197	1.427000	0.47276	0.563000	0.77884	CGA	.	.	none		0.517	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1			A	77325285	G	A	77325285	4	1	29	1	0	0	0	0	0	1	0	0	263	1095	38	1	397	1	ADAMTS18	16	77325285	Nonsense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	6390295	77325285	13029468	729	12970											
OSGIN1	29948	hgsc.bcm.edu	37	chr16	83992895	83992895	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctctggtatctgcctgtcctAcctgctctccggctacacac	5	12	7	17	1	3	0	0	0	3	0	5	0	4	0	4	2	4	3	4	2	3	3	rs150635654	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:83992895A>G	ENST00000343939.2	+	4	730	c.347A>G	c.(346-348)tAc>tGc	p.Y116C	OSGIN1_ENST00000361711.3_Missense_Mutation_p.Y33C|OSGIN1_ENST00000393306.1_Missense_Mutation_p.Y33C|OSGIN1_ENST00000565123.1_Missense_Mutation_p.Y33C			Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	116					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						TGCCTGTCCTACCTGCTCTCC	0.627													A|||	2	0.000399361	0.0	0.0	5008	,	,		14501	0.0		0.002	False		,,,				2504	0.0				p.Y33C		Atlas-SNP	.											.	OSGIN1	33	.	0			c.A98G						PASS	.	A	CYS/TYR,CYS/TYR,CYS/TYR	2,4398	4.2+/-10.8	0,2,2198	149	127	134		347,98,98	4.7	1	16	dbSNP_134	134	21,8579	16.0+/-53.3	0,21,4279	yes	missense,missense,missense	OSGIN1	NM_013370.3,NM_182980.2,NM_182981.2	194,194,194	0,23,6477	GG,GA,AA		0.2442,0.0455,0.1769	probably-damaging,probably-damaging,probably-damaging	116/561,33/478,33/478	83992895	23,12977	2200	4300	6500	SO:0001583	missense	29948	exon3			TGTCCTACCTGCT	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.347A>G	16.37:g.83992895A>G	ENSP00000343376:p.Tyr116Cys	80	0	0		79	37	0.468354	NM_182981	Q52M33|Q86UQ1|Q96S88|Q9BZ70	Missense_Mutation	SNP	ENST00000343939.2	37		0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	A	16.64	3.178546	0.57692	4.55E-4	0.002442	ENSG00000140961	ENST00000343939;ENST00000361711;ENST00000393306	T;T;T	0.44881	0.91;0.91;0.91	4.66	4.66	0.58398	.	0.000000	0.85682	D	0.000000	T	0.59838	0.2223	L	0.59436	1.845	0.54753	D	0.99998	D	0.89917	1.0	D	0.87578	0.998	T	0.63752	-0.6566	10	0.87932	D	0	-0.215	13.2677	0.60144	1.0:0.0:0.0:0.0	.	116	Q9UJX0	OSGI1_HUMAN	C	116;33;33	ENSP00000343376:Y116C;ENSP00000355374:Y33C;ENSP00000376983:Y33C	ENSP00000343376:Y116C	Y	+	2	0	OSGIN1	82550396	1.000000	0.71417	1.000000	0.80357	0.364000	0.29643	9.277000	0.95755	1.744000	0.51775	0.172000	0.16884	TAC	A|0.999;G|0.001	0.001	strong		0.627	OSGIN1-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000269081.1	NM_013370		G	83992895	A	G	83992895	3	3	29	1	0	0	0	0	1	0	0	0	11298	391	14	3	361	3	OSGIN1	16	83992895	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	6667610	83992895	6361858	730	12971											
MBTPS1	8720	hgsc.bcm.edu	37	chr16	84125394	84125394	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgatgctgaggtttaacacGtcgatcttctttaaaatggc	10	13	9	9	3	2	1	0	1	2	0	3	3	2	1	1	2	2	2	1	2	3	5	rs113848224	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:84125394G>A	ENST00000343411.3	-	7	1401	c.906C>T	c.(904-906)gaC>gaT	p.D302D	MBTPS1_ENST00000569770.1_5'UTR	NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	302	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						GGTTTAACACGTCGATCTTCT	0.443																																					p.D302D		Atlas-SNP	.											.	MBTPS1	85	.	0			c.C906T						PASS	.	G		0,4400		0,0,2200	103	96	98		906	-6.2	0.1	16	dbSNP_132	98	9,8591	7.1+/-27.0	1,7,4292	yes	coding-synonymous	MBTPS1	NM_003791.2		1,7,6492	AA,AG,GG		0.1047,0.0,0.0692		302/1053	84125394	9,12991	2200	4300	6500	SO:0001819	synonymous_variant	8720	exon7			TAACACGTCGATC	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.906C>T	16.37:g.84125394G>A		120	0	0		90	36	0.4	NM_003791	A8K6V8|Q24JQ2|Q9UF67	Silent	SNP	ENST00000343411.3	37	CCDS10941.1																																																																																			G|0.998;A|0.002	0.002	strong		0.443	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269080.2	NM_003791		A	84125394	G	A	84125394	2	1	29	1	0	0	0	0	0	0	0	1	9370	1136	40	1		1	MBTPS1	16	84125394	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	132499	84125394	6229359	731	12972											
CRISPLD2	83716	hgsc.bcm.edu	37	chr16	84900645	84900645	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acctctgcggtcaactacatGagtgagtctaggccgtcctc	8	10	10	13	2	3	2	1	2	2	0	5	2	4	2	3	2	3	0	3	2	3	2	rs149615348	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:84900645G>A	ENST00000262424.5	+	7	1076	c.852G>A	c.(850-852)atG>atA	p.M284I	CRISPLD2_ENST00000567845.1_Splice_Site_p.M283I|CRISPLD2_ENST00000564567.1_Splice_Site_p.M284I	NM_031476.3	NP_113664.1	Q9H0B8	CRLD2_HUMAN	cysteine-rich secretory protein LCCL domain containing 2	284	LCCL 1. {ECO:0000255|PROSITE- ProRule:PRU00123}.				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						TCAACTACATGAGTGAGTCTA	0.582													G|||	13	0.00259585	0.0008	0.0058	5008	,	,		15855	0.0		0.007	False		,,,				2504	0.001				p.M284I		Atlas-SNP	.											.	CRISPLD2	36	.	0			c.G852A						PASS	.	G	ILE/MET	7,4391	12.9+/-30.5	0,7,2192	98	86	90		852	5.4	1	16	dbSNP_134	90	67,8533	41.2+/-98.3	1,65,4234	yes	missense-near-splice	CRISPLD2	NM_031476.3	10	1,72,6426	AA,AG,GG		0.7791,0.1592,0.5693	benign	284/498	84900645	74,12924	2199	4300	6499	SO:0001630	splice_region_variant	83716	exon7			CTACATGAGTGAG	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.853+1G>A	16.37:g.84900645G>A		79	0	0		54	24	0.444444	NM_031476	D3DUM0|Q6P590|Q6UWH0|Q6UXC6|Q96IB1|Q96K61	Missense_Mutation	SNP	ENST00000262424.5	37	CCDS10949.1	7	0.003205128205128205	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	15.98	2.991514	0.54041	0.001592	0.007791	ENSG00000103196	ENST00000262424	D	0.88818	-2.43	5.36	5.36	0.76844	LCCL (3);	0.291378	0.41938	D	0.000792	D	0.85687	0.5754	M	0.71581	2.175	0.80722	D	1	B;B;B	0.28933	0.179;0.019;0.228	B;B;B	0.30855	0.084;0.013;0.121	D	0.86000	0.1494	10	0.51188	T	0.08	.	16.5865	0.84728	0.0:0.0:1.0:0.0	.	284;284;284	Q9H0B8;Q9H0B8-2;Q9H0B8-3	CRLD2_HUMAN;.;.	I	284	ENSP00000262424:M284I	ENSP00000262424:M284I	M	+	3	0	CRISPLD2	83458146	1.000000	0.71417	1.000000	0.80357	0.670000	0.39368	5.753000	0.68736	2.514000	0.84764	0.561000	0.74099	ATG	G|0.994;A|0.006	0.006	strong		0.582	CRISPLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269086.2	NM_031476	Missense_Mutation	A	84900645	G	A	84900645	5	1	29	1	0	0	0	0	0	0	1	0	3885	1304	45	2	874	2	CRISPLD2	16	84900645	Splice_Site	SNP	G	TCGA-GR-7351-01A-11D-2210-10	775251	84900645	5454108	732	12973											
KLHDC4	54758	hgsc.bcm.edu	37	chr16	87782322	87782322	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ggccaaatgcaggacccagaGatccttgtagtggtagaact	12	8	12	9	0	0	2	0	0	0	2	1	4	1	3	3	3	2	3	3	3	4	3	rs3751727	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:87782322G>C	ENST00000270583.5	-	5	521	c.463C>G	c.(463-465)Ctc>Gtc	p.L155V	KLHDC4_ENST00000347925.5_Missense_Mutation_p.L155V|RP11-278A23.2_ENST00000563036.1_RNA|KLHDC4_ENST00000353170.5_Missense_Mutation_p.L98V	NM_017566.3	NP_060036.2	Q8TBB5	KLDC4_HUMAN	kelch domain containing 4	155			L -> V (in dbSNP:rs3751727).							breast(2)|endometrium(3)|lung(10)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(2)	21				BRCA - Breast invasive adenocarcinoma(80;0.0283)		AGGACCCAGAGATCCTTGTAG	0.557													G|||	128	0.0255591	0.0121	0.0101	5008	,	,		19581	0.0546		0.0278	False		,,,				2504	0.0225				p.L155V		Atlas-SNP	.											.	KLHDC4	45	.	0			c.C463G						PASS	.	G	VAL/LEU,VAL/LEU,VAL/LEU	59,4337	57.4+/-93.9	0,59,2139	177	175	175		292,463,463	5	1	16	dbSNP_107	175	249,8351	97.7+/-159.3	6,237,4057	yes	missense,missense,missense	KLHDC4	NM_001184854.1,NM_001184856.1,NM_017566.3	32,32,32	6,296,6196	CC,CG,GG		2.8953,1.3421,2.37	possibly-damaging,possibly-damaging,possibly-damaging	98/464,155/490,155/521	87782322	308,12688	2198	4300	6498	SO:0001583	missense	54758	exon5			CCCAGAGATCCTT	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.463C>G	16.37:g.87782322G>C	ENSP00000270583:p.Leu155Val	51	0	0		70	28	0.4	NM_001184856	D3DUN3|D3DUN4|D3DUN5|Q96F29|Q9BVN3	Missense_Mutation	SNP	ENST00000270583.5	37	CCDS10963.1	58	0.026556776556776556	5	0.01016260162601626	1	0.0027624309392265192	32	0.055944055944055944	20	0.026385224274406333	G	25.5	4.645314	0.87859	0.013421	0.028953	ENSG00000104731	ENST00000270583;ENST00000347925;ENST00000353170	T;T;T	0.62232	0.04;0.04;0.04	4.97	4.97	0.65823	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.34366	0.0895	M	0.75615	2.305	0.80722	D	1	D;D;D	0.89917	0.992;1.0;0.999	D;D;D	0.80764	0.976;0.994;0.988	T	0.64782	-0.6326	10	0.46703	T	0.11	0.8402	17.5767	0.87952	0.0:0.0:1.0:0.0	rs3751727;rs17699822;rs52805401;rs3751727	98;155;155	Q8TBB5-2;Q8TBB5-3;Q8TBB5	.;.;KLDC4_HUMAN	V	155;155;98	ENSP00000270583:L155V;ENSP00000325717:L155V;ENSP00000262530:L98V	ENSP00000270583:L155V	L	-	1	0	KLHDC4	86339823	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.891000	0.92485	2.450000	0.82876	0.561000	0.74099	CTC	G|0.974;C|0.026	0.026	strong		0.557	KLHDC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269109.2	NM_017566		C	87782322	G	C	87782322	3	2	29	1	0	0	0	0	1	0	0	0	8367	942	33	4	1127	4	KLHDC4	16	87782322	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2881677	87782322	2572431	733	12974											
CDH15	1013	hgsc.bcm.edu	37	chr16	89260195	89260195	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atcagccagctgcgtcacccGacagcgctgagcctgcctct	7	7	10	17	3	3	1	2	1	1	0	3	2	3	1	4	0	6	2	4	0	0	0	rs62068507	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:89260195G>A	ENST00000289746.2	+	13	2090	c.2025G>A	c.(2023-2025)ccG>ccA	p.P675P		NM_004933.2	NP_004924.1	P55291	CAD15_HUMAN	cadherin 15, type 1, M-cadherin (myotubule)	675					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)		TGCGTCACCCGACAGCGCTGA	0.706													G|||	16	0.00319489	0.0015	0.0029	5008	,	,		8843	0.0		0.0109	False		,,,				2504	0.001				p.P675P		Atlas-SNP	.											.	CDH15	54	.	0			c.G2025A						PASS	.	G		9,4279		0,9,2135	14	15	14		2025	-3.6	0	16	dbSNP_129	14	75,8425		0,75,4175	no	coding-synonymous	CDH15	NM_004933.2		0,84,6310	AA,AG,GG		0.8824,0.2099,0.6569		675/815	89260195	84,12704	2144	4250	6394	SO:0001819	synonymous_variant	1013	exon13			TCACCCGACAGCG	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.2025G>A	16.37:g.89260195G>A		20	0	0		13	7	0.538462	NM_004933		Silent	SNP	ENST00000289746.2	37	CCDS10976.1																																																																																			G|0.995;A|0.005	0.005	strong		0.706	CDH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269920.1	NM_004933		A	89260195	G	A	89260195	2	1	29	1	0	0	0	0	0	0	0	1	3102	1045	37	1		1	CDH15	16	89260195	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1477873	89260195	1094558	734	12975											
CHMP1A	5119	hgsc.bcm.edu	37	chr16	89715813	89715813	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccactgcgtctacgcgggaCgccatccgaagccagttcac	8	6	11	16	5	2	0	1	0	1	0	3	2	3	1	4	1	3	1	4	1	2	2	rs201479143	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:89715813C>T	ENST00000397901.3	-	4	454	c.198G>A	c.(196-198)gcG>gcA	p.A66A	CHMP1A_ENST00000253475.5_Missense_Mutation_p.V60I|CHMP1A_ENST00000535997.2_Silent_p.A2A|CHMP1A_ENST00000550102.1_Silent_p.A66A|CHMP1A_ENST00000547614.1_5'UTR	NM_002768.3	NP_002759.2	Q9HD42	CHM1A_HUMAN	charged multivesicular body protein 1A	66					cytokinesis (GO:0000910)|gene silencing (GO:0016458)|mitotic chromosome condensation (GO:0007076)|negative regulation of transcription by glucose (GO:0045014)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|proteolysis (GO:0006508)|transcription, DNA-templated (GO:0006351)|vesicle-mediated transport (GO:0016192)	condensed nuclear chromosome (GO:0000794)|early endosome (GO:0005769)|endomembrane system (GO:0012505)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|nuclear matrix (GO:0016363)	metallopeptidase activity (GO:0008237)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|ovary(1)	3		all_lung(18;3.07e-05)|all_hematologic(23;0.0256)		BRCA - Breast invasive adenocarcinoma(80;0.048)		CTACGCGGGACGCCATCCGAA	0.592													C|||	2	0.000399361	0.0	0.0	5008	,	,		14103	0.001		0.001	False		,,,				2504	0.0				p.V60I		Atlas-SNP	.											.	CHMP1A	15	.	0			c.G178A						PASS	.	C	ILE/VAL,	1,4321		0,1,2160	90	104	100		178,198	-6.3	1	16		100	14,8498		0,14,4242	yes	missense,coding-synonymous	CHMP1A	NM_001083314.1,NM_002768.2	29,	0,15,6402	TT,TC,CC		0.1645,0.0231,0.1169	,	60/241,66/197	89715813	15,12819	2161	4256	6417	SO:0001819	synonymous_variant	5119	exon3			GCGGGACGCCATC	U58048	CCDS45552.1	16q24.3	2011-09-21	2011-09-21	2007-03-20	ENSG00000131165	ENSG00000131165		"Charged multivesicular body proteins"	8740	protein-coding gene	gene with protein product		164010	"procollagen (type III) N-endopeptidase", "chromatin modifying protein 1A"	PRSM1, PCOLN3		11559748, 11559747	Standard	NM_002768		Approved	KIAA0047, CHMP1, Vps46A	uc002fnu.4	Q9HD42	OTTHUMG00000169521	ENST00000397901.3:c.198G>A	16.37:g.89715813C>T		92	0	0		80	44	0.55	NM_001083314	A2RU09|Q14468|Q15779|Q96G31	Missense_Mutation	SNP	ENST00000397901.3	37	CCDS45552.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	12.40	1.926176	0.34002	2.31E-4	0.001645	ENSG00000131165	ENST00000253475	.	.	.	5.38	-6.34	0.01982	.	0.936287	0.08656	N	0.913147	T	0.18215	0.0437	.	.	.	0.19945	N	0.999941	B	0.23891	0.093	B	0.17098	0.017	T	0.32107	-0.9919	8	0.87932	D	0	0.3661	0.8968	0.01265	0.1559:0.2634:0.2432:0.3375	.	60	A6NG32	.	I	60	.	ENSP00000253475:V60I	V	-	1	0	CHMP1A	88243314	0.000000	0.05858	0.964000	0.40570	0.730000	0.41778	-4.815000	0.00182	-0.773000	0.04596	-0.258000	0.10820	GTC	C|0.999;T|0.001	0.001	strong		0.592	CHMP1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404581.1	NM_002768		T	89715813	C	T	89715813	2	4	29	1	0	0	0	0	0	0	0	1	3354	536	19	1		1	CHMP1A	16	89715813	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	455618	89715813	638940	735	12976											
C16orf7	9605	hgsc.bcm.edu	37	chr16	89783205	89783205	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcttcagcatcttggaggtGtcggggggcacagtttcccc	6	10	14	11	1	2	0	1	0	1	0	4	1	3	1	2	5	2	4	2	5	0	3	rs118114589	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr16:89783205G>A	ENST00000389386.3	-	3	325	c.201C>T	c.(199-201)gaC>gaT	p.D67D	VPS9D1-AS1_ENST00000562298.1_RNA|VPS9D1_ENST00000561976.1_5'UTR|VPS9D1-AS1_ENST00000562866.1_RNA	NM_004913.2	NP_004904.2	Q9Y2B5	VP9D1_HUMAN	VPS9 domain containing 1	67					ATP synthesis coupled proton transport (GO:0015986)		GTPase activator activity (GO:0005096)|transporter activity (GO:0005215)										TCTTGGAGGTGTCGGGGGGCA	0.597													g|||	127	0.0253594	0.0015	0.0173	5008	,	,		12625	0.001		0.0249	False		,,,				2504	0.089				p.D67D		Atlas-SNP	.											.	.	.	.	0			c.C201T						PASS	.			16,3858		0,16,1921	17	20	19		201	-1.8	0.1	16	dbSNP_132	19	197,8037		1,195,3921	no	coding-synonymous	C16orf7	NM_004913.2		1,211,5842	AA,AG,GG		2.3925,0.413,1.7592		67/632	89783205	213,11895	1937	4117	6054	SO:0001819	synonymous_variant	9605	exon3			GGAGGTGTCGGGG	AB018551	CCDS42220.1	16q24.3	2012-10-09	2012-10-09	2012-10-09	ENSG00000075399	ENSG00000075399			13526	protein-coding gene	gene with protein product			"chromosome 16 open reading frame 7"	C16orf7		10231027	Standard	NM_004913		Approved	ATP-BL	uc002fom.1	Q9Y2B5	OTTHUMG00000173219	ENST00000389386.3:c.201C>T	16.37:g.89783205G>A		60	0	0		52	29	0.557692	NM_004913		Silent	SNP	ENST00000389386.3	37	CCDS42220.1																																																																																			G|0.988;A|0.012	0.012	strong		0.597	VPS9D1-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422508.1	NM_004913		A	89783205	G	A	89783205	2	1	29	1	0	0	0	0	0	0	0	1	1830	1368	48	2		2	C16orf7	16	89783205	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	67392	89783205	571548	736	12977											
MYO1C	4641	hgsc.bcm.edu	37	chr17	1382889	1382889	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgcccgccccactcaccctGgtcagatacttgagctggtt	6	10	9	16	1	2	2	2	1	0	1	2	2	2	2	4	2	3	2	4	2	1	3	rs146685153		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:1382889G>A	ENST00000575158.1	-	8	1088	c.912C>T	c.(910-912)acC>acT	p.T304T	MYO1C_ENST00000573198.1_5'UTR|MYO1C_ENST00000438665.2_Silent_p.T320T|MYO1C_ENST00000359786.5_Silent_p.T339T|MYO1C_ENST00000545534.2_Silent_p.T315T|MYO1C_ENST00000361007.2_Silent_p.T304T			Q12965	MYO1E_HUMAN	myosin IC	309	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)		CACTCACCCTGGTCAGATACT	0.662																																					p.T339T		Atlas-SNP	.											.	MYO1C	57	.	0			c.C1017T						PASS	.	G	,,	0,4406		0,0,2203	63	47	52		1017,960,912	2.9	1	17	dbSNP_134	52	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	MYO1C	NM_001080779.1,NM_001080950.1,NM_033375.4	,,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,,	339/1064,320/1045,304/1029	1382889	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	4641	exon8			CACCCTGGTCAGA	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.912C>T	17.37:g.1382889G>A		138	0	0		123	57	0.463415	NM_001080779	Q14778	Silent	SNP	ENST00000575158.1	37	CCDS11003.1																																																																																			G|1.000;A|0.000	0.000	weak		0.662	MYO1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438694.2			A	1382889	G	A	1382889	2	1	29	1	0	0	0	0	0	0	0	1	10079	1335	47	2		2	MYO1C	17	1382889	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10		1382889	79812321	737	12978											
RTN4RL1	146760	hgsc.bcm.edu	37	chr17	1840732	1840732	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacttgtagaggtagagggcGtgaagcttcaccaggccctg	9	8	14	10	1	1	3	1	1	0	2	1	3	1	3	2	3	1	3	2	3	3	4	rs372962204		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:1840732G>A	ENST00000331238.6	-	2	863	c.384C>T	c.(382-384)caC>caT	p.H128H		NM_178568.2	NP_848663.1			reticulon 4 receptor-like 1											breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|prostate(2)|skin(1)	11						GGTAGAGGGCGTGAAGCTTCA	0.657																																					p.H128H	GBM(68;949 1139 14865 32798 38342)	Atlas-SNP	.											.	RTN4RL1	21	.	0			c.C384T						PASS	.	G		2,4392		0,2,2195	49	55	53		384	-4.3	0.9	17		53	0,8582		0,0,4291	no	coding-synonymous	RTN4RL1	NM_178568.2		0,2,6486	AA,AG,GG		0.0,0.0455,0.0154		128/442	1840732	2,12974	2197	4291	6488	SO:0001819	synonymous_variant	146760	exon2			GAGGGCGTGAAGC	AF532859	CCDS45569.1	17p13.3	2008-02-05				ENSG00000185924			21329	protein-coding gene	gene with protein product	"nogo-66 receptor homolog 2"	610461					Standard	NM_178568		Approved	NGRH2, NgR3, DKFZp547J144	uc002ftp.3	Q86UN2		ENST00000331238.6:c.384C>T	17.37:g.1840732G>A		66	0	0		76	38	0.5	NM_178568		Silent	SNP	ENST00000331238.6	37	CCDS45569.1																																																																																			.	.	weak		0.657	RTN4RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450155.2	NM_178568		A	1840732	G	A	1840732	2	1	29	1	0	0	0	0	0	0	0	1	13746	1136	40	1		1	RTN4RL1	17	1840732	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	457843	1840732	79354478	738	12979											
TSR1	55720	hgsc.bcm.edu	37	chr17	2237939	2237941	+	In_Frame_Del	DEL	CCA	CCA	-																															gcctgaaattttcaaggtgcCcaccaagttattctcttcac																								rs570684854	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	CCA	CCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:2237939_2237941delCCA	ENST00000301364.5	-	5	1885_1887	c.806_808delTGG	c.(805-810)gtgggc>ggc	p.V269del	SGSM2_ENST00000268989.3_5'Flank|SGSM2_ENST00000574563.1_5'Flank|TSR1_ENST00000576112.2_In_Frame_Del_p.V253del|SGSM2_ENST00000426855.2_5'Flank	NM_018128.4	NP_060598.3	Q2NL82	TSR1_HUMAN	TSR1, 20S rRNA accumulation, homolog (S. cerevisiae)	269					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						TTCAAGGTGCCCACCAAGTTATT	0.443														7	0.00139776	0.0	0.0029	5008	,	,		18232	0.0		0.005	False		,,,				2504	0.0				p.269_270del		Pindel,Atlas-Indel	.											.	TSR1	57	.	0			c.807_809del						PASS	.			4,4252		0,4,2124						5.4	1			110	47,8205		2,43,4081	no	coding	TSR1	NM_018128.4		2,47,6205	A1A1,A1R,RR		0.5696,0.094,0.4077				51,12457				SO:0001651	inframe_deletion	55720	exon5			.	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.806_808delTGG	17.37:g.2237942_2237944delCCA	ENSP00000301364:p.Val269del	110	0	.		87	29	0.333	NM_018128	Q8WUY5|Q9NVT0|Q9P2E6	In_Frame_Del	DEL	ENST00000301364.5	37	CCDS32525.1																																																																																			.	.	none		0.443	TSR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438180.2	NM_018128		-	2237941	CCA	-	2237939	7	5	29	1	0	1	0	1	0	0	0	0	16679	623	22	0	1650	0	TSR1	17	2237939	In_Frame_Del	DEL	CCA	TCGA-GR-7351-01A-11D-2210-10	397207	2237939	78957271	739	12980											
DHX33	56919	hgsc.bcm.edu	37	chr17	5364393	5364393	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gccattgaaatactgagagaAcaggtccacatccatcgtag	14	8	9	10	1	0	3	0	2	0	1	3	4	2	3	3	1	2	1	3	1	4	3	rs141223137	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:5364393A>G	ENST00000225296.3	-	4	915	c.715T>C	c.(715-717)Ttc>Ctc	p.F239L	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	239	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						TACTGAGAGAACAGGTCCACA	0.507													A|||	6	0.00119808	0.0	0.0014	5008	,	,		16225	0.0		0.005	False		,,,				2504	0.0				p.F239L		Atlas-SNP	.											DHX33,NS,carcinoma,+2,3	DHX33	41	3	0			c.T715C						PASS	.	A	LEU/PHE,LEU/PHE	2,4404	2.1+/-5.4	0,2,2201	153	142	146		196,715	6.1	1	17	dbSNP_134	146	45,8555	29.6+/-80.5	0,45,4255	yes	missense,missense	DHX33	NM_001199699.1,NM_020162.3	22,22	0,47,6456	GG,GA,AA		0.5233,0.0454,0.3614	probably-damaging,probably-damaging	66/535,239/708	5364393	47,12959	2203	4300	6503	SO:0001583	missense	56919	exon4			GAGAGAACAGGTC	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.715T>C	17.37:g.5364393A>G	ENSP00000225296:p.Phe239Leu	61	0	0		70	28	0.4	NM_020162	B4DHF9|Q4G149|Q5CZ73|Q9H5M9	Missense_Mutation	SNP	ENST00000225296.3	37	CCDS11072.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	A	36	5.656465	0.96724	4.54E-4	0.005233	ENSG00000005100	ENST00000225296	T	0.23348	1.91	6.07	6.07	0.98685	DEAD-like helicase (2);	0.000000	0.85682	D	0.000000	T	0.38825	0.1055	M	0.63428	1.95	0.80722	D	1	D	0.63880	0.993	P	0.62014	0.897	T	0.36311	-0.9753	10	0.87932	D	0	.	15.81	0.78552	1.0:0.0:0.0:0.0	.	239	Q9H6R0	DHX33_HUMAN	L	239	ENSP00000225296:F239L	ENSP00000225296:F239L	F	-	1	0	DHX33	5305117	1.000000	0.71417	0.996000	0.52242	0.990000	0.78478	9.271000	0.95698	2.326000	0.78906	0.533000	0.62120	TTC	A|0.996;G|0.004	0.004	strong		0.507	DHX33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219826.2	NM_020162		G	5364393	A	G	5364393	3	3	29	1	0	0	0	0	1	0	0	0	4508	43	2	3	1444	3	DHX33	17	5364393	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	3126454	5364393	75830817	740	12981											
AIPL1	23746	hgsc.bcm.edu	37	chr17	6337404	6337404	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tcatcacatttcatggtgcgGaaatgaaagatcacctagtc	13	11	8	9	1	4	2	4	1	0	1	5	3	4	3	1	2	1	0	1	2	3	2	rs11650007	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:6337404G>A	ENST00000381129.3	-	2	191	c.111C>T	c.(109-111)ttC>ttT	p.F37F	AIPL1_ENST00000570466.1_Intron|AIPL1_ENST00000574506.1_Intron|AIPL1_ENST00000575265.1_Silent_p.F37F|AIPL1_ENST00000576776.1_Silent_p.F37F|AIPL1_ENST00000250087.5_Silent_p.F37F|AIPL1_ENST00000576307.1_Intron|AIPL1_ENST00000571740.1_Silent_p.F37F	NM_001033055.1|NM_014336.3	NP_001028227.1|NP_055151.3	Q9NZN9	AIPL1_HUMAN	aryl hydrocarbon receptor interacting protein-like 1	37					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)		TCATGGTGCGGAAATGAAAGA	0.567													G|||	31	0.0061901	0.0	0.0043	5008	,	,		18369	0.0		0.0278	False		,,,				2504	0.0				p.F37F		Atlas-SNP	.											.	AIPL1	34	.	0			c.C111T						PASS	.	G	,,	36,4370	39.2+/-71.8	0,36,2167	118	83	95	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	111,,111	3.8	1	17	dbSNP_120	95	238,8362	95.0+/-156.8	1,236,4063	no	coding-synonymous,intron,coding-synonymous	AIPL1	NM_001033054.1,NM_001033055.1,NM_014336.3	,,	1,272,6230	AA,AG,GG		2.7674,0.8171,2.1067	,,	37/322,,37/385	6337404	274,12732	2203	4300	6503	SO:0001819	synonymous_variant	23746	exon2			GGTGCGGAAATGA	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.111C>T	17.37:g.6337404G>A		100	0	0		89	38	0.426966	NM_014336	D3DTM4|Q659W3|Q659W4|Q6ZZB6|Q8N6A0|Q9H873|Q9NS10	Silent	SNP	ENST00000381129.3	37	CCDS11075.1																																																																																			G|0.983;A|0.017	0.017	strong		0.567	AIPL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219828.3	NM_014336		A	6337404	G	A	6337404	2	1	29	1	0	0	0	0	0	0	0	1	436	1165	41	2		2	AIPL1	17	6337404	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	973011	6337404	74857806	741	12982											
FBXO39	162517	hgsc.bcm.edu	37	chr17	6684003	6684003	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caggtcatctggggtatgtcCtgggccaagctggccaggca	7	8	15	11	0	2	0	1	0	1	0	3	0	3	0	3	6	1	3	3	6	2	1	rs17731806	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:6684003C>G	ENST00000321535.4	+	2	946	c.816C>G	c.(814-816)tcC>tcG	p.S272S		NM_153230.2	NP_694962.1	Q8N4B4	FBX39_HUMAN	F-box protein 39	272										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						GGGGTATGTCCTGGGCCAAGC	0.542													C|||	120	0.0239617	0.0023	0.0216	5008	,	,		21815	0.0		0.0447	False		,,,				2504	0.0583				p.S272S		Atlas-SNP	.											.	FBXO39	50	.	0			c.C816G						PASS	.	C		63,4343	59.3+/-96.0	0,63,2140	75	63	67		816	0.6	1	17	dbSNP_123	67	472,8128	139.8+/-196.4	16,440,3844	no	coding-synonymous	FBXO39	NM_153230.2		16,503,5984	GG,GC,CC		5.4884,1.4299,4.1135		272/443	6684003	535,12471	2203	4300	6503	SO:0001819	synonymous_variant	162517	exon2			TATGTCCTGGGCC	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.816C>G	17.37:g.6684003C>G		42	0	0		49	28	0.571429	NM_153230		Silent	SNP	ENST00000321535.4	37	CCDS11082.1																																																																																			C|0.963;G|0.037	0.037	strong		0.542	FBXO39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219866.2	NM_153230		G	6684003	C	G	6684003	2	3	29	1	0	0	0	0	0	0	0	1	5755	668	24	4		4	FBXO39	17	6684003	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	346599	6684003	74511207	742	12983											
SLC16A11	162515	hgsc.bcm.edu	37	chr17	6946357	6946357	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aaccatcaccacggggcgggCcccccagcgcgtgctcaggg	7	3	14	17	4	2	0	2	0	0	0	2	0	2	0	5	4	3	1	5	4	1	0	rs75636181	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:6946357C>A	ENST00000308009.1	-	2	647	c.310G>T	c.(310-312)Gcc>Tcc	p.A104S	SLC16A11_ENST00000447225.1_Missense_Mutation_p.A80S	NM_153357.1	NP_699188.1	Q8NCK7	MOT11_HUMAN	solute carrier family 16, member 11	104					lipid metabolic process (GO:0006629)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			endometrium(2)|kidney(2)|lung(2)|ovary(1)|skin(2)	9						ACGGGGCGGGCCCCCCAGCGC	0.692													.|||	101	0.0201677	0.0023	0.0303	5008	,	,		13501	0.0		0.0676	False		,,,				2504	0.0092				p.A104S		Atlas-SNP	.											SLC16A11,NS,carcinoma,0,1	SLC16A11	25	1	0			c.G310T						PASS	.	C	SER/ALA	70,4266		0,70,2098	10	14	13		310	3.1	1	17	dbSNP_131	13	545,7977		24,497,3740	no	missense	SLC16A11	NM_153357.1	99	24,567,5838	AA,AC,CC		6.3952,1.6144,4.783	benign	104/472	6946357	615,12243	2168	4261	6429	SO:0001583	missense	162515	exon2			GGCGGGCCCCCCA	AK074674	CCDS11086.1	17p13.2	2013-07-18	2013-07-18		ENSG00000174326	ENSG00000174326		"Solute carriers"	23093	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 11"	615765	"solute carrier family 16 (monocarboxylic acid transporters), member 11"				Standard	NM_153357		Approved	FLJ90193, MCT11	uc002gei.1	Q8NCK7	OTTHUMG00000102087	ENST00000308009.1:c.310G>T	17.37:g.6946357C>A	ENSP00000310490:p.Ala104Ser	68	0	0		28	17	0.607143	NM_153357		Missense_Mutation	SNP	ENST00000308009.1	37	CCDS11086.1	71	0.03250915750915751	1	0.0020325203252032522	17	0.04696132596685083	0	0.0	53	0.06992084432717678	C	10.57	1.386498	0.25031	0.016144	0.063952	ENSG00000174326	ENST00000308009;ENST00000447225	T;T	0.37411	1.2;1.2	5.18	3.09	0.35607	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.319287	0.34046	N	0.004302	T	0.01156	0.0038	N	0.03238	-0.38	0.38818	P	0.04442900000000005	B	0.15719	0.014	B	0.20955	0.032	T	0.08743	-1.0707	9	0.27785	T	0.31	.	11.0985	0.48160	0.5302:0.4698:0.0:0.0	.	104	Q8NCK7	MOT11_HUMAN	S	104;80	ENSP00000310490:A104S;ENSP00000394449:A80S	ENSP00000310490:A104S	A	-	1	0	SLC16A11	6887081	0.001000	0.12720	1.000000	0.80357	0.945000	0.59286	-0.023000	0.12456	0.676000	0.31285	0.555000	0.69702	GCC	C|0.967;A|0.033	0.033	strong		0.692	SLC16A11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219921.1	NM_153357		A	6946357	C	A	6946357	3	1	29	1	0	0	0	0	1	0	0	0	14419	739	26	4	1117	4	SLC16A11	17	6946357	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	262354	6946357	74248853	743	12984											
C17orf74	201243	hgsc.bcm.edu	37	chr17	7330307	7330307	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcggtgtcccggaacgccCggcctgaggcccagggctgc	4	5	15	17	4	0	1	0	1	0	0	2	2	1	2	5	5	2	1	5	5	1	0	rs146528431	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:7330307C>T	ENST00000333870.3	+	3	1071	c.997C>T	c.(997-999)Cgg>Tgg	p.R333W	RP11-104H15.7_ENST00000575310.1_RNA|C17orf74_ENST00000574034.1_3'UTR	NM_175734.4	NP_783861.3	Q0P670	CQ074_HUMAN	chromosome 17 open reading frame 74	333						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)				CCGGAACGCCCGGCCTGAGGC	0.692													C|||	17	0.00339457	0.0008	0.0072	5008	,	,		14183	0.0		0.0099	False		,,,				2504	0.001				p.R333W		Atlas-SNP	.											.	C17orf74	56	.	0			c.C997T						PASS	.	C	TRP/ARG	6,3938		0,6,1966	17	21	20		997	1.3	0	17	dbSNP_134	20	69,8203		0,69,4067	no	missense	C17orf74	NM_175734.4	101	0,75,6033	TT,TC,CC		0.8341,0.1521,0.6139	probably-damaging	333/502	7330307	75,12141	1972	4136	6108	SO:0001583	missense	201243	exon3			AACGCCCGGCCTG	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.997C>T	17.37:g.7330307C>T	ENSP00000328061:p.Arg333Trp	77	0	0		61	41	0.672131	NM_175734		Missense_Mutation	SNP	ENST00000333870.3	37	CCDS42255.1	14	0.00641025641025641	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	8	0.010554089709762533	C	4.791	0.147015	0.09134	0.001521	0.008341	ENSG00000184560	ENST00000333870	T	0.37058	1.22	4.59	1.29	0.21616	.	0.000000	0.34828	N	0.003652	T	0.16896	0.0406	L	0.32530	0.975	0.09310	N	1	B	0.15719	0.014	B	0.06405	0.002	T	0.16394	-1.0404	10	0.87932	D	0	-6.0266	5.6303	0.17506	0.355:0.5485:0.0:0.0964	.	333	Q0P670	CQ074_HUMAN	W	333	ENSP00000328061:R333W	ENSP00000328061:R333W	R	+	1	2	C17orf74	7271031	0.002000	0.14202	0.000000	0.03702	0.007000	0.05969	-0.278000	0.08490	0.091000	0.17302	-0.320000	0.08662	CGG	C|0.995;T|0.005	0.005	strong		0.692	C17orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440933.2	NM_175734		T	7330307	C	T	7330307	3	4	29	1	0	0	0	0	1	0	0	0	1881	643	23	1	1007	1	C17orf74	17	7330307	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	383950	7330307	73864903	744	12985											
MYH10	4628	hgsc.bcm.edu	37	chr17	8402769	8402769	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatctgtctccaggccctgcTtgttcttctctagatttgct	4	18	7	12	0	4	1	0	0	4	1	6	1	4	1	2	1	2	3	2	1	2	6			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:8402769T>G	ENST00000269243.4	-	28	3815	c.3677A>C	c.(3676-3678)aAg>aCg	p.K1226T	MYH10_ENST00000379980.4_Missense_Mutation_p.K1242T|MYH10_ENST00000360416.3_Missense_Mutation_p.K1257T|MYH10_ENST00000396239.1_Missense_Mutation_p.K1247T	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	1226					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						CAGGCCCTGCTTGTTCTTCTC	0.473																																					p.K1257T		Atlas-SNP	.											.	MYH10	148	.	0			c.A3770C						PASS	.						108	103	105					17																	8402769		2203	4300	6503	SO:0001583	missense	4628	exon30			CCCTGCTTGTTCT	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.3677A>C	17.37:g.8402769T>G	ENSP00000269243:p.Lys1226Thr	160	0	0		154	50	0.324675	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Missense_Mutation	SNP	ENST00000269243.4	37	CCDS11144.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.190916	0.78789	.	.	ENSG00000133026	ENST00000269243;ENST00000360416;ENST00000396239;ENST00000379980	D;D;D;D	0.85171	-1.95;-1.95;-1.95;-1.95	5.03	5.03	0.67393	Myosin tail (1);	0.106621	0.64402	D	0.000005	D	0.92358	0.7575	M	0.83692	2.655	0.54753	D	0.999986	D;D;D	0.55605	0.972;0.965;0.972	D;D;D	0.70227	0.968;0.945;0.968	D	0.93517	0.6858	10	0.87932	D	0	.	14.9308	0.70914	0.0:0.0:0.0:1.0	.	1235;1257;1226	B2RWP9;F8VTL3;P35580	.;.;MYH10_HUMAN	T	1226;1257;1247;1242	ENSP00000269243:K1226T;ENSP00000353590:K1257T;ENSP00000379539:K1247T;ENSP00000369315:K1242T	ENSP00000269243:K1226T	K	-	2	0	MYH10	8343494	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.961000	0.63681	2.114000	0.64651	0.533000	0.62120	AAG	.	.	none		0.473	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			G	8402769	T	G	8402769	3	3	29	1	0	0	0	0	1	0	0	0	10039	1609	56	5	2309	5	MYH10	17	8402769	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	1072462	8402769	72792441	745	12986											
MYH13	8735	hgsc.bcm.edu	37	chr17	10222310	10222310	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcctcctccaggtccctgcGcattttctggaactcagcct	5	11	9	16	1	2	0	1	0	1	0	5	1	5	1	5	3	3	1	5	3	1	2	rs200861648	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:10222310G>A	ENST00000418404.3	-	26	3698	c.3535C>T	c.(3535-3537)Cgc>Tgc	p.R1179C	MYH13_ENST00000252172.4_Missense_Mutation_p.R1179C|RP11-401O9.4_ENST00000609088.1_RNA|RP11-401O9.3_ENST00000577743.1_RNA			Q9UKX3	MYH13_HUMAN	myosin, heavy chain 13, skeletal muscle	1179					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						AGGTCCCTGCGCATTTTCTGG	0.582													G|||	2	0.000399361	0.0	0.0014	5008	,	,		17738	0.0		0.001	False		,,,				2504	0.0				p.R1179C		Atlas-SNP	.											MYH13_ENST00000252172,right_upper_lobe,carcinoma,0,2	MYH13	533	2	0			c.C3535T						PASS	.	G	CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	132	135	134		3535	4.1	1	17	dbSNP_132	134	6,8594	5.0+/-18.6	0,6,4294	no	missense	MYH13	NM_003802.2	180	0,8,6495	AA,AG,GG		0.0698,0.0454,0.0615	probably-damaging	1179/1939	10222310	8,12998	2203	4300	6503	SO:0001583	missense	8735	exon27			CCCTGCGCATTTT	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.3535C>T	17.37:g.10222310G>A	ENSP00000404570:p.Arg1179Cys	155	0	0		138	56	0.405797	NM_003802	O95252|Q9P0U8	Missense_Mutation	SNP	ENST00000418404.3	37	CCDS45613.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	17.64	3.438775	0.62955	4.54E-4	6.98E-4	ENSG00000006788	ENST00000252172	D	0.84070	-1.8	4.05	4.05	0.47172	Myosin tail (1);	.	.	.	.	D	0.93867	0.8038	H	0.97983	4.12	0.44862	D	0.997876	D	0.89917	1.0	D	0.97110	1.0	D	0.95113	0.8240	9	0.87932	D	0	.	11.9523	0.52962	0.0:0.0:0.8264:0.1735	.	1179	Q9UKX3	MYH13_HUMAN	C	1179	ENSP00000252172:R1179C	ENSP00000252172:R1179C	R	-	1	0	MYH13	10163035	1.000000	0.71417	0.972000	0.41901	0.989000	0.77384	4.380000	0.59581	2.236000	0.73375	0.591000	0.81541	CGC	G|1.000;A|0.000	0.000	strong		0.582	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	10222310	G	A	10222310	3	1	29	1	0	0	0	0	1	0	0	0	10041	1087	38	1	2341	1	MYH13	17	10222310	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1819541	10222310	70972900	746	12987											
TNFRSF13B	23495	hgsc.bcm.edu	37	chr17	16843666	16843666	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagacttggccggactttgaCggggccttgagcggggctgg	6	8	18	9	3	0	3	0	2	0	1	0	4	0	4	2	7	1	1	2	7	1	3	rs104894649		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:16843666C>T	ENST00000261652.2	-	4	617	c.605G>A	c.(604-606)cGt>cAt	p.R202H	TNFRSF13B_ENST00000579315.1_Intron|TNFRSF13B_ENST00000437538.2_Missense_Mutation_p.R156H|TNFRSF13B_ENST00000581616.2_5'Flank|TNFRSF13B_ENST00000583789.1_Missense_Mutation_p.R156H	NM_012452.2	NP_036584.1	O14836	TR13B_HUMAN	tumor necrosis factor receptor superfamily, member 13B	202			R -> H (in CVID2). {ECO:0000269|PubMed:16007086}.		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						CGGACTTTGACGGGGCCTTGA	0.652									IgA Deficiency, Selective				.|||	1	0.000199681	0.0	0.0	5008	,	,		16946	0.0		0.0	False		,,,				2504	0.001				p.R202H		Atlas-SNP	.											.	TNFRSF13B	34	.	0			c.G605A	GRCh37	CM052923	TNFRSF13B	M	rs104894649	PASS	.	C	HIS/ARG	2,4404	4.2+/-10.8	0,2,2201	93	100	98	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	605	2	0	17	dbSNP_132	98	7,8593	5.7+/-21.5	0,7,4293	yes	missense	TNFRSF13B	NM_012452.2	29	0,9,6494	TT,TC,CC		0.0814,0.0454,0.0692	benign	202/294	16843666	9,12997	2203	4300	6503	SO:0001583	missense	23495	exon4	Familial Cancer Database	IGAD1, IGAD2	CTTTGACGGGGCC	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.605G>A	17.37:g.16843666C>T	ENSP00000261652:p.Arg202His	46	0	0		61	32	0.52459	NM_012452	B2R8B0|B7Z6V8|Q32LX4|Q7Z6F5	Missense_Mutation	SNP	ENST00000261652.2	37	CCDS11181.1	.	.	.	.	.	.	.	.	.	.	c	7.351	0.622884	0.14193	4.54E-4	8.14E-4	ENSG00000240505	ENST00000437538;ENST00000261652	D;D	0.93488	-3.23;-3.2	3.03	2.01	0.26516	.	0.476795	0.19299	N	0.117685	D	0.83543	0.5277	N	0.19112	0.55	0.09310	A	1.25395e-09	B;P	0.34892	0.3;0.474	B;B	0.25140	0.058;0.043	T	0.82168	-0.0591	9	0.54805	T	0.06	0.0038	6.5787	0.22581	0.0:0.8475:0.0:0.1525	.	156;202	O14836-2;O14836	.;TR13B_HUMAN	H	156;202	ENSP00000413453:R156H;ENSP00000261652:R202H	ENSP00000261652:R202H	R	-	2	0	TNFRSF13B	16784391	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.497000	0.22514	0.552000	0.29026	0.558000	0.71614	CGT	C|0.999;T|0.001	0.001	strong		0.652	TNFRSF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131474.2			T	16843666	C	T	16843666	3	4	29	1	0	0	0	0	1	0	0	0	16302	536	19	1	284	1	TNFRSF13B	17	16843666	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	6621356	16843666	64351544	747	12988											
NT5M	56953	hgsc.bcm.edu	37	chr17	17250197	17250197	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgcagctgcagcccccccGccgcaggctgcactcgtggg	4	5	13	19	3	0	0	0	0	0	0	1	0	0	0	5	2	5	6	5	2	0	0	rs145194793	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:17250197G>A	ENST00000389022.4	+	5	839	c.623G>A	c.(622-624)cGc>cAc	p.R208H	NT5M_ENST00000582909.1_3'UTR	NM_020201.3	NP_064586.1	Q9NPB1	NT5M_HUMAN	5',3'-nucleotidase, mitochondrial	208					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						CAGCCCCCCCGCCGCAGGCTG	0.677													G|||	8	0.00159744	0.0	0.0	5008	,	,		15949	0.0		0.007	False		,,,				2504	0.001				p.R208H		Atlas-SNP	.											.	NT5M	17	.	0			c.G623A						PASS	.	G	HIS/ARG	7,4395		0,7,2194	30	36	34		623	-0.1	0.4	17	dbSNP_134	34	40,8552		0,40,4256	yes	missense	NT5M	NM_020201.3	29	0,47,6450	AA,AG,GG		0.4655,0.159,0.3617	possibly-damaging	208/229	17250197	47,12947	2201	4296	6497	SO:0001583	missense	56953	exon5			CCCCCCGCCGCAG	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.623G>A	17.37:g.17250197G>A	ENSP00000373674:p.Arg208His	63	0	0		77	40	0.519481	NM_020201		Missense_Mutation	SNP	ENST00000389022.4	37	CCDS32581.1	5|5	0.0022893772893772895|0.0022893772893772895	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	5|5	0.006596306068601583|0.006596306068601583	G|G	13.76|13.76	2.332091|2.332091	0.41297|0.41297	0.00159|0.00159	0.004655|0.004655	ENSG00000205309|ENSG00000205309	ENST00000446264|ENST00000389022	.|T	.|0.41400	.|1.0	5.79|5.79	-0.0825|-0.0825	0.13697|0.13697	.|HAD-like domain (2);	0.532662|.	0.21888|.	N|.	0.067623|.	T|T	0.25901|0.25901	0.0631|0.0631	L|L	0.31420|0.31420	0.93|0.93	0.09310|0.09310	N|N	1|1	B|D;P	0.27971|0.52996	0.196|0.957;0.926	B|P;P	0.17098|0.48270	0.017|0.572;0.572	T|T	0.15235|0.15235	-1.0444|-1.0444	9|9	0.59425|0.59425	D|D	0.04|0.04	-10.4946|-10.4946	6.402|6.402	0.21644|0.21644	0.3077:0.0:0.5678:0.1245|0.3077:0.0:0.5678:0.1245	.|.	207|214;208	F6S3X3|Q2I378;Q9NPB1	.|.;NT5M_HUMAN	T|H	207|208	.|ENSP00000373674:R208H	ENSP00000390695:A207T|ENSP00000373674:R208H	A|R	+|+	1|2	0|0	NT5M|NT5M	17190922|17190922	0.735000|0.735000	0.28153|0.28153	0.378000|0.378000	0.26068|0.26068	0.070000|0.070000	0.16714|0.16714	1.114000|1.114000	0.31196|0.31196	0.377000|0.377000	0.24735|0.24735	-0.254000|-0.254000	0.11334|0.11334	GCC|CGC	G|0.997;A|0.003	0.003	strong		0.677	NT5M-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446045.1			A	17250197	G	A	17250197	3	1	29	1	0	0	0	0	1	0	0	0	10703	1087	38	1	641	1	NT5M	17	17250197	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	406531	17250197	63945013	748	12989											
FAM83G	644815	hgsc.bcm.edu	37	chr17	18881605	18881605	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctctgcttccacagctggtgCtgggcgctggcctgggaggt	3	10	16	12	1	1	0	0	0	1	0	2	1	2	1	2	5	3	4	2	5	0	1	rs201344489	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:18881605C>A	ENST00000388995.6	-	5	1597	c.1374G>T	c.(1372-1374)caG>caT	p.Q458H	SLC5A10_ENST00000317977.6_Intron|SLC5A10_ENST00000395643.2_Intron|SLC5A10_ENST00000395647.2_Intron|SLC5A10_ENST00000395642.1_Intron|SLC5A10_ENST00000417251.2_Intron|SLC5A10_ENST00000395645.3_Intron|FAM83G_ENST00000345041.4_Missense_Mutation_p.Q458H|FAM83G_ENST00000585154.2_Missense_Mutation_p.Q458H			A6ND36	FA83G_HUMAN	family with sequence similarity 83, member G	458					BMP signaling pathway (GO:0030509)	cytosol (GO:0005829)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(3)|stomach(1)	22						ACAGCTGGTGCTGGGCGCTGG	0.642													C|||	8	0.00159744	0.0	0.0014	5008	,	,		16140	0.001		0.004	False		,,,				2504	0.002				p.Q458H		Atlas-SNP	.											.	FAM83G	51	.	0			c.G1374T						PASS	.	C	HIS/GLN,,	11,4201		0,11,2095	19	24	22		1374,,	3.6	1	17		22	79,8385		0,79,4153	yes	missense,intron,intron	SLC5A10,FAM83G	NM_001039999.2,NM_001042450.1,NM_152351.3	24,,	0,90,6248	AA,AC,CC		0.9334,0.2612,0.71	possibly-damaging,,	458/824,,	18881605	90,12586	2106	4232	6338	SO:0001583	missense	644815	exon5			CTGGTGCTGGGCG	AK123558	CCDS42276.1	17p11.2	2014-05-01	2006-03-22		ENSG00000188522	ENSG00000188522			32554	protein-coding gene	gene with protein product	"protein associated with SMAD1"	615886				24554596	Standard	NM_001039999		Approved	FLJ41564, PAWS1	uc002guw.3	A6ND36	OTTHUMG00000059411	ENST00000388995.6:c.1374G>T	17.37:g.18881605C>A	ENSP00000373647:p.Gln458His	119	0	0		119	72	0.605042	NM_001039999	Q3KQZ4|Q6ZW60	Missense_Mutation	SNP	ENST00000388995.6	37	CCDS42276.1	5	0.0022893772893772895	0	0.0	0	0.0	1	0.0017482517482517483	4	0.005277044854881266	C	17.35	3.367567	0.61513	0.002612	0.009334	ENSG00000188522	ENST00000388995;ENST00000345041	T;T	0.14022	2.54;2.54	5.62	3.62	0.41486	.	1.902850	0.02950	N	0.141633	T	0.27798	0.0684	L	0.56769	1.78	0.26245	N	0.978812	D	0.89917	1.0	D	0.73380	0.98	T	0.02457	-1.1156	10	0.51188	T	0.08	-18.311	8.5714	0.33572	0.0:0.7088:0.0:0.2912	.	458	A6ND36	FA83G_HUMAN	H	458	ENSP00000373647:Q458H;ENSP00000343279:Q458H	ENSP00000343279:Q458H	Q	-	3	2	FAM83G	18822330	0.999000	0.42202	0.997000	0.53966	0.984000	0.73092	0.631000	0.24568	0.732000	0.32470	0.655000	0.94253	CAG	C|0.998;A|0.002	0.002	strong		0.642	FAM83G-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253108.4			A	18881605	C	A	18881605	3	1	29	1	0	0	0	0	1	0	0	0	5647	796	28	4	1105	4	FAM83G	17	18881605	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1631408	18881605	62313605	749	12990											
ALDH3A2	224	hgsc.bcm.edu	37	chr17	19575096	19575096	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	atactttttctcatcagcgtCcctgtttattaaaaagttta	11	18	4	8	1	2	0	2	0	1	0	4	0	3	0	1	0	2	2	1	0	6	8	rs61737992	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:19575096C>T	ENST00000176643.6	+	9	1716	c.1270C>T	c.(1270-1272)Ccc>Tcc	p.P424S	ALDH3A2_ENST00000579855.1_Missense_Mutation_p.P424S|ALDH3A2_ENST00000395575.2_Missense_Mutation_p.P424S|ALDH3A2_ENST00000581518.1_Missense_Mutation_p.P424S|ALDH3A2_ENST00000339618.4_Missense_Mutation_p.P424S|ALDH3A2_ENST00000571163.1_Intron			P51648	AL3A2_HUMAN	aldehyde dehydrogenase 3 family, member A2	424					cellular aldehyde metabolic process (GO:0006081)|central nervous system development (GO:0007417)|epidermis development (GO:0008544)|oxidation-reduction process (GO:0055114)|peripheral nervous system development (GO:0007422)|phytol metabolic process (GO:0033306)|sesquiterpenoid metabolic process (GO:0006714)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)|peroxisome (GO:0005777)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|long-chain-alcohol oxidase activity (GO:0046577)|long-chain-aldehyde dehydrogenase activity (GO:0050061)|medium-chain-aldehyde dehydrogenase activity (GO:0052814)			endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(2)|ovary(2)|prostate(1)	13	all_cancers(12;1.39e-05)|all_epithelial(12;0.00158)|Breast(13;0.245)					TCATCAGCGTCCCTGTTTATT	0.388													C|||	12	0.00239617	0.0	0.0058	5008	,	,		18840	0.0		0.007	False		,,,				2504	0.001				p.P424S		Atlas-SNP	.											.	ALDH3A2	41	.	0			c.C1270T						PASS	.	C	SER/PRO,SER/PRO	2,4404	4.2+/-10.8	0,2,2201	104	110	108		1270,1270	-1.8	0.7	17	dbSNP_129	108	58,8542	35.9+/-90.5	0,58,4242	yes	missense,missense	ALDH3A2	NM_000382.2,NM_001031806.1	74,74	0,60,6443	TT,TC,CC		0.6744,0.0454,0.4613	benign,benign	424/486,424/509	19575096	60,12946	2203	4300	6503	SO:0001583	missense	224	exon9			CAGCGTCCCTGTT	L47162	CCDS11210.1, CCDS32589.1	17p11.2	2010-05-07			ENSG00000072210	ENSG00000072210	1.2.1.3	"Aldehyde dehydrogenases"	403	protein-coding gene	gene with protein product	"fatty aldehyde dehydrogenase"	609523		SLS, ALDH10		7894487	Standard	NM_000382		Approved	FALDH	uc002gwa.1	P51648	OTTHUMG00000059471	ENST00000176643.6:c.1270C>T	17.37:g.19575096C>T	ENSP00000176643:p.Pro424Ser	102	0	0		104	50	0.480769	NM_001031806	Q6I9T3|Q93011|Q96J37	Missense_Mutation	SNP	ENST00000176643.6	37	CCDS11210.1	7	0.003205128205128205	0	0.0	3	0.008287292817679558	0	0.0	4	0.005277044854881266	C	2.583	-0.296965	0.05532	4.54E-4	0.006744	ENSG00000072210	ENST00000176643;ENST00000395575;ENST00000339618	D;D;D	0.83591	-1.74;-1.74;-1.74	6.06	-1.82	0.07857	Aldehyde/histidinol dehydrogenase (1);	0.872349	0.10601	N	0.655669	T	0.46852	0.1414	N	0.02830	-0.485	0.43603	D	0.99596	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.51172	-0.8739	10	0.02654	T	1	-4.9546	8.2837	0.31915	0.0:0.1298:0.4471:0.423	rs61737992	424;424	P51648;P51648-2	AL3A2_HUMAN;.	S	424	ENSP00000176643:P424S;ENSP00000378942:P424S;ENSP00000345774:P424S	ENSP00000176643:P424S	P	+	1	0	ALDH3A2	19515688	0.000000	0.05858	0.736000	0.30914	0.993000	0.82548	-0.852000	0.04308	-0.339000	0.08401	0.650000	0.86243	CCC	C|0.996;T|0.004	0.004	strong		0.388	ALDH3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132268.1			T	19575096	C	T	19575096	3	4	29	1	0	0	0	0	1	0	0	0	498	855	30	2	1304	2	ALDH3A2	17	19575096	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	693491	19575096	61620114	750	12991											
FNDC8	54752	hgsc.bcm.edu	37	chr17	33454198	33454198	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctttgcagggatgctggaggGggagctgaacaaactcagct	10	8	15	8	0	1	1	1	1	0	0	1	4	1	4	0	4	6	4	0	4	2	1	rs147725468		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:33454198G>T	ENST00000158009.5	+	2	462	c.347G>T	c.(346-348)gGg>gTg	p.G116V		NM_017559.2	NP_060029.1	Q8TC99	FNDC8_HUMAN	fibronectin type III domain containing 8	116						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)		ATGCTGGAGGGGGAGCTGAAC	0.567													G|||	1	0.000199681	0.0	0.0	5008	,	,		20327	0.0		0.001	False		,,,				2504	0.0				p.G116V		Atlas-SNP	.											.	FNDC8	28	.	0			c.G347T						PASS	.	G	VAL/GLY	2,4404	4.2+/-10.8	0,2,2201	133	136	135		347	5.4	0.2	17	dbSNP_134	135	10,8590	7.7+/-29.5	0,10,4290	yes	missense	FNDC8	NM_017559.2	109	0,12,6491	TT,TG,GG		0.1163,0.0454,0.0923	probably-damaging	116/325	33454198	12,12994	2203	4300	6503	SO:0001583	missense	54752	exon2			TGGAGGGGGAGCT	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.347G>T	17.37:g.33454198G>T	ENSP00000158009:p.Gly116Val	61	0	0		84	49	0.583333	NM_017559	B2R9G6|Q9UFC2	Missense_Mutation	SNP	ENST00000158009.5	37	CCDS11290.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	20.4	3.975927	0.74360	4.54E-4	0.001163	ENSG00000073598	ENST00000158009	T	0.35973	1.28	5.38	5.38	0.77491	.	0.000000	0.50627	D	0.000111	T	0.46776	0.1410	L	0.27053	0.805	0.46521	D	0.999088	D	0.89917	1.0	D	0.74674	0.984	T	0.45086	-0.9285	10	0.87932	D	0	-20.0231	14.5032	0.67737	0.0:0.0:1.0:0.0	.	116	Q8TC99	FNDC8_HUMAN	V	116	ENSP00000158009:G116V	ENSP00000158009:G116V	G	+	2	0	FNDC8	30478311	0.998000	0.40836	0.228000	0.23943	0.985000	0.73830	4.167000	0.58209	2.794000	0.96219	0.655000	0.94253	GGG	G|0.999;T|0.001	0.001	strong		0.567	FNDC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256459.2	NM_017559		T	33454198	G	T	33454198	3	4	29	1	0	0	0	0	1	0	0	0	5982	1232	43	4	353	4	FNDC8	17	33454198	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	13879102	33454198	47741012	751	12992											
SLFN5	162394	hgsc.bcm.edu	37	chr17	33592323	33592323	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgagttgcagtggcctccccCctccctcagaccagtatcca	7	9	8	17	0	1	2	1	1	0	1	4	2	4	2	7	1	1	3	7	1	1	2	rs113644060	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:33592323C>G	ENST00000299977.4	+	5	2240	c.2092C>G	c.(2092-2094)Cct>Gct	p.P698A	SLFN5_ENST00000542451.1_3'UTR	NM_144975.3	NP_659412.3	Q08AF3	SLFN5_HUMAN	schlafen family member 5	698					cell differentiation (GO:0030154)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(8)|liver(2)|lung(6)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	34		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0191)		TGGCCTCCCCCCTCCCTCAGA	0.498													C|||	97	0.019369	0.0265	0.0259	5008	,	,		18966	0.0		0.0179	False		,,,				2504	0.0266				p.P698A		Atlas-SNP	.											.	SLFN5	92	.	0			c.C2092G						PASS	.	C	ALA/PRO	131,4275	95.3+/-134.0	1,129,2073	110	108	109		2092	-6.3	0	17	dbSNP_132	109	213,8387	89.4+/-151.6	4,205,4091	yes	missense	SLFN5	NM_144975.3	27	5,334,6164	GG,GC,CC		2.4767,2.9732,2.6449	benign	698/892	33592323	344,12662	2203	4300	6503	SO:0001583	missense	162394	exon5			CTCCCCCCTCCCT	BX647942	CCDS32619.1	17q12	2006-04-05				ENSG00000166750			28286	protein-coding gene	gene with protein product		614952				9846487	Standard	NM_144975		Approved	MGC19764	uc002hjf.4	Q08AF3		ENST00000299977.4:c.2092C>G	17.37:g.33592323C>G	ENSP00000299977:p.Pro698Ala	127	0	0		140	64	0.457143	NM_144975	Q08AF2|Q8WU54|Q96A82	Missense_Mutation	SNP	ENST00000299977.4	37	CCDS32619.1	37	0.01694139194139194	13	0.026422764227642278	7	0.019337016574585635	0	0.0	17	0.022427440633245383	c	0.035	-1.311433	0.01342	0.029732	0.024767	ENSG00000166750	ENST00000299977	T	0.01804	4.63	3.14	-6.29	0.02013	.	3.015190	0.01558	N	0.019980	T	0.00552	0.0018	N	0.25647	0.755	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.46190	-0.9209	10	0.13108	T	0.6	.	10.9039	0.47069	0.0:0.194:0.6988:0.1073	.	698	Q08AF3	SLFN5_HUMAN	A	698	ENSP00000299977:P698A	ENSP00000299977:P698A	P	+	1	0	SLFN5	30616436	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.066000	0.01385	-1.019000	0.03358	-0.259000	0.10710	CCT	C|0.975;G|0.025	0.025	strong		0.498	SLFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448649.2	NM_144975		G	33592323	C	G	33592323	3	3	29	1	0	0	0	0	1	0	0	0	14752	623	22	4	2106	4	SLFN5	17	33592323	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	138125	33592323	47602887	752	12993											
SLFN11	91607	hgsc.bcm.edu	37	chr17	33680127	33680127	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttttctcttaggaaagtttTccgggtctctgctcggcaga	6	15	11	9	2	2	1	0	0	2	1	6	2	3	2	1	3	1	4	1	3	2	5	rs143643982		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:33680127T>C	ENST00000394566.1	-	7	2226	c.1954A>G	c.(1954-1956)Aaa>Gaa	p.K652E	SLFN11_ENST00000308377.4_Missense_Mutation_p.K652E	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	652					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)		AGGAAAGTTTTCCGGGTCTCT	0.383													T|||	1	0.000199681	0.0	0.0	5008	,	,		20114	0.0		0.001	False		,,,				2504	0.0				p.K652E		Atlas-SNP	.											.	SLFN11	112	.	0			c.A1954G						PASS	.	T	GLU/LYS,GLU/LYS,GLU/LYS,GLU/LYS,GLU/LYS	0,4406		0,0,2203	79	78	79		1954,1954,1954,1954,1954	4	0.9	17	dbSNP_134	79	6,8594	1.2+/-3.3	0,6,4294	no	missense,missense,missense,missense,missense	SLFN11	NM_001104587.1,NM_001104588.1,NM_001104589.1,NM_001104590.1,NM_152270.3	56,56,56,56,56	0,6,6497	CC,CT,TT		0.0698,0.0,0.0461	benign,benign,benign,benign,benign	652/902,652/902,652/902,652/902,652/902	33680127	6,13000	2203	4300	6503	SO:0001583	missense	91607	exon5			AAGTTTTCCGGGT	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.1954A>G	17.37:g.33680127T>C	ENSP00000378067:p.Lys652Glu	43	0	0		47	26	0.553191	NM_152270	E1P643|Q8N3S8|Q8N762|Q8TEE0	Missense_Mutation	SNP	ENST00000394566.1	37	CCDS11294.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	t	14.77	2.635559	0.47049	0.0	6.98E-4	ENSG00000172716	ENST00000308377;ENST00000394566	D;D	0.84298	-1.83;-1.83	4.0	4.0	0.46444	Domain of unknown function DUF2075 (1);	0.126128	0.36101	N	0.002788	D	0.82449	0.5039	M	0.71296	2.17	0.23693	N	0.9971	B	0.21606	0.058	B	0.25405	0.06	T	0.71464	-0.4585	10	0.33940	T	0.23	.	9.4902	0.38955	0.0:0.0:0.0:1.0	.	652	Q7Z7L1	SLN11_HUMAN	E	652	ENSP00000312402:K652E;ENSP00000378067:K652E	ENSP00000312402:K652E	K	-	1	0	SLFN11	30704240	0.994000	0.37717	0.934000	0.37439	0.057000	0.15508	3.073000	0.50057	1.799000	0.52666	0.533000	0.62120	AAA	T|0.999;C|0.001	0.001	strong		0.383	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1	NM_152270		C	33680127	T	C	33680127	3	2	29	1	0	0	0	0	1	0	0	0	14748	1792	62	3	755	3	SLFN11	17	33680127	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	87804	33680127	47515083	753	12994											
KRTAP1-3	81850	hgsc.bcm.edu	37	chr17	39191027	39191027	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tggagccgcatgtcccactgGtggagcagctgggatatcca	8	8	14	11	1	0	0	0	0	0	0	2	3	2	3	3	4	3	3	3	4	1	1	rs140428118	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39191027G>A	ENST00000344363.5	-	1	80	c.47C>T	c.(46-48)aCc>aTc	p.T16I		NM_030966.1	NP_112228.1	Q8IUG1	KRA13_HUMAN	keratin associated protein 1-3	16						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)			TGTCCCACTGGTGGAGCAGCT	0.582													g|||	7	0.00139776	0.0	0.0043	5008	,	,		17184	0.0		0.004	False		,,,				2504	0.0				p.T16I		Atlas-SNP	.											.	KRTAP1-3	18	.	0			c.C47T						PASS	.	G	ILE/THR	2,3942		0,2,1970	52	59	56		47	3.2	0.8	17	dbSNP_134	56	33,8297		0,33,4132	no	missense	KRTAP1-3	NM_030966.1	89	0,35,6102	AA,AG,GG		0.3962,0.0507,0.2852	benign	16/168	39191027	35,12239	1972	4165	6137	SO:0001583	missense	81850	exon1			CCACTGGTGGAGC	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.47C>T	17.37:g.39191027G>A	ENSP00000344420:p.Thr16Ile	166	0	0		145	76	0.524138	NM_030966	Q07628|Q8IUG0|Q9BYS2	Missense_Mutation	SNP	ENST00000344363.5	37	CCDS42323.1	7	0.003205128205128205	0	0.0	3	0.008287292817679558	0	0.0	4	0.005277044854881266	G	8.061	0.768110	0.15983	5.07E-4	0.003962	ENSG00000221880	ENST00000344363	T	0.34275	1.37	4.17	3.21	0.36854	.	.	.	.	.	T	0.20861	0.0502	.	.	.	0.30763	N	0.743898	B	0.17852	0.024	B	0.27170	0.077	T	0.19257	-1.0311	8	0.40728	T	0.16	.	8.0851	0.30767	0.109:0.0:0.891:0.0	.	16	Q8IUG1	KRA13_HUMAN	I	16	ENSP00000344420:T16I	ENSP00000344420:T16I	T	-	2	0	KRTAP1-3	36444553	0.424000	0.25490	0.846000	0.33378	0.296000	0.27459	2.395000	0.44459	1.338000	0.45544	0.563000	0.77884	ACC	G|0.997;A|0.003	0.003	strong		0.582	KRTAP1-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257687.1			A	39191027	G	A	39191027	3	1	29	1	0	0	0	0	1	0	0	0	8512	1261	44	2	460	2	KRTAP1-3	17	39191027	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	5510900	39191027	42004183	754	12995											
KRTAP4-5	85289	hgsc.bcm.edu	37	chr17	39305774	39305775	+	In_Frame_Ins	INS	-	-	TGGCAGCAGCTGGGG																															tggtcctgcagcaggtggtcINStggcagcagcaggggcggca																								rs137947981|rs535144703|rs141265645|rs58117746	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	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	1	Substitution - Missense(1)	lung(1)	c.246_247insCCCCAGCTGCTGCCA						PASS	.																																			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	17.37:g.39305774_39305775insTGGCAGCAGCTGGGG	ENSP00000340546:p.Cys81_Gln82insHisProSerCysCys	22	0	0		31	17	0.548387	NM_033188		In_Frame_Ins	INS	ENST00000343246.4	37	CCDS32650.1																																																																																			.	.	none		0.653	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1			TGGCAGCAGCTGGGG	39305775	-	TGGCAGCAGCTGGGG	39305774	7	5	29	1	0	1	1	0	0	0	0	0	8563	912	32	0	303	0	KRTAP4-5	17	39305774	In_Frame_Ins	INS	-	TCGA-GR-7351-01A-11D-2210-10	114747	39305774	41889436	755	12996											
KRTAP9-2	83899	hgsc.bcm.edu	37	chr17	39383217	39383217	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccaaaccagctgtgggtccaGctgtggccagagcagctcct	8	7	12	14	0	0	1	0	0	0	1	2	1	2	1	5	2	5	4	5	2	1	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39383217G>A	ENST00000377721.3	+	1	318	c.311G>A	c.(310-312)aGc>aAc	p.S104N	KRTAP9-2_ENST00000455970.2_Missense_Mutation_p.S88N	NM_031961.2	NP_114167.2	Q9BYQ4	KRA92_HUMAN	keratin associated protein 9-2	104	17 X 5 AA repeats of C-C-[RQVSGE]-[SPTQ]- [TASP].					keratin filament (GO:0045095)				large_intestine(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			TGTGGGTCCAGCTGTGGCCAG	0.622																																					p.S104N		Atlas-SNP	.											.	KRTAP9-2	24	.	0			c.G311A						PASS	.						54	57	56					17																	39383217		2202	4293	6495	SO:0001583	missense	83899	exon1			GGTCCAGCTGTGG	AJ406946	CCDS32651.1	17q21.2	2013-06-25			ENSG00000239886	ENSG00000239886		"Keratin associated proteins"	16926	protein-coding gene	gene with protein product						11279113	Standard	NM_031961		Approved	KAP9.2	uc002hwf.3	Q9BYQ4	OTTHUMG00000133609	ENST00000377721.3:c.311G>A	17.37:g.39383217G>A	ENSP00000366950:p.Ser104Asn	148	0	0		132	42	0.318182	NM_031961	Q17RK8|Q2TB15|Q6ISF6	Missense_Mutation	SNP	ENST00000377721.3	37	CCDS32651.1	.	.	.	.	.	.	.	.	.	.	.	11.14	1.551968	0.27739	.	.	ENSG00000239886	ENST00000377721;ENST00000455970	T;T	0.01838	4.61;4.61	2.56	2.56	0.30785	.	.	.	.	.	T	0.02970	0.0088	M	0.67700	2.07	0.19300	N	0.999971	P	0.48016	0.904	B	0.36922	0.236	T	0.43605	-0.9381	9	0.48119	T	0.1	.	6.8345	0.23929	0.0:0.0:0.7231:0.2769	.	104	Q9BYQ4	KRA92_HUMAN	N	104;88	ENSP00000366950:S104N;ENSP00000398325:S88N	ENSP00000366950:S104N	S	+	2	0	KRTAP9-2	36636743	0.898000	0.30612	0.791000	0.31998	0.013000	0.08279	0.446000	0.21694	1.736000	0.51660	0.494000	0.49563	AGC	.	.	none		0.622	KRTAP9-2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257717.1			A	39383217	G	A	39383217	3	1	29	1	0	0	0	0	1	0	0	0	8582	971	34	2	313	2	KRTAP9-2	17	39383217	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	77443	39383217	41811993	756	12997											
KRT33A	3883	hgsc.bcm.edu	37	chr17	39502917	39502917	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcgtgttttccagagagtCtcgctgtggtggggaagatt	7	12	15	7	2	1	2	0	0	1	2	3	4	2	3	1	3	1	2	1	3	1	3	rs144588166		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:39502917C>A	ENST00000007735.3	-	6	924	c.880G>T	c.(880-882)Gac>Tac	p.D294Y		NM_004138.3	NP_004129.2	O76009	KT33A_HUMAN	keratin 33A	294	Coil 2.|Rod.					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)				TCCAGAGAGTCTCGCTGTGGT	0.562													C|||	1	0.000199681	0.0	0.0014	5008	,	,		17962	0.0		0.0	False		,,,				2504	0.0				p.D294Y		Atlas-SNP	.											.	KRT33A	53	.	0			c.G880T						PASS	.	C	TYR/ASP	1,4405	2.1+/-5.4	0,1,2202	48	47	47		880	-1.6	0.8	17	dbSNP_134	47	16,8584	11.9+/-42.8	0,16,4284	yes	missense	KRT33A	NM_004138.2	160	0,17,6486	AA,AC,CC		0.186,0.0227,0.1307	benign	294/405	39502917	17,12989	2203	4300	6503	SO:0001583	missense	3883	exon6			GAGAGTCTCGCTG	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.880G>T	17.37:g.39502917C>A	ENSP00000007735:p.Asp294Tyr	92	0	0		73	30	0.410959	NM_004138	B2RA87|Q6NTB9|Q6ZZB9	Missense_Mutation	SNP	ENST00000007735.3	37	CCDS11388.1	.	.	.	.	.	.	.	.	.	.	C	6.070	0.381145	0.11466	2.27E-4	0.00186	ENSG00000006059	ENST00000007735	D	0.89552	-2.53	4.55	-1.56	0.08532	Filament (1);	0.271361	0.32671	N	0.005792	D	0.87853	0.6282	M	0.85197	2.74	0.20196	N	0.999928	B	0.12630	0.006	B	0.23852	0.049	T	0.80407	-0.1395	10	0.59425	D	0.04	.	9.8523	0.41064	0.0:0.6084:0.0:0.3916	.	294	O76009	KT33A_HUMAN	Y	294	ENSP00000007735:D294Y	ENSP00000007735:D294Y	D	-	1	0	KRT33A	36756443	0.000000	0.05858	0.756000	0.31282	0.062000	0.15995	-0.572000	0.05881	-0.282000	0.09128	-0.302000	0.09304	GAC	C|0.999;A|0.001	0.001	strong		0.562	KRT33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257295.1	NM_004138		A	39502917	C	A	39502917	3	1	29	1	0	0	0	0	1	0	0	0	8478	913	32	4	342	4	KRT33A	17	39502917	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	119700	39502917	41692293	757	12998											
STAT3	6774	hgsc.bcm.edu	37	chr17	40475330	40475330	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cacaaggtcaatgatattgtCcagccagacccagaaggaga	15	6	10	10	0	1	4	1	1	0	3	2	5	2	4	3	2	1	0	3	2	4	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:40475330C>A	ENST00000264657.5	-	19	2008	c.1696G>T	c.(1696-1698)Gac>Tac	p.D566Y	STAT3_ENST00000404395.3_Missense_Mutation_p.D566Y|STAT3_ENST00000585517.1_Missense_Mutation_p.D566Y|STAT3_ENST00000389272.3_Missense_Mutation_p.D468Y|STAT3_ENST00000588969.1_Missense_Mutation_p.D566Y	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)	566					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)	p.D566N(1)		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)		ATGATATTGTCCAGCCAGACC	0.507									Hyperimmunoglobulin E Recurrent Infection Syndrome		OREG0024421	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D566Y		Atlas-SNP	.											STAT3,NS,lymphoid_neoplasm,0,1	STAT3	268	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G1696T						PASS	.						111	105	107					17																	40475330		2203	4300	6503	SO:0001583	missense	6774	exon19	Familial Cancer Database	HIES, Hyper IgE syndrome, autosomal dominant (Job syndrome) / recessive	TATTGTCCAGCCA	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.1696G>T	17.37:g.40475330C>A	ENSP00000264657:p.Asp566Tyr	87	0	0	893	102	33	0.323529	NM_003150	A8K7B8|K7ENL3|O14916|Q9BW54	Missense_Mutation	SNP	ENST00000264657.5	37	CCDS32656.1	.	.	.	.	.	.	.	.	.	.	C	32	5.120901	0.94385	.	.	ENSG00000168610	ENST00000264657;ENST00000389272;ENST00000404395	D;D;D	0.89343	-2.5;-2.5;-2.5	5.9	5.9	0.94986	STAT transcription factor, DNA-binding (1);p53-like transcription factor, DNA-binding (1);EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.89347	0.6689	L	0.31157	0.91	0.80722	D	1	P;P;P	0.41131	0.693;0.739;0.739	P;P;P	0.51266	0.533;0.664;0.664	D	0.87296	0.2302	10	0.35671	T	0.21	-26.7334	20.2754	0.98485	0.0:1.0:0.0:0.0	.	566;566;566	P40763-2;P40763;B5BTZ6	.;STAT3_HUMAN;.	Y	566;468;566	ENSP00000264657:D566Y;ENSP00000373923:D468Y;ENSP00000384943:D566Y	ENSP00000264657:D566Y	D	-	1	0	STAT3	37728856	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.708000	0.84633	2.793000	0.96121	0.609000	0.83330	GAC	.	.	none		0.507	STAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319353.3	NM_139276, NM_003150		A	40475330	C	A	40475330	3	1	29	1	0	0	0	0	1	0	0	0	15281	855	30	4	640	4	STAT3	17	40475330	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	972413	40475330	40719880	758	12999											
NBR1	4077	hgsc.bcm.edu	37	chr17	41342737	41342737	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gttgtgggctcctctgaaccGttctgtcactcaaagtactc	7	13	9	12	1	4	1	2	1	2	0	6	1	5	1	2	1	2	4	2	1	3	3	rs200554551	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:41342737G>A	ENST00000422280.1	+	9	1266	c.807G>A	c.(805-807)ccG>ccA	p.P269P	NBR1_ENST00000341165.6_Silent_p.P269P|NBR1_ENST00000590996.1_Silent_p.P269P|NBR1_ENST00000589872.1_Silent_p.P269P|NBR1_ENST00000542611.1_Silent_p.P248P|NBR1_ENST00000389312.4_Silent_p.P269P	NM_031858.2	NP_114064.1	Q14596	NBR1_HUMAN	neighbor of BRCA1 gene 1	269					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)		CCTCTGAACCGTTCTGTCACT	0.483													G|||	4	0.000798722	0.0	0.0014	5008	,	,		18864	0.0		0.003	False		,,,				2504	0.0				p.P269P		Atlas-SNP	.											.	NBR1	55	.	0			c.G807A						PASS	.	G	,,	5,3885		0,5,1940	141	135	137		807,807,807	-11.9	0	17		137	53,8223		0,53,4085	no	coding-synonymous,coding-synonymous,coding-synonymous	NBR1	NM_005899.3,NM_031858.2,NM_031862.2	,,	0,58,6025	AA,AG,GG		0.6404,0.1285,0.4767	,,	269/967,269/967,269/967	41342737	58,12108	1945	4138	6083	SO:0001819	synonymous_variant	4077	exon9			TGAACCGTTCTGT	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.807G>A	17.37:g.41342737G>A		124	0	0		107	48	0.448598	NM_031862	Q13173|Q15026|Q5J7Q8|Q96GB6|Q9NRF7	Silent	SNP	ENST00000422280.1	37	CCDS45694.1																																																																																			G|0.997;A|0.003	0.003	strong		0.483	NBR1-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453461.1	NM_005899		A	41342737	G	A	41342737	2	1	29	1	0	0	0	0	0	0	0	1	10209	1132	40	1		1	NBR1	17	41342737	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	867407	41342737	39852473	759	13000											
WNT9B	7484	hgsc.bcm.edu	37	chr17	44953637	44953637	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagagtggcctcaggaccacGtgtaagtgccatggcgtatc	10	8	13	10	2	1	1	1	0	0	1	2	2	1	2	3	3	1	2	3	3	3	2	rs62071993	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:44953637G>A	ENST00000290015.2	+	4	680	c.627G>A	c.(625-627)acG>acA	p.T209T	WNT9B_ENST00000393461.2_Silent_p.T209T	NM_003396.1	NP_003387.1	O14905	WNT9B_HUMAN	wingless-type MMTV integration site family, member 9B	209					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)			TCAGGACCACGTGTAAGTGCC	0.647													G|||	8	0.00159744	0.0008	0.0014	5008	,	,		20087	0.0		0.006	False		,,,				2504	0.0				p.T209T		Atlas-SNP	.											.	WNT9B	37	.	0			c.G627A						PASS	.	G		8,4398	14.3+/-33.2	0,8,2195	62	53	56		627	-3.8	1	17	dbSNP_129	56	47,8553	31.2+/-83.2	0,47,4253	no	coding-synonymous	WNT9B	NM_003396.1		0,55,6448	AA,AG,GG		0.5465,0.1816,0.4229		209/358	44953637	55,12951	2203	4300	6503	SO:0001819	synonymous_variant	7484	exon4			GACCACGTGTAAG	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.627G>A	17.37:g.44953637G>A		106	0	0		120	60	0.5	NM_003396	Q6UXT4|Q96Q09	Silent	SNP	ENST00000290015.2	37	CCDS11506.1																																																																																			G|0.997;A|0.003	0.003	strong		0.647	WNT9B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440433.1	NM_003396		A	44953637	G	A	44953637	2	1	29	1	0	0	0	0	0	0	0	1	17414	1132	40	1		1	WNT9B	17	44953637	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	3610900	44953637	36241573	760	13001											
ZNF652	22834	hgsc.bcm.edu	37	chr17	47394825	47394825	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ccttaacagcatgcacgtcaGacactgctcttgtctccctg	8	11	7	15	1	3	1	1	0	2	1	4	1	3	1	2	0	4	3	2	0	1	2	rs181916483	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:47394825G>C	ENST00000362063.2	-	2	581	c.263C>G	c.(262-264)tCt>tGt	p.S88C	ZNF652_ENST00000430262.2_Missense_Mutation_p.S88C	NM_014897.2	NP_055712.1	Q9Y2D9	ZN652_HUMAN	zinc finger protein 652	88	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)			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)			ATGCACGTCAGACACTGCTCT	0.463													G|||	3	0.000599042	0.0	0.0014	5008	,	,		22639	0.0		0.002	False		,,,				2504	0.0				p.S88C		Atlas-SNP	.											ZNF652,NS,haematopoietic_neoplasm,0,3	ZNF652	54	3	0			c.C263G						PASS	.	G	CYS/SER,CYS/SER	1,4405	4.2+/-10.8	0,1,2202	179	142	155		263,263	5.7	1	17		155	12,8588	9.1+/-34.3	0,12,4288	yes	missense,missense	ZNF652	NM_001145365.1,NM_014897.2	112,112	0,13,6490	CC,CG,GG		0.1395,0.0227,0.1	possibly-damaging,possibly-damaging	88/607,88/607	47394825	13,12993	2203	4300	6503	SO:0001583	missense	22834	exon2			ACGTCAGACACTG	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.263C>G	17.37:g.47394825G>C	ENSP00000354686:p.Ser88Cys	226	1	0.00442478		211	108	0.511848	NM_001145365	A4QPD9|Q5H9Q0	Missense_Mutation	SNP	ENST00000362063.2	37	CCDS32677.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	9.061	0.994478	0.19043	2.27E-4	0.001395	ENSG00000198740	ENST00000362063;ENST00000430262	D;D	0.98958	-5.27;-5.27	5.74	5.74	0.90152	.	0.448368	0.27371	N	0.019676	D	0.94663	0.8279	N	0.14661	0.345	0.26476	N	0.975184	P	0.34462	0.454	B	0.29524	0.103	D	0.90267	0.4305	10	0.56958	D	0.05	-5.273	10.1922	0.43032	0.0:0.1844:0.6819:0.1337	.	88	Q9Y2D9	ZN652_HUMAN	C	88	ENSP00000354686:S88C;ENSP00000416305:S88C	ENSP00000354686:S88C	S	-	2	0	ZNF652	44749824	0.998000	0.40836	0.974000	0.42286	0.980000	0.70556	2.293000	0.43558	2.715000	0.92844	0.655000	0.94253	TCT	G|0.998;C|0.002	0.002	strong		0.463	ZNF652-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364524.1	NM_014897		C	47394825	G	C	47394825	3	2	29	1	0	0	0	0	1	0	0	0	18080	942	33	4	1577	4	ZNF652	17	47394825	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2441188	47394825	33800385	761	13002											
COL1A1	1277	hgsc.bcm.edu	37	chr17	48269167	48269167	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accttagcaccatcgttgccGggagcaccgttggcccctcg	6	8	11	16	4	0	0	0	0	0	0	2	1	0	1	6	2	3	4	6	2	1	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:48269167G>A	ENST00000225964.5	-	31	2227	c.2109C>T	c.(2107-2109)ccC>ccT	p.P703P		NM_000088.3	NP_000079	P02452	CO1A1_HUMAN	collagen, type I, alpha 1	703	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)	CATCGTTGCCGGGAGCACCGT	0.677			T	"PDGFB, USP6"	"dermatofibrosarcoma protuberans, aneurysmal bone cyst "		Osteogenesis imperfecta																														p.P703P		Atlas-SNP	.		Dom	yes		17	17q21.31-q22	1277	"collagen, type I, alpha 1"	yes	M	COL1A1,NS,carcinoma,-2,2	COL1A1	158	2	0			c.C2109T						scavenged	.						30	31	31					17																	48269167		2202	4298	6500	SO:0001819	synonymous_variant	1277	exon31			GTTGCCGGGAGCA	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.2109C>T	17.37:g.48269167G>A		29	0	0		38	3	0.0789474	NM_000088	O76045|P78441|Q13896|Q13902|Q13903|Q14037|Q14992|Q15176|Q15201|Q16050|Q59F64|Q7KZ30|Q7KZ34|Q8IVI5|Q8N473|Q9UML6|Q9UMM7	Silent	SNP	ENST00000225964.5	37	CCDS11561.1																																																																																			.	.	none		0.677	COL1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309036.2			A	48269167	G	A	48269167	2	1	29	1	0	0	0	0	0	0	0	1	3679	1103	39	1		1	COL1A1	17	48269167	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	874342	48269167	32926043	762	13003											
RSAD1	55316	hgsc.bcm.edu	37	chr17	48561871	48561871	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcgaacaaggaggtgcaggaGctgctggagcggggcctact	9	5	18	9	2	0	0	0	0	0	0	0	4	0	3	1	6	6	3	1	6	3	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:48561871G>A	ENST00000258955.2	+	8	1261	c.1176G>A	c.(1174-1176)gaG>gaA	p.E392E		NM_018346.1	NP_060816.1	Q9HA92	RSAD1_HUMAN	radical S-adenosyl methionine domain containing 1	392					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)			AGGTGCAGGAGCTGCTGGAGC	0.647																																					p.E392E		Atlas-SNP	.											RSAD1,NS,carcinoma,+2,1	RSAD1	36	1	0			c.G1176A						PASS	.						56	58	58					17																	48561871		2203	4300	6503	SO:0001819	synonymous_variant	55316	exon8			GCAGGAGCTGCTG	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.1176G>A	17.37:g.48561871G>A		34	0	0		43	12	0.27907	NM_018346	B4DMW0|Q53HV8|Q86VC4|Q9BRY7|Q9NUS7	Silent	SNP	ENST00000258955.2	37	CCDS11569.1																																																																																			.	.	none		0.647	RSAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367413.1	NM_018346		A	48561871	G	A	48561871	2	1	29	1	0	0	0	0	0	0	0	1	13709	962	34	2		2	RSAD1	17	48561871	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	292704	48561871	32633339	763	13004											
MRC2	9902	hgsc.bcm.edu	37	chr17	60766283	60766283	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgggacgatcggagctgcaCggaggagacccatggcttca	9	6	15	11	3	1	1	1	0	0	1	2	6	1	4	1	5	2	3	1	5	0	1	rs201851897		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:60766283C>T	ENST00000303375.5	+	23	3698	c.3296C>T	c.(3295-3297)aCg>aTg	p.T1099M	MRC2_ENST00000580916.1_3'UTR|MRC2_ENST00000446119.2_Missense_Mutation_p.R45W	NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	1099	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						CGGAGCTGCACGGAGGAGACC	0.672													C|||	1	0.000199681	0.0	0.0	5008	,	,		19199	0.001		0.0	False		,,,				2504	0.0				p.T1099M		Atlas-SNP	.											MRC2,NS,carcinoma,0,1	MRC2	126	1	0			c.C3296T						PASS	.	C	MET/THR	0,4406		0,0,2203	46	39	42		3296	-1.2	0	17		42	1,8599	1.2+/-3.3	0,1,4299	no	missense	MRC2	NM_006039.3	81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	1099/1480	60766283	1,13005	2203	4300	6503	SO:0001583	missense	9902	exon23			GCTGCACGGAGGA	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.3296C>T	17.37:g.60766283C>T	ENSP00000307513:p.Thr1099Met	135	0	0		118	35	0.29661	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Missense_Mutation	SNP	ENST00000303375.5	37	CCDS11634.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0017482517482517483|0.0017482517482517483	0|0	0.0|0.0	C|C	14.28|14.28	2.487814|2.487814	0.44249|0.44249	0.0|0.0	1.16E-4|1.16E-4	ENSG00000011028|ENSG00000011028	ENST00000446119|ENST00000303375	T|T	0.03301|0.20200	3.98|2.09	4.73|4.73	-1.2|-1.2	0.09554|0.09554	.|C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	.|0.935369	.|0.09211	.|N	.|0.833271	T|T	0.21841|0.21841	0.0526|0.0526	M|M	0.75447|0.75447	2.3|2.3	0.09310|0.09310	N|N	1|1	B|B	0.02656|0.17038	0.0|0.02	B|B	0.01281|0.12837	0.0|0.008	T|T	0.35649|0.35649	-0.9780|-0.9780	9|10	0.38643|0.51188	T|T	0.18|0.08	0.3399|0.3399	5.0404|5.0404	0.14456|0.14456	0.1411:0.3507:0.0:0.5082|0.1411:0.3507:0.0:0.5082	.|.	45|1099	E7EME3|Q9UBG0	.|MRC2_HUMAN	W|M	45|1099	ENSP00000400445:R45W|ENSP00000307513:T1099M	ENSP00000400445:R45W|ENSP00000307513:T1099M	R|T	+|+	1|2	2|0	MRC2|MRC2	58120015|58120015	0.003000|0.003000	0.15002|0.15002	0.023000|0.023000	0.16930|0.16930	0.918000|0.918000	0.54935|0.54935	0.763000|0.763000	0.26517|0.26517	-0.035000|-0.035000	0.13691|0.13691	0.561000|0.561000	0.74099|0.74099	CGG|ACG	C|1.000;T|0.000	0.000	strong		0.672	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1			T	60766283	C	T	60766283	3	4	29	1	0	0	0	0	1	0	0	0	9767	536	19	1	3386	1	MRC2	17	60766283	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	12204412	60766283	20428927	764	13005											
LIMD2	80774	hgsc.bcm.edu	37	chr17	61776651	61776651	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgggcggctcctgcagccTggaacatggctcgttggagg	5	8	16	12	2	0	0	0	0	0	0	2	2	1	2	3	6	3	4	3	6	1	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:61776651T>A	ENST00000259006.3	-	2	166	c.8A>T	c.(7-9)cAg>cTg	p.Q3L	LIMD2_ENST00000582055.1_5'Flank|LIMD2_ENST00000578061.1_Missense_Mutation_p.Q3L|LIMD2_ENST00000578402.1_Missense_Mutation_p.Q3L|LIMD2_ENST00000578993.1_Missense_Mutation_p.Q3L|LIMD2_ENST00000583211.1_5'UTR	NM_030576.3	NP_085053.1	Q9BT23	LIMD2_HUMAN	LIM domain containing 2	3							zinc ion binding (GO:0008270)			kidney(1)|lung(2)	3						TCCTGCAGCCTGGAACATGGC	0.716																																					p.Q3L		Atlas-SNP	.											.	LIMD2	6	.	0			c.A8T						PASS	.						12	16	15					17																	61776651		2182	4271	6453	SO:0001583	missense	80774	exon2			GCAGCCTGGAACA	AK092301	CCDS11641.1	17q23.3	2006-02-03				ENSG00000136490			28142	protein-coding gene	gene with protein product						12477932	Standard	NM_030576		Approved	MGC10986	uc002jbj.4	Q9BT23		ENST00000259006.3:c.8A>T	17.37:g.61776651T>A	ENSP00000259006:p.Gln3Leu	112	0	0		96	20	0.208333	NM_030576	D3DU16|Q96S91	Missense_Mutation	SNP	ENST00000259006.3	37	CCDS11641.1	.	.	.	.	.	.	.	.	.	.	T	17.08	3.298889	0.60195	.	.	ENSG00000136490	ENST00000259006	T	0.77358	-1.09	4.43	4.43	0.53597	.	0.000000	0.64402	D	0.000011	T	0.66218	0.2767	L	0.27053	0.805	0.80722	D	1	B	0.18461	0.028	B	0.11329	0.006	T	0.66176	-0.5989	10	0.87932	D	0	-18.1445	12.0851	0.53691	0.0:0.0:0.0:1.0	.	3	Q9BT23	LIMD2_HUMAN	L	3	ENSP00000259006:Q3L	ENSP00000259006:Q3L	Q	-	2	0	LIMD2	59130383	0.970000	0.33590	1.000000	0.80357	0.975000	0.68041	1.307000	0.33516	1.856000	0.53863	0.379000	0.24179	CAG	.	.	none		0.716	LIMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443877.1	NM_030576		A	61776651	T	A	61776651	3	1	29	1	0	0	0	0	1	0	0	0	8808	1580	55	5	391	5	LIMD2	17	61776651	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	1010368	61776651	19418559	765	13006											
KCNJ2	3759	hgsc.bcm.edu	37	chr17	68171425	68171425	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgtgtggacattcgctggcGgtggatgctggttatcttct	4	15	15	7	2	2	0	0	0	2	0	3	2	2	2	0	5	1	3	0	5	1	3	rs199473653		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:68171425G>A	ENST00000243457.3	+	2	628	c.245G>A	c.(244-246)cGg>cAg	p.R82Q	KCNJ2_ENST00000535240.1_Missense_Mutation_p.R82Q	NM_000891.2	NP_000882.1	P63252	KCNJ2_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 2	82					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)					ATTCGCTGGCGGTGGATGCTG	0.512																																					p.R82Q		Atlas-SNP	.											.	KCNJ2	74	.	0			c.G245A	GRCh37	CM053932	KCNJ2	M		PASS	.						220	164	183					17																	68171425		2203	4300	6503	SO:0001583	missense	3759	exon2			GCTGGCGGTGGAT	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.245G>A	17.37:g.68171425G>A	ENSP00000243457:p.Arg82Gln	285	0	0		306	85	0.277778	NM_000891	O15110|P48049	Missense_Mutation	SNP	ENST00000243457.3	37	CCDS11688.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.689148	0.88735	.	.	ENSG00000123700	ENST00000535240;ENST00000243457	D;D	0.95788	-3.81;-3.81	5.66	5.66	0.87406	Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);	0.000000	0.85682	D	0.000000	D	0.98692	0.9561	H	0.96889	3.9	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99379	1.0922	9	.	.	.	.	19.7433	0.96241	0.0:0.0:1.0:0.0	.	82	P63252	IRK2_HUMAN	Q	82	ENSP00000441848:R82Q;ENSP00000243457:R82Q	.	R	+	2	0	KCNJ2	65683020	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.869000	0.99810	2.662000	0.90505	0.555000	0.69702	CGG	.	.	weak		0.512	KCNJ2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450889.1	NM_000891		A	68171425	G	A	68171425	3	1	29	1	0	0	0	0	1	0	0	0	8060	1116	39	1	247	1	KCNJ2	17	68171425	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	6394774	68171425	13023785	766	13007											
GPRC5C	55890	hgsc.bcm.edu	37	chr17	72436078	72436078	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cgtggggcatcgtcctggagGccgtggctggggcgggcatt	3	8	20	10	4	0	0	0	0	0	0	2	1	1	1	2	8	0	3	2	8	0	1	rs148895616	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:72436078G>A	ENST00000481232.1	+	2	809	c.298G>A	c.(298-300)Gcc>Acc	p.A100T	GPRC5C_ENST00000342648.5_Intron|GPRC5C_ENST00000392629.2_Missense_Mutation_p.A67T|GPRC5C_ENST00000392627.1_Missense_Mutation_p.A100T			Q9NQ84	GPC5C_HUMAN	G protein-coupled receptor, class C, group 5, member C	55					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						CGTCCTGGAGGCCGTGGCTGG	0.657																																					p.A100T		Atlas-SNP	.											.	GPRC5C	92	.	0			c.G298A						PASS	.	G	THR/ALA,THR/ALA	0,4406		0,0,2203	59	57	58		199,298	5.6	1	17	dbSNP_134	58	13,8587	9.8+/-36.6	0,13,4287	yes	missense,missense	GPRC5C	NM_018653.3,NM_022036.2	58,58	0,13,6490	AA,AG,GG		0.1512,0.0,0.1	possibly-damaging,possibly-damaging	67/454,100/487	72436078	13,12993	2203	4300	6503	SO:0001583	missense	55890	exon2			CTGGAGGCCGTGG	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	ENST00000481232.1:c.298G>A	17.37:g.72436078G>A	ENSP00000462147:p.Ala100Thr	40	0	0		29	15	0.517241	NM_022036	B5BUN4|Q2NL85|Q9NZG5	Missense_Mutation	SNP	ENST00000481232.1	37		.	.	.	.	.	.	.	.	.	.	G	9.841	1.191113	0.21954	0.0	0.001512	ENSG00000170412	ENST00000392627;ENST00000342648;ENST00000392629;ENST00000392628	T	0.22134	1.97	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.32376	0.0827	L	0.46670	1.46	0.58432	D	0.999995	P;P;P;D	0.52996	0.714;0.714;0.812;0.957	B;B;B;P	0.52758	0.194;0.194;0.355;0.708	T	0.00628	-1.1637	10	0.28530	T	0.3	-6.6765	18.5	0.90877	0.0:0.0:1.0:0.0	.	55;55;67;55	A8MXZ4;Q9NQ84;Q9NQ84-2;Q9BSP0	.;GPC5C_HUMAN;.;.	T	55;100;67;55	ENSP00000376405:A67T	ENSP00000340595:A100T	A	+	1	0	GPRC5C	69947673	1.000000	0.71417	0.995000	0.50966	0.171000	0.22731	5.341000	0.65964	2.616000	0.88540	0.561000	0.74099	GCC	G|0.999;A|0.001	0.001	strong		0.657	GPRC5C-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000145095.2			A	72436078	G	A	72436078	3	1	29	1	0	0	0	0	1	0	0	0	6735	1203	42	2	312	2	GPRC5C	17	72436078	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	4264653	72436078	8759132	767	13008											
RECQL5	9400	hgsc.bcm.edu	37	chr17	73657118	73657118	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcctccatccagtcgttctgCaccagcgttctttcagaggc	6	12	8	15	2	3	1	1	0	2	1	7	1	6	1	4	1	2	3	4	1	0	3	rs149970344		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:73657118C>T	ENST00000317905.5	-	6	1062	c.903G>A	c.(901-903)gtG>gtA	p.V301V	RECQL5_ENST00000423245.2_Silent_p.V274V|RECQL5_ENST00000584999.1_Silent_p.V301V|RECQL5_ENST00000420326.2_Silent_p.V301V|RECQL5_ENST00000340830.5_Silent_p.V301V	NM_004259.6	NP_004250.4	O94762	RECQ5_HUMAN	RecQ protein-like 5	301	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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)			AGTCGTTCTGCACCAGCGTTC	0.498								Other identified genes with known or suspected DNA repair function																													p.V301V		Atlas-SNP	.											.	RECQL5	77	.	0			c.G903A						PASS	.	C	,,	1,4405	2.1+/-5.4	0,1,2202	164	134	144		903,903,903	0.8	1	17	dbSNP_134	144	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	RECQL5	NM_001003715.3,NM_001003716.3,NM_004259.6	,,	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	,,	301/436,301/411,301/992	73657118	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	9400	exon6			GTTCTGCACCAGC	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.903G>A	17.37:g.73657118C>T		152	0	0		155	61	0.393548	NM_001003715	Q9H0B1|Q9P1W7|Q9UNC8	Silent	SNP	ENST00000317905.5	37	CCDS42380.1																																																																																			C|1.000;T|0.000	0.000	weak		0.498	RECQL5-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448207.1	NM_004259		T	73657118	C	T	73657118	2	4	29	1	0	0	0	0	0	0	0	1	13218	697	25	2		2	RECQL5	17	73657118	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1221040	73657118	7538092	768	13009											
MRPL38	64978	hgsc.bcm.edu	37	chr17	73895744	73895744	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttcagccacccggttacccGggatgttggttctgggagga	6	10	14	11	2	2	0	1	0	1	0	2	3	2	3	3	5	2	3	3	5	1	4	rs1128878		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:73895744G>A	ENST00000309352.3	-	7	1259	c.722C>T	c.(721-723)cCg>cTg	p.P241L	MRPL38_ENST00000409963.3_Missense_Mutation_p.P57L|RP11-552F3.10_ENST00000587267.1_RNA|MRPL38_ENST00000585475.1_5'Flank|TRIM65_ENST00000269383.3_5'Flank	NM_032478.3	NP_115867.2	Q96DV4	RM38_HUMAN	mitochondrial ribosomal protein L38	241						mitochondrion (GO:0005739)|ribosome (GO:0005840)				ovary(1)|pancreas(1)|prostate(2)|skin(1)	5			all cancers(21;0.000154)|Epithelial(20;0.000156)|BRCA - Breast invasive adenocarcinoma(9;0.00936)|LUSC - Lung squamous cell carcinoma(166;0.154)			CCGGTTACCCGGGATGTTGGT	0.612													G|||	1	0.000199681	0.0	0.0	5008	,	,		17869	0.0		0.001	False		,,,				2504	0.0				p.P241L		Atlas-SNP	.											.	MRPL38	26	.	0			c.C722T						PASS	.	G	LEU/PRO	2,4404	4.2+/-10.8	0,2,2201	37	38	38		722	5.9	1	17	dbSNP_86	38	11,8583	8.4+/-32.0	0,11,4286	yes	missense	MRPL38	NM_032478.3	98	0,13,6487	AA,AG,GG		0.128,0.0454,0.1	probably-damaging	241/381	73895744	13,12987	2203	4297	6500	SO:0001583	missense	64978	exon7			TTACCCGGGATGT	AB051345	CCDS11733.2	17q23-q25	2012-09-13			ENSG00000204316	ENSG00000204316		"Mitochondrial ribosomal proteins / large subunits"	14033	protein-coding gene	gene with protein product		611844				11543634	Standard	NM_032478		Approved	RPML3, MRP-L3, HSPC262, MGC4810	uc010wso.1	Q96DV4	OTTHUMG00000152977	ENST00000309352.3:c.722C>T	17.37:g.73895744G>A	ENSP00000308275:p.Pro241Leu	54	0	0		57	21	0.368421	NM_032478	B3KN96|Q96Q66|Q9P0B9	Missense_Mutation	SNP	ENST00000309352.3	37	CCDS11733.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	35	5.459407	0.96240	4.54E-4	0.00128	ENSG00000204316	ENST00000309352;ENST00000409963	T;T	0.59224	0.48;0.28	5.87	5.87	0.94306	.	0.048517	0.85682	N	0.000000	T	0.81054	0.4743	H	0.97103	3.94	0.80722	D	1	D	0.63046	0.992	P	0.52514	0.701	D	0.87262	0.2280	10	0.87932	D	0	-13.2193	20.2144	0.98291	0.0:0.0:1.0:0.0	rs1128878;rs17352818	241	Q96DV4	RM38_HUMAN	L	241;57	ENSP00000308275:P241L;ENSP00000387085:P57L	ENSP00000308275:P241L	P	-	2	0	MRPL38	71407339	1.000000	0.71417	0.969000	0.41365	0.933000	0.57130	8.872000	0.92352	2.791000	0.96007	0.511000	0.50034	CCG	G|0.999;A|0.001	0.001	strong		0.612	MRPL38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328829.1	NM_032478		A	73895744	G	A	73895744	3	1	29	1	0	0	0	0	1	0	0	0	9810	1116	39	1	432	1	MRPL38	17	73895744	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	238626	73895744	7299466	769	13010											
EVPL	2125	hgsc.bcm.edu	37	chr17	74003525	74003525	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcatccagcccttctggaCggcctcgcccaccgagagcc	6	5	12	18	3	1	1	0	0	1	1	3	3	2	2	6	3	2	1	6	3	0	1	rs141706835		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:74003525C>T	ENST00000301607.3	-	22	6014	c.5761G>A	c.(5761-5763)Gtc>Atc	p.V1921I	EVPL_ENST00000586740.1_Missense_Mutation_p.V1943I|TEN1-CDK3_ENST00000567351.1_RNA	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1921	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						CCCTTCTGGACGGCCTCGCCC	0.662													C|||	1	0.000199681	0.0	0.0	5008	,	,		16834	0.0		0.0	False		,,,				2504	0.001				p.V1921I		Atlas-SNP	.											EVPL,colon,carcinoma,0,1	EVPL	155	1	0			c.G5761A						PASS	.	C	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	47	41	43		5761	-7.3	0.1	17	dbSNP_134	43	2,8598	2.2+/-6.3	0,2,4298	yes	missense	EVPL	NM_001988.2	29	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	benign	1921/2034	74003525	3,13003	2203	4300	6503	SO:0001583	missense	2125	exon22			TCTGGACGGCCTC	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.5761G>A	17.37:g.74003525C>T	ENSP00000301607:p.Val1921Ile	68	0	0		66	33	0.5	NM_001988	A0AUV5	Missense_Mutation	SNP	ENST00000301607.3	37	CCDS11737.1	.	.	.	.	.	.	.	.	.	.	C	8.608	0.888553	0.17540	2.27E-4	2.33E-4	ENSG00000167880	ENST00000301607	T	0.66460	-0.21	5.48	-7.34	0.01427	.	0.382752	0.26463	N	0.024227	T	0.45013	0.1321	N	0.22421	0.69	0.09310	N	0.999999	B;B	0.30605	0.039;0.287	B;B	0.23574	0.025;0.047	T	0.03121	-1.1070	10	0.24483	T	0.36	-16.312	19.1581	0.93520	0.0:0.8769:0.0:0.1231	.	1943;1921	B7ZLH8;Q92817	.;EVPL_HUMAN	I	1921	ENSP00000301607:V1921I	ENSP00000301607:V1921I	V	-	1	0	EVPL	71515120	0.000000	0.05858	0.123000	0.21794	0.698000	0.40448	-0.195000	0.09546	-1.270000	0.02433	-0.291000	0.09656	GTC	C|1.000;T|0.000	0.000	weak		0.662	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988		T	74003525	C	T	74003525	3	4	29	1	0	0	0	0	1	0	0	0	5294	536	19	1	344	1	EVPL	17	74003525	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	107781	74003525	7191685	770	13011											
QRICH2	84074	hgsc.bcm.edu	37	chr17	74303550	74303550	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ccgtgtgcgtgctcaccctgGcaaagctgagctcctcggcg	5	8	13	15	4	1	1	1	1	0	0	3	1	2	1	3	2	4	4	3	2	1	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:74303550G>A	ENST00000262765.5	-	1	211	c.32C>T	c.(31-33)gCc>gTc	p.A11V		NM_032134.1	NP_115510.1	Q9H0J4	QRIC2_HUMAN	glutamine rich 2	11										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						GCTCACCCTGGCAAAGCTGAG	0.701																																					p.A11V		Atlas-SNP	.											.	QRICH2	143	.	0			c.C32T						PASS	.						56	51	53					17																	74303550		2203	4300	6503	SO:0001583	missense	84074	exon1			ACCCTGGCAAAGC	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.32C>T	17.37:g.74303550G>A	ENSP00000262765:p.Ala11Val	129	0	0		97	4	0.0412371	NM_032134	A2RRE1|Q96LM3	Missense_Mutation	SNP	ENST00000262765.5	37	CCDS32741.1	.	.	.	.	.	.	.	.	.	.	G	9.558	1.117648	0.20877	.	.	ENSG00000129646	ENST00000262765;ENST00000301613	T	0.08546	3.08	4.13	3.15	0.36227	.	.	.	.	.	T	0.05502	0.0145	N	0.14661	0.345	0.09310	N	1	B	0.29552	0.248	B	0.29077	0.098	T	0.38542	-0.9656	9	0.45353	T	0.12	11.3655	8.1866	0.31343	0.1154:0.0:0.8846:0.0	.	11	Q9H0J4	QRIC2_HUMAN	V	11	ENSP00000262765:A11V	ENSP00000262765:A11V	A	-	2	0	QRICH2	71815145	0.000000	0.05858	0.001000	0.08648	0.031000	0.12232	0.085000	0.14912	0.845000	0.35118	0.411000	0.27672	GCC	.	.	none		0.701	QRICH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395140.1	NM_032134		A	74303550	G	A	74303550	3	1	29	1	0	0	0	0	1	0	0	0	12895	1203	42	2	5035	2	QRICH2	17	74303550	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	300025	74303550	6891660	771	13012											
USP36	57602	hgsc.bcm.edu	37	chr17	76823425	76823425	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaaagcggaagtgtcgggcGatctctaaaagaggaagaaa	16	5	13	7	3	1	2	0	0	1	2	3	5	1	4	1	3	1	0	1	3	6	1	rs143701541	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:76823425G>T	ENST00000542802.3	-	6	1034	c.591C>A	c.(589-591)atC>atA	p.I197I	USP36_ENST00000312010.6_Silent_p.I197I|USP36_ENST00000589424.1_Silent_p.I197I|USP36_ENST00000590546.2_Silent_p.I197I			Q9P275	UBP36_HUMAN	ubiquitin specific peptidase 36	197	USP.				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)			AGTGTCGGGCGATCTCTAAAA	0.552													G|||	58	0.0115815	0.0015	0.0101	5008	,	,		12480	0.0		0.0308	False		,,,				2504	0.0184				p.I197I		Atlas-SNP	.											.	USP36	243	.	0			c.C591A						PASS	.	G		26,4380	31.7+/-61.6	0,26,2177	43	37	39		591	-7.7	0.8	17	dbSNP_134	39	261,8339	101.9+/-163.1	4,253,4043	no	coding-synonymous	USP36	NM_025090.3		4,279,6220	TT,TG,GG		3.0349,0.5901,2.2067		197/1124	76823425	287,12719	2203	4300	6503	SO:0001819	synonymous_variant	57602	exon6			TCGGGCGATCTCT	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.591C>A	17.37:g.76823425G>T		27	0	0		38	22	0.578947	NM_025090	Q05C98|Q05DD0|Q6IQ38|Q8NDM8|Q9NVC8	Silent	SNP	ENST00000542802.3	37	CCDS32755.1																																																																																			G|0.980;T|0.020	0.020	strong		0.552	USP36-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437472.3	NM_025090		T	76823425	G	T	76823425	2	4	29	1	0	0	0	0	0	0	0	1	17082	1048	37	4		4	USP36	17	76823425	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2519875	76823425	4371785	772	13013											
ENGASE	64772	hgsc.bcm.edu	37	chr17	77075631	77075631	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taccactggcagtgcatcgaCgtctttgtgtacttcagcca	8	12	9	12	2	2	0	1	0	1	0	3	1	2	0	2	1	4	3	2	1	2	4	rs3744182	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:77075631C>T	ENST00000579016.1	+	4	477	c.477C>T	c.(475-477)gaC>gaT	p.D159D	ENGASE_ENST00000539857.2_Intron	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	159						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						AGTGCATCGACGTCTTTGTGT	0.587													C|||	721	0.14397	0.3865	0.0893	5008	,	,		19787	0.0476		0.0427	False		,,,				2504	0.0583				p.D159D		Atlas-SNP	.											ENGASE,NS,carcinoma,+2,2	ENGASE	55	2	0			c.C477T						PASS	.	C		1255,2959		185,885,1037	134	156	149		477	5.2	1	17	dbSNP_107	149	329,8093		3,323,3885	no	coding-synonymous	ENGASE	NM_001042573.1		188,1208,4922	TT,TC,CC		3.9064,29.7817,12.5356		159/744	77075631	1584,11052	2107	4211	6318	SO:0001819	synonymous_variant	64772	exon4			CATCGACGTCTTT	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.477C>T	17.37:g.77075631C>T		84	0	0		72	23	0.319444	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Silent	SNP	ENST00000579016.1	37	CCDS42394.1																																																																																			C|0.878;T|0.122	0.122	strong		0.587	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759		T	77075631	C	T	77075631	2	4	29	1	0	0	0	0	0	0	0	1	5120	535	19	1		1	ENGASE	17	77075631	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	252206	77075631	4119579	773	13014											
ENPP7	339221	hgsc.bcm.edu	37	chr17	77709383	77709383	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacgtctacaagaaggaggCgttccccgaggccttccact	9	7	10	15	3	1	1	0	0	1	1	3	3	3	2	5	3	1	1	5	3	3	3	rs148221256	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:77709383C>T	ENST00000328313.5	+	3	1162	c.941C>T	c.(940-942)gCg>gTg	p.A314V		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)			AAGAAGGAGGCGTTCCCCGAG	0.607													C|||	5	0.000998403	0.0	0.0	5008	,	,		12692	0.005		0.0	False		,,,				2504	0.0				p.A314V		Atlas-SNP	.											.	ENPP7	63	.	0			c.C941T						PASS	.						79	69	72					17																	77709383		2203	4300	6503	SO:0001583	missense	339221	exon3			AGGAGGCGTTCCC	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.941C>T	17.37:g.77709383C>T	ENSP00000332656:p.Ala314Val	85	0	0		73	23	0.315068	NM_178543		Missense_Mutation	SNP	ENST00000328313.5	37	CCDS11763.1	4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	C	9.525	1.109390	0.20714	.	.	ENSG00000182156	ENST00000328313	T	0.75367	-0.93	5.16	-10.3	0.00346	Alkaline-phosphatase-like, core domain (1);	2.191760	0.03750	N	0.256410	T	0.39545	0.1082	N	0.05383	-0.06	0.09310	N	1	B	0.18310	0.027	B	0.12837	0.008	T	0.42207	-0.9465	10	0.52906	T	0.07	-0.5261	5.6555	0.17640	0.5382:0.2657:0.0617:0.1344	.	314	Q6UWV6	ENPP7_HUMAN	V	314	ENSP00000332656:A314V	ENSP00000332656:A314V	A	+	2	0	ENPP7	75323978	0.003000	0.15002	0.000000	0.03702	0.013000	0.08279	0.718000	0.25866	-2.154000	0.00792	-2.138000	0.00339	GCG	C|0.998;T|0.002	0.002	strong		0.607	ENPP7-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437038.1	NM_178543		T	77709383	C	T	77709383	3	4	29	1	0	0	0	0	1	0	0	0	5137	768	27	1	951	1	ENPP7	17	77709383	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	633752	77709383	3485827	774	13015											
CARD14	79092	hgsc.bcm.edu	37	chr17	78157961	78157961	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgaaggacgagatgctcaGcctctcgctgcactatagca	10	8	11	12	2	2	2	1	1	1	1	3	4	2	3	1	1	4	5	1	1	3	2	rs114688446	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:78157961G>A	ENST00000573882.1	+	6	1135	c.599G>A	c.(598-600)aGc>aAc	p.S200N	CARD14_ENST00000392434.2_5'Flank|CARD14_ENST00000344227.2_Missense_Mutation_p.S200N|CARD14_ENST00000570421.1_Missense_Mutation_p.S200N			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	200			S -> N (in dbSNP:rs114688446). {ECO:0000269|PubMed:22521419}.		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)			GAGATGCTCAGCCTCTCGCTG	0.652													G|||	11	0.00219649	0.0	0.0029	5008	,	,		18540	0.0		0.002	False		,,,				2504	0.0072				p.S200N		Atlas-SNP	.											.	CARD14	98	.	0			c.G599A						PASS	.						28	21	24					17																	78157961		2186	4282	6468	SO:0001583	missense	79092	exon4			TGCTCAGCCTCTC	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.599G>A	17.37:g.78157961G>A	ENSP00000458715:p.Ser200Asn	68	0	0		73	34	0.465753	NM_024110	B8QQJ3|Q9BVB5	Missense_Mutation	SNP	ENST00000573882.1	37	CCDS11768.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	G	0.004	-2.372545	0.00209	.	.	ENSG00000141527	ENST00000344227	T	0.34072	1.38	3.58	-3.66	0.04489	.	0.717962	0.13758	N	0.364763	T	0.06735	0.0172	N	0.02916	-0.46	0.19945	N	0.999944	B	0.02656	0.0	B	0.04013	0.001	T	0.32214	-0.9915	10	0.02654	T	1	-3.1167	5.8528	0.18701	0.5403:0.1435:0.3162:0.0	.	200	Q9BXL6	CAR14_HUMAN	N	200	ENSP00000344549:S200N	ENSP00000344549:S200N	S	+	2	0	CARD14	75772556	0.000000	0.05858	0.001000	0.08648	0.037000	0.13140	-0.119000	0.10676	-0.492000	0.06687	-0.479000	0.04858	AGC	A|0.001;G|0.994;T|0.005	0.001	strong		0.652	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1			A	78157961	G	A	78157961	3	1	29	1	0	0	0	0	1	0	0	0	2648	971	34	2	609	2	CARD14	17	78157961	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	448578	78157961	3037249	775	13016											
ACTG1	71	hgsc.bcm.edu	37	chr17	79479099	79479099	+	Missense_Mutation	SNP	G	G	T																															aatggggtacttcagggtcaGgatgccacgcttgctctggg																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79479099G>T	ENST00000575842.1	-	2	619	c.193C>A	c.(193-195)Ctg>Atg	p.L65M	ACTG1_ENST00000331925.2_Missense_Mutation_p.L65M|RP13-766D20.2_ENST00000430912.1_RNA|ACTG1_ENST00000573283.1_Missense_Mutation_p.L65M|ACTG1_ENST00000575087.1_Missense_Mutation_p.L65M|AC139149.1_ENST00000584254.1_RNA			P63261	ACTG_HUMAN	actin, gamma 1	65					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)			TTCAGGGTCAGGATGCCACGC	0.642																																					p.L65M		Atlas-SNP	.											.	ACTG1	55	.	0			c.C193A						PASS	.						71	69	69					17																	79479099		2203	4300	6503	SO:0001583	missense	71	exon3			GGGTCAGGATGCC		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.193C>A	17.37:g.79479099G>T	ENSP00000458162:p.Leu65Met	74	0	0		37	10	0.27027	NM_001614	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000575842.1	37	CCDS11782.1	.	.	.	.	.	.	.	.	.	.	G	7.842	0.722186	0.15372	.	.	ENSG00000184009	ENST00000331925;ENST00000447294	D	0.94723	-3.5	3.99	1.97	0.26223	.	0.000000	0.52532	U	0.000061	D	0.97356	0.9135	M	0.91663	3.23	0.41069	D	0.985436	D	0.61697	0.99	D	0.83275	0.996	D	0.96801	0.9589	10	0.87932	D	0	.	11.7241	0.51700	0.1712:0.0:0.8288:0.0	.	65	P63261	ACTG_HUMAN	M	65	ENSP00000331514:L65M	ENSP00000331514:L65M	L	-	1	2	ACTG1	77093694	1.000000	0.71417	0.992000	0.48379	0.176000	0.22953	7.295000	0.78780	0.055000	0.16094	-1.119000	0.02030	CTG	.	.	none		0.642	ACTG1-012	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439935.2	NM_001614		T	79479099	G	T	79479099	3	4	29	1	0	0	0	0	1	0	0	0	196	991	35	4	950	4	ACTG1	17	79479099	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1321138	79479099	1716111	776	13017	165	3									
ACTG1	71	hgsc.bcm.edu	37	chr17	79479101	79479101	+	Missense_Mutation	SNP	A	A	T																															tggggtacttcagggtcaggAtgccacgcttgctctgggcc																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79479101A>T	ENST00000575842.1	-	2	617	c.191T>A	c.(190-192)aTc>aAc	p.I64N	ACTG1_ENST00000331925.2_Missense_Mutation_p.I64N|RP13-766D20.2_ENST00000430912.1_RNA|ACTG1_ENST00000573283.1_Missense_Mutation_p.I64N|ACTG1_ENST00000575087.1_Missense_Mutation_p.I64N|AC139149.1_ENST00000584254.1_RNA			P63261	ACTG_HUMAN	actin, gamma 1	64					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)			CAGGGTCAGGATGCCACGCTT	0.637																																					p.I64N		Atlas-SNP	.											ACTG1,spleen,lymphoid_neoplasm,0,1	ACTG1	55	1	0			c.T191A						PASS	.						71	69	69					17																	79479101		2203	4300	6503	SO:0001583	missense	71	exon3			GTCAGGATGCCAC		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.191T>A	17.37:g.79479101A>T	ENSP00000458162:p.Ile64Asn	73	0	0		37	10	0.27027	NM_001614	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000575842.1	37	CCDS11782.1	.	.	.	.	.	.	.	.	.	.	A	7.994	0.753990	0.15778	.	.	ENSG00000184009	ENST00000331925;ENST00000447294	D	0.90676	-2.71	3.88	3.88	0.44766	.	0.000000	0.64402	U	0.000002	D	0.90528	0.7032	M	0.83223	2.63	0.53688	D	0.999974	B	0.11235	0.004	B	0.20577	0.03	D	0.89491	0.3757	10	0.87932	D	0	.	11.8408	0.52353	1.0:0.0:0.0:0.0	.	64	P63261	ACTG_HUMAN	N	64	ENSP00000331514:I64N	ENSP00000331514:I64N	I	-	2	0	ACTG1	77093696	1.000000	0.71417	0.988000	0.46212	0.263000	0.26337	8.617000	0.90927	1.634000	0.50500	0.460000	0.39030	ATC	.	.	none		0.637	ACTG1-012	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439935.2	NM_001614		T	79479101	A	T	79479101	3	4	29	1	0	0	0	0	1	0	0	0	196	333	12	5	952	5	ACTG1	17	79479101	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	2	79479101	1716109	777	13018	165	3									
ACTG1	71	hgsc.bcm.edu	37	chr17	79479108	79479108	+	Missense_Mutation	SNP	G	G	A																															cttcagggtcaggatgccacGcttgctctgggcctcgtcgc																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79479108G>A	ENST00000575842.1	-	2	610	c.184C>T	c.(184-186)Cgt>Tgt	p.R62C	ACTG1_ENST00000331925.2_Missense_Mutation_p.R62C|RP13-766D20.2_ENST00000430912.1_RNA|ACTG1_ENST00000573283.1_Missense_Mutation_p.R62C|ACTG1_ENST00000575087.1_Missense_Mutation_p.R62C|AC139149.1_ENST00000584254.1_RNA			P63261	ACTG_HUMAN	actin, gamma 1	62					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)			AGGATGCCACGCTTGCTCTGG	0.627																																					p.R62C		Atlas-SNP	.											.	ACTG1	55	.	0			c.C184T						PASS	.						70	68	68					17																	79479108		2203	4300	6503	SO:0001583	missense	71	exon3			TGCCACGCTTGCT		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.184C>T	17.37:g.79479108G>A	ENSP00000458162:p.Arg62Cys	69	0	0		37	9	0.243243	NM_001614	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000575842.1	37	CCDS11782.1	.	.	.	.	.	.	.	.	.	.	G	12.19	1.863019	0.32884	.	.	ENSG00000184009	ENST00000331925;ENST00000447294	D	0.90955	-2.76	3.99	0.23	0.15372	Actin, conserved site (1);	0.000000	0.64402	U	0.000005	D	0.94341	0.8181	H	0.98786	4.33	0.58432	D	0.999991	P	0.50819	0.939	P	0.45406	0.479	D	0.94108	0.7368	10	0.87932	D	0	.	11.3287	0.49463	0.0:0.0:0.2975:0.7025	.	62	P63261	ACTG_HUMAN	C	62	ENSP00000331514:R62C	ENSP00000331514:R62C	R	-	1	0	ACTG1	77093703	1.000000	0.71417	0.758000	0.31321	0.728000	0.41692	3.215000	0.51169	0.236000	0.21180	0.563000	0.77884	CGT	.	.	none		0.627	ACTG1-012	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439935.2	NM_001614		A	79479108	G	A	79479108	3	1	29	1	0	0	0	0	1	0	0	0	196	1087	38	1	959	1	ACTG1	17	79479108	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	7	79479108	1716102	778	13019	165	3									
C17orf70	80233	hgsc.bcm.edu	37	chr17	79517729	79517729	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gggcatttgggtcaccagggGctgacctggaggtgaccagg	7	7	18	9	0	1	2	1	2	0	0	1	3	1	3	3	7	0	2	3	7	0	1	rs62076033	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79517729G>A	ENST00000327787.8	-	3	837	c.791C>T	c.(790-792)gCc>gTc	p.A264V	C17orf70_ENST00000537152.1_Missense_Mutation_p.A113V|C17orf70_ENST00000425898.2_5'Flank			Q0VG06	FP100_HUMAN	chromosome 17 open reading frame 70	264					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)			GTCACCAGGGGCTGACCTGGA	0.597													G|||	13	0.00259585	0.0	0.0029	5008	,	,		17976	0.001		0.005	False		,,,				2504	0.0051				p.A264V		Atlas-SNP	.											.	C17orf70	79	.	0			c.C791T						PASS	.	G	VAL/ALA	2,4404	4.2+/-10.8	0,2,2201	50	49	49		791	1.3	0	17	dbSNP_129	49	35,8565	24.0+/-70.4	1,33,4266	yes	missense	C17orf70	NM_025161.5	64	1,35,6467	AA,AG,GG		0.407,0.0454,0.2845	possibly-damaging	264/882	79517729	37,12969	2203	4300	6503	SO:0001583	missense	80233	exon3			CCAGGGGCTGACC	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.791C>T	17.37:g.79517729G>A	ENSP00000333283:p.Ala264Val	83	0	0		79	36	0.455696	NM_025161	A6NNM1|Q8N3F7|Q9BV13|Q9H6K7|Q9H7E8	Missense_Mutation	SNP	ENST00000327787.8	37	CCDS32765.2	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	G	14.74	2.625913	0.46840	4.54E-4	0.00407	ENSG00000185504	ENST00000327787;ENST00000537152;ENST00000541246;ENST00000544302	T;T	0.34472	1.36;1.36	4.34	1.27	0.21489	.	0.691562	0.13293	N	0.398824	T	0.24547	0.0595	L	0.51422	1.61	0.09310	N	1	P	0.40731	0.728	P	0.46076	0.503	T	0.16837	-1.0389	10	0.42905	T	0.14	.	0.873	0.01218	0.2856:0.159:0.3926:0.1628	rs62076033	264	Q0VG06	FP100_HUMAN	V	264;113;113;113	ENSP00000333283:A264V;ENSP00000440151:A113V	ENSP00000333283:A264V	A	-	2	0	C17orf70	77128171	0.931000	0.31567	0.028000	0.17463	0.604000	0.37047	2.557000	0.45871	0.129000	0.18514	0.563000	0.77884	GCC	G|0.997;A|0.003	0.003	strong		0.597	C17orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396170.1	NM_025161		A	79517729	G	A	79517729	3	1	29	1	0	0	0	0	1	0	0	0	1879	1203	42	2	1882	2	C17orf70	17	79517729	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	38621	79517729	1677481	779	13020											
MAFG	4097	hgsc.bcm.edu	37	chr17	79880565	79880565	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggacgaggggccccaggccGgcggcaagggggccccgggc	5	0	22	14	4	0	0	0	0	0	0	0	2	0	1	5	9	0	1	5	9	1	0	rs61752690	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79880565G>A	ENST00000357736.4	-	3	620	c.405C>T	c.(403-405)gcC>gcT	p.A135A	MAFG_ENST00000392366.3_Silent_p.A135A|RP11-498C9.12_ENST00000580897.1_RNA	NM_002359.3|NM_032711.3	NP_002350.1|NP_116100.2	O15525	MAFG_HUMAN	v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog G	135					adult behavior (GO:0030534)|blood coagulation (GO:0007596)|in utero embryonic development (GO:0001701)|regulation of cell proliferation (GO:0042127)|regulation of cellular pH (GO:0030641)|regulation of epidermal cell differentiation (GO:0045604)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|lung(1)	3	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.0165)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			GCCCCAGGCCGGCGGCAAGGG	0.716													G|||	6	0.00119808	0.0	0.0014	5008	,	,		11901	0.0		0.003	False		,,,				2504	0.002				p.A135A		Atlas-SNP	.											.	MAFG	9	.	0			c.C405T						PASS	.	G	,	5,4303		0,5,2149	10	11	10		405,405	-2.1	0	17	dbSNP_129	10	60,8350		0,60,4145	no	coding-synonymous,coding-synonymous	MAFG	NM_002359.3,NM_032711.3	,	0,65,6294	AA,AG,GG		0.7134,0.1161,0.5111	,	135/163,135/163	79880565	65,12653	2154	4205	6359	SO:0001819	synonymous_variant	4097	exon3			CAGGCCGGCGGCA	AF059195	CCDS11793.1	17q25.3	2013-07-09	2013-07-09		ENSG00000197063	ENSG00000197063			6781	protein-coding gene	gene with protein product	"transcription factor MafG", "basic leucine zipper transcription factor MafG"	602020				9763667	Standard	NM_002359		Approved	MGC13090, MGC20149	uc002kcm.3	O15525		ENST00000357736.4:c.405C>T	17.37:g.79880565G>A		14	0	0		12	7	0.583333	NM_032711		Silent	SNP	ENST00000357736.4	37	CCDS11793.1																																																																																			A|0.002;G|0.998	0.002	strong		0.716	MAFG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439980.1	NM_002359		A	79880565	G	A	79880565	2	1	29	1	0	0	0	0	0	0	0	1	9169	1103	39	1		1	MAFG	17	79880565	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	362836	79880565	1314645	780	13021											
ASPSCR1	79058	hgsc.bcm.edu	37	chr17	79941511	79941511	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaagctggagatggtgccCgcttcccggagccgtgaggg	6	6	17	12	3	0	2	0	1	0	1	1	4	1	3	4	4	3	2	4	4	1	1	rs11539917	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr17:79941511C>T	ENST00000306739.4	+	3	337	c.240C>T	c.(238-240)ccC>ccT	p.P80P	ASPSCR1_ENST00000581647.1_Silent_p.P80P|ASPSCR1_ENST00000306729.7_Silent_p.P80P|ASPSCR1_ENST00000580534.1_Silent_p.P3P	NM_024083.3	NP_076988.1	Q9BZE9	ASPC1_HUMAN	alveolar soft part sarcoma chromosome region, candidate 1	80					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)			AGATGGTGCCCGCTTCCCGGA	0.622			T	TFE3	alveolar soft part sarcoma								C|||	63	0.0125799	0.0015	0.0231	5008	,	,		12243	0.0		0.0209	False		,,,				2504	0.0245				p.P80P		Atlas-SNP	.		Dom	yes		17	17q25	79058	"alveolar soft part sarcoma chromosome region, candidate 1"		M	ASPSCR1_ENST00000306729,colon,carcinoma,0,1	ASPSCR1	27	1	0			c.C240T						PASS	.	C		22,4384	29.0+/-57.7	0,22,2181	80	63	69		240	-8	0	17	dbSNP_120	69	162,8438	76.3+/-139.0	2,158,4140	no	coding-synonymous	ASPSCR1	NM_024083.2		2,180,6321	TT,TC,CC		1.8837,0.4993,1.4147		80/554	79941511	184,12822	2203	4300	6503	SO:0001819	synonymous_variant	79058	exon3			GGTGCCCGCTTCC	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.240C>T	17.37:g.79941511C>T		59	0	0		47	29	0.617021	NM_001251888	A8K3K9|Q7Z6N7|Q8WV59|Q96LS5|Q96M40	Silent	SNP	ENST00000306739.4	37	CCDS11796.1																																																																																			C|0.988;T|0.012	0.012	strong		0.622	ASPSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441972.1	NM_024083		T	79941511	C	T	79941511	2	4	29	1	0	0	0	0	0	0	0	1	1059	639	23	1		1	ASPSCR1	17	79941511	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	60946	79941511	1253699	781	13022											
CLUL1	27098	hgsc.bcm.edu	37	chr18	618015	618015	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gggaacatgaagccgccactCttggtgtttattgtgtgtct	7	14	12	8	1	2	1	0	1	2	0	2	2	2	2	2	2	2	1	2	2	3	4	rs116985056	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:618015C>G	ENST00000400606.2	+	2	160	c.15C>G	c.(13-15)ctC>ctG	p.L5L	CLUL1_ENST00000540035.1_Silent_p.L57L|CLUL1_ENST00000579494.1_Silent_p.L5L|CLUL1_ENST00000580436.1_3'UTR|CLUL1_ENST00000581619.1_Silent_p.L30L|CLUL1_ENST00000338387.7_Silent_p.L5L	NM_014410.4	NP_055225.1	Q15846	CLUL1_HUMAN	clusterin-like 1 (retinal)	5					cell death (GO:0008219)	extracellular region (GO:0005576)				NS(1)|breast(1)|endometrium(5)|large_intestine(5)|liver(2)|lung(7)|ovary(2)|skin(1)	24						AGCCGCCACTCTTGGTGTTTA	0.438													C|||	2	0.000399361	0.0	0.0	5008	,	,		19800	0.0		0.001	False		,,,				2504	0.001				p.L5L		Atlas-SNP	.											.	CLUL1	57	.	0			c.C15G						PASS	.	C	,	2,3954		0,2,1976	110	111	111		15,15	2.3	0.6	18	dbSNP_132	111	21,8311		0,21,4145	no	coding-synonymous,coding-synonymous	CLUL1	NM_014410.4,NM_199167.1	,	0,23,6121	GG,GC,CC		0.252,0.0506,0.1872	,	5/467,5/467	618015	23,12265	1978	4166	6144	SO:0001819	synonymous_variant	27098	exon2			GCCACTCTTGGTG	D63813	CCDS42405.1, CCDS74187.1	18p11.32	2008-07-28				ENSG00000079101			2096	protein-coding gene	gene with protein product						10675623, 14507903	Standard	NM_199167		Approved		uc002kkq.3	Q15846		ENST00000400606.2:c.15C>G	18.37:g.618015C>G		109	0	0		91	30	0.32967	NM_199167	A0FDN7	Silent	SNP	ENST00000400606.2	37	CCDS42405.1																																																																																			C|0.999;G|0.001	0.001	strong		0.438	CLUL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441183.1			G	618015	C	G	618015	2	3	29	1	0	0	0	0	0	0	0	1	3572	900	32	4		4	CLUL1	18	618015	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10		618015	77459233	782	13023											
LAMA1	284217	hgsc.bcm.edu	37	chr18	6950847	6950847	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttctgcctttgccaaggtcAaacatgaagtggaggcggcc	9	9	13	10	1	2	1	1	1	1	0	2	2	2	2	3	4	3	1	3	4	3	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:6950847A>C	ENST00000389658.3	-	58	8424	c.8331T>G	c.(8329-8331)ttT>ttG	p.F2777L		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2777	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)				TGCCAAGGTCAAACATGAAGT	0.572																																					p.F2777L		Atlas-SNP	.											.	LAMA1	458	.	0			c.T8331G						PASS	.						117	100	105					18																	6950847		2203	4300	6503	SO:0001583	missense	284217	exon58			AAGGTCAAACATG	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.8331T>G	18.37:g.6950847A>C	ENSP00000374309:p.Phe2777Leu	110	0	0		103	27	0.262136	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	A	12.70	2.017652	0.35606	.	.	ENSG00000101680	ENST00000389658	T	0.73575	-0.76	5.5	0.425	0.16473	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	0.200169	0.45126	D	0.000391	T	0.60130	0.2245	L	0.39514	1.22	0.37392	D	0.9125	B;B	0.28350	0.083;0.208	B;B	0.33690	0.028;0.168	T	0.45512	-0.9256	10	0.20519	T	0.43	.	5.6623	0.17676	0.5896:0.1311:0.2793:0.0	.	2777;107	P25391;B3KSD8	LAMA1_HUMAN;.	L	2777	ENSP00000374309:F2777L	ENSP00000374309:F2777L	F	-	3	2	LAMA1	6940847	1.000000	0.71417	0.995000	0.50966	0.400000	0.30750	2.104000	0.41815	-0.144000	0.11314	-0.441000	0.05720	TTT	.	.	none		0.572	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		C	6950847	A	C	6950847	3	2	29	1	0	0	0	0	1	0	0	0	8614	127	5	5	920	5	LAMA1	18	6950847	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	6332832	6950847	71126401	783	13024											
DSG2	1829	hgsc.bcm.edu	37	chr18	29126108	29126108	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttctaggcaggcgcaaaaggTagctacacctcttcctgacc	10	9	9	13	1	2	1	0	1	2	0	3	1	3	1	3	3	2	4	3	3	5	5	rs142841727	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:29126108T>G	ENST00000261590.8	+	15	2968	c.2759T>G	c.(2758-2760)gTa>gGa	p.V920G	RP11-75N4.2_ENST00000583706.1_RNA	NM_001943.3	NP_001934.2	Q14126	DSG2_HUMAN	desmoglein 2	920			V -> G (in dbSNP:rs142841727). {ECO:0000269|PubMed:18678517, ECO:0000269|PubMed:19863551}.		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)			GCGCAAAAGGTAGCTACACCT	0.458													T|||	16	0.00319489	0.0	0.0101	5008	,	,		21083	0.0		0.0089	False		,,,				2504	0.0				p.V920G		Atlas-SNP	.											DSG2,NS,lymphoid_neoplasm,0,1	DSG2	115	1	0			c.T2759G	GRCh37	CM070920	DSG2	M	rs142841727	PASS	.	T	GLY/VAL	6,3890		0,6,1942	86	84	85		2759	2.5	0	18	dbSNP_134	85	41,8229		0,41,4094	yes	missense	DSG2	NM_001943.3	109	0,47,6036	GG,GT,TT		0.4958,0.154,0.3863	benign	920/1119	29126108	47,12119	1948	4135	6083	SO:0001583	missense	1829	exon15			AAAAGGTAGCTAC	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.2759T>G	18.37:g.29126108T>G	ENSP00000261590:p.Val920Gly	116	0	0		107	53	0.495327	NM_001943	Q4KKU6	Missense_Mutation	SNP	ENST00000261590.8	37	CCDS42423.1	8	0.003663003663003663	0	0.0	4	0.011049723756906077	0	0.0	4	0.005277044854881266	T	4.378	0.069751	0.08436	0.00154	0.004958	ENSG00000046604	ENST00000261590	T	0.77877	-1.13	4.9	2.5	0.30297	.	0.296289	0.24470	N	0.038257	T	0.53142	0.1778	L	0.36672	1.1	0.09310	N	0.999999	P	0.39282	0.666	B	0.32864	0.154	T	0.48714	-0.9011	10	0.38643	T	0.18	.	6.805	0.23772	0.0:0.29:0.0:0.71	.	920	Q14126	DSG2_HUMAN	G	920	ENSP00000261590:V920G	ENSP00000261590:V920G	V	+	2	0	DSG2	27380106	0.000000	0.05858	0.024000	0.17045	0.571000	0.35966	0.145000	0.16157	0.438000	0.26450	-0.250000	0.11733	GTA	T|0.995;G|0.005	0.005	strong		0.458	DSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447506.1	NM_001943		G	29126108	T	G	29126108	3	3	29	1	0	0	0	0	1	0	0	0	4779	1638	57	5	2817	5	DSG2	18	29126108	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	22175261	29126108	48951140	784	13025											
ASXL3	80816	hgsc.bcm.edu	37	chr18	31326554	31326554	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgtagcatgcctggttgtaCgataagagctgagtgaaaga	12	10	14	5	1	0	4	0	2	0	2	0	5	0	4	1	1	4	5	1	1	4	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:31326554C>T	ENST00000269197.5	+	12	6742	c.6742C>T	c.(6742-6744)Cga>Tga	p.R2248*		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	2248					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						CCTGGTTGTACGATAAGAGCT	0.458																																					p.R2248X		Atlas-SNP	.											ASXL3_ENST00000269197,NS,carcinoma,-1,1	ASXL3	405	1	0			c.C6742T						PASS	.						109	104	106					18																	31326554		1994	4172	6166	SO:0001587	stop_gained	80816	exon12			GTTGTACGATAAG	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.6742C>T	18.37:g.31326554C>T	ENSP00000269197:p.Arg2248*	21	0	0		20	7	0.35	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Nonsense_Mutation	SNP	ENST00000269197.5	37	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	C	46	12.156967	0.99642	.	.	ENSG00000141431	ENST00000269197	.	.	.	6.03	6.03	0.97812	.	.	.	.	.	.	.	.	.	.	.	0.49051	D	0.999744	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	20.5666	0.99351	0.0:1.0:0.0:0.0	.	.	.	.	X	2248	.	ENSP00000269197:R2248X	R	+	1	2	ASXL3	29580552	0.999000	0.42202	0.998000	0.56505	0.883000	0.51084	3.717000	0.54911	2.854000	0.98071	0.655000	0.94253	CGA	.	.	none		0.458	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			T	31326554	C	T	31326554	4	4	29	1	0	0	0	0	0	1	0	0	1068	528	19	1	6788	1	ASXL3	18	31326554	Nonsense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2200446	31326554	46750694	785	13026											
KIAA1632	57724	hgsc.bcm.edu	37	chr18	43514856	43514856	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctctccacctggtgcatgaGgtagaagagcttccacagca	10	8	11	12	0	1	3	0	1	1	2	3	3	2	3	3	2	3	5	3	2	2	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:43514856G>A	ENST00000282041.5	-	11	2210	c.2176C>T	c.(2176-2178)Ctc>Ttc	p.L726F		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	726					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						TGGTGCATGAGGTAGAAGAGC	0.562																																					p.L726F		Atlas-SNP	.											.	EPG5	199	.	0			c.C2176T						PASS	.						65	66	66					18																	43514856		2017	4185	6202	SO:0001583	missense	57724	exon11			GCATGAGGTAGAA	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.2176C>T	18.37:g.43514856G>A	ENSP00000282041:p.Leu726Phe	120	0	0		140	60	0.428571	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	.	.	.	.	.	.	.	.	.	.	G	16.72	3.201595	0.58234	.	.	ENSG00000152223	ENST00000282041	T	0.12879	2.64	5.49	3.59	0.41128	.	0.761961	0.12243	N	0.486318	T	0.12305	0.0299	L	0.50333	1.59	0.36997	D	0.895098	B;B	0.13145	0.007;0.007	B;B	0.09377	0.004;0.004	T	0.08330	-1.0727	10	0.25751	T	0.34	-7.8907	6.4791	0.22053	0.0758:0.1864:0.6245:0.1132	.	726;726	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	F	726	ENSP00000282041:L726F	ENSP00000282041:L726F	L	-	1	0	EPG5	41768854	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	2.282000	0.43461	1.451000	0.47736	-0.150000	0.13652	CTC	.	.	none		0.562	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964		A	43514856	G	A	43514856	3	1	29	1	0	0	0	0	1	0	0	0	8258	1000	35	2	5699	2	KIAA1632	18	43514856	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	12188302	43514856	34562392	786	13027											
ME2	4200	hgsc.bcm.edu	37	chr18	48447462	48447462	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aggctgctcttggaattgcaAatcttatagttatgtctatg	10	16	9	6	0	3	0	0	0	3	0	3	1	3	1	0	2	2	4	0	2	6	6	rs59409558	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr18:48447462A>C	ENST00000321341.5	+	10	1233	c.961A>C	c.(961-963)Aat>Cat	p.N321H	ME2_ENST00000382927.3_Missense_Mutation_p.N321H	NM_002396.4	NP_002387.1	P23368	MAOM_HUMAN	malic enzyme 2, NAD(+)-dependent, mitochondrial	321					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)		TGGAATTGCAAATCTTATAGT	0.318													A|||	30	0.00599042	0.0	0.0058	5008	,	,		15027	0.003		0.0149	False		,,,				2504	0.0082				p.N321H		Atlas-SNP	.											.	ME2	49	.	0			c.A961C						PASS	.	A	HIS/ASN,HIS/ASN	20,4386	27.2+/-55.0	0,20,2183	53	55	54		961,961	5.9	1	18	dbSNP_129	54	99,8495	55.2+/-116.2	0,99,4198	yes	missense,missense	ME2	NM_001168335.1,NM_002396.4	68,68	0,119,6381	CC,CA,AA		1.152,0.4539,0.9154	benign,benign	321/480,321/585	48447462	119,12881	2203	4297	6500	SO:0001583	missense	4200	exon10			ATTGCAAATCTTA	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.961A>C	18.37:g.48447462A>C	ENSP00000321070:p.Asn321His	82	0	0		108	47	0.435185	NM_001168335	B2R8J2|Q9BWL6|Q9BYG1|Q9H4B2	Missense_Mutation	SNP	ENST00000321341.5	37	CCDS11948.1	15	0.006868131868131868	0	0.0	3	0.008287292817679558	2	0.0034965034965034965	10	0.013192612137203167	A	11.52	1.662037	0.29515	0.004539	0.01152	ENSG00000082212	ENST00000321341;ENST00000382927	T;T	0.31769	1.48;1.48	5.92	5.92	0.95590	Malic enzyme, NAD-binding (2);NAD(P)-binding domain (1);	0.042144	0.85682	D	0.000000	T	0.23451	0.0567	L	0.52364	1.645	0.58432	D	0.999997	B;B	0.09022	0.002;0.0	B;B	0.10450	0.005;0.003	T	0.02805	-1.1108	10	0.32370	T	0.25	-20.0102	15.3462	0.74340	1.0:0.0:0.0:0.0	rs59409558	321;321	Q9BWL6;P23368	.;MAOM_HUMAN	H	321	ENSP00000321070:N321H;ENSP00000372384:N321H	ENSP00000321070:N321H	N	+	1	0	ME2	46701460	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.360000	0.59455	2.267000	0.75376	0.528000	0.53228	AAT	A|0.991;C|0.009	0.009	strong		0.318	ME2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255991.1	NM_002396		C	48447462	A	C	48447462	3	2	29	1	0	0	0	0	1	0	0	0	9427	14	1	5	995	5	ME2	18	48447462	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	4932606	48447462	29629786	787	13028											
HCN2	610	hgsc.bcm.edu	37	chr19	605093	605093	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acctatgacctggccagcgcGgtgatgaggatctgcaatct	9	9	12	11	2	2	3	0	3	2	0	2	4	2	4	3	3	2	1	3	3	2	1	rs55839339	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:605093G>A	ENST00000251287.2	+	3	1142	c.1089G>A	c.(1087-1089)gcG>gcA	p.A363A		NM_001194.3	NP_001185.3	Q9UL51	HCN2_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 2	363					cell-cell signaling (GO:0007267)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|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)|voltage-gated potassium channel complex (GO:0008076)	cAMP binding (GO:0030552)|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)			endometrium(5)|lung(4)	9		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)		TGGCCAGCGCGGTGATGAGGA	0.642													g|||	35	0.00698882	0.003	0.0159	5008	,	,		9413	0.002		0.0139	False		,,,				2504	0.0041				p.A363A	Melanoma(145;1175 2427 8056 36306)	Atlas-SNP	.											.	HCN2	36	.	0			c.G1089A						PASS	.	G		34,4372		0,34,2169	89	73	79		1089	-6.8	0.8	19	dbSNP_129	79	170,8424		3,164,4130	no	coding-synonymous	HCN2	NM_001194.3		3,198,6299	AA,AG,GG		1.9781,0.7717,1.5692		363/890	605093	204,12796	2203	4297	6500	SO:0001819	synonymous_variant	610	exon3			CAGCGCGGTGATG	AF064877	CCDS12035.1	19p13	2011-07-05				ENSG00000099822		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	4846	protein-coding gene	gene with protein product		602781		BCNG2		9405696, 9630217, 16382102	Standard	NM_001194		Approved	BCNG-2, HAC-1	uc002lpe.3	Q9UL51		ENST00000251287.2:c.1089G>A	19.37:g.605093G>A		82	0	0		72	34	0.472222	NM_001194	O60742|O60743|O75267|Q9UBS2	Silent	SNP	ENST00000251287.2	37	CCDS12035.1																																																																																			G|0.984;A|0.016	0.016	strong		0.642	HCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452100.1	NM_001194		A	605093	G	A	605093	2	1	29	1	0	0	0	0	0	0	0	1	7006	1103	39	1		1	HCN2	19	605093	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10		605093	58523890	788	13029											
ABCA7	10347	hgsc.bcm.edu	37	chr19	1056183	1056183	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcctggcggggccctcgacCgtgtcctgaaaaacctcaca	8	7	11	15	3	1	1	1	1	0	0	3	2	2	1	5	3	2	0	5	3	2	0	rs144562001	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:1056183C>T	ENST00000263094.6	+	32	4588	c.4357C>T	c.(4357-4359)Cgt>Tgt	p.R1453C	ABCA7_ENST00000433129.1_Missense_Mutation_p.R1453C|ABCA7_ENST00000435683.2_Missense_Mutation_p.R1315C	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1453					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)		GGCCCTCGACCGTGTCCTGAA	0.677																																					p.R1453C		Atlas-SNP	.											.	ABCA7	174	.	0			c.C4357T						PASS	.	C	CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	46	50	49		4357	3.3	0	19	dbSNP_134	49	6,8594	4.3+/-15.6	0,6,4294	yes	missense	ABCA7	NM_019112.3	180	0,8,6495	TT,TC,CC		0.0698,0.0454,0.0615	probably-damaging	1453/2147	1056183	8,12998	2203	4300	6503	SO:0001583	missense	10347	exon32			CTCGACCGTGTCC	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.4357C>T	19.37:g.1056183C>T	ENSP00000263094:p.Arg1453Cys	36	0	0		39	20	0.512821	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	C	15.59	2.878421	0.51801	4.54E-4	6.98E-4	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.87334	-2.24;-2.24	3.28	3.28	0.37604	.	.	.	.	.	D	0.91744	0.7389	M	0.80028	2.48	0.24069	N	0.995988	D	0.62365	0.991	P	0.58970	0.849	D	0.83846	0.0260	9	0.87932	D	0	.	11.7386	0.51780	0.0:1.0:0.0:0.0	.	1453	Q8IZY2	ABCA7_HUMAN	C	1453	ENSP00000263094:R1453C;ENSP00000414062:R1453C	ENSP00000263094:R1453C	R	+	1	0	ABCA7	1007183	0.004000	0.15560	0.040000	0.18447	0.052000	0.14988	1.048000	0.30379	1.859000	0.53934	0.561000	0.74099	CGT	C|0.999;G|0.000;T|0.000	0.000	strong		0.677	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112		T	1056183	C	T	1056183	3	4	29	1	0	0	0	0	1	0	0	0	37	652	23	1	4479	1	ABCA7	19	1056183	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	451090	1056183	58072800	789	13030											
FEM1A	55527	hgsc.bcm.edu	37	chr19	4793128	4793128	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtacgccctggacatgcaacAgagcaacctggagcctctga	11	6	11	13	1	1	2	0	1	1	1	1	4	1	4	3	2	6	3	3	2	3	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:4793128A>C	ENST00000269856.3	+	1	1401	c.1262A>C	c.(1261-1263)cAg>cCg	p.Q421P	AC005523.2_ENST00000596170.1_RNA|AC005523.2_ENST00000601192.1_RNA|AC005523.3_ENST00000598782.1_lincRNA	NM_018708.2	NP_061178.1	Q9BSK4	FEM1A_HUMAN	fem-1 homolog a (C. elegans)	421					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)		GACATGCAACAGAGCAACCTG	0.602																																					p.Q421P		Atlas-SNP	.											.	FEM1A	41	.	0			c.A1262C						PASS	.						64	66	65					19																	4793128		2203	4299	6502	SO:0001583	missense	55527	exon1			TGCAACAGAGCAA	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.1262A>C	19.37:g.4793128A>C	ENSP00000269856:p.Gln421Pro	43	0	0		52	20	0.384615	NM_018708	B2RDI3|Q711P8|Q9NPN7|Q9NPW8	Missense_Mutation	SNP	ENST00000269856.3	37	CCDS12135.1	.	.	.	.	.	.	.	.	.	.	A	18.10	3.547381	0.65311	.	.	ENSG00000141965	ENST00000269856	T	0.58652	0.32	5.07	5.07	0.68467	Tetratricopeptide-like helical (1);	0.000000	0.64402	U	0.000001	T	0.80481	0.4631	M	0.91406	3.205	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	D	0.84430	0.0576	10	0.52906	T	0.07	-21.7521	14.8247	0.70101	1.0:0.0:0.0:0.0	.	421	Q9BSK4	FEM1A_HUMAN	P	421	ENSP00000269856:Q421P	ENSP00000269856:Q421P	Q	+	2	0	FEM1A	4744128	1.000000	0.71417	0.993000	0.49108	0.698000	0.40448	9.119000	0.94362	1.906000	0.55180	0.402000	0.26972	CAG	.	.	none		0.602	FEM1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459000.1			C	4793128	A	C	4793128	3	2	29	1	0	0	0	0	1	0	0	0	5817	188	7	5	1264	5	FEM1A	19	4793128	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	3736945	4793128	54335855	790	13031											
PRR22	163154	hgsc.bcm.edu	37	chr19	5783840	5783840	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gtagggcaagagaaactgggGccccccgggtgcctgctggt	7	6	17	11	1	0	1	0	0	0	1	0	2	0	1	4	5	3	3	4	5	3	1	rs576156353	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:5783840G>C	ENST00000419421.2	-	3	522	c.418C>G	c.(418-420)Ccc>Gcc	p.P140A		NM_001134316.1	NP_001127788.1	Q8IZ63	PRR22_HUMAN	proline rich 22	140	Pro-rich.									endometrium(2)|large_intestine(1)|prostate(1)|urinary_tract(1)	5						AGAAACTGGGGCCCCCCGGGT	0.716													G|||	2	0.000399361	0.0	0.0	5008	,	,		10475	0.0		0.001	False		,,,				2504	0.001				p.P140A		Atlas-SNP	.											.	PRR22	25	.	0			c.C418G						PASS	.																																			SO:0001583	missense	163154	exon3			ACTGGGGCCCCCC	BC023278	CCDS45933.1	19p13.3	2012-12-20			ENSG00000212123	ENSG00000212123			28354	protein-coding gene	gene with protein product						12477932	Standard	NM_001134316		Approved	MGC24975	uc010xiv.1	Q8IZ63	OTTHUMG00000180553	ENST00000419421.2:c.418C>G	19.37:g.5783840G>C	ENSP00000407653:p.Pro140Ala	19	0	0		36	14	0.388889	NM_001134316	E9PB31	Missense_Mutation	SNP	ENST00000419421.2	37	CCDS45933.1	.	.	.	.	.	.	.	.	.	.	G	10.36	1.329912	0.24167	.	.	ENSG00000212123	ENST00000419421	T	0.50277	0.75	4.55	3.49	0.39957	.	.	.	.	.	T	0.37919	0.1021	L	0.32530	0.975	0.27285	N	0.957999	P;P	0.40332	0.713;0.713	B;B	0.37304	0.162;0.246	T	0.26224	-1.0109	9	0.87932	D	0	-5.6709	12.2151	0.54402	0.0:0.1737:0.8263:0.0	.	140;138	E9PB31;Q8IZ63	.;PRR22_HUMAN	A	140	ENSP00000407653:P140A	ENSP00000407653:P140A	P	-	1	0	PRR22	5734840	0.003000	0.15002	0.252000	0.24328	0.010000	0.07245	0.703000	0.25646	1.096000	0.41439	-0.479000	0.04858	CCC	.	.	none		0.716	PRR22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368523.1	NM_153359		C	5783840	G	C	5783840	3	2	29	1	0	0	0	0	1	0	0	0	12605	1203	42	4	854	4	PRR22	19	5783840	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	990712	5783840	53345143	791	13032											
ZNF414	84330	hgsc.bcm.edu	37	chr19	8576390	8576390	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgagggcgcgtcggagccgCcctggggtcttcgggggctg	2	7	20	12	5	1	1	0	1	1	0	3	2	1	2	2	6	1	1	2	6	0	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:8576390C>T	ENST00000255616.8	-	6	1006	c.905G>A	c.(904-906)gGc>gAc	p.G302D	ZNF414_ENST00000393927.4_Missense_Mutation_p.G302D	NM_032370.2	NP_115746.2	Q96IQ9	ZN414_HUMAN	zinc finger protein 414	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)			lung(2)	2						GTCGGAGCCGCCCTGGGGTCT	0.706																																					p.G302D		Atlas-SNP	.											.	ZNF414	25	.	0			c.G905A						PASS	.						18	24	22					19																	8576390		2197	4295	6492	SO:0001583	missense	84330	exon6			GAGCCGCCCTGGG	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.905G>A	19.37:g.8576390C>T	ENSP00000255616:p.Gly302Asp	100	0	0		103	57	0.553398	NM_032370	A8MY94	Missense_Mutation	SNP	ENST00000255616.8	37	CCDS12205.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.266899	0.80469	.	.	ENSG00000133250	ENST00000393927;ENST00000255616	T;T	0.14766	2.48;2.48	4.53	4.53	0.55603	.	0.000000	0.52532	D	0.000080	T	0.25717	0.0626	L	0.29908	0.895	0.37759	D	0.926255	D;D	0.89917	1.0;0.998	D;D	0.91635	0.999;0.924	T	0.09185	-1.0686	10	0.72032	D	0.01	-19.322	14.3348	0.66581	0.0:1.0:0.0:0.0	.	302;302	Q96IQ9;A8MY94	ZN414_HUMAN;.	D	302	ENSP00000377504:G302D;ENSP00000255616:G302D	ENSP00000255616:G302D	G	-	2	0	ZNF414	8482390	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	2.815000	0.48018	2.231000	0.72958	0.313000	0.20887	GGC	.	.	none		0.706	ZNF414-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000460199.2	NM_032370		T	8576390	C	T	8576390	3	4	29	1	0	0	0	0	1	0	0	0	17906	739	26	2	293	2	ZNF414	19	8576390	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2792550	8576390	50552593	792	13033											
OR7G3	390883	hgsc.bcm.edu	37	chr19	9237554	9237554	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gaacagcatgaagaggatggGctgcagctccggatcccctg	10	6	14	11	1	0	2	0	1	0	1	2	5	2	4	3	3	4	4	3	3	2	0	rs138008445	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9237554G>A	ENST00000305444.2	-	1	72	c.73C>T	c.(73-75)Ccc>Tcc	p.P25S		NM_001001958.1	NP_001001958.1	Q8NG95	OR7G3_HUMAN	olfactory receptor, family 7, subfamily G, member 3	25						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						AAGAGGATGGGCTGCAGCTCC	0.517													G|||	11	0.00219649	0.0038	0.0014	5008	,	,		18583	0.0		0.004	False		,,,				2504	0.001				p.P25S		Atlas-SNP	.											.	OR7G3	41	.	0			c.C73T						PASS	.	G	SER/PRO	18,4388	25.3+/-52.1	0,18,2185	83	79	80		73	1.8	0.4	19	dbSNP_134	80	45,8555	30.1+/-81.4	0,45,4255	yes	missense	OR7G3	NM_001001958.1	74	0,63,6440	AA,AG,GG		0.5233,0.4085,0.4844	benign	25/313	9237554	63,12943	2203	4300	6503	SO:0001583	missense	390883	exon1			GGATGGGCTGCAG		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.73C>T	19.37:g.9237554G>A	ENSP00000302867:p.Pro25Ser	113	0	0		132	62	0.469697	NM_001001958	Q6IFJ6|Q96R99	Missense_Mutation	SNP	ENST00000305444.2	37	CCDS32899.1	5	0.0022893772893772895	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	10.52	1.371909	0.24857	0.004085	0.005233	ENSG00000170920	ENST00000305444	T	0.00424	7.45	4.02	1.83	0.25207	.	0.925765	0.08843	N	0.885581	T	0.00300	0.0009	M	0.71581	2.175	0.22050	N	0.999397	P	0.45474	0.859	B	0.34242	0.178	T	0.49960	-0.8883	10	0.54805	T	0.06	.	7.5109	0.27573	0.0906:0.0:0.7443:0.1651	.	25	Q8NG95	OR7G3_HUMAN	S	25	ENSP00000302867:P25S	ENSP00000302867:P25S	P	-	1	0	OR7G3	9098554	0.000000	0.05858	0.355000	0.25773	0.017000	0.09413	-0.911000	0.04050	0.469000	0.27268	-0.259000	0.10710	CCC	G|0.995;A|0.005	0.005	strong		0.517	OR7G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384611.1			A	9237554	G	A	9237554	3	1	29	1	0	0	0	0	1	0	0	0	11233	1203	42	2	868	2	OR7G3	19	9237554	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	661164	9237554	49891429	793	13034											
ZNF561	93134	hgsc.bcm.edu	37	chr19	9721218	9721218	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agacttgtggatgtagtgaaGgctttcccacattccttaca	10	13	9	9	0	0	2	0	1	0	1	2	3	2	3	2	2	1	2	2	2	3	5	rs138137635		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:9721218G>A	ENST00000302851.3	-	6	1482	c.1119C>T	c.(1117-1119)gcC>gcT	p.A373A	ZNF561_ENST00000354661.4_Silent_p.A237A|ZNF561_ENST00000326044.5_3'UTR|ZNF561_ENST00000424629.1_Silent_p.A304A|ZNF561_ENST00000495503.1_5'Flank	NM_152289.2	NP_689502.2	Q8N587	ZN561_HUMAN	zinc finger protein 561	373					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						ATGTAGTGAAGGCTTTCCCAC	0.438													G|||	1	0.000199681	0.0	0.0014	5008	,	,		21339	0.0		0.0	False		,,,				2504	0.0				p.A373A		Atlas-SNP	.											.	ZNF561	64	.	0			c.C1119T						PASS	.	G		0,4406		0,0,2203	124	116	119		1119	-0.2	0	19	dbSNP_134	119	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous	ZNF561	NM_152289.2		0,11,6492	AA,AG,GG		0.1279,0.0,0.0846		373/487	9721218	11,12995	2203	4300	6503	SO:0001819	synonymous_variant	93134	exon6			AGTGAAGGCTTTC	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.1119C>T	19.37:g.9721218G>A		57	0	0		61	33	0.540984	NM_152289	B4E2Q8|Q6PJS0	Silent	SNP	ENST00000302851.3	37	CCDS12216.2																																																																																			G|0.999;A|0.001	0.001	strong		0.438	ZNF561-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347272.2	NM_152289		A	9721218	G	A	9721218	2	1	29	1	0	0	0	0	0	0	0	1	18007	987	35	2		2	ZNF561	19	9721218	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	483664	9721218	49407765	794	13035											
KEAP1	9817	hgsc.bcm.edu	37	chr19	10602344	10602344	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	caccccgatgcggttacgggGcacgctcatgggggcgcagg	6	5	17	13	5	1	0	1	0	0	0	1	1	1	0	2	6	2	4	2	6	1	1	rs147613351		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:10602344G>A	ENST00000171111.5	-	3	1781	c.1234C>T	c.(1234-1236)Ccc>Tcc	p.P412S	KEAP1_ENST00000588024.1_5'Flank|CTC-429L19.3_ENST00000592671.1_RNA|KEAP1_ENST00000393623.2_Missense_Mutation_p.P412S	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	412					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)	CGGTTACGGGGCACGCTCATG	0.652													G|||	1	0.000199681	0.0	0.0	5008	,	,		15649	0.0		0.001	False		,,,				2504	0.0				p.P412S		Atlas-SNP	.											.	KEAP1	182	.	0			c.C1234T						PASS	.	G	SER/PRO,SER/PRO	0,4402		0,0,2201	34	29	31		1234,1234	5.6	1	19	dbSNP_134	31	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	KEAP1	NM_012289.3,NM_203500.1	74,74	0,5,6496	AA,AG,GG		0.0581,0.0,0.0385	probably-damaging,probably-damaging	412/625,412/625	10602344	5,12997	2201	4300	6501	SO:0001583	missense	9817	exon3			TACGGGGCACGCT	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.1234C>T	19.37:g.10602344G>A	ENSP00000171111:p.Pro412Ser	115	0	0		98	43	0.438776	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Missense_Mutation	SNP	ENST00000171111.5	37	CCDS12239.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	14.70	2.612736	0.46631	0.0	5.81E-4	ENSG00000079999	ENST00000171111;ENST00000393623	T;T	0.79749	-1.3;-1.3	5.6	5.6	0.85130	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	D	0.88336	0.6409	M	0.66297	2.02	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	D	0.87234	0.2262	10	0.41790	T	0.15	.	17.1192	0.86697	0.0:0.0:1.0:0.0	.	412	Q14145	KEAP1_HUMAN	S	412	ENSP00000171111:P412S;ENSP00000377245:P412S	ENSP00000171111:P412S	P	-	1	0	KEAP1	10463344	1.000000	0.71417	0.955000	0.39395	0.717000	0.41224	4.656000	0.61483	2.662000	0.90505	0.655000	0.94253	CCC	G|1.000;A|0.000	0.000	strong		0.652	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289		A	10602344	G	A	10602344	3	1	29	1	0	0	0	0	1	0	0	0	8150	1203	42	2	656	2	KEAP1	19	10602344	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	881126	10602344	48526639	795	13036											
ECSIT	51295	hgsc.bcm.edu	37	chr19	11617020	11617020	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagctctggccctgctgctgTcgctgcaggttgtcgtcttc	2	14	12	13	2	2	0	0	0	2	0	5	0	2	0	1	2	4	6	1	2	1	3	rs34645543	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:11617020T>G	ENST00000270517.7	-	8	1410	c.1275A>C	c.(1273-1275)cgA>cgC	p.R425R	ZNF653_ENST00000293771.5_5'Flank|ZNF653_ENST00000593191.1_5'Flank|ECSIT_ENST00000588998.1_3'UTR|ECSIT_ENST00000591104.1_3'UTR|CTC-398G3.6_ENST00000585656.1_5'Flank|ECSIT_ENST00000591352.1_5'Flank|ECSIT_ENST00000417981.2_Silent_p.R211R|ECSIT_ENST00000252440.7_3'UTR	NM_016581.4	NP_057665.2	Q9BQ95	ECSIT_HUMAN	ECSIT signalling integrator	425					BMP signaling pathway (GO:0030509)|innate immune response (GO:0045087)|mesoderm formation (GO:0001707)|oxidation-reduction process (GO:0055114)|regulation of oxidoreductase activity (GO:0051341)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	oxidoreductase activity, acting on NAD(P)H (GO:0016651)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	11						CCTGCTGCTGTCGCTGCAGGT	0.677													T|||	4	0.000798722	0.0	0.0014	5008	,	,		16330	0.0		0.003	False		,,,				2504	0.0				p.R425R		Atlas-SNP	.											.	ECSIT	32	.	0			c.A1275C						PASS	.	T	,,	3,4303		0,3,2150	52	53	53		,633,1275	0.6	0.9	19	dbSNP_126	53	13,8423		1,11,4206	no	utr-3,coding-synonymous,coding-synonymous	ECSIT	NM_001142464.2,NM_001142465.2,NM_016581.4	,,	1,14,6356	GG,GT,TT		0.1541,0.0697,0.1256	,,	,211/218,425/432	11617020	16,12726	2153	4218	6371	SO:0001819	synonymous_variant	51295	exon8			CTGCTGTCGCTGC	BC005119	CCDS12262.1, CCDS45979.1, CCDS45980.1, CCDS59353.1	19p13.2	2013-05-24	2013-05-24			ENSG00000130159		"Mitochondrial respiratory chain complex assembly factors"	29548	protein-coding gene	gene with protein product	"signaling intermediate in Toll pathway evolutionarily conserved ortholog (mouse)"	608388	"ECSIT homolog (Drosophila)"			10465784, 22982022	Standard	NM_001142464		Approved	SITPEC	uc002msb.3	Q9BQ95		ENST00000270517.7:c.1275A>C	19.37:g.11617020T>G		32	0	0		44	26	0.590909	NM_016581	E9PAN9|K7EMM0|Q96HQ7|Q9NYI1	Silent	SNP	ENST00000270517.7	37	CCDS12262.1																																																																																			T|0.999;G|0.001	0.001	strong		0.677	ECSIT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442603.2	NM_016581		G	11617020	T	G	11617020	2	3	29	1	0	0	0	0	0	0	0	1	4902	1654	58	5		5	ECSIT	19	11617020	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	1014676	11617020	47511963	796	13037											
ZNF763	284390	hgsc.bcm.edu	37	chr19	12087921	12087921	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgggctttgctggatatttcGcagaggaaactctacaggga	10	11	13	7	1	1	1	0	0	1	1	2	4	1	4	0	4	3	3	0	4	3	4	rs376310072	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:12087921G>C	ENST00000358987.3	+	2	199	c.72G>C	c.(70-72)tcG>tcC	p.S24S	ZNF763_ENST00000538752.1_Silent_p.S44S|ZNF763_ENST00000590798.1_Silent_p.S44S|ZNF763_ENST00000545530.1_Intron|ZNF763_ENST00000343949.5_Silent_p.S27S|ZNF763_ENST00000591944.1_Silent_p.S93S|ZNF763_ENST00000592625.1_Silent_p.S24S			Q0D2J5	ZN763_HUMAN	zinc finger protein 763	24	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)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)	15						TGGATATTTCGCAGAGGAAAC	0.493													N|||	4	0.000798722	0.0023	0.0	5008	,	,		18630	0.0		0.001	False		,,,				2504	0.0				p.S27S		Atlas-SNP	.											ZNF763,NS,carcinoma,+1,2	ZNF763	31	2	0			c.G81C						scavenged	.						150	152	151					19																	12087921		2203	4300	6503	SO:0001819	synonymous_variant	284390	exon2			TATTTCGCAGAGG	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.72G>C	19.37:g.12087921G>C		137	1	0.00729927		96	9	0.09375	NM_001012753	B3KRU3|B4DRE7	Silent	SNP	ENST00000358987.3	37																																																																																				.	.	alt		0.493	ZNF763-002	KNOWN	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000344158.1	NM_001012753		C	12087921	G	C	12087921	2	2	29	1	0	0	0	0	0	0	0	1	18152	1074	38	4		4	ZNF763	19	12087921	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	470901	12087921	47041062	797	13038											
BEST2	54831	hgsc.bcm.edu	37	chr19	12866544	12866544	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cctgtgtgtgcccatcttcaCcctcttgcagttcttcttct	3	17	6	15	0	6	0	1	0	5	0	6	0	6	0	3	0	2	2	3	0	0	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:12866544C>T	ENST00000549706.1	+	7	1154	c.830C>T	c.(829-831)aCc>aTc	p.T277I	BEST2_ENST00000042931.1_Missense_Mutation_p.T277I|BEST2_ENST00000553030.1_Missense_Mutation_p.T277I			Q8NFU1	BEST2_HUMAN	bestrophin 2	277					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						CCCATCTTCACCCTCTTGCAG	0.577																																					p.T277I		Atlas-SNP	.											.	BEST2	35	.	0			c.C830T						PASS	.						105	107	106					19																	12866544		2064	4233	6297	SO:0001583	missense	54831	exon6			TCTTCACCCTCTT	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.830C>T	19.37:g.12866544C>T	ENSP00000448310:p.Thr277Ile	123	0	0		147	21	0.142857	NM_017682	Q53YQ8|Q9NXP0	Missense_Mutation	SNP	ENST00000549706.1	37	CCDS42506.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.547910	0.86022	.	.	ENSG00000039987	ENST00000549706;ENST00000553030;ENST00000042931	D;D;D	0.99005	-5.32;-5.32;-5.32	4.58	4.58	0.56647	.	0.000000	0.85682	D	0.000000	D	0.99554	0.9840	H	0.97265	3.97	0.80722	D	1	D	0.69078	0.997	D	0.76071	0.987	D	0.97764	1.0222	10	0.87932	D	0	-32.3086	16.2931	0.82759	0.0:1.0:0.0:0.0	.	277	Q8NFU1	BEST2_HUMAN	I	277	ENSP00000448310:T277I;ENSP00000447203:T277I;ENSP00000042931:T277I	ENSP00000042931:T277I	T	+	2	0	BEST2	12727544	1.000000	0.71417	1.000000	0.80357	0.824000	0.46624	7.507000	0.81676	2.362000	0.80069	0.650000	0.86243	ACC	.	.	none		0.577	BEST2-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403343.1	NM_017682		T	12866544	C	T	12866544	3	4	29	1	0	0	0	0	1	0	0	0	1405	507	18	2	852	2	BEST2	19	12866544	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	778623	12866544	46262439	798	13039											
OR7A10	390892	hgsc.bcm.edu	37	chr19	14952301	14952301	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcataatgaccatgtagtgcAgagggtgacagatggccaca	13	8	12	8	0	1	4	1	2	0	2	1	4	1	4	2	2	1	2	2	2	2	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:14952301A>C	ENST00000248058.1	-	1	388	c.389T>G	c.(388-390)cTg>cGg	p.L130R		NM_001005190.1	NP_001005190.1	O76100	OR7AA_HUMAN	olfactory receptor, family 7, subfamily A, member 10	130						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)					CATGTAGTGCAGAGGGTGACA	0.463																																					p.L130R		Atlas-SNP	.											.	OR7A10	33	.	0			c.T389G						PASS	.						88	80	82					19																	14952301		2203	4300	6503	SO:0001583	missense	390892	exon1			TAGTGCAGAGGGT		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.389T>G	19.37:g.14952301A>C	ENSP00000248058:p.Leu130Arg	88	0	0		100	49	0.49	NM_001005190	Q6IFP0|Q96R97	Missense_Mutation	SNP	ENST00000248058.1	37	CCDS32936.1	.	.	.	.	.	.	.	.	.	.	a	12.67	2.008986	0.35415	.	.	ENSG00000127515	ENST00000248058	T	0.01516	4.81	2.8	2.8	0.32819	GPCR, rhodopsin-like superfamily (1);	0.000000	0.31747	U	0.007131	T	0.15912	0.0383	H	0.97983	4.12	0.30328	N	0.786887	D	0.89917	1.0	D	0.80764	0.994	T	0.18745	-1.0327	10	0.87932	D	0	.	9.1033	0.36683	1.0:0.0:0.0:0.0	.	130	O76100	OR7AA_HUMAN	R	130	ENSP00000248058:L130R	ENSP00000248058:L130R	L	-	2	0	OR7A10	14813301	1.000000	0.71417	0.951000	0.38953	0.026000	0.11368	7.589000	0.82641	1.306000	0.44926	0.163000	0.16589	CTG	.	.	none		0.463	OR7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466520.1	NM_001005190		C	14952301	A	C	14952301	3	2	29	1	0	0	0	0	1	0	0	0	11223	188	7	5	544	5	OR7A10	19	14952301	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	2085757	14952301	44176682	799	13040											
BRD4	23476	hgsc.bcm.edu	37	chr19	15349962	15349962	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgctcctctttctcccgagcGgcgcggcggaactgctcgaa	5	8	12	16	7	2	0	0	0	2	0	5	3	3	1	2	3	3	2	2	3	2	1	rs118000160	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:15349962G>A	ENST00000263377.2	-	18	3911	c.3690C>T	c.(3688-3690)gcC>gcT	p.A1230A		NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	1230	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)			TCTCCCGAGCGGCGCGGCGGA	0.657			T	C15orf55	lethal midline carcinoma of young people								g|||	13	0.00259585	0.0008	0.0029	5008	,	,		15419	0.0		0.004	False		,,,				2504	0.0061				p.A1230A		Atlas-SNP	.		Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	.	BRD4	172	.	0			c.C3690T						PASS	.			4,4402	8.1+/-20.4	0,4,2199	29	31	30		3690	-9.5	0	19	dbSNP_132	30	66,8532	38.8+/-94.9	0,66,4233	no	coding-synonymous	BRD4	NM_058243.2		0,70,6432	AA,AG,GG		0.7676,0.0908,0.5383		1230/1363	15349962	70,12934	2203	4299	6502	SO:0001819	synonymous_variant	23476	exon18			CCGAGCGGCGCGG	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.3690C>T	19.37:g.15349962G>A		116	0	0		104	55	0.528846	NM_058243	O60433|Q4G0X8|Q86YS8|Q96PD3	Silent	SNP	ENST00000263377.2	37	CCDS12328.1																																																																																			G|0.997;A|0.003	0.003	strong		0.657	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243		A	15349962	G	A	15349962	2	1	29	1	0	0	0	0	0	0	0	1	1506	1103	39	1		1	BRD4	19	15349962	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	397661	15349962	43779021	800	13041											
AKAP8L	26993	hgsc.bcm.edu	37	chr19	15491357	15491357	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgctccagcttcttgctgaTgagcttgttgttgagaatac	7	14	11	9	1	1	3	0	3	1	1	2	4	2	3	1	0	4	6	1	0	2	6			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:15491357T>C	ENST00000397410.5	-	13	1733	c.1603A>G	c.(1603-1605)Atc>Gtc	p.I535V	AKAP8L_ENST00000595465.2_Missense_Mutation_p.I474V|AKAP8_ENST00000269701.2_5'Flank|AC005785.2_ENST00000597164.2_RNA	NM_014371.2	NP_055186.2	Q9ULX6	AKP8L_HUMAN	A kinase (PRKA) anchor protein 8-like	535						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						TTCTTGCTGATGAGCTTGTTG	0.617																																					p.I535V		Atlas-SNP	.											.	AKAP8L	64	.	0			c.A1603G						PASS	.						62	69	67					19																	15491357		2040	4188	6228	SO:0001583	missense	26993	exon13			TGCTGATGAGCTT	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.1603A>G	19.37:g.15491357T>C	ENSP00000380557:p.Ile535Val	98	0	0		93	48	0.516129	NM_014371	B4DJ74|B5BU90|O94792|Q96J58|Q9NRQ0|Q9UGM0	Missense_Mutation	SNP	ENST00000397410.5	37	CCDS46005.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.096921	0.76870	.	.	ENSG00000011243	ENST00000397410	T	0.43294	0.95	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.49508	0.1561	N	0.25890	0.77	0.42859	D	0.994105	P;P	0.47604	0.898;0.898	D;D	0.68192	0.956;0.956	T	0.49606	-0.8922	10	0.45353	T	0.12	-15.6199	12.1116	0.53842	0.0:0.0:0.0:1.0	.	474;535	B4DJ74;Q9ULX6	.;AKP8L_HUMAN	V	535	ENSP00000380557:I535V	ENSP00000380557:I535V	I	-	1	0	AKAP8L	15352357	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.505000	0.60421	1.854000	0.53819	0.459000	0.35465	ATC	.	.	none		0.617	AKAP8L-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461301.2	NM_014371		C	15491357	T	C	15491357	3	2	29	1	0	0	0	0	1	0	0	0	458	1464	51	3	345	3	AKAP8L	19	15491357	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	141395	15491357	43637626	801	13042											
AP1M1	8907	hgsc.bcm.edu	37	chr19	16318904	16318904	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gttatcatctacgagctgctGgacgagctcatggacttcgg	8	11	12	10	3	3	0	2	0	1	0	4	4	3	2	0	3	4	4	0	3	2	3	rs143435975	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:16318904G>C	ENST00000291439.3	+	4	791	c.342G>C	c.(340-342)ctG>ctC	p.L114L	AP1M1_ENST00000429941.2_Silent_p.L114L|AP1M1_ENST00000541844.1_Silent_p.L42L|AP1M1_ENST00000590756.1_Silent_p.L42L|AP1M1_ENST00000444449.2_Silent_p.L114L	NM_032493.3	NP_115882.1	Q9BXS5	AP1M1_HUMAN	adaptor-related protein complex 1, mu 1 subunit	114					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						ACGAGCTGCTGGACGAGCTCA	0.622													G|||	3	0.000599042	0.0	0.0	5008	,	,		16238	0.001		0.002	False		,,,				2504	0.0				p.L114L		Atlas-SNP	.											.	AP1M1	48	.	0			c.G342C						PASS	.	G	,	8,4398	14.3+/-33.2	0,8,2195	112	104	107		342,342	1.5	1	19	dbSNP_134	107	56,8544	34.8+/-89.0	0,56,4244	no	coding-synonymous,coding-synonymous	AP1M1	NM_001130524.1,NM_032493.3	,	0,64,6439	CC,CG,GG		0.6512,0.1816,0.4921	,	114/436,114/424	16318904	64,12942	2203	4300	6503	SO:0001819	synonymous_variant	8907	exon4			GCTGCTGGACGAG		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.342G>C	19.37:g.16318904G>C		109	0	0		112	58	0.517857	NM_001130524	Q4TTY5	Silent	SNP	ENST00000291439.3	37	CCDS12342.1																																																																																			G|0.996;C|0.004	0.004	strong		0.622	AP1M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460492.1	NM_032493		C	16318904	G	C	16318904	2	2	29	1	0	0	0	0	0	0	0	1	734	1335	47	4		4	AP1M1	19	16318904	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	827547	16318904	42810079	802	13043											
USHBP1	83878	hgsc.bcm.edu	37	chr19	17367354	17367354	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgggccagcctgggtccccaGaatggcctgcaccatggctt	6	8	13	14	0	0	1	0	0	0	1	1	1	1	1	6	4	2	2	6	4	1	1	rs141680124	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:17367354G>A	ENST00000252597.3	-	9	1569	c.1396C>T	c.(1396-1398)Ctg>Ttg	p.L466L	USHBP1_ENST00000431146.2_Silent_p.L402L|AC010646.3_ENST00000594059.1_5'Flank	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						TGGGTCCCCAGAATGGCCTGC	0.612													G|||	21	0.00419329	0.0	0.013	5008	,	,		18612	0.0		0.007	False		,,,				2504	0.0051				p.L466L		Atlas-SNP	.											.	USHBP1	85	.	0			c.C1396T						PASS	.	G		11,4395	19.1+/-41.9	0,11,2192	74	77	76		1396	3.8	1	19	dbSNP_134	76	96,8504	51.9+/-112.3	0,96,4204	no	coding-synonymous	USHBP1	NM_031941.3		0,107,6396	AA,AG,GG		1.1163,0.2497,0.8227		466/704	17367354	107,12899	2203	4300	6503	SO:0001819	synonymous_variant	83878	exon9			TCCCCAGAATGGC	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.1396C>T	19.37:g.17367354G>A		60	0	0		54	31	0.574074	NM_031941		Silent	SNP	ENST00000252597.3	37	CCDS12353.1																																																																																			G|0.992;A|0.008	0.008	strong		0.612	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941		A	17367354	G	A	17367354	2	1	29	1	0	0	0	0	0	0	0	1	17052	933	33	2		2	USHBP1	19	17367354	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1048450	17367354	41761629	803	13044											
ARRDC2	27106	hgsc.bcm.edu	37	chr19	18121454	18121454	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagagccccttcccgcttccGcaggaccccgacatgagcct	7	6	9	19	3	0	2	0	1	0	1	2	4	2	3	7	1	2	2	7	1	0	2	rs147293119	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:18121454G>C	ENST00000222250.4	+	7	1229	c.1086G>C	c.(1084-1086)ccG>ccC	p.P362P	ARRDC2_ENST00000379656.3_Silent_p.P357P	NM_015683.1	NP_056498.1	Q8TBH0	ARRD2_HUMAN	arrestin domain containing 2	362					signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|prostate(1)	12						TCCCGCTTCCGCAGGACCCCG	0.637													G|||	9	0.00179712	0.0	0.0029	5008	,	,		17520	0.0		0.007	False		,,,				2504	0.0				p.P362P		Atlas-SNP	.											.	ARRDC2	60	.	0			c.G1086C						PASS	.	G	,	2,4404	4.2+/-10.8	0,2,2201	63	62	63		1071,1086	-6.8	0	19	dbSNP_134	63	28,8572	20.4+/-63.3	0,28,4272	no	coding-synonymous,coding-synonymous	ARRDC2	NM_001025604.1,NM_015683.1	,	0,30,6473	CC,CG,GG		0.3256,0.0454,0.2307	,	357/403,362/408	18121454	30,12976	2203	4300	6503	SO:0001819	synonymous_variant	27106	exon7			GCTTCCGCAGGAC		CCDS12370.1, CCDS32956.1	19p13.12	2008-02-05				ENSG00000105643			25225	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015683		Approved	CLONE24945, PP2703	uc002nhv.3	Q8TBH0		ENST00000222250.4:c.1086G>C	19.37:g.18121454G>C		34	0	0		48	25	0.520833	NM_015683	B2RBG9|O95895|Q6ZRV9|Q8WYG6	Silent	SNP	ENST00000222250.4	37	CCDS12370.1																																																																																			G|0.998;C|0.002	0.002	strong		0.637	ARRDC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466845.1	NM_015683		C	18121454	G	C	18121454	2	2	29	1	0	0	0	0	0	0	0	1	983	1074	38	4		4	ARRDC2	19	18121454	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	754100	18121454	41007529	804	13045											
TSHZ3	57616	hgsc.bcm.edu	37	chr19	31770506	31770506	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcatggcaggaaaactcggCggccggggagttctggtagc	8	8	16	9	3	2	0	1	0	1	0	3	2	2	2	1	7	2	3	1	7	3	3	rs111618794	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:31770506C>T	ENST00000240587.4	-	2	520	c.193G>A	c.(193-195)Gcc>Acc	p.A65T		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	65					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)					GAAAACTCGGCGGCCGGGGAG	0.592													C|||	6	0.00119808	0.0	0.0043	5008	,	,		15202	0.0		0.003	False		,,,				2504	0.0				p.A65T		Atlas-SNP	.											TSHZ3_ENST00000240587,NS,carcinoma,+2,1	TSHZ3	549	1	0			c.G193A						PASS	.	C	THR/ALA	0,3914		0,0,1957	32	34	34		193	5.9	0.2	19	dbSNP_132	34	14,8248		0,14,4117	yes	missense	TSHZ3	NM_020856.2	58	0,14,6074	TT,TC,CC		0.1695,0.0,0.115	possibly-damaging	65/1082	31770506	14,12162	1957	4131	6088	SO:0001583	missense	57616	exon2			ACTCGGCGGCCGG	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.193G>A	19.37:g.31770506C>T	ENSP00000240587:p.Ala65Thr	71	0	0		41	19	0.463415	NM_020856	Q9H0G6|Q9P254	Missense_Mutation	SNP	ENST00000240587.4	37	CCDS12421.2	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	16.97	3.269545	0.59540	0.0	0.001695	ENSG00000121297	ENST00000240587	T	0.12984	2.63	5.92	5.92	0.95590	.	0.000000	0.64402	U	0.000001	T	0.24736	0.0600	L	0.40543	1.245	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	T	0.00394	-1.1767	10	0.87932	D	0	-15.0968	20.3116	0.98642	0.0:1.0:0.0:0.0	.	65	Q63HK5	TSH3_HUMAN	T	65	ENSP00000240587:A65T	ENSP00000240587:A65T	A	-	1	0	TSHZ3	36462346	1.000000	0.71417	0.217000	0.23759	0.270000	0.26580	5.737000	0.68606	2.793000	0.96121	0.650000	0.86243	GCC	C|0.998;T|0.002	0.002	strong		0.592	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		T	31770506	C	T	31770506	3	4	29	1	0	0	0	0	1	0	0	0	16640	768	27	1	3056	1	TSHZ3	19	31770506	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	13649052	31770506	27358477	805	13046											
RHPN2	85415	hgsc.bcm.edu	37	chr19	33517507	33517507	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagctcagctccagccgcaCttgctcccgcacctttgagt	7	9	9	16	2	1	1	1	1	0	0	3	2	3	1	4	0	4	5	4	0	1	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:33517507C>T	ENST00000254260.3	-	3	252	c.217G>A	c.(217-219)Gtg>Atg	p.V73M	RHPN2_ENST00000400226.4_De_novo_Start_OutOfFrame	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	73					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)		p.V73M(2)		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)					TCCAGCCGCACTTGCTCCCGC	0.552																																					p.V73M		Atlas-SNP	.											RHPN2,face,carcinoma,0,2	RHPN2	107	2	2	Substitution - Missense(2)	NS(1)|skin(1)	c.G217A						scavenged	.						84	83	83					19																	33517507		2203	4300	6503	SO:0001583	missense	85415	exon3			GCCGCACTTGCTC	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.217G>A	19.37:g.33517507C>T	ENSP00000254260:p.Val73Met	15	0	0		23	2	0.0869565	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	C	18.08	3.542997	0.65198	.	.	ENSG00000131941	ENST00000254260	T	0.39787	1.06	3.88	3.88	0.44766	.	0.000000	0.85682	D	0.000000	T	0.64853	0.2636	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.71984	-0.4427	10	0.87932	D	0	11.9954	16.025	0.80536	0.0:1.0:0.0:0.0	.	73	Q8IUC4	RHPN2_HUMAN	M	73	ENSP00000254260:V73M	ENSP00000254260:V73M	V	-	1	0	RHPN2	38209347	1.000000	0.71417	1.000000	0.80357	0.343000	0.28985	7.267000	0.78462	2.167000	0.68274	0.557000	0.71058	GTG	.	.	none		0.552	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103		T	33517507	C	T	33517507	3	4	29	1	0	0	0	0	1	0	0	0	13366	565	20	2	1895	2	RHPN2	19	33517507	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1747001	33517507	25611476	806	13047											
CHST8	64377	hgsc.bcm.edu	37	chr19	34262922	34262922	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aacccacagagagggtcactCgggacttatccagtggggcc	10	6	13	12	1	1	1	1	0	0	1	3	3	2	2	3	4	1	0	3	4	2	1	rs149660944	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:34262922C>T	ENST00000262622.4	+	4	987	c.229C>T	c.(229-231)Cgg>Tgg	p.R77W	CHST8_ENST00000434302.1_Missense_Mutation_p.R77W|CHST8_ENST00000438847.3_Missense_Mutation_p.R77W	NM_022467.3	NP_071912.2	Q9H2A9	CHST8_HUMAN	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 8	77			R -> W (probable disease-associated mutation found in generalized non- inflammatory peeling skin syndrome type A; results in decreased enzyme activity; the mutant protein shows reduced glycosylation; dbSNP:rs149660944). {ECO:0000269|PubMed:22289416}.		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)					GAGGGTCACTCGGGACTTATC	0.652													C|||	7	0.00139776	0.0	0.0058	5008	,	,		12973	0.0		0.003	False		,,,				2504	0.0				p.R77W		Atlas-SNP	.											.	CHST8	70	.	0			c.C229T						PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG	3,4395	6.2+/-15.9	0,3,2196	34	44	41		229,229,229	4	0	19	dbSNP_134	41	62,8536	38.3+/-94.2	0,62,4237	yes	missense,missense,missense	CHST8	NM_001127895.1,NM_001127896.1,NM_022467.3	101,101,101	0,65,6433	TT,TC,CC		0.7211,0.0682,0.5002	possibly-damaging,possibly-damaging,possibly-damaging	77/425,77/425,77/425	34262922	65,12931	2199	4299	6498	SO:0001583	missense	64377	exon5			GTCACTCGGGACT	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.229C>T	19.37:g.34262922C>T	ENSP00000262622:p.Arg77Trp	112	0	0		103	51	0.495146	NM_001127895	Q9H3N2	Missense_Mutation	SNP	ENST00000262622.4	37	CCDS12433.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	14.66	2.600258	0.46423	6.82E-4	0.007211	ENSG00000124302	ENST00000434302;ENST00000438847;ENST00000262622	T;T;T	0.75704	-0.96;-0.96;-0.96	5.08	4.01	0.46588	.	2.113150	0.02181	N	0.060503	T	0.57710	0.2072	N	0.24115	0.695	0.09310	N	1	P	0.51537	0.946	B	0.37422	0.249	T	0.60786	-0.7194	10	0.72032	D	0.01	-13.224	12.9913	0.58620	0.0:0.8358:0.1642:0.0	.	77	Q9H2A9	CHST8_HUMAN	W	77	ENSP00000392604:R77W;ENSP00000393879:R77W;ENSP00000262622:R77W	ENSP00000262622:R77W	R	+	1	2	CHST8	38954762	0.000000	0.05858	0.002000	0.10522	0.019000	0.09904	0.297000	0.19101	1.067000	0.40740	0.478000	0.44815	CGG	C|0.995;T|0.005	0.005	strong		0.652	CHST8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451453.1	NM_022467		T	34262922	C	T	34262922	3	4	29	1	0	0	0	0	1	0	0	0	3412	875	31	1	239	1	CHST8	19	34262922	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	745415	34262922	24866061	807	13048											
MRPS12	6183	hgsc.bcm.edu	37	chr19	39421979	39421979	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggcctcaacacgtccctaacTtgtggtaagtgggggacttg	8	10	13	10	1	1	0	1	0	0	0	2	1	2	1	2	4	2	1	2	4	3	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:39421979T>G	ENST00000407800.2	+	1	386	c.45T>G	c.(43-45)acT>acG	p.T15T	MRPS12_ENST00000308018.4_Silent_p.T15T|SARS2_ENST00000221431.6_5'Flank|SARS2_ENST00000600042.1_5'Flank|SARS2_ENST00000430193.3_5'Flank|SARS2_ENST00000594171.1_5'Flank|CTC-360G5.8_ENST00000599996.1_Intron|MRPS12_ENST00000402029.3_Silent_p.T15T|SARS2_ENST00000448145.2_Intron	NM_021107.1	NP_066930.1	O15235	RT12_HUMAN	mitochondrial ribosomal protein S12	15					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|small ribosomal subunit (GO:0015935)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(1)|large_intestine(1)	2	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)			CGTCCCTAACTTGTGGTAAGT	0.592																																					p.T15T		Atlas-SNP	.											.	MRPS12	11	.	0			c.T45G						PASS	.						119	111	114					19																	39421979		2203	4300	6503	SO:0001819	synonymous_variant	6183	exon2			CCTAACTTGTGGT	Y11681	CCDS12525.1	19q13.1-q13.2	2012-09-13			ENSG00000128626	ENSG00000128626		"Mitochondrial ribosomal proteins / small subunits"	10380	protein-coding gene	gene with protein product		603021		RPMS12		9545647, 9790755	Standard	NM_021107		Approved	RPS12, RPSM12	uc002oke.3	O15235		ENST00000407800.2:c.45T>G	19.37:g.39421979T>G		84	0	0		94	27	0.287234	NM_033362	Q53X98	Silent	SNP	ENST00000407800.2	37	CCDS12525.1																																																																																			.	.	none		0.592	MRPS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463154.1			G	39421979	T	G	39421979	2	3	29	1	0	0	0	0	0	0	0	1	9832	1596	56	5		5	MRPS12	19	39421979	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	5159057	39421979	19707004	808	13049											
CYP2A7	1549	hgsc.bcm.edu	37	chr19	41382544	41382544	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagctggggtctctcagcacGgagcccagcatagggaacac	11	5	13	12	1	2	0	1	0	1	0	3	2	2	2	1	4	5	3	1	4	3	1	rs116333747	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:41382544G>A	ENST00000301146.4	-	8	1732	c.1191C>T	c.(1189-1191)tcC>tcT	p.S397S	CTC-490E21.12_ENST00000601627.1_Intron|CYP2A7_ENST00000291764.3_Silent_p.S346S	NM_000764.2	NP_000755.2	P20853	CP2A7_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 7	397						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)			CTCTCAGCACGGAGCCCAGCA	0.552													.|||	29	0.00579073	0.0144	0.0	5008	,	,		19465	0.0		0.004	False		,,,				2504	0.0061				p.S397S		Atlas-SNP	.											.	CYP2A7	71	.	0			c.C1191T						PASS	.	G	,	46,4360	48.9+/-83.8	1,44,2158	112	98	103		1191,1038	-3	0.6	19	dbSNP_132	103	55,8545	33.8+/-87.4	2,51,4247	no	coding-synonymous,coding-synonymous	CYP2A7	NM_000764.2,NM_030589.2	,	3,95,6405	AA,AG,GG		0.6395,1.044,0.7766	,	397/495,346/444	41382544	101,12905	2203	4300	6503	SO:0001819	synonymous_variant	1549	exon8			CAGCACGGAGCCC	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.1191C>T	19.37:g.41382544G>A		202	0	0		254	119	0.468504	NM_000764	Q13121	Silent	SNP	ENST00000301146.4	37	CCDS12569.1																																																																																			G|0.992;A|0.008	0.008	strong		0.552	CYP2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463269.2	NM_030589		A	41382544	G	A	41382544	2	1	29	1	0	0	0	0	0	0	0	1	4165	1103	39	1		1	CYP2A7	19	41382544	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1960565	41382544	17746439	809	13050											
CYP2B6	1555	hgsc.bcm.edu	37	chr19	41497346	41497346	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttgggaaaccttctgcagAtggatagaagaggcctactc	11	11	11	8	0	1	3	0	0	1	3	2	5	1	5	2	3	3	1	2	3	4	5	rs35303484	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:41497346A>G	ENST00000324071.4	+	1	143	c.136A>G	c.(136-138)Atg>Gtg	p.M46V	CYP2B6_ENST00000598834.1_3'UTR	NM_000767.4	NP_000758.1	P20813	CP2B6_HUMAN	cytochrome P450, family 2, subfamily B, polypeptide 6	46			M -> V (in allele CYP2B6*11; dbSNP:rs35303484). {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)	CCTTCTGCAGATGGATAGAAG	0.567													A|||	6	0.00119808	0.0008	0.0	5008	,	,		18573	0.0		0.004	False		,,,				2504	0.001				p.M46V		Atlas-SNP	.											.	CYP2B6	79	.	0			c.A136G	GRCh37	CM042692	CYP2B6	M	rs35303484	PASS	.	A	VAL/MET	5,4401	9.9+/-24.2	0,5,2198	147	165	159		136	0.6	0.8	19	dbSNP_126	159	32,8568	22.2+/-67.0	0,32,4268	no	missense	CYP2B6	NM_000767.4	21	0,37,6466	GG,GA,AA		0.3721,0.1135,0.2845	benign	46/492	41497346	37,12969	2203	4300	6503	SO:0001583	missense	1555	exon1			CTGCAGATGGATA	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.136A>G	19.37:g.41497346A>G	ENSP00000324648:p.Met46Val	28	0	0		32	16	0.5	NM_000767	B4DWP3|Q2V565|Q9UK46	Missense_Mutation	SNP	ENST00000324071.4	37	CCDS12570.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	7.340	0.620661	0.14193	0.001135	0.003721	ENSG00000197408	ENST00000324071	T	0.01228	5.14	3.1	0.644	0.17776	.	0.174316	0.40064	U	0.001199	T	0.01061	0.0035	N	0.17901	0.54	0.40857	D	0.983801	P	0.40431	0.717	B	0.38106	0.265	T	0.71886	-0.4457	10	0.35671	T	0.21	.	6.9443	0.24510	0.5213:0.4787:0.0:0.0	rs35303484	46	P20813	CP2B6_HUMAN	V	46	ENSP00000324648:M46V	ENSP00000324648:M46V	M	+	1	0	CYP2B6	46189186	1.000000	0.71417	0.845000	0.33349	0.095000	0.18619	0.538000	0.23160	0.388000	0.25054	-1.020000	0.02445	ATG	A|0.997;G|0.003;T|0.000	0.003	strong		0.567	CYP2B6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463260.1	NM_000767		G	41497346	A	G	41497346	3	3	29	1	0	0	0	0	1	0	0	0	4166	333	12	3	138	3	CYP2B6	19	41497346	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	114802	41497346	17631637	810	13051											
CYP2S1	29785	hgsc.bcm.edu	37	chr19	41703793	41703793	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcgaggagctgatccaggcGgaggcccggtgtctggtgga	6	6	20	9	3	1	1	0	1	1	0	2	5	2	4	2	8	1	1	2	8	0	0	rs57266494	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:41703793G>A	ENST00000310054.4	+	3	669	c.453G>A	c.(451-453)gcG>gcA	p.A151A	CYP2S1_ENST00000542619.1_Intron	NM_030622.6	NP_085125.1	Q96SQ9	CP2S1_HUMAN	cytochrome P450, family 2, subfamily S, polypeptide 1	151					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(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(2)	14						TGATCCAGGCGGAGGCCCGGT	0.622													g|||	45	0.00898562	0.0015	0.0144	5008	,	,		15828	0.0		0.0288	False		,,,				2504	0.0041				p.A151A		Atlas-SNP	.											.	CYP2S1	47	.	0			c.G453A						PASS	.	G		44,4362	46.7+/-81.2	1,42,2160	57	56	56		453	-9.7	0.2	19	dbSNP_129	56	368,8232	121.7+/-180.7	6,356,3938	no	coding-synonymous	CYP2S1	NM_030622.6		7,398,6098	AA,AG,GG		4.2791,0.9986,3.1678		151/505	41703793	412,12594	2203	4300	6503	SO:0001819	synonymous_variant	29785	exon3			CCAGGCGGAGGCC	AA301039	CCDS12573.1	19q13.2	2013-11-11	2003-01-14		ENSG00000167600	ENSG00000167600		"Cytochrome P450s"	15654	protein-coding gene	gene with protein product		611529	"cytochrome P450, subfamily IIS, polypeptide 1"			11181079	Standard	NM_030622		Approved		uc002opw.3	Q96SQ9	OTTHUMG00000182721	ENST00000310054.4:c.453G>A	19.37:g.41703793G>A		46	0	0		52	22	0.423077	NM_030622	Q9BZ66	Silent	SNP	ENST00000310054.4	37	CCDS12573.1																																																																																			G|0.975;A|0.025	0.025	strong		0.622	CYP2S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463287.1			A	41703793	G	A	41703793	2	1	29	1	0	0	0	0	0	0	0	1	4176	1103	39	1		1	CYP2S1	19	41703793	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	206447	41703793	17425190	811	13052											
CEACAM1	634	hgsc.bcm.edu	37	chr19	43031318	43031318	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggatgcattggggtatattGtctctcgaccgctgtttgcg	5	14	14	8	3	1	0	0	0	1	0	3	2	1	1	1	3	2	4	1	3	2	5	rs199627333		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:43031318G>A	ENST00000161559.6	-	2	433	c.299C>T	c.(298-300)aCa>aTa	p.T100I	CEACAM1_ENST00000358394.3_Missense_Mutation_p.T100I|CEACAM1_ENST00000308072.4_Missense_Mutation_p.T60I|CEACAM1_ENST00000351134.3_Missense_Mutation_p.T100I|LIPE-AS1_ENST00000594624.2_RNA|CEACAM1_ENST00000403461.1_Missense_Mutation_p.T100I|CEACAM1_ENST00000352591.5_Missense_Mutation_p.T100I|LIPE-AS1_ENST00000457234.2_RNA|CEACAM1_ENST00000599389.1_Missense_Mutation_p.T100I|CEACAM1_ENST00000403444.3_Missense_Mutation_p.T100I|LIPE-AS1_ENST00000594688.1_RNA	NM_001712.4	NP_001703.2	P13688	CEAM1_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein)	100	Ig-like V-type.				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)	GGGGTATATTGTCTCTCGACC	0.473																																					p.T100I		Atlas-SNP	.											.	CEACAM1	43	.	0			c.C299T						PASS	.						358	304	322					19																	43031318		2203	4300	6503	SO:0001583	missense	634	exon2			TATATTGTCTCTC	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.299C>T	19.37:g.43031318G>A	ENSP00000161559:p.Thr100Ile	275	0	0		313	13	0.0415335	NM_001184816	A6NE38|A8MY49|O60430|Q069I7|Q13854|Q13857|Q13858|Q13859|Q13860|Q15600|Q15601|Q16170|Q5UB49|Q7KYP5|Q96CA7|Q9UQV9	Missense_Mutation	SNP	ENST00000161559.6	37	CCDS12609.1	.	.	.	.	.	.	.	.	.	.	g	8.472	0.857824	0.17178	.	.	ENSG00000079385	ENST00000161559;ENST00000358394;ENST00000351134;ENST00000446434;ENST00000378065;ENST00000352591;ENST00000403444;ENST00000403461;ENST00000308072;ENST00000377806;ENST00000344391;ENST00000403136	T;T;T;T;T;T;T	0.68479	-0.33;-0.33;-0.33;-0.33;-0.33;-0.33;-0.33	4.41	-0.431	0.12295	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.46737	0.1408	L	0.33485	1.01	0.09310	N	1	B;B;B;B;B;B;B;B;B;B	0.31989	0.35;0.005;0.001;0.003;0.001;0.005;0.197;0.012;0.022;0.054	B;B;B;B;B;B;B;B;B;B	0.30495	0.103;0.005;0.003;0.006;0.002;0.01;0.116;0.007;0.051;0.026	T	0.26710	-1.0095	9	0.24483	T	0.36	.	3.4213	0.07395	0.1214:0.1385:0.5979:0.1422	.	100;100;100;100;100;100;100;100;100;100	P13688-7;P13688-10;P13688-3;P13688-4;P13688-2;P13688-11;P13688-6;P13688-5;P13688-8;P13688	.;.;.;.;.;.;.;.;.;CEAM1_HUMAN	I	100;100;100;127;60;100;100;100;60;100;100;100	ENSP00000161559:T100I;ENSP00000351165:T100I;ENSP00000325946:T100I;ENSP00000244291:T100I;ENSP00000384709:T100I;ENSP00000384083:T100I;ENSP00000312184:T60I	ENSP00000161559:T100I	T	-	2	0	CEACAM1	47723158	0.000000	0.05858	0.003000	0.11579	0.001000	0.01503	-1.426000	0.02443	-0.044000	0.13491	-2.357000	0.00240	ACA	.	.	weak		0.473	CEACAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321190.2	NM_001712		A	43031318	G	A	43031318	3	1	29	1	0	0	0	0	1	0	0	0	3189	1377	48	2	1410	2	CEACAM1	19	43031318	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1327525	43031318	16097665	812	13053											
PSG11	5680	hgsc.bcm.edu	37	chr19	43519324	43519324	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgccagtggctgagttacgaGcagagcaagcatagagccca	12	5	13	11	2	0	3	0	1	0	2	0	4	0	3	2	1	5	5	2	1	3	2	rs139355393		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:43519324G>A	ENST00000401740.1	-	4	1011	c.908C>T	c.(907-909)gCt>gTt	p.A303V	PSG11_ENST00000595312.1_5'Flank|PSG11_ENST00000320078.7_Missense_Mutation_p.A303V|PSG11_ENST00000306322.7_Missense_Mutation_p.A181V|PSG11_ENST00000403486.1_Missense_Mutation_p.A181V			Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 11	312	Ig-like C2-type 2.				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)				TGAGTTACGAGCAGAGCAAGC	0.458													.|||	1	0.000199681	0.0	0.0	5008	,	,		20595	0.001		0.0	False		,,,				2504	0.0				p.A303V		Atlas-SNP	.											.	PSG11	57	.	0			c.C908T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA	2,4396	4.2+/-10.8	1,0,2198	147	142	144		542,908,542	-2	0	19	dbSNP_134	144	6,8588	5.0+/-18.6	0,6,4291	yes	missense,missense,missense	PSG11	NM_001113410.1,NM_002785.2,NM_203287.1	64,64,64	1,6,6489	AA,AG,GG		0.0698,0.0455,0.0616	,,	181/214,303/336,181/214	43519324	8,12984	2199	4297	6496	SO:0001583	missense	5680	exon4			TTACGAGCAGAGC	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.908C>T	19.37:g.43519324G>A	ENSP00000384995:p.Ala303Val	120	0	0		102	49	0.480392	NM_002785	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000401740.1	37	CCDS12614.2	.	.	.	.	.	.	.	.	.	.	g	0	-2.632599	0.00115	4.55E-4	6.98E-4	ENSG00000243130	ENST00000320078;ENST00000403486;ENST00000306322;ENST00000401740	T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03	0.976	-1.95	0.07548	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.56645	0.1999	L	0.31926	0.97	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.003	T	0.45716	-0.9242	9	0.02654	T	1	.	4.5197	0.11954	0.5126:0.0:0.4874:0.0	.	181;303	Q9UQ72-2;Q9UQ72	.;PSG11_HUMAN	V	303;181;181;303	ENSP00000319140:A303V;ENSP00000385427:A181V;ENSP00000304913:A181V;ENSP00000384995:A303V	ENSP00000304913:A181V	A	-	2	0	PSG11	48211164	0.000000	0.05858	0.001000	0.08648	0.039000	0.13416	-1.321000	0.02697	-1.482000	0.01860	-1.207000	0.01640	GCT	G|1.000;A|0.000	0.000	weak		0.458	PSG11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323079.1	NM_002785		A	43519324	G	A	43519324	3	1	29	1	0	0	0	0	1	0	0	0	12666	971	34	2	107	2	PSG11	19	43519324	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	488006	43519324	15609659	813	13054											
ZNF285	26974	hgsc.bcm.edu	37	chr19	44890654	44890654	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttataatgtttctctctgctCatgtagtctttgatgagtca	8	19	7	7	0	5	2	2	2	3	0	6	2	5	2	0	0	1	3	0	0	3	5	rs149238831	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:44890654C>T	ENST00000330997.4	-	4	1817	c.1753G>A	c.(1753-1755)Gag>Aag	p.E585K	ZNF285_ENST00000544719.2_Missense_Mutation_p.E585K|ZNF285_ENST00000591679.1_Missense_Mutation_p.E592K|CTC-512J12.6_ENST00000588212.1_Intron	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	585					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						TCTCTCTGCTCATGTAGTCTT	0.418																																					p.E585K		Atlas-SNP	.											.	ZNF285	86	.	0			c.G1753A						PASS	.						127	107	113					19																	44890654		2203	4300	6503	SO:0001583	missense	26974	exon4			TCTGCTCATGTAG	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.1753G>A	19.37:g.44890654C>T	ENSP00000333595:p.Glu585Lys	108	0	0		100	15	0.15	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Missense_Mutation	SNP	ENST00000330997.4	37	CCDS12638.1	9	0.004120879120879121	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	3.493	-0.103371	0.06967	.	.	ENSG00000062370	ENST00000544719;ENST00000330997	T	0.05996	3.36	1.94	-3.87	0.04218	.	.	.	.	.	T	0.02494	0.0076	N	0.26092	0.79	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.41124	-0.9526	9	0.87932	D	0	.	1.2743	0.02027	0.168:0.3012:0.3374:0.1934	.	609;585	B7ZLR9;Q96NJ3	.;ZN285_HUMAN	K	608;585	ENSP00000333595:E585K	ENSP00000333595:E585K	E	-	1	0	ZNF285	49582494	0.793000	0.28825	0.000000	0.03702	0.035000	0.12851	0.746000	0.26275	-1.954000	0.01025	0.454000	0.30748	GAG	C|0.995;T|0.005	0.005	strong		0.418	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354		T	44890654	C	T	44890654	3	4	29	1	0	0	0	0	1	0	0	0	17837	835	29	2	23	2	ZNF285	19	44890654	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1371330	44890654	14238329	814	13055											
RSPH6A	81492	hgsc.bcm.edu	37	chr19	46313918	46313918	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctccactccgggtgaacagCgccttctgtttctccgccat	5	11	8	17	3	2	1	0	1	2	0	5	1	4	1	6	1	2	1	6	1	1	2	rs141102105		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:46313918C>G	ENST00000221538.3	-	2	973	c.831G>C	c.(829-831)gcG>gcC	p.A277A	RSPH6A_ENST00000597055.1_Silent_p.A277A|RSPH6A_ENST00000600188.1_Silent_p.A13A	NM_030785.3	NP_110412.1	Q9H0K4	RSH6A_HUMAN	radial spoke head 6 homolog A (Chlamydomonas)	277						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						GGGTGAACAGCGCCTTCTGTT	0.637													C|||	1	0.000199681	0.0	0.0	5008	,	,		17889	0.0		0.001	False		,,,				2504	0.0				p.A277A		Atlas-SNP	.											RSPH6A,NS,carcinoma,-2,1	RSPH6A	70	1	0			c.G831C						PASS	.	C		4,4402	9.9+/-24.2	0,4,2199	143	127	133		831	-3.8	1	19	dbSNP_134	133	44,8556	27.9+/-77.7	0,44,4256	no	coding-synonymous	RSPH6A	NM_030785.3		0,48,6455	GG,GC,CC		0.5116,0.0908,0.3691		277/718	46313918	48,12958	2203	4300	6503	SO:0001819	synonymous_variant	81492	exon2			GAACAGCGCCTTC	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.831G>C	19.37:g.46313918C>G		93	0	0		64	33	0.515625	NM_030785	Q53FE2|Q6PEZ9	Silent	SNP	ENST00000221538.3	37	CCDS12675.1																																																																																			C|0.997;G|0.003	0.003	strong		0.637	RSPH6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461657.1			G	46313918	C	G	46313918	2	3	29	1	0	0	0	0	0	0	0	1	13722	755	27	4		4	RSPH6A	19	46313918	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1423264	46313918	12815065	815	13056											
SYMPK	8189	hgsc.bcm.edu	37	chr19	46320218	46320218	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgaagccctcccacaccttGgggtacttccacacctgaac	10	8	7	16	0	0	2	0	2	0	0	2	2	2	2	5	2	3	1	5	2	3	3	rs140350780		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:46320218G>A	ENST00000245934.7	-	24	3340	c.3096C>T	c.(3094-3096)ccC>ccT	p.P1032P	RSPH6A_ENST00000597055.1_5'Flank|SYMPK_ENST00000598155.1_5'UTR|RSPH6A_ENST00000221538.3_5'Flank	NM_004819.2	NP_004810.2	Q92797	SYMPK_HUMAN	symplekin	1032					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)		CCCACACCTTGGGGTACTTCC	0.632											OREG0025562	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0.0	0.0	5008	,	,		15216	0.0		0.001	False		,,,				2504	0.0				p.P1032P		Atlas-SNP	.											.	SYMPK	104	.	0			c.C3096T						PASS	.	G		1,4385		0,1,2192	24	22	23		3096	4.7	1	19	dbSNP_134	23	38,8512		0,38,4237	no	coding-synonymous	SYMPK	NM_004819.2		0,39,6429	AA,AG,GG		0.4444,0.0228,0.3015		1032/1275	46320218	39,12897	2193	4275	6468	SO:0001819	synonymous_variant	8189	exon24			CACCTTGGGGTAC	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.3096C>T	19.37:g.46320218G>A		110	0	0	938	92	47	0.51087	NM_004819	O00521|O00689|O00733|Q59GT5|Q8N2U5	Silent	SNP	ENST00000245934.7	37	CCDS12676.2																																																																																			G|0.997;A|0.003	0.003	strong		0.632	SYMPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316581.1	NM_004819		A	46320218	G	A	46320218	2	1	29	1	0	0	0	0	0	0	0	1	15454	1335	47	2		2	SYMPK	19	46320218	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	6300	46320218	12808765	816	13057											
DHX34	9704	hgsc.bcm.edu	37	chr19	47858526	47858526	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggtcatcctcatgtcggcCaccatcaacatctcgctctt	9	11	6	15	2	5	0	3	0	2	0	8	0	6	0	3	2	1	1	3	2	2	1	rs138629177		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:47858526C>T	ENST00000328771.4	+	3	1285	c.936C>T	c.(934-936)gcC>gcT	p.A312A		NM_014681.5	NP_055496.2	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	312	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				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)		TCATGTCGGCCACCATCAACA	0.587																																					p.A312A		Atlas-SNP	.											.	DHX34	98	.	0			c.C936T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	162	144	150		936	2.2	1	19	dbSNP_134	150	0,8600		0,0,4300	no	coding-synonymous	DHX34	NM_014681.5		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		312/1144	47858526	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9704	exon3			GTCGGCCACCATC	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.936C>T	19.37:g.47858526C>T		122	0	0		105	53	0.504762	NM_014681	B4DMY8	Silent	SNP	ENST00000328771.4	37	CCDS12700.1																																																																																			C|1.000;T|0.000	0.000	weak		0.587	DHX34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314313.3	NM_014681		T	47858526	C	T	47858526	2	4	29	1	0	0	0	0	0	0	0	1	4509	581	21	2		2	DHX34	19	47858526	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1538308	47858526	11270457	817	13058											
IZUMO1	284359	hgsc.bcm.edu	37	chr19	49245518	49245518	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcctgatgccagtttaacTcacagtccaggatcatgtct	11	11	8	11	0	3	1	2	1	1	0	4	2	4	2	3	1	3	1	3	1	2	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:49245518T>G	ENST00000332955.2	-	7	1095	c.548A>C	c.(547-549)gAg>gCg	p.E183A	RASIP1_ENST00000222145.4_5'Flank	NM_182575.2	NP_872381.2	Q8IYV9	IZUM1_HUMAN	izumo sperm-egg fusion 1	183	Ig-like C2-type.				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)		CCAGTTTAACTCACAGTCCAG	0.478																																					p.E183A		Atlas-SNP	.											.	IZUMO1	30	.	0			c.A548C						PASS	.						186	168	174					19																	49245518		2203	4300	6503	SO:0001583	missense	284359	exon7			TTTAACTCACAGT	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.548A>C	19.37:g.49245518T>G	ENSP00000327786:p.Glu183Ala	134	0	0		129	31	0.24031	NM_182575	Q6Q8P6|Q6Q8P7	Missense_Mutation	SNP	ENST00000332955.2	37	CCDS12732.1	.	.	.	.	.	.	.	.	.	.	T	13.61	2.287181	0.40494	.	.	ENSG00000182264	ENST00000332955	D	0.83992	-1.79	4.57	2.39	0.29439	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	1.196760	0.05963	N	0.641060	T	0.73063	0.3539	L	0.29908	0.895	0.09310	N	1	P	0.42518	0.782	B	0.37888	0.26	T	0.59392	-0.7463	10	0.31617	T	0.26	-14.0882	7.3146	0.26493	0.3508:0.0:0.0:0.6491	.	183	Q8IYV9	IZUM1_HUMAN	A	183	ENSP00000327786:E183A	ENSP00000327786:E183A	E	-	2	0	IZUMO1	53937330	0.076000	0.21285	0.015000	0.15790	0.791000	0.44710	0.781000	0.26774	0.316000	0.23135	0.459000	0.35465	GAG	.	.	none		0.478	IZUMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466189.1	NM_182575		G	49245518	T	G	49245518	3	3	29	1	0	0	0	0	1	0	0	0	7942	1551	54	5	520	5	IZUMO1	19	49245518	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	1386992	49245518	9883465	818	13059											
HRC	3270	hgsc.bcm.edu	37	chr19	49658345	49658345	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agctctgctgatgcctcctcGgagagcccggcgactccagt	6	8	12	15	3	1	2	0	1	1	1	4	4	3	2	4	2	4	2	4	2	0	0	rs117942355	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:49658345G>A	ENST00000252825.4	-	1	336	c.150C>T	c.(148-150)tcC>tcT	p.S50S	TRPM4_ENST00000427978.2_5'Flank|TRPM4_ENST00000355712.5_5'Flank|TRPM4_ENST00000252826.5_5'Flank|HRC_ENST00000595625.1_Silent_p.S50S	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	50					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)		ATGCCTCCTCGGAGAGCCCGG	0.597													g|||	2	0.000399361	0.0	0.0014	5008	,	,		17990	0.001		0.0	False		,,,				2504	0.0				p.S50S	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.C150T						PASS	.	A		0,4406		0,0,2203	147	132	137		150	-4.7	0	19	dbSNP_132	137	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	HRC	NM_002152.2		0,4,6499	AA,AG,GG		0.0465,0.0,0.0308		50/700	49658345	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			CTCCTCGGAGAGC		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.150C>T	19.37:g.49658345G>A		67	0	0		61	27	0.442623	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	37	CCDS12759.1																																																																																			G|1.000;A|0.000	0.000	strong		0.597	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152		A	49658345	G	A	49658345	2	1	29	1	0	0	0	0	0	0	0	1	7361	1103	39	1		1	HRC	19	49658345	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	412827	49658345	9470638	819	13060											
NUP62	23636	hgsc.bcm.edu	37	chr19	50412396	50412396	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttggagcagttgctattgaCgcaaagaggctgggcccagt	9	9	15	8	1	0	2	0	1	0	1	0	3	0	3	1	3	2	6	1	3	2	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:50412396C>T	ENST00000596217.1	-	2	2556	c.669G>A	c.(667-669)gcG>gcA	p.A223A	NUP62_ENST00000597029.1_Silent_p.A223A|NUP62_ENST00000413454.1_Silent_p.A223A|NUP62_ENST00000600583.1_5'Flank|NUP62_ENST00000352066.3_Silent_p.A223A|NUP62_ENST00000422090.2_Silent_p.A223A|IL4I1_ENST00000341114.3_Intron|IL4I1_ENST00000595948.1_Intron|NUP62_ENST00000597723.1_Silent_p.A223A			P37198	NUP62_HUMAN	nucleoporin 62kDa	223	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)		TTGCTATTGACGCAAAGAGGC	0.642																																					p.A223A		Atlas-SNP	.											NUP62,NS,carcinoma,0,2	NUP62	50	2	0			c.G669A						PASS	.						94	87	89					19																	50412396		2203	4300	6503	SO:0001819	synonymous_variant	23636	exon3			TATTGACGCAAAG	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.669G>A	19.37:g.50412396C>T		66	0	0		85	39	0.458824	NM_153719	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	Silent	SNP	ENST00000596217.1	37	CCDS12788.1																																																																																			.	.	none		0.642	NUP62-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464991.1	NM_153719		T	50412396	C	T	50412396	2	4	29	1	0	0	0	0	0	0	0	1	10777	523	19	1		1	NUP62	19	50412396	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	754051	50412396	8716587	820	13061											
ETFB	2109	hgsc.bcm.edu	37	chr19	51857774	51857774	+	Intron	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccttctctcatccagccatTcctgggtaccagggacatct	7	12	7	15	0	3	0	1	0	2	0	7	1	6	1	5	2	2	1	5	2	1	3	rs143144671	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:51857774T>G	ENST00000309244.4	-	2	149				CTD-2616J11.9_ENST00000600974.1_RNA|ETFB_ENST00000354232.4_Missense_Mutation_p.E40A|CTD-2616J11.11_ENST00000600067.1_Intron	NM_001985.2	NP_001976.1	P38117	ETFB_HUMAN	electron-transfer-flavoprotein, beta polypeptide						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)		ATCCAGCCATTCCTGGGTACC	0.522													t|||	4	0.000798722	0.0	0.0029	5008	,	,		18122	0.0		0.002	False		,,,				2504	0.0				p.E40A		Atlas-SNP	.											.	ETFB	46	.	0			c.A119C						PASS	.	T	ALA/GLU,	3,4403	6.2+/-15.9	0,3,2200	88	83	85		119,	-3.9	0	19	dbSNP_134	85	31,8569	21.6+/-65.8	0,31,4269	yes	missense,intron	ETFB	NM_001014763.1,NM_001985.2	107,	0,34,6469	GG,GT,TT		0.3605,0.0681,0.2614	possibly-damaging,	40/347,	51857774	34,12972	2203	4300	6503	SO:0001627	intron_variant	2109	exon1			AGCCATTCCTGGG	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.58-212A>C	19.37:g.51857774T>G		67	0	0		71	42	0.591549	NM_001014763	A8K766|B3KNY2|Q6IBH7|Q71RF6|Q9Y3S7	Missense_Mutation	SNP	ENST00000309244.4	37	CCDS12828.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	t	12.37	1.918726	0.33908	6.81E-4	0.003605	ENSG00000105379	ENST00000354232	D	0.85339	-1.97	2.49	-3.88	0.04205	.	.	.	.	.	T	0.68430	0.3000	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.50558	-0.8814	7	.	.	.	.	4.1225	0.10112	0.0:0.1914:0.3562:0.4524	.	40	P38117-2	.	A	40	ENSP00000346173:E40A	.	E	-	2	0	ETFB	56549586	0.000000	0.05858	0.000000	0.03702	0.054000	0.15201	-0.697000	0.05098	-1.056000	0.03205	-0.319000	0.08680	GAA	T|0.998;G|0.002	0.002	strong		0.522	ETFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464273.1			G	51857774	T	G	51857774	1	3	29	0	1	0	0	0	0	0	0	0	5272	1783	62	5		5	ETFB	19	51857774	Intron	SNP	T	TCGA-GR-7351-01A-11D-2210-10	1445378	51857774	7271209	821	13062											
ZNF577	84765	hgsc.bcm.edu	37	chr19	52375854	52375854	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggccacattcacttcattTgtgaggcttattctctgttc	6	16	9	10	0	3	1	2	1	1	0	5	1	3	1	1	3	0	2	1	3	1	6			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:52375854T>G	ENST00000301399.5	-	7	1754	c.1389A>C	c.(1387-1389)acA>acC	p.T463T	ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000420592.1_Silent_p.T404T|ZNF577_ENST00000412216.1_Intron|ZNF577_ENST00000451628.2_Silent_p.T404T	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	463					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)		TCACTTCATTTGTGAGGCTTA	0.363																																					p.T463T		Atlas-SNP	.											.	ZNF577	63	.	0			c.A1389C						PASS	.						59	57	57					19																	52375854		2203	4300	6503	SO:0001819	synonymous_variant	84765	exon7			TTCATTTGTGAGG	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.1389A>C	19.37:g.52375854T>G		63	0	0		73	18	0.246575	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Silent	SNP	ENST00000301399.5	37	CCDS12842.2																																																																																			.	.	none		0.363	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679		G	52375854	T	G	52375854	2	3	29	1	0	0	0	0	0	0	0	1	18024	1799	63	5		5	ZNF577	19	52375854	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	518080	52375854	6753129	822	13063											
ZNF577	84765	hgsc.bcm.edu	37	chr19	52375907	52375907	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aactacaaaggcttgatttcTtggaaaaggttgttccacaa	14	12	8	7	0	1	1	0	1	1	0	2	2	2	2	1	3	2	3	1	3	6	6			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:52375907T>G	ENST00000301399.5	-	7	1701	c.1336A>C	c.(1336-1338)Aga>Cga	p.R446R	ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000420592.1_Silent_p.R387R|ZNF577_ENST00000412216.1_Intron|ZNF577_ENST00000451628.2_Silent_p.R387R	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	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(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)		GCTTGATTTCTTGGAAAAGGT	0.398																																					p.R446R		Atlas-SNP	.											ZNF577,colon,carcinoma,+1,1	ZNF577	63	1	0			c.A1336C						PASS	.						67	63	64					19																	52375907		2203	4300	6503	SO:0001819	synonymous_variant	84765	exon7			GATTTCTTGGAAA	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.1336A>C	19.37:g.52375907T>G		83	0	0		76	17	0.223684	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Silent	SNP	ENST00000301399.5	37	CCDS12842.2																																																																																			.	.	none		0.398	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679		G	52375907	T	G	52375907	2	3	29	1	0	0	0	0	0	0	0	1	18024	1617	56	5		5	ZNF577	19	52375907	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	53	52375907	6753076	823	13064											
NLRP12	91662	hgsc.bcm.edu	37	chr19	54313944	54313944	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccgaattaagctgttaagAagcagctccgtgggccgttt	9	12	11	9	3	0	1	0	0	0	1	2	2	2	1	3	1	3	5	3	1	4	4	rs142063194	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54313944A>C	ENST00000324134.6	-	3	1137	c.969T>G	c.(967-969)ctT>ctG	p.L323L	NLRP12_ENST00000391772.1_Silent_p.L323L|NLRP12_ENST00000391773.1_Silent_p.L323L|NLRP12_ENST00000354278.3_Silent_p.L323L|NLRP12_ENST00000391775.3_Silent_p.L323L|NLRP12_ENST00000535162.1_Silent_p.L323L|NLRP12_ENST00000345770.5_Silent_p.L323L|NLRP12_ENST00000351894.4_Silent_p.L323L	NM_001277126.1|NM_144687.2	NP_001264055.1|NP_653288.1	P59046	NAL12_HUMAN	NLR family, pyrin domain containing 12	323	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)		AGCTGTTAAGAAGCAGCTCCG	0.562													A|||	22	0.00439297	0.0	0.0086	5008	,	,		17335	0.0		0.007	False		,,,				2504	0.0092				p.S323R		Atlas-SNP	.											.	NLRP12	236	.	0			c.C969G						PASS	.	A		9,4397	15.5+/-35.6	0,9,2194	49	52	51		969	-8.6	0	19	dbSNP_134	51	117,8483	61.0+/-122.8	0,117,4183	no	coding-synonymous	NLRP12	NM_144687.2		0,126,6377	CC,CA,AA		1.3605,0.2043,0.9688		323/1062	54313944	126,12880	2203	4300	6503	SO:0001819	synonymous_variant	91662	exon3			GTTAAGAAGCAGC	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.969T>G	19.37:g.54313944A>C		51	0	0		51	27	0.529412	NM_144687	A8MTQ2|B3KTE7|Q8NEU4|Q9BY26	Missense_Mutation	SNP	ENST00000324134.6	37	CCDS12864.1																																																																																			A|0.991;C|0.009	0.009	strong		0.562	NLRP12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000134340.1	NM_144687		C	54313944	A	C	54313944	2	2	29	1	0	0	0	0	0	0	0	1	10483	233	9	5		5	NLRP12	19	54313944	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	1938037	54313944	4815039	824	13065											
MBOAT7	79143	hgsc.bcm.edu	37	chr19	54687453	54687453	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tagctgagtgtctccatcagGgagggcacgtcgggcagcag	8	7	16	10	2	2	1	1	1	1	0	4	2	2	2	1	3	2	4	1	3	1	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:54687453G>A	ENST00000245615.1	-	5	924	c.444C>T	c.(442-444)tcC>tcT	p.S148S	MBOAT7_ENST00000474910.1_5'UTR|MBOAT7_ENST00000431666.2_Silent_p.S75S|MBOAT7_ENST00000391754.1_Silent_p.S148S|MBOAT7_ENST00000338624.6_Silent_p.S75S	NM_024298.3	NP_077274.3	Q96N66	MBOA7_HUMAN	membrane bound O-acyltransferase domain containing 7	148					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)					TCTCCATCAGGGAGGGCACGT	0.612																																					p.S148S	NSCLC(97;826 2151 10470 22540)	Atlas-SNP	.											.	MBOAT7	37	.	0			c.C444T						PASS	.						121	93	102					19																	54687453		2203	4300	6503	SO:0001819	synonymous_variant	79143	exon5			CATCAGGGAGGGC	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.444C>T	19.37:g.54687453G>A		121	0	0		121	40	0.330579	NM_001146082	A9C4B6|B0V3I5|B4DQ87|Q05DF0|Q7L5N2|Q99908|Q9BPV2|Q9BRE9	Silent	SNP	ENST00000245615.1	37	CCDS12883.1																																																																																			.	.	none		0.612	MBOAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142203.1	NM_024298		A	54687453	G	A	54687453	2	1	29	1	0	0	0	0	0	0	0	1	9367	1219	43	2		2	MBOAT7	19	54687453	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	373509	54687453	4441530	825	13066											
NLRP8	126205	hgsc.bcm.edu	37	chr19	56473502	56473502	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgtttgcaacgaatgataaGctggaagtcctgactatgac	12	11	11	7	1	0	3	0	3	0	0	1	5	1	4	1	1	3	3	1	1	5	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:56473502G>C	ENST00000291971.3	+	4	2183	c.2112G>C	c.(2110-2112)aaG>aaC	p.K704N	NLRP8_ENST00000590542.1_Missense_Mutation_p.K704N	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	704					neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		CGAATGATAAGCTGGAAGTCC	0.512																																					p.K704N		Atlas-SNP	.											.	NLRP8	225	.	0			c.G2112C						PASS	.						210	177	188					19																	56473502		2203	4300	6503	SO:0001583	missense	126205	exon4			TGATAAGCTGGAA	AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"Nucleotide-binding domain and leucine rich repeat containing"	22940	protein-coding gene	gene with protein product	"nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"	609659	"NACHT, leucine rich repeat and PYD containing 8"	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.2112G>C	19.37:g.56473502G>C	ENSP00000291971:p.Lys704Asn	159	0	0		150	8	0.0533333	NM_176811	Q7RTR4	Missense_Mutation	SNP	ENST00000291971.3	37	CCDS12937.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.472569	0.00167	.	.	ENSG00000179709	ENST00000291971	D	0.88046	-2.33	1.93	-3.87	0.04218	.	.	.	.	.	T	0.54919	0.1888	N	0.00793	-1.18	0.09310	N	1	B;B	0.10296	0.003;0.001	B;B	0.08055	0.003;0.002	T	0.54754	-0.8246	9	0.02654	T	1	.	5.0641	0.14572	0.0:0.4982:0.2851:0.2166	.	704;704	Q86W28-2;Q86W28	.;NALP8_HUMAN	N	704	ENSP00000291971:K704N	ENSP00000291971:K704N	K	+	3	2	NLRP8	61165314	0.002000	0.14202	0.000000	0.03702	0.010000	0.07245	-0.448000	0.06820	-1.456000	0.01921	-0.428000	0.05917	AAG	.	.	none		0.512	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811		C	56473502	G	C	56473502	3	2	29	1	0	0	0	0	1	0	0	0	10492	962	34	4	2126	4	NLRP8	19	56473502	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1786049	56473502	2655481	826	13067											
NLRP5	126206	hgsc.bcm.edu	37	chr19	56549518	56549518	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accagggagtaatgcctctcAgtgatgccttgagagtctcc	9	10	11	11	0	2	2	1	2	2	1	4	4	2	3	4	1	2	1	4	1	1	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:56549518A>G	ENST00000390649.3	+	10	2743	c.2743A>G	c.(2743-2745)Agt>Ggt	p.S915G		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	915					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)		AATGCCTCTCAGTGATGCCTT	0.517																																					p.S915G		Atlas-SNP	.											.	NLRP5	217	.	0			c.A2743G						PASS	.						132	134	133					19																	56549518		2108	4229	6337	SO:0001583	missense	126206	exon10			CCTCTCAGTGATG	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.2743A>G	19.37:g.56549518A>G	ENSP00000375063:p.Ser915Gly	127	0	0		133	24	0.180451	NM_153447	A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	37	CCDS12938.1	.	.	.	.	.	.	.	.	.	.	A	4.665	0.123582	0.08931	.	.	ENSG00000171487	ENST00000390649	T	0.52526	0.66	3.59	1.27	0.21489	.	0.882081	0.09271	N	0.825144	T	0.26738	0.0654	N	0.13272	0.32	0.09310	N	1	B	0.06786	0.001	B	0.14023	0.01	T	0.22068	-1.0227	10	0.29301	T	0.29	.	4.0597	0.09832	0.212:0.0:0.2079:0.5801	.	915	P59047	NALP5_HUMAN	G	915	ENSP00000375063:S915G	ENSP00000375063:S915G	S	+	1	0	NLRP5	61241330	0.956000	0.32656	0.012000	0.15200	0.003000	0.03518	0.996000	0.29719	0.045000	0.15804	-0.408000	0.06270	AGT	.	.	none		0.517	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447		G	56549518	A	G	56549518	3	3	29	1	0	0	0	0	1	0	0	0	10489	188	7	3	2781	3	NLRP5	19	56549518	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	76016	56549518	2579465	827	13068											
ZNF543	125919	hgsc.bcm.edu	37	chr19	57839629	57839630	+	In_Frame_Ins	INS	-	-	GCG																															tgggaaggcttttaaccgcaINSggtcacacctcacacggcac																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:57839629_57839630insGCG	ENST00000321545.4	+	4	1144_1145	c.799_800insGCG	c.(799-801)agg>aGCGgg	p.267_267R>SG		NM_213598.3	NP_998763.2	Q08ER8	ZN543_HUMAN	zinc finger protein 543	267					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)		TTTTAACCGCAGGTCACACCTC	0.51																																					p.R267delinsSG		Pindel,Atlas-Indel	.											.	ZNF543	61	.	0			c.799_800insGCG						PASS	.			0,4264		0,0,2132						2.6	0.3			64	1,8253		0,1,4126	no	coding	ZNF543	NM_213598.3		0,1,6258	A1A1,A1R,RR		0.0121,0.0,0.0080				1,12517				SO:0001652	inframe_insertion	125919	exon4			.	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		Exception_encountered	19.37:g.57839629_57839630insGCG	ENSP00000322545:p.Arg267delinsSerGly	55	0	.		47	20	0.426	NM_213598	Q495U9|Q495V0|Q6ZMP4|Q8NCX4	In_Frame_Ins	INS	ENST00000321545.4	37	CCDS33130.1																																																																																			.	.	none		0.51	ZNF543-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465780.1	XM_064865		GCG	57839630	-	GCG	57839629	7	5	29	1	0	1	1	0	0	0	0	0	17991	179	7	0	813	0	ZNF543	19	57839629	In_Frame_Ins	INS	-	TCGA-GR-7351-01A-11D-2210-10	1290111	57839629	1289354	828	13069											
ZNF417	147687	hgsc.bcm.edu	37	chr19	58420416	58420416	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aatgatttcccacattccttGcactcatagggcctttctcc	8	14	5	14	0	2	1	1	1	1	0	5	1	4	1	4	1	1	1	4	1	2	5	rs150518835	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr19:58420416G>A	ENST00000312026.5	-	3	1394	c.1230C>T	c.(1228-1230)tgC>tgT	p.C410C	ZNF417_ENST00000536263.1_Silent_p.C211C|ZNF417_ENST00000595559.1_Silent_p.C409C|CTD-2583A14.9_ENST00000602124.1_Intron	NM_152475.2	NP_689688.2	Q8TAU3	ZN417_HUMAN	zinc finger protein 417	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)			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)		CACATTCCTTGCACTCATAGG	0.453													G|||	37	0.00738818	0.0	0.0086	5008	,	,		23472	0.0		0.0298	False		,,,				2504	0.001				p.C410C		Atlas-SNP	.											.	ZNF417	44	.	0			c.C1230T						PASS	.	G		24,4382		0,24,2179	108	100	103		1230	-1.5	0	19	dbSNP_134	103	215,8385		5,205,4090	no	coding-synonymous	ZNF417	NM_152475.2		5,229,6269	AA,AG,GG		2.5,0.5447,1.8376		410/576	58420416	239,12767	2203	4300	6503	SO:0001819	synonymous_variant	147687	exon3			TTCCTTGCACTCA	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.1230C>T	19.37:g.58420416G>A		79	0	0		80	25	0.3125	NM_152475	B4DEU1	Silent	SNP	ENST00000312026.5	37	CCDS12965.1																																																																																			G|0.984;A|0.016	0.016	strong		0.453	ZNF417-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466860.1	NM_152475		A	58420416	G	A	58420416	2	1	29	1	0	0	0	0	0	0	0	1	17909	1311	46	2		2	ZNF417	19	58420416	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	580787	58420416	708567	829	13070											
UBOX5	22888	hgsc.bcm.edu	37	chr20	3102636	3102636	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagagccacatcctgaggcaGgttctctgaggtgaccagca	10	7	12	12	0	1	4	0	3	1	1	3	4	2	4	3	3	2	3	3	3	0	1	rs148731933	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:3102636G>C	ENST00000217173.2	-	3	1120	c.649C>G	c.(649-651)Ctg>Gtg	p.L217V	UBOX5_ENST00000348031.2_Missense_Mutation_p.L217V|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						TCCTGAGGCAGGTTCTCTGAG	0.607																																					p.L217V		Atlas-SNP	.											UBOX5,NS,carcinoma,+2,1	UBOX5	47	1	0			c.C649G						PASS	.	G	VAL/LEU,VAL/LEU	1,4405	2.1+/-5.4	0,1,2202	48	43	45		649,649	2.2	0	20	dbSNP_134	45	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	UBOX5	NM_014948.2,NM_199415.1	32,32	0,7,6496	CC,CG,GG		0.0698,0.0227,0.0538	benign,benign	217/542,217/488	3102636	7,12999	2203	4300	6503	SO:0001583	missense	22888	exon3			GAGGCAGGTTCTC	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.649C>G	20.37:g.3102636G>C	ENSP00000217173:p.Leu217Val	49	0	0		54	27	0.5	NM_014948		Missense_Mutation	SNP	ENST00000217173.2	37	CCDS13046.1	.	.	.	.	.	.	.	.	.	.	G	1.639	-0.517024	0.04171	2.27E-4	6.98E-4	ENSG00000185019	ENST00000217173;ENST00000348031	T;T	0.35048	1.33;1.33	5.42	2.19	0.27852	.	0.745856	0.12057	U	0.503558	T	0.20333	0.0489	N	0.17082	0.46	0.09310	N	1	B;B;B	0.09022	0.001;0.002;0.001	B;B;B	0.08055	0.003;0.003;0.003	T	0.17379	-1.0371	10	0.41790	T	0.15	-0.1066	5.4175	0.16382	0.0649:0.227:0.4742:0.2339	.	217;217;217	Q53GQ5;Q86X87;O94941	.;.;RNF37_HUMAN	V	217	ENSP00000217173:L217V;ENSP00000311726:L217V	ENSP00000217173:L217V	L	-	1	2	UBOX5	3050636	0.015000	0.18098	0.036000	0.18154	0.082000	0.17680	0.438000	0.21559	0.617000	0.30160	0.563000	0.77884	CTG	G|1.000;C|0.000	0.000	strong		0.607	UBOX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077706.2	NM_014948		C	3102636	G	C	3102636	3	2	29	1	0	0	0	0	1	0	0	0	16909	991	35	4	988	4	UBOX5	20	3102636	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10		3102636	59922884	830	13071											
CENPB	1059	hgsc.bcm.edu	37	chr20	3766137	3766137	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcggtagtggcccttcacctGctggaccactcccctctcca	5	9	9	18	1	2	0	1	0	1	0	4	1	3	1	6	3	1	2	6	3	1	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:3766137G>T	ENST00000379751.4	-	1	1200	c.994C>A	c.(994-996)Cag>Aag	p.Q332K	CDC25B_ENST00000344256.6_5'Flank|CDC25B_ENST00000379598.5_5'Flank	NM_001810.5	NP_001801.1	P07199	CENPB_HUMAN	centromere protein B, 80kDa	332					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						CCCTTCACCTGCTGGACCACT	0.682																																					p.Q332K		Atlas-SNP	.											.	CENPB	24	.	0			c.C994A						PASS	.						18	16	17					20																	3766137		2199	4293	6492	SO:0001583	missense	1059	exon1			TCACCTGCTGGAC	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.994C>A	20.37:g.3766137G>T	ENSP00000369075:p.Gln332Lys	88	0	0		73	35	0.479452	NM_001810	Q96EI4	Missense_Mutation	SNP	ENST00000379751.4	37	CCDS13064.1	.	.	.	.	.	.	.	.	.	.	g	14.57	2.576145	0.45902	.	.	ENSG00000125817	ENST00000379751	T	0.41065	1.01	4.04	4.04	0.47022	.	0.000000	0.35646	U	0.003063	T	0.32645	0.0836	L	0.36672	1.1	0.32344	N	0.559389	B	0.28258	0.205	B	0.19148	0.024	T	0.48456	-0.9034	10	0.56958	D	0.05	-12.9621	13.6906	0.62544	0.0:0.0:1.0:0.0	.	332	P07199	CENPB_HUMAN	K	332	ENSP00000369075:Q332K	ENSP00000369075:Q332K	Q	-	1	0	CENPB	3714137	0.999000	0.42202	1.000000	0.80357	0.986000	0.74619	2.752000	0.47516	1.801000	0.52704	0.457000	0.33378	CAG	.	.	none		0.682	CENPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077772.2	NM_001810		T	3766137	G	T	3766137	3	4	29	1	0	0	0	0	1	0	0	0	3229	1328	46	4	809	4	CENPB	20	3766137	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	663501	3766137	59259383	831	13072											
SNAP25	6616	hgsc.bcm.edu	37	chr20	10258375	10258375	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgctgcaactggttgaagagGtaagaagtgacagtatttta	13	12	12	4	0	0	4	0	2	0	2	0	4	0	4	0	2	3	5	0	2	6	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:10258375G>A	ENST00000254976.2	+	3	325		c.e3+1		SNAP25-AS1_ENST00000421143.2_RNA|SNAP25-AS1_ENST00000453544.1_RNA|SNAP25_ENST00000304886.2_Splice_Site	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)	GGTTGAAGAGGTAAGAAGTGA	0.398																																					.		Atlas-SNP	.											.	SNAP25	79	.	0			c.114+1G>A						PASS	.						103	92	95					20																	10258375		2203	4300	6503	SO:0001630	splice_region_variant	6616	exon3			GAAGAGGTAAGAA		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.114+1G>A	20.37:g.10258375G>A		40	0	0		20	5	0.25	NM_130811	B2RAU4|D3DW16|D3DW17|P13795|P36974|P70557|P70558|Q53EM2|Q5U0B5|Q8IXK3|Q96FM2|Q9BR45	Splice_Site	SNP	ENST00000254976.2	37	CCDS13110.1	.	.	.	.	.	.	.	.	.	.	G	19.89	3.911425	0.72983	.	.	ENSG00000132639	ENST00000254976;ENST00000304886;ENST00000430336	.	.	.	5.58	5.58	0.84498	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.5584	0.95363	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SNAP25	10206375	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	8.749000	0.91619	2.618000	0.88619	0.655000	0.94253	.	.	.	none		0.398	SNAP25-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077976.3	NM_130811	Intron	A	10258375	G	A	10258375	5	1	29	1	0	0	0	0	0	0	1	0	14845	1275	44	2	121	2	SNAP25	20	10258375	Splice_Site	SNP	G	TCGA-GR-7351-01A-11D-2210-10	6492238	10258375	52767145	832	13073											
SPTLC3	55304	hgsc.bcm.edu	37	chr20	13145471	13145471	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggcacaagaagtcagcacGtcctgagctctatgatgaga	12	7	11	11	2	2	4	1	3	1	2	3	5	3	4	2	1	2	3	2	1	3	1	rs200308499		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:13145471G>A	ENST00000399002.2	+	12	1890	c.1616G>A	c.(1615-1617)cGt>cAt	p.R539H		NM_018327.2	NP_060797.2	Q9NUV7	SPTC3_HUMAN	serine palmitoyltransferase, long chain base subunit 3	539					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						AAGTCAGCACGTCCTGAGCTC	0.443																																					p.R539H		Atlas-SNP	.											.	SPTLC3	78	.	0			c.G1616A						PASS	.	G	HIS/ARG	1,3895		0,1,1947	91	85	87		1616	-1.5	0	20		87	0,8278		0,0,4139	yes	missense	SPTLC3	NM_018327.2	29	0,1,6086	AA,AG,GG		0.0,0.0257,0.0082	benign	539/553	13145471	1,12173	1948	4139	6087	SO:0001583	missense	55304	exon12			CAGCACGTCCTGA	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.1616G>A	20.37:g.13145471G>A	ENSP00000381968:p.Arg539His	89	0	0		94	28	0.297872	NM_018327	A2A2I4|B9EK64|Q05DQ8|Q5T1U4|Q9H1L1|Q9H1Z0	Missense_Mutation	SNP	ENST00000399002.2	37	CCDS13115.2	.	.	.	.	.	.	.	.	.	.	G	7.900	0.734107	0.15574	2.57E-4	0.0	ENSG00000172296	ENST00000399002	D	0.95885	-3.84	5.69	-1.45	0.08828	.	0.883465	0.09800	U	0.754214	D	0.89622	0.6768	N	0.16743	0.435	0.19300	N	0.999975	B	0.11235	0.004	B	0.06405	0.002	T	0.77547	-0.2547	10	0.41790	T	0.15	-1.3251	12.8449	0.57823	0.4423:0.0:0.5577:0.0	.	539	Q9NUV7	SPTC3_HUMAN	H	539	ENSP00000381968:R539H	ENSP00000381968:R539H	R	+	2	0	SPTLC3	13093471	0.035000	0.19736	0.002000	0.10522	0.074000	0.17049	0.997000	0.29731	-0.126000	0.11682	-0.136000	0.14681	CGT	.	.	weak		0.443	SPTLC3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254544.1	NM_018327		A	13145471	G	A	13145471	3	1	29	1	0	0	0	0	1	0	0	0	15140	1145	40	1	1662	1	SPTLC3	20	13145471	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2887096	13145471	49880049	833	13074											
SEL1L2	80343	hgsc.bcm.edu	37	chr20	13912308	13912308	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttccttttattcttattttaCgttgattcttctttttctcc	4	26	2	9	1	4	1	0	1	4	0	6	1	5	1	2	0	1	1	2	0	3	12	rs143129534	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:13912308C>T	ENST00000284951.5	-	3	298	c.224G>A	c.(223-225)cGt>cAt	p.R75H	SEL1L2_ENST00000486903.1_5'UTR|SEL1L2_ENST00000378072.5_Missense_Mutation_p.R75H			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	75						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						TCTTATTTTACGTTGATTCTT	0.244													C|||	36	0.0071885	0.0008	0.0101	5008	,	,		15470	0.0		0.0219	False		,,,				2504	0.0061				p.R75H		Atlas-SNP	.											SEL1L2,colon,carcinoma,-1,1	SEL1L2	103	1	0			c.G224A						scavenged	.	C	HIS/ARG	12,3540		0,12,1764	57	50	52		224	-5.1	0	20	dbSNP_134	52	162,7902		1,160,3871	no	missense	SEL1L2	NM_025229.1	29	1,172,5635	TT,TC,CC		2.0089,0.3378,1.4979	benign	75/689	13912308	174,11442	1776	4032	5808	SO:0001583	missense	80343	exon3			ATTTTACGTTGAT	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.224G>A	20.37:g.13912308C>T	ENSP00000284951:p.Arg75His	98	1	0.0102041		108	40	0.37037	NM_001271539	B4DXX5	Missense_Mutation	SNP	ENST00000284951.5	37		24	0.01098901098901099	0	0.0	5	0.013812154696132596	0	0.0	19	0.025065963060686015	C	2.707	-0.269735	0.05716	0.003378	0.020089	ENSG00000101251	ENST00000378072;ENST00000284951	T;T	0.23147	1.92;2.23	5.11	-5.07	0.02938	.	1.668320	0.03077	N	0.157986	T	0.03695	0.0105	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	0.25847	-1.0120	10	0.14252	T	0.57	3.976	12.3194	0.54977	0.0:0.6944:0.0:0.3056	.	75;75	B4DXX5;Q5TEA6	.;SE1L2_HUMAN	H	75	ENSP00000367312:R75H;ENSP00000284951:R75H	ENSP00000284951:R75H	R	-	2	0	SEL1L2	13860308	0.016000	0.18221	0.000000	0.03702	0.311000	0.27955	-1.651000	0.01989	-0.970000	0.03569	-0.290000	0.09829	CGT	C|0.988;T|0.012	0.012	strong		0.244	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229		T	13912308	C	T	13912308	3	4	29	1	0	0	0	0	1	0	0	0	14026	536	19	1	1914	1	SEL1L2	20	13912308	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	766837	13912308	49113212	834	13075											
SNX5	27131	hgsc.bcm.edu	37	chr20	17933265	17933265	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccaggaaaacatgaaagttgCgatctttactgagaacaggg	15	8	11	7	1	1	2	0	2	1	1	1	5	1	3	1	2	4	1	1	2	5	3	rs145056868		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:17933265C>T	ENST00000377768.3	-	6	791	c.479G>A	c.(478-480)cGc>cAc	p.R160H	SNX5_ENST00000377759.4_Missense_Mutation_p.R160H|SNX5_ENST00000483485.1_5'UTR	NM_152227.1	NP_689413.1	Q9Y5X3	SNX5_HUMAN	sorting nexin 5	160	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				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						ATGAAAGTTGCGATCTTTACT	0.368													C|||	1	0.000199681	0.0	0.0	5008	,	,		21023	0.0		0.001	False		,,,				2504	0.0				p.R160H		Atlas-SNP	.											.	SNX5	38	.	0			c.G479A						PASS	.	C	HIS/ARG,HIS/ARG	0,4406		0,0,2203	73	69	71		479,479	5.7	1	20	dbSNP_134	71	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	SNX5	NM_014426.2,NM_152227.1	29,29	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign,benign	160/405,160/405	17933265	2,13004	2203	4300	6503	SO:0001583	missense	27131	exon5			AAGTTGCGATCTT	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	ENST00000377768.3:c.479G>A	20.37:g.17933265C>T	ENSP00000366998:p.Arg160His	77	0	0		55	30	0.545455	NM_014426	B7ZKN3|D3DW26|Q52LC4|Q7KZN0|Q9BWP0	Missense_Mutation	SNP	ENST00000377768.3	37	CCDS13130.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	5.968	0.362556	0.11296	0.0	2.33E-4	ENSG00000089006	ENST00000377768;ENST00000377759;ENST00000431277;ENST00000419004	T;T;T;T	0.38240	1.15;1.15;1.15;1.15	5.66	5.66	0.87406	Phox homologous domain (5);	0.254317	0.45361	D	0.000366	T	0.15565	0.0375	N	0.03154	-0.405	0.41418	D	0.987781	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.18935	-1.0321	10	0.21540	T	0.41	.	8.5702	0.33565	0.0:0.7445:0.1402:0.1153	.	181;160	B7Z476;Q9Y5X3	.;SNX5_HUMAN	H	160;160;123;125	ENSP00000366998:R160H;ENSP00000366988:R160H;ENSP00000404448:R123H;ENSP00000406731:R125H	ENSP00000366988:R160H	R	-	2	0	SNX5	17881265	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	2.153000	0.42282	2.831000	0.97527	0.650000	0.86243	CGC	C|1.000;T|0.000	0.000	strong		0.368	SNX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078137.4			T	17933265	C	T	17933265	3	4	29	1	0	0	0	0	1	0	0	0	14920	768	27	1	771	1	SNX5	20	17933265	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	4020957	17933265	45092255	835	13076											
SNX5	27131	hgsc.bcm.edu	37	chr20	17949050	17949050	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctcctcctgctgctgcagcaActcgggaaccgcggccatgg	6	7	12	16	3	0	0	0	0	0	0	3	1	2	1	4	3	6	4	4	3	2	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:17949050A>G	ENST00000377768.3	-	2	331	c.19T>C	c.(19-21)Ttg>Ctg	p.L7L	MGME1_ENST00000377710.5_5'Flank|SNX5_ENST00000606602.1_Silent_p.L7L|SNX5_ENST00000481323.1_Silent_p.L7L|SNX5_ENST00000486039.1_Silent_p.L7L|MGME1_ENST00000377704.4_5'Flank|SNX5_ENST00000377759.4_Silent_p.L7L|MGME1_ENST00000377709.1_5'Flank|SNX5_ENST00000606557.1_Silent_p.L7L	NM_152227.1	NP_689413.1	Q9Y5X3	SNX5_HUMAN	sorting nexin 5	7					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						TGCTGCAGCAACTCGGGAACC	0.721																																					p.L7L		Atlas-SNP	.											SNX5,NS,lymphoid_neoplasm,+2,1	SNX5	38	1	0			c.T19C						scavenged	.						5	5	5					20																	17949050		1766	3420	5186	SO:0001819	synonymous_variant	27131	exon1			GCAGCAACTCGGG	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	ENST00000377768.3:c.19T>C	20.37:g.17949050A>G		114	2	0.0175439		63	16	0.253968	NM_014426	B7ZKN3|D3DW26|Q52LC4|Q7KZN0|Q9BWP0	Silent	SNP	ENST00000377768.3	37	CCDS13130.1																																																																																			.	.	none		0.721	SNX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078137.4			G	17949050	A	G	17949050	2	3	29	1	0	0	0	0	0	0	0	1	14920	40	2	3		3	SNX5	20	17949050	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	15785	17949050	45076470	836	13077											
RIN2	54453	hgsc.bcm.edu	37	chr20	19937289	19937289	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacaaggatggtggctattcCgaggaagaggacgtgaagac	13	6	15	7	2	0	3	0	1	0	2	1	7	1	6	1	5	0	1	1	5	4	2	rs368413043		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:19937289C>T	ENST00000255006.6	+	4	485	c.336C>T	c.(334-336)tcC>tcT	p.S112S	RIN2_ENST00000484638.1_3'UTR|RIN2_ENST00000440354.2_Silent_p.S63S	NM_001242581.1|NM_018993.3	NP_001229510.1|NP_061866.1	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	63	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)			autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	27						GTGGCTATTCCGAGGAAGAGG	0.567																																					p.S112S		Atlas-SNP	.											.	RIN2	126	.	0			c.C336T						PASS	.	C	,	2,4094		0,2,2046	48	52	51		336,189	-10.5	0	20		51	10,8368		0,10,4179	no	coding-synonymous,coding-synonymous	RIN2	NM_001242581.1,NM_018993.3	,	0,12,6225	TT,TC,CC		0.1194,0.0488,0.0962	,	112/945,63/896	19937289	12,12462	2048	4189	6237	SO:0001819	synonymous_variant	54453	exon4			CTATTCCGAGGAA	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.336C>T	20.37:g.19937289C>T		55	0	0		66	33	0.5	NM_001242581	Q00425|Q5TFT8|Q9BQL3|Q9H071	Silent	SNP	ENST00000255006.6	37	CCDS56182.1																																																																																			.	.	weak		0.567	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1			T	19937289	C	T	19937289	2	4	29	1	0	0	0	0	0	0	0	1	13387	639	23	1		1	RIN2	20	19937289	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1988239	19937289	43088231	837	13078											
RIN2	54453	hgsc.bcm.edu	37	chr20	19955473	19955473	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgcagccagaccaacggggcCctgtgctttattaatcccct	8	10	9	14	1	0	1	0	0	0	1	1	1	1	1	5	2	4	2	5	2	3	3	rs41306763	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:19955473C>T	ENST00000255006.6	+	8	1100	c.951C>T	c.(949-951)gcC>gcT	p.A317A	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	268					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						CCAACGGGGCCCTGTGCTTTA	0.557													C|||	23	0.00459265	0.0008	0.0072	5008	,	,		13957	0.0		0.0169	False		,,,				2504	0.0				p.A317A		Atlas-SNP	.											.	RIN2	126	.	0			c.C951T						PASS	.	C	,	12,3852		0,12,1920	66	71	70		951,804	3.5	1	20	dbSNP_127	70	188,8048		2,184,3932	no	coding-synonymous,coding-synonymous	RIN2	NM_001242581.1,NM_018993.3	,	2,196,5852	TT,TC,CC		2.2827,0.3106,1.6529	,	317/945,268/896	19955473	200,11900	1932	4118	6050	SO:0001819	synonymous_variant	54453	exon8			CGGGGCCCTGTGC	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.951C>T	20.37:g.19955473C>T		61	0	0		105	53	0.504762	NM_001242581	Q00425|Q5TFT8|Q9BQL3|Q9H071	Silent	SNP	ENST00000255006.6	37	CCDS56182.1																																																																																			C|0.990;T|0.010	0.010	strong		0.557	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1			T	19955473	C	T	19955473	2	4	29	1	0	0	0	0	0	0	0	1	13387	610	22	2		2	RIN2	20	19955473	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	18184	19955473	43070047	838	13079											
FOXA2	3170	hgsc.bcm.edu	37	chr20	22563684	22563684	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgacatgttcatggagcccgCgctcatgttgcccgagccgc	6	8	12	15	5	2	0	2	0	0	0	2	3	2	1	3	1	3	3	3	1	0	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:22563684C>T	ENST00000377115.4	-	3	359	c.178G>A	c.(178-180)Gcg>Acg	p.A60T	FOXA2_ENST00000419308.2_Missense_Mutation_p.A66T	NM_153675.2	NP_710141.1	Q9Y261	FOXA2_HUMAN	forkhead box A2	60	Transactivation domain 1. {ECO:0000250}.				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)					ATGGAGCCCGCGCTCATGTTG	0.692																																					p.A66T		Atlas-SNP	.											.	FOXA2	48	.	0			c.G196A						PASS	.						48	50	50					20																	22563684		2200	4291	6491	SO:0001583	missense	3170	exon2			AGCCCGCGCTCAT	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.178G>A	20.37:g.22563684C>T	ENSP00000366319:p.Ala60Thr	83	0	0		68	27	0.397059	NM_021784	Q8WUW4|Q96DF7	Missense_Mutation	SNP	ENST00000377115.4	37	CCDS13147.1	.	.	.	.	.	.	.	.	.	.	C	4.203	0.036488	0.08148	.	.	ENSG00000125798	ENST00000377115;ENST00000419308;ENST00000319993	D;D;D	0.90504	-2.68;-2.68;-2.68	4.42	2.29	0.28610	Fork-head N-terminal (1);	.	.	.	.	D	0.85008	0.5599	L	0.50333	1.59	0.53005	D	0.999967	B;B	0.10296	0.003;0.003	B;B	0.08055	0.002;0.003	T	0.76610	-0.2896	9	0.22706	T	0.39	.	8.3158	0.32100	0.0:0.7519:0.1567:0.0914	.	60;66	Q9Y261;B0ZTD4	FOXA2_HUMAN;.	T	60;60;66	ENSP00000366319:A60T;ENSP00000400341:A60T;ENSP00000315955:A66T	ENSP00000315955:A66T	A	-	1	0	FOXA2	22511684	0.376000	0.25098	0.994000	0.49952	0.994000	0.84299	1.624000	0.37018	0.827000	0.34685	0.467000	0.42956	GCG	.	.	none		0.692	FOXA2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078289.1			T	22563684	C	T	22563684	3	4	29	1	0	0	0	0	1	0	0	0	5998	768	27	1	1199	1	FOXA2	20	22563684	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2608211	22563684	40461836	839	13080											
C20orf3	57136	hgsc.bcm.edu	37	chr20	24954303	24954303	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	caagggcccgaaccaaaccgGgcaatggtctctatttcacc	11	7	9	14	2	2	0	1	0	1	0	3	1	2	0	4	3	2	1	4	3	5	2	rs148400044	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:24954303G>C	ENST00000217456.2	-	4	689	c.399C>G	c.(397-399)gcC>gcG	p.A133A	APMAP_ENST00000447138.1_Silent_p.A133A|RNU6-1257P_ENST00000384625.1_RNA	NM_020531.2	NP_065392.1	Q9HDC9	APMAP_HUMAN	adipocyte plasma membrane associated protein	133					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)										AACCAAACCGGGCAATGGTCT	0.448													G|||	3	0.000599042	0.0	0.0	5008	,	,		19675	0.0		0.001	False		,,,				2504	0.002				p.A133A		Atlas-SNP	.											.	APMAP	3	.	0			c.C399G						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	107	92	97		399	0	1	20	dbSNP_134	97	11,8589	9.1+/-34.3	0,11,4289	no	coding-synonymous	C20orf3	NM_020531.2		0,13,6490	CC,CG,GG		0.1279,0.0454,0.1		133/417	24954303	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	57136	exon4			AAACCGGGCAATG	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.399C>G	20.37:g.24954303G>C		98	0	0		102	57	0.558824	NM_020531	A8K514|B4DXG1|Q6UVZ8|Q9GZS8|Q9NUB2	Silent	SNP	ENST00000217456.2	37	CCDS13166.1	.	.	.	.	.	.	.	.	.	.	G	9.501	1.103322	0.20632	4.54E-4	0.001279	ENSG00000101474	ENST00000451442	.	.	.	5.43	0.0444	0.14225	.	.	.	.	.	T	0.50360	0.1611	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33752	-0.9856	4	.	.	.	-17.6727	5.067	0.14587	0.3047:0.2599:0.4354:0.0	.	.	.	.	R	118	.	.	P	-	2	0	C20orf3	24902303	0.804000	0.28969	0.963000	0.40424	0.854000	0.48673	-0.233000	0.09041	-0.200000	0.10300	-0.150000	0.13652	CCC	G|0.998;C|0.002	0.002	strong		0.448	APMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078380.2	NM_020531		C	24954303	G	C	24954303	2	2	29	1	0	0	0	0	0	0	0	1	2111	1219	43	4		4	C20orf3	20	24954303	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2390619	24954303	38071217	840	13081											
ZNF341	84905	hgsc.bcm.edu	37	chr20	32376748	32376748	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagagacacatgttgatccaCgagcccttcaagaaatacaa	17	7	7	10	1	1	3	1	1	0	2	2	5	2	3	2	0	2	1	2	0	5	3	rs34260449	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:32376748C>T	ENST00000375200.1	+	13	2297	c.1932C>T	c.(1930-1932)caC>caT	p.H644H	RP4-553F4.6_ENST00000423074.1_RNA|RP4-553F4.6_ENST00000439444.1_RNA|ZNF341_ENST00000342427.2_Silent_p.H637H|RP4-553F4.6_ENST00000443171.1_RNA	NM_001282933.1	NP_001269862.1	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	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)			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						TGTTGATCCACGAGCCCTTCA	0.552													C|||	60	0.0119808	0.0	0.0159	5008	,	,		17759	0.001		0.0318	False		,,,				2504	0.0164				p.H637H		Atlas-SNP	.											.	ZNF341	73	.	0			c.C1911T						PASS	.	C		17,4389	25.3+/-52.1	0,17,2186	121	99	106		1911	-4.3	1	20	dbSNP_126	106	180,8420	82.6+/-145.2	2,176,4122	no	coding-synonymous	ZNF341	NM_032819.3		2,193,6308	TT,TC,CC		2.093,0.3858,1.5147		637/848	32376748	197,12809	2203	4300	6503	SO:0001819	synonymous_variant	84905	exon13			GATCCACGAGCCC	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.1932C>T	20.37:g.32376748C>T		180	0	0		142	75	0.528169	NM_032819	A2RUF4|B2RXE5|B7ZM09|Q5JXM8|Q96ST5	Silent	SNP	ENST00000375200.1	37																																																																																				C|0.985;T|0.015	0.015	strong		0.552	ZNF341-201	KNOWN	basic	protein_coding	protein_coding				T	32376748	C	T	32376748	2	4	29	1	0	0	0	0	0	0	0	1	17872	535	19	1		1	ZNF341	20	32376748	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	7422445	32376748	30648772	841	13082											
ASIP	434	hgsc.bcm.edu	37	chr20	32856838	32856838	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gtggtgcggccccggaccccCctatctgcgccctgcgtggc	2	7	14	18	4	1	0	0	0	1	0	1	1	1	1	6	4	3	0	6	4	1	1	rs36093428	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:32856838C>A	ENST00000568305.1	+	4	466	c.264C>A	c.(262-264)ccC>ccA	p.P88P	RP4-785G19.5_ENST00000512005.1_RNA|ASIP_ENST00000374954.3_Silent_p.P88P			P42127	ASIP_HUMAN	agouti signaling protein	88					adult feeding behavior (GO:0008343)|cell-cell signaling (GO:0007267)|generation of precursor metabolites and energy (GO:0006091)|genetic imprinting (GO:0071514)|hormone-mediated signaling pathway (GO:0009755)|melanin biosynthetic process (GO:0042438)|melanosome organization (GO:0032438)|melanosome transport (GO:0032402)|regulation of molecular function, epigenetic (GO:0040030)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	receptor binding (GO:0005102)			central_nervous_system(1)|lung(2)	3						CCCGGACCCCCCTATCTGCGC	0.706													C|||	31	0.0061901	0.0008	0.0144	5008	,	,		11685	0.0		0.0199	False		,,,				2504	0.0				p.P88P		Atlas-SNP	.											.	ASIP	6	.	0			c.C264A						PASS	.	C		3,4325		0,3,2161	9	11	11		264	-1.8	0	20	dbSNP_126	11	48,8490		0,48,4221	no	coding-synonymous	ASIP	NM_001672.2		0,51,6382	AA,AC,CC		0.5622,0.0693,0.3964		88/133	32856838	51,12815	2164	4269	6433	SO:0001819	synonymous_variant	434	exon3			GACCCCCCTATCT		CCDS13232.1	20q11.2-q12	2010-06-24	2010-06-24		ENSG00000101440	ENSG00000101440			745	protein-coding gene	gene with protein product	"nonagouti homolog (mouse)"	600201	"agouti (mouse)-signaling protein", "agouti signaling protein, nonagouti homolog (mouse)"	AGTIL		7937887, 7757071	Standard	NM_001672		Approved	ASP	uc002xah.1	P42127	OTTHUMG00000032289	ENST00000568305.1:c.264C>A	20.37:g.32856838C>A		62	0	0		53	35	0.660377	NM_001672	Q3SXL2	Silent	SNP	ENST00000568305.1	37	CCDS13232.1																																																																																			C|0.994;A|0.006	0.006	strong		0.706	ASIP-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430541.1			A	32856838	C	A	32856838	2	1	29	1	0	0	0	0	0	0	0	1	1043	610	22	4		4	ASIP	20	32856838	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	480090	32856838	30168682	842	13083											
MMP24	10893	hgsc.bcm.edu	37	chr20	33842284	33842284	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ataccccaaaagtgggtgagCtagacacgcggaaagctatt	14	7	11	9	2	0	2	0	1	0	1	0	3	0	3	2	2	3	2	2	2	6	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:33842284C>A	ENST00000246186.6	+	4	629	c.544C>A	c.(544-546)Cta>Ata	p.L182I	MMP24-AS1_ENST00000454184.1_RNA|MMP24-AS1_ENST00000456350.1_RNA|MMP24-AS1_ENST00000566203.2_RNA|MMP24-AS1_ENST00000453892.1_RNA|EDEM2_ENST00000540582.1_Intron|MMP24-AS1_ENST00000438751.1_RNA|MMP24-AS1_ENST00000433764.1_RNA	NM_006690.3	NP_006681.1	Q9Y5R2	MMP24_HUMAN	matrix metallopeptidase 24 (membrane-inserted)	182					cell-cell adhesion (GO:0098609)|cell-cell adhesion mediated by cadherin (GO:0044331)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|glial cell differentiation (GO:0010001)|neuronal stem cell maintenance (GO:0097150)|positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network membrane (GO:0032588)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|large_intestine(1)|lung(2)|prostate(2)|skin(5)	14			BRCA - Breast invasive adenocarcinoma(18;0.00252)		Marimastat(DB00786)	AGTGGGTGAGCTAGACACGCG	0.493																																					p.L182I		Atlas-SNP	.											.	MMP24	35	.	0			c.C544A						PASS	.						180	179	179					20																	33842284		2001	4179	6180	SO:0001583	missense	10893	exon4			GGTGAGCTAGACA	AF131284	CCDS46593.1	20q11.2	2008-07-16	2005-08-08		ENSG00000125966	ENSG00000125966			7172	protein-coding gene	gene with protein product	"membrane-type 5 matrix metalloproteinase"	604871	"matrix metalloproteinase 24 (membrane-inserted)"			10363975	Standard	NM_006690		Approved	MT5-MMP	uc002xbu.2	Q9Y5R2	OTTHUMG00000032330	ENST00000246186.6:c.544C>A	20.37:g.33842284C>A	ENSP00000246186:p.Leu182Ile	72	0	0		57	15	0.263158	NM_006690	B7ZBG8|Q9H440	Missense_Mutation	SNP	ENST00000246186.6	37	CCDS46593.1	.	.	.	.	.	.	.	.	.	.	C	12.12	1.843928	0.32606	.	.	ENSG00000125966	ENST00000246186;ENST00000540655	T	0.21031	2.03	5.53	4.59	0.56863	Peptidase M10, metallopeptidase (1);Peptidase, metallopeptidase (1);Metallopeptidase, catalytic domain (1);	0.207502	0.41605	D	0.000843	T	0.11024	0.0269	N	0.11560	0.145	0.36654	D	0.877557	B	0.06786	0.001	B	0.12837	0.008	T	0.17623	-1.0363	10	0.24483	T	0.36	.	10.288	0.43579	0.1343:0.7942:0.0:0.0714	.	182	Q9Y5R2	MMP24_HUMAN	I	182;130	ENSP00000246186:L182I	ENSP00000246186:L182I	L	+	1	2	MMP24	33305700	0.998000	0.40836	0.997000	0.53966	0.910000	0.53928	0.975000	0.29449	1.580000	0.49851	0.655000	0.94253	CTA	.	.	none		0.493	MMP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078851.4	NM_006690		A	33842284	C	A	33842284	3	1	29	1	0	0	0	0	1	0	0	0	9670	796	28	4	308	4	MMP24	20	33842284	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	985446	33842284	29183236	843	13084											
MMP24	10893	hgsc.bcm.edu	37	chr20	33855126	33855126	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aggccccctcggccgcccctCggggaccggccatccacacc	5	3	11	22	4	0	0	0	0	0	0	3	1	1	1	9	5	0	0	9	5	0	0	rs560750597		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:33855126C>T	ENST00000246186.6	+	6	1183	c.1098C>T	c.(1096-1098)ctC>ctT	p.L366L	MMP24-AS1_ENST00000454184.1_RNA|MMP24-AS1_ENST00000456350.1_RNA|MMP24-AS1_ENST00000566203.2_RNA|MMP24-AS1_ENST00000453892.1_RNA|EDEM2_ENST00000540582.1_Intron|RP4-614O4.11_ENST00000444717.1_RNA|MMP24-AS1_ENST00000438751.1_RNA|MMP24-AS1_ENST00000433764.1_RNA	NM_006690.3	NP_006681.1	Q9Y5R2	MMP24_HUMAN	matrix metallopeptidase 24 (membrane-inserted)	366					cell-cell adhesion (GO:0098609)|cell-cell adhesion mediated by cadherin (GO:0044331)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|glial cell differentiation (GO:0010001)|neuronal stem cell maintenance (GO:0097150)|positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)|trans-Golgi network membrane (GO:0032588)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|large_intestine(1)|lung(2)|prostate(2)|skin(5)	14			BRCA - Breast invasive adenocarcinoma(18;0.00252)		Marimastat(DB00786)	GGCCGCCCCTCGGGGACCGGC	0.632													C|||	1	0.000199681	0.0	0.0	5008	,	,		15710	0.0		0.0	False		,,,				2504	0.001				p.L366L		Atlas-SNP	.											.	MMP24	35	.	0			c.C1098T						PASS	.						20	25	23					20																	33855126		1916	4120	6036	SO:0001819	synonymous_variant	10893	exon6			GCCCCTCGGGGAC	AF131284	CCDS46593.1	20q11.2	2008-07-16	2005-08-08		ENSG00000125966	ENSG00000125966			7172	protein-coding gene	gene with protein product	"membrane-type 5 matrix metalloproteinase"	604871	"matrix metalloproteinase 24 (membrane-inserted)"			10363975	Standard	NM_006690		Approved	MT5-MMP	uc002xbu.2	Q9Y5R2	OTTHUMG00000032330	ENST00000246186.6:c.1098C>T	20.37:g.33855126C>T		85	0	0		97	4	0.0412371	NM_006690	B7ZBG8|Q9H440	Silent	SNP	ENST00000246186.6	37	CCDS46593.1																																																																																			.	.	none		0.632	MMP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078851.4	NM_006690		T	33855126	C	T	33855126	2	4	29	1	0	0	0	0	0	0	0	1	9670	871	31	1		1	MMP24	20	33855126	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	12842	33855126	29170394	844	13085											
PIGT	51604	hgsc.bcm.edu	37	chr20	44048224	44048224	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcagtgcatatccgccctgtTtgcagagtaagtcatgggga	9	10	13	9	1	1	1	1	0	0	1	2	2	2	2	2	2	2	5	2	2	2	3	rs147475258		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:44048224T>C	ENST00000279036.6	+	5	755	c.675T>C	c.(673-675)gtT>gtC	p.V225V	PIGT_ENST00000535404.1_Silent_p.V70V|PIGT_ENST00000341555.5_Intron|PIGT_ENST00000543458.2_Silent_p.V169V|PIGT_ENST00000279035.9_Silent_p.V123V|PIGT_ENST00000372689.5_Silent_p.V225V|PIGT_ENST00000545755.1_5'UTR	NM_015937.5	NP_057021.2	Q969N2	PIGT_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class T	225					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|neuron apoptotic process (GO:0051402)|neuron differentiation (GO:0030182)|post-translational protein modification (GO:0043687)	cytoplasmic membrane-bounded vesicle (GO:0016023)|endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)	GPI-anchor transamidase activity (GO:0003923)			breast(1)|endometrium(2)|kidney(5)|large_intestine(4)|lung(7)|pancreas(1)|skin(1)|stomach(1)	22		Myeloproliferative disorder(115;0.0122)				TCCGCCCTGTTTGCAGAGTAA	0.552													T|||	1	0.000199681	0.0008	0.0	5008	,	,		20797	0.0		0.0	False		,,,				2504	0.0				p.V225V		Atlas-SNP	.											.	PIGT	85	.	0			c.T675C						PASS	.	T	,,,	1,4405	2.1+/-5.4	0,1,2202	111	99	103		507,675,369,675	-2.1	0.4	20	dbSNP_134	103	27,8573	18.5+/-59.3	0,27,4273	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PIGT	NM_001184728.1,NM_001184729.1,NM_001184730.1,NM_015937.4	,,,	0,28,6475	CC,CT,TT		0.314,0.0227,0.2153	,,,	169/523,225/512,123/477,225/579	44048224	28,12978	2203	4300	6503	SO:0001819	synonymous_variant	51604	exon5			CCCTGTTTGCAGA		CCDS13353.1, CCDS54464.1, CCDS54465.1, CCDS54466.1	20q12-q13.12	2013-02-26	2006-06-28		ENSG00000124155	ENSG00000124155		"Phosphatidylinositol glycan anchor biosynthesis"	14938	protein-coding gene	gene with protein product	"GPI transamidase subunit"	610272	"phosphatidylinositol glycan, class T"			15713669	Standard	NM_015937		Approved		uc002xoh.3	Q969N2	OTTHUMG00000032574	ENST00000279036.6:c.675T>C	20.37:g.44048224T>C		57	0	0		88	35	0.397727	NM_001184729	B2RND5|B7Z3N1|B7Z7I8|E1P622|G8JLF5|Q2NL69|Q7Z3N7|Q9BQY7|Q9BQY8|Q9UJG6|Q9Y2Z5	Silent	SNP	ENST00000279036.6	37	CCDS13353.1																																																																																			T|0.999;C|0.001	0.001	strong		0.552	PIGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079434.2	NM_015937		C	44048224	T	C	44048224	2	2	29	1	0	0	0	0	0	0	0	1	11908	1828	64	3		3	PIGT	20	44048224	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	10193098	44048224	18977296	845	13086											
PCIF1	63935	hgsc.bcm.edu	37	chr20	44574722	44574722	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctgcctttgagaggttcctgCcccgggtctggtgtcttctc	2	14	12	13	1	3	1	0	1	3	1	5	2	4	1	4	3	2	1	4	3	0	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:44574722C>T	ENST00000372409.3	+	13	1760	c.1396C>T	c.(1396-1398)Ccc>Tcc	p.P466S	PCIF1_ENST00000479348.1_3'UTR	NM_022104.3	NP_071387.1	Q9H4Z3	PCIF1_HUMAN	PDX1 C-terminal inhibiting factor 1	466					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						GAGGTTCCTGCCCCGGGTCTG	0.632																																					p.P466S		Atlas-SNP	.											.	PCIF1	51	.	0			c.C1396T						PASS	.						127	120	122					20																	44574722		2203	4300	6503	SO:0001583	missense	63935	exon13			TTCCTGCCCCGGG	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.1396C>T	20.37:g.44574722C>T	ENSP00000361486:p.Pro466Ser	61	0	0		83	22	0.26506	NM_022104	E1P5P1|Q54AB9|Q9NT85	Missense_Mutation	SNP	ENST00000372409.3	37	CCDS13388.1	.	.	.	.	.	.	.	.	.	.	C	9.569	1.120426	0.20877	.	.	ENSG00000100982	ENST00000372409;ENST00000443130	.	.	.	5.14	5.14	0.70334	Phosphorylated CTD interacting factor 1, WW domain (1);	0.168415	0.56097	D	0.000036	T	0.29491	0.0735	N	0.04768	-0.165	0.38097	D	0.937137	B	0.21688	0.059	B	0.22152	0.038	T	0.22138	-1.0225	9	0.20519	T	0.43	-14.9956	10.9093	0.47099	0.0:0.914:0.0:0.086	.	466	Q9H4Z3	PCIF1_HUMAN	S	466	.	ENSP00000361486:P466S	P	+	1	0	PCIF1	44008129	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.613000	0.54152	2.696000	0.92011	0.456000	0.33151	CCC	.	.	none		0.632	PCIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079550.1	NM_022104		T	44574722	C	T	44574722	3	4	29	1	0	0	0	0	1	0	0	0	11589	739	26	2	1438	2	PCIF1	20	44574722	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	526498	44574722	18450798	846	13087											
SLC9A8	23315	hgsc.bcm.edu	37	chr20	48503306	48503306	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagggcaacactgtggagtcGgagcacctgtcggagctcac	9	6	14	12	2	1	0	1	0	0	0	3	3	1	3	1	4	3	3	1	4	1	0	rs73125686	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:48503306G>A	ENST00000361573.2	+	15	1551	c.1509G>A	c.(1507-1509)tcG>tcA	p.S503S	SLC9A8_ENST00000541138.1_Silent_p.S203S|SLC9A8_ENST00000490250.1_3'UTR|SLC9A8_ENST00000417961.1_Silent_p.S519S|SLC9A8_ENST00000539601.1_Silent_p.S284S			Q9Y2E8	SL9A8_HUMAN	solute carrier family 9, subfamily A (NHE8, cation proton antiporter 8), member 8	503					ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	potassium:proton antiporter activity (GO:0015386)|sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	30			BRCA - Breast invasive adenocarcinoma(9;3.91e-07)			CTGTGGAGTCGGAGCACCTGT	0.662													G|||	7	0.00139776	0.0	0.0	5008	,	,		18613	0.0		0.007	False		,,,				2504	0.0				p.S519S		Atlas-SNP	.											.	SLC9A8	63	.	0			c.G1557A						PASS	.	G		14,4392	21.2+/-45.6	0,14,2189	107	86	93		1509	-5.8	1	20	dbSNP_130	93	53,8547	33.8+/-87.4	0,53,4247	no	coding-synonymous	SLC9A8	NM_015266.1		0,67,6436	AA,AG,GG		0.6163,0.3177,0.5151		503/582	48503306	67,12939	2203	4300	6503	SO:0001819	synonymous_variant	23315	exon15			GGAGTCGGAGCAC	AB023156	CCDS13421.1, CCDS58774.1	20q13.13	2013-05-22	2012-03-22		ENSG00000197818	ENSG00000197818		"Solute carriers"	20728	protein-coding gene	gene with protein product		612730	"solute carrier family 9 (sodium/hydrogen exchanger), isoform 8", "solute carrier family 9 (sodium/hydrogen exchanger), member 8"			12409279	Standard	NM_001260491		Approved	KIAA0939, NHE8	uc002xuv.2	Q9Y2E8	OTTHUMG00000032710	ENST00000361573.2:c.1509G>A	20.37:g.48503306G>A		64	0	0		105	55	0.52381	NM_001260491	B4DTQ8|Q2M1U9|Q68CZ8|Q9BX15|Q9Y507	Silent	SNP	ENST00000361573.2	37	CCDS13421.1																																																																																			G|0.996;A|0.004	0.004	strong		0.662	SLC9A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106483.3	XM_030524		A	48503306	G	A	48503306	2	1	29	1	0	0	0	0	0	0	0	1	14735	1103	39	1		1	SLC9A8	20	48503306	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	3928584	48503306	14522214	847	13088											
ZNF831	128611	hgsc.bcm.edu	37	chr20	57768655	57768655	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	catcccagaagcaggatgccGatcccggggaggtgccaggg	9	4	16	12	2	0	1	0	0	0	1	2	4	2	3	4	5	3	1	4	5	1	0	rs61743779	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:57768655G>A	ENST00000371030.2	+	1	2581	c.2581G>A	c.(2581-2583)Gat>Aat	p.D861N		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	861							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)					GCAGGATGCCGATCCCGGGGA	0.652													.|||	19	0.00379393	0.0106	0.0	5008	,	,		13970	0.0		0.004	False		,,,				2504	0.001				p.D861N		Atlas-SNP	.											.	ZNF831	287	.	0			c.G2581A						PASS	.	G	ASN/ASP	37,3899		0,37,1931	32	39	37		2581	4	0	20	dbSNP_129	37	78,8218		0,78,4070	yes	missense	ZNF831	NM_178457.1	23	0,115,6001	AA,AG,GG		0.9402,0.94,0.9402	possibly-damaging	861/1678	57768655	115,12117	1968	4148	6116	SO:0001583	missense	128611	exon1			GATGCCGATCCCG	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.2581G>A	20.37:g.57768655G>A	ENSP00000360069:p.Asp861Asn	61	0	0		53	30	0.566038	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	37	CCDS42894.1	9	0.004120879120879121	5	0.01016260162601626	0	0.0	0	0.0	4	0.005277044854881266	G	14.30	2.493208	0.44352	0.0094	0.009402	ENSG00000124203	ENST00000371030	T	0.06687	3.27	4.91	3.95	0.45737	.	1.458410	0.04186	N	0.327383	T	0.07818	0.0196	L	0.27053	0.805	0.09310	N	1	D	0.58268	0.982	P	0.47102	0.537	T	0.34378	-0.9831	10	0.51188	T	0.08	-1.9265	9.8204	0.40878	0.0972:0.0:0.9028:0.0	rs61743779	861	Q5JPB2	ZN831_HUMAN	N	861	ENSP00000360069:D861N	ENSP00000360069:D861N	D	+	1	0	ZNF831	57202050	0.000000	0.05858	0.015000	0.15790	0.009000	0.06853	-0.138000	0.10374	1.186000	0.42985	0.655000	0.94253	GAT	G|0.996;A|0.004	0.004	strong		0.652	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457		A	57768655	G	A	57768655	3	1	29	1	0	0	0	0	1	0	0	0	18200	1058	37	1	2583	1	ZNF831	20	57768655	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	9265349	57768655	5256865	848	13089											
LAMA5	3911	hgsc.bcm.edu	37	chr20	60898891	60898891	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgggtgcggccgcctcgCaggacacagccctcggcgaa	7	4	14	16	5	0	0	0	0	0	0	2	2	0	1	3	4	2	1	3	4	1	0	rs138911913		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:60898891C>T	ENST00000252999.3	-	44	5856	c.5790G>A	c.(5788-5790)ctG>ctA	p.L1930L		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1930	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)			GGCCGCCTCGCAGGACACAGC	0.687													.|||	1	0.000199681	0.0	0.0	5008	,	,		15565	0.0		0.001	False		,,,				2504	0.0				p.L1930L		Atlas-SNP	.											.	LAMA5	268	.	0			c.G5790A						PASS	.	C		1,4363		0,1,2181	21	23	22		5790	-2	0.1	20	dbSNP_134	22	32,8540		0,32,4254	no	coding-synonymous	LAMA5	NM_005560.3		0,33,6435	TT,TC,CC		0.3733,0.0229,0.2551		1930/3696	60898891	33,12903	2182	4286	6468	SO:0001819	synonymous_variant	3911	exon44			GCCTCGCAGGACA	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.5790G>A	20.37:g.60898891C>T		78	0	0		51	23	0.45098	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			C|0.999;T|0.001	0.001	strong		0.687	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		T	60898891	C	T	60898891	2	4	29	1	0	0	0	0	0	0	0	1	8618	697	25	2		2	LAMA5	20	60898891	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	3130236	60898891	2126629	849	13090											
OGFR	11054	hgsc.bcm.edu	37	chr20	61444660	61444660	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	catcggagaccccaggccccCgcccggcaggacctgcaggg	7	2	14	18	3	0	1	0	0	0	1	1	3	0	2	6	5	1	2	6	5	0	0	rs61743079		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:61444660C>A	ENST00000290291.6	+	7	1718	c.1693C>A	c.(1693-1695)Cgc>Agc	p.R565S	OGFR_ENST00000370461.1_Missense_Mutation_p.R513S	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	565	7 X 20 AA approximate tandem repeats of [ST]-P-S-E-T-P-G-P-[SR]-P-A-G-P-[AT]- [GR]-D-E-P-A-[EK].				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)					CCCAGGCCCCCGCCCGGCAGG	0.741																																					p.R565S		Atlas-SNP	.											OGFR,NS,neuroblastoma,0,1	OGFR	63	1	0			c.C1693A						scavenged	.						3	6	5					20																	61444660		1281	3014	4295	SO:0001583	missense	11054	exon7			GGCCCCCGCCCGG	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.1693C>A	20.37:g.61444660C>A	ENSP00000290291:p.Arg565Ser	4	0	0		8	3	0.375	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Missense_Mutation	SNP	ENST00000290291.6	37	CCDS13504.1	.	.	.	.	.	.	.	.	.	.	A	0.130	-1.114132	0.01799	.	.	ENSG00000060491	ENST00000290291;ENST00000357163;ENST00000370469;ENST00000370461	T;T	0.54866	0.55;0.55	1.46	-2.91	0.05631	.	.	.	.	.	T	0.23649	0.0572	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	0.19031	-1.0318	9	0.11182	T	0.66	.	0.4172	0.00450	0.232:0.1649:0.1659:0.4372	rs61743079	565;548;565	B3KMQ6;Q05BV5;Q9NZT2	.;.;OGFR_HUMAN	S	565;545;400;513	ENSP00000290291:R565S;ENSP00000359491:R513S	ENSP00000290291:R565S	R	+	1	0	OGFR	60915105	0.000000	0.05858	0.002000	0.10522	0.017000	0.09413	-0.466000	0.06672	-1.870000	0.01139	-1.293000	0.01348	CGC	C|0.981;A|0.019	0.019	weak		0.741	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1			A	61444660	C	A	61444660	3	1	29	1	0	0	0	0	1	0	0	0	10852	652	23	4	1719	4	OGFR	20	61444660	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	545769	61444660	1580860	850	13091											
COL9A3	1299	hgsc.bcm.edu	37	chr20	61452556	61452556	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtctgggacccccggggccGcccgggctgggggtgagtat	4	6	19	12	3	1	1	0	1	1	0	1	2	1	2	4	6	0	2	4	6	1	1	rs149690829	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:61452556G>A	ENST00000343916.3	+	6	336	c.333G>A	c.(331-333)ccG>ccA	p.P111P		NM_001853.3	NP_001844.3	Q14050	CO9A3_HUMAN	collagen, type IX, alpha 3	111	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)					CCCCGGGGCCGCCCGGGCTGG	0.617													G|||	2	0.000399361	0.0	0.0	5008	,	,		16029	0.001		0.0	False		,,,				2504	0.001				p.P111P		Atlas-SNP	.											.	COL9A3	70	.	0			c.G333A						PASS	.	G		0,4396		0,0,2198	40	47	45		333	-9.7	0	20	dbSNP_134	45	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	COL9A3	NM_001853.3		0,1,6497	AA,AG,GG		0.0116,0.0,0.0077		111/685	61452556	1,12995	2198	4300	6498	SO:0001819	synonymous_variant	1299	exon6			GGGGCCGCCCGGG	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.333G>A	20.37:g.61452556G>A		61	0	0		51	27	0.529412	NM_001853	Q13681|Q9H4G9|Q9UPE2	Silent	SNP	ENST00000343916.3	37	CCDS13505.1																																																																																			G|1.000;A|0.000	0.000	strong		0.617	COL9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080071.2	NM_001853		A	61452556	G	A	61452556	2	1	29	1	0	0	0	0	0	0	0	1	3711	1074	38	1		1	COL9A3	20	61452556	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	7896	61452556	1572964	851	13092											
PRIC285	85441	hgsc.bcm.edu	37	chr20	62194238	62194238	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcgccctgcagctgcccctgCggcgtccgtgacgcctccca	3	6	12	20	5	0	1	0	1	0	0	2	1	2	1	6	1	4	2	6	1	0	0	rs34996572	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr20:62194238C>T	ENST00000467148.1	-	8	6006	c.5937G>A	c.(5935-5937)ccG>ccA	p.P1979P	HELZ2_ENST00000427522.2_Silent_p.P1410P	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	1979					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)										GCTGCCCCTGCGGCGTCCGTG	0.657													C|||	71	0.0141773	0.0008	0.0303	5008	,	,		15702	0.001		0.0408	False		,,,				2504	0.0072				p.P1979P		Atlas-SNP	.											.	.	.	.	0			c.G5937A						PASS	.	C	,	23,4271		0,23,2124	10	11	11		5937,4230	-9.2	0	20	dbSNP_126	11	243,8151		3,237,3957	no	coding-synonymous,coding-synonymous	PRIC285	NM_001037335.2,NM_033405.3	,	3,260,6081	TT,TC,CC		2.8949,0.5356,2.0965	,	1979/2650,1410/2081	62194238	266,12422	2147	4197	6344	SO:0001819	synonymous_variant	85441	exon9			CCCCTGCGGCGTC	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.5937G>A	20.37:g.62194238C>T		67	0	0		70	33	0.471429	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	37	CCDS33508.1																																																																																			C|0.984;T|0.016	0.016	strong		0.657	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		T	62194238	C	T	62194238	2	4	29	1	0	0	0	0	0	0	0	1	12497	755	27	1		1	PRIC285	20	62194238	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	741682	62194238	831282	852	13093											
TMPRSS15	5651	hgsc.bcm.edu	37	chr21	19704490	19704490	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caaaaggtcctccacagtccGctgaaaaggaaagcaatggg	15	5	11	10	1	0	1	0	1	0	0	3	2	3	2	3	3	1	2	3	3	6	0	rs146718638		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:19704490G>A	ENST00000284885.3	-	14	1598	c.1565C>T	c.(1564-1566)aCg>aTg	p.T522M		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	522						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						TCCACAGTCCGCTGAAAAGGA	0.383													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17327	0.0		0.0	False		,,,				2504	0.0				p.T522M		Atlas-SNP	.											.	TMPRSS15	189	.	0			c.C1565T						PASS	.	G	MET/THR	0,4406		0,0,2203	102	101	102		1565	5.4	1	21	dbSNP_134	102	6,8594	5.0+/-18.6	0,6,4294	yes	missense-near-splice	TMPRSS15	NM_002772.2	81	0,6,6497	AA,AG,GG		0.0698,0.0,0.0461	probably-damaging	522/1020	19704490	6,13000	2203	4300	6503	SO:0001630	splice_region_variant	5651	exon14			CAGTCCGCTGAAA		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.1565-1C>T	21.37:g.19704490G>A		62	0	0		84	36	0.428571	NM_002772	Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	37	CCDS13571.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.095356	0.76870	0.0	6.98E-4	ENSG00000154646	ENST00000284885	D	0.87179	-2.22	5.43	5.43	0.79202	CUB (1);	0.124734	0.53938	D	0.000053	D	0.91758	0.7393	L	0.60455	1.87	0.42859	D	0.994106	D	0.89917	1.0	D	0.67382	0.951	D	0.90913	0.4777	9	.	.	.	.	18.1722	0.89749	0.0:0.0:1.0:0.0	.	522	P98073	ENTK_HUMAN	M	522	ENSP00000284885:T522M	.	T	-	2	0	TMPRSS15	18626361	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	4.749000	0.62155	2.705000	0.92388	0.650000	0.86243	ACG	G|1.000;A|0.000	0.000	weak		0.383	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772	Missense_Mutation	A	19704490	G	A	19704490	5	1	29	1	0	0	0	0	0	0	1	0	16261	1101	38	1	1542	1	TMPRSS15	21	19704490	Splice_Site	SNP	G	TCGA-GR-7351-01A-11D-2210-10		19704490	28425405	853	13094											
KRTAP27-1	643812	hgsc.bcm.edu	37	chr21	31709723	31709723	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagggcctggaattggagtaAgtagtttggacaactccggg	10	9	15	7	1	0	0	0	0	0	0	1	3	1	3	2	5	1	3	2	5	4	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:31709723A>C	ENST00000382835.2	-	1	289	c.264T>G	c.(262-264)acT>acG	p.T88T		NM_001077711.1	NP_001071179.1	Q3LI81	KR271_HUMAN	keratin associated protein 27-1	88						intermediate filament (GO:0005882)				endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(1)	18						AATTGGAGTAAGTAGTTTGGA	0.488																																					p.T88T		Atlas-SNP	.											.	KRTAP27-1	53	.	0			c.T264G						PASS	.						149	145	146					21																	31709723		2203	4300	6503	SO:0001819	synonymous_variant	643812	exon1			GGAGTAAGTAGTT	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.264T>G	21.37:g.31709723A>C		157	0	0		230	45	0.195652	NM_001077711		Silent	SNP	ENST00000382835.2	37	CCDS33532.1																																																																																			.	.	none		0.488	KRTAP27-1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132470.3	NM_001077711		C	31709723	A	C	31709723	2	2	29	1	0	0	0	0	0	0	0	1	8553	59	3	5		5	KRTAP27-1	21	31709723	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	12005233	31709723	16420172	854	13095											
KRTAP13-2	337959	hgsc.bcm.edu	37	chr21	31744062	31744062	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctgtaacaaggagactggCagctcctagaagccaagtag	13	7	12	9	0	1	2	0	0	1	2	2	3	2	2	2	2	3	4	2	2	6	3	rs150635388	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:31744062C>A	ENST00000399889.2	-	1	495	c.470G>T	c.(469-471)tGc>tTc	p.C157F		NM_181621.3	NP_853652.1	Q52LG2	KR132_HUMAN	keratin associated protein 13-2	157						intermediate filament (GO:0005882)				endometrium(1)|kidney(1)|lung(14)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	21						AGGAGACTGGCAGCTCCTAGA	0.507													C|||	5	0.000998403	0.0	0.0014	5008	,	,		18428	0.0		0.004	False		,,,				2504	0.0				p.C157F		Atlas-SNP	.											KRTAP13-2,NS,carcinoma,0,1	KRTAP13-2	29	1	0			c.G470T						PASS	.	C	PHE/CYS	1,4405	2.1+/-5.4	0,1,2202	72	67	69		470	-1	0	21	dbSNP_134	69	22,8578	16.0+/-53.3	0,22,4278	yes	missense	KRTAP13-2	NM_181621.3	205	0,23,6480	AA,AC,CC		0.2558,0.0227,0.1768	benign	157/176	31744062	23,12983	2203	4300	6503	SO:0001583	missense	337959	exon1			GACTGGCAGCTCC	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.470G>T	21.37:g.31744062C>A	ENSP00000382777:p.Cys157Phe	105	0	0		110	65	0.590909	NM_181621		Missense_Mutation	SNP	ENST00000399889.2	37	CCDS13589.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	0.070	-1.205164	0.01568	2.27E-4	0.002558	ENSG00000182816	ENST00000399889	T	0.02863	4.13	5.02	-0.986	0.10252	.	0.755961	0.11281	N	0.580344	T	0.01940	0.0061	N	0.17564	0.495	0.09310	N	1	B	0.13594	0.008	B	0.14023	0.01	T	0.48281	-0.9049	10	0.21540	T	0.41	.	8.3543	0.32321	0.4947:0.4264:0.0:0.0789	.	157	Q52LG2	KR132_HUMAN	F	157	ENSP00000382777:C157F	ENSP00000382777:C157F	C	-	2	0	KRTAP13-2	30665933	0.106000	0.21978	0.001000	0.08648	0.976000	0.68499	-0.467000	0.06664	-0.305000	0.08831	0.655000	0.94253	TGC	C|0.999;A|0.001	0.001	strong		0.507	KRTAP13-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128245.1			A	31744062	C	A	31744062	3	1	29	1	0	0	0	0	1	0	0	0	8532	710	25	4	61	4	KRTAP13-2	21	31744062	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	34339	31744062	16385833	855	13096											
KRTAP19-5	337972	hgsc.bcm.edu	37	chr21	31874240	31874240	+	Missense_Mutation	SNP	T	T	C																															atagcatgatggacggcagcTgcggtatccatagcctccga																								rs117415039	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:31874240T>C	ENST00000334151.2	-	1	195	c.169A>G	c.(169-171)Agc>Ggc	p.S57G		NM_181611.1	NP_853642.1	Q3LI72	KR195_HUMAN	keratin associated protein 19-5	57						intermediate filament (GO:0005882)				endometrium(1)|large_intestine(5)|lung(4)|pancreas(1)|prostate(1)	12						GGACGGCAGCTGCGGTATCCA	0.527													T|||	28	0.00559105	0.0015	0.0072	5008	,	,		17008	0.0		0.0189	False		,,,				2504	0.002				p.S57G		Atlas-SNP	.											.	KRTAP19-5	32	.	0			c.A169G						PASS	.						111	109	110					21																	31874240		2203	4300	6503	SO:0001583	missense	337972	exon1			GGCAGCTGCGGTA	AP001708	CCDS13597.1	21q22.1	2006-03-13			ENSG00000186977	ENSG00000186977		"Keratin associated proteins"	18940	protein-coding gene	gene with protein product						12359730	Standard	NM_181611		Approved	KAP19.5	uc011ada.2	Q3LI72	OTTHUMG00000057774	ENST00000334151.2:c.169A>G	21.37:g.31874240T>C	ENSP00000334985:p.Ser57Gly	57	0	0		65	24	0.369231	NM_181611	A4IF22	Missense_Mutation	SNP	ENST00000334151.2	37	CCDS13597.1	.	.	.	.	.	.	.	.	.	.	T	10.24	1.296388	0.23650	.	.	ENSG00000186977	ENST00000334151	T	0.10288	2.89	5.16	3.98	0.46160	.	2.005650	0.03059	U	0.155572	T	0.11623	0.0283	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.29579	-1.0007	9	0.87932	D	0	-2.7636	8.509	0.33206	0.8243:0.0:0.0:0.1757	.	57	Q3LI72	KR195_HUMAN	G	57	ENSP00000334985:S57G	ENSP00000334985:S57G	S	-	1	0	KRTAP19-5	30796111	0.634000	0.27190	0.008000	0.14137	0.219000	0.24729	1.424000	0.34848	0.904000	0.36572	-0.417000	0.06048	AGC	T|0.975;C|0.025	0.025	strong		0.527	KRTAP19-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128226.2			C	31874240	T	C	31874240	3	2	29	1	0	0	0	0	1	0	0	0	8541	1580	55	3	52	3	KRTAP19-5	21	31874240	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	130178	31874240	16255655	856	13097	166	2									
KRTAP19-5	337972	hgsc.bcm.edu	37	chr21	31874241	31874241	+	Silent	SNP	G	G	T																															tagcatgatggacggcagctGcggtatccatagcctccgaa																								rs150340950	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:31874241G>T	ENST00000334151.2	-	1	194	c.168C>A	c.(166-168)cgC>cgA	p.R56R		NM_181611.1	NP_853642.1	Q3LI72	KR195_HUMAN	keratin associated protein 19-5	56						intermediate filament (GO:0005882)				endometrium(1)|large_intestine(5)|lung(4)|pancreas(1)|prostate(1)	12						GACGGCAGCTGCGGTATCCAT	0.527													G|||	28	0.00559105	0.0015	0.0072	5008	,	,		17028	0.0		0.0189	False		,,,				2504	0.002				p.R56R		Atlas-SNP	.											KRTAP19-5,NS,carcinoma,-2,1	KRTAP19-5	32	1	0			c.C168A						PASS	.						112	110	110					21																	31874241		2203	4300	6503	SO:0001819	synonymous_variant	337972	exon1			GCAGCTGCGGTAT	AP001708	CCDS13597.1	21q22.1	2006-03-13			ENSG00000186977	ENSG00000186977		"Keratin associated proteins"	18940	protein-coding gene	gene with protein product						12359730	Standard	NM_181611		Approved	KAP19.5	uc011ada.2	Q3LI72	OTTHUMG00000057774	ENST00000334151.2:c.168C>A	21.37:g.31874241G>T		57	0	0		66	23	0.348485	NM_181611	A4IF22	Silent	SNP	ENST00000334151.2	37	CCDS13597.1																																																																																			G|0.975;T|0.025	0.025	strong		0.527	KRTAP19-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128226.2			T	31874241	G	T	31874241	2	4	29	1	0	0	0	0	0	0	0	1	8541	1306	46	4		4	KRTAP19-5	21	31874241	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1	31874241	16255654	857	13098	166	2									
HUNK	30811	hgsc.bcm.edu	37	chr21	33368191	33368191	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cagccctcaggctcgcttatGacacagattcagaacaccaa	13	7	7	14	1	2	3	2	1	0	2	3	3	2	3	2	1	2	2	2	1	3	2	rs138721520	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:33368191G>C	ENST00000270112.2	+	10	1776	c.1416G>C	c.(1414-1416)atG>atC	p.M472I	HUNK_ENST00000465574.1_3'UTR	NM_014586.1	NP_055401.1	P57058	HUNK_HUMAN	hormonally up-regulated Neu-associated kinase	472					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						GCTCGCTTATGACACAGATTC	0.532													G|||	7	0.00139776	0.0053	0.0	5008	,	,		19053	0.0		0.0	False		,,,				2504	0.0				p.M472I		Atlas-SNP	.											.	HUNK	74	.	0			c.G1416C						PASS	.	G	ILE/MET	34,4372	39.2+/-71.8	0,34,2169	57	54	55		1416	0.3	0	21	dbSNP_134	55	0,8600		0,0,4300	yes	missense	HUNK	NM_014586.1	10	0,34,6469	CC,CG,GG		0.0,0.7717,0.2614	benign	472/715	33368191	34,12972	2203	4300	6503	SO:0001583	missense	30811	exon10			GCTTATGACACAG	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.1416G>C	21.37:g.33368191G>C	ENSP00000270112:p.Met472Ile	162	0	0		180	106	0.588889	NM_014586		Missense_Mutation	SNP	ENST00000270112.2	37	CCDS13610.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	0.003	-2.395865	0.00198	0.007717	0.0	ENSG00000142149	ENST00000270112;ENST00000439107	T	0.63417	-0.04	4.34	0.337	0.15966	.	0.591295	0.16443	N	0.214240	T	0.22126	0.0533	N	0.01576	-0.805	0.09310	N	0.999994	B	0.02656	0.0	B	0.01281	0.0	T	0.18023	-1.0350	10	0.25751	T	0.34	-4.655	9.205	0.37285	0.0:0.4763:0.443:0.0807	.	472	P57058	HUNK_HUMAN	I	472;86	ENSP00000270112:M472I	ENSP00000270112:M472I	M	+	3	0	HUNK	32290062	0.393000	0.25237	0.004000	0.12327	0.031000	0.12232	0.727000	0.25999	-0.133000	0.11537	-0.867000	0.03001	ATG	G|0.998;C|0.002	0.002	strong		0.532	HUNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192782.1	NM_014586		C	33368191	G	C	33368191	3	2	29	1	0	0	0	0	1	0	0	0	7467	1290	45	4	1454	4	HUNK	21	33368191	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1493950	33368191	14761704	858	13099											
SETD4	54093	hgsc.bcm.edu	37	chr21	37420606	37420606	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcaagtgtgtggtcacttacTtagtaatgtatgcccctaag	10	13	10	8	0	1	0	1	0	0	0	1	0	1	0	2	1	2	3	2	1	6	5			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:37420606T>G	ENST00000399215.1	-	4	1668	c.296A>C	c.(295-297)aAg>aCg	p.K99T	SETD4_ENST00000481477.1_Intron|SETD4_ENST00000399201.1_Splice_Site_p.K75T|SETD4_ENST00000399212.1_Splice_Site_p.K75T|SETD4_ENST00000399205.1_Splice_Site_p.K75T|SETD4_ENST00000399207.1_Splice_Site_p.K99T|SETD4_ENST00000399208.2_Splice_Site_p.K99T|SETD4_ENST00000332131.4_Splice_Site_p.K99T			Q9NVD3	SETD4_HUMAN	SET domain containing 4	99	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.						methyltransferase activity (GO:0008168)			autonomic_ganglia(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	15						GGTCACTTACTTAGTAATGTA	0.463																																					p.K99T		Atlas-SNP	.											.	SETD4	37	.	0			c.A296C						PASS	.						368	302	324					21																	37420606		2203	4300	6503	SO:0001630	splice_region_variant	54093	exon5			ACTTACTTAGTAA	AK001660	CCDS13640.1, CCDS42923.1, CCDS74791.1, CCDS74792.1	21q22.13	2006-02-15	2006-02-15	2006-02-15	ENSG00000185917	ENSG00000185917			1258	protein-coding gene	gene with protein product			"chromosome 21 open reading frame 27", "chromosome 21 open reading frame 18"	C21orf27, C21orf18			Standard	XM_005261000		Approved		uc021wiy.1	Q9NVD3	OTTHUMG00000086483	ENST00000399215.1:c.296+1A>C	21.37:g.37420606T>G		63	0	0		71	15	0.211268	NM_001007259	B4DT14|D3DSG2|D3DSG4|Q8NE19|Q9BU46	Missense_Mutation	SNP	ENST00000399215.1	37	CCDS13640.1	.	.	.	.	.	.	.	.	.	.	T	14.46	2.540882	0.45280	.	.	ENSG00000185917	ENST00000399215;ENST00000399212;ENST00000332131;ENST00000399205;ENST00000399208;ENST00000399201;ENST00000399207;ENST00000424303;ENST00000429161;ENST00000446166	T;T;T;T;T;T;T;T;T;T	0.15139	2.45;2.45;2.45;2.45;2.45;2.45;2.45;2.45;2.45;2.45	5.25	2.89	0.33648	SET domain (1);	0.203653	0.52532	D	0.000080	T	0.11110	0.0271	L	0.34521	1.04	0.80722	D	1	B;B;B;P	0.36086	0.08;0.147;0.241;0.536	B;B;B;B	0.36378	0.077;0.061;0.202;0.223	T	0.21280	-1.0250	9	.	.	.	6.6449	5.4075	0.16330	0.0:0.152:0.1478:0.7002	.	75;99;75;99	A8MTS1;C9JWV5;Q9NVD3-3;Q9NVD3	.;.;.;SETD4_HUMAN	T	99;75;99;75;99;75;99;99;99;75	ENSP00000382163:K99T;ENSP00000382161:K75T;ENSP00000329189:K99T;ENSP00000382156:K75T;ENSP00000382159:K99T;ENSP00000382152:K75T;ENSP00000382158:K99T;ENSP00000399998:K99T;ENSP00000396837:K99T;ENSP00000413318:K75T	.	K	-	2	0	SETD4	36342476	1.000000	0.71417	0.998000	0.56505	0.965000	0.64279	1.283000	0.33237	0.345000	0.23873	0.460000	0.39030	AAG	.	.	none		0.463	SETD4-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194456.1	NM_017438	Missense_Mutation	G	37420606	T	G	37420606	5	3	29	1	0	0	0	0	0	0	1	0	14148	1623	56	5	1077	5	SETD4	21	37420606	Splice_Site	SNP	T	TCGA-GR-7351-01A-11D-2210-10	4052415	37420606	10709289	859	13100											
BRWD1	54014	hgsc.bcm.edu	37	chr21	40582823	40582823	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cagttgctttcaacatagttCgtagctctgatgcttttttt	7	19	7	8	1	2	1	1	1	1	0	3	1	2	1	0	0	4	6	0	0	3	8	rs75046572	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:40582823C>T	ENST00000333229.2	-	35	4260	c.3933G>A	c.(3931-3933)acG>acA	p.T1311T	BRWD1_ENST00000342449.3_Silent_p.T1311T|BRWD1_ENST00000380800.3_Silent_p.T1311T	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	1311					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)				CAACATAGTTCGTAGCTCTGA	0.348													C|||	89	0.0177716	0.0023	0.0519	5008	,	,		18539	0.0109		0.0348	False		,,,				2504	0.0041				p.T1311T	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.G3933A						PASS	.	C	,	35,4371	39.2+/-71.8	0,35,2168	104	97	99		3933,3933	-4.7	0	21	dbSNP_131	99	378,8222	122.2+/-181.2	11,356,3933	no	coding-synonymous,coding-synonymous	BRWD1	NM_018963.4,NM_033656.3	,	11,391,6101	TT,TC,CC		4.3953,0.7944,3.1755	,	1311/2321,1311/2270	40582823	413,12593	2203	4300	6503	SO:0001819	synonymous_variant	54014	exon35			ATAGTTCGTAGCT	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.3933G>A	21.37:g.40582823C>T		74	0	0		116	74	0.637931	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Silent	SNP	ENST00000333229.2	37	CCDS13662.1																																																																																			C|0.970;T|0.030	0.030	strong		0.348	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		T	40582823	C	T	40582823	2	4	29	1	0	0	0	0	0	0	0	1	1527	871	31	1		1	BRWD1	21	40582823	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	3162217	40582823	7547072	860	13101											
UMODL1	89766	hgsc.bcm.edu	37	chr21	43557637	43557637	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgctggtggcgggaacagcCacccttctgatcgtgcgcta	6	9	14	12	3	1	1	0	1	1	0	2	2	1	2	2	3	4	2	2	3	2	2	rs200233807	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:43557637C>T	ENST00000408910.2	+	22	3864	c.3864C>T	c.(3862-3864)gcC>gcT	p.A1288A	UMODL1_ENST00000400424.2_Silent_p.A1216A|UMODL1_ENST00000408989.2_Silent_p.A1416A|UMODL1_ENST00000400423.2_3'UTR|UMODL1_ENST00000400427.1_Silent_p.A1344A	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	1288					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						CGGGAACAGCCACCCTTCTGA	0.547													C|||	3	0.000599042	0.0	0.0	5008	,	,		15307	0.0		0.002	False		,,,				2504	0.001				p.A1416A	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.C4248T						PASS	.	C	,,,	1,4129		0,1,2064	149	157	154		3864,4032,3648,4248	-6.1	0	21		154	14,8372		0,14,4179	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	,,,	0,15,6243	TT,TC,CC		0.1669,0.0242,0.1198	,,,	1288/1319,1344/1375,1216/1247,1416/1447	43557637	15,12501	2065	4193	6258	SO:0001819	synonymous_variant	89766	exon21			AACAGCCACCCTT		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.3864C>T	21.37:g.43557637C>T		131	0	0		205	127	0.619512	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Silent	SNP	ENST00000408910.2	37	CCDS42936.1																																																																																			C|0.999;T|0.001	0.001	strong		0.547	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2			T	43557637	C	T	43557637	2	4	29	1	0	0	0	0	0	0	0	1	16995	581	21	2		2	UMODL1	21	43557637	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2974814	43557637	4572258	861	13102											
DNMT3L	29947	hgsc.bcm.edu	37	chr21	45670790	45670790	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggctgcctggcttgggcCgtgcgtactgcaggagccgg	3	8	19	11	3	0	0	0	0	0	0	0	1	0	1	3	6	5	4	3	6	1	2	rs113593938	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:45670790C>T	ENST00000418993.1	-	10	1295	c.812G>A	c.(811-813)cGg>cAg	p.R271Q	DNMT3L_ENST00000270172.3_Missense_Mutation_p.R271Q|AP001059.5_ENST00000442785.1_RNA	NM_175867.2	NP_787063.1	Q9UJW3	DNM3L_HUMAN	DNA (cytosine-5-)-methyltransferase 3-like	271					chorionic trophoblast cell differentiation (GO:0060718)|DNA methylation (GO:0006306)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|placenta development (GO:0001890)|positive regulation of catalytic activity (GO:0043085)|regulation of gene expression by genetic imprinting (GO:0006349)|spermatogenesis (GO:0007283)	condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(3)	11				Colorectal(79;0.0165)|READ - Rectum adenocarcinoma(84;0.0781)		TGGCTTGGGCCGTGCGTACTG	0.657													C|||	10	0.00199681	0.0	0.0043	5008	,	,		10001	0.0		0.007	False		,,,				2504	0.0				p.R271Q		Atlas-SNP	.											.	DNMT3L	33	.	0			c.G812A						PASS	.	C	GLN/ARG,GLN/ARG	4,4402	8.1+/-20.4	0,4,2199	45	39	41		812,812	1.6	0	21	dbSNP_132	41	43,8557	28.5+/-78.6	1,41,4258	yes	missense,missense	DNMT3L	NM_013369.2,NM_175867.1	43,43	1,45,6457	TT,TC,CC		0.5,0.0908,0.3614	possibly-damaging,possibly-damaging	271/388,271/387	45670790	47,12959	2203	4300	6503	SO:0001583	missense	29947	exon10			TTGGGCCGTGCGT	AF194032	CCDS13705.1	21q22.3	2008-07-31			ENSG00000142182	ENSG00000142182			2980	protein-coding gene	gene with protein product	"cytosine-5-methyltransferase 3-like protein", "human cytosine-5-methyltransferase 3-like protein"	606588				10857753	Standard	NM_013369		Approved	MGC1090	uc002zeh.2	Q9UJW3	OTTHUMG00000086914	ENST00000418993.1:c.812G>A	21.37:g.45670790C>T	ENSP00000412862:p.Arg271Gln	110	0	0		159	88	0.553459	NM_013369	E9PB42|Q9BUJ4	Missense_Mutation	SNP	ENST00000418993.1	37	CCDS46650.1	9|9	0.004120879120879121|0.004120879120879121	0|0	0.0|0.0	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	7|7	0.009234828496042216|0.009234828496042216	C|C	8.432|8.432	0.848933|0.848933	0.17034|0.17034	9.08E-4|9.08E-4	0.005|0.005	ENSG00000142182|ENSG00000142182	ENST00000436357|ENST00000270172;ENST00000418993;ENST00000431166	.|T;T;T	.|0.32753	.|1.44;1.44;1.44	3.53|3.53	1.61|1.61	0.23674|0.23674	.|.	.|0.311404	.|0.28815	.|N	.|0.014056	T|T	0.19604|0.19604	0.0471|0.0471	M|M	0.75777|0.75777	2.31|2.31	0.24644|0.24644	N|N	0.99355|0.99355	.|B;B	.|0.29115	.|0.233;0.233	.|B;B	.|0.09377	.|0.004;0.004	T|T	0.19582|0.19582	-1.0301|-1.0301	5|10	.|0.59425	.|D	.|0.04	-5.898|-5.898	5.0926|5.0926	0.14715|0.14715	0.2011:0.6813:0.0:0.1176|0.2011:0.6813:0.0:0.1176	.|.	.|271;271	.|Q9UJW3-2;Q9UJW3	.|.;DNM3L_HUMAN	S|Q	66|271;271;256	.|ENSP00000270172:R271Q;ENSP00000412862:R271Q;ENSP00000400242:R256Q	.|ENSP00000270172:R271Q	G|R	-|-	1|2	0|0	DNMT3L|DNMT3L	44495218|44495218	0.001000|0.001000	0.12720|0.12720	0.014000|0.014000	0.15608|0.15608	0.045000|0.045000	0.14185|0.14185	-0.211000|-0.211000	0.09332|0.09332	0.229000|0.229000	0.21039|0.21039	0.555000|0.555000	0.69702|0.69702	GGC|CGG	C|0.996;T|0.004	0.004	strong		0.657	DNMT3L-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000195820.1	NM_013369		T	45670790	C	T	45670790	3	4	29	1	0	0	0	0	1	0	0	0	4680	652	23	1	363	1	DNMT3L	21	45670790	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2113153	45670790	2459105	862	13103											
C21orf29	54084	hgsc.bcm.edu	37	chr21	45949769	45949769	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gacagcaccgccagcggggcGttcctgctgggacacagcct	7	5	14	15	3	0	0	0	0	0	0	1	2	1	1	4	3	4	3	4	3	0	1	rs117791519	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:45949769G>A	ENST00000323084.4	-	5	767	c.702C>T	c.(700-702)aaC>aaT	p.N234N	TSPEAR_ENST00000397916.1_Silent_p.N166N	NM_001272037.1|NM_144991.2	NP_001258966.1|NP_659428.2	Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	234	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						CCAGCGGGGCGTTCCTGCTGG	0.632													G|||	11	0.00219649	0.0015	0.0014	5008	,	,		17868	0.0		0.008	False		,,,				2504	0.0				p.N234N		Atlas-SNP	.											.	TSPEAR	110	.	0			c.C702T						PASS	.	G		4,4402	8.1+/-20.4	0,4,2199	40	45	44		702	-5.5	0	21	dbSNP_132	44	51,8549	32.8+/-85.7	0,51,4249	no	coding-synonymous	TSPEAR	NM_144991.2		0,55,6448	AA,AG,GG		0.593,0.0908,0.4229		234/670	45949769	55,12951	2203	4300	6503	SO:0001819	synonymous_variant	54084	exon5			CGGGGCGTTCCTG	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.702C>T	21.37:g.45949769G>A		36	0	0		57	40	0.701754	NM_144991		Silent	SNP	ENST00000323084.4	37	CCDS13712.1																																																																																			G|0.996;A|0.004	0.004	strong		0.632	TSPEAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098761.1	NM_144991		A	45949769	G	A	45949769	2	1	29	1	0	0	0	0	0	0	0	1	2126	1136	40	1		1	C21orf29	21	45949769	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	278979	45949769	2180126	863	13104											
ITGB2	3689	hgsc.bcm.edu	37	chr21	46330667	46330667	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagggagagcagccccaccaGggcgagcagtggggggcgca	9	1	20	11	2	0	1	0	0	0	1	0	4	0	1	3	5	3	3	3	5	0	0	rs5030667	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:46330667G>A	ENST00000397850.2	-	3	483	c.31C>T	c.(31-33)Ctg>Ttg	p.L11L	ITGB2_ENST00000397852.1_Silent_p.L11L|ITGB2_ENST00000355153.4_Silent_p.L11L|ITGB2_ENST00000397854.3_Silent_p.L11L|ITGB2_ENST00000397857.1_Silent_p.L11L|ITGB2_ENST00000523126.1_5'Flank|ITGB2_ENST00000302347.5_Silent_p.L11L|ITGB2_ENST00000397846.3_Silent_p.L11L			P05107	ITB2_HUMAN	integrin, beta 2 (complement component 3 receptor 3 and 4 subunit)	11					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)	AGCCCCACCAGGGCGAGCAGT	0.657													G|||	71	0.0141773	0.0189	0.0144	5008	,	,		19347	0.0		0.0278	False		,,,				2504	0.0082				p.L11L		Atlas-SNP	.											.	ITGB2	107	.	0			c.C31T						PASS	.	G	,	67,4339	61.1+/-98.1	1,65,2137	39	43	42		31,31	2.9	0.2	21	dbSNP_113	42	257,8343	97.7+/-159.3	5,247,4048	no	coding-synonymous,coding-synonymous	ITGB2	NM_000211.3,NM_001127491.1	,	6,312,6185	AA,AG,GG		2.9884,1.5207,2.4912	,	11/770,11/770	46330667	324,12682	2203	4300	6503	SO:0001819	synonymous_variant	3689	exon2			CCACCAGGGCGAG	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.31C>T	21.37:g.46330667G>A		80	0	0		74	28	0.378378	NM_000211	B3KTS8|D3DSM1|Q16418|Q53HS5|Q9UD72	Silent	SNP	ENST00000397850.2	37	CCDS13716.1																																																																																			G|0.975;A|0.025	0.025	strong		0.657	ITGB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206566.2	NM_000211		A	46330667	G	A	46330667	2	1	29	1	0	0	0	0	0	0	0	1	7903	991	35	2		2	ITGB2	21	46330667	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	380898	46330667	1799228	864	13105											
DIP2A	23181	hgsc.bcm.edu	37	chr21	47971585	47971585	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgatcgtggggaacctggttGctgggaagagaatcgctcag	9	9	16	7	2	1	2	1	1	0	1	3	5	1	4	1	4	2	3	1	4	3	1	rs574049766		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr21:47971585G>T	ENST00000417564.2	+	24	2899	c.2878G>T	c.(2878-2880)Gct>Tct	p.A960S	DIP2A_ENST00000318711.7_Missense_Mutation_p.A961S|DIP2A_ENST00000400274.1_Missense_Mutation_p.A956S|DIP2A_ENST00000427143.2_Missense_Mutation_p.A896S			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	960					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)		GAACCTGGTTGCTGGGAAGAG	0.562													G|||	1	0.000199681	0.0	0.0	5008	,	,		17861	0.0		0.001	False		,,,				2504	0.0				p.A960S		Atlas-SNP	.											.	DIP2A	332	.	0			c.G2878T						PASS	.						34	36	36					21																	47971585		1996	4193	6189	SO:0001583	missense	23181	exon24			CTGGTTGCTGGGA	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.2878G>T	21.37:g.47971585G>T	ENSP00000392066:p.Ala960Ser	66	0	0		95	32	0.336842	NM_015151	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Missense_Mutation	SNP	ENST00000417564.2	37	CCDS46655.1	.	.	.	.	.	.	.	.	.	.	G	12.04	1.819361	0.32145	.	.	ENSG00000160305	ENST00000400274;ENST00000427143;ENST00000318711;ENST00000417564	T;T;T;T	0.22945	1.94;1.94;1.94;1.93	5.34	3.46	0.39613	.	0.000000	0.85682	D	0.000000	T	0.20129	0.0484	L	0.42245	1.32	0.58432	D	0.999999	B;B;B	0.27117	0.132;0.038;0.168	B;B;B	0.31191	0.081;0.013;0.125	T	0.04268	-1.0964	10	0.02654	T	1	-11.1468	13.3584	0.60642	0.0:0.0:0.7124:0.2876	.	961;896;960	E9PER1;E7EMA5;Q14689	.;.;DIP2A_HUMAN	S	956;896;961;960	ENSP00000383133:A956S;ENSP00000400528:A896S;ENSP00000323633:A961S;ENSP00000392066:A960S	ENSP00000323633:A961S	A	+	1	0	DIP2A	46796013	1.000000	0.71417	0.991000	0.47740	0.997000	0.91878	3.230000	0.51286	0.565000	0.29255	0.655000	0.94253	GCT	.	.	none		0.562	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151		T	47971585	G	T	47971585	3	4	29	1	0	0	0	0	1	0	0	0	4529	1319	46	4	3054	4	DIP2A	21	47971585	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1640918	47971585	158310	865	13106											
DGCR2	9993	hgsc.bcm.edu	37	chr22	19028744	19028744	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgcagcggcgtgaggcccGtgccaaacccgtctgggccg	6	5	16	14	5	1	1	0	1	1	0	1	2	1	1	4	3	4	1	4	3	1	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:19028744G>A	ENST00000263196.7	-	9	1470	c.1223C>T	c.(1222-1224)aCg>aTg	p.T408M	DGCR2_ENST00000537045.1_Missense_Mutation_p.T367M|DGCR2_ENST00000545799.1_3'UTR	NM_001184781.1|NM_005137.2	NP_001171710.1|NP_005128.1	P98153	IDD_HUMAN	DiGeorge syndrome critical region gene 2	408					cell adhesion (GO:0007155)|cognition (GO:0050890)|organ morphogenesis (GO:0009887)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)	18	Colorectal(54;0.0993)					CGTGAGGCCCGTGCCAAACCC	0.587																																					p.T408M		Atlas-SNP	.											.	DGCR2	45	.	0			c.C1223T						PASS	.						91	79	83					22																	19028744		2203	4300	6503	SO:0001583	missense	9993	exon9			AGGCCCGTGCCAA	D79985	CCDS33598.1, CCDS54496.1	22q11.21	2008-06-12			ENSG00000070413	ENSG00000070413			2845	protein-coding gene	gene with protein product	"integral membrane protein DGCR2"	600594				7655455, 8630060	Standard	NM_005137		Approved	KIAA0163, LAN, IDD, DGS-C, SEZ-12	uc002zoq.1	P98153	OTTHUMG00000150141	ENST00000263196.7:c.1223C>T	22.37:g.19028744G>A	ENSP00000263196:p.Thr408Met	72	0	0		72	4	0.0555556	NM_005137	A6NIB5|A8K6K5|B5TY34|B7Z935	Missense_Mutation	SNP	ENST00000263196.7	37	CCDS33598.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.571021	0.86542	.	.	ENSG00000070413	ENST00000537045;ENST00000263196	T;D	0.97352	0.76;-4.35	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	D	0.98340	0.9449	M	0.69823	2.125	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.98951	1.0794	10	0.87932	D	0	.	20.0384	0.97572	0.0:0.0:1.0:0.0	.	364;408	B7Z3T5;P98153	.;IDD_HUMAN	M	367;408	ENSP00000440062:T367M;ENSP00000263196:T408M	ENSP00000263196:T408M	T	-	2	0	DGCR2	17408744	1.000000	0.71417	0.970000	0.41538	0.412000	0.31113	9.744000	0.98853	2.837000	0.97791	0.655000	0.94253	ACG	.	.	none		0.587	DGCR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316504.1	NM_005137		A	19028744	G	A	19028744	3	1	29	1	0	0	0	0	1	0	0	0	4463	1145	40	1	437	1	DGCR2	22	19028744	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10		19028744	32275822	866	13107											
HIRA	7290	hgsc.bcm.edu	37	chr22	19385570	19385570	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttatccacgctgcatgaggcTagccaggcatcgtggggaga	9	8	14	10	2	0	2	0	1	0	1	2	3	1	2	2	4	2	4	2	4	2	2	rs373432911		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:19385570T>C	ENST00000263208.5	-	6	694	c.438A>G	c.(436-438)ctA>ctG	p.L146L	HIRA_ENST00000546308.1_Silent_p.L102L|HIRA_ENST00000541063.1_Silent_p.L102L|HIRA_ENST00000464189.1_5'Flank|HIRA_ENST00000340170.4_Silent_p.L146L	NM_003325.3	NP_003316.3	P54198	HIRA_HUMAN	histone cell cycle regulator	146					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)					TGCATGAGGCTAGCCAGGCAT	0.517																																					p.L146L		Atlas-SNP	.											.	HIRA	100	.	0			c.A438G						PASS	.	T		0,4406		0,0,2203	103	85	91		438	-3.9	1	22		91	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	HIRA	NM_003325.3		0,2,6501	CC,CT,TT		0.0233,0.0,0.0154		146/1018	19385570	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	7290	exon6			TGAGGCTAGCCAG	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.438A>G	22.37:g.19385570T>C		77	0	0		86	49	0.569767	NM_003325	Q05BU9|Q8IXN2	Silent	SNP	ENST00000263208.5	37	CCDS13759.1																																																																																			.	.	weak		0.517	HIRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316488.2	NM_003325		C	19385570	T	C	19385570	2	2	29	1	0	0	0	0	0	0	0	1	7129	1509	53	3		3	HIRA	22	19385570	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	356826	19385570	31918996	867	13108											
PRAME	23532	hgsc.bcm.edu	37	chr22	22893394	22893394	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaagagctccctgggcagcaActccagggcggcaatggcca	10	4	14	13	1	0	1	0	0	0	1	2	2	2	1	3	4	3	4	3	4	3	0	rs41310248	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:22893394A>T	ENST00000398741.1	-	4	445	c.139T>A	c.(139-141)Ttg>Atg	p.L47M	PRAME_ENST00000402697.1_Missense_Mutation_p.L47M|PRAME_ENST00000406503.1_Missense_Mutation_p.L47M|PRAME_ENST00000485532.1_5'UTR|PRAME_ENST00000543184.1_Missense_Mutation_p.L47M|PRAME_ENST00000539862.1_Missense_Mutation_p.L31M|PRAME_ENST00000424204.2_Missense_Mutation_p.L31M|PRAME_ENST00000405655.3_Missense_Mutation_p.L47M|PRAME_ENST00000398743.2_Missense_Mutation_p.L47M	NM_206955.1	NP_996838.1	P78395	PRAME_HUMAN	preferentially expressed antigen in melanoma	47					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)		CTGGGCAGCAACTCCAGGGCG	0.617													A|||	32	0.00638978	0.0023	0.0072	5008	,	,		11531	0.0		0.0209	False		,,,				2504	0.0031				p.L47M	Melanoma(73;1707 1838 15168 27201)	Atlas-SNP	.											.	PRAME	78	.	0			c.T139A						PASS	.	A	MET/LEU,MET/LEU,MET/LEU,MET/LEU,MET/LEU	29,4377	36.0+/-67.5	0,29,2174	73	74	73		139,139,139,139,139	-5.9	0	22	dbSNP_127	73	296,8304	107.6+/-168.3	7,282,4011	yes	missense,missense,missense,missense,missense	PRAME	NM_006115.3,NM_206953.1,NM_206954.1,NM_206955.1,NM_206956.1	15,15,15,15,15	7,311,6185	TT,TA,AA		3.4419,0.6582,2.4988	benign,benign,benign,benign,benign	47/510,47/510,47/510,47/510,47/510	22893394	325,12681	2203	4300	6503	SO:0001583	missense	23532	exon4			GCAGCAACTCCAG	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.139T>A	22.37:g.22893394A>T	ENSP00000381726:p.Leu47Met	45	0	0		41	25	0.609756	NM_206954	B2R6Y7|O43481|Q8IXN8	Missense_Mutation	SNP	ENST00000398741.1	37	CCDS13801.1	26|26	0.011904761904761904|0.011904761904761904	3|3	0.006097560975609756|0.006097560975609756	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	19|19	0.025065963060686015|0.025065963060686015	a|a	13.46|13.46	2.244046|2.244046	0.39697|0.39697	0.006582|0.006582	0.034419|0.034419	ENSG00000185686|ENSG00000185686	ENST00000398743;ENST00000543184;ENST00000398741;ENST00000405655;ENST00000539862;ENST00000402697;ENST00000424204;ENST00000439106;ENST00000420709;ENST00000406503;ENST00000403441|ENST00000438888	T;T;T;T;T;T;T;T;T;T;T|.	0.04758|.	3.56;3.56;3.56;3.56;3.56;3.56;3.56;3.56;3.56;3.56;3.56|.	3.36|3.36	-5.92|-5.92	0.02261|0.02261	.|.	1.473330|.	0.03603|.	N|.	0.233652|.	T|T	0.13756|0.13756	0.0333|0.0333	L|L	0.52573|0.52573	1.65|1.65	0.09310|0.09310	N|N	1|1	D|.	0.54601|.	0.967|.	P|.	0.55161|.	0.77|.	T|T	0.32824|0.32824	-0.9892|-0.9892	10|5	0.54805|.	T|.	0.06|.	.|.	5.1917|5.1917	0.15212|0.15212	0.6477:0.151:0.1109:0.0904|0.6477:0.151:0.1109:0.0904	rs41310248|rs41310248	47|.	P78395|.	PRAME_HUMAN|.	M|D	47;47;47;47;31;47;31;47;47;47;47|70	ENSP00000381728:L47M;ENSP00000445675:L47M;ENSP00000381726:L47M;ENSP00000384343:L47M;ENSP00000445097:L31M;ENSP00000385198:L47M;ENSP00000407342:L31M;ENSP00000407320:L47M;ENSP00000412318:L47M;ENSP00000384058:L47M;ENSP00000385091:L47M|.	ENSP00000381726:L47M|.	L|V	-|-	1|2	2|0	PRAME|PRAME	21223394|21223394	0.000000|0.000000	0.05858|0.05858	0.005000|0.005000	0.12908|0.12908	0.668000|0.668000	0.39293|0.39293	-2.016000|-2.016000	0.01446|0.01446	-1.139000|-1.139000	0.02881|0.02881	-0.213000|-0.213000	0.12676|0.12676	TTG|GTT	A|0.978;T|0.022	0.022	strong		0.617	PRAME-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321644.1	NM_206953		T	22893394	A	T	22893394	3	4	29	1	0	0	0	0	1	0	0	0	12436	40	2	5	1402	5	PRAME	22	22893394	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	3507824	22893394	28411172	868	13109											
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230370	23230370	+	Frame_Shift_Del	DEL	A	A	-																															gcgcccaatggttgcaccgcAaagcggggacccagaccctg																								rs538001103	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:23230370delA	ENST00000526893.1	+	1	411	c.137delA	c.(136-138)caafs	p.Q46fs	IGLL5_ENST00000531372.1_Frame_Shift_Del_p.Q46fs|IGLL5_ENST00000532223.2_Frame_Shift_Del_p.Q46fs|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	46						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GTTGCACCGCAAAGCGGGGAC	0.682																																					p.Q46fs		Pindel,Atlas-Indel	.											.	IGLL5	26	.	0			c.136delC						PASS	.																																			SO:0001589	frameshift_variant	100423062	exon1			.	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.137delA	22.37:g.23230370delA	ENSP00000431254:p.Gln46fs	144	0	.		45	10	0.222	NM_001178126		Frame_Shift_Del	DEL	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.682	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		-	23230370	A	-	23230370	7	5	29	1	0	1	0	1	0	0	0	0	7603	130	5	0	139	0	IGLL5	22	23230370	Frame_Shift_Del	DEL	A	TCGA-GR-7351-01A-11D-2210-10	336976	23230370	28074196	869	13110											
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230404	23230404	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccctggagcctcagttggAagcagccgatccagcctgcg	8	6	13	14	2	1	0	1	0	0	0	2	4	2	2	5	2	5	2	5	2	1	1	rs115653109	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:23230404A>C	ENST00000526893.1	+	1	445	c.171A>C	c.(169-171)ggA>ggC	p.G57G	IGLL5_ENST00000531372.1_Silent_p.G57G|IGLL5_ENST00000532223.2_Silent_p.G57G|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	57						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CCTCAGTTGGAAGCAGCCGAT	0.662																																					p.E22A		Atlas-SNP	.											.	IGLL5	26	.	0			c.A65C						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			AGTTGGAAGCAGC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.171A>C	22.37:g.23230404A>C		141	0	0		41	12	0.292683	NM_001256296		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			A|0.999;G|0.001	.	alt		0.662	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		C	23230404	A	C	23230404	2	2	29	1	0	0	0	0	0	0	0	1	7603	233	9	5		5	IGLL5	22	23230404	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	34	23230404	28074162	870	13111											
MN1	4330	hgsc.bcm.edu	37	chr22	28192809	28192809	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagggcgccaacgtcttgtcGtcgtccgcgctgtccaccag	5	8	12	16	6	1	0	0	0	1	0	5	0	3	0	4	1	1	1	4	1	1	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:28192809G>A	ENST00000302326.4	-	1	4677	c.3723C>T	c.(3721-3723)gaC>gaT	p.D1241D		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	1241					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						ACGTCTTGTCGTCGTCCGCGC	0.607			T	ETV6	"AML, meningioma"																																p.D1241D		Atlas-SNP	.		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"L, O"	.	MN1	122	.	0			c.C3723T						PASS	.						91	97	95					22																	28192809		2149	4245	6394	SO:0001819	synonymous_variant	4330	exon1			CTTGTCGTCGTCC	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.3723C>T	22.37:g.28192809G>A		81	0	0		96	30	0.3125	NM_002430	A9Z1V9	Silent	SNP	ENST00000302326.4	37	CCDS42998.1																																																																																			.	.	none		0.607	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430		A	28192809	G	A	28192809	2	1	29	1	0	0	0	0	0	0	0	1	9682	1136	40	1		1	MN1	22	28192809	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	4962405	28192809	23111757	871	13112											
ZNRF3	84133	hgsc.bcm.edu	37	chr22	29445817	29445817	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tggccgactgcccaggcagcGacagcagcagcagcagcagc	10	2	14	15	2	0	0	0	0	0	0	0	2	0	0	2	2	8	6	2	2	0	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:29445817G>A	ENST00000544604.2	+	8	1823	c.1648G>A	c.(1648-1650)Gac>Aac	p.D550N	ZNRF3_ENST00000332811.4_Missense_Mutation_p.D450N|ZNRF3_ENST00000406323.3_Missense_Mutation_p.D450N|ZNRF3_ENST00000402174.1_Missense_Mutation_p.D450N	NM_001206998.1	NP_001193927.1	Q9ULT6	ZNRF3_HUMAN	zinc and ring finger 3	550					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						CCCAGgcagcgacagcagcag	0.662																																					p.D550N		Atlas-SNP	.											.	ZNRF3	75	.	0			c.G1648A						PASS	.						14	17	16					22																	29445817		1965	3949	5914	SO:0001583	missense	84133	exon8			GGCAGCGACAGCA	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.1648G>A	22.37:g.29445817G>A	ENSP00000443824:p.Asp550Asn	110	0	0		86	27	0.313953	NM_001206998	B3KU18|Q6ICH1|Q6NTF8|Q8WU18	Missense_Mutation	SNP	ENST00000544604.2	37	CCDS56225.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.650547	0.87958	.	.	ENSG00000183579	ENST00000544604;ENST00000332811;ENST00000462485;ENST00000402174;ENST00000406323	T;T;T;T	0.80738	-1.41;-1.41;-1.41;-1.41	5.44	5.44	0.79542	.	0.289400	0.41712	D	0.000829	D	0.88672	0.6500	M	0.61703	1.905	0.52501	D	0.999951	D	0.89917	1.0	D	0.85130	0.997	D	0.89083	0.3477	10	0.62326	D	0.03	-1.1774	18.24	0.89965	0.0:0.0:1.0:0.0	.	550	Q9ULT6	ZNRF3_HUMAN	N	550;450;257;450;450	ENSP00000443824:D550N;ENSP00000328614:D450N;ENSP00000384456:D450N;ENSP00000384553:D450N	ENSP00000328614:D450N	D	+	1	0	ZNRF3	27775817	1.000000	0.71417	0.999000	0.59377	0.844000	0.47949	9.357000	0.97099	2.546000	0.85860	0.655000	0.94253	GAC	.	.	none		0.662	ZNRF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320943.2	XM_290972		A	29445817	G	A	29445817	3	1	29	1	0	0	0	0	1	0	0	0	18228	1058	37	1	1374	1	ZNRF3	22	29445817	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1253008	29445817	21858749	872	13113											
HORMAD2	150280	hgsc.bcm.edu	37	chr22	30518155	30518155	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gagaacagcactactgagatCgcccatcagggtctagactg	12	7	11	11	1	2	3	1	1	1	3	3	5	2	3	1	1	3	1	1	1	3	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:30518155C>T	ENST00000336726.6	+	10	1126	c.771C>T	c.(769-771)atC>atT	p.I257I	HORMAD2_ENST00000403975.1_Silent_p.I257I	NM_152510.2	NP_689723.1	Q8N7B1	HORM2_HUMAN	HORMA domain containing 2	257					meiotic nuclear division (GO:0007126)|meiotic sister chromatid cohesion (GO:0051177)	chromosome (GO:0005694)|nucleus (GO:0005634)				large_intestine(1)|lung(1)	2			Epithelial(10;0.125)			CTACTGAGATCGCCCATCAGG	0.408																																					p.I257I		Atlas-SNP	.											.	HORMAD2	12	.	0			c.C771T						PASS	.						51	51	51					22																	30518155		1918	4128	6046	SO:0001819	synonymous_variant	150280	exon10			TGAGATCGCCCAT	AK098703	CCDS46683.1	22q12.2	2014-01-21			ENSG00000176635	ENSG00000176635			28383	protein-coding gene	gene with protein product						12477932	Standard	NM_152510		Approved	MGC26710, CT46.2	uc003agy.3	Q8N7B1	OTTHUMG00000150881	ENST00000336726.6:c.771C>T	22.37:g.30518155C>T		106	0	0		107	52	0.485981	NM_152510	B5MEB2|Q8NHR2	Silent	SNP	ENST00000336726.6	37	CCDS46683.1																																																																																			.	.	none		0.408	HORMAD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320416.2	NM_152510		T	30518155	C	T	30518155	2	4	29	1	0	0	0	0	0	0	0	1	7296	874	31	1		1	HORMAD2	22	30518155	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	1072338	30518155	20786411	873	13114											
LARGE	9215	hgsc.bcm.edu	37	chr22	34000460	34000460	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tagaagtccacacgcacagcGggcaccatccaggtctggaa	12	5	11	13	2	1	1	0	0	1	1	3	2	3	2	3	3	1	2	3	3	3	1	rs36002910	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:34000460G>A	ENST00000354992.2	-	6	1147	c.576C>T	c.(574-576)ccC>ccT	p.P192P	LARGE_ENST00000337431.2_Silent_p.P192P|LARGE_ENST00000437602.2_Silent_p.P192P|LARGE_ENST00000397394.2_Silent_p.P192P|LARGE_ENST00000402320.1_Silent_p.P192P	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	192					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)				CACGCACAGCGGGCACCATCC	0.567													G|||	72	0.014377	0.0015	0.0216	5008	,	,		19700	0.0		0.0477	False		,,,				2504	0.0072				p.P192P	Colon(70;397 1175 4573 19089 45288)	Atlas-SNP	.											.	LARGE	98	.	0			c.C576T						PASS	.	G	,	24,4382	30.8+/-60.4	0,24,2179	139	115	123		576,576	-7.5	0.9	22	dbSNP_126	123	253,8347	100.1+/-161.6	6,241,4053	no	coding-synonymous,coding-synonymous	LARGE	NM_004737.4,NM_133642.3	,	6,265,6232	AA,AG,GG		2.9419,0.5447,2.1298	,	192/757,192/757	34000460	277,12729	2203	4300	6503	SO:0001819	synonymous_variant	9215	exon6			CACAGCGGGCACC	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.576C>T	22.37:g.34000460G>A		86	0	0		104	67	0.644231	NM_004737	B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	Silent	SNP	ENST00000354992.2	37	CCDS13912.1																																																																																			G|0.979;A|0.021	0.021	strong		0.567	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320515.2	NM_133642		A	34000460	G	A	34000460	2	1	29	1	0	0	0	0	0	0	0	1	8636	1103	39	1		1	LARGE	22	34000460	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	3482305	34000460	17304106	874	13115											
MYH9	4627	hgsc.bcm.edu	37	chr22	36690158	36690158	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgcagcttggtgaccttgtCggccagctctgtgcgcacgc	4	10	13	14	3	1	1	0	1	1	0	2	1	1	1	2	2	4	4	2	2	0	2	rs147031322		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:36690158C>T	ENST00000216181.5	-	28	4047	c.3817G>A	c.(3817-3819)Gac>Aac	p.D1273N		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1273					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)	p.D1273N(1)		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						GTGACCTTGTCGGCCAGCTCT	0.657			T	ALK	ALCL		"Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"		Hereditary Macrothrombocytopenia, MYH9-associated																												p.D1273N		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"myosin, heavy polypeptide 9, non-muscle"	yes	L	MYH9,rectum,carcinoma,0,1	MYH9	225	1	1	Substitution - Missense(1)	large_intestine(1)	c.G3817A						PASS	.	C	ASN/ASP	0,4406		0,0,2203	68	65	66		3817	5	1	22	dbSNP_134	66	2,8598	2.2+/-6.3	0,2,4298	no	missense	MYH9	NM_002473.4	23	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	1273/1961	36690158	2,13004	2203	4300	6503	SO:0001583	missense	4627	exon28	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	CCTTGTCGGCCAG		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.3817G>A	22.37:g.36690158C>T	ENSP00000216181:p.Asp1273Asn	48	0	0		49	20	0.408163	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Missense_Mutation	SNP	ENST00000216181.5	37	CCDS13927.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.608292	0.87258	0.0	2.33E-4	ENSG00000100345	ENST00000216181	D	0.82893	-1.66	4.98	4.98	0.66077	Myosin tail (1);	0.107359	0.64402	D	0.000006	T	0.77096	0.4080	N	0.20986	0.625	0.80722	D	1	B	0.28178	0.202	B	0.35353	0.201	T	0.72497	-0.4275	10	0.25751	T	0.34	.	18.6261	0.91340	0.0:1.0:0.0:0.0	.	1273	P35579	MYH9_HUMAN	N	1273	ENSP00000216181:D1273N	ENSP00000216181:D1273N	D	-	1	0	MYH9	35020104	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.954000	0.70298	2.454000	0.82982	0.561000	0.74099	GAC	C|1.000;T|0.000	0.000	weak		0.657	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473		T	36690158	C	T	36690158	3	4	29	1	0	0	0	0	1	0	0	0	10051	884	31	1	2121	1	MYH9	22	36690158	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	2689698	36690158	14614408	875	13116											
TXN2	25828	hgsc.bcm.edu	37	chr22	36872873	36872873	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gccaccatcttctctaacctCggccccaggatcttgcaggg	7	9	9	16	1	3	0	0	0	3	0	5	1	3	1	5	3	2	1	5	3	1	3	rs150502647	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:36872873C>T	ENST00000216185.2	-	3	760	c.294G>A	c.(292-294)ccG>ccA	p.P98P	TXN2_ENST00000416967.1_5'UTR|TXN2_ENST00000487725.1_5'UTR|TXN2_ENST00000403313.1_Silent_p.P98P			Q99757	THIOM_HUMAN	thioredoxin 2	98	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						TCTCTAACCTCGGCCCCAGGA	0.547													c|||	24	0.00479233	0.0	0.0144	5008	,	,		17737	0.0		0.0099	False		,,,				2504	0.0041				p.P98P		Atlas-SNP	.											.	TXN2	15	.	0			c.G294A						PASS	.	C		6,4400	11.4+/-27.6	0,6,2197	191	152	165		294	-10.3	0	22	dbSNP_134	165	81,8519	46.7+/-105.8	2,77,4221	no	coding-synonymous	TXN2	NM_012473.3		2,83,6418	TT,TC,CC		0.9419,0.1362,0.6689		98/167	36872873	87,12919	2203	4300	6503	SO:0001819	synonymous_variant	25828	exon3			TAACCTCGGCCCC	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.294G>A	22.37:g.36872873C>T		120	0	0		138	67	0.485507	NM_012473	Q5JZA0|Q6FH60|Q9UH29	Silent	SNP	ENST00000216185.2	37	CCDS13928.1																																																																																			C|0.993;T|0.007	0.007	strong		0.547	TXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319016.1	NM_012473		T	36872873	C	T	36872873	2	4	29	1	0	0	0	0	0	0	0	1	16806	871	31	1		1	TXN2	22	36872873	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	182715	36872873	14431693	876	13117											
ATF4	468	hgsc.bcm.edu	37	chr22	39917561	39917561	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctaggtctcttagatgattaCctggaggtggccaagcactt	9	12	11	9	0	1	2	0	1	1	1	2	3	1	3	2	4	2	1	2	4	4	4	rs375843215		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:39917561C>T	ENST00000337304.2	+	1	993	c.111C>T	c.(109-111)taC>taT	p.Y37Y	ATF4_ENST00000396680.1_Silent_p.Y37Y|ATF4_ENST00000404241.2_Silent_p.Y37Y	NM_001675.2	NP_001666.2	P18848	ATF4_HUMAN	activating transcription factor 4	37					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)	TAGATGATTACCTGGAGGTGG	0.577																																					p.Y37Y		Atlas-SNP	.											.	ATF4	27	.	0			c.C111T						PASS	.	C	,	0,4406		0,0,2203	63	62	63		111,111	3.3	1	22		63	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ATF4	NM_001675.2,NM_182810.1	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	37/352,37/352	39917561	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	468	exon1			TGATTACCTGGAG	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.111C>T	22.37:g.39917561C>T		112	0	0		100	45	0.45	NM_001675	Q9UH31	Silent	SNP	ENST00000337304.2	37	CCDS13996.1																																																																																			.	.	weak		0.577	ATF4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321305.1	NM_001675		T	39917561	C	T	39917561	2	4	29	1	0	0	0	0	0	0	0	1	1082	518	18	2		2	ATF4	22	39917561	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	3044688	39917561	11387005	877	13118											
PARVB	29780	hgsc.bcm.edu	37	chr22	44495953	44495953	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagaacgaggagcgcacgAtgattgaccccacttccaag	13	5	12	11	3	0	3	0	2	0	1	1	7	1	4	3	2	2	1	3	2	2	2	rs56194750	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:44495953A>G	ENST00000338758.7	+	3	286	c.223A>G	c.(223-225)Atg>Gtg	p.M75V	PARVB_ENST00000404989.1_Missense_Mutation_p.M38V|PARVB_ENST00000406477.3_Missense_Mutation_p.M108V|PARVB_ENST00000477795.1_3'UTR	NM_013327.4	NP_037459.2	Q9HBI1	PARVB_HUMAN	parvin, beta	75					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)				GGAGCGCACGATGATTGACCC	0.572													A|||	3	0.000599042	0.0	0.0014	5008	,	,		18925	0.0		0.002	False		,,,				2504	0.0				p.M108V		Atlas-SNP	.											.	PARVB	44	.	0			c.A322G						PASS	.	A	VAL/MET,VAL/MET	4,4402	8.1+/-20.4	0,4,2199	123	100	108		322,223	3.5	0.9	22	dbSNP_129	108	35,8565	23.4+/-69.3	0,35,4265	yes	missense,missense	PARVB	NM_001003828.2,NM_013327.4	21,21	0,39,6464	GG,GA,AA		0.407,0.0908,0.2999	benign,benign	108/398,75/365	44495953	39,12967	2203	4300	6503	SO:0001583	missense	29780	exon4			CGCACGATGATTG	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.223A>G	22.37:g.44495953A>G	ENSP00000342492:p.Met75Val	79	0	0		66	35	0.530303	NM_001003828	B0QYM8|B0QYN1|B2R9X6|Q5TGJ5|Q86X93|Q96PN1|Q9NSP7|Q9UGT3|Q9Y368|Q9Y3L6|Q9Y3L7	Missense_Mutation	SNP	ENST00000338758.7	37	CCDS14056.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	A	12.33	1.905546	0.33628	9.08E-4	0.00407	ENSG00000188677	ENST00000406477;ENST00000338758;ENST00000402876;ENST00000444029;ENST00000404989	T;T;T;T;T	0.34275	1.37;1.37;1.37;1.37;1.37	4.5	3.45	0.39498	Calponin homology domain (1);	0.131379	0.64402	N	0.000001	T	0.31513	0.0799	L	0.52905	1.665	0.47511	D	0.999442	B;B;B;B	0.16166	0.005;0.001;0.003;0.016	B;B;B;B	0.23018	0.006;0.005;0.008;0.043	T	0.07908	-1.0748	10	0.40728	T	0.16	-2.8779	7.5657	0.27876	0.8909:0.0:0.1091:0.0	rs56194750	75;38;75;108	A6NG58;B0QYM8;Q9HBI1;Q9HBI1-2	.;.;PARVB_HUMAN;.	V	108;75;75;73;38	ENSP00000384515:M108V;ENSP00000342492:M75V;ENSP00000385331:M75V;ENSP00000393758:M73V;ENSP00000384353:M38V	ENSP00000342492:M75V	M	+	1	0	PARVB	42827286	1.000000	0.71417	0.919000	0.36401	0.989000	0.77384	4.938000	0.63519	0.585000	0.29608	0.460000	0.39030	ATG	A|0.997;G|0.003	0.003	strong		0.572	PARVB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319518.2	NM_001003828		G	44495953	A	G	44495953	3	3	29	1	0	0	0	0	1	0	0	0	11478	333	12	3	452	3	PARVB	22	44495953	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	4578392	44495953	6808613	878	13119											
WNT7B	7477	hgsc.bcm.edu	37	chr22	46319203	46319203	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttgcactccagctgcatccGgtcctctagaacctgcgggt	6	10	10	15	2	1	1	0	0	1	1	4	1	4	1	4	2	5	3	4	2	2	2	rs147287645		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:46319203G>A	ENST00000339464.4	-	4	957	c.583C>T	c.(583-585)Cgg>Tgg	p.R195W	WNT7B_ENST00000409496.3_Missense_Mutation_p.R199W|WNT7B_ENST00000410089.1_Missense_Mutation_p.R179W	NM_058238.2	NP_478679.1	P56706	WNT7B_HUMAN	wingless-type MMTV integration site family, member 7B	195					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)		AGCTGCATCCGGTCCTCTAGA	0.657																																					p.R195W		Atlas-SNP	.											.	WNT7B	45	.	0			c.C583T						PASS	.	G	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	35	32	33		583	2.2	1	22	dbSNP_134	33	0,8598		0,0,4299	no	missense	WNT7B	NM_058238.2	101	0,1,6501	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	195/350	46319203	1,13003	2203	4299	6502	SO:0001583	missense	7477	exon4			GCATCCGGTCCTC	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.583C>T	22.37:g.46319203G>A	ENSP00000341032:p.Arg195Trp	63	0	0		66	18	0.272727	NM_058238	B8A596|Q96Q12	Missense_Mutation	SNP	ENST00000339464.4	37	CCDS33667.1	.	.	.	.	.	.	.	.	.	.	G	11.59	1.685148	0.29872	2.27E-4	0.0	ENSG00000188064	ENST00000339464;ENST00000410089;ENST00000409496	T;T;T	0.76578	-1.03;-1.03;-1.03	3.33	2.19	0.27852	.	0.060599	0.64402	U	0.000011	T	0.79639	0.4480	L	0.58810	1.83	0.80722	D	1	P;D	0.63046	0.939;0.992	P;P	0.56916	0.809;0.809	T	0.77787	-0.2457	10	0.38643	T	0.18	.	9.4282	0.38592	0.0:0.0:0.6255:0.3745	.	199;195	A8K0G1;P56706	.;WNT7B_HUMAN	W	195;179;199	ENSP00000341032:R195W;ENSP00000386781:R179W;ENSP00000386546:R199W	ENSP00000341032:R195W	R	-	1	2	WNT7B	44697867	1.000000	0.71417	1.000000	0.80357	0.264000	0.26372	2.986000	0.49370	1.579000	0.49836	0.305000	0.20034	CGG	G|1.000;A|0.000	0.000	weak		0.657	WNT7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336418.1	NM_058238		A	46319203	G	A	46319203	3	1	29	1	0	0	0	0	1	0	0	0	17410	1115	39	1	470	1	WNT7B	22	46319203	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	1823250	46319203	4985363	879	13120											
CELSR1	9620	hgsc.bcm.edu	37	chr22	46761565	46761565	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	accagcccagaggacacgccGagcttctggatcccttcatc	9	7	9	16	2	2	1	1	0	1	1	4	4	3	3	4	2	2	1	4	2	0	2	rs34184256	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:46761565G>C	ENST00000262738.3	-	31	8321	c.8322C>G	c.(8320-8322)ctC>ctG	p.L2774L		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2774					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)		AGGACACGCCGAGCTTCTGGA	0.617													g|||	53	0.0105831	0.0	0.0086	5008	,	,		11875	0.002		0.0109	False		,,,				2504	0.0348				p.L2774L		Atlas-SNP	.											.	CELSR1	242	.	0			c.C8322G						PASS	.	C		3,4357		0,3,2177	21	20	20		8322	-1.4	1	22	dbSNP_126	20	114,8458		1,112,4173	no	coding-synonymous	CELSR1	NM_014246.1		1,115,6350	CC,CG,GG		1.3299,0.0688,0.9047		2774/3015	46761565	117,12815	2180	4286	6466	SO:0001819	synonymous_variant	9620	exon31			CACGCCGAGCTTC	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.8322C>G	22.37:g.46761565G>C		103	0	0		87	29	0.333333	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	37	CCDS14076.1																																																																																			G|0.992;C|0.008	0.008	strong		0.617	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		C	46761565	G	C	46761565	2	2	29	1	0	0	0	0	0	0	0	1	3223	1045	37	4		4	CELSR1	22	46761565	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	442362	46761565	4543001	880	13121											
CELSR1	9620	hgsc.bcm.edu	37	chr22	46762360	46762360	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcccgtcaccgaaggtggtGttgcagttgagggagcgctg	6	8	18	9	3	1	1	1	1	0	0	1	3	1	2	2	4	2	4	2	4	1	2	rs56325154	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:46762360G>A	ENST00000262738.3	-	30	8222	c.8223C>T	c.(8221-8223)aaC>aaT	p.N2741N		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2741					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)		CGAAGGTGGTGTTGCAGTTGA	0.652													.|||	56	0.0111821	0.0008	0.0058	5008	,	,		12394	0.002		0.0139	False		,,,				2504	0.0358				p.N2741N		Atlas-SNP	.											.	CELSR1	242	.	0			c.C8223T						PASS	.			10,4078		0,10,2034	52	38	43		8223	4.5	1	22	dbSNP_129	43	87,7807		0,87,3860	no	coding-synonymous	CELSR1	NM_014246.1		0,97,5894	AA,AG,GG		1.1021,0.2446,0.8095		2741/3015	46762360	97,11885	2044	3947	5991	SO:0001819	synonymous_variant	9620	exon30			GGTGGTGTTGCAG	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.8223C>T	22.37:g.46762360G>A		95	0	0		107	52	0.485981	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	37	CCDS14076.1																																																																																			G|0.993;A|0.007	0.007	strong		0.652	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		A	46762360	G	A	46762360	2	1	29	1	0	0	0	0	0	0	0	1	3223	1368	48	2		2	CELSR1	22	46762360	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	795	46762360	4542206	881	13122											
SBF1	6305	hgsc.bcm.edu	37	chr22	50893668	50893668	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccacctggtgtacgcagtcCaggaactgcaggaagacggg	10	5	14	12	2	0	1	0	0	0	1	1	3	1	3	3	4	3	3	3	4	3	1	rs374064130		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chr22:50893668C>G	ENST00000390679.3	-	32	4645	c.4461G>C	c.(4459-4461)ctG>ctC	p.L1487L	SBF1_ENST00000476293.1_5'Flank|SBF1_ENST00000380817.3_Silent_p.L1513L|SBF1_ENST00000348911.6_Silent_p.L1488L			O95248	MTMR5_HUMAN	SET binding factor 1	1487	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)		GTACGCAGTCCAGGAACTGCA	0.677																																					p.L1513L		Atlas-SNP	.											.	SBF1	211	.	0			c.G4539C						PASS	.	C		0,4196		0,0,2098	24	32	29		4539	1.8	1	22		29	4,8394		0,4,4195	no	coding-synonymous	SBF1	NM_002972.2		0,4,6293	GG,GC,CC		0.0476,0.0,0.0318		1513/1894	50893668	4,12590	2098	4199	6297	SO:0001819	synonymous_variant	6305	exon33			GCAGTCCAGGAAC	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.4461G>C	22.37:g.50893668C>G		57	0	0		56	35	0.625	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Silent	SNP	ENST00000390679.3	37		.	.	.	.	.	.	.	.	.	.	C	8.810	0.934901	0.18206	0.0	4.76E-4	ENSG00000100241	ENST00000418590	.	.	.	3.84	1.75	0.24633	.	.	.	.	.	T	0.56411	0.1983	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52087	-0.8622	4	.	.	.	.	8.9063	0.35526	0.0:0.7398:0.0:0.2602	.	.	.	.	R	47	.	.	G	-	1	0	SBF1	49240534	0.349000	0.24870	1.000000	0.80357	0.978000	0.69477	-0.281000	0.08456	0.969000	0.38237	0.563000	0.77884	GGA	.	.	weak		0.677	SBF1-201	KNOWN	basic	protein_coding	protein_coding				G	50893668	C	G	50893668	2	3	29	1	0	0	0	0	0	0	0	1	13873	581	21	4		4	SBF1	22	50893668	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	4131308	50893668	410898	882	13123											
PPP2R3B	28227	hgsc.bcm.edu	37	chrX	322294	322294	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaatgctttggctcgtggccGggggcagaggctcttctttc	4	12	15	10	2	2	1	0	0	2	1	4	2	2	1	1	5	1	4	1	5	1	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:322294G>A	ENST00000390665.3	-	2	374	c.356C>T	c.(355-357)cCg>cTg	p.P119L		NM_013239.4	NP_037371.2	Q9Y5P8	P2R3B_HUMAN	protein phosphatase 2, regulatory subunit B'', beta	119					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)				GCTCGTGGCCGGGGGCAGAGG	0.582																																					p.P119L		Atlas-SNP	.											.	PPP2R3B	43	.	0			c.C356T						PASS	.	G	LEU/PRO	6,4186		0,6,2090	145	177	166		356	1.6	0	X		166	0,8416		0,0,4208	no	missense	PPP2R3B	NM_013239.4	98	0,6,6298	AA,AG,GG		0.0,0.1431,0.0476	possibly-damaging	119/576	322294	6,12602	2096	4208	6304	SO:0001583	missense	28227	exon2			GTGGCCGGGGGCA	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.356C>T	X.37:g.322294G>A	ENSP00000375080:p.Pro119Leu	310	0	0		241	161	0.66805	NM_013239	Q6P4G9|Q7RTT1|Q96H01	Missense_Mutation	SNP	ENST00000390665.3	37	CCDS14104.1	.	.	.	.	.	.	.	.	.	.	G	11.55	1.671721	0.29693	0.001431	0.0	ENSG00000167393	ENST00000390665;ENST00000381625	T;T	0.32515	1.45;1.45	1.62	1.62	0.23740	.	0.285142	0.27172	U	0.020583	T	0.23846	0.0577	L	0.61218	1.895	0.20196	N	0.999928	P	0.47762	0.9	B	0.33521	0.165	T	0.23511	-1.0186	10	0.87932	D	0	.	8.9681	0.35890	0.0:0.0:1.0:0.0	.	119	Q9Y5P8	P2R3B_HUMAN	L	119;91	ENSP00000375080:P119L;ENSP00000371038:P91L	ENSP00000371038:P91L	P	-	2	0	PPP2R3B	242294	1.000000	0.71417	0.013000	0.15412	0.073000	0.16967	4.432000	0.59922	0.579000	0.29504	0.115000	0.15696	CCG	.	.	weak		0.582	PPP2R3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055577.2	NM_013239		A	322294	G	A	322294	3	1	29	1	0	0	0	0	1	0	0	0	12401	1116	39	1	1419	1	PPP2R3B	23	322294	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10		322294	154948266	883	13124											
P2RY8	286530	hgsc.bcm.edu	37	chrX	1585084	1585084	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcgggtacaggacccccAggaagcgctccacgctgata	10	5	13	13	3	0	2	0	2	0	0	1	4	1	4	3	3	3	3	3	3	3	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:1585084A>C	ENST00000381297.4	-	2	578	c.368T>G	c.(367-369)cTg>cGg	p.L123R	P2RY8_ENST00000460672.1_5'Flank	NM_178129.4	NP_835230.1	Q86VZ1	P2RY8_HUMAN	purinergic receptor P2Y, G-protein coupled, 8	123						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(13)|prostate(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)				CAGGACCCCCAGGAAGCGCTC	0.632			T	CRLF2	"B-ALL, Downs associated ALL"																																p.L123R		Atlas-SNP	.		Dom	yes		"X,Y"	Xp22.3; Yp11.3	286530	"purinergic receptor P2Y, G-protein coupled, 8"		L	.	P2RY8	53	.	0			c.T368G						PASS	.						88	85	86					X																	1585084		2202	4296	6498	SO:0001583	missense	286530	exon2			ACCCCCAGGAAGC	AA804531	CCDS14115.1	Xp22.33 and Yp11.3	2012-08-08			ENSG00000182162	ENSG00000182162		"Pseudoautosomal regions / PAR1", "Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	15524	protein-coding gene	gene with protein product		300525				11004484	Standard	NM_178129		Approved	P2Y8	uc004cpz.2	Q86VZ1	OTTHUMG00000021060	ENST00000381297.4:c.368T>G	X.37:g.1585084A>C	ENSP00000370697:p.Leu123Arg	120	0	0		87	15	0.172414	NM_178129		Missense_Mutation	SNP	ENST00000381297.4	37	CCDS14115.1	.	.	.	.	.	.	.	.	.	.	a	14.57	2.573664	0.45902	.	.	ENSG00000182162	ENST00000381297	T	0.46819	0.86	2.26	2.26	0.28386	GPCR, rhodopsin-like superfamily (1);	0.242138	0.29300	U	0.012559	T	0.65428	0.2690	M	0.80028	2.48	0.09310	N	1	D	0.69078	0.997	D	0.70487	0.969	T	0.56836	-0.7913	10	0.72032	D	0.01	.	9.9318	0.41528	1.0:0.0:0.0:0.0	.	123	Q86VZ1	P2RY8_HUMAN	R	123	ENSP00000370697:L123R	ENSP00000370697:L123R	L	-	2	0	P2RY8	1545084	1.000000	0.71417	0.995000	0.50966	0.350000	0.29205	7.120000	0.77153	0.611000	0.30052	0.230000	0.17803	CTG	.	.	none		0.632	P2RY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055602.1	NM_178129		C	1585084	A	C	1585084	3	2	29	1	0	0	0	0	1	0	0	0	11364	188	7	5	715	5	P2RY8	23	1585084	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	1262790	1585084	153685476	884	13125											
VCX3B	425054	hgsc.bcm.edu	37	chrX	8434346	8434346	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agtcaggagagccaggtggaGgaaccactgagtcaggagag	13	4	17	7	0	2	3	2	1	0	2	2	7	2	5	2	5	2	0	2	5	1	0	rs808146		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:8434346G>A	ENST00000381032.1	+	3	970	c.663G>A	c.(661-663)gaG>gaA	p.E221E	VCX3B_ENST00000381029.4_Silent_p.E189E|VCX3B_ENST00000440654.2_Silent_p.E171E|VCX3B_ENST00000453306.1_Intron|VCX3B_ENST00000444481.1_Silent_p.E191E	NM_001001888.3	NP_001001888.3	Q9H321	VCX3B_HUMAN	variable charge, X-linked 3B	221	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						GCCAGGTGGAGGAACCACTGA	0.557																																					p.E221E		Atlas-SNP	.											.	VCX3B	34	.	0			c.G663A						PASS	.	G		1,3807		0,0,1,1626,555	90	176	147		663	-1.1	0	X	dbSNP_86	147	8,6662		1,5,1,2418,1821	no	coding-synonymous	VCX3B	NM_001001888.3		1,5,2,4044,2376	AA,AG,A,GG,G		0.1199,0.0263,0.0859		221/247	8434346	9,10469	2182	4246	6428	SO:0001819	synonymous_variant	425054	exon3			GGTGGAGGAACCA		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.663G>A	X.37:g.8434346G>A		326	0	0		450	135	0.3	NM_001001888	C9JS46|Q4KN12	Silent	SNP	ENST00000381032.1	37	CCDS48077.2																																																																																			.	.	weak		0.557	VCX3B-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055691.1			A	8434346	G	A	8434346	2	1	29	1	0	0	0	0	0	0	0	1	17160	991	35	2		2	VCX3B	23	8434346	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	6849262	8434346	146836214	885	13126											
OFD1	8481	hgsc.bcm.edu	37	chrX	13786875	13786875	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagaaggctccctagtggaCacgctgcaatctagtgacaa	13	7	10	11	1	1	2	0	1	1	1	2	3	2	3	1	2	1	3	1	2	6	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:13786875C>T	ENST00000340096.6	+	22	3294	c.2967C>T	c.(2965-2967)gaC>gaT	p.D989D	OFD1_ENST00000490265.1_3'UTR|OFD1_ENST00000380567.1_Silent_p.D849D|OFD1_ENST00000380550.3_Silent_p.D949D	NM_003611.2	NP_003602.1	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1	989	Mediates the interaction with SDCCAG8.				axoneme assembly (GO:0035082)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation (GO:2000314)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|gamma-tubulin binding (GO:0043015)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	25						CCCTAGTGGACACGCTGCAAT	0.378																																					p.D989D		Atlas-SNP	.											.	OFD1	109	.	0			c.C2967T						PASS	.						155	148	150					X																	13786875		2203	4300	6503	SO:0001819	synonymous_variant	8481	exon22			AGTGGACACGCTG	Y15164	CCDS14157.1	Xp22	2014-06-18			ENSG00000046651	ENSG00000046651			2567	protein-coding gene	gene with protein product		300170	"retinitis pigmentosa 23 (X-linked recessive)"	CXorf5, RP23		9722947, 9215688, 22619378	Standard	NM_003611		Approved	71-7A, JBTS10	uc004cvp.4	O75665	OTTHUMG00000021159	ENST00000340096.6:c.2967C>T	X.37:g.13786875C>T		157	0	0		211	48	0.227488	NM_003611	B9ZVU5|O75666|Q4VAK4	Silent	SNP	ENST00000340096.6	37	CCDS14157.1																																																																																			.	.	none		0.378	OFD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055808.1	NM_003611		T	13786875	C	T	13786875	2	4	29	1	0	0	0	0	0	0	0	1	10847	477	17	2		2	OFD1	23	13786875	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	5352529	13786875	141483685	886	13127											
CXorf58	254158	hgsc.bcm.edu	37	chrX	23933912	23933912	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cagtgtaaaattagattcagGtaatgtatctatgctgattt	13	16	8	4	0	2	2	1	1	1	1	2	2	2	2	0	1	1	4	0	1	6	7	rs62584865	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:23933912G>A	ENST00000379211.3	+	4	860		c.e4+1			NM_001169574.1|NM_152761.2	NP_001163045.1|NP_689974.2	Q96LI9	CX058_HUMAN	chromosome X open reading frame 58											breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|prostate(1)	14						TTAGATTCAGGTAATGTATCT	0.308													G|||	15	0.00397351	0.0	0.0029	3775	,	,		14821	0.0		0.006	False		,,,				2504	0.0072				.		Atlas-SNP	.											.	CXorf58	53	.	0			c.311+1G>A						PASS	.	G	,	9,3825		0,5,4,1627,566	51	43	46		,	5.8	1	X	dbSNP_129	46	128,6599		0,98,30,2330,1841	yes	splice-5,splice-5	CXorf58	NM_001169574.1,NM_152761.2	,	0,103,34,3957,2407	AA,AG,A,GG,G		1.9028,0.2347,1.2972	,	,	23933912	137,10424	2202	4299	6501	SO:0001630	splice_region_variant	254158	exon4			ATTCAGGTAATGT	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.311+1G>A	X.37:g.23933912G>A		77	0	0		110	40	0.363636	NM_001169574		Splice_Site	SNP	ENST00000379211.3	37	CCDS14209.1	6	0.003616636528028933	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005291005291005291	g	13.92	2.380686	0.42207	0.002347	0.019028	ENSG00000165182	ENST00000379211;ENST00000435707	.	.	.	5.85	5.85	0.93711	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8642	0.79052	0.0:0.0:1.0:0.0	rs62584865	.	.	.	.	-1	.	.	.	+	.	.	CXorf58	23843833	1.000000	0.71417	1.000000	0.80357	0.383000	0.30230	5.194000	0.65125	2.460000	0.83146	0.540000	0.68198	.	G|0.991;A|0.009	0.009	strong		0.308	CXorf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056071.1	NM_152761	Intron	A	23933912	G	A	23933912	5	1	29	1	0	0	0	0	0	0	1	0	4116	1275	44	2	322	2	CXorf58	23	23933912	Splice_Site	SNP	G	TCGA-GR-7351-01A-11D-2210-10	10147037	23933912	131336648	887	13128											
FAM48B2	170067	hgsc.bcm.edu	37	chrX	24329897	24329908	+	IGR	DEL	AGCAGGAGCAGG	AGCAGGAGCAGG	-																															gcagctaaagcaggagcagcAgcaggagcaggagcaggagc																										TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	AGCAGGAGCAGG	AGCAGGAGCAGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:24329897_24329908delAGCAGGAGCAGG								AC096509.1 (25103 upstream) : AC004552.1 (37017 downstream)																							caggagcagcagcaggagcaggagcaggagca	0.604																																					p.509_513del		Atlas-Indel	.											.	.	.	.	0			c.1526_1537del						PASS	.																																			SO:0001628	intergenic_variant	170067	exon1			.																													X.37:g.24329897_24329908delAGCAGGAGCAGG		101	0	0		153	38	0.248366	NM_001136233		In_Frame_Del	DEL		37																																																																																				.	.	none	0	0.604									-	24329908	AGCAGGAGCAGG	-	24329897	6	5	29	0	1	1	0	1	0	0	0	0	5582	175	7	0		0	FAM48B2	23	24329897	IGR	DEL	AGCAGGAGCAGG	TCGA-GR-7351-01A-11D-2210-10	395985	24329897	130940663	888	13129											
FAM48B1	100130302	hgsc.bcm.edu	37	chrX	24382374	24382388	+	IGR	DEL	TGCTGCTGCTGCTGC	TGCTGCTGCTGCTGC	-																															ttttctgctgctgctgctatTgctgctgctgctgctgctgc																								rs371342199		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	TGCTGCTGCTGCTGC	TGCTGCTGCTGCTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:24382374_24382388delTGCTGCTGCTGCTGC								AC004552.1 (15351 upstream) : PDK3 (100949 downstream)																							ctgctgctattgctgctgctgctgctgctgctgct	0.577																																					p.499_504del		Atlas-Indel	.											.	.	.	.	0			c.1496_1510del						PASS	.																																			SO:0001628	intergenic_variant	100130302	exon1			.																													X.37:g.24382374_24382388delTGCTGCTGCTGCTGC		131	0	0		195	52	0.266667	NM_001136234		In_Frame_Del	DEL		37																																																																																				.	.	alt	0	0.577									-	24382388	TGCTGCTGCTGCTGC	-	24382374	6	5	29	0	1	1	0	1	0	0	0	0	5581	1800	63	0		0	FAM48B1	23	24382374	IGR	DEL	TGCTGCTGCTGCTGC	TCGA-GR-7351-01A-11D-2210-10	52477	24382374	130888186	889	13130											
OTC	5009	hgsc.bcm.edu	37	chrX	38262964	38262964	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgatgagcgcagcgaaattcGgaatgcaccttcaggcagct	11	8	12	10	3	1	2	1	2	0	0	2	4	1	3	1	2	4	4	1	2	2	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:38262964G>A	ENST00000039007.4	+	6	786	c.634G>A	c.(634-636)Gga>Aga	p.G212R	TM4SF2_ENST00000465127.1_Intron	NM_000531.5	NP_000522.3	P00480	OTC_HUMAN	ornithine carbamoyltransferase	212					ammonia homeostasis (GO:0097272)|arginine biosynthetic process (GO:0006526)|cellular nitrogen compound metabolic process (GO:0034641)|citrulline biosynthetic process (GO:0019240)|liver development (GO:0001889)|midgut development (GO:0007494)|ornithine catabolic process (GO:0006593)|protein homotrimerization (GO:0070207)|response to biotin (GO:0070781)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|ornithine carbamoyltransferase activity (GO:0004585)|phosphate ion binding (GO:0042301)|phospholipid binding (GO:0005543)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22					L-Citrulline(DB00155)|L-Ornithine(DB00129)	AGCGAAATTCGGAATGCACCT	0.463																																					p.G212R		Atlas-SNP	.											.	OTC	60	.	0			c.G634A						PASS	.						105	84	91					X																	38262964		2202	4300	6502	SO:0001583	missense	5009	exon6			AAATTCGGAATGC	K02100	CCDS14247.1	Xp21.1	2014-06-28			ENSG00000036473	ENSG00000036473	2.1.3.3		8512	protein-coding gene	gene with protein product		300461					Standard	NM_000531		Approved		uc004def.4	P00480	OTTHUMG00000022727	ENST00000039007.4:c.634G>A	X.37:g.38262964G>A	ENSP00000039007:p.Gly212Arg	47	0	0		59	18	0.305085	NM_000531	A8K9P2|D3DWB0|Q3KNR1|Q6B0I1|Q9NYJ5	Missense_Mutation	SNP	ENST00000039007.4	37	CCDS14247.1	.	.	.	.	.	.	.	.	.	.	g	31	5.090646	0.94149	.	.	ENSG00000036473	ENST00000039007	D	0.99329	-5.75	5.91	5.91	0.95273	Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99658	0.9873	H	0.96547	3.84	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97657	1.0158	10	0.87932	D	0	-23.1274	19.2113	0.93757	0.0:0.0:1.0:0.0	.	212	P00480	OTC_HUMAN	R	212	ENSP00000039007:G212R	ENSP00000039007:G212R	G	+	1	0	OTC	38147908	1.000000	0.71417	0.597000	0.28824	0.891000	0.51852	9.417000	0.97391	2.488000	0.83962	0.594000	0.82650	GGA	.	.	none		0.463	OTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059006.2			A	38262964	G	A	38262964	3	1	29	1	0	0	0	0	1	0	0	0	11310	1117	39	1	656	1	OTC	23	38262964	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	13880590	38262964	117007596	890	13131											
USP11	8237	hgsc.bcm.edu	37	chrX	47092423	47092423	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcgcacagctgcgttggctGtagaagagaacggacggcga	10	6	15	10	5	0	2	0	0	0	2	1	5	0	3	0	3	3	5	0	3	3	2	rs149757747	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:47092423G>A	ENST00000218348.3	+	1	110	c.110G>A	c.(109-111)tGt>tAt	p.C37Y	USP11_ENST00000377107.2_5'UTR	NM_004651.3	NP_004642.2	P51784	UBP11_HUMAN	ubiquitin specific peptidase 11	37					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|ovary(3)|pancreas(1)|stomach(1)	40						TGCGTTGGCTGTAGAAGAGAA	0.647																																					p.C37Y		Atlas-SNP	.											.	USP11	93	.	0			c.G110A						PASS	.	G	TYR/CYS	0,3835		0,0,0,1632,571	25	23	24		110	4.4	0	X	dbSNP_134	24	7,6721		0,4,3,2424,1869	yes	missense	USP11	NM_004651.3	194	0,4,3,4056,2440	AA,AG,A,GG,G		0.104,0.0,0.0663	possibly-damaging	37/964	47092423	7,10556	2203	4300	6503	SO:0001583	missense	8237	exon1			TTGGCTGTAGAAG	U44839	CCDS14277.1	Xp11.23	2008-02-05	2005-08-08		ENSG00000102226	ENSG00000102226		"Ubiquitin-specific peptidases"	12609	protein-coding gene	gene with protein product		300050	"ubiquitin specific protease 11"			12838346	Standard	XM_005272674		Approved	UHX1	uc004dhp.3	P51784	OTTHUMG00000021437	ENST00000218348.3:c.110G>A	X.37:g.47092423G>A	ENSP00000218348:p.Cys37Tyr	70	0	0		81	21	0.259259	NM_004651	B2RTX1|Q8IUG6|Q9BWE1	Missense_Mutation	SNP	ENST00000218348.3	37	CCDS14277.1	.	.	.	.	.	.	.	.	.	.	G	12.59	1.984787	0.35036	0.0	0.00104	ENSG00000102226	ENST00000218348	T	0.21191	2.02	4.39	4.39	0.52855	.	.	.	.	.	T	0.12305	0.0299	N	0.08118	0	0.09310	N	1	B	0.18461	0.028	B	0.14578	0.011	T	0.15065	-1.0450	9	0.49607	T	0.09	2.5884	11.9698	0.53058	0.0:0.0:1.0:0.0	.	37	P51784	UBP11_HUMAN	Y	37	ENSP00000218348:C37Y	ENSP00000218348:C37Y	C	+	2	0	USP11	46977367	0.010000	0.17322	0.005000	0.12908	0.733000	0.41908	1.525000	0.35953	2.111000	0.64477	0.513000	0.50165	TGT	G|1.000;A|0.000	0.000	strong		0.647	USP11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_004651		A	47092423	G	A	47092423	3	1	29	1	0	0	0	0	1	0	0	0	17057	1377	48	2	112	2	USP11	23	47092423	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	8829459	47092423	108178137	891	13132											
ZNF81	347344	hgsc.bcm.edu	37	chrX	47774599	47774599	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aagcccaaatctcattctttCacagaaaagaccccataaac	17	8	3	13	0	3	2	2	0	2	2	4	2	3	2	3	0	2	0	3	0	6	3	rs186251256		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:47774599C>T	ENST00000376954.1	+	6	922	c.554C>T	c.(553-555)tCa>tTa	p.S185L	ZNF81_ENST00000338637.7_Missense_Mutation_p.S185L			P51508	ZNF81_HUMAN	zinc finger protein 81	185			S -> L (in dbSNP:rs186251256). {ECO:0000269|PubMed:15121780}.		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)				CTCATTCTTTCACAGAAAAGA	0.328													C|||	17	0.00450331	0.0	0.0058	3775	,	,		14189	0.0		0.0129	False		,,,				2504	0.0				p.S185L		Atlas-SNP	.											.	ZNF81	60	.	0			c.C554T						PASS	.	C	LEU/SER	8,3049		0,7,1,1237,568	40	36	38		554	3.2	1	X		38	104,6250		0,78,26,2215,1742	yes	missense	ZNF81	NM_007137.3	145	0,85,27,3452,2310	TT,TC,T,CC,C		1.6368,0.2617,1.1901	probably-damaging	185/662	47774599	112,9299	1813	4061	5874	SO:0001583	missense	347344	exon5			TTCTTTCACAGAA	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.554C>T	X.37:g.47774599C>T	ENSP00000366153:p.Ser185Leu	198	0	0		279	197	0.706093	NM_007137	Q6RX22|Q96QH6	Missense_Mutation	SNP	ENST00000376954.1	37	CCDS43933.1	14	0.008438818565400843	0	0.0	4	0.011049723756906077	0	0.0	10	0.013227513227513227	C	15.24	2.774871	0.49786	0.002617	0.016368	ENSG00000197779	ENST00000376954;ENST00000338637	T;T	0.06068	3.35;3.35	4.04	3.18	0.36537	.	0.228496	0.22784	N	0.055692	T	0.02083	0.0065	N	0.21448	0.665	0.29252	N	0.871902	B	0.18610	0.029	B	0.15484	0.013	T	0.20840	-1.0263	10	0.39692	T	0.17	.	9.0083	0.36127	0.0:0.8864:0.0:0.1136	.	185	P51508	ZNF81_HUMAN	L	185	ENSP00000366153:S185L;ENSP00000341151:S185L	ENSP00000341151:S185L	S	+	2	0	ZNF81	47659543	0.000000	0.05858	0.973000	0.42090	0.625000	0.37756	-0.284000	0.08422	1.067000	0.40740	0.600000	0.82982	TCA	C|0.992;T|0.008	0.008	strong		0.328	ZNF81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056455.2	NM_007137		T	47774599	C	T	47774599	3	4	29	1	0	0	0	0	1	0	0	0	18189	838	29	2	568	2	ZNF81	23	47774599	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	682176	47774599	107495961	892	13133											
SSX3	10214	hgsc.bcm.edu	37	chrX	48213499	48213499	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtctgtgacccgtttattaCgcatgaaagatgggaggatg	11	11	13	6	2	1	3	0	2	1	1	1	5	1	5	1	2	1	2	1	2	3	3			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:48213499C>T	ENST00000298396.2	-	4	267	c.215G>A	c.(214-216)cGt>cAt	p.R72H	SSX3_ENST00000376895.1_5'Flank|SSX3_ENST00000376893.3_Missense_Mutation_p.R72H	NM_021014.2	NP_066294.1	Q99909	SSX3_HUMAN	synovial sarcoma, X breakpoint 3	72	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)			endometrium(3)|large_intestine(1)|lung(9)	13						CCGTTTATTACGCATGAAAGA	0.478																																					p.R72H	Colon(37;227 826 19399 40970 48007)	Atlas-SNP	.											.	SSX3	64	.	0			c.G215A						PASS	.						135	120	125					X																	48213499		2203	4300	6503	SO:0001583	missense	10214	exon4			TTATTACGCATGA	U90840	CCDS14291.1	Xp11.23	2009-06-17			ENSG00000165584	ENSG00000165584			11337	protein-coding gene	gene with protein product		300325				8697803, 9378559	Standard	NM_021014		Approved	CT5.3	uc004djd.1	Q99909	OTTHUMG00000021489	ENST00000298396.2:c.215G>A	X.37:g.48213499C>T	ENSP00000298396:p.Arg72His	187	0	0		278	109	0.392086	NM_021014	O60223|Q5JQZ3|Q9BRW7	Missense_Mutation	SNP	ENST00000298396.2	37	CCDS14291.1	.	.	.	.	.	.	.	.	.	.	c	0.954	-0.705443	0.03255	.	.	ENSG00000165584	ENST00000298396;ENST00000376893	T;T	0.09630	3.01;2.96	1.52	-0.417	0.12347	Krueppel-associated box (2);Krueppel-associated box-related (1);	2.446520	0.01248	N	0.008799	T	0.08447	0.0210	N	0.25647	0.755	0.09310	N	1	B;B	0.14438	0.01;0.003	B;B	0.11329	0.006;0.002	T	0.30119	-0.9989	10	0.35671	T	0.21	.	4.0257	0.09687	0.0:0.5359:0.0:0.4641	.	72;72	Q9BRW7;Q99909	.;SSX3_HUMAN	H	72	ENSP00000298396:R72H;ENSP00000366090:R72H	ENSP00000298396:R72H	R	-	2	0	SSX3	48098443	0.000000	0.05858	0.005000	0.12908	0.020000	0.10135	-0.082000	0.11304	-0.233000	0.09797	-1.164000	0.01763	CGT	.	.	none		0.478	SSX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056486.1	NM_021014		T	48213499	C	T	48213499	3	4	29	1	0	0	0	0	1	0	0	0	15220	536	19	1	418	1	SSX3	23	48213499	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	438900	48213499	107057061	893	13134											
SUV39H1	6839	hgsc.bcm.edu	37	chrX	48558888	48558888	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggactgtctgtgggcacccaCtggaggctgctgcccggggg	4	7	18	12	1	1	0	0	0	1	0	1	2	1	2	2	6	2	3	2	6	0	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:48558888C>T	ENST00000376687.3	+	3	762	c.572C>T	c.(571-573)aCt>aTt	p.T191I	SUV39H1_ENST00000453214.2_Intron|SUV39H1_ENST00000337852.6_Missense_Mutation_p.T202I|AF196970.3_ENST00000416061.1_RNA	NM_003173.2	NP_003164.1	O43463	SUV91_HUMAN	suppressor of variegation 3-9 homolog 1 (Drosophila)	191	Pre-SET. {ECO:0000255|PROSITE- ProRule:PRU00157}.				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						TGGGCACCCACTGGAGGCTGC	0.632																																					p.T191I		Atlas-SNP	.											.	SUV39H1	36	.	0			c.C572T						PASS	.						52	41	45					X																	48558888		2203	4300	6503	SO:0001583	missense	6839	exon3			CACCCACTGGAGG	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.572C>T	X.37:g.48558888C>T	ENSP00000365877:p.Thr191Ile	86	0	0		94	52	0.553191	NM_003173	B2R6E8|B4DST0|Q53G60|Q6FHK6	Missense_Mutation	SNP	ENST00000376687.3	37	CCDS14304.1	.	.	.	.	.	.	.	.	.	.	C	13.44	2.237725	0.39598	.	.	ENSG00000101945	ENST00000337852;ENST00000376687;ENST00000448548;ENST00000422496	D;D	0.89270	-2.49;-2.49	4.93	3.13	0.36017	Pre-SET zinc-binding sub-group (1);Pre-SET domain (2);	0.478513	0.21039	N	0.081202	T	0.77246	0.4102	N	0.19112	0.55	0.09310	N	0.999999	B;B	0.11235	0.004;0.002	B;B	0.15870	0.014;0.014	T	0.63278	-0.6673	10	0.36615	T	0.2	.	4.2419	0.10652	0.1806:0.6131:0.0:0.2062	.	202;191	B4DST0;O43463	.;SUV91_HUMAN	I	202;191;189;49	ENSP00000337976:T202I;ENSP00000365877:T191I	ENSP00000337976:T202I	T	+	2	0	SUV39H1	48443832	0.019000	0.18553	0.882000	0.34594	0.989000	0.77384	1.055000	0.30467	0.858000	0.35431	0.502000	0.49764	ACT	.	.	none		0.632	SUV39H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058909.1	NM_003173		T	48558888	C	T	48558888	3	4	29	1	0	0	0	0	1	0	0	0	15427	565	20	2	582	2	SUV39H1	23	48558888	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	345389	48558888	106711672	894	13135											
PLP2	5355	hgsc.bcm.edu	37	chrX	49029758	49029758	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcttccgaaccctcatagcGgcaatcctctacctgatcac	9	11	5	16	2	4	1	2	1	2	0	6	2	6	1	4	1	3	1	4	1	4	4	rs145837656		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:49029758G>A	ENST00000376327.5	+	3	348	c.273G>A	c.(271-273)gcG>gcA	p.A91A	PLP2_ENST00000376322.3_Silent_p.A91A	NM_002668.2	NP_002659.1	Q04941	PLP2_HUMAN	proteolipid protein 2 (colonic epithelium-enriched)	91	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.		A -> S (in dbSNP:rs1802969).		chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chemokine binding (GO:0019956)|ion transmembrane transporter activity (GO:0015075)			endometrium(3)|large_intestine(1)|lung(6)|urinary_tract(3)	13						CCCTCATAGCGGCAATCCTCT	0.542																																					p.A91A		Atlas-SNP	.											.	PLP2	25	.	0			c.G273A						PASS	.	G		2,3833		0,2,0,1630,571	138	108	118		273	-10.7	0	X	dbSNP_134	118	3,6725		0,2,1,2426,1871	no	coding-synonymous	PLP2	NM_002668.2		0,4,1,4056,2442	AA,AG,A,GG,G		0.0446,0.0522,0.0473		91/153	49029758	5,10558	2203	4300	6503	SO:0001819	synonymous_variant	5355	exon3			CATAGCGGCAATC	L09604	CCDS14319.1	Xp11.23	2008-08-01			ENSG00000102007	ENSG00000102007			9087	protein-coding gene	gene with protein product	"A4 differentiation-dependent protein"	300112				8470895, 7622043	Standard	NM_002668		Approved	A4, A4-LSB, MGC126187	uc004dmx.3	Q04941	OTTHUMG00000021513	ENST00000376327.5:c.273G>A	X.37:g.49029758G>A		38	0	0		60	24	0.4	NM_002668	A6NDT7|Q32MM8	Silent	SNP	ENST00000376327.5	37	CCDS14319.1																																																																																			G|1.000;A|0.000	0.000	weak		0.542	PLP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056540.1	NM_002668		A	49029758	G	A	49029758	2	1	29	1	0	0	0	0	0	0	0	1	12114	1103	39	1		1	PLP2	23	49029758	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	470870	49029758	106240802	895	13136											
CACNA1F	778	hgsc.bcm.edu	37	chrX	49081230	49081230	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccctaatacaaacctggtgaCcttaaagatcctgaggaggc	13	8	9	11	0	0	3	0	2	0	1	1	4	1	4	4	3	2	0	4	3	5	3	rs141010716	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:49081230C>T	ENST00000376265.2	-	14	1964	c.1903G>A	c.(1903-1905)Gtc>Atc	p.V635I	CACNA1F_ENST00000376251.1_Missense_Mutation_p.V570I|CACNA1F_ENST00000480889.1_5'Flank|CACNA1F_ENST00000323022.5_Missense_Mutation_p.V624I	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	635			V -> I (in CSNB2A; dbSNP:rs141010716). {ECO:0000269|PubMed:12187427}.		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)	AACCTGGTGACCTTAAAGATC	0.562													c|||	8	0.00211921	0.0023	0.0	3775	,	,		12808	0.0		0.005	False		,,,				2504	0.0				p.V635I		Atlas-SNP	.											.	CACNA1F	218	.	0			c.G1903A	GRCh37	CM023777	CACNA1F	M	rs141010716	PASS	.		ILE/VAL	4,3806		0,4,0,1623,556	36	30	32		1903	3.4	1	X	dbSNP_134	32	22,6662		0,14,8,2408,1832	yes	missense	CACNA1F	NM_005183.2	29	0,18,8,4031,2388	TT,TC,T,CC,C		0.3291,0.105,0.2478	benign	635/1978	49081230	26,10468	2183	4262	6445	SO:0001583	missense	778	exon14			TGGTGACCTTAAA	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.1903G>A	X.37:g.49081230C>T	ENSP00000365441:p.Val635Ile	55	0	0		69	47	0.681159	NM_005183	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Missense_Mutation	SNP	ENST00000376265.2	37	CCDS35253.1	5	0.0030138637733574444	2	0.0040650406504065045	0	0.0	0	0.0	2	0.0026455026455026454	.	4.653	0.121374	0.08881	0.00105	0.003291	ENSG00000102001	ENST00000376251;ENST00000323022;ENST00000376265	D;D;D	0.98221	-4.8;-4.8;-4.8	3.39	3.39	0.38822	Ion transport (1);	0.501276	0.19185	N	0.120568	D	0.95172	0.8435	L	0.33137	0.985	0.29467	N	0.857304	B;P	0.39216	0.192;0.664	B;B	0.38842	0.094;0.283	D	0.90937	0.4794	10	0.15952	T	0.53	.	13.2338	0.59958	0.0:1.0:0.0:0.0	.	624;635	F5CIQ9;O60840	.;CAC1F_HUMAN	I	570;624;635	ENSP00000365427:V570I;ENSP00000321618:V624I;ENSP00000365441:V635I	ENSP00000321618:V624I	V	-	1	0	CACNA1F	48968174	0.963000	0.33076	1.000000	0.80357	0.222000	0.24845	0.688000	0.25422	1.298000	0.44778	0.273000	0.19326	GTC	C|0.997;T|0.003	0.003	strong		0.562	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183		T	49081230	C	T	49081230	3	4	29	1	0	0	0	0	1	0	0	0	2545	507	18	2	4170	2	CACNA1F	23	49081230	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	51472	49081230	106189330	896	13137											
ITIH5L	347365	hgsc.bcm.edu	37	chrX	54783779	54783779	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actgctgggacctgtggaacTtgagattgtatttgggaatg	9	13	14	5	0	0	1	0	1	0	1	0	5	0	4	1	3	2	2	1	3	3	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:54783779T>C	ENST00000218436.6	-	8	2757	c.2728A>G	c.(2728-2730)Agt>Ggt	p.S910G		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	910	Pro-rich.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.S910R(1)									CCTGTGGAACTTGAGATTGTA	0.557																																					p.S910G		Atlas-SNP	.											.	.	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A2728G						PASS	.						100	89	93					X																	54783779		2203	4300	6503	SO:0001583	missense	347365	exon8			TGGAACTTGAGAT	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.2728A>G	X.37:g.54783779T>C	ENSP00000218436:p.Ser910Gly	55	0	0		94	7	0.0744681	NM_198510	A6NN03	Missense_Mutation	SNP	ENST00000218436.6	37	CCDS14361.1	.	.	.	.	.	.	.	.	.	.	T	6.767	0.510364	0.12883	.	.	ENSG00000102313	ENST00000218436	T	0.02656	4.21	3.38	0.712	0.18167	.	1.639110	0.04365	U	0.358064	T	0.02342	0.0072	N	0.19112	0.55	0.09310	N	1	B	0.30326	0.276	B	0.25759	0.063	T	0.43702	-0.9375	10	0.56958	D	0.05	.	3.6381	0.08157	0.2181:0.0:0.2212:0.5607	.	910	Q6UXX5	ITH5L_HUMAN	G	910	ENSP00000218436:S910G	ENSP00000218436:S910G	S	-	1	0	ITIH5L	54800504	0.004000	0.15560	0.001000	0.08648	0.081000	0.17604	0.363000	0.20301	-0.043000	0.13513	0.412000	0.27726	AGT	.	.	none		0.557	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510		C	54783779	T	C	54783779	3	2	29	1	0	0	0	0	1	0	0	0	7917	1609	56	3	1237	3	ITIH5L	23	54783779	Missense_Mutation	SNP	T	TCGA-GR-7351-01A-11D-2210-10	5702549	54783779	100486781	897	13138											
FAM123B	139285	hgsc.bcm.edu	37	chrX	63412987	63412987	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagatacccttcttgccaccAaagagtttcatggcagtttt	10	13	7	11	0	2	2	1	0	1	2	2	2	2	2	3	1	2	3	3	1	2	6			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:63412987A>G	ENST00000330258.3	-	2	452	c.180T>C	c.(178-180)ttT>ttC	p.F60F	AMER1_ENST00000374869.3_Silent_p.F60F|AMER1_ENST00000403336.1_Silent_p.F60F	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	60					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)									TCTTGCCACCAAAGAGTTTCA	0.532																																					p.F60F		Atlas-SNP	.											.	.	.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.T180C						PASS	.						181	147	159					X																	63412987		2203	4300	6503	SO:0001819	synonymous_variant	139285	exon2			GCCACCAAAGAGT	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.180T>C	X.37:g.63412987A>G		73	0	0		123	51	0.414634	NM_152424	A2IB86|Q8N885	Silent	SNP	ENST00000330258.3	37	CCDS14377.2																																																																																			.	.	none		0.532	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		G	63412987	A	G	63412987	2	3	29	1	0	0	0	0	0	0	0	1	5428	127	5	3		3	FAM123B	23	63412987	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	8629208	63412987	91857573	898	13139											
GLRA4	441509	hgsc.bcm.edu	37	chrX	102974119	102974119	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggacaggatgacgatgagtaGgctggggatgtacatctgaa	12	8	16	5	1	1	3	0	3	1	0	1	7	1	6	0	5	1	3	0	5	3	2	rs41300882	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:102974119G>A	ENST00000372617.4	-	7	1219	c.799C>T	c.(799-801)Cta>Tta	p.L267L	GLRA4_ENST00000469567.1_5'Flank	NM_001024452.2	NP_001019623.2	Q5JXX5	GLRA4_HUMAN	glycine receptor, alpha 4	267						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						ACGATGAGTAGGCTGGGGATG	0.557													G|||	11	0.00291391	0.0	0.0014	3775	,	,		14691	0.0		0.007	False		,,,				2504	0.0031				p.L267L		Atlas-SNP	.											.	GLRA4	86	.	0			c.C799T						PASS	.	G	,	8,3827		0,7,1,1625,570	156	159	158		799,799	4.9	1	X	dbSNP_127	158	87,6640		1,60,25,2367,1846	no	coding-synonymous,coding-synonymous	GLRA4	NM_001024452.2,NM_001172285.1	,	1,67,26,3992,2416	AA,AG,A,GG,G		1.2933,0.2086,0.8995	,	267/418,267/343	102974119	95,10467	2203	4299	6502	SO:0001819	synonymous_variant	441509	exon7			TGAGTAGGCTGGG	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.799C>T	X.37:g.102974119G>A		128	0	0		196	141	0.719388	NM_001024452		Silent	SNP	ENST00000372617.4	37	CCDS43980.2																																																																																			G|0.995;A|0.005	0.005	strong		0.557	GLRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057742.2	NM_001024452		A	102974119	G	A	102974119	2	1	29	1	0	0	0	0	0	0	0	1	6465	991	35	2		2	GLRA4	23	102974119	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	39561132	102974119	52296441	899	13140											
RGAG1	57529	hgsc.bcm.edu	37	chrX	109696758	109696758	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctttaatgtcagccatggcTtctggagagatgtctatgcc	8	13	10	10	0	3	1	1	0	2	1	3	3	3	2	3	2	2	1	3	2	2	4			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:109696758T>G	ENST00000465301.2	+	3	3159	c.2913T>G	c.(2911-2913)gcT>gcG	p.A971A	RGAG1_ENST00000540313.1_Silent_p.A971A	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	971										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						CAGCCATGGCTTCTGGAGAGA	0.512																																					p.A971A		Atlas-SNP	.											.	RGAG1	168	.	0			c.T2913G						PASS	.						144	138	140					X																	109696758		2203	4300	6503	SO:0001819	synonymous_variant	57529	exon3			CATGGCTTCTGGA	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.2913T>G	X.37:g.109696758T>G		62	0	0		71	24	0.338028	NM_020769	Q9P2M8	Silent	SNP	ENST00000465301.2	37	CCDS14552.1																																																																																			.	.	none		0.512	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769		G	109696758	T	G	109696758	2	3	29	1	0	0	0	0	0	0	0	1	13289	1596	56	5		5	RGAG1	23	109696758	Silent	SNP	T	TCGA-GR-7351-01A-11D-2210-10	6722639	109696758	45573802	900	13141											
ODZ1	10178	hgsc.bcm.edu	37	chrX	123539063	123539063	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatctccatcccgctggcaaAagtgacacgcagggaaccat	12	6	10	13	2	1	1	0	1	1	0	3	3	2	2	3	2	1	3	3	2	3	0			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:123539063A>C	ENST00000371130.3	-	26	5251	c.5188T>G	c.(5188-5190)Ttt>Gtt	p.F1730V	STAG2_ENST00000469481.1_Intron|TENM1_ENST00000422452.2_Missense_Mutation_p.F1737V	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1730					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)										CCGCTGGCAAAAGTGACACGC	0.547																																					p.F1737V		Atlas-SNP	.											.	.	.	.	0			c.T5209G						PASS	.						82	68	73					X																	123539063		2203	4300	6503	SO:0001583	missense	10178	exon27			TGGCAAAAGTGAC	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.5188T>G	X.37:g.123539063A>C	ENSP00000360171:p.Phe1730Val	39	0	0		60	25	0.416667	NM_001163278	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	A	15.51	2.855583	0.51376	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.85013	-1.93;-1.89	5.56	5.56	0.83823	.	0.188786	0.47093	D	0.000251	T	0.79203	0.4406	L	0.40543	1.245	0.42964	D	0.99441	B;B;B	0.24483	0.104;0.049;0.059	B;B;B	0.19148	0.024;0.024;0.021	T	0.74612	-0.3607	10	0.23302	T	0.38	.	14.742	0.69464	1.0:0.0:0.0:0.0	.	1736;1737;1730	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	V	1730;1737	ENSP00000360171:F1730V;ENSP00000403954:F1737V	ENSP00000360171:F1730V	F	-	1	0	ODZ1	123366744	1.000000	0.71417	0.958000	0.39756	0.887000	0.51463	5.898000	0.69838	1.862000	0.54008	0.486000	0.48141	TTT	.	.	none		0.547	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253		C	123539063	A	C	123539063	3	2	29	1	0	0	0	0	1	0	0	0	10843	14	1	5	3013	5	ODZ1	23	123539063	Missense_Mutation	SNP	A	TCGA-GR-7351-01A-11D-2210-10	13842305	123539063	31731497	901	13142											
UTP14A	10813	hgsc.bcm.edu	37	chrX	129045815	129045815	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccctgtcgtcctgaagaaccGgcaggcagagcagctggttt	8	8	13	12	2	0	3	0	1	0	2	2	3	1	3	3	3	3	5	3	3	2	1			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:129045815G>A	ENST00000394422.3	+	6	483	c.455G>A	c.(454-456)cGg>cAg	p.R152Q	UTP14A_ENST00000371042.3_5'Flank|RP4-537K23.4_ENST00000432062.1_RNA|UTP14A_ENST00000371051.5_Missense_Mutation_p.R98Q|UTP14A_ENST00000425117.2_Intron	NM_006649.3	NP_006640.2	Q9BVJ6	UT14A_HUMAN	UTP14, U3 small nucleolar ribonucleoprotein, homolog A (yeast)	152					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						CTGAAGAACCGGCAGGCAGAG	0.507																																					p.R152Q		Atlas-SNP	.											.	UTP14A	74	.	0			c.G455A						PASS	.						90	86	87					X																	129045815		2203	4300	6503	SO:0001583	missense	10813	exon6			AGAACCGGCAGGC	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.455G>A	X.37:g.129045815G>A	ENSP00000377944:p.Arg152Gln	66	0	0		66	17	0.257576	NM_006649	A8K7A3|A8MVQ1|B4DQ08|E9PEL7|Q5JYF1	Missense_Mutation	SNP	ENST00000394422.3	37	CCDS14615.1	.	.	.	.	.	.	.	.	.	.	G	10.68	1.418778	0.25552	.	.	ENSG00000156697	ENST00000394422;ENST00000371051	T;T	0.30981	1.51;1.51	5.43	5.43	0.79202	.	0.173156	0.53938	D	0.000060	T	0.43787	0.1263	M	0.87682	2.9	0.80722	D	1	B;B	0.26258	0.145;0.019	B;B	0.20577	0.018;0.03	T	0.48068	-0.9067	10	0.56958	D	0.05	-5.4583	18.3408	0.90304	0.0:0.0:1.0:0.0	.	98;152	F8WD00;Q9BVJ6	.;UT14A_HUMAN	Q	152;98	ENSP00000377944:R152Q;ENSP00000360090:R98Q	ENSP00000360090:R98Q	R	+	2	0	UTP14A	128873496	1.000000	0.71417	0.986000	0.45419	0.160000	0.22226	3.602000	0.54066	2.270000	0.75569	0.411000	0.27672	CGG	.	.	none		0.507	UTP14A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058221.1	NM_006649		A	129045815	G	A	129045815	3	1	29	1	0	0	0	0	1	0	0	0	17110	1116	39	1	477	1	UTP14A	23	129045815	Missense_Mutation	SNP	G	TCGA-GR-7351-01A-11D-2210-10	5506752	129045815	26224745	902	13143											
TFDP3	51270	hgsc.bcm.edu	37	chrX	132351703	132351703	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccgtaagttctgacagttCtgagccgagttggtggtcag	8	11	13	9	2	3	2	1	2	2	0	3	3	3	2	2	2	1	4	2	2	1	4	rs35745873	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:132351703C>A	ENST00000310125.4	-	1	673	c.585G>T	c.(583-585)caG>caT	p.Q195H		NM_016521.2	NP_057605.3	Q5H9I0	TFDP3_HUMAN	transcription factor Dp family, member 3	195	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)					TCTGACAGTTCTGAGCCGAGT	0.438													C|||	85	0.0225166	0.0098	0.0187	3775	,	,		16569	0.002		0.0288	False		,,,				2504	0.0286				p.Q195H		Atlas-SNP	.											.	TFDP3	92	.	0			c.G585T						PASS	.	C	HIS/GLN	36,3799		0,29,7,1603,564	104	97	99		585	0.2	0	X	dbSNP_126	99	262,6466		3,197,59,2228,1813	yes	missense	TFDP3	NM_016521.2	24	3,226,66,3831,2377	AA,AC,A,CC,C		3.8942,0.9387,2.8212	probably-damaging	195/406	132351703	298,10265	2203	4300	6503	SO:0001583	missense	51270	exon1			ACAGTTCTGAGCC	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.585G>T	X.37:g.132351703C>A	ENSP00000385461:p.Gln195His	71	0	0		84	28	0.333333	NM_016521	Q6DK49|Q9NZ54	Missense_Mutation	SNP	ENST00000310125.4	37	CCDS14636.2	43	0.02591922845087402	5	0.010245901639344262	6	0.01675977653631285	2	0.0034965034965034965	14	0.01907356948228883	c	11.08	1.534355	0.27475	0.009387	0.038942	ENSG00000183434	ENST00000310125	T	0.27104	1.69	0.208	0.208	0.15221	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor DP, C-terminal (1);	.	.	.	.	T	0.13628	0.0330	M	0.83774	2.66	0.09310	P	0.9999988559	P	0.46142	0.873	P	0.55087	0.768	T	0.41998	-0.9477	8	0.87932	D	0	.	6.1509	0.20310	0.0:0.9996:0.0:4.0E-4	rs35745873;rs35745873	195	Q5H9I0	TFDP3_HUMAN	H	195	ENSP00000385461:Q195H	ENSP00000385461:Q195H	Q	-	3	2	TFDP3	132179369	0.998000	0.40836	0.018000	0.16275	0.019000	0.09904	0.277000	0.18734	0.268000	0.21939	0.271000	0.19318	CAG	C|0.978;A|0.022	0.022	strong		0.438	TFDP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058337.1	NM_016521		A	132351703	C	A	132351703	3	1	29	1	0	0	0	0	1	0	0	0	15814	912	32	4	636	4	TFDP3	23	132351703	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	3305888	132351703	22918857	903	13144											
TFDP3	51270	hgsc.bcm.edu	37	chrX	132352230	132352230	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	ggggcggctggtctggttctCgtccattaagaccttgagtt	5	13	14	9	2	2	2	0	1	2	1	4	2	3	2	2	5	0	3	2	5	1	4	rs28455963	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:132352230C>G	ENST00000310125.4	-	1	146	c.58G>C	c.(58-60)Gag>Cag	p.E20Q		NM_016521.2	NP_057605.3	Q5H9I0	TFDP3_HUMAN	transcription factor Dp family, member 3	20					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)					GTCTGGTTCTCGTCCATTAAG	0.483													G|||	383	0.101457	0.2247	0.0389	3775	,	,		13274	0.002		0.0288	False		,,,				2504	0.0286				p.E20Q		Atlas-SNP	.											.	TFDP3	92	.	0			c.G58C						PASS	.	G	GLN/GLU	304,905		40,182,42,295,133	63	47	52		58	0.2	0	X	dbSNP_125	52	85,2306		3,62,17,735,774	yes	missense	TFDP3	NM_016521.2	29	43,244,59,1030,907	GG,GC,G,CC,C		3.555,25.1447,10.8056	benign	20/406	132352230	389,3211	692	1591	2283	SO:0001583	missense	51270	exon1			GGTTCTCGTCCAT	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.58G>C	X.37:g.132352230C>G	ENSP00000385461:p.Glu20Gln	66	0	0		134	52	0.38806	NM_016521	Q6DK49|Q9NZ54	Missense_Mutation	SNP	ENST00000310125.4	37	CCDS14636.2	154	0.09282700421940929	74	0.17703349282296652	13	0.03651685393258427	2	0.0034965034965034965	14	0.01907356948228883	G	0.008	-1.897626	0.00517	0.251447	0.03555	ENSG00000183434	ENST00000310125	T	0.19806	2.12	0.235	0.235	0.15431	.	.	.	.	.	T	0.00012	0.0000	N	0.00260	-1.75	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34378	-0.9831	7	0.02654	T	1	.	.	.	.	rs28455963	20	Q5H9I0	TFDP3_HUMAN	Q	20	ENSP00000385461:E20Q	ENSP00000385461:E20Q	E	-	1	0	TFDP3	132179896	0.988000	0.35896	0.016000	0.15963	0.016000	0.09150	0.556000	0.23438	-0.705000	0.05035	-0.699000	0.03677	GAG	C|0.877;G|0.123	0.123	strong		0.483	TFDP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058337.1	NM_016521		G	132352230	C	G	132352230	3	3	29	1	0	0	0	0	1	0	0	0	15814	893	31	4	1163	4	TFDP3	23	132352230	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	527	132352230	22918330	904	13145											
SLITRK2	84631	hgsc.bcm.edu	37	chrX	144906370	144906370	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttatatggaactcccaggaaAtgctttgtggggcagtcaaa	12	11	11	7	0	1	0	1	0	0	0	2	2	2	2	1	4	2	2	1	4	5	3	rs45540333	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:144906370A>G	ENST00000370490.1	+	1	6682	c.2427A>G	c.(2425-2427)aaA>aaG	p.K809K	SLITRK2_ENST00000413937.2_Silent_p.K809K|SLITRK2_ENST00000434188.2_Silent_p.K809K|SLITRK2_ENST00000428560.2_Silent_p.K809K|TMEM257_ENST00000408967.2_5'Flank|SLITRK2_ENST00000447897.2_Silent_p.K809K			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	809					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)					CTCCCAGGAAATGCTTTGTGG	0.443													A|||	45	0.0119205	0.0008	0.0086	3775	,	,		14242	0.0		0.0209	False		,,,				2504	0.0174				p.K809K		Atlas-SNP	.											.	SLITRK2	221	.	0			c.A2427G						PASS	.	A	,,,,,,,	12,3823		0,11,1,1621,570	95	93	94		2427,2427,2427,2427,2427,2427,2427,2427	5.4	1	X	dbSNP_127	94	173,6555		1,120,51,2307,1821	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	,,,,,,,	1,131,52,3928,2391	GG,GA,G,AA,A		2.5713,0.3129,1.7514	,,,,,,,	809/846,809/846,809/846,809/846,809/846,809/846,809/846,809/846	144906370	185,10378	2203	4300	6503	SO:0001819	synonymous_variant	84631	exon5			CAGGAAATGCTTT	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.2427A>G	X.37:g.144906370A>G		130	0	0		174	122	0.701149	NM_001144005	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Silent	SNP	ENST00000370490.1	37	CCDS14680.1																																																																																			A|0.986;G|0.014	0.014	strong		0.443	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		G	144906370	A	G	144906370	2	3	29	1	0	0	0	0	0	0	0	1	14758	98	4	3		3	SLITRK2	23	144906370	Silent	SNP	A	TCGA-GR-7351-01A-11D-2210-10	12554140	144906370	10364190	905	13146											
FMR1	2332	hgsc.bcm.edu	37	chrX	146993715	146993715	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aagatggaggagctggtggtGgaagtgcggggctccaatgg	9	7	20	5	1	0	1	0	0	0	1	1	4	1	4	1	8	2	2	1	8	3	0	rs111485627	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:146993715G>T	ENST00000370475.4	+	1	146	c.18G>T	c.(16-18)gtG>gtT	p.V6V	FMR1_ENST00000334557.6_Silent_p.V6V|FMR1-AS1_ENST00000598667.1_RNA|FMR1_ENST00000370477.1_Silent_p.V6V|FMR1-AS1_ENST00000596112.1_RNA|FMR1_ENST00000370470.1_Silent_p.V6V|FMR1_ENST00000370471.3_Silent_p.V6V|FMR1_ENST00000439526.2_Silent_p.V6V|FMR1-AS1_ENST00000594922.1_RNA|FMR1_ENST00000218200.8_Silent_p.V6V	NM_002024.5	NP_002015.1	Q06787	FMR1_HUMAN	fragile X mental retardation 1	6	Agenet-like 1.				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)					AGCTGGTGGTGGAAGTGCGGG	0.677									Fragile X syndrome				G|||	15	0.00397351	0.0	0.0029	3775	,	,		5155	0.0		0.0129	False		,,,				2504	0.0				p.V6V		Atlas-SNP	.											.	FMR1	93	.	0			c.G18T						PASS	.	G	,,,,	6,3525		0,6,0,1538,443	76	50	59		18,18,18,18,18	4	1	X	dbSNP_132	59	79,6026		0,62,17,2208,1548	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FMR1	NM_001185075.1,NM_001185076.1,NM_001185081.1,NM_001185082.1,NM_002024.5	,,,,	0,68,17,3746,1991	TT,TG,T,GG,G		1.294,0.1699,0.8821	,,,,	6/538,6/612,6/517,6/587,6/633	146993715	85,9551	1987	3835	5822	SO:0001819	synonymous_variant	2332	exon1	Familial Cancer Database	Martin-Bell syndrome, FRAXA syndrome	GGTGGTGGAAGTG	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.18G>T	X.37:g.146993715G>T		89	0	0		123	27	0.219512	NM_002024	A6NNH4|D3DWT0|D3DWT1|D3DWT2|G8JL90|Q16578|Q5PQZ6|Q99054	Silent	SNP	ENST00000370475.4	37	CCDS14682.1																																																																																			C|0.000;G|0.987;T|0.013	0.013	strong		0.677	FMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058655.1	NM_002024		T	146993715	G	T	146993715	2	4	29	1	0	0	0	0	0	0	0	1	5968	1335	47	4		4	FMR1	23	146993715	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	2087345	146993715	8276845	906	13147											
TREX2	11219	hgsc.bcm.edu	37	chrX	152710522	152710522	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcacacagcagggggaaatCataatcaaagccattgtggg	14	6	13	8	0	2	0	2	0	0	0	2	1	2	1	1	4	2	2	1	4	3	2			TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:152710522C>A	ENST00000334497.2	-	11	1637	c.496G>T	c.(496-498)Gat>Tat	p.D166Y	TREX2_ENST00000338525.2_Missense_Mutation_p.D123Y|HAUS7_ENST00000484394.1_5'Flank|TREX2_ENST00000370231.2_Missense_Mutation_p.D123Y|TREX2_ENST00000330912.2_Missense_Mutation_p.D123Y|TREX2_ENST00000402951.1_Missense_Mutation_p.D166Y|TREX2_ENST00000370232.1_Missense_Mutation_p.D166Y|TREX2_ENST00000393862.2_Missense_Mutation_p.D123Y|TREX2_ENST00000414588.1_Missense_Mutation_p.D165Y			Q9BQ50	TREX2_HUMAN	three prime repair exonuclease 2	166					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)					AGGGGGAAATCATAATCAAAG	0.692								Editing and processing nucleases																													p.D123Y		Atlas-SNP	.											.	TREX2	36	.	0			c.G367T						PASS	.						7	6	7					X																	152710522		2093	4103	6196	SO:0001583	missense	11219	exon2			GGAAATCATAATC	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.496G>T	X.37:g.152710522C>A	ENSP00000334993:p.Asp166Tyr	21	0	0		20	7	0.35	NM_080701	Q45F08|Q9UN77	Missense_Mutation	SNP	ENST00000334497.2	37		.	.	.	.	.	.	.	.	.	.	C	18.63	3.664993	0.67700	.	.	ENSG00000183479	ENST00000393862;ENST00000330912;ENST00000338525;ENST00000334497;ENST00000370232;ENST00000402951;ENST00000414588;ENST00000370231	D;D;D;D;D;D;D;D	0.85258	-1.96;-1.96;-1.96;-1.96;-1.96;-1.96;-1.96;-1.96	5.01	5.01	0.66863	Exonuclease (1);Exonuclease, RNase T/DNA polymerase III (1);Ribonuclease H-like (1);	0.000000	0.50627	U	0.000120	D	0.92721	0.7686	M	0.85041	2.73	0.47374	D	0.999401	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93907	0.7193	10	0.87932	D	0	-19.851	14.7609	0.69604	0.0:1.0:0.0:0.0	.	165;166	Q06S70;Q9BQ50	.;TREX2_HUMAN	Y	123;123;123;166;166;166;165;123	ENSP00000377442:D123Y;ENSP00000333441:D123Y;ENSP00000345218:D123Y;ENSP00000334993:D166Y;ENSP00000359252:D166Y;ENSP00000386078:D166Y;ENSP00000401692:D165Y;ENSP00000359251:D123Y	ENSP00000333441:D123Y	D	-	1	0	TREX2	152363716	0.982000	0.34865	0.989000	0.46669	0.687000	0.40016	2.609000	0.46317	2.067000	0.61834	0.468000	0.43344	GAT	.	.	none		0.692	TREX2-001	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000060966.1	NM_080701		A	152710522	C	A	152710522	3	1	29	1	0	0	0	0	1	0	0	0	16492	826	29	4	346	4	TREX2	23	152710522	Missense_Mutation	SNP	C	TCGA-GR-7351-01A-11D-2210-10	5716807	152710522	2560038	907	13148											
PLXNB3	5365	hgsc.bcm.edu	37	chrX	153043896	153043896	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tctccggcgagctaccaggaGatgaactctgctttggctga	8	10	12	11	2	2	3	0	2	2	1	3	5	2	3	2	3	4	3	2	3	2	2	rs144872102	byFrequency	TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:153043896G>A	ENST00000361971.5	+	34	5634	c.5520G>A	c.(5518-5520)gaG>gaA	p.E1840E	SRPK3_ENST00000370104.1_5'Flank|SRPK3_ENST00000370108.3_5'Flank|SRPK3_ENST00000370100.1_5'Flank|SRPK3_ENST00000370101.3_5'Flank|PLXNB3_ENST00000538776.1_Silent_p.E1493E|SRPK3_ENST00000393786.3_5'Flank|PLXNB3_ENST00000538966.1_Silent_p.E1863E|SRPK3_ENST00000489426.1_De_novo_Start_OutOfFrame	NM_005393.2	NP_005384.2	Q9ULL4	PLXB3_HUMAN	plexin B3	1840					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)					GCTACCAGGAGATGAACTCTG	0.647													G|||	2	0.000529801	0.0	0.0	3775	,	,		13514	0.0		0.002	False		,,,				2504	0.0				p.E1863E		Atlas-SNP	.											.	PLXNB3	208	.	0			c.G5589A						PASS	.	G	,	1,3834		0,1,0,1631,571	43	41	42		5589,5520	2.4	1	X	dbSNP_134	42	8,6720		0,5,3,2423,1869	no	coding-synonymous,coding-synonymous	PLXNB3	NM_001163257.1,NM_005393.2	,	0,6,3,4054,2440	AA,AG,A,GG,G		0.1189,0.0261,0.0852	,	1863/1933,1840/1910	153043896	9,10554	2203	4300	6503	SO:0001819	synonymous_variant	5365	exon35			CCAGGAGATGAAC	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.5520G>A	X.37:g.153043896G>A		62	0	0		76	47	0.618421	NM_001163257	B7Z3E6|F5H773|Q9HDA4	Silent	SNP	ENST00000361971.5	37	CCDS14729.1																																																																																			G|0.999;A|0.001	0.001	strong		0.647	PLXNB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061063.1			A	153043896	G	A	153043896	2	1	29	1	0	0	0	0	0	0	0	1	12134	933	33	2		2	PLXNB3	23	153043896	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	333374	153043896	2226664	908	13149											
HCFC1	3054	hgsc.bcm.edu	37	chrX	153223257	153223257	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgatctgagtcacaggaccCgtggacgcctggcctgtgac	8	8	13	12	2	2	3	1	3	1	0	2	5	2	5	3	3	0	0	3	3	0	0	rs3027888		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:153223257C>T	ENST00000310441.7	-	12	3075	c.2109G>A	c.(2107-2109)acG>acA	p.T703T	HCFC1_ENST00000369984.4_Silent_p.T703T|HCFC1_ENST00000354233.3_Silent_p.T634T|HCFC1_ENST00000461098.1_5'Flank	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	703	Interaction with SIN3A.				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)					TCACAGGACCCGTGGACGCCT	0.552													C|||	17	0.00450331	0.0	0.0	3775	,	,		16219	0.0		0.004	False		,,,				2504	0.0133				p.T703T		Atlas-SNP	.											.	HCFC1	284	.	0			c.G2109A						PASS	.	C		4,3432		0,4,0,1429,570	83	86	85		2109	-10.5	0.2	X	dbSNP_102	85	55,6449		0,39,16,2314,1782	no	coding-synonymous	HCFC1	NM_005334.2		0,43,16,3743,2352	TT,TC,T,CC,C		0.8456,0.1164,0.5936		703/2036	153223257	59,9881	2003	4151	6154	SO:0001819	synonymous_variant	3054	exon12			AGGACCCGTGGAC		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.2109G>A	X.37:g.153223257C>T		66	0	0		98	22	0.22449	NM_005334	Q6P4G5	Silent	SNP	ENST00000310441.7	37	CCDS44020.1																																																																																			C|0.998;T|0.002	0.002	strong		0.552	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061099.4	NM_005334		T	153223257	C	T	153223257	2	4	29	1	0	0	0	0	0	0	0	1	7000	639	23	1		1	HCFC1	23	153223257	Silent	SNP	C	TCGA-GR-7351-01A-11D-2210-10	179361	153223257	2047303	909	13150											
HCFC1	3054	hgsc.bcm.edu	37	chrX	153227753	153227753	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctgggcttattccacgtcagGgtgtctgcagagagacggag	8	9	15	9	2	2	2	1	0	1	2	3	4	3	3	1	3	1	2	1	3	1	2	rs372516617		TCGA-GR-7351-01A-11D-2210-10	TCGA-GR-7351-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	dff37268-b20d-4489-a9af-6238d218ebcf	60d6b362-2bad-47dd-99c9-ad7df3203fd6	g.chrX:153227753G>C	ENST00000310441.7	-	5	1683	c.717C>G	c.(715-717)acC>acG	p.T239T	HCFC1_ENST00000369984.4_Silent_p.T239T|HCFC1_ENST00000354233.3_Silent_p.T239T|HCFC1_ENST00000461098.1_5'Flank	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	239					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)					TCCACGTCAGGGTGTCTGCAG	0.562																																					p.T239T		Atlas-SNP	.											.	HCFC1	284	.	0			c.C717G						PASS	.	G		1,3672		0,1,0,1550,571	56	58	58		717	-11.2	0.1	X		58	5,6605		0,4,1,2392,1817	no	coding-synonymous	HCFC1	NM_005334.2		0,5,1,3942,2388	CC,CG,C,GG,G		0.0756,0.0272,0.0583		239/2036	153227753	6,10277	2122	4214	6336	SO:0001819	synonymous_variant	3054	exon5			CGTCAGGGTGTCT		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.717C>G	X.37:g.153227753G>C		26	0	0		48	10	0.208333	NM_005334	Q6P4G5	Silent	SNP	ENST00000310441.7	37	CCDS44020.1																																																																																			.	.	weak		0.562	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061099.4	NM_005334		C	153227753	G	C	153227753	2	2	29	1	0	0	0	0	0	0	0	1	7000	1219	43	4		4	HCFC1	23	153227753	Silent	SNP	G	TCGA-GR-7351-01A-11D-2210-10	4496	153227753	2042807	910	13151											
KLHL17	339451	hgsc.bcm.edu	37	chr1	899824	899824	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgtacgtggcagggggcaaCgacggcaccagctgcctcaa	9	5	14	13	3	1	0	1	0	0	0	1	1	1	0	2	4	4	5	2	4	3	1	rs201807567	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:899824C>T	ENST00000338591.3	+	11	1721	c.1614C>T	c.(1612-1614)aaC>aaT	p.N538N	PLEKHN1_ENST00000379409.2_5'Flank|PLEKHN1_ENST00000379407.3_5'Flank|PLEKHN1_ENST00000379410.3_5'Flank	NM_198317.2	NP_938073.1	Q6TDP4	KLH17_HUMAN	kelch-like family member 17	538	Interaction with F-actin. {ECO:0000250}.				actin cytoskeleton organization (GO:0030036)|brain development (GO:0007420)|protein ubiquitination (GO:0016567)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|dendrite cytoplasm (GO:0032839)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	protein complex scaffold (GO:0032947)			central_nervous_system(1)|kidney(2)|lung(3)|prostate(2)|upper_aerodigestive_tract(1)|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)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.52e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.59e-23)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.000469)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		CAGGGGGCAACGACGGCACCA	0.667													C|||	11	0.00219649	0.0	0.0014	5008	,	,		10445	0.001		0.006	False		,,,				2504	0.0031				p.N538N		Atlas-SNP	.											.	KLHL17	31	.	0			c.C1614T						PASS	.	C		1,4119		0,1,2059	15	16	16		1614	-2.8	1	1		16	27,8173		0,27,4073	no	coding-synonymous	KLHL17	NM_198317.2		0,28,6132	TT,TC,CC		0.3293,0.0243,0.2273		538/643	899824	28,12292	2060	4100	6160	SO:0001819	synonymous_variant	339451	exon11			GGGCAACGACGGC	AY423763	CCDS30550.1	1p36	2013-01-30	2013-01-30		ENSG00000187961	ENSG00000187961		"Kelch-like", "BTB/POZ domain containing"	24023	protein-coding gene	gene with protein product	"actinfilin"		"kelch-like 17 (Drosophila)"			12063253	Standard	NM_198317		Approved		uc001aca.2	Q6TDP4	OTTHUMG00000040721	ENST00000338591.3:c.1614C>T	1.37:g.899824C>T		88	0	0		48	38	0.791667	NM_198317	Q5SV94	Silent	SNP	ENST00000338591.3	37	CCDS30550.1																																																																																			C|0.996;T|0.004	0.004	strong		0.667	KLHL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097875.3	NM_198317		T	899824	C	T	899824	2	4	30	1	0	0	0	0	0	0	0	1	8381	535	19	1		1	KLHL17	1	899824	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10		899824	248350797	1	13152											
WDR8	49856	hgsc.bcm.edu	37	chr1	3551828	3551828	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgtacgtggacaacaaccGgccatccaatgagtacagca	13	6	10	12	2	0	1	0	1	0	0	1	2	1	2	3	2	5	4	3	2	5	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:3551828G>A	ENST00000270708.7	-	7	707	c.634C>T	c.(634-636)Cgg>Tgg	p.R212W	WRAP73_ENST00000378322.3_Missense_Mutation_p.R212W	NM_017818.3	NP_060288.3	Q9P2S5	WRP73_HUMAN	WD repeat containing, antisense to TP73	212						centrosome (GO:0005813)|cytoplasm (GO:0005737)				endometrium(2)|kidney(1)|large_intestine(5)|lung(3)|pancreas(1)	12						GACAACAACCGGCCATCCAAT	0.542																																					p.R212W		Atlas-SNP	.											WRAP73,NS,carcinoma,+1,1	WRAP73	43	1	0			c.C634T						PASS	.						80	80	80					1																	3551828		2203	4300	6503	SO:0001583	missense	49856	exon7			ACAACCGGCCATC	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.634C>T	1.37:g.3551828G>A	ENSP00000270708:p.Arg212Trp	157	0	0		118	48	0.40678	NM_017818	Q5T0D6|Q9BUH7|Q9NTK7|Q9NX56	Missense_Mutation	SNP	ENST00000270708.7	37	CCDS48.1	.	.	.	.	.	.	.	.	.	.	G	16.60	3.168380	0.57584	.	.	ENSG00000116213	ENST00000270708;ENST00000378322;ENST00000419924	T;T	0.49139	3.34;0.79	5.65	5.65	0.86999	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.77226	0.4099	H	0.94423	3.535	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83414	0.0029	10	0.87932	D	0	-63.099	15.1585	0.72761	0.0:0.0:0.8584:0.1416	.	212	Q9P2S5	WRP73_HUMAN	W	212;212;183	ENSP00000270708:R212W;ENSP00000367573:R212W	ENSP00000270708:R212W	R	-	1	2	WRAP73	3541688	1.000000	0.71417	1.000000	0.80357	0.053000	0.15095	5.938000	0.70170	2.652000	0.90054	0.655000	0.94253	CGG	.	.	none		0.542	WRAP73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001470.1			A	3551828	G	A	3551828	3	1	30	1	0	0	0	0	1	0	0	0	17344	1115	39	1	772	1	WDR8	1	3551828	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2652004	3551828	245698793	2	13153											
C1orf127	148345	hgsc.bcm.edu	37	chr1	11017141	11017141	+	Intron	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ctcaccagccatagtggcagGagctcagcagaggtgttcag	10	7	13	11	0	3	1	3	0	0	1	3	2	3	2	2	3	3	4	2	3	1	2	rs75810903	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:11017141G>A	ENST00000377008.4	-	7	724				C1orf127_ENST00000377004.4_Silent_p.L239L			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127											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)		ATAGTGGCAGGAGCTCAGCAG	0.602													G|||	16	0.00319489	0.0008	0.0014	5008	,	,		15143	0.002		0.0099	False		,,,				2504	0.002				p.L239L		Atlas-SNP	.											.	C1orf127	134	.	0			c.C717T						PASS	.	G		3,1381		0,3,689	33	41	38		717	-4.9	0	1	dbSNP_132	38	36,3146		0,36,1555	yes	coding-synonymous	C1orf127	NM_001170754.1		0,39,2244	AA,AG,GG		1.1314,0.2168,0.8541		239/824	11017141	39,4527	692	1591	2283	SO:0001627	intron_variant	148345	exon8			TGGCAGGAGCTCA	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.277+500C>T	1.37:g.11017141G>A		40	0	0		52	29	0.557692	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Silent	SNP	ENST00000377008.4	37		8	0.003663003663003663	0	0.0	0	0.0	1	0.0017482517482517483	7	0.009234828496042216	G	3.484	-0.105372	0.06967	0.002168	0.011314	ENSG00000175262	ENST00000520253	.	.	.	5.39	-4.9	0.03094	.	.	.	.	.	T	0.19208	0.0461	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.32025	-0.9922	4	.	.	.	.	6.7834	0.23659	0.1109:0.62:0.1446:0.1245	.	.	.	.	F	217	.	.	S	-	2	0	C1orf127	10939728	0.067000	0.21026	0.024000	0.17045	0.510000	0.34073	-0.085000	0.11250	-0.691000	0.05135	0.561000	0.74099	TCC	G|0.996;A|0.004	0.004	strong		0.602	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507		A	11017141	G	A	11017141	1	1	30	0	1	0	0	0	0	0	0	0	1996	1161	41	2		2	C1orf127	1	11017141	Intron	SNP	G	TCGA-GR-7353-01A-11D-2210-10	7465313	11017141	238233480	3	13154											
MTHFR	4524	hgsc.bcm.edu	37	chr1	11855269	11855269	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactggccagaagctcctggCacaggctcacggccagctcg	8	5	12	16	2	1	1	1	0	0	1	3	1	2	1	3	4	2	4	3	4	1	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:11855269C>T	ENST00000376592.1	-	5	1045	c.917G>A	c.(916-918)tGc>tAc	p.C306Y	MTHFR_ENST00000376590.3_Missense_Mutation_p.C306Y|MTHFR_ENST00000376583.3_Missense_Mutation_p.C347Y|MTHFR_ENST00000376585.1_Missense_Mutation_p.C347Y			P42898	MTHR_HUMAN	methylenetetrahydrofolate reductase (NAD(P)H)	306					blood circulation (GO:0008015)|cellular amino acid metabolic process (GO:0006520)|folic acid metabolic process (GO:0046655)|homocysteine metabolic process (GO:0050667)|methionine biosynthetic process (GO:0009086)|response to drug (GO:0042493)|response to folic acid (GO:0051593)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to vitamin B2 (GO:0033274)|S-adenosylmethionine metabolic process (GO:0046500)|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)|neuron projection (GO:0043005)	flavin adenine dinucleotide binding (GO:0050660)|methylenetetrahydrofolate reductase (NAD(P)H) activity (GO:0004489)|modified amino acid binding (GO:0072341)|NADP binding (GO:0050661)			NS(4)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33	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)|Hepatocellular(190;0.00826)|Ovarian(437;0.00965)|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)	Benazepril(DB00542)|Cyanocobalamin(DB00115)|Fluorouracil(DB00544)|Folic Acid(DB00158)|L-Methionine(DB00134)|Menadione(DB00170)|Methotrexate(DB00563)|Riboflavin(DB00140)|Tetrahydrofolic acid(DB00116)	AAGCTCCTGGCACAGGCTCAC	0.592																																					p.C306Y		Atlas-SNP	.											.	MTHFR	65	.	0			c.G917A						PASS	.						80	80	80					1																	11855269		2203	4300	6503	SO:0001583	missense	4524	exon6			TCCTGGCACAGGC	BC053509	CCDS137.1	1p36.3	2014-09-17	2010-05-04		ENSG00000177000	ENSG00000177000	1.5.1.20		7436	protein-coding gene	gene with protein product		607093	"5,10-methylenetetrahydrofolate reductase (NADPH)"			7920641	Standard	NM_005957		Approved		uc001atc.2	P42898	OTTHUMG00000002277	ENST00000376592.1:c.917G>A	1.37:g.11855269C>T	ENSP00000365777:p.Cys306Tyr	93	0	0		66	10	0.151515	NM_005957	B2R7A6|Q5SNW6|Q5SNW9|Q7Z6M6|Q8IU73|Q9UQR2	Missense_Mutation	SNP	ENST00000376592.1	37	CCDS137.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.600241	0.87055	.	.	ENSG00000177000	ENST00000376592;ENST00000376583;ENST00000376590;ENST00000376585	D;D;D;D	0.92495	-3.05;-3.05;-3.05;-3.05	5.09	5.09	0.68999	.	0.084158	0.85682	D	0.000000	D	0.97359	0.9136	H	0.96239	3.79	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.69479	0.964;0.963	D	0.98609	1.0662	10	0.87932	D	0	.	17.8468	0.88732	0.0:1.0:0.0:0.0	.	306;347	P42898;Q5SNW6	MTHR_HUMAN;.	Y	306;347;306;347	ENSP00000365777:C306Y;ENSP00000365767:C347Y;ENSP00000365775:C306Y;ENSP00000365770:C347Y	ENSP00000365767:C347Y	C	-	2	0	MTHFR	11777856	1.000000	0.71417	1.000000	0.80357	0.836000	0.47400	7.085000	0.76875	2.517000	0.84864	0.462000	0.41574	TGC	.	.	none		0.592	MTHFR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000006538.1	NM_005957		T	11855269	C	T	11855269	3	4	30	1	0	0	0	0	1	0	0	0	9940	710	25	2	1081	2	MTHFR	1	11855269	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	838128	11855269	237395352	4	13155											
CTRC	11330	hgsc.bcm.edu	37	chr1	15772212	15772212	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agaagccggtagtctacaccCgggtgtccgcctacatcgac	9	7	11	14	4	1	1	0	0	1	1	3	2	2	1	4	2	3	1	4	2	4	3	rs121909293	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:15772212C>T	ENST00000375949.4	+	7	786	c.760C>T	c.(760-762)Cgg>Tgg	p.R254W	CTRC_ENST00000483406.1_3'UTR|CTRC_ENST00000375943.2_3'UTR	NM_007272.2	NP_009203.2	Q99895	CTRC_HUMAN	chymotrypsin C (caldecrin)	254	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		Missing (in PCTT; associated with disease susceptibility; results in reduced protein secretion and loss of activity). {ECO:0000269|PubMed:18172691}.|R -> Q (found in a patient with chronic pancreatitis; unknown pathological significance; mutant protein secretion, activity and trypsin-mediated degradation are comparable to those of wild-type). {ECO:0000269|PubMed:19407484}.|R -> W (in PCTT; associated with susceptibility to disease; results in reduced secretion; normal activity; the mutant undergoes proteolytic degradation during trypsin-mediated activation; dbSNP:rs121909293). {ECO:0000269|PubMed:18059268, ECO:0000269|PubMed:18172691, ECO:0000269|PubMed:22580415, ECO:0000269|PubMed:23135764}.		proteolysis (GO:0006508)		peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)	13		Breast(348;0.000207)|all_lung(284;0.00021)|Colorectal(325;0.000257)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)|Hepatocellular(190;0.0634)		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)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		AGTCTACACCCGGGTGTCCGC	0.632													C|||	8	0.00159744	0.0	0.0	5008	,	,		15935	0.0		0.008	False		,,,				2504	0.0				p.R254W		Atlas-SNP	.											.	CTRC	28	.	0			c.C760T	GRCh37	CM080169	CTRC	M	rs121909293	PASS	.	C	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	81	82	82	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	760	4.7	1	1	dbSNP_133	82	33,8567	22.8+/-68.1	0,33,4267	yes	missense	CTRC	NM_007272.2	101	0,34,6469	TT,TC,CC		0.3837,0.0227,0.2614	probably-damaging	254/269	15772212	34,12972	2203	4300	6503	SO:0001583	missense	11330	exon7			TACACCCGGGTGT	BC015118	CCDS156.1	1p36.21	2009-02-18			ENSG00000162438	ENSG00000162438	3.4.21.2		2523	protein-coding gene	gene with protein product	"elastase 4"	601405				8635596	Standard	NM_007272		Approved	CLCR, ELA4	uc001awi.1	Q99895	OTTHUMG00000002255	ENST00000375949.4:c.760C>T	1.37:g.15772212C>T	ENSP00000365116:p.Arg254Trp	63	0	0		37	10	0.27027	NM_007272	A8K082|O00765|Q9NUH5	Missense_Mutation	SNP	ENST00000375949.4	37	CCDS156.1	9	0.004120879120879121	0	0.0	0	0.0	0	0.0	9	0.011873350923482849	C	19.97	3.925157	0.73213	2.27E-4	0.003837	ENSG00000162438	ENST00000375949	D	0.94793	-3.52	4.68	4.68	0.58851	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.053971	0.85682	D	0.000000	D	0.97244	0.9099	H	0.94808	3.585	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96153	0.9109	10	0.87932	D	0	-43.8301	16.7021	0.85357	0.0:1.0:0.0:0.0	.	254	Q99895	CTRC_HUMAN	W	254	ENSP00000365116:R254W	ENSP00000365116:R254W	R	+	1	2	CTRC	15644799	0.930000	0.31532	1.000000	0.80357	0.586000	0.36452	1.189000	0.32114	2.606000	0.88127	0.650000	0.86243	CGG	C|0.997;T|0.003	0.003	strong		0.632	CTRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006435.1	NM_007272		T	15772212	C	T	15772212	3	4	30	1	0	0	0	0	1	0	0	0	4029	643	23	1	786	1	CTRC	1	15772212	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	3916943	15772212	233478409	5	13156											
PADI2	11240	hgsc.bcm.edu	37	chr1	17410253	17410253	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atcgcctcggtttaggtactGgaagcagaccttcagctcac	9	10	10	12	2	2	1	2	0	0	1	4	2	2	2	2	3	3	4	2	3	3	4	rs142403504	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:17410253G>A	ENST00000375486.4	-	9	1081	c.1018C>T	c.(1018-1020)Cag>Tag	p.Q340*	PADI2_ENST00000375481.1_Nonsense_Mutation_p.Q340*|PADI2_ENST00000444885.2_Nonsense_Mutation_p.Q224*|PADI2_ENST00000466151.1_5'Flank	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	340					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)	TTTAGGTACTGGAAGCAGACC	0.522													G|||	4	0.000798722	0.0	0.0	5008	,	,		20901	0.0		0.001	False		,,,				2504	0.0031				p.Q340X		Atlas-SNP	.											.	PADI2	72	.	0			c.C1018T						PASS	.	G	stop/GLN	1,4405	2.1+/-5.4	0,1,2202	140	133	135		1018	5.8	1	1	dbSNP_134	135	30,8570	21.0+/-64.5	0,30,4270	yes	stop-gained	PADI2	NM_007365.2		0,31,6472	AA,AG,GG		0.3488,0.0227,0.2384		340/666	17410253	31,12975	2203	4300	6503	SO:0001587	stop_gained	11240	exon9			GGTACTGGAAGCA	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.1018C>T	1.37:g.17410253G>A	ENSP00000364635:p.Gln340*	219	0	0		121	35	0.289256	NM_007365	Q96DA7|Q9UPN2	Nonsense_Mutation	SNP	ENST00000375486.4	37	CCDS177.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	38	7.248142	0.98161	2.27E-4	0.003488	ENSG00000117115	ENST00000375486;ENST00000444885;ENST00000375481	.	.	.	5.77	5.77	0.91146	.	0.267496	0.41605	D	0.000847	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.13853	T	0.58	-37.1678	13.5666	0.61822	0.0:0.2539:0.7461:0.0	.	.	.	.	X	340;224;340	.	ENSP00000364630:Q340X	Q	-	1	0	PADI2	17282840	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.120000	0.64685	2.724000	0.93272	0.561000	0.74099	CAG	G|0.998;A|0.002	0.002	strong		0.522	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1			A	17410253	G	A	17410253	4	1	30	1	0	0	0	0	0	1	0	0	11387	1357	47	2	1011	2	PADI2	1	17410253	Nonsense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1638041	17410253	231840368	6	13157											
ALDH4A1	8659	hgsc.bcm.edu	37	chr1	19212007	19212007	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgaggatctcagccctgcgcGgcccactcagcatgtctgcc	6	7	11	17	3	3	0	2	0	2	0	4	2	3	1	3	2	4	1	3	2	0	0	rs139640415	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:19212007G>A	ENST00000375341.3	-	5	670	c.413C>T	c.(412-414)cCg>cTg	p.P138L	ALDH4A1_ENST00000538839.1_Missense_Mutation_p.P138L|MIR4695_ENST00000577305.1_RNA|RP13-279N23.2_ENST00000494072.3_3'UTR|ALDH4A1_ENST00000290597.5_Missense_Mutation_p.P138L|ALDH4A1_ENST00000454547.1_5'UTR|ALDH4A1_ENST00000538309.1_Missense_Mutation_p.P78L	NM_003748.3	NP_003739.2	P30038	AL4A1_HUMAN	aldehyde dehydrogenase 4 family, member A1	138					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)		AGCCCTGCGCGGCCCACTCAG	0.672													G|||	6	0.00119808	0.0008	0.0014	5008	,	,		10477	0.0		0.004	False		,,,				2504	0.0				p.P138L		Atlas-SNP	.											ALDH4A1_ENST00000375341,NS,carcinoma,+1,2	ALDH4A1	72	2	0			c.C413T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO	12,4392		0,12,2190	27	25	26		233,413,413	3.5	0.7	1	dbSNP_134	26	12,8588		0,12,4288	yes	missense,missense,missense	ALDH4A1	NM_001161504.1,NM_003748.3,NM_170726.2	98,98,98	0,24,6478	AA,AG,GG		0.1395,0.2725,0.1846	possibly-damaging,possibly-damaging,possibly-damaging	78/504,138/564,138/564	19212007	24,12980	2202	4300	6502	SO:0001583	missense	8659	exon5			CTGCGCGGCCCAC	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.413C>T	1.37:g.19212007G>A	ENSP00000364490:p.Pro138Leu	98	0	0		44	32	0.727273	NM_003748	A8K1Q7|B4DGE4|D2D4A3|Q16882|Q53HU4|Q5JNV6|Q8IZ38|Q96IF0|Q9UDI6	Missense_Mutation	SNP	ENST00000375341.3	37	CCDS188.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	14.66	2.601317	0.46423	0.002725	0.001395	ENSG00000159423	ENST00000290597;ENST00000375341;ENST00000538839;ENST00000538309;ENST00000375335;ENST00000454547;ENST00000375334;ENST00000432718	T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57	5.41	3.54	0.40534	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.237912	0.43416	D	0.000562	T	0.42177	0.1191	M	0.83852	2.665	0.80722	D	1	D	0.53151	0.958	P	0.47864	0.559	T	0.40553	-0.9557	10	0.48119	T	0.1	-36.7716	10.2054	0.43109	0.0751:0.1365:0.7884:0.0	.	138	P30038	AL4A1_HUMAN	L	138;138;138;78;122;36;78;122	ENSP00000290597:P138L;ENSP00000364490:P138L;ENSP00000446071:P138L;ENSP00000442988:P78L;ENSP00000393209:P122L	ENSP00000290597:P138L	P	-	2	0	ALDH4A1	19084594	1.000000	0.71417	0.671000	0.29857	0.115000	0.19883	6.100000	0.71473	0.667000	0.31107	-0.264000	0.10439	CCG	G|0.999;A|0.001	0.001	strong		0.672	ALDH4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006954.1			A	19212007	G	A	19212007	3	1	30	1	0	0	0	0	1	0	0	0	501	1116	39	1	1322	1	ALDH4A1	1	19212007	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1801754	19212007	230038614	7	13158											
SFN	2810	hgsc.bcm.edu	37	chr1	27190149	27190149	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	catcattgactcagcccggtCagcctaccaggaggccatgg	9	7	11	14	1	3	1	3	1	0	0	3	2	3	2	4	4	3	0	4	4	1	2	rs78707984		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:27190149C>T	ENST00000339276.4	+	1	517	c.446C>T	c.(445-447)tCa>tTa	p.S149L		NM_006142.3	NP_006133.1	Q9Y3B8	ORN_HUMAN	stratifin	0	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)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(2)	9		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)|all cancers(4;2.1e-52)|Epithelial(14;2.31e-52)|OV - Ovarian serous cystadenocarcinoma(117;8.22e-30)|Colorectal(126;1.31e-09)|COAD - Colon adenocarcinoma(152;3.45e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000501)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)|GBM - Glioblastoma multiforme(114;0.0767)|Lung(427;0.215)		TCAGCCCGGTCAGCCTACCAG	0.602																																					p.S149L		Atlas-SNP	.											.	SFN	20	.	0			c.C446T						PASS	.	C	LEU/SER	0,4406		0,0,2203	85	83	84		446	5.1	0.7	1	dbSNP_131	84	2,8598	2.2+/-6.3	0,2,4298	yes	missense	SFN	NM_006142.3	145	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	149/249	27190149	2,13004	2203	4300	6503	SO:0001583	missense	2810	exon1			CCCGGTCAGCCTA	BC023552	CCDS288.1	1p36.11	2008-02-05			ENSG00000175793	ENSG00000175793			10773	protein-coding gene	gene with protein product	"14-3-3 sigma"	601290				8515476	Standard	NM_006142		Approved	YWHAS	uc001bnc.1	P31947	OTTHUMG00000004093	ENST00000339276.4:c.446C>T	1.37:g.27190149C>T	ENSP00000340989:p.Ser149Leu	48	0	0		41	11	0.268293	NM_006142	B2R532|Q32Q18|Q53FT1|Q6FIC6|Q9UFY7	Missense_Mutation	SNP	ENST00000339276.4	37	CCDS288.1	.	.	.	.	.	.	.	.	.	.	C	12.17	1.858571	0.32791	0.0	2.33E-4	ENSG00000175793	ENST00000339276;ENST00000538651	T	0.43688	0.94	6.06	5.1	0.69264	14-3-3 domain (4);	0.906876	0.09400	N	0.807339	T	0.20780	0.0500	N	0.02368	-0.58	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.05402	-1.0887	10	0.25751	T	0.34	-0.5242	11.3178	0.49403	0.1716:0.7101:0.1183:0.0	.	149	P31947	1433S_HUMAN	L	149;117	ENSP00000340989:S149L	ENSP00000340989:S149L	S	+	2	0	SFN	27062736	0.144000	0.22641	0.733000	0.30861	0.993000	0.82548	2.150000	0.42254	2.871000	0.98454	0.655000	0.94253	TCA	.	.	weak		0.602	SFN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011709.1	NM_006142		T	27190149	C	T	27190149	3	4	30	1	0	0	0	0	1	0	0	0	14174	838	29	2	448	2	SFN	1	27190149	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	7978142	27190149	222060472	8	13159											
SFN	2810	hgsc.bcm.edu	37	chr1	27190196	27190196	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaagaaggagatgccgcccAccaaccccatccgcctgggc	10	3	11	17	2	0	2	0	0	0	2	1	3	1	2	7	2	2	1	7	2	3	0	rs77755255		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:27190196A>T	ENST00000339276.4	+	1	564	c.493A>T	c.(493-495)Acc>Tcc	p.T165S		NM_006142.3	NP_006133.1	Q9Y3B8	ORN_HUMAN	stratifin	0	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)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(2)	9		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)|all cancers(4;2.1e-52)|Epithelial(14;2.31e-52)|OV - Ovarian serous cystadenocarcinoma(117;8.22e-30)|Colorectal(126;1.31e-09)|COAD - Colon adenocarcinoma(152;3.45e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000501)|STAD - Stomach adenocarcinoma(196;0.000588)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|READ - Rectum adenocarcinoma(331;0.0419)|GBM - Glioblastoma multiforme(114;0.0767)|Lung(427;0.215)		GATGCCGCCCACCAACCCCAT	0.617																																					p.T165S		Atlas-SNP	.											.	SFN	20	.	0			c.A493T						PASS	.						90	84	86					1																	27190196		2203	4300	6503	SO:0001583	missense	2810	exon1			CCGCCCACCAACC	BC023552	CCDS288.1	1p36.11	2008-02-05			ENSG00000175793	ENSG00000175793			10773	protein-coding gene	gene with protein product	"14-3-3 sigma"	601290				8515476	Standard	NM_006142		Approved	YWHAS	uc001bnc.1	P31947	OTTHUMG00000004093	ENST00000339276.4:c.493A>T	1.37:g.27190196A>T	ENSP00000340989:p.Thr165Ser	59	0	0		37	6	0.162162	NM_006142	B2R532|Q32Q18|Q53FT1|Q6FIC6|Q9UFY7	Missense_Mutation	SNP	ENST00000339276.4	37	CCDS288.1	.	.	.	.	.	.	.	.	.	.	A	28.4	4.919577	0.92249	.	.	ENSG00000175793	ENST00000339276;ENST00000538651	T	0.46819	0.86	5.91	5.91	0.95273	14-3-3 domain (4);	0.000000	0.85682	D	0.000000	T	0.73938	0.3651	M	0.89715	3.055	0.36736	D	0.881953	D	0.53885	0.963	D	0.65443	0.935	T	0.83349	-0.0004	10	0.87932	D	0	-45.3648	16.0112	0.80404	1.0:0.0:0.0:0.0	.	165	P31947	1433S_HUMAN	S	165;133	ENSP00000340989:T165S	ENSP00000340989:T165S	T	+	1	0	SFN	27062783	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.335000	0.96500	2.255000	0.74692	0.533000	0.62120	ACC	.	.	weak		0.617	SFN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011709.1	NM_006142		T	27190196	A	T	27190196	3	4	30	1	0	0	0	0	1	0	0	0	14174	159	6	5	495	5	SFN	1	27190196	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	47	27190196	222060425	9	13160											
XKR8	55113	hgsc.bcm.edu	37	chr1	28290155	28290155	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagacggcaccacagctcacGctggtgctggccatcatgct	8	7	12	14	2	2	1	2	0	0	1	2	2	2	1	2	3	3	5	2	3	0	0	rs142513353	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:28290155G>A	ENST00000373884.5	+	2	1049	c.441G>A	c.(439-441)acG>acA	p.T147T	XKR8_ENST00000481387.1_3'UTR	NM_018053.2	NP_060523.2	Q9H6D3	XKR8_HUMAN	XK, Kell blood group complex subunit-related family, member 8	147					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)		CACAGCTCACGCTGGTGCTGG	0.627													G|||	10	0.00199681	0.0	0.0043	5008	,	,		17805	0.0		0.007	False		,,,				2504	0.0				p.T147T		Atlas-SNP	.											.	XKR8	15	.	0			c.G441A						PASS	.	G		3,4403	4.2+/-10.8	0,3,2200	23	20	21		441	-1.9	1	1	dbSNP_134	21	31,8569	19.8+/-62.0	0,31,4269	no	coding-synonymous	XKR8	NM_018053.2		0,34,6469	AA,AG,GG		0.3605,0.0681,0.2614		147/396	28290155	34,12972	2203	4300	6503	SO:0001819	synonymous_variant	55113	exon2			GCTCACGCTGGTG	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.441G>A	1.37:g.28290155G>A		201	0	0		128	16	0.125	NM_018053		Silent	SNP	ENST00000373884.5	37	CCDS315.1																																																																																			G|0.997;A|0.003	0.003	strong		0.627	XKR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011175.1	NM_018053		A	28290155	G	A	28290155	2	1	30	1	0	0	0	0	0	0	0	1	17452	1074	38	1		1	XKR8	1	28290155	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1099959	28290155	220960466	10	13161											
EYA3	2140	hgsc.bcm.edu	37	chr1	28304899	28304899	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggttacctgtttggctgcaaTttcttcatctcgtccatctc	5	17	7	12	1	4	0	1	0	3	0	7	0	5	0	2	2	2	4	2	2	2	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:28304899T>C	ENST00000373871.3	-	17	1867	c.1627A>G	c.(1627-1629)Att>Gtt	p.I543V	EYA3_ENST00000540618.1_Missense_Mutation_p.I497V|EYA3_ENST00000373863.3_Missense_Mutation_p.I497V|EYA3_ENST00000436342.2_Missense_Mutation_p.I417V|EYA3_ENST00000373864.1_Missense_Mutation_p.I386V|EYA3_ENST00000545175.1_Missense_Mutation_p.I490V	NM_001282561.1|NM_001282562.1	NP_001269490.1|NP_001269491.1	Q99504	EYA3_HUMAN	EYA transcriptional coactivator and phosphatase 3	543					anatomical structure morphogenesis (GO:0009653)|double-strand break repair (GO:0006302)|histone dephosphorylation (GO:0016576)|multicellular organismal development (GO:0007275)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of DNA repair (GO:0045739)|regulation of transcription, DNA-templated (GO:0006355)|response to ionizing radiation (GO:0010212)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	15		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000432)|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;0.0484)|OV - Ovarian serous cystadenocarcinoma(117;1.25e-24)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;2.8e-06)|STAD - Stomach adenocarcinoma(196;0.00364)|KIRC - Kidney renal clear cell carcinoma(1967;0.00378)|BRCA - Breast invasive adenocarcinoma(304;0.00718)|READ - Rectum adenocarcinoma(331;0.0642)		TTGGCTGCAATTTCTTCATCT	0.368																																					p.I543V		Atlas-SNP	.											.	EYA3	38	.	0			c.A1627G						PASS	.						207	200	202					1																	28304899		2203	4300	6503	SO:0001583	missense	2140	exon17			CTGCAATTTCTTC	U81602	CCDS316.1, CCDS60050.1, CCDS60051.1, CCDS60052.1	1p36	2014-06-19	2014-06-19		ENSG00000158161	ENSG00000158161		"Protein tyrosine phosphatases / Asp-based PTPs"	3521	protein-coding gene	gene with protein product		601655	"eyes absent (Drosophila) homolog 3", "eyes absent homolog 3 (Drosophila)"			9020840	Standard	NM_001990		Approved	DKFZp686C132	uc001bpi.2	Q99504	OTTHUMG00000003916	ENST00000373871.3:c.1627A>G	1.37:g.28304899T>C	ENSP00000362978:p.Ile543Val	253	0	0		155	40	0.258065	NM_001990	A8K190|B4DIR7|B4DNZ7|O95463|Q8IVX7|Q99813	Missense_Mutation	SNP	ENST00000373871.3	37	CCDS316.1	.	.	.	.	.	.	.	.	.	.	T	8.394	0.840482	0.16891	.	.	ENSG00000158161	ENST00000373871;ENST00000436342;ENST00000373864;ENST00000540618;ENST00000545175;ENST00000373863	D;D;D;D;D;D	0.88046	-2.33;-2.33;-2.33;-2.33;-2.33;-2.33	5.54	5.54	0.83059	EYA (1);Haloacid dehalogenase-like hydrolase (1);	0.254205	0.46145	D	0.000317	T	0.77805	0.4185	N	0.22421	0.69	0.28710	N	0.903603	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.06405	0.001;0.001;0.002	T	0.67074	-0.5762	10	0.28530	T	0.3	-12.8991	10.8241	0.46622	0.0:0.0757:0.0:0.9243	.	497;497;543	B4DIR7;Q8IVX7;Q99504	.;.;EYA3_HUMAN	V	543;417;386;497;490;497	ENSP00000362978:I543V;ENSP00000405587:I417V;ENSP00000362971:I386V;ENSP00000442558:I497V;ENSP00000442280:I490V;ENSP00000362970:I497V	ENSP00000362970:I497V	I	-	1	0	EYA3	28177486	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.160000	0.42348	2.107000	0.64212	0.402000	0.26972	ATT	.	.	none		0.368	EYA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011184.1	NM_001990		C	28304899	T	C	28304899	3	2	30	1	0	0	0	0	1	0	0	0	5332	1493	52	3	102	3	EYA3	1	28304899	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	14744	28304899	220945722	11	13162											
BAI2	576	hgsc.bcm.edu	37	chr1	32193185	32193185	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgttgggacaagctggggcGctccccagggctgggcttat	6	9	16	10	1	0	0	0	0	0	0	1	1	1	1	2	5	1	5	2	5	2	2	rs41263977	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:32193185G>A	ENST00000373658.3	-	33	4935	c.4594C>T	c.(4594-4596)Cgc>Tgc	p.R1532C	BAI2_ENST00000398556.3_Missense_Mutation_p.R1447C|BAI2_ENST00000398547.1_Missense_Mutation_p.R1446C|BAI2_ENST00000398538.1_Missense_Mutation_p.R1501C|BAI2_ENST00000398542.1_Missense_Mutation_p.R1413C|BAI2_ENST00000257070.4_Missense_Mutation_p.R1498C|BAI2_ENST00000465256.1_5'UTR|BAI2_ENST00000440175.2_Missense_Mutation_p.R1122C|BAI2_ENST00000373655.2_Missense_Mutation_p.R1531C|BAI2_ENST00000527361.1_Missense_Mutation_p.R1498C	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	1532					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)		AAGCTGGGGCGCTCCCCAGGG	0.612													G|||	12	0.00239617	0.0	0.0	5008	,	,		14744	0.0		0.0089	False		,,,				2504	0.0031				p.R1532C		Atlas-SNP	.											.	BAI2	128	.	0			c.C4594T						PASS	.	G	CYS/ARG	7,4399	12.9+/-30.5	0,7,2196	20	20	20		4594	3.3	1	1	dbSNP_127	20	77,8523	44.9+/-103.4	0,77,4223	yes	missense	BAI2	NM_001703.2	180	0,84,6419	AA,AG,GG		0.8953,0.1589,0.6459	probably-damaging	1532/1586	32193185	84,12922	2203	4300	6503	SO:0001583	missense	576	exon33			TGGGGCGCTCCCC	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.4594C>T	1.37:g.32193185G>A	ENSP00000362762:p.Arg1532Cys	108	0	0		78	58	0.74359	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Missense_Mutation	SNP	ENST00000373658.3	37	CCDS346.2	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	G	14.71	2.616398	0.46736	0.001589	0.008953	ENSG00000121753	ENST00000398556;ENST00000398547;ENST00000373658;ENST00000373655;ENST00000398542;ENST00000257070;ENST00000527361;ENST00000440175;ENST00000398538	T;T;T;T;T;T;T;T;T	0.48201	3.33;1.62;3.33;3.33;1.8;3.33;3.33;1.46;0.82	4.29	3.3	0.37823	.	0.412552	0.18103	N	0.151610	T	0.47911	0.1471	L	0.52011	1.625	0.39636	D	0.970247	P;D;D;P;D;D	0.76494	0.95;0.999;0.981;0.95;0.999;0.988	B;P;P;B;P;B	0.59825	0.409;0.864;0.608;0.409;0.735;0.295	T	0.58267	-0.7666	10	0.87932	D	0	.	11.0708	0.48002	0.0:0.0:0.8153:0.1847	rs41263977	1498;1520;1122;1531;1532;1501	O60241-4;O60241-3;B4DKC3;O60241-2;O60241;A2A3C2	.;.;.;.;BAI2_HUMAN;.	C	1447;1446;1532;1531;1413;1498;1498;1122;1501	ENSP00000381564:R1447C;ENSP00000381555:R1446C;ENSP00000362762:R1532C;ENSP00000362759:R1531C;ENSP00000381550:R1413C;ENSP00000257070:R1498C;ENSP00000435397:R1498C;ENSP00000391071:R1122C;ENSP00000381548:R1501C	ENSP00000257070:R1498C	R	-	1	0	BAI2	31965772	0.999000	0.42202	0.997000	0.53966	0.941000	0.58515	4.208000	0.58486	2.401000	0.81631	0.561000	0.74099	CGC	G|0.994;A|0.006	0.006	strong		0.612	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703		A	32193185	G	A	32193185	3	1	30	1	0	0	0	0	1	0	0	0	1299	1087	38	1	167	1	BAI2	1	32193185	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	3888286	32193185	217057436	12	13163											
BAI2	576	hgsc.bcm.edu	37	chr1	32196453	32196453	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacggtgcgaggcatggtcCggctgcgctcccctggctcg	3	7	16	15	5	0	0	0	0	0	0	3	1	2	0	3	5	2	5	3	5	0	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:32196453C>T	ENST00000373658.3	-	29	4669	c.4328G>A	c.(4327-4329)cGg>cAg	p.R1443Q	BAI2_ENST00000398556.3_Missense_Mutation_p.R1358Q|BAI2_ENST00000398547.1_Missense_Mutation_p.R1376Q|BAI2_ENST00000398538.1_Missense_Mutation_p.R1431Q|BAI2_ENST00000398542.1_Missense_Mutation_p.R1343Q|BAI2_ENST00000257070.4_Missense_Mutation_p.R1410Q|BAI2_ENST00000465256.1_5'UTR|BAI2_ENST00000440175.2_Missense_Mutation_p.R1052Q|BAI2_ENST00000373655.2_Missense_Mutation_p.R1443Q|BAI2_ENST00000527361.1_Missense_Mutation_p.R1410Q	NM_001703.2	NP_001694.2	O60241	BAI2_HUMAN	brain-specific angiogenesis inhibitor 2	1443					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.R1443Q(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)		AGGCATGGTCCGGCTGCGCTC	0.632																																					p.R1443Q		Atlas-SNP	.											BAI2,colon,carcinoma,0,1	BAI2	128	1	1	Substitution - Missense(1)	large_intestine(1)	c.G4328A						PASS	.						40	51	47					1																	32196453		2202	4299	6501	SO:0001583	missense	576	exon29			ATGGTCCGGCTGC	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.4328G>A	1.37:g.32196453C>T	ENSP00000362762:p.Arg1443Gln	85	0	0		39	4	0.102564	NM_001703	B9EGK9|Q5T6K0|Q8NGW8|Q96GZ9	Missense_Mutation	SNP	ENST00000373658.3	37	CCDS346.2	.	.	.	.	.	.	.	.	.	.	C	26.3	4.729029	0.89390	.	.	ENSG00000121753	ENST00000398556;ENST00000398547;ENST00000373658;ENST00000373655;ENST00000398542;ENST00000257070;ENST00000527361;ENST00000440175;ENST00000398538	T;T;T;T;T;T;T;T;T	0.47528	1.52;1.76;0.92;0.92;1.89;0.84;0.84;1.55;0.95	5.74	5.74	0.90152	.	0.000000	0.39274	N	0.001419	T	0.61763	0.2373	L	0.48642	1.525	0.51767	D	0.999934	D;D;D;D;D;D;D	0.89917	0.996;0.996;0.999;1.0;0.996;0.994;1.0	P;P;P;D;P;P;D	0.63957	0.883;0.77;0.743;0.92;0.883;0.594;0.92	T	0.52902	-0.8513	10	0.31617	T	0.26	.	19.9066	0.97010	0.0:1.0:0.0:0.0	.	1410;1431;1052;1358;1443;1443;1431	O60241-4;O60241-3;B4DKC3;A2A3C6;O60241-2;O60241;A2A3C2	.;.;.;.;.;BAI2_HUMAN;.	Q	1358;1376;1443;1443;1343;1410;1410;1052;1431	ENSP00000381564:R1358Q;ENSP00000381555:R1376Q;ENSP00000362762:R1443Q;ENSP00000362759:R1443Q;ENSP00000381550:R1343Q;ENSP00000257070:R1410Q;ENSP00000435397:R1410Q;ENSP00000391071:R1052Q;ENSP00000381548:R1431Q	ENSP00000257070:R1410Q	R	-	2	0	BAI2	31969040	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.447000	0.60020	2.884000	0.98904	0.655000	0.94253	CGG	.	.	none		0.632	BAI2-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000381838.1	NM_001703		T	32196453	C	T	32196453	3	4	30	1	0	0	0	0	1	0	0	0	1299	652	23	1	449	1	BAI2	1	32196453	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	3268	32196453	217054168	13	13164											
S100PBP	64766	hgsc.bcm.edu	37	chr1	33292189	33292189	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgctctgcttgataaggaCgagactgattcgtccaaaga	12	10	11	8	2	1	4	0	2	1	2	3	7	2	5	1	1	2	2	1	1	2	3	rs41265867	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:33292189C>T	ENST00000373475.5	+	3	743	c.489C>T	c.(487-489)gaC>gaT	p.D163D	S100PBP_ENST00000398243.3_Silent_p.D163D|S100PBP_ENST00000373476.1_Silent_p.D163D|S100PBP_ENST00000356689.3_3'UTR	NM_022753.3	NP_073590.2			S100P binding protein											endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|stomach(1)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)				TTGATAAGGACGAGACTGATT	0.378													c|||	29	0.00579073	0.0008	0.0058	5008	,	,		22086	0.0		0.0159	False		,,,				2504	0.0082				p.D163D		Atlas-SNP	.											.	S100PBP	31	.	0			c.C489T						PASS	.	T	,	9,4397	15.5+/-35.6	0,9,2194	69	71	70		489,489	-8.8	0.3	1	dbSNP_127	70	67,8533	40.8+/-97.7	1,65,4234	no	coding-synonymous,coding-synonymous	S100PBP	NM_001017406.1,NM_022753.2	,	1,74,6428	TT,TC,CC		0.7791,0.2043,0.5843	,	163/342,163/409	33292189	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	64766	exon3			TAAGGACGAGACT	BX647916	CCDS30666.1	1p35.1	2008-02-05			ENSG00000116497	ENSG00000116497			25768	protein-coding gene	gene with protein product	"S100P binding protein 1"	611889				12477932	Standard	NM_022753		Approved	FLJ12903, S100PBPR	uc001bwc.4	Q96BU1	OTTHUMG00000003955	ENST00000373475.5:c.489C>T	1.37:g.33292189C>T		36	0	0		26	20	0.769231	NM_001256121		Silent	SNP	ENST00000373475.5	37	CCDS30666.1																																																																																			C|0.992;T|0.008	0.008	strong		0.378	S100PBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011266.1	NM_022753		T	33292189	C	T	33292189	2	4	30	1	0	0	0	0	0	0	0	1	13806	535	19	1		1	S100PBP	1	33292189	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1095736	33292189	215958432	14	13165											
KIAA0319L	79932	hgsc.bcm.edu	37	chr1	35972375	35972375	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatacagcaggtctgagtgcAgctctgggtgggctctgcct	6	10	15	10	0	3	1	0	1	3	0	3	2	3	1	1	3	5	4	1	3	1	1			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:35972375A>T	ENST00000325722.3	-	3	738	c.504T>A	c.(502-504)gcT>gcA	p.A168A		NM_024874.4	NP_079150.3	Q8IZA0	K319L_HUMAN	KIAA0319-like	168						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)				GTCTGAGTGCAGCTCTGGGTG	0.502																																					p.A168A		Atlas-SNP	.											.	KIAA0319L	156	.	0			c.T504A						PASS	.						121	117	118					1																	35972375		2203	4300	6503	SO:0001819	synonymous_variant	79932	exon3			GAGTGCAGCTCTG	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.504T>A	1.37:g.35972375A>T		161	0	0		103	29	0.281553	NM_024874	B1AN13|D3DPR8|O95010|Q6PJJ7|Q7L1C9|Q8N2B3|Q8NDA0|Q8WY39|Q8WYZ5|Q96IC3|Q96JJ0|Q9BUW6|Q9H7V0	Silent	SNP	ENST00000325722.3	37	CCDS390.1	.	.	.	.	.	.	.	.	.	.	A	0.044	-1.271484	0.01421	.	.	ENSG00000142687	ENST00000431916	.	.	.	5.78	-1.12	0.09808	.	.	.	.	.	T	0.22166	0.0534	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.28459	-1.0043	4	.	.	.	-0.4253	4.2445	0.10665	0.5279:0.2944:0.0697:0.108	.	.	.	.	S	32	.	.	C	-	1	0	KIAA0319L	35744962	0.905000	0.30787	0.001000	0.08648	0.083000	0.17756	0.332000	0.19751	0.104000	0.17725	0.533000	0.62120	TGC	.	.	none		0.502	KIAA0319L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012684.2	NM_024874		T	35972375	A	T	35972375	2	4	30	1	0	0	0	0	0	0	0	1	8178	175	7	5		5	KIAA0319L	1	35972375	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	2680186	35972375	213278246	15	13166											
CSF3R	1441	hgsc.bcm.edu	37	chr1	36937106	36937106	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ataggccacaagggccacctCctgggcttctgaaggcaggt	9	7	13	12	0	1	1	0	1	1	0	2	1	2	1	4	5	0	2	4	5	3	2	rs3918019	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:36937106C>T	ENST00000373106.1	-	10	1760	c.1213G>A	c.(1213-1215)Gag>Aag	p.E405K	CSF3R_ENST00000373103.1_Missense_Mutation_p.E405K|CSF3R_ENST00000331941.5_Missense_Mutation_p.E405K|CSF3R_ENST00000418048.2_Missense_Mutation_p.E405K|CSF3R_ENST00000338937.5_Missense_Mutation_p.E405K|CSF3R_ENST00000373104.1_Missense_Mutation_p.E405K|CSF3R_ENST00000487540.2_5'UTR|CSF3R_ENST00000361632.4_Missense_Mutation_p.E405K|CSF3R_ENST00000440588.2_Missense_Mutation_p.E405K	NM_000760.3	NP_000751.1	Q99062	CSF3R_HUMAN	colony stimulating factor 3 receptor (granulocyte)	405	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.		E -> K (in dbSNP:rs3918019). {ECO:0000269|Ref.4}.		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)	AGGGCCACCTCCTGGGCTTCT	0.612													C|||	8	0.00159744	0.0	0.0014	5008	,	,		17751	0.0		0.007	False		,,,				2504	0.0				p.E405K		Atlas-SNP	.											.	CSF3R	157	.	0			c.G1213A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU	3,4403	6.2+/-15.9	0,3,2200	103	111	108		1213,1213,1213	3.3	0.9	1	dbSNP_108	108	37,8563	25.7+/-73.6	1,35,4264	yes	missense,missense,missense	CSF3R	NM_000760.3,NM_156039.3,NM_172313.2	56,56,56	1,38,6464	TT,TC,CC		0.4302,0.0681,0.3076	possibly-damaging,possibly-damaging,possibly-damaging	405/837,405/864,405/784	36937106	40,12966	2203	4300	6503	SO:0001583	missense	1441	exon10			CCACCTCCTGGGC	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.1213G>A	1.37:g.36937106C>T	ENSP00000362198:p.Glu405Lys	105	0	0		73	50	0.684932	NM_156039		Missense_Mutation	SNP	ENST00000373106.1	37	CCDS413.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	15.35	2.808248	0.50421	6.81E-4	0.004302	ENSG00000119535	ENST00000373106;ENST00000373104;ENST00000373103;ENST00000361632;ENST00000331941;ENST00000418048;ENST00000338937;ENST00000440588	T;T;T;T;T;T;T;T	0.18338	2.22;2.22;2.22;2.22;2.22;2.22;2.22;2.22	5.2	3.3	0.37823	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.580572	0.20168	N	0.097787	T	0.05686	0.0149	L	0.33485	1.01	0.25352	N	0.988858	P;P;P;B	0.48764	0.915;0.902;0.651;0.028	B;B;B;B	0.36092	0.217;0.194;0.057;0.038	T	0.14952	-1.0454	10	0.06236	T	0.91	-11.2121	7.3658	0.26772	0.0:0.7939:0.0:0.2061	rs3918019;rs3918019	405;405;405;405	E1B6W6;Q99062-3;Q99062;Q99062-4	.;.;CSF3R_HUMAN;.	K	405	ENSP00000362198:E405K;ENSP00000362196:E405K;ENSP00000362195:E405K;ENSP00000355406:E405K;ENSP00000332180:E405K;ENSP00000401588:E405K;ENSP00000345013:E405K;ENSP00000397568:E405K	ENSP00000332180:E405K	E	-	1	0	CSF3R	36709693	0.102000	0.21896	0.923000	0.36655	0.788000	0.44548	1.384000	0.34396	0.561000	0.29186	-0.258000	0.10820	GAG	C|0.996;T|0.004	0.004	strong		0.612	CSF3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021997.2	NM_156039		T	36937106	C	T	36937106	3	4	30	1	0	0	0	0	1	0	0	0	3939	864	30	2	1519	2	CSF3R	1	36937106	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	964731	36937106	212313515	16	13167											
KIAA0754	643314	hgsc.bcm.edu	37	chr1	39879340	39879340	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggagcccgcctccccagctGctgcagtgcccaccccagag	7	4	11	19	1	0	1	0	0	0	1	1	2	1	2	7	1	5	3	7	1	0	0	rs141110458	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:39879340G>C	ENST00000530275.1	+	1	3190	c.2995G>C	c.(2995-2997)Gct>Cct	p.A999P	MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000289893.4_Intron|MACF1_ENST00000372915.3_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	999	Ala-rich.									central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	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)			CTCCCCAGCTGCTGCAGTGCC	0.711													G|||	13	0.00259585	0.0	0.0029	5008	,	,		10576	0.001		0.006	False		,,,				2504	0.0041				p.A1135P		Atlas-SNP	.											.	KIAA0754	93	.	0			c.G3403C						PASS	.	G	,PRO/ALA,	5,3513		0,5,1754	6	9	8		,3403,	0.2	0	1	dbSNP_134	8	77,7935		0,77,3929	no	intron,missense,intron	MACF1,KIAA0754	NM_012090.4,NM_015038.1,NM_033044.3	,27,	0,82,5683	CC,CG,GG		0.9611,0.1421,0.7112	,probably-damaging,	,1135/1428,	39879340	82,11448	1759	4006	5765	SO:0001583	missense	643314	exon1			CCAGCTGCTGCAG			1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.2995G>C	1.37:g.39879340G>C	ENSP00000431179:p.Ala999Pro	140	0	0		61	37	0.606557	NM_015038	E9PMC2|Q6ZSB2	Missense_Mutation	SNP	ENST00000530275.1	37		22	0.010073260073260074	7	0.014227642276422764	5	0.013812154696132596	7	0.012237762237762238	3	0.00395778364116095	G	13.78	2.338002	0.41398	0.001421	0.009611	ENSG00000255103	ENST00000530275	T	0.24151	1.87	4.56	0.241	0.15494	.	.	.	.	.	T	0.13243	0.0321	N	0.14661	0.345	0.09310	N	1	D	0.56968	0.978	P	0.54706	0.759	T	0.10337	-1.0634	9	0.25751	T	0.34	.	2.6328	0.04949	0.0953:0.1583:0.4215:0.3249	.	999	O94854	K0754_HUMAN	P	999	ENSP00000431179:A999P	ENSP00000431179:A999P	A	+	1	0	RP4-562N20.1	39651927	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-0.456000	0.06754	0.200000	0.20447	0.498000	0.49722	GCT	G|0.990;C|0.010	0.010	strong		0.711	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038		C	39879340	G	C	39879340	3	2	30	1	0	0	0	0	1	0	0	0	8201	1319	46	4	3405	4	KIAA0754	1	39879340	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2942234	39879340	209371281	17	13168											
KIAA0754	643314	hgsc.bcm.edu	37	chr1	39879397	39879435	+	In_Frame_Del	DEL	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	-																															ctcctgcagtgcccaccccaGaggaatccgcctccgcagct																								rs371382486|rs55976345|rs541496808|rs199726261|rs548996855|rs112569629|rs201613510	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:39879397_39879435delGAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	ENST00000530275.1	+	1	3247_3285	c.3052_3090delGAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	c.(3052-3090)gaggaatccgcctccgcagctgttgcagtgcccacccccdel	p.EESASAAVAVPTP1018del	MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000289893.4_Intron|MACF1_ENST00000372915.3_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	1018	Ala-rich.									central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	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)			GCCCACCCCAGAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCCGAGGAATCTG	0.682																																					p.1153_1166del		Pindel	.											.	KIAA0754	93	.	0			c.3459_3497del						PASS	.		,,	832,2850		248,336,1257					,,	0	0			18	1888,6000		448,992,2504	no	intron,coding,intron	MACF1,KIAA0754	NM_033044.3,NM_015038.1,NM_012090.4	,,	696,1328,3761	A1A1,A1R,RR		23.9351,22.5964,23.5091	,,	,,		2720,8850				SO:0001651	inframe_deletion	643314	exon1			.			1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.3052_3090delGAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	1.37:g.39879397_39879435delGAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	ENSP00000431179:p.Glu1018_Pro1030del	197	0	.		65	19	0.292	NM_015038	E9PMC2|Q6ZSB2	In_Frame_Del	DEL	ENST00000530275.1	37																																																																																				.	.	none		0.682	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038		-	39879435	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	-	39879397	7	5	30	1	0	1	0	1	0	0	0	0	8201	943	33	0	3462	0	KIAA0754	1	39879397	In_Frame_Del	DEL	GAGGAATCCGCCTCCGCAGCTGTTGCAGTGCCCACCCCC	TCGA-GR-7353-01A-11D-2210-10	57	39879397	209371224	18	13169	167	3									
KIAA0754	643314	hgsc.bcm.edu	37	chr1	39879405	39879405	+	Silent	SNP	C	C	T																															gtgcccaccccagaggaatcCgcctccgcagctgttgcagt																								rs548996855|rs199726261		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:39879405C>T	ENST00000530275.1	+	1	3255	c.3060C>T	c.(3058-3060)tcC>tcT	p.S1020S	MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000289893.4_Intron|MACF1_ENST00000372915.3_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	1020	Ala-rich.									central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	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)			CAGAGGAATCCGCCTCCGCAG	0.682																																					p.S1156S		Atlas-SNP	.											.	KIAA0754	93	.	0			c.C3468T						PASS	.						18	21	20					1																	39879405		1939	4131	6070	SO:0001819	synonymous_variant	643314	exon1			GGAATCCGCCTCC			1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.3060C>T	1.37:g.39879405C>T		206	0	0		55	20	0.363636	NM_015038	E9PMC2|Q6ZSB2	Silent	SNP	ENST00000530275.1	37																																																																																				.	.	none		0.682	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038		T	39879405	C	T	39879405	2	4	30	1	0	0	0	0	0	0	0	1	8201	639	23	1		1	KIAA0754	1	39879405	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	8	39879405	209371216	19	13170	167	3									
KIAA0754	643314	hgsc.bcm.edu	37	chr1	39879410	39879410	+	Missense_Mutation	SNP	C	C	T																															caccccagaggaatccgcctCcgcagctgttgcagtgccca																										TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:39879410C>T	ENST00000530275.1	+	1	3260	c.3065C>T	c.(3064-3066)tCc>tTc	p.S1022F	MACF1_ENST00000564288.1_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000289893.4_Intron|MACF1_ENST00000372915.3_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	1022	Ala-rich.									central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	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)			GAATCCGCCTCCGCAGCTGTT	0.687																																					p.S1158F		Atlas-SNP	.											KIAA0754_ENST00000530275,NS,carcinoma,-1,2	KIAA0754	93	2	0			c.C3473T						scavenged	.						18	22	21					1																	39879410		1946	4130	6076	SO:0001583	missense	643314	exon1			CCGCCTCCGCAGC			1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.3065C>T	1.37:g.39879410C>T	ENSP00000431179:p.Ser1022Phe	206	0	0		58	9	0.155172	NM_015038	E9PMC2|Q6ZSB2	Missense_Mutation	SNP	ENST00000530275.1	37		.	.	.	.	.	.	.	.	.	.	N	12.12	1.842527	0.32606	.	.	ENSG00000255103	ENST00000530275	T	0.24350	1.86	4.0	2.07	0.26955	.	.	.	.	.	T	0.15522	0.0374	N	0.08118	0	0.09310	N	1	P	0.42203	0.773	P	0.44422	0.449	T	0.11299	-1.0593	9	0.72032	D	0.01	.	6.6382	0.22895	0.1876:0.5829:0.2295:0.0	.	1022	O94854	K0754_HUMAN	F	1022	ENSP00000431179:S1022F	ENSP00000431179:S1022F	S	+	2	0	RP4-562N20.1	39651997	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.547000	0.02186	0.468000	0.27243	0.391000	0.25812	TCC	.	.	none		0.687	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038		T	39879410	C	T	39879410	3	4	30	1	0	0	0	0	1	0	0	0	8201	855	30	2	3475	2	KIAA0754	1	39879410	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	5	39879410	209371211	20	13171	167	3									
HIVEP3	59269	hgsc.bcm.edu	37	chr1	41978959	41978959	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtttgcgggctagtggtggaCggctgcctgcttctttgctt	2	15	15	9	2	1	0	0	0	1	0	1	1	1	1	1	4	4	5	1	4	1	5	rs144265546		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:41978959C>T	ENST00000372583.1	-	8	6818	c.5933G>A	c.(5932-5934)cGt>cAt	p.R1978H	HIVEP3_ENST00000429157.2_Missense_Mutation_p.R1978H|HIVEP3_ENST00000372584.1_Missense_Mutation_p.R1978H|HIVEP3_ENST00000247584.5_Missense_Mutation_p.R1978H|HIVEP3_ENST00000460604.1_5'UTR	NM_024503.4	NP_078779.2	Q5T1R4	ZEP3_HUMAN	human immunodeficiency virus type I enhancer binding protein 3	1978					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)				TAGTGGTGGACGGCTGCCTGC	0.612													C|||	1	0.000199681	0.0	0.0	5008	,	,		16700	0.001		0.0	False		,,,				2504	0.0				p.R1978H		Atlas-SNP	.											HIVEP3,NS,carcinoma,-1,1	HIVEP3	235	1	0			c.G5933A						PASS	.	C	HIS/ARG,HIS/ARG	0,4394		0,0,2197	59	66	64		5933,5933	0.9	0.1	1	dbSNP_134	64	1,8581		0,1,4290	no	missense,missense	HIVEP3	NM_001127714.2,NM_024503.4	29,29	0,1,6487	TT,TC,CC		0.0117,0.0,0.0077	benign,benign	1978/2406,1978/2407	41978959	1,12975	2197	4291	6488	SO:0001583	missense	59269	exon8			GGTGGACGGCTGC	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.5933G>A	1.37:g.41978959C>T	ENSP00000361664:p.Arg1978His	398	1	0.00251256		266	194	0.729323	NM_024503	A7YY91|Q5T1R5|Q9BZS0|Q9HCL7	Missense_Mutation	SNP	ENST00000372583.1	37	CCDS463.1	.	.	.	.	.	.	.	.	.	.	C	3.314	-0.140096	0.06669	0.0	1.17E-4	ENSG00000127124	ENST00000372584;ENST00000372583;ENST00000247584;ENST00000429157	T;T;T;T	0.06849	3.27;3.25;3.25;3.27	4.9	0.906	0.19314	.	0.511179	0.16205	N	0.224759	T	0.04452	0.0122	N	0.17082	0.46	0.09310	N	1	B;B	0.15930	0.015;0.009	B;B	0.12156	0.007;0.003	T	0.43475	-0.9389	10	0.23891	T	0.37	-0.7167	5.8783	0.18842	0.0:0.5722:0.1291:0.2987	.	1978;1978	Q5T1R4-2;Q5T1R4	.;ZEP3_HUMAN	H	1978	ENSP00000361665:R1978H;ENSP00000361664:R1978H;ENSP00000247584:R1978H;ENSP00000410828:R1978H	ENSP00000247584:R1978H	R	-	2	0	HIVEP3	41751546	0.136000	0.22515	0.136000	0.22124	0.344000	0.29017	0.195000	0.17155	-0.021000	0.14009	-0.150000	0.13652	CGT	C|1.000;T|0.000	0.000	weak		0.612	HIVEP3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000016978.1	NM_024503		T	41978959	C	T	41978959	3	4	30	1	0	0	0	0	1	0	0	0	7197	536	19	1	1295	1	HIVEP3	1	41978959	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	2099549	41978959	207271662	21	13172											
CLDN19	149461	hgsc.bcm.edu	37	chr1	43201614	43201614	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgttgggtctctctggctcCgggcatgtgcagcagaggaa	6	10	15	10	1	2	1	0	0	2	1	4	2	3	2	1	4	2	5	1	4	1	1	rs9660973	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:43201614C>T	ENST00000296387.1	-	4	751	c.561G>A	c.(559-561)ccG>ccA	p.P187P	CLDN19_ENST00000372539.3_Silent_p.P187P|CLDN19_ENST00000539749.1_Missense_Mutation_p.R159Q	NM_001123395.1|NM_148960.2	NP_001116867.1|NP_683763.2	Q8N6F1	CLD19_HUMAN	claudin 19	187					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)				TCTCTGGCTCCGGGCATGTGC	0.677													c|||	260	0.0519169	0.1006	0.0389	5008	,	,		16585	0.001		0.0398	False		,,,				2504	0.0603				p.R159Q		Atlas-SNP	.											.	CLDN19	21	.	0			c.G476A						PASS	.		,GLN/ARG,	396,3984		9,378,1803	30	28	29		561,476,561	-8.6	0	1	dbSNP_119	29	351,8217		5,341,3938	yes	coding-synonymous,missense,coding-synonymous	CLDN19	NM_001123395.1,NM_001185117.1,NM_148960.2	,43,	14,719,5741	TT,TC,CC		4.0966,9.0411,5.7692	,,	187/212,159/219,187/225	43201614	747,12201	2190	4284	6474	SO:0001819	synonymous_variant	149461	exon3			TGGCTCCGGGCAT	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.561G>A	1.37:g.43201614C>T		216	0	0		134	45	0.335821	NM_001185117	B7Z5I2|F5H5P9|Q5QT57|Q8N8X0	Missense_Mutation	SNP	ENST00000296387.1	37	CCDS471.1	98	0.04487179487179487	48	0.0975609756097561	19	0.052486187845303865	0	0.0	31	0.040897097625329816	c	11.52	1.664047	0.29604	0.090411	0.040966	ENSG00000164007	ENST00000539749	D	0.86627	-2.15	4.31	-8.62	0.00881	.	.	.	.	.	T	0.07458	0.0188	.	.	.	0.23260	N	0.998023	B	0.10296	0.003	B	0.04013	0.001	T	0.48714	-0.9011	8	0.72032	D	0.01	.	2.721	0.05201	0.2173:0.0855:0.367:0.3302	rs9660973;rs9660973	159	F5H5P9	.	Q	159	ENSP00000443229:R159Q	ENSP00000443229:R159Q	R	-	2	0	CLDN19	42974201	0.000000	0.05858	0.016000	0.15963	0.624000	0.37722	-2.658000	0.00852	-3.151000	0.00230	-0.516000	0.04426	CGG	C|0.945;T|0.055	0.055	strong		0.677	CLDN19-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019788.1	NM_148960		T	43201614	C	T	43201614	2	4	30	1	0	0	0	0	0	0	0	1	3482	652	23	1		1	CLDN19	1	43201614	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1222655	43201614	206049007	22	13173											
LEPRE1	64175	hgsc.bcm.edu	37	chr1	43212926	43212926	+	Intron	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agcaccagctgctctcacccGctcgagctgctctcacccgc	6	7	8	20	3	2	0	2	0	2	0	5	1	2	0	3	0	5	6	3	0	0	0	rs67014447	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:43212926G>A	ENST00000296388.5	-	14	2107				LEPRE1_ENST00000397054.3_Missense_Mutation_p.A691V|LEPRE1_ENST00000236040.4_Missense_Mutation_p.A691V|LEPRE1_ENST00000462474.1_5'UTR			Q32P28	P3H1_HUMAN	leucine proline-enriched proteoglycan (leprecan) 1						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)	GCTCTCACCCGCTCGAGCTGC	0.627											OREG0013422	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	-|||	310	0.061901	0.1384	0.0389	5008	,	,		19053	0.001		0.0398	False		,,,				2504	0.0603				p.A691V		Atlas-SNP	.											.	LEPRE1	130	.	0			c.C2072T						PASS	.	-	VAL/ALA,	584,3822		33,518,1652	61	61	61		2072,		0	1	dbSNP_130	61	378,8222		7,364,3929	yes	missense,intron	LEPRE1	NM_001146289.1,NM_022356.3	64,	40,882,5581	AA,AG,GG		4.3953,13.2547,7.3966	,	691/698,	43212926	962,12044	2203	4300	6503	SO:0001627	intron_variant	64175	exon14			TCACCCGCTCGAG	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.2055+16C>T	1.37:g.43212926G>A		65	0	0	914	45	11	0.244444	NM_001146289	Q7KZR4|Q96BR8|Q96SK8|Q96SL5|Q96SN3|Q9H6K3|Q9HC86|Q9HC87	Missense_Mutation	SNP	ENST00000296388.5	37	CCDS472.2	112	0.05128205128205128	61	0.12398373983739837	19	0.052486187845303865	0	0.0	32	0.04221635883905013	-	0.009	-1.803442	0.00611	0.132547	0.043953	ENSG00000117385	ENST00000397054;ENST00000236040	T;T	0.37411	1.2;1.28	.	.	.	.	.	.	.	.	T	0.00241	0.0007	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.19224	-1.0312	4	0.21540	T	0.41	.	.	.	.	.	691	Q32P28-3	.	V	691	ENSP00000380245:A691V;ENSP00000236040:A691V	ENSP00000236040:A691V	A	-	2	0	LEPRE1	42985513	0.009000	0.17119	0.014000	0.15608	0.025000	0.11179	-0.234000	0.09028	0.000000	0.14550	0.000000	0.15137	GCG	G|0.936;A|0.064	0.064	strong		0.627	LEPRE1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019790.2	NM_022356		A	43212926	G	A	43212926	1	1	30	0	1	0	0	0	0	0	0	0	8738	1087	38	1		1	LEPRE1	1	43212926	Intron	SNP	G	TCGA-GR-7353-01A-11D-2210-10	11312	43212926	206037695	23	13174											
EBNA1BP2	10969	hgsc.bcm.edu	37	chr1	43630156	43630156	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctctcttgttcgttttccAggtctcttctacagaaaaag	8	17	6	10	1	4	1	0	0	4	1	8	1	5	1	1	1	1	2	1	1	3	7	rs11559311	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:43630156A>C	ENST00000236051.2	-	9	1020	c.879T>G	c.(877-879)ccT>ccG	p.P293P	EBNA1BP2_ENST00000431635.2_Silent_p.P348P	NM_006824.2	NP_006815.2	Q99848	EBP2_HUMAN	EBNA1 binding protein 2	293					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)				TTCGTTTTCCAGGTCTCTTCT	0.443													A|||	410	0.081869	0.2405	0.0605	5008	,	,		19601	0.001		0.0368	False		,,,				2504	0.0123				p.P348P		Atlas-SNP	.											.	EBNA1BP2	37	.	0			c.T1044G						PASS	.	A	,	913,3493	351.1+/-311.1	102,709,1392	176	155	162		1044,879	-0.3	1	1	dbSNP_120	162	356,8244	119.7+/-179.0	6,344,3950	no	coding-synonymous,coding-synonymous	EBNA1BP2	NM_001159936.1,NM_006824.2	,	108,1053,5342	CC,CA,AA		4.1395,20.7217,9.757	,	348/362,293/307	43630156	1269,11737	2203	4300	6503	SO:0001819	synonymous_variant	10969	exon10			TTTTCCAGGTCTC	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.879T>G	1.37:g.43630156A>C		148	0	0		119	87	0.731092	NM_001159936	Q96A66	Silent	SNP	ENST00000236051.2	37	CCDS478.1																																																																																			A|0.912;C|0.088	0.088	strong		0.443	EBNA1BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019015.1			C	43630156	A	C	43630156	2	2	30	1	0	0	0	0	0	0	0	1	4887	175	7	5		5	EBNA1BP2	1	43630156	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	417230	43630156	205620465	24	13175											
WDR65	149465	hgsc.bcm.edu	37	chr1	43638436	43638436	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgggagatcatgtcagccgtGgtagctcagacgctgcatgt	8	9	14	10	3	3	2	3	0	0	2	3	3	3	2	1	2	3	4	1	2	1	1	rs6695238	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:43638436G>T	ENST00000372492.4	+	2	336	c.12G>T	c.(10-12)gtG>gtT	p.V4V	EBNA1BP2_ENST00000431635.2_5'Flank|EBNA1BP2_ENST00000236051.2_5'Flank|WDR65_ENST00000528956.1_Silent_p.V4V|EBNA1BP2_ENST00000472982.1_5'Flank	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		4										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)				TGTCAGCCGTGGTAGCTCAGA	0.547													G|||	341	0.0680911	0.1899	0.0576	5008	,	,		10442	0.001		0.0368	False		,,,				2504	0.0123				p.V4V		Atlas-SNP	.											.	WDR65	76	.	0			c.G12T						PASS	.	G	,,	714,3692	295.6+/-283.7	65,584,1554	116	104	108		12,12,12	2.1	1	1	dbSNP_116	108	354,8246	119.5+/-178.9	6,342,3952	no	coding-synonymous,coding-synonymous,coding-synonymous	WDR65	NM_001167965.1,NM_001167966.1,NM_152498.3	,,	71,926,5506	TT,TG,GG		4.1163,16.2052,8.2116	,,	4/699,4/699,4/699	43638436	1068,11938	2203	4300	6503	SO:0001819	synonymous_variant	149465	exon2			AGCCGTGGTAGCT																												ENST00000372492.4:c.12G>T	1.37:g.43638436G>T		175	0	0		69	53	0.768116	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Silent	SNP	ENST00000372492.4	37																																																																																				G|0.920;T|0.080	0.080	strong		0.547	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1			T	43638436	G	T	43638436	2	4	30	1	0	0	0	0	0	0	0	1	17331	1335	47	4		4	WDR65	1	43638436	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	8280	43638436	205612185	25	13176											
C1orf84	23334	hgsc.bcm.edu	37	chr1	43870071	43870071	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgattccacaggggagatCttgtttgatgaagttttcca	10	14	11	6	0	1	4	0	3	1	1	3	6	3	4	2	2	0	2	2	2	1	5	rs41312024	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:43870071C>A	ENST00000562955.1	+	4	348	c.348C>A	c.(346-348)atC>atA	p.I116I	SZT2_ENST00000310739.4_Silent_p.I116I|SZT2_ENST00000372450.4_Silent_p.I114I	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	116					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						CAGGGGAGATCTTGTTTGATG	0.562													C|||	18	0.00359425	0.0	0.0058	5008	,	,		18752	0.0		0.0139	False		,,,				2504	0.0				p.I116I		Atlas-SNP	.											.	SZT2	383	.	0			c.C348A						PASS	.	C		15,4391	22.3+/-47.3	0,15,2188	95	91	93		348	1.4	1	1	dbSNP_127	93	147,8453	71.0+/-133.6	0,147,4153	no	coding-synonymous	SZT2	NM_015284.3		0,162,6341	AA,AC,CC		1.7093,0.3404,1.2456		116/3376	43870071	162,12844	2203	4300	6503	SO:0001819	synonymous_variant	23334	exon4			GGAGATCTTGTTT	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.348C>A	1.37:g.43870071C>A		147	0	0		83	68	0.819277	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Silent	SNP	ENST00000562955.1	37	CCDS30694.2																																																																																			C|0.990;A|0.010	0.010	strong		0.562	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284		A	43870071	C	A	43870071	2	1	30	1	0	0	0	0	0	0	0	1	2063	903	32	4		4	C1orf84	1	43870071	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	231635	43870071	205380550	26	13177											
PTCH2	8643	hgsc.bcm.edu	37	chr1	45294295	45294295	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcgctgcagacactcgccCatgcgctcctgccaggacag	7	6	12	16	3	0	1	0	0	0	1	2	2	1	2	3	1	4	3	3	1	0	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:45294295C>T	ENST00000372192.3	-	12	1603	c.1473G>A	c.(1471-1473)atG>atA	p.M491I	PTCH2_ENST00000447098.2_Missense_Mutation_p.M491I	NM_003738.4	NP_003729.3	Q9Y6C5	PTC2_HUMAN	patched 2	491	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				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)					GACACTCGCCCATGCGCTCCT	0.632									Basal Cell Nevus syndrome																												p.M491I		Atlas-SNP	.											.	PTCH2	96	.	0			c.G1473A						PASS	.						71	55	60					1																	45294295		2202	4300	6502	SO:0001583	missense	8643	exon12	Familial Cancer Database	Gorlin syndrome, Gorlin-Golz syndrome, Naevoid Basal Cell Carcinoma syndrome, NBCCS	CTCGCCCATGCGC	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.1473G>A	1.37:g.45294295C>T	ENSP00000361266:p.Met491Ile	102	0	0		67	4	0.0597015	NM_001166292	O95341|O95856|Q53Z57|Q5QP87|Q6UX14	Missense_Mutation	SNP	ENST00000372192.3	37	CCDS516.1	.	.	.	.	.	.	.	.	.	.	C	13.56	2.275107	0.40194	.	.	ENSG00000117425	ENST00000447098;ENST00000372192	D;D	0.94184	-3.37;-3.37	4.47	-3.0	0.05480	Sterol-sensing domain (1);	0.196196	0.35320	N	0.003287	T	0.79776	0.4504	N	0.05467	-0.045	0.29800	N	0.832513	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.003	T	0.68228	-0.5464	10	0.18276	T	0.48	-34.0928	7.4614	0.27298	0.1257:0.1735:0.0:0.7008	.	491;491	Q9Y6C5-2;Q9Y6C5	.;PTC2_HUMAN	I	491	ENSP00000389703:M491I;ENSP00000361266:M491I	ENSP00000361266:M491I	M	-	3	0	PTCH2	45066882	0.000000	0.05858	0.640000	0.29408	0.929000	0.56500	-3.137000	0.00588	-0.491000	0.06697	0.462000	0.41574	ATG	.	.	none		0.632	PTCH2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023428.4	NM_003738		T	45294295	C	T	45294295	3	4	30	1	0	0	0	0	1	0	0	0	12743	594	21	2	2202	2	PTCH2	1	45294295	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1424224	45294295	203956326	27	13178											
CPT2	1376	hgsc.bcm.edu	37	chr1	53668099	53668099	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	taaacatacaagctacatttCgggtaggtaggctgggctgt	11	11	12	7	1	0	0	0	0	0	0	1	0	0	0	0	4	4	5	0	4	7	6	rs74315294	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:53668099C>T	ENST00000371486.3	+	3	853	c.338C>T	c.(337-339)tCg>tTg	p.S113L	CPT2_ENST00000468572.1_3'UTR	NM_000098.2	NP_000089.1	P23786	CPT2_HUMAN	carnitine palmitoyltransferase 2	113			S -> L (in CPT2D; muscular form; frequent mutation; dbSNP:rs74315294). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:15622536, ECO:0000269|PubMed:8358442, ECO:0000269|PubMed:9758712}.		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)	AGCTACATTTCGGGTAGGTAG	0.418													C|||	3	0.000599042	0.0008	0.0014	5008	,	,		20386	0.0		0.001	False		,,,				2504	0.0				p.S113L		Atlas-SNP	.											CPT2,right_upper_lobe,carcinoma,0,1	CPT2	34	1	0			c.C338T	GRCh37	CM930171	CPT2	M	rs74315294	PASS	.	C	LEU/SER	2,4404	4.2+/-10.8	0,2,2201	92	89	90	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	338	5.9	1	1	dbSNP_131	90	16,8584	11.9+/-42.8	0,16,4284	yes	missense	CPT2	NM_000098.2	145	0,18,6485	TT,TC,CC		0.186,0.0454,0.1384	probably-damaging	113/659	53668099	18,12988	2203	4300	6503	SO:0001583	missense	1376	exon3			ACATTTCGGGTAG	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.338C>T	1.37:g.53668099C>T	ENSP00000360541:p.Ser113Leu	162	0	0		123	78	0.634146	NM_000098	B2R6S0|Q5SW68|Q9BQ26	Missense_Mutation	SNP	ENST00000371486.3	37	CCDS575.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	33	5.265643	0.95399	4.54E-4	0.00186	ENSG00000157184	ENST00000371486	D	0.90676	-2.71	5.88	5.88	0.94601	.	0.064942	0.64402	D	0.000004	D	0.96889	0.8984	H	0.94306	3.52	0.80722	A	1	D	0.76494	0.999	D	0.73708	0.981	D	0.97157	0.9835	9	0.66056	D	0.02	-1.9784	19.8509	0.96740	0.0:1.0:0.0:0.0	.	113	P23786	CPT2_HUMAN	L	113	ENSP00000360541:S113L	ENSP00000360541:S113L	S	+	2	0	CPT2	53440687	1.000000	0.71417	1.000000	0.80357	0.773000	0.43773	6.952000	0.75989	2.797000	0.96272	0.561000	0.74099	TCG	C|0.999;T|0.001	0.001	strong		0.418	CPT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024757.1	NM_000098		T	53668099	C	T	53668099	3	4	30	1	0	0	0	0	1	0	0	0	3836	893	31	1	348	1	CPT2	1	53668099	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	8373804	53668099	195582522	28	13179											
ALG6	29929	hgsc.bcm.edu	37	chr1	63902524	63902524	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cagtcatcactatggtgcttCtgacgttgatgactgtcaca	9	13	9	10	1	4	3	3	3	1	0	4	3	4	3	0	1	1	2	0	1	1	3	rs41285372	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:63902524C>G	ENST00000371108.4	+	15	1662	c.1357C>G	c.(1357-1359)Ctg>Gtg	p.L453V	ALG6_ENST00000263440.4_Missense_Mutation_p.L455V|ALG6_ENST00000494765.1_3'UTR	NM_013339.3	NP_037471.2	Q9Y672	ALG6_HUMAN	ALG6, alpha-1,3-glucosyltransferase	453					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						TATGGTGCTTCTGACGTTGAT	0.383													C|||	21	0.00419329	0.0008	0.0043	5008	,	,		18422	0.0		0.0159	False		,,,				2504	0.001				p.L453V		Atlas-SNP	.											.	ALG6	33	.	0			c.C1357G						PASS	.	C	VAL/LEU	24,4382	30.8+/-60.4	1,22,2180	227	214	219		1357	3.2	1	1	dbSNP_127	219	152,8448	72.9+/-135.5	1,150,4149	yes	missense	ALG6	NM_013339.3	32	2,172,6329	GG,GC,CC		1.7674,0.5447,1.3532	possibly-damaging	453/508	63902524	176,12830	2203	4300	6503	SO:0001583	missense	29929	exon15			GTGCTTCTGACGT	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.1357C>G	1.37:g.63902524C>G	ENSP00000360149:p.Leu453Val	275	0	0		180	135	0.75	NM_013339	B3KMU2|Q5SXR9|Q9H3I0	Missense_Mutation	SNP	ENST00000371108.4	37	CCDS30735.1	13	0.005952380952380952	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	C	16.45	3.125406	0.56721	0.005447	0.017674	ENSG00000088035	ENST00000371108;ENST00000263440;ENST00000423077	D;D	0.83755	-1.76;-1.76	5.06	3.19	0.36642	.	0.079049	0.53938	D	0.000045	D	0.86100	0.5852	M	0.73962	2.25	0.58432	D	0.999999	D;D	0.89917	1.0;0.977	D;D	0.87578	0.998;0.919	D	0.85509	0.1196	10	0.45353	T	0.12	-16.66	11.1039	0.48190	0.0:0.8472:0.0:0.1528	rs41285372	200;455	B4DHV8;A2A2G4	.;.	V	453;455;200	ENSP00000360149:L453V;ENSP00000263440:L455V	ENSP00000263440:L455V	L	+	1	2	ALG6	63675112	0.985000	0.35326	0.997000	0.53966	0.749000	0.42624	2.010000	0.40913	0.647000	0.30713	0.484000	0.47621	CTG	C|0.987;G|0.013	0.013	strong		0.383	ALG6-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025330.2	NM_013339		G	63902524	C	G	63902524	3	3	30	1	0	0	0	0	1	0	0	0	522	912	32	4	1411	4	ALG6	1	63902524	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	10234425	63902524	185348097	29	13180											
C1orf141	400757	hgsc.bcm.edu	37	chr1	67558870	67558874	+	Frame_Shift_Del	DEL	TCATT	TCATT	-																															aaattttccagtttgggcacTcatttcatgaataacagctt																								rs200104842|rs373816272|rs577736835	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TCATT	TCATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:67558870_67558874delTCATT	ENST00000371007.2	-	8	1126_1130	c.1017_1021delAATGA	c.(1015-1023)gaaatgagtfs	p.MS340fs	C1orf141_ENST00000544837.1_Frame_Shift_Del_p.MS340fs|C1orf141_ENST00000371006.1_Frame_Shift_Del_p.MS340fs	NM_001276351.1	NP_001263280.1	Q5JVX7	CA141_HUMAN	chromosome 1 open reading frame 141	340										NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|skin(1)	18						GTTTGGGCACTCATTTCATGAATAA	0.361														19	0.00379393	0.0023	0.0072	5008	,	,		16889	0.0		0.0109	False		,,,				2504	0.0				p.340_341del		Atlas-Indel	.											.	C1orf141	58	.	0			c.1018_1022del						PASS	.			10,4244		0,10,2117						-2.1	0			110	69,8177		2,65,4056	no	frameshift	C1orf141	NM_001013674.1		2,75,6173	A1A1,A1R,RR		0.8368,0.2351,0.632				79,12421				SO:0001589	frameshift_variant	400757	exon8			.	BC090886	CCDS30745.1, CCDS72804.1	1p31.2	2012-07-23			ENSG00000203963	ENSG00000203963			32044	protein-coding gene	gene with protein product							Standard	NM_001276351		Approved		uc001ddm.2	Q5JVX7	OTTHUMG00000009406	ENST00000371007.2:c.1017_1021delAATGA	1.37:g.67558870_67558874delTCATT	ENSP00000360046:p.Met340fs	267	0	0		125	14	0.112	NM_001276351	Q0P5P5|Q5JVX5	Frame_Shift_Del	DEL	ENST00000371007.2	37	CCDS30745.1																																																																																			TCATT|0.994;-|0.006	0.006	strong		0.361	C1orf141-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026096.2	NM_001013674		-	67558874	TCATT	-	67558870	7	5	30	1	0	1	0	1	0	0	0	0	2003	1551	54	0	185	0	C1orf141	1	67558870	Frame_Shift_Del	DEL	TCATT	TCGA-GR-7353-01A-11D-2210-10	3656346	67558870	181691751	30	13181											
RPE65	6121	hgsc.bcm.edu	37	chr1	68914353	68914353	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacagttcctccacagtttcAaacagtttcttgtaaccacc	11	12	5	13	0	2	0	1	0	1	0	4	1	4	0	4	0	2	4	4	0	2	5	rs62642581		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:68914353A>G	ENST00000262340.5	-	2	101	c.48T>C	c.(46-48)ttT>ttC	p.F16F		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	16					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						CCACAGTTTCAAACAGTTTCT	0.488													A|||	1	0.000199681	0.0	0.0	5008	,	,		14614	0.0		0.001	False		,,,				2504	0.0				p.F16F		Atlas-SNP	.											.	RPE65	87	.	0			c.T48C						PASS	.	A		1,4405	2.1+/-5.4	0,1,2202	116	100	106	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	48	-4.9	0.9	1	dbSNP_129	106	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	RPE65	NM_000329.2		0,6,6497	GG,GA,AA		0.0581,0.0227,0.0461		16/534	68914353	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	6121	exon2			AGTTTCAAACAGT	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.48T>C	1.37:g.68914353A>G		158	0	0		97	25	0.257732	NM_000329	A8K1L0|Q5T9U3	Silent	SNP	ENST00000262340.5	37	CCDS643.1																																																																																			A|1.000;G|0.000	0.000	strong		0.488	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329		G	68914353	A	G	68914353	2	3	30	1	0	0	0	0	0	0	0	1	13560	127	5	3		3	RPE65	1	68914353	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	1355483	68914353	180336268	31	13182											
ST6GALNAC5	81849	hgsc.bcm.edu	37	chr1	77510008	77510008	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atccgcatgaatgacgccccCacacgcggctatgggcgtga	9	6	12	14	5	0	3	0	3	0	0	1	3	1	3	3	2	0	2	3	2	2	1	rs35763299	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:77510008C>A	ENST00000477717.1	+	3	616	c.381C>A	c.(379-381)ccC>ccA	p.P127P		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	127					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						ATGACGCCCCCACACGCGGCT	0.622													C|||	75	0.014976	0.0015	0.0331	5008	,	,		20009	0.0		0.0398	False		,,,				2504	0.0102				p.P127P		Atlas-SNP	.											.	ST6GALNAC5	59	.	0			c.C381A						PASS	.	C		17,4389	22.3+/-47.3	1,15,2187	65	59	61		381	1.6	1	1	dbSNP_126	61	232,8368	94.0+/-155.9	5,222,4073	no	coding-synonymous	ST6GALNAC5	NM_030965.1		6,237,6260	AA,AC,CC		2.6977,0.3858,1.9145		127/337	77510008	249,12757	2203	4300	6503	SO:0001819	synonymous_variant	81849	exon3			CGCCCCCACACGC		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.381C>A	1.37:g.77510008C>A		111	0	0		65	19	0.292308	NM_030965	B1AK82	Silent	SNP	ENST00000477717.1	37	CCDS673.1																																																																																			T|0.009;C|0.980;A|0.010	0.010	strong		0.622	ST6GALNAC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026692.2	NM_030965		A	77510008	C	A	77510008	2	1	30	1	0	0	0	0	0	0	0	1	15242	581	21	4		4	ST6GALNAC5	1	77510008	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	8595655	77510008	171740613	32	13183											
GBP1	2633	hgsc.bcm.edu	37	chr1	89523911	89523911	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaaagtttcatctttttgaCtggtacctagaaaaacattt	14	16	5	6	0	2	2	1	1	1	1	2	2	2	2	1	1	2	2	1	1	6	7	rs75161612	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:89523911C>T	ENST00000370473.4	-	6	857	c.638G>A	c.(637-639)aGt>aAt	p.S213N	GBP1_ENST00000484970.1_5'Flank	NM_002053.2	NP_002044.2	P32455	GBP1_HUMAN	guanylate binding protein 1, interferon-inducible	213	GB1/RHD3-type G.|GTPase domain (Globular).				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)	cytosol (GO:0005829)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			endometrium(7)|kidney(4)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	30		Lung NSC(277;0.123)		all cancers(265;0.0156)|Epithelial(280;0.0291)		ATCTTTTTGACTGGTACCTAG	0.368													.|||	91	0.0181709	0.0053	0.0159	5008	,	,		16962	0.0		0.0298	False		,,,				2504	0.044				p.S213N		Atlas-SNP	.											.	GBP1	68	.	0			c.G638A						PASS	.	C	ASN/SER	30,4374	31.7+/-61.6	0,30,2172	97	109	105		638	-2.4	0	1	dbSNP_131	105	220,8380	88.4+/-150.7	1,218,4081	yes	missense	GBP1	NM_002053.2	46	1,248,6253	TT,TC,CC		2.5581,0.6812,1.9225	benign	213/593	89523911	250,12754	2202	4300	6502	SO:0001583	missense	2633	exon6			TTTTGACTGGTAC	BC002666	CCDS718.1	1p22.2	2011-03-09	2011-03-09		ENSG00000117228	ENSG00000117228			4182	protein-coding gene	gene with protein product		600411	"guanylate binding protein 1, interferon-inducible, 67kDa"			7518790	Standard	NM_002053		Approved		uc001dmx.2	P32455	OTTHUMG00000010614	ENST00000370473.4:c.638G>A	1.37:g.89523911C>T	ENSP00000359504:p.Ser213Asn	55	0	0		27	27	1	NM_002053	D3DT26|Q5T8M1	Missense_Mutation	SNP	ENST00000370473.4	37	CCDS718.1	27	0.012362637362637362	4	0.008130081300813009	6	0.016574585635359115	0	0.0	17	0.022427440633245383	C	0.084	-1.178538	0.01633	0.006812	0.025581	ENSG00000117228	ENST00000370473;ENST00000542693	T	0.73789	-0.78	4.48	-2.37	0.06643	Guanylate-binding protein, N-terminal (1);	1.837820	0.02201	N	0.062280	T	0.24928	0.0605	N	0.11845	0.185	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.15925	-1.0420	10	0.06757	T	0.87	.	5.8264	0.18556	0.0:0.432:0.1405:0.4275	.	213	P32455	GBP1_HUMAN	N	213;176	ENSP00000359504:S213N	ENSP00000359504:S213N	S	-	2	0	GBP1	89296499	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-2.686000	0.00834	-0.598000	0.05806	0.313000	0.20887	AGT	C|0.981;T|0.019	0.019	strong		0.368	GBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029289.3	NM_002053		T	89523911	C	T	89523911	3	4	30	1	0	0	0	0	1	0	0	0	6281	565	20	2	1164	2	GBP1	1	89523911	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	12013903	89523911	159726710	33	13184											
GBP7	388646	hgsc.bcm.edu	37	chr1	89599013	89599013	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccctctccatcttcttcttGagttgagctatgttttcctg	4	19	6	12	0	4	2	0	2	4	0	7	2	6	2	3	0	1	3	3	0	1	7	rs115671591	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:89599013G>T	ENST00000294671.2	-	10	1728	c.1590C>A	c.(1588-1590)ctC>ctA	p.L530L		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	530						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)		TCTTCTTCTTGAGTTGAGCTA	0.438													G|||	103	0.0205671	0.0068	0.0159	5008	,	,		22297	0.0119		0.0278	False		,,,				2504	0.044				p.L530L		Atlas-SNP	.											.	GBP7	57	.	0			c.C1590A						PASS	.	G		38,4366	41.6+/-74.8	0,38,2164	290	265	273		1590	-6.5	0	1	dbSNP_132	273	216,8384	90.9+/-153.0	1,214,4085	no	coding-synonymous	GBP7	NM_207398.2		1,252,6249	TT,TG,GG		2.5116,0.8629,1.9532		530/639	89599013	254,12750	2202	4300	6502	SO:0001819	synonymous_variant	388646	exon10			CTTCTTGAGTTGA	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.1590C>A	1.37:g.89599013G>T		473	0	0		274	272	0.992701	NM_207398		Silent	SNP	ENST00000294671.2	37	CCDS720.1																																																																																			G|0.979;T|0.021	0.021	strong		0.438	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398		T	89599013	G	T	89599013	2	4	30	1	0	0	0	0	0	0	0	1	6287	1277	45	4		4	GBP7	1	89599013	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	75102	89599013	159651608	34	13185											
GBP7	388646	hgsc.bcm.edu	37	chr1	89613280	89613280	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctgggcactagtgtataGtcctgttcaatcttcttttt	6	20	7	8	0	4	0	1	0	3	0	5	0	5	0	1	1	0	3	1	1	4	8	rs115454072	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:89613280G>A	ENST00000294671.2	-	8	1473	c.1335C>T	c.(1333-1335)gaC>gaT	p.D445D		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	445						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)		CTAGTGTATAGTCCTGTTCAA	0.443													G|||	115	0.0229633	0.0166	0.0159	5008	,	,		18197	0.0119		0.0278	False		,,,				2504	0.0429				p.D445D		Atlas-SNP	.											.	GBP7	57	.	0			c.C1335T						PASS	.	G		71,4335	64.1+/-101.4	0,71,2132	171	171	171		1335	-0.8	0	1	dbSNP_132	171	215,8385	90.6+/-152.8	1,213,4086	no	coding-synonymous	GBP7	NM_207398.2		1,284,6218	AA,AG,GG		2.5,1.6114,2.199		445/639	89613280	286,12720	2203	4300	6503	SO:0001819	synonymous_variant	388646	exon8			TGTATAGTCCTGT	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.1335C>T	1.37:g.89613280G>A		300	0	0		159	158	0.993711	NM_207398		Silent	SNP	ENST00000294671.2	37	CCDS720.1																																																																																			G|0.976;A|0.024	0.024	strong		0.443	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398		A	89613280	G	A	89613280	2	1	30	1	0	0	0	0	0	0	0	1	6287	1020	36	2		2	GBP7	1	89613280	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	14267	89613280	159637341	35	13186											
GBP4	115361	hgsc.bcm.edu	37	chr1	89655787	89655787	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tccatgaagactgcaatggcTtccctctcacaggctgcatg	9	10	9	13	0	1	2	1	1	1	1	4	2	3	2	2	2	2	4	2	2	2	1	rs41305862	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:89655787T>C	ENST00000355754.6	-	7	1228	c.1131A>G	c.(1129-1131)gaA>gaG	p.E377E		NM_052941.4	NP_443173.2	Q96PP9	GBP4_HUMAN	guanylate binding protein 4	377						cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(19)|skin(1)|stomach(2)|urinary_tract(1)	33				all cancers(265;0.00723)|Epithelial(280;0.0291)		CTGCAATGGCTTCCCTCTCAC	0.532													T|||	109	0.0217652	0.0113	0.0159	5008	,	,		18719	0.0119		0.0278	False		,,,				2504	0.044				p.E377E		Atlas-SNP	.											.	GBP4	89	.	0			c.A1131G						PASS	.	T		52,4354	52.3+/-87.9	0,52,2151	103	97	99		1131	0.2	1	1	dbSNP_127	99	216,8384	90.9+/-153.0	1,214,4085	no	coding-synonymous	GBP4	NM_052941.4		1,266,6236	CC,CT,TT		2.5116,1.1802,2.0606		377/641	89655787	268,12738	2203	4300	6503	SO:0001819	synonymous_variant	115361	exon7			AATGGCTTCCCTC	AF288814	CCDS721.1	1p22.2	2008-02-05			ENSG00000162654	ENSG00000162654			20480	protein-coding gene	gene with protein product		612466				16689661	Standard	NM_052941		Approved	Mpa2	uc001dnb.3	Q96PP9	OTTHUMG00000010663	ENST00000355754.6:c.1131A>G	1.37:g.89655787T>C		306	0	0		166	158	0.951807	NM_052941	B2R630|Q05D63|Q6NSL0|Q86T99	Silent	SNP	ENST00000355754.6	37	CCDS721.1																																																																																			T|0.977;C|0.023	0.023	strong		0.532	GBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029409.1	NM_052941		C	89655787	T	C	89655787	2	2	30	1	0	0	0	0	0	0	0	1	6284	1606	56	3		3	GBP4	1	89655787	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	42507	89655787	159594834	36	13187											
SLC44A3	126969	hgsc.bcm.edu	37	chr1	95322903	95322903	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aactttaggagctgcccaggTtatggaaggcggccaagtgg	10	8	15	8	1	0	0	0	0	0	0	0	2	0	2	2	6	3	2	2	6	5	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:95322903T>C	ENST00000271227.6	+	10	1187	c.1085T>C	c.(1084-1086)gTt>gCt	p.V362A	SLC44A3_ENST00000530397.1_3'UTR|SLC44A3_ENST00000446120.2_Missense_Mutation_p.V326A|RP11-465K1.2_ENST00000422162.1_RNA|SLC44A3_ENST00000532427.1_Missense_Mutation_p.V282A|SLC44A3_ENST00000529450.1_Missense_Mutation_p.V330A|SLC44A3_ENST00000467909.1_Missense_Mutation_p.V314A|SLC44A3_ENST00000527077.1_Missense_Mutation_p.V294A	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	362					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)	GCTGCCCAGGTTATGGAAGGC	0.443																																					p.V362A		Atlas-SNP	.											.	SLC44A3	109	.	0			c.T1085C						PASS	.						114	102	106					1																	95322903		2203	4300	6503	SO:0001583	missense	126969	exon10			CCCAGGTTATGGA	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.1085T>C	1.37:g.95322903T>C	ENSP00000271227:p.Val362Ala	213	1	0.00469484		112	59	0.526786	NM_001114106	B4DVY4|B4E1M4|B7ZA08|E9PJH2|E9PJY8|Q6UWT1|Q7Z6C5|Q9BWY7	Missense_Mutation	SNP	ENST00000271227.6	37	CCDS44176.1	.	.	.	.	.	.	.	.	.	.	T	4.282	0.051417	0.08291	.	.	ENSG00000143036	ENST00000446120;ENST00000271227;ENST00000527077;ENST00000529450;ENST00000467909;ENST00000532427	T;T;T;T;T;T	0.21191	2.02;2.02;2.02;2.02;2.02;2.02	4.7	3.58	0.41010	.	0.152963	0.30401	N	0.009710	T	0.07593	0.0191	L	0.59436	1.845	0.09310	N	0.999997	P;B;B;P;P	0.34462	0.454;0.05;0.007;0.454;0.454	B;B;B;B;B	0.34931	0.192;0.037;0.011;0.192;0.192	T	0.25293	-1.0136	10	0.20519	T	0.43	-12.261	8.0786	0.30731	0.0:0.1799:0.0:0.8201	.	282;326;294;330;362	E9PIC5;Q8N4M1-3;E9PJY8;E9PJH2;Q8N4M1	.;.;.;.;CTL3_HUMAN	A	326;362;294;330;314;282	ENSP00000389143:V326A;ENSP00000271227:V362A;ENSP00000433641:V294A;ENSP00000431836:V330A;ENSP00000432789:V314A;ENSP00000436661:V282A	ENSP00000271227:V362A	V	+	2	0	SLC44A3	95095491	0.928000	0.31464	0.625000	0.29200	0.926000	0.56050	1.389000	0.34453	0.851000	0.35264	0.533000	0.62120	GTT	.	.	none		0.443	SLC44A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029544.3	NM_152369		C	95322903	T	C	95322903	3	2	30	1	0	0	0	0	1	0	0	0	14652	1725	60	3	1123	3	SLC44A3	1	95322903	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	5667116	95322903	153927718	37	13188											
C1orf59	113802	hgsc.bcm.edu	37	chr1	109200108	109200108	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgatccactaaatttttaaCgaactggtaccgctgtctgt	10	15	7	9	2	1	1	0	1	1	0	2	2	2	1	2	1	3	2	2	1	5	6	rs36100901	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:109200108C>T	ENST00000370032.5	-	3	535	c.115G>A	c.(115-117)Gtt>Att	p.V39I	HENMT1_ENST00000493676.1_5'UTR|HENMT1_ENST00000402983.1_Missense_Mutation_p.V39I|HENMT1_ENST00000370031.1_Missense_Mutation_p.V39I	NM_144584.2	NP_653185.2	Q5T8I9	HENMT_HUMAN	HEN1 methyltransferase homolog 1 (Arabidopsis)	39					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						AAATTTTTAACGAACTGGTAC	0.383													C|||	62	0.0123802	0.0053	0.0202	5008	,	,		17554	0.0		0.0288	False		,,,				2504	0.0123				p.V39I		Atlas-SNP	.											.	HENMT1	38	.	0			c.G115A						PASS	.	C	ILE/VAL,ILE/VAL	22,4384	29.0+/-57.7	0,22,2181	112	113	113		115,115	3.7	0.2	1	dbSNP_126	113	219,8381	91.4+/-153.5	2,215,4083	yes	missense,missense	HENMT1	NM_001102592.1,NM_144584.2	29,29	2,237,6264	TT,TC,CC		2.5465,0.4993,1.853	possibly-damaging,possibly-damaging	39/394,39/394	109200108	241,12765	2203	4300	6503	SO:0001583	missense	113802	exon3			TTTTAACGAACTG		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.115G>A	1.37:g.109200108C>T	ENSP00000359049:p.Val39Ile	111	0	0		69	53	0.768116	NM_144584	A8MRR6|B1AM16|B1AM17|Q96EJ7|Q96NN0	Missense_Mutation	SNP	ENST00000370032.5	37	CCDS787.1	29	0.013278388278388278	4	0.008130081300813009	4	0.011049723756906077	0	0.0	21	0.027704485488126648	C	15.44	2.833273	0.50951	0.004993	0.025465	ENSG00000162639	ENST00000402983;ENST00000370031;ENST00000370032;ENST00000420055	T;T;T;T	0.38077	1.16;1.16;1.16;1.16	5.62	3.68	0.42216	.	0.067024	0.64402	D	0.000015	T	0.31327	0.0793	L	0.41573	1.285	0.48185	D	0.999609	D	0.76494	0.999	D	0.66979	0.948	T	0.05733	-1.0867	10	0.32370	T	0.25	.	8.5831	0.33642	0.0:0.813:0.0:0.187	rs36100901	39	Q5T8I9	HENMT_HUMAN	I	39	ENSP00000385655:V39I;ENSP00000359048:V39I;ENSP00000359049:V39I;ENSP00000403953:V39I	ENSP00000359048:V39I	V	-	1	0	HENMT1	109001631	0.607000	0.26958	0.229000	0.23960	0.264000	0.26372	0.956000	0.29202	1.292000	0.44672	0.655000	0.94253	GTT	C|0.984;T|0.016	0.016	strong		0.383	HENMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030592.1	NM_144584		T	109200108	C	T	109200108	3	4	30	1	0	0	0	0	1	0	0	0	2053	536	19	1	1090	1	C1orf59	1	109200108	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	13877205	109200108	140050513	38	13189											
KIAA1324	57535	hgsc.bcm.edu	37	chr1	109714593	109714593	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caatctggcaccgttaacttCgaatactactatccagactc	12	11	5	13	2	1	1	0	0	1	1	4	2	2	1	2	1	3	2	2	1	6	5	rs112023388	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:109714593C>T	ENST00000369939.3	+	4	756	c.573C>T	c.(571-573)ttC>ttT	p.F191F	KIAA1324_ENST00000529753.1_Silent_p.F191F	NM_020775.4	NP_065826	Q6UXG2	K1324_HUMAN	KIAA1324	191					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)		CCGTTAACTTCGAATACTACT	0.537																																					p.F191F		Atlas-SNP	.											.	KIAA1324	77	.	0			c.C573T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	156	133	141		573	-3.8	1	1	dbSNP_132	141	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	KIAA1324	NM_020775.3		0,4,6499	TT,TC,CC		0.0349,0.0227,0.0308		191/1014	109714593	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	57535	exon4			TAACTTCGAATAC	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.573C>T	1.37:g.109714593C>T		267	0	0		160	122	0.7625	NM_020775	Q08AE6|Q5T5C9|Q5T5D0|Q5T5D1|Q9P2M2	Silent	SNP	ENST00000369939.3	37	CCDS794.1																																																																																			C|0.999;T|0.001	0.001	strong		0.537	KIAA1324-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032389.2	NM_020775		T	109714593	C	T	109714593	2	4	30	1	0	0	0	0	0	0	0	1	8232	883	31	1		1	KIAA1324	1	109714593	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	514485	109714593	139536028	39	13190											
DDX20	11218	hgsc.bcm.edu	37	chr1	112309230	112309230	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agacttaaagagggggctagCcagagagctaagcagagccg	14	4	15	8	1	0	4	0	0	0	4	0	5	0	4	2	2	4	3	2	2	4	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:112309230C>T	ENST00000369702.4	+	11	2804	c.2184C>T	c.(2182-2184)agC>agT	p.S728S	DDX20_ENST00000475700.1_Silent_p.S336S	NM_007204.4	NP_009135.4	Q9UHI6	DDX20_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 20	728					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)		AGGGGGCTAGCCAGAGAGCTA	0.483																																					p.S728S		Atlas-SNP	.											.	DDX20	50	.	0			c.C2184T						PASS	.						65	67	66					1																	112309230		2203	4300	6503	SO:0001819	synonymous_variant	11218	exon11			GGCTAGCCAGAGA	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.2184C>T	1.37:g.112309230C>T		132	0	0		87	4	0.045977	NM_007204	B4DWV7|Q96F72|Q9NVM3|Q9UF59|Q9UIY0|Q9Y659	Silent	SNP	ENST00000369702.4	37	CCDS842.1																																																																																			.	.	none		0.483	DDX20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033063.2	NM_007204		T	112309230	C	T	112309230	2	4	30	1	0	0	0	0	0	0	0	1	4350	738	26	2		2	DDX20	1	112309230	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	2594637	112309230	136941391	40	13191											
CSDE1	7812	hgsc.bcm.edu	37	chr1	115269685	115269685	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtttcaccccacagtcatcAtaagcaataatgccatcctc	13	10	4	14	0	3	0	3	0	0	0	5	0	4	0	4	0	2	2	4	0	3	3	rs150190370	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:115269685A>G	ENST00000358528.4	-	13	1809	c.1383T>C	c.(1381-1383)taT>taC	p.Y461Y	CSDE1_ENST00000534699.1_Silent_p.Y461Y|CSDE1_ENST00000438362.2_Silent_p.Y507Y|CSDE1_ENST00000261443.5_Silent_p.Y430Y|CSDE1_ENST00000530886.1_Silent_p.Y331Y|Y_RNA_ENST00000365030.1_RNA|CSDE1_ENST00000369530.1_Silent_p.Y476Y|CSDE1_ENST00000339438.6_Silent_p.Y430Y	NM_001007553.2	NP_001007554.1	O75534	CSDE1_HUMAN	cold shock domain containing E1, RNA-binding	461	CSD 6.				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)		CACAGTCATCATAAGCAATAA	0.368													A|||	7	0.00139776	0.0	0.0	5008	,	,		18398	0.0069		0.0	False		,,,				2504	0.0				p.Y507Y		Atlas-SNP	.											.	CSDE1	145	.	0			c.T1521C						PASS	.						140	122	128					1																	115269685		2203	4300	6503	SO:0001819	synonymous_variant	7812	exon14			GTCATCATAAGCA		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.1383T>C	1.37:g.115269685A>G		181	0	0		84	5	0.0595238	NM_001242891	A8K281|E9PGZ0|G5E9Q2|O94961|Q5TF04|Q5TF05|Q68DF1|Q68DI9|Q9Y2S4	Silent	SNP	ENST00000358528.4	37	CCDS30812.1																																																																																			A|0.997;G|0.003	0.003	strong		0.368	CSDE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033397.1	NM_007158		G	115269685	A	G	115269685	2	3	30	1	0	0	0	0	0	0	0	1	3931	224	8	3		3	CSDE1	1	115269685	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	2960455	115269685	133980936	41	13192											
FAM46C	54855	hgsc.bcm.edu	37	chr1	118166385	118166385	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttcaaaaccacttcgctgaaGaagagagaagcaagtacgac	17	6	9	9	2	1	4	1	1	0	3	2	6	1	4	1	0	3	3	1	0	7	3	rs145471785	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:118166385G>A	ENST00000369448.3	+	2	1142	c.895G>A	c.(895-897)Gaa>Aaa	p.E299K		NM_017709.3	NP_060179.2	Q5VWP2	FA46C_HUMAN	family with sequence similarity 46, member C	299										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|lung(7)|ovary(1)|upper_aerodigestive_tract(1)	15	Lung SC(450;0.225)	all_cancers(81;0.000101)|all_lung(203;3.4e-06)|all_epithelial(167;4.98e-06)|Lung NSC(69;2.33e-05)		Lung(183;0.0576)|LUSC - Lung squamous cell carcinoma(189;0.192)|Colorectal(144;0.247)		CTTCGCTGAAGAAGAGAGAAG	0.517			"Mis, F, O"		MM					Multiple Myeloma(3;1.13e-06)			G|||	13	0.00259585	0.0	0.0029	5008	,	,		22262	0.0		0.0089	False		,,,				2504	0.002				p.E299K		Atlas-SNP	.		Rec	yes		1	1p12	54855	"family with sequence similarity 46, member C"		L	.	FAM46C	25	.	0			c.G895A						PASS	.	G	LYS/GLU	5,4401	9.9+/-24.2	0,5,2198	123	116	118		895	5.7	0.9	1	dbSNP_134	118	91,8509	51.1+/-111.2	1,89,4210	yes	missense	FAM46C	NM_017709.3	56	1,94,6408	AA,AG,GG		1.0581,0.1135,0.7381	possibly-damaging	299/392	118166385	96,12910	2203	4300	6503	SO:0001583	missense	54855	exon2			GCTGAAGAAGAGA	BC036516	CCDS896.1	1p12	2008-02-05			ENSG00000183508	ENSG00000183508			24712	protein-coding gene	gene with protein product		613952				12477932	Standard	NM_017709		Approved	FLJ20202	uc001ehe.3	Q5VWP2	OTTHUMG00000013703	ENST00000369448.3:c.895G>A	1.37:g.118166385G>A	ENSP00000358458:p.Glu299Lys	113	0	0		53	39	0.735849	NM_017709	A3KMG2|Q8NE25|Q9NXK0	Missense_Mutation	SNP	ENST00000369448.3	37	CCDS896.1	11	0.005036630036630037	0	0.0	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	G	22.3	4.273089	0.80580	0.001135	0.010581	ENSG00000183508	ENST00000369448	T	0.22945	1.93	5.7	5.7	0.88788	Domain of unknown function DUF1693 (1);	0.079249	0.51477	D	0.000094	T	0.27454	0.0674	M	0.79693	2.465	0.80722	D	1	B	0.26902	0.163	B	0.34452	0.183	T	0.05131	-1.0904	10	0.33940	T	0.23	-11.7413	18.8168	0.92079	0.0:0.0:1.0:0.0	.	299	Q5VWP2	FA46C_HUMAN	K	299	ENSP00000358458:E299K	ENSP00000358458:E299K	E	+	1	0	FAM46C	117967908	1.000000	0.71417	0.894000	0.35097	0.979000	0.70002	5.244000	0.65400	2.686000	0.91538	0.655000	0.94253	GAA	G|0.995;A|0.005	0.005	strong		0.517	FAM46C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038424.1	NM_017709		A	118166385	G	A	118166385	3	1	30	1	0	0	0	0	1	0	0	0	5575	943	33	2	897	2	FAM46C	1	118166385	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2896700	118166385	131084236	42	13193											
HSD3B1	3283	hgsc.bcm.edu	37	chr1	120056849	120056849	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atgtggcctgggcccacattCtggccttgagggccctgcag	5	9	14	13	0	1	1	0	1	1	0	1	1	1	1	4	4	1	1	4	4	0	2	rs141977722	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:120056849C>T	ENST00000369413.3	+	4	848	c.703C>T	c.(703-705)Ctg>Ttg	p.L235L	HSD3B1_ENST00000528909.1_Silent_p.L235L|HSD3B1_ENST00000235547.6_Silent_p.L237L			P14060	3BHS1_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	235					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)	GGCCCACATTCTGGCCTTGAG	0.512													C|||	2	0.000399361	0.0	0.0	5008	,	,		18576	0.0		0.002	False		,,,				2504	0.0				p.L235L		Atlas-SNP	.											.	HSD3B1	53	.	0			c.C703T						PASS	.	C		0,4406		0,0,2203	64	69	68		703	1.2	1	1	dbSNP_134	68	20,8580	11.2+/-40.8	0,20,4280	no	coding-synonymous	HSD3B1	NM_000862.2		0,20,6483	TT,TC,CC		0.2326,0.0,0.1538		235/374	120056849	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	3283	exon4			CACATTCTGGCCT	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.703C>T	1.37:g.120056849C>T		128	0	0		175	65	0.371429	NM_000862	A8K691|Q14545|Q8IV65	Silent	SNP	ENST00000369413.3	37	CCDS903.1																																																																																			C|0.998;T|0.002	0.002	strong		0.512	HSD3B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034993.3	NM_000862		T	120056849	C	T	120056849	2	4	30	1	0	0	0	0	0	0	0	1	7399	912	32	2		2	HSD3B1	1	120056849	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1890464	120056849	129193772	43	13194											
ZNF697	90874	hgsc.bcm.edu	37	chr1	120166528	120166528	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccgactccccagggagagAtgtcgcctccagggaagtac	9	6	13	13	2	0	1	0	0	0	1	3	5	2	3	5	2	2	1	5	2	2	1	rs374393078		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:120166528A>G	ENST00000421812.2	-	3	557	c.438T>C	c.(436-438)caT>caC	p.H146H		NM_001080470.1	NP_001073939.1	Q5TEC3	ZN697_HUMAN	zinc finger protein 697	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)			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)		CCAGGGAGAGATGTCGCCTCC	0.706																																					p.H146H		Atlas-SNP	.											.	ZNF697	26	.	0			c.T438C						PASS	.	A		1,3997		0,1,1998	15	19	18		438	-2.7	0.9	1		18	0,8274		0,0,4137	no	coding-synonymous	ZNF697	NM_001080470.1		0,1,6135	GG,GA,AA		0.0,0.025,0.0081		146/546	120166528	1,12271	1999	4137	6136	SO:0001819	synonymous_variant	90874	exon3			GGAGAGATGTCGC	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.438T>C	1.37:g.120166528A>G		158	0	0		162	40	0.246914	NM_001080470	Q96IT2	Silent	SNP	ENST00000421812.2	37	CCDS44202.1																																																																																			.	.	none		0.706	ZNF697-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036349.3	XM_371286		G	120166528	A	G	120166528	2	3	30	1	0	0	0	0	0	0	0	1	18115	330	12	3		3	ZNF697	1	120166528	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	109679	120166528	129084093	44	13195											
NBPF14	25832	hgsc.bcm.edu	37	chr1	148004783	148004783	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttccacttccatcagcatgCtgttgagcctgcaaaaggag	10	10	9	12	0	1	1	1	1	0	0	3	2	3	2	3	1	4	4	3	1	2	3	rs147480284	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:148004783C>A	ENST00000369219.1	-	22	2547	c.2531G>T	c.(2530-2532)aGc>aTc	p.S844I				Q5TI25	NBPFE_HUMAN	neuroblastoma breakpoint family, member 14	844	NBPF 10. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)		p.S844I(1)		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)					CATCAGCATGCTGTTGAGCCT	0.453													-|||	73	0.0145767	0.0008	0.0187	5008	,	,		15184	0.001		0.0537	False		,,,				2504	0.0041				p.S844I		Atlas-SNP	.											NBPF14,NS,adenoma,0,2	NBPF14	107	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2531T						scavenged	.	C	ILE/SER	84,3292		31,22,1635	72	122	108		2531	0.5	0	1	dbSNP_134	108	565,7627		134,297,3665	no	missense	NBPF14	NM_015383.1	142	165,319,5300	AA,AC,CC		6.897,2.4882,5.6103	possibly-damaging	844/922	148004783	649,10919	1688	4096	5784	SO:0001583	missense	25832	exon22			AGCATGCTGTTGA	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.2531G>T	1.37:g.148004783C>A	ENSP00000358221:p.Ser844Ile	529	2	0.00378072		412	393	0.953883	NM_015383	Q5TI23|Q8IX76|Q9UJI9	Missense_Mutation	SNP	ENST00000369219.1	37		61|61	0.027930402930402932|0.027930402930402932	1|1	0.0020325203252032522|0.0020325203252032522	6|6	0.016574585635359115|0.016574585635359115	0|0	0.0|0.0	54|54	0.0712401055408971|0.0712401055408971	c|c	9.996|9.996	1.232277|1.232277	0.22626|0.22626	0.024882|0.024882	0.06897|0.06897	ENSG00000122497|ENSG00000122497	ENST00000310701|ENST00000369219;ENST00000369368	.|T	.|0.06608	.|3.28	0.464|0.464	0.464|0.464	0.16706|0.16706	.|DUF1220 (2);	.|.	.|.	.|.	.|.	T|T	0.02571|0.02571	0.0078|0.0078	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	1|1	.|B;P;P	.|0.51653	.|0.228;0.947;0.858	.|B;P;P	.|0.54026	.|0.215;0.699;0.74	T|T	0.48068|0.48068	-0.9067|-0.9067	4|8	.|0.21014	.|T	.|0.42	.|.	.|.	.|.	.|.	.|.	.|192;825;844	.|F8WEX8;B4DH59;Q5TI25	.|.;.;NBPFE_HUMAN	S|I	850|844;192	.|ENSP00000358221:S844I	.|ENSP00000358221:S844I	A|S	-|-	1|2	0|0	NBPF14|NBPF14	146471407|146471407	0.009000|0.009000	0.17119|0.17119	0.004000|0.004000	0.12327|0.12327	0.011000|0.011000	0.07611|0.07611	0.685000|0.685000	0.25378|0.25378	0.550000|0.550000	0.28991|0.28991	0.388000|0.388000	0.25769|0.25769	GCA|AGC	C|0.960;A|0.040	0.040	strong		0.453	NBPF14-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_015383		A	148004783	C	A	148004783	3	1	30	1	0	0	0	0	1	0	0	0	10203	797	28	4	238	4	NBPF14	1	148004783	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	27838255	148004783	101245838	45	13196											
SF3B4	10262	hgsc.bcm.edu	37	chr1	149895866	149895866	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagcgtggggatgtcctaaGccatgagggccatggtgtgc	7	8	16	10	1	0	1	0	1	0	0	1	2	1	2	4	4	3	0	4	4	1	1			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:149895866G>A	ENST00000271628.8	-	5	1538	c.954C>T	c.(952-954)ggC>ggT	p.G318G		NM_005850.4	NP_005841.1	Q15427	SF3B4_HUMAN	splicing factor 3b, subunit 4, 49kDa	318					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)			GATGTCCTAAGCCATGAGGGC	0.542																																					p.G318G		Atlas-SNP	.											.	SF3B4	37	.	0			c.C954T						PASS	.						12	13	13					1																	149895866		2197	4296	6493	SO:0001819	synonymous_variant	10262	exon5			TCCTAAGCCATGA	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.954C>T	1.37:g.149895866G>A		101	0	0		120	31	0.258333	NM_005850	Q5SZ63	Silent	SNP	ENST00000271628.8	37	CCDS941.1																																																																																			.	.	none		0.542	SF3B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033753.1	NM_005850		A	149895866	G	A	149895866	2	1	30	1	0	0	0	0	0	0	0	1	14168	958	34	2		2	SF3B4	1	149895866	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1891083	149895866	99354755	46	13197											
TCHH	7062	hgsc.bcm.edu	37	chr1	152083806	152083806	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctcttcagcagctgctggcgCctctcttcctccggctcctc	2	12	8	19	2	3	0	1	0	2	0	8	0	6	0	4	2	3	4	4	2	0	2	rs200947543	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:152083806C>T	ENST00000368804.1	-	2	1886	c.1887G>A	c.(1885-1887)agG>agA	p.R629R		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	629	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)			GCTGCTGGCGCCTCTCTTCCT	0.677													c|||	18	0.00359425	0.0008	0.0043	5008	,	,		15925	0.0		0.0129	False		,,,				2504	0.001				p.R629R		Atlas-SNP	.											.	TCHH	275	.	0			c.G1887A						PASS	.			8,3992		0,8,1992	34	40	38		1887	-0.7	0	1	dbSNP_134	38	85,8265		1,83,4091	no	coding-synonymous	TCHH	NM_007113.2		1,91,6083	TT,TC,CC		1.018,0.2,0.753		629/1944	152083806	93,12257	2000	4175	6175	SO:0001819	synonymous_variant	7062	exon3			CTGGCGCCTCTCT	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.1887G>A	1.37:g.152083806C>T		136	0	0		206	127	0.616505	NM_007113	Q5VUI3	Silent	SNP	ENST00000368804.1	37	CCDS41396.1																																																																																			C|0.993;T|0.007	0.007	strong		0.677	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		T	152083806	C	T	152083806	2	4	30	1	0	0	0	0	0	0	0	1	15715	738	26	2		2	TCHH	1	152083806	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	2187940	152083806	97166815	47	13198											
C1orf43	25912	hgsc.bcm.edu	37	chr1	154184993	154184993	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggtatcaatgagtgctttgcGtacacccttgaaaggcgtac	10	11	11	9	2	1	2	1	2	0	0	1	2	1	2	1	2	4	4	1	2	5	5	rs144385115	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:154184993G>A	ENST00000368521.5	-	5	646	c.448C>T	c.(448-450)Cgc>Tgc	p.R150C	C1orf43_ENST00000350592.3_Missense_Mutation_p.R116C|C1orf43_ENST00000368516.1_Missense_Mutation_p.R116C|C1orf43_ENST00000368518.1_Missense_Mutation_p.R150C|C1orf43_ENST00000362076.4_Missense_Mutation_p.R98C|C1orf43_ENST00000368519.1_Missense_Mutation_p.R132C	NM_001098616.1	NP_001092086.1	Q9BWL3	CA043_HUMAN	chromosome 1 open reading frame 43	150						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)					AGTGCTTTGCGTACACCCTTG	0.498													G|||	22	0.00439297	0.0008	0.0101	5008	,	,		19963	0.0		0.0119	False		,,,				2504	0.002				p.R150C		Atlas-SNP	.											.	C1orf43	36	.	0			c.C448T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG	6,4400	11.4+/-27.6	0,6,2197	90	82	85		448,346,292	3.5	1	1	dbSNP_134	85	70,8530	41.7+/-99.0	0,70,4230	yes	missense,missense,missense	C1orf43	NM_001098616.1,NM_015449.2,NM_138740.2	180,180,180	0,76,6427	AA,AG,GG		0.814,0.1362,0.5843	benign,benign,benign	150/254,116/220,98/202	154184993	76,12930	2203	4300	6503	SO:0001583	missense	25912	exon5			CTTTGCGTACACC	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.448C>T	1.37:g.154184993G>A	ENSP00000357507:p.Arg150Cys	168	0	0		156	84	0.538462	NM_001098616	A8K3G8|D3DV72|D3DV74|Q5M801|Q5VU73|Q5VU83|Q96HP7|Q9UFU2|Q9UGL7|Q9UGL8|Q9Y2R6	Missense_Mutation	SNP	ENST00000368521.5	37	CCDS41404.1	16	0.007326007326007326	0	0.0	5	0.013812154696132596	0	0.0	11	0.014511873350923483	G	15.45	2.837975	0.50951	0.001362	0.00814	ENSG00000143612	ENST00000350592;ENST00000368521;ENST00000362076;ENST00000368519;ENST00000368518;ENST00000368516	.	.	.	5.39	3.5	0.40072	Dehydrogenase, multihelical (1);	0.150760	0.64402	D	0.000008	T	0.32466	0.0830	L	0.58101	1.795	0.53005	D	0.999961	B;B;B;B;B	0.14012	0.007;0.007;0.004;0.003;0.009	B;B;B;B;B	0.14023	0.002;0.002;0.01;0.002;0.003	T	0.31503	-0.9941	9	0.54805	T	0.06	-17.9839	5.6172	0.17438	0.0749:0.1395:0.6412:0.1444	.	132;116;150;98;116	Q9BWL3-5;Q9BWL3-2;Q9BWL3;Q9BWL3-4;Q09GN0	.;.;CA043_HUMAN;.;.	C	116;150;98;132;150;116	.	ENSP00000271925:R116C	R	-	1	0	C1orf43	152451617	1.000000	0.71417	0.998000	0.56505	0.792000	0.44763	4.784000	0.62411	0.821000	0.34540	0.585000	0.79938	CGC	G|0.994;A|0.006	0.006	strong		0.498	C1orf43-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087664.2	NM_015449		A	154184993	G	A	154184993	3	1	30	1	0	0	0	0	1	0	0	0	2042	1145	40	1	325	1	C1orf43	1	154184993	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2101187	154184993	95065628	48	13199											
DCST1	149095	hgsc.bcm.edu	37	chr1	155019698	155019698	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ataaactggaggtgaaggtcGggggagactccatgctagcc	11	7	15	8	1	0	2	0	1	0	1	2	4	1	3	2	5	3	1	2	5	4	2	rs200041699	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:155019698G>A	ENST00000295542.1	+	14	1618	c.1522G>A	c.(1522-1524)Ggg>Agg	p.G508R	RP11-307C12.11_ENST00000452962.1_RNA|DCST1_ENST00000368419.2_Missense_Mutation_p.G508R|DCST1_ENST00000392480.1_Missense_Mutation_p.G508R|DCST1_ENST00000423025.2_Missense_Mutation_p.G483R	NM_152494.3	NP_689707.2	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1	508						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)			GGTGAAGGTCGGGGGAGACTC	0.542													G|||	2	0.000399361	0.0015	0.0	5008	,	,		18587	0.0		0.0	False		,,,				2504	0.0				p.G508R		Atlas-SNP	.											.	DCST1	69	.	0			c.G1522A						PASS	.	G	ARG/GLY,ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	82	81	81		1447,1522	4.9	0	1		81	0,8600		0,0,4300	no	missense,missense	DCST1	NM_001143687.2,NM_152494.3	125,125	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	483/682,508/707	155019698	1,13005	2203	4300	6503	SO:0001583	missense	149095	exon14			AAGGTCGGGGGAG	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.1522G>A	1.37:g.155019698G>A	ENSP00000295542:p.Gly508Arg	184	0	0		253	144	0.56917	NM_152494	B4DXA0|E9PHV3|Q5T198|Q6P1W6|Q71S70|Q96M70	Missense_Mutation	SNP	ENST00000295542.1	37	CCDS1083.1	.	.	.	.	.	.	.	.	.	.	G	14.31	2.496614	0.44352	2.27E-4	0.0	ENSG00000163357	ENST00000295542;ENST00000392480;ENST00000423025;ENST00000368419	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	4.88	4.88	0.63580	Dendritic cell-specific transmembrane protein-like (1);	0.308295	0.33005	N	0.005381	T	0.20455	0.0492	L	0.40543	1.245	0.19300	N	0.999974	D;P	0.57571	0.98;0.932	P;P	0.54060	0.741;0.741	T	0.06899	-1.0801	10	0.13853	T	0.58	-11.7727	13.7183	0.62712	0.0:0.0:1.0:0.0	.	483;508	E9PHV3;Q5T197	.;DCST1_HUMAN	R	508;508;483;508	ENSP00000295542:G508R;ENSP00000376271:G508R;ENSP00000387369:G483R;ENSP00000357404:G508R	ENSP00000295542:G508R	G	+	1	0	DCST1	153286322	1.000000	0.71417	0.023000	0.16930	0.036000	0.12997	4.814000	0.62627	2.688000	0.91661	0.655000	0.94253	GGG	G|0.999;A|0.001	0.001	weak		0.542	DCST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099006.1	NM_152494		A	155019698	G	A	155019698	3	1	30	1	0	0	0	0	1	0	0	0	4304	1116	39	1	1572	1	DCST1	1	155019698	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	834705	155019698	94230923	49	13200											
ETV3L	440695	hgsc.bcm.edu	37	chr1	157069134	157069134	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tctgccgggagcctggggacGactcggctttgtaggcccaa	6	8	15	12	3	1	0	0	0	1	0	2	3	1	2	3	5	2	2	3	5	2	2	rs61730132	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:157069134G>A	ENST00000454449.2	-	2	379	c.95C>T	c.(94-96)tCg>tTg	p.S32L		NM_001004341.2	NP_001004341.1	Q6ZN32	ETV3L_HUMAN	ets variant 3-like	32					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)				GCCTGGGGACGACTCGGCTTT	0.642													G|||	26	0.00519169	0.0008	0.0029	5008	,	,		17095	0.0		0.0109	False		,,,				2504	0.0123				p.S32L		Atlas-SNP	.											.	ETV3L	73	.	0			c.C95T						PASS	.	G	LEU/SER	5,4401	9.9+/-24.2	0,5,2198	51	51	51		95	4	1	1	dbSNP_129	51	74,8526	43.6+/-101.6	0,74,4226	yes	missense	ETV3L	NM_001004341.2	145	0,79,6424	AA,AG,GG		0.8605,0.1135,0.6074	probably-damaging	32/362	157069134	79,12927	2203	4300	6503	SO:0001583	missense	440695	exon2			GGGGACGACTCGG	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.95C>T	1.37:g.157069134G>A	ENSP00000430271:p.Ser32Leu	150	0	0		231	94	0.406926	NM_001004341		Missense_Mutation	SNP	ENST00000454449.2	37	CCDS30893.1	11	0.005036630036630037	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	G	24.7	4.556591	0.86231	0.001135	0.008605	ENSG00000253831	ENST00000454449	T	0.12255	2.7	4.96	4.03	0.46877	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.32802	N	0.005635	T	0.16685	0.0401	L	0.34521	1.04	0.40492	D	0.980559	D	0.89917	1.0	D	0.78314	0.991	T	0.02625	-1.1132	10	0.87932	D	0	.	14.2718	0.66155	0.0:0.1505:0.8495:0.0	rs61730132	32	Q6ZN32	ETV3L_HUMAN	L	32	ENSP00000430271:S32L	ENSP00000430271:S32L	S	-	2	0	ETV3L	155335758	1.000000	0.71417	0.954000	0.39281	0.918000	0.54935	5.422000	0.66453	1.271000	0.44313	0.655000	0.94253	TCG	G|0.994;A|0.006	0.006	strong		0.642	ETV3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099024.2	NM_001004341		A	157069134	G	A	157069134	3	1	30	1	0	0	0	0	1	0	0	0	5282	1059	37	1	1006	1	ETV3L	1	157069134	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2049436	157069134	92181487	50	13201											
CD1B	910	hgsc.bcm.edu	37	chr1	158299358	158299358	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacccacacgggctttgggtAgaatcctgagacatggcaca	11	7	11	12	1	0	2	0	1	0	2	1	3	1	2	2	3	0	3	2	3	2	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:158299358A>G	ENST00000368168.3	-	4	795	c.688T>C	c.(688-690)Tac>Cac	p.Y230H		NM_001764.2	NP_001755.1	P29016	CD1B_HUMAN	CD1b molecule	230	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)					GGCTTTGGGTAGAATCCTGAG	0.587																																					p.Y230H		Atlas-SNP	.											CD1B,colon,carcinoma,+1,1	CD1B	78	1	0			c.T688C						PASS	.						91	87	88					1																	158299358		2203	4300	6503	SO:0001583	missense	910	exon4			TTGGGTAGAATCC	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.688T>C	1.37:g.158299358A>G	ENSP00000357150:p.Tyr230His	325	0	0		396	231	0.583333	NM_001764	Q5TDK9|Q5TDL0|Q9UMM2	Missense_Mutation	SNP	ENST00000368168.3	37	CCDS1176.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.94|12.94	2.086996|2.086996	0.36855|0.36855	.|.	.|.	ENSG00000158485|ENSG00000158485	ENST00000451207|ENST00000368168	.|T	.|0.03920	.|3.76	4.26|4.26	1.9|1.9	0.25705|0.25705	.|Immunoglobulin-like (1);MHC class I-like antigen recognition (1);Immunoglobulin C1-set (2);	.|0.196307	.|0.25509	.|N	.|0.030200	T|T	0.04952|0.04952	0.0133|0.0133	M|M	0.64080|0.64080	1.96|1.96	0.28660|0.28660	N|N	0.9062|0.9062	.|D;P	.|0.54397	.|0.966;0.888	.|P;P	.|0.59546	.|0.859;0.668	T|T	0.22556|0.22556	-1.0213|-1.0213	5|10	.|0.44086	.|T	.|0.13	-8.3888|-8.3888	5.8437|5.8437	0.18647|0.18647	0.7803:0.0:0.2197:0.0|0.7803:0.0:0.2197:0.0	.|.	.|230;230	.|P29016;P29016-2	.|CD1B_HUMAN;.	P|H	197|230	.|ENSP00000357150:Y230H	.|ENSP00000357150:Y230H	L|Y	-|-	2|1	0|0	CD1B|CD1B	156565982|156565982	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.977000|0.977000	0.68977|0.68977	0.587000|0.587000	0.23909|0.23909	0.280000|0.280000	0.22209|0.22209	0.533000|0.533000	0.62120|0.62120	CTA|TAC	.	.	none		0.587	CD1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046350.2	NM_001764		G	158299358	A	G	158299358	3	3	30	1	0	0	0	0	1	0	0	0	2977	420	15	3	325	3	CD1B	1	158299358	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	1230224	158299358	90951263	51	13202											
MNDA	4332	hgsc.bcm.edu	37	chr1	158817521	158817521	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttaatcttcttttgcagaaaAgcgtacacaagaagaacaca	17	10	6	8	1	2	3	0	0	2	3	2	3	2	3	0	0	4	2	0	0	7	5			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:158817521A>G	ENST00000368141.4	+	6	1252	c.991A>G	c.(991-993)Agc>Ggc	p.S331G		NM_002432.1	NP_002423.1	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	331	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)					TTTGCAGAAAAGCGTACACAA	0.368																																					p.S331G		Atlas-SNP	.											MNDA,colon,carcinoma,0,2	MNDA	147	2	0			c.A991G						PASS	.						95	93	94					1																	158817521		2203	4300	6503	SO:0001583	missense	4332	exon6			CAGAAAAGCGTAC	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.991A>G	1.37:g.158817521A>G	ENSP00000357123:p.Ser331Gly	77	0	0		120	5	0.0416667	NM_002432		Missense_Mutation	SNP	ENST00000368141.4	37	CCDS1177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	4.768|4.768	0.142801|0.142801	0.09083|0.09083	.|.	.|.	ENSG00000163563|ENSG00000163563	ENST00000438394|ENST00000368141	T|T	0.19394|0.14766	2.15|2.48	4.15|4.15	0.259|0.259	0.15583|0.15583	.|HIN-200/IF120x (2);Nucleic acid-binding, OB-fold (1);	.|1.196580	.|0.06409	.|N	.|0.720183	T|T	0.02727|0.02727	0.0082|0.0082	N|N	0.24115|0.24115	0.695|0.695	0.09310|0.09310	N|N	0.999996|0.999996	.|B	.|0.33777	.|0.425	.|B	.|0.33121	.|0.158	T|T	0.45205|0.45205	-0.9277|-0.9277	7|10	0.72032|0.40728	D|T	0.01|0.16	0.0539|0.0539	5.0869|5.0869	0.14687|0.14687	0.4576:0.3654:0.0:0.1771|0.4576:0.3654:0.0:0.1771	.|.	.|331	.|P41218	.|MNDA_HUMAN	R|G	36|331	ENSP00000406800:K36R|ENSP00000357123:S331G	ENSP00000406800:K36R|ENSP00000357123:S331G	K|S	+|+	2|1	0|0	MNDA|MNDA	157084145|157084145	0.104000|0.104000	0.21937|0.21937	0.136000|0.136000	0.22124|0.22124	0.082000|0.082000	0.17680|0.17680	0.152000|0.152000	0.16302|0.16302	-0.064000|-0.064000	0.13043|0.13043	0.460000|0.460000	0.39030|0.39030	AAG|AGC	.	.	none		0.368	MNDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059069.1	NM_002432		G	158817521	A	G	158817521	3	3	30	1	0	0	0	0	1	0	0	0	9685	72	3	3	1009	3	MNDA	1	158817521	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	518163	158817521	90433100	52	13203											
ALDH9A1	223	hgsc.bcm.edu	37	chr1	165664562	165664562	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tttgactccatattttaaaaGcagcctttgcattttgaaca	12	16	5	8	0	0	2	0	2	0	0	1	2	1	2	2	0	4	2	2	0	4	7			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:165664562G>A	ENST00000354775.4	-	2	558	c.254C>T	c.(253-255)gCt>gTt	p.A85V	ALDH9A1_ENST00000461664.1_5'UTR|ALDH9A1_ENST00000538148.1_5'UTR	NM_000696.3	NP_000687.3	P49189	AL9A1_HUMAN	aldehyde dehydrogenase 9 family, member A1	61					carnitine biosynthetic process (GO:0045329)|cellular aldehyde metabolic process (GO:0006081)|cellular nitrogen compound metabolic process (GO:0034641)|hormone metabolic process (GO:0042445)|kidney development (GO:0001822)|liver development (GO:0001889)|neurotransmitter biosynthetic process (GO:0042136)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	1-pyrroline dehydrogenase activity (GO:0033737)|3-chloroallyl aldehyde dehydrogenase activity (GO:0004028)|4-trimethylammoniobutyraldehyde dehydrogenase activity (GO:0047105)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|amine binding (GO:0043176)|aminobutyraldehyde dehydrogenase activity (GO:0019145)|NAD binding (GO:0051287)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	21	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)					TATTTTAAAAGCAGCCTTTGC	0.398																																					p.A85V	Ovarian(179;1583 2014 18106 33801 42447)	Atlas-SNP	.											.	ALDH9A1	75	.	0			c.C254T						PASS	.						99	98	98					1																	165664562		2203	4300	6503	SO:0001583	missense	223	exon2			TTAAAAGCAGCCT	U34252	CCDS1250.2	1q22-q23	2008-02-05			ENSG00000143149	ENSG00000143149		"Aldehyde dehydrogenases"	412	protein-coding gene	gene with protein product		602733		ALDH7, ALDH4, ALDH9		8112751, 8786138	Standard	NM_000696		Approved	E3	uc001gdh.1	P49189	OTTHUMG00000034677	ENST00000354775.4:c.254C>T	1.37:g.165664562G>A	ENSP00000346827:p.Ala85Val	100	0	0		99	23	0.232323	NM_000696	B2R6X1|B4DXY7|Q5VV90|Q6LCL1|Q9NZT7	Missense_Mutation	SNP	ENST00000354775.4	37	CCDS1250.2	.	.	.	.	.	.	.	.	.	.	G	22.0	4.232550	0.79688	.	.	ENSG00000143149	ENST00000354775	D	0.94330	-3.4	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	D	0.96318	0.8799	M	0.81179	2.53	0.52099	D	0.999942	D;D	0.76494	0.999;0.999	D;D	0.72625	0.978;0.978	D	0.96736	0.9543	9	0.87932	D	0	.	16.7765	0.85552	0.0:0.0:1.0:0.0	.	75;85	B4DX14;B9EKV4	.;.	V	85	ENSP00000346827:A85V	ENSP00000346827:A85V	A	-	2	0	ALDH9A1	163931186	1.000000	0.71417	1.000000	0.80357	0.478000	0.33099	7.115000	0.77110	2.545000	0.85829	0.655000	0.94253	GCT	.	.	none		0.398	ALDH9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083899.1			A	165664562	G	A	165664562	3	1	30	1	0	0	0	0	1	0	0	0	506	971	34	2	1342	2	ALDH9A1	1	165664562	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	6847041	165664562	83586059	53	13204											
FMO4	2329	hgsc.bcm.edu	37	chr1	171303626	171303626	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caatcactatgaaaaccagcGtgattgaatttacagaaacc	17	9	6	9	1	1	4	1	3	0	1	1	4	1	4	2	0	4	0	2	0	7	4	rs573059844		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:171303626G>A	ENST00000367749.3	+	8	1234	c.904G>A	c.(904-906)Gtg>Atg	p.V302M		NM_002022.1	NP_002013.1	P31512	FMO4_HUMAN	flavin containing monooxygenase 4	302					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)					GAAAACCAGCGTGATTGAATT	0.378																																					p.V302M	Pancreas(24;816 862 7754 7993 32832)	Atlas-SNP	.											FMO4,caecum,carcinoma,0,1	FMO4	64	1	0			c.G904A						PASS	.						70	73	72					1																	171303626		2203	4300	6503	SO:0001583	missense	2329	exon8			ACCAGCGTGATTG	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.904G>A	1.37:g.171303626G>A	ENSP00000356723:p.Val302Met	133	0	0		170	51	0.3	NM_002022	Q53XR0	Missense_Mutation	SNP	ENST00000367749.3	37	CCDS1295.1	.	.	.	.	.	.	.	.	.	.	G	13.75	2.331649	0.41297	.	.	ENSG00000076258	ENST00000367749	T	0.61040	0.14	5.66	4.76	0.60689	.	0.135375	0.48286	D	0.000184	T	0.74680	0.3748	M	0.92880	3.355	0.46954	D	0.999265	D	0.89917	1.0	D	0.85130	0.997	T	0.80939	-0.1158	10	0.72032	D	0.01	-15.5018	10.7486	0.46196	0.1469:0.0:0.8531:0.0	.	302	P31512	FMO4_HUMAN	M	302	ENSP00000356723:V302M	ENSP00000356723:V302M	V	+	1	0	FMO4	169570250	0.823000	0.29233	0.380000	0.26093	0.043000	0.13939	1.146000	0.31589	1.387000	0.46486	-0.128000	0.14901	GTG	.	.	none		0.378	FMO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086223.1	NM_002022		A	171303626	G	A	171303626	3	1	30	1	0	0	0	0	1	0	0	0	5965	1145	40	1	926	1	FMO4	1	171303626	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	5639064	171303626	77946995	54	13205											
FMO4	2329	hgsc.bcm.edu	37	chr1	171303810	171303810	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcccttaaacctagagagagCgacattagccatcatcggcc	12	8	8	13	2	1	2	1	0	0	2	3	4	2	2	4	1	3	0	4	1	4	3	rs144578261	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:171303810C>T	ENST00000367749.3	+	8	1418	c.1088C>T	c.(1087-1089)gCg>gTg	p.A363V		NM_002022.1	NP_002013.1	P31512	FMO4_HUMAN	flavin containing monooxygenase 4	363					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)					CTAGAGAGAGCGACATTAGCC	0.403													C|||	2	0.000399361	0.0	0.0	5008	,	,		19559	0.0		0.0	False		,,,				2504	0.002				p.A363V	Pancreas(24;816 862 7754 7993 32832)	Atlas-SNP	.											FMO4,NS,NS,-1,1	FMO4	64	1	0			c.C1088T						scavenged	.	C	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	87	88	88		1088	5.6	0.1	1	dbSNP_134	88	3,8597	3.0+/-9.4	0,3,4297	yes	missense	FMO4	NM_002022.1	64	0,4,6499	TT,TC,CC		0.0349,0.0227,0.0308	benign	363/559	171303810	4,13002	2203	4300	6503	SO:0001583	missense	2329	exon8			AGAGAGCGACATT	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.1088C>T	1.37:g.171303810C>T	ENSP00000356723:p.Ala363Val	111	1	0.00900901		156	63	0.403846	NM_002022	Q53XR0	Missense_Mutation	SNP	ENST00000367749.3	37	CCDS1295.1	.	.	.	.	.	.	.	.	.	.	C	15.89	2.966086	0.53507	2.27E-4	3.49E-4	ENSG00000076258	ENST00000367749	T	0.58060	0.36	5.63	5.63	0.86233	.	0.633406	0.17137	N	0.185613	T	0.43919	0.1269	M	0.66939	2.045	0.38079	D	0.936608	P	0.38048	0.616	B	0.33568	0.166	T	0.56780	-0.7922	10	0.87932	D	0	-2.4899	19.2618	0.93971	0.0:1.0:0.0:0.0	.	363	P31512	FMO4_HUMAN	V	363	ENSP00000356723:A363V	ENSP00000356723:A363V	A	+	2	0	FMO4	169570434	0.106000	0.21978	0.117000	0.21633	0.428000	0.31595	3.801000	0.55545	2.632000	0.89209	0.650000	0.86243	GCG	C|1.000;T|0.000	0.000	weak		0.403	FMO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086223.1	NM_002022		T	171303810	C	T	171303810	3	4	30	1	0	0	0	0	1	0	0	0	5965	768	27	1	1110	1	FMO4	1	171303810	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	184	171303810	77946811	55	13206											
LAMC1	3915	hgsc.bcm.edu	37	chr1	183079729	183079729	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tagactgtgaaaagtgtcttCctttcttcaatgaccggccg	9	13	9	10	2	3	3	1	2	2	1	4	3	4	3	3	1	0	0	3	1	4	4	rs142614579	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:183079729C>T	ENST00000258341.4	+	4	1218	c.961C>T	c.(961-963)Cct>Tct	p.P321S		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	321	Laminin EGF-like 1. {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						AAAGTGTCTTCCTTTCTTCAA	0.473																																					p.P321S		Atlas-SNP	.											.	LAMC1	176	.	0			c.C961T						PASS	.	C	SER/PRO	3,4403	6.2+/-15.9	0,3,2200	188	184	186		961	4.9	0.3	1	dbSNP_134	186	4,8596	3.7+/-12.6	0,4,4296	yes	missense	LAMC1	NM_002293.3	74	0,7,6496	TT,TC,CC		0.0465,0.0681,0.0538	probably-damaging	321/1610	183079729	7,12999	2203	4300	6503	SO:0001583	missense	3915	exon4			TGTCTTCCTTTCT	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.961C>T	1.37:g.183079729C>T	ENSP00000258341:p.Pro321Ser	162	0	0		203	122	0.600985	NM_002293	Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	37	CCDS1351.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.382348	0.82792	6.81E-4	4.65E-4	ENSG00000135862	ENST00000258341	T	0.62498	0.02	4.87	4.87	0.63330	EGF-like, laminin (4);	0.054481	0.85682	D	0.000000	T	0.76026	0.3930	M	0.79475	2.455	0.80722	D	1	P	0.46142	0.873	P	0.54026	0.74	T	0.80443	-0.1380	10	0.87932	D	0	.	17.9961	0.89184	0.0:1.0:0.0:0.0	.	321	P11047	LAMC1_HUMAN	S	321	ENSP00000258341:P321S	ENSP00000258341:P321S	P	+	1	0	LAMC1	181346352	0.998000	0.40836	0.254000	0.24359	0.975000	0.68041	3.714000	0.54889	2.239000	0.73571	0.305000	0.20034	CCT	C|0.999;T|0.001	0.001	strong		0.473	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293		T	183079729	C	T	183079729	3	4	30	1	0	0	0	0	1	0	0	0	8623	855	30	2	975	2	LAMC1	1	183079729	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	11775919	183079729	66170892	56	13207											
LAMC1	3915	hgsc.bcm.edu	37	chr1	183091040	183091040	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagtccatgtgtgctttgcGcctgcaatggacacagcgag	9	9	12	11	2	0	0	0	0	0	0	1	2	1	1	2	1	4	2	2	1	1	1	rs147401305	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:183091040G>A	ENST00000258341.4	+	12	2430	c.2173G>A	c.(2173-2175)Gcc>Acc	p.A725T		NM_002293.3	NP_002284.3	P11047	LAMC1_HUMAN	laminin, gamma 1 (formerly LAMB2)	725	Laminin EGF-like 6. {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)	p.A725S(1)		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						TGTGCTTTGCGCCTGCAATGG	0.478																																					p.A725T		Atlas-SNP	.											LAMC1,NS,carcinoma,0,1	LAMC1	176	1	1	Substitution - Missense(1)	lung(1)	c.G2173A						scavenged	.	G	THR/ALA	3,4403	6.2+/-15.9	0,3,2200	132	117	122		2173	1.5	0.5	1	dbSNP_134	122	4,8596	3.7+/-12.6	0,4,4296	yes	missense	LAMC1	NM_002293.3	58	0,7,6496	AA,AG,GG		0.0465,0.0681,0.0538	benign	725/1610	183091040	7,12999	2203	4300	6503	SO:0001583	missense	3915	exon12			CTTTGCGCCTGCA	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.2173G>A	1.37:g.183091040G>A	ENSP00000258341:p.Ala725Thr	103	1	0.00970874		146	88	0.60274	NM_002293	Q5VYE7	Missense_Mutation	SNP	ENST00000258341.4	37	CCDS1351.1	.	.	.	.	.	.	.	.	.	.	G	1.387	-0.581931	0.03827	6.81E-4	4.65E-4	ENSG00000135862	ENST00000258341	T	0.61627	0.09	5.17	1.54	0.23209	EGF-like, laminin (3);	0.249221	0.46442	N	0.000296	T	0.17959	0.0431	N	0.00621	-1.32	0.19945	N	0.999948	B	0.02656	0.0	B	0.04013	0.001	T	0.29027	-1.0025	10	0.07990	T	0.79	.	5.4496	0.16556	0.6007:0.0:0.2809:0.1184	.	725	P11047	LAMC1_HUMAN	T	725	ENSP00000258341:A725T	ENSP00000258341:A725T	A	+	1	0	LAMC1	181357663	0.001000	0.12720	0.533000	0.28001	0.645000	0.38454	0.530000	0.23036	0.013000	0.14918	-0.946000	0.02672	GCC	G|0.999;A|0.001	0.001	strong		0.478	LAMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085954.2	NM_002293		A	183091040	G	A	183091040	3	1	30	1	0	0	0	0	1	0	0	0	8623	1087	38	1	2219	1	LAMC1	1	183091040	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	11311	183091040	66159581	57	13208											
ZNF281	23528	hgsc.bcm.edu	37	chr1	200378495	200378495	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aacccccaggaggtcctctgCgaggggaaggccgcggctga	8	4	16	13	3	1	1	0	1	1	0	2	4	2	3	4	6	2	1	4	6	2	0	rs374232799	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:200378495C>T	ENST00000294740.3	-	2	463	c.339G>A	c.(337-339)tcG>tcA	p.S113S	ZNF281_ENST00000367352.3_Silent_p.S77S|ZNF281_ENST00000367353.1_Silent_p.S113S	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	113					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						AGGTCCTCTGCGAGGGGAAGG	0.662																																					p.S113S		Atlas-SNP	.											.	ZNF281	74	.	0			c.G339A						PASS	.	C		0,4176		0,0,2088	7	6	6		339	3.2	1	1		6	2,8178		0,2,4088	no	coding-synonymous	ZNF281	NM_012482.3		0,2,6176	TT,TC,CC		0.0244,0.0,0.0162		113/896	200378495	2,12354	2088	4090	6178	SO:0001819	synonymous_variant	23528	exon2			CCTCTGCGAGGGG	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.339G>A	1.37:g.200378495C>T		43	0	0		38	26	0.684211	NM_012482	A6NF48|B3KMX2|Q5RKW5|Q9NY92	Silent	SNP	ENST00000294740.3	37	CCDS1402.1																																																																																			.	.	none		0.662	ZNF281-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086879.2	NM_012482		T	200378495	C	T	200378495	2	4	30	1	0	0	0	0	0	0	0	1	17833	755	27	1		1	ZNF281	1	200378495	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	17287455	200378495	48872126	58	13209											
IPO9	55705	hgsc.bcm.edu	37	chr1	201798367	201798367	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggcggcagctggtgcggcCtccgggctgccgggtccagt	2	6	19	14	5	0	0	0	0	0	0	2	0	2	0	4	6	3	3	4	6	0	0	rs537589191		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:201798367C>T	ENST00000361565.4	+	1	99	c.30C>T	c.(28-30)gcC>gcT	p.A10A	IPO9_ENST00000464348.1_3'UTR|IPO9-AS1_ENST00000421159.1_RNA|IPO9-AS1_ENST00000421449.1_RNA|IPO9-AS1_ENST00000413035.1_RNA	NM_018085.4	NP_060555.2	Q96P70	IPO9_HUMAN	importin 9	10					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						CTGGTGCGGCCTCCGGGCTGC	0.711													C|||	1	0.000199681	0.0	0.0	5008	,	,		9698	0.0		0.0	False		,,,				2504	0.001				p.A10A		Atlas-SNP	.											.	IPO9	98	.	0			c.C30T						PASS	.						10	12	12					1																	201798367		2164	4234	6398	SO:0001819	synonymous_variant	55705	exon1			TGCGGCCTCCGGG	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.30C>T	1.37:g.201798367C>T		44	0	0		60	19	0.316667	NM_018085	B1ASV5|Q8N1Y1|Q8N3I2|Q8NCG9|Q96SU6|Q9NW01|Q9P0A8|Q9ULM8	Silent	SNP	ENST00000361565.4	37	CCDS1415.1																																																																																			.	.	none		0.711	IPO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087088.1	NM_018085		T	201798367	C	T	201798367	2	4	30	1	0	0	0	0	0	0	0	1	7808	668	24	2		2	IPO9	1	201798367	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1419872	201798367	47452254	59	13210											
SLC26A9	115019	hgsc.bcm.edu	37	chr1	205884508	205884508	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagggcggtcagggtctctgCgtgaaacatgctcccgaaca	9	7	13	12	3	2	1	1	1	1	0	4	2	3	1	1	3	4	1	1	3	2	0	rs147005854		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:205884508C>T	ENST00000367135.3	-	21	2466	c.2353G>A	c.(2353-2355)Gca>Aca	p.A785T	SLC26A9_ENST00000340781.4_Missense_Mutation_p.A785T|SLC26A9_ENST00000367134.2_Missense_Mutation_p.A785T	NM_052934.3	NP_443166.1	Q7LBE3	S26A9_HUMAN	solute carrier family 26 (anion exchanger), member 9	785					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)			AGGGTCTCTGCGTGAAACATG	0.577													C|||	1	0.000199681	0.0	0.0	5008	,	,		19734	0.0		0.001	False		,,,				2504	0.0				p.A785T		Atlas-SNP	.											.	SLC26A9	176	.	0			c.G2353A						PASS	.	C	THR/ALA,THR/ALA	1,4405	2.1+/-5.4	0,1,2202	108	98	102		2353,2353	-10.9	0	1	dbSNP_134	102	8,8592	5.7+/-21.5	0,8,4292	yes	missense,missense	SLC26A9	NM_052934.3,NM_134325.2	58,58	0,9,6494	TT,TC,CC		0.093,0.0227,0.0692	benign,benign	785/792,785/888	205884508	9,12997	2203	4300	6503	SO:0001583	missense	115019	exon21			TCTCTGCGTGAAA	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.2353G>A	1.37:g.205884508C>T	ENSP00000356103:p.Ala785Thr	180	0	0		254	88	0.346457	NM_134325	A7E2V6|B1AVM8|B1AVM9|B7ZKK2|Q96PK9|Q96RN0	Missense_Mutation	SNP	ENST00000367135.3	37	CCDS30990.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	3.411	-0.120195	0.06838	2.27E-4	9.3E-4	ENSG00000174502	ENST00000340781;ENST00000367135;ENST00000367134	D;D;D	0.92699	-3.09;-2.98;-3.09	5.44	-10.9	0.00192	.	1.255410	0.05466	N	0.552214	T	0.76772	0.4034	N	0.04508	-0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.65307	-0.6200	10	0.11794	T	0.64	.	10.9011	0.47051	0.2271:0.5876:0.0:0.1853	.	785;785	Q7LBE3;B1AVM8	S26A9_HUMAN;.	T	785	ENSP00000341682:A785T;ENSP00000356103:A785T;ENSP00000356102:A785T	ENSP00000341682:A785T	A	-	1	0	SLC26A9	204151131	0.000000	0.05858	0.035000	0.18076	0.935000	0.57460	-2.719000	0.00812	-3.835000	0.00101	-1.327000	0.01280	GCA	C|0.999;T|0.001	0.001	strong		0.577	SLC26A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087742.1	NM_052934		T	205884508	C	T	205884508	3	4	30	1	0	0	0	0	1	0	0	0	14539	768	27	1	322	1	SLC26A9	1	205884508	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	4086141	205884508	43366113	60	13211											
AVPR1B	553	hgsc.bcm.edu	37	chr1	206225260	206225260	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagcatcaacaccatctcaCgggccaagatccgaacagtg	13	5	9	14	2	2	1	2	0	1	1	4	2	3	1	3	1	3	2	3	1	3	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:206225260C>G	ENST00000367126.4	+	1	1285	c.820C>G	c.(820-822)Cgg>Ggg	p.R274G	RP11-38J22.3_ENST00000425896.1_RNA	NM_000707.3	NP_000698.1	P47901	V1BR_HUMAN	arginine vasopressin receptor 1B	274					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)	CACCATCTCACGGGCCAAGAT	0.597																																					p.R274G		Atlas-SNP	.											.	AVPR1B	47	.	0			c.C820G						PASS	.						71	68	69					1																	206225260		2203	4300	6503	SO:0001583	missense	553	exon1			ATCTCACGGGCCA	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.820C>G	1.37:g.206225260C>G	ENSP00000356094:p.Arg274Gly	144	0	0		190	39	0.205263	NM_000707	B0M0J6|Q5TZ00	Missense_Mutation	SNP	ENST00000367126.4	37	CCDS30994.1	.	.	.	.	.	.	.	.	.	.	C	14.44	2.537242	0.45176	.	.	ENSG00000198049	ENST00000367126	T	0.40756	1.02	5.34	-0.645	0.11475	GPCR, rhodopsin-like superfamily (1);	0.081659	0.48767	D	0.000165	T	0.65974	0.2743	M	0.85777	2.775	0.25895	N	0.983424	D	0.89917	1.0	D	0.83275	0.996	T	0.67189	-0.5733	10	0.72032	D	0.01	-31.1727	16.7694	0.85533	0.7528:0.2472:0.0:0.0	.	274	P47901	V1BR_HUMAN	G	274	ENSP00000356094:R274G	ENSP00000356094:R274G	R	+	1	2	AVPR1B	204391883	0.001000	0.12720	0.110000	0.21437	0.836000	0.47400	0.017000	0.13399	-0.086000	0.12550	0.462000	0.41574	CGG	.	.	none		0.597	AVPR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087996.1	NM_000707		G	206225260	C	G	206225260	3	3	30	1	0	0	0	0	1	0	0	0	1232	527	19	4	822	4	AVPR1B	1	206225260	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	340752	206225260	43025361	61	13212											
LIN9	286826	hgsc.bcm.edu	37	chr1	226474035	226474035	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaaaaacattatttttaccTccgtggttttcccataagcc	12	14	4	11	1	0	0	0	0	0	0	2	0	2	0	4	1	3	1	4	1	5	7			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:226474035T>C	ENST00000328205.5	-	6	1116	c.571A>G	c.(571-573)Aga>Gga	p.R191G	LIN9_ENST00000481685.1_Splice_Site_p.R156G|LIN9_ENST00000366801.1_Splice_Site_p.R140G	NM_173083.3	NP_775106.2	Q5TKA1	LIN9_HUMAN	lin-9 DREAM MuvB core complex component	175	Sufficient for interaction with RB1.				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)		TATTTTTACCTCCGTGGTTTT	0.348																																					p.R191G	Ovarian(197;1696 2974 11248 14117)	Atlas-SNP	.											.	LIN9	57	.	0			c.A571G						PASS	.						50	55	53					1																	226474035		2202	4298	6500	SO:0001630	splice_region_variant	286826	exon6			TTTACCTCCGTGG	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.572+1A>G	1.37:g.226474035T>C		79	0	0		99	5	0.050505	NM_173083	Q5U5L8|Q5U7E1|Q6PI55|Q6ZTV4|Q7Z3J1	Missense_Mutation	SNP	ENST00000328205.5	37	CCDS1553.1	.	.	.	.	.	.	.	.	.	.	T	16.75	3.208799	0.58343	.	.	ENSG00000183814	ENST00000460719;ENST00000328205;ENST00000366808;ENST00000366801;ENST00000481685;ENST00000366807	.	.	.	5.85	5.85	0.93711	.	0.042455	0.85682	D	0.000000	D	0.86033	0.5836	M	0.93062	3.375	0.80722	D	1	D;P;D	0.62365	0.989;0.884;0.991	D;P;D	0.78314	0.916;0.891;0.991	D	0.89383	0.3683	9	0.87932	D	0	.	16.2265	0.82298	0.0:0.0:0.0:1.0	.	156;175;325	C9J5J4;Q5TKA1;B1ANK3	.;LIN9_HUMAN;.	G	151;191;246;140;156;325	.	ENSP00000329102:R191G	R	-	1	2	LIN9	224540658	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.751000	0.62169	2.233000	0.73108	0.533000	0.62120	AGA	.	.	none		0.348	LIN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091523.2	NM_173083	Missense_Mutation	C	226474035	T	C	226474035	5	2	30	1	0	0	0	0	0	0	1	0	8822	1565	54	3	1145	3	LIN9	1	226474035	Splice_Site	SNP	T	TCGA-GR-7353-01A-11D-2210-10	20248775	226474035	22776586	62	13213											
C1orf35	79169	hgsc.bcm.edu	37	chr1	228290223	228290223	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggtccacgcccttctcctcGgggtcgcctccttcccgctt	1	11	9	20	5	1	0	0	0	1	0	7	0	4	0	6	3	0	1	6	3	0	3	rs377443672	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:228290223G>C	ENST00000272139.4	-	4	564	c.330C>G	c.(328-330)ccC>ccG	p.P110P	C1orf35_ENST00000472617.1_5'UTR	NM_024319.2	NP_077295.1	Q9BU76	MMTA2_HUMAN	chromosome 1 open reading frame 35	110							poly(A) RNA binding (GO:0044822)			large_intestine(1)|lung(1)|skin(1)	3		Prostate(94;0.0488)				CCTTCTCCTCGGGGTCGCCTC	0.721													G|||	5	0.000998403	0.0008	0.0014	5008	,	,		9295	0.0		0.003	False		,,,				2504	0.0				p.P110P		Atlas-SNP	.											.	C1orf35	17	.	0			c.C330G						PASS	.	G		0,4340		0,0,2170	10	13	12		330	-8.1	0.6	1		12	9,8471		0,9,4231	no	coding-synonymous	C1orf35	NM_024319.2		0,9,6401	CC,CG,GG		0.1061,0.0,0.0702		110/264	228290223	9,12811	2170	4240	6410	SO:0001819	synonymous_variant	79169	exon4			CTCCTCGGGGTCG	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.330C>G	1.37:g.228290223G>C		148	0	0		175	66	0.377143	NM_024319	Q6P5Y0|Q6ZTZ6|Q6ZWA6|Q8IZH3	Silent	SNP	ENST00000272139.4	37	CCDS1566.1																																																																																			.	.	none		0.721	C1orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092245.1	NM_024319		C	228290223	G	C	228290223	2	2	30	1	0	0	0	0	0	0	0	1	2040	1103	39	4		4	C1orf35	1	228290223	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1816188	228290223	20960398	63	13214											
TSNAX	7257	hgsc.bcm.edu	37	chr1	231665038	231665038	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	aaaaggaagcatgacaatttCccacataaccaaagaagaga	21	5	7	8	0	0	3	0	1	0	2	1	5	1	4	2	1	2	1	2	1	7	2	rs138421350	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:231665038C>T	ENST00000366639.4	+	2	212	c.54C>T	c.(52-54)ttC>ttT	p.F18F	RP11-295G20.2_ENST00000450783.1_RNA|TSNAX-DISC1_ENST00000602962.1_Silent_p.F18F|RP11-295G20.2_ENST00000440665.1_RNA|RP11-295G20.2_ENST00000425412.1_RNA|RP11-295G20.2_ENST00000416221.1_RNA|TSNAX_ENST00000602825.1_3'UTR|RP11-295G20.2_ENST00000454631.1_RNA	NM_005999.2	NP_005990.1	Q99598	TSNAX_HUMAN	translin-associated factor X	18					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)				ATGACAATTTCCCACATAACC	0.398													C|||	3	0.000599042	0.0	0.0014	5008	,	,		18625	0.0		0.0	False		,,,				2504	0.002				p.F18F		Atlas-SNP	.											.	TSNAX	14	.	0			c.C54T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	174	158	163		54	2.5	1	1	dbSNP_134	163	8,8592	7.1+/-27.0	0,8,4292	no	coding-synonymous	TSNAX	NM_005999.2		0,10,6493	TT,TC,CC		0.093,0.0454,0.0769		18/291	231665038	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	7257	exon2			CAATTTCCCACAT	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.54C>T	1.37:g.231665038C>T		143	0	0		190	67	0.352632	NM_005999	B1APC6	Silent	SNP	ENST00000366639.4	37	CCDS1596.1																																																																																			C|0.999;T|0.001	0.001	strong		0.398	TSNAX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095267.2	NM_005999		T	231665038	C	T	231665038	2	4	30	1	0	0	0	0	0	0	0	1	16646	854	30	2		2	TSNAX	1	231665038	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	3374815	231665038	17585583	64	13215											
DISC1	27185	hgsc.bcm.edu	37	chr1	231902975	231902975	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcttgcacgtgtccatcaCgagacgagactggcttcttc	8	10	10	13	3	2	2	1	0	1	2	4	4	3	2	1	1	2	3	1	1	0	3	rs28930675	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:231902975C>T	ENST00000602281.1	+	5	1411	c.1358C>T	c.(1357-1359)aCg>aTg	p.T453M	TSNAX-DISC1_ENST00000602962.1_3'UTR|DISC1_ENST00000539444.1_Missense_Mutation_p.T453M|DISC1_ENST00000366633.3_Missense_Mutation_p.T453M|DISC1_ENST00000366637.3_5'UTR|DISC1_ENST00000439617.2_Missense_Mutation_p.T453M|DISC1_ENST00000535983.1_Missense_Mutation_p.T453M|DISC1_ENST00000366636.4_Missense_Mutation_p.T453M|DISC1_ENST00000537876.1_Missense_Mutation_p.T453M|DISC1_ENST00000602873.1_Missense_Mutation_p.T103M	NM_001164542.1|NM_001164544.1	NP_001158014.1|NP_001158016.1	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	453	Interaction with TRAF3IP1.|Necessary and sufficient for interaction with PCNT and localization at the centrosome.|Required for localization to punctate cytoplasmic foci.				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)				GTGTCCATCACGAGACGAGAC	0.507													C|||	7	0.00139776	0.0008	0.0	5008	,	,		18597	0.0		0.001	False		,,,				2504	0.0051				p.T485M		Atlas-SNP	.											.	DISC1	207	.	0			c.C1454T						PASS	.	C	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	1,4405	2.1+/-5.4	0,1,2202	111	98	102		1358,1358,1454,1358,1358,,1358,1358,1358,1358,1358,1358,1358,1358,308,1358	3.7	0.2	1	dbSNP_125	102	25,8575	18.5+/-59.3	0,25,4275	yes	missense,missense,missense,missense,missense,intron,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	DISC1	NM_001012957.1,NM_001012959.1,NM_001164537.1,NM_001164538.1,NM_001164539.1,NM_001164540.1,NM_001164541.1,NM_001164542.1,NM_001164544.1,NM_001164545.1,NM_001164546.1,NM_001164547.1,NM_001164548.1,NM_001164549.1,NM_001164556.1,NM_018662.2	81,81,81,81,81,,81,81,81,81,81,81,81,81,81,81	0,26,6477	TT,TC,CC		0.2907,0.0227,0.1999	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	453/833,453/679,485/887,453/804,453/756,,453/696,453/682,453/663,453/580,453/560,453/560,453/552,453/548,103/202,453/855	231902975	26,12980	2203	4300	6503	SO:0001583	missense	27185	exon6			CCATCACGAGACG	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.1358C>T	1.37:g.231902975C>T	ENSP00000473425:p.Thr453Met	108	0	0		124	32	0.258065	NM_001164537	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Missense_Mutation	SNP	ENST00000602281.1	37	CCDS59205.1	3	0.0013736263736263737	2	0.0040650406504065045	0	0.0	0	0.0	1	0.0013192612137203166	C	12.61	1.989191	0.35131	2.27E-4	0.002907	ENSG00000162946	ENST00000439617;ENST00000366637;ENST00000366636;ENST00000366638;ENST00000535983;ENST00000537876;ENST00000366633;ENST00000539444;ENST00000295051;ENST00000535944	T;T;T;T;T;T;T;T	0.13901	2.92;2.73;2.72;2.57;2.9;2.57;2.57;2.55	3.74	3.74	0.42951	.	0.423266	0.24527	N	0.037752	T	0.23572	0.0570	M	0.62723	1.935	0.20638	N	0.999871	D;D;D;D;D;D;D;P;D;D;P;D;D;D;D;D;D;P	0.64830	0.992;0.992;0.988;0.983;0.989;0.966;0.979;0.941;0.994;0.988;0.941;0.994;0.988;0.979;0.988;0.979;0.988;0.941	P;P;P;P;P;B;B;B;P;P;B;P;P;B;P;B;P;B	0.54346	0.731;0.749;0.504;0.516;0.512;0.367;0.434;0.407;0.663;0.663;0.236;0.663;0.59;0.434;0.59;0.434;0.663;0.236	T	0.03413	-1.1039	10	0.59425	D	0.04	-3.9113	9.0698	0.36486	0.0:0.8923:0.0:0.1077	rs28930675	485;485;453;453;453;453;453;103;453;453;453;453;453;453;453;453;453;453	C4P096;E2QRA4;C4P0A3;C4P098;C4P0A1;C4P0A4;A6NLH2;C4P0C1;C4P0A5;C4P095;C4P0B6;C4P0C4;C4P0B1;A7E2W8;Q5T409;Q9NRI5-2;Q9NRI5;Q9NRI5-3	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;DISC1_HUMAN;.	M	453;453;453;485;453;453;453;453;453;453	ENSP00000403888:T453M;ENSP00000355596:T453M;ENSP00000443996:T453M;ENSP00000440909:T453M;ENSP00000355593:T453M;ENSP00000440953:T453M;ENSP00000295051:T453M;ENSP00000441193:T453M	ENSP00000295051:T453M	T	+	2	0	DISC1	229969598	0.470000	0.25854	0.174000	0.22961	0.391000	0.30476	1.717000	0.37991	2.063000	0.61619	0.655000	0.94253	ACG	C|0.998;T|0.002	0.002	strong		0.507	DISC1-019	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467451.1	NM_018662		T	231902975	C	T	231902975	3	4	30	1	0	0	0	0	1	0	0	0	4540	536	19	1	1739	1	DISC1	1	231902975	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	237937	231902975	17347646	65	13216											
ARID4B	51742	hgsc.bcm.edu	37	chr1	235383742	235383742	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgtttcattttcctccttaaCttttatttcttttacatttt	6	26	1	8	0	2	0	1	0	1	0	4	0	4	0	2	0	2	1	2	0	3	11	rs148132837		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:235383742C>G	ENST00000264183.3	-	15	1779	c.1282G>C	c.(1282-1284)Gtt>Ctt	p.V428L	ARID4B_ENST00000366603.2_Missense_Mutation_p.V428L|ARID4B_ENST00000349213.3_Missense_Mutation_p.V428L	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	428	Glu-rich.				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)			TCCTCCTTAACTTTTATTTCT	0.348													C|||	1	0.000199681	0.0	0.0	5008	,	,		14311	0.0		0.001	False		,,,				2504	0.0				p.V428L		Atlas-SNP	.											.	ARID4B	142	.	0			c.G1282C						PASS	.	C	LEU/VAL,LEU/VAL,LEU/VAL	0,4406		0,0,2203	128	118	121		1282,1282,1282	-0.5	1	1	dbSNP_134	121	9,8585	7.1+/-27.0	0,9,4288	yes	missense,missense,missense	ARID4B	NM_001206794.1,NM_016374.5,NM_031371.3	32,32,32	0,9,6491	GG,GC,CC		0.1047,0.0,0.0692	benign,benign,benign	428/1313,428/1313,428/1227	235383742	9,12991	2203	4297	6500	SO:0001583	missense	51742	exon15			CCTTAACTTTTAT	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.1282G>C	1.37:g.235383742C>G	ENSP00000264183:p.Val428Leu	405	0	0		487	158	0.324435	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	37	CCDS31061.1	.	.	.	.	.	.	.	.	.	.	C	5.309	0.242397	0.10077	0.0	0.001047	ENSG00000054267	ENST00000391856;ENST00000349213;ENST00000366603;ENST00000264183;ENST00000439834;ENST00000418304	T;T;T;T	0.22945	1.95;1.93;1.93;1.97	5.29	-0.47	0.12131	.	0.806611	0.11942	N	0.514583	T	0.13586	0.0329	N	0.19112	0.55	0.25879	N	0.983618	B;B;B;B	0.12013	0.005;0.005;0.005;0.003	B;B;B;B	0.15052	0.007;0.012;0.007;0.003	T	0.36986	-0.9725	10	0.09084	T	0.74	-3.7761	10.6262	0.45508	0.0:0.4311:0.0:0.5689	.	109;428;428;428	Q4LE39-4;Q4LE39-3;Q4LE39-2;Q4LE39	.;.;.;ARI4B_HUMAN	L	428	ENSP00000264184:V428L;ENSP00000355562:V428L;ENSP00000264183:V428L;ENSP00000391497:V428L	ENSP00000264183:V428L	V	-	1	0	ARID4B	233450365	0.953000	0.32496	0.997000	0.53966	0.690000	0.40134	-0.041000	0.12084	-0.034000	0.13713	0.609000	0.83330	GTT	C|0.999;G|0.001	0.001	strong		0.348	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374		G	235383742	C	G	235383742	3	3	30	1	0	0	0	0	1	0	0	0	920	565	20	4	2696	4	ARID4B	1	235383742	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	3480767	235383742	13866879	66	13217											
AHCTF1	25909	hgsc.bcm.edu	37	chr1	247051714	247051714	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatgcagactagcaggaggAtattttcctgtgcctccttc	9	12	9	11	0	0	1	0	0	0	1	3	3	2	3	3	2	3	2	3	2	2	5	rs144599339	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:247051714A>G	ENST00000391829.2	-	18	2373	c.2250T>C	c.(2248-2250)taT>taC	p.Y750Y	AHCTF1_ENST00000470300.1_5'UTR|AHCTF1_ENST00000326225.3_Silent_p.Y759Y|AHCTF1_ENST00000366508.1_Silent_p.Y785Y			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	750	Necessary for cytoplasmic 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)			TAGCAGGAGGATATTTTCCTG	0.463													A|||	13	0.00259585	0.0	0.0014	5008	,	,		18465	0.0		0.006	False		,,,				2504	0.0061				p.Y759Y	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.T2277C						PASS	.	A		3,4403	6.2+/-15.9	0,3,2200	134	125	128		2277	-1.4	1	1	dbSNP_134	128	54,8546	33.8+/-87.4	0,54,4246	no	coding-synonymous	AHCTF1	NM_015446.4		0,57,6446	GG,GA,AA		0.6279,0.0681,0.4383		759/2276	247051714	57,12949	2203	4300	6503	SO:0001819	synonymous_variant	25909	exon18			AGGAGGATATTTT		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.2250T>C	1.37:g.247051714A>G		477	1	0.00209644		565	328	0.580531	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Silent	SNP	ENST00000391829.2	37																																																																																				A|0.997;G|0.003	0.003	strong		0.463	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446		G	247051714	A	G	247051714	2	3	30	1	0	0	0	0	0	0	0	1	408	340	12	3		3	AHCTF1	1	247051714	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	11667972	247051714	2198907	67	13218											
OR2T8	343172	hgsc.bcm.edu	37	chr1	248084470	248084471	+	Frame_Shift_Ins	INS	-	-	G																															tctcctgattcactgggaccINSaccggctccacacgcccatg																								rs140846339|rs149623571|rs547311711	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr1:248084470_248084471insG	ENST00000319968.4	+	1	151_152	c.151_152insG	c.(151-153)cacfs	p.H51fs		NM_001005522.1	NP_001005522.1	A6NH00	OR2T8_HUMAN	olfactory receptor, family 2, subfamily T, member 8	51						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H51D(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(20)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34	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;0.0211)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			TCACTGGGACCACCGGCTCCAC	0.535																																					p.H51fs		Atlas-Indel	.											OR2T8,rectum,carcinoma,0,2	OR2T8	67	2	1	Substitution - Missense(1)	large_intestine(1)	c.151_152insG						PASS	.																																			SO:0001589	frameshift_variant	343172	exon1			.		CCDS31100.1	1q44	2012-08-09		2004-03-10	ENSG00000177462	ENSG00000177462		"GPCR / Class A : Olfactory receptors"	15020	protein-coding gene	gene with protein product				OR2T8P			Standard	XM_005273117		Approved		uc010pzc.2	A6NH00	OTTHUMG00000040205	Exception_encountered	1.37:g.248084470_248084471insG	ENSP00000326225:p.His51fs	726	0	0		441	69	0.156463	NM_001005522		Frame_Shift_Ins	INS	ENST00000319968.4	37	CCDS31100.1																																																																																			.	.	none		0.535	OR2T8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096862.1	NM_001005522		G	248084471	-	G	248084470	7	5	30	1	0	1	1	0	0	0	0	0	11039	594	21	0	153	0	OR2T8	1	248084470	Frame_Shift_Ins	INS	-	TCGA-GR-7353-01A-11D-2210-10	1032756	248084470	1166151	68	13219											
ITSN2	50618	hgsc.bcm.edu	37	chr2	24426581	24426581	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcatgcagcagcagtcggcGggtcatagggcctttgcttt	6	11	13	11	2	2	0	2	0	0	0	3	0	2	0	1	3	4	4	1	3	1	3	rs140804905	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:24426581G>A	ENST00000355123.4	-	40	5451	c.5008C>T	c.(5008-5010)Cgc>Tgc	p.R1670C	AC008073.9_ENST00000429717.1_RNA|ITSN2_ENST00000361999.3_Missense_Mutation_p.R1643C	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	1670					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)					AGCAGTCGGCGGGTCATAGGG	0.507													G|||	4	0.000798722	0.0023	0.0	5008	,	,		16966	0.0		0.001	False		,,,				2504	0.0				p.R1670C		Atlas-SNP	.											.	ITSN2	224	.	0			c.C5008T						PASS	.	G	CYS/ARG,CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	82	83	83		5008,4927	4.5	1	2	dbSNP_134	83	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	ITSN2	NM_006277.2,NM_019595.3	180,180	0,6,6497	AA,AG,GG		0.0465,0.0454,0.0461	probably-damaging,probably-damaging	1670/1698,1643/1671	24426581	6,13000	2203	4300	6503	SO:0001583	missense	50618	exon40			GTCGGCGGGTCAT	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.5008C>T	2.37:g.24426581G>A	ENSP00000347244:p.Arg1670Cys	82	0	0		77	32	0.415584	NM_006277	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Missense_Mutation	SNP	ENST00000355123.4	37	CCDS1710.2	5	0.0022893772893772895	4	0.008130081300813009	0	0.0	0	0.0	1	0.0013192612137203166	G	16.42	3.118003	0.56505	4.54E-4	4.65E-4	ENSG00000198399	ENST00000361999;ENST00000355123;ENST00000380868	T;T;T	0.67523	-0.27;-0.27;-0.27	5.46	4.52	0.55395	C2 calcium/lipid-binding domain, CaLB (1);	0.412335	0.15639	U	0.251972	T	0.69611	0.3130	L	0.54323	1.7	0.53005	D	0.999968	D;D	0.89917	1.0;1.0	D;P	0.65773	0.938;0.869	T	0.73877	-0.3844	10	0.87932	D	0	.	11.956	0.52981	0.0:0.0:0.6677:0.3323	.	1643;1670	Q9NZM3-2;Q9NZM3	.;ITSN2_HUMAN	C	1643;1670;1643	ENSP00000354561:R1643C;ENSP00000347244:R1670C;ENSP00000370250:R1643C	ENSP00000347244:R1670C	R	-	1	0	ITSN2	24280085	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	4.498000	0.60373	2.735000	0.93741	0.561000	0.74099	CGC	G|0.999;A|0.001	0.001	strong		0.507	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277		A	24426581	G	A	24426581	3	1	30	1	0	0	0	0	1	0	0	0	7936	1116	39	1	89	1	ITSN2	2	24426581	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10		24426581	218772792	69	13220											
ALK	238	hgsc.bcm.edu	37	chr2	30143499	30143499	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gtggaaagcagcagcggcagGagccacaggagcccgatggc	11	2	17	11	2	0	0	0	0	0	0	0	4	0	3	2	5	5	3	2	5	1	0	rs4358080	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:30143499G>C	ENST00000389048.3	-	1	933	c.27C>G	c.(25-27)ctC>ctG	p.L9L	ALK_ENST00000431873.1_Silent_p.L9L	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	9					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)	GCAGCGGCAGGAGCCACAGGA	0.736			"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				C|||	4476	0.89377	0.8003	0.938	5008	,	,		12200	0.998		0.8837	False		,,,				2504	0.8916				p.L9L		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"L, E, M"	.	ALK	533	.	0			c.C27G						PASS	.	C		2838,380		1249,340,20	3	5	4		27	2.1	1	2	dbSNP_111	4	6073,509		2805,463,23	no	coding-synonymous	ALK	NM_004304.4		4054,803,43	CC,CG,GG		7.7332,11.8086,9.0714		9/1621	30143499	8911,889	1609	3291	4900	SO:0001819	synonymous_variant	238	exon1	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	CGGCAGGAGCCAC	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.27C>G	2.37:g.30143499G>C		0	0	.		4	4	1	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			G|0.120;C|0.880	0.880	strong		0.736	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304		C	30143499	G	C	30143499	2	2	30	1	0	0	0	0	0	0	0	1	525	1161	41	4		4	ALK	2	30143499	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	5716918	30143499	213055874	70	13221											
XDH	7498	hgsc.bcm.edu	37	chr2	31606682	31606682	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgggcagacaatcataggAaacagcatattcttgaactt	14	10	9	8	0	2	2	1	1	1	1	2	3	2	3	0	2	3	3	0	2	5	5	rs145596057	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:31606682A>G	ENST00000379416.3	-	10	873	c.825T>C	c.(823-825)ttT>ttC	p.F275F	XDH_ENST00000491727.1_5'UTR	NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	275	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)	CAATCATAGGAAACAGCATAT	0.493													A|||	2	0.000399361	0.0	0.0	5008	,	,		18724	0.0		0.002	False		,,,				2504	0.0				p.F275F	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.T825C						PASS	.	A		1,4405	2.1+/-5.4	0,1,2202	115	101	106		825	0.8	0.9	2	dbSNP_134	106	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	XDH	NM_000379.3		0,15,6488	GG,GA,AA		0.1628,0.0227,0.1153		275/1334	31606682	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	7498	exon10			CATAGGAAACAGC	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.825T>C	2.37:g.31606682A>G		165	0	0		166	85	0.512048	NM_000379	Q16681|Q16712|Q4PJ16	Silent	SNP	ENST00000379416.3	37	CCDS1775.1																																																																																			A|0.999;G|0.001	0.001	strong		0.493	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379		G	31606682	A	G	31606682	2	3	30	1	0	0	0	0	0	0	0	1	17441	243	9	3		3	XDH	2	31606682	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	1463183	31606682	211592691	71	13222											
FAM98A	25940	hgsc.bcm.edu	37	chr2	33820635	33820635	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caagcacagagtttggtaaaCtcgggggaactggctccagc	11	7	13	10	1	0	1	0	0	0	1	2	2	1	2	1	4	4	4	1	4	4	2	rs72785999	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:33820635C>T	ENST00000238823.8	-	2	263	c.123G>A	c.(121-123)gaG>gaA	p.E41E	FAM98A_ENST00000498340.1_5'UTR|FAM98A_ENST00000441530.2_5'UTR|FAM98A_ENST00000403368.1_Silent_p.E41E			Q8NCA5	FA98A_HUMAN	family with sequence similarity 98, member A	41							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)					GTTTGGTAAACTCGGGGGAAC	0.448													C|||	15	0.00299521	0.0	0.0029	5008	,	,		15482	0.0		0.0099	False		,,,				2504	0.0031				p.E41E		Atlas-SNP	.											.	FAM98A	42	.	0			c.G123A						PASS	.	C		11,4395	17.9+/-39.9	1,9,2193	105	107	106		123	4.1	1	2	dbSNP_130	106	74,8526	42.2+/-99.7	0,74,4226	no	coding-synonymous	FAM98A	NM_015475.3		1,83,6419	TT,TC,CC		0.8605,0.2497,0.6535		41/519	33820635	85,12921	2203	4300	6503	SO:0001819	synonymous_variant	25940	exon2			GGTAAACTCGGGG		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.123G>A	2.37:g.33820635C>T		133	0	0		171	94	0.549708	NM_015475	B2RNA2|Q9Y3Y6	Silent	SNP	ENST00000238823.8	37	CCDS33179.1																																																																																			C|0.995;T|0.005	0.005	strong		0.448	FAM98A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325457.2	NM_015475		T	33820635	C	T	33820635	2	4	30	1	0	0	0	0	0	0	0	1	5664	564	20	2		2	FAM98A	2	33820635	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	2213953	33820635	209378738	72	13223											
DHX57	90957	hgsc.bcm.edu	37	chr2	39042718	39042718	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgggcccttttctcaattTcccttgctctgagcccttcc	3	16	6	16	0	2	1	1	1	2	0	5	1	4	1	4	1	2	1	4	1	1	6	rs150735204	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:39042718T>G	ENST00000295373.6	-	20	3677	c.3551A>C	c.(3550-3552)gAa>gCa	p.E1184A		NM_198963.1	NP_945314.1	Q6P158	DHX57_HUMAN	DEAH (Asp-Glu-Ala-Asp/His) box polypeptide 57	1184							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)				TTTCTCAATTTCCCTTGCTCT	0.453													T|||	11	0.00219649	0.0	0.0043	5008	,	,		19870	0.0		0.007	False		,,,				2504	0.001				p.E1184A	Melanoma(191;1090 2095 4375 23729 47341)	Atlas-SNP	.											DHX57,NS,carcinoma,0,1	DHX57	127	1	0			c.A3551C						PASS	.	T	ALA/GLU	5,4401	9.9+/-24.2	0,5,2198	222	207	212		3551	5.3	1	2	dbSNP_134	212	63,8537	39.3+/-95.6	0,63,4237	yes	missense	DHX57	NM_198963.1	107	0,68,6435	GG,GT,TT		0.7326,0.1135,0.5228	benign	1184/1387	39042718	68,12938	2203	4300	6503	SO:0001583	missense	90957	exon20			TCAATTTCCCTTG	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.3551A>C	2.37:g.39042718T>G	ENSP00000295373:p.Glu1184Ala	112	0	0		123	61	0.495935	NM_198963	A2RRC7|Q53SI4|Q6P9G1|Q7Z6H3|Q8NG17|Q96M33	Missense_Mutation	SNP	ENST00000295373.6	37	CCDS1800.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	11.33	1.606871	0.28623	0.001135	0.007326	ENSG00000163214	ENST00000295373	T	0.02787	4.16	5.29	5.29	0.74685	Domain of unknown function DUF1605 (1);	0.241073	0.29046	N	0.013302	T	0.01489	0.0048	N	0.11560	0.145	0.46078	D	0.99885	B;B	0.10296	0.003;0.001	B;B	0.13407	0.009;0.001	T	0.57069	-0.7874	10	0.13470	T	0.59	.	15.5408	0.76043	0.0:0.0:0.0:1.0	.	1184;576	Q6P158;Q59G60	DHX57_HUMAN;.	A	1184	ENSP00000295373:E1184A	ENSP00000295373:E1184A	E	-	2	0	DHX57	38896222	1.000000	0.71417	0.992000	0.48379	0.948000	0.59901	5.728000	0.68531	2.120000	0.65058	0.460000	0.39030	GAA	T|0.996;G|0.004	0.004	strong		0.453	DHX57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219940.2	NM_145646		G	39042718	T	G	39042718	3	3	30	1	0	0	0	0	1	0	0	0	4515	1783	62	5	629	5	DHX57	2	39042718	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	5222083	39042718	204156655	73	13224											
C2orf34	79823	hgsc.bcm.edu	37	chr2	44942450	44942450	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcaagacatcatcacaaggaAtcagaaggctggtgtgttta	14	9	11	7	0	3	2	3	0	0	2	3	3	3	3	0	3	0	3	0	3	5	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:44942450A>G	ENST00000378494.3	+	7	625	c.581A>G	c.(580-582)aAt>aGt	p.N194S		NM_024766.4	NP_079042.1	Q7Z624	CMKMT_HUMAN	calmodulin-lysine N-methyltransferase	194						Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	calmodulin-lysine N-methyltransferase activity (GO:0018025)			breast(2)|large_intestine(3)|lung(5)	10						ATCACAAGGAATCAGAAGGCT	0.363																																					p.N194S		Atlas-SNP	.											.	CAMKMT	20	.	0			c.A581G						PASS	.						87	92	90					2																	44942450		2203	4300	6503	SO:0001583	missense	79823	exon7			CAAGGAATCAGAA		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.581A>G	2.37:g.44942450A>G	ENSP00000367755:p.Asn194Ser	99	0	0		106	45	0.424528	NM_024766	Q4ZG15|Q53SS6|Q8N6P5|Q9H5G8	Missense_Mutation	SNP	ENST00000378494.3	37	CCDS1820.1	.	.	.	.	.	.	.	.	.	.	A	17.82	3.482904	0.63962	.	.	ENSG00000143919	ENST00000378494	T	0.12879	2.64	5.52	5.52	0.82312	.	0.086330	0.85682	D	0.000000	T	0.39279	0.1072	M	0.89478	3.035	0.80722	D	1	D	0.56746	0.977	P	0.61874	0.895	T	0.42050	-0.9474	10	0.72032	D	0.01	-12.628	10.9403	0.47270	0.8434:0.1566:0.0:0.0	.	194	Q7Z624	CMKMT_HUMAN	S	194	ENSP00000367755:N194S	ENSP00000367755:N194S	N	+	2	0	CAMKMT	44795954	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	5.066000	0.64351	2.104000	0.64026	0.528000	0.53228	AAT	.	.	none		0.363	CAMKMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250678.2	NM_024766		G	44942450	A	G	44942450	3	3	30	1	0	0	0	0	1	0	0	0	2165	101	4	3	607	3	C2orf34	2	44942450	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	5899732	44942450	198256923	74	13225											
MSH2	4436	hgsc.bcm.edu	37	chr2	47630528	47630528	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acccagggggtgatcaagtaCatggggccggcaggtgaggg	9	5	19	8	1	1	2	1	2	0	0	1	2	1	2	2	7	1	2	2	7	2	1			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:47630528C>T	ENST00000233146.2	+	1	421	c.198C>T	c.(196-198)taC>taT	p.Y66Y	MSH2_ENST00000543555.1_5'UTR|MSH2_ENST00000406134.1_Silent_p.Y66Y	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	66					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)			TGATCAAGTACATGGGGCCGG	0.706			"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.Y66Y		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.C198T						PASS	.						9	12	11					2																	47630528		2186	4271	6457	SO:0001819	synonymous_variant	4436	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	CAAGTACATGGGG	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.198C>T	2.37:g.47630528C>T		171	0	0		111	62	0.558559	NM_000251	B4E2Z2|O75488	Silent	SNP	ENST00000233146.2	37	CCDS1834.1																																																																																			.	.	none		0.706	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3			T	47630528	C	T	47630528	2	4	30	1	0	0	0	0	0	0	0	1	9879	489	17	2		2	MSH2	2	47630528	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	2688078	47630528	195568845	75	13226											
DNAH6	1768	hgsc.bcm.edu	37	chr2	84926756	84926756	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agcaaagtgcgtcagaagctGcacattgttctctgcatgag	11	10	11	9	1	2	2	1	1	1	1	3	2	2	2	0	0	5	5	0	0	2	2	rs74514752	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:84926756G>A	ENST00000237449.6	+	47	7724	c.7716G>A	c.(7714-7716)ctG>ctA	p.L2572L	DNAH6_ENST00000389394.3_Silent_p.L2572L			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	2572	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						GTCAGAAGCTGCACATTGTTC	0.408													G|||	23	0.00459265	0.0023	0.0101	5008	,	,		20442	0.0		0.0109	False		,,,				2504	0.002				p.L2572L		Atlas-SNP	.											.	DNAH6	194	.	0			c.G7716A						PASS	.	G		3,1381		0,3,689	113	92	99		7716	-0.2	1	2	dbSNP_132	99	43,3139		1,41,1549	no	coding-synonymous	DNAH6	NM_001370.1		1,44,2238	AA,AG,GG		1.3514,0.2168,1.0074		2572/4159	84926756	46,4520	692	1591	2283	SO:0001819	synonymous_variant	1768	exon48			GAAGCTGCACATT	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.7716G>A	2.37:g.84926756G>A		94	0	0		85	38	0.447059	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	37	CCDS46348.1																																																																																			G|0.994;A|0.006	0.006	strong		0.408	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		A	84926756	G	A	84926756	2	1	30	1	0	0	0	0	0	0	0	1	4607	1306	46	2		2	DNAH6	2	84926756	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	37296228	84926756	158272617	76	13227											
COX5B	1329	hgsc.bcm.edu	37	chr2	98264478	98264478	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggtgaagaggacaataccagCgtcgtctggttttggctgca	9	10	14	8	2	1	2	0	1	1	1	2	3	1	3	1	4	3	3	1	4	3	3	rs142899936		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:98264478C>T	ENST00000258424.2	+	4	344	c.297C>T	c.(295-297)agC>agT	p.S99S	COX5B_ENST00000464949.1_3'UTR	NM_001862.2	NP_001853.2	P10606	COX5B_HUMAN	cytochrome c oxidase subunit Vb	99					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						ACAATACCAGCGTCGTCTGGT	0.522																																					p.S99S		Atlas-SNP	.											.	COX5B	9	.	0			c.C297T						PASS	.	C		1,4405		0,1,2202	65	61	62		297	-3.5	0.1	2	dbSNP_134	62	1,8599		0,1,4299	no	coding-synonymous	COX5B	NM_001862.2		0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154		99/130	98264478	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	1329	exon4			TACCAGCGTCGTC	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.297C>T	2.37:g.98264478C>T		182	0	0		151	58	0.384106	NM_001862	Q53YB7|Q96J18|Q99610	Silent	SNP	ENST00000258424.2	37	CCDS2032.1																																																																																			C|1.000;T|0.000	0.000	weak		0.522	COX5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252972.2	NM_001862		T	98264478	C	T	98264478	2	4	30	1	0	0	0	0	0	0	0	1	3775	767	27	1		1	COX5B	2	98264478	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	13337722	98264478	144934895	77	13228											
MGAT4A	11320	hgsc.bcm.edu	37	chr2	99271976	99271976	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtaatctaggttttgctttgTtctccatctgaaataaacat	11	17	6	7	0	3	1	0	1	3	0	4	1	3	1	1	1	2	4	1	1	5	7	rs61748145	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:99271976T>C	ENST00000264968.3	-	7	1069	c.706A>G	c.(706-708)Aca>Gca	p.T236A	MGAT4A_ENST00000461884.1_5'Flank|MGAT4A_ENST00000414521.2_Missense_Mutation_p.T108A|MGAT4A_ENST00000393487.1_Missense_Mutation_p.T236A|MGAT4A_ENST00000409391.1_Missense_Mutation_p.T236A			Q9UM21	MGT4A_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme A	236					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						TTTTGCTTTGTTCTCCATCTG	0.279													T|||	17	0.00339457	0.0008	0.0043	5008	,	,		20215	0.0		0.0099	False		,,,				2504	0.0031				p.T236A		Atlas-SNP	.											.	MGAT4A	51	.	0			c.A706G						PASS	.	T	ALA/THR,ALA/THR	12,4394	21.2+/-45.6	0,12,2191	94	88	90		322,706	5.1	1	2	dbSNP_129	90	92,8506	51.9+/-112.3	0,92,4207	yes	missense,missense	MGAT4A	NM_001160154.1,NM_012214.2	58,58	0,104,6398	CC,CT,TT		1.07,0.2724,0.7998	possibly-damaging,possibly-damaging	108/424,236/536	99271976	104,12900	2203	4299	6502	SO:0001583	missense	11320	exon8			GCTTTGTTCTCCA	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.706A>G	2.37:g.99271976T>C	ENSP00000264968:p.Thr236Ala	99	0	0		98	48	0.489796	NM_012214	B4E2R6|D3DVH6|E9PEN2|Q53S97|Q86Z15	Missense_Mutation	SNP	ENST00000264968.3	37	CCDS2036.1	8	0.003663003663003663	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	4	0.005277044854881266	T	24.9	4.578058	0.86645	0.002724	0.0107	ENSG00000071073	ENST00000393487;ENST00000414521;ENST00000264968;ENST00000409391	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.12	5.12	0.69794	.	0.093140	0.85682	D	0.000000	T	0.63046	0.2478	M	0.90082	3.085	0.80722	D	1	D;D	0.76494	0.999;0.997	D;D	0.83275	0.996;0.992	T	0.73883	-0.3842	10	0.52906	T	0.07	-3.5017	14.3832	0.66926	0.0:0.0:0.0:1.0	rs61748145	108;236	E9PEN2;Q9UM21	.;MGT4A_HUMAN	A	236;108;236;236	ENSP00000377127:T236A;ENSP00000404889:T108A;ENSP00000264968:T236A;ENSP00000386841:T236A	ENSP00000264968:T236A	T	-	1	0	MGAT4A	98638408	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.938000	0.87678	2.044000	0.60594	0.533000	0.62120	ACA	T|0.993;C|0.007	0.007	strong		0.279	MGAT4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252988.2	NM_012214		C	99271976	T	C	99271976	3	2	30	1	0	0	0	0	1	0	0	0	9554	1725	60	3	1016	3	MGAT4A	2	99271976	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	1007498	99271976	143927397	78	13229											
PAX8	7849	hgsc.bcm.edu	37	chr2	113976146	113976146	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgtggcagtggtgggcggTgcactcggccttgatgtgga	4	9	19	9	3	0	1	0	1	0	0	1	2	0	2	2	6	1	2	2	6	0	1	rs368201100	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:113976146T>C	ENST00000429538.3	-	12	1511	c.1317A>G	c.(1315-1317)gcA>gcG	p.A439A	PAX8_ENST00000397647.3_3'UTR|PAX8_ENST00000263335.7_3'UTR|PAX8_ENST00000348715.5_3'UTR|AC016683.6_ENST00000456685.1_RNA	NM_003466.3	NP_003457.1	Q06710	PAX8_HUMAN	paired box 8	439					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						TGGTGGGCGGTGCACTCGGCC	0.517			T	PPARG	follicular thyroid		Thyroid dysgenesis						T|||	8	0.00159744	0.0	0.0014	5008	,	,		17403	0.0		0.006	False		,,,				2504	0.001				p.A439A	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.A1317G						PASS	.	T	,,,	6,3874		0,6,1934	34	40	38		1317,,,	-6.1	0	2		38	37,8203		0,37,4083	no	coding-synonymous,utr-3,utr-3,utr-3	PAX8	NM_003466.3,NM_013952.3,NM_013953.3,NM_013992.3	,,,	0,43,6017	CC,CT,TT		0.449,0.1546,0.3548	,,,	439/451,,,	113976146	43,12077	1940	4120	6060	SO:0001819	synonymous_variant	7849	exon12			GGGCGGTGCACTC	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.1317A>G	2.37:g.113976146T>C		54	0	0		70	32	0.457143	NM_003466	Q09155|Q16337|Q16338|Q16339|Q4ZG35|Q96J49	Silent	SNP	ENST00000429538.3	37	CCDS46398.1	.	.	.	.	.	.	.	.	.	.	T	0.123	-1.122781	0.01785	0.001546	0.00449	ENSG00000125618	ENST00000468980	.	.	.	5.34	-6.12	0.02124	.	.	.	.	.	T	0.51907	0.1702	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56056	-0.8042	4	.	.	.	.	10.6988	0.45915	0.1148:0.5796:0.0:0.3056	.	.	.	.	A	162	.	.	T	-	1	0	PAX8	113692617	0.000000	0.05858	0.014000	0.15608	0.065000	0.16274	-4.294000	0.00258	-0.902000	0.03886	-1.054000	0.02325	ACC	.	.	weak		0.517	PAX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250353.5			C	113976146	T	C	113976146	2	2	30	1	0	0	0	0	0	0	0	1	11494	1683	59	3		3	PAX8	2	113976146	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	14704170	113976146	129223227	79	13230											
PCDP1	200373	hgsc.bcm.edu	37	chr2	120383248	120383248	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agaaagattggccaagcaaaAcaatcgatagcacaaggtga	19	5	10	7	1	0	3	0	1	0	2	1	4	0	3	1	2	3	2	1	2	7	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:120383248A>G	ENST00000413369.3	+	15	1587	c.1500A>G	c.(1498-1500)aaA>aaG	p.K500K	PCDP1_ENST00000602047.1_Silent_p.K214K|PCDP1_ENST00000597189.1_3'UTR	NM_001271049.1	NP_001257978																Colorectal(110;0.196)					GCCAAGCAAAACAATCGATAG	0.428																																					p.K500K		Atlas-SNP	.											.	.	.	.	0			c.A1500G						PASS	.						130	111	117					2																	120383248		2203	4300	6503	SO:0001819	synonymous_variant	0	exon15			AGCAAAACAATCG																												ENST00000413369.3:c.1500A>G	2.37:g.120383248A>G		134	0	0		113	36	0.318584	NM_001271049		Silent	SNP	ENST00000413369.3	37	CCDS33282.2	.	.	.	.	.	.	.	.	.	.	A	2.807	-0.247935	0.05867	.	.	ENSG00000163075	ENST00000443972;ENST00000413057	.	.	.	4.45	0.852	0.18995	.	.	.	.	.	T	0.30885	0.0779	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.25082	-1.0142	4	.	.	.	-6.3731	6.1027	0.20057	0.6942:0.0:0.3058:0.0	.	.	.	.	S	59;48	.	.	N	+	2	0	AC069154.2	120099718	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	0.160000	0.16462	0.142000	0.18901	0.533000	0.62120	AAC	.	.	none		0.428	PCDP1-006	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464236.1			G	120383248	A	G	120383248	2	3	30	1	0	0	0	0	0	0	0	1	11581	40	2	3		3	PCDP1	2	120383248	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	6407102	120383248	122816125	80	13231											
PTPN4	5775	hgsc.bcm.edu	37	chr2	120734589	120734589	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agatttgtatgtgaagctatTttgaaagtttatgaagaagg	14	15	11	1	0	0	5	0	3	0	2	0	5	0	5	0	1	1	3	0	1	7	7			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:120734589T>A	ENST00000263708.2	+	27	3495	c.2724T>A	c.(2722-2724)atT>atA	p.I908I	PTPN4_ENST00000544261.1_Silent_p.I541I	NM_002830.3	NP_002821.1	P29074	PTN4_HUMAN	protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)	908	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)			endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|urinary_tract(1)	30					Alendronate(DB00630)	GTGAAGCTATTTTGAAAGTTT	0.328																																					p.I908I		Atlas-SNP	.											PTPN4,NS,carcinoma,+2,1	PTPN4	89	1	0			c.T2724A						PASS	.						53	54	54					2																	120734589		2202	4299	6501	SO:0001819	synonymous_variant	5775	exon27			AGCTATTTTGAAA		CCDS2129.1	2q14.2	2011-06-09			ENSG00000088179	ENSG00000088179		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9656	protein-coding gene	gene with protein product		176878				1648233	Standard	NM_002830		Approved	PTPMEG	uc002tmf.2	P29074	OTTHUMG00000131436	ENST00000263708.2:c.2724T>A	2.37:g.120734589T>A		119	0	0		133	51	0.383459	NM_002830	B2RBV8|Q9UDA7	Silent	SNP	ENST00000263708.2	37	CCDS2129.1	.	.	.	.	.	.	.	.	.	.	T	4.925	0.171834	0.09391	.	.	ENSG00000088179	ENST00000441089	.	.	.	5.12	3.96	0.45880	.	.	.	.	.	T	0.55016	0.1894	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50048	-0.8873	4	.	.	.	.	6.0894	0.19985	0.1433:0.0767:0.0:0.78	.	.	.	.	I	201	.	.	F	+	1	0	PTPN4	120451059	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	2.465000	0.45075	0.798000	0.33994	0.528000	0.53228	TTT	.	.	none		0.328	PTPN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254233.2			A	120734589	T	A	120734589	2	1	30	1	0	0	0	0	0	0	0	1	12805	1829	64	5		5	PTPN4	2	120734589	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	351341	120734589	122464784	81	13232											
GLI2	2736	hgsc.bcm.edu	37	chr2	121742124	121742124	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctccggaagcatgtgaaaacGgtccacggcccagatgccca	11	5	11	14	3	0	2	0	1	0	1	2	3	2	3	4	3	3	1	4	3	3	0	rs61732852	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:121742124G>A	ENST00000452319.1	+	12	1821	c.1761G>A	c.(1759-1761)acG>acA	p.T587T	GLI2_ENST00000314490.11_Silent_p.T259T|GLI2_ENST00000361492.4_Silent_p.T587T|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)				ATGTGAAAACGGTCCACGGCC	0.597													G|||	22	0.00439297	0.0	0.0043	5008	,	,		19759	0.0		0.0139	False		,,,				2504	0.0051				p.T587T		Atlas-SNP	.											.	GLI2	187	.	0			c.G1761A						PASS	.	G		13,4393	19.1+/-41.9	0,13,2190	154	147	149		1761	-9	0.3	2	dbSNP_129	149	117,8483	61.7+/-123.6	0,117,4183	no	coding-synonymous	GLI2	NM_005270.4		0,130,6373	AA,AG,GG		1.3605,0.2951,0.9995		587/1587	121742124	130,12876	2203	4300	6503	SO:0001819	synonymous_variant	2736	exon11			GAAAACGGTCCAC		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.1761G>A	2.37:g.121742124G>A		206	0	0		180	83	0.461111	NM_005270		Silent	SNP	ENST00000452319.1	37	CCDS33283.1																																																																																			G|0.991;A|0.009	0.009	strong		0.597	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		A	121742124	G	A	121742124	2	1	30	1	0	0	0	0	0	0	0	1	6446	1103	39	1		1	GLI2	2	121742124	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1007535	121742124	121457249	82	13233											
GLI2	2736	hgsc.bcm.edu	37	chr2	121742307	121742307	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacgtcagagccatcaagacCgagagctccggggtaagcgg	11	4	14	12	4	2	3	2	0	0	3	3	4	3	3	3	3	3	2	3	3	2	1	rs13008360	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:121742307C>T	ENST00000452319.1	+	12	2004	c.1944C>T	c.(1942-1944)acC>acT	p.T648T	GLI2_ENST00000314490.11_Silent_p.T320T|GLI2_ENST00000361492.4_Silent_p.T648T|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)				CCATCAAGACCGAGAGCTCCG	0.701													C|||	40	0.00798722	0.0015	0.0101	5008	,	,		16587	0.0		0.0308	False		,,,				2504	0.0				p.T648T		Atlas-SNP	.											GLI2,NS,carcinoma,0,1	GLI2	187	1	0			c.C1944T						scavenged	.	C		26,4366		0,26,2170	21	22	22		1944	-5.5	1	2	dbSNP_121	22	229,8367		4,221,4073	no	coding-synonymous	GLI2	NM_005270.4		4,247,6243	TT,TC,CC		2.664,0.592,1.9634		648/1587	121742307	255,12733	2196	4298	6494	SO:0001819	synonymous_variant	2736	exon11			CAAGACCGAGAGC		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.1944C>T	2.37:g.121742307C>T		126	1	0.00793651		84	47	0.559524	NM_005270		Silent	SNP	ENST00000452319.1	37	CCDS33283.1																																																																																			C|0.984;T|0.016	0.016	strong		0.701	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		T	121742307	C	T	121742307	2	4	30	1	0	0	0	0	0	0	0	1	6446	639	23	1		1	GLI2	2	121742307	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	183	121742307	121457066	83	13234											
CYP27C1	339761	hgsc.bcm.edu	37	chr2	127956964	127956964	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agactcaccgtgtcgacgccGgccagcagcatctcagtcac	9	6	10	16	4	3	1	3	0	1	1	5	2	3	1	3	1	2	2	3	1	0	0	rs149542135	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:127956964G>A	ENST00000335247.7	-	4	670	c.540C>T	c.(538-540)gcC>gcT	p.A180A	CYP27C1_ENST00000409327.1_Silent_p.A180A	NM_001001665.3	NP_001001665.3	Q4G0S4	C27C1_HUMAN	cytochrome P450, family 27, subfamily C, polypeptide 1	180						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)		TGTCGACGCCGGCCAGCAGCA	0.582													G|||	2	0.000399361	0.0	0.0	5008	,	,		19906	0.0		0.002	False		,,,				2504	0.0				p.A180A		Atlas-SNP	.											.	CYP27C1	52	.	0			c.C540T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	158	139	145		540	-2.6	0.9	2	dbSNP_134	145	16,8584	11.2+/-40.8	1,14,4285	no	coding-synonymous	CYP27C1	NM_001001665.3		1,15,6487	AA,AG,GG		0.186,0.0227,0.1307		180/373	127956964	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	339761	exon4			GACGCCGGCCAGC	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.540C>T	2.37:g.127956964G>A		175	0	0		141	72	0.510638	NM_001001665	Q6ZNI7	Silent	SNP	ENST00000335247.7	37	CCDS33285.1																																																																																			G|0.999;A|0.001	0.001	strong		0.582	CYP27C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331046.1	NM_001001665		A	127956964	G	A	127956964	2	1	30	1	0	0	0	0	0	0	0	1	4162	1103	39	1		1	CYP27C1	2	127956964	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	6214657	127956964	115242409	84	13235											
HS6ST1	9394	hgsc.bcm.edu	37	chr2	129025800	129025800	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcggcccggctcgtcggcaTcctcccgcggcagtgcctcc	2	6	13	20	7	0	0	0	0	0	0	5	0	3	0	5	4	1	3	5	4	0	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:129025800T>C	ENST00000259241.6	-	2	1185	c.1172A>G	c.(1171-1173)gAt>gGt	p.D391G		NM_004807.2	NP_004798.3	O60243	H6ST1_HUMAN	heparan sulfate 6-O-sulfotransferase 1	391					angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|labyrinthine layer blood vessel development (GO:0060716)|lung alveolus development (GO:0048286)|neuron development (GO:0048666)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)|sulfotransferase activity (GO:0008146)			endometrium(3)|liver(1)|lung(7)|pancreas(1)|prostate(2)|skin(1)	15	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.117)		CTCGTCGGCATCCTCCCGCGG	0.692																																					p.D391G		Atlas-SNP	.											.	HS6ST1	31	.	0			c.A1172G						PASS	.						21	23	22					2																	129025800		2013	4161	6174	SO:0001583	missense	9394	exon2			TCGGCATCCTCCC	AB006179	CCDS42748.1	2q21	2010-03-19		2002-08-23	ENSG00000136720	ENSG00000136720		"Sulfotransferases, membrane-bound"	5201	protein-coding gene	gene with protein product		604846		HS6ST		9535912	Standard	NM_004807		Approved		uc002tpt.4	O60243	OTTHUMG00000153542	ENST00000259241.6:c.1172A>G	2.37:g.129025800T>C	ENSP00000259241:p.Asp391Gly	140	0	0		96	5	0.0520833	NM_004807	B4DEP2|B4DJ29|Q53SL2|Q9BVI1	Missense_Mutation	SNP	ENST00000259241.6	37	CCDS42748.1	.	.	.	.	.	.	.	.	.	.	T	6.511	0.462424	0.12342	.	.	ENSG00000136720	ENST00000259241	D	0.82893	-1.66	4.19	2.98	0.34508	.	0.419922	0.27622	N	0.018544	T	0.70710	0.3255	L	0.29908	0.895	0.32984	D	0.524007	B	0.02656	0.0	B	0.01281	0.0	T	0.65726	-0.6098	9	.	.	.	-2.5669	9.8137	0.40840	0.0:0.0842:0.0:0.9158	.	391	O60243	H6ST1_HUMAN	G	391	ENSP00000259241:D391G	.	D	-	2	0	HS6ST1	128742270	0.994000	0.37717	0.051000	0.19133	0.159000	0.22180	2.428000	0.44749	0.558000	0.29135	0.260000	0.18958	GAT	.	.	none		0.692	HS6ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331572.1	NM_004807		C	129025800	T	C	129025800	3	2	30	1	0	0	0	0	1	0	0	0	7379	1435	50	3	67	3	HS6ST1	2	129025800	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	1068836	129025800	114173573	85	13236											
ORC4L	5000	hgsc.bcm.edu	37	chr2	148730367	148730367	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agagttactctctccatggaGagcagttcttttcagcagct	9	13	9	10	0	3	2	1	0	2	2	5	3	4	2	1	1	4	5	1	1	1	4	rs2307397	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:148730367G>C	ENST00000392857.5	-	4	273	c.166C>G	c.(166-168)Ctc>Gtc	p.L56V	ORC4_ENST00000542387.1_5'UTR|ORC4_ENST00000392858.1_Missense_Mutation_p.L56V|ORC4_ENST00000536575.1_Intron|ORC4_ENST00000535373.1_Missense_Mutation_p.L56V|ORC4_ENST00000264169.2_Missense_Mutation_p.L56V|ORC4_ENST00000540442.1_5'UTR	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	56			L -> V (in dbSNP:rs2307397). {ECO:0000269|Ref.4}.		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						TCTCCATGGAGAGCAGTTCTT	0.358													G|||	86	0.0171725	0.0045	0.0288	5008	,	,		13467	0.0		0.0447	False		,,,				2504	0.0153				p.L56V		Atlas-SNP	.											.	ORC4	40	.	0			c.C166G						PASS	.	G	VAL/LEU,,,VAL/LEU,VAL/LEU,VAL/LEU	51,4355	51.6+/-87.1	1,49,2153	73	75	74		166,,,166,166,166	2.3	1	2	dbSNP_100	74	464,8136	138.3+/-195.1	13,438,3849	yes	missense,intron,utr-5,missense,missense,missense	ORC4	NM_001190879.2,NM_001190881.2,NM_001190882.2,NM_002552.4,NM_181741.3,NM_181742.3	32,,,32,32,32	14,487,6002	CC,CG,GG		5.3953,1.1575,3.9597	benign,,,benign,benign,benign	56/437,,,56/437,56/437,56/437	148730367	515,12491	2203	4300	6503	SO:0001583	missense	5000	exon4			CATGGAGAGCAGT	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.166C>G	2.37:g.148730367G>C	ENSP00000376597:p.Leu56Val	223	0	0		206	122	0.592233	NM_002552	B7Z3D0|B7Z5F1|D3DP86|F5H069|Q96C42	Missense_Mutation	SNP	ENST00000392857.5	37	CCDS2187.1	56	0.02564102564102564	6	0.012195121951219513	14	0.03867403314917127	0	0.0	36	0.047493403693931395	G	9.786	1.176749	0.21704	0.011575	0.053953	ENSG00000115947	ENST00000264169;ENST00000535373;ENST00000392858;ENST00000392857;ENST00000416719;ENST00000457954;ENST00000440042	T;T;T;T;T;T;T	0.60920	0.15;0.15;0.15;0.15;0.15;0.15;0.15	5.88	2.28	0.28536	.	0.171869	0.51477	N	0.000088	T	0.03608	0.0103	N	0.01257	-0.925	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	0.01961	-1.1239	10	0.26408	T	0.33	-4.2923	4.915	0.13842	0.0:0.2245:0.1536:0.6219	rs2307397;rs17219015;rs56449945;rs2307397	56;56;56	B7Z2M4;A8K7H4;O43929	.;.;ORC4_HUMAN	V	56	ENSP00000264169:L56V;ENSP00000441953:L56V;ENSP00000376598:L56V;ENSP00000376597:L56V;ENSP00000413939:L56V;ENSP00000391484:L56V;ENSP00000403105:L56V	ENSP00000264169:L56V	L	-	1	0	ORC4	148446837	0.997000	0.39634	1.000000	0.80357	0.885000	0.51271	0.434000	0.21494	0.487000	0.27698	-0.266000	0.10368	CTC	G|0.964;C|0.036	0.036	strong		0.358	ORC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254797.3	NM_181742		C	148730367	G	C	148730367	3	2	30	1	0	0	0	0	1	0	0	0	11273	942	33	4	1188	4	ORC4L	2	148730367	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	19704567	148730367	94469006	86	13237											
LY75	4065	hgsc.bcm.edu	37	chr2	160697271	160697271	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agagtccgatccataaggaaGagttgtgaaggagcgcctgc	12	7	14	8	2	0	3	0	1	0	2	2	6	2	5	3	2	2	1	3	2	3	2	rs147904044	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:160697271G>A	ENST00000263636.4	-	25	3503	c.3476C>T	c.(3475-3477)tCt>tTt	p.S1159F	LY75-CD302_ENST00000504764.1_Missense_Mutation_p.S1159F|LY75_ENST00000553424.1_Missense_Mutation_p.S1159F|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.S1159F|LY75_ENST00000554112.1_Missense_Mutation_p.S1159F	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1159	C-type lectin 7. {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)		CCATAAGGAAGAGTTGTGAAG	0.483													G|||	6	0.00119808	0.0	0.0043	5008	,	,		18429	0.0		0.003	False		,,,				2504	0.0				p.S1159F		Atlas-SNP	.											.	LY75	151	.	0			c.C3476T						PASS	.	G	PHE/SER,PHE/SER,PHE/SER	8,4398	14.3+/-33.2	0,8,2195	150	143	145		3476,3476,3476	3.5	0	2	dbSNP_134	145	45,8555	27.9+/-77.7	0,45,4255	yes	missense,missense,missense	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	155,155,155	0,53,6450	AA,AG,GG		0.5233,0.1816,0.4075	benign,benign,benign	1159/1874,1159/1818,1159/1723	160697271	53,12953	2203	4300	6503	SO:0001583	missense	4065	exon25			AAGGAAGAGTTGT	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.3476C>T	2.37:g.160697271G>A	ENSP00000263636:p.Ser1159Phe	125	0	0		132	61	0.462121	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	5	0.0022893772893772895	0	0.0	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	8.582	0.882464	0.17467	0.001816	0.005233	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16	5.35	3.48	0.39840	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	.	.	.	.	T	0.24392	0.0591	L	0.50919	1.6	0.18873	N	0.999983	P;P;D	0.57571	0.899;0.952;0.98	P;P;P	0.56700	0.509;0.642;0.804	T	0.05194	-1.0900	9	0.44086	T	0.13	-0.8422	10.0198	0.42035	0.0:0.1485:0.6974:0.1541	.	1159;1159;1159	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	F	1159	ENSP00000451511:S1159F;ENSP00000451446:S1159F;ENSP00000263636:S1159F;ENSP00000423463:S1159F;ENSP00000421035:S1159F	ENSP00000423463:S1159F	S	-	2	0	LY75;LY75-CD302	160405517	0.933000	0.31639	0.011000	0.14972	0.281000	0.26958	1.035000	0.30216	0.570000	0.29347	0.655000	0.94253	TCT	G|0.996;A|0.004	0.004	strong		0.483	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1			A	160697271	G	A	160697271	3	1	30	1	0	0	0	0	1	0	0	0	9108	942	33	2	1736	2	LY75	2	160697271	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	11966904	160697271	82502102	87	13238											
LY75	4065	hgsc.bcm.edu	37	chr2	160735174	160735174	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tagtcagattgcagtttgttCcaaaagggacctcatcctca	11	12	8	10	0	3	1	3	0	0	1	5	2	5	2	3	1	1	3	3	1	3	4	rs147820690	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:160735174C>T	ENST00000263636.4	-	10	1601	c.1574G>A	c.(1573-1575)gGa>gAa	p.G525E	LY75-CD302_ENST00000504764.1_Missense_Mutation_p.G525E|LY75_ENST00000553424.1_Missense_Mutation_p.G525E|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.G525E|LY75_ENST00000554112.1_Missense_Mutation_p.G525E	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	525	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)		GCAGTTTGTTCCAAAAGGGAC	0.388													C|||	3	0.000599042	0.0	0.0014	5008	,	,		20519	0.0		0.002	False		,,,				2504	0.0				p.G525E		Atlas-SNP	.											.	LY75	151	.	0			c.G1574A						PASS	.	C	GLU/GLY,GLU/GLY,GLU/GLY	5,4401	9.9+/-24.2	0,5,2198	173	156	162		1574,1574,1574	4.4	1	2	dbSNP_134	162	23,8577	16.6+/-54.9	0,23,4277	yes	missense,missense,missense	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	98,98,98	0,28,6475	TT,TC,CC		0.2674,0.1135,0.2153	probably-damaging,probably-damaging,probably-damaging	525/1874,525/1818,525/1723	160735174	28,12978	2203	4300	6503	SO:0001583	missense	4065	exon10			TTTGTTCCAAAAG	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.1574G>A	2.37:g.160735174C>T	ENSP00000263636:p.Gly525Glu	209	0	0		220	125	0.568182	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	19.40	3.820467	0.71028	0.001135	0.002674	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.51817	0.69;2.98;2.96;0.69;2.98	5.31	4.43	0.53597	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (2);	0.234809	0.21795	N	0.069012	T	0.66877	0.2834	M	0.73598	2.24	0.48901	D	0.999726	B;D;D;D	0.89917	0.41;1.0;1.0;1.0	P;D;D;D	0.97110	0.45;0.999;1.0;1.0	T	0.67313	-0.5702	10	0.41790	T	0.15	-18.7866	13.1585	0.59531	0.0:0.9209:0.0:0.0791	.	143;525;525;525	Q59H44;O60449-3;O60449;O60449-2	.;.;LY75_HUMAN;.	E	525	ENSP00000451511:G525E;ENSP00000451446:G525E;ENSP00000263636:G525E;ENSP00000423463:G525E;ENSP00000421035:G525E	ENSP00000423463:G525E	G	-	2	0	LY75;LY75-CD302	160443420	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.886000	0.56190	1.367000	0.46095	0.650000	0.86243	GGA	C|0.998;T|0.002	0.002	strong		0.388	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1			T	160735174	C	T	160735174	3	4	30	1	0	0	0	0	1	0	0	0	9108	855	30	2	3698	2	LY75	2	160735174	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	37903	160735174	82464199	88	13239											
SCN7A	6332	hgsc.bcm.edu	37	chr2	167319011	167319011	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatcaggatttatgccagctTttacacacacatatccttca	12	13	5	11	0	2	0	2	0	0	0	3	2	3	1	2	1	3	1	2	1	3	6			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:167319011T>A	ENST00000409855.1	-	9	1097	c.971A>T	c.(970-972)aAa>aTa	p.K324I		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	324					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)	TATGCCAGCTTTTACACACAC	0.373																																					p.K324I		Atlas-SNP	.											.	SCN7A	410	.	0			c.A971T						PASS	.						71	63	66					2																	167319011		1845	4102	5947	SO:0001583	missense	6332	exon9			CCAGCTTTTACAC	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.971A>T	2.37:g.167319011T>A	ENSP00000386796:p.Lys324Ile	137	0	0		112	59	0.526786	NM_002976		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	T	25.1	4.598912	0.87055	.	.	ENSG00000136546	ENST00000409855;ENST00000259060;ENST00000419992;ENST00000441411	D;D;D	0.98717	-5.09;-5.09;-5.09	4.43	4.43	0.53597	Ion transport (1);	0.000000	0.52532	D	0.000071	D	0.99010	0.9662	M	0.83603	2.65	0.42436	D	0.992693	D	0.89917	1.0	D	0.91635	0.999	D	0.99839	1.1060	10	0.87932	D	0	.	12.8081	0.57626	0.0:0.0:0.0:1.0	.	324	Q01118	SCN7A_HUMAN	I	324	ENSP00000386796:K324I;ENSP00000413699:K324I;ENSP00000403846:K324I	ENSP00000259060:K324I	K	-	2	0	SCN7A	167027257	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.043000	0.64208	1.747000	0.51819	0.477000	0.44152	AAA	.	.	none		0.373	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1			A	167319011	T	A	167319011	3	1	30	1	0	0	0	0	1	0	0	0	13938	1841	64	5	4145	5	SCN7A	2	167319011	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	6583837	167319011	75880362	89	13240											
XIRP2	129446	hgsc.bcm.edu	37	chr2	168115158	168115158	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatgatgccagaaaatcataAagaaaatttgaataagaata	22	9	7	3	0	1	5	1	2	0	3	1	6	1	5	1	0	1	0	1	0	10	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:168115158A>C	ENST00000409728.1	+	11	2290	c.2201A>C	c.(2200-2202)aAa>aCa	p.K734T	XIRP2_ENST00000409273.1_3'UTR|XIRP2_ENST00000420519.1_Missense_Mutation_p.K734T|XIRP2_ENST00000409605.1_Missense_Mutation_p.K479T|XIRP2_ENST00000409043.1_Missense_Mutation_p.K701T|XIRP2_ENST00000295237.9_3'UTR|XIRP2_ENST00000409756.2_Missense_Mutation_p.K701T|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						GAAAATCATAAAGAAAATTTG	0.294																																					p.K734T		Atlas-SNP	.											.	XIRP2	914	.	0			c.A2201C						PASS	.						28	27	27					2																	168115158		1807	4068	5875	SO:0001583	missense	129446	exon11			ATCATAAAGAAAA	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.2201A>C	2.37:g.168115158A>C	ENSP00000386619:p.Lys734Thr	88	0	0		85	37	0.435294	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	37	CCDS56143.1	.	.	.	.	.	.	.	.	.	.	A	14.20	2.463028	0.43736	.	.	ENSG00000163092	ENST00000409043;ENST00000409728;ENST00000409756;ENST00000420519;ENST00000409605	D;D;D;D;D	0.82167	-1.54;-1.54;-1.54;-1.54;-1.58	5.61	3.21	0.36854	.	.	.	.	.	D	0.87597	0.6217	.	.	.	0.80722	D	1	D;D	0.67145	0.996;0.996	P;P	0.62298	0.9;0.9	D	0.85431	0.1149	8	0.87932	D	0	.	5.8857	0.18880	0.7743:0.0:0.0791:0.1466	.	701;734	A4UGR9-4;A4UGR9-6	.;.	T	701;734;701;734;479	ENSP00000386454:K701T;ENSP00000386619:K734T;ENSP00000386724:K701T;ENSP00000415541:K734T;ENSP00000386981:K479T	ENSP00000386454:K701T	K	+	2	0	XIRP2	167823404	1.000000	0.71417	0.366000	0.25914	0.381000	0.30169	2.375000	0.44283	0.407000	0.25591	0.418000	0.28097	AAA	.	.	none		0.294	XIRP2-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333552.1	NM_152381		C	168115158	A	C	168115158	3	2	30	1	0	0	0	0	1	0	0	0	17445	14	1	5	11519	5	XIRP2	2	168115158	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	796147	168115158	75084215	90	13241											
HOXD10	3236	hgsc.bcm.edu	37	chr2	176983923	176983923	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	aagatgagccgagagaaccgGatccgagaactgaccgccaa	15	3	12	11	4	0	5	0	2	0	3	1	9	1	6	5	1	3	0	5	1	4	0	rs33913965	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:176983923G>C	ENST00000249501.4	+	2	1242	c.987G>C	c.(985-987)cgG>cgC	p.R329R	HOXD-AS2_ENST00000440016.2_RNA|HOXD10_ENST00000490088.2_3'UTR	NM_002148.3	NP_002139.2	P28358	HXD10_HUMAN	homeobox D10	329					adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|neuromuscular process (GO:0050905)|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)|spinal cord motor neuron cell fate specification (GO:0021520)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)		GAGAGAACCGGATCCGAGAAC	0.562													G|||	37	0.00738818	0.0015	0.0187	5008	,	,		10062	0.0		0.0209	False		,,,				2504	0.001				p.R329R		Atlas-SNP	.											.	HOXD10	65	.	0			c.G987C						PASS	.	G		18,4388	25.3+/-52.1	0,18,2185	45	48	47		987	3.9	1	2	dbSNP_126	47	193,8407	84.8+/-147.2	1,191,4108	no	coding-synonymous	HOXD10	NM_002148.3		1,209,6293	CC,CG,GG		2.2442,0.4085,1.6223		329/341	176983923	211,12795	2203	4300	6503	SO:0001819	synonymous_variant	3236	exon2			GAACCGGATCCGA		CCDS2266.1	2q31.1	2014-09-17	2005-12-22		ENSG00000128710	ENSG00000128710		"Homeoboxes / ANTP class : HOXL subclass"	5133	protein-coding gene	gene with protein product		142984	"homeo box D10"	HOX4, HOX4D		1973146, 1358459	Standard	NM_002148		Approved		uc002ukj.3	P28358	OTTHUMG00000132511	ENST00000249501.4:c.987G>C	2.37:g.176983923G>C		128	0	0		159	77	0.484277	NM_002148	Q6NT10	Silent	SNP	ENST00000249501.4	37	CCDS2266.1																																																																																			G|0.984;C|0.016	0.016	strong		0.562	HOXD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255692.2			C	176983923	G	C	176983923	2	2	30	1	0	0	0	0	0	0	0	1	7328	1161	41	4		4	HOXD10	2	176983923	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	8868765	176983923	66215450	91	13242											
DUSP19	142679	hgsc.bcm.edu	37	chr2	183951796	183951796	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tattcttaatgttgcatatgGagttgaaaatgctttcctca	11	17	7	6	0	2	1	1	1	1	0	3	2	3	2	1	1	2	4	1	1	5	7	rs368865344		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:183951796G>A	ENST00000354221.4	+	3	477	c.302G>A	c.(301-303)gGa>gAa	p.G101E	DUSP19_ENST00000342619.6_Intron|AC064871.3_ENST00000444562.1_RNA|DUSP19_ENST00000469344.1_Intron	NM_080876.3	NP_543152.1	Q8WTR2	DUS19_HUMAN	dual specificity phosphatase 19	101					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 protein kinase activity (GO:0006469)|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 protein kinase activity (GO:0045860)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	JUN kinase phosphatase activity (GO:0008579)|MAP-kinase scaffold activity (GO:0005078)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein kinase activator activity (GO:0030295)|protein kinase inhibitor activity (GO:0004860)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/threonine phosphatase activity (GO:0008330)			breast(1)|kidney(2)|large_intestine(3)|lung(6)|ovary(4)|pancreas(1)	17						GTTGCATATGGAGTTGAAAAT	0.333																																					p.G101E		Atlas-SNP	.											.	DUSP19	41	.	0			c.G302A						PASS	.		GLU/GLY,	0,4404		0,0,2202	112	111	111		302,	5.4	1	2		111	1,8599	1.2+/-3.3	0,1,4299	no	missense,intron	DUSP19	NM_080876.3,NM_001142314.1	98,	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,	101/218,	183951796	1,13003	2202	4300	6502	SO:0001583	missense	142679	exon3			CATATGGAGTTGA	AB038770	CCDS2289.1, CCDS46469.1	2q32.1	2011-06-09			ENSG00000162999	ENSG00000162999		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"	18894	protein-coding gene	gene with protein product		611437					Standard	NM_080876		Approved	SKRP1, DUSP17	uc002upd.3	Q8WTR2	OTTHUMG00000132622	ENST00000354221.4:c.302G>A	2.37:g.183951796G>A	ENSP00000346160:p.Gly101Glu	57	0	0		48	17	0.354167	NM_080876	B2RA79|Q547H4|Q8WYN4	Missense_Mutation	SNP	ENST00000354221.4	37	CCDS2289.1	.	.	.	.	.	.	.	.	.	.	g	18.99	3.739002	0.69304	0.0	1.16E-4	ENSG00000162999	ENST00000354221	D	0.83506	-1.73	5.38	5.38	0.77491	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.199838	0.53938	D	0.000058	T	0.79106	0.4390	L	0.35341	1.055	0.80722	D	1	P	0.42908	0.793	P	0.46885	0.53	T	0.74284	-0.3715	10	0.02654	T	1	.	19.5054	0.95113	0.0:0.0:1.0:0.0	.	101	Q8WTR2	DUS19_HUMAN	E	101	ENSP00000346160:G101E	ENSP00000346160:G101E	G	+	2	0	DUSP19	183660041	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.691000	0.91279	2.674000	0.91012	0.651000	0.88453	GGA	.	.	weak		0.333	DUSP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255866.1			A	183951796	G	A	183951796	3	1	30	1	0	0	0	0	1	0	0	0	4820	1174	41	2	312	2	DUSP19	2	183951796	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	6967873	183951796	59247577	92	13243											
ANKAR	150709	hgsc.bcm.edu	37	chr2	190569908	190569908	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttgcatcattattgctctctGtaggaaggatcctagtttgc	8	16	9	8	0	2	0	1	0	1	0	4	2	3	2	1	2	3	4	1	2	4	6	rs116660656	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:190569908G>A	ENST00000520309.1	+	8	1956	c.1868G>A	c.(1867-1869)tGt>tAt	p.C623Y	ANKAR_ENST00000431575.2_Missense_Mutation_p.C552Y|ANKAR_ENST00000281412.6_Missense_Mutation_p.C387Y|ANKAR_ENST00000438402.2_Missense_Mutation_p.C623Y|ANKAR_ENST00000313581.4_Missense_Mutation_p.C623Y	NM_144708.3	NP_653309.3	Q7Z5J8	ANKAR_HUMAN	ankyrin and armadillo repeat containing	623				C -> Y (in Ref. 3; AAH47413). {ECO:0000305}.		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)			ATTGCTCTCTGTAGGAAGGAT	0.403													G|||	40	0.00798722	0.0008	0.0058	5008	,	,		17427	0.0		0.0258	False		,,,				2504	0.0092				p.C623Y		Atlas-SNP	.											.	ANKAR	184	.	0			c.G1868A						PASS	.	G	TYR/CYS	15,4391	21.2+/-45.6	0,15,2188	145	141	142		1868	3	1	2	dbSNP_132	142	236,8364	95.9+/-157.7	3,230,4067	yes	missense	ANKAR	NM_144708.3	194	3,245,6255	AA,AG,GG		2.7442,0.3404,1.9299	benign	623/1435	190569908	251,12755	2203	4300	6503	SO:0001583	missense	150709	exon8			CTCTCTGTAGGAA	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.1868G>A	2.37:g.190569908G>A	ENSP00000427882:p.Cys623Tyr	306	0	0		235	110	0.468085	NM_144708	Q3ZCS6|Q4G0M2|Q6ZU02	Missense_Mutation	SNP	ENST00000520309.1	37	CCDS33351.2	23	0.010531135531135532	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	20	0.026385224274406333	G	15.26	2.781995	0.49891	0.003404	0.027442	ENSG00000151687	ENST00000520309;ENST00000313581;ENST00000438402;ENST00000431575;ENST00000281412	T;T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09;-0.09	5.84	2.97	0.34412	.	0.580099	0.16803	N	0.198888	T	0.30039	0.0752	L	0.33792	1.035	0.40694	D	0.982421	.	.	.	.	.	.	T	0.23762	-1.0179	8	0.35671	T	0.21	-1.9537	7.6426	0.28303	0.4252:0.0:0.5748:0.0	.	.	.	.	Y	623;623;623;552;387	ENSP00000427882:C623Y;ENSP00000313513:C623Y;ENSP00000397243:C623Y;ENSP00000393043:C552Y;ENSP00000281412:C387Y	ENSP00000281412:C387Y	C	+	2	0	ANKAR	190278153	0.095000	0.21747	0.981000	0.43875	0.973000	0.67179	0.169000	0.16641	0.332000	0.23536	-0.345000	0.07892	TGT	G|0.983;A|0.017	0.017	strong		0.403	ANKAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335045.3	NM_144708		A	190569908	G	A	190569908	3	1	30	1	0	0	0	0	1	0	0	0	623	1377	48	2	1894	2	ANKAR	2	190569908	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	6618112	190569908	52629465	93	13244											
CASP8	841	hgsc.bcm.edu	37	chr2	202137432	202137432	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggaaagttggacatcctgaaAagagtctgtgcccaaatcaa	15	8	10	8	0	2	2	1	1	1	1	3	4	3	4	2	2	1	1	2	2	5	1			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:202137432A>G	ENST00000432109.2	+	5	672	c.483A>G	c.(481-483)aaA>aaG	p.K161K	CASP8_ENST00000264275.5_Silent_p.K193K|CASP8_ENST00000358485.4_Silent_p.K220K|CASP8_ENST00000392259.2_Silent_p.K161K|CASP8_ENST00000392258.3_Silent_p.K161K|CASP8_ENST00000323492.7_Silent_p.K161K|CASP8_ENST00000392266.3_Silent_p.K161K|CASP8_ENST00000264274.9_Silent_p.K161K	NM_033355.3	NP_203519.1	Q14790	CASP8_HUMAN	caspase 8, apoptosis-related cysteine peptidase	161	DED 2. {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						ACATCCTGAAAAGAGTCTGTG	0.438										HNSCC(4;0.00038)																											p.K220K	Melanoma(82;831 1348 20716 36952 40159)	Atlas-SNP	.											.	CASP8	272	.	0			c.A660G						PASS	.						154	157	156					2																	202137432		2203	4300	6503	SO:0001819	synonymous_variant	841	exon4			CCTGAAAAGAGTC	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.483A>G	2.37:g.202137432A>G		139	0	0		107	71	0.663551	NM_001080125	O14676|Q14791|Q14792|Q14793|Q14794|Q14795|Q14796|Q15780|Q15806|Q53TT5|Q8TDI1|Q8TDI2|Q8TDI3|Q8TDI4|Q8TDI5|Q96T22|Q9C0K4|Q9UQ81	Silent	SNP	ENST00000432109.2	37	CCDS2342.1																																																																																			.	.	none		0.438	CASP8-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000336853.2	NM_001228		G	202137432	A	G	202137432	2	3	30	1	0	0	0	0	0	0	0	1	2679	11	1	3		3	CASP8	2	202137432	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	11567524	202137432	41061941	94	13245											
PIKFYVE	200576	hgsc.bcm.edu	37	chr2	209168942	209168942	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cccgacagtgactcagtgaaCtccgtggaaggacactctga	11	7	11	12	2	2	3	1	3	1	0	3	6	3	5	2	2	1	0	2	2	2	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:209168942C>T	ENST00000264380.4	+	11	1526	c.1368C>T	c.(1366-1368)aaC>aaT	p.N456N	PIKFYVE_ENST00000392202.3_Silent_p.N359N|PIKFYVE_ENST00000407449.1_Silent_p.N456N|PIKFYVE_ENST00000308862.6_Silent_p.N370N	NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	456					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						ACTCAGTGAACTCCGTGGAAG	0.443																																					p.N456N		Atlas-SNP	.											.	PIKFYVE	223	.	0			c.C1368T						PASS	.						125	120	122					2																	209168942		2203	4300	6503	SO:0001819	synonymous_variant	200576	exon11			AGTGAACTCCGTG	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.1368C>T	2.37:g.209168942C>T		93	0	0		59	42	0.711864	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Silent	SNP	ENST00000264380.4	37	CCDS2382.1																																																																																			.	.	none		0.443	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040		T	209168942	C	T	209168942	2	4	30	1	0	0	0	0	0	0	0	1	11933	564	20	2		2	PIKFYVE	2	209168942	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	7031510	209168942	34030431	95	13246											
SPAG16	79582	hgsc.bcm.edu	37	chr2	215013915	215013915	+	Frame_Shift_Del	DEL	T	T	-																															gggttacaaagctgtgggacTttcggaagctgttaccaatt																										TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:215013915delT	ENST00000331683.5	+	15	1740	c.1645delT	c.(1645-1647)tttfs	p.F549fs	SPAG16_ENST00000374309.3_Frame_Shift_Del_p.F455fs	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	549					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)		GCTGTGGGACTTTCGGAAGCT	0.368																																					p.D548fs		Pindel,Atlas-Indel	.											.	SPAG16	134	.	0			c.1644delC						PASS	.						166	165	165					2																	215013915		2203	4300	6503	SO:0001589	frameshift_variant	79582	exon15			.	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.1645delT	2.37:g.215013915delT	ENSP00000332592:p.Phe549fs	307	0	.		179	55	0.307	NM_024532	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Frame_Shift_Del	DEL	ENST00000331683.5	37	CCDS2396.1																																																																																			.	.	none		0.368	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532		-	215013915	T	-	215013915	7	5	30	1	0	1	0	1	0	0	0	0	14993	1609	56	0	1719	0	SPAG16	2	215013915	Frame_Shift_Del	DEL	T	TCGA-GR-7353-01A-11D-2210-10	5844973	215013915	28185458	96	13247											
FN1	2335	hgsc.bcm.edu	37	chr2	216248820	216248820	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tgacagcatacacagtgatgGtataatcaactccaggttta	14	11	8	8	0	1	2	1	2	0	0	2	2	2	2	1	2	3	3	1	2	5	5			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:216248820G>T	ENST00000359671.1	-	29	4809	c.4544C>A	c.(4543-4545)aCc>aAc	p.T1515N	FN1_ENST00000432072.2_Missense_Mutation_p.T1606N|FN1_ENST00000357009.2_Missense_Mutation_p.T1515N|FN1_ENST00000490833.1_5'Flank|FN1_ENST00000323926.6_Missense_Mutation_p.T1606N|FN1_ENST00000354785.4_Missense_Mutation_p.T1606N|FN1_ENST00000421182.1_Missense_Mutation_p.T1515N|FN1_ENST00000336916.4_Missense_Mutation_p.T1515N|FN1_ENST00000346544.3_Missense_Mutation_p.T1515N|FN1_ENST00000357867.4_Missense_Mutation_p.T1515N|FN1_ENST00000345488.5_Missense_Mutation_p.T1515N|FN1_ENST00000356005.4_Missense_Mutation_p.T1515N|FN1_ENST00000446046.1_Missense_Mutation_p.T1515N|FN1_ENST00000443816.1_Missense_Mutation_p.T1515N			P02751	FINC_HUMAN	fibronectin 1	1515	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)	CACAGTGATGGTATAATCAAC	0.498																																					p.T1606N		Atlas-SNP	.											.	FN1	521	.	0			c.C4817A						PASS	.						131	120	123					2																	216248820		2203	4300	6503	SO:0001583	missense	2335	exon30			GTGATGGTATAAT		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.4544C>A	2.37:g.216248820G>T	ENSP00000352696:p.Thr1515Asn	114	0	0		71	19	0.267606	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	Missense_Mutation	SNP	ENST00000359671.1	37		.	.	.	.	.	.	.	.	.	.	G	20.8	4.046748	0.75846	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000346544;ENST00000345488;ENST00000357009;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005;ENST00000456923	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.57907	0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37;0.37	5.83	4.94	0.65067	.	0.000000	0.64402	D	0.000001	T	0.63331	0.2502	L	0.39898	1.24	0.27525	N	0.951287	D;D;D;D;D;P;D;D;D;D	0.76494	0.999;0.999;0.999;0.997;0.999;0.922;0.999;0.999;0.999;0.995	D;D;D;D;D;P;D;D;D;D	0.83275	0.977;0.995;0.996;0.969;0.987;0.905;0.987;0.977;0.977;0.969	T	0.56426	-0.7981	10	0.46703	T	0.11	.	14.3418	0.66633	0.0705:0.0:0.9295:0.0	.	1606;1606;1515;1515;1515;1515;1516;1515;1515;1606	P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15	.;.;.;.;.;.;.;.;.;.	N	1515;1606;1515;1515;1606;1516;1515;1515;1515;1515;1515;1515;1606;1515;322	ENSP00000394423:T1515N;ENSP00000323534:T1606N;ENSP00000338200:T1515N;ENSP00000350534:T1515N;ENSP00000346839:T1606N;ENSP00000352696:T1515N;ENSP00000265312:T1515N;ENSP00000273049:T1515N;ENSP00000349509:T1515N;ENSP00000410422:T1515N;ENSP00000415018:T1515N;ENSP00000399538:T1606N;ENSP00000348285:T1515N;ENSP00000416139:T322N	ENSP00000265313:T1516N	T	-	2	0	FN1	215957065	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	6.391000	0.73208	2.756000	0.94617	0.655000	0.94253	ACC	.	.	none		0.498	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		T	216248820	G	T	216248820	3	4	30	1	0	0	0	0	1	0	0	0	5970	1261	44	4	2684	4	FN1	2	216248820	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1234905	216248820	26950553	97	13248											
TNS1	7145	hgsc.bcm.edu	37	chr2	218682757	218682757	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgtgggtctccgatcctccGgggtagaatagccaccatag	8	9	13	11	2	1	1	0	0	1	1	4	2	3	1	5	3	1	1	5	3	4	3	rs140104262	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:218682757G>A	ENST00000171887.4	-	24	4438	c.3986C>T	c.(3985-3987)cCg>cTg	p.P1329L	TNS1_ENST00000430930.1_Missense_Mutation_p.P1308L|TNS1_ENST00000419504.1_Missense_Mutation_p.P1316L	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1329					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)		CCGATCCTCCGGGGTAGAATA	0.662													G|||	4	0.000798722	0.0	0.0	5008	,	,		15504	0.0		0.003	False		,,,				2504	0.001				p.P1329L		Atlas-SNP	.											TNS1,NS,carcinoma,+1,1	TNS1	251	1	0			c.C3986T						PASS	.	G	LEU/PRO	1,4405		0,1,2202	22	23	23		3986	4.6	1	2	dbSNP_134	23	21,8577		0,21,4278	yes	missense	TNS1	NM_022648.4	98	0,22,6480	AA,AG,GG		0.2442,0.0227,0.1692	possibly-damaging	1329/1736	218682757	22,12982	2203	4299	6502	SO:0001583	missense	7145	exon24			TCCTCCGGGGTAG	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.3986C>T	2.37:g.218682757G>A	ENSP00000171887:p.Pro1329Leu	73	0	0		39	37	0.948718	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	18.68	3.675106	0.67928	2.27E-4	0.002442	ENSG00000079308	ENST00000171887;ENST00000446688;ENST00000419504;ENST00000430930	D;T;D;D	0.94138	-3.36;1.7;-3.36;-3.36	4.57	4.57	0.56435	.	0.605025	0.15502	N	0.258967	D	0.94853	0.8337	L	0.50333	1.59	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.998	P;P;P	0.58721	0.844;0.754;0.826	D	0.95184	0.8302	10	0.87932	D	0	.	17.5631	0.87912	0.0:0.0:1.0:0.0	.	1329;1308;1316	Q9HBL0;E9PGF5;E9PF55	TENS1_HUMAN;.;.	L	1329;467;1316;1308	ENSP00000171887:P1329L;ENSP00000394171:P467L;ENSP00000408724:P1316L;ENSP00000406016:P1308L	ENSP00000171887:P1329L	P	-	2	0	TNS1	218391002	1.000000	0.71417	0.989000	0.46669	0.311000	0.27955	6.993000	0.76245	2.368000	0.80403	0.563000	0.77884	CCG	G|0.999;A|0.001	0.001	strong		0.662	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		A	218682757	G	A	218682757	3	1	30	1	0	0	0	0	1	0	0	0	16358	1116	39	1	1261	1	TNS1	2	218682757	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2433937	218682757	24516616	98	13249											
CCDC108	255101	hgsc.bcm.edu	37	chr2	219890814	219890814	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aatagctgtggcctcgtgccCgcaccgtcaggcaccaggat	8	7	12	14	3	1	0	1	0	0	0	2	1	1	1	4	3	2	3	4	3	2	1	rs114017706	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:219890814C>T	ENST00000341552.5	-	14	2362	c.2279G>A	c.(2278-2280)cGg>cAg	p.R760Q	CCDC108_ENST00000453220.1_Missense_Mutation_p.R760Q|CCDC108_ENST00000441968.1_Missense_Mutation_p.R760Q	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	760						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)		GCCTCGTGCCCGCACCGTCAG	0.597													C|||	75	0.014976	0.0499	0.0086	5008	,	,		20085	0.0		0.002	False		,,,				2504	0.001				p.R760Q		Atlas-SNP	.											CCDC108,right_upper_lobe,carcinoma,+1,1	CCDC108	208	1	0			c.G2279A						PASS	.	C	GLN/ARG	149,4257	103.8+/-142.4	1,147,2055	80	71	74		2279	-1.5	0	2	dbSNP_132	74	5,8595	4.3+/-15.6	0,5,4295	yes	missense	CCDC108	NM_194302.2	43	1,152,6350	TT,TC,CC		0.0581,3.3818,1.1841	possibly-damaging	760/1926	219890814	154,12852	2203	4300	6503	SO:0001583	missense	255101	exon14			CGTGCCCGCACCG	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.2279G>A	2.37:g.219890814C>T	ENSP00000340776:p.Arg760Gln	230	0	0		164	47	0.286585	NM_194302	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Missense_Mutation	SNP	ENST00000341552.5	37	CCDS2430.2	21	0.009615384615384616	16	0.032520325203252036	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	C	12.23	1.874254	0.33069	0.033818	5.81E-4	ENSG00000181378	ENST00000341552;ENST00000441968;ENST00000453220	T;T;T	0.06068	3.35;3.35;3.35	4.87	-1.46	0.08800	.	0.698236	0.11855	N	0.522902	T	0.01454	0.0047	L	0.55103	1.725	0.09310	N	1	P	0.39404	0.672	B	0.28139	0.086	T	0.34428	-0.9829	10	0.35671	T	0.21	-7.944	6.1253	0.20176	0.0:0.4501:0.1226:0.4273	.	760	Q6ZU64	CC108_HUMAN	Q	760	ENSP00000340776:R760Q;ENSP00000413377:R760Q;ENSP00000409117:R760Q	ENSP00000340776:R760Q	R	-	2	0	CCDC108	219599058	0.000000	0.05858	0.003000	0.11579	0.588000	0.36517	-0.972000	0.03802	-0.213000	0.10094	0.561000	0.74099	CGG	C|0.989;T|0.011	0.011	strong		0.597	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302		T	219890814	C	T	219890814	3	4	30	1	0	0	0	0	1	0	0	0	2745	652	23	1	3586	1	CCDC108	2	219890814	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1208057	219890814	23308559	99	13250											
FAM134A	79137	hgsc.bcm.edu	37	chr2	220046155	220046155	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcagagacagagagtgaaagCgaggcagagctggctggctt	12	5	17	7	1	0	4	0	1	0	3	0	7	0	4	0	3	2	5	0	3	1	1	rs548711754		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:220046155C>T	ENST00000430297.2	+	7	985	c.849C>T	c.(847-849)agC>agT	p.S283S		NM_024293.4	NP_077269.3	Q8NC44	F134A_HUMAN	family with sequence similarity 134, member A	283						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(2)	19		Renal(207;0.0915)		Epithelial(149;8.92e-07)|all cancers(144;0.000151)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGAGTGAAAGCGAGGCAGAGC	0.542													C|||	1	0.000199681	0.0	0.0	5008	,	,		18963	0.0		0.0	False		,,,				2504	0.001				p.S283S		Atlas-SNP	.											FAM134A,colon,carcinoma,0,1	FAM134A	34	1	0			c.C849T						PASS	.						56	57	57					2																	220046155		2203	4300	6503	SO:0001819	synonymous_variant	79137	exon7			TGAAAGCGAGGCA	AK074983	CCDS2434.1	2q36.1	2008-02-05	2007-05-01	2007-05-01	ENSG00000144567	ENSG00000144567			28450	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 17"	C2orf17			Standard	NM_024293		Approved	MGC3035	uc002vjw.4	Q8NC44	OTTHUMG00000154577	ENST00000430297.2:c.849C>T	2.37:g.220046155C>T		82	0	0		74	18	0.243243	NM_024293	Q6P1P5|Q9H0K7	Silent	SNP	ENST00000430297.2	37	CCDS2434.1																																																																																			.	.	none		0.542	FAM134A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336147.2	NM_024293		T	220046155	C	T	220046155	2	4	30	1	0	0	0	0	0	0	0	1	5450	767	27	1		1	FAM134A	2	220046155	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	155341	220046155	23153218	100	13251											
EPHA4	2043	hgsc.bcm.edu	37	chr2	222301160	222301160	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggatcatcctcaagcactcGggacatgccaaaatcagaca	14	6	8	13	2	3	1	3	0	0	1	5	3	4	3	2	2	2	1	2	2	3	0	rs56159060		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:222301160G>T	ENST00000281821.2	-	13	2346	c.2305C>A	c.(2305-2307)Cga>Aga	p.R769R	EPHA4_ENST00000392071.4_Silent_p.R718R|EPHA4_ENST00000409854.1_Silent_p.R769R|EPHA4_ENST00000409938.1_Silent_p.R769R	NM_004438.3	NP_004429.1	P54764	EPHA4_HUMAN	EPH receptor A4	769	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)		TCAAGCACTCGGGACATGCCA	0.488																																					p.R769R		Atlas-SNP	.											.	EPHA4	263	.	0			c.C2305A						PASS	.						101	83	89					2																	222301160		2203	4300	6503	SO:0001819	synonymous_variant	2043	exon13			GCACTCGGGACAT	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.2305C>A	2.37:g.222301160G>T		106	0	0		71	16	0.225352	NM_004438	A8K2P1|B2R601|B7Z6Q8|Q2M380	Silent	SNP	ENST00000281821.2	37	CCDS2447.1																																																																																			.	.	weak		0.488	EPHA4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256836.3			T	222301160	G	T	222301160	2	4	30	1	0	0	0	0	0	0	0	1	5171	1124	39	4		4	EPHA4	2	222301160	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2255005	222301160	20898213	101	13252											
SP140L	93349	hgsc.bcm.edu	37	chr2	231226371	231226371	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaagaaagtgatcgaaaagAaagggaagagaggcctgaca	19	3	13	6	1	0	5	0	2	0	3	1	8	0	6	2	2	0	0	2	2	6	0	rs190007801	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:231226371A>G	ENST00000415673.2	+	5	568	c.482A>G	c.(481-483)gAa>gGa	p.E161G	SP140L_ENST00000444636.1_Missense_Mutation_p.E161G|SP140L_ENST00000396563.4_Missense_Mutation_p.E161G|SP140L_ENST00000458341.1_Missense_Mutation_p.E74G|SP140L_ENST00000243810.6_Missense_Mutation_p.E161G	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	161						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|skin(1)	20						GATCGAAAAGAAAGGGAAGAG	0.403													A|||	2	0.000399361	0.0015	0.0	5008	,	,		23304	0.0		0.0	False		,,,				2504	0.0				p.E161G		Atlas-SNP	.											.	SP140L	68	.	0			c.A482G						PASS	.	A	GLY/GLU	3,4039		0,3,2018	62	59	60		482	0.9	0	2		60	0,8456		0,0,4228	yes	missense	SP140L	NM_138402.4	98	0,3,6246	GG,GA,AA		0.0,0.0742,0.024	probably-damaging	161/581	231226371	3,12495	2021	4228	6249	SO:0001583	missense	93349	exon5			GAAAAGAAAGGGA	BC004921	CCDS46538.1	2q37.1	2013-01-28			ENSG00000185404	ENSG00000185404		"Zinc fingers, PHD-type"	25105	protein-coding gene	gene with protein product						12477932	Standard	NM_138402		Approved		uc010fxm.1	Q9H930	OTTHUMG00000153730	ENST00000415673.2:c.482A>G	2.37:g.231226371A>G	ENSP00000397911:p.Glu161Gly	103	0	0		89	4	0.0449438	NM_138402	Q2M375|Q4ZG65|Q9BSP3	Missense_Mutation	SNP	ENST00000415673.2	37	CCDS46538.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	A	9.805	1.181709	0.21787	7.42E-4	0.0	ENSG00000185404	ENST00000444636;ENST00000415673;ENST00000243810;ENST00000396563;ENST00000458341	D;T;D;D;T	0.85171	-1.82;-1.45;-1.82;-1.95;0.58	2.13	0.943	0.19531	.	.	.	.	.	D	0.84284	0.5438	L	0.44542	1.39	0.09310	N	1	D;B	0.67145	0.996;0.028	P;B	0.61722	0.893;0.007	T	0.71220	-0.4657	9	0.31617	T	0.26	.	3.9572	0.09395	0.811:0.0:0.189:0.0	.	74;161	Q9H930-3;Q9H930-4	.;.	G	161;161;161;161;74	ENSP00000395195:E161G;ENSP00000397911:E161G;ENSP00000243810:E161G;ENSP00000379811:E161G;ENSP00000395223:E74G	ENSP00000243810:E161G	E	+	2	0	SP140L	230934615	0.001000	0.12720	0.001000	0.08648	0.010000	0.07245	0.491000	0.22419	0.268000	0.21939	0.254000	0.18369	GAA	A|0.999;G|0.001	0.001	strong		0.403	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1	NM_138402		G	231226371	A	G	231226371	3	3	30	1	0	0	0	0	1	0	0	0	14978	246	9	3	500	3	SP140L	2	231226371	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	8925211	231226371	11973002	102	13253											
USP40	55230	hgsc.bcm.edu	37	chr2	234429744	234429744	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	catactagtgacccatttctCttccttggtcaacaagctgt	9	14	6	12	0	2	1	1	1	1	0	4	1	3	1	2	1	3	1	2	1	4	5			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:234429744C>T	ENST00000427112.2	-	16	2250	c.2215G>A	c.(2215-2217)Gag>Aag	p.E739K	USP40_ENST00000251722.6_Missense_Mutation_p.E739K|USP40_ENST00000450966.1_Missense_Mutation_p.E751K			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	739					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)		ACCCATTTCTCTTCCTTGGTC	0.368																																					p.E751K		Atlas-SNP	.											USP40_ENST00000450966,caecum,carcinoma,+2,2	USP40	174	2	0			c.G2251A						scavenged	.						84	77	79					2																	234429744		1842	4083	5925	SO:0001583	missense	55230	exon16			ATTTCTCTTCCTT	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.2215G>A	2.37:g.234429744C>T	ENSP00000387898:p.Glu739Lys	60	0	0		67	6	0.0895522	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	37	CCDS46547.1	.	.	.	.	.	.	.	.	.	.	C	8.295	0.818600	0.16607	.	.	ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112;ENST00000452724	T;T;T;T	0.50548	0.74;0.74;0.74;0.74	4.75	2.88	0.33553	.	2.303910	0.01545	N	0.019397	T	0.37376	0.1001	L	0.29908	0.895	0.09310	N	1	B;B	0.28055	0.126;0.199	B;B	0.26770	0.033;0.073	T	0.22836	-1.0205	10	0.12430	T	0.62	.	9.1947	0.37220	0.0:0.8191:0.0:0.1809	.	739;751	Q9NVE5;Q9NVE5-3	UBP40_HUMAN;.	K	751;739;739;34	ENSP00000415434:E751K;ENSP00000251722:E739K;ENSP00000387898:E739K;ENSP00000408853:E34K	ENSP00000251722:E739K	E	-	1	0	USP40	234094483	0.026000	0.19158	0.801000	0.32222	0.504000	0.33889	1.443000	0.35057	1.208000	0.43306	0.585000	0.79938	GAG	.	.	none		0.368	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294		T	234429744	C	T	234429744	3	4	30	1	0	0	0	0	1	0	0	0	17087	922	32	2	1556	2	USP40	2	234429744	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	3203373	234429744	8769629	103	13254											
COL6A3	1293	hgsc.bcm.edu	37	chr2	238280553	238280553	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcctggtctgcgttcctggcGatcgtgaaaggggccacgcc	5	9	14	13	4	1	1	0	1	1	0	4	2	3	1	4	4	1	1	4	4	1	1	rs35114079	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:238280553G>A	ENST00000295550.4	-	9	4559	c.4107C>T	c.(4105-4107)atC>atT	p.I1369I	COL6A3_ENST00000392003.2_Silent_p.I962I|COL6A3_ENST00000353578.4_Silent_p.I1163I|COL6A3_ENST00000346358.4_Silent_p.I1169I|COL6A3_ENST00000472056.1_Silent_p.I762I|COL6A3_ENST00000409809.1_Silent_p.I1163I|COL6A3_ENST00000347401.3_Silent_p.I1168I|COL6A3_ENST00000392004.3_Silent_p.I1163I	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	1369	Nonhelical region.|VWFA 7. {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)		CGTTCCTGGCGATCGTGAAAG	0.612													G|||	14	0.00279553	0.0015	0.0014	5008	,	,		16527	0.0		0.006	False		,,,				2504	0.0051				p.I1369I		Atlas-SNP	.											.	COL6A3	608	.	0			c.C4107T						PASS	.	G	,,,,	7,4399	12.9+/-30.5	0,7,2196	60	56	57		4107,2886,3489,2286,3489	-9.3	0	2	dbSNP_126	57	71,8529	42.2+/-99.7	0,71,4229	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057164.4,NM_057165.4,NM_057166.4,NM_057167.3	,,,,	0,78,6425	AA,AG,GG		0.8256,0.1589,0.5997	,,,,	1369/3178,962/1037,1163/1238,762/2571,1163/2972	238280553	78,12928	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon9			CCTGGCGATCGTG	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.4107C>T	2.37:g.238280553G>A		127	0	0		77	28	0.363636	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			G|0.994;A|0.006	0.006	strong		0.612	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		A	238280553	G	A	238280553	2	1	30	1	0	0	0	0	0	0	0	1	3703	1048	37	1		1	COL6A3	2	238280553	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	3850809	238280553	4918820	104	13255											
RBM44	375316	hgsc.bcm.edu	37	chr2	238742968	238742968	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agtgagaataagacataaagGttttctgaatggcttatcta	15	13	9	4	0	2	3	0	2	2	2	2	4	2	3	0	2	0	2	0	2	7	6			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:238742968G>A	ENST00000409864.1	+	15	3337	c.3083G>A	c.(3082-3084)gGt>gAt	p.G1028D	RBM44_ENST00000316997.4_Missense_Mutation_p.G1028D			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	1027						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)		AGACATAAAGGTTTTCTGAAT	0.318																																					p.G1028D		Atlas-SNP	.											.	RBM44	167	.	0			c.G3083A						PASS	.						38	37	37					2																	238742968		1804	4054	5858	SO:0001583	missense	375316	exon15			ATAAAGGTTTTCT	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.3083G>A	2.37:g.238742968G>A	ENSP00000386727:p.Gly1028Asp	297	1	0.003367		262	128	0.48855	NM_001080504	A0AUW3	Missense_Mutation	SNP	ENST00000409864.1	37	CCDS46554.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.962568	0.74016	.	.	ENSG00000177483	ENST00000316997;ENST00000409864	T;T	0.69561	-0.41;-0.41	4.96	4.96	0.65561	.	.	.	.	.	T	0.81351	0.4804	M	0.74881	2.28	0.43275	D	0.995234	D	0.89917	1.0	D	0.91635	0.999	D	0.83952	0.0317	9	0.87932	D	0	-15.9804	15.6834	0.77391	0.0:0.0:1.0:0.0	.	1027	Q6ZP01	RBM44_HUMAN	D	1028	ENSP00000321179:G1028D;ENSP00000386727:G1028D	ENSP00000321179:G1028D	G	+	2	0	RBM44	238407707	1.000000	0.71417	0.812000	0.32479	0.977000	0.68977	6.062000	0.71155	2.297000	0.77311	0.484000	0.47621	GGT	.	.	none		0.318	RBM44-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328733.2	NM_001080504		A	238742968	G	A	238742968	3	1	30	1	0	0	0	0	1	0	0	0	13153	1261	44	2	3137	2	RBM44	2	238742968	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	462415	238742968	4456405	105	13256											
AQP12A	375318	hgsc.bcm.edu	37	chr2	241631499	241631499	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgctgcctggagatgaggacGctggtcgagctcgggccctg	5	8	17	11	3	0	2	0	1	0	1	2	5	0	3	2	4	3	3	2	4	0	0	rs200769008		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:241631499G>A	ENST00000337801.4	+	2	201	c.132G>A	c.(130-132)acG>acA	p.T44T	AQP12A_ENST00000429564.1_Silent_p.T56T|AC011298.2_ENST00000407635.2_lincRNA	NM_198998.2	NP_945349.1	Q8IXF9	AQ12A_HUMAN	aquaporin 12A	44						integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(2)|kidney(3)|large_intestine(2)|lung(7)	14		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;2.2e-31)|all cancers(36;1.08e-28)|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;7.52e-06)|Lung(119;0.00163)|LUSC - Lung squamous cell carcinoma(224;0.008)|Colorectal(34;0.0124)|COAD - Colon adenocarcinoma(134;0.0757)		AGATGAGGACGCTGGTCGAGC	0.701													g|||	1	0.000199681	0.0	0.0	5008	,	,		12447	0.0		0.001	False		,,,				2504	0.0				p.T44T		Atlas-SNP	.											AQP12A,NS,carcinoma,+1,1	AQP12A	32	1	0			c.G132A						PASS	.						25	37	33					2																	241631499		2147	4265	6412	SO:0001819	synonymous_variant	375318	exon2			GAGGACGCTGGTC	AB040748		2q37.3	2013-06-03	2005-05-26	2005-05-26	ENSG00000184945	ENSG00000184945		"Ion channels / Aquaporins"	19941	protein-coding gene	gene with protein product		609789	"aquaporin 12"	AQP12			Standard	NM_198998		Approved		uc002vzu.3	Q8IXF9	OTTHUMG00000183906	ENST00000337801.4:c.132G>A	2.37:g.241631499G>A		191	0	0		110	49	0.445455	NM_198998		Silent	SNP	ENST00000337801.4	37																																																																																				G|0.998;A|0.002	0.002	weak		0.701	AQP12A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257185.2	NM_198998		A	241631499	G	A	241631499	2	1	30	1	0	0	0	0	0	0	0	1	824	1074	38	1		1	AQP12A	2	241631499	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2888531	241631499	1567874	106	13257											
FARP2	9855	hgsc.bcm.edu	37	chr2	242373714	242373714	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caaaagccgtcttcttcagcCggggctcctccttcagatac	8	10	8	15	2	4	1	2	0	2	1	6	1	6	1	4	2	3	1	4	2	3	4	rs372818608		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:242373714C>T	ENST00000264042.3	+	10	1179	c.1009C>T	c.(1009-1011)Cgg>Tgg	p.R337W	FARP2_ENST00000373287.4_Missense_Mutation_p.R337W|FARP2_ENST00000545004.1_Missense_Mutation_p.R337W	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	337					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)		CTTCTTCAGCCGGGGCTCCTC	0.463																																					p.R337W		Atlas-SNP	.											.	FARP2	92	.	0			c.C1009T						PASS	.	C	TRP/ARG	2,4404	4.2+/-10.8	0,2,2201	78	81	80		1009	4.1	1	2		80	0,8600		0,0,4300	no	missense	FARP2	NM_014808.2	101	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging	337/1055	242373714	2,13004	2203	4300	6503	SO:0001583	missense	9855	exon10			TTCAGCCGGGGCT	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.1009C>T	2.37:g.242373714C>T	ENSP00000264042:p.Arg337Trp	121	0	0		90	4	0.0444444	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Missense_Mutation	SNP	ENST00000264042.3	37	CCDS33424.1	.	.	.	.	.	.	.	.	.	.	C	18.78	3.696420	0.68386	4.54E-4	0.0	ENSG00000006607	ENST00000264042;ENST00000545004;ENST00000373287;ENST00000413432	D;D;D;D	0.86432	-2.12;-2.12;-2.12;-2.12	5.04	4.13	0.48395	FERM adjacent (FA) (1);	0.062830	0.64402	D	0.000012	D	0.93851	0.8033	M	0.88105	2.93	0.58432	D	0.999995	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.94179	0.7430	10	0.66056	D	0.02	.	12.8745	0.57982	0.3929:0.6071:0.0:0.0	.	337;337;337	O94887-2;F5GZ84;O94887	.;.;FARP2_HUMAN	W	337;337;337;24	ENSP00000264042:R337W;ENSP00000443876:R337W;ENSP00000362384:R337W;ENSP00000412772:R24W	ENSP00000264042:R337W	R	+	1	2	FARP2	242022387	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.660000	0.37397	1.023000	0.39654	0.557000	0.71058	CGG	.	.	weak		0.463	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1			T	242373714	C	T	242373714	3	4	30	1	0	0	0	0	1	0	0	0	5685	643	23	1	1043	1	FARP2	2	242373714	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	742215	242373714	825659	107	13258											
FARP2	9855	hgsc.bcm.edu	37	chr2	242396209	242396209	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctccctccagccggaagagcCccctgagtctgagccctgca	7	6	10	18	1	1	3	0	2	1	1	3	4	3	4	6	1	4	1	6	1	1	0	rs145630778		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr2:242396209C>A	ENST00000264042.3	+	14	1629	c.1459C>A	c.(1459-1461)Ccc>Acc	p.P487T	FARP2_ENST00000373287.4_Missense_Mutation_p.P487T|FARP2_ENST00000545004.1_Missense_Mutation_p.P487T	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	487	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)		CCGGAAGAGCCCCCTGAGTCT	0.617													C|||	1	0.000199681	0.0	0.0	5008	,	,		17269	0.0		0.001	False		,,,				2504	0.0				p.P487T		Atlas-SNP	.											.	FARP2	92	.	0			c.C1459A						PASS	.	C	THR/PRO	0,4406		0,0,2203	85	85	85		1459	3	0.2	2	dbSNP_134	85	1,8599	2.2+/-6.3	0,1,4299	yes	missense	FARP2	NM_014808.2	38	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	benign	487/1055	242396209	1,13005	2203	4300	6503	SO:0001583	missense	9855	exon14			AAGAGCCCCCTGA	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.1459C>A	2.37:g.242396209C>A	ENSP00000264042:p.Pro487Thr	266	1	0.0037594		258	120	0.465116	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Missense_Mutation	SNP	ENST00000264042.3	37	CCDS33424.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	10.91	1.485420	0.26686	0.0	1.16E-4	ENSG00000006607	ENST00000264042;ENST00000545004;ENST00000373287	T;T;D	0.81499	-0.98;-1.49;-1.5	5.18	3.03	0.35002	.	0.717669	0.13260	N	0.401364	T	0.67552	0.2905	L	0.32530	0.975	0.26033	N	0.981711	P;B;B	0.34724	0.465;0.328;0.22	B;B;B	0.34242	0.178;0.124;0.058	T	0.53322	-0.8455	10	0.12103	T	0.63	.	9.2186	0.37362	0.0:0.7326:0.0:0.2674	.	487;487;487	O94887-2;F5GZ84;O94887	.;.;FARP2_HUMAN	T	487	ENSP00000264042:P487T;ENSP00000443876:P487T;ENSP00000362384:P487T	ENSP00000264042:P487T	P	+	1	0	FARP2	242044882	1.000000	0.71417	0.234000	0.24042	0.857000	0.48899	3.646000	0.54396	1.195000	0.43115	-0.192000	0.12808	CCC	C|1.000;A|0.000	0.000	strong		0.617	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1			A	242396209	C	A	242396209	3	1	30	1	0	0	0	0	1	0	0	0	5685	623	22	4	1509	4	FARP2	2	242396209	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	22495	242396209	803164	108	13259											
C3orf32	51066	hgsc.bcm.edu	37	chr3	8675447	8675447	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccacaaagctgaggagggCttcccgggccacctcctccg	7	6	12	16	2	0	1	0	1	0	0	4	2	4	2	6	3	1	2	6	3	1	1	rs112366230	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:8675447C>T	ENST00000317371.4	-	11	1403	c.178G>A	c.(178-180)Gcc>Acc	p.A60T	SSUH2_ENST00000341795.3_Missense_Mutation_p.A60T|SSUH2_ENST00000415132.1_Missense_Mutation_p.A60T|SSUH2_ENST00000544814.1_Missense_Mutation_p.A82T			Q9Y2M2	SSUH2_HUMAN	ssu-2 homolog (C. elegans)	60						cytoplasm (GO:0005737)											CTGAGGAGGGCTTCCCGGGCC	0.657													C|||	67	0.0133786	0.0424	0.0086	5008	,	,		13880	0.0		0.003	False		,,,				2504	0.002				p.A82T		Atlas-SNP	.											.	.	.	.	0			c.G244A						PASS	.	C	THR/ALA	156,4248		3,150,2049	27	30	29		178	5.1	1	3	dbSNP_132	29	73,8519		1,71,4224	yes	missense	C3orf32	NM_015931.1	58	4,221,6273	TT,TC,CC		0.8496,3.5422,1.7621	probably-damaging	60/354	8675447	229,12767	2202	4296	6498	SO:0001583	missense	51066	exon4			GGAGGGCTTCCCG	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.178G>A	3.37:g.8675447C>T	ENSP00000324551:p.Ala60Thr	157	0	0		182	96	0.527473	NM_001256748	A6NFA9|B3KS84|B7Z6E3|F5H2S5|Q7Z7K4	Missense_Mutation	SNP	ENST00000317371.4	37	CCDS2568.1	16	0.007326007326007326	13	0.026422764227642278	3	0.008287292817679558	0	0.0	0	0.0	C	21.1	4.092595	0.76756	0.035422	0.008496	ENSG00000125046	ENST00000341795;ENST00000317371;ENST00000415132;ENST00000544814;ENST00000427408	T;T;T;T;T	0.54675	0.61;0.61;0.59;0.61;0.56	5.14	5.14	0.70334	.	0.000000	0.85682	D	0.000000	T	0.43897	0.1268	M	0.83953	2.67	0.46061	D	0.998843	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.68416	-0.5414	10	0.72032	D	0.01	-39.6842	14.128	0.65235	0.0:1.0:0.0:0.0	.	82;60	F5H2S5;Q9Y2M2	.;CC032_HUMAN	T	60;60;60;82;82	ENSP00000339150:A60T;ENSP00000324551:A60T;ENSP00000410757:A60T;ENSP00000439378:A82T;ENSP00000401289:A82T	ENSP00000324551:A60T	A	-	1	0	C3orf32	8650447	1.000000	0.71417	1.000000	0.80357	0.339000	0.28857	4.952000	0.63618	2.407000	0.81776	0.484000	0.47621	GCC	C|0.986;T|0.014	0.014	strong		0.657	SSUH2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337900.1	NM_015931		T	8675447	C	T	8675447	3	4	30	1	0	0	0	0	1	0	0	0	2224	797	28	2	919	2	C3orf32	3	8675447	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10		8675447	189346983	109	13260											
OXNAD1	92106	hgsc.bcm.edu	37	chr3	16336381	16336381	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agggttgatttctttattccAggagtctctgtggttggtgg	5	17	14	5	0	2	1	0	1	2	0	4	2	3	2	1	5	0	2	1	5	1	6			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:16336381A>G	ENST00000285083.5	+	6	774	c.309A>G	c.(307-309)ccA>ccG	p.P103P	OXNAD1_ENST00000606098.1_Silent_p.P103P|OXNAD1_ENST00000544043.1_Silent_p.P121P|OXNAD1_ENST00000605932.1_Silent_p.P103P|OXNAD1_ENST00000435829.2_Silent_p.P121P	NM_138381.3	NP_612390.1	Q96HP4	OXND1_HUMAN	oxidoreductase NAD-binding domain containing 1	103	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.					mitochondrion (GO:0005739)	oxidoreductase activity (GO:0016491)			endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|skin(2)	13						TCTTTATTCCAGGAGTCTCTG	0.363																																					p.P103P		Atlas-SNP	.											.	OXNAD1	31	.	0			c.A309G						PASS	.						140	143	142					3																	16336381		2203	4300	6503	SO:0001819	synonymous_variant	92106	exon6			TATTCCAGGAGTC	AL832787	CCDS2630.1	3p25-p24	2010-03-19			ENSG00000154814	ENSG00000154814			25128	protein-coding gene	gene with protein product						12477932	Standard	NM_138381		Approved	MGC15763	uc003caw.3	Q96HP4	OTTHUMG00000129867	ENST00000285083.5:c.309A>G	3.37:g.16336381A>G		216	0	0		214	94	0.439252	NM_138381	Q2HYC7|Q59FA4	Silent	SNP	ENST00000285083.5	37	CCDS2630.1																																																																																			.	.	none		0.363	OXNAD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252109.1	NM_138381		G	16336381	A	G	16336381	2	3	30	1	0	0	0	0	0	0	0	1	11342	175	7	3		3	OXNAD1	3	16336381	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	7660934	16336381	181686049	110	13261											
RFTN1	23180	hgsc.bcm.edu	37	chr3	16419238	16419238	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacttactccctgagagtggCtcttcatgcacctccaaggg	8	11	9	13	0	2	1	1	1	1	1	4	2	4	1	3	2	3	2	3	2	3	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:16419238C>G	ENST00000334133.4	-	5	1085	c.813G>C	c.(811-813)gaG>gaC	p.E271D	RFTN1_ENST00000432519.1_Missense_Mutation_p.E235D	NM_015150.1	NP_055965.1	Q14699	RFTN1_HUMAN	raftlin, lipid raft linker 1	271					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						CTGAGAGTGGCTCTTCATGCA	0.512																																					p.E271D		Atlas-SNP	.											.	RFTN1	79	.	0			c.G813C						PASS	.						64	68	67					3																	16419238		2203	4300	6503	SO:0001583	missense	23180	exon5			GAGTGGCTCTTCA	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.813G>C	3.37:g.16419238C>G	ENSP00000334153:p.Glu271Asp	101	0	0		135	37	0.274074	NM_015150	Q0D2G0|Q496Y2|Q4QQI7|Q5JB48|Q7Z7P2	Missense_Mutation	SNP	ENST00000334133.4	37	CCDS33712.1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.443891	0.43429	.	.	ENSG00000131378	ENST00000432519;ENST00000334133;ENST00000451036	T;T;T	0.49139	1.5;1.5;0.79	4.67	-0.787	0.10943	.	0.907323	0.09628	N	0.776624	T	0.33527	0.0866	L	0.36672	1.1	0.21290	N	0.999731	B;B	0.18461	0.028;0.028	B;B	0.16722	0.016;0.016	T	0.27971	-1.0058	10	0.44086	T	0.13	-34.4945	5.6878	0.17813	0.0:0.4135:0.1371:0.4494	.	235;271	G3XAJ6;Q14699	.;RFTN1_HUMAN	D	235;271;271	ENSP00000403926:E235D;ENSP00000334153:E271D;ENSP00000403997:E271D	ENSP00000334153:E271D	E	-	3	2	RFTN1	16394242	0.002000	0.14202	0.103000	0.21229	0.791000	0.44710	-0.043000	0.12043	-0.073000	0.12842	0.561000	0.74099	GAG	.	.	none		0.512	RFTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346908.1	NM_015150		G	16419238	C	G	16419238	3	3	30	1	0	0	0	0	1	0	0	0	13273	796	28	4	947	4	RFTN1	3	16419238	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	82857	16419238	181603192	111	13262											
PLCL2	23228	hgsc.bcm.edu	37	chr3	17053613	17053613	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gtattcaagaatgcccagccCcctatacgggatgccacaga	12	7	9	13	1	1	2	1	0	0	2	1	3	1	3	4	1	4	1	4	1	5	4	rs61751588	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:17053613C>T	ENST00000418129.2	+	2	2862	c.2397C>T	c.(2395-2397)ccC>ccT	p.P799P	PLCL2_ENST00000396755.2_Silent_p.P799P|PLCL2_ENST00000432376.1_Silent_p.P799P	NM_001144382.1	NP_001137854.1	Q9UPR0	PLCL2_HUMAN	phospholipase C-like 2	925	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				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						ATGCCCAGCCCCCTATACGGG	0.438													C|||	34	0.00678914	0.0008	0.0043	5008	,	,		17519	0.0		0.0258	False		,,,				2504	0.0041				p.P799P		Atlas-SNP	.											.	PLCL2	145	.	0			c.C2397T						PASS	.	C	,	19,4387	24.3+/-50.5	1,17,2185	60	65	64		2779,2397	-0.4	1	3	dbSNP_129	64	175,8423	75.1+/-137.7	3,169,4127	yes	coding-synonymous,coding-synonymous	PLCL2	NM_001144382.1,NM_015184.5	,	4,186,6312	TT,TC,CC		2.0354,0.4312,1.4918	,	925/1128,799/1002	17053613	194,12810	2203	4299	6502	SO:0001819	synonymous_variant	23228	exon2			CCAGCCCCCTATA	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.2397C>T	3.37:g.17053613C>T		70	0	0		51	22	0.431373	NM_015184	A8K5V4|Q8N498|Q9H8L0|Q9UFP9	Silent	SNP	ENST00000418129.2	37	CCDS33713.1	23	0.010531135531135532	0	0.0	2	0.0055248618784530384	0	0.0	21	0.027704485488126648	C	9.281	1.048206	0.19827	0.004312	0.020354	ENSG00000154822	ENST00000419842	T	0.20069	2.1	5.53	-0.419	0.12340	.	0.164246	0.53938	D	0.000054	T	0.04407	0.0121	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.12142	-1.0559	7	0.10636	T	0.68	.	9.1754	0.37109	0.4233:0.203:0.3736:0.0	rs61751588	.	.	.	L	543	ENSP00000404433:P543L	ENSP00000404433:P543L	P	+	2	0	PLCL2	17028617	0.893000	0.30496	0.989000	0.46669	0.984000	0.73092	-0.009000	0.12765	0.255000	0.21593	0.491000	0.48974	CCC	C|0.987;T|0.013	0.013	strong		0.438	PLCL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340250.3			T	17053613	C	T	17053613	2	4	30	1	0	0	0	0	0	0	0	1	12049	610	22	2		2	PLCL2	3	17053613	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	634375	17053613	180968817	112	13263											
DLEC1	9940	hgsc.bcm.edu	37	chr3	38125704	38125704	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgctacctgcgagtcctccCgccttccacgccatacttcg	5	9	7	20	5	0	0	0	0	0	0	4	1	3	0	7	0	3	1	7	0	2	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:38125704C>T	ENST00000308059.6	+	7	1250	c.1229C>T	c.(1228-1230)cCg>cTg	p.P410L	DLEC1_ENST00000346219.3_Missense_Mutation_p.P410L|DLEC1_ENST00000452631.2_Missense_Mutation_p.P410L|DLEC1_ENST00000469151.1_3'UTR					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)		CGAGTCCTCCCGCCTTCCACG	0.453																																					p.P410L		Atlas-SNP	.											.	DLEC1	278	.	0			c.C1229T						PASS	.						110	121	117					3																	38125704		2083	4217	6300	SO:0001583	missense	9940	exon7			TCCTCCCGCCTTC	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.1229C>T	3.37:g.38125704C>T	ENSP00000308597:p.Pro410Leu	159	0	0		178	89	0.5	NM_007337		Missense_Mutation	SNP	ENST00000308059.6	37	CCDS2672.2	.	.	.	.	.	.	.	.	.	.	c	23.3	4.394599	0.83011	.	.	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.08984	3.03;3.05;3.27	5.4	5.4	0.78164	.	0.060013	0.64402	D	0.000002	T	0.32882	0.0844	M	0.80422	2.495	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;0.999	T	0.03545	-1.1026	10	0.56958	D	0.05	-17.7606	17.9203	0.88964	0.0:1.0:0.0:0.0	.	410;410;410;410	A1L305;F8W6T4;Q9Y238-3;Q9Y238	.;.;.;DLEC1_HUMAN	L	410	ENSP00000308597:P410L;ENSP00000315914:P410L;ENSP00000410427:P410L	ENSP00000308597:P410L	P	+	2	0	DLEC1	38100708	0.999000	0.42202	0.891000	0.34965	0.768000	0.43524	5.469000	0.66749	2.532000	0.85374	0.524000	0.50904	CCG	.	.	none		0.453	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337		T	38125704	C	T	38125704	3	4	30	1	0	0	0	0	1	0	0	0	4554	652	23	1	1255	1	DLEC1	3	38125704	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	21072091	38125704	159896726	113	13264											
XIRP1	165904	hgsc.bcm.edu	37	chr3	39227495	39227495	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtgggtcaaaggtcctcaCgggatgagcggtgtagatgc	9	8	17	7	2	2	2	2	1	0	1	3	3	3	3	1	5	2	1	1	5	2	1	rs142860074	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:39227495C>T	ENST00000340369.3	-	2	3670	c.3442G>A	c.(3442-3444)Gtg>Atg	p.V1148M	XIRP1_ENST00000396251.1_Intron|XIRP1_ENST00000421646.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	1148					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)	p.V1148M(1)		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)		AAGGTCCTCACGGGATGAGCG	0.617																																					p.V1148M		Atlas-SNP	.											XIRP1,colon,carcinoma,0,1	XIRP1	173	1	1	Substitution - Missense(1)	large_intestine(1)	c.G3442A						PASS	.	C	,MET/VAL	1,4405	2.1+/-5.4	0,1,2202	59	60	60		,3442	1.6	0	3	dbSNP_134	60	7,8593	5.7+/-21.5	0,7,4293	yes	intron,missense	XIRP1	NM_001198621.1,NM_194293.2	,21	0,8,6495	TT,TC,CC		0.0814,0.0227,0.0615	,possibly-damaging	,1148/1844	39227495	8,12998	2203	4300	6503	SO:0001583	missense	165904	exon2			TCCTCACGGGATG	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.3442G>A	3.37:g.39227495C>T	ENSP00000343140:p.Val1148Met	113	0	0		146	77	0.527397	NM_194293	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	37	CCDS2683.1	.	.	.	.	.	.	.	.	.	.	C	5.679	0.309769	0.10733	2.27E-4	8.14E-4	ENSG00000168334	ENST00000340369	T	0.06142	3.34	4.39	1.58	0.23477	.	0.713130	0.12138	U	0.496126	T	0.05686	0.0149	L	0.43152	1.355	0.09310	N	1	B	0.28208	0.203	B	0.14578	0.011	T	0.34054	-0.9844	10	0.45353	T	0.12	.	6.8454	0.23984	0.0:0.6999:0.0:0.3001	.	1148	Q702N8	XIRP1_HUMAN	M	1148	ENSP00000343140:V1148M	ENSP00000343140:V1148M	V	-	1	0	XIRP1	39202499	0.840000	0.29493	0.025000	0.17156	0.219000	0.24729	1.440000	0.35024	0.227000	0.20999	0.561000	0.74099	GTG	C|0.999;T|0.001	0.001	strong		0.617	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522		T	39227495	C	T	39227495	3	4	30	1	0	0	0	0	1	0	0	0	17444	536	19	1	2093	1	XIRP1	3	39227495	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1101791	39227495	158794935	114	13265											
TGM4	7047	hgsc.bcm.edu	37	chr3	44948563	44948563	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctcatctggttggtgaagAtggtgaatgggcaggaggag	9	9	19	4	0	2	3	1	2	1	1	2	5	2	5	0	7	0	3	0	7	2	1			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:44948563A>G	ENST00000296125.4	+	10	1266	c.1198A>G	c.(1198-1200)Atg>Gtg	p.M400V		NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	400					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)	GTTGGTGAAGATGGTGAATGG	0.498																																					p.M400V		Atlas-SNP	.											.	TGM4	82	.	0			c.A1198G						PASS	.						140	128	132					3																	44948563		2203	4300	6503	SO:0001583	missense	7047	exon10			GTGAAGATGGTGA	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.1198A>G	3.37:g.44948563A>G	ENSP00000296125:p.Met400Val	270	0	0		230	117	0.508696	NM_003241	Q16707|Q96QN4	Missense_Mutation	SNP	ENST00000296125.4	37	CCDS2723.1	.	.	.	.	.	.	.	.	.	.	A	5.841	0.339412	0.11069	.	.	ENSG00000163810	ENST00000296125	T	0.20738	2.05	2.03	-4.07	0.03975	.	0.468908	0.16456	U	0.213616	T	0.04048	0.0113	N	0.01048	-1.04	0.09310	N	1	B	0.19073	0.033	B	0.08055	0.003	T	0.22765	-1.0207	10	0.33141	T	0.24	.	0.4585	0.00512	0.3471:0.1383:0.2793:0.2353	.	400	P49221	TGM4_HUMAN	V	400	ENSP00000296125:M400V	ENSP00000296125:M400V	M	+	1	0	TGM4	44923567	0.002000	0.14202	0.000000	0.03702	0.112000	0.19704	-0.168000	0.09925	-1.271000	0.02430	-0.710000	0.03640	ATG	.	.	none		0.498	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241		G	44948563	A	G	44948563	3	3	30	1	0	0	0	0	1	0	0	0	15847	333	12	3	1236	3	TGM4	3	44948563	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	5721068	44948563	153073867	115	13266											
CCR2	729230	hgsc.bcm.edu	37	chr3	46399226	46399226	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgtcctcatcttaataaacTgcaaaaagctgaagtgcttg	13	12	7	9	1	2	1	1	1	1	0	4	1	3	1	1	0	4	3	1	0	6	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:46399226T>G	ENST00000400888.2	+	1	247	c.208T>G	c.(208-210)Tgc>Ggc	p.C70G	CCR2_ENST00000445132.2_Missense_Mutation_p.C70G|CCR2_ENST00000465202.1_Intron|CCR2_ENST00000292301.4_Missense_Mutation_p.C70G			P41597	CCR2_HUMAN	chemokine (C-C motif) receptor 2	70					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)		CTTAATAAACTGCAAAAAGCT	0.488																																					p.C70G		Atlas-SNP	.											.	CCR2	103	.	0			c.T208G						PASS	.						199	182	188					3																	46399226		1568	3582	5150	SO:0001583	missense	729230	exon2			ATAAACTGCAAAA		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.208T>G	3.37:g.46399226T>G	ENSP00000383681:p.Cys70Gly	380	1	0.00263158		353	141	0.399433	NM_001123041	A0AVQ3|B2RMT0|Q4VBL2	Missense_Mutation	SNP	ENST00000400888.2	37	CCDS43078.1	.	.	.	.	.	.	.	.	.	.	T	15.03	2.712653	0.48517	.	.	ENSG00000121807	ENST00000445132;ENST00000292301;ENST00000421659;ENST00000400888	T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57	4.41	4.41	0.53225	GPCR, rhodopsin-like superfamily (1);	0.097576	0.46145	D	0.000305	T	0.81403	0.4815	M	0.73430	2.235	0.31410	N	0.675649	D;P	0.76494	0.999;0.851	D;P	0.71184	0.972;0.794	T	0.80899	-0.1176	10	0.25106	T	0.35	.	13.9659	0.64209	0.0:0.0:0.0:1.0	.	70;70	P41597;Q4VBL2	CCR2_HUMAN;.	G	70	ENSP00000399285:C70G;ENSP00000292301:C70G;ENSP00000396736:C70G;ENSP00000383681:C70G	ENSP00000292301:C70G	C	+	1	0	CCR2	46374230	1.000000	0.71417	0.988000	0.46212	0.949000	0.60115	1.614000	0.36911	1.774000	0.52232	0.528000	0.53228	TGC	.	.	none		0.488	CCR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344292.1	NM_000647		G	46399226	T	G	46399226	3	3	30	1	0	0	0	0	1	0	0	0	2943	1580	55	5	210	5	CCR2	3	46399226	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	1450663	46399226	151623204	116	13267											
LTF	4057	hgsc.bcm.edu	37	chr3	46496910	46496910	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctgcaccgggaacacagctGgctgagaagaacctggccac	11	5	12	13	1	1	2	0	1	1	2	1	4	1	3	3	3	4	3	3	3	3	0	rs145526650	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:46496910G>A	ENST00000231751.4	-	5	817	c.522C>T	c.(520-522)gcC>gcT	p.A174A	LTF_ENST00000417439.1_Silent_p.A174A|LTF_ENST00000426532.2_Silent_p.A130A	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	174	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)	p.A174A(1)		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)		GAACACAGCTGGCTGAGAAGA	0.567													G|||	5	0.000998403	0.0008	0.0	5008	,	,		21912	0.0		0.004	False		,,,				2504	0.0				p.A174A		Atlas-SNP	.											LTF,NS,carcinoma,0,1	LTF	98	1	1	Substitution - coding silent(1)	kidney(1)	c.C522T						PASS	.	G	,	5,4401	9.9+/-24.2	0,5,2198	99	80	86		390,522	0.6	0.3	3	dbSNP_134	86	34,8566	23.4+/-69.3	0,34,4266	no	coding-synonymous,coding-synonymous	LTF	NM_001199149.1,NM_002343.3	,	0,39,6464	AA,AG,GG		0.3953,0.1135,0.2999	,	130/667,174/711	46496910	39,12967	2203	4300	6503	SO:0001819	synonymous_variant	4057	exon5			ACAGCTGGCTGAG		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.522C>T	3.37:g.46496910G>A		196	0	0		161	80	0.496894	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Silent	SNP	ENST00000231751.4	37	CCDS33747.1	3	0.0013736263736263737	1	0.0020325203252032522	0	0.0	0	0.0	2	0.002638522427440633	G	10.21	1.287664	0.23478	0.001135	0.003953	ENSG00000012223	ENST00000443743	.	.	.	4.89	0.614	0.17603	.	.	.	.	.	T	0.64057	0.2564	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.64972	-0.6281	5	0.72032	D	0.01	0.0819	10.0059	0.41957	0.0:0.428:0.4338:0.1382	.	.	.	.	L	107	.	ENSP00000393737:P107L	P	-	2	0	LTF	46471914	0.807000	0.29009	0.279000	0.24732	0.998000	0.95712	1.015000	0.29963	0.190000	0.20209	0.655000	0.94253	CCA	G|0.998;A|0.002	0.002	strong		0.567	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343		A	46496910	G	A	46496910	2	1	30	1	0	0	0	0	0	0	0	1	9088	1335	47	2		2	LTF	3	46496910	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	97684	46496910	151525520	117	13268											
PTH1R	5745	hgsc.bcm.edu	37	chr3	46939456	46939456	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ttatgacttcaatcacaaagGtgaggcctgctggaaggggt	11	10	13	7	0	2	2	2	2	0	0	2	3	2	3	1	5	1	1	1	5	4	2	rs201472450		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:46939456G>C	ENST00000313049.5	+	4	627		c.e4+1		PTH1R_ENST00000418619.1_Splice_Site|PTH1R_ENST00000490109.1_Splice_Site|PTH1R_ENST00000449590.1_Splice_Site|PTH1R_ENST00000430002.2_Splice_Site			Q03431	PTH1R_HUMAN	parathyroid hormone 1 receptor						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)	AATCACAAAGGTGAGGCCTGC	0.612																																					.		Atlas-SNP	.											.	PTH1R	49	.	0			c.424+1G>C						PASS	.						61	63	62					3																	46939456		2203	4300	6503	SO:0001630	splice_region_variant	5745	exon6			ACAAAGGTGAGGC		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.424+1G>C	3.37:g.46939456G>C		123	0	0		147	49	0.333333	NM_000316	Q2M1U3	Splice_Site	SNP	ENST00000313049.5	37	CCDS2747.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.198211	0.79015	.	.	ENSG00000160801	ENST00000449590;ENST00000418619;ENST00000427125;ENST00000430002;ENST00000313049	.	.	.	5.24	5.24	0.73138	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3295	0.83004	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PTH1R	46914460	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	9.292000	0.96076	2.448000	0.82819	0.561000	0.74099	.	.	.	weak		0.612	PTH1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257481.1	NM_000316	Intron	C	46939456	G	C	46939456	5	2	30	1	0	0	0	0	0	0	1	0	12771	1275	44	4	439	4	PTH1R	3	46939456	Splice_Site	SNP	G	TCGA-GR-7353-01A-11D-2210-10	442546	46939456	151082974	118	13269											
PTPN23	25930	hgsc.bcm.edu	37	chr3	47453659	47453659	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cattacctgcatcagcggccGctgcacacgcccatcattgt	8	9	8	16	3	2	0	2	0	0	0	2	0	2	0	3	1	4	3	3	1	1	2	rs147959396	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:47453659G>T	ENST00000265562.4	+	22	4226	c.4149G>T	c.(4147-4149)ccG>ccT	p.P1383P	PTPN23_ENST00000431726.1_Silent_p.P1257P	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	1383	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)		ATCAGCGGCCGCTGCACACGC	0.627													G|||	5	0.000998403	0.0	0.0043	5008	,	,		20941	0.0		0.002	False		,,,				2504	0.0				p.P1383P		Atlas-SNP	.											.	PTPN23	85	.	0			c.G4149T						PASS	.	G		6,4400	11.4+/-27.6	0,6,2197	53	52	53		4149	-1.4	1	3	dbSNP_134	53	35,8565	24.0+/-70.4	0,35,4265	no	coding-synonymous	PTPN23	NM_015466.2		0,41,6462	TT,TG,GG		0.407,0.1362,0.3152		1383/1637	47453659	41,12965	2203	4300	6503	SO:0001819	synonymous_variant	25930	exon22			GCGGCCGCTGCAC	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.4149G>T	3.37:g.47453659G>T		175	0	0		259	140	0.540541	NM_015466	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Silent	SNP	ENST00000265562.4	37	CCDS2754.1																																																																																			G|0.997;T|0.003	0.003	strong		0.627	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	NM_015466		T	47453659	G	T	47453659	2	4	30	1	0	0	0	0	0	0	0	1	12803	1074	38	4		4	PTPN23	3	47453659	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	514203	47453659	150568771	119	13270											
NCKIPSD	51517	hgsc.bcm.edu	37	chr3	48717276	48717276	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccaggacagactcgaactcGtttctcttgcacattttctt	8	14	7	12	2	2	1	0	0	2	1	5	3	2	2	1	1	2	2	1	1	1	5	rs562394435		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:48717276G>A	ENST00000294129.2	-	7	1427	c.1308C>T	c.(1306-1308)aaC>aaT	p.N436N	NCKIPSD_ENST00000416649.2_Silent_p.N429N|NCKIPSD_ENST00000341520.4_Silent_p.N436N	NM_016453.2	NP_057537.1	Q9NZQ3	SPN90_HUMAN	NCK interacting protein with SH3 domain	436					cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|NLS-bearing protein import into nucleus (GO:0006607)|signal transduction (GO:0007165)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	cytoskeletal protein binding (GO:0008092)			endometrium(1)|large_intestine(3)|lung(6)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		ACTCGAACTCGTTTCTCTTGC	0.522													G|||	1	0.000199681	0.0	0.0	5008	,	,		24484	0.0		0.0	False		,,,				2504	0.001				p.N436N		Atlas-SNP	.											.	NCKIPSD	52	.	0			c.C1308T						PASS	.						138	123	128					3																	48717276		2203	4300	6503	SO:0001819	synonymous_variant	51517	exon7			GAACTCGTTTCTC	AF178432	CCDS2776.1, CCDS46827.1	3p21	2008-07-18			ENSG00000213672	ENSG00000213672			15486	protein-coding gene	gene with protein product	"dia interacting protein", "diaphanous protein interacting protein", "SH3 protein interacting with Nck, 90 kDa"	606671				10648423, 10619843	Standard	NM_016453		Approved	AF3P21, SPIN90, ORF1, WISH, WASLBP, DIP1	uc003cun.3	Q9NZQ3	OTTHUMG00000133542	ENST00000294129.2:c.1308C>T	3.37:g.48717276G>A		166	0	0		123	67	0.544715	NM_016453	B4DFL5|Q6GU34|Q6SPF3|Q8TC10|Q9UGM8	Silent	SNP	ENST00000294129.2	37	CCDS2776.1	.	.	.	.	.	.	.	.	.	.	G	5.849	0.340768	0.11069	.	.	ENSG00000213672	ENST00000415281	.	.	.	5.2	-3.89	0.04193	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2642	0.54668	0.5461:0.0:0.4539:0.0	.	.	.	.	X	172	.	.	R	-	1	2	NCKIPSD	48692280	0.845000	0.29573	0.068000	0.19968	0.913000	0.54294	-0.007000	0.12810	-1.032000	0.03304	-1.326000	0.01283	CGA	.	.	none		0.522	NCKIPSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257520.1	NM_016453		A	48717276	G	A	48717276	2	1	30	1	0	0	0	0	0	0	0	1	10234	1136	40	1		1	NCKIPSD	3	48717276	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1263617	48717276	149305154	120	13271											
RBM6	10180	hgsc.bcm.edu	37	chr3	50005373	50005373	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaggtagggatgctcctcCatctgacttcaggggccggg	7	8	15	11	1	2	2	1	1	1	1	4	3	4	3	3	5	1	2	3	5	1	2	rs142246877	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:50005373C>T	ENST00000266022.4	+	3	774	c.515C>T	c.(514-516)cCa>cTa	p.P172L	RBM6_ENST00000422955.1_Intron|RBM6_ENST00000441115.1_Intron|RBM6_ENST00000443081.1_Missense_Mutation_p.P40L|RBM6_ENST00000539992.1_Intron|RBM6_ENST00000442092.1_Intron	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	172					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)		GATGCTCCTCCATCTGACTTC	0.473													C|||	5	0.000998403	0.0	0.0014	5008	,	,		17453	0.0		0.003	False		,,,				2504	0.001				p.P172L		Atlas-SNP	.											.	RBM6	85	.	0			c.C515T						PASS	.	C	,LEU/PRO	7,4399	12.9+/-30.5	0,7,2196	61	63	62		,515	5.9	1	3	dbSNP_134	62	37,8563	25.7+/-73.6	0,37,4263	yes	intron,missense	RBM6	NM_001167582.1,NM_005777.2	,98	0,44,6459	TT,TC,CC		0.4302,0.1589,0.3383	,probably-damaging	,172/1124	50005373	44,12962	2203	4300	6503	SO:0001583	missense	10180	exon3			CTCCTCCATCTGA	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.515C>T	3.37:g.50005373C>T	ENSP00000266022:p.Pro172Leu	112	0	0		102	49	0.480392	NM_005777	O60549|O75524|Q86SS3	Missense_Mutation	SNP	ENST00000266022.4	37	CCDS2809.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	14.30	2.493001	0.44352	0.001589	0.004302	ENSG00000004534	ENST00000266022;ENST00000443081	T;T	0.34472	1.43;1.36	5.88	5.88	0.94601	.	0.109289	0.41396	D	0.000894	T	0.32315	0.0825	L	0.40543	1.245	0.80722	D	1	B	0.31383	0.321	B	0.25614	0.062	T	0.03910	-1.0993	9	.	.	.	-3.6177	20.2405	0.98372	0.0:1.0:0.0:0.0	.	172	P78332	RBM6_HUMAN	L	172;40	ENSP00000266022:P172L;ENSP00000396466:P40L	.	P	+	2	0	RBM6	49980377	0.965000	0.33210	0.985000	0.45067	0.994000	0.84299	4.345000	0.59360	2.797000	0.96272	0.561000	0.74099	CCA	C|0.997;T|0.003	0.003	strong		0.473	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777		T	50005373	C	T	50005373	3	4	30	1	0	0	0	0	1	0	0	0	13159	594	21	2	521	2	RBM6	3	50005373	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1288097	50005373	148017057	121	13272											
RBM6	10180	hgsc.bcm.edu	37	chr3	50005855	50005855	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cttttggcattcagaagggaGaatttgagcattcagaaaca	14	11	10	6	0	2	4	2	1	0	3	2	5	2	4	0	2	2	2	0	2	3	5	rs143972186	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:50005855G>A	ENST00000266022.4	+	3	1256	c.997G>A	c.(997-999)Gaa>Aaa	p.E333K	RBM6_ENST00000422955.1_Intron|RBM6_ENST00000441115.1_Intron|RBM6_ENST00000443081.1_Missense_Mutation_p.E201K|RBM6_ENST00000539992.1_Intron|RBM6_ENST00000442092.1_Intron	NM_005777.2	NP_005768.1	P78332	RBM6_HUMAN	RNA binding motif protein 6	333					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)		TCAGAAGGGAGAATTTGAGCA	0.423													G|||	5	0.000998403	0.0	0.0014	5008	,	,		21143	0.0		0.003	False		,,,				2504	0.001				p.E333K		Atlas-SNP	.											.	RBM6	85	.	0			c.G997A						PASS	.	G	,LYS/GLU	7,4399	12.9+/-30.5	0,7,2196	81	72	75		,997	6	1	3	dbSNP_134	75	37,8563	25.1+/-72.6	0,37,4263	yes	intron,missense	RBM6	NM_001167582.1,NM_005777.2	,56	0,44,6459	AA,AG,GG		0.4302,0.1589,0.3383	,probably-damaging	,333/1124	50005855	44,12962	2203	4300	6503	SO:0001583	missense	10180	exon3			AAGGGAGAATTTG	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.997G>A	3.37:g.50005855G>A	ENSP00000266022:p.Glu333Lys	219	1	0.00456621		205	106	0.517073	NM_005777	O60549|O75524|Q86SS3	Missense_Mutation	SNP	ENST00000266022.4	37	CCDS2809.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	16.90	3.249072	0.59103	0.001589	0.004302	ENSG00000004534	ENST00000266022;ENST00000443081	T;T	0.38887	1.11;1.15	6.04	6.04	0.98038	.	0.128334	0.51477	D	0.000098	T	0.49695	0.1572	L	0.27053	0.805	0.80722	D	1	D	0.69078	0.997	D	0.75020	0.985	T	0.35574	-0.9783	9	.	.	.	-13.7992	13.7331	0.62802	0.0698:0.0:0.9302:0.0	.	333	P78332	RBM6_HUMAN	K	333;201	ENSP00000266022:E333K;ENSP00000396466:E201K	.	E	+	1	0	RBM6	49980859	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	4.840000	0.62817	2.873000	0.98535	0.561000	0.74099	GAA	G|0.997;A|0.003	0.003	strong		0.423	RBM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345528.4	NM_005777		A	50005855	G	A	50005855	3	1	30	1	0	0	0	0	1	0	0	0	13159	943	33	2	1003	2	RBM6	3	50005855	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	482	50005855	148016575	122	13273											
PARP3	10039	hgsc.bcm.edu	37	chr3	51981769	51981769	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgcagttattggcatgaaGtgtggggcccaccatgtcgg	7	11	14	9	1	0	1	0	1	0	0	1	1	0	1	2	4	1	3	2	4	2	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:51981769G>A	ENST00000417220.2	+	11	1778	c.1290G>A	c.(1288-1290)aaG>aaA	p.K430K	PARP3_ENST00000398755.3_Silent_p.K437K|PARP3_ENST00000486510.1_3'UTR|PARP3_ENST00000431474.1_Silent_p.K430K			Q9Y6F1	PARP3_HUMAN	poly (ADP-ribose) polymerase family, member 3	430	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				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)		TTGGCATGAAGTGTGGGGCCC	0.602																																					p.K437K		Atlas-SNP	.											.	PARP3	90	.	0			c.G1311A						PASS	.						95	100	98					3																	51981769		2053	4189	6242	SO:0001819	synonymous_variant	10039	exon10			CATGAAGTGTGGG	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.1290G>A	3.37:g.51981769G>A		103	0	0		97	57	0.587629	NM_001003931	Q8NER9|Q96CG2|Q9UG81	Silent	SNP	ENST00000417220.2	37	CCDS43097.1																																																																																			.	.	none		0.602	PARP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000348612.2	NM_005485.4		A	51981769	G	A	51981769	2	1	30	1	0	0	0	0	0	0	0	1	11471	1020	36	2		2	PARP3	3	51981769	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1975914	51981769	146040661	123	13274											
CCDC66	285331	hgsc.bcm.edu	37	chr3	56628033	56628033	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgaggaacgagacagacgaCgacaaaaacaattagagcat	19	5	10	7	3	0	4	0	1	0	3	0	8	0	5	0	1	3	1	0	1	5	2	rs150364083	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:56628033C>T	ENST00000394672.3	+	10	1451	c.1381C>T	c.(1381-1383)Cga>Tga	p.R461*	CCDC66_ENST00000436465.2_Nonsense_Mutation_p.R461*|CCDC66_ENST00000326595.7_Nonsense_Mutation_p.R427*	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	461					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)		AGACAGACGACGACAAAAACA	0.373													C|||	3	0.000599042	0.0	0.0014	5008	,	,		20246	0.0		0.002	False		,,,				2504	0.0				p.R461X		Atlas-SNP	.											.	CCDC66	145	.	0			c.C1381T						PASS	.	C	stop/ARG,stop/ARG	4,4402	9.9+/-24.2	0,4,2199	180	168	172		1279,1381	4.9	1	3	dbSNP_134	172	66,8534	39.8+/-96.3	0,66,4234	yes	stop-gained,stop-gained	CCDC66	NM_001012506.4,NM_001141947.1	,	0,70,6433	TT,TC,CC		0.7674,0.0908,0.5382	,	427/915,461/949	56628033	70,12936	2203	4300	6503	SO:0001587	stop_gained	285331	exon10			AGACGACGACAAA	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.1381C>T	3.37:g.56628033C>T	ENSP00000378167:p.Arg461*	163	0	0		125	51	0.408	NM_001141947	B3KWL8|Q4VC34|Q8N949	Nonsense_Mutation	SNP	ENST00000394672.3	37	CCDS46852.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	37	6.393245	0.97529	9.08E-4	0.007674	ENSG00000180376	ENST00000422222;ENST00000394672;ENST00000326595;ENST00000436465	.	.	.	5.81	4.86	0.63082	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.6425	15.6712	0.77279	0.1457:0.8543:0.0:0.0	.	.	.	.	X	417;461;427;461	.	ENSP00000326050:R427X	R	+	1	2	CCDC66	56603073	1.000000	0.71417	0.994000	0.49952	0.977000	0.68977	3.573000	0.53856	2.739000	0.93911	0.585000	0.79938	CGA	C|0.996;T|0.004	0.004	strong		0.373	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506		T	56628033	C	T	56628033	4	4	30	1	0	0	0	0	0	1	0	0	2840	528	19	1	1419	1	CCDC66	3	56628033	Nonsense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	4646264	56628033	141394397	124	13275											
SUCLG2	8801	hgsc.bcm.edu	37	chr3	67579535	67579535	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgttaaatgaacacctcctTtcaaaccactattgaagaca	15	12	4	10	0	1	3	1	2	0	1	2	3	2	3	3	0	2	1	3	0	6	5	rs74675534	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:67579535T>C	ENST00000307227.5	-	3	329	c.302A>G	c.(301-303)aAa>aGa	p.K101R	SUCLG2_ENST00000492795.1_Missense_Mutation_p.K101R|SUCLG2_ENST00000493112.1_Missense_Mutation_p.K101R	NM_003848.3	NP_003839.2	Q96I99	SUCB2_HUMAN	succinate-CoA ligase, GDP-forming, beta subunit	101	ATP-grasp.				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)	AACACCTCCTTTCAAACCACT	0.383													T|||	9	0.00179712	0.0008	0.0	5008	,	,		17705	0.0		0.007	False		,,,				2504	0.001				p.K101R		Atlas-SNP	.											.	SUCLG2	95	.	0			c.A302G						PASS	.	T	ARG/LYS,ARG/LYS	6,3664		0,6,1829	156	147	150		302,302	5	1	3	dbSNP_131	150	86,8080		1,84,3998	yes	missense,missense	SUCLG2	NM_001177599.1,NM_003848.3	26,26	1,90,5827	CC,CT,TT		1.0531,0.1635,0.7773	benign,benign	101/441,101/433	67579535	92,11744	1835	4083	5918	SO:0001583	missense	8801	exon3			CCTCCTTTCAAAC	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.302A>G	3.37:g.67579535T>C	ENSP00000307432:p.Lys101Arg	129	0	0		102	57	0.558824	NM_001177599	C9JVT2|O95195|Q6NUH7|Q86VX8|Q8WUQ1	Missense_Mutation	SNP	ENST00000307227.5	37	CCDS43104.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	T	17.48	3.401307	0.62288	0.001635	0.010531	ENSG00000172340	ENST00000493112;ENST00000307227;ENST00000541608;ENST00000492795	T;T;T	0.70399	-0.48;-0.48;-0.48	5.01	5.01	0.66863	ATP-grasp fold, subdomain 1 (1);ATP-grasp fold, succinyl-CoA synthetase-type (1);	0.143233	0.64402	D	0.000006	T	0.73666	0.3616	M	0.88775	2.98	0.80722	D	1	B	0.25955	0.138	B	0.36766	0.232	T	0.79006	-0.1979	10	0.66056	D	0.02	.	14.7526	0.69536	0.0:0.0:0.0:1.0	.	101	Q96I99	SUCB2_HUMAN	R	101;101;53;101	ENSP00000419325:K101R;ENSP00000307432:K101R;ENSP00000417589:K101R	ENSP00000307432:K101R	K	-	2	0	SUCLG2	67662225	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.957000	0.87870	1.884000	0.54569	0.377000	0.23210	AAA	T|0.993;C|0.007	0.007	strong		0.383	SUCLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351993.1	NM_003848		C	67579535	T	C	67579535	3	2	30	1	0	0	0	0	1	0	0	0	15380	1841	64	3	1176	3	SUCLG2	3	67579535	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	10951502	67579535	130442895	125	13276											
GBE1	2632	hgsc.bcm.edu	37	chr3	81720086	81720086	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccagttttttgtatgggtacGaaaatggattccaaccatct	11	14	8	8	1	1	0	0	0	1	0	2	2	2	1	3	2	2	3	3	2	5	6			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:81720086G>A	ENST00000429644.2	-	3	975	c.332C>T	c.(331-333)tCg>tTg	p.S111L	GBE1_ENST00000489715.1_Missense_Mutation_p.S70L|GBE1_ENST00000477426.1_5'UTR	NM_000158.3	NP_000149	Q04446	GLGB_HUMAN	glucan (1,4-alpha-), branching enzyme 1	111					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)	p.S111L(1)		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)		GTATGGGTACGAAAATGGATT	0.338									Glycogen Storage Disease, type IV																												p.S111L		Atlas-SNP	.											GBE1_ENST00000429644,colon,carcinoma,0,1	GBE1	111	1	1	Substitution - Missense(1)	large_intestine(1)	c.C332T						PASS	.						64	60	61					3																	81720086		1816	4085	5901	SO:0001583	missense	2632	exon3	Familial Cancer Database	Andersen Disease, Brancher deficiency	GGGTACGAAAATG		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.332C>T	3.37:g.81720086G>A	ENSP00000410833:p.Ser111Leu	95	0	0		104	35	0.336538	NM_000158	B3KWV3|Q96EN0	Missense_Mutation	SNP	ENST00000429644.2	37	CCDS54612.1	.	.	.	.	.	.	.	.	.	.	G	19.31	3.802766	0.70682	.	.	ENSG00000114480	ENST00000429644;ENST00000264326;ENST00000489715	T;T	0.18657	2.2;2.21	5.5	3.72	0.42706	Immunoglobulin E-set (1);Glycoside hydrolase, family 13, N-terminal (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.30386	0.0763	L	0.57536	1.79	0.38321	D	0.943534	P;D	0.54207	0.888;0.965	B;P	0.51055	0.3;0.657	T	0.14309	-1.0477	10	0.66056	D	0.02	-3.5779	11.1977	0.48722	0.1509:0.0:0.8491:0.0	.	70;111	E9PGM4;Q04446	.;GLGB_HUMAN	L	111;162;70	ENSP00000410833:S111L;ENSP00000419638:S70L	ENSP00000264326:S162L	S	-	2	0	GBE1	81802776	1.000000	0.71417	0.699000	0.30290	0.813000	0.45954	5.642000	0.67888	0.694000	0.31654	0.650000	0.86243	TCG	.	.	none		0.338	GBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352760.2			A	81720086	G	A	81720086	3	1	30	1	0	0	0	0	1	0	0	0	6278	1059	37	1	1832	1	GBE1	3	81720086	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	14140551	81720086	116302344	126	13277											
TMEM45A	55076	hgsc.bcm.edu	37	chr3	100274090	100274090	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	aggtcatgccctccctggaaCcttcttttttattattggtc	6	17	7	11	0	2	0	1	0	1	0	4	1	3	1	3	3	2	0	3	3	3	6	rs200878698		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:100274090C>A	ENST00000323523.4	+	2	348	c.35C>A	c.(34-36)aCc>aAc	p.T12N	TMEM45A_ENST00000462884.1_3'UTR|TMEM45A_ENST00000403410.1_Missense_Mutation_p.T28N	NM_018004.1	NP_060474.1	Q9NWC5	TM45A_HUMAN	transmembrane protein 45A	12						integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)	11						CTCCCTGGAACCTTCTTTTTT	0.368																																					p.T12N		Atlas-SNP	.											TMEM45A,NS,carcinoma,+1,1	TMEM45A	35	1	0			c.C35A						PASS	.	C	ASN/THR	0,4406		0,0,2203	166	176	172		35	-0.4	0.6	3		172	2,8598	2.2+/-6.3	0,2,4298	yes	missense	TMEM45A	NM_018004.1	65	0,2,6501	AA,AC,CC		0.0233,0.0,0.0154	benign	12/276	100274090	2,13004	2203	4300	6503	SO:0001583	missense	55076	exon2			CTGGAACCTTCTT	AK000996	CCDS2937.1	3q12.2	2005-02-04			ENSG00000181458	ENSG00000181458			25480	protein-coding gene	gene with protein product						12477932	Standard	XM_005247568		Approved	FLJ10134, DERP7	uc003dtz.1	Q9NWC5	OTTHUMG00000150327	ENST00000323523.4:c.35C>A	3.37:g.100274090C>A	ENSP00000319009:p.Thr12Asn	195	0	0		156	68	0.435897	NM_018004	Q53YW5	Missense_Mutation	SNP	ENST00000323523.4	37	CCDS2937.1	.	.	.	.	.	.	.	.	.	.	C	11.78	1.740553	0.30865	0.0	2.33E-4	ENSG00000181458	ENST00000323523;ENST00000403410;ENST00000449609	T;T;T	0.50001	1.39;1.38;0.76	5.84	-0.364	0.12553	.	0.370601	0.35349	N	0.003273	T	0.45135	0.1327	M	0.62723	1.935	0.25270	N	0.989529	B;P	0.47106	0.22;0.89	B;B	0.39876	0.036;0.312	T	0.52711	-0.8539	10	0.59425	D	0.04	0.3845	17.6844	0.88253	0.0:0.1546:0.7715:0.0738	.	28;12	C9J9Z5;Q9NWC5	.;TM45A_HUMAN	N	12;28;28	ENSP00000319009:T12N;ENSP00000385089:T28N;ENSP00000405597:T28N	ENSP00000319009:T12N	T	+	2	0	TMEM45A	101756780	1.000000	0.71417	0.567000	0.28434	0.432000	0.31715	0.710000	0.25748	-0.406000	0.07588	-0.150000	0.13652	ACC	.	.	weak		0.368	TMEM45A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317571.1	NM_018004		A	100274090	C	A	100274090	3	1	30	1	0	0	0	0	1	0	0	0	16184	507	18	4	37	4	TMEM45A	3	100274090	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	18554004	100274090	97748340	127	13278											
TFG	10342	hgsc.bcm.edu	37	chr3	100455433	100455433	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatccagggccacccagtgcTcctgcagaagatcgttcagg	9	8	11	13	1	1	2	1	0	0	2	4	2	3	2	4	2	2	3	4	2	2	2	rs12562	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:100455433T>G	ENST00000240851.4	+	6	934	c.594T>G	c.(592-594)gcT>gcG	p.A198A	TFG_ENST00000418917.2_Silent_p.A198A|TFG_ENST00000476228.1_Silent_p.A198A|TFG_ENST00000490574.1_Silent_p.A198A	NM_001195478.1|NM_001195479.1|NM_006070.5	NP_001182407.1|NP_001182408.1|NP_006061.2	Q92734	TFG_HUMAN	TRK-fused gene	198					cell death (GO:0008219)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	signal transducer activity (GO:0004871)		TFG/NR4A3(2)|TFG/NTRK1_ENST00000392302(5)|TFG/ALK(9)	large_intestine(4)|lung(2)|prostate(1)|stomach(1)	8						CACCCAGTGCTCCTGCAGAAG	0.507			T	"NTRK1, ALK"	"papillary thyroid, ALCL, NSCLC"								T|||	2	0.000399361	0.0	0.0	5008	,	,		17057	0.0		0.002	False		,,,				2504	0.0				p.A198A		Atlas-SNP	.		Dom	yes		3	3q11-q12	10342	TRK-fused gene		"E, L"	.	TFG	42	.	0			c.T594G						PASS	.	T	,,,	9,4397	15.5+/-35.6	0,9,2194	69	63	65		594,594,594,594	2.6	1	3	dbSNP_52	65	69,8531	41.7+/-99.0	0,69,4231	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TFG	NM_001007565.2,NM_001195478.1,NM_001195479.1,NM_006070.5	,,,	0,78,6425	GG,GT,TT		0.8023,0.2043,0.5997	,,,	198/401,198/401,198/397,198/401	100455433	78,12928	2203	4300	6503	SO:0001819	synonymous_variant	10342	exon6			CAGTGCTCCTGCA	BC009241	CCDS2939.1, CCDS56266.1	3q12.2	2013-03-13	2001-12-04		ENSG00000114354	ENSG00000114354			11758	protein-coding gene	gene with protein product		602498				9169129, 23479643	Standard	NM_001007565		Approved	TF6, FLJ36137, SPG57	uc003dui.3	Q92734	OTTHUMG00000159085	ENST00000240851.4:c.594T>G	3.37:g.100455433T>G		244	0	0		256	132	0.515625	NM_006070	D3DN49|G5E9V1|Q15656|Q969I2	Silent	SNP	ENST00000240851.4	37	CCDS2939.1																																																																																			T|0.993;G|0.007	0.007	strong		0.507	TFG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353242.1	NM_006070		G	100455433	T	G	100455433	2	3	30	1	0	0	0	0	0	0	0	1	15821	1538	54	5		5	TFG	3	100455433	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	181343	100455433	97566997	128	13279											
KIAA2018	205717	hgsc.bcm.edu	37	chr3	113376113	113376113	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcttgttgttgttgctgttgCtgctgctgctgctgctgctg	0	18	14	9	0	0	0	0	0	0	0	0	0	0	0	0	0	8	13	0	0	0	5	rs62265537|rs59601191|rs112313093|rs59990801|rs397990842|rs10606566		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:113376113C>T	ENST00000478658.1	-	5	4433	c.4416G>A	c.(4414-4416)caG>caA	p.Q1472Q	KIAA2018_ENST00000316407.4_Silent_p.Q1472Q|KIAA2018_ENST00000491165.1_Intron			Q68DE3	K2018_HUMAN	KIAA2018	1472	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						gttgctgttgctgctgctgct	0.502																																					p.Q1472Q		Atlas-SNP	.											KIAA2018,rectum,carcinoma,0,1	KIAA2018	180	1	0			c.G4416A						scavenged	.						68	71	70					3																	113376113		2188	4274	6462	SO:0001819	synonymous_variant	205717	exon7			CTGTTGCTGCTGC	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.4416G>A	3.37:g.113376113C>T		106	0	0		69	3	0.0434783	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	37	CCDS43133.1																																																																																			.	.	weak		0.502	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899		T	113376113	C	T	113376113	2	4	30	1	0	0	0	0	0	0	0	1	8277	796	28	2		2	KIAA2018	3	113376113	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	12920680	113376113	84646317	129	13280											
PARP14	54625	hgsc.bcm.edu	37	chr3	122419292	122419292	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacaaaattcctccccaaacActgtaatcatcaatgagtta	17	10	3	11	0	2	1	2	1	0	0	4	1	4	1	3	0	2	2	3	0	7	3	rs7632072	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:122419292A>G	ENST00000474629.2	+	6	2157	c.1891A>G	c.(1891-1893)Act>Gct	p.T631A		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	631					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)		CTCCCCAAACACTGTAATCAT	0.348													A|||	278	0.0555112	0.1218	0.0576	5008	,	,		21423	0.001		0.0487	False		,,,				2504	0.0276				p.T631A		Atlas-SNP	.											.	PARP14	242	.	0			c.A1891G						PASS	.	A	ALA/THR	342,3342		18,306,1518	31	30	31		1891	2.1	0	3	dbSNP_116	31	361,7841		5,351,3745	yes	missense	PARP14	NM_017554.2	58	23,657,5263	GG,GA,AA		4.4014,9.2834,5.9145	probably-damaging	631/1802	122419292	703,11183	1842	4101	5943	SO:0001583	missense	54625	exon6			CCAAACACTGTAA	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.1891A>G	3.37:g.122419292A>G	ENSP00000418194:p.Thr631Ala	104	0	0		72	32	0.444444	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	37	CCDS46894.1	111	0.050824175824175824	49	0.09959349593495935	22	0.06077348066298342	1	0.0017482517482517483	39	0.051451187335092345	A	13.04	2.119612	0.37436	0.092834	0.044014	ENSG00000173193	ENST00000474629;ENST00000398162	T	0.10099	2.91	6.06	2.12	0.27331	.	0.174182	0.39759	N	0.001269	T	0.00271	0.0008	M	0.66939	2.045	0.09310	N	1	P;B	0.38827	0.649;0.376	B;B	0.33690	0.168;0.055	T	0.30268	-0.9984	10	0.36615	T	0.2	.	3.82	0.08832	0.663:0.1354:0.0717:0.1299	rs7632072;rs52827643;rs7632072	631;631	Q460N5-4;Q460N5	.;PAR14_HUMAN	A	631;550	ENSP00000418194:T631A	ENSP00000381228:T550A	T	+	1	0	PARP14	123901982	0.014000	0.17966	0.001000	0.08648	0.003000	0.03518	1.250000	0.32850	0.497000	0.27926	0.533000	0.62120	ACT	A|0.950;G|0.050	0.050	strong		0.348	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554		G	122419292	A	G	122419292	3	3	30	1	0	0	0	0	1	0	0	0	11467	159	6	3	1913	3	PARP14	3	122419292	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	9043179	122419292	75603138	130	13281											
MYLK	4638	hgsc.bcm.edu	37	chr3	123419422	123419422	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccttctcaggcacgggggTcttggaagtccccttcttgg	5	11	12	13	1	3	0	1	0	3	0	5	1	4	1	3	5	0	1	3	5	1	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:123419422T>C	ENST00000475616.1	-	15	2892	c.2893A>G	c.(2893-2895)Acc>Gcc	p.T965A	MYLK_ENST00000346322.5_Missense_Mutation_p.T896A|MYLK_ENST00000510775.1_5'Flank|MYLK_ENST00000360304.3_Missense_Mutation_p.T965A|MYLK_ENST00000360772.3_Missense_Mutation_p.T965A|MYLK_ENST00000359169.1_Missense_Mutation_p.T965A			Q15746	MYLK_HUMAN	myosin light chain kinase	965	5 X 28 AA approximate tandem repeats.				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)		GGCACGGGGGTCTTGGAAGTC	0.572																																					p.T965A		Atlas-SNP	.											.	MYLK	224	.	0			c.A2893G						PASS	.						49	48	48					3																	123419422		2203	4300	6503	SO:0001583	missense	4638	exon18			CGGGGGTCTTGGA	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.2893A>G	3.37:g.123419422T>C	ENSP00000418335:p.Thr965Ala	76	0	0		71	5	0.0704225	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	37	CCDS46896.1	.	.	.	.	.	.	.	.	.	.	T	6.416	0.444842	0.12164	.	.	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000346322;ENST00000475616	T;T;T;T;T	0.64260	-0.09;-0.04;-0.09;-0.04;-0.04	5.2	2.46	0.29980	.	.	.	.	.	T	0.43344	0.1243	L	0.28556	0.865	0.80722	D	1	B;B;B;B;B;B	0.15141	0.0;0.001;0.005;0.012;0.003;0.0	B;B;B;B;B;B	0.14023	0.001;0.005;0.01;0.006;0.004;0.001	T	0.14364	-1.0475	9	0.15499	T	0.54	.	7.056	0.25099	0.0:0.1566:0.1276:0.7157	.	965;43;896;965;896;965	Q15746-6;Q15746-7;Q15746-4;Q15746-3;Q15746-2;Q15746	.;.;.;.;.;MYLK_HUMAN	A	965;965;965;896;965	ENSP00000354004:T965A;ENSP00000353452:T965A;ENSP00000352088:T965A;ENSP00000320622:T896A;ENSP00000418335:T965A	ENSP00000320622:T896A	T	-	1	0	MYLK	124902112	0.997000	0.39634	1.000000	0.80357	0.951000	0.60555	0.367000	0.20382	0.835000	0.34877	-0.434000	0.05882	ACC	.	.	none		0.572	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025		C	123419422	T	C	123419422	3	2	30	1	0	0	0	0	1	0	0	0	10065	1667	58	3	2919	3	MYLK	3	123419422	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	1000130	123419422	74603008	131	13282											
CHST13	166012	hgsc.bcm.edu	37	chr3	126260995	126260995	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gccgccttccagaggcgctaCggtgcacgcatcgttcagcg	6	7	13	15	6	1	1	1	0	0	1	3	1	2	1	3	2	3	4	3	2	1	3	rs7614066	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:126260995C>T	ENST00000319340.2	+	3	650	c.600C>T	c.(598-600)taC>taT	p.Y200Y		NM_152889.2	NP_690849.1	Q8NET6	CHSTD_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 13	200					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)		AGAGGCGCTACGGTGCACGCA	0.721													C|||	273	0.0545128	0.1248	0.0288	5008	,	,		7896	0.002		0.0258	False		,,,				2504	0.0613				p.Y200Y		Atlas-SNP	.											.	CHST13	21	.	0			c.C600T						PASS	.	C		331,3793		10,311,1741	6	7	6		600	-5.3	0.2	3	dbSNP_116	6	189,7819		2,185,3817	no	coding-synonymous	CHST13	NM_152889.2		12,496,5558	TT,TC,CC		2.3601,8.0262,4.2862		200/342	126260995	520,11612	2062	4004	6066	SO:0001819	synonymous_variant	166012	exon3			GCGCTACGGTGCA	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.600C>T	3.37:g.126260995C>T		16	0	0		18	11	0.611111	NM_152889	Q3SYA3|Q3SYA5	Silent	SNP	ENST00000319340.2	37	CCDS3039.1																																																																																			C|0.956;T|0.044	0.044	strong		0.721	CHST13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370201.2	NM_152889		T	126260995	C	T	126260995	2	4	30	1	0	0	0	0	0	0	0	1	3403	547	19	1		1	CHST13	3	126260995	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	2841573	126260995	71761435	132	13283											
PLXNA1	5361	hgsc.bcm.edu	37	chr3	126741041	126741041	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcgcagcttctccatgcgCgaccgcgggaatgtggcctc	6	7	13	15	5	1	0	0	0	1	0	3	2	1	1	3	2	3	2	3	2	1	1	rs150052583	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:126741041C>T	ENST00000393409.2	+	21	4152	c.4152C>T	c.(4150-4152)cgC>cgT	p.R1384R	PLXNA1_ENST00000251772.4_Silent_p.R1361R	NM_032242.3	NP_115618.3	Q9UIW2	PLXA1_HUMAN	plexin A1	1384					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)		TCTCCATGCGCGACCGCGGGA	0.612													C|||	28	0.00559105	0.0038	0.0101	5008	,	,		22692	0.001		0.0129	False		,,,				2504	0.002				p.R1384R		Atlas-SNP	.											PLXNA1,colon,carcinoma,+2,1	PLXNA1	185	1	0			c.C4152T						PASS	.	C		11,4393	17.9+/-39.9	0,11,2191	62	54	56		4152	-5.4	0.9	3	dbSNP_134	56	93,8505	53.1+/-113.8	0,93,4206	no	coding-synonymous	PLXNA1	NM_032242.3		0,104,6397	TT,TC,CC		1.0816,0.2498,0.7999		1384/1897	126741041	104,12898	2202	4299	6501	SO:0001819	synonymous_variant	5361	exon21			CATGCGCGACCGC	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.4152C>T	3.37:g.126741041C>T		206	0	0		150	67	0.446667	NM_032242		Silent	SNP	ENST00000393409.2	37	CCDS33847.2																																																																																			C|0.992;T|0.008	0.008	strong		0.612	PLXNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356451.1	NM_032242		T	126741041	C	T	126741041	2	4	30	1	0	0	0	0	0	0	0	1	12128	755	27	1		1	PLXNA1	3	126741041	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	480046	126741041	71281389	133	13284											
COL6A6	131873	hgsc.bcm.edu	37	chr3	130282383	130282383	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaacctgaaggccatggccaCgtctcagtttcatttcaacc	11	10	7	13	1	3	1	3	1	1	0	4	1	3	1	4	2	2	1	4	2	3	2	rs114511272	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:130282383C>A	ENST00000358511.6	+	2	567	c.536C>A	c.(535-537)aCg>aAg	p.T179K	COL6A6_ENST00000453409.2_Missense_Mutation_p.T179K	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	179	Nonhelical region.|VWFA 1. {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)		p.T179M(1)		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						GCCATGGCCACGTCTCAGTTT	0.468													C|||	43	0.00858626	0.0008	0.0072	5008	,	,		19242	0.006		0.0189	False		,,,				2504	0.0123				p.T179K		Atlas-SNP	.											COL6A6_ENST00000358511,colon,carcinoma,-1,3	COL6A6	497	3	1	Substitution - Missense(1)	breast(1)	c.C536A						PASS	.	C	LYS/THR	13,3867		0,13,1927	72	72	72		536	5.3	0.9	3	dbSNP_132	72	129,8135		1,127,4004	yes	missense	COL6A6	NM_001102608.1	78	1,140,5931	AA,AC,CC		1.561,0.3351,1.1693	probably-damaging	179/2264	130282383	142,12002	1940	4132	6072	SO:0001583	missense	131873	exon2			TGGCCACGTCTCA	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.536C>A	3.37:g.130282383C>A	ENSP00000351310:p.Thr179Lys	232	1	0.00431034		207	91	0.439614	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Missense_Mutation	SNP	ENST00000358511.6	37	CCDS46911.1	18	0.008241758241758242	0	0.0	2	0.0055248618784530384	2	0.0034965034965034965	14	0.018469656992084433	C	23.3	4.401156	0.83120	0.003351	0.01561	ENSG00000206384	ENST00000358511;ENST00000453409	T;T	0.78246	-1.16;-1.16	5.3	5.3	0.74995	von Willebrand factor, type A (3);	0.000000	0.64402	D	0.000008	T	0.79516	0.4459	M	0.71206	2.165	0.42732	D	0.993717	D	0.89917	1.0	D	0.97110	1.0	T	0.82671	-0.0342	10	0.39692	T	0.17	.	18.0868	0.89460	0.0:1.0:0.0:0.0	.	179	A6NMZ7	CO6A6_HUMAN	K	179	ENSP00000351310:T179K;ENSP00000399236:T179K	ENSP00000351310:T179K	T	+	2	0	COL6A6	131765073	0.889000	0.30405	0.859000	0.33776	0.964000	0.63967	1.641000	0.37197	2.652000	0.90054	0.561000	0.74099	ACG	C|0.992;A|0.008	0.008	strong		0.468	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608		A	130282383	C	A	130282383	3	1	30	1	0	0	0	0	1	0	0	0	3705	536	19	4	542	4	COL6A6	3	130282383	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	3541342	130282383	67740047	134	13285											
DNAJC13	23317	hgsc.bcm.edu	37	chr3	132241682	132241682	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctcgtataggttcgaattaCgttaatgaaatttctaccaa	13	14	6	8	3	1	1	0	1	1	0	3	2	1	1	2	1	2	3	2	1	8	7	rs145242123	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:132241682C>T	ENST00000260818.6	+	49	5932	c.5684C>T	c.(5683-5685)aCg>aTg	p.T1895M		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	1895					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						GTTCGAATTACGTTAATGAAA	0.333													C|||	3	0.000599042	0.0	0.0029	5008	,	,		18811	0.0		0.001	False		,,,				2504	0.0				p.T1895M		Atlas-SNP	.											.	DNAJC13	253	.	0			c.C5684T						PASS	.	C	MET/THR	1,4405	2.1+/-5.4	0,1,2202	51	51	51		5684	5.2	1	3	dbSNP_134	51	12,8588	8.4+/-32.0	0,12,4288	yes	missense	DNAJC13	NM_015268.3	81	0,13,6490	TT,TC,CC		0.1395,0.0227,0.1	benign	1895/2244	132241682	13,12993	2203	4300	6503	SO:0001583	missense	23317	exon49			GAATTACGTTAAT	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.5684C>T	3.37:g.132241682C>T	ENSP00000260818:p.Thr1895Met	138	0	0		125	70	0.56	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	37	CCDS33857.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	8.466	0.856381	0.17106	2.27E-4	0.001395	ENSG00000138246	ENST00000260818;ENST00000538066	T	0.49720	0.77	6.08	5.2	0.72013	Armadillo-like helical (1);Armadillo-type fold (1);	0.122360	0.56097	N	0.000036	T	0.42720	0.1215	L	0.58810	1.83	0.31740	N	0.635937	B	0.13145	0.007	B	0.06405	0.002	T	0.47156	-0.9139	10	0.33940	T	0.23	.	9.9625	0.41704	0.0:0.7534:0.0:0.2466	.	1895	O75165	DJC13_HUMAN	M	1895;542	ENSP00000260818:T1895M	ENSP00000260818:T1895M	T	+	2	0	DNAJC13	133724372	0.797000	0.28877	0.995000	0.50966	0.605000	0.37080	1.532000	0.36029	0.919000	0.36945	-0.797000	0.03246	ACG	C|0.998;T|0.002	0.002	strong		0.333	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268		T	132241682	C	T	132241682	3	4	30	1	0	0	0	0	1	0	0	0	4634	536	19	1	5874	1	DNAJC13	3	132241682	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1959299	132241682	65780748	135	13286											
MED12L	116931	hgsc.bcm.edu	37	chr3	151150568	151150568	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccacagcaaggagtgactccGtatgggcatccttcacactt	10	9	9	13	1	1	1	1	1	0	0	3	2	3	2	3	2	1	3	3	2	2	3	rs142871635	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:151150568G>A	ENST00000474524.1	+	43	6452	c.6414G>A	c.(6412-6414)ccG>ccA	p.P2138P	MED12L_ENST00000273432.4_Silent_p.P1802P	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	2138						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)			GAGTGACTCCGTATGGGCATC	0.393													G|||	4	0.000798722	0.0	0.0029	5008	,	,		20900	0.0		0.002	False		,,,				2504	0.0				p.P2138P		Atlas-SNP	.											.	MED12L	271	.	0			c.G6414A						PASS	.	G		3,4403	6.2+/-15.9	0,3,2200	111	98	102		6414	-3	1	3	dbSNP_134	102	37,8563	24.6+/-71.5	0,37,4263	no	coding-synonymous	MED12L	NM_053002.4		0,40,6463	AA,AG,GG		0.4302,0.0681,0.3076		2138/2146	151150568	40,12966	2203	4300	6503	SO:0001819	synonymous_variant	116931	exon43			GACTCCGTATGGG	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.6414G>A	3.37:g.151150568G>A		173	0	0		166	90	0.542169	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Silent	SNP	ENST00000474524.1	37	CCDS33876.1																																																																																			G|0.997;A|0.003	0.003	strong		0.393	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002		A	151150568	G	A	151150568	2	1	30	1	0	0	0	0	0	0	0	1	9438	1132	40	1		1	MED12L	3	151150568	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	18908886	151150568	46871862	136	13287											
SLITRK3	22865	hgsc.bcm.edu	37	chr3	164906800	164906800	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctctgggcaaagaacttccaGctcaatagtgcgcacatcac	12	8	8	13	1	3	1	2	0	1	1	4	1	4	1	1	1	3	3	1	1	4	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:164906800G>T	ENST00000475390.1	-	2	2262	c.1819C>A	c.(1819-1821)Ctg>Atg	p.L607M	SLITRK3_ENST00000241274.3_Missense_Mutation_p.L607M			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	607	LRRCT 2.				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						AGAACTTCCAGCTCAATAGTG	0.542										HNSCC(40;0.11)																											p.L607M		Atlas-SNP	.											.	SLITRK3	263	.	0			c.C1819A						PASS	.						61	57	58					3																	164906800		2203	4300	6503	SO:0001583	missense	22865	exon2			CTTCCAGCTCAAT	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.1819C>A	3.37:g.164906800G>T	ENSP00000420091:p.Leu607Met	111	0	0		87	15	0.172414	NM_014926	Q1RMY6	Missense_Mutation	SNP	ENST00000475390.1	37	CCDS3197.1	.	.	.	.	.	.	.	.	.	.	G	6.538	0.467489	0.12402	.	.	ENSG00000121871	ENST00000475390;ENST00000241274	T;T	0.54675	0.56;0.56	5.76	4.8	0.61643	Cysteine-rich flanking region, C-terminal (1);	0.000000	0.30185	N	0.010219	T	0.32133	0.0819	N	0.10809	0.05	0.33093	D	0.538255	B	0.12013	0.005	B	0.11329	0.006	T	0.36890	-0.9729	10	0.45353	T	0.12	-9.1664	9.2667	0.37645	0.0785:0.0:0.7817:0.1398	.	607	O94933	SLIK3_HUMAN	M	607	ENSP00000420091:L607M;ENSP00000241274:L607M	ENSP00000241274:L607M	L	-	1	2	SLITRK3	166389494	0.021000	0.18746	0.997000	0.53966	0.879000	0.50718	0.452000	0.21795	1.403000	0.46800	0.655000	0.94253	CTG	.	.	none		0.542	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926		T	164906800	G	T	164906800	3	4	30	1	0	0	0	0	1	0	0	0	14759	962	34	4	1118	4	SLITRK3	3	164906800	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	13756232	164906800	33115630	137	13288											
FNDC3B	64778	hgsc.bcm.edu	37	chr3	172061988	172061988	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccagagctggagtgcaccgtCggcaacctgcttcctggaac	8	7	12	14	2	0	1	0	0	0	1	2	3	1	3	4	3	5	4	4	3	2	1	rs200807692		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:172061988C>T	ENST00000336824.4	+	19	2289	c.2190C>T	c.(2188-2190)gtC>gtT	p.V730V	FNDC3B_ENST00000416957.1_Silent_p.V730V|FNDC3B_ENST00000415807.2_Silent_p.V730V	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	730	Fibronectin type-III 5. {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)		AGTGCACCGTCGGCAACCTGC	0.567													C|||	1	0.000199681	0.0	0.0	5008	,	,		18074	0.001		0.0	False		,,,				2504	0.0				p.V730V		Atlas-SNP	.											.	FNDC3B	118	.	0			c.C2190T						PASS	.						183	166	172					3																	172061988		2203	4300	6503	SO:0001819	synonymous_variant	64778	exon19			CACCGTCGGCAAC	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.2190C>T	3.37:g.172061988C>T		216	0	0		178	90	0.505618	NM_001135095	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Silent	SNP	ENST00000336824.4	37	CCDS3217.1																																																																																			C|1.000;T|0.000	0.000	strong		0.567	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763		T	172061988	C	T	172061988	2	4	30	1	0	0	0	0	0	0	0	1	5978	871	31	1		1	FNDC3B	3	172061988	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	7155188	172061988	25960442	138	13289											
APOD	347	hgsc.bcm.edu	37	chr3	195306289	195306289	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgtccctctgccgcaccgAagaggccagccagtgcggaa	8	6	12	15	3	1	1	0	0	1	1	2	3	2	2	5	2	3	1	5	2	2	1	rs5952	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:195306289A>G	ENST00000343267.3	-	2	405	c.44T>C	c.(43-45)tTc>tCc	p.F15S		NM_001647.3	NP_001638.1	P05090	APOD_HUMAN	apolipoprotein D	15			F -> S (in dbSNP:rs5952). {ECO:0000269|PubMed:10391209}.		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)		TGCCGCACCGAAGAGGCCAGC	0.582													A|||	7	0.00139776	0.0	0.0043	5008	,	,		18597	0.0		0.004	False		,,,				2504	0.0				p.F15S		Atlas-SNP	.											.	APOD	28	.	0			c.T44C						PASS	.	A	SER/PHE	6,4400	9.9+/-24.2	0,6,2197	41	44	43		44	1.6	0	3	dbSNP_52	43	54,8546	30.1+/-81.4	0,54,4246	yes	missense	APOD	NM_001647.3	155	0,60,6443	GG,GA,AA		0.6279,0.1362,0.4613	benign	15/190	195306289	60,12946	2203	4300	6503	SO:0001583	missense	347	exon2			GCACCGAAGAGGC		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.44T>C	3.37:g.195306289A>G	ENSP00000345179:p.Phe15Ser	50	0	0		53	24	0.45283	NM_001647	B2R579|D3DNW6|Q6IBG6	Missense_Mutation	SNP	ENST00000343267.3	37	CCDS33925.1	7	0.003205128205128205	0	0.0	3	0.008287292817679558	0	0.0	4	0.005277044854881266	A	12.13	1.844610	0.32606	0.001362	0.006279	ENSG00000189058	ENST00000343267;ENST00000421243;ENST00000453131	T;T;T	0.21031	2.03;2.03;2.03	5.68	1.61	0.23674	Calycin (1);	0.701798	0.13384	N	0.391946	T	0.11196	0.0273	L	0.38175	1.15	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.06405	0.002;0.002	T	0.19976	-1.0289	10	0.62326	D	0.03	-0.2464	7.3764	0.26831	0.7035:0.0:0.2965:0.0	rs5952	15;15	B4DGC3;P05090	.;APOD_HUMAN	S	15;43;15	ENSP00000345179:F15S;ENSP00000415235:F43S;ENSP00000393076:F15S	ENSP00000345179:F15S	F	-	2	0	APOD	196787578	0.127000	0.22367	0.000000	0.03702	0.009000	0.06853	1.338000	0.33873	0.434000	0.26340	0.533000	0.62120	TTC	A|0.996;G|0.004	0.004	strong		0.582	APOD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342004.1	NM_001647		G	195306289	A	G	195306289	3	3	30	1	0	0	0	0	1	0	0	0	801	246	9	3	541	3	APOD	3	195306289	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	23244301	195306289	2716141	139	13290											
PAK2	5062	hgsc.bcm.edu	37	chr3	196529917	196529917	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaacagtgggctcgattactAcagacctccaatatcaccaa	14	8	7	12	1	1	1	1	0	0	1	3	3	2	1	3	1	3	1	3	1	6	3	rs183020057	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:196529917A>G	ENST00000327134.3	+	4	640	c.318A>G	c.(316-318)ctA>ctG	p.L106L		NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	106	Autoregulatory region. {ECO:0000250}.|GTPase-binding. {ECO:0000250}.				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)		CTCGATTACTACAGACCTCCA	0.378													A|||	5	0.000998403	0.0008	0.0	5008	,	,		19631	0.001		0.001	False		,,,				2504	0.002				p.L106L		Atlas-SNP	.											.	PAK2	113	.	0			c.A318G						PASS	.						93	81	85					3																	196529917		2203	4300	6503	SO:0001819	synonymous_variant	5062	exon4			ATTACTACAGACC	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.318A>G	3.37:g.196529917A>G		180	0	0		214	10	0.046729	NM_002577	Q13154|Q6ISC3	Silent	SNP	ENST00000327134.3	37	CCDS3321.1																																																																																			A|1.000;G|0.000	0.000	strong		0.378	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577		G	196529917	A	G	196529917	2	3	30	1	0	0	0	0	0	0	0	1	11410	378	14	3		3	PAK2	3	196529917	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	1223628	196529917	1492513	140	13291											
KIAA0226	9711	hgsc.bcm.edu	37	chr3	197408085	197408085	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaggatcattccagatcttaAtgagcaggtccttggagaag	12	10	12	7	0	2	3	1	1	1	2	4	6	4	4	2	3	1	1	2	3	2	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr3:197408085A>C	ENST00000296343.5	-	16	2344	c.2345T>G	c.(2344-2346)aTt>aGt	p.I782S	KIAA0226_ENST00000389665.5_Missense_Mutation_p.I807S|KIAA0226_ENST00000273582.5_Missense_Mutation_p.I737S	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	782					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)		CCAGATCTTAATGAGCAGGTC	0.517																																					p.I782S	Esophageal Squamous(3;167 355 3763 15924)	Atlas-SNP	.											.	KIAA0226	136	.	0			c.T2345G						PASS	.						149	144	145					3																	197408085		2034	4226	6260	SO:0001583	missense	9711	exon16			ATCTTAATGAGCA	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.2345T>G	3.37:g.197408085A>C	ENSP00000296343:p.Ile782Ser	172	0	0		156	75	0.480769	NM_014687	Q96CK5	Missense_Mutation	SNP	ENST00000296343.5	37	CCDS43195.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	A|A|A	1.156|1.156|1.156	-0.645279|-0.645279|-0.645279	0.03531|0.03531|0.03531	.|.|.	.|.|.	ENSG00000145016|ENSG00000145016|ENSG00000145016	ENST00000413360|ENST00000273582;ENST00000296343;ENST00000389665|ENST00000415452	.|.|.	.|.|.	.|.|.	4.55|4.55|4.55	0.842|0.842|0.842	0.18927|0.18927|0.18927	.|.|.	.|0.449024|.	.|0.23137|.	.|N|.	.|0.051520|.	T|T|T	0.07052|0.07052|0.07052	0.0179|0.0179|0.0179	N|N|N	0.00413|0.00413|0.00413	-1.525|-1.525|-1.525	0.09310|0.09310|0.09310	N|N|N	1|1|1	.|B;B;B|.	.|0.06786|.	.|0.001;0.0;0.001|.	.|B;B;B|.	.|0.10450|.	.|0.003;0.0;0.005|.	T|T|T	0.39035|0.39035|0.39035	-0.9633|-0.9633|-0.9633	5|9|5	.|0.07990|.	.|T|.	.|0.79|.	.|.|.	5.7617|5.7617|5.7617	0.18203|0.18203|0.18203	0.394:0.4484:0.1575:0.0|0.394:0.4484:0.1575:0.0|0.394:0.4484:0.1575:0.0	.|.|.	.|807;737;782|.	.|Q92622-3;Q92622-2;Q92622|.	.|.;.;RUBIC_HUMAN|.	Q|S|V	743|737;782;807|566	.|.|.	.|ENSP00000273582:I737S|.	H|I|L	-|-|-	3|2|1	2|0|2	KIAA0226|KIAA0226|KIAA0226	198892482|198892482|198892482	0.950000|0.950000|0.950000	0.32346|0.32346|0.32346	0.220000|0.220000|0.220000	0.23810|0.23810|0.23810	0.992000|0.992000|0.992000	0.81027|0.81027|0.81027	1.068000|1.068000|1.068000	0.30629|0.30629|0.30629	0.353000|0.353000|0.353000	0.24079|0.24079|0.24079	0.454000|0.454000|0.454000	0.30748|0.30748|0.30748	CAT|ATT|TTA	.	.	none		0.517	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901		C	197408085	A	C	197408085	3	2	30	1	0	0	0	0	1	0	0	0	8171	101	4	5	593	5	KIAA0226	3	197408085	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	878168	197408085	614345	141	13292											
ZNF732	654254	hgsc.bcm.edu	37	chr4	289877	289877	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctctatacaaattctgctggGcagggtccaggcatttccac	9	11	9	12	0	2	0	0	0	2	0	4	0	4	0	2	3	2	3	2	3	3	4	rs62619793	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:289877G>T	ENST00000419098.1	-	2	81	c.71C>A	c.(70-72)gCc>gAc	p.A24D		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						ATTCTGCTGGGCAGGGTCCAG	0.423													.|||	191	0.038139	0.0968	0.0317	5008	,	,		17640	0.0		0.0298	False		,,,				2504	0.0112				p.A23D		Atlas-SNP	.											.	ZNF732	117	.	0			c.C68A						PASS	.						33	32	32					4																	289877		692	1590	2282	SO:0001583	missense	654254	exon1			TGCTGGGCAGGGT	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.71C>A	4.37:g.289877G>T	ENSP00000415774:p.Ala24Asp	326	1	0.00306748		291	138	0.474227	NM_001137608		Missense_Mutation	SNP	ENST00000419098.1	37	CCDS46990.1	90	0.04120879120879121	57	0.11585365853658537	11	0.03038674033149171	0	0.0	22	0.029023746701846966	G	6.253	0.414829	0.11870	.	.	ENSG00000186777	ENST00000419098	T	0.02525	4.26	1.22	1.22	0.21188	Krueppel-associated box (4);	.	.	.	.	T	0.00109	0.0003	M	0.88310	2.945	0.80722	P	0.0	B	0.20368	0.044	B	0.28991	0.097	T	0.03566	-1.1024	8	0.72032	D	0.01	.	5.3307	0.15930	0.0:0.0:1.0:0.0	rs62619793	24	B4DXR9	ZN732_HUMAN	D	24	ENSP00000415774:A24D	ENSP00000415774:A24D	A	-	2	0	ZNF732	279877	0.000000	0.05858	0.082000	0.20525	0.084000	0.17831	-1.252000	0.02880	0.300000	0.22699	0.305000	0.20034	GCC	G|0.958;T|0.042	0.042	strong		0.423	ZNF732-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000357937.2	NM_001137608		T	289877	G	T	289877	3	4	30	1	0	0	0	0	1	0	0	0	18138	1203	42	4	1698	4	ZNF732	4	289877	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10		289877	190864399	142	13293											
GAK	2580	hgsc.bcm.edu	37	chr4	843536	843536	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccatgaagatcatcttggcGtgctgctcgtacggctgccc	6	11	11	13	3	2	2	1	1	1	1	4	2	3	2	2	2	4	4	2	2	2	2	rs55904229	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:843536G>A	ENST00000314167.4	-	28	3971	c.3861C>T	c.(3859-3861)caC>caT	p.H1287H	GAK_ENST00000511163.1_Silent_p.H1208H|GAK_ENST00000509566.1_5'UTR	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	1287	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				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)		TCATCTTGGCGTGCTGCTCGT	0.672													G|||	9	0.00179712	0.0008	0.0	5008	,	,		14022	0.0		0.006	False		,,,				2504	0.002				p.H1287H		Atlas-SNP	.											.	GAK	104	.	0			c.C3861T						PASS	.	G		7,4399	12.9+/-30.5	0,7,2196	51	49	50		3861	-7.5	0	4	dbSNP_129	50	55,8545	34.3+/-88.2	0,55,4245	no	coding-synonymous	GAK	NM_005255.2		0,62,6441	AA,AG,GG		0.6395,0.1589,0.4767		1287/1312	843536	62,12944	2203	4300	6503	SO:0001819	synonymous_variant	2580	exon28			CTTGGCGTGCTGC	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.3861C>T	4.37:g.843536G>A		279	0	0		268	132	0.492537	NM_005255	Q5U4P5|Q9BVY6	Silent	SNP	ENST00000314167.4	37	CCDS3340.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	1.270	-0.613465	0.03690	0.001589	0.006395	ENSG00000178950	ENST00000511980	.	.	.	4.76	-7.48	0.01360	.	.	.	.	.	T	0.45458	0.1343	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59005	-0.7535	4	.	.	.	-0.8575	11.9205	0.52789	0.7915:0.1057:0.1028:0.0	rs55904229	.	.	.	M	443	.	.	T	-	2	0	GAK	833536	0.555000	0.26530	0.003000	0.11579	0.228000	0.25075	-0.100000	0.10990	-1.556000	0.01695	-0.796000	0.03273	ACG	G|0.997;A|0.003	0.003	strong		0.672	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255		A	843536	G	A	843536	2	1	30	1	0	0	0	0	0	0	0	1	6203	1136	40	1		1	GAK	4	843536	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	553659	843536	190310740	143	13294											
TACC3	10460	hgsc.bcm.edu	37	chr4	1729958	1729958	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgaagccctgggctgccctGcgggtgtgggcacccccgtg	3	6	17	15	3	0	0	0	0	0	0	0	1	0	0	4	3	3	2	4	3	1	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:1729958G>T	ENST00000313288.4	+	4	935	c.829G>T	c.(829-831)Gcg>Tcg	p.A277S		NM_006342.2	NP_006333.1	Q9Y6A5	TACC3_HUMAN	transforming, acidic coiled-coil containing protein 3	277					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)			GGGCTGCCCTGCGGGTGTGGG	0.667																																					p.A277S	Ovarian(120;482 2294 11894 35824)	Atlas-SNP	.											.	TACC3	69	.	0			c.G829T						PASS	.						15	17	16					4																	1729958		2193	4293	6486	SO:0001583	missense	10460	exon4			TGCCCTGCGGGTG	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.829G>T	4.37:g.1729958G>T	ENSP00000326550:p.Ala277Ser	67	0	0		95	59	0.621053	NM_006342	Q2NKK4|Q3KQS5|Q9UMQ1	Missense_Mutation	SNP	ENST00000313288.4	37	CCDS3352.1	.	.	.	.	.	.	.	.	.	.	G	3.044	-0.196772	0.06259	.	.	ENSG00000013810	ENST00000313288	T	0.10477	2.87	3.55	-3.23	0.05109	.	10.642000	0.00481	U	0.000126	T	0.04907	0.0132	N	0.08118	0	0.09310	N	1	B;B	0.16396	0.017;0.004	B;B	0.12837	0.008;0.004	T	0.30736	-0.9968	10	0.10636	T	0.68	0.0017	4.8773	0.13662	0.3038:0.2546:0.4416:0.0	.	277;277	B4DYJ1;Q9Y6A5	.;TACC3_HUMAN	S	277	ENSP00000326550:A277S	ENSP00000326550:A277S	A	+	1	0	TACC3	1699756	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.169000	0.09911	-0.955000	0.03636	0.563000	0.77884	GCG	.	.	none		0.667	TACC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000203730.2			T	1729958	G	T	1729958	3	4	30	1	0	0	0	0	1	0	0	0	15518	1319	46	4	839	4	TACC3	4	1729958	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	886422	1729958	189424318	144	13295											
SH3TC1	54436	hgsc.bcm.edu	37	chr4	8229140	8229140	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gggcggctgtgcagcaggagGctcaagctgtcccaggcccg	6	5	17	13	2	1	0	1	0	0	0	2	1	2	1	2	5	3	5	2	5	1	0	rs141562329	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:8229140G>T	ENST00000245105.3	+	12	1786	c.1719G>T	c.(1717-1719)agG>agT	p.R573S	SH3TC1_ENST00000514274.1_3'UTR|SH3TC1_ENST00000539824.1_Missense_Mutation_p.R497S	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	573										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						GCAGCAGGAGGCTCAAGCTGT	0.692													G|||	13	0.00259585	0.0	0.0	5008	,	,		15676	0.001		0.003	False		,,,				2504	0.0092				p.R573S	NSCLC(145;2298 2623 35616 37297)	Atlas-SNP	.											.	SH3TC1	105	.	0			c.G1719T						PASS	.	G	SER/ARG	0,4340		0,0,2170	35	40	38		1719	2.4	0.8	4	dbSNP_134	38	18,8450		0,18,4216	yes	missense	SH3TC1	NM_018986.3	110	0,18,6386	TT,TG,GG		0.2126,0.0,0.1405	possibly-damaging	573/1337	8229140	18,12790	2170	4234	6404	SO:0001583	missense	54436	exon12			CAGGAGGCTCAAG	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.1719G>T	4.37:g.8229140G>T	ENSP00000245105:p.Arg573Ser	97	0	0		93	40	0.430108	NM_018986	Q4W5G5	Missense_Mutation	SNP	ENST00000245105.3	37	CCDS3399.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	15.49	2.849206	0.51270	0.0	0.002126	ENSG00000125089	ENST00000382516;ENST00000245105;ENST00000539824;ENST00000535265	T;T	0.79845	-1.31;-1.31	4.51	2.42	0.29668	Tetratricopeptide-like helical (1);	0.373920	0.30003	N	0.010654	T	0.79639	0.4480	L	0.49126	1.545	0.09310	N	1	P	0.48911	0.917	P	0.50314	0.637	T	0.71394	-0.4606	10	0.66056	D	0.02	-17.1056	10.2336	0.43268	0.2842:0.0:0.7158:0.0	.	573	Q8TE82	S3TC1_HUMAN	S	311;573;497;402	ENSP00000245105:R573S;ENSP00000441045:R497S	ENSP00000245105:R573S	R	+	3	2	SH3TC1	8280040	0.976000	0.34144	0.808000	0.32385	0.871000	0.50021	0.768000	0.26590	0.892000	0.36259	-0.254000	0.11334	AGG	G|0.999;T|0.001	0.001	strong		0.692	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986		T	8229140	G	T	8229140	3	4	30	1	0	0	0	0	1	0	0	0	14276	1194	42	4	1761	4	SH3TC1	4	8229140	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	6499182	8229140	182925136	145	13296											
BOD1L	259282	hgsc.bcm.edu	37	chr4	13602793	13602793	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcttccacatgctctaccaCagtaccaatctgactgtccc	10	10	5	16	0	2	1	0	1	2	0	4	1	4	1	4	0	4	3	4	0	3	3	rs199927242		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:13602793C>G	ENST00000040738.5	-	10	5866	c.5731G>C	c.(5731-5733)Gtg>Ctg	p.V1911L		NM_148894.2	NP_683692.2	Q8NFC6	BD1L1_HUMAN	biorientation of chromosomes in cell division 1-like 1	1911						nucleus (GO:0005634)	DNA binding (GO:0003677)										TGCTCTACCACAGTACCAATC	0.443													C|||	1	0.000199681	0.0008	0.0	5008	,	,		23179	0.0		0.0	False		,,,				2504	0.0				p.V1911L		Atlas-SNP	.											.	.	.	.	0			c.G5731C						PASS	.	C	LEU/VAL	1,4405	2.1+/-5.4	0,1,2202	119	118	118		5731	2.8	0	4		118	1,8599	1.2+/-3.3	0,1,4299	yes	missense	BOD1L	NM_148894.2	32	0,2,6501	GG,GC,CC		0.0116,0.0227,0.0154	benign	1911/3052	13602793	2,13004	2203	4300	6503	SO:0001583	missense	259282	exon10			CTACCACAGTACC	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.5731G>C	4.37:g.13602793C>G	ENSP00000040738:p.Val1911Leu	160	0	0		147	68	0.462585	NM_148894	Q6P0M8|Q96AL1|Q9H6G0|Q9NTD6|Q9P2L9	Missense_Mutation	SNP	ENST00000040738.5	37	CCDS3411.2	.	.	.	.	.	.	.	.	.	.	C	5.583	0.292461	0.10567	2.27E-4	1.16E-4	ENSG00000038219	ENST00000040738	T	0.08807	3.05	4.79	2.8	0.32819	.	0.896444	0.09441	N	0.801789	T	0.06050	0.0157	N	0.19112	0.55	0.09310	N	1	B	0.22003	0.063	B	0.19148	0.024	T	0.40232	-0.9574	10	0.33940	T	0.23	0.4353	7.6976	0.28604	0.0:0.7633:0.0:0.2367	.	1911	Q8NFC6	BOD1L_HUMAN	L	1911	ENSP00000040738:V1911L	ENSP00000040738:V1911L	V	-	1	0	BOD1L	13211891	0.000000	0.05858	0.001000	0.08648	0.053000	0.15095	0.762000	0.26503	0.812000	0.34326	0.561000	0.74099	GTG	.	.	weak		0.443	BOD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207321.1	NM_148894		G	13602793	C	G	13602793	3	3	30	1	0	0	0	0	1	0	0	0	1483	478	17	4	3492	4	BOD1L	4	13602793	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	5373653	13602793	177551483	146	13297											
DHX15	1665	hgsc.bcm.edu	37	chr4	24550580	24550580	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacaatggaatgattttaatGtcaccaacttcagggcccaa	14	11	7	9	0	2	1	2	1	0	0	2	2	2	2	2	2	2	0	2	2	6	4	rs33972724	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:24550580G>A	ENST00000336812.4	-	6	1302	c.1146C>T	c.(1144-1146)gaC>gaT	p.D382D		NM_001358.2	NP_001349.2	O43143	DHX15_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 15	382	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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)				TGATTTTAATGTCACCAACTT	0.393													G|||	25	0.00499201	0.0015	0.013	5008	,	,		15491	0.0		0.0139	False		,,,				2504	0.0				p.D382D		Atlas-SNP	.											.	DHX15	69	.	0			c.C1146T						PASS	.	G		11,4395	17.9+/-39.9	0,11,2192	124	111	115		1146	3.2	1	4	dbSNP_126	115	108,8492	59.1+/-120.7	0,108,4192	no	coding-synonymous	DHX15	NM_001358.2		0,119,6384	AA,AG,GG		1.2558,0.2497,0.915		382/796	24550580	119,12887	2203	4300	6503	SO:0001819	synonymous_variant	1665	exon6			TTTAATGTCACCA	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.1146C>T	4.37:g.24550580G>A		102	0	0		92	39	0.423913	NM_001358	Q9NQT7	Silent	SNP	ENST00000336812.4	37	CCDS33966.1																																																																																			G|0.991;A|0.009	0.009	strong		0.393	DHX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360143.1	NM_001358		A	24550580	G	A	24550580	2	1	30	1	0	0	0	0	0	0	0	1	4503	1368	48	2		2	DHX15	4	24550580	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	10947787	24550580	166603696	147	13298											
ARAP2	116984	hgsc.bcm.edu	37	chr4	36230634	36230634	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agaacccaaattcaggtgtgGttcctctgcagtggggaagt	10	10	13	8	0	2	1	1	0	1	1	3	2	3	2	2	4	2	2	2	4	3	2	rs141442791	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:36230634G>A	ENST00000303965.4	-	2	964	c.475C>T	c.(475-477)Cca>Tca	p.P159S		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	159					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						TTCAGGTGTGGTTCCTCTGCA	0.393													G|||	7	0.00139776	0.0	0.0014	5008	,	,		20594	0.0		0.006	False		,,,				2504	0.0				p.P159S		Atlas-SNP	.											.	ARAP2	210	.	0			c.C475T						PASS	.	G	SER/PRO	3,4403	4.2+/-10.8	0,3,2200	69	65	67		475	-0.6	0	4	dbSNP_134	67	16,8584	11.9+/-42.8	0,16,4284	yes	missense	ARAP2	NM_015230.3	74	0,19,6484	AA,AG,GG		0.186,0.0681,0.1461	benign	159/1705	36230634	19,12987	2203	4300	6503	SO:0001583	missense	116984	exon2			GGTGTGGTTCCTC	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.475C>T	4.37:g.36230634G>A	ENSP00000302895:p.Pro159Ser	82	0	0		94	43	0.457447	NM_015230	Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Missense_Mutation	SNP	ENST00000303965.4	37	CCDS3441.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	5.262	0.233857	0.09969	6.81E-4	0.00186	ENSG00000047365	ENST00000303965	T	0.62639	0.01	5.5	-0.558	0.11796	.	0.647728	0.14546	N	0.312977	T	0.34395	0.0896	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.0;0.001	T	0.12889	-1.0530	10	0.16420	T	0.52	.	3.6174	0.08082	0.3113:0.0:0.427:0.2617	.	89;159	A7E2A5;Q8WZ64	.;ARAP2_HUMAN	S	159	ENSP00000302895:P159S	ENSP00000302895:P159S	P	-	1	0	ARAP2	35907029	0.888000	0.30383	0.021000	0.16686	0.262000	0.26303	1.029000	0.30140	0.010000	0.14839	0.650000	0.86243	CCA	G|0.998;A|0.002	0.002	strong		0.393	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230		A	36230634	G	A	36230634	3	1	30	1	0	0	0	0	1	0	0	0	839	1261	44	2	4767	2	ARAP2	4	36230634	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	11680054	36230634	154923642	148	13299											
EXOC1	55763	hgsc.bcm.edu	37	chr4	56737278	56737278	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atattctagaaccacatggaCttggccaaaggtcatataaa	16	10	7	8	0	2	1	1	0	1	1	2	2	2	2	2	3	1	0	2	3	7	6			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:56737278C>G	ENST00000381295.2	+	7	1191	c.843C>G	c.(841-843)gaC>gaG	p.D281E	EXOC1_ENST00000349598.6_Missense_Mutation_p.D281E|EXOC1_ENST00000346134.7_Missense_Mutation_p.D281E	NM_001024924.1	NP_001020095.1	Q9NV70	EXOC1_HUMAN	exocyst complex component 1	281					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)					ACCACATGGACTTGGCCAAAG	0.448																																					p.D281E		Atlas-SNP	.											.	EXOC1	103	.	0			c.C843G						PASS	.						98	86	90					4																	56737278		2203	4300	6503	SO:0001583	missense	55763	exon7			CATGGACTTGGCC	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.843C>G	4.37:g.56737278C>G	ENSP00000370695:p.Asp281Glu	198	0	0		158	77	0.487342	NM_018261	Q504V4|Q8WUE7|Q96T15|Q9NZE4	Missense_Mutation	SNP	ENST00000381295.2	37	CCDS3502.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.040304	0.75732	.	.	ENSG00000090989	ENST00000381295;ENST00000346134;ENST00000349598	.	.	.	5.97	4.23	0.50019	.	0.043036	0.85682	D	0.000000	T	0.63510	0.2517	L	0.58669	1.825	0.58432	D	0.999993	D;P	0.76494	0.999;0.95	D;P	0.80764	0.994;0.836	T	0.59669	-0.7411	9	0.11182	T	0.66	.	6.0347	0.19699	0.0:0.7065:0.0:0.2935	.	281;281	Q9NV70-2;Q9NV70	.;EXOC1_HUMAN	E	281	.	ENSP00000326514:D281E	D	+	3	2	EXOC1	56432035	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	1.604000	0.36804	2.833000	0.97629	0.585000	0.79938	GAC	.	.	none		0.448	EXOC1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361799.1	NM_018261		G	56737278	C	G	56737278	3	3	30	1	0	0	0	0	1	0	0	0	5303	564	20	4	865	4	EXOC1	4	56737278	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	20506644	56737278	134416998	149	13300											
MUC7	4589	hgsc.bcm.edu	37	chr4	71347333	71347333	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acccacaccttctgcaactaCaccagctccaccgtcttccc	9	8	3	21	1	2	0	0	0	2	0	4	0	4	0	6	0	4	2	6	0	2	3	rs72655156	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:71347333C>T	ENST00000304887.5	+	3	1062	c.872C>T	c.(871-873)aCa>aTa	p.T291I	MUC7_ENST00000413702.1_Missense_Mutation_p.T291I|MUC7_ENST00000456088.1_Missense_Mutation_p.T291I	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted	291	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)			TCTGCAACTACACCAGCTCCA	0.562													-|||	28	0.00559105	0.0	0.0086	5008	,	,		22130	0.0		0.0199	False		,,,				2504	0.002				p.T291I		Atlas-SNP	.											.	MUC7	91	.	0			c.C872T						PASS	.	C	ILE/THR,ILE/THR,ILE/THR	16,4390		0,16,2187	389	355	367		872,872,872	1.5	0	4	dbSNP_131	367	195,8405		1,193,4106	yes	missense,missense,missense	MUC7	NM_001145006.1,NM_001145007.1,NM_152291.2	89,89,89	1,209,6293	TT,TC,CC		2.2674,0.3631,1.6223	probably-damaging,probably-damaging,probably-damaging	291/378,291/378,291/378	71347333	211,12795	2203	4300	6503	SO:0001583	missense	4589	exon4			CAACTACACCAGC	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.872C>T	4.37:g.71347333C>T	ENSP00000302021:p.Thr291Ile	398	1	0.00251256		409	185	0.452323	NM_001145007	Q9UCD7|Q9UCD8	Missense_Mutation	SNP	ENST00000304887.5	37	CCDS3541.1	24	0.01098901098901099	0	0.0	6	0.016574585635359115	0	0.0	18	0.023746701846965697	-	9.647	1.140465	0.21205	0.003631	0.022674	ENSG00000171195	ENST00000413702;ENST00000456088;ENST00000304887	T;T;T	0.58210	0.35;0.35;0.35	1.52	1.52	0.23074	.	.	.	.	.	T	0.36276	0.0961	N	0.19112	0.55	0.09310	N	1	D	0.71674	0.998	D	0.74023	0.982	T	0.28713	-1.0035	8	.	.	.	.	8.9663	0.35879	0.0:1.0:0.0:0.0	.	291	Q8TAX7	MUC7_HUMAN	I	291	ENSP00000407422:T291I;ENSP00000400585:T291I;ENSP00000302021:T291I	.	T	+	2	0	MUC7	71381922	0.384000	0.25164	0.002000	0.10522	0.002000	0.02628	3.421000	0.52742	1.122000	0.41944	0.505000	0.49811	ACA	C|0.985;T|0.015	0.015	strong		0.562	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291		T	71347333	C	T	71347333	3	4	30	1	0	0	0	0	1	0	0	0	9990	478	17	2	878	2	MUC7	4	71347333	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	14610055	71347333	119806943	150	13301											
NUP54	53371	hgsc.bcm.edu	37	chr4	77038912	77038912	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catcctgatttgagacatcaAttcatttagtcggccctaaa	12	13	6	10	1	2	2	2	2	0	1	4	3	3	2	2	1	0	0	2	1	4	5	rs144785979	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:77038912A>T	ENST00000264883.3	-	11	1440	c.1300T>A	c.(1300-1302)Ttg>Atg	p.L434M	NUP54_ENST00000514987.1_Missense_Mutation_p.L386M|NUP54_ENST00000342467.6_Missense_Mutation_p.L218M|NUP54_ENST00000458189.2_Missense_Mutation_p.L254M	NM_017426.2	NP_059122.2	Q7Z3B4	NUP54_HUMAN	nucleoporin 54kDa	434	9 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 targeting (GO:0006605)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)	nucleocytoplasmic transporter activity (GO:0005487)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(3)|skin(1)|stomach(1)	19						TGAGACATCAATTCATTTAGT	0.373													A|||	2	0.000399361	0.0	0.0	5008	,	,		20100	0.0		0.002	False		,,,				2504	0.0				p.L434M		Atlas-SNP	.											.	NUP54	48	.	0			c.T1300A						PASS	.	A	MET/LEU	1,4405	2.1+/-5.4	0,1,2202	116	109	111		1300	-1.2	1	4	dbSNP_134	111	4,8594	3.7+/-12.6	0,4,4295	yes	missense	NUP54	NM_017426.2	15	0,5,6497	TT,TA,AA		0.0465,0.0227,0.0384	possibly-damaging	434/508	77038912	5,12999	2203	4299	6502	SO:0001583	missense	53371	exon11			ACATCAATTCATT	AF157322	CCDS3576.1, CCDS63998.1	4q21.1	2008-07-03	2002-08-29		ENSG00000138750	ENSG00000138750			17359	protein-coding gene	gene with protein product		607607	"nucleoporin 54kD"			8707840	Standard	NM_017426		Approved		uc003hjs.3	Q7Z3B4	OTTHUMG00000130098	ENST00000264883.3:c.1300T>A	4.37:g.77038912A>T	ENSP00000264883:p.Leu434Met	251	0	0		256	115	0.449219	NM_017426	B2RCK7|B4DT35|Q96EA7|Q9NVL5|Q9P0I1	Missense_Mutation	SNP	ENST00000264883.3	37	CCDS3576.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	13.35	2.209809	0.39003	2.27E-4	4.65E-4	ENSG00000138750	ENST00000264883;ENST00000342467;ENST00000514987;ENST00000458189	.	.	.	5.88	-1.16	0.09678	.	0.000000	0.64402	D	0.000001	T	0.64757	0.2627	M	0.75615	2.305	0.47905	D	0.999546	P;P;D	0.52996	0.926;0.918;0.957	P;B;P	0.56612	0.802;0.436;0.802	T	0.64419	-0.6412	9	0.49607	T	0.09	-7.8541	9.651	0.39897	0.1989:0.1983:0.6027:0.0	.	386;218;434	B4DT35;Q7Z3B4-2;Q7Z3B4	.;.;NUP54_HUMAN	M	434;218;386;254	.	ENSP00000264883:L434M	L	-	1	2	NUP54	77257936	0.991000	0.36638	0.980000	0.43619	0.416000	0.31233	0.731000	0.26058	-0.151000	0.11176	-2.917000	0.00090	TTG	A|0.999;T|0.001	0.001	strong		0.373	NUP54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252402.3			T	77038912	A	T	77038912	3	4	30	1	0	0	0	0	1	0	0	0	10776	98	4	5	231	5	NUP54	4	77038912	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	5691579	77038912	114115364	151	13302											
TET2	54790	hgsc.bcm.edu	37	chr4	106196819	106196819	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttagaccaaatgtacatcatGtagggaaattgcctccttat	13	13	7	8	0	1	1	1	0	0	1	2	2	2	2	3	1	2	2	3	1	6	5	rs142312318	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:106196819G>T	ENST00000540549.1	+	11	6012	c.5152G>T	c.(5152-5154)Gta>Tta	p.V1718L	TET2_ENST00000380013.4_Missense_Mutation_p.V1718L|TET2_ENST00000545826.1_3'UTR|TET2_ENST00000513237.1_Missense_Mutation_p.V1739L			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1718			V -> L (in refractory anemia with ringed sideroblasts; somatic mutation in an acute myeloid leukemia sample; dbSNP:rs142312318). {ECO:0000269|PubMed:19372255, ECO:0000269|PubMed:19420352}.		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)	p.V1718L(6)		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)		TGTACATCATGTAGGGAAATT	0.418			"Mis N, F"		MDS								G|||	3	0.000599042	0.0	0.0014	5008	,	,		23074	0.0		0.001	False		,,,				2504	0.001				p.V1718L		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	TET2,NS,lymphoid_neoplasm,0,8	TET2	1762	8	6	Substitution - Missense(6)	haematopoietic_and_lymphoid_tissue(6)	c.G5152T						PASS	.	G	LEU/VAL	1,1383		0,1,691	114	95	101		5152	-2.3	0	4	dbSNP_134	101	21,3161		0,21,1570	yes	missense	TET2	NM_001127208.2	32	0,22,2261	TT,TG,GG		0.66,0.0723,0.4818	possibly-damaging	1718/2003	106196819	22,4544	692	1591	2283	SO:0001583	missense	54790	exon11			CATCATGTAGGGA	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.5152G>T	4.37:g.106196819G>T	ENSP00000442788:p.Val1718Leu	263	0	0		200	95	0.475	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Missense_Mutation	SNP	ENST00000540549.1	37	CCDS47120.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	0.311	-0.968065	0.02232	7.23E-4	0.0066	ENSG00000168769	ENST00000540549;ENST00000513237;ENST00000380013	T;T;T	0.02158	4.42;4.42;4.42	5.16	-2.29	0.06805	Methylcytosine dioxygenase TET, double-stranded beta helix fold domain (1);	.	.	.	.	T	0.00998	0.0033	N	0.21583	0.68	0.09310	N	1	B;B	0.13145	0.007;0.007	B;B	0.17433	0.018;0.012	T	0.49011	-0.8983	9	0.08837	T	0.75	-0.48	5.6612	0.17670	0.3513:0.2405:0.4082:0.0	.	1739;1718	E7EQS8;Q6N021	.;TET2_HUMAN	L	1718;1739;1718	ENSP00000442788:V1718L;ENSP00000425443:V1739L;ENSP00000369351:V1718L	ENSP00000369351:V1718L	V	+	1	0	TET2	106416268	0.000000	0.05858	0.000000	0.03702	0.066000	0.16364	-0.054000	0.11826	-0.328000	0.08539	-0.373000	0.07131	GTA	G|0.999;T|0.001	0.001	strong		0.418	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628		T	106196819	G	T	106196819	3	4	30	1	0	0	0	0	1	0	0	0	15785	1377	48	4	5275	4	TET2	4	106196819	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	29157907	106196819	84957457	152	13303											
NDST3	9348	hgsc.bcm.edu	37	chr4	118975189	118975189	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggctacaaacaggaaaatGaactctctgagacggcttca	14	8	10	9	1	2	2	1	2	1	1	3	4	2	3	0	3	3	2	0	3	5	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:118975189G>T	ENST00000296499.5	+	2	527	c.124G>T	c.(124-126)Gaa>Taa	p.E42*	NDST3_ENST00000433996.2_Nonsense_Mutation_p.E42*	NM_004784.2	NP_004775.1	O95803	NDST3_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 3	42	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						ACAGGAAAATGAACTCTCTGA	0.423																																					p.E42X		Atlas-SNP	.											.	NDST3	107	.	0			c.G124T						PASS	.						122	119	120					4																	118975189		2203	4300	6503	SO:0001587	stop_gained	9348	exon2			GAAAATGAACTCT	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.124G>T	4.37:g.118975189G>T	ENSP00000296499:p.Glu42*	224	1	0.00446429		123	60	0.487805	NM_004784	B4DI67|Q4W5C1|Q4W5D0|Q6UWC5|Q9UP21	Nonsense_Mutation	SNP	ENST00000296499.5	37	CCDS3708.1	.	.	.	.	.	.	.	.	.	.	G	36	5.624220	0.96660	.	.	ENSG00000164100	ENST00000296499;ENST00000433996	.	.	.	5.82	4.98	0.66077	.	0.262983	0.39083	N	0.001477	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	.	11.9424	0.52909	0.0:0.1318:0.7311:0.1371	.	.	.	.	X	42	.	ENSP00000296499:E42X	E	+	1	0	NDST3	119194637	1.000000	0.71417	0.305000	0.25099	0.920000	0.55202	7.237000	0.78164	1.441000	0.47550	0.650000	0.86243	GAA	.	.	none		0.423	NDST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256517.4	NM_004784		T	118975189	G	T	118975189	4	4	30	1	0	0	0	0	0	1	0	0	10266	1291	45	4	126	4	NDST3	4	118975189	Nonsense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	12778370	118975189	72179087	153	13304											
PRDM5	11107	hgsc.bcm.edu	37	chr4	121737704	121737704	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacaaacctggcatccccccGgcaagtctcctggtgctgct	7	8	9	17	1	1	0	0	0	1	0	3	0	2	0	5	3	3	4	5	3	2	0	rs190835070		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:121737704G>A	ENST00000264808.3	-	7	1009	c.769C>T	c.(769-771)Cgg>Tgg	p.R257W	PRDM5_ENST00000515109.1_Missense_Mutation_p.R226W|PRDM5_ENST00000428209.2_Missense_Mutation_p.R226W	NM_018699.2	NP_061169.2	Q9NQX1	PRDM5_HUMAN	PR domain containing 5	257					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						GCATCCCCCCGGCAAGTCTCC	0.493													G|||	1	0.000199681	0.0	0.0	5008	,	,		18108	0.0		0.001	False		,,,				2504	0.0				p.R257W		Atlas-SNP	.											PRDM5,NS,carcinoma,+1,1	PRDM5	76	1	0			c.C769T						scavenged	.	G	TRP/ARG	0,4406		0,0,2203	55	51	52		769	4.2	0.9	4		52	2,8598	2.2+/-6.3	0,2,4298	no	missense	PRDM5	NM_018699.2	101	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	257/631	121737704	2,13004	2203	4300	6503	SO:0001583	missense	11107	exon7			CCCCCCGGCAAGT	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.769C>T	4.37:g.121737704G>A	ENSP00000264808:p.Arg257Trp	99	1	0.010101		78	24	0.307692	NM_018699	Q0VAI9|Q0VAJ0|Q6NXQ7	Missense_Mutation	SNP	ENST00000264808.3	37	CCDS3716.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	23.5	4.419624	0.83559	0.0	2.33E-4	ENSG00000138738	ENST00000264808;ENST00000515109;ENST00000428209	T;T;T	0.15372	2.43;2.43;2.43	6.07	4.24	0.50183	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.270689	0.41396	D	0.000900	T	0.29321	0.0730	L	0.48362	1.52	0.80722	D	1	D;D;D	0.76494	0.978;0.999;0.978	B;P;B	0.56916	0.425;0.809;0.306	T	0.04635	-1.0937	10	0.87932	D	0	-1.8067	14.4681	0.67497	0.0:0.0:0.5912:0.4088	.	226;226;257	Q0VAI9;Q9NQX1-2;Q9NQX1	.;.;PRDM5_HUMAN	W	257;226;226	ENSP00000264808:R257W;ENSP00000422309:R226W;ENSP00000404832:R226W	ENSP00000264808:R257W	R	-	1	2	PRDM5	121957154	1.000000	0.71417	0.861000	0.33841	0.998000	0.95712	3.119000	0.50422	1.546000	0.49388	0.655000	0.94253	CGG	G|1.000;A|0.000	0.000	strong		0.493	PRDM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256528.2			A	121737704	G	A	121737704	3	1	30	1	0	0	0	0	1	0	0	0	12472	1115	39	1	1163	1	PRDM5	4	121737704	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2762515	121737704	69416572	154	13305											
FAT4	79633	hgsc.bcm.edu	37	chr4	126241565	126241565	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aacatgagaattggtgaactCgtgtcctctgttactgcaac	11	12	9	9	1	1	2	0	2	1	1	3	3	2	2	1	1	5	2	1	1	5	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:126241565C>T	ENST00000394329.3	+	1	4012	c.3999C>T	c.(3997-3999)ctC>ctT	p.L1333L		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1333	Cadherin 13. {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.L1333L(4)		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						TTGGTGAACTCGTGTCCTCTG	0.358																																					p.L1333L		Atlas-SNP	.											FAT4_ENST00000394329,NS,carcinoma,0,2	FAT4	1752	2	4	Substitution - coding silent(4)	lung(4)	c.C3999T						PASS	.						139	131	133					4																	126241565		1890	4108	5998	SO:0001819	synonymous_variant	79633	exon1			TGAACTCGTGTCC	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.3999C>T	4.37:g.126241565C>T		154	0	0		93	54	0.580645	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																			.	.	none		0.358	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126241565	C	T	126241565	2	4	30	1	0	0	0	0	0	0	0	1	5700	871	31	1		1	FAT4	4	126241565	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	4503861	126241565	64912711	155	13306											
PHF17	79960	hgsc.bcm.edu	37	chr4	129792787	129792787	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccagagagctttttgggtttAgaaaagacctttgcagaagc	12	11	11	7	0	0	4	0	0	0	4	0	5	0	4	2	1	3	3	2	1	4	5	rs6850940	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:129792787A>G	ENST00000226319.6	+	11	2179	c.1899A>G	c.(1897-1899)ttA>ttG	p.L633L	PHF17_ENST00000512960.1_Silent_p.L633L|PHF17_ENST00000452328.2_Silent_p.L621L	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						TTTTGGGTTTAGAAAAGACCT	0.483													G|||	111	0.0221645	0.0734	0.0144	5008	,	,		18630	0.0		0.002	False		,,,				2504	0.002				p.L633L		Atlas-SNP	.											.	PHF17	63	.	0			c.A1899G						PASS	.	G		329,4077	793.1+/-415.2	13,303,1887	62	66	65		1899	-4.7	0.1	4	dbSNP_116	65	10,8590	817.4+/-406.9	0,10,4290	no	coding-synonymous	PHF17	NM_199320.2		13,313,6177	GG,GA,AA		0.1163,7.4671,2.6065		633/843	129792787	339,12667	2203	4300	6503	SO:0001819	synonymous_variant	79960	exon11			GGGTTTAGAAAAG																												ENST00000226319.6:c.1899A>G	4.37:g.129792787A>G		117	0	0		86	22	0.255814	NM_199320		Silent	SNP	ENST00000226319.6	37	CCDS34062.1																																																																																			A|0.972;G|0.028	0.028	strong		0.483	PHF17-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364280.1			G	129792787	A	G	129792787	2	3	30	1	0	0	0	0	0	0	0	1	11837	417	15	3		3	PHF17	4	129792787	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	3551222	129792787	61361489	156	13307											
PHF17	79960	hgsc.bcm.edu	37	chr4	129792873	129792873	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccatgggaaaagaagagacaAtcgttttcattgtgatctca	14	11	9	7	1	2	3	2	1	1	2	4	5	2	4	1	1	0	1	1	1	4	3	rs6855813	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:129792873A>G	ENST00000226319.6	+	11	2265	c.1985A>G	c.(1984-1986)aAt>aGt	p.N662S	PHF17_ENST00000512960.1_Missense_Mutation_p.N662S|PHF17_ENST00000452328.2_Missense_Mutation_p.N650S	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						AGAAGAGACAATCGTTTTCAT	0.423													A|||	112	0.0223642	0.0734	0.0144	5008	,	,		21259	0.001		0.002	False		,,,				2504	0.002				p.N662S		Atlas-SNP	.											.	PHF17	63	.	0			c.A1985G						PASS	.	A	SER/ASN	329,4077	170.5+/-200.9	13,303,1887	77	76	76		1985	2.2	1	4	dbSNP_116	76	11,8589	8.4+/-32.0	0,11,4289	yes	missense	PHF17	NM_199320.2	46	13,314,6176	GG,GA,AA		0.1279,7.4671,2.6142	benign	662/843	129792873	340,12666	2203	4300	6503	SO:0001583	missense	79960	exon11			GAGACAATCGTTT																												ENST00000226319.6:c.1985A>G	4.37:g.129792873A>G	ENSP00000226319:p.Asn662Ser	128	0	0		96	21	0.21875	NM_199320		Missense_Mutation	SNP	ENST00000226319.6	37	CCDS34062.1	50	0.022893772893772892	43	0.08739837398373984	5	0.013812154696132596	0	0.0	2	0.002638522427440633	A	0.959	-0.703925	0.03255	0.074671	0.001279	ENSG00000077684	ENST00000226319;ENST00000452328;ENST00000512960;ENST00000535321	T;T;T	0.38401	1.14;1.15;1.14	4.59	2.25	0.28309	.	0.840784	0.11323	N	0.575875	T	0.00580	0.0019	N	0.04880	-0.145	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.17349	-1.0372	9	.	.	.	.	7.662	0.28409	0.7588:0.0:0.2412:0.0	rs6855813;rs6855813	650;662	Q6IE81-2;Q6IE81	.;JADE1_HUMAN	S	662;650;662;662	ENSP00000226319:N662S;ENSP00000388015:N650S;ENSP00000425730:N662S	.	N	+	2	0	PHF17	130012323	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	1.779000	0.38624	0.910000	0.36722	0.533000	0.62120	AAT	A|0.972;G|0.028	0.028	strong		0.423	PHF17-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364280.1			G	129792873	A	G	129792873	3	3	30	1	0	0	0	0	1	0	0	0	11837	101	4	3	2050	3	PHF17	4	129792873	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	86	129792873	61361403	157	13308											
CLGN	1047	hgsc.bcm.edu	37	chr4	141313500	141313500	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtttgtggtatacatatgtcGgtttttttatactctgtatc	7	21	8	5	1	1	0	0	0	1	0	3	0	1	0	0	2	2	4	0	2	6	10	rs34492995	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:141313500G>A	ENST00000325617.5	-	13	1964	c.1524C>T	c.(1522-1524)acC>acT	p.T508T	CLGN_ENST00000537281.1_Silent_p.T508T|CLGN_ENST00000414773.1_Silent_p.T508T	NM_004362.2	NP_004353.1	O14967	CLGN_HUMAN	calmegin	508					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)					TACATATGTCGGTTTTTTTAT	0.333													G|||	19	0.00379393	0.0008	0.0043	5008	,	,		16252	0.0		0.0139	False		,,,				2504	0.001				p.T508T		Atlas-SNP	.											.	CLGN	76	.	0			c.C1524T						PASS	.	G	,	10,4396	16.8+/-37.8	0,10,2193	129	123	125		1524,1524	-9.4	0	4	dbSNP_126	125	131,8469	66.7+/-129.0	3,125,4172	no	coding-synonymous,coding-synonymous	CLGN	NM_001130675.1,NM_004362.2	,	3,135,6365	AA,AG,GG		1.5233,0.227,1.0841	,	508/611,508/611	141313500	141,12865	2203	4300	6503	SO:0001819	synonymous_variant	1047	exon14			TATGTCGGTTTTT	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.1524C>T	4.37:g.141313500G>A		223	0	0		163	117	0.717791	NM_001130675	B3KS90|B4DXV8|D3DNY8	Silent	SNP	ENST00000325617.5	37	CCDS3751.1																																																																																			G|0.992;A|0.008	0.008	strong		0.333	CLGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257272.2	NM_004362		A	141313500	G	A	141313500	2	1	30	1	0	0	0	0	0	0	0	1	3526	1103	39	1		1	CLGN	4	141313500	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	11520627	141313500	49840776	158	13309											
POU4F2	5458	hgsc.bcm.edu	37	chr4	147561804	147561804	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcgctgcgccagagaagcgCtcgctcgaagcctactttgc	8	8	11	14	5	0	1	0	0	0	1	3	3	0	1	2	0	5	3	2	0	3	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:147561804C>T	ENST00000281321.3	+	2	1322	c.1074C>T	c.(1072-1074)cgC>cgT	p.R358R	AC093887.1_ENST00000584185.1_RNA	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN	POU class 4 homeobox 2	358					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)					CAGAGAAGCGCTCGCTCGAAG	0.602																																					p.R358R		Atlas-SNP	.											POU4F2,caecum,carcinoma,+1,1	POU4F2	83	1	0			c.C1074T						scavenged	.						74	77	76					4																	147561804		2203	4300	6503	SO:0001819	synonymous_variant	5458	exon2			GAAGCGCTCGCTC	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.1074C>T	4.37:g.147561804C>T		74	0	0		55	3	0.0545455	NM_004575	B1PJR6|B2RC84|Q13883|Q14987	Silent	SNP	ENST00000281321.3	37	CCDS34074.1																																																																																			.	.	none		0.602	POU4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367020.1	NM_004575		T	147561804	C	T	147561804	2	4	30	1	0	0	0	0	0	0	0	1	12288	784	28	2		2	POU4F2	4	147561804	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	6248304	147561804	43592472	159	13310											
KIAA0922	23240	hgsc.bcm.edu	37	chr4	154388363	154388363	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	attttttggtgttcctgcagCgattgagccgttgccgaacg	6	14	12	9	4	0	1	0	1	0	0	1	3	1	1	3	1	5	3	3	1	1	6	rs78441178	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:154388363C>T	ENST00000409663.3	+	2	177	c.125C>T	c.(124-126)gCg>gTg	p.A42V	KIAA0922_ENST00000440693.1_Splice_Site_p.A42V|KIAA0922_ENST00000409959.3_Splice_Site_p.A42V	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	42						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)				GTTCCTGCAGCGATTGAGCCG	0.577													c|||	2	0.000399361	0.0	0.0	5008	,	,		18938	0.0		0.002	False		,,,				2504	0.0				p.A42V		Atlas-SNP	.											.	KIAA0922	214	.	0			c.C125T						PASS	.		VAL/ALA,VAL/ALA	1,1383		0,1,691	198	177	183		125,125	4.2	1	4	dbSNP_131	183	15,3167		0,15,1576	yes	missense-near-splice,missense-near-splice	KIAA0922	NM_001131007.1,NM_015196.3	64,64	0,16,2267	TT,TC,CC		0.4714,0.0723,0.3504	benign,benign	42/1611,42/1610	154388363	16,4550	692	1591	2283	SO:0001630	splice_region_variant	23240	exon2			CTGCAGCGATTGA	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.125-1C>T	4.37:g.154388363C>T		218	0	0		137	93	0.678832	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	37	CCDS3783.2	.	.	.	.	.	.	.	.	.	.	c	15.31	2.796674	0.50208	7.23E-4	0.004714	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959	T;T;T	0.28255	1.89;1.62;1.9	5.23	4.19	0.49359	.	.	.	.	.	T	0.27798	0.0684	L	0.55481	1.735	0.27301	N	0.957589	B;B	0.32526	0.374;0.257	B;B	0.29942	0.109;0.051	T	0.08827	-1.0703	8	.	.	.	.	10.079	0.42377	0.0:0.8247:0.0:0.1753	.	42;42	A2VDJ0-5;A2VDJ0	.;T131L_HUMAN	V	42	ENSP00000386574:A42V;ENSP00000409663:A42V;ENSP00000386787:A42V	.	A	+	2	0	KIAA0922	154607813	0.991000	0.36638	1.000000	0.80357	0.988000	0.76386	1.197000	0.32211	2.442000	0.82660	0.550000	0.68814	GCG	.	.	weak		0.577	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196	Missense_Mutation	T	154388363	C	T	154388363	5	4	30	1	0	0	0	0	0	0	1	0	8210	782	27	1	131	1	KIAA0922	4	154388363	Splice_Site	SNP	C	TCGA-GR-7353-01A-11D-2210-10	6826559	154388363	36765913	160	13311											
DDX60L	91351	hgsc.bcm.edu	37	chr4	169294859	169294859	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	agcaaatcattatctgtgttCcccgaaagacaaacaaatgg	16	9	7	9	1	2	1	1	0	1	1	3	2	3	1	2	1	2	2	2	1	5	2	rs13133439	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:169294859C>T	ENST00000511577.1	-	35	4981	c.4734G>A	c.(4732-4734)ggG>ggA	p.G1578G	DDX60L_ENST00000260184.7_Silent_p.G1578G			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	1578							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)		TATCTGTGTTCCCCGAAAGAC	0.408													C|||	44	0.00878594	0.0008	0.013	5008	,	,		21270	0.0		0.0298	False		,,,				2504	0.0041				p.G1578G		Atlas-SNP	.											DDX60L,NS,carcinoma,-2,1	DDX60L	116	1	0			c.G4734A						PASS	.	C		31,4315	30.8+/-60.4	0,31,2142	266	268	267		4734	-2	0.1	4	dbSNP_121	267	333,8255	111.4+/-171.7	8,317,3969	no	coding-synonymous	DDX60L	NM_001012967.1		8,348,6111	TT,TC,CC		3.8775,0.7133,2.8143		1578/1707	169294859	364,12570	2173	4294	6467	SO:0001819	synonymous_variant	91351	exon35			TGTGTTCCCCGAA	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.4734G>A	4.37:g.169294859C>T		373	0	0		210	51	0.242857	NM_001012967	Q96ND6	Silent	SNP	ENST00000511577.1	37																																																																																				C|0.979;T|0.021	0.021	strong		0.408	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967		T	169294859	C	T	169294859	2	4	30	1	0	0	0	0	0	0	0	1	4381	842	30	2		2	DDX60L	4	169294859	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	14906496	169294859	21859417	161	13312											
PALLD	23022	hgsc.bcm.edu	37	chr4	169819835	169819835	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaatgccagtaactttcacAtgtagagtggctggaaatcc	12	10	11	8	0	1	1	1	0	0	1	2	3	2	3	2	3	2	3	2	3	4	3	rs113676921	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:169819835A>G	ENST00000505667.1	+	14	2615	c.2442A>G	c.(2440-2442)acA>acG	p.T814T	PALLD_ENST00000507735.1_Silent_p.T310T|CBR4_ENST00000509108.1_Intron|PALLD_ENST00000261509.6_Silent_p.T797T|PALLD_ENST00000512127.1_Silent_p.T415T|PALLD_ENST00000335742.7_Silent_p.T639T			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	1021	Interaction with ARGBP2, SPIN90, SRC and PFN1.|Interaction with EPS8. {ECO:0000250}.|Pro-rich.				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)		TAACTTTCACATGTAGAGTGG	0.423									Pancreatic Cancer, Familial Clustering of				A|||	7	0.00139776	0.0	0.0	5008	,	,		19745	0.0		0.007	False		,,,				2504	0.0				p.T814T	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.A2442G						PASS	.	A	,,,	3,4403	6.2+/-15.9	0,3,2200	103	98	100		2442,1245,930,2391	-7	0.9	4	dbSNP_132	100	48,8552	30.7+/-82.3	0,48,4252	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PALLD	NM_001166108.1,NM_001166109.1,NM_001166110.1,NM_016081.3	,,,	0,51,6452	GG,GA,AA		0.5581,0.0681,0.3921	,,,	814/1124,415/778,310/673,797/1107	169819835	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	23022	exon14	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	TTTCACATGTAGA	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.2442A>G	4.37:g.169819835A>G		119	0	0		70	47	0.671429	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Silent	SNP	ENST00000505667.1	37	CCDS54818.1																																																																																			A|0.996;G|0.004	0.004	strong		0.423	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081		G	169819835	A	G	169819835	2	3	30	1	0	0	0	0	0	0	0	1	11416	204	8	3		3	PALLD	4	169819835	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	524976	169819835	21334441	162	13313											
VEGFC	7424	hgsc.bcm.edu	37	chr4	177713326	177713326	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacgcagacctaccgtggccTcgcccgcgtcgggctccgcg	5	5	13	18	8	0	1	0	0	0	1	3	1	1	1	5	2	2	2	5	2	2	1	rs55728985	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:177713326T>A	ENST00000280193.2	-	1	555	c.140A>T	c.(139-141)gAg>gTg	p.E47V		NM_005429.2	NP_005420	P49767	VEGFC_HUMAN	vascular endothelial growth factor C	47					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)		TACCGTGGCCTCGCCCGCGTC	0.716													T|||	7	0.00139776	0.0	0.0043	5008	,	,		9648	0.0		0.004	False		,,,				2504	0.0				p.E47V		Atlas-SNP	.											VEGFC,NS,carcinoma,-1,1	VEGFC	94	1	0			c.A140T						PASS	.	T	VAL/GLU	1,3751		0,1,1875	18	22	21		140	3.1	1	4	dbSNP_129	21	43,8131		0,43,4044	yes	missense	VEGFC	NM_005429.2	121	0,44,5919	AA,AT,TT		0.5261,0.0267,0.3689	benign	47/421	177713326	44,11882	1876	4087	5963	SO:0001583	missense	7424	exon1			GTGGCCTCGCCCG	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.140A>T	4.37:g.177713326T>A	ENSP00000280193:p.Glu47Val	25	0	0		15	4	0.266667	NM_005429	B2R9Q8	Missense_Mutation	SNP	ENST00000280193.2	37	CCDS43285.1	.	.	.	.	.	.	.	.	.	.	T	17.21	3.330343	0.60743	2.67E-4	0.005261	ENSG00000150630	ENST00000280193	.	.	.	4.3	3.13	0.36017	.	0.089559	0.43110	D	0.000613	T	0.44829	0.1312	L	0.57536	1.79	0.38259	D	0.941825	D	0.59357	0.985	P	0.50270	0.636	T	0.57590	-0.7785	9	0.72032	D	0.01	-12.749	6.7656	0.23564	0.0:0.1111:0.0:0.8889	rs55728985;rs62617087	47	P49767	VEGFC_HUMAN	V	47	.	ENSP00000280193:E47V	E	-	2	0	VEGFC	177950320	0.986000	0.35501	0.998000	0.56505	0.332000	0.28634	1.525000	0.35953	1.577000	0.49804	0.254000	0.18369	GAG	T|0.996;A|0.004	0.004	strong		0.716	VEGFC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361991.1	NM_005429		A	177713326	T	A	177713326	3	1	30	1	0	0	0	0	1	0	0	0	17167	1551	54	5	1150	5	VEGFC	4	177713326	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	7893491	177713326	13440950	163	13314											
ODZ3	55714	hgsc.bcm.edu	37	chr4	183721088	183721088	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgagagcgacctgggcacgCtgcggttgaccagcggccgc	6	4	16	15	6	0	2	0	1	0	1	0	4	0	2	4	3	3	3	4	3	0	1			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:183721088C>T	ENST00000511685.1	+	28	7807	c.7684C>T	c.(7684-7686)Ctg>Ttg	p.L2562L	TENM3_ENST00000406950.2_Silent_p.L2562L			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	2562					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)										CCTGGGCACGCTGCGGTTGAC	0.632																																					p.L2562L		Atlas-SNP	.											.	.	.	.	0			c.C7684T						PASS	.						23	30	28					4																	183721088		2175	4263	6438	SO:0001819	synonymous_variant	55714	exon27			GGCACGCTGCGGT	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.7684C>T	4.37:g.183721088C>T		198	0	0		101	5	0.049505	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Silent	SNP	ENST00000511685.1	37	CCDS47165.1																																																																																			.	.	none		0.632	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			T	183721088	C	T	183721088	2	4	30	1	0	0	0	0	0	0	0	1	10845	796	28	2		2	ODZ3	4	183721088	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	6007762	183721088	7433188	164	13315											
WWC2	80014	hgsc.bcm.edu	37	chr4	184192231	184192231	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgttttctttcacttacatAggctggaactcagatcagcc	9	15	7	10	0	4	1	3	0	1	1	4	2	4	2	1	2	3	2	1	2	3	6			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:184192231A>G	ENST00000403733.3	+	16	2599		c.e16-1		WWC2_ENST00000504005.1_Splice_Site|WWC2_ENST00000513834.1_Splice_Site|WWC2_ENST00000448232.2_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)		TCACTTACATAGGCTGGAACT	0.318																																					.		Atlas-SNP	.											WWC2,NS,carcinoma,0,1	WWC2	78	1	0			c.2401-2A>G						scavenged	.						30	29	29					4																	184192231		2203	4296	6499	SO:0001630	splice_region_variant	80014	exon16			TTACATAGGCTGG	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.2401-1A>G	4.37:g.184192231A>G		144	0	0		68	3	0.0441176	NM_024949	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Splice_Site	SNP	ENST00000403733.3	37	CCDS34109.2	.	.	.	.	.	.	.	.	.	.	A	18.71	3.681262	0.68042	.	.	ENSG00000151718	ENST00000403733;ENST00000513834;ENST00000448232;ENST00000504005	.	.	.	5.33	5.33	0.75918	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4782	0.75501	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	WWC2	184429225	1.000000	0.71417	0.938000	0.37757	0.976000	0.68499	7.743000	0.85020	2.237000	0.73441	0.460000	0.39030	.	.	.	none		0.318	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949	Intron	G	184192231	A	G	184192231	5	3	30	1	0	0	0	0	0	0	1	0	17427	434	15	3	2461	3	WWC2	4	184192231	Splice_Site	SNP	A	TCGA-GR-7353-01A-11D-2210-10	471143	184192231	6962045	165	13316											
FAM149A	25854	hgsc.bcm.edu	37	chr4	187078745	187078745	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaaacagagagaaacattgAaagtggctggaaacagattt	20	7	10	4	0	0	4	0	1	0	3	0	6	0	5	0	2	3	1	0	2	5	2	rs113168248	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:187078745A>G	ENST00000356371.5	+	8	1474	c.1474A>G	c.(1474-1476)Aaa>Gaa	p.K492E	FAM149A_ENST00000227065.4_Missense_Mutation_p.K201E|FAM149A_ENST00000389354.5_Missense_Mutation_p.K201E|FAM149A_ENST00000514829.1_3'UTR|FAM149A_ENST00000502970.1_Missense_Mutation_p.K201E|FAM149A_ENST00000514153.1_Missense_Mutation_p.K201E|FAM149A_ENST00000503432.1_Missense_Mutation_p.K201E			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	492										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)		AGAAACATTGAAAGTGGCTGG	0.468													A|||	11	0.00219649	0.0008	0.0043	5008	,	,		20772	0.0		0.007	False		,,,				2504	0.0				p.K201E		Atlas-SNP	.											.	FAM149A	52	.	0			c.A601G						PASS	.	A	GLU/LYS,GLU/LYS	6,4400	11.4+/-27.6	0,6,2197	70	80	77		601,601	3.5	0.1	4	dbSNP_132	77	62,8538	37.8+/-93.5	0,62,4238	yes	missense,missense	FAM149A	NM_001006655.2,NM_015398.2	56,56	0,68,6435	GG,GA,AA		0.7209,0.1362,0.5228	benign,benign	201/483,201/483	187078745	68,12938	2203	4300	6503	SO:0001583	missense	25854	exon7			ACATTGAAAGTGG	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.1474A>G	4.37:g.187078745A>G	ENSP00000348732:p.Lys492Glu	41	0	0		38	5	0.131579	NM_001006655	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	Missense_Mutation	SNP	ENST00000356371.5	37		8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	A	8.161	0.789539	0.16258	0.001362	0.007209	ENSG00000109794	ENST00000503432;ENST00000356371;ENST00000227065;ENST00000502970;ENST00000514153;ENST00000389354	T;T;T;T;T;T	0.13420	2.68;2.59;2.68;2.68;2.68;2.68	5.97	3.47	0.39725	.	0.209202	0.42821	D	0.000654	T	0.08403	0.0209	L	0.53729	1.69	0.09310	N	1	P;B;P	0.42692	0.525;0.217;0.787	B;B;B	0.40199	0.182;0.089;0.322	T	0.13602	-1.0503	10	0.22706	T	0.39	-18.2705	6.3912	0.21587	0.7847:0.0:0.0763:0.139	.	492;492;201	A5PLN7-3;A5PLN7;B4DHZ9	.;F149A_HUMAN;.	E	201;492;201;201;201;201	ENSP00000426835:K201E;ENSP00000348732:K492E;ENSP00000227065:K201E;ENSP00000427155:K201E;ENSP00000424380:K201E;ENSP00000374005:K201E	ENSP00000227065:K201E	K	+	1	0	FAM149A	187315739	0.986000	0.35501	0.050000	0.19076	0.009000	0.06853	3.318000	0.51975	1.056000	0.40484	0.524000	0.50904	AAA	A|0.995;G|0.005	0.005	strong		0.468	FAM149A-201	KNOWN	basic	protein_coding	protein_coding		NM_001006655		G	187078745	A	G	187078745	3	3	30	1	0	0	0	0	1	0	0	0	5460	247	9	3	619	3	FAM149A	4	187078745	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	2886514	187078745	4075531	166	13317											
FAM149A	25854	hgsc.bcm.edu	37	chr4	187088399	187088399	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgctgctcacacatggacagGtcaaagtattttgacaggtc	11	11	10	9	0	2	1	2	1	0	0	3	2	2	2	0	3	2	3	0	3	2	3	rs111681837	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:187088399G>T	ENST00000356371.5	+	13	2231	c.2231G>T	c.(2230-2232)gGt>gTt	p.G744V	FAM149A_ENST00000227065.4_Missense_Mutation_p.G453V|FAM149A_ENST00000389354.5_Missense_Mutation_p.G453V|FAM149A_ENST00000502970.1_Missense_Mutation_p.G453V|FAM149A_ENST00000514153.1_Missense_Mutation_p.G453V|FAM149A_ENST00000503432.1_Missense_Mutation_p.G453V			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	744										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)		ACATGGACAGGTCAAAGTATT	0.373													G|||	8	0.00159744	0.0008	0.0014	5008	,	,		20278	0.0		0.006	False		,,,				2504	0.0				p.G453V		Atlas-SNP	.											.	FAM149A	52	.	0			c.G1358T						PASS	.	G	VAL/GLY,VAL/GLY	7,4399	12.9+/-30.5	0,7,2196	126	128	128		1358,1358	4.8	1	4	dbSNP_132	128	58,8542	35.9+/-90.5	0,58,4242	yes	missense,missense	FAM149A	NM_001006655.2,NM_015398.2	109,109	0,65,6438	TT,TG,GG		0.6744,0.1589,0.4998	probably-damaging,probably-damaging	453/483,453/483	187088399	65,12941	2203	4300	6503	SO:0001583	missense	25854	exon12			GGACAGGTCAAAG	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.2231G>T	4.37:g.187088399G>T	ENSP00000348732:p.Gly744Val	276	0	0		165	48	0.290909	NM_001006655	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	Missense_Mutation	SNP	ENST00000356371.5	37		6|6|6	0.0027472527472527475|0.0027472527472527475|0.0027472527472527475	0|0|0	0.0|0.0|0.0	1|1|1	0.0027624309392265192|0.0027624309392265192|0.0027624309392265192	0|0|0	0.0|0.0|0.0	5|5|5	0.006596306068601583|0.006596306068601583|0.006596306068601583	G|G|G	20.2|20.2|20.2	3.945034|3.945034|3.945034	0.73672|0.73672|0.73672	0.001589|0.001589|0.001589	0.006744|0.006744|0.006744	ENSG00000109794|ENSG00000109794|ENSG00000109794	ENST00000503432;ENST00000356371;ENST00000227065;ENST00000502970;ENST00000514153;ENST00000389354|ENST00000512271|ENST00000510843;ENST00000502894	T;T;T;T;T;T|.|.	0.15372|.|.	2.56;2.43;2.56;2.56;2.56;2.56|.|.	5.62|5.62|5.62	4.77|4.77|4.77	0.60923|0.60923|0.60923	.|.|.	0.309873|.|.	0.32518|.|.	N|.|.	0.005996|.|.	T|T|T	0.64360|0.64360|0.64360	0.2591|0.2591|0.2591	M|M|M	0.65975|0.65975|0.65975	2.015|2.015|2.015	0.52501|0.52501|0.52501	D|D|D	0.999951|0.999951|0.999951	D;D|.|.	0.76494|.|.	0.999;0.999|.|.	D;D|.|.	0.74023|.|.	0.982;0.961|.|.	T|T|T	0.67356|0.67356|0.67356	-0.5691|-0.5691|-0.5691	10|5|5	0.87932|.|.	D|.|.	0|.|.	-13.1821|-13.1821|-13.1821	13.7969|13.7969|13.7969	0.63177|0.63177|0.63177	0.0766:0.0:0.9234:0.0|0.0766:0.0:0.9234:0.0|0.0766:0.0:0.9234:0.0	.|.|.	743;744|.|.	A5PLN7-3;A5PLN7|.|.	.;F149A_HUMAN|.|.	V|S|F	453;744;453;453;453;453|129|131;14	ENSP00000426835:G453V;ENSP00000348732:G744V;ENSP00000227065:G453V;ENSP00000427155:G453V;ENSP00000424380:G453V;ENSP00000374005:G453V|.|.	ENSP00000227065:G453V|.|.	G|R|V	+|+|+	2|3|1	0|2|0	FAM149A|FAM149A|FAM149A	187325393|187325393|187325393	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.965000|0.965000|0.965000	0.64279|0.64279|0.64279	4.047000|4.047000|4.047000	0.57383|0.57383|0.57383	2.652000|2.652000|2.652000	0.90054|0.90054|0.90054	0.591000|0.591000|0.591000	0.81541|0.81541|0.81541	GGT|AGG|GTC	G|0.995;T|0.005	0.005	strong		0.373	FAM149A-201	KNOWN	basic	protein_coding	protein_coding		NM_001006655		T	187088399	G	T	187088399	3	4	30	1	0	0	0	0	1	0	0	0	5460	1261	44	4	1396	4	FAM149A	4	187088399	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	9654	187088399	4065877	167	13318											
MTNR1A	4543	hgsc.bcm.edu	37	chr4	187455329	187455329	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aagtggaaaaccaccacggcGatggtgtaggcggagctgac	12	5	15	9	3	0	1	0	1	0	0	0	4	0	3	2	5	2	2	2	5	4	1	rs8192549	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr4:187455329G>A	ENST00000307161.5	-	2	768	c.567C>T	c.(565-567)atC>atT	p.I189I	RP11-215A19.2_ENST00000509111.1_Intron	NM_005958.3	NP_005949.1	P48039	MTR1A_HUMAN	melatonin receptor 1A	189					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)	CCACCACGGCGATGGTGTAGG	0.577													G|||	48	0.00958466	0.0015	0.0101	5008	,	,		20839	0.001		0.0298	False		,,,				2504	0.0082				p.I189I		Atlas-SNP	.											.	MTNR1A	46	.	0			c.C567T						PASS	.	G		29,4377	36.0+/-67.5	0,29,2174	136	131	133		567	-9.9	0	4	dbSNP_117	133	312,8288	111.0+/-171.3	3,306,3991	no	coding-synonymous	MTNR1A	NM_005958.3		3,335,6165	AA,AG,GG		3.6279,0.6582,2.6219		189/351	187455329	341,12665	2203	4300	6503	SO:0001819	synonymous_variant	4543	exon2			CACGGCGATGGTG		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.567C>T	4.37:g.187455329G>A		83	0	0		65	13	0.2	NM_005958	A0AVC5|B0M0L2	Silent	SNP	ENST00000307161.5	37	CCDS3848.1																																																																																			G|0.977;A|0.023	0.023	strong		0.577	MTNR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360189.1			A	187455329	G	A	187455329	2	1	30	1	0	0	0	0	0	0	0	1	9960	1048	37	1		1	MTNR1A	4	187455329	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	366930	187455329	3698947	168	13319											
CEP72	55722	hgsc.bcm.edu	37	chr5	637637	637637	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctctatatctcagactccAtggataccgaggactcggcc	9	10	8	14	2	2	1	1	0	2	1	6	4	3	3	3	3	1	0	3	3	3	3	rs62000999	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:637637A>G	ENST00000264935.5	+	7	1000	c.910A>G	c.(910-912)Atg>Gtg	p.M304V	CEP72_ENST00000444221.1_3'UTR	NM_018140.3	NP_060610.2	Q9P209	CEP72_HUMAN	centrosomal protein 72kDa	304					G2/M transition of mitotic cell cycle (GO:0000086)|gamma-tubulin complex localization (GO:0033566)|mitotic cell cycle (GO:0000278)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)				autonomic_ganglia(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(5)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	20			Epithelial(17;0.000339)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|Lung(60;0.0863)			CTCAGACTCCATGGATACCGA	0.527													G|||	22	0.00439297	0.0008	0.0043	5008	,	,		20995	0.0		0.0169	False		,,,				2504	0.001				p.M304V		Atlas-SNP	.											.	CEP72	53	.	0			c.A910G						PASS	.	G	VAL/MET	8,4398	822.5+/-416.5	0,8,2195	64	69	67		910	-9.5	0	5	dbSNP_129	67	180,8420	810.6+/-407.1	1,178,4121	yes	missense	CEP72	NM_018140.3	21	1,186,6316	GG,GA,AA		2.093,0.1816,1.4455	benign	304/648	637637	188,12818	2203	4300	6503	SO:0001583	missense	55722	exon7			GACTCCATGGATA	BC000132	CCDS34126.1	5p15.33	2014-02-20			ENSG00000112877	ENSG00000112877			25547	protein-coding gene	gene with protein product						10819331	Standard	NM_018140		Approved	KIAA1519, FLJ10565	uc003jbf.3	Q9P209	OTTHUMG00000161745	ENST00000264935.5:c.910A>G	5.37:g.637637A>G	ENSP00000264935:p.Met304Val	221	0	0		193	91	0.471503	NM_018140	B4DR26|Q9BV03|Q9BWM3|Q9NVR4	Missense_Mutation	SNP	ENST00000264935.5	37	CCDS34126.1	13	0.005952380952380952	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	G	0.015	-1.560185	0.00910	0.001816	0.02093	ENSG00000112877	ENST00000264935	T	0.06768	3.26	4.76	-9.52	0.00578	.	2.230810	0.01420	N	0.014329	T	0.01029	0.0034	N	0.00926	-1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.34104	-0.9842	10	0.02654	T	1	0.5272	10.8012	0.46489	0.691:0.1782:0.1307:0.0	rs62000999	304	Q9P209	CEP72_HUMAN	V	304	ENSP00000264935:M304V	ENSP00000264935:M304V	M	+	1	0	CEP72	690637	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.554000	0.00926	-2.567000	0.00470	-1.050000	0.02344	ATG	A|0.989;G|0.011	0.011	strong		0.527	CEP72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365967.3	NM_018140		G	637637	A	G	637637	3	3	30	1	0	0	0	0	1	0	0	0	3262	217	8	3	936	3	CEP72	5	637637	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10		637637	180277623	169	13320											
PAPD7	11044	hgsc.bcm.edu	37	chr5	6753013	6753013	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttactatacctccaccgaccCtaggggttgctcctgttcct	6	13	7	15	1	0	0	0	0	0	0	3	1	3	0	6	2	3	3	6	2	4	6	rs28381429	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:6753013C>T	ENST00000230859.6	+	12	1426	c.1297C>T	c.(1297-1299)Cta>Tta	p.L433L		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	663	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						TCCACCGACCCTAGGGGTTGC	0.532													C|||	74	0.0147764	0.0	0.0159	5008	,	,		17117	0.0		0.0288	False		,,,				2504	0.0348				p.L433L	NSCLC(7;212 333 5667 23379 46547)	Atlas-SNP	.											.	PAPD7	69	.	0			c.C1297T						PASS	.	C	,,	25,4381	32.6+/-62.9	0,25,2178	103	97	99		1297,757,1297	2.2	1	5	dbSNP_125	99	247,8353	97.0+/-158.7	3,241,4056	no	coding-synonymous,coding-synonymous,coding-synonymous	PAPD7	NM_001171805.1,NM_001171806.1,NM_006999.4	,,	3,266,6234	TT,TC,CC		2.8721,0.5674,2.0913	,,	433/542,253/363,433/543	6753013	272,12734	2203	4300	6503	SO:0001819	synonymous_variant	11044	exon12			CCGACCCTAGGGG	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.1297C>T	5.37:g.6753013C>T		219	0	0		210	89	0.42381	NM_001171805	A8K1E2|M1JCE6|O43289|Q17RZ1|Q9Y6C1	Silent	SNP	ENST00000230859.6	37	CCDS3871.1																																																																																			C|0.979;T|0.021	0.021	strong		0.532	PAPD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206904.1	NM_006999		T	6753013	C	T	6753013	2	4	30	1	0	0	0	0	0	0	0	1	11435	680	24	2		2	PAPD7	5	6753013	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	6115376	6753013	174162247	170	13321											
TRIO	7204	hgsc.bcm.edu	37	chr5	14304588	14304588	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtatatgagcaacgtggatTcatggtgtaaagcttgcggt	11	12	13	5	2	1	1	1	1	0	0	1	2	1	2	0	3	4	4	0	3	5	5			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:14304588T>G	ENST00000344204.4	+	8	1411	c.1387T>G	c.(1387-1389)Tca>Gca	p.S463A	TRIO_ENST00000509967.2_Missense_Mutation_p.S414A|TRIO_ENST00000537187.1_Missense_Mutation_p.S463A	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	463					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)					CAACGTGGATTCATGGTGTAA	0.373																																					p.S463A		Atlas-SNP	.											.	TRIO	305	.	0			c.T1387G						PASS	.						177	160	166					5																	14304588		2203	4300	6503	SO:0001583	missense	7204	exon8			GTGGATTCATGGT	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.1387T>G	5.37:g.14304588T>G	ENSP00000339299:p.Ser463Ala	151	0	0		168	81	0.482143	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Missense_Mutation	SNP	ENST00000344204.4	37	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	T	12.03	1.816676	0.32145	.	.	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000509967;ENST00000513206	T;T;T	0.65178	-0.14;-0.11;0.53	5.18	5.18	0.71444	.	0.080894	0.56097	D	0.000034	T	0.43366	0.1244	N	0.12831	0.26	0.48135	D	0.999591	B;B;B	0.22983	0.0;0.078;0.004	B;B;B	0.27380	0.002;0.079;0.001	T	0.35351	-0.9792	10	0.08599	T	0.76	.	15.0541	0.71897	0.0:0.0:0.0:1.0	.	414;463;463	F5H228;O75962-5;O75962	.;.;TRIO_HUMAN	A	463;463;414;150	ENSP00000339299:S463A;ENSP00000446348:S463A;ENSP00000445592:S414A	ENSP00000339299:S463A	S	+	1	0	TRIO	14357588	1.000000	0.71417	0.995000	0.50966	0.971000	0.66376	2.719000	0.47244	1.966000	0.57179	0.528000	0.53228	TCA	.	.	none		0.373	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		G	14304588	T	G	14304588	3	3	30	1	0	0	0	0	1	0	0	0	16567	1783	62	5	1417	5	TRIO	5	14304588	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	7551575	14304588	166610672	171	13322											
ZNF622	90441	hgsc.bcm.edu	37	chr5	16465442	16465442	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtcctttctccaagttcttTtcattcatcatctccacttt	7	19	2	13	0	6	0	3	0	3	0	9	0	7	0	3	0	0	1	3	0	1	6			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:16465442T>C	ENST00000308683.2	-	1	459	c.333A>G	c.(331-333)gaA>gaG	p.E111E		NM_033414.2	NP_219482.1	Q969S3	ZN622_HUMAN	zinc finger protein 622	111					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						CCAAGTTCTTTTCATTCATCA	0.562																																					p.E111E		Atlas-SNP	.											ZNF622,NS,carcinoma,-2,1	ZNF622	49	1	0			c.A333G						PASS	.						167	152	157					5																	16465442		2203	4300	6503	SO:0001819	synonymous_variant	90441	exon1			GTTCTTTTCATTC	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.333A>G	5.37:g.16465442T>C		147	0	0		143	66	0.461538	NM_033414		Silent	SNP	ENST00000308683.2	37	CCDS3886.1																																																																																			.	.	none		0.562	ZNF622-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207105.1	NM_033414		C	16465442	T	C	16465442	2	2	30	1	0	0	0	0	0	0	0	1	18061	1838	64	3		3	ZNF622	5	16465442	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	2160854	16465442	164449818	172	13323											
C5orf42	65250	hgsc.bcm.edu	37	chr5	37153871	37153871	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	atgtagatctagcatttcagGcttggggaaatcctgttcta	10	14	10	7	0	3	1	1	0	2	1	4	2	4	2	1	3	1	4	1	3	4	6	rs77014998	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:37153871G>T	ENST00000508244.1	-	40	8275	c.8182C>A	c.(8182-8184)Cct>Act	p.P2728T	C5orf42_ENST00000274258.7_Missense_Mutation_p.P1626T|C5orf42_ENST00000425232.2_Missense_Mutation_p.P2728T			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2728						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)			AGCATTTCAGGCTTGGGGAAA	0.358													G|||	13	0.00259585	0.0	0.0058	5008	,	,		19975	0.0		0.0089	False		,,,				2504	0.0				p.P2728T		Atlas-SNP	.											.	C5orf42	422	.	0			c.C8182A						PASS	.	G	THR/PRO	20,4386	27.2+/-55.0	0,20,2183	93	83	86		8182	2.3	0	5	dbSNP_131	86	99,8501	54.4+/-115.2	1,97,4202	yes	missense	C5orf42	NM_023073.3	38	1,117,6385	TT,TG,GG		1.1512,0.4539,0.915	benign	2728/3198	37153871	119,12887	2203	4300	6503	SO:0001583	missense	65250	exon41			TTTCAGGCTTGGG		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.8182C>A	5.37:g.37153871G>T	ENSP00000421690:p.Pro2728Thr	122	0	0		90	34	0.377778	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	9	0.004120879120879121	0	0.0	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	G	3.383	-0.126029	0.06795	0.004539	0.011512	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.17854	2.25;2.25;2.35;2.34	5.41	2.29	0.28610	.	1.705140	0.03544	N	0.224372	T	0.07052	0.0179	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.29274	-1.0017	10	0.16420	T	0.52	.	4.6926	0.12788	0.1913:0.0:0.5443:0.2644	.	2728;1626	E9PH94;Q9H799	.;CE042_HUMAN	T	2728;2728;1626;1794;1662	ENSP00000421690:P2728T;ENSP00000389014:P2728T;ENSP00000274258:P1626T;ENSP00000424223:P1794T	ENSP00000274258:P1626T	P	-	1	0	C5orf42	37189628	0.000000	0.05858	0.000000	0.03702	0.592000	0.36648	0.288000	0.18939	0.645000	0.30675	0.591000	0.81541	CCT	G|0.992;T|0.008	0.008	strong		0.358	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		T	37153871	G	T	37153871	3	4	30	1	0	0	0	0	1	0	0	0	2303	1203	42	4	1459	4	C5orf42	5	37153871	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	20688429	37153871	143761389	173	13324											
OSMR	9180	hgsc.bcm.edu	37	chr5	38904082	38904082	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccataaggaataatttcacaTatttgtgtcagattgaactc	14	14	6	7	0	2	2	2	1	0	1	3	3	2	3	1	1	1	0	1	1	5	6	rs35117676	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:38904082T>C	ENST00000274276.3	+	8	1492	c.1090T>C	c.(1090-1092)Tat>Cat	p.Y364H		NM_003999.2	NP_003990.1	Q99650	OSMR_HUMAN	oncostatin M receptor	364	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	oncostatin-M receptor complex (GO:0005900)	growth factor binding (GO:0019838)|oncostatin-M receptor activity (GO:0004924)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(8)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	46	all_lung(31;0.000365)					TAATTTCACATATTTGTGTCA	0.328													T|||	18	0.00359425	0.0	0.0072	5008	,	,		18317	0.0		0.0109	False		,,,				2504	0.002				p.Y364H		Atlas-SNP	.											.	OSMR	133	.	0			c.T1090C						PASS	.	T	HIS/TYR	16,4390	24.3+/-50.5	0,16,2187	61	63	62		1090	-1.3	0	5	dbSNP_126	62	124,8474	64.9+/-127.2	1,122,4176	yes	missense	OSMR	NM_003999.2	83	1,138,6363	CC,CT,TT		1.4422,0.3631,1.0766	benign	364/980	38904082	140,12864	2203	4299	6502	SO:0001583	missense	9180	exon8			TTCACATATTTGT	U60805	CCDS3928.1, CCDS54847.1	5p13.2	2013-02-11			ENSG00000145623	ENSG00000145623		"Fibronectin type III domain containing"	8507	protein-coding gene	gene with protein product		601743				8999038	Standard	NM_001168355		Approved	OSMRB	uc003jln.2	Q99650	OTTHUMG00000090811	ENST00000274276.3:c.1090T>C	5.37:g.38904082T>C	ENSP00000274276:p.Tyr364His	387	1	0.00258398		365	171	0.468493	NM_003999	Q6P4E8|Q96QJ6	Missense_Mutation	SNP	ENST00000274276.3	37	CCDS3928.1	13	0.005952380952380952	0	0.0	3	0.008287292817679558	0	0.0	10	0.013192612137203167	T	12.79	2.044954	0.36085	0.003631	0.014422	ENSG00000145623	ENST00000274276	T	0.53640	0.61	5.75	-1.26	0.09376	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.457709	0.22766	N	0.055885	T	0.19644	0.0472	N	0.22421	0.69	0.09310	N	1	P	0.48640	0.913	B	0.37601	0.254	T	0.25222	-1.0138	10	0.87932	D	0	.	9.3318	0.38027	0.0:0.32:0.0:0.68	rs35117676	364	Q99650	OSMR_HUMAN	H	364	ENSP00000274276:Y364H	ENSP00000274276:Y364H	Y	+	1	0	OSMR	38939839	0.001000	0.12720	0.002000	0.10522	0.020000	0.10135	-0.039000	0.12124	-0.126000	0.11682	-0.408000	0.06270	TAT	T|0.991;C|0.009	0.009	strong		0.328	OSMR-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000207609.2	NM_003999		C	38904082	T	C	38904082	3	2	30	1	0	0	0	0	1	0	0	0	11301	1406	49	3	1154	3	OSMR	5	38904082	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	1750211	38904082	142011178	174	13325											
PRKAA1	5562	hgsc.bcm.edu	37	chr5	40765280	40765280	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcatcaatcatggttgaactAtatgatggatcctcaggaaa	14	12	8	7	0	4	2	4	2	0	0	5	4	5	4	1	3	1	1	1	3	5	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:40765280A>G	ENST00000397128.2	-	7	890	c.882T>C	c.(880-882)taT>taC	p.Y294Y	PRKAA1_ENST00000354209.3_Silent_p.Y309Y	NM_006251.5|NM_206907.3	NP_006242.5|NP_996790.3	Q13131	AAPK1_HUMAN	protein kinase, AMP-activated, alpha 1 catalytic subunit	294					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)	TGGTTGAACTATATGATGGAT	0.388																																					p.Y309Y		Atlas-SNP	.											.	PRKAA1	27	.	0			c.T927C						PASS	.						126	115	118					5																	40765280		1838	4091	5929	SO:0001819	synonymous_variant	5562	exon8			TGAACTATATGAT		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.882T>C	5.37:g.40765280A>G		277	0	0		306	131	0.428105	NM_206907	A8MTQ6|B2R7E1|O00286|Q5D0E1|Q86VS1|Q9UNQ4	Silent	SNP	ENST00000397128.2	37	CCDS3932.2																																																																																			.	.	none		0.388	PRKAA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253833.2	NM_006251		G	40765280	A	G	40765280	2	3	30	1	0	0	0	0	0	0	0	1	12505	456	16	3		3	PRKAA1	5	40765280	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	1861198	40765280	140149980	175	13326											
ADAMTS6	11174	hgsc.bcm.edu	37	chr5	64756136	64756136	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttaaaggttcgataaaataCtcttcatcttctgtagcaat	13	16	5	7	1	4	0	1	0	3	0	5	1	4	0	0	1	2	3	0	1	7	8			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:64756136C>T	ENST00000536360.1	-	4	1305	c.492G>A	c.(490-492)gaG>gaA	p.E164E				Q9UKP5	ATS6_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 6	164						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)		CGATAAAATACTCTTCATCTT	0.308																																					p.E164E		Atlas-SNP	.											.	ADAMTS6	174	.	0			c.G492A						PASS	.						109	114	112					5																	64756136		2203	4300	6503	SO:0001819	synonymous_variant	11174	exon4			AAAATACTCTTCA	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.492G>A	5.37:g.64756136C>T		113	0	0		114	8	0.0701754	NM_197941	Q59EX6|Q5IR87|Q5IR88|Q5IR89|Q68DL1	Silent	SNP	ENST00000536360.1	37																																																																																				.	.	none		0.308	ADAMTS6-201	KNOWN	basic	protein_coding	protein_coding		NM_197941		T	64756136	C	T	64756136	2	4	30	1	0	0	0	0	0	0	0	1	270	564	20	2		2	ADAMTS6	5	64756136	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	23990856	64756136	116159124	176	13327											
ERBB2IP	55914	hgsc.bcm.edu	37	chr5	65350044	65350044	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggccccacaagtggcccacaAtctgcacctcaaatatatgg	12	7	8	14	0	2	0	1	0	1	0	2	0	2	0	4	3	1	1	4	3	5	2	rs35278406	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:65350044A>G	ENST00000284037.5	+	21	3287	c.2898A>G	c.(2896-2898)caA>caG	p.Q966Q	ERBB2IP_ENST00000380939.2_Silent_p.Q966Q|ERBB2IP_ENST00000380943.2_Silent_p.Q966Q|ERBB2IP_ENST00000380938.2_Silent_p.Q966Q|ERBB2IP_ENST00000380935.1_Silent_p.Q966Q|ERBB2IP_ENST00000506030.1_Silent_p.Q966Q|ERBB2IP_ENST00000511297.1_Silent_p.Q962Q|ERBB2IP_ENST00000380936.1_Silent_p.Q966Q|ERBB2IP_ENST00000508515.1_Silent_p.Q966Q|ERBB2IP_ENST00000416865.2_Intron	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	966					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)		GTGGCCCACAATCTGCACCTC	0.398													A|||	87	0.0173722	0.0008	0.0159	5008	,	,		17609	0.0		0.0388	False		,,,				2504	0.0368				p.Q966Q		Atlas-SNP	.											.	ERBB2IP	120	.	0			c.A2898G						PASS	.	A	,	33,4363		0,33,2165	71	79	76		2898,2898	-5.2	0.5	5	dbSNP_126	76	343,8255		5,333,3961	no	coding-synonymous,coding-synonymous	ERBB2IP	NM_001006600.1,NM_018695.2	,	5,366,6126	GG,GA,AA		3.9893,0.7507,2.8936	,	966/1303,966/1372	65350044	376,12618	2198	4299	6497	SO:0001819	synonymous_variant	55914	exon21			CCCACAATCTGCA		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.2898A>G	5.37:g.65350044A>G		97	0	0		94	33	0.351064	NM_001253699	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Silent	SNP	ENST00000284037.5	37	CCDS58953.1																																																																																			A|0.974;G|0.026	0.026	strong		0.398	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695		G	65350044	A	G	65350044	2	3	30	1	0	0	0	0	0	0	0	1	5209	98	4	3		3	ERBB2IP	5	65350044	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	593908	65350044	115565216	177	13328											
WDR41	55255	hgsc.bcm.edu	37	chr5	76728996	76728996	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagtcaccattctcctctaaTttttgaaataatcttaaact	14	16	2	9	0	4	1	1	1	3	0	5	1	4	1	2	0	1	0	2	0	6	6	rs72769029	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:76728996T>C	ENST00000296679.4	-	13	1719	c.1344A>G	c.(1342-1344)aaA>aaG	p.K448K	WDR41_ENST00000512033.1_5'UTR|WDR41_ENST00000507029.1_Silent_p.K393K|WDR41_ENST00000414719.2_Silent_p.K194K	NM_018268.2	NP_060738.2	Q9HAD4	WDR41_HUMAN	WD repeat domain 41	448						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)		TCTCCTCTAATTTTTGAAATA	0.368													T|||	83	0.0165735	0.0015	0.0245	5008	,	,		17492	0.0		0.0338	False		,,,				2504	0.0307				p.K448K		Atlas-SNP	.											.	WDR41	29	.	0			c.A1344G						PASS	.	T		21,4383	27.2+/-55.0	0,21,2181	118	121	120		1344	-0.2	1	5	dbSNP_130	120	238,8362	96.8+/-158.5	5,228,4067	no	coding-synonymous	WDR41	NM_018268.2		5,249,6248	CC,CT,TT		2.7674,0.4768,1.9917		448/460	76728996	259,12745	2202	4300	6502	SO:0001819	synonymous_variant	55255	exon13			CTCTAATTTTTGA	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.1344A>G	5.37:g.76728996T>C		218	2	0.00917431		221	219	0.99095	NM_018268	B4DT55|Q7Z792|Q8IWG3|Q8IXA9|Q8NDA7|Q9NV62	Silent	SNP	ENST00000296679.4	37	CCDS4038.1																																																																																			T|0.979;C|0.021	0.021	strong		0.368	WDR41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220014.2	NM_018268		C	76728996	T	C	76728996	2	2	30	1	0	0	0	0	0	0	0	1	17309	1490	52	3		3	WDR41	5	76728996	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	11378952	76728996	104186264	178	13329											
MTX3	345778	hgsc.bcm.edu	37	chr5	79286042	79286042	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaccatgtcgtcttcagttgTcaaaattggtacatcgccta	11	13	7	10	2	3	0	2	0	1	0	5	0	3	0	2	1	2	2	2	1	5	5	rs371364933		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:79286042T>A	ENST00000512528.1	-	3	189	c.169A>T	c.(169-171)Aca>Tca	p.T57S	MTX3_ENST00000512560.1_5'UTR|MTX3_ENST00000509852.1_Missense_Mutation_p.T57S			Q5HYI7	MTX3_HUMAN	metaxin 3	57					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)		TCTTCAGTTGTCAAAATTGGT	0.358																																					p.T57S		Atlas-SNP	.											.	MTX3	29	.	0			c.A169T						PASS	.	T	SER/THR,	0,3672		0,0,1836	86	78	81		169,	4.7	1	5		81	2,8158		0,2,4078	no	missense,utr-5	MTX3	NM_001010891.4,NM_001167741.1	58,	0,2,5914	AA,AT,TT		0.0245,0.0,0.0169	benign,	57/249,	79286042	2,11830	1836	4080	5916	SO:0001583	missense	345778	exon3			CAGTTGTCAAAAT	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.169A>T	5.37:g.79286042T>A	ENSP00000424798:p.Thr57Ser	380	0	0		349	162	0.464183	NM_001010891	B4DL65|E9PB57|Q7Z380|Q8NB92	Missense_Mutation	SNP	ENST00000512528.1	37		.	.	.	.	.	.	.	.	.	.	T	8.983	0.975725	0.18736	0.0	2.45E-4	ENSG00000177034	ENST00000328496;ENST00000509852;ENST00000512528;ENST00000418095	T;T	0.42513	0.97;0.97	5.86	4.69	0.59074	.	0.541563	0.21589	N	0.072127	T	0.30885	0.0779	L	0.35644	1.08	0.28755	N	0.901208	B;B	0.10296	0.003;0.001	B;B	0.09377	0.002;0.004	T	0.18116	-1.0347	10	0.33141	T	0.24	-2.1085	8.1501	0.31134	0.1203:0.0663:0.0:0.8134	.	57;57	Q5HYI7-4;Q5HYI7	.;MTX3_HUMAN	S	57	ENSP00000423302:T57S;ENSP00000424798:T57S	ENSP00000331672:T57S	T	-	1	0	MTX3	79321798	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.676000	0.37565	1.036000	0.39998	-0.290000	0.09829	ACA	.	.	weak		0.358	MTX3-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372567.1	XM_293971		A	79286042	T	A	79286042	3	1	30	1	0	0	0	0	1	0	0	0	9978	1667	58	5	797	5	MTX3	5	79286042	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	2557046	79286042	101629218	179	13330											
PGGT1B	5229	hgsc.bcm.edu	37	chr5	114557642	114557643	+	Frame_Shift_Ins	INS	-	-	A																															cctgttcaattctttttctgINSaaaaaacttcttctagttta																										TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:114557642_114557643insA	ENST00000419445.1	-	7	741_742	c.721_722insT	c.(721-723)tcafs	p.S241fs	PGGT1B_ENST00000514178.1_5'UTR|PGGT1B_ENST00000379615.3_Intron	NM_005023.3	NP_005014.2	P53609	PGTB1_HUMAN	protein geranylgeranyltransferase type I, beta subunit	241					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)		TTCTTTTTCTGAAAAAACTTCT	0.351																																					p.S241fs		Pindel,Atlas-Indel	.											.	PGGT1B	26	.	0			c.722_723insT						PASS	.																																			SO:0001589	frameshift_variant	5229	exon7			.		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.722dupT	5.37:g.114557648_114557648dupA	ENSP00000404676:p.Ser241fs	475	0	.		423	73	0.173	NM_005023	Q5MJP9	Frame_Shift_Ins	INS	ENST00000419445.1	37	CCDS4116.1																																																																																			.	.	none		0.351	PGGT1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250855.2	NM_005023		A	114557643	-	A	114557642	7	5	30	1	0	1	1	0	0	0	0	0	11798	1294	45	0	423	0	PGGT1B	5	114557642	Frame_Shift_Ins	INS	-	TCGA-GR-7353-01A-11D-2210-10	35271600	114557642	66357618	180	13331											
AQPEP	206338	hgsc.bcm.edu	37	chr5	115298898	115298898	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ggtgctggagctcagtgagcCcctgaaacctggtagcagct	8	8	14	11	0	1	2	1	2	0	0	1	3	1	3	3	3	6	5	3	3	2	1	rs145336539	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:115298898C>T	ENST00000357872.4	+	1	708	c.584C>T	c.(583-585)cCc>cTc	p.P195L	AQPEP_ENST00000395528.2_5'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		195						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										CTCAGTGAGCCCCTGAAACCT	0.622													C|||	16	0.00319489	0.0008	0.0086	5008	,	,		14129	0.0		0.008	False		,,,				2504	0.001				p.P195L		Atlas-SNP	.											.	.	.	.	0			c.C584T						PASS	.	C	LEU/PRO	3,4397		0,3,2197	21	22	22		584	4.6	0.9	5	dbSNP_134	22	39,8545		0,39,4253	yes	missense	AQPEP	NM_173800.4	98	0,42,6450	TT,TC,CC		0.4543,0.0682,0.3235	benign	195/991	115298898	42,12942	2200	4292	6492	SO:0001583	missense	0	exon1			GTGAGCCCCTGAA																												ENST00000357872.4:c.584C>T	5.37:g.115298898C>T	ENSP00000350541:p.Pro195Leu	131	0	0		131	56	0.427481	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Missense_Mutation	SNP	ENST00000357872.4	37	CCDS4124.1	7	0.003205128205128205	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	3	0.00395778364116095	C	8.710	0.911797	0.17907	6.82E-4	0.004543	ENSG00000172901	ENST00000357872;ENST00000379578	T	0.02656	4.21	4.6	4.6	0.57074	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	1.383950	0.04803	N	0.433838	T	0.03305	0.0096	L	0.43554	1.36	0.80722	D	1	B	0.27013	0.166	B	0.25614	0.062	T	0.41963	-0.9479	10	0.35671	T	0.21	.	12.9406	0.58340	0.0:1.0:0.0:0.0	.	195	Q6Q4G3	AMPQ_HUMAN	L	195;184	ENSP00000350541:P195L	ENSP00000350541:P195L	P	+	2	0	AC010282.1	115326797	0.002000	0.14202	0.891000	0.34965	0.178000	0.23041	1.441000	0.35035	2.105000	0.64084	0.655000	0.94253	CCC	C|0.997;T|0.003	0.003	strong		0.622	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1			T	115298898	C	T	115298898	3	4	30	1	0	0	0	0	1	0	0	0	834	623	22	2	586	2	AQPEP	5	115298898	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	741256	115298898	65616362	181	13332											
AQPEP	206338	hgsc.bcm.edu	37	chr5	115351066	115351066	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaaacaaagaagaaaagatTcaacttgcttatgcaatgag	20	8	7	6	0	1	4	1	1	0	3	1	4	1	4	0	0	4	2	0	0	8	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:115351066T>A	ENST00000357872.4	+	17	2692	c.2568T>A	c.(2566-2568)atT>atA	p.I856I	AQPEP_ENST00000515454.1_3'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		856						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										AAGAAAAGATTCAACTTGCTT	0.343																																					p.I856I		Atlas-SNP	.											FLJ90650,caecum,carcinoma,0,1	.	.	1	0			c.T2568A						scavenged	.						91	87	88					5																	115351066		2202	4300	6502	SO:0001819	synonymous_variant	0	exon17			AAAGATTCAACTT																												ENST00000357872.4:c.2568T>A	5.37:g.115351066T>A		31	0	0		35	3	0.0857143	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Silent	SNP	ENST00000357872.4	37	CCDS4124.1																																																																																			.	.	none		0.343	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1			A	115351066	T	A	115351066	2	1	30	1	0	0	0	0	0	0	0	1	834	1771	62	5		5	AQPEP	5	115351066	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	52168	115351066	65564194	182	13333											
CDKL3	51265	hgsc.bcm.edu	37	chr5	133655067	133655067	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acatgaactatatctgccaaCaatccattaagctttggata	15	12	5	9	0	1	1	0	1	1	0	2	2	2	2	2	1	4	1	2	1	7	5	rs373913998	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:133655067C>T	ENST00000265334.4	-	6	892	c.774G>A	c.(772-774)ttG>ttA	p.L258L	CTD-2410N18.4_ENST00000518409.1_RNA|CDKL3_ENST00000435211.1_Silent_p.L258L|CDKL3_ENST00000536186.1_Intron|CDKL3_ENST00000609654.1_Silent_p.L69L|CDKL3_ENST00000523054.1_Silent_p.L69L|CDKL3_ENST00000521755.1_Intron|CDKL3_ENST00000521118.1_Silent_p.L258L|CDKL3_ENST00000435240.2_5'UTR|CDKL3_ENST00000609383.1_Intron|CDKL3_ENST00000522501.1_5'UTR|CDKL3_ENST00000523832.1_Silent_p.L258L	NM_001113575.1	NP_001107047.1	Q8IVW4	CDKL3_HUMAN	cyclin-dependent kinase-like 3	258	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|prostate(3)	11			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TATCTGCCAACAATCCATTAA	0.428													C|||	3	0.000599042	0.0	0.0014	5008	,	,		15912	0.0		0.002	False		,,,				2504	0.0				p.L258L		Atlas-SNP	.											.	CDKL3	76	.	0			c.G774A						PASS	.	C	,	0,3060		0,0,1530	87	84	85		774,774	1.5	1	5		85	13,6839		0,13,3413	no	coding-synonymous,coding-synonymous	CDKL3	NM_001113575.1,NM_016508.3	,	0,13,4943	TT,TC,CC		0.1897,0.0,0.1312	,	258/593,258/456	133655067	13,9899	1530	3426	4956	SO:0001819	synonymous_variant	51265	exon6			TGCCAACAATCCA	AF130372	CCDS47264.1, CCDS47265.1, CCDS75303.1	5q31.1	2014-09-09			ENSG00000006837	ENSG00000006837	2.7.11.22	"Cyclin-dependent kinases"	15483	protein-coding gene	gene with protein product	"serine-threonine protein kinase NKIAMRE"	608459				10463609	Standard	NM_016508		Approved	NKIAMRE	uc003kzf.4	Q8IVW4	OTTHUMG00000186341	ENST00000265334.4:c.774G>A	5.37:g.133655067C>T		23	0	0		42	21	0.5	NM_001113575	D3DQA0|D3DQA1|Q9P114	Silent	SNP	ENST00000265334.4	37	CCDS47264.1																																																																																			.	.	weak		0.428	CDKL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377697.1	NM_001113575		T	133655067	C	T	133655067	2	4	30	1	0	0	0	0	0	0	0	1	3157	477	17	2		2	CDKL3	5	133655067	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	18304001	133655067	47260193	183	13334											
SAR1B	51128	hgsc.bcm.edu	37	chr5	133945288	133945288	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tcttcttttgactctaacagCctttcgtggtctgcacaatc	7	16	6	12	1	4	1	0	1	4	0	6	1	4	1	1	1	3	1	1	1	2	5	rs140899111	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:133945288C>T	ENST00000402673.2	-	5	599	c.321G>A	c.(319-321)agG>agA	p.R107R	SAR1B_ENST00000502539.1_Silent_p.R39R|SAR1B_ENST00000439578.1_Silent_p.R107R|SAR1B_ENST00000509937.1_Silent_p.R39R|SAR1B_ENST00000507419.1_Silent_p.R39R	NM_016103.3	NP_057187.1	Q9Y6B6	SAR1B_HUMAN	secretion associated, Ras related GTPase 1B	107					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)			ACTCTAACAGCCTTTCGTGGT	0.393													C|||	4	0.000798722	0.0	0.0	5008	,	,		20631	0.0		0.004	False		,,,				2504	0.0				p.R107R		Atlas-SNP	.											.	SAR1B	19	.	0			c.G321A						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	129	118	122		321,321	1.9	1	5	dbSNP_134	122	15,8585	11.2+/-40.8	0,15,4285	no	coding-synonymous,coding-synonymous	SAR1B	NM_001033503.2,NM_016103.3	,	0,16,6487	TT,TC,CC		0.1744,0.0227,0.123	,	107/199,107/199	133945288	16,12990	2203	4300	6503	SO:0001819	synonymous_variant	51128	exon6			TAACAGCCTTTCG	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.321G>A	5.37:g.133945288C>T		138	0	0		145	56	0.386207	NM_001033503	D3DQA4|Q567T4	Silent	SNP	ENST00000402673.2	37	CCDS4177.1																																																																																			C|0.999;T|0.001	0.001	strong		0.393	SAR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251158.2	NM_016103		T	133945288	C	T	133945288	2	4	30	1	0	0	0	0	0	0	0	1	13855	738	26	2		2	SAR1B	5	133945288	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	290221	133945288	46969972	184	13335											
CDC23	8697	hgsc.bcm.edu	37	chr5	137533901	137533901	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcttaccaattacacagcaCgtttctacacgatatttatc	12	15	3	11	2	2	0	0	0	2	0	3	1	2	0	1	0	4	2	1	0	6	8			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:137533901C>T	ENST00000394886.2	-	9	1029	c.999G>A	c.(997-999)acG>acA	p.T333T		NM_004661.3	NP_004652.2	Q9UJX2	CDC23_HUMAN	cell division cycle 23	333					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)			TTACACAGCACGTTTCTACAC	0.313																																					p.T333T		Atlas-SNP	.											.	CDC23	46	.	0			c.G999A						PASS	.						77	81	79					5																	137533901		2203	4300	6503	SO:0001819	synonymous_variant	8697	exon9			ACAGCACGTTTCT	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.999G>A	5.37:g.137533901C>T		80	0	0		93	48	0.516129	NM_004661	A8K6E5|B4E3A2|B7WP05|D3DQB7|O75433|Q53FN2|Q9BS73	Silent	SNP	ENST00000394886.2	37	CCDS4200.2																																																																																			.	.	none		0.313	CDC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251275.2			T	137533901	C	T	137533901	2	4	30	1	0	0	0	0	0	0	0	1	3063	523	19	1		1	CDC23	5	137533901	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	3588613	137533901	43381359	185	13336											
PCDHA4	56144	hgsc.bcm.edu	37	chr5	140188353	140188353	+	Silent	SNP	G	G	A																															cagccgctggaccacgaggaGctagagctgctgcagtttca																								rs561061447	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140188353G>A	ENST00000530339.1	+	1	1581	c.1581G>A	c.(1579-1581)gaG>gaA	p.E527E	PCDHA4_ENST00000356878.4_Silent_p.E527E|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Silent_p.E527E	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	527	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)			ACCACGAGGAGCTAGAGCTGC	0.652													.|||	115	0.0229633	0.003	0.0389	5008	,	,		17480	0.0		0.0755	False		,,,				2504	0.0082				p.E527E		Atlas-SNP	.											.	PCDHA4	419	.	0			c.G1581A						PASS	.						71	76	74					5																	140188353		2203	4300	6503	SO:0001819	synonymous_variant	56144	exon1			CGAGGAGCTAGAG	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.1581G>A	5.37:g.140188353G>A		136	0	0		65	12	0.184615	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			.	.	none		0.652	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		A	140188353	G	A	140188353	2	1	30	1	0	0	0	0	0	0	0	1	11535	962	34	2		2	PCDHA4	5	140188353	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2654452	140188353	40726907	186	13337	168	3									
PCDHA4	56144	hgsc.bcm.edu	37	chr5	140188354	140188354	+	Missense_Mutation	SNP	C	C	G																															agccgctggaccacgaggagCtagagctgctgcagtttcag																								rs142480630	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140188354C>G	ENST00000530339.1	+	1	1582	c.1582C>G	c.(1582-1584)Cta>Gta	p.L528V	PCDHA4_ENST00000356878.4_Missense_Mutation_p.L528V|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Missense_Mutation_p.L528V	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	528	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)			CCACGAGGAGCTAGAGCTGCT	0.652													.|||	115	0.0229633	0.003	0.0389	5008	,	,		17618	0.0		0.0755	False		,,,				2504	0.0082				p.L528V		Atlas-SNP	.											PCDHA4_ENST00000530339,NS,carcinoma,0,8	PCDHA4	419	8	0			c.C1582G						PASS	.						70	75	74					5																	140188354		2203	4300	6503	SO:0001583	missense	56144	exon1			GAGGAGCTAGAGC	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.1582C>G	5.37:g.140188354C>G	ENSP00000435300:p.Leu528Val	133	0	0		64	11	0.171875	NM_031500	O75285|Q2M253	Missense_Mutation	SNP	ENST00000530339.1	37	CCDS54916.1	.	.	.	.	.	.	.	.	.	.	c	11.23	1.577307	0.28092	.	.	ENSG00000204967	ENST00000512229;ENST00000356878;ENST00000530339	T;T;T	0.51325	0.71;0.71;0.71	4.18	2.19	0.27852	Cadherin (5);Cadherin-like (1);	0.000000	0.28952	U	0.013601	T	0.34948	0.0915	N	0.25332	0.735	0.20764	N	0.999854	P;B;B	0.43662	0.814;0.101;0.207	B;B;B	0.43508	0.422;0.421;0.214	T	0.15150	-1.0447	10	0.51188	T	0.08	.	8.8809	0.35374	0.2588:0.4914:0.2498:0.0	.	528;528;528	Q9UN74-2;Q9UN74;D6RA20	.;PCDA4_HUMAN;.	V	528	ENSP00000423470:L528V;ENSP00000349344:L528V;ENSP00000435300:L528V	ENSP00000349344:L528V	L	+	1	2	PCDHA4	140168538	0.000000	0.05858	1.000000	0.80357	0.984000	0.73092	-1.847000	0.01675	0.874000	0.35823	0.580000	0.79431	CTA	C|0.999;G|0.001	0.001	weak		0.652	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		G	140188354	C	G	140188354	3	3	30	1	0	0	0	0	1	0	0	0	11535	796	28	4	1584	4	PCDHA4	5	140188354	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1	140188354	40726906	187	13338	168	3									
PCDHA4	56144	hgsc.bcm.edu	37	chr5	140188356	140188356	+	Silent	SNP	A	A	G																															ccgctggaccacgaggagctAgagctgctgcagtttcaggt																								rs144593807	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140188356A>G	ENST00000530339.1	+	1	1584	c.1584A>G	c.(1582-1584)ctA>ctG	p.L528L	PCDHA4_ENST00000356878.4_Silent_p.L528L|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Silent_p.L528L	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	528	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)			ACGAGGAGCTAGAGCTGCTGC	0.652													.|||	115	0.0229633	0.003	0.0389	5008	,	,		17817	0.0		0.0755	False		,,,				2504	0.0082				p.L528L		Atlas-SNP	.											PCDHA4_ENST00000530339,NS,carcinoma,+2,8	PCDHA4	419	8	0			c.A1584G						PASS	.	A	,,,,,	11,4395		0,11,2192	70	75	73		,,,1584,,1584	1.3	1	5	dbSNP_134	73	57,8543		9,39,4252	no	intron,intron,intron,coding-synonymous,intron,coding-synonymous	PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_031411.1,NM_031500.1	,,,,,	9,50,6444	GG,GA,AA		0.6628,0.2497,0.5228	,,,,,	,,,528/948,,528/799	140188356	68,12938	2203	4300	6503	SO:0001819	synonymous_variant	56144	exon1			GGAGCTAGAGCTG	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.1584A>G	5.37:g.140188356A>G		133	0	0		63	11	0.174603	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			A|0.976;G|0.024	0.024	strong		0.652	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		G	140188356	A	G	140188356	2	3	30	1	0	0	0	0	0	0	0	1	11535	407	15	3		3	PCDHA4	5	140188356	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	2	140188356	40726904	188	13339	168	3									
PCDHA10	56139	hgsc.bcm.edu	37	chr5	140237158	140237158	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cgctgtcgagctacgtgtcgGtgcacgcggagagcggcaag	7	6	17	11	7	0	1	0	0	0	1	2	3	0	1	0	3	4	4	0	3	2	1	rs142356019	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140237158G>A	ENST00000307360.5	+	1	1525	c.1525G>A	c.(1525-1527)Gtg>Atg	p.V509M	PCDHA5_ENST00000529619.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000506939.2_Missense_Mutation_p.V509M|PCDHA4_ENST00000512229.2_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	509	Cadherin 5. {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)			CTACGTGTCGGTGCACGCGGA	0.697													.|||	119	0.023762	0.0121	0.0346	5008	,	,		14546	0.0		0.0716	False		,,,				2504	0.0072				p.V509M		Atlas-SNP	.											.	PCDHA10	358	.	0			c.G1525A						PASS	.	G	,MET/VAL,,,,,,,,,,,MET/VAL,MET/VAL	120,4272		4,112,2080	66	73	71		,1525,,,,,,,,,,,1525,1525	3.6	1	5	dbSNP_134	71	477,8069		47,383,3843	no	intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,missense	PCDHA9,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031859.1,NM_031860.1	,21,,,,,,,,,,,21,21	51,495,5923	AA,AG,GG		5.5816,2.7322,4.6143	,,,,,,,,,,,,,	,509/949,,,,,,,,,,,509/845,509/686	140237158	597,12341	2196	4273	6469	SO:0001583	missense	56139	exon1			GTGTCGGTGCACG	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.1525G>A	5.37:g.140237158G>A	ENSP00000304234:p.Val509Met	211	0	0		139	62	0.446043	NM_031859	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	37	CCDS54921.1	87	0.03983516483516483	9	0.018292682926829267	19	0.052486187845303865	0	0.0	59	0.07783641160949868	G	14.28	2.487603	0.44249	0.027322	0.055816	ENSG00000250120	ENST00000506939;ENST00000307360	T;T	0.67698	-0.28;-0.28	3.63	3.63	0.41609	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.17323	0.0416	M	0.64404	1.975	0.43489	P	0.004271000000000025	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.993	T	0.65446	-0.6166	8	0.59425	D	0.04	.	9.6727	0.40021	0.0974:0.0:0.9026:0.0	.	509;509;509	Q9Y5I2-3;Q9Y5I2;Q9Y5I2-2	.;PCDAA_HUMAN;.	M	509	ENSP00000421030:V509M;ENSP00000304234:V509M	ENSP00000304234:V509M	V	+	1	0	PCDHA10	140217342	.	.	0.998000	0.56505	0.648000	0.38561	.	.	2.007000	0.58848	0.561000	0.74099	GTG	G|0.957;A|0.043	0.043	strong		0.697	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		A	140237158	G	A	140237158	3	1	30	1	0	0	0	0	1	0	0	0	11529	1261	44	2	1527	2	PCDHA10	5	140237158	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	48802	140237158	40678102	189	13340											
PCDHA12	56137	hgsc.bcm.edu	37	chr5	140256807	140256807	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttagcgagttggtaccgcggTcggtgggtgcgggccacgtg	4	9	19	9	6	0	0	0	0	0	0	1	1	0	0	2	5	3	2	2	5	2	3	rs199811254		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140256807T>A	ENST00000398631.2	+	1	1750	c.1750T>A	c.(1750-1752)Tcg>Acg	p.S584T	PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	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)			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)			GGTACCGCGGTCGGTGGGTGC	0.682													.|||	1	0.000199681	0.0	0.0	5008	,	,		17689	0.0		0.001	False		,,,				2504	0.0				p.S584T	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											PCDHA12,NS,carcinoma,-1,2	PCDHA12	196	2	0			c.T1750A						PASS	.	T	,,,THR/SER,,,,,,,,,,,,THR/SER	1,4405	2.1+/-5.4	0,1,2202	221	209	213		,,,1750,,,,,,,,,,,,1750	-1.4	0	5		213	5,8591	4.3+/-15.6	0,5,4293	no	intron,intron,intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHA9,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031864.1	,,,58,,,,,,,,,,,,58	0,6,6495	AA,AT,TT		0.0582,0.0227,0.0461	,,,,,,,,,,,,,,,	,,,584/942,,,,,,,,,,,,584/793	140256807	6,12996	2203	4298	6501	SO:0001583	missense	56137	exon1			CCGCGGTCGGTGG	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.1750T>A	5.37:g.140256807T>A	ENSP00000381628:p.Ser584Thr	295	0	0		224	117	0.522321	NM_018903	O75278|Q2M1N8	Missense_Mutation	SNP	ENST00000398631.2	37	CCDS47285.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	4.945	0.175589	0.09391	2.27E-4	5.82E-4	ENSG00000251664	ENST00000398631	T	0.39229	1.09	4.71	-1.37	0.09056	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.33760	0.0874	M	0.69185	2.1	0.09310	N	1	B;B	0.33212	0.232;0.402	B;B	0.32762	0.152;0.082	T	0.37549	-0.9701	9	0.59425	D	0.04	.	1.4327	0.02337	0.276:0.0817:0.2678:0.3745	.	584;584	Q9UN75-2;Q9UN75	.;PCDAC_HUMAN	T	584	ENSP00000381628:S584T	ENSP00000381628:S584T	S	+	1	0	PCDHA12	140236991	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.529000	0.06186	-0.138000	0.11434	-0.516000	0.04426	TCG	T|0.999;A|0.001	0.001	strong		0.682	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		A	140256807	T	A	140256807	3	1	30	1	0	0	0	0	1	0	0	0	11531	1667	58	5	1752	5	PCDHA12	5	140256807	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	19649	140256807	40658453	190	13341											
PCDHA12	56137	hgsc.bcm.edu	37	chr5	140256920	140256920	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcggtcggcgcgcacatcccGttccacgtggggctgtacac	5	7	14	15	6	0	0	0	0	0	0	3	0	2	0	2	4	1	4	2	4	1	2	rs115718636	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140256920G>C	ENST00000398631.2	+	1	1863	c.1863G>C	c.(1861-1863)ccG>ccC	p.P621P	PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	621	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)			CGCACATCCCGTTCCACGTGG	0.672													.|||	111	0.0221645	0.0129	0.0303	5008	,	,		17234	0.0		0.0656	False		,,,				2504	0.0072				p.P621P	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											PCDHA12,colon,carcinoma,0,2	PCDHA12	196	2	0			c.G1863C						PASS	.	G	,,,,,,,,,,,,,,,	117,4289	87.8+/-126.4	0,117,2086	228	205	213		,,,1863,,,,,,,,,,,,1863	-0.7	0.9	5	dbSNP_132	213	437,8161	133.5+/-191.0	11,415,3873	no	intron,intron,intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031864.1	,,,,,,,,,,,,,,,	11,532,5959	CC,CG,GG		5.0826,2.6555,4.2602	,,,,,,,,,,,,,,,	,,,621/942,,,,,,,,,,,,621/793	140256920	554,12450	2203	4299	6502	SO:0001819	synonymous_variant	56137	exon1			CATCCCGTTCCAC	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.1863G>C	5.37:g.140256920G>C		368	1	0.00271739		298	150	0.503356	NM_018903	O75278|Q2M1N8	Silent	SNP	ENST00000398631.2	37	CCDS47285.1																																																																																			G|0.959;C|0.041	0.041	strong		0.672	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		C	140256920	G	C	140256920	2	2	30	1	0	0	0	0	0	0	0	1	11531	1132	40	4		4	PCDHA12	5	140256920	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	113	140256920	40658340	191	13342											
PCDHA13	56136	hgsc.bcm.edu	37	chr5	140262582	140262582	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gacaacgccccggaattttaCcaatccgtttataaagtgac	13	10	7	11	3	0	1	0	1	0	0	1	3	1	2	4	1	2	1	4	1	7	5			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140262582C>G	ENST00000289272.2	+	1	729	c.729C>G	c.(727-729)taC>taG	p.Y243*	PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA13_ENST00000409494.1_Nonsense_Mutation_p.Y243*|PCDHA10_ENST00000506939.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	243	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)			CGGAATTTTACCAATCCGTTT	0.453																																					p.Y243X	Melanoma(147;1739 1852 5500 27947 37288)	Atlas-SNP	.											.	PCDHA13	213	.	0			c.C729G						PASS	.						72	71	71					5																	140262582		2203	4300	6503	SO:0001587	stop_gained	56136	exon1			ATTTTACCAATCC	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.729C>G	5.37:g.140262582C>G	ENSP00000289272:p.Tyr243*	133	0	0		141	49	0.347518	NM_031865	O75277	Nonsense_Mutation	SNP	ENST00000289272.2	37	CCDS4240.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.998714	0.54147	.	.	ENSG00000239389	ENST00000409494;ENST00000289272	.	.	.	5.58	-0.292	0.12839	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	1.8341	0.03136	0.1235:0.1792:0.3522:0.345	.	.	.	.	X	243	.	ENSP00000289272:Y243X	Y	+	3	2	PCDHA13	140242766	0.000000	0.05858	0.101000	0.21167	0.535000	0.34838	-1.244000	0.02902	-0.053000	0.13289	0.561000	0.74099	TAC	.	.	none		0.453	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904		G	140262582	C	G	140262582	4	3	30	1	0	0	0	0	0	1	0	0	11532	518	18	4	731	4	PCDHA13	5	140262582	Nonsense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	5662	140262582	40652678	192	13343											
PCDHGB4	8641	hgsc.bcm.edu	37	chr5	140768442	140768442	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatgattgcgcaatgcacaGtggaggtagaagtcatagat	14	9	13	5	1	1	3	1	1	0	2	1	5	1	4	0	2	2	3	0	2	5	3	rs201053346		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140768442G>T	ENST00000519479.1	+	1	991	c.991G>T	c.(991-993)Gtg>Ttg	p.V331L	PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_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	331	Cadherin 3. {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)			GCAATGCACAGTGGAGGTAGA	0.413																																					p.V331L		Atlas-SNP	.											.	PCDHGB4	125	.	0			c.G991T						PASS	.	G	LEU/VAL,,,,,,,,,,,LEU/VAL	0,3830		0,0,1915	86	80	82		991,,,,,,,,,,,991	4.2	0.1	5		82	3,8283		0,3,4140	yes	missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHGB4,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_032098.1	32,,,,,,,,,,,32	0,3,6055	TT,TG,GG		0.0362,0.0,0.0248	,,,,,,,,,,,	331/924,,,,,,,,,,,331/804	140768442	3,12113	1915	4143	6058	SO:0001583	missense	8641	exon1			TGCACAGTGGAGG	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.991G>T	5.37:g.140768442G>T	ENSP00000428288:p.Val331Leu	64	0	0		77	33	0.428571	NM_032098	O15099|Q2M267|Q9UN64	Missense_Mutation	SNP	ENST00000519479.1	37	CCDS54928.1	.	.	.	.	.	.	.	.	.	.	.	13.67	2.306759	0.40795	0.0	3.62E-4	ENSG00000253953	ENST00000519479	T	0.01787	4.64	5.09	4.2	0.49525	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.06781	0.0173	M	0.74389	2.26	0.25118	N	0.990664	P;D	0.55385	0.918;0.971	P;P	0.53102	0.596;0.718	T	0.09552	-1.0669	9	0.49607	T	0.09	.	14.1498	0.65375	0.0773:0.0:0.9227:0.0	.	331;331	Q9UN71-2;Q9UN71	.;PCDGG_HUMAN	L	331	ENSP00000428288:V331L	ENSP00000428288:V331L	V	+	1	0	PCDHGB4	140748626	0.998000	0.40836	0.109000	0.21407	0.063000	0.16089	2.244000	0.43124	2.525000	0.85131	0.655000	0.94253	GTG	.	.	weak		0.413	PCDHGB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374745.1	NM_003736		T	140768442	G	T	140768442	3	4	30	1	0	0	0	0	1	0	0	0	11574	1029	36	4	993	4	PCDHGB4	5	140768442	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	505860	140768442	40146818	193	13344											
PCDHGA8	9708	hgsc.bcm.edu	37	chr5	140773812	140773812	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcttttccttgactgcacacGaccccgacagccaggagaat	10	9	8	14	2	1	2	0	1	1	1	2	5	2	2	4	1	2	1	4	1	1	3	rs144796076	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140773812G>A	ENST00000398604.2	+	1	1432	c.1432G>A	c.(1432-1434)Gac>Aac	p.D478N	PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	478	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(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)			GACTGCACACGACCCCGACAG	0.547													.|||	10	0.00199681	0.0	0.0029	5008	,	,		17412	0.0		0.007	False		,,,				2504	0.001				p.D478N		Atlas-SNP	.											.	PCDHGA8	146	.	0			c.G1432A						PASS	.	G	,ASN/ASP,,,,,,,,,,,ASN/ASP	4,4204		0,4,2100	51	55	53		,1432,,,,,,,,,,,1432	5.1	0.4	5	dbSNP_134	53	26,8436		0,26,4205	yes	intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHGB4,PCDHGA8,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_014004.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_032088.1	,23,,,,,,,,,,,23	0,30,6305	AA,AG,GG		0.3073,0.0951,0.2368	,,,,,,,,,,,,	,478/821,,,,,,,,,,,478/933	140773812	30,12640	2104	4231	6335	SO:0001583	missense	9708	exon1			GCACACGACCCCG	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.1432G>A	5.37:g.140773812G>A	ENSP00000381605:p.Asp478Asn	166	0	0		182	78	0.428571	NM_014004	A7MCZ4|O15039	Missense_Mutation	SNP	ENST00000398604.2	37	CCDS47291.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	.	16.62	3.173397	0.57584	9.51E-4	0.003073	ENSG00000253767	ENST00000398604	T	0.74526	-0.85	5.06	5.06	0.68205	Cadherin (4);Cadherin-like (1);	0.000000	0.32273	U	0.006322	D	0.91958	0.7453	H	0.99970	5.12	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95745	0.8787	10	0.87932	D	0	.	18.0785	0.89435	0.0:0.0:1.0:0.0	.	478;478	Q9Y5G5;Q9Y5G5-2	PCDG8_HUMAN;.	N	478	ENSP00000381605:D478N	ENSP00000381605:D478N	D	+	1	0	PCDHGA8	140753996	1.000000	0.71417	0.373000	0.26003	0.201000	0.24016	9.595000	0.98260	2.366000	0.80165	0.655000	0.94253	GAC	G|0.996;A|0.004	0.004	strong		0.547	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088		A	140773812	G	A	140773812	3	1	30	1	0	0	0	0	1	0	0	0	11569	1058	37	1	1434	1	PCDHGA8	5	140773812	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	5370	140773812	40141448	194	13345											
PCDHGA8	9708	hgsc.bcm.edu	37	chr5	140774076	140774076	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcccgagatcctgtaccccGccctccccacagacggttcc	6	6	8	21	4	0	2	0	0	0	2	3	3	3	2	8	1	1	2	8	1	1	2	rs367855808		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:140774076G>T	ENST00000398604.2	+	1	1696	c.1696G>T	c.(1696-1698)Gcc>Tcc	p.A566S	PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	566					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)			CCTGTACCCCGCCCTCCCCAC	0.667																																					p.A566S		Atlas-SNP	.											.	PCDHGA8	146	.	0			c.G1696T						PASS	.	A	,SER/ALA,,,,,,,,,,,SER/ALA	0,4406		0,0,2203	91	106	101		,1696,,,,,,,,,,,1696	-10.1	0	5		101	1,8595		0,1,4297	no	intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHGB4,PCDHGA8,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_014004.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_032088.1	,99,,,,,,,,,,,99	0,1,6500	TT,TG,GG		0.0116,0.0,0.0077	,,,,,,,,,,,,	,566/821,,,,,,,,,,,566/933	140774076	1,13001	2203	4298	6501	SO:0001583	missense	9708	exon1			TACCCCGCCCTCC	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.1696G>T	5.37:g.140774076G>T	ENSP00000381605:p.Ala566Ser	172	0	0		182	83	0.456044	NM_014004	A7MCZ4|O15039	Missense_Mutation	SNP	ENST00000398604.2	37	CCDS47291.1	.	.	.	.	.	.	.	.	.	.	.	0.012	-1.677464	0.00751	0.0	1.16E-4	ENSG00000253767	ENST00000398604	T	0.46063	0.88	5.06	-10.1	0.00402	Cadherin-like (1);	1.441770	0.05974	N	0.642917	T	0.13329	0.0323	N	0.02379	-0.575	0.09310	N	1	B;B	0.21071	0.051;0.004	B;B	0.19391	0.025;0.006	T	0.11767	-1.0574	10	0.07813	T	0.8	.	9.2393	0.37486	0.6616:0.0594:0.0798:0.1992	.	566;566	Q9Y5G5;Q9Y5G5-2	PCDG8_HUMAN;.	S	566	ENSP00000381605:A566S	ENSP00000381605:A566S	A	+	1	0	PCDHGA8	140754260	0.000000	0.05858	0.000000	0.03702	0.625000	0.37756	-8.772000	0.00017	-3.686000	0.00121	-1.652000	0.00757	GCC	.	.	weak		0.667	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088		T	140774076	G	T	140774076	3	4	30	1	0	0	0	0	1	0	0	0	11569	1087	38	4	1698	4	PCDHGA8	5	140774076	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	264	140774076	40141184	195	13346											
SPRY4	81848	hgsc.bcm.edu	37	chr5	141693948	141693948	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcaggcagggcagcaccacGgagagagcacccatgaagga	14	1	15	11	1	0	2	0	1	0	1	0	5	0	4	2	4	3	5	2	4	1	0	rs145360326	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:141693948G>A	ENST00000434127.2	-	2	969	c.726C>T	c.(724-726)tcC>tcT	p.S242S	SPRY4_ENST00000344120.4_Silent_p.S265S|SPRY4_ENST00000503582.1_5'Flank	NM_001127496.1	NP_001120968.1	Q9C004	SPY4_HUMAN	sprouty homolog 4 (Drosophila)	242	Cys-rich.|SPR. {ECO:0000255|PROSITE- ProRule:PRU00572}.				multicellular organismal development (GO:0007275)|negative regulation of MAP kinase activity (GO:0043407)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)		p.S265S(3)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(1)	18		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAGCACCACGGAGAGAGCAC	0.682									Testicular Cancer, Familial Clustering of																												p.S265S		Atlas-SNP	.											SPRY4,rectum,carcinoma,0,2	SPRY4	31	2	3	Substitution - coding silent(3)	lung(2)|large_intestine(1)	c.C795T						PASS	.	G	,	2,4404	4.2+/-10.8	0,2,2201	60	60	60		726,795	0.7	1	5	dbSNP_134	60	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	SPRY4	NM_001127496.1,NM_030964.3	,	0,7,6496	AA,AG,GG		0.0581,0.0454,0.0538	,	242/300,265/323	141693948	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	81848	exon3	Familial Cancer Database		CACCACGGAGAGA	AF227516	CCDS4274.1, CCDS47296.1	5q31.3	2010-08-05			ENSG00000187678	ENSG00000187678			15533	protein-coding gene	gene with protein product		607984				16465403	Standard	NM_030964		Approved		uc010jgi.1	Q9C004	OTTHUMG00000129663	ENST00000434127.2:c.726C>T	5.37:g.141693948G>A		251	0	0		229	108	0.471616	NM_030964	A4FVB2|A4FVB3|Q6QIX2|Q9C003	Silent	SNP	ENST00000434127.2	37	CCDS47296.1																																																																																			G|0.999;A|0.001	0.001	strong		0.682	SPRY4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370652.1			A	141693948	G	A	141693948	2	1	30	1	0	0	0	0	0	0	0	1	15123	1103	39	1		1	SPRY4	5	141693948	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	919872	141693948	39221312	196	13347											
GPR151	134391	hgsc.bcm.edu	37	chr5	145894882	145894882	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacagccaagctacccattcGgggagccacaagagagcaga	14	3	11	13	1	0	2	0	0	0	2	1	4	0	3	3	2	5	2	3	2	3	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:145894882G>A	ENST00000311104.2	-	1	871	c.795C>T	c.(793-795)ccC>ccT	p.P265P		NM_194251.2	NP_919227.2	Q8TDV0	GP151_HUMAN	G protein-coupled receptor 151	265						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)			CTACCCATTCGGGGAGCCACA	0.507																																					p.P265P	Pancreas(78;420 1386 18535 37114 49710)	Atlas-SNP	.											.	GPR151	35	.	0			c.C795T						PASS	.						54	56	56					5																	145894882		2203	4300	6503	SO:0001819	synonymous_variant	134391	exon1			CCATTCGGGGAGC	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.795C>T	5.37:g.145894882G>A		94	0	0		113	32	0.283186	NM_194251	Q86SN8|Q8NGV2	Silent	SNP	ENST00000311104.2	37	CCDS34266.1																																																																																			.	.	none		0.507	GPR151-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373457.1	NM_194251		A	145894882	G	A	145894882	2	1	30	1	0	0	0	0	0	0	0	1	6665	1103	39	1		1	GPR151	5	145894882	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	4200934	145894882	35020378	197	13348											
PDE6A	5145	hgsc.bcm.edu	37	chr5	149265875	149265875	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgtggtcaatgtcatggcaGaaagcagcagtgaccatggc	11	8	13	9	0	2	2	2	1	0	1	2	2	2	2	1	3	2	3	1	3	2	0	rs61733360	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:149265875G>A	ENST00000255266.5	-	14	1910	c.1791C>T	c.(1789-1791)ttC>ttT	p.F597F		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	597					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)	p.F597F(1)		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)	TGTCATGGCAGAAAGCAGCAG	0.527													G|||	133	0.0265575	0.003	0.0749	5008	,	,		20466	0.0119		0.0308	False		,,,				2504	0.0348				p.F597F		Atlas-SNP	.											PDE6A,NS,carcinoma,0,1	PDE6A	98	1	1	Substitution - coding silent(1)	stomach(1)	c.C1791T						PASS	.	G		37,4369	43.1+/-76.7	0,37,2166	155	130	138		1791	5.7	1	5	dbSNP_129	138	325,8275	114.6+/-174.5	8,309,3983	no	coding-synonymous	PDE6A	NM_000440.2		8,346,6149	AA,AG,GG		3.7791,0.8398,2.7833		597/861	149265875	362,12644	2203	4300	6503	SO:0001819	synonymous_variant	5145	exon14			ATGGCAGAAAGCA		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.1791C>T	5.37:g.149265875G>A		159	0	0		163	79	0.484663	NM_000440	Q0P638	Silent	SNP	ENST00000255266.5	37	CCDS4299.1																																																																																			G|0.969;A|0.031	0.031	strong		0.527	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2			A	149265875	G	A	149265875	2	1	30	1	0	0	0	0	0	0	0	1	11654	933	33	2		2	PDE6A	5	149265875	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	3370993	149265875	31649385	198	13349											
ZNF300	91975	hgsc.bcm.edu	37	chr5	150275835	150275835	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagaacaatcataaggtttCtccccagtatgagttctctg	11	13	7	10	0	4	2	2	1	2	1	6	2	4	2	2	1	1	3	2	1	4	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:150275835C>A	ENST00000274599.5	-	6	1386	c.966G>T	c.(964-966)gaG>gaT	p.E322D	ZNF300_ENST00000446148.2_Missense_Mutation_p.E338D|ZNF300_ENST00000418587.2_Missense_Mutation_p.E286D|ZNF300_ENST00000394226.2_Missense_Mutation_p.E322D|ZNF300_ENST00000427179.1_3'UTR	NM_052860.2	NP_443092.1	Q96RE9	ZN300_HUMAN	zinc finger protein 300	322					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)			CATAAGGTTTCTCCCCAGTAT	0.398																																					p.E338D		Atlas-SNP	.											.	ZNF300	69	.	0			c.G1014T						PASS	.						84	89	87					5																	150275835		2202	4299	6501	SO:0001583	missense	91975	exon7			AGGTTTCTCCCCA	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.966G>T	5.37:g.150275835C>A	ENSP00000274599:p.Glu322Asp	126	0	0		102	26	0.254902	NM_001172831	A8MY91|B3KU35|B4DU78|F5GWS1|Q06DQ3|Q17RP3|Q5H9N5	Missense_Mutation	SNP	ENST00000274599.5	37	CCDS4311.2	.	.	.	.	.	.	.	.	.	.	C	17.05	3.289152	0.59976	.	.	ENSG00000145908	ENST00000446148;ENST00000274599;ENST00000418587;ENST00000394226	T;T;T;T	0.26810	1.71;1.71;1.71;1.71	3.59	2.71	0.32032	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.29817	0.0745	L	0.41961	1.31	0.26287	N	0.97818	P	0.47484	0.896	P	0.50136	0.632	T	0.08432	-1.0722	9	0.72032	D	0.01	.	8.7303	0.34494	0.0:0.8839:0.0:0.1161	.	322	Q96RE9	ZN300_HUMAN	D	338;322;286;322	ENSP00000397178:E338D;ENSP00000274599:E322D;ENSP00000392593:E286D;ENSP00000377773:E322D	ENSP00000274599:E322D	E	-	3	2	ZNF300	150256028	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.994000	0.40757	0.846000	0.35142	0.563000	0.77884	GAG	.	.	none		0.398	ZNF300-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_052860		A	150275835	C	A	150275835	3	1	30	1	0	0	0	0	1	0	0	0	17846	912	32	4	852	4	ZNF300	5	150275835	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1009960	150275835	30639425	199	13350											
GLRA1	2741	hgsc.bcm.edu	37	chr5	151208500	151208500	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	accttgtgatgtctccgcttCctcctgaatcggagcagctc	6	12	9	14	2	1	2	0	2	1	0	6	3	3	3	4	1	2	3	4	1	1	2	rs75463357	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:151208500C>T	ENST00000455880.2	-	8	1327	c.1041G>A	c.(1039-1041)agG>agA	p.R347R	GLRA1_ENST00000545569.1_Silent_p.R264R|GLRA1_ENST00000274576.4_Silent_p.R347R			P23415	GLRA1_HUMAN	glycine receptor, alpha 1	347					acrosome reaction (GO:0007340)|action potential (GO:0001508)|adult walking behavior (GO:0007628)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|muscle contraction (GO:0006936)|negative regulation of transmission of nerve impulse (GO:0051970)|neuromuscular process controlling posture (GO:0050884)|neuropeptide signaling pathway (GO:0007218)|positive regulation of acrosome reaction (GO:2000344)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|righting reflex (GO:0060013)|startle response (GO:0001964)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|external side of plasma membrane (GO:0009897)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|glycine binding (GO:0016594)|taurine binding (GO:0030977)|transmitter-gated ion channel activity (GO:0022824)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	23		all_hematologic(541;0.0341)|Medulloblastoma(196;0.0912)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Ethanol(DB00898)|Ginkgo biloba(DB01381)|Glycine(DB00145)|Halothane(DB01159)|Isoflurane(DB00753)|Lindane(DB00431)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	GTCTCCGCTTCCTCCTGAATC	0.468													C|||	42	0.00838658	0.0008	0.0159	5008	,	,		21283	0.0		0.0258	False		,,,				2504	0.0041				p.R347R		Atlas-SNP	.											.	GLRA1	61	.	0			c.G1041A						PASS	.	C	,	23,4383	30.8+/-60.4	0,23,2180	172	167	169		1041,1041	4.2	1	5	dbSNP_132	169	209,8391	89.2+/-151.4	5,199,4096	no	coding-synonymous,coding-synonymous	GLRA1	NM_000171.3,NM_001146040.1	,	5,222,6276	TT,TC,CC		2.4302,0.522,1.7838	,	347/450,347/458	151208500	232,12774	2203	4300	6503	SO:0001819	synonymous_variant	2741	exon8			CCGCTTCCTCCTG		CCDS4320.1, CCDS54942.1	5q33.1	2012-02-07	2008-01-24		ENSG00000145888	ENSG00000145888		"Ligand-gated ion channels / Glycine receptors"	4326	protein-coding gene	gene with protein product	"startle disease/hyperekplexia", "stiff person syndrome"	138491	"glycine receptor, alpha 1 (startle disease/hyperekplexia)"	STHE		1355335, 8298642	Standard	NM_000171		Approved		uc003lut.3	P23415	OTTHUMG00000130121	ENST00000455880.2:c.1041G>A	5.37:g.151208500C>T		66	0	0		71	35	0.492958	NM_000171	B2R6T3|Q14C77|Q6DJV9	Silent	SNP	ENST00000455880.2	37	CCDS54942.1																																																																																			C|0.983;T|0.017	0.017	strong		0.468	GLRA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373959.1			T	151208500	C	T	151208500	2	4	30	1	0	0	0	0	0	0	0	1	6462	854	30	2		2	GLRA1	5	151208500	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	932665	151208500	29706760	200	13351											
IL12B	3593	hgsc.bcm.edu	37	chr5	158750329	158750329	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cggataccaatccaattctaCgacataaactggaatgcaca	16	8	6	11	2	1	0	0	0	1	0	2	3	2	2	2	2	4	1	2	2	7	4	rs3213096	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr5:158750329C>T	ENST00000231228.2	-	3	552	c.97G>A	c.(97-99)Gta>Ata	p.V33I		NM_002187.2	NP_002178.2	P29460	IL12B_HUMAN	interleukin 12B	33	Ig-like C2-type.		V -> I (in dbSNP:rs3213096). {ECO:0000269|Ref.5}.		cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|defense response to Gram-negative bacterium (GO:0050829)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|interferon-gamma biosynthetic process (GO:0042095)|natural killer cell activation (GO:0030101)|natural killer cell activation involved in immune response (GO:0002323)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of cell adhesion (GO:0045785)|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 biosynthetic process (GO:0045078)|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 lymphocyte proliferation (GO:0050671)|positive regulation of memory T cell differentiation (GO:0043382)|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 directed against tumor cell target (GO:0002860)|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 activation (GO:0051135)|positive regulation of NK T cell proliferation (GO:0051142)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|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 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 cytokine biosynthetic process (GO:0042035)|regulation of tyrosine phosphorylation of Stat1 protein (GO:0042510)|response to UV-B (GO:0010224)|sensory perception of pain (GO:0019233)|sexual reproduction (GO:0019953)|T-helper 1 type immune response (GO:0042088)|T-helper cell differentiation (GO:0042093)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|interleukin-12 complex (GO:0043514)|interleukin-23 complex (GO:0070743)|membrane (GO:0016020)	cytokine receptor activity (GO:0004896)|identical protein binding (GO:0042802)|interleukin-12 alpha subunit binding (GO:0042164)|interleukin-12 receptor binding (GO:0005143)|protein heterodimerization activity (GO:0046982)			cervix(1)|endometrium(1)|large_intestine(5)|lung(4)	11	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)			TCCAATTCTACGACATAAACT	0.502													C|||	19	0.00379393	0.0	0.0043	5008	,	,		20539	0.0		0.0099	False		,,,				2504	0.0061				p.V33I		Atlas-SNP	.											.	IL12B	30	.	0			c.G97A						PASS	.	C	ILE/VAL	7,4399	12.9+/-30.5	0,7,2196	61	56	58		97	5.2	0.9	5	dbSNP_106	58	49,8551	31.2+/-83.2	0,49,4251	yes	missense	IL12B	NM_002187.2	29	0,56,6447	TT,TC,CC		0.5698,0.1589,0.4306	benign	33/329	158750329	56,12950	2203	4300	6503	SO:0001583	missense	3593	exon3			ATTCTACGACATA	M65290	CCDS4346.1	5q31.1-q33.1	2014-09-17	2014-04-04		ENSG00000113302	ENSG00000113302		"Interleukins and interleukin receptors", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	5970	protein-coding gene	gene with protein product	"natural killer cell stimulatory factor-2", "cytotoxic lymphocyte maturation factor 2, p40", "interleukin 12, p40", "natural killer cell stimulatory factor, 40 kD subunit", "interleukin-12 beta chain", "IL12, subunit p40"	161561	"interleukin 12B (natural killer cell stimulatory factor 2, cytotoxic lymphocyte maturation factor 2, p40)"	NKSF2		1673147	Standard	NM_002187		Approved	CLMF, IL-12B, NKSF, CLMF2	uc003lxr.1	P29460	OTTHUMG00000130307	ENST00000231228.2:c.97G>A	5.37:g.158750329C>T	ENSP00000231228:p.Val33Ile	57	0	0		63	29	0.460317	NM_002187		Missense_Mutation	SNP	ENST00000231228.2	37	CCDS4346.1	13	0.005952380952380952	0	0.0	3	0.008287292817679558	0	0.0	10	0.013192612137203167	C	9.248	1.040122	0.19669	0.001589	0.005698	ENSG00000113302	ENST00000231228	T	0.22743	1.94	6.02	5.16	0.70880	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.054974	0.64402	D	0.000001	T	0.20210	0.0486	M	0.79475	2.455	0.45791	D	0.998676	B	0.09022	0.002	B	0.12156	0.007	T	0.03473	-1.1033	10	0.46703	T	0.11	-3.6912	11.4605	0.50208	0.0:0.9177:0.0:0.0823	rs3213096;rs17056679;rs17875310;rs52806839;rs56592501;rs3213096	33	P29460	IL12B_HUMAN	I	33	ENSP00000231228:V33I	ENSP00000231228:V33I	V	-	1	0	IL12B	158682907	0.822000	0.29219	0.877000	0.34402	0.087000	0.18053	1.240000	0.32731	1.568000	0.49683	-0.137000	0.14449	GTA	C|0.994;T|0.006	0.006	strong		0.502	IL12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252652.2	NM_002187		T	158750329	C	T	158750329	3	4	30	1	0	0	0	0	1	0	0	0	7634	536	19	1	909	1	IL12B	5	158750329	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	7541829	158750329	22164931	201	13352											
PRPF4B	8899	hgsc.bcm.edu	37	chr6	4044109	4044109	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tctgaaccaagcagcccccaGagcagtacgagaacacgatc	14	4	9	14	2	1	3	0	1	1	2	2	5	1	3	3	0	6	3	3	0	4	1	rs12195092	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:4044109G>A	ENST00000337659.6	+	6	1813	c.1713G>A	c.(1711-1713)caG>caA	p.Q571Q	PRPF4B_ENST00000538861.1_Silent_p.Q557Q	NM_003913.4	NP_003904.3	Q13523	PRP4B_HUMAN	pre-mRNA processing factor 4B	571					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)				GCAGCCCCCAGAGCAGTACGA	0.398													G|||	30	0.00599042	0.0015	0.0058	5008	,	,		18977	0.0		0.0219	False		,,,				2504	0.002				p.Q571Q		Atlas-SNP	.											.	PRPF4B	140	.	0			c.G1713A						PASS	.	G		15,4391	22.3+/-47.3	0,15,2188	90	85	87		1713	4.5	1	6	dbSNP_120	87	218,8382	91.4+/-153.5	1,216,4083	no	coding-synonymous	PRPF4B	NM_003913.4		1,231,6271	AA,AG,GG		2.5349,0.3404,1.7915		571/1008	4044109	233,12773	2203	4300	6503	SO:0001819	synonymous_variant	8899	exon6			CCCCCAGAGCAGT	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.1713G>A	6.37:g.4044109G>A		163	0	0		119	56	0.470588	NM_003913	A8K5C9|Q5D0F6|Q5TAY8|Q8IVC3|Q8TDP2|Q96QT7|Q9UEE6	Silent	SNP	ENST00000337659.6	37	CCDS4488.1																																																																																			G|0.982;A|0.018	0.018	strong		0.398	PRPF4B-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314018.2			A	4044109	G	A	4044109	2	1	30	1	0	0	0	0	0	0	0	1	12585	933	33	2		2	PRPF4B	6	4044109	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10		4044109	167070958	202	13353											
RREB1	6239	hgsc.bcm.edu	37	chr6	7189437	7189437	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accactcatgcagcatctgcGgaaagtcactgagctcggcc	10	7	10	14	2	3	1	2	1	1	0	4	2	3	2	2	2	4	3	2	2	1	0	rs201588284		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:7189437G>A	ENST00000349384.6	+	6	621	c.307G>A	c.(307-309)Gga>Aga	p.G103R	RREB1_ENST00000379933.3_Missense_Mutation_p.G103R|RREB1_ENST00000379938.2_Missense_Mutation_p.G103R|Y_RNA_ENST00000364613.1_RNA|RREB1_ENST00000334984.6_Missense_Mutation_p.G103R	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	103					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)				CAGCATCTGCGGAAAGTCACT	0.557													G|||	1	0.000199681	0.0	0.0	5008	,	,		18775	0.001		0.0	False		,,,				2504	0.0				p.G103R		Atlas-SNP	.											RREB1_ENST00000379938,NS,carcinoma,-2,2	RREB1	242	2	0			c.G307A						PASS	.						67	53	57					6																	7189437		2203	4300	6503	SO:0001583	missense	6239	exon6			ATCTGCGGAAAGT	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.307G>A	6.37:g.7189437G>A	ENSP00000305560:p.Gly103Arg	40	0	0		59	31	0.525424	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	32	5.181977	0.94885	.	.	ENSG00000124782	ENST00000379933;ENST00000491191;ENST00000379938;ENST00000471433;ENST00000349384;ENST00000334984;ENST00000483150	T;T;T;T;T;T;T	0.66460	3.19;-0.21;3.19;3.19;3.19;3.19;3.19	5.65	5.65	0.86999	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000016	T	0.80177	0.4575	M	0.75447	2.3	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.997;0.962	T	0.80759	-0.1239	10	0.62326	D	0.03	-55.3388	19.7284	0.96174	0.0:0.0:1.0:0.0	.	103;103;103	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	R	103	ENSP00000369265:G103R;ENSP00000420519:G103R;ENSP00000369270:G103R;ENSP00000420299:G103R;ENSP00000305560:G103R;ENSP00000335574:G103R;ENSP00000419511:G103R	ENSP00000335574:G103R	G	+	1	0	RREB1	7134436	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.304000	0.78882	2.668000	0.90789	0.591000	0.81541	GGA	G|0.999;A|0.001	0.001	strong		0.557	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1			A	7189437	G	A	7189437	3	1	30	1	0	0	0	0	1	0	0	0	13694	1117	39	1	317	1	RREB1	6	7189437	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	3145328	7189437	163925630	203	13354											
HIVEP1	3096	hgsc.bcm.edu	37	chr6	12164308	12164308	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agcagacttctgtagccagcGcaaaccaggtcagcaggacc	12	5	11	13	1	2	1	1	0	1	1	2	2	2	2	3	2	5	4	3	2	2	2	rs181056704		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:12164308G>A	ENST00000379388.2	+	9	8103	c.7771G>A	c.(7771-7773)Gca>Aca	p.A2591T	HIVEP1_ENST00000541134.1_Missense_Mutation_p.A456T	NM_002114.2	NP_002105.2	P15822	ZEP1_HUMAN	human immunodeficiency virus type I enhancer binding protein 1	2591					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)				TGTAGCCAGCGCAAACCAGGT	0.537													G|||	1	0.000199681	0.0	0.0	5008	,	,		21442	0.0		0.001	False		,,,				2504	0.0				p.A2591T		Atlas-SNP	.											.	HIVEP1	242	.	0			c.G7771A						PASS	.	G	THR/ALA	3,4009		0,3,2003	70	78	76		7771	3.3	0	6		76	31,8333		0,31,4151	yes	missense	HIVEP1	NM_002114.2	58	0,34,6154	AA,AG,GG		0.3706,0.0748,0.2747	benign	2591/2719	12164308	34,12342	2006	4182	6188	SO:0001583	missense	3096	exon9			GCCAGCGCAAACC	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.7771G>A	6.37:g.12164308G>A	ENSP00000368698:p.Ala2591Thr	120	0	0		117	58	0.495726	NM_002114	B2RTU3|Q14122|Q5MPB1|Q5VW60	Missense_Mutation	SNP	ENST00000379388.2	37	CCDS43426.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	16.33	3.092661	0.56075	7.48E-4	0.003706	ENSG00000095951	ENST00000379388;ENST00000541134;ENST00000542327	T;T	0.31769	2.99;1.48	5.23	3.27	0.37495	.	0.224672	0.22869	N	0.054645	T	0.07007	0.0178	L	0.38175	1.15	0.09310	N	1	P	0.35155	0.487	B	0.20955	0.032	T	0.13098	-1.0522	10	0.37606	T	0.19	-6.4409	6.6498	0.22955	0.0763:0.2109:0.5992:0.1136	.	2591	P15822	ZEP1_HUMAN	T	2591;456;573	ENSP00000368698:A2591T;ENSP00000445617:A456T	ENSP00000368698:A2591T	A	+	1	0	HIVEP1	12272294	0.000000	0.05858	0.005000	0.12908	0.319000	0.28217	0.217000	0.17603	1.173000	0.42796	0.580000	0.79431	GCA	G|0.999;A|0.001	0.001	strong		0.537	HIVEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039870.2	NM_002114		A	12164308	G	A	12164308	3	1	30	1	0	0	0	0	1	0	0	0	7195	1087	38	1	7801	1	HIVEP1	6	12164308	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	4974871	12164308	158950759	204	13355											
HIST1H1A	3024	hgsc.bcm.edu	37	chr6	26017397	26017397	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgccttgggttttacagcCttagctttagcagggctttt	5	15	11	10	1	0	0	0	0	0	0	0	0	0	0	3	2	4	4	3	2	3	8			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:26017397C>G	ENST00000244573.3	-	1	643	c.564G>C	c.(562-564)aaG>aaC	p.K188N		NM_005325.3	NP_005316.1	Q02539	H11_HUMAN	histone cluster 1, H1a	188					nucleosome assembly (GO:0006334)|spermatogenesis (GO:0007283)	nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|ovary(3)|prostate(1)	13						GTTTTACAGCCTTAGCTTTAG	0.453																																					p.K188N		Atlas-SNP	.											.	HIST1H1A	25	.	0			c.G564C						PASS	.						151	159	156					6																	26017397		2203	4300	6503	SO:0001583	missense	3024	exon1			TACAGCCTTAGCT	AF531299	CCDS4569.1	6p22.1	2012-11-16	2006-10-11	2003-02-21	ENSG00000124610	ENSG00000124610		"Histones / Replication-dependent"	4715	protein-coding gene	gene with protein product		142709	"H1 histone family, member 1", "histone 1, H1a"	H1F1		2759094, 12408966	Standard	NM_005325		Approved	H1.1, H1a	uc003nfo.3	Q02539	OTTHUMG00000016413	ENST00000244573.3:c.564G>C	6.37:g.26017397C>G	ENSP00000244573:p.Lys188Asn	292	1	0.00342466		251	125	0.498008	NM_005325	Q3MJ34	Missense_Mutation	SNP	ENST00000244573.3	37	CCDS4569.1	.	.	.	.	.	.	.	.	.	.	N	10.43	1.346702	0.24426	.	.	ENSG00000124610	ENST00000244573	T	0.20463	2.07	4.31	4.31	0.51392	.	0.070517	0.56097	D	0.000038	T	0.09949	0.0244	L	0.45352	1.415	0.51482	D	0.99992	P	0.37636	0.603	B	0.28385	0.089	T	0.08269	-1.0730	10	0.56958	D	0.05	-13.3791	16.683	0.85297	0.0:1.0:0.0:0.0	.	188	Q02539	H11_HUMAN	N	188	ENSP00000244573:K188N	ENSP00000244573:K188N	K	-	3	2	HIST1H1A	26125376	0.881000	0.30235	0.884000	0.34674	0.057000	0.15508	0.342000	0.19926	2.320000	0.78422	0.609000	0.83330	AAG	.	.	none		0.453	HIST1H1A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043884.1	NM_005325		G	26017397	C	G	26017397	3	3	30	1	0	0	0	0	1	0	0	0	7131	680	24	4	87	4	HIST1H1A	6	26017397	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	13853089	26017397	145097670	205	13356											
HIST1H1E	3008	hgsc.bcm.edu	37	chr6	26157009	26157009	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gcgcggccaaggccaagaagCcagcaggagcggcgaagaag	13	0	17	11	4	0	2	0	0	0	2	0	4	0	3	3	4	3	1	3	4	5	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:26157009C>T	ENST00000304218.3	+	1	451	c.391C>T	c.(391-393)Cca>Tca	p.P131S	HIST1H2BD_ENST00000377777.4_5'Flank|HIST1H2BD_ENST00000289316.2_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	131					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						GGCCAAGAAGCCAGCAGGAGC	0.642																																					p.P131S		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.C391T						PASS	.						16	22	20					6																	26157009		2201	4297	6498	SO:0001583	missense	3008	exon1			AAGAAGCCAGCAG	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.391C>T	6.37:g.26157009C>T	ENSP00000307705:p.Pro131Ser	103	0	0		109	35	0.321101	NM_005321	Q4VB25	Missense_Mutation	SNP	ENST00000304218.3	37	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	3.113	-0.182313	0.06340	.	.	ENSG00000168298	ENST00000304218	T	0.25579	1.79	5.51	-0.293	0.12835	.	0.186307	0.47455	N	0.000233	T	0.04634	0.0126	L	0.38175	1.15	0.48975	D	0.999731	B	0.10296	0.003	B	0.08055	0.003	T	0.29731	-1.0002	10	0.11182	T	0.66	0.2785	3.53	0.07773	0.114:0.485:0.2269:0.1741	.	131	P10412	H14_HUMAN	S	131	ENSP00000307705:P131S	ENSP00000307705:P131S	P	+	1	0	HIST1H1E	26264988	0.865000	0.29922	0.579000	0.28588	0.041000	0.13682	0.334000	0.19787	0.052000	0.16007	0.561000	0.74099	CCA	.	.	none		0.642	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321		T	26157009	C	T	26157009	3	4	30	1	0	0	0	0	1	0	0	0	7135	739	26	2	393	2	HIST1H1E	6	26157009	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	139612	26157009	144958058	206	13357											
BTN2A2	10385	hgsc.bcm.edu	37	chr6	26384092	26384092	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acttctccctgccagcctccCtcctcctcctcctgctcctc	2	12	3	24	0	1	0	0	0	1	0	9	0	7	0	9	0	3	1	9	0	0	1	rs546542545		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:26384092C>T	ENST00000356709.4	+	2	154	c.43C>T	c.(43-45)Ctc>Ttc	p.L15F	BTN2A2_ENST00000482536.1_Missense_Mutation_p.L15F|BTN2A2_ENST00000416795.2_Missense_Mutation_p.L15F|BTN2A2_ENST00000469230.1_Missense_Mutation_p.L15F|BTN2A2_ENST00000352867.2_Missense_Mutation_p.L15F|BTN2A2_ENST00000432533.2_Missense_Mutation_p.L15F	NM_001197240.1|NM_006995.4	NP_001184169.1|NP_008926.2	Q8WVV5	BT2A2_HUMAN	butyrophilin, subfamily 2, member A2	15					negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of cellular metabolic process (GO:0031324)|negative regulation of cytokine secretion (GO:0050710)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|large_intestine(5)|lung(13)	23						GCCAGCCTCcctcctcctcct	0.587																																					p.L15F		Atlas-SNP	.											BTN2A2_ENST00000432533,bladder,carcinoma,-1,2	BTN2A2	87	2	0			c.C43T						scavenged	.						191	138	156					6																	26384092		2203	4300	6503	SO:0001583	missense	10385	exon2			GCCTCCCTCCTCC	U90550	CCDS4606.1, CCDS4607.1, CCDS56401.1, CCDS56402.1, CCDS56403.1	6p22.1	2014-01-14			ENSG00000124508	ENSG00000124508		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / C2-set domain containing", "Butyrophilins"	1137	protein-coding gene	gene with protein product		613591				10354554, 9149941	Standard	NM_006995		Approved	BTF2, BT2.2, BTN2.2	uc003nhq.3	Q8WVV5	OTTHUMG00000014452	ENST00000356709.4:c.43C>T	6.37:g.26384092C>T	ENSP00000349143:p.Leu15Phe	125	0	0		125	6	0.048	NM_181531	A6NM84|B4DE97|B4DQ01|E9PH07|O00480	Missense_Mutation	SNP	ENST00000356709.4	37	CCDS4606.1	.	.	.	.	.	.	.	.	.	.	c	14.03	2.412871	0.42817	.	.	ENSG00000124508	ENST00000469230;ENST00000356709;ENST00000352867;ENST00000493275;ENST00000472507;ENST00000482536;ENST00000432533;ENST00000416795;ENST00000494184;ENST00000483410	T;T;T;T;T;T;D;T;T;T	0.90444	3.76;1.1;0.43;4.24;3.36;-0.21;-2.67;1.1;2.29;3.8	2.01	1.1	0.20463	.	0.656368	0.12607	N	0.454165	T	0.62085	0.2399	N	0.08118	0	0.21675	N	0.999591	B;B;B;B;B;B	0.24132	0.003;0.008;0.098;0.014;0.003;0.003	B;B;B;B;B;B	0.15052	0.002;0.003;0.012;0.006;0.002;0.002	T	0.57562	-0.7790	10	0.87932	D	0	.	4.8159	0.13367	0.0:0.8071:0.0:0.1929	.	15;15;15;15;15;15	E9PH07;B4DQ01;B4E3J1;Q8WVV5-2;A6NM84;Q8WVV5	.;.;.;.;.;BT2A2_HUMAN	F	15	ENSP00000417472:L15F;ENSP00000349143:L15F;ENSP00000337117:L15F;ENSP00000418857:L15F;ENSP00000419226:L15F;ENSP00000419451:L15F;ENSP00000394241:L15F;ENSP00000399308:L15F;ENSP00000417511:L15F;ENSP00000418176:L15F	ENSP00000337117:L15F	L	+	1	0	BTN2A2	26492071	0.000000	0.05858	0.368000	0.25939	0.580000	0.36256	-0.390000	0.07332	0.383000	0.24910	0.298000	0.19748	CTC	.	.	none		0.587	BTN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040117.1			T	26384092	C	T	26384092	3	4	30	1	0	0	0	0	1	0	0	0	1563	681	24	2	45	2	BTN2A2	6	26384092	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	227083	26384092	144730975	207	13358											
HLA-DRB5	3127	hgsc.bcm.edu	37	chr6	32489753	32489753	+	Missense_Mutation	SNP	C	C	T																															aggtgtccaccgcggcgcgcCtgtcttccaggaagtccttc																								rs41544215	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:32489753C>T	ENST00000374975.3	-	2	361	c.299G>A	c.(298-300)aGg>aAg	p.R100K		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						CGCGGCGCGCCTGTCTTCCAG	0.662																																					p.R100K		Atlas-SNP	.											.	HLA-DRB5	31	.	0			c.G299A						PASS	.	C	LYS/ARG	193,3701		62,69,1816	36	32	33		299	-9.4	0	6	dbSNP_127	33	210,7310		48,114,3598	no	missense	HLA-DRB5	NM_002125.3	26	110,183,5414	TT,TC,CC		2.7926,4.9563,3.5308	benign	100/267	32489753	403,11011	1947	3760	5707	SO:0001583	missense	3127	exon2			GCGCGCCTGTCTT		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.299G>A	6.37:g.32489753C>T	ENSP00000364114:p.Arg100Lys	2	0	0		27	25	0.925926	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	92	0.04212454212454213	32	0.06504065040650407	21	0.058011049723756904	9	0.015734265734265736	30	0.0395778364116095	.	4.604	0.112185	0.08831	0.049563	0.027926	ENSG00000198502	ENST00000374975	T	0.00314	8.14	4.72	-9.43	0.00607	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (3);MHC classes I/II-like antigen recognition protein (1);	5.372110	0.00166	N	0.000006	T	0.00039	0.0001	N	0.11756	0.17	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.29942	0.006;0.109	T	0.39014	-0.9634	10	0.10636	T	0.68	.	2.9021	0.05709	0.1516:0.3667:0.2298:0.2519	.	27;100	Q29973;Q30154	.;DRB5_HUMAN	K	100	ENSP00000364114:R100K	ENSP00000364114:R100K	R	-	2	0	HLA-DRB5	32597731	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-12.951000	0.00001	-4.402000	0.00051	-2.111000	0.00353	AGG	T|0.078;C|0.922	0.078	strong		0.662	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125		T	32489753	C	T	32489753	3	4	30	1	0	0	0	0	1	0	0	0	7218	681	24	2	521	2	HLA-DRB5	6	32489753	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	6105661	32489753	138625314	208	13359	169	2									
HLA-DRB5	3127	hgsc.bcm.edu	37	chr6	32489754	32489754	+	Missense_Mutation	SNP	T	T	C																															ggtgtccaccgcggcgcgccTgtcttccaggaagtccttct																								rs41551116|rs201925120	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:32489754T>C	ENST00000374975.3	-	2	360	c.298A>G	c.(298-300)Agg>Ggg	p.R100G		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						GCGGCGCGCCTGTCTTCCAGG	0.667													T|||	280	0.0559105	0.084	0.0605	5008	,	,		4296	0.0317		0.0626	False		,,,				2504	0.0327				p.R100G		Atlas-SNP	.											.	HLA-DRB5	31	.	0			c.A298G						PASS	.						36	32	33					6																	32489754		1942	3732	5674	SO:0001583	missense	3127	exon2			CGCGCCTGTCTTC		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.298A>G	6.37:g.32489754T>C	ENSP00000364114:p.Arg100Gly	2	0	0		29	27	0.931035	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	10.39	1.336269	0.24253	.	.	ENSG00000198502	ENST00000374975	T	0.00349	7.99	4.72	-9.43	0.00607	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (3);MHC classes I/II-like antigen recognition protein (1);	5.372110	0.00166	N	0.000006	T	0.00300	0.0009	H	0.95950	3.745	0.09310	N	1	P;B	0.35155	0.487;0.304	B;P	0.58266	0.344;0.836	T	0.48536	-0.9027	10	0.66056	D	0.02	.	0.4687	0.00528	0.2086:0.2516:0.2378:0.302	rs41551116	27;100	Q29973;Q30154	.;DRB5_HUMAN	G	100	ENSP00000364114:R100G	ENSP00000364114:R100G	R	-	1	2	HLA-DRB5	32597732	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-6.530000	0.00062	-5.722000	0.00010	-3.428000	0.00037	AGG	T|0.952;C|0.047	0.047	strong		0.667	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125		C	32489754	T	C	32489754	3	2	30	1	0	0	0	0	1	0	0	0	7218	1579	55	3	522	3	HLA-DRB5	6	32489754	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	1	32489754	138625313	209	13360	169	2									
KCNK16	83795	hgsc.bcm.edu	37	chr6	39284148	39284148	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggatcagcgccagccacgcCaggcccaggaggatccagat	11	3	13	14	2	1	1	1	0	0	1	2	4	2	4	5	4	2	0	5	4	0	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:39284148C>T	ENST00000373229.5	-	5	745	c.732G>A	c.(730-732)ctG>ctA	p.L244L	KCNK16_ENST00000437525.2_Silent_p.L244L|KCNK17_ENST00000373231.4_5'Flank|KCNK16_ENST00000507712.1_Intron|KCNK16_ENST00000425054.2_Intron|KCNK17_ENST00000453413.2_5'Flank|KCNK16_ENST00000373227.4_Intron	NM_032115.3	NP_115491.1	Q96T55	KCNKG_HUMAN	potassium channel, subfamily K, member 16	244					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						CCAGCCACGCCAGGCCCAGGA	0.627																																					p.L244L		Atlas-SNP	.											.	KCNK16	59	.	0			c.G732A						PASS	.						32	34	33					6																	39284148		2203	4300	6503	SO:0001819	synonymous_variant	83795	exon5			CCACGCCAGGCCC	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.732G>A	6.37:g.39284148C>T		89	0	0		89	46	0.516854	NM_001135106	B5TJL9|Q2M2N9|Q5TCF3|Q6X6Z3|Q6X6Z4|Q6X6Z5|Q9H591	Silent	SNP	ENST00000373229.5	37	CCDS4843.1																																																																																			.	.	none		0.627	KCNK16-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000040452.2	NM_032115		T	39284148	C	T	39284148	2	4	30	1	0	0	0	0	0	0	0	1	8072	581	21	2		2	KCNK16	6	39284148	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	6794394	39284148	131830919	210	13361											
TREML4	285852	hgsc.bcm.edu	37	chr6	41196169	41196169	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aacagatctgggctggaatgGcctggggtggggtccacacc	8	7	16	10	0	1	1	0	0	1	1	2	2	2	2	3	7	1	1	3	7	2	0	rs112680060	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:41196169G>T	ENST00000341495.2	+	1	108	c.4G>T	c.(4-6)Gcc>Tcc	p.A2S	TREML4_ENST00000448827.2_Missense_Mutation_p.A2S	NM_198153.2	NP_937796.1	Q6UXN2	TRML4_HUMAN	triggering receptor expressed on myeloid cells-like 4	2						extracellular region (GO:0005576)				breast(1)|endometrium(1)|large_intestine(1)|lung(4)|skin(1)	8	Ovarian(28;0.0327)|Colorectal(47;0.196)					GGCTGGAATGGCCTGGGGTGG	0.607													G|||	141	0.028155	0.0	0.0159	5008	,	,		17102	0.006		0.0129	False		,,,				2504	0.1135				p.A2S		Atlas-SNP	.											.	TREML4	25	.	0			c.G4T						PASS	.	G	SER/ALA	7,4399		0,7,2196	37	37	37		4	2	0.3	6	dbSNP_132	37	57,8543		0,57,4243	yes	missense	TREML4	NM_198153.2	99	0,64,6439	TT,TG,GG		0.6628,0.1589,0.4921	possibly-damaging	2/201	41196169	64,12942	2203	4300	6503	SO:0001583	missense	285852	exon1			GGAATGGCCTGGG	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.4G>T	6.37:g.41196169G>T	ENSP00000342570:p.Ala2Ser	75	0	0		85	46	0.541176	NM_198153	B7ZL92	Missense_Mutation	SNP	ENST00000341495.2	37	CCDS34446.1	16	0.007326007326007326	0	0.0	6	0.016574585635359115	0	0.0	10	0.013192612137203167	.	12.79	2.044341	0.36085	0.001589	0.006628	ENSG00000188056	ENST00000341495;ENST00000445267;ENST00000448827	T;T	0.09445	2.98;2.98	3.94	2.05	0.26809	.	.	.	.	.	T	0.05273	0.0140	N	0.14661	0.345	0.09310	N	1	D	0.76494	0.999	D	0.63381	0.914	T	0.22800	-1.0206	9	0.72032	D	0.01	-18.3792	4.7235	0.12929	0.1155:0.0:0.6718:0.2127	.	2	Q6UXN2	TRML4_HUMAN	S	2	ENSP00000342570:A2S;ENSP00000418078:A2S	ENSP00000342570:A2S	A	+	1	0	TREML4	41304147	0.595000	0.26857	0.269000	0.24586	0.017000	0.09413	0.825000	0.27393	0.395000	0.25257	0.591000	0.81541	GCC	G|0.995;T|0.005	0.005	strong		0.607	TREML4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043873.2			T	41196169	G	T	41196169	3	4	30	1	0	0	0	0	1	0	0	0	16489	1203	42	4	6	4	TREML4	6	41196169	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1912021	41196169	129918898	211	13362											
KLC4	89953	hgsc.bcm.edu	37	chr6	43039340	43039340	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tctggatgcatgcagaggagCgggaggaaatgagcaaagtg	13	6	17	5	1	1	2	0	1	1	1	1	6	1	6	0	4	4	3	0	4	2	0	rs41274918	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:43039340C>T	ENST00000394056.2	+	11	1786	c.1291C>T	c.(1291-1293)Cgg>Tgg	p.R431W	KLC4_ENST00000347162.5_Missense_Mutation_p.R431W|KLC4_ENST00000259708.3_Missense_Mutation_p.R449W|KLC4_ENST00000453940.2_Missense_Mutation_p.R354W|KLC4_ENST00000479388.1_Missense_Mutation_p.R431W|RP11-387M24.5_ENST00000606123.1_RNA|KLC4_ENST00000394058.1_Missense_Mutation_p.R431W			Q9NSK0	KLC4_HUMAN	kinesin light chain 4	431						cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)	p.R431W(1)		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)			TGCAGAGGAGCGGGAGGAAAT	0.587													C|||	3	0.000599042	0.0	0.0	5008	,	,		17649	0.0		0.002	False		,,,				2504	0.001				p.R449W		Atlas-SNP	.											KLC4,colon,carcinoma,0,1	KLC4	89	1	1	Substitution - Missense(1)	large_intestine(1)	c.C1345T						scavenged	.	C	TRP/ARG,TRP/ARG,TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	59	61	60		1291,1291,1345	5.8	1	6	dbSNP_127	60	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	KLC4	NM_201521.1,NM_201522.1,NM_201523.1	101,101,101	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging,probably-damaging,probably-damaging	431/620,431/620,449/638	43039340	2,13004	2203	4300	6503	SO:0001583	missense	89953	exon10			GAGGAGCGGGAGG	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.1291C>T	6.37:g.43039340C>T	ENSP00000377620:p.Arg431Trp	280	2	0.00714286		251	134	0.533865	NM_201523	B3KNY4|B3KPI3|B3KSQ3|B4DME9|Q66K28|Q96EG6	Missense_Mutation	SNP	ENST00000394056.2	37	CCDS4883.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	17.58	3.423957	0.62733	2.27E-4	1.16E-4	ENSG00000137171	ENST00000347162;ENST00000453940;ENST00000259708;ENST00000479388;ENST00000394056;ENST00000394058	T;T;T;T;T;T	0.80824	-1.4;-1.38;-1.42;-1.4;-1.4;-1.4	5.83	5.83	0.93111	.	0.000000	0.56097	D	0.000022	D	0.88381	0.6421	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	0.937;0.999;0.998	D	0.87053	0.2148	10	0.36615	T	0.2	-22.2004	14.7934	0.69860	0.1783:0.8217:0.0:0.0	rs41274918	354;449;431	B4DME9;Q9NSK0-3;Q9NSK0	.;.;KLC4_HUMAN	W	431;354;449;431;431;431	ENSP00000340221:R431W;ENSP00000395806:R354W;ENSP00000259708:R449W;ENSP00000418031:R431W;ENSP00000377620:R431W;ENSP00000377622:R431W	ENSP00000259708:R449W	R	+	1	2	KLC4	43147318	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.659000	0.37387	2.765000	0.95021	0.555000	0.69702	CGG	C|0.999;T|0.001	0.001	strong		0.587	KLC4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040579.2	NM_138343		T	43039340	C	T	43039340	3	4	30	1	0	0	0	0	1	0	0	0	8345	759	27	1	1452	1	KLC4	6	43039340	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1843171	43039340	128075727	212	13363											
MAD2L1BP	9587	hgsc.bcm.edu	37	chr6	43608220	43608220	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tccgaaccacggcttgggaaGactacatttggttccaggca	10	9	11	11	2	0	1	0	0	0	1	2	3	2	2	3	4	2	3	3	4	3	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:43608220G>A	ENST00000372171.4	+	3	832	c.775G>A	c.(775-777)Gac>Aac	p.D259N	MAD2L1BP_ENST00000451025.2_Missense_Mutation_p.D291N	NM_014628.2	NP_055443.1	Q15013	MD2BP_HUMAN	MAD2L1 binding protein	259					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)			GGCTTGGGAAGACTACATTTG	0.493																																					p.D291N		Atlas-SNP	.											.	MAD2L1BP	12	.	0			c.G871A						PASS	.						51	48	49					6																	43608220		2203	4300	6503	SO:0001583	missense	9587	exon4			TGGGAAGACTACA	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.775G>A	6.37:g.43608220G>A	ENSP00000361244:p.Asp259Asn	100	0	0		101	30	0.29703	NM_001003690	B4DLV3|E9PAT7|Q6IBB1	Missense_Mutation	SNP	ENST00000372171.4	37	CCDS4904.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.831484	0.91036	.	.	ENSG00000124688	ENST00000451025;ENST00000372171	T	0.57752	0.38	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.57227	0.2039	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.62511	-0.6839	10	0.72032	D	0.01	-18.5445	16.7112	0.85386	0.0:0.0:1.0:0.0	.	259;291	Q15013;E9PAT7	MD2BP_HUMAN;.	N	291;259	ENSP00000410818:D291N	ENSP00000361244:D259N	D	+	1	0	MAD2L1BP	43716198	1.000000	0.71417	0.997000	0.53966	0.568000	0.35870	6.281000	0.72632	2.365000	0.80145	0.555000	0.69702	GAC	.	.	none		0.493	MAD2L1BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040692.2	NM_014628		A	43608220	G	A	43608220	3	1	30	1	0	0	0	0	1	0	0	0	9158	942	33	2	935	2	MAD2L1BP	6	43608220	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	568880	43608220	127506847	213	13364											
MUT	4594	hgsc.bcm.edu	37	chr6	49425446	49425446	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagcaataattttcatggaTggttctggaggaaaaatgta	14	13	10	4	0	3	0	2	0	1	0	3	3	3	3	0	4	1	3	0	4	5	5	rs138085432	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:49425446T>C	ENST00000274813.3	-	3	838	c.711A>G	c.(709-711)ccA>ccG	p.P237P		NM_000255.3	NP_000246.2	P22033	MUTA_HUMAN	methylmalonyl CoA mutase	237					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)	TTTTCATGGATGGTTCTGGAG	0.313													T|||	53	0.0105831	0.0023	0.0101	5008	,	,		17146	0.0		0.0129	False		,,,				2504	0.0307				p.P237P		Atlas-SNP	.											.	MUT	70	.	0			c.A711G						PASS	.	T		23,4379	28.1+/-56.4	0,23,2178	57	51	53		711	0.7	1	6	dbSNP_134	53	115,8475	58.3+/-119.8	1,113,4181	no	coding-synonymous	MUT	NM_000255.3		1,136,6359	CC,CT,TT		1.3388,0.5225,1.0622		237/751	49425446	138,12854	2201	4295	6496	SO:0001819	synonymous_variant	4594	exon3			CATGGATGGTTCT		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.711A>G	6.37:g.49425446T>C		69	0	0		117	46	0.393162	NM_000255	A8K953|Q5SYZ3|Q96B11|Q9UD64	Silent	SNP	ENST00000274813.3	37	CCDS4924.1																																																																																			T|0.991;C|0.009	0.009	strong		0.313	MUT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040854.1			C	49425446	T	C	49425446	2	2	30	1	0	0	0	0	0	0	0	1	10000	1451	51	3		3	MUT	6	49425446	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	5817226	49425446	121689621	214	13365											
COL21A1	81578	hgsc.bcm.edu	37	chr6	56035495	56035495	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acttgtgagccattaattacGctggttgttgtaaataataa	13	15	8	5	1	0	1	0	1	0	0	0	1	0	1	1	1	2	4	1	1	6	8	rs41271846	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:56035495G>A	ENST00000244728.5	-	5	1375	c.978C>T	c.(976-978)agC>agT	p.S326S	COL21A1_ENST00000535941.1_Silent_p.S326S|COL21A1_ENST00000370819.1_Silent_p.S326S	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	326	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(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)			CATTAATTACGCTGGTTGTTG	0.358													G|||	9	0.00179712	0.0	0.0	5008	,	,		17653	0.0		0.005	False		,,,				2504	0.0041				p.S326S		Atlas-SNP	.											.	COL21A1	201	.	0			c.C978T						PASS	.	G		7,3729		0,7,1861	79	71	74		978	1.5	0.6	6	dbSNP_127	74	72,8136		1,70,4033	no	coding-synonymous	COL21A1	NM_030820.3		1,77,5894	AA,AG,GG		0.8772,0.1874,0.6614		326/958	56035495	79,11865	1868	4104	5972	SO:0001819	synonymous_variant	81578	exon5			AATTACGCTGGTT	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.978C>T	6.37:g.56035495G>A		118	0	0		113	53	0.469027	NM_030820	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Silent	SNP	ENST00000244728.5	37	CCDS55025.1																																																																																			G|0.997;A|0.003	0.003	strong		0.358	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2			A	56035495	G	A	56035495	2	1	30	1	0	0	0	0	0	0	0	1	3682	1078	38	1		1	COL21A1	6	56035495	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	6610049	56035495	115079572	215	13366											
DST	667	hgsc.bcm.edu	37	chr6	56457044	56457044	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caataggttcagataagtgtTtgctcgctgtggcctcacag	9	12	11	9	1	2	1	2	0	0	1	3	1	2	1	1	2	1	4	1	2	3	4	rs186813964	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:56457044T>C	ENST00000361203.3	-	45	12213	c.12206A>G	c.(12205-12207)aAa>aGa	p.K4069R	DST_ENST00000370788.2_Missense_Mutation_p.K1983R|DST_ENST00000370754.5_Missense_Mutation_p.K4249R|DST_ENST00000446842.2_Missense_Mutation_p.K3745R|DST_ENST00000244364.6_Missense_Mutation_p.K1657R|DST_ENST00000312431.6_Missense_Mutation_p.K4069R|DST_ENST00000370769.4_Missense_Mutation_p.K4071R|DST_ENST00000421834.2_Missense_Mutation_p.K1983R			Q03001	DYST_HUMAN	dystonin	4069					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)			AGATAAGTGTTTGCTCGCTGT	0.428													T|||	12	0.00239617	0.0	0.0029	5008	,	,		16441	0.0		0.004	False		,,,				2504	0.0061				p.K1657R		Atlas-SNP	.											DST_ENST00000370769,NS,lymphoid_neoplasm,0,2	DST	1427	2	0			c.A4970G						PASS	.	T	ARG/LYS	2,3780		0,2,1889	81	80	81		4970	3.2	1	6		81	44,8184		0,44,4070	yes	missense	DST	NM_015548.4	26	0,46,5959	CC,CT,TT		0.5348,0.0529,0.383	benign	1657/5172	56457044	46,11964	1891	4114	6005	SO:0001583	missense	667	exon30			AAGTGTTTGCTCG	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.12206A>G	6.37:g.56457044T>C	ENSP00000354508:p.Lys4069Arg	197	0	0		131	64	0.48855	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	37		4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	T	12.87	2.068920	0.36470	5.29E-4	0.005348	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T;T	0.51325	1.35;1.35;1.35;1.35;1.35;0.71;1.35;1.35	5.8	3.23	0.37069	.	0.226724	0.30177	N	0.010236	T	0.17492	0.0420	L	0.41710	1.295	0.24732	N	0.993083	B;B;B;B;B	0.15473	0.01;0.011;0.005;0.013;0.004	B;B;B;B;B	0.22880	0.013;0.042;0.011;0.028;0.012	T	0.08722	-1.0708	9	0.15952	T	0.53	.	10.2141	0.43158	0.0:0.1428:0.0:0.8572	.	1983;4071;4249;4069;1657	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	R	1657;4249;4071;1983;3745;4069;1983;4069	ENSP00000244364:K1657R;ENSP00000359790:K4249R;ENSP00000359805:K4071R;ENSP00000400883:K1983R;ENSP00000393645:K3745R;ENSP00000307959:K4069R;ENSP00000359824:K1983R;ENSP00000354508:K4069R	ENSP00000244364:K1657R	K	-	2	0	DST	56565003	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	1.130000	0.31393	0.376000	0.24707	0.528000	0.53228	AAA	T|0.998;C|0.002	0.002	strong		0.428	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		C	56457044	T	C	56457044	3	2	30	1	0	0	0	0	1	0	0	0	4785	1841	64	3	10765	3	DST	6	56457044	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	421549	56457044	114658023	216	13367											
COL12A1	1303	hgsc.bcm.edu	37	chr6	75836079	75836079	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttccttacccactggcttatAtactattttatatccaagaa	12	16	3	10	0	0	1	0	0	0	1	2	1	2	1	3	1	2	1	3	1	9	9	rs200450866		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:75836079A>G	ENST00000322507.8	-	39	6757	c.6448T>C	c.(6448-6450)Tat>Cat	p.Y2150H	COL12A1_ENST00000416123.2_Missense_Mutation_p.Y2150H|COL12A1_ENST00000345356.6_Missense_Mutation_p.Y986H|COL12A1_ENST00000483888.2_Missense_Mutation_p.Y2150H	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	2150	Fibronectin type-III 17. {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						ACTGGCTTATATACTATTTTA	0.428																																					p.Y2150H		Atlas-SNP	.											.	COL12A1	385	.	0			c.T6448C						PASS	.	A	HIS/TYR,HIS/TYR	0,3684		0,0,1842	108	103	105		6448,2956	5.7	1	6		105	3,8163		0,3,4080	yes	missense,missense	COL12A1	NM_004370.5,NM_080645.2	83,83	0,3,5922	GG,GA,AA		0.0367,0.0,0.0253	probably-damaging,probably-damaging	2150/3064,986/1900	75836079	3,11847	1842	4083	5925	SO:0001583	missense	1303	exon39			GCTTATATACTAT	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.6448T>C	6.37:g.75836079A>G	ENSP00000325146:p.Tyr2150His	100	0	0		84	40	0.47619	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.498898	0.85069	0.0	3.67E-4	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000345356;ENST00000416123;ENST00000483888	T;T;T;T	0.62639	0.01;0.01;0.01;0.01	5.7	5.7	0.88788	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.78786	0.4338	M	0.86805	2.84	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.83385	0.0014	10	0.87932	D	0	.	15.9743	0.80049	1.0:0.0:0.0:0.0	.	986;2150	Q99715-2;Q99715	.;COCA1_HUMAN	H	2150;2150;986;2150;2150	ENSP00000325146:Y2150H;ENSP00000305147:Y986H;ENSP00000412864:Y2150H;ENSP00000421216:Y2150H	ENSP00000325146:Y2150H	Y	-	1	0	COL12A1	75892799	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	8.905000	0.92613	2.173000	0.68751	0.528000	0.53228	TAT	.	.	weak		0.428	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		G	75836079	A	G	75836079	3	3	30	1	0	0	0	0	1	0	0	0	3671	449	16	3	2855	3	COL12A1	6	75836079	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	19379035	75836079	95278988	217	13368											
RNGTT	8732	hgsc.bcm.edu	37	chr6	89614521	89614521	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatcctcatcctcatcttcGtcttcatcatcctcaaaaca	10	13	1	17	1	7	0	5	0	2	0	11	0	10	0	4	0	1	0	4	0	2	2	rs139029923		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:89614521G>A	ENST00000369485.4	-	6	783	c.597C>T	c.(595-597)gaC>gaT	p.D199D	RNGTT_ENST00000538899.1_Silent_p.D139D|RNGTT_ENST00000369475.3_Silent_p.D199D|RNGTT_ENST00000265607.6_Silent_p.D199D	NM_003800.3	NP_003791.3	O60942	MCE1_HUMAN	RNA guanylyltransferase and 5'-phosphatase	199	Asp/Glu-rich.|TPase.				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)		CCTCATCTTCGTCTTCATCAT	0.428																																					p.D199D		Atlas-SNP	.											.	RNGTT	52	.	0			c.C597T						PASS	.	G		0,4406		0,0,2203	108	91	97		597	-10.6	0.9	6	dbSNP_134	97	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RNGTT	NM_003800.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		199/598	89614521	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8732	exon6			ATCTTCGTCTTCA	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.597C>T	6.37:g.89614521G>A		227	0	0		206	103	0.5	NM_003800	E1P513|E1P514|O43483|O60257|O60351|Q5TCW8|Q8WUM8	Silent	SNP	ENST00000369485.4	37	CCDS5017.1																																																																																			G|1.000;A|0.000	0.000	weak		0.428	RNGTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041469.1			A	89614521	G	A	89614521	2	1	30	1	0	0	0	0	0	0	0	1	13518	1136	40	1		1	RNGTT	6	89614521	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	13778442	89614521	81500546	218	13369											
MDN1	23195	hgsc.bcm.edu	37	chr6	90500067	90500067	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgcagacagactcaaccagCacataagacctaagggccag	15	5	9	12	0	1	3	1	0	0	3	1	3	1	3	3	1	3	2	3	1	3	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:90500067C>T	ENST00000369393.3	-	6	1024	c.909G>A	c.(907-909)gtG>gtA	p.V303V	MDN1_ENST00000428876.1_Silent_p.V303V			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	303					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)		ACTCAACCAGCACATAAGACC	0.478																																					p.V303V		Atlas-SNP	.											.	MDN1	478	.	0			c.G909A						PASS	.						164	169	167					6																	90500067		2203	4300	6503	SO:0001819	synonymous_variant	23195	exon6			AACCAGCACATAA	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.909G>A	6.37:g.90500067C>T		114	0	0		130	6	0.0461538	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	37	CCDS5024.1																																																																																			.	.	none		0.478	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			T	90500067	C	T	90500067	2	4	30	1	0	0	0	0	0	0	0	1	9424	697	25	2		2	MDN1	6	90500067	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	885546	90500067	80615000	219	13370											
SLC22A16	85413	hgsc.bcm.edu	37	chr6	110763935	110763935	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagacttcatgccaatgaatTccatcacatagacaaacccc	15	8	5	13	0	2	3	2	1	0	2	3	4	3	3	4	0	2	0	4	0	4	3	rs41288594	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:110763935T>C	ENST00000368919.3	-	4	761	c.695A>G	c.(694-696)gAa>gGa	p.E232G	RN7SL617P_ENST00000485298.2_RNA|SLC22A16_ENST00000456137.2_3'UTR|SLC22A16_ENST00000439654.1_Missense_Mutation_p.E232G|SLC22A16_ENST00000330550.4_Missense_Mutation_p.E198G	NM_033125.3	NP_149116.2	Q86VW1	S22AG_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 16	232					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)	GCCAATGAATTCCATCACATA	0.428													T|||	33	0.00658946	0.003	0.0144	5008	,	,		19307	0.0		0.0099	False		,,,				2504	0.0092				p.E232G		Atlas-SNP	.											.	SLC22A16	81	.	0			c.A695G						PASS	.	T	GLY/GLU	28,4378	31.7+/-61.6	0,28,2175	71	69	69		695	4.7	0.2	6	dbSNP_127	69	186,8414	80.4+/-143.0	1,184,4115	yes	missense	SLC22A16	NM_033125.2	98	1,212,6290	CC,CT,TT		2.1628,0.6355,1.6454	probably-damaging	232/578	110763935	214,12792	2203	4300	6503	SO:0001583	missense	85413	exon4			ATGAATTCCATCA		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.695A>G	6.37:g.110763935T>C	ENSP00000357915:p.Glu232Gly	91	0	0		107	52	0.485981	NM_033125	O14567|Q5JXM1|Q8IUG8|Q8IZD5|Q96M90|Q96RU0	Missense_Mutation	SNP	ENST00000368919.3	37	CCDS5084.1	15	0.006868131868131868	4	0.008130081300813009	6	0.016574585635359115	0	0.0	5	0.006596306068601583	T	16.01	3.001806	0.54254	0.006355	0.021628	ENSG00000004809	ENST00000368919;ENST00000451557;ENST00000330550;ENST00000439654;ENST00000434949;ENST00000437378	D;D;D;D;D;D	0.86694	-2.16;-2.16;-2.16;-2.16;-2.16;-2.16	4.74	4.74	0.60224	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.95053	0.8398	H	0.97023	3.925	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.993	D	0.96626	0.9463	10	0.87932	D	0	.	14.2102	0.65759	0.0:0.0:0.0:1.0	rs41288594	232;198	Q86VW1;Q86VW1-2	S22AG_HUMAN;.	G	232;149;198;232;62;189	ENSP00000357915:E232G;ENSP00000395642:E149G;ENSP00000328583:E198G;ENSP00000408799:E232G;ENSP00000409306:E62G;ENSP00000416310:E189G	ENSP00000328583:E198G	E	-	2	0	SLC22A16	110870628	1.000000	0.71417	0.215000	0.23724	0.120000	0.20174	7.301000	0.78850	1.762000	0.52044	0.533000	0.62120	GAA	T|0.985;C|0.015	0.015	strong		0.428	SLC22A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043428.1	NM_033125		C	110763935	T	C	110763935	3	2	30	1	0	0	0	0	1	0	0	0	14462	1783	62	3	1058	3	SLC22A16	6	110763935	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	20263868	110763935	60351132	220	13371											
HS3ST5	222537	hgsc.bcm.edu	37	chr6	114378722	114378722	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgacgacatgaaattgctcaAttggaaagtatttcaaccac	15	10	7	9	2	2	1	2	1	0	0	2	4	2	2	1	1	2	2	1	1	5	4	rs17793043	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:114378722A>T	ENST00000312719.5	-	5	1928	c.740T>A	c.(739-741)aTt>aAt	p.I247N	RP3-399L15.3_ENST00000523087.1_RNA|RP3-399L15.3_ENST00000519104.1_RNA|RP3-399L15.3_ENST00000519270.1_RNA|HS3ST5_ENST00000411826.1_Missense_Mutation_p.I247N			Q8IZT8	HS3S5_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	247			I -> N (in dbSNP:rs17793043).		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)		AAATTGCTCAATTGGAAAGTA	0.443													A|||	15	0.00299521	0.0	0.0043	5008	,	,		19731	0.0		0.0119	False		,,,				2504	0.0				p.I247N		Atlas-SNP	.											.	HS3ST5	80	.	0			c.T740A						PASS	.	A	ASN/ILE	7,4399	12.9+/-30.5	0,7,2196	192	185	187		740	6.1	1	6	dbSNP_123	187	90,8510	51.1+/-111.2	0,90,4210	yes	missense	HS3ST5	NM_153612.3	149	0,97,6406	TT,TA,AA		1.0465,0.1589,0.7458	possibly-damaging	247/347	114378722	97,12909	2203	4300	6503	SO:0001583	missense	222537	exon2			TGCTCAATTGGAA	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.740T>A	6.37:g.114378722A>T	ENSP00000427888:p.Ile247Asn	247	0	0		199	105	0.527638	NM_153612	A8K1J2|Q52LI2|Q8N285	Missense_Mutation	SNP	ENST00000312719.5	37	CCDS34517.1	12	0.005494505494505495	0	0.0	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	A	11.94	1.789740	0.31685	0.001589	0.010465	ENSG00000249853	ENST00000312719;ENST00000411826	D;D	0.81579	-1.51;-1.51	6.06	6.06	0.98353	Sulfotransferase domain (1);	0.055484	0.64402	D	0.000001	T	0.65471	0.2694	L	0.58101	1.795	0.47698	D	0.999498	B	0.32302	0.363	B	0.27796	0.083	T	0.66826	-0.5825	10	0.15499	T	0.54	.	16.6093	0.84858	1.0:0.0:0.0:0.0	rs17793043;rs17793043	247	Q8IZT8	HS3S5_HUMAN	N	247	ENSP00000427888:I247N;ENSP00000440332:I247N	ENSP00000427888:I247N	I	-	2	0	HS3ST5	114485415	1.000000	0.71417	0.992000	0.48379	0.873000	0.50193	6.369000	0.73109	2.324000	0.78689	0.533000	0.62120	ATT	A|0.994;T|0.006	0.006	strong		0.443	HS3ST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041911.2	NM_153612		T	114378722	A	T	114378722	3	4	30	1	0	0	0	0	1	0	0	0	7377	101	4	5	304	5	HS3ST5	6	114378722	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	3614787	114378722	56736345	221	13372											
SLC35F1	222553	hgsc.bcm.edu	37	chr6	118588185	118588185	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgttttgtgatcccagtcGtgattttgctctcctggttc	4	18	9	10	1	1	2	0	2	1	0	5	2	2	2	2	1	1	3	2	1	0	5			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:118588185G>A	ENST00000360388.4	+	4	706	c.505G>A	c.(505-507)Gtg>Atg	p.V169M		NM_001029858.3	NP_001025029.2	Q5T1Q4	S35F1_HUMAN	solute carrier family 35, member F1	169					transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(3)|kidney(1)|large_intestine(7)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				GBM - Glioblastoma multiforme(226;0.217)		GATCCCAGTCGTGATTTTGCT	0.498																																					p.V169M		Atlas-SNP	.											SLC35F1,bladder,carcinoma,-2,2	SLC35F1	65	2	0			c.G505A						scavenged	.						387	354	365					6																	118588185		2203	4300	6503	SO:0001583	missense	222553	exon4			CCAGTCGTGATTT	BC028615	CCDS34524.1	6q22.31	2013-05-22			ENSG00000196376	ENSG00000196376		"Solute carriers"	21483	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 169"	C6orf169			Standard	NM_001029858		Approved	dJ230I3.1	uc003pxx.4	Q5T1Q4	OTTHUMG00000015460	ENST00000360388.4:c.505G>A	6.37:g.118588185G>A	ENSP00000353557:p.Val169Met	366	2	0.00546448		379	117	0.308707	NM_001029858	E1P564|Q1RMG1|Q4G0U9|Q4G167|Q6N007	Missense_Mutation	SNP	ENST00000360388.4	37	CCDS34524.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.974196	0.74246	.	.	ENSG00000196376	ENST00000360388	T	0.71341	-0.56	4.99	4.99	0.66335	.	0.143231	0.46442	D	0.000299	T	0.80788	0.4690	M	0.84433	2.695	0.58432	D	0.999996	D	0.53312	0.959	P	0.55713	0.782	D	0.83597	0.0126	10	0.72032	D	0.01	-26.7614	18.8278	0.92125	0.0:0.0:1.0:0.0	.	169	Q5T1Q4	S35F1_HUMAN	M	169	ENSP00000353557:V169M	ENSP00000353557:V169M	V	+	1	0	SLC35F1	118694878	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	3.849000	0.55910	2.756000	0.94617	0.561000	0.74099	GTG	.	.	none		0.498	SLC35F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041991.2	XM_167044		A	118588185	G	A	118588185	3	1	30	1	0	0	0	0	1	0	0	0	14603	1145	40	1	519	1	SLC35F1	6	118588185	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	4209463	118588185	52526882	222	13373											
VNN2	8875	hgsc.bcm.edu	37	chr6	133073844	133073844	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgttgaaagtcaccaactcCggcttttcagggacattaaa	12	11	9	9	1	2	1	2	1	0	0	3	2	3	2	2	2	1	2	2	2	4	4	rs33980664	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:133073844C>T	ENST00000326499.6	-	4	706	c.582G>A	c.(580-582)ccG>ccA	p.P194P	RP1-55C23.7_ENST00000430895.1_RNA|VNN2_ENST00000526192.1_5'Flank|VNN2_ENST00000525289.1_Intron|VNN2_ENST00000525270.1_Silent_p.P141P	NM_004665.2	NP_004656	O95498	VNN2_HUMAN	vanin 2	194	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				cellular component movement (GO:0006928)|pantothenate metabolic process (GO:0015939)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	pantetheine hydrolase activity (GO:0017159)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(155;0.00237)|GBM - Glioblastoma multiforme(226;0.0267)		TCACCAACTCCGGCTTTTCAG	0.408													C|||	85	0.0169728	0.0023	0.049	5008	,	,		19553	0.004		0.0278	False		,,,				2504	0.0164				p.P194P		Atlas-SNP	.											.	VNN2	83	.	0			c.G582A						PASS	.	C	,,	24,4382	29.0+/-57.7	0,24,2179	119	115	116		,582,423	-10.8	0	6	dbSNP_126	116	294,8306	108.0+/-168.7	6,282,4012	no	intron,coding-synonymous,coding-synonymous	VNN2	NM_001242350.1,NM_004665.2,NM_078488.1	,,	6,306,6191	TT,TC,CC		3.4186,0.5447,2.445	,,	,194/521,141/468	133073844	318,12688	2203	4300	6503	SO:0001819	synonymous_variant	8875	exon4			CAACTCCGGCTTT	AB026705	CCDS5161.1, CCDS5162.1, CCDS56451.1	6q23-q24	2013-02-13			ENSG00000112303	ENSG00000112303	3.5.1.92	"Vanins"	12706	protein-coding gene	gene with protein product	"pantetheinase"	603571				9790769, 11491533	Standard	NM_078488		Approved	FOAP-4, GPI-80	uc003qdt.3	O95498	OTTHUMG00000015588	ENST00000326499.6:c.582G>A	6.37:g.133073844C>T		84	0	0		95	45	0.473684	NM_004665	A0AUZ3|A6NDY1|A8K4E3|A8K7W0|B2DFZ0|B2DFZ1|B2DFZ2|B2DFZ3|F6XL73|Q2XUN1|Q9UJF3|Q9UMW2	Silent	SNP	ENST00000326499.6	37	CCDS5161.1																																																																																			C|0.976;T|0.024	0.024	strong		0.408	VNN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042264.2			T	133073844	C	T	133073844	2	4	30	1	0	0	0	0	0	0	0	1	17198	639	23	1		1	VNN2	6	133073844	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	14485659	133073844	38041223	223	13374											
IFNGR1	3459	hgsc.bcm.edu	37	chr6	137540423	137540423	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtgcccatctcagccctgctCacaccctgcatgacaagggg	8	7	10	16	0	2	1	2	1	1	0	3	1	2	1	3	2	4	2	3	2	1	0	rs17181471	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:137540423C>T	ENST00000367739.4	-	1	163	c.42G>A	c.(40-42)gtG>gtA	p.V14V	IFNGR1_ENST00000367735.2_5'UTR|IFNGR1_ENST00000543628.1_5'Flank|IFNGR1_ENST00000478333.1_5'UTR	NM_000416.2	NP_000407.1	P15260	INGR1_HUMAN	interferon gamma receptor 1	14					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)	CAGCCCTGCTCACACCCTGCA	0.687													C|||	22	0.00439297	0.0015	0.0086	5008	,	,		14299	0.0		0.0119	False		,,,				2504	0.002				p.V14V		Atlas-SNP	.											.	IFNGR1	46	.	0			c.G42A						PASS	.	C		10,4392	15.5+/-35.6	0,10,2191	43	42	42		42	3.2	0	6	dbSNP_123	42	58,8542	32.8+/-85.7	0,58,4242	no	coding-synonymous	IFNGR1	NM_000416.2		0,68,6433	TT,TC,CC		0.6744,0.2272,0.523		14/490	137540423	68,12934	2201	4300	6501	SO:0001819	synonymous_variant	3459	exon1			CCTGCTCACACCC		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.42G>A	6.37:g.137540423C>T		179	0	0		131	52	0.396947	NM_000416	B4DFT7|E1P587|Q53Y96	Silent	SNP	ENST00000367739.4	37	CCDS5185.1																																																																																			C|0.995;T|0.005	0.005	strong		0.687	IFNGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042401.1			T	137540423	C	T	137540423	2	4	30	1	0	0	0	0	0	0	0	1	7558	813	29	2		2	IFNGR1	6	137540423	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	4466579	137540423	33574644	224	13375											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152712440	152712440	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gtgacagccgtttctccaggGtgtctttgctcccaagagtg	6	12	12	11	1	2	2	0	1	2	1	4	2	3	2	3	1	2	2	3	1	1	2	rs117480635	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:152712440G>T	ENST00000367255.5	-	52	8577	c.7976C>A	c.(7975-7977)aCc>aAc	p.T2659N	SYNE1_ENST00000341594.5_Missense_Mutation_p.T2698N|SYNE1_ENST00000265368.4_Missense_Mutation_p.T2659N|SYNE1_ENST00000423061.1_Missense_Mutation_p.T2666N|SYNE1_ENST00000448038.1_Missense_Mutation_p.T2666N	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2659					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)		TTTCTCCAGGGTGTCTTTGCT	0.507										HNSCC(10;0.0054)			G|||	8	0.00159744	0.0	0.0	5008	,	,		15514	0.0		0.006	False		,,,				2504	0.002				p.T2666N		Atlas-SNP	.											.	SYNE1	3227	.	0			c.C7997A						PASS	.	G	ASN/THR,ASN/THR	4,4402	8.1+/-20.4	0,4,2199	109	104	106		7997,7976	5	0	6	dbSNP_132	106	30,8570	20.4+/-63.3	0,30,4270	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	65,65	0,34,6469	TT,TG,GG		0.3488,0.0908,0.2614	possibly-damaging,possibly-damaging	2666/8750,2659/8798	152712440	34,12972	2203	4300	6503	SO:0001583	missense	23345	exon52			TCCAGGGTGTCTT	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.7976C>A	6.37:g.152712440G>T	ENSP00000356224:p.Thr2659Asn	104	0	0		117	55	0.470085	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	37	CCDS5236.2	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	9.754	1.168155	0.21621	9.08E-4	0.003488	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.54279	0.67;0.67;0.58;0.67;0.79	5.91	5.04	0.67666	.	0.341353	0.25419	N	0.030816	T	0.31638	0.0803	M	0.62723	1.935	0.24214	N	0.995468	P;B;B;P	0.39696	0.612;0.413;0.413;0.683	B;B;B;B	0.40602	0.203;0.179;0.179;0.334	T	0.19095	-1.0316	10	0.17832	T	0.49	.	11.5958	0.50972	0.1855:0.0:0.8145:0.0	.	2642;2659;2659;2666	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	N	2659;2666;2659;2666;2698	ENSP00000356224:T2659N;ENSP00000396024:T2666N;ENSP00000265368:T2659N;ENSP00000390975:T2666N;ENSP00000341887:T2698N	ENSP00000265368:T2659N	T	-	2	0	SYNE1	152754133	0.997000	0.39634	0.010000	0.14722	0.702000	0.40608	3.098000	0.50259	1.500000	0.48636	0.655000	0.94253	ACC	G|0.998;T|0.002	0.002	strong		0.507	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152712440	G	T	152712440	3	4	30	1	0	0	0	0	1	0	0	0	15460	1261	44	4	18870	4	SYNE1	6	152712440	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	15172017	152712440	18402627	225	13376											
SYNJ2	8871	hgsc.bcm.edu	37	chr6	158516882	158516882	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaccacctctggaggcgcCgcctcttgtgcccaaggtac	6	7	11	17	2	2	0	0	0	2	0	2	1	2	1	6	3	2	1	6	3	2	2	rs137935231	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:158516882C>T	ENST00000355585.4	+	27	4052	c.3977C>T	c.(3976-3978)cCg>cTg	p.P1326L	SYNJ2_ENST00000367112.1_Missense_Mutation_p.P411L|SYNJ2_ENST00000367122.2_Missense_Mutation_p.P1281L	NM_001178088.1|NM_003898.3	NP_001171559.1|NP_003889.1	O15056	SYNJ2_HUMAN	synaptojanin 2	1326	Pro-rich.				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)		CTGGAGGCGCCGCCTCTTGTG	0.657																																					p.P1326L		Atlas-SNP	.											.	SYNJ2	111	.	0			c.C3977T						PASS	.	C	LEU/PRO,LEU/PRO	5,4401	9.9+/-24.2	0,5,2198	42	50	48		3266,3977	2.8	0	6	dbSNP_134	48	23,8577	16.6+/-54.9	1,21,4278	yes	missense,missense	SYNJ2	NM_001178088.1,NM_003898.3	98,98	1,26,6476	TT,TC,CC		0.2674,0.1135,0.2153	benign,benign	1089/1260,1326/1497	158516882	28,12978	2203	4300	6503	SO:0001583	missense	8871	exon27			AGGCGCCGCCTCT	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.3977C>T	6.37:g.158516882C>T	ENSP00000347792:p.Pro1326Leu	60	0	0		59	30	0.508475	NM_003898	Q5TA13|Q5TA16|Q5TA19|Q86XK0|Q8IZA8|Q9H226	Missense_Mutation	SNP	ENST00000355585.4	37	CCDS5254.1	.	.	.	.	.	.	.	.	.	.	C	13.26	2.185571	0.38609	0.001135	0.002674	ENSG00000078269	ENST00000367122;ENST00000355585;ENST00000367112	D;D;T	0.93133	-3.17;-3.16;0.83	5.57	2.76	0.32466	.	0.687143	0.13870	N	0.357073	T	0.79516	0.4459	L	0.55481	1.735	0.09310	N	1	B;P	0.48998	0.066;0.918	B;B	0.35510	0.01;0.204	T	0.67898	-0.5551	10	0.25106	T	0.35	.	9.5075	0.39056	0.0:0.7068:0.0:0.2932	.	721;1326	B4DLC4;O15056	.;SYNJ2_HUMAN	L	1281;1326;411	ENSP00000356089:P1281L;ENSP00000347792:P1326L;ENSP00000356079:P411L	ENSP00000347792:P1326L	P	+	2	0	SYNJ2	158436870	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.511000	0.22739	-1.335000	0.02241	-2.210000	0.00300	CCG	C|0.997;T|0.003	0.003	strong		0.657	SYNJ2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042858.2			T	158516882	C	T	158516882	3	4	30	1	0	0	0	0	1	0	0	0	15468	652	23	1	4083	1	SYNJ2	6	158516882	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	5804442	158516882	12598185	226	13377											
FNDC1	84624	hgsc.bcm.edu	37	chr6	159667972	159667972	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gactgacactgcagtacctaCggaagaggcctacgttatat	12	9	10	10	2	0	2	0	1	0	1	0	4	0	3	2	2	4	3	2	2	6	5	rs61746218	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:159667972C>T	ENST00000297267.9	+	15	4861	c.4661C>T	c.(4660-4662)aCg>aTg	p.T1554M	FNDC1_ENST00000340366.6_Missense_Mutation_p.T1491M	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1554					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)		GCAGTACCTACGGAAGAGGCC	0.428													C|||	17	0.00339457	0.0008	0.0058	5008	,	,		18897	0.0		0.004	False		,,,				2504	0.0082				p.T1554M		Atlas-SNP	.											.	FNDC1	250	.	0			c.C4661T						PASS	.	C	MET/THR	6,3840		0,6,1917	133	128	129		4661	5.5	0.8	6	dbSNP_129	129	65,8205		0,65,4070	yes	missense	FNDC1	NM_032532.2	81	0,71,5987	TT,TC,CC		0.786,0.156,0.586	probably-damaging	1554/1895	159667972	71,12045	1923	4135	6058	SO:0001583	missense	84624	exon15			TACCTACGGAAGA	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.4661C>T	6.37:g.159667972C>T	ENSP00000297267:p.Thr1554Met	136	0	0		104	42	0.403846	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	8	0.003663003663003663	0	0.0	5	0.013812154696132596	0	0.0	3	0.00395778364116095	C	14.60	2.584588	0.46110	0.00156	0.00786	ENSG00000164694	ENST00000297267;ENST00000340366	T;T	0.09817	2.94;3.75	5.54	5.54	0.83059	.	0.207947	0.41001	D	0.000969	T	0.10294	0.0252	M	0.64997	1.995	0.33849	D	0.632415	D	0.56746	0.977	P	0.45794	0.493	T	0.04796	-1.0926	9	.	.	.	-21.4287	17.2366	0.87000	0.0:1.0:0.0:0.0	rs61746218	1554	Q4ZHG4	FNDC1_HUMAN	M	1554;1491	ENSP00000297267:T1554M;ENSP00000342460:T1491M	.	T	+	2	0	FNDC1	159587962	0.988000	0.35896	0.765000	0.31456	0.577000	0.36160	2.989000	0.49393	2.588000	0.87417	0.591000	0.81541	ACG	C|0.995;T|0.005	0.005	strong		0.428	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532		T	159667972	C	T	159667972	3	4	30	1	0	0	0	0	1	0	0	0	5976	536	19	1	4719	1	FNDC1	6	159667972	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1151090	159667972	11447095	227	13378											
TCP1	6950	hgsc.bcm.edu	37	chr6	160201577	160201577	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tttcttcaccttccaaattgGccagggttgacagaatagtt	10	14	8	9	0	2	2	1	1	1	1	3	2	3	2	3	2	0	2	3	2	3	7	rs148556538	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:160201577G>C	ENST00000321394.7	-	9	1275	c.995C>G	c.(994-996)gCc>gGc	p.A332G	SNORA20_ENST00000384662.1_RNA|TCP1_ENST00000420894.2_Missense_Mutation_p.A332G|TCP1_ENST00000392168.2_Missense_Mutation_p.A177G|TCP1_ENST00000544255.1_Missense_Mutation_p.A108G	NM_030752.2	NP_110379.2	P17987	TCPA_HUMAN	t-complex 1	332					'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)		TTCCAAATTGGCCAGGGTTGA	0.388													G|||	9	0.00179712	0.0068	0.0	5008	,	,		19426	0.0		0.0	False		,,,				2504	0.0				p.A332G		Atlas-SNP	.											.	TCP1	37	.	0			c.C995G						PASS	.	G	GLY/ALA,GLY/ALA	13,4393	17.9+/-39.9	0,13,2190	101	102	102		530,995	5.8	1	6	dbSNP_134	102	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	TCP1	NM_001008897.1,NM_030752.2	60,60	0,14,6489	CC,CG,GG		0.0116,0.2951,0.1076	possibly-damaging,possibly-damaging	177/402,332/557	160201577	14,12992	2203	4300	6503	SO:0001583	missense	6950	exon9			AAATTGGCCAGGG	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.995C>G	6.37:g.160201577G>C	ENSP00000317334:p.Ala332Gly	209	1	0.00478469		196	101	0.515306	NM_030752	E1P5B2|Q15556|Q5TCM3	Missense_Mutation	SNP	ENST00000321394.7	37	CCDS5269.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.242607	0.79912	0.002951	1.16E-4	ENSG00000120438	ENST00000321394;ENST00000544255;ENST00000420894;ENST00000392168;ENST00000539756	T;T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1;-1.1	5.76	5.76	0.90799	.	0.140834	0.64402	D	0.000003	T	0.81683	0.4874	M	0.84683	2.71	0.58432	D	0.999999	P;P	0.43024	0.798;0.53	P;P	0.45538	0.484;0.456	D	0.83565	0.0109	10	0.56958	D	0.05	-13.3037	20.3242	0.98691	0.0:0.0:1.0:0.0	.	332;332	E7ERF2;P17987	.;TCPA_HUMAN	G	332;108;332;177;130	ENSP00000317334:A332G;ENSP00000439447:A108G;ENSP00000390159:A332G;ENSP00000376008:A177G;ENSP00000441345:A130G	ENSP00000317334:A332G	A	-	2	0	TCP1	160121567	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.269000	0.78482	2.882000	0.98803	0.655000	0.94253	GCC	G|0.999;C|0.001	0.001	strong		0.388	TCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042917.2	NM_030752		C	160201577	G	C	160201577	3	2	30	1	0	0	0	0	1	0	0	0	15724	1203	42	4	691	4	TCP1	6	160201577	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	533605	160201577	10913490	228	13379											
MAP3K4	4216	hgsc.bcm.edu	37	chr6	161508880	161508880	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctatctgcttctgaccaagcAcggtgatcgagcccgtgatt	8	11	10	12	3	2	3	0	3	2	0	3	4	2	3	2	1	3	2	2	1	2	3	rs35533223	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:161508880A>C	ENST00000392142.4	+	10	2865	c.2717A>C	c.(2716-2718)cAc>cCc	p.H906P	MAP3K4_ENST00000366920.2_Missense_Mutation_p.H906P|MAP3K4_ENST00000366919.2_Missense_Mutation_p.H906P|MAP3K4_ENST00000348824.7_Missense_Mutation_p.H906P	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	906			H -> P (in dbSNP:rs35533223). {ECO:0000269|PubMed:17344846}.		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)		CTGACCAAGCACGGTGATCGA	0.512													A|||	57	0.0113818	0.0023	0.0159	5008	,	,		20328	0.0		0.0278	False		,,,				2504	0.0153				p.H906P		Atlas-SNP	.											.	MAP3K4	364	.	0			c.A2717C						PASS	.	A	PRO/HIS,PRO/HIS	36,4370	40.8+/-73.8	0,36,2167	139	112	121		2717,2717	2	0	6	dbSNP_126	121	344,8256	117.7+/-177.3	5,334,3961	yes	missense,missense	MAP3K4	NM_005922.2,NM_006724.2	77,77	5,370,6128	CC,CA,AA		4.0,0.8171,2.9217	possibly-damaging,possibly-damaging	906/1609,906/1559	161508880	380,12626	2203	4300	6503	SO:0001583	missense	4216	exon10			CCAAGCACGGTGA	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.2717A>C	6.37:g.161508880A>C	ENSP00000375986:p.His906Pro	101	0	0		116	60	0.517241	NM_006724	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Missense_Mutation	SNP	ENST00000392142.4	37	CCDS34565.1	32	0.014652014652014652	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	22	0.029023746701846966	A	13.59	2.282961	0.40394	0.008171	0.04	ENSG00000085511	ENST00000366919;ENST00000392142;ENST00000540111;ENST00000366920;ENST00000348824	T;T;T;T	0.70749	-0.5;-0.49;-0.49;-0.51	5.73	1.95	0.26073	.	0.192782	0.44483	D	0.000443	T	0.48696	0.1514	L	0.60455	1.87	0.33817	D	0.628597	B;P;P	0.42993	0.305;0.797;0.472	B;B;B	0.43623	0.245;0.425;0.261	T	0.40059	-0.9583	10	0.33141	T	0.24	-6.8869	6.1099	0.20094	0.7457:0.0:0.1333:0.121	rs35533223	906;906;906	F5H538;Q9Y6R4-2;Q9Y6R4	.;.;M3K4_HUMAN	P	906	ENSP00000355886:H906P;ENSP00000375986:H906P;ENSP00000355887:H906P;ENSP00000297332:H906P	ENSP00000297332:H906P	H	+	2	0	MAP3K4	161428870	1.000000	0.71417	0.000000	0.03702	0.003000	0.03518	4.880000	0.63107	0.483000	0.27608	0.533000	0.62120	CAC	A|0.976;C|0.024	0.024	strong		0.512	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3			C	161508880	A	C	161508880	3	2	30	1	0	0	0	0	1	0	0	0	9261	159	6	5	2755	5	MAP3K4	6	161508880	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	1307303	161508880	9606187	229	13380											
AGPAT4	56895	hgsc.bcm.edu	37	chr6	161567601	161567601	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggccgagcactcgtcatcGtcttcagggatgtcttccag	7	10	11	13	3	4	0	2	0	2	0	7	2	5	1	2	2	1	1	2	2	0	2	rs16892215	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:161567601G>A	ENST00000320285.4	-	7	1010	c.798C>T	c.(796-798)gaC>gaT	p.D266D	AGPAT4_ENST00000457520.2_Silent_p.D104D|AGPAT4_ENST00000366911.5_3'UTR|AGPAT4_ENST00000366908.5_3'UTR	NM_020133.2	NP_064518.1	Q9NRZ5	PLCD_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 4	266					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)		ACTCGTCATCGTCTTCAGGGA	0.592													G|||	117	0.0233626	0.0802	0.0072	5008	,	,		18454	0.006		0.0	False		,,,				2504	0.0				p.D266D		Atlas-SNP	.											.	AGPAT4	50	.	0			c.C798T						PASS	.	G		263,4143	150.3+/-184.3	10,243,1950	126	102	110		798	-9.9	0	6	dbSNP_123	110	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	AGPAT4	NM_020133.2		10,245,6248	AA,AG,GG		0.0233,5.9691,2.0375		266/379	161567601	265,12741	2203	4300	6503	SO:0001819	synonymous_variant	56895	exon7			GTCATCGTCTTCA	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.798C>T	6.37:g.161567601G>A		77	0	0		76	36	0.473684	NM_020133	B4DSF9|Q5TEF0	Silent	SNP	ENST00000320285.4	37	CCDS5280.1	47	0.02152014652014652	37	0.07520325203252033	4	0.011049723756906077	6	0.01048951048951049	0	0.0	G	0.145	-1.097373	0.01843	0.059691	2.33E-4	ENSG00000026652	ENST00000437165	.	.	.	4.95	-9.9	0.00461	.	.	.	.	.	T	0.43366	0.1244	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68112	-0.5495	4	.	.	.	-42.6356	14.5465	0.68035	0.7342:0.1664:0.0994:0.0	rs16892215;rs16892215	.	.	.	M	45	.	.	T	-	2	0	AGPAT4	161487591	0.004000	0.15560	0.014000	0.15608	0.025000	0.11179	-1.069000	0.03444	-3.051000	0.00260	-0.997000	0.02515	ACG	G|0.975;A|0.025	0.025	strong		0.592	AGPAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042983.1	NM_020133		A	161567601	G	A	161567601	2	1	30	1	0	0	0	0	0	0	0	1	389	1136	40	1		1	AGPAT4	6	161567601	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	58721	161567601	9547466	230	13381											
PARK2	5071	hgsc.bcm.edu	37	chr6	162864492	162864492	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gggaaaccatggctggagttGaacctgacaaacactgacca	14	6	11	10	0	0	3	0	3	0	0	0	5	0	5	3	3	3	2	3	3	3	1			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:162864492G>C	ENST00000366898.1	-	2	123	c.21C>G	c.(19-21)ttC>ttG	p.F7L	PARK2_ENST00000366894.1_5'UTR|PARK2_ENST00000366897.1_Missense_Mutation_p.F7L|PARK2_ENST00000338468.3_5'UTR|PARK2_ENST00000366896.1_Missense_Mutation_p.F7L|PARK2_ENST00000366892.1_Missense_Mutation_p.F7L	NM_004562.2	NP_004553.2	O60260	PRKN2_HUMAN	parkin RBR E3 ubiquitin protein ligase	7	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				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)		GGCTGGAGTTGAACCTGACAA	0.498																																					p.F7L		Atlas-SNP	.											.	PARK2	96	.	0			c.C21G						PASS	.						108	93	98					6																	162864492		2203	4300	6503	SO:0001583	missense	5071	exon2			GGAGTTGAACCTG		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.21C>G	6.37:g.162864492G>C	ENSP00000355865:p.Phe7Leu	118	0	0		129	35	0.271318	NM_004562	A3FG77|A8K975|D3JZW7|D3K2X0|Q5TFV8|Q5VVX4|Q6Q2I6|Q8NI41|Q8NI43|Q8NI44|Q8WW07	Missense_Mutation	SNP	ENST00000366898.1	37	CCDS5281.1	.	.	.	.	.	.	.	.	.	.	G	18.43	3.621739	0.66787	.	.	ENSG00000185345	ENST00000366898;ENST00000366897;ENST00000366896;ENST00000366892;ENST00000542682	D;D;D;D	0.95885	-3.84;-3.84;-3.84;-3.84	5.63	5.63	0.86233	Ubiquitin supergroup (1);Ubiquitin (1);	0.058575	0.64402	D	0.000002	D	0.96367	0.8815	M	0.61703	1.905	0.33112	D	0.540611	D;P;D;D	0.76494	0.999;0.88;0.997;0.995	D;D;D;D	0.80764	0.994;0.946;0.958;0.958	D	0.95572	0.8639	10	0.44086	T	0.13	.	14.8348	0.70175	0.0:0.0:0.8561:0.1438	.	7;7;7;7	O60260-5;Q5VVX3;Q5VVX4;O60260	.;.;.;PRKN2_HUMAN	L	7;7;7;7;6	ENSP00000355865:F7L;ENSP00000355863:F7L;ENSP00000355862:F7L;ENSP00000355858:F7L	ENSP00000355858:F7L	F	-	3	2	PARK2	162784482	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.700000	0.54786	2.805000	0.96524	0.655000	0.94253	TTC	.	.	none		0.498	PARK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042995.1			C	162864492	G	C	162864492	3	2	30	1	0	0	0	0	1	0	0	0	11458	1281	45	4	1420	4	PARK2	6	162864492	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1296891	162864492	8250575	231	13382											
C6orf70	55780	hgsc.bcm.edu	37	chr6	170169688	170169688	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtccccgcataagagatcAtttaagccacggggagatca	12	7	12	10	2	2	2	2	0	0	2	3	4	3	2	3	3	1	1	3	3	2	3	rs61738268	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr6:170169688A>G	ENST00000366773.3	+	12	1145	c.1112A>G	c.(1111-1113)cAt>cGt	p.H371R	ERMARD_ENST00000392095.4_Missense_Mutation_p.H245R|ERMARD_ENST00000418781.3_Missense_Mutation_p.H371R|ERMARD_ENST00000366772.2_Missense_Mutation_p.H371R|RP1-266L20.9_ENST00000586101.1_RNA|ERMARD_ENST00000588451.1_Missense_Mutation_p.H235R	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	371					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											ATAAGAGATCATTTAAGCCAC	0.388													A|||	37	0.00738818	0.0	0.013	5008	,	,		16813	0.0		0.0119	False		,,,				2504	0.0164				p.H371R		Atlas-SNP	.											.	C6orf70	63	.	0			c.A1112G						PASS	.	A	ARG/HIS	5,4401		0,5,2198	58	54	56		1112	-4.5	0	6	dbSNP_129	56	108,8492		2,104,4194	yes	missense	C6orf70	NM_018341.1	29	2,109,6392	GG,GA,AA		1.2558,0.1135,0.8688	benign	371/679	170169688	113,12893	2203	4300	6503	SO:0001583	missense	55780	exon12			GAGATCATTTAAG	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.1112A>G	6.37:g.170169688A>G	ENSP00000355735:p.His371Arg	77	0	0		61	25	0.409836	NM_018341	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Missense_Mutation	SNP	ENST00000366773.3	37	CCDS34576.1	20	0.009157509157509158	0	0.0	8	0.022099447513812154	0	0.0	12	0.0158311345646438	.	0.029	-1.347487	0.01266	0.001135	0.012558	ENSG00000130023	ENST00000366773;ENST00000366772;ENST00000418781;ENST00000392095;ENST00000366771	T;T	0.35605	1.3;1.36	5.34	-4.53	0.03462	.	0.650998	0.14673	N	0.305256	T	0.06690	0.0171	N	0.12502	0.225	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.0	B;B;B	0.09377	0.004;0.003;0.001	T	0.34254	-0.9836	10	0.20519	T	0.43	.	15.5024	0.75709	0.816:0.0:0.184:0.0	rs61738268	371;371;371	Q5T6L9-3;Q5T6L9-2;Q5T6L9	.;.;CF070_HUMAN	R	371;371;371;245;19	ENSP00000355735:H371R;ENSP00000375945:H245R	ENSP00000355733:H19R	H	+	2	0	C6orf70	169911613	0.000000	0.05858	0.000000	0.03702	0.473000	0.32948	-1.487000	0.02310	-0.732000	0.04856	-0.426000	0.05927	CAT	A|0.991;G|0.009	0.009	strong		0.388	ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2	NM_018341		G	170169688	A	G	170169688	3	3	30	1	0	0	0	0	1	0	0	0	2372	217	8	3	1158	3	C6orf70	6	170169688	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	7305196	170169688	945379	232	13383											
C7orf27	221927	hgsc.bcm.edu	37	chr7	2577809	2577809	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtcgctgctctcggccagcGtgctccgcaggccctccagg	3	7	14	17	4	1	0	0	0	1	0	5	0	3	0	4	4	3	4	4	4	0	0	rs375916445		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:2577809G>A	ENST00000340611.4	-	14	2616	c.2360C>T	c.(2359-2361)aCg>aTg	p.T787M	BRAT1_ENST00000473879.1_5'Flank	NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	787					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						CTCGGCCAGCGTGCTCCGCAG	0.701																																					p.T787M		Atlas-SNP	.											.	BRAT1	57	.	0			c.C2360T						PASS	.						22	22	22					7																	2577809		2187	4272	6459	SO:0001583	missense	221927	exon14			GCCAGCGTGCTCC	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.2360C>T	7.37:g.2577809G>A	ENSP00000339637:p.Thr787Met	65	0	0		72	53	0.736111	NM_152743	A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	Missense_Mutation	SNP	ENST00000340611.4	37	CCDS5334.1	.	.	.	.	.	.	.	.	.	.	G	9.550	1.115689	0.20795	.	.	ENSG00000106009	ENST00000340611	T	0.30981	1.51	5.42	4.53	0.55603	.	0.648485	0.17239	N	0.181608	T	0.24851	0.0603	N	0.14661	0.345	0.09310	N	1	D	0.76494	0.999	P	0.50490	0.642	T	0.05209	-1.0899	10	0.34782	T	0.22	-11.8434	10.0764	0.42362	0.0:0.189:0.6795:0.1314	.	787	Q6PJG6	BRAT1_HUMAN	M	787	ENSP00000339637:T787M	ENSP00000339637:T787M	T	-	2	0	BRAT1	2544335	0.005000	0.15991	0.006000	0.13384	0.041000	0.13682	1.359000	0.34113	1.239000	0.43787	0.561000	0.74099	ACG	.	.	weak		0.701	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239305.2	NM_152743		A	2577809	G	A	2577809	3	1	30	1	0	0	0	0	1	0	0	0	2384	1145	40	1	109	1	C7orf27	7	2577809	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10		2577809	156560854	233	13384											
HDAC9	9734	hgsc.bcm.edu	37	chr7	18687542	18687542	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttactttagagggaaagccAcccaacagcagccaccaggc	13	5	10	13	0	0	1	0	0	0	1	0	2	0	2	4	2	5	2	4	2	4	3	rs35614472	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:18687542A>T	ENST00000432645.2	+	9	1161	c.1161A>T	c.(1159-1161)ccA>ccT	p.P387P	HDAC9_ENST00000406451.4_Silent_p.P387P|HDAC9_ENST00000524023.1_Silent_p.P310P|HDAC9_ENST00000405010.3_Silent_p.P387P|HDAC9_ENST00000406072.1_Silent_p.P374P|HDAC9_ENST00000417496.2_Silent_p.P385P|HDAC9_ENST00000401921.1_Silent_p.P346P|HDAC9_ENST00000441542.2_Silent_p.P390P|HDAC9_ENST00000456174.2_Silent_p.P359P|HDAC9_ENST00000428307.2_Silent_p.P343P	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	387					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)	AGGGAAAGCCACCCAACAGCA	0.502													A|||	19	0.00379393	0.0015	0.0043	5008	,	,		17684	0.0		0.0139	False		,,,				2504	0.0				p.P390P		Atlas-SNP	.											.	HDAC9	560	.	0			c.A1170T						PASS	.	A	,,,,,,,,	7,4069		0,7,2031	39	40	39		1155,1029,1038,930,1077,1161,1161,1161,1170	-5	0.7	7	dbSNP_126	39	115,8287		0,115,4086	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HDAC9	NM_001204144.1,NM_001204145.1,NM_001204146.1,NM_001204147.1,NM_001204148.1,NM_014707.1,NM_058176.2,NM_178423.1,NM_178425.2	,,,,,,,,	0,122,6117	TT,TA,AA		1.3687,0.1717,0.9777	,,,,,,,,	385/589,343/547,346/550,310/514,359/563,387/591,387/1012,387/1067,390/1070	18687542	122,12356	2038	4201	6239	SO:0001819	synonymous_variant	9734	exon9			AAAGCCACCCAAC	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.1161A>T	7.37:g.18687542A>T		90	0	0		88	34	0.386364	NM_178425	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Silent	SNP	ENST00000432645.2	37	CCDS47555.1																																																																																			A|0.992;T|0.008	0.008	strong		0.502	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1			T	18687542	A	T	18687542	2	4	30	1	0	0	0	0	0	0	0	1	7023	146	6	5		5	HDAC9	7	18687542	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	16109733	18687542	140451121	234	13385											
KLHL7	55975	hgsc.bcm.edu	37	chr7	23212627	23212627	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catgggctggtatttgtaaaAgacaagatatttgctgtggg	11	13	13	4	0	0	2	0	0	0	2	0	2	0	2	0	3	1	4	0	3	5	5	rs118185564	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:23212627A>G	ENST00000339077.5	+	10	1683	c.1440A>G	c.(1438-1440)aaA>aaG	p.K480K	KLHL7_ENST00000545443.1_Silent_p.K458K|AC005082.1_ENST00000366347.4_Intron|KLHL7_ENST00000322231.7_Silent_p.K458K|KLHL7_ENST00000542558.1_Silent_p.K255K|KLHL7_ENST00000409689.1_Silent_p.K432K|KLHL7_ENST00000539124.1_Silent_p.K404K	NM_001031710.2	NP_001026880.2	Q8IXQ5	KLHL7_HUMAN	kelch-like family member 7	480					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						TATTTGTAAAAGACAAGATAT	0.368													A|||	17	0.00339457	0.0008	0.0	5008	,	,		17141	0.0		0.0139	False		,,,				2504	0.002				p.K480K		Atlas-SNP	.											.	KLHL7	102	.	0			c.A1440G						PASS	.	A	,	8,4398	14.3+/-33.2	0,8,2195	283	269	273		1440,1296	2.2	1	7	dbSNP_132	273	53,8547	33.8+/-87.4	0,53,4247	no	coding-synonymous,coding-synonymous	KLHL7	NM_001031710.2,NM_018846.4	,	0,61,6442	GG,GA,AA		0.6163,0.1816,0.469	,	480/587,432/539	23212627	61,12945	2203	4300	6503	SO:0001819	synonymous_variant	55975	exon10			TGTAAAAGACAAG		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.1440A>G	7.37:g.23212627A>G		297	0	0		437	278	0.636156	NM_001031710	A4D144|B7Z5I9|G5E9G3|Q7Z765|Q96MV2|Q9BQF8|Q9UDQ9	Silent	SNP	ENST00000339077.5	37	CCDS34609.1																																																																																			A|0.994;G|0.006	0.006	strong		0.368	KLHL7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326860.3	NM_018846		G	23212627	A	G	23212627	2	3	30	1	0	0	0	0	0	0	0	1	8403	69	3	3		3	KLHL7	7	23212627	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	4525085	23212627	135926036	235	13386											
DFNA5	1687	hgsc.bcm.edu	37	chr7	24789386	24789386	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gaaaattcctggttgctttgGcaaacattttgaaagctcca	12	13	8	8	0	0	1	0	1	0	0	2	2	2	1	2	2	3	4	2	2	4	5			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:24789386G>A	ENST00000342947.3	-	2	433	c.8C>T	c.(7-9)gCc>gTc	p.A3V	DFNA5_ENST00000409970.1_Intron|DFNA5_ENST00000409775.3_Missense_Mutation_p.A3V|DFNA5_ENST00000545231.1_5'UTR|DFNA5_ENST00000419307.1_Intron	NM_004403.2	NP_004394.1	O60443	DFNA5_HUMAN	deafness, autosomal dominant 5	3					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						GGTTGCTTTGGCAAACATTTT	0.333																																					p.A3V	GBM(78;184 1250 20134 20900 23600)	Atlas-SNP	.											.	DFNA5	51	.	0			c.C8T						PASS	.						79	85	83					7																	24789386		2203	4300	6503	SO:0001583	missense	1687	exon2			GCTTTGGCAAACA	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.8C>T	7.37:g.24789386G>A	ENSP00000339587:p.Ala3Val	113	0	0		114	29	0.254386	NM_001127453	A4D156|B2RAX9|B3KT05|O14590|Q08AQ8|Q9UBV3	Missense_Mutation	SNP	ENST00000342947.3	37	CCDS5389.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.670665	0.88348	.	.	ENSG00000105928	ENST00000342947;ENST00000409775	T;T	0.25414	1.8;1.8	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.54498	0.1862	M	0.80847	2.515	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	T	0.57230	-0.7847	10	0.59425	D	0.04	-24.0835	16.4772	0.84135	0.0:0.1308:0.8692:0.0	.	3;3	A4FTY0;O60443	.;DFNA5_HUMAN	V	3	ENSP00000339587:A3V;ENSP00000386670:A3V	ENSP00000339587:A3V	A	-	2	0	DFNA5	24755911	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	5.414000	0.66405	2.606000	0.88127	0.655000	0.94253	GCC	.	.	none		0.333	DFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214060.2	NM_004403		A	24789386	G	A	24789386	3	1	30	1	0	0	0	0	1	0	0	0	4456	1203	42	2	1518	2	DFNA5	7	24789386	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1576759	24789386	134349277	236	13387											
HOXA7	3204	hgsc.bcm.edu	37	chr7	27196116	27196116	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	attttggaacagagaagcccCcgccgtatatttgctaaaaa	14	10	8	9	2	0	1	0	0	0	1	0	3	0	2	3	1	3	2	3	1	7	6	rs78410337	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:27196116C>T	ENST00000242159.3	-	1	182	c.49G>A	c.(49-51)Ggg>Agg	p.G17R	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	17					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						AGAGAAGCCCCCGCCGTATAT	0.532													C|||	13	0.00259585	0.0	0.0029	5008	,	,		12045	0.0		0.0109	False		,,,				2504	0.0				p.G17R		Atlas-SNP	.											.	HOXA7	34	.	0			c.G49A						PASS	.	C	ARG/GLY	18,4380		0,18,2181	64	81	75		49	5.2	1	7	dbSNP_131	75	98,8490		0,98,4196	yes	missense	HOXA7	NM_006896.3	125	0,116,6377	TT,TC,CC		1.1411,0.4093,0.8933	probably-damaging	17/231	27196116	116,12870	2199	4294	6493	SO:0001583	missense	3204	exon1			AAGCCCCCGCCGT		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.49G>A	7.37:g.27196116C>T	ENSP00000242159:p.Gly17Arg	116	0	0		164	47	0.286585	NM_006896	A4D191|O43368|O43486|O95655|Q9NSC8|Q9UDM1	Missense_Mutation	SNP	ENST00000242159.3	37	CCDS5408.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	32	5.110578	0.94292	0.004093	0.011411	ENSG00000122592	ENST00000242159;ENST00000519842	T;D	0.82081	1.53;-1.57	5.21	5.21	0.72293	.	0.121540	0.52532	D	0.000067	T	0.79834	0.4514	M	0.84948	2.725	0.80722	D	1	P	0.40144	0.704	B	0.31390	0.129	D	0.86042	0.1520	10	0.87932	D	0	.	18.7386	0.91765	0.0:1.0:0.0:0.0	.	17	P31268	HXA7_HUMAN	R	17	ENSP00000242159:G17R;ENSP00000428563:G17R	ENSP00000242159:G17R	G	-	1	0	HOXA7	27162641	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.510000	0.81708	2.599000	0.87857	0.561000	0.74099	GGG	C|0.993;T|0.007	0.007	strong		0.532	HOXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358695.1			T	27196116	C	T	27196116	3	4	30	1	0	0	0	0	1	0	0	0	7306	623	22	2	651	2	HOXA7	7	27196116	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	2406730	27196116	131942547	237	13388											
FAM188B	84182	hgsc.bcm.edu	37	chr7	30868352	30868352	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gagctgggtgccctgcggctCggtaggtgcagcgggtgcct	3	8	19	11	3	0	0	0	0	0	0	1	1	0	0	2	5	6	4	2	5	1	1	rs201645679		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:30868352C>T	ENST00000265299.6	+	6	1208	c.1131C>T	c.(1129-1131)ctC>ctT	p.L377L	INMT-FAM188B_ENST00000458257.1_3'UTR	NM_032222.2	NP_115598.2	Q4G0A6	F188B_HUMAN	family with sequence similarity 188, member B	377										endometrium(1)|large_intestine(5)|lung(19)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CCCTGCGGCTCGGTAGGTGCA	0.582																																					p.L377L		Atlas-SNP	.											.	FAM188B	62	.	0			c.C1131T						PASS	.	C		0,4054		0,0,2027	115	119	118		1131	-6.6	0.3	7		118	1,8369		0,1,4184	yes	coding-synonymous-near-splice	FAM188B	NM_032222.2		0,1,6211	TT,TC,CC		0.0119,0.0,0.0080		377/758	30868352	1,12423	2027	4185	6212	SO:0001630	splice_region_variant	84182	exon6			GCGGCTCGGTAGG	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.1132+1C>T	7.37:g.30868352C>T		80	0	0		98	48	0.489796	NM_032222	Q71AZ7|Q9H6D2	Silent	SNP	ENST00000265299.6	37	CCDS43565.1																																																																																			C|0.999;T|0.001	0.001	weak		0.582	FAM188B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327962.1	NM_032222	Silent	T	30868352	C	T	30868352	5	4	30	1	0	0	0	0	0	0	1	0	5520	898	31	1	1153	1	FAM188B	7	30868352	Splice_Site	SNP	C	TCGA-GR-7353-01A-11D-2210-10	3672236	30868352	128270311	238	13389											
ADCYAP1R1	117	hgsc.bcm.edu	37	chr7	31104520	31104520	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggagaagatccagagggccaAtgagctgatgggcttcaatg	12	7	15	7	0	1	5	1	2	0	3	2	6	2	5	2	3	1	2	2	3	3	1	rs144472289	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:31104520A>G	ENST00000304166.4	+	3	414	c.125A>G	c.(124-126)aAt>aGt	p.N42S	ADCYAP1R1_ENST00000409363.1_Missense_Mutation_p.N42S|ADCYAP1R1_ENST00000396211.2_Missense_Mutation_p.N42S|ADCYAP1R1_ENST00000409489.1_Missense_Mutation_p.N42S	NM_001118.4|NM_001199635.1|NM_001199636.1	NP_001109.2|NP_001186564.1|NP_001186565.1	P41586	PACR_HUMAN	adenylate cyclase activating polypeptide 1 (pituitary) receptor type I	42					activation of adenylate cyclase activity (GO:0007190)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)|vasoactive intestinal polypeptide receptor activity (GO:0004999)			endometrium(1)|large_intestine(4)|liver(2)|lung(24)|ovary(1)|skin(2)|stomach(1)	35						CAGAGGGCCAATGAGCTGATG	0.557													A|||	10	0.00199681	0.0	0.0014	5008	,	,		21493	0.0		0.0089	False		,,,				2504	0.0				p.N42S	Ovarian(44;225 1186 2158 11092)	Atlas-SNP	.											.	ADCYAP1R1	78	.	0			c.A125G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN,SER/ASN	1,4405	2.1+/-5.4	0,1,2202	81	70	74		125,125,125,125	4.4	1	7	dbSNP_134	74	42,8556	27.4+/-76.7	0,42,4257	yes	missense,missense,missense,missense	ADCYAP1R1	NM_001118.4,NM_001199635.1,NM_001199636.1,NM_001199637.1	46,46,46,46	0,43,6459	GG,GA,AA		0.4885,0.0227,0.3307	benign,benign,benign,benign	42/469,42/497,42/496,42/448	31104520	43,12961	2203	4299	6502	SO:0001583	missense	117	exon3			GGGCCAATGAGCT		CCDS5433.1, CCDS56480.1, CCDS56481.1	7p14.3	2012-09-20			ENSG00000078549	ENSG00000078549		"GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"	242	protein-coding gene	gene with protein product	"PACAP receptor 1"	102981				7902709	Standard	NM_001199635		Approved	PAC1, PACAPR, PAC1R	uc003tcg.3	P41586	OTTHUMG00000023884	ENST00000304166.4:c.125A>G	7.37:g.31104520A>G	ENSP00000306620:p.Asn42Ser	85	0	0		139	69	0.496403	NM_001118	A8K1Y1|B7ZLA7|B8ZZK3|Q17S10	Missense_Mutation	SNP	ENST00000304166.4	37	CCDS5433.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	A	13.14	2.147275	0.37923	2.27E-4	0.004885	ENSG00000078549	ENST00000304166;ENST00000409363;ENST00000431811;ENST00000396211;ENST00000409489	T;T;T;T;T	0.52057	0.68;1.16;0.98;0.68;0.68	5.58	4.36	0.52297	GPCR, family 2, extracellular hormone receptor domain (1);	0.257434	0.36066	N	0.002816	T	0.21186	0.0510	N	0.22421	0.69	0.30532	N	0.767307	B;B;B;B;B	0.11235	0.004;0.002;0.004;0.001;0.004	B;B;B;B;B	0.15052	0.012;0.007;0.007;0.0;0.004	T	0.14952	-1.0454	10	0.09590	T	0.72	.	8.9845	0.35986	0.8131:0.1869:0.0:0.0	.	42;42;42;42;42	B7ZLA7;Q17S10;E9PFU5;B8ZZK3;P41586	.;.;.;.;PACR_HUMAN	S	42	ENSP00000306620:N42S;ENSP00000387335:N42S;ENSP00000400893:N42S;ENSP00000379514:N42S;ENSP00000386395:N42S	ENSP00000306620:N42S	N	+	2	0	ADCYAP1R1	31071045	0.041000	0.20044	0.992000	0.48379	0.984000	0.73092	1.464000	0.35288	2.115000	0.64714	0.460000	0.39030	AAT	A|0.997;G|0.003	0.003	strong		0.557	ADCYAP1R1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215041.3	NM_001118		G	31104520	A	G	31104520	3	3	30	1	0	0	0	0	1	0	0	0	303	101	4	3	131	3	ADCYAP1R1	7	31104520	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	236168	31104520	128034143	239	13390											
CCDC129	223075	hgsc.bcm.edu	37	chr7	31682829	31682829	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttccttcatgttgactctgaGgccccacgagaagaggaaag	11	9	11	10	1	2	4	1	2	1	2	3	6	3	5	3	2	0	1	3	2	2	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:31682829G>C	ENST00000407970.3	+	11	1883	c.1845G>C	c.(1843-1845)gaG>gaC	p.E615D	CCDC129_ENST00000409210.1_Missense_Mutation_p.E523D|CCDC129_ENST00000319386.3_Missense_Mutation_p.E467D|CCDC129_ENST00000451887.2_Missense_Mutation_p.E641D	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	615										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						TTGACTCTGAGGCCCCACGAG	0.498																																					p.E641D		Atlas-SNP	.											.	CCDC129	127	.	0			c.G1923C						PASS	.						119	112	114					7																	31682829		2203	4300	6503	SO:0001583	missense	223075	exon11			CTCTGAGGCCCCA	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.1845G>C	7.37:g.31682829G>C	ENSP00000384416:p.Glu615Asp	68	0	0		91	26	0.285714	NM_001257968	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Missense_Mutation	SNP	ENST00000407970.3	37	CCDS5435.2	.	.	.	.	.	.	.	.	.	.	G	12.14	1.847181	0.32606	.	.	ENSG00000180347	ENST00000319386;ENST00000407970;ENST00000451887;ENST00000538406;ENST00000409210	T;T;T;T	0.19394	2.15;2.42;2.41;2.16	6.02	1.06	0.20224	.	0.998383	0.08108	N	0.996656	T	0.18509	0.0444	L	0.55103	1.725	0.09310	N	1	B;B;B;B	0.24186	0.025;0.099;0.099;0.099	B;B;B;B	0.26202	0.022;0.067;0.067;0.067	T	0.38373	-0.9664	10	0.22706	T	0.39	-6.6287	3.9948	0.09553	0.2297:0.0:0.4889:0.2814	.	641;625;615;467	F5H3V5;F5H2J8;Q6ZRS4;Q6ZRS4-2	.;.;CC129_HUMAN;.	D	467;615;641;625;523	ENSP00000313062:E467D;ENSP00000384416:E615D;ENSP00000395835:E641D;ENSP00000387214:E523D	ENSP00000313062:E467D	E	+	3	2	CCDC129	31649354	0.017000	0.18338	0.000000	0.03702	0.307000	0.27823	0.200000	0.17257	-0.075000	0.12798	0.655000	0.94253	GAG	.	.	none		0.498	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300		C	31682829	G	C	31682829	3	2	30	1	0	0	0	0	1	0	0	0	2766	991	35	4	1883	4	CCDC129	7	31682829	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	578309	31682829	127455834	240	13391											
KIAA0895	23366	hgsc.bcm.edu	37	chr7	36366404	36366404	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagttccctgtcagtcagttCattcacttccatgatcttct	7	16	5	13	0	6	1	4	1	2	0	8	1	8	1	2	0	0	2	2	0	0	5	rs191576648		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:36366404C>T	ENST00000297063.6	-	7	1578	c.1528G>A	c.(1528-1530)Gaa>Aaa	p.E510K	KIAA0895_ENST00000453212.1_Missense_Mutation_p.E265K|KIAA0895_ENST00000338533.5_Missense_Mutation_p.E497K|KIAA0895_ENST00000440378.1_Missense_Mutation_p.E507K|KIAA0895_ENST00000317020.6_Missense_Mutation_p.E459K|KIAA0895_ENST00000436884.1_Missense_Mutation_p.E407K	NM_001100425.1	NP_001093895.1	Q8NCT3	K0895_HUMAN	KIAA0895	510										breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						TCAGTCAGTTCATTCACTTCC	0.418													C|||	1	0.000199681	0.0	0.0014	5008	,	,		16857	0.0		0.0	False		,,,				2504	0.0				p.E510K		Atlas-SNP	.											.	KIAA0895	89	.	0			c.G1528A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	0,3788		0,0,1894	180	169	172		1528,1519,1489,1219,1375	5.6	1	7		172	1,8201		0,1,4100	no	missense,missense,missense,missense,missense	KIAA0895	NM_001100425.1,NM_001199706.1,NM_001199707.1,NM_001199708.1,NM_015314.2	56,56,56,56,56	0,1,5994	TT,TC,CC		0.0122,0.0,0.0083	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	510/521,507/518,497/508,407/418,459/470	36366404	1,11989	1894	4101	5995	SO:0001583	missense	23366	exon7			TCAGTTCATTCAC	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.1528G>A	7.37:g.36366404C>T	ENSP00000297063:p.Glu510Lys	171	0	0		246	100	0.406504	NM_001100425	B4DF35|B7ZLT4|B9EGB9|O94969|Q0VGC1|Q7Z4L2	Missense_Mutation	SNP	ENST00000297063.6	37	CCDS43570.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	15.36	2.811535	0.50527	0.0	1.22E-4	ENSG00000164542	ENST00000297063;ENST00000338533;ENST00000317020;ENST00000440378;ENST00000436884;ENST00000453212	.	.	.	5.6	5.6	0.85130	.	0.205140	0.51477	D	0.000096	T	0.45856	0.1363	L	0.33485	1.01	0.80722	D	1	B;B;B;B;B	0.31548	0.018;0.019;0.009;0.328;0.001	B;B;B;B;B	0.30495	0.023;0.023;0.015;0.116;0.004	T	0.43310	-0.9399	9	0.02654	T	1	-22.975	19.9925	0.97371	0.0:1.0:0.0:0.0	.	507;407;510;497;459	B7ZLT4;B4DF35;Q8NCT3;Q8NCT3-2;Q8NCT3-3	.;.;K0895_HUMAN;.;.	K	510;497;459;507;407;265	.	ENSP00000297063:E510K	E	-	1	0	KIAA0895	36332929	0.998000	0.40836	0.990000	0.47175	0.994000	0.84299	1.435000	0.34969	2.818000	0.97014	0.655000	0.94253	GAA	C|1.000;T|0.000	0.000	strong		0.418	KIAA0895-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337717.1	NM_015314		T	36366404	C	T	36366404	3	4	30	1	0	0	0	0	1	0	0	0	8206	835	29	2	38	2	KIAA0895	7	36366404	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	4683575	36366404	122772259	241	13392											
IKZF1	10320	hgsc.bcm.edu	37	chr7	50459542	50459542	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtcgccaaacgtaagagctcTatgcctcagaaatttcttgg	11	11	9	10	2	3	2	1	0	2	2	4	2	3	2	2	1	3	2	2	1	4	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:50459542T>C	ENST00000331340.3	+	7	986	c.831T>C	c.(829-831)tcT>tcC	p.S277S	IKZF1_ENST00000343574.5_Silent_p.S190S|IKZF1_ENST00000438033.1_Silent_p.S190S|IKZF1_ENST00000439701.1_Silent_p.S235S|IKZF1_ENST00000346667.4_Intron|IKZF1_ENST00000359197.5_Silent_p.S235S|IKZF1_ENST00000440768.2_3'UTR|IKZF1_ENST00000357364.4_Intron|IKZF1_ENST00000349824.4_Intron	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)	277					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)				GTAAGAGCTCTATGCCTCAGA	0.413			"D,T"	BCL6	"ALL, DLBCL"																																p.S277S		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.T831C						PASS	.						60	59	59					7																	50459542		1858	4109	5967	SO:0001819	synonymous_variant	10320	exon7			GAGCTCTATGCCT	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.831T>C	7.37:g.50459542T>C		83	0	0		80	4	0.05	NM_006060	A4D260|B4E0Z1|D3DVM5|O00598|Q53XL2|Q69BM4|Q8WVA3	Silent	SNP	ENST00000331340.3	37																																																																																				.	.	none		0.413	IKZF1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000342242.1	NM_006060		C	50459542	T	C	50459542	2	2	30	1	0	0	0	0	0	0	0	1	7623	1509	53	3		3	IKZF1	7	50459542	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	14093138	50459542	108679121	242	13393											
EGFR	1956	hgsc.bcm.edu	37	chr7	55268916	55268916	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catttgccaagtcctacagaCtccaacttctaccgtgccct	9	11	5	16	1	1	1	0	0	1	1	3	1	3	1	5	0	5	0	5	0	4	4	rs2293347|rs587778251	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:55268916C>T	ENST00000275493.2	+	25	3159	c.2982C>T	c.(2980-2982)gaC>gaT	p.D994D	EGFR_ENST00000454757.2_Silent_p.D941D|EGFR_ENST00000442591.1_Intron|EGFR_ENST00000455089.1_Silent_p.D949D	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	994					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)	GTCCTACAGACTCCAACTTCT	0.512		8	"A, O, Mis"		"glioma, NSCLC"	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			t|||	710	0.141773	0.0129	0.1542	5008	,	,		18651	0.247		0.1113	False		,,,				2504	0.2301				p.D994D		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.C2982T						PASS	.	T		121,4285	90.6+/-129.3	1,119,2083	151	139	143		2982	3.8	1	7	dbSNP_100	143	795,7805	185.7+/-233.4	42,711,3547	no	coding-synonymous	EGFR	NM_005228.3		43,830,5630	TT,TC,CC		9.2442,2.7463,7.0429		994/1211	55268916	916,12090	2203	4300	6503	SO:0001819	synonymous_variant	1956	exon25	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	TACAGACTCCAAC		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.2982C>T	7.37:g.55268916C>T		206	0	0		252	85	0.337302	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																			C|0.894;T|0.106	0.106	strong		0.512	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228		T	55268916	C	T	55268916	2	4	30	1	0	0	0	0	0	0	0	1	4969	564	20	2		2	EGFR	7	55268916	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	4809374	55268916	103869747	243	13394											
ZNF679	168417	hgsc.bcm.edu	37	chr7	63727212	63727212	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtcttgctaatcataagagtAtgcatactggagagaaaccc	14	10	9	8	0	2	2	1	0	1	2	2	4	2	3	1	1	4	3	1	1	5	5	rs571908143		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:63727212A>T	ENST00000421025.1	+	5	1470	c.1201A>T	c.(1201-1203)Atg>Ttg	p.M401L	ZNF679_ENST00000255746.4_Missense_Mutation_p.M401L	NM_001159524.1|NM_153363.2	NP_001152996.1|NP_699194.2	Q8IYX0	ZN679_HUMAN	zinc finger protein 679	401					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						TCATAAGAGTATGCATACTGG	0.333																																					p.M401L		Atlas-SNP	.											.	ZNF679	80	.	0			c.A1201T						PASS	.						25	25	25					7																	63727212		692	1591	2283	SO:0001583	missense	168417	exon5			AAGAGTATGCATA	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.1201A>T	7.37:g.63727212A>T	ENSP00000416809:p.Met401Leu	46	0	0		43	33	0.767442	NM_153363		Missense_Mutation	SNP	ENST00000421025.1	37	CCDS47592.1	.	.	.	.	.	.	.	.	.	.	A	11.30	1.598500	0.28445	.	.	ENSG00000197123	ENST00000421025;ENST00000255746	T;T	0.00949	5.51;5.51	0.819	0.819	0.18785	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00440	0.0014	N	0.00801	-1.175	0.20196	N	0.999922	B	0.06786	0.001	B	0.09377	0.004	T	0.46952	-0.9154	9	0.72032	D	0.01	.	5.4486	0.16550	1.0:0.0:0.0:0.0	.	401	Q8IYX0	ZN679_HUMAN	L	401	ENSP00000416809:M401L;ENSP00000255746:M401L	ENSP00000255746:M401L	M	+	1	0	ZNF679	63364647	0.000000	0.05858	0.487000	0.27428	0.488000	0.33401	0.021000	0.13489	0.165000	0.19558	0.163000	0.16589	ATG	.	.	none		0.333	ZNF679-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344317.2	NM_153363		T	63727212	A	T	63727212	3	4	30	1	0	0	0	0	1	0	0	0	18101	449	16	5	1215	5	ZNF679	7	63727212	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	8458296	63727212	95411451	244	13395											
HIP1	3092	hgsc.bcm.edu	37	chr7	75171262	75171262	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaatccatctcttggcgtttGatctgtgtcagcgtcatgct	6	15	10	10	2	4	1	2	1	2	0	6	2	5	1	1	1	2	2	1	1	1	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:75171262G>A	ENST00000336926.6	-	29	2954	c.2928C>T	c.(2926-2928)atC>atT	p.I976I	HIP1_ENST00000434438.2_Silent_p.I925I	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	976	I/LWEQ. {ECO:0000255|PROSITE- ProRule:PRU00292}.				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						CTTGGCGTTTGATCTGTGTCA	0.463			T	PDGFRB	CMML																																p.I976I		Atlas-SNP	.		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	HIP1,NS,carcinoma,-2,1	HIP1	91	1	0			c.C2928T						PASS	.						180	162	168					7																	75171262		2203	4300	6503	SO:0001819	synonymous_variant	3092	exon29			GCGTTTGATCTGT	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.2928C>T	7.37:g.75171262G>A		256	0	0		317	72	0.227129	NM_005338	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Silent	SNP	ENST00000336926.6	37	CCDS34669.1																																																																																			.	.	none		0.463	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338		A	75171262	G	A	75171262	2	1	30	1	0	0	0	0	0	0	0	1	7123	1280	45	2		2	HIP1	7	75171262	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	11444050	75171262	83967401	245	13396											
PION	54103	hgsc.bcm.edu	37	chr7	76984961	76984961	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtaagtaaacagccacataaTagtctatagaagagaaagat	20	8	8	5	0	1	3	0	0	1	3	1	4	1	3	1	0	2	2	1	0	9	6	rs375426636		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:76984961T>C	ENST00000257626.7	-	15	1109	c.1031A>G	c.(1030-1032)tAt>tGt	p.Y344C		NM_017439.3	NP_059135.2	A4D1B5	GSAP_HUMAN	gamma-secretase activating protein	344					positive regulation of beta-amyloid formation (GO:1902004)|regulation of proteolysis (GO:0030162)	trans-Golgi network (GO:0005802)	beta-amyloid binding (GO:0001540)										AGCCACATAATAGTCTATAGA	0.393																																					p.Y344C		Atlas-SNP	.											.	PION	74	.	0			c.A1031G						PASS	.						95	98	97					7																	76984961		2203	4300	6503	SO:0001583	missense	54103	exon15			ACATAATAGTCTA		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.1031A>G	7.37:g.76984961T>C	ENSP00000257626:p.Tyr344Cys	112	0	0		163	106	0.650307	NM_017439	A4D1B6|Q3MJC0|Q8ND73|Q9UMH3|Q9Y4L9	Missense_Mutation	SNP	ENST00000257626.7	37	CCDS34672.2	.	.	.	.	.	.	.	.	.	.	T	11.76	1.734928	0.30774	.	.	ENSG00000186088	ENST00000257626	T	0.19669	2.13	5.87	1.96	0.26148	.	0.000000	0.64402	U	0.000007	T	0.18964	0.0455	M	0.69823	2.125	0.80722	D	1	B;B	0.29508	0.246;0.119	B;B	0.28139	0.086;0.048	T	0.03739	-1.1008	9	.	.	.	.	4.7934	0.13259	0.1393:0.1571:0.0:0.7037	.	344;344	A4D1B5-3;A4D1B5	.;GSAP_HUMAN	C	344	ENSP00000257626:Y344C	.	Y	-	2	0	PION	76822897	0.986000	0.35501	0.774000	0.31636	0.613000	0.37349	0.377000	0.20552	1.056000	0.40484	0.533000	0.62120	TAT	.	.	weak		0.393	GSAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318672.2	NM_017439		C	76984961	T	C	76984961	3	2	30	1	0	0	0	0	1	0	0	0	11943	1406	49	3	1601	3	PION	7	76984961	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	1813699	76984961	82153702	246	13397											
SEMA3C	10512	hgsc.bcm.edu	37	chr7	80380645	80380645	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgtctcacatcttgtcttcGgctcctcctgcaagtgcaga	7	13	8	13	1	3	1	1	0	3	1	7	1	5	1	2	1	2	3	2	1	1	2	rs138526129		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:80380645G>T	ENST00000265361.3	-	16	2212	c.1651C>A	c.(1651-1653)Cga>Aga	p.R551R	SEMA3C_ENST00000544525.1_Silent_p.R569R|SEMA3C_ENST00000419255.2_Silent_p.R551R	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	551					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						TCTTGTCTTCGGCTCCTCCTG	0.388																																					p.R551R		Atlas-SNP	.											.	SEMA3C	106	.	0			c.C1651A						PASS	.	G		0,4406		0,0,2203	155	137	143		1651	4.7	1	7	dbSNP_134	143	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SEMA3C	NM_006379.3		0,1,6502	TT,TG,GG		0.0116,0.0,0.0077		551/752	80380645	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	10512	exon16			GTCTTCGGCTCCT	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.1651C>A	7.37:g.80380645G>T		210	0	0		251	151	0.601594	NM_006379	B4DRL8	Silent	SNP	ENST00000265361.3	37	CCDS5596.1																																																																																			G|1.000;T|0.000	0.000	weak		0.388	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379		T	80380645	G	T	80380645	2	4	30	1	0	0	0	0	0	0	0	1	14041	1124	39	4		4	SEMA3C	7	80380645	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	3395684	80380645	78758018	247	13398											
CACNA2D1	781	hgsc.bcm.edu	37	chr7	81635083	81635083	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagcaaatttcatcttactgTaaaacgtggtgtcagtcttt	11	15	8	7	1	4	0	2	0	2	0	4	1	4	0	0	1	3	2	0	1	4	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:81635083T>C	ENST00000356253.5	-	17	1768	c.1513A>G	c.(1513-1515)Aca>Gca	p.T505A	CACNA2D1_ENST00000356860.3_Missense_Mutation_p.T505A|CACNA2D1_ENST00000464354.1_5'UTR			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	505	Cache.				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)	CATCTTACTGTAAAACGTGGT	0.358																																					p.T505A		Atlas-SNP	.											.	CACNA2D1	191	.	0			c.A1513G						PASS	.						123	117	119					7																	81635083		2203	4299	6502	SO:0001583	missense	781	exon17			TTACTGTAAAACG	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.1513A>G	7.37:g.81635083T>C	ENSP00000348589:p.Thr505Ala	380	0	0		475	107	0.225263	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Missense_Mutation	SNP	ENST00000356253.5	37		.	.	.	.	.	.	.	.	.	.	T	17.74	3.464121	0.63513	.	.	ENSG00000153956	ENST00000356860;ENST00000284088;ENST00000356253	T;T	0.06608	3.28;3.28	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.10165	0.0249	L	0.58669	1.825	0.80722	D	1	B	0.19445	0.036	B	0.20384	0.029	T	0.02885	-1.1098	10	0.56958	D	0.05	-20.1301	15.0578	0.71927	0.0:0.0:0.0:1.0	.	505	P54289-2	.	A	505	ENSP00000349320:T505A;ENSP00000348589:T505A	ENSP00000284088:T505A	T	-	1	0	CACNA2D1	81473019	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	7.672000	0.83956	2.040000	0.60383	0.482000	0.46254	ACA	.	.	none		0.358	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding				C	81635083	T	C	81635083	3	2	30	1	0	0	0	0	1	0	0	0	2550	1638	57	3	1854	3	CACNA2D1	7	81635083	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	1254438	81635083	77503580	248	13399											
PCLO	27445	hgsc.bcm.edu	37	chr7	82451984	82451984	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggactactatgggatttcTcaatggtgggaacctgcatg	10	11	12	8	0	1	0	1	0	1	0	2	3	1	3	1	4	3	1	1	4	4	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:82451984T>G	ENST00000333891.9	-	20	14955	c.14618A>C	c.(14617-14619)gAg>gCg	p.E4873A	PCLO_ENST00000426442.2_5'UTR|PCLO_ENST00000423517.2_Missense_Mutation_p.E4873A	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						ATGGGATTTCTCAATGGTGGG	0.438																																					p.E4873A		Atlas-SNP	.											.	PCLO	1506	.	0			c.A14618C						PASS	.						231	226	228					7																	82451984		1967	4169	6136	SO:0001583	missense	27445	exon20			GATTTCTCAATGG	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.14618A>C	7.37:g.82451984T>G	ENSP00000334319:p.Glu4873Ala	60	0	0		62	12	0.193548	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	14.77	2.635321	0.47049	.	.	ENSG00000186472	ENST00000333891;ENST00000423517;ENST00000380195	T;T	0.18174	2.29;2.23	5.05	5.05	0.67936	.	.	.	.	.	T	0.30823	0.0777	L	0.29908	0.895	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.998;0.997	D;D;D;D	0.87578	0.998;0.998;0.991;0.98	T	0.06826	-1.0805	9	0.87932	D	0	.	15.0845	0.72142	0.0:0.0:0.0:1.0	.	4873;4873;294;361	Q9Y6V0-5;Q9Y6V0-6;Q9Y6V0-3;Q32P40	.;.;.;.	A	4873;4873;360	ENSP00000334319:E4873A;ENSP00000388393:E4873A	ENSP00000334319:E4873A	E	-	2	0	PCLO	82289920	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.619000	0.83057	2.023000	0.59567	0.533000	0.62120	GAG	.	.	none		0.438	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		G	82451984	T	G	82451984	3	3	30	1	0	0	0	0	1	0	0	0	11592	1551	54	5	851	5	PCLO	7	82451984	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	816901	82451984	76686679	249	13400											
AKAP9	10142	hgsc.bcm.edu	37	chr7	91660861	91660861	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggagtgaaagaggaaacaaaTatcgttaagttgcttgaaaa	18	9	11	3	1	0	3	0	2	0	1	1	5	0	5	0	2	2	3	0	2	7	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:91660861T>C	ENST00000359028.2	+	17	4542	c.4317T>C	c.(4315-4317)aaT>aaC	p.N1439N	AKAP9_ENST00000356239.3_Silent_p.N1427N|AKAP9_ENST00000358100.2_Silent_p.N1439N			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	1439					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)			AGGAAACAAATATCGTTAAGT	0.284			T	BRAF	papillary thyroid																																p.N1427N		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.T4281C						PASS	.						121	128	126					7																	91660861		2202	4297	6499	SO:0001819	synonymous_variant	10142	exon16			AACAAATATCGTT	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.4317T>C	7.37:g.91660861T>C		87	0	0		91	6	0.0659341	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Silent	SNP	ENST00000359028.2	37																																																																																				.	.	none		0.284	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751		C	91660861	T	C	91660861	2	2	30	1	0	0	0	0	0	0	0	1	459	1403	49	3		3	AKAP9	7	91660861	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	9208877	91660861	67477802	250	13401											
C7orf64	84060	hgsc.bcm.edu	37	chr7	92158154	92158154	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tcgagcggcggggagctaggGagtttatttgatcaccacgt	8	10	15	8	4	1	1	1	1	0	0	2	4	1	3	1	4	2	2	1	4	2	4	rs117787377	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:92158154G>A	ENST00000265732.5	+	1	68	c.27G>A	c.(25-27)ggG>ggA	p.G9G	PEX1_ENST00000438045.1_5'Flank|PEX1_ENST00000428214.1_5'Flank|RBM48_ENST00000481551.1_Silent_p.G9G|PEX1_ENST00000248633.4_5'Flank	NM_032120.2	NP_115496.2	Q5RL73	RBM48_HUMAN	RNA binding motif protein 48	9						nucleus (GO:0005634)	RNA binding (GO:0003723)										GGGAGCTAGGGAGTTTATTTG	0.552													G|||	20	0.00399361	0.0008	0.0029	5008	,	,		17571	0.0		0.0149	False		,,,				2504	0.002				p.G9G		Atlas-SNP	.											.	.	.	.	0			c.G27A						PASS	.	G		18,3950		0,18,1966	70	75	74		27	-4	0	7	dbSNP_132	74	123,8149		0,123,4013	no	coding-synonymous	C7orf64	NM_032120.2		0,141,5979	AA,AG,GG		1.4869,0.4536,1.152		9/368	92158154	141,12099	1984	4136	6120	SO:0001819	synonymous_variant	84060	exon1			GCTAGGGAGTTTA	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.27G>A	7.37:g.92158154G>A		172	0	0		266	167	0.62782	NM_032120	B7Z2K5|B7ZL51|Q5H9T2|Q8IYW7|Q96NS0|Q9H0V7	Silent	SNP	ENST00000265732.5	37	CCDS43615.1																																																																																			G|0.992;A|0.008	0.008	strong		0.552	RBM48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356076.1	NM_032120		A	92158154	G	A	92158154	2	1	30	1	0	0	0	0	0	0	0	1	2412	1161	41	2		2	C7orf64	7	92158154	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	497293	92158154	66980509	251	13402											
SAMD9	54809	hgsc.bcm.edu	37	chr7	92734358	92734358	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaactttatttttcgtaatGtccttagagctggtcccatc	8	17	6	10	1	1	1	1	0	0	1	5	1	3	1	2	1	2	2	2	1	4	6	rs200454238		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:92734358G>A	ENST00000379958.2	-	3	1322	c.1053C>T	c.(1051-1053)gaC>gaT	p.D351D		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	351						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)		p.S348fs*47(1)		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)			TTTTCGTAATGTCCTTAGAGC	0.323																																					p.D351D		Atlas-SNP	.											.	SAMD9	239	.	1	Deletion - Frameshift(1)	breast(1)	c.C1053T						PASS	.	G	,	0,4402		0,0,2201	97	95	96		1053,1053	2.4	0.1	7		96	4,8594	3.7+/-12.6	0,4,4295	no	coding-synonymous,coding-synonymous	SAMD9	NM_001193307.1,NM_017654.3	,	0,4,6496	AA,AG,GG		0.0465,0.0,0.0308	,	351/1590,351/1590	92734358	4,12996	2201	4299	6500	SO:0001819	synonymous_variant	54809	exon2			CGTAATGTCCTTA	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.1053C>T	7.37:g.92734358G>A		128	0	0		198	68	0.343434	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Silent	SNP	ENST00000379958.2	37	CCDS34680.1																																																																																			G|0.999;A|0.001	0.001	weak		0.323	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654		A	92734358	G	A	92734358	2	1	30	1	0	0	0	0	0	0	0	1	13841	1368	48	2		2	SAMD9	7	92734358	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	576204	92734358	66404305	252	13403											
ZKSCAN5	23660	hgsc.bcm.edu	37	chr7	99129744	99129744	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atcagagaatccatactggtGagaaaccttttcaatgtaaa	16	11	7	7	0	2	2	2	1	0	2	3	4	3	2	2	1	2	1	2	1	6	4	rs150395462	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:99129744G>C	ENST00000394170.2	+	7	2643	c.2392G>C	c.(2392-2394)Gag>Cag	p.E798Q	ZKSCAN5_ENST00000326775.5_Missense_Mutation_p.E798Q|ZKSCAN5_ENST00000451158.1_Missense_Mutation_p.E798Q	NM_014569.3	NP_055384.1	Q9Y2L8	ZKSC5_HUMAN	zinc finger with KRAB and SCAN domains 5	798					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(3)|endometrium(1)|kidney(1)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	21	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)					CCATACTGGTGAGAAACCTTT	0.398													G|||	4	0.000798722	0.0	0.0014	5008	,	,		20675	0.0		0.003	False		,,,				2504	0.0				p.E798Q		Atlas-SNP	.											.	ZKSCAN5	63	.	0			c.G2392C						PASS	.	G	GLN/GLU,GLN/GLU	5,4401	11.4+/-27.6	0,5,2198	85	91	89		2392,2392	5	1	7	dbSNP_134	89	61,8539	38.8+/-94.9	1,59,4240	yes	missense,missense	ZKSCAN5	NM_014569.3,NM_145102.2	29,29	1,64,6438	CC,CG,GG		0.7093,0.1135,0.5075	probably-damaging,probably-damaging	798/840,798/840	99129744	66,12940	2203	4300	6503	SO:0001583	missense	23660	exon7			ACTGGTGAGAAAC	AF170025	CCDS5667.1	7q22	2013-01-09	2007-02-20	2007-02-20	ENSG00000196652	ENSG00000196652		"Zinc fingers, C2H2-type", "-", "-", "-"	12867	protein-coding gene	gene with protein product		611272	"zinc finger protein homologous to Zfp95 in mouse", "zinc finger protein 95 homolog (mouse)"	ZFP95		10585779	Standard	NM_014569		Approved	ZNF914, ZSCAN37	uc003uqv.3	Q9Y2L8	OTTHUMG00000156749	ENST00000394170.2:c.2392G>C	7.37:g.99129744G>C	ENSP00000377725:p.Glu798Gln	77	0	0		100	54	0.54	NM_145102	A4D280|D6W5S9	Missense_Mutation	SNP	ENST00000394170.2	37	CCDS5667.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	23.4	4.411517	0.83340	0.001135	0.007093	ENSG00000196652	ENST00000326775;ENST00000451158;ENST00000394170	T;T;T	0.25912	1.77;1.77;1.77	5.03	5.03	0.67393	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.116325	0.38720	N	0.001586	T	0.42177	0.1191	M	0.70595	2.14	0.50171	D	0.99985	D;D	0.76494	0.999;0.999	D;D	0.70935	0.971;0.971	T	0.45556	-0.9253	10	0.72032	D	0.01	.	16.2692	0.82607	0.0:0.0:1.0:0.0	.	798;798	Q8N718;Q9Y2L8	.;ZKSC5_HUMAN	Q	798	ENSP00000322872:E798Q;ENSP00000392104:E798Q;ENSP00000377725:E798Q	ENSP00000322872:E798Q	E	+	1	0	ZKSCAN5	98967680	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.485000	0.66850	2.782000	0.95742	0.655000	0.94253	GAG	G|0.996;C|0.004	0.004	strong		0.398	ZKSCAN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345597.1	NM_014569		C	99129744	G	C	99129744	3	2	30	1	0	0	0	0	1	0	0	0	17705	1291	45	4	2414	4	ZKSCAN5	7	99129744	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	6395386	99129744	60008919	253	13404											
TRIP6	7205	hgsc.bcm.edu	37	chr7	100465747	100465747	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	caggggctccctgcagacagGgggggccttcgccctggaag	6	5	17	13	1	0	1	0	0	0	1	2	2	1	2	3	6	1	2	3	6	1	1	rs139351872	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100465747G>T	ENST00000200457.4	+	3	615	c.255G>T	c.(253-255)agG>agT	p.R85S		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)					CTGCAGACAGGGGGGGCCTTC	0.647													G|||	4	0.000798722	0.0015	0.0014	5008	,	,		15814	0.0		0.001	False		,,,				2504	0.0				p.R85S		Atlas-SNP	.											.	TRIP6	45	.	0			c.G255T						PASS	.	G	SER/ARG	2,4404	4.2+/-10.8	0,2,2201	40	45	43		255	-0.6	0	7	dbSNP_134	43	6,8594	4.3+/-15.6	0,6,4294	yes	missense	TRIP6	NM_003302.2	110	0,8,6495	TT,TG,GG		0.0698,0.0454,0.0615	probably-damaging	85/477	100465747	8,12998	2203	4300	6503	SO:0001583	missense	7205	exon3			AGACAGGGGGGGC	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.255G>T	7.37:g.100465747G>T	ENSP00000200457:p.Arg85Ser	180	0	0		212	71	0.334906	NM_003302	A4D2E7|F2ZC07|F2ZC08|O15170|O15275|Q9BTB2|Q9BUE5|Q9BXP3|Q9UNT4	Missense_Mutation	SNP	ENST00000200457.4	37	CCDS5708.1	3	0.0013736263736263737	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	7.094	0.572692	0.13623	4.54E-4	6.98E-4	ENSG00000087077	ENST00000200457	T	0.62364	0.03	4.67	-0.581	0.11713	.	0.120807	0.53938	D	0.000055	T	0.51210	0.1661	L	0.47716	1.5	0.23101	N	0.998297	P	0.47762	0.9	P	0.44518	0.452	T	0.49113	-0.8973	10	0.35671	T	0.21	.	7.89	0.29672	0.5076:0.0:0.4924:0.0	.	85	Q15654	TRIP6_HUMAN	S	85	ENSP00000200457:R85S	ENSP00000200457:R85S	R	+	3	2	TRIP6	100303683	0.884000	0.30299	0.018000	0.16275	0.003000	0.03518	0.211000	0.17474	-0.471000	0.06891	-1.022000	0.02435	AGG	C|0.000;G|0.999;T|0.001	0.001	strong		0.647	TRIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347151.2	NM_003302		T	100465747	G	T	100465747	3	4	30	1	0	0	0	0	1	0	0	0	16574	1223	43	4	265	4	TRIP6	7	100465747	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1336003	100465747	58672916	254	13405											
TRIP6	7205	hgsc.bcm.edu	37	chr7	100465824	100465824	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggccgagctgaatgggggtcGgggtcatgcgtcacggcgac	6	6	19	10	5	2	1	2	1	0	0	3	3	2	1	1	6	2	1	1	6	1	0	rs2437100	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100465824G>A	ENST00000200457.4	+	3	692	c.332G>A	c.(331-333)cGg>cAg	p.R111Q		NM_003302.2	NP_003293.2	Q15654	TRIP6_HUMAN	thyroid hormone receptor interactor 6	111			R -> Q (in dbSNP:rs2437100). {ECO:0000269|PubMed:15489334}.		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)					AATGGGGGTCGGGGTCATGCG	0.672													G|||	32	0.00638978	0.0008	0.0058	5008	,	,		14361	0.0		0.0268	False		,,,				2504	0.0				p.R111Q		Atlas-SNP	.											.	TRIP6	45	.	0			c.G332A						PASS	.	G	GLN/ARG	21,4385	29.0+/-57.7	0,21,2182	41	41	41		332	4.5	0.8	7	dbSNP_100	41	176,8424	80.6+/-143.3	1,174,4125	yes	missense	TRIP6	NM_003302.2	43	1,195,6307	AA,AG,GG		2.0465,0.4766,1.5147	probably-damaging	111/477	100465824	197,12809	2203	4300	6503	SO:0001583	missense	7205	exon3			GGGGTCGGGGTCA	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.332G>A	7.37:g.100465824G>A	ENSP00000200457:p.Arg111Gln	71	0	0		105	73	0.695238	NM_003302	A4D2E7|F2ZC07|F2ZC08|O15170|O15275|Q9BTB2|Q9BUE5|Q9BXP3|Q9UNT4	Missense_Mutation	SNP	ENST00000200457.4	37	CCDS5708.1	26	0.011904761904761904	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	23	0.030343007915567283	G	18.42	3.619897	0.66787	0.004766	0.020465	ENSG00000087077	ENST00000200457	T	0.59502	0.26	4.53	4.53	0.55603	.	0.374538	0.26931	N	0.021774	T	0.33089	0.0851	L	0.47716	1.5	0.28405	N	0.918477	D	0.69078	0.997	P	0.53518	0.728	T	0.40646	-0.9552	10	0.11794	T	0.64	.	12.7393	0.57241	0.0:0.0:1.0:0.0	rs2437100	111	Q15654	TRIP6_HUMAN	Q	111	ENSP00000200457:R111Q	ENSP00000200457:R111Q	R	+	2	0	TRIP6	100303760	0.997000	0.39634	0.757000	0.31301	0.054000	0.15201	3.870000	0.56070	2.074000	0.62210	0.455000	0.32223	CGG	G|0.985;A|0.015	0.015	strong		0.672	TRIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347151.2	NM_003302		A	100465824	G	A	100465824	3	1	30	1	0	0	0	0	1	0	0	0	16574	1116	39	1	342	1	TRIP6	7	100465824	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	77	100465824	58672839	255	13406											
MUC17	140453	hgsc.bcm.edu	37	chr7	100677355	100677355	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgcaatcagcaccctttcAacaactcctgttgacaccag	11	10	5	15	0	3	1	2	1	1	0	4	1	4	1	3	0	4	3	3	0	3	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100677355A>C	ENST00000306151.4	+	3	2722	c.2658A>C	c.(2656-2658)tcA>tcC	p.S886S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	886	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)					GCACCCTTTCAACAACTCCTG	0.498																																					p.S886S		Atlas-SNP	.											.	MUC17	804	.	0			c.A2658C						PASS	.						292	289	290					7																	100677355		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			CCTTTCAACAACT	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.2658A>C	7.37:g.100677355A>C		162	0	0		302	23	0.0761589	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			.	.	none		0.498	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		C	100677355	A	C	100677355	2	2	30	1	0	0	0	0	0	0	0	1	9983	117	5	5		5	MUC17	7	100677355	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	211531	100677355	58461308	256	13407			1	57		9	9	5460	N	T_G_A	1.304015e-12
MUC17	140453	hgsc.bcm.edu	37	chr7	100678032	100678032	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgcctgtcagcaccaggcTggtggtcagttctgaggcta	6	11	14	10	0	3	1	2	1	1	0	3	1	3	1	2	4	2	4	2	4	1	2	rs147173571		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678032T>C	ENST00000306151.4	+	3	3399	c.3335T>C	c.(3334-3336)cTg>cCg	p.L1112P		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1112	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)					AGCACCAGGCTGGTGGTCAGT	0.512																																					p.L1112P		Atlas-SNP	.											.	MUC17	804	.	0			c.T3335C						PASS	.						494	394	428					7																	100678032		2203	4300	6503	SO:0001583	missense	140453	exon3			CCAGGCTGGTGGT	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.3335T>C	7.37:g.100678032T>C	ENSP00000302716:p.Leu1112Pro	206	0	0		753	89	0.118194	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	0.149	-1.093913	0.01858	.	.	ENSG00000169876	ENST00000306151	T	0.03212	4.01	0.693	-0.391	0.12446	.	.	.	.	.	T	0.01320	0.0043	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48055	-0.9068	8	0.25751	T	0.34	.	.	.	.	.	1112	Q685J3	MUC17_HUMAN	P	1112	ENSP00000302716:L1112P	ENSP00000302716:L1112P	L	+	2	0	MUC17	100464752	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-6.070000	0.00082	-0.165000	0.10908	-1.364000	0.01208	CTG	.	.	weak		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		C	100678032	T	C	100678032	3	2	30	1	0	0	0	0	1	0	0	0	9983	1580	55	3	3345	3	MUC17	7	100678032	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	677	100678032	58460631	257	13408			1	57		9	9	5460	N	T_G_A	1.304015e-12
MUC17	140453	hgsc.bcm.edu	37	chr7	100678693	100678693	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcatgccaacctcaacttaTagtgaaggaagaactccttt	14	10	7	10	0	1	2	1	1	0	1	2	3	2	3	3	1	5	1	3	1	7	3	rs78176991	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678693T>C	ENST00000306151.4	+	3	4060	c.3996T>C	c.(3994-3996)taT>taC	p.Y1332Y		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1332	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)					CCTCAACTTATAGTGAAGGAA	0.448																																					p.Y1332Y		Atlas-SNP	.											.	MUC17	804	.	0			c.T3996C						PASS	.						241	232	235					7																	100678693		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			AACTTATAGTGAA	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.3996T>C	7.37:g.100678693T>C		200	0	0		264	39	0.147727	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			T|0.994;C|0.006	0.006	strong		0.448	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		C	100678693	T	C	100678693	2	2	30	1	0	0	0	0	0	0	0	1	9983	1413	49	3		3	MUC17	7	100678693	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	661	100678693	58459970	258	13409			1	57		9	9	5460	N	T_G_A	1.304015e-12
MUC17	140453	hgsc.bcm.edu	37	chr7	100678988	100678988	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcacccctgggaccacttctGctgaagccacttcatctcct	7	10	7	17	0	3	1	1	1	2	0	4	2	3	2	5	1	2	2	5	1	1	2	rs71286276		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100678988G>A	ENST00000306151.4	+	3	4355	c.4291G>A	c.(4291-4293)Gct>Act	p.A1431T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1431	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)	p.A1431T(1)		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)					GACCACTTCTGCTGAAGCCAC	0.488																																					p.A1431T		Atlas-SNP	.											MUC17,NS,carcinoma,0,2	MUC17	804	2	1	Substitution - Missense(1)	kidney(1)	c.G4291A						scavenged	.						207	222	217					7																	100678988		2203	4300	6503	SO:0001583	missense	140453	exon3			ACTTCTGCTGAAG	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.4291G>A	7.37:g.100678988G>A	ENSP00000302716:p.Ala1431Thr	120	0	0		205	12	0.0585366	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	a	3.722	-0.057377	0.07317	.	.	ENSG00000169876	ENST00000306151	T	0.02656	4.21	0.982	-0.425	0.12317	.	.	.	.	.	T	0.01558	0.0050	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48779	-0.9005	9	0.02654	T	1	.	4.4511	0.11621	0.488:0.0:0.512:0.0	.	1431	Q685J3	MUC17_HUMAN	T	1431	ENSP00000302716:A1431T	ENSP00000302716:A1431T	A	+	1	0	MUC17	100465708	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-2.968000	0.00669	-0.790000	0.04492	-1.616000	0.00795	GCT	.	.	none		0.488	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100678988	G	A	100678988	3	1	30	1	0	0	0	0	1	0	0	0	9983	1319	46	2	4301	2	MUC17	7	100678988	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	295	100678988	58459675	259	13410			1	57		9	9	5460	N	T_G_A	1.304015e-12
MUC17	140453	hgsc.bcm.edu	37	chr7	100680463	100680463	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atgccaacctcaactcctagGgaaggaaggcctccattaac	13	7	8	13	0	1	0	1	0	0	0	3	2	3	2	5	3	4	0	5	3	6	2	rs368849364	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100680463G>T	ENST00000306151.4	+	3	5830	c.5766G>T	c.(5764-5766)agG>agT	p.R1922S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1922	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)					CAACTCCTAGGGAAGGAAGGC	0.507																																					p.R1922S		Atlas-SNP	.											.	MUC17	804	.	0			c.G5766T						PASS	.						242	242	242					7																	100680463		2203	4300	6503	SO:0001583	missense	140453	exon3			TCCTAGGGAAGGA	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.5766G>T	7.37:g.100680463G>T	ENSP00000302716:p.Arg1922Ser	157	0	0		204	19	0.0931373	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	N	0.015	-1.561399	0.00903	.	.	ENSG00000169876	ENST00000306151	T	0.02787	4.16	0.932	-1.86	0.07760	.	.	.	.	.	T	0.00998	0.0033	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39210	-0.9625	9	0.06494	T	0.89	.	3.4094	0.07353	0.2058:0.0:0.3687:0.4255	.	1922	Q685J3	MUC17_HUMAN	S	1922	ENSP00000302716:R1922S	ENSP00000302716:R1922S	R	+	3	2	MUC17	100467183	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.905000	0.00338	-2.952000	0.00293	-2.056000	0.00403	AGG	.	.	alt		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		T	100680463	G	T	100680463	3	4	30	1	0	0	0	0	1	0	0	0	9983	1223	43	4	5776	4	MUC17	7	100680463	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1475	100680463	58458200	260	13411			1	57		9	9	5460	N	T_G_A	1.304015e-12
MUC17	140453	hgsc.bcm.edu	37	chr7	100681345	100681345	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgccaacctcaactcctagTgaaggaagcactccattcac	13	8	6	14	0	2	1	2	1	0	0	4	2	4	2	4	1	4	1	4	1	5	2	rs142097516		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100681345T>G	ENST00000306151.4	+	3	6712	c.6648T>G	c.(6646-6648)agT>agG	p.S2216R		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2216	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)					CAACTCCTAGTGAAGGAAGCA	0.507																																					p.S2216R		Atlas-SNP	.											.	MUC17	804	.	0			c.T6648G						PASS	.						343	338	340					7																	100681345		2203	4300	6503	SO:0001583	missense	140453	exon3			TCCTAGTGAAGGA	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.6648T>G	7.37:g.100681345T>G	ENSP00000302716:p.Ser2216Arg	177	0	0		249	23	0.0923695	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	T	2.901	-0.227411	0.06022	.	.	ENSG00000169876	ENST00000306151	T	0.02606	4.23	1.11	-2.01	0.07410	.	.	.	.	.	T	0.01489	0.0048	N	0.14661	0.345	0.09310	N	1	B	0.24963	0.115	B	0.13407	0.009	T	0.49351	-0.8949	9	0.18710	T	0.47	.	4.0824	0.09932	0.3049:0.0:0.0:0.695	.	2216	Q685J3	MUC17_HUMAN	R	2216	ENSP00000302716:S2216R	ENSP00000302716:S2216R	S	+	3	2	MUC17	100468065	0.013000	0.17824	0.006000	0.13384	0.003000	0.03518	-0.741000	0.04855	0.459000	0.27016	0.113000	0.15668	AGT	.	.	weak		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		G	100681345	T	G	100681345	3	3	30	1	0	0	0	0	1	0	0	0	9983	1693	59	5	6658	5	MUC17	7	100681345	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	882	100681345	58457318	261	13412			1	57		9	9	5460	N	T_G_A	1.304015e-12
MUC17	140453	hgsc.bcm.edu	37	chr7	100681917	100681917	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtgtgcctgtcagcaccaTgccggtggtcagttctgagg	7	10	14	10	1	3	1	2	1	1	0	3	1	3	1	3	3	3	2	3	3	1	1	rs111633703	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100681917T>G	ENST00000306151.4	+	3	7284	c.7220T>G	c.(7219-7221)aTg>aGg	p.M2407R		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2407	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)					GTCAGCACCATGCCGGTGGTC	0.507																																					p.M2407R		Atlas-SNP	.											.	MUC17	804	.	0			c.T7220G						PASS	.						383	363	370					7																	100681917		2203	4300	6503	SO:0001583	missense	140453	exon3			GCACCATGCCGGT	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.7220T>G	7.37:g.100681917T>G	ENSP00000302716:p.Met2407Arg	217	0	0		326	16	0.0490798	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	N	0.009	-1.819708	0.00595	.	.	ENSG00000169876	ENST00000306151	T	0.02216	4.39	0.679	-1.36	0.09085	.	.	.	.	.	T	0.01156	0.0038	N	0.14661	0.345	0.09310	N	1	P	0.35139	0.486	B	0.22601	0.04	T	0.50311	-0.8843	9	0.17832	T	0.49	.	7.4277	0.27109	0.0:0.7775:0.0:0.2225	.	2407	Q685J3	MUC17_HUMAN	R	2407	ENSP00000302716:M2407R	ENSP00000302716:M2407R	M	+	2	0	MUC17	100468637	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.128000	0.10531	-1.293000	0.02362	-1.602000	0.00811	ATG	T|0.996;C|0.004	.	alt		0.507	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		G	100681917	T	G	100681917	3	3	30	1	0	0	0	0	1	0	0	0	9983	1464	51	5	7230	5	MUC17	7	100681917	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	572	100681917	58456746	262	13413			1	57		9	9	5460	N	T_G_A	1.304015e-12
MUC17	140453	hgsc.bcm.edu	37	chr7	100682117	100682117	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggtggtcagttctgaggctGgcaccctttccacaactcct	6	11	10	14	1	2	1	1	1	1	0	4	1	4	1	3	4	1	3	3	4	1	2	rs555953599	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100682117G>A	ENST00000306151.4	+	3	7484	c.7420G>A	c.(7420-7422)Ggc>Agc	p.G2474S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2474	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)					TTCTGAGGCTGGCACCCTTTC	0.522													N|||	3	0.000599042	0.0	0.0	5008	,	,		27478	0.0		0.0	False		,,,				2504	0.0031				p.G2474S		Atlas-SNP	.											MUC17,right_upper_lobe,carcinoma,-2,1	MUC17	804	1	0			c.G7420A						scavenged	.																																			SO:0001583	missense	140453	exon3			GAGGCTGGCACCC	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.7420G>A	7.37:g.100682117G>A	ENSP00000302716:p.Gly2474Ser	187	0	0		238	15	0.0630252	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	N	2.617	-0.289370	0.05605	.	.	ENSG00000169876	ENST00000306151	T	0.03468	3.92	0.869	-0.297	0.12820	.	.	.	.	.	T	0.01254	0.0041	N	0.02916	-0.46	0.09310	N	1	B	0.27286	0.174	B	0.19148	0.024	T	0.45131	-0.9282	9	0.02654	T	1	.	5.8185	0.18514	0.4085:0.0:0.5915:0.0	.	2474	Q685J3	MUC17_HUMAN	S	2474	ENSP00000302716:G2474S	ENSP00000302716:G2474S	G	+	1	0	MUC17	100468837	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.476000	0.06591	-0.655000	0.05387	-1.616000	0.00795	GGC	.	.	none		0.522	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100682117	G	A	100682117	3	1	30	1	0	0	0	0	1	0	0	0	9983	1348	47	2	7430	2	MUC17	7	100682117	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	200	100682117	58456546	263	13414			1	57		9	9	5460	N	T_G_A	1.304015e-12
MUC17	140453	hgsc.bcm.edu	37	chr7	100682814	100682814	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagcaccacgctgttggccaAttctgaggctagcacccttt	8	10	9	14	1	1	1	0	1	1	0	1	1	1	1	3	2	2	5	3	2	2	4	rs201007776		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100682814A>G	ENST00000306151.4	+	3	8181	c.8117A>G	c.(8116-8118)aAt>aGt	p.N2706S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2706	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)					CTGTTGGCCAATTCTGAGGCT	0.493																																					p.N2706S		Atlas-SNP	.											MUC17,NS,carcinoma,0,1	MUC17	804	1	0			c.A8117G						scavenged	.						245	255	251					7																	100682814		2203	4300	6503	SO:0001583	missense	140453	exon3			TGGCCAATTCTGA	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.8117A>G	7.37:g.100682814A>G	ENSP00000302716:p.Asn2706Ser	139	2	0.0143885		198	15	0.0757576	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	0.044	-1.274581	0.01410	.	.	ENSG00000169876	ENST00000306151	T	0.02015	4.5	0.37	-0.741	0.11112	.	.	.	.	.	T	0.00754	0.0025	N	0.02539	-0.55	0.09310	N	1	B	0.17667	0.023	B	0.08055	0.003	T	0.43065	-0.9414	9	0.06236	T	0.91	.	0.1449	0.00087	0.2508:0.246:0.2581:0.2451	.	2706	Q685J3	MUC17_HUMAN	S	2706	ENSP00000302716:N2706S	ENSP00000302716:N2706S	N	+	2	0	MUC17	100469534	0.000000	0.05858	0.001000	0.08648	0.021000	0.10359	-0.783000	0.04638	-2.048000	0.00907	-1.389000	0.01157	AAT	A|0.999;G|0.001	0.001	weak		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		G	100682814	A	G	100682814	3	3	30	1	0	0	0	0	1	0	0	0	9983	101	4	3	8127	3	MUC17	7	100682814	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	697	100682814	58455849	264	13415			1	57		9	9	5460	N	T_G_A	1.304015e-12
TRIM56	81844	hgsc.bcm.edu	37	chr7	100730707	100730707	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagacactgccctgcctgcaTacctactgccaagactgcct	10	8	7	16	0	0	2	0	0	0	2	0	2	0	2	5	0	7	1	5	0	4	2	rs372702476		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:100730707T>C	ENST00000306085.6	+	3	411	c.114T>C	c.(112-114)caT>caC	p.H38H		NM_030961.1	NP_112223.1	Q9BRZ2	TRI56_HUMAN	tripartite motif containing 56	38					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)					CCTGCCTGCATACCTACTGCC	0.687																																					p.H38H	Ovarian(89;1092 1379 22756 38989 39611)	Atlas-SNP	.											.	TRIM56	123	.	0			c.T114C						PASS	.	T		0,4242		0,0,2121	51	62	58		114	-1.4	1	7		58	2,8486		0,2,4242	no	coding-synonymous	TRIM56	NM_030961.1		0,2,6363	CC,CT,TT		0.0236,0.0,0.0157		38/756	100730707	2,12728	2121	4244	6365	SO:0001819	synonymous_variant	81844	exon3			CCTGCATACCTAC	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.114T>C	7.37:g.100730707T>C		60	0	0		67	20	0.298507	NM_030961	Q6PJS5|Q86VT6|Q8N2H8|Q8NAC0|Q9H031	Silent	SNP	ENST00000306085.6	37	CCDS43625.1																																																																																			.	.	weak		0.687	TRIM56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347185.1	NM_030961		C	100730707	T	C	100730707	2	2	30	1	0	0	0	0	0	0	0	1	16545	1403	49	3		3	TRIM56	7	100730707	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	47893	100730707	58407956	265	13416											
RELN	5649	hgsc.bcm.edu	37	chr7	103292201	103292201	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cagtgtgaaggagggaccagGagcgcccatggttggtagaa	11	6	17	7	1	0	2	0	1	0	1	0	5	0	5	2	5	1	2	2	5	3	2	rs78008536	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:103292201G>A	ENST00000428762.1	-	15	1958	c.1799C>T	c.(1798-1800)tCc>tTc	p.S600F	RELN_ENST00000424685.2_Missense_Mutation_p.S600F|RELN_ENST00000343529.5_Missense_Mutation_p.S600F	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	600					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)		GAGGGACCAGGAGCGCCCATG	0.473													G|||	30	0.00599042	0.0008	0.013	5008	,	,		15954	0.0		0.0169	False		,,,				2504	0.0031				p.S600F	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.C1799T						PASS	.	G	PHE/SER,PHE/SER	12,4394	19.1+/-41.9	0,12,2191	72	58	63		1799,1799	5.8	1	7	dbSNP_131	63	130,8470	66.3+/-128.7	1,128,4171	yes	missense,missense	RELN	NM_005045.3,NM_173054.2	155,155	1,140,6362	AA,AG,GG		1.5116,0.2724,1.0918	probably-damaging,probably-damaging	600/3461,600/3459	103292201	142,12864	2203	4300	6503	SO:0001583	missense	5649	exon15			GACCAGGAGCGCC		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.1799C>T	7.37:g.103292201G>A	ENSP00000392423:p.Ser600Phe	102	0	0		163	71	0.435583	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	19	0.0086996336996337	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	13	0.017150395778364115	G	26.8	4.768385	0.90020	0.002724	0.015116	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.34072	1.38;1.38;1.38	5.8	5.8	0.92144	.	0.055760	0.85682	D	0.000000	T	0.30947	0.0781	L	0.47016	1.485	0.51767	D	0.999932	P;P	0.52061	0.95;0.612	P;B	0.54238	0.746;0.424	T	0.20907	-1.0261	10	0.87932	D	0	.	15.5384	0.76021	0.0:0.1373:0.8627:0.0	.	600;600	P78509-2;P78509	.;RELN_HUMAN	F	600	ENSP00000392423:S600F;ENSP00000345694:S600F;ENSP00000388446:S600F	ENSP00000345694:S600F	S	-	2	0	RELN	103079437	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.513000	0.81739	2.758000	0.94735	0.563000	0.77884	TCC	G|0.990;A|0.010	0.010	strong		0.473	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045		A	103292201	G	A	103292201	3	1	30	1	0	0	0	0	1	0	0	0	13235	1174	41	2	8787	2	RELN	7	103292201	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2561494	103292201	55846462	266	13417											
PPP1R3A	5506	hgsc.bcm.edu	37	chr7	113519637	113519637	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ataatcttccttagaagatcCttcttctgttgattctttga	9	19	5	8	0	4	4	0	2	4	2	6	4	6	4	2	0	0	1	2	0	3	8	rs371962450		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:113519637C>G	ENST00000284601.3	-	4	1578	c.1510G>C	c.(1510-1512)Gga>Cga	p.G504R		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	504					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						TTAGAAGATCCTTCTTCTGTT	0.318																																					p.G504R		Atlas-SNP	.											.	PPP1R3A	317	.	0			c.G1510C						PASS	.						63	60	61					7																	113519637		2203	4299	6502	SO:0001583	missense	5506	exon4			AAGATCCTTCTTC	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.1510G>C	7.37:g.113519637C>G	ENSP00000284601:p.Gly504Arg	188	0	0		181	53	0.292818	NM_002711	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Missense_Mutation	SNP	ENST00000284601.3	37	CCDS5759.1	.	.	.	.	.	.	.	.	.	.	C	9.621	1.133935	0.21123	.	.	ENSG00000154415	ENST00000284601;ENST00000449795	T;T	0.29655	2.51;1.56	6.02	2.73	0.32206	.	0.930568	0.09052	N	0.855709	T	0.19604	0.0471	N	0.25144	0.715	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.28586	-1.0039	10	0.13853	T	0.58	-0.2141	9.1988	0.37244	0.0:0.6562:0.0:0.3437	.	504	Q16821	PPR3A_HUMAN	R	504;183	ENSP00000284601:G504R;ENSP00000401278:G183R	ENSP00000284601:G504R	G	-	1	0	PPP1R3A	113306873	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.331000	0.19733	0.826000	0.34661	0.655000	0.94253	GGA	.	.	none		0.318	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711		G	113519637	C	G	113519637	3	3	30	1	0	0	0	0	1	0	0	0	12383	690	24	4	1862	4	PPP1R3A	7	113519637	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	10227436	113519637	45619026	267	13418											
MET	4233	hgsc.bcm.edu	37	chr7	116397572	116397572	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatggccacgggacaacacaAtacagtacattctcctatgt	14	9	7	11	1	1	0	0	0	1	0	2	1	1	1	2	2	3	1	2	2	6	4	rs13223756	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:116397572A>G	ENST00000318493.6	+	7	2131	c.1944A>G	c.(1942-1944)caA>caG	p.Q648Q	MET_ENST00000397752.3_Silent_p.Q648Q|MET_ENST00000436117.2_Silent_p.Q648Q			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0	Arg/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)			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)			GGACAACACAATACAGTACAT	0.318			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				A|||	941	0.187899	0.1089	0.1254	5008	,	,		17860	0.2728		0.2048	False		,,,				2504	0.2342				p.Q648Q		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.A1944G						PASS	.	A	,	486,3224		27,432,1396	93	92	92		1944,1944	-6.5	0	7	dbSNP_121	92	1521,6665		129,1263,2701	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	156,1695,4097	GG,GA,AA		18.5805,13.0997,16.8712	,	648/1391,648/1409	116397572	2007,9889	1855	4093	5948	SO:0001819	synonymous_variant	4233	exon7	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	AACACAATACAGT	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.1944A>G	7.37:g.116397572A>G		98	0	0		159	103	0.647799	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			A|0.817;G|0.183	0.183	strong		0.318	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			G	116397572	A	G	116397572	2	3	30	1	0	0	0	0	0	0	0	1	9494	98	4	3		3	MET	7	116397572	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	2877935	116397572	42741091	268	13419											
C7orf58	79974	hgsc.bcm.edu	37	chr7	120737809	120737809	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	atcagggaatgcaattaaagCcgagtacttcgagtcacctt	13	10	9	9	2	2	0	2	0	0	0	3	3	2	1	2	1	3	2	2	1	5	4	rs144805034	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:120737809C>T	ENST00000310396.5	+	6	1140	c.673C>T	c.(673-675)Ccg>Tcg	p.P225S	CPED1_ENST00000450913.2_Missense_Mutation_p.P225S|CPED1_ENST00000423795.1_Missense_Mutation_p.P5S	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	225						endoplasmic reticulum (GO:0005783)											GCAATTAAAGCCGAGTACTTC	0.428													C|||	5	0.000998403	0.0	0.0	5008	,	,		18641	0.0		0.005	False		,,,				2504	0.0				p.P225S		Atlas-SNP	.											.	.	.	.	0			c.C673T						PASS	.	C	SER/PRO,SER/PRO	6,4400	11.4+/-27.6	0,6,2197	148	144	146		673,673	4.8	0	7	dbSNP_134	146	58,8542	36.4+/-91.3	0,58,4242	yes	missense,missense	C7orf58	NM_001105533.1,NM_024913.4	74,74	0,64,6439	TT,TC,CC		0.6744,0.1362,0.4921	possibly-damaging,possibly-damaging	225/784,225/1027	120737809	64,12942	2203	4300	6503	SO:0001583	missense	79974	exon5			TTAAAGCCGAGTA		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.673C>T	7.37:g.120737809C>T	ENSP00000309772:p.Pro225Ser	171	0	0		89	73	0.820225	NM_001105533	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Missense_Mutation	SNP	ENST00000310396.5	37	CCDS34739.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	13.55	2.271428	0.40194	0.001362	0.006744	ENSG00000106034	ENST00000310396;ENST00000428526;ENST00000450913;ENST00000423795;ENST00000443817	T;T;T;T;T	0.43294	0.95;0.95;0.95;2.02;1.61	5.75	4.82	0.62117	.	1.300280	0.04908	N	0.452653	T	0.30324	0.0761	L	0.40543	1.245	0.24671	N	0.993418	P;B;B	0.39216	0.664;0.435;0.116	B;B;B	0.38500	0.275;0.157;0.043	T	0.11767	-1.0574	10	0.18710	T	0.47	-16.7029	11.2559	0.49054	0.1821:0.8179:0.0:0.0	.	5;225;225	G5E9U2;A4D0V7-2;A4D0V7	.;.;CG058_HUMAN	S	225;225;225;5;5	ENSP00000309772:P225S;ENSP00000398082:P225S;ENSP00000406122:P225S;ENSP00000415573:P5S;ENSP00000391952:P5S	ENSP00000309772:P225S	P	+	1	0	C7orf58	120525045	0.038000	0.19896	0.015000	0.15790	0.699000	0.40488	0.642000	0.24735	2.710000	0.92621	0.557000	0.71058	CCG	C|0.996;T|0.004	0.004	strong		0.428	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913		T	120737809	C	T	120737809	3	4	30	1	0	0	0	0	1	0	0	0	2407	739	26	2	691	2	C7orf58	7	120737809	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	4340237	120737809	38400854	269	13420											
TSGA14	95681	hgsc.bcm.edu	37	chr7	130051013	130051013	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttccagtgtttgatcagagAgggaagcaacttggatgatc	11	11	12	7	0	1	3	1	2	0	1	3	6	2	5	1	2	2	2	1	2	2	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:130051013A>G	ENST00000223208.5	-	5	497	c.227T>C	c.(226-228)cTc>cCc	p.L76P	CEP41_ENST00000541543.1_Missense_Mutation_p.L60P|CEP41_ENST00000343969.5_Missense_Mutation_p.L76P	NM_001257158.1|NM_018718.2	NP_001244087.1|NP_061188.1	Q9BYV8	CEP41_HUMAN	centrosomal protein 41kDa	76					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)											TTGATCAGAGAGGGAAGCAAC	0.403																																					p.L76P		Atlas-SNP	.											TSGA14,NS,carcinoma,+1,1	.	.	1	0			c.T227C						PASS	.						167	153	157					7																	130051013		2203	4300	6503	SO:0001583	missense	95681	exon5			TCAGAGAGGGAAG	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.227T>C	7.37:g.130051013A>G	ENSP00000223208:p.Leu76Pro	128	0	0		71	54	0.760563	NM_018718	A4D1M0|B4DQ35|F5H0V6|Q7Z496|Q86TM1|Q8NFU8|Q9H6A3|Q9NPV3	Missense_Mutation	SNP	ENST00000223208.5	37	CCDS5821.1	.	.	.	.	.	.	.	.	.	.	A	22.9	4.350277	0.82132	.	.	ENSG00000106477	ENST00000223208;ENST00000541543;ENST00000343969;ENST00000492389;ENST00000472739;ENST00000477003;ENST00000475282;ENST00000469826	D;D;D;D;D;D;D;D	0.90620	-2.7;-2.33;-2.66;-2.35;-2.34;-2.36;-1.84;-1.5	5.93	5.93	0.95920	Rhodanese-like (1);	0.242522	0.36409	N	0.002614	D	0.94371	0.8190	M	0.67953	2.075	0.80722	D	1	D;D;D	0.76494	0.999;0.997;0.997	D;D;D	0.71656	0.974;0.916;0.909	D	0.94745	0.7922	10	0.72032	D	0.01	-10.3632	15.1976	0.73104	1.0:0.0:0.0:0.0	.	60;76;76	F5H0V6;Q9BYV8-2;Q9BYV8	.;.;CEP41_HUMAN	P	76;60;76;41;41;73;41;63	ENSP00000223208:L76P;ENSP00000445888:L60P;ENSP00000342738:L76P;ENSP00000419192:L41P;ENSP00000417593:L41P;ENSP00000420670:L73P;ENSP00000418363:L41P;ENSP00000418712:L63P	ENSP00000223208:L76P	L	-	2	0	TSGA14	129838249	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.635000	0.67841	2.273000	0.75805	0.482000	0.46254	CTC	.	.	none		0.403	CEP41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349702.2	NM_018718		G	130051013	A	G	130051013	3	3	30	1	0	0	0	0	1	0	0	0	16635	304	11	3	922	3	TSGA14	7	130051013	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	9313204	130051013	29087650	270	13421											
EXOC4	60412	hgsc.bcm.edu	37	chr7	133689801	133689801	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgccattgaagaggccatgAgcgccagccttcagcagcac	10	5	12	14	2	1	3	1	2	0	1	1	3	1	3	4	1	4	2	4	1	1	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:133689801A>G	ENST00000253861.4	+	16	2514	c.2485A>G	c.(2485-2487)Agc>Ggc	p.S829G	EXOC4_ENST00000539845.1_Missense_Mutation_p.S728G|EXOC4_ENST00000541309.1_Missense_Mutation_p.S117G|EXOC4_ENST00000545148.1_Missense_Mutation_p.S439G	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	829					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)				AGAGGCCATGAGCGCCAGCCT	0.493																																					p.S829G		Atlas-SNP	.											EXOC4_ENST00000545148,NS,carcinoma,0,2	EXOC4	118	2	0			c.A2485G						PASS	.						131	125	127					7																	133689801		2203	4300	6503	SO:0001583	missense	60412	exon16			GCCATGAGCGCCA	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.2485A>G	7.37:g.133689801A>G	ENSP00000253861:p.Ser829Gly	122	0	0		61	9	0.147541	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Missense_Mutation	SNP	ENST00000253861.4	37	CCDS5829.1	.	.	.	.	.	.	.	.	.	.	A	15.04	2.714902	0.48622	.	.	ENSG00000131558	ENST00000253861;ENST00000546185;ENST00000539845;ENST00000545148;ENST00000541309	.	.	.	5.44	4.28	0.50868	.	0.052853	0.85682	D	0.000000	T	0.53867	0.1823	L	0.46819	1.47	0.45239	D	0.998246	B;B;B	0.17038	0.001;0.02;0.001	B;B;B	0.25759	0.003;0.063;0.001	T	0.50363	-0.8837	9	0.48119	T	0.1	.	8.4959	0.33127	0.8499:0.0:0.1501:0.0	.	361;439;829	B7Z689;F5GZT1;Q96A65	.;.;EXOC4_HUMAN	G	829;448;728;439;117	.	ENSP00000253861:S829G	S	+	1	0	EXOC4	133340341	1.000000	0.71417	0.997000	0.53966	0.966000	0.64601	4.678000	0.61641	0.903000	0.36546	0.402000	0.26972	AGC	.	.	none		0.493	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807		G	133689801	A	G	133689801	3	3	30	1	0	0	0	0	1	0	0	0	5308	304	11	3	2556	3	EXOC4	7	133689801	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	3638788	133689801	25448862	271	13422											
AKR1B15	441282	hgsc.bcm.edu	37	chr7	134261174	134261174	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcaaagcacaaaaaaaccAcagcccaggtaccatatttt	17	7	5	12	0	0	0	0	0	0	0	0	0	0	0	3	1	5	3	3	1	6	4	rs2458502	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:134261174A>G	ENST00000457545.2	+	9	1077	c.817A>G	c.(817-819)Aca>Gca	p.T273A	AKR1B15_ENST00000423958.1_Missense_Mutation_p.T245A	NM_001080538.2	NP_001074007.2	C9JRZ8	AK1BF_HUMAN	aldo-keto reductase family 1, member B15	273							oxidoreductase activity (GO:0016491)			endometrium(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|urinary_tract(1)	18						CAAAAAAACCACAGCCCAGGT	0.448													A|||	5	0.000998403	0.0	0.0029	5008	,	,		21387	0.0		0.003	False		,,,				2504	0.0				p.T273A		Atlas-SNP	.											.	AKR1B15	105	.	0			c.A817G						PASS	.	A	ALA/THR	7,4399	12.9+/-30.5	0,7,2196	64	71	68		817	-6.9	0	7	dbSNP_100	68	48,8552	31.2+/-83.2	0,48,4252	no	missense	AKR1B15	NM_001080538.2	58	0,55,6448	GG,GA,AA		0.5581,0.1589,0.4229	benign	273/345	134261174	55,12951	2203	4300	6503	SO:0001583	missense	441282	exon9			AAAACCACAGCCC		CCDS47715.1, CCDS47715.2	7q33	2009-09-09			ENSG00000227471	ENSG00000227471		"Aldo-keto reductases"	37281	protein-coding gene	gene with protein product							Standard	NM_001080538		Approved		uc011kpr.2	C9JRZ8	OTTHUMG00000155376	ENST00000457545.2:c.817A>G	7.37:g.134261174A>G	ENSP00000389289:p.Thr273Ala	91	0	0		77	17	0.220779	NM_001080538	C9J3V2	Missense_Mutation	SNP	ENST00000457545.2	37	CCDS47715.2	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	a	0.028	-1.354403	0.01256	0.001589	0.005581	ENSG00000227471	ENST00000457545;ENST00000423958	T;T	0.16324	2.35;2.35	3.46	-6.91	0.01649	NADP-dependent oxidoreductase domain (3);	.	.	.	.	T	0.03178	0.0093	N	0.03071	-0.42	0.09310	N	0.999998	B;B	0.10296	0.0;0.003	B;B	0.12156	0.001;0.007	T	0.33904	-0.9850	9	0.33141	T	0.24	.	2.4069	0.04414	0.2716:0.2406:0.3777:0.1102	rs2458502	245;273	C9JRZ8-2;C9JRZ8	.;AK1BF_HUMAN	A	273;245	ENSP00000389289:T273A;ENSP00000397009:T245A	ENSP00000397009:T245A	T	+	1	0	AKR1B15	133911714	0.000000	0.05858	0.001000	0.08648	0.157000	0.22087	-5.815000	0.00096	-2.183000	0.00763	-1.140000	0.01884	ACA	A|0.998;G|0.002	0.002	strong		0.448	AKR1B15-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339726.2			G	134261174	A	G	134261174	3	3	30	1	0	0	0	0	1	0	0	0	468	159	6	3	843	3	AKR1B15	7	134261174	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	571373	134261174	24877489	272	13423											
CNOT4	4850	hgsc.bcm.edu	37	chr7	135098310	135098310	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acatgcagtcaggttttggaCactgcatattctttaagaag	12	13	9	7	0	2	1	1	0	1	1	2	2	2	2	0	2	2	3	0	2	3	6			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:135098310C>T	ENST00000315544.5	-	6	893	c.614G>A	c.(613-615)tGt>tAt	p.C205Y	CNOT4_ENST00000361528.4_Missense_Mutation_p.C205Y|CNOT4_ENST00000356162.4_Missense_Mutation_p.C205Y|CNOT4_ENST00000541284.1_Missense_Mutation_p.C205Y|CNOT4_ENST00000414802.1_Missense_Mutation_p.C205Y|CNOT4_ENST00000451834.1_Missense_Mutation_p.C205Y|CNOT4_ENST00000428680.2_Missense_Mutation_p.C205Y|CNOT4_ENST00000423368.2_Missense_Mutation_p.C205Y	NM_001190848.1	NP_001177777.1	O95628	CNOT4_HUMAN	CCR4-NOT transcription complex, subunit 4	205					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						AGGTTTTGGACACTGCATATT	0.418																																					p.C205Y	Ovarian(51;766 1130 5502 35047 50875)	Atlas-SNP	.											.	CNOT4	146	.	0			c.G614A						PASS	.						130	118	122					7																	135098310		1876	4110	5986	SO:0001583	missense	4850	exon6			TTTGGACACTGCA	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.614G>A	7.37:g.135098310C>T	ENSP00000326731:p.Cys205Tyr	242	0	0		133	72	0.541353	NM_001190850	B7Z6I4|E7ET38|F8VQP3|O95339|O95627|Q8IYM7|Q8NCL0|Q9NPQ1|Q9NZN6	Missense_Mutation	SNP	ENST00000315544.5	37	CCDS55166.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.043251	0.75732	.	.	ENSG00000080802	ENST00000541284;ENST00000451834;ENST00000423368;ENST00000262563;ENST00000361528;ENST00000414802;ENST00000356162;ENST00000428680;ENST00000315544	D;D;T;D;T;T;D;D	0.82619	-1.52;-1.57;-1.44;-1.51;-1.38;-1.38;-1.63;-1.56	5.95	5.07	0.68467	Zinc finger, CCCH-type (1);	0.000000	0.85682	D	0.000000	D	0.92756	0.7697	M	0.91612	3.225	0.80722	D	1	D;D;D;D;B;D	0.89917	1.0;1.0;1.0;1.0;0.16;0.997	D;D;D;D;B;D	0.97110	0.999;1.0;0.999;1.0;0.051;0.991	D	0.94292	0.7529	10	0.87932	D	0	-12.3216	15.3196	0.74112	0.0:0.9329:0.0:0.0671	.	205;205;205;205;205;205	E7ET38;F8VQP3;O95628;O95628-2;O95628-4;O95628-8	.;.;CNOT4_HUMAN;.;.;.	Y	205	ENSP00000445508:C205Y;ENSP00000388491:C205Y;ENSP00000406777:C205Y;ENSP00000354673:C205Y;ENSP00000416532:C205Y;ENSP00000348485:C205Y;ENSP00000399108:C205Y;ENSP00000326731:C205Y	ENSP00000262563:C205Y	C	-	2	0	CNOT4	134748850	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.506000	0.81665	1.527000	0.49086	0.563000	0.77884	TGT	.	.	none		0.418	CNOT4-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_013316		T	135098310	C	T	135098310	3	4	30	1	0	0	0	0	1	0	0	0	3623	478	17	2	1434	2	CNOT4	7	135098310	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	837136	135098310	24040353	273	13424											
SSPO	23145	hgsc.bcm.edu	37	chr7	149485557	149485557	+	RNA	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgaggggactctgctgcaCggtgtgtagagtgacaaagg	9	7	16	9	2	1	2	0	1	1	1	1	4	1	3	1	4	2	3	1	4	2	1	rs73168056	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:149485557C>T	ENST00000378016.2	+	0	3963							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)			CTCTGCTGCACGGTGTGTAGA	0.652													C|||	65	0.0129792	0.0008	0.0548	5008	,	,		20320	0.0		0.0209	False		,,,				2504	0.0051				p.H1321H		Atlas-SNP	.											.	.	.	.	0			c.C3963T						PASS	.	C		18,4176		1,16,2080	34	41	39		3967	-6.3	0.6	7	dbSNP_130	39	136,8306		1,134,4086	yes	coding-notMod3-near-splice	SSPO	NM_198455.2		2,150,6166	TT,TC,CC		1.611,0.4292,1.2187			149485557	154,12482	2097	4221	6318			23145	exon27			GCTGCACGGTGTG	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.149485557C>T		117	0	0		86	15	0.174419	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				C|0.986;T|0.014	0.014	strong		0.652	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				T	149485557	C	T	149485557	1	4	30	0	1	0	0	0	0	0	0	0	15204	550	19	1		1	SSPO	7	149485557	RNA	SNP	C	TCGA-GR-7353-01A-11D-2210-10	14387247	149485557	9653106	274	13425											
SSPO	23145	hgsc.bcm.edu	37	chr7	149489540	149489540	+	RNA	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgccaagacggacggccccGacgctgccgactcaacccgg	8	3	12	18	6	1	1	1	0	0	1	1	4	1	2	5	3	3	1	5	3	2	0	rs199795943	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:149489540G>A	ENST00000378016.2	+	0	5693							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)			GGACGGCCCCGACGCTGCCGA	0.692													G|||	7	0.00139776	0.0	0.0014	5008	,	,		15662	0.0		0.005	False		,,,				2504	0.001				p.R1898Q		Atlas-SNP	.											.	.	.	.	0			c.G5693A						PASS	.	G		2,4260		0,2,2129	14	21	19		5697	-0.2	0.1	7		19	30,8422		0,30,4196	no	coding-notMod3	SSPO	NM_198455.2		0,32,6325	AA,AG,GG		0.3549,0.0469,0.2517			149489540	32,12682	2131	4226	6357			23145	exon37			GGCCCCGACGCTG	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.149489540G>A		27	0	0		7	5	0.714286	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				G|0.998;A|0.002	0.002	weak		0.692	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				A	149489540	G	A	149489540	1	1	30	0	1	0	0	0	0	0	0	0	15204	1058	37	1		1	SSPO	7	149489540	RNA	SNP	G	TCGA-GR-7353-01A-11D-2210-10	3983	149489540	9649123	275	13426											
SSPO	23145	hgsc.bcm.edu	37	chr7	149519742	149519742	+	RNA	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcggctggatggccacttccGgccttgccttatcagcaact	6	10	11	14	2	1	0	1	0	0	0	2	1	2	1	4	4	3	2	4	4	2	3	rs201102091	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr7:149519742G>A	ENST00000378016.2	+	0	13232							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)			GGCCACTTCCGGCCTTGCCTT	0.687													G|||	6	0.00119808	0.0	0.0029	5008	,	,		15642	0.0		0.003	False		,,,				2504	0.001				p.R4411Q		Atlas-SNP	.											.	.	.	.	0			c.G13232A						PASS	.	G		5,3807		0,5,1901	6	8	8		13246	4	1	7		8	36,8100		0,36,4032	yes	coding-notMod3	SSPO	NM_198455.2		0,41,5933	AA,AG,GG		0.4425,0.1312,0.3432			149519742	41,11907	1906	4068	5974			23145	exon91			ACTTCCGGCCTTG	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.149519742G>A		118	0	0		48	11	0.229167	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				.	.	weak		0.687	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript				A	149519742	G	A	149519742	1	1	30	0	1	0	0	0	0	0	0	0	15204	1116	39	1		1	SSPO	7	149519742	RNA	SNP	G	TCGA-GR-7353-01A-11D-2210-10	30202	149519742	9618921	276	13427											
PCM1	5108	hgsc.bcm.edu	37	chr8	17824674	17824674	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tactaacttttcatcatttgCaccaggtaggtgacttaacc	11	14	6	10	0	2	1	2	1	0	0	2	1	2	1	2	2	4	2	2	2	4	7	rs565676613		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:17824674C>T	ENST00000519253.1	+	21	3658	c.3407C>T	c.(3406-3408)gCa>gTa	p.A1136V	PCM1_ENST00000325083.8_Missense_Mutation_p.A1136V|PCM1_ENST00000524226.1_Missense_Mutation_p.A1137V			Q15154	PCM1_HUMAN	pericentriolar material 1	1136					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)	p.A1136V(1)	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)		TCATCATTTGCACCAGGTAGG	0.353			T	"RET, JAK2"	"papillary thyroid, CML, MPD"																																p.A1136V		Atlas-SNP	.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"E, L"	PCM1,colon,carcinoma,0,1	PCM1	120	1	1	Substitution - Missense(1)	large_intestine(1)	c.C3407T						PASS	.						43	42	42					8																	17824674		1826	4087	5913	SO:0001583	missense	5108	exon21			CATTTGCACCAGG		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.3407C>T	8.37:g.17824674C>T	ENSP00000431099:p.Ala1136Val	144	0	0		134	82	0.61194	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	37		.	.	.	.	.	.	.	.	.	.	C	15.01	2.707472	0.48412	.	.	ENSG00000078674	ENST00000325083;ENST00000519253;ENST00000524226	T;T;T	0.56776	0.44;0.44;0.44	5.7	4.83	0.62350	.	0.317735	0.40302	N	0.001125	T	0.32882	0.0844	N	0.14661	0.345	0.80722	D	1	P;B;P	0.35575	0.51;0.001;0.51	B;B;B	0.31442	0.13;0.004;0.13	T	0.19976	-1.0289	10	0.40728	T	0.16	-3.1369	11.1977	0.48722	0.0:0.8595:0.0:0.1405	.	1136;1137;1136	E7ETA6;E7EV56;Q15154	.;.;PCM1_HUMAN	V	1136;1136;1137	ENSP00000327077:A1136V;ENSP00000431099:A1136V;ENSP00000430521:A1137V	ENSP00000327077:A1136V	A	+	2	0	PCM1	17868954	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	2.612000	0.46343	1.584000	0.49913	-0.151000	0.13558	GCA	.	.	none		0.353	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197		T	17824674	C	T	17824674	3	4	30	1	0	0	0	0	1	0	0	0	11593	710	25	2	3481	2	PCM1	8	17824674	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10		17824674	128539348	277	13428											
PCM1	5108	hgsc.bcm.edu	37	chr8	17847418	17847418	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acccataaaataagtgagcaAaatgatgctgataatgctag	18	9	8	6	0	0	3	0	3	0	0	0	3	0	3	1	0	3	3	1	0	7	4	rs145539051	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:17847418A>G	ENST00000519253.1	+	27	4712	c.4461A>G	c.(4459-4461)caA>caG	p.Q1487Q	PCM1_ENST00000325083.8_Silent_p.Q1487Q|PCM1_ENST00000327578.8_Silent_p.Q186Q|PCM1_ENST00000524226.1_Silent_p.Q1433Q			Q15154	PCM1_HUMAN	pericentriolar material 1	1487	Interaction with HAP1.				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)		TAAGTGAGCAAAATGATGCTG	0.308			T	"RET, JAK2"	"papillary thyroid, CML, MPD"								A|||	18	0.00359425	0.0015	0.0058	5008	,	,		18234	0.0		0.0099	False		,,,				2504	0.002				p.Q1487Q		Atlas-SNP	.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"E, L"	.	PCM1	120	.	0			c.A4461G						PASS	.	A		13,3403		0,13,1695	86	80	82		4461	-1.6	1	8	dbSNP_134	82	106,7508		0,106,3701	no	coding-synonymous	PCM1	NM_006197.3		0,119,5396	GG,GA,AA		1.3922,0.3806,1.0789		1487/2025	17847418	119,10911	1708	3807	5515	SO:0001819	synonymous_variant	5108	exon27			TGAGCAAAATGAT		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.4461A>G	8.37:g.17847418A>G		79	0	0		97	45	0.463918	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Silent	SNP	ENST00000519253.1	37		13	0.005952380952380952	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	A	5.205	0.223287	0.09863	0.003806	0.013922	ENSG00000078674	ENST00000522275	.	.	.	5.17	-1.58	0.08479	.	.	.	.	.	T	0.33498	0.0865	.	.	.	0.52099	D	0.999945	.	.	.	.	.	.	T	0.24476	-1.0159	4	.	.	.	-4.1258	2.8152	0.05454	0.5136:0.1104:0.2686:0.1075	.	.	.	.	R	227	.	.	K	+	2	0	PCM1	17891698	0.998000	0.40836	0.990000	0.47175	0.774000	0.43823	0.689000	0.25437	-0.140000	0.11394	-2.258000	0.00281	AAA	A|0.991;G|0.009	0.009	strong		0.308	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197		G	17847418	A	G	17847418	2	3	30	1	0	0	0	0	0	0	0	1	11593	11	1	3		3	PCM1	8	17847418	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	22744	17847418	128516604	278	13429											
POLR3D	661	hgsc.bcm.edu	37	chr8	22107986	22107986	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cacgtgaagcacaaacttgtAtgttcccctgattttgaatc	11	13	7	10	1	0	3	0	3	0	0	2	3	1	3	2	0	2	3	2	0	4	5	rs75142930	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:22107986A>G	ENST00000397802.4	+	8	1367	c.1152A>G	c.(1150-1152)gtA>gtG	p.V384V	POLR3D_ENST00000306433.4_Silent_p.V384V			P05423	RPC4_HUMAN	polymerase (RNA) III (DNA directed) polypeptide D, 44kDa	384					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)	p.V384V(1)		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)		ACAAACTTGTATGTTCCCCTG	0.552													A|||	158	0.0315495	0.0038	0.1124	5008	,	,		19379	0.006		0.0507	False		,,,				2504	0.0184				p.V384V		Atlas-SNP	.											POLR3D,NS,adenoma,0,2	POLR3D	26	2	1	Substitution - coding silent(1)	stomach(1)	c.A1152G						PASS	.	A		52,4354	52.9+/-88.7	0,52,2151	213	183	193		1152	-4.8	1	8	dbSNP_132	193	454,8146	136.7+/-193.7	6,442,3852	no	coding-synonymous	POLR3D	NM_001722.2		6,494,6003	GG,GA,AA		5.2791,1.1802,3.8905		384/399	22107986	506,12500	2203	4300	6503	SO:0001819	synonymous_variant	661	exon9			ACTTGTATGTTCC	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.1152A>G	8.37:g.22107986A>G		124	0	0		186	53	0.284946	NM_001722	Q6FI28|Q9BPV7|Q9BPZ1|Q9BXB3	Silent	SNP	ENST00000397802.4	37	CCDS34858.1																																																																																			A|0.958;G|0.042	0.042	strong		0.552	POLR3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375434.2	NM_001722		G	22107986	A	G	22107986	2	3	30	1	0	0	0	0	0	0	0	1	12240	436	16	3		3	POLR3D	8	22107986	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	4260568	22107986	124256036	279	13430											
ADAM7	8756	hgsc.bcm.edu	37	chr8	24333985	24333985	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcacaataaactaaggaacCgaatttggggaatggtcaat	16	9	9	7	1	2	0	2	0	0	0	2	3	2	2	1	4	2	0	1	4	8	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:24333985C>T	ENST00000175238.6	+	8	756	c.673C>T	c.(673-675)Cga>Tga	p.R225*	RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|ADAM7_ENST00000520720.1_5'UTR|ADAM7_ENST00000380789.1_Nonsense_Mutation_p.R225*	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	225	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)		ACTAAGGAACCGAATTTGGGG	0.328																																					p.R225X		Atlas-SNP	.											ADAM7,NS,carcinoma,-1,4	ADAM7	165	4	0			c.C673T						PASS	.						114	106	109					8																	24333985		2203	4300	6503	SO:0001587	stop_gained	8756	exon8			AGGAACCGAATTT	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.673C>T	8.37:g.24333985C>T	ENSP00000175238:p.Arg225*	69	0	0		103	37	0.359223	NM_003817	A8K8X7|O75959|Q6PEJ6	Nonsense_Mutation	SNP	ENST00000175238.6	37	CCDS6045.1	.	.	.	.	.	.	.	.	.	.	C	37	6.589310	0.97688	.	.	ENSG00000069206	ENST00000175238;ENST00000380789;ENST00000335595	.	.	.	5.38	2.32	0.28847	.	0.000000	0.46145	D	0.000301	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.9142	0.47126	0.496:0.504:0.0:0.0	.	.	.	.	X	225;225;40	.	ENSP00000175238:R225X	R	+	1	2	ADAM7	24389875	0.428000	0.25522	0.898000	0.35279	0.991000	0.79684	0.270000	0.18607	0.721000	0.32231	0.591000	0.81541	CGA	.	.	none		0.328	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817		T	24333985	C	T	24333985	4	4	30	1	0	0	0	0	0	1	0	0	251	644	23	1	703	1	ADAM7	8	24333985	Nonsense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	2225999	24333985	122030037	280	13431											
PBK	55872	hgsc.bcm.edu	37	chr8	27685663	27685663	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accccagtaccaaagccaagCttctgcataaacggagaggc	14	5	9	13	1	1	1	0	0	1	1	1	2	1	1	4	2	5	3	4	2	5	3	rs55973425	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:27685663C>T	ENST00000301905.4	-	3	574	c.111G>A	c.(109-111)aaG>aaA	p.K37K	PBK_ENST00000522944.1_Silent_p.K37K	NM_018492.2	NP_060962.2	Q96KB5	TOPK_HUMAN	PDZ binding kinase	37	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)		CAAAGCCAAGCTTCTGCATAA	0.299													C|||	5	0.000998403	0.0008	0.0	5008	,	,		16110	0.0		0.004	False		,,,				2504	0.0				p.K37K		Atlas-SNP	.											.	PBK	29	.	0			c.G111A						PASS	.	C		7,4399	11.4+/-27.6	0,7,2196	64	70	68		111	4.9	1	8	dbSNP_129	68	27,8573	18.5+/-59.3	0,27,4273	no	coding-synonymous	PBK	NM_018492.2		0,34,6469	TT,TC,CC		0.314,0.1589,0.2614		37/323	27685663	34,12972	2203	4300	6503	SO:0001819	synonymous_variant	55872	exon3			GCCAAGCTTCTGC	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.111G>A	8.37:g.27685663C>T		69	0	0		97	41	0.42268	NM_018492	B4DX68|D3DST2|Q9NPD9|Q9NYL7|Q9NZK6	Silent	SNP	ENST00000301905.4	37	CCDS6063.1																																																																																			C|0.998;T|0.002	0.002	strong		0.299	PBK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219952.2	NM_018492		T	27685663	C	T	27685663	2	4	30	1	0	0	0	0	0	0	0	1	11497	796	28	2		2	PBK	8	27685663	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	3351678	27685663	118678359	281	13432											
KCNU1	157855	hgsc.bcm.edu	37	chr8	36788597	36788597	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatagctgcacgtcgctcttGtctggaagaaaccggtgtaa	10	10	12	9	3	2	1	0	0	2	1	3	3	2	2	1	2	3	4	1	2	4	3	rs190224798	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:36788597G>C	ENST00000399881.3	+	25	2902	c.2865G>C	c.(2863-2865)ttG>ttC	p.L955F	KCNU1_ENST00000518904.1_3'UTR	NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1	955					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)		CGTCGCTCTTGTCTGGAAGAA	0.443													G|||	3	0.000599042	0.0008	0.0014	5008	,	,		17383	0.0		0.0	False		,,,				2504	0.001				p.L955F		Atlas-SNP	.											.	KCNU1	359	.	0			c.G2865C						PASS	.	G	PHE/LEU	4,3820		0,4,1908	137	131	133		2865	0.5	0	8		133	18,8248		0,18,4115	yes	missense	KCNU1	NM_001031836.2	22	0,22,6023	CC,CG,GG		0.2178,0.1046,0.182	possibly-damaging	955/1150	36788597	22,12068	1912	4133	6045	SO:0001583	missense	157855	exon25			GCTCTTGTCTGGA	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.2865G>C	8.37:g.36788597G>C	ENSP00000382770:p.Leu955Phe	156	0	0		218	61	0.279817	NM_001031836		Missense_Mutation	SNP	ENST00000399881.3	37	CCDS55220.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	11.00	1.510137	0.27036	0.001046	0.002178	ENSG00000215262	ENST00000399881	T	0.39229	1.09	5.41	0.468	0.16732	.	2.385820	0.03106	U	0.161774	T	0.44705	0.1306	M	0.73962	2.25	0.09310	N	1	B	0.12013	0.005	B	0.10450	0.005	T	0.34453	-0.9828	10	0.87932	D	0	0.6019	4.979	0.14155	0.0865:0.1259:0.6256:0.162	.	955	A8MYU2	KCNU1_HUMAN	F	955	ENSP00000382770:L955F	ENSP00000382770:L955F	L	+	3	2	KCNU1	36907755	0.001000	0.12720	0.000000	0.03702	0.009000	0.06853	0.833000	0.27504	-0.142000	0.11354	0.650000	0.86243	TTG	G|1.000;C|0.000	0.000	strong		0.443	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836		C	36788597	G	C	36788597	3	2	30	1	0	0	0	0	1	0	0	0	8102	1368	48	4	2963	4	KCNU1	8	36788597	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	9102934	36788597	109575425	282	13433											
PLAT	5327	hgsc.bcm.edu	37	chr8	42044965	42044965	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgatggcgtctggcctccGcccgctgtagggcttctggg	2	10	15	14	3	2	1	0	1	2	0	3	1	3	1	4	4	0	3	4	4	1	2	rs2020921	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:42044965G>A	ENST00000220809.4	-	6	746	c.490C>T	c.(490-492)Cgg>Tgg	p.R164W	PLAT_ENST00000429089.2_Missense_Mutation_p.R164W|PLAT_ENST00000352041.3_Missense_Mutation_p.R118W|PLAT_ENST00000519510.1_Intron|PLAT_ENST00000429710.2_Intron|PLAT_ENST00000524009.1_Intron|PLAT_ENST00000270189.6_Missense_Mutation_p.R164W	NM_000930.3	NP_000921.1	P00750	TPA_HUMAN	plasminogen activator, tissue	164	Kringle 1. {ECO:0000255|PROSITE- ProRule:PRU00121}.		R -> W (in dbSNP:rs2020921). {ECO:0000269|Ref.12}.		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)	TCTGGCCTCCGCCCGCTGTAG	0.652													G|||	34	0.00678914	0.0038	0.0029	5008	,	,		20354	0.0		0.0229	False		,,,				2504	0.0041				p.R164W		Atlas-SNP	.											PLAT,NS,carcinoma,+1,1	PLAT	62	1	0			c.C490T						PASS	.	G	TRP/ARG,TRP/ARG	22,4384	29.0+/-57.7	0,22,2181	43	42	43		490,352	1.9	0.3	8	dbSNP_94	43	191,8409	83.4+/-145.9	2,187,4111	yes	missense,missense	PLAT	NM_000930.3,NM_033011.2	101,101	2,209,6292	AA,AG,GG		2.2209,0.4993,1.6377	benign,benign	164/563,118/517	42044965	213,12793	2203	4300	6503	SO:0001583	missense	5327	exon6			GCCTCCGCCCGCT		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.490C>T	8.37:g.42044965G>A	ENSP00000220809:p.Arg164Trp	37	0	0		60	35	0.583333	NM_000930	A8K022|B2R8E8|Q15103|Q503B0|Q6PJA5|Q7Z7N2|Q86YK8|Q9BU99|Q9BZW1	Missense_Mutation	SNP	ENST00000220809.4	37	CCDS6126.1	20	0.009157509157509158	3	0.006097560975609756	2	0.0055248618784530384	0	0.0	15	0.01978891820580475	G	11.06	1.529003	0.27387	0.004993	0.022209	ENSG00000104368	ENST00000270189;ENST00000429089;ENST00000220809;ENST00000352041;ENST00000520523	T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29	5.95	1.92	0.25849	Kringle (4);Kringle-like fold (1);	0.147675	0.64402	N	0.000015	T	0.33614	0.0869	L	0.35288	1.05	0.34497	D	0.705653	B;B;B	0.24920	0.114;0.036;0.037	B;B;B	0.24848	0.035;0.021;0.056	T	0.47169	-0.9138	10	0.51188	T	0.08	.	5.6142	0.17422	0.0641:0.1146:0.4484:0.3729	rs2020921;rs2020921	164;118;164	B8ZX62;P00750-3;P00750	.;.;TPA_HUMAN	W	164;164;164;118;164	ENSP00000270189:R164W;ENSP00000392045:R164W;ENSP00000220809:R164W;ENSP00000270188:R118W;ENSP00000428797:R164W	ENSP00000220809:R164W	R	-	1	2	PLAT	42164122	0.009000	0.17119	0.283000	0.24790	0.227000	0.25037	1.460000	0.35244	0.376000	0.24707	0.655000	0.94253	CGG	G|0.987;A|0.013	0.013	strong		0.652	PLAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377100.1	NM_000930		A	42044965	G	A	42044965	3	1	30	1	0	0	0	0	1	0	0	0	12030	1086	38	1	1234	1	PLAT	8	42044965	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	5256368	42044965	104319057	283	13434											
IKBKB	3551	hgsc.bcm.edu	37	chr8	42174380	42174380	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	caggaagcgggcctggcgttGatccccgataagcctgccac	8	6	13	14	3	0	1	0	1	0	0	1	3	1	2	5	3	3	1	5	3	2	2	rs56230731	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:42174380G>A	ENST00000520810.1	+	11	1269	c.1083G>A	c.(1081-1083)ttG>ttA	p.L361L	IKBKB_ENST00000522147.1_Intron|IKBKB_ENST00000416505.2_Silent_p.L302L|IKBKB_ENST00000520835.1_Silent_p.L359L|IKBKB_ENST00000379708.3_Silent_p.L138L	NM_001556.2	NP_001547.1	O14920	IKKB_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta	361					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)	GCCTGGCGTTGATCCCCGATA	0.582													G|||	19	0.00379393	0.0008	0.0014	5008	,	,		17740	0.0		0.0169	False		,,,				2504	0.0				p.L361L		Atlas-SNP	.											.	IKBKB	88	.	0			c.G1083A						PASS	.	G	,,	14,4392	21.2+/-45.6	0,14,2189	82	76	78		1077,906,1083	4.6	1	8	dbSNP_129	78	128,8472	65.6+/-127.9	1,126,4173	no	coding-synonymous,coding-synonymous,coding-synonymous	IKBKB	NM_001190720.2,NM_001242778.1,NM_001556.2	,,	1,140,6362	AA,AG,GG		1.4884,0.3177,1.0918	,,	359/755,302/698,361/757	42174380	142,12864	2203	4300	6503	SO:0001819	synonymous_variant	3551	exon11			GGCGTTGATCCCC	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.1083G>A	8.37:g.42174380G>A		106	0	0		115	37	0.321739	NM_001556	B4DZ30|B4E0U4|O75327	Silent	SNP	ENST00000520810.1	37	CCDS6128.1																																																																																			G|0.991;A|0.009	0.009	strong		0.582	IKBKB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377214.1			A	42174380	G	A	42174380	2	1	30	1	0	0	0	0	0	0	0	1	7620	1281	45	2		2	IKBKB	8	42174380	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	129415	42174380	104189642	284	13435											
PCMTD1	115294	hgsc.bcm.edu	37	chr8	52733127	52733127	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttacccacaaatacgtaagtGttaattctctgtttaactct	12	16	4	9	1	2	0	0	0	2	0	3	0	2	0	1	0	3	3	1	0	6	7			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:52733127G>A	ENST00000360540.5	-	7	1264	c.858C>T	c.(856-858)aaC>aaT	p.N286N	PCMTD1_ENST00000544451.1_Silent_p.N210N|PCMTD1_ENST00000519559.1_5'UTR|PCMTD1_ENST00000522514.1_Silent_p.N286N	NM_052937.2	NP_443169.2	Q96MG8	PCMD1_HUMAN	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	286						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)				ATACGTAAGTGTTAATTCTCT	0.398																																					p.N286N		Atlas-SNP	.											.	PCMTD1	73	.	0			c.C858T						PASS	.						189	188	188					8																	52733127		2203	4300	6503	SO:0001819	synonymous_variant	115294	exon6			GTAAGTGTTAATT		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.858C>T	8.37:g.52733127G>A		400	0	0		518	28	0.0540541	NM_052937	Q96FK9	Silent	SNP	ENST00000360540.5	37	CCDS6148.1																																																																																			.	.	none		0.398	PCMTD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377909.2	NM_052937		A	52733127	G	A	52733127	2	1	30	1	0	0	0	0	0	0	0	1	11595	1368	48	2		2	PCMTD1	8	52733127	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	10558747	52733127	93630895	285	13436											
RP1	6101	hgsc.bcm.edu	37	chr8	55541738	55541738	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaatcctggcatgtgtggcAatgcagacaccacatcagtg	13	8	10	10	0	1	1	1	0	0	1	2	1	2	1	2	2	1	3	2	2	3	0	rs147009600	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:55541738A>C	ENST00000220676.1	+	4	5444	c.5296A>C	c.(5296-5298)Aat>Cat	p.N1766H		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1766					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)			CATGTGTGGCAATGCAGACAC	0.438													A|||	2	0.000399361	0.0	0.0	5008	,	,		23417	0.0		0.0	False		,,,				2504	0.002				p.N1766H	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.A5296C						PASS	.	A	HIS/ASN	0,4406		0,0,2203	95	92	93		5296	3.5	0.9	8	dbSNP_134	93	6,8594	5.0+/-18.6	0,6,4294	yes	missense	RP1	NM_006269.1	68	0,6,6497	CC,CA,AA		0.0698,0.0,0.0461	benign	1766/2157	55541738	6,13000	2203	4300	6503	SO:0001583	missense	6101	exon4			TGTGGCAATGCAG	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.5296A>C	8.37:g.55541738A>C	ENSP00000220676:p.Asn1766His	184	0	0		100	15	0.15	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	A	8.388	0.839077	0.16891	0.0	6.98E-4	ENSG00000104237	ENST00000220676	T	0.47177	0.85	5.93	3.47	0.39725	.	0.241833	0.28977	N	0.013529	T	0.35941	0.0949	L	0.33485	1.01	0.26317	N	0.977733	B	0.18461	0.028	B	0.15870	0.014	T	0.16041	-1.0416	10	0.30078	T	0.28	.	12.782	0.57483	0.6029:0.397:0.0:0.0	.	1766	P56715	RP1_HUMAN	H	1766	ENSP00000220676:N1766H	ENSP00000220676:N1766H	N	+	1	0	RP1	55704291	0.998000	0.40836	0.854000	0.33618	0.698000	0.40448	3.291000	0.51764	0.454000	0.26884	0.533000	0.62120	AAT	A|0.999;C|0.001	0.001	strong		0.438	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		C	55541738	A	C	55541738	3	2	30	1	0	0	0	0	1	0	0	0	13547	130	5	5	5306	5	RP1	8	55541738	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	2808611	55541738	90822284	286	13437											
IMPAD1	54928	hgsc.bcm.edu	37	chr8	57906042	57906042	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caggccgaagaggctgaagcGgccggccaagaagcccgagt	11	2	16	12	4	0	3	0	1	0	2	0	5	0	3	4	4	2	1	4	4	4	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:57906042G>A	ENST00000262644.4	-	1	361	c.103C>T	c.(103-105)Cgc>Tgc	p.R35C		NM_017813.4	NP_060283.3	Q9NX62	IMPA3_HUMAN	inositol monophosphatase domain containing 1	35					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)				AGGCTGAAGCGGCCGGCCAAG	0.741																																					p.R35C		Atlas-SNP	.											.	IMPAD1	27	.	0			c.C103T						PASS	.						2	2	2					8																	57906042		1082	2103	3185	SO:0001583	missense	54928	exon1			TGAAGCGGCCGGC		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.103C>T	8.37:g.57906042G>A	ENSP00000262644:p.Arg35Cys	11	0	0		8	6	0.75	NM_017813	Q6NVY7	Missense_Mutation	SNP	ENST00000262644.4	37	CCDS6169.1	.	.	.	.	.	.	.	.	.	.	G	15.72	2.915816	0.52546	.	.	ENSG00000104331	ENST00000262644	T	0.52983	0.64	5.05	4.17	0.49024	.	0.059812	0.64402	D	0.000007	T	0.36771	0.0979	N	0.24115	0.695	0.80722	D	1	D	0.69078	0.997	P	0.47470	0.548	T	0.24512	-1.0158	10	0.72032	D	0.01	-34.6783	7.4777	0.27387	0.0852:0.0:0.7506:0.1642	.	35	Q9NX62	IMPA3_HUMAN	C	35	ENSP00000262644:R35C	ENSP00000262644:R35C	R	-	1	0	IMPAD1	58068596	1.000000	0.71417	1.000000	0.80357	0.001000	0.01503	2.643000	0.46604	1.123000	0.41961	-0.266000	0.10368	CGC	.	.	none		0.741	IMPAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378665.1	NM_017813		A	57906042	G	A	57906042	3	1	30	1	0	0	0	0	1	0	0	0	7734	1116	39	1	996	1	IMPAD1	8	57906042	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2364304	57906042	88457980	287	13438											
CLVS1	157807	hgsc.bcm.edu	37	chr8	62370916	62370916	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcaccagctaatacacccTgaatttttgccctctgaatt	10	14	4	13	0	2	2	1	2	1	0	2	2	2	2	3	0	3	1	3	0	4	6	rs72657068	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:62370916T>G	ENST00000519846.1	+	6	1264	c.792T>G	c.(790-792)ccT>ccG	p.P264P	CLVS1_ENST00000325897.4_Silent_p.P264P|CLVS1_ENST00000518592.1_5'UTR			Q8IUQ0	CLVS1_HUMAN	clavesin 1	264	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)			endometrium(3)|kidney(4)|large_intestine(4)|lung(21)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	41						TAATACACCCTGAATTTTTGC	0.408													T|||	8	0.00159744	0.0	0.0029	5008	,	,		18914	0.0		0.002	False		,,,				2504	0.0041				p.P264P		Atlas-SNP	.											.	CLVS1	74	.	0			c.T792G						PASS	.	T		0,4406		0,0,2203	128	121	123		792	0	1	8	dbSNP_130	123	28,8572	19.8+/-62.0	0,28,4272	no	coding-synonymous	CLVS1	NM_173519.2		0,28,6475	GG,GT,TT		0.3256,0.0,0.2153		264/355	62370916	28,12978	2203	4300	6503	SO:0001819	synonymous_variant	157807	exon5			ACACCCTGAATTT	AY094971	CCDS6176.1	8q12.1	2009-10-14	2009-10-14	2009-10-14		ENSG00000177182			23139	protein-coding gene	gene with protein product		611292	"retinaldehyde binding protein 1-like 1"	RLBP1L1		16802092, 19651769	Standard	NM_173519		Approved	MGC34646, CRALBPL, C6orf212L	uc003xuh.3	Q8IUQ0		ENST00000519846.1:c.792T>G	8.37:g.62370916T>G		47	0	0		24	8	0.333333	NM_173519	B2R7M5|C8UZT3|Q8NB32	Silent	SNP	ENST00000519846.1	37	CCDS6176.1																																																																																			T|0.998;G|0.002	0.002	strong		0.408	CLVS1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378323.1	NM_173519		G	62370916	T	G	62370916	2	3	30	1	0	0	0	0	0	0	0	1	3573	1567	55	5		5	CLVS1	8	62370916	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	4464874	62370916	83993106	288	13439											
LRRC67	286187	hgsc.bcm.edu	37	chr8	67926717	67926717	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atacatgaaatacaattgttTtgtaggtacaagtgggtcag	14	13	10	4	0	1	1	1	1	0	0	1	1	1	1	0	2	3	3	0	2	7	7			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:67926717T>C	ENST00000324682.5	-	3	384	c.240A>G	c.(238-240)caA>caG	p.Q80Q	PPP1R42_ENST00000522909.1_Silent_p.Q80Q|PPP1R42_ENST00000517834.1_Intron	NM_001013626.2	NP_001013648.1	Q7Z4L9	PPR42_HUMAN	protein phosphatase 1, regulatory subunit 42	80					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)										TACAATTGTTTTGTAGGTACA	0.274																																					p.Q80Q		Atlas-SNP	.											.	PPP1R42	2	.	0			c.A240G						PASS	.						97	109	105					8																	67926717		2203	4294	6497	SO:0001819	synonymous_variant	286187	exon3			ATTGTTTTGTAGG	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.240A>G	8.37:g.67926717T>C		127	0	0		73	60	0.821918	NM_001013626		Silent	SNP	ENST00000324682.5	37	CCDS34902.1																																																																																			.	.	none		0.274	PPP1R42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380034.2	NM_001013626		C	67926717	T	C	67926717	2	2	30	1	0	0	0	0	0	0	0	1	9028	1838	64	3		3	LRRC67	8	67926717	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	5555801	67926717	78437305	289	13440											
XKR9	389668	hgsc.bcm.edu	37	chr8	71646201	71646201	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgtggatgctgagtgttgtaCttctactattcttaaatgtt	8	18	9	6	1	2	1	0	1	2	0	2	2	2	2	0	1	3	4	0	1	5	8	rs61734026	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:71646201C>T	ENST00000408926.3	+	5	1198	c.664C>T	c.(664-666)Ctt>Ttt	p.L222F	XKR9_ENST00000520273.1_Intron|XKR9_ENST00000520030.1_Missense_Mutation_p.L222F	NM_001011720.1	NP_001011720.1	Q5GH70	XKR9_HUMAN	XK, Kell blood group complex subunit-related family, member 9	222						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)			GAGTGTTGTACTTCTACTATT	0.313													C|||	24	0.00479233	0.0	0.0101	5008	,	,		16387	0.0		0.0149	False		,,,				2504	0.002				p.L222F		Atlas-SNP	.											.	XKR9	43	.	0			c.C664T						PASS	.	C	PHE/LEU	7,4399	15.5+/-35.6	0,7,2196	189	188	188		664	4.7	1	8	dbSNP_129	188	110,8486	57.5+/-118.9	1,108,4189	yes	missense	XKR9	NM_001011720.1	22	1,115,6385	TT,TC,CC		1.2797,0.1589,0.8999	possibly-damaging	222/374	71646201	117,12885	2203	4298	6501	SO:0001583	missense	389668	exon5			GTTGTACTTCTAC	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.664C>T	8.37:g.71646201C>T	ENSP00000386141:p.Leu222Phe	365	0	0		461	266	0.577007	NM_001011720	B2RNS9|B9EH74	Missense_Mutation	SNP	ENST00000408926.3	37	CCDS34905.1	12	0.005494505494505495	0	0.0	3	0.008287292817679558	0	0.0	9	0.011873350923482849	C	14.17	2.456518	0.43634	0.001589	0.012797	ENSG00000221947	ENST00000408926;ENST00000520030	T;T	0.70749	-0.51;-0.51	4.69	4.69	0.59074	.	0.000000	0.85682	D	0.000000	T	0.57975	0.2090	M	0.62723	1.935	0.53688	D	0.999976	P	0.42993	0.797	B	0.39840	0.311	T	0.66097	-0.6008	10	0.49607	T	0.09	-22.2782	9.9909	0.41870	0.0:0.8431:0.0:0.1569	rs61734026	222	Q5GH70	XKR9_HUMAN	F	222	ENSP00000386141:L222F;ENSP00000431088:L222F	ENSP00000386141:L222F	L	+	1	0	XKR9	71808755	0.999000	0.42202	1.000000	0.80357	0.982000	0.71751	1.792000	0.38754	2.597000	0.87782	0.563000	0.77884	CTT	C|0.990;T|0.010	0.010	strong		0.313	XKR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378752.1	NM_001011720		T	71646201	C	T	71646201	3	4	30	1	0	0	0	0	1	0	0	0	17453	565	20	2	674	2	XKR9	8	71646201	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	3719484	71646201	74717821	290	13441											
VPS13B	157680	hgsc.bcm.edu	37	chr8	100874154	100874154	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcttcgacagggcctgtcccGgctgggcatcagcctgcttg	4	9	14	14	2	1	0	1	0	0	0	3	1	2	0	3	3	2	4	3	3	0	2	rs149318176	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:100874154G>A	ENST00000358544.2	+	58	11381	c.11270G>A	c.(11269-11271)cGg>cAg	p.R3757Q	VPS13B_ENST00000395996.1_3'UTR|VPS13B_ENST00000357162.2_Missense_Mutation_p.R3732Q	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	3757					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)			GGCCTGTCCCGGCTGGGCATC	0.677													G|||	5	0.000998403	0.0	0.0014	5008	,	,		14908	0.0		0.001	False		,,,				2504	0.0031				p.R3757Q	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.G11270A						PASS	.	G	GLN/ARG,GLN/ARG	0,4392		0,0,2196	16	18	18		11270,11195	5.8	1	8	dbSNP_134	18	23,8565		0,23,4271	yes	missense,missense	VPS13B	NM_017890.3,NM_152564.3	43,43	0,23,6467	AA,AG,GG		0.2678,0.0,0.1772	probably-damaging,probably-damaging	3757/4023,3732/3998	100874154	23,12957	2196	4294	6490	SO:0001583	missense	157680	exon58			TGTCCCGGCTGGG	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.11270G>A	8.37:g.100874154G>A	ENSP00000351346:p.Arg3757Gln	61	0	0		83	28	0.337349	NM_017890	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	.	.	.	.	.	.	.	.	.	.	G	35	5.463122	0.96257	0.0	0.002678	ENSG00000132549	ENST00000357162;ENST00000358544	T;T	0.69306	-0.39;-0.39	5.78	5.78	0.91487	Autophagy-related, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.77260	0.4104	L	0.40543	1.245	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.87578	0.948;0.998	T	0.74873	-0.3516	10	0.41790	T	0.15	.	20.0204	0.97499	0.0:0.0:1.0:0.0	.	3732;3757	Q7Z7G8-2;Q7Z7G8	.;VP13B_HUMAN	Q	3732;3757	ENSP00000349685:R3732Q;ENSP00000351346:R3757Q	ENSP00000349685:R3732Q	R	+	2	0	VPS13B	100943330	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.628000	0.83189	2.729000	0.93468	0.650000	0.86243	CGG	G|0.998;A|0.002	0.002	strong		0.677	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		A	100874154	G	A	100874154	3	1	30	1	0	0	0	0	1	0	0	0	17205	1116	39	1	11690	1	VPS13B	8	100874154	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	29227953	100874154	45489868	291	13442											
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110447512	110447512	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tggactagcacagaatgtagGgggtgaagagttctactttg	11	11	14	5	0	1	3	0	1	1	2	1	4	1	4	0	3	2	3	0	3	5	5	rs142972518	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:110447512G>C	ENST00000378402.5	+	29	3538	c.3434G>C	c.(3433-3435)gGg>gCg	p.G1145A		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1145	IPT/TIG 4.				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)			CAGAATGTAGGGGGTGAAGAG	0.443										HNSCC(38;0.096)			G|||	58	0.0115815	0.0015	0.0101	5008	,	,		18338	0.0		0.0268	False		,,,				2504	0.0225				p.G1145A		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.G3434C						PASS	.	G	ALA/GLY	15,3743		0,15,1864	197	197	197		3434	-2.3	0	8	dbSNP_134	197	167,8083		3,161,3961	yes	missense	PKHD1L1	NM_177531.4	60	3,176,5825	CC,CG,GG		2.0242,0.3991,1.5157	benign	1145/4244	110447512	182,11826	1879	4125	6004	SO:0001583	missense	93035	exon29			ATGTAGGGGGTGA	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.3434G>C	8.37:g.110447512G>C	ENSP00000367655:p.Gly1145Ala	209	0	0		251	97	0.386454	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	27	0.012362637362637362	0	0.0	5	0.013812154696132596	0	0.0	22	0.029023746701846966	G	2.585	-0.296544	0.05532	0.003991	0.020242	ENSG00000205038	ENST00000378402	D	0.85702	-2.02	6.07	-2.3	0.06785	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.912531	0.09435	N	0.802529	T	0.53142	0.1778	L	0.34521	1.04	0.09310	N	1	B	0.16396	0.017	B	0.21360	0.034	T	0.50074	-0.8870	10	0.12103	T	0.63	.	12.0147	0.53307	0.3405:0.0:0.6595:0.0	.	1145	Q86WI1	PKHL1_HUMAN	A	1145	ENSP00000367655:G1145A	ENSP00000367655:G1145A	G	+	2	0	PKHD1L1	110516688	0.005000	0.15991	0.000000	0.03702	0.004000	0.04260	0.643000	0.24750	-0.303000	0.08856	-0.768000	0.03414	GGG	G|0.986;C|0.014	0.014	strong		0.443	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		C	110447512	G	C	110447512	3	2	30	1	0	0	0	0	1	0	0	0	11981	1232	43	4	3548	4	PKHD1L1	8	110447512	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	9573358	110447512	35916510	292	13443											
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110510964	110510964	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccccatgcaggaatcatgAgttacaatgccatcagtggc	12	8	10	11	0	2	1	2	1	0	0	2	2	2	2	3	2	4	2	3	2	3	1	rs191412861	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:110510964A>C	ENST00000378402.5	+	67	10896	c.10792A>C	c.(10792-10794)Agt>Cgt	p.S3598R		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3598					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)			AGGAATCATGAGTTACAATGC	0.408										HNSCC(38;0.096)			A|||	28	0.00559105	0.0008	0.0072	5008	,	,		16193	0.0		0.005	False		,,,				2504	0.0174				p.S3598R		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.A10792C						PASS	.	A	ARG/SER	2,3744		0,2,1871	81	77	78		10792	6	1	8		78	48,8134		1,46,4044	yes	missense	PKHD1L1	NM_177531.4	110	1,48,5915	CC,CA,AA		0.5867,0.0534,0.4192	probably-damaging	3598/4244	110510964	50,11878	1873	4091	5964	SO:0001583	missense	93035	exon67			ATCATGAGTTACA	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.10792A>C	8.37:g.110510964A>C	ENSP00000367655:p.Ser3598Arg	149	0	0		217	73	0.336406	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	5	0.0022893772893772895	0	0.0	3	0.008287292817679558	0	0.0	2	0.002638522427440633	A	26.4	4.731514	0.89390	5.34E-4	0.005867	ENSG00000205038	ENST00000378402;ENST00000526472	D;D	0.86865	-2.18;-1.99	6.02	6.02	0.97574	.	0.109105	0.64402	D	0.000010	D	0.83723	0.5316	M	0.78637	2.42	0.40619	D	0.981744	B	0.25719	0.132	B	0.22601	0.04	D	0.84175	0.0436	10	0.59425	D	0.04	.	14.5014	0.67724	1.0:0.0:0.0:0.0	.	3598	Q86WI1	PKHL1_HUMAN	R	3598;526	ENSP00000367655:S3598R;ENSP00000437376:S526R	ENSP00000367655:S3598R	S	+	1	0	PKHD1L1	110580140	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	7.683000	0.84093	2.299000	0.77371	0.528000	0.53228	AGT	A|0.997;C|0.003	0.003	strong		0.408	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		C	110510964	A	C	110510964	3	2	30	1	0	0	0	0	1	0	0	0	11981	304	11	5	11058	5	PKHD1L1	8	110510964	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	63452	110510964	35853058	293	13444											
CSMD3	114788	hgsc.bcm.edu	37	chr8	113363466	113363466	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctggcatacatgtaatgtgaGagtgaccctacataaacaaa	16	9	8	8	0	0	2	0	2	0	1	0	3	0	2	1	1	3	2	1	1	6	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:113363466G>A	ENST00000297405.5	-	40	6507	c.6263C>T	c.(6262-6264)tCt>tTt	p.S2088F	CSMD3_ENST00000352409.3_Missense_Mutation_p.S2018F|CSMD3_ENST00000455883.2_Missense_Mutation_p.S1984F|CSMD3_ENST00000343508.3_Missense_Mutation_p.S2048F	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2088	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						TGTAATGTGAGAGTGACCCTA	0.294										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.S2088F		Atlas-SNP	.											.	CSMD3	2325	.	0			c.C6263T						PASS	.						120	122	121					8																	113363466		2203	4292	6495	SO:0001583	missense	114788	exon40			ATGTGAGAGTGAC	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.6263C>T	8.37:g.113363466G>A	ENSP00000297405:p.Ser2088Phe	80	0	0		89	20	0.224719	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.226833	0.79576	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16	4.32	4.32	0.51571	Complement control module (2);Sushi/SCR/CCP (3);	0.087525	0.48286	D	0.000186	T	0.79919	0.4529	M	0.81614	2.55	0.54753	D	0.999985	D;P;D	0.89917	0.973;0.921;1.0	P;P;D	0.79784	0.847;0.722;0.993	T	0.82573	-0.0390	10	0.54805	T	0.06	.	17.3411	0.87296	0.0:0.0:1.0:0.0	.	1984;2088;2048	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	F	2048;2088;1358;1984;2018	ENSP00000345799:S2048F;ENSP00000297405:S2088F;ENSP00000341558:S1358F;ENSP00000412263:S1984F;ENSP00000343124:S2018F	ENSP00000297405:S2088F	S	-	2	0	CSMD3	113432642	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.772000	0.85439	2.380000	0.81148	0.650000	0.86243	TCT	.	.	none		0.294	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113363466	G	A	113363466	3	1	30	1	0	0	0	0	1	0	0	0	3948	942	33	2	4988	2	CSMD3	8	113363466	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2852502	113363466	33000556	294	13445											
TG	7038	hgsc.bcm.edu	37	chr8	133899008	133899008	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttcagtttaccaccaaccCaaagagactccagcaaaacc	15	6	4	16	0	1	1	1	0	0	1	2	2	2	1	6	0	4	2	6	0	5	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:133899008C>A	ENST00000220616.4	+	9	1431	c.1391C>A	c.(1390-1392)cCa>cAa	p.P464Q	TG_ENST00000377869.1_Missense_Mutation_p.P464Q	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	464					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)		ACCACCAACCCAAAGAGACTC	0.463																																					p.P464Q		Atlas-SNP	.											.	TG	416	.	0			c.C1391A						PASS	.						57	63	61					8																	133899008		2203	4300	6503	SO:0001583	missense	7038	exon9			CCAACCCAAAGAG	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.1391C>A	8.37:g.133899008C>A	ENSP00000220616:p.Pro464Gln	76	0	0		170	72	0.423529	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.164144	0.78339	.	.	ENSG00000042832	ENST00000377869;ENST00000220616;ENST00000535932	D;T	0.81499	-1.5;-1.43	5.8	5.8	0.92144	.	0.190696	0.37348	N	0.002135	D	0.88894	0.6561	M	0.72894	2.215	0.40203	D	0.977531	D	0.76494	0.999	D	0.66602	0.945	D	0.88843	0.3314	10	0.52906	T	0.07	.	19.0314	0.92959	0.0:1.0:0.0:0.0	.	464	P01266	THYG_HUMAN	Q	464	ENSP00000367100:P464Q;ENSP00000220616:P464Q	ENSP00000220616:P464Q	P	+	2	0	TG	133968190	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.334000	0.65923	2.740000	0.93945	0.650000	0.86243	CCA	.	.	none		0.463	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235		A	133899008	C	A	133899008	3	1	30	1	0	0	0	0	1	0	0	0	15828	594	21	4	1425	4	TG	8	133899008	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	20535542	133899008	12465014	295	13446											
FAM135B	51059	hgsc.bcm.edu	37	chr8	139263158	139263158	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagacaggtggaaatagtcGaacatgaccgggacctggtg	13	6	14	8	2	0	2	0	1	0	1	1	5	0	4	2	4	1	0	2	4	3	1			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:139263158G>T	ENST00000395297.1	-	6	638	c.468C>A	c.(466-468)ttC>ttA	p.F156L		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	156										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)			GGAAATAGTCGAACATGACCG	0.597										HNSCC(54;0.14)																											p.F156L		Atlas-SNP	.											.	FAM135B	423	.	0			c.C468A						PASS	.						128	140	136					8																	139263158		2096	4217	6313	SO:0001583	missense	51059	exon6			ATAGTCGAACATG	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.468C>A	8.37:g.139263158G>T	ENSP00000378710:p.Phe156Leu	122	0	0		137	74	0.540146	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Missense_Mutation	SNP	ENST00000395297.1	37	CCDS6375.2	.	.	.	.	.	.	.	.	.	.	G	22.8	4.340691	0.81911	.	.	ENSG00000147724	ENST00000395297	T	0.72282	-0.64	5.47	-3.38	0.04883	.	0.000000	0.85682	D	0.000000	D	0.82449	0.5039	M	0.84585	2.705	0.44652	D	0.99763	D	0.89917	1.0	D	0.91635	0.999	D	0.83531	0.0091	10	0.87932	D	0	-21.2002	14.2536	0.66035	0.5756:0.0:0.4243:0.0	.	156	Q49AJ0	F135B_HUMAN	L	156	ENSP00000378710:F156L	ENSP00000276737:F156L	F	-	3	2	FAM135B	139332340	0.004000	0.15560	0.973000	0.42090	0.969000	0.65631	-0.976000	0.03786	-0.602000	0.05775	-0.254000	0.11334	TTC	.	.	none		0.597	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912		T	139263158	G	T	139263158	3	4	30	1	0	0	0	0	1	0	0	0	5454	1049	37	4	3812	4	FAM135B	8	139263158	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	5364150	139263158	7100864	296	13447											
GPR20	2843	hgsc.bcm.edu	37	chr8	142367350	142367350	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggtggagcagacccggcCgcgacagtgcacacatgatg	9	5	14	13	3	0	2	0	1	0	1	0	4	0	3	3	3	2	2	3	3	0	0	rs201039593	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:142367350C>T	ENST00000377741.3	-	2	764	c.674G>A	c.(673-675)cGg>cAg	p.R225Q	CTD-3064M3.3_ENST00000562459.1_RNA	NM_005293.2	NP_005284.2	Q99678	GPR20_HUMAN	G protein-coupled receptor 20	225					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(3)|lung(4)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	15	all_cancers(97;4.32e-16)|all_epithelial(106;6.61e-14)|Lung NSC(106;9.4e-06)|all_lung(105;1.35e-05)|Ovarian(258;0.0303)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0415)			CAGACCCGGCCGCGACAGTGC	0.652													C|||	4	0.000798722	0.0008	0.0	5008	,	,		18546	0.0		0.003	False		,,,				2504	0.0				p.R225Q		Atlas-SNP	.											.	GPR20	43	.	0			c.G674A						PASS	.	C	GLN/ARG	4,4162		0,4,2079	10	9	9		674	3.7	0.2	8	dbSNP_134	9	52,8166		1,50,4058	yes	missense	GPR20	NM_005293.2	43	1,54,6137	TT,TC,CC		0.6328,0.096,0.4522	probably-damaging	225/359	142367350	56,12328	2083	4109	6192	SO:0001583	missense	2843	exon2			CCCGGCCGCGACA	U66579	CCDS34949.1	8q24.3	2012-08-21				ENSG00000204882		"GPCR / Class A : Orphans"	4475	protein-coding gene	gene with protein product		601908				18347022	Standard	NM_005293		Approved		uc003ywf.3	Q99678		ENST00000377741.3:c.674G>A	8.37:g.142367350C>T	ENSP00000366970:p.Arg225Gln	20	0	0		20	20	1	NM_005293	Q17R96	Missense_Mutation	SNP	ENST00000377741.3	37	CCDS34949.1	.	.	.	.	.	.	.	.	.	.	C	10.82	1.459179	0.26248	9.6E-4	0.006328	ENSG00000204882	ENST00000377741	T	0.41400	1.0	4.77	3.67	0.42095	GPCR, rhodopsin-like superfamily (1);	0.643696	0.13570	U	0.378104	T	0.29684	0.0741	L	0.35793	1.09	0.09310	N	1	D	0.55800	0.973	P	0.48166	0.569	T	0.06588	-1.0818	10	0.32370	T	0.25	-20.3414	9.5849	0.39510	0.0:0.8396:0.0:0.1604	.	225	Q99678	GPR20_HUMAN	Q	225	ENSP00000366970:R225Q	ENSP00000366970:R225Q	R	-	2	0	GPR20	142436532	0.004000	0.15560	0.175000	0.22980	0.085000	0.17905	0.829000	0.27449	2.197000	0.70478	0.462000	0.41574	CGG	.	.	weak		0.652	GPR20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378968.1	NM_005293		T	142367350	C	T	142367350	3	4	30	1	0	0	0	0	1	0	0	0	6688	652	23	1	406	1	GPR20	8	142367350	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	3104192	142367350	3996672	297	13448											
RHPN1	114822	hgsc.bcm.edu	37	chr8	144462841	144462841	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgccgcgtcctgcgcgaggtGgacctgcttcgggctgtgat	3	10	16	12	5	0	1	0	1	0	0	2	3	1	2	3	3	3	2	3	3	0	1	rs117282246	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:144462841G>A	ENST00000289013.6	+	11	1400	c.1299G>A	c.(1297-1299)gtG>gtA	p.V433V		NM_052924.2	NP_443156.2	Q8TCX5	RHPN1_HUMAN	rhophilin, Rho GTPase binding protein 1	458	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)			TGCGCGAGGTGGACCTGCTTC	0.687													g|||	20	0.00399361	0.0	0.0	5008	,	,		17518	0.0		0.0129	False		,,,				2504	0.0072				p.V433V		Atlas-SNP	.											.	RHPN1	76	.	0			c.G1299A						PASS	.	G		7,4217		0,7,2105	19	23	21		1299	2.5	0.9	8	dbSNP_132	21	71,8371		0,71,4150	no	coding-synonymous	RHPN1	NM_052924.2		0,78,6255	AA,AG,GG		0.841,0.1657,0.6158		433/671	144462841	78,12588	2112	4221	6333	SO:0001819	synonymous_variant	114822	exon11			CGAGGTGGACCTG	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.1299G>A	8.37:g.144462841G>A		233	0	0		210	95	0.452381	NM_052924	Q8TAV1|Q96PV9	Silent	SNP	ENST00000289013.6	37	CCDS47927.1																																																																																			G|0.994;A|0.006	0.006	strong		0.687	RHPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381417.1			A	144462841	G	A	144462841	2	1	30	1	0	0	0	0	0	0	0	1	13365	1335	47	2		2	RHPN1	8	144462841	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2095491	144462841	1901181	298	13449											
SCRIB	23513	hgsc.bcm.edu	37	chr8	144885669	144885669	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgtcaggcccagcaggctctGctggttcacctccaacagcc	7	7	10	17	1	3	0	2	0	1	0	4	0	4	0	4	3	4	4	4	3	1	1	rs138257744	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:144885669G>C	ENST00000320476.3	-	24	3493	c.3487C>G	c.(3487-3489)Cag>Gag	p.Q1163E	SCRIB_ENST00000356994.2_Missense_Mutation_p.Q1163E|SCRIB_ENST00000377533.3_Missense_Mutation_p.Q1082E	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	1163	Interaction with ARHGEF7.|PDZ 4. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)			AGCAGGCTCTGCTGGTTCACC	0.692													G|||	17	0.00339457	0.0	0.0	5008	,	,		11201	0.0169		0.0	False		,,,				2504	0.0				p.Q1163E	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.C3487G						PASS	.	G	GLU/GLN,GLU/GLN	2,4362		0,2,2180	20	20	20		3487,3487	4.8	1	8	dbSNP_134	20	0,8554		0,0,4277	yes	missense,missense	SCRIB	NM_015356.3,NM_182706.3	29,29	0,2,6457	CC,CG,GG		0.0,0.0458,0.0155	possibly-damaging,possibly-damaging	1163/1631,1163/1656	144885669	2,12916	2182	4277	6459	SO:0001583	missense	23513	exon24			GGCTCTGCTGGTT	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.3487C>G	8.37:g.144885669G>C	ENSP00000322938:p.Gln1163Glu	21	0	0		15	9	0.6	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Missense_Mutation	SNP	ENST00000320476.3	37	CCDS6411.1	7|7	0.003205128205128205|0.003205128205128205	0|0	0.0|0.0	0|0	0.0|0.0	7|7	0.012237762237762238|0.012237762237762238	0|0	0.0|0.0	G|G	17.95|17.95	3.514052|3.514052	0.64522|0.64522	4.58E-4|4.58E-4	0.0|0.0	ENSG00000180900|ENSG00000180900	ENST00000526832|ENST00000356994;ENST00000320476;ENST00000377533;ENST00000377539	.|T;T;T	.|0.27256	.|1.68;1.68;1.68	4.82|4.82	4.82|4.82	0.62117|0.62117	.|PDZ/DHR/GLGF (4);	.|.	.|.	.|.	.|.	T|T	0.16085|0.16085	0.0387|0.0387	N|N	0.10618|0.10618	0.005|0.005	0.24765|0.24765	N|N	0.99291|0.99291	.|P;P	.|0.48089	.|0.855;0.905	.|P;P	.|0.50860	.|0.634;0.652	T|T	0.13629|0.13629	-1.0502|-1.0502	5|9	.|0.30854	.|T	.|0.27	.|.	15.1122|15.1122	0.72368|0.72368	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1163;1163	.|Q14160;Q14160-3	.|SCRIB_HUMAN;.	G|E	158|1163;1163;1082;532	.|ENSP00000349486:Q1163E;ENSP00000322938:Q1163E;ENSP00000366756:Q1082E	.|ENSP00000322938:Q1163E	A|Q	-|-	2|1	0|0	SCRIB|SCRIB	144957657|144957657	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.913000|0.913000	0.54294|0.54294	5.594000|5.594000	0.67557|0.67557	2.222000|2.222000	0.72286|0.72286	0.456000|0.456000	0.33151|0.33151	GCA|CAG	G|0.999;C|0.001	0.001	strong		0.692	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356		C	144885669	G	C	144885669	3	2	30	1	0	0	0	0	1	0	0	0	13952	1328	46	4	1536	4	SCRIB	8	144885669	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	422828	144885669	1478353	299	13450											
PLEC	5339	hgsc.bcm.edu	37	chr8	144991925	144991925	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcctggaagagggagatgaGcttcccagagtaggggtcct	9	7	17	8	0	0	4	0	1	0	3	2	6	2	5	3	5	1	2	3	5	2	2	rs189061273	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:144991925G>A	ENST00000322810.4	-	32	12644	c.12475C>T	c.(12475-12477)Ctc>Ttc	p.L4159F	PLEC_ENST00000345136.3_Missense_Mutation_p.L4022F|PLEC_ENST00000357649.2_Missense_Mutation_p.L4026F|PLEC_ENST00000354589.3_Missense_Mutation_p.L4022F|PLEC_ENST00000436759.2_Missense_Mutation_p.L4049F|PLEC_ENST00000354958.2_Missense_Mutation_p.L4000F|PLEC_ENST00000356346.3_Missense_Mutation_p.L4008F|PLEC_ENST00000398774.2_Missense_Mutation_p.L3990F|PLEC_ENST00000527096.1_Missense_Mutation_p.L4045F	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	4159	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						AGGGAGATGAGCTTCCCAGAG	0.637													G|||	14	0.00279553	0.0	0.0	5008	,	,		18649	0.0139		0.0	False		,,,				2504	0.0				p.L4159F		Atlas-SNP	.											PLEC_ENST00000436759,bladder,carcinoma,+2,3	PLEC	1144	3	0			c.C12475T						PASS	.						49	57	54					8																	144991925		2110	4197	6307	SO:0001583	missense	5339	exon32			AGATGAGCTTCCC	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.12475C>T	8.37:g.144991925G>A	ENSP00000323856:p.Leu4159Phe	96	0	0		102	63	0.617647	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	10	0.004578754578754579	0	0.0	0	0.0	10	0.017482517482517484	0	0.0	G	8.561	0.877675	0.17395	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	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	4.98	4.98	0.66077	.	0.420113	0.19781	U	0.106211	T	0.37758	0.1015	N	0.14661	0.345	0.34450	D	0.700616	P;P;P;P;P;P;P;P	0.49090	0.919;0.919;0.919;0.868;0.919;0.919;0.919;0.919	P;P;P;B;P;P;P;P	0.45506	0.483;0.483;0.483;0.289;0.483;0.483;0.483;0.483	T	0.63637	-0.6592	10	0.54805	T	0.06	.	13.0686	0.59048	0.0:0.0:0.8393:0.1607	.	4049;4008;4000;4159;3990;4022;4026;4022	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	F	4022;4026;4022;3990;4159;4000;4008;4049;4045	ENSP00000344848:L4022F;ENSP00000350277:L4026F;ENSP00000346602:L4022F;ENSP00000381756:L3990F;ENSP00000323856:L4159F;ENSP00000347044:L4000F;ENSP00000348702:L4008F;ENSP00000388180:L4049F;ENSP00000434583:L4045F	ENSP00000323856:L4159F	L	-	1	0	PLEC	145063913	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.222000	0.32515	2.597000	0.87782	0.549000	0.68633	CTC	G|0.995;A|0.005	0.005	strong		0.637	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		A	144991925	G	A	144991925	3	1	30	1	0	0	0	0	1	0	0	0	12061	971	34	2	1583	2	PLEC	8	144991925	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	106256	144991925	1372097	300	13451											
PLEC	5339	hgsc.bcm.edu	37	chr8	145006143	145006143	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctccttcaggtgtgcctcgaTacagcagcacagctgtagca	9	9	10	13	1	1	0	1	0	0	0	3	1	2	0	2	1	6	5	2	1	2	3	rs189137260	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:145006143T>C	ENST00000322810.4	-	18	2720	c.2551A>G	c.(2551-2553)Atc>Gtc	p.I851V	PLEC_ENST00000345136.3_Missense_Mutation_p.I714V|PLEC_ENST00000357649.2_Missense_Mutation_p.I718V|PLEC_ENST00000354589.3_Missense_Mutation_p.I714V|PLEC_ENST00000436759.2_Missense_Mutation_p.I741V|PLEC_ENST00000354958.2_Missense_Mutation_p.I692V|PLEC_ENST00000356346.3_Missense_Mutation_p.I700V|PLEC_ENST00000398774.2_Missense_Mutation_p.I682V|PLEC_ENST00000527096.1_Missense_Mutation_p.I737V	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	851	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						TGTGCCTCGATACAGCAGCAC	0.682													T|||	7	0.00139776	0.0	0.0	5008	,	,		12293	0.0069		0.0	False		,,,				2504	0.0				p.I851V		Atlas-SNP	.											.	PLEC	1144	.	0			c.A2551G						PASS	.						18	23	21					8																	145006143		2101	4235	6336	SO:0001583	missense	5339	exon18			CCTCGATACAGCA	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.2551A>G	8.37:g.145006143T>C	ENSP00000323856:p.Ile851Val	114	0	0		154	83	0.538961	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	11	0.005036630036630037	1	0.0020325203252032522	1	0.0027624309392265192	7	0.012237762237762238	2	0.002638522427440633	T	10.35	1.327031	0.24080	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	D;D;D;D;D;D;D;D;D	0.88975	-2.45;-2.45;-2.45;-2.45;-2.45;-2.45;-2.45;-2.45;-2.45	4.2	0.331	0.15933	.	0.000000	0.64402	U	0.000016	T	0.69949	0.3168	N	0.21545	0.675	0.34771	D	0.73369	B;B;B;B;B;B;B;B	0.06786	0.001;0.001;0.001;0.001;0.001;0.001;0.001;0.001	B;B;B;B;B;B;B;B	0.09377	0.004;0.004;0.004;0.002;0.004;0.004;0.004;0.004	T	0.62872	-0.6762	10	0.23302	T	0.38	.	5.975	0.19373	0.0:0.1853:0.1515:0.6631	.	741;700;692;851;682;714;718;714	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	V	714;718;714;682;851;692;700;741;737	ENSP00000344848:I714V;ENSP00000350277:I718V;ENSP00000346602:I714V;ENSP00000381756:I682V;ENSP00000323856:I851V;ENSP00000347044:I692V;ENSP00000348702:I700V;ENSP00000388180:I741V;ENSP00000434583:I737V	ENSP00000323856:I851V	I	-	1	0	PLEC	145078131	0.157000	0.22836	0.190000	0.23270	0.782000	0.44232	0.054000	0.14205	0.208000	0.20626	0.372000	0.22366	ATC	T|0.995;C|0.005	0.005	strong		0.682	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		C	145006143	T	C	145006143	3	2	30	1	0	0	0	0	1	0	0	0	12061	1406	49	3	11563	3	PLEC	8	145006143	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	14218	145006143	1357879	301	13452											
GPAA1	8733	hgsc.bcm.edu	37	chr8	145138063	145138063	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcgggcatcgcctggttcttGgcgctggttttcccgccgct	1	12	14	14	5	1	0	0	0	1	0	3	0	2	0	3	4	0	5	3	4	0	4	rs138412600	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:145138063G>A	ENST00000355091.4	+	2	232	c.111G>A	c.(109-111)ttG>ttA	p.L37L	GPAA1_ENST00000361036.6_Intron	NM_003801.3	NP_003792.1	O43292	GPAA1_HUMAN	glycosylphosphatidylinositol anchor attachment 1	37					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)			CCTGGTTCTTGGCGCTGGTTT	0.677													G|||	22	0.00439297	0.0008	0.0014	5008	,	,		12607	0.0		0.0189	False		,,,				2504	0.001				p.L37L		Atlas-SNP	.											.	GPAA1	40	.	0			c.G111A						PASS	.	G		16,4062		0,16,2023	24	29	27		111	4	1	8	dbSNP_134	27	153,8217		3,147,4035	no	coding-synonymous	GPAA1	NM_003801.3		3,163,6058	AA,AG,GG		1.828,0.3923,1.3576		37/622	145138063	169,12279	2039	4185	6224	SO:0001819	synonymous_variant	8733	exon2			GTTCTTGGCGCTG	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.111G>A	8.37:g.145138063G>A		177	0	0		225	76	0.337778	NM_003801	Q9NSS0|Q9UQ31	Silent	SNP	ENST00000355091.4	37	CCDS43776.1																																																																																			G|0.993;A|0.007	0.007	strong		0.677	GPAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384070.1	NM_003801		A	145138063	G	A	145138063	2	1	30	1	0	0	0	0	0	0	0	1	6595	1339	47	2		2	GPAA1	8	145138063	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	131920	145138063	1225959	302	13453											
CPSF1	29894	hgsc.bcm.edu	37	chr8	145624559	145624559	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcgcccacggcggcattggCacagggtccaatgttcagga	8	7	13	13	3	1	0	1	0	0	0	3	1	2	1	2	5	0	3	2	5	1	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:145624559C>T	ENST00000349769.3	-	15	1520	c.1426G>A	c.(1426-1428)Gcc>Acc	p.A476T	MIR1234_ENST00000408875.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	476					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)			GCGGCATTGGCACAGGGTCCA	0.701																																					p.A476T	NSCLC(133;1088 1848 27708 34777 35269)	Atlas-SNP	.											.	CPSF1	92	.	0			c.G1426A						PASS	.						8	9	9					8																	145624559		2182	4242	6424	SO:0001583	missense	29894	exon15			CATTGGCACAGGG	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.1426G>A	8.37:g.145624559C>T	ENSP00000339353:p.Ala476Thr	103	0	0		153	36	0.235294	NM_013291	Q96AF0	Missense_Mutation	SNP	ENST00000349769.3	37	CCDS34966.1	.	.	.	.	.	.	.	.	.	.	C	15.45	2.836638	0.50951	.	.	ENSG00000071894	ENST00000349769	T	0.39406	1.08	5.62	5.62	0.85841	.	0.054386	0.64402	D	0.000001	T	0.34308	0.0893	L	0.32530	0.975	0.58432	D	0.999999	B	0.18310	0.027	B	0.19666	0.026	T	0.09292	-1.0681	10	0.17832	T	0.49	-17.6509	17.1693	0.86825	0.0:1.0:0.0:0.0	.	476	Q10570	CPSF1_HUMAN	T	476	ENSP00000339353:A476T	ENSP00000339353:A476T	A	-	1	0	CPSF1	145595367	1.000000	0.71417	0.995000	0.50966	0.082000	0.17680	5.468000	0.66743	2.658000	0.90341	0.561000	0.74099	GCC	.	.	none		0.701	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291		T	145624559	C	T	145624559	3	4	30	1	0	0	0	0	1	0	0	0	3826	710	25	2	3001	2	CPSF1	8	145624559	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	486496	145624559	739463	303	13454											
ZNF16	7564	hgsc.bcm.edu	37	chr8	146157265	146157265	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttaaggctcgagttctggCtgaaggcttttccacattca	8	15	9	9	1	2	1	1	1	1	0	4	2	3	1	1	3	0	4	1	3	2	6	rs80044147	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr8:146157265C>T	ENST00000276816.4	-	4	1094	c.908G>A	c.(907-909)aGc>aAc	p.S303N	ZNF16_ENST00000394909.2_Missense_Mutation_p.S303N	NM_001029976.2	NP_001025147.2	P17020	ZNF16_HUMAN	zinc finger protein 16	303	Required for nuclear localization.				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)		CGAGTTCTGGCTGAAGGCTTT	0.478													C|||	5	0.000998403	0.0008	0.0	5008	,	,		20412	0.0		0.004	False		,,,				2504	0.0				p.S303N		Atlas-SNP	.											.	ZNF16	80	.	0			c.G908A						PASS	.	C	ASN/SER,ASN/SER	9,4397	15.5+/-35.6	0,9,2194	72	72	72		908,908	3.1	1	8	dbSNP_132	72	31,8569	22.2+/-67.0	0,31,4269	yes	missense,missense	ZNF16	NM_001029976.2,NM_006958.2	46,46	0,40,6463	TT,TC,CC		0.3605,0.2043,0.3076	benign,benign	303/683,303/683	146157265	40,12966	2203	4300	6503	SO:0001583	missense	7564	exon3			TTCTGGCTGAAGG	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.908G>A	8.37:g.146157265C>T	ENSP00000276816:p.Ser303Asn	137	0	0		159	48	0.301887	NM_006958	B3KXM4|D3DWP2|Q45SH7|Q96FG0|Q9NRA4	Missense_Mutation	SNP	ENST00000276816.4	37	CCDS6437.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	8.817	0.936690	0.18206	0.002043	0.003605	ENSG00000170631	ENST00000276816;ENST00000394909	T;T	0.19394	2.15;2.15	4.02	3.11	0.35812	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11110	0.0271	N	0.17594	0.5	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.12268	-1.0554	9	0.42905	T	0.14	.	3.0488	0.06162	0.1772:0.5474:0.1724:0.103	.	303	P17020	ZNF16_HUMAN	N	303	ENSP00000276816:S303N;ENSP00000378369:S303N	ENSP00000276816:S303N	S	-	2	0	ZNF16	146128069	0.000000	0.05858	1.000000	0.80357	0.988000	0.76386	-1.354000	0.02614	2.056000	0.61249	0.563000	0.77884	AGC	C|0.998;T|0.002	0.002	strong		0.478	ZNF16-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000382978.1	NM_006958		T	146157265	C	T	146157265	3	4	30	1	0	0	0	0	1	0	0	0	17753	797	28	2	1144	2	ZNF16	8	146157265	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	532706	146157265	206757	304	13455											
DOCK8	81704	hgsc.bcm.edu	37	chr9	304670	304670	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tccgaaacagacgtttgagtCggaaaccttggagtgcagtg	11	9	13	8	3	0	2	0	1	0	1	2	5	1	4	2	2	3	2	2	2	2	2	rs146490788	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:304670C>T	ENST00000453981.1	+	5	606	c.494C>T	c.(493-495)tCg>tTg	p.S165L	DOCK8_ENST00000432829.2_Missense_Mutation_p.S97L|DOCK8_ENST00000469391.1_Missense_Mutation_p.S97L			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	165					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)		ACGTTTGAGTCGGAAACCTTG	0.463																																					p.S165L		Atlas-SNP	.											.	DOCK8	401	.	0			c.C494T						PASS	.	C	LEU/SER,LEU/SER,LEU/SER	3,4403	6.2+/-15.9	0,3,2200	127	134	132		290,290,494	6	1	9	dbSNP_134	132	7,8593	5.7+/-21.5	0,7,4293	yes	missense,missense,missense	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	145,145,145	0,10,6493	TT,TC,CC		0.0814,0.0681,0.0769	benign,benign,benign	97/2000,97/2032,165/2100	304670	10,12996	2203	4300	6503	SO:0001583	missense	81704	exon5			TTGAGTCGGAAAC	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.494C>T	9.37:g.304670C>T	ENSP00000408464:p.Ser165Leu	67	0	0		58	30	0.517241	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Missense_Mutation	SNP	ENST00000453981.1	37	CCDS6440.2	.	.	.	.	.	.	.	.	.	.	C	18.68	3.676168	0.67928	6.81E-4	8.14E-4	ENSG00000107099	ENST00000453981;ENST00000287364;ENST00000432829;ENST00000487230;ENST00000469391	T;T;T;T	0.32272	2.59;2.59;1.46;2.59	6.02	6.02	0.97574	.	0.139758	0.49916	D	0.000133	T	0.41971	0.1182	N	0.19112	0.55	0.58432	D	0.999999	B;D;B	0.89917	0.158;1.0;0.031	B;D;B	0.83275	0.029;0.996;0.006	T	0.11203	-1.0597	10	0.25751	T	0.34	.	18.7213	0.91694	0.0:1.0:0.0:0.0	.	97;165;165	E9PH09;A2A349;Q8NF50	.;.;DOCK8_HUMAN	L	165;165;97;97;97	ENSP00000408464:S165L;ENSP00000394888:S97L;ENSP00000418318:S97L;ENSP00000419438:S97L	ENSP00000287364:S165L	S	+	2	0	DOCK8	294670	0.999000	0.42202	1.000000	0.80357	0.993000	0.82548	5.226000	0.65299	2.865000	0.98341	0.655000	0.94253	TCG	C|0.999;T|0.001	0.001	strong		0.463	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307		T	304670	C	T	304670	3	4	30	1	0	0	0	0	1	0	0	0	4695	893	31	1	512	1	DOCK8	9	304670	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10		304670	140908761	305	13456											
GLIS3	169792	hgsc.bcm.edu	37	chr9	4286248	4286248	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcctgagggcatcttgaGatggaggttgttagcaaggc	8	11	14	8	0	1	2	0	2	1	1	3	4	3	3	2	4	1	4	2	4	2	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:4286248G>T	ENST00000381971.3	-	2	771	c.178C>A	c.(178-180)Ctc>Atc	p.L60I		NM_001042413.1	NP_001035878.1	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3	0	Ser-rich.				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)		GGCATCTTGAGATGGAGGTTG	0.592																																					p.L60I		Atlas-SNP	.											.	GLIS3	152	.	0			c.C178A						PASS	.						64	70	68					9																	4286248		2088	4214	6302	SO:0001583	missense	169792	exon2			TCTTGAGATGGAG	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	ENST00000381971.3:c.178C>A	9.37:g.4286248G>T	ENSP00000371398:p.Leu60Ile	149	0	0		145	55	0.37931	NM_001042413	B1AL19|Q1PHK5	Missense_Mutation	SNP	ENST00000381971.3	37	CCDS43784.1	.	.	.	.	.	.	.	.	.	.	G	15.26	2.781727	0.49891	.	.	ENSG00000107249	ENST00000381971;ENST00000477901;ENST00000481827	T	0.12361	2.69	5.75	5.75	0.90469	.	.	.	.	.	T	0.19765	0.0475	N	0.24115	0.695	0.29128	N	0.879822	D;P	0.63880	0.993;0.882	P;P	0.61397	0.888;0.477	T	0.06409	-1.0828	9	0.62326	D	0.03	.	8.9189	0.35599	0.1588:0.0:0.8412:0.0	.	60;60	F8WEV9;Q8NEA6-2	.;.	I	60	ENSP00000371398:L60I	ENSP00000371398:L60I	L	-	1	0	GLIS3	4276248	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	3.698000	0.54771	2.711000	0.92665	0.655000	0.94253	CTC	.	.	none		0.592	GLIS3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354776.1	NM_152629		T	4286248	G	T	4286248	3	4	30	1	0	0	0	0	1	0	0	0	6455	942	33	4	2654	4	GLIS3	9	4286248	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	3981578	4286248	136927183	306	13457											
C9orf150	286343	hgsc.bcm.edu	37	chr9	12775855	12775855	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacccctgcggggggagcggTggtggtggcggcggcggcgg	2	4	25	10	6	0	0	0	0	0	0	0	2	0	1	2	11	2	0	2	11	0	0	rs572021640		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:12775855T>C	ENST00000319264.3	+	1	836	c.141T>C	c.(139-141)ggT>ggC	p.G47G	LURAP1L_ENST00000489107.1_3'UTR|RP11-3L8.3_ENST00000417638.1_RNA	NM_203403.1	NP_981948.1	Q8IV03	LUR1L_HUMAN	leucine rich adaptor protein 1-like	50	Gly-rich.		Missing.														GGGGGAgcggtggtggtggcg	0.677																																					p.G47G		Atlas-SNP	.											.	.	.	.	0			c.T141C						PASS	.						5	6	5					9																	12775855		2076	4056	6132	SO:0001819	synonymous_variant	286343	exon1			GAGCGGTGGTGGT	AK095824	CCDS6473.1	9p22.3	2012-02-01	2012-02-01	2012-02-01	ENSG00000153714	ENSG00000153714			31452	protein-coding gene	gene with protein product	"similar to DNA segment, Chr 4, Brigham & Womens Genetics 0951 expressed"		"chromosome 9 open reading frame 150"	C9orf150		12766061	Standard	NM_203403		Approved	MGC46502, FLJ38505, bA3L8.2	uc003zkw.3	Q8IV03	OTTHUMG00000019557	ENST00000319264.3:c.141T>C	9.37:g.12775855T>C		15	0	0		17	7	0.411765	NM_203403	Q5VZX7|Q8N923|Q8NCG2	Silent	SNP	ENST00000319264.3	37	CCDS6473.1																																																																																			.	.	none		0.677	LURAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051730.1	NM_203403		C	12775855	T	C	12775855	2	2	30	1	0	0	0	0	0	0	0	1	2464	1683	59	3		3	C9orf150	9	12775855	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	8489607	12775855	128437576	307	13458											
CNTLN	54875	hgsc.bcm.edu	37	chr9	17135322	17135322	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagcgcgcccatggggtccAgacggctagagggcatctcg	7	6	15	13	4	2	2	1	0	1	2	4	2	3	2	2	4	1	2	2	4	1	1			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:17135322A>G	ENST00000380647.3	+	1	343	c.259A>G	c.(259-261)Aga>Gga	p.R87G	CNTLN_ENST00000380641.4_Missense_Mutation_p.R87G|CNTLN_ENST00000425824.1_Missense_Mutation_p.R87G|CNTLN_ENST00000484374.1_3'UTR|CNTLN_ENST00000262360.5_Missense_Mutation_p.R87G			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	87					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)		CATGGGGTCCAGACGGCTAGA	0.652																																					p.R87G		Atlas-SNP	.											.	CNTLN	128	.	0			c.A259G						PASS	.						22	28	26					9																	17135322		1996	4163	6159	SO:0001583	missense	54875	exon1			GGGTCCAGACGGC	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.259A>G	9.37:g.17135322A>G	ENSP00000370021:p.Arg87Gly	76	0	0		49	12	0.244898	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Missense_Mutation	SNP	ENST00000380647.3	37	CCDS43789.1	.	.	.	.	.	.	.	.	.	.	A	13.10	2.135748	0.37728	.	.	ENSG00000044459	ENST00000380647;ENST00000425824;ENST00000262360;ENST00000380641	T;T;T;T	0.14516	2.5;2.5;2.5;2.5	5.4	-5.91	0.02269	.	.	.	.	.	T	0.04182	0.0116	N	0.08118	0	0.09310	N	1	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.41395	-0.9511	9	0.13470	T	0.59	.	2.1611	0.03825	0.2599:0.2501:0.3609:0.1291	.	87;87;87;87	C9J1F9;Q9NXG0-2;Q9NXG0-3;B1AMC8	.;.;.;.	G	87	ENSP00000370021:R87G;ENSP00000392798:R87G;ENSP00000262360:R87G;ENSP00000370015:R87G	ENSP00000262360:R87G	R	+	1	2	CNTLN	17125322	0.756000	0.28383	0.210000	0.23637	0.766000	0.43426	-0.298000	0.08265	-1.336000	0.02238	-0.478000	0.04885	AGA	.	.	none		0.652	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738		G	17135322	A	G	17135322	3	3	30	1	0	0	0	0	1	0	0	0	3641	180	7	3	261	3	CNTLN	9	17135322	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	4359467	17135322	124078109	308	13459											
IFNA21	3452	hgsc.bcm.edu	37	chr9	21166423	21166423	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggttgccatcaaactcctcCtgggggaatccaaagtcatg	10	10	10	11	0	2	0	2	0	0	0	5	1	5	1	4	3	2	1	4	3	3	1	rs1053884	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:21166423C>T	ENST00000380225.1	-	1	236	c.189G>A	c.(187-189)caG>caA	p.Q63Q		NM_002175.2	NP_002166.2	P01568	IFN21_HUMAN	interferon, alpha 21	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)|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)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(3)	14				GBM - Glioblastoma multiforme(5;1.93e-187)|Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		CAAACTCCTCCTGGGGGAATC	0.502													C|||	25	0.00499201	0.0151	0.0072	5008	,	,		20179	0.0		0.0	False		,,,				2504	0.0				p.Q63Q		Atlas-SNP	.											.	IFNA21	25	.	0			c.G189A						PASS	.	C		49,4357		0,49,2154	135	136	135		189	3.1	0	9	dbSNP_86	135	7,8593		0,7,4293	no	coding-synonymous	IFNA21	NM_002175.2		0,56,6447	TT,TC,CC		0.0814,1.1121,0.4306		63/190	21166423	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	3452	exon1			CTCCTCCTGGGGG		CCDS6497.1	9p22	2010-12-10			ENSG00000137080	ENSG00000137080		"Interferons"	5424	protein-coding gene	gene with protein product	"leukocyte interferon protein"	147584				1385305	Standard	NM_002175		Approved	IFN-alphaI	uc003zom.2	P01568	OTTHUMG00000019653	ENST00000380225.1:c.189G>A	9.37:g.21166423C>T		243	0	0		232	121	0.521552	NM_002175	Q14608|Q5VWD1|Q7M4Q4	Silent	SNP	ENST00000380225.1	37	CCDS6497.1																																																																																			C|0.996;T|0.004	0.004	strong		0.502	IFNA21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051882.1	NM_002175		T	21166423	C	T	21166423	2	4	30	1	0	0	0	0	0	0	0	1	7547	680	24	2		2	IFNA21	9	21166423	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	4031101	21166423	120047008	309	13460											
IFNA1	3439	hgsc.bcm.edu	37	chr9	21440916	21440916	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agaaactcccctgatgaatgCggactccatcttggctgtga	10	10	10	11	1	1	4	0	3	1	1	3	5	3	5	3	2	2	1	3	2	2	1	rs2230050	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:21440916C>T	ENST00000276927.1	+	1	477	c.410C>T	c.(409-411)gCg>gTg	p.A137V		NM_024013.2	NP_076918.1	P01562	IFNA1_HUMAN	interferon, alpha 1	137			A -> V (in alpha-1B; dbSNP:rs2230050). {ECO:0000269|Ref.9}.		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)			kidney(1)|large_intestine(1)|lung(3)|ovary(2)	7				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0173)		CTGATGAATGCGGACTCCATC	0.498													c|||	118	0.0235623	0.0764	0.013	5008	,	,		18884	0.001		0.005	False		,,,				2504	0.002				p.A137V		Atlas-SNP	.											IFNA1,NS,carcinoma,-1,1	IFNA1	21	1	0			c.C410T						scavenged	.	C	VAL/ALA	264,3734		11,242,1746	17	21	19		410	0.5	0	9	dbSNP_134	19	25,8205		0,25,4090	no	missense	IFNA1	NM_024013.2	64	11,267,5836	TT,TC,CC		0.3038,6.6033,2.3634	benign	137/190	21440916	289,11939	1999	4115	6114	SO:0001583	missense	3439	exon1			TGAATGCGGACTC		CCDS6508.1	9p22	2010-12-10			ENSG00000197919	ENSG00000197919		"Interferons"	5417	protein-coding gene	gene with protein product	"IFN-alpha 1b", "interferon alpha 1b"	147660				1385305	Standard	NM_024013		Approved	IFNA@, IFL, IFN, IFN-ALPHA, IFNA13, IFN-alphaD	uc003zpd.2	P01562	OTTHUMG00000019673	ENST00000276927.1:c.410C>T	9.37:g.21440916C>T	ENSP00000276927:p.Ala137Val	714	0	0		634	176	0.277603	NM_024013	D4Q9M8|Q14605|Q2M1L8|Q52LB8|Q5VYQ2|Q7M4Q1|Q8WZ68|Q9UMJ3	Missense_Mutation	SNP	ENST00000276927.1	37	CCDS6508.1	.	.	.	.	.	.	.	.	.	.	C	7.309	0.614657	0.14129	0.066033	0.003038	ENSG00000197919	ENST00000276927	T	0.05580	3.42	3.12	0.511	0.16989	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.388379	0.22170	N	0.063657	T	0.00271	0.0008	N	0.11927	0.2	0.09310	N	1	B	0.09022	0.002	B	0.13407	0.009	T	0.43702	-0.9375	10	0.39692	T	0.17	.	3.5529	0.07853	0.5394:0.2403:0.0:0.2203	.	137	P01562	IFNA1_HUMAN	V	137	ENSP00000276927:A137V	ENSP00000276927:A137V	A	+	2	0	IFNA1	21430916	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.127000	0.15790	-0.015000	0.14150	-0.607000	0.04081	GCG	C|0.946;T|0.054	0.054	strong		0.498	IFNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051902.1	NM_024013		T	21440916	C	T	21440916	3	4	30	1	0	0	0	0	1	0	0	0	7540	768	27	1	412	1	IFNA1	9	21440916	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	274493	21440916	119772515	310	13461											
CCL27	10850	hgsc.bcm.edu	37	chr9	34661945	34661945	+	Frame_Shift_Del	DEL	C	C	-																															ttggctattgggggcttcagCccattttccttagcatccca																										TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:34661945delC	ENST00000259631.4	-	3	393	c.335delG	c.(334-336)ggcfs	p.G112fs	RP11-195F19.30_ENST00000564224.1_RNA|CCL27_ENST00000557161.1_5'UTR	NM_006664.2	NP_006655.1	Q9Y4X3	CCL27_HUMAN	chemokine (C-C motif) ligand 27	112					cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|immune response (GO:0006955)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)			kidney(1)|large_intestine(3)|ovary(1)	5	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.173)		GGGGCTTCAGCCCATTTTCCT	0.448																																					p.G112fs		Pindel,Atlas-Indel	.											.	CCL27	6	.	0			c.336delC						PASS	.						88	97	94					9																	34661945		2203	4300	6503	SO:0001589	frameshift_variant	10850	exon3			.	AJ243542	CCDS6569.1	9p13	2014-05-16	2002-08-22	2002-08-23	ENSG00000213927	ENSG00000213927		"Chemokine ligands", "Endogenous ligands"	10626	protein-coding gene	gene with protein product	"CC chemokine ILC", "IL-11 Ralpha-locus chemokine", "cutaneous T-cell attracting chemokine"	604833	"small inducible cytokine subfamily A (Cys-Cys), member 27"	SCYA27		10556532, 10588729	Standard	NM_006664		Approved	ALP, ILC, CTACK, skinkine, ESkine, PESKY, CTAK	uc003zvm.1	Q9Y4X3	OTTHUMG00000019834	ENST00000259631.4:c.335delG	9.37:g.34661945delC	ENSP00000259631:p.Gly112fs	122	0	.		107	32	0.299	NM_006664		Frame_Shift_Del	DEL	ENST00000259631.4	37	CCDS6569.1																																																																																			.	.	none		0.448	CCL27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052228.1	NM_006664		-	34661945	C	-	34661945	7	5	30	1	0	1	0	1	0	0	0	0	2901	739	26	0	7	0	CCL27	9	34661945	Frame_Shift_Del	DEL	C	TCGA-GR-7353-01A-11D-2210-10	13221029	34661945	106551486	311	13462											
FRMPD1	22844	hgsc.bcm.edu	37	chr9	37733752	37733752	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tatttctgctgcccagctacGtttaaattatctacagatcc	10	15	5	11	1	2	1	0	0	2	1	3	1	3	1	2	0	5	3	2	0	6	7	rs140800271	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:37733752G>A	ENST00000539465.1	+	12	1741	c.1148G>A	c.(1147-1149)cGt>cAt	p.R383H	FRMPD1_ENST00000541302.1_Missense_Mutation_p.R252H|FRMPD1_ENST00000536622.1_Missense_Mutation_p.R205H|FRMPD1_ENST00000377765.3_Missense_Mutation_p.R383H|RP11-613M10.9_ENST00000540557.1_Intron			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	383	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.					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)		GCCCAGCTACGTTTAAATTAT	0.343													G|||	16	0.00319489	0.0015	0.0101	5008	,	,		20643	0.0		0.007	False		,,,				2504	0.0				p.R383H		Atlas-SNP	.											.	FRMPD1	237	.	0			c.G1148A						PASS	.	G	HIS/ARG	4,4402	8.1+/-20.4	0,4,2199	143	146	145		1148	5.2	1	9	dbSNP_134	145	29,8571	21.0+/-64.5	0,29,4271	yes	missense	FRMPD1	NM_014907.2	29	0,33,6470	AA,AG,GG		0.3372,0.0908,0.2537	probably-damaging	383/1579	37733752	33,12973	2203	4300	6503	SO:0001583	missense	22844	exon12			AGCTACGTTTAAA	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.1148G>A	9.37:g.37733752G>A	ENSP00000444411:p.Arg383His	109	0	0		126	64	0.507937	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	37	CCDS6612.1	11	0.005036630036630037	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	5	0.006596306068601583	G	25.5	4.643088	0.87859	9.08E-4	0.003372	ENSG00000070601	ENST00000377765;ENST00000539465;ENST00000536622;ENST00000541302	T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16	5.16	5.16	0.70880	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);	0.000000	0.85682	D	0.000000	T	0.81049	0.4742	L	0.60455	1.87	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.64687	0.923;0.928	D	0.84554	0.0646	10	0.66056	D	0.02	-11.2075	16.1394	0.81513	0.0:0.0:1.0:0.0	.	252;383	B4DZC8;Q5SYB0	.;FRPD1_HUMAN	H	383;383;205;252	ENSP00000366995:R383H;ENSP00000444411:R383H;ENSP00000437762:R205H;ENSP00000444804:R252H	ENSP00000366995:R383H	R	+	2	0	FRMPD1	37723752	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.626000	0.83164	2.400000	0.81607	0.609000	0.83330	CGT	G|0.997;A|0.003	0.003	strong		0.343	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		A	37733752	G	A	37733752	3	1	30	1	0	0	0	0	1	0	0	0	6065	1145	40	1	1190	1	FRMPD1	9	37733752	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	3071807	37733752	103479679	312	13463											
TJP2	9414	hgsc.bcm.edu	37	chr9	71851969	71851969	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctggggtgaagaagaaccTgaggaaaagtcgggaagacc	14	5	16	6	1	1	5	0	2	1	3	2	7	1	7	2	4	1	0	2	4	6	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:71851969T>C	ENST00000377245.4	+	14	2304	c.2096T>C	c.(2095-2097)cTg>cCg	p.L699P	TJP2_ENST00000539225.1_Missense_Mutation_p.L730P|TJP2_ENST00000453658.2_Missense_Mutation_p.L676P|TJP2_ENST00000348208.4_Missense_Mutation_p.L699P|TJP2_ENST00000535702.1_Missense_Mutation_p.L703P|TJP2_ENST00000265384.7_Missense_Mutation_p.L699P	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	699	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				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						AAGAAGAACCTGAGGAAAAGT	0.532																																					p.L730P		Atlas-SNP	.											.	TJP2	120	.	0			c.T2189C						PASS	.						155	165	162					9																	71851969		2203	4300	6503	SO:0001583	missense	9414	exon14			AGAACCTGAGGAA	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.2096T>C	9.37:g.71851969T>C	ENSP00000366453:p.Leu699Pro	155	0	0		148	68	0.459459	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Missense_Mutation	SNP	ENST00000377245.4	37	CCDS6627.1	.	.	.	.	.	.	.	.	.	.	T	16.54	3.152156	0.57259	.	.	ENSG00000119139	ENST00000453658;ENST00000377245;ENST00000348208;ENST00000265384;ENST00000535702;ENST00000539225	T;T;T;T;T;T	0.12361	2.72;2.69;2.72;2.71;2.7;2.74	5.77	5.77	0.91146	Src homology-3 domain (1);Guanylate kinase/L-type calcium channel (1);Guanylate kinase (1);	0.374098	0.27927	N	0.017282	T	0.36853	0.0982	M	0.82056	2.57	0.58432	D	0.999998	P;P;D;D;D	0.67145	0.853;0.919;0.963;0.996;0.995	P;P;P;D;D	0.68943	0.502;0.888;0.679;0.95;0.961	T	0.19386	-1.0307	10	0.87932	D	0	.	10.6932	0.45884	0.0:0.0712:0.0:0.9288	.	730;703;699;699;699	F5H301;F5H886;Q9UDY2-2;Q9UDY2;Q9UDY2-5	.;.;.;ZO2_HUMAN;.	P	676;699;699;699;703;730	ENSP00000392178:L676P;ENSP00000366453:L699P;ENSP00000345893:L699P;ENSP00000265384:L699P;ENSP00000442090:L703P;ENSP00000438262:L730P	ENSP00000265384:L699P	L	+	2	0	TJP2	71041789	0.994000	0.37717	0.014000	0.15608	0.620000	0.37586	6.251000	0.72441	2.330000	0.79161	0.528000	0.53228	CTG	.	.	none		0.532	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629		C	71851969	T	C	71851969	3	2	30	1	0	0	0	0	1	0	0	0	15945	1580	55	3	2307	3	TJP2	9	71851969	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	34118217	71851969	69361462	313	13464											
NOL8	55035	hgsc.bcm.edu	37	chr9	95076771	95076771	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgtgaggccgcttgaatcAgaccgctcttcctgtgaagc	8	10	12	11	2	2	4	1	3	1	1	3	5	3	4	3	1	1	2	3	1	2	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:95076771A>C	ENST00000535387.1	-	6	2135	c.2136T>G	c.(2134-2136)tcT>tcG	p.S712S	NOL8_ENST00000358855.4_Silent_p.S644S|NOL8_ENST00000442668.2_Silent_p.S712S|NOL8_ENST00000545558.1_Silent_p.S712S|NOL8_ENST00000542053.1_Silent_p.S644S					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						CGCTTGAATCAGACCGCTCTT	0.428																																					p.S712S		Atlas-SNP	.											.	NOL8	118	.	0			c.T2136G						PASS	.						57	51	53					9																	95076771		1899	4115	6014	SO:0001819	synonymous_variant	55035	exon7			TGAATCAGACCGC	AB109030	CCDS47993.1, CCDS59135.1	9q22.32	2013-02-12	2004-01-12	2004-01-14	ENSG00000198000	ENSG00000198000		"RNA binding motif (RRM) containing"	23387	protein-coding gene	gene with protein product		611534	"chromosome 9 open reading frame 34"	C9orf34		12477932	Standard	NM_017948		Approved	FLJ20736, Nop132	uc022bjx.1	Q76FK4	OTTHUMG00000020221	ENST00000535387.1:c.2136T>G	9.37:g.95076771A>C		98	0	0		90	24	0.266667	NM_017948		Silent	SNP	ENST00000535387.1	37	CCDS47993.1																																																																																			.	.	none		0.428	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948		C	95076771	A	C	95076771	2	2	30	1	0	0	0	0	0	0	0	1	10536	175	7	5		5	NOL8	9	95076771	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	23224802	95076771	46136660	314	13465											
PTCH1	5727	hgsc.bcm.edu	37	chr9	98244242	98244242	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacacttacaggaggtatgcTgtcccagactgtaatttcgc	10	11	9	11	1	0	1	0	0	0	1	2	2	1	2	1	2	2	3	1	2	3	4	rs1805154	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:98244242T>C	ENST00000331920.6	-	5	1034	c.735A>G	c.(733-735)acA>acG	p.T245T	PTCH1_ENST00000437951.1_Silent_p.T179T|PTCH1_ENST00000429896.2_Silent_p.T94T|PTCH1_ENST00000418258.1_Silent_p.T94T|PTCH1_ENST00000468211.2_Silent_p.T179T|PTCH1_ENST00000375274.2_Silent_p.T244T|PTCH1_ENST00000548379.1_5'UTR|PTCH1_ENST00000421141.1_Silent_p.T94T|PTCH1_ENST00000430669.2_Silent_p.T179T	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	245					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)				GGAGGTATGCTGTCCCAGACT	0.388													T|||	47	0.00938498	0.0023	0.0202	5008	,	,		17942	0.0		0.0249	False		,,,				2504	0.0051				p.T245T		Atlas-SNP	.											.	PTCH1	1850	.	0			c.A735G						PASS	.	T	,,,,,,	30,4376	34.3+/-65.2	0,30,2173	84	70	75		735,537,732,282,282,282,282	-2.5	1	9	dbSNP_89	75	329,8271	115.2+/-175.0	4,321,3975	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTCH1	NM_000264.3,NM_001083602.1,NM_001083603.1,NM_001083604.1,NM_001083605.1,NM_001083606.1,NM_001083607.1	,,,,,,	4,351,6148	CC,CT,TT		3.8256,0.6809,2.7603	,,,,,,	245/1448,179/1382,244/1447,94/1297,94/1297,94/1297,94/1297	98244242	359,12647	2203	4300	6503	SO:0001819	synonymous_variant	5727	exon5			GTATGCTGTCCCA	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.735A>G	9.37:g.98244242T>C		106	0	0		95	45	0.473684	NM_000264	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Silent	SNP	ENST00000331920.6	37	CCDS6714.1																																																																																			T|0.976;C|0.024	0.024	strong		0.388	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		C	98244242	T	C	98244242	2	2	30	1	0	0	0	0	0	0	0	1	12742	1567	55	3		3	PTCH1	9	98244242	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	3167471	98244242	42969189	315	13466											
TBC1D2	55357	hgsc.bcm.edu	37	chr9	100961704	100961704	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtcctcgctggcacagccctCggacacagctctgcgccggg	5	6	13	17	4	1	0	0	0	1	0	4	1	2	1	3	3	3	3	3	3	0	0	rs34769888	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:100961704C>T	ENST00000375066.5	-	13	2804	c.2713G>A	c.(2713-2715)Gag>Aag	p.E905K	TBC1D2_ENST00000375064.1_3'UTR|TBC1D2_ENST00000342112.5_Missense_Mutation_p.E698K|TBC1D2_ENST00000375063.1_Missense_Mutation_p.E456K	NM_018421.3	NP_060891.3	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2	916					positive regulation of Rab GTPase activity (GO:0032851)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)	cadherin binding (GO:0045296)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.55e-37)		GCACAGCCCTCGGACACAGCT	0.682													C|||	20	0.00399361	0.0	0.0043	5008	,	,		15710	0.0		0.006	False		,,,				2504	0.0112				p.E916K		Atlas-SNP	.											.	TBC1D2	70	.	0			c.G2746A						PASS	.	C	LYS/GLU	11,4395	16.8+/-37.8	0,11,2192	62	64	63		2713	3.5	0	9	dbSNP_126	63	80,8518	45.8+/-104.6	1,78,4220	yes	missense	TBC1D2	NM_018421.3	56	1,89,6412	TT,TC,CC		0.9304,0.2497,0.6998	benign	905/918	100961704	91,12913	2203	4299	6502	SO:0001583	missense	55357	exon13			AGCCCTCGGACAC	AY026527	CCDS35080.1, CCDS59137.1, CCDS75865.1	9q22.32	2011-11-30			ENSG00000095383	ENSG00000095383			18026	protein-coding gene	gene with protein product	"prostate antigen recognized and identified by SEREX"	609871					Standard	NM_018421		Approved	PARIS1, TBC1D2A, Armus	uc011lvb.2	Q9BYX2	OTTHUMG00000020343	ENST00000375066.5:c.2713G>A	9.37:g.100961704C>T	ENSP00000364207:p.Glu905Lys	144	0	0		135	64	0.474074	NM_001267571	B3KWD1|B4DQ05|B9A6J7|Q59EU0|Q5TBQ5|Q6IPC7|Q7L1K8|Q8WYT1|Q9H6A2|Q9NSH4	Missense_Mutation	SNP	ENST00000375066.5	37	CCDS35080.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	C	16.15	3.041987	0.55003	0.002497	0.009304	ENSG00000095383	ENST00000375066;ENST00000342112;ENST00000375063	T;T;T	0.08896	3.04;3.5;3.11	5.34	3.5	0.40072	.	0.512441	0.20582	N	0.089520	T	0.04907	0.0132	L	0.57536	1.79	0.09310	N	0.999999	B;B	0.33919	0.306;0.432	B;B	0.22386	0.017;0.039	T	0.33317	-0.9873	10	0.13470	T	0.59	.	9.2808	0.37727	0.0:0.8294:0.0:0.1706	rs34769888	916;905	Q9BYX2;Q9BYX2-2	TBD2A_HUMAN;.	K	905;698;456	ENSP00000364207:E905K;ENSP00000341567:E698K;ENSP00000364203:E456K	ENSP00000341567:E698K	E	-	1	0	TBC1D2	100001525	0.612000	0.27000	0.033000	0.17914	0.033000	0.12548	1.029000	0.30140	0.641000	0.30601	0.511000	0.50034	GAG	C|0.994;T|0.006	0.006	strong		0.682	TBC1D2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053367.1	NM_018421		T	100961704	C	T	100961704	3	4	30	1	0	0	0	0	1	0	0	0	15623	893	31	1	44	1	TBC1D2	9	100961704	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	2717462	100961704	40251727	316	13467											
TBC1D2	55357	hgsc.bcm.edu	37	chr9	100971024	100971024	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agcacccggcggagcttgtcGgggaagctggaggtggggca	7	5	20	9	3	0	0	0	0	0	0	1	3	0	3	1	8	3	4	1	8	1	1	rs148143158	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:100971024G>A	ENST00000375064.1	-	9	2114	c.2076C>T	c.(2074-2076)ccC>ccT	p.P692P	TBC1D2_ENST00000342112.5_Silent_p.P474P|TBC1D2_ENST00000375066.5_Silent_p.P692P|TBC1D2_ENST00000493589.2_5'UTR|TBC1D2_ENST00000375063.1_Silent_p.P232P	NM_001267571.1	NP_001254500.1	Q9BYX2	TBD2A_HUMAN	TBC1 domain family, member 2	692	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				positive regulation of Rab GTPase activity (GO:0032851)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)	cadherin binding (GO:0045296)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24		Myeloproliferative disorder(762;0.0255)		OV - Ovarian serous cystadenocarcinoma(323;2.55e-37)		GGAGCTTGTCGGGGAAGCTGG	0.642													G|||	16	0.00319489	0.0	0.0043	5008	,	,		18428	0.0		0.004	False		,,,				2504	0.0092				p.P692P		Atlas-SNP	.											TBC1D2_ENST00000375063,NS,carcinoma,0,2	TBC1D2	70	2	0			c.C2076T						PASS	.	G		9,4397	14.3+/-33.2	0,9,2194	90	89	90		2076	-2.2	1	9	dbSNP_134	90	37,8563	24.6+/-71.5	0,37,4263	yes	coding-synonymous	TBC1D2	NM_018421.3		0,46,6457	AA,AG,GG		0.4302,0.2043,0.3537		692/918	100971024	46,12960	2203	4300	6503	SO:0001819	synonymous_variant	55357	exon9			CTTGTCGGGGAAG	AY026527	CCDS35080.1, CCDS59137.1, CCDS75865.1	9q22.32	2011-11-30			ENSG00000095383	ENSG00000095383			18026	protein-coding gene	gene with protein product	"prostate antigen recognized and identified by SEREX"	609871					Standard	NM_018421		Approved	PARIS1, TBC1D2A, Armus	uc011lvb.2	Q9BYX2	OTTHUMG00000020343	ENST00000375064.1:c.2076C>T	9.37:g.100971024G>A		243	0	0		245	121	0.493878	NM_001267571	B3KWD1|B4DQ05|B9A6J7|Q59EU0|Q5TBQ5|Q6IPC7|Q7L1K8|Q8WYT1|Q9H6A2|Q9NSH4	Silent	SNP	ENST00000375064.1	37																																																																																				G|0.996;A|0.004	0.004	strong		0.642	TBC1D2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000053366.1	NM_018421		A	100971024	G	A	100971024	2	1	30	1	0	0	0	0	0	0	0	1	15623	1103	39	1		1	TBC1D2	9	100971024	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	9320	100971024	40242407	317	13468											
IKBKAP	8518	hgsc.bcm.edu	37	chr9	111665215	111665215	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catggtttaatagccagagaAggtgactctgcaagattcac	13	10	10	8	0	2	3	1	1	1	2	2	4	2	3	1	2	2	2	1	2	4	4	rs35054425	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:111665215A>C	ENST00000374647.5	-	16	2065	c.1758T>G	c.(1756-1758)ccT>ccG	p.P586P	IKBKAP_ENST00000537196.1_Silent_p.P237P	NM_003640.3	NP_003631.2	O95163	ELP1_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein	586					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						TAGCCAGAGAAGGTGACTCTG	0.423													A|||	73	0.0145767	0.0015	0.0058	5008	,	,		15642	0.0		0.0089	False		,,,				2504	0.0593				p.P586P		Atlas-SNP	.											.	IKBKAP	122	.	0			c.T1758G						PASS	.	A		8,4398	12.9+/-30.5	0,8,2195	84	84	84		1758	-1.3	1	9	dbSNP_126	84	131,8469	67.0+/-129.4	1,129,4170	no	coding-synonymous	IKBKAP	NM_003640.3		1,137,6365	CC,CA,AA		1.5233,0.1816,1.0687		586/1333	111665215	139,12867	2203	4300	6503	SO:0001819	synonymous_variant	8518	exon16			CAGAGAAGGTGAC	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.1758T>G	9.37:g.111665215A>C		133	0	0		118	50	0.423729	NM_003640	Q5JSV2|Q9H327|Q9UG87	Silent	SNP	ENST00000374647.5	37	CCDS6773.1																																																																																			A|0.990;C|0.010	0.010	strong		0.423	IKBKAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053574.1			C	111665215	A	C	111665215	2	2	30	1	0	0	0	0	0	0	0	1	7619	59	3	5		5	IKBKAP	9	111665215	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	10694191	111665215	29548216	318	13469											
PRPF4	9128	hgsc.bcm.edu	37	chr9	116045007	116045007	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagaagtctaaaaagtccaaAgaagaggtagaacatgtctt	18	8	10	5	0	2	4	0	0	2	4	3	5	3	4	1	1	1	1	1	1	8	3	rs148684386	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:116045007A>C	ENST00000374198.4	+	4	579	c.477A>C	c.(475-477)aaA>aaC	p.K159N	PRPF4_ENST00000488937.1_3'UTR|PRPF4_ENST00000374199.4_Missense_Mutation_p.K158N	NM_001244926.1|NM_004697.4	NP_001231855.1|NP_004688.2	O43172	PRP4_HUMAN	pre-mRNA processing factor 4	159					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						AAAAGTCCAAAGAAGAGGTAG	0.348																																					p.K159N		Atlas-SNP	.											.	PRPF4	56	.	0			c.A477C						PASS	.	A	ASN/LYS	1,4405	2.1+/-5.4	0,1,2202	78	76	77		477	3.5	1	9	dbSNP_134	77	3,8597	2.2+/-6.3	0,3,4297	yes	missense	PRPF4	NM_004697.3	94	0,4,6499	CC,CA,AA		0.0349,0.0227,0.0308	benign	159/523	116045007	4,13002	2203	4300	6503	SO:0001583	missense	9128	exon4			GTCCAAAGAAGAG	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.477A>C	9.37:g.116045007A>C	ENSP00000363313:p.Lys159Asn	162	0	0		127	61	0.480315	NM_004697	O43445|O43864|Q5T1M8|Q96DG2|Q96IK4	Missense_Mutation	SNP	ENST00000374198.4	37	CCDS6791.1	.	.	.	.	.	.	.	.	.	.	A	12.32	1.901787	0.33535	2.27E-4	3.49E-4	ENSG00000136875	ENST00000374199;ENST00000374198	T;T	0.63417	-0.04;0.01	5.9	3.5	0.40072	.	0.381275	0.33005	N	0.005394	T	0.45054	0.1323	L	0.29908	0.895	0.44012	D	0.996725	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.22521	-1.0214	10	0.35671	T	0.21	.	6.3671	0.21461	0.7403:0.1367:0.123:0.0	.	174;159	Q59EL4;O43172	.;PRP4_HUMAN	N	158;159	ENSP00000363315:K158N;ENSP00000363313:K159N	ENSP00000363313:K159N	K	+	3	2	PRPF4	115084828	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	1.947000	0.40293	0.462000	0.27095	0.460000	0.39030	AAA	A|0.999;C|0.001	0.001	strong		0.348	PRPF4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053708.2	NM_004697		C	116045007	A	C	116045007	3	2	30	1	0	0	0	0	1	0	0	0	12582	69	3	5	491	5	PRPF4	9	116045007	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	4379792	116045007	25168424	319	13470											
HDHD3	81932	hgsc.bcm.edu	37	chr9	116136262	116136262	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagtctcagaccccgtgtgcGgcactccctcagggtgtcct	5	9	11	16	2	2	1	2	0	1	1	5	1	4	1	4	2	1	1	4	2	0	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:116136262G>A	ENST00000238379.5	-	2	1270	c.373C>T	c.(373-375)Cgc>Tgc	p.R125C	HDHD3_ENST00000374180.3_Missense_Mutation_p.R125C|HDHD3_ENST00000485934.1_5'UTR	NM_031219.2	NP_112496.1	Q9BSH5	HDHD3_HUMAN	haloacid dehalogenase-like hydrolase domain containing 3	125						mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			large_intestine(2)|liver(1)	3						CCCCGTGTGCGGCACTCCCTC	0.597																																					p.R125C		Atlas-SNP	.											.	HDHD3	10	.	0			c.C373T						PASS	.						120	127	125					9																	116136262		2203	4300	6503	SO:0001583	missense	81932	exon2			GTGTGCGGCACTC	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.373C>T	9.37:g.116136262G>A	ENSP00000238379:p.Arg125Cys	116	0	0		145	75	0.517241	NM_031219	B2RD47	Missense_Mutation	SNP	ENST00000238379.5	37	CCDS6793.1	.	.	.	.	.	.	.	.	.	.	G	14.42	2.529009	0.44969	.	.	ENSG00000119431	ENST00000238379;ENST00000374180	T;T	0.06687	3.27;3.27	5.76	5.76	0.90799	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (2);	0.421114	0.26963	N	0.021610	T	0.34861	0.0912	M	0.92507	3.315	0.53688	D	0.999974	D	0.89917	1.0	P	0.62089	0.898	T	0.34775	-0.9815	10	0.87932	D	0	-14.3793	13.8598	0.63552	0.0:0.0:0.8475:0.1525	.	125	Q9BSH5	HDHD3_HUMAN	C	125	ENSP00000238379:R125C;ENSP00000363295:R125C	ENSP00000238379:R125C	R	-	1	0	HDHD3	115176083	0.955000	0.32602	0.998000	0.56505	0.238000	0.25445	1.482000	0.35486	2.721000	0.93114	0.655000	0.94253	CGC	.	.	none		0.597	HDHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053731.1	NM_031219		A	116136262	G	A	116136262	3	1	30	1	0	0	0	0	1	0	0	0	7033	1116	39	1	386	1	HDHD3	9	116136262	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	91255	116136262	25077169	320	13471											
ASTN2	23245	hgsc.bcm.edu	37	chr9	119770495	119770495	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttggccgggtttaaccagtcGgagatgtccaggtagctccc	7	10	13	11	2	0	1	0	0	0	1	3	2	2	1	4	4	2	3	4	4	2	4	rs61736198	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:119770495G>A	ENST00000313400.4	-	7	1567	c.1467C>T	c.(1465-1467)tcC>tcT	p.S489S	ASTN2_ENST00000361477.3_5'UTR|ASTN2_ENST00000373996.3_Silent_p.S489S|ASTN2_ENST00000361209.2_Silent_p.S438S			O75129	ASTN2_HUMAN	astrotactin 2	489					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						TTAACCAGTCGGAGATGTCCA	0.512													G|||	38	0.00758786	0.0008	0.0058	5008	,	,		20493	0.0159		0.0089	False		,,,				2504	0.0082				p.S438S		Atlas-SNP	.											.	ASTN2	307	.	0			c.C1314T						PASS	.	G		8,4398	14.3+/-33.2	0,8,2195	112	96	101		1314	-9.3	0.4	9	dbSNP_129	101	42,8558	28.5+/-78.6	1,40,4259	no	coding-synonymous	ASTN2	NM_014010.4		1,48,6454	AA,AG,GG		0.4884,0.1816,0.3844		438/1289	119770495	50,12956	2203	4300	6503	SO:0001819	synonymous_variant	23245	exon6			CCAGTCGGAGATG	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.1467C>T	9.37:g.119770495G>A		189	0	0		225	101	0.448889	NM_014010	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Silent	SNP	ENST00000313400.4	37																																																																																				G|0.994;A|0.006	0.006	strong		0.512	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010		A	119770495	G	A	119770495	2	1	30	1	0	0	0	0	0	0	0	1	1065	1103	39	1		1	ASTN2	9	119770495	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	3634233	119770495	21442936	321	13472											
CCBL1	883	hgsc.bcm.edu	37	chr9	131600394	131600394	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcatgggctcgtagcagtcaAaaaagggttcgatgatgatg	12	10	13	6	2	2	2	2	2	0	0	4	3	2	2	0	2	1	4	0	2	4	2	rs371451324		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:131600394A>G	ENST00000302586.3	-	5	536	c.374T>C	c.(373-375)tTt>tCt	p.F125S	CCBL1_ENST00000436267.2_Missense_Mutation_p.F219S|CCBL1_ENST00000483599.1_5'UTR|CCBL1_ENST00000320665.6_Missense_Mutation_p.F75S	NM_001122671.1|NM_004059.4	NP_001116143.1|NP_004050.3	Q16773	KAT1_HUMAN	cysteine conjugate-beta lyase, cytoplasmic	125					cellular amino acid biosynthetic process (GO:0008652)|cellular modified amino acid metabolic process (GO:0006575)|cellular nitrogen compound metabolic process (GO:0034641)|kynurenine metabolic process (GO:0070189)|L-kynurenine catabolic process (GO:0097053)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-S-conjugate beta-lyase activity (GO:0047804)|glutamine-phenylpyruvate transaminase activity (GO:0047316)|kynurenine-oxoglutarate transaminase activity (GO:0016212)|L-glutamine:pyruvate aminotransferase activity (GO:0047945)|L-phenylalanine-oxaloacetate transaminase activity (GO:0036141)|L-phenylalanine:pyruvate aminotransferase activity (GO:0047312)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(1)|skin(1)	18					L-Glutamine(DB00130)	GTAGCAGTCAAAAAAGGGTTC	0.542																																					p.F125S		Atlas-SNP	.											.	CCBL1	36	.	0			c.T374C						PASS	.	A	SER/PHE,SER/PHE,SER/PHE	0,4402		0,0,2201	165	174	171		374,224,374	5.1	1	9		171	1,8585	1.2+/-3.3	0,1,4292	no	missense,missense,missense	CCBL1	NM_001122671.1,NM_001122672.1,NM_004059.4	155,155,155	0,1,6493	GG,GA,AA		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging	125/423,75/373,125/423	131600394	1,12987	2201	4293	6494	SO:0001583	missense	883	exon5			CAGTCAAAAAAGG	Y17448	CCDS43884.1, CCDS48038.1, CCDS75915.1	9q34.11	2008-03-11	2008-03-11		ENSG00000171097	ENSG00000171097	2.6.1.64		1564	protein-coding gene	gene with protein product	"glutamine transaminase K", "kyneurenine aminotransferase"	600547	"cysteine conjugate-beta lyase; cytoplasmic (glutamine transaminase K, kyneurenine aminotransferase)"			7883047	Standard	NM_001122671		Approved	KATI, GTK	uc004bwh.3	Q16773	OTTHUMG00000020767	ENST00000302586.3:c.374T>C	9.37:g.131600394A>G	ENSP00000302227:p.Phe125Ser	234	1	0.0042735		197	99	0.502538	NM_001122671	Q5T275|Q8N191	Missense_Mutation	SNP	ENST00000302586.3	37	CCDS43884.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.698125	0.88830	0.0	1.16E-4	ENSG00000171097	ENST00000302586;ENST00000320665;ENST00000436267;ENST00000451800;ENST00000416084	D;D;D;D;D	0.91351	-2.83;-2.83;-2.83;-2.83;-2.83	5.12	5.12	0.69794	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	0.96731	0.8933	H	0.95950	3.745	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	D	0.97818	1.0255	10	0.87932	D	0	-33.2894	13.7717	0.63029	1.0:0.0:0.0:0.0	.	219;125;75;125;125	B7Z4W5;A8K563;Q16773-2;Q16773;Q5T278	.;.;.;KAT1_HUMAN;.	S	125;75;219;125;125	ENSP00000302227:F125S;ENSP00000317342:F75S;ENSP00000399415:F219S;ENSP00000390377:F125S;ENSP00000412402:F125S	ENSP00000302227:F125S	F	-	2	0	CCBL1	130640215	1.000000	0.71417	0.977000	0.42913	0.944000	0.59088	6.220000	0.72237	1.927000	0.55829	0.528000	0.53228	TTT	.	.	weak		0.542	CCBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054521.2			G	131600394	A	G	131600394	3	3	30	1	0	0	0	0	1	0	0	0	2734	14	1	3	930	3	CCBL1	9	131600394	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	11829899	131600394	9613037	322	13473											
ASB6	140459	hgsc.bcm.edu	37	chr9	132401753	132401753	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccggctggttccgcaggacGgcgatgtgcaaggccgtgta	6	8	16	11	5	0	0	0	0	0	0	2	2	2	1	3	5	1	5	3	5	2	2	rs144137235		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:132401753G>A	ENST00000277458.4	-	3	495	c.330C>T	c.(328-330)gcC>gcT	p.A110A	ASB6_ENST00000277459.4_Silent_p.A110A|ASB6_ENST00000450050.2_Silent_p.A31A|RP11-483H20.4_ENST00000455074.1_RNA	NM_017873.3	NP_060343.1	Q9NWX5	ASB6_HUMAN	ankyrin repeat and SOCS box containing 6	110					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)				TCCGCAGGACGGCGATGTGCA	0.607													G|||	1	0.000199681	0.0	0.0	5008	,	,		18818	0.0		0.001	False		,,,				2504	0.0				p.A110A		Atlas-SNP	.											.	ASB6	31	.	0			c.C330T						PASS	.	G	,,	1,4405	2.1+/-5.4	0,1,2202	55	53	54		330,330,330	-7.5	0.4	9	dbSNP_134	54	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	ASB6	NM_001202403.1,NM_017873.3,NM_177999.2	,,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	,,	110/393,110/422,110/198	132401753	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	140459	exon3			CAGGACGGCGATG		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.330C>T	9.37:g.132401753G>A		82	0	0		81	34	0.419753	NM_017873	Q5SZB7|Q9BV15	Silent	SNP	ENST00000277458.4	37	CCDS6924.1																																																																																			G|0.999;A|0.001	0.001	strong		0.607	ASB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054594.1	NM_017873		A	132401753	G	A	132401753	2	1	30	1	0	0	0	0	0	0	0	1	1027	1103	39	1		1	ASB6	9	132401753	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	801359	132401753	8811678	323	13474											
GTF3C4	9329	hgsc.bcm.edu	37	chr9	135546021	135546021	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caggcccgggtggggcccgcGgacgacgggcctgcgccgtc	3	3	19	16	7	0	0	0	0	0	0	1	2	0	1	4	6	1	0	4	6	0	0	rs146201597	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:135546021G>A	ENST00000372146.4	+	1	600	c.36G>A	c.(34-36)gcG>gcA	p.A12A	DDX31_ENST00000544003.1_5'Flank|DDX31_ENST00000372153.1_5'Flank|DDX31_ENST00000480876.1_5'Flank|GTF3C4_ENST00000483873.2_Silent_p.A12A|DDX31_ENST00000310532.2_5'Flank|DDX31_ENST00000372159.3_5'Flank	NM_012204.2	NP_036336.2	Q9UKN8	TF3C4_HUMAN	general transcription factor IIIC, polypeptide 4, 90kDa	12					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)		TGGGGCCCGCGGACGACGGGC	0.771													G|||	81	0.0161741	0.0045	0.0202	5008	,	,		9102	0.0		0.0338	False		,,,				2504	0.0276				p.A12A	Pancreas(142;417 1875 11086 31973 47667)	Atlas-SNP	.											.	GTF3C4	53	.	0			c.G36A						PASS	.	G		13,2385		0,13,1186	3	4	4		36	2.4	0.9	9	dbSNP_134	4	168,5390		0,168,2611	no	coding-synonymous	GTF3C4	NM_012204.2		0,181,3797	AA,AG,GG		3.0227,0.5421,2.275		12/823	135546021	181,7775	1199	2779	3978	SO:0001819	synonymous_variant	9329	exon1			GCCCGCGGACGAC	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.36G>A	9.37:g.135546021G>A		13	0	0		9	8	0.888889	NM_012204	Q5VZJ7	Silent	SNP	ENST00000372146.4	37	CCDS6953.1																																																																																			G|0.986;A|0.014	0.014	strong		0.771	GTF3C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054792.1			A	135546021	G	A	135546021	2	1	30	1	0	0	0	0	0	0	0	1	6884	1103	39	1		1	GTF3C4	9	135546021	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	3144268	135546021	5667410	324	13475											
GBGT1	26301	hgsc.bcm.edu	37	chr9	136029138	136029138	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccgccaggcagccatgatGccattggccttgtccgccag	6	8	11	16	2	0	1	0	1	0	0	2	1	2	1	7	2	2	1	7	2	0	2	rs35902535	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:136029138G>A	ENST00000372040.3	-	7	1181	c.870C>T	c.(868-870)ggC>ggT	p.G290G	GBGT1_ENST00000540636.1_Silent_p.G273G|GBGT1_ENST00000372043.3_Missense_Mutation_p.A284V|RALGDS_ENST00000542690.1_Intron|GBGT1_ENST00000472281.1_5'UTR	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	290					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)		CAGCCATGATGCCATTGGCCT	0.587													G|||	210	0.0419329	0.0333	0.0403	5008	,	,		17659	0.002		0.0795	False		,,,				2504	0.0573				p.G290G		Atlas-SNP	.											.	GBGT1	25	.	0			c.C870T						PASS	.	G		200,4206	124.9+/-162.1	8,184,2011	121	113	116		870	2.3	1	9	dbSNP_126	116	618,7982	160.3+/-213.4	16,586,3698	no	coding-synonymous	GBGT1	NM_021996.4		24,770,5709	AA,AG,GG		7.186,4.5393,6.2894		290/348	136029138	818,12188	2203	4300	6503	SO:0001819	synonymous_variant	26301	exon7			CATGATGCCATTG	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.870C>T	9.37:g.136029138G>A		122	0	0		140	68	0.485714	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Silent	SNP	ENST00000372040.3	37	CCDS6960.1	105	0.04807692307692308	21	0.042682926829268296	15	0.04143646408839779	2	0.0034965034965034965	67	0.08839050131926121	G	12.72	2.022220	0.35701	0.045393	0.07186	ENSG00000148288	ENST00000372043	T	0.23348	1.91	5.38	2.31	0.28768	.	.	.	.	.	T	0.01287	0.0042	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.00460	-1.1726	6	0.87932	D	0	-15.1162	5.0909	0.14708	0.2677:0.3054:0.4269:0.0	rs35902535;rs62638711	.	.	.	V	284	ENSP00000361113:A284V	ENSP00000361113:A284V	A	-	2	0	GBGT1	135018959	0.629000	0.27146	0.992000	0.48379	0.929000	0.56500	0.761000	0.26489	0.542000	0.28846	0.561000	0.74099	GCA	G|0.944;A|0.056	0.056	strong		0.587	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996		A	136029138	G	A	136029138	2	1	30	1	0	0	0	0	0	0	0	1	6280	1306	46	2		2	GBGT1	9	136029138	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	483117	136029138	5184293	325	13476											
GBGT1	26301	hgsc.bcm.edu	37	chr9	136029645	136029645	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaggactggatgaaatgagtGtacctagtgatgatcacccg	13	9	12	7	1	1	4	1	4	0	0	1	6	1	6	2	2	1	1	2	2	4	2	rs35898523	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:136029645G>T	ENST00000372040.3	-	7	674	c.363C>A	c.(361-363)taC>taA	p.Y121*	GBGT1_ENST00000540636.1_Nonsense_Mutation_p.Y104*|GBGT1_ENST00000372043.3_Intron|RALGDS_ENST00000542690.1_Intron|GBGT1_ENST00000372038.3_Missense_Mutation_p.H134N|GBGT1_ENST00000472281.1_5'UTR	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	121					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)		TGAAATGAGTGTACCTAGTGA	0.587													G|||	215	0.0429313	0.034	0.0418	5008	,	,		18455	0.002		0.0815	False		,,,				2504	0.0583				p.Y121X		Atlas-SNP	.											GBGT1,NS,carcinoma,-2,1	GBGT1	25	1	0			c.C363A						PASS	.	G	stop/TYR	199,4207	121.7+/-159.2	8,183,2012	39	40	39		363	1.5	0.9	9	dbSNP_126	39	629,7971	155.7+/-209.7	18,593,3689	yes	stop-gained	GBGT1	NM_021996.4		26,776,5701	TT,TG,GG		7.314,4.5166,6.3663		121/348	136029645	828,12178	2203	4300	6503	SO:0001587	stop_gained	26301	exon7			ATGAGTGTACCTA	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.363C>A	9.37:g.136029645G>T	ENSP00000361110:p.Tyr121*	24	0	0		23	7	0.304348	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Nonsense_Mutation	SNP	ENST00000372040.3	37	CCDS6960.1	108|108	0.04945054945054945|0.04945054945054945	23|23	0.046747967479674794|0.046747967479674794	16|16	0.04419889502762431|0.04419889502762431	2|2	0.0034965034965034965|0.0034965034965034965	67|67	0.08839050131926121|0.08839050131926121	G|G	17.35|17.35	3.367115|3.367115	0.61513|0.61513	0.045166|0.045166	0.07314|0.07314	ENSG00000148288|ENSG00000148288	ENST00000372038|ENST00000372040;ENST00000540636	T|.	0.36157|.	1.27|.	5.38|5.38	1.47|1.47	0.22746|0.22746	.|.	.|0.137701	.|0.50627	.|D	.|0.000106	T|.	0.01156|.	0.0038|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.02358|.	-1.1171|.	6|.	0.05833|0.07813	T|T	0.94|0.8	-15.2709|-15.2709	6.0904|6.0904	0.19991|0.19991	0.2143:0.0:0.6535:0.1322|0.2143:0.0:0.6535:0.1322	rs35898523;rs62638704|rs35898523;rs62638704	.|.	.|.	.|.	N|X	134|121;104	ENSP00000361108:H134N|.	ENSP00000361108:H134N|ENSP00000361110:Y121X	H|Y	-|-	1|3	0|2	GBGT1|GBGT1	135019466|135019466	0.883000|0.883000	0.30277|0.30277	0.900000|0.900000	0.35374|0.35374	0.243000|0.243000	0.25628|0.25628	0.687000|0.687000	0.25407|0.25407	0.008000|0.008000	0.14787|0.14787	0.491000|0.491000	0.48974|0.48974	CAC|TAC	G|0.941;T|0.059	0.059	strong		0.587	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996		T	136029645	G	T	136029645	4	4	30	1	0	0	0	0	0	1	0	0	6280	1372	48	4	684	4	GBGT1	9	136029645	Nonsense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	507	136029645	5183786	326	13477											
COL5A1	1289	hgsc.bcm.edu	37	chr9	137734084	137734084	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatcgtggacatcatgttcAatgacttcggtgaagcgtca	10	11	10	10	3	3	2	3	2	0	0	5	3	3	3	1	2	1	1	1	2	2	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:137734084A>G	ENST00000371817.3	+	66	5866	c.5452A>G	c.(5452-5454)Aat>Gat	p.N1818D		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	1818	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)		CATCATGTTCAATGACTTCGG	0.577																																					p.N1818D		Atlas-SNP	.											.	COL5A1	323	.	0			c.A5452G						PASS	.						129	125	126					9																	137734084		2203	4300	6503	SO:0001583	missense	1289	exon66			ATGTTCAATGACT	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.5452A>G	9.37:g.137734084A>G	ENSP00000360882:p.Asn1818Asp	156	0	0		144	68	0.472222	NM_000093	Q15094|Q5SUX4	Missense_Mutation	SNP	ENST00000371817.3	37	CCDS6982.1	.	.	.	.	.	.	.	.	.	.	A	16.41	3.114962	0.56505	.	.	ENSG00000130635	ENST00000371817;ENST00000355306	T	0.73152	-0.72	4.72	4.72	0.59763	Fibrillar collagen, C-terminal (4);	0.069214	0.53938	U	0.000046	T	0.69278	0.3093	M	0.70595	2.14	0.42323	D	0.992266	P	0.38280	0.625	B	0.37508	0.252	T	0.70575	-0.4834	10	0.33940	T	0.23	.	14.1846	0.65598	1.0:0.0:0.0:0.0	.	1818	P20908	CO5A1_HUMAN	D	1818;355	ENSP00000360882:N1818D	ENSP00000347458:N355D	N	+	1	0	COL5A1	136873905	1.000000	0.71417	0.986000	0.45419	0.997000	0.91878	9.057000	0.93889	1.765000	0.52091	0.460000	0.39030	AAT	.	.	none		0.577	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093		G	137734084	A	G	137734084	3	3	30	1	0	0	0	0	1	0	0	0	3698	130	5	3	5714	3	COL5A1	9	137734084	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	1704439	137734084	3479347	327	13478											
C9orf172	389813	hgsc.bcm.edu	37	chr9	139740436	139740436	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gccgcgcgggcgagggcctgGgccgcaactggtacgtgacg	5	4	19	13	7	0	1	0	1	0	0	0	2	0	1	3	4	2	2	3	4	2	1	rs375030600		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:139740436G>A	ENST00000436881.1	+	1	1570	c.1570G>A	c.(1570-1572)Ggc>Agc	p.G524S	PHPT1_ENST00000371661.1_5'Flank|PHPT1_ENST00000545326.1_5'Flank	NM_001080482.2	NP_001073951.2	C9J069	CI172_HUMAN	chromosome 9 open reading frame 172	524										endometrium(2)|large_intestine(1)|lung(6)	9						CGAGGGCCTGGGCCGCAACTG	0.711																																					p.G524S		Atlas-SNP	.											.	C9orf172	23	.	0			c.G1570A						PASS	.	G	SER/GLY	0,3880		0,0,1940	7	8	8		1570	1.4	1	9		8	1,8013		0,1,4006	no	missense	C9orf172	NM_001080482.2	56	0,1,5946	AA,AG,GG		0.0125,0.0,0.0084	possibly-damaging	524/977	139740436	1,11893	1940	4007	5947	SO:0001583	missense	389813	exon1			GGCCTGGGCCGCA		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.1570G>A	9.37:g.139740436G>A	ENSP00000412388:p.Gly524Ser	81	0	0		63	37	0.587302	NM_001080482		Missense_Mutation	SNP	ENST00000436881.1	37	CCDS48059.1	.	.	.	.	.	.	.	.	.	.	.	7.729	0.698804	0.15106	0.0	1.25E-4	ENSG00000232434	ENST00000436881	.	.	.	3.54	1.41	0.22369	.	.	.	.	.	T	0.18718	0.0449	N	0.12746	0.255	0.26736	N	0.970498	P	0.36683	0.565	B	0.34385	0.181	T	0.12319	-1.0552	8	0.30078	T	0.28	-13.7135	9.0585	0.36421	0.2261:0.0:0.7739:0.0	.	524	C9J069	CI172_HUMAN	S	524	.	ENSP00000412388:G524S	G	+	1	0	C9orf172	138860257	0.337000	0.24766	0.990000	0.47175	0.802000	0.45316	0.645000	0.24782	0.670000	0.31165	0.472000	0.43445	GGC	.	.	weak		0.711	C9orf172-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080482		A	139740436	G	A	139740436	3	1	30	1	0	0	0	0	1	0	0	0	2473	1232	43	2	1572	2	C9orf172	9	139740436	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2006352	139740436	1472995	328	13479											
PHPT1	29085	hgsc.bcm.edu	37	chr9	139744524	139744524	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaggctgcgactgtgagtgtCtgggcggcgggcgcatctcc	5	8	17	11	4	2	1	0	1	2	0	3	2	2	1	1	4	1	2	1	4	1	0	rs8666	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:139744524C>T	ENST00000247665.10	+	2	557	c.220C>T	c.(220-222)Ctg>Ttg	p.L74L	MAMDC4_ENST00000317446.2_5'Flank|MAMDC4_ENST00000445819.1_5'Flank|PHPT1_ENST00000371661.1_Silent_p.L74L|PHPT1_ENST00000492540.1_3'UTR|PHPT1_ENST00000545326.1_Silent_p.L74L	NM_014172.4	NP_054891.2	Q9NRX4	PHP14_HUMAN	phosphohistidine phosphatase 1	74					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)		CTGTGAGTGTCTGGGCGGCGG	0.662													C|||	214	0.0427316	0.0015	0.0202	5008	,	,		14400	0.0089		0.0318	False		,,,				2504	0.1605				p.L74L		Atlas-SNP	.											.	PHPT1	14	.	0			c.C220T						PASS	.	C	,	33,4373		0,33,2170	104	100	101		220,220	4.6	1	9	dbSNP_52	101	283,8317		5,273,4022	no	coding-synonymous,coding-synonymous	PHPT1	NM_001135861.1,NM_014172.4	,	5,306,6192	TT,TC,CC		3.2907,0.749,2.4296	,	74/125,74/126	139744524	316,12690	2203	4300	6503	SO:0001819	synonymous_variant	29085	exon2			GAGTGTCTGGGCG	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.220C>T	9.37:g.139744524C>T		167	0	0		176	82	0.465909	NM_001135861	B1AMX0|B1AMX1|Q9H0Y3	Silent	SNP	ENST00000247665.10	37	CCDS7009.1																																																																																			C|0.972;T|0.028	0.028	strong		0.662	PHPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055150.1	NM_014172		T	139744524	C	T	139744524	2	4	30	1	0	0	0	0	0	0	0	1	11869	912	32	2		2	PHPT1	9	139744524	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	4088	139744524	1468907	329	13480											
FBXW5	54461	hgsc.bcm.edu	37	chr9	139836694	139836694	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagaaagtgccgcaagccCtccttggcgtgggcgggggc	6	6	16	13	3	0	1	0	0	0	1	2	1	2	1	4	4	2	1	4	4	2	1	rs34391108	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr9:139836694C>T	ENST00000325285.3	-	6	979	c.900G>A	c.(898-900)gaG>gaA	p.E300E	FBXW5_ENST00000483559.1_5'UTR	NM_018998.3	NP_061871.1	Q969U6	FBXW5_HUMAN	F-box and WD repeat domain containing 5	300					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)		GCCGCAAGCCCTCCTTGGCGT	0.711													C|||	176	0.0351438	0.0023	0.0259	5008	,	,		15047	0.004		0.0477	False		,,,				2504	0.1053				p.E300E		Atlas-SNP	.											.	FBXW5	36	.	0			c.G900A						PASS	.	C		38,4292		1,36,2128	11	14	13		900	0.9	0.9	9	dbSNP_126	13	318,8216		4,310,3953	no	coding-synonymous	FBXW5	NM_018998.2		5,346,6081	TT,TC,CC		3.7263,0.8776,2.7674		300/567	139836694	356,12508	2165	4267	6432	SO:0001819	synonymous_variant	54461	exon6			CAAGCCCTCCTTG	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.900G>A	9.37:g.139836694C>T		40	0	0		7	6	0.857143	NM_018998	B2RDZ6|Q59ET5|Q5SPZ8|Q5SPZ9|Q5SQ00|Q5SQ02|Q5SQ03|Q5SQ04|Q8WY79|Q96GJ6|Q9BSU8|Q9H6A8|Q9HBQ6|Q9NSZ3	Silent	SNP	ENST00000325285.3	37	CCDS7014.1																																																																																			C|0.975;T|0.025	0.025	strong		0.711	FBXW5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055227.1	NM_018998		T	139836694	C	T	139836694	2	4	30	1	0	0	0	0	0	0	0	1	5776	680	24	2		2	FBXW5	9	139836694	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	92170	139836694	1376737	330	13481											
LARP4B	23185	hgsc.bcm.edu	37	chr10	909711	909711	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctattttcaggcagagagtcAtattctgagggacccagagc	11	10	11	9	0	3	3	2	1	1	2	3	5	3	4	1	2	1	1	1	2	2	5			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:909711A>G	ENST00000316157.3	-	4	442	c.402T>C	c.(400-402)taT>taC	p.Y134Y		NM_015155.1	NP_055970.1	Q92615	LAR4B_HUMAN	La ribonucleoprotein domain family, member 4B	134					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						GCAGAGAGTCATATTCTGAGG	0.473																																					p.Y134Y		Atlas-SNP	.											.	LARP4B	110	.	0			c.T402C						PASS	.						99	100	100					10																	909711		2203	4300	6503	SO:0001819	synonymous_variant	23185	exon5			AGAGTCATATTCT	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.402T>C	10.37:g.909711A>G		112	0	0		70	10	0.142857	NM_015155	A7MD20|Q5T3R3|Q5T3R4|Q5T3R5|Q68CY4	Silent	SNP	ENST00000316157.3	37	CCDS31131.1																																																																																			.	.	none		0.473	LARP4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046395.2	NM_015155		G	909711	A	G	909711	2	3	30	1	0	0	0	0	0	0	0	1	8640	224	8	3		3	LARP4B	10	909711	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10		909711	134625036	331	13482											
RBM17	84991	hgsc.bcm.edu	37	chr10	6139078	6139078	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaccagtgactcaaaaacagAaggctggtccaaaaacttca	17	6	8	10	0	2	2	2	1	0	1	3	3	3	2	2	2	2	1	2	2	5	1			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:6139078A>G	ENST00000446108.1	+	2	694	c.50A>G	c.(49-51)gAa>gGa	p.E17G	RBM17_ENST00000379888.4_Missense_Mutation_p.E17G	NM_001145547.1	NP_001139019.1	Q96I25	SPF45_HUMAN	RNA binding motif protein 17	17					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						TCAAAAACAGAAGGCTGGTCC	0.468																																					p.E17G		Atlas-SNP	.											.	RBM17	45	.	0			c.A50G						PASS	.						106	106	106					10																	6139078		2203	4300	6503	SO:0001583	missense	84991	exon2			AAACAGAAGGCTG	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.50A>G	10.37:g.6139078A>G	ENSP00000388638:p.Glu17Gly	174	0	0		118	5	0.0423729	NM_001145547	Q96GY6	Missense_Mutation	SNP	ENST00000446108.1	37	CCDS7077.1	.	.	.	.	.	.	.	.	.	.	A	19.61	3.859257	0.71834	.	.	ENSG00000134453	ENST00000379888;ENST00000432931;ENST00000446108;ENST00000418631	T;T;T;T	0.56611	0.45;0.45;0.45;0.45	4.64	3.5	0.40072	.	0.049423	0.85682	N	0.000000	T	0.41534	0.1163	L	0.51422	1.61	0.80722	D	1	P	0.39216	0.664	B	0.32928	0.155	T	0.25502	-1.0130	10	0.40728	T	0.16	-25.6691	10.0431	0.42171	0.9194:0.0:0.0806:0.0	.	17	Q96I25	SPF45_HUMAN	G	17	ENSP00000369218:E17G;ENSP00000408214:E17G;ENSP00000388638:E17G;ENSP00000402303:E17G	ENSP00000369218:E17G	E	+	2	0	RBM17	6179084	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.815000	0.91973	0.738000	0.32606	0.377000	0.23210	GAA	.	.	none		0.468	RBM17-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046635.1	NM_032905		G	6139078	A	G	6139078	3	3	30	1	0	0	0	0	1	0	0	0	13134	246	9	3	52	3	RBM17	10	6139078	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	5229367	6139078	129395669	332	13483											
ITIH2	3698	hgsc.bcm.edu	37	chr10	7759736	7759736	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tatctgcaacctggacggctGgccaaacacttagaggtaag	12	8	11	10	1	1	1	0	0	1	1	1	2	1	2	2	4	3	3	2	4	5	3	rs370987991		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:7759736G>A	ENST00000358415.4	+	6	781	c.615G>A	c.(613-615)ctG>ctA	p.L205L	ITIH2_ENST00000480387.1_3'UTR|ITIH2_ENST00000379587.4_Silent_p.L194L	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	205					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						CTGGACGGCTGGCCAAACACT	0.507																																					p.L205L		Atlas-SNP	.											.	ITIH2	144	.	0			c.G615A						PASS	.	G		0,4406		0,0,2203	129	125	126		615	3.3	1	10		126	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	ITIH2	NM_002216.2		0,4,6499	AA,AG,GG		0.0465,0.0,0.0308		205/947	7759736	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	3698	exon6			ACGGCTGGCCAAA	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.615G>A	10.37:g.7759736G>A		154	0	0		122	86	0.704918	NM_002216	Q14659|Q15484|Q5T986	Silent	SNP	ENST00000358415.4	37	CCDS31141.1																																																																																			.	.	none		0.507	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216		A	7759736	G	A	7759736	2	1	30	1	0	0	0	0	0	0	0	1	7913	1335	47	2		2	ITIH2	10	7759736	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1620658	7759736	127775011	333	13484											
FAM171A1	221061	hgsc.bcm.edu	37	chr10	15256368	15256368	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gggggtgtgcaggtccccttCgccgcccggagacatcattt	5	9	14	13	3	1	1	1	0	0	1	3	2	2	1	4	4	1	1	4	4	0	2	rs143772901	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:15256368C>T	ENST00000378116.4	-	8	1225	c.1219G>A	c.(1219-1221)Gaa>Aaa	p.E407K	FAM171A1_ENST00000477161.1_5'UTR	NM_001010924.1	NP_001010924.1	Q5VUB5	F1711_HUMAN	family with sequence similarity 171, member A1	407						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						AGGTCCCCTTCGCCGCCCGGA	0.622													C|||	2	0.000399361	0.0	0.0	5008	,	,		16253	0.0		0.0	False		,,,				2504	0.002				p.E407K		Atlas-SNP	.											.	FAM171A1	252	.	0			c.G1219A						PASS	.	C	LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	58	62	61		1219	5.1	0.1	10	dbSNP_134	61	5,8595	4.3+/-15.6	0,5,4295	yes	missense	FAM171A1	NM_001010924.1	56	0,6,6497	TT,TC,CC		0.0581,0.0227,0.0461	probably-damaging	407/891	15256368	6,13000	2203	4300	6503	SO:0001583	missense	221061	exon8			CCCCTTCGCCGCC	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.1219G>A	10.37:g.15256368C>T	ENSP00000367356:p.Glu407Lys	94	0	0		58	21	0.362069	NM_001010924	D3DRT9|Q32M49|Q8N4I0	Missense_Mutation	SNP	ENST00000378116.4	37	CCDS31154.1	.	.	.	.	.	.	.	.	.	.	C	16.76	3.213121	0.58452	2.27E-4	5.81E-4	ENSG00000148468	ENST00000378116;ENST00000396781	T	0.35421	1.31	5.14	5.14	0.70334	.	0.101232	0.64402	D	0.000003	T	0.51092	0.1654	M	0.72894	2.215	0.80722	D	1	D	0.54397	0.966	P	0.51101	0.659	T	0.51965	-0.8638	10	0.45353	T	0.12	-22.4632	18.8133	0.92068	0.0:1.0:0.0:0.0	.	407	Q5VUB5	F1711_HUMAN	K	407;408	ENSP00000367356:E407K	ENSP00000367356:E407K	E	-	1	0	FAM171A1	15296374	1.000000	0.71417	0.106000	0.21319	0.055000	0.15305	7.103000	0.77014	2.667000	0.90743	0.563000	0.77884	GAA	C|1.000;T|0.000	0.000	weak		0.622	FAM171A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046984.1	XM_167709		T	15256368	C	T	15256368	3	4	30	1	0	0	0	0	1	0	0	0	5495	893	31	1	1457	1	FAM171A1	10	15256368	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	7496632	15256368	120278379	334	13485											
TRDMT1	1787	hgsc.bcm.edu	37	chr10	17243610	17243610	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccgcccacgccgctgtatagCtccagcacccgcaggggctc	6	5	11	19	4	0	0	0	0	0	0	2	0	1	0	5	2	2	6	5	2	2	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:17243610C>T	ENST00000377799.3	-	1	71	c.24G>A	c.(22-24)gaG>gaA	p.E8E	TRDMT1_ENST00000412821.3_Silent_p.E8E|TRDMT1_ENST00000457442.2_5'UTR|TRDMT1_ENST00000358282.7_Silent_p.E8E|TRDMT1_ENST00000351358.4_Silent_p.E8E|TRDMT1_ENST00000377766.5_Silent_p.E8E|TRDMT1_ENST00000488990.1_Silent_p.E8E	NM_004412.5	NP_004403.1	O14717	TRDMT_HUMAN	tRNA aspartic acid methyltransferase 1	8	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)	CGCTGTATAGCTCCAGCACCC	0.706																																					p.E8E		Atlas-SNP	.											.	TRDMT1	46	.	0			c.G24A						PASS	.						11	12	12					10																	17243610		1939	3647	5586	SO:0001819	synonymous_variant	1787	exon1			GTATAGCTCCAGC	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.24G>A	10.37:g.17243610C>T		44	0	0		18	12	0.666667	NM_004412	B0YJ02|B0YJ03|B0YJ07|B0YJ08|O43669|Q86WW6	Silent	SNP	ENST00000377799.3	37	CCDS7114.1																																																																																			.	.	none		0.706	TRDMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047024.3	NM_004412		T	17243610	C	T	17243610	2	4	30	1	0	0	0	0	0	0	0	1	16482	796	28	2		2	TRDMT1	10	17243610	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1987242	17243610	118291137	335	13486											
GAD2	2572	hgsc.bcm.edu	37	chr10	26575277	26575277	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctcttctctcttgtagggaTtgatgcagaattgcaaccaa	10	14	8	9	0	3	2	0	1	3	1	5	3	3	3	1	1	3	3	1	1	4	5	rs531559223		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:26575277T>C	ENST00000376261.3	+	13	1743	c.1240T>C	c.(1240-1242)Ttg>Ctg	p.L414L	GAD2_ENST00000259271.3_Silent_p.L414L	NM_001134366.1	NP_001127838.1	Q05329	DCE2_HUMAN	glutamate decarboxylase 2 (pancreatic islets and brain, 65kDa)	414					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						CTTGTAGGGATTGATGCAGAA	0.363													T|||	1	0.000199681	0.0	0.0	5008	,	,		18191	0.0		0.0	False		,,,				2504	0.001				p.L414L		Atlas-SNP	.											.	GAD2	116	.	0			c.T1240C						PASS	.						102	91	95					10																	26575277		2203	4300	6503	SO:0001819	synonymous_variant	2572	exon13			TAGGGATTGATGC	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.1240T>C	10.37:g.26575277T>C		84	0	0		56	15	0.267857	NM_000818	Q9UD87	Silent	SNP	ENST00000376261.3	37	CCDS7149.1																																																																																			.	.	none		0.363	GAD2-001	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047255.1	NM_000818		C	26575277	T	C	26575277	2	2	30	1	0	0	0	0	0	0	0	1	6188	1490	52	3		3	GAD2	10	26575277	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	9331667	26575277	108959470	336	13487											
PARD3	56288	hgsc.bcm.edu	37	chr10	34630575	34630575	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtcggctgaatcactgatTgcagccttggcccaagtacc	9	9	10	13	1	1	2	1	2	0	0	2	2	1	2	3	2	3	3	3	2	3	3	rs141191270	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:34630575T>A	ENST00000374789.3	-	16	2722	c.2397A>T	c.(2395-2397)gcA>gcT	p.A799A	PARD3_ENST00000545260.1_Silent_p.A739A|PARD3_ENST00000545693.1_Silent_p.A783A|PARD3_ENST00000346874.4_Silent_p.A799A|PARD3_ENST00000350537.4_Silent_p.A783A|PARD3_ENST00000374794.3_Silent_p.A739A|PARD3_ENST00000374773.1_Silent_p.A796A|PARD3_ENST00000374790.3_Silent_p.A739A|PARD3_ENST00000374776.1_Silent_p.A783A|PARD3_ENST00000544292.1_Silent_p.A513A|PARD3_ENST00000374788.3_Silent_p.A796A|PARD3_ENST00000340077.5_Silent_p.A796A	NM_019619.3	NP_062565.2	Q8TEW0	PARD3_HUMAN	par-3 family cell polarity regulator	799	Interacts with PRKCI and PRKCZ. {ECO:0000250}.				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)				AATCACTGATTGCAGCCTTGG	0.478																																					p.A799A		Atlas-SNP	.											.	PARD3	131	.	0			c.A2397T						PASS	.	T	,,,,,,,,,,	3,4403	6.2+/-15.9	0,3,2200	128	117	120		2388,2349,2397,2349,2349,2217,2217,2388,2388,2349,2397	-11.3	0	10	dbSNP_134	120	2,8598	3.0+/-9.4	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PARD3	NM_001184785.1,NM_001184786.1,NM_001184787.1,NM_001184788.1,NM_001184789.1,NM_001184790.1,NM_001184791.1,NM_001184792.1,NM_001184793.1,NM_001184794.1,NM_019619.3	,,,,,,,,,,	0,5,6498	AA,AT,TT		0.0233,0.0681,0.0384	,,,,,,,,,,	796/1354,783/1341,799/1320,783/1311,783/1274,739/1267,739/1245,796/1032,796/1001,783/989,799/1357	34630575	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	56288	exon16			ACTGATTGCAGCC	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.2397A>T	10.37:g.34630575T>A		118	0	0		88	69	0.784091	NM_001184787	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																																																																																			T|0.999;A|0.001	0.001	strong		0.478	PARD3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047527.1	NM_019619		A	34630575	T	A	34630575	2	1	30	1	0	0	0	0	0	0	0	1	11452	1799	63	5		5	PARD3	10	34630575	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	8055298	34630575	100904172	337	13488											
ZNF33A	7581	hgsc.bcm.edu	37	chr10	38345409	38345409	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatggatattagaaatttccAgccacaagtcagcctccata	15	10	6	10	0	1	1	1	0	0	1	3	2	3	2	4	1	2	0	4	1	6	4	rs71491230	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:38345409A>G	ENST00000458705.2	+	5	2512	c.2354A>G	c.(2353-2355)cAg>cGg	p.Q785R	ZNF33A_ENST00000469037.2_Intron|ZNF33A_ENST00000432900.2_Missense_Mutation_p.Q792R|ZNF33A_ENST00000374618.3_Missense_Mutation_p.Q786R|ZNF33A_ENST00000307441.9_Missense_Mutation_p.Q785R			Q06730	ZN33A_HUMAN	zinc finger protein 33A	785					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.Q785R(1)		cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						AGAAATTTCCAGCCACAAGTC	0.383													A|||	3	0.000599042	0.0	0.0	5008	,	,		18653	0.0		0.003	False		,,,				2504	0.0				p.Q786R		Atlas-SNP	.											ZNF33A,NS,carcinoma,0,1	ZNF33A	103	1	1	Substitution - Missense(1)	lung(1)	c.A2357G						PASS	.	A	ARG/GLN,ARG/GLN	2,4404	4.2+/-10.8	0,2,2201	61	61	61		2357,2354	0.6	0	10	dbSNP_130	61	25,8575	17.3+/-56.4	0,25,4275	yes	missense,missense	ZNF33A	NM_006954.1,NM_006974.2	43,43	0,27,6476	GG,GA,AA		0.2907,0.0454,0.2076	benign,benign	786/812,785/811	38345409	27,12979	2203	4300	6503	SO:0001583	missense	7581	exon5			ATTTCCAGCCACA	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.2354A>G	10.37:g.38345409A>G	ENSP00000387713:p.Gln785Arg	162	0	0		95	24	0.252632	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Missense_Mutation	SNP	ENST00000458705.2	37	CCDS31182.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	7.459	0.644218	0.14451	4.54E-4	0.002907	ENSG00000189180	ENST00000374618;ENST00000432900;ENST00000458705;ENST00000307441	T;T;T;T	0.07327	3.2;3.46;3.2;3.2	1.92	0.561	0.17285	.	.	.	.	.	T	0.03827	0.0108	N	0.08118	0	0.09310	N	1	B;B;B	0.15141	0.012;0.007;0.012	B;B;B	0.09377	0.004;0.002;0.004	T	0.40961	-0.9535	9	0.87932	D	0	.	2.6079	0.04883	0.4659:0.2692:0.0:0.2649	.	792;785;786	F6TH33;Q06730;F8WAJ5	.;ZN33A_HUMAN;.	R	786;792;785;785	ENSP00000363747:Q786R;ENSP00000402467:Q792R;ENSP00000387713:Q785R;ENSP00000304268:Q785R	ENSP00000304268:Q785R	Q	+	2	0	ZNF33A	38385415	0.000000	0.05858	0.007000	0.13788	0.142000	0.21351	-0.152000	0.10159	-0.018000	0.14079	0.260000	0.18958	CAG	A|0.998;G|0.002	0.002	strong		0.383	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974		G	38345409	A	G	38345409	3	3	30	1	0	0	0	0	1	0	0	0	17869	188	7	3	2371	3	ZNF33A	10	38345409	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	3714834	38345409	97189338	338	13489											
ZNF33A	7581	hgsc.bcm.edu	37	chr10	38345455	38345455	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagagtattcacactgtggAgaaagccctgatgacatcct	12	10	9	10	0	2	4	2	2	0	2	3	5	3	4	2	1	1	1	2	1	2	2	rs12242343	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:38345455A>G	ENST00000458705.2	+	5	2558	c.2400A>G	c.(2398-2400)ggA>ggG	p.G800G	ZNF33A_ENST00000469037.2_Intron|ZNF33A_ENST00000432900.2_Silent_p.G807G|ZNF33A_ENST00000374618.3_Silent_p.G801G|ZNF33A_ENST00000307441.9_Silent_p.G800G			Q06730	ZN33A_HUMAN	zinc finger protein 33A	800					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						CACACTGTGGAGAAAGCCCTG	0.388													A|||	140	0.0279553	0.0915	0.013	5008	,	,		18836	0.0		0.0099	False		,,,				2504	0.0				p.G801G		Atlas-SNP	.											.	ZNF33A	103	.	0			c.A2403G						PASS	.	A	,	359,4047	175.9+/-205.1	19,321,1863	61	59	60		2403,2400	1.9	0.1	10	dbSNP_120	60	53,8547	32.3+/-84.9	0,53,4247	no	coding-synonymous,coding-synonymous	ZNF33A	NM_006954.1,NM_006974.2	,	19,374,6110	GG,GA,AA		0.6163,8.148,3.1678	,	801/812,800/811	38345455	412,12594	2203	4300	6503	SO:0001819	synonymous_variant	7581	exon5			CTGTGGAGAAAGC	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.2400A>G	10.37:g.38345455A>G		102	0	0		66	17	0.257576	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Silent	SNP	ENST00000458705.2	37	CCDS31182.1																																																																																			A|0.968;G|0.032	0.032	strong		0.388	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974		G	38345455	A	G	38345455	2	3	30	1	0	0	0	0	0	0	0	1	17869	291	11	3		3	ZNF33A	10	38345455	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	46	38345455	97189292	339	13490											
ZNF33B	7582	hgsc.bcm.edu	37	chr10	43089278	43089278	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtgtgtgatctctgatgttTagtgaggtttgacttctccc	5	18	11	7	0	2	4	0	4	2	0	4	4	2	4	1	1	0	2	1	1	1	4	rs71505624	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:43089278T>C	ENST00000359467.3	-	5	1234	c.1120A>G	c.(1120-1122)Aaa>Gaa	p.K374E	ZNF33B_ENST00000486187.1_RNA	NM_006955.1	NP_008886.1	Q06732	ZN33B_HUMAN	zinc finger protein 33B	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)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(15)|skin(1)|stomach(1)	29						CTCTGATGTTTAGTGAGGTTT	0.433													t|||	7	0.00139776	0.0	0.0014	5008	,	,		20809	0.0		0.004	False		,,,				2504	0.002				p.K374E	Melanoma(137;1247 1767 16772 25727 43810)	Atlas-SNP	.											.	ZNF33B	78	.	0			c.A1120G						PASS	.	T	GLU/LYS	2,4404	4.2+/-10.8	0,2,2201	117	117	117		1120	2.3	1	10	dbSNP_130	117	20,8580	14.6+/-50.1	0,20,4280	yes	missense	ZNF33B	NM_006955.1	56	0,22,6481	CC,CT,TT		0.2326,0.0454,0.1692	probably-damaging	374/779	43089278	22,12984	2203	4300	6503	SO:0001583	missense	7582	exon5			GATGTTTAGTGAG	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.1120A>G	10.37:g.43089278T>C	ENSP00000352444:p.Lys374Glu	200	0	0		174	33	0.189655	NM_006955	Q06731|Q32MA2|Q86XY8|Q8NDW3	Missense_Mutation	SNP	ENST00000359467.3	37	CCDS7198.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	T	5.009	0.187437	0.09547	4.54E-4	0.002326	ENSG00000196693	ENST00000359467;ENST00000395836	T	0.19394	2.15	2.28	2.28	0.28536	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.38548	N	0.001658	T	0.17959	0.0431	N	0.12569	0.235	0.09310	N	1	D	0.76494	0.999	D	0.69479	0.964	T	0.13548	-1.0505	10	0.02654	T	1	.	8.5071	0.33195	0.0:0.0:0.0:1.0	.	374	Q06732	ZN33B_HUMAN	E	374;340	ENSP00000352444:K374E	ENSP00000352444:K374E	K	-	1	0	ZNF33B	42409284	0.000000	0.05858	1.000000	0.80357	0.981000	0.71138	-0.059000	0.11731	1.324000	0.45282	0.341000	0.21757	AAA	T|0.998;C|0.002	0.002	strong		0.433	ZNF33B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_006955		C	43089278	T	C	43089278	3	2	30	1	0	0	0	0	1	0	0	0	17870	1763	61	3	1220	3	ZNF33B	10	43089278	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	4743823	43089278	92445469	340	13491											
ZNF33B	7582	hgsc.bcm.edu	37	chr10	43089370	43089370	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctctgatgtcgagtgagaTgtgacttctcccagaaagct	9	11	10	11	1	2	4	0	3	2	2	4	6	2	4	2	0	1	1	2	0	1	1	rs71505625	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:43089370T>A	ENST00000359467.3	-	5	1142	c.1028A>T	c.(1027-1029)cAt>cTt	p.H343L	ZNF33B_ENST00000486187.1_RNA	NM_006955.1	NP_008886.1	Q06732	ZN33B_HUMAN	zinc finger protein 33B	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)|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						TCGAGTGAGATGTGACTTCTC	0.413													t|||	7	0.00139776	0.0	0.0014	5008	,	,		22122	0.0		0.004	False		,,,				2504	0.002				p.H343L	Melanoma(137;1247 1767 16772 25727 43810)	Atlas-SNP	.											.	ZNF33B	78	.	0			c.A1028T						PASS	.	T	LEU/HIS	2,4404	4.2+/-10.8	0,2,2201	121	119	120		1028	2.3	1	10	dbSNP_130	120	20,8580	14.6+/-50.1	0,20,4280	no	missense	ZNF33B	NM_006955.1	99	0,22,6481	AA,AT,TT		0.2326,0.0454,0.1692	probably-damaging	343/779	43089370	22,12984	2203	4300	6503	SO:0001583	missense	7582	exon5			GTGAGATGTGACT	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.1028A>T	10.37:g.43089370T>A	ENSP00000352444:p.His343Leu	215	0	0		132	23	0.174242	NM_006955	Q06731|Q32MA2|Q86XY8|Q8NDW3	Missense_Mutation	SNP	ENST00000359467.3	37	CCDS7198.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	T	4.540	0.100297	0.08731	4.54E-4	0.002326	ENSG00000196693	ENST00000359467;ENST00000395836	T	0.18338	2.22	2.28	2.28	0.28536	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.207772	0.24160	N	0.040988	T	0.09774	0.0240	N	0.20483	0.58	0.09310	N	0.999998	B	0.10296	0.003	B	0.08055	0.003	T	0.24119	-1.0169	10	0.32370	T	0.25	.	8.5071	0.33195	0.0:0.0:0.0:1.0	.	343	Q06732	ZN33B_HUMAN	L	343;309	ENSP00000352444:H343L	ENSP00000352444:H343L	H	-	2	0	ZNF33B	42409376	0.000000	0.05858	0.998000	0.56505	0.966000	0.64601	0.224000	0.17738	1.324000	0.45282	0.341000	0.21757	CAT	T|0.998;A|0.002	0.002	strong		0.413	ZNF33B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_006955		A	43089370	T	A	43089370	3	1	30	1	0	0	0	0	1	0	0	0	17870	1464	51	5	1312	5	ZNF33B	10	43089370	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	92	43089370	92445377	341	13492											
SYT15	83849	hgsc.bcm.edu	37	chr10	46967514	46967514	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccgctcatcgggcagcaggTagagcttcaccagggggctg	7	6	16	12	2	2	1	2	0	0	1	3	1	2	1	2	4	2	6	2	4	1	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:46967514T>C	ENST00000374321.4	-	4	629	c.563A>G	c.(562-564)tAc>tGc	p.Y188C	SYT15_ENST00000503753.1_Missense_Mutation_p.Y188C|RP11-38L15.3_ENST00000506914.1_RNA|SYT15_ENST00000374323.4_Missense_Mutation_p.Y241C|SYT15_ENST00000374325.3_Missense_Mutation_p.Y188C	NM_031912.4	NP_114118.2	Q9BQS2	SYT15_HUMAN	synaptotagmin XV	188	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						GGGCAGCAGGTAGAGCTTCAC	0.592																																					p.Y188C	Ovarian(57;1152 1428 19651 37745)	Atlas-SNP	.											.	SYT15	165	.	0			c.A563G						PASS	.						68	81	77					10																	46967514		2071	4211	6282	SO:0001583	missense	83849	exon4			AGCAGGTAGAGCT	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.563A>G	10.37:g.46967514T>C	ENSP00000363441:p.Tyr188Cys	141	0	0		145	15	0.103448	NM_031912	A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	Missense_Mutation	SNP	ENST00000374321.4	37	CCDS44376.1	.	.	.	.	.	.	.	.	.	.	.	15.71	2.913590	0.52439	.	.	ENSG00000204176	ENST00000416127;ENST00000374325;ENST00000503753;ENST00000374330;ENST00000374323;ENST00000374321;ENST00000512997	T;T;T;T;T	0.09073	3.02;3.02;3.02;3.02;3.02	4.92	4.92	0.64577	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.238169	0.42964	D	0.000627	T	0.09818	0.0241	L	0.51914	1.62	0.34918	D	0.748104	B;B	0.20550	0.005;0.046	B;B	0.21708	0.013;0.036	T	0.12400	-1.0549	9	.	.	.	.	12.8277	0.57728	0.0:0.0:0.0:1.0	.	188;188	Q9BQS2;Q9BQS2-2	SYT15_HUMAN;.	C	188;188;188;27;241;188;72	ENSP00000363445:Y188C;ENSP00000427607:Y188C;ENSP00000363443:Y241C;ENSP00000363441:Y188C;ENSP00000424803:Y72C	.	Y	-	2	0	SYT15	46387520	1.000000	0.71417	0.996000	0.52242	0.871000	0.50021	5.085000	0.64468	1.974000	0.57490	0.533000	0.62120	TAC	.	.	none		0.592	SYT15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367008.1	NM_031912		C	46967514	T	C	46967514	3	2	30	1	0	0	0	0	1	0	0	0	15486	1638	57	3	776	3	SYT15	10	46967514	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	3878144	46967514	88567233	342	13493											
CHAT	1103	hgsc.bcm.edu	37	chr10	50854637	50854637	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caggaggcgtggagctcagcGacacccacagggcactccag	10	3	14	14	2	1	0	1	0	0	0	2	3	2	2	2	4	2	2	2	4	0	0	rs8178991	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:50854637G>A	ENST00000337653.2	+	8	1351	c.1198G>A	c.(1198-1200)Gac>Aac	p.D400N	CHAT_ENST00000351556.3_Missense_Mutation_p.D282N|CHAT_ENST00000455728.2_Missense_Mutation_p.D282N|CHAT_ENST00000395559.2_Missense_Mutation_p.D282N|CHAT_ENST00000339797.1_Missense_Mutation_p.D282N|CHAT_ENST00000395562.2_Missense_Mutation_p.D318N	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	400			D -> N (in dbSNP:rs8178991).		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)	GGAGCTCAGCGACACCCACAG	0.637													G|||	30	0.00599042	0.0015	0.0101	5008	,	,		20906	0.0		0.0199	False		,,,				2504	0.001				p.D400N		Atlas-SNP	.											.	CHAT	162	.	0			c.G1198A						PASS	.	G	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	21,4385	29.0+/-57.7	0,21,2182	92	81	84		844,952,844,1198,844,844,844	4.3	0.9	10	dbSNP_117	84	189,8411	85.0+/-147.5	4,181,4115	yes	missense,missense,missense,missense,missense,missense,missense	CHAT	NM_001142929.1,NM_001142933.1,NM_001142934.1,NM_020549.4,NM_020984.3,NM_020985.3,NM_020986.3	23,23,23,23,23,23,23	4,202,6297	AA,AG,GG		2.1977,0.4766,1.6146	benign,benign,benign,benign,benign,benign,benign	282/631,318/667,282/631,400/749,282/631,282/631,282/631	50854637	210,12796	2203	4300	6503	SO:0001583	missense	1103	exon8			CTCAGCGACACCC	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.1198G>A	10.37:g.50854637G>A	ENSP00000337103:p.Asp400Asn	141	0	0		104	104	1	NM_020549	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Missense_Mutation	SNP	ENST00000337653.2	37	CCDS7232.1	19	0.0086996336996337	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	15	0.01978891820580475	G	19.11	3.763636	0.69878	0.004766	0.021977	ENSG00000070748	ENST00000339797;ENST00000351556;ENST00000395559;ENST00000337653;ENST00000395562;ENST00000455728	T;T;T;T;T;T	0.81415	-1.49;-1.49;-1.49;-1.49;-1.49;-1.49	5.27	4.34	0.51931	.	0.099000	0.64402	D	0.000003	T	0.72277	0.3440	M	0.78223	2.4	0.58432	D	0.999996	B;D	0.56968	0.339;0.978	B;P	0.48524	0.096;0.58	T	0.78738	-0.2087	10	0.51188	T	0.08	-24.4513	10.8728	0.46894	0.0727:0.1312:0.7961:0.0	rs8178991	282;400	F8W8I2;P28329	.;CLAT_HUMAN	N	282;282;282;400;318;282	ENSP00000343486:D282N;ENSP00000345878:D282N;ENSP00000378926:D282N;ENSP00000337103:D400N;ENSP00000378929:D318N;ENSP00000390521:D282N	ENSP00000337103:D400N	D	+	1	0	CHAT	50524643	1.000000	0.71417	0.898000	0.35279	0.926000	0.56050	4.110000	0.57831	1.162000	0.42619	0.655000	0.94253	GAC	G|0.986;A|0.014	0.014	strong		0.637	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549		A	50854637	G	A	50854637	3	1	30	1	0	0	0	0	1	0	0	0	3315	1058	37	1	1272	1	CHAT	10	50854637	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	3887123	50854637	84680110	343	13494											
OGDHL	55753	hgsc.bcm.edu	37	chr10	50959965	50959965	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaaacttctgccggatccaCtggcactgctccacatcgtt	8	11	7	15	2	2	0	1	0	1	0	5	1	4	1	3	2	3	3	3	2	1	2	rs7090775	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:50959965C>T	ENST00000374103.4	-	6	742	c.657G>A	c.(655-657)caG>caA	p.Q219Q	OGDHL_ENST00000419399.1_Silent_p.Q162Q|OGDHL_ENST00000432695.1_Silent_p.Q10Q	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	219					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						GCCGGATCCACTGGCACTGCT	0.592													C|||	274	0.0547125	0.0877	0.0331	5008	,	,		19769	0.004		0.0219	False		,,,				2504	0.1115				p.Q219Q		Atlas-SNP	.											.	OGDHL	149	.	0			c.G657A						PASS	.	C	,,	263,4143	150.3+/-184.3	10,243,1950	193	187	189		486,30,657	4.7	1	10	dbSNP_116	189	287,8313	107.8+/-168.5	4,279,4017	no	coding-synonymous,coding-synonymous,coding-synonymous	OGDHL	NM_001143996.1,NM_001143997.1,NM_018245.2	,,	14,522,5967	TT,TC,CC		3.3372,5.9691,4.2288	,,	162/954,10/802,219/1011	50959965	550,12456	2203	4300	6503	SO:0001819	synonymous_variant	55753	exon6			GATCCACTGGCAC	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.657G>A	10.37:g.50959965C>T		184	0	0		92	73	0.793478	NM_018245	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Silent	SNP	ENST00000374103.4	37	CCDS7234.1																																																																																			C|0.960;T|0.040	0.040	strong		0.592	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245		T	50959965	C	T	50959965	2	4	30	1	0	0	0	0	0	0	0	1	10849	564	20	2		2	OGDHL	10	50959965	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	105328	50959965	84574782	344	13495											
CTNNA3	29119	hgsc.bcm.edu	37	chr10	68535222	68535222	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtctgcgaaggtctcttgTcttcttacacatgttgtcta	6	17	8	10	1	5	0	0	0	5	0	6	1	5	0	0	1	2	1	0	1	3	5			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:68535222T>C	ENST00000433211.2	-	8	1282	c.1108A>G	c.(1108-1110)Aca>Gca	p.T370A	CTNNA3_ENST00000373744.4_Missense_Mutation_p.T370A	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						AGGTCTCTTGTCTTCTTACAC	0.378																																					p.T370A		Atlas-SNP	.											.	CTNNA3	401	.	0			c.A1108G						PASS	.						187	177	180					10																	68535222		2203	4300	6503	SO:0001583	missense	29119	exon8			CTCTTGTCTTCTT	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.1108A>G	10.37:g.68535222T>C	ENSP00000389714:p.Thr370Ala	175	0	0		102	6	0.0588235	NM_013266		Missense_Mutation	SNP	ENST00000433211.2	37	CCDS7269.1	.	.	.	.	.	.	.	.	.	.	T	15.09	2.731133	0.48939	.	.	ENSG00000183230	ENST00000433211;ENST00000373744	T;T	0.40756	1.02;1.02	6.16	5.04	0.67666	.	0.092451	0.47093	D	0.000247	T	0.48607	0.1509	M	0.82716	2.605	0.80722	D	1	B;B	0.26744	0.158;0.006	B;B	0.33196	0.159;0.012	T	0.53287	-0.8460	10	0.52906	T	0.07	-22.6925	9.8846	0.41253	0.0:0.0786:0.0:0.9214	.	370;370	Q9UI47-2;Q9UI47	.;CTNA3_HUMAN	A	370	ENSP00000389714:T370A;ENSP00000362849:T370A	ENSP00000362849:T370A	T	-	1	0	CTNNA3	68205228	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.998000	0.63927	2.367000	0.80283	0.528000	0.53228	ACA	.	.	none		0.378	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048282.2	NM_013266		C	68535222	T	C	68535222	3	2	30	1	0	0	0	0	1	0	0	0	4016	1667	58	3	1623	3	CTNNA3	10	68535222	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	17575257	68535222	66999525	345	13496											
PBLD	64081	hgsc.bcm.edu	37	chr10	70066553	70066553	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aacagcagcaggattcccacGaaatgctcttgctgtgaatg	12	9	10	10	1	1	1	0	1	1	0	2	3	2	2	1	1	5	4	1	1	3	2	rs12359690	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:70066553G>A	ENST00000358769.2	-	2	251	c.49C>T	c.(49-51)Cgt>Tgt	p.R17C	PBLD_ENST00000432941.1_Missense_Mutation_p.R17C|PBLD_ENST00000495025.2_Missense_Mutation_p.R17C|PBLD_ENST00000309049.4_Missense_Mutation_p.R17C	NM_022129.3	NP_071412.2	P30039	PBLD_HUMAN	phenazine biosynthesis-like protein domain containing	17			R -> C (in dbSNP:rs12359690). {ECO:0000269|PubMed:15806103}.		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						GGATTCCCACGAAATGCTCTT	0.383													G|||	117	0.0233626	0.0461	0.0245	5008	,	,		18502	0.0		0.0318	False		,,,				2504	0.0072				p.R17C		Atlas-SNP	.											.	PBLD	53	.	0			c.C49T						PASS	.	G	CYS/ARG,CYS/ARG	186,4220	119.6+/-157.3	6,174,2023	89	82	85		49,49	0.5	0.9	10	dbSNP_120	85	399,8201	127.2+/-185.5	8,383,3909	yes	missense,missense	PBLD	NM_001033083.1,NM_022129.3	180,180	14,557,5932	AA,AG,GG		4.6395,4.2215,4.4979	benign,benign	17/281,17/289	70066553	585,12421	2203	4300	6503	SO:0001583	missense	64081	exon2			TCCCACGAAATGC	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.49C>T	10.37:g.70066553G>A	ENSP00000351619:p.Arg17Cys	264	0	0		117	117	1	NM_022129	A8MZJ3|C9JIM0|Q9HCC2	Missense_Mutation	SNP	ENST00000358769.2	37	CCDS7277.2	53	0.024267399267399268	25	0.0508130081300813	8	0.022099447513812154	0	0.0	20	0.026385224274406333	G	11.72	1.723233	0.30503	0.042215	0.046395	ENSG00000108187	ENST00000358769;ENST00000309049;ENST00000432941;ENST00000277795	T;T;T;T	0.31510	1.49;1.49;1.49;1.49	5.51	0.525	0.17072	.	0.445102	0.24249	N	0.040187	T	0.04363	0.0120	L	0.55017	1.72	0.21416	N	0.999695	B;B;B	0.16802	0.002;0.019;0.008	B;B;B	0.16289	0.001;0.015;0.007	T	0.11641	-1.0579	10	0.56958	D	0.05	0.3367	8.8276	0.35065	0.4705:0.0:0.5295:0.0	rs12359690;rs52804292;rs12359690	17;17;17	F8W7D0;C9JIM0;P30039	.;.;PBLD_HUMAN	C	17	ENSP00000351619:R17C;ENSP00000308466:R17C;ENSP00000395534:R17C;ENSP00000277795:R17C	ENSP00000277795:R17C	R	-	1	0	PBLD	69736559	0.038000	0.19896	0.910000	0.35882	0.979000	0.70002	-0.107000	0.10873	-0.157000	0.11059	-1.002000	0.02502	CGT	G|0.961;A|0.039	0.039	strong		0.383	PBLD-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048314.1	NM_022129		A	70066553	G	A	70066553	3	1	30	1	0	0	0	0	1	0	0	0	11498	1058	37	1	942	1	PBLD	10	70066553	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1531331	70066553	65468194	346	13497											
RUFY2	55680	hgsc.bcm.edu	37	chr10	70143826	70143826	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acctctaggtgctgctgtgtTttcattaaaatcaatttatt	10	18	6	7	0	3	0	2	0	1	0	3	0	3	0	1	1	2	3	1	1	5	7			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:70143826T>C	ENST00000602465.1	-	9	904	c.804A>G	c.(802-804)aaA>aaG	p.K268K	RUFY2_ENST00000472394.2_5'UTR|RUFY2_ENST00000454950.2_Silent_p.K210K|RUFY2_ENST00000388768.2_Silent_p.K303K|RUFY2_ENST00000399200.2_Silent_p.K234K			Q8WXA3	RUFY2_HUMAN	RUN and FYVE domain containing 2	317						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						GCTGCTGTGTTTTCATTAAAA	0.323																																					p.K303K		Atlas-SNP	.											.	RUFY2	58	.	0			c.A909G						PASS	.						146	131	136					10																	70143826		1832	4084	5916	SO:0001819	synonymous_variant	55680	exon9			CTGTGTTTTCATT	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.804A>G	10.37:g.70143826T>C		132	0	0		84	4	0.047619	NM_017987	B3KXB2|B4DFR0|Q5TC48|Q8IW33|Q96P51|Q9P1Z1	Silent	SNP	ENST00000602465.1	37																																																																																				.	.	none		0.323	RUFY2-010	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467567.1	NM_017987		C	70143826	T	C	70143826	2	2	30	1	0	0	0	0	0	0	0	1	13754	1838	64	3		3	RUFY2	10	70143826	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	77273	70143826	65390921	347	13498											
DNA2	1763	hgsc.bcm.edu	37	chr10	70178965	70178965	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaatatcagagggactgcaTccagcctaaatagaaaaaga	18	6	8	9	0	1	3	1	0	0	3	2	4	2	4	3	1	2	1	3	1	7	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:70178965T>C	ENST00000358410.3	-	19	2843	c.2793A>G	c.(2791-2793)ggA>ggG	p.G931G	DNA2_ENST00000399180.2_Silent_p.G1017G|DNA2_ENST00000399179.2_Silent_p.G693G	NM_001080449.2	NP_001073918.2	P51530	DNA2_HUMAN	DNA replication helicase/nuclease 2	931	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						AGGGACTGCATCCAGCCTAAA	0.323																																					p.G931G		Atlas-SNP	.											.	DNA2	76	.	0			c.A2793G						PASS	.						54	46	49					10																	70178965		1838	4091	5929	SO:0001819	synonymous_variant	1763	exon19			ACTGCATCCAGCC	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.2793A>G	10.37:g.70178965T>C		49	0	0		38	19	0.5	NM_001080449	Q2NKM1|Q5TC49|Q5TC50|Q6P455|Q6PI80|Q7Z6H9|Q8N346	Silent	SNP	ENST00000358410.3	37		.	.	.	.	.	.	.	.	.	.	T	8.699	0.909289	0.17833	.	.	ENSG00000138346	ENST00000440722	.	.	.	5.39	-0.794	0.10918	.	.	.	.	.	T	0.50990	0.1648	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40997	-0.9533	4	.	.	.	.	5.9261	0.19112	0.3798:0.0:0.2894:0.3308	.	.	.	.	V	253	.	.	M	-	1	0	DNA2	69848971	1.000000	0.71417	0.989000	0.46669	0.871000	0.50021	0.478000	0.22212	0.009000	0.14813	0.482000	0.46254	ATG	.	.	none		0.323	DNA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048334.2			C	70178965	T	C	70178965	2	2	30	1	0	0	0	0	0	0	0	1	4598	1422	50	3		3	DNA2	10	70178965	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	35139	70178965	65355782	348	13499											
KIAA1274	27143	hgsc.bcm.edu	37	chr10	72291172	72291172	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tccagggccttggacccgggGtccgggtggagagcctggag	5	6	19	11	2	0	1	0	0	0	1	2	4	2	3	5	7	1	0	5	7	0	1	rs61737673	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:72291172G>A	ENST00000263563.6	+	5	863	c.595G>A	c.(595-597)Gtc>Atc	p.V199I		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	199						cytosol (GO:0005829)											TGGACCCGGGGTCCGGGTGGA	0.602													G|||	67	0.0133786	0.003	0.0216	5008	,	,		18858	0.0		0.0388	False		,,,				2504	0.0092				p.V199I		Atlas-SNP	.											.	.	.	.	0			c.G595A						PASS	.	G	ILE/VAL	38,4368	41.6+/-74.8	0,38,2165	64	58	60		595	1.1	0	10	dbSNP_129	60	276,8324	104.2+/-165.2	3,270,4027	yes	missense	KIAA1274	NM_014431.2	29	3,308,6192	AA,AG,GG		3.2093,0.8625,2.4143	benign	199/857	72291172	314,12692	2203	4300	6503	SO:0001583	missense	27143	exon5			CCCGGGGTCCGGG	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.595G>A	10.37:g.72291172G>A	ENSP00000263563:p.Val199Ile	92	0	0		54	13	0.240741	NM_014431	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Missense_Mutation	SNP	ENST00000263563.6	37	CCDS31215.1	33	0.01510989010989011	0	0.0	10	0.027624309392265192	0	0.0	23	0.030343007915567283	G	2.180	-0.387703	0.04932	0.008625	0.032093	ENSG00000107719	ENST00000263563;ENST00000373214	T	0.21932	1.98	5.08	1.08	0.20341	.	0.896709	0.09766	N	0.758599	T	0.04588	0.0125	L	0.33753	1.03	0.09310	N	1	B	0.09022	0.002	B	0.11329	0.006	T	0.37033	-0.9723	10	0.18710	T	0.47	-16.1671	6.6817	0.23123	0.2174:0.3405:0.442:0.0	rs61737673	199	Q9ULE6	PALD_HUMAN	I	199	ENSP00000263563:V199I	ENSP00000263563:V199I	V	+	1	0	KIAA1274	71961178	0.013000	0.17824	0.003000	0.11579	0.070000	0.16714	0.778000	0.26732	0.091000	0.17302	0.655000	0.94253	GTC	G|0.979;A|0.021	0.021	strong		0.602	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431		A	72291172	G	A	72291172	3	1	30	1	0	0	0	0	1	0	0	0	8229	1261	44	2	609	2	KIAA1274	10	72291172	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2112207	72291172	63243575	349	13500											
PRF1	5551	hgsc.bcm.edu	37	chr10	72360197	72360197	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctgggctgcaaagttggcTgcctgtgagtgtgagccggc	5	11	16	9	1	1	2	0	2	1	0	1	2	1	2	2	3	3	4	2	3	1	2	rs116554195	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:72360197T>C	ENST00000441259.1	-	2	622	c.462A>G	c.(460-462)gcA>gcG	p.A154A	PRF1_ENST00000373209.2_Silent_p.A154A	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	154	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						CAAAGTTGGCTGCCTGTGAGT	0.612			M			"various leukaemia, lymphoma"	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis				T|||	76	0.0151757	0.0378	0.0086	5008	,	,		17805	0.0		0.0109	False		,,,				2504	0.0092				p.A154A		Atlas-SNP	.	yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	.	PRF1	64	.	0			c.A462G						PASS	.	T	,	135,4271	95.7+/-134.4	1,133,2069	81	71	74		462,462	-8.4	0	10	dbSNP_132	74	71,8529	41.7+/-99.0	0,71,4229	no	coding-synonymous,coding-synonymous	PRF1	NM_001083116.1,NM_005041.4	,	1,204,6298	CC,CT,TT		0.8256,3.064,1.5839	,	154/556,154/556	72360197	206,12800	2203	4300	6503	SO:0001819	synonymous_variant	5551	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GTTGGCTGCCTGT	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.462A>G	10.37:g.72360197T>C		235	0	0		126	92	0.730159	NM_001083116	B2R6X4|Q59F57|Q86WX7	Silent	SNP	ENST00000441259.1	37	CCDS7305.1																																																																																			T|0.987;C|0.013	0.013	strong		0.612	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041		C	72360197	T	C	72360197	2	2	30	1	0	0	0	0	0	0	0	1	12490	1567	55	3		3	PRF1	10	72360197	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	69025	72360197	63174550	350	13501											
PRF1	5551	hgsc.bcm.edu	37	chr10	72360224	72360224	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtgtgagccggccacagaCacatgcacattgctggtggg	9	7	15	10	1	0	2	0	1	0	1	0	3	0	2	2	3	3	2	2	3	0	1	rs115281140	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:72360224C>T	ENST00000441259.1	-	2	595	c.435G>A	c.(433-435)gtG>gtA	p.V145V	PRF1_ENST00000373209.2_Silent_p.V145V	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	145	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						CGGCCACAGACACATGCACAT	0.612			M			"various leukaemia, lymphoma"	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis				C|||	64	0.0127796	0.0287	0.0086	5008	,	,		16983	0.0		0.0109	False		,,,				2504	0.0092				p.V145V		Atlas-SNP	.	yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	PRF1,NS,carcinoma,-2,1	PRF1	64	1	0			c.G435A						scavenged	.	C	,	88,4318	73.6+/-111.7	1,86,2116	88	76	80		435,435	2.8	0	10	dbSNP_132	80	71,8529	41.7+/-99.0	0,71,4229	no	coding-synonymous,coding-synonymous	PRF1	NM_001083116.1,NM_005041.4	,	1,157,6345	TT,TC,CC		0.8256,1.9973,1.2225	,	145/556,145/556	72360224	159,12847	2203	4300	6503	SO:0001819	synonymous_variant	5551	exon2	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	CACAGACACATGC	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.435G>A	10.37:g.72360224C>T		226	2	0.00884956		119	87	0.731092	NM_001083116	B2R6X4|Q59F57|Q86WX7	Silent	SNP	ENST00000441259.1	37	CCDS7305.1																																																																																			C|0.990;T|0.010	0.010	strong		0.612	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041		T	72360224	C	T	72360224	2	4	30	1	0	0	0	0	0	0	0	1	12490	465	17	2		2	PRF1	10	72360224	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	27	72360224	63174523	351	13502											
ANXA7	310	hgsc.bcm.edu	37	chr10	75139952	75139952	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttatactctggttctcatcaCgatttccctgcaaaagagaa	12	13	6	10	1	3	1	2	0	2	1	5	3	4	1	1	1	2	2	1	1	5	4	rs10159690	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:75139952C>T	ENST00000372921.5	-	10	982	c.926G>A	c.(925-927)cGt>cAt	p.R309H	RP11-537A6.9_ENST00000427492.1_RNA|ANXA7_ENST00000535178.1_Missense_Mutation_p.R179H	NM_001156.3	NP_001147.1	P20073	ANXA7_HUMAN	annexin A7	331					autophagy (GO:0006914)|cell proliferation (GO:0008283)|cellular calcium ion homeostasis (GO:0006874)|cellular water homeostasis (GO:0009992)|epithelial cell differentiation (GO:0030855)|hemostasis (GO:0007599)|membrane fusion (GO:0061025)|negative regulation of gene expression (GO:0010629)|regulation of cell shape (GO:0008360)|response to calcium ion (GO:0051592)|response to organic cyclic compound (GO:0014070)|response to salt stress (GO:0009651)|social behavior (GO:0035176)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|integrin binding (GO:0005178)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	26	Prostate(51;0.0119)					GTTCTCATCACGATTTCCCTG	0.388																																					p.R331H		Atlas-SNP	.											ANXA7,colon,carcinoma,-1,1	ANXA7	50	1	0			c.G992A						scavenged	.						159	156	157					10																	75139952		2203	4300	6503	SO:0001583	missense	310	exon11			TCATCACGATTTC	J04543	CCDS7325.1, CCDS7326.1	10q22.2	2005-11-09			ENSG00000138279	ENSG00000138279		"Annexins"	545	protein-coding gene	gene with protein product		186360		ANX7		7515686	Standard	NM_001156		Approved		uc001jtz.2	P20073	OTTHUMG00000018463	ENST00000372921.5:c.926G>A	10.37:g.75139952C>T	ENSP00000362012:p.Arg309His	89	0	0		62	3	0.0483871	NM_004034	Q5F2H3|Q5T0M6|Q5T0M7	Missense_Mutation	SNP	ENST00000372921.5	37	CCDS7325.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.416323	0.83449	.	.	ENSG00000138279	ENST00000372921;ENST00000372919;ENST00000535178	T;T;T	0.17370	2.28;2.28;2.28	6.17	4.27	0.50696	.	0.000000	0.85682	D	0.000000	T	0.55226	0.1907	H	0.98178	4.165	0.51767	D	0.999933	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.997;0.998;0.996;0.998;0.997	T	0.68469	-0.5400	10	0.87932	D	0	.	10.012	0.41992	0.1369:0.7898:0.0:0.0733	rs10159690;rs10159690	309;309;236;309;331	Q53HM8;B2R7L2;B4DWU2;P20073-2;P20073	.;.;.;.;ANXA7_HUMAN	H	309;331;179	ENSP00000362012:R309H;ENSP00000362010:R331H;ENSP00000442864:R179H	ENSP00000362010:R331H	R	-	2	0	ANXA7	74809958	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	4.762000	0.62250	1.575000	0.49775	0.655000	0.94253	CGT	C|0.994;T|0.006	0.006	strong		0.388	ANXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048646.2	NM_001156		T	75139952	C	T	75139952	3	4	30	1	0	0	0	0	1	0	0	0	723	536	19	1	490	1	ANXA7	10	75139952	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	2779728	75139952	60394795	352	13503											
RPS24	6229	hgsc.bcm.edu	37	chr10	79814612	79814612	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctccccaccctgtggacggTgacttggtcctccacttgcc	4	11	9	17	1	1	1	0	1	1	0	4	2	3	2	6	3	1	0	6	3	0	2	rs2257155	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:79814612T>C	ENST00000440692.1	+	5	856	c.714T>C	c.(712-714)ggT>ggC	p.G238G	RPS24_ENST00000476545.1_3'UTR	NM_001142285.1	NP_001135757.1	P62847	RS24_HUMAN	ribosomal protein S24	0					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)			ctgtggacggtgacttggtcc	0.572													T|||	3	0.000599042	0.0	0.0014	5008	,	,		17704	0.0		0.002	False		,,,				2504	0.0				p.G238G		Atlas-SNP	.											.	RPS24	23	.	0			c.T714C						PASS	.	T		0,1384		0,0,692	105	103	104		714	-1.1	0	10	dbSNP_100	104	10,3172		0,10,1581	no	coding-synonymous	RPS24	NM_001142285.1		0,10,2273	CC,CT,TT		0.3143,0.0,0.219		238/290	79814612	10,4556	692	1591	2283	SO:0001819	synonymous_variant	6229	exon5			GGACGGTGACTTG	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	ENST00000440692.1:c.714T>C	10.37:g.79814612T>C		169	0	0		94	67	0.712766	NM_001142285	E7EPK6|P16632|Q5T0P7|Q5T0P8|Q7Z3D1	Silent	SNP	ENST00000440692.1	37	CCDS44443.1																																																																																			T|1.000;|0.000	.	weak		0.572	RPS24-202	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001026		C	79814612	T	C	79814612	2	2	30	1	0	0	0	0	0	0	0	1	13650	1683	59	3		3	RPS24	10	79814612	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	4674660	79814612	55720135	353	13504											
ANXA11	311	hgsc.bcm.edu	37	chr10	81917486	81917486	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcgctgcgagacaccatgaTgcgaatcagggtccggtcct	8	8	12	13	4	1	2	1	1	0	1	4	4	3	2	3	2	2	1	3	2	1	0	rs1802932	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:81917486T>C	ENST00000438331.1	-	16	1851	c.1369A>G	c.(1369-1371)Atc>Gtc	p.I457V	ANXA11_ENST00000422982.3_Missense_Mutation_p.I457V|ANXA11_ENST00000372231.3_Missense_Mutation_p.I457V|ANXA11_ENST00000535999.1_Missense_Mutation_p.I457V|ANXA11_ENST00000360615.4_Missense_Mutation_p.I457V|ANXA11_ENST00000265447.4_Missense_Mutation_p.I457V|ANXA11_ENST00000537102.1_Missense_Mutation_p.I424V	NM_145869.1	NP_665876.1	P50995	ANX11_HUMAN	annexin A11	457			I -> V (in dbSNP:rs1802932).		cytokinesis, completion of separation (GO:0007109)|phagocytosis (GO:0006909)|response to calcium ion (GO:0051592)	azurophil granule (GO:0042582)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|specific granule (GO:0042581)|spindle (GO:0005819)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|MHC class II protein complex binding (GO:0023026)|phosphatidylethanolamine binding (GO:0008429)|poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)			endometrium(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(2)|urinary_tract(1)	17	Prostate(51;0.00985)|all_epithelial(25;0.0951)		Colorectal(32;0.109)			GACACCATGATGCGAATCAGG	0.597													t|||	17	0.00339457	0.0	0.0029	5008	,	,		20944	0.0		0.0139	False		,,,				2504	0.001				p.I457V		Atlas-SNP	.											.	ANXA11	32	.	0			c.A1369G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE	13,4393	20.2+/-43.8	0,13,2190	127	110	116		1369,1369,1369	5.2	1	10	dbSNP_89	116	105,8495	57.5+/-118.9	1,103,4196	yes	missense,missense,missense	ANXA11	NM_001157.2,NM_145868.1,NM_145869.1	29,29,29	1,116,6386	CC,CT,TT		1.2209,0.2951,0.9073	benign,benign,benign	457/506,457/506,457/506	81917486	118,12888	2203	4300	6503	SO:0001583	missense	311	exon15			CCATGATGCGAAT	L19605	CCDS7364.1, CCDS60576.1	10q22.3	2005-11-09			ENSG00000122359	ENSG00000122359		"Annexins"	535	protein-coding gene	gene with protein product		602572		ANX11		7508441, 9503022	Standard	NM_001157		Approved		uc001kbt.1	P50995	OTTHUMG00000018604	ENST00000438331.1:c.1369A>G	10.37:g.81917486T>C	ENSP00000398610:p.Ile457Val	121	0	0		64	39	0.609375	NM_145868	B4DVE7	Missense_Mutation	SNP	ENST00000438331.1	37	CCDS7364.1	15	0.006868131868131868	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	12	0.0158311345646438	T	13.99	2.402389	0.42613	0.002951	0.012209	ENSG00000122359	ENST00000372231;ENST00000422982;ENST00000438331;ENST00000372234;ENST00000360615;ENST00000265447;ENST00000535999;ENST00000424188;ENST00000537102;ENST00000372219	T;T;T;T;T;T;T	0.08984	3.03;3.03;3.03;3.03;3.03;3.03;3.03	5.17	5.17	0.71159	Annexin repeat, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.03739	0.0106	L	0.28192	0.835	0.50313	D	0.999865	B;B;B	0.33345	0.284;0.409;0.409	B;B;B	0.38225	0.103;0.268;0.268	T	0.45614	-0.9249	10	0.27082	T	0.32	.	13.2804	0.60210	0.0:0.0:0.0:1.0	rs1802932;rs1802932	557;457;457	B7Z6L0;Q5T0G8;P50995	.;.;ANX11_HUMAN	V	457;457;457;457;457;457;457;364;424;104	ENSP00000361305:I457V;ENSP00000404412:I457V;ENSP00000398610:I457V;ENSP00000353827:I457V;ENSP00000265447:I457V;ENSP00000441748:I457V;ENSP00000441400:I424V	ENSP00000265447:I457V	I	-	1	0	ANXA11	81907466	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	4.665000	0.61547	2.082000	0.62665	0.460000	0.39030	ATC	T|0.992;C|0.008	0.008	strong		0.597	ANXA11-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049044.1	NM_145869		C	81917486	T	C	81917486	3	2	30	1	0	0	0	0	1	0	0	0	716	1464	51	3	156	3	ANXA11	10	81917486	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	2102874	81917486	53617261	354	13505											
HECTD2	143279	hgsc.bcm.edu	37	chr10	93221018	93221018	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gttttcattttagggaagatGtagaaaaagttaagtcatca	15	14	9	3	0	3	2	3	0	0	2	3	3	3	3	0	1	0	3	0	1	6	6	rs61754655	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:93221018G>A	ENST00000298068.5	+	4	509	c.415G>A	c.(415-417)Gta>Ata	p.V139I	HECTD2_ENST00000371681.4_Missense_Mutation_p.V139I|HECTD2_ENST00000536715.1_5'Flank|HECTD2_ENST00000446394.1_Missense_Mutation_p.V139I	NM_182765.3	NP_877497	Q5U5R9	HECD2_HUMAN	HECT domain containing E3 ubiquitin protein ligase 2	139					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						TAGGGAAGATGTAGAAAAAGT	0.284													G|||	4	0.000798722	0.0	0.0029	5008	,	,		12787	0.0		0.002	False		,,,				2504	0.0				p.V139I	NSCLC(12;376 469 1699 39910 41417)	Atlas-SNP	.											.	HECTD2	60	.	0			c.G415A						PASS	.	G	ILE/VAL,ILE/VAL	4,4400	8.1+/-20.4	0,4,2198	101	114	109		415,415	-0.3	1	10	dbSNP_129	109	54,8530	34.3+/-88.2	0,54,4238	yes	missense,missense	HECTD2	NM_173497.2,NM_182765.3	29,29	0,58,6436	AA,AG,GG		0.6291,0.0908,0.4466	benign,benign	139/208,139/777	93221018	58,12930	2202	4292	6494	SO:0001583	missense	143279	exon4			GAAGATGTAGAAA	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.415G>A	10.37:g.93221018G>A	ENSP00000298068:p.Val139Ile	176	0	0		101	76	0.752475	NM_173497	Q5VZ97|Q5VZ98|Q5VZ99|Q8N1X7|Q8TCP5	Missense_Mutation	SNP	ENST00000298068.5	37	CCDS7414.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	10.46	1.357431	0.24598	9.08E-4	0.006291	ENSG00000165338	ENST00000446394;ENST00000371681;ENST00000298068	T;T;T	0.46819	1.19;0.86;1.2	5.1	-0.347	0.12617	.	0.414930	0.24467	N	0.038276	T	0.18383	0.0441	L	0.27053	0.805	0.80722	D	1	B;B;B	0.16603	0.0;0.0;0.018	B;B;B	0.10450	0.0;0.0;0.005	T	0.05402	-1.0887	10	0.15499	T	0.54	.	4.2595	0.10733	0.4162:0.0:0.3307:0.2531	rs61754655	139;139;139	E7ERR3;Q5U5R9;Q5VZ98	.;HECD2_HUMAN;.	I	139	ENSP00000401023:V139I;ENSP00000360746:V139I;ENSP00000298068:V139I	ENSP00000298068:V139I	V	+	1	0	HECTD2	93210998	0.670000	0.27512	0.997000	0.53966	0.982000	0.71751	-0.199000	0.09491	-0.086000	0.12550	0.467000	0.42956	GTA	G|0.997;A|0.003	0.003	strong		0.284	HECTD2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098620.1			A	93221018	G	A	93221018	3	1	30	1	0	0	0	0	1	0	0	0	7049	1377	48	2	429	2	HECTD2	10	93221018	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	11303532	93221018	42313729	355	13506											
FAM178A	55719	hgsc.bcm.edu	37	chr10	102716222	102716222	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcacagaaacactttgtgctActctgtggggctttggaaaa	11	11	11	8	0	1	1	0	0	1	1	1	2	1	2	0	3	3	3	0	3	4	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:102716222A>G	ENST00000238961.4	+	18	3887	c.3345A>G	c.(3343-3345)ctA>ctG	p.L1115L	FAM178A_ENST00000370269.3_Silent_p.L1115L	NM_018121.3	NP_060591.3	Q8IX21	F178A_HUMAN	family with sequence similarity 178, member A	1115						chromatin (GO:0000785)|extracellular space (GO:0005615)|nucleus (GO:0005634)											ACTTTGTGCTACTCTGTGGGG	0.328																																					p.L1115L		Atlas-SNP	.											.	FAM178A	9	.	0			c.A3345G						PASS	.						145	143	144					10																	102716222		2203	4300	6503	SO:0001819	synonymous_variant	55719	exon18			TGTGCTACTCTGT	AF460991	CCDS7500.1, CCDS44470.1, CCDS65918.1	10q24.31	2008-07-18	2008-07-18	2008-07-18	ENSG00000119906	ENSG00000119906			17814	protein-coding gene	gene with protein product		610348	"chromosome 10 open reading frame 6"	C10orf6		12459258	Standard	NM_018121		Approved	FLJ10512, FLJ25012	uc001krs.3	Q8IX21	OTTHUMG00000018919	ENST00000238961.4:c.3345A>G	10.37:g.102716222A>G		127	0	0		98	4	0.0408163	NM_001136123	A8K950|B1AL17|Q5W0L8|Q6GMU6|Q9NPE8	Silent	SNP	ENST00000238961.4	37	CCDS7500.1																																																																																			.	.	none		0.328	FAM178A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049897.3			G	102716222	A	G	102716222	2	3	30	1	0	0	0	0	0	0	0	1	5508	378	14	3		3	FAM178A	10	102716222	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	9495204	102716222	32818525	356	13507											
NOLC1	9221	hgsc.bcm.edu	37	chr10	103919738	103919738	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccaagaaggctgtggagaaGcagcagcctgtggaaagcag	13	4	15	9	0	0	2	0	0	0	2	0	4	0	3	2	3	4	4	2	3	4	0	rs143372447	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:103919738G>A	ENST00000605788.1	+	8	1180	c.945G>A	c.(943-945)aaG>aaA	p.K315K	NOLC1_ENST00000603742.1_Silent_p.K34K|NOLC1_ENST00000405356.1_Silent_p.K325K|NOLC1_ENST00000488254.2_Silent_p.K316K	NM_001284389.1|NM_004741.3	NP_001271318.1|NP_004732.2	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	315	11 X 12 AA approximate repeats of an acidic serine cluster.|Interacts with RPA194.				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)		CTGTGGAGAAGCAGCAGCCTG	0.572													G|||	15	0.00299521	0.0	0.0014	5008	,	,		18044	0.0		0.004	False		,,,				2504	0.0102				p.K315K		Atlas-SNP	.											.	NOLC1	61	.	0			c.G945A						PASS	.	G		7,4399	12.9+/-30.5	0,7,2196	38	40	39		945	4.7	1	10	dbSNP_134	39	30,8570	19.8+/-62.0	0,30,4270	no	coding-synonymous	NOLC1	NM_004741.3		0,37,6466	AA,AG,GG		0.3488,0.1589,0.2845		315/700	103919738	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	9221	exon8			GGAGAAGCAGCAG	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.945G>A	10.37:g.103919738G>A		53	0	0		73	16	0.219178	NM_004741	Q15030|Q5VV70|Q9BUV3	Silent	SNP	ENST00000605788.1	37	CCDS7530.1																																																																																			G|0.998;A|0.002	0.002	strong		0.572	NOLC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050012.2	NM_004741		A	103919738	G	A	103919738	2	1	30	1	0	0	0	0	0	0	0	1	10538	962	34	2		2	NOLC1	10	103919738	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1203516	103919738	31615009	357	13508											
CNNM2	54805	hgsc.bcm.edu	37	chr10	104678801	104678801	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagatggagaagagcaagtcCtattacctgtgcacgtcgct	12	9	11	9	2	0	3	0	0	0	3	2	4	1	3	2	1	3	3	2	1	5	2	rs117691462	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:104678801C>T	ENST00000369878.4	+	1	752	c.564C>T	c.(562-564)tcC>tcT	p.S188S	CNNM2_ENST00000433628.2_Silent_p.S188S|CNNM2_ENST00000369875.3_Silent_p.S188S	NM_017649.4	NP_060119.3	Q9H8M5	CNNM2_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 2	188					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)		AGAGCAAGTCCTATTACCTGT	0.652													C|||	8	0.00159744	0.0008	0.0	5008	,	,		13685	0.0		0.007	False		,,,				2504	0.0				p.S188S		Atlas-SNP	.											.	CNNM2	119	.	0			c.C564T						PASS	.	C	,,	2,4402		0,2,2200	96	104	102		564,564,564	2.6	1	10	dbSNP_132	102	46,8548		0,46,4251	no	coding-synonymous,coding-synonymous,coding-synonymous	CNNM2	NM_017649.3,NM_199076.1,NM_199077.1	,,	0,48,6451	TT,TC,CC		0.5353,0.0454,0.3693	,,	188/876,188/854,188/553	104678801	48,12950	2202	4297	6499	SO:0001819	synonymous_variant	54805	exon1			CAAGTCCTATTAC	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.564C>T	10.37:g.104678801C>T		134	0	0		75	62	0.826667	NM_199076	Q5T569|Q5T570|Q8WU59|Q9H952|Q9NRK5|Q9NXT4	Silent	SNP	ENST00000369878.4	37	CCDS44474.1																																																																																			C|0.996;T|0.004	0.004	strong		0.652	CNNM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050113.3	NM_017649		T	104678801	C	T	104678801	2	4	30	1	0	0	0	0	0	0	0	1	3615	668	24	2		2	CNNM2	10	104678801	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	759063	104678801	30855946	358	13509											
VWA2	340706	hgsc.bcm.edu	37	chr10	116045993	116045993	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccttgcggcaggcggcagaGcgtggcttcgggagcgccac	5	5	18	13	5	0	1	0	0	0	1	1	2	0	2	2	5	3	3	2	5	0	2	rs566742651	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:116045993G>A	ENST00000392982.3	+	11	1543	c.1293G>A	c.(1291-1293)gaG>gaA	p.E431E	VWA2_ENST00000603594.1_Silent_p.E431E			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	431	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)		AGGCGGCAGAGCGTGGCTTCG	0.662																																					p.E431E		Atlas-SNP	.											.	VWA2	64	.	0			c.G1293A						PASS	.						56	49	51					10																	116045993		2203	4299	6502	SO:0001819	synonymous_variant	340706	exon11			GGCAGAGCGTGGC	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.1293G>A	10.37:g.116045993G>A		117	0	0		89	43	0.483146	NM_001272046	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Silent	SNP	ENST00000392982.3	37																																																																																				.	.	none		0.662	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496		A	116045993	G	A	116045993	2	1	30	1	0	0	0	0	0	0	0	1	17254	962	34	2		2	VWA2	10	116045993	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	11367192	116045993	19488754	359	13510											
PNLIPRP3	119548	hgsc.bcm.edu	37	chr10	118231317	118231317	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tctgttaaactcagtggaagCgaagtcactcaaggaactgt	13	10	10	8	1	4	0	3	0	1	0	4	3	4	2	0	2	3	1	0	2	6	1			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:118231317C>T	ENST00000369230.3	+	10	1244	c.1098C>T	c.(1096-1098)agC>agT	p.S366S		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	366	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)		TCAGTGGAAGCGAAGTCACTC	0.453																																					p.S366S		Atlas-SNP	.											.	PNLIPRP3	101	.	0			c.C1098T						PASS	.						203	209	207					10																	118231317		2203	4300	6503	SO:0001819	synonymous_variant	119548	exon10			TGGAAGCGAAGTC	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.1098C>T	10.37:g.118231317C>T		233	0	0		200	86	0.43	NM_001011709		Silent	SNP	ENST00000369230.3	37	CCDS31292.1																																																																																			.	.	none		0.453	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404		T	118231317	C	T	118231317	2	4	30	1	0	0	0	0	0	0	0	1	12161	767	27	1		1	PNLIPRP3	10	118231317	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	2185324	118231317	17303430	360	13511											
C10orf46	143384	hgsc.bcm.edu	37	chr10	120489828	120489828	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcataggatatggggatataGtcaccaggactctgagttaa	13	11	11	6	0	3	1	2	1	1	0	3	4	3	4	1	4	0	1	1	4	5	5	rs41284412	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:120489828G>A	ENST00000369151.3	-	2	945	c.462C>T	c.(460-462)gaC>gaT	p.D154D	CACUL1_ENST00000340214.4_Silent_p.D154D	NM_153810.4	NP_722517.3	Q86Y37	CACL1_HUMAN	CDK2-associated, cullin domain 1	154					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)										TGGGGATATAGTCACCAGGAC	0.348													G|||	4	0.000798722	0.0	0.0	5008	,	,		19535	0.0		0.004	False		,,,				2504	0.0				p.D154D		Atlas-SNP	.											.	.	.	.	0			c.C462T						PASS	.	G		3,3659		0,3,1828	125	121	122		462	5.7	1	10	dbSNP_127	122	41,8135		0,41,4047	no	coding-synonymous	C10orf46	NM_153810.4		0,44,5875	AA,AG,GG		0.5015,0.0819,0.3717		154/370	120489828	44,11794	1831	4088	5919	SO:0001819	synonymous_variant	143384	exon2			GATATAGTCACCA	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.462C>T	10.37:g.120489828G>A		137	0	0		104	54	0.519231	NM_153810	Q5XPL7|Q8IY11|Q8N7S4	Silent	SNP	ENST00000369151.3	37	CCDS41570.1																																																																																			G|0.998;A|0.002	0.002	strong		0.348	CACUL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050612.2	NM_153810		A	120489828	G	A	120489828	2	1	30	1	0	0	0	0	0	0	0	1	1606	1020	36	2		2	C10orf46	10	120489828	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2258511	120489828	15044919	361	13512											
EIF3A	8661	hgsc.bcm.edu	37	chr10	120819176	120819187	+	In_Frame_Del	DEL	AAGGAACCAAAG	AAGGAACCAAAG	-																															cagttggaaagcatcaacaaAaggaaccaaagaagtcaaac																								rs374628063		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	AAGGAACCAAAG	AAGGAACCAAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:120819176_120819187delAAGGAACCAAAG	ENST00000369144.3	-	10	1497_1508	c.1370_1381delCTTTGGTTCCTT	c.(1369-1383)tctttggttcctttt>ttt	p.SLVP457del	SNORA19_ENST00000410656.1_RNA|EIF3A_ENST00000541549.1_In_Frame_Del_p.SLVP423del|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)	p.P460F(1)		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)		GCATCAACAAAAGGAACCAAAGAAGTCAAACG	0.434																																					p.457_461del		Atlas-Indel	.											.	EIF3A	142	.	1	Substitution - Missense(1)	skin(1)	c.1371_1382del						PASS	.																																			SO:0001651	inframe_deletion	8661	exon10			.	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.1370_1381delCTTTGGTTCCTT	10.37:g.120819176_120819187delAAGGAACCAAAG	ENSP00000358140:p.Ser457_Pro460del	215	0	0		176	25	0.142045	NM_003750	B7ZBG9|Q6IBN8|Q96TD5	In_Frame_Del	DEL	ENST00000369144.3	37	CCDS7608.1																																																																																			.	.	none		0.434	EIF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050634.1	NM_003750		-	120819187	AAGGAACCAAAG	-	120819176	7	5	30	1	0	1	0	1	0	0	0	0	5014	14	1	0	2819	0	EIF3A	10	120819176	In_Frame_Del	DEL	AAGGAACCAAAG	TCGA-GR-7353-01A-11D-2210-10	329348	120819176	14715571	362	13513											
TACC2	10579	hgsc.bcm.edu	37	chr10	123846252	123846252	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagacttcagggagcacatcGccaagatcttcgagaagcct	12	7	10	12	2	2	3	1	0	1	3	4	5	2	4	2	1	2	1	2	1	2	2	rs201709460		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:123846252G>A	ENST00000369005.1	+	4	4577	c.4237G>A	c.(4237-4239)Gcc>Acc	p.A1413T	TACC2_ENST00000453444.2_Missense_Mutation_p.A1413T|TACC2_ENST00000334433.3_Missense_Mutation_p.A1413T|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000515603.1_Missense_Mutation_p.A1413T|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515273.1_Missense_Mutation_p.A1413T	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	1413					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)				GGAGCACATCGCCAAGATCTT	0.592													G|||	0	0.0	0.0	0.0	5008	,	,		19162	0.0		0.0	False		,,,				2504	0.0				p.A1413T		Atlas-SNP	.											.	TACC2	271	.	0			c.G4237A						PASS	.	G	,THR/ALA	0,4406		0,0,2203	70	67	68		,4237	4.2	1	10		68	1,8599	1.2+/-3.3	0,1,4299	yes	intron,missense	TACC2	NM_206861.1,NM_206862.2	,58	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,benign	,1413/2949	123846252	1,13005	2203	4300	6503	SO:0001583	missense	10579	exon4			CACATCGCCAAGA	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.4237G>A	10.37:g.123846252G>A	ENSP00000358001:p.Ala1413Thr	106	0	0		119	51	0.428571	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	3.835	-0.035002	0.07543	0.0	1.16E-4	ENSG00000138162	ENST00000369005;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000453444;ENST00000340076	T;T;T;T;T	0.02301	4.35;4.46;4.37;4.35;4.46	5.27	4.15	0.48705	.	0.234704	0.22121	N	0.064340	T	0.00936	0.0031	N	0.02539	-0.55	0.22280	N	0.999238	B;B;B	0.10296	0.003;0.003;0.003	B;B;B	0.01281	0.0;0.0;0.0	T	0.47724	-0.9095	10	0.02654	T	1	-6.9253	7.1361	0.25529	0.8892:0.0:0.1108:0.0	.	1413;1413;1413	E9PBC6;E7EMZ9;O95359	.;.;TACC2_HUMAN	T	1413;1413;1413;1413;1413;1403	ENSP00000358001:A1413T;ENSP00000424467:A1413T;ENSP00000427618:A1413T;ENSP00000334280:A1413T;ENSP00000395048:A1413T	ENSP00000334280:A1413T	A	+	1	0	TACC2	123836242	1.000000	0.71417	1.000000	0.80357	0.731000	0.41821	3.191000	0.50981	0.855000	0.35359	0.549000	0.68633	GCC	G|0.999;A|0.001	0.001	strong		0.592	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			A	123846252	G	A	123846252	3	1	30	1	0	0	0	0	1	0	0	0	15517	1087	38	1	4247	1	TACC2	10	123846252	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	3027076	123846252	11688495	363	13514											
DMBT1	1755	hgsc.bcm.edu	37	chr10	124351974	124351974	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggccccaggaaatgcccggtTtggccagggctcaggaccca	8	5	14	14	1	1	0	1	0	0	0	1	2	1	2	5	6	1	2	5	6	1	1			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:124351974T>G	ENST00000338354.3	+	20	2469	c.2363T>G	c.(2362-2364)tTt>tGt	p.F788C	DMBT1_ENST00000368955.3_Missense_Mutation_p.F778C|DMBT1_ENST00000368956.2_Intron|DMBT1_ENST00000368909.3_Missense_Mutation_p.F788C|DMBT1_ENST00000344338.3_Missense_Mutation_p.F778C|DMBT1_ENST00000330163.4_Intron|DMBT1_ENST00000359586.6_Intron			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	788	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)				AATGCCCGGTTTGGCCAGGGC	0.617																																					p.F788C	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.T2363G						PASS	.						172	135	147					10																	124351974		1994	4114	6108	SO:0001583	missense	1755	exon20			CCCGGTTTGGCCA		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.2363T>G	10.37:g.124351974T>G	ENSP00000342210:p.Phe788Cys	90	0	0		78	26	0.333333	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	37		.	.	.	.	.	.	.	.	.	.	T	8.174	0.792281	0.16258	.	.	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000344338;ENST00000368909;ENST00000368955	T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13	3.86	3.86	0.44501	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	.	.	.	.	D	0.84547	0.5496	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	0.97110	1.0;0.998;0.998;0.999	D	0.86955	0.2088	9	0.87932	D	0	.	8.6056	0.33771	0.1713:0.0:0.0:0.8286	.	549;788;778;788	Q9UGM3-4;Q9UGM3-6;Q9UGM3-3;Q9UGM3	.;.;.;DMBT1_HUMAN	C	788;788;788;788;788;788;778;788;778	ENSP00000342210:F788C;ENSP00000343175:F778C;ENSP00000357905:F788C;ENSP00000357951:F778C	ENSP00000342210:F788C	F	+	2	0	DMBT1	124341964	1.000000	0.71417	0.015000	0.15790	0.070000	0.16714	3.795000	0.55499	1.525000	0.49052	0.456000	0.33151	TTT	.	.	none		0.617	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406		G	124351974	T	G	124351974	3	3	30	1	0	0	0	0	1	0	0	0	4579	1841	64	5	2441	5	DMBT1	10	124351974	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	505722	124351974	11182773	364	13515											
DOCK1	1793	hgsc.bcm.edu	37	chr10	129046371	129046371	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggaaaatgaggactgatgtgGtagtaagtgtccctttcacc	11	11	12	7	0	1	2	1	2	0	0	2	4	2	4	2	3	0	2	2	3	4	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:129046371G>A	ENST00000280333.6	+	28	2993	c.2884G>A	c.(2884-2886)Gta>Ata	p.V962I	DOCK1_ENST00000484400.1_3'UTR	NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	962					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)		GACTGATGTGGTAGTAAGTGT	0.388																																					p.V962I		Atlas-SNP	.											.	DOCK1	188	.	0			c.G2884A						PASS	.						112	103	106					10																	129046371		1898	4109	6007	SO:0001583	missense	1793	exon28			GATGTGGTAGTAA	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.2884G>A	10.37:g.129046371G>A	ENSP00000280333:p.Val962Ile	193	0	0		186	85	0.456989	NM_001380	A9Z1Z5	Missense_Mutation	SNP	ENST00000280333.6	37		.	.	.	.	.	.	.	.	.	.	G	11.06	1.528362	0.27299	.	.	ENSG00000150760	ENST00000280333	T	0.21734	1.99	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.11495	0.0280	N	0.10733	0.035	0.80722	D	1	B;B	0.24426	0.01;0.103	B;B	0.18871	0.015;0.023	T	0.11084	-1.0602	10	0.07030	T	0.85	.	19.1025	0.93279	0.0:0.0:1.0:0.0	.	962;962	B2RUU3;Q14185	.;DOCK1_HUMAN	I	962	ENSP00000280333:V962I	ENSP00000280333:V962I	V	+	1	0	DOCK1	128936361	1.000000	0.71417	0.997000	0.53966	0.630000	0.37929	6.639000	0.74314	2.491000	0.84063	0.563000	0.77884	GTA	.	.	none		0.388	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380		A	129046371	G	A	129046371	3	1	30	1	0	0	0	0	1	0	0	0	4686	1261	44	2	2994	2	DOCK1	10	129046371	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	4694397	129046371	6488376	365	13516											
MKI67	4288	hgsc.bcm.edu	37	chr10	129909929	129909929	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaaagatcttccttaaagTccattttttggttggaaatg	11	16	8	6	0	1	2	0	1	1	1	3	3	3	3	2	2	0	1	2	2	4	6			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr10:129909929T>G	ENST00000368654.3	-	11	2615	c.2240A>C	c.(2239-2241)gAc>gCc	p.D747A	MKI67_ENST00000368653.3_Missense_Mutation_p.D387A|MKI67_ENST00000484853.1_5'UTR	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	747					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)				TTCCTTAAAGTCCATTTTTTG	0.348																																					p.D747A		Atlas-SNP	.											.	MKI67	363	.	0			c.A2240C						PASS	.						99	97	97					10																	129909929		2203	4300	6503	SO:0001583	missense	4288	exon11			TTAAAGTCCATTT	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.2240A>C	10.37:g.129909929T>G	ENSP00000357643:p.Asp747Ala	85	0	0		67	28	0.41791	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	T	17.07	3.295801	0.60086	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609;ENST00000368652	T;T	0.01584	4.77;4.75	5.18	4.01	0.46588	.	0.000000	0.45867	D	0.000331	T	0.06872	0.0175	M	0.64404	1.975	0.09310	N	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.79784	0.993;0.973;0.976	T	0.09975	-1.0650	10	0.72032	D	0.01	.	7.2985	0.26408	0.0:0.0771:0.1574:0.7655	.	746;387;747	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	A	747;387;746;322	ENSP00000357643:D747A;ENSP00000357642:D387A	ENSP00000357641:D322A	D	-	2	0	MKI67	129799919	0.017000	0.18338	0.150000	0.22450	0.353000	0.29299	1.086000	0.30853	0.937000	0.37394	0.533000	0.62120	GAC	.	.	none		0.348	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417		G	129909929	T	G	129909929	3	3	30	1	0	0	0	0	1	0	0	0	9607	1667	58	5	7550	5	MKI67	10	129909929	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	863558	129909929	5624818	366	13517											
C11orf35	256329	hgsc.bcm.edu	37	chr11	556584	556584	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ctgggtgagtgggttttctgGagatctagagagagcagcgc	8	10	17	6	1	2	4	0	1	2	3	2	6	2	4	0	3	2	2	0	3	1	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:556584G>A	ENST00000329451.3	-	9	1043	c.981C>T	c.(979-981)ctC>ctT	p.L327L	RP11-496I9.1_ENST00000527620.1_RNA|RP11-496I9.1_ENST00000527113.1_RNA	NM_173573.2	NP_775844.2	Q8IXW0	LMTD2_HUMAN		327										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)		GGGTTTTCTGGAGATCTAGAG	0.657																																					p.L327L		Atlas-SNP	.											.	C11orf35	22	.	0			c.C981T						PASS	.						20	20	20					11																	556584		2172	4248	6420	SO:0001819	synonymous_variant	256329	exon9			TTTCTGGAGATCT																												ENST00000329451.3:c.981C>T	11.37:g.556584G>A		67	0	0		45	28	0.622222	NM_173573		Silent	SNP	ENST00000329451.3	37	CCDS7701.1																																																																																			.	.	none		0.657	C11orf35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254973.2			A	556584	G	A	556584	2	1	30	1	0	0	0	0	0	0	0	1	1640	1161	41	2		2	C11orf35	11	556584	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10		556584	134449932	367	13518											
MUC2	4583	hgsc.bcm.edu	37	chr11	1093481	1093481	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcacacagaccccaaccaCggtactcatcaccaccacca	13	3	5	20	2	2	1	2	0	0	1	2	1	2	1	6	2	2	2	6	2	2	1	rs547164370	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1093481C>T	ENST00000441003.2	+	30	5327	c.5300C>T	c.(5299-5301)aCg>aTg	p.T1767M	MUC2_ENST00000333592.6_Missense_Mutation_p.T55M|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Splice_Site_p.T1734M	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0					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)	accccaaccacggtactcatc	0.612													c|||	7	0.00139776	0.0	0.0014	5008	,	,		26176	0.005		0.001	False		,,,				2504	0.0				p.T1767M		Atlas-SNP	.											.	MUC2	614	.	0			c.C5300T						PASS	.																																			SO:0001583	missense	4583	exon30			CAACCACGGTACT	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.5300C>T	11.37:g.1093481C>T	ENSP00000415183:p.Thr1767Met	72	0	0		69	20	0.289855	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	3.092	-0.186712	0.06340	.	.	ENSG00000198788	ENST00000441003;ENST00000359061;ENST00000333592	T;T;T	0.12879	2.64;3.12;2.78	1.77	-3.54	0.04653	.	0.173549	0.20316	U	0.094725	T	0.06325	0.0163	.	.	.	0.09310	N	1	B	0.33073	0.396	B	0.24848	0.056	T	0.14952	-1.0454	9	0.66056	D	0.02	.	1.3227	0.02119	0.1446:0.3605:0.1442:0.3508	.	1767	E7EUV1	.	M	1767;1734;55	ENSP00000415183:T1767M;ENSP00000351956:T1734M;ENSP00000331373:T55M	ENSP00000331373:T55M	T	+	2	0	MUC2	1083481	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.581000	0.23819	-1.920000	0.01069	-1.152000	0.01820	ACG	.	.	none		0.612	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		T	1093481	C	T	1093481	3	4	30	1	0	0	0	0	1	0	0	0	9984	536	19	1	5418	1	MUC2	11	1093481	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	536897	1093481	133913035	368	13519											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1269655	1269655	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacaaccagggccaccggcTctgtggccaccccctcttcc	6	6	8	21	1	2	0	0	0	2	0	3	0	3	0	8	3	1	1	8	3	1	1			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:1269655T>G	ENST00000529681.1	+	31	11603	c.11545T>G	c.(11545-11547)Tct>Gct	p.S3849A	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.S3852A	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3849	11 X approximate tandem repeats, Ser/Thr- rich.|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)		GGCCACCGGCTCTGTGGCCAC	0.642																																					p.S3849A		Atlas-SNP	.											.	MUC5B	473	.	0			c.T11545G						PASS	.						118	137	131					11																	1269655		2065	4172	6237	SO:0001583	missense	727897	exon31			ACCGGCTCTGTGG	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.11545T>G	11.37:g.1269655T>G	ENSP00000436812:p.Ser3849Ala	219	0	0		341	98	0.28739	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	T	1.973	-0.435940	0.04636	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.21031	2.03;2.21	0.58	-1.16	0.09678	.	.	.	.	.	T	0.17152	0.0412	M	0.75264	2.295	0.09310	N	1	P;P	0.40476	0.718;0.718	B;B	0.28385	0.089;0.089	T	0.10154	-1.0642	9	0.87932	D	0	.	4.7328	0.12974	0.0:0.2164:0.0:0.7836	.	4377;3852	A7Y9J9;E9PBJ0	.;.	A	3849;3852;3793;3754	ENSP00000436812:S3849A;ENSP00000415793:S3852A	ENSP00000343037:S3793A	S	+	1	0	MUC5B	1226231	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	-5.111000	0.00150	-0.567000	0.06046	0.163000	0.16589	TCT	.	.	none		0.642	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		G	1269655	T	G	1269655	3	3	30	1	0	0	0	0	1	0	0	0	9988	1551	54	5	11676	5	MUC5B	11	1269655	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	176174	1269655	133736861	369	13520											
TSPAN32	10077	hgsc.bcm.edu	37	chr11	2325427	2325427	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagggaggcccagggcctcaTggcaggggtgagttcattgt	7	8	18	8	0	2	1	2	1	0	0	2	3	2	2	2	6	0	2	2	6	0	2	rs61744929	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:2325427T>C	ENST00000182290.4	+	3	409	c.272T>C	c.(271-273)aTg>aCg	p.M91T	C11orf21_ENST00000470369.1_5'Flank|TSPAN32_ENST00000483227.1_3'UTR|C11orf21_ENST00000381153.3_5'Flank|TSPAN32_ENST00000451520.2_Missense_Mutation_p.M80T|TSPAN32_ENST00000381121.3_Missense_Mutation_p.M91T	NM_139022.2	NP_620591.3	Q96QS1	TSN32_HUMAN	tetraspanin 32	91					cell-cell signaling (GO:0007267)|cytoskeleton organization (GO:0007010)|defense response to protozoan (GO:0042832)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of cell proliferation (GO:0008285)|negative regulation of myeloid dendritic cell activation (GO:0030886)|platelet aggregation (GO:0070527)|regulation of defense response to virus (GO:0050688)	cell surface (GO:0009986)|integrin alphaIIb-beta3 complex (GO:0070442)|intracellular (GO:0005622)				breast(1)|central_nervous_system(1)|lung(4)|ovary(1)|skin(1)	8		all_epithelial(84;4.89e-05)|Breast(177;0.000962)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|all_neural(188;0.00791)|Lung NSC(207;0.209)		BRCA - Breast invasive adenocarcinoma(625;0.000533)|LUSC - Lung squamous cell carcinoma(625;0.082)|Lung(200;0.153)		CAGGGCCTCATGGCAGGGGTG	0.632													T|||	19	0.00379393	0.0015	0.0043	5008	,	,		16077	0.0		0.0099	False		,,,				2504	0.0041				p.M91T		Atlas-SNP	.											.	TSPAN32	19	.	0			c.T272C						PASS	.	T	THR/MET	8,4390		0,8,2191	37	34	35		272	4.1	1	11	dbSNP_129	35	119,8465		0,119,4173	yes	missense	TSPAN32	NM_139022.2	81	0,127,6364	CC,CT,TT		1.3863,0.1819,0.9783	benign	91/321	2325427	127,12855	2199	4292	6491	SO:0001583	missense	10077	exon3			GCCTCATGGCAGG	AF176070	CCDS7733.1	11p15	2013-02-14	2005-08-16	2005-08-16	ENSG00000064201	ENSG00000064201		"Tetraspanins"	13410	protein-coding gene	gene with protein product		603853	"pan-hematopoietic expression"	TSSC6, PHEMX		10072438, 10950922	Standard	NM_139022		Approved		uc001lvy.1	Q96QS1	OTTHUMG00000009762	ENST00000182290.4:c.272T>C	11.37:g.2325427T>C	ENSP00000182290:p.Met91Thr	36	0	0		36	14	0.388889	NM_139022	Q96KX4|Q9HC50|Q9HC51|Q9Y5U1	Missense_Mutation	SNP	ENST00000182290.4	37	CCDS7733.1	8	0.003663003663003663	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	T	10.19	1.282156	0.23392	0.001819	0.013863	ENSG00000064201	ENST00000182290;ENST00000381121;ENST00000451520;ENST00000444307;ENST00000381117	T;T;T;T	0.79554	-1.28;-1.28;-1.28;-1.24	4.12	4.12	0.48240	.	0.146307	0.30649	N	0.009173	T	0.78572	0.4304	L	0.51422	1.61	0.31276	N	0.691117	D;D;P;D;P;D	0.63880	0.993;0.978;0.936;0.991;0.948;0.978	P;P;P;P;P;P	0.60609	0.877;0.649;0.556;0.736;0.684;0.733	T	0.80294	-0.1443	10	0.42905	T	0.14	-24.6332	9.7847	0.40668	0.0:0.0:0.0:1.0	rs61744929	78;91;61;91;91;80	B4DQ90;Q96QS1-5;G3XAG6;Q96QS1-3;Q96QS1;F8WCN6	.;.;.;.;TSN32_HUMAN;.	T	91;91;80;61;61	ENSP00000182290:M91T;ENSP00000370513:M91T;ENSP00000405205:M80T;ENSP00000370509:M61T	ENSP00000182290:M91T	M	+	2	0	TSPAN32	2282003	0.988000	0.35896	1.000000	0.80357	0.169000	0.22640	0.386000	0.20702	1.636000	0.50526	0.443000	0.29094	ATG	T|0.992;C|0.008	0.008	strong		0.632	TSPAN32-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026912.2	NM_139024		C	2325427	T	C	2325427	3	2	30	1	0	0	0	0	1	0	0	0	16662	1464	51	3	282	3	TSPAN32	11	2325427	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	1055772	2325427	132681089	370	13521											
TRPM5	29850	hgsc.bcm.edu	37	chr11	2434799	2434799	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcggccatgtccccccacCagatcctggtcaggaaggcc	7	6	11	17	1	1	1	1	0	0	1	3	2	3	2	7	4	1	0	7	4	1	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:2434799C>A	ENST00000155858.6	-	13	1918	c.1910G>T	c.(1909-1911)tGg>tTg	p.W637L	TRPM5_ENST00000452833.1_Missense_Mutation_p.W639L|TRPM5_ENST00000533060.1_Missense_Mutation_p.W637L|TRPM5_ENST00000528453.1_Missense_Mutation_p.W637L	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)		GTCCCCCCACCAGATCCTGGT	0.642																																					p.W637L	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.G1910T						PASS	.						54	53	53					11																	2434799		2202	4299	6501	SO:0001583	missense	29850	exon13			CCCCACCAGATCC	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.1910G>T	11.37:g.2434799C>A	ENSP00000155858:p.Trp637Leu	388	1	0.00257732		392	126	0.321429	NM_014555		Missense_Mutation	SNP	ENST00000155858.6	37	CCDS31340.1	.	.	.	.	.	.	.	.	.	.	C	21.3	4.130183	0.77549	.	.	ENSG00000070985	ENST00000533881;ENST00000155858;ENST00000452833;ENST00000533060;ENST00000528453;ENST00000437542	T;T;T;T;T	0.80738	-1.41;-1.41;-1.41;-1.41;-1.41	3.97	3.97	0.46021	.	0.000000	0.64402	D	0.000001	D	0.90448	0.7009	M	0.87381	2.88	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	D	0.92548	0.6047	10	0.87932	D	0	-15.2033	15.4027	0.74855	0.0:1.0:0.0:0.0	.	637;639;637	E9PRW0;Q9NZQ8-2;Q9NZQ8	.;.;TRPM5_HUMAN	L	631;637;639;637;637;637	ENSP00000434383:W631L;ENSP00000155858:W637L;ENSP00000387965:W639L;ENSP00000434121:W637L;ENSP00000436809:W637L	ENSP00000155858:W637L	W	-	2	0	TRPM5	2391375	1.000000	0.71417	1.000000	0.80357	0.754000	0.42855	7.383000	0.79741	1.940000	0.56252	0.313000	0.20887	TGG	.	.	none		0.642	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555		A	2434799	C	A	2434799	3	1	30	1	0	0	0	0	1	0	0	0	16604	595	21	4	1635	4	TRPM5	11	2434799	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	109372	2434799	132571717	371	13522											
TRPM5	29850	hgsc.bcm.edu	37	chr11	2436464	2436464	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagaaggccggtggccccgCgggtggctcccgggcctgct	3	5	19	14	4	0	1	0	0	0	1	1	2	1	1	5	7	1	2	5	7	1	0	rs34551253	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:2436464C>T	ENST00000155858.6	-	9	1374	c.1366G>A	c.(1366-1368)Gcg>Acg	p.A456T	TRPM5_ENST00000452833.1_Missense_Mutation_p.A458T|TRPM5_ENST00000533060.1_Missense_Mutation_p.A456T|TRPM5_ENST00000528453.1_Missense_Mutation_p.A456T	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)		GGTGGCCCCGCGGGTGGCTCC	0.716													C|||	54	0.0107827	0.0023	0.0245	5008	,	,		13476	0.001		0.0308	False		,,,				2504	0.002				p.A456T	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.G1366A						PASS	.	C	THR/ALA	35,4235		1,33,2101	7	9	9		1366	-6.4	0	11	dbSNP_126	9	273,8141		6,261,3940	yes	missense	TRPM5	NM_014555.3	58	7,294,6041	TT,TC,CC		3.2446,0.8197,2.4283	benign	456/1166	2436464	308,12376	2135	4207	6342	SO:0001583	missense	29850	exon9			GCCCCGCGGGTGG	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.1366G>A	11.37:g.2436464C>T	ENSP00000155858:p.Ala456Thr	15	0	0		10	6	0.6	NM_014555		Missense_Mutation	SNP	ENST00000155858.6	37	CCDS31340.1	35	0.016025641025641024	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	22	0.029023746701846966	C	0.009	-1.820965	0.00595	0.008197	0.032446	ENSG00000070985	ENST00000533881;ENST00000155858;ENST00000452833;ENST00000533060;ENST00000528453;ENST00000437542	T;T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31;-0.31	3.19	-6.37	0.01963	.	1.134030	0.06672	N	0.766349	T	0.14227	0.0344	N	0.08118	0	0.09310	N	1	B;B;B	0.13594	0.005;0.005;0.008	B;B;B	0.09377	0.002;0.001;0.004	T	0.05517	-1.0880	10	0.14252	T	0.57	0.2166	1.5474	0.02568	0.2706:0.3676:0.1989:0.1629	rs34551253	456;458;456	E9PRW0;Q9NZQ8-2;Q9NZQ8	.;.;TRPM5_HUMAN	T	450;456;458;456;456;456	ENSP00000434383:A450T;ENSP00000155858:A456T;ENSP00000387965:A458T;ENSP00000434121:A456T;ENSP00000436809:A456T	ENSP00000155858:A456T	A	-	1	0	TRPM5	2393040	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-2.025000	0.01435	-3.859000	0.00098	-1.579000	0.00862	GCG	C|0.983;T|0.017	0.017	strong		0.716	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555		T	2436464	C	T	2436464	3	4	30	1	0	0	0	0	1	0	0	0	16604	768	27	1	2195	1	TRPM5	11	2436464	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1665	2436464	132570052	372	13523											
RRM1	6240	hgsc.bcm.edu	37	chr11	4154851	4154851	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcctatggcatgaagagaTgaaaaaccagattattgcat	15	9	11	6	0	0	4	0	2	0	2	0	5	0	4	2	2	2	2	2	2	5	3	rs145770432	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:4154851T>C	ENST00000300738.5	+	17	2168	c.1964T>C	c.(1963-1965)aTg>aCg	p.M655T	RRM1_ENST00000423050.2_Missense_Mutation_p.M558T|RRM1_ENST00000534285.1_Missense_Mutation_p.M433T|RRM1_ENST00000537197.1_Missense_Mutation_p.M317T	NM_001033.3	NP_001024.1	P23921	RIR1_HUMAN	ribonucleotide reductase M1	655					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)	CATGAAGAGATGAAAAACCAG	0.403													T|||	2	0.000399361	0.0	0.0	5008	,	,		20309	0.0		0.002	False		,,,				2504	0.0				p.M655T	NSCLC(45;1345 1376 6258 22925)|Ovarian(34;894 1053 6175 12768)	Atlas-SNP	.											.	RRM1	31	.	0			c.T1964C						PASS	.	T	THR/MET	1,4401	2.1+/-5.4	0,1,2200	111	103	106		1964	5.5	1	11	dbSNP_134	106	2,8594	2.2+/-6.3	0,2,4296	yes	missense	RRM1	NM_001033.3	81	0,3,6496	CC,CT,TT		0.0233,0.0227,0.0231	benign	655/793	4154851	3,12995	2201	4298	6499	SO:0001583	missense	6240	exon17			AAGAGATGAAAAA	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.1964T>C	11.37:g.4154851T>C	ENSP00000300738:p.Met655Thr	118	0	0		112	40	0.357143	NM_001033	Q9UNN2	Missense_Mutation	SNP	ENST00000300738.5	37	CCDS7750.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	17.36	3.368737	0.61624	2.27E-4	2.33E-4	ENSG00000167325	ENST00000300738;ENST00000423050;ENST00000536894;ENST00000534285;ENST00000543838;ENST00000537197	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	5.52	5.52	0.82312	Ribonucleoside-diphosphate reductase, alpha subunit (1);Ribonucleotide reductase large subunit, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.45736	0.1357	M	0.75884	2.315	0.80722	D	1	P	0.42757	0.789	B	0.38264	0.269	T	0.55179	-0.8181	10	0.87932	D	0	-17.4615	14.8104	0.69992	0.0:0.0:0.0:1.0	.	655	P23921	RIR1_HUMAN	T	655;558;568;433;433;317	ENSP00000300738:M655T;ENSP00000390539:M558T;ENSP00000431464:M433T;ENSP00000442148:M317T	ENSP00000300738:M655T	M	+	2	0	RRM1	4111427	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.698000	0.84413	2.092000	0.63282	0.533000	0.62120	ATG	T|0.999;C|0.001	0.001	strong		0.403	RRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257197.1	NM_001033		C	4154851	T	C	4154851	3	2	30	1	0	0	0	0	1	0	0	0	13696	1464	51	3	2030	3	RRM1	11	4154851	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	1718387	4154851	130851665	373	13524											
OR51I1	390063	hgsc.bcm.edu	37	chr11	5461861	5461861	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatctccttggttttcacaCtgtagatgatagggttgagc	8	14	12	7	0	2	3	1	2	1	1	3	4	2	4	1	3	1	3	1	3	2	6	rs76233016	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:5461861C>G	ENST00000380211.1	-	1	883	c.884G>C	c.(883-885)aGt>aCt	p.S295T	HBG2_ENST00000380252.1_Intron|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA	NM_001005288.2	NP_001005288.1	Q9H343	O51I1_HUMAN	olfactory receptor, family 51, subfamily I, member 1	295					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(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)		GGTTTTCACACTGTAGATGAT	0.478													C|||	18	0.00359425	0.0	0.0086	5008	,	,		19623	0.0		0.0119	False		,,,				2504	0.0				p.S295T		Atlas-SNP	.											.	OR51I1	66	.	0			c.G884C						PASS	.	C	THR/SER	11,4391	17.9+/-39.9	0,11,2190	120	114	116		884	4.5	1	11	dbSNP_132	116	50,8544	31.7+/-84.0	0,50,4247	yes	missense	OR51I1	NM_001005288.2	58	0,61,6437	GG,GC,CC		0.5818,0.2499,0.4694	benign	295/315	5461861	61,12935	2201	4297	6498	SO:0001583	missense	390063	exon1			TTCACACTGTAGA	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.884G>C	11.37:g.5461861C>G	ENSP00000369559:p.Ser295Thr	149	0	0		125	75	0.6	NM_001005288	B9EKW2|Q6IF33	Missense_Mutation	SNP	ENST00000380211.1	37	CCDS31382.1	13	0.005952380952380952	0	0.0	3	0.008287292817679558	0	0.0	10	0.013192612137203167	C	10.13	1.265693	0.23136	0.002499	0.005818	ENSG00000167359	ENST00000321307;ENST00000380211	T	0.37752	1.18	5.47	4.54	0.55810	.	0.096735	0.47093	D	0.000243	T	0.26774	0.0655	M	0.75884	2.315	0.25867	N	0.983753	P	0.48764	0.915	B	0.32677	0.15	T	0.37526	-0.9702	10	0.51188	T	0.08	.	14.2494	0.66009	0.0:0.7161:0.2839:0.0	.	295	Q9H343	O51I1_HUMAN	T	292;295	ENSP00000369559:S295T	ENSP00000439622:S292T	S	-	2	0	OR51I1	5418437	0.045000	0.20229	0.998000	0.56505	0.339000	0.28857	2.449000	0.44935	1.289000	0.44618	0.551000	0.68910	AGT	C|0.994;G|0.006	0.006	strong		0.478	OR51I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143399.1	NM_001005288		G	5461861	C	G	5461861	3	3	30	1	0	0	0	0	1	0	0	0	11109	565	20	4	64	4	OR51I1	11	5461861	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1307010	5461861	129544655	374	13525											
ZNF215	7762	hgsc.bcm.edu	37	chr11	6962879	6962879	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctggctcacgaacaggcaaaCcacaggtgaattaggattct	13	8	10	10	1	2	1	1	1	1	0	2	3	2	2	1	4	2	2	1	4	4	2	rs141940336	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:6962879C>T	ENST00000278319.5	+	4	1066	c.478C>T	c.(478-480)Cca>Tca	p.P160S	ZNF215_ENST00000527171.1_3'UTR|ZNF215_ENST00000414517.2_Missense_Mutation_p.P160S|ZNF215_ENST00000529903.1_Missense_Mutation_p.P160S	NM_013250.2	NP_037382.2	Q9UL58	ZN215_HUMAN	zinc finger protein 215	160					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)		AACAGGCAAACCACAGGTGAA	0.413																																					p.P160S		Atlas-SNP	.											.	ZNF215	72	.	0			c.C478T						PASS	.	C	SER/PRO	0,4402		0,0,2201	90	86	87		478	1.1	0	11	dbSNP_134	87	2,8590	2.2+/-6.3	0,2,4294	yes	missense	ZNF215	NM_013250.2	74	0,2,6495	TT,TC,CC		0.0233,0.0,0.0154	benign	160/518	6962879	2,12992	2201	4296	6497	SO:0001583	missense	7762	exon4			GGCAAACCACAGG	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.478C>T	11.37:g.6962879C>T	ENSP00000278319:p.Pro160Ser	83	0	0		87	40	0.45977	NM_013250	Q96C84	Missense_Mutation	SNP	ENST00000278319.5	37	CCDS7775.1	.	.	.	.	.	.	.	.	.	.	C	0.861	-0.735158	0.03111	0.0	2.33E-4	ENSG00000149054	ENST00000278319;ENST00000414517;ENST00000529903	T;T;T	0.00768	5.72;5.72;5.72	4.32	1.07	0.20283	Krueppel-associated box (1);	0.585459	0.14355	N	0.324834	T	0.00328	0.0010	N	0.01705	-0.755	0.34821	D	0.738729	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.31998	-0.9923	10	0.02654	T	1	4.8197	5.2224	0.15375	0.0:0.4366:0.0:0.5634	.	160;160;160	B4DYW9;Q96C84;Q9UL58	.;.;ZN215_HUMAN	S	160	ENSP00000278319:P160S;ENSP00000393202:P160S;ENSP00000432306:P160S	ENSP00000278319:P160S	P	+	1	0	ZNF215	6919455	0.000000	0.05858	0.000000	0.03702	0.091000	0.18340	0.273000	0.18662	0.419000	0.25927	0.591000	0.81541	CCA	C|1.000;T|0.000	0.000	strong		0.413	ZNF215-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384550.1			T	6962879	C	T	6962879	3	4	30	1	0	0	0	0	1	0	0	0	17786	507	18	2	484	2	ZNF215	11	6962879	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1501018	6962879	128043637	375	13526											
NLRP10	338322	hgsc.bcm.edu	37	chr11	7981822	7981822	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtagtcgttactactcaggAaagcggcaagcctggggcca	10	7	14	10	2	1	0	1	0	0	0	2	1	1	1	2	5	4	3	2	5	5	3	rs143403695	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:7981822A>G	ENST00000328600.2	-	2	1498	c.1337T>C	c.(1336-1338)tTc>tCc	p.F446S		NM_176821.3	NP_789791.1	Q86W26	NAL10_HUMAN	NLR family, pyrin domain containing 10	446	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)		ACTACTCAGGAAAGCGGCAAG	0.488																																					p.F446S		Atlas-SNP	.											.	NLRP10	146	.	0			c.T1337C						PASS	.	A	SER/PHE	1,4401		0,1,2200	99	109	106		1337	3.7	0.2	11	dbSNP_134	106	1,8591		0,1,4295	yes	missense	NLRP10	NM_176821.3	155	0,2,6495	GG,GA,AA		0.0116,0.0227,0.0154	possibly-damaging	446/656	7981822	2,12992	2201	4296	6497	SO:0001583	missense	338322	exon2			CTCAGGAAAGCGG	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.1337T>C	11.37:g.7981822A>G	ENSP00000327763:p.Phe446Ser	63	0	0		53	34	0.641509	NM_176821	Q2M3C4|Q6JGT0	Missense_Mutation	SNP	ENST00000328600.2	37	CCDS7784.1	.	.	.	.	.	.	.	.	.	.	A	10.78	1.446070	0.25987	2.27E-4	1.16E-4	ENSG00000182261	ENST00000328600	D	0.87103	-2.21	4.86	3.73	0.42828	.	0.000000	0.42548	D	0.000691	D	0.92205	0.7528	M	0.83012	2.62	0.09310	N	1	D	0.76494	0.999	D	0.75484	0.986	D	0.84554	0.0646	10	0.87932	D	0	.	7.3185	0.26513	0.8987:0.0:0.1013:0.0	.	446	Q86W26	NAL10_HUMAN	S	446	ENSP00000327763:F446S	ENSP00000327763:F446S	F	-	2	0	NLRP10	7938398	0.997000	0.39634	0.178000	0.23040	0.011000	0.07611	6.425000	0.73370	0.828000	0.34709	0.533000	0.62120	TTC	A|0.999;G|0.001	0.001	strong		0.488	NLRP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385705.1	NM_176821		G	7981822	A	G	7981822	3	3	30	1	0	0	0	0	1	0	0	0	10481	246	9	3	634	3	NLRP10	11	7981822	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	1018943	7981822	127024694	376	13527											
COPB1	1315	hgsc.bcm.edu	37	chr11	14515829	14515829	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagttgttttaggaacaattTcccaaaataccagaagtaat	16	12	7	6	0	0	1	0	0	0	1	1	3	1	2	2	1	2	3	2	1	8	6			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:14515829T>C	ENST00000249923.3	-	3	548	c.248A>G	c.(247-249)gAa>gGa	p.E83G	PSMA1_ENST00000419365.2_3'UTR|PSMA1_ENST00000555531.1_3'UTR|COPB1_ENST00000439561.2_Missense_Mutation_p.E83G	NM_016451.4	NP_057535.1	P53618	COPB_HUMAN	coatomer protein complex, subunit beta 1	83					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						AGGAACAATTTCCCAAAATAC	0.363																																					p.E83G		Atlas-SNP	.											.	COPB1	81	.	0			c.A248G						PASS	.						84	88	87					11																	14515829		2200	4294	6494	SO:0001583	missense	1315	exon3			ACAATTTCCCAAA	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.248A>G	11.37:g.14515829T>C	ENSP00000249923:p.Glu83Gly	112	0	0		124	55	0.443548	NM_001144062	D3DQX0|Q6GTT7|Q9NTK2|Q9UNW7	Missense_Mutation	SNP	ENST00000249923.3	37	CCDS7815.1	.	.	.	.	.	.	.	.	.	.	T	29.3	4.997254	0.93167	.	.	ENSG00000129083	ENST00000249923;ENST00000439561;ENST00000534234;ENST00000529866;ENST00000534771	T;T;T;T;T	0.27890	1.64;1.64;1.64;1.64;1.64	5.31	5.31	0.75309	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.68540	0.3012	H	0.96142	3.775	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80137	-0.1508	10	0.87932	D	0	-14.0469	15.2851	0.73822	0.0:0.0:0.0:1.0	.	83	P53618	COPB_HUMAN	G	83	ENSP00000249923:E83G;ENSP00000397873:E83G;ENSP00000436383:E83G;ENSP00000431530:E83G;ENSP00000436401:E83G	ENSP00000249923:E83G	E	-	2	0	COPB1	14472405	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	2.004000	0.58718	0.533000	0.62120	GAA	.	.	none		0.363	COPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386410.1	NM_016451		C	14515829	T	C	14515829	3	2	30	1	0	0	0	0	1	0	0	0	3730	1783	62	3	2693	3	COPB1	11	14515829	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	6534007	14515829	120490687	377	13528											
PIK3C2A	5286	hgsc.bcm.edu	37	chr11	17158120	17158120	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcgacaccatctaaagcaCtacagatttttcttacagct	12	13	4	12	1	3	1	0	0	3	1	4	2	3	1	1	0	4	2	1	0	4	5	rs61733866	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:17158120C>T	ENST00000265970.7	-	8	1756	c.1757G>A	c.(1756-1758)aGt>aAt	p.S586N	PIK3C2A_ENST00000531428.1_Intron|PIK3C2A_ENST00000540361.1_Missense_Mutation_p.S206N	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	586					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						ATCTAAAGCACTACAGATTTT	0.328													C|||	32	0.00638978	0.0	0.0043	5008	,	,		16548	0.0		0.005	False		,,,				2504	0.0245				p.S586N		Atlas-SNP	.											.	PIK3C2A	148	.	0			c.G1757A						PASS	.	C	ASN/SER	8,4390	15.5+/-35.6	0,8,2191	114	109	111		1757	4.6	1	11	dbSNP_129	111	97,8489	53.1+/-113.8	0,97,4196	yes	missense	PIK3C2A	NM_002645.2	46	0,105,6387	TT,TC,CC		1.1297,0.1819,0.8087	benign	586/1687	17158120	105,12879	2199	4293	6492	SO:0001583	missense	5286	exon8			AAAGCACTACAGA	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.1757G>A	11.37:g.17158120C>T	ENSP00000265970:p.Ser586Asn	104	0	0		77	39	0.506494	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	37	CCDS7824.1	9	0.004120879120879121	0	0.0	4	0.011049723756906077	0	0.0	5	0.006596306068601583	C	11.39	1.626054	0.28978	0.001819	0.011297	ENSG00000011405	ENST00000265970;ENST00000540361;ENST00000544896	T;T	0.62788	0.0;0.38	5.5	4.58	0.56647	.	0.440892	0.29995	N	0.010680	T	0.36908	0.0984	L	0.35723	1.085	0.32142	N	0.585417	B	0.23735	0.09	B	0.21360	0.034	T	0.43393	-0.9394	10	0.10377	T	0.69	-8.3308	7.5542	0.27814	0.0:0.7019:0.1477:0.1504	.	586	O00443	P3C2A_HUMAN	N	586;206;586	ENSP00000265970:S586N;ENSP00000438687:S206N	ENSP00000265970:S586N	S	-	2	0	PIK3C2A	17114696	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.729000	0.47327	1.459000	0.47892	0.561000	0.74099	AGT	C|0.992;T|0.008	0.008	strong		0.328	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645		T	17158120	C	T	17158120	3	4	30	1	0	0	0	0	1	0	0	0	11918	565	20	2	3403	2	PIK3C2A	11	17158120	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	2642291	17158120	117848396	378	13529											
NAV2	89797	hgsc.bcm.edu	37	chr11	19735325	19735325	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gcgcccatcctgcacgtgccCccggcccgggcgggccccca	3	3	13	22	5	0	0	0	0	0	0	1	0	1	0	7	3	2	1	7	3	0	0	rs11828836	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:19735325C>A	ENST00000396087.3	+	1	183	c.84C>A	c.(82-84)ccC>ccA	p.P28P	RP11-359E10.1_ENST00000603468.1_lincRNA|NAV2_ENST00000349880.4_Silent_p.P28P|NAV2_ENST00000360655.4_Intron|NAV2_ENST00000396085.1_Silent_p.P28P	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	28					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						TGCACGTgcccccggcccggg	0.662													C|||	112	0.0223642	0.0825	0.0043	5008	,	,		13608	0.0		0.0	False		,,,				2504	0.0				p.P28P		Atlas-SNP	.											.	NAV2	255	.	0			c.C84A						PASS	.	C	,,	269,4121		8,253,1934	20	22	21		,84,84	4.4	1	11	dbSNP_120	21	5,8571		0,5,4283	no	intron,coding-synonymous,coding-synonymous	NAV2	NM_001111018.1,NM_145117.4,NM_182964.5	,,	8,258,6217	AA,AC,CC		0.0583,6.1276,2.1132	,,	,28/2430,28/2433	19735325	274,12692	2195	4288	6483	SO:0001819	synonymous_variant	89797	exon1			CGTGCCCCCGGCC	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.84C>A	11.37:g.19735325C>A		38	0	0		21	9	0.428571	NM_145117	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	37	CCDS58126.1																																																																																			C|0.975;A|0.025	0.025	strong		0.662	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117		A	19735325	C	A	19735325	2	1	30	1	0	0	0	0	0	0	0	1	10193	610	22	4		4	NAV2	11	19735325	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	2577205	19735325	115271191	379	13530											
MAPK8IP1	9479	hgsc.bcm.edu	37	chr11	45924057	45924057	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gcacagccacccagatggcaCctccgggtggtccccctgct	6	6	11	18	1	0	1	0	0	0	1	2	1	2	1	6	3	2	3	6	3	0	0	rs117665789	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:45924057C>T	ENST00000241014.2	+	5	909	c.739C>T	c.(739-741)Cct>Tct	p.P247S	MAPK8IP1_ENST00000395629.2_Missense_Mutation_p.P237S	NM_005456.3	NP_005447.1	Q9UQF2	JIP1_HUMAN	mitogen-activated protein kinase 8 interacting protein 1	247	JNK-binding domain (JBD).				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)		CCAGATGGCACCTCCGGGTGG	0.706													C|||	16	0.00319489	0.0	0.0029	5008	,	,		13357	0.0		0.0109	False		,,,				2504	0.0031				p.P247S		Atlas-SNP	.											.	MAPK8IP1	51	.	0			c.C739T						PASS	.	C	SER/PRO	7,4359		0,7,2176	11	14	13		739	4.5	0.9	11	dbSNP_132	13	88,8478		0,88,4195	yes	missense	MAPK8IP1	NM_005456.3	74	0,95,6371	TT,TC,CC		1.0273,0.1603,0.7346	possibly-damaging	247/712	45924057	95,12837	2183	4283	6466	SO:0001583	missense	9479	exon5			ATGGCACCTCCGG		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.739C>T	11.37:g.45924057C>T	ENSP00000241014:p.Pro247Ser	114	0	0		72	37	0.513889	NM_005456	D3DQP4|O43407	Missense_Mutation	SNP	ENST00000241014.2	37	CCDS7916.1	10	0.004578754578754579	0	0.0	0	0.0	2	0.0034965034965034965	8	0.010554089709762533	C	13.85	2.358998	0.41801	0.001603	0.010273	ENSG00000121653	ENST00000241014;ENST00000395629	T;T	0.36699	1.24;1.25	4.51	4.51	0.55191	.	0.065445	0.64402	D	0.000011	T	0.18551	0.0445	N	0.24115	0.695	0.45541	D	0.998496	P	0.43750	0.816	B	0.37267	0.245	T	0.03514	-1.1029	10	0.27785	T	0.31	-3.6985	17.7712	0.88493	0.0:1.0:0.0:0.0	.	247	Q9UQF2	JIP1_HUMAN	S	247;237	ENSP00000241014:P247S;ENSP00000378991:P237S	ENSP00000241014:P247S	P	+	1	0	MAPK8IP1	45880633	0.428000	0.25522	0.877000	0.34402	0.627000	0.37826	3.856000	0.55964	2.504000	0.84457	0.561000	0.74099	CCT	C|0.993;T|0.007	0.007	strong		0.706	MAPK8IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259405.1	NM_005456		T	45924057	C	T	45924057	3	4	30	1	0	0	0	0	1	0	0	0	9293	507	18	2	757	2	MAPK8IP1	11	45924057	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	26188732	45924057	89082459	380	13531											
MYBPC3	4607	hgsc.bcm.edu	37	chr11	47365164	47365164	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggtaggccggctccagctTcttctgaaaggctgagcacc	7	9	12	13	1	2	2	0	2	2	0	3	2	3	2	3	4	2	5	3	4	2	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:47365164T>C	ENST00000545968.1	-	13	1156	c.1102A>G	c.(1102-1104)Aag>Gag	p.K368E	MYBPC3_ENST00000256993.4_Missense_Mutation_p.K368E|MYBPC3_ENST00000399249.2_Missense_Mutation_p.K368E	NM_000256.3	NP_000247.2	Q14896	MYPC3_HUMAN	myosin binding protein C, cardiac	368	Ig-like C2-type 2.				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)		GGCTCCAGCTTCTTCTGAAAG	0.647																																					p.K368E		Atlas-SNP	.											.	MYBPC3	102	.	0			c.A1102G						PASS	.						52	50	51					11																	47365164		1941	4129	6070	SO:0001583	missense	4607	exon13			CCAGCTTCTTCTG	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.1102A>G	11.37:g.47365164T>C	ENSP00000442795:p.Lys368Glu	89	0	0		97	4	0.0412371	NM_000256	A5PL00|Q16410|Q6R2F7|Q9UE27|Q9UM53	Missense_Mutation	SNP	ENST00000545968.1	37	CCDS53621.1	.	.	.	.	.	.	.	.	.	.	t	25.9	4.686390	0.88639	.	.	ENSG00000134571	ENST00000545968;ENST00000399249;ENST00000256993	T;T;T	0.67865	-0.29;-0.29;-0.29	4.99	4.99	0.66335	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.79587	0.4471	M	0.77616	2.38	0.46396	D	0.999024	D	0.69078	0.997	D	0.68621	0.959	T	0.80899	-0.1176	9	0.51188	T	0.08	.	11.5285	0.50595	0.0:0.0:0.1496:0.8504	.	368	Q14896	MYPC3_HUMAN	E	368	ENSP00000442795:K368E;ENSP00000382193:K368E;ENSP00000256993:K368E	ENSP00000256993:K368E	K	-	1	0	MYBPC3	47321740	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.639000	0.54339	2.103000	0.63969	0.456000	0.33151	AAG	.	.	none		0.647	MYBPC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392271.3			C	47365164	T	C	47365164	3	2	30	1	0	0	0	0	1	0	0	0	10022	1792	62	3	2806	3	MYBPC3	11	47365164	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	1441107	47365164	87641352	381	13532											
SLC39A13	91252	hgsc.bcm.edu	37	chr11	47431764	47431764	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccagccggccctccggagccGggggactgcgacggcctgtc	4	4	16	17	5	0	0	0	0	0	0	2	3	1	2	6	5	3	0	6	5	0	0	rs35741412	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:47431764G>A	ENST00000362021.4	+	2	161	c.119G>A	c.(118-120)cGg>cAg	p.R40Q	RP11-750H9.5_ENST00000532943.1_RNA|SLC39A13_ENST00000354884.4_Missense_Mutation_p.R40Q|SLC39A13_ENST00000524928.1_Missense_Mutation_p.R40Q|RP11-750H9.5_ENST00000532340.1_RNA|SLC39A13_ENST00000533076.1_Missense_Mutation_p.R40Q|SLC39A13_ENST00000531974.1_Missense_Mutation_p.R40Q	NM_001128225.2	NP_001121697	Q96H72	S39AD_HUMAN	solute carrier family 39 (zinc transporter), member 13	40					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)		CTCCGGAGCCGGGGGACTGCG	0.687													G|||	38	0.00758786	0.0015	0.013	5008	,	,		13659	0.0		0.0258	False		,,,				2504	0.001				p.R40Q		Atlas-SNP	.											.	SLC39A13	18	.	0			c.G119A						PASS	.	G	GLN/ARG,GLN/ARG	15,4387	20.2+/-43.8	0,15,2186	30	36	34		119,119	2.8	0.9	11	dbSNP_126	34	214,8382	84.5+/-147.0	2,210,4086	yes	missense,missense	SLC39A13	NM_001128225.2,NM_152264.4	43,43	2,225,6272	AA,AG,GG		2.4895,0.3408,1.7618	benign,benign	40/372,40/365	47431764	229,12769	2201	4298	6499	SO:0001583	missense	91252	exon2			GGAGCCGGGGGAC		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.119G>A	11.37:g.47431764G>A	ENSP00000354689:p.Arg40Gln	131	0	0		98	54	0.55102	NM_152264	D3DQR6|D3DQR7|E9PLY1|E9PQV3|Q659D9|Q8N7C9|Q8WV10	Missense_Mutation	SNP	ENST00000362021.4	37	CCDS44592.1	25	0.011446886446886446	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	17	0.022427440633245383	G	12.31	1.899337	0.33535	0.003408	0.024895	ENSG00000165915	ENST00000533076;ENST00000531974;ENST00000531419;ENST00000531865;ENST00000362021;ENST00000354884;ENST00000526614;ENST00000527091;ENST00000524928	T;T;T;T;T;T;T;T;T	0.70869	-0.49;0.97;0.96;-0.52;-0.38;-0.19;-0.03;0.97;0.91	5.05	2.85	0.33270	.	1.028510	0.07690	N	0.938611	T	0.29850	0.0746	N	0.14661	0.345	0.21527	N	0.999657	B;B;B	0.21688	0.019;0.013;0.059	B;B;B	0.13407	0.001;0.003;0.009	T	0.31194	-0.9952	10	0.07813	T	0.8	-1.9191	2.8954	0.05689	0.0997:0.1541:0.5026:0.2436	rs35741412;rs61897433	40;40;40	Q96H72;Q96H72-2;E9PNE7	S39AD_HUMAN;.;.	Q	40	ENSP00000434290:R40Q;ENSP00000435845:R40Q;ENSP00000432302:R40Q;ENSP00000434684:R40Q;ENSP00000354689:R40Q;ENSP00000346956:R40Q;ENSP00000432499:R40Q;ENSP00000435076:R40Q;ENSP00000437186:R40Q	ENSP00000346956:R40Q	R	+	2	0	SLC39A13	47388340	1.000000	0.71417	0.932000	0.37286	0.500000	0.33767	1.734000	0.38166	0.884000	0.36064	0.491000	0.48974	CGG	G|0.984;A|0.016	0.016	strong		0.687	SLC39A13-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395652.1	NM_152264		A	47431764	G	A	47431764	3	1	30	1	0	0	0	0	1	0	0	0	14631	1116	39	1	121	1	SLC39A13	11	47431764	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	66600	47431764	87574752	382	13533											
OR4A5	81318	hgsc.bcm.edu	37	chr11	51411918	51411918	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagaaagggagactgtacaCaacaatttgaaacgcagaat	19	6	9	7	1	0	4	0	1	0	3	0	5	0	4	0	1	3	2	0	1	6	2	rs150995059	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:51411918C>T	ENST00000319760.6	-	1	530	c.478G>A	c.(478-480)Gtg>Atg	p.V160M		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	160						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)				AGACTGTACACAACAATTTGA	0.448													.|||	15	0.00299521	0.0008	0.0014	5008	,	,		21527	0.0		0.0089	False		,,,				2504	0.0041				p.V160M		Atlas-SNP	.											.	OR4A5	116	.	0			c.G478A						PASS	.	C	MET/VAL	10,4392		0,10,2191	79	71	74		478	1	0.1	11	dbSNP_134	74	109,8483		1,107,4188	no	missense	OR4A5	NM_001005272.3	21	1,117,6379	TT,TC,CC		1.2686,0.2272,0.9158	benign	160/316	51411918	119,12875	2201	4296	6497	SO:0001583	missense	81318	exon1			TGTACACAACAAT	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.478G>A	11.37:g.51411918C>T	ENSP00000367664:p.Val160Met	143	0	0		148	72	0.486486	NM_001005272	Q6IF84	Missense_Mutation	SNP	ENST00000319760.6	37	CCDS31497.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	.	2.005	-0.428430	0.04701	0.002272	0.012686	ENSG00000221840	ENST00000319760	T	0.00130	8.69	1.93	0.984	0.19773	GPCR, rhodopsin-like superfamily (1);	0.547041	0.15102	N	0.280442	T	0.00073	0.0002	N	0.11673	0.155	0.09310	N	0.999999	B	0.33739	0.422	B	0.41666	0.363	T	0.03493	-1.1031	10	0.33141	T	0.24	.	4.1454	0.10214	0.0:0.6238:0.0:0.3762	.	160	Q8NH83	OR4A5_HUMAN	M	160	ENSP00000367664:V160M	ENSP00000367664:V160M	V	-	1	0	OR4A5	51268494	0.000000	0.05858	0.070000	0.20053	0.214000	0.24535	-0.808000	0.04515	0.371000	0.24564	0.162000	0.16502	GTG	C|0.993;T|0.007	0.007	strong		0.448	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272		T	51411918	C	T	51411918	3	4	30	1	0	0	0	0	1	0	0	0	11052	478	17	2	473	2	OR4A5	11	51411918	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	3980154	51411918	83594598	383	13534											
OR5AS1	219447	hgsc.bcm.edu	37	chr11	55798278	55798278	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cgctatgcagccatctgcaaCccactgctctatactacact	10	10	5	16	1	2	0	0	0	2	0	2	0	2	0	2	0	7	4	2	0	5	4	rs148523609	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:55798278C>T	ENST00000313555.1	+	1	384	c.384C>T	c.(382-384)aaC>aaT	p.N128N		NM_001001921.1	NP_001001921.1	Q8N127	O5AS1_HUMAN	olfactory receptor, family 5, subfamily AS, 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)			endometrium(7)|large_intestine(7)|liver(1)|lung(22)|ovary(3)|prostate(4)|skin(3)|stomach(1)	48	Esophageal squamous(21;0.00693)					CCATCTGCAACCCACTGCTCT	0.468													C|||	14	0.00279553	0.0008	0.0014	5008	,	,		20153	0.0		0.0089	False		,,,				2504	0.0031				p.N128N		Atlas-SNP	.											.	OR5AS1	121	.	0			c.C384T						PASS	.	C		12,4390	21.2+/-45.6	0,12,2189	150	122	132		384	-1.9	0.3	11	dbSNP_134	132	106,8486	57.5+/-118.9	1,104,4191	no	coding-synonymous	OR5AS1	NM_001001921.1		1,116,6380	TT,TC,CC		1.2337,0.2726,0.9081		128/325	55798278	118,12876	2201	4296	6497	SO:0001819	synonymous_variant	219447	exon1			CTGCAACCCACTG	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.384C>T	11.37:g.55798278C>T		335	1	0.00298507		295	136	0.461017	NM_001001921	Q6IFB8	Silent	SNP	ENST00000313555.1	37	CCDS31516.1																																																																																			C|0.993;T|0.007	0.007	strong		0.468	OR5AS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391538.1	NM_001001921		T	55798278	C	T	55798278	2	4	30	1	0	0	0	0	0	0	0	1	11155	506	18	2		2	OR5AS1	11	55798278	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	4386360	55798278	79208238	384	13535											
OR8K5	219453	hgsc.bcm.edu	37	chr11	55927584	55927584	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgacagtagaattaccaagAtcaacaaaagccaaatgtct	19	8	6	8	0	2	3	1	1	1	2	2	3	2	3	2	0	3	1	2	0	8	2	rs141612231	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:55927584A>T	ENST00000313447.1	-	1	209	c.210T>A	c.(208-210)gaT>gaA	p.D70E		NM_001004058.2	NP_001004058.2	Q8NH50	OR8K5_HUMAN	olfactory receptor, family 8, subfamily K, member 5	70						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)				AATTACCAAGATCAACAAAAG	0.403													A|||	5	0.000998403	0.0015	0.0	5008	,	,		21723	0.0		0.003	False		,,,				2504	0.0				p.D70E		Atlas-SNP	.											.	OR8K5	82	.	0			c.T210A						PASS	.	A	GLU/ASP	4,4398	8.1+/-20.4	0,4,2197	109	108	109		210	-1.8	1	11	dbSNP_134	109	44,8548	29.6+/-80.5	0,44,4252	yes	missense	OR8K5	NM_001004058.2	45	0,48,6449	TT,TA,AA		0.5121,0.0909,0.3694	probably-damaging	70/308	55927584	48,12946	2201	4296	6497	SO:0001583	missense	219453	exon1			ACCAAGATCAACA	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.210T>A	11.37:g.55927584A>T	ENSP00000323853:p.Asp70Glu	177	0	0		193	99	0.512953	NM_001004058	Q6IFB5	Missense_Mutation	SNP	ENST00000313447.1	37	CCDS31521.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	15.04	2.715189	0.48622	9.09E-4	0.005121	ENSG00000181752	ENST00000313447	T	0.01152	5.26	3.87	-1.8	0.07907	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.01976	0.0062	L	0.43701	1.375	0.23260	N	0.998023	D	0.89917	1.0	D	0.83275	0.996	T	0.45381	-0.9265	9	0.87932	D	0	.	4.7748	0.13173	0.4794:0.0:0.3737:0.1469	.	70	Q8NH50	OR8K5_HUMAN	E	70	ENSP00000323853:D70E	ENSP00000323853:D70E	D	-	3	2	OR8K5	55684160	0.000000	0.05858	0.991000	0.47740	0.512000	0.34134	-1.621000	0.02044	-0.081000	0.12662	-0.377000	0.06932	GAT	A|0.998;T|0.002	0.002	strong		0.403	OR8K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391543.1	NM_001004058		T	55927584	A	T	55927584	3	4	30	1	0	0	0	0	1	0	0	0	11254	330	12	5	716	5	OR8K5	11	55927584	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	129306	55927584	79078932	385	13536											
OR9G1	390174	hgsc.bcm.edu	37	chr11	56468225	56468225	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggctgccgtggcttatgaccGctacgtggccatctccaagc	6	9	12	14	3	1	1	0	1	1	0	2	1	1	1	4	3	3	3	4	3	3	2	rs148651508	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:56468225G>A	ENST00000312153.1	+	1	362	c.362G>A	c.(361-363)cGc>cAc	p.R121H		NM_001005213.1	NP_001005213.1	Q8NH87	OR9G1_HUMAN	olfactory receptor, family 9, subfamily G, member 1	121						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R121P(1)		breast(2)|kidney(1)|lung(25)|stomach(2)|upper_aerodigestive_tract(1)	31						GCTTATGACCGCTACGTGGCC	0.527													G|||	5	0.000998403	0.0	0.0	5008	,	,		17980	0.0		0.0	False		,,,				2504	0.0051				p.R121H		Atlas-SNP	.											OR9G1,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	lung(1)	c.G362A						scavenged	.	G	HIS/ARG	6,4396	4.2+/-10.8	0,6,2195	134	124	127		362	0.5	0.7	11	dbSNP_134	127	5,8587	4.3+/-15.6	0,5,4291	yes	missense	OR9G1	NM_001005213.1	29	0,11,6486	AA,AG,GG		0.0582,0.1363,0.0847	benign	121/306	56468225	11,12983	2201	4296	6497	SO:0001583	missense	504191	exon1			ATGACCGCTACGT	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.362G>A	11.37:g.56468225G>A	ENSP00000309012:p.Arg121His	289	2	0.00692042		298	76	0.255034	NM_001013358	Q6IEU9|Q8NGQ0	Missense_Mutation	SNP	ENST00000312153.1	37	CCDS31536.1	.	.	.	.	.	.	.	.	.	.	G	9.545	1.114336	0.20795	0.001363	5.82E-4	ENSG00000174914	ENST00000312153	T	0.77489	-1.1	4.54	0.508	0.16972	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000040	T	0.76147	0.3947	M	0.88842	2.985	0.33993	D	0.649336	B	0.28026	0.198	B	0.26969	0.075	T	0.74272	-0.3719	10	0.72032	D	0.01	-11.8484	5.9681	0.19336	0.2233:0.0:0.6439:0.1329	.	121	Q8NH87	OR9G1_HUMAN	H	121	ENSP00000309012:R121H	ENSP00000309012:R121H	R	+	2	0	OR9G1	56224801	0.996000	0.38824	0.684000	0.30055	0.041000	0.13682	2.226000	0.42963	0.004000	0.14682	-0.203000	0.12734	CGC	G|1.000;A|0.000	0.000	weak		0.527	OR9G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393253.1	NM_001005213		A	56468225	G	A	56468225	3	1	30	1	0	0	0	0	1	0	0	0	11259	1087	38	1	364	1	OR9G1	11	56468225	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	540641	56468225	78538291	386	13537											
OR10V1	390201	hgsc.bcm.edu	37	chr11	59480759	59480759	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtgtctgcacaagccaggCgcatgactgcaggcatgtca	9	8	13	11	1	2	1	1	1	1	0	2	1	2	1	1	2	3	4	1	2	1	0	rs141649641	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:59480759C>T	ENST00000307552.2	-	1	578	c.560G>A	c.(559-561)cGc>cAc	p.R187H	STX3_ENST00000300150.7_5'Flank	NM_001005324.1	NP_001005324.1	Q8NGI7	O10V1_HUMAN	olfactory receptor, family 10, subfamily V, member 1	187						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						ACAAGCCAGGCGCATGACTGC	0.483													C|||	3	0.000599042	0.0	0.0	5008	,	,		23804	0.0		0.003	False		,,,				2504	0.0				p.R187H		Atlas-SNP	.											.	OR10V1	40	.	0			c.G560A						PASS	.	C	HIS/ARG	5,4397	9.9+/-24.2	0,5,2196	104	89	94		560	0	1	11	dbSNP_134	94	31,8559	21.6+/-65.8	0,31,4264	yes	missense	OR10V1	NM_001005324.1	29	0,36,6460	TT,TC,CC		0.3609,0.1136,0.2771	benign	187/310	59480759	36,12956	2201	4295	6496	SO:0001583	missense	390201	exon1			GCCAGGCGCATGA	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.560G>A	11.37:g.59480759C>T	ENSP00000302199:p.Arg187His	102	0	0		94	52	0.553191	NM_001005324	Q6IFD9|Q96R50	Missense_Mutation	SNP	ENST00000307552.2	37	CCDS31565.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	9.722	1.159943	0.21454	0.001136	0.003609	ENSG00000172289	ENST00000307552	T	0.00137	8.68	4.47	-0.0376	0.13883	GPCR, rhodopsin-like superfamily (1);	0.258733	0.25869	N	0.027762	T	0.00109	0.0003	L	0.37800	1.135	0.24816	N	0.992619	B	0.31383	0.321	B	0.32149	0.141	T	0.28681	-1.0036	10	0.54805	T	0.06	.	5.0568	0.14537	0.142:0.5452:0.0:0.3128	.	187	Q8NGI7	O10V1_HUMAN	H	187	ENSP00000302199:R187H	ENSP00000302199:R187H	R	-	2	0	OR10V1	59237335	0.000000	0.05858	0.993000	0.49108	0.635000	0.38103	-1.103000	0.03329	-0.105000	0.12132	-0.545000	0.04230	CGC	C|0.998;T|0.002	0.002	strong		0.483	OR10V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394517.1	NM_001005324		T	59480759	C	T	59480759	3	4	30	1	0	0	0	0	1	0	0	0	10929	768	27	1	373	1	OR10V1	11	59480759	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	3012534	59480759	75525757	387	13538											
VWCE	220001	hgsc.bcm.edu	37	chr11	61053895	61053895	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggaggaggttacacattcGtcaatgtctggaaagacaga	14	8	12	7	1	2	2	1	0	1	2	3	5	2	5	0	4	1	1	0	4	3	2	rs146572904	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:61053895G>A	ENST00000335613.5	-	5	818	c.432C>T	c.(430-432)gaC>gaT	p.D144D		NM_152718.2	NP_689931.2	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	144	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					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						TTACACATTCGTCAATGTCTG	0.547													g|||	6	0.00119808	0.0	0.0014	5008	,	,		23016	0.0		0.005	False		,,,				2504	0.0				p.D144D		Atlas-SNP	.											.	VWCE	84	.	0			c.C432T						PASS	.	A		2,4404	4.2+/-10.8	0,2,2201	89	77	81		432	-10.6	0	11	dbSNP_134	81	22,8576	16.6+/-54.9	0,22,4277	no	coding-synonymous	VWCE	NM_152718.2		0,24,6478	AA,AG,GG		0.2559,0.0454,0.1846		144/956	61053895	24,12980	2203	4299	6502	SO:0001819	synonymous_variant	220001	exon5			ACATTCGTCAATG	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.432C>T	11.37:g.61053895G>A		56	0	0		64	26	0.40625	NM_152718	A5PKV0|Q7Z7L6|Q86WK8	Silent	SNP	ENST00000335613.5	37	CCDS8002.1																																																																																			G|0.998;A|0.002	0.002	strong		0.547	VWCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398811.1	NM_152718		A	61053895	G	A	61053895	2	1	30	1	0	0	0	0	0	0	0	1	17260	1136	40	1		1	VWCE	11	61053895	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1573136	61053895	73952621	388	13539											
GANAB	23193	hgsc.bcm.edu	37	chr11	62397114	62397114	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggacaaaggggcgttccaTgcccccagagcgctgtctca	9	6	12	14	2	1	1	1	0	1	1	3	2	2	2	3	3	2	2	3	3	1	1	rs76572368	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:62397114T>C	ENST00000356638.3	-	15	1796	c.1780A>G	c.(1780-1782)Atg>Gtg	p.M594V	GANAB_ENST00000534779.1_Missense_Mutation_p.M502V|GANAB_ENST00000346178.4_Missense_Mutation_p.M616V|GANAB_ENST00000540933.1_Missense_Mutation_p.M497V	NM_198334.1	NP_938148.1	Q14697	GANAB_HUMAN	glucosidase, alpha; neutral AB	594					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)	GGGCGTTCCATGCCCCCAGAG	0.597													T|||	89	0.0177716	0.0008	0.0389	5008	,	,		20960	0.001		0.0547	False		,,,				2504	0.0051				p.M616V	Melanoma(23;1005 1074 15747 18937)	Atlas-SNP	.											.	GANAB	110	.	0			c.A1846G						PASS	.	T	VAL/MET,VAL/MET	28,4376	31.7+/-61.6	0,28,2174	37	37	37		1780,1846	-4.7	0.1	11	dbSNP_131	37	362,8236	115.7+/-175.5	10,342,3947	yes	missense,missense	GANAB	NM_198334.1,NM_198335.2	21,21	10,370,6121	CC,CT,TT		4.2103,0.6358,2.9995	benign,benign	594/945,616/967	62397114	390,12612	2202	4299	6501	SO:0001583	missense	23193	exon16			GTTCCATGCCCCC	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.1780A>G	11.37:g.62397114T>C	ENSP00000349053:p.Met594Val	205	0	0		228	92	0.403509	NM_198335	A6NC20|Q8WTS9|Q9P0X0	Missense_Mutation	SNP	ENST00000356638.3	37	CCDS8026.1	53	0.024267399267399268	0	0.0	14	0.03867403314917127	0	0.0	39	0.051451187335092345	T	7.943	0.743196	0.15642	0.006358	0.042103	ENSG00000089597	ENST00000346178;ENST00000356638;ENST00000534779;ENST00000540933	D;D;D;D	0.91068	-2.78;-2.78;-2.78;-2.78	5.31	-4.7	0.03288	Glycoside hydrolase, superfamily (1);	0.908173	0.09646	N	0.774318	T	0.25419	0.0618	N	0.00368	-1.59	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	0.53961	-0.8364	10	0.29301	T	0.29	0.5168	8.9385	0.35715	0.0:0.4806:0.1198:0.3996	.	480;502;594;616	B4DIW2;E9PKU7;Q14697;Q14697-2	.;.;GANAB_HUMAN;.	V	616;594;502;497	ENSP00000340466:M616V;ENSP00000349053:M594V;ENSP00000435306:M502V;ENSP00000442962:M497V	ENSP00000340466:M616V	M	-	1	0	GANAB	62153690	0.000000	0.05858	0.133000	0.22050	0.980000	0.70556	-1.352000	0.02619	-0.731000	0.04862	0.533000	0.62120	ATG	T|0.974;C|0.026	0.026	strong		0.597	GANAB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395689.1	NM_198334		C	62397114	T	C	62397114	3	2	30	1	0	0	0	0	1	0	0	0	6241	1464	51	3	1094	3	GANAB	11	62397114	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	1343219	62397114	72609402	389	13540											
SCYL1	57410	hgsc.bcm.edu	37	chr11	65293819	65293819	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagagtggtcagagagaaGtggtgggtgactgggggcag	9	6	22	4	0	1	4	1	1	0	3	1	5	1	4	0	6	0	2	0	6	1	0	rs75169347	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:65293819G>A	ENST00000270176.5	+	4	677	c.600G>A	c.(598-600)aaG>aaA	p.K200K	SCYL1_ENST00000527009.1_Silent_p.K57K|SCYL1_ENST00000533862.1_Silent_p.K200K|SCYL1_ENST00000525364.1_Silent_p.K200K|SCYL1_ENST00000524944.1_Silent_p.K200K|SCYL1_ENST00000279270.6_Silent_p.K200K|SCYL1_ENST00000420247.2_Silent_p.K200K	NM_020680.3	NP_065731.3	Q96KG9	NTKL_HUMAN	SCY1-like 1 (S. cerevisiae)	200	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						TCAGAGAGAAGTGGTGGGTGA	0.657													G|||	91	0.0181709	0.0015	0.0303	5008	,	,		16563	0.0		0.0616	False		,,,				2504	0.0061				p.K200K		Atlas-SNP	.											.	SCYL1	76	.	0			c.G600A						PASS	.	G	,	34,4166		0,34,2066	16	19	18		600,600	-1.8	0.8	11	dbSNP_131	18	504,7942		14,476,3733	no	coding-synonymous,coding-synonymous	SCYL1	NM_001048218.1,NM_020680.3	,	14,510,5799	AA,AG,GG		5.9673,0.8095,4.2543	,	200/792,200/809	65293819	538,12108	2100	4223	6323	SO:0001819	synonymous_variant	57410	exon4			AGAGAAGTGGTGG	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.600G>A	11.37:g.65293819G>A		141	0	0		140	64	0.457143	NM_020680	A6NJF1|Q96G50|Q96KG8|Q96KH1|Q9HAW5|Q9HBL3|Q9NR53	Silent	SNP	ENST00000270176.5	37	CCDS41672.1																																																																																			G|0.968;A|0.032	0.032	strong		0.657	SCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389159.2	NM_020680		A	65293819	G	A	65293819	2	1	30	1	0	0	0	0	0	0	0	1	13962	1020	36	2		2	SCYL1	11	65293819	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2896705	65293819	69712697	390	13541											
EHBP1L1	254102	hgsc.bcm.edu	37	chr11	65349037	65349037	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggcagccagcccaggacacGgcccccaccccagcccctcg	8	1	10	22	2	0	0	0	0	0	0	1	1	0	1	8	3	3	1	8	3	0	0	rs74684453	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:65349037G>A	ENST00000309295.4	+	9	1159	c.894G>A	c.(892-894)acG>acA	p.T298T		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	298						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						CCCAGGACACGGCCCCCACCC	0.677													G|||	34	0.00678914	0.0008	0.0086	5008	,	,		13897	0.0		0.0239	False		,,,				2504	0.0031				p.T298T		Atlas-SNP	.											.	EHBP1L1	64	.	0			c.G894A						PASS	.	G		13,3719		0,13,1853	8	9	9		894	3	0.8	11	dbSNP_134	9	194,7914		2,190,3862	no	coding-synonymous	EHBP1L1	NM_001099409.1		2,203,5715	AA,AG,GG		2.3927,0.3483,1.7483		298/1524	65349037	207,11633	1866	4054	5920	SO:0001819	synonymous_variant	254102	exon9			GGACACGGCCCCC	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.894G>A	11.37:g.65349037G>A		195	0	0		209	92	0.440191	NM_001099409	Q8TB89|Q9H7M7	Silent	SNP	ENST00000309295.4	37	CCDS44649.1																																																																																			G|0.989;A|0.011	0.011	strong		0.677	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658		A	65349037	G	A	65349037	2	1	30	1	0	0	0	0	0	0	0	1	4978	1103	39	1		1	EHBP1L1	11	65349037	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	55218	65349037	69657479	391	13542											
MRGPRF	116535	hgsc.bcm.edu	37	chr11	68773089	68773089	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttggcagagcgctggcgcCgtcgggcccggcactccacg	4	5	16	16	6	0	1	0	0	0	1	2	1	1	1	3	4	1	4	3	4	0	1	rs151254404		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:68773089C>T	ENST00000309099.6	-	3	1071	c.689G>A	c.(688-690)cGg>cAg	p.R230Q	RP11-554A11.5_ENST00000562506.1_RNA|MRGPRF_ENST00000441623.1_Missense_Mutation_p.R230Q	NM_145015.4	NP_659452.3	Q96AM1	MRGRF_HUMAN	MAS-related GPR, member F	230						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)			GCGCTGGCGCCGTCGGGCCCG	0.627																																					p.R230Q		Atlas-SNP	.											.	MRGPRF	22	.	0			c.G689A						PASS	.	C	GLN/ARG,GLN/ARG	0,4368		0,0,2184	33	26	28		689,689	3.3	0.9	11	dbSNP_134	28	4,8528		0,4,4262	yes	missense,missense	MRGPRF	NM_001098515.1,NM_145015.4	43,43	0,4,6446	TT,TC,CC		0.0469,0.0,0.031	probably-damaging,probably-damaging	230/344,230/344	68773089	4,12896	2184	4266	6450	SO:0001583	missense	116535	exon3			TGGCGCCGTCGGG	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.689G>A	11.37:g.68773089C>T	ENSP00000309782:p.Arg230Gln	122	0	0		118	56	0.474576	NM_001098515	B3KV43|Q8NBK8	Missense_Mutation	SNP	ENST00000309099.6	37	CCDS8188.1	.	.	.	.	.	.	.	.	.	.	C	12.99	2.103907	0.37145	0.0	4.69E-4	ENSG00000172935	ENST00000441623;ENST00000309099;ENST00000421543	T;T	0.43294	0.95;0.95	5.25	3.27	0.37495	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39146	N	0.001445	T	0.27765	0.0683	L	0.54323	1.7	0.25460	N	0.987926	P	0.38827	0.649	B	0.30572	0.117	T	0.10917	-1.0609	10	0.14656	T	0.56	-24.2612	6.393	0.21597	0.0:0.7165:0.1856:0.0979	.	230	Q96AM1	MRGRF_HUMAN	Q	230;230;202	ENSP00000403660:R230Q;ENSP00000309782:R230Q	ENSP00000309782:R230Q	R	-	2	0	MRGPRF	68529665	0.064000	0.20934	0.913000	0.36048	0.963000	0.63663	0.101000	0.15251	1.215000	0.43411	0.561000	0.74099	CGG	C|1.000;T|0.000	0.000	weak		0.627	MRGPRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396875.1	NM_145015		T	68773089	C	T	68773089	3	4	30	1	0	0	0	0	1	0	0	0	9774	652	23	1	346	1	MRGPRF	11	68773089	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	3424052	68773089	66233427	392	13543											
CCND1	595	hgsc.bcm.edu	37	chr11	69457987	69457987	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagctgtgcatctacaccgaCaactccatccggcccgagga	11	6	9	15	3	1	0	0	0	1	0	3	3	3	1	4	2	4	2	4	2	3	1	rs371689281		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:69457987C>T	ENST00000227507.2	+	2	614	c.387C>T	c.(385-387)gaC>gaT	p.D129D	CCND1_ENST00000536559.1_Intron	NM_053056.2	NP_444284.1	P24385	CCND1_HUMAN	cyclin D1	129	Cyclin N-terminal.				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)	TCTACACCGACAACTCCATCC	0.687			T	"IGH@, FSTL3"	"CLL, B-ALL, breast"					Multiple Myeloma(6;0.086)																											p.D129D	Pancreas(65;393 884 2788 21700 24360 27795 36895)	Atlas-SNP	.		Dom	yes		11	11q13	595	cyclin D1		"L, E"	.	CCND1	107	.	0			c.C387T						PASS	.	C		0,4378		0,0,2189	38	36	37		387	3.7	1	11		37	2,8578		0,2,4288	no	coding-synonymous	CCND1	NM_053056.2		0,2,6477	TT,TC,CC		0.0233,0.0,0.0154		129/296	69457987	2,12956	2189	4290	6479	SO:0001819	synonymous_variant	595	exon2			CACCGACAACTCC	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.387C>T	11.37:g.69457987C>T		47	0	0		42	18	0.428571	NM_053056	Q6LEF0	Silent	SNP	ENST00000227507.2	37	CCDS8191.1																																																																																			.	.	weak		0.687	CCND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396775.2	NM_053056		T	69457987	C	T	69457987	2	4	30	1	0	0	0	0	0	0	0	1	2918	477	17	2		2	CCND1	11	69457987	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	684898	69457987	65548529	393	13544											
GDPD5	81544	hgsc.bcm.edu	37	chr11	75150971	75150971	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agggtgaaggagaccaggtcGgcagtgacccacatgagaca	13	4	15	9	1	0	4	0	3	0	2	1	6	0	4	2	4	0	1	2	4	1	0	rs115438239	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:75150971G>A	ENST00000336898.3	-	15	2346	c.1509C>T	c.(1507-1509)gcC>gcT	p.A503A	GDPD5_ENST00000376282.3_Silent_p.A384A|GDPD5_ENST00000533805.1_Silent_p.A258A|GDPD5_ENST00000526177.1_Silent_p.A365A|GDPD5_ENST00000443276.2_3'UTR|GDPD5_ENST00000533784.1_Silent_p.A384A|GDPD5_ENST00000529721.1_Silent_p.A503A	NM_030792.6	NP_110419.5	Q8WTR4	GDPD5_HUMAN	glycerophosphodiester phosphodiesterase domain containing 5	503					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						AGACCAGGTCGGCAGTGACCC	0.612													G|||	10	0.00199681	0.0008	0.0	5008	,	,		19335	0.003		0.006	False		,,,				2504	0.0				p.A503A		Atlas-SNP	.											.	GDPD5	49	.	0			c.C1509T						PASS	.	G		2,4398	4.2+/-10.8	0,2,2198	124	101	109		1509	-7.7	0.7	11	dbSNP_132	109	27,8559	19.2+/-60.6	0,27,4266	no	coding-synonymous	GDPD5	NM_030792.6		0,29,6464	AA,AG,GG		0.3145,0.0455,0.2233		503/606	75150971	29,12957	2200	4293	6493	SO:0001819	synonymous_variant	81544	exon15			CAGGTCGGCAGTG	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.1509C>T	11.37:g.75150971G>A		115	0	0		117	62	0.529915	NM_030792	Q49AQ5|Q6UX76|Q7Z4S0|Q8N781|Q8NCB7|Q8TB77	Silent	SNP	ENST00000336898.3	37	CCDS8238.1																																																																																			G|0.997;A|0.003	0.003	strong		0.612	GDPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384409.1	NM_030792		A	75150971	G	A	75150971	2	1	30	1	0	0	0	0	0	0	0	1	6335	1103	39	1		1	GDPD5	11	75150971	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	5692984	75150971	59855545	394	13545											
MYO7A	4647	hgsc.bcm.edu	37	chr11	76918411	76918411	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggctgctcctcaagtcctcAgagggattcagcctctttgt	7	12	10	12	0	4	1	3	0	1	1	6	2	6	2	3	2	2	2	3	2	1	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:76918411A>G	ENST00000409709.3	+	42	6092	c.5820A>G	c.(5818-5820)tcA>tcG	p.S1940S	MYO7A_ENST00000605744.1_3'UTR|MYO7A_ENST00000409619.2_Silent_p.S1891S|MYO7A_ENST00000458637.2_Silent_p.S1902S	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	1940	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						TCAAGTCCTCAGAGGGATTCA	0.572																																					p.S1940S		Atlas-SNP	.											.	MYO7A	164	.	0			c.A5820G						PASS	.						40	45	43					11																	76918411		2062	4191	6253	SO:0001819	synonymous_variant	4647	exon42			GTCCTCAGAGGGA	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.5820A>G	11.37:g.76918411A>G		112	0	0		118	72	0.610169	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Silent	SNP	ENST00000409709.3	37	CCDS53683.1																																																																																			.	.	none		0.572	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260		G	76918411	A	G	76918411	2	3	30	1	0	0	0	0	0	0	0	1	10091	175	7	3		3	MYO7A	11	76918411	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	1767440	76918411	58088105	395	13546											
ODZ4	26011	hgsc.bcm.edu	37	chr11	78369573	78369573	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cacaaagtaatgggtatccaCcccatcaatggtgaagtgca	14	8	9	10	0	1	1	1	1	0	0	2	1	2	1	3	2	1	3	3	2	5	2	rs75922333	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:78369573C>T	ENST00000278550.7	-	34	8302	c.7840G>A	c.(7840-7842)Gtg>Atg	p.V2614M		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	2614					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)										TGGGTATCCACCCCATCAATG	0.557													C|||	17	0.00339457	0.0023	0.0014	5008	,	,		20854	0.0		0.0129	False		,,,				2504	0.0				p.V2614M		Atlas-SNP	.											.	.	.	.	0			c.G7840A						PASS	.	C	MET/VAL	16,4072		0,16,2028	44	47	46		7840	1.8	0.7	11	dbSNP_131	46	155,8247		2,151,4048	yes	missense	ODZ4	NM_001098816.2	21	2,167,6076	TT,TC,CC		1.8448,0.3914,1.3691	benign	2614/2770	78369573	171,12319	2044	4201	6245	SO:0001583	missense	26011	exon34			TATCCACCCCATC	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.7840G>A	11.37:g.78369573C>T	ENSP00000278550:p.Val2614Met	106	0	0		105	47	0.447619	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	37	CCDS44688.1	14	0.00641025641025641	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	10	0.013192612137203167	C	9.623	1.134402	0.21123	0.003914	0.018448	ENSG00000149256	ENST00000278550	D	0.89485	-2.52	5.65	1.78	0.24846	.	0.375145	0.29273	N	0.012631	T	0.59595	0.2205	N	0.08118	0	0.27241	N	0.959155	B	0.13145	0.007	B	0.09377	0.004	T	0.54022	-0.8355	9	.	.	.	.	9.0578	0.36416	0.0:0.5855:0.0:0.4145	.	2614	Q6N022	TEN4_HUMAN	M	2614	ENSP00000278550:V2614M	.	V	-	1	0	ODZ4	78047221	0.005000	0.15991	0.705000	0.30386	0.942000	0.58702	-0.244000	0.08903	0.185000	0.20105	-0.137000	0.14449	GTG	C|0.990;T|0.010	0.010	strong		0.557	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			T	78369573	C	T	78369573	3	4	30	1	0	0	0	0	1	0	0	0	10846	507	18	2	473	2	ODZ4	11	78369573	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1451162	78369573	56636943	396	13547											
UBTFL1	0	hgsc.bcm.edu	37	chr11	89819431	89819431	+	IGR	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctttccaaagaggccccttaCtgcttacaatcgcttcttca	9	13	5	14	1	2	1	1	0	1	1	4	1	3	1	3	1	3	2	3	1	4	5			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:89819431C>T								TRIM49C (12873 upstream) : SNORD56 (32127 downstream)																							AGGCCCCTTACTGCTTACAAT	0.428																																					p.T105I		Atlas-SNP	.											.	.	.	.	0			c.C314T						PASS	.						97	72	80					11																	89819431		682	1559	2241	SO:0001628	intergenic_variant	642623	exon1			CCCTTACTGCTTA																													11.37:g.89819431C>T		321	1	0.00311526		411	270	0.656934	NM_001143975		Missense_Mutation	SNP		37																																																																																				.	.	none	0	0.428									T	89819431	C	T	89819431	1	4	30	0	1	0	0	0	0	0	0	0	16925	565	20	2		2	UBTFL1	11	89819431	IGR	SNP	C	TCGA-GR-7353-01A-11D-2210-10	11449858	89819431	45187085	397	13548											
FAT3	120114	hgsc.bcm.edu	37	chr11	92257991	92257991	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgttgtcatggaaaactctCcaaaggacgtatctgtcatt	11	13	8	9	1	4	0	2	0	2	0	5	2	4	2	1	2	1	2	1	2	4	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:92257991C>A	ENST00000298047.6	+	2	3501	c.3484C>A	c.(3484-3486)Cca>Aca	p.P1162T	FAT3_ENST00000409404.2_Missense_Mutation_p.P1162T|FAT3_ENST00000541502.1_Missense_Mutation_p.P1162T|FAT3_ENST00000525166.1_Missense_Mutation_p.P1012T			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	1162	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)				GGAAAACTCTCCAAAGGACGT	0.418										TCGA Ovarian(4;0.039)																											p.P1162T		Atlas-SNP	.											.	FAT3	1822	.	0			c.C3484A						PASS	.						58	58	58					11																	92257991		1968	4167	6135	SO:0001583	missense	120114	exon2			AACTCTCCAAAGG	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.3484C>A	11.37:g.92257991C>A	ENSP00000298047:p.Pro1162Thr	134	0	0		200	123	0.615	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	C	21.8	4.197532	0.79015	.	.	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000541502;ENST00000525166	T;T;T;T	0.54675	0.56;0.56;0.56;0.56	5.66	5.66	0.87406	.	.	.	.	.	T	0.68933	0.3055	L	0.58925	1.835	0.51482	D	0.999922	D	0.89917	1.0	D	0.91635	0.999	T	0.68969	-0.5269	9	0.54805	T	0.06	.	15.2581	0.73601	0.0:0.8603:0.1397:0.0	.	1162	Q8TDW7-3	.	T	1162;1162;1162;1012	ENSP00000298047:P1162T;ENSP00000387040:P1162T;ENSP00000443786:P1162T;ENSP00000432586:P1012T	ENSP00000298047:P1162T	P	+	1	0	FAT3	91897639	1.000000	0.71417	0.998000	0.56505	0.955000	0.61496	5.946000	0.70234	2.682000	0.91365	0.650000	0.86243	CCA	.	.	none		0.418	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		A	92257991	C	A	92257991	3	1	30	1	0	0	0	0	1	0	0	0	5699	855	30	4	3490	4	FAT3	11	92257991	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	2438560	92257991	42748525	398	13549											
FAT3	120114	hgsc.bcm.edu	37	chr11	92568149	92568149	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgctgtggccactgtcaacAtcaacctcacagatgttaat	11	10	8	12	1	3	1	3	0	0	1	3	1	3	1	2	1	2	2	2	1	3	1	rs75651194	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:92568149A>G	ENST00000298047.6	+	14	10002	c.9985A>G	c.(9985-9987)Atc>Gtc	p.I3329V	FAT3_ENST00000409404.2_Missense_Mutation_p.I3329V|FAT3_ENST00000525166.1_Missense_Mutation_p.I3179V			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3329	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)				CACTGTCAACATCAACCTCAC	0.498										TCGA Ovarian(4;0.039)			A|||	27	0.00539137	0.0008	0.0115	5008	,	,		16819	0.0		0.0119	False		,,,				2504	0.0061				p.I3329V		Atlas-SNP	.											.	FAT3	1822	.	0			c.A9985G						PASS	.	A	VAL/ILE	2,3912		0,2,1955	50	51	51		9985	3.2	1	11	dbSNP_133	51	113,8195		2,109,4043	yes	missense	FAT3	NM_001008781.2	29	2,111,5998	GG,GA,AA		1.3601,0.0511,0.9409	benign	3329/4558	92568149	115,12107	1957	4154	6111	SO:0001583	missense	120114	exon14			GTCAACATCAACC	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.9985A>G	11.37:g.92568149A>G	ENSP00000298047:p.Ile3329Val	118	0	0		183	50	0.273224	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		13	0.005952380952380952	0	0.0	5	0.013812154696132596	0	0.0	8	0.010554089709762533	A	3.371	-0.128480	0.06753	5.11E-4	0.013601	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.35421	1.31;1.31;1.31	5.46	3.17	0.36434	.	.	.	.	.	T	0.15652	0.0377	N	0.20574	0.59	0.80722	D	1	B	0.13594	0.008	B	0.18263	0.021	T	0.04128	-1.0975	9	0.28530	T	0.3	.	8.4034	0.32601	0.7733:0.0:0.2267:0.0	.	3329	Q8TDW7-3	.	V	3329;3329;3179	ENSP00000298047:I3329V;ENSP00000387040:I3329V;ENSP00000432586:I3179V	ENSP00000298047:I3329V	I	+	1	0	FAT3	92207797	1.000000	0.71417	1.000000	0.80357	0.122000	0.20287	1.781000	0.38644	0.897000	0.36392	-0.256000	0.11100	ATC	A|0.991;G|0.009	0.009	strong		0.498	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		G	92568149	A	G	92568149	3	3	30	1	0	0	0	0	1	0	0	0	5699	217	8	3	10039	3	FAT3	11	92568149	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	310158	92568149	42438367	399	13550											
YAP1	10413	hgsc.bcm.edu	37	chr11	102094424	102094424	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caaaatccagtgtcttctccCgggatgtctcaggaattgag	10	11	10	10	1	3	1	1	1	3	0	6	3	4	3	2	2	0	0	2	2	3	2	rs61749258	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:102094424C>T	ENST00000282441.5	+	7	1492	c.1104C>T	c.(1102-1104)ccC>ccT	p.P368P	YAP1_ENST00000526343.1_Silent_p.P314P|YAP1_ENST00000524575.1_Silent_p.P190P|YAP1_ENST00000531439.1_Silent_p.P352P|YAP1_ENST00000537274.1_Silent_p.P356P|YAP1_ENST00000345877.2_Silent_p.P318P	NM_001130145.2|NM_001282101.1	NP_001123617.1|NP_001269030.1	P46937	YAP1_HUMAN	Yes-associated protein 1	368	Transactivation domain.				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)		TGTCTTCTCCCGGGATGTCTC	0.438													C|||	15	0.00299521	0.0	0.0029	5008	,	,		20533	0.0		0.008	False		,,,				2504	0.0051				p.P368P	Colon(50;247 1103 7861 28956)	Atlas-SNP	.											.	YAP1	45	.	0			c.C1104T						PASS	.	C	,,,	13,4393	20.2+/-43.8	0,13,2190	108	97	101		1104,1056,570,942	-11	0.2	11	dbSNP_129	101	81,8517	46.7+/-105.8	0,81,4218	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	YAP1	NM_001130145.2,NM_001195044.1,NM_001195045.1,NM_006106.4	,,,	0,94,6408	TT,TC,CC		0.9421,0.2951,0.7229	,,,	368/505,352/489,190/327,314/451	102094424	94,12910	2203	4299	6502	SO:0001819	synonymous_variant	10413	exon7			TTCTCCCGGGATG		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.1104C>T	11.37:g.102094424C>T		156	1	0.00641026		316	209	0.661392	NM_001130145	B4DTY1|B7ZA01|E3WEB5|E3WEB6|E9PRV2|F5H202|K0KQ18|K0KYZ8|K0L195|K0L1G3|Q7Z574|Q8IUY9	Silent	SNP	ENST00000282441.5	37	CCDS44716.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	C	8.228	0.803942	0.16467	0.002951	0.009421	ENSG00000137693	ENST00000529029	.	.	.	5.49	-11.0	0.00169	.	0.114641	0.64402	D	0.000010	T	0.27866	0.0686	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56019	-0.8048	6	0.39692	T	0.17	.	1.2473	0.01975	0.1961:0.1395:0.2166:0.4477	rs61749258	.	.	.	L	122	.	ENSP00000431626:P122L	P	+	2	0	YAP1	101599634	0.700000	0.27796	0.231000	0.23993	0.968000	0.65278	-0.459000	0.06728	-2.745000	0.00377	-1.083000	0.02208	CCG	C|0.995;T|0.005	0.005	strong		0.438	YAP1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394151.1	NM_006106		T	102094424	C	T	102094424	2	4	30	1	0	0	0	0	0	0	0	1	17481	639	23	1		1	YAP1	11	102094424	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	9526275	102094424	32912092	400	13551											
BIRC3	330	hgsc.bcm.edu	37	chr11	102195297	102195297	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttgatgaaaagcgccaacacGtttgaactgaaatacgactt	15	10	8	8	3	0	4	0	4	0	0	0	5	0	4	1	0	4	1	1	0	6	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:102195297G>A	ENST00000263464.3	+	2	2807	c.57G>A	c.(55-57)acG>acA	p.T19T	BIRC3_ENST00000532808.1_Silent_p.T19T	NM_001165.4	NP_001156.1	Q13489	BIRC3_HUMAN	baculoviral IAP repeat containing 3	19					apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of necroptotic process (GO:0060546)|negative regulation of phosphorylation (GO:0042326)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|protein heterooligomerization (GO:0051291)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|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)|spermatogenesis (GO:0007283)|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)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|ovary(3)|skin(1)	21	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)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0146)		GCGCCAACACGTTTGAACTGA	0.413			T	MALT1	MALT																																p.T19T		Atlas-SNP	.		Dom	yes		11	11q22-q23	330	baculoviral IAP repeat-containing 3		L	.	BIRC3	56	.	0			c.G57A						PASS	.						144	129	134					11																	102195297		2203	4299	6502	SO:0001819	synonymous_variant	330	exon2			CAACACGTTTGAA	L49432	CCDS8315.1	11q22	2011-01-25	2011-01-25			ENSG00000023445		"Baculoviral IAP repeat containing", "RING-type (C3HC4) zinc fingers"	591	protein-coding gene	gene with protein product	"apoptosis inhibitor 2", "TNFR2-TRAF signaling complex protein", "mammalian IAP homolog C", "inhibitor of apoptosis protein 1"	601721	"baculoviral IAP repeat-containing 3"	API2		8552191, 8548810	Standard	NM_001165		Approved	cIAP2, hiap-1, MIHC, RNF49, MALT2, c-IAP2	uc001pgx.3	Q13489		ENST00000263464.3:c.57G>A	11.37:g.102195297G>A		315	0	0		442	95	0.214932	NM_001165	Q16628|Q9HC27|Q9UP46	Silent	SNP	ENST00000263464.3	37	CCDS8315.1																																																																																			.	.	none		0.413	BIRC3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394159.1	NM_001165		A	102195297	G	A	102195297	2	1	30	1	0	0	0	0	0	0	0	1	1436	1132	40	1		1	BIRC3	11	102195297	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	100873	102195297	32811219	401	13552											
BIRC3	330	hgsc.bcm.edu	37	chr11	102195984	102195984	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acttcaagatacacagtttcTaatctgagcatgcagacaca	15	10	6	10	0	3	3	1	1	2	2	3	3	3	3	0	0	3	3	0	0	3	4	rs147757750		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:102195984T>A	ENST00000263464.3	+	2	3494	c.744T>A	c.(742-744)tcT>tcA	p.S248S	BIRC3_ENST00000532808.1_Silent_p.S248S	NM_001165.4	NP_001156.1	Q13489	BIRC3_HUMAN	baculoviral IAP repeat containing 3	248					apoptotic process (GO:0006915)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of necroptotic process (GO:0060546)|negative regulation of phosphorylation (GO:0042326)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|protein heterooligomerization (GO:0051291)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|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)|spermatogenesis (GO:0007283)|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)|cytosol (GO:0005829)|membrane raft (GO:0045121)|nucleus (GO:0005634)|protein complex (GO:0043234)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|ovary(3)|skin(1)	21	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)|LUSC - Lung squamous cell carcinoma(19;0.151)	BRCA - Breast invasive adenocarcinoma(274;0.0146)		ACACAGTTTCTAATCTGAGCA	0.423			T	MALT1	MALT																																p.S248S		Atlas-SNP	.		Dom	yes		11	11q22-q23	330	baculoviral IAP repeat-containing 3		L	BIRC3,colon,carcinoma,+2,2	BIRC3	56	2	0			c.T744A						PASS	.						75	76	76					11																	102195984		2203	4299	6502	SO:0001819	synonymous_variant	330	exon2			AGTTTCTAATCTG	L49432	CCDS8315.1	11q22	2011-01-25	2011-01-25			ENSG00000023445		"Baculoviral IAP repeat containing", "RING-type (C3HC4) zinc fingers"	591	protein-coding gene	gene with protein product	"apoptosis inhibitor 2", "TNFR2-TRAF signaling complex protein", "mammalian IAP homolog C", "inhibitor of apoptosis protein 1"	601721	"baculoviral IAP repeat-containing 3"	API2		8552191, 8548810	Standard	NM_001165		Approved	cIAP2, hiap-1, MIHC, RNF49, MALT2, c-IAP2	uc001pgx.3	Q13489		ENST00000263464.3:c.744T>A	11.37:g.102195984T>A		66	0	0		106	20	0.188679	NM_001165	Q16628|Q9HC27|Q9UP46	Silent	SNP	ENST00000263464.3	37	CCDS8315.1																																																																																			T|1.000;C|0.000	.	alt		0.423	BIRC3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394159.1	NM_001165		A	102195984	T	A	102195984	2	1	30	1	0	0	0	0	0	0	0	1	1436	1509	53	5		5	BIRC3	11	102195984	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	687	102195984	32810532	402	13553											
MMP8	4317	hgsc.bcm.edu	37	chr11	102593273	102593273	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtccagagtttcctcattTggcttccccgtcacattcaa	8	14	6	13	1	3	1	3	0	0	1	6	1	6	1	4	1	0	2	4	1	1	4	rs12803000	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:102593273T>G	ENST00000236826.3	-	2	332	c.234A>C	c.(232-234)ccA>ccC	p.P78P		NM_002424.2	NP_002415.1	P22894	MMP8_HUMAN	matrix metallopeptidase 8 (neutrophil collagenase)	78					collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|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)|metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(4)|skin(6)|stomach(1)|urinary_tract(1)	32	all_cancers(8;0.00092)|all_epithelial(12;0.00389)|Lung NSC(15;0.227)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0555)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.189)	BRCA - Breast invasive adenocarcinoma(274;0.0141)	Marimastat(DB00786)	TTTCCTCATTTGGCTTCCCCG	0.458													T|||	131	0.0261581	0.0015	0.036	5008	,	,		21789	0.0089		0.0417	False		,,,				2504	0.0542				p.P78P		Atlas-SNP	.											MMP8,face,malignant_melanoma,-2,1	MMP8	68	1	0			c.A234C						PASS	.	T		38,4368	43.1+/-76.7	0,38,2165	179	174	175		234	-5.5	0	11	dbSNP_121	175	441,8155	133.6+/-191.1	13,415,3870	no	coding-synonymous	MMP8	NM_002424.2		13,453,6035	GG,GT,TT		5.1303,0.8625,3.684		78/468	102593273	479,12523	2203	4298	6501	SO:0001819	synonymous_variant	4317	exon2			CTCATTTGGCTTC	J05556	CCDS8320.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000118113	ENSG00000118113	3.4.24.34		7175	protein-coding gene	gene with protein product		120355	"matrix metalloproteinase 8 (neutrophil collagenase)"	CLG1			Standard	NM_002424		Approved		uc001phe.2	P22894	OTTHUMG00000167587	ENST00000236826.3:c.234A>C	11.37:g.102593273T>G		343	0	0		579	141	0.243523	NM_002424	Q45F99	Silent	SNP	ENST00000236826.3	37	CCDS8320.1	50	0.022893772893772892	1	0.0020325203252032522	15	0.04143646408839779	3	0.005244755244755245	31	0.040897097625329816	T	9.744	1.165560	0.21538	0.008625	0.051303	ENSG00000118113	ENST00000438475	.	.	.	5.73	-5.47	0.02600	.	.	.	.	.	T	0.02571	0.0078	.	.	.	0.28932	N	0.891481	.	.	.	.	.	.	T	0.28586	-1.0039	4	.	.	.	.	1.8071	0.03083	0.1913:0.251:0.3608:0.1968	rs12803000;rs12803000	.	.	.	Q	54	.	.	K	-	1	0	MMP8	102098483	0.000000	0.05858	0.021000	0.16686	0.916000	0.54674	-2.650000	0.00858	-0.504000	0.06577	0.533000	0.62120	AAA	T|0.966;G|0.034	0.034	strong		0.458	MMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395223.1	NM_002424		G	102593273	T	G	102593273	2	3	30	1	0	0	0	0	0	0	0	1	9677	1799	63	5		5	MMP8	11	102593273	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	397289	102593273	32413243	403	13554											
MMP8	4317	hgsc.bcm.edu	37	chr11	102595579	102595579	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gaaatggaagcgtcttcaggGagaacatgatcttctcttca	12	11	10	8	1	5	2	2	1	3	1	6	5	5	3	0	2	2	0	0	2	3	3	rs17099450	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:102595579G>C	ENST00000236826.3	-	1	106	c.8C>G	c.(7-9)tCc>tGc	p.S3C		NM_002424.2	NP_002415.1	P22894	MMP8_HUMAN	matrix metallopeptidase 8 (neutrophil collagenase)	3			S -> C (in dbSNP:rs17099450). {ECO:0000269|Ref.2}.		collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|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)|metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase activity (GO:0004252)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(3)|kidney(1)|large_intestine(4)|lung(11)|ovary(4)|skin(6)|stomach(1)|urinary_tract(1)	32	all_cancers(8;0.00092)|all_epithelial(12;0.00389)|Lung NSC(15;0.227)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0555)|Lung(13;0.0828)|LUSC - Lung squamous cell carcinoma(19;0.151)|all cancers(10;0.189)	BRCA - Breast invasive adenocarcinoma(274;0.0141)	Marimastat(DB00786)	CGTCTTCAGGGAGAACATGAT	0.468													G|||	199	0.0397364	0.0514	0.0389	5008	,	,		18266	0.0089		0.0417	False		,,,				2504	0.0542				p.S3C		Atlas-SNP	.											.	MMP8	68	.	0			c.C8G						PASS	.	G	CYS/SER	213,4193	130.2+/-166.9	7,199,1997	147	154	152		8	-10.2	0	11	dbSNP_123	152	441,8157	133.9+/-191.4	13,415,3871	yes	missense	MMP8	NM_002424.2	112	20,614,5868	CC,CG,GG		5.1291,4.8343,5.0292	benign	3/468	102595579	654,12350	2203	4299	6502	SO:0001583	missense	4317	exon1			TTCAGGGAGAACA	J05556	CCDS8320.1	11q21-q22	2008-02-05	2005-08-08		ENSG00000118113	ENSG00000118113	3.4.24.34		7175	protein-coding gene	gene with protein product		120355	"matrix metalloproteinase 8 (neutrophil collagenase)"	CLG1			Standard	NM_002424		Approved		uc001phe.2	P22894	OTTHUMG00000167587	ENST00000236826.3:c.8C>G	11.37:g.102595579G>C	ENSP00000236826:p.Ser3Cys	200	0	0		335	80	0.238806	NM_002424	Q45F99	Missense_Mutation	SNP	ENST00000236826.3	37	CCDS8320.1	73	0.033424908424908424	23	0.046747967479674794	16	0.04419889502762431	3	0.005244755244755245	31	0.040897097625329816	G	11.83	1.756524	0.31137	0.048343	0.051291	ENSG00000118113	ENST00000236826	T	0.13901	2.55	5.26	-10.2	0.00374	.	5.605950	0.00166	N	0.000000	T	0.00815	0.0027	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24368	-1.0162	10	0.52906	T	0.07	.	0.229	0.00177	0.2519:0.1874:0.2546:0.3061	rs17099450;rs52812571;rs17099450	3	P22894	MMP8_HUMAN	C	3	ENSP00000236826:S3C	ENSP00000236826:S3C	S	-	2	0	MMP8	102100789	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.482000	0.02320	-1.792000	0.01259	-1.067000	0.02272	TCC	G|0.946;C|0.054	0.054	strong		0.468	MMP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395223.1	NM_002424		C	102595579	G	C	102595579	3	2	30	1	0	0	0	0	1	0	0	0	9677	1174	41	4	1435	4	MMP8	11	102595579	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2306	102595579	32410937	404	13555											
ALKBH8	91801	hgsc.bcm.edu	37	chr11	107375703	107375703	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttcctgagagtcattaatgCgggggacagaagatgccgag	11	8	14	8	2	1	3	1	1	0	3	2	6	2	4	2	2	2	0	2	2	2	2	rs139390837	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:107375703C>T	ENST00000428149.2	-	12	1827	c.1676G>A	c.(1675-1677)cGc>cAc	p.R559H	ALKBH8_ENST00000429370.1_Intron|ALKBH8_ENST00000417449.2_Missense_Mutation_p.R562H|ALKBH8_ENST00000389568.3_Missense_Mutation_p.R559H	NM_138775.2	NP_620130.2	Q96BT7	ALKB8_HUMAN	alkB, alkylation repair homolog 8 (E. coli)	559	Methyltransferase domain.				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)		GTCATTAATGCGGGGGACAGA	0.453													C|||	7	0.00139776	0.0038	0.0014	5008	,	,		20733	0.0		0.001	False		,,,				2504	0.0				p.R559H		Atlas-SNP	.											.	ALKBH8	88	.	0			c.G1676A						PASS	.	C	HIS/ARG	1,1383		0,1,691	118	98	104		1676	2.1	0	11	dbSNP_134	104	0,3182		0,0,1591	yes	missense	ALKBH8	NM_138775.2	29	0,1,2282	TT,TC,CC		0.0,0.0723,0.0219	benign	559/665	107375703	1,4565	692	1591	2283	SO:0001583	missense	91801	exon12			TTAATGCGGGGGA	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.1676G>A	11.37:g.107375703C>T	ENSP00000415885:p.Arg559His	91	0	0		133	36	0.270677	NM_138775	B1Q2M0|B4DEF6|Q8N989	Missense_Mutation	SNP	ENST00000428149.2	37	CCDS8337.2	4	0.0018315018315018315	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	4.450	0.083419	0.08533	7.23E-4	0.0	ENSG00000137760	ENST00000428149;ENST00000389568;ENST00000417449	T;T;T	0.45668	0.89;0.89;0.89	5.07	2.13	0.27403	.	0.956250	0.08831	N	0.887349	T	0.20251	0.0487	N	0.08118	0	0.09310	N	1	B;B	0.25351	0.124;0.001	B;B	0.08055	0.003;0.0	T	0.18272	-1.0342	10	0.42905	T	0.14	-2.6235	4.1101	0.10055	0.0872:0.3134:0.4508:0.1486	.	559;562	Q96BT7;Q96BT7-4	ALKB8_HUMAN;.	H	559;559;562	ENSP00000415885:R559H;ENSP00000374219:R559H;ENSP00000397673:R562H	ENSP00000374219:R559H	R	-	2	0	ALKBH8	106880913	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-0.511000	0.06321	0.241000	0.21283	-0.865000	0.03005	CGC	C|0.998;T|0.002	0.002	strong		0.453	ALKBH8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347071.2	NM_138775		T	107375703	C	T	107375703	3	4	30	1	0	0	0	0	1	0	0	0	533	768	27	1	322	1	ALKBH8	11	107375703	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	4780124	107375703	27630813	405	13556											
NPAT	4863	hgsc.bcm.edu	37	chr11	108044204	108044204	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tattggtatatcaggctgatCaggctgtaactgagattcac	11	13	10	7	0	3	2	3	2	0	1	3	3	3	2	0	3	1	4	0	3	4	6			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:108044204C>G	ENST00000278612.8	-	13	1612	c.1507G>C	c.(1507-1509)Gat>Cat	p.D503H	NPAT_ENST00000610253.1_5'UTR	NM_002519.2	NP_002510.2	Q14207	NPAT_HUMAN	nuclear protein, ataxia-telangiectasia locus	503					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)		TCAGGCTGATCAGGCTGTAAC	0.368																																					p.D503H		Atlas-SNP	.											.	NPAT	124	.	0			c.G1507C						PASS	.						127	122	123					11																	108044204		1867	4096	5963	SO:0001583	missense	4863	exon13			GCTGATCAGGCTG	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.1507G>C	11.37:g.108044204C>G	ENSP00000278612:p.Asp503His	207	0	0		386	99	0.256477	NM_002519	A8K1V5|A8K6M2|Q13632|Q14967|Q16580|Q86W55|Q8IWE9	Missense_Mutation	SNP	ENST00000278612.8	37	CCDS41710.1	.	.	.	.	.	.	.	.	.	.	C	4.278	0.050716	0.08243	.	.	ENSG00000149308	ENST00000278612	T	0.28069	1.63	6.08	4.21	0.49690	.	0.380295	0.29493	N	0.011997	T	0.44265	0.1285	M	0.62723	1.935	0.29803	N	0.832279	D;P	0.56287	0.975;0.956	P;P	0.56960	0.81;0.551	T	0.46289	-0.9202	10	0.62326	D	0.03	-4.1581	9.7917	0.40710	0.1397:0.7908:0.0:0.0695	.	503;503	B9EG70;Q14207	.;NPAT_HUMAN	H	503	ENSP00000278612:D503H	ENSP00000278612:D503H	D	-	1	0	NPAT	107549414	0.946000	0.32159	0.671000	0.29857	0.037000	0.13140	0.380000	0.20602	0.897000	0.36392	-0.181000	0.13052	GAT	.	.	none		0.368	NPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389506.2	NM_002519		G	108044204	C	G	108044204	3	3	30	1	0	0	0	0	1	0	0	0	10575	826	29	4	2800	4	NPAT	11	108044204	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	668501	108044204	26962312	406	13557											
ATM	472	hgsc.bcm.edu	37	chr11	108106435	108106435	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtcaagaactcttaaattatAtcatggatacagtgaaagat	17	12	7	5	0	3	3	2	1	1	2	3	4	3	4	0	1	2	0	0	1	8	4	rs148590073	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:108106435A>G	ENST00000452508.2	+	6	559	c.370A>G	c.(370-372)Atc>Gtc	p.I124V	ATM_ENST00000278616.4_Missense_Mutation_p.I124V			Q13315	ATM_HUMAN	ATM serine/threonine kinase	124					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)	CTTAAATTATATCATGGATAC	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)			A|||	7	0.00139776	0.0053	0.0	5008	,	,		18157	0.0		0.0	False		,,,				2504	0.0				p.I124V		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	.	ATM	1657	.	0			c.A370G	GRCh37	CD000908	ATM	D	rs148590073	PASS	.	A	VAL/ILE	35,4367	40.0+/-72.8	0,35,2166	113	116	115		370	0.4	1	11	dbSNP_134	115	0,8596		0,0,4298	yes	missense	ATM	NM_000051.3	29	0,35,6464	GG,GA,AA		0.0,0.7951,0.2693	benign	124/3057	108106435	35,12963	2201	4298	6499	SO:0001583	missense	472	exon5	Familial Cancer Database	AT, Louis-Bar syndrome	AATTATATCATGG	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.370A>G	11.37:g.108106435A>G	ENSP00000388058:p.Ile124Val	135	0	0		212	64	0.301887	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	A	5.116	0.207058	0.09704	0.007951	0.0	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.70045	-0.45;-0.45;-0.45	5.62	0.39	0.16275	Telomere-length maintenance and DNA damage repair (1);	0.272984	0.36101	N	0.002796	T	0.18130	0.0435	N	0.00801	-1.175	0.22581	N	0.998968	B	0.06786	0.001	B	0.08055	0.003	T	0.31724	-0.9933	10	0.06494	T	0.89	.	5.4836	0.16737	0.294:0.0:0.5308:0.1751	.	124	Q13315	ATM_HUMAN	V	124	ENSP00000435747:I124V;ENSP00000278616:I124V;ENSP00000388058:I124V	ENSP00000278616:I124V	I	+	1	0	ATM	107611645	0.996000	0.38824	0.976000	0.42696	0.990000	0.78478	0.866000	0.27954	0.174000	0.19809	0.477000	0.44152	ATC	A|0.997;G|0.003	0.003	strong		0.308	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		G	108106435	A	G	108106435	3	3	30	1	0	0	0	0	1	0	0	0	1109	449	16	3	384	3	ATM	11	108106435	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	62231	108106435	26900081	407	13558											
EXPH5	23086	hgsc.bcm.edu	37	chr11	108383560	108383560	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagcatcaagggaagaatTctttgatggtgaggaatctg	13	10	14	4	0	3	3	1	2	2	1	3	6	3	6	0	4	1	1	0	4	4	2	rs10890850	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:108383560T>A	ENST00000265843.4	-	6	2784	c.2674A>T	c.(2674-2676)Aat>Tat	p.N892Y	EXPH5_ENST00000428840.1_Missense_Mutation_p.N816Y|EXPH5_ENST00000443411.1_Missense_Mutation_p.N704Y|EXPH5_ENST00000524840.1_5'Flank|EXPH5_ENST00000525344.1_Missense_Mutation_p.N885Y	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	892			N -> Y (in dbSNP:rs10890850).		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)		AGGGAAGAATTCTTTGATGGT	0.438													T|||	270	0.0539137	0.1316	0.0115	5008	,	,		19382	0.0119		0.002	False		,,,				2504	0.0757				p.N892Y		Atlas-SNP	.											.	EXPH5	193	.	0			c.A2674T						PASS	.	T	TYR/ASN	493,3909	229.8+/-244.2	29,435,1737	182	167	172		2674	-2	0	11	dbSNP_120	172	9,8587	7.1+/-27.0	0,9,4289	yes	missense	EXPH5	NM_015065.2	143	29,444,6026	AA,AT,TT		0.1047,11.1995,3.8621	benign	892/1990	108383560	502,12496	2201	4298	6499	SO:0001583	missense	23086	exon6			AAGAATTCTTTGA		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.2674A>T	11.37:g.108383560T>A	ENSP00000265843:p.Asn892Tyr	152	0	0		211	60	0.28436	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	59	0.027014652014652016	46	0.09349593495934959	5	0.013812154696132596	7	0.012237762237762238	1	0.0013192612137203166	T	14.92	2.680490	0.47886	0.111995	0.001047	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.04603	4.17;4.1;3.95;4.17;4.02;3.59	5.74	-1.97	0.07503	.	0.712890	0.13437	N	0.387972	T	0.00109	0.0003	L	0.44542	1.39	0.09310	N	1	P	0.49090	0.919	B	0.43445	0.42	T	0.40813	-0.9543	10	0.72032	D	0.01	-0.8859	6.5046	0.22188	0.0:0.4682:0.1578:0.3739	rs10890850;rs10890850	892	Q8NEV8	EXPH5_HUMAN	Y	892;816;704;885;816;704	ENSP00000265843:N892Y;ENSP00000391966:N816Y;ENSP00000411390:N704Y;ENSP00000432546:N885Y;ENSP00000432683:N816Y;ENSP00000446434:N704Y	ENSP00000265843:N892Y	N	-	1	0	EXPH5	107888770	0.000000	0.05858	0.002000	0.10522	0.230000	0.25150	-0.173000	0.09854	-0.270000	0.09285	0.460000	0.39030	AAT	T|0.967;A|0.033	0.033	strong		0.438	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		A	108383560	T	A	108383560	3	1	30	1	0	0	0	0	1	0	0	0	5324	1783	62	5	3299	5	EXPH5	11	108383560	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	277125	108383560	26622956	408	13559											
HTR3B	9177	hgsc.bcm.edu	37	chr11	113803108	113803108	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaggtggtctctgcgtgcAgtttagagacatatgctttt	7	15	11	8	1	1	1	0	0	1	1	3	2	2	1	1	2	3	3	1	2	2	5	rs72466469	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:113803108A>C	ENST00000260191.2	+	5	723	c.466A>C	c.(466-468)Agt>Cgt	p.S156R	HTR3B_ENST00000537778.1_Missense_Mutation_p.S145R	NM_006028.4	NP_006019.1	O95264	5HT3B_HUMAN	5-hydroxytryptamine (serotonin) receptor 3B, ionotropic	156			S -> R (in dbSNP:rs72466469). {ECO:0000269|PubMed:15293096, ECO:0000269|PubMed:15389765, ECO:0000269|PubMed:21179162}.		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)	CTCTGCGTGCAGTTTAGAGAC	0.438													A|||	9	0.00179712	0.0	0.0043	5008	,	,		21219	0.0		0.006	False		,,,				2504	0.0				p.S156R		Atlas-SNP	.											.	HTR3B	50	.	0			c.A466C	GRCh37	CM083528	HTR3B	M	rs72466469	PASS	.	A	ARG/SER	2,4400	2.1+/-5.4	0,2,2199	179	153	162		466	0.7	0.2	11	dbSNP_130	162	69,8523	41.7+/-99.0	2,65,4229	yes	missense	HTR3B	NM_006028.4	110	2,67,6428	CC,CA,AA		0.8031,0.0454,0.5464	possibly-damaging	156/442	113803108	71,12923	2201	4296	6497	SO:0001583	missense	9177	exon5			GCGTGCAGTTTAG	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.466A>C	11.37:g.113803108A>C	ENSP00000260191:p.Ser156Arg	245	1	0.00408163		345	220	0.637681	NM_006028	B0YJ23|Q0VJC3	Missense_Mutation	SNP	ENST00000260191.2	37	CCDS8364.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	A	16.36	3.101980	0.56183	4.54E-4	0.008031	ENSG00000149305	ENST00000260191;ENST00000537778	T;T	0.79554	-1.28;-1.28	5.82	0.729	0.18266	Neurotransmitter-gated ion-channel ligand-binding (3);	0.421195	0.29473	N	0.012047	T	0.75317	0.3833	L	0.52905	1.665	0.33014	D	0.527966	D;P	0.56287	0.975;0.934	P;P	0.59643	0.861;0.643	T	0.77107	-0.2710	10	0.37606	T	0.19	-0.5361	4.9411	0.13965	0.6577:0.0:0.2158:0.1265	.	145;156	O95264-2;O95264	.;5HT3B_HUMAN	R	156;145	ENSP00000260191:S156R;ENSP00000443118:S145R	ENSP00000260191:S156R	S	+	1	0	HTR3B	113308318	0.181000	0.23161	0.166000	0.22797	0.877000	0.50540	0.873000	0.28052	0.144000	0.18951	-0.376000	0.06991	AGT	A|0.996;C|0.004	0.004	strong		0.438	HTR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398842.1	NM_006028		C	113803108	A	C	113803108	3	2	30	1	0	0	0	0	1	0	0	0	7454	188	7	5	484	5	HTR3B	11	113803108	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	5419548	113803108	21203408	409	13560											
SIK3	23387	hgsc.bcm.edu	37	chr11	116719841	116719841	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgggaccaacatacataagCatcgtcgctgttctggatcg	10	10	11	10	3	1	0	0	0	1	0	4	2	1	2	1	2	3	3	1	2	3	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:116719841C>T	ENST00000292055.4	-	21	3531	c.3496G>A	c.(3496-3498)Gct>Act	p.A1166T	SIK3_ENST00000542607.1_Missense_Mutation_p.A1106T|SIK3_ENST00000488337.1_5'UTR|SIK3_ENST00000446921.2_Missense_Mutation_p.A1164T|SIK3_ENST00000434315.2_Missense_Mutation_p.A1005T|AP006216.12_ENST00000444200.1_RNA|SIK3_ENST00000375288.1_Missense_Mutation_p.A501T|SIK3_ENST00000375300.1_Missense_Mutation_p.A1224T	NM_025164.3	NP_079440.3	Q9Y2K2	SIK3_HUMAN	SIK family kinase 3	1166					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						CATACATAAGCATCGTCGCTG	0.602																																					p.A1166T		Atlas-SNP	.											.	SIK3	112	.	0			c.G3496A						PASS	.						170	122	139					11																	116719841		2201	4292	6493	SO:0001583	missense	23387	exon21			CATAAGCATCGTC	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.3496G>A	11.37:g.116719841C>T	ENSP00000292055:p.Ala1166Thr	326	1	0.00306748		461	306	0.663774	NM_025164	A1A5A8|Q59FY2|Q5M9N1|Q6P3R6|Q8IYM8|Q9HA50	Missense_Mutation	SNP	ENST00000292055.4	37	CCDS8379.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.5|28.5	4.921494|4.921494	0.92249|0.92249	.|.	.|.	ENSG00000160584|ENSG00000160584	ENST00000375300;ENST00000292055;ENST00000375288;ENST00000542607;ENST00000434315|ENST00000445177;ENST00000454905;ENST00000446921	T;T;T;D;T|.	0.81821|.	-1.44;-1.42;0.59;-1.54;-1.17|.	5.26|5.26	4.35|4.35	0.52113|0.52113	.|.	0.000000|.	0.41194|.	U|.	0.000938|.	T|T	0.56108|0.56108	0.1963|0.1963	L|L	0.36672|0.36672	1.1|1.1	0.58432|0.58432	D|D	0.999998|0.999998	D;D;D;B|.	0.89917|.	1.0;1.0;1.0;0.117|.	D;D;D;B|.	0.87578|.	0.998;0.998;0.998;0.138|.	T|T	0.52087|0.52087	-0.8622|-0.8622	10|5	0.87932|.	D|.	0|.	.|.	13.8208|13.8208	0.63320|0.63320	0.0:0.9254:0.0:0.0746|0.0:0.9254:0.0:0.0746	.|.	1106;1005;1166;501|.	A1A5A8;A1A5A9;Q9Y2K2;Q9Y2K2-2|.	.;.;SIK3_HUMAN;.|.	T|Y	1224;1166;501;1106;1005|1265;5;1128	ENSP00000364449:A1224T;ENSP00000292055:A1166T;ENSP00000364437:A501T;ENSP00000438108:A1106T;ENSP00000415873:A1005T|.	ENSP00000292055:A1166T|.	A|C	-|-	1|2	0|0	SIK3|SIK3	116225051|116225051	1.000000|1.000000	0.71417|0.71417	0.978000|0.978000	0.43139|0.43139	0.993000|0.993000	0.82548|0.82548	7.456000|7.456000	0.80751|0.80751	1.223000|1.223000	0.43536|0.43536	0.557000|0.557000	0.71058|0.71058	GCT|TGC	.	.	none		0.602	SIK3-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_025164		T	116719841	C	T	116719841	3	4	30	1	0	0	0	0	1	0	0	0	14334	710	25	2	307	2	SIK3	11	116719841	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	2916733	116719841	18286675	410	13561											
CEP164	22897	hgsc.bcm.edu	37	chr11	117222691	117222691	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	caagaaggacagagacccccCcaaaagttcgctggtgagtc	13	5	11	12	1	0	3	0	1	0	2	2	5	0	4	3	2	0	2	3	2	4	1	rs143659874	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:117222691C>A	ENST00000278935.3	+	5	527	c.380C>A	c.(379-381)cCc>cAc	p.P127H		NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	127	Interaction with ATRIP.				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)		AGAGACCCCCCCAAAAGTTCG	0.517													C|||	9	0.00179712	0.0	0.0014	5008	,	,		16611	0.0		0.008	False		,,,				2504	0.0				p.P127H		Atlas-SNP	.											.	CEP164	121	.	0			c.C380A						PASS	.	C	HIS/PRO	3,4385		0,3,2191	21	23	22		380	4.9	0.1	11	dbSNP_134	22	39,8503		0,39,4232	yes	missense	CEP164	NM_014956.4	77	0,42,6423	AA,AC,CC		0.4566,0.0684,0.3248	possibly-damaging	127/1461	117222691	42,12888	2194	4271	6465	SO:0001583	missense	22897	exon4			ACCCCCCCAAAAG	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.380C>A	11.37:g.117222691C>A	ENSP00000278935:p.Pro127His	35	0	0		49	38	0.77551	NM_001271933	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	37	CCDS31683.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	10.48	1.362097	0.24684	6.84E-4	0.004566	ENSG00000110274	ENST00000533153;ENST00000278935;ENST00000525416;ENST00000545330;ENST00000529538	T;T;T	0.63744	-0.05;0.32;-0.06	5.81	4.89	0.63831	.	1.313720	0.05171	N	0.499480	T	0.60945	0.2308	L	0.36672	1.1	0.09310	N	1	P;P;D;P	0.63046	0.947;0.906;0.992;0.924	B;B;P;P	0.53146	0.36;0.258;0.719;0.562	T	0.57551	-0.7792	9	.	.	.	-0.0023	14.4821	0.67590	0.0:0.6025:0.3975:0.0	.	127;81;127;127	E9PI34;B7Z884;Q9UPV0;Q9UPV0-2	.;.;CE164_HUMAN;.	H	81;127;81;81;127	ENSP00000436034:P81H;ENSP00000278935:P127H;ENSP00000435759:P81H	.	P	+	2	0	CEP164	116727901	0.001000	0.12720	0.138000	0.22173	0.013000	0.08279	1.218000	0.32467	1.422000	0.47177	0.655000	0.94253	CCC	C|0.998;A|0.002	0.002	strong		0.517	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1	NM_014956		A	117222691	C	A	117222691	3	1	30	1	0	0	0	0	1	0	0	0	3251	623	22	4	390	4	CEP164	11	117222691	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	502850	117222691	17783825	411	13562											
TMPRSS13	84000	hgsc.bcm.edu	37	chr11	117789317	117789317	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagccggagatgcccgggcTggagatgcctgggctggaga	8	5	19	9	2	0	4	0	0	0	4	0	7	0	4	3	5	3	2	3	5	0	0	rs201746372|rs58754377|rs201369736		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:117789317T>C	ENST00000430170.2	-	2	345	c.258A>G	c.(256-258)ccA>ccG	p.P86P	TMPRSS13_ENST00000445164.2_Silent_p.P86P|TMPRSS13_ENST00000526090.1_Silent_p.P86P|TMPRSS13_ENST00000524993.1_Silent_p.P86P|TMPRSS13_ENST00000528626.1_Silent_p.P86P	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	86	13 X 5 AA repeats of A-S-P-A-[GLQR].|Ala-rich.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.Q83_A87delQASPA(1)		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)		ATGCCCGGGCTGGAGATGCCT	0.652																																					p.P86P		Atlas-SNP	.											TMPRSS13,caecum,carcinoma,0,1	TMPRSS13	75	1	1	Deletion - In frame(1)	urinary_tract(1)	c.A258G						PASS	.						34	41	38					11																	117789317		1955	4135	6090	SO:0001819	synonymous_variant	84000	exon2			CCGGGCTGGAGAT	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.258A>G	11.37:g.117789317T>C		118	0	0		268	13	0.0485075	NM_001206790	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	Silent	SNP	ENST00000430170.2	37	CCDS58185.1																																																																																			.	.	weak		0.652	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046		C	117789317	T	C	117789317	2	2	30	1	0	0	0	0	0	0	0	1	16260	1567	55	3		3	TMPRSS13	11	117789317	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	566626	117789317	17217199	412	13563											
UBE4A	9354	hgsc.bcm.edu	37	chr11	118253436	118253436	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgttctgcaactttcagtaTgcaccccaacttgcagaggc	9	11	9	12	0	2	1	1	0	1	1	2	1	2	1	2	1	5	5	2	1	3	4	rs567105943		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:118253436T>C	ENST00000431736.2	+	13	2235	c.2163T>C	c.(2161-2163)taT>taC	p.Y721Y	UBE4A_ENST00000545354.1_Silent_p.Y186Y|UBE4A_ENST00000252108.3_Silent_p.Y714Y					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)		ACTTTCAGTATGCACCCCAAC	0.498																																					p.Y721Y		Atlas-SNP	.											.	UBE4A	97	.	0			c.T2163C						PASS	.						180	167	172					11																	118253436		2200	4296	6496	SO:0001819	synonymous_variant	9354	exon13			TCAGTATGCACCC	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.2163T>C	11.37:g.118253436T>C		85	0	0		110	76	0.690909	NM_004788		Silent	SNP	ENST00000431736.2	37	CCDS8396.1																																																																																			.	.	none		0.498	UBE4A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398143.1	NM_004788		C	118253436	T	C	118253436	2	2	30	1	0	0	0	0	0	0	0	1	16897	1471	51	3		3	UBE4A	11	118253436	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	464119	118253436	16753080	413	13564											
NLRX1	79671	hgsc.bcm.edu	37	chr11	119050906	119050906	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctgggcagcggaaggcatGccctggatgaggtgaacttg	8	8	17	8	1	0	2	0	2	0	0	0	4	0	4	1	5	4	3	1	5	2	1	rs45450295	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:119050906G>A	ENST00000409109.1	+	7	2763	c.2176G>A	c.(2176-2178)Gcc>Acc	p.A726T	NLRX1_ENST00000292199.2_Missense_Mutation_p.A726T|NLRX1_ENST00000525863.1_Missense_Mutation_p.A726T|NLRX1_ENST00000409265.4_Missense_Mutation_p.A726T|NLRX1_ENST00000409991.1_Missense_Mutation_p.A726T	NM_001282144.1	NP_001269073.1	Q86UT6	NLRX1_HUMAN	NLR family member X1	726	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)		CGGAAGGCATGCCCTGGATGA	0.637													G|||	45	0.00898562	0.0295	0.0043	5008	,	,		18736	0.0		0.002	False		,,,				2504	0.001				p.A726T		Atlas-SNP	.											.	NLRX1	128	.	0			c.G2176A						PASS	.	G	THR/ALA,THR/ALA	162,4238	104.3+/-142.8	2,158,2040	51	47	49		2176,2176	-0.9	0.9	11	dbSNP_127	49	41,8549	26.3+/-74.7	0,41,4254	yes	missense,missense	NLRX1	NM_024618.2,NM_170722.1	58,58	2,199,6294	AA,AG,GG		0.4773,3.6818,1.5627	benign,benign	726/976,726/922	119050906	203,12787	2200	4295	6495	SO:0001583	missense	79671	exon7			AGGCATGCCCTGG	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.2176G>A	11.37:g.119050906G>A	ENSP00000387334:p.Ala726Thr	234	0	0		428	99	0.231308	NM_024618	A8K6Q1|B3KPK2|B3KTA2|Q7RTR3|Q96D51|Q9H724	Missense_Mutation	SNP	ENST00000409109.1	37	CCDS8416.1	13	0.005952380952380952	11	0.022357723577235773	0	0.0	0	0.0	2	0.002638522427440633	G	5.185	0.219615	0.09863	0.036818	0.004773	ENSG00000160703	ENST00000409991;ENST00000292199;ENST00000409265;ENST00000409109;ENST00000525863	T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73	5.17	-0.941	0.10402	.	0.788838	0.11541	N	0.553714	T	0.04588	0.0125	N	0.08118	0	0.18873	N	0.999983	B;B	0.15473	0.013;0.0	B;B	0.12156	0.007;0.002	T	0.16867	-1.0388	10	0.13108	T	0.6	.	3.8077	0.08783	0.1544:0.3464:0.3861:0.1131	rs45450295	726;726	Q86UT6-2;Q86UT6	.;NLRX1_HUMAN	T	726	ENSP00000386851:A726T;ENSP00000292199:A726T;ENSP00000386858:A726T;ENSP00000387334:A726T;ENSP00000433442:A726T	ENSP00000292199:A726T	A	+	1	0	NLRX1	118556116	0.000000	0.05858	0.911000	0.35937	0.797000	0.45037	-0.202000	0.09451	0.162000	0.19483	0.313000	0.20887	GCC	G|0.988;A|0.012	0.012	strong		0.637	NLRX1-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335403.1	NM_170722		A	119050906	G	A	119050906	3	1	30	1	0	0	0	0	1	0	0	0	10494	1319	46	2	2198	2	NLRX1	11	119050906	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	797470	119050906	15955610	414	13565											
CDON	50937	hgsc.bcm.edu	37	chr11	125873796	125873796	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccaaaggaagccctcactcaCctttgctggttcggaaggta	10	9	10	12	1	2	0	2	0	0	0	3	2	2	2	3	4	2	3	3	4	4	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr11:125873796C>T	ENST00000392693.3	-	10	2154		c.e10+1		CDON_ENST00000531738.1_Splice_Site|CDON_ENST00000263577.7_Splice_Site	NM_001243597.1|NM_016952.4	NP_001230526.1|NP_058648.4	Q4KMG0	CDON_HUMAN	cell adhesion associated, oncogene regulated						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)		CCCTCACTCACCTTTGCTGGT	0.458																																					.		Atlas-SNP	.											.	CDON	137	.	0			c.2026+1G>A						PASS	.						83	75	78					11																	125873796		2201	4299	6500	SO:0001630	splice_region_variant	50937	exon11			CACTCACCTTTGC	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.2026+1G>A	11.37:g.125873796C>T		60	0	0		97	5	0.0515464	NM_001243597	O14631	Splice_Site	SNP	ENST00000392693.3	37	CCDS58192.1	.	.	.	.	.	.	.	.	.	.	C	14.26	2.483812	0.44147	.	.	ENSG00000064309	ENST00000392693;ENST00000531738;ENST00000263577	.	.	.	6.08	6.08	0.98989	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.6634	0.99662	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CDON	125379006	1.000000	0.71417	1.000000	0.80357	0.161000	0.22273	7.440000	0.80464	2.894000	0.99253	0.655000	0.94253	.	.	.	none		0.458	CDON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386749.2	NM_016952	Intron	T	125873796	C	T	125873796	5	4	30	1	0	0	0	0	0	0	1	0	3172	521	18	2	1811	2	CDON	11	125873796	Splice_Site	SNP	C	TCGA-GR-7353-01A-11D-2210-10	6822890	125873796	9132720	415	13566											
GPR162	27239	hgsc.bcm.edu	37	chr12	6935995	6935995	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aaagacacaggttggaggacGaggaggacgaggaagaggct	15	3	18	5	2	0	2	0	0	0	2	0	9	0	7	0	7	0	2	0	7	2	1	rs138514784|rs138578985|rs58069762	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:6935995G>A	ENST00000311268.3	+	5	2180	c.1393G>A	c.(1393-1395)Gag>Aag	p.E465K	LEPREL2_ENST00000396725.2_RNA|LEPREL2_ENST00000606935.1_RNA|LEPREL2_ENST00000251761.8_RNA|GPR162_ENST00000382315.3_Missense_Mutation_p.E161K|GPR162_ENST00000428545.2_Missense_Mutation_p.E181K	NM_019858.1	NP_062832.1	Q16538	GP162_HUMAN	G protein-coupled receptor 162	465						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						GTTGGAGGACGAGGAGGACGA	0.652																																					p.E465K		Atlas-SNP	.											GPR162,bladder,carcinoma,0,1	GPR162	55	1	0			c.G1393A						scavenged	.	G	LYS/GLU,LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	50	62	58		541,1393	3.8	0.9	12	dbSNP_134	58	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	GPR162	NM_014449.1,NM_019858.1	56,56	0,4,6499	AA,AG,GG		0.0349,0.0227,0.0308	benign,benign	181/305,465/589	6935995	4,13002	2203	4300	6503	SO:0001583	missense	27239	exon5			GAGGACGAGGAGG	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.1393G>A	12.37:g.6935995G>A	ENSP00000311528:p.Glu465Lys	76	1	0.0131579		97	57	0.587629	NM_019858	Q16664|Q59EH5|Q66K56	Missense_Mutation	SNP	ENST00000311268.3	37	CCDS8563.1	.	.	.	.	.	.	.	.	.	.	G	7.227	0.598598	0.13939	2.27E-4	3.49E-4	ENSG00000250510	ENST00000311268;ENST00000428545;ENST00000382315	T;T;T	0.43688	3.1;0.94;0.94	4.7	3.79	0.43588	.	.	.	.	.	T	0.21145	0.0509	N	0.08118	0	0.22389	N	0.999148	B;B	0.27679	0.133;0.185	B;B	0.18561	0.022;0.013	T	0.10776	-1.0615	9	0.36615	T	0.2	.	7.9273	0.29883	0.0:0.268:0.5194:0.2126	.	181;465	Q16538-2;Q16538	.;GP162_HUMAN	K	465;181;161	ENSP00000311528:E465K;ENSP00000399670:E181K;ENSP00000371752:E161K	ENSP00000311528:E465K	E	+	1	0	GPR162	6806256	0.985000	0.35326	0.882000	0.34594	0.215000	0.24574	2.459000	0.45023	1.299000	0.44798	0.491000	0.48974	GAG	G|1.000;A|0.000	0.000	weak		0.652	GPR162-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399478.1	NM_019858		A	6935995	G	A	6935995	3	1	30	1	0	0	0	0	1	0	0	0	6674	1059	37	1	1426	1	GPR162	12	6935995	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10		6935995	126915900	416	13567											
PTPN6	5777	hgsc.bcm.edu	37	chr12	7067226	7067226	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcacgcagggcccatcatcGtgcactgcaggtgaggatga	9	7	13	12	2	2	2	2	2	0	0	3	3	2	3	1	3	2	3	1	3	0	0	rs62621988		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:7067226G>A	ENST00000318974.9	+	11	1595	c.1351G>A	c.(1351-1353)Gtg>Atg	p.V451M	PTPN6_ENST00000456013.1_Missense_Mutation_p.V451M|PTPN6_ENST00000399448.1_Missense_Mutation_p.V453M|PTPN6_ENST00000447931.2_Missense_Mutation_p.V412M	NM_002831.5	NP_002822.2	P29350	PTN6_HUMAN	protein tyrosine phosphatase, non-receptor type 6	451	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						GCCCATCATCGTGCACTGCAG	0.532													G|||	1	0.000199681	0.0	0.0	5008	,	,		-128	0.0		0.001	False		,,,				2504	0.0				p.V453M		Atlas-SNP	.											.	PTPN6	42	.	0			c.G1357A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL	2,4098		0,2,2048	36	38	38		1351,1357,1351	5.1	1	12	dbSNP_129	38	12,8396		0,12,4192	yes	missense,missense,missense	PTPN6	NM_002831.5,NM_080548.4,NM_080549.3	21,21,21	0,14,6240	AA,AG,GG		0.1427,0.0488,0.1119	probably-damaging,probably-damaging,probably-damaging	451/596,453/598,451/625	7067226	14,12494	2050	4204	6254	SO:0001583	missense	5777	exon11			ATCATCGTGCACT		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.1351G>A	12.37:g.7067226G>A	ENSP00000326010:p.Val451Met	41	0	0		22	11	0.5	NM_080548	A8K306|G3V0F8|Q969V8|Q9UK67	Missense_Mutation	SNP	ENST00000318974.9	37	CCDS44820.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	19.88	3.908893	0.72868	4.88E-4	0.001427	ENSG00000111679	ENST00000399448;ENST00000447931;ENST00000318974;ENST00000456013	D;D;D;D	0.91124	-2.79;-2.79;-2.79;-2.79	5.08	5.08	0.68730	Protein-tyrosine phosphatase, receptor/non-receptor type (4);Protein-tyrosine/Dual-specificity phosphatase (1);	0.140227	0.48767	D	0.000171	D	0.97480	0.9175	H	0.98646	4.29	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	0.999;0.998;0.998;0.998;0.999	D	0.99410	1.0930	10	0.87932	D	0	.	18.4653	0.90752	0.0:0.0:1.0:0.0	rs62621988	439;412;451;451;453	B4DPS0;P29350-2;G3V0F8;P29350;Q53XS4	.;.;.;PTN6_HUMAN;.	M	453;412;451;451	ENSP00000382376:V453M;ENSP00000415979:V412M;ENSP00000326010:V451M;ENSP00000391592:V451M	ENSP00000326010:V451M	V	+	1	0	PTPN6	6937487	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	4.603000	0.61105	2.346000	0.79739	0.561000	0.74099	GTG	G|0.999;A|0.001	0.001	strong		0.532	PTPN6-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400023.1	NM_002831		A	7067226	G	A	7067226	3	1	30	1	0	0	0	0	1	0	0	0	12807	1145	40	1	1411	1	PTPN6	12	7067226	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	131231	7067226	126784669	417	13568											
C12orf59	120939	hgsc.bcm.edu	37	chr12	10332198	10332198	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gagtccgagttcatgtcgtgGcggcctcagccctgctgtat	5	11	13	12	3	2	0	2	0	0	0	4	2	3	0	3	2	2	3	3	2	1	2	rs140071448		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:10332198G>T	ENST00000381923.2	+	2	429	c.25G>T	c.(25-27)Gcg>Tcg	p.A9S	TMEM52B_ENST00000298530.3_Missense_Mutation_p.W3C|TMEM52B_ENST00000536952.1_Missense_Mutation_p.A9S			Q4KMG9	TM52B_HUMAN	transmembrane protein 52B	9						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											TCATGTCGTGGCGGCCTCAGC	0.478													G|||	1	0.000199681	0.0	0.0	5008	,	,		17529	0.0		0.001	False		,,,				2504	0.0				p.W3C		Atlas-SNP	.											.	.	.	.	0			c.G9T						PASS	.	G	CYS/TRP	0,4406		0,0,2203	183	173	176		9	-5.3	0	12	dbSNP_134	176	3,8597	3.0+/-9.4	0,3,4297	yes	missense	C12orf59	NM_153022.2	215	0,3,6500	TT,TG,GG		0.0349,0.0,0.0231	benign	3/164	10332198	3,13003	2203	4300	6503	SO:0001583	missense	120939	exon1			GTCGTGGCGGCCT	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.25G>T	12.37:g.10332198G>T	ENSP00000371348:p.Ala9Ser	163	0	0		118	54	0.457627	NM_153022	Q96NA7	Missense_Mutation	SNP	ENST00000381923.2	37		1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	G|G	8.571|8.571	0.879998|0.879998	0.17467|0.17467	0.0|0.0	3.49E-4|3.49E-4	ENSG00000165685|ENSG00000165685	ENST00000381923;ENST00000543484;ENST00000536952|ENST00000298530	.|.	.|.	.|.	5.3|5.3	-5.3|-5.3	0.02738|0.02738	.|.	1.353820|.	0.04491|.	N|.	0.379462|.	T|T	0.25754|0.25754	0.0627|0.0627	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	B|B	0.02656|0.02656	0.0|0.0	B|B	0.01281|0.01281	0.0|0.0	T|T	0.29366|0.29366	-1.0014|-1.0014	8|7	0.38643|0.87932	T|D	0.18|0	1.6513|1.6513	4.7738|4.7738	0.13169|0.13169	0.3682:0.0:0.3801:0.2518|0.3682:0.0:0.3801:0.2518	.|.	9|3	Q4KMG9|Q4KMG9-2	CL059_HUMAN|.	S|C	9|3	.|.	ENSP00000371348:A9S|ENSP00000298530:W3C	A|W	+|+	1|3	0|0	C12orf59|C12orf59	10223465|10223465	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-0.493000|-0.493000	0.06459|0.06459	-1.165000|-1.165000	0.02786|0.02786	-1.197000|-1.197000	0.01672|0.01672	GCG|TGG	G|1.000;T|0.000	0.000	strong		0.478	TMEM52B-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000399645.1	NM_153022		T	10332198	G	T	10332198	3	4	30	1	0	0	0	0	1	0	0	0	1704	1212	42	4	11	4	C12orf59	12	10332198	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	3264972	10332198	123519697	418	13569											
PRB3	5544	hgsc.bcm.edu	37	chr12	11421004	11421004	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggttgcctccttgtgggggtCgtccttctggctttcctgga	1	15	14	11	1	1	0	0	0	1	0	5	1	4	1	4	5	1	2	4	5	0	4	rs71455364		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:11421004C>T	ENST00000279573.7	-	3	314	c.179G>A	c.(178-180)cGa>cAa	p.R60Q	PRB3_ENST00000538488.1_Missense_Mutation_p.R60Q|PRB3_ENST00000381842.3_Missense_Mutation_p.R60Q|PRB3_ENST00000440870.3_5'UTR			Q04118	PRB3_HUMAN	proline-rich protein BstNI subfamily 3	60	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.			R -> P (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)			TTGTGGGGGTCGTCCTTCTGG	0.627																																					p.R60Q		Atlas-SNP	.											.	PRB3	84	.	0			c.G179A						PASS	.						160	173	168					12																	11421004		2198	4296	6494	SO:0001583	missense	5544	exon3			GGGGGTCGTCCTT			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.179G>A	12.37:g.11421004C>T	ENSP00000279573:p.Arg60Gln	108	0	0		73	27	0.369863	NM_006249	Q15188|Q4VAY3|Q4VAY4|Q7M4M9|Q9UCT9	Missense_Mutation	SNP	ENST00000279573.7	37		.	.	.	.	.	.	.	.	.	.	.	3.985	-0.005638	0.07773	.	.	ENSG00000197870	ENST00000381842;ENST00000538488	T;T	0.04119	3.7;3.7	0.763	-1.53	0.08611	.	0.242690	0.19335	U	0.116811	T	0.02610	0.0079	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46233	-0.9206	9	0.13470	T	0.59	.	5.5053	0.16850	0.0:0.3072:0.4664:0.2265	.	60	Q04118	PRB3_HUMAN	Q	60	ENSP00000371264:R60Q;ENSP00000442626:R60Q	ENSP00000279573:R60Q	R	-	2	0	PRB3	11312271	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.005000	0.00315	-4.132000	0.00071	-2.937000	0.00087	CGA	C|0.500;G|0.500	.	alt		0.627	PRB3-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000402119.5	NM_006249		T	11421004	C	T	11421004	3	4	30	1	0	0	0	0	1	0	0	0	12456	884	31	1	758	1	PRB3	12	11421004	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1088806	11421004	122430891	419	13570											
PTPRO	5800	hgsc.bcm.edu	37	chr12	15661564	15661564	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgcagcacgtgagtgtccacGttttaagctcaaccactgcc	9	9	9	14	3	1	1	1	1	0	0	2	1	2	1	3	0	4	4	3	0	2	2	rs71459181	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:15661564G>A	ENST00000281171.4	+	7	1657	c.1327G>A	c.(1327-1329)Gtt>Att	p.V443I	PTPRO_ENST00000543886.1_Missense_Mutation_p.V443I|PTPRO_ENST00000348962.2_Missense_Mutation_p.V443I	NM_030667.2	NP_109592.1	Q16827	PTPRO_HUMAN	protein tyrosine phosphatase, receptor type, O	443	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)				GAGTGTCCACGTTTTAAGCTC	0.502													G|||	18	0.00359425	0.0008	0.0072	5008	,	,		18994	0.0		0.0089	False		,,,				2504	0.0031				p.V443I		Atlas-SNP	.											.	PTPRO	148	.	0			c.G1327A						PASS	.	G	ILE/VAL,ILE/VAL	14,4392	22.3+/-47.3	0,14,2189	100	93	95		1327,1327	4.6	0.2	12	dbSNP_130	95	121,8479	62.8+/-124.8	2,117,4181	yes	missense,missense	PTPRO	NM_002848.3,NM_030667.2	29,29	2,131,6370	AA,AG,GG		1.407,0.3177,1.038	benign,benign	443/1189,443/1217	15661564	135,12871	2203	4300	6503	SO:0001583	missense	5800	exon7			GTCCACGTTTTAA	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.1327G>A	12.37:g.15661564G>A	ENSP00000281171:p.Val443Ile	198	0	0		198	109	0.550505	NM_002848	A0AV39|Q13101|Q8IYG3|Q9UBF0|Q9UBT5	Missense_Mutation	SNP	ENST00000281171.4	37	CCDS8675.1	10	0.004578754578754579	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	G	14.57	2.576090	0.45902	0.003177	0.01407	ENSG00000151490	ENST00000281171;ENST00000543886;ENST00000348962	T;T;T	0.57752	0.38;0.38;0.38	5.44	4.55	0.56014	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.46442	D	0.000284	T	0.20941	0.0504	N	0.12182	0.205	0.80722	D	1	P;P;B	0.40398	0.669;0.716;0.233	B;B;B	0.28385	0.053;0.089;0.04	T	0.07751	-1.0756	10	0.28530	T	0.3	.	12.3796	0.55299	0.0767:0.0:0.9233:0.0	.	443;443;443	Q16827-2;Q16827;Q8IYG3	.;PTPRO_HUMAN;.	I	443	ENSP00000281171:V443I;ENSP00000444173:V443I;ENSP00000343434:V443I	ENSP00000281171:V443I	V	+	1	0	PTPRO	15552831	0.869000	0.29996	0.175000	0.22980	0.976000	0.68499	1.352000	0.34033	1.537000	0.49254	0.655000	0.94253	GTT	G|0.991;A|0.009	0.009	strong		0.502	PTPRO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401079.1			A	15661564	G	A	15661564	3	1	30	1	0	0	0	0	1	0	0	0	12824	1145	40	1	1353	1	PTPRO	12	15661564	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	4240560	15661564	118190331	420	13571											
PPHLN1	51535	hgsc.bcm.edu	37	chr12	42839923	42839923	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccccggaagaaacgggttcGtcggacgacacagcttcgtc	9	6	13	13	6	0	1	0	0	0	1	4	4	0	3	2	3	2	2	2	3	2	2	rs201876048	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:42839923G>A	ENST00000395568.2	+	12	1265	c.1181G>A	c.(1180-1182)cGt>cAt	p.R394H	PPHLN1_ENST00000317560.9_Intron|PPHLN1_ENST00000432191.2_Missense_Mutation_p.R370H|PPHLN1_ENST00000256678.8_Missense_Mutation_p.R299H	NM_016488.6	NP_057572.5	Q8NEY8	PPHLN_HUMAN	periphilin 1	394					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)		aaacgggttcgtcggacgaca	0.622													G|||	3	0.000599042	0.0	0.0014	5008	,	,		11704	0.0		0.002	False		,,,				2504	0.0				p.R394H		Atlas-SNP	.											.	PPHLN1	101	.	0			c.G1181A						PASS	.	G	HIS/ARG,HIS/ARG	1,4325		0,1,2162	7	8	8		1109,1181	0.2	0.1	12		8	18,8426		0,18,4204	yes	missense,missense	PPHLN1	NM_001143787.1,NM_016488.6	29,29	0,19,6366	AA,AG,GG		0.2132,0.0231,0.1488	probably-damaging,probably-damaging	370/435,394/459	42839923	19,12751	2163	4222	6385	SO:0001583	missense	51535	exon12			GGGTTCGTCGGAC	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.1181G>A	12.37:g.42839923G>A	ENSP00000378935:p.Arg394His	92	0	0		93	47	0.505376	NM_016488	E9PAX8|Q86YT2|Q8IXN3|Q8TB09|Q96NB9|Q9NXL4|Q9P0P6|Q9P0R9	Missense_Mutation	SNP	ENST00000395568.2	37	CCDS31777.1	.	.	.	.	.	.	.	.	.	.	G	5.312	0.242935	0.10077	2.31E-4	0.002132	ENSG00000134283	ENST00000395568;ENST00000256678;ENST00000432191	.	.	.	0.158	0.158	0.14942	.	0.000000	0.85682	U	0.000000	T	0.12263	0.0298	N	0.02011	-0.69	0.09310	N	1	B;B;B;B	0.06786	0.001;0.001;0.001;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.20706	-1.0267	8	0.87932	D	0	.	.	.	.	.	299;345;370;394	F8W6A0;B7Z695;Q8NEY8-3;Q8NEY8	.;.;.;PPHLN_HUMAN	H	394;299;370	.	ENSP00000256678:R299H	R	+	2	0	PPHLN1	41126190	0.328000	0.24687	0.148000	0.22405	0.150000	0.21749	0.251000	0.18257	0.202000	0.20498	0.205000	0.17691	CGT	.	.	weak		0.622	PPHLN1-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404047.1	NM_201515		A	42839923	G	A	42839923	3	1	30	1	0	0	0	0	1	0	0	0	12324	1145	40	1	1433	1	PPHLN1	12	42839923	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	27178359	42839923	91011972	421	13572											
DBX2	440097	hgsc.bcm.edu	37	chr12	45444426	45444426	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgcgttccgtagggcgccccGgcggggctaacttgttcggc	3	8	16	14	7	0	0	0	0	0	0	2	0	1	0	3	5	1	4	3	5	2	5			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:45444426G>A	ENST00000332700.6	-	1	456	c.285C>T	c.(283-285)gcC>gcT	p.A95A	RP11-478B9.1_ENST00000548424.1_RNA	NM_001004329.2	NP_001004329.2	Q6ZNG2	DBX2_HUMAN	developing brain homeobox 2	95					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)		AGGGCGCCCCGGCGGGGCTAA	0.721																																					p.A95A		Atlas-SNP	.											.	DBX2	45	.	0			c.C285T						PASS	.						4	5	5					12																	45444426		1972	3943	5915	SO:0001819	synonymous_variant	440097	exon1			CGCCCCGGCGGGG		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.285C>T	12.37:g.45444426G>A		84	0	0		68	21	0.308824	NM_001004329		Silent	SNP	ENST00000332700.6	37	CCDS31781.1																																																																																			.	.	none		0.721	DBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404810.1	NM_001004329		A	45444426	G	A	45444426	2	1	30	1	0	0	0	0	0	0	0	1	4262	1103	39	1		1	DBX2	12	45444426	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2604503	45444426	88407469	422	13573											
AMIGO2	91523	hgsc.bcm.edu	37	chr12	47471287	47471287	+	5'Flank	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgagtcagatttccccctcGtggactttaggatgccctca	7	12	9	13	1	2	2	2	1	0	1	4	4	3	4	3	2	1	0	3	2	1	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:47471287G>A	ENST00000546455.1	+	0	0				AMIGO2_ENST00000429635.1_Missense_Mutation_p.T500M|AMIGO2_ENST00000321382.3_Missense_Mutation_p.T500M|AMIGO2_ENST00000550413.1_Missense_Mutation_p.T500M|AMIGO2_ENST00000266581.4_Missense_Mutation_p.T500M			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B								hydrolase activity (GO:0016787)										TTTCCCCCTCGTGGACTTTAG	0.468																																					p.T500M		Atlas-SNP	.											AMIGO2,NS,carcinoma,-1,1	AMIGO2	50	1	0			c.C1499T						PASS	.						70	66	67					12																	47471287		2203	4300	6503	SO:0001631	upstream_gene_variant	347902	exon2			CCCCTCGTGGACT	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		12.37:g.47471287G>A	Exception_encountered	167	0	0		130	56	0.430769	NM_181847	Q96B20	Missense_Mutation	SNP	ENST00000546455.1	37	CCDS8752.1	.	.	.	.	.	.	.	.	.	.	G	13.07	2.126383	0.37533	.	.	ENSG00000139211	ENST00000266581;ENST00000550413;ENST00000429635;ENST00000321382	T;T;T;T	0.49432	0.78;0.78;0.78;0.78	5.09	5.09	0.68999	.	0.380800	0.28647	N	0.014620	T	0.40839	0.1133	L	0.44542	1.39	0.25929	N	0.983015	P	0.47910	0.902	B	0.36666	0.23	T	0.47209	-0.9135	10	0.51188	T	0.08	-0.3923	18.3695	0.90402	0.0:0.0:1.0:0.0	.	500	Q86SJ2	AMGO2_HUMAN	M	500	ENSP00000266581:T500M;ENSP00000449034:T500M;ENSP00000406020:T500M;ENSP00000320848:T500M	ENSP00000266581:T500M	T	-	2	0	AMIGO2	45757554	0.970000	0.33590	0.047000	0.18901	0.988000	0.76386	4.115000	0.57865	2.745000	0.94114	0.561000	0.74099	ACG	.	.	none		0.468	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371		A	47471287	G	A	47471287	1	1	30	0	1	0	0	0	0	0	0	0	576	1145	40	1		1	AMIGO2	12	47471287	5'Flank	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2026861	47471287	86380608	423	13574											
CELA1	1990	hgsc.bcm.edu	37	chr12	51739625	51739625	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcagtccctccgactacgCgggcattggtttccggaagg	6	9	12	14	4	1	0	1	0	0	0	4	2	4	1	4	4	1	2	4	4	2	3	rs74336876	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:51739625C>T	ENST00000293636.1	-	2	93	c.53G>A	c.(52-54)cGc>cAc	p.R18H		NM_001971.5	NP_001962.3	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1	18					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						TCCGACTACGCGGGCATTGGT	0.592													C|||	14	0.00279553	0.0	0.0043	5008	,	,		15127	0.0		0.0089	False		,,,				2504	0.002				p.R18H		Atlas-SNP	.											.	CELA1	39	.	0			c.G53A						PASS	.	C	HIS/ARG	12,4382		0,12,2185	58	52	54		53	5	1	12	dbSNP_131	54	66,8516		0,66,4225	yes	missense	CELA1	NM_001971.5	29	0,78,6410	TT,TC,CC		0.7691,0.2731,0.6011	probably-damaging	18/259	51739625	78,12898	2197	4291	6488	SO:0001583	missense	1990	exon2			ACTACGCGGGCAT		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.53G>A	12.37:g.51739625C>T	ENSP00000293636:p.Arg18His	66	0	0		53	26	0.490566	NM_001971	Q5MLF0|Q6DJT0|Q6ISM6	Missense_Mutation	SNP	ENST00000293636.1	37	CCDS8812.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	27.9	4.875832	0.91664	0.002731	0.007691	ENSG00000139610	ENST00000293636	D	0.94966	-3.57	5.03	5.03	0.67393	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (1);	0.000000	0.85682	D	0.000000	D	0.95950	0.8681	M	0.76002	2.32	0.58432	D	0.999999	D	0.89917	1.0	D	0.91635	0.999	D	0.95423	0.8509	10	0.87932	D	0	-29.8305	17.5406	0.87846	0.0:1.0:0.0:0.0	.	18	Q9UNI1	CELA1_HUMAN	H	18	ENSP00000293636:R18H	ENSP00000293636:R18H	R	-	2	0	CELA1	50025892	0.999000	0.42202	0.998000	0.56505	0.793000	0.44817	6.004000	0.70709	2.503000	0.84419	0.563000	0.77884	CGC	C|0.995;T|0.005	0.005	strong		0.592	CELA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394901.1	NM_001971		T	51739625	C	T	51739625	3	4	30	1	0	0	0	0	1	0	0	0	3212	768	27	1	751	1	CELA1	12	51739625	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	4268338	51739625	82112270	424	13575											
KRT1	3848	hgsc.bcm.edu	37	chr12	53069243	53069243	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acctccggagccgtagctgcTacctccggagccatagctgc	7	7	11	16	3	0	0	0	0	0	0	2	2	2	2	6	2	7	4	6	2	3	3	rs77846840|rs540699806|rs267607656	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:53069243T>C	ENST00000252244.3	-	9	1727	c.1669A>G	c.(1669-1671)Agc>Ggc	p.S557G		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	557	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.S557_G563delSSYGSGG(3)		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						ccgtagctgctacctccggag	0.682																																					p.S557G		Atlas-SNP	.											.	KRT1	110	.	3	Deletion - In frame(3)	prostate(2)|central_nervous_system(1)	c.A1669G						PASS	.						4	4	4					12																	53069243		1805	3566	5371	SO:0001583	missense	3848	exon9			AGCTGCTACCTCC	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.1669A>G	12.37:g.53069243T>C	ENSP00000252244:p.Ser557Gly	17	0	0		25	8	0.32	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Missense_Mutation	SNP	ENST00000252244.3	37	CCDS8836.1	.	.	.	.	.	.	.	.	.	.	t	12.77	2.037794	0.35989	.	.	ENSG00000167768	ENST00000252244	T	0.81247	-1.47	3.63	0.628	0.17681	.	.	.	.	.	T	0.54711	0.1875	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48490	-0.9031	8	0.07644	T	0.81	.	5.639	0.17552	0.0:0.6406:0.1602:0.1993	.	557	P04264	K2C1_HUMAN	G	557	ENSP00000252244:S557G	ENSP00000252244:S557G	S	-	1	0	KRT1	51355510	0.000000	0.05858	0.034000	0.17996	0.201000	0.24016	-0.192000	0.09587	-0.104000	0.12154	-1.598000	0.00824	AGC	T|0.500;C|0.500	0.500	weak		0.682	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121		C	53069243	T	C	53069243	3	2	30	1	0	0	0	0	1	0	0	0	8456	1522	53	3	269	3	KRT1	12	53069243	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	1329618	53069243	80782652	425	13576											
KRT77	374454	hgsc.bcm.edu	37	chr12	53090181	53090181	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggacgacaaagtcattctcGctgccagtcctcttgttgat	9	12	9	11	2	3	1	1	1	2	0	5	3	4	2	2	1	1	2	2	1	1	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:53090181G>A	ENST00000341809.3	-	3	820	c.792C>T	c.(790-792)agC>agT	p.S264S	KRT77_ENST00000537195.1_Silent_p.S31S|RP11-641A6.3_ENST00000547533.1_RNA	NM_175078.2	NP_778253.2	Q7Z794	K2C1B_HUMAN	keratin 77	264	Coil 1B.|Rod.					cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.S264S(1)		NS(2)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						AGTCATTCTCGCTGCCAGTCC	0.567																																					p.S264S		Atlas-SNP	.											KRT77,NS,carcinoma,0,1	KRT77	58	1	1	Substitution - coding silent(1)	lung(1)	c.C792T						scavenged	.						176	125	142					12																	53090181		2203	4300	6503	SO:0001819	synonymous_variant	374454	exon3			ATTCTCGCTGCCA	BK000975	CCDS8837.1	12q13.13	2013-06-25	2006-07-17	2006-07-17	ENSG00000189182	ENSG00000189182		"-", "Intermediate filaments type II, keratins (basic)"	20411	protein-coding gene	gene with protein product		611158	"keratin 1B"	KRT1B		11683385, 16831889	Standard	NM_175078		Approved		uc001saw.3	Q7Z794	OTTHUMG00000169450	ENST00000341809.3:c.792C>T	12.37:g.53090181G>A		51	1	0.0196078		56	27	0.482143	NM_175078	Q7RTS8	Silent	SNP	ENST00000341809.3	37	CCDS8837.1																																																																																			.	.	none		0.567	KRT77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404111.1	NM_175078		A	53090181	G	A	53090181	2	1	30	1	0	0	0	0	0	0	0	1	8499	1078	38	1		1	KRT77	12	53090181	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	20938	53090181	80761714	426	13577											
CBX5	23468	hgsc.bcm.edu	37	chr12	54639963	54639963	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgatcttttctggttccaGtcctctctcaaagccccgag	8	13	7	13	1	4	1	1	1	3	0	7	2	6	1	4	1	1	1	4	1	2	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:54639963G>A	ENST00000439541.2	-	4	486	c.361C>T	c.(361-363)Ctg>Ttg	p.L121L	CBX5_ENST00000209875.4_Silent_p.L121L|CBX5_ENST00000550411.1_Silent_p.L121L	NM_001127321.1	NP_001120793.1	P45973	CBX5_HUMAN	chromobox homolog 5	121	Chromo 2; shadow subtype. {ECO:0000255|PROSITE-ProRule:PRU00053}.|Interaction with ASXL1.				blood coagulation (GO:0007596)|negative regulation of transcription, DNA-templated (GO:0045892)|viral process (GO:0016032)	chromocenter (GO:0010369)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear heterochromatin (GO:0005720)|nuclear pericentric heterochromatin (GO:0031618)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|methylated histone binding (GO:0035064)|protein binding, bridging (GO:0030674)|repressing transcription factor binding (GO:0070491)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)	8						TCTGGTTCCAGTCCTCTCTCA	0.403																																					p.L121L	Colon(153;588 2459 18334 48613)	Atlas-SNP	.											.	CBX5	24	.	0			c.C361T						PASS	.						196	176	183					12																	54639963		2203	4300	6503	SO:0001819	synonymous_variant	23468	exon4			GTTCCAGTCCTCT	U26311	CCDS8875.1	12q13.13	2010-07-06	2010-06-24		ENSG00000094916	ENSG00000094916			1555	protein-coding gene	gene with protein product	"HP1 alpha homolog (Drosophila)"	604478	"chromobox homolog 5 (Drosophila HP1 alpha)", "chromobox homolog 5 (HP1 alpha homolog, Drosophila)"			8663349	Standard	NM_012117		Approved	HP1Hs-alpha, HP1, HP1-ALPHA	uc001sfj.4	P45973		ENST00000439541.2:c.361C>T	12.37:g.54639963G>A		191	0	0		159	73	0.459119	NM_012117	B2R8T9	Silent	SNP	ENST00000439541.2	37	CCDS8875.1																																																																																			.	.	none		0.403	CBX5-004	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000405468.1	NM_012117		A	54639963	G	A	54639963	2	1	30	1	0	0	0	0	0	0	0	1	2723	1020	36	2		2	CBX5	12	54639963	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1549782	54639963	79211932	427	13578											
HNRNPA1	3178	hgsc.bcm.edu	37	chr12	54676630	54676630	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggtggatatggtggcagtggGgatggctataatggatttgg	8	12	19	2	0	0	0	0	0	0	0	0	3	0	3	0	9	0	2	0	9	3	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:54676630G>A	ENST00000340913.6	+	7	776	c.723G>A	c.(721-723)ggG>ggA	p.G241G	HNRNPA1_ENST00000330752.8_Silent_p.G228G|RP11-968A15.8_ENST00000553061.1_RNA|HNRNPA1_ENST00000546500.1_Silent_p.G241G|CBX5_ENST00000209875.4_5'Flank|HNRNPA1_ENST00000547276.1_Intron	NM_002136.2|NM_031157.2	NP_002127.1|NP_112420.1	P09651	ROA1_HUMAN	heterogeneous nuclear ribonucleoprotein A1	241	Gly-rich.				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						gtggcagtggggatggctata	0.398																																					p.G241G	Colon(83;502 1289 8436 16406 24870)	Atlas-SNP	.											.	HNRNPA1	72	.	0			c.G723A						PASS	.						34	33	34					12																	54676630		2008	3945	5953	SO:0001819	synonymous_variant	3178	exon7			CAGTGGGGATGGC	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.723G>A	12.37:g.54676630G>A		125	0	0		104	38	0.365385	NM_002136	A8K4Z8|Q3MIB7|Q6PJZ7	Silent	SNP	ENST00000340913.6	37	CCDS44909.1																																																																																			.	.	none		0.398	HNRNPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000405480.1	NM_031157		A	54676630	G	A	54676630	2	1	30	1	0	0	0	0	0	0	0	1	7266	1219	43	2		2	HNRNPA1	12	54676630	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	36667	54676630	79175265	428	13579											
DCD	117159	hgsc.bcm.edu	37	chr12	55038536	55038536	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acgtctttaacgtcatggacGgctcctaggacagccacaga	11	8	10	12	3	2	1	1	0	1	1	3	3	3	3	2	3	2	1	2	3	2	3	rs139716642		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:55038536G>A	ENST00000293371.6	-	5	483	c.294C>T	c.(292-294)gcC>gcT	p.A98A	DCD_ENST00000456047.2_Missense_Mutation_p.R120C	NM_053283.2	NP_444513.1	P81605	DCD_HUMAN	dermcidin	98					defense response to bacterium (GO:0042742)|defense response to fungus (GO:0050832)|killing of cells of other organism (GO:0031640)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	peptidase activity (GO:0008233)|poly(A) RNA binding (GO:0044822)			large_intestine(2)|lung(2)|ovary(1)|skin(1)	6		Myeloproliferative disorder(1001;0.0255)				CGTCATGGACGGCTCCTAGGA	0.488																																					p.A98A		Atlas-SNP	.											.	DCD	20	.	0			c.C294T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	31	28	29		294	-1.2	0	12	dbSNP_134	29	2,8596	2.2+/-6.3	0,2,4297	no	coding-synonymous	DCD	NM_053283.2		0,3,6499	AA,AG,GG		0.0233,0.0227,0.0231		98/111	55038536	3,13001	2203	4299	6502	SO:0001819	synonymous_variant	117159	exon5			ATGGACGGCTCCT	AF144011	CCDS8884.1, CCDS73478.1	12q13.1	2008-08-04				ENSG00000161634			14669	protein-coding gene	gene with protein product	"proteolysis inducing factor", "preproteolysin", "diffusible survival/evasion peptide", "survival promoting peptide"	606634				11694882	Standard	XM_005268627		Approved	AIDD, PIF, DSEP, HCAP, DCD-1	uc001sgj.3	P81605	OTTHUMG00000169937	ENST00000293371.6:c.294C>T	12.37:g.55038536G>A		214	0	0		238	120	0.504202	NM_053283	A5JHP2|A5JHP3|P58461|Q53YJ2	Silent	SNP	ENST00000293371.6	37	CCDS8884.1	.	.	.	.	.	.	.	.	.	.	G	3.323	-0.138330	0.06669	2.27E-4	2.33E-4	ENSG00000161634	ENST00000456047	.	.	.	2.5	-1.22	0.09494	.	.	.	.	.	T	0.28433	0.0703	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.29212	-1.0019	7	0.87932	D	0	.	6.2481	0.20830	0.2528:0.0:0.7472:0.0	.	120	A5JHP3	.	C	120	.	ENSP00000406773:R120C	R	-	1	0	DCD	53324803	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.482000	0.06544	-0.129000	0.11620	-0.440000	0.05779	CGT	G|1.000;A|0.000	0.000	weak		0.488	DCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406617.1	NM_053283		A	55038536	G	A	55038536	2	1	30	1	0	0	0	0	0	0	0	1	4285	1103	39	1		1	DCD	12	55038536	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	361906	55038536	78813359	429	13580											
MMP19	4327	hgsc.bcm.edu	37	chr12	56236136	56236136	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	atacacctcatagcttctcaCctcagagcctcggtgatatc	10	11	6	14	1	3	2	3	1	1	1	6	2	3	2	3	1	3	1	3	1	3	4	rs145293054		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:56236136C>T	ENST00000322569.4	-	2	265		c.e2+1		MMP19_ENST00000409200.3_Splice_Site|MMP19_ENST00000548629.1_Splice_Site|MMP19_ENST00000547487.1_Splice_Site	NM_002429.4	NP_002420.1	Q99542	MMP19_HUMAN	matrix metallopeptidase 19						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)	TAGCTTCTCACCTCAGAGCCT	0.498													C|||	1	0.000199681	0.0	0.0	5008	,	,		19637	0.0		0.001	False		,,,				2504	0.0				.		Atlas-SNP	.											.	MMP19	61	.	0			c.173+1G>A						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	154	119	131			6.1	1	12	dbSNP_134	131	17,8583	12.6+/-44.7	0,17,4283	yes	splice-5	MMP19	NM_002429.4		0,18,6485	TT,TC,CC		0.1977,0.0227,0.1384			56236136	18,12988	2203	4300	6503	SO:0001630	splice_region_variant	4327	exon3			TTCTCACCTCAGA	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.173+1G>A	12.37:g.56236136C>T		227	1	0.00440529		230	117	0.508696	NM_002429	B4E030|O15278|O95606|Q99580	Splice_Site	SNP	ENST00000322569.4	37	CCDS8895.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	24.7	4.564157	0.86335	2.27E-4	0.001977	ENSG00000123342	ENST00000322569;ENST00000548629;ENST00000409200	.	.	.	6.08	6.08	0.98989	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4349	0.94788	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MMP19	54522403	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	4.839000	0.62810	2.894000	0.99253	0.655000	0.94253	.	C|0.999;T|0.001	0.001	strong		0.498	MMP19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408023.1	NM_002429	Intron	T	56236136	C	T	56236136	5	4	30	1	0	0	0	0	0	0	1	0	9666	521	18	2	1384	2	MMP19	12	56236136	Splice_Site	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1197600	56236136	77615759	430	13581											
C12orf26	84190	hgsc.bcm.edu	37	chr12	82792792	82792792	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaagaaaggaaagtgcaaaaTaaagttaaaaataaagctga	25	6	8	2	0	0	2	0	1	0	1	0	3	0	3	0	1	2	3	0	1	12	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:82792792T>G	ENST00000248306.3	+	4	819	c.750T>G	c.(748-750)aaT>aaG	p.N250K	METTL25_ENST00000547357.1_3'UTR	NM_032230.2	NP_115606.2	Q8N6Q8	MET25_HUMAN	methyltransferase like 25	250							methyltransferase activity (GO:0008168)										AAGTGCAAAATAAAGTTAAAA	0.343																																					p.N250K		Atlas-SNP	.											.	.	.	.	0			c.T750G						PASS	.						60	57	58					12																	82792792		2203	4299	6502	SO:0001583	missense	84190	exon4			GCAAAATAAAGTT	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.750T>G	12.37:g.82792792T>G	ENSP00000248306:p.Asn250Lys	48	0	0		31	11	0.354839	NM_032230	Q9H5Y3	Missense_Mutation	SNP	ENST00000248306.3	37	CCDS9024.1	.	.	.	.	.	.	.	.	.	.	T	0.058	-1.231429	0.01505	.	.	ENSG00000127720	ENST00000248306	T	0.29142	1.58	5.39	-0.792	0.10925	.	1.047890	0.07359	N	0.883727	T	0.07548	0.0190	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.30119	-0.9989	10	0.05525	T	0.97	-2.823	1.9271	0.03319	0.1244:0.1816:0.1292:0.5648	.	250	Q8N6Q8	CL026_HUMAN	K	250	ENSP00000248306:N250K	ENSP00000248306:N250K	N	+	3	2	C12orf26	81316923	0.162000	0.22906	0.000000	0.03702	0.023000	0.10783	0.214000	0.17541	-0.265000	0.09352	-0.418000	0.06021	AAT	.	.	none		0.343	METTL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408192.1	NM_032230		G	82792792	T	G	82792792	3	3	30	1	0	0	0	0	1	0	0	0	1681	1403	49	5	764	5	C12orf26	12	82792792	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	26556656	82792792	51059103	431	13582											
SLC6A15	55117	hgsc.bcm.edu	37	chr12	85257230	85257230	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gtatttaccttatcttcaatCcatgcgttatagccaggagg	10	14	8	9	1	2	0	1	0	1	0	3	1	3	1	3	2	3	2	3	2	6	7			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:85257230C>A	ENST00000266682.5	-	11	2347	c.1806G>T	c.(1804-1806)tgG>tgT	p.W602C	SLC6A15_ENST00000309283.7_Missense_Mutation_p.W310C|SLC6A15_ENST00000552192.1_Missense_Mutation_p.W495C	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15	602					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						TATCTTCAATCCATGCGTTAT	0.303																																					p.W602C		Atlas-SNP	.											.	SLC6A15	159	.	0			c.G1806T						PASS	.						85	91	89					12																	85257230		2203	4296	6499	SO:0001583	missense	55117	exon11			TTCAATCCATGCG	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.1806G>T	12.37:g.85257230C>A	ENSP00000266682:p.Trp602Cys	247	0	0		241	76	0.315353	NM_182767	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Missense_Mutation	SNP	ENST00000266682.5	37	CCDS9026.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.283503	0.80803	.	.	ENSG00000072041	ENST00000309283;ENST00000266682;ENST00000552192;ENST00000548267	T;T;T	0.75704	-0.96;-0.96;-0.96	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	D	0.90417	0.7000	M	0.93241	3.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	D	0.92239	0.5799	10	0.87932	D	0	.	19.8516	0.96743	0.0:1.0:0.0:0.0	.	310;602	F8WJN6;Q9H2J7	.;S6A15_HUMAN	C	310;602;495;80	ENSP00000311645:W310C;ENSP00000266682:W602C;ENSP00000450145:W495C	ENSP00000266682:W602C	W	-	3	0	SLC6A15	83781361	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.395000	0.79876	2.685000	0.91497	0.585000	0.79938	TGG	.	.	none		0.303	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767		A	85257230	C	A	85257230	3	1	30	1	0	0	0	0	1	0	0	0	14693	856	30	4	394	4	SLC6A15	12	85257230	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	2464438	85257230	48594665	432	13583											
LRRIQ1	84125	hgsc.bcm.edu	37	chr12	85450426	85450426	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gatcactctcactaacatcaGaaaattccaaagatgtaaga	18	9	5	9	0	3	3	3	0	1	3	5	4	4	3	1	0	1	1	1	0	5	3	rs74720621	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:85450426G>A	ENST00000393217.2	+	8	1916	c.1855G>A	c.(1855-1857)Gaa>Aaa	p.E619K		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	619										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)		ACTAACATCAGAAAATTCCAA	0.284													G|||	17	0.00339457	0.0	0.0029	5008	,	,		17719	0.0		0.0149	False		,,,				2504	0.0				p.E619K		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.G1855A						PASS	.	G	LYS/GLU	5,4371		0,5,2183	24	25	24		1855	5.3	0.2	12	dbSNP_132	24	96,8474		0,96,4189	yes	missense	LRRIQ1	NM_001079910.1	56	0,101,6372	AA,AG,GG		1.1202,0.1143,0.7802	possibly-damaging	619/1723	85450426	101,12845	2188	4285	6473	SO:0001583	missense	84125	exon8			ACATCAGAAAATT	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.1855G>A	12.37:g.85450426G>A	ENSP00000376910:p.Glu619Lys	118	0	0		99	46	0.464646	NM_001079910	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	37	CCDS41816.1	13	0.005952380952380952	0	0.0	1	0.0027624309392265192	0	0.0	12	0.0158311345646438	G	18.93	3.728055	0.69074	0.001143	0.011202	ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393217	T	0.53423	0.62	5.32	5.32	0.75619	.	0.664291	0.13539	N	0.380378	T	0.25606	0.0623	L	0.29908	0.895	0.29964	N	0.819151	P;P	0.47350	0.807;0.894	B;B	0.43950	0.294;0.437	T	0.20571	-1.0271	10	0.41790	T	0.15	.	13.6724	0.62434	0.0767:0.0:0.9233:0.0	.	619;594	Q96JM4;C9JI57	LRIQ1_HUMAN;.	K	619;594;619	ENSP00000376910:E619K	ENSP00000256007:E619K	E	+	1	0	LRRIQ1	83974557	1.000000	0.71417	0.163000	0.22734	0.028000	0.11728	3.334000	0.52097	2.640000	0.89533	0.591000	0.81541	GAA	G|0.992;A|0.008	0.008	strong		0.284	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		A	85450426	G	A	85450426	3	1	30	1	0	0	0	0	1	0	0	0	9038	943	33	2	1881	2	LRRIQ1	12	85450426	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	193196	85450426	48401469	433	13584											
PLXNC1	10154	hgsc.bcm.edu	37	chr12	94631496	94631496	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcgacattagggaaaagcaaCgtgatagtaacgggagcaaa	17	6	12	6	3	0	1	0	1	0	0	1	4	0	3	0	2	4	3	0	2	7	3	rs2230755	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:94631496C>T	ENST00000258526.4	+	10	2286	c.2037C>T	c.(2035-2037)aaC>aaT	p.N679N		NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1	679					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						GGAAAAGCAACGTGATAGTAA	0.398													C|||	306	0.0611022	0.1566	0.0591	5008	,	,		21079	0.0119		0.0298	False		,,,				2504	0.0164				p.N679N		Atlas-SNP	.											.	PLXNC1	135	.	0			c.C2037T						PASS	.	C		589,3817	259.5+/-263.1	47,495,1661	94	80	85		2037	-3.6	0.9	12	dbSNP_98	85	296,8304	108.8+/-169.4	5,286,4009	no	coding-synonymous	PLXNC1	NM_005761.2		52,781,5670	TT,TC,CC		3.4419,13.3681,6.8046		679/1569	94631496	885,12121	2203	4300	6503	SO:0001819	synonymous_variant	10154	exon10			AAGCAACGTGATA	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.2037C>T	12.37:g.94631496C>T		82	0	0		54	12	0.222222	NM_005761	Q59H25	Silent	SNP	ENST00000258526.4	37	CCDS9049.1																																																																																			C|0.929;T|0.071	0.071	strong		0.398	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2			T	94631496	C	T	94631496	2	4	30	1	0	0	0	0	0	0	0	1	12135	535	19	1		1	PLXNC1	12	94631496	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	9181070	94631496	39220399	434	13585											
LTA4H	4048	hgsc.bcm.edu	37	chr12	96408716	96408716	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaataagctacatcagggTctatatctgtcagatcaacc	15	10	7	9	0	5	2	3	0	2	2	5	2	5	2	1	1	3	1	1	1	7	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:96408716T>C	ENST00000228740.2	-	12	1262	c.1121A>G	c.(1120-1122)gAc>gGc	p.D374G	LTA4H_ENST00000548375.1_5'UTR|LTA4H_ENST00000413268.2_Missense_Mutation_p.D350G|LTA4H_ENST00000552789.1_Missense_Mutation_p.D350G	NM_000895.2	NP_000886.1	P09960	LKHA4_HUMAN	leukotriene A4 hydrolase	374					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)	TACATCAGGGTCTATATCTGT	0.393																																					p.D374G		Atlas-SNP	.											.	LTA4H	38	.	0			c.A1121G						PASS	.						172	157	162					12																	96408716		2203	4300	6503	SO:0001583	missense	4048	exon12			TCAGGGTCTATAT	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.1121A>G	12.37:g.96408716T>C	ENSP00000228740:p.Asp374Gly	148	0	0		185	8	0.0432432	NM_000895	B4DNQ9|F8VV40|Q6IAT6|Q9UCT7	Missense_Mutation	SNP	ENST00000228740.2	37	CCDS9059.1	.	.	.	.	.	.	.	.	.	.	T	17.73	3.461791	0.63513	.	.	ENSG00000111144	ENST00000228740;ENST00000552789;ENST00000413268	T;T;T	0.02944	4.1;4.1;4.1	6.07	6.07	0.98685	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.16599	0.0399	M	0.88512	2.96	0.80722	D	1	P;P;D	0.53312	0.502;0.698;0.959	P;P;P	0.57846	0.499;0.736;0.828	T	0.00350	-1.1797	10	0.52906	T	0.07	-23.543	16.6277	0.84984	0.0:0.0:0.0:1.0	.	350;350;374	P09960-3;F8VV40;P09960	.;.;LKHA4_HUMAN	G	374;350;350	ENSP00000228740:D374G;ENSP00000449958:D350G;ENSP00000395051:D350G	ENSP00000228740:D374G	D	-	2	0	LTA4H	94932847	1.000000	0.71417	0.996000	0.52242	0.627000	0.37826	5.728000	0.68531	2.330000	0.79161	0.528000	0.53228	GAC	.	.	none		0.393	LTA4H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408655.1	NM_000895		C	96408716	T	C	96408716	3	2	30	1	0	0	0	0	1	0	0	0	9078	1667	58	3	746	3	LTA4H	12	96408716	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	1777220	96408716	37443179	435	13586											
ELK3	2004	hgsc.bcm.edu	37	chr12	96641452	96641452	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggcaccgacatcggctccatCgccctcaacagcccagccct	8	5	8	20	3	1	0	1	0	0	0	4	1	2	0	5	2	3	2	5	2	1	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:96641452C>T	ENST00000228741.3	+	3	1268	c.942C>T	c.(940-942)atC>atT	p.I314I	ELK3_ENST00000552142.1_Intron	NM_005230.2	NP_005221.2	P41970	ELK3_HUMAN	ELK3, ETS-domain protein (SRF accessory protein 2)	314					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)					TCGGCTCCATCGCCCTCAACA	0.592																																					p.I314I		Atlas-SNP	.											.	ELK3	36	.	0			c.C942T						PASS	.						37	35	36					12																	96641452		2203	4299	6502	SO:0001819	synonymous_variant	2004	exon3			CTCCATCGCCCTC	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.942C>T	12.37:g.96641452C>T		24	0	0		19	9	0.473684	NM_005230	B2R6S6|Q6FG57|Q6GU29|Q9UD17	Silent	SNP	ENST00000228741.3	37	CCDS9060.1																																																																																			.	.	none		0.592	ELK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408694.1	NM_005230		T	96641452	C	T	96641452	2	4	30	1	0	0	0	0	0	0	0	1	5062	874	31	1		1	ELK3	12	96641452	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	232736	96641452	37210443	436	13587											
BTBD11	121551	hgsc.bcm.edu	37	chr12	108011971	108011971	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgctcgcccagccagagaaGgagaagagtgatatcctgtc	11	7	12	11	1	0	4	0	1	0	3	3	6	1	4	3	1	2	1	3	1	3	1	rs56296886	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:108011971G>A	ENST00000280758.5	+	10	2796	c.2268G>A	c.(2266-2268)aaG>aaA	p.K756K	BTBD11_ENST00000490090.2_Silent_p.K756K|BTBD11_ENST00000420571.2_Intron|BTBD11_ENST00000357167.4_Silent_p.K293K|RP11-128P10.1_ENST00000548473.1_RNA	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	756						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						AGCCAGAGAAGGAGAAGAGTG	0.597													G|||	9	0.00179712	0.0015	0.0043	5008	,	,		20060	0.0		0.003	False		,,,				2504	0.001				p.K756K		Atlas-SNP	.											.	BTBD11	122	.	0			c.G2268A						PASS	.	G	,	6,4400	11.4+/-27.6	0,6,2197	62	65	64		879,2268	4.7	1	12	dbSNP_129	64	70,8530	41.7+/-99.0	0,70,4230	no	coding-synonymous,coding-synonymous	BTBD11	NM_001017523.1,NM_001018072.1	,	0,76,6427	AA,AG,GG		0.814,0.1362,0.5843	,	293/642,756/1105	108011971	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	121551	exon10			AGAGAAGGAGAAG	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.2268G>A	12.37:g.108011971G>A		82	0	0		64	28	0.4375	NM_001018072	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Silent	SNP	ENST00000280758.5	37	CCDS31893.1																																																																																			G|0.996;A|0.004	0.004	strong		0.597	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322		A	108011971	G	A	108011971	2	1	30	1	0	0	0	0	0	0	0	1	1541	991	35	2		2	BTBD11	12	108011971	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	11370519	108011971	25839924	437	13588											
PRDM4	11108	hgsc.bcm.edu	37	chr12	108140191	108140191	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagggataggcgcggtcacaCagagtacaccctgtagatgg	11	6	15	9	2	1	2	1	0	0	2	1	4	1	3	1	4	1	2	1	4	3	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:108140191C>T	ENST00000228437.5	-	6	1596	c.1137G>A	c.(1135-1137)ctG>ctA	p.L379L	RP11-864J10.4_ENST00000546714.1_RNA	NM_012406.3	NP_036538.3	Q9UKN5	PRDM4_HUMAN	PR domain containing 4	379					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						CGCGGTCACACAGAGTACACC	0.458																																					p.L379L		Atlas-SNP	.											PRDM4,bladder,carcinoma,-1,1	PRDM4	64	1	0			c.G1137A						PASS	.						86	83	84					12																	108140191		2203	4300	6503	SO:0001819	synonymous_variant	11108	exon6			GTCACACAGAGTA	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.1137G>A	12.37:g.108140191C>T		122	0	0		109	46	0.422018	NM_012406	Q9UFA6	Silent	SNP	ENST00000228437.5	37	CCDS9115.1																																																																																			.	.	none		0.458	PRDM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406546.1	NM_012406		T	108140191	C	T	108140191	2	4	30	1	0	0	0	0	0	0	0	1	12471	465	17	2		2	PRDM4	12	108140191	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	128220	108140191	25711704	438	13589											
SSH1	54434	hgsc.bcm.edu	37	chr12	109198832	109198832	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gccagggccatgcctcttacGagataaagatgatcgaagat	13	8	11	9	2	1	4	0	1	1	3	2	6	1	4	3	1	2	0	3	1	4	2	rs140151008	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:109198832G>A	ENST00000326495.5	-	10	1047	c.954C>T	c.(952-954)ctC>ctT	p.L318L	SSH1_ENST00000551165.1_Splice_Site_p.L318L|SSH1_ENST00000326470.5_Splice_Site_p.L329L|SSH1_ENST00000360239.3_Splice_Site_p.S22L	NM_018984.3	NP_061857.3	Q8WYL5	SSH1_HUMAN	slingshot protein phosphatase 1	318	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						TGCCTCTTACGAGATAAAGAT	0.433													G|||	17	0.00339457	0.0	0.0	5008	,	,		19464	0.0		0.004	False		,,,				2504	0.0133				p.L329L		Atlas-SNP	.											.	SSH1	144	.	0			c.C987T						PASS	.	G	,,	6,4400	12.9+/-30.5	0,6,2197	125	118	120		954,987,954	-1.8	1	12	dbSNP_134	120	63,8537	38.8+/-94.9	0,63,4237	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	SSH1	NM_001161330.1,NM_001161331.1,NM_018984.3	,,	0,69,6434	AA,AG,GG		0.7326,0.1362,0.5305	,,	318/693,329/704,318/1050	109198832	69,12937	2203	4300	6503	SO:0001630	splice_region_variant	54434	exon9			TCTTACGAGATAA	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.954+1C>T	12.37:g.109198832G>A		132	0	0		132	63	0.477273	NM_001161331	Q6P6C0|Q8N9A7|Q8WYL3|Q8WYL4|Q9P2P8	Silent	SNP	ENST00000326495.5	37	CCDS9121.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	18.44	3.625527	0.66901	0.001362	0.007326	ENSG00000084112	ENST00000360239	D	0.86164	-2.08	5.13	-1.82	0.07857	.	.	.	.	.	T	0.67268	0.2875	.	.	.	0.27735	N	0.944678	B	0.19935	0.04	B	0.06405	0.002	T	0.55798	-0.8084	7	.	.	.	-29.1082	7.2487	0.26138	0.3231:0.4661:0.2108:0.0	.	22	Q8WYL5-4	.	L	22	ENSP00000353374:S22L	.	S	-	2	0	SSH1	107722961	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	1.002000	0.29796	-0.089000	0.12484	0.655000	0.94253	TCG	G|0.996;A|0.004	0.004	strong		0.433	SSH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403724.1	NM_018984	Silent	A	109198832	G	A	109198832	5	1	30	1	0	0	0	0	0	0	1	0	15199	1072	37	1	2405	1	SSH1	12	109198832	Splice_Site	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1058641	109198832	24653063	439	13590											
ATXN2	6311	hgsc.bcm.edu	37	chr12	111907956	111907956	+	Nonsense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gagccccgtactgagttgctGaagaagatactaaaccaggc	13	7	11	10	1	0	4	0	2	0	2	0	5	0	4	3	1	5	3	3	1	6	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:111907956G>C	ENST00000377617.3	-	20	3433	c.3272C>G	c.(3271-3273)tCa>tGa	p.S1091*	ATXN2_ENST00000608853.1_Nonsense_Mutation_p.S931*|ATXN2_ENST00000550104.1_3'UTR|ATXN2_ENST00000389153.4_Nonsense_Mutation_p.S828*|ATXN2_ENST00000542287.2_Nonsense_Mutation_p.S826*|ATXN2_ENST00000535949.1_Nonsense_Mutation_p.S802*	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	1091					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						CTGAGTTGCTGAAGAAGATAC	0.453																																					p.S1091X		Atlas-SNP	.											.	ATXN2	99	.	0			c.C3272G						PASS	.						218	172	188					12																	111907956		2203	4300	6503	SO:0001587	stop_gained	6311	exon20			GTTGCTGAAGAAG	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.3272C>G	12.37:g.111907956G>C	ENSP00000366843:p.Ser1091*	183	0	0		174	54	0.310345	NM_002973	A6NLD4|Q6ZQZ7|Q99493	Nonsense_Mutation	SNP	ENST00000377617.3	37	CCDS31902.1	.	.	.	.	.	.	.	.	.	.	G	41	8.647790	0.98899	.	.	ENSG00000204842	ENST00000389154;ENST00000389153;ENST00000377617;ENST00000482777;ENST00000542287;ENST00000535949;ENST00000550844	.	.	.	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	-12.4094	19.6783	0.95946	0.0:0.0:1.0:0.0	.	.	.	.	X	146;828;1091;110;826;802;16	.	ENSP00000366843:S1091X	S	-	2	0	ATXN2	110392339	1.000000	0.71417	0.973000	0.42090	0.782000	0.44232	9.301000	0.96167	2.724000	0.93272	0.585000	0.79938	TCA	.	.	none		0.453	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973		C	111907956	G	C	111907956	4	2	30	1	0	0	0	0	0	1	0	0	1211	1294	45	4	693	4	ATXN2	12	111907956	Nonsense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2709124	111907956	21943939	440	13591											
DDX54	79039	hgsc.bcm.edu	37	chr12	113596866	113596866	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgcttggtcttgagttccGggcggactcggcctgcaggg	3	10	17	11	3	1	1	0	1	1	0	3	2	2	2	2	5	2	4	2	5	0	3	rs1048889	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:113596866G>A	ENST00000306014.5	-	20	2489	c.2462C>T	c.(2461-2463)cCg>cTg	p.P821L	DDX54_ENST00000314045.7_Missense_Mutation_p.P822L|Y_RNA_ENST00000363029.1_RNA|CCDC42B_ENST00000335621.6_3'UTR|DDX54_ENST00000549271.1_5'UTR	NM_024072.3	NP_076977.3	Q8TDD1	DDX54_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	821			P -> L (in dbSNP:rs1048889).		ATP catabolic process (GO:0006200)|intracellular estrogen receptor signaling pathway (GO:0030520)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						CTTGAGTTCCGGGCGGACTCG	0.662													G|||	124	0.0247604	0.0023	0.0432	5008	,	,		15410	0.0		0.0805	False		,,,				2504	0.0102				p.P822L		Atlas-SNP	.											.	DDX54	73	.	0			c.C2465T						PASS	.	G	LEU/PRO,,LEU/PRO	56,4350		1,54,2148	17	19	18		2465,,2462	5.1	0.9	12	dbSNP_86	18	498,8102		16,466,3818	yes	missense,utr-3,missense	DDX54,CCDC42B	NM_001111322.1,NM_001144872.1,NM_024072.3	98,,98	17,520,5966	AA,AG,GG		5.7907,1.271,4.2596	benign,,benign	822/883,,821/882	113596866	554,12452	2203	4300	6503	SO:0001583	missense	79039	exon20			AGTTCCGGGCGGA	AF144056	CCDS31907.1, CCDS44984.1	12q24.11	2006-01-30				ENSG00000123064		"DEAD-boxes"	20084	protein-coding gene	gene with protein product		611665				12466272	Standard	NM_001111322		Approved	MGC2835, APR-5, DP97	uc001tuq.4	Q8TDD1	OTTHUMG00000169676	ENST00000306014.5:c.2462C>T	12.37:g.113596866G>A	ENSP00000304072:p.Pro821Leu	117	0	0		86	36	0.418605	NM_001111322	Q86YT8|Q9BRZ1	Missense_Mutation	SNP	ENST00000306014.5	37	CCDS31907.1	80	0.03663003663003663	3	0.006097560975609756	16	0.04419889502762431	0	0.0	61	0.08047493403693931	G	14.61	2.587399	0.46110	0.01271	0.057907	ENSG00000123064	ENST00000314045;ENST00000306014	T;T	0.09350	2.99;2.99	5.06	5.06	0.68205	.	0.218861	0.40908	D	0.000994	T	0.00496	0.0016	L	0.29908	0.895	0.20074	P	0.9999367728	B;B	0.17667	0.009;0.023	B;B	0.15870	0.013;0.014	T	0.23797	-1.0178	9	0.33141	T	0.24	.	16.5805	0.84713	0.0:0.0:1.0:0.0	rs1048889;rs1048889	822;821	Q8TDD1-2;Q8TDD1	.;DDX54_HUMAN	L	822;821	ENSP00000323858:P822L;ENSP00000304072:P821L	ENSP00000304072:P821L	P	-	2	0	DDX54	112081249	1.000000	0.71417	0.886000	0.34754	0.404000	0.30871	8.858000	0.92256	2.509000	0.84616	0.561000	0.74099	CCG	G|0.963;A|0.037	0.037	strong		0.662	DDX54-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405435.1	NM_024072		A	113596866	G	A	113596866	3	1	30	1	0	0	0	0	1	0	0	0	4374	1116	39	1	187	1	DDX54	12	113596866	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1688910	113596866	20255029	441	13592											
DDX54	79039	hgsc.bcm.edu	37	chr12	113600940	113600940	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccagccagccactcaccccCgctcgctgtcaaagtccttg	7	7	7	20	2	2	0	2	0	0	0	4	0	3	0	6	0	2	2	6	0	1	1	rs11564	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:113600940C>T	ENST00000306014.5	-	16	2105	c.2078G>A	c.(2077-2079)cGg>cAg	p.R693Q	DDX54_ENST00000314045.7_Missense_Mutation_p.R693Q|DDX54_ENST00000549271.1_5'Flank	NM_024072.3	NP_076977.3	Q8TDD1	DDX54_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 54	693			R -> Q (in dbSNP:rs11564).		ATP catabolic process (GO:0006200)|intracellular estrogen receptor signaling pathway (GO:0030520)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						CACTCACCCCCGCTCGCTGTC	0.637													C|||	155	0.0309505	0.025	0.0447	5008	,	,		15348	0.0		0.0805	False		,,,				2504	0.0102				p.R693Q		Atlas-SNP	.											.	DDX54	73	.	0			c.G2078A						PASS	.	C	GLN/ARG,GLN/ARG	115,4291	85.8+/-124.5	1,113,2089	47	54	52		2078,2078	4.2	1	12	dbSNP_52	52	501,8099	142.3+/-198.5	14,473,3813	yes	missense,missense	DDX54	NM_001111322.1,NM_024072.3	43,43	15,586,5902	TT,TC,CC		5.8256,2.6101,4.7363	possibly-damaging,possibly-damaging	693/883,693/882	113600940	616,12390	2203	4300	6503	SO:0001583	missense	79039	exon16			CACCCCCGCTCGC	AF144056	CCDS31907.1, CCDS44984.1	12q24.11	2006-01-30				ENSG00000123064		"DEAD-boxes"	20084	protein-coding gene	gene with protein product		611665				12466272	Standard	NM_001111322		Approved	MGC2835, APR-5, DP97	uc001tuq.4	Q8TDD1	OTTHUMG00000169676	ENST00000306014.5:c.2078G>A	12.37:g.113600940C>T	ENSP00000304072:p.Arg693Gln	101	0	0		103	45	0.436893	NM_024072	Q86YT8|Q9BRZ1	Missense_Mutation	SNP	ENST00000306014.5	37	CCDS31907.1	86	0.039377289377289376	8	0.016260162601626018	16	0.04419889502762431	0	0.0	62	0.08179419525065963	C	17.30	3.355570	0.61293	0.026101	0.058256	ENSG00000123064	ENST00000314045;ENST00000306014	T;T	0.11277	2.79;2.8	5.1	4.21	0.49690	.	0.112829	0.56097	D	0.000030	T	0.00666	0.0022	M	0.73598	2.24	0.19575	P	0.9999672619	B;B	0.25486	0.127;0.078	B;B	0.18561	0.022;0.01	T	0.10359	-1.0633	9	0.21014	T	0.42	.	13.0042	0.58694	0.0:0.9213:0.0:0.0787	rs11564;rs1130231;rs3188910;rs17296035;rs17354493;rs34797478	693;693	Q8TDD1-2;Q8TDD1	.;DDX54_HUMAN	Q	693	ENSP00000323858:R693Q;ENSP00000304072:R693Q	ENSP00000304072:R693Q	R	-	2	0	DDX54	112085323	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.529000	0.60588	1.146000	0.42352	0.643000	0.83706	CGG	C|0.954;T|0.046	0.046	strong		0.637	DDX54-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405435.1	NM_024072		T	113600940	C	T	113600940	3	4	30	1	0	0	0	0	1	0	0	0	4374	652	23	1	590	1	DDX54	12	113600940	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	4074	113600940	20250955	442	13593											
TPCN1	53373	hgsc.bcm.edu	37	chr12	113733830	113733830	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcagcagcagtgcagccccCgccgcccagcagcccccagg	7	2	11	21	2	1	0	1	0	0	0	1	0	1	0	6	1	6	4	6	1	0	0	rs61943642	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:113733830C>T	ENST00000335509.6	+	28	2714	c.2400C>T	c.(2398-2400)ccC>ccT	p.P800P	TPCN1_ENST00000392569.4_Silent_p.P732P|TPCN1_ENST00000541517.1_Silent_p.P872P|TPCN1_ENST00000550785.1_Silent_p.P872P	NM_017901.4	NP_060371.2	Q9ULQ1	TPC1_HUMAN	two pore segment channel 1	800					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						GTGCAGCCCCCGCCGCCCAGC	0.617													C|||	123	0.0245607	0.0023	0.0461	5008	,	,		11380	0.0		0.0775	False		,,,				2504	0.0102				p.P872P		Atlas-SNP	.											.	TPCN1	109	.	0			c.C2616T						PASS	.	C	,	60,4340	48.9+/-83.8	2,56,2142	27	32	30		2616,2400	0.7	0	12	dbSNP_129	30	498,8102	133.3+/-190.8	13,472,3815	no	coding-synonymous,coding-synonymous	TPCN1	NM_001143819.1,NM_017901.4	,	15,528,5957	TT,TC,CC		5.7907,1.3636,4.2923	,	872/889,800/817	113733830	558,12442	2200	4300	6500	SO:0001819	synonymous_variant	53373	exon29			AGCCCCCGCCGCC	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.2400C>T	12.37:g.113733830C>T		158	0	0		121	60	0.495868	NM_001143819	A7E258|Q86XS9|Q8NC20	Silent	SNP	ENST00000335509.6	37	CCDS31908.1																																																																																			C|0.958;T|0.042	0.042	strong		0.617	TPCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405156.3	NM_017901		T	113733830	C	T	113733830	2	4	30	1	0	0	0	0	0	0	0	1	16410	639	23	1		1	TPCN1	12	113733830	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	132890	113733830	20118065	443	13594											
GCN1L1	10985	hgsc.bcm.edu	37	chr12	120602208	120602208	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcttaaagcccccaagagAggacagcagcttccgaactg	13	5	10	13	1	0	1	0	0	0	1	1	4	1	2	3	1	5	3	3	1	4	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:120602208A>G	ENST00000300648.6	-	18	1792	c.1780T>C	c.(1780-1782)Tct>Cct	p.S594P		NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	594					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)					CCCCCAAGAGAGGACAGCAGC	0.622																																					p.S594P		Atlas-SNP	.											.	GCN1L1	207	.	0			c.T1780C						PASS	.						75	80	78					12																	120602208		1969	4161	6130	SO:0001583	missense	10985	exon18			CAAGAGAGGACAG	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.1780T>C	12.37:g.120602208A>G	ENSP00000300648:p.Ser594Pro	107	0	0		94	4	0.0425532	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	37	CCDS41847.1	.	.	.	.	.	.	.	.	.	.	A	16.79	3.220268	0.58560	.	.	ENSG00000089154	ENST00000300648	T	0.05199	3.48	5.83	4.67	0.58626	Armadillo-like helical (1);Domain of unknown function DUF3554 (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.17619	0.0423	M	0.74881	2.28	0.80722	D	1	D	0.54047	0.964	P	0.54590	0.756	T	0.01570	-1.1322	10	0.30854	T	0.27	.	13.3498	0.60595	0.8686:0.1314:0.0:0.0	.	594	Q92616	GCN1L_HUMAN	P	594	ENSP00000300648:S594P	ENSP00000300648:S594P	S	-	1	0	GCN1L1	119086591	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	5.545000	0.67237	1.022000	0.39626	0.533000	0.62120	TCT	.	.	none		0.622	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1			G	120602208	A	G	120602208	3	3	30	1	0	0	0	0	1	0	0	0	6307	304	11	3	6399	3	GCN1L1	12	120602208	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	6868378	120602208	13249687	444	13595											
HNF1A	6927	hgsc.bcm.edu	37	chr12	121437114	121437114	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtggcccagtacacccacacGggcctgctcccgcagactat	8	6	10	17	2	0	1	0	0	0	1	1	1	1	1	4	2	2	3	4	2	2	2	rs55834942	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:121437114G>A	ENST00000257555.6	+	8	1771	c.1545G>A	c.(1543-1545)acG>acA	p.T515T	HNF1A_ENST00000541395.1_Silent_p.T515T|RP11-216P16.2_ENST00000606238.1_RNA|HNF1A_ENST00000544413.1_Silent_p.T515T			P20823	HNF1A_HUMAN	HNF1 homeobox A	515					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)					ACACCCACACGGGCCTGCTCC	0.677									Hepatic Adenoma, Familial Clustering of				.|||	315	0.0628994	0.0121	0.1095	5008	,	,		16172	0.001		0.1988	False		,,,				2504	0.0225				p.T515T		Atlas-SNP	.											HNF1A,brain,glioma,0,4	HNF1A	302	4	0			c.G1545A						PASS	.	G		175,4231	113.3+/-151.4	4,167,2032	68	70	70		1545	-7.7	0.9	12	dbSNP_129	70	1654,6944	303.3+/-306.4	156,1342,2801	yes	coding-synonymous	HNF1A	NM_000545.5		160,1509,4833	AA,AG,GG		19.237,3.9719,14.0649		515/632	121437114	1829,11175	2203	4299	6502	SO:0001819	synonymous_variant	6927	exon8	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CCACACGGGCCTG	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.1545G>A	12.37:g.121437114G>A		230	1	0.00434783		241	117	0.485477	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Silent	SNP	ENST00000257555.6	37	CCDS9209.1																																																																																			G|0.860;A|0.140	0.140	strong		0.677	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545		A	121437114	G	A	121437114	2	1	30	1	0	0	0	0	0	0	0	1	7260	1103	39	1		1	HNF1A	12	121437114	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	834906	121437114	12414781	445	13596											
GPR133	283383	hgsc.bcm.edu	37	chr12	131620650	131620650	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgggtctttggcgtgcttgCtgtcaacggttgtgctgtgg	2	15	17	7	2	2	0	1	0	1	0	2	0	2	0	0	4	4	4	0	4	1	3	rs61746588	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:131620650C>T	ENST00000261654.5	+	22	2895	c.2336C>T	c.(2335-2337)gCt>gTt	p.A779V	GPR133_ENST00000376682.4_Missense_Mutation_p.A465V|GPR133_ENST00000540207.1_3'UTR|GPR133_ENST00000535015.1_Missense_Mutation_p.A811V|GPR133_ENST00000543617.1_Missense_Mutation_p.A298V	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	779					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)		GGCGTGCTTGCTGTCAACGGT	0.622													C|||	11	0.00219649	0.0	0.0086	5008	,	,		20891	0.0		0.003	False		,,,				2504	0.002				p.A779V		Atlas-SNP	.											.	GPR133	136	.	0			c.C2336T						PASS	.	C	VAL/ALA	7,4399	12.9+/-30.5	0,7,2196	288	182	218		2336	3.7	0	12	dbSNP_129	218	49,8551	31.7+/-84.0	0,49,4251	yes	missense	GPR133	NM_198827.3	64	0,56,6447	TT,TC,CC		0.5698,0.1589,0.4306	probably-damaging	779/875	131620650	56,12950	2203	4300	6503	SO:0001583	missense	283383	exon22			TGCTTGCTGTCAA	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.2336C>T	12.37:g.131620650C>T	ENSP00000261654:p.Ala779Val	238	0	0		197	82	0.416244	NM_198827	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Missense_Mutation	SNP	ENST00000261654.5	37	CCDS9272.1	6	0.0027472527472527475	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	12.69	2.013191	0.35511	0.001589	0.005698	ENSG00000111452	ENST00000261654;ENST00000535015;ENST00000376682;ENST00000543617	T;T;T;T	0.42900	1.32;1.31;0.96;0.96	4.6	3.71	0.42584	GPCR, family 2-like (1);	0.000000	0.85682	D	0.000000	T	0.36991	0.0987	M	0.63428	1.95	0.58432	D	0.999998	P;P;B	0.42123	0.586;0.771;0.333	P;B;B	0.48089	0.566;0.444;0.348	T	0.18713	-1.0328	10	0.17369	T	0.5	.	10.3596	0.43984	0.0:0.902:0.0:0.098	rs61746588	811;132;779	B7ZLF7;Q9NSM3;Q6QNK2	.;.;GP133_HUMAN	V	779;811;465;298	ENSP00000261654:A779V;ENSP00000444425:A811V;ENSP00000365872:A465V;ENSP00000438021:A298V	ENSP00000261654:A779V	A	+	2	0	GPR133	130186603	1.000000	0.71417	0.036000	0.18154	0.315000	0.28087	4.744000	0.62118	0.913000	0.36797	0.491000	0.48974	GCT	C|0.997;T|0.003	0.003	strong		0.622	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827		T	131620650	C	T	131620650	3	4	30	1	0	0	0	0	1	0	0	0	6651	797	28	2	2422	2	GPR133	12	131620650	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	10183536	131620650	2231245	446	13597											
POLE	5426	hgsc.bcm.edu	37	chr12	133253180	133253180	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataatctggtctgtctcagcAtcaggaaacttgaggggcag	11	10	12	8	0	4	1	2	1	3	0	5	2	4	2	0	4	2	2	0	4	2	2	rs139075637	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr12:133253180A>T	ENST00000320574.5	-	9	904	c.861T>A	c.(859-861)gaT>gaA	p.D287E	POLE_ENST00000535270.1_Missense_Mutation_p.D260E	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	287					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)	CTGTCTCAGCATCAGGAAACT	0.498								DNA polymerases (catalytic subunits)					A|||	2	0.000399361	0.0	0.0	5008	,	,		20902	0.0		0.002	False		,,,				2504	0.0				p.D287E		Atlas-SNP	.											.	POLE	416	.	0			c.T861A						PASS	.	A	GLU/ASP	1,4405	2.1+/-5.4	0,1,2202	115	99	105		861	1.9	1	12	dbSNP_134	105	11,8589	8.4+/-32.0	0,11,4289	yes	missense	POLE	NM_006231.2	45	0,12,6491	TT,TA,AA		0.1279,0.0227,0.0923	probably-damaging	287/2287	133253180	12,12994	2203	4300	6503	SO:0001583	missense	5426	exon9			CTCAGCATCAGGA		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.861T>A	12.37:g.133253180A>T	ENSP00000322570:p.Asp287Glu	223	0	0		167	91	0.54491	NM_006231	Q13533|Q86VH9	Missense_Mutation	SNP	ENST00000320574.5	37	CCDS9278.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	22.2	4.257395	0.80246	2.27E-4	0.001279	ENSG00000177084	ENST00000320574;ENST00000455752;ENST00000535270;ENST00000539006;ENST00000376577	T;T;T;T	0.48201	3.07;3.07;3.07;0.82	5.49	1.9	0.25705	DNA-directed DNA polymerase, family B, exonuclease domain (1);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.62841	0.2461	M	0.71206	2.165	0.51233	D	0.999917	D;D	0.89917	1.0;1.0	D;D	0.83275	0.992;0.996	T	0.62469	-0.6848	10	0.87932	D	0	.	8.9216	0.35615	0.718:0.0:0.282:0.0	.	260;287	F5H1D6;Q07864	.;DPOE1_HUMAN	E	287;298;260;67;222	ENSP00000322570:D287E;ENSP00000406383:D298E;ENSP00000445753:D260E;ENSP00000442519:D67E	ENSP00000322570:D287E	D	-	3	2	POLE	131763253	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	1.156000	0.31712	0.376000	0.24707	-0.441000	0.05720	GAT	A|0.999;T|0.001	0.001	strong		0.498	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231		T	133253180	A	T	133253180	3	4	30	1	0	0	0	0	1	0	0	0	12205	214	8	5	6163	5	POLE	12	133253180	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	1632530	133253180	598715	447	13598											
ZDHHC20	253832	hgsc.bcm.edu	37	chr13	21976996	21976996	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcagctgacatttttcacaaTatctgatagctacatgaaag	14	13	6	8	0	3	3	2	3	1	0	3	3	3	3	0	0	3	2	0	0	5	5			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:21976996T>C	ENST00000400590.3	-	5	578	c.380A>G	c.(379-381)tAt>tGt	p.Y127C	ZDHHC20_ENST00000320220.9_Missense_Mutation_p.Y127C|ZDHHC20_ENST00000415724.1_Missense_Mutation_p.Y127C|ZDHHC20_ENST00000382466.3_Missense_Mutation_p.Y127C|ZDHHC20_ENST00000494731.1_5'UTR|ZDHHC20_ENST00000542645.1_Missense_Mutation_p.Y64C			Q5W0Z9	ZDH20_HUMAN	zinc finger, DHHC-type containing 20	127					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)		TTTTTCACAATATCTGATAGC	0.353																																					p.Y127C		Atlas-SNP	.											.	ZDHHC20	36	.	0			c.A380G						PASS	.						65	62	63					13																	21976996		1862	4106	5968	SO:0001583	missense	253832	exon5			TCACAATATCTGA	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.380A>G	13.37:g.21976996T>C	ENSP00000383433:p.Tyr127Cys	41	0	0		51	32	0.627451	NM_153251	A8MTV9|C9JG20|I6L9D4|Q2TB82|Q6NVU8	Missense_Mutation	SNP	ENST00000400590.3	37		.	.	.	.	.	.	.	.	.	.	T	19.89	3.910520	0.72983	.	.	ENSG00000180776	ENST00000400590;ENST00000320220;ENST00000382466;ENST00000542645;ENST00000415724	T;T;T;T;T	0.27256	1.68;1.68;1.68;1.68;1.68	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.62270	0.2414	H	0.96489	3.83	0.80722	D	1	D;P	0.63046	0.992;0.812	P;D	0.63381	0.908;0.914	T	0.76348	-0.2992	10	0.87932	D	0	-33.8396	15.3153	0.74069	0.0:0.0:0.0:1.0	.	64;127	B4DRN8;Q5W0Z9-3	.;.	C	127;127;127;64;127	ENSP00000383433:Y127C;ENSP00000313583:Y127C;ENSP00000371905:Y127C;ENSP00000443236:Y64C;ENSP00000401232:Y127C	ENSP00000313583:Y127C	Y	-	2	0	ZDHHC20	20874996	1.000000	0.71417	0.973000	0.42090	0.820000	0.46376	4.578000	0.60929	2.069000	0.61940	0.533000	0.62120	TAT	.	.	none		0.353	ZDHHC20-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000045994.1	NM_153251		C	21976996	T	C	21976996	3	2	30	1	0	0	0	0	1	0	0	0	17626	1406	49	3	716	3	ZDHHC20	13	21976996	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10		21976996	93192882	448	13599											
SACS	26278	hgsc.bcm.edu	37	chr13	23904298	23904298	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cactttttgttgcataaaatTttcaagttttattatgatac	12	20	4	5	0	1	1	1	1	0	0	1	1	1	1	0	0	2	3	0	0	6	10	rs34382952	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:23904298T>G	ENST00000382292.3	-	9	13990	c.13717A>C	c.(13717-13719)Aat>Cat	p.N4573H	SACS_ENST00000402364.1_Missense_Mutation_p.N3823H|SACS_ENST00000382298.3_Missense_Mutation_p.N4573H			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	4573					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)		TGCATAAAATTTTCAAGTTTT	0.348													T|||	15	0.00299521	0.0008	0.0058	5008	,	,		9531	0.0		0.0099	False		,,,				2504	0.0				p.N4573H		Atlas-SNP	.											.	SACS	871	.	0			c.A13717C						PASS	.	T	HIS/ASN	5,4401	9.9+/-24.2	0,5,2198	66	67	67		13717	5.8	1	13	dbSNP_126	67	40,8560	26.3+/-74.7	0,40,4260	yes	missense	SACS	NM_014363.4	68	0,45,6458	GG,GT,TT		0.4651,0.1135,0.346	possibly-damaging	4573/4580	23904298	45,12961	2203	4300	6503	SO:0001583	missense	26278	exon10			TAAAATTTTCAAG	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.13717A>C	13.37:g.23904298T>G	ENSP00000371729:p.Asn4573His	85	0	0		124	50	0.403226	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	8	0.003663003663003663	0	0.0	3	0.008287292817679558	0	0.0	5	0.006596306068601583	T	18.35	3.603679	0.66445	0.001135	0.004651	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.86366	-2.11;-2.11;-2.11	5.85	5.85	0.93711	.	0.089079	0.85682	D	0.000000	T	0.79627	0.4478	N	0.03608	-0.345	0.35519	D	0.801247	D	0.56521	0.976	P	0.59595	0.86	D	0.88793	0.3279	10	0.59425	D	0.04	.	16.2271	0.82306	0.0:0.0:0.0:1.0	rs34382952	4573	Q9NZJ4	SACS_HUMAN	H	4573;3823;4573	ENSP00000371729:N4573H;ENSP00000385844:N3823H;ENSP00000371735:N4573H	ENSP00000371729:N4573H	N	-	1	0	SACS	22802298	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	6.258000	0.72487	2.234000	0.73211	0.460000	0.39030	AAT	T|0.997;G|0.003	0.003	strong		0.348	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		G	23904298	T	G	23904298	3	3	30	1	0	0	0	0	1	0	0	0	13819	1841	64	5	26	5	SACS	13	23904298	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	1927302	23904298	91265580	449	13600											
FLT3	2322	hgsc.bcm.edu	37	chr13	28623525	28623525	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gagcagcctgcattacctacGatggtaaccaaagctgattg	12	9	10	10	1	0	1	0	1	0	0	0	3	0	1	3	1	7	4	3	1	4	4	rs146983744	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:28623525G>A	ENST00000241453.7	-	8	1113	c.1032C>T	c.(1030-1032)atC>atT	p.I344I	FLT3_ENST00000537084.1_Silent_p.I344I|FLT3_ENST00000380982.4_Silent_p.I344I	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	344					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)	CATTACCTACGATGGTAACCA	0.398			"Mis, O"		"AML, ALL"																																p.I344I		Atlas-SNP	.		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	.	FLT3	15525	.	0			c.C1032T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	245	216	226		1032	3.8	1	13	dbSNP_134	226	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	FLT3	NM_004119.2		0,7,6496	AA,AG,GG		0.0698,0.0227,0.0538		344/994	28623525	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	2322	exon8			ACCTACGATGGTA	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.1032C>T	13.37:g.28623525G>A		145	0	0		133	74	0.556391	NM_004119	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Silent	SNP	ENST00000241453.7	37	CCDS31953.1																																																																																			G|0.999;A|0.001	0.001	strong		0.398	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044319.2			A	28623525	G	A	28623525	2	1	30	1	0	0	0	0	0	0	0	1	5950	1048	37	1		1	FLT3	13	28623525	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	4719227	28623525	86546353	450	13601											
KL	9365	hgsc.bcm.edu	37	chr13	33635910	33635910	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaattacataaacgaagcTctcaaaggtaaggagcccta	17	7	8	9	1	1	1	1	0	1	1	2	3	1	2	1	2	4	2	1	2	8	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:33635910T>C	ENST00000380099.3	+	4	2702	c.2694T>C	c.(2692-2694)gcT>gcC	p.A898A	KL_ENST00000487852.1_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	898	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)		TAAACGAAGCTCTCAAAGGTA	0.473																																					p.A898A		Atlas-SNP	.											.	KL	106	.	0			c.T2694C						PASS	.						77	81	79					13																	33635910		2203	4300	6503	SO:0001819	synonymous_variant	9365	exon4			CGAAGCTCTCAAA	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.2694T>C	13.37:g.33635910T>C		17	0	0		18	11	0.611111	NM_004795	Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Silent	SNP	ENST00000380099.3	37	CCDS9347.1																																																																																			.	.	none		0.473	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1			C	33635910	T	C	33635910	2	2	30	1	0	0	0	0	0	0	0	1	8340	1538	54	3		3	KL	13	33635910	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	5012385	33635910	81533968	451	13602											
COG3	83548	hgsc.bcm.edu	37	chr13	46104849	46104849	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caagtcttccagaagttccaCgctctgttaaaggaagagtt	12	11	9	9	1	2	2	0	0	2	2	4	3	4	3	2	1	0	4	2	1	5	4	rs62637564	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:46104849C>T	ENST00000349995.5	+	22	2503	c.2391C>T	c.(2389-2391)caC>caT	p.H797H		NM_031431.3	NP_113619	Q96JB2	COG3_HUMAN	component of oligomeric golgi complex 3	797					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)		AGAAGTTCCACGCTCTGTTAA	0.393													T|||	189	0.0377396	0.115	0.0144	5008	,	,		16886	0.0		0.0169	False		,,,				2504	0.0102				p.H797H	Ovarian(150;1048 1859 18083 21577 42700)	Atlas-SNP	.											.	COG3	52	.	0			c.C2391T						PASS	.	T		363,4043		11,341,1851	114	109	111		2391	-3.4	0.3	13	dbSNP_129	111	174,8426		4,166,4130	no	coding-synonymous	COG3	NM_031431.3		15,507,5981	TT,TC,CC		2.0233,8.2388,4.1289		797/829	46104849	537,12469	2203	4300	6503	SO:0001819	synonymous_variant	83548	exon22			GTTCCACGCTCTG	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.2391C>T	13.37:g.46104849C>T		106	0	0		122	61	0.5	NM_031431	B2RAW5|Q5VT70|Q8IXX4|Q9BZ92	Silent	SNP	ENST00000349995.5	37	CCDS9398.1																																																																																			C|0.964;T|0.036	0.036	strong		0.393	COG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044777.2			T	46104849	C	T	46104849	2	4	30	1	0	0	0	0	0	0	0	1	3661	535	19	1		1	COG3	13	46104849	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	12468939	46104849	69065029	452	13603											
HTR2A	3356	hgsc.bcm.edu	37	chr13	47469939	47469939	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atcagaagtgttagcttctcCggagttaaagtcattactgt	11	14	9	7	1	3	1	2	0	1	1	4	2	3	2	1	1	2	3	1	1	5	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:47469939C>T	ENST00000378688.4	-	1	234	c.103G>A	c.(103-105)Gga>Aga	p.G35R	HTR2A_ENST00000542664.1_Missense_Mutation_p.G35R|HTR2A_ENST00000543956.1_Intron			P28223	5HT2A_HUMAN	5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupled	35					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)	TTAGCTTCTCCGGAGTTAAAG	0.428																																					p.G35R		Atlas-SNP	.											.	HTR2A	98	.	0			c.G103A						PASS	.						102	100	101					13																	47469939		2203	4300	6503	SO:0001583	missense	3356	exon2			CTTCTCCGGAGTT	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.103G>A	13.37:g.47469939C>T	ENSP00000367959:p.Gly35Arg	84	0	0		81	42	0.518519	NM_000621	B2RAC5|B4DZ79|F5GWE8|Q5T8C0	Missense_Mutation	SNP	ENST00000378688.4	37	CCDS9405.1	.	.	.	.	.	.	.	.	.	.	C	1.837	-0.468315	0.04445	.	.	ENSG00000102468	ENST00000378688;ENST00000542664	T;T	0.54866	0.55;0.55	5.49	1.83	0.25207	.	0.180503	0.39407	N	0.001371	T	0.29588	0.0738	N	0.17082	0.46	0.23309	N	0.997934	B	0.15473	0.013	B	0.08055	0.003	T	0.18272	-1.0342	10	0.13853	T	0.58	.	8.1078	0.30896	0.0:0.6054:0.0:0.3946	.	35	P28223	5HT2A_HUMAN	R	35	ENSP00000367959:G35R;ENSP00000437737:G35R	ENSP00000367959:G35R	G	-	1	0	HTR2A	46367940	0.018000	0.18449	0.035000	0.18076	0.996000	0.88848	0.190000	0.17057	0.028000	0.15324	0.585000	0.79938	GGA	.	.	none		0.428	HTR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044835.3	NM_000621		T	47469939	C	T	47469939	3	4	30	1	0	0	0	0	1	0	0	0	7450	661	23	1	1324	1	HTR2A	13	47469939	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1365090	47469939	67699939	453	13604											
SLAIN1	122060	hgsc.bcm.edu	37	chr13	78320801	78320801	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aatttgatcatttgccaccaCctcagcctcgtcttccaaga	10	12	5	14	1	3	2	2	1	1	1	5	2	4	2	5	0	2	0	5	0	2	3	rs144139933	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:78320801C>G	ENST00000466548.1	+	5	1029	c.1003C>G	c.(1003-1005)Cct>Gct	p.P335A	SLAIN1_ENST00000314070.5_Intron|SLAIN1_ENST00000465831.1_3'UTR|SLAIN1_ENST00000267219.8_Missense_Mutation_p.P116A|SLAIN1_ENST00000418532.1_Missense_Mutation_p.P116A|SLAIN1_ENST00000351546.3_Missense_Mutation_p.P72A|SLAIN1_ENST00000358679.3_Missense_Mutation_p.P72A|SLAIN1_ENST00000488699.1_Missense_Mutation_p.P193A	NM_001242868.1	NP_001229797.1	Q8ND83	SLAI1_HUMAN	SLAIN motif family, member 1	335										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)		TTTGCCACCACCTCAGCCTCG	0.468													C|||	6	0.00119808	0.0	0.0014	5008	,	,		19409	0.0		0.005	False		,,,				2504	0.0				p.P357A		Atlas-SNP	.											.	SLAIN1	43	.	0			c.C1069G						PASS	.	C	ALA/PRO,ALA/PRO,,,ALA/PRO,ALA/PRO	2,4404	4.2+/-10.8	0,2,2201	158	150	153		577,1069,,,211,214	5.9	1	13	dbSNP_134	153	21,8579	16.6+/-54.9	0,21,4279	yes	missense,missense,intron,intron,missense,missense	SLAIN1	NM_001040153.3,NM_001242868.1,NM_001242869.1,NM_001242870.1,NM_001242871.1,NM_144595.3	27,27,,,27,27	0,23,6480	GG,GC,CC		0.2442,0.0454,0.1768	probably-damaging,probably-damaging,,,probably-damaging,probably-damaging	193/427,357/591,,,71/305,72/306	78320801	23,12983	2203	4300	6503	SO:0001583	missense	122060	exon4			CCACCACCTCAGC	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.1003C>G	13.37:g.78320801C>G	ENSP00000419730:p.Pro335Ala	181	0	0		181	95	0.524862	NM_001242868	A8K0Z9|B7Z209|Q5T6P4|Q5T6P7|Q8ND10|Q96NV0	Missense_Mutation	SNP	ENST00000466548.1	37		5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	20.3	3.960845	0.74016	4.54E-4	0.002442	ENSG00000139737	ENST00000466548;ENST00000389459;ENST00000418532;ENST00000442759;ENST00000446759;ENST00000488699;ENST00000267219;ENST00000351546;ENST00000441784;ENST00000462234;ENST00000496045;ENST00000474663;ENST00000358679	.	.	.	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.73489	0.3593	M	0.69823	2.125	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.998	D;D;D	0.71414	0.973;0.973;0.96	T	0.74697	-0.3578	8	.	.	.	-15.4977	20.3325	0.98724	0.0:1.0:0.0:0.0	.	71;193;335	B7Z326;B7Z209;Q8ND83	.;.;SLAI1_HUMAN	A	335;335;116;116;166;193;116;72;72;72;72;72;72	.	.	P	+	1	0	SLAIN1	77218802	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.733000	0.68571	2.805000	0.96524	0.655000	0.94253	CCT	C|0.999;G|0.001	0.001	strong		0.468	SLAIN1-009	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000355018.1	NM_144595		G	78320801	C	G	78320801	3	3	30	1	0	0	0	0	1	0	0	0	14380	507	18	4	356	4	SLAIN1	13	78320801	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	30850862	78320801	36849077	454	13605											
CUL4A	8451	hgsc.bcm.edu	37	chr13	113909008	113909008	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atgaggccttctcttccaggGgaagaaggaattccaggtgt	10	10	13	8	0	1	2	0	1	1	1	4	4	3	4	3	5	0	0	3	5	3	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr13:113909008G>A	ENST00000375440.4	+	17	1838	c.1754G>A	c.(1753-1755)gGg>gAg	p.G585E	CUL4A_ENST00000451881.1_Splice_Site_p.G485E|CUL4A_ENST00000375441.3_Splice_Site_p.G485E|CUL4A_ENST00000326335.4_Splice_Site_p.G485E	NM_001008895.1	NP_001008895.1	Q13619	CUL4A_HUMAN	cullin 4A	585					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)			CTCTTCCAGGGGAAGAAGGAA	0.443																																					p.G585E		Atlas-SNP	.											.	CUL4A	50	.	0			c.G1754A						PASS	.						138	130	133					13																	113909008		2203	4300	6503	SO:0001630	splice_region_variant	8451	exon17			TCCAGGGGAAGAA	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.1753-1G>A	13.37:g.113909008G>A		98	0	0		104	53	0.509615	NM_001008895	A2A2W2|O75834|Q589T6|Q5TC62|Q6UP08|Q9UP17	Missense_Mutation	SNP	ENST00000375440.4	37	CCDS41908.1	.	.	.	.	.	.	.	.	.	.	G	18.32	3.598067	0.66332	.	.	ENSG00000139842	ENST00000375441;ENST00000451881;ENST00000326335;ENST00000375440	T;T;T;T	0.74106	-0.81;-0.81;-0.81;-0.81	5.3	5.3	0.74995	Cullin, N-terminal (1);Cullin homology (2);	0.000000	0.85682	D	0.000000	T	0.72203	0.3431	M	0.61703	1.905	0.80722	D	1	P;P	0.42161	0.772;0.772	B;B	0.41036	0.346;0.346	T	0.74077	-0.3781	10	0.46703	T	0.11	-31.6571	12.6463	0.56735	0.0762:0.0:0.9238:0.0	.	585;585	Q13619;A8MSH7	CUL4A_HUMAN;.	E	485;485;485;585	ENSP00000364590:G485E;ENSP00000389118:G485E;ENSP00000322132:G485E;ENSP00000364589:G585E	ENSP00000322132:G485E	G	+	2	0	CUL4A	112957009	1.000000	0.71417	0.998000	0.56505	0.908000	0.53690	7.668000	0.83897	2.627000	0.88993	0.561000	0.74099	GGG	.	.	none		0.443	CUL4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045888.3	NM_003589	Missense_Mutation	A	113909008	G	A	113909008	5	1	30	1	0	0	0	0	0	0	1	0	4059	1246	43	2	1820	2	CUL4A	13	113909008	Splice_Site	SNP	G	TCGA-GR-7353-01A-11D-2210-10	35588207	113909008	1260870	455	13606											
CHD8	57680	hgsc.bcm.edu	37	chr14	21862616	21862616	+	Frame_Shift_Del	DEL	A	A	-																															aaacgtagacaccactcgatAaaaatcagtttgttcacgcc																										TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:21862616delA	ENST00000557364.1	-	31	5682	c.5419delT	c.(5419-5421)tatfs	p.Y1807fs	SNORD9_ENST00000362566.1_RNA|CHD8_ENST00000555962.1_5'Flank|CHD8_ENST00000430710.3_Frame_Shift_Del_p.Y1528fs|CHD8_ENST00000399982.2_Frame_Shift_Del_p.Y1807fs|SNORD8_ENST00000363915.1_RNA			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	1807					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)		ACCACTCGATAAAAATCAGTT	0.413																																					p.Y1807fs		Pindel,Atlas-Indel	.											.	CHD8	339	.	0			c.5420delA						PASS	.						53	52	52					14																	21862616		1958	4159	6117	SO:0001589	frameshift_variant	57680	exon30			.	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.5419delT	14.37:g.21862616delA	ENSP00000451601:p.Tyr1807fs	121	0	.		156	30	0.192	NM_001170629	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Frame_Shift_Del	DEL	ENST00000557364.1	37	CCDS53885.1																																																																																			.	.	none		0.413	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920		-	21862616	A	-	21862616	7	5	30	1	0	1	0	1	0	0	0	0	3333	362	13	0	2358	0	CHD8	14	21862616	Frame_Shift_Del	DEL	A	TCGA-GR-7353-01A-11D-2210-10		21862616	85486924	456	13607											
CDH24	64403	hgsc.bcm.edu	37	chr14	23523353	23523353	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaggcaggaggctaaccttGcggacagtgaggagcccgtc	10	5	15	11	2	0	1	0	1	0	0	1	4	0	4	2	5	3	2	2	5	1	2	rs139832060	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:23523353G>T	ENST00000267383.5	-	5	1061	c.969C>A	c.(967-969)cgC>cgA	p.R323R	CDH24_ENST00000554034.1_Silent_p.R323R|CDH24_ENST00000397359.3_Silent_p.R323R|CDH24_ENST00000487137.2_Silent_p.R323R			Q86UP0	CAD24_HUMAN	cadherin 24, type 2	323	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)	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)		GGCTAACCTTGCGGACAGTGA	0.547													G|||	8	0.00159744	0.0	0.0029	5008	,	,		20441	0.0		0.0	False		,,,				2504	0.0061				p.R323R		Atlas-SNP	.											.	CDH24	129	.	0			c.C969A						PASS	.	G	,	4,4400		0,4,2198	78	72	74		969,969	0.3	1	14	dbSNP_134	74	41,8553		0,41,4256	yes	coding-synonymous,coding-synonymous	CDH24	NM_022478.3,NM_144985.3	,	0,45,6454	TT,TG,GG		0.4771,0.0908,0.3462	,	323/820,323/782	23523353	45,12953	2202	4297	6499	SO:0001819	synonymous_variant	64403	exon6			AACCTTGCGGACA	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.969C>A	14.37:g.23523353G>T		35	0	0		51	34	0.666667	NM_022478	D3DS44|Q86UP1|Q9NT84	Silent	SNP	ENST00000267383.5	37	CCDS9585.1																																																																																			G|0.997;T|0.003	0.003	strong		0.547	CDH24-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257241.2	NM_022478		T	23523353	G	T	23523353	2	4	30	1	0	0	0	0	0	0	0	1	3111	1306	46	4		4	CDH24	14	23523353	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1660737	23523353	83826187	457	13608											
MYH6	4624	hgsc.bcm.edu	37	chr14	23862710	23862710	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatccagcccagccatctcCtctgttaggttcttcacctg	6	13	6	16	0	5	0	2	0	3	0	7	0	6	0	5	1	2	2	5	1	1	3	rs145274612	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:23862710C>T	ENST00000356287.3	-	22	2975	c.2946G>A	c.(2944-2946)gaG>gaA	p.E982E	MYH6_ENST00000405093.3_Silent_p.E982E			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	982					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)		CAGCCATCTCCTCTGTTAGGT	0.537													C|||	21	0.00419329	0.0	0.0101	5008	,	,		22617	0.0		0.0119	False		,,,				2504	0.002				p.E982E		Atlas-SNP	.											.	MYH6	274	.	0			c.G2946A						PASS	.	C		9,4397	15.5+/-35.6	0,9,2194	181	177	178		2946	3.3	1	14	dbSNP_134	178	103,8497	56.0+/-117.1	0,103,4197	no	coding-synonymous	MYH6	NM_002471.3		0,112,6391	TT,TC,CC		1.1977,0.2043,0.8611		982/1940	23862710	112,12894	2203	4300	6503	SO:0001819	synonymous_variant	4624	exon23			CATCTCCTCTGTT	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.2946G>A	14.37:g.23862710C>T		306	1	0.00326797		422	277	0.656398	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Silent	SNP	ENST00000356287.3	37	CCDS9600.1																																																																																			C|0.992;T|0.008	0.008	strong		0.537	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3			T	23862710	C	T	23862710	2	4	30	1	0	0	0	0	0	0	0	1	10047	680	24	2		2	MYH6	14	23862710	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	339357	23862710	83486830	458	13609											
THTPA	79178	hgsc.bcm.edu	37	chr14	24026046	24026046	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gcggctgcaggagttgggggGcaccctggagtaccgggtca	6	6	19	10	2	1	0	1	0	0	0	1	2	1	2	2	7	2	5	2	7	1	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24026046G>A	ENST00000288014.6	+	1	816	c.80G>A	c.(79-81)gGc>gAc	p.G27D	THTPA_ENST00000554789.1_Missense_Mutation_p.G27D|RP11-66N24.4_ENST00000553985.1_RNA|RP11-66N24.4_ENST00000555446.1_RNA|THTPA_ENST00000404535.3_Missense_Mutation_p.G27D|RP11-66N24.4_ENST00000556354.1_RNA|THTPA_ENST00000554970.1_Missense_Mutation_p.G27D|THTPA_ENST00000556015.1_Missense_Mutation_p.G27D			Q9BU02	THTPA_HUMAN	thiamine triphosphatase	27	CYTH. {ECO:0000255|PROSITE- ProRule:PRU01044}.				dephosphorylation (GO:0016311)|generation of precursor metabolites and energy (GO:0006091)|small molecule metabolic process (GO:0044281)|thiamine diphosphate metabolic process (GO:0042357)|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)	hydrolase activity (GO:0016787)|magnesium ion binding (GO:0000287)|thiamin-triphosphatase activity (GO:0050333)			large_intestine(1)|prostate(2)	3	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00643)		GAGTTGGGGGGCACCCTGGAG	0.607																																					p.G27D		Atlas-SNP	.											.	THTPA	11	.	0			c.G80A						PASS	.						53	43	46					14																	24026046		2203	4300	6503	SO:0001583	missense	79178	exon2			TGGGGGGCACCCT	AF432862	CCDS32053.1, CCDS58306.1, CCDS58307.1	14q11.2	2011-04-28					3.6.1.28		18987	protein-coding gene	gene with protein product		611612				11827967	Standard	NR_046051		Approved	THTPASE	uc001wkh.5	Q9BU02		ENST00000288014.6:c.80G>A	14.37:g.24026046G>A	ENSP00000288014:p.Gly27Asp	126	0	0		158	93	0.588608	NM_001256321	D3DS50|G3V4J3	Missense_Mutation	SNP	ENST00000288014.6	37	CCDS32053.1	.	.	.	.	.	.	.	.	.	.	G	19.29	3.799652	0.70567	.	.	ENSG00000157306	ENST00000404535;ENST00000288014;ENST00000557630;ENST00000556015;ENST00000554970;ENST00000554789	T;T;T;T;T;T	0.49139	0.79;0.79;0.79;0.79;0.79;0.79	5.91	0.674	0.17946	CYTH domain (2);CYTH-like domain (1);	0.428933	0.25484	N	0.030357	T	0.66268	0.2772	M	0.76170	2.325	0.28533	N	0.91246	P;D	0.56746	0.928;0.977	P;P	0.60473	0.564;0.875	T	0.71155	-0.4675	10	0.62326	D	0.03	-1.7363	20.3036	0.98618	0.0:0.7093:0.2907:0.0	.	27;27	G3V4J3;Q9BU02	.;THTPA_HUMAN	D	27	ENSP00000384580:G27D;ENSP00000288014:G27D;ENSP00000452281:G27D;ENSP00000451835:G27D;ENSP00000452465:G27D;ENSP00000450459:G27D	ENSP00000288014:G27D	G	+	2	0	THTPA	23095886	0.623000	0.27094	0.764000	0.31436	0.880000	0.50808	0.727000	0.25999	-0.142000	0.11354	0.655000	0.94253	GGC	.	.	none		0.607	THTPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413800.2			A	24026046	G	A	24026046	3	1	30	1	0	0	0	0	1	0	0	0	15896	1203	42	2	82	2	THTPA	14	24026046	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	163336	24026046	83323494	459	13610											
DHRS4	10901	hgsc.bcm.edu	37	chr14	24424346	24424346	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caggcggtggccacgctgcaGggggaggggctgagcgtgac	6	4	21	10	3	0	2	0	2	0	0	0	3	0	3	1	7	2	3	1	7	0	0	rs4981491		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24424346G>A	ENST00000313250.5	+	2	434	c.231G>A	c.(229-231)caG>caA	p.Q77Q	DHRS4_ENST00000559632.1_Silent_p.Q77Q|DHRS4_ENST00000397075.3_Silent_p.Q77Q|DHRS4_ENST00000558263.1_Silent_p.Q77Q|DHRS4_ENST00000421831.1_Silent_p.Q59Q|DHRS4_ENST00000558581.1_Silent_p.Q77Q|DHRS4_ENST00000543741.2_Silent_p.Q77Q|DHRS4_ENST00000308178.8_Silent_p.Q59Q|DHRS4_ENST00000382761.3_Silent_p.Q59Q|DHRS4-AS1_ENST00000556379.1_RNA|DHRS4_ENST00000397074.3_Silent_p.Q77Q|DHRS4_ENST00000397073.2_Silent_p.Q59Q	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	77					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)	CCACGCTGCAGGGGGAGGGGC	0.701																																					p.Q77Q		Atlas-SNP	.											.	DHRS4	22	.	0			c.G231A						PASS	.						37	42	40					14																	24424346		2203	4299	6502	SO:0001819	synonymous_variant	10901	exon2			GCTGCAGGGGGAG	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.231G>A	14.37:g.24424346G>A		324	0	0		432	92	0.212963	NM_021004	B2RB10|B7WNS9|D3YTB8|E2QRL8|O95162|Q20CR0|Q2LC19|Q2LE81|Q58IU4|Q6E0Y1|Q6UWU3|Q71UQ6|Q8TD03|Q9H3N5|Q9NV08	Silent	SNP	ENST00000313250.5	37	CCDS9605.1																																																																																			.	.	weak		0.701	DHRS4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071857.3			A	24424346	G	A	24424346	2	1	30	1	0	0	0	0	0	0	0	1	4494	991	35	2		2	DHRS4	14	24424346	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	398300	24424346	82925194	460	13611											
DHRS4	10901	hgsc.bcm.edu	37	chr14	24435542	24435542	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccttgctgggcctgaccaaGaccctggccatagagctggc	7	7	13	14	0	0	3	0	1	0	2	0	3	0	3	5	3	2	2	5	3	2	2	rs11556285		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24435542G>T	ENST00000313250.5	+	6	785	c.582G>T	c.(580-582)aaG>aaT	p.K194N	DHRS4_ENST00000559632.1_Intron|DHRS4_ENST00000397075.3_Intron|DHRS4_ENST00000558263.1_Intron|DHRS4_ENST00000421831.1_Missense_Mutation_p.K142N|DHRS4_ENST00000558581.1_Missense_Mutation_p.K160N|DHRS4_ENST00000543741.2_Intron|DHRS4_ENST00000308178.8_Intron|DHRS4_ENST00000382761.3_Intron|DHRS4_ENST00000397074.3_Intron|DHRS4_ENST00000397073.2_Intron	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	194					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)	GCCTGACCAAGACCCTGGCCA	0.502																																					p.K194N		Atlas-SNP	.											.	DHRS4	22	.	0			c.G582T						PASS	.																																			SO:0001583	missense	10901	exon6			GACCAAGACCCTG	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.582G>T	14.37:g.24435542G>T	ENSP00000326219:p.Lys194Asn	1032	1	0.000968992		1415	159	0.112367	NM_021004	B2RB10|B7WNS9|D3YTB8|E2QRL8|O95162|Q20CR0|Q2LC19|Q2LE81|Q58IU4|Q6E0Y1|Q6UWU3|Q71UQ6|Q8TD03|Q9H3N5|Q9NV08	Missense_Mutation	SNP	ENST00000313250.5	37	CCDS9605.1	.	.	.	.	.	.	.	.	.	.	G	11.78	1.739826	0.30865	.	.	ENSG00000157326	ENST00000313250;ENST00000421831	T;T	0.46063	0.88;0.88	3.53	2.63	0.31362	Short-chain dehydrogenase/reductase, conserved site (1);NAD(P)-binding domain (1);	0.294117	0.30639	N	0.009188	T	0.54838	0.1883	M	0.82056	2.57	0.80722	D	1	B;P	0.39862	0.326;0.692	B;P	0.52823	0.238;0.71	T	0.54609	-0.8268	10	0.72032	D	0.01	.	5.9644	0.19316	0.251:0.0:0.749:0.0	rs11556285;rs11556285	160;194	Q9BTZ2-4;Q9BTZ2	.;DHRS4_HUMAN	N	194;142	ENSP00000326219:K194N;ENSP00000404147:K142N	ENSP00000326219:K194N	K	+	3	2	DHRS4	23505382	1.000000	0.71417	0.998000	0.56505	0.689000	0.40095	1.961000	0.40432	0.599000	0.29845	0.580000	0.79431	AAG	G|0.998;T|0.002	0.002	weak		0.502	DHRS4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071857.3			T	24435542	G	T	24435542	3	4	30	1	0	0	0	0	1	0	0	0	4494	933	33	4	604	4	DHRS4	14	24435542	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	11196	24435542	82913998	461	13612											
LRRC16B	90668	hgsc.bcm.edu	37	chr14	24534270	24534270	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtttcactttcgccggcccCggagcttcaagggggacagg	6	9	14	12	3	2	0	2	0	0	0	3	2	2	2	3	5	1	2	3	5	1	3	rs117833529	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24534270C>T	ENST00000342740.5	+	33	3338	c.3184C>T	c.(3184-3186)Cgg>Tgg	p.R1062W	LRRC16B_ENST00000334420.7_Missense_Mutation_p.R158W	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	1062				R -> W (in Ref. 2; CAD38886). {ECO:0000305}.		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)		TCGCCGGCCCCGGAGCTTCAA	0.716													C|||	108	0.0215655	0.0015	0.0418	5008	,	,		8025	0.0		0.0368	False		,,,				2504	0.0409				p.R1062W		Atlas-SNP	.											.	LRRC16B	120	.	0			c.C3184T						PASS	.	C	TRP/ARG	23,3751		0,23,1864	19	24	22		3184	2.8	1	14	dbSNP_132	22	255,7637		2,251,3693	yes	missense	LRRC16B	NM_138360.3	101	2,274,5557	TT,TC,CC		3.2311,0.6094,2.383	probably-damaging	1062/1373	24534270	278,11388	1887	3946	5833	SO:0001583	missense	90668	exon33			CGGCCCCGGAGCT	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.3184C>T	14.37:g.24534270C>T	ENSP00000340467:p.Arg1062Trp	59	0	0		69	35	0.507246	NM_138360	Q8TEF7|Q96HS9	Missense_Mutation	SNP	ENST00000342740.5	37	CCDS32054.1	46	0.021062271062271064	2	0.0040650406504065045	19	0.052486187845303865	0	0.0	25	0.032981530343007916	C	12.56	1.973870	0.34848	0.006094	0.032311	ENSG00000186648	ENST00000342740;ENST00000334420	T;T	0.60797	1.2;0.16	4.66	2.77	0.32553	.	0.254810	0.20948	N	0.082818	T	0.29389	0.0732	L	0.59436	1.845	0.28233	N	0.926034	D;D	0.89917	1.0;0.999	D;P	0.80764	0.994;0.876	T	0.48725	-0.9010	10	0.87932	D	0	-13.2657	9.764	0.40550	0.3756:0.6244:0.0:0.0	.	158;1062	Q8ND23-2;Q8ND23	.;LR16B_HUMAN	W	1062;158	ENSP00000340467:R1062W;ENSP00000334701:R158W	ENSP00000334701:R158W	R	+	1	2	LRRC16B	23604110	0.999000	0.42202	1.000000	0.80357	0.602000	0.36980	1.625000	0.37029	0.375000	0.24679	-0.348000	0.07805	CGG	C|0.976;T|0.024	0.024	strong		0.716	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360		T	24534270	C	T	24534270	3	4	30	1	0	0	0	0	1	0	0	0	8981	643	23	1	3314	1	LRRC16B	14	24534270	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	98728	24534270	82815270	462	13613											
C14orf21	161424	hgsc.bcm.edu	37	chr14	24772373	24772373	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttgccctggtgggggcctgtCgcagagttggggcctaccaa	5	9	16	11	1	0	1	0	0	0	1	1	1	0	1	4	5	2	2	4	5	2	3	rs147123517	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24772373C>T	ENST00000267425.3	+	6	1330	c.1237C>T	c.(1237-1239)Cgc>Tgc	p.R413C	NOP9_ENST00000396802.3_Missense_Mutation_p.R413C	NM_174913.1	NP_777573.1	Q86U38	NOP9_HUMAN	NOP9 nucleolar protein	413							poly(A) RNA binding (GO:0044822)										GGGGGCCTGTCGCAGAGTTGG	0.557													C|||	8	0.00159744	0.0	0.0014	5008	,	,		16884	0.0		0.007	False		,,,				2504	0.0				p.R413C		Atlas-SNP	.											.	.	.	.	0			c.C1237T						PASS	.	C	CYS/ARG	4,4402	6.2+/-15.9	0,4,2199	70	71	71		1237	4.2	1	14	dbSNP_134	71	45,8555	30.1+/-81.4	0,45,4255	yes	missense	C14orf21	NM_174913.1	180	0,49,6454	TT,TC,CC		0.5233,0.0908,0.3767	probably-damaging	413/637	24772373	49,12957	2203	4300	6503	SO:0001583	missense	161424	exon6			GCCTGTCGCAGAG		CCDS9624.1, CCDS66616.1	14q12	2012-12-10	2012-12-10	2012-06-06	ENSG00000196943	ENSG00000196943			19826	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 21", "NOP9 nucleolar protein homolog (yeast)"	C14orf21		21653694	Standard	XM_005267385		Approved		uc001wol.1	Q86U38	OTTHUMG00000029342	ENST00000267425.3:c.1237C>T	14.37:g.24772373C>T	ENSP00000267425:p.Arg413Cys	156	0	0		281	94	0.33452	NM_174913	A8MY76|Q8IVF0|Q8TBS6	Missense_Mutation	SNP	ENST00000267425.3	37	CCDS9624.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	18.19	3.567896	0.65651	9.08E-4	0.005233	ENSG00000196943	ENST00000267425;ENST00000396802	T;T	0.32753	1.48;1.44	5.16	4.25	0.50352	.	0.224065	0.38897	N	0.001525	T	0.35189	0.0923	L	0.54323	1.7	0.43536	D	0.995829	D	0.76494	0.999	P	0.59288	0.855	T	0.23013	-1.0200	10	0.52906	T	0.07	-4.9362	11.1833	0.48642	0.4521:0.5479:0.0:0.0	.	413	Q86U38	CN021_HUMAN	C	413	ENSP00000267425:R413C;ENSP00000380020:R413C	ENSP00000267425:R413C	R	+	1	0	C14orf21	23842213	0.869000	0.29996	1.000000	0.80357	0.909000	0.53808	0.630000	0.24553	1.356000	0.45884	0.563000	0.77884	CGC	C|0.996;T|0.004	0.004	strong		0.557	NOP9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073186.2			T	24772373	C	T	24772373	3	4	30	1	0	0	0	0	1	0	0	0	1771	884	31	1	1259	1	C14orf21	14	24772373	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	238103	24772373	82577167	463	13614											
CIDEB	27141	hgsc.bcm.edu	37	chr14	24775287	24775287	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acgtcaaaggtgaatcgggcGatgtccttgctgtgcttggg	7	11	15	8	3	1	1	1	1	0	0	3	2	2	1	1	3	2	2	1	3	2	2	rs139893717	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:24775287G>A	ENST00000336557.5	-	7	1695	c.393C>T	c.(391-393)atC>atT	p.I131I	CIDEB_ENST00000554411.1_Silent_p.I131I|LTB4R2_ENST00000528054.1_5'Flank|NOP9_ENST00000267425.3_3'UTR|CIDEB_ENST00000258807.5_Silent_p.I131I			Q9UHD4	CIDEB_HUMAN	cell death-inducing DFFA-like effector b	131					apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|regulation of apoptotic process (GO:0042981)	cytosol (GO:0005829)|lipid particle (GO:0005811)	identical protein binding (GO:0042802)			NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|urinary_tract(1)	7				GBM - Glioblastoma multiforme(265;0.0181)		TGAATCGGGCGATGTCCTTGC	0.527													G|||	8	0.00159744	0.0	0.0072	5008	,	,		21522	0.0		0.002	False		,,,				2504	0.001				p.I131I		Atlas-SNP	.											.	CIDEB	17	.	0			c.C393T						PASS	.	G		9,4397	15.5+/-35.6	0,9,2194	196	166	176		393	0.1	1	14	dbSNP_134	176	72,8528	43.1+/-100.9	1,70,4229	no	coding-synonymous	CIDEB	NM_014430.2		1,79,6423	AA,AG,GG		0.8372,0.2043,0.6228		131/220	24775287	81,12925	2203	4300	6503	SO:0001819	synonymous_variant	27141	exon6			TCGGGCGATGTCC	AF190901	CCDS32056.1	14q12	2012-09-20			ENSG00000136305	ENSG00000136305			1977	protein-coding gene	gene with protein product		604441				10619428, 10837461	Standard	XM_005267540		Approved		uc001woo.3	Q9UHD4	OTTHUMG00000171555	ENST00000336557.5:c.393C>T	14.37:g.24775287G>A		53	0	0		83	53	0.638554	NM_014430	D3DS73|Q546V8|Q9NNW9	Silent	SNP	ENST00000336557.5	37	CCDS32056.1																																																																																			G|0.995;A|0.005	0.005	strong		0.527	CIDEB-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414120.1			A	24775287	G	A	24775287	2	1	30	1	0	0	0	0	0	0	0	1	3428	1048	37	1		1	CIDEB	14	24775287	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2914	24775287	82574253	464	13615											
AKAP6	9472	hgsc.bcm.edu	37	chr14	33014876	33014876	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgacaaatgctgctcaaccCtcctctgagactgtgcagca	10	9	8	14	0	2	2	1	2	1	1	3	3	3	2	2	0	5	4	2	0	2	0	rs375820695		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:33014876C>T	ENST00000280979.4	+	4	1187	c.1017C>T	c.(1015-1017)ccC>ccT	p.P339P	AKAP6_ENST00000557354.1_Silent_p.P339P|AKAP6_ENST00000557272.1_Silent_p.P339P	NM_004274.4	NP_004265.3	Q13023	AKAP6_HUMAN	A kinase (PRKA) anchor protein 6	339					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)		CTGCTCAACCCTCCTCTGAGA	0.498																																					p.P339P	Melanoma(49;821 1200 7288 13647 42351)	Atlas-SNP	.											.	AKAP6	308	.	0			c.C1017T						PASS	.	C		0,4406		0,0,2203	71	62	65		1017	0.4	0	14		65	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	AKAP6	NM_004274.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		339/2320	33014876	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9472	exon4			TCAACCCTCCTCT	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.1017C>T	14.37:g.33014876C>T		89	0	0		123	51	0.414634	NM_004274	A7E242|A7E2D4|O15028	Silent	SNP	ENST00000280979.4	37	CCDS9644.1																																																																																			.	.	weak		0.498	AKAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276617.2	NM_004274		T	33014876	C	T	33014876	2	4	30	1	0	0	0	0	0	0	0	1	455	668	24	2		2	AKAP6	14	33014876	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	8239589	33014876	74334664	465	13616											
NPAS3	64067	hgsc.bcm.edu	37	chr14	34247747	34247747	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacttcatccatgctgaagaCgtggagggcatcaggcacag	11	7	12	11	1	2	2	2	1	0	1	3	3	3	3	1	3	1	3	1	3	1	1	rs147070037	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:34247747C>T	ENST00000356141.4	+	9	1122	c.1122C>T	c.(1120-1122)gaC>gaT	p.D374D	NPAS3_ENST00000551492.1_Silent_p.D379D|NPAS3_ENST00000346562.2_Silent_p.D342D|NPAS3_ENST00000548645.1_Silent_p.D344D|NPAS3_ENST00000357798.5_Silent_p.D361D			Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3	374	PAC.|PAS 2. {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)		ATGCTGAAGACGTGGAGGGCA	0.493													C|||	3	0.000599042	0.0	0.0	5008	,	,		19225	0.0		0.003	False		,,,				2504	0.0				p.D374D		Atlas-SNP	.											.	NPAS3	266	.	0			c.C1122T						PASS	.	C	,,,	1,4405	2.1+/-5.4	0,1,2202	117	102	107		1122,1032,1026,1083	-6.6	0.2	14	dbSNP_134	107	20,8580	14.6+/-50.1	0,20,4280	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NPAS3	NM_001164749.1,NM_001165893.1,NM_022123.2,NM_173159.2	,,,	0,21,6482	TT,TC,CC		0.2326,0.0227,0.1615	,,,	374/934,344/904,342/902,361/921	34247747	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	64067	exon9			TGAAGACGTGGAG	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.1122C>T	14.37:g.34247747C>T		133	0	0		166	108	0.650602	NM_001164749	Q86US6|Q86US7|Q8IXF2|Q9BY81|Q9H323|Q9Y4L8	Silent	SNP	ENST00000356141.4	37	CCDS53891.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	8.823	0.937989	0.18206	2.27E-4	0.002326	ENSG00000151322	ENST00000552874	.	.	.	6.03	-6.63	0.01807	.	.	.	.	.	T	0.67552	0.2905	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.70385	-0.4886	4	.	.	.	.	19.2046	0.93724	0.0:0.2337:0.0:0.7663	.	.	.	.	M	121	.	.	T	+	2	0	NPAS3	33317498	0.002000	0.14202	0.183000	0.23137	0.952000	0.60782	-1.517000	0.02248	-1.491000	0.01840	-0.226000	0.12346	ACG	C|0.999;T|0.001	0.001	strong		0.493	NPAS3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276645.1			T	34247747	C	T	34247747	2	4	30	1	0	0	0	0	0	0	0	1	10573	535	19	1		1	NPAS3	14	34247747	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1232871	34247747	73101793	466	13617											
TXNDC16	57544	hgsc.bcm.edu	37	chr14	52981664	52981664	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtagtcccatacacaaaaGcggcttccatgactgctctg	11	10	8	12	1	1	1	0	1	1	0	3	1	3	1	2	1	3	3	2	1	4	3	rs117463339	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:52981664G>C	ENST00000281741.4	-	8	910	c.539C>G	c.(538-540)gCt>gGt	p.A180G	TXNDC16_ENST00000554399.1_Intron	NM_001160047.1|NM_020784.2	NP_001153519.1|NP_065835.2	Q9P2K2	TXD16_HUMAN	thioredoxin domain containing 16	180				A -> G (in Ref. 1; BAA92582). {ECO:0000305}.	cell redox homeostasis (GO:0045454)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|prostate(3)|skin(1)	21	Breast(41;0.0716)					ATACACAAAAGCGGCTTCCAT	0.363													G|||	73	0.0145767	0.0061	0.0101	5008	,	,		18339	0.004		0.0258	False		,,,				2504	0.0286				p.A180G		Atlas-SNP	.											.	TXNDC16	59	.	0			c.C539G						PASS	.	G	GLY/ALA,GLY/ALA	36,4370	40.8+/-73.8	0,36,2167	130	133	132		524,539	5.7	1	14	dbSNP_132	132	264,8334	102.1+/-163.3	2,260,4037	yes	missense,missense	TXNDC16	NM_001160047.1,NM_020784.2	60,60	2,296,6204	CC,CG,GG		3.0705,0.8171,2.307	probably-damaging,probably-damaging	175/821,180/826	52981664	300,12704	2203	4299	6502	SO:0001583	missense	57544	exon8			ACAAAAGCGGCTT	AB037765	CCDS32083.1	14q22.1	2007-08-16	2007-08-16	2007-08-16		ENSG00000087301			19965	protein-coding gene	gene with protein product			"KIAA1344"	KIAA1344			Standard	NM_020784		Approved		uc001wzs.3	Q9P2K2		ENST00000281741.4:c.539C>G	14.37:g.52981664G>C	ENSP00000281741:p.Ala180Gly	67	0	0		100	37	0.37	NM_020784	A5PKW9|A7E260|A7MD07|B9EH67|Q9H9W7	Missense_Mutation	SNP	ENST00000281741.4	37	CCDS32083.1	33	0.01510989010989011	3	0.006097560975609756	7	0.019337016574585635	0	0.0	23	0.030343007915567283	G	25.2	4.612167	0.87258	0.008171	0.030705	ENSG00000087301	ENST00000281741	T	0.36157	1.27	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.36717	0.0977	M	0.72894	2.215	0.54753	D	0.999984	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.54510	-0.8283	10	0.87932	D	0	-44.0895	17.2216	0.86959	0.0:0.0:1.0:0.0	.	175;180	B7ZME4;Q9P2K2	.;TXD16_HUMAN	G	180	ENSP00000281741:A180G	ENSP00000281741:A180G	A	-	2	0	TXNDC16	52051414	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	5.007000	0.63984	2.681000	0.91329	0.563000	0.77884	GCT	G|0.979;C|0.021	0.021	strong		0.363	TXNDC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411681.1	XM_051699		C	52981664	G	C	52981664	3	2	30	1	0	0	0	0	1	0	0	0	16810	971	34	4	1994	4	TXNDC16	14	52981664	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	18733917	52981664	54367876	467	13618											
CGRRF1	10668	hgsc.bcm.edu	37	chr14	55005083	55005083	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaaaagagcaagataaagaCaaaccgaagactctttgaag	21	5	8	7	1	1	5	0	1	1	4	1	6	1	5	1	0	2	1	1	0	8	2	rs202061859		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:55005083C>T	ENST00000216420.7	+	6	1113	c.981C>T	c.(979-981)gaC>gaT	p.D327D		NM_006568.2	NP_006559.1	Q99675	CGRF1_HUMAN	cell growth regulator with ring finger domain 1	327					cell cycle arrest (GO:0007050)|negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(3)|kidney(2)|lung(5)|ovary(2)|stomach(1)	13						AAGATAAAGACAAACCGAAGA	0.383																																					p.D327D		Atlas-SNP	.											.	CGRRF1	30	.	0			c.C981T						PASS	.	C		0,4406		0,0,2203	71	67	69		981	1.5	0.2	14		69	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	CGRRF1	NM_006568.2		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		327/333	55005083	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	10668	exon6			TAAAGACAAACCG	BC015063	CCDS9719.1	14q22.2	2013-09-20			ENSG00000100532	ENSG00000100532		"RING-type (C3HC4) zinc fingers"	15528	protein-coding gene	gene with protein product		606138				8968090	Standard	NM_006568		Approved	CGR19, RNF197	uc001xay.3	Q99675	OTTHUMG00000140308	ENST00000216420.7:c.981C>T	14.37:g.55005083C>T		87	0	0		98	32	0.326531	NM_006568	Q96BX2	Silent	SNP	ENST00000216420.7	37	CCDS9719.1																																																																																			C|0.999;T|0.001	0.001	weak		0.383	CGRRF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276905.2	NM_006568		T	55005083	C	T	55005083	2	4	30	1	0	0	0	0	0	0	0	1	3308	477	17	2		2	CGRRF1	14	55005083	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	2023419	55005083	52344457	468	13619											
SAMD4A	23034	hgsc.bcm.edu	37	chr14	55226987	55226987	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaccacccccgaggctcgcCgccgggagccccaggccccg	5	1	13	22	5	0	0	0	0	0	0	1	2	0	1	9	3	1	2	9	3	0	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:55226987C>T	ENST00000554335.1	+	7	1948	c.1285C>T	c.(1285-1287)Cgc>Tgc	p.R429C	SAMD4A_ENST00000357634.3_Missense_Mutation_p.R428C|SAMD4A_ENST00000555192.1_Missense_Mutation_p.R20C|SAMD4A_ENST00000251091.5_Missense_Mutation_p.R341C|SAMD4A_ENST00000392067.3_Missense_Mutation_p.R429C			Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4A	429					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						CGAGGCTCGCCGCCGGGAGCC	0.716																																					p.R429C		Atlas-SNP	.											.	SAMD4A	68	.	0			c.C1285T						PASS	.																																			SO:0001583	missense	23034	exon6			GCTCGCCGCCGGG	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.1285C>T	14.37:g.55226987C>T	ENSP00000452535:p.Arg429Cys	45	0	0		46	32	0.695652	NM_015589	A8MPZ5|Q0VA96|Q6PEW4	Missense_Mutation	SNP	ENST00000554335.1	37	CCDS32084.2	.	.	.	.	.	.	.	.	.	.	C	13.96	2.391816	0.42410	.	.	ENSG00000020577	ENST00000554335;ENST00000392067;ENST00000305831;ENST00000251091;ENST00000357634;ENST00000555192	.	.	.	5.07	3.07	0.35406	.	0.889887	0.09934	N	0.736892	T	0.23451	0.0567	N	0.14661	0.345	0.24451	N	0.994482	B;D;P	0.53151	0.012;0.958;0.474	B;P;B	0.50617	0.002;0.646;0.093	T	0.09271	-1.0682	9	0.51188	T	0.08	-15.041	3.4091	0.07352	0.288:0.5045:0.1175:0.09	.	20;341;429	G3V2R1;Q9UPU9-3;Q9UPU9	.;.;SMAG1_HUMAN	C	429;429;341;340;428;20	.	ENSP00000251091:R58C	R	+	1	0	SAMD4A	54296737	0.921000	0.31238	0.318000	0.25279	0.343000	0.28985	1.821000	0.39041	1.331000	0.45412	0.609000	0.83330	CGC	.	.	none		0.716	SAMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411186.1	NM_015589		T	55226987	C	T	55226987	3	4	30	1	0	0	0	0	1	0	0	0	13836	652	23	1	1304	1	SAMD4A	14	55226987	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	221904	55226987	52122553	469	13620											
C14orf37	145407	hgsc.bcm.edu	37	chr14	58605734	58605734	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgaggggacacctgactcagTaggtgtggaaacaccagggc	11	6	15	9	0	1	2	1	2	0	0	1	4	1	4	2	5	1	1	2	5	2	1	rs61741497	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:58605734T>C	ENST00000267485.7	-	2	537	c.343A>G	c.(343-345)Act>Gct	p.T115A	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	115						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						CCTGACTCAGTAGGTGTGGAA	0.478													T|||	8	0.00159744	0.0	0.0029	5008	,	,		21817	0.0		0.006	False		,,,				2504	0.0				p.T115A		Atlas-SNP	.											.	C14orf37	87	.	0			c.A343G						PASS	.	T	ALA/THR	8,4398	15.5+/-35.6	0,8,2195	85	81	82		343	2.1	0.1	14	dbSNP_129	82	62,8538	37.4+/-92.8	3,56,4241	yes	missense	C14orf37	NM_001001872.2	58	3,64,6436	CC,CT,TT		0.7209,0.1816,0.5382	possibly-damaging	115/775	58605734	70,12936	2203	4300	6503	SO:0001583	missense	145407	exon2			ACTCAGTAGGTGT		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.343A>G	14.37:g.58605734T>C	ENSP00000267485:p.Thr115Ala	153	1	0.00653595		212	140	0.660377	NM_001001872	A8K8Z8|Q6P5Q1|Q86TY1	Missense_Mutation	SNP	ENST00000267485.7	37	CCDS32089.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	T	9.312	1.055831	0.19907	0.001816	0.007209	ENSG00000139971	ENST00000267485;ENST00000438670	T	0.21734	1.99	5.82	2.06	0.26882	.	0.429079	0.24436	N	0.038557	T	0.13415	0.0325	M	0.62723	1.935	0.19300	N	0.99997	B;P;B;B	0.40970	0.208;0.734;0.208;0.208	B;B;B;B	0.39503	0.084;0.301;0.084;0.084	T	0.09729	-1.0661	10	0.37606	T	0.19	-2.845	4.9334	0.13928	0.0:0.2244:0.1493:0.6264	.	153;115;115;115	B4DMS4;Q86TY3-2;A8K990;Q86TY3	.;.;.;CN037_HUMAN	A	115;153	ENSP00000267485:T115A	ENSP00000267485:T115A	T	-	1	0	C14orf37	57675487	0.014000	0.17966	0.120000	0.21714	0.017000	0.09413	-0.048000	0.11944	0.106000	0.17784	0.533000	0.62120	ACT	T|0.995;C|0.005	0.005	strong		0.478	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872		C	58605734	T	C	58605734	3	2	30	1	0	0	0	0	1	0	0	0	1773	1638	57	3	2009	3	C14orf37	14	58605734	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	3378747	58605734	48743806	470	13621											
ARID4A	5926	hgsc.bcm.edu	37	chr14	58831995	58831995	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacctgtagtataattgtacAagagagagagagcagagaga	17	8	12	4	0	0	5	0	0	0	5	0	8	0	5	1	0	3	4	1	0	6	6	rs377087834		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:58831995A>G	ENST00000355431.3	+	20	3561	c.3188A>G	c.(3187-3189)cAa>cGa	p.Q1063R	ARID4A_ENST00000348476.3_Missense_Mutation_p.Q1063R|ARID4A_ENST00000395168.3_Missense_Mutation_p.Q1063R|ARID4A_ENST00000431317.2_Missense_Mutation_p.Q1063R	NM_002892.3	NP_002883.3	P29374	ARI4A_HUMAN	AT rich interactive domain 4A (RBP1-like)	1063					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						ATAATTGTACAAGAGAGAGAG	0.383																																					p.Q1063R		Atlas-SNP	.											.	ARID4A	222	.	0			c.A3188G						PASS	.	A	ARG/GLN,ARG/GLN,ARG/GLN	1,4395		0,1,2197	59	61	60		3188,3188,3188	4.2	0.6	14		60	2,8576		0,2,4287	no	missense,missense,missense	ARID4A	NM_002892.3,NM_023000.2,NM_023001.2	43,43,43	0,3,6484	GG,GA,AA		0.0233,0.0227,0.0231	benign,benign,benign	1063/1258,1063/1204,1063/1189	58831995	3,12971	2198	4289	6487	SO:0001583	missense	5926	exon20			TTGTACAAGAGAG	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.3188A>G	14.37:g.58831995A>G	ENSP00000347602:p.Gln1063Arg	84	0	0		99	42	0.424242	NM_002892	Q15991|Q15992|Q15993	Missense_Mutation	SNP	ENST00000355431.3	37	CCDS9732.1	.	.	.	.	.	.	.	.	.	.	A	6.768	0.510652	0.12883	2.27E-4	2.33E-4	ENSG00000032219	ENST00000355431;ENST00000348476;ENST00000395168;ENST00000431317;ENST00000417477	T;T;T;T;T	0.17370	2.43;2.43;2.46;2.43;2.28	5.46	4.25	0.50352	.	0.533378	0.21403	N	0.075117	T	0.12817	0.0311	L	0.44542	1.39	0.30980	N	0.722581	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.09377	0.003;0.002;0.004	T	0.08973	-1.0696	10	0.17832	T	0.49	-11.3967	7.5328	0.27693	0.6734:0.2537:0.0729:0.0	.	1063;1063;1063	P29374-3;P29374;P29374-2	.;ARI4A_HUMAN;.	R	1063;1063;1063;1063;741	ENSP00000347602:Q1063R;ENSP00000344556:Q1063R;ENSP00000378597:Q1063R;ENSP00000397368:Q1063R;ENSP00000416053:Q741R	ENSP00000344556:Q1063R	Q	+	2	0	ARID4A	57901748	1.000000	0.71417	0.605000	0.28930	0.958000	0.62258	3.193000	0.50997	2.082000	0.62665	0.455000	0.32223	CAA	.	.	weak		0.383	ARID4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276927.2	NM_023001		G	58831995	A	G	58831995	3	3	30	1	0	0	0	0	1	0	0	0	919	130	5	3	3262	3	ARID4A	14	58831995	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	226261	58831995	48517545	471	13622											
PLEKHH1	57475	hgsc.bcm.edu	37	chr14	68053807	68053807	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttagattgcagaagctacctTcatcatggccagctatatga	12	12	8	9	0	2	3	2	1	0	2	2	3	2	3	2	1	4	3	2	1	5	6	rs118013098	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:68053807T>G	ENST00000329153.5	+	29	4082	c.3950T>G	c.(3949-3951)tTc>tGc	p.F1317C	PLEKHH1_ENST00000417684.2_Silent_p.L258L	NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	1317	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)		GAAGCTACCTTCATCATGGCC	0.498													T|||	7	0.00139776	0.0	0.0	5008	,	,		18391	0.0		0.007	False		,,,				2504	0.0				p.F1317C		Atlas-SNP	.											.	PLEKHH1	118	.	0			c.T3950G						PASS	.	T	CYS/PHE	4,3938		0,4,1967	61	66	64		3950	5.5	0.9	14	dbSNP_132	64	38,8266		0,38,4114	yes	missense	PLEKHH1	NM_020715.2	205	0,42,6081	GG,GT,TT		0.4576,0.1015,0.343	benign	1317/1365	68053807	42,12204	1971	4152	6123	SO:0001583	missense	57475	exon29			CTACCTTCATCAT	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.3950T>G	14.37:g.68053807T>G	ENSP00000330278:p.Phe1317Cys	199	0	0		255	159	0.623529	NM_020715	A6H8X6|Q6PJL4|Q6ZWC7	Missense_Mutation	SNP	ENST00000329153.5	37	CCDS45128.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	T	21.5	4.152327	0.78001	0.001015	0.004576	ENSG00000054690	ENST00000329153	T	0.71461	-0.57	5.54	5.54	0.83059	FERM domain (1);	0.398053	0.28989	N	0.013497	T	0.49508	0.1561	N	0.19112	0.55	0.80722	D	1	B	0.14012	0.009	B	0.12156	0.007	T	0.52351	-0.8587	10	0.48119	T	0.1	.	14.4073	0.67090	0.0:0.0:0.0:1.0	.	1317	Q9ULM0	PKHH1_HUMAN	C	1317	ENSP00000330278:F1317C	ENSP00000330278:F1317C	F	+	2	0	PLEKHH1	67123560	0.960000	0.32886	0.910000	0.35882	0.977000	0.68977	4.841000	0.62824	2.326000	0.78906	0.533000	0.62120	TTC	T|0.997;G|0.003	0.003	strong		0.498	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054		G	68053807	T	G	68053807	3	3	30	1	0	0	0	0	1	0	0	0	12085	1783	62	5	4060	5	PLEKHH1	14	68053807	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	9221812	68053807	39295733	472	13623											
DPF3	8110	hgsc.bcm.edu	37	chr14	73137882	73137882	+	Intron	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atctgctgtgggcgaaccccGgccactgcggcgtcctcgac	5	7	13	16	5	1	0	0	0	1	0	3	2	2	0	4	3	3	1	4	3	1	0	rs202093453		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:73137882G>A	ENST00000556509.1	-	8	871				DPF3_ENST00000546183.1_Missense_Mutation_p.R356W|DPF3_ENST00000541685.1_Missense_Mutation_p.R346W|DPF3_ENST00000557704.1_5'UTR	NM_001280542.1	NP_001267471.1	Q92784	DPF3_HUMAN	D4, zinc and double PHD fingers, family 3						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)		GGCGAACCCCGGCCACTGCGG	0.547													G|||	1	0.000199681	0.0	0.0014	5008	,	,		16614	0.0		0.0	False		,,,				2504	0.0				p.R346W		Atlas-SNP	.											.	DPF3	117	.	0			c.C1036T						PASS	.	G	TRP/ARG	1,4029		0,1,2014	55	57	56		1036	4.8	1	14		56	8,8334		0,8,4163	yes	missense	DPF3	NM_012074.3	101	0,9,6177	AA,AG,GG		0.0959,0.0248,0.0727	benign	346/358	73137882	9,12363	2015	4171	6186	SO:0001627	intron_variant	8110	exon9			AACCCCGGCCACT	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.871+3065C>T	14.37:g.73137882G>A		86	0	0		139	91	0.654676	NM_012074	A8MSI3|B7Z276|F5H575|Q32UJ0|Q6P9E6|Q6ZT41|Q9H7Y5	Missense_Mutation	SNP	ENST00000556509.1	37		.	.	.	.	.	.	.	.	.	.	G	17.16	3.317391	0.60524	2.48E-4	9.59E-4	ENSG00000205683	ENST00000541685;ENST00000546183	T;T	0.67523	-0.25;-0.27	5.79	4.82	0.62117	.	.	.	.	.	T	0.47619	0.1455	N	0.08118	0	0.27889	N	0.939402	D;P	0.60160	0.987;0.923	P;B	0.44561	0.453;0.237	T	0.42155	-0.9468	9	0.87932	D	0	.	7.5751	0.27931	0.0:0.117:0.3984:0.4846	.	356;346	F5H575;Q92784-2	.;.	W	346;356	ENSP00000441640:R346W;ENSP00000444662:R356W	ENSP00000381791:R401W	R	-	1	2	DPF3	72207635	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	1.667000	0.37471	1.366000	0.46076	0.655000	0.94253	CGG	.	.	weak		0.547	DPF3-004	NOVEL	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000413152.2			A	73137882	G	A	73137882	1	1	30	0	1	0	0	0	0	0	0	0	4720	1115	39	1		1	DPF3	14	73137882	Intron	SNP	G	TCGA-GR-7353-01A-11D-2210-10	5084075	73137882	34211658	473	13624											
ACOT4	122970	hgsc.bcm.edu	37	chr14	74060476	74060476	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctcttggaatatcgagccagCctccttgctggccatggctt	6	12	10	13	1	1	0	0	0	1	0	3	2	2	1	4	3	3	2	4	3	2	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:74060476C>A	ENST00000326303.4	+	2	782	c.528C>A	c.(526-528)agC>agA	p.S176R		NM_152331.3	NP_689544.3	Q8N9L9	ACOT4_HUMAN	acyl-CoA thioesterase 4	176					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)		ATCGAGCCAGCCTCCTTGCTG	0.463																																					p.S176R		Atlas-SNP	.											.	ACOT4	25	.	0			c.C528A						PASS	.						102	96	98					14																	74060476		2203	4300	6503	SO:0001583	missense	122970	exon2			AGCCAGCCTCCTT	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.528C>A	14.37:g.74060476C>A	ENSP00000323071:p.Ser176Arg	98	0	0		181	85	0.469613	NM_152331	Q17RF4|Q5BKT6|Q86TX0|Q86TX1|Q96N88	Missense_Mutation	SNP	ENST00000326303.4	37	CCDS9817.1	.	.	.	.	.	.	.	.	.	.	C	18.69	3.677650	0.68042	.	.	ENSG00000177465	ENST00000326303	T	0.39592	1.07	5.25	2.34	0.29019	.	0.451951	0.27437	N	0.019371	T	0.64427	0.2597	M	0.91561	3.22	0.37397	D	0.912664	D	0.76494	0.999	D	0.66979	0.948	T	0.68573	-0.5373	10	0.87932	D	0	-1.9598	6.2571	0.20879	0.0:0.6343:0.1404:0.2253	.	176	Q8N9L9	ACOT4_HUMAN	R	176	ENSP00000323071:S176R	ENSP00000323071:S176R	S	+	3	2	ACOT4	73130229	0.523000	0.26274	1.000000	0.80357	0.995000	0.86356	-0.120000	0.10660	0.554000	0.29061	0.561000	0.74099	AGC	.	.	none		0.463	ACOT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404298.2	NM_152331		A	74060476	C	A	74060476	3	1	30	1	0	0	0	0	1	0	0	0	153	738	26	4	534	4	ACOT4	14	74060476	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	922594	74060476	33289064	474	13625											
C14orf4	64207	hgsc.bcm.edu	37	chr14	77493809	77493809	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgctgttgctgctgctgctgCtgctgttgctgttgctgttg	0	18	14	9	0	0	0	0	0	0	0	0	0	0	0	0	0	9	13	0	0	0	4	rs61991638		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:77493809C>T	ENST00000238647.3	-	1	1225	c.327G>A	c.(325-327)caG>caA	p.Q109Q		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	109	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						gctgctgctgctgctgttgct	0.687																																					p.Q109Q		Atlas-SNP	.											.	IRF2BPL	40	.	0			c.G327A						PASS	.						2	2	2					14																	77493809		1179	2145	3324	SO:0001819	synonymous_variant	64207	exon1			CTGCTGCTGCTGT	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.327G>A	14.37:g.77493809C>T		15	0	0		13	4	0.307692	NM_024496	Q8NDQ2|Q96JG2|Q9H3I7	Silent	SNP	ENST00000238647.3	37	CCDS9854.1																																																																																			C|0.978;T|0.022	0.022	strong		0.687	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1	NM_024496		T	77493809	C	T	77493809	2	4	30	1	0	0	0	0	0	0	0	1	1775	796	28	2		2	C14orf4	14	77493809	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	3433333	77493809	29855731	475	13626											
ISM2	145501	hgsc.bcm.edu	37	chr14	77942316	77942316	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagctgcggccctggtgctcGtcctgtaggctcacagggct	5	9	14	13	2	1	0	1	0	0	0	3	0	2	0	2	4	3	5	2	4	2	1	rs3742732	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:77942316G>A	ENST00000342219.4	-	7	1394	c.1338C>T	c.(1336-1338)gaC>gaT	p.D446D	ISM2_ENST00000493585.1_3'UTR|ISM2_ENST00000393684.3_Silent_p.D358D|ISM2_ENST00000412904.1_Silent_p.D365D|ISM2_ENST00000429906.1_Silent_p.D365D	NM_199296.2	NP_954993.1	Q6H9L7	ISM2_HUMAN	isthmin 2	446	AMOP. {ECO:0000255|PROSITE- ProRule:PRU00347}.					extracellular region (GO:0005576)				endometrium(3)|large_intestine(4)|lung(11)|prostate(1)|skin(1)|urinary_tract(1)	21						CCTGGTGCTCGTCCTGTAGGC	0.652													G|||	322	0.0642971	0.0363	0.1571	5008	,	,		17437	0.0149		0.0765	False		,,,				2504	0.0746				p.D446D		Atlas-SNP	.											.	ISM2	68	.	0			c.C1338T						PASS	.	G	,	210,4196	127.8+/-164.7	6,198,1999	36	38	37		,1338	-3	0.3	14	dbSNP_107	37	775,7825	179.2+/-228.4	32,711,3557	no	utr-3,coding-synonymous	ISM2	NM_182509.3,NM_199296.2	,	38,909,5556	AA,AG,GG		9.0116,4.7662,7.5734	,	,446/572	77942316	985,12021	2203	4300	6503	SO:0001819	synonymous_variant	145501	exon7			GTGCTCGTCCTGT	AK056709	CCDS9864.1, CCDS45143.1	14q24.3	2013-05-15	2013-05-15	2008-12-23	ENSG00000100593	ENSG00000100593			23176	protein-coding gene	gene with protein product	"thrombospondin and AMOP containing isthmin-like 1"	612684	"thrombospondin, type I domain-containing 3", "thrombospondin, type I, domain containing 3", "isthmin 2 homolog (zebrafish)"	THSD3		15194193	Standard	NM_199296		Approved	FLJ32147, TAIL1	uc001xtz.3	Q6H9L7	OTTHUMG00000158563	ENST00000342219.4:c.1338C>T	14.37:g.77942316G>A		12	0	0		14	7	0.5	NM_199296	A8K6D5|O95432|Q495U5|Q68CN3|Q86TQ7|Q86TW3|Q86TW4|Q8N501|Q8NBL0	Silent	SNP	ENST00000342219.4	37	CCDS9864.1																																																																																			G|0.930;A|0.070	0.070	strong		0.652	ISM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351309.1	NM_182509		A	77942316	G	A	77942316	2	1	30	1	0	0	0	0	0	0	0	1	7870	1136	40	1		1	ISM2	14	77942316	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	448507	77942316	29407224	476	13627											
ADCK1	57143	hgsc.bcm.edu	37	chr14	78399654	78399654	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggcagatcaacctccatgagCtcatcctgcgtgtgaagggg	9	8	13	11	1	2	3	2	2	0	1	4	3	4	3	3	3	3	2	3	3	2	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:78399654C>T	ENST00000238561.5	+	11	1591	c.1492C>T	c.(1492-1494)Ctc>Ttc	p.L498F	ADCK1_ENST00000556560.1_3'UTR|ADCK1_ENST00000341211.5_Missense_Mutation_p.L430F	NM_020421.3	NP_065154.2	Q86TW2	ADCK1_HUMAN	aarF domain containing kinase 1	505						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)		CCTCCATGAGCTCATCCTGCG	0.517																																					p.L498F		Atlas-SNP	.											.	ADCK1	81	.	0			c.C1492T						PASS	.						130	122	124					14																	78399654		2203	4300	6503	SO:0001583	missense	57143	exon11			CATGAGCTCATCC	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.1492C>T	14.37:g.78399654C>T	ENSP00000238561:p.Leu498Phe	217	0	0		268	122	0.455224	NM_020421	B3KUD5|Q6PD65|Q9UIE6	Missense_Mutation	SNP	ENST00000238561.5	37	CCDS9869.1	.	.	.	.	.	.	.	.	.	.	C	8.266	0.812185	0.16537	.	.	ENSG00000063761	ENST00000238561;ENST00000341211	T;T	0.68479	-0.33;1.07	5.58	4.66	0.58398	.	0.194806	0.45126	N	0.000398	T	0.58104	0.2099	L	0.50333	1.59	0.80722	D	1	B;B;B	0.09022	0.001;0.002;0.001	B;B;B	0.12837	0.003;0.008;0.007	T	0.52555	-0.8560	10	0.23302	T	0.38	-20.9933	10.9445	0.47294	0.0:0.9076:0.0:0.0924	.	505;430;498	Q86TW2;Q9UIE6;Q86TW2-2	ADCK1_HUMAN;.;.	F	498;430	ENSP00000238561:L498F;ENSP00000339663:L430F	ENSP00000238561:L498F	L	+	1	0	ADCK1	77469407	1.000000	0.71417	0.458000	0.27068	0.072000	0.16883	2.926000	0.48892	1.298000	0.44778	0.655000	0.94253	CTC	.	.	none		0.517	ADCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413864.1	NM_020421		T	78399654	C	T	78399654	3	4	30	1	0	0	0	0	1	0	0	0	288	797	28	2	1530	2	ADCK1	14	78399654	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	457338	78399654	28949886	477	13628											
GTF2A1	2957	hgsc.bcm.edu	37	chr14	81686832	81686832	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gccaccgaaccacgtccttaCcacggtgtttgtatttgccg	7	11	9	14	4	0	0	0	0	0	0	1	1	1	0	6	1	3	2	6	1	3	4	rs201410281		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:81686832C>G	ENST00000553612.1	-	1	434		c.e1+1		GTF2A1_ENST00000434192.2_Intron	NM_001278940.1|NM_015859.3	NP_001265869.1|NP_056943.1	P52655	TF2AA_HUMAN	general transcription factor IIA, 1, 19/37kDa						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)		CACGTCCTTACCACGGTGTTT	0.577																																					.		Atlas-SNP	.											.	GTF2A1	34	.	0			c.30+1G>C						PASS	.						39	40	40					14																	81686832		2202	4293	6495	SO:0001630	splice_region_variant	2957	exon2			TCCTTACCACGGT	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.30+1G>C	14.37:g.81686832C>G		32	0	0		74	21	0.283784	NM_015859	Q3KNQ9	Splice_Site	SNP	ENST00000553612.1	37	CCDS9873.1	.	.	.	.	.	.	.	.	.	.	C	16.74	3.205504	0.58234	.	.	ENSG00000165417	ENST00000553612	.	.	.	3.35	3.35	0.38373	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.2408	0.59995	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GTF2A1	80756585	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	5.468000	0.66743	1.400000	0.46741	0.305000	0.20034	.	C|1.000;T|0.000	.	alt		0.577	GTF2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413309.1	NM_015859	Intron	G	81686832	C	G	81686832	5	3	30	1	0	0	0	0	0	0	1	0	6861	521	18	4	1135	4	GTF2A1	14	81686832	Splice_Site	SNP	C	TCGA-GR-7353-01A-11D-2210-10	3287178	81686832	25662708	478	13629											
PTPN21	11099	hgsc.bcm.edu	37	chr14	88946343	88946343	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgtaggcgtacgagctgcCgatgttgaggtttcgcagcg	6	10	16	9	5	0	1	0	1	0	0	1	3	0	1	1	2	4	7	1	2	2	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:88946343C>T	ENST00000556564.1	-	13	1716	c.1432G>A	c.(1432-1434)Ggc>Agc	p.G478S	PTPN21_ENST00000328736.3_Missense_Mutation_p.G478S	NM_007039.3	NP_008970.2	Q16825	PTN21_HUMAN	protein tyrosine phosphatase, non-receptor type 21	478					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						TACGAGCTGCCGATGTTGAGG	0.667																																					p.G478S		Atlas-SNP	.											.	PTPN21	113	.	0			c.G1432A						PASS	.						36	37	37					14																	88946343		2203	4300	6503	SO:0001583	missense	11099	exon13			AGCTGCCGATGTT	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.1432G>A	14.37:g.88946343C>T	ENSP00000452414:p.Gly478Ser	55	0	0		49	4	0.0816327	NM_007039		Missense_Mutation	SNP	ENST00000556564.1	37	CCDS9884.1	.	.	.	.	.	.	.	.	.	.	C	14.33	2.502634	0.44455	.	.	ENSG00000070778	ENST00000328736;ENST00000556564	T;T	0.72051	-0.62;-0.62	5.38	4.48	0.54585	.	0.111045	0.64402	D	0.000007	T	0.50000	0.1590	L	0.27053	0.805	0.47621	D	0.999473	P	0.41214	0.742	B	0.31946	0.138	T	0.49428	-0.8941	10	0.21014	T	0.42	.	10.7907	0.46432	0.0:0.8548:0.0:0.1452	.	478	Q16825	PTN21_HUMAN	S	478	ENSP00000330276:G478S;ENSP00000452414:G478S	ENSP00000330276:G478S	G	-	1	0	PTPN21	88016096	0.997000	0.39634	0.667000	0.29798	0.960000	0.62799	3.056000	0.49923	2.528000	0.85240	0.561000	0.74099	GGC	.	.	none		0.667	PTPN21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410303.1			T	88946343	C	T	88946343	3	4	30	1	0	0	0	0	1	0	0	0	12801	652	23	1	2120	1	PTPN21	14	88946343	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	7259511	88946343	18403197	479	13630											
TDP1	55775	hgsc.bcm.edu	37	chr14	90458308	90458308	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agacagctgaaaaacagaatTggctgcattcctattttcag	14	11	8	8	0	1	3	1	1	0	2	2	3	2	3	1	1	3	3	1	1	4	5			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:90458308T>C	ENST00000335725.4	+	13	1664	c.1414T>C	c.(1414-1416)Tgg>Cgg	p.W472R	TDP1_ENST00000357382.3_Missense_Mutation_p.W233R|TDP1_ENST00000393452.3_Missense_Mutation_p.W472R|TDP1_ENST00000555880.1_Missense_Mutation_p.W472R|TDP1_ENST00000393454.2_Missense_Mutation_p.W472R	NM_018319.3	NP_060789.2	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	472					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)		AAAACAGAATTGGCTGCATTC	0.318								Repair of DNA-protein crosslinks																													p.W472R		Atlas-SNP	.											.	TDP1	47	.	0			c.T1414C						PASS	.						120	124	123					14																	90458308		2203	4299	6502	SO:0001583	missense	55775	exon13			CAGAATTGGCTGC	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.1414T>C	14.37:g.90458308T>C	ENSP00000337353:p.Trp472Arg	80	0	0		89	15	0.168539	NM_018319	Q2HXX4|Q86TV8|Q96BK7|Q9NZM7|Q9NZM8	Missense_Mutation	SNP	ENST00000335725.4	37	CCDS9888.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.69|17.69	3.452357|3.452357	0.63290|0.63290	.|.	.|.	ENSG00000042088|ENSG00000042088	ENST00000556063|ENST00000393452;ENST00000393454;ENST00000335725;ENST00000357382;ENST00000555880	.|T;T;T;T;T	.|0.44881	.|0.91;0.91;0.91;0.91;0.91	5.94|5.94	4.76|4.76	0.60689|0.60689	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.68842|0.68842	0.3045|0.3045	M|M	0.90483|0.90483	3.12|3.12	0.80722|0.80722	D|D	1|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	.|0.998;0.998;0.999;0.99;0.999	T|T	0.73789|0.73789	-0.3872|-0.3872	5|10	.|0.66056	.|D	.|0.02	-23.862|-23.862	11.4452|11.4452	0.50118|0.50118	0.1353:0.0:0.0:0.8647|0.1353:0.0:0.0:0.8647	.|.	.|472;472;472;233;472	.|G3V2F4;E7EPD8;B2RDI0;Q86TV8;Q9NUW8	.|.;.;.;.;TYDP1_HUMAN	S|R	112|472;472;472;233;472	.|ENSP00000377098:W472R;ENSP00000377099:W472R;ENSP00000337353:W472R;ENSP00000349952:W233R;ENSP00000450628:W472R	.|ENSP00000337353:W472R	L|W	+|+	2|1	0|0	TDP1|TDP1	89528061|89528061	1.000000|1.000000	0.71417|0.71417	0.926000|0.926000	0.36857|0.36857	0.998000|0.998000	0.95712|0.95712	6.735000|6.735000	0.74806|0.74806	1.015000|1.015000	0.39444|0.39444	0.459000|0.459000	0.35465|0.35465	TTG|TGG	.	.	none		0.318	TDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411239.1	NM_018319		C	90458308	T	C	90458308	3	2	30	1	0	0	0	0	1	0	0	0	15743	1812	63	3	1456	3	TDP1	14	90458308	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	1511965	90458308	16891232	480	13631											
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102508056	102508056	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagccgctcgacctgacccaCattgtgggcacagaggtaat	10	7	11	13	2	0	2	0	1	0	1	1	3	0	2	3	2	1	3	3	2	1	2	rs10129889	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:102508056C>A	ENST00000360184.4	+	65	12251	c.12087C>A	c.(12085-12087)caC>caA	p.H4029Q	RP11-1017G21.4_ENST00000557242.1_RNA|RP11-1017G21.4_ENST00000553701.1_RNA|RP11-1017G21.4_ENST00000557551.1_RNA	NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	4029	AAA 6. {ECO:0000250}.		H -> Q (in dbSNP:rs10129889). {ECO:0000269|PubMed:9205841, ECO:0000269|Ref.4}.		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						ACCTGACCCACATTGTGGGCA	0.602													C|||	496	0.0990415	0.2784	0.0519	5008	,	,		19868	0.002		0.0696	False		,,,				2504	0.0204				p.H4029Q		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.C12087A						PASS	.	C	GLN/HIS	1199,3207	418.7+/-338.4	164,871,1168	59	61	60		12087	4.6	1	14	dbSNP_119	60	534,8066	148.8+/-204.0	20,494,3786	yes	missense	DYNC1H1	NM_001376.4	24	184,1365,4954	AA,AC,CC		6.2093,27.2129,13.3246	benign	4029/4647	102508056	1733,11273	2203	4300	6503	SO:0001583	missense	1778	exon65			GACCCACATTGTG	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.12087C>A	14.37:g.102508056C>A	ENSP00000348965:p.His4029Gln	131	0	0		143	48	0.335664	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	37	CCDS9966.1	203	0.09294871794871795	138	0.2804878048780488	20	0.055248618784530384	0	0.0	45	0.059366754617414245	C	7.360	0.624576	0.14193	0.272129	0.062093	ENSG00000197102	ENST00000360184	T	0.07908	3.15	5.61	4.59	0.56863	Dynein heavy chain (1);	0.094690	0.64402	D	0.000001	T	0.00012	0.0000	N	0.03154	-0.405	0.22112	P	0.999354976	B	0.06786	0.001	B	0.04013	0.001	T	0.48570	-0.9024	9	0.18710	T	0.47	.	8.1177	0.30953	0.0:0.7299:0.0:0.2701	rs10129889;rs17292699;rs17292706;rs17541554;rs57501843;rs10129889	4029	Q14204	DYHC1_HUMAN	Q	4029	ENSP00000348965:H4029Q	ENSP00000348965:H4029Q	H	+	3	2	DYNC1H1	101577809	0.995000	0.38212	0.984000	0.44739	0.984000	0.73092	0.450000	0.21762	1.256000	0.44068	0.655000	0.94253	CAC	C|0.882;A|0.118	0.118	strong		0.602	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		A	102508056	C	A	102508056	3	1	30	1	0	0	0	0	1	0	0	0	4843	477	17	4	12345	4	DYNC1H1	14	102508056	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	12049748	102508056	4841484	481	13632											
RCOR1	23186	hgsc.bcm.edu	37	chr14	103173756	103173756	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gctgatttgcccaactttacCcctttcccagatgagtggac	8	12	8	13	0	0	3	0	2	0	1	1	4	1	4	4	1	3	1	4	1	2	4	rs149418829	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:103173756C>A	ENST00000570597.1	+	5	558	c.558C>A	c.(556-558)acC>acA	p.T186T	RCOR1_ENST00000262241.6_Silent_p.T189T			Q9UKL0	RCOR1_HUMAN	REST corepressor 1	186	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						CCAACTTTACCCCTTTCCCAG	0.363													C|||	31	0.0061901	0.0	0.0202	5008	,	,		16191	0.0		0.0129	False		,,,				2504	0.0041				p.T189T		Atlas-SNP	.											.	RCOR1	39	.	0			c.C567A						PASS	.	C		14,4392	21.2+/-45.6	0,14,2189	134	136	136		558	3.1	1	14	dbSNP_134	136	96,8504	53.1+/-113.8	0,96,4204	no	coding-synonymous	RCOR1	NM_015156.3		0,110,6393	AA,AC,CC		1.1163,0.3177,0.8458		186/483	103173756	110,12896	2203	4300	6503	SO:0001819	synonymous_variant	23186	exon5			CTTTACCCCTTTC	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.558C>A	14.37:g.103173756C>A		161	0	0		162	51	0.314815	NM_015156	Q15044|Q6P2I9|Q86VG5	Silent	SNP	ENST00000570597.1	37																																																																																				C|0.990;A|0.010	0.010	strong		0.363	RCOR1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015156		A	103173756	C	A	103173756	2	1	30	1	0	0	0	0	0	0	0	1	13197	610	22	4		4	RCOR1	14	103173756	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	665700	103173756	4175784	482	13633											
TRAF3	7187	hgsc.bcm.edu	37	chr14	103336727	103336727	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cacctggtgctgtgcagcccGaagcagaccgagtgtgggca	8	6	15	12	2	0	1	0	0	0	1	0	3	0	1	3	2	4	4	3	2	1	0	rs142350527	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:103336727G>A	ENST00000560371.1	+	2	406	c.189G>A	c.(187-189)ccG>ccA	p.P63P	TRAF3_ENST00000392745.2_Silent_p.P63P|TRAF3_ENST00000539721.1_Silent_p.P63P|TRAF3_ENST00000347662.4_Silent_p.P63P|TRAF3_ENST00000351691.5_Silent_p.P63P	NM_003300.3|NM_145725.2	NP_003291.2|NP_663777.1	Q13114	TRAF3_HUMAN	TNF receptor-associated factor 3	63					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)		TGTGCAGCCCGAAGCAGACCG	0.617													G|||	23	0.00459265	0.0	0.0159	5008	,	,		16014	0.0		0.0119	False		,,,				2504	0.0				p.P63P		Atlas-SNP	.											.	TRAF3	60	.	0			c.G189A						PASS	.	G	,,,	8,4398	14.3+/-33.2	0,8,2195	76	65	68		189,189,189,189	-10.9	0.4	14	dbSNP_134	68	28,8572	19.8+/-62.0	0,28,4272	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRAF3	NM_001199427.1,NM_003300.3,NM_145725.2,NM_145726.2	,,,	0,36,6467	AA,AG,GG		0.3256,0.1816,0.2768	,,,	63/486,63/569,63/569,63/544	103336727	36,12970	2203	4300	6503	SO:0001819	synonymous_variant	7187	exon3			CAGCCCGAAGCAG	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.189G>A	14.37:g.103336727G>A		82	0	0		93	37	0.397849	NM_145726	B7Z8C4|Q12990|Q13076|Q13947|Q6AZX1|Q9UNL1	Silent	SNP	ENST00000560371.1	37	CCDS9975.1																																																																																			G|0.996;A|0.004	0.004	strong		0.617	TRAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415735.1	NM_145725		A	103336727	G	A	103336727	2	1	30	1	0	0	0	0	0	0	0	1	16454	1045	37	1		1	TRAF3	14	103336727	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	162971	103336727	4012813	483	13634											
KLC1	3831	hgsc.bcm.edu	37	chr14	104143806	104143806	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcactttacagacgtcaaggCaaatttgaagctgcagaaac	15	8	9	9	1	1	3	1	1	0	2	1	3	1	3	0	1	4	4	0	1	5	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:104143806C>T	ENST00000348520.6	+	12	1753	c.1434C>T	c.(1432-1434)ggC>ggT	p.G478G	KLC1_ENST00000452929.2_Silent_p.G478G|KLC1_ENST00000553286.1_Silent_p.G478G|KLC1_ENST00000380038.3_Silent_p.G478G|RP11-73M18.2_ENST00000472726.2_Silent_p.G650G|KLC1_ENST00000347839.6_Silent_p.G478G|KLC1_ENST00000554280.1_Silent_p.G478G|KLC1_ENST00000557575.1_Silent_p.G478G|KLC1_ENST00000555836.1_Silent_p.G478G|KLC1_ENST00000445352.4_Silent_p.G476G|KLC1_ENST00000557450.1_Silent_p.G478G|KLC1_ENST00000246489.7_Silent_p.G478G|KLC1_ENST00000334553.6_Silent_p.G478G|KLC1_ENST00000389744.4_Silent_p.G478G	NM_182923.3	NP_891553.2	Q07866	KLC1_HUMAN	kinesin light chain 1	478					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)				GACGTCAAGGCAAATTTGAAG	0.418																																					p.G478G		Atlas-SNP	.											.	KLC1	54	.	0			c.C1434T						PASS	.						145	141	143					14																	104143806		2203	4300	6503	SO:0001819	synonymous_variant	3831	exon12			TCAAGGCAAATTT	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.1434C>T	14.37:g.104143806C>T		98	0	0		126	35	0.277778	NM_182923	A6NF62|F8VTM4|Q7RTM2|Q7RTM3|Q7RTM5|Q7RTP9|Q7RTQ3|Q7RTQ5|Q7RTQ6|Q86SF5|Q86TF5|Q86V74|Q86V75|Q86V76|Q86V77|Q86V78|Q86V79|Q96H62	Silent	SNP	ENST00000348520.6	37	CCDS41996.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.60|10.60	1.396952|1.396952	0.25205|0.25205	.|.	.|.	ENSG00000126214|ENSG00000126214	ENST00000553325;ENST00000553436;ENST00000555856|ENST00000537046	.|.	.|.	.|.	5.52|5.52	2.56|2.56	0.30785|0.30785	.|.	.|.	.|.	.|.	.|.	T|.	0.72350|.	0.3449|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.71869|.	-0.4462|.	4|.	.|.	.|.	.|.	-15.9577|-15.9577	17.9404|17.9404	0.89025|0.89025	0.0:0.7802:0.2198:0.0|0.0:0.7802:0.2198:0.0	.|.	.|.	.|.	.|.	V|X	58;54;52|84	.|.	.|.	A|Q	+|+	2|1	0|0	KLC1|KLC1	103213559|103213559	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.964000|0.964000	0.63967|0.63967	1.666000|1.666000	0.37460|0.37460	0.313000|0.313000	0.23062|0.23062	0.655000|0.655000	0.94253|0.94253	GCA|CAA	.	.	none		0.418	KLC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402947.2	NM_005552		T	104143806	C	T	104143806	2	4	30	1	0	0	0	0	0	0	0	1	8342	697	25	2		2	KLC1	14	104143806	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	807079	104143806	3205734	484	13635											
XRCC3	7517	hgsc.bcm.edu	37	chr14	104174950	104174950	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggttggtcagtctcttcaaGtctggtccagaaaagtgtaa	11	12	11	7	0	4	1	2	0	2	1	6	1	5	1	1	3	0	2	1	3	4	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:104174950G>T	ENST00000553264.1	-	3	898	c.102C>A	c.(100-102)gaC>gaA	p.D34E	XRCC3_ENST00000554974.1_Intron|XRCC3_ENST00000352127.7_Missense_Mutation_p.D34E|XRCC3_ENST00000555055.1_Missense_Mutation_p.D34E|XRCC3_ENST00000554913.1_Missense_Mutation_p.D34E|AL049840.1_ENST00000429169.1_5'Flank|XRCC3_ENST00000445556.1_Missense_Mutation_p.D34E			O43542	XRCC3_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 3	34					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|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)|response to organic substance (GO:0010033)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Rad51C-XRCC3 complex (GO:0033065)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)			endometrium(1)|large_intestine(1)|ovary(1)|prostate(1)	4		Melanoma(154;0.155)|all_epithelial(191;0.19)		Epithelial(152;0.239)		GTCTCTTCAAGTCTGGTCCAG	0.498								Direct reversal of damage;Homologous recombination																													p.D34E		Atlas-SNP	.											.	XRCC3	16	.	0			c.C102A						PASS	.						119	104	109					14																	104174950		2203	4300	6503	SO:0001583	missense	7517	exon5			CTTCAAGTCTGGT	AF035586	CCDS9984.1	14q32.3	2006-05-04				ENSG00000126215			12830	protein-coding gene	gene with protein product	"RAD51-like"	600675				7603995	Standard	NM_001100118		Approved		uc001ynz.4	O43542		ENST00000553264.1:c.102C>A	14.37:g.104174950G>T	ENSP00000451974:p.Asp34Glu	83	0	0		144	46	0.319444	NM_005432	O43568|Q9BU18	Missense_Mutation	SNP	ENST00000553264.1	37	CCDS9984.1	.	.	.	.	.	.	.	.	.	.	G	7.232	0.599455	0.13939	.	.	ENSG00000126215	ENST00000554913;ENST00000352127;ENST00000553264;ENST00000555055;ENST00000445556;ENST00000553361;ENST00000556980;ENST00000555964;ENST00000556682;ENST00000553332;ENST00000554170	T;T;T;T;T;T;T;T	0.60299	1.06;1.06;1.06;1.06;1.06;0.2;0.68;0.59	5.44	-0.127	0.13510	.	0.095213	0.64402	D	0.000001	T	0.35038	0.0918	L	0.45228	1.405	0.23754	N	0.996937	P	0.39535	0.677	B	0.31686	0.134	T	0.36335	-0.9752	10	0.10377	T	0.69	-0.0139	6.7499	0.23482	0.4232:0.0:0.4621:0.1147	.	34	O43542	XRCC3_HUMAN	E	34	ENSP00000451362:D34E;ENSP00000343392:D34E;ENSP00000451974:D34E;ENSP00000452598:D34E;ENSP00000412990:D34E;ENSP00000451118:D34E;ENSP00000451252:D34E;ENSP00000451173:D34E	ENSP00000343392:D34E	D	-	3	2	XRCC3	103244703	0.756000	0.28383	0.283000	0.24790	0.039000	0.13416	0.177000	0.16801	0.039000	0.15632	-0.918000	0.02743	GAC	.	.	none		0.498	XRCC3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414631.1	NM_005432		T	104174950	G	T	104174950	3	4	30	1	0	0	0	0	1	0	0	0	17469	1020	36	4	962	4	XRCC3	14	104174950	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	31144	104174950	3174590	485	13636											
INF2	64423	hgsc.bcm.edu	37	chr14	105179184	105179184	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggccagcatctcggccttccGggcactggatgagctgtttg	5	10	14	12	2	1	1	0	1	1	0	3	2	2	2	3	4	2	4	3	4	0	2	rs142678449	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105179184G>A	ENST00000392634.4	+	18	2742	c.2630G>A	c.(2629-2631)cGg>cAg	p.R877Q	INF2_ENST00000330634.7_Missense_Mutation_p.R877Q	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	inverted formin, FH2 and WH2 domain containing	877	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)		TCGGCCTTCCGGGCACTGGAT	0.677													G|||	28	0.00559105	0.0023	0.013	5008	,	,		17221	0.0		0.0089	False		,,,				2504	0.0072				p.R877Q		Atlas-SNP	.											.	INF2	148	.	0			c.G2630A						PASS	.	G	GLN/ARG,GLN/ARG	6,4024		0,6,2009	24	28	27		2630,2630	-4.1	0	14	dbSNP_134	27	89,8255		2,85,4085	yes	missense,missense	INF2	NM_022489.3,NM_001031714.3	43,43	2,91,6094	AA,AG,GG		1.0666,0.1489,0.7677	benign,benign	877/1250,877/1241	105179184	95,12279	2015	4172	6187	SO:0001583	missense	64423	exon18			CCTTCCGGGCACT	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.2630G>A	14.37:g.105179184G>A	ENSP00000376410:p.Arg877Gln	121	0	0		145	50	0.344828	NM_022489	Q27J83|Q69YL8|Q6P1X7|Q6PK22|Q86TR7|Q9BRM1|Q9H6N1	Missense_Mutation	SNP	ENST00000392634.4	37	CCDS9989.2	16	0.007326007326007326	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	6	0.0079155672823219	G	13.65	2.300727	0.40694	0.001489	0.010666	ENSG00000203485	ENST00000330634;ENST00000392634	T;T	0.17213	2.29;2.29	5.06	-4.11	0.03928	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	1.264760	0.05384	N	0.537746	T	0.05731	0.0150	L	0.27053	0.805	0.09310	N	1	B;B	0.24882	0.093;0.113	B;B	0.17722	0.008;0.019	T	0.31308	-0.9948	10	0.17369	T	0.5	.	14.103	0.65070	0.6837:0.0:0.3163:0.0	.	877;877	Q27J81-2;Q27J81	.;INF2_HUMAN	Q	877	ENSP00000376406:R877Q;ENSP00000376410:R877Q	ENSP00000252527:R345Q	R	+	2	0	INF2	104250229	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.660000	0.05317	-1.495000	0.01831	0.561000	0.74099	CGG	G|0.992;A|0.008	0.008	strong		0.677	INF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074371.4	NM_022489		A	105179184	G	A	105179184	3	1	30	1	0	0	0	0	1	0	0	0	7743	1116	39	1	2700	1	INF2	14	105179184	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1004234	105179184	2170356	486	13637											
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105411619	105411619	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatctccaccttgggcaggTgccctttgaggccagctccc	5	9	11	16	0	1	1	0	1	1	0	3	1	2	1	5	3	2	3	5	3	0	2	rs200461684		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105411619T>C	ENST00000333244.5	-	7	10288	c.10169A>G	c.(10168-10170)cAc>cGc	p.H3390R	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3390						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)			CTTGGGCAGGTGCCCTTTGAG	0.627													.|||	1	0.000199681	0.0	0.0	5008	,	,		17915	0.0		0.001	False		,,,				2504	0.0				p.H3390R		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A10169G						PASS	.	T	ARG/HIS	1,3791		0,1,1895	149	161	157		10169	4.2	0.8	14		157	10,8194		0,10,4092	no	missense	AHNAK2	NM_138420.2	29	0,11,5987	CC,CT,TT		0.1219,0.0264,0.0917	probably-damaging	3390/5796	105411619	11,11985	1896	4102	5998	SO:0001583	missense	113146	exon7			GGCAGGTGCCCTT	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.10169A>G	14.37:g.105411619T>C	ENSP00000353114:p.His3390Arg	156	0	0		246	96	0.390244	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	t	2.101	-0.406153	0.04832	2.64E-4	0.001219	ENSG00000185567	ENST00000333244	T	0.01902	4.57	4.22	4.22	0.49857	.	.	.	.	.	T	0.07007	0.0178	M	0.82923	2.615	0.09310	N	1	D	0.59357	0.985	P	0.52109	0.69	T	0.24977	-1.0145	9	0.17832	T	0.49	.	8.3292	0.32175	0.0:0.0:0.2686:0.7314	.	3390	Q8IVF2	AHNK2_HUMAN	R	3390	ENSP00000353114:H3390R	ENSP00000353114:H3390R	H	-	2	0	AHNAK2	104482664	0.865000	0.29922	0.833000	0.33012	0.077000	0.17291	3.174000	0.50847	1.792000	0.52537	0.402000	0.26972	CAC	T|0.999;C|0.001	0.001	weak		0.627	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		C	105411619	T	C	105411619	3	2	30	1	0	0	0	0	1	0	0	0	415	1696	59	3	7222	3	AHNAK2	14	105411619	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	232435	105411619	1937921	487	13638											
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105413220	105413220	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgcggatgtcagtggtcttAagatccccttgcatggaggg	8	11	14	8	1	2	1	1	0	1	1	3	3	3	3	2	4	2	1	2	4	1	2	rs151173659	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105413220A>C	ENST00000333244.5	-	7	8687	c.8568T>G	c.(8566-8568)ctT>ctG	p.L2856L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2856						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)			CAGTGGTCTTAAGATCCCCTT	0.637													.|||	57	0.0113818	0.0386	0.0029	5008	,	,		17917	0.0		0.0	False		,,,				2504	0.0041				p.L2856L		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T8568G						PASS	.	G		157,3765		7,143,1811	126	144	138		8568	0	0	14	dbSNP_134	138	6,8298		0,6,4146	no	coding-synonymous	AHNAK2	NM_138420.2		7,149,5957	CC,CA,AA		0.0723,4.0031,1.3332		2856/5796	105413220	163,12063	1961	4152	6113	SO:0001819	synonymous_variant	113146	exon7			GGTCTTAAGATCC	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.8568T>G	14.37:g.105413220A>C		205	1	0.00487805		249	167	0.670683	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.994;C|0.006	0.006	strong		0.637	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		C	105413220	A	C	105413220	2	2	30	1	0	0	0	0	0	0	0	1	415	349	13	5		5	AHNAK2	14	105413220	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	1601	105413220	1936320	488	13639											
AHNAK2	113146	hgsc.bcm.edu	37	chr14	105413649	105413649	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggccctctgggagtttcacAtccacctggccagcctggac	6	9	11	15	0	2	0	1	0	1	0	3	2	3	2	5	4	1	1	5	4	0	1	rs201545349	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105413649A>G	ENST00000333244.5	-	7	8258	c.8139T>C	c.(8137-8139)gaT>gaC	p.D2713D	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2713						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)			GGAGTTTCACATCCACCTGGC	0.612													.|||	29	0.00579073	0.0174	0.0	5008	,	,		17337	0.0		0.0	False		,,,				2504	0.0061				p.D2713D		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,-2,1	AHNAK2	719	1	0			c.T8139C						scavenged	.						130	144	139					14																	105413649		1936	4121	6057	SO:0001819	synonymous_variant	113146	exon7			TTTCACATCCACC	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.8139T>C	14.37:g.105413649A>G		239	2	0.0083682		281	13	0.0462633	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.998;G|0.002	0.002	weak		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420		G	105413649	A	G	105413649	2	3	30	1	0	0	0	0	0	0	0	1	415	214	8	3		3	AHNAK2	14	105413649	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	429	105413649	1935891	489	13640											
C14orf79	122616	hgsc.bcm.edu	37	chr14	105457923	105457923	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcccgttgccaggagaactTctttcttgttctcggaatag	7	14	10	10	2	3	1	0	0	3	1	5	3	4	2	2	2	2	2	2	2	3	6	rs61745867	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr14:105457923T>A	ENST00000547315.1	+	3	1304	c.665T>A	c.(664-666)tTc>tAc	p.F222Y	C14orf79_ENST00000549584.1_3'UTR|C14orf79_ENST00000550614.1_5'UTR|C14orf79_ENST00000549240.1_5'UTR	NM_174891.3	NP_777551.2	Q96F83	CN079_HUMAN	chromosome 14 open reading frame 79	222										breast(1)|endometrium(1)|lung(1)	3		all_cancers(154;0.0798)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.00326)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0181)			CAGGAGAACTTCTTTCTTGTT	0.542													T|||	24	0.00479233	0.0015	0.0072	5008	,	,		18114	0.0		0.0099	False		,,,				2504	0.0072				p.F222Y		Atlas-SNP	.											.	C14orf79	13	.	0			c.T665A						PASS	.	T	TYR/PHE	9,3843		0,9,1917	132	123	126		665	2.4	0	14	dbSNP_129	126	169,8123		4,161,3981	yes	missense	C14orf79	NM_174891.3	22	4,170,5898	AA,AT,TT		2.0381,0.2336,1.4657	benign	222/326	105457923	178,11966	1926	4146	6072	SO:0001583	missense	122616	exon3			AGAACTTCTTTCT		CCDS42000.1	14q32.33	2012-09-25			ENSG00000140104	ENSG00000140104			20126	protein-coding gene	gene with protein product							Standard	NM_174891		Approved		uc001ypy.1	Q96F83	OTTHUMG00000170474	ENST00000547315.1:c.665T>A	14.37:g.105457923T>A	ENSP00000450114:p.Phe222Tyr	116	0	0		159	69	0.433962	NM_174891	B2RPK9|Q9BTP4	Missense_Mutation	SNP	ENST00000547315.1	37	CCDS42000.1	11|11	0.005036630036630037|0.005036630036630037	1|1	0.0020325203252032522|0.0020325203252032522	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	8|8	0.010554089709762533|0.010554089709762533	T|T	3.056|3.056	-0.194267|-0.194267	0.06259|0.06259	0.002336|0.002336	0.020381|0.020381	ENSG00000140104|ENSG00000140104	ENST00000547315|ENST00000551606	.|.	.|.	.|.	3.62|3.62	2.43|2.43	0.29744|0.29744	.|.	1.254200|.	0.06177|.	N|.	0.678664|.	T|T	0.21103|0.21103	0.0508|0.0508	N|N	0.19112|0.19112	0.55|0.55	0.39067|0.39067	D|D	0.960632|0.960632	B|.	0.14805|.	0.011|.	B|.	0.08055|.	0.003|.	T|T	0.05241|0.05241	-1.0897|-1.0897	9|5	0.29301|.	T|.	0.29|.	-3.7825|-3.7825	6.0924|6.0924	0.20001|0.20001	0.2279:0.0:0.0:0.7721|0.2279:0.0:0.0:0.7721	rs61745867|rs61745867	222|.	Q96F83|.	CN079_HUMAN|.	Y|T	222|116	.|.	ENSP00000450114:F222Y|.	F|S	+|+	2|1	0|0	C14orf79|C14orf79	104528968|104528968	0.021000|0.021000	0.18746|0.18746	0.010000|0.010000	0.14722|0.14722	0.012000|0.012000	0.07955|0.07955	2.128000|2.128000	0.42045|0.42045	0.298000|0.298000	0.22638|0.22638	0.378000|0.378000	0.23410|0.23410	TTC|TCT	T|0.990;A|0.010	0.010	strong		0.542	C14orf79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409318.1	NM_174891		A	105457923	T	A	105457923	3	1	30	1	0	0	0	0	1	0	0	0	1782	1783	62	5	675	5	C14orf79	14	105457923	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	44274	105457923	1891617	490	13641											
HERC2	8924	hgsc.bcm.edu	37	chr15	28459393	28459393	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcagcgaggcctgcgggcgCaccctgcgccgcctcagcgt	4	5	15	17	6	2	0	2	0	0	0	2	1	2	0	4	2	4	1	4	2	0	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:28459393C>T	ENST00000261609.7	-	41	6492	c.6384G>A	c.(6382-6384)gtG>gtA	p.V2128V		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)		CCTGCGGGCGCACCCTGCGCC	0.672																																					p.V2128V		Atlas-SNP	.											.	HERC2	501	.	0			c.G6384A						PASS	.						24	25	25					15																	28459393		2195	4293	6488	SO:0001819	synonymous_variant	8924	exon41			CGGGCGCACCCTG	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.6384G>A	15.37:g.28459393C>T		82	0	0		53	45	0.849057	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			.	.	none		0.672	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667		T	28459393	C	T	28459393	2	4	30	1	0	0	0	0	0	0	0	1	7067	697	25	2		2	HERC2	15	28459393	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10		28459393	74071999	491	13642											
APBA2	321	hgsc.bcm.edu	37	chr15	29368269	29368269	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcctaacagacaaagaaggtGgcatcatttccaagttttgt	13	12	8	8	0	1	2	1	0	0	2	3	2	3	2	2	2	1	2	2	2	4	4	rs149285403	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:29368269G>A	ENST00000558402.1	+	7	1643	c.1044G>A	c.(1042-1044)gtG>gtA	p.V348V	APBA2_ENST00000561069.1_Silent_p.V348V|APBA2_ENST00000411764.1_Silent_p.V348V|APBA2_ENST00000558259.1_Silent_p.V348V|APBA2_ENST00000558330.1_Silent_p.V348V			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	348					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)		CAAAGAAGGTGGCATCATTTC	0.378																																					p.V348V		Atlas-SNP	.											.	APBA2	132	.	0			c.G1044A						PASS	.	G	,	2,4404	4.2+/-10.8	0,2,2201	185	185	185		1044,1044	3.9	1	15	dbSNP_134	185	18,8582	13.3+/-46.6	0,18,4282	no	coding-synonymous,coding-synonymous	APBA2	NM_001130414.1,NM_005503.3	,	0,20,6483	AA,AG,GG		0.2093,0.0454,0.1538	,	348/738,348/750	29368269	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	321	exon5			GAAGGTGGCATCA	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.1044G>A	15.37:g.29368269G>A		138	0	0		95	76	0.8	NM_005503	E9PGI4|O60571|Q5XKC0	Silent	SNP	ENST00000558402.1	37	CCDS10022.1																																																																																			G|0.999;A|0.001	0.001	strong		0.378	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503		A	29368269	G	A	29368269	2	1	30	1	0	0	0	0	0	0	0	1	757	1335	47	2		2	APBA2	15	29368269	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	908876	29368269	73163123	492	13643											
TJP1	7082	hgsc.bcm.edu	37	chr15	30026582	30026582	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatttgtaaaatctacgttgTttacctaataaataagattt	15	18	4	4	1	1	1	0	0	1	1	1	1	1	1	1	0	2	3	1	0	9	11	rs2229517	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:30026582T>C	ENST00000346128.6	-	12	1886	c.1412A>G	c.(1411-1413)aAc>aGc	p.N471S	TJP1_ENST00000400011.2_Missense_Mutation_p.N475S|TJP1_ENST00000356107.6_Missense_Mutation_p.N471S|TJP1_ENST00000545208.2_Missense_Mutation_p.N471S	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	471	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.		N -> S (in dbSNP:rs2229517). {ECO:0000269|Ref.3}.		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)		ATCTACGTTGTTTACCTAATA	0.348													T|||	24	0.00479233	0.003	0.0014	5008	,	,		17609	0.0		0.0109	False		,,,				2504	0.0082				p.N471S	Melanoma(77;681 1843 6309 6570)	Atlas-SNP	.											.	TJP1	140	.	0			c.A1412G						PASS	.	T	SER/ASN,SER/ASN	7,3635		0,7,1814	99	89	92		1412,1412	5.4	1	15	dbSNP_98	92	108,8050		0,108,3971	yes	missense,missense	TJP1	NM_003257.3,NM_175610.2	46,46	0,115,5785	CC,CT,TT		1.3239,0.1922,0.9746	benign,benign	471/1749,471/1669	30026582	115,11685	1821	4079	5900	SO:0001583	missense	7082	exon12			ACGTTGTTTACCT		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.1412A>G	15.37:g.30026582T>C	ENSP00000281537:p.Asn471Ser	135	0	0		61	43	0.704918	NM_175610	B4E3K1|Q2NKP3|Q4ZGJ6	Missense_Mutation	SNP	ENST00000346128.6	37	CCDS42007.1	16	0.007326007326007326	3	0.006097560975609756	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	T	16.63	3.176786	0.57692	0.001922	0.013239	ENSG00000104067	ENST00000346128;ENST00000400011;ENST00000545208;ENST00000400007;ENST00000356107	T;T;T;T	0.59224	0.28;0.28;0.28;0.28	5.36	5.36	0.76844	Src homology-3 domain (1);PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.72550	0.3474	M	0.85945	2.785	0.80722	D	1	B;D;B;D	0.89917	0.009;1.0;0.009;0.998	B;D;B;D	0.87578	0.04;0.998;0.04;0.994	T	0.79434	-0.1805	9	.	.	.	.	15.6385	0.76977	0.0:0.0:0.0:1.0	rs2229517;rs45612033	464;471;471;475	A9CQZ8;Q07157-2;Q07157;G5E9E7	.;.;ZO1_HUMAN;.	S	471;475;471;471;471	ENSP00000281537:N471S;ENSP00000382890:N475S;ENSP00000441202:N471S;ENSP00000348416:N471S	.	N	-	2	0	TJP1	27813874	1.000000	0.71417	1.000000	0.80357	0.762000	0.43233	7.997000	0.88414	2.147000	0.66899	0.477000	0.44152	AAC	T|0.991;C|0.009	0.009	strong		0.348	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		C	30026582	T	C	30026582	3	2	30	1	0	0	0	0	1	0	0	0	15944	1725	60	3	3902	3	TJP1	15	30026582	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	658313	30026582	72504810	493	13644											
C15orf41	84529	hgsc.bcm.edu	37	chr15	36989578	36989578	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gacttgcttctagagaaaaaCctgtccttcctaggtaagta	12	12	8	9	0	1	1	0	0	1	1	3	3	3	1	3	1	2	3	3	1	6	7	rs117638434	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:36989578C>T	ENST00000566621.1	+	8	781	c.531C>T	c.(529-531)aaC>aaT	p.N177N	C15orf41_ENST00000567389.1_Silent_p.N79N|C15orf41_ENST00000437989.2_Silent_p.N177N|C15orf41_ENST00000565792.1_3'UTR|C15orf41_ENST00000562877.1_Silent_p.N79N|C15orf41_ENST00000338183.4_Silent_p.N79N|C15orf41_ENST00000569302.1_Silent_p.N177N	NM_001130010.1	NP_001123482.1	Q9Y2V0	CO041_HUMAN	chromosome 15 open reading frame 41	177										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)		TAGAGAAAAACCTGTCCTTCC	0.408													C|||	22	0.00439297	0.0	0.0014	5008	,	,		15677	0.0		0.0209	False		,,,				2504	0.0				p.N177N		Atlas-SNP	.											.	C15orf41	24	.	0			c.C531T						PASS	.	C	,	17,3791		0,17,1887	183	184	184		531,237	-0.8	1	15	dbSNP_132	184	99,8177		1,97,4040	no	coding-synonymous,coding-synonymous	C15orf41	NM_001130010.1,NM_032499.4	,	1,114,5927	TT,TC,CC		1.1962,0.4464,0.9599	,	177/282,79/184	36989578	116,11968	1904	4138	6042	SO:0001819	synonymous_variant	84529	exon8			GAAAAACCTGTCC	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.531C>T	15.37:g.36989578C>T		196	0	0		110	84	0.763636	NM_001130010	B2RD87	Silent	SNP	ENST00000566621.1	37	CCDS45215.1																																																																																			C|0.992;T|0.008	0.008	strong		0.408	C15orf41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419741.1	NM_032499		T	36989578	C	T	36989578	2	4	30	1	0	0	0	0	0	0	0	1	1797	506	18	2		2	C15orf41	15	36989578	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	6962996	36989578	65541814	494	13645											
THBS1	7057	hgsc.bcm.edu	37	chr15	39880818	39880818	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cgtagtcgtctctgcaacaaCcccacaccccagtttggagg	9	8	9	15	2	1	0	0	0	1	0	3	1	1	1	4	2	3	3	4	2	3	2	rs41338344	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:39880818C>T	ENST00000260356.5	+	10	1728	c.1563C>T	c.(1561-1563)aaC>aaT	p.N521N		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	521	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				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)		TCTGCAACAACCCCACACCCC	0.537													C|||	64	0.0127796	0.003	0.0274	5008	,	,		20155	0.0		0.0318	False		,,,				2504	0.0092				p.N521N		Atlas-SNP	.											.	THBS1	106	.	0			c.C1563T						PASS	.	C		34,4366	39.2+/-71.8	0,34,2166	94	89	91		1563	4.8	1	15	dbSNP_127	91	301,8293	109.6+/-170.1	4,293,4000	no	coding-synonymous	THBS1	NM_003246.2		4,327,6166	TT,TC,CC		3.5024,0.7727,2.5781		521/1171	39880818	335,12659	2200	4297	6497	SO:0001819	synonymous_variant	7057	exon10			CAACAACCCCACA		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.1563C>T	15.37:g.39880818C>T		80	0	0		54	15	0.277778	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	37	CCDS32194.1																																																																																			C|0.975;T|0.025	0.025	strong		0.537	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246		T	39880818	C	T	39880818	2	4	30	1	0	0	0	0	0	0	0	1	15868	506	18	2		2	THBS1	15	39880818	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	2891240	39880818	62650574	495	13646											
C15orf52	388115	hgsc.bcm.edu	37	chr15	40629995	40629995	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtctctgtgccgggcgaggcGggctaggtcgatctgctccc	3	9	16	13	4	2	0	0	0	2	0	5	2	3	0	2	4	2	2	2	4	1	1	rs149438052	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:40629995G>A	ENST00000559313.1	-	6	760	c.745C>T	c.(745-747)Cgc>Tgc	p.R249C	C15orf52_ENST00000557973.1_5'Flank|C15orf52_ENST00000397536.2_Missense_Mutation_p.R39C	NM_207380.2	NP_997263.2	Q6ZUT6	CO052_HUMAN	chromosome 15 open reading frame 52	249							poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	19		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;9.06e-06)|Colorectal(105;0.0107)|BRCA - Breast invasive adenocarcinoma(123;0.0505)|READ - Rectum adenocarcinoma(2;0.0649)|Lung(196;0.0781)|LUAD - Lung adenocarcinoma(183;0.0841)		CGGGCGAGGCGGGCTAGGTCG	0.711																																					p.R249C		Atlas-SNP	.											.	C15orf52	47	.	0			c.C745T						PASS	.						23	24	24					15																	40629995		2202	4298	6500	SO:0001583	missense	388115	exon6			CGAGGCGGGCTAG	AK124643	CCDS10055.2	15q15.1	2007-06-14			ENSG00000188549	ENSG00000188549			33488	protein-coding gene	gene with protein product							Standard	NM_207380		Approved	FLJ43339	uc001zlh.4	Q6ZUT6	OTTHUMG00000129981	ENST00000559313.1:c.745C>T	15.37:g.40629995G>A	ENSP00000453969:p.Arg249Cys	93	0	0		48	18	0.375	NM_207380	B9EIQ8|Q68DG9|Q6ZTM3|Q6ZU22	Missense_Mutation	SNP	ENST00000559313.1	37	CCDS10055.2	.	.	.	.	.	.	.	.	.	.	G	26.7	4.764787	0.90020	.	.	ENSG00000188549	ENST00000382688;ENST00000397536;ENST00000397535	T	0.72942	-0.7	4.63	4.63	0.57726	.	0.092822	0.45867	D	0.000338	D	0.82637	0.5080	M	0.74258	2.255	0.58432	D	0.999992	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	D	0.84930	0.0859	10	0.87932	D	0	-13.7074	12.996	0.58646	0.0:0.0:1.0:0.0	.	39;181;249	Q6ZUT6-2;Q6ZUT6-3;Q6ZUT6	.;.;CO052_HUMAN	C	249;39;181	ENSP00000380670:R39C	ENSP00000372135:R249C	R	-	1	0	C15orf52	38417287	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.805000	0.38883	2.097000	0.63578	0.563000	0.77884	CGC	A|0.001;G|0.999	0.001	strong		0.711	C15orf52-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319567.2	NM_207380		A	40629995	G	A	40629995	3	1	30	1	0	0	0	0	1	0	0	0	1802	1116	39	1	883	1	C15orf52	15	40629995	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	749177	40629995	61901397	496	13647											
CAPN3	825	hgsc.bcm.edu	37	chr15	42702836	42702836	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tccggcaccatcaacagctaCgagatgcgaaatgcagtcaa	14	6	9	12	3	2	1	2	0	0	1	3	3	3	1	2	1	5	3	2	1	4	1	rs147774793	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:42702836C>T	ENST00000397163.3	+	21	2454	c.2235C>T	c.(2233-2235)taC>taT	p.Y745Y	CAPN3_ENST00000561817.1_Silent_p.Y80Y|CAPN3_ENST00000349748.3_Silent_p.Y653Y|CAPN3_ENST00000562199.1_3'UTR|CAPN3_ENST00000397204.4_Silent_p.Y80Y|CAPN3_ENST00000569136.1_Silent_p.Y80Y|CAPN3_ENST00000357568.3_Silent_p.Y739Y|RP11-164J13.1_ENST00000495723.1_RNA|CAPN3_ENST00000337571.4_Silent_p.Y80Y|CAPN3_ENST00000356316.3_Silent_p.Y652Y|CAPN3_ENST00000397200.4_Silent_p.Y233Y|CAPN3_ENST00000318023.7_Silent_p.Y739Y	NM_000070.2	NP_000061.1	P20807	CAN3_HUMAN	calpain 3, (p94)	745	Domain IV.|EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				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)		TCAACAGCTACGAGATGCGAA	0.517																																					p.Y745Y		Atlas-SNP	.											.	CAPN3	172	.	0			c.C2235T	GRCh37	CM051887	CAPN3	M	rs147774793	PASS	.	C	,,,,,	2,4404	4.2+/-10.8	0,2,2201	65	59	61		2235,2217,1959,699,240,240	-3.8	1	15	dbSNP_134	61	9,8589	7.1+/-27.0	0,9,4290	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CAPN3	NM_000070.2,NM_024344.1,NM_173087.1,NM_173088.1,NM_173089.1,NM_173090.1	,,,,,	0,11,6491	TT,TC,CC		0.1047,0.0454,0.0846	,,,,,	745/822,739/816,653/730,233/310,80/157,80/157	42702836	11,12993	2203	4299	6502	SO:0001819	synonymous_variant	825	exon21			CAGCTACGAGATG	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.2235C>T	15.37:g.42702836C>T		116	0	0		89	20	0.224719	NM_000070	A6H8K6|Q7L4R0|Q9BQC8|Q9BTU4|Q9Y5S6|Q9Y5S7	Silent	SNP	ENST00000397163.3	37	CCDS45245.1																																																																																			C|0.999;T|0.001	0.001	strong		0.517	CAPN3-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421075.1			T	42702836	C	T	42702836	2	4	30	1	0	0	0	0	0	0	0	1	2630	547	19	1		1	CAPN3	15	42702836	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	2072841	42702836	59828556	497	13648											
GNB5	10681	hgsc.bcm.edu	37	chr15	52433397	52433397	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggtgtgcatagcaacagaCttctttttggcagccatgtt	8	15	10	8	0	1	1	0	0	1	1	1	1	1	1	1	2	4	4	1	2	2	6	rs17612637	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:52433397C>T	ENST00000261837.7	-	7	632	c.567G>A	c.(565-567)aaG>aaA	p.K189K	GNB5_ENST00000559348.1_5'Flank|GNB5_ENST00000396335.4_Intron|CTD-2184D3.7_ENST00000560613.1_RNA|GNB5_ENST00000358784.7_Silent_p.K147K|CTD-2184D3.7_ENST00000557898.1_RNA	NM_016194.3	NP_057278.2	O14775	GBB5_HUMAN	guanine nucleotide binding protein (G protein), beta 5	189					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)		TAGCAACAGACTTCTTTTTGG	0.473													C|||	82	0.0163738	0.0008	0.0389	5008	,	,		18151	0.0		0.0368	False		,,,				2504	0.0174				p.K189K		Atlas-SNP	.											.	GNB5	28	.	0			c.G567A						PASS	.	C	,	35,4355	39.2+/-71.8	1,33,2161	166	150	155		441,567	5.3	1	15	dbSNP_123	155	317,8269	112.5+/-172.7	4,309,3980	no	coding-synonymous,coding-synonymous	GNB5	NM_006578.3,NM_016194.3	,	5,342,6141	TT,TC,CC		3.6921,0.7973,2.7127	,	147/354,189/396	52433397	352,12624	2195	4293	6488	SO:0001819	synonymous_variant	10681	exon7			AACAGACTTCTTT	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.567G>A	15.37:g.52433397C>T		186	0	0		94	24	0.255319	NM_016194	B2RBR5|Q9HAU9|Q9UFT3	Silent	SNP	ENST00000261837.7	37	CCDS10149.1																																																																																			C|0.973;G|0.000;T|0.027	0.027	strong		0.473	GNB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254842.1			T	52433397	C	T	52433397	2	4	30	1	0	0	0	0	0	0	0	1	6529	564	20	2		2	GNB5	15	52433397	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	9730561	52433397	50097995	498	13649											
GNB5	10681	hgsc.bcm.edu	37	chr15	52446260	52446260	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccagggcctccacccgctcCgccacctggtgcactggaat	6	6	10	19	2	0	0	0	0	0	0	2	1	2	1	7	3	1	2	7	3	1	0	rs35581121	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:52446260C>T	ENST00000261837.7	-	4	317	c.252G>A	c.(250-252)gcG>gcA	p.A84A	GNB5_ENST00000560116.1_Silent_p.A42A|GNB5_ENST00000396335.4_Silent_p.A42A|GNB5_ENST00000358784.7_Silent_p.A42A	NM_016194.3	NP_057278.2	O14775	GBB5_HUMAN	guanine nucleotide binding protein (G protein), beta 5	84					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)		CCACCCGCTCCGCCACCTGGT	0.562													C|||	84	0.0167732	0.0008	0.0389	5008	,	,		18869	0.001		0.0378	False		,,,				2504	0.0174				p.A84A		Atlas-SNP	.											.	GNB5	28	.	0			c.G252A						PASS	.	C	,	36,4354	40.0+/-72.8	1,34,2160	79	67	71		126,252	-11.1	0	15	dbSNP_126	71	317,8269	112.5+/-172.7	4,309,3980	no	coding-synonymous,coding-synonymous	GNB5	NM_006578.3,NM_016194.3	,	5,343,6140	TT,TC,CC		3.6921,0.82,2.7204	,	42/354,84/396	52446260	353,12623	2195	4293	6488	SO:0001819	synonymous_variant	10681	exon4			CCGCTCCGCCACC	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.252G>A	15.37:g.52446260C>T		51	0	0		26	6	0.230769	NM_016194	B2RBR5|Q9HAU9|Q9UFT3	Silent	SNP	ENST00000261837.7	37	CCDS10149.1																																																																																			C|0.973;T|0.027	0.027	strong		0.562	GNB5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254842.1			T	52446260	C	T	52446260	2	4	30	1	0	0	0	0	0	0	0	1	6529	639	23	1		1	GNB5	15	52446260	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	12863	52446260	50085132	499	13650											
MYO5A	4644	hgsc.bcm.edu	37	chr15	52635394	52635394	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtaatccagagcagatgaTcttccatgcaaaaggaacaa	16	8	9	8	0	1	3	0	1	1	2	3	4	3	4	2	2	3	3	2	2	5	2	rs61731219	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:52635394T>A	ENST00000399231.3	-	31	4203	c.3960A>T	c.(3958-3960)agA>agT	p.R1320S	MYO5A_ENST00000553916.1_Intron|MYO5A_ENST00000358212.6_Splice_Site_p.R1320S|MYO5A_ENST00000356338.6_Intron|MYO5A_ENST00000399233.2_Splice_Site_p.R1317S	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	1320					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)		GAGCAGATGATCTTCCATGCA	0.408													T|||	58	0.0115815	0.0023	0.0072	5008	,	,		19797	0.0		0.0437	False		,,,				2504	0.0061				p.R1320S		Atlas-SNP	.											.	MYO5A	145	.	0			c.A3960T						PASS	.	T	SER/ARG,	24,3884		0,24,1930	92	85	87		3960,	5.9	1	15	dbSNP_129	87	339,7997		6,327,3835	yes	missense-near-splice,intron	MYO5A	NM_000259.3,NM_001142495.1	110,	6,351,5765	AA,AT,TT		4.0667,0.6141,2.9647	benign,	1320/1856,	52635394	363,11881	1954	4168	6122	SO:0001630	splice_region_variant	4644	exon31			AGATGATCTTCCA		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.3960-1A>T	15.37:g.52635394T>A		152	0	0		56	48	0.857143	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	37	CCDS42037.1	37	0.01694139194139194	0	0.0	4	0.011049723756906077	0	0.0	33	0.04353562005277045	T	15.01	2.706322	0.48412	0.006141	0.040667	ENSG00000197535	ENST00000399231;ENST00000399233;ENST00000358212;ENST00000399228	T;T;T;T	0.04454	3.62;3.62;3.62;3.62	5.87	5.87	0.94306	.	0.059846	0.64402	D	0.000003	T	0.02807	0.0084	L	0.43152	1.355	0.80722	D	1	D;D;P	0.61080	0.989;0.989;0.495	D;D;B	0.75020	0.985;0.985;0.034	T	0.05566	-1.0877	10	0.38643	T	0.18	.	10.8931	0.47006	0.0:0.0783:0.0:0.9217	rs61731219	110;113;1320	Q9UES5;O95317;Q9Y4I1	.;.;MYO5A_HUMAN	S	1320;1317;1320;110	ENSP00000382177:R1320S;ENSP00000382179:R1317S;ENSP00000350945:R1320S;ENSP00000382174:R110S	ENSP00000350945:R1320S	R	-	3	2	MYO5A	50422686	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.751000	0.55165	2.236000	0.73375	0.528000	0.53228	AGA	T|0.955;A|0.045	0.045	strong		0.408	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259	Missense_Mutation	A	52635394	T	A	52635394	5	1	30	1	0	0	0	0	0	0	1	0	10087	1449	50	5	1651	5	MYO5A	15	52635394	Splice_Site	SNP	T	TCGA-GR-7353-01A-11D-2210-10	189134	52635394	49895998	500	13651											
VPS13C	54832	hgsc.bcm.edu	37	chr15	62253954	62253954	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctgtgggatgactataaccgGtgctttcaaatcaatattga	12	13	9	7	1	2	2	2	2	0	0	2	3	2	3	1	2	2	1	1	2	5	5			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:62253954G>T	ENST00000261517.5	-	35	3815	c.3742C>A	c.(3742-3744)Ccg>Acg	p.P1248T	VPS13C_ENST00000395898.3_Missense_Mutation_p.P1205T|VPS13C_ENST00000395896.4_Missense_Mutation_p.P1248T|VPS13C_ENST00000249837.3_Missense_Mutation_p.P1205T	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						ACTATAACCGGTGCTTTCAAA	0.458																																					p.P1248T		Atlas-SNP	.											.	VPS13C	506	.	0			c.C3742A						PASS	.						111	110	111					15																	62253954		2203	4300	6503	SO:0001583	missense	54832	exon35			TAACCGGTGCTTT	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.3742C>A	15.37:g.62253954G>T	ENSP00000261517:p.Pro1248Thr	168	0	0		109	8	0.0733945	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.186000	0.78789	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.14893	2.47;2.47;2.47	5.76	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.49474	0.1559	M	0.90309	3.105	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.76071	0.987;0.982;0.974;0.971	T	0.61520	-0.7046	10	0.87932	D	0	.	14.8531	0.70313	0.0689:0.0:0.9311:0.0	.	1205;1248;1205;1248	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	T	1205;1248;1248;1248	ENSP00000249837:P1205T;ENSP00000261517:P1248T;ENSP00000379233:P1248T	ENSP00000249837:P1205T	P	-	1	0	VPS13C	60041246	1.000000	0.71417	0.936000	0.37596	0.978000	0.69477	9.476000	0.97823	1.434000	0.47414	0.563000	0.77884	CCG	.	.	none		0.458	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		T	62253954	G	T	62253954	3	4	30	1	0	0	0	0	1	0	0	0	17206	1261	44	4	7751	4	VPS13C	15	62253954	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	9618560	62253954	40277438	501	13652											
PLEKHO2	80301	hgsc.bcm.edu	37	chr15	65158047	65158047	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acctgggctaagggagaagcGgaaggagctggtgaccctct	10	6	16	9	1	1	2	0	1	1	1	1	5	1	4	2	5	2	2	2	5	3	1	rs77456635	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:65158047G>A	ENST00000323544.4	+	6	1561	c.1433G>A	c.(1432-1434)cGg>cAg	p.R478Q	AC069368.3_ENST00000437723.1_Intron	NM_001195059.1|NM_025201.4	NP_001181988.1|NP_079477.2	Q8TD55	PKHO2_HUMAN	pleckstrin homology domain containing, family O member 2	478										NS(1)|breast(1)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	25						AGGGAGAAGCGGAAGGAGCTG	0.607													G|||	49	0.00978435	0.0008	0.0115	5008	,	,		19769	0.0		0.0239	False		,,,				2504	0.0164				p.R478Q		Atlas-SNP	.											.	PLEKHO2	50	.	0			c.G1433A						PASS	.	G	GLN/ARG,GLN/ARG	33,4371	36.0+/-67.5	0,33,2169	30	31	31		1283,1433	-0.6	1	15	dbSNP_132	31	242,8356	95.2+/-157.0	5,232,4062	yes	missense,missense	PLEKHO2	NM_001195059.1,NM_025201.4	43,43	5,265,6231	AA,AG,GG		2.8146,0.7493,2.1151	benign,benign	428/441,478/491	65158047	275,12727	2202	4299	6501	SO:0001583	missense	80301	exon6			AGAAGCGGAAGGA	AF318373	CCDS10196.1, CCDS73739.1	15q22.31	2013-01-10	2007-12-14	2007-12-14	ENSG00000241839	ENSG00000241839		"Pleckstrin homology (PH) domain containing"	30026	protein-coding gene	gene with protein product			"pleckstrin homology domain containing, family Q member 1"	PLEKHQ1		12477932	Standard	NM_025201		Approved	DKFZp761K2312, PP1628, pp9099	uc002anv.3	Q8TD55	OTTHUMG00000133050	ENST00000323544.4:c.1433G>A	15.37:g.65158047G>A	ENSP00000326706:p.Arg478Gln	24	0	0		17	13	0.764706	NM_025201	Q7L4H4|Q8WYS8	Missense_Mutation	SNP	ENST00000323544.4	37	CCDS10196.1	27	0.012362637362637362	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	21	0.027704485488126648	G	12.58	1.980799	0.34942	0.007493	0.028146	ENSG00000241839	ENST00000323544	T	0.31510	1.49	5.13	-0.638	0.11500	.	0.335637	0.24633	N	0.036878	T	0.04907	0.0132	N	0.19112	0.55	0.28088	N	0.931902	B;B	0.23490	0.086;0.026	B;B	0.16722	0.016;0.004	T	0.22068	-1.0227	10	0.17832	T	0.49	.	8.772	0.34737	0.5539:0.0:0.4461:0.0	.	428;478	Q8TD55-2;Q8TD55	.;PKHO2_HUMAN	Q	478	ENSP00000326706:R478Q	ENSP00000326706:R478Q	R	+	2	0	PLEKHO2	62945100	0.998000	0.40836	0.993000	0.49108	0.988000	0.76386	0.377000	0.20552	-0.025000	0.13918	-0.275000	0.10095	CGG	G|0.982;A|0.018	0.018	strong		0.607	PLEKHO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256659.1	NM_025201		A	65158047	G	A	65158047	3	1	30	1	0	0	0	0	1	0	0	0	12094	1116	39	1	1455	1	PLEKHO2	15	65158047	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2904093	65158047	37373345	502	13653											
RASL12	51285	hgsc.bcm.edu	37	chr15	65357558	65357558	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggggagtagtttcttacccaAgttggggtcatattcactga	9	13	12	7	0	3	1	2	1	1	0	3	2	3	2	1	4	1	3	1	4	4	6	rs36045000	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:65357558A>G	ENST00000220062.4	-	2	433	c.157T>C	c.(157-159)Ttg>Ctg	p.L53L	RASL12_ENST00000434605.2_Silent_p.L42L|RASL12_ENST00000421977.3_Intron	NM_016563.2	NP_057647.1	Q9NYN1	RASLC_HUMAN	RAS-like, family 12	53					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	GTP binding (GO:0005525)			lung(1)|ovary(1)|skin(1)|urinary_tract(1)	4						TTCTTACCCAAGTTGGGGTCA	0.562													A|||	47	0.00938498	0.0227	0.0029	5008	,	,		17164	0.0		0.0129	False		,,,				2504	0.002				p.L53L		Atlas-SNP	.											.	RASL12	32	.	0			c.T157C						PASS	.	A		83,4321	68.7+/-106.4	0,83,2119	133	97	110		157	3.4	1	15	dbSNP_126	110	115,8481	59.8+/-121.6	2,111,4185	no	coding-synonymous	RASL12	NM_016563.2		2,194,6304	GG,GA,AA		1.3378,1.8847,1.5231		53/267	65357558	198,12802	2202	4298	6500	SO:0001819	synonymous_variant	51285	exon2			TACCCAAGTTGGG	AF233588	CCDS10200.1	15q11.2-q22.33	2014-05-09			ENSG00000103710	ENSG00000103710			30289	protein-coding gene	gene with protein product	"Ras family member Ris"					12107412	Standard	NM_016563		Approved	RIS	uc002aoi.1	Q9NYN1	OTTHUMG00000133115	ENST00000220062.4:c.157T>C	15.37:g.65357558A>G		144	0	0		101	18	0.178218	NM_016563	B2RC29|B4DJW2|B4DU82	Silent	SNP	ENST00000220062.4	37	CCDS10200.1																																																																																			A|0.987;G|0.013	0.013	strong		0.562	RASL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256782.2	NM_016563		G	65357558	A	G	65357558	2	3	30	1	0	0	0	0	0	0	0	1	13098	69	3	3		3	RASL12	15	65357558	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	199511	65357558	37173834	503	13654											
MAP2K1	5604	hgsc.bcm.edu	37	chr15	66727483	66727483	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgggagaactgaaggatgacGactttgagaagatcagtgag	14	8	15	4	1	1	6	1	4	0	3	1	10	1	7	0	2	1	0	0	2	3	1			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:66727483G>A	ENST00000307102.5	+	2	730	c.199G>A	c.(199-201)Gac>Aac	p.D67N		NM_002755.3	NP_002746.1	Q02750	MP2K1_HUMAN	mitogen-activated protein kinase kinase 1	67					activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cellular senescence (GO:0090398)|chemotaxis (GO:0006935)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|Golgi inheritance (GO:0048313)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|keratinocyte differentiation (GO:0030216)|labyrinthine layer development (GO:0060711)|MAPK cascade (GO:0000165)|melanosome transport (GO:0032402)|mitotic nuclear division (GO:0007067)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell proliferation (GO:0008285)|negative regulation of homotypic cell-cell adhesion (GO:0034111)|neurotrophin TRK receptor signaling pathway (GO:0048011)|placenta blood vessel development (GO:0060674)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|protein heterooligomerization (GO:0051291)|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)|regulation of vascular smooth muscle contraction (GO:0003056)|response to axon injury (GO:0048678)|response to glucocorticoid (GO:0051384)|response to oxidative stress (GO:0006979)|signal transduction (GO:0007165)|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)|vesicle transport along microtubule (GO:0047496)	cell cortex (GO:0005938)|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)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase activity (GO:0004672)|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)|receptor signaling protein tyrosine phosphatase activity (GO:0004728)	p.D67N(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(8)|urinary_tract(1)	20					Bosutinib(DB06616)|Trametinib(DB08911)	GAAGGATGACGACTTTGAGAA	0.547																																					p.D67N		Atlas-SNP	.											MAP2K1,NS,lymphoid_neoplasm,0,5	MAP2K1	115	5	1	Substitution - Missense(1)	large_intestine(1)	c.G199A	GRCh37	CM076269	MAP2K1	M		PASS	.						188	174	179					15																	66727483		2201	4299	6500	SO:0001583	missense	5604	exon2			GATGACGACTTTG	L11284	CCDS10216.1	15q22.1-q22.33	2014-09-17			ENSG00000169032	ENSG00000169032	2.7.12.2	"Mitogen-activated protein kinase cascade / Kinase kinases"	6840	protein-coding gene	gene with protein product		176872		PRKMK1		9465908, 8388392	Standard	NM_002755		Approved	MEK1, MAPKK1	uc010bhq.3	Q02750	OTTHUMG00000133196	ENST00000307102.5:c.199G>A	15.37:g.66727483G>A	ENSP00000302486:p.Asp67Asn	141	0	0		97	54	0.556701	NM_002755		Missense_Mutation	SNP	ENST00000307102.5	37	CCDS10216.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	36|36	5.691697|5.691697	0.96793|0.96793	.|.	.|.	ENSG00000169032|ENSG00000169032	ENST00000307102|ENST00000425818	D|.	0.93859|.	-3.3|.	5.24|5.24	5.24|5.24	0.73138|0.73138	Protein kinase-like domain (1);|.	0.091006|.	0.85682|.	D|.	0.000000|.	T|T	0.76133|0.76133	0.3945|0.3945	M|M	0.73962|0.73962	2.25|2.25	0.80722|0.80722	D|D	1|1	D;D|.	0.76494|.	0.999;0.993|.	D;P|.	0.64687|.	0.928;0.638|.	T|T	0.76211|0.76211	-0.3042|-0.3042	10|5	0.72032|.	D|.	0.01|.	-32.7633|-32.7633	17.8302|17.8302	0.88680|0.88680	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	45;67|.	B4DFY5;Q02750|.	.;MP2K1_HUMAN|.	N|Q	67|6	ENSP00000302486:D67N|.	ENSP00000302486:D67N|.	D|R	+|+	1|2	0|0	MAP2K1|MAP2K1	64514537|64514537	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.983000|0.983000	0.72400|0.72400	9.723000|9.723000	0.98772|0.98772	2.443000|2.443000	0.82685|0.82685	0.591000|0.591000	0.81541|0.81541	GAC|CGA	.	.	none		0.547	MAP2K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256906.4			A	66727483	G	A	66727483	3	1	30	1	0	0	0	0	1	0	0	0	9245	1058	37	1	205	1	MAP2K1	15	66727483	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1369925	66727483	35803909	504	13655											
PIAS1	8554	hgsc.bcm.edu	37	chr15	68479959	68479959	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctacactcgtctcggttttTcccgtatacctcctcacaga	7	13	5	16	3	2	1	1	0	1	1	6	1	4	1	4	1	2	2	4	1	3	5			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:68479959T>C	ENST00000249636.6	+	14	1890	c.1742T>C	c.(1741-1743)tTc>tCc	p.F581S	PIAS1_ENST00000545237.1_Missense_Mutation_p.F583S	NM_016166.1	NP_057250.1	O75925	PIAS1_HUMAN	protein inhibitor of activated STAT, 1	581	4 X 4 AA repeats of N-T-S-L.|Ser-rich.				androgen receptor signaling pathway (GO:0030521)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of smooth muscle cell differentiation (GO:0051152)|positive regulation of transcription, DNA-templated (GO:0045893)|protein sumoylation (GO:0016925)|protein-DNA complex assembly (GO:0065004)|regulation of cell proliferation (GO:0042127)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|SUMO ligase activity (GO:0019789)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)	24						TCTCGGTTTTTCCCGTATACC	0.498																																					p.F581S		Atlas-SNP	.											PIAS1,NS,carcinoma,-1,1	PIAS1	42	1	0			c.T1742C						PASS	.						87	84	85					15																	68479959		1919	4137	6056	SO:0001583	missense	8554	exon14			GGTTTTTCCCGTA	AF077951	CCDS45290.1	15q	2011-10-11	2002-04-19	2002-04-19		ENSG00000033800		"Zinc fingers, MIZ-type"	2752	protein-coding gene	gene with protein product	"zinc finger, MIZ-type containing 3"	603566	"DEAD/H (Asp-Glu-Ala-Asp/His) box binding protein 1"	DDXBP1		9724754, 9177271	Standard	XM_005254735		Approved	GBP, GU/RH-II, ZMIZ3	uc002aqz.3	O75925		ENST00000249636.6:c.1742T>C	15.37:g.68479959T>C	ENSP00000249636:p.Phe581Ser	272	0	0		171	16	0.0935673	NM_016166	B2RB67|B3KSY9|C5J4B4|Q147X4|Q99751|Q9UN02	Missense_Mutation	SNP	ENST00000249636.6	37	CCDS45290.1	.	.	.	.	.	.	.	.	.	.	T	17.16	3.317953	0.60524	.	.	ENSG00000033800	ENST00000249636;ENST00000545237	T;T	0.33216	1.43;1.42	5.74	5.74	0.90152	.	0.103576	0.64402	D	0.000002	T	0.26011	0.0634	L	0.39898	1.24	0.51233	D	0.999913	P	0.40000	0.698	B	0.32211	0.142	T	0.07233	-1.0783	10	0.87932	D	0	-15.7775	16.0292	0.80564	0.0:0.0:0.0:1.0	.	581	O75925	PIAS1_HUMAN	S	581;583	ENSP00000249636:F581S;ENSP00000438574:F583S	ENSP00000249636:F581S	F	+	2	0	PIAS1	66267013	1.000000	0.71417	0.918000	0.36340	0.518000	0.34316	7.420000	0.80191	2.187000	0.69744	0.533000	0.62120	TTC	.	.	none		0.498	PIAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419642.2			C	68479959	T	C	68479959	3	2	30	1	0	0	0	0	1	0	0	0	11884	1783	62	3	1796	3	PIAS1	15	68479959	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	1752476	68479959	34051433	505	13656											
ITGA11	22801	hgsc.bcm.edu	37	chr15	68606192	68606192	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcttccttggtgctgtccCgctcattactgtcactgcaa	5	15	8	13	1	3	0	2	0	1	0	5	0	5	0	2	1	3	3	2	1	2	3	rs368307734		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:68606192C>T	ENST00000315757.7	-	23	2893	c.2807G>A	c.(2806-2808)cGg>cAg	p.R936Q	ITGA11_ENST00000423218.2_Missense_Mutation_p.R936Q	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	936					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						GGTGCTGTCCCGCTCATTACT	0.637																																					p.R936Q		Atlas-SNP	.											.	ITGA11	110	.	0			c.G2807A						PASS	.	C	GLN/ARG	0,4316		0,0,2158	80	84	83		2807	2.6	1	15		83	2,8508		0,2,4253	no	missense	ITGA11	NM_001004439.1	43	0,2,6411	TT,TC,CC		0.0235,0.0,0.0156	benign	936/1189	68606192	2,12824	2158	4255	6413	SO:0001583	missense	22801	exon23			CTGTCCCGCTCAT	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.2807G>A	15.37:g.68606192C>T	ENSP00000327290:p.Arg936Gln	158	0	0		100	78	0.78	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	37	CCDS45291.1	.	.	.	.	.	.	.	.	.	.	C	10.57	1.386513	0.25031	0.0	2.35E-4	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000535491	T;T	0.39997	1.05;1.05	4.94	2.58	0.30949	Integrin alpha-2 (1);	0.362684	0.31071	N	0.008308	T	0.14657	0.0354	N	0.02539	-0.55	0.22581	N	0.998964	B;B	0.09022	0.002;0.0	B;B	0.13407	0.009;0.001	T	0.24297	-1.0164	10	0.15499	T	0.54	.	5.5239	0.16947	0.1525:0.0858:0.0:0.7617	.	936;936	A8K8T0;Q9UKX5	.;ITA11_HUMAN	Q	936;936;571	ENSP00000327290:R936Q;ENSP00000403392:R936Q	ENSP00000327290:R936Q	R	-	2	0	ITGA11	66393246	0.984000	0.35163	0.987000	0.45799	0.698000	0.40448	2.853000	0.48317	0.228000	0.21019	-0.367000	0.07326	CGG	.	.	weak		0.637	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211		T	68606192	C	T	68606192	3	4	30	1	0	0	0	0	1	0	0	0	7883	652	23	1	791	1	ITGA11	15	68606192	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	126233	68606192	33925200	506	13657											
PKM2	5315	hgsc.bcm.edu	37	chr15	72501072	72501072	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgccttgcggatgaatgaCgcaaacaccatatcaacatc	14	8	8	11	2	1	2	1	2	0	0	2	4	1	3	2	1	4	1	2	1	4	2	rs11558376	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:72501072C>T	ENST00000335181.5	-	6	829	c.726G>A	c.(724-726)gcG>gcA	p.A242A	PKM_ENST00000389093.3_Silent_p.A242A|PKM_ENST00000568459.1_Silent_p.A242A|PKM_ENST00000568883.1_Silent_p.A77A|PKM_ENST00000565184.1_Silent_p.A242A|PKM_ENST00000319622.6_Silent_p.A242A|PKM_ENST00000565154.1_Silent_p.A242A|PKM_ENST00000449901.2_Silent_p.A227A	NM_002654.4	NP_002645.3	P14618	KPYM_HUMAN	pyruvate kinase, muscle	242					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|programmed cell death (GO:0012501)|small molecule metabolic process (GO:0044281)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|potassium ion binding (GO:0030955)|pyruvate kinase activity (GO:0004743)			endometrium(1)|lung(7)	8					Pyruvic acid(DB00119)	GGATGAATGACGCAAACACCA	0.493													C|||	4	0.000798722	0.0	0.0	5008	,	,		21170	0.0		0.004	False		,,,				2504	0.0				p.A316A		Atlas-SNP	.											PKM2,NS,neuroblastoma,-1,2	PKM	25	2	0			c.G948A						PASS	.	C	,,,,,,	1,4397	2.1+/-5.4	0,1,2198	203	180	188		948,504,681,741,726,726,726	-10.5	0.5	15	dbSNP_120	188	15,8579	11.2+/-40.8	0,15,4282	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PKM2	NM_001206796.1,NM_001206797.1,NM_001206798.1,NM_001206799.1,NM_002654.4,NM_182470.2,NM_182471.2	,,,,,,	0,16,6480	TT,TC,CC		0.1745,0.0227,0.1232	,,,,,,	316/606,168/458,227/517,247/537,242/532,242/532,242/532	72501072	16,12976	2199	4297	6496	SO:0001819	synonymous_variant	5315	exon7			GAATGACGCAAAC	M23725	CCDS32284.1, CCDS32285.1, CCDS55972.1, CCDS73752.1	15q23	2012-10-02		2012-05-23	ENSG00000067225	ENSG00000067225	2.7.1.40		9021	protein-coding gene	gene with protein product		179050		PKM2		2040271	Standard	NM_002654		Approved	THBP1, OIP3, PK3	uc002atr.1	P14618	OTTHUMG00000172709	ENST00000335181.5:c.726G>A	15.37:g.72501072C>T		140	1	0.00714286		85	64	0.752941	NM_001206796	A6NFK3|B2R5N8|B3KRY0|B4DFX8|B4DUU6|P14786|Q53GK4|Q96E76|Q9BWB5|Q9UCV6|Q9UPF2	Silent	SNP	ENST00000335181.5	37	CCDS32284.1																																																																																			C|0.999;T|0.001	0.001	strong		0.493	PKM-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420056.1			T	72501072	C	T	72501072	2	4	30	1	0	0	0	0	0	0	0	1	11986	523	19	1		1	PKM2	15	72501072	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	3894880	72501072	30030320	507	13658											
SCAMP5	192683	hgsc.bcm.edu	37	chr15	75308976	75308976	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaacctggtgggctgtctcgCgtggctgatcggaggcgggg	4	8	20	9	4	1	1	0	1	1	0	3	3	1	2	1	7	1	2	1	7	1	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:75308976C>T	ENST00000361900.6	+	5	386	c.179C>T	c.(178-180)gCg>gTg	p.A60V	SCAMP5_ENST00000562212.1_Missense_Mutation_p.A60V|SCAMP5_ENST00000568081.1_5'Flank|SCAMP5_ENST00000545456.1_Intron|SCAMP5_ENST00000565923.1_3'UTR|SCAMP5_ENST00000425597.3_Missense_Mutation_p.A60V	NM_001178111.1	NP_001171582.1	Q8TAC9	SCAM5_HUMAN	secretory carrier membrane protein 5	60					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						GGCTGTCTCGCGTGGCTGATC	0.612																																					p.A60V		Atlas-SNP	.											.	SCAMP5	34	.	0			c.C179T						PASS	.						107	111	109					15																	75308976		2165	4255	6420	SO:0001583	missense	192683	exon5			GTCTCGCGTGGCT	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.179C>T	15.37:g.75308976C>T	ENSP00000355387:p.Ala60Val	118	0	0		67	33	0.492537	NM_001178111	B3KPJ7|B7Z762|D3DW71|Q8N3M4	Missense_Mutation	SNP	ENST00000361900.6	37	CCDS45306.1	.	.	.	.	.	.	.	.	.	.	C	31	5.087901	0.94100	.	.	ENSG00000198794	ENST00000361900;ENST00000425597	T;T	0.18016	2.24;2.24	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	T	0.33118	0.0852	L	0.45352	1.415	0.80722	D	1	P;D	0.71674	0.842;0.998	B;D	0.63793	0.214;0.918	T	0.03443	-1.1036	10	0.59425	D	0.04	-8.1334	17.2941	0.87166	0.0:1.0:0.0:0.0	.	60;60	Q8TAC9-2;Q8TAC9	.;SCAM5_HUMAN	V	60	ENSP00000355387:A60V;ENSP00000406547:A60V	ENSP00000355387:A60V	A	+	2	0	SCAMP5	73096029	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.681000	0.84073	2.391000	0.81399	0.561000	0.74099	GCG	.	.	none		0.612	SCAMP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420015.2	NM_138967		T	75308976	C	T	75308976	3	4	30	1	0	0	0	0	1	0	0	0	13889	768	27	1	189	1	SCAMP5	15	75308976	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	2807904	75308976	27222416	508	13659											
CSPG4	1464	hgsc.bcm.edu	37	chr15	75982119	75982119	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gggctgatagtcagcagctgGgtgaaattggcaaagacagg	12	7	16	6	0	1	3	1	2	0	1	1	3	1	3	0	4	2	4	0	4	3	2	rs199778089	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:75982119G>T	ENST00000308508.5	-	3	1379	c.1287C>A	c.(1285-1287)acC>acA	p.T429T		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	429	Globular or compact configuration stabilized by disulfide bonds.|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						TCAGCAGCTGGGTGAAATTGG	0.642																																					p.T429T		Atlas-SNP	.											CSPG4,NS,neuroblastoma,0,1	CSPG4	175	1	0			c.C1287A						PASS	.						34	34	34					15																	75982119		2197	4291	6488	SO:0001819	synonymous_variant	1464	exon3			CAGCTGGGTGAAA	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.1287C>A	15.37:g.75982119G>T		134	0	0		88	15	0.170455	NM_001897	D3DW77|Q92675	Silent	SNP	ENST00000308508.5	37	CCDS10284.1																																																																																			G|0.997;T|0.003	0.003	strong		0.642	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		T	75982119	G	T	75982119	2	4	30	1	0	0	0	0	0	0	0	1	3962	1219	43	4		4	CSPG4	15	75982119	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	673143	75982119	26549273	509	13660											
HMG20A	10363	hgsc.bcm.edu	37	chr15	77750802	77750802	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccctttttgcagatgaagAcggttccaaggagagtaatg	11	10	12	8	1	0	4	0	1	0	3	1	5	1	4	3	2	1	3	3	2	3	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:77750802A>G	ENST00000381714.3	+	3	481	c.53A>G	c.(52-54)gAc>gGc	p.D18G	HMG20A_ENST00000336216.4_Missense_Mutation_p.D18G	NM_018200.2	NP_060670.1	Q9NP66	HM20A_HUMAN	high mobility group 20A	18					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|negative regulation of neuron differentiation (GO:0045665)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	18						GCAGATGAAGACGGTTCCAAG	0.423																																					p.D18G		Atlas-SNP	.											.	HMG20A	48	.	0			c.A53G						PASS	.						94	94	94					15																	77750802		2196	4294	6490	SO:0001583	missense	10363	exon3			ATGAAGACGGTTC	AF146222	CCDS10295.1	15q24	2011-07-01	2011-04-05		ENSG00000140382	ENSG00000140382		"High mobility group / Non-canonical"	5001	protein-coding gene	gene with protein product	"HMG box domain containing 1"	605534	"high-mobility group 20A"			10773667	Standard	NM_018200		Approved	HMGX1, FLJ10739, HMGXB1	uc002bcr.3	Q9NP66	OTTHUMG00000143729	ENST00000381714.3:c.53A>G	15.37:g.77750802A>G	ENSP00000371133:p.Asp18Gly	88	0	0		63	5	0.0793651	NM_018200	A6NHY3|D3DW78|Q53G31|Q9NSF6	Missense_Mutation	SNP	ENST00000381714.3	37	CCDS10295.1	.	.	.	.	.	.	.	.	.	.	A	15.39	2.820448	0.50633	.	.	ENSG00000140382	ENST00000336216;ENST00000381714	T;T	0.70986	-0.53;-0.53	5.76	5.76	0.90799	.	0.067632	0.64402	D	0.000012	T	0.67011	0.2848	N	0.24115	0.695	0.44816	D	0.997829	B;P	0.46395	0.247;0.877	B;P	0.49829	0.053;0.623	T	0.71431	-0.4595	10	0.66056	D	0.02	-17.0189	14.3238	0.66505	1.0:0.0:0.0:0.0	.	18;18	Q9NP66;Q9NP66-2	HM20A_HUMAN;.	G	18	ENSP00000336856:D18G;ENSP00000371133:D18G	ENSP00000336856:D18G	D	+	2	0	HMG20A	75537857	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.672000	0.68102	2.200000	0.70718	0.460000	0.39030	GAC	.	.	none		0.423	HMG20A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419512.2	NM_018200		G	77750802	A	G	77750802	3	3	30	1	0	0	0	0	1	0	0	0	7230	275	10	3	55	3	HMG20A	15	77750802	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	1768683	77750802	24780590	510	13661											
ST20	400410	hgsc.bcm.edu	37	chr15	80191280	80191280	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caaagttgtttatttaaaagTagaagtatgtgttggcaatc	14	15	9	3	0	0	1	0	0	0	1	1	1	0	1	0	1	0	6	0	1	8	8	rs184575290	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:80191280T>A	ENST00000478497.1	-	3	912	c.233A>T	c.(232-234)tAc>tTc	p.Y78F	ST20-MTHFS_ENST00000494999.1_Intron|MTHFS_ENST00000258874.3_5'Flank|ST20-MTHFS_ENST00000479961.1_Intron|ST20_ENST00000485386.1_Missense_Mutation_p.Y78F|ST20_ENST00000562759.1_Missense_Mutation_p.Y78F|MTHFS_ENST00000559722.1_5'Flank	NM_001100879.1	NP_001094349.1	Q9HBF5	ST20_HUMAN	suppressor of tumorigenicity 20	78					extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)	mitochondrial outer membrane (GO:0005741)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			kidney(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4						TATTTAAAAGTAGAAGTATGT	0.333													T|||	3	0.000599042	0.0	0.0	5008	,	,		18184	0.0		0.003	False		,,,				2504	0.0				p.Y78F		Atlas-SNP	.											ST20,NS,carcinoma,+1,1	ST20	9	1	0			c.A233T						PASS	.	T	PHE/TYR,PHE/TYR,PHE/TYR,	3,4391	6.2+/-15.9	0,3,2194	74	78	77		233,233,233,	-1.1	0	15		77	29,8561	17.9+/-57.8	0,29,4266	yes	missense,missense,missense,intron	ST20,ST20-MTHFS	NM_001100879.1,NM_001100880.2,NM_001199757.1,NM_001199760.1	22,22,22,	0,32,6460	AA,AT,TT		0.3376,0.0683,0.2465	possibly-damaging,possibly-damaging,possibly-damaging,	78/80,78/80,78/80,	80191280	32,12952	2197	4295	6492	SO:0001583	missense	400410	exon3			TAAAAGTAGAAGT	AF249277	CCDS42067.1	15q25.1	2007-07-16				ENSG00000180953			33520	protein-coding gene	gene with protein product							Standard	NM_001100879		Approved	HCCS-1		Q9HBF5		ENST00000478497.1:c.233A>T	15.37:g.80191280T>A	ENSP00000453502:p.Tyr78Phe	285	1	0.00350877		129	87	0.674419	NM_001199757		Missense_Mutation	SNP	ENST00000478497.1	37	CCDS42067.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	12.63	1.994958	0.35226	6.83E-4	0.003376	ENSG00000180953	ENST00000322484;ENST00000417278	.	.	.	1.78	-1.14	0.09741	.	.	.	.	.	T	0.16854	0.0405	.	.	.	0.09310	N	1	P	0.46020	0.871	B	0.31812	0.136	T	0.13150	-1.0520	7	0.87932	D	0	.	5.9491	0.19235	0.0:0.0:0.5632:0.4368	.	78	Q9HBF5	ST20_HUMAN	F	78	.	ENSP00000319125:Y78F	Y	-	2	0	ST20	77978335	0.002000	0.14202	0.000000	0.03702	0.446000	0.32137	-0.513000	0.06305	-0.277000	0.09193	0.172000	0.16884	TAC	T|0.998;A|0.002	0.002	strong		0.333	ST20-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416728.2			A	80191280	T	A	80191280	3	1	30	1	0	0	0	0	1	0	0	0	15228	1638	57	5	10	5	ST20	15	80191280	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	2440478	80191280	22340112	511	13662											
AP3B2	8120	hgsc.bcm.edu	37	chr15	83378366	83378366	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgcttgtagtcggaggagaaGatgccgccgctcgcggggtc	6	7	17	11	6	0	2	0	0	0	2	3	4	0	3	2	4	1	3	2	4	2	2	rs200226421	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:83378366G>A	ENST00000261722.3	-	1	300	c.93C>T	c.(91-93)atC>atT	p.I31I	AP3B2_ENST00000535348.1_Silent_p.I31I|AP3B2_ENST00000561455.1_5'Flank|AC105339.1_ENST00000440479.1_lincRNA|AP3B2_ENST00000542200.1_Silent_p.I31I|AP3B2_ENST00000535359.1_Silent_p.I31I	NM_004644.3	NP_004635.2	Q13367	AP3B2_HUMAN	adaptor-related protein complex 3, beta 2 subunit	31					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)			CGGAGGAGAAGATGCCGCCGC	0.761													G|||	25	0.00499201	0.0008	0.0029	5008	,	,		8047	0.0		0.0199	False		,,,				2504	0.002				p.I31I		Atlas-SNP	.											.	AP3B2	103	.	0			c.C93T						PASS	.	G		0,2962		0,0,1481	2	3	3		93	1.7	1	15		3	42,6932		0,42,3445	no	coding-synonymous	AP3B2	NM_004644.3		0,42,4926	AA,AG,GG		0.6022,0.0,0.4227		31/1083	83378366	42,9894	1481	3487	4968	SO:0001819	synonymous_variant	8120	exon1			GGAGAAGATGCCG	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.93C>T	15.37:g.83378366G>A		10	0	0		12	10	0.833333	NM_004644	A4Z4T7|B7ZKR7|B7ZKS0|O14808|Q52LY8	Silent	SNP	ENST00000261722.3	37	CCDS45331.1																																																																																			.	.	weak		0.761	AP3B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397463.1			A	83378366	G	A	83378366	2	1	30	1	0	0	0	0	0	0	0	1	745	932	33	2		2	AP3B2	15	83378366	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	3187086	83378366	19153026	512	13663											
PDE8A	5151	hgsc.bcm.edu	37	chr15	85610349	85610349	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	accaaggaggctcaggctgtCcttgcctgtttcctggacaa	8	10	11	12	0	1	0	1	0	0	0	3	2	3	2	4	4	1	3	4	4	2	2	rs35666574	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:85610349C>T	ENST00000310298.4	+	4	600	c.348C>T	c.(346-348)gtC>gtT	p.V116V	PDE8A_ENST00000557957.1_Silent_p.V44V|PDE8A_ENST00000394553.1_Silent_p.V116V|PDE8A_ENST00000557819.2_3'UTR|PDE8A_ENST00000339708.5_Silent_p.V116V			O60658	PDE8A_HUMAN	phosphodiesterase 8A	116					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)	CTCAGGCTGTCCTTGCCTGTT	0.448													C|||	64	0.0127796	0.0098	0.0058	5008	,	,		19685	0.0		0.0408	False		,,,				2504	0.0061				p.V116V		Atlas-SNP	.											.	PDE8A	50	.	0			c.C348T						PASS	.	C	,	60,4346	58.1+/-94.6	0,60,2143	164	138	147		348,348	0.2	1	15	dbSNP_126	147	280,8318	105.6+/-166.5	7,266,4026	no	coding-synonymous,coding-synonymous	PDE8A	NM_002605.2,NM_173454.1	,	7,326,6169	TT,TC,CC		3.2566,1.3618,2.6146	,	116/830,116/784	85610349	340,12664	2203	4299	6502	SO:0001819	synonymous_variant	5151	exon3			GGCTGTCCTTGCC	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.348C>T	15.37:g.85610349C>T		105	0	0		73	62	0.849315	NM_173454	B3KXE6|H0YMZ7|Q6P9H3|Q969I1|Q96PC9|Q96PD0|Q96PD1|Q96T71|Q9UMB7|Q9UMC3	Silent	SNP	ENST00000310298.4	37	CCDS10336.1																																																																																			C|0.976;T|0.024	0.024	strong		0.448	PDE8A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000309018.1	NM_002605		T	85610349	C	T	85610349	2	4	30	1	0	0	0	0	0	0	0	1	11662	842	30	2		2	PDE8A	15	85610349	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	2231983	85610349	16921043	513	13664											
AGBL1	123624	hgsc.bcm.edu	37	chr15	86790936	86790936	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agagcagtgaaccgaggctaCgtcaccagcctgctcgggct	9	6	13	13	3	1	2	1	1	0	1	2	3	1	2	3	2	5	4	3	2	2	1	rs371409529		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:86790936C>T	ENST00000441037.2	+	6	518	c.423C>T	c.(421-423)taC>taT	p.Y141Y	AGBL1_ENST00000421325.2_Silent_p.Y141Y	NM_152336.2	NP_689549.2	Q96MI9	CBPC4_HUMAN	ATP/GTP binding protein-like 1	141					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						ACCGAGGCTACGTCACCAGCC	0.597																																					p.Y141Y		Atlas-SNP	.											AGBL1,bladder,carcinoma,0,1	AGBL1	151	1	0			c.C423T						PASS	.						25	27	26					15																	86790936		2139	4253	6392	SO:0001819	synonymous_variant	123624	exon6			AGGCTACGTCACC	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.423C>T	15.37:g.86790936C>T		135	0	0		105	80	0.761905	NM_152336	A1A4X5|A6NJH6|C9JHL5	Silent	SNP	ENST00000441037.2	37	CCDS58398.1																																																																																			.	.	alt		0.597	AGBL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314929.5	NM_152336		T	86790936	C	T	86790936	2	4	30	1	0	0	0	0	0	0	0	1	375	547	19	1		1	AGBL1	15	86790936	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1180587	86790936	15740456	514	13665											
HAPLN3	145864	hgsc.bcm.edu	37	chr15	89424765	89424765	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaggagcggtgcctcagccCgatggccaccagcacgtcct	9	5	12	15	3	1	0	1	0	0	0	2	2	2	1	5	3	4	1	5	3	1	0	rs140982817	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:89424765C>T	ENST00000359595.3	-	3	530	c.316G>A	c.(316-318)Ggg>Agg	p.G106R	HAPLN3_ENST00000562889.1_Missense_Mutation_p.G168R	NM_178232.2	NP_839946.1	Q96S86	HPLN3_HUMAN	hyaluronan and proteoglycan link protein 3	106	Ig-like V-type. {ECO:0000305}.				cell adhesion (GO:0007155)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	17	Lung NSC(78;0.0392)|all_lung(78;0.077)				Hyaluronan(DB08818)	TGCCTCAGCCCGATGGCCACC	0.662													C|||	3	0.000599042	0.0	0.0029	5008	,	,		18397	0.0		0.001	False		,,,				2504	0.0				p.G106R		Atlas-SNP	.											HAPLN3,caecum,carcinoma,0,1	HAPLN3	43	1	0			c.G316A						PASS	.	C	ARG/GLY	2,4398	4.2+/-10.8	0,2,2198	95	76	83		316	4.2	0.4	15	dbSNP_134	83	55,8543	34.8+/-89.0	0,55,4244	yes	missense	HAPLN3	NM_178232.2	125	0,57,6442	TT,TC,CC		0.6397,0.0455,0.4385	probably-damaging	106/361	89424765	57,12941	2200	4299	6499	SO:0001583	missense	145864	exon3			TCAGCCCGATGGC	AY262759	CCDS10346.1	15q26.1	2013-01-11			ENSG00000140511	ENSG00000140511		"Immunoglobulin superfamily / V-set domain containing"	21446	protein-coding gene	gene with protein product			"extracellular link domain containing, 1"	EXLD1		12663660	Standard	NM_178232		Approved	HsT19883	uc002bnc.3	Q96S86	OTTHUMG00000148680	ENST00000359595.3:c.316G>A	15.37:g.89424765C>T	ENSP00000352606:p.Gly106Arg	112	0	0		70	21	0.3	NM_178232	A8K7P0	Missense_Mutation	SNP	ENST00000359595.3	37	CCDS10346.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	17.60	3.429872	0.62844	4.55E-4	0.006397	ENSG00000140511	ENST00000359595	T	0.65364	-0.15	4.21	4.21	0.49690	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.77705	0.4170	M	0.90369	3.11	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.85370	0.1113	10	0.87932	D	0	-31.7116	15.5717	0.76345	0.0:1.0:0.0:0.0	.	106;106	A8K7T8;Q96S86	.;HPLN3_HUMAN	R	106	ENSP00000352606:G106R	ENSP00000352606:G106R	G	-	1	0	HAPLN3	87225769	1.000000	0.71417	0.441000	0.26858	0.188000	0.23474	7.032000	0.76498	1.870000	0.54199	0.650000	0.86243	GGG	C|0.998;T|0.002	0.002	strong		0.662	HAPLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309070.1	NM_178232		T	89424765	C	T	89424765	3	4	30	1	0	0	0	0	1	0	0	0	6965	652	23	1	778	1	HAPLN3	15	89424765	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	2633829	89424765	13106627	515	13666											
FURIN	5045	hgsc.bcm.edu	37	chr15	91424029	91424029	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctagagattgaaaacaccagCgaagccaacaactatggtac	17	6	8	10	1	0	2	0	1	0	1	0	4	0	2	2	1	6	1	2	1	8	4	rs142489043	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:91424029C>T	ENST00000268171.3	+	14	1944	c.1665C>T	c.(1663-1665)agC>agT	p.S555S		NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	555					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)			AAAACACCAGCGAAGCCAACA	0.557													C|||	4	0.000798722	0.0	0.0	5008	,	,		19315	0.0		0.004	False		,,,				2504	0.0				p.S555S		Atlas-SNP	.											.	FURIN	85	.	0			c.C1665T						PASS	.	C		0,4396		0,0,2198	85	83	84		1665	-7.6	0.8	15	dbSNP_134	84	36,8560	25.1+/-72.6	0,36,4262	no	coding-synonymous	FURIN	NM_002569.2		0,36,6460	TT,TC,CC		0.4188,0.0,0.2771		555/795	91424029	36,12956	2198	4298	6496	SO:0001819	synonymous_variant	5045	exon14			CACCAGCGAAGCC	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.1665C>T	15.37:g.91424029C>T		195	0	0		143	30	0.20979	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Silent	SNP	ENST00000268171.3	37	CCDS10364.1																																																																																			C|0.997;T|0.003	0.003	strong		0.557	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569		T	91424029	C	T	91424029	2	4	30	1	0	0	0	0	0	0	0	1	6107	767	27	1		1	FURIN	15	91424029	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1999264	91424029	11107363	516	13667											
MAN2A2	4122	hgsc.bcm.edu	37	chr15	91452566	91452566	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcctgccccagggcagccctGcttctggaccaataccggaa	8	7	10	16	1	1	0	0	0	1	0	2	2	2	2	6	3	4	2	6	3	3	2	rs148266546		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:91452566G>A	ENST00000559717.1	+	9	1665	c.1206G>A	c.(1204-1206)ctG>ctA	p.L402L	MAN2A2_ENST00000430376.2_5'Flank|MAN2A2_ENST00000431652.2_5'UTR|MAN2A2_ENST00000360468.3_Silent_p.L402L			P49641	MA2A2_HUMAN	mannosidase, alpha, class 2A, member 2	402					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)			GGGCAGCCCTGCTTCTGGACC	0.572													G|||	1	0.000199681	0.0	0.0014	5008	,	,		17474	0.0		0.0	False		,,,				2504	0.0				p.L402L		Atlas-SNP	.											.	MAN2A2	99	.	0			c.G1206A						PASS	.	G		0,4396		0,0,2198	56	55	55		1206	4.8	1	15	dbSNP_134	55	4,8592	3.7+/-12.6	0,4,4294	no	coding-synonymous	MAN2A2	NM_006122.2		0,4,6492	AA,AG,GG		0.0465,0.0,0.0308		402/1151	91452566	4,12988	2198	4298	6496	SO:0001819	synonymous_variant	4122	exon8			AGCCCTGCTTCTG	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.1206G>A	15.37:g.91452566G>A		101	0	0		62	6	0.0967742	NM_006122	A6NH12|A8K1E8|Q13754	Silent	SNP	ENST00000559717.1	37	CCDS32332.1																																																																																			G|1.000;A|0.000	0.000	strong		0.572	MAN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418246.5	NM_006122		A	91452566	G	A	91452566	2	1	30	1	0	0	0	0	0	0	0	1	9224	1306	46	2		2	MAN2A2	15	91452566	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	28537	91452566	11078826	517	13668											
MEF2A	4205	hgsc.bcm.edu	37	chr15	100250918	100250918	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgtcgctgggacaggtgtcGgcctggcagcagcaccacct	6	7	14	14	2	0	0	0	0	0	0	2	1	0	1	3	4	2	4	3	4	0	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:100250918G>A	ENST00000557785.1	+	10	1414	c.1065G>A	c.(1063-1065)tcG>tcA	p.S355S	MEF2A_ENST00000557942.1_Silent_p.S363S|MEF2A_ENST00000453228.2_Silent_p.S355S|MEF2A_ENST00000558812.1_Silent_p.S295S|MEF2A_ENST00000354410.5_Silent_p.S357S|MEF2A_ENST00000338042.6_Silent_p.S364S|MEF2A_ENST00000449277.2_Silent_p.S287S	NM_001171894.1	NP_001165365.1	Q02078	MEF2A_HUMAN	myocyte enhancer factor 2A	365					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)			GACAGGTGTCGGCCTGGCAGC	0.537																																					p.S357S		Atlas-SNP	.											.	MEF2A	138	.	0			c.G1071A						PASS	.						51	53	53					15																	100250918		2046	4203	6249	SO:0001819	synonymous_variant	4205	exon10			GGTGTCGGCCTGG		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.1065G>A	15.37:g.100250918G>A		139	0	0		97	71	0.731959	NM_005587	B4DFQ7|F6XG23|O43814|Q14223|Q14224|Q59GX4|Q7Z6C9|Q96D14	Silent	SNP	ENST00000557785.1	37	CCDS53978.1																																																																																			.	.	none		0.537	MEF2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415985.1			A	100250918	G	A	100250918	2	1	30	1	0	0	0	0	0	0	0	1	9464	1103	39	1		1	MEF2A	15	100250918	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	8798352	100250918	2280474	518	13669											
LRRK1	79705	hgsc.bcm.edu	37	chr15	101567971	101567971	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtggagcagacgcccgacaaCgacatcaaggactacgagga	14	3	13	11	4	1	1	1	0	0	1	1	7	1	4	1	3	3	1	1	3	3	1	rs41535348	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr15:101567971C>T	ENST00000388948.3	+	19	3014	c.2655C>T	c.(2653-2655)aaC>aaT	p.N885N	LRRK1_ENST00000284395.5_Silent_p.N882N	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)			CGCCCGACAACGACATCAAGG	0.632													C|||	18	0.00359425	0.0008	0.0029	5008	,	,		18583	0.0		0.008	False		,,,				2504	0.0072				p.N885N		Atlas-SNP	.											.	LRRK1	310	.	0			c.C2655T						PASS	.	C		6,4338		0,6,2166	26	37	34		2655	-8.9	0	15	dbSNP_127	34	87,8451		0,87,4182	no	coding-synonymous	LRRK1	NM_024652.3		0,93,6348	TT,TC,CC		1.019,0.1381,0.7219		885/2016	101567971	93,12789	2172	4269	6441	SO:0001819	synonymous_variant	79705	exon19			CGACAACGACATC	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.2655C>T	15.37:g.101567971C>T		183	0	0		129	31	0.24031	NM_024652		Silent	SNP	ENST00000388948.3	37	CCDS42086.1																																																																																			C|0.995;T|0.005	0.005	strong		0.632	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652		T	101567971	C	T	101567971	2	4	30	1	0	0	0	0	0	0	0	1	9041	535	19	1		1	LRRK1	15	101567971	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1317053	101567971	963421	519	13670											
TMEM8A	58986	hgsc.bcm.edu	37	chr16	427452	427452	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cccgggggccgggtgggaaaCgttgacggaggcattgcttc	6	7	18	10	4	0	1	0	1	0	0	1	3	0	3	2	6	2	3	2	6	1	3	rs146645376	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:427452C>T	ENST00000431232.2	-	3	593	c.433G>A	c.(433-435)Gtt>Att	p.V145I	TMEM8A_ENST00000250930.3_5'UTR|TMEM8A_ENST00000476735.1_5'UTR	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	145					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						GGGTGGGAAACGTTGACGGAG	0.692											OREG0003703	type=REGULATORY REGION|Gene=TMEM8|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	3	0.000599042	0.0	0.0014	5008	,	,		15162	0.0		0.002	False		,,,				2504	0.0				p.V145I		Atlas-SNP	.											.	TMEM8A	49	.	0			c.G433A						PASS	.	C	ILE/VAL	1,4383		0,1,2191	20	21	21		433	-2.8	0.7	16	dbSNP_134	21	21,8571		0,21,4275	yes	missense	TMEM8A	NM_021259.2	29	0,22,6466	TT,TC,CC		0.2444,0.0228,0.1695	benign	145/772	427452	22,12954	2192	4296	6488	SO:0001583	missense	58986	exon3			GGGAAACGTTGAC	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.433G>A	16.37:g.427452C>T	ENSP00000401338:p.Val145Ile	124	0	0	588	166	76	0.457831	NM_021259	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Missense_Mutation	SNP	ENST00000431232.2	37	CCDS10407.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	2.751	-0.260131	0.05791	2.28E-4	0.002444	ENSG00000129925	ENST00000431232	T	0.22945	1.93	4.59	-2.78	0.05859	.	0.629806	0.14558	N	0.312254	T	0.09158	0.0226	N	0.16833	0.445	0.80722	D	1	B	0.16396	0.017	B	0.06405	0.002	T	0.28364	-1.0046	10	0.15066	T	0.55	-0.0054	12.862	0.57918	0.0:0.1718:0.0:0.8282	.	145	Q9HCN3	TMM8A_HUMAN	I	145	ENSP00000401338:V145I	ENSP00000401338:V145I	V	-	1	0	TMEM8A	367453	0.069000	0.21087	0.699000	0.30290	0.293000	0.27360	-0.831000	0.04405	-0.760000	0.04677	0.563000	0.77884	GTT	C|0.998;T|0.002	0.002	strong		0.692	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259		T	427452	C	T	427452	3	4	30	1	0	0	0	0	1	0	0	0	16229	536	19	1	1926	1	TMEM8A	16	427452	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10		427452	89927301	520	13671											
CHTF18	63922	hgsc.bcm.edu	37	chr16	841238	841238	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacgagaggccttcccggaaGcccaggcccagtgttgagcc	8	5	13	15	2	0	2	0	1	0	1	1	4	1	3	5	3	2	1	5	3	1	2	rs151271197	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:841238G>A	ENST00000262315.9	+	8	1035	c.972G>A	c.(970-972)aaG>aaA	p.K324K	RPUSD1_ENST00000007264.2_5'Flank|RPUSD1_ENST00000567114.1_5'Flank|CHTF18_ENST00000455171.2_Silent_p.K352K|RPUSD1_ENST00000565809.1_5'Flank|CHTF18_ENST00000317063.6_Silent_p.K519K|CHTF18_ENST00000491530.1_3'UTR	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	324					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)				CTTCCCGGAAGCCCAGGCCCA	0.642													G|||	27	0.00539137	0.0	0.0058	5008	,	,		18196	0.0		0.008	False		,,,				2504	0.0153				p.K324K		Atlas-SNP	.											.	CHTF18	52	.	0			c.G972A						PASS	.	G		5,4119		0,5,2057	19	24	22		972	1.3	1	16	dbSNP_134	22	86,8280		1,84,4098	no	coding-synonymous	CHTF18	NM_022092.2		1,89,6155	AA,AG,GG		1.028,0.1212,0.7286		324/976	841238	91,12399	2062	4183	6245	SO:0001819	synonymous_variant	63922	exon8			CCGGAAGCCCAGG	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.972G>A	16.37:g.841238G>A		76	0	0		79	41	0.518987	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Silent	SNP	ENST00000262315.9	37	CCDS45371.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	G	1.548	-0.540090	0.04053	0.001212	0.01028	ENSG00000127586	ENST00000426047	.	.	.	4.85	1.28	0.21552	.	.	.	.	.	T	0.43787	0.1263	.	.	.	0.41571	D	0.988681	.	.	.	.	.	.	T	0.36768	-0.9734	4	.	.	.	-39.2725	5.5091	0.16870	0.4904:0.0:0.5096:0.0	.	.	.	.	T	220	.	.	A	+	1	0	CHTF18	781239	0.890000	0.30428	0.994000	0.49952	0.848000	0.48234	0.510000	0.22723	0.579000	0.29504	0.579000	0.79373	GCC	G|0.995;A|0.005	0.005	strong		0.642	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092		A	841238	G	A	841238	2	1	30	1	0	0	0	0	0	0	0	1	3416	962	34	2		2	CHTF18	16	841238	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	413786	841238	89513515	521	13672											
TELO2	9894	hgsc.bcm.edu	37	chr16	1555505	1555505	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccaacaccccgtgcctgcCagaggcagccgtctctcagc	7	6	9	19	2	2	1	1	0	1	1	4	1	3	1	6	1	5	1	6	1	1	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:1555505C>T	ENST00000262319.6	+	16	2216	c.1937C>T	c.(1936-1938)cCa>cTa	p.P646L	TELO2_ENST00000564507.1_3'UTR	NM_016111.3	NP_057195.2	Q9Y4R8	TELO2_HUMAN	telomere maintenance 2	646					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)				CCGTGCCTGCCAGAGGCAGCC	0.667																																					p.P646L		Atlas-SNP	.											.	TELO2	44	.	0			c.C1937T						PASS	.						33	37	36					16																	1555505		2198	4297	6495	SO:0001583	missense	9894	exon16			GCCTGCCAGAGGC	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.1937C>T	16.37:g.1555505C>T	ENSP00000262319:p.Pro646Leu	102	0	0		131	61	0.465649	NM_016111	D3DU73|O75168|Q7LDV4|Q9BR21	Missense_Mutation	SNP	ENST00000262319.6	37	CCDS32363.1	.	.	.	.	.	.	.	.	.	.	C	9.403	1.078424	0.20227	.	.	ENSG00000100726	ENST00000437914;ENST00000262319	T	0.14893	2.47	3.64	1.62	0.23740	.	0.309815	0.24107	N	0.041482	T	0.12305	0.0299	L	0.50333	1.59	0.21147	N	0.999776	B	0.26635	0.155	B	0.20384	0.029	T	0.27706	-1.0066	10	0.22706	T	0.39	-0.0024	5.4471	0.16541	0.1965:0.693:0.0:0.1106	.	646	Q9Y4R8	TELO2_HUMAN	L	169;646	ENSP00000262319:P646L	ENSP00000262319:P646L	P	+	2	0	TELO2	1495506	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.334000	0.19787	0.069000	0.16605	-1.436000	0.01078	CCA	.	.	none		0.667	TELO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103602.2	NM_016111		T	1555505	C	T	1555505	3	4	30	1	0	0	0	0	1	0	0	0	15772	594	21	2	1995	2	TELO2	16	1555505	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	714267	1555505	88799248	522	13673											
ABCA3	21	hgsc.bcm.edu	37	chr16	2329071	2329071	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtacatgaccagcatctcccGgcctgtcatgtggtccagca	8	9	10	14	1	2	1	1	1	1	0	4	1	3	1	4	2	3	3	4	2	1	1	rs146709251	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2329071G>A	ENST00000301732.5	-	29	5120	c.4420C>T	c.(4420-4422)Cgg>Tgg	p.R1474W	ABCA3_ENST00000382381.3_Missense_Mutation_p.R1416W	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	1474	ABC transporter 2. {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)	AGCATCTCCCGGCCTGTCATG	0.677													G|||	11	0.00219649	0.0	0.0	5008	,	,		18482	0.0		0.0109	False		,,,				2504	0.0				p.R1474W		Atlas-SNP	.											.	ABCA3	176	.	0			c.C4420T						PASS	.	G	TRP/ARG	1,4395	2.1+/-5.4	0,1,2197	56	57	57		4420	3.3	1	16	dbSNP_134	57	31,8569	22.2+/-67.0	0,31,4269	yes	missense	ABCA3	NM_001089.2	101	0,32,6466	AA,AG,GG		0.3605,0.0227,0.2462	probably-damaging	1474/1705	2329071	32,12964	2198	4300	6498	SO:0001583	missense	21	exon29			TCTCCCGGCCTGT	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.4420C>T	16.37:g.2329071G>A	ENSP00000301732:p.Arg1474Trp	134	0	0		143	67	0.468531	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Missense_Mutation	SNP	ENST00000301732.5	37	CCDS10466.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	G	13.04	2.118520	0.37436	2.27E-4	0.003605	ENSG00000167972	ENST00000301732;ENST00000382381	D	0.94613	-3.47	5.35	3.32	0.38043	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.057559	0.64402	N	0.000002	D	0.92414	0.7592	M	0.76328	2.33	0.80722	D	1	P;P	0.43024	0.798;0.689	P;P	0.47573	0.55;0.466	D	0.90607	0.4549	10	0.56958	D	0.05	.	9.1349	0.36868	0.0781:0.0:0.7721:0.1498	.	1478;1474	Q4LE27;Q99758	.;ABCA3_HUMAN	W	1474;1478	ENSP00000301732:R1474W	ENSP00000301732:R1474W	R	-	1	2	ABCA3	2269072	1.000000	0.71417	0.998000	0.56505	0.958000	0.62258	2.466000	0.45084	0.580000	0.29522	0.561000	0.74099	CGG	G|0.997;A|0.003	0.003	strong		0.677	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089		A	2329071	G	A	2329071	3	1	30	1	0	0	0	0	1	0	0	0	33	1115	39	1	714	1	ABCA3	16	2329071	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	773566	2329071	88025682	523	13674											
AMDHD2	51005	hgsc.bcm.edu	37	chr16	2577943	2577943	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagttgggccgtagccacgaAgtgatccgggcgctgacggc	7	6	17	11	5	0	2	0	2	0	0	1	4	1	2	3	3	1	3	3	3	2	2	rs182580356	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2577943A>C	ENST00000293971.6	+	5	679	c.585A>C	c.(583-585)gaA>gaC	p.E195D	AMDHD2_ENST00000565570.1_Intron|ATP6C_ENST00000569317.1_Missense_Mutation_p.E148D|AMDHD2_ENST00000413459.3_Missense_Mutation_p.E195D|AMDHD2_ENST00000302956.4_Missense_Mutation_p.E195D|CEMP1_ENST00000382350.1_Intron	NM_015944.3	NP_057028.2	Q9Y303	NAGA_HUMAN	amidohydrolase domain containing 2	195					carbohydrate metabolic process (GO:0005975)|N-acetylglucosamine metabolic process (GO:0006044)|N-acetylneuraminate catabolic process (GO:0019262)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|N-acetylglucosamine-6-phosphate deacetylase activity (GO:0008448)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(3)|skin(2)|urinary_tract(2)	19						GTAGCCACGAAGTGATCCGGG	0.682													G|||	5	0.000998403	0.0	0.0043	5008	,	,		13543	0.0		0.002	False		,,,				2504	0.0				p.E195D		Atlas-SNP	.											.	AMDHD2	33	.	0			c.A585C						PASS	.	A	ASP/GLU,ASP/GLU	2,4356		0,2,2177	11	15	13		585,585	-1.5	0.9	16		13	22,8546		0,22,4262	yes	missense,missense	AMDHD2	NM_001145815.1,NM_015944.3	45,45	0,24,6439	CC,CA,AA		0.2568,0.0459,0.1857	benign,benign	195/595,195/440	2577943	24,12902	2179	4284	6463	SO:0001583	missense	51005	exon5			CCACGAAGTGATC	AF132948	CCDS10471.1, CCDS53984.1	16p13.3	2008-02-05			ENSG00000162066	ENSG00000162066			24262	protein-coding gene	gene with protein product						10810093	Standard	NM_001145815		Approved	CGI-14	uc010uwc.2	Q9Y303	OTTHUMG00000128866	ENST00000293971.6:c.585A>C	16.37:g.2577943A>C	ENSP00000293971:p.Glu195Asp	39	0	0		18	10	0.555556	NM_001145815	B4DL77|Q8WV54	Missense_Mutation	SNP	ENST00000293971.6	37		3	0.0013736263736263737	0	0.0	3	0.008287292817679558	0	0.0	0	0.0	A	11.47	1.647305	0.29246	4.59E-4	0.002568	ENSG00000162066	ENST00000413459;ENST00000302956;ENST00000293971	D;D;D	0.99948	-8.65;-8.65;-8.65	5.32	-1.49	0.08718	Amidohydrolase 1 (1);Metal-dependent hydrolase, composite domain (1);	0.163396	0.52532	D	0.000061	D	0.99420	0.9795	L	0.35414	1.06	0.80722	D	1	B;B;B	0.19706	0.038;0.002;0.002	B;B;B	0.28553	0.091;0.029;0.017	D	0.99978	1.2301	10	0.27082	T	0.32	-22.327	10.5895	0.45302	0.3942:0.0:0.6058:0.0	.	195;195;195	Q9Y303-3;Q9Y303;Q9Y303-2	.;NAGA_HUMAN;.	D	195	ENSP00000391596:E195D;ENSP00000307481:E195D;ENSP00000293971:E195D	ENSP00000293971:E195D	E	+	3	2	AMDHD2	2517944	1.000000	0.71417	0.855000	0.33649	0.188000	0.23474	0.819000	0.27308	-0.235000	0.09767	-0.146000	0.13790	GAA	A|0.999;C|0.001	0.001	strong		0.682	AMDHD2-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000435652.1	NM_015944		C	2577943	A	C	2577943	3	2	30	1	0	0	0	0	1	0	0	0	568	69	3	5	603	5	AMDHD2	16	2577943	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	248872	2577943	87776810	524	13675											
SRRM2	23524	hgsc.bcm.edu	37	chr16	2816519	2816519	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccgaaggagatctcgatctcGcacatctccagtaactcgaa	12	8	8	13	4	3	1	0	0	3	1	7	5	3	1	2	1	1	2	2	1	3	1	rs138447860	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2816519G>A	ENST00000301740.8	+	11	6539	c.5990G>A	c.(5989-5991)cGc>cAc	p.R1997H		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	1997	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						TCTCGATCTCGCACATCTCCA	0.577													G|||	10	0.00199681	0.0	0.0043	5008	,	,		17504	0.0		0.007	False		,,,				2504	0.0				p.R1997H		Atlas-SNP	.											.	SRRM2	263	.	0			c.G5990A						PASS	.	G	HIS/ARG	3,4393	6.2+/-15.9	0,3,2195	71	75	74		5990	5.3	1	16	dbSNP_134	74	50,8550	32.3+/-84.9	0,50,4250	yes	missense	SRRM2	NM_016333.3	29	0,53,6445	AA,AG,GG		0.5814,0.0682,0.4078	probably-damaging	1997/2753	2816519	53,12943	2198	4300	6498	SO:0001583	missense	23524	exon11			GATCTCGCACATC	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.5990G>A	16.37:g.2816519G>A	ENSP00000301740:p.Arg1997His	87	0	0		99	48	0.484848	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	37	CCDS32373.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	11.77	1.736455	0.30774	6.82E-4	0.005814	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933	T	0.24908	1.83	5.26	5.26	0.73747	.	0.000000	0.53938	D	0.000043	T	0.23572	0.0570	N	0.08118	0	0.35761	D	0.820188	D	0.76494	0.999	D	0.69654	0.965	T	0.48198	-0.9056	10	0.62326	D	0.03	-6.3676	16.354	0.83228	0.0:0.0:1.0:0.0	.	1997	Q9UQ35	SRRM2_HUMAN	H	1997;1997;1249	ENSP00000301740:R1997H	ENSP00000301740:R1997H	R	+	2	0	SRRM2	2756520	0.967000	0.33354	0.988000	0.46212	0.988000	0.76386	3.451000	0.52964	2.466000	0.83321	0.650000	0.86243	CGC	G|0.997;A|0.003	0.003	strong		0.577	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			A	2816519	G	A	2816519	3	1	30	1	0	0	0	0	1	0	0	0	15184	1087	38	1	6028	1	SRRM2	16	2816519	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	238576	2816519	87538234	525	13676											
SRRM2	23524	hgsc.bcm.edu	37	chr16	2819196	2819196	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcatcttcctcctcctcGtcgtcttcctccccttcccc	1	15	2	23	2	3	0	1	0	2	0	12	0	10	0	9	0	0	0	9	0	0	3	rs150110237	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:2819196G>C	ENST00000301740.8	+	12	8481	c.7932G>C	c.(7930-7932)tcG>tcC	p.S2644S	AC092117.2_ENST00000581119.1_RNA|SRRM2_ENST00000574593.1_3'UTR	NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	2644	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						cctcctcctcgtcgtcttcct	0.597													C|||	9	0.00179712	0.0068	0.0	5008	,	,		18150	0.0		0.0	False		,,,				2504	0.0				p.S2644S		Atlas-SNP	.											.	SRRM2	263	.	0			c.G7932C						PASS	.	C		24,4372	823.0+/-416.5	0,24,2174	112	112	112		7932	-3.7	0.1	16	dbSNP_134	112	5,8595	819.0+/-406.8	0,5,4295	no	coding-synonymous	SRRM2	NM_016333.3		0,29,6469	CC,CG,GG		0.0581,0.546,0.2231		2644/2753	2819196	29,12967	2198	4300	6498	SO:0001819	synonymous_variant	23524	exon12			CTCCTCGTCGTCT	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.7932G>C	16.37:g.2819196G>C		83	0	0		77	22	0.285714	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Silent	SNP	ENST00000301740.8	37	CCDS32373.1																																																																																			G|0.998;C|0.002	0.002	strong		0.597	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1			C	2819196	G	C	2819196	2	2	30	1	0	0	0	0	0	0	0	1	15184	1132	40	4		4	SRRM2	16	2819196	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2677	2819196	87535557	526	13677											
TRAP1	10131	hgsc.bcm.edu	37	chr16	3724365	3724365	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgggcacgtagaagatgctgCggatgttgagcggtgcgtcc	7	8	17	9	5	0	3	0	1	0	2	1	4	1	4	1	3	4	4	1	3	2	2	rs145715008		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:3724365C>T	ENST00000246957.5	-	9	1107	c.1019G>A	c.(1018-1020)cGc>cAc	p.R340H	TRAP1_ENST00000573872.1_5'UTR|TRAP1_ENST00000575671.1_Missense_Mutation_p.R131H|TRAP1_ENST00000538171.1_Missense_Mutation_p.R287H	NM_016292.2	NP_057376.2	Q12931	TRAP1_HUMAN	TNF receptor-associated protein 1	340					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)				GAAGATGCTGCGGATGTTGAG	0.602													C|||	1	0.000199681	0.0	0.0	5008	,	,		20813	0.001		0.0	False		,,,				2504	0.0				p.R340H		Atlas-SNP	.											TRAP1,colon,carcinoma,-1,1	TRAP1	53	1	0			c.G1019A						PASS	.	C	HIS/ARG	2,4392	4.2+/-10.8	0,2,2195	160	102	122		1019	5.8	1	16	dbSNP_134	122	9,8591	7.1+/-27.0	0,9,4291	yes	missense	TRAP1	NM_016292.2	29	0,11,6486	TT,TC,CC		0.1047,0.0455,0.0847	possibly-damaging	340/705	3724365	11,12983	2197	4300	6497	SO:0001583	missense	10131	exon9			ATGCTGCGGATGT	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.1019G>A	16.37:g.3724365C>T	ENSP00000246957:p.Arg340His	138	0	0		163	90	0.552147	NM_016292	B4DR68|D3DUC8|F5H897|O43642|O75235|Q9UHL5	Missense_Mutation	SNP	ENST00000246957.5	37	CCDS10508.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	21.3	4.131985	0.77662	4.55E-4	0.001047	ENSG00000126602	ENST00000246957;ENST00000538171	T;T	0.12569	2.67;2.67	5.82	5.82	0.92795	Ribosomal protein S5 domain 2-type fold (1);	0.000000	0.85682	D	0.000000	T	0.18759	0.0450	L	0.49256	1.55	0.80722	D	1	P;P	0.36944	0.518;0.574	B;B	0.36922	0.152;0.236	T	0.00768	-1.1574	10	0.87932	D	0	-32.3858	19.0936	0.93240	0.0:1.0:0.0:0.0	.	287;340	F5H897;Q12931	.;TRAP1_HUMAN	H	340;287	ENSP00000246957:R340H;ENSP00000442070:R287H	ENSP00000246957:R340H	R	-	2	0	TRAP1	3664366	1.000000	0.71417	1.000000	0.80357	0.202000	0.24057	7.424000	0.80242	2.757000	0.94681	0.655000	0.94253	CGC	C|0.999;T|0.001	0.001	strong		0.602	TRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251586.2	NM_016292		T	3724365	C	T	3724365	3	4	30	1	0	0	0	0	1	0	0	0	16470	768	27	1	1135	1	TRAP1	16	3724365	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	905169	3724365	86630388	527	13678											
CREBBP	1387	hgsc.bcm.edu	37	chr16	3808872	3808872	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tactggaattccgaggagctGgggatctacaggctgccgga	9	8	15	9	2	1	0	0	0	1	0	2	5	2	4	2	6	4	2	2	6	3	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:3808872G>A	ENST00000262367.5	-	17	4161	c.3352C>T	c.(3352-3354)Cag>Tag	p.Q1118*	CREBBP_ENST00000382070.3_Nonsense_Mutation_p.Q1080*	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1118	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				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)		CCGAGGAGCTGGGGATCTACA	0.433			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.Q1118X		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.C3352T						PASS	.						83	81	81					16																	3808872		2197	4300	6497	SO:0001587	stop_gained	1387	exon17			GGAGCTGGGGATC	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.3352C>T	16.37:g.3808872G>A	ENSP00000262367:p.Gln1118*	136	0	0		141	44	0.312057	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Nonsense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	G	49	15.347356	0.99831	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070	.	.	.	5.05	5.05	0.67936	.	0.000000	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.16420	T	0.52	-9.7097	18.7675	0.91879	0.0:0.0:1.0:0.0	.	.	.	.	X	1118;1148;1080	.	ENSP00000262367:Q1118X	Q	-	1	0	CREBBP	3748873	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.034000	0.64152	2.499000	0.84300	0.561000	0.74099	CAG	.	.	none		0.433	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		A	3808872	G	A	3808872	4	1	30	1	0	0	0	0	0	1	0	0	3863	1357	47	2	4036	2	CREBBP	16	3808872	Nonsense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	84507	3808872	86545881	528	13679											
ANKS3	124401	hgsc.bcm.edu	37	chr16	4776685	4776685	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gttggcattggctccactgtCcaagaggaacctgaccatgt	9	10	11	11	0	0	2	0	1	0	1	2	3	2	3	4	3	1	3	4	3	2	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:4776685C>T	ENST00000304283.4	-	5	760	c.466G>A	c.(466-468)Gac>Aac	p.D156N	ANKS3_ENST00000585773.1_Missense_Mutation_p.D83N|ANKS3_ENST00000450067.2_Intron|ANKS3_ENST00000592711.1_Intron|ANKS3_ENST00000446014.2_Missense_Mutation_p.D27N	NM_133450.3	NP_597707.1	Q6ZW76	ANKS3_HUMAN	ankyrin repeat and sterile alpha motif domain containing 3	156										endometrium(5)|kidney(4)|large_intestine(3)|lung(5)|prostate(1)|stomach(1)	19						GCTCCACTGTCCAAGAGGAAC	0.567																																					p.D156N		Atlas-SNP	.											.	ANKS3	44	.	0			c.G466A						PASS	.						95	78	84					16																	4776685		2197	4300	6497	SO:0001583	missense	124401	exon5			CACTGTCCAAGAG	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.466G>A	16.37:g.4776685C>T	ENSP00000304586:p.Asp156Asn	91	0	0		102	5	0.0490196	NM_133450	B4DWU4|D3DUE2|Q8TF25	Missense_Mutation	SNP	ENST00000304283.4	37	CCDS10520.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.496348	0.85069	.	.	ENSG00000168096	ENST00000304283;ENST00000446014	T;T	0.65732	-0.12;-0.17	5.35	5.35	0.76521	Ankyrin repeat-containing domain (4);	0.136125	0.64402	D	0.000003	T	0.66317	0.2777	L	0.41573	1.285	0.80722	D	1	P	0.47253	0.892	P	0.51055	0.657	T	0.68416	-0.5414	10	0.62326	D	0.03	-17.1943	18.4258	0.90608	0.0:1.0:0.0:0.0	.	156	Q6ZW76	ANKS3_HUMAN	N	156;27	ENSP00000304586:D156N;ENSP00000406796:D27N	ENSP00000304586:D156N	D	-	1	0	ANKS3	4716686	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.445000	0.80570	2.675000	0.91044	0.555000	0.69702	GAC	.	.	none		0.567	ANKS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251642.3	NM_133450		T	4776685	C	T	4776685	3	4	30	1	0	0	0	0	1	0	0	0	690	855	30	2	1556	2	ANKS3	16	4776685	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	967813	4776685	85578068	529	13680											
CLEC16A	23274	hgsc.bcm.edu	37	chr16	11272330	11272330	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacagccagcctgtcccccaGcctcgtccctgcccggcagc	5	5	10	21	2	0	0	0	0	0	0	3	1	2	0	7	1	5	1	7	1	0	0	rs72650689	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:11272330G>A	ENST00000409790.1	+	24	3175	c.2945G>A	c.(2944-2946)aGc>aAc	p.S982N	CLEC16A_ENST00000381822.2_Missense_Mutation_p.S69N	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						CTGTCCCCCAGCCTCGTCCCT	0.637													G|||	14	0.00279553	0.0008	0.0	5008	,	,		18303	0.0		0.0089	False		,,,				2504	0.0041				p.S982N		Atlas-SNP	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2945A						PASS	.	G	ASN/SER	6,4296		0,6,2145	63	77	72		2945	4.6	1	16	dbSNP_130	72	64,8436		0,64,4186	yes	missense	CLEC16A	NM_015226.2	46	0,70,6331	AA,AG,GG		0.7529,0.1395,0.5468	possibly-damaging	982/1054	11272330	70,12732	2151	4250	6401	SO:0001583	missense	23274	exon23			CCCCCAGCCTCGT	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.2945G>A	16.37:g.11272330G>A	ENSP00000387122:p.Ser982Asn	106	0	0		96	44	0.458333	NM_015226		Missense_Mutation	SNP	ENST00000409790.1	37	CCDS45409.1	9	0.004120879120879121	0	0.0	0	0.0	0	0.0	9	0.011873350923482849	G	26.8	4.771612	0.90108	0.001395	0.007529	ENSG00000038532	ENST00000409790;ENST00000542102;ENST00000381822	T	0.55930	0.49	4.64	4.64	0.57946	.	0.000000	0.85682	D	0.000000	T	0.52058	0.1711	L	0.27053	0.805	0.38000	D	0.934194	D;D	0.67145	0.996;0.967	D;P	0.75484	0.986;0.878	T	0.65878	-0.6061	10	0.72032	D	0.01	-25.0792	15.032	0.71713	0.0:0.0:1.0:0.0	.	69;982	Q2KHT3-3;Q2KHT3	.;CL16A_HUMAN	N	982;982;69	ENSP00000387122:S982N	ENSP00000371244:S69N	S	+	2	0	CLEC16A	11179831	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	6.910000	0.75741	2.304000	0.77564	0.655000	0.94253	AGC	A|0.006;G|0.994	0.006	strong		0.637	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226		A	11272330	G	A	11272330	3	1	30	1	0	0	0	0	1	0	0	0	3502	971	34	2	3035	2	CLEC16A	16	11272330	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	6495645	11272330	79082423	530	13681											
USP31	57478	hgsc.bcm.edu	37	chr16	23091371	23091371	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtccatagggccgtctccacGgggaccaatgcgatggcaaa	10	6	13	12	3	1	0	0	0	1	0	3	2	2	1	4	4	1	1	4	4	3	1			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:23091371G>A	ENST00000219689.7	-	13	2071	c.2072C>T	c.(2071-2073)cCg>cTg	p.P691L		NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	333	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)		CCGTCTCCACGGGGACCAATG	0.562																																					p.P691L		Atlas-SNP	.											.	USP31	122	.	0			c.C2072T						PASS	.						126	109	114					16																	23091371		2197	4300	6497	SO:0001583	missense	57478	exon13			CTCCACGGGGACC	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.2072C>T	16.37:g.23091371G>A	ENSP00000219689:p.Pro691Leu	248	0	0		264	15	0.0568182	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000219689.7	37	CCDS10607.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.393555	0.83011	.	.	ENSG00000103404	ENST00000219689	T	0.10005	2.92	4.91	3.96	0.45880	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	U	0.000000	T	0.25791	0.0628	L	0.50993	1.605	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.00641	-1.1631	10	0.59425	D	0.04	-16.8435	12.2435	0.54558	0.0829:0.0:0.9171:0.0	.	691	Q70CQ4	UBP31_HUMAN	L	691	ENSP00000219689:P691L	ENSP00000219689:P691L	P	-	2	0	USP31	22998872	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	9.471000	0.97696	1.058000	0.40530	0.557000	0.71058	CCG	.	.	none		0.562	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718		A	23091371	G	A	23091371	3	1	30	1	0	0	0	0	1	0	0	0	17077	1116	39	1	2002	1	USP31	16	23091371	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	11819041	23091371	67263382	531	13682											
IL21R	50615	hgsc.bcm.edu	37	chr16	27460436	27460436	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggcgggctcacccctggcCggcctggatatggacacgtt	6	7	15	13	3	1	0	1	0	0	0	1	3	1	2	4	6	0	2	4	6	1	2	rs3093408		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:27460436C>T	ENST00000337929.3	+	9	1922	c.1449C>T	c.(1447-1449)gcC>gcT	p.A483A	IL21R_ENST00000564089.1_Silent_p.A483A|IL21R-AS1_ENST00000563191.1_RNA|IL21R_ENST00000395754.4_Silent_p.A483A|IL21R_ENST00000395755.1_Silent_p.A483A	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	483					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						CACCCCTGGCCGGCCTGGATA	0.672			T	BCL6	NHL								C|||	1	0.000199681	0.0	0.0014	5008	,	,		18843	0.0		0.0	False		,,,				2504	0.0				p.A505A		Atlas-SNP	.		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	.	IL21R	95	.	0			c.C1515T						PASS	.	C	,,	0,4394		0,0,2197	41	38	39		1449,1449,1515	-7.6	0	16	dbSNP_103	39	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	IL21R	NM_021798.3,NM_181078.2,NM_181079.4	,,	0,3,6494	TT,TC,CC		0.0349,0.0,0.0231	,,	483/539,483/539,505/561	27460436	3,12991	2197	4300	6497	SO:0001819	synonymous_variant	50615	exon10			CCTGGCCGGCCTG	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.1449C>T	16.37:g.27460436C>T		131	0	0		105	55	0.52381	NM_181079	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Silent	SNP	ENST00000337929.3	37	CCDS10630.1																																																																																			C|0.999;T|0.001	0.001	strong		0.672	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078		T	27460436	C	T	27460436	2	4	30	1	0	0	0	0	0	0	0	1	7680	639	23	1		1	IL21R	16	27460436	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	4369065	27460436	62894317	532	13683											
ASPHD1	253982	hgsc.bcm.edu	37	chr16	29917177	29917177	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	accccaacgtggcaggggctGagcgccaggccctcgacttt	7	6	13	15	3	0	1	0	1	0	0	1	2	0	1	4	4	2	2	4	4	1	1			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:29917177G>A	ENST00000308748.5	+	3	1384	c.1132G>A	c.(1132-1134)Gag>Aag	p.E378K	ASPHD1_ENST00000483405.1_Missense_Mutation_p.E97K	NM_181718.3	NP_859069.2	Q5U4P2	ASPH1_HUMAN	aspartate beta-hydroxylase domain containing 1	378					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						GGCAGGGGCTGAGCGCCAGGC	0.637																																					p.E378K		Atlas-SNP	.											.	ASPHD1	28	.	0			c.G1132A						PASS	.						70	60	64					16																	29917177		2197	4300	6497	SO:0001583	missense	253982	exon3			GGGGCTGAGCGCC	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.1132G>A	16.37:g.29917177G>A	ENSP00000311447:p.Glu378Lys	111	0	0		99	56	0.565657	NM_181718	A0AVE3|B7ZLZ3|Q8IW63|Q8N316|Q96H00	Missense_Mutation	SNP	ENST00000308748.5	37	CCDS10660.1	.	.	.	.	.	.	.	.	.	.	G	36	5.897740	0.97081	.	.	ENSG00000174939	ENST00000414952;ENST00000308748	T;T	0.59364	0.27;0.27	5.76	5.76	0.90799	.	0.000000	0.64402	D	0.000001	T	0.80177	0.4575	M	0.86953	2.85	0.80722	D	1	D	0.76494	0.999	D	0.75020	0.985	T	0.82938	-0.0209	10	0.87932	D	0	-22.1497	18.742	0.91777	0.0:0.0:1.0:0.0	.	378	Q5U4P2	ASPH1_HUMAN	K	378	ENSP00000388036:E378K;ENSP00000311447:E378K	ENSP00000311447:E378K	E	+	1	0	ASPHD1	29824678	1.000000	0.71417	0.923000	0.36655	0.980000	0.70556	9.149000	0.94659	2.728000	0.93425	0.655000	0.94253	GAG	.	.	none		0.637	ASPHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255163.2	NM_181718		A	29917177	G	A	29917177	3	1	30	1	0	0	0	0	1	0	0	0	1054	1291	45	2	1142	2	ASPHD1	16	29917177	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2456741	29917177	60437576	533	13684											
YPEL3	83719	hgsc.bcm.edu	37	chr16	30106716	30106716	+	5'UTR	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccgggggcagtggccccaCgcggggagcggcccacgggg	4	1	22	14	5	0	0	0	0	0	0	0	1	0	1	4	9	1	1	4	9	0	0	rs184524218	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:30106716C>A	ENST00000398838.4	-	0	187				RP11-455F5.3_ENST00000515455.2_RNA|YPEL3_ENST00000398841.1_Missense_Mutation_p.V30L|YPEL3_ENST00000562641.1_Missense_Mutation_p.V30L|YPEL3_ENST00000566595.1_5'UTR|YPEL3_ENST00000565479.1_Intron|YPEL3_ENST00000563788.1_5'UTR|YPEL3_ENST00000566134.1_5'UTR	NM_001145524.1	NP_001138996.1	P61236	YPEL3_HUMAN	yippee-like 3 (Drosophila)							nucleus (GO:0005634)				endometrium(1)|lung(2)	3						AGTGGCCCCACGCGGGGAGCG	0.672													C|||	16	0.00319489	0.0	0.0014	5008	,	,		14972	0.0		0.0129	False		,,,				2504	0.002				p.V30L		Atlas-SNP	.											.	YPEL3	5	.	0			c.G88T						PASS	.	C	,LEU/VAL	6,3864		0,6,1929	23	26	25		,88	3.5	1	16		25	108,8124		0,108,4008	yes	utr-5,missense	YPEL3	NM_001145524.1,NM_031477.4	,32	0,114,5937	AA,AC,CC		1.312,0.155,0.942	,	,30/158	30106716	114,11988	1935	4116	6051	SO:0001623	5_prime_UTR_variant	83719	exon1			GCCCCACGCGGGG	AF305622	CCDS42147.1, CCDS45459.1	16p11	2008-02-05							18327	protein-coding gene	gene with protein product		609724					Standard	NM_031477		Approved	MGC10500	uc002dwm.3	P61236		ENST00000398838.4:c.-27G>T	16.37:g.30106716C>A		44	0	0		37	24	0.648649	NM_031477	Q65Z99|Q86VK6|Q9BSJ4|Q9CQB6	Missense_Mutation	SNP	ENST00000398838.4	37	CCDS45459.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	C	13.01	2.110837	0.37242	0.00155	0.01312	ENSG00000090238	ENST00000398841	.	.	.	3.52	3.52	0.40303	.	0.000000	0.30109	N	0.010388	T	0.16128	0.0388	.	.	.	0.21627	N	0.999613	B	0.06786	0.001	B	0.06405	0.002	T	0.11591	-1.0581	8	0.10902	T	0.67	-5.6356	10.7694	0.46314	0.0:0.8051:0.1949:0.0	.	30	P61236-2	.	L	30	.	ENSP00000381821:V30L	V	-	1	0	YPEL3	30014217	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.998000	0.49465	1.811000	0.52892	0.561000	0.74099	GTG	C|0.995;A|0.005	0.005	strong		0.672	YPEL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434043.1	NM_031477		A	30106716	C	A	30106716	1	1	30	0	1	0	0	0	0	0	0	0	17506	536	19	4		4	YPEL3	16	30106716	5'UTR	SNP	C	TCGA-GR-7353-01A-11D-2210-10	189539	30106716	60248037	534	13685											
SRCAP	10847	hgsc.bcm.edu	37	chr16	30732558	30732558	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggacctcacggcctcccaCgccaaccttgtccctaaagc	8	7	8	18	2	1	0	1	0	0	0	3	1	3	1	6	2	2	0	6	2	3	2	rs149248373	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:30732558C>A	ENST00000262518.4	+	21	3687	c.3302C>A	c.(3301-3303)aCg>aAg	p.T1101K	SRCAP_ENST00000395059.2_Missense_Mutation_p.T1101K|SRCAP_ENST00000344771.4_Intron	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	1101	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)			CGGCCTCCCACGCCAACCTTG	0.602													C|||	9	0.00179712	0.0	0.0014	5008	,	,		17448	0.0		0.006	False		,,,				2504	0.002				p.T1101K		Atlas-SNP	.											.	SRCAP	298	.	0			c.C3302A						PASS	.	C	LYS/THR	5,4389	9.9+/-24.2	0,5,2192	109	118	115		3302	4.4	0.9	16	dbSNP_134	115	75,8525	44.0+/-102.2	0,75,4225	yes	missense	SRCAP	NM_006662.2	78	0,80,6417	AA,AC,CC		0.8721,0.1138,0.6157	possibly-damaging	1101/3231	30732558	80,12914	2197	4300	6497	SO:0001583	missense	10847	exon21			CTCCCACGCCAAC	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.3302C>A	16.37:g.30732558C>A	ENSP00000262518:p.Thr1101Lys	124	0	0		127	60	0.472441	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	37	CCDS10689.2	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	11.98	1.799401	0.31869	0.001138	0.008721	ENSG00000080603	ENST00000262518;ENST00000395059	D;D	0.91351	-2.83;-2.72	5.36	4.41	0.53225	.	.	.	.	.	T	0.75759	0.3893	N	0.14661	0.345	0.80722	D	1	P;P	0.38020	0.615;0.481	B;B	0.38954	0.286;0.149	T	0.74940	-0.3493	9	0.28530	T	0.3	-1.5386	7.321	0.26528	0.0:0.7419:0.17:0.0881	.	1101;1101	Q6ZRS2-2;Q6ZRS2	.;SRCAP_HUMAN	K	1101	ENSP00000262518:T1101K;ENSP00000378499:T1101K	ENSP00000262518:T1101K	T	+	2	0	SRCAP	30640059	0.102000	0.21896	0.924000	0.36721	0.955000	0.61496	1.191000	0.32138	1.499000	0.48617	0.557000	0.71058	ACG	C|0.996;A|0.004	0.004	strong		0.602	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		A	30732558	C	A	30732558	3	1	30	1	0	0	0	0	1	0	0	0	15150	536	19	4	3376	4	SRCAP	16	30732558	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	625842	30732558	59622195	535	13686											
ZNF668	79759	hgsc.bcm.edu	37	chr16	31072912	31072912	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccagccccgcccctgctgccGgggcggctgaactctcacct	4	6	11	20	3	1	1	1	1	1	0	2	1	1	1	7	3	4	2	7	3	1	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:31072912G>A	ENST00000538906.1	-	3	2121	c.1337C>T	c.(1336-1338)cCg>cTg	p.P446L	ZNF668_ENST00000417110.2_Missense_Mutation_p.G34R|ZNF668_ENST00000539836.3_Missense_Mutation_p.P469L|ZNF668_ENST00000394983.2_Missense_Mutation_p.P446L|ZNF668_ENST00000535577.1_Missense_Mutation_p.P446L|ZNF668_ENST00000426488.2_Missense_Mutation_p.P469L|ZNF668_ENST00000300849.4_Missense_Mutation_p.P446L	NM_001172668.1	NP_001166139	Q96K58	ZN668_HUMAN	zinc finger protein 668	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(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	27						CCCTGCTGCCGGGGCGGCTGA	0.711																																					p.P469L	Colon(181;1111 1980 5060 10512 25785)	Atlas-SNP	.											.	ZNF668	121	.	0			c.C1406T						PASS	.						32	40	37					16																	31072912		2194	4298	6492	SO:0001583	missense	79759	exon4			GCTGCCGGGGCGG		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.1337C>T	16.37:g.31072912G>A	ENSP00000440149:p.Pro446Leu	20	0	0		20	9	0.45	NM_001172669	C9JHH8|F5H7E7|Q59EV1|Q8N669|Q9H8L4	Missense_Mutation	SNP	ENST00000538906.1	37	CCDS10701.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.02|11.02	1.515722|1.515722	0.27123|0.27123	.|.	.|.	ENSG00000232748|ENSG00000167394	ENST00000417110|ENST00000539836;ENST00000535577;ENST00000538906;ENST00000394983;ENST00000300849	.|T;T;T;T;T	.|0.08546	.|3.08;3.09;3.09;3.09;3.09	4.84|4.84	4.84|4.84	0.62591|0.62591	.|.	.|0.000000	.|0.40302	.|N	.|0.001138	T|T	0.07548|0.07548	0.0190|0.0190	N|N	0.08118|0.08118	0|0	0.80722|0.80722	D|D	1|1	.|D	.|0.69078	.|0.997	.|P	.|0.50708	.|0.648	T|T	0.51702|0.51702	-0.8672|-0.8672	6|10	0.87932|0.21540	D|T	0|0.41	-20.0419|-20.0419	14.9766|14.9766	0.71277|0.71277	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|446	.|Q96K58	.|ZN668_HUMAN	R|L	34|469;446;446;446;446	.|ENSP00000442573:P469L;ENSP00000441349:P446L;ENSP00000440149:P446L;ENSP00000378434:P446L;ENSP00000300849:P446L	ENSP00000391989:G34R|ENSP00000300849:P446L	G|P	+|-	1|2	0|0	AC135050.1|ZNF668	30980413|30980413	0.837000|0.837000	0.29446|0.29446	0.637000|0.637000	0.29366|0.29366	0.430000|0.430000	0.31655|0.31655	1.657000|1.657000	0.37366|0.37366	2.531000|2.531000	0.85337|0.85337	0.462000|0.462000	0.41574|0.41574	GGG|CCG	.	.	none		0.711	ZNF668-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108516.2	NM_024706		A	31072912	G	A	31072912	3	1	30	1	0	0	0	0	1	0	0	0	18090	1116	39	1	526	1	ZNF668	16	31072912	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	340354	31072912	59281841	536	13687											
ABCC11	85320	hgsc.bcm.edu	37	chr16	48226458	48226458	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagagcttgttgtgcagggcCgtggatgccttcctcgtgac	6	11	14	10	2	0	2	0	1	0	1	2	3	1	3	3	2	3	3	3	2	1	3	rs144318062		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:48226458C>T	ENST00000394747.1	-	19	3028	c.2679G>A	c.(2677-2679)acG>acA	p.T893T	ABCC11_ENST00000353782.5_Silent_p.T893T|ABCC11_ENST00000394748.1_Silent_p.T893T|ABCC11_ENST00000356608.2_Silent_p.T893T|ABCC11_ENST00000537808.1_3'UTR	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	893	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				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)	TGTGCAGGGCCGTGGATGCCT	0.552																																					p.T893T		Atlas-SNP	.											.	ABCC11	177	.	0			c.G2679A						PASS	.	C	,,	0,4402		0,0,2201	90	82	85		2679,2679,2679	-9.9	0	16	dbSNP_134	85	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	ABCC11	NM_032583.3,NM_033151.3,NM_145186.2	,,	0,1,6500	TT,TC,CC		0.0116,0.0,0.0077	,,	893/1383,893/1383,893/1345	48226458	1,13001	2201	4300	6501	SO:0001819	synonymous_variant	85320	exon19			CAGGGCCGTGGAT	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.2679G>A	16.37:g.48226458C>T		148	0	0		141	116	0.822695	NM_033151	Q8TDJ0|Q96JA6|Q9BX80	Silent	SNP	ENST00000394747.1	37	CCDS10732.1																																																																																			C|1.000;T|0.000	0.000	weak		0.552	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583		T	48226458	C	T	48226458	2	4	30	1	0	0	0	0	0	0	0	1	51	639	23	1		1	ABCC11	16	48226458	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	17153546	48226458	42128295	537	13688											
IRX6	79190	hgsc.bcm.edu	37	chr16	55362625	55362625	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cctgcagaagttactgctagCcaggaggcccgggggctccg	7	6	15	13	2	0	1	0	0	0	1	1	2	1	2	4	4	4	4	4	4	3	2	rs199714803		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:55362625C>T	ENST00000290552.7	+	5	2067	c.735C>T	c.(733-735)agC>agT	p.S245S	RP11-26L20.3_ENST00000558730.2_RNA	NM_024335.2	NP_077311.2	P78412	IRX6_HUMAN	iroquois homeobox 6	245					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(2)|central_nervous_system(5)|endometrium(3)|kidney(2)|large_intestine(6)|liver(2)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	33						TTACTGCTAGCCAGGAGGCCC	0.582																																					p.S245S		Atlas-SNP	.											.	IRX6	66	.	0			c.C735T						PASS	.																																			SO:0001819	synonymous_variant	79190	exon5			TGCTAGCCAGGAG	AF319966	CCDS32449.1	16q12.2	2011-06-20	2007-07-13	2003-01-10		ENSG00000159387		"Homeoboxes / TALE class"	14675	protein-coding gene	gene with protein product		606196	"iroquois homeobox protein 7", "iroquois homeobox protein 6"	IRX7			Standard	NM_024335		Approved	IRX-3	uc002ehy.3	P78412		ENST00000290552.7:c.735C>T	16.37:g.55362625C>T		34	0	0		42	36	0.857143	NM_024335	B2RN06|Q7Z2K0	Silent	SNP	ENST00000290552.7	37	CCDS32449.1																																																																																			C|0.999;T|0.001	0.001	weak		0.582	IRX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417445.4	NM_024335		T	55362625	C	T	55362625	2	4	30	1	0	0	0	0	0	0	0	1	7857	738	26	2		2	IRX6	16	55362625	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	7136167	55362625	34992128	538	13689											
COQ9	57017	hgsc.bcm.edu	37	chr16	57490480	57490480	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcagtgagctaatactgcAttttgtgacccagtgcaata	11	12	10	8	0	0	2	0	2	0	0	0	2	0	2	1	1	4	4	1	1	4	5	rs191446011		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:57490480A>C	ENST00000262507.6	+	4	512	c.443A>C	c.(442-444)cAt>cCt	p.H148P	COQ9_ENST00000567933.1_Intron|COQ9_ENST00000567072.1_Missense_Mutation_p.H148P	NM_020312.3	NP_064708.1	O75208	COQ9_HUMAN	coenzyme Q9	148					mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|ubiquinone biosynthetic process (GO:0006744)	mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)	16						CTAATACTGCATTTTGTGACC	0.532													A|||	1	0.000199681	0.0	0.0	5008	,	,		22372	0.0		0.001	False		,,,				2504	0.0				p.H148P		Atlas-SNP	.											.	COQ9	30	.	0			c.A443C						PASS	.	A	PRO/HIS	0,4396		0,0,2198	143	123	130		443	5.6	1	16		130	2,8598	2.2+/-6.3	0,2,4298	no	missense	COQ9	NM_020312.3	77	0,2,6496	CC,CA,AA		0.0233,0.0,0.0154	probably-damaging	148/319	57490480	2,12994	2198	4300	6498	SO:0001583	missense	57017	exon4			TACTGCATTTTGT	BC064946	CCDS32459.1	16q13	2013-10-18	2013-10-18	2006-01-13	ENSG00000088682	ENSG00000088682			25302	protein-coding gene	gene with protein product		612837	"chromosome 16 open reading frame 49", "coenzyme Q9 homolog (yeast)", "coenzyme Q9 homolog (S. cerevisiae)"	C16orf49		19375058	Standard	NM_020312		Approved	DKFZP434K046	uc002elq.3	O75208		ENST00000262507.6:c.443A>C	16.37:g.57490480A>C	ENSP00000262507:p.His148Pro	163	0	0		175	24	0.137143	NM_020312	A8K3L2|Q7L5V7|Q7Z5T6|Q8NBL4|Q9NTJ2|Q9P056	Missense_Mutation	SNP	ENST00000262507.6	37	CCDS32459.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	23.2	4.387434	0.82902	0.0	2.33E-4	ENSG00000088682	ENST00000262507	.	.	.	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	D	0.84133	0.5405	M	0.88450	2.955	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;0.996;0.998;0.998	D	0.86577	0.1851	9	0.54805	T	0.06	-11.6483	14.9239	0.70862	1.0:0.0:0.0:0.0	.	148;148;148;148	B4E0U3;B4DIV2;B4DEE3;O75208	.;.;.;COQ9_HUMAN	P	148	.	ENSP00000262507:H148P	H	+	2	0	COQ9	56047981	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	8.700000	0.91322	2.117000	0.64856	0.460000	0.39030	CAT	A|1.000;C|0.000	0.000	strong		0.532	COQ9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432598.3	NM_020312		C	57490480	A	C	57490480	3	2	30	1	0	0	0	0	1	0	0	0	3753	217	8	5	457	5	COQ9	16	57490480	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	2127855	57490480	32864273	539	13690											
CDH1	999	hgsc.bcm.edu	37	chr16	68855966	68855966	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtctgatgtgaatgacaacGcccccataccagaacctcga	12	8	8	13	2	1	4	0	3	1	1	2	5	1	4	4	0	3	0	4	0	4	1	rs35187787	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:68855966G>A	ENST00000261769.5	+	12	1965	c.1774G>A	c.(1774-1776)Gcc>Acc	p.A592T	CDH1_ENST00000562836.1_3'UTR|CDH1_ENST00000422392.2_Missense_Mutation_p.A531T|RP11-354M1.2_ENST00000563916.1_RNA	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	592	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.		A -> T (in a thyroid cancer sample; may play a role in colorectal carcinogenesis; dbSNP:rs35187787). {ECO:0000269|PubMed:11562785, ECO:0000269|PubMed:8985087}.		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.A592T(4)		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)		GAATGACAACGCCCCCATACC	0.458			"Mis, N, F, S"		"lobular breast, gastric"	gastric			Hereditary Diffuse Gastric Cancer				G|||	6	0.00119808	0.0008	0.0029	5008	,	,		21048	0.0		0.002	False		,,,				2504	0.001				p.A592T		Atlas-SNP	.	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"		E	CDH1,NS,carcinoma,0,4	CDH1	535	4	4	Substitution - Missense(4)	breast(2)|thyroid(1)|stomach(1)	c.G1774A	GRCh37	CM994192	CDH1	M	rs35187787	PASS	.	G	THR/ALA	5,4391	9.9+/-24.2	0,5,2193	133	121	125		1774	5.6	0.1	16	dbSNP_126	125	54,8546	34.3+/-88.2	0,54,4246	yes	missense	CDH1	NM_004360.3	58	0,59,6439	AA,AG,GG		0.6279,0.1137,0.454	possibly-damaging	592/883	68855966	59,12937	2198	4300	6498	SO:0001583	missense	999	exon12	Familial Cancer Database	HDGC	GACAACGCCCCCA	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.1774G>A	16.37:g.68855966G>A	ENSP00000261769:p.Ala592Thr	171	0	0		161	21	0.130435	NM_004360	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Missense_Mutation	SNP	ENST00000261769.5	37	CCDS10869.1	3	0.0013736263736263737	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	15.26	2.781583	0.49891	0.001137	0.006279	ENSG00000039068	ENST00000261769;ENST00000379120;ENST00000268794;ENST00000422392	T;T	0.61627	0.09;0.09	5.56	5.56	0.83823	Cadherin (4);Cadherin conserved site (1);Cadherin-like (2);	0.595783	0.14702	N	0.303477	T	0.45816	0.1361	L	0.45744	1.44	0.34229	D	0.676292	P;P	0.51791	0.948;0.492	B;B	0.38156	0.266;0.092	T	0.68153	-0.5484	10	0.87932	D	0	.	19.1853	0.93641	0.0:0.0:1.0:0.0	rs35187787	531;592	Q9UII8;P12830	.;CADH1_HUMAN	T	592;610;592;531	ENSP00000261769:A592T;ENSP00000414946:A531T	ENSP00000261769:A592T	A	+	1	0	CDH1	67413467	1.000000	0.71417	0.149000	0.22428	0.254000	0.26022	8.900000	0.92551	2.641000	0.89580	0.536000	0.68110	GCC	A|0.003;G|0.997	0.003	strong		0.458	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360		A	68855966	G	A	68855966	3	1	30	1	0	0	0	0	1	0	0	0	3097	1087	38	1	1820	1	CDH1	16	68855966	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	11365486	68855966	21498787	540	13691											
TAT	6898	hgsc.bcm.edu	37	chr16	71602660	71602660	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcagcaactaaccgctccGtgaactccacatcgttctca	10	9	6	16	3	2	1	2	1	1	0	6	1	4	1	3	0	4	4	3	0	3	2	rs142634310	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:71602660G>A	ENST00000355962.4	-	11	1311	c.1178C>T	c.(1177-1179)aCg>aTg	p.T393M	RP11-432I5.1_ENST00000561529.1_RNA	NM_000353.2	NP_000344.1	P17735	ATTY_HUMAN	tyrosine aminotransferase	393					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)	TAACCGCTCCGTGAACTCCAC	0.517																																					p.T393M	Melanoma(198;542 2142 10292 21661 50033)|Esophageal Squamous(48;487 1013 5572 44395 52594)	Atlas-SNP	.											.	TAT	80	.	0			c.C1178T						PASS	.	G	MET/THR	0,4396		0,0,2198	82	69	73		1178	4.9	1	16	dbSNP_134	73	3,8597	3.0+/-9.4	0,3,4297	yes	missense	TAT	NM_000353.2	81	0,3,6495	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging	393/455	71602660	3,12993	2198	4300	6498	SO:0001583	missense	6898	exon11			CGCTCCGTGAACT		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.1178C>T	16.37:g.71602660G>A	ENSP00000348234:p.Thr393Met	148	0	0		156	32	0.205128	NM_000353	B2R8I1|D3DWS2	Missense_Mutation	SNP	ENST00000355962.4	37	CCDS10903.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.353229	0.82132	0.0	3.49E-4	ENSG00000198650	ENST00000355962	D	0.90676	-2.71	5.93	4.93	0.64822	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);	0.000000	0.85682	D	0.000000	D	0.94089	0.8105	L	0.55103	1.725	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.93537	0.6874	10	0.49607	T	0.09	-17.5761	18.7826	0.91941	0.0:0.1252:0.8748:0.0	.	393	P17735	ATTY_HUMAN	M	393	ENSP00000348234:T393M	ENSP00000348234:T393M	T	-	2	0	TAT	70160161	1.000000	0.71417	0.970000	0.41538	0.977000	0.68977	7.610000	0.82949	2.826000	0.97356	0.655000	0.94253	ACG	G|0.999;A|0.001	0.001	strong		0.517	TAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268989.1			A	71602660	G	A	71602660	3	1	30	1	0	0	0	0	1	0	0	0	15605	1145	40	1	194	1	TAT	16	71602660	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2746694	71602660	18752093	541	13692											
RFWD3	55159	hgsc.bcm.edu	37	chr16	74664698	74664698	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctggctttctgagctactaActcctgcacatgactgctcg	7	12	8	14	1	1	2	0	2	1	0	3	2	2	2	2	1	5	4	2	1	2	3	rs78796563	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:74664698A>G	ENST00000361070.4	-	10	1832	c.1735T>C	c.(1735-1737)Tta>Cta	p.L579L	RFWD3_ENST00000571750.1_Silent_p.L579L	NM_018124.3	NP_060594.3	Q6PCD5	RFWD3_HUMAN	ring finger and WD repeat domain 3	579					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)	p.L579L(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	26						TGAGCTACTAACTCCTGCACA	0.473													A|||	67	0.0133786	0.0023	0.0259	5008	,	,		18719	0.0		0.0288	False		,,,				2504	0.0174				p.L579L		Atlas-SNP	.											RFWD3,NS,carcinoma,0,1	RFWD3	49	1	1	Substitution - coding silent(1)	lung(1)	c.T1735C						PASS	.	A		28,4368	32.6+/-62.9	1,26,2171	94	70	78		1735	3.5	0.3	16	dbSNP_132	78	267,8333	102.3+/-163.5	4,259,4037	no	coding-synonymous	RFWD3	NM_018124.3		5,285,6208	GG,GA,AA		3.1047,0.6369,2.2699		579/775	74664698	295,12701	2198	4300	6498	SO:0001819	synonymous_variant	55159	exon10			CTACTAACTCCTG	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.1735T>C	16.37:g.74664698A>G		91	0	0		87	16	0.183908	NM_018124	A8K585|B2RE35|D3DUJ8|Q5XKR3|Q9H9Q3|Q9NVT4	Silent	SNP	ENST00000361070.4	37	CCDS32486.1																																																																																			A|0.981;G|0.019	0.019	strong		0.473	RFWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436506.2	NM_018124		G	74664698	A	G	74664698	2	3	30	1	0	0	0	0	0	0	0	1	13276	40	2	3		3	RFWD3	16	74664698	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	3062038	74664698	15690055	542	13693											
MLKL	197259	hgsc.bcm.edu	37	chr16	74709233	74709233	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	caacctcaccactggctgagCcagtcttcacattcttcacc	9	10	5	17	0	5	1	3	1	2	0	5	1	5	1	4	1	2	1	4	1	1	3	rs144526386	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:74709233C>A	ENST00000306247.7	-	4	944	c.605G>T	c.(604-606)gGc>gTc	p.G202V	MLKL_ENST00000308807.7_Intron	NM_001142497.1	NP_001135969.1			mixed lineage kinase domain-like											breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(6)|skin(1)|stomach(2)	19						ACTGGCTGAGCCAGTCTTCAC	0.493													C|||	51	0.0101837	0.0023	0.0144	5008	,	,		19105	0.0		0.0209	False		,,,				2504	0.0174				p.G202V		Atlas-SNP	.											.	MLKL	51	.	0			c.G605T						PASS	.	C	VAL/GLY,	17,4379	23.3+/-48.9	0,17,2181	113	108	110		605,	-1	0	16	dbSNP_134	110	162,8438	76.3+/-139.0	2,158,4140	yes	missense,intron	MLKL	NM_001142497.1,NM_152649.2	109,	2,175,6321	AA,AC,CC		1.8837,0.3867,1.3773	,	202/264,	74709233	179,12817	2198	4300	6498	SO:0001583	missense	197259	exon4			GCTGAGCCAGTCT	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		ENST00000306247.7:c.605G>T	16.37:g.74709233C>A	ENSP00000303118:p.Gly202Val	126	0	0		122	25	0.204918	NM_001142497		Missense_Mutation	SNP	ENST00000306247.7	37	CCDS45528.1	23	0.010531135531135532	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	15	0.01978891820580475	C	8.923	0.961462	0.18583	0.003867	0.018837	ENSG00000168404	ENST00000306247	T	0.12147	2.71	4.96	-1.05	0.10036	.	.	.	.	.	T	0.14313	0.0346	.	.	.	0.09310	N	1	D	0.67145	0.996	D	0.65573	0.936	T	0.07501	-1.0769	8	0.48119	T	0.1	.	8.2986	0.32001	0.0:0.4852:0.0:0.5148	.	202	Q8NB16-2	.	V	202	ENSP00000303118:G202V	ENSP00000303118:G202V	G	-	2	0	MLKL	73266734	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	-0.620000	0.05565	-0.228000	0.09869	-0.374000	0.07098	GGC	C|0.986;A|0.014	0.014	strong		0.493	MLKL-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000436402.1	NM_152649		A	74709233	C	A	74709233	3	1	30	1	0	0	0	0	1	0	0	0	9628	739	26	4	198	4	MLKL	16	74709233	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	44535	74709233	15645520	543	13694											
PKD1L2	114780	hgsc.bcm.edu	37	chr16	81232294	81232294	+	RNA	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggaacagccaggcggcaaaTcccaaatggctctccaaagc	13	4	10	14	2	1	0	0	0	1	0	3	1	2	1	3	4	3	2	3	4	4	0	rs61734110	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:81232294T>C	ENST00000525539.1	-	0	1515				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						AGGCGGCAAATCCCAAATGGC	0.582													T|||	154	0.0307508	0.0325	0.0317	5008	,	,		20196	0.004		0.0716	False		,,,				2504	0.0133				p.I506V		Atlas-SNP	.											.	PKD1L2	361	.	0			c.A1516G						PASS	.	T	VAL/ILE,VAL/ILE	168,3844		1,166,1839	51	52	51		1516,1516	2.8	0.5	16	dbSNP_129	51	526,7782		17,492,3645	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	29,29	18,658,5484	CC,CT,TT		6.3312,4.1874,5.6331	benign,benign	506/992,506/2460	81232294	694,11626	2006	4154	6160			114780	exon7			GGCAAATCCCAAA	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		16.37:g.81232294T>C		122	0	0		109	88	0.807339	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		85|85	0.03891941391941392|0.03891941391941392	17|17	0.034552845528455285|0.034552845528455285	16|16	0.04419889502762431|0.04419889502762431	1|1	0.0017482517482517483|0.0017482517482517483	51|51	0.06728232189973615|0.06728232189973615	T|T	0.006|0.006	-2.058861|-2.058861	0.00390|0.00390	0.041874|0.041874	0.063312|0.063312	ENSG00000166473|ENSG00000166473	ENST00000526632|ENST00000337114	.|T	.|0.01279	.|5.06	5.08|5.08	2.75|2.75	0.32379|0.32379	.|Egg jelly receptor, REJ-like (1);	.|1.001100	.|0.08058	.|N	.|0.997623	T|T	0.00144|0.00144	0.0004|0.0004	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|B;B	.|0.16603	.|0.018;0.006	.|B;B	.|0.17722	.|0.019;0.004	T|T	0.50127|0.50127	-0.8864|-0.8864	4|9	.|0.22706	.|T	.|0.39	-3.0E-4|-3.0E-4	8.8296|8.8296	0.35076|0.35076	0.0:0.2087:0.0:0.7913|0.0:0.2087:0.0:0.7913	.|.	.|506;506	.|Q7Z442-3;Q7Z442	.|.;PK1L2_HUMAN	G|V	33|506	.|ENSP00000337397:I506V	.|ENSP00000337397:I506V	D|I	-|-	2|1	0|0	PKD1L2|PKD1L2	79789795|79789795	0.000000|0.000000	0.05858|0.05858	0.487000|0.487000	0.27428|0.27428	0.041000|0.041000	0.13682|0.13682	0.422000|0.422000	0.21296|0.21296	0.790000|0.790000	0.33803|0.33803	-0.398000|-0.398000	0.06409|0.06409	GAT|ATT	T|0.956;C|0.044	0.044	strong		0.582	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2			C	81232294	T	C	81232294	1	2	30	0	1	0	0	0	0	0	0	0	11974	1435	50	3		3	PKD1L2	16	81232294	RNA	SNP	T	TCGA-GR-7353-01A-11D-2210-10	6523061	81232294	9122459	544	13695											
OSGIN1	29948	hgsc.bcm.edu	37	chr16	83998922	83998922	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtggtcctcgccacaggcacGttcgacagcccggcccggct	5	6	13	17	5	0	0	0	0	0	0	3	1	1	0	4	4	1	3	4	4	0	1	rs146347192		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:83998922G>A	ENST00000343939.2	+	7	1376	c.993G>A	c.(991-993)acG>acA	p.T331T	OSGIN1_ENST00000393306.1_Silent_p.T248T|OSGIN1_ENST00000361711.3_Silent_p.T248T			Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	331					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						CCACAGGCACGTTCGACAGCC	0.697																																					p.T248T		Atlas-SNP	.											OSGIN1,NS,carcinoma,+2,1	OSGIN1	33	1	0			c.G744A						scavenged	.	G	,,	0,4398		0,0,2199	26	31	29		993,744,744	-8.1	0	16	dbSNP_134	29	2,8580		0,2,4289	no	coding-synonymous,coding-synonymous,coding-synonymous	OSGIN1	NM_013370.3,NM_182980.2,NM_182981.2	,,	0,2,6488	AA,AG,GG		0.0233,0.0,0.0154	,,	331/561,248/478,248/478	83998922	2,12978	2199	4291	6490	SO:0001819	synonymous_variant	29948	exon6			AGGCACGTTCGAC	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.993G>A	16.37:g.83998922G>A		35	0	0		28	4	0.142857	NM_182981	Q52M33|Q86UQ1|Q96S88|Q9BZ70	Silent	SNP	ENST00000343939.2	37																																																																																				G|1.000;A|0.000	0.000	weak		0.697	OSGIN1-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000269081.1	NM_013370		A	83998922	G	A	83998922	2	1	30	1	0	0	0	0	0	0	0	1	11298	1132	40	1		1	OSGIN1	16	83998922	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2766628	83998922	6355831	545	13696											
OSGIN1	29948	hgsc.bcm.edu	37	chr16	83999548	83999548	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacaacttcgtgaggtttgTgcaggggggcgccttggctg	5	10	18	8	2	0	1	0	1	0	0	1	2	0	2	1	6	2	3	1	6	1	3	rs62640905	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:83999548T>C	ENST00000343939.2	+	7	2002	c.1619T>C	c.(1618-1620)gTg>gCg	p.V540A	NECAB2_ENST00000305202.4_5'Flank|OSGIN1_ENST00000393306.1_Missense_Mutation_p.V457A|OSGIN1_ENST00000361711.3_Missense_Mutation_p.V457A			Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	540					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						GTGAGGTTTGTGCAGGGGGGC	0.662													T|||	40	0.00798722	0.0	0.013	5008	,	,		17559	0.0		0.0278	False		,,,				2504	0.0031				p.V457A		Atlas-SNP	.											.	OSGIN1	33	.	0			c.T1370C						PASS	.	T	ALA/VAL,ALA/VAL,ALA/VAL	14,4370		0,14,2178	14	15	15		1619,1370,1370	4.4	1	16	dbSNP_129	15	218,8354		5,208,4073	yes	missense,missense,missense	OSGIN1	NM_013370.3,NM_182980.2,NM_182981.2	64,64,64	5,222,6251	CC,CT,TT		2.5432,0.3193,1.7907	possibly-damaging,possibly-damaging,possibly-damaging	540/561,457/478,457/478	83999548	232,12724	2192	4286	6478	SO:0001583	missense	29948	exon6			GGTTTGTGCAGGG	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.1619T>C	16.37:g.83999548T>C	ENSP00000343376:p.Val540Ala	76	0	0		53	43	0.811321	NM_182981	Q52M33|Q86UQ1|Q96S88|Q9BZ70	Missense_Mutation	SNP	ENST00000343939.2	37		27	0.012362637362637362	0	0.0	6	0.016574585635359115	0	0.0	21	0.027704485488126648	T	16.86	3.238732	0.58995	0.003193	0.025432	ENSG00000140961	ENST00000343939;ENST00000361711;ENST00000393306	T;T;T	0.37411	1.2;1.2;1.2	4.37	4.37	0.52481	.	0.065516	0.64402	D	0.000009	T	0.15739	0.0379	M	0.63428	1.95	0.80722	D	1	D	0.58268	0.982	B	0.44315	0.446	T	0.04811	-1.0925	10	0.24483	T	0.36	-26.2537	12.7349	0.57218	0.0:0.0:0.0:1.0	rs62640905	540	Q9UJX0	OSGI1_HUMAN	A	540;457;457	ENSP00000343376:V540A;ENSP00000355374:V457A;ENSP00000376983:V457A	ENSP00000343376:V540A	V	+	2	0	OSGIN1	82557049	1.000000	0.71417	0.954000	0.39281	0.681000	0.39784	7.645000	0.83430	1.606000	0.50161	0.260000	0.18958	GTG	T|0.985;C|0.015	0.015	strong		0.662	OSGIN1-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000269081.1	NM_013370		C	83999548	T	C	83999548	3	2	30	1	0	0	0	0	1	0	0	0	11298	1696	59	3	1645	3	OSGIN1	16	83999548	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	626	83999548	6355205	546	13697											
MTHFSD	64779	hgsc.bcm.edu	37	chr16	86585743	86585743	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tttgatgttttggcaagccaGataagacccctagttaggca	11	12	10	8	0	0	3	0	1	0	2	0	3	0	3	3	2	1	4	3	2	4	6	rs34005514	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr16:86585743G>C	ENST00000360900.6	-	3	158	c.133C>G	c.(133-135)Ctg>Gtg	p.L45V	MTHFSD_ENST00000543303.2_Intron|MTHFSD_ENST00000568037.1_Intron|MTHFSD_ENST00000322911.6_Missense_Mutation_p.L44V|MTHFSD_ENST00000381214.5_Intron|MTHFSD_ENST00000546093.1_Intron	NM_001159380.1	NP_001152852.1	Q2M296	MTHSD_HUMAN	methenyltetrahydrofolate synthetase domain containing	45			L -> V (in dbSNP:rs34005514).				nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(3)|lung(6)|skin(1)	11						TGGCAAGCCAGATAAGACCCC	0.473													G|||	95	0.0189696	0.0053	0.0274	5008	,	,		19532	0.004		0.0517	False		,,,				2504	0.0133				p.L45V		Atlas-SNP	.											.	MTHFSD	52	.	0			c.C133G						PASS	.	G	VAL/LEU,,,VAL/LEU,VAL/LEU	43,3753		0,43,1855	151	153	152		133,,,73,130	-0.4	0.6	16	dbSNP_126	152	398,7840		14,370,3735	yes	missense,intron,intron,missense,missense	MTHFSD	NM_001159377.1,NM_001159378.1,NM_001159379.1,NM_001159380.1,NM_022764.2	32,,,32,32	14,413,5590	CC,CG,GG		4.8313,1.1328,3.6646	,,,,	45/384,,,25/364,44/383	86585743	441,11593	1898	4119	6017	SO:0001583	missense	64779	exon3			AAGCCAGATAAGA	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.133C>G	16.37:g.86585743G>C	ENSP00000354152:p.Leu45Val	130	0	0		142	113	0.795775	NM_001159377	A8MQ77|B7ZLC0|B7ZLC2|D3DUM9|E9PAM1|Q9H878|Q9H954	Missense_Mutation	SNP	ENST00000360900.6	37	CCDS54047.1	55	0.025183150183150184	2	0.0040650406504065045	8	0.022099447513812154	4	0.006993006993006993	41	0.05408970976253298	G	10.80	1.453214	0.26161	0.011328	0.048313	ENSG00000103248	ENST00000543303;ENST00000360900;ENST00000322911	T;T	0.41400	1.0;1.0	5.93	-0.438	0.12268	5-formyltetrahydrofolate cyclo-ligase-like domain (1);	1.474430	0.04126	N	0.317098	T	0.04724	0.0128	N	0.04297	-0.235	0.09310	N	1	B;B	0.17465	0.022;0.017	B;B	0.23852	0.049;0.029	T	0.23726	-1.0180	10	0.35671	T	0.21	-11.0693	14.9226	0.70851	0.0:0.419:0.4829:0.0981	rs34005514	45;44	Q2M296;Q2M296-2	MTHSD_HUMAN;.	V	43;45;44	ENSP00000354152:L45V;ENSP00000326777:L44V	ENSP00000326777:L44V	L	-	1	2	MTHFSD	85143244	0.057000	0.20700	0.564000	0.28396	0.964000	0.63967	0.453000	0.21811	0.070000	0.16634	0.655000	0.94253	CTG	G|0.968;C|0.032	0.032	strong		0.473	MTHFSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432182.1	NM_022764		C	86585743	G	C	86585743	3	2	30	1	0	0	0	0	1	0	0	0	9942	933	33	4	1042	4	MTHFSD	16	86585743	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2586195	86585743	3769010	547	13698											
VPS53	55275	hgsc.bcm.edu	37	chr17	534812	534812	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggtgccctgggaaggaaacGcttcttcaaaatctgccagg	10	9	12	10	1	3	0	1	0	2	0	3	2	3	2	2	4	3	1	2	4	4	2	rs138639431		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:534812G>A	ENST00000571805.1	-	8	801	c.665C>T	c.(664-666)gCg>gTg	p.A222V	VPS53_ENST00000576149.1_5'UTR|VPS53_ENST00000291074.5_Missense_Mutation_p.A193V|VPS53_ENST00000437048.2_Missense_Mutation_p.A222V|VPS53_ENST00000446250.2_Missense_Mutation_p.A24V|VPS53_ENST00000401468.3_Intron|VPS53_ENST00000574029.1_Intron			Q5VIR6	VPS53_HUMAN	vacuolar protein sorting 53 homolog (S. cerevisiae)	222					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)		GGAAGGAAACGCTTCTTCAAA	0.502													G|||	1	0.000199681	0.0	0.0	5008	,	,		21279	0.0		0.001	False		,,,				2504	0.0				p.A222V		Atlas-SNP	.											.	VPS53	109	.	0			c.C665T						PASS	.	G	VAL/ALA,VAL/ALA	0,4406		0,0,2203	153	117	129		665,578	5.8	1	17	dbSNP_134	129	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	VPS53	NM_001128159.2,NM_018289.3	64,64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	222/833,193/671	534812	1,13005	2203	4300	6503	SO:0001583	missense	55275	exon8			GGAAACGCTTCTT		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.665C>T	17.37:g.534812G>A	ENSP00000459312:p.Ala222Val	98	0	0		109	47	0.431193	NM_001128159	A8K2S8|B3FH42|Q8WYW3|Q9BRR2|Q9BY02|Q9NV25	Missense_Mutation	SNP	ENST00000571805.1	37		1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	24.9	4.586261	0.86851	0.0	1.16E-4	ENSG00000141252	ENST00000437048;ENST00000446250;ENST00000291074;ENST00000389040	T;T;T;T	0.32988	1.43;1.43;1.43;1.43	5.82	5.82	0.92795	Vps53-like, N-terminal (1);	0.212444	0.49305	D	0.000142	T	0.42899	0.1223	M	0.61703	1.905	0.80722	D	1	P;P;P;P	0.51537	0.946;0.786;0.821;0.786	P;B;B;B	0.47402	0.546;0.286;0.409;0.286	T	0.33548	-0.9864	10	0.62326	D	0.03	-8.2413	19.0968	0.93255	0.0:0.0:1.0:0.0	.	222;24;222;193	Q5VIR6-4;G3V0H8;Q5VIR6;Q5VIR6-2	.;.;VPS53_HUMAN;.	V	222;24;193;222	ENSP00000401435:A222V;ENSP00000394386:A24V;ENSP00000291074:A193V;ENSP00000373692:A222V	ENSP00000291074:A193V	A	-	2	0	VPS53	481562	1.000000	0.71417	0.995000	0.50966	0.981000	0.71138	9.199000	0.95003	2.756000	0.94617	0.563000	0.77884	GCG	G|1.000;A|0.000	0.000	strong		0.502	VPS53-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000436940.2	NM_018289		A	534812	G	A	534812	3	1	30	1	0	0	0	0	1	0	0	0	17230	1087	38	1	1908	1	VPS53	17	534812	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10		534812	80660398	548	13699											
ABR	29	hgsc.bcm.edu	37	chr17	970419	970419	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggctggcctcagactcctcGggggatggaaacaccaggtc	8	6	15	12	1	1	1	1	0	0	1	4	3	2	3	3	6	1	1	3	6	1	0	rs199545490		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:970419G>A	ENST00000302538.5	-	10	1226	c.1080C>T	c.(1078-1080)ccC>ccT	p.P360P	ABR_ENST00000536794.2_Silent_p.P142P|ABR_ENST00000574437.1_Silent_p.P314P|ABR_ENST00000291107.2_Silent_p.P323P|ABR_ENST00000544583.2_Silent_p.P314P	NM_001282149.1|NM_021962.3	NP_001269078.1|NP_068781.2	Q12979	ABR_HUMAN	active BCR-related	360	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)		CAGACTCCTCGGGGGATGGAA	0.582																																					p.P360P	Esophageal Squamous(197;2016 2115 4129 29033 46447)	Atlas-SNP	.											ABR,colon,carcinoma,0,1	ABR	119	1	0			c.C1080T						scavenged	.						35	33	34					17																	970419		2203	4300	6503	SO:0001819	synonymous_variant	29	exon10			CTCCTCGGGGGAT	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.1080C>T	17.37:g.970419G>A		66	1	0.0151515		73	40	0.547945	NM_021962	B3KW89|B7Z6H7|D3DTH3|D3DTH4|F5H3S2|F5H8B3|Q13693|Q13694	Silent	SNP	ENST00000302538.5	37	CCDS10999.1																																																																																			G|0.999;A|0.001	0.001	weak		0.582	ABR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206675.4			A	970419	G	A	970419	2	1	30	1	0	0	0	0	0	0	0	1	99	1103	39	1		1	ABR	17	970419	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	435607	970419	80224791	549	13700											
CTNS	1497	hgsc.bcm.edu	37	chr17	3563221	3563221	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acgtgctcctggacttcaccGggggcagcttcagcctcctg	5	9	12	15	2	2	0	2	0	0	0	4	1	4	1	4	3	3	3	4	3	0	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:3563221G>A	ENST00000046640.3	+	11	1515	c.922G>A	c.(922-924)Ggg>Agg	p.G308R	CTNS_ENST00000381870.3_Missense_Mutation_p.G308R|CTNS_ENST00000441220.2_Missense_Mutation_p.G200R|CTNS_ENST00000414524.2_Missense_Mutation_p.G161R|RP11-235E17.6_ENST00000575741.1_RNA	NM_004937.2	NP_004928.2	O60931	CTNS_HUMAN	cystinosin, lysosomal cystine transporter	308	PQ-loop 2.		G -> R (in CTNS). {ECO:0000269|PubMed:10556299, ECO:0000269|PubMed:12825071, ECO:0000269|PubMed:9792862}.|G -> V (in CTNS). {ECO:0000269|PubMed:12204010}.		adult walking behavior (GO:0007628)|ATP metabolic process (GO:0046034)|brain development (GO:0007420)|cellular amino acid metabolic process (GO:0006520)|cognition (GO:0050890)|glutathione metabolic process (GO:0006749)|grooming behavior (GO:0007625)|L-cystine transport (GO:0015811)|lens development in camera-type eye (GO:0002088)|long-term memory (GO:0007616)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	L-cystine transmembrane transporter activity (GO:0015184)			NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)	10				COAD - Colon adenocarcinoma(5;0.0829)	L-Cystine(DB00138)	GGACTTCACCGGGGGCAGCTT	0.617																																					p.G308R		Atlas-SNP	.											.	CTNS	42	.	0			c.G922A	GRCh37	CM980460	CTNS	M		PASS	.						59	57	58					17																	3563221		2203	4300	6503	SO:0001583	missense	1497	exon11			TTCACCGGGGGCA	AJ222967	CCDS11031.1, CCDS32530.1	17p13	2011-06-07	2011-06-07		ENSG00000040531	ENSG00000040531			2518	protein-coding gene	gene with protein product		606272	"cystinosis, nephropathic"			9537412, 15128704	Standard	NM_004937		Approved	CTNS-LSB, PQLC4	uc002fwa.3	O60931	OTTHUMG00000090693	ENST00000046640.3:c.922G>A	17.37:g.3563221G>A	ENSP00000046640:p.Gly308Arg	134	0	0		174	46	0.264368	NM_001031681	D3DTJ5|Q8IZ01|Q9UNK6	Missense_Mutation	SNP	ENST00000046640.3	37	CCDS11031.1	.	.	.	.	.	.	.	.	.	.	g	35	5.491019	0.96339	.	.	ENSG00000040531	ENST00000046640;ENST00000381870;ENST00000441220;ENST00000414524	D;D;D;D	0.99507	-6.04;-6.04;-6.04;-6.04	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	D	0.99684	0.9881	H	0.94345	3.525	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.97688	1.0177	10	0.87932	D	0	-16.3759	18.5632	0.91108	0.0:0.0:1.0:0.0	.	200;308;308	F8W6Z1;O60931;O60931-2	.;CTNS_HUMAN;.	R	308;308;200;161	ENSP00000046640:G308R;ENSP00000371294:G308R;ENSP00000411465:G200R;ENSP00000395471:G161R	ENSP00000046640:G308R	G	+	1	0	CTNS	3509970	1.000000	0.71417	0.967000	0.41034	0.984000	0.73092	9.168000	0.94781	2.712000	0.92718	0.561000	0.74099	GGG	.	.	none		0.617	CTNS-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317696.1	NM_004937		A	3563221	G	A	3563221	3	1	30	1	0	0	0	0	1	0	0	0	4023	1116	39	1	956	1	CTNS	17	3563221	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2592802	3563221	77631989	550	13701											
SPNS2	124976	hgsc.bcm.edu	37	chr17	4434031	4434031	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacctcttcaccaagaacacGcgtacgctcatgctgtccgt	9	9	8	15	4	3	1	2	0	1	1	4	2	4	1	3	0	3	3	3	0	3	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:4434031G>A	ENST00000329078.3	+	4	888	c.678G>A	c.(676-678)acG>acA	p.T226T		NM_001124758.1	NP_001118230.1	Q8IVW8	SPNS2_HUMAN	spinster homolog 2 (Drosophila)	226					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						CCAAGAACACGCGTACGCTCA	0.627																																					p.T226T		Atlas-SNP	.											SPNS2,colon,carcinoma,+1,1	SPNS2	24	1	0			c.G678A						PASS	.						69	61	63					17																	4434031		1568	3582	5150	SO:0001819	synonymous_variant	124976	exon4			GAACACGCGTACG	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.678G>A	17.37:g.4434031G>A		201	0	0		205	103	0.502439	NM_001124758	B9A1T3	Silent	SNP	ENST00000329078.3	37	CCDS42237.1																																																																																			.	.	none		0.627	SPNS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438802.1			A	4434031	G	A	4434031	2	1	30	1	0	0	0	0	0	0	0	1	15090	1074	38	1		1	SPNS2	17	4434031	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	870810	4434031	76761179	551	13702											
ALOX12B	242	hgsc.bcm.edu	37	chr17	7989492	7989492	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttgtgcaggcggatgatgAtgagctcacccaggtcctga	8	10	13	10	1	1	4	1	4	0	0	2	5	2	5	2	3	2	2	2	3	0	1	rs542947562		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:7989492A>G	ENST00000319144.4	-	2	454	c.194T>C	c.(193-195)aTc>aCc	p.I65T	MIR4314_ENST00000583321.1_RNA	NM_001139.2	NP_001130.1	O75342	LX12B_HUMAN	arachidonate 12-lipoxygenase, 12R type	65	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						GCGGATGATGATGAGCTCACC	0.612										Multiple Myeloma(8;0.094)			A|||	1	0.000199681	0.0	0.0	5008	,	,		19749	0.0		0.001	False		,,,				2504	0.0				p.I65T		Atlas-SNP	.											.	ALOX12B	61	.	0			c.T194C						PASS	.						111	90	97					17																	7989492		2203	4300	6503	SO:0001583	missense	242	exon2			ATGATGATGAGCT	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.194T>C	17.37:g.7989492A>G	ENSP00000315167:p.Ile65Thr	275	0	0		266	130	0.488722	NM_001139		Missense_Mutation	SNP	ENST00000319144.4	37	CCDS11129.1	.	.	.	.	.	.	.	.	.	.	A	14.64	2.595105	0.46318	.	.	ENSG00000179477	ENST00000319144	T	0.63417	-0.04	4.58	3.48	0.39840	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	0.253600	0.39909	N	0.001228	T	0.46502	0.1396	N	0.21142	0.635	0.29604	N	0.847425	B	0.29955	0.263	B	0.29440	0.102	T	0.49504	-0.8933	10	0.62326	D	0.03	-23.0942	10.4946	0.44770	0.8365:0.1635:0.0:0.0	.	65	O75342	LX12B_HUMAN	T	65	ENSP00000315167:I65T	ENSP00000315167:I65T	I	-	2	0	ALOX12B	7930217	0.990000	0.36364	0.952000	0.39060	0.922000	0.55478	7.844000	0.86867	0.765000	0.33221	0.529000	0.55759	ATC	.	.	none		0.612	ALOX12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226984.3			G	7989492	A	G	7989492	3	3	30	1	0	0	0	0	1	0	0	0	537	333	12	3	1967	3	ALOX12B	17	7989492	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	3555461	7989492	73205718	552	13703											
C17orf68	80169	hgsc.bcm.edu	37	chr17	8135446	8135446	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggtggggtccctctgggccGgtgggatctgtctgaggtgt	3	11	19	8	1	3	1	0	1	3	0	4	2	4	2	2	7	0	0	2	7	0	0	rs3027235	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:8135446G>A	ENST00000315684.8	-	13	2167	c.2160C>T	c.(2158-2160)acC>acT	p.T720T		NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	720					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						CCTCTGGGCCGGTGGGATCTG	0.577													G|||	217	0.0433307	0.087	0.1009	5008	,	,		17092	0.0099		0.0139	False		,,,				2504	0.0082				p.T720T		Atlas-SNP	.											.	CTC1	75	.	0			c.C2160T						PASS	.	G		260,3684		9,242,1721	21	22	22		2160	2.3	0	17	dbSNP_102	22	124,8160		3,118,4021	no	coding-synonymous	CTC1	NM_025099.5		12,360,5742	AA,AG,GG		1.4969,6.5923,3.1403		720/1218	8135446	384,11844	1972	4142	6114	SO:0001819	synonymous_variant	80169	exon13			TGGGCCGGTGGGA	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.2160C>T	17.37:g.8135446G>A		79	0	0		73	28	0.383562	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Silent	SNP	ENST00000315684.8	37	CCDS42259.1																																																																																			G|0.964;A|0.036	0.036	strong		0.577	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099		A	8135446	G	A	8135446	2	1	30	1	0	0	0	0	0	0	0	1	1878	1103	39	1		1	C17orf68	17	8135446	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	145954	8135446	73059764	553	13704											
MYH10	4628	hgsc.bcm.edu	37	chr17	8396176	8396176	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaccgtgaggtcgtccagcTcctgctgcaggcggttcttg	4	10	13	14	3	1	1	0	1	1	0	4	1	3	1	4	3	3	4	4	3	0	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:8396176T>C	ENST00000269243.4	-	31	4421	c.4283A>G	c.(4282-4284)gAg>gGg	p.E1428G	MYH10_ENST00000396239.1_Missense_Mutation_p.E1449G|MYH10_ENST00000360416.3_Missense_Mutation_p.E1459G|MYH10_ENST00000379980.4_Missense_Mutation_p.E1444G	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	1428					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						GTCGTCCAGCTCCTGCTGCAG	0.607																																					p.E1459G		Atlas-SNP	.											.	MYH10	148	.	0			c.A4376G						PASS	.						80	71	74					17																	8396176		2203	4300	6503	SO:0001583	missense	4628	exon33			TCCAGCTCCTGCT	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.4283A>G	17.37:g.8396176T>C	ENSP00000269243:p.Glu1428Gly	125	0	0		91	4	0.043956	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Missense_Mutation	SNP	ENST00000269243.4	37	CCDS11144.1	.	.	.	.	.	.	.	.	.	.	T	31	5.091155	0.94149	.	.	ENSG00000133026	ENST00000269243;ENST00000360416;ENST00000396239;ENST00000379980	D;D;D;D	0.85629	-2.01;-2.01;-2.01;-2.01	5.31	5.31	0.75309	Myosin tail (1);	0.000000	0.85682	D	0.000000	D	0.94820	0.8327	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;1.0;1.0	D	0.96370	0.9273	10	0.87932	D	0	.	15.4317	0.75105	0.0:0.0:0.0:1.0	.	1437;1459;1428	B2RWP9;F8VTL3;P35580	.;.;MYH10_HUMAN	G	1428;1459;1449;1444	ENSP00000269243:E1428G;ENSP00000353590:E1459G;ENSP00000379539:E1449G;ENSP00000369315:E1444G	ENSP00000269243:E1428G	E	-	2	0	MYH10	8336901	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.825000	0.86693	2.224000	0.72417	0.528000	0.53228	GAG	.	.	none		0.607	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			C	8396176	T	C	8396176	3	2	30	1	0	0	0	0	1	0	0	0	10039	1551	54	3	1691	3	MYH10	17	8396176	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	260730	8396176	72799034	554	13705											
USP43	124739	hgsc.bcm.edu	37	chr17	9580092	9580092	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgtcaccttggtcttcccctCtaagagccagcggttcctgc	5	12	9	15	1	3	1	1	0	2	1	5	1	5	1	5	2	3	1	5	2	1	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:9580092C>G	ENST00000285199.7	+	5	959	c.863C>G	c.(862-864)tCt>tGt	p.S288C	USP43_ENST00000570827.2_3'UTR|USP43_ENST00000570475.1_Missense_Mutation_p.S288C	NM_001267576.1|NM_153210.4	NP_001254505.1|NP_694942.3	Q70EL4	UBP43_HUMAN	ubiquitin specific peptidase 43	288	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						GTCTTCCCCTCTAAGAGCCAG	0.542																																					p.S288C		Atlas-SNP	.											.	USP43	65	.	0			c.C863G						PASS	.						91	93	93					17																	9580092		2015	4165	6180	SO:0001583	missense	124739	exon5			TCCCCTCTAAGAG	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.863C>G	17.37:g.9580092C>G	ENSP00000285199:p.Ser288Cys	264	0	0		256	28	0.109375	NM_001267576	A6NDT9|B7ZLT9|B7ZVX5|Q8N2C5|Q96DQ6	Missense_Mutation	SNP	ENST00000285199.7	37	CCDS45610.1	.	.	.	.	.	.	.	.	.	.	C	12.78	2.041149	0.35989	.	.	ENSG00000154914	ENST00000285199	T	0.10099	2.91	4.62	2.55	0.30701	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.387701	0.24601	N	0.037138	T	0.12475	0.0303	L	0.50847	1.595	0.09310	N	0.999998	B;B	0.12630	0.001;0.006	B;B	0.23852	0.01;0.049	T	0.18999	-1.0319	10	0.52906	T	0.07	-3.9205	12.7709	0.57421	0.0:0.7264:0.2736:0.0	.	288;288	B7ZVX5;Q70EL4	.;UBP43_HUMAN	C	288	ENSP00000285199:S288C	ENSP00000285199:S288C	S	+	2	0	USP43	9520817	0.587000	0.26791	0.707000	0.30419	0.997000	0.91878	2.000000	0.40816	0.537000	0.28751	0.555000	0.69702	TCT	.	.	none		0.542	USP43-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439855.3	NM_153210		G	9580092	C	G	9580092	3	3	30	1	0	0	0	0	1	0	0	0	17089	913	32	4	881	4	USP43	17	9580092	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1183916	9580092	71615118	555	13706											
CDRT1	374286	hgsc.bcm.edu	37	chr17	15519029	15519029	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaggaagggatgtgtgctgAgttttggctgtccaatagac	11	11	14	5	0	0	2	0	1	0	1	1	4	1	4	1	3	1	3	1	3	4	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:15519029A>C	ENST00000395906.3	-	2	599	c.600T>G	c.(598-600)acT>acG	p.T200T	RP11-385D13.1_ENST00000455584.2_Silent_p.T510T	NM_006382.3	NP_006373.2	O95170	CDRT1_HUMAN	CMT1A duplicated region transcript 1	200										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)		ATGTGTGCTGAGTTTTGGCTG	0.468																																					p.T200T		Atlas-SNP	.											.	CDRT1	83	.	0			c.T600G						PASS	.						58	62	61					17																	15519029		2202	4297	6499	SO:0001819	synonymous_variant	374286	exon2			GTGCTGAGTTTTG	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.600T>G	17.37:g.15519029A>C		295	0	0		272	32	0.117647	NM_006382	O43848|O95611	Silent	SNP	ENST00000395906.3	37	CCDS45619.1	.	.	.	.	.	.	.	.	.	.	A	3.489	-0.104310	0.06967	.	.	ENSG00000251537	ENST00000455584	.	.	.	3.68	2.66	0.31614	.	.	.	.	.	T	0.27349	0.0671	.	.	.	0.09310	N	0.999996	.	.	.	.	.	.	T	0.18085	-1.0348	4	.	.	.	.	5.4733	0.16682	0.1721:0.0:0.8279:0.0	.	.	.	.	R	525	.	.	L	-	2	0	RP11-385D13.1	15459754	0.007000	0.16637	0.004000	0.12327	0.024000	0.10985	1.274000	0.33132	1.021000	0.39600	0.454000	0.30748	CTC	.	.	none		0.468	CDRT1-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448127.1	NM_006382		C	15519029	A	C	15519029	2	2	30	1	0	0	0	0	0	0	0	1	3176	291	11	5		5	CDRT1	17	15519029	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	5938937	15519029	65676181	556	13707											
DRG2	1819	hgsc.bcm.edu	37	chr17	18003919	18003919	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatctcctttaactcgacaGtcacgctgacccagtgctcg	8	10	8	15	3	2	1	1	1	1	0	5	2	2	1	2	0	2	3	2	0	1	2	rs143296623	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:18003919G>A	ENST00000225729.3	+	7	715	c.577G>A	c.(577-579)Gtc>Atc	p.V193I	DRG2_ENST00000583355.1_Intron|DRG2_ENST00000395726.4_Missense_Mutation_p.V193I	NM_001388.4	NP_001379.1	P55039	DRG2_HUMAN	developmentally regulated GTP binding protein 2	193	OBG-type G. {ECO:0000255|PROSITE- ProRule:PRU01047}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)	p.V193fs*2(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	14	all_neural(463;0.228)					TAACTCGACAGTCACGCTGAC	0.562													G|||	13	0.00259585	0.0	0.0086	5008	,	,		22449	0.0		0.006	False		,,,				2504	0.001				p.V193I		Atlas-SNP	.											.	DRG2	27	.	1	Deletion - Frameshift(1)	ovary(1)	c.G577A						PASS	.	G	ILE/VAL	4,4402	8.1+/-20.4	0,4,2199	91	78	82		577	5.3	1	17	dbSNP_134	82	47,8553	30.1+/-81.4	0,47,4253	yes	missense	DRG2	NM_001388.3	29	0,51,6452	AA,AG,GG		0.5465,0.0908,0.3921	benign	193/365	18003919	51,12955	2203	4300	6503	SO:0001583	missense	1819	exon7			TCGACAGTCACGC	X80754	CCDS11191.1	17p13-p12	2008-07-18	2001-11-28		ENSG00000108591	ENSG00000108591			3030	protein-coding gene	gene with protein product		602986	"developmentally regulated GTP-binding protein 2"			9605870, 7929244	Standard	NM_001388		Approved		uc002gsh.2	P55039	OTTHUMG00000059399	ENST00000225729.3:c.577G>A	17.37:g.18003919G>A	ENSP00000225729:p.Val193Ile	83	0	0		102	51	0.5	NM_001388	B2R8G5|Q53Y50|Q9BWB2	Missense_Mutation	SNP	ENST00000225729.3	37	CCDS11191.1	8	0.003663003663003663	0	0.0	3	0.008287292817679558	0	0.0	5	0.006596306068601583	G	14.49	2.551381	0.45383	9.08E-4	0.005465	ENSG00000108591	ENST00000395726;ENST00000225729	T;T	0.30182	1.54;1.54	5.29	5.29	0.74685	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.29491	0.0735	M	0.66378	2.025	0.80722	D	1	B;B	0.18310	0.027;0.015	B;B	0.12837	0.008;0.008	T	0.16305	-1.0407	10	0.59425	D	0.04	-21.1669	18.9395	0.92600	0.0:0.0:1.0:0.0	.	193;193	A8MZF9;P55039	.;DRG2_HUMAN	I	193	ENSP00000379076:V193I;ENSP00000225729:V193I	ENSP00000225729:V193I	V	+	1	0	DRG2	17944644	1.000000	0.71417	0.952000	0.39060	0.257000	0.26127	7.764000	0.85297	2.484000	0.83849	0.462000	0.41574	GTC	G|0.996;A|0.004	0.004	strong		0.562	DRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132075.3	NM_001388		A	18003919	G	A	18003919	3	1	30	1	0	0	0	0	1	0	0	0	4764	1029	36	2	603	2	DRG2	17	18003919	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2484890	18003919	63191291	557	13708											
TMEM199	147007	hgsc.bcm.edu	37	chr17	26684707	26684707	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctagatatggcgtcctcttTgcttgcgggcgagcgattgg	5	12	15	9	4	1	1	0	0	1	1	2	3	2	1	1	3	3	2	1	3	2	5			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:26684707T>A	ENST00000292114.3	+	1	104	c.14T>A	c.(13-15)tTg>tAg	p.L5*	POLDIP2_ENST00000003607.4_5'Flank|TMEM199_ENST00000395404.3_5'Flank|CTB-96E2.3_ENST00000591482.1_RNA|TMEM199_ENST00000581386.1_3'UTR|POLDIP2_ENST00000540200.1_5'Flank|MIR4723_ENST00000585070.1_RNA|TMEM199_ENST00000509083.1_Nonsense_Mutation_p.L5*	NM_152464.1	NP_689677.1	Q8N511	TM199_HUMAN	transmembrane protein 199	5						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)		GCGTCCTCTTTGCTTGCGGGC	0.692																																					p.L5X		Atlas-SNP	.											.	TMEM199	15	.	0			c.T14A						PASS	.						46	53	50					17																	26684707		2203	4299	6502	SO:0001587	stop_gained	147007	exon1			CCTCTTTGCTTGC	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	ENST00000292114.3:c.14T>A	17.37:g.26684707T>A	ENSP00000292114:p.Leu5*	49	0	0		41	16	0.390244	NM_152464		Nonsense_Mutation	SNP	ENST00000292114.3	37	CCDS11228.1	.	.	.	.	.	.	.	.	.	.	T	18.87	3.715363	0.68844	.	.	ENSG00000244045	ENST00000292114;ENST00000509083	.	.	.	4.87	3.78	0.43462	.	0.423693	0.22233	N	0.062791	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.4721	9.6131	0.39674	0.0:0.0:0.1765:0.8235	.	.	.	.	X	5	.	ENSP00000292114:L5X	L	+	2	0	TMEM199	23708834	0.068000	0.21057	0.001000	0.08648	0.003000	0.03518	2.583000	0.46094	0.861000	0.35504	-0.313000	0.08912	TTG	.	.	none		0.692	TMEM199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255676.2	NM_152464		A	26684707	T	A	26684707	4	1	30	1	0	0	0	0	0	1	0	0	16135	1821	63	5	16	5	TMEM199	17	26684707	Nonsense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	8680788	26684707	54510503	558	13709											
UTP6	55813	hgsc.bcm.edu	37	chr17	30200750	30200750	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cttcactccactctgcccagGaaatccacaatggcagacaa	13	7	6	15	0	2	1	1	0	1	1	4	2	4	2	3	2	1	1	3	2	3	1	rs267604797		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:30200750G>A	ENST00000261708.4	-	15	1465	c.1328C>T	c.(1327-1329)tCc>tTc	p.S443F	CTC-542B22.2_ENST00000583236.1_lincRNA	NM_018428.2	NP_060898.2	Q9NYH9	UTP6_HUMAN	UTP6, small subunit (SSU) processome component, homolog (yeast)	443					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)				CTCTGCCCAGGAAATCCACAA	0.428																																					p.S443F		Atlas-SNP	.											.	UTP6	46	.	0			c.C1328T						PASS	.						199	189	192					17																	30200750		2203	4300	6503	SO:0001583	missense	55813	exon15			GCCCAGGAAATCC	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.1328C>T	17.37:g.30200750G>A	ENSP00000261708:p.Ser443Phe	69	0	0		51	4	0.0784314	NM_018428	Q8IX96|Q96BL2|Q9NQ91	Missense_Mutation	SNP	ENST00000261708.4	37	CCDS11269.1	.	.	.	.	.	.	.	.	.	.	G	11.40	1.626443	0.28978	.	.	ENSG00000108651	ENST00000261708	T	0.34859	1.34	5.1	2.71	0.32032	Tetratricopeptide-like helical (1);	0.326861	0.31301	N	0.007891	T	0.18841	0.0452	L	0.29908	0.895	0.29239	N	0.872766	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.15636	-1.0430	10	0.08837	T	0.75	-7.7125	4.5063	0.11889	0.3816:0.0:0.6184:0.0	.	443;443	B3KQ21;Q9NYH9	.;UTP6_HUMAN	F	443	ENSP00000261708:S443F	ENSP00000261708:S443F	S	-	2	0	UTP6	27224863	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	4.107000	0.57811	1.291000	0.44653	0.650000	0.86243	TCC	.	.	none		0.428	UTP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256265.2	NM_018428		A	30200750	G	A	30200750	3	1	30	1	0	0	0	0	1	0	0	0	17117	1174	41	2	485	2	UTP6	17	30200750	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	3516043	30200750	50994460	559	13710											
SPACA3	124912	hgsc.bcm.edu	37	chr17	31322691	31322691	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaactggccagagtgctacAtgacttcgggctggacggat	9	9	14	9	2	0	3	0	2	0	1	1	5	0	5	1	4	3	2	1	4	2	2	rs28963	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:31322691A>G	ENST00000269053.3	+	2	369	c.299A>G	c.(298-300)cAt>cGt	p.H100R	SPACA3_ENST00000394637.2_3'UTR|SPACA3_ENST00000580599.1_Missense_Mutation_p.H31R|SPACA3_ENST00000394638.1_Intron	NM_173847.3	NP_776246.1	Q8IXA5	SACA3_HUMAN	sperm acrosome associated 3	100			H -> R (in dbSNP:rs28963).		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)			AGAGTGCTACATGACTTCGGG	0.612																																					p.H100R		Atlas-SNP	.											.	SPACA3	35	.	0			c.A299G						PASS	.	A	ARG/HIS	1,4405	2.1+/-5.4	0,1,2202	102	67	79		299	-1	0	17	dbSNP_76	79	14,8586	10.5+/-38.8	0,14,4286	yes	missense	SPACA3	NM_173847.3	29	0,15,6488	GG,GA,AA		0.1628,0.0227,0.1153	benign	100/216	31322691	15,12991	2203	4300	6503	SO:0001583	missense	124912	exon2			TGCTACATGACTT	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.299A>G	17.37:g.31322691A>G	ENSP00000269053:p.His100Arg	245	0	0		203	101	0.497537	NM_173847	Q7Z4Y5	Missense_Mutation	SNP	ENST00000269053.3	37	CCDS11275.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	a|a	2.934|2.934	-0.220387|-0.220387	0.06061|0.06061	2.27E-4|2.27E-4	0.001628|0.001628	ENSG00000141316|ENSG00000141316	ENST00000269053;ENST00000394637|ENST00000411740	T|.	0.67345|.	-0.26|.	3.82|3.82	-0.968|-0.968	0.10313|0.10313	Lysozyme-like domain (1);|.	0.660523|.	0.13489|.	N|.	0.384114|.	T|T	0.16642|0.16642	0.0400|0.0400	N|N	0.05230|0.05230	-0.09|-0.09	0.09310|0.09310	N|N	1|1	B|.	0.06786|.	0.001|.	B|.	0.08055|.	0.003|.	T|T	0.20739|0.20739	-1.0266|-1.0266	10|6	0.39692|0.87932	T|D	0.17|0	-7.1977|-7.1977	3.9109|3.9109	0.09202|0.09202	0.4882:0.1912:0.3206:0.0|0.4882:0.1912:0.3206:0.0	rs28963;rs52826872;rs28963|rs28963;rs52826872;rs28963	100|.	Q8IXA5|.	SACA3_HUMAN|.	R|V	100;101|1	ENSP00000269053:H100R|.	ENSP00000269053:H100R|ENSP00000392807:M1V	H|M	+|+	2|1	0|0	SPACA3|SPACA3	28346804|28346804	0.026000|0.026000	0.19158|0.19158	0.000000|0.000000	0.03702|0.03702	0.607000|0.607000	0.37147|0.37147	2.419000|2.419000	0.44671|0.44671	-0.692000|-0.692000	0.05128|0.05128	-0.443000|-0.443000	0.05667|0.05667	CAT|ATG	A|0.998;G|0.002	0.002	strong		0.612	SPACA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256380.1	NM_173847		G	31322691	A	G	31322691	3	3	30	1	0	0	0	0	1	0	0	0	14988	217	8	3	305	3	SPACA3	17	31322691	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	1121941	31322691	49872519	560	13711											
SLFN12	55106	hgsc.bcm.edu	37	chr17	33749758	33749758	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaagtagttaccattctgcAtgaagtctaagtactcagga	14	11	9	7	0	3	1	1	1	2	0	3	3	3	2	1	1	3	4	1	1	6	5	rs138003670	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:33749758A>G	ENST00000394562.1	-	4	813	c.290T>C	c.(289-291)aTg>aCg	p.M97T	SLFN12_ENST00000452764.3_Missense_Mutation_p.M97T|SLFN12_ENST00000304905.5_Missense_Mutation_p.M97T|SLFN12_ENST00000460530.1_5'Flank			Q8IYM2	SLN12_HUMAN	schlafen family member 12	97							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)		ACCATTCTGCATGAAGTCTAA	0.358													A|||	8	0.00159744	0.0	0.0	5008	,	,		20665	0.0		0.006	False		,,,				2504	0.002				p.M97T		Atlas-SNP	.											.	SLFN12	56	.	0			c.T290C						PASS	.	A	THR/MET	3,4403	6.2+/-15.9	0,3,2200	70	70	70		290	0.7	0.1	17	dbSNP_134	70	31,8569	21.6+/-65.8	0,31,4269	yes	missense	SLFN12	NM_018042.3	81	0,34,6469	GG,GA,AA		0.3605,0.0681,0.2614	benign	97/579	33749758	34,12972	2203	4300	6503	SO:0001583	missense	55106	exon2			TTCTGCATGAAGT	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.290T>C	17.37:g.33749758A>G	ENSP00000378063:p.Met97Thr	146	0	0		117	53	0.452991	NM_018042	A8K711|Q9NP47	Missense_Mutation	SNP	ENST00000394562.1	37	CCDS11295.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	a	12.33	1.906264	0.33628	6.81E-4	0.003605	ENSG00000172123	ENST00000394562;ENST00000304905;ENST00000452764;ENST00000447040	T;T;T;T	0.22945	3.79;3.79;3.79;1.93	3.27	0.658	0.17855	.	.	.	.	.	T	0.19406	0.0466	L	0.58583	1.82	0.09310	N	1	P	0.51791	0.948	P	0.46362	0.514	T	0.09975	-1.0650	9	0.46703	T	0.11	.	5.5093	0.16872	0.5168:0.0:0.0:0.4831	.	97	Q8IYM2	SLN12_HUMAN	T	97	ENSP00000378063:M97T;ENSP00000302077:M97T;ENSP00000394903:M97T;ENSP00000398315:M97T	ENSP00000302077:M97T	M	-	2	0	SLFN12	30773871	0.062000	0.20869	0.071000	0.20095	0.053000	0.15095	0.162000	0.16501	-0.026000	0.13895	0.358000	0.22013	ATG	A|0.998;G|0.002	0.002	strong		0.358	SLFN12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256491.1	NM_018042		G	33749758	A	G	33749758	3	3	30	1	0	0	0	0	1	0	0	0	14749	217	8	3	1458	3	SLFN12	17	33749758	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	2427067	33749758	47445452	561	13712											
MLLT6	4302	hgsc.bcm.edu	37	chr17	36868976	36868976	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaagaacgccttaagcagaaGcacaagaagcggcctgagtc	16	4	11	10	2	0	4	0	1	0	3	1	4	0	4	2	1	4	2	2	1	6	1			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:36868976G>A	ENST00000325718.7	+	8	844	c.753G>A	c.(751-753)aaG>aaA	p.K251K	CTB-58E17.9_ENST00000579499.1_RNA|MLLT6_ENST00000378137.5_Silent_p.K251K	NM_005937.3	NP_005928	P55198	AF17_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 6	251					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)					TTAAGCAGAAGCACAAGAAGC	0.587			T	MLL	AL																																p.K251K		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.G753A						PASS	.						108	104	105					17																	36868976		2203	4300	6503	SO:0001819	synonymous_variant	4302	exon8			GCAGAAGCACAAG		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.753G>A	17.37:g.36868976G>A		107	0	0		123	34	0.276423	NM_005937	Q59F28|Q96IU3|Q9H5F6|Q9UF49	Silent	SNP	ENST00000325718.7	37	CCDS11327.1																																																																																			.	.	none		0.587	MLLT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256799.1	NM_005937		A	36868976	G	A	36868976	2	1	30	1	0	0	0	0	0	0	0	1	9639	962	34	2		2	MLLT6	17	36868976	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	3119218	36868976	44326234	562	13713											
CDK12	51755	hgsc.bcm.edu	37	chr17	37627387	37627387	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctagaaaagagaacagttcAgtagaggctaaggattcagg	16	7	12	6	0	2	3	2	0	0	3	2	5	2	4	1	3	1	3	1	3	6	5	rs56158954	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:37627387A>G	ENST00000447079.4	+	2	1335	c.1302A>G	c.(1300-1302)tcA>tcG	p.S434S	CDK12_ENST00000430627.2_Silent_p.S434S	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	434					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						AGAACAGTTCAGTAGAGGCTA	0.428			"Mis, N, F"		serous ovarian					TCGA Ovarian(9;0.13)			A|||	28	0.00559105	0.0	0.0115	5008	,	,		17944	0.0		0.0179	False		,,,				2504	0.002				p.S434S		Atlas-SNP	.		Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	CDK12,NS,carcinoma,0,1	CDK12	161	1	0			c.A1302G						PASS	.	A	,	21,4385	28.1+/-56.4	0,21,2182	68	69	69		1302,1302	2.7	1	17	dbSNP_129	69	170,8430	77.8+/-140.4	1,168,4131	no	coding-synonymous,coding-synonymous	CDK12	NM_015083.1,NM_016507.2	,	1,189,6313	GG,GA,AA		1.9767,0.4766,1.4686	,	434/1482,434/1491	37627387	191,12815	2203	4300	6503	SO:0001819	synonymous_variant	51755	exon2			CAGTTCAGTAGAG	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.1302A>G	17.37:g.37627387A>G		68	0	0		59	33	0.559322	NM_016507	A7E2B2|B4DYX4|B9EIQ6|O94978	Silent	SNP	ENST00000447079.4	37	CCDS11337.1																																																																																			A|0.987;G|0.013	0.013	strong		0.428	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507		G	37627387	A	G	37627387	2	3	30	1	0	0	0	0	0	0	0	1	3130	175	7	3		3	CDK12	17	37627387	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	758411	37627387	43567823	563	13714											
TOP2A	7153	hgsc.bcm.edu	37	chr17	38546274	38546274	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttagagtcagaatcatcagaAgtggatggcttccttttgcg	10	13	11	7	1	3	3	3	0	0	3	4	4	4	4	1	2	1	1	1	2	3	4	rs17680289	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:38546274A>C	ENST00000423485.1	-	34	4568	c.4410T>G	c.(4408-4410)acT>acG	p.T1470T	Y_RNA_ENST00000410949.1_RNA	NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	1470					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)	AATCATCAGAAGTGGATGGCT	0.433													A|||	34	0.00678914	0.0015	0.0101	5008	,	,		17725	0.0		0.0209	False		,,,				2504	0.0041				p.T1470T		Atlas-SNP	.											.	TOP2A	124	.	0			c.T4410G						PASS	.	A		13,3797		0,13,1892	69	66	67		4410	0.4	0.8	17	dbSNP_123	67	163,8085		1,161,3962	no	coding-synonymous	TOP2A	NM_001067.3		1,174,5854	CC,CA,AA		1.9762,0.3412,1.4596		1470/1532	38546274	176,11882	1905	4124	6029	SO:0001819	synonymous_variant	7153	exon34			ATCAGAAGTGGAT		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.4410T>G	17.37:g.38546274A>C		198	0	0		166	87	0.524096	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Silent	SNP	ENST00000423485.1	37	CCDS45672.1																																																																																			A|0.988;C|0.012	0.012	strong		0.433	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1			C	38546274	A	C	38546274	2	2	30	1	0	0	0	0	0	0	0	1	16380	59	3	5		5	TOP2A	17	38546274	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	918887	38546274	42648936	564	13715											
TOP2A	7153	hgsc.bcm.edu	37	chr17	38564363	38564363	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggataagcgtacactcagtGgagtttcggccccctaaaat	12	9	10	10	2	1	0	1	0	0	0	2	2	1	2	2	3	2	2	2	3	4	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:38564363G>A	ENST00000423485.1	-	12	1514	c.1356C>T	c.(1354-1356)tcC>tcT	p.S452S		NM_001067.3	NP_001058.2	P11388	TOP2A_HUMAN	topoisomerase (DNA) II alpha 170kDa	452					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)	TACACTCAGTGGAGTTTCGGC	0.403																																					p.S452S		Atlas-SNP	.											.	TOP2A	124	.	0			c.C1356T						PASS	.						39	37	37					17																	38564363		1832	4080	5912	SO:0001819	synonymous_variant	7153	exon12			CTCAGTGGAGTTT		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.1356C>T	17.37:g.38564363G>A		43	0	0		58	27	0.465517	NM_001067	B2RTS1|Q71UN1|Q71UQ5|Q9HB24|Q9HB25|Q9HB26|Q9UP44|Q9UQP9	Silent	SNP	ENST00000423485.1	37	CCDS45672.1																																																																																			.	.	none		0.403	TOP2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338035.1			A	38564363	G	A	38564363	2	1	30	1	0	0	0	0	0	0	0	1	16380	1335	47	2		2	TOP2A	17	38564363	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	18089	38564363	42630847	565	13716											
KRTAP1-1	81851	hgsc.bcm.edu	37	chr17	39197304	39197304	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtctgggcggcaccacctgaTacgggtgctcacagctccac	7	7	12	15	2	2	1	1	1	1	0	3	1	3	1	3	3	3	3	3	3	1	1			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:39197304T>C	ENST00000306271.4	-	1	409	c.346A>G	c.(346-348)Atc>Gtc	p.I116V		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	116						keratin filament (GO:0045095)		p.I116V(1)		NS(2)|endometrium(2)|kidney(5)|lung(4)|prostate(1)	14		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			CACCACCTGATACGGGTGCTC	0.662																																					p.I116V		Atlas-SNP	.											KRTAP1-1,NS,malignant_melanoma,0,1	KRTAP1-1	23	1	1	Substitution - Missense(1)	NS(1)	c.A346G						PASS	.						22	27	25					17																	39197304		2019	4148	6167	SO:0001583	missense	81851	exon1			ACCTGATACGGGT	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.346A>G	17.37:g.39197304T>C	ENSP00000305975:p.Ile116Val	156	0	0		135	13	0.0962963	NM_030967	A6NC32|Q96S60|Q96S67	Missense_Mutation	SNP	ENST00000306271.4	37	CCDS42324.1	.	.	.	.	.	.	.	.	.	.	T	8.173	0.792133	0.16258	.	.	ENSG00000188581	ENST00000306271;ENST00000543328	T	0.29655	1.56	4.28	-1.23	0.09465	.	.	.	.	.	T	0.12135	0.0295	N	0.03253	-0.375	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.34079	-0.9843	9	0.20046	T	0.44	.	9.4726	0.38851	0.0:0.573:0.0:0.427	.	116	Q07627	KRA11_HUMAN	V	116;106	ENSP00000305975:I116V	ENSP00000305975:I116V	I	-	1	0	KRTAP1-1	36450830	0.132000	0.22450	0.024000	0.17045	0.516000	0.34256	0.017000	0.13399	-0.199000	0.10317	0.529000	0.55759	ATC	.	.	none		0.662	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967		C	39197304	T	C	39197304	3	2	30	1	0	0	0	0	1	0	0	0	8511	1406	49	3	191	3	KRTAP1-1	17	39197304	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	632941	39197304	41997906	566	13717											
KAT2A	2648	hgsc.bcm.edu	37	chr17	40265751	40265751	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcggcagtactcgctgtcCggggggttgtactcgcgaca	6	8	15	12	5	0	0	0	0	0	0	3	1	1	0	1	4	3	5	1	4	2	3	rs147642400	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:40265751C>T	ENST00000225916.5	-	18	2483	c.2430G>A	c.(2428-2430)ccG>ccA	p.P810P	DHX58_ENST00000251642.3_5'Flank	NM_021078.2	NP_066564.2	Q92830	KAT2A_HUMAN	K(lysine) acetyltransferase 2A	810	Bromo. {ECO:0000255|PROSITE- ProRule:PRU00035}.				cell proliferation (GO:0008283)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|histone H3-K14 acetylation (GO:0044154)|in utero embryonic development (GO:0001701)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|positive regulation of gluconeogenesis (GO:0045722)|regulation of protein stability (GO:0031647)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|somitogenesis (GO:0001756)|telencephalon development (GO:0021537)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|extracellular space (GO:0005615)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	chromatin binding (GO:0003682)|H3 histone acetyltransferase activity (GO:0010484)|histone acetyltransferase activity (GO:0004402)|histone acetyltransferase activity (H4-K12 specific) (GO:0043997)|histone deacetylase binding (GO:0042826)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						ACTCGCTGTCCGGGGGGTTGT	0.612													C|||	7	0.00139776	0.0008	0.0029	5008	,	,		17799	0.0		0.004	False		,,,				2504	0.0				p.P810P		Atlas-SNP	.											.	KAT2A	54	.	0			c.G2430A						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	34	35	34		2430	-10.1	0.6	17	dbSNP_134	34	54,8546	32.3+/-84.9	0,54,4246	no	coding-synonymous	KAT2A	NM_021078.2		0,55,6448	TT,TC,CC		0.6279,0.0227,0.4229		810/838	40265751	55,12951	2203	4300	6503	SO:0001819	synonymous_variant	2648	exon18			GCTGTCCGGGGGG	AF029777	CCDS11417.1	17q12-q21	2011-07-01	2008-07-04	2008-07-04	ENSG00000108773	ENSG00000108773		"Chromatin-modifying enzymes / K-acetyltransferases"	4201	protein-coding gene	gene with protein product		602301	"GCN5 general control of amino-acid synthesis 5-like 2 (yeast)"	GCN5L2		8552087	Standard	NM_021078		Approved	GCN5, PCAF-b	uc002hyx.2	Q92830	OTTHUMG00000133504	ENST00000225916.5:c.2430G>A	17.37:g.40265751C>T		35	0	0		54	15	0.277778	NM_021078	Q8N1A2|Q9UCW1	Silent	SNP	ENST00000225916.5	37	CCDS11417.1																																																																																			C|0.998;T|0.002	0.002	strong		0.612	KAT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257458.1	NM_021078		T	40265751	C	T	40265751	2	4	30	1	0	0	0	0	0	0	0	1	7990	639	23	1		1	KAT2A	17	40265751	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1068447	40265751	40929459	567	13718											
FZD2	2535	hgsc.bcm.edu	37	chr17	42636477	42636477	+	Frame_Shift_Del	DEL	C	C	-																															gctctacacagtgcccgccaCcatcgtcatcgcttgctact																										TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:42636477delC	ENST00000315323.3	+	1	1553	c.1421delC	c.(1420-1422)accfs	p.T474fs		NM_001466.3	NP_001457.1	Q14332	FZD2_HUMAN	frizzled class receptor 2	474					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)		GTGCCCGCCACCATCGTCATC	0.632																																					p.T474fs		Pindel,Atlas-Indel	.											.	FZD2	81	.	0			c.1420delA						PASS	.						73	59	64					17																	42636477		2203	4300	6503	SO:0001589	frameshift_variant	2535	exon1			.	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.1421delC	17.37:g.42636477delC	ENSP00000323901:p.Thr474fs	96	0	.		90	19	0.211	NM_001466	Q0VG82	Frame_Shift_Del	DEL	ENST00000315323.3	37	CCDS11484.1																																																																																			.	.	none		0.632	FZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457806.1	NM_001466		-	42636477	C	-	42636477	7	5	30	1	0	1	0	1	0	0	0	0	6138	507	18	0	1423	0	FZD2	17	42636477	Frame_Shift_Del	DEL	C	TCGA-GR-7353-01A-11D-2210-10	2370726	42636477	38558733	568	13719											
KPNB1	3837	hgsc.bcm.edu	37	chr17	45734285	45734285	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgcctcacagtgtgtggcTggtattgcttgtgcagagat	6	14	13	8	0	2	1	1	0	1	1	2	2	2	1	1	2	3	4	1	2	1	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:45734285T>C	ENST00000290158.4	+	4	749	c.342T>C	c.(340-342)gcT>gcC	p.A114A	KPNB1_ENST00000537679.1_5'Flank|KPNB1_ENST00000540627.1_5'UTR|KPNB1_ENST00000535458.2_5'UTR|KPNB1_ENST00000577918.1_3'UTR	NM_001276453.1|NM_002265.4	NP_001263382.1|NP_002256.2	Q14974	IMB1_HUMAN	karyopherin (importin) beta 1	114					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						AGTGTGTGGCTGGTATTGCTT	0.468																																					p.H114H		Atlas-SNP	.											.	KPNB1	58	.	0			c.C342C						PASS	.						138	121	127					17																	45734285		2203	4300	6503	SO:0001819	synonymous_variant	3837	exon4			TGTGGCTGGTATT	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.342T>C	17.37:g.45734285T>C		146	0	0		111	46	0.414414	NM_002265	B7ZAV6|D3DTT3|Q14637|Q53XN2|Q96J27	Silent	SNP	ENST00000290158.4	37	CCDS11513.1																																																																																			.	.	none		0.468	KPNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089755.2	NM_002265		C	45734285	T	C	45734285	2	2	30	1	0	0	0	0	0	0	0	1	8444	1567	55	3		3	KPNB1	17	45734285	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	3097808	45734285	35460925	569	13720											
HOXB5	3215	hgsc.bcm.edu	37	chr17	46669730	46669730	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgccgtcgccgggtcaggtaGcggttgaagtggaactcctt	6	9	15	11	5	1	1	1	1	0	0	3	2	2	2	3	4	2	2	3	4	3	3	rs36049616	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:46669730G>T	ENST00000239151.5	-	2	929	c.651C>A	c.(649-651)cgC>cgA	p.R217R	HOXB-AS3_ENST00000480872.1_RNA|HOXB3_ENST00000552000.2_Intron|HOXB3_ENST00000472863.1_5'Flank|HOXB-AS3_ENST00000476204.1_RNA|HOXB-AS3_ENST00000474040.1_RNA|HOXB-AS3_ENST00000467155.2_RNA|HOXB-AS3_ENST00000492897.3_RNA|HOXB3_ENST00000476342.1_5'Flank|HOXB-AS3_ENST00000487849.3_RNA|HOXB3_ENST00000498678.1_5'Flank|HOXB3_ENST00000460160.1_5'Flank|HOXB-AS3_ENST00000465846.2_RNA|HOXB-AS3_ENST00000429755.4_RNA	NM_002147.3	NP_002138.1	P09067	HXB5_HUMAN	homeobox B5	217					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						GGGTCAGGTAGCGGTTGAAGT	0.612													G|||	144	0.028754	0.0734	0.0346	5008	,	,		11348	0.0		0.0179	False		,,,				2504	0.0051				p.R217R		Atlas-SNP	.											.	HOXB5	20	.	0			c.C651A						PASS	.	G		301,4105	165.8+/-197.2	13,275,1915	105	105	105		651	4.2	1	17	dbSNP_126	105	301,8299	109.4+/-169.9	6,289,4005	no	coding-synonymous	HOXB5	NM_002147.3		19,564,5920	TT,TG,GG		3.5,6.8316,4.6286		217/270	46669730	602,12404	2203	4300	6503	SO:0001819	synonymous_variant	3215	exon2			CAGGTAGCGGTTG		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.651C>A	17.37:g.46669730G>T		187	0	0		203	76	0.374384	NM_002147	B2RC69|P09069|Q17RP4	Silent	SNP	ENST00000239151.5	37	CCDS11530.1																																																																																			G|0.960;T|0.040	0.040	strong		0.612	HOXB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358148.2			T	46669730	G	T	46669730	2	4	30	1	0	0	0	0	0	0	0	1	7313	958	34	4		4	HOXB5	17	46669730	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	935445	46669730	34525480	570	13721											
HOXB8	3218	hgsc.bcm.edu	37	chr17	46690777	46690777	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatacctcgattcgccgcttAcgagtcagatagggattaaa	12	10	10	9	4	1	1	1	0	0	1	3	5	1	2	2	1	2	1	2	1	5	5	rs45441492	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:46690777A>G	ENST00000239144.4	-	2	753	c.519T>C	c.(517-519)cgT>cgC	p.R173R	HOXB8_ENST00000576562.1_Silent_p.R172R|HOXB7_ENST00000239165.7_5'Flank|HOXB7_ENST00000567101.2_Intron	NM_024016.3	NP_076921.1	P17481	HXB8_HUMAN	homeobox B8	173					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						TTCGCCGCTTACGAGTCAGAT	0.557													G|||	304	0.0607029	0.1536	0.0519	5008	,	,		8833	0.001		0.0278	False		,,,				2504	0.0368				p.R173R		Atlas-SNP	.											.	HOXB8	26	.	0			c.T519C						PASS	.	G		658,3748	764.6+/-413.3	52,554,1597	106	101	102		519	3.1	1	17	dbSNP_127	102	459,8141	798.8+/-407.4	16,427,3857	no	coding-synonymous	HOXB8	NM_024016.3		68,981,5454	GG,GA,AA		5.3372,14.9342,8.5883		173/244	46690777	1117,11889	2203	4300	6503	SO:0001819	synonymous_variant	3218	exon2			CCGCTTACGAGTC		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.519T>C	17.37:g.46690777A>G		221	1	0.00452489		182	180	0.989011	NM_024016	Q9H1I2	Silent	SNP	ENST00000239144.4	37	CCDS11533.1																																																																																			A|0.924;G|0.076	0.076	strong		0.557	HOXB8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358092.3			G	46690777	A	G	46690777	2	3	30	1	0	0	0	0	0	0	0	1	7316	378	14	3		3	HOXB8	17	46690777	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	21047	46690777	34504433	571	13722											
TTLL6	284076	hgsc.bcm.edu	37	chr17	46877017	46877017	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcccctggtttgatttctttCactgtccgggtgatgaatat	6	17	9	9	1	2	3	1	3	1	0	4	3	4	3	3	2	0	1	3	2	2	4	rs201225285	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:46877017C>T	ENST00000393382.3	-	6	858	c.717G>A	c.(715-717)gtG>gtA	p.V239V		NM_001130918.1	NP_001124390.1			tubulin tyrosine ligase-like family, member 6											endometrium(1)|large_intestine(5)|lung(9)|prostate(1)|skin(2)	18						TGATTTCTTTCACTGTCCGGG	0.428																																					p.V239V		Atlas-SNP	.											.	TTLL6	113	.	0			c.G717A						PASS	.						173	141	151					17																	46877017		692	1591	2283	SO:0001819	synonymous_variant	284076	exon6			TTCTTTCACTGTC	AK093127	CCDS11537.2, CCDS45724.1	17q21.32	2013-02-14			ENSG00000170703	ENSG00000170703		"Tubulin tyrosine ligase-like family"	26664	protein-coding gene	gene with protein product		610849				15890843	Standard	NM_173623		Approved	FLJ35808	uc021tzm.1	Q8N841	OTTHUMG00000156978	ENST00000393382.3:c.717G>A	17.37:g.46877017C>T		189	0	0		148	63	0.425676	NM_001130918		Silent	SNP	ENST00000393382.3	37	CCDS45724.1																																																																																			C|0.996;T|0.004	0.004	strong		0.428	TTLL6-003	KNOWN	downstream_ATG|non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346939.3	NM_173623		T	46877017	C	T	46877017	2	4	30	1	0	0	0	0	0	0	0	1	16746	813	29	2		2	TTLL6	17	46877017	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	186240	46877017	34318193	572	13723											
ABCC3	8714	hgsc.bcm.edu	37	chr17	48745035	48745035	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagcaggtggagggcatcAggcagggtgagctccagctg	9	6	18	8	0	1	2	1	2	0	0	2	3	2	3	1	5	3	5	1	5	1	0	rs11568601	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:48745035A>C	ENST00000285238.8	+	12	1632	c.1552A>C	c.(1552-1554)Agg>Cgg	p.R518R	ABCC3_ENST00000427699.1_Silent_p.R518R	NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	518	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				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)	GGAGGGCATCAGGCAGGGTGA	0.622													A|||	26	0.00519169	0.0015	0.0058	5008	,	,		22136	0.0		0.0189	False		,,,				2504	0.001				p.R518R		Atlas-SNP	.											.	ABCC3	138	.	0			c.A1552C						PASS	.	A	,	21,4385	28.1+/-56.4	0,21,2182	72	58	63		1552,1552	1.7	1	17	dbSNP_126	63	219,8381	91.1+/-153.3	3,213,4084	no	coding-synonymous,coding-synonymous	ABCC3	NM_001144070.1,NM_003786.3	,	3,234,6266	CC,CA,AA		2.5465,0.4766,1.8453	,	518/573,518/1528	48745035	240,12766	2203	4300	6503	SO:0001819	synonymous_variant	8714	exon12			GGCATCAGGCAGG	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.1552A>C	17.37:g.48745035A>C		80	0	0		100	45	0.45	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Silent	SNP	ENST00000285238.8	37	CCDS32681.1																																																																																			A|0.984;C|0.016	0.016	strong		0.622	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038		C	48745035	A	C	48745035	2	2	30	1	0	0	0	0	0	0	0	1	54	179	7	5		5	ABCC3	17	48745035	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	1868018	48745035	32450175	573	13724											
MSI2	124540	hgsc.bcm.edu	37	chr17	55752389	55752389	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaacagcccaggacctgtcGccgatctctacggccctgcc	7	6	9	19	3	1	0	0	0	1	0	3	2	1	1	6	2	4	0	6	2	2	1	rs116924898	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:55752389G>A	ENST00000284073.2	+	12	1056	c.847G>A	c.(847-849)Gcc>Acc	p.A283T	MSI2_ENST00000579505.1_3'UTR|MSI2_ENST00000442934.2_Missense_Mutation_p.A222T|MSI2_ENST00000416426.2_Missense_Mutation_p.A279T	NM_138962.2	NP_620412.1	Q96DH6	MSI2H_HUMAN	musashi RNA-binding protein 2	283						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)		AGGACCTGTCGCCGATCTCTA	0.687			T	HOXA9	CML								G|||	15	0.00299521	0.0008	0.0043	5008	,	,		15149	0.0		0.0099	False		,,,				2504	0.001				p.A283T		Atlas-SNP	.		Dom	yes		17	17q23.2	124540	musashi homolog 2 (Drosophila)		L	.	MSI2	52	.	0			c.G847A						PASS	.	G	THR/ALA	7,4399	11.4+/-27.6	0,7,2196	47	58	55		847	4.5	1	17	dbSNP_132	55	94,8500	49.8+/-109.6	0,94,4203	yes	missense	MSI2	NM_138962.2	58	0,101,6399	AA,AG,GG		1.0938,0.1589,0.7769	probably-damaging	283/329	55752389	101,12899	2203	4297	6500	SO:0001583	missense	124540	exon12			CCTGTCGCCGATC	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.847G>A	17.37:g.55752389G>A	ENSP00000284073:p.Ala283Thr	142	0	0		120	57	0.475	NM_138962	Q7Z6M7|Q8N9T4	Missense_Mutation	SNP	ENST00000284073.2	37	CCDS11596.1	12	0.005494505494505495	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	G	25.8	4.674614	0.88445	0.001589	0.010938	ENSG00000153944	ENST00000416426;ENST00000284073;ENST00000442934	D;D;D	0.85773	-2.03;-2.03;-2.03	4.48	4.48	0.54585	.	0.000000	0.85682	D	0.000000	D	0.87014	0.6072	M	0.63428	1.95	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.71656	0.959;0.974	D	0.85771	0.1355	10	0.15952	T	0.53	.	17.1487	0.86773	0.0:0.0:1.0:0.0	.	279;283	B4DHE8;Q96DH6	.;MSI2H_HUMAN	T	279;283;222	ENSP00000414671:A279T;ENSP00000284073:A283T;ENSP00000392607:A222T	ENSP00000284073:A283T	A	+	1	0	MSI2	53107388	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.418000	0.97395	2.038000	0.60285	0.491000	0.48974	GCC	A|0.007;C|0.000;G|0.992	0.007	strong		0.687	MSI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441813.1			A	55752389	G	A	55752389	3	1	30	1	0	0	0	0	1	0	0	0	9885	1087	38	1	988	1	MSI2	17	55752389	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	7007354	55752389	25442821	574	13725											
SFRS1	6426	hgsc.bcm.edu	37	chr17	56083705	56083705	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acacaaccagtacactcaccAgagacaaccactctgttttc	14	8	4	15	0	2	1	1	0	1	1	3	2	2	1	3	0	3	2	3	0	3	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:56083705A>G	ENST00000258962.4	-	2	586	c.378T>C	c.(376-378)tcT>tcC	p.S126S	SRSF1_ENST00000582730.2_Splice_Site_p.S126S|SRSF1_ENST00000584773.1_Splice_Site_p.S126S|RP11-159D12.5_ENST00000578794.1_5'Flank|SRSF1_ENST00000585096.1_Intron|SRSF1_ENST00000581497.1_5'Flank	NM_006924.4	NP_008855.1	Q07955	SRSF1_HUMAN	serine/arginine-rich splicing factor 1	126	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				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						TACACTCACCAGAGACAACCA	0.527																																					p.S126S		Atlas-SNP	.											.	SRSF1	41	.	0			c.T378C						PASS	.						44	53	50					17																	56083705		2125	4165	6290	SO:0001630	splice_region_variant	6426	exon2			CTCACCAGAGACA		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.379+1T>C	17.37:g.56083705A>G		197	0	0		174	56	0.321839	NM_006924	B2R6Z7|D3DTZ3|Q13809	Silent	SNP	ENST00000258962.4	37	CCDS11600.1																																																																																			.	.	none		0.527	SRSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443335.1	NM_006924	Silent	G	56083705	A	G	56083705	5	3	30	1	0	0	0	0	0	0	1	0	14180	202	7	3	434	3	SFRS1	17	56083705	Splice_Site	SNP	A	TCGA-GR-7353-01A-11D-2210-10	331316	56083705	25111505	575	13726											
HEATR6	63897	hgsc.bcm.edu	37	chr17	58153586	58153586	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tcggcaagcctggacaagaaGagcactaacgtcctaccaaa	15	5	9	12	2	0	2	0	0	0	2	2	3	1	3	3	2	4	2	3	2	6	2	rs552733926		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:58153586G>C	ENST00000184956.6	-	2	248	c.232C>G	c.(232-234)Ctt>Gtt	p.L78V	HEATR6_ENST00000585712.1_5'Flank|HEATR6_ENST00000585976.1_Missense_Mutation_p.L78V	NM_022070.4	NP_071353.4	Q6AI08	HEAT6_HUMAN	HEAT repeat containing 6	78							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)			TGGACAAGAAGAGCACTAACG	0.368																																					p.L78V		Atlas-SNP	.											.	HEATR6	98	.	0			c.C232G						PASS	.						62	55	57					17																	58153586		2203	4300	6503	SO:0001583	missense	63897	exon2			CAAGAAGAGCACT	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.232C>G	17.37:g.58153586G>C	ENSP00000184956:p.Leu78Val	15	0	0		24	12	0.5	NM_022070	B3KXP3|Q6MZX1|Q6MZY2|Q8TDM9|Q9H6B3|Q9H6M7	Missense_Mutation	SNP	ENST00000184956.6	37	CCDS11623.1	.	.	.	.	.	.	.	.	.	.	G	13.22	2.171512	0.38315	.	.	ENSG00000068097	ENST00000184956	T	0.44083	0.93	5.1	3.9	0.45041	Armadillo-like helical (1);	0.069197	0.56097	D	0.000024	T	0.32852	0.0843	M	0.64997	1.995	0.35789	D	0.822271	B	0.31077	0.307	B	0.24701	0.055	T	0.50423	-0.8830	10	0.62326	D	0.03	-11.8567	3.2759	0.06898	0.166:0.0:0.5802:0.2538	.	78	Q6AI08	HEAT6_HUMAN	V	78	ENSP00000184956:L78V	ENSP00000184956:L78V	L	-	1	0	HEATR6	55508368	0.992000	0.36948	1.000000	0.80357	0.989000	0.77384	0.478000	0.22212	2.557000	0.86248	0.644000	0.83932	CTT	.	.	none		0.368	HEATR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449165.1	NM_022070		C	58153586	G	C	58153586	3	2	30	1	0	0	0	0	1	0	0	0	7042	942	33	4	3389	4	HEATR6	17	58153586	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2069881	58153586	23041624	576	13727											
ACE	1636	hgsc.bcm.edu	37	chr17	61573777	61573777	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actttgtcagcttcatcatcCagttccagttccacgaggca	9	12	7	13	1	3	0	3	0	0	0	6	1	6	0	3	1	1	4	3	1	0	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:61573777C>A	ENST00000290866.4	+	23	3427	c.3403C>A	c.(3403-3405)Cag>Aag	p.Q1135K	ACE_ENST00000421982.2_Intron|ACE_ENST00000413513.3_Intron|ACE_ENST00000490216.2_Missense_Mutation_p.Q561K|ACE_ENST00000290863.6_Missense_Mutation_p.Q561K|ACE_ENST00000428043.1_Missense_Mutation_p.Q1135K|ACE_ENST00000577647.1_Missense_Mutation_p.Q561K	NM_000789.3	NP_000780.1	P12821	ACE_HUMAN	angiotensin I converting enzyme	1135	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)	CTTCATCATCCAGTTCCAGTT	0.657																																					p.Q1135K		Atlas-SNP	.											.	ACE	187	.	0			c.C3403A						PASS	.						104	99	100					17																	61573777		2203	4300	6503	SO:0001583	missense	1636	exon23			ATCATCCAGTTCC	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.3403C>A	17.37:g.61573777C>A	ENSP00000290866:p.Gln1135Lys	245	1	0.00408163		248	124	0.5	NM_000789	B0LPF0|B4DXI3|E7EU16|P22966|Q53YX9|Q59GY8|Q7M4L4	Missense_Mutation	SNP	ENST00000290866.4	37	CCDS11637.1	.	.	.	.	.	.	.	.	.	.	C	13.51	2.258736	0.39896	.	.	ENSG00000159640	ENST00000290866;ENST00000428043;ENST00000290863	T;T;T	0.37584	1.19;1.19;1.19	5.17	5.17	0.71159	.	0.000000	0.85682	D	0.000000	T	0.73110	0.3545	H	0.95950	3.745	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.81914	0.922;0.995	T	0.83186	-0.0086	10	0.87932	D	0	-44.5904	18.2622	0.90039	0.0:1.0:0.0:0.0	.	561;1135	P12821-3;P12821	.;ACE_HUMAN	K	1135;1135;561	ENSP00000290866:Q1135K;ENSP00000397593:Q1135K;ENSP00000290863:Q561K	ENSP00000290863:Q561K	Q	+	1	0	ACE	58927509	1.000000	0.71417	1.000000	0.80357	0.328000	0.28507	7.726000	0.84824	2.393000	0.81446	0.484000	0.47621	CAG	.	.	none		0.657	ACE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337675.2			A	61573777	C	A	61573777	3	1	30	1	0	0	0	0	1	0	0	0	136	595	21	4	3696	4	ACE	17	61573777	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	3420191	61573777	19621433	577	13728											
SDK2	54549	hgsc.bcm.edu	37	chr17	71344769	71344769	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatttctgagggcttctccGtcaggctgctgctctctgca	5	13	11	12	1	4	2	1	1	3	1	6	2	4	2	1	2	3	5	1	2	0	2	rs199591952		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:71344769G>A	ENST00000392650.3	-	44	6134	c.6134C>T	c.(6133-6135)aCg>aTg	p.T2045M	SDK2_ENST00000410094.1_5'UTR|SDK2_ENST00000388726.3_Missense_Mutation_p.T2026M	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	2045					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						GGGCTTCTCCGTCAGGCTGCT	0.637													G|||	1	0.000199681	0.0	0.0	5008	,	,		16899	0.001		0.0	False		,,,				2504	0.0				p.T2045M		Atlas-SNP	.											.	SDK2	219	.	0			c.C6134T						PASS	.						61	54	56					17																	71344769		2203	4299	6502	SO:0001583	missense	54549	exon44			TTCTCCGTCAGGC	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.6134C>T	17.37:g.71344769G>A	ENSP00000376421:p.Thr2045Met	88	0	0		67	34	0.507463	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Missense_Mutation	SNP	ENST00000392650.3	37	CCDS45769.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	23.3	4.399737	0.83120	.	.	ENSG00000069188	ENST00000409227;ENST00000392650;ENST00000388726;ENST00000424778;ENST00000316893;ENST00000410094	T;T;T	0.62941	-0.01;0.03;1.29	4.81	4.81	0.61882	.	0.000000	0.85682	D	0.000000	T	0.76905	0.4053	M	0.62723	1.935	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.76575	0.983;0.988	T	0.80042	-0.1548	10	0.87932	D	0	.	16.6634	0.85247	0.0:0.0:1.0:0.0	.	2045;2026	Q58EX2;Q58EX2-3	SDK2_HUMAN;.	M	1669;2045;2026;1202;2045;386	ENSP00000376421:T2045M;ENSP00000373378:T2026M;ENSP00000407098:T1202M	ENSP00000324967:T2045M	T	-	2	0	SDK2	68856364	1.000000	0.71417	0.919000	0.36401	0.935000	0.57460	7.721000	0.84768	2.204000	0.70986	0.563000	0.77884	ACG	A|0.000;G|1.000	0.000	strong		0.637	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064		A	71344769	G	A	71344769	3	1	30	1	0	0	0	0	1	0	0	0	13984	1145	40	1	392	1	SDK2	17	71344769	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	9770992	71344769	9850441	578	13729											
GGA3	23163	hgsc.bcm.edu	37	chr17	73234805	73234806	+	Frame_Shift_Ins	INS	-	-	TCTG																															tggggctaaatggagagagtINStctgtcccagaaggtggctg																										TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:73234805_73234806insTCTG	ENST00000245541.6	-	16	2204_2205	c.1988_1989insCAGA	c.(1987-1989)gaafs	p.E663fs	GGA3_ENST00000582486.1_Frame_Shift_Ins_p.E591fs|GGA3_ENST00000582717.1_Frame_Shift_Ins_p.E591fs|GGA3_ENST00000578348.1_Frame_Shift_Ins_p.E541fs|GGA3_ENST00000351904.7_Frame_Shift_Ins_p.E630fs|GGA3_ENST00000538886.1_Frame_Shift_Ins_p.E541fs	NM_138619.2	NP_619525.1	Q9NZ52	GGA3_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 3	663	GAE. {ECO:0000255|PROSITE- ProRule:PRU00093}.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|endosome (GO:0005768)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)			breast(2)|endometrium(3)|large_intestine(4)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	20			all cancers(21;2.39e-06)|Epithelial(20;2.38e-05)			ATGGAGAGAGTTCTGTCCCAGA	0.535											OREG0024729	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E663fs		Pindel,Atlas-Indel	.											GGA3,NS,carcinoma,0,1	GGA3	54	1	0			c.1989_1990insCAGA						PASS	.																																			SO:0001589	frameshift_variant	23163	exon16			.	AF190864	CCDS11716.1, CCDS11717.1, CCDS54164.1, CCDS58597.1	17q25	2010-02-12	2010-02-12			ENSG00000125447			17079	protein-coding gene	gene with protein product		606006				10747089, 10749927	Standard	NR_033345		Approved	KIAA0154	uc002jni.2	Q9NZ52		ENST00000245541.6:c.1985_1988dupCAGA	17.37:g.73234806_73234809dupTCTG	ENSP00000245541:p.Glu663fs	203	0	.	1143	205	45	0.22	NM_138619	B7Z7E2|B7Z7M9|J3KRN0|Q15017|Q6IS16|Q9UJY3	Frame_Shift_Ins	INS	ENST00000245541.6	37	CCDS11717.1																																																																																			.	.	none		0.535	GGA3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446645.1	NM_138619		TCTG	73234806	-	TCTG	73234805	7	5	30	1	0	1	1	0	0	0	0	0	6362	1722	60	0	278	0	GGA3	17	73234805	Frame_Shift_Ins	INS	-	TCGA-GR-7353-01A-11D-2210-10	1890036	73234805	7960405	579	13730											
RHBDF2	79651	hgsc.bcm.edu	37	chr17	74473329	74473329	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatccctcggaagtagctggCagagagtgggggggactcaa	10	6	17	8	1	1	1	1	0	0	1	3	5	2	3	1	5	1	3	1	5	3	1	rs140433374		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:74473329C>T	ENST00000313080.4	-	8	1213	c.940G>A	c.(940-942)Gcc>Acc	p.A314T	RHBDF2_ENST00000389760.4_Missense_Mutation_p.A285T|RHBDF2_ENST00000592378.1_5'Flank|RHBDF2_ENST00000591885.1_Missense_Mutation_p.A285T	NM_024599.5	NP_078875.4	Q6PJF5	RHDF2_HUMAN	rhomboid 5 homolog 2 (Drosophila)	314					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						AAGTAGCTGGCAGAGAGTGGG	0.582													C|||	1	0.000199681	0.0	0.0014	5008	,	,		17105	0.0		0.0	False		,,,				2504	0.0				p.A314T		Atlas-SNP	.											.	RHBDF2	57	.	0			c.G940A						PASS	.	C	THR/ALA,THR/ALA	0,4404		0,0,2202	30	35	33		853,940	5.5	1	17	dbSNP_134	33	9,8591	6.4+/-24.3	0,9,4291	yes	missense,missense	RHBDF2	NM_001005498.3,NM_024599.5	58,58	0,9,6493	TT,TC,CC		0.1047,0.0,0.0692	possibly-damaging,possibly-damaging	285/828,314/857	74473329	9,12995	2202	4300	6502	SO:0001583	missense	79651	exon8			AGCTGGCAGAGAG	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.940G>A	17.37:g.74473329C>T	ENSP00000322775:p.Ala314Thr	158	0	0		138	74	0.536232	NM_024599	A6NEM3|A8K801|Q5U607|Q5YGQ8|Q9H6E9	Missense_Mutation	SNP	ENST00000313080.4	37	CCDS32743.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	27.4	4.830924	0.91036	0.0	0.001047	ENSG00000129667	ENST00000313080;ENST00000389760;ENST00000389762	T;T	0.69561	-0.41;-0.41	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	T	0.78566	0.4303	L	0.56769	1.78	0.50632	D	0.999886	D;P;P;P	0.69078	0.997;0.866;0.891;0.799	D;P;B;P	0.67548	0.952;0.507;0.439;0.615	T	0.73920	-0.3830	10	0.26408	T	0.33	-38.8792	19.4819	0.95013	0.0:1.0:0.0:0.0	.	285;260;314;285	B7Z8H4;Q6ZWP8;Q6PJF5;Q6PJF5-2	.;.;RHDF2_HUMAN;.	T	314;285;260	ENSP00000322775:A314T;ENSP00000374410:A285T	ENSP00000322775:A314T	A	-	1	0	RHBDF2	71984924	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.534000	0.67167	2.595000	0.87683	0.655000	0.94253	GCC	C|0.999;T|0.001	0.001	strong		0.582	RHBDF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450134.1	NM_024599		T	74473329	C	T	74473329	3	4	30	1	0	0	0	0	1	0	0	0	13335	710	25	2	1678	2	RHBDF2	17	74473329	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1238524	74473329	6721881	580	13731											
DNAH17	8632	hgsc.bcm.edu	37	chr17	76488794	76488794	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccttggggtccaggtccacGgcgaccggcttcctcttcag	4	9	13	15	3	2	0	1	0	1	0	5	1	5	0	5	5	0	1	5	5	0	3	rs76641546	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:76488794G>A	ENST00000585328.1	-	42	6571	c.6447C>T	c.(6445-6447)gcC>gcT	p.A2149A	DNAH17_ENST00000586052.1_5'Flank|RP11-559N14.5_ENST00000591373.1_RNA|RP11-559N14.5_ENST00000585969.1_RNA|RP11-559N14.5_ENST00000588565.1_RNA|DNAH17_ENST00000389840.5_Silent_p.A2140A	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	2140	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(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)			CCAGGTCCACGGCGACCGGCT	0.587													G|||	17	0.00339457	0.0	0.0043	5008	,	,		16651	0.0		0.0139	False		,,,				2504	0.0				p.A2154A		Atlas-SNP	.											.	DNAH17	347	.	0			c.C6462T						PASS	.	G		7,3935		0,7,1964	63	67	66		6462	-9.5	0	17	dbSNP_133	66	78,8248		1,76,4086	no	coding-synonymous	DNAH17	NM_173628.3		1,83,6050	AA,AG,GG		0.9368,0.1776,0.6929		2154/4463	76488794	85,12183	1971	4163	6134	SO:0001819	synonymous_variant	8632	exon42			GTCCACGGCGACC	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.6447C>T	17.37:g.76488794G>A		137	0	0		129	68	0.527132	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				G|0.994;A|0.006	0.006	strong		0.587	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		A	76488794	G	A	76488794	2	1	30	1	0	0	0	0	0	0	0	1	4603	1103	39	1		1	DNAH17	17	76488794	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2015465	76488794	4706416	581	13732											
HGS	9146	hgsc.bcm.edu	37	chr17	79660570	79660570	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ccacttccaccactgagctgCcccccgagtacctgaccagc	8	6	7	20	1	0	2	0	2	0	0	1	3	1	2	8	0	4	2	8	0	1	2	rs150616739		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:79660570C>T	ENST00000329138.4	+	9	835	c.700C>T	c.(700-702)Ccc>Tcc	p.P234S		NM_004712.4	NP_004703.1	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine kinase substrate	234	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)			CACTGAGCTGCCCCCCGAGTA	0.682																																					p.P234S		Atlas-SNP	.											.	HGS	54	.	0			c.C700T						PASS	.	C	SER/PRO	0,4406		0,0,2203	84	67	72		700	4.4	1	17	dbSNP_134	72	2,8598	2.2+/-6.3	0,2,4298	yes	missense	HGS	NM_004712.4	74	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	234/778	79660570	2,13004	2203	4300	6503	SO:0001583	missense	9146	exon9			GAGCTGCCCCCCG	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.700C>T	17.37:g.79660570C>T	ENSP00000331201:p.Pro234Ser	264	1	0.00378788		223	117	0.524664	NM_004712	Q9NR36	Missense_Mutation	SNP	ENST00000329138.4	37	CCDS11784.1	.	.	.	.	.	.	.	.	.	.	C	32	5.166816	0.94768	0.0	2.33E-4	ENSG00000185359	ENST00000329138;ENST00000442335	T	0.42900	0.96	4.39	4.39	0.52855	.	0.184051	0.48767	D	0.000171	T	0.61223	0.2330	M	0.82323	2.585	0.80722	D	1	P	0.47545	0.897	P	0.54924	0.764	T	0.65557	-0.6139	10	0.40728	T	0.16	-24.3068	16.3019	0.82825	0.0:1.0:0.0:0.0	.	234	O14964	HGS_HUMAN	S	234	ENSP00000331201:P234S	ENSP00000331201:P234S	P	+	1	0	HGS	77270975	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	7.258000	0.78371	2.138000	0.66242	0.655000	0.94253	CCC	C|1.000;T|0.000	0.000	weak		0.682	HGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440541.1	NM_004712		T	79660570	C	T	79660570	3	4	30	1	0	0	0	0	1	0	0	0	7096	739	26	2	734	2	HGS	17	79660570	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	3171776	79660570	1534640	582	13733											
CCDC57	284001	hgsc.bcm.edu	37	chr17	80059690	80059690	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcatccctggggtggcaatGcctgcctgcatcttgacggg	5	11	13	12	1	2	1	1	1	1	0	3	1	3	1	3	4	3	2	3	4	1	2	rs61735692	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:80059690G>A	ENST00000389641.4	-	18	2655	c.2619C>T	c.(2617-2619)ggC>ggT	p.G873G	CCDC57_ENST00000392347.1_Silent_p.G873G			Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	873										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)			GGGTGGCAATGCCTGCCTGCA	0.602													G|||	69	0.013778	0.0038	0.0288	5008	,	,		17944	0.0		0.0398	False		,,,				2504	0.0041				p.G872G		Atlas-SNP	.											.	CCDC57	102	.	0			c.C2616T						PASS	.	G		46,4056		0,46,2005	64	71	69		2616	0.4	0	17	dbSNP_129	69	420,7976		15,390,3793	no	coding-synonymous	CCDC57	NM_198082.2		15,436,5798	AA,AG,GG		5.0024,1.1214,3.7286		872/916	80059690	466,12032	2051	4198	6249	SO:0001819	synonymous_variant	284001	exon17			GGCAATGCCTGCC	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.2619C>T	17.37:g.80059690G>A		121	0	0		101	49	0.485149	NM_198082	A6NP51|A8MQC7|Q8IWG2|Q8TER3	Silent	SNP	ENST00000389641.4	37		46	0.021062271062271064	5	0.01016260162601626	7	0.019337016574585635	0	0.0	34	0.044854881266490766	G	3.247	-0.154002	0.06585	0.011214	0.050024	ENSG00000176155	ENST00000392345	.	.	.	2.53	0.444	0.16592	.	.	.	.	.	T	0.03871	0.0109	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	T	0.15896	-1.0421	4	.	.	.	.	4.2507	0.10693	0.4561:0.0:0.5439:0.0	.	.	.	.	V	185	.	.	A	-	2	0	CCDC57	77652979	0.001000	0.12720	0.001000	0.08648	0.000000	0.00434	0.849000	0.27723	0.392000	0.25172	-0.224000	0.12420	GCA	G|0.975;A|0.025	0.025	strong		0.602	CCDC57-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000277182.3	NM_198082		A	80059690	G	A	80059690	2	1	30	1	0	0	0	0	0	0	0	1	2829	1306	46	2		2	CCDC57	17	80059690	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	399120	80059690	1135520	583	13734											
C17orf62	79415	hgsc.bcm.edu	37	chr17	80404555	80404555	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcagcctgtgacgtagaagaGcttccagcccaggctatctg	9	8	12	12	1	1	3	0	1	1	2	2	3	2	3	3	1	3	4	3	1	3	3	rs72857481	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr17:80404555G>A	ENST00000437807.2	-	5	462	c.145C>T	c.(145-147)Ctc>Ttc	p.L49F	C17orf62_ENST00000585080.1_Missense_Mutation_p.L49F|C17orf62_ENST00000306645.5_Missense_Mutation_p.L49F|C17orf62_ENST00000434650.2_Missense_Mutation_p.L35F|C17orf62_ENST00000578913.1_Missense_Mutation_p.L49F|C17orf62_ENST00000577732.1_Missense_Mutation_p.L49F|C17orf62_ENST00000585064.1_Missense_Mutation_p.L49F|C17orf62_ENST00000583617.1_Missense_Mutation_p.L49F|C17orf62_ENST00000342572.8_Intron|C17orf62_ENST00000577436.1_Missense_Mutation_p.L35F|C17orf62_ENST00000336995.7_Intron|C17orf62_ENST00000583359.1_5'UTR|C17orf62_ENST00000578919.1_Missense_Mutation_p.L49F	NM_001193653.1|NM_001193657.1	NP_001180582.1|NP_001180586.1	Q9BQA9	CQ062_HUMAN	chromosome 17 open reading frame 62	49						integral component of membrane (GO:0016021)				breast(2)|large_intestine(2)|skin(2)|urinary_tract(2)	8	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			ACGTAGAAGAGCTTCCAGCCC	0.647													G|||	34	0.00678914	0.0	0.0072	5008	,	,		17150	0.0		0.0229	False		,,,				2504	0.0061				p.L49F		Atlas-SNP	.											.	C17orf62	23	.	0			c.C145T						PASS	.	G	PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU	15,4391	22.3+/-47.3	0,15,2188	96	93	94		145,145,103,145,145,145,145	2.6	1	17	dbSNP_130	94	165,8435	77.5+/-140.1	1,163,4136	yes	missense,missense,missense,missense,missense,missense,missense	C17orf62	NM_001033046.3,NM_001100407.2,NM_001100408.2,NM_001193653.1,NM_001193654.1,NM_001193655.1,NM_001193657.1	22,22,22,22,22,22,22	1,178,6324	AA,AG,GG		1.9186,0.3404,1.384	benign,benign,benign,benign,benign,benign,benign	49/188,49/188,35/174,49/188,49/188,49/188,49/188	80404555	180,12826	2203	4300	6503	SO:0001583	missense	79415	exon5			AGAAGAGCTTCCA	AK074950	CCDS32776.1, CCDS45817.1	17q25.3	2014-06-09			ENSG00000178927	ENSG00000178927			28672	protein-coding gene	gene with protein product							Standard	NM_001100407		Approved	MGC4368, FLJ90469	uc021ufr.1	Q9BQA9		ENST00000437807.2:c.145C>T	17.37:g.80404555G>A	ENSP00000388909:p.Leu49Phe	66	0	0		73	31	0.424658	NM_001193657	E1B6X3|Q96NR1	Missense_Mutation	SNP	ENST00000437807.2	37	CCDS32776.1	20	0.009157509157509158	0	0.0	2	0.0055248618784530384	0	0.0	18	0.023746701846965697	G	11.50	1.658734	0.29515	0.003404	0.019186	ENSG00000178927	ENST00000437807;ENST00000306645;ENST00000434650	.	.	.	4.96	2.58	0.30949	.	.	.	.	.	T	0.35098	0.0920	L	0.41824	1.3	0.80722	D	1	B;B	0.12013	0.002;0.005	B;B	0.14023	0.006;0.01	T	0.46679	-0.9174	8	0.52906	T	0.07	.	11.0231	0.47730	0.1877:0.0:0.8123:0.0	.	35;49	E1B6X3;Q9BQA9	.;CQ062_HUMAN	F	49;49;35	.	ENSP00000307765:L49F	L	-	1	0	C17orf62	77997844	1.000000	0.71417	1.000000	0.80357	0.608000	0.37181	3.151000	0.50670	1.086000	0.41228	0.561000	0.74099	CTC	G|0.989;A|0.011	0.011	strong		0.647	C17orf62-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443260.1	NM_001033046		A	80404555	G	A	80404555	3	1	30	1	0	0	0	0	1	0	0	0	1872	971	34	2	434	2	C17orf62	17	80404555	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	344865	80404555	790655	584	13735											
LAMA1	284217	hgsc.bcm.edu	37	chr18	7080048	7080048	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctgggactttgccaccagtTattggtgccatctatggcat	7	13	11	10	0	1	0	0	0	1	0	1	1	1	1	3	3	2	3	3	3	2	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:7080048T>C	ENST00000389658.3	-	3	364	c.271A>G	c.(271-273)Aac>Gac	p.N91D	RP11-76K13.3_ENST00000581502.1_RNA	NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	91	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)				TGCCACCAGTTATTGGTGCCA	0.418																																					p.N91D		Atlas-SNP	.											.	LAMA1	458	.	0			c.A271G						PASS	.						167	135	146					18																	7080048		2203	4300	6503	SO:0001583	missense	284217	exon3			ACCAGTTATTGGT	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.271A>G	18.37:g.7080048T>C	ENSP00000374309:p.Asn91Asp	315	0	0		246	116	0.471545	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	T	16.50	3.140937	0.56936	.	.	ENSG00000101680	ENST00000389658	T	0.75821	-0.97	5.61	4.45	0.53987	Laminin, N-terminal (3);	0.245554	0.40908	D	0.000990	T	0.60495	0.2273	L	0.31526	0.94	0.29065	N	0.883622	B	0.19200	0.034	B	0.16289	0.015	T	0.57911	-0.7729	10	0.72032	D	0.01	.	7.2768	0.26290	0.0:0.0731:0.157:0.7699	.	91	P25391	LAMA1_HUMAN	D	91	ENSP00000374309:N91D	ENSP00000374309:N91D	N	-	1	0	LAMA1	7070048	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	2.279000	0.43435	0.964000	0.38108	0.533000	0.62120	AAC	.	.	none		0.418	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559		C	7080048	T	C	7080048	3	2	30	1	0	0	0	0	1	0	0	0	8614	1754	61	3	9200	3	LAMA1	18	7080048	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10		7080048	70997200	585	13736											
NPC1	4864	hgsc.bcm.edu	37	chr18	21123523	21123523	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagggtttccccttgaagaCgttcatctctcttaaaaaaa	12	12	6	11	1	3	2	1	1	2	1	5	2	4	2	3	1	0	2	3	1	5	4	rs375047023		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:21123523C>T	ENST00000269228.5	-	14	2695	c.2141G>A	c.(2140-2142)cGt>cAt	p.R714H	NPC1_ENST00000540608.1_5'UTR|NPC1_ENST00000412552.2_Missense_Mutation_p.R396H	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	714	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				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)					CCCTTGAAGACGTTCATCTCT	0.403																																					p.R714H		Atlas-SNP	.											.	NPC1	114	.	0			c.G2141A						PASS	.	C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	64	66	65		2141	4.9	1	18		65	1,8599	1.2+/-3.3	0,1,4299	no	missense	NPC1	NM_000271.4	29	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging	714/1279	21123523	2,13004	2203	4300	6503	SO:0001583	missense	4864	exon14			TGAAGACGTTCAT	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.2141G>A	18.37:g.21123523C>T	ENSP00000269228:p.Arg714His	21	0	0		15	9	0.6	NM_000271	B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	37	CCDS11878.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.719159	0.89205	2.27E-4	1.16E-4	ENSG00000141458	ENST00000269228;ENST00000412552;ENST00000540608	D;D	0.95949	-3.86;-3.86	5.79	4.93	0.64822	Sterol-sensing domain (1);	0.000000	0.85682	D	0.000000	D	0.95918	0.8671	L	0.60067	1.865	0.80722	D	1	D;D	0.61697	0.99;0.99	P;P	0.54889	0.679;0.763	D	0.95741	0.8783	10	0.56958	D	0.05	-14.1977	14.8323	0.70156	0.0:0.9311:0.0:0.0689	.	725;714	Q59GR1;O15118	.;NPC1_HUMAN	H	714;396;559	ENSP00000269228:R714H;ENSP00000408606:R396H	ENSP00000269228:R714H	R	-	2	0	NPC1	19377521	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.448000	0.80631	1.472000	0.48140	-0.142000	0.14014	CGT	.	.	weak		0.403	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271		T	21123523	C	T	21123523	3	4	30	1	0	0	0	0	1	0	0	0	10579	536	19	1	1743	1	NPC1	18	21123523	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	14043475	21123523	56953725	586	13737											
DSG1	1828	hgsc.bcm.edu	37	chr18	28919763	28919763	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttaacattcaaagttttggtAatgacgacaggactaataca	16	12	7	6	1	1	1	1	1	0	0	1	3	1	2	0	2	2	2	0	2	5	7			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:28919763A>C	ENST00000257192.4	+	11	1674	c.1462A>C	c.(1462-1464)Aat>Cat	p.N488H		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	488	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				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)			AAGTTTTGGTAATGACGACAG	0.328																																					p.N488H		Atlas-SNP	.											DSG1,NS,carcinoma,-2,1	DSG1	176	1	0			c.A1462C						PASS	.						80	81	81					18																	28919763		2203	4300	6503	SO:0001583	missense	1828	exon11			TTTGGTAATGACG	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.1462A>C	18.37:g.28919763A>C	ENSP00000257192:p.Asn488His	166	0	0		138	52	0.376812	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	.	.	.	.	.	.	.	.	.	.	A	4.359	0.066056	0.08388	.	.	ENSG00000134760	ENST00000257192	T	0.58210	0.35	3.05	-5.83	0.02325	Cadherin (2);	3.162780	0.00531	N	0.000201	T	0.32675	0.0837	N	0.22421	0.69	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.16689	-1.0394	10	0.72032	D	0.01	.	0.9696	0.01413	0.2735:0.1294:0.3832:0.2139	.	488	Q02413	DSG1_HUMAN	H	488	ENSP00000257192:N488H	ENSP00000257192:N488H	N	+	1	0	DSG1	27173761	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.215000	0.09279	-0.831000	0.04256	-0.574000	0.04147	AAT	.	.	none		0.328	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942		C	28919763	A	C	28919763	3	2	30	1	0	0	0	0	1	0	0	0	4778	362	13	5	1504	5	DSG1	18	28919763	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	7796240	28919763	49157485	587	13738											
MEP1B	4225	hgsc.bcm.edu	37	chr18	29782953	29782953	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctggagaaacaaactatatAtcagtgttcaagggcagtgg	14	9	12	6	0	2	1	2	0	0	1	2	2	2	1	0	3	2	3	0	3	6	4	rs71361372	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:29782953A>G	ENST00000269202.6	+	6	395	c.348A>G	c.(346-348)atA>atG	p.I116M	MEP1B_ENST00000581447.1_Missense_Mutation_p.I116M	NM_005925.2	NP_005916.2	Q16820	MEP1B_HUMAN	meprin A, beta	116	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						CAAACTATATATCAGTGTTCA	0.413													A|||	36	0.0071885	0.0015	0.0086	5008	,	,		20162	0.0		0.0129	False		,,,				2504	0.0153				p.I116M		Atlas-SNP	.											.	MEP1B	54	.	0			c.A348G						PASS	.	A	MET/ILE	13,3787		0,13,1887	83	81	82		348	1.2	1	18	dbSNP_130	82	141,8103		3,135,3984	yes	missense	MEP1B	NM_005925.2	10	3,148,5871	GG,GA,AA		1.7103,0.3421,1.2786	probably-damaging	116/702	29782953	154,11890	1900	4122	6022	SO:0001583	missense	4225	exon6			CTATATATCAGTG	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.348A>G	18.37:g.29782953A>G	ENSP00000269202:p.Ile116Met	37	0	0		39	24	0.615385	NM_005925	B7ZM35|B9EGL6|Q670J1	Missense_Mutation	SNP	ENST00000269202.6	37	CCDS45846.1	16	0.007326007326007326	0	0.0	5	0.013812154696132596	0	0.0	11	0.014511873350923483	A	18.72	3.684857	0.68157	0.003421	0.017103	ENSG00000141434	ENST00000269202	T	0.70749	-0.51	5.72	1.22	0.21188	Peptidase, metallopeptidase (1);Peptidase M12A, astacin (1);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.74199	0.3685	M	0.91972	3.26	0.38390	D	0.945362	D	0.89917	1.0	D	0.81914	0.995	T	0.80837	-0.1204	10	0.87932	D	0	-18.6302	8.2453	0.31684	0.5426:0.3346:0.0:0.1228	.	116	Q16820	MEP1B_HUMAN	M	116	ENSP00000269202:I116M	ENSP00000269202:I116M	I	+	3	3	MEP1B	28036951	1.000000	0.71417	0.998000	0.56505	0.974000	0.67602	1.052000	0.30429	0.376000	0.24707	0.533000	0.62120	ATA	A|0.992;G|0.008	0.008	strong		0.413	MEP1B-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447755.1	NM_005925		G	29782953	A	G	29782953	3	3	30	1	0	0	0	0	1	0	0	0	9485	439	16	3	370	3	MEP1B	18	29782953	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	863190	29782953	48294295	588	13739											
C18orf34	374864	hgsc.bcm.edu	37	chr18	30928852	30928852	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caagtaggaggaacaactttAcctctcttttctcctggttt	9	15	7	10	0	2	0	0	0	2	0	4	2	2	2	2	3	3	2	2	3	5	6	rs140419270	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:30928852A>G	ENST00000383096.3	-	8	640		c.e8+1		CCDC178_ENST00000300227.8_Splice_Site|CCDC178_ENST00000406524.2_Splice_Site|CCDC178_ENST00000583930.1_Splice_Site|CCDC178_ENST00000402325.1_Splice_Site|CCDC178_ENST00000579916.1_Intron|CCDC178_ENST00000403303.1_Splice_Site|CCDC178_ENST00000579947.1_Splice_Site			Q5BJE1	CC178_HUMAN	coiled-coil domain containing 178									p.?(2)									GAACAACTTTACCTCTCTTTT	0.323													A|||	8	0.00159744	0.0	0.0029	5008	,	,		15391	0.0		0.005	False		,,,				2504	0.001				.		Atlas-SNP	.											.	.	.	.	2	Unknown(2)	lung(2)	c.457+2T>C						PASS	.	A	,	5,4401	9.9+/-24.2	0,5,2198	132	111	118		,	4.2	0.8	18	dbSNP_134	118	31,8569	21.6+/-65.8	0,31,4269	yes	splice-5,splice-5	C18orf34	NM_001105528.1,NM_198995.2	,	0,36,6467	GG,GA,AA		0.3605,0.1135,0.2768	,	,	30928852	36,12970	2203	4300	6503	SO:0001630	splice_region_variant	374864	exon8			AACTTTACCTCTC	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.457+1T>C	18.37:g.30928852A>G		77	0	0		62	24	0.387097	NM_001105528	A6NDC6|J3KS92|Q6ZP67|Q6ZU20	Splice_Site	SNP	ENST00000383096.3	37	CCDS42424.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	A	12.87	2.068210	0.36470	0.001135	0.003605	ENSG00000166960	ENST00000403303;ENST00000383096;ENST00000300227;ENST00000406524;ENST00000402325;ENST00000399177	.	.	.	4.24	4.24	0.50183	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.0289	0.42087	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C18orf34	29182850	0.994000	0.37717	0.791000	0.31998	0.061000	0.15899	3.552000	0.53705	2.144000	0.66660	0.533000	0.62120	.	A|0.997;G|0.003	0.003	strong		0.323	CCDC178-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255373.2	NM_198995	Intron	G	30928852	A	G	30928852	5	3	30	1	0	0	0	0	0	0	1	0	1904	405	14	3	2208	3	C18orf34	18	30928852	Splice_Site	SNP	A	TCGA-GR-7353-01A-11D-2210-10	1145899	30928852	47148396	589	13740											
SIGLEC15	284266	hgsc.bcm.edu	37	chr18	43422149	43422149	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagccaccatgtgctcaccGtgaggagtccctcagccacc	8	6	9	18	1	2	1	2	1	0	0	3	2	3	2	7	1	3	1	7	1	0	0	rs143689799	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:43422149G>A	ENST00000389474.3	+	6	1201	c.984G>A	c.(982-984)ccG>ccA	p.P328P	SIGLEC15_ENST00000546268.1_Silent_p.P174P|SIGLEC15_ENST00000602118.2_3'UTR	NM_213602.2	NP_998767.1	Q6ZMC9	SIG15_HUMAN	sialic acid binding Ig-like lectin 15	328					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						TGTGCTCACCGTGAGGAGTCC	0.562													G|||	8	0.00159744	0.0015	0.0	5008	,	,		18230	0.0		0.006	False		,,,				2504	0.0				p.P328P		Atlas-SNP	.											.	SIGLEC15	10	.	0			c.G984A						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	73	69	70		984	-8.6	0	18	dbSNP_134	70	27,8573	19.2+/-60.6	0,27,4273	no	coding-synonymous	SIGLEC15	NM_213602.2		0,29,6474	AA,AG,GG		0.314,0.0454,0.223		328/329	43422149	29,12977	2203	4300	6503	SO:0001819	synonymous_variant	284266	exon6			CTCACCGTGAGGA	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.984G>A	18.37:g.43422149G>A		131	0	0		115	61	0.530435	NM_213602	A8K2Y5|B4DVQ9	Silent	SNP	ENST00000389474.3	37	CCDS32819.1																																																																																			G|0.997;A|0.003	0.003	strong		0.562	SIGLEC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410768.2	NM_213602		A	43422149	G	A	43422149	2	1	30	1	0	0	0	0	0	0	0	1	14325	1132	40	1		1	SIGLEC15	18	43422149	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	12493297	43422149	34655099	590	13741											
TCEB3B	51224	hgsc.bcm.edu	37	chr18	44560337	44560337	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctctctgactggctttcctgGacaggaggcaatttcttagc	7	13	10	11	0	2	1	0	1	2	0	4	3	3	3	1	4	1	2	1	4	2	3	rs3744864	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:44560337G>T	ENST00000332567.4	-	1	1651	c.1299C>A	c.(1297-1299)gtC>gtA	p.V433V	KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000356157.7_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	433					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						GGCTTTCCTGGACAGGAGGCA	0.567													G|||	26	0.00519169	0.0	0.0159	5008	,	,		17739	0.001		0.0139	False		,,,				2504	0.0				p.V433V		Atlas-SNP	.											TCEB3B,NS,carcinoma,-1,1	TCEB3B	141	1	0			c.C1299A						PASS	.	G	,	11,4393	16.8+/-37.8	0,11,2191	81	78	79		1299,	1	0	18	dbSNP_107	79	97,8503	53.6+/-114.3	0,97,4203	no	coding-synonymous,intron	TCEB3B,KATNAL2	NM_016427.2,NM_031303.2	,	0,108,6394	TT,TG,GG		1.1279,0.2498,0.8305	,	433/754,	44560337	108,12896	2202	4300	6502	SO:0001819	synonymous_variant	51224	exon1			TTCCTGGACAGGA	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.1299C>A	18.37:g.44560337G>T		119	0	0		122	53	0.434426	NM_016427	Q9P2V9	Silent	SNP	ENST00000332567.4	37	CCDS11932.1																																																																																			G|0.992;T|0.008	0.008	strong		0.567	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427		T	44560337	G	T	44560337	2	4	30	1	0	0	0	0	0	0	0	1	15697	1161	41	4		4	TCEB3B	18	44560337	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1138188	44560337	33516911	591	13742											
CCDC11	220136	hgsc.bcm.edu	37	chr18	47788544	47788544	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgatggctgcgtcggattcTttctagatggtgctcagctc	5	14	12	10	2	3	2	1	1	2	1	5	3	3	3	0	3	3	3	0	3	1	3	rs112087763	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:47788544T>G	ENST00000398545.4	-	2	232	c.115A>C	c.(115-117)Aga>Cga	p.R39R		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)		CGTCGGATTCTTTCTAGATGG	0.438													T|||	6	0.00119808	0.0	0.0014	5008	,	,		19087	0.0		0.004	False		,,,				2504	0.001				p.R39R		Atlas-SNP	.											.	CCDC11	59	.	0			c.A115C						PASS	.	T		1,3831		0,1,1915	113	108	109		115	4	0.2	18	dbSNP_132	109	24,8220		0,24,4098	no	coding-synonymous	CCDC11	NM_145020.3		0,25,6013	GG,GT,TT		0.2911,0.0261,0.207		39/515	47788544	25,12051	1916	4122	6038	SO:0001819	synonymous_variant	220136	exon2			GGATTCTTTCTAG																												ENST00000398545.4:c.115A>C	18.37:g.47788544T>G		100	0	0		121	53	0.438017	NM_145020		Silent	SNP	ENST00000398545.4	37	CCDS11940.2																																																																																			T|0.997;G|0.003	0.003	strong		0.438	CCDC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255922.3			G	47788544	T	G	47788544	2	3	30	1	0	0	0	0	0	0	0	1	2748	1617	56	5		5	CCDC11	18	47788544	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	3228207	47788544	30288704	592	13743											
CDH19	28513	hgsc.bcm.edu	37	chr18	64172434	64172434	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgtatcttcttctccacccCcttcatcatcatattggaat	8	16	3	14	0	6	0	3	0	3	0	7	1	6	1	3	1	0	1	3	1	3	6	rs55874520	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:64172434C>G	ENST00000262150.2	-	12	2226	c.1934G>C	c.(1933-1935)gGg>gCg	p.G645A	CDH19_ENST00000540086.1_3'UTR	NM_021153.3	NP_066976.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	0	Cadherin 6. {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)				TTCTCCACCCCCTTCATCATC	0.403													c|||	35	0.00698882	0.0015	0.0101	5008	,	,		14403	0.0		0.0258	False		,,,				2504	0.0				p.G645A		Atlas-SNP	.											.	CDH19	141	.	0			c.G1934C						PASS	.	C	ALA/GLY	26,4380	29.0+/-57.7	0,26,2177	169	169	169		1934	5.2	0.8	18	dbSNP_129	169	219,8381	83.1+/-145.7	3,213,4084	yes	missense	CDH19	NM_021153.2	60	3,239,6261	GG,GC,CC		2.5465,0.5901,1.8837	probably-damaging	645/773	64172434	245,12761	2203	4300	6503	SO:0001583	missense	28513	exon12			CCACCCCCTTCAT	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.1934G>C	18.37:g.64172434C>G	ENSP00000262150:p.Gly645Ala	239	0	0		201	97	0.482587	NM_021153	O15098	Missense_Mutation	SNP	ENST00000262150.2	37	CCDS11994.1	25	0.011446886446886446	0	0.0	5	0.013812154696132596	0	0.0	20	0.026385224274406333	c	19.92	3.917129	0.73098	0.005901	0.025465	ENSG00000071991	ENST00000262150	D	0.85556	-2.0	5.18	5.18	0.71444	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	D	0.87030	0.6076	M	0.91717	3.235	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	D	0.90204	0.4259	10	0.87932	D	0	.	19.0693	0.93126	0.0:1.0:0.0:0.0	rs55874520	645	Q9H159	CAD19_HUMAN	A	645	ENSP00000262150:G645A	ENSP00000262150:G645A	G	-	2	0	CDH19	62323414	1.000000	0.71417	0.759000	0.31340	0.423000	0.31445	7.284000	0.78650	2.564000	0.86499	0.650000	0.86243	GGG	C|0.983;G|0.017	0.017	strong		0.403	CDH19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256219.1	NM_021153		G	64172434	C	G	64172434	3	3	30	1	0	0	0	0	1	0	0	0	3106	623	22	4	388	4	CDH19	18	64172434	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	16383890	64172434	13904814	593	13744											
RTTN	25914	hgsc.bcm.edu	37	chr18	67755252	67755252	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcaccatactacattctgaCtggtccagaagaatgttcac	12	10	7	12	1	2	3	1	1	1	2	3	3	3	3	2	1	2	2	2	1	4	4	rs376382612		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:67755252C>G	ENST00000255674.6	-	31	4561	c.4275G>C	c.(4273-4275)caG>caC	p.Q1425H	RTTN_ENST00000454359.1_3'UTR|RTTN_ENST00000437017.1_Missense_Mutation_p.Q1425H	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	1425					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)				TACATTCTGACTGGTCCAGAA	0.483																																					p.Q1425H		Atlas-SNP	.											.	RTTN	184	.	0			c.G4275C						PASS	.	C	HIS/GLN	0,3862		0,0,1931	100	98	98		4275	-1	1	18		98	1,8241		0,1,4120	no	missense	RTTN	NM_173630.3	24	0,1,6051	GG,GC,CC		0.0121,0.0,0.0083	benign	1425/2227	67755252	1,12103	1931	4121	6052	SO:0001583	missense	25914	exon31			TTCTGACTGGTCC	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.4275G>C	18.37:g.67755252C>G	ENSP00000255674:p.Gln1425His	70	0	0		59	26	0.440678	NM_173630	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Missense_Mutation	SNP	ENST00000255674.6	37	CCDS42443.1	.	.	.	.	.	.	.	.	.	.	C	12.24	1.878046	0.33162	0.0	1.21E-4	ENSG00000176225	ENST00000255674;ENST00000437017	T;T	0.68331	-0.32;-0.32	5.45	-0.961	0.10337	Armadillo-like helical (1);	0.110450	0.64402	D	0.000007	T	0.43389	0.1245	L	0.35414	1.06	0.80722	D	1	P	0.34934	0.476	B	0.26094	0.066	T	0.10428	-1.0630	10	0.40728	T	0.16	.	5.2259	0.15393	0.2225:0.4534:0.0:0.3242	.	1425	Q86VV8	RTTN_HUMAN	H	1425	ENSP00000255674:Q1425H;ENSP00000399520:Q1425H	ENSP00000255674:Q1425H	Q	-	3	2	RTTN	65906232	0.988000	0.35896	0.987000	0.45799	0.968000	0.65278	0.302000	0.19192	0.074000	0.16767	0.484000	0.47621	CAG	.	.	weak		0.483	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630		G	67755252	C	G	67755252	3	3	30	1	0	0	0	0	1	0	0	0	13752	564	20	4	2481	4	RTTN	18	67755252	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	3582818	67755252	10321996	594	13745											
NETO1	81832	hgsc.bcm.edu	37	chr18	70526301	70526301	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtaaagttcaatgcactgtcTtggagcggctgtaaagaaga	13	10	12	6	1	2	2	1	0	1	2	2	3	2	3	0	2	2	5	0	2	6	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:70526301T>C	ENST00000327305.6	-	4	886	c.229A>G	c.(229-231)Aga>Gga	p.R77G	NETO1_ENST00000580049.1_5'UTR|NETO1_ENST00000299430.2_Missense_Mutation_p.R76G|NETO1_ENST00000397929.1_Missense_Mutation_p.R76G|NETO1_ENST00000583169.1_Missense_Mutation_p.R77G	NM_138966.3	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 1	77	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)		ATGCACTGTCTTGGAGCGGCT	0.368																																					p.R77G		Atlas-SNP	.											.	NETO1	178	.	0			c.A229G						PASS	.						57	57	57					18																	70526301		2203	4300	6503	SO:0001583	missense	81832	exon4			ACTGTCTTGGAGC	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.229A>G	18.37:g.70526301T>C	ENSP00000313088:p.Arg77Gly	144	0	0		150	51	0.34	NM_001201465	Q86W85|Q8ND78|Q8TDF4	Missense_Mutation	SNP	ENST00000327305.6	37	CCDS12000.1	.	.	.	.	.	.	.	.	.	.	T	9.808	1.182281	0.21787	.	.	ENSG00000166342	ENST00000327305;ENST00000299430;ENST00000397929	T;T;T	0.23754	1.89;1.89;2.15	5.35	5.35	0.76521	CUB (5);	0.000000	0.64402	D	0.000003	T	0.23532	0.0569	N	0.01482	-0.84	0.80722	D	1	D;D;P	0.76494	0.999;0.989;0.592	D;D;B	0.80764	0.994;0.985;0.241	T	0.50233	-0.8852	10	0.25751	T	0.34	-24.7403	15.6405	0.76997	0.0:0.0:0.0:1.0	.	76;76;77	Q8TDF5-1;Q8TDF5-2;Q8TDF5	.;.;NETO1_HUMAN	G	77;76;76	ENSP00000313088:R77G;ENSP00000299430:R76G;ENSP00000381024:R76G	ENSP00000299430:R76G	R	-	1	2	NETO1	68677281	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.054000	0.57434	2.159000	0.67721	0.533000	0.62120	AGA	.	.	none		0.368	NETO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256301.2	NM_138999		C	70526301	T	C	70526301	3	2	30	1	0	0	0	0	1	0	0	0	10348	1617	56	3	1409	3	NETO1	18	70526301	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	2771049	70526301	7550947	595	13746											
TSHZ1	10194	hgsc.bcm.edu	37	chr18	72998296	72998296	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtgctgaagtgcatgtacTgtggacactcctttgagtcc	8	12	12	9	0	0	2	0	2	0	0	2	3	2	3	2	2	3	3	2	2	2	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr18:72998296T>C	ENST00000580243.1	+	2	1282	c.934T>C	c.(934-936)Tgt>Cgt	p.C312R	TSHZ1_ENST00000322038.5_Missense_Mutation_p.C267R			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	312					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)		GTGCATGTACTGTGGACACTC	0.557																																					p.C267R		Atlas-SNP	.											.	TSHZ1	104	.	0			c.T799C						PASS	.						150	122	131					18																	72998296		2203	4300	6503	SO:0001583	missense	10194	exon2			ATGTACTGTGGAC	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.934T>C	18.37:g.72998296T>C	ENSP00000464391:p.Cys312Arg	199	0	0		159	50	0.314465	NM_005786	O60534|Q4LE29|Q53EU4	Missense_Mutation	SNP	ENST00000580243.1	37		.	.	.	.	.	.	.	.	.	.	T	10.93	1.490440	0.26686	.	.	ENSG00000179981	ENST00000322038	D	0.83755	-1.76	5.38	5.38	0.77491	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);	0.000000	0.85682	D	0.000000	D	0.89942	0.6861	M	0.65498	2.005	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	D	0.90801	0.4694	10	0.87932	D	0	-17.6812	15.4172	0.74980	0.0:0.0:0.0:1.0	.	312	Q6ZSZ6	TSH1_HUMAN	R	267	ENSP00000323584:C267R	ENSP00000323584:C267R	C	+	1	0	TSHZ1	71127284	1.000000	0.71417	0.989000	0.46669	0.982000	0.71751	7.694000	0.84235	2.512000	0.84698	0.561000	0.74099	TGT	.	.	none		0.557	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786		C	72998296	T	C	72998296	3	2	30	1	0	0	0	0	1	0	0	0	16638	1580	55	3	801	3	TSHZ1	18	72998296	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	2471995	72998296	5078952	596	13747											
TCF3	6929	hgsc.bcm.edu	37	chr19	1615393	1615393	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agttggcacatgcgccccagCtccttaaaggcctcgttgat	8	10	10	13	2	0	1	0	1	0	0	2	1	1	1	4	2	2	4	4	2	2	3	rs143212973	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:1615393C>T	ENST00000262965.5	-	18	2057	c.1713G>A	c.(1711-1713)gaG>gaA	p.E571E	TCF3_ENST00000395423.3_Silent_p.E575E|TCF3_ENST00000588136.1_Intron|TCF3_ENST00000344749.5_Intron|TCF3_ENST00000453954.2_Intron|RNU6-1223P_ENST00000517124.1_RNA	NM_003200.3	NP_003191.1	Q9HCS4	TF7L1_HUMAN	transcription factor 3	0					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)		TGCGCCCCAGCTCCTTAAAGG	0.637			T	"PBX1, HLF, TFPT"	pre B-ALL								C|||	6	0.00119808	0.0	0.0	5008	,	,		14615	0.0		0.006	False		,,,				2504	0.0				p.E571E		Atlas-SNP	.		Dom	yes		19	19p13.3	6929	transcription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47)		L	.	TCF3	72	.	0			c.G1713A						PASS	.	C	,	12,4394	20.2+/-43.8	0,12,2191	98	97	97		,1713	3.4	1	19	dbSNP_134	97	52,8548	33.8+/-87.4	2,48,4250	no	intron,coding-synonymous	TCF3	NM_001136139.2,NM_003200.3	,	2,60,6441	TT,TC,CC		0.6047,0.2724,0.4921	,	,571/655	1615393	64,12942	2203	4300	6503	SO:0001819	synonymous_variant	6929	exon18			CCCCAGCTCCTTA	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.1713G>A	19.37:g.1615393C>T		99	0	0		74	37	0.5	NM_003200	Q53R97|Q6PD70|Q9NP00	Silent	SNP	ENST00000262965.5	37	CCDS12074.1																																																																																			C|0.997;T|0.003	0.003	strong		0.637	TCF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449367.1	NM_003200		T	1615393	C	T	1615393	2	4	30	1	0	0	0	0	0	0	0	1	15709	796	28	2		2	TCF3	19	1615393	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10		1615393	57513590	597	13748											
REXO1	57455	hgsc.bcm.edu	37	chr19	1827927	1827927	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggcctcatcttctgagtcTgagaaccttgcatcgcaact	8	11	9	13	2	4	2	1	2	3	1	5	3	4	2	2	1	3	2	2	1	2	2	rs144940979	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:1827927T>G	ENST00000170168.4	-	2	955	c.861A>C	c.(859-861)tcA>tcC	p.S287S	REXO1_ENST00000587524.1_5'UTR	NM_020695.3	NP_065746.3	Q8N1G1	REXO1_HUMAN	REX1, RNA exonuclease 1 homolog (S. cerevisiae)	287						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)		CTTCTGAGTCTGAGAACCTTG	0.672													.|||	3	0.000599042	0.0	0.0	5008	,	,		13621	0.0		0.003	False		,,,				2504	0.0				p.S287S		Atlas-SNP	.											.	REXO1	55	.	0			c.A861C						PASS	.	T		0,4404		0,0,2202	41	44	43		861	-8.3	0.1	19	dbSNP_134	43	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	REXO1	NM_020695.3		0,14,6488	GG,GT,TT		0.1628,0.0,0.1077		287/1222	1827927	14,12990	2202	4300	6502	SO:0001819	synonymous_variant	57455	exon2			TGAGTCTGAGAAC	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.861A>C	19.37:g.1827927T>G		128	0	0		138	71	0.514493	NM_020695	Q9ULT2	Silent	SNP	ENST00000170168.4	37	CCDS32866.1																																																																																			T|0.999;G|0.001	0.001	strong		0.672	REXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449200.1	NM_020695		G	1827927	T	G	1827927	2	3	30	1	0	0	0	0	0	0	0	1	13256	1567	55	5		5	REXO1	19	1827927	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	212534	1827927	57301056	598	13749											
SF3A2	8175	hgsc.bcm.edu	37	chr19	2248152	2248153	+	In_Frame_Ins	INS	-	-	GGAGTCCACCCTCCAGCCCCC																															gggtccaccccccagctcctINSggagtccaccctccagcccc																								rs59267791|rs539335935	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:2248152_2248153insGGAGTCCACCCTCCAGCCCCC	ENST00000221494.5	+	9	1420_1421	c.1002_1003insGGAGTCCACCCTCCAGCCCCC	c.(1003-1005)gga>GGAGTCCACCCTCCAGCCCCCgga	p.335_335G>GVHPPAPG	AMH_ENST00000221496.4_5'Flank|MIR4321_ENST00000592276.1_RNA	NM_007165.4	NP_009096.2	Q15428	SF3A2_HUMAN	splicing factor 3a, subunit 2, 66kDa	335	Pro-rich.				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)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(2)	4		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)		CCCCAGCTCCTGGAGTCCACCC	0.733																																					p.P334delinsPGVHPPAP		Pindel	.											SF3A2,colon,carcinoma,0,1	SF3A2	22	1	0			c.1002_1003insGGAGTCCACCCTCCAGCCCCC						PASS	.																																			SO:0001652	inframe_insertion	8175	exon9			.	L21990	CCDS12084.1	19p13.3	2012-10-02	2002-08-29		ENSG00000104897	ENSG00000104897			10766	protein-coding gene	gene with protein product		600796	"splicing factor 3a, subunit 2, 66kD"			8211113, 8541848	Standard	NM_007165		Approved	SF3a66, SAP62, PRPF11, Prp11	uc002lvg.3	Q15428	OTTHUMG00000180414	ENST00000221494.5:c.1003_1023dupGGAGTCCACCCTCCAGCCCCC	19.37:g.2248152_2248153insGGAGTCCACCCTCCAGCCCCC	ENSP00000221494:p.ValHisProProAlaProGly363dup	28	0	.		16	10	0.625	NM_007165	B2RBU1|D6W605|O75245	In_Frame_Ins	INS	ENST00000221494.5	37	CCDS12084.1																																																																																			.	.	none		0.733	SF3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451268.3			GGAGTCCACCCTCCAGCCCCC	2248153	-	GGAGTCCACCCTCCAGCCCCC	2248152	7	5	30	1	0	1	1	0	0	0	0	0	14162	1567	55	0	1032	0	SF3A2	19	2248152	In_Frame_Ins	INS	-	TCGA-GR-7353-01A-11D-2210-10	420225	2248152	56880831	599	13750											
SF3A2	8175	hgsc.bcm.edu	37	chr19	2248185	2248185	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagcccccggggttcacccAccagcccccggagtccaccc	6	3	9	23	2	1	0	1	0	0	0	2	1	2	1	9	3	2	1	9	3	0	1			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:2248185A>T	ENST00000221494.5	+	9	1453	c.1035A>T	c.(1033-1035)ccA>ccT	p.P345P	AMH_ENST00000221496.4_5'Flank|MIR4321_ENST00000592276.1_RNA	NM_007165.4	NP_009096.2	Q15428	SF3A2_HUMAN	splicing factor 3a, subunit 2, 66kDa	345	Pro-rich.				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)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(1)|lung(2)	4		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)		GGGTTCACCCACCAGCCCCCG	0.741																																					p.P345P		Atlas-SNP	.											SF3A2,colon,carcinoma,0,1	SF3A2	22	1	0			c.A1035T						scavenged	.						2	3	3					19																	2248185		1454	3177	4631	SO:0001819	synonymous_variant	8175	exon9			TCACCCACCAGCC	L21990	CCDS12084.1	19p13.3	2012-10-02	2002-08-29		ENSG00000104897	ENSG00000104897			10766	protein-coding gene	gene with protein product		600796	"splicing factor 3a, subunit 2, 66kD"			8211113, 8541848	Standard	NM_007165		Approved	SF3a66, SAP62, PRPF11, Prp11	uc002lvg.3	Q15428	OTTHUMG00000180414	ENST00000221494.5:c.1035A>T	19.37:g.2248185A>T		24	0	0		15	10	0.666667	NM_007165	B2RBU1|D6W605|O75245	Silent	SNP	ENST00000221494.5	37	CCDS12084.1																																																																																			.	.	none		0.741	SF3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451268.3			T	2248185	A	T	2248185	2	4	30	1	0	0	0	0	0	0	0	1	14162	146	6	5		5	SF3A2	19	2248185	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	33	2248185	56880798	600	13751											
ZNF556	80032	hgsc.bcm.edu	37	chr19	2877426	2877426	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcagtgtggaaaactcttcaCccattcctcatccctgataa	11	12	5	13	0	4	1	3	1	1	0	6	2	6	2	3	1	1	0	3	1	3	3	rs34849844	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:2877426C>T	ENST00000307635.2	+	4	557	c.470C>T	c.(469-471)aCc>aTc	p.T157I	ZNF556_ENST00000586426.1_Missense_Mutation_p.T156I	NM_024967.1	NP_079243.1	Q9HAH1	ZN556_HUMAN	zinc finger protein 556	157					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)		AAACTCTTCACCCATTCCTCA	0.423													C|||	33	0.00658946	0.0015	0.0101	5008	,	,		20726	0.001		0.0159	False		,,,				2504	0.0072				p.T157I		Atlas-SNP	.											.	ZNF556	73	.	0			c.C470T						PASS	.	C	ILE/THR	15,4391	22.3+/-47.3	0,15,2188	136	123	127		470	-0.3	0	19	dbSNP_126	127	157,8443	74.8+/-137.4	3,151,4146	yes	missense	ZNF556	NM_024967.1	89	3,166,6334	TT,TC,CC		1.8256,0.3404,1.3225	benign	157/457	2877426	172,12834	2203	4300	6503	SO:0001583	missense	80032	exon4			TCTTCACCCATTC	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.470C>T	19.37:g.2877426C>T	ENSP00000302603:p.Thr157Ile	94	0	0		65	36	0.553846	NM_024967	Q96GM3	Missense_Mutation	SNP	ENST00000307635.2	37	CCDS12097.1	15	0.006868131868131868	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	9	0.011873350923482849	C	8.841	0.942299	0.18281	0.003404	0.018256	ENSG00000172000	ENST00000307635	T	0.28666	1.6	2.27	-0.272	0.12919	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09291	0.0229	L	0.35487	1.065	0.09310	N	1	B	0.30068	0.267	B	0.24541	0.054	T	0.14924	-1.0455	9	0.44086	T	0.13	.	5.1815	0.15161	0.1587:0.4899:0.3514:0.0	rs34849844;rs62126859	157	Q9HAH1	ZN556_HUMAN	I	157	ENSP00000302603:T157I	ENSP00000302603:T157I	T	+	2	0	ZNF556	2828426	0.000000	0.05858	0.004000	0.12327	0.205000	0.24178	-3.911000	0.00336	0.139000	0.18822	0.407000	0.27541	ACC	C|0.987;T|0.013	0.013	strong		0.423	ZNF556-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451638.2	NM_024967		T	2877426	C	T	2877426	3	4	30	1	0	0	0	0	1	0	0	0	18002	507	18	2	484	2	ZNF556	19	2877426	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	629241	2877426	56251557	601	13752											
PIP5K1C	23396	hgsc.bcm.edu	37	chr19	3633473	3633473	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggccgggggggcctgggCgctatagtggagcggggagt	5	5	24	7	3	0	0	0	0	0	0	0	3	0	3	2	9	1	1	2	9	2	2	rs35014191	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:3633473C>T	ENST00000335312.3	-	17	2054	c.1966G>A	c.(1966-1968)Gcc>Acc	p.A656T	PIP5K1C_ENST00000539785.1_Intron	NM_001195733.1|NM_012398.2	NP_001182662.1|NP_036530.1	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, gamma	656	Mediates interaction with TLN2.				actin cytoskeleton organization (GO:0030036)|adherens junction assembly (GO:0034333)|axon guidance (GO:0007411)|clathrin-mediated endocytosis (GO:0072583)|cytoskeletal anchoring at plasma membrane (GO:0007016)|neutrophil chemotaxis (GO:0030593)|phagocytosis (GO:0006909)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet aggregation (GO:0070527)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle exocytosis (GO:0016079)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|uropod (GO:0001931)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)			large_intestine(3)|ovary(1)|skin(3)|stomach(2)	9		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)		GGGGCCTGGGCGCTATAGTGG	0.701													C|||	34	0.00678914	0.0129	0.0058	5008	,	,		11951	0.0		0.006	False		,,,				2504	0.0072				p.A656T	Esophageal Squamous(135;99 1744 12852 27186 39851)	Atlas-SNP	.											PIP5K1C_ENST00000335312,NS,carcinoma,+1,1	PIP5K1C	63	1	0			c.G1966A						PASS	.	C	,THR/ALA	21,4373		0,21,2176	17	22	20		,1966	-6.2	0.2	19	dbSNP_126	20	101,8487		0,101,4193	no	intron,missense	PIP5K1C	NM_001195733.1,NM_012398.2	,58	0,122,6369	TT,TC,CC		1.1761,0.4779,0.9398	,benign	,656/669	3633473	122,12860	2197	4294	6491	SO:0001583	missense	23396	exon17			CCTGGGCGCTATA	AB011161	CCDS32872.1, CCDS56074.1, CCDS74257.1	19p13.3	2012-10-02			ENSG00000186111	ENSG00000186111			8996	protein-coding gene	gene with protein product		606102				9535851	Standard	NM_001195733		Approved	PIP5Kgamma, KIAA0589, LCCS3	uc002lyj.2	O60331	OTTHUMG00000180870	ENST00000335312.3:c.1966G>A	19.37:g.3633473C>T	ENSP00000335333:p.Ala656Thr	111	0	0		95	53	0.557895	NM_012398	B7Z9E7|C6GIJ7|C6GIJ8|Q7LE07	Missense_Mutation	SNP	ENST00000335312.3	37	CCDS32872.1	12	0.005494505494505495	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	6.504	0.461201	0.12342	0.004779	0.011761	ENSG00000186111	ENST00000335312	T	0.25912	1.77	3.39	-6.18	0.02085	.	0.500976	0.17660	N	0.166351	T	0.05227	0.0139	N	0.03608	-0.345	0.58432	D	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.37979	-0.9682	10	0.07813	T	0.8	-8.2929	12.3675	0.55236	0.0:0.2685:0.0:0.7315	rs35014191	656	O60331	PI51C_HUMAN	T	656	ENSP00000335333:A656T	ENSP00000335333:A656T	A	-	1	0	PIP5K1C	3584473	0.551000	0.26497	0.185000	0.23176	0.746000	0.42486	-0.496000	0.06436	-1.205000	0.02645	-0.657000	0.03884	GCC	C|0.992;T|0.008	0.008	strong		0.701	PIP5K1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453432.2	NM_012398		T	3633473	C	T	3633473	3	4	30	1	0	0	0	0	1	0	0	0	11950	768	27	1	48	1	PIP5K1C	19	3633473	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	756047	3633473	55495510	602	13753											
PLIN4	729359	hgsc.bcm.edu	37	chr19	4513549	4513549	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tccatggcccctgtgaccccGctggacaccacctccttggt	5	9	9	18	1	0	1	0	1	0	0	2	2	2	2	8	3	0	1	8	3	0	1	rs146566557	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:4513549G>A	ENST00000301286.3	-	3	380	c.381C>T	c.(379-381)agC>agT	p.S127S		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	127	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						CTGTGACCCCGCTGGACACCA	0.667													G|||	4	0.000798722	0.0008	0.0	5008	,	,		17859	0.001		0.002	False		,,,				2504	0.0				p.S127S		Atlas-SNP	.											.	PLIN4	191	.	0			c.C381T						PASS	.	G		2,3976		0,2,1987	26	30	29		381	-10.7	0	19	dbSNP_134	29	37,8263		0,37,4113	no	coding-synonymous	PLIN4	NM_001080400.1		0,39,6100	AA,AG,GG		0.4458,0.0503,0.3176		127/1358	4513549	39,12239	1989	4150	6139	SO:0001819	synonymous_variant	729359	exon3			GACCCCGCTGGAC	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.381C>T	19.37:g.4513549G>A		80	0	0		89	47	0.52809	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			G|0.998;A|0.002	0.002	strong		0.667	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901		A	4513549	G	A	4513549	2	1	30	1	0	0	0	0	0	0	0	1	12101	1078	38	1		1	PLIN4	19	4513549	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	880076	4513549	54615434	603	13754											
PLIN3	10226	hgsc.bcm.edu	37	chr19	4861381	4861381	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtcacctgggtgctgccaTcagcctctgccccgtcggca	4	9	11	17	2	3	0	2	0	1	0	4	0	3	0	5	2	4	2	5	2	0	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:4861381T>C	ENST00000221957.4	-	2	202	c.26A>G	c.(25-27)gAt>gGt	p.D9G	PLIN3_ENST00000592528.1_Missense_Mutation_p.D9G|PLIN3_ENST00000585479.1_Missense_Mutation_p.D9G	NM_001164189.1|NM_001164194.1|NM_005817.4	NP_001157661.1|NP_001157666.1|NP_005808.3	O60664	PLIN3_HUMAN	perilipin 3	9					vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)|membrane (GO:0016020)				cervix(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9					Galsulfase(DB01279)|Idursulfase(DB01271)	GGTGCTGCCATCAGCCTCTGC	0.627																																					p.D9G		Atlas-SNP	.											PLIN3,NS,carcinoma,-1,1	PLIN3	36	1	0			c.A26G						PASS	.						113	91	98					19																	4861381		2203	4300	6503	SO:0001583	missense	10226	exon2			CTGCCATCAGCCT	AF051314	CCDS12137.1, CCDS59337.1, CCDS59338.1	19p13.3	2009-08-12	2009-08-12	2009-08-12		ENSG00000105355		"Perilipins"	16893	protein-coding gene	gene with protein product	"cargo selection protein (mannose 6 phosphate receptor binding protein)", "placental protein 17", "MPR-BINDING PROTEIN, 47-KD"	602702	"mannose-6-phosphate receptor binding protein 1"	M6PRBP1		9590177, 6856484, 19638644	Standard	NM_005817		Approved	TIP47, PP17	uc002mbj.2	O60664		ENST00000221957.4:c.26A>G	19.37:g.4861381T>C	ENSP00000221957:p.Asp9Gly	42	0	0		48	13	0.270833	NM_001164189	A8K4Y9|K7EQF4|Q53G77|Q9BS03|Q9UBD7|Q9UP92	Missense_Mutation	SNP	ENST00000221957.4	37	CCDS12137.1	.	.	.	.	.	.	.	.	.	.	T	7.718	0.696623	0.15106	.	.	ENSG00000105355	ENST00000221957	T	0.05925	3.37	3.24	-1.14	0.09741	.	1.247070	0.05815	U	0.614699	T	0.05135	0.0137	L	0.29908	0.895	0.09310	N	1	B;B	0.15930	0.015;0.009	B;B	0.16722	0.016;0.007	T	0.45731	-0.9241	10	0.27785	T	0.31	-22.7586	5.44	0.16501	0.0:0.161:0.5605:0.2785	.	9;9	O60664-3;O60664	.;PLIN3_HUMAN	G	9	ENSP00000221957:D9G	ENSP00000221957:D9G	D	-	2	0	PLIN3	4812381	0.000000	0.05858	0.000000	0.03702	0.106000	0.19336	0.176000	0.16782	0.042000	0.15717	0.379000	0.24179	GAT	.	.	none		0.627	PLIN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000450436.1	NM_005817		C	4861381	T	C	4861381	3	2	30	1	0	0	0	0	1	0	0	0	12100	1435	50	3	1306	3	PLIN3	19	4861381	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	347832	4861381	54267602	604	13755											
RFX2	5990	hgsc.bcm.edu	37	chr19	6013057	6013057	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actgcgtgtcctcctgcagcCggttcagtggtgagtccggc	4	10	14	13	3	1	1	1	1	0	0	4	1	4	1	4	3	3	2	4	3	0	1			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:6013057C>T	ENST00000303657.5	-	8	988	c.839G>A	c.(838-840)cGg>cAg	p.R280Q	RFX2_ENST00000592546.1_Missense_Mutation_p.R255Q|CTC-232P5.1_ENST00000587836.1_RNA|RFX2_ENST00000359161.3_Missense_Mutation_p.R280Q	NM_000635.3	NP_000626.2	P48378	RFX2_HUMAN	regulatory factor X, 2 (influences HLA class II expression)	280					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						CTCCTGCAGCCGGTTCAGTGG	0.612																																					p.R280Q	Colon(38;171 817 19800 47433 48051)	Atlas-SNP	.											.	RFX2	60	.	0			c.G839A						PASS	.						126	122	123					19																	6013057		2203	4300	6503	SO:0001583	missense	5990	exon8			TGCAGCCGGTTCA		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.839G>A	19.37:g.6013057C>T	ENSP00000306335:p.Arg280Gln	42	0	0		56	25	0.446429	NM_000635	A8K581|B3KNC4|Q6IQ44|Q8SNA2	Missense_Mutation	SNP	ENST00000303657.5	37	CCDS12157.1	.	.	.	.	.	.	.	.	.	.	C	19.57	3.851655	0.71719	.	.	ENSG00000087903	ENST00000303657;ENST00000359161;ENST00000537791	T;D	0.92149	-0.1;-2.98	4.99	2.84	0.33178	.	0.059667	0.64402	D	0.000002	D	0.88385	0.6422	M	0.65320	2	0.80722	D	1	P;P	0.41848	0.763;0.651	B;B	0.37387	0.248;0.087	D	0.84345	0.0529	10	0.37606	T	0.19	-48.0962	9.5849	0.39510	0.0:0.7782:0.1427:0.0791	.	255;280	P48378-2;P48378	.;RFX2_HUMAN	Q	280;255;67	ENSP00000306335:R280Q;ENSP00000352076:R255Q	ENSP00000306335:R280Q	R	-	2	0	RFX2	5964057	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.746000	0.62133	0.611000	0.30052	0.557000	0.71058	CGG	.	.	none		0.612	RFX2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452687.1	NM_000635		T	6013057	C	T	6013057	3	4	30	1	0	0	0	0	1	0	0	0	13278	652	23	1	1376	1	RFX2	19	6013057	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1151676	6013057	53115926	605	13756											
KHSRP	8570	hgsc.bcm.edu	37	chr19	6415735	6415735	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggggtccgcggccgctgcAgctgctttgcctgcaggaga	4	9	16	12	3	0	1	0	0	0	1	1	2	1	1	3	4	5	5	3	4	0	2	rs145698454	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:6415735A>G	ENST00000398148.3	-	17	1790	c.1698T>C	c.(1696-1698)gcT>gcC	p.A566A	MIR3940_ENST00000579148.1_RNA	NM_003685.2	NP_003676.2	Q92945	FUBP2_HUMAN	KH-type splicing regulatory protein	566	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)	p.A566A(1)		breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|liver(1)|lung(6)|skin(1)|soft_tissue(1)	17						CGGCCGCTGCAGCTGCTTTGC	0.706													A|||	32	0.00638978	0.0008	0.0144	5008	,	,		11509	0.0		0.0139	False		,,,				2504	0.0072				p.A566A	Colon(55;593 1006 2067 9135 22980)	Atlas-SNP	.											KHSRP,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	KHSRP	51	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.T1698C						PASS	.	A		3,3369		0,3,1683	4	6	5		1698	-10.1	0	19	dbSNP_134	5	31,7415		0,31,3692	no	coding-synonymous	KHSRP	NM_003685.2		0,34,5375	GG,GA,AA		0.4163,0.089,0.3143		566/712	6415735	34,10784	1686	3723	5409	SO:0001819	synonymous_variant	8570	exon17			CGCTGCAGCTGCT	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.1698T>C	19.37:g.6415735A>G		48	0	0		31	10	0.322581	NM_003685	O00301|Q59EZ9|Q5U4P6|Q9UNT5|Q9UQH5	Silent	SNP	ENST00000398148.3	37	CCDS45936.1																																																																																			A|0.994;G|0.006	0.006	strong		0.706	KHSRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453305.1			G	6415735	A	G	6415735	2	3	30	1	0	0	0	0	0	0	0	1	8160	175	7	3		3	KHSRP	19	6415735	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	402678	6415735	52713248	606	13757											
GPR108	56927	hgsc.bcm.edu	37	chr19	6733582	6733582	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgccctccactccgctcaccGtgatgtcgaatggatgctcc	6	10	9	16	3	1	1	1	1	0	0	5	3	4	2	5	1	2	2	5	1	1	0	rs201134279	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:6733582G>A	ENST00000264080.7	-	8	748	c.722C>T	c.(721-723)aCg>aTg	p.T241M	GPR108_ENST00000598626.1_5'Flank|GPR108_ENST00000430424.4_De_novo_Start_InFrame	NM_001080452.1	NP_001073921.1	Q9NPR9	GP108_HUMAN	G protein-coupled receptor 108	241						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|large_intestine(4)|lung(4)|skin(1)|urinary_tract(1)	13						TCCGCTCACCGTGATGTCGAA	0.632													G|||	21	0.00419329	0.0	0.0	5008	,	,		16071	0.0		0.005	False		,,,				2504	0.0164				p.T241M		Atlas-SNP	.											.	GPR108	35	.	0			c.C722T						PASS	.	G	MET/THR	11,4095		0,11,2042	81	79	80		722	3.9	1	19		80	45,8347		0,45,4151	yes	missense-near-splice	GPR108	NM_001080452.1	81	0,56,6193	AA,AG,GG		0.5362,0.2679,0.4481	probably-damaging	241/544	6733582	56,12442	2053	4196	6249	SO:0001630	splice_region_variant	56927	exon8			CTCACCGTGATGT		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.723+1C>T	19.37:g.6733582G>A		159	1	0.00628931		129	129	1	NM_001080452	B9EJD7	Missense_Mutation	SNP	ENST00000264080.7	37	CCDS42479.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	32	5.147240	0.94603	0.002679	0.005362	ENSG00000125734	ENST00000264080	T	0.26373	1.74	3.92	3.92	0.45320	.	0.198041	0.28600	U	0.014764	T	0.38665	0.1049	M	0.70595	2.14	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	T	0.34700	-0.9818	10	0.48119	T	0.1	-26.584	11.595	0.50968	0.0:0.0:1.0:0.0	.	241	Q9NPR9	GP108_HUMAN	M	241	ENSP00000264080:T241M	ENSP00000264080:T241M	T	-	2	0	GPR108	6684582	0.981000	0.34729	0.999000	0.59377	0.813000	0.45954	1.961000	0.40432	2.172000	0.68678	0.555000	0.69702	ACG	G|0.995;A|0.005	0.005	strong		0.632	GPR108-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407508.2		Missense_Mutation	A	6733582	G	A	6733582	5	1	30	1	0	0	0	0	0	0	1	0	6632	1159	40	1	953	1	GPR108	19	6733582	Splice_Site	SNP	G	TCGA-GR-7353-01A-11D-2210-10	317847	6733582	52395401	607	13758											
STXBP2	6813	hgsc.bcm.edu	37	chr19	7712050	7712050	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcctctcggccgccaggaCgccgtggaggaccggctgga	5	5	16	15	5	1	0	0	0	1	0	2	4	1	4	5	6	1	1	5	6	0	0	rs146425381	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:7712050C>T	ENST00000221283.5	+	17	1486	c.1455C>T	c.(1453-1455)gaC>gaT	p.D485D	STXBP2_ENST00000414284.2_Silent_p.D482D|STXBP2_ENST00000441779.2_Silent_p.D496D|STXBP2_ENST00000602355.1_Silent_p.D20D	NM_006949.2	NP_008880.2	Q15833	STXB2_HUMAN	syntaxin binding protein 2	485					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						GCCGCCAGGACGCCGTGGAGG	0.721													C|||	3	0.000599042	0.0	0.0014	5008	,	,		13459	0.0		0.002	False		,,,				2504	0.0				p.D496D		Atlas-SNP	.											.	STXBP2	63	.	0			c.C1488T						PASS	.	C	,	0,4384		0,0,2192	22	28	26		1446,1455	-3.5	0.5	19	dbSNP_134	26	14,8528		0,14,4257	no	coding-synonymous,coding-synonymous	STXBP2	NM_001127396.1,NM_006949.2	,	0,14,6449	TT,TC,CC		0.1639,0.0,0.1083	,	482/591,485/594	7712050	14,12912	2192	4271	6463	SO:0001819	synonymous_variant	6813	exon17			CCAGGACGCCGTG	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.1455C>T	19.37:g.7712050C>T		57	0	0		50	15	0.3	NM_001272034	B4E175|E7EQD5|Q9BU65	Silent	SNP	ENST00000221283.5	37	CCDS12181.1																																																																																			C|0.999;T|0.001	0.001	strong		0.721	STXBP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460963.1	NM_006949		T	7712050	C	T	7712050	2	4	30	1	0	0	0	0	0	0	0	1	15368	535	19	1		1	STXBP2	19	7712050	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	978468	7712050	51416933	608	13759											
ZNF560	147741	hgsc.bcm.edu	37	chr19	9579809	9579809	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcccatttaatgtttttaaaCaaaaattatcttgccaaagg	15	15	4	7	0	1	0	0	0	1	0	2	0	2	0	2	1	2	1	2	1	7	7	rs61737643	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:9579809C>A	ENST00000301480.4	-	9	797	c.584G>T	c.(583-585)tGt>tTt	p.C195F		NM_152476.2	NP_689689.2	Q96MR9	ZN560_HUMAN	zinc finger protein 560	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)			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						TGTTTTTAAACAAAAATTATC	0.313													C|||	5	0.000998403	0.0	0.0029	5008	,	,		18821	0.0		0.003	False		,,,				2504	0.0				p.C195F		Atlas-SNP	.											.	ZNF560	162	.	0			c.G584T						PASS	.	C	PHE/CYS	6,4398		0,6,2196	29	30	30		584	0.9	0	19	dbSNP_129	30	23,8571		0,23,4274	yes	missense	ZNF560	NM_152476.2	205	0,29,6470	AA,AC,CC		0.2676,0.1362,0.2231	possibly-damaging	195/791	9579809	29,12969	2202	4297	6499	SO:0001583	missense	147741	exon9			TTTAAACAAAAAT	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.584G>T	19.37:g.9579809C>A	ENSP00000301480:p.Cys195Phe	251	0	0		194	85	0.438144	NM_152476	Q495S9|Q495T1	Missense_Mutation	SNP	ENST00000301480.4	37	CCDS12214.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	4.197	0.035323	0.08148	0.001362	0.002676	ENSG00000198028	ENST00000301480	T	0.05258	3.47	1.99	0.933	0.19471	.	.	.	.	.	T	0.01940	0.0061	N	0.13098	0.295	0.09310	N	1	B	0.32010	0.351	B	0.19148	0.024	T	0.43637	-0.9379	9	0.38643	T	0.18	.	3.29	0.06945	0.0:0.5484:0.2782:0.1734	.	195	Q96MR9	ZN560_HUMAN	F	195	ENSP00000301480:C195F	ENSP00000301480:C195F	C	-	2	0	ZNF560	9440809	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-0.516000	0.06282	0.386000	0.24997	0.555000	0.69702	TGT	C|0.997;A|0.003	0.003	strong		0.313	ZNF560-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449901.1	NM_152476		A	9579809	C	A	9579809	3	1	30	1	0	0	0	0	1	0	0	0	18006	478	17	4	1796	4	ZNF560	19	9579809	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1867759	9579809	49549174	609	13760											
TYK2	7297	hgsc.bcm.edu	37	chr19	10463118	10463118	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cctggctctcaccgtgggggGgctctggctggagtcacagt	4	9	16	12	1	3	0	2	0	2	0	4	1	3	1	2	6	0	3	2	6	0	0	rs34536443	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:10463118G>C	ENST00000525621.1	-	23	3791	c.3310C>G	c.(3310-3312)Ccc>Gcc	p.P1104A	TYK2_ENST00000524462.1_Missense_Mutation_p.P919A|TYK2_ENST00000529422.1_Intron|TYK2_ENST00000264818.6_Missense_Mutation_p.P1104A	NM_003331.4	NP_003322.3	P29597	TYK2_HUMAN	tyrosine kinase 2	1104	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.		P -> A (in dbSNP:rs34536443). {ECO:0000269|PubMed:17344846}.		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)			ACCGTGGGGGGGCTCTGGCTG	0.592													g|||	51	0.0101837	0.0015	0.0202	5008	,	,		14995	0.0		0.0288	False		,,,				2504	0.0061				p.P1104A		Atlas-SNP	.											.	TYK2	126	.	0			c.C3310G	GRCh37	CM070300	TYK2	M	rs34536443	PASS	.	G	ALA/PRO	30,4376	36.0+/-67.5	0,30,2173	69	76	73		3310	4.3	1	19	dbSNP_126	73	347,8253	117.0+/-176.6	4,339,3957	yes	missense	TYK2	NM_003331.4	27	4,369,6130	CC,CG,GG		4.0349,0.6809,2.8987	probably-damaging	1104/1188	10463118	377,12629	2203	4300	6503	SO:0001583	missense	7297	exon23			TGGGGGGGCTCTG		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.3310C>G	19.37:g.10463118G>C	ENSP00000431885:p.Pro1104Ala	213	1	0.00469484		260	160	0.615385	NM_003331	Q6QB10|Q96CH0	Missense_Mutation	SNP	ENST00000525621.1	37	CCDS12236.1	31	0.014194139194139194	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	23	0.030343007915567283	G	24.3	4.511294	0.85389	0.006809	0.040349	ENSG00000105397	ENST00000524462;ENST00000525621;ENST00000264818;ENST00000543792;ENST00000529739	T;T;T;D	0.82344	-1.32;-1.32;-1.32;-1.6	5.35	4.32	0.51571	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.273195	0.25750	N	0.028545	T	0.71617	0.3361	M	0.72118	2.19	0.80722	D	1	D	0.89917	1.0	D	0.72982	0.979	T	0.82143	-0.0603	10	0.87932	D	0	-42.3966	11.8328	0.52305	0.0853:0.0:0.9147:0.0	rs34536443	1104	P29597	TYK2_HUMAN	A	919;1104;1104;851;127	ENSP00000433203:P919A;ENSP00000431885:P1104A;ENSP00000264818:P1104A;ENSP00000436155:P127A	ENSP00000264818:P1104A	P	-	1	0	TYK2	10324118	1.000000	0.71417	0.978000	0.43139	0.888000	0.51559	7.317000	0.79018	1.283000	0.44513	0.549000	0.68633	CCC	G|0.975;C|0.025	0.025	strong		0.592	TYK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389443.1			C	10463118	G	C	10463118	3	2	30	1	0	0	0	0	1	0	0	0	16825	1232	43	4	265	4	TYK2	19	10463118	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	883309	10463118	48665865	610	13761											
CCDC159	126075	hgsc.bcm.edu	37	chr19	11465311	11465311	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctcctgggactctgactcCgactgtgaccaggacctctc	6	9	9	17	1	2	2	0	2	2	0	5	5	4	4	5	2	0	0	5	2	0	0	rs374274390	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:11465311C>T	ENST00000588790.1	+	12	1275	c.828C>T	c.(826-828)tcC>tcT	p.S276S	DKFZP761J1410_ENST00000251473.5_5'Flank|DKFZP761J1410_ENST00000591608.1_5'Flank|CCDC159_ENST00000458408.1_Silent_p.S276S			P0C7I6	CC159_HUMAN	coiled-coil domain containing 159	391										endometrium(1)|large_intestine(1)|lung(2)|ovary(1)	5						ACTCTGACTCCGACTGTGACC	0.647													C|||	3	0.000599042	0.0	0.0	5008	,	,		16082	0.0		0.002	False		,,,				2504	0.001				p.S276S		Atlas-SNP	.											.	CCDC159	35	.	0			c.C828T						PASS	.	C		3,4397		0,3,2197	31	39	36		828	-8.8	0	19		36	33,8555		0,33,4261	no	coding-synonymous	CCDC159	NM_001080503.2		0,36,6458	TT,TC,CC		0.3843,0.0682,0.2772		276/298	11465311	36,12952	2200	4294	6494	SO:0001819	synonymous_variant	126075	exon10			TGACTCCGACTGT	BC038439	CCDS45976.1	19p13.2	2010-02-17			ENSG00000183401	ENSG00000183401			26996	protein-coding gene	gene with protein product							Standard	NM_001080503		Approved		uc010xlt.2	P0C7I6		ENST00000588790.1:c.828C>T	19.37:g.11465311C>T		133	0	0		124	59	0.475806	NM_001080503	B4DEG3|B4DWR8|B4E133|B7ZAM4	Silent	SNP	ENST00000588790.1	37	CCDS45976.1																																																																																			.	.	weak		0.647	CCDC159-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458761.1	NM_001080503		T	11465311	C	T	11465311	2	4	30	1	0	0	0	0	0	0	0	1	2793	639	23	1		1	CCDC159	19	11465311	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1002193	11465311	47663672	611	13762											
C19orf39	126074	hgsc.bcm.edu	37	chr19	11486354	11486354	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccgcctacctcattgccttaCttctagacacagctgcccac	8	10	5	18	1	2	1	1	0	1	1	2	1	2	1	5	0	5	1	5	0	3	5	rs146815699	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:11486354C>A	ENST00000312423.2	+	2	411	c.352C>A	c.(352-354)Ctt>Att	p.L118I	CTD-2342J14.6_ENST00000590399.1_RNA	NM_175871.3	NP_787067.2	Q6NVH7	SWAP1_HUMAN	SWIM-type zinc finger 7 associated protein 1	118					ATP catabolic process (GO:0006200)|double-strand break repair via homologous recombination (GO:0000724)|protein stabilization (GO:0050821)	nucleus (GO:0005634)|Shu complex (GO:0097196)	ATPase activity (GO:0016887)|single-stranded DNA binding (GO:0003697)										CATTGCCTTACTTCTAGACAC	0.652													C|||	3	0.000599042	0.0	0.0014	5008	,	,		17164	0.0		0.002	False		,,,				2504	0.0				p.L118I		Atlas-SNP	.											.	.	.	.	0			c.C352A						PASS	.	C	ILE/LEU	5,4401	9.9+/-24.2	0,5,2198	73	72	72		352	5.3	1	19	dbSNP_134	72	39,8561	26.8+/-75.7	0,39,4261	yes	missense	C19orf39	NM_175871.3	5	0,44,6459	AA,AC,CC		0.4535,0.1135,0.3383	possibly-damaging	118/230	11486354	44,12962	2203	4300	6503	SO:0001583	missense	126074	exon2			GCCTTACTTCTAG	AK092438	CCDS12259.1	19p13.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000173928	ENSG00000173928			26638	protein-coding gene	gene with protein product	"zinc finger, SWIM-type containing 7 associated protein 1", "SWS1-associated protein 1"	614536	"chromosome 19 open reading frame 39"	C19orf39		21965664	Standard	NM_175871		Approved	FLJ35119, ZSWIM7AP1, SWS1AP1	uc002mrg.1	Q6NVH7		ENST00000312423.2:c.352C>A	19.37:g.11486354C>A	ENSP00000310008:p.Leu118Ile	70	0	0		66	25	0.378788	NM_175871	Q8NAM1	Missense_Mutation	SNP	ENST00000312423.2	37	CCDS12259.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	24.3	4.520751	0.85495	0.001135	0.004535	ENSG00000173928	ENST00000312423	T	0.41400	1.0	5.32	5.32	0.75619	.	0.000000	0.64402	D	0.000007	T	0.63307	0.2500	M	0.65975	2.015	0.45216	D	0.998223	D	0.76494	0.999	D	0.87578	0.998	T	0.65038	-0.6265	10	0.59425	D	0.04	-11.7403	15.9252	0.79611	0.0:1.0:0.0:0.0	.	118	Q6NVH7	CS039_HUMAN	I	118	ENSP00000310008:L118I	ENSP00000310008:L118I	L	+	1	0	C19orf39	11347354	1.000000	0.71417	0.998000	0.56505	0.762000	0.43233	4.466000	0.60148	2.489000	0.83994	0.655000	0.94253	CTT	C|0.997;A|0.003	0.003	strong		0.652	SWSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458789.1	NM_175871		A	11486354	C	A	11486354	3	1	30	1	0	0	0	0	1	0	0	0	1924	565	20	4	358	4	C19orf39	19	11486354	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	21043	11486354	47642629	612	13763											
ZNF433	163059	hgsc.bcm.edu	37	chr19	12126128	12126128	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccatgatatcgaaaggagctCgaacagttgaaggatctgcc	13	8	11	9	2	1	2	0	2	1	0	3	6	1	4	2	2	3	2	2	2	4	2	rs79356451		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:12126128C>T	ENST00000344980.6	-	4	1724	c.1554G>A	c.(1552-1554)tcG>tcA	p.S518S	CTD-2006C1.2_ENST00000406892.2_RNA|ZNF433_ENST00000419886.2_Silent_p.S483S|CTD-2006C1.2_ENST00000495324.1_RNA|CTD-2006C1.2_ENST00000476474.1_RNA	NM_001080411.1	NP_001073880.1	Q8N7K0	ZN433_HUMAN	zinc finger protein 433	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)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(1)|prostate(1)|skin(1)	14						GAAAGGAGCTCGAACAGTTGA	0.433													C|||	1	0.000199681	0.0	0.0	5008	,	,		23439	0.0		0.001	False		,,,				2504	0.0				p.S518S		Atlas-SNP	.											ZNF433,colon,carcinoma,-1,2	ZNF433	49	2	0			c.G1554A						scavenged	.	C		0,4398		0,0,2199	71	76	74		1554	-2.4	0	19	dbSNP_132	74	4,8594	3.7+/-12.6	0,4,4295	no	coding-synonymous	ZNF433	NM_001080411.1		0,4,6494	TT,TC,CC		0.0465,0.0,0.0308		518/674	12126128	4,12992	2199	4299	6498	SO:0001819	synonymous_variant	163059	exon4			GGAGCTCGAACAG	AK098300	CCDS45983.1	19p13.13	2013-01-08			ENSG00000197647	ENSG00000197647		"Zinc fingers, C2H2-type", "-"	20811	protein-coding gene	gene with protein product							Standard	NM_001080411		Approved	FLJ40981	uc002msy.1	Q8N7K0	OTTHUMG00000156427	ENST00000344980.6:c.1554G>A	19.37:g.12126128C>T		163	1	0.00613497		153	84	0.54902	NM_001080411	Q86VX3	Silent	SNP	ENST00000344980.6	37	CCDS45983.1																																																																																			C|0.999;T|0.001	0.001	strong		0.433	ZNF433-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403716.1	NM_152602		T	12126128	C	T	12126128	2	4	30	1	0	0	0	0	0	0	0	1	17922	871	31	1		1	ZNF433	19	12126128	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	639774	12126128	47002855	613	13764											
CACNA1A	773	hgsc.bcm.edu	37	chr19	13395957	13395959	+	In_Frame_Del	DEL	TCC	TCC	-																															cgtcttccccacggtcgtctTcctcctcctccttcttctct																										TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:13395957_13395959delTCC	ENST00000360228.5	-	21	3614_3616	c.3615_3617delGGA	c.(3613-3618)gaggaa>gaa	p.1205_1206EE>E	CACNA1A_ENST00000573710.2_In_Frame_Del_p.1206_1207EE>E	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	1206	Poly-Glu.				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)	ACGGtcgtcttcctcctcctcct	0.552																																					p.1207_1207del		Pindel,Atlas-Indel	.											.	CACNA1A	715	.	0			c.3619_3621del						PASS	.		,,,,	3,3657		1,1,1828					,,,,	-3.5	0.6			103	12,7868		0,12,3928	no	coding,coding,coding,coding,coding	CACNA1A	NM_023035.2,NM_001174080.1,NM_001127222.1,NM_001127221.1,NM_000068.3	,,,,	1,13,5756	A1A1,A1R,RR		0.1523,0.082,0.13	,,,,	,,,,		15,11525				SO:0001651	inframe_deletion	773	exon21			.	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.3615_3617delGGA	19.37:g.13395966_13395968delTCC	ENSP00000353362:p.Glu1206del	170	0	.		172	45	0.262	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	In_Frame_Del	DEL	ENST00000360228.5	37	CCDS45998.1																																																																																			.	.	none		0.552	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		-	13395959	TCC	-	13395957	7	5	30	1	0	1	0	1	0	0	0	0	2540	1783	62	0	4113	0	CACNA1A	19	13395957	In_Frame_Del	DEL	TCC	TCGA-GR-7353-01A-11D-2210-10	1269829	13395957	45733026	614	13765											
CACNA1A	773	hgsc.bcm.edu	37	chr19	13409407	13409407	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctccctccgcgcgtccccctCgtacgtggctggagcgccat	3	8	11	19	6	0	0	0	0	0	0	4	1	3	1	5	2	2	2	5	2	1	1	rs16024	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:13409407C>T	ENST00000360228.5	-	19	3039	c.3040G>A	c.(3040-3042)Gag>Aag	p.E1014K	CACNA1A_ENST00000573710.2_Missense_Mutation_p.E1015K	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	1015					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)	GCGTCCCCCTCGTACGTGGCT	0.687													C|||	6	0.00119808	0.0008	0.0029	5008	,	,		9081	0.0		0.003	False		,,,				2504	0.0				p.E1015K		Atlas-SNP	.											.	CACNA1A	715	.	0			c.G3043A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	0,3196		0,0,1598	22	22	22		3052,3043,3040,3043,3052	3.5	0	19	dbSNP_54	22	35,6103		0,35,3034	yes	missense,missense,missense,missense,missense	CACNA1A	NM_000068.3,NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2	56,56,56,56,56	0,35,4632	TT,TC,CC		0.5702,0.0,0.375	benign,benign,benign,benign,benign	1018/2267,1015/2262,1014/2507,1015/2264,1018/2513	13409407	35,9299	1598	3069	4667	SO:0001583	missense	773	exon19			CCCCCTCGTACGT	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.3040G>A	19.37:g.13409407C>T	ENSP00000353362:p.Glu1014Lys	141	0	0		122	58	0.47541	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Missense_Mutation	SNP	ENST00000360228.5	37	CCDS45998.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	8.418	0.845757	0.16963	0.0	0.005702	ENSG00000141837	ENST00000360228;ENST00000418012;ENST00000357018;ENST00000325084	D	0.95853	-3.83	3.54	3.54	0.40534	.	2.783830	0.01492	N	0.017126	D	0.89213	0.6651	L	0.36672	1.1	0.34650	D	0.721503	B;B;B	0.31599	0.0;0.33;0.222	B;B;B	0.17098	0.0;0.017;0.015	T	0.74842	-0.3527	10	0.06236	T	0.91	.	13.8911	0.63740	0.0:1.0:0.0:0.0	rs16024;rs16024	1015;1018;1014	O00555;E9PD31;Q9NS88	CAC1A_HUMAN;.;.	K	1014;1018;1015;1015	ENSP00000353362:E1014K	ENSP00000317661:E1015K	E	-	1	0	CACNA1A	13270407	0.456000	0.25744	0.039000	0.18376	0.035000	0.12851	1.820000	0.39032	1.541000	0.49316	0.462000	0.41574	GAG	C|0.997;T|0.003	0.003	strong		0.687	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068		T	13409407	C	T	13409407	3	4	30	1	0	0	0	0	1	0	0	0	2540	893	31	1	4698	1	CACNA1A	19	13409407	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	13450	13409407	45719576	615	13766											
LPHN1	22859	hgsc.bcm.edu	37	chr19	14288369	14288369	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gacatgatcttgaaggcgtcCggcaggtagcactgcacatt	10	9	12	10	2	1	2	0	2	1	0	2	3	2	2	1	3	2	4	1	3	2	3	rs146417164	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:14288369C>T	ENST00000340736.6	-	3	555	c.258G>A	c.(256-258)ccG>ccA	p.P86P	LPHN1_ENST00000361434.3_Silent_p.P86P	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	86	SUEL-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00260}.				calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|heterophilic cell-cell adhesion (GO:0007157)|neuropeptide signaling pathway (GO:0007218)|positive regulation of synapse maturation (GO:0090129)	axon (GO:0030424)|cell junction (GO:0030054)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TGAAGGCGTCCGGCAGGTAGC	0.572													C|||	26	0.00519169	0.0	0.0086	5008	,	,		18398	0.002		0.0179	False		,,,				2504	0.0				p.P86P		Atlas-SNP	.											.	LPHN1	107	.	0			c.G258A						PASS	.	C	,	8,4398	14.3+/-33.2	0,8,2195	137	114	122		258,258	-9.7	0	19	dbSNP_134	122	104,8496	57.2+/-118.5	1,102,4197	no	coding-synonymous,coding-synonymous	LPHN1	NM_001008701.2,NM_014921.4	,	1,110,6392	TT,TC,CC		1.2093,0.1816,0.8611	,	86/1475,86/1470	14288369	112,12894	2203	4300	6503	SO:0001819	synonymous_variant	22859	exon3			GGCGTCCGGCAGG	AB020628	CCDS12307.1, CCDS32928.1	19p13.2	2014-08-08				ENSG00000072071		"-", "GPCR / Class B : Orphans"	20973	protein-coding gene	gene with protein product						10994649	Standard	NM_014921		Approved	KIAA0821, CIRL1, LEC2	uc010xnn.2	O94910		ENST00000340736.6:c.258G>A	19.37:g.14288369C>T		140	0	0		119	62	0.521008	NM_001008701	Q96IE7|Q9BU07|Q9HAR3	Silent	SNP	ENST00000340736.6	37	CCDS32928.1																																																																																			C|0.992;T|0.008	0.008	strong		0.572	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921		T	14288369	C	T	14288369	2	4	30	1	0	0	0	0	0	0	0	1	8924	639	23	1		1	LPHN1	19	14288369	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	878962	14288369	44840614	616	13767											
DNAJB1	3337	hgsc.bcm.edu	37	chr19	14629138	14629138	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcgccgcgggccaggcccaaCgtctggtagtagtctttacc	6	8	13	14	4	2	0	0	0	2	0	2	0	2	0	4	3	2	2	4	3	4	4	rs141518218	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:14629138C>T	ENST00000254322.2	-	1	94	c.24G>A	c.(22-24)acG>acA	p.T8T	DNAJB1_ENST00000396969.4_Intron	NM_006145.1	NP_006136.1	P25685	DNJB1_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 1	8	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				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)		CCAGGCCCAACGTCTGGTAGT	0.711													C|||	8	0.00159744	0.0	0.0014	5008	,	,		9495	0.0		0.004	False		,,,				2504	0.0031				p.T8T		Atlas-SNP	.											.	DNAJB1	38	.	0			c.G24A						PASS	.	C		8,4394		0,8,2193	27	26	27		24	1.7	1	19	dbSNP_134	27	67,8527		0,67,4230	no	coding-synonymous	DNAJB1	NM_006145.1		0,75,6423	TT,TC,CC		0.7796,0.1817,0.5771		8/341	14629138	75,12921	2201	4297	6498	SO:0001819	synonymous_variant	3337	exon1			GCCCAACGTCTGG	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.24G>A	19.37:g.14629138C>T		61	0	0		36	20	0.555556	NM_006145	B4DX52	Silent	SNP	ENST00000254322.2	37	CCDS12312.1																																																																																			C|0.995;T|0.005	0.005	strong		0.711	DNAJB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465987.1	NM_006145		T	14629138	C	T	14629138	2	4	30	1	0	0	0	0	0	0	0	1	4617	523	19	1		1	DNAJB1	19	14629138	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	340769	14629138	44499845	617	13768											
SLC1A6	6511	hgsc.bcm.edu	37	chr19	15083555	15083555	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	accgtcagcagaatgaaggcGtttcggcgcaggaagcgcag	11	5	15	10	5	1	2	1	1	0	1	2	3	1	3	1	3	2	4	1	3	3	1	rs115001292	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:15083555G>A	ENST00000221742.3	-	1	175	c.168C>T	c.(166-168)aaC>aaT	p.N56N	SLC1A6_ENST00000600144.1_Silent_p.N56N|SLC1A6_ENST00000430939.2_Missense_Mutation_p.R61C|SLC1A6_ENST00000598504.1_Silent_p.N56N|SLC1A6_ENST00000544886.2_Silent_p.N56N	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	56					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						GAATGAAGGCGTTTCGGCGCA	0.637													G|||	44	0.00878594	0.0	0.0245	5008	,	,		19459	0.0		0.0239	False		,,,				2504	0.0031				p.N56N		Atlas-SNP	.											.	SLC1A6	111	.	0			c.C168T						PASS	.	G		7,4393		0,7,2193	29	29	29		168	-4.8	0.9	19	dbSNP_132	29	53,8547		1,51,4248	no	coding-synonymous	SLC1A6	NM_005071.1		1,58,6441	AA,AG,GG		0.6163,0.1591,0.4615		56/565	15083555	60,12940	2200	4300	6500	SO:0001819	synonymous_variant	6511	exon4			GAAGGCGTTTCGG		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.168C>T	19.37:g.15083555G>A		133	0	0		110	57	0.518182	NM_001272087	Q8N753	Silent	SNP	ENST00000221742.3	37	CCDS12321.1	26	0.011904761904761904	0	0.0	6	0.016574585635359115	0	0.0	20	0.026385224274406333	G	10.63	1.404119	0.25291	0.001591	0.006163	ENSG00000105143	ENST00000430939	T	0.75260	-0.92	4.46	-4.79	0.03200	.	.	.	.	.	T	0.37865	0.1019	.	.	.	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.32771	-0.9894	8	0.87932	D	0	-17.863	10.8289	0.46649	0.7382:0.0:0.2618:0.0	.	61	E7EV13	.	C	61	ENSP00000409386:R61C	ENSP00000409386:R61C	R	-	1	0	SLC1A6	14944555	0.036000	0.19791	0.931000	0.37212	0.642000	0.38348	-0.826000	0.04429	-0.758000	0.04690	0.313000	0.20887	CGC	G|0.993;A|0.007	0.007	strong		0.637	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071		A	15083555	G	A	15083555	2	1	30	1	0	0	0	0	0	0	0	1	14451	1136	40	1		1	SLC1A6	19	15083555	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	454417	15083555	44045428	618	13769											
FAM32A	26017	hgsc.bcm.edu	37	chr19	16301759	16301759	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattcccaaagtcagctggaCgaagtagccgcctgccccca	10	6	9	16	2	1	0	1	0	0	0	2	2	2	1	5	1	3	2	5	1	3	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:16301759C>T	ENST00000263384.7	+	4	357	c.332C>T	c.(331-333)aCg>aTg	p.T111M	FAM32A_ENST00000588367.1_Missense_Mutation_p.T93M|CTD-2562J15.4_ENST00000591038.1_RNA|FAM32A_ENST00000589852.1_Missense_Mutation_p.T91M	NM_014077.2	NP_054796.1	Q9Y421	FA32A_HUMAN	family with sequence similarity 32, member A	111					apoptotic process (GO:0006915)|cell cycle (GO:0007049)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.T111M(1)		lung(1)	1						GTCAGCTGGACGAAGTAGCCG	0.557																																					p.T111M		Atlas-SNP	.											FAM32A,NS,carcinoma,0,1	FAM32A	6	1	1	Substitution - Missense(1)	lung(1)	c.C332T						PASS	.						73	61	65					19																	16301759		2203	4300	6503	SO:0001583	missense	26017	exon4			GCTGGACGAAGTA	BC000639	CCDS12341.1	19p13.12-p13.11	2013-09-19			ENSG00000105058	ENSG00000105058			24563	protein-coding gene	gene with protein product		614554				11230166, 10810093	Standard	NM_014077		Approved	DKFZP586O0120	uc002ndt.3	Q9Y421	OTTHUMG00000182279	ENST00000263384.7:c.332C>T	19.37:g.16301759C>T	ENSP00000263384:p.Thr111Met	127	0	0		131	53	0.40458	NM_014077	Q9BT02	Missense_Mutation	SNP	ENST00000263384.7	37	CCDS12341.1	.	.	.	.	.	.	.	.	.	.	C	16.01	2.999969	0.54147	.	.	ENSG00000105058	ENST00000263384	.	.	.	3.99	2.94	0.34122	.	0.000000	0.85682	D	0.000000	T	0.44307	0.1287	M	0.72576	2.205	0.80722	D	1	P	0.40144	0.704	B	0.28465	0.09	T	0.48747	-0.9008	9	0.66056	D	0.02	-16.2628	9.4497	0.38719	0.0:0.8985:0.0:0.1015	.	111	Q9Y421	FA32A_HUMAN	M	111	.	ENSP00000263384:T111M	T	+	2	0	FAM32A	16162759	1.000000	0.71417	0.841000	0.33234	0.578000	0.36192	5.807000	0.69157	0.793000	0.33875	0.462000	0.41574	ACG	.	.	none		0.557	FAM32A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460346.1	NM_014077		T	16301759	C	T	16301759	3	4	30	1	0	0	0	0	1	0	0	0	5560	536	19	1	346	1	FAM32A	19	16301759	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1218204	16301759	42827224	619	13770											
MYO9B	4650	hgsc.bcm.edu	37	chr19	17306074	17306074	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggacaagagcaaaccatgtGgcagcccaagggttcaggaa	15	4	13	9	0	1	1	1	0	0	1	1	3	1	3	2	4	3	3	2	4	4	1	rs112900956	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:17306074G>A	ENST00000594824.1	+	22	3985	c.3838G>A	c.(3838-3840)Ggc>Agc	p.G1280S	MYO9B_ENST00000397274.2_Missense_Mutation_p.G1280S|MYO9B_ENST00000595618.1_Missense_Mutation_p.G1280S			Q13459	MYO9B_HUMAN	myosin IXB	1280	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						CAAACCATGTGGCAGCCCAAG	0.701													G|||	19	0.00379393	0.0008	0.0029	5008	,	,		13079	0.0		0.0129	False		,,,				2504	0.0031				p.G1280S		Atlas-SNP	.											MYO9B_ENST00000319396,adrenal_gland,adrenal_cortical_adenoma,0,2	MYO9B	264	2	0			c.G3838A						PASS	.	G	SER/GLY,SER/GLY	11,3783		0,11,1886	20	27	25		3838,3838	-3.2	0	19	dbSNP_132	25	119,8027		0,119,3954	yes	missense,missense	MYO9B	NM_001130065.1,NM_004145.3	56,56	0,130,5840	AA,AG,GG		1.4608,0.2899,1.0888	benign,benign	1280/2023,1280/2158	17306074	130,11810	1897	4073	5970	SO:0001583	missense	4650	exon22			CCATGTGGCAGCC		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.3838G>A	19.37:g.17306074G>A	ENSP00000471367:p.Gly1280Ser	89	0	0		65	40	0.615385	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Missense_Mutation	SNP	ENST00000594824.1	37		12	0.005494505494505495	0	0.0	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	G	5.753	0.323409	0.10900	0.002899	0.014608	ENSG00000099331	ENST00000397274	D	0.83673	-1.75	5.28	-3.16	0.05217	.	1.740110	0.03022	N	0.150866	T	0.65123	0.2661	L	0.34521	1.04	0.09310	N	1	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.06405	0.0;0.0;0.002	T	0.56932	-0.7897	10	0.07030	T	0.85	.	10.5091	0.44851	0.645:0.0:0.355:0.0	.	1280;1280;1286	Q13459;B0I1T6;Q4LE74	MYO9B_HUMAN;.;.	S	1280	ENSP00000380444:G1280S	ENSP00000380444:G1280S	G	+	1	0	MYO9B	17167074	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.479000	0.06567	-0.339000	0.08401	-0.367000	0.07326	GGC	G|0.994;A|0.006	0.006	strong		0.701	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1			A	17306074	G	A	17306074	3	1	30	1	0	0	0	0	1	0	0	0	10094	1348	47	2	3920	2	MYO9B	19	17306074	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1004315	17306074	41822909	620	13771											
MEF2B	100271849	hgsc.bcm.edu	37	chr19	19257101	19257102	+	Intron	INS	-	-	G																															ctgggctgggaggacacggcINSggggggcccatcacccctcg																										TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:19257101_19257102insG	ENST00000602424.2	-	9	1496				MEF2B_ENST00000424583.2_Frame_Shift_Ins_p.A288fs|MEF2B_ENST00000410050.1_Frame_Shift_Ins_p.A295fs|MEF2B_ENST00000409224.1_Frame_Shift_Ins_p.A291fs|MEF2BNB-MEF2B_ENST00000602276.1_5'Flank|MEF2B_ENST00000162023.5_Frame_Shift_Ins_p.A288fs|MEF2BNB-MEF2B_ENST00000514819.3_Intron|MEF2BNB-MEF2B_ENST00000444486.3_Intron|MEF2B_ENST00000409447.2_Intron	NM_005919.3	NP_005910.1	Q02080	MEF2B_HUMAN	myocyte enhancer factor 2B						muscle organ development (GO:0007517)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cell junction (GO:0030054)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|haematopoietic_and_lymphoid_tissue(21)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(5;0.00011)|Epithelial(12;0.00412)			GAGGACACGGCGGGGGGCCCAT	0.703											OREG0025379	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A288fs		Atlas-Indel	.											.	MEF2B	41	.	0			c.862_863insC						PASS	.																																			SO:0001627	intron_variant	100271849	exon8			.	X63380	CCDS12394.1, CCDS46024.1	19p13.11	2010-05-12	2007-04-24					"Myocyte enhancer factors"	6995	protein-coding gene	gene with protein product		600661				1516833, 8575763	Standard	NM_001145785		Approved	RSRFR2	uc002nll.2	Q02080		ENST00000602424.2:c.769+261->C	19.37:g.19257107_19257107dupG		21	0	0	731	33	11	0.333333	NM_001145785	A0AV80|B4DVH7|B7ZVY1|G5E9M1	Frame_Shift_Ins	INS	ENST00000602424.2	37	CCDS12394.1																																																																																			.	.	none		0.703	MEF2B-202	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_005919		G	19257102	-	G	19257101	6	5	30	0	1	1	1	0	0	0	0	0	9465	768	27	0		0	MEF2B	19	19257101	Intron	INS	-	TCGA-GR-7353-01A-11D-2210-10	1951027	19257101	39871882	621	13772											
GATAD2A	54815	hgsc.bcm.edu	37	chr19	19612027	19612027	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcgggaggagaagagcggCgccatcatgtgtgagaactg	10	6	18	7	3	1	3	1	1	0	3	1	6	1	4	1	4	2	0	1	4	2	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:19612027C>T	ENST00000360315.3	+	9	1614	c.1302C>T	c.(1300-1302)ggC>ggT	p.G434G	GATAD2A_ENST00000252577.5_Silent_p.G434G|GATAD2A_ENST00000358713.3_Silent_p.G434G|GATAD2A_ENST00000537887.1_Silent_p.G63G|GATAD2A_ENST00000429563.2_Silent_p.G262G|GATAD2A_ENST00000404158.1_Silent_p.G435G	NM_017660.3	NP_060130.3	Q86YP4	P66A_HUMAN	GATA zinc finger domain containing 2A	434	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						AGAAGAGCGGCGCCATCATGT	0.627																																					p.G434G		Atlas-SNP	.											GATAD2A_ENST00000360315,colon,carcinoma,+2,2	GATAD2A	81	2	0			c.C1302T						PASS	.						49	40	43					19																	19612027		2203	4300	6503	SO:0001819	synonymous_variant	54815	exon9			GAGCGGCGCCATC	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.1302C>T	19.37:g.19612027C>T		228	1	0.00438596		226	108	0.477876	NM_017660	B5MC40|Q7L3J2|Q96F28|Q9NPU2|Q9NXS1	Silent	SNP	ENST00000360315.3	37	CCDS12402.2	.	.	.	.	.	.	.	.	.	.	C	7.688	0.690376	0.15039	.	.	ENSG00000167491	ENST00000418032	.	.	.	5.76	-11.5	0.00074	.	.	.	.	.	T	0.34279	0.0892	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52087	-0.8622	4	.	.	.	-20.9578	3.2541	0.06826	0.2384:0.4298:0.078:0.2537	.	.	.	.	C	61	.	.	R	+	1	0	GATAD2A	19473027	0.000000	0.05858	0.006000	0.13384	0.808000	0.45660	-5.377000	0.00127	-4.065000	0.00077	-0.158000	0.13435	CGC	.	.	none		0.627	GATAD2A-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326671.4	NM_017660		T	19612027	C	T	19612027	2	4	30	1	0	0	0	0	0	0	0	1	6268	755	27	1		1	GATAD2A	19	19612027	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	354926	19612027	39516956	622	13773											
NDUFA13	51079	hgsc.bcm.edu	37	chr19	19627083	19627083	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgaagcaggacatgcctccGccggggggctatgggcccat	7	6	16	12	2	0	1	0	1	0	0	1	2	1	2	4	5	2	2	4	5	2	1	rs11552886		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:19627083G>C	ENST00000507754.4	+	1	520	c.36G>C	c.(34-36)ccG>ccC	p.P12P	NDUFA13_ENST00000512771.3_Silent_p.P12P|TSSK6_ENST00000360913.3_5'Flank|CTC-260F20.3_ENST00000555938.1_Silent_p.P12P|NDUFA13_ENST00000428459.2_Silent_p.P12P|TSSK6_ENST00000585580.3_5'Flank|YJEFN3_ENST00000608404.1_Silent_p.P12P|NDUFA13_ENST00000503283.1_Silent_p.P12P|NDUFA13_ENST00000252576.5_Silent_p.P95P|CTC-260F20.3_ENST00000586674.1_3'UTR			Q9P0J0	NDUAD_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13	12					apoptotic signaling pathway (GO:0097190)|cellular metabolic process (GO:0044237)|cellular response to interferon-beta (GO:0035458)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell growth (GO:0030308)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of peptidase activity (GO:0010952)|positive regulation of protein catabolic process (GO:0045732)|protein import into mitochondrial inner membrane (GO:0045039)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain (GO:0005746)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|NADH dehydrogenase activity (GO:0003954)	p.P95P(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)	12						ACATGCCTCCGCCGGGGGGCT	0.622																																					p.P12P		Atlas-SNP	.											NDUFA13,NS,carcinoma,0,1	NDUFA13	17	1	1	Substitution - coding silent(1)	ovary(1)	c.G36C						scavenged	.						38	43	41					19																	19627083		2203	4300	6503	SO:0001819	synonymous_variant	51079	exon1			GCCTCCGCCGGGG	AF261134	CCDS12404.1, CCDS12404.2	19p13.11	2011-07-04			ENSG00000186010	ENSG00000186010		"Mitochondrial respiratory chain complex / Complex I"	17194	protein-coding gene	gene with protein product	"complex I B16.6 subunit"	609435				12837546, 10924506, 15367666	Standard	NM_015965		Approved	CGI-39, CDA016, GRIM-19, GRIM19, B16.6		Q9P0J0	OTTHUMG00000162211	ENST00000507754.4:c.36G>C	19.37:g.19627083G>C		262	2	0.00763359		243	112	0.460905	NM_015965	B4DF76|K7EK58|Q6PKI0|Q9H2L3|Q9Y327	Silent	SNP	ENST00000507754.4	37	CCDS12404.2																																																																																			.	.	alt		0.622	NDUFA13-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367916.6	NM_015965		C	19627083	G	C	19627083	2	2	30	1	0	0	0	0	0	0	0	1	10272	1074	38	4		4	NDUFA13	19	19627083	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	15056	19627083	39501900	623	13774											
LPAR2	9170	hgsc.bcm.edu	37	chr19	19737992	19737992	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtcagccccagtgccaccacGaccacatccttgggccgcca	8	5	9	19	2	1	0	1	0	0	0	2	1	2	0	8	1	2	0	8	1	0	1	rs150741448	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:19737992G>A	ENST00000542587.1	-	5	1004	c.102C>T	c.(100-102)gtC>gtT	p.V34V	LPAR2_ENST00000407877.3_Silent_p.V34V|LPAR2_ENST00000589311.1_5'Flank|LPAR2_ENST00000586703.1_Silent_p.V34V			Q9HBW0	LPAR2_HUMAN	lysophosphatidic acid receptor 2	34					activation of MAPK activity (GO:0000187)|activation of phospholipase C activity (GO:0007202)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of Rho protein signal transduction (GO:0035025)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|lysophosphatidic acid receptor activity (GO:0070915)			breast(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|urinary_tract(1)	10						GTGCCACCACGACCACATCCT	0.592													G|||	7	0.00139776	0.0	0.0029	5008	,	,		18269	0.0		0.005	False		,,,				2504	0.0				p.V34V		Atlas-SNP	.											.	LPAR2	28	.	0			c.C102T						PASS	.	G		4,4400	6.2+/-15.9	0,4,2198	33	32	33		102	-8.9	0.4	19	dbSNP_134	33	39,8561	24.0+/-70.4	0,39,4261	no	coding-synonymous	LPAR2	NM_004720.5		0,43,6459	AA,AG,GG		0.4535,0.0908,0.3307		34/352	19737992	43,12961	2202	4300	6502	SO:0001819	synonymous_variant	9170	exon2			CACCACGACCACA	AF011466	CCDS12407.1	19p12	2012-08-08	2008-04-11	2008-04-11		ENSG00000064547		"GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"	3168	protein-coding gene	gene with protein product		605110	"endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 4"	EDG4		9525886, 9804623	Standard	NM_004720		Approved	EDG-4, LPA2	uc002nnb.4	Q9HBW0		ENST00000542587.1:c.102C>T	19.37:g.19737992G>A		66	0	0		75	35	0.466667	NM_004720	O00543|O43431	Silent	SNP	ENST00000542587.1	37	CCDS12407.1																																																																																			G|0.997;A|0.003	0.003	strong		0.592	LPAR2-003	KNOWN	alternative_5_UTR|non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460544.1	NM_004720		A	19737992	G	A	19737992	2	1	30	1	0	0	0	0	0	0	0	1	8914	1045	37	1		1	LPAR2	19	19737992	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	110909	19737992	39390991	624	13775											
ZNF85	7639	hgsc.bcm.edu	37	chr19	21133078	21133078	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtccttactaaacataagatAattcataccggagaaaaatt	18	11	5	7	1	1	2	1	0	0	2	2	3	2	2	2	1	3	0	2	1	8	7	rs142868740	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:21133078A>G	ENST00000328178.8	+	4	1871	c.1758A>G	c.(1756-1758)atA>atG	p.I586M	ZNF85_ENST00000601023.1_Missense_Mutation_p.I527M|ZNF85_ENST00000345030.6_Missense_Mutation_p.I553M	NM_001256173.1|NM_003429.4	NP_001243102.1|NP_003420.2	Q03923	ZNF85_HUMAN	zinc finger protein 85	586					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						AACATAAGATAATTCATACCG	0.284													.|||	2	0.000399361	0.0	0.0	5008	,	,		18633	0.0		0.001	False		,,,				2504	0.001				p.I616M		Atlas-SNP	.											.	ZNF85	72	.	0			c.A1848G						PASS	.	A	MET/ILE	0,4396		0,0,2198	18	19	19		1758	1.3	0	19	dbSNP_134	19	12,8550		0,12,4269	yes	missense	ZNF85	NM_003429.4	10	0,12,6467	GG,GA,AA		0.1402,0.0,0.0926	benign	586/596	21133078	12,12946	2198	4281	6479	SO:0001583	missense	7639	exon5			TAAGATAATTCAT	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.1758A>G	19.37:g.21133078A>G	ENSP00000329793:p.Ile586Met	99	0	0		98	46	0.469388	NM_001256171	B9ZVP4|Q6NVI0	Missense_Mutation	SNP	ENST00000328178.8	37	CCDS32977.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	.	0.029	-1.346964	0.01266	0.0	0.001402	ENSG00000105750	ENST00000328178;ENST00000345030;ENST00000421385	T;T	0.07444	3.19;3.19	1.27	1.27	0.21489	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04407	0.0121	N	0.12471	0.22	0.80722	D	1	P;B;P	0.44816	0.478;0.082;0.844	B;B;B	0.40165	0.272;0.002;0.321	T	0.48906	-0.8993	9	0.72032	D	0.01	.	5.3151	0.15850	0.7085:0.2915:0.0:0.0	.	553;527;586	Q03923-2;Q49A12;Q03923	.;.;ZNF85_HUMAN	M	586;553;461	ENSP00000329793:I586M;ENSP00000342340:I553M	ENSP00000329793:I586M	I	+	3	3	ZNF85	20924918	0.001000	0.12720	0.044000	0.18714	0.048000	0.14542	0.031000	0.13710	0.528000	0.28580	0.329000	0.21502	ATA	A|0.999;G|0.001	0.001	strong		0.284	ZNF85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463430.1	NM_003429		G	21133078	A	G	21133078	3	3	30	1	0	0	0	0	1	0	0	0	18208	352	13	3	1772	3	ZNF85	19	21133078	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	1395086	21133078	37995905	625	13776											
ZNF493	284443	hgsc.bcm.edu	37	chr19	21607252	21607252	+	Missense_Mutation	SNP	T	T	A																															cacaagataattcatactgaTaagaaaccctacaaatgtga																								rs142288436	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:21607252T>A	ENST00000355504.4	+	2	1673	c.1407T>A	c.(1405-1407)gaT>gaA	p.D469E	ZNF493_ENST00000392288.2_Missense_Mutation_p.D597E|CTD-2561J22.3_ENST00000600810.1_Intron	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	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)|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						TTCATACTGATAAGAAACCCT	0.333													.|||	3	0.000599042	0.0	0.0	5008	,	,		19829	0.0		0.003	False		,,,				2504	0.0				p.D597E		Atlas-SNP	.											.	ZNF493	178	.	0			c.T1791A						PASS	.						33	33	33					19																	21607252		2200	4298	6498	SO:0001583	missense	284443	exon4			TACTGATAAGAAA	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.1407T>A	19.37:g.21607252T>A	ENSP00000347691:p.Asp469Glu	77	0	0		66	11	0.166667	NM_001076678	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	1.434	-0.569466	0.03910	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	T;T	0.16897	2.31;2.31	1.06	-2.12	0.07165	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.05731	0.0150	N	0.02674	-0.535	0.09310	N	1	B;B	0.09022	0.001;0.002	B;B	0.08055	0.003;0.002	T	0.31336	-0.9947	9	0.66056	D	0.02	.	3.2801	0.06912	0.5296:0.0:0.2843:0.1862	.	469;597	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	E	597;469	ENSP00000376110:D597E;ENSP00000347691:D469E	ENSP00000347691:D469E	D	+	3	2	ZNF493	21399092	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-1.688000	0.01925	-3.330000	0.00186	-3.393000	0.00039	GAT	.	.	weak		0.333	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		A	21607252	T	A	21607252	3	1	30	1	0	0	0	0	1	0	0	0	17959	1403	49	5	1868	5	ZNF493	19	21607252	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	474174	21607252	37521731	626	13777	170	2									
ZNF493	284443	hgsc.bcm.edu	37	chr19	21607253	21607253	+	Missense_Mutation	SNP	A	A	G																															acaagataattcatactgatAagaaaccctacaaatgtgaa																								rs150159158	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:21607253A>G	ENST00000355504.4	+	2	1674	c.1408A>G	c.(1408-1410)Aag>Gag	p.K470E	ZNF493_ENST00000392288.2_Missense_Mutation_p.K598E|CTD-2561J22.3_ENST00000600810.1_Intron	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	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)|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						TCATACTGATAAGAAACCCTA	0.338													.|||	3	0.000599042	0.0	0.0	5008	,	,		19874	0.0		0.003	False		,,,				2504	0.0				p.K598E		Atlas-SNP	.											.	ZNF493	178	.	0			c.A1792G						PASS	.						33	33	33					19																	21607253		2201	4298	6499	SO:0001583	missense	284443	exon4			ACTGATAAGAAAC	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.1408A>G	19.37:g.21607253A>G	ENSP00000347691:p.Lys470Glu	75	0	0		65	11	0.169231	NM_001076678	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	0.006	-2.049581	0.00394	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	T;T	0.12672	2.66;2.66	1.06	-2.12	0.07165	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01940	0.0061	N	0.00191	-1.88	0.38843	D	0.956104	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.50575	-0.8812	9	0.02654	T	1	.	4.9183	0.13856	0.3932:0.1603:0.4464:0.0	.	470;598	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	E	598;470	ENSP00000376110:K598E;ENSP00000347691:K470E	ENSP00000347691:K470E	K	+	1	0	ZNF493	21399093	0.015000	0.18098	0.000000	0.03702	0.000000	0.00434	0.849000	0.27723	-2.911000	0.00308	-2.864000	0.00100	AAG	.	.	weak		0.338	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		G	21607253	A	G	21607253	3	3	30	1	0	0	0	0	1	0	0	0	17959	363	13	3	1869	3	ZNF493	19	21607253	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	1	21607253	37521730	627	13778	170	2									
ZNF676	163223	hgsc.bcm.edu	37	chr19	22364230	22364230	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggttaagtttattataacCttctttgtgcacgttacact	9	18	6	8	1	1	0	0	0	1	0	1	0	1	0	1	1	3	4	1	1	5	8			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:22364230C>A	ENST00000397121.2	-	3	606	c.289G>T	c.(289-291)Ggt>Tgt	p.G97C		NM_001001411.2	NP_001001411.2	Q8N7Q3	ZN676_HUMAN	zinc finger protein 676	97					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)				TTATTATAACCTTCTTTGTGC	0.313																																					p.G97C		Atlas-SNP	.											ZNF676,NS,carcinoma,+1,2	ZNF676	146	2	0			c.G289T						PASS	.						131	121	124					19																	22364230		1971	4181	6152	SO:0001583	missense	163223	exon3			TATAACCTTCTTT	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.289G>T	19.37:g.22364230C>A	ENSP00000380310:p.Gly97Cys	292	1	0.00342466		282	100	0.35461	NM_001001411	A8MVX5	Missense_Mutation	SNP	ENST00000397121.2	37	CCDS42539.1	.	.	.	.	.	.	.	.	.	.	.	0.866	-0.733679	0.03111	.	.	ENSG00000196109	ENST00000397121	T	0.07688	3.17	0.398	-0.797	0.10909	.	.	.	.	.	T	0.09247	0.0228	M	0.70842	2.15	0.09310	N	1	B	0.16396	0.017	B	0.16289	0.015	T	0.33650	-0.9860	9	0.37606	T	0.19	.	4.101	0.10014	0.6355:0.3645:0.0:0.0	.	97	Q8N7Q3	ZN676_HUMAN	C	97	ENSP00000380310:G97C	ENSP00000380310:G97C	G	-	1	0	ZNF676	22156070	0.000000	0.05858	0.011000	0.14972	0.153000	0.21895	-0.155000	0.10115	-0.683000	0.05190	0.186000	0.17326	GGT	.	.	none		0.313	ZNF676-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464392.1	NM_001001411		A	22364230	C	A	22364230	3	1	30	1	0	0	0	0	1	0	0	0	18098	681	24	4	1481	4	ZNF676	19	22364230	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	756977	22364230	36764753	628	13779											
ZNF91	7644	hgsc.bcm.edu	37	chr19	23544515	23544515	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtatgaataaacttatgtatAgtaagatttgaagatcgatt	16	15	8	2	1	0	4	0	2	0	2	1	5	0	4	0	0	1	3	0	0	9	8			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:23544515A>T	ENST00000300619.7	-	4	1471	c.1266T>A	c.(1264-1266)acT>acA	p.T422T	ZNF91_ENST00000596528.1_5'Flank|ZNF91_ENST00000397082.2_Silent_p.T390T|ZNF91_ENST00000599743.1_Intron	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	422					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)				ACTTATGTATAGTAAGATTTG	0.338																																					p.T422T		Atlas-SNP	.											ZNF91_ENST00000300619,NS,lymphoid_neoplasm,-1,2	ZNF91	349	2	0			c.T1266A						PASS	.						13	13	13					19																	23544515		1849	4026	5875	SO:0001819	synonymous_variant	7644	exon4			ATGTATAGTAAGA	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.1266T>A	19.37:g.23544515A>T		115	0	0		111	37	0.333333	NM_003430	A8K5E1|B7Z6G6	Silent	SNP	ENST00000300619.7	37	CCDS42541.1																																																																																			.	.	none		0.338	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430		T	23544515	A	T	23544515	2	4	30	1	0	0	0	0	0	0	0	1	18215	407	15	5		5	ZNF91	19	23544515	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	1180285	23544515	35584468	629	13780											
TSHZ3	57616	hgsc.bcm.edu	37	chr19	31769293	31769293	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtcgacttccttcttgaccTccacattcagttttggggag	6	15	9	11	1	2	1	1	1	1	0	5	3	4	2	3	2	0	1	3	2	0	6	rs143453460	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:31769293T>C	ENST00000240587.4	-	2	1733	c.1406A>G	c.(1405-1407)gAg>gGg	p.E469G		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	469			E -> G (in dbSNP:rs143453460). {ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:19745106}.		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)					CTTCTTGACCTCCACATTCAG	0.542													T|||	18	0.00359425	0.0	0.0086	5008	,	,		18888	0.0		0.0099	False		,,,				2504	0.002				p.E469G		Atlas-SNP	.											TSHZ3_ENST00000240587,NS,carcinoma,+1,2	TSHZ3	549	2	0			c.A1406G						PASS	.	T	GLY/GLU	8,4398	12.9+/-30.5	0,8,2195	152	154	153		1406	5.6	1	19	dbSNP_134	153	102,8498	54.8+/-115.7	0,102,4198	yes	missense	TSHZ3	NM_020856.2	98	0,110,6393	CC,CT,TT		1.186,0.1816,0.8458	probably-damaging	469/1082	31769293	110,12896	2203	4300	6503	SO:0001583	missense	57616	exon2			TTGACCTCCACAT	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.1406A>G	19.37:g.31769293T>C	ENSP00000240587:p.Glu469Gly	209	1	0.00478469		199	108	0.542714	NM_020856	Q9H0G6|Q9P254	Missense_Mutation	SNP	ENST00000240587.4	37	CCDS12421.2	11	0.005036630036630037	0	0.0	5	0.013812154696132596	0	0.0	6	0.0079155672823219	T	18.15	3.560653	0.65538	0.001816	0.01186	ENSG00000121297	ENST00000240587	T	0.38077	1.16	5.55	5.55	0.83447	.	0.052145	0.85682	D	0.000000	T	0.49898	0.1584	M	0.67397	2.05	0.80722	D	1	D	0.71674	0.998	D	0.72982	0.979	T	0.54957	-0.8215	10	0.44086	T	0.13	-30.6092	15.7178	0.77681	0.0:0.0:0.0:1.0	.	469	Q63HK5	TSH3_HUMAN	G	469	ENSP00000240587:E469G	ENSP00000240587:E469G	E	-	2	0	TSHZ3	36461133	1.000000	0.71417	1.000000	0.80357	0.865000	0.49528	5.849000	0.69465	2.099000	0.63709	0.533000	0.62120	GAG	T|0.991;C|0.009	0.009	strong		0.542	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856		C	31769293	T	C	31769293	3	2	30	1	0	0	0	0	1	0	0	0	16640	1551	54	3	1843	3	TSHZ3	19	31769293	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	8224778	31769293	27359690	630	13781											
DMKN	93099	hgsc.bcm.edu	37	chr19	36002421	36002421	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctgccactgctgctgccAccactgctgctgccattgtt	4	12	9	16	0	0	0	0	0	0	0	0	0	0	0	4	0	8	6	4	0	0	2	rs72334573	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:36002421A>G	ENST00000339686.3	-	5	986	c.810T>C	c.(808-810)ggT>ggC	p.G270G	DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000440396.1_Silent_p.G270G|DMKN_ENST00000424570.2_Silent_p.G270G|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000451297.2_Silent_p.G270G|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000447113.2_Silent_p.G270G|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000418261.1_Silent_p.G270G|DMKN_ENST00000462126.1_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	270	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)			tgctgctgccaccactgctgc	0.652																																					p.G270G		Atlas-SNP	.											DMKN,colon,carcinoma,0,1	DMKN	116	1	0			c.T810C						PASS	.						30	23	25					19																	36002421		2166	4245	6411	SO:0001819	synonymous_variant	93099	exon5			GCTGCCACCACTG	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.810T>C	19.37:g.36002421A>G		35	0	0		72	6	0.0833333	NM_001126058	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Silent	SNP	ENST00000339686.3	37	CCDS12463.1																																																																																			.	.	none		0.652	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317		G	36002421	A	G	36002421	2	3	30	1	0	0	0	0	0	0	0	1	4584	146	6	3		3	DMKN	19	36002421	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	4233128	36002421	23126562	631	13782											
TYROBP	7305	hgsc.bcm.edu	37	chr19	36398454	36398454	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcacgatccctgccagcacGcccgggctcaccgtagagca	9	5	10	17	4	2	1	2	0	0	1	3	2	3	1	4	1	3	4	4	1	1	1	rs111477177	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:36398454G>C	ENST00000262629.4	-	3	189	c.123C>G	c.(121-123)ggC>ggG	p.G41G	TYROBP_ENST00000424586.3_Silent_p.G30G|TYROBP_ENST00000589517.1_Silent_p.G41G|TYROBP_ENST00000544690.2_Silent_p.G30G|TYROBP_ENST00000585901.2_Silent_p.G41G	NM_003332.3|NM_198125.2	NP_003323.1|NP_937758.1	O43914	TYOBP_HUMAN	TYRO protein tyrosine kinase binding protein	41					axon guidance (GO:0007411)|cellular defense response (GO:0006968)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|intracellular signal transduction (GO:0035556)|macrophage activation involved in immune response (GO:0002281)|neutrophil activation involved in immune response (GO:0002283)|regulation of immune response (GO:0050776)|regulation of osteoclast development (GO:2001204)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|receptor binding (GO:0005102)|receptor signaling protein activity (GO:0005057)			NS(1)|central_nervous_system(1)|large_intestine(1)|lung(4)|skin(1)	8	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)			CTGCCAGCACGCCCGGGCTCA	0.672													G|||	56	0.0111821	0.0008	0.0202	5008	,	,		16218	0.0		0.0348	False		,,,				2504	0.0061				p.G41G		Atlas-SNP	.											TYROBP,NS,carcinoma,-2,1	TYROBP	15	1	0			c.C123G						scavenged	.	G	,,,	36,4370	36.8+/-68.6	0,36,2167	36	38	37		90,90,123,123	-10.3	0	19	dbSNP_132	37	366,8234	115.9+/-175.7	8,350,3942	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TYROBP	NM_001173514.1,NM_001173515.1,NM_003332.3,NM_198125.2	,,,	8,386,6109	CC,CG,GG		4.2558,0.8171,3.0909	,,,	30/103,30/102,41/114,41/113	36398454	402,12604	2203	4300	6503	SO:0001819	synonymous_variant	7305	exon3			CAGCACGCCCGGG	AF019563	CCDS12482.1, CCDS46058.1, CCDS54255.1, CCDS59378.1	19q13.1	2014-09-17				ENSG00000011600			12449	protein-coding gene	gene with protein product	"killer activating receptor associated protein", "DNAX-activation protein 12"	604142		PLOSL		9490415, 10888890	Standard	NM_003332		Approved	DAP12, PLO-SL, KARAP	uc002ocm.3	O43914		ENST00000262629.4:c.123C>G	19.37:g.36398454G>C		133	2	0.0150376		108	46	0.425926	NM_198125	A8K2X0|F5H389|Q6FGA5|Q9UMT3	Silent	SNP	ENST00000262629.4	37	CCDS12482.1																																																																																			A|0.000;C|0.024;G|0.976	0.024	strong		0.672	TYROBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457397.1			C	36398454	G	C	36398454	2	2	30	1	0	0	0	0	0	0	0	1	16830	1074	38	4		4	TYROBP	19	36398454	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	396033	36398454	22730529	632	13783											
ZNF345	25850	hgsc.bcm.edu	37	chr19	37368535	37368535	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgaatgtggtaaggcctttaGttttggatcagcccttactc	8	15	10	8	0	1	1	1	1	0	0	2	2	1	2	2	3	2	2	2	3	4	6	rs112729744	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:37368535G>C	ENST00000529555.1	+	2	1591	c.803G>C	c.(802-804)aGt>aCt	p.S268T	ZNF345_ENST00000420450.1_Missense_Mutation_p.S268T|ZNF345_ENST00000432005.2_Intron|ZNF345_ENST00000589046.1_Missense_Mutation_p.S268T|ZNF345_ENST00000526123.1_Intron			Q14585	ZN345_HUMAN	zinc finger protein 345	268					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)			AAGGCCTTTAGTTTTGGATCA	0.418													G|||	10	0.00199681	0.0	0.0058	5008	,	,		21427	0.0		0.006	False		,,,				2504	0.0				p.S268T		Atlas-SNP	.											.	ZNF345	68	.	0			c.G803C						PASS	.	G	THR/SER,THR/SER,THR/SER,THR/SER,THR/SER	11,4395	16.8+/-37.8	0,11,2192	84	87	86		803,803,803,803,803	1.6	1	19	dbSNP_132	86	106,8494	57.2+/-118.5	1,104,4195	no	missense,missense,missense,missense,missense	ZNF345	NM_001242472.1,NM_001242474.1,NM_001242475.1,NM_001242476.1,NM_003419.4	58,58,58,58,58	1,115,6387	CC,CG,GG		1.2326,0.2497,0.8996	benign,benign,benign,benign,benign	268/489,268/489,268/489,268/489,268/489	37368535	117,12889	2203	4300	6503	SO:0001583	missense	25850	exon4			CCTTTAGTTTTGG	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.803G>C	19.37:g.37368535G>C	ENSP00000431202:p.Ser268Thr	123	0	0		131	70	0.534351	NM_001242476		Missense_Mutation	SNP	ENST00000529555.1	37	CCDS12497.1	7	0.003205128205128205	0	0.0	3	0.008287292817679558	0	0.0	4	0.005277044854881266	G	4.013	-0.000126	0.07819	0.002497	0.012326	ENSG00000251247	ENST00000420450;ENST00000529555;ENST00000344705	T;T	0.07567	3.18;3.18	3.96	1.58	0.23477	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04815	0.0130	L	0.31371	0.925	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.33929	-0.9849	9	0.35671	T	0.21	.	11.5634	0.50792	0.0:0.5461:0.4539:0.0	.	268	Q14585	ZN345_HUMAN	T	268;268;32	ENSP00000431216:S268T;ENSP00000431202:S268T	ENSP00000442320:S32T	S	+	2	0	ZNF345	42060375	0.000000	0.05858	1.000000	0.80357	0.994000	0.84299	-0.912000	0.04046	0.347000	0.23924	0.561000	0.74099	AGT	G|0.993;C|0.007	0.007	strong		0.418	ZNF345-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388258.1			C	37368535	G	C	37368535	3	2	30	1	0	0	0	0	1	0	0	0	17874	1029	36	4	805	4	ZNF345	19	37368535	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	970081	37368535	21760448	633	13784											
ZNF345	25850	hgsc.bcm.edu	37	chr19	37369032	37369032	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aatgtaaggagtgtgggaagGctttttatagtggctcaagc	11	12	14	4	0	1	0	1	0	0	0	1	2	1	2	0	4	1	3	0	4	6	5			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:37369032G>C	ENST00000529555.1	+	2	2088	c.1300G>C	c.(1300-1302)Gct>Cct	p.A434P	ZNF345_ENST00000420450.1_Missense_Mutation_p.A434P|ZNF345_ENST00000432005.2_Intron|ZNF345_ENST00000589046.1_Missense_Mutation_p.A434P|ZNF345_ENST00000526123.1_Intron			Q14585	ZN345_HUMAN	zinc finger protein 345	434					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)			GTGTGGGAAGGCTTTTTATAG	0.423																																					p.A434P		Atlas-SNP	.											.	ZNF345	68	.	0			c.G1300C						PASS	.						79	81	80					19																	37369032		2203	4300	6503	SO:0001583	missense	25850	exon4			GGGAAGGCTTTTT	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.1300G>C	19.37:g.37369032G>C	ENSP00000431202:p.Ala434Pro	97	0	0		101	56	0.554455	NM_001242476		Missense_Mutation	SNP	ENST00000529555.1	37	CCDS12497.1	.	.	.	.	.	.	.	.	.	.	G	10.40	1.340040	0.24339	.	.	ENSG00000251247	ENST00000420450;ENST00000529555;ENST00000344705	T;T	0.14391	2.51;2.51	3.0	-0.576	0.11731	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13586	0.0329	M	0.64260	1.97	0.09310	N	1	B	0.26041	0.14	B	0.29663	0.105	T	0.35549	-0.9784	9	0.72032	D	0.01	.	3.2328	0.06754	0.3529:0.0:0.4485:0.1985	.	434	Q14585	ZN345_HUMAN	P	434;434;198	ENSP00000431216:A434P;ENSP00000431202:A434P	ENSP00000442320:A198P	A	+	1	0	ZNF345	42060872	0.000000	0.05858	0.250000	0.24296	0.522000	0.34438	-1.705000	0.01896	-0.091000	0.12440	0.655000	0.94253	GCT	.	.	none		0.423	ZNF345-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388258.1			C	37369032	G	C	37369032	3	2	30	1	0	0	0	0	1	0	0	0	17874	1203	42	4	1302	4	ZNF345	19	37369032	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	497	37369032	21759951	634	13785											
HNRNPL	3191	hgsc.bcm.edu	37	chr19	39331198	39331198	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggggttgctgccagggtcAcctgtggagagagaaaacag	10	8	16	7	0	1	2	1	0	0	2	1	4	1	2	2	4	3	2	2	4	2	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:39331198A>T	ENST00000221419.5	-	7	1248	c.882T>A	c.(880-882)ggT>ggA	p.G294G	AC104534.3_ENST00000594769.1_5'Flank|HNRNPL_ENST00000600873.1_Splice_Site_p.G161G	NM_001533.2	NP_001524.2	P14866	HNRPL_HUMAN	heterogeneous nuclear ribonucleoprotein L	294					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)			TGCCAGGGTCACCTGTGGAGA	0.602																																					p.G294G		Atlas-SNP	.											.	HNRNPL	67	.	0			c.T882A						PASS	.						27	27	27					19																	39331198		2199	4299	6498	SO:0001630	splice_region_variant	3191	exon7			AGGGTCACCTGTG	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.881-1T>A	19.37:g.39331198A>T		94	0	0		90	30	0.333333	NM_001533	A6ND69|A6NIT8|Q9H3P3	Silent	SNP	ENST00000221419.5	37	CCDS33015.1																																																																																			.	.	none		0.602	HNRNPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462670.1		Silent	T	39331198	A	T	39331198	5	4	30	1	0	0	0	0	0	0	1	0	7279	173	6	5	915	5	HNRNPL	19	39331198	Splice_Site	SNP	A	TCGA-GR-7353-01A-11D-2210-10	1962166	39331198	19797785	635	13786											
NFKBIB	4793	hgsc.bcm.edu	37	chr19	39399416	39399416	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acagcagccgcagccaaaccCggctgcctcccaccccagcc	9	2	8	22	2	0	0	0	0	0	0	1	0	1	0	8	1	6	3	8	1	1	0	rs17886215		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:39399416C>T	ENST00000313582.5	+	6	1049	c.1015C>T	c.(1015-1017)Cgg>Tgg	p.R339W	NFKBIB_ENST00000392079.3_3'UTR	NM_002503.4	NP_002494.2	Q15653	IKBB_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, beta	339			R -> W (in dbSNP:rs17886215). {ECO:0000269|Ref.3}.		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)			CAGCCAAACCCGGCTGCCTCC	0.547																																					p.R339W	Pancreas(165;1492 2005 6979 7739 34483)	Atlas-SNP	.											.	NFKBIB	23	.	0			c.C1015T						PASS	.	C	,TRP/ARG	0,4406		0,0,2203	81	89	87		,1015	0.3	0	19	dbSNP_124	87	3,8597	3.0+/-9.4	0,3,4297	yes	utr-3,missense	NFKBIB	NM_001001716.1,NM_002503.4	,101	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	,possibly-damaging	,339/357	39399416	3,13003	2203	4300	6503	SO:0001583	missense	4793	exon6			CAAACCCGGCTGC	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.1015C>T	19.37:g.39399416C>T	ENSP00000312988:p.Arg339Trp	109	0	0		127	58	0.456693	NM_002503	A8K3F4|Q96BJ7	Missense_Mutation	SNP	ENST00000313582.5	37	CCDS12524.1	.	.	.	.	.	.	.	.	.	.	C	11.78	1.739866	0.30865	0.0	3.49E-4	ENSG00000104825	ENST00000313582	T	0.54675	0.56	5.08	0.314	0.15847	.	1.956000	0.02482	N	0.088598	T	0.36690	0.0976	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.28650	-1.0037	10	0.56958	D	0.05	1.3469	2.9887	0.05977	0.1946:0.4876:0.0:0.3178	rs17886215;rs17886215	339	Q15653	IKBB_HUMAN	W	339	ENSP00000312988:R339W	ENSP00000312988:R339W	R	+	1	2	NFKBIB	44091256	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	-0.182000	0.09726	0.293000	0.22520	0.655000	0.94253	CGG	C|0.998;T|0.002	0.002	strong		0.547	NFKBIB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438155.1	NM_002503		T	39399416	C	T	39399416	3	4	30	1	0	0	0	0	1	0	0	0	10387	643	23	1	1085	1	NFKBIB	19	39399416	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	68218	39399416	19729567	636	13787											
MAP3K10	4294	hgsc.bcm.edu	37	chr19	40712040	40712040	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgctcaagctgcgggaaggcGgcagccacatcagcctgccc	8	5	13	15	2	2	0	2	0	0	0	2	1	2	1	3	3	6	3	3	3	2	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:40712040G>A	ENST00000253055.3	+	5	1699	c.1411G>A	c.(1411-1413)Ggc>Agc	p.G471S	AC118344.1_ENST00000408124.1_RNA	NM_002446.3	NP_002437.2	Q02779	M3K10_HUMAN	mitogen-activated protein kinase kinase kinase 10	471				G -> S (in Ref. 2; CAA88531). {ECO:0000305}.|LKLREGGSHISLPSGF -> AQAAGRRQPHQPALWL (in Ref. 3). {ECO:0000305}.	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)	p.G471C(1)		NS(1)|breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	24						GCGGGAAGGCGGCAGCCACAT	0.657																																					p.G471S		Atlas-SNP	.											.	MAP3K10	70	.	1	Substitution - Missense(1)	lung(1)	c.G1411A						PASS	.						16	19	18					19																	40712040		2094	4126	6220	SO:0001583	missense	4294	exon5			GAAGGCGGCAGCC	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.1411G>A	19.37:g.40712040G>A	ENSP00000253055:p.Gly471Ser	168	0	0		144	80	0.555556	NM_002446	Q12761|Q14871	Missense_Mutation	SNP	ENST00000253055.3	37	CCDS12549.1	.	.	.	.	.	.	.	.	.	.	G	14.82	2.649911	0.47362	.	.	ENSG00000130758	ENST00000253055	T	0.73469	-0.75	4.53	-1.14	0.09741	.	0.279022	0.41097	N	0.000942	T	0.56790	0.2009	L	0.28192	0.835	0.31735	N	0.636552	B	0.15930	0.015	B	0.21917	0.037	T	0.51568	-0.8689	10	0.41790	T	0.15	.	8.6882	0.34251	0.5148:0.0:0.4852:0.0	.	471	Q02779	M3K10_HUMAN	S	471	ENSP00000253055:G471S	ENSP00000253055:G471S	G	+	1	0	MAP3K10	45403880	0.376000	0.25098	0.585000	0.28666	0.988000	0.76386	-0.143000	0.10296	-0.078000	0.12730	0.491000	0.48974	GGC	.	.	none		0.657	MAP3K10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462552.1	NM_002446		A	40712040	G	A	40712040	3	1	30	1	0	0	0	0	1	0	0	0	9253	1116	39	1	1429	1	MAP3K10	19	40712040	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1312624	40712040	18416943	637	13788											
PRX	57716	hgsc.bcm.edu	37	chr19	40909695	40909695	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccctctttgccgccgcccgcTacgttgatgccgctgacccc	3	9	9	20	5	1	2	0	2	1	0	1	2	1	2	7	0	3	3	7	0	1	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:40909695T>G	ENST00000324001.7	-	5	372	c.102A>C	c.(100-102)gtA>gtC	p.V34V	PRX_ENST00000291825.7_Silent_p.V34V	NM_181882.2	NP_870998.2	Q9BXM0	PRAX_HUMAN	periaxin	34	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)			CGCCGCCCGCTACGTTGATGC	0.692																																					p.V34V		Atlas-SNP	.											.	PRX	151	.	0			c.A102C						PASS	.						15	14	14					19																	40909695		2193	4294	6487	SO:0001819	synonymous_variant	57716	exon5			GCCCGCTACGTTG	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.102A>C	19.37:g.40909695T>G		159	0	0		116	56	0.482759	NM_181882	Q9BXL9|Q9HCF2	Silent	SNP	ENST00000324001.7	37	CCDS33028.1																																																																																			.	.	none		0.692	PRX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462582.1	NM_020956		G	40909695	T	G	40909695	2	3	30	1	0	0	0	0	0	0	0	1	12654	1509	53	5		5	PRX	19	40909695	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	197655	40909695	18219288	638	13789											
CYP2A6	1548	hgsc.bcm.edu	37	chr19	41356246	41356246	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccggaggcagcttccccttgCtcttcctctgctgccaaaca	6	10	8	17	1	2	0	0	0	2	0	4	1	4	1	5	2	5	4	5	2	1	3	rs28399435	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:41356246C>T	ENST00000301141.5	-	1	106	c.86G>A	c.(85-87)aGc>aAc	p.S29N	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	29			S -> N (in allele CYP2A6*14; dbSNP:rs28399435). {ECO:0000269|PubMed:15469410, ECO:0000269|PubMed:15618701, ECO:0000269|PubMed:2726448}.		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)	CTTCCCCTTGCTCTTCCTCTG	0.557													.|||	70	0.0139776	0.0023	0.0173	5008	,	,		17142	0.0		0.0328	False		,,,				2504	0.0225				p.S29N		Atlas-SNP	.											.	CYP2A6	69	.	0			c.G86A						PASS	.	C	ASN/SER	45,4361		2,41,2160	108	92	98		86	-3.7	0	19	dbSNP_125	98	350,8248		12,326,3961	no	missense	CYP2A6	NM_000762.5	46	14,367,6121	TT,TC,CC		4.0707,1.0213,3.0375	benign	29/495	41356246	395,12609	2203	4299	6502	SO:0001583	missense	1548	exon1			CCCTTGCTCTTCC	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.86G>A	19.37:g.41356246C>T	ENSP00000301141:p.Ser29Asn	341	1	0.00293255		330	166	0.50303	NM_000762	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Missense_Mutation	SNP	ENST00000301141.5	37	CCDS12568.1	34	0.015567765567765568	0	0.0	6	0.016574585635359115	0	0.0	28	0.036939313984168866	-	5.795	0.330971	0.10956	0.010213	0.040707	ENSG00000255974	ENST00000301141	T	0.69435	-0.4	2.86	-3.66	0.04489	.	1.227710	0.05870	U	0.624444	T	0.21427	0.0516	L	0.40543	1.245	0.09310	N	1	B	0.20671	0.047	B	0.27262	0.078	T	0.26677	-1.0096	10	0.22706	T	0.39	.	6.2921	0.21065	0.5064:0.3714:0.1222:0.0	rs28399435;rs57299031	29	P11509	CP2A6_HUMAN	N	29	ENSP00000301141:S29N	ENSP00000301141:S29N	S	-	2	0	CYP2A6	46048086	0.000000	0.05858	0.001000	0.08648	0.019000	0.09904	-2.019000	0.01442	-0.197000	0.10350	0.173000	0.16961	AGC	C|0.975;T|0.025	0.025	strong		0.557	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762		T	41356246	C	T	41356246	3	4	30	1	0	0	0	0	1	0	0	0	4164	797	28	2	1434	2	CYP2A6	19	41356246	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	446551	41356246	17772737	639	13790											
PSG11	5680	hgsc.bcm.edu	37	chr19	43528921	43528921	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgtgtaaggtgtaggatcCtgcgtcctcccgggtgacat	7	11	14	9	2	0	1	0	1	0	0	3	3	3	2	3	3	1	2	3	3	2	2	rs558961472	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:43528921C>G	ENST00000401740.1	-	2	455	c.352G>C	c.(352-354)Gga>Cga	p.G118R	PSG11_ENST00000403486.1_Intron|PSG11_ENST00000306322.7_Intron|PSG11_ENST00000320078.7_Missense_Mutation_p.G118R			Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 11	118	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)				GTGTAGGATCCTGCGTCCTCC	0.458													.|||	2	0.000399361	0.0	0.0	5008	,	,		20669	0.0		0.0	False		,,,				2504	0.002				p.G118R		Atlas-SNP	.											PSG11,NS,carcinoma,+2,1	PSG11	57	1	0			c.G352C						scavenged	.						154	147	150					19																	43528921		2199	4294	6493	SO:0001583	missense	5680	exon2			AGGATCCTGCGTC	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.352G>C	19.37:g.43528921C>G	ENSP00000384995:p.Gly118Arg	310	0	0		359	27	0.0752089	NM_002785	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Missense_Mutation	SNP	ENST00000401740.1	37	CCDS12614.2	.	.	.	.	.	.	.	.	.	.	c	10.99	1.507740	0.27036	.	.	ENSG00000243130	ENST00000320078;ENST00000401740	T;T	0.11821	2.74;2.74	0.929	0.929	0.19449	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.32912	0.0845	M	0.79805	2.47	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.05354	-1.0890	9	0.59425	D	0.04	.	5.2086	0.15304	0.0:1.0:0.0:0.0	.	118	Q9UQ72	PSG11_HUMAN	R	118	ENSP00000319140:G118R;ENSP00000384995:G118R	ENSP00000319140:G118R	G	-	1	0	PSG11	48220761	0.007000	0.16637	0.011000	0.14972	0.029000	0.11900	0.559000	0.23485	0.795000	0.33922	0.184000	0.17185	GGA	.	.	none		0.458	PSG11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323079.1	NM_002785		G	43528921	C	G	43528921	3	3	30	1	0	0	0	0	1	0	0	0	12666	690	24	4	671	4	PSG11	19	43528921	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	2172675	43528921	15600062	640	13791											
PSG2	5670	hgsc.bcm.edu	37	chr19	43575982	43575982	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttttgtcctgattgctgaaaCttcccattaattgtccaaga	10	16	6	9	0	0	3	0	2	0	1	3	3	3	3	3	0	2	1	3	0	3	6	rs150568950	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:43575982C>T	ENST00000406487.1	-	4	932	c.834G>A	c.(832-834)aaG>aaA	p.K278K		NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	278	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)				ATTGCTGAAACTTCCCATTAA	0.448													C|||	3	0.000599042	0.0008	0.0014	5008	,	,		20458	0.0		0.001	False		,,,				2504	0.0				p.K278K		Atlas-SNP	.											PSG2,NS,carcinoma,-1,1	PSG2	84	1	0			c.G834A						PASS	.	C		6,4398	825.3+/-416.5	0,6,2196	190	199	196		834	-1.7	0	19	dbSNP_134	196	32,8566	817.7+/-406.9	0,32,4267	no	coding-synonymous	PSG2	NM_031246.3		0,38,6463	TT,TC,CC		0.3722,0.1362,0.2923		278/336	43575982	38,12964	2202	4299	6501	SO:0001819	synonymous_variant	5670	exon4			CTGAAACTTCCCA		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.834G>A	19.37:g.43575982C>T		249	1	0.00401606		234	108	0.461538	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Silent	SNP	ENST00000406487.1	37	CCDS12616.1																																																																																			C|0.998;T|0.002	0.002	strong		0.448	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246		T	43575982	C	T	43575982	2	4	30	1	0	0	0	0	0	0	0	1	12667	564	20	2		2	PSG2	19	43575982	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	47061	43575982	15553001	641	13792											
ZNF235	9310	hgsc.bcm.edu	37	chr19	44793278	44793278	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctcttgatttgccagcatgAaagctctcccagtgaaaagc	11	11	8	11	0	2	3	0	3	2	0	4	3	2	3	2	0	4	2	2	0	3	2	rs141976678	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:44793278A>G	ENST00000291182.4	-	5	412	c.310T>C	c.(310-312)Tca>Cca	p.S104P	ZNF235_ENST00000589248.1_Intron|ZNF235_ENST00000589799.1_Intron	NM_004234.4	NP_004225.3	Q14590	ZN235_HUMAN	zinc finger protein 235	104					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)				TGCCAGCATGAAAGCTCTCCC	0.418																																					p.S104P		Atlas-SNP	.											.	ZNF235	60	.	0			c.T310C						PASS	.	A	PRO/SER	3,4403	4.2+/-10.8	0,3,2200	56	58	57		310	0.9	0.6	19	dbSNP_134	57	8,8592	4.3+/-15.6	0,8,4292	yes	missense	ZNF235	NM_004234.4	74	0,11,6492	GG,GA,AA		0.093,0.0681,0.0846	benign	104/739	44793278	11,12995	2203	4300	6503	SO:0001583	missense	9310	exon5			AGCATGAAAGCTC	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.310T>C	19.37:g.44793278A>G	ENSP00000291182:p.Ser104Pro	133	0	0		121	62	0.512397	NM_004234	B4DTQ7|O14898|O14899|Q17RR8	Missense_Mutation	SNP	ENST00000291182.4	37	CCDS33048.1	.	.	.	.	.	.	.	.	.	.	A	11.66	1.706086	0.30232	6.81E-4	9.3E-4	ENSG00000159917	ENST00000433015;ENST00000391957;ENST00000291182;ENST00000359844	T	0.05855	3.38	4.18	0.951	0.19579	.	0.487586	0.15465	N	0.260936	T	0.03695	0.0105	N	0.13003	0.285	0.20074	N	0.999938	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.42068	-0.9473	10	0.33940	T	0.23	.	7.7635	0.28965	0.7099:0.0:0.2901:0.0	.	100;104	Q14590-2;Q14590	.;ZN235_HUMAN	P	100;104;104;26	ENSP00000291182:S104P	ENSP00000291182:S104P	S	-	1	0	ZNF235	49485118	0.001000	0.12720	0.635000	0.29338	0.938000	0.57974	0.195000	0.17155	0.279000	0.22186	0.379000	0.24179	TCA	A|0.999;G|0.001	0.001	strong		0.418	ZNF235-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460732.1			G	44793278	A	G	44793278	3	3	30	1	0	0	0	0	1	0	0	0	17803	246	9	3	1910	3	ZNF235	19	44793278	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	1217296	44793278	14335705	642	13793											
ZNF285	26974	hgsc.bcm.edu	37	chr19	44891009	44891009	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgtgaagaacagagctataCgcaaaatcctttccacacac	15	8	7	11	1	0	3	0	1	0	2	2	3	2	3	2	0	3	2	2	0	6	3	rs139913772	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:44891009C>T	ENST00000330997.4	-	4	1462	c.1398G>A	c.(1396-1398)gcG>gcA	p.A466A	ZNF285_ENST00000591679.1_Silent_p.A473A|ZNF285_ENST00000544719.2_Silent_p.A466A|CTC-512J12.6_ENST00000588212.1_Intron	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	466					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						CAGAGCTATACGCAAAATCCT	0.423																																					p.A466A		Atlas-SNP	.											ZNF285,NS,carcinoma,0,2	ZNF285	86	2	0			c.G1398A						PASS	.	T		0,4406		0,0,2203	84	85	85		1398	-6.9	0	19	dbSNP_134	85	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	ZNF285	NM_152354.3		0,8,6495	TT,TC,CC		0.093,0.0,0.0615		466/591	44891009	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	26974	exon4			GCTATACGCAAAA	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.1398G>A	19.37:g.44891009C>T		236	0	0		200	84	0.42	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Silent	SNP	ENST00000330997.4	37	CCDS12638.1																																																																																			C|0.999;T|0.001	0.001	strong		0.423	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354		T	44891009	C	T	44891009	2	4	30	1	0	0	0	0	0	0	0	1	17837	523	19	1		1	ZNF285	19	44891009	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	97731	44891009	14237974	643	13794											
CEACAM20	125931	hgsc.bcm.edu	37	chr19	45024535	45024535	+	RNA	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtcagctcaaggggctcacTccgggcccggctgccccagt	5	6	14	16	2	3	0	3	0	0	0	4	0	4	0	4	5	2	3	4	5	1	0	rs200961907		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:45024535T>C	ENST00000454753.1	-	0	1281							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)				AGGGGCTCACTCCGGGCCCGG	0.592																																					p.S335G		Atlas-SNP	.											.	CEACAM20	31	.	0			c.A1003G						PASS	.		GLY/SER,GLY/SER,GLY/SER,GLY/SER	1,3869		0,1,1934	45	47	46		1003,1003,1003,1003	4.3	0	19		46	7,8257		0,7,4125	yes	missense,missense,missense,missense	CEACAM20	NM_001102597.1,NM_001102598.1,NM_001102599.1,NM_001102600.1	56,56,56,56	0,8,6059	CC,CT,TT		0.0847,0.0258,0.0659	probably-damaging,probably-damaging,probably-damaging,probably-damaging	335/597,335/492,335/504,335/585	45024535	8,12126	1935	4132	6067			125931	exon5			GCTCACTCCGGGC	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		19.37:g.45024535T>C		70	0	0		86	43	0.5	NM_001102600		Missense_Mutation	SNP	ENST00000454753.1	37																																																																																				T|0.996;C|0.004	0.004	weak		0.592	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444		C	45024535	T	C	45024535	1	2	30	0	1	0	0	0	0	0	0	0	3193	1551	54	3		3	CEACAM20	19	45024535	RNA	SNP	T	TCGA-GR-7353-01A-11D-2210-10	133526	45024535	14104448	644	13795											
PVR	5817	hgsc.bcm.edu	37	chr19	45153113	45153113	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	acacagctgaggttcagaagGtccagctcactggagagcca	12	6	12	11	0	2	3	2	1	0	2	3	4	3	3	2	3	3	3	2	3	1	1	rs35959395	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:45153113G>C	ENST00000425690.3	+	3	759	c.460G>C	c.(460-462)Gtc>Ctc	p.V154L	PVR_ENST00000403059.4_Missense_Mutation_p.V154L|PVR_ENST00000406449.4_Missense_Mutation_p.V154L|CTB-171A8.1_ENST00000590796.1_RNA|PVR_ENST00000344956.4_Missense_Mutation_p.V154L	NM_006505.3	NP_006496.3	P15151	PVR_HUMAN	poliovirus receptor	154	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)		GGTTCAGAAGGTCCAGCTCAC	0.602													G|||	6	0.00119808	0.0	0.0	5008	,	,		16803	0.0		0.006	False		,,,				2504	0.0				p.V154L		Atlas-SNP	.											.	PVR	23	.	0			c.G460C						PASS	.	G	LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL	2,4404	4.2+/-10.8	0,2,2201	121	129	126		460,460,460,460	-0.5	0	19	dbSNP_126	126	19,8581	11.9+/-42.8	0,19,4281	yes	missense,missense,missense,missense	PVR	NM_001135768.1,NM_001135769.1,NM_001135770.1,NM_006505.3	32,32,32,32	0,21,6482	CC,CG,GG		0.2209,0.0454,0.1615	probably-damaging,probably-damaging,probably-damaging,probably-damaging	154/373,154/365,154/393,154/418	45153113	21,12985	2203	4300	6503	SO:0001583	missense	5817	exon3			CAGAAGGTCCAGC	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.460G>C	19.37:g.45153113G>C	ENSP00000402060:p.Val154Leu	155	0	0		133	60	0.451128	NM_001135769	B4DTS9|P15152|Q15267|Q15268|Q96BJ1	Missense_Mutation	SNP	ENST00000425690.3	37	CCDS12640.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	15.03	2.712862	0.48517	4.54E-4	0.002209	ENSG00000073008	ENST00000344956;ENST00000425690;ENST00000406449;ENST00000403059	T;T;T;T	0.76316	-1.01;-1.01;-1.01;-1.01	4.35	-0.515	0.11954	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);	1.055660	0.07497	N	0.906707	D	0.86493	0.5946	M	0.90309	3.105	0.09310	N	1	P;D;D;D	0.59767	0.842;0.983;0.983;0.986	P;D;D;D	0.74023	0.698;0.957;0.969;0.982	T	0.70328	-0.4902	10	0.20046	T	0.44	.	4.0615	0.09841	0.3186:0.1848:0.4966:0.0	rs35959395	154;154;154;154	P15151-2;P15151-3;P15151-4;P15151	.;.;.;PVR_HUMAN	L	154	ENSP00000340870:V154L;ENSP00000402060:V154L;ENSP00000383907:V154L;ENSP00000385344:V154L	ENSP00000340870:V154L	V	+	1	0	PVR	49844953	0.005000	0.15991	0.000000	0.03702	0.020000	0.10135	0.802000	0.27069	-0.290000	0.09025	-0.339000	0.08088	GTC	G|0.999;C|0.001	0.001	strong		0.602	PVR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323017.2	NM_006505		C	45153113	G	C	45153113	3	2	30	1	0	0	0	0	1	0	0	0	12852	1261	44	4	470	4	PVR	19	45153113	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	128578	45153113	13975870	645	13796											
CKM	1158	hgsc.bcm.edu	37	chr19	45815163	45815163	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acttccctttgaactcgcccGtcaggctgttgagagctatg	7	12	10	12	2	1	2	1	2	0	1	3	3	2	2	2	1	2	3	2	1	2	4	rs17357122	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:45815163G>A	ENST00000221476.3	-	5	671	c.497C>T	c.(496-498)aCg>aTg	p.T166M		NM_001824.4	NP_001815.2	P06732	KCRM_HUMAN	creatine kinase, muscle	166	Phosphagen kinase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00843}.		T -> M (in dbSNP:rs17357122).		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)	GAACTCGCCCGTCAGGCTGTT	0.597													G|||	14	0.00279553	0.0015	0.0043	5008	,	,		15490	0.0		0.007	False		,,,				2504	0.002				p.T166M		Atlas-SNP	.											.	CKM	40	.	0			c.C497T						PASS	.	G	MET/THR	12,4394	19.1+/-41.9	0,12,2191	77	61	67		497	4.6	1	19	dbSNP_123	67	66,8534	40.8+/-97.7	0,66,4234	yes	missense	CKM	NM_001824.3	81	0,78,6425	AA,AG,GG		0.7674,0.2724,0.5997	possibly-damaging	166/382	45815163	78,12928	2203	4300	6503	SO:0001583	missense	1158	exon5			TCGCCCGTCAGGC	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.497C>T	19.37:g.45815163G>A	ENSP00000221476:p.Thr166Met	189	0	0		152	58	0.381579	NM_001824	Q96QL9	Missense_Mutation	SNP	ENST00000221476.3	37	CCDS12659.1	9	0.004120879120879121	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	g	17.70	3.454039	0.63290	0.002724	0.007674	ENSG00000104879	ENST00000221476	T	0.24151	1.87	4.64	4.64	0.57946	ATP:guanido phosphotransferase, catalytic domain (2);Glutamine synthetase/guanido kinase, catalytic domain (1);	0.255179	0.38959	N	0.001515	T	0.32734	0.0839	M	0.84683	2.71	0.42644	D	0.99342	P	0.49185	0.92	P	0.45998	0.5	T	0.51164	-0.8740	10	0.72032	D	0.01	-36.3443	15.0589	0.71936	0.0:0.0:1.0:0.0	rs17357122;rs52824783;rs17357122	166	P06732	KCRM_HUMAN	M	166	ENSP00000221476:T166M	ENSP00000221476:T166M	T	-	2	0	CKM	50507003	0.984000	0.35163	0.997000	0.53966	0.892000	0.51952	2.104000	0.41815	2.421000	0.82119	0.556000	0.70494	ACG	G|0.995;A|0.005	0.005	strong		0.597	CKM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457569.1			A	45815163	G	A	45815163	3	1	30	1	0	0	0	0	1	0	0	0	3450	1145	40	1	664	1	CKM	19	45815163	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	662050	45815163	13313820	646	13797											
QPCTL	54814	hgsc.bcm.edu	37	chr19	46202131	46202131	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccacttccctcgcacggtcCgctggttccatcggctgagg	4	9	12	16	4	0	1	0	1	0	0	5	1	3	1	4	4	0	4	4	4	0	2	rs145016874	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:46202131C>T	ENST00000012049.5	+	5	1080	c.859C>T	c.(859-861)Cgc>Tgc	p.R287C	QPCTL_ENST00000366382.4_Missense_Mutation_p.R193C	NM_017659.3	NP_060129.2	Q9NXS2	QPCTL_HUMAN	glutaminyl-peptide cyclotransferase-like	287					peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase (GO:0017186)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glutaminyl-peptide cyclotransferase activity (GO:0016603)|zinc ion binding (GO:0008270)			breast(1)|cervix(2)|endometrium(1)|lung(5)|skin(1)|stomach(1)	11		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0059)|GBM - Glioblastoma multiforme(486;0.0882)|Epithelial(262;0.208)		TCGCACGGTCCGCTGGTTCCA	0.617													C|||	3	0.000599042	0.0	0.0	5008	,	,		15872	0.0		0.002	False		,,,				2504	0.001				p.R287C		Atlas-SNP	.											.	QPCTL	24	.	0			c.C859T						PASS	.	C	CYS/ARG,CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	81	80	81		577,859	3.8	1	19	dbSNP_134	81	11,8589	8.4+/-32.0	0,11,4289	yes	missense,missense	QPCTL	NM_001163377.1,NM_017659.3	180,180	0,13,6490	TT,TC,CC		0.1279,0.0454,0.1	probably-damaging,probably-damaging	193/289,287/383	46202131	13,12993	2203	4300	6503	SO:0001583	missense	54814	exon5			ACGGTCCGCTGGT	AK000091	CCDS12672.1, CCDS54282.1	19q13.32	2014-09-04			ENSG00000011478	ENSG00000011478			25952	protein-coding gene	gene with protein product	"glutaminyl cyclase-like"						Standard	NM_017659		Approved	FLJ20084	uc010xxr.2	Q9NXS2	OTTHUMG00000182131	ENST00000012049.5:c.859C>T	19.37:g.46202131C>T	ENSP00000012049:p.Arg287Cys	113	0	0		92	45	0.48913	NM_017659	Q53HE4|Q96F74	Missense_Mutation	SNP	ENST00000012049.5	37	CCDS12672.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	17.33	3.362347	0.61403	4.54E-4	0.001279	ENSG00000011478	ENST00000012049;ENST00000366382	T;T	0.51071	0.72;0.72	5.93	3.83	0.44106	Peptidase M28 (1);	0.342596	0.33772	N	0.004570	T	0.63212	0.2492	M	0.88450	2.955	0.58432	D	0.999993	D	0.71674	0.998	P	0.56700	0.804	T	0.64580	-0.6374	10	0.39692	T	0.17	-1.3625	8.816	0.34996	0.0:0.8542:0.0:0.1458	.	287	Q9NXS2	QPCTL_HUMAN	C	287;193	ENSP00000012049:R287C;ENSP00000387944:R193C	ENSP00000012049:R287C	R	+	1	0	QPCTL	50893971	0.932000	0.31603	0.997000	0.53966	0.627000	0.37826	1.506000	0.35747	2.826000	0.97356	0.655000	0.94253	CGC	C|0.999;T|0.001	0.001	strong		0.617	QPCTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459656.1	NM_017659		T	46202131	C	T	46202131	3	4	30	1	0	0	0	0	1	0	0	0	12890	652	23	1	877	1	QPCTL	19	46202131	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	386968	46202131	12926852	647	13798											
DMPK	1760	hgsc.bcm.edu	37	chr19	46273740	46273740	+	3'UTR	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cccggagtcgaagacagttcTagggttcagggagcgcgggc	8	6	17	10	4	2	1	1	0	1	1	3	4	2	3	1	4	1	2	1	4	2	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:46273740T>C	ENST00000291270.4	-	0	2021				DMPK_ENST00000600757.1_Nonstop_Mutation_p.*636W|SIX5_ENST00000560168.1_5'Flank|DMPK_ENST00000458663.2_Nonstop_Mutation_p.*626W|AC074212.6_ENST00000586251.1_RNA|DMPK_ENST00000354227.5_3'UTR|SIX5_ENST00000317578.6_5'Flank|AC074212.5_ENST00000559756.1_RNA|AC074212.5_ENST00000592217.2_RNA|DMPK_ENST00000447742.2_3'UTR|AC074212.6_ENST00000591530.1_RNA|DMPK_ENST00000343373.4_3'UTR|AC074212.6_ENST00000586498.1_RNA|AC074212.6_ENST00000590076.1_RNA	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)		AAGACAGTTCTAGGGTTCAGG	0.716											OREG0025561	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.X626W	Esophageal Squamous(35;307 869 9153 24033 28903)	Atlas-SNP	.											.	DMPK	74	.	0			c.A1877G						PASS	.						7	8	8					19																	46273740		1840	3549	5389	SO:0001624	3_prime_UTR_variant	1760	exon15			CAGTTCTAGGGTT	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.*6A>G	19.37:g.46273740T>C		157	0	0	938	95	45	0.473684	NM_001081562	E5KR08|Q16205|Q6P5Z6	Missense_Mutation	SNP	ENST00000291270.4	37	CCDS12674.1	.	.	.	.	.	.	.	.	.	.	t	17.91	3.504333	0.64410	.	.	ENSG00000104936	ENST00000458663	.	.	.	4.05	4.05	0.47172	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.3258	0.37993	0.0:0.0:0.0:1.0	.	.	.	.	W	626	.	.	X	-	2	0	DMPK	50965580	1.000000	0.71417	0.967000	0.41034	0.514000	0.34195	1.865000	0.39479	1.712000	0.51347	0.454000	0.30748	TAG	.	.	none		0.716	DMPK-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460572.1	NM_004409		C	46273740	T	C	46273740	1	2	30	0	1	0	0	0	0	0	0	0	4586	1535	53	3		3	DMPK	19	46273740	3'UTR	SNP	T	TCGA-GR-7353-01A-11D-2210-10	71609	46273740	12855243	648	13799											
SAE1	10055	hgsc.bcm.edu	37	chr19	47700542	47700542	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatcccagttctgatacataTgaggaagattctgagttgtt	11	14	10	6	0	2	4	0	3	2	1	3	6	3	5	1	1	1	3	1	1	3	6	rs117605411	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:47700542T>C	ENST00000270225.7	+	7	854	c.786T>C	c.(784-786)taT>taC	p.Y262Y	SAE1_ENST00000392776.3_Intron|SAE1_ENST00000598840.1_Silent_p.Y181Y|SAE1_ENST00000540850.1_Silent_p.Y88Y|SAE1_ENST00000413379.3_Intron	NM_005500.2	NP_005491.1	Q9UBE0	SAE1_HUMAN	SUMO1 activating enzyme subunit 1	262					cellular protein metabolic process (GO:0044267)|positive regulation of catalytic activity (GO:0043085)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)|protein ubiquitination (GO:0016567)|regulation of mitotic cell cycle (GO:0007346)|SMT3-dependent protein catabolic process (GO:0019950)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP-dependent protein binding (GO:0043008)|enzyme activator activity (GO:0008047)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|ubiquitin activating enzyme activity (GO:0004839)			endometrium(3)|large_intestine(5)|lung(4)|ovary(1)	13		all_cancers(25;1.13e-05)|all_lung(116;0.000192)|all_epithelial(76;0.000274)|Lung NSC(112;0.000446)|all_neural(266;0.0652)|Ovarian(192;0.15)		all cancers(93;0.00013)|OV - Ovarian serous cystadenocarcinoma(262;0.000146)|Epithelial(262;0.00697)|GBM - Glioblastoma multiforme(486;0.0278)		CTGATACATATGAGGAAGATT	0.408													T|||	23	0.00459265	0.0	0.0014	5008	,	,		19443	0.001		0.005	False		,,,				2504	0.0164				p.Y262Y		Atlas-SNP	.											.	SAE1	50	.	0			c.T786C						PASS	.	T	,,	9,4397	14.3+/-33.2	0,9,2194	213	193	200		,,786	-4.8	0	19	dbSNP_132	200	27,8573	19.2+/-60.6	0,27,4273	no	intron,intron,coding-synonymous	SAE1	NM_001145713.1,NM_001145714.1,NM_005500.2	,,	0,36,6467	CC,CT,TT		0.314,0.2043,0.2768	,,	,,262/347	47700542	36,12970	2203	4300	6503	SO:0001819	synonymous_variant	10055	exon7			TACATATGAGGAA	BC018271	CCDS12696.1, CCDS54284.1, CCDS54285.1	19q13.32	2013-09-26				ENSG00000142230		"Ubiquitin-like modifier activating enzymes"	30660	protein-coding gene	gene with protein product	"activator Of sumo 1"	613294				10187858, 9920803, 10217437	Standard	NM_005500		Approved	AOS1, FLJ3091, Sua1	uc002pgc.3	Q9UBE0		ENST00000270225.7:c.786T>C	19.37:g.47700542T>C		238	0	0		190	74	0.389474	NM_005500	B2RDP5|B3KMQ2|F5GXX7|G3XAK6|O95717|Q9P020	Silent	SNP	ENST00000270225.7	37	CCDS12696.1																																																																																			T|0.997;C|0.003	0.003	strong		0.408	SAE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466775.1	NM_005500		C	47700542	T	C	47700542	2	2	30	1	0	0	0	0	0	0	0	1	13820	1471	51	3		3	SAE1	19	47700542	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	1426802	47700542	11428441	649	13800											
CCDC9	26093	hgsc.bcm.edu	37	chr19	47774358	47774358	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gtgaccatgatgaccgctggGagacaaaagaaggggcagca	14	4	15	8	1	0	5	0	3	0	2	0	6	0	5	2	3	1	3	2	3	3	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:47774358G>C	ENST00000221922.6	+	11	1327	c.1105G>C	c.(1105-1107)Gag>Cag	p.E369Q		NM_015603.2	NP_056418.1	Q9Y3X0	CCDC9_HUMAN	coiled-coil domain containing 9	369							poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|urinary_tract(1)	12		all_cancers(25;0.0432)|all_epithelial(76;0.00812)|Medulloblastoma(540;0.0208)|all_neural(266;0.0416)|Hepatocellular(1079;0.114)		OV - Ovarian serous cystadenocarcinoma(262;8.51e-95)|Epithelial(262;1.15e-92)|all cancers(93;7.67e-84)|GBM - Glioblastoma multiforme(486;0.024)|STAD - Stomach adenocarcinoma(1328;0.183)		TGACCGCTGGGAGACAAAAGA	0.622																																					p.E369Q		Atlas-SNP	.											.	CCDC9	37	.	0			c.G1105C						PASS	.						35	35	35					19																	47774358		2198	4285	6483	SO:0001583	missense	26093	exon11			CGCTGGGAGACAA	AL050284	CCDS12698.1	19q13.33	2008-02-05				ENSG00000105321			24560	protein-coding gene	gene with protein product						11230166	Standard	NM_015603		Approved	DKFZP586M1019	uc010xym.2	Q9Y3X0		ENST00000221922.6:c.1105G>C	19.37:g.47774358G>C	ENSP00000221922:p.Glu369Gln	150	0	0		145	72	0.496552	NM_015603		Missense_Mutation	SNP	ENST00000221922.6	37	CCDS12698.1	.	.	.	.	.	.	.	.	.	.	.	13.05	2.122654	0.37436	.	.	ENSG00000105321	ENST00000221922;ENST00000504556	T	0.58358	0.34	4.34	4.34	0.51931	.	0.059852	0.64402	D	0.000005	T	0.69043	0.3067	M	0.69823	2.125	0.45025	D	0.998043	D	0.67145	0.996	D	0.75484	0.986	T	0.72080	-0.4398	10	0.62326	D	0.03	-22.8191	12.1997	0.54317	0.0:0.0:1.0:0.0	.	369	Q9Y3X0	CCDC9_HUMAN	Q	369;351	ENSP00000221922:E369Q	ENSP00000221922:E369Q	E	+	1	0	CCDC9	52466198	1.000000	0.71417	1.000000	0.80357	0.463000	0.32649	2.962000	0.49176	2.213000	0.71641	0.305000	0.20034	GAG	.	.	none		0.622	CCDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466917.1	NM_015603		C	47774358	G	C	47774358	3	2	30	1	0	0	0	0	1	0	0	0	2869	1175	41	4	1143	4	CCDC9	19	47774358	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	73816	47774358	11354625	650	13801											
SYNGR4	23546	hgsc.bcm.edu	37	chr19	48879375	48879375	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acctggcattccaggacctcCgaaatgatgctccagtccct	9	9	8	15	1	0	1	0	1	0	0	4	3	4	2	6	2	1	2	6	2	1	1			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:48879375C>T	ENST00000344846.2	+	5	755	c.505C>T	c.(505-507)Cga>Tga	p.R169*	SYNGR4_ENST00000601610.1_Missense_Mutation_p.P145L|SYNGR4_ENST00000595322.1_Missense_Mutation_p.P73L	NM_012451.3	NP_036583.2	O95473	SNG4_HUMAN	synaptogyrin 4	169	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.					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)		CCAGGACCTCCGAAATGATGC	0.602																																					p.R169X		Atlas-SNP	.											SYNGR4,NS,carcinoma,-2,3	SYNGR4	31	3	0			c.C505T						PASS	.						104	98	100					19																	48879375		2203	4300	6503	SO:0001587	stop_gained	23546	exon5			GACCTCCGAAATG	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.505C>T	19.37:g.48879375C>T	ENSP00000344041:p.Arg169*	147	0	0		147	38	0.258503	NM_012451	Q3KP58	Nonsense_Mutation	SNP	ENST00000344846.2	37	CCDS12717.1	.	.	.	.	.	.	.	.	.	.	C	36	5.676643	0.96764	.	.	ENSG00000105467	ENST00000344846	.	.	.	5.61	4.55	0.56014	.	0.948152	0.08692	N	0.907770	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.6799	7.5531	0.27808	0.1663:0.7504:0.0:0.0833	.	.	.	.	X	169	.	ENSP00000344041:R169X	R	+	1	2	SYNGR4	53571187	0.522000	0.26266	0.855000	0.33649	0.846000	0.48090	0.827000	0.27421	1.480000	0.48289	0.555000	0.69702	CGA	.	.	none		0.602	SYNGR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465704.1			T	48879375	C	T	48879375	4	4	30	1	0	0	0	0	0	1	0	0	15466	644	23	1	519	1	SYNGR4	19	48879375	Nonsense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1105017	48879375	10249608	651	13802											
GRIN2D	2906	hgsc.bcm.edu	37	chr19	48945044	48945044	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggaagctggacgccttcatCtacgatgctgcagtgctcaa	10	9	11	11	2	3	0	2	0	1	0	3	3	3	2	1	2	5	4	1	2	3	2	rs144676582	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:48945044C>T	ENST00000263269.3	+	11	2359	c.2271C>T	c.(2269-2271)atC>atT	p.I757I		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	757					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)	ACGCCTTCATCTACGATGCTG	0.617													C|||	6	0.00119808	0.0	0.0058	5008	,	,		20158	0.0		0.002	False		,,,				2504	0.0				p.I757I		Atlas-SNP	.											.	GRIN2D	76	.	0			c.C2271T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	55	46	49		2271	2.5	1	19	dbSNP_134	49	29,8571	19.2+/-60.6	0,29,4271	no	coding-synonymous	GRIN2D	NM_000836.2		0,31,6472	TT,TC,CC		0.3372,0.0454,0.2384		757/1337	48945044	31,12975	2203	4300	6503	SO:0001819	synonymous_variant	2906	exon11			CTTCATCTACGAT	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.2271C>T	19.37:g.48945044C>T		120	0	0		102	48	0.470588	NM_000836		Silent	SNP	ENST00000263269.3	37	CCDS12719.1																																																																																			C|0.998;T|0.002	0.002	strong		0.617	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1			T	48945044	C	T	48945044	2	4	30	1	0	0	0	0	0	0	0	1	6791	903	32	2		2	GRIN2D	19	48945044	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	65669	48945044	10183939	652	13803											
SULT2B1	6820	hgsc.bcm.edu	37	chr19	49102605	49102610	+	In_Frame_Del	DEL	CCAGCC	CCAGCC	-																															gcgtgagcccagacccaactCcagccccagccccagccccg																								rs16989366|rs535907004		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	CCAGCC	CCAGCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:49102605_49102610delCCAGCC	ENST00000201586.2	+	7	1218_1223	c.1040_1045delCCAGCC	c.(1039-1047)tccagcccc>tcc	p.SP352del	SULT2B1_ENST00000323090.4_In_Frame_Del_p.SP337del	NM_177973.1	NP_814444.1	O00204	ST2B1_HUMAN	sulfotransferase family, cytosolic, 2B, member 1	352	Pro/Ser-rich.				3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	alcohol sulfotransferase activity (GO:0004027)|steroid sulfotransferase activity (GO:0050294)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|skin(2)|urinary_tract(1)	11		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;0.000115)|all cancers(93;0.000147)|GBM - Glioblastoma multiforme(486;0.00707)|Epithelial(262;0.0178)		agacccaactccagccccagccccag	0.66																																					p.347_348del		Pindel,Atlas-Indel	.											.	SULT2B1	72	.	0			c.1039_1044del						PASS	.		,	1,4133		0,1,2066					,	-3.9	0		dbSNP_126	21	16,8050		0,16,4017	no	coding,coding	SULT2B1	NM_177973.1,NM_004605.2	,	0,17,6083	A1A1,A1R,RR		0.1984,0.0242,0.1393	,	,		17,12183				SO:0001651	inframe_deletion	6820	exon7			.	U92314	CCDS12723.1, CCDS12724.1	19q13.3	2008-02-05				ENSG00000088002		"Sulfotransferases, cytosolic"	11459	protein-coding gene	gene with protein product		604125				9799594	Standard	NM_177973		Approved	HSST2	uc002pjl.3	O00204		ENST00000201586.2:c.1040_1045delCCAGCC	19.37:g.49102611_49102616delCCAGCC	ENSP00000201586:p.Ser352_Pro353del	244	0	.		203	38	0.187	NM_177973	O00205|O75814	In_Frame_Del	DEL	ENST00000201586.2	37	CCDS12723.1																																																																																			.	.	none		0.66	SULT2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466140.1	NM_004605		-	49102610	CCAGCC	-	49102605	7	5	30	1	0	1	0	1	0	0	0	0	15397	855	30	0	1092	0	SULT2B1	19	49102605	In_Frame_Del	DEL	CCAGCC	TCGA-GR-7353-01A-11D-2210-10	157561	49102605	10026378	653	13804											
SCAF1	58506	hgsc.bcm.edu	37	chr19	50154607	50154607	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcccaggtgacgagagccccCgcccggacgcgcagcccaca	8	2	12	19	5	0	2	0	1	0	1	1	4	1	3	5	2	2	1	5	2	0	0	rs146455893	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:50154607C>T	ENST00000360565.3	+	7	1085	c.961C>T	c.(961-963)Cgc>Tgc	p.R321C		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	321					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)		CGAGAGCCCCCGCCCGGACGC	0.697																																					p.R321C		Atlas-SNP	.											.	SCAF1	78	.	0			c.C961T						PASS	.	C	CYS/ARG	2,4400		0,2,2199	18	19	19		961	0.7	0.2	19	dbSNP_134	19	5,8591		0,5,4293	no	missense	SCAF1	NM_021228.2	180	0,7,6492	TT,TC,CC		0.0582,0.0454,0.0539	possibly-damaging	321/1313	50154607	7,12991	2201	4298	6499	SO:0001583	missense	58506	exon7			AGCCCCCGCCCGG	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.961C>T	19.37:g.50154607C>T	ENSP00000353769:p.Arg321Cys	20	0	0		19	16	0.842105	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Missense_Mutation	SNP	ENST00000360565.3	37	CCDS33074.1	.	.	.	.	.	.	.	.	.	.	C	14.64	2.595518	0.46318	4.54E-4	5.82E-4	ENSG00000126461	ENST00000360565	T	0.34275	1.37	4.47	0.683	0.17998	.	1.130880	0.06849	N	0.797016	T	0.19685	0.0473	N	0.08118	0	0.09310	N	0.999999	P	0.44281	0.831	B	0.36186	0.219	T	0.23547	-1.0185	9	.	.	.	-2.8823	14.2469	0.65995	0.0:0.4311:0.5689:0.0	.	321	Q9H7N4	SFR19_HUMAN	C	321	ENSP00000353769:R321C	.	R	+	1	0	SCAF1	54846419	0.000000	0.05858	0.200000	0.23457	0.964000	0.63967	-0.197000	0.09518	0.401000	0.25424	0.591000	0.81541	CGC	A|0.000;C|0.999;T|0.001	0.001	strong		0.697	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228		T	50154607	C	T	50154607	3	4	30	1	0	0	0	0	1	0	0	0	13883	652	23	1	983	1	SCAF1	19	50154607	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1052002	50154607	8974376	654	13805											
PNKP	11284	hgsc.bcm.edu	37	chr19	50364914	50364914	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggcggtgaagaggaagcagCggcaggggacgcccgcggct	8	3	20	10	5	0	2	0	1	0	1	0	4	0	4	1	7	2	3	1	7	2	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:50364914C>T	ENST00000322344.3	-	15	1446	c.1337G>A	c.(1336-1338)cGc>cAc	p.R446H	PNKP_ENST00000600573.1_Missense_Mutation_p.R415H|AC018766.5_ENST00000601893.1_RNA|PNKP_ENST00000596014.1_Missense_Mutation_p.R446H|AC018766.5_ENST00000599259.1_RNA|PNKP_ENST00000600910.1_Silent_p.P409P|AC018766.5_ENST00000593654.1_RNA|AC018766.4_ENST00000596624.1_RNA	NM_007254.3	NP_009185.2	Q96T60	PNKP_HUMAN	polynucleotide kinase 3'-phosphatase	446	Kinase. {ECO:0000250}.				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)		GAGGAAGCAGCGGCAGGGGAC	0.741								Other BER factors																													p.R446H		Atlas-SNP	.											.	PNKP	71	.	0			c.G1337A						PASS	.						4	8	7					19																	50364914		1965	3897	5862	SO:0001583	missense	11284	exon15			AAGCAGCGGCAGG	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.1337G>A	19.37:g.50364914C>T	ENSP00000323511:p.Arg446His	25	0	0		24	4	0.166667	NM_007254	Q9BUL2|Q9P1V2|Q9UKU8|Q9UNF8|Q9UNI0	Missense_Mutation	SNP	ENST00000322344.3	37	CCDS12783.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.885414	0.91814	.	.	ENSG00000039650	ENST00000322344	T	0.48201	0.82	3.96	3.96	0.45880	.	0.000000	0.64402	D	0.000003	T	0.66626	0.2808	M	0.77313	2.365	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.69435	-0.5146	10	0.54805	T	0.06	-17.9148	11.6883	0.51499	0.0:1.0:0.0:0.0	.	407;446	Q9BUL2;Q96T60	.;PNKP_HUMAN	H	446	ENSP00000323511:R446H	ENSP00000323511:R446H	R	-	2	0	PNKP	55056726	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	3.989000	0.56958	2.226000	0.72624	0.557000	0.71058	CGC	.	.	none		0.741	PNKP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465830.1	NM_007254		T	50364914	C	T	50364914	3	4	30	1	0	0	0	0	1	0	0	0	12156	768	27	1	240	1	PNKP	19	50364914	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	210307	50364914	8764069	655	13806											
MYBPC2	4606	hgsc.bcm.edu	37	chr19	50944294	50944294	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acctccggggcatgctgaagCggctgaaaaaggctaaggtc	11	6	14	10	2	0	2	0	2	0	0	2	2	1	2	2	5	2	4	2	5	4	1	rs374005339		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:50944294C>T	ENST00000357701.5	+	8	781	c.730C>T	c.(730-732)Cgg>Tgg	p.R244W		NM_004533.3	NP_004524.3	Q14324	MYPC2_HUMAN	myosin binding protein C, fast type	244					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)		CATGCTGAAGCGGCTGAAAAA	0.602																																					p.R244W		Atlas-SNP	.											.	MYBPC2	103	.	0			c.C730T						PASS	.		TRP/ARG	1,4181		0,1,2090	32	34	34		730	2.2	1	19		34	1,8491		0,1,4245	no	missense	MYBPC2	NM_004533.3	101	0,2,6335	TT,TC,CC		0.0118,0.0239,0.0158	probably-damaging	244/1142	50944294	2,12672	2091	4246	6337	SO:0001583	missense	4606	exon8			CTGAAGCGGCTGA		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.730C>T	19.37:g.50944294C>T	ENSP00000350332:p.Arg244Trp	178	0	0		203	12	0.0591133	NM_004533	A1L4G9	Missense_Mutation	SNP	ENST00000357701.5	37	CCDS46152.1	.	.	.	.	.	.	.	.	.	.	.	15.42	2.829530	0.50845	2.39E-4	1.18E-4	ENSG00000086967	ENST00000357701	T	0.59638	0.25	3.33	2.23	0.28157	.	0.000000	0.33477	U	0.004875	T	0.69975	0.3171	M	0.66297	2.02	0.35743	D	0.818838	D	0.89917	1.0	D	0.97110	1.0	T	0.76391	-0.2976	10	0.66056	D	0.02	.	9.7381	0.40401	0.368:0.632:0.0:0.0	.	244	Q14324	MYPC2_HUMAN	W	244	ENSP00000350332:R244W	ENSP00000350332:R244W	R	+	1	2	MYBPC2	55636106	1.000000	0.71417	0.999000	0.59377	0.797000	0.45037	1.612000	0.36889	0.910000	0.36722	0.298000	0.19748	CGG	.	.	weak		0.602	MYBPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464751.1	NM_004533		T	50944294	C	T	50944294	3	4	30	1	0	0	0	0	1	0	0	0	10021	759	27	1	760	1	MYBPC2	19	50944294	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	579380	50944294	8184689	656	13807											
LRRC4B	94030	hgsc.bcm.edu	37	chr19	51051935	51051935	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aggccacggggcaggaggtgGccggcggggagccccctccg	5	2	20	14	4	0	0	0	0	0	0	1	2	1	2	5	9	1	1	5	9	0	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:51051935G>A	ENST00000599957.1	-	2	358	c.161C>T	c.(160-162)gCc>gTc	p.A54V	LRRC4B_ENST00000389201.3_Missense_Mutation_p.A54V			Q9NT99	LRC4B_HUMAN	leucine rich repeat containing 4B	54	LRRNT.				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)		GCAGGAGGTGGCCGGCGGGGA	0.716																																					p.A54V		Atlas-SNP	.											.	LRRC4B	89	.	0			c.C161T						PASS	.						5	7	6					19																	51051935		1891	4047	5938	SO:0001583	missense	94030	exon2			GAGGTGGCCGGCG	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.161C>T	19.37:g.51051935G>A	ENSP00000471502:p.Ala54Val	38	0	0		33	19	0.575758	NM_001080457	Q3ZCQ4|Q58F20	Missense_Mutation	SNP	ENST00000599957.1	37	CCDS42595.1	.	.	.	.	.	.	.	.	.	.	G	18.91	3.724144	0.68959	.	.	ENSG00000131409	ENST00000389201;ENST00000535879	T	0.44083	0.93	3.66	2.57	0.30868	.	0.000000	0.56097	U	0.000023	T	0.35393	0.0930	M	0.68317	2.08	0.40088	D	0.976213	B	0.29432	0.244	B	0.18871	0.023	T	0.19224	-1.0312	10	0.33940	T	0.23	.	8.9339	0.35688	0.0:0.229:0.771:0.0	.	54	Q9NT99	LRC4B_HUMAN	V	54	ENSP00000373853:A54V	ENSP00000373853:A54V	A	-	2	0	LRRC4B	55743747	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	4.242000	0.58714	0.830000	0.34757	0.544000	0.68410	GCC	.	.	none		0.716	LRRC4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464907.1	NM_001080457		A	51051935	G	A	51051935	3	1	30	1	0	0	0	0	1	0	0	0	9016	1203	42	2	1988	2	LRRC4B	19	51051935	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	107641	51051935	8077048	657	13808											
FPR3	2359	hgsc.bcm.edu	37	chr19	52327479	52327479	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccatagtccttaccttaccaAatttcatcttctggactaca	11	14	3	13	0	3	0	1	0	2	0	4	1	4	1	4	1	3	0	4	1	5	6			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:52327479A>T	ENST00000339223.4	+	2	657	c.478A>T	c.(478-480)Aat>Tat	p.N160Y	FPR3_ENST00000595991.1_Missense_Mutation_p.N160Y	NM_002030.3	NP_002021.3	P25089	FPR3_HUMAN	formyl peptide receptor 3	160					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						TACCTTACCAAATTTCATCTT	0.478																																					p.N160Y		Atlas-SNP	.											.	FPR3	66	.	0			c.A478T						PASS	.						134	122	126					19																	52327479		2203	4300	6503	SO:0001583	missense	2359	exon2			TTACCAAATTTCA		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.478A>T	19.37:g.52327479A>T	ENSP00000341821:p.Asn160Tyr	258	0	0		243	97	0.399177	NM_002030		Missense_Mutation	SNP	ENST00000339223.4	37	CCDS12841.1	.	.	.	.	.	.	.	.	.	.	.	0	-2.601169	0.00123	.	.	ENSG00000187474	ENST00000339223	T	0.36520	1.25	2.34	-4.67	0.03319	GPCR, rhodopsin-like superfamily (1);	0.726121	0.12818	N	0.436647	T	0.08268	0.0206	N	0.00926	-1.1	0.09310	N	1	B	0.06786	0.001	B	0.16722	0.016	T	0.19712	-1.0297	10	0.02654	T	1	.	6.9341	0.24457	0.6963:0.0:0.1696:0.1341	.	160	P25089	FPR3_HUMAN	Y	160	ENSP00000341821:N160Y	ENSP00000341821:N160Y	N	+	1	0	FPR3	57019291	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.708000	0.05035	-1.822000	0.01211	-1.486000	0.00981	AAT	.	.	none		0.478	FPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466914.1	NM_002030		T	52327479	A	T	52327479	3	4	30	1	0	0	0	0	1	0	0	0	6048	14	1	5	480	5	FPR3	19	52327479	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	1275544	52327479	6801504	658	13809											
VN1R2	317701	hgsc.bcm.edu	37	chr19	53761857	53761857	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttatttctacactctcttGtctctgcacacggagagaaa	10	14	6	11	1	3	1	0	0	3	1	5	3	3	2	0	1	2	1	0	1	3	5	rs112986288	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:53761857G>T	ENST00000341702.3	+	1	313	c.229G>T	c.(229-231)Gtc>Ttc	p.V77F		NM_173856.2	NP_776255.2	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	77					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)		acactctcttgtctctgcaca	0.483													G|||	37	0.00738818	0.0	0.0072	5008	,	,		16666	0.0		0.0139	False		,,,				2504	0.0184				p.V77F		Atlas-SNP	.											.	VN1R2	71	.	0			c.G229T						PASS	.	G	PHE/VAL	8,4376		0,8,2184	35	35	35		229	0.1	0	19	dbSNP_132	35	78,8498		1,76,4211	no	missense	VN1R2	NM_173856.2	50	1,84,6395	TT,TG,GG		0.9095,0.1825,0.6636	benign	77/396	53761857	86,12874	2192	4288	6480	SO:0001583	missense	317701	exon1			TCTCTTGTCTCTG	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.229G>T	19.37:g.53761857G>T	ENSP00000351244:p.Val77Phe	65	0	0		55	22	0.4	NM_173856	A1L411|Q8TDU4	Missense_Mutation	SNP	ENST00000341702.3	37	CCDS12862.1	13	0.005952380952380952	0	0.0	4	0.011049723756906077	0	0.0	9	0.011873350923482849	G	5.291	0.239112	0.10023	0.001825	0.009095	ENSG00000196131	ENST00000341702	T	0.10192	2.9	0.0465	0.0465	0.14256	.	.	.	.	.	T	0.02929	0.0087	N	0.08118	0	0.09310	N	1	B	0.25169	0.119	B	0.12837	0.008	T	0.38001	-0.9681	9	0.72032	D	0.01	.	2.6651	0.05041	0.4852:0.0:0.5147:0.0	.	77	Q8NFZ6	VN1R2_HUMAN	F	77	ENSP00000351244:V77F	ENSP00000351244:V77F	V	+	1	0	VN1R2	58453669	0.000000	0.05858	0.022000	0.16811	0.022000	0.10575	-1.105000	0.03323	0.132000	0.18615	0.134000	0.15878	GTC	G|0.994;T|0.006	0.006	strong		0.483	VN1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464285.1	NM_173856		T	53761857	G	T	53761857	3	4	30	1	0	0	0	0	1	0	0	0	17194	1377	48	4	231	4	VN1R2	19	53761857	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1434378	53761857	5367126	659	13810											
ZNF845	91664	hgsc.bcm.edu	37	chr19	53856776	53856776	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaagtgtaatgaatgtggcAaggtttttaatcgaaaagca	16	11	10	4	1	0	1	0	1	0	0	1	2	0	1	0	2	1	4	0	2	7	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:53856776A>G	ENST00000595091.1	+	5	3067	c.2848A>G	c.(2848-2850)Aag>Gag	p.K950E	ZNF845_ENST00000458035.1_Missense_Mutation_p.K950E			Q96IR2	ZN845_HUMAN	zinc finger protein 845	950					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						TGAATGTGGCAAGGTTTTTAA	0.343																																					p.K950E		Atlas-SNP	.											.	ZNF845	101	.	0			c.A2848G						PASS	.						26	24	25					19																	53856776		692	1589	2281	SO:0001583	missense	91664	exon4			TGTGGCAAGGTTT	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.2848A>G	19.37:g.53856776A>G	ENSP00000470005:p.Lys950Glu	145	0	0		156	7	0.0448718	NM_138374		Missense_Mutation	SNP	ENST00000595091.1	37	CCDS46170.1	.	.	.	.	.	.	.	.	.	.	A	12.64	1.999115	0.35226	.	.	ENSG00000213799	ENST00000458035;ENST00000427984	T	0.27104	1.69	2.04	2.04	0.26737	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.27933	0.0688	M	0.71036	2.16	0.21802	N	0.999532	B	0.02656	0.0	B	0.06405	0.002	T	0.25984	-1.0116	9	0.62326	D	0.03	.	8.7997	0.34901	1.0:0.0:0.0:0.0	.	950	Q96IR2	ZN845_HUMAN	E	950;866	ENSP00000388311:K950E	ENSP00000412086:K866E	K	+	1	0	ZNF845	58548588	0.001000	0.12720	0.001000	0.08648	0.060000	0.15804	1.472000	0.35376	0.918000	0.36919	0.338000	0.21704	AAG	.	.	none		0.343	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908		G	53856776	A	G	53856776	3	3	30	1	0	0	0	0	1	0	0	0	18206	131	5	3	2858	3	ZNF845	19	53856776	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	94919	53856776	5272207	660	13811											
LILRA4	23547	hgsc.bcm.edu	37	chr19	54848144	54848144	+	Missense_Mutation	SNP	T	T	A																															gctccaggggctcactggggTgagacagcaggtaggggttg																								rs74869671	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:54848144T>A	ENST00000291759.4	-	6	1279	c.1223A>T	c.(1222-1224)cAc>cTc	p.H408L	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	408	Ig-like C2-type 4.				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)		CTCACTGGGGTGAGACAGCAG	0.592													T|||	74	0.0147764	0.0333	0.0014	5008	,	,		17775	0.0		0.001	False		,,,				2504	0.0286				p.H408L		Atlas-SNP	.											.	LILRA4	91	.	0			c.A1223T						PASS	.	T	LEU/HIS	1,4405		0,1,2202	111	91	98		1223	-1.7	0	19	dbSNP_131	98	1,8599		0,1,4299	no	missense	LILRA4	NM_012276.3	99	0,2,6501	AA,AT,TT		0.0116,0.0227,0.0154	benign	408/500	54848144	2,13004	2203	4300	6503	SO:0001583	missense	23547	exon6			CTGGGGTGAGACA	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.1223A>T	19.37:g.54848144T>A	ENSP00000291759:p.His408Leu	233	0	0		179	18	0.100559	NM_012276	Q32MC4	Missense_Mutation	SNP	ENST00000291759.4	37	CCDS12890.1	.	.	.	.	.	.	.	.	.	.	.	5.063	0.197370	0.09599	2.27E-4	1.16E-4	ENSG00000239961	ENST00000291759	T	0.00691	5.84	2.4	-1.74	0.08056	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	3.662820	0.00932	N	0.002721	T	0.00754	0.0025	L	0.35414	1.06	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.49437	-0.8940	10	0.17832	T	0.49	.	3.0817	0.06265	0.4319:0.0:0.22:0.3481	.	408	P59901	LIRA4_HUMAN	L	408	ENSP00000291759:H408L	ENSP00000291759:H408L	H	-	2	0	LILRA4	59539956	0.000000	0.05858	0.001000	0.08648	0.029000	0.11900	-2.031000	0.01427	-0.517000	0.06461	-0.714000	0.03626	CAC	T|0.995;A|0.005	0.005	strong		0.592	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276		A	54848144	T	A	54848144	3	1	30	1	0	0	0	0	1	0	0	0	8796	1696	59	5	288	5	LILRA4	19	54848144	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	991368	54848144	4280839	661	13812	171	2									
LILRA4	23547	hgsc.bcm.edu	37	chr19	54848145	54848145	+	Missense_Mutation	SNP	G	G	A																															ctccaggggctcactggggtGagacagcaggtaggggttgg																								rs75547479	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:54848145G>A	ENST00000291759.4	-	6	1278	c.1222C>T	c.(1222-1224)Cac>Tac	p.H408Y	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	408	Ig-like C2-type 4.				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)		TCACTGGGGTGAGACAGCAGG	0.592													G|||	74	0.0147764	0.0333	0.0014	5008	,	,		17303	0.0		0.001	False		,,,				2504	0.0286				p.H408Y		Atlas-SNP	.											.	LILRA4	91	.	0			c.C1222T						PASS	.						112	91	98					19																	54848145		2203	4300	6503	SO:0001583	missense	23547	exon6			TGGGGTGAGACAG	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.1222C>T	19.37:g.54848145G>A	ENSP00000291759:p.His408Tyr	235	0	0		182	19	0.104396	NM_012276	Q32MC4	Missense_Mutation	SNP	ENST00000291759.4	37	CCDS12890.1	.	.	.	.	.	.	.	.	.	.	.	6.455	0.452105	0.12283	.	.	ENSG00000239961	ENST00000291759	T	0.00724	5.78	2.4	0.177	0.15054	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	3.662820	0.00932	N	0.002721	T	0.01523	0.0049	M	0.81341	2.54	0.09310	N	1	B	0.14438	0.01	B	0.09377	0.004	T	0.56056	-0.8042	10	0.20519	T	0.43	.	4.4089	0.11423	0.3496:0.0:0.6504:0.0	.	408	P59901	LIRA4_HUMAN	Y	408	ENSP00000291759:H408Y	ENSP00000291759:H408Y	H	-	1	0	LILRA4	59539957	0.000000	0.05858	0.008000	0.14137	0.035000	0.12851	-1.057000	0.03486	0.109000	0.17891	0.455000	0.32223	CAC	A|0.005;G|0.995	0.005	strong		0.592	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276		A	54848145	G	A	54848145	3	1	30	1	0	0	0	0	1	0	0	0	8796	1290	45	2	289	2	LILRA4	19	54848145	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1	54848145	4280838	662	13813	171	2									
LILRA4	23547	hgsc.bcm.edu	37	chr19	54848826	54848826	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggggctgccggccagggCgctgggggaggccatcggcc	3	4	20	14	3	0	0	0	0	0	0	1	1	0	1	5	8	1	2	5	8	0	0	rs145556773	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:54848826C>T	ENST00000291759.4	-	5	853	c.797G>A	c.(796-798)cGc>cAc	p.R266H	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	266	Ig-like C2-type 3.				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)		CCGGCCAGGGCGCTGGGGGAG	0.657													C|||	7	0.00139776	0.0	0.0029	5008	,	,		12832	0.0		0.005	False		,,,				2504	0.0				p.R266H		Atlas-SNP	.											.	LILRA4	91	.	0			c.G797A						PASS	.	C	HIS/ARG	1,4403		0,1,2201	22	24	23		797	-5	0	19	dbSNP_134	23	56,8542		0,56,4243	yes	missense	LILRA4	NM_012276.3	29	0,57,6444	TT,TC,CC		0.6513,0.0227,0.4384	benign	266/500	54848826	57,12945	2202	4299	6501	SO:0001583	missense	23547	exon5			CCAGGGCGCTGGG	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.797G>A	19.37:g.54848826C>T	ENSP00000291759:p.Arg266His	205	0	0		175	95	0.542857	NM_012276	Q32MC4	Missense_Mutation	SNP	ENST00000291759.4	37	CCDS12890.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	.	0.012	-1.661083	0.00772	2.27E-4	0.006513	ENSG00000239961	ENST00000291759	T	0.12879	2.64	2.51	-5.02	0.02982	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	2.356960	0.01819	N	0.033919	T	0.07593	0.0191	L	0.46157	1.445	0.09310	N	1	B	0.12630	0.006	B	0.18561	0.022	T	0.26326	-1.0106	10	0.18710	T	0.47	.	3.0012	0.06015	0.1276:0.1549:0.1272:0.5903	.	266	P59901	LIRA4_HUMAN	H	266	ENSP00000291759:R266H	ENSP00000291759:R266H	R	-	2	0	LILRA4	59540638	0.000000	0.05858	0.000000	0.03702	0.041000	0.13682	-2.350000	0.01092	-2.651000	0.00424	-0.391000	0.06502	CGC	C|0.997;T|0.003	0.003	strong		0.657	LILRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140229.2	NM_012276		T	54848826	C	T	54848826	3	4	30	1	0	0	0	0	1	0	0	0	8796	768	27	1	718	1	LILRA4	19	54848826	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	681	54848826	4280157	663	13814											
U2AF2	11338	hgsc.bcm.edu	37	chr19	56181019	56181019	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gtcaagtccatcgagatcccCcggcctgtggacggcgtcga	7	7	13	14	5	1	1	1	0	0	1	5	4	3	2	4	3	0	0	4	3	1	0	rs147666260	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr19:56181019C>T	ENST00000308924.4	+	11	1294	c.1254C>T	c.(1252-1254)ccC>ccT	p.P418P	U2AF2_ENST00000590551.1_Silent_p.P250P|CTD-2537I9.12_ENST00000585940.1_RNA|CTD-2537I9.12_ENST00000589456.1_RNA|CTD-2537I9.13_ENST00000592252.1_RNA|U2AF2_ENST00000450554.2_Silent_p.P414P			P26368	U2AF2_HUMAN	U2 small nuclear RNA auxiliary factor 2	418	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)			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)		TCGAGATCCCCCGGCCTGTGG	0.657													C|||	15	0.00299521	0.0	0.0101	5008	,	,		16186	0.0		0.008	False		,,,				2504	0.0				p.P418P		Atlas-SNP	.											.	U2AF2	62	.	0			c.C1254T						PASS	.	C	,	9,4397	15.5+/-35.6	0,9,2194	123	111	115		1242,1254	-0.6	1	19	dbSNP_134	115	87,8513	48.5+/-108.0	1,85,4214	no	coding-synonymous,coding-synonymous	U2AF2	NM_001012478.1,NM_007279.2	,	1,94,6408	TT,TC,CC		1.0116,0.2043,0.7381	,	414/472,418/476	56181019	96,12910	2203	4300	6503	SO:0001819	synonymous_variant	11338	exon11			GATCCCCCGGCCT	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.1254C>T	19.37:g.56181019C>T		151	0	0		162	81	0.5	NM_007279	Q96HC5	Silent	SNP	ENST00000308924.4	37	CCDS12933.1																																																																																			C|0.994;T|0.006	0.006	strong		0.657	U2AF2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453599.1	NM_007279		T	56181019	C	T	56181019	2	4	30	1	0	0	0	0	0	0	0	1	16838	610	22	2		2	U2AF2	19	56181019	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1332193	56181019	2947964	664	13815											
FERMT1	55612	hgsc.bcm.edu	37	chr20	6078246	6078246	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agaatggcccacctggcttgCtcatagagttggtttattcg	8	13	11	9	1	1	2	1	0	0	2	2	2	1	2	2	3	1	4	2	3	3	6	rs149893089		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:6078246C>T	ENST00000217289.4	-	7	1670	c.882G>A	c.(880-882)gaG>gaA	p.E294E	FERMT1_ENST00000536936.1_Silent_p.E37E	NM_017671.4	NP_060141.3	Q9BQL6	FERM1_HUMAN	fermitin family member 1	294	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						ACCTGGCTTGCTCATAGAGTT	0.393													T|||	1	0.000199681	0.0	0.0	5008	,	,		15796	0.0		0.0	False		,,,				2504	0.001				p.E294E		Atlas-SNP	.											.	FERMT1	106	.	0			c.G882A						PASS	.	T		1,4405	826.1+/-416.6	0,1,2202	143	135	138		882	0.8	1	20	dbSNP_134	138	5,8595	819.0+/-406.8	0,5,4295	no	coding-synonymous	FERMT1	NM_017671.4		0,6,6497	TT,TC,CC		0.0581,0.0227,0.0461		294/678	6078246	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	55612	exon7			GGCTTGCTCATAG	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.882G>A	20.37:g.6078246C>T		159	0	0		157	74	0.471338	NM_017671	D3DW10|Q8IX34|Q8IYH2|Q9NWM2|Q9NXQ3	Silent	SNP	ENST00000217289.4	37	CCDS13098.1																																																																																			C|0.999;T|0.001	0.001	strong		0.393	FERMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077908.2	NM_017671		T	6078246	C	T	6078246	2	4	30	1	0	0	0	0	0	0	0	1	5825	796	28	2		2	FERMT1	20	6078246	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10		6078246	56947274	665	13816											
PAK7	57144	hgsc.bcm.edu	37	chr20	9523244	9523244	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gtttctcaccttgtgtaggtCcttcactcttggaggtaaac	7	15	9	10	0	3	0	2	0	2	0	5	1	4	1	2	3	1	3	2	3	3	6	rs150828790	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:9523244C>T	ENST00000378429.3	-	10	2539	c.1993G>A	c.(1993-1995)Gac>Aac	p.D665N	PAK7_ENST00000378423.1_Missense_Mutation_p.D665N|PAK7_ENST00000353224.5_Missense_Mutation_p.D665N	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	665	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)			TTGTGTAGGTCCTTCACTCTT	0.478													C|||	3	0.000599042	0.0008	0.0	5008	,	,		20256	0.0		0.002	False		,,,				2504	0.0				p.D665N		Atlas-SNP	.											.	PAK7	194	.	0			c.G1993A						PASS	.	C	ASN/ASP,ASN/ASP	0,4406		0,0,2203	156	158	157		1993,1993	5.5	1	20	dbSNP_134	157	18,8582	13.3+/-46.6	0,18,4282	yes	missense,missense	PAK7	NM_020341.3,NM_177990.2	23,23	0,18,6485	TT,TC,CC		0.2093,0.0,0.1384	benign,benign	665/720,665/720	9523244	18,12988	2203	4300	6503	SO:0001583	missense	57144	exon9			GTAGGTCCTTCAC	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.1993G>A	20.37:g.9523244C>T	ENSP00000367686:p.Asp665Asn	159	0	0		189	96	0.507937	NM_177990	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	SNP	ENST00000378429.3	37	CCDS13107.1	3	0.0013736263736263737	1	0.0020325203252032522	0	0.0	0	0.0	2	0.002638522427440633	C	13.57	2.276632	0.40294	0.0	0.002093	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423	T;T;T	0.13538	2.58;2.58;2.58	5.48	5.48	0.80851	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.042605	0.85682	D	0.000000	T	0.12263	0.0298	N	0.25992	0.78	0.58432	D	0.999996	B	0.09022	0.002	B	0.10450	0.005	T	0.15492	-1.0435	9	.	.	.	.	19.3557	0.94412	0.0:1.0:0.0:0.0	.	665	Q9P286	PAK7_HUMAN	N	665	ENSP00000367686:D665N;ENSP00000322957:D665N;ENSP00000367679:D665N	.	D	-	1	0	PAK7	9471244	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.034000	0.57289	2.597000	0.87782	0.655000	0.94253	GAC	C|0.999;T|0.001	0.001	strong		0.478	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1			T	9523244	C	T	9523244	3	4	30	1	0	0	0	0	1	0	0	0	11414	855	30	2	174	2	PAK7	20	9523244	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	3444998	9523244	53502276	666	13817											
CSRP2BP	57325	hgsc.bcm.edu	37	chr20	18168099	18168099	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	attctttctgaggctccggcGctgatgcgaatacagctcac	8	11	10	12	3	3	2	1	2	2	0	4	3	4	2	1	2	3	3	1	2	2	3	rs376874386		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:18168099G>A	ENST00000435364.3	+	10	2686	c.2345G>A	c.(2344-2346)cGc>cAc	p.R782H	CSRP2BP_ENST00000377681.3_Missense_Mutation_p.R781H|CSRP2BP_ENST00000489634.2_Missense_Mutation_p.R654H	NM_020536.4	NP_065397	Q9H8E8	CSR2B_HUMAN	CSRP2 binding protein	782	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				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						AGGCTCCGGCGCTGATGCGAA	0.413																																					p.R782H		Atlas-SNP	.											.	CSRP2BP	80	.	0			c.G2345A						PASS	.	G	HIS/ARG	0,4406		0,0,2203	73	73	73		2345	5.9	1	20		73	1,8599	1.2+/-3.3	0,1,4299	no	missense	CSRP2BP	NM_020536.4	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	782/783	18168099	1,13005	2203	4300	6503	SO:0001583	missense	57325	exon10			TCCGGCGCTGATG	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.2345G>A	20.37:g.18168099G>A	ENSP00000392318:p.Arg782His	66	0	0		65	29	0.446154	NM_020536	A2A2I5|Q96GW6|Q96IH3|Q9HBF0|Q9UIY5	Missense_Mutation	SNP	ENST00000435364.3	37	CCDS13133.1	.	.	.	.	.	.	.	.	.	.	G	36	5.598337	0.96614	0.0	1.16E-4	ENSG00000149474	ENST00000278816;ENST00000377681;ENST00000435364;ENST00000489634	T;T;T;T	0.28666	1.6;1.61;1.6;1.63	5.87	5.87	0.94306	GCN5-related N-acetyltransferase (GNAT) domain (1);	0.000000	0.85682	D	0.000000	T	0.58779	0.2146	M	0.72576	2.205	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.58945	-0.7546	10	0.87932	D	0	.	20.2147	0.98293	0.0:0.0:1.0:0.0	.	654;782	Q9H8E8-2;Q9H8E8	.;CSR2B_HUMAN	H	782;781;782;654	ENSP00000278816:R782H;ENSP00000366909:R781H;ENSP00000392318:R782H;ENSP00000425909:R654H	ENSP00000278816:R782H	R	+	2	0	CSRP2BP	18116099	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.750000	0.98875	2.785000	0.95823	0.591000	0.81541	CGC	.	.	weak		0.413	CSRP2BP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078152.5	NM_020536		A	18168099	G	A	18168099	3	1	30	1	0	0	0	0	1	0	0	0	3970	1087	38	1	2383	1	CSRP2BP	20	18168099	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	8644855	18168099	44857421	667	13818											
C20orf112	140688	hgsc.bcm.edu	37	chr20	31044059	31044059	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttgatgggctgatcctcggcGgccgtggtgaagtccatggg	5	10	17	9	3	0	3	0	3	0	0	3	3	2	3	3	5	0	1	3	5	1	1	rs570929204	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:31044059G>A	ENST00000359676.5	-	3	391	c.249C>T	c.(247-249)gcC>gcT	p.A83A	RP5-1184F4.5_ENST00000442179.1_RNA|C20orf112_ENST00000475781.1_5'UTR	NM_001256798.1|NM_080616.4	NP_001243727.1|NP_542183.2	Q96MY1	NOL4L_HUMAN		83						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|kidney(2)|large_intestine(5)|lung(5)	15						GATCCTCGGCGGCCGTGGTGA	0.687													G|||	4	0.000798722	0.0	0.0	5008	,	,		17312	0.0		0.0	False		,,,				2504	0.0041				p.A327A		Atlas-SNP	.											.	C20orf112	39	.	0			c.C981T						PASS	.						43	40	41					20																	31044059		2203	4298	6501	SO:0001819	synonymous_variant	140688	exon6			CTCGGCGGCCGTG																												ENST00000359676.5:c.249C>T	20.37:g.31044059G>A		181	0	0		152	71	0.467105	NM_001256798	Q5JYB7|Q6P0Y4|Q9BR34|Q9NQF6	Silent	SNP	ENST00000359676.5	37	CCDS13202.1																																																																																			.	.	none		0.687	C20orf112-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078628.2			A	31044059	G	A	31044059	2	1	30	1	0	0	0	0	0	0	0	1	2083	1103	39	1		1	C20orf112	20	31044059	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	12875960	31044059	31981461	668	13819											
C20orf70	140683	hgsc.bcm.edu	37	chr20	31761919	31761919	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actccctcatcctggatgtcAaagctgaaccgatcgatgat	11	10	8	12	2	2	2	2	2	0	0	5	5	4	3	3	1	2	1	3	1	2	0	rs17304572	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:31761919A>G	ENST00000253362.2	+	4	483	c.337A>G	c.(337-339)Aaa>Gaa	p.K113E	BPIFA2_ENST00000354932.5_Missense_Mutation_p.K113E			Q96DR5	BPIA2_HUMAN	BPI fold containing family A, member 2	113			K -> E (in dbSNP:rs17304572).			extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)										CCTGGATGTCAAAGCTGAACC	0.507													A|||	36	0.0071885	0.0008	0.0447	5008	,	,		20651	0.0		0.003	False		,,,				2504	0.001				p.K113E		Atlas-SNP	.											.	.	.	.	0			c.A337G						PASS	.	A	GLU/LYS	9,4397	15.5+/-35.6	0,9,2194	190	130	150		337	0.5	0	20	dbSNP_123	150	65,8535	39.3+/-95.6	0,65,4235	yes	missense	BPIFA2	NM_080574.2	56	0,74,6429	GG,GA,AA		0.7558,0.2043,0.569	possibly-damaging	113/250	31761919	74,12932	2203	4300	6503	SO:0001583	missense	140683	exon4			GATGTCAAAGCTG	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.337A>G	20.37:g.31761919A>G	ENSP00000253362:p.Lys113Glu	148	0	0		126	58	0.460317	NM_080574	Q9BQQ0	Missense_Mutation	SNP	ENST00000253362.2	37	CCDS13214.1	15	0.006868131868131868	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	4	0.005277044854881266	A	14.94	2.685424	0.47991	0.002043	0.007558	ENSG00000131050	ENST00000253362;ENST00000354932	T;T	0.05580	3.42;3.42	4.11	0.538	0.17150	.	0.626240	0.15043	N	0.283766	T	0.02767	0.0083	L	0.50919	1.6	0.09310	N	1	P	0.41624	0.757	B	0.43728	0.429	T	0.30001	-0.9993	10	0.15952	T	0.53	-20.1787	3.5768	0.07937	0.5707:0.2098:0.2195:0.0	rs17304572;rs52835642;rs56630818;rs17304572	113	Q96DR5	BPIA2_HUMAN	E	113	ENSP00000253362:K113E;ENSP00000347012:K113E	ENSP00000253362:K113E	K	+	1	0	BPIFA2	31225580	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	0.427000	0.21379	0.060000	0.16281	0.459000	0.35465	AAA	A|0.994;G|0.006	0.006	strong		0.507	BPIFA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257117.1	NM_080574		G	31761919	A	G	31761919	3	3	30	1	0	0	0	0	1	0	0	0	2118	131	5	3	347	3	C20orf70	20	31761919	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	717860	31761919	31263601	669	13820											
CEP250	11190	hgsc.bcm.edu	37	chr20	34092076	34092076	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcatcaggaggaggctgcccGggcccgggctgaggctctgc	5	5	18	13	2	2	1	1	1	1	0	2	3	2	3	2	6	2	4	2	6	0	0	rs56259282	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:34092076G>A	ENST00000397527.1	+	30	6599	c.5879G>A	c.(5878-5880)cGg>cAg	p.R1960Q	CEP250_ENST00000342580.4_Missense_Mutation_p.R1904Q	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	1960	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)			GAGGCTGCCCGGGCCCGGGCT	0.657													G|||	24	0.00479233	0.0008	0.0115	5008	,	,		18767	0.0		0.0119	False		,,,				2504	0.0031				p.R1960Q		Atlas-SNP	.											.	CEP250	141	.	0			c.G5879A						PASS	.	G	GLN/ARG	9,4369		0,9,2180	9	11	10		5879	-4	0	20	dbSNP_129	10	103,8479		2,99,4190	yes	missense	CEP250	NM_007186.3	43	2,108,6370	AA,AG,GG		1.2002,0.2056,0.8642	benign	1960/2443	34092076	112,12848	2189	4291	6480	SO:0001583	missense	11190	exon30			CTGCCCGGGCCCG	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.5879G>A	20.37:g.34092076G>A	ENSP00000380661:p.Arg1960Gln	43	0	0		40	19	0.475	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	ENST00000397527.1	37	CCDS13255.1	15	0.006868131868131868	0	0.0	8	0.022099447513812154	0	0.0	7	0.009234828496042216	G	2.257	-0.370208	0.05069	0.002056	0.012002	ENSG00000126001	ENST00000397527;ENST00000342580;ENST00000422671	T;T;T	0.41065	3.05;3.04;1.01	4.95	-4.04	0.04010	.	1.940040	0.02640	N	0.105311	T	0.11836	0.0288	L	0.29908	0.895	0.09310	N	1	B	0.13594	0.008	B	0.08055	0.003	T	0.05550	-1.0878	10	0.12430	T	0.62	.	0.1713	0.00113	0.3233:0.1493:0.21:0.3175	rs56259282	1960	Q9BV73	CP250_HUMAN	Q	1960;1904;448	ENSP00000380661:R1960Q;ENSP00000341541:R1904Q;ENSP00000395992:R448Q	ENSP00000341541:R1904Q	R	+	2	0	CEP250	33555490	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.281000	0.08456	-0.484000	0.06763	-0.733000	0.03571	CGG	G|0.993;A|0.007	0.007	strong		0.657	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186		A	34092076	G	A	34092076	3	1	30	1	0	0	0	0	1	0	0	0	3254	1116	39	1	5985	1	CEP250	20	34092076	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	2330157	34092076	28933444	670	13821											
RIMS4	140730	hgsc.bcm.edu	37	chr20	43386414	43386414	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaccgatctccacatccccTggaagaggcaccaagagatg	13	5	10	13	1	1	3	0	0	1	3	3	6	2	4	5	2	0	1	5	2	2	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:43386414T>A	ENST00000372851.3	-	4	416		c.e4-2		RIMS4_ENST00000541604.2_Splice_Site	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)				CCACATCCCCTGGAAGAGGCA	0.562																																					.		Atlas-SNP	.											.	RIMS4	47	.	0			c.353-2A>T						PASS	.						83	69	74					20																	43386414		2203	4300	6503	SO:0001630	splice_region_variant	140730	exon5			ATCCCCTGGAAGA		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	ENST00000372851.3:c.350-2A>T	20.37:g.43386414T>A		81	0	0		80	26	0.325	NM_001205317	A4FU94|E1P613|Q3MI44|Q5JWT7	Splice_Site	SNP	ENST00000372851.3	37	CCDS13338.1	.	.	.	.	.	.	.	.	.	.	T	18.70	3.680306	0.68042	.	.	ENSG00000101098	ENST00000372851;ENST00000541604	.	.	.	5.91	5.91	0.95273	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3453	0.83126	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	RIMS4	42819828	1.000000	0.71417	0.999000	0.59377	0.492000	0.33523	8.040000	0.89188	2.261000	0.74972	0.533000	0.62120	.	.	.	none		0.562	RIMS4-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000101027.2	NM_182970	Intron	A	43386414	T	A	43386414	5	1	30	1	0	0	0	0	0	0	1	0	13385	1594	55	5	473	5	RIMS4	20	43386414	Splice_Site	SNP	T	TCGA-GR-7353-01A-11D-2210-10	9294338	43386414	19639106	671	13822											
PCIF1	63935	hgsc.bcm.edu	37	chr20	44575932	44575932	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagctcaccggagcccctgTccttcatcgtgttcatccct	6	11	8	16	2	3	1	3	0	0	1	6	2	5	2	5	1	2	2	5	1	0	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:44575932T>C	ENST00000372409.3	+	16	2102	c.1738T>C	c.(1738-1740)Tcc>Ccc	p.S580P	PCIF1_ENST00000479348.1_3'UTR	NM_022104.3	NP_071387.1	Q9H4Z3	PCIF1_HUMAN	PDX1 C-terminal inhibiting factor 1	580					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						GGAGCCCCTGTCCTTCATCGT	0.622																																					p.S580P		Atlas-SNP	.											.	PCIF1	51	.	0			c.T1738C						PASS	.						79	81	80					20																	44575932		2203	4300	6503	SO:0001583	missense	63935	exon16			CCCCTGTCCTTCA	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.1738T>C	20.37:g.44575932T>C	ENSP00000361486:p.Ser580Pro	110	0	0		104	6	0.0576923	NM_022104	E1P5P1|Q54AB9|Q9NT85	Missense_Mutation	SNP	ENST00000372409.3	37	CCDS13388.1	.	.	.	.	.	.	.	.	.	.	T	23.1	4.371687	0.82573	.	.	ENSG00000100982	ENST00000372409;ENST00000443130	.	.	.	5.03	5.03	0.67393	Phosphorylated CTD interacting factor 1, WW domain (1);	0.000000	0.85682	D	0.000000	D	0.84306	0.5443	M	0.90542	3.125	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.87621	0.2510	9	0.72032	D	0.01	-30.1299	14.0902	0.64984	0.0:0.0:0.0:1.0	.	580;580	B7Z5U5;Q9H4Z3	.;PCIF1_HUMAN	P	580	.	ENSP00000361486:S580P	S	+	1	0	PCIF1	44009339	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	5.925000	0.70062	2.114000	0.64651	0.374000	0.22700	TCC	.	.	none		0.622	PCIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079550.1	NM_022104		C	44575932	T	C	44575932	3	2	30	1	0	0	0	0	1	0	0	0	11589	1667	58	3	1792	3	PCIF1	20	44575932	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	1189518	44575932	18449588	672	13823											
ATP9A	10079	hgsc.bcm.edu	37	chr20	50346491	50346491	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggggcctggcctcccctccaCcgcagcatctcagccactcg	5	6	10	20	2	1	0	1	0	1	0	5	0	3	0	7	3	2	2	7	3	0	0	rs142435125	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:50346491C>A	ENST00000338821.5	-	2	359	c.95G>T	c.(94-96)gGt>gTt	p.G32V	ATP9A_ENST00000477492.1_5'UTR|ATP9A_ENST00000402822.1_Missense_Mutation_p.G32V|ATP9A_ENST00000311637.5_Missense_Mutation_p.G17V	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	32					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						CTCCCCTCCACCGCAGCATCT	0.597													C|||	30	0.00599042	0.0	0.0014	5008	,	,		17873	0.0		0.003	False		,,,				2504	0.0266				p.G32V		Atlas-SNP	.											.	ATP9A	135	.	0			c.G95T						PASS	.	C	VAL/GLY	3,4403	6.2+/-15.9	0,3,2200	90	85	87		95	5.3	1	20	dbSNP_134	87	36,8564	24.6+/-71.5	0,36,4264	yes	missense	ATP9A	NM_006045.1	109	0,39,6464	AA,AC,CC		0.4186,0.0681,0.2999	benign	32/1048	50346491	39,12967	2203	4300	6503	SO:0001583	missense	10079	exon2			CCTCCACCGCAGC	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.95G>T	20.37:g.50346491C>A	ENSP00000342481:p.Gly32Val	46	0	0		57	27	0.473684	NM_006045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Missense_Mutation	SNP	ENST00000338821.5	37	CCDS33489.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	18.40	3.615508	0.66672	6.81E-4	0.004186	ENSG00000054793	ENST00000311637;ENST00000338821;ENST00000402822	T;T;T	0.54071	0.59;0.59;0.59	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.52108	0.1714	L	0.43152	1.355	0.58432	D	0.999996	B;P	0.36789	0.073;0.57	B;B	0.39805	0.31;0.147	T	0.53995	-0.8359	10	0.51188	T	0.08	-14.3884	19.2362	0.93861	0.0:1.0:0.0:0.0	.	32;32	O75110-2;O75110	.;ATP9A_HUMAN	V	17;32;32	ENSP00000309086:G17V;ENSP00000342481:G32V;ENSP00000385875:G32V	ENSP00000309086:G17V	G	-	2	0	ATP9A	49779898	1.000000	0.71417	0.997000	0.53966	0.922000	0.55478	7.257000	0.78362	2.608000	0.88229	0.563000	0.77884	GGT	C|0.997;A|0.003	0.003	strong		0.597	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045		A	50346491	C	A	50346491	3	1	30	1	0	0	0	0	1	0	0	0	1198	507	18	4	3156	4	ATP9A	20	50346491	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	5770559	50346491	12679029	673	13824											
SALL4	57167	hgsc.bcm.edu	37	chr20	50407255	50407255	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cactggaacggtctctccccGgtgtgggtgcgataatgcat	7	10	13	11	3	1	0	0	0	1	0	3	2	2	1	2	4	3	1	2	4	2	1	rs201329321		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:50407255G>A	ENST00000217086.4	-	2	1878	c.1767C>T	c.(1765-1767)acC>acT	p.T589T	SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000395997.3_Intron|SALL4_ENST00000371539.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	589					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						GTCTCTCCCCGGTGTGGGTGC	0.507													G|||	1	0.000199681	0.0	0.0	5008	,	,		19405	0.001		0.0	False		,,,				2504	0.0				p.T589T		Atlas-SNP	.											.	SALL4	168	.	0			c.C1767T						PASS	.						93	82	86					20																	50407255		2203	4300	6503	SO:0001819	synonymous_variant	57167	exon2			CTCCCCGGTGTGG	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.1767C>T	20.37:g.50407255G>A		136	0	0		168	50	0.297619	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																			G|1.000;A|0.000	0.000	strong		0.507	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3			A	50407255	G	A	50407255	2	1	30	1	0	0	0	0	0	0	0	1	13828	1103	39	1		1	SALL4	20	50407255	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	60764	50407255	12618265	674	13825											
ZNF217	7764	hgsc.bcm.edu	37	chr20	52192595	52192595	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcagtattgctggcactcCgattacagaaatagtctctt	10	13	8	10	1	1	1	0	0	1	1	3	2	2	1	1	1	3	4	1	1	4	5	rs61748378	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:52192595C>T	ENST00000371471.2	-	4	3133	c.2708G>A	c.(2707-2709)cGg>cAg	p.R903Q	RP4-724E16.2_ENST00000424252.1_RNA|ZNF217_ENST00000302342.3_Missense_Mutation_p.R903Q			O75362	ZN217_HUMAN	zinc finger protein 217	903					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)			GCTGGCACTCCGATTACAGAA	0.562													C|||	57	0.0113818	0.0008	0.0231	5008	,	,		18605	0.0		0.0368	False		,,,				2504	0.0031				p.R903Q		Atlas-SNP	.											.	ZNF217	227	.	0			c.G2708A						PASS	.	C	GLN/ARG	36,4370	40.8+/-73.8	0,36,2167	63	61	62		2708	5.3	0.1	20	dbSNP_129	62	340,8260	117.6+/-177.1	6,328,3966	yes	missense	ZNF217	NM_006526.2	43	6,364,6133	TT,TC,CC		3.9535,0.8171,2.891	probably-damaging	903/1049	52192595	376,12630	2203	4300	6503	SO:0001583	missense	7764	exon3			GCACTCCGATTAC	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.2708G>A	20.37:g.52192595C>T	ENSP00000360526:p.Arg903Gln	197	1	0.00507614		157	82	0.522293	NM_006526	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	37	CCDS13443.1	40	0.018315018315018316	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	29	0.03825857519788918	C	15.18	2.755994	0.49362	0.008171	0.039535	ENSG00000171940	ENST00000371471;ENST00000302342;ENST00000395971	T;T	0.13196	2.61;2.61	5.26	5.26	0.73747	.	0.510022	0.19366	N	0.116007	T	0.02267	0.0070	L	0.39147	1.195	0.09310	N	0.999997	P	0.43938	0.822	B	0.32342	0.144	T	0.17531	-1.0366	10	0.87932	D	0	-20.7069	13.2311	0.59945	0.0:0.9214:0.0:0.0786	rs61748378	903	O75362	ZN217_HUMAN	Q	903;903;63	ENSP00000360526:R903Q;ENSP00000304308:R903Q	ENSP00000304308:R903Q	R	-	2	0	ZNF217	51626002	0.953000	0.32496	0.078000	0.20375	0.006000	0.05464	2.935000	0.48963	2.450000	0.82876	0.650000	0.86243	CGG	C|0.976;T|0.024	0.024	strong		0.562	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		T	52192595	C	T	52192595	3	4	30	1	0	0	0	0	1	0	0	0	17787	652	23	1	446	1	ZNF217	20	52192595	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1785340	52192595	10832925	675	13826											
CYP24A1	1591	hgsc.bcm.edu	37	chr20	52790027	52790027	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctgaggggacgtgtacgccGtagatgtcaccagtctcggg	7	8	16	10	4	2	2	1	1	1	1	3	3	2	3	2	3	1	3	2	3	2	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:52790027G>A	ENST00000216862.3	-	1	485	c.92C>T	c.(91-93)aCg>aTg	p.T31M	CYP24A1_ENST00000395954.3_5'Flank|CYP24A1_ENST00000395955.3_Missense_Mutation_p.T31M	NM_000782.4	NP_000773.2	Q07973	CP24A_HUMAN	cytochrome P450, family 24, subfamily A, polypeptide 1	31					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)	CGTGTACGCCGTAGATGTCAC	0.701																																					p.T31M		Atlas-SNP	.											.	CYP24A1	75	.	0			c.C92T						PASS	.						11	10	10					20																	52790027		2182	4282	6464	SO:0001583	missense	1591	exon1			TACGCCGTAGATG	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.92C>T	20.37:g.52790027G>A	ENSP00000216862:p.Thr31Met	80	0	0		39	13	0.333333	NM_000782	Q15807|Q32ML3|Q5I2W7	Missense_Mutation	SNP	ENST00000216862.3	37	CCDS33491.1	.	.	.	.	.	.	.	.	.	.	G	8.351	0.830799	0.16820	.	.	ENSG00000019186	ENST00000216862;ENST00000395955	T;T	0.71222	-0.53;-0.55	5.27	-0.451	0.12214	.	0.815815	0.11464	N	0.561406	T	0.40372	0.1114	N	0.08118	0	0.09310	N	0.999999	P;P	0.43024	0.521;0.798	B;B	0.35182	0.128;0.197	T	0.29731	-1.0002	10	0.35671	T	0.21	-0.5016	3.5654	0.07897	0.0786:0.2999:0.3524:0.2691	.	31;31	Q32ML3;Q07973	.;CP24A_HUMAN	M	31	ENSP00000216862:T31M;ENSP00000379285:T31M	ENSP00000216862:T31M	T	-	2	0	CYP24A1	52223434	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.239000	0.18023	-0.332000	0.08489	-0.309000	0.09137	ACG	.	.	none		0.701	CYP24A1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079769.2			A	52790027	G	A	52790027	3	1	30	1	0	0	0	0	1	0	0	0	4156	1145	40	1	1496	1	CYP24A1	20	52790027	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	597432	52790027	10235493	676	13827											
C20orf85	128602	hgsc.bcm.edu	37	chr20	56735761	56735761	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cagaccacccagggcttcatCggctggagatctgcagtgcc	8	7	12	14	1	2	2	1	0	1	2	3	3	2	2	3	3	2	3	3	3	0	1	rs61749694	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:56735761C>T	ENST00000371168.3	+	4	358	c.297C>T	c.(295-297)atC>atT	p.I99I		NM_178456.2	NP_848551.1	Q9H1P6	CT085_HUMAN	chromosome 20 open reading frame 85	99			I -> V (in dbSNP:rs17440813).							kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	13	all_epithelial(3;5.99e-14)|Lung NSC(12;0.000152)|all_lung(29;0.000518)|Melanoma(10;0.118)		BRCA - Breast invasive adenocarcinoma(13;5.53e-12)|Epithelial(14;7.42e-08)|all cancers(14;7.19e-07)			AGGGCTTCATCGGCTGGAGAT	0.577													C|||	9	0.00179712	0.0	0.0029	5008	,	,		19067	0.0		0.007	False		,,,				2504	0.0				p.I99I		Atlas-SNP	.											.	C20orf85	35	.	0			c.C297T						PASS	.	C		6,4400	9.9+/-24.2	0,6,2197	46	40	42		297	1.3	1	20	dbSNP_129	42	43,8557	27.9+/-77.7	0,43,4257	no	coding-synonymous	C20orf85	NM_178456.2		0,49,6454	TT,TC,CC		0.5,0.1362,0.3767		99/138	56735761	49,12957	2203	4300	6503	SO:0001819	synonymous_variant	128602	exon4			CTTCATCGGCTGG	AL354776	CCDS13465.1	20q13.32	2012-10-29			ENSG00000124237	ENSG00000124237			16216	protein-coding gene	gene with protein product	"Low in Lung Cancer 1"						Standard	NM_178456		Approved	bA196N14.1, LLC1	uc002xyv.3	Q9H1P6	OTTHUMG00000032836	ENST00000371168.3:c.297C>T	20.37:g.56735761C>T		90	0	0		80	36	0.45	NM_178456		Silent	SNP	ENST00000371168.3	37	CCDS13465.1																																																																																			C|0.997;T|0.003	0.003	strong		0.577	C20orf85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079866.2	NM_178456		T	56735761	C	T	56735761	2	4	30	1	0	0	0	0	0	0	0	1	2122	874	31	1		1	C20orf85	20	56735761	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	3945734	56735761	6289759	677	13828											
TUBB1	81027	hgsc.bcm.edu	37	chr20	57598808	57598808	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	caaaggccactacacggaggGagccgagctgatcgagaatg	13	4	14	10	3	0	2	0	1	0	1	1	6	0	4	2	3	3	1	2	3	3	1	rs41303899	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:57598808G>A	ENST00000217133.1	+	4	595	c.326G>A	c.(325-327)gGa>gAa	p.G109E		NM_030773.3	NP_110400.1	Q9H4B7	TBB1_HUMAN	tubulin, beta 1 class VI	109					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|protein polymerization (GO:0051258)|spindle assembly (GO:0051225)	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)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|skin(2)	16	all_lung(29;0.00711)		Colorectal(105;0.109)		Cabazitaxel(DB06772)|Colchicine(DB01394)|Docetaxel(DB01248)|Paclitaxel(DB01229)|Vindesine(DB00309)	TACACGGAGGGAGCCGAGCTG	0.592													G|||	4	0.000798722	0.0	0.0029	5008	,	,		16838	0.0		0.002	False		,,,				2504	0.0				p.G109E		Atlas-SNP	.											TUBB1,mucosal,malignant_melanoma,+1,1	TUBB1	42	1	0			c.G326A						PASS	.	G	GLU/GLY	2,4404	4.2+/-10.8	0,2,2201	83	91	89		326	5.4	1	20	dbSNP_127	89	12,8588	9.1+/-34.3	0,12,4288	yes	missense	TUBB1	NM_030773.3	98	0,14,6489	AA,AG,GG		0.1395,0.0454,0.1076	probably-damaging	109/452	57598808	14,12992	2203	4300	6503	SO:0001583	missense	81027	exon4			CGGAGGGAGCCGA	AJ292757	CCDS13475.1	20q13.32	2014-09-17	2011-10-10		ENSG00000101162	ENSG00000101162		"Tubulins"	16257	protein-coding gene	gene with protein product	"class VI beta-tubulin"	612901	"tubulin, beta 1"				Standard	NM_030773		Approved	dJ543J19.4	uc002yak.3	Q9H4B7	OTTHUMG00000032860	ENST00000217133.1:c.326G>A	20.37:g.57598808G>A	ENSP00000217133:p.Gly109Glu	113	0	0		124	59	0.475806	NM_030773		Missense_Mutation	SNP	ENST00000217133.1	37	CCDS13475.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	17.48	3.399586	0.62177	4.54E-4	0.001395	ENSG00000101162	ENST00000217133	T	0.75821	-0.97	5.39	5.39	0.77823	Tubulin/FtsZ, GTPase domain (4);	0.000000	0.85682	D	0.000000	D	0.94374	0.8191	H	0.99993	5.38	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97591	1.0117	10	0.87932	D	0	.	18.1143	0.89546	0.0:0.0:1.0:0.0	rs41303899	109	Q9H4B7	TBB1_HUMAN	E	109	ENSP00000217133:G109E	ENSP00000217133:G109E	G	+	2	0	TUBB1	57032203	1.000000	0.71417	0.952000	0.39060	0.158000	0.22134	9.824000	0.99380	2.537000	0.85549	0.655000	0.94253	GGA	G|0.999;A|0.001	0.001	strong		0.592	TUBB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079903.1	NM_030773		A	57598808	G	A	57598808	3	1	30	1	0	0	0	0	1	0	0	0	16768	1174	41	2	340	2	TUBB1	20	57598808	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	863047	57598808	5426712	678	13829											
DIDO1	11083	hgsc.bcm.edu	37	chr20	61528044	61528044	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acggctcccaccaaagcagcGgagccagggaacttcttgga	11	5	12	13	2	1	0	0	0	1	0	2	3	2	3	3	4	4	2	3	4	2	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:61528044G>A	ENST00000266070.4	-	7	2218	c.1893C>T	c.(1891-1893)tcC>tcT	p.S631S	DIDO1_ENST00000395343.1_Silent_p.S631S|DIDO1_ENST00000395340.1_Silent_p.S631S|DIDO1_ENST00000395335.2_Silent_p.S631S	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	631					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)					CCAAAGCAGCGGAGCCAGGGA	0.647																																					p.S631S	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.C1893T						PASS	.						46	52	50					20																	61528044		2203	4300	6503	SO:0001819	synonymous_variant	11083	exon7			AGCAGCGGAGCCA	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.1893C>T	20.37:g.61528044G>A		91	0	0		109	53	0.486239	NM_080797	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Silent	SNP	ENST00000266070.4	37	CCDS33506.1																																																																																			.	.	none		0.647	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		A	61528044	G	A	61528044	2	1	30	1	0	0	0	0	0	0	0	1	4524	1103	39	1		1	DIDO1	20	61528044	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	3929236	61528044	1497476	679	13830											
RTEL1	51750	hgsc.bcm.edu	37	chr20	62322290	62322290	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	acagcgggcggggagccctgGcgaggagcaggtacagttcc	8	4	18	11	3	0	0	0	0	0	0	1	3	1	2	2	6	4	3	2	6	1	2	rs190887884	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr20:62322290G>A	ENST00000360203.5	+	27	2871	c.2546G>A	c.(2545-2547)gGc>gAc	p.G849D	RTEL1_ENST00000370018.3_Missense_Mutation_p.G849D|RTEL1_ENST00000508582.2_Missense_Mutation_p.G873D|RTEL1-TNFRSF6B_ENST00000482936.1_Missense_Mutation_p.G849D|RTEL1_ENST00000318100.4_Missense_Mutation_p.G849D|RTEL1_ENST00000370003.1_Missense_Mutation_p.G94D					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)			GGGAGCCCTGGCGAGGAGCAG	0.687													G|||	23	0.00459265	0.0023	0.0058	5008	,	,		15022	0.0		0.0099	False		,,,				2504	0.0061				p.G873D		Atlas-SNP	.											.	RTEL1	114	.	0			c.G2618A						PASS	.	G	ASP/GLY,ASP/GLY	9,4167		0,9,2079	14	15	14		2546,2618	-0.1	0	20		14	113,8185		0,113,4036	yes	missense,missense	RTEL1	NM_016434.3,NM_032957.4	94,94	0,122,6115	AA,AG,GG		1.3618,0.2155,0.978	benign,benign	849/1220,873/1244	62322290	122,12352	2088	4149	6237	SO:0001583	missense	51750	exon27			GCCCTGGCGAGGA	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.2546G>A	20.37:g.62322290G>A	ENSP00000353332:p.Gly849Asp	53	0	0		34	13	0.382353	NM_032957		Missense_Mutation	SNP	ENST00000360203.5	37		13	0.005952380952380952	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	G	11.51	1.659474	0.29515	0.002155	0.013618	ENSG00000258366	ENST00000370018;ENST00000318100;ENST00000508582;ENST00000360203;ENST00000370003	T;T;T;T;T	0.09255	3.0;3.0;3.0;3.0;3.0	4.77	-0.131	0.13494	.	0.888187	0.09800	N	0.754121	T	0.04679	0.0127	L	0.34521	1.04	0.09310	N	1	B;B;B;B	0.34290	0.052;0.447;0.003;0.008	B;B;B;B	0.35413	0.075;0.202;0.017;0.046	T	0.38972	-0.9636	10	0.23302	T	0.38	-13.4816	2.5812	0.04818	0.4374:0.0:0.343:0.2196	.	873;94;849;849	Q9NZ71-7;Q9NZ71-5;Q9NZ71;Q9NZ71-6	.;.;RTEL1_HUMAN;.	D	849;849;873;849;94	ENSP00000359035:G849D;ENSP00000322287:G849D;ENSP00000424307:G873D;ENSP00000353332:G849D;ENSP00000359020:G94D	ENSP00000353332:G849D	G	+	2	0	AL353715.1	61792734	0.001000	0.12720	0.005000	0.12908	0.006000	0.05464	0.096000	0.15147	0.093000	0.17368	-0.217000	0.12591	GGC	G|0.994;A|0.006	0.006	strong		0.687	RTEL1-011	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000289781.1	NM_032957		A	62322290	G	A	62322290	3	1	30	1	0	0	0	0	1	0	0	0	13735	1203	42	2	2648	2	RTEL1	20	62322290	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	794246	62322290	703230	680	13831											
USP25	29761	hgsc.bcm.edu	37	chr21	17181168	17181168	+	Nonsense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acacaaattattagattggtTagaagatgccttccaaatga	16	12	7	6	0	0	4	0	1	0	3	1	4	1	4	2	1	1	1	2	1	6	5			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:17181168T>G	ENST00000285679.6	+	8	1190	c.821T>G	c.(820-822)tTa>tGa	p.L274*	USP25_ENST00000547201.1_3'UTR|USP25_ENST00000285681.2_Nonsense_Mutation_p.L274*|USP25_ENST00000351097.5_Intron|USP25_ENST00000400183.2_Nonsense_Mutation_p.L274*	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	274	USP.				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)		TTAGATTGGTTAGAAGATGCC	0.333																																					p.L274X		Atlas-SNP	.											.	USP25	156	.	0			c.T821G						PASS	.						76	73	74					21																	17181168		2203	4300	6503	SO:0001587	stop_gained	29761	exon8			ATTGGTTAGAAGA	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.821T>G	21.37:g.17181168T>G	ENSP00000285679:p.Leu274*	55	0	0		80	15	0.1875	NM_013396	C0LSZ0|Q6DHZ9|Q9H9W1	Nonsense_Mutation	SNP	ENST00000285679.6	37	CCDS33515.1	.	.	.	.	.	.	.	.	.	.	T	39	7.408059	0.98265	.	.	ENSG00000155313	ENST00000285681;ENST00000285679;ENST00000400183	.	.	.	4.83	4.83	0.62350	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.7222	0.69314	0.0:0.0:0.0:1.0	.	.	.	.	X	274	.	ENSP00000285679:L274X	L	+	2	0	USP25	16103039	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.651000	0.83577	1.928000	0.55862	0.482000	0.46254	TTA	.	.	none		0.333	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1			G	17181168	T	G	17181168	4	3	30	1	0	0	0	0	0	1	0	0	17071	1764	61	5	851	5	USP25	21	17181168	Nonsense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10		17181168	30948727	681	13832											
KRTAP13-3	337960	hgsc.bcm.edu	37	chr21	31797919	31797919	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcagggagcagcagctattGgatccaaaaccccgagaccc	12	5	10	14	1	1	1	1	0	0	1	2	4	2	3	4	2	4	3	4	2	3	2	rs73356706	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:31797919G>A	ENST00000390690.2	-	1	367	c.312C>T	c.(310-312)tcC>tcT	p.S104S		NM_181622.1	NP_853653.1	Q3SY46	KR133_HUMAN	keratin associated protein 13-3	104						intermediate filament (GO:0005882)				endometrium(1)|large_intestine(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	14						AGCAGCTATTGGATCCAAAAC	0.532													-|||	210	0.0419329	0.1505	0.0144	5008	,	,		18568	0.0		0.001	False		,,,				2504	0.0				p.S104S		Atlas-SNP	.											.	KRTAP13-3	47	.	0			c.C312T						PASS	.	G		432,3908		23,386,1761	51	57	55		312	3.4	0.3	21	dbSNP_130	55	9,8569		0,9,4280	no	coding-synonymous	KRTAP13-3	NM_181622.1		23,395,6041	AA,AG,GG		0.1049,9.9539,3.4138		104/173	31797919	441,12477	2170	4289	6459	SO:0001819	synonymous_variant	337960	exon1			GCTATTGGATCCA	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.312C>T	21.37:g.31797919G>A		108	0	0		171	61	0.356725	NM_181622	Q3LI78	Silent	SNP	ENST00000390690.2	37	CCDS13591.1																																																																																			G|0.975;A|0.025	0.025	strong		0.532	KRTAP13-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128228.2			A	31797919	G	A	31797919	2	1	30	1	0	0	0	0	0	0	0	1	8533	1335	47	2		2	KRTAP13-3	21	31797919	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	14616751	31797919	16331976	682	13833											
KRTAP13-4	284827	hgsc.bcm.edu	37	chr21	31802629	31802629	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgctctagaaacttctcctcCcgctcctttgggggctacct	5	13	8	15	1	2	1	0	0	2	1	5	1	4	1	4	2	3	3	4	2	3	4	rs73356729	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:31802629C>T	ENST00000334068.2	+	1	58	c.36C>T	c.(34-36)tcC>tcT	p.S12S		NM_181600.1	NP_853631.1	Q3LI77	KR134_HUMAN	keratin associated protein 13-4	12						intermediate filament (GO:0005882)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	15						ACTTCTCCTCCCGCTCCTTTG	0.547													-|||	220	0.0439297	0.1581	0.0144	5008	,	,		18637	0.0		0.001	False		,,,				2504	0.0				p.S12S	NSCLC(196;2401 3038 18004 35753)	Atlas-SNP	.											.	KRTAP13-4	46	.	0			c.C36T						PASS	.	C		473,3933		25,423,1755	109	111	110		36	0.1	0.1	21	dbSNP_130	110	10,8590		0,10,4290	no	coding-synonymous	KRTAP13-4	NM_181600.1		25,433,6045	TT,TC,CC		0.1163,10.7354,3.7137		12/161	31802629	483,12523	2203	4300	6503	SO:0001819	synonymous_variant	284827	exon1			CTCCTCCCGCTCC	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.36C>T	21.37:g.31802629C>T		181	0	0		240	79	0.329167	NM_181600	A2RRL3	Silent	SNP	ENST00000334068.2	37	CCDS13592.1																																																																																			C|0.963;T|0.037	0.037	strong		0.547	KRTAP13-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128222.1			T	31802629	C	T	31802629	2	4	30	1	0	0	0	0	0	0	0	1	8534	610	22	2		2	KRTAP13-4	21	31802629	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	4710	31802629	16327266	683	13834											
KRTAP19-6	337973	hgsc.bcm.edu	37	chr21	31914019	31914019	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atccttcacggcatgatgggCggcagcagccatatctatag	10	9	11	11	2	2	1	1	1	1	0	3	1	3	1	2	3	2	3	2	3	3	4	rs77807247	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:31914019C>T	ENST00000334046.5	-	1	164	c.134G>A	c.(133-135)cGc>cAc	p.R45H		NM_181612.2	NP_853643.1	Q3LI70	KR196_HUMAN	keratin associated protein 19-6	45						intermediate filament (GO:0005882)				breast(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	9						GCATGATGGGCGGCAGCAGCC	0.498													c|||	161	0.0321486	0.1135	0.0115	5008	,	,		14661	0.0		0.001	False		,,,				2504	0.002				p.R45H		Atlas-SNP	.											.	KRTAP19-6	16	.	0			c.G134A						PASS	.	C	HIS/ARG	371,4035	188.5+/-214.9	13,345,1845	110	120	116		134	-6.1	0	21	dbSNP_131	116	12,8588	9.8+/-36.6	0,12,4288	yes	missense	KRTAP19-6	NM_181612.2	29	13,357,6133	TT,TC,CC		0.1395,8.4203,2.9448	benign	45/59	31914019	383,12623	2203	4300	6503	SO:0001583	missense	337973	exon1			GATGGGCGGCAGC	AP001708	CCDS13598.1	21q22.1	2010-09-30			ENSG00000186925	ENSG00000186925		"Keratin associated proteins"	18941	protein-coding gene	gene with protein product						12359730	Standard	NM_181612		Approved	KAP19.6	uc002yok.1	Q3LI70	OTTHUMG00000057779	ENST00000334046.5:c.134G>A	21.37:g.31914019C>T	ENSP00000375107:p.Arg45His	111	0	0		141	47	0.333333	NM_181612	Q3LI71	Missense_Mutation	SNP	ENST00000334046.5	37	CCDS13598.1	64	0.029304029304029304	58	0.11788617886178862	6	0.016574585635359115	0	0.0	0	0.0	c	6.926	0.540492	0.13250	0.084203	0.001395	ENSG00000186925	ENST00000334046;ENST00000437381	T	0.11169	2.8	4.39	-6.09	0.02145	.	0.598882	0.13443	N	0.387478	T	0.00109	0.0003	.	.	.	0.09310	N	1	B	0.12013	0.005	B	0.04013	0.001	T	0.32587	-0.9901	9	0.87932	D	0	-1.818	7.3473	0.26670	0.1168:0.3112:0.0:0.5719	.	45	Q3LI70	KR196_HUMAN	H	45	ENSP00000375107:R45H	ENSP00000375107:R45H	R	-	2	0	KRTAP19-6	30835890	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.929000	0.03976	-1.347000	0.02208	-1.903000	0.00527	CGC	C|0.969;T|0.031	0.031	strong		0.498	KRTAP19-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128231.4			T	31914019	C	T	31914019	3	4	30	1	0	0	0	0	1	0	0	0	8542	768	27	1	46	1	KRTAP19-6	21	31914019	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	111390	31914019	16215876	684	13835											
KRTAP6-1	337966	hgsc.bcm.edu	37	chr21	31986163	31986163	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atagccatagcccaggcctcCatagccacagaacccatagc	13	5	7	16	0	0	1	0	0	0	1	1	1	1	1	6	1	5	0	6	1	5	4	rs138494765		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:31986163C>T	ENST00000329122.2	-	1	86	c.61G>A	c.(61-63)Gga>Aga	p.G21R	KRTAP20-1_ENST00000334664.2_5'Flank	NM_181602.1	NP_853633.1	Q3LI64	KRA61_HUMAN	keratin associated protein 6-1	21						cytosol (GO:0005829)|intermediate filament (GO:0005882)				breast(2)|endometrium(1)|lung(7)	10						CCCAGGCCTCCATAGCCACAG	0.592																																					p.G21R		Atlas-SNP	.											.	KRTAP6-1	21	.	0			c.G61A						PASS	.	C	ARG/GLY	0,4406		0,0,2203	181	178	179		61	3.1	1	21	dbSNP_134	179	2,8598	2.2+/-6.3	0,2,4298	yes	missense	KRTAP6-1	NM_181602.1	125	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	21/72	31986163	2,13004	2203	4300	6503	SO:0001583	missense	337966	exon1			GGCCTCCATAGCC	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.61G>A	21.37:g.31986163C>T	ENSP00000332690:p.Gly21Arg	267	0	0		383	158	0.412533	NM_181602		Missense_Mutation	SNP	ENST00000329122.2	37	CCDS13602.1	.	.	.	.	.	.	.	.	.	.	C	11.99	1.802250	0.31869	0.0	2.33E-4	ENSG00000184724	ENST00000329122	T	0.23552	1.9	4.91	3.08	0.35506	.	0.237368	0.21800	U	0.068932	T	0.20740	0.0499	.	.	.	0.26580	N	0.973391	B	0.28552	0.215	B	0.28991	0.097	T	0.17899	-1.0354	9	0.87932	D	0	.	8.6058	0.33773	0.0:0.7606:0.1541:0.0853	.	21	Q3LI64	KRA61_HUMAN	R	21	ENSP00000332690:G21R	ENSP00000332690:G21R	G	-	1	0	KRTAP6-1	30908034	0.000000	0.05858	0.982000	0.44146	0.940000	0.58332	-1.080000	0.03407	0.786000	0.33708	0.643000	0.83706	GGA	C|1.000;T|0.000	0.000	weak		0.592	KRTAP6-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128240.2	NM_181602		T	31986163	C	T	31986163	3	4	30	1	0	0	0	0	1	0	0	0	8578	603	21	2	158	2	KRTAP6-1	21	31986163	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	72144	31986163	16143732	685	13836											
BRWD1	54014	hgsc.bcm.edu	37	chr21	40574434	40574434	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acctaccaactcaggaattaTttttgtctgagattttaacc	12	15	5	9	0	2	1	1	1	1	1	2	3	2	2	3	1	3	0	3	1	5	6	rs144295288	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:40574434T>C	ENST00000333229.2	-	38	4729	c.4402A>G	c.(4402-4404)Ata>Gta	p.I1468V	BRWD1_ENST00000380800.3_Missense_Mutation_p.I1468V|BRWD1_ENST00000342449.3_Missense_Mutation_p.I1468V	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	1468					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)				TCAGGAATTATTTTTGTCTGA	0.398													T|||	7	0.00139776	0.0	0.0	5008	,	,		18729	0.0		0.007	False		,,,				2504	0.0				p.I1468V	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.A4402G						PASS	.	T	VAL/ILE,VAL/ILE	6,4400	9.9+/-24.2	0,6,2197	72	67	69		4402,4402	3.4	0.7	21	dbSNP_134	69	46,8554	29.0+/-79.6	2,42,4256	yes	missense,missense	BRWD1	NM_018963.4,NM_033656.3	29,29	2,48,6453	CC,CT,TT		0.5349,0.1362,0.3998	benign,benign	1468/2321,1468/2270	40574434	52,12954	2203	4300	6503	SO:0001583	missense	54014	exon38			GAATTATTTTTGT	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.4402A>G	21.37:g.40574434T>C	ENSP00000330753:p.Ile1468Val	115	0	0		151	55	0.364238	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	37	CCDS13662.1	6|6	0.0027472527472527475|0.0027472527472527475	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	6|6	0.0079155672823219|0.0079155672823219	T|T	0.007|0.007	-1.938401|-1.938401	0.00484|0.00484	0.001362|0.001362	0.005349|0.005349	ENSG00000185658|ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800;ENST00000380783|ENST00000424441	T;T;T|.	0.52983|.	0.64;0.66;0.73|.	5.27|5.27	3.39|3.39	0.38822|0.38822	.|.	0.692467|.	0.13487|.	N|.	0.384267|.	T|T	0.04815|0.04815	0.0130|0.0130	N|N	0.00436|0.00436	-1.5|-1.5	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;0.0|.	T|T	0.33727|0.33727	-0.9857|-0.9857	10|5	0.24483|.	T|.	0.36|.	-2.138|-2.138	4.6929|4.6929	0.12790|0.12790	0.0:0.5271:0.151:0.3219|0.0:0.5271:0.151:0.3219	.|.	1468;1468;1468|.	Q9NSI6-3;Q9NSI6-2;Q9NSI6|.	.;.;BRWD1_HUMAN|.	V|S	1468;1468;1468;424|405	ENSP00000330753:I1468V;ENSP00000344333:I1468V;ENSP00000370178:I1468V|.	ENSP00000330753:I1468V|.	I|N	-|-	1|2	0|0	BRWD1|BRWD1	39496304|39496304	0.054000|0.054000	0.20591|0.20591	0.729000|0.729000	0.30791|0.30791	0.351000|0.351000	0.29236|0.29236	0.360000|0.360000	0.20250|0.20250	0.608000|0.608000	0.30000|0.30000	-0.177000|-0.177000	0.13119|0.13119	ATA|AAT	T|0.997;C|0.003	0.003	strong		0.398	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656		C	40574434	T	C	40574434	3	2	30	1	0	0	0	0	1	0	0	0	1527	1493	52	3	2819	3	BRWD1	21	40574434	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	8588271	40574434	7555461	686	13837											
RSPH1	89765	hgsc.bcm.edu	37	chr21	43913112	43913112	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccgaattcgtagctcccttcGtaggtgtccccgttgggtag	5	12	12	12	4	0	0	0	0	0	0	4	1	2	0	4	2	1	5	4	2	4	6			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:43913112G>A	ENST00000291536.3	-	2	299	c.132C>T	c.(130-132)taC>taT	p.Y44Y	RSPH1_ENST00000398352.3_Intron	NM_080860.2	NP_543136.1	Q8WYR4	RSPH1_HUMAN	radial spoke head 1 homolog (Chlamydomonas)	44					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						AGCTCCCTTCGTAGGTGTCCC	0.498																																					p.Y44Y	Esophageal Squamous(23;63 706 6286 10288 12913)	Atlas-SNP	.											RSPH1,NS,carcinoma,0,1	RSPH1	36	1	0			c.C132T						PASS	.						262	232	242					21																	43913112		2203	4300	6503	SO:0001819	synonymous_variant	89765	exon2			CCCTTCGTAGGTG	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.132C>T	21.37:g.43913112G>A		148	0	0		251	62	0.247012	NM_080860	A8MWV0|B2RBN9|Q3MJA1	Silent	SNP	ENST00000291536.3	37	CCDS13688.1																																																																																			.	.	none		0.498	RSPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195379.1			A	43913112	G	A	43913112	2	1	30	1	0	0	0	0	0	0	0	1	13717	1140	40	1		1	RSPH1	21	43913112	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	3338678	43913112	4216783	687	13838											
CBS	875	hgsc.bcm.edu	37	chr21	44483101	44483101	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggatgaagtcgtagccgaTcccttccacctcgtaggttg	7	10	13	11	3	0	1	0	1	0	0	4	3	2	2	4	3	1	3	4	3	3	4			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:44483101T>C	ENST00000398165.3	-	10	1175	c.916A>G	c.(916-918)Atc>Gtc	p.I306V	CBS_ENST00000352178.5_Missense_Mutation_p.I306V|CBS_ENST00000398158.1_Missense_Mutation_p.I306V|CBS_ENST00000359624.3_Missense_Mutation_p.I306V|CBS_ENST00000544202.1_Missense_Mutation_p.I218V|CBS_ENST00000398168.1_Missense_Mutation_p.I306V	NM_000071.2	NP_000062.1	P35520	CBS_HUMAN	cystathionine-beta-synthase	306					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)	TCGTAGCCGATCCCTTCCACC	0.632																																					p.I306V		Atlas-SNP	.											.	CBS	85	.	0			c.A916G						PASS	.						145	121	129					21																	44483101		2203	4300	6503	SO:0001583	missense	875	exon10			AGCCGATCCCTTC	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.916A>G	21.37:g.44483101T>C	ENSP00000381231:p.Ile306Val	106	0	0		120	27	0.225	NM_000071	B2R993|D3DSK4|Q99425|Q9BWC5	Missense_Mutation	SNP	ENST00000398165.3	37	CCDS13693.1	.	.	.	.	.	.	.	.	.	.	T	17.87	3.494781	0.64186	.	.	ENSG00000160200	ENST00000398158;ENST00000398165;ENST00000359624;ENST00000352178;ENST00000398168;ENST00000539520;ENST00000544202	D;D;D;D;D;D	0.97066	-4.23;-4.23;-4.23;-4.23;-4.23;-4.23	4.67	4.67	0.58626	Pyridoxal phosphate-dependent enzyme, beta subunit (2);	0.000000	0.85682	D	0.000000	D	0.97766	0.9267	M	0.82056	2.57	0.49798	D	0.99982	P;P	0.46784	0.573;0.884	P;P	0.57720	0.775;0.826	D	0.97377	0.9980	10	0.38643	T	0.18	-21.5015	12.3672	0.55234	0.0:0.0:0.0:1.0	.	306;263	P35520;B7Z2D6	CBS_HUMAN;.	V	306;306;306;306;306;263;218	ENSP00000381225:I306V;ENSP00000381231:I306V;ENSP00000352643:I306V;ENSP00000344460:I306V;ENSP00000381234:I306V;ENSP00000439332:I218V	ENSP00000344460:I306V	I	-	1	0	CBS	43356170	1.000000	0.71417	0.122000	0.21767	0.415000	0.31203	6.807000	0.75201	1.740000	0.51718	0.482000	0.46254	ATC	.	.	none		0.632	CBS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195525.1	NM_000071		C	44483101	T	C	44483101	3	2	30	1	0	0	0	0	1	0	0	0	2713	1435	50	3	771	3	CBS	21	44483101	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	569989	44483101	3646794	688	13839											
KRTAP10-3	386682	hgsc.bcm.edu	37	chr21	45978210	45978210	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agcatgaagaggaagccccaGagcagacgggcacacagcag	15	1	14	11	1	0	4	0	1	0	3	0	5	0	5	2	2	4	4	2	2	2	0	rs200250794		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr21:45978210G>C	ENST00000391620.1	-	1	433	c.389C>G	c.(388-390)tCt>tGt	p.S130C	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron	NM_198696.2	NP_941969.2	P60369	KR103_HUMAN	keratin associated protein 10-3	130	18 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				kidney(1)|lung(4)|prostate(1)|skin(1)	7						GGAAGCCCCAGAgcagacggg	0.657																																					p.S130C		Atlas-SNP	.											.	KRTAP10-3	17	.	0			c.C389G						PASS	.	G	,CYS/SER	0,4406		0,0,2203	154	157	156		,389	0.3	0.9	21		156	4,8596	3.7+/-12.6	0,4,4296	no	intron,missense	TSPEAR,KRTAP10-3	NM_144991.2,NM_198696.2	,112	0,4,6499	CC,CG,GG		0.0465,0.0,0.0308	,benign	,130/222	45978210	4,13002	2203	4300	6503	SO:0001583	missense	386682	exon1			GCCCCAGAGCAGA	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.389C>G	21.37:g.45978210G>C	ENSP00000375478:p.Ser130Cys	165	0	0		199	118	0.592965	NM_198696	A3KN67|Q70LJ4	Missense_Mutation	SNP	ENST00000391620.1	37	CCDS42956.1	.	.	.	.	.	.	.	.	.	.	g	0.926	-0.714347	0.03206	0.0	4.65E-4	ENSG00000212935	ENST00000391620	T	0.00672	5.89	3.53	0.295	0.15752	.	.	.	.	.	T	0.00496	0.0016	N	0.13168	0.305	0.24401	N	0.994705	B	0.09022	0.002	B	0.12156	0.007	T	0.43972	-0.9358	9	0.02654	T	1	.	7.3519	0.26695	0.0:0.4413:0.4219:0.1367	.	130	P60369	KR103_HUMAN	C	130	ENSP00000375478:S130C	ENSP00000375478:S130C	S	-	2	0	KRTAP10-3	44802638	0.172000	0.23043	0.877000	0.34402	0.106000	0.19336	1.422000	0.34826	0.267000	0.21916	0.561000	0.74099	TCT	G|0.999;C|0.001	0.001	weak		0.657	KRTAP10-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128031.1			C	45978210	G	C	45978210	3	2	30	1	0	0	0	0	1	0	0	0	8519	942	33	4	280	4	KRTAP10-3	21	45978210	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1495109	45978210	2151685	689	13840											
CLTCL1	8218	hgsc.bcm.edu	37	chr22	19175095	19175095	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagatgatccttcttgcagAgctccacgctctgggcccac	8	9	10	14	1	2	3	0	1	2	2	4	4	4	3	3	1	2	3	3	1	0	2	rs182434700	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:19175095A>C	ENST00000263200.10	-	29	4652	c.4580T>G	c.(4579-4581)cTc>cGc	p.L1527R	CLTCL1_ENST00000427926.1_Missense_Mutation_p.L1527R|CLTCL1_ENST00000353891.5_Intron|CLTCL1_ENST00000442042.2_Intron	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	1527	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)					CTTCTTGCAGAGCTCCACGCT	0.572			T	?	ALCL								A|||	5	0.000998403	0.0038	0.0	5008	,	,		20542	0.0		0.0	False		,,,				2504	0.0				p.L1527R		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"clathrin, heavy polypeptide-like 1"		L	.	CLTCL1	115	.	0			c.T4580G						PASS	.	A	ARG/LEU,	6,4150		0,6,2072	102	110	107		4580,	4.1	1	22		107	2,8418		0,2,4208	yes	missense,intron	CLTCL1	NM_007098.3,NM_001835.3	102,	0,8,6280	CC,CA,AA		0.0238,0.1444,0.0636	probably-damaging,	1527/1641,	19175095	8,12568	2078	4210	6288	SO:0001583	missense	8218	exon29			TTGCAGAGCTCCA		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.4580T>G	22.37:g.19175095A>C	ENSP00000445677:p.Leu1527Arg	209	1	0.00478469		185	90	0.486486	NM_007098	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	37	CCDS46662.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	23.2	4.381943	0.82792	0.001444	2.38E-4	ENSG00000070371	ENST00000263200;ENST00000427926	T;T	0.29917	1.55;1.55	4.13	4.13	0.48395	.	0.000000	0.64402	D	0.000002	T	0.62392	0.2424	M	0.91038	3.17	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.72434	-0.4295	10	0.87932	D	0	-15.1854	13.2908	0.60270	1.0:0.0:0.0:0.0	.	1527	P53675	CLH2_HUMAN	R	1527	ENSP00000445677:L1527R;ENSP00000441158:L1527R	ENSP00000445677:L1527R	L	-	2	0	CLTCL1	17555095	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.286000	0.89916	1.738000	0.51689	0.533000	0.62120	CTC	A|0.999;C|0.001	0.001	strong		0.572	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098		C	19175095	A	C	19175095	3	2	30	1	0	0	0	0	1	0	0	0	3569	304	11	5	358	5	CLTCL1	22	19175095	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10		19175095	32129471	690	13841											
CLTCL1	8218	hgsc.bcm.edu	37	chr22	19175133	19175133	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caccagttattgcccttgtaCagataggccgcaatgcacct	10	10	8	13	1	0	1	0	0	0	1	0	1	0	1	4	1	3	4	4	1	4	5	rs187075533	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:19175133C>A	ENST00000263200.10	-	29	4614	c.4542G>T	c.(4540-4542)ctG>ctT	p.L1514L	CLTCL1_ENST00000427926.1_Silent_p.L1514L|CLTCL1_ENST00000353891.5_Intron|CLTCL1_ENST00000442042.2_Intron	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	1514	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)					TGCCCTTGTACAGATAGGCCG	0.552			T	?	ALCL								C|||	5	0.000998403	0.0038	0.0	5008	,	,		22029	0.0		0.0	False		,,,				2504	0.0				p.L1514L		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"clathrin, heavy polypeptide-like 1"		L	.	CLTCL1	115	.	0			c.G4542T						PASS	.	C	,	6,4122		0,6,2058	103	106	105		,4542	0.4	0.8	22		105	2,8402		0,2,4200	no	intron,coding-synonymous	CLTCL1	NM_001835.3,NM_007098.3	,	0,8,6258	AA,AC,CC		0.0238,0.1453,0.0638	,	,1514/1641	19175133	8,12524	2064	4202	6266	SO:0001819	synonymous_variant	8218	exon29			CTTGTACAGATAG		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.4542G>T	22.37:g.19175133C>A		278	0	0		215	108	0.502326	NM_007098	B7Z7U5|Q14017|Q15808|Q15809	Silent	SNP	ENST00000263200.10	37	CCDS46662.1																																																																																			C|0.999;A|0.001	0.001	strong		0.552	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098		A	19175133	C	A	19175133	2	1	30	1	0	0	0	0	0	0	0	1	3569	465	17	4		4	CLTCL1	22	19175133	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	38	19175133	32129433	691	13842											
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230408	23230408	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggagcctcagttggaagcAgccgatccagcctgcggagc	8	6	14	13	2	1	0	1	0	0	0	2	4	2	3	4	3	6	2	4	3	1	1	rs552295669		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:23230408A>C	ENST00000526893.1	+	1	449	c.175A>C	c.(175-177)Agc>Cgc	p.S59R	IGLL5_ENST00000532223.2_Missense_Mutation_p.S59R|IGLL5_ENST00000531372.1_Missense_Mutation_p.S59R|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	59						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						AGTTGGAAGCAGCCGATCCAG	0.657																																					p.S59R		Atlas-SNP	.											.	IGLL5	26	.	0			c.A175C						PASS	.																																			SO:0001583	missense	100423062	exon1			GGAAGCAGCCGAT	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.175A>C	22.37:g.23230408A>C	ENSP00000431254:p.Ser59Arg	164	0	0		145	38	0.262069	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	A	12.14	1.848880	0.32699	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00593	6.34;6.35	3.92	-0.722	0.11184	.	.	.	.	.	T	0.00496	0.0016	L	0.29908	0.895	0.09310	N	1	B	0.21821	0.061	B	0.15870	0.014	T	0.45175	-0.9279	9	0.72032	D	0.01	.	3.8729	0.09044	0.4764:0.1955:0.3281:0.0	.	59	B9A064	IGLL5_HUMAN	R	59	ENSP00000436353:S59R;ENSP00000431254:S59R	ENSP00000431254:S59R	S	+	1	0	IGLL5	21560408	0.001000	0.12720	0.000000	0.03702	0.007000	0.05969	0.203000	0.17315	-0.212000	0.10109	0.523000	0.50628	AGC	.	.	none		0.657	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		C	23230408	A	C	23230408	3	2	30	1	0	0	0	0	1	0	0	0	7603	188	7	5	177	5	IGLL5	22	23230408	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	4055275	23230408	28074158	692	13843											
CABIN1	23523	hgsc.bcm.edu	37	chr22	24567795	24567795	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgccagctgactctgtccagCggcccagtgatgctcacacc	7	8	10	16	1	2	2	1	2	1	0	3	2	3	2	4	1	4	2	4	1	0	0	rs145513360	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:24567795C>T	ENST00000398319.2	+	34	6257	c.5872C>T	c.(5872-5874)Cgg>Tgg	p.R1958W	CABIN1_ENST00000405822.2_Missense_Mutation_p.R1879W|CABIN1_ENST00000263119.5_Missense_Mutation_p.R1958W|CABIN1_ENST00000485008.1_3'UTR|CABIN1_ENST00000337989.7_Missense_Mutation_p.R383W	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	1958					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						CTCTGTCCAGCGGCCCAGTGA	0.607													C|||	3	0.000599042	0.0	0.0	5008	,	,		19053	0.0		0.003	False		,,,				2504	0.0				p.R1958W		Atlas-SNP	.											.	CABIN1	153	.	0			c.C5872T						PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	123	115	118		5872,5722,5872	2.7	0.9	22	dbSNP_134	118	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense,missense	CABIN1	NM_001199281.1,NM_001201429.1,NM_012295.3	101,101,101	0,4,6499	TT,TC,CC		0.0465,0.0,0.0308	probably-damaging,probably-damaging,probably-damaging	1958/2221,1908/2171,1958/2221	24567795	4,13002	2203	4300	6503	SO:0001583	missense	23523	exon34			GTCCAGCGGCCCA	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.5872C>T	22.37:g.24567795C>T	ENSP00000381364:p.Arg1958Trp	141	0	0		160	94	0.5875	NM_001199281	G5E9F3|Q6PHY0|Q9Y460	Missense_Mutation	SNP	ENST00000398319.2	37	CCDS13823.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	17.75	3.465698	0.63513	0.0	4.65E-4	ENSG00000099991	ENST00000263119;ENST00000405822;ENST00000398319;ENST00000337989;ENST00000403176	T;T;T;T	0.19806	2.12;2.12;2.12;2.12	4.9	2.7	0.31948	.	0.150708	0.43110	D	0.000609	T	0.30008	0.0751	N	0.24115	0.695	0.39027	D	0.959857	D;D	0.89917	0.999;1.0	P;D	0.79784	0.9;0.993	T	0.12192	-1.0557	10	0.72032	D	0.01	.	12.406	0.55441	0.3019:0.698:0.0:0.0	.	1879;1958	G5E9F3;Q9Y6J0	.;CABIN_HUMAN	W	1958;1879;1958;383;382	ENSP00000263119:R1958W;ENSP00000384694:R1879W;ENSP00000381364:R1958W;ENSP00000336991:R383W	ENSP00000263119:R1958W	R	+	1	2	CABIN1	22897795	0.011000	0.17503	0.915000	0.36163	0.505000	0.33919	0.127000	0.15790	0.689000	0.31550	0.650000	0.86243	CGG	C|0.999;T|0.001	0.001	strong		0.607	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295		T	24567795	C	T	24567795	3	4	30	1	0	0	0	0	1	0	0	0	2530	759	27	1	6002	1	CABIN1	22	24567795	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1337387	24567795	26736771	693	13844											
CRYBB3	1417	hgsc.bcm.edu	37	chr22	25603052	25603052	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccggctaccgtgggcgccAgtacgtgtttgagcggggcg	4	7	17	13	6	0	1	0	1	0	0	0	1	0	1	4	4	3	3	4	4	2	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:25603052A>G	ENST00000215855.2	+	6	589	c.509A>G	c.(508-510)cAg>cGg	p.Q170R	CRYBB3_ENST00000404334.1_3'UTR	NM_004076.3	NP_004067.1	P26998	CRBB3_HUMAN	crystallin, beta B3	170	Beta/gamma crystallin 'Greek key' 4. {ECO:0000255|PROSITE-ProRule:PRU00028}.				visual perception (GO:0007601)		structural constituent of eye lens (GO:0005212)			large_intestine(2)|lung(2)|prostate(1)	5						CGTGGGCGCCAGTACGTGTTT	0.647																																					p.V170G		Atlas-SNP	.											.	CRYBB3	13	.	0			c.T509G						PASS	.						57	52	54					22																	25603052		2201	4300	6501	SO:0001583	missense	1417	exon6			GGCGCCAGTACGT		CCDS13830.1	22q11.23	2008-06-10			ENSG00000100053	ENSG00000100053			2400	protein-coding gene	gene with protein product		123630		CRYB3		8999933	Standard	NM_004076		Approved		uc003abo.2	P26998	OTTHUMG00000150869	ENST00000215855.2:c.509A>G	22.37:g.25603052A>G	ENSP00000215855:p.Gln170Arg	150	0	0		127	51	0.401575	NM_004076	Q3B7S9|Q3T1B7|Q6ISK6|Q92965|Q9UH09	Missense_Mutation	SNP	ENST00000215855.2	37	CCDS13830.1	.	.	.	.	.	.	.	.	.	.	A	27.3	4.816949	0.90790	.	.	ENSG00000100053	ENST00000215855	T	0.80123	-1.34	4.87	4.87	0.63330	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.000000	0.85682	D	0.000000	D	0.92001	0.7466	H	0.94222	3.51	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93900	0.7187	10	0.87932	D	0	.	13.2896	0.60264	1.0:0.0:0.0:0.0	.	170	P26998	CRBB3_HUMAN	R	170	ENSP00000215855:Q170R	ENSP00000215855:Q170R	Q	+	2	0	CRYBB3	23933052	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.664000	0.91139	1.804000	0.52760	0.459000	0.35465	CAG	.	.	none		0.647	CRYBB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320352.1	NM_004076		G	25603052	A	G	25603052	3	3	30	1	0	0	0	0	1	0	0	0	3914	188	7	3	527	3	CRYBB3	22	25603052	Missense_Mutation	SNP	A	TCGA-GR-7353-01A-11D-2210-10	1035257	25603052	25701514	694	13845											
MYO18B	84700	hgsc.bcm.edu	37	chr22	26164700	26164700	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccaggccccaagcccaagggCccggcgagggggtgcgacca	8	1	16	16	3	0	0	0	0	0	0	0	2	0	0	6	5	2	0	6	5	2	0			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:26164700C>T	ENST00000407587.2	+	4	986	c.817C>T	c.(817-819)Ccc>Tcc	p.P273S	MYO18B_ENST00000335473.7_Missense_Mutation_p.P273S|MYO18B_ENST00000536101.1_Missense_Mutation_p.P273S			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	273						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						AGCCCAAGGGCCCGGCGAGGG	0.627																																					p.P273S		Atlas-SNP	.											.	MYO18B	322	.	0			c.C817T						PASS	.						16	20	19					22																	26164700		1895	4089	5984	SO:0001583	missense	84700	exon4			CAAGGGCCCGGCG	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.817C>T	22.37:g.26164700C>T	ENSP00000386096:p.Pro273Ser	60	0	0		53	31	0.584906	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		.	.	.	.	.	.	.	.	.	.	c	11.33	1.607898	0.28623	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.86366	-2.09;-2.09;-2.11	3.13	-3.41	0.04839	.	0.695036	0.11932	N	0.515636	T	0.74176	0.3682	L	0.27053	0.805	0.09310	N	1	B;B;B	0.28291	0.131;0.103;0.206	B;B;B	0.25291	0.018;0.059;0.04	T	0.63278	-0.6673	10	0.66056	D	0.02	.	5.8765	0.18832	0.0:0.3595:0.3875:0.253	.	273;273;273	Q8IUG5;F5GXR6;F5GYU7	MY18B_HUMAN;.;.	S	273	ENSP00000441229:P273S;ENSP00000334563:P273S;ENSP00000386096:P273S	ENSP00000334563:P273S	P	+	1	0	MYO18B	24494700	0.000000	0.05858	0.001000	0.08648	0.367000	0.29736	-0.514000	0.06298	-0.256000	0.09473	0.306000	0.20318	CCC	.	.	none		0.627	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		T	26164700	C	T	26164700	3	4	30	1	0	0	0	0	1	0	0	0	10075	739	26	2	827	2	MYO18B	22	26164700	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	561648	26164700	25139866	695	13846											
MYH9	4627	hgsc.bcm.edu	37	chr22	36689434	36689434	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cttggcctcctcctcctcctCcagctgctcccggaaggaat	5	10	8	18	1	0	0	0	0	0	0	6	2	6	2	7	3	2	2	7	3	2	1			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:36689434C>T	ENST00000216181.5	-	30	4266	c.4036G>A	c.(4036-4038)Gag>Aag	p.E1346K		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1346					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						TCCTCCTCCTCCAGCTGCTCC	0.637			T	ALK	ALCL		"Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"		Hereditary Macrothrombocytopenia, MYH9-associated																												p.E1346K		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"myosin, heavy polypeptide 9, non-muscle"	yes	L	.	MYH9	225	.	0			c.G4036A						PASS	.						80	76	77					22																	36689434		2203	4300	6503	SO:0001583	missense	4627	exon30	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	CCTCCTCCAGCTG		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.4036G>A	22.37:g.36689434C>T	ENSP00000216181:p.Glu1346Lys	75	0	0		100	4	0.04	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Missense_Mutation	SNP	ENST00000216181.5	37	CCDS13927.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.763943	0.89932	.	.	ENSG00000100345	ENST00000216181	D	0.84070	-1.8	5.0	2.88	0.33553	Myosin tail (1);	0.000000	0.85682	D	0.000000	D	0.90974	0.7162	M	0.88906	2.99	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.90771	0.4672	10	0.87932	D	0	.	10.4603	0.44575	0.0:0.7922:0.1347:0.0731	.	1346	P35579	MYH9_HUMAN	K	1346	ENSP00000216181:E1346K	ENSP00000216181:E1346K	E	-	1	0	MYH9	35019380	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	5.997000	0.70646	0.607000	0.29982	0.491000	0.48974	GAG	.	.	none		0.637	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473		T	36689434	C	T	36689434	3	4	30	1	0	0	0	0	1	0	0	0	10051	864	30	2	1894	2	MYH9	22	36689434	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	10524734	36689434	14615132	696	13847											
SLC16A8	23539	hgsc.bcm.edu	37	chr22	38477275	38477275	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccatcaggaacttggtgacgGcgtacacggcgaaggcgcgg	9	5	16	11	6	1	1	1	1	0	0	1	3	1	2	1	6	2	1	1	6	3	2	rs75640043	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:38477275G>A	ENST00000320521.5	-	4	878	c.770C>T	c.(769-771)gCc>gTc	p.A257V	SLC16A8_ENST00000469516.1_Intron	NM_013356.2	NP_037488.2	O95907	MOT3_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 8	257					blood coagulation (GO:0007596)|cellular metabolic process (GO:0044237)|lactate transmembrane transport (GO:0035873)|lactate transport (GO:0015727)|leukocyte migration (GO:0050900)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lactate transmembrane transporter activity (GO:0015129)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			kidney(1)|large_intestine(1)|prostate(1)	3	Melanoma(58;0.045)				Pyruvic acid(DB00119)	CTTGGTGACGGCGTACACGGC	0.721													G|||	140	0.0279553	0.0053	0.0533	5008	,	,		11403	0.003		0.0785	False		,,,				2504	0.0143				p.A257V		Atlas-SNP	.											SLC16A8,NS,carcinoma,0,1	SLC16A8	13	1	0			c.C770T						PASS	.	G	VAL/ALA	70,4292		2,66,2113	18	17	17		770	-0.7	0.9	22	dbSNP_131	17	783,7775		28,727,3524	yes	missense	SLC16A8	NM_013356.2	64	30,793,5637	AA,AG,GG		9.1493,1.6048,6.6022	benign	257/505	38477275	853,12067	2181	4279	6460	SO:0001583	missense	23539	exon4			GTGACGGCGTACA	AF132610	CCDS13966.1	22q12.3-q13.2	2013-07-18	2013-07-18		ENSG00000100156	ENSG00000100156		"Solute carriers"	16270	protein-coding gene	gene with protein product	"monocarboxylate transporter 3"	610409	"solute carrier 16 (monocarboxylic acid transporters), member 8"			10493836	Standard	NM_013356		Approved	MCT3, REMP	uc003auu.3	O95907	OTTHUMG00000151196	ENST00000320521.5:c.770C>T	22.37:g.38477275G>A	ENSP00000321735:p.Ala257Val	94	0	0		46	44	0.956522	NM_013356	Q9UBE2	Missense_Mutation	SNP	ENST00000320521.5	37	CCDS13966.1	82	0.037545787545787544	5	0.01016260162601626	13	0.03591160220994475	2	0.0034965034965034965	62	0.08179419525065963	G	13.23	2.173754	0.38413	0.016048	0.091493	ENSG00000100156	ENST00000320521	T	0.55930	0.49	3.34	-0.715	0.11215	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.106640	0.06977	N	0.819091	T	0.01870	0.0059	L	0.41124	1.26	0.22975	N	0.998482	B	0.19583	0.037	B	0.24974	0.057	T	0.10428	-1.0630	10	0.20046	T	0.44	.	7.5375	0.27719	0.4057:0.0:0.5943:0.0	.	257	O95907	MOT3_HUMAN	V	257	ENSP00000321735:A257V	ENSP00000321735:A257V	A	-	2	0	SLC16A8	36807221	0.995000	0.38212	0.948000	0.38648	0.931000	0.56810	2.753000	0.47524	-0.042000	0.13535	0.313000	0.20887	GCC	G|0.951;A|0.049	0.049	strong		0.721	SLC16A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321724.1	NM_013356		A	38477275	G	A	38477275	3	1	30	1	0	0	0	0	1	0	0	0	14429	1203	42	2	752	2	SLC16A8	22	38477275	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1787841	38477275	12827291	697	13848											
APOBEC3F	200316	hgsc.bcm.edu	37	chr22	39441478	39441478	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgtacagtgaaggtcagcCattcatgccttggtacaaat	11	12	10	8	0	2	1	2	1	0	0	2	1	2	1	2	2	4	2	2	2	4	4	rs138934952	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:39441478C>A	ENST00000308521.5	+	4	854	c.497C>A	c.(496-498)cCa>cAa	p.P166Q	APOBEC3G_ENST00000452957.2_Intron	NM_145298.5	NP_660341.2	Q8IUX4	ABC3F_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3F	166					base conversion or substitution editing (GO:0016553)|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 single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral process (GO:0048525)|positive regulation of defense response to virus by host (GO:0002230)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|ribonucleoprotein complex (GO:0030529)	cytidine deaminase activity (GO:0004126)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|skin(2)	16	Melanoma(58;0.04)					GAAGGTCAGCCATTCATGCCT	0.527													C|||	9	0.00179712	0.0	0.0	5008	,	,		22581	0.0		0.0089	False		,,,				2504	0.0				p.P166Q		Atlas-SNP	.											.	APOBEC3F	37	.	0			c.C497A						PASS	.	C	GLN/PRO	1,4405		0,1,2202	363	299	321		497	-1.4	0	22	dbSNP_134	321	13,8587		0,13,4287	no	missense	APOBEC3F	NM_145298.5	76	0,14,6489	AA,AC,CC		0.1512,0.0227,0.1076	benign	166/374	39441478	14,12992	2203	4300	6503	SO:0001583	missense	200316	exon4			GTCAGCCATTCAT	BC038808	CCDS33648.1, CCDS33649.1	22q13.1-q13.2	2008-05-15			ENSG00000128394	ENSG00000128394		"Apolipoprotein B mRNA editing enzymes"	17356	protein-coding gene	gene with protein product		608993				11863358, 17121840	Standard	NM_145298		Approved	ARP8, BK150C2.4.MRNA, KA6	uc003aww.3	Q8IUX4	OTTHUMG00000151080	ENST00000308521.5:c.497C>A	22.37:g.39441478C>A	ENSP00000309749:p.Pro166Gln	455	0	0		425	197	0.463529	NM_145298	B0QYD4|Q45F03|Q6ICH3|Q7Z2N2|Q7Z2N5	Missense_Mutation	SNP	ENST00000308521.5	37	CCDS33648.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	.	5.006	0.186780	0.09547	2.27E-4	0.001512	ENSG00000128394	ENST00000308521	T	0.63096	-0.02	2.27	-1.43	0.08884	APOBEC-like, C-terminal (1);Cytidine deaminase-like (1);	.	.	.	.	T	0.30386	0.0763	N	0.25825	0.765	0.09310	N	1	B	0.18741	0.03	B	0.17433	0.018	T	0.15292	-1.0442	9	0.20519	T	0.43	.	1.0452	0.01568	0.2303:0.3935:0.226:0.1502	.	166	Q8IUX4	ABC3F_HUMAN	Q	166	ENSP00000309749:P166Q	ENSP00000309749:P166Q	P	+	2	0	APOBEC3F	37771424	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.825000	0.04433	-0.226000	0.09899	0.400000	0.26472	CCA	C|0.998;A|0.002	0.002	strong		0.527	APOBEC3F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321216.1	NM_145298		A	39441478	C	A	39441478	3	1	30	1	0	0	0	0	1	0	0	0	793	594	21	4	650	4	APOBEC3F	22	39441478	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	964203	39441478	11863088	698	13849											
EP300	2033	hgsc.bcm.edu	37	chr22	41546158	41546158	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	agagcacagcagcgtctgttCctaccccaacagcaccgctg	10	6	9	16	2	1	1	0	0	1	1	2	1	2	1	4	0	6	5	4	0	2	2	rs148884710	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:41546158C>A	ENST00000263253.7	+	14	3992	c.2773C>A	c.(2773-2775)Cct>Act	p.P925T		NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	925					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)	p.P925T(1)		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						AGCGTCTGTTCCTACCCCAAC	0.522			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome				C|||	8	0.00159744	0.0	0.0014	5008	,	,		20472	0.0		0.007	False		,,,				2504	0.0				p.P925T		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	EP300,NS,lymphoid_neoplasm,0,1	EP300	367	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C2773A						PASS	.	C	THR/PRO	10,4394	16.8+/-37.8	0,10,2192	64	48	53		2773	3.8	0.9	22	dbSNP_134	53	55,8545	35.3+/-89.8	3,49,4248	yes	missense	EP300	NM_001429.3	38	3,59,6440	AA,AC,CC		0.6395,0.2271,0.4998	benign	925/2415	41546158	65,12939	2202	4300	6502	SO:0001583	missense	2033	exon14	Familial Cancer Database	Broad Thumb-Hallux syndrome	TCTGTTCCTACCC	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.2773C>A	22.37:g.41546158C>A	ENSP00000263253:p.Pro925Thr	59	0	0		58	33	0.568965	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	13.29	2.193769	0.38707	0.002271	0.006395	ENSG00000100393	ENST00000263253	D	0.83992	-1.79	5.92	3.85	0.44370	.	0.135740	0.33401	N	0.004949	T	0.68183	0.2973	L	0.47716	1.5	0.35741	D	0.818666	B	0.13594	0.008	B	0.16722	0.016	T	0.67608	-0.5627	10	0.22706	T	0.39	-8.5427	8.0505	0.30575	0.0:0.7318:0.1307:0.1375	.	925	Q09472	EP300_HUMAN	T	925	ENSP00000263253:P925T	ENSP00000263253:P925T	P	+	1	0	EP300	39876104	0.960000	0.32886	0.934000	0.37439	0.957000	0.61999	1.349000	0.33998	0.859000	0.35456	-0.373000	0.07131	CCT	C|0.995;A|0.005	0.005	strong		0.522	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		A	41546158	C	A	41546158	3	1	30	1	0	0	0	0	1	0	0	0	5150	855	30	4	2827	4	EP300	22	41546158	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	2104680	41546158	9758408	699	13850											
CYP2D6	1565	hgsc.bcm.edu	37	chr22	42525089	42525089	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcctcctcggtcacccactGctccagcgacttcttgccca	5	9	8	19	2	2	0	1	0	1	0	5	1	4	0	5	2	3	1	5	2	0	2	rs78482768	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:42525089G>C	ENST00000360608.5	-	3	565	c.451C>G	c.(451-453)Cag>Gag	p.Q151E	CYP2D6_ENST00000389970.3_Missense_Mutation_p.Q151E|CYP2D6_ENST00000359033.4_Intron|NDUFA6-AS1_ENST00000608288.1_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|NDUFA6-AS1_ENST00000608491.1_RNA|NDUFA6-AS1_ENST00000439129.1_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	151					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)	GTCACCCACTGCTCCAGCGAC	0.677													G|||	6	0.00119808	0.0	0.0014	5008	,	,		16419	0.0		0.005	False		,,,				2504	0.0				p.Q151E		Atlas-SNP	.											.	CYP2D6	104	.	0			c.C451G						PASS	.	G	GLU/GLN,	5,4131		0,5,2063	19	23	22		451,	2	1	22	dbSNP_131	22	28,8350		1,26,4162	no	missense,intron	CYP2D6	NM_000106.4,NM_001025161.1	29,	1,31,6225	CC,CG,GG		0.3342,0.1209,0.2637	benign,	151/498,	42525089	33,12481	2068	4189	6257	SO:0001583	missense	1565	exon3			CCCACTGCTCCAG	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.451C>G	22.37:g.42525089G>C	ENSP00000353820:p.Gln151Glu	119	0	0		102	52	0.509804	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Missense_Mutation	SNP	ENST00000360608.5	37	CCDS46721.1	.	.	.	.	.	.	.	.	.	.	g	0.009	-1.841892	0.00573	0.001209	0.003342	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000413640	T;T	0.77877	-1.13;-1.13	4.18	1.97	0.26223	.	0.756605	0.11656	N	0.542295	T	0.52008	0.1708	N	0.11341	0.13	0.22684	N	0.998852	B	0.10296	0.003	B	0.08055	0.003	T	0.38929	-0.9638	10	0.02654	T	1	.	6.6787	0.23108	0.1016:0.3458:0.5526:0.0	.	151	Q6NWU0	.	E	151;151;100	ENSP00000353820:Q151E;ENSP00000374620:Q151E	ENSP00000353820:Q151E	Q	-	1	0	CYP2D6	40855033	0.005000	0.15991	0.998000	0.56505	0.063000	0.16089	0.273000	0.18662	0.442000	0.26555	0.305000	0.20034	CAG	G|1.000;|0.000	.	weak		0.677	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1			C	42525089	G	C	42525089	3	2	30	1	0	0	0	0	1	0	0	0	4171	1328	46	4	1070	4	CYP2D6	22	42525089	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	978931	42525089	8779477	700	13851											
CYP2D6	1565	hgsc.bcm.edu	37	chr22	42526775	42526775	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cactatcacggccaggggcaCcagtgcttctagccccatac	9	7	9	16	1	2	0	1	0	1	0	2	0	2	0	4	3	3	2	4	3	3	4	rs72549358	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:42526775C>T	ENST00000360608.5	-	1	133	c.19G>A	c.(19-21)Gtg>Atg	p.V7M	CYP2D6_ENST00000389970.3_Missense_Mutation_p.V7M|CYP2D6_ENST00000359033.4_Missense_Mutation_p.V7M|NDUFA6-AS1_ENST00000608288.1_RNA|NDUFA6-AS1_ENST00000416037.2_RNA|NDUFA6-AS1_ENST00000608491.1_RNA|NDUFA6-AS1_ENST00000439129.1_RNA	NM_000106.5	NP_000097	P10635	CP2D6_HUMAN	cytochrome P450, family 2, subfamily D, polypeptide 6	7					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)	GCCAGGGGCACCAGTGCTTCT	0.652													C|||	6	0.00119808	0.0	0.0014	5008	,	,		19268	0.0		0.005	False		,,,				2504	0.0				p.V7M		Atlas-SNP	.											.	CYP2D6	104	.	0			c.G19A						PASS	.	C	MET/VAL,MET/VAL	6,4376		0,6,2185	37	37	37		19,19	0.1	0	22	dbSNP_130	37	27,8549		0,27,4261	no	missense,missense	CYP2D6	NM_001025161.1,NM_000106.4	21,21	0,33,6446	TT,TC,CC		0.3148,0.1369,0.2547	benign,benign	7/447,7/498	42526775	33,12925	2191	4288	6479	SO:0001583	missense	1565	exon1			GGGGCACCAGTGC	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.19G>A	22.37:g.42526775C>T	ENSP00000353820:p.Val7Met	308	1	0.00324675		289	154	0.532872	NM_000106	Q16752|Q2XND6|Q2XND7|Q2XNE0|Q6B012|Q6NXU8	Missense_Mutation	SNP	ENST00000360608.5	37	CCDS46721.1	.	.	.	.	.	.	.	.	.	.	C	1.817	-0.473201	0.04445	0.001369	0.003148	ENSG00000100197	ENST00000360608;ENST00000389970;ENST00000359033	T;T;T	0.37058	1.22;1.22;1.22	3.46	0.0648	0.14354	.	3.717790	0.00802	N	0.001421	T	0.18964	0.0455	N	0.08118	0	0.09310	N	1	B;B	0.13145	0.007;0.007	B;B	0.08055	0.003;0.002	T	0.12578	-1.0542	10	0.34782	T	0.22	.	2.8284	0.05491	0.2852:0.448:0.0:0.2668	.	7;7	Q6NXU8;Q6NWU0	.;.	M	7	ENSP00000353820:V7M;ENSP00000374620:V7M;ENSP00000351927:V7M	ENSP00000351927:V7M	V	-	1	0	CYP2D6	40856719	0.001000	0.12720	0.013000	0.15412	0.004000	0.04260	-0.451000	0.06795	0.050000	0.15949	-0.350000	0.07774	GTG	C|0.996;T|0.004	0.004	strong		0.652	CYP2D6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320525.1			T	42526775	C	T	42526775	3	4	30	1	0	0	0	0	1	0	0	0	4171	507	18	2	1510	2	CYP2D6	22	42526775	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	1686	42526775	8777791	701	13852											
FAM118A	55007	hgsc.bcm.edu	37	chr22	45719125	45719125	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gttatcgggactggcgtcagCgcagcagtggcccccggaat	7	7	15	12	4	1	0	1	0	0	0	2	2	1	2	2	4	2	3	2	4	2	1	rs138980075	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:45719125C>T	ENST00000216214.3	+	4	951	c.117C>T	c.(115-117)agC>agT	p.S39S	FAM118A_ENST00000405673.1_Silent_p.S39S|FAM118A_ENST00000441876.2_Silent_p.S39S	NM_001104595.1	NP_001098065.1	Q9NWS6	F118A_HUMAN	family with sequence similarity 118, member A	39						integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(1)	11		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		CTGGCGTCAGCGCAGCAGTGG	0.572													C|||	10	0.00199681	0.0	0.0014	5008	,	,		17209	0.0		0.006	False		,,,				2504	0.0031				p.S39S		Atlas-SNP	.											.	FAM118A	32	.	0			c.C117T						PASS	.	C	,	2,4404	4.2+/-10.8	0,2,2201	44	49	47		117,117	-11.3	0	22	dbSNP_134	47	36,8564	23.4+/-69.3	0,36,4264	no	coding-synonymous,coding-synonymous	FAM118A	NM_001104595.1,NM_017911.2	,	0,38,6465	TT,TC,CC		0.4186,0.0454,0.2922	,	39/358,39/358	45719125	38,12968	2203	4300	6503	SO:0001819	synonymous_variant	55007	exon3			CGTCAGCGCAGCA	BC013696	CCDS14065.1	22q13.3	2006-04-26	2006-04-26	2006-04-26	ENSG00000100376	ENSG00000100376			1313	protein-coding gene	gene with protein product			"chromosome 22 open reading frame 8"	C22orf8		12477932	Standard	NM_001104595		Approved	FLJ20635, bK268H5.C22.4	uc003bga.4	Q9NWS6	OTTHUMG00000151338	ENST00000216214.3:c.117C>T	22.37:g.45719125C>T		165	0	0		175	83	0.474286	NM_017911	B3KWG4|B4DY02|Q5TII5|Q96CY3	Silent	SNP	ENST00000216214.3	37	CCDS14065.1																																																																																			C|0.997;T|0.003	0.003	strong		0.572	FAM118A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322260.1	NM_017911		T	45719125	C	T	45719125	2	4	30	1	0	0	0	0	0	0	0	1	5416	767	27	1		1	FAM118A	22	45719125	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	3192350	45719125	5585441	702	13853											
BRD1	23774	hgsc.bcm.edu	37	chr22	50187853	50187853	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggagccgctggacttcatagCgcaggtgaggtcgagcatgt	8	8	16	9	3	1	1	1	1	0	0	2	4	1	3	1	4	3	3	1	4	1	2	rs35331092	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50187853C>T	ENST00000216267.8	-	6	2674	c.2188G>A	c.(2188-2190)Gct>Act	p.A730T	BRD1_ENST00000342989.5_Missense_Mutation_p.A325T|BRD1_ENST00000404034.1_Missense_Mutation_p.A730T|BRD1_ENST00000542442.1_Missense_Mutation_p.A418T|BRD1_ENST00000404760.1_Missense_Mutation_p.A730T|BRD1_ENST00000457780.2_Missense_Mutation_p.A730T	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	730			A -> T (in dbSNP:rs35331092).		histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			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)		GACTTCATAGCGCAGGTGAGG	0.607													C|||	342	0.0682907	0.0825	0.0317	5008	,	,		18559	0.003		0.0596	False		,,,				2504	0.1513				p.A730T		Atlas-SNP	.											.	BRD1	144	.	0			c.G2188A						PASS	.	C	THR/ALA	422,3984	206.5+/-228.1	21,380,1802	59	63	62		2188	-0.9	0.4	22	dbSNP_126	62	590,8010	156.4+/-210.3	24,542,3734	yes	missense	BRD1	NM_014577.1	58	45,922,5536	TT,TC,CC		6.8605,9.5778,7.781	benign	730/1059	50187853	1012,11994	2203	4300	6503	SO:0001583	missense	23774	exon6			TCATAGCGCAGGT	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.2188G>A	22.37:g.50187853C>T	ENSP00000216267:p.Ala730Thr	110	0	0		100	59	0.59	NM_014577	A6ZJA4	Missense_Mutation	SNP	ENST00000216267.8	37	CCDS14080.1	96	0.04395604395604396	41	0.08333333333333333	12	0.03314917127071823	0	0.0	43	0.05672823218997362	C	14.17	2.456934	0.43634	0.095778	0.068605	ENSG00000100425	ENST00000216267;ENST00000404034;ENST00000404760;ENST00000457780;ENST00000542442;ENST00000342989;ENST00000419212	T;T;T;T;T;T	0.28255	2.57;2.57;2.58;2.44;1.62;2.01	5.4	-0.94	0.10405	.	0.418477	0.26248	N	0.025479	T	0.00754	0.0025	L	0.39898	1.24	0.28355	P	0.9207138	P;P;P;D	0.54964	0.948;0.63;0.788;0.969	B;B;B;B	0.43728	0.247;0.12;0.169;0.429	T	0.07654	-1.0761	9	0.31617	T	0.26	.	21.7236	0.99959	0.1644:0.8356:0.0:0.0	rs35331092	730;325;730;730	Q86X06;B7Z926;O95696;O95696-2	.;.;BRD1_HUMAN;.	T	730;730;730;730;418;325;190	ENSP00000216267:A730T;ENSP00000384076:A730T;ENSP00000385858:A730T;ENSP00000410042:A730T;ENSP00000437514:A418T;ENSP00000345886:A325T	ENSP00000216267:A730T	A	-	1	0	BRD1	48573857	0.065000	0.20965	0.369000	0.25952	0.980000	0.70556	0.428000	0.21395	-0.460000	0.07003	0.655000	0.94253	GCT	C|0.936;T|0.064	0.064	strong		0.607	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577		T	50187853	C	T	50187853	3	4	30	1	0	0	0	0	1	0	0	0	1503	768	27	1	1016	1	BRD1	22	50187853	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	4468728	50187853	1116713	703	13854											
BRD1	23774	hgsc.bcm.edu	37	chr22	50217387	50217387	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcgcagtgcgactccttctcGaagcggtccatcaggaactc	8	9	10	14	4	2	0	1	0	1	0	7	3	4	1	2	2	3	1	2	2	2	1	rs11912787	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50217387G>A	ENST00000216267.8	-	1	1065	c.579C>T	c.(577-579)ttC>ttT	p.F193F	BRD1_ENST00000342989.5_5'Flank|BRD1_ENST00000404034.1_Silent_p.F193F|BRD1_ENST00000542442.1_5'Flank|BRD1_ENST00000459821.1_5'Flank|BRD1_ENST00000404760.1_Silent_p.F193F|BRD1_ENST00000457780.2_Silent_p.F193F	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	193					histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			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)		ACTCCTTCTCGAAGCGGTCCA	0.602													G|||	508	0.101438	0.1664	0.0432	5008	,	,		21111	0.003		0.0746	False		,,,				2504	0.184				p.F193F		Atlas-SNP	.											.	BRD1	144	.	0			c.C579T						PASS	.	G		801,3605	322.9+/-297.8	69,663,1471	72	61	65		579	-5.2	1	22	dbSNP_120	65	702,7898	172.6+/-223.3	31,640,3629	no	coding-synonymous	BRD1	NM_014577.1		100,1303,5100	AA,AG,GG		8.1628,18.1798,11.5562		193/1059	50217387	1503,11503	2203	4300	6503	SO:0001819	synonymous_variant	23774	exon1			CTTCTCGAAGCGG	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.579C>T	22.37:g.50217387G>A		112	0	0		116	57	0.491379	NM_014577	A6ZJA4	Silent	SNP	ENST00000216267.8	37	CCDS14080.1																																																																																			G|0.899;A|0.101	0.101	strong		0.602	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577		A	50217387	G	A	50217387	2	1	30	1	0	0	0	0	0	0	0	1	1503	1049	37	1		1	BRD1	22	50217387	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	29534	50217387	1087179	704	13855											
PANX2	56666	hgsc.bcm.edu	37	chr22	50617671	50617671	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcctcatcgccaccttcgacGagccgagaacggtcgtgagt	8	8	11	14	6	1	2	1	1	0	1	5	5	2	2	4	1	2	0	4	1	1	1			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chr22:50617671G>A	ENST00000395842.2	+	3	1999	c.1999G>A	c.(1999-2001)Gag>Aag	p.E667K	PANX2_ENST00000159647.5_Silent_p.T638T	NM_052839.3	NP_443071.2	Q96RD6	PANX2_HUMAN	pannexin 2	667					ion transport (GO:0006811)|protein hexamerization (GO:0034214)|response to ischemia (GO:0002931)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction hemi-channel activity (GO:0055077)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(1)|skin(1)	7		all_cancers(38;1.14e-10)|all_epithelial(38;2.12e-09)|all_lung(38;7.01e-05)|Breast(42;0.000523)|Lung NSC(38;0.0018)|Ovarian(80;0.0365)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.105)		CACCTTCGACGAGCCGAGAAC	0.697																																					p.E667K		Atlas-SNP	.											.	PANX2	69	.	0			c.G1999A						PASS	.						49	43	45					22																	50617671		2203	4297	6500	SO:0001583	missense	56666	exon3			TTCGACGAGCCGA		CCDS14085.2, CCDS54544.1	22q13.33	2011-12-05			ENSG00000073150	ENSG00000073150		"Ion channels / Pannexins"	8600	protein-coding gene	gene with protein product		608421				14702039, 14597722	Standard	NM_052839		Approved	hPANX2, PX2	uc003bjn.4	Q96RD6	OTTHUMG00000044649	ENST00000395842.2:c.1999G>A	22.37:g.50617671G>A	ENSP00000379183:p.Glu667Lys	146	0	0		127	44	0.346457	NM_052839	B7Z684|Q96RD5|Q9UGX8	Missense_Mutation	SNP	ENST00000395842.2	37	CCDS14085.2	.	.	.	.	.	.	.	.	.	.	G	22.1	4.250501	0.80024	.	.	ENSG00000073150	ENST00000395842;ENST00000401643	T	0.33216	1.42	3.72	3.72	0.42706	.	0.000000	0.37304	U	0.002153	T	0.55529	0.1926	.	.	.	0.46279	D	0.998968	D	0.76494	0.999	D	0.68621	0.959	T	0.64744	-0.6335	9	0.87932	D	0	-23.7117	15.9969	0.80256	0.0:0.0:1.0:0.0	.	667	Q96RD6	PANX2_HUMAN	K	667;344	ENSP00000379183:E667K	ENSP00000379183:E667K	E	+	1	0	PANX2	48959798	1.000000	0.71417	0.946000	0.38457	0.282000	0.26991	6.495000	0.73665	2.081000	0.62600	0.313000	0.20887	GAG	.	.	none		0.697	PANX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075010.3	NM_052839		A	50617671	G	A	50617671	3	1	30	1	0	0	0	0	1	0	0	0	11430	1059	37	1	2009	1	PANX2	22	50617671	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	400284	50617671	686895	705	13856											
MXRA5	25878	hgsc.bcm.edu	37	chrX	3248333	3248333	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gacgttaagccgttgaaagcTtgagggtggataaactcgat	12	10	13	6	3	0	2	0	2	0	0	1	5	0	3	1	2	3	3	1	2	4	4	rs372395776		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:3248333T>C	ENST00000217939.6	-	4	589	c.435A>G	c.(433-435)caA>caG	p.Q145Q		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	145						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)				CGTTGAAAGCTTGAGGGTGGA	0.488																																					p.Q145Q		Atlas-SNP	.											.	MXRA5	815	.	0			c.A435G						PASS	.	T		1,3834		0,0,1,1632,570	118	96	103		435	-7.1	0	X		103	1,6727		0,0,1,2428,1871	no	coding-synonymous	MXRA5	NM_015419.3		0,0,2,4060,2441	CC,CT,C,TT,T		0.0149,0.0261,0.0189		145/2829	3248333	2,10561	2203	4300	6503	SO:0001819	synonymous_variant	25878	exon4			GAAAGCTTGAGGG	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.435A>G	X.37:g.3248333T>C		397	2	0.00503778		176	171	0.971591	NM_015419	Q6P1M7|Q9Y3Y8	Silent	SNP	ENST00000217939.6	37	CCDS14124.1																																																																																			.	.	weak		0.488	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419		C	3248333	T	C	3248333	2	2	30	1	0	0	0	0	0	0	0	1	10012	1606	56	3		3	MXRA5	23	3248333	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10		3248333	152022227	706	13857											
FRMPD4	9758	hgsc.bcm.edu	37	chrX	12720127	12720127	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aaaatctccctcaaatacatCgagtaagtgttgactctcag	14	11	6	10	1	3	1	2	1	2	0	6	2	3	1	1	0	1	2	1	0	5	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:12720127C>T	ENST00000380682.1	+	10	1574	c.1068C>T	c.(1066-1068)atC>atT	p.I356I		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	356	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)	p.I346I(1)		breast(1)|central_nervous_system(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)	22						TCAAATACATCGAGTAAGTGT	0.468											OREG0019670	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I356I		Atlas-SNP	.											.	FRMPD4	214	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1068T						PASS	.						124	103	110					X																	12720127		2203	4300	6503	SO:0001819	synonymous_variant	9758	exon10			ATACATCGAGTAA	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.1068C>T	X.37:g.12720127C>T		101	0	0	682	39	39	1	NM_014728	A8K0X9|O15032	Silent	SNP	ENST00000380682.1	37	CCDS35201.1																																																																																			.	.	none		0.468	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712		T	12720127	C	T	12720127	2	4	30	1	0	0	0	0	0	0	0	1	6067	874	31	1		1	FRMPD4	23	12720127	Silent	SNP	C	TCGA-GR-7353-01A-11D-2210-10	9471794	12720127	142550433	707	13858											
KLHL34	257240	hgsc.bcm.edu	37	chrX	21675125	21675125	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagcggctggcgggagggcGtcgtgtggtagttgagggcc	4	8	22	7	4	0	2	0	2	0	0	1	3	0	3	1	6	1	3	1	6	1	2			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:21675125G>A	ENST00000379499.2	-	1	1323	c.782C>T	c.(781-783)aCg>aTg	p.T261M		NM_153270.1	NP_695002.1	Q8N239	KLH34_HUMAN	kelch-like family member 34	261						extracellular space (GO:0005615)				cervix(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(11)|ovary(2)|urinary_tract(1)	26						GCGGGAGGGCGTCGTGTGGTA	0.706													G|||	1	0.000264901	0.0	0.0	3775	,	,		9852	0.0		0.0	False		,,,				2504	0.001				p.T261M		Atlas-SNP	.											.	KLHL34	76	.	0			c.C782T						PASS	.						16	18	17					X																	21675125		2197	4282	6479	SO:0001583	missense	257240	exon1			GAGGGCGTCGTGT	AK092279	CCDS14199.1	Xp22.12	2013-02-22	2013-02-22		ENSG00000185915	ENSG00000185915		"Kelch-like", "BTB/POZ domain containing"	26634	protein-coding gene	gene with protein product			"kelch-like 34 (Drosophila)"				Standard	NM_153270		Approved	FLJ34960, RP11-450P7.3	uc004czz.1	Q8N239	OTTHUMG00000021234	ENST00000379499.2:c.782C>T	X.37:g.21675125G>A	ENSP00000368813:p.Thr261Met	203	0	0		87	83	0.954023	NM_153270		Missense_Mutation	SNP	ENST00000379499.2	37	CCDS14199.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.747283	0.00086	.	.	ENSG00000185915	ENST00000379499	T	0.72394	-0.65	4.76	3.89	0.44902	.	0.552287	0.18919	N	0.127528	T	0.38480	0.1042	N	0.01168	-0.975	0.09310	N	1	B	0.20887	0.049	B	0.12837	0.008	T	0.24693	-1.0153	10	0.27082	T	0.32	.	8.1602	0.31194	0.0844:0.0:0.7565:0.1591	.	261	Q8N239	KLH34_HUMAN	M	261	ENSP00000368813:T261M	ENSP00000368813:T261M	T	-	2	0	KLHL34	21585046	0.003000	0.15002	0.038000	0.18304	0.365000	0.29674	1.693000	0.37742	0.990000	0.38787	0.422000	0.28245	ACG	.	.	none		0.706	KLHL34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056022.1	NM_153270		A	21675125	G	A	21675125	3	1	30	1	0	0	0	0	1	0	0	0	8396	1145	40	1	1156	1	KLHL34	23	21675125	Missense_Mutation	SNP	G	TCGA-GR-7353-01A-11D-2210-10	8954998	21675125	133595435	708	13859											
SYTL5	94122	hgsc.bcm.edu	37	chrX	37935844	37935844	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttcttagcaagttcagatcGgcaaccagaggagaaatcat	14	9	9	9	1	3	3	2	0	1	3	4	4	3	3	1	2	2	3	1	2	4	3	rs12558731	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:37935844G>A	ENST00000357972.5	+	6	1125	c.579G>A	c.(577-579)tcG>tcA	p.S193S	TM4SF2_ENST00000465127.1_Intron|SYTL5_ENST00000297875.2_Silent_p.S193S|SYTL5_ENST00000456733.2_Silent_p.S193S			Q8TDW5	SYTL5_HUMAN	synaptotagmin-like 5	193					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						AGTTCAGATCGGCAACCAGAG	0.338													A|||	12	0.00317881	0.0015	0.013	3775	,	,		12229	0.0		0.001	False		,,,				2504	0.0				p.S193S		Atlas-SNP	.											.	SYTL5	72	.	0			c.G579A						PASS	.	A	,,	5,3828		0,4,1,1627,570	68	52	57		579,579,579	5.2	1	X	dbSNP_120	57	75,6653		0,55,20,2373,1852	no	coding-synonymous,coding-synonymous,coding-synonymous	SYTL5	NM_001163334.1,NM_001163335.1,NM_138780.2	,,	0,59,21,4000,2422	AA,AG,A,GG,G		1.1147,0.1304,0.7575	,,	193/753,193/731,193/731	37935844	80,10481	2202	4300	6502	SO:0001819	synonymous_variant	94122	exon5			CAGATCGGCAACC		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.579G>A	X.37:g.37935844G>A		146	0	0		41	40	0.97561	NM_001163334	A2RRF2	Silent	SNP	ENST00000357972.5	37	CCDS14244.1																																																																																			G|0.993;A|0.007	0.007	strong		0.338	SYTL5-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080883.1	NM_138780		A	37935844	G	A	37935844	2	1	30	1	0	0	0	0	0	0	0	1	15501	1103	39	1		1	SYTL5	23	37935844	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	16260719	37935844	117334716	709	13860											
BCOR	54880	hgsc.bcm.edu	37	chrX	39932808	39932808	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggccgggggctggcccacGtgctgaataacggatggtgt	6	8	18	9	3	0	1	0	1	0	0	0	2	0	2	2	6	2	2	2	6	2	1	rs144606152	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:39932808G>A	ENST00000378444.4	-	4	2019	c.1791C>T	c.(1789-1791)caC>caT	p.H597H	BCOR_ENST00000397354.3_Silent_p.H597H|BCOR_ENST00000342274.4_Silent_p.H597H|BCOR_ENST00000378455.4_Silent_p.H597H	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	597					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						GCTGGCCCACGTGCTGAATAA	0.607			"F, N, S, T"	RARA	"retinoblastoma, AML, APL(translocation)"		oculo-facio-cardio-dental genetic						G|||	63	0.0166887	0.0015	0.0159	3775	,	,		12801	0.0		0.0437	False		,,,				2504	0.0061				p.H597H		Atlas-SNP	.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	.	0			c.C1791T						PASS	.	G	,,,	22,3811		0,19,3,1612,568	68	65	66		1791,1791,1791,1791	-1.4	0.9	X	dbSNP_134	66	372,6356		5,260,102,2163,1770	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BCOR	NM_001123383.1,NM_001123384.1,NM_001123385.1,NM_017745.5	,,,	5,279,105,3775,2338	AA,AG,A,GG,G		5.5291,0.574,3.7307	,,,	597/1722,597/1704,597/1756,597/1722	39932808	394,10167	2202	4300	6502	SO:0001819	synonymous_variant	54880	exon4			GCCCACGTGCTGA	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.1791C>T	X.37:g.39932808G>A		90	0	0		38	36	0.947368	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Silent	SNP	ENST00000378444.4	37	CCDS48093.1																																																																																			G|0.963;A|0.037	0.037	strong		0.607	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745		A	39932808	G	A	39932808	2	1	30	1	0	0	0	0	0	0	0	1	1386	1136	40	1		1	BCOR	23	39932808	Silent	SNP	G	TCGA-GR-7353-01A-11D-2210-10	1996964	39932808	115337752	710	13861											
PAGE5	90737	hgsc.bcm.edu	37	chrX	55247817	55247817	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgttttcagtgagagataTgagtgagcatgtaacaagat	13	14	11	3	0	1	5	1	3	0	2	1	6	1	5	0	0	2	3	0	0	3	5	rs61745114	byFrequency	TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:55247817T>C	ENST00000289619.5	+	2	307	c.62T>C	c.(61-63)aTg>aCg	p.M21T	PAGE5_ENST00000374952.1_Start_Codon_SNP_p.M1T|PAGE5_ENST00000374955.3_Start_Codon_SNP_p.M1T	NM_130467.3	NP_569734.2	Q96GU1	PAGE5_HUMAN	P antigen family, member 5 (prostate associated)	21										breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	8						GTGAGAGATATGAGTGAGCAT	0.363													T|||	7	0.0018543	0.0	0.0	3775	,	,		11913	0.0		0.006	False		,,,				2504	0.001				p.M21T		Atlas-SNP	.											.	PAGE5	20	.	0			c.T62C						PASS	.	T	THR/MET,THR/MET	11,3824		0,11,0,1621,571	98	80	86		2,62	1.1	0	X	dbSNP_129	86	80,6648		0,52,28,2376,1844	yes	missense,missense	PAGE5	NM_001013435.1,NM_130467.3	81,81	0,63,28,3997,2415	CC,CT,C,TT,T		1.1891,0.2868,0.8615	probably-damaging,probably-damaging	1/111,21/131	55247817	91,10472	2203	4300	6503	SO:0001583	missense	90737	exon2			GAGATATGAGTGA	AJ344352	CCDS14368.1, CCDS35306.1	Xp11.22	2009-08-18			ENSG00000158639	ENSG00000158639			29992	protein-coding gene	gene with protein product	"cancer/testis antigen family 16, member 1", "cancer/testis antigen family 16, member 2"					11920606, 11992404	Standard	XM_006724613		Approved	PAGE-5, CT16.1, CT16.2	uc004duk.3	Q96GU1	OTTHUMG00000021650	ENST00000289619.5:c.62T>C	X.37:g.55247817T>C	ENSP00000289619:p.Met21Thr	622	0	0		278	272	0.978417	NM_130467	Q2NL97|Q5JUL0|Q8WWL9	Missense_Mutation	SNP	ENST00000289619.5	37	CCDS14368.1	4	0.0024110910186859553	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	.	9.512	1.106093	0.20632	0.002868	0.011891	ENSG00000158639	ENST00000289619;ENST00000374955;ENST00000374952	T;T;T	0.50813	1.66;1.75;0.73	1.09	1.09	0.20402	.	.	.	.	.	T	0.49081	0.1536	M	0.67397	2.05	0.54753	D	0.999989	D	0.60160	0.987	D	0.66196	0.942	T	0.55205	-0.8177	9	0.87932	D	0	.	4.0529	0.09803	0.0:0.0:0.0:1.0	rs61745114	21	Q96GU1	GGEE1_HUMAN	T	21;1;1	ENSP00000289619:M21T;ENSP00000364093:M1T;ENSP00000364090:M1T	ENSP00000289619:M21T	M	+	2	0	PAGE5	55264542	0.381000	0.25140	0.020000	0.16555	0.069000	0.16628	0.969000	0.29370	0.677000	0.31305	0.231000	0.17811	ATG	T|0.994;C|0.006	0.006	strong		0.363	PAGE5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056861.1	NM_130467		C	55247817	T	C	55247817	3	2	30	1	0	0	0	0	1	0	0	0	11402	1464	51	3	68	3	PAGE5	23	55247817	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	15315009	55247817	100022743	711	13862											
MED12	9968	hgsc.bcm.edu	37	chrX	70351982	70351982	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atcgaggttttccaacagtcAgcagagacagggtcatcttc	11	10	10	10	1	3	1	2	0	1	1	6	3	4	1	1	2	2	2	1	2	1	3	rs376058351		TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:70351982A>C	ENST00000374080.3	+	30	4211	c.4179A>C	c.(4177-4179)tcA>tcC	p.S1393S	MED12_ENST00000374102.1_Silent_p.S1393S|MED12_ENST00000333646.6_Silent_p.S1393S			Q93074	MED12_HUMAN	mediator complex subunit 12	1393					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)					TCCAACAGTCAGCAGAGACAG	0.512			"M, S"		uterine leiomyoma		Opitz-Kaveggia Syndrome																														p.S1393S		Atlas-SNP	.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12	984	.	0			c.A4179C						PASS	.	A		0,3657		0,0,1543,571	83	76	78		4179	-8.8	0.4	X		78	2,6605		0,2,2395,1813	no	coding-synonymous	MED12	NM_005120.2		0,2,3938,2384	CC,CA,AA,A		0.0303,0.0,0.0195		1393/2178	70351982	2,10262	2114	4210	6324	SO:0001819	synonymous_variant	9968	exon30			ACAGTCAGCAGAG	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.4179A>C	X.37:g.70351982A>C		429	0	0		213	207	0.971831	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Silent	SNP	ENST00000374080.3	37	CCDS43970.1																																																																																			.	.	weak		0.512	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120		C	70351982	A	C	70351982	2	2	30	1	0	0	0	0	0	0	0	1	9437	175	7	5		5	MED12	23	70351982	Silent	SNP	A	TCGA-GR-7353-01A-11D-2210-10	15104165	70351982	84918578	712	13863											
NAP1L3	4675	hgsc.bcm.edu	37	chrX	92927728	92927728	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttctttagggttttcttcTtcctcaccctctaagggagg	5	18	8	10	0	5	0	1	0	4	0	6	1	6	1	2	3	0	1	2	3	2	9			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:92927728T>C	ENST00000373079.3	-	1	839	c.576A>G	c.(574-576)gaA>gaG	p.E192E	FAM133A_ENST00000538690.1_5'Flank|FAM133A_ENST00000355813.5_5'Flank|NAP1L3_ENST00000475430.2_Silent_p.E185E|FAM133A_ENST00000332647.4_5'Flank|FAM133A_ENST00000322139.4_5'Flank	NM_004538.5	NP_004529.2	Q99457	NP1L3_HUMAN	nucleosome assembly protein 1-like 3	192	Glu-rich.				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						GGTTTTCTTCTTCCTCACCCT	0.438																																					p.E192E		Atlas-SNP	.											.	NAP1L3	81	.	0			c.A576G						PASS	.						80	79	79					X																	92927728		2203	4300	6503	SO:0001819	synonymous_variant	4675	exon1			TTCTTCTTCCTCA		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.576A>G	X.37:g.92927728T>C		159	0	0		78	5	0.0641026	NM_004538	B2RCM0|O60788	Silent	SNP	ENST00000373079.3	37	CCDS14465.1																																																																																			.	.	none		0.438	NAP1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057449.1	NM_004538		C	92927728	T	C	92927728	2	2	30	1	0	0	0	0	0	0	0	1	10167	1606	56	3		3	NAP1L3	23	92927728	Silent	SNP	T	TCGA-GR-7353-01A-11D-2210-10	22575746	92927728	62342832	713	13864											
VSIG1	340547	hgsc.bcm.edu	37	chrX	107320447	107320447	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	agcctgccccagagcctgccCcaggatcagagcctatggca	9	5	11	16	0	1	2	1	0	0	2	1	3	1	3	7	2	5	1	7	2	1	1			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:107320447C>T	ENST00000217957.5	+	7	1117	c.1000C>T	c.(1000-1002)Cca>Tca	p.P334S	VSIG1_ENST00000415430.3_Missense_Mutation_p.P370S	NM_182607.4	NP_872413.1	Q86XK7	VSIG1_HUMAN	V-set and immunoglobulin domain containing 1	334						integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	17						agagcctgccccagGATCAGA	0.562																																					p.P370S		Atlas-SNP	.											.	VSIG1	126	.	0			c.C1108T						PASS	.						75	69	71					X																	107320447		2203	4300	6503	SO:0001583	missense	340547	exon8			CCTGCCCCAGGAT	BX648658	CCDS14535.1, CCDS55474.1	Xq22.3	2013-01-29			ENSG00000101842	ENSG00000101842		"Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	28675	protein-coding gene	gene with protein product		300620				12477932	Standard	NM_182607		Approved	MGC44287	uc011msk.2	Q86XK7	OTTHUMG00000022175	ENST00000217957.5:c.1000C>T	X.37:g.107320447C>T	ENSP00000217957:p.Pro334Ser	127	0	0		71	4	0.056338	NM_001170553	C9J4P2|Q6MZS4	Missense_Mutation	SNP	ENST00000217957.5	37	CCDS14535.1	.	.	.	.	.	.	.	.	.	.	C	4.558	0.103573	0.08731	.	.	ENSG00000101842	ENST00000415430;ENST00000217957	T;T	0.61274	0.12;0.12	3.5	-7.0	0.01599	.	1.931450	0.02302	N	0.071290	T	0.38427	0.1040	L	0.43152	1.355	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.48445	-0.9035	10	0.05436	T	0.98	.	3.3355	0.07100	0.1048:0.1372:0.4102:0.3478	.	370;334	C9J4P2;Q86XK7	.;VSIG1_HUMAN	S	370;334	ENSP00000402219:P370S;ENSP00000217957:P334S	ENSP00000217957:P334S	P	+	1	0	VSIG1	107207103	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.489000	0.00226	-2.917000	0.00306	-4.471000	0.00005	CCA	.	.	none		0.562	VSIG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057858.1	NM_182607		T	107320447	C	T	107320447	3	4	30	1	0	0	0	0	1	0	0	0	17237	623	22	2	1138	2	VSIG1	23	107320447	Missense_Mutation	SNP	C	TCGA-GR-7353-01A-11D-2210-10	14392719	107320447	47950113	714	13865											
GAB3	139716	hgsc.bcm.edu	37	chrX	153925443	153925443	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctggtaagagatgcatgtTcccggatgatcgagaggttt	9	12	13	7	2	0	3	0	1	0	2	3	6	2	4	2	3	1	4	2	3	1	3			TCGA-GR-7353-01A-11D-2210-10	TCGA-GR-7353-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8e2c3217-6e8f-4f19-b00f-d551799c527e	694ae665-129e-4f77-8739-c727be952b33	g.chrX:153925443T>C	ENST00000369575.3	-	7	1419	c.1388A>G	c.(1387-1389)gAa>gGa	p.E463G	GAB3_ENST00000496390.1_5'UTR|GAB3_ENST00000424127.2_Missense_Mutation_p.E464G	NM_001081573.1|NM_080612.2	NP_001075042.1|NP_542179.1	Q8WWW8	GAB3_HUMAN	GRB2-associated binding protein 3	463					macrophage differentiation (GO:0030225)					NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)	25	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)					AGATGCATGTTCCCGGATGAT	0.537																																					p.E464G		Atlas-SNP	.											.	GAB3	73	.	0			c.A1391G						PASS	.						146	123	131					X																	153925443		2203	4300	6503	SO:0001583	missense	139716	exon7			GCATGTTCCCGGA	AY057989	CCDS14760.1, CCDS48198.1, CCDS65357.1	Xq28	2013-01-10			ENSG00000160219	ENSG00000160219		"Pleckstrin homology (PH) domain containing"	17515	protein-coding gene	gene with protein product	"DOS/Gab family member 3", "Gab3 scaffolding protein"	300482				11739737	Standard	XM_005274648		Approved		uc004fmk.1	Q8WWW8	OTTHUMG00000024245	ENST00000369575.3:c.1388A>G	X.37:g.153925443T>C	ENSP00000358588:p.Glu463Gly	158	0	0		74	4	0.0540541	NM_001081573	A6NHF8|E9PB44	Missense_Mutation	SNP	ENST00000369575.3	37	CCDS14760.1	.	.	.	.	.	.	.	.	.	.	T	14.91	2.675913	0.47886	.	.	ENSG00000160219	ENST00000369575;ENST00000369568;ENST00000424127	T;T;T	0.30448	1.53;1.53;1.53	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	T	0.60418	0.2267	M	0.88031	2.925	0.39665	D	0.970665	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.996;0.997;0.996	T	0.69884	-0.5024	10	0.87932	D	0	-15.0336	12.0037	0.53246	0.0:0.0:0.0:1.0	.	464;464;463	A6NHF8;E9PB44;Q8WWW8	.;.;GAB3_HUMAN	G	463;464;464	ENSP00000358588:E463G;ENSP00000358581:E464G;ENSP00000399588:E464G	ENSP00000358581:E464G	E	-	2	0	GAB3	153578637	1.000000	0.71417	0.875000	0.34327	0.065000	0.16274	5.325000	0.65869	1.808000	0.52836	0.486000	0.48141	GAA	.	.	none		0.537	GAB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061192.2	NM_001081573		C	153925443	T	C	153925443	3	2	30	1	0	0	0	0	1	0	0	0	6158	1783	62	3	388	3	GAB3	23	153925443	Missense_Mutation	SNP	T	TCGA-GR-7353-01A-11D-2210-10	46604996	153925443	1345117	715	13866											
UBR4	23352	hgsc.bcm.edu	37	chr1	19503103	19503103	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gacctgatgagaaatgcttaGaccagttttcttctacttct	10	15	7	9	0	3	3	0	2	3	2	3	5	3	3	2	0	2	2	2	0	3	6			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:19503103G>C	ENST00000375254.3	-	20	2783	c.2756C>G	c.(2755-2757)tCt>tGt	p.S919C	UBR4_ENST00000375217.2_Missense_Mutation_p.S919C|UBR4_ENST00000375226.2_Missense_Mutation_p.S919C|UBR4_ENST00000375267.2_Missense_Mutation_p.S919C	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	919					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)		GAAATGCTTAGACCAGTTTTC	0.468																																					p.S919C		Atlas-SNP	.											.	UBR4	415	.	0			c.C2756G						PASS	.						104	99	101					1																	19503103		2203	4300	6503	SO:0001583	missense	23352	exon20			TGCTTAGACCAGT	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.2756C>G	1.37:g.19503103G>C	ENSP00000364403:p.Ser919Cys	100	0	0		99	30	0.30303	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	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	G	13.91	2.379097	0.42207	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000419533	T;T;T;T	0.40225	1.04;1.04;1.04;1.04	5.97	4.02	0.46733	.	0.441462	0.24085	N	0.041697	T	0.23249	0.0562	N	0.08118	0	0.80722	D	1	B	0.28512	0.214	B	0.24541	0.054	T	0.11867	-1.0570	10	0.62326	D	0.03	.	12.3615	0.55205	0.0678:0.1211:0.8112:0.0	.	919	Q5T4S7	UBR4_HUMAN	C	919;919;919;919;135	ENSP00000364403:S919C;ENSP00000364416:S919C;ENSP00000364365:S919C;ENSP00000364374:S919C	ENSP00000364365:S919C	S	-	2	0	UBR4	19375690	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.809000	0.55606	2.836000	0.97738	0.655000	0.94253	TCT	.	.	none		0.468	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		C	19503103	G	C	19503103	3	2	31	1	0	0	0	0	1	0	0	0	16919	942	33	4	13143	4	UBR4	1	19503103	Missense_Mutation	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10		19503103	229747518	1	13867											
RAP1GAP	5909	hgsc.bcm.edu	37	chr1	21928279	21928279	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctggggtcttctgaccagccGgagggctctccctgcggggc	3	8	16	14	2	3	1	0	1	3	0	4	2	3	2	3	6	2	1	3	6	0	1			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:21928279G>A	ENST00000374765.4	-	20	1750	c.1550C>T	c.(1549-1551)cCg>cTg	p.P517L	RAP1GAP_ENST00000290101.4_Missense_Mutation_p.P581L|RAP1GAP_ENST00000374761.2_Missense_Mutation_p.P548L|RAP1GAP_ENST00000374763.2_Missense_Mutation_p.P602L|RAP1GAP_ENST00000542643.2_Missense_Mutation_p.P543L	NM_002885.2	NP_002876.2	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein	517					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)		CTGACCAGCCGGAGGGCTCTC	0.672																																					p.P581L		Atlas-SNP	.											.	RAP1GAP	119	.	0			c.C1742T						PASS	.						45	43	43					1																	21928279		2203	4300	6503	SO:0001583	missense	5909	exon20			CCAGCCGGAGGGC	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.1550C>T	1.37:g.21928279G>A	ENSP00000363897:p.Pro517Leu	31	0	0		28	6	0.214286	NM_001145658	J3QSS6|O75062|Q5T3S9|Q5T3T4|Q7Z5S8|Q9UQ51	Missense_Mutation	SNP	ENST00000374765.4	37	CCDS218.1	.	.	.	.	.	.	.	.	.	.	g	22.3	4.275461	0.80580	.	.	ENSG00000076864	ENST00000290101;ENST00000374761;ENST00000542643;ENST00000374765;ENST00000374763;ENST00000374758	D;D;D;D	0.89050	-2.43;-2.43;-2.46;-2.42	4.72	4.72	0.59763	.	0.411353	0.23279	N	0.049923	D	0.84875	0.5569	L	0.39633	1.23	0.52501	D	0.999951	D;P;B;P	0.54397	0.966;0.913;0.041;0.913	B;B;B;B	0.43018	0.405;0.121;0.006;0.121	D	0.84295	0.0502	10	0.32370	T	0.25	-7.3773	15.211	0.73225	0.0:0.0:1.0:0.0	.	543;517;547;517	P47736-2;P47736;P47736-3;Q7Z5S8	.;RPGP1_HUMAN;.;.	L	581;548;543;517;547;602	ENSP00000290101:P581L;ENSP00000363893:P548L;ENSP00000441661:P543L;ENSP00000363897:P517L	ENSP00000290101:P581L	P	-	2	0	RAP1GAP	21800866	1.000000	0.71417	0.984000	0.44739	0.994000	0.84299	7.049000	0.76613	2.452000	0.82932	0.556000	0.70494	CCG	.	.	none		0.672	RAP1GAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019759.2	NM_002885		A	21928279	G	A	21928279	3	1	31	1	0	0	0	0	1	0	0	0	13052	1116	39	1	461	1	RAP1GAP	1	21928279	Missense_Mutation	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10	2425176	21928279	227322342	2	13868											
ARID1A	8289	hgsc.bcm.edu	37	chr1	27101097	27101097	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccaatttccattccagtttgGccgagaccgtgtctctgcac	7	12	8	14	2	1	1	0	0	1	1	4	2	3	1	5	1	1	2	5	1	1	3			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:27101097G>C	ENST00000324856.7	+	18	4750	c.4379G>C	c.(4378-4380)gGc>gCc	p.G1460A	ARID1A_ENST00000457599.2_Intron|ARID1A_ENST00000540690.1_Intron|ARID1A_ENST00000374152.2_Missense_Mutation_p.G1077A	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1460					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)		TTCCAGTTTGGCCGAGACCGT	0.582			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.G1460A		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.G4379C						PASS	.						69	73	72					1																	27101097		2203	4300	6503	SO:0001583	missense	8289	exon18			AGTTTGGCCGAGA	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.4379G>C	1.37:g.27101097G>C	ENSP00000320485:p.Gly1460Ala	114	0	0		124	38	0.306452	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.76|18.76	3.691728|3.691728	0.68271|0.68271	.|.	.|.	ENSG00000117713|ENSG00000117713	ENST00000324856;ENST00000374152|ENST00000430799	T;T|.	0.02606|.	4.39;4.23|.	5.54|5.54	4.63|4.63	0.57726|0.57726	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.59838|0.59838	0.2223|0.2223	L|L	0.43923|0.43923	1.385|1.385	0.80722|0.80722	D|D	1|1	D;P;D|.	0.89917|.	1.0;0.952;0.982|.	D;P;P|.	0.87578|.	0.998;0.607;0.73|.	T|T	0.57545|0.57545	-0.7793|-0.7793	10|5	0.37606|.	T|.	0.19|.	-10.3623|-10.3623	14.2699|14.2699	0.66145|0.66145	0.0706:0.0:0.9294:0.0|0.0706:0.0:0.9294:0.0	.|.	1077;1460;1113|.	O14497-3;O14497;Q4LE49|.	.;ARI1A_HUMAN;.|.	A|C	1460;1077|356	ENSP00000320485:G1460A;ENSP00000363267:G1077A|.	ENSP00000320485:G1460A|.	G|W	+|+	2|3	0|0	ARID1A|ARID1A	26973684|26973684	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	6.134000|6.134000	0.71689|0.71689	1.586000|1.586000	0.49944|0.49944	0.650000|0.650000	0.86243|0.86243	GGC|TGG	.	.	none		0.582	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		C	27101097	G	C	27101097	3	2	31	1	0	0	0	0	1	0	0	0	913	1203	42	4	4449	4	ARID1A	1	27101097	Missense_Mutation	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10	5172818	27101097	222149524	3	13869											
NSUN4	387338	hgsc.bcm.edu	37	chr1	46806573	46806654	+	Splice_Site	DEL	TCGATATAAGAAGAAATGGGTAAGGTCCGGCTGGGGGCGCAGGAGGGAAAAGTGAGGGTGGAAACTTCTCCAGTCTTTCCGT	TCGATATAAGAAGAAATGGGTAAGGTCCGGCTGGGGGCGCAGGAGGGAAAAGTGAGGGTGGAAACTTCTCCAGTCTTTCCGT	-																															gcgacggtcccgcggagacaTcgatataagaagaaatgggt																								rs546723714|rs41293279		TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	TCGATATAAGAAGAAATGGGTAAGGTCCGGCTGGGGGCGCAGGAGGGAAAAGTGAGGGTGGAAACTTCTCCAGTCTTTCCGT	TCGATATAAGAAGAAATGGGTAAGGTCCGGCTGGGGGCGCAGGAGGGAAAAGTGAGGGTGGAAACTTCTCCAGTCTTTCCGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:46806573_46806654delTCGATATAAGAAGAAATGGGTAAGGTCCGGCTGGGGGCGCAGGAGGGAAAAGTGAGGGTGGAAACTTCTCCAGTCTTTCCGT	ENST00000474844.1	+	1	725_743	c.75_93delTCGATATAAGAAGAAATGGGTAAGGTCCGGCTGGGGGCGCAGGAGGGAAAAGTGAGGGTGGAAACTTCTCCAGTCTTTCCGT	c.(73-93)catcgatataagaagaaatgg>ca	p.HRYKKKW25fs	NSUN4_ENST00000536062.1_5'UTR|NSUN4_ENST00000537428.1_5'Flank	NM_199044.3	NP_950245.2	Q96CB9	NSUN4_HUMAN	NOP2/Sun domain family, member 4	25					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)					CGCGGAGACATCGATATAAGAAGAAATGGGTAAGGTCCGGCTGGGGGCGCAGGAGGGAAAAGTGAGGGTGGAAACTTCTCCAGTCTTTCCGTTTCCCGGCCC	0.603											OREG0013456	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.25_31del		Pindel	.											.	NSUN4	26	.	0			c.74_93del						PASS	.																																			SO:0001630	splice_region_variant	387338	exon1			.	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.93+1TCGATATAAGAAGAAATGGGTAAGGTCCGGCTGGGGGCGCAGGAGGGAAAAGTGAGGGTGGAAACTTCTCCAGTCTTTCCGT>-	1.37:g.46806573_46806654delTCGATATAAGAAGAAATGGGTAAGGTCCGGCTGGGGGCGCAGGAGGGAAAAGTGAGGGTGGAAACTTCTCCAGTCTTTCCGT		0	0	.	942	13	13	1	NM_199044	A8K6S6|B3KQ50|B4DHA4|Q5TDF7|Q96AN8|Q9HAJ8	Frame_Shift_Del	DEL	ENST00000474844.1	37	CCDS534.1																																																																																			.	.	none		0.603	NSUN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021427.1	NM_199044	Frame_Shift_Del	-	46806654	TCGATATAAGAAGAAATGGGTAAGGTCCGGCTGGGGGCGCAGGAGGGAAAAGTGAGGGTGGAAACTTCTCCAGTCTTTCCGT	-	46806573	8	5	31	1	0	1	0	1	0	0	1	0	10689	1432	50	0	77	0	NSUN4	1	46806573	Splice_Site	DEL	TCGATATAAGAAGAAATGGGTAAGGTCCGGCTGGGGGCGCAGGAGGGAAAAGTGAGGGTGGAAACTTCTCCAGTCTTTCCGT	TCGA-GR-A4D4-01A-11D-A31X-10	19705476	46806573	202444048	4	13870											
LRP8	7804	hgsc.bcm.edu	37	chr1	53755315	53755315	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccaccgttcgtggatgcaGtggccgttgtcacaggtgaa	7	11	13	10	3	1	1	1	1	0	0	3	2	2	2	3	3	1	3	3	3	1	3			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:53755315G>C	ENST00000306052.6	-	3	392	c.291C>G	c.(289-291)caC>caG	p.H97Q	LRP8_ENST00000371454.2_Missense_Mutation_p.H97Q|RP4-784A16.2_ENST00000421637.1_RNA|LRP8_ENST00000347547.2_Missense_Mutation_p.H97Q|LRP8_ENST00000354412.3_Missense_Mutation_p.H97Q|LRP8_ENST00000465675.1_5'UTR|RP4-784A16.3_ENST00000450469.1_RNA	NM_004631.4	NP_004622.2	Q14114	LRP8_HUMAN	low density lipoprotein receptor-related protein 8, apolipoprotein e receptor	97	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.				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						CGTGGATGCAGTGGCCGTTGT	0.612																																					p.H97Q		Atlas-SNP	.											.	LRP8	58	.	0			c.C291G						PASS	.						103	73	83					1																	53755315		2203	4300	6503	SO:0001583	missense	7804	exon3			GATGCAGTGGCCG	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.291C>G	1.37:g.53755315G>C	ENSP00000303634:p.His97Gln	35	0	0		40	9	0.225	NM_004631	B1AMT6|B1AMT7|B1AMT8|O14968|Q86V27|Q99876|Q9BR78	Missense_Mutation	SNP	ENST00000306052.6	37	CCDS578.1	.	.	.	.	.	.	.	.	.	.	G	15.42	2.827526	0.50845	.	.	ENSG00000157193	ENST00000306052;ENST00000371454;ENST00000354412;ENST00000347547	D;D;D;D	0.94897	-3.55;-3.55;-3.55;-3.55	5.33	5.33	0.75918	.	.	.	.	.	D	0.90232	0.6946	N	0.16266	0.395	0.22280	N	0.999238	B;B;B;B	0.34372	0.028;0.451;0.259;0.049	B;B;B;B	0.43701	0.034;0.225;0.428;0.055	T	0.79593	-0.1739	9	0.09843	T	0.71	.	11.9452	0.52924	0.0826:0.0:0.9174:0.0	.	97;97;97;97	Q14114-2;Q14114-4;Q14114-3;Q14114	.;.;.;LRP8_HUMAN	Q	97	ENSP00000303634:H97Q;ENSP00000360509:H97Q;ENSP00000346391:H97Q;ENSP00000334522:H97Q	ENSP00000303634:H97Q	H	-	3	2	LRP8	53527903	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	1.925000	0.40074	2.778000	0.95560	0.655000	0.94253	CAC	.	.	none		0.612	LRP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024699.1	NM_004631		C	53755315	G	C	53755315	3	2	31	1	0	0	0	0	1	0	0	0	8972	1020	36	4	2668	4	LRP8	1	53755315	Missense_Mutation	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10	6948742	53755315	195495306	5	13871											
ATG4C	84938	hgsc.bcm.edu	37	chr1	63300503	63300503	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatcttttgtagatgtcagcAtaaaggatttccctcttgag	11	15	8	7	0	3	2	1	1	2	1	4	3	4	3	1	1	1	2	1	1	4	6			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:63300503A>C	ENST00000317868.4	+	9	1276	c.1069A>C	c.(1069-1071)Ata>Cta	p.I357L	ATG4C_ENST00000371120.3_Missense_Mutation_p.I357L	NM_032852.3	NP_116241.2	Q96DT6	ATG4C_HUMAN	autophagy related 4C, cysteine peptidase	357					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						AGATGTCAGCATAAAGGATTT	0.343																																					p.I357L		Atlas-SNP	.											.	ATG4C	96	.	0			c.A1069C						PASS	.						162	140	147					1																	63300503		2203	4300	6503	SO:0001583	missense	84938	exon9			GTCAGCATAAAGG	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.1069A>C	1.37:g.63300503A>C	ENSP00000322159:p.Ile357Leu	167	0	0		135	28	0.207407	NM_178221	A6NLR8|D3DQ58|Q96K04	Missense_Mutation	SNP	ENST00000317868.4	37	CCDS623.1	.	.	.	.	.	.	.	.	.	.	A	11.55	1.672343	0.29693	.	.	ENSG00000125703	ENST00000317868;ENST00000371120;ENST00000540025;ENST00000414558	T;T	0.40476	1.03;1.03	5.24	2.91	0.33838	.	0.176121	0.64402	D	0.000009	T	0.21550	0.0519	L	0.61387	1.9	0.35343	D	0.786638	B	0.25667	0.131	B	0.32393	0.145	T	0.03750	-1.1007	10	0.27785	T	0.31	-13.9202	8.0732	0.30701	0.7766:0.0:0.2234:0.0	.	357	Q96DT6	ATG4C_HUMAN	L	357;357;357;101	ENSP00000322159:I357L;ENSP00000360161:I357L	ENSP00000322159:I357L	I	+	1	0	ATG4C	63073091	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	5.058000	0.64300	0.411000	0.25702	-0.334000	0.08254	ATA	.	.	none		0.343	ATG4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025332.2	NM_032852		C	63300503	A	C	63300503	3	2	31	1	0	0	0	0	1	0	0	0	1098	217	8	5	1099	5	ATG4C	1	63300503	Missense_Mutation	SNP	A	TCGA-GR-A4D4-01A-11D-A31X-10	9545188	63300503	185950118	6	13872											
FPGT	8790	hgsc.bcm.edu	37	chr1	74670196	74670196	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccatgtacattgatttcccCttaaatatgaatcctggaat	12	14	6	9	0	0	2	0	2	0	0	2	3	2	3	4	1	1	1	4	1	6	5			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:74670196C>T	ENST00000609362.1	+	4	502	c.465C>T	c.(463-465)ccC>ccT	p.P155P	FPGT_ENST00000524915.1_Intron|TNNI3K_ENST00000370891.2_Intron|FPGT-TNNI3K_ENST00000533006.1_Intron|FPGT_ENST00000467578.2_3'UTR|FPGT-TNNI3K_ENST00000370895.1_Intron|FPGT-TNNI3K_ENST00000557284.2_Intron|FPGT-TNNI3K_ENST00000370899.3_Intron|FPGT_ENST00000534056.1_Intron|FPGT-TNNI3K_ENST00000370893.1_Intron|FPGT_ENST00000370894.5_Intron|FPGT_ENST00000370898.3_Silent_p.P168P	NM_003838.4	NP_003829.3	O14772	FPGT_HUMAN	fucose-1-phosphate guanylyltransferase	155					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						TTGATTTCCCCTTAAATATGA	0.353																																					p.P155P		Atlas-SNP	.											.	FPGT	77	.	0			c.C465T						PASS	.						110	114	112					1																	74670196		2203	4300	6503	SO:0001819	synonymous_variant	8790	exon4			TTTCCCCTTAAAT	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.465C>T	1.37:g.74670196C>T		152	0	0		154	54	0.350649	NM_003838	A6NMH3|B4DRX2|B4E2Y7|E9PNQ2|Q8N5J7	Silent	SNP	ENST00000609362.1	37	CCDS663.1																																																																																			.	.	none		0.353	FPGT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	74670196	C	T	74670196	2	4	31	1	0	0	0	0	0	0	0	1	6045	668	24	2		2	FPGT	1	74670196	Silent	SNP	C	TCGA-GR-A4D4-01A-11D-A31X-10	11369693	74670196	174580425	7	13873											
C1orf51	148523	hgsc.bcm.edu	37	chr1	150256253	150256253	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tttatacctcctctcacagaCctactcaatgggctgaagat	11	12	6	12	0	2	3	2	1	1	2	4	3	3	3	3	1	2	1	3	1	5	4			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:150256253C>T	ENST00000290363.5	+	2	854	c.405C>T	c.(403-405)gaC>gaT	p.D135D	C1orf51_ENST00000369094.1_Silent_p.D47D|C1orf51_ENST00000369095.1_Silent_p.D135D|C1orf51_ENST00000469255.1_Intron	NM_144697.2	NP_653298.1	Q8N365	CIART_HUMAN		135					circadian regulation of gene expression (GO:0032922)|locomotor rhythm (GO:0045475)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|E-box binding (GO:0070888)			endometrium(3)|large_intestine(2)|lung(3)|urinary_tract(2)	10	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)			CTCTCACAGACCTACTCAATG	0.428																																					p.D135D		Atlas-SNP	.											.	C1orf51	35	.	0			c.C405T						PASS	.						121	106	111					1																	150256253		2203	4300	6503	SO:0001819	synonymous_variant	148523	exon2			CACAGACCTACTC																												ENST00000290363.5:c.405C>T	1.37:g.150256253C>T		155	0	0		121	36	0.297521	NM_144697	B2RD43|D3DV01|Q8N795|Q96MG6	Silent	SNP	ENST00000290363.5	37	CCDS949.1																																																																																			.	.	none		0.428	C1orf51-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035058.1			T	150256253	C	T	150256253	2	4	31	1	0	0	0	0	0	0	0	1	2045	506	18	2		2	C1orf51	1	150256253	Silent	SNP	C	TCGA-GR-A4D4-01A-11D-A31X-10	75586057	150256253	98994368	8	13874											
CADM3	57863	hgsc.bcm.edu	37	chr1	159166170	159166170	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	acagacacaccaactgcgatGattaggccagaccctcccca	13	5	7	16	1	0	3	0	1	0	2	1	4	1	3	5	1	2	0	5	1	2	1			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:159166170G>C	ENST00000368125.4	+	6	865	c.708G>C	c.(706-708)atG>atC	p.M236I	CADM3_ENST00000368124.4_Missense_Mutation_p.M270I|CTA-134P22.2_ENST00000415675.2_RNA	NM_001127173.1	NP_001120645.1	Q8N126	CADM3_HUMAN	cell adhesion molecule 3	236	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)					CAACTGCGATGATTAGGCCAG	0.517											OREG0013913	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.M270I		Atlas-SNP	.											.	CADM3	118	.	0			c.G810C						PASS	.						206	142	164					1																	159166170		2203	4300	6503	SO:0001583	missense	57863	exon7			TGCGATGATTAGG	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.708G>C	1.37:g.159166170G>C	ENSP00000357107:p.Met236Ile	109	0	0	1799	86	22	0.255814	NM_021189	Q8IZQ9|Q9NVJ5|Q9UJP1	Missense_Mutation	SNP	ENST00000368125.4	37	CCDS44251.1	.	.	.	.	.	.	.	.	.	.	G	11.19	1.565133	0.27915	.	.	ENSG00000162706	ENST00000368124;ENST00000368125;ENST00000416746	T;T;T	0.52295	2.56;2.56;0.67	4.78	4.78	0.61160	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.755390	0.12781	N	0.439679	T	0.19846	0.0477	N	0.11927	0.2	0.30714	N	0.748991	B;B;B	0.22211	0.001;0.066;0.011	B;B;B	0.32393	0.004;0.145;0.014	T	0.20207	-1.0282	10	0.48119	T	0.1	.	13.1756	0.59624	0.0:0.0:1.0:0.0	.	190;236;270	Q8N126-3;Q8N126;Q8N126-2	.;CADM3_HUMAN;.	I	270;236;190	ENSP00000357106:M270I;ENSP00000357107:M236I;ENSP00000387802:M190I	ENSP00000357106:M270I	M	+	3	0	CADM3	157432794	0.998000	0.40836	0.525000	0.27900	0.306000	0.27790	2.465000	0.45075	2.470000	0.83445	0.655000	0.94253	ATG	.	.	none		0.517	CADM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090330.1	NM_021189		C	159166170	G	C	159166170	3	2	31	1	0	0	0	0	1	0	0	0	2570	1290	45	4	836	4	CADM3	1	159166170	Missense_Mutation	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10	8909917	159166170	90084451	9	13875											
TPR	7175	hgsc.bcm.edu	37	chr1	186306183	186306183	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgactttcaagtgattttgAttttgtttcagcttggttga	7	21	9	4	0	2	4	2	4	0	0	2	4	2	4	0	1	1	3	0	1	1	9			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:186306183A>T	ENST00000367478.4	-	32	4764	c.4468T>A	c.(4468-4470)Tca>Aca	p.S1490T		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	1490					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)		AGTGATTTTGATTTTGTTTCA	0.423			T	NTRK1	papillary thyroid																																p.S1490T		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.T4468A						PASS	.						231	209	216					1																	186306183		1900	4128	6028	SO:0001583	missense	7175	exon32			ATTTTGATTTTGT	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.4468T>A	1.37:g.186306183A>T	ENSP00000356448:p.Ser1490Thr	103	0	0		89	18	0.202247	NM_003292	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	37	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	A	7.171	0.587708	0.13812	.	.	ENSG00000047410	ENST00000367478	T	0.22336	1.96	5.91	-5.49	0.02584	Seryl-tRNA synthetase, class IIa, N-terminal (1);	0.471414	0.24638	N	0.036825	T	0.02571	0.0078	N	0.00162	-1.95	0.19945	N	0.999941	B	0.02656	0.0	B	0.01281	0.0	T	0.43294	-0.9400	10	0.07030	T	0.85	.	7.7025	0.28632	0.2781:0.1562:0.0:0.5657	.	1490	P12270	TPR_HUMAN	T	1490	ENSP00000356448:S1490T	ENSP00000356448:S1490T	S	-	1	0	TPR	184572806	1.000000	0.71417	0.927000	0.36925	0.836000	0.47400	0.896000	0.28377	-0.614000	0.05687	0.533000	0.62120	TCA	.	.	none		0.423	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		T	186306183	A	T	186306183	3	4	31	1	0	0	0	0	1	0	0	0	16431	333	12	5	2703	5	TPR	1	186306183	Missense_Mutation	SNP	A	TCGA-GR-A4D4-01A-11D-A31X-10	27140013	186306183	62944438	10	13876											
ASPM	259266	hgsc.bcm.edu	37	chr1	197069752	197069752	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctatatagtaaaaactgttTtctggtttgccacgtcctaa	11	16	6	8	1	2	0	0	0	2	0	3	0	3	0	2	1	2	3	2	1	7	8			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:197069752T>G	ENST00000367409.4	-	18	8885	c.8629A>C	c.(8629-8631)Aaa>Caa	p.K2877Q	ASPM_ENST00000294732.7_Intron|ASPM_ENST00000367408.1_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2877	IQ 32. {ECO:0000255|PROSITE- ProRule:PRU00116}.				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						AAAAACTGTTTTCTGGTTTGC	0.373																																					p.K2877Q		Atlas-SNP	.											.	ASPM	444	.	0			c.A8629C						PASS	.						52	55	54					1																	197069752		2203	4298	6501	SO:0001583	missense	259266	exon18			ACTGTTTTCTGGT	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.8629A>C	1.37:g.197069752T>G	ENSP00000356379:p.Lys2877Gln	151	0	0		110	30	0.272727	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	37	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	T	11.88	1.769791	0.31320	.	.	ENSG00000066279	ENST00000367409;ENST00000367406	T	0.35789	1.29	4.76	4.76	0.60689	.	0.827867	0.10966	N	0.614361	T	0.48714	0.1515	L	0.49571	1.57	0.28913	N	0.89257	D;D	0.60160	0.969;0.987	D;P	0.70227	0.968;0.9	T	0.38001	-0.9681	10	0.31617	T	0.26	.	5.7651	0.18221	0.1604:0.0847:0.0:0.7549	.	863;2877	E7EQ84;Q8IZT6	.;ASPM_HUMAN	Q	2877;863	ENSP00000356379:K2877Q	ENSP00000356376:K863Q	K	-	1	0	ASPM	195336375	0.003000	0.15002	0.093000	0.20910	0.442000	0.32017	0.921000	0.28718	1.908000	0.55244	0.460000	0.39030	AAA	.	.	none		0.373	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		G	197069752	T	G	197069752	3	3	31	1	0	0	0	0	1	0	0	0	1056	1850	64	5	1848	5	ASPM	1	197069752	Missense_Mutation	SNP	T	TCGA-GR-A4D4-01A-11D-A31X-10	10763569	197069752	52180869	11	13877											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228564799	228564799	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgggagaaggccagcgggCgggcgctggccgccaagatc	7	3	19	12	4	0	2	0	0	0	2	1	3	0	2	3	5	1	2	3	5	2	0	rs541725106		TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:228564799C>T	ENST00000422127.1	+	101	23130	c.23086C>T	c.(23086-23088)Cgg>Tgg	p.R7696W	OBSCN_ENST00000570156.2_Missense_Mutation_p.R8653W|OBSCN_ENST00000366707.4_Missense_Mutation_p.R5330W	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	7696	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)				GGCCAGCGGGCGGGCGCTGGC	0.687													C|||	1	0.000199681	0.0	0.0	5008	,	,		15332	0.001		0.0	False		,,,				2504	0.0				p.R8653W		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C25957T						PASS	.						13	17	15					1																	228564799		2005	4163	6168	SO:0001583	missense	84033	exon112			AGCGGGCGGGCGC	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.23086C>T	1.37:g.228564799C>T	ENSP00000409493:p.Arg7696Trp	31	0	0		52	17	0.326923	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	37	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.50|16.50	3.139945|3.139945	0.56936|0.56936	.|.	.|.	ENSG00000154358|ENSG00000154358	ENST00000441106|ENST00000422127;ENST00000366707	.|T;T	.|0.66995	.|-0.24;-0.24	4.82|4.82	4.82|4.82	0.62117|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);	.|0.259072	.|0.31660	.|N	.|0.007272	T|T	0.78610|0.78610	0.4310|0.4310	M|M	0.89214|0.89214	3.015|3.015	0.58432|0.58432	D|D	0.999991|0.999991	.|D	.|0.71674	.|0.998	.|P	.|0.54210	.|0.745	T|T	0.82948|0.82948	-0.0204|-0.0204	5|10	.|0.72032	.|D	.|0.01	.|.	11.3533|11.3533	0.49600|0.49600	0.3162:0.6838:0.0:0.0|0.3162:0.6838:0.0:0.0	.|.	.|7696	.|Q5VST9	.|OBSCN_HUMAN	V|W	2312|7696;5330	.|ENSP00000409493:R7696W;ENSP00000355668:R5330W	.|ENSP00000355668:R5330W	A|R	+|+	2|1	0|2	OBSCN|OBSCN	226631422|226631422	0.056000|0.056000	0.20664|0.20664	0.048000|0.048000	0.18961|0.18961	0.006000|0.006000	0.05464|0.05464	1.933000|1.933000	0.40153|0.40153	2.239000|2.239000	0.73571|0.73571	0.313000|0.313000	0.20887|0.20887	GCG|CGG	.	.	none		0.687	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228564799	C	T	228564799	3	4	31	1	0	0	0	0	1	0	0	0	10821	759	27	1	24694	1	OBSCN	1	228564799	Missense_Mutation	SNP	C	TCGA-GR-A4D4-01A-11D-A31X-10	31495047	228564799	20685822	12	13878											
TBCE	6905	hgsc.bcm.edu	37	chr1	235590506	235590506	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgtcatcatgggatgaagTgatacacattgctgatcagc	11	12	11	7	0	3	3	3	3	0	0	3	4	3	4	0	1	3	2	0	1	2	3			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:235590506T>C	ENST00000366601.3	+	6	688	c.512T>C	c.(511-513)gTg>gCg	p.V171A	TBCE_ENST00000472011.1_3'UTR|RP11-293G6__A.2_ENST00000430613.2_RNA|TBCE_ENST00000543662.1_Missense_Mutation_p.V171A|TBCE_ENST00000406207.1_Missense_Mutation_p.V171A			Q15813	TBCE_HUMAN	tubulin folding cofactor E	171					'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)			TGGGATGAAGTGATACACATT	0.363																																					p.V171A		Atlas-SNP	.											.	TBCE	40	.	0			c.T512C						PASS	.						140	133	135					1																	235590506		2203	4300	6503	SO:0001583	missense	6905	exon6			ATGAAGTGATACA	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.512T>C	1.37:g.235590506T>C	ENSP00000355560:p.Val171Ala	69	0	0		80	28	0.35	NM_003193	A8K8C2|B7Z3P1	Missense_Mutation	SNP	ENST00000366601.3	37	CCDS1605.1	.	.	.	.	.	.	.	.	.	.	T	17.11	3.304959	0.60305	.	.	ENSG00000116957	ENST00000366601;ENST00000406207;ENST00000543662	T;T;T	0.39229	1.09;1.09;1.09	5.43	5.43	0.79202	.	0.061993	0.64402	D	0.000005	T	0.65450	0.2692	M	0.83483	2.645	0.58432	D	0.999999	D;D;D	0.69078	0.997;0.97;0.991	D;P;P	0.65773	0.938;0.539;0.905	T	0.71148	-0.4677	10	0.72032	D	0.01	-16.6054	14.0172	0.64531	0.0:0.0:0.0:1.0	.	171;171;171	B7Z3P1;A8K8C2;Q15813	.;.;TBCE_HUMAN	A	171	ENSP00000355560:V171A;ENSP00000384571:V171A;ENSP00000439170:V171A	ENSP00000355560:V171A	V	+	2	0	TBCE	233657129	0.999000	0.42202	0.949000	0.38748	0.473000	0.32948	4.558000	0.60789	2.189000	0.69895	0.443000	0.29094	GTG	.	.	none		0.363	TBCE-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000096458.3	NM_003193		C	235590506	T	C	235590506	3	2	31	1	0	0	0	0	1	0	0	0	15649	1696	59	3	530	3	TBCE	1	235590506	Missense_Mutation	SNP	T	TCGA-GR-A4D4-01A-11D-A31X-10	7025707	235590506	13660115	13	13879											
ZP4	57829	hgsc.bcm.edu	37	chr1	238049158	238049158	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gattgggagagagttgctacTtactgagtagctgcagctga	10	11	14	6	0	0	3	0	2	0	1	0	6	0	4	0	1	6	6	0	1	3	5			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr1:238049158T>G	ENST00000366570.4	-	7	1026	c.868A>C	c.(868-870)Agt>Cgt	p.S290R	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	290	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)			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)			GAGTTGCTACTTACTGAGTAG	0.483																																					p.S290R	NSCLC(166;160 2029 11600 18754 19936)	Atlas-SNP	.											.	ZP4	161	.	0			c.A868C						PASS	.						149	144	146					1																	238049158		2203	4300	6503	SO:0001583	missense	57829	exon7			TGCTACTTACTGA	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.868A>C	1.37:g.238049158T>G	ENSP00000355529:p.Ser290Arg	80	0	0		70	19	0.271429	NM_021186	B2RAE1	Missense_Mutation	SNP	ENST00000366570.4	37	CCDS1615.1	.	.	.	.	.	.	.	.	.	.	T	13.47	2.248183	0.39697	.	.	ENSG00000116996	ENST00000366570	D	0.82619	-1.63	4.32	1.89	0.25635	Zona pellucida sperm-binding protein (3);	0.550821	0.19053	N	0.123987	T	0.71134	0.3304	L	0.31804	0.96	0.09310	N	1	B	0.11235	0.004	B	0.17979	0.02	T	0.57341	-0.7828	10	0.34782	T	0.22	-1.9444	8.4328	0.32769	0.0:0.0:0.412:0.588	.	290	Q12836	ZP4_HUMAN	R	290	ENSP00000355529:S290R	ENSP00000355529:S290R	S	-	1	0	ZP4	236115781	0.002000	0.14202	0.000000	0.03702	0.817000	0.46193	1.245000	0.32790	0.194000	0.20326	0.528000	0.53228	AGT	.	.	none		0.483	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1			G	238049158	T	G	238049158	3	3	31	1	0	0	0	0	1	0	0	0	18233	1609	56	5	778	5	ZP4	1	238049158	Missense_Mutation	SNP	T	TCGA-GR-A4D4-01A-11D-A31X-10	2458652	238049158	11201463	14	13880											
LPIN1	23175	hgsc.bcm.edu	37	chr2	11955228	11955228	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttcaggaatggatataaatTtctctactgttctgcccgtg	9	16	8	8	1	3	0	1	0	2	0	4	2	3	2	1	2	2	1	1	2	5	6			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr2:11955228T>A	ENST00000256720.2	+	17	2249	c.2156T>A	c.(2155-2157)tTt>tAt	p.F719Y	LPIN1_ENST00000404113.2_Missense_Mutation_p.F220Y|LPIN1_ENST00000449576.2_Missense_Mutation_p.F804Y|LPIN1_ENST00000425416.2_Missense_Mutation_p.F725Y|LPIN1_ENST00000396097.1_Missense_Mutation_p.F449Y|LPIN1_ENST00000396099.1_Missense_Mutation_p.F761Y	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	719	C-LIP.				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)		GGATATAAATTTCTCTACTGT	0.502																																					p.F804Y		Atlas-SNP	.											.	LPIN1	99	.	0			c.T2411A						PASS	.						53	52	52					2																	11955228		2203	4300	6503	SO:0001583	missense	23175	exon19			ATAAATTTCTCTA	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.2156T>A	2.37:g.11955228T>A	ENSP00000256720:p.Phe719Tyr	125	0	0		119	23	0.193277	NM_001261428	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Missense_Mutation	SNP	ENST00000256720.2	37	CCDS1682.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.551618	0.86127	.	.	ENSG00000134324	ENST00000449576;ENST00000396099;ENST00000425416;ENST00000256720;ENST00000396097;ENST00000404113	T;T;T;T;T;T	0.77229	-1.08;-1.08;-1.08;-1.08;-1.08;-1.08	4.69	4.69	0.59074	HAD-like domain (2);LNS2, Lipin/Ned1/Smp2 (2);	0.000000	0.85682	D	0.000000	D	0.88991	0.6588	M	0.87547	2.89	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.998;0.999;0.986	D	0.91033	0.4865	10	0.87932	D	0	-18.1031	14.1851	0.65601	0.0:0.0:0.0:1.0	.	220;804;719	B4DET9;F5GY24;Q14693	.;.;LPIN1_HUMAN	Y	804;761;725;719;449;220	ENSP00000397908:F804Y;ENSP00000379406:F761Y;ENSP00000401522:F725Y;ENSP00000256720:F719Y;ENSP00000379404:F449Y;ENSP00000386120:F220Y	ENSP00000256720:F719Y	F	+	2	0	LPIN1	11872679	1.000000	0.71417	0.997000	0.53966	0.775000	0.43874	7.544000	0.82117	1.752000	0.51891	0.533000	0.62120	TTT	.	.	none		0.502	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693		A	11955228	T	A	11955228	3	1	31	1	0	0	0	0	1	0	0	0	8927	1841	64	5	2218	5	LPIN1	2	11955228	Missense_Mutation	SNP	T	TCGA-GR-A4D4-01A-11D-A31X-10		11955228	231244145	15	13881											
ANKRD44	91526	hgsc.bcm.edu	37	chr2	197878306	197878306	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgcgccctgattgataagcGcttccacacattctgtgtgt	8	13	9	11	2	1	2	0	2	1	0	2	2	2	2	2	0	2	1	2	0	1	4	rs145800695	byFrequency	TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr2:197878306G>A	ENST00000328737.2	-	18	1854	c.1778C>T	c.(1777-1779)gCg>gTg	p.A593V	ANKRD44_ENST00000450567.1_Missense_Mutation_p.A593V|ANKRD44_ENST00000337207.5_Missense_Mutation_p.A593V|ANKRD44_ENST00000282272.8_Missense_Mutation_p.A610V			Q8N8A2	ANR44_HUMAN	ankyrin repeat domain 44	618										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)			ATTGATAAGCGCTTCCACACA	0.507													G|||	8	0.00159744	0.0061	0.0	5008	,	,		20126	0.0		0.0	False		,,,				2504	0.0				p.A618V		Atlas-SNP	.											ANKRD44_ENST00000424317,NS,carcinoma,+1,2	ANKRD44	281	2	0			c.C1853T						scavenged	.	G	VAL/ALA	35,4371	40.8+/-73.8	0,35,2168	220	208	212		1853	4.4	1	2	dbSNP_134	212	0,8600		0,0,4300	yes	missense	ANKRD44	NM_001195144.1	64	0,35,6468	AA,AG,GG		0.0,0.7944,0.2691	benign	618/994	197878306	35,12971	2203	4300	6503	SO:0001583	missense	91526	exon18			ATAAGCGCTTCCA	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.1778C>T	2.37:g.197878306G>A	ENSP00000331516:p.Ala593Val	134	1	0.00746269		130	32	0.246154	NM_001195144	Q53SL9|Q6P480|Q86VL5|Q8IZ72|Q9UFA4	Missense_Mutation	SNP	ENST00000328737.2	37		5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	3.291	-0.144875	0.06627	0.007944	0.0	ENSG00000065413	ENST00000424317;ENST00000282272;ENST00000328737;ENST00000450567;ENST00000337207;ENST00000422886	T;T;T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06;-0.06;-0.06	4.43	4.43	0.53597	.	0.060668	0.64402	D	0.000003	T	0.53786	0.1818	N	0.21240	0.645	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.52631	-0.8550	10	0.12103	T	0.63	.	10.8392	0.46704	0.0862:0.0:0.9138:0.0	.	636	Q8N8A2-2	.	V	433;610;593;593;593;293	ENSP00000403415:A433V;ENSP00000282272:A610V;ENSP00000331516:A593V;ENSP00000402420:A593V;ENSP00000338794:A593V;ENSP00000416319:A293V	ENSP00000282272:A610V	A	-	2	0	ANKRD44	197586551	0.996000	0.38824	0.993000	0.49108	0.714000	0.41099	2.528000	0.45624	2.294000	0.77228	0.655000	0.94253	GCG	G|0.997;A|0.003	0.003	strong		0.507	ANKRD44-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335113.1	NM_153697		A	197878306	G	A	197878306	3	1	31	1	0	0	0	0	1	0	0	0	672	1087	38	1	1017	1	ANKRD44	2	197878306	Missense_Mutation	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10	185923078	197878306	45321067	16	13882											
FARSB	10056	hgsc.bcm.edu	37	chr2	223504317	223504317	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acctgcaaatattctgatgtAatttctcctgaagttcaatg	12	15	6	8	0	3	2	1	2	2	0	4	2	3	2	2	0	1	3	2	0	5	5			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr2:223504317A>T	ENST00000281828.6	-	5	700	c.437T>A	c.(436-438)tTa>tAa	p.L146*	FARSB_ENST00000536361.1_Nonsense_Mutation_p.L47*	NM_005687.3	NP_005678.3	Q9NSD9	SYFB_HUMAN	phenylalanyl-tRNA synthetase, beta subunit	146					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)	ATTCTGATGTAATTTCTCCTG	0.423																																					p.L146X		Atlas-SNP	.											.	FARSB	49	.	0			c.T437A						PASS	.						126	123	124					2																	223504317		2203	4300	6503	SO:0001587	stop_gained	10056	exon5			TGATGTAATTTCT	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.437T>A	2.37:g.223504317A>T	ENSP00000281828:p.Leu146*	94	0	0		101	20	0.19802	NM_005687	B4DFM0|O95708|Q4ZFX1|Q57ZJ5|Q9NZZ6	Nonsense_Mutation	SNP	ENST00000281828.6	37	CCDS2454.1	.	.	.	.	.	.	.	.	.	.	A	40	8.314864	0.98757	.	.	ENSG00000116120	ENST00000281828;ENST00000536361	.	.	.	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.0598	16.2824	0.82697	1.0:0.0:0.0:0.0	.	.	.	.	X	146;47	.	ENSP00000281828:L146X	L	-	2	0	FARSB	223212561	1.000000	0.71417	0.160000	0.22671	0.957000	0.61999	8.826000	0.92034	2.250000	0.74265	0.533000	0.62120	TTA	.	.	none		0.423	FARSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256855.2	NM_005687		T	223504317	A	T	223504317	4	4	31	1	0	0	0	0	0	1	0	0	5688	372	13	5	1384	5	FARSB	2	223504317	Nonsense_Mutation	SNP	A	TCGA-GR-A4D4-01A-11D-A31X-10	25626011	223504317	19695056	17	13883											
COL4A3	1285	hgsc.bcm.edu	37	chr2	228172583	228172583	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	acagtgccactctacagtggGttttcttttctttttgtaca	7	18	7	9	0	3	0	0	0	3	0	3	0	3	0	1	1	3	2	1	1	2	8			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr2:228172583G>A	ENST00000396578.3	+	48	4572	c.4410G>A	c.(4408-4410)ggG>ggA	p.G1470G	AC097662.2_ENST00000433324.1_RNA|AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000396588.2_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	1470	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)		TCTACAGTGGGTTTTCTTTTC	0.498																																					p.G1470G		Atlas-SNP	.											.	COL4A3	293	.	0			c.G4410A						PASS	.						91	87	88					2																	228172583		1900	4112	6012	SO:0001819	synonymous_variant	1285	exon48			CAGTGGGTTTTCT		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.4410G>A	2.37:g.228172583G>A		180	0	0		147	38	0.258503	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Silent	SNP	ENST00000396578.3	37	CCDS42829.1																																																																																			.	.	none		0.498	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091		A	228172583	G	A	228172583	2	1	31	1	0	0	0	0	0	0	0	1	3693	1248	44	2		2	COL4A3	2	228172583	Silent	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10	4668266	228172583	15026790	18	13884											
SPHKAP	80309	hgsc.bcm.edu	37	chr2	228881444	228881444	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggctgtttacattcggtaaCagagtctttcctcgggcaat	8	13	11	9	2	1	1	0	0	1	1	4	1	2	1	1	3	2	4	1	3	3	5			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr2:228881444C>T	ENST00000392056.3	-	7	4172	c.4126G>A	c.(4126-4128)Gtt>Att	p.V1376I	SPHKAP_ENST00000344657.5_Missense_Mutation_p.V1376I	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1376						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)		CATTCGGTAACAGAGTCTTTC	0.473																																					p.V1376I		Atlas-SNP	.											.	SPHKAP	750	.	0			c.G4126A						PASS	.						75	77	76					2																	228881444		2203	4300	6503	SO:0001583	missense	80309	exon7			CGGTAACAGAGTC		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.4126G>A	2.37:g.228881444C>T	ENSP00000375909:p.Val1376Ile	103	0	0		80	19	0.2375	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	.	.	.	.	.	.	.	.	.	.	C	8.953	0.968624	0.18659	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.13089	2.62;2.62	5.14	0.496	0.16896	.	1.516350	0.03499	N	0.217772	T	0.05135	0.0137	N	0.02315	-0.6	0.09310	N	1	B;B;B	0.15141	0.002;0.002;0.012	B;B;B	0.15484	0.001;0.004;0.013	T	0.31998	-0.9923	10	0.18276	T	0.48	.	2.5383	0.04719	0.0973:0.3926:0.2658:0.2443	.	407;1376;1376	B3KR30;Q2M3C7;Q2M3C7-2	.;SPKAP_HUMAN;.	I	1376	ENSP00000375909:V1376I;ENSP00000339886:V1376I	ENSP00000339886:V1376I	V	-	1	0	SPHKAP	228589688	0.000000	0.05858	0.000000	0.03702	0.144000	0.21451	-0.174000	0.09839	-0.056000	0.13221	0.655000	0.94253	GTT	.	.	none		0.473	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		T	228881444	C	T	228881444	3	4	31	1	0	0	0	0	1	0	0	0	15063	478	17	2	1000	2	SPHKAP	2	228881444	Missense_Mutation	SNP	C	TCGA-GR-A4D4-01A-11D-A31X-10	708861	228881444	14317929	19	13885											
RBM44	375316	hgsc.bcm.edu	37	chr2	238726640	238726644	+	Frame_Shift_Del	DEL	ACATT	ACATT	-																															tgcaccttgaaaatcctagcAcattaccacaggataaagct																										TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	ACATT	ACATT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr2:238726640_238726644delACATT	ENST00000409864.1	+	3	1335_1339	c.1081_1085delACATT	c.(1081-1086)acattafs	p.TL361fs	RBM44_ENST00000316997.4_Frame_Shift_Del_p.TL361fs|RBM44_ENST00000444524.2_Intron			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	360						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)		AAATCCTAGCACATTACCACAGGAT	0.332																																					p.360_362del		Atlas-Indel	.											.	RBM44	167	.	0			c.1080_1084del						PASS	.																																			SO:0001589	frameshift_variant	375316	exon3			.	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.1081_1085delACATT	2.37:g.238726640_238726644delACATT	ENSP00000386727:p.Thr361fs	410	0	0		345	50	0.144928	NM_001080504	A0AUW3	Frame_Shift_Del	DEL	ENST00000409864.1	37	CCDS46554.1																																																																																			.	.	none		0.332	RBM44-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328733.2	NM_001080504		-	238726644	ACATT	-	238726640	7	5	31	1	0	1	0	1	0	0	0	0	13153	159	6	0	1087	0	RBM44	2	238726640	Frame_Shift_Del	DEL	ACATT	TCGA-GR-A4D4-01A-11D-A31X-10	9845196	238726640	4472733	20	13886	172	2									
RBM44	375316	hgsc.bcm.edu	37	chr2	238726642	238726647	+	In_Frame_Del	DEL	ATTACC	ATTACC	-																															caccttgaaaatcctagcacAttaccacaggataaagcttt																								rs201162171		TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	ATTACC	ATTACC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr2:238726642_238726647delATTACC	ENST00000409864.1	+	3	1337_1342	c.1083_1088delATTACC	c.(1081-1089)acattacca>aca	p.LP362del	RBM44_ENST00000316997.4_In_Frame_Del_p.LP362del|RBM44_ENST00000444524.2_Intron			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	361						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)		ATCCTAGCACATTACCACAGGATAAA	0.33																																					p.361_363del		Pindel	.											.	RBM44	167	.	0			c.1082_1087del						PASS	.																																			SO:0001651	inframe_deletion	375316	exon3			.	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.1083_1088delATTACC	2.37:g.238726642_238726647delATTACC	ENSP00000386727:p.Leu362_Pro363del	0	0	.		40	40	1	NM_001080504	A0AUW3	In_Frame_Del	DEL	ENST00000409864.1	37	CCDS46554.1																																																																																			.	.	none		0.33	RBM44-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328733.2	NM_001080504		-	238726647	ATTACC	-	238726642	7	5	31	1	0	1	0	1	0	0	0	0	13153	204	8	0	1089	0	RBM44	2	238726642	In_Frame_Del	DEL	ATTACC	TCGA-GR-A4D4-01A-11D-A31X-10	2	238726642	4472731	21	13887	172	2									
ABI3BP	25890	hgsc.bcm.edu	37	chr3	100497214	100497214	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggtggcaagggtgggcggCgagtccctgggattgtggat	5	9	21	6	2	0	0	0	0	0	0	1	3	1	2	1	7	0	1	1	7	1	1	rs564595054	byFrequency	TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr3:100497214C>T	ENST00000284322.5	-	26	2223	c.2114G>A	c.(2113-2115)cGc>cAc	p.R705H	ABI3BP_ENST00000383691.4_Missense_Mutation_p.R659H|ABI3BP_ENST00000471714.1_Missense_Mutation_p.R1407H	NM_015429.3	NP_056244.2	Q7Z7G0	TARSH_HUMAN	ABI family, member 3 (NESH) binding protein	705	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						GGGTGGGCGGCGAGTCCCTGG	0.403													C|||	2	0.000399361	0.0008	0.0	5008	,	,		12839	0.0		0.0	False		,,,				2504	0.001				p.R705H		Atlas-SNP	.											ABI3BP_ENST00000383691,colon,carcinoma,-1,2	ABI3BP	305	2	0			c.G2114A						scavenged	.						95	94	94					3																	100497214		1866	4097	5963	SO:0001583	missense	25890	exon26			GGGCGGCGAGTCC	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.2114G>A	3.37:g.100497214C>T	ENSP00000284322:p.Arg705His	57	0	0		52	3	0.0576923	NM_015429	B3KSL4|Q6ZW20|Q6ZW22|Q9C082|Q9UFI6	Missense_Mutation	SNP	ENST00000284322.5	37	CCDS46880.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.38|12.38	1.919848|1.919848	0.33908|0.33908	.|.	.|.	ENSG00000154175|ENSG00000154175	ENST00000495591|ENST00000471714;ENST00000284322;ENST00000383692;ENST00000429331;ENST00000383691;ENST00000486770	.|T;T;T	.|0.23147	.|2.28;1.96;1.92	5.79|5.79	1.33|1.33	0.21861|0.21861	.|.	.|0.493767	.|0.20611	.|N	.|0.088971	T|T	0.14270|0.14270	0.0345|0.0345	L|L	0.43152|0.43152	1.355|1.355	0.09310|0.09310	N|N	1|1	.|B;B;P;B	.|0.35456	.|0.037;0.027;0.502;0.01	.|B;B;B;B	.|0.22753	.|0.006;0.007;0.041;0.004	T|T	0.13575|0.13575	-1.0504|-1.0504	5|10	.|0.41790	.|T	.|0.15	-1.1719|-1.1719	4.1604|4.1604	0.10280|0.10280	0.0:0.3549:0.3169:0.3282|0.0:0.3549:0.3169:0.3282	.|.	.|659;705;1407;414	.|B4DSV9;Q7Z7G0;D3YTG3;D3YTD6	.|.;TARSH_HUMAN;.;.	T|H	761|1407;705;414;116;659;117	.|ENSP00000420524:R1407H;ENSP00000284322:R705H;ENSP00000373189:R659H	.|ENSP00000284322:R705H	A|R	-|-	1|2	0|0	ABI3BP|ABI3BP	101979904|101979904	0.123000|0.123000	0.22298|0.22298	0.538000|0.538000	0.28064|0.28064	0.889000|0.889000	0.51656|0.51656	-0.086000|-0.086000	0.11233|0.11233	0.812000|0.812000	0.34326|0.34326	0.462000|0.462000	0.41574|0.41574	GCC|CGC	.	.	none		0.403	ABI3BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353260.1			T	100497214	C	T	100497214	3	4	31	1	0	0	0	0	1	0	0	0	91	768	27	1	1153	1	ABI3BP	3	100497214	Missense_Mutation	SNP	C	TCGA-GR-A4D4-01A-11D-A31X-10		100497214	97525216	22	13888											
CHST2	9435	hgsc.bcm.edu	37	chr3	142839977	142839977	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggcagctgggggcgcccaGggccgcctccggccgggccg	3	2	20	16	5	0	0	0	0	0	0	1	1	1	0	6	6	1	2	6	6	0	0	rs185111962	byFrequency	TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr3:142839977G>A	ENST00000309575.3	+	2	1703	c.319G>A	c.(319-321)Ggg>Agg	p.G107R		NM_004267.4	NP_004258.2	Q9Y4C5	CHST2_HUMAN	carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2	107					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						ggggcgcccagggccgcctcc	0.761													G|||	32	0.00638978	0.0008	0.0115	5008	,	,		9166	0.0		0.0179	False		,,,				2504	0.0051				p.G107R		Atlas-SNP	.											.	CHST2	67	.	0			c.G319A						PASS	.	G	ARG/GLY	6,3188		0,6,1591	2	2	2		319	2.4	0.8	3		2	29,6187		0,29,3079	no	missense	CHST2	NM_004267.4	125	0,35,4670	AA,AG,GG		0.4665,0.1879,0.3719	benign	107/531	142839977	35,9375	1597	3108	4705	SO:0001583	missense	9435	exon2			CGCCCAGGGCCGC	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.319G>A	3.37:g.142839977G>A	ENSP00000307911:p.Gly107Arg	1	0	0		13	9	0.692308	NM_004267	D3DNG5|Q2M370|Q9GZN5|Q9UED5|Q9Y6F2	Missense_Mutation	SNP	ENST00000309575.3	37	CCDS3129.1	22	0.010073260073260074	6	0.012195121951219513	4	0.011049723756906077	0	0.0	12	0.0158311345646438	G	4.642	0.119345	0.08881	0.001879	0.004665	ENSG00000175040	ENST00000309575	D	0.97041	-4.22	3.3	2.42	0.29668	.	.	.	.	.	D	0.85225	0.5648	N	0.14661	0.345	0.27986	N	0.935857	B	0.06786	0.001	B	0.08055	0.003	T	0.82478	-0.0437	9	0.51188	T	0.08	-12.4417	4.825	0.13412	0.1239:0.2213:0.6548:0.0	.	107	Q9Y4C5	CHST2_HUMAN	R	107	ENSP00000307911:G107R	ENSP00000307911:G107R	G	+	1	0	CHST2	144322667	0.000000	0.05858	0.845000	0.33349	0.137000	0.21094	-0.018000	0.12568	0.947000	0.37659	0.407000	0.27541	GGG	G|0.990;A|0.010	0.010	strong		0.761	CHST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354850.1	NM_004267		A	142839977	G	A	142839977	3	1	31	1	0	0	0	0	1	0	0	0	3406	1000	35	2	321	2	CHST2	3	142839977	Missense_Mutation	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10	42342763	142839977	55182453	23	13889											
OCIAD1	54940	hgsc.bcm.edu	37	chr4	48835428	48835428	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtaaaaagacatagggccTgattacattccaacagagga	16	8	10	7	0	0	3	0	1	0	2	1	4	1	4	2	3	2	1	2	3	6	4			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr4:48835428T>A	ENST00000381473.3	+	3	487	c.69T>A	c.(67-69)ccT>ccA	p.P23P	OCIAD1_ENST00000513391.2_Silent_p.P23P|OCIAD1_ENST00000444354.2_Silent_p.P23P|OCIAD1_ENST00000508293.1_Silent_p.P23P|OCIAD1_ENST00000264312.7_Silent_p.P23P|OCIAD1_ENST00000509122.1_Intron|OCIAD1_ENST00000512981.1_3'UTR|OCIAD1_ENST00000506801.1_Intron|OCIAD1_ENST00000396448.2_Silent_p.P23P|OCIAD1_ENST00000425583.2_Silent_p.P23P	NM_001079839.2	NP_001073308.1	Q9NX40	OCAD1_HUMAN	OCIA domain containing 1	23	OCIA.					endosome (GO:0005768)|membrane (GO:0016020)|mitochondrion (GO:0005739)				breast(2)|large_intestine(2)|lung(2)|prostate(1)|skin(2)	9						ACATAGGGCCTGATTACATTC	0.328																																					p.P28P		Atlas-SNP	.											.	OCIAD1	27	.	0			c.T84A						PASS	.						62	65	64					4																	48835428		2203	4300	6503	SO:0001819	synonymous_variant	54940	exon3			AGGGCCTGATTAC	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.69T>A	4.37:g.48835428T>A		290	0	0		324	82	0.253086	NM_001168254	C9K030|G8JLN7|Q9BZE8	Silent	SNP	ENST00000381473.3	37	CCDS3484.1																																																																																			.	.	none		0.328	OCIAD1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361812.3	NM_017830		A	48835428	T	A	48835428	2	1	31	1	0	0	0	0	0	0	0	1	10826	1567	55	5		5	OCIAD1	4	48835428	Silent	SNP	T	TCGA-GR-A4D4-01A-11D-A31X-10		48835428	142318848	24	13890											
AGA	175	hgsc.bcm.edu	37	chr4	178355534	178355534	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcacaaactaagaagtcatAccttggcaggaagcgcatca	15	8	8	10	1	3	1	3	0	0	1	3	2	3	2	1	2	3	2	1	2	5	4			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr4:178355534A>G	ENST00000264595.2	-	7	934		c.e7+1		AGA_ENST00000506853.1_5'Flank	NM_000027.3|NM_001171988.1	NP_000018.2|NP_001165459.1	P20933	ASPG_HUMAN	aspartylglucosaminidase						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)		AAGAAGTCATACCTTGGCAGG	0.448																																					.		Atlas-SNP	.											.	AGA	39	.	0			c.806+2T>C						PASS	.						127	124	125					4																	178355534		2203	4300	6503	SO:0001630	splice_region_variant	175	exon8			AGTCATACCTTGG	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.806+1T>C	4.37:g.178355534A>G		235	0	0		199	55	0.276382	NM_000027	B2R7H2|D3DP47|Q4W5Q2|Q6FHN6|Q9UCK6|Q9UCK7|Q9UCK8	Splice_Site	SNP	ENST00000264595.2	37	CCDS3829.1	.	.	.	.	.	.	.	.	.	.	A	12.58	1.980000	0.34942	.	.	ENSG00000038002	ENST00000264595;ENST00000502310	.	.	.	5.41	5.41	0.78517	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1232	0.72460	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	AGA	178592528	1.000000	0.71417	0.913000	0.36048	0.145000	0.21501	8.511000	0.90535	2.059000	0.61396	0.528000	0.53228	.	.	.	none		0.448	AGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361916.1	NM_000027	Intron	G	178355534	A	G	178355534	5	3	31	1	0	0	0	0	0	0	1	0	365	405	14	3	244	3	AGA	4	178355534	Splice_Site	SNP	A	TCGA-GR-A4D4-01A-11D-A31X-10	129520106	178355534	12798742	25	13891											
ENC1	8507	hgsc.bcm.edu	37	chr5	73930903	73930903	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggccggtacagtccacctgtTttcacactgatcgtaacact	9	11	8	13	2	1	1	1	1	0	0	3	1	2	1	3	2	2	3	3	2	2	4			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr5:73930903T>C	ENST00000302351.4	-	2	2538	c.1408A>G	c.(1408-1410)Aac>Gac	p.N470D	ENC1_ENST00000510316.1_Missense_Mutation_p.N397D|ENC1_ENST00000509284.1_5'Flank|ENC1_ENST00000537006.1_Missense_Mutation_p.N470D	NM_003633.3	NP_003624.1	O14682	ENC1_HUMAN	ectodermal-neural cortex 1 (with BTB domain)	470					multicellular organismal development (GO:0007275)|negative regulation of translation (GO:0017148)|nervous system development (GO:0007399)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	20		all_lung(232;0.0154)|Lung NSC(167;0.0331)|Ovarian(174;0.0798)		OV - Ovarian serous cystadenocarcinoma(47;1.45e-59)		GTCCACCTGTTTTCACACTGA	0.507																																					p.N470D		Atlas-SNP	.											.	ENC1	56	.	0			c.A1408G						PASS	.						50	56	54					5																	73930903		2203	4300	6503	SO:0001583	missense	8507	exon2			ACCTGTTTTCACA	AF059611	CCDS4021.1, CCDS58958.1	5q13	2013-01-30	2013-01-30		ENSG00000171617	ENSG00000171617		"Kelch-like", "BTB/POZ domain containing"	3345	protein-coding gene	gene with protein product	"kelch-like family member 37"	605173	"ectodermal-neural cortex 1 (with BTB-like domain)"	NRPB		9305847, 9566959	Standard	NM_003633		Approved	PIG10, ENC-1, TP53I10, KLHL37	uc003kdc.5	O14682	OTTHUMG00000102059	ENST00000302351.4:c.1408A>G	5.37:g.73930903T>C	ENSP00000306356:p.Asn470Asp	61	0	0		59	21	0.355932	NM_003633	B4DHJ1|E9PFU0|O75464|Q9UPG9	Missense_Mutation	SNP	ENST00000302351.4	37	CCDS4021.1	.	.	.	.	.	.	.	.	.	.	T	15.43	2.830609	0.50845	.	.	ENSG00000171617	ENST00000302351;ENST00000510316;ENST00000537006	T;T;T	0.66638	-0.22;-0.22;-0.22	5.89	5.89	0.94794	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.58850	0.2151	L	0.33668	1.02	0.80722	D	1	B	0.12013	0.005	B	0.11329	0.006	T	0.55159	-0.8184	10	0.54805	T	0.06	.	16.3123	0.82883	0.0:0.0:0.0:1.0	.	470	O14682	ENC1_HUMAN	D	470;397;470	ENSP00000306356:N470D;ENSP00000423804:N397D;ENSP00000446289:N470D	ENSP00000306356:N470D	N	-	1	0	ENC1	73966659	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.254000	0.74563	0.459000	0.35465	AAC	.	.	none		0.507	ENC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219862.2	NM_003633		C	73930903	T	C	73930903	3	2	31	1	0	0	0	0	1	0	0	0	5115	1841	64	3	365	3	ENC1	5	73930903	Missense_Mutation	SNP	T	TCGA-GR-A4D4-01A-11D-A31X-10		73930903	106984357	26	13892											
ODZ2	57451	hgsc.bcm.edu	37	chr5	167645245	167645245	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccaccaagtcagcatcattgCgggacgccccatgcactgcc	9	6	9	17	2	2	0	2	0	0	0	2	1	2	1	5	1	4	2	5	1	1	1			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr5:167645245C>T	ENST00000518659.1	+	23	4388	c.4349C>T	c.(4348-4350)gCg>gTg	p.A1450V	TENM2_ENST00000520394.1_Missense_Mutation_p.A1211V|TENM2_ENST00000545108.1_Missense_Mutation_p.A1449V|TENM2_ENST00000403607.2_Missense_Mutation_p.A1274V|TENM2_ENST00000519204.1_Missense_Mutation_p.A1329V	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	1450					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)										AGCATCATTGCGGGACGCCCC	0.502																																					p.A1441V		Atlas-SNP	.											ODZ2_ENST00000519204,NS,carcinoma,-1,3	.	.	3	0			c.C4322T						PASS	.						209	215	213					5																	167645245		2180	4278	6458	SO:0001583	missense	57451	exon23			TCATTGCGGGACG	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.4349C>T	5.37:g.167645245C>T	ENSP00000429430:p.Ala1450Val	110	0	0		102	28	0.27451	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	37		.	.	.	.	.	.	.	.	.	.	C	22.2	4.263444	0.80358	.	.	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.90563	-2.69;-2.69;-2.69;-2.69;-2.69	5.71	5.71	0.89125	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.95743	0.8615	M	0.80183	2.485	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;0.987	D	0.95724	0.8769	10	0.87932	D	0	.	19.8677	0.96824	0.0:1.0:0.0:0.0	.	1449;1450;1211	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	V	1450;1449;1329;1211;1274	ENSP00000429430:A1450V;ENSP00000438635:A1449V;ENSP00000428964:A1329V;ENSP00000427874:A1211V;ENSP00000384905:A1274V	ENSP00000384905:A1274V	A	+	2	0	ODZ2	167577823	1.000000	0.71417	0.982000	0.44146	0.989000	0.77384	6.089000	0.71384	2.709000	0.92574	0.655000	0.94253	GCG	.	.	none		0.502	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679		T	167645245	C	T	167645245	3	4	31	1	0	0	0	0	1	0	0	0	10844	768	27	1	4412	1	ODZ2	5	167645245	Missense_Mutation	SNP	C	TCGA-GR-A4D4-01A-11D-A31X-10	93714342	167645245	13270015	27	13893											
HIST1H1C	3006	hgsc.bcm.edu	37	chr6	26056500	26056500	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagagaaactccgctacgctCtttagaggcggccacagcct	10	7	10	14	3	1	2	0	0	1	2	2	3	2	2	3	2	3	2	3	2	3	3	rs372319415		TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr6:26056500C>T	ENST00000343677.2	-	1	199	c.157G>A	c.(157-159)Gag>Aag	p.E53K		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	53	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				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						CCGCTACGCTCTTTAGAGGCG	0.552																																					p.E53K		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.G157A						PASS	.						65	74	71					6																	26056500		2203	4300	6503	SO:0001583	missense	3006	exon1			TACGCTCTTTAGA	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.157G>A	6.37:g.26056500C>T	ENSP00000339566:p.Glu53Lys	108	0	0		117	66	0.564103	NM_005319	A8K4I2	Missense_Mutation	SNP	ENST00000343677.2	37	CCDS4577.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.297068	0.81025	.	.	ENSG00000187837	ENST00000343677	T	0.35048	1.33	5.73	5.73	0.89815	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.180300	0.47852	D	0.000208	T	0.72350	0.3449	H	0.97635	4.045	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.81922	-0.0711	10	0.87932	D	0	-77.7995	19.248	0.93909	0.0:1.0:0.0:0.0	.	53	P16403	H12_HUMAN	K	53	ENSP00000339566:E53K	ENSP00000339566:E53K	E	-	1	0	HIST1H1C	26164479	1.000000	0.71417	1.000000	0.80357	0.065000	0.16274	5.774000	0.68906	2.861000	0.98227	0.655000	0.94253	GAG	.	.	alt		0.552	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319		T	26056500	C	T	26056500	3	4	31	1	0	0	0	0	1	0	0	0	7133	922	32	2	488	2	HIST1H1C	6	26056500	Missense_Mutation	SNP	C	TCGA-GR-A4D4-01A-11D-A31X-10		26056500	145058567	28	13894											
KIAA1949	170954	hgsc.bcm.edu	37	chr6	30652888	30652888	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctgcggaactgttgccttggGcctcccttgtcagggtctcg	3	12	13	13	2	2	0	1	0	1	0	4	1	3	1	3	3	3	1	3	3	1	3			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr6:30652888G>T	ENST00000274853.3	-	1	2784	c.908C>A	c.(907-909)gCc>gAc	p.A303D	PPP1R18_ENST00000488324.1_Intron|NRM_ENST00000470733.1_5'Flank|PPP1R18_ENST00000399199.3_Missense_Mutation_p.A303D	NM_133471.3	NP_597728.1	Q6NYC8	PPR18_HUMAN	protein phosphatase 1, regulatory subunit 18	303						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.A303V(1)									GTTGCCTTGGGCCTCCCTTGT	0.572																																					p.A303D		Atlas-SNP	.											KIAA1949,rectum,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	large_intestine(1)	c.C908A						PASS	.						88	107	101					6																	30652888		1431	2652	4083	SO:0001583	missense	170954	exon2			CCTTGGGCCTCCC	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.908C>A	6.37:g.30652888G>T	ENSP00000274853:p.Ala303Asp	56	0	0		65	5	0.0769231	NM_001134870	A2AB01|A2AIB8|A4UBI6|A6NCB7|A8MSS7|B7ZCV7|Q68CK8|Q6ZTV1|Q6ZUJ6|Q8NDQ4|Q8TF52|Q9BRL9	Missense_Mutation	SNP	ENST00000274853.3	37	CCDS43444.1	.	.	.	.	.	.	.	.	.	.	G	7.611	0.674709	0.14841	.	.	ENSG00000146112	ENST00000274853;ENST00000399199;ENST00000376424	T;T	0.23950	1.88;1.88	5.27	-3.84	0.04256	.	1.204620	0.06234	N	0.689171	T	0.05731	0.0150	L	0.27053	0.805	0.09310	N	1	B	0.29432	0.244	B	0.29176	0.099	T	0.42882	-0.9425	10	0.48119	T	0.1	0.5484	6.0357	0.19706	0.3447:0.3544:0.3008:0.0	.	303	Q6NYC8	PPR18_HUMAN	D	303	ENSP00000274853:A303D;ENSP00000382150:A303D	ENSP00000274853:A303D	A	-	2	0	KIAA1949	30760867	0.000000	0.05858	0.000000	0.03702	0.165000	0.22458	-0.144000	0.10280	-0.347000	0.08299	0.561000	0.74099	GCC	.	.	none		0.572	PPP1R18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076498.2	NM_133471		T	30652888	G	T	30652888	3	4	31	1	0	0	0	0	1	0	0	0	8272	1203	42	4	945	4	KIAA1949	6	30652888	Missense_Mutation	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10	4596388	30652888	140462179	29	13895											
KCTD20	222658	hgsc.bcm.edu	37	chr6	36454876	36454876	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggagatattaatgcatcAcccaccccaagtggatgaac	14	7	8	12	0	1	2	1	1	0	1	1	4	1	3	4	2	2	1	4	2	4	2			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr6:36454876A>C	ENST00000373731.2	+	8	1575	c.1184A>C	c.(1183-1185)cAc>cCc	p.H395P	KCTD20_ENST00000449081.2_Missense_Mutation_p.H229P|KCTD20_ENST00000544295.1_Missense_Mutation_p.H149P|KCTD20_ENST00000474988.1_3'UTR|KCTD20_ENST00000536244.1_Missense_Mutation_p.H250P	NM_173562.3	NP_775833.2	Q7Z5Y7	KCD20_HUMAN	potassium channel tetramerization domain containing 20	395					protein homooligomerization (GO:0051260)					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|skin(1)	15						TTAATGCATCACCCACCCCAA	0.502																																					p.H395P		Atlas-SNP	.											KCTD20,NS,lymphoid_neoplasm,+1,1	KCTD20	37	1	0			c.A1184C						scavenged	.						214	214	214					6																	36454876		2203	4300	6503	SO:0001583	missense	222658	exon8			TGCATCACCCACC	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.1184A>C	6.37:g.36454876A>C	ENSP00000362836:p.His395Pro	186	1	0.00537634		184	40	0.217391	NM_173562	B4DZD3|B4E2Q3|F5H3T3|Q5W105|Q69YQ7|Q8IZ55	Missense_Mutation	SNP	ENST00000373731.2	37	CCDS4821.1	.	.	.	.	.	.	.	.	.	.	A	17.15	3.315570	0.60524	.	.	ENSG00000112078	ENST00000373731;ENST00000544295;ENST00000449081;ENST00000536244	T;T	0.44881	0.91;0.97	5.91	5.91	0.95273	.	0.121605	0.56097	D	0.000028	T	0.10551	0.0258	N	0.04508	-0.205	0.51012	D	0.9999	B;B	0.12013	0.004;0.005	B;B	0.12156	0.007;0.006	T	0.12528	-1.0544	10	0.27785	T	0.31	-22.5018	12.2309	0.54486	0.8582:0.1418:0.0:0.0	.	229;395	Q7Z5Y7-2;Q7Z5Y7	.;KCD20_HUMAN	P	395;149;229;250	ENSP00000362836:H395P;ENSP00000439118:H250P	ENSP00000362836:H395P	H	+	2	0	KCTD20	36562854	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	4.355000	0.59424	2.252000	0.74401	0.533000	0.62120	CAC	.	.	none		0.502	KCTD20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040345.2	NM_173562		C	36454876	A	C	36454876	3	2	31	1	0	0	0	0	1	0	0	0	8117	159	6	5	1210	5	KCTD20	6	36454876	Missense_Mutation	SNP	A	TCGA-GR-A4D4-01A-11D-A31X-10	5801988	36454876	134660191	30	13896											
COL21A1	81578	hgsc.bcm.edu	37	chr6	56006741	56006741	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacatacttgtattcctggaGatcctggaacacctggtgtc	9	12	9	11	0	0	1	0	0	0	1	3	3	2	2	3	3	2	1	3	3	3	4	rs575546564		TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr6:56006741G>T	ENST00000244728.5	-	11	1872	c.1475C>A	c.(1474-1476)tCt>tAt	p.S492Y	COL21A1_ENST00000535941.1_Missense_Mutation_p.S492Y|COL21A1_ENST00000370819.1_Missense_Mutation_p.S489Y	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	492	Collagen-like 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(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)			TATTCCTGGAGATCCTGGAAC	0.274																																					p.S492Y		Atlas-SNP	.											.	COL21A1	201	.	0			c.C1475A						PASS	.						46	45	46					6																	56006741		911	2069	2980	SO:0001583	missense	81578	exon11			CCTGGAGATCCTG	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.1475C>A	6.37:g.56006741G>T	ENSP00000244728:p.Ser492Tyr	155	0	0		125	27	0.216	NM_030820	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Missense_Mutation	SNP	ENST00000244728.5	37	CCDS55025.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.876|8.876	0.950487|0.950487	0.18431|0.18431	.|.	.|.	ENSG00000124749|ENSG00000124749	ENST00000456983|ENST00000244728;ENST00000370819;ENST00000535941;ENST00000370811	.|D;D;D	.|0.92858	.|-3.12;-3.12;-3.12	5.27|5.27	4.39|4.39	0.52855|0.52855	.|.	.|0.116551	.|0.37715	.|N	.|0.001980	D|D	0.91192|0.91192	0.7225|0.7225	M|M	0.64170|0.64170	1.965|1.965	0.58432|0.58432	D|D	0.999996|0.999996	.|P;D	.|0.57257	.|0.955;0.979	.|P;P	.|0.55222	.|0.566;0.771	D|D	0.91203|0.91203	0.4993|0.4993	5|10	.|0.59425	.|D	.|0.04	.|.	9.1386|9.1386	0.36890|0.36890	0.0978:0.0:0.9022:0.0|0.0978:0.0:0.9022:0.0	.|.	.|489;492	.|Q96P44-3;Q96P44	.|.;COLA1_HUMAN	I|Y	56|492;489;492;489	.|ENSP00000244728:S492Y;ENSP00000359855:S489Y;ENSP00000444384:S492Y	.|ENSP00000244728:S492Y	L|S	-|-	1|2	0|0	COL21A1|COL21A1	56114700|56114700	0.981000|0.981000	0.34729|0.34729	0.814000|0.814000	0.32528|0.32528	0.926000|0.926000	0.56050|0.56050	3.065000|3.065000	0.49994|0.49994	2.624000|2.624000	0.88883|0.88883	0.655000|0.655000	0.94253|0.94253	CTC|TCT	.	.	none		0.274	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2			T	56006741	G	T	56006741	3	4	31	1	0	0	0	0	1	0	0	0	3682	942	33	4	1478	4	COL21A1	6	56006741	Missense_Mutation	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10	19551865	56006741	115108326	31	13897											
HDAC2	3066	hgsc.bcm.edu	37	chr6	114262899	114262899	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatctgttttttcaccactgTtgtccttggatttatcttct	5	22	5	9	0	4	0	1	0	3	0	5	1	5	1	2	1	0	2	2	1	2	9			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr6:114262899T>A	ENST00000519065.1	-	13	1785	c.1409A>T	c.(1408-1410)aAc>aTc	p.N470I	HDAC2_ENST00000368632.2_Missense_Mutation_p.N440I|HDAC2_ENST00000398283.2_Missense_Mutation_p.N564I|HDAC2_ENST00000519108.1_Missense_Mutation_p.N440I			Q92769	HDAC2_HUMAN	histone deacetylase 2	470					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)	TTCACCACTGTTGTCCTTGGA	0.259																																					p.N470I		Atlas-SNP	.											.	HDAC2	102	.	0			c.A1409T						PASS	.						69	67	68					6																	114262899		1809	4070	5879	SO:0001583	missense	3066	exon13			CCACTGTTGTCCT	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.1409A>T	6.37:g.114262899T>A	ENSP00000430432:p.Asn470Ile	98	0	0		74	20	0.27027	NM_001527	B3KRS5|B4DL58|E1P561|Q5SRI8|Q5SZ86|Q8NEH4	Missense_Mutation	SNP	ENST00000519065.1	37	CCDS43493.2	.	.	.	.	.	.	.	.	.	.	T	14.56	2.570458	0.45798	.	.	ENSG00000196591	ENST00000519065;ENST00000398283;ENST00000519108;ENST00000368632	T;T;T;T	0.74421	-0.8;-0.84;-0.8;-0.8	5.76	-1.27	0.09347	.	0.077961	0.52532	D	0.000075	T	0.27900	0.0687	N	0.02802	-0.49	0.38410	D	0.945915	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.03157	-1.1066	10	0.37606	T	0.19	-17.9783	10.9454	0.47297	0.0:0.4618:0.0:0.5382	.	440;470	B3KRS5;Q92769	.;HDAC2_HUMAN	I	470;564;440;440	ENSP00000430432:N470I;ENSP00000381331:N564I;ENSP00000430008:N440I;ENSP00000357621:N440I	ENSP00000357621:N440I	N	-	2	0	HDAC2	114369592	0.695000	0.27747	0.882000	0.34594	0.996000	0.88848	-0.363000	0.07593	-0.108000	0.12066	0.528000	0.53228	AAC	.	.	none		0.259	HDAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041909.2			A	114262899	T	A	114262899	3	1	31	1	0	0	0	0	1	0	0	0	7016	1725	60	5	65	5	HDAC2	6	114262899	Missense_Mutation	SNP	T	TCGA-GR-A4D4-01A-11D-A31X-10	58256158	114262899	56852168	32	13898			1	58		2	2	14	T		3.863383e-05
HDAC2	3066	hgsc.bcm.edu	37	chr6	114262912	114262912	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accactgttgtccttggattTatcttcttccttaacgtcta	7	18	5	11	1	3	0	0	0	3	0	5	1	5	1	3	1	1	1	3	1	3	8			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr6:114262912T>G	ENST00000519065.1	-	13	1772	c.1396A>C	c.(1396-1398)Aaa>Caa	p.K466Q	HDAC2_ENST00000368632.2_Missense_Mutation_p.K436Q|HDAC2_ENST00000398283.2_Missense_Mutation_p.K560Q|HDAC2_ENST00000519108.1_Missense_Mutation_p.K436Q			Q92769	HDAC2_HUMAN	histone deacetylase 2	466					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)	TCCTTGGATTTATCTTCTTCC	0.234																																					p.K466Q		Atlas-SNP	.											.	HDAC2	102	.	0			c.A1396C						PASS	.						64	62	63					6																	114262912		1805	4060	5865	SO:0001583	missense	3066	exon13			TGGATTTATCTTC	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.1396A>C	6.37:g.114262912T>G	ENSP00000430432:p.Lys466Gln	95	0	0		76	20	0.263158	NM_001527	B3KRS5|B4DL58|E1P561|Q5SRI8|Q5SZ86|Q8NEH4	Missense_Mutation	SNP	ENST00000519065.1	37	CCDS43493.2	.	.	.	.	.	.	.	.	.	.	T	17.37	3.372576	0.61624	.	.	ENSG00000196591	ENST00000519065;ENST00000398283;ENST00000519108;ENST00000368632	T;T;T;T	0.75260	-0.87;-0.92;-0.87;-0.87	5.76	5.76	0.90799	.	0.075114	0.56097	D	0.000037	T	0.62575	0.2439	L	0.40543	1.245	0.48696	D	0.999691	D;B	0.57899	0.981;0.137	P;B	0.49637	0.617;0.019	T	0.61540	-0.7042	10	0.21014	T	0.42	-36.1428	14.6077	0.68493	0.0:0.0:0.0:1.0	.	436;466	B3KRS5;Q92769	.;HDAC2_HUMAN	Q	466;560;436;436	ENSP00000430432:K466Q;ENSP00000381331:K560Q;ENSP00000430008:K436Q;ENSP00000357621:K436Q	ENSP00000357621:K436Q	K	-	1	0	HDAC2	114369605	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	4.297000	0.59061	2.323000	0.78572	0.528000	0.53228	AAA	.	.	none		0.234	HDAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041909.2			G	114262912	T	G	114262912	3	3	31	1	0	0	0	0	1	0	0	0	7016	1763	61	5	78	5	HDAC2	6	114262912	Missense_Mutation	SNP	T	TCGA-GR-A4D4-01A-11D-A31X-10	13	114262912	56852155	33	13899			1	58		2	2	14	T		3.863383e-05
CARD11	84433	hgsc.bcm.edu	37	chr7	2977614	2977614	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgcttgtacatttcacagTcctttcccagggtcgagcac	7	12	10	12	1	1	0	1	0	0	0	4	1	3	0	2	2	3	3	2	2	1	4			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr7:2977614T>A	ENST00000396946.4	-	8	1473	c.1070A>T	c.(1069-1071)gAc>gTc	p.D357V		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	357					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.D350V(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)		CATTTCACAGTCCTTTCCCAG	0.567			Mis		DLBCL																																p.D357V		Atlas-SNP	.		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	CARD11,NS,lymphoid_neoplasm,0,4	CARD11	339	4	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.A1070T						PASS	.						153	124	134					7																	2977614		2203	4300	6503	SO:0001583	missense	84433	exon8			TCACAGTCCTTTC	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.1070A>T	7.37:g.2977614T>A	ENSP00000380150:p.Asp357Val	48	0	0		44	23	0.522727	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	T	24.8	4.568717	0.86439	.	.	ENSG00000198286	ENST00000396946	T	0.35605	1.3	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.56906	0.2017	M	0.64997	1.995	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.60682	-0.7215	10	0.72032	D	0.01	-47.8827	13.8813	0.63684	0.0:0.0:0.0:1.0	.	357	Q9BXL7	CAR11_HUMAN	V	357	ENSP00000380150:D357V	ENSP00000380150:D357V	D	-	2	0	CARD11	2944140	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.794000	0.85869	1.878000	0.54408	0.482000	0.46254	GAC	.	.	none		0.567	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		A	2977614	T	A	2977614	3	1	31	1	0	0	0	0	1	0	0	0	2647	1667	58	5	2466	5	CARD11	7	2977614	Missense_Mutation	SNP	T	TCGA-GR-A4D4-01A-11D-A31X-10		2977614	156161049	34	13900											
TXNDC3	51314	hgsc.bcm.edu	37	chr7	37907335	37907335	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagtttgtctcttttatgaCaagtggcttaagctatattc	10	17	8	6	0	1	2	0	1	1	1	3	2	1	2	0	1	1	3	0	1	5	7			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr7:37907335C>G	ENST00000199447.4	+	11	1025	c.653C>G	c.(652-654)aCa>aGa	p.T218R	EPDR1_ENST00000476620.1_Intron|NME8_ENST00000440017.1_Missense_Mutation_p.T218R	NM_016616.4	NP_057700.3	Q8N427	TXND3_HUMAN	NME/NM23 family member 8	218	NDK 1.				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)										TCTTTTATGACAAGTGGCTTA	0.398																																					p.T218R		Atlas-SNP	.											.	.	.	.	0			c.C653G						PASS	.						128	121	123					7																	37907335		2203	4300	6503	SO:0001583	missense	51314	exon11			TTATGACAAGTGG	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.653C>G	7.37:g.37907335C>G	ENSP00000199447:p.Thr218Arg	145	0	0		138	29	0.210145	NM_016616	Q9NZH1	Missense_Mutation	SNP	ENST00000199447.4	37	CCDS5452.1	.	.	.	.	.	.	.	.	.	.	C	12.78	2.039377	0.35989	.	.	ENSG00000086288	ENST00000199447;ENST00000440017	T;T	0.50001	0.76;0.76	5.1	4.21	0.49690	.	0.000000	0.47093	D	0.000242	T	0.67335	0.2882	M	0.87758	2.905	0.31171	N	0.703179	D	0.58970	0.984	D	0.66847	0.947	T	0.71009	-0.4716	10	0.62326	D	0.03	-34.9938	8.5596	0.33503	0.0:0.8992:0.0:0.1007	.	218	Q8N427	TXND3_HUMAN	R	218	ENSP00000199447:T218R;ENSP00000397063:T218R	ENSP00000199447:T218R	T	+	2	0	TXNDC3	37873860	0.195000	0.23338	0.984000	0.44739	0.025000	0.11179	0.270000	0.18607	2.756000	0.94617	0.563000	0.77884	ACA	.	.	none		0.398	NME8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219946.1	NM_016616		G	37907335	C	G	37907335	3	3	31	1	0	0	0	0	1	0	0	0	16813	478	17	4	687	4	TXNDC3	7	37907335	Missense_Mutation	SNP	C	TCGA-GR-A4D4-01A-11D-A31X-10	34929721	37907335	121231328	35	13901											
ATXN7L1	222255	hgsc.bcm.edu	37	chr7	105254603	105254603	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acctgtctcactatgtccgcGgggccgccgggcagcgaggt	5	7	15	14	5	1	0	1	0	1	0	3	1	2	0	4	4	1	1	4	4	1	1	rs147930086	byFrequency	TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr7:105254603G>A	ENST00000419735.3	-	10	2223	c.2178C>T	c.(2176-2178)ccC>ccT	p.P726P	ATXN7L1_ENST00000477775.1_Silent_p.P602P|ATXN7L1_ENST00000388807.4_Silent_p.P386P	NM_020725.1	NP_065776.1	Q9ULK2	AT7L1_HUMAN	ataxin 7-like 1	726	Ser-rich.									endometrium(1)|large_intestine(4)|lung(5)	10						CTATGTCCGCGGGGCCGCCGG	0.647													G|||	4	0.000798722	0.0015	0.0014	5008	,	,		15422	0.0		0.001	False		,,,				2504	0.0				p.P726P		Atlas-SNP	.											.	ATXN7L1	56	.	0			c.C2178T						PASS	.						29	29	29					7																	105254603		692	1591	2283	SO:0001819	synonymous_variant	222255	exon10			GTCCGCGGGGCCG	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.2178C>T	7.37:g.105254603G>A		57	0	0		81	24	0.296296	NM_020725	A4D0Q2|B4DTS1|Q8N2T0	Silent	SNP	ENST00000419735.3	37	CCDS47682.1																																																																																			G|0.998;A|0.002	0.002	strong		0.647	ATXN7L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349037.2			A	105254603	G	A	105254603	2	1	31	1	0	0	0	0	0	0	0	1	1216	1103	39	1		1	ATXN7L1	7	105254603	Silent	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10	67347268	105254603	53884060	36	13902											
ERICH1	157697	hgsc.bcm.edu	37	chr8	623759	623759	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctctcccacgccttcccctTcattgctgctgtcctcgggc	2	12	7	20	2	2	0	1	0	1	0	6	0	4	0	6	1	2	2	6	1	0	3			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr8:623759T>G	ENST00000262109.7	-	4	670	c.593A>C	c.(592-594)gAa>gCa	p.E198A	ERICH1_ENST00000522706.1_Missense_Mutation_p.E104A|ERICH1_ENST00000518277.1_5'Flank	NM_207332.1	NP_997215.1	Q86X53	ERIC1_HUMAN	glutamate-rich 1	198	Glu-rich.									endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)	20		Colorectal(14;0.158)|Ovarian(12;0.17)|Myeloproliferative disorder(644;0.185)|Hepatocellular(245;0.236)		Epithelial(5;3.29e-14)|BRCA - Breast invasive adenocarcinoma(11;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(5;3.65e-06)|READ - Rectum adenocarcinoma(1;0.0325)		GCCTTCCCCTTCATTGCTGCT	0.547																																					p.E198A		Atlas-SNP	.											.	ERICH1	50	.	0			c.A593C						PASS	.						92	87	89					8																	623759		2203	4300	6503	SO:0001583	missense	157697	exon4			TCCCCTTCATTGC		CCDS5955.1	8p23.3	2005-09-01			ENSG00000104714	ENSG00000104714			27234	protein-coding gene	gene with protein product							Standard	NM_207332		Approved		uc003wph.3	Q86X53	OTTHUMG00000129163	ENST00000262109.7:c.593A>C	8.37:g.623759T>G	ENSP00000262109:p.Glu198Ala	73	0	0		69	10	0.144928	NM_207332	A8K2J9|Q9P063	Missense_Mutation	SNP	ENST00000262109.7	37	CCDS5955.1	.	.	.	.	.	.	.	.	.	.	T	13.57	2.275783	0.40294	.	.	ENSG00000104714	ENST00000543819;ENST00000522706;ENST00000262109	T;T	0.39787	1.06;1.08	5.84	5.84	0.93424	.	0.402558	0.26883	N	0.022004	T	0.46698	0.1406	L	0.34521	1.04	0.28111	N	0.930986	D;D;D	0.69078	0.997;0.997;0.997	D;D;D	0.66196	0.91;0.91;0.942	T	0.38672	-0.9650	10	0.19147	T	0.46	-8.068	9.445	0.38693	0.1582:0.0:0.0:0.8418	.	198;198;104	B4DMI5;Q86X53;E5RHA3	.;ERIC1_HUMAN;.	A	198;104;198	ENSP00000428635:E104A;ENSP00000262109:E198A	ENSP00000262109:E198A	E	-	2	0	ERICH1	613759	0.869000	0.29996	0.467000	0.27180	0.016000	0.09150	2.241000	0.43097	2.216000	0.71823	0.533000	0.62120	GAA	.	.	none		0.547	ERICH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251228.3	NM_207332		G	623759	T	G	623759	3	3	31	1	0	0	0	0	1	0	0	0	5232	1783	62	5	750	5	ERICH1	8	623759	Missense_Mutation	SNP	T	TCGA-GR-A4D4-01A-11D-A31X-10		623759	145740263	37	13903											
SLC7A2	6542	hgsc.bcm.edu	37	chr8	17409482	17409482	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgcagctggttctctctgcGccttgtcaacaaggtacatt	7	13	9	12	2	3	0	1	0	2	0	5	0	3	0	1	2	4	4	1	2	3	4	rs139867348		TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr8:17409482G>A	ENST00000494857.1	+	7	1260	c.1042G>A	c.(1042-1044)Gcc>Acc	p.A348T	SLC7A2_ENST00000522656.1_Missense_Mutation_p.A348T|SLC7A2_ENST00000398090.3_Missense_Mutation_p.A388T|SLC7A2_ENST00000470360.1_Missense_Mutation_p.A388T|SLC7A2_ENST00000004531.10_Missense_Mutation_p.A388T	NM_001008539.3	NP_001008539.3	P52569	CTR2_HUMAN	solute carrier family 7 (cationic amino acid transporter, y+ system), member 2	348					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)	p.A348T(1)|p.A388T(1)		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)	TTCTCTCTGCGCCTTGTCAAC	0.478																																					p.A388T		Atlas-SNP	.											SLC7A2_ENST00000470360,NS,carcinoma,0,4	SLC7A2	157	4	2	Substitution - Missense(2)	endometrium(2)	c.G1162A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	1,4405	2.1+/-5.4	0,1,2202	80	80	80		1042,1162,1162	5.3	1	8	dbSNP_134	80	0,8600		0,0,4300	no	missense,missense,missense	SLC7A2	NM_001008539.3,NM_001164771.1,NM_003046.5	58,58,58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging,probably-damaging	348/659,388/699,388/698	17409482	1,13005	2203	4300	6503	SO:0001583	missense	6542	exon6			CTCTGCGCCTTGT	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.1042G>A	8.37:g.17409482G>A	ENSP00000419140:p.Ala348Thr	149	0	0		134	41	0.30597	NM_001164771	B7ZL54|O15291|O15292|Q14CQ6|Q6NSZ7|Q86TC6	Missense_Mutation	SNP	ENST00000494857.1	37	CCDS34852.1	.	.	.	.	.	.	.	.	.	.	G	31	5.064440	0.93898	2.27E-4	0.0	ENSG00000003989	ENST00000494857;ENST00000522656;ENST00000470360;ENST00000004531;ENST00000398090	D;D;D;D;D	0.90444	-2.67;-2.67;-2.67;-2.67;-2.67	5.26	5.26	0.73747	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.95465	0.8527	M	0.79258	2.445	0.80722	D	1	D;D;D	0.89917	0.992;1.0;1.0	P;D;D	0.91635	0.761;0.989;0.999	D	0.95700	0.8748	10	0.87932	D	0	.	19.2416	0.93887	0.0:0.0:1.0:0.0	.	388;388;348	P52569-3;P52569-2;P52569	.;.;CTR2_HUMAN	T	348;348;388;388;388	ENSP00000419140:A348T;ENSP00000430464:A348T;ENSP00000419873:A388T;ENSP00000004531:A388T;ENSP00000381164:A388T	ENSP00000004531:A388T	A	+	1	0	SLC7A2	17453860	1.000000	0.71417	0.994000	0.49952	0.926000	0.56050	9.869000	0.99810	2.621000	0.88768	0.655000	0.94253	GCC	G|1.000;A|0.000	0.000	weak		0.478	SLC7A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253367.3	NM_003046		A	17409482	G	A	17409482	3	1	31	1	0	0	0	0	1	0	0	0	14712	1087	38	1	1184	1	SLC7A2	8	17409482	Missense_Mutation	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10	16785723	17409482	128954540	38	13904											
KIAA1967	57805	hgsc.bcm.edu	37	chr8	22472491	22472491	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgcaggcccagactggcatTgatttgagcggctgtaccaa	9	8	13	11	2	0	3	0	2	0	1	0	3	0	3	2	3	2	4	2	3	2	3			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr8:22472491T>A	ENST00000308511.4	+	11	1431	c.1182T>A	c.(1180-1182)atT>atA	p.I394I	RP11-582J16.5_ENST00000521025.1_RNA|CCAR2_ENST00000389279.3_Silent_p.I394I|CCAR2_ENST00000520861.1_Silent_p.I69I			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	394					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage checkpoint (GO:2000003)|regulation of circadian rhythm (GO:0042752)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of protein stability (GO:0031647)|response to UV (GO:0009411)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|DBIRD complex (GO:0044609)|mitochondrial matrix (GO:0005759)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)										AGACTGGCATTGATTTGAGCG	0.642																																					p.I394I		Atlas-SNP	.											.	KIAA1967	72	.	0			c.T1182A						PASS	.						43	32	36					8																	22472491		2202	4297	6499	SO:0001819	synonymous_variant	57805	exon11			TGGCATTGATTTG	AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941			23360	protein-coding gene	gene with protein product	"deleted in breast cancer"	607359	"KIAA1967"	KIAA1967		12370419	Standard	NM_021174		Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.1182T>A	8.37:g.22472491T>A		38	0	0		46	14	0.304348	NM_021174	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Silent	SNP	ENST00000308511.4	37	CCDS34863.1	.	.	.	.	.	.	.	.	.	.	T	8.519	0.868204	0.17250	.	.	ENSG00000158941	ENST00000520738	.	.	.	5.53	-8.45	0.00946	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-15.7173	8.7499	0.34609	0.0777:0.1142:0.0771:0.7309	.	.	.	.	X	86	.	.	L	+	2	0	KIAA1967	22528436	0.238000	0.23825	0.522000	0.27862	0.623000	0.37688	-0.487000	0.06505	-1.792000	0.01259	-0.290000	0.09829	TTG	.	.	none		0.642	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174		A	22472491	T	A	22472491	2	1	31	1	0	0	0	0	0	0	0	1	8274	1800	63	5		5	KIAA1967	8	22472491	Silent	SNP	T	TCGA-GR-A4D4-01A-11D-A31X-10	5063009	22472491	123891531	39	13905											
FNTA	2339	hgsc.bcm.edu	37	chr8	42940407	42940407	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcacagaaaatgactcaccAacaaatgtacagcaataaca	21	5	5	10	0	1	2	1	1	0	1	1	2	1	2	1	0	5	3	1	0	7	2			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr8:42940407A>T	ENST00000302279.3	+	9	1316	c.1122A>T	c.(1120-1122)ccA>ccT	p.P374P	FNTA_ENST00000529687.1_Silent_p.P223P|FNTA_ENST00000342116.4_Silent_p.P307P	NM_002027.2	NP_002018.1	P49354	FNTA_HUMAN	farnesyltransferase, CAAX box, alpha	374					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)			ATGACTCACCAACAAATGTAC	0.393																																					p.P374P		Atlas-SNP	.											.	FNTA	34	.	0			c.A1122T						PASS	.						99	85	90					8																	42940407		2203	4300	6503	SO:0001819	synonymous_variant	2339	exon9			CTCACCAACAAAT	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.1122A>T	8.37:g.42940407A>T		379	0	0		343	97	0.282799	NM_002027	A6NJW0|Q53XJ9|Q9UDC1	Silent	SNP	ENST00000302279.3	37	CCDS6140.1																																																																																			.	.	none		0.393	FNTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383178.1	NM_002027		T	42940407	A	T	42940407	2	4	31	1	0	0	0	0	0	0	0	1	5985	117	5	5		5	FNTA	8	42940407	Silent	SNP	A	TCGA-GR-A4D4-01A-11D-A31X-10	20467916	42940407	103423615	40	13906											
ANKRD46	157567	hgsc.bcm.edu	37	chr8	101541987	101541987	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaaagccgcttggaataattAaagtccccatcaatacaggc	16	8	7	10	1	1	0	1	0	0	0	2	1	2	1	3	2	2	1	3	2	8	4			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr8:101541987A>T	ENST00000520552.1	-	3	236	c.75T>A	c.(73-75)ttT>ttA	p.F25L	ANKRD46_ENST00000335659.3_Missense_Mutation_p.F25L|ANKRD46_ENST00000519316.1_Missense_Mutation_p.F25L|ANKRD46_ENST00000519597.1_Missense_Mutation_p.F25L|ANKRD46_ENST00000520311.1_Missense_Mutation_p.F25L	NM_001270379.1	NP_001257308.1	Q86W74	ANR46_HUMAN	ankyrin repeat domain 46	25						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)			TGGAATAATTAAAGTCCCCAT	0.468																																					p.F25L		Atlas-SNP	.											.	ANKRD46	13	.	0			c.T75A						PASS	.						74	70	71					8																	101541987		2203	4300	6503	SO:0001583	missense	157567	exon3			ATAATTAAAGTCC	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.75T>A	8.37:g.101541987A>T	ENSP00000429015:p.Phe25Leu	150	0	0		138	38	0.275362	NM_001270378	Q6P9B7	Missense_Mutation	SNP	ENST00000520552.1	37	CCDS59109.1	.	.	.	.	.	.	.	.	.	.	A	9.293	1.051020	0.19827	.	.	ENSG00000186106	ENST00000520552;ENST00000335659;ENST00000519597;ENST00000520311;ENST00000519316;ENST00000358990;ENST00000524072;ENST00000523000;ENST00000521345	T;T;T;T;T;T;T;T;T	0.61040	0.18;0.18;0.18;0.18;0.18;0.18;0.18;0.18;0.14	5.78	0.537	0.17144	Ankyrin repeat-containing domain (4);	0.178647	0.51477	D	0.000097	T	0.17831	0.0428	N	0.00960	-1.095	0.43740	D	0.99623	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.31861	-0.9928	10	0.02654	T	1	.	5.2114	0.15318	0.5244:0.1482:0.3274:0.0	.	25;25	Q86W74-2;Q86W74	.;ANR46_HUMAN	L	25	ENSP00000429015:F25L;ENSP00000335287:F25L;ENSP00000430056:F25L;ENSP00000428388:F25L;ENSP00000430827:F25L;ENSP00000351881:F25L;ENSP00000430357:F25L;ENSP00000430800:F25L;ENSP00000429647:F25L	ENSP00000335287:F25L	F	-	3	2	ANKRD46	101611163	0.999000	0.42202	1.000000	0.80357	0.986000	0.74619	0.814000	0.27239	0.139000	0.18822	0.533000	0.62120	TTT	.	.	none		0.468	ANKRD46-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379899.1	NM_198401		T	101541987	A	T	101541987	3	4	31	1	0	0	0	0	1	0	0	0	674	359	13	5	623	5	ANKRD46	8	101541987	Missense_Mutation	SNP	A	TCGA-GR-A4D4-01A-11D-A31X-10	58601580	101541987	44822035	41	13907											
ZNF706	51123	hgsc.bcm.edu	37	chr8	102212299	102212299	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgctctcaaagtgctgcttGaaggtcttagggtctggcat	7	14	12	8	0	3	1	1	1	3	0	4	1	3	1	0	3	3	4	0	3	3	3			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr8:102212299G>T	ENST00000520347.1	-	3	3118	c.162C>A	c.(160-162)ttC>ttA	p.F54L	ZNF706_ENST00000518336.1_Missense_Mutation_p.F54L|ZNF706_ENST00000519882.1_Missense_Mutation_p.F54L|ZNF706_ENST00000517844.1_Missense_Mutation_p.F54L|ZNF706_ENST00000520984.1_Missense_Mutation_p.F54L|ZNF706_ENST00000311212.4_Missense_Mutation_p.F54L|ZNF706_ENST00000521272.1_Missense_Mutation_p.F54L|ZNF706_ENST00000519744.1_Intron			Q9Y5V0	ZN706_HUMAN	zinc finger protein 706	54							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)			AGTGCTGCTTGAAGGTCTTAG	0.368																																					p.F54L		Atlas-SNP	.											.	ZNF706	12	.	0			c.C162A						PASS	.						163	147	152					8																	102212299		2203	4300	6503	SO:0001583	missense	51123	exon4			CTGCTTGAAGGTC	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.162C>A	8.37:g.102212299G>T	ENSP00000430823:p.Phe54Leu	130	0	0		110	5	0.0454545	NM_001042510	A8K362	Missense_Mutation	SNP	ENST00000520347.1	37	CCDS6291.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.3|26.3	4.728806|4.728806	0.89390|0.89390	.|.	.|.	ENSG00000120963|ENSG00000120963	ENST00000520984;ENST00000311212;ENST00000517844;ENST00000520347;ENST00000519882;ENST00000521272;ENST00000518336|ENST00000519103	.|.	.|.	.|.	5.87|5.87	5.0|5.0	0.66597|0.66597	Zinc finger, C2H2-like (1);|.	0.044791|.	0.85682|.	D|.	0.000000|.	T|.	0.70824|.	0.3268|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	P|.	0.40534|.	0.72|.	P|.	0.48704|.	0.587|.	T|.	0.70260|.	-0.4921|.	8|.	0.28530|.	T|.	0.3|.	.|.	15.045|15.045	0.71822|0.71822	0.0678:0.0:0.9321:0.0|0.0678:0.0:0.9321:0.0	.|.	54|.	Q9Y5V0|.	ZN706_HUMAN|.	L|X	54|35	.|.	ENSP00000311768:F54L|.	F|S	-|-	3|2	2|0	ZNF706|ZNF706	102281475|102281475	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	3.646000|3.646000	0.54396|0.54396	1.500000|1.500000	0.48636|0.48636	0.655000|0.655000	0.94253|0.94253	TTC|TCA	.	.	none		0.368	ZNF706-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380477.1	NM_016096		T	102212299	G	T	102212299	3	4	31	1	0	0	0	0	1	0	0	0	18125	1281	45	4	72	4	ZNF706	8	102212299	Missense_Mutation	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10	670312	102212299	44151723	42	13908											
C8orf85	441376	hgsc.bcm.edu	37	chr8	117950758	117950758	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggcggcgcgggaggagcaGagctggacgggcgttgaggc	6	3	23	9	6	0	2	0	1	0	1	0	5	0	5	0	7	2	3	0	7	0	1	rs111477672	byFrequency	TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr8:117950758G>T	ENST00000378279.3	+	1	321	c.276G>T	c.(274-276)caG>caT	p.Q92H		NM_001025357.2	NP_001020528.1	Q4LEZ3	AARD_HUMAN	alanine and arginine rich domain containing protein	92	Ala/Arg-rich.				lung development (GO:0030324)												GGGAGGAgcagagctggacgg	0.761													G|||	75	0.014976	0.0015	0.0159	5008	,	,		9938	0.0		0.0547	False		,,,				2504	0.0072				p.Q92H		Atlas-SNP	.											.	.	.	.	0			c.G276T						PASS	.						2	3	2					8																	117950758		1194	2634	3828	SO:0001583	missense	441376	exon1			GGAGCAGAGCTGG	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.276G>T	8.37:g.117950758G>T	ENSP00000367528:p.Gln92His	1	0	0		11	10	0.909091	NM_001025357	A5PKU8	Missense_Mutation	SNP	ENST00000378279.3	37	CCDS34935.1	53	0.024267399267399268	5	0.01016260162601626	7	0.019337016574585635	0	0.0	41	0.05408970976253298	G	7.346	0.621816	0.14193	.	.	ENSG00000205002	ENST00000378279	T	0.32515	1.45	3.52	0.485	0.16830	.	1.349340	0.05344	N	0.530724	T	0.05456	0.0144	N	0.24115	0.695	0.09310	N	1	D	0.60160	0.987	P	0.57548	0.823	T	0.06445	-1.0826	10	0.30854	T	0.27	-0.5551	2.1438	0.03782	0.1165:0.1949:0.4883:0.2002	.	92	Q4LEZ3	AARD_HUMAN	H	92	ENSP00000367528:Q92H	ENSP00000367528:Q92H	Q	+	3	2	C8orf85	118019939	0.000000	0.05858	0.004000	0.12327	0.408000	0.30992	0.044000	0.13992	-0.030000	0.13804	0.455000	0.32223	CAG	G|0.976;T|0.024	0.024	strong		0.761	AARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381195.1	NM_001025357		T	117950758	G	T	117950758	3	4	31	1	0	0	0	0	1	0	0	0	2443	933	33	4	278	4	C8orf85	8	117950758	Missense_Mutation	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10	15738459	117950758	28413264	43	13909											
SMARCA2	6595	hgsc.bcm.edu	37	chr9	2039777	2039785	+	In_Frame_Del	DEL	CAGCAGCAG	CAGCAGCAG	-																															agcaacaacagcagcagcaaCagcagcagcagcagcagcag																								rs376509101|rs145170448|rs62639301	byFrequency	TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	CAGCAGCAG	CAGCAGCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr9:2039777_2039785delCAGCAGCAG	ENST00000382203.1	+	4	876_884	c.667_675delCAGCAGCAG	c.(667-675)cagcagcagdel	p.QQQ235del	RP11-264I13.2_ENST00000426860.1_RNA|SMARCA2_ENST00000382194.1_In_Frame_Del_p.QQQ235del|SMARCA2_ENST00000357248.2_In_Frame_Del_p.QQQ235del|SMARCA2_ENST00000349721.2_In_Frame_Del_p.QQQ235del|SMARCA2_ENST00000491574.1_3'UTR			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)		gcagcagcaacagcagcagcagcagcagc	0.622																																					p.222_225del		Atlas-Indel	.											SMARCA2_ENST00000349721,NS,carcinoma,0,2	SMARCA2	313	2	0			c.666_674del						PASS	.																																			SO:0001651	inframe_deletion	6595	exon4			.	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.667_675delCAGCAGCAG	9.37:g.2039786_2039794delCAGCAGCAG	ENSP00000371638:p.Gln235_Gln237del	100	0	0		93	13	0.139785	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	In_Frame_Del	DEL	ENST00000382203.1	37	CCDS34977.1																																																																																			.	.	alt		0.622	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070		-	2039785	CAGCAGCAG	-	2039777	7	5	31	1	0	1	0	1	0	0	0	0	14784	479	17	0	677	0	SMARCA2	9	2039777	In_Frame_Del	DEL	CAGCAGCAG	TCGA-GR-A4D4-01A-11D-A31X-10		2039777	139173654	44	13910											
TEK	7010	hgsc.bcm.edu	37	chr9	27204915	27204915	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtcttcctgcacagcaccagCggacctcggaggggggaaga	9	5	15	12	2	1	1	0	0	1	1	3	4	2	4	3	5	3	2	3	5	1	1	rs561507573		TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr9:27204915C>T	ENST00000380036.4	+	14	2658	c.2216C>T	c.(2215-2217)gCg>gTg	p.A739V	TEK_ENST00000406359.4_Missense_Mutation_p.A696V|TEK_ENST00000519097.1_Missense_Mutation_p.A592V	NM_000459.3	NP_000450	Q02763	TIE2_HUMAN	TEK tyrosine kinase, endothelial	739					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)	ACAGCACCAGCGGACCTCGGA	0.507													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18299	0.0		0.0	False		,,,				2504	0.0				p.A739V		Atlas-SNP	.											.	TEK	250	.	0			c.C2216T						PASS	.						131	120	124					9																	27204915		2203	4300	6503	SO:0001583	missense	7010	exon14			CACCAGCGGACCT	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.2216C>T	9.37:g.27204915C>T	ENSP00000369375:p.Ala739Val	65	0	0		57	17	0.298246	NM_000459	A8K6W0|B4DH20|B4DHD3|D3DRK5|E7EWI2|Q5TCU2|Q8IV34	Missense_Mutation	SNP	ENST00000380036.4	37	CCDS6519.1	.	.	.	.	.	.	.	.	.	.	C	10.56	1.385178	0.25031	.	.	ENSG00000120156	ENST00000519097;ENST00000380036;ENST00000406359	T;T;T	0.74632	-0.83;-0.85;-0.86	6.02	0.534	0.17127	Fibronectin, type III (1);	1.391580	0.04700	N	0.415659	T	0.56046	0.1959	N	0.24115	0.695	0.09310	N	1	B;B;B;B	0.24426	0.0;0.054;0.0;0.103	B;B;B;B	0.20577	0.0;0.03;0.0;0.01	T	0.38265	-0.9669	10	0.27082	T	0.32	.	1.3342	0.02141	0.4257:0.2524:0.1303:0.1916	.	592;772;696;739	E7EWI2;Q59HG2;B4DHD3;Q02763	.;.;.;TIE2_HUMAN	V	592;739;696	ENSP00000430686:A592V;ENSP00000369375:A739V;ENSP00000383977:A696V	ENSP00000369375:A739V	A	+	2	0	TEK	27194915	0.000000	0.05858	0.000000	0.03702	0.057000	0.15508	-0.246000	0.08878	0.351000	0.24027	-0.311000	0.09066	GCG	.	.	none		0.507	TEK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051965.3			T	27204915	C	T	27204915	3	4	31	1	0	0	0	0	1	0	0	0	15766	768	27	1	2270	1	TEK	9	27204915	Missense_Mutation	SNP	C	TCGA-GR-A4D4-01A-11D-A31X-10	25165138	27204915	114008516	45	13911											
PTCH1	5727	hgsc.bcm.edu	37	chr9	98241333	98241333	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atggctgccgctttgtcctcGttccagttgatgtgtgagac	5	14	12	10	2	0	2	0	2	0	1	3	3	2	2	3	1	1	4	3	1	0	3	rs201602238		TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr9:98241333G>C	ENST00000331920.6	-	8	1463	c.1164C>G	c.(1162-1164)aaC>aaG	p.N388K	PTCH1_ENST00000429896.2_Missense_Mutation_p.N237K|PTCH1_ENST00000418258.1_Missense_Mutation_p.N237K|PTCH1_ENST00000375274.2_Missense_Mutation_p.N387K|PTCH1_ENST00000548379.1_5'Flank|PTCH1_ENST00000421141.1_Missense_Mutation_p.N237K|PTCH1_ENST00000430669.2_Missense_Mutation_p.N322K|PTCH1_ENST00000437951.1_Missense_Mutation_p.N322K	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	388					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)				CTTTGTCCTCGTTCCAGTTGA	0.537																																					p.N388K		Atlas-SNP	.											.	PTCH1	1850	.	0			c.C1164G						PASS	.						173	128	143					9																	98241333		2203	4300	6503	SO:0001583	missense	5727	exon8			GTCCTCGTTCCAG	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.1164C>G	9.37:g.98241333G>C	ENSP00000332353:p.Asn388Lys	108	0	0		105	30	0.285714	NM_000264	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	G	18.57	3.652082	0.67472	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000430669;ENST00000429896;ENST00000375274;ENST00000375271	D;D;D;D;D;D;D;D	0.90955	-2.7;-2.69;-2.68;-2.68;-2.69;-2.68;-2.7;-2.76	6.17	-9.99	0.00435	.	0.000000	0.85682	D	0.000000	D	0.92251	0.7542	M	0.68593	2.085	0.37604	D	0.920694	D;D;D;D	0.56746	0.976;0.971;0.976;0.977	P;P;P;P	0.61533	0.89;0.875;0.875;0.889	D	0.92850	0.6296	10	0.45353	T	0.12	-28.9913	22.0603	0.99966	0.7933:0.0:0.2067:0.0	.	237;322;387;388	Q13635-4;Q13635-3;Q13635-2;Q13635	.;.;.;PTC1_HUMAN	K	388;322;237;237;322;237;387;105	ENSP00000332353:N388K;ENSP00000389744:N322K;ENSP00000399981:N237K;ENSP00000396135:N237K;ENSP00000410287:N322K;ENSP00000414823:N237K;ENSP00000364423:N387K;ENSP00000364420:N105K	ENSP00000332353:N388K	N	-	3	2	PTCH1	97281154	0.001000	0.12720	0.416000	0.26546	0.846000	0.48090	-1.360000	0.02600	-2.160000	0.00786	-0.940000	0.02684	AAC	G|1.000;A|0.000	.	alt		0.537	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264		C	98241333	G	C	98241333	3	2	31	1	0	0	0	0	1	0	0	0	12742	1136	40	4	3243	4	PTCH1	9	98241333	Missense_Mutation	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10	71036418	98241333	42972098	46	13912											
STRBP	55342	hgsc.bcm.edu	37	chr9	125923280	125923280	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaccatttggcatgtcgaagAgacgccaaggcgttcaggca	12	7	12	10	3	1	1	1	0	0	1	2	3	1	1	2	3	1	3	2	3	3	2			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr9:125923280A>G	ENST00000348403.5	-	7	1032	c.603T>C	c.(601-603)tcT>tcC	p.S201S	STRBP_ENST00000447404.2_Silent_p.S201S|STRBP_ENST00000360998.3_Silent_p.S187S	NM_018387.4	NP_060857.2	Q96SI9	STRBP_HUMAN	spermatid perinuclear RNA binding protein	201	DZF. {ECO:0000255|PROSITE- ProRule:PRU01040}.				cellular component movement (GO:0006928)|mechanosensory behavior (GO:0007638)|multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(6)|prostate(1)|skin(2)	26						CATGTCGAAGAGACGCCAAGG	0.388																																					p.S201S		Atlas-SNP	.											.	STRBP	73	.	0			c.T603C						PASS	.						46	44	45					9																	125923280		2203	4300	6503	SO:0001819	synonymous_variant	55342	exon7			TCGAAGAGACGCC	AK002169	CCDS6851.1, CCDS55337.1	9q33.1-q33.3	2008-08-29	2001-11-28		ENSG00000165209	ENSG00000165209			16462	protein-coding gene	gene with protein product		611138	"spermatid perinuclear RNA-binding protein", "interleukin enhancer binding factor 3-like"	ILF3L			Standard	NM_018387		Approved	FLJ11307, SPNR	uc004bns.3	Q96SI9	OTTHUMG00000020636	ENST00000348403.5:c.603T>C	9.37:g.125923280A>G		298	0	0		318	95	0.298742	NM_018387	Q32NB9|Q9BUE1|Q9BXG4|Q9H0B4|Q9H7V1|Q9NUK4	Silent	SNP	ENST00000348403.5	37	CCDS6851.1																																																																																			.	.	none		0.388	STRBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053982.1			G	125923280	A	G	125923280	2	3	31	1	0	0	0	0	0	0	0	1	15342	291	11	3		3	STRBP	9	125923280	Silent	SNP	A	TCGA-GR-A4D4-01A-11D-A31X-10	27681947	125923280	15290151	47	13913											
FAM73B	84895	hgsc.bcm.edu	37	chr9	131821550	131821550	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acagcatgctgctagacctcGgtgagctgggcccagtgcag	8	7	14	12	1	0	2	0	1	0	1	1	2	0	2	2	2	5	5	2	2	1	1			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr9:131821550G>A	ENST00000358369.4	+	7	1019	c.793G>A	c.(793-795)Gag>Aag	p.E265K	FAM73B_ENST00000277475.5_Splice_Site_p.R305Q|FAM73B_ENST00000406926.2_Splice_Site_p.E265K	NM_032809.2	NP_116198.2	Q7L4E1	FA73B_HUMAN	family with sequence similarity 73, member B	265					bone development (GO:0060348)	integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(2)|lung(7)|skin(1)	13						GCTAGACCTCGGTGAGCTGGG	0.642																																					p.E265K		Atlas-SNP	.											.	FAM73B	37	.	0			c.G793A						PASS	.						26	22	23					9																	131821550		2198	4297	6495	SO:0001630	splice_region_variant	84895	exon7			GACCTCGGTGAGC	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.793+1G>A	9.37:g.131821550G>A		65	0	0		72	20	0.277778	NM_032809	Q8NBM3|Q8TEJ6|Q969E6	Missense_Mutation	SNP	ENST00000358369.4	37	CCDS6917.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.6|20.6	4.009961|4.009961	0.75046|0.75046	.|.	.|.	ENSG00000148343|ENSG00000148343	ENST00000358369;ENST00000406926|ENST00000277475	T;T|T	0.23147|0.16597	1.92;1.92|2.33	5.13|5.13	5.13|5.13	0.70059|0.70059	.|.	0.052634|.	0.85682|.	D|.	0.000000|.	T|T	0.34193|0.34193	0.0889|0.0889	M|M	0.71581|0.71581	2.175|2.175	0.35587|0.35587	D|D	0.806755|0.806755	D;D|.	0.89917|.	1.0;0.982|.	D;P|.	0.83275|.	0.996;0.85|.	T|T	0.32402|0.32402	-0.9908|-0.9908	10|7	0.62326|0.23302	D|T	0.03|0.38	-27.6397|-27.6397	17.5609|17.5609	0.87906|0.87906	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	329;265|.	B4DZP8;Q7L4E1|.	.;FA73B_HUMAN|.	K|Q	265|305	ENSP00000351138:E265K;ENSP00000384662:E265K|ENSP00000277475:R305Q	ENSP00000351138:E265K|ENSP00000277475:R305Q	E|R	+|+	1|2	0|0	FAM73B|FAM73B	130861371|130861371	1.000000|1.000000	0.71417|0.71417	0.962000|0.962000	0.40283|0.40283	0.122000|0.122000	0.20287|0.20287	9.238000|9.238000	0.95380|0.95380	2.376000|2.376000	0.81061|0.81061	0.491000|0.491000	0.48974|0.48974	GAG|CGA	.	.	none		0.642	FAM73B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054542.7	NM_032809	Missense_Mutation	A	131821550	G	A	131821550	5	1	31	1	0	0	0	0	0	0	1	0	5626	1130	39	1	815	1	FAM73B	9	131821550	Splice_Site	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10	5898270	131821550	9391881	48	13914											
FAS	355	hgsc.bcm.edu	37	chr10	90770574	90770574	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attccactaattgtttggggTaagttcttgctttgttcaaa	9	18	8	6	0	2	0	1	0	1	0	3	0	3	0	1	2	1	5	1	2	3	9			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr10:90770574T>A	ENST00000355279.2	+	6	568		c.e6+2		FAS_ENST00000355740.2_Splice_Site|FAS_ENST00000313771.5_Splice_Site|FAS_ENST00000357339.2_Intron|FAS_ENST00000352159.4_Splice_Site			P49327	FAS_HUMAN	Fas cell surface death receptor						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)	TTGTTTGGGGTAAGTTCTTGC	0.368																																					.		Atlas-SNP	.											.	FAS	47	.	0			c.568+2T>A						PASS	.						248	222	231					10																	90770574		2203	4300	6503	SO:0001630	splice_region_variant	355	exon6			TTGGGGTAAGTTC	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.568+2T>A	10.37:g.90770574T>A		153	0	0		92	35	0.380435	NM_152872	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Splice_Site	SNP	ENST00000355279.2	37	CCDS7395.1	.	.	.	.	.	.	.	.	.	.	T	11.07	1.530798	0.27387	.	.	ENSG00000026103	ENST00000540197;ENST00000355740;ENST00000352159;ENST00000355279;ENST00000371875	.	.	.	3.9	3.9	0.45041	.	.	.	.	.	.	.	.	.	.	.	0.54753	D	0.999987	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.4431	0.38681	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	FAS	90760554	0.996000	0.38824	0.241000	0.24154	0.039000	0.13416	1.607000	0.36836	2.012000	0.59069	0.528000	0.53228	.	.	.	none		0.368	FAS-011	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000049280.2		Intron	A	90770574	T	A	90770574	5	1	31	1	0	0	0	0	0	0	1	0	5689	1652	57	5	592	5	FAS	10	90770574	Splice_Site	SNP	T	TCGA-GR-A4D4-01A-11D-A31X-10		90770574	44764173	49	13915											
MUC2	4583	hgsc.bcm.edu	37	chr11	1093342	1093342	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	ccggcacacagaccccaaccCcgacacccatctccaccacc	11	2	4	24	2	1	1	0	0	1	1	2	2	1	1	9	1	1	1	9	1	1	0	rs55695633		TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr11:1093342C>A	ENST00000441003.2	+	30	5188	c.5161C>A	c.(5161-5163)Ccg>Acg	p.P1721T	MUC2_ENST00000359061.5_Missense_Mutation_p.P1688T|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_Missense_Mutation_p.P9T	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)	gaccccaaccccgacacccat	0.642																																					p.P1721T		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,-2,2	MUC2	614	2	0			c.C5161A						scavenged	.						234	273	260					11																	1093342		1973	3751	5724	SO:0001583	missense	4583	exon30			CCAACCCCGACAC	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.5161C>A	11.37:g.1093342C>A	ENSP00000415183:p.Pro1721Thr	68	2	0.0294118		74	9	0.121622	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	5.758	0.324335	0.10900	.	.	ENSG00000198788	ENST00000441003;ENST00000359061;ENST00000333592	T;T;T	0.04917	3.53;3.69;3.76	1.4	0.392	0.16288	.	2.679550	0.04278	N	0.343350	T	0.06325	0.0163	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42832	-0.9428	9	0.87932	D	0	.	6.4437	0.21865	0.291:0.709:0.0:0.0	.	1721	E7EUV1	.	T	1721;1688;9	ENSP00000415183:P1721T;ENSP00000351956:P1688T;ENSP00000331373:P9T	ENSP00000331373:P9T	P	+	1	0	MUC2	1083342	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-2.316000	0.01123	-0.071000	0.12886	-1.119000	0.02030	CCG	.	.	alt		0.642	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		A	1093342	C	A	1093342	3	1	31	1	0	0	0	0	1	0	0	0	9984	623	22	4	5279	4	MUC2	11	1093342	Missense_Mutation	SNP	C	TCGA-GR-A4D4-01A-11D-A31X-10		1093342	133913174	50	13916											
ART5	116969	hgsc.bcm.edu	37	chr11	3661044	3661044	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcctgtataggggccccaaaGcaagttgttagagagaagag	13	7	14	7	0	0	3	0	0	0	3	0	4	0	3	3	2	1	4	3	2	6	4			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr11:3661044G>A	ENST00000397068.3	-	2	1007	c.615C>T	c.(613-615)tgC>tgT	p.C205C	TRPC2_ENST00000526541.1_RNA|ART5_ENST00000359918.4_Silent_p.C205C|ART5_ENST00000397067.3_Intron	NM_053017.3	NP_443750.2	Q96L15	NAR5_HUMAN	ADP-ribosyltransferase 5	205					protein ADP-ribosylation (GO:0006471)	extracellular region (GO:0005576)|membrane (GO:0016020)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|NAD+ nucleosidase activity (GO:0003953)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(6)|ovary(1)	11		Medulloblastoma(188;0.0025)|Breast(177;0.00328)|all_neural(188;0.0227)		BRCA - Breast invasive adenocarcinoma(625;0.0336)|LUSC - Lung squamous cell carcinoma(625;0.19)		GGGCCCCAAAGCAAGTTGTTA	0.542																																					p.C205C		Atlas-SNP	.											.	ART5	38	.	0			c.C615T						PASS	.						74	87	82					11																	3661044		2201	4298	6499	SO:0001819	synonymous_variant	116969	exon2			CCCAAAGCAAGTT	Y16835	CCDS7743.1, CCDS73242.1	11p15.4	2008-02-05			ENSG00000167311	ENSG00000167311			24049	protein-coding gene	gene with protein product		610625				11587854, 10448534	Standard	NM_001079536		Approved		uc001lyb.1	Q96L15	OTTHUMG00000011842	ENST00000397068.3:c.615C>T	11.37:g.3661044G>A		144	0	0		94	28	0.297872	NM_053017	C9IYG7|Q6UX84|Q86W02	Silent	SNP	ENST00000397068.3	37	CCDS7743.1	.	.	.	.	.	.	.	.	.	.	G	8.700	0.909544	0.17833	.	.	ENSG00000167311	ENST00000453353	.	.	.	6.17	1.32	0.21799	.	.	.	.	.	T	0.58764	0.2145	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53380	-0.8447	4	.	.	.	-28.2147	10.4319	0.44413	0.3324:0.0:0.6676:0.0	.	.	.	.	F	162	.	.	L	-	1	0	ART5	3617620	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.992000	0.40737	0.351000	0.24027	0.655000	0.94253	CTT	.	.	none		0.542	ART5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032760.2	NM_053017		A	3661044	G	A	3661044	2	1	31	1	0	0	0	0	0	0	0	1	1000	963	34	2		2	ART5	11	3661044	Silent	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10	2567702	3661044	131345472	51	13917											
ACCS	84680	hgsc.bcm.edu	37	chr11	44092850	44092850	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gagaacaaactctgctttgaCctgctgtcctggcgggtaag	9	10	12	10	1	1	2	0	1	1	1	2	3	2	2	2	2	4	3	2	2	3	2			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr11:44092850C>T	ENST00000263776.8	+	3	767	c.333C>T	c.(331-333)gaC>gaT	p.D111D	CTD-2609K8.3_ENST00000531268.1_RNA|ACCS_ENST00000533208.1_3'UTR|ACCS_ENST00000432284.2_Silent_p.D111D	NM_001127219.1|NM_032592.3	NP_001120691.1|NP_115981.1	Q96QU6	1A1L1_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)	111					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						TCTGCTTTGACCTGCTGTCCT	0.577																																					p.D111D	Esophageal Squamous(158;148 1889 8077 23160 41213)	Atlas-SNP	.											.	ACCS	64	.	0			c.C333T						PASS	.						126	116	119					11																	44092850		2203	4300	6503	SO:0001819	synonymous_variant	84680	exon3			CTTTGACCTGCTG	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.333C>T	11.37:g.44092850C>T		112	0	0		87	18	0.206897	NM_032592	B4E219|Q8WUL4|Q96LX5	Silent	SNP	ENST00000263776.8	37	CCDS7907.1																																																																																			.	.	none		0.577	ACCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389721.1	NM_032592		T	44092850	C	T	44092850	2	4	31	1	0	0	0	0	0	0	0	1	133	506	18	2		2	ACCS	11	44092850	Silent	SNP	C	TCGA-GR-A4D4-01A-11D-A31X-10	40431806	44092850	90913666	52	13918											
DGKZ	8525	hgsc.bcm.edu	37	chr11	46397091	46397091	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggatggcgagccctgcaagcTtgcagcctcacgcatccgca	8	6	12	15	3	1	0	1	0	0	0	2	2	2	1	3	2	5	5	3	2	1	1			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr11:46397091T>G	ENST00000454345.1	+	21	2509	c.2384T>G	c.(2383-2385)cTt>cGt	p.L795R	DGKZ_ENST00000421244.2_Missense_Mutation_p.L607R|DGKZ_ENST00000343674.6_Missense_Mutation_p.L623R|DGKZ_ENST00000395574.3_Missense_Mutation_p.L573R|MIR4688_ENST00000577966.1_RNA|DGKZ_ENST00000528615.1_Missense_Mutation_p.L385R|DGKZ_ENST00000318201.8_Missense_Mutation_p.L584R|DGKZ_ENST00000543978.1_Intron|DGKZ_ENST00000532868.2_Missense_Mutation_p.L611R|DGKZ_ENST00000456247.2_Missense_Mutation_p.L606R|DGKZ_ENST00000527911.1_Missense_Mutation_p.L607R	NM_001105540.1	NP_001099010.1	Q13574	DGKZ_HUMAN	diacylglycerol kinase, zeta	795					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)		CCCTGCAAGCTTGCAGCCTCA	0.692																																					p.L795R		Atlas-SNP	.											.	DGKZ	199	.	0			c.T2384G						PASS	.						30	31	31					11																	46397091		2192	4294	6486	SO:0001583	missense	8525	exon21			GCAAGCTTGCAGC	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.2384T>G	11.37:g.46397091T>G	ENSP00000412178:p.Leu795Arg	59	0	0		76	21	0.276316	NM_001105540	B7Z2M9|B7Z6M3|E9PPW4|F6UCU9|G3V0F6|J3KNJ6|O00542|Q6ZVG7|Q8IVW9	Missense_Mutation	SNP	ENST00000454345.1	37	CCDS41640.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.2|25.2	4.618080|4.618080	0.87359|0.87359	.|.	.|.	ENSG00000149091|ENSG00000149091	ENST00000343674;ENST00000528615;ENST00000395574;ENST00000532868;ENST00000527911;ENST00000456247;ENST00000421244;ENST00000318201;ENST00000454345|ENST00000524869	T;T;T;T;T;T;T;T;T|T	0.27557|0.45276	2.24;2.45;2.44;2.5;3.42;2.25;2.32;2.44;1.66|0.9	4.19|4.19	4.19|4.19	0.49359|0.49359	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.55481|0.55481	0.1923|0.1923	M|M	0.72479|0.72479	2.2|2.2	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D;D;D|.	0.89917|.	1.0;0.999;1.0;1.0;1.0;1.0;1.0;1.0;1.0|.	D;D;D;D;D;D;D;D;D|.	0.85130|.	0.996;0.987;0.993;0.996;0.996;0.997;0.997;0.992;0.996|.	T|T	0.55774|0.55774	-0.8088|-0.8088	10|8	0.87932|0.36615	D|T	0|0.2	.|.	13.7246|13.7246	0.62750|0.62750	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	584;572;550;607;795;606;607;573;623|.	B7Z2M9;B7Z6M3;B7Z8F6;E9PPW4;Q13574;Q13574-2;G3V0F6;A8MVN1;Q6ZVG7|.	.;.;.;.;DGKZ_HUMAN;.;.;.;.|.	R|V	623;385;573;572;607;606;607;584;795|162	ENSP00000343065:L623R;ENSP00000434719:L385R;ENSP00000378941:L573R;ENSP00000436273:L572R;ENSP00000436291:L607R;ENSP00000395684:L606R;ENSP00000391021:L607R;ENSP00000320340:L584R;ENSP00000412178:L795R|ENSP00000434016:L162V	ENSP00000320340:L584R|ENSP00000434016:L162V	L|L	+|+	2|1	0|2	DGKZ|DGKZ	46353667|46353667	1.000000|1.000000	0.71417|0.71417	0.834000|0.834000	0.33040|0.33040	0.929000|0.929000	0.56500|0.56500	7.581000|7.581000	0.82535|0.82535	1.904000|1.904000	0.55121|0.55121	0.379000|0.379000	0.24179|0.24179	CTT|TTG	.	.	none		0.692	DGKZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389772.1	NM_001105540		G	46397091	T	G	46397091	3	3	31	1	0	0	0	0	1	0	0	0	4476	1609	56	5	2909	5	DGKZ	11	46397091	Missense_Mutation	SNP	T	TCGA-GR-A4D4-01A-11D-A31X-10	2304241	46397091	88609425	53	13919											
BBS1	582	hgsc.bcm.edu	37	chr11	66294208	66294208	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccccaccagcccaggccatGaaactcaatgtgccccgaaa	12	4	7	18	1	1	1	1	1	0	0	1	2	1	1	7	1	3	0	7	1	3	0			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr11:66294208G>T	ENST00000318312.7	+	13	1320	c.1269G>T	c.(1267-1269)atG>atT	p.M423I	BBS1_ENST00000393994.2_Missense_Mutation_p.M294I|CTD-3074O7.11_ENST00000419755.3_Missense_Mutation_p.M460I|BBS1_ENST00000529766.1_3'UTR|ZDHHC24_ENST00000526986.1_Intron|BBS1_ENST00000455748.2_Missense_Mutation_p.M326I	NM_024649.4	NP_078925.3	Q8NFJ9	BBS1_HUMAN	Bardet-Biedl syndrome 1	423					cilium assembly (GO:0042384)|Golgi to plasma membrane protein transport (GO:0043001)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	patched binding (GO:0005113)|RNA polymerase II repressing transcription factor binding (GO:0001103)|smoothened binding (GO:0005119)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	28						CCCAGGCCATGAAACTCAATG	0.587									Bardet-Biedl syndrome																												p.M423I	GBM(152;173 2612 9770 10137)	Atlas-SNP	.											.	BBS1	58	.	0			c.G1269T						PASS	.						159	151	153					11																	66294208		2200	4295	6495	SO:0001583	missense	582	exon13	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	GGCCATGAAACTC	AF503941	CCDS8142.1	11q13	2013-01-08			ENSG00000174483	ENSG00000174483			966	protein-coding gene	gene with protein product		209901				9039982, 12567324	Standard	NM_024649		Approved	FLJ23590	uc001oij.1	Q8NFJ9	OTTHUMG00000167110	ENST00000318312.7:c.1269G>T	11.37:g.66294208G>T	ENSP00000317469:p.Met423Ile	118	0	0		125	23	0.184	NM_024649	Q32MM9|Q32MN0|Q96SN4	Missense_Mutation	SNP	ENST00000318312.7	37	CCDS8142.1	.	.	.	.	.	.	.	.	.	.	G	0.378	-0.930525	0.02359	.	.	ENSG00000256349;ENSG00000174483;ENSG00000174483;ENSG00000174483	ENST00000419755;ENST00000318312;ENST00000455748;ENST00000393994	D;D;D;D	0.96300	-3.89;-3.97;-3.8;-3.7	4.69	-2.72	0.05968	.	.	.	.	.	T	0.78604	0.4309	N	0.00525	-1.395	0.09310	N	1	B;B;B;B;B;B	0.06786	0.0;0.001;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.06405	0.0;0.002;0.0;0.001;0.0;0.001	T	0.75838	-0.3176	9	0.07175	T	0.84	.	0.5633	0.00683	0.354:0.1232:0.2725:0.2503	.	98;326;294;311;423;460	B4DH75;E7EQH1;Q32MM9;Q4G0L2;Q8NFJ9;Q8NFJ9-2	.;.;.;.;BBS1_HUMAN;.	I	460;423;326;294	ENSP00000398526:M460I;ENSP00000317469:M423I;ENSP00000405764:M326I;ENSP00000377563:M294I	ENSP00000317469:M423I	M	+	3	0	BBS1;CTD-3074O7.11	66050784	0.001000	0.12720	0.002000	0.10522	0.787000	0.44495	-0.617000	0.05584	-0.634000	0.05538	-0.150000	0.13652	ATG	.	.	none		0.587	BBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393235.2			T	66294208	G	T	66294208	3	4	31	1	0	0	0	0	1	0	0	0	1335	1290	45	4	1319	4	BBS1	11	66294208	Missense_Mutation	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10	19897117	66294208	68712308	54	13920											
AMOTL1	154810	hgsc.bcm.edu	37	chr11	94602519	94602519	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcacacagactgacaagaGtgccgagctcttctggccca	11	6	10	14	1	2	3	0	1	2	2	2	4	2	3	2	1	3	2	2	1	1	1			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr11:94602519G>A	ENST00000433060.2	+	12	2786	c.2645G>A	c.(2644-2646)aGt>aAt	p.S882N	AMOTL1_ENST00000317829.8_Missense_Mutation_p.S832N|AMOTL1_ENST00000317837.9_Missense_Mutation_p.S469N	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	882					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)				ACTGACAAGAGTGCCGAGCTC	0.652																																					p.S882N		Atlas-SNP	.											.	AMOTL1	95	.	0			c.G2645A						PASS	.						36	46	43					11																	94602519		2173	4278	6451	SO:0001583	missense	154810	exon12			ACAAGAGTGCCGA	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.2645G>A	11.37:g.94602519G>A	ENSP00000387739:p.Ser882Asn	103	0	0		87	25	0.287356	NM_130847	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Missense_Mutation	SNP	ENST00000433060.2	37	CCDS44712.1	.	.	.	.	.	.	.	.	.	.	G	13.27	2.187928	0.38609	.	.	ENSG00000166025	ENST00000317829;ENST00000317837;ENST00000433060	T;T;T	0.19669	2.15;2.34;2.13	5.48	4.56	0.56223	.	0.181464	0.49916	D	0.000126	T	0.20618	0.0496	L	0.54323	1.7	0.21020	N	0.999801	B;B	0.11235	0.004;0.001	B;B	0.13407	0.009;0.004	T	0.16012	-1.0417	10	0.20046	T	0.44	-6.9791	12.7542	0.57325	0.0:0.1248:0.7455:0.1297	.	832;882	Q8IY63-2;Q8IY63	.;AMOL1_HUMAN	N	832;469;882	ENSP00000320968:S832N;ENSP00000323474:S469N;ENSP00000387739:S882N	ENSP00000320968:S832N	S	+	2	0	AMOTL1	94242167	1.000000	0.71417	0.483000	0.27378	0.247000	0.25773	6.087000	0.71362	1.299000	0.44798	0.561000	0.74099	AGT	.	.	none		0.652	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847		A	94602519	G	A	94602519	3	1	31	1	0	0	0	0	1	0	0	0	583	1029	36	2	2691	2	AMOTL1	11	94602519	Missense_Mutation	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10	28308311	94602519	40403997	55	13921											
DYNC2H1	79659	hgsc.bcm.edu	37	chr11	103070165	103070165	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gttttctccaaagatttccaGaggatatgaactgaagcagt	13	12	9	7	0	1	4	0	2	1	2	3	5	2	5	2	1	2	2	2	1	4	4			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr11:103070165G>C	ENST00000375735.2	+	49	8192	c.8048G>C	c.(8047-8049)aGa>aCa	p.R2683T	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.R2683T|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	2683	AAA 4. {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)		AAGATTTCCAGAGGATATGAA	0.403																																					p.R2683T		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.G8048C						PASS	.						85	78	80					11																	103070165		1882	4126	6008	SO:0001583	missense	79659	exon49			TTTCCAGAGGATA	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.8048G>C	11.37:g.103070165G>C	ENSP00000364887:p.Arg2683Thr	121	0	0		88	30	0.340909	NM_001377	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.848139	0.91277	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.44083	0.93;0.93	6.17	6.17	0.99709	Dynein heavy chain, P-loop containing D4 domain (1);	0.000000	0.64402	U	0.000005	T	0.69242	0.3089	M	0.92649	3.33	0.80722	D	1	D;P	0.56287	0.975;0.86	P;P	0.53722	0.733;0.535	T	0.75966	-0.3131	10	0.87932	D	0	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	2683;2683	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	T	2683	ENSP00000364887:R2683T;ENSP00000381167:R2683T	ENSP00000364887:R2683T	R	+	2	0	DYNC2H1	102575375	1.000000	0.71417	0.996000	0.52242	0.994000	0.84299	9.766000	0.98957	2.941000	0.99782	0.655000	0.94253	AGA	.	.	none		0.403	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652		C	103070165	G	C	103070165	3	2	31	1	0	0	0	0	1	0	0	0	4848	942	33	4	8242	4	DYNC2H1	11	103070165	Missense_Mutation	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10	8467646	103070165	31936351	56	13922											
ATM	472	hgsc.bcm.edu	37	chr11	108202718	108202718	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	accagaggtagccagaagaaGcagaataactaaaaatgtgc	19	5	10	7	0	0	4	0	0	0	4	0	4	0	4	2	1	4	2	2	1	8	3			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr11:108202718G>C	ENST00000452508.2	+	53	7931	c.7742G>C	c.(7741-7743)aGc>aCc	p.S2581T	C11orf65_ENST00000525729.1_Intron|ATM_ENST00000278616.4_Missense_Mutation_p.S2581T			Q13315	ATM_HUMAN	ATM serine/threonine kinase	2581					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)	GCCAGAAGAAGCAGAATAACT	0.368			"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.S2581T		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"L, O"	.	ATM	1657	.	0			c.G7742C						PASS	.						88	87	87					11																	108202718		2201	4298	6499	SO:0001583	missense	472	exon52	Familial Cancer Database	AT, Louis-Bar syndrome	GAAGAAGCAGAAT	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.7742G>C	11.37:g.108202718G>C	ENSP00000388058:p.Ser2581Thr	125	0	0		116	30	0.258621	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	.	.	.	.	.	.	.	.	.	.	G	4.758	0.141006	0.09083	.	.	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.79141	-1.24;-1.24	5.18	3.26	0.37387	Armadillo-type fold (1);	0.434069	0.29040	N	0.013336	T	0.70979	0.3286	M	0.72894	2.215	0.80722	D	1	B	0.17667	0.023	B	0.15484	0.013	T	0.59941	-0.7359	10	0.15952	T	0.53	.	7.6319	0.28245	0.1605:0.1368:0.7027:0.0	.	2581	Q13315	ATM_HUMAN	T	2581	ENSP00000278616:S2581T;ENSP00000388058:S2581T	ENSP00000278616:S2581T	S	+	2	0	ATM	107707928	0.281000	0.24258	0.637000	0.29366	0.172000	0.22775	0.471000	0.22100	0.537000	0.28751	-0.282000	0.10007	AGC	.	.	none		0.368	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051		C	108202718	G	C	108202718	3	2	31	1	0	0	0	0	1	0	0	0	1109	971	34	4	7944	4	ATM	11	108202718	Missense_Mutation	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10	5132553	108202718	26803798	57	13923											
RNF214	257160	hgsc.bcm.edu	37	chr11	117109653	117109653	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagcagcttgcctccaggaaTtgctctgaagagaaatcccc	12	8	9	12	0	1	2	0	1	1	1	3	4	3	3	4	1	4	3	4	1	4	2			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr11:117109653T>C	ENST00000531452.1	+	3	490	c.444T>C	c.(442-444)aaT>aaC	p.N148N	RNF214_ENST00000300650.4_Silent_p.N148N|RNF214_ENST00000530849.1_Intron|RNF214_ENST00000531287.1_Intron	NM_001077239.1|NM_001278249.1	NP_001070707.1|NP_001265178.1	Q8ND24	RN214_HUMAN	ring finger protein 214	148							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)		CCTCCAGGAATTGCTCTGAAG	0.537																																					p.N148N		Atlas-SNP	.											.	RNF214	54	.	0			c.T444C						PASS	.						55	58	57					11																	117109653		1953	4151	6104	SO:0001819	synonymous_variant	257160	exon3			CAGGAATTGCTCT	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.444T>C	11.37:g.117109653T>C		78	0	0		67	14	0.208955	NM_207343	B2RUW0|B4DTD1	Silent	SNP	ENST00000531452.1	37	CCDS41720.1																																																																																			.	.	none		0.537	RNF214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392884.1	NM_001077239		C	117109653	T	C	117109653	2	2	31	1	0	0	0	0	0	0	0	1	13493	1490	52	3		3	RNF214	11	117109653	Silent	SNP	T	TCGA-GR-A4D4-01A-11D-A31X-10	8906935	117109653	17896863	58	13924											
ABCC9	10060	hgsc.bcm.edu	37	chr12	21998615	21998615	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tagtctatagctacaatgacCgaatgcttcaaaagcttaga	15	11	7	8	1	2	2	1	1	1	1	2	3	2	2	1	0	4	3	1	0	9	6			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr12:21998615C>T	ENST00000261201.4	-	24	3017	c.3018G>A	c.(3016-3018)tcG>tcA	p.S1006S	RP11-729I10.2_ENST00000539874.1_RNA|ABCC9_ENST00000261200.4_Silent_p.S1006S|ABCC9_ENST00000345162.2_Silent_p.S970S	NM_005691.2	NP_005682.2	O60706	ABCC9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 9	1006	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				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)	CTACAATGACCGAATGCTTCA	0.433																																					p.S1006S		Atlas-SNP	.											ABCC9,colon,carcinoma,-1,1	ABCC9	411	1	0			c.G3018A						PASS	.						118	103	108					12																	21998615		2203	4300	6503	SO:0001819	synonymous_variant	10060	exon24			AATGACCGAATGC	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.3018G>A	12.37:g.21998615C>T		81	0	0		47	17	0.361702	NM_005691	O60707	Silent	SNP	ENST00000261201.4	37	CCDS8694.1																																																																																			.	.	none		0.433	ABCC9-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402230.1	NM_005691		T	21998615	C	T	21998615	2	4	31	1	0	0	0	0	0	0	0	1	59	639	23	1		1	ABCC9	12	21998615	Silent	SNP	C	TCGA-GR-A4D4-01A-11D-A31X-10		21998615	111853280	59	13925											
CS	1431	hgsc.bcm.edu	37	chr12	56676685	56676685	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccagttaccagcagccaaaAtaagccctcaggcaggggtt	12	7	10	12	0	1	0	1	0	0	0	2	0	2	0	4	3	4	4	4	3	4	3			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr12:56676685A>C	ENST00000351328.3	-	5	548	c.358T>G	c.(358-360)Ttt>Gtt	p.F120V	CS_ENST00000542324.2_Missense_Mutation_p.F107V|CS_ENST00000548567.1_Missense_Mutation_p.F54V	NM_004077.2	NP_004068.2	O75390	CISY_HUMAN	citrate synthase	120					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)		AGCAGCCAAAATAAGCCCTCA	0.483																																					p.F120V		Atlas-SNP	.											.	CS	44	.	0			c.T358G						PASS	.						109	111	110					12																	56676685		2203	4300	6503	SO:0001583	missense	1431	exon5			GCCAAAATAAGCC		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.358T>G	12.37:g.56676685A>C	ENSP00000342056:p.Phe120Val	71	0	0		83	23	0.277108	NM_004077	Q71UT9|Q7KZH0|Q96FZ8|Q9BWN8	Missense_Mutation	SNP	ENST00000351328.3	37	CCDS8913.1	.	.	.	.	.	.	.	.	.	.	A	28.4	4.920811	0.92249	.	.	ENSG00000062485	ENST00000548567;ENST00000351328;ENST00000542324;ENST00000549221;ENST00000548041;ENST00000551936;ENST00000550734;ENST00000551253;ENST00000552688;ENST00000546554;ENST00000551473;ENST00000547298;ENST00000551137;ENST00000550655;ENST00000551968;ENST00000550159;ENST00000551430	.	.	.	4.61	4.61	0.57282	Citrate synthase-like, large alpha subdomain (1);Citrate synthase-like, core (1);	0.000000	0.85682	D	0.000000	D	0.85053	0.5609	H	0.95187	3.635	0.80722	D	1	P;P;P;P	0.51057	0.892;0.941;0.941;0.941	P;P;P;P	0.60682	0.783;0.809;0.752;0.878	D	0.89441	0.3723	9	0.87932	D	0	-12.2063	13.7141	0.62687	1.0:0.0:0.0:0.0	.	54;107;75;120	B7Z1E1;B4DJV2;B3KTN4;O75390	.;.;.;CISY_HUMAN	V	54;120;107;45;120;54;54;54;84;70;54;54;54;120;92;54;54	.	ENSP00000342056:F120V	F	-	1	0	CS	54962952	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.542000	0.90647	2.023000	0.59567	0.528000	0.53228	TTT	.	.	none		0.483	CS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408588.2	NM_004077		C	56676685	A	C	56676685	3	2	31	1	0	0	0	0	1	0	0	0	3926	101	4	5	1070	5	CS	12	56676685	Missense_Mutation	SNP	A	TCGA-GR-A4D4-01A-11D-A31X-10	34678070	56676685	77175210	60	13926											
CS	1431	hgsc.bcm.edu	37	chr12	56676766	56676766	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agggatactaaagcctcggaAacggatgcccttgagagagg	13	6	14	8	2	0	2	0	1	0	1	1	6	0	5	2	4	4	0	2	4	4	3			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr12:56676766A>C	ENST00000351328.3	-	5	467	c.277T>G	c.(277-279)Ttc>Gtc	p.F93V	CS_ENST00000542324.2_Missense_Mutation_p.F80V|CS_ENST00000548567.1_Missense_Mutation_p.F27V	NM_004077.2	NP_004068.2	O75390	CISY_HUMAN	citrate synthase	93					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)		AAGCCTCGGAAACGGATGCCC	0.483																																					p.F93V		Atlas-SNP	.											.	CS	44	.	0			c.T277G						PASS	.						75	79	78					12																	56676766		2203	4300	6503	SO:0001583	missense	1431	exon5			CTCGGAAACGGAT		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.277T>G	12.37:g.56676766A>C	ENSP00000342056:p.Phe93Val	45	0	0		55	16	0.290909	NM_004077	Q71UT9|Q7KZH0|Q96FZ8|Q9BWN8	Missense_Mutation	SNP	ENST00000351328.3	37	CCDS8913.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.719196	0.89205	.	.	ENSG00000062485	ENST00000548567;ENST00000351328;ENST00000542324;ENST00000549221;ENST00000548041;ENST00000551936;ENST00000550734;ENST00000551253;ENST00000552688;ENST00000551473;ENST00000547298;ENST00000551137;ENST00000550655;ENST00000550159;ENST00000551430	.	.	.	4.55	4.55	0.56014	Citrate synthase-like, large alpha subdomain (1);Citrate synthase-like, core (1);	0.000000	0.85682	D	0.000000	D	0.87418	0.6172	H	0.97758	4.07	0.80722	D	1	D;D;D;D	0.76494	0.998;0.999;0.997;0.999	D;D;D;D	0.79108	0.987;0.992;0.986;0.992	D	0.91554	0.5259	9	0.87932	D	0	-14.8489	13.594	0.61978	1.0:0.0:0.0:0.0	.	27;80;48;93	B7Z1E1;B4DJV2;B3KTN4;O75390	.;.;.;CISY_HUMAN	V	27;93;80;18;93;27;27;27;57;27;27;27;93;27;27	.	ENSP00000342056:F93V	F	-	1	0	CS	54963033	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.639000	0.91023	1.995000	0.58328	0.528000	0.53228	TTC	.	.	none		0.483	CS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408588.2	NM_004077		C	56676766	A	C	56676766	3	2	31	1	0	0	0	0	1	0	0	0	3926	14	1	5	1151	5	CS	12	56676766	Missense_Mutation	SNP	A	TCGA-GR-A4D4-01A-11D-A31X-10	81	56676766	77175129	61	13927											
STAB2	55576	hgsc.bcm.edu	37	chr12	104071379	104071379	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cgcatcctgtttgtatgtggGtcccgggcaggtaggttgga	5	12	16	8	2	0	0	0	0	0	0	2	1	2	1	2	5	0	6	2	5	2	4			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr12:104071379G>A	ENST00000388887.2	+	25	2999	c.2795G>A	c.(2794-2796)gGt>gAt	p.G932D		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						TTGTATGTGGGTCCCGGGCAG	0.547																																					p.G932D		Atlas-SNP	.											.	STAB2	370	.	0			c.G2795A						PASS	.						83	81	82					12																	104071379		2203	4300	6503	SO:0001583	missense	55576	exon25			ATGTGGGTCCCGG	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.2795G>A	12.37:g.104071379G>A	ENSP00000373539:p.Gly932Asp	56	0	0		60	9	0.15	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	37	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	G	18.51	3.638706	0.67130	.	.	ENSG00000136011	ENST00000388887	T	0.64438	-0.1	5.55	5.55	0.83447	Growth factor, receptor (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	T	0.79890	0.4524	M	0.78916	2.43	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	T	0.78365	-0.2232	10	0.37606	T	0.19	.	18.2638	0.90044	0.0:0.0:1.0:0.0	.	932	Q8WWQ8	STAB2_HUMAN	D	932	ENSP00000373539:G932D	ENSP00000373539:G932D	G	+	2	0	STAB2	102595509	1.000000	0.71417	0.996000	0.52242	0.194000	0.23727	8.757000	0.91657	2.623000	0.88846	0.563000	0.77884	GGT	.	.	none		0.547	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			A	104071379	G	A	104071379	3	1	31	1	0	0	0	0	1	0	0	0	15253	1261	44	2	2893	2	STAB2	12	104071379	Missense_Mutation	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10	47394613	104071379	29780516	62	13928											
MED13L	23389	hgsc.bcm.edu	37	chr12	116408551	116408551	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcagtgcagtacttcggccaAaaacagagcccattgtgaca	13	8	9	11	1	1	2	1	1	0	1	2	2	1	2	2	1	4	2	2	1	3	3			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr12:116408551A>C	ENST00000281928.3	-	27	6121	c.5915T>G	c.(5914-5916)tTt>tGt	p.F1972C		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	1972						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)		ACTTCGGCCAAAAACAGAGCC	0.423																																					p.F1972C		Atlas-SNP	.											.	MED13L	193	.	0			c.T5915G						PASS	.						108	91	97					12																	116408551		2203	4300	6503	SO:0001583	missense	23389	exon27			CGGCCAAAAACAG	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.5915T>G	12.37:g.116408551A>C	ENSP00000281928:p.Phe1972Cys	94	0	0		94	14	0.148936	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Missense_Mutation	SNP	ENST00000281928.3	37	CCDS9177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	25.1|25.1	4.606136|4.606136	0.87157|0.87157	.|.	.|.	ENSG00000123066|ENSG00000123066	ENST00000281928|ENST00000552447	D|.	0.84370|.	-1.84|.	5.55|5.55	5.55|5.55	0.83447|0.83447	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.79112|0.79112	0.4391|0.4391	M|M	0.84846|0.84846	2.72|2.72	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|T	0.81389|0.81389	-0.0955|-0.0955	10|6	0.72032|.	D|.	0.01|.	.|.	15.8583|15.8583	0.79000|0.79000	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	1972|.	Q71F56|.	MD13L_HUMAN|.	C|L	1972|176	ENSP00000281928:F1972C|.	ENSP00000281928:F1972C|.	F|F	-|-	2|3	0|2	MED13L|MED13L	114892934|114892934	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	8.761000|8.761000	0.91691|0.91691	2.326000|2.326000	0.78906|0.78906	0.533000|0.533000	0.62120|0.62120	TTT|TTT	.	.	none		0.423	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3			C	116408551	A	C	116408551	3	2	31	1	0	0	0	0	1	0	0	0	9440	14	1	5	737	5	MED13L	12	116408551	Missense_Mutation	SNP	A	TCGA-GR-A4D4-01A-11D-A31X-10	12337172	116408551	17443344	63	13929											
CENPJ	55835	hgsc.bcm.edu	37	chr13	25479846	25479846	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggatctcgagggctcagacActttatgttttatgctttcc	8	15	9	9	1	2	1	1	0	1	1	4	3	3	2	1	2	1	3	1	2	2	5			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr13:25479846A>G	ENST00000381884.4	-	7	2515	c.2330T>C	c.(2329-2331)gTg>gCg	p.V777A	CENPJ_ENST00000545981.1_Missense_Mutation_p.V777A	NM_018451.4	NP_060921.3	Q9HC77	CENPJ_HUMAN	centromere protein J	777					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)		GGGCTCAGACACTTTATGTTT	0.393																																					p.V777A		Atlas-SNP	.											.	CENPJ	116	.	0			c.T2330C						PASS	.						175	167	170					13																	25479846		2203	4300	6503	SO:0001583	missense	55835	exon7			TCAGACACTTTAT	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.2330T>C	13.37:g.25479846A>G	ENSP00000371308:p.Val777Ala	94	0	0		50	23	0.46	NM_018451	Q2KHM6|Q5JPD5|Q5T6R5|Q96KS5|Q9C067	Missense_Mutation	SNP	ENST00000381884.4	37	CCDS9310.1	.	.	.	.	.	.	.	.	.	.	A	0.113	-1.135609	0.01742	.	.	ENSG00000151849	ENST00000381884;ENST00000545981;ENST00000445729	T;T	0.35236	1.32;1.91	5.53	-11.1	0.00147	.	0.821166	0.10737	N	0.639900	T	0.12944	0.0314	L	0.35288	1.05	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33701	-0.9858	10	0.07482	T	0.82	.	0.2461	0.00199	0.2284:0.2381:0.2221:0.3114	.	777	Q9HC77	CENPJ_HUMAN	A	777	ENSP00000371308:V777A;ENSP00000441090:V777A	ENSP00000371308:V777A	V	-	2	0	CENPJ	24377846	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.506000	0.06359	-2.029000	0.00930	-2.802000	0.00113	GTG	.	.	none		0.393	CENPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044209.1	NM_018451		G	25479846	A	G	25479846	3	3	31	1	0	0	0	0	1	0	0	0	3236	159	6	3	1730	3	CENPJ	13	25479846	Missense_Mutation	SNP	A	TCGA-GR-A4D4-01A-11D-A31X-10		25479846	89690032	64	13930											
CARS2	79587	hgsc.bcm.edu	37	chr13	111340323	111340323	+	Missense_Mutation	SNP	C	C	A																															tgccatgtcctgcttgaagtCttcctcataaagactggcga																										TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr13:111340323C>A	ENST00000257347.4	-	4	499	c.436G>T	c.(436-438)Gac>Tac	p.D146Y	CARS2_ENST00000535398.1_5'UTR	NM_024537.2	NP_078813.1	Q9HA77	SYCM_HUMAN	cysteinyl-tRNA synthetase 2, mitochondrial (putative)	146					cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|prostate(4)|skin(1)	13	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;0.163)		L-Cysteine(DB00151)	TGCTTGAAGTCTTCCTCATAA	0.532																																					p.D146Y		Atlas-SNP	.											.	CARS2	37	.	0			c.G436T						PASS	.						79	69	72					13																	111340323		2203	4300	6503	SO:0001583	missense	79587	exon4			TGAAGTCTTCCTC	BC007220	CCDS9514.1	13q34	2011-07-01	2007-02-22		ENSG00000134905	ENSG00000134905	6.1.1.16	"Aminoacyl tRNA synthetases / Class I"	25695	protein-coding gene	gene with protein product	"cysteine tRNA ligase 2, mitochondrial (putative)"	612800				15779907	Standard	NM_024537		Approved	FLJ12118	uc001vrd.2	Q9HA77	OTTHUMG00000017347	ENST00000257347.4:c.436G>T	13.37:g.111340323C>A	ENSP00000257347:p.Asp146Tyr	90	0	0		55	16	0.290909	NM_024537	Q8NI84|Q96IV4	Missense_Mutation	SNP	ENST00000257347.4	37	CCDS9514.1	.	.	.	.	.	.	.	.	.	.	C	12.70	2.015505	0.35511	.	.	ENSG00000134905	ENST00000257347;ENST00000542709	T	0.31247	1.5	4.71	3.86	0.44501	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.322809	0.31834	N	0.006995	T	0.44808	0.1311	L	0.51914	1.62	0.39637	D	0.970261	D	0.55385	0.971	P	0.62491	0.903	T	0.41342	-0.9514	10	0.49607	T	0.09	-3.3731	12.2493	0.54589	0.0:0.9143:0.0:0.0857	.	146	Q9HA77	SYCM_HUMAN	Y	146;137	ENSP00000257347:D146Y	ENSP00000257347:D146Y	D	-	1	0	CARS2	110138324	1.000000	0.71417	0.749000	0.31150	0.586000	0.36452	4.335000	0.59298	1.086000	0.41228	0.557000	0.71058	GAC	.	.	none		0.532	CARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045772.3	NM_024537		A	111340323	C	A	111340323	3	1	31	1	0	0	0	0	1	0	0	0	2660	913	32	4	1306	4	CARS2	13	111340323	Missense_Mutation	SNP	C	TCGA-GR-A4D4-01A-11D-A31X-10	85860477	111340323	3829555	65	13931	173	2									
CARS2	79587	hgsc.bcm.edu	37	chr13	111340329	111340329	+	Missense_Mutation	SNP	C	C	T																															gtcctgcttgaagtcttcctCataaagactggcgagggaag																										TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr13:111340329C>T	ENST00000257347.4	-	4	493	c.430G>A	c.(430-432)Gag>Aag	p.E144K	CARS2_ENST00000535398.1_5'UTR	NM_024537.2	NP_078813.1	Q9HA77	SYCM_HUMAN	cysteinyl-tRNA synthetase 2, mitochondrial (putative)	144					cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|prostate(4)|skin(1)	13	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;0.163)		L-Cysteine(DB00151)	AAGTCTTCCTCATAAAGACTG	0.532																																					p.E144K		Atlas-SNP	.											.	CARS2	37	.	0			c.G430A						PASS	.						75	66	69					13																	111340329		2203	4300	6503	SO:0001583	missense	79587	exon4			CTTCCTCATAAAG	BC007220	CCDS9514.1	13q34	2011-07-01	2007-02-22		ENSG00000134905	ENSG00000134905	6.1.1.16	"Aminoacyl tRNA synthetases / Class I"	25695	protein-coding gene	gene with protein product	"cysteine tRNA ligase 2, mitochondrial (putative)"	612800				15779907	Standard	NM_024537		Approved	FLJ12118	uc001vrd.2	Q9HA77	OTTHUMG00000017347	ENST00000257347.4:c.430G>A	13.37:g.111340329C>T	ENSP00000257347:p.Glu144Lys	81	0	0		52	16	0.307692	NM_024537	Q8NI84|Q96IV4	Missense_Mutation	SNP	ENST00000257347.4	37	CCDS9514.1	.	.	.	.	.	.	.	.	.	.	C	15.43	2.831407	0.50845	.	.	ENSG00000134905	ENST00000257347;ENST00000542709	T	0.35973	1.28	4.71	3.85	0.44370	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	T	0.64962	0.2646	M	0.89478	3.035	0.58432	D	0.999996	D	0.89917	1.0	D	0.91635	0.999	T	0.72301	-0.4334	10	0.62326	D	0.03	-30.7203	14.0156	0.64523	0.0:0.8467:0.1533:0.0	.	144	Q9HA77	SYCM_HUMAN	K	144;135	ENSP00000257347:E144K	ENSP00000257347:E144K	E	-	1	0	CARS2	110138330	1.000000	0.71417	0.472000	0.27241	0.023000	0.10783	5.937000	0.70162	1.073000	0.40885	-0.310000	0.09108	GAG	.	.	none		0.532	CARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045772.3	NM_024537		T	111340329	C	T	111340329	3	4	31	1	0	0	0	0	1	0	0	0	2660	835	29	2	1312	2	CARS2	13	111340329	Missense_Mutation	SNP	C	TCGA-GR-A4D4-01A-11D-A31X-10	6	111340329	3829549	66	13932	173	2									
CARS2	79587	hgsc.bcm.edu	37	chr13	111340366	111340366	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagcgggggaaatattcatCtgcagaaggattagatgtgc	13	9	14	5	1	2	2	1	0	1	2	2	5	2	4	0	3	3	1	0	3	5	3			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr13:111340366C>A	ENST00000257347.4	-	4	457		c.e4-1		CARS2_ENST00000535398.1_Splice_Site	NM_024537.2	NP_078813.1	Q9HA77	SYCM_HUMAN	cysteinyl-tRNA synthetase 2, mitochondrial (putative)						cysteinyl-tRNA aminoacylation (GO:0006423)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|cysteine-tRNA ligase activity (GO:0004817)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(2)|prostate(4)|skin(1)	13	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;0.163)		L-Cysteine(DB00151)	AAATATTCATCTGCAGAAGGA	0.517																																					.		Atlas-SNP	.											.	CARS2	37	.	0			c.394-1G>T						PASS	.						54	50	52					13																	111340366		2203	4300	6503	SO:0001630	splice_region_variant	79587	exon5			ATTCATCTGCAGA	BC007220	CCDS9514.1	13q34	2011-07-01	2007-02-22		ENSG00000134905	ENSG00000134905	6.1.1.16	"Aminoacyl tRNA synthetases / Class I"	25695	protein-coding gene	gene with protein product	"cysteine tRNA ligase 2, mitochondrial (putative)"	612800				15779907	Standard	NM_024537		Approved	FLJ12118	uc001vrd.2	Q9HA77	OTTHUMG00000017347	ENST00000257347.4:c.394-1G>T	13.37:g.111340366C>A		57	0	0		42	13	0.309524	NM_024537	Q8NI84|Q96IV4	Splice_Site	SNP	ENST00000257347.4	37	CCDS9514.1	.	.	.	.	.	.	.	.	.	.	C	11.58	1.679757	0.29783	.	.	ENSG00000134905	ENST00000257347;ENST00000542709	.	.	.	4.93	4.93	0.64822	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.2901	0.87153	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CARS2	110138367	1.000000	0.71417	0.997000	0.53966	0.112000	0.19704	5.947000	0.70242	2.433000	0.82419	0.557000	0.71058	.	.	.	none		0.517	CARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045772.3	NM_024537	Intron	A	111340366	C	A	111340366	5	1	31	1	0	0	0	0	0	0	1	0	2660	927	32	4	1349	4	CARS2	13	111340366	Splice_Site	SNP	C	TCGA-GR-A4D4-01A-11D-A31X-10	37	111340366	3829512	67	13933											
ANKRD10	55608	hgsc.bcm.edu	37	chr13	111532094	111532094	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gttcagttctgggatgctttCagcagtgtccccaaacccgt	7	12	10	12	1	3	0	2	0	1	0	4	1	4	1	3	1	3	4	3	1	1	3			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr13:111532094C>G	ENST00000267339.2	-	6	1287	c.1153G>C	c.(1153-1155)Gaa>Caa	p.E385Q	ANKRD10_ENST00000375758.5_3'UTR	NM_017664.2	NP_060134.2	Q9NXR5	ANR10_HUMAN	ankyrin repeat domain 10	385								p.E385K(1)		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)			GGGATGCTTTCAGCAGTGTCC	0.567																																					p.E385Q		Atlas-SNP	.											ANKRD10,NS,carcinoma,0,1	ANKRD10	24	1	1	Substitution - Missense(1)	lung(1)	c.G1153C						PASS	.						152	107	122					13																	111532094		2203	4300	6503	SO:0001583	missense	55608	exon6			TGCTTTCAGCAGT	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.1153G>C	13.37:g.111532094C>G	ENSP00000267339:p.Glu385Gln	58	0	0		35	19	0.542857	NM_017664	Q5VW12|Q9BV12	Missense_Mutation	SNP	ENST00000267339.2	37	CCDS9520.1	.	.	.	.	.	.	.	.	.	.	C	17.55	3.417175	0.62511	.	.	ENSG00000088448	ENST00000267339	T	0.77750	-1.12	5.52	5.52	0.82312	.	0.053640	0.64402	D	0.000001	D	0.88388	0.6423	M	0.75264	2.295	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.89186	0.3547	10	0.87932	D	0	-17.5215	19.4338	0.94783	0.0:1.0:0.0:0.0	.	385	Q9NXR5	ANR10_HUMAN	Q	385	ENSP00000267339:E385Q	ENSP00000267339:E385Q	E	-	1	0	ANKRD10	110330095	1.000000	0.71417	0.259000	0.24435	0.152000	0.21847	5.793000	0.69060	2.598000	0.87819	0.650000	0.86243	GAA	.	.	none		0.567	ANKRD10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045783.1			G	111532094	C	G	111532094	3	3	31	1	0	0	0	0	1	0	0	0	638	835	29	4	113	4	ANKRD10	13	111532094	Missense_Mutation	SNP	C	TCGA-GR-A4D4-01A-11D-A31X-10	191728	111532094	3637784	68	13934											
CHD8	57680	hgsc.bcm.edu	37	chr14	21884030	21884031	+	Frame_Shift_Ins	INS	-	-	T																															atatccaggtcctctgtataINStttttttcgcttaacttggc																										TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr14:21884030_21884031insT	ENST00000557364.1	-	6	2015_2016	c.1752_1753insA	c.(1750-1755)aaatatfs	p.Y585fs	CHD8_ENST00000399982.2_Frame_Shift_Ins_p.Y585fs|CHD8_ENST00000555962.1_Intron|CHD8_ENST00000430710.3_Frame_Shift_Ins_p.Y306fs			Q9HCK8	CHD8_HUMAN	chromodomain helicase DNA binding protein 8	585					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)		TCCTCTGTATATTTTTTTCGCT	0.396																																					p.Y585fs		Pindel,Atlas-Indel	.											.	CHD8	339	.	0			c.1753_1754insA						PASS	.																																			SO:0001589	frameshift_variant	57680	exon5			.	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.1753dupA	14.37:g.21884037_21884037dupT	ENSP00000451601:p.Tyr585fs	0	0	.		22	22	1	NM_001170629	Q4G0D8|Q68DQ0|Q6DKH9|Q6P440|Q6ZNL7|Q8N3Z9|Q8NCY4|Q8TBR9|Q96F26	Frame_Shift_Ins	INS	ENST00000557364.1	37	CCDS53885.1																																																																																			.	.	none		0.396	CHD8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410436.1	NM_020920		T	21884031	-	T	21884030	7	5	31	1	0	1	1	0	0	0	0	0	3333	449	16	0	6124	0	CHD8	14	21884030	Frame_Shift_Ins	INS	-	TCGA-GR-A4D4-01A-11D-A31X-10		21884030	85465510	69	13935											
FBXO34	55030	hgsc.bcm.edu	37	chr14	55817618	55817618	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtggaaaggatgagggaggtTaacagcaggtgctaccaacc	13	6	15	7	0	0	1	0	1	0	0	0	4	0	4	2	5	5	3	2	5	4	2			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr14:55817618T>G	ENST00000313833.4	+	2	755	c.510T>G	c.(508-510)gtT>gtG	p.V170V	FBXO34_ENST00000440021.1_Silent_p.V170V	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	170										breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						TGAGGGAGGTTAACAGCAGGT	0.473																																					p.V170V		Atlas-SNP	.											.	FBXO34	61	.	0			c.T510G						PASS	.						88	75	79					14																	55817618		2203	4300	6503	SO:0001819	synonymous_variant	55030	exon2			GGAGGTTAACAGC	AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"F-boxes /  "other""	20201	protein-coding gene	gene with protein product		609104	"F-box only protein 34"				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.510T>G	14.37:g.55817618T>G		134	0	0		109	26	0.238532	NM_017943	Q2VPB5|Q4VBP5|Q86TY4	Silent	SNP	ENST00000313833.4	37	CCDS32086.1																																																																																			.	.	none		0.473	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1			G	55817618	T	G	55817618	2	3	31	1	0	0	0	0	0	0	0	1	5752	1741	61	5		5	FBXO34	14	55817618	Silent	SNP	T	TCGA-GR-A4D4-01A-11D-A31X-10	33933588	55817618	51531922	70	13936											
SGPP1	81537	hgsc.bcm.edu	37	chr14	64165346	64165346	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aactagagaacaccagcaggGaataagaatcagtccatata	19	6	8	8	0	1	2	1	0	0	2	2	4	2	3	2	1	3	1	2	1	8	4			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr14:64165346G>T	ENST00000247225.6	-	2	809	c.715C>A	c.(715-717)Ccc>Acc	p.P239T		NM_030791.2	NP_110418.1	Q9BX95	SGPP1_HUMAN	sphingosine-1-phosphate phosphatase 1	239					extrinsic apoptotic signaling pathway (GO:0097191)|intrinsic apoptotic signaling pathway (GO:0097193)|small molecule metabolic process (GO:0044281)|sphinganine-1-phosphate metabolic process (GO:0006668)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	sphingosine-1-phosphate phosphatase activity (GO:0042392)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(4)|skin(2)	10				OV - Ovarian serous cystadenocarcinoma(108;0.0056)|all cancers(60;0.0141)|BRCA - Breast invasive adenocarcinoma(234;0.103)		CACCAGCAGGGAATAAGAATC	0.289																																					p.P239T		Atlas-SNP	.											.	SGPP1	29	.	0			c.C715A						PASS	.						64	64	64					14																	64165346		2203	4295	6498	SO:0001583	missense	81537	exon2			AGCAGGGAATAAG	AJ293294	CCDS9760.1	14q23.1	2003-09-17			ENSG00000126821	ENSG00000126821			17720	protein-coding gene	gene with protein product		612826				10859351	Standard	NM_030791		Approved		uc001xgj.3	Q9BX95	OTTHUMG00000029080	ENST00000247225.6:c.715C>A	14.37:g.64165346G>T	ENSP00000247225:p.Pro239Thr	449	0	0		457	97	0.212254	NM_030791	B2RAH0|Q9H189	Missense_Mutation	SNP	ENST00000247225.6	37	CCDS9760.1	.	.	.	.	.	.	.	.	.	.	G	9.884	1.202340	0.22121	.	.	ENSG00000126821	ENST00000247225	T	0.51574	0.7	5.6	2.62	0.31277	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.568287	0.19623	N	0.109879	T	0.13243	0.0321	N	0.00873	-1.125	0.27550	N	0.950526	B	0.17038	0.02	B	0.14578	0.011	T	0.11012	-1.0605	10	0.22109	T	0.4	-25.1553	1.6276	0.02726	0.1449:0.2663:0.343:0.2458	.	239	Q9BX95	SGPP1_HUMAN	T	239	ENSP00000247225:P239T	ENSP00000247225:P239T	P	-	1	0	SGPP1	63235099	0.916000	0.31088	1.000000	0.80357	0.996000	0.88848	0.599000	0.24089	1.500000	0.48636	-0.165000	0.13383	CCC	.	.	none		0.289	SGPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072626.3	NM_030791		T	64165346	G	T	64165346	3	4	31	1	0	0	0	0	1	0	0	0	14234	1174	41	4	618	4	SGPP1	14	64165346	Missense_Mutation	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10	8347728	64165346	43184194	71	13937											
MTHFD1	4522	hgsc.bcm.edu	37	chr14	64921449	64921449	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ttctttccccagggctttggGaatctccccatctgcatggc	5	13	9	14	0	3	0	0	0	3	0	5	1	4	1	4	3	1	2	4	3	1	3			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr14:64921449G>A	ENST00000545908.1	+	26	2971	c.2742G>A	c.(2740-2742)ggG>ggA	p.G914G	ZBTB25_ENST00000555220.1_Intron|MTHFD1_ENST00000216605.8_Silent_p.G858G|MTHFD1_ENST00000556284.1_3'UTR|ZBTB25_ENST00000555424.1_Intron			P11586	C1TC_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolate cyclohydrolase, formyltetrahydrofolate synthetase	858	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)	AGGGCTTTGGGAATCTCCCCA	0.488																																					p.G858G	Colon(18;220 581 13419 18191 31512)|GBM(126;343 1658 28700 44425 52519)	Atlas-SNP	.											.	MTHFD1	61	.	0			c.G2574A						PASS	.						103	91	95					14																	64921449		2203	4300	6503	SO:0001819	synonymous_variant	4522	exon26			CTTTGGGAATCTC	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.2742G>A	14.37:g.64921449G>A		79	0	0		75	27	0.36	NM_005956	B2R5Y2|G3V2B8|Q86VC9|Q9BVP5	Silent	SNP	ENST00000545908.1	37																																																																																				.	.	none		0.488	MTHFD1-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000412167.1			A	64921449	G	A	64921449	2	1	31	1	0	0	0	0	0	0	0	1	9936	1161	41	2		2	MTHFD1	14	64921449	Silent	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10	756103	64921449	42428091	72	13938											
C14orf145	145508	hgsc.bcm.edu	37	chr14	81329188	81329188	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcatctctctctccagttcCtgaagccgccgctccacccg	5	9	7	20	4	2	1	0	1	2	0	7	1	5	1	6	0	1	3	6	0	1	1			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr14:81329188C>A	ENST00000555265.1	-	9	1050	c.675G>T	c.(673-675)caG>caT	p.Q225H	CEP128_ENST00000281129.3_Missense_Mutation_p.Q225H|CEP128_ENST00000216517.6_Missense_Mutation_p.Q225H			Q6ZU80	CE128_HUMAN	centrosomal protein 128kDa	225						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						TCTCCAGTTCCTGAAGCCGCC	0.478																																					p.Q225H		Atlas-SNP	.											.	CEP128	146	.	0			c.G675T						PASS	.						74	67	69					14																	81329188		2203	4300	6503	SO:0001583	missense	145508	exon8			CAGTTCCTGAAGC	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.675G>T	14.37:g.81329188C>A	ENSP00000451162:p.Gln225His	52	0	0		39	19	0.487179	NM_152446	B9EK52|Q86X97|Q96ML4	Missense_Mutation	SNP	ENST00000555265.1	37	CCDS32130.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.21|19.21	3.784243|3.784243	0.70222|0.70222	.|.	.|.	ENSG00000100629|ENSG00000100629	ENST00000281129;ENST00000555265;ENST00000393619;ENST00000216517|ENST00000554827	T;T;T|.	0.55052|.	1.18;1.18;0.54|.	6.08|6.08	2.89|2.89	0.33648|0.33648	.|.	0.069385|.	0.64402|.	D|.	0.000016|.	T|T	0.64843|0.64843	0.2635|0.2635	M|M	0.70275|0.70275	2.135|2.135	0.80722|0.80722	D|D	1|1	D;D;D|.	0.57257|.	0.979;0.963;0.963|.	P;P;P|.	0.60473|.	0.875;0.875;0.81|.	T|T	0.63207|0.63207	-0.6689|-0.6689	10|5	0.72032|.	D|.	0.01|.	.|.	10.0884|10.0884	0.42432|0.42432	0.0:0.6984:0.0:0.3016|0.0:0.6984:0.0:0.3016	.|.	225;106;225|.	Q6ZU80-3;Q8N3Z7;Q6ZU80|.	.;.;CE128_HUMAN|.	H|M	225|104	ENSP00000281129:Q225H;ENSP00000451162:Q225H;ENSP00000216517:Q225H|.	ENSP00000216517:Q225H|.	Q|R	-|-	3|2	2|0	CEP128|CEP128	80398941|80398941	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.815000|0.815000	0.46073|0.46073	1.282000|1.282000	0.33226|0.33226	0.919000|0.919000	0.36945|0.36945	0.655000|0.655000	0.94253|0.94253	CAG|AGG	.	.	none		0.478	CEP128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413415.1	NM_152446		A	81329188	C	A	81329188	3	1	31	1	0	0	0	0	1	0	0	0	1751	680	24	4	2677	4	C14orf145	14	81329188	Missense_Mutation	SNP	C	TCGA-GR-A4D4-01A-11D-A31X-10	16407739	81329188	26020352	73	13939											
CHTF18	63922	hgsc.bcm.edu	37	chr16	841239	841239	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	acgagaggccttcccggaagCccaggcccagtgttgagccg	8	5	14	14	3	0	2	0	1	0	1	1	4	1	3	5	3	2	1	5	3	1	2			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr16:841239C>T	ENST00000262315.9	+	8	1036	c.973C>T	c.(973-975)Ccc>Tcc	p.P325S	CHTF18_ENST00000491530.1_3'UTR|CHTF18_ENST00000455171.2_Missense_Mutation_p.P353S|RPUSD1_ENST00000007264.2_5'Flank|CHTF18_ENST00000317063.6_Missense_Mutation_p.P520S|RPUSD1_ENST00000567114.1_5'Flank|RPUSD1_ENST00000565809.1_5'Flank	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	325					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)				TTCCCGGAAGCCCAGGCCCAG	0.647																																					p.P325S		Atlas-SNP	.											.	CHTF18	52	.	0			c.C973T						PASS	.						19	24	22					16																	841239		2062	4183	6245	SO:0001583	missense	63922	exon8			CGGAAGCCCAGGC	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.973C>T	16.37:g.841239C>T	ENSP00000262315:p.Pro325Ser	31	0	0		55	29	0.527273	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Missense_Mutation	SNP	ENST00000262315.9	37	CCDS45371.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.52|10.52	1.373536|1.373536	0.24857|0.24857	.|.	.|.	ENSG00000127586|ENSG00000127586	ENST00000426047|ENST00000317063;ENST00000455171;ENST00000262315	.|T;T;T	.|0.10573	.|2.86;2.9;2.88	4.85|4.85	0.255|0.255	0.15561|0.15561	.|.	.|0.459860	.|0.21606	.|N	.|0.071879	T|T	0.09730|0.09730	0.0239|0.0239	M|M	0.74647|0.74647	2.275|2.275	0.35423|0.35423	D|D	0.79339|0.79339	.|B;B	.|0.32467	.|0.372;0.139	.|B;B	.|0.29942	.|0.109;0.017	T|T	0.13282|0.13282	-1.0515|-1.0515	5|10	.|0.25106	.|T	.|0.35	-14.7794|-14.7794	2.5691|2.5691	0.04790|0.04790	0.1507:0.5277:0.1468:0.1748|0.1507:0.5277:0.1468:0.1748	.|.	.|353;325	.|Q8WVB6-2;Q8WVB6	.|.;CTF18_HUMAN	V|S	220|520;353;325	.|ENSP00000313029:P520S;ENSP00000406252:P353S;ENSP00000262315:P325S	.|ENSP00000262315:P325S	A|P	+|+	2|1	0|0	CHTF18|CHTF18	781240|781240	0.863000|0.863000	0.29885|0.29885	0.995000|0.995000	0.50966|0.50966	0.896000|0.896000	0.52359|0.52359	0.552000|0.552000	0.23376|0.23376	0.190000|0.190000	0.20209|0.20209	0.579000|0.579000	0.79373|0.79373	GCC|CCC	.	.	none		0.647	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092		T	841239	C	T	841239	3	4	31	1	0	0	0	0	1	0	0	0	3416	739	26	2	1003	2	CHTF18	16	841239	Missense_Mutation	SNP	C	TCGA-GR-A4D4-01A-11D-A31X-10		841239	89513514	74	13940											
CREBBP	1387	hgsc.bcm.edu	37	chr16	3786764	3786764	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtgggtggcaatggaagaTgtaatcatctccttcacttg	10	12	12	7	0	3	1	2	0	1	1	4	2	3	2	1	4	0	2	1	4	3	3			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr16:3786764T>A	ENST00000262367.5	-	27	5256	c.4447A>T	c.(4447-4449)Atc>Ttc	p.I1483F	CREBBP_ENST00000382070.3_Missense_Mutation_p.I1445F	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1483	CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.|Cys/His-rich.|Interaction with TRERF1.				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)		CAATGGAAGATGTAATCATCT	0.512			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.I1483F		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	CREBBP,colon,carcinoma,+1,4	CREBBP	546	4	0			c.A4447T						PASS	.						225	192	203					16																	3786764		2197	4300	6497	SO:0001583	missense	1387	exon27			GGAAGATGTAATC	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.4447A>T	16.37:g.3786764T>A	ENSP00000262367:p.Ile1483Phe	160	0	0		194	43	0.221649	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	t	21.2	4.116784	0.77323	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.94793	-3.52;-3.52	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	D	0.97598	0.9213	M	0.90814	3.15	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.98516	1.0621	10	0.87932	D	0	-22.4571	14.6308	0.68655	0.0:0.0:0.0:1.0	.	1513;1483	Q4LE28;Q92793	.;CBP_HUMAN	F	1483;1513;1445;72	ENSP00000262367:I1483F;ENSP00000371502:I1445F	ENSP00000262367:I1483F	I	-	1	0	CREBBP	3726765	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.997000	0.88414	2.107000	0.64212	0.459000	0.35465	ATC	.	.	none		0.512	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		A	3786764	T	A	3786764	3	1	31	1	0	0	0	0	1	0	0	0	3863	1464	51	5	2901	5	CREBBP	16	3786764	Missense_Mutation	SNP	T	TCGA-GR-A4D4-01A-11D-A31X-10	2945525	3786764	86567989	75	13941											
GSPT1	2935	hgsc.bcm.edu	37	chr16	12009383	12009383	+	Intron	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttgacgttgagttgccggctGaaggccgcgctgaggttctc	5	11	15	10	4	1	4	0	4	1	0	2	4	1	4	2	3	1	5	2	3	1	4			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr16:12009383G>C	ENST00000420576.2	-	1	41				GSPT1_ENST00000439887.2_Missense_Mutation_p.F65L|GSPT1_ENST00000434724.2_Missense_Mutation_p.F65L|AC007216.1_ENST00000583357.1_RNA	NM_001130007.1	NP_001123479.1	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						GTTGCCGGCTGAAGGCCGCGC	0.761																																					p.F65L		Atlas-SNP	.											.	GSPT1	71	.	0			c.C195G						PASS	.						10	13	12					16																	12009383		1526	3533	5059	SO:0001627	intron_variant	2935	exon1			CCGGCTGAAGGCC	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		ENST00000420576.2:c.61+515C>G	16.37:g.12009383G>C		47	0	0		101	22	0.217822	NM_001130006	J3KQG6|Q96GF2	Missense_Mutation	SNP	ENST00000420576.2	37	CCDS45414.1	.	.	.	.	.	.	.	.	.	.	g	13.05	2.121366	0.37436	.	.	ENSG00000103342	ENST00000434724;ENST00000439887	T;T	0.34472	1.42;1.36	5.09	4.13	0.48395	.	0.638850	0.14978	U	0.287426	T	0.24586	0.0596	.	.	.	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.003	T	0.03922	-1.0992	9	0.19590	T	0.45	-5.7554	10.5732	0.45212	0.0913:0.0:0.9087:0.0	.	65;62	E7EQZ3;Q96GF2	.;.	L	65	ENSP00000398131:F65L;ENSP00000408399:F65L	ENSP00000398131:F65L	F	-	3	2	GSPT1	11916884	1.000000	0.71417	1.000000	0.80357	0.072000	0.16883	2.931000	0.48932	1.129000	0.42072	0.457000	0.33378	TTC	.	.	none		0.761	GSPT1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421514.1	NM_002094		C	12009383	G	C	12009383	1	2	31	0	1	0	0	0	0	0	0	0	6835	1281	45	4		4	GSPT1	16	12009383	Intron	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10	8222619	12009383	78345370	76	13942											
RBBP6	5930	hgsc.bcm.edu	37	chr16	24557518	24557518	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatgctctgattcctaagaaTtcttctgtaattgttagaag	12	16	7	6	0	3	3	0	1	3	2	4	3	4	3	1	0	1	3	1	0	6	7			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr16:24557518T>A	ENST00000319715.4	+	2	633	c.201T>A	c.(199-201)aaT>aaA	p.N67K	RBBP6_ENST00000452655.2_Missense_Mutation_p.N67K|RBBP6_ENST00000381039.3_Missense_Mutation_p.N67K|RBBP6_ENST00000348022.2_Missense_Mutation_p.N67K	NM_006910.4	NP_008841.2	Q7Z6E9	RBBP6_HUMAN	retinoblastoma binding protein 6	67	DWNN. {ECO:0000255|PROSITE- ProRule:PRU00612}.				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)		TTCCTAAGAATTCTTCTGTAA	0.299																																					p.N67K		Atlas-SNP	.											.	RBBP6	158	.	0			c.T201A						PASS	.						39	42	41					16																	24557518		2192	4278	6470	SO:0001583	missense	5930	exon2			TAAGAATTCTTCT		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.201T>A	16.37:g.24557518T>A	ENSP00000317872:p.Asn67Lys	82	0	0		107	31	0.28972	NM_018703	Q147T5|Q15290|Q6DKH4|Q6P4C2|Q6YNC9|Q7Z6E8|Q8N0V2|Q96PH3|Q9H3I8|Q9H5M5|Q9NPX4	Missense_Mutation	SNP	ENST00000319715.4	37	CCDS10621.1	.	.	.	.	.	.	.	.	.	.	T	21.1	4.103777	0.76983	.	.	ENSG00000122257	ENST00000381039;ENST00000452655;ENST00000319715;ENST00000348022	T;T;T;T	0.45668	0.89;0.89;0.89;0.89	6.08	1.31	0.21738	DWNN domain (2);	0.091915	0.64402	D	0.000001	T	0.64148	0.2572	M	0.86573	2.825	0.51767	D	0.999934	D;D;D;D	0.76494	0.999;0.996;0.997;0.996	D;D;D;P	0.74023	0.982;0.937;0.962;0.894	T	0.66380	-0.5938	10	0.87932	D	0	-31.0125	10.2634	0.43441	0.0:0.4392:0.0:0.5608	.	67;67;67;67	Q7Z6E9-4;Q7Z6E9-2;Q7Z6E9;Q7Z6E9-3	.;.;RBBP6_HUMAN;.	K	67	ENSP00000370427:N67K;ENSP00000390537:N67K;ENSP00000317872:N67K;ENSP00000316291:N67K	ENSP00000317872:N67K	N	+	3	2	RBBP6	24465019	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	1.119000	0.31258	0.161000	0.19458	0.482000	0.46254	AAT	.	.	none		0.299	RBBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214067.2	NM_006910		A	24557518	T	A	24557518	3	1	31	1	0	0	0	0	1	0	0	0	13118	1490	52	5	207	5	RBBP6	16	24557518	Missense_Mutation	SNP	T	TCGA-GR-A4D4-01A-11D-A31X-10	12548135	24557518	65797235	77	13943											
TBC1D10B	26000	hgsc.bcm.edu	37	chr16	30381303	30381303	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	cggggccggagcagaggtctCggccgaccccgggacccagg	6	2	18	15	5	1	1	0	0	1	1	2	4	1	3	5	7	1	1	5	7	0	0	rs12930787	byFrequency	TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr16:30381303C>G	ENST00000409939.3	-	1	282	c.202G>C	c.(202-204)Gag>Cag	p.E68Q		NM_015527.3	NP_056342.3	Q4KMP7	TB10B_HUMAN	TBC1 domain family, member 10B	68	Pro-rich.				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)			gcAGAGGTCTCGGCCGACCCC	0.786													G|||	1131	0.225839	0.2224	0.2219	5008	,	,		5407	0.0794		0.327	False		,,,				2504	0.2802				p.E68Q		Atlas-SNP	.											.	TBC1D10B	32	.	0			c.G202C						PASS	.						1	1	1					16																	30381303		132	419	551	SO:0001583	missense	26000	exon1			AGGTCTCGGCCGA	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.202G>C	16.37:g.30381303C>G	ENSP00000386538:p.Glu68Gln	0	0	.		5	5	1	NM_015527	B9A6L0|Q6IN54|Q6P530|Q71RG7|Q86VC5|Q9H8Z2|Q9NUN6|Q9UFP2	Missense_Mutation	SNP	ENST00000409939.3	37	CCDS10676.2	476	0.21794871794871795	101	0.20528455284552846	86	0.23756906077348067	47	0.08216783216783216	242	0.31926121372031663	G	0.004	-2.356799	0.00214	.	.	ENSG00000169221	ENST00000409939	T	0.04156	3.69	3.57	-0.0103	0.13997	.	.	.	.	.	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45366	-0.9266	8	0.02654	T	1	.	5.7944	0.18379	0.2033:0.4717:0.325:0.0	rs12930787	68	Q4KMP7	TB10B_HUMAN	Q	68	ENSP00000386538:E68Q	ENSP00000386538:E68Q	E	-	1	0	TBC1D10B	30288804	0.000000	0.05858	0.000000	0.03702	0.178000	0.23041	0.290000	0.18975	-0.070000	0.12908	-0.647000	0.03941	GAG	C|0.776;G|0.224	0.224	strong		0.786	TBC1D10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255527.3	NM_015527		G	30381303	C	G	30381303	3	3	31	1	0	0	0	0	1	0	0	0	15614	893	31	4	2260	4	TBC1D10B	16	30381303	Missense_Mutation	SNP	C	TCGA-GR-A4D4-01A-11D-A31X-10	5823785	30381303	59973450	78	13944											
ZNF768	79724	hgsc.bcm.edu	37	chr16	30537265	30537265	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aaactctgggctttgtggctCaaacccagggctctggggtt	7	11	13	10	0	3	0	1	0	2	0	3	0	3	0	1	5	2	4	1	5	2	2			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr16:30537265C>G	ENST00000380412.5	-	2	371	c.196G>C	c.(196-198)Gag>Cag	p.E66Q	ZNF747_ENST00000535210.1_3'UTR|ZNF768_ENST00000562803.1_Missense_Mutation_p.E35Q|ZNF747_ENST00000569360.1_3'UTR	NM_024671.3	NP_078947.3	Q9H5H4	ZN768_HUMAN	zinc finger protein 768	66	Pro-rich.				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						CTTTGTGGCTCAAACCCAGGG	0.547																																					p.E66Q		Atlas-SNP	.											.	ZNF768	28	.	0			c.G196C						PASS	.						73	78	76					16																	30537265		2197	4300	6497	SO:0001583	missense	79724	exon2			GTGGCTCAAACCC	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.196G>C	16.37:g.30537265C>G	ENSP00000369777:p.Glu66Gln	56	0	0		87	18	0.206897	NM_024671	Q569L7|Q96CX4	Missense_Mutation	SNP	ENST00000380412.5	37	CCDS10681.2	.	.	.	.	.	.	.	.	.	.	C	15.07	2.723574	0.48728	.	.	ENSG00000169957	ENST00000380412;ENST00000538507	T	0.06687	3.27	4.28	4.28	0.50868	.	0.204949	0.24429	N	0.038613	T	0.07773	0.0195	N	0.24115	0.695	0.80722	D	1	B	0.23937	0.094	B	0.32149	0.141	T	0.37430	-0.9706	10	0.24483	T	0.36	-4.1654	14.2663	0.66121	0.0:1.0:0.0:0.0	.	66	Q9H5H4	ZN768_HUMAN	Q	66;35	ENSP00000369777:E66Q	ENSP00000369777:E66Q	E	-	1	0	ZNF768	30444766	0.990000	0.36364	0.998000	0.56505	0.992000	0.81027	2.717000	0.47227	2.236000	0.73375	0.561000	0.74099	GAG	.	.	none		0.547	ZNF768-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255522.2	NM_024671		G	30537265	C	G	30537265	3	3	31	1	0	0	0	0	1	0	0	0	18156	835	29	4	1430	4	ZNF768	16	30537265	Missense_Mutation	SNP	C	TCGA-GR-A4D4-01A-11D-A31X-10	155962	30537265	59817488	79	13945											
TP53	7157	hgsc.bcm.edu	37	chr17	7574035	7574035	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcgctcacgcccacggatcTgcagcaacagaggaggggga	11	3	15	12	3	2	1	1	0	1	1	2	4	2	4	1	4	4	3	1	4	1	0			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr17:7574035T>C	ENST00000269305.4	-	10	1183		c.e10-2		TP53_ENST00000359597.4_Intron|TP53_ENST00000445888.2_Splice_Site|TP53_ENST00000413465.2_Intron|TP53_ENST00000420246.2_Splice_Site|TP53_ENST00000455263.2_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.?(10)|p.0?(8)|p.I332fs*49(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)	CCCACGGATCTGCAGCAACAG	0.507		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_ENST00000269305,NS,carcinoma,0,13	TP53	33396	13	19	Unknown(10)|Whole gene deletion(8)|Insertion - Frameshift(1)	lung(5)|haematopoietic_and_lymphoid_tissue(4)|bone(4)|central_nervous_system(2)|liver(2)|stomach(1)|breast(1)	c.994-2A>G						PASS	.						44	36	38					17																	7574035		2203	4300	6503	SO:0001630	splice_region_variant	7157	exon11	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;	CGGATCTGCAGCA	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.994-2A>G	17.37:g.7574035T>C		93	0	0		63	26	0.412698	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	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	12.31	1.898270	0.33535	.	.	ENSG00000141510	ENST00000269305;ENST00000445888;ENST00000396473	.	.	.	5.13	5.13	0.70059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.1784	0.59641	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	TP53	7514760	1.000000	0.71417	0.937000	0.37676	0.131000	0.20780	6.590000	0.74085	2.061000	0.61500	0.459000	0.35465	.	.	.	none		0.507	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Intron	C	7574035	T	C	7574035	5	2	31	1	0	0	0	0	0	0	1	0	16396	1594	55	3	197	3	TP53	17	7574035	Splice_Site	SNP	T	TCGA-GR-A4D4-01A-11D-A31X-10		7574035	73621175	80	13946											
KRTAP4-5	85289	hgsc.bcm.edu	37	chr17	39305783	39305784	+	In_Frame_Ins	INS	-	-	CTGGGGCGGCAGCAG																															agcaggtggtctggcagcagINScaggggcggcagcagctgga																										TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr17:39305783_39305784insCTGGGGCGGCAGCAG	ENST00000343246.4	-	1	270_271	c.236_237insCTGCTGCCGCCCCAG	c.(235-237)tgc>tgCTGCTGCCGCCCCAGc	p.79_80insCCRPS		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	79	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].		C -> CCCRPS.		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)			tctggcagcagcaggggcggca	0.653																																					p.C79delinsCCCRPS		Atlas-Indel	.											KRTAP4-5,colon,carcinoma,-2,3	KRTAP4-5	34	3	0			c.237_238insCTGCTGCCGCCCCAG						PASS	.																																			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.236_237insCTGCTGCCGCCCCAG	17.37:g.39305783_39305784insCTGGGGCGGCAGCAG	ENSP00000340546:p.Cys79_Cys80insCysCysArgProSer	53	0	0		58	30	0.517241	NM_033188		In_Frame_Ins	INS	ENST00000343246.4	37	CCDS32650.1																																																																																			.	.	none		0.653	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1			CTGGGGCGGCAGCAG	39305784	-	CTGGGGCGGCAGCAG	39305783	7	5	31	1	0	1	1	0	0	0	0	0	8563	963	34	0	312	0	KRTAP4-5	17	39305783	In_Frame_Ins	INS	-	TCGA-GR-A4D4-01A-11D-A31X-10	31731748	39305783	41889427	81	13947											
SLC4A1	6521	hgsc.bcm.edu	37	chr17	42336903	42336903	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctctgaatccgggggaatcTtttccagaattccagatggt	9	12	10	10	1	2	3	0	1	2	2	5	4	5	4	4	3	0	0	4	3	3	3			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr17:42336903T>C	ENST00000262418.6	-	8	811	c.656A>G	c.(655-657)aAg>aGg	p.K219R	AC003043.1_ENST00000597382.1_Intron|SLC4A1_ENST00000471005.1_5'Flank	NM_000342.3	NP_000333.1	P02730	B3AT_HUMAN	solute carrier family 4 (anion exchanger), member 1 (Diego blood group)	219	Globular.				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)		CGGGGGAATCTTTTCCAGAAT	0.597																																					p.K219R		Atlas-SNP	.											.	SLC4A1	104	.	0			c.A656G						PASS	.						95	88	90					17																	42336903		2203	4300	6503	SO:0001583	missense	6521	exon8			GGAATCTTTTCCA		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.656A>G	17.37:g.42336903T>C	ENSP00000262418:p.Lys219Arg	74	0	0		95	4	0.0421053	NM_000342	G4V2I6|P78487|Q1ZZ45|Q4KKW9|Q4VB84|Q9UCY7|Q9UDJ1	Missense_Mutation	SNP	ENST00000262418.6	37	CCDS11481.1	.	.	.	.	.	.	.	.	.	.	t	6.620	0.482756	0.12581	.	.	ENSG00000004939	ENST00000262418	T	0.69435	-0.4	5.34	1.89	0.25635	Bicarbonate transporter, cytoplasmic (2);Phosphotransferase/anion transporter (1);	0.483231	0.23159	N	0.051267	T	0.61035	0.2315	M	0.65975	2.015	0.39099	D	0.961257	B;B	0.20671	0.008;0.047	B;B	0.28916	0.012;0.096	T	0.52147	-0.8614	10	0.31617	T	0.26	.	6.9872	0.24735	0.0:0.0962:0.1395:0.7643	.	219;219	E2RVJ0;P02730	.;B3AT_HUMAN	R	219	ENSP00000262418:K219R	ENSP00000262418:K219R	K	-	2	0	SLC4A1	39692429	1.000000	0.71417	0.817000	0.32601	0.144000	0.21451	2.477000	0.45180	0.048000	0.15891	-0.666000	0.03841	AAG	.	.	none		0.597	SLC4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346194.1	NM_000342		C	42336903	T	C	42336903	3	2	31	1	0	0	0	0	1	0	0	0	14665	1609	56	3	2131	3	SLC4A1	17	42336903	Missense_Mutation	SNP	T	TCGA-GR-A4D4-01A-11D-A31X-10	3031120	42336903	38858307	82	13948											
SPOP	8405	hgsc.bcm.edu	37	chr17	47696644	47696644	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attcaggatggagaatttgaAttttgcccgaacttcactct	11	14	8	8	1	3	2	2	1	1	1	3	5	3	3	1	2	2	0	1	2	3	5			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr17:47696644A>T	ENST00000393328.2	-	5	669	c.304T>A	c.(304-306)Ttc>Atc	p.F102I	SPOP_ENST00000503676.1_Missense_Mutation_p.F102I|SPOP_ENST00000393331.3_Missense_Mutation_p.F102I|SPOP_ENST00000504102.1_Missense_Mutation_p.F102I|SPOP_ENST00000347630.2_Missense_Mutation_p.F102I|SPOP_ENST00000513080.1_5'Flank	NM_003563.3	NP_003554.1	O43791	SPOP_HUMAN	speckle-type POZ protein	102	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.|Required for nuclear localization.				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						GAGAATTTGAATTTTGCCCGA	0.408										Prostate(2;0.17)																											p.F102I		Atlas-SNP	.											SPOP,NS,adenoma,+1,3	SPOP	91	3	0			c.T304A						PASS	.						147	136	140					17																	47696644		2203	4300	6503	SO:0001583	missense	8405	exon4			ATTTGAATTTTGC	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.304T>A	17.37:g.47696644A>T	ENSP00000377001:p.Phe102Ile	98	0	0		114	33	0.289474	NM_001007228	B2R6S3|D3DTW7|Q53HJ1	Missense_Mutation	SNP	ENST00000393328.2	37	CCDS11551.1	.	.	.	.	.	.	.	.	.	.	A	31	5.059254	0.93846	.	.	ENSG00000121067	ENST00000393328;ENST00000393331;ENST00000347630;ENST00000504102;ENST00000503676;ENST00000513872;ENST00000509079;ENST00000505581;ENST00000507970;ENST00000514121;ENST00000515508	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	5.52	5.52	0.82312	TRAF-type (1);TRAF-like (1);MATH (3);	0.000000	0.85682	D	0.000000	D	0.83459	0.5259	M	0.87180	2.865	0.80722	D	1	D	0.76494	0.999	D	0.69824	0.966	D	0.86433	0.1762	10	0.72032	D	0.01	-11.8278	15.4649	0.75390	1.0:0.0:0.0:0.0	.	102	O43791	SPOP_HUMAN	I	102;102;102;102;102;55;102;102;102;102;102	ENSP00000377001:F102I;ENSP00000377004:F102I;ENSP00000240327:F102I;ENSP00000425905:F102I;ENSP00000420908:F102I;ENSP00000426986:F102I;ENSP00000420960:F102I;ENSP00000426262:F102I;ENSP00000424119:F102I;ENSP00000426537:F102I	ENSP00000240327:F102I	F	-	1	0	SPOP	45051643	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.135000	0.94478	2.317000	0.78254	0.460000	0.39030	TTC	.	.	none		0.408	SPOP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365154.2	NM_003563		T	47696644	A	T	47696644	3	4	31	1	0	0	0	0	1	0	0	0	15099	101	4	5	848	5	SPOP	17	47696644	Missense_Mutation	SNP	A	TCGA-GR-A4D4-01A-11D-A31X-10	5359741	47696644	33498566	83	13949											
TEX2	55852	hgsc.bcm.edu	37	chr17	62290117	62290117	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagtgggggagggggaggatGaggtacacatagacacacat	13	6	17	5	0	0	2	0	1	0	1	0	5	0	5	0	6	1	1	0	6	3	3			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr17:62290117G>T	ENST00000583097.1	-	2	1633	c.1461C>A	c.(1459-1461)ctC>ctA	p.L487L	TEX2_ENST00000258991.3_Silent_p.L487L|TEX2_ENST00000584379.1_Silent_p.L487L			Q8IWB9	TEX2_HUMAN	testis expressed 2	487					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)		GGGGGAGGATGAGGTACACAT	0.512																																					p.L487L		Atlas-SNP	.											.	TEX2	89	.	0			c.C1461A						PASS	.						96	93	94					17																	62290117		2203	4300	6503	SO:0001819	synonymous_variant	55852	exon2			GAGGATGAGGTAC	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.1461C>A	17.37:g.62290117G>T		119	0	0		146	44	0.30137	NM_018469	Q6AHZ5|Q8N3L0|Q9C0C5	Silent	SNP	ENST00000583097.1	37																																																																																				.	.	none		0.512	TEX2-003	KNOWN	alternative_5_UTR|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000443745.1	NM_018469		T	62290117	G	T	62290117	2	4	31	1	0	0	0	0	0	0	0	1	15796	1277	45	4		4	TEX2	17	62290117	Silent	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10	14593473	62290117	18905093	84	13950											
CACNG5	27091	hgsc.bcm.edu	37	chr17	64881273	64881273	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcccctccgacatctccagCgaggcctccctgcagatgaa	9	6	9	17	2	1	2	0	1	1	1	4	4	3	2	6	1	3	1	6	1	1	0			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr17:64881273C>T	ENST00000533854.1	+	6	981	c.744C>T	c.(742-744)agC>agT	p.S248S	CACNG5_ENST00000307139.3_Silent_p.S248S			Q9UF02	CCG5_HUMAN	calcium channel, voltage-dependent, gamma subunit 5	248				SAGVMSVYLFMKRYTAEDMYRPHPGFYRPRLSNCSDYSGQF LHPDAWVRGRSPSDISSEASLQMNSNYPALLKCPDYDQMSS SPC -> VKPVTLSMDRLGLGTAPLSRGEWGWGRRDIPQPF WTPDHPLYFPSSSQNVSLSYLSGSPPARMSPGPCSCPHVHF PPHSSCVLCRPQPREMRQAPAASPSSAVFSL (in Ref. 1; AAF03089). {ECO:0000305}.	regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	ion transmembrane transporter activity (GO:0015075)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(6)|pancreas(1)|prostate(1)|skin(2)	24			BRCA - Breast invasive adenocarcinoma(6;1.61e-08)			ACATCTCCAGCGAGGCCTCCC	0.637																																					p.S248S		Atlas-SNP	.											.	CACNG5	77	.	0			c.C744T						PASS	.						54	48	50					17																	64881273		2203	4300	6503	SO:0001819	synonymous_variant	27091	exon5			CTCCAGCGAGGCC	AF148220	CCDS11665.1	17q24	2004-02-16				ENSG00000075429		"Calcium channel subunits"	1409	protein-coding gene	gene with protein product		606405				10613843	Standard	NM_145811		Approved		uc010wqj.2	Q9UF02		ENST00000533854.1:c.744C>T	17.37:g.64881273C>T		37	0	0		45	16	0.355556	NM_145811	A8K2A6|Q547R3|Q8WXS7|Q9UHM3	Silent	SNP	ENST00000533854.1	37	CCDS11665.1																																																																																			.	.	none		0.637	CACNG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389882.1	NM_014404, NM_145811		T	64881273	C	T	64881273	2	4	31	1	0	0	0	0	0	0	0	1	2562	767	27	1		1	CACNG5	17	64881273	Silent	SNP	C	TCGA-GR-A4D4-01A-11D-A31X-10	2591156	64881273	16313937	85	13951											
PITPNC1	26207	hgsc.bcm.edu	37	chr17	65574302	65574302	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatttgcttttctcccacagTgttcctttctgccgaaattc	7	17	5	12	1	2	0	0	0	2	0	5	1	3	0	3	0	2	2	3	0	2	6			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr17:65574302T>A	ENST00000581322.1	+	5	295	c.295T>A	c.(295-297)Tgt>Agt	p.C99S	PITPNC1_ENST00000580974.1_Splice_Site_p.C99S|PITPNC1_ENST00000299954.9_Missense_Mutation_p.C99S|PITPNC1_ENST00000335257.6_Missense_Mutation_p.C99S			Q9UKF7	PITC1_HUMAN	phosphatidylinositol transfer protein, cytoplasmic 1	99					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)			TCTCCCACAGTGTTCCTTTCT	0.423																																					p.C99S		Atlas-SNP	.											.	PITPNC1	47	.	0			c.T295A						PASS	.						73	72	72					17																	65574302		1943	4146	6089	SO:0001630	splice_region_variant	26207	exon5			CCACAGTGTTCCT	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.295-1T>A	17.37:g.65574302T>A		65	0	0		53	19	0.358491	NM_012417	A8K473|J3QR20|Q96I07	Missense_Mutation	SNP	ENST00000581322.1	37	CCDS58588.1	.	.	.	.	.	.	.	.	.	.	T	14.85	2.659119	0.47467	.	.	ENSG00000154217	ENST00000335257;ENST00000299954	T;T	0.44482	0.92;0.92	5.47	5.47	0.80525	START-like domain (1);	0.000000	0.85682	D	0.000000	T	0.61375	0.2342	M	0.66560	2.04	0.80722	D	1	D;D	0.69078	0.996;0.997	D;D	0.74348	0.983;0.978	T	0.58736	-0.7584	10	0.30854	T	0.27	-4.8363	15.4926	0.75619	0.0:0.0:0.0:1.0	.	99;99	Q9UKF7;Q9UKF7-2	PITC1_HUMAN;.	S	99	ENSP00000335618:C99S;ENSP00000299954:C99S	ENSP00000299954:C99S	C	+	1	0	PITPNC1	63004764	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.332000	0.79203	2.198000	0.70561	0.459000	0.35465	TGT	.	.	none		0.423	PITPNC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447194.1	NM_012417	Missense_Mutation	A	65574302	T	A	65574302	5	1	31	1	0	0	0	0	0	0	1	0	11958	1710	59	5	313	5	PITPNC1	17	65574302	Splice_Site	SNP	T	TCGA-GR-A4D4-01A-11D-A31X-10	693029	65574302	15620908	86	13952											
PODNL1	79883	hgsc.bcm.edu	37	chr19	14043787	14043787	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gccagtgggcaggcccatggGcagccgggttagctgattcc	6	7	16	12	1	0	1	0	1	0	0	1	1	1	1	4	4	2	4	4	4	1	2			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr19:14043787G>A	ENST00000339560.5	-	8	1543	c.1270C>T	c.(1270-1272)Ccc>Tcc	p.P424S	PODNL1_ENST00000538517.2_Missense_Mutation_p.P333S|PODNL1_ENST00000254320.3_Missense_Mutation_p.P342S|PODNL1_ENST00000538371.2_Missense_Mutation_p.P422S	NM_024825.3	NP_079101.3	Q6PEZ8	PONL1_HUMAN	podocan-like 1	424	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)			AGGCCCATGGGCAGCCGGGTT	0.706																																					p.P424S		Atlas-SNP	.											.	PODNL1	27	.	0			c.C1270T						PASS	.						7	9	8					19																	14043787		2152	4212	6364	SO:0001583	missense	79883	exon8			CCATGGGCAGCCG	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.1270C>T	19.37:g.14043787G>A	ENSP00000345175:p.Pro424Ser	19	0	0		39	14	0.358974	NM_024825	B7Z564|Q9H5G9	Missense_Mutation	SNP	ENST00000339560.5	37	CCDS12300.1	.	.	.	.	.	.	.	.	.	.	G	20.2	3.948115	0.73787	.	.	ENSG00000132000	ENST00000538371;ENST00000538517;ENST00000339560;ENST00000545071;ENST00000254320	T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16	4.89	4.89	0.63831	.	0.000000	0.48286	D	0.000183	D	0.87553	0.6206	M	0.79475	2.455	0.44555	D	0.997517	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	0.88485	0.3071	10	0.54805	T	0.06	.	14.9488	0.71054	0.0:0.0:1.0:0.0	.	422;342;333;424	F5H7F9;B7Z3M0;G3V1J6;Q6PEZ8	.;.;.;PONL1_HUMAN	S	422;333;424;274;342	ENSP00000442553:P422S;ENSP00000440080:P333S;ENSP00000345175:P424S;ENSP00000254320:P342S	ENSP00000254320:P342S	P	-	1	0	PODNL1	13904787	1.000000	0.71417	0.995000	0.50966	0.372000	0.29890	8.738000	0.91569	2.271000	0.75665	0.453000	0.30009	CCC	.	.	none		0.706	PODNL1-003	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457967.1	NM_024825		A	14043787	G	A	14043787	3	1	31	1	0	0	0	0	1	0	0	0	12188	1203	42	2	272	2	PODNL1	19	14043787	Missense_Mutation	SNP	G	TCGA-GR-A4D4-01A-11D-A31X-10		14043787	45085196	87	13953											
RYR1	6261	hgsc.bcm.edu	37	chr19	38931449	38931449	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gcagctcaagctctgcctggCcgccgagggcttcggcaacc	6	6	13	16	3	2	0	1	0	1	0	3	1	2	0	4	3	4	5	4	3	2	1			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr19:38931449C>T	ENST00000359596.3	+	2	110	c.110C>T	c.(109-111)gCc>gTc	p.A37V	RYR1_ENST00000355481.4_Missense_Mutation_p.A37V|RYR1_ENST00000360985.3_Missense_Mutation_p.A37V			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	37					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)	CTCTGCCTGGCCGCCGAGGGC	0.682																																					p.A37V		Atlas-SNP	.											.	RYR1	708	.	0			c.C110T						PASS	.						17	17	17					19																	38931449		2196	4289	6485	SO:0001583	missense	6261	exon2			GCCTGGCCGCCGA	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.110C>T	19.37:g.38931449C>T	ENSP00000352608:p.Ala37Val	116	0	0		92	29	0.315217	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	c	15.49	2.848708	0.51164	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.98419	-4.92;-4.92;-4.92	4.68	4.68	0.58851	Inositol 1,4,5-trisphosphate/ryanodine receptor (1);	0.302095	0.25291	U	0.031737	D	0.98548	0.9515	M	0.77820	2.39	0.34501	D	0.706091	D;D	0.89917	0.994;1.0	P;D	0.68039	0.642;0.955	D	0.99967	1.1892	10	0.87932	D	0	.	11.0484	0.47872	0.0:0.8112:0.1888:0.0	.	37;37	P21817-2;P21817	.;RYR1_HUMAN	V	37	ENSP00000352608:A37V;ENSP00000347667:A37V;ENSP00000354254:A37V	ENSP00000347667:A37V	A	+	2	0	RYR1	43623289	1.000000	0.71417	0.988000	0.46212	0.475000	0.33008	5.618000	0.67722	2.150000	0.67090	0.556000	0.70494	GCC	.	.	none		0.682	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			T	38931449	C	T	38931449	3	4	31	1	0	0	0	0	1	0	0	0	13783	739	26	2	116	2	RYR1	19	38931449	Missense_Mutation	SNP	C	TCGA-GR-A4D4-01A-11D-A31X-10	24887662	38931449	20197534	88	13954											
POU2F2	5452	hgsc.bcm.edu	37	chr19	42600030	42600030	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcgaagcgggaaatggtcgTctggctgaagtcgttgccgt	7	10	15	9	5	1	1	0	1	1	0	4	3	1	2	1	3	2	2	1	3	3	1			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr19:42600030T>C	ENST00000526816.2	-	9	730	c.715A>G	c.(715-717)Acg>Gcg	p.T239A	POU2F2_ENST00000389341.5_Missense_Mutation_p.T223A|POU2F2_ENST00000560558.1_Missense_Mutation_p.T184A|POU2F2_ENST00000560398.1_Missense_Mutation_p.T245A|POU2F2_ENST00000529952.1_Missense_Mutation_p.T239A|POU2F2_ENST00000342301.4_Missense_Mutation_p.T239A|POU2F2_ENST00000529067.1_Missense_Mutation_p.T223A|POU2F2_ENST00000533720.1_Missense_Mutation_p.T223A			P09086	PO2F2_HUMAN	POU class 2 homeobox 2	239	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				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)	GAAATGGTCGTCTGGCTGAAG	0.627																																					p.T239A		Atlas-SNP	.											POU2F2_ENST00000292077,NS,lymphoid_neoplasm,0,8	POU2F2	106	8	0			c.A715G						PASS	.						119	118	118					19																	42600030		2203	4300	6503	SO:0001583	missense	5452	exon9			TGGTCGTCTGGCT		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.715A>G	19.37:g.42600030T>C	ENSP00000431603:p.Thr239Ala	73	0	0		94	29	0.308511	NM_001207025	Q16648|Q7M4M8|Q9BRS4	Missense_Mutation	SNP	ENST00000526816.2	37	CCDS56095.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.957613	0.73902	.	.	ENSG00000028277	ENST00000389341;ENST00000342301;ENST00000292077;ENST00000533720;ENST00000526816;ENST00000529067;ENST00000529952	D;D;D;D;D	0.85861	-2.04;-2.04;-2.04;-2.04;-2.04	4.38	2.18	0.27775	POU-specific (4);Lambda repressor-like, DNA-binding (2);POU (1);	0.247967	0.39834	N	0.001250	D	0.91492	0.7314	M	0.88310	2.945	0.52501	D	0.999956	D;P;B	0.76494	0.999;0.953;0.262	D;D;B	0.79784	0.993;0.938;0.37	D	0.89325	0.3643	10	0.87932	D	0	.	6.8485	0.24003	0.15:0.0:0.1568:0.6932	.	223;239;223	P09086-4;P09086;P09086-3	.;PO2F2_HUMAN;.	A	223;239;239;223;238;223;239	ENSP00000373992:T223A;ENSP00000339369:T239A;ENSP00000437221:T223A;ENSP00000437224:T223A;ENSP00000436988:T239A	ENSP00000292077:T239A	T	-	1	0	POU2F2	47291870	1.000000	0.71417	0.972000	0.41901	0.994000	0.84299	7.819000	0.86621	0.269000	0.21961	0.454000	0.30748	ACG	.	.	none		0.627	POU2F2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387329.3			C	42600030	T	C	42600030	3	2	31	1	0	0	0	0	1	0	0	0	12281	1667	58	3	748	3	POU2F2	19	42600030	Missense_Mutation	SNP	T	TCGA-GR-A4D4-01A-11D-A31X-10	3668581	42600030	16528953	89	13955											
FKRP	79147	hgsc.bcm.edu	37	chr19	47258887	47258887	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggagttcgaggcatttgaCaacgcggtgcccgagctggt	7	8	16	10	5	0	1	0	1	0	0	1	4	0	2	1	4	3	3	1	4	1	2			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr19:47258887C>G	ENST00000318584.5	+	4	477	c.180C>G	c.(178-180)gaC>gaG	p.D60E	FKRP_ENST00000600646.1_Intron|FKRP_ENST00000391909.3_Missense_Mutation_p.D60E	NM_001039885.2|NM_024301.4	NP_001034974.1|NP_077277.1	Q9H9S5	FKRP_HUMAN	fukutin related protein	60					glycoprotein biosynthetic process (GO:0009101)|protein processing (GO:0016485)	dystrophin-associated glycoprotein complex (GO:0016010)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|rough endoplasmic reticulum (GO:0005791)|sarcolemma (GO:0042383)	transferase activity (GO:0016740)			NS(1)|large_intestine(1)|lung(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	7		all_epithelial(76;5.08e-05)|Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000541)|all cancers(93;0.00128)|Epithelial(262;0.0207)|GBM - Glioblastoma multiforme(486;0.0336)		AGGCATTTGACAACGCGGTGC	0.706																																					p.D60E		Atlas-SNP	.											.	FKRP	16	.	0			c.C180G						PASS	.						37	30	32					19																	47258887		2201	4300	6501	SO:0001583	missense	79147	exon4			ATTTGACAACGCG	AJ314847	CCDS12691.1	19q13.32	2014-09-17			ENSG00000181027	ENSG00000181027			17997	protein-coding gene	gene with protein product		606596				11592034, 11741828	Standard	NM_024301		Approved	LGMD2I, MDC1C	uc002pfp.2	Q9H9S5		ENST00000318584.5:c.180C>G	19.37:g.47258887C>G	ENSP00000326570:p.Asp60Glu	61	0	0		46	26	0.565217	NM_024301	A8K5G7	Missense_Mutation	SNP	ENST00000318584.5	37	CCDS12691.1	.	.	.	.	.	.	.	.	.	.	C	1.655	-0.512864	0.04200	.	.	ENSG00000181027	ENST00000391909;ENST00000318584	D;D	0.99277	-5.67;-5.67	4.79	4.79	0.61399	.	0.056531	0.64402	D	0.000002	D	0.92996	0.7771	N	0.01209	-0.955	0.38410	D	0.945893	B	0.20261	0.043	B	0.14023	0.01	D	0.91027	0.4861	10	0.02654	T	1	-33.5211	8.247	0.31695	0.1748:0.6561:0.1691:0.0	.	60	Q9H9S5	FKRP_HUMAN	E	60	ENSP00000375776:D60E;ENSP00000326570:D60E	ENSP00000326570:D60E	D	+	3	2	FKRP	51950727	0.999000	0.42202	1.000000	0.80357	0.801000	0.45260	0.458000	0.21892	2.491000	0.84063	0.555000	0.69702	GAC	.	.	none		0.706	FKRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465473.1	NM_024301		G	47258887	C	G	47258887	3	3	31	1	0	0	0	0	1	0	0	0	5925	477	17	4	182	4	FKRP	19	47258887	Missense_Mutation	SNP	C	TCGA-GR-A4D4-01A-11D-A31X-10	4658857	47258887	11870096	90	13956											
PTPRA	5786	hgsc.bcm.edu	37	chr20	3007337	3007337	+	Nonsense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccccttcccaattcagaagtTaacatcaatcaaaatccaga	16	9	3	13	0	3	2	3	0	0	2	5	2	5	2	4	0	1	1	4	0	6	3			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr20:3007337T>G	ENST00000216877.6	+	17	1992	c.1592T>G	c.(1591-1593)tTa>tGa	p.L531*	PTPRA_ENST00000425918.2_Nonsense_Mutation_p.L551*|PTPRA_ENST00000358719.4_Nonsense_Mutation_p.L396*|PTPRA_ENST00000356147.3_Nonsense_Mutation_p.L531*|PTPRA_ENST00000318266.5_Nonsense_Mutation_p.L531*|PTPRA_ENST00000380393.3_Nonsense_Mutation_p.L540*|PTPRA_ENST00000399903.2_Nonsense_Mutation_p.L540*	NM_080840.2	NP_543030.1	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	540					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						ATTCAGAAGTTAACATCAATC	0.463																																					p.L540X		Atlas-SNP	.											.	PTPRA	75	.	0			c.T1619G						PASS	.						80	64	69					20																	3007337		2203	4300	6503	SO:0001587	stop_gained	5786	exon22			AGAAGTTAACATC		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.1592T>G	20.37:g.3007337T>G	ENSP00000216877:p.Leu531*	89	0	0		80	24	0.3	NM_002836	A8K2G8|D3DVX5|Q14513|Q7Z2I2|Q96TD9	Nonsense_Mutation	SNP	ENST00000216877.6	37	CCDS13039.1	.	.	.	.	.	.	.	.	.	.	T	38	7.281920	0.98186	.	.	ENSG00000132670	ENST00000380393;ENST00000216877;ENST00000399903;ENST00000358719;ENST00000542217;ENST00000425918;ENST00000318266;ENST00000356147	.	.	.	5.49	5.49	0.81192	.	0.000000	0.64402	U	0.000007	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.8803	0.79197	0.0:0.0:0.0:1.0	.	.	.	.	X	540;531;540;396;150;551;531;531	.	ENSP00000216877:L531X	L	+	2	0	PTPRA	2955337	1.000000	0.71417	0.993000	0.49108	0.192000	0.23643	7.997000	0.88414	2.203000	0.70933	0.459000	0.35465	TTA	.	.	none		0.463	PTPRA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077682.3			G	3007337	T	G	3007337	4	3	31	1	0	0	0	0	0	1	0	0	12810	1764	61	5	1677	5	PTPRA	20	3007337	Nonsense_Mutation	SNP	T	TCGA-GR-A4D4-01A-11D-A31X-10		3007337	60018183	91	13957											
SIGLEC1	6614	hgsc.bcm.edu	37	chr20	3679921	3679921	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgggcccggcagtggtatgAgccggcgtcagtgctggagg	5	6	19	11	4	1	1	1	1	0	0	1	2	1	2	3	6	2	3	3	6	1	1			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr20:3679921A>G	ENST00000344754.4	-	7	1713	c.1714T>C	c.(1714-1716)Tca>Cca	p.S572P	SIGLEC1_ENST00000202578.4_Missense_Mutation_p.S572P	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	572	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						CAGTGGTATGAGCCGGCGTCA	0.672																																					p.S572P		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.T1714C						PASS	.						18	17	17					20																	3679921		2202	4296	6498	SO:0001583	missense	6614	exon7			GGTATGAGCCGGC	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.1714T>C	20.37:g.3679921A>G	ENSP00000341141:p.Ser572Pro	99	0	0		117	5	0.042735	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Missense_Mutation	SNP	ENST00000344754.4	37	CCDS13060.1	.	.	.	.	.	.	.	.	.	.	A	15.50	2.852055	0.51270	.	.	ENSG00000088827	ENST00000344754;ENST00000202578	T;T	0.12672	2.66;2.66	5.46	4.3	0.51218	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.000000	0.34986	N	0.003523	T	0.24122	0.0584	L	0.39898	1.24	0.37064	D	0.898214	D;D	0.76494	0.999;0.999	D;D	0.91635	0.999;0.994	T	0.05321	-1.0892	10	0.35671	T	0.21	.	8.8204	0.35023	0.8101:0.1899:0.0:0.0	.	572;572	Q9BZZ2;Q9BZZ2-3	SN_HUMAN;.	P	572	ENSP00000341141:S572P;ENSP00000202578:S572P	ENSP00000202578:S572P	S	-	1	0	SIGLEC1	3627921	0.258000	0.24033	0.989000	0.46669	0.183000	0.23260	0.313000	0.19415	2.081000	0.62600	0.533000	0.62120	TCA	.	.	none		0.672	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068		G	3679921	A	G	3679921	3	3	31	1	0	0	0	0	1	0	0	0	14320	304	11	3	3475	3	SIGLEC1	20	3679921	Missense_Mutation	SNP	A	TCGA-GR-A4D4-01A-11D-A31X-10	672584	3679921	59345599	92	13958											
SULF2	55959	hgsc.bcm.edu	37	chr20	46331406	46331406	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtattcattaagatacttccCgaagaaagctgcggagggag	13	9	12	7	2	1	2	1	0	0	2	2	5	2	4	1	2	3	2	1	2	5	5			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr20:46331406C>T	ENST00000359930.4	-	4	1275	c.424G>A	c.(424-426)Ggg>Agg	p.G142R	SULF2_ENST00000361612.4_Missense_Mutation_p.G142R|SULF2_ENST00000484875.1_Missense_Mutation_p.G142R|SULF2_ENST00000467815.1_Missense_Mutation_p.G142R	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	142					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						AGATACTTCCCGAAGAAAGCT	0.512																																					p.G142R		Atlas-SNP	.											.	SULF2	131	.	0			c.G424A						PASS	.						40	35	37					20																	46331406		2203	4300	6503	SO:0001583	missense	55959	exon4			ACTTCCCGAAGAA	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.424G>A	20.37:g.46331406C>T	ENSP00000353007:p.Gly142Arg	42	0	0		52	12	0.230769	NM_001161841	E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	Missense_Mutation	SNP	ENST00000359930.4	37	CCDS13408.1	.	.	.	.	.	.	.	.	.	.	C	33	5.285132	0.95517	.	.	ENSG00000196562	ENST00000359930;ENST00000484875;ENST00000361612;ENST00000467815;ENST00000437955	D;D;D;D;D	0.99859	-4.83;-4.83;-4.83;-4.83;-7.24	5.08	5.08	0.68730	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.99924	0.9965	H	0.98833	4.345	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	0.95859	0.8881	10	0.87932	D	0	-19.458	18.4712	0.90776	0.0:1.0:0.0:0.0	.	142;142;142	G3XAE6;Q8IWU5-2;Q8IWU5	.;.;SULF2_HUMAN	R	142	ENSP00000353007:G142R;ENSP00000418290:G142R;ENSP00000354662:G142R;ENSP00000418442:G142R;ENSP00000410026:G142R	ENSP00000353007:G142R	G	-	1	0	SULF2	45764813	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	7.814000	0.86154	2.355000	0.79922	0.561000	0.74099	GGG	.	.	none		0.512	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1	NM_018837		T	46331406	C	T	46331406	3	4	31	1	0	0	0	0	1	0	0	0	15386	652	23	1	2260	1	SULF2	20	46331406	Missense_Mutation	SNP	C	TCGA-GR-A4D4-01A-11D-A31X-10	42651485	46331406	16694114	93	13959											
DYRK1A	1859	hgsc.bcm.edu	37	chr21	38862627	38862627	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgcgcaacagatgtgcactgCactgcttttccttgcgactc	7	12	9	13	2	0	1	0	0	0	1	2	2	1	1	1	0	6	4	1	0	1	3			TCGA-GR-A4D4-01A-11D-A31X-10	TCGA-GR-A4D4-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	8f63ab7f-314f-4c7f-92cc-4f512ca6478e	32dbeee5-dae4-41d3-ac37-873569dcc6a9	g.chr21:38862627C>T	ENST00000398960.2	+	6	890	c.815C>T	c.(814-816)gCa>gTa	p.A272V	DYRK1A_ENST00000338785.3_Missense_Mutation_p.A272V|DYRK1A_ENST00000321219.8_Missense_Mutation_p.A272V|DYRK1A_ENST00000451934.1_Missense_Mutation_p.A272V|DYRK1A_ENST00000339659.4_Missense_Mutation_p.A263V|DYRK1A_ENST00000455387.2_Missense_Mutation_p.A44V|DYRK1A_ENST00000398956.2_Missense_Mutation_p.A272V	NM_001396.3|NM_130438.2	NP_001387.2|NP_569122.1	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A	272	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						ATGTGCACTGCACTGCTTTTC	0.428																																					p.A272V	Melanoma(114;464 1602 31203 43785 45765)	Atlas-SNP	.											.	DYRK1A	85	.	0			c.C815T						PASS	.						107	97	100					21																	38862627		2203	4300	6503	SO:0001583	missense	1859	exon6			GCACTGCACTGCT	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.815C>T	21.37:g.38862627C>T	ENSP00000381932:p.Ala272Val	148	0	0		142	36	0.253521	NM_001396	O60769|Q92582|Q92810|Q9UNM5	Missense_Mutation	SNP	ENST00000398960.2	37	CCDS42925.1	.	.	.	.	.	.	.	.	.	.	C	36	5.715261	0.96830	.	.	ENSG00000157540	ENST00000338785;ENST00000339659;ENST00000321219;ENST00000451934;ENST00000398960;ENST00000398956;ENST00000455387	T;T;T;T;T;T;T	0.31510	1.49;1.49;1.49;1.49;1.49;1.49;1.49	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);	0.000000	0.85682	D	0.000000	T	0.56558	0.1993	M	0.64997	1.995	0.80722	D	1	D;D;D;D;D	0.89917	0.988;0.988;1.0;1.0;0.988	P;P;D;D;P	0.79108	0.683;0.683;0.992;0.968;0.761	T	0.55289	-0.8164	10	0.87932	D	0	.	20.2989	0.98608	0.0:1.0:0.0:0.0	.	272;272;272;263;272	Q13627-3;Q13627-4;Q13627;Q13627-2;Q13627-5	.;.;DYR1A_HUMAN;.;.	V	272;263;272;272;272;272;44	ENSP00000342690:A272V;ENSP00000340373:A263V;ENSP00000319032:A272V;ENSP00000416089:A272V;ENSP00000381932:A272V;ENSP00000381929:A272V;ENSP00000407854:A44V	ENSP00000319032:A272V	A	+	2	0	DYRK1A	37784497	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.741000	0.84997	2.794000	0.96219	0.573000	0.79308	GCA	.	.	none		0.428	DYRK1A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194804.1	NM_001396		T	38862627	C	T	38862627	3	4	31	1	0	0	0	0	1	0	0	0	4856	710	25	2	837	2	DYRK1A	21	38862627	Missense_Mutation	SNP	C	TCGA-GR-A4D4-01A-11D-A31X-10		38862627	9267268	94	13960											
CHD5	26038	hgsc.bcm.edu	37	chr1	6196687	6196687	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaatcttgtagctgtttaaGaccctaaaaaactgagggga	14	11	9	7	0	2	2	1	1	1	1	2	3	2	3	1	2	2	3	1	2	6	5			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr1:6196687G>T	ENST00000262450.3	-	17	2685	c.2586C>A	c.(2584-2586)gtC>gtA	p.V862V	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)		AGCTGTTTAAGACCCTAAAAA	0.602																																					p.V862V		Atlas-SNP	.											.	CHD5	267	.	0			c.C2586A						PASS	.						43	53	50					1																	6196687		2203	4300	6503	SO:0001819	synonymous_variant	26038	exon17			GTTTAAGACCCTA	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.2586C>A	1.37:g.6196687G>T		85	0	0		72	7	0.0972222	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Silent	SNP	ENST00000262450.3	37	CCDS57.1																																																																																			.	.	none		0.602	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557		T	6196687	G	T	6196687	2	4	32	1	0	0	0	0	0	0	0	1	3330	929	33	4		4	CHD5	1	6196687	Silent	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10		6196687	243053934	1	13961											
BCAR3	8412	hgsc.bcm.edu	37	chr1	94032925	94032925	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatggttcagcatgatttcaCagctctggtcgtttttttcc	7	17	8	9	1	3	1	2	1	1	0	5	1	4	1	1	2	2	4	1	2	1	5			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr1:94032925C>G	ENST00000370244.1	-	13	2498	c.2210G>C	c.(2209-2211)tGt>tCt	p.C737S	BCAR3_ENST00000260502.6_Missense_Mutation_p.C737S|BCAR3_ENST00000539242.1_Missense_Mutation_p.C413S|BCAR3_ENST00000370247.3_Missense_Mutation_p.C646S|BCAR3_ENST00000370243.1_Missense_Mutation_p.C737S	NM_001261408.1	NP_001248337.1	O75815	BCAR3_HUMAN	breast cancer anti-estrogen resistance 3	737	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				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)		CATGATTTCACAGCTCTGGTC	0.517																																					p.C737S		Atlas-SNP	.											.	BCAR3	62	.	0			c.G2210C						PASS	.						168	143	152					1																	94032925		2203	4300	6503	SO:0001583	missense	8412	exon11			ATTTCACAGCTCT	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.2210G>C	1.37:g.94032925C>G	ENSP00000359264:p.Cys737Ser	116	0	0		97	4	0.0412371	NM_001261409	D3DT43|Q5TEW3|Q6UW40|Q9BR50	Missense_Mutation	SNP	ENST00000370244.1	37	CCDS745.1	.	.	.	.	.	.	.	.	.	.	C	34	5.336461	0.95758	.	.	ENSG00000137936	ENST00000370247;ENST00000260502;ENST00000370244;ENST00000370243;ENST00000539242	T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52	5.85	5.85	0.93711	Guanine-nucleotide dissociation stimulator CDC25 (2);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.46946	0.1419	M	0.64404	1.975	0.80722	D	1	P;D	0.69078	0.769;0.997	P;D	0.64877	0.456;0.93	T	0.35126	-0.9801	10	0.56958	D	0.05	-21.5128	20.1577	0.98120	0.0:1.0:0.0:0.0	.	737;646	O75815;Q5TEW3	BCAR3_HUMAN;.	S	646;737;737;737;413	ENSP00000359267:C646S;ENSP00000260502:C737S;ENSP00000359264:C737S;ENSP00000359263:C737S;ENSP00000441343:C413S	ENSP00000260502:C737S	C	-	2	0	BCAR3	93805513	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.461000	0.80834	2.767000	0.95098	0.655000	0.94253	TGT	.	.	none		0.517	BCAR3-003	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028420.1			G	94032925	C	G	94032925	3	3	32	1	0	0	0	0	1	0	0	0	1349	478	17	4	275	4	BCAR3	1	94032925	Missense_Mutation	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10	87836238	94032925	155217696	2	13962											
DNTTIP2	30836	hgsc.bcm.edu	37	chr1	94341909	94341909	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtctgatgaatcttcttcacTtttttcatcctcttcctctt	5	21	3	12	0	7	2	2	2	5	0	9	2	9	2	2	0	0	0	2	0	1	7			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr1:94341909T>C	ENST00000436063.2	-	2	1639	c.1582A>G	c.(1582-1584)Agt>Ggt	p.S528G	DNTTIP2_ENST00000460191.1_5'UTR	NM_014597.4	NP_055412.2	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 2	528					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.S528G(1)		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)		tcttcttcacttttttcatcc	0.368																																					p.S528G		Atlas-SNP	.											DNTTIP2,lymph_node,lymphoid_neoplasm,0,1	DNTTIP2	59	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.A1582G						PASS	.						137	120	125					1																	94341909		1856	4045	5901	SO:0001583	missense	30836	exon2			CTTCACTTTTTTC	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.1582A>G	1.37:g.94341909T>C	ENSP00000411010:p.Ser528Gly	125	0	0		90	7	0.0777778	NM_014597	Q12987|Q53H59|Q5TFJ4|Q6TLI0|Q76MJ8|Q86WX9	Missense_Mutation	SNP	ENST00000436063.2	37	CCDS44174.1	.	.	.	.	.	.	.	.	.	.	T	10.41	1.341819	0.24339	.	.	ENSG00000067334	ENST00000436063	T	0.17528	2.27	4.36	3.22	0.36961	.	2.882460	0.00834	N	0.001686	T	0.07098	0.0180	L	0.56769	1.78	0.28783	N	0.899718	B	0.29716	0.255	B	0.24394	0.053	T	0.17776	-1.0358	10	0.39692	T	0.17	.	5.0473	0.14490	0.0:0.3543:0.0:0.6457	.	528	Q5QJE6	TDIF2_HUMAN	G	528	ENSP00000411010:S528G	ENSP00000352137:S528G	S	-	1	0	DNTTIP2	94114497	0.172000	0.23043	0.804000	0.32291	0.784000	0.44337	0.933000	0.28897	0.992000	0.38840	0.533000	0.62120	AGT	.	.	none		0.368	DNTTIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028317.2	NM_014597		C	94341909	T	C	94341909	3	2	32	1	0	0	0	0	1	0	0	0	4684	1609	56	3	712	3	DNTTIP2	1	94341909	Missense_Mutation	SNP	T	TCGA-GR-A4D5-01A-11D-A31X-10	308984	94341909	154908712	3	13963											
IGSF3	3321	hgsc.bcm.edu	37	chr1	117142613	117142613	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tggaggtcctctccgccagtCgcgtccaggtgttgttgtag	4	12	14	11	3	1	0	0	0	1	0	5	1	3	1	4	3	0	3	4	3	1	3	rs76151115	byFrequency	TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr1:117142613C>T	ENST00000369486.3	-	7	2744	c.1979G>A	c.(1978-1980)cGa>cAa	p.R660Q	IGSF3_ENST00000369483.1_Missense_Mutation_p.R680Q|IGSF3_ENST00000318837.6_Missense_Mutation_p.R680Q	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	660	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)		CTCCGCCAGTCGCGTCCAGGT	0.612																																					p.R680Q		Atlas-SNP	.											.	IGSF3	294	.	0			c.G2039A						PASS	.						69	54	59					1																	117142613		2203	4300	6503	SO:0001583	missense	3321	exon8			GCCAGTCGCGTCC	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.1979G>A	1.37:g.117142613C>T	ENSP00000358498:p.Arg660Gln	39	0	0		46	10	0.217391	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	C	12.58	1.979753	0.34942	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.03212	4.01;4.04;4.04	4.56	2.7	0.31948	Immunoglobulin subtype (1);	0.270543	0.31010	N	0.008430	T	0.01353	0.0044	L	0.29908	0.895	0.36040	D	0.840027	D;D;D	0.59767	0.982;0.986;0.986	B;P;P	0.45310	0.345;0.476;0.476	T	0.64071	-0.6493	10	0.22706	T	0.39	-28.9658	8.7768	0.34767	0.0:0.8142:0.0:0.1858	.	680;660;680	O75054-2;O75054;A6NJZ6	.;IGSF3_HUMAN;.	Q	660;680;680	ENSP00000358498:R660Q;ENSP00000358495:R680Q;ENSP00000321184:R680Q	ENSP00000321184:R680Q	R	-	2	0	IGSF3	116944136	0.789000	0.28775	0.602000	0.28890	0.526000	0.34562	2.194000	0.42668	0.550000	0.28991	-0.384000	0.06662	CGA	C|0.967;T|0.033	0.033	strong		0.612	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542		T	117142613	C	T	117142613	3	4	32	1	0	0	0	0	1	0	0	0	7610	884	31	1	1625	1	IGSF3	1	117142613	Missense_Mutation	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10	22800704	117142613	132108008	4	13964											
SDHC	6391	hgsc.bcm.edu	37	chr1	161326591	161326591	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gctaagtttgcacttgtcttCcctctcatgtatcatacctg	7	16	6	12	0	3	0	2	0	2	0	5	0	4	0	2	0	2	4	2	0	3	6			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr1:161326591C>T	ENST00000367975.2	+	5	515	c.366C>T	c.(364-366)ttC>ttT	p.F122F	SDHC_ENST00000342751.4_Intron|SDHC_ENST00000392169.2_Silent_p.F69F|SDHC_ENST00000470743.3_3'UTR|SDHC_ENST00000513009.1_Intron|SDHC_ENST00000432287.2_Silent_p.F88F	NM_003001.3	NP_002992.1	Q99643	C560_HUMAN	succinate dehydrogenase complex, subunit C, integral membrane protein, 15kDa	122					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|oxidation-reduction process (GO:0055114)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)|respiratory chain complex II (GO:0045273)	electron carrier activity (GO:0009055)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|succinate dehydrogenase activity (GO:0000104)			urinary_tract(1)	1	all_cancers(52;6.96e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Succinic acid(DB00139)	CACTTGTCTTCCCTCTCATGT	0.483			"Mis, N, F"			"paraganglioma, pheochromocytoma"			Familial Paragangliomas;Carney-Stratakis syndrome																												p.F122F		Atlas-SNP	.	yes	Rec		Familial paraganglioma	1	1q21	6391	"succinate dehydrogenase complex, subunit C, integral membrane protein, 15kDa"		O	.	SDHC	19	.	0			c.C366T						PASS	.						170	158	162					1																	161326591		2203	4300	6503	SO:0001819	synonymous_variant	6391	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;Carney-Stratakis dyad, Paraganglioma-Gastric Stromal Sarcoma dyad	TGTCTTCCCTCTC	D49737	CCDS1230.1, CCDS41431.1, CCDS41432.1, CCDS44263.1, CCDS60330.1	1q23.3	2014-09-17	2002-08-29		ENSG00000143252	ENSG00000143252		"Mitochondrial respiratory chain complex / Complex II"	10682	protein-coding gene	gene with protein product		602413	"succinate dehydrogenase complex, subunit C, integral membrane protein, 15kD"	PGL3		9533030, 12658451	Standard	NM_001278172		Approved		uc001gag.3	Q99643	OTTHUMG00000034468	ENST00000367975.2:c.366C>T	1.37:g.161326591C>T		102	0	0		83	6	0.0722892	NM_003001	O75609|Q3C259|Q3C2D8|Q3C2H4|Q5VTH3	Silent	SNP	ENST00000367975.2	37	CCDS1230.1																																																																																			.	.	none		0.483	SDHC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083316.2	NM_003001		T	161326591	C	T	161326591	2	4	32	1	0	0	0	0	0	0	0	1	13981	854	30	2		2	SDHC	1	161326591	Silent	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10	44183978	161326591	87924030	5	13965											
CTSE	1510	hgsc.bcm.edu	37	chr1	206329027	206329027	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcaccattaacggagtcccCtataccctcagcccaactgc	10	9	5	17	1	2	0	2	0	0	0	3	1	3	1	5	1	5	0	5	1	4	4			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr1:206329027C>T	ENST00000360218.2	+	7	955	c.851C>T	c.(850-852)cCt>cTt	p.P284L	CTSE_ENST00000432969.2_Missense_Mutation_p.P209L|CTSE_ENST00000361052.3_Silent_p.P336P|CTSE_ENST00000358184.2_Silent_p.P331P	NM_148964.2	NP_683865.1	P14091	CATE_HUMAN	cathepsin E	0					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)			ACGGAGTCCCCTATACCCTCA	0.527																																					p.P284L		Atlas-SNP	.											.	CTSE	72	.	0			c.C851T						PASS	.						166	135	146					1																	206329027		2203	4300	6503	SO:0001583	missense	1510	exon7			AGTCCCCTATACC	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	ENST00000360218.2:c.851C>T	1.37:g.206329027C>T	ENSP00000353350:p.Pro284Leu	125	0	0		113	9	0.079646	NM_148964	Q5TZ01|Q5TZ02|Q9NY58|Q9UCE3|Q9UCE4	Missense_Mutation	SNP	ENST00000360218.2	37	CCDS1461.1	.	.	.	.	.	.	.	.	.	.	c	12.35	1.910655	0.33721	.	.	ENSG00000196188	ENST00000360218;ENST00000432969	T;T	0.62788	0.67;0.0	5.3	2.21	0.28008	.	0.643045	0.15132	N	0.278775	T	0.44973	0.1319	.	.	.	0.24200	N	0.995516	B;B	0.14438	0.006;0.01	B;B	0.13407	0.004;0.009	T	0.41360	-0.9513	9	0.87932	D	0	.	2.459	0.04537	0.1543:0.4224:0.2816:0.1417	.	209;284	B4DNU8;P14091-2	.;.	L	284;209	ENSP00000353350:P284L;ENSP00000394607:P209L	ENSP00000353350:P284L	P	+	2	0	CTSE	204495650	0.000000	0.05858	0.775000	0.31657	0.173000	0.22820	-0.176000	0.09811	0.717000	0.32145	0.637000	0.83480	CCT	.	.	none		0.527	CTSE-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000087999.1	NM_001910		T	206329027	C	T	206329027	3	4	32	1	0	0	0	0	1	0	0	0	4035	681	24	2	1023	2	CTSE	1	206329027	Missense_Mutation	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10	45002436	206329027	42921594	6	13966											
CDC42BPA	8476	hgsc.bcm.edu	37	chr1	227279603	227279603	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaccttatcaagttcactcGtcagctttttattttcttca	8	19	3	11	1	6	0	5	0	1	0	7	0	6	0	1	0	1	2	1	0	3	8	rs56119119		TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr1:227279603G>A	ENST00000366769.3	-	16	3630	c.2339C>T	c.(2338-2340)aCg>aTg	p.T780M	CDC42BPA_ENST00000366767.3_Missense_Mutation_p.T699M|CDC42BPA_ENST00000535525.1_Missense_Mutation_p.T780M|CDC42BPA_ENST00000366764.2_Missense_Mutation_p.T780M|CDC42BPA_ENST00000366766.2_Missense_Mutation_p.T780M|CDC42BPA_ENST00000334218.5_Missense_Mutation_p.T780M|CDC42BPA_ENST00000366765.3_Missense_Mutation_p.T780M	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)				AAGTTCACTCGTCAGCTTTTT	0.313																																					p.T780M		Atlas-SNP	.											CDC42BPA_ENST00000366769,NS,carcinoma,0,3	CDC42BPA	528	3	0			c.C2339T						PASS	.	G	MET/THR,MET/THR	0,4402		0,0,2201	182	173	176		2339,2096	5.1	1	1	dbSNP_129	176	4,8588	3.7+/-12.6	0,4,4292	yes	missense,missense	CDC42BPA	NM_003607.3,NM_014826.4	81,81	0,4,6493	AA,AG,GG		0.0466,0.0,0.0308	benign,benign	780/1720,699/1639	227279603	4,12990	2201	4296	6497	SO:0001583	missense	8476	exon16			TCACTCGTCAGCT	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.2339C>T	1.37:g.227279603G>A	ENSP00000355731:p.Thr780Met	120	0	0		83	5	0.060241	NM_003607		Missense_Mutation	SNP	ENST00000366769.3	37	CCDS1558.1	.	.	.	.	.	.	.	.	.	.	G	18.63	3.665839	0.67700	0.0	4.66E-4	ENSG00000143776	ENST00000366769;ENST00000366767;ENST00000334218;ENST00000366766;ENST00000366764;ENST00000366762;ENST00000535525;ENST00000366765	T;T;T;T;T;T;T	0.66460	-0.21;0.96;-0.21;-0.19;0.96;-0.19;-0.21	5.09	5.09	0.68999	.	0.054763	0.85682	D	0.000000	T	0.71426	0.3338	N	0.25485	0.75	0.31652	N	0.646716	D;B;D;B;B	0.58620	0.983;0.055;0.976;0.121;0.26	P;B;D;B;B	0.63033	0.73;0.02;0.91;0.065;0.095	T	0.72915	-0.4147	10	0.40728	T	0.16	.	18.855	0.92247	0.0:0.0:1.0:0.0	rs56119119	780;780;699;780;780	F5H5N0;Q5VT25-4;Q5VT25-3;Q5VT25-5;Q5VT25-2	.;.;.;.;.	M	780;699;780;780;780;44;780;780	ENSP00000355731:T780M;ENSP00000355729:T699M;ENSP00000335341:T780M;ENSP00000355728:T780M;ENSP00000355726:T780M;ENSP00000443275:T780M;ENSP00000355727:T780M	ENSP00000335341:T780M	T	-	2	0	CDC42BPA	225346226	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.769000	0.91742	2.537000	0.85549	0.557000	0.71058	ACG	G|1.000;A|0.000	0.000	weak		0.313	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826		A	227279603	G	A	227279603	3	1	32	1	0	0	0	0	1	0	0	0	3074	1145	40	1	2904	1	CDC42BPA	1	227279603	Missense_Mutation	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10	20950576	227279603	21971018	7	13967											
APOB	338	hgsc.bcm.edu	37	chr2	21239442	21239442	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgaggtcaacatcaaaatcCggaatttggacttcactgga	13	9	9	10	2	3	0	3	0	0	0	4	4	4	3	2	4	1	0	2	4	4	2	rs200281277	byFrequency	TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr2:21239442C>T	ENST00000233242.1	-	21	3328	c.3201G>A	c.(3199-3201)ccG>ccA	p.P1067P		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1067					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)					CATCAAAATCCGGAATTTGGA	0.433													C|||	2	0.000399361	0.0	0.0	5008	,	,		18827	0.002		0.0	False		,,,				2504	0.0				p.P1067P		Atlas-SNP	.											.	APOB	761	.	0			c.G3201A						PASS	.						139	124	129					2																	21239442		2203	4300	6503	SO:0001819	synonymous_variant	338	exon21			AAAATCCGGAATT	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.3201G>A	2.37:g.21239442C>T		202	0	0		136	12	0.0882353	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Silent	SNP	ENST00000233242.1	37	CCDS1703.1																																																																																			C|1.000;T|0.000	0.000	strong		0.433	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			T	21239442	C	T	21239442	2	4	32	1	0	0	0	0	0	0	0	1	785	639	23	1		1	APOB	2	21239442	Silent	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10		21239442	221959931	8	13968											
NRXN1	9378	hgsc.bcm.edu	37	chr2	50765586	50765586	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gatatctttgctttggccatCgatgaacaaatccctgatgc	10	13	8	10	1	1	2	0	2	1	0	3	4	2	2	2	1	3	1	2	1	3	3	rs202137841		TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr2:50765586C>T	ENST00000406316.2	-	10	3424	c.1948G>A	c.(1948-1950)Gat>Aat	p.D650N	NRXN1_ENST00000406859.3_Missense_Mutation_p.D650N|NRXN1_ENST00000401669.2_Missense_Mutation_p.D650N|NRXN1_ENST00000331040.5_5'UTR|NRXN1_ENST00000402717.3_Missense_Mutation_p.D642N|NRXN1_ENST00000404971.1_Missense_Mutation_p.D690N|NRXN1_ENST00000405472.3_Missense_Mutation_p.D642N	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	650	Laminin G-like 3. {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)			CTTTGGCCATCGATGAACAAA	0.512																																					p.D690N		Atlas-SNP	.											.	NRXN1	1118	.	0			c.G2068A						PASS	.						207	221	216					2																	50765586		2198	4299	6497	SO:0001583	missense	9378	exon11			GGCCATCGATGAA	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.1948G>A	2.37:g.50765586C>T	ENSP00000384311:p.Asp650Asn	171	0	0		110	12	0.109091	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Missense_Mutation	SNP	ENST00000406316.2	37	CCDS54360.1	.	.	.	.	.	.	.	.	.	.	C	27.6	4.849430	0.91277	.	.	ENSG00000179915	ENST00000404971;ENST00000406316;ENST00000405472;ENST00000401669;ENST00000536085;ENST00000402717;ENST00000406859	T;T;T;T;T;T	0.63744	-0.06;-0.06;-0.06;-0.06;-0.06;-0.06	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.71187	0.3310	L	0.38175	1.15	0.50632	D	0.999885	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.991	T	0.65265	-0.6210	10	0.22706	T	0.39	.	18.8479	0.92215	0.0:1.0:0.0:0.0	.	690;650;642	Q9ULB1-3;F8WB18;A7E294	.;.;.	N	690;650;642;650;691;642;650	ENSP00000385142:D690N;ENSP00000384311:D650N;ENSP00000434015:D642N;ENSP00000385017:D650N;ENSP00000385434:D642N;ENSP00000385681:D650N	ENSP00000385017:D650N	D	-	1	0	NRXN1	50619090	1.000000	0.71417	0.636000	0.29352	0.971000	0.66376	7.651000	0.83577	2.682000	0.91365	0.585000	0.79938	GAT	.	.	alt		0.512	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2			T	50765586	C	T	50765586	3	4	32	1	0	0	0	0	1	0	0	0	10674	884	31	1	2894	1	NRXN1	2	50765586	Missense_Mutation	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10	29526144	50765586	192433787	9	13969											
ADRA2B	151	hgsc.bcm.edu	37	chr2	96781704	96781704	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agaaagggatgatgagcgtgGccaccaggatgtcggcggcg	10	5	18	8	4	0	3	0	2	0	1	1	5	0	5	2	5	1	0	2	5	1	0			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr2:96781704G>A	ENST00000409345.3	-	1	280	c.185C>T	c.(184-186)gCc>gTc	p.A62V		NM_000682.5	NP_000673	P18089	ADA2B_HUMAN	adrenoceptor alpha 2B	62					activation of MAPK activity by adrenergic receptor signaling pathway (GO:0071883)|activation of protein kinase B activity (GO:0032148)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|MAPK cascade (GO:0000165)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of norepinephrine secretion (GO:0010700)|platelet activation (GO:0030168)|positive regulation of blood pressure (GO:0045777)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of uterine smooth muscle contraction (GO:0070474)|regulation of vascular smooth muscle contraction (GO:0003056)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha2-adrenergic receptor activity (GO:0004938)|epinephrine binding (GO:0051379)			endometrium(2)|large_intestine(2)|lung(9)|ovary(3)	16					Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Apraclonidine(DB00964)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bethanidine(DB00217)|Brimonidine(DB00484)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Desipramine(DB01151)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Etomidate(DB00292)|Fenoldopam(DB00800)|Guanabenz(DB00629)|Guanfacine(DB01018)|Lisuride(DB00589)|Loxapine(DB00408)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Prazosin(DB00457)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Tizanidine(DB00697)|Tolazoline(DB00797)|Trimipramine(DB00726)|Xylometazoline(DB06694)|Yohimbine(DB01392)|Ziprasidone(DB00246)	GATGAGCGTGGCCACCAGGAT	0.657																																					p.A62V		Atlas-SNP	.											.	ADRA2B	115	.	0			c.C185T						PASS	.						45	51	49					2																	96781704		2202	4300	6502	SO:0001583	missense	151	exon1			AGCGTGGCCACCA	M34041	CCDS56129.1	2q11.1	2014-05-06	2012-05-09		ENSG00000222040	ENSG00000274286		"GPCR / Class A : Adrenoceptors : alpha"	282	protein-coding gene	gene with protein product		104260	"adrenergic, alpha-2B-, receptor"	ADRA2L1, ADRA2RL1		2164221	Standard	NM_000682		Approved	ADRARL1	uc021vlh.1	P18089	OTTHUMG00000188276	ENST00000409345.3:c.185C>T	2.37:g.96781704G>A	ENSP00000387281:p.Ala62Val	142	0	0		117	9	0.0769231	NM_000682	Q4TUH9|Q53RF2|Q9BZK0	Missense_Mutation	SNP	ENST00000409345.3	37	CCDS56129.1	.	.	.	.	.	.	.	.	.	.	g	29.4	5.000455	0.93227	.	.	ENSG00000222040	ENST00000409345	T	0.13538	2.58	4.48	4.48	0.54585	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.48537	0.1505	H	0.95950	3.745	0.54753	D	0.999982	D	0.69078	0.997	D	0.65323	0.934	T	0.66408	-0.5931	9	0.87932	D	0	.	14.755	0.69557	0.0:0.0:1.0:0.0	.	62	P18089	ADA2B_HUMAN	V	62	ENSP00000387281:A62V	ENSP00000387281:A62V	A	-	2	0	ADRA2B	96145431	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.654000	0.98509	2.334000	0.79466	0.450000	0.29827	GCC	.	.	none		0.657	ADRA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334990.1			A	96781704	G	A	96781704	3	1	32	1	0	0	0	0	1	0	0	0	338	1203	42	2	1162	2	ADRA2B	2	96781704	Missense_Mutation	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10	46016118	96781704	146417669	10	13970											
CXCR4	7852	hgsc.bcm.edu	37	chr2	136875620	136875620	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgaaactggacttacactgAtcccctccatggtaaccgct	10	11	7	13	1	0	2	0	2	0	0	2	3	2	3	4	2	3	2	4	2	3	3			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr2:136875620A>C	ENST00000241393.3	-	1	115	c.11T>G	c.(10-12)aTc>aGc	p.I4S	CXCR4_ENST00000409817.1_5'Flank|CXCR4_ENST00000466288.1_5'Flank	NM_003467.2	NP_003458.1	P61073	CXCR4_HUMAN	chemokine (C-X-C motif) receptor 4	4	Important for chemokine binding, signaling and HIV-1 coreceptor activity.				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)	ACTTACACTGATCCCCTCCAT	0.557																																					p.I4S		Atlas-SNP	.											.	CXCR4	51	.	0			c.T11G						PASS	.						55	61	59					2																	136875620		1947	4140	6087	SO:0001583	missense	7852	exon1			ACACTGATCCCCT	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.11T>G	2.37:g.136875620A>C	ENSP00000241393:p.Ile4Ser	61	0	0		56	5	0.0892857	NM_003467	B2R5N0|O60835|P30991|P56438|Q53S69|Q9BXA0|Q9UKN2	Missense_Mutation	SNP	ENST00000241393.3	37	CCDS46420.1	.	.	.	.	.	.	.	.	.	.	A	14.24	2.476334	0.44044	.	.	ENSG00000121966	ENST00000241393	T	0.60548	0.18	4.14	4.14	0.48551	.	.	.	.	.	T	0.38931	0.1059	N	0.14661	0.345	0.24453	N	0.994476	B	0.14012	0.009	B	0.15484	0.013	T	0.15235	-1.0444	9	0.30854	T	0.27	.	9.8281	0.40925	1.0:0.0:0.0:0.0	.	4	P61073	CXCR4_HUMAN	S	4	ENSP00000241393:I4S	ENSP00000241393:I4S	I	-	2	0	CXCR4	136592090	0.206000	0.23470	0.143000	0.22291	0.767000	0.43475	2.871000	0.48459	2.091000	0.63221	0.455000	0.32223	ATC	.	.	none		0.557	CXCR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331732.1			C	136875620	A	C	136875620	3	2	32	1	0	0	0	0	1	0	0	0	4095	333	12	5	1082	5	CXCR4	2	136875620	Missense_Mutation	SNP	A	TCGA-GR-A4D5-01A-11D-A31X-10	40093916	136875620	106323753	11	13971											
PTPRG	5793	hgsc.bcm.edu	37	chr3	62189308	62189308	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagaagagtggggtgacccaCgctgccgaggagcggaatca	11	4	17	9	3	1	3	1	1	0	2	1	7	1	5	2	4	2	1	2	4	2	0	rs150936656		TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr3:62189308C>T	ENST00000474889.1	+	12	2216	c.1839C>T	c.(1837-1839)caC>caT	p.H613H	PTPRG_ENST00000295874.10_Silent_p.H613H	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	613					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)		GGGTGACCCACGCTGCCGAGG	0.602																																					p.H613H		Atlas-SNP	.											.	PTPRG	153	.	0			c.C1839T						PASS	.	C		0,4346		0,0,2173	87	56	66		1839	-0.8	0	3	dbSNP_134	66	1,8519		0,1,4259	no	coding-synonymous	PTPRG	NM_002841.3		0,1,6432	TT,TC,CC		0.0117,0.0,0.0078		613/1446	62189308	1,12865	2173	4260	6433	SO:0001819	synonymous_variant	5793	exon12			GACCCACGCTGCC	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.1839C>T	3.37:g.62189308C>T		179	0	0		125	16	0.128	NM_002841	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Silent	SNP	ENST00000474889.1	37	CCDS2895.1																																																																																			C|1.000;T|0.000	0.000	weak		0.602	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841		T	62189308	C	T	62189308	2	4	32	1	0	0	0	0	0	0	0	1	12817	535	19	1		1	PTPRG	3	62189308	Silent	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10		62189308	135833122	12	13972											
CRIPAK	285464	hgsc.bcm.edu	37	chr4	1389063	1389063	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	tgcccgcctgctcacgtgccGatgtggagtgcccgcctgct	3	9	13	16	4	1	0	1	0	0	0	1	2	1	1	5	1	5	2	5	1	0	0	rs148588369	byFrequency	TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr4:1389063G>C	ENST00000324803.4	+	1	3724	c.764G>C	c.(763-765)cGa>cCa	p.R255P		NM_175918.3	NP_787114.2	Q8N1N5	CRPAK_HUMAN	cysteine-rich PAK1 inhibitor	255					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of protein kinase activity (GO:0006469)|regulation of cytoskeleton organization (GO:0051493)|response to estrogen (GO:0043627)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R255P(1)		NS(3)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(1)	35			OV - Ovarian serous cystadenocarcinoma(23;0.0106)			CTCACGTGCCGATGTGGAGTG	0.682													g|||	168	0.0335463	0.087	0.013	5008	,	,		12257	0.0169		0.007	False		,,,				2504	0.0204				p.R255P		Atlas-SNP	.											CRIPAK,NS,carcinoma,0,1	CRIPAK	185	1	1	Substitution - Missense(1)	prostate(1)	c.G764C						scavenged	.	C	PRO/ARG	237,4167		9,219,1974	160	142	148		764	-0.2	0	4	dbSNP_134	148	16,8582		2,12,4285	no	missense	CRIPAK	NM_175918.3	103	11,231,6259	CC,CG,GG		0.1861,5.3815,1.9459	probably-damaging	255/447	1389063	253,12749	2202	4299	6501	SO:0001583	missense	285464	exon1			CGTGCCGATGTGG	AK096209	CCDS3349.1	4p16.3	2011-02-10	2006-09-04		ENSG00000179979	ENSG00000179979			26619	protein-coding gene	gene with protein product		610203	"cysteine-rich PAK1inhibitor"			16278681	Standard	NM_175918		Approved	FLJ34443	uc003gdf.2	Q8N1N5	OTTHUMG00000121131	ENST00000324803.4:c.764G>C	4.37:g.1389063G>C	ENSP00000323978:p.Arg255Pro	48	1	0.0208333		43	4	0.0930233	NM_175918	Q8NB03	Missense_Mutation	SNP	ENST00000324803.4	37	CCDS3349.1	.	.	.	.	.	.	.	.	.	.	-	0.914	-0.718231	0.03182	0.053815	0.001861	ENSG00000179979	ENST00000324803;ENST00000382944	T	0.22743	1.94	0.815	-0.148	0.13424	Post-SET domain (1);	.	.	.	.	T	0.01061	0.0035	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.34675	-0.9819	9	0.07482	T	0.82	.	4.0747	0.09899	0.0:0.5464:0.2553:0.1983	.	255	Q8N1N5	CRPAK_HUMAN	P	255;197	ENSP00000323978:R255P	ENSP00000323978:R255P	R	+	2	0	CRIPAK	1379063	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.274000	0.01163	-1.652000	0.01502	-2.723000	0.00131	CGA	G|0.982;C|0.018	0.018	strong		0.682	CRIPAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241607.2	NM_175918		C	1389063	G	C	1389063	3	2	32	1	0	0	0	0	1	0	0	0	3879	1058	37	4	766	4	CRIPAK	4	1389063	Missense_Mutation	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10		1389063	189765213	13	13973											
CPZ	8532	hgsc.bcm.edu	37	chr4	8608504	8608504	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacgagcgggaggcagaacgCgcagaacctggatctgaacc	12	3	15	11	4	1	3	0	1	1	2	1	7	1	5	2	3	4	2	2	3	3	0			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr4:8608504C>T	ENST00000360986.4	+	6	1121	c.947C>T	c.(946-948)gCg>gTg	p.A316V	CPZ_ENST00000429646.2_5'UTR|CPZ_ENST00000382480.2_Missense_Mutation_p.A179V|CPZ_ENST00000315782.6_Missense_Mutation_p.A305V	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	316					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						AGGCAGAACGCGCAGAACCTG	0.657																																					p.A316V		Atlas-SNP	.											CPZ,rectum,carcinoma,+1,1	CPZ	95	1	0			c.C947T						PASS	.						70	69	69					4																	8608504		2203	4300	6503	SO:0001583	missense	8532	exon6			AGAACGCGCAGAA	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.947C>T	4.37:g.8608504C>T	ENSP00000354255:p.Ala316Val	208	0	0		157	15	0.0955414	NM_001014447	O00520|Q96MX2	Missense_Mutation	SNP	ENST00000360986.4	37	CCDS33953.1	.	.	.	.	.	.	.	.	.	.	c	17.32	3.359187	0.61403	.	.	ENSG00000109625	ENST00000360986;ENST00000382480;ENST00000315782	T;T;T	0.03920	3.76;3.76;3.76	3.31	3.31	0.37934	Peptidase M14, carboxypeptidase A (2);	0.202783	0.41605	N	0.000853	T	0.08044	0.0201	M	0.85197	2.74	0.80722	D	1	P;B	0.37207	0.587;0.17	B;B	0.23574	0.047;0.013	T	0.14531	-1.0469	10	0.49607	T	0.09	-20.6085	12.9837	0.58579	0.0:1.0:0.0:0.0	.	305;316	Q66K79-2;Q66K79	.;CBPZ_HUMAN	V	316;179;305	ENSP00000354255:A316V;ENSP00000371920:A179V;ENSP00000315074:A305V	ENSP00000315074:A305V	A	+	2	0	CPZ	8659404	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	5.155000	0.64900	1.672000	0.50884	0.450000	0.29827	GCG	.	.	none		0.657	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652		T	8608504	C	T	8608504	3	4	32	1	0	0	0	0	1	0	0	0	3841	768	27	1	969	1	CPZ	4	8608504	Missense_Mutation	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10	7219441	8608504	182545772	14	13974											
KDR	3791	hgsc.bcm.edu	37	chr4	55968617	55968617	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgcatgagacttcgatgctTtccccaatacttgtcgtctg	7	14	9	11	2	1	1	0	1	1	1	4	3	2	1	2	0	3	2	2	0	2	4			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr4:55968617T>G	ENST00000263923.4	-	14	2341	c.2046A>C	c.(2044-2046)gaA>gaC	p.E682D		NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	682	Ig-like C2-type 7.				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)	CTTCGATGCTTTCCCCAATAC	0.438			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)																											p.E682D		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	.	KDR	307	.	0			c.A2046C						PASS	.						191	160	171					4																	55968617		2203	4300	6503	SO:0001583	missense	3791	exon14			GATGCTTTCCCCA	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.2046A>C	4.37:g.55968617T>G	ENSP00000263923:p.Glu682Asp	173	0	0		111	6	0.0540541	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	37	CCDS3497.1	.	.	.	.	.	.	.	.	.	.	T	4.280	0.051088	0.08243	.	.	ENSG00000128052	ENST00000263923	D	0.82344	-1.6	6.02	0.114	0.14639	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.105014	0.64402	D	0.000004	T	0.65616	0.2708	N	0.11364	0.135	0.39576	D	0.969365	B	0.27140	0.169	B	0.36030	0.216	T	0.48833	-0.9000	10	0.09590	T	0.72	.	9.6807	0.40067	0.0:0.3153:0.0:0.6847	.	682	P35968	VGFR2_HUMAN	D	682	ENSP00000263923:E682D	ENSP00000263923:E682D	E	-	3	2	KDR	55663374	1.000000	0.71417	0.988000	0.46212	0.095000	0.18619	0.945000	0.29056	-0.165000	0.10908	0.533000	0.62120	GAA	.	.	none		0.438	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			G	55968617	T	G	55968617	3	3	32	1	0	0	0	0	1	0	0	0	8148	1838	64	5	2092	5	KDR	4	55968617	Missense_Mutation	SNP	T	TCGA-GR-A4D5-01A-11D-A31X-10	47360113	55968617	135185659	15	13975											
TIGD2	166815	hgsc.bcm.edu	37	chr4	90034738	90034738	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtacttctgggtgtaggtcaAgcagagagagaatcatcatt	12	11	12	6	0	4	2	3	0	1	2	4	4	4	2	0	2	2	3	0	2	4	4			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr4:90034738A>G	ENST00000317005.2	+	1	771	c.613A>G	c.(613-615)Agc>Ggc	p.S205G	FAM13A_ENST00000502459.1_5'Flank|RP11-84C13.1_ENST00000603357.1_lincRNA	NM_145715.2	NP_663761.1	Q4W5G0	TIGD2_HUMAN	tigger transposable element derived 2	205	DDE.					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)		GTGTAGGTCAAGCAGAGAGAG	0.413																																					p.S205G		Atlas-SNP	.											.	TIGD2	36	.	0			c.A613G						PASS	.						74	77	76					4																	90034738		2203	4299	6502	SO:0001583	missense	166815	exon1			AGGTCAAGCAGAG	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.613A>G	4.37:g.90034738A>G	ENSP00000317170:p.Ser205Gly	145	0	0		97	7	0.0721649	NM_145715		Missense_Mutation	SNP	ENST00000317005.2	37	CCDS3633.1	.	.	.	.	.	.	.	.	.	.	a	4.701	0.130320	0.08981	.	.	ENSG00000180346	ENST00000317005	T	0.41065	1.01	3.97	3.97	0.46021	.	0.000000	0.39083	U	0.001480	T	0.32852	0.0843	L	0.53671	1.685	0.26228	N	0.979052	B	0.16166	0.016	B	0.15052	0.012	T	0.14839	-1.0458	10	0.17832	T	0.49	-3.6072	7.4637	0.27310	0.7792:0.2208:0.0:0.0	.	205	Q4W5G0	TIGD2_HUMAN	G	205	ENSP00000317170:S205G	ENSP00000317170:S205G	S	+	1	0	TIGD2	90253761	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	4.010000	0.57117	1.682000	0.51000	0.446000	0.29264	AGC	.	.	none		0.413	TIGD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253545.2	NM_145715		G	90034738	A	G	90034738	3	3	32	1	0	0	0	0	1	0	0	0	15911	72	3	3	615	3	TIGD2	4	90034738	Missense_Mutation	SNP	A	TCGA-GR-A4D5-01A-11D-A31X-10	34066121	90034738	101119538	16	13976											
MSH3	4437	hgsc.bcm.edu	37	chr5	79950715	79950715	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gcgctgcagcggctgcagcgGccgcagcggccgcagcgccc	4	2	17	18	7	0	0	0	0	0	0	0	0	0	0	3	3	6	6	3	3	0	0	rs144776112|rs201874762		TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr5:79950715G>C	ENST00000265081.6	+	1	249	c.169G>C	c.(169-171)Gcc>Ccc	p.A57P	DHFR_ENST00000513048.1_5'Flank|DHFR_ENST00000439211.2_5'UTR|DHFR_ENST00000511032.1_5'Flank|DHFR_ENST00000504396.1_5'Flank|DHFR_ENST00000505337.1_5'Flank	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	57	Poly-Ala.		Missing. {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8942985}.		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)		ggctgcagcggccgcagcggc	0.692								Mismatch excision repair (MMR)																													p.A57P	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											MSH3_ENST00000265081,NS,carcinoma,0,1	MSH3	129	1	0			c.G169C						PASS	.						7	7	7					5																	79950715		2089	4077	6166	SO:0001583	missense	4437	exon1			GCAGCGGCCGCAG	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.169G>C	5.37:g.79950715G>C	ENSP00000265081:p.Ala57Pro	15	0	0		47	17	0.361702	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	37	CCDS34195.1	362	0.16575091575091574	115	0.23373983739837398	67	0.1850828729281768	32	0.055944055944055944	148	0.19525065963060687	-	0.222	-1.028222	0.02045	.	.	ENSG00000113318	ENST00000265081	D	0.87256	-2.23	.	.	.	.	.	.	.	.	T	0.00039	0.0001	N	0.03608	-0.345	0.80722	P	0.0	.	.	.	.	.	.	T	0.02983	-1.1086	3	.	.	.	.	.	.	.	.	57	P20585	MSH3_HUMAN	P	57	ENSP00000265081:A57P	.	A	+	1	0	MSH3	79986471	0.041000	0.20044	0.049000	0.19019	0.152000	0.21847	0.000000	0.12993	0.000000	0.14550	0.000000	0.15137	GCC	G|0.835;C|0.165	0.165	strong		0.692	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		C	79950715	G	C	79950715	3	2	32	1	0	0	0	0	1	0	0	0	9880	1203	42	4	171	4	MSH3	5	79950715	Missense_Mutation	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10		79950715	100964545	17	13977											
PCDHA4	56144	hgsc.bcm.edu	37	chr5	140186810	140186810	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagcggccaggaatcccggcGtctgctgctcttacttcttc	6	11	10	14	3	3	0	0	0	3	0	5	1	4	1	2	3	4	2	2	3	3	3			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr5:140186810G>A	ENST00000530339.1	+	1	38	c.38G>A	c.(37-39)cGt>cAt	p.R13H	PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Missense_Mutation_p.R13H|PCDHA4_ENST00000356878.4_Missense_Mutation_p.R13H	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	13					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)			GAATCCCGGCGTCTGCTGCTC	0.522																																					p.R13H		Atlas-SNP	.											.	PCDHA4	419	.	0			c.G38A						PASS	.						77	86	83					5																	140186810		2203	4300	6503	SO:0001583	missense	56144	exon1			CCCGGCGTCTGCT	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.38G>A	5.37:g.140186810G>A	ENSP00000435300:p.Arg13His	111	0	0		80	6	0.075	NM_031500	O75285|Q2M253	Missense_Mutation	SNP	ENST00000530339.1	37	CCDS54916.1	.	.	.	.	.	.	.	.	.	.	g	9.674	1.147430	0.21288	.	.	ENSG00000204967	ENST00000512229;ENST00000356878;ENST00000530339	T;T;T	0.52526	0.71;0.66;0.68	4.55	2.63	0.31362	.	0.435566	0.16599	U	0.207426	T	0.37100	0.0991	L	0.60455	1.87	0.09310	N	1	B;B;B	0.17268	0.021;0.007;0.007	B;B;B	0.10450	0.005;0.004;0.002	T	0.22906	-1.0203	10	0.13470	T	0.59	.	6.4619	0.21960	0.1637:0.1655:0.6708:0.0	.	13;13;13	Q9UN74-2;Q9UN74;D6RA20	.;PCDA4_HUMAN;.	H	13	ENSP00000423470:R13H;ENSP00000349344:R13H;ENSP00000435300:R13H	ENSP00000349344:R13H	R	+	2	0	PCDHA4	140166994	0.056000	0.20664	0.746000	0.31095	0.800000	0.45204	1.920000	0.40025	0.980000	0.38523	0.467000	0.42956	CGT	.	.	none		0.522	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		A	140186810	G	A	140186810	3	1	32	1	0	0	0	0	1	0	0	0	11535	1145	40	1	40	1	PCDHA4	5	140186810	Missense_Mutation	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10	60236095	140186810	40728450	18	13978											
PCDHA12	56137	hgsc.bcm.edu	37	chr5	140257190	140257190	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtgcggtgtccagcctgctGgtgctcacgctgctgctgta	3	12	14	12	2	1	0	1	0	0	0	2	0	2	0	2	2	6	6	2	2	1	1			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr5:140257190G>C	ENST00000398631.2	+	1	2133	c.2133G>C	c.(2131-2133)ctG>ctC	p.L711L	PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	711					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)			CCAGCCTGCTGGTGCTCACGC	0.677																																					p.L711L	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											.	PCDHA12	196	.	0			c.G2133C						PASS	.						40	39	40					5																	140257190		2203	4300	6503	SO:0001819	synonymous_variant	56137	exon1			CCTGCTGGTGCTC	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.2133G>C	5.37:g.140257190G>C		122	0	0		95	15	0.157895	NM_018903	O75278|Q2M1N8	Silent	SNP	ENST00000398631.2	37	CCDS47285.1																																																																																			.	.	none		0.677	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903		C	140257190	G	C	140257190	2	2	32	1	0	0	0	0	0	0	0	1	11531	1335	47	4		4	PCDHA12	5	140257190	Silent	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10	70380	140257190	40658070	19	13979											
PCDHGA6	56109	hgsc.bcm.edu	37	chr5	140755640	140755640	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtcacgctcaccgtggccGtggccgacaggatccccgac	6	6	12	17	5	2	0	2	0	0	0	3	3	3	1	5	3	0	1	5	3	0	0			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr5:140755640G>A	ENST00000517434.1	+	1	1990	c.1990G>A	c.(1990-1992)Gtg>Atg	p.V664M	PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA4_ENST00000571252.1_Intron	NM_018919.2|NM_032086.1	NP_061742.1|NP_114475.1	Q9Y5G7	PCDG6_HUMAN	protocadherin gamma subfamily A, 6	664	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)|large_intestine(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CACCGTGGCCGTGGCCGACAG	0.682																																					p.V664M		Atlas-SNP	.											.	PCDHGA6	219	.	0			c.G1990A						PASS	.						22	29	27					5																	140755640		2192	4276	6468	SO:0001583	missense	56109	exon1			GTGGCCGTGGCCG	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.1990G>A	5.37:g.140755640G>A	ENSP00000429601:p.Val664Met	169	0	0		150	11	0.0733333	NM_018919	A6H8K7|B2RN55|Q9Y5D1	Missense_Mutation	SNP	ENST00000517434.1	37	CCDS54926.1	.	.	.	.	.	.	.	.	.	.	.	10.61	1.399613	0.25291	.	.	ENSG00000253731	ENST00000517434	T	0.68181	-0.31	5.02	2.93	0.34026	Cadherin (4);Cadherin-like (1);	0.311695	0.16920	N	0.194119	T	0.78027	0.4219	H	0.94698	3.57	0.21147	N	0.999772	D;D	0.65815	0.982;0.995	P;P	0.53146	0.597;0.719	T	0.70992	-0.4721	10	0.72032	D	0.01	.	2.9236	0.05777	0.1869:0.1835:0.5086:0.121	.	664;664	Q9Y5G7-2;Q9Y5G7	.;PCDG6_HUMAN	M	664	ENSP00000429601:V664M	ENSP00000429601:V664M	V	+	1	0	PCDHGA6	140735824	0.513000	0.26194	0.153000	0.22517	0.120000	0.20174	0.792000	0.26929	0.603000	0.29913	0.563000	0.77884	GTG	.	.	none		0.682	PCDHGA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374743.1	NM_018919		A	140755640	G	A	140755640	3	1	32	1	0	0	0	0	1	0	0	0	11567	1145	40	1	1992	1	PCDHGA6	5	140755640	Missense_Mutation	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10	498450	140755640	40159620	20	13980											
HIST1H2AC	8334	hgsc.bcm.edu	37	chr6	26124712	26124712	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgcatcatcccgcgccacttGcagctggccatccgcaacga	8	6	9	18	5	1	0	1	0	0	0	3	1	3	0	4	1	3	4	4	1	1	1			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr6:26124712G>A	ENST00000602637.1	+	1	282	c.252G>A	c.(250-252)ttG>ttA	p.L84L	HIST1H2BC_ENST00000396984.1_5'Flank|HIST1H2AC_ENST00000377791.2_Silent_p.L84L|HIST1H2BC_ENST00000314332.5_5'Flank			Q93077	H2A1C_HUMAN	histone cluster 1, H2ac	84						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|lung(5)	12						CGCGCCACTTGCAGCTGGCCA	0.632																																					p.L84L		Atlas-SNP	.											.	HIST1H2AC	29	.	0			c.G252A						PASS	.						107	103	105					6																	26124712		2203	4300	6503	SO:0001819	synonymous_variant	8334	exon1			CCACTTGCAGCTG	Z80778	CCDS4585.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000180573	ENSG00000180573		"Histones / Replication-dependent"	4733	protein-coding gene	gene with protein product		602794	"H2A histone family, member L", "histone 1, H2ac"	H2AFL		9119399, 12408966	Standard	NM_003512		Approved		uc003ngm.3	Q93077	OTTHUMG00000014428	ENST00000602637.1:c.252G>A	6.37:g.26124712G>A		195	0	0		183	12	0.0655738	NM_003512	B2R4F7|O00775|O00776|O00777|O00778|Q540R1	Silent	SNP	ENST00000602637.1	37	CCDS4585.1																																																																																			.	.	none		0.632	HIST1H2AC-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468023.1	NM_003512		A	26124712	G	A	26124712	2	1	32	1	0	0	0	0	0	0	0	1	7139	1310	46	2		2	HIST1H2AC	6	26124712	Silent	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10		26124712	144990355	21	13981											
LTA	4049	hgsc.bcm.edu	37	chr6	31541106	31541106	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggagagcaaacacggaccGtgccttcctccaggatggtt	9	8	12	12	2	0	1	0	0	0	1	2	4	2	3	4	4	3	2	4	4	1	2	rs148093456		TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr6:31541106G>A	ENST00000454783.1	+	4	512	c.254G>A	c.(253-255)cGt>cAt	p.R85H	LTA_ENST00000418386.2_Missense_Mutation_p.R85H|TNF_ENST00000449264.2_5'Flank	NM_001159740.2	NP_001153212.1	P01374	TNFB_HUMAN	lymphotoxin alpha	85					apoptotic process (GO:0006915)|cell-cell signaling (GO:0007267)|defense response to Gram-positive bacterium (GO:0050830)|humoral immune response (GO:0006959)|lymph node development (GO:0048535)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of growth of symbiont in host (GO:0044130)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chronic inflammatory response to antigenic stimulus (GO:0002876)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of interferon-gamma production (GO:0032729)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|membrane (GO:0016020)	receptor binding (GO:0005102)			endometrium(2)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9					Etanercept(DB00005)	AACACGGACCGTGCCTTCCTC	0.562																																					p.R85H		Atlas-SNP	.											.	LTA	18	.	0			c.G254A						PASS	.	G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	98	83	88		254,254	2.1	0	6	dbSNP_134	88	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	LTA	NM_000595.2,NM_001159740.1	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	85/206,85/206	31541106	1,13005	2203	4300	6503	SO:0001583	missense	4049	exon4			CGGACCGTGCCTT	X01393	CCDS4701.1	6p21.3	2013-05-22	2013-05-22		ENSG00000226979	ENSG00000226979		"Tumor necrosis factor (ligand) superfamily"	6709	protein-coding gene	gene with protein product	"TNF superfamily member 1"	153440	"lymphotoxin alpha (TNF superfamily, member 1)"	TNFB		2995927, 3001529	Standard	NM_001159740		Approved	TNFSF1, LT	uc011dnu.2	P01374	OTTHUMG00000031135	ENST00000454783.1:c.254G>A	6.37:g.31541106G>A	ENSP00000403495:p.Arg85His	61	0	0		68	4	0.0588235	NM_001159740	Q8N4C3|Q9UKS8	Missense_Mutation	SNP	ENST00000454783.1	37	CCDS4701.1	.	.	.	.	.	.	.	.	.	.	G	1.401	-0.578112	0.03854	0.0	1.16E-4	ENSG00000226979	ENST00000454783;ENST00000418386;ENST00000436827	D;D	0.94613	-3.47;-3.47	5.16	2.13	0.27403	Tumour necrosis factor (3);Tumour necrosis factor-like (2);	0.498096	0.22853	N	0.054821	T	0.68375	0.2994	N	0.04203	-0.255	0.09310	N	1	B;B;B	0.33198	0.022;0.401;0.007	B;B;B	0.23150	0.007;0.044;0.004	T	0.66114	-0.6004	10	0.38643	T	0.18	-22.6602	5.1779	0.15145	0.514:0.0:0.486:0.0	.	85;85;85	E7ET53;F8WB56;P01374	.;.;TNFB_HUMAN	H	85	ENSP00000403495:R85H;ENSP00000413450:R85H	ENSP00000413450:R85H	R	+	2	0	LTA	31649085	0.000000	0.05858	0.001000	0.08648	0.036000	0.12997	0.082000	0.14847	0.269000	0.21961	-0.140000	0.14226	CGT	G|1.000;A|0.000	0.000	weak		0.562	LTA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259097.1			A	31541106	G	A	31541106	3	1	32	1	0	0	0	0	1	0	0	0	9077	1145	40	1	264	1	LTA	6	31541106	Missense_Mutation	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10	5416394	31541106	139573961	22	13982											
HLA-DMB	3109	hgsc.bcm.edu	37	chr6	32905038	32905038	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	agggggttaaggctaaatggGagagggtctggtatgtccag	10	9	18	4	0	1	1	0	0	1	1	2	2	2	1	1	6	0	3	1	6	4	3			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr6:32905038G>A	ENST00000418107.2	-	3	795	c.533C>T	c.(532-534)tCc>tTc	p.S178F	AL645941.1_ENST00000390777.1_RNA|HLA-DMB_ENST00000416244.2_Missense_Mutation_p.S178F	NM_002118.4	NP_002109.2	P28068	DMB_HUMAN	major histocompatibility complex, class II, DM beta	178	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|immune response (GO:0006955)|MHC class II protein complex assembly (GO:0002399)|peptide antigen assembly with MHC class II protein complex (GO:0002503)|positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:2001190)|positive regulation of T cell proliferation (GO:0042102)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)	MHC class II protein complex binding (GO:0023026)			breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13						GGCTAAATGGGAGAGGGTCTG	0.557																																					p.S178F		Atlas-SNP	.											.	HLA-DMB	38	.	0			c.C533T						PASS	.						146	111	123					6																	32905038		2203	4300	6503	SO:0001583	missense	3109	exon3			AAATGGGAGAGGG		CCDS4760.1	6p21.3	2014-05-16			ENSG00000242574	ENSG00000242574		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4935	protein-coding gene	gene with protein product		142856				1922365	Standard	NM_002118		Approved	D6S221E, RING7	uc003ocl.2	P28068	OTTHUMG00000031176	ENST00000418107.2:c.533C>T	6.37:g.32905038G>A	ENSP00000398890:p.Ser178Phe	187	0	0		166	11	0.0662651	NM_002118	O77936|Q13012|Q29751|Q58ZE2|Q5SNZ8|Q5STC4|Q9XRX2	Missense_Mutation	SNP	ENST00000418107.2	37	CCDS4760.1	.	.	.	.	.	.	.	.	.	.	G	13.15	2.151635	0.38021	.	.	ENSG00000242574	ENST00000438510;ENST00000446948;ENST00000418107;ENST00000416244	T;T;T	0.04234	3.67;5.59;5.59	4.56	4.56	0.56223	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.240788	0.29892	N	0.010929	T	0.16041	0.0386	M	0.89287	3.02	0.28561	N	0.911108	D;D;D;D;D	0.89917	1.0;1.0;0.998;1.0;1.0	D;D;D;D;D	0.97110	0.983;1.0;0.969;0.994;1.0	T	0.01460	-1.1349	10	0.87932	D	0	.	13.0126	0.58739	0.0:0.0:1.0:0.0	.	178;178;60;67;178	E9PD01;A2AAT3;B0V061;B0V062;P28068	.;.;.;.;DMB_HUMAN	F	60;178;178;178	ENSP00000390848:S60F;ENSP00000398890:S178F;ENSP00000391010:S178F	ENSP00000391010:S178F	S	-	2	0	HLA-DMB	33013016	0.107000	0.21998	0.515000	0.27774	0.121000	0.20230	2.070000	0.41491	2.524000	0.85096	0.494000	0.49563	TCC	.	.	none		0.557	HLA-DMB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076340.2	NM_002118		A	32905038	G	A	32905038	3	1	32	1	0	0	0	0	1	0	0	0	7208	1174	41	2	274	2	HLA-DMB	6	32905038	Missense_Mutation	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10	1363932	32905038	138210029	23	13983											
EFHC1	114327	hgsc.bcm.edu	37	chr6	52344014	52344014	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gacaaccctgtctactatggCcccagtgacttcttcattgg	8	12	8	13	0	3	1	1	1	2	0	3	2	3	1	3	2	2	0	3	2	3	5			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr6:52344014C>G	ENST00000371068.5	+	8	1561	c.1458C>G	c.(1456-1458)ggC>ggG	p.G486G	EFHC1_ENST00000433625.2_Silent_p.G395G|EFHC1_ENST00000538167.1_Silent_p.G467G	NM_018100.3	NP_060570.2	Q5JVL4	EFHC1_HUMAN	EF-hand domain (C-terminal) containing 1	486	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)					TCTACTATGGCCCCAGTGACT	0.443																																					p.G486G		Atlas-SNP	.											.	EFHC1	68	.	0			c.C1458G						PASS	.						123	112	115					6																	52344014		2203	4300	6503	SO:0001819	synonymous_variant	114327	exon8			CTATGGCCCCAGT	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.1458C>G	6.37:g.52344014C>G		81	0	0		60	5	0.0833333	NM_018100	B4DMU3|F5GZD8|Q5XKM4|Q6E1U7|Q6E1U8|Q8WUL2|Q9NVW6	Silent	SNP	ENST00000371068.5	37	CCDS4942.1																																																																																			.	.	none		0.443	EFHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040905.2	NM_018100		G	52344014	C	G	52344014	2	3	32	1	0	0	0	0	0	0	0	1	4948	726	26	4		4	EFHC1	6	52344014	Silent	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10	19438976	52344014	118771053	24	13984											
TMEM30A	55754	hgsc.bcm.edu	37	chr6	75969072	75969072	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	taatgttttacctttaaatcGttcttccaggttgtctcctc	7	19	5	10	1	2	0	0	0	2	0	6	0	3	0	3	1	1	3	3	1	4	8			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr6:75969072G>A	ENST00000230461.6	-	5	1005	c.676C>T	c.(676-678)Cga>Tga	p.R226*	TMEM30A_ENST00000475111.2_Nonsense_Mutation_p.R190*|TMEM30A_ENST00000370050.5_Nonsense_Mutation_p.R107*	NM_018247.3	NP_060717.1	Q9NV96	CC50A_HUMAN	transmembrane protein 30A	226					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)		p.R226*(1)		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						CCTTTAAATCGTTCTTCCAGG	0.308																																					p.R226X		Atlas-SNP	.											TMEM30A,caecum,carcinoma,0,2	TMEM30A	40	2	1	Substitution - Nonsense(1)	lung(1)	c.C676T						PASS	.						74	79	77					6																	75969072		2203	4298	6501	SO:0001587	stop_gained	55754	exon5			TAAATCGTTCTTC	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.676C>T	6.37:g.75969072G>A	ENSP00000230461:p.Arg226*	392	0	0		271	15	0.0553506	NM_018247	A8K9V8|E1P539|Q658Z3|Q96H09|Q9NSL9	Nonsense_Mutation	SNP	ENST00000230461.6	37	CCDS4983.1	.	.	.	.	.	.	.	.	.	.	G	39	7.311733	0.98203	.	.	ENSG00000112697	ENST00000230461;ENST00000545449;ENST00000370050;ENST00000475111	.	.	.	5.51	2.43	0.29744	.	0.572479	0.17857	N	0.159668	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	.	10.4926	0.44760	0.0:0.1178:0.5054:0.3768	.	.	.	.	X	226;210;107;190	.	ENSP00000230461:R226X	R	-	1	2	TMEM30A	76025792	0.004000	0.15560	1.000000	0.80357	0.933000	0.57130	0.839000	0.27586	0.724000	0.32296	0.655000	0.94253	CGA	.	.	none		0.308	TMEM30A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041248.2	NM_018247		A	75969072	G	A	75969072	4	1	32	1	0	0	0	0	0	1	0	0	16168	1153	40	1	421	1	TMEM30A	6	75969072	Nonsense_Mutation	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10	23625058	75969072	95145995	25	13985											
TNFAIP3	7128	hgsc.bcm.edu	37	chr6	138200148	138200148	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttggatcccgggaagtgccaAgcctgcctccaggatgttac	8	9	12	12	1	0	0	0	0	0	0	2	3	2	3	5	3	4	1	5	3	3	2	rs202233466		TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr6:138200148A>G	ENST00000237289.4	+	7	1632	c.1566A>G	c.(1564-1566)caA>caG	p.Q522Q		NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	522	Interaction with TNIP1. {ECO:0000250}.				apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|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 interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|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 protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		GGAAGTGCCAAGCCTGCCTCC	0.572			"D, N, F"		"marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"																																p.Q522Q	GBM(130;153 1739 22295 28918 47987)	Atlas-SNP	.		Rec	yes		6	6q23	7128	"tumor necrosis factor, alpha-induced protein 3"		L	.	TNFAIP3	340	.	25	Whole gene deletion(25)	haematopoietic_and_lymphoid_tissue(25)	c.A1566G						PASS	.						74	79	77					6																	138200148		2203	4300	6503	SO:0001819	synonymous_variant	7128	exon7			GTGCCAAGCCTGC	M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"OTU domain containing"	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.1566A>G	6.37:g.138200148A>G		82	0	0		61	4	0.0655738	NM_001270507	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Silent	SNP	ENST00000237289.4	37	CCDS5187.1																																																																																			A|0.999;G|0.001	0.001	weak		0.572	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1			G	138200148	A	G	138200148	2	3	32	1	0	0	0	0	0	0	0	1	16289	69	3	3		3	TNFAIP3	6	138200148	Silent	SNP	A	TCGA-GR-A4D5-01A-11D-A31X-10	62231076	138200148	32914919	26	13986											
DGKI	9162	hgsc.bcm.edu	37	chr7	137206621	137206621	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttccaacttacaagcttctcGgagtttctccttgtcatagt	8	16	6	11	1	3	0	1	0	2	0	6	1	4	1	2	1	3	2	2	1	4	6			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr7:137206621G>A	ENST00000288490.5	-	21	2239	c.2239C>T	c.(2239-2241)Cga>Tga	p.R747*	DGKI_ENST00000446122.1_Nonsense_Mutation_p.R747*|DGKI_ENST00000424189.2_Nonsense_Mutation_p.R768*|DGKI_ENST00000453654.2_Nonsense_Mutation_p.R447*	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	747					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						CAAGCTTCTCGGAGTTTCTCC	0.443																																					p.R747X		Atlas-SNP	.											.	DGKI	335	.	0			c.C2239T						PASS	.						115	98	104					7																	137206621		2203	4300	6503	SO:0001587	stop_gained	9162	exon21			CTTCTCGGAGTTT	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.2239C>T	7.37:g.137206621G>A	ENSP00000288490:p.Arg747*	81	0	0		86	4	0.0465116	NM_004717	A4D1Q9|Q9NZ49	Nonsense_Mutation	SNP	ENST00000288490.5	37	CCDS5845.1	.	.	.	.	.	.	.	.	.	.	G	43	9.936638	0.99299	.	.	ENSG00000157680	ENST00000453654;ENST00000540376;ENST00000424189;ENST00000288490;ENST00000446122	.	.	.	5.77	5.77	0.91146	.	0.060212	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06494	T	0.89	.	19.9576	0.97228	0.0:0.0:1.0:0.0	.	.	.	.	X	447;695;768;747;747	.	ENSP00000288490:R747X	R	-	1	2	DGKI	136857161	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.753000	0.62183	2.885000	0.99019	0.655000	0.94253	CGA	.	.	none		0.443	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717		A	137206621	G	A	137206621	4	1	32	1	0	0	0	0	0	1	0	0	4473	1124	39	1	1014	1	DGKI	7	137206621	Nonsense_Mutation	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10		137206621	21932042	27	13987											
CSMD3	114788	hgsc.bcm.edu	37	chr8	113267635	113267635	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tttttccttgggcaggtataCcagggtcaccacaaaacttt	10	13	8	10	0	1	0	1	0	0	0	2	0	2	0	3	3	2	2	3	3	4	6			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr8:113267635C>A	ENST00000297405.5	-	62	10128	c.9884G>T	c.(9883-9885)gGt>gTt	p.G3295V	CSMD3_ENST00000352409.3_Missense_Mutation_p.G3225V|CSMD3_ENST00000343508.3_Missense_Mutation_p.G3255V|CSMD3_ENST00000455883.2_Missense_Mutation_p.G3126V	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3295	Sushi 26. {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						GGCAGGTATACCAGGGTCACC	0.388										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.G3295V		Atlas-SNP	.											CSMD3_ENST00000343508,caecum,carcinoma,-1,4	CSMD3	2325	4	0			c.G9884T						PASS	.						98	92	94					8																	113267635		2203	4300	6503	SO:0001583	missense	114788	exon62			GGTATACCAGGGT	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.9884G>T	8.37:g.113267635C>A	ENSP00000297405:p.Gly3295Val	135	0	0		91	6	0.0659341	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	22.8	4.337760	0.81911	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11;-0.11	4.99	4.99	0.66335	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.64402	D	0.000001	T	0.80757	0.4684	M	0.84156	2.68	0.80722	D	1	D;D;B	0.89917	1.0;1.0;0.355	D;D;B	0.97110	1.0;1.0;0.359	T	0.79895	-0.1610	10	0.34782	T	0.22	.	18.485	0.90825	0.0:1.0:0.0:0.0	.	3126;3295;3255	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	V	3255;3295;2565;3126;3225	ENSP00000345799:G3255V;ENSP00000297405:G3295V;ENSP00000341558:G2565V;ENSP00000412263:G3126V;ENSP00000343124:G3225V	ENSP00000297405:G3295V	G	-	2	0	CSMD3	113336811	1.000000	0.71417	0.991000	0.47740	0.841000	0.47740	7.581000	0.82535	2.601000	0.87937	0.650000	0.86243	GGT	.	.	none		0.388	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		A	113267635	C	A	113267635	3	1	32	1	0	0	0	0	1	0	0	0	3948	507	18	4	1279	4	CSMD3	8	113267635	Missense_Mutation	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10		113267635	33096387	28	13988											
SMARCA2	6595	hgsc.bcm.edu	37	chr9	2081900	2081900	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggaatcttagccgatgaaatGgggcttggaaagaccataca	14	8	12	7	1	1	2	0	1	1	1	1	5	1	4	2	4	2	1	2	4	5	3			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr9:2081900G>A	ENST00000382203.1	+	15	2462	c.2253G>A	c.(2251-2253)atG>atA	p.M751I	SMARCA2_ENST00000357248.2_Missense_Mutation_p.M751I|SMARCA2_ENST00000382194.1_Missense_Mutation_p.M751I|SMARCA2_ENST00000349721.2_Missense_Mutation_p.M751I			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	751	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				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)		CCGATGAAATGGGGCTTGGAA	0.433																																					p.M751I		Atlas-SNP	.											SMARCA2_ENST00000349721,NS,carcinoma,+2,2	SMARCA2	313	2	0			c.G2253A						PASS	.						217	181	193					9																	2081900		2203	4300	6503	SO:0001583	missense	6595	exon15			TGAAATGGGGCTT	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.2253G>A	9.37:g.2081900G>A	ENSP00000371638:p.Met751Ile	94	0	0		92	11	0.119565	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Missense_Mutation	SNP	ENST00000382203.1	37	CCDS34977.1	.	.	.	.	.	.	.	.	.	.	G	19.71	3.878109	0.72294	.	.	ENSG00000080503	ENST00000349721;ENST00000357248;ENST00000382203;ENST00000382194	D;D;D;D	0.94497	-3.44;-3.44;-3.44;-3.44	5.41	5.41	0.78517	DEAD-like helicase (2);SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.98801	0.9596	H	0.99634	4.67	0.80722	D	1	D;P;P	0.89917	1.0;0.908;0.925	D;D;D	0.91635	0.999;0.922;0.954	D	0.99395	1.0926	10	0.87932	D	0	-33.1543	19.1951	0.93684	0.0:0.0:1.0:0.0	.	352;751;751	B4DK35;P51531-2;P51531	.;.;SMCA2_HUMAN	I	751	ENSP00000265773:M751I;ENSP00000349788:M751I;ENSP00000371638:M751I;ENSP00000371629:M751I	ENSP00000265773:M751I	M	+	3	0	SMARCA2	2071900	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.552000	0.86080	0.591000	0.81541	ATG	.	.	none		0.433	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070		A	2081900	G	A	2081900	3	1	32	1	0	0	0	0	1	0	0	0	14784	1348	47	2	2307	2	SMARCA2	9	2081900	Missense_Mutation	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10		2081900	139131531	29	13989											
TLN1	7094	hgsc.bcm.edu	37	chr9	35724043	35724043	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaggccttgtcaaaggagaCagggtgggagccattcagga	12	6	15	8	0	2	1	2	0	0	1	2	4	2	3	2	5	1	0	2	5	1	2			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr9:35724043C>T	ENST00000314888.9	-	7	1041	c.688G>A	c.(688-690)Gtc>Atc	p.V230I	TLN1_ENST00000540444.1_Missense_Mutation_p.V230I	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	230	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				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)			TCAAAGGAGACAGGGTGGGAG	0.562																																					p.V230I		Atlas-SNP	.											.	TLN1	185	.	0			c.G688A						PASS	.						157	138	145					9																	35724043		2203	4300	6503	SO:0001583	missense	7094	exon7			AGGAGACAGGGTG	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.688G>A	9.37:g.35724043C>T	ENSP00000316029:p.Val230Ile	115	0	0		72	8	0.111111	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	37	CCDS35009.1	.	.	.	.	.	.	.	.	.	.	C	17.40	3.380291	0.61845	.	.	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.79033	-1.23;-1.23	5.48	5.48	0.80851	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.064498	0.64402	D	0.000009	T	0.76104	0.3941	L	0.50919	1.6	0.80722	D	1	B;B	0.26445	0.149;0.005	B;B	0.28709	0.093;0.086	T	0.73052	-0.4104	10	0.49607	T	0.09	-29.9777	19.387	0.94560	0.0:1.0:0.0:0.0	.	230;230	Q5TCU5;Q9Y490	.;TLN1_HUMAN	I	230	ENSP00000316029:V230I;ENSP00000442981:V230I	ENSP00000316029:V230I	V	-	1	0	TLN1	35714043	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.056000	0.71111	2.572000	0.86782	0.655000	0.94253	GTC	.	.	none		0.562	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		T	35724043	C	T	35724043	3	4	32	1	0	0	0	0	1	0	0	0	15962	478	17	2	7141	2	TLN1	9	35724043	Missense_Mutation	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10	33642143	35724043	105489388	30	13990											
TRPM3	80036	hgsc.bcm.edu	37	chr9	73461394	73461394	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agttttggctggagttcaaaGttctgcaggcccccatggac	8	11	12	10	0	2	0	1	0	1	0	2	2	2	2	2	4	1	5	2	4	1	4			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr9:73461394G>A	ENST00000377111.2	-	4	819	c.576C>T	c.(574-576)aaC>aaT	p.N192N	TRPM3_ENST00000377105.1_Silent_p.N39N|TRPM3_ENST00000377106.1_Silent_p.N39N|TRPM3_ENST00000377097.3_Silent_p.N39N|TRPM3_ENST00000377101.1_Silent_p.N39N|TRPM3_ENST00000408909.2_Silent_p.N39N|TRPM3_ENST00000358082.3_Silent_p.N39N|TRPM3_ENST00000396292.4_Silent_p.N39N|TRPM3_ENST00000377110.3_Silent_p.N192N|TRPM3_ENST00000396280.5_Silent_p.N39N|TRPM3_ENST00000357533.2_Silent_p.N194N|TRPM3_ENST00000396285.1_Silent_p.N39N|TRPM3_ENST00000423814.3_Silent_p.N194N|TRPM3_ENST00000361823.5_Silent_p.N39N|TRPM3_ENST00000360823.2_Silent_p.N39N|TRPM3_ENST00000396283.1_Silent_p.N39N	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	192					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						GGAGTTCAAAGTTCTGCAGGC	0.483																																					p.N192N		Atlas-SNP	.											.	TRPM3	700	.	0			c.C576T						PASS	.						148	151	150					9																	73461394		2203	4300	6503	SO:0001819	synonymous_variant	80036	exon4			TTCAAAGTTCTGC	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.576C>T	9.37:g.73461394G>A		156	0	0		128	14	0.109375	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Silent	SNP	ENST00000377111.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.226|9.226	1.034597|1.034597	0.19590|0.19590	.|.	.|.	ENSG00000083067|ENSG00000083067	ENST00000396280|ENST00000377097	.|.	.|.	.|.	6.01|6.01	3.19|3.19	0.36642|0.36642	.|.	.|.	.|.	.|.	.|.	T|T	0.57829|0.57829	0.2080|0.2080	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.52983|0.52983	-0.8502|-0.8502	4|4	.|.	.|.	.|.	-20.7118|-20.7118	8.1451|8.1451	0.31106|0.31106	0.4047:0.0:0.5953:0.0|0.4047:0.0:0.5953:0.0	.|.	.|.	.|.	.|.	F|I	39|82	.|.	.|.	L|T	-|-	1|2	0|0	TRPM3|TRPM3	72651214|72651214	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	1.447000|1.447000	0.35101|0.35101	0.899000|0.899000	0.36444|0.36444	0.650000|0.650000	0.86243|0.86243	CTT|ACT	.	.	none		0.483	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945		A	73461394	G	A	73461394	2	1	32	1	0	0	0	0	0	0	0	1	16602	1020	36	2		2	TRPM3	9	73461394	Silent	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10	37737351	73461394	67752037	31	13991											
PALM2	114299	hgsc.bcm.edu	37	chr9	112642863	112642863	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgggagaaatggctgctgcaGggcatacccgctggaactgc	9	6	15	11	2	0	1	0	0	0	1	0	3	0	2	1	4	5	5	1	4	3	1			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr9:112642863G>T	ENST00000374531.2	+	4	239	c.165G>T	c.(163-165)caG>caT	p.Q55H	PALM2_ENST00000448454.2_Missense_Mutation_p.Q55H|AKAP2_ENST00000555236.1_Missense_Mutation_p.Q53H|PALM2_ENST00000483909.1_Missense_Mutation_p.Q53H|PALM2-AKAP2_ENST00000302798.7_Missense_Mutation_p.Q53H|AKAP2_ENST00000510514.5_Missense_Mutation_p.Q53H|PALM2-AKAP2_ENST00000374530.3_Missense_Mutation_p.Q53H|PALM2_ENST00000314527.4_Missense_Mutation_p.Q53H	NM_001037293.2	NP_001032370.1	Q8IXS6	PALM2_HUMAN	paralemmin 2	55					regulation of cell shape (GO:0008360)	plasma membrane (GO:0005886)				breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(2)|skin(3)|upper_aerodigestive_tract(1)	18						GGCTGCTGCAGGGCATACCCG	0.517																																					p.Q55H		Atlas-SNP	.											.	PALM2	51	.	0			c.G165T						PASS	.						97	84	89					9																	112642863		2203	4300	6503	SO:0001583	missense	114299	exon4			GCTGCAGGGCATA	AJ312216	CCDS35099.1, CCDS48002.1, CCDS48002.2	9q31.3	2009-10-16			ENSG00000243444	ENSG00000243444			15845	protein-coding gene	gene with protein product						11478809	Standard	NM_001037293		Approved			Q8IXS6	OTTHUMG00000020479	ENST00000374531.2:c.165G>T	9.37:g.112642863G>T	ENSP00000363656:p.Gln55His	68	0	0		75	4	0.0533333	NM_001037293	A9Z1X9|Q8N9D5|Q96DU1	Missense_Mutation	SNP	ENST00000374531.2	37	CCDS35099.1	.	.	.	.	.	.	.	.	.	.	G	18.67	3.674599	0.67928	.	.	ENSG00000243444;ENSG00000243444;ENSG00000243444;ENSG00000243444;ENSG00000243444;ENSG00000157654;ENSG00000157654;ENSG00000157654;ENSG00000241978;ENSG00000241978	ENST00000374531;ENST00000448454;ENST00000483909;ENST00000314527;ENST00000497711;ENST00000374530;ENST00000413420;ENST00000302798;ENST00000555236;ENST00000510514	T;T;T;T;T;T;T;T;T;T	0.32515	1.82;1.84;1.81;1.84;1.45;2.09;1.81;2.09;2.09;2.09	5.36	3.09	0.35607	.	0.639479	0.14359	N	0.324569	T	0.43122	0.1233	L	0.40543	1.245	0.30980	N	0.722632	D;D;D;D	0.89917	0.997;0.997;0.995;1.0	D;D;D;D	0.83275	0.995;0.995;0.99;0.996	T	0.41822	-0.9487	10	0.87932	D	0	-11.3524	8.4766	0.33016	0.2302:0.0:0.7698:0.0	.	53;53;55;55	Q9Y2D5-6;Q9Y2D5-4;Q8IXS6;D3YTA4	.;.;PALM2_HUMAN;.	H	55;55;53;53;39;53;53;53;53;53	ENSP00000363656:Q55H;ENSP00000400206:Q55H;ENSP00000417525:Q53H;ENSP00000323805:Q53H;ENSP00000419747:Q39H;ENSP00000363654:Q53H;ENSP00000397839:Q53H;ENSP00000305861:Q53H;ENSP00000451476:Q53H;ENSP00000421522:Q53H	ENSP00000305861:Q53H	Q	+	3	2	PALM2-AKAP2;PALM2;AKAP2	111682684	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.503000	0.22610	1.390000	0.46547	0.650000	0.86243	CAG	.	.	none		0.517	PALM2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053604.1	NM_001037293		T	112642863	G	T	112642863	3	4	32	1	0	0	0	0	1	0	0	0	11418	991	35	4	179	4	PALM2	9	112642863	Missense_Mutation	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10	39181469	112642863	28570568	32	13992											
PAPPA	5069	hgsc.bcm.edu	37	chr9	118989774	118989774	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggtgcagtatgcttccaacGcttcctccccaatgccctgc	6	11	8	16	1	0	0	0	0	0	0	3	0	3	0	5	1	5	4	5	1	3	3			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr9:118989774G>A	ENST00000328252.3	+	6	2545	c.2176G>A	c.(2176-2178)Gct>Act	p.A726T	PAPPA_ENST00000534838.1_Intron	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	726					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						TGCTTCCAACGCTTCCTCCCC	0.542																																					p.A726T		Atlas-SNP	.											PAPPA,NS,carcinoma,-2,1	PAPPA	243	1	0			c.G2176A						PASS	.						152	131	138					9																	118989774		2203	4300	6503	SO:0001583	missense	5069	exon6			TCCAACGCTTCCT		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.2176G>A	9.37:g.118989774G>A	ENSP00000330658:p.Ala726Thr	44	0	0		41	7	0.170732	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Missense_Mutation	SNP	ENST00000328252.3	37	CCDS6813.1	.	.	.	.	.	.	.	.	.	.	G	33	5.254603	0.95336	.	.	ENSG00000182752	ENST00000328252;ENST00000443904	T	0.03004	4.08	5.85	5.85	0.93711	.	0.047663	0.85682	D	0.000000	T	0.18341	0.0440	M	0.75615	2.305	0.80722	D	1	D;D	0.76494	0.999;0.994	P;P	0.62089	0.898;0.592	T	0.00015	-1.2398	10	0.87932	D	0	-25.4983	20.1624	0.98139	0.0:0.0:1.0:0.0	.	170;726	E7EMD3;Q13219	.;PAPP1_HUMAN	T	726;170	ENSP00000330658:A726T	ENSP00000330658:A726T	A	+	1	0	PAPPA	118029595	1.000000	0.71417	0.985000	0.45067	0.987000	0.75469	7.400000	0.79949	2.764000	0.94973	0.591000	0.81541	GCT	.	.	none		0.542	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581		A	118989774	G	A	118989774	3	1	32	1	0	0	0	0	1	0	0	0	11441	1087	38	1	2198	1	PAPPA	9	118989774	Missense_Mutation	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10	6346911	118989774	22223657	33	13993											
AKR1C4	1109	hgsc.bcm.edu	37	chr10	5248268	5248268	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agtgtaaggatgcaggattgGccaagtccatcggggtgtca	10	9	15	7	1	1	0	1	0	0	0	3	2	2	2	2	5	1	2	2	5	2	2			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr10:5248268G>A	ENST00000380448.1	+	7	731	c.478G>A	c.(478-480)Gcc>Acc	p.A160T	AKR1C4_ENST00000263126.1_Missense_Mutation_p.A160T			P17516	AK1C4_HUMAN	aldo-keto reductase family 1, member C4	160					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						TGCAGGATTGGCCAAGTCCAT	0.493																																					p.A160T		Atlas-SNP	.											.	AKR1C4	57	.	0			c.G478A						PASS	.						160	140	147					10																	5248268		2203	4300	6503	SO:0001583	missense	1109	exon5			GGATTGGCCAAGT	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.478G>A	10.37:g.5248268G>A	ENSP00000369814:p.Ala160Thr	181	0	0		143	11	0.0769231	NM_001818	Q5T6A3|Q8WW84|Q9NS54	Missense_Mutation	SNP	ENST00000380448.1	37	CCDS7064.1	.	.	.	.	.	.	.	.	.	.	G	5.716	0.316610	0.10845	.	.	ENSG00000198610	ENST00000380448;ENST00000263126	T;T	0.52754	0.65;0.65	3.16	1.2	0.21068	Aldo/keto reductase, conserved site (1);NADP-dependent oxidoreductase domain (3);	0.432537	0.20662	N	0.088006	T	0.23649	0.0572	N	0.11201	0.11	0.33351	D	0.571106	B	0.12013	0.005	B	0.18263	0.021	T	0.15896	-1.0421	10	0.25106	T	0.35	.	6.7199	0.23325	0.2549:0.0:0.7451:0.0	.	160	P17516	AK1C4_HUMAN	T	160	ENSP00000369814:A160T;ENSP00000263126:A160T	ENSP00000263126:A160T	A	+	1	0	AKR1C4	5238268	0.194000	0.23325	0.735000	0.30896	0.146000	0.21551	0.134000	0.15932	0.019000	0.15079	0.313000	0.20887	GCC	.	.	none		0.493	AKR1C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046543.2	NM_001818		A	5248268	G	A	5248268	3	1	32	1	0	0	0	0	1	0	0	0	472	1203	42	2	496	2	AKR1C4	10	5248268	Missense_Mutation	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10		5248268	130286479	34	13994											
CDH23	64072	hgsc.bcm.edu	37	chr10	73537483	73537483	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtggatgagaatgataacgCgcccatgttccagcagcccc	10	8	11	12	2	0	2	0	2	0	1	1	4	1	3	4	1	3	2	4	1	2	2	rs370762269	byFrequency	TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr10:73537483C>T	ENST00000224721.6	+	38	4912	c.4907C>T	c.(4906-4908)gCg>gTg	p.A1636V		NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	1631	Cadherin 16. {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						AATGATAACGCGCCCATGTTC	0.587													C|||	5	0.000998403	0.0	0.0	5008	,	,		20989	0.0		0.0	False		,,,				2504	0.0051				p.A1631V		Atlas-SNP	.											.	CDH23	365	.	0			c.C4892T						PASS	.	C	VAL/ALA	0,4192		0,0,2096	52	54	53		4892	5.8	0	10		53	3,8429		0,3,4213	no	missense	CDH23	NM_022124.5	64	0,3,6309	TT,TC,CC		0.0356,0.0,0.0238	benign	1631/3355	73537483	3,12621	2096	4216	6312	SO:0001583	missense	64072	exon37			ATAACGCGCCCAT	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.4907C>T	10.37:g.73537483C>T	ENSP00000224721:p.Ala1636Val	83	0	0		69	6	0.0869565	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Missense_Mutation	SNP	ENST00000224721.6	37		.	.	.	.	.	.	.	.	.	.	C	15.30	2.791860	0.50102	0.0	3.56E-4	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721	.	.	.	5.75	5.75	0.90469	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.119943	0.56097	D	0.000029	T	0.66187	0.2764	L	0.58510	1.815	0.80722	D	1	B	0.13145	0.007	B	0.09377	0.004	T	0.59883	-0.7370	9	0.37606	T	0.19	.	19.938	0.97149	0.0:1.0:0.0:0.0	.	1631	Q9H251	CAD23_HUMAN	V	1636;1631;1634	.	ENSP00000224721:A1636V	A	+	2	0	CDH23	73207489	0.989000	0.36119	0.034000	0.17996	0.188000	0.23474	4.843000	0.62838	2.732000	0.93576	0.650000	0.86243	GCG	.	.	none		0.587	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836		T	73537483	C	T	73537483	3	4	32	1	0	0	0	0	1	0	0	0	3110	768	27	1	5387	1	CDH23	10	73537483	Missense_Mutation	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10	68289215	73537483	61997264	35	13995											
SMPD1	6609	hgsc.bcm.edu	37	chr11	6412880	6412880	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aaaccccctagccccccagcCccaggtgcccctgtcagccg	7	4	8	22	1	1	0	1	0	0	0	1	0	1	0	10	1	5	0	10	1	2	1			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr11:6412880C>T	ENST00000342245.4	+	2	753	c.585C>T	c.(583-585)gcC>gcT	p.A195A	SMPD1_ENST00000533196.1_Intron|SMPD1_ENST00000356761.2_Silent_p.A195A|SMPD1_ENST00000299397.3_Silent_p.A195A|SMPD1_ENST00000527275.1_Silent_p.A194A	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	193					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)	GCCCCCCAGCCCCAGGTGCCC	0.617																																					p.A195A		Atlas-SNP	.											.	SMPD1	108	.	0			c.C585T						PASS	.						6	6	6					11																	6412880		2114	4096	6210	SO:0001819	synonymous_variant	6609	exon2			CCCAGCCCCAGGT	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.585C>T	11.37:g.6412880C>T		33	0	0		36	13	0.361111	NM_000543	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	Silent	SNP	ENST00000342245.4	37	CCDS44531.1																																																																																			.	.	none		0.617	SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543		T	6412880	C	T	6412880	2	4	32	1	0	0	0	0	0	0	0	1	14819	610	22	2		2	SMPD1	11	6412880	Silent	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10		6412880	128593636	36	13996											
DGKZ	8525	hgsc.bcm.edu	37	chr11	46387868	46387868	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggccctggagaggggcagcAgcggcccagcagcgtggggc	7	2	20	12	2	0	1	0	0	0	1	0	2	0	1	2	7	4	3	2	7	0	0	rs1317826	byFrequency	TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr11:46387868A>G	ENST00000454345.1	+	2	187	c.62A>G	c.(61-63)cAg>cGg	p.Q21R	DGKZ_ENST00000527911.1_Intron|DGKZ_ENST00000525434.1_3'UTR|DGKZ_ENST00000343674.6_Intron|DGKZ_ENST00000421244.2_Intron|DGKZ_ENST00000456247.2_Intron|DGKZ_ENST00000395574.3_Intron|DGKZ_ENST00000528615.1_Intron|DGKZ_ENST00000318201.8_Intron|DGKZ_ENST00000543978.1_Intron|DGKZ_ENST00000532868.2_Intron	NM_001105540.1	NP_001099010.1	Q13574	DGKZ_HUMAN	diacylglycerol kinase, zeta	21			Q -> R (in dbSNP:rs1317826). {ECO:0000269|PubMed:9159104}.		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)		GAGGGGCAGCAGCGGCCCAGC	0.701													G|||	2181	0.435503	0.9107	0.2493	5008	,	,		13838	0.1458		0.3111	False		,,,				2504	0.3517				p.Q21R		Atlas-SNP	.											.	DGKZ	199	.	0			c.A62G						PASS	.	G	ARG/GLN,,,,,,	2682,930		1027,628,151	8	9	9		62,,,,,,	4.5	1	11	dbSNP_88	9	2229,5713		386,1457,2128	yes	missense,intron,intron,intron,intron,intron,intron	DGKZ	NM_001105540.1,NM_001199266.1,NM_001199267.1,NM_001199268.1,NM_003646.3,NM_201532.2,NM_201533.3	43,,,,,,	1413,2085,2279	GG,GA,AA		28.066,25.7475,42.5048	benign,,,,,,	21/1118,,,,,,	46387868	4911,6643	1806	3971	5777	SO:0001583	missense	8525	exon2			GGCAGCAGCGGCC	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.62A>G	11.37:g.46387868A>G	ENSP00000412178:p.Gln21Arg	0	0	.		17	7	0.411765	NM_001105540	B7Z2M9|B7Z6M3|E9PPW4|F6UCU9|G3V0F6|J3KNJ6|O00542|Q6ZVG7|Q8IVW9	Missense_Mutation	SNP	ENST00000454345.1	37	CCDS41640.1	872	0.3992673992673993	446	0.9065040650406504	95	0.26243093922651933	97	0.16958041958041958	234	0.3087071240105541	G	2.360	-0.346808	0.05208	0.742525	0.28066	ENSG00000149091	ENST00000454345	T	0.64260	-0.09	4.53	4.53	0.55603	.	0.291635	0.22594	N	0.058046	T	0.00012	0.0000	N	0.02916	-0.46	0.09310	P	1.0	B	0.02656	0.0	B	0.01281	0.0	T	0.40961	-0.9535	9	0.02654	T	1	.	13.0604	0.59003	0.0784:0.0:0.9216:0.0	rs1317826	21	Q13574	DGKZ_HUMAN	R	21	ENSP00000412178:Q21R	ENSP00000412178:Q21R	Q	+	2	0	DGKZ	46344444	1.000000	0.71417	0.991000	0.47740	0.097000	0.18754	3.832000	0.55783	1.049000	0.40321	-0.213000	0.12676	CAG	A|0.609;G|0.391	0.391	strong		0.701	DGKZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389772.1	NM_001105540		G	46387868	A	G	46387868	3	3	32	1	0	0	0	0	1	0	0	0	4476	188	7	3	508	3	DGKZ	11	46387868	Missense_Mutation	SNP	A	TCGA-GR-A4D5-01A-11D-A31X-10	39974988	46387868	88618648	37	13997											
OR9Q2	219957	hgsc.bcm.edu	37	chr11	57958226	57958226	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggctgtgctgtgggagcaCggcacaaccatctcccaggc	7	7	13	14	1	1	0	0	0	1	0	2	1	1	1	2	4	3	4	2	4	1	0			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr11:57958226C>T	ENST00000311591.3	+	1	321	c.264C>T	c.(262-264)caC>caT	p.H88H		NM_001005283.2	NP_001005283.1	Q8NGE9	OR9Q2_HUMAN	olfactory receptor, family 9, subfamily Q, member 2	88						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)|large_intestine(3)|lung(24)|ovary(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	41		Breast(21;0.0589)				TGTGGGAGCACGGCACAACCA	0.567																																					p.H88H		Atlas-SNP	.											OR9Q2,NS,carcinoma,+2,1	OR9Q2	78	1	0			c.C264T						scavenged	.						182	132	149					11																	57958226		2201	4296	6497	SO:0001819	synonymous_variant	219957	exon1			GGAGCACGGCACA	AB065859	CCDS31544.1	11q12.1	2012-08-09		2004-03-10	ENSG00000186513	ENSG00000186513		"GPCR / Class A : Olfactory receptors"	15328	protein-coding gene	gene with protein product				OR9Q2P			Standard	NM_001005283		Approved		uc010rka.2	Q8NGE9	OTTHUMG00000167414	ENST00000311591.3:c.264C>T	11.37:g.57958226C>T		58	1	0.0172414		52	12	0.230769	NM_001005283		Silent	SNP	ENST00000311591.3	37	CCDS31544.1																																																																																			.	.	none		0.567	OR9Q2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394540.1	NM_001005283		T	57958226	C	T	57958226	2	4	32	1	0	0	0	0	0	0	0	1	11265	535	19	1		1	OR9Q2	11	57958226	Silent	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10	11570358	57958226	77048290	38	13998											
PHLDB1	23187	hgsc.bcm.edu	37	chr11	118526582	118526582	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcccagaagaggtttttcCgcttcactatggtgactgag	8	13	10	10	1	1	4	1	2	0	2	3	4	3	4	2	2	0	2	2	2	2	5	rs149980232		TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr11:118526582C>T	ENST00000361417.2	+	23	4384	c.3973C>T	c.(3973-3975)Cgc>Tgc	p.R1325C	PHLDB1_ENST00000524713.1_Intron|PHLDB1_ENST00000534672.1_Intron|PHLDB1_ENST00000356063.5_Intron|PHLDB1_ENST00000527898.1_Intron	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	1325	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.									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)		GAGGTTTTTCCGCTTCACTAT	0.542													C|||	1	0.000199681	0.0	0.0	5008	,	,		18829	0.001		0.0	False		,,,				2504	0.0				p.R1325C		Atlas-SNP	.											.	PHLDB1	103	.	0			c.C3973T						PASS	.						189	178	182					11																	118526582		2200	4295	6495	SO:0001583	missense	23187	exon22			TTTTTCCGCTTCA		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.3973C>T	11.37:g.118526582C>T	ENSP00000354498:p.Arg1325Cys	42	0	0		38	10	0.263158	NM_001144758	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Missense_Mutation	SNP	ENST00000361417.2	37	CCDS8401.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	12.88	2.070482	0.36566	.	.	ENSG00000019144	ENST00000361417	T	0.31510	1.49	5.25	1.91	0.25777	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.745951	0.12817	N	0.436765	T	0.14960	0.0361	N	0.02916	-0.46	0.80722	D	1	B	0.31968	0.349	B	0.32022	0.139	T	0.10337	-1.0634	10	0.54805	T	0.06	1.0934	12.4647	0.55751	0.5992:0.4008:0.0:0.0	.	1325	Q86UU1	PHLB1_HUMAN	C	1325	ENSP00000354498:R1325C	ENSP00000354498:R1325C	R	+	1	0	PHLDB1	118031792	0.944000	0.32072	0.991000	0.47740	0.999000	0.98932	0.095000	0.15127	0.211000	0.20683	0.650000	0.86243	CGC	C|1.000;T|0.000	0.000	strong		0.542	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157		T	118526582	C	T	118526582	3	4	32	1	0	0	0	0	1	0	0	0	11860	652	23	1	4055	1	PHLDB1	11	118526582	Missense_Mutation	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10	60568356	118526582	16479934	39	13999											
PEX5	5830	hgsc.bcm.edu	37	chr12	7343151	7343151	+	Intron	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttgaggtggaaagcccaggtGcagcctctgaggcagtgagt	9	8	16	8	0	1	3	0	3	1	0	1	4	1	4	2	4	3	2	2	4	1	1			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr12:7343151G>C	ENST00000455147.2	+	3	727				PEX5_ENST00000545220.1_Intron|RP11-273B20.3_ENST00000545794.1_RNA|PEX5_ENST00000420616.2_Intron|PEX5_ENST00000434354.2_Missense_Mutation_p.A60P|PEX5_ENST00000266564.3_Intron|PEX5_ENST00000266563.5_Intron|PEX5_ENST00000412720.2_Intron|RP11-273B20.3_ENST00000543061.1_RNA	NM_001131026.1	NP_001124498.1	P50542	PEX5_HUMAN	peroxisomal biogenesis factor 5						cell development (GO:0048468)|cerebral cortex cell migration (GO:0021795)|cerebral cortex neuron differentiation (GO:0021895)|endoplasmic reticulum organization (GO:0007029)|fatty acid beta-oxidation (GO:0006635)|mitochondrial membrane organization (GO:0007006)|negative regulation of protein homotetramerization (GO:1901094)|neuromuscular process (GO:0050905)|neuron migration (GO:0001764)|positive regulation of multicellular organism growth (GO:0040018)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, docking (GO:0016560)|protein import into peroxisome matrix, translocation (GO:0016561)|protein import into peroxisome membrane (GO:0045046)|protein targeting to peroxisome (GO:0006625)|protein tetramerization (GO:0051262)|very long-chain fatty acid metabolic process (GO:0000038)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	enzyme binding (GO:0019899)|peroxisome matrix targeting signal-1 binding (GO:0005052)|peroxisome targeting sequence binding (GO:0000268)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|small GTPase binding (GO:0031267)			breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)	21						AAGCCCAGGTGCAGCCTCTGA	0.632																																					p.A60P		Atlas-SNP	.											PEX5_ENST00000434354,colon,carcinoma,-2,3	PEX5	63	3	0			c.G178C						scavenged	.						10	12	12					12																	7343151		2163	4228	6391	SO:0001627	intron_variant	5830	exon2			CCAGGTGCAGCCT	U19721	CCDS8576.1, CCDS44822.1, CCDS44823.1, CCDS44824.1, CCDS73433.1	12p	2013-01-10	2004-03-17	2004-03-19		ENSG00000139197		"Tetratricopeptide (TTC) repeat domain containing"	9719	protein-coding gene	gene with protein product		600414	"peroxisome receptor 1"	PXR1			Standard	NM_000319		Approved	PTS1R	uc010sgc.2	P50542		ENST00000455147.2:c.147+31G>C	12.37:g.7343151G>C		37	2	0.0540541		43	9	0.209302	NM_001131023	A8K891|B4DZ45|B7ZAD5|D3DUT8|Q15115|Q15266|Q96FN7	Missense_Mutation	SNP	ENST00000455147.2	37	CCDS44823.1	.	.	.	.	.	.	.	.	.	.	G	4.863	0.160424	0.09287	.	.	ENSG00000139197	ENST00000434354;ENST00000396637	D;D	0.87650	-2.28;-2.1	.	.	.	.	.	.	.	.	T	0.73024	0.3534	.	.	.	0.09310	N	0.999999	P	0.42993	0.797	B	0.31191	0.125	T	0.61525	-0.7045	5	.	.	.	.	.	.	.	.	60	B4DZ45	.	P	60	ENSP00000407401:A60P;ENSP00000379877:A60P	.	A	+	1	0	PEX5	7234418	0.000000	0.05858	0.005000	0.12908	0.094000	0.18550	0.032000	0.13732	0.502000	0.28037	0.000000	0.15137	GCA	.	.	none		0.632	PEX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398611.1	NM_000319		C	7343151	G	C	7343151	1	2	32	0	1	0	0	0	0	0	0	0	11757	1319	46	4		4	PEX5	12	7343151	Intron	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10		7343151	126508744	40	14000											
PIK3C2G	5288	hgsc.bcm.edu	37	chr12	18443868	18443868	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctactacagcatttccgtatCagctcttttctaagaccaag	11	13	5	12	1	3	1	1	0	2	1	4	1	4	1	2	0	4	3	2	0	5	7			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr12:18443868C>G	ENST00000266497.5	+	3	879	c.841C>G	c.(841-843)Cag>Gag	p.Q281E	PIK3C2G_ENST00000535651.1_Missense_Mutation_p.Q281E|RERGL_ENST00000541632.1_Intron|PIK3C2G_ENST00000536967.1_3'UTR|PIK3C2G_ENST00000538779.1_Missense_Mutation_p.Q281E|PIK3C2G_ENST00000433979.1_Missense_Mutation_p.Q281E			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	281					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)				ATTTCCGTATCAGCTCTTTTC	0.333																																					p.Q281E		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.C841G						PASS	.						70	65	67					12																	18443868		1831	4080	5911	SO:0001583	missense	5288	exon4			CCGTATCAGCTCT	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.841C>G	12.37:g.18443868C>G	ENSP00000266497:p.Gln281Glu	270	0	0		187	23	0.122995	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	37	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	C	3.777	-0.046403	0.07407	.	.	ENSG00000139144	ENST00000535651;ENST00000433979;ENST00000266497;ENST00000538779	T;T;T;T	0.41400	1.0;1.0;1.0;1.0	4.07	3.17	0.36434	Phosphoinositide 3-kinase, ras-binding (1);	1.575750	0.03477	N	0.214491	T	0.33411	0.0862	L	0.36672	1.1	0.09310	N	1	B;B;B	0.20164	0.042;0.034;0.012	B;B;B	0.25506	0.061;0.036;0.037	T	0.30794	-0.9966	10	0.02654	T	1	-0.5465	9.0175	0.36179	0.2401:0.7599:0.0:0.0	.	280;281;281	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	E	281	ENSP00000443850:Q281E;ENSP00000404845:Q281E;ENSP00000266497:Q281E;ENSP00000445381:Q281E	ENSP00000266497:Q281E	Q	+	1	0	PIK3C2G	18335135	0.097000	0.21791	0.040000	0.18447	0.115000	0.19883	0.564000	0.23563	1.294000	0.44707	0.644000	0.83932	CAG	.	.	none		0.333	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570		G	18443868	C	G	18443868	3	3	32	1	0	0	0	0	1	0	0	0	11920	827	29	4	851	4	PIK3C2G	12	18443868	Missense_Mutation	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10	11100717	18443868	115408027	41	14001											
KCNC2	3747	hgsc.bcm.edu	37	chr12	75601404	75601404	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcggggcagtgcagcttgccGgtgcggtagtaattgagcac	7	8	17	9	3	0	1	0	1	0	0	0	1	0	1	1	4	5	6	1	4	2	4			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr12:75601404G>A	ENST00000549446.1	-	2	1040	c.360C>T	c.(358-360)acC>acT	p.T120T	KCNC2_ENST00000548513.1_Silent_p.T120T|KCNC2_ENST00000350228.2_Silent_p.T120T|KCNC2_ENST00000540018.1_Silent_p.T120T|KCNC2_ENST00000298972.1_Silent_p.T120T|KCNC2_ENST00000341669.3_Silent_p.T120T|KCNC2_ENST00000393288.2_Silent_p.T120T|KCNC2_ENST00000550433.1_Silent_p.T120T	NM_001260497.1|NM_139137.3	NP_001247426.1|NP_631875.1	Q96PR1	KCNC2_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 2	120					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)	p.T120T(2)		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)	GCAGCTTGCCGGTGCGGTAGT	0.692																																					p.T120T		Atlas-SNP	.											KCNC2_ENST00000549446,colon,carcinoma,0,2	KCNC2	239	2	2	Substitution - coding silent(2)	large_intestine(2)	c.C360T						PASS	.						28	32	31					12																	75601404		2203	4298	6501	SO:0001819	synonymous_variant	3747	exon2			CTTGCCGGTGCGG	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.360C>T	12.37:g.75601404G>A		151	0	0		158	12	0.0759494	NM_139137	B7Z231|F5H030|J3KPP5|Q4LE77|Q86W09|Q8N1V9|Q96PR0	Silent	SNP	ENST00000549446.1	37	CCDS9007.1																																																																																			.	.	none		0.692	KCNC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405581.2	NM_153748		A	75601404	G	A	75601404	2	1	32	1	0	0	0	0	0	0	0	1	8024	1103	39	1		1	KCNC2	12	75601404	Silent	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10	57157536	75601404	58250491	42	14002											
STAB2	55576	hgsc.bcm.edu	37	chr12	104031890	104031890	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacatgccaagaaggctaccGtggggatggccaagtgtgct	10	8	14	9	1	0	1	0	0	0	1	0	2	0	2	3	4	4	2	3	4	5	2	rs374968745		TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr12:104031890G>A	ENST00000388887.2	+	8	1010	c.806G>A	c.(805-807)cGt>cAt	p.R269H		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						GAAGGCTACCGTGGGGATGGC	0.498																																					p.R269H		Atlas-SNP	.											STAB2,rectum,carcinoma,0,1	STAB2	370	1	0			c.G806A						PASS	.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	177	151	160		806	-10.7	0	12		160	1,8599		0,1,4299	no	missense	STAB2	NM_017564.9	29	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	benign	269/2552	104031890	2,13004	2203	4300	6503	SO:0001583	missense	55576	exon8			GCTACCGTGGGGA	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.806G>A	12.37:g.104031890G>A	ENSP00000373539:p.Arg269His	133	0	0		93	7	0.0752688	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	37	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	G	0.287	-0.982590	0.02180	2.27E-4	1.16E-4	ENSG00000136011	ENST00000388887	T	0.04970	3.52	5.34	-10.7	0.00240	EGF domain, merozoite surface protein 1-like (1);Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1);	0.796511	0.11661	N	0.541825	T	0.03348	0.0097	N	0.20986	0.625	0.09310	N	0.999999	B	0.14438	0.01	B	0.09377	0.004	T	0.32508	-0.9904	10	0.26408	T	0.33	.	12.2094	0.54371	0.3687:0.0:0.539:0.0924	.	269	Q8WWQ8	STAB2_HUMAN	H	269	ENSP00000373539:R269H	ENSP00000373539:R269H	R	+	2	0	STAB2	102556020	0.000000	0.05858	0.000000	0.03702	0.453000	0.32348	-1.459000	0.02370	-2.678000	0.00410	-1.036000	0.02392	CGT	.	.	weak		0.498	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1			A	104031890	G	A	104031890	3	1	32	1	0	0	0	0	1	0	0	0	15253	1145	40	1	836	1	STAB2	12	104031890	Missense_Mutation	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10	28430486	104031890	29820005	43	14003											
DAO	1610	hgsc.bcm.edu	37	chr12	109278847	109278847	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgccctctgcatccatgagcGctaccactcagtcctgcagc	7	8	8	18	2	2	1	1	1	1	0	4	1	4	1	4	0	5	3	4	0	1	1	rs200257378		TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr12:109278847G>A	ENST00000228476.3	+	2	269	c.65G>A	c.(64-66)cGc>cAc	p.R22H	DAO_ENST00000551281.1_Missense_Mutation_p.R22H	NM_001917.4	NP_001908.3	P14920	OXDA_HUMAN	D-amino-acid oxidase	22					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)	ATCCATGAGCGCTACCACTCA	0.622													G|||	1	0.000199681	0.0	0.0	5008	,	,		17707	0.001		0.0	False		,,,				2504	0.0				p.R22H		Atlas-SNP	.											DAO,colon,carcinoma,0,1	DAO	58	1	0			c.G65A						PASS	.						121	97	105					12																	109278847		2203	4300	6503	SO:0001583	missense	1610	exon2			ATGAGCGCTACCA	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.65G>A	12.37:g.109278847G>A	ENSP00000228476:p.Arg22His	79	0	0		56	8	0.142857	NM_001917	B2R7I5|Q16758|Q8N6R2	Missense_Mutation	SNP	ENST00000228476.3	37	CCDS9122.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	11.86	1.763654	0.31228	.	.	ENSG00000110887	ENST00000551281;ENST00000228476;ENST00000547166	T;T;T	0.48836	0.8;0.8;0.87	5.44	-0.879	0.10613	FAD dependent oxidoreductase (1);NAD(P)-binding domain (1);	0.534143	0.23139	N	0.051487	T	0.23806	0.0576	N	0.20357	0.565	0.32875	D	0.509703	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.0	T	0.15925	-1.0420	10	0.17832	T	0.49	.	5.3692	0.16131	0.4709:0.0:0.3964:0.1328	.	22;22	P14920;Q7Z312	OXDA_HUMAN;.	H	22	ENSP00000446853:R22H;ENSP00000228476:R22H;ENSP00000447104:R22H	ENSP00000228476:R22H	R	+	2	0	DAO	107802976	0.210000	0.23517	0.459000	0.27081	0.960000	0.62799	0.606000	0.24194	-0.056000	0.13221	-0.218000	0.12543	CGC	G|1.000;A|0.000	0.000	strong		0.622	DAO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403682.1			A	109278847	G	A	109278847	3	1	32	1	0	0	0	0	1	0	0	0	4233	1087	38	1	67	1	DAO	12	109278847	Missense_Mutation	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10	5246957	109278847	24573048	44	14004											
TCTN1	79600	hgsc.bcm.edu	37	chr12	111066588	111066588	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acagataaacctgcattatcCtttattaatccagaagtacc	15	12	4	10	0	0	2	0	0	0	2	2	2	2	2	4	0	3	2	4	0	7	6			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr12:111066588C>T	ENST00000551590.1	+	4	645	c.489C>T	c.(487-489)tcC>tcT	p.S163S	TCTN1_ENST00000397655.3_Silent_p.S163S|TCTN1_ENST00000397659.4_Silent_p.S163S|RN7SL387P_ENST00000581015.1_RNA|HVCN1_ENST00000548312.1_Intron|TCTN1_ENST00000377654.3_5'UTR|TCTN1_ENST00000550703.2_Silent_p.S163S|TCTN1_ENST00000551555.2_3'UTR			Q2MV58	TECT1_HUMAN	tectonic family member 1	163					central nervous system interneuron axonogenesis (GO:0021956)|cilium morphogenesis (GO:0060271)|dorsal/ventral neural tube patterning (GO:0021904)|in utero embryonic development (GO:0001701)|neural tube formation (GO:0001841)|regulation of smoothened signaling pathway (GO:0008589)|somatic motor neuron differentiation (GO:0021523)|telencephalon development (GO:0021537)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|membrane (GO:0016020)|TCTN-B9D complex (GO:0036038)				NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(9)|urinary_tract(1)	15						CTGCATTATCCTTTATTAATC	0.259																																					p.S163S		Atlas-SNP	.											.	TCTN1	37	.	0			c.C489T						PASS	.						89	83	85					12																	111066588		1796	4060	5856	SO:0001819	synonymous_variant	79600	exon4			ATTATCCTTTATT	AK055891	CCDS41833.1, CCDS41834.1, CCDS41835.1	12q24.11	2011-09-07			ENSG00000204852	ENSG00000204852		"Tectonic proteins"	26113	protein-coding gene	gene with protein product		609863				16357211	Standard	NM_001082537		Approved	FLJ21127, TECT1, JBTS13	uc001trn.4	Q2MV58	OTTHUMG00000150051	ENST00000551590.1:c.489C>T	12.37:g.111066588C>T		76	0	0		57	5	0.0877193	NM_024549	A8MX11|Q49A60|Q6P5X1|Q6UXW2|Q8NAE9|Q96N72|Q9H798	Silent	SNP	ENST00000551590.1	37	CCDS41835.1																																																																																			.	.	none		0.259	TCTN1-001	KNOWN	non_canonical_TEC|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316016.2	NM_024549		T	111066588	C	T	111066588	2	4	32	1	0	0	0	0	0	0	0	1	15737	668	24	2		2	TCTN1	12	111066588	Silent	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10	1787741	111066588	22785307	45	14005											
C14orf50	145376	hgsc.bcm.edu	37	chr14	65054033	65054033	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gttcaacattcctcgcaggaGgcgtgaagatgaggaatcag	12	8	13	8	2	2	3	2	2	0	1	4	5	3	5	1	3	1	2	1	3	3	2			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr14:65054033G>T	ENST00000298705.1	+	10	929	c.833G>T	c.(832-834)aGg>aTg	p.R278M	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	278					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										CCTCGCAGGAGGCGTGAAGAT	0.438																																					p.R278M		Atlas-SNP	.											.	.	.	.	0			c.G833T						PASS	.						118	117	117					14																	65054033		2203	4300	6503	SO:0001583	missense	145376	exon10			GCAGGAGGCGTGA		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.833G>T	14.37:g.65054033G>T	ENSP00000298705:p.Arg278Met	105	0	0		95	4	0.0421053	NM_172365	Q6NTH6	Missense_Mutation	SNP	ENST00000298705.1	37	CCDS9767.1	.	.	.	.	.	.	.	.	.	.	G	16.18	3.049283	0.55218	.	.	ENSG00000165807	ENST00000298705	T	0.33438	1.41	5.55	1.56	0.23342	.	0.366248	0.26227	N	0.025588	T	0.23688	0.0573	L	0.36672	1.1	0.24361	N	0.994873	P	0.48230	0.907	B	0.44163	0.443	T	0.09357	-1.0678	10	0.62326	D	0.03	-18.651	7.233	0.26053	0.6839:0.0:0.3161:0.0	.	278	Q96LQ0	PPR36_HUMAN	M	278	ENSP00000298705:R278M	ENSP00000298705:R278M	R	+	2	0	C14orf50	64123786	0.167000	0.22975	0.989000	0.46669	0.940000	0.58332	0.403000	0.20982	0.404000	0.25506	-0.302000	0.09304	AGG	.	.	none		0.438	PPP1R36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280667.1	NM_172365		T	65054033	G	T	65054033	3	4	32	1	0	0	0	0	1	0	0	0	1779	1000	35	4	871	4	C14orf50	14	65054033	Missense_Mutation	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10		65054033	42295507	46	14006											
ADSSL1	122622	hgsc.bcm.edu	37	chr14	105204722	105204722	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctcatgcaggcaacggggTggtcatccacttgccaggct	7	9	12	13	1	2	0	2	0	1	0	4	0	3	0	2	5	3	3	2	5	1	1			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr14:105204722T>C	ENST00000330877.2	+	3	390	c.305T>C	c.(304-306)gTg>gCg	p.V102A	ADSSL1_ENST00000332972.5_Missense_Mutation_p.V145A	NM_152328.3	NP_689541.1			adenylosuccinate synthase like 1											central_nervous_system(1)|cervix(1)|kidney(1)|lung(5)|ovary(2)|prostate(1)	11		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00153)|OV - Ovarian serous cystadenocarcinoma(23;0.0148)|Epithelial(46;0.0396)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.18)		GGCAACGGGGTGGTCATCCAC	0.527																																					p.V145A		Atlas-SNP	.											ADSSL1,NS,carcinoma,-1,1	ADSSL1	37	1	0			c.T434C						scavenged	.						108	93	98					14																	105204722		2203	4300	6503	SO:0001583	missense	122622	exon3			ACGGGGTGGTCAT	AK095921	CCDS9990.1, CCDS9991.1	14q32.33	2010-08-05			ENSG00000185100	ENSG00000185100			20093	protein-coding gene	gene with protein product		612498					Standard	NM_199165		Approved	FLJ38602	uc001ype.3	Q8N142		ENST00000330877.2:c.305T>C	14.37:g.105204722T>C	ENSP00000331260:p.Val102Ala	67	0	0		50	3	0.06	NM_199165		Missense_Mutation	SNP	ENST00000330877.2	37	CCDS9990.1	.	.	.	.	.	.	.	.	.	.	T	18.43	3.623044	0.66901	.	.	ENSG00000185100	ENST00000330877;ENST00000332972	T;T	0.54479	0.57;0.57	3.64	3.64	0.41730	.	0.000000	0.85682	D	0.000000	T	0.71333	0.3327	M	0.81682	2.555	0.80722	D	1	D;D	0.64830	0.993;0.994	D;D	0.72338	0.973;0.977	T	0.75822	-0.3182	10	0.87932	D	0	-3.9478	12.2559	0.54623	0.0:0.0:0.0:1.0	.	145;102	Q8N142-2;Q8N142	.;PURA1_HUMAN	A	102;145	ENSP00000331260:V102A;ENSP00000333019:V145A	ENSP00000331260:V102A	V	+	2	0	ADSSL1	104275767	1.000000	0.71417	0.806000	0.32338	0.630000	0.37929	7.699000	0.84547	1.297000	0.44761	0.402000	0.26972	GTG	.	.	none		0.527	ADSSL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410529.1			C	105204722	T	C	105204722	3	2	32	1	0	0	0	0	1	0	0	0	348	1696	59	3	640	3	ADSSL1	14	105204722	Missense_Mutation	SNP	T	TCGA-GR-A4D5-01A-11D-A31X-10	40150689	105204722	2144818	47	14007											
BTBD12	84464	hgsc.bcm.edu	37	chr16	3633415	3633415	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgtgaggactggctctcGtcctcggagtctgagtccag	5	10	15	11	2	2	2	0	2	2	0	6	4	4	4	2	4	0	2	2	4	0	0	rs140844106	byFrequency	TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr16:3633415G>T	ENST00000294008.3	-	14	5476	c.4836C>A	c.(4834-4836)gaC>gaA	p.D1612E	RP11-461A8.1_ENST00000573982.1_lincRNA	NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	1612	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						ACTGGCTCTCGTCCTCGGAGT	0.602								Direct reversal of damage																													p.D1612E		Atlas-SNP	.											.	SLX4	173	.	0			c.C4836A						PASS	.						89	85	86					16																	3633415		2197	4300	6497	SO:0001583	missense	84464	exon14			GCTCTCGTCCTCG	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.4836C>A	16.37:g.3633415G>T	ENSP00000294008:p.Asp1612Glu	108	0	0		99	4	0.040404	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	.	.	.	.	.	.	.	.	.	.	G	14.49	2.550284	0.45383	.	.	ENSG00000188827	ENST00000294008	T	0.01279	5.06	5.64	-11.3	0.00108	.	0.338393	0.30830	N	0.008795	T	0.00754	0.0025	L	0.33245	0.995	0.21064	N	0.999799	P	0.38020	0.615	B	0.28638	0.092	T	0.35624	-0.9781	10	0.30078	T	0.28	.	9.2116	0.37322	0.5432:0.2303:0.2265:0.0	.	1612	Q8IY92	SLX4_HUMAN	E	1612	ENSP00000294008:D1612E	ENSP00000294008:D1612E	D	-	3	2	SLX4	3573416	0.000000	0.05858	0.004000	0.12327	0.552000	0.35366	-2.093000	0.01353	-1.628000	0.01548	-0.238000	0.12139	GAC	G|1.000;A|0.000	.	alt		0.602	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444		T	3633415	G	T	3633415	3	4	32	1	0	0	0	0	1	0	0	0	1542	1136	40	4	676	4	BTBD12	16	3633415	Missense_Mutation	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10		3633415	86721338	48	14008											
CDC27	996	hgsc.bcm.edu	37	chr17	45216113	45216113	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggttaacatacctctggcgAatttttatccatgtctgtta	9	17	7	8	1	2	0	0	0	2	0	3	1	3	0	2	2	2	2	2	2	5	6			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr17:45216113A>G	ENST00000066544.3	-	13	1789	c.1696T>C	c.(1696-1698)Tcg>Ccg	p.S566P	CDC27_ENST00000527547.1_Missense_Mutation_p.S565P|CDC27_ENST00000446365.2_Missense_Mutation_p.S505P|CDC27_ENST00000531206.1_Missense_Mutation_p.S572P	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	566					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						ACCTCTGGCGAATTTTTATCC	0.353																																					p.S572P		Atlas-SNP	.											CDC27_ENST00000531206,caecum,carcinoma,+1,6	CDC27	337	6	0			c.T1714C						scavenged	.						50	55	53					17																	45216113		2201	4299	6500	SO:0001583	missense	996	exon13			CTGGCGAATTTTT	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.1696T>C	17.37:g.45216113A>G	ENSP00000066544:p.Ser566Pro	50	0	0		48	2	0.0416667	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	A	25.3	4.623261	0.87460	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547	T;T;T;T	0.39229	1.09;1.09;1.09;1.09	5.62	5.62	0.85841	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.058252	0.64402	D	0.000001	T	0.71417	0.3337	M	0.92367	3.3	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;1.0;0.998	D;D;D;D	0.73380	0.98;0.961;0.975;0.924	T	0.79176	-0.1911	10	0.87932	D	0	-9.281	13.77	0.63019	1.0:0.0:0.0:0.0	.	505;565;572;566	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	P	566;572;505;565	ENSP00000066544:S566P;ENSP00000434614:S572P;ENSP00000392802:S505P;ENSP00000437339:S565P	ENSP00000066544:S566P	S	-	1	0	CDC27	42571112	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	8.962000	0.93254	2.141000	0.66446	0.528000	0.53228	TCG	.	.	none		0.353	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2			G	45216113	A	G	45216113	3	3	32	1	0	0	0	0	1	0	0	0	3068	246	9	3	806	3	CDC27	17	45216113	Missense_Mutation	SNP	A	TCGA-GR-A4D5-01A-11D-A31X-10		45216113	35979097	49	14009											
PPM1E	22843	hgsc.bcm.edu	37	chr17	56833454	56833454	+	Silent	SNP	G	G	A																															tgcggcggcggcgagccggaGccggaacccgaacccgaacc																								rs77856248		TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr17:56833454G>A	ENST00000308249.2	+	1	225	c.96G>A	c.(94-96)gaG>gaA	p.E32E		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)			Gcgagccggagccggaacccg	0.667																																					p.E32E		Atlas-SNP	.											PPM1E,colon,carcinoma,0,1	PPM1E	97	1	0			c.G96A						scavenged	.						14	20	18					17																	56833454		2185	4284	6469	SO:0001819	synonymous_variant	22843	exon1			GCCGGAGCCGGAA	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.96G>A	17.37:g.56833454G>A		235	1	0.00425532		200	9	0.045	NM_014906	Q8N8J9|Q96DB8	Silent	SNP	ENST00000308249.2	37	CCDS11613.1																																																																																			.	.	weak		0.667	PPM1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445458.1	NM_014906		A	56833454	G	A	56833454	2	1	32	1	0	0	0	0	0	0	0	1	12350	962	34	2		2	PPM1E	17	56833454	Silent	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10	11617341	56833454	24361756	50	14010	174	2	1	59		4	2	44	N	G_C	8.889429e-05
PPM1E	22843	hgsc.bcm.edu	37	chr17	56833457	56833457	+	Silent	SNP	G	G	C																															ggcggcggcgagccggagccGgaacccgaacccgaacccga																								rs3834568|rs201186780|rs74256772	byFrequency	TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr17:56833457G>C	ENST00000308249.2	+	1	228	c.99G>C	c.(97-99)ccG>ccC	p.P33P		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)			agccggagccggaacccgaac	0.672																																					p.P33P		Atlas-SNP	.											PPM1E,colon,carcinoma,0,1	PPM1E	97	1	0			c.G99C						PASS	.						14	20	18					17																	56833457		2188	4284	6472	SO:0001819	synonymous_variant	22843	exon1			GGAGCCGGAACCC	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.99G>C	17.37:g.56833457G>C		226	0	0		195	11	0.0564103	NM_014906	Q8N8J9|Q96DB8	Silent	SNP	ENST00000308249.2	37	CCDS11613.1																																																																																			.	.	weak		0.672	PPM1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445458.1	NM_014906		C	56833457	G	C	56833457	2	2	32	1	0	0	0	0	0	0	0	1	12350	1103	39	4		4	PPM1E	17	56833457	Silent	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10	3	56833457	24361753	51	14011	174	2	1	59		4	2	44	N	G_C	8.889429e-05
PPM1E	22843	hgsc.bcm.edu	37	chr17	56833490	56833490	+	Silent	SNP	G	G	A																															gaacccgaacccgaacccgaGtccgagcccgagcccgaacc																								rs59676153		TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr17:56833490G>A	ENST00000308249.2	+	1	261	c.132G>A	c.(130-132)gaG>gaA	p.E44E		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)			ccgaacccgagtccgagcccg	0.706																																					p.E44E		Atlas-SNP	.											PPM1E,colon,carcinoma,0,1	PPM1E	97	1	0			c.G132A						scavenged	.																																			SO:0001819	synonymous_variant	22843	exon1			ACCCGAGTCCGAG	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.132G>A	17.37:g.56833490G>A		231	1	0.004329		203	31	0.152709	NM_014906	Q8N8J9|Q96DB8	Silent	SNP	ENST00000308249.2	37	CCDS11613.1																																																																																			.	.	weak		0.706	PPM1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445458.1	NM_014906		A	56833490	G	A	56833490	2	1	32	1	0	0	0	0	0	0	0	1	12350	1020	36	2		2	PPM1E	17	56833490	Silent	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10	33	56833490	24361720	52	14012	175	2	1	59		4	2	44	N	G_C	8.889429e-05
PPM1E	22843	hgsc.bcm.edu	37	chr17	56833497	56833497	+	Missense_Mutation	SNP	C	C	T																															aacccgaacccgagtccgagCccgagcccgaacctgaactg																								rs61052860		TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr17:56833497C>T	ENST00000308249.2	+	1	268	c.139C>T	c.(139-141)Ccc>Tcc	p.P47S		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)			cgagtccgagcccgagcccga	0.701																																					p.P47S		Atlas-SNP	.											PPM1E,colon,carcinoma,0,1	PPM1E	97	1	0			c.C139T						PASS	.						15	17	16					17																	56833497		2188	4270	6458	SO:0001583	missense	22843	exon1			TCCGAGCCCGAGC	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.139C>T	17.37:g.56833497C>T	ENSP00000312411:p.Pro47Ser	232	0	0		202	20	0.0990099	NM_014906	Q8N8J9|Q96DB8	Missense_Mutation	SNP	ENST00000308249.2	37	CCDS11613.1	.	.	.	.	.	.	.	.	.	.	C	9.492	1.100828	0.20552	.	.	ENSG00000175175	ENST00000308249	T	0.22336	1.96	4.15	3.1	0.35709	.	.	.	.	.	T	0.09202	0.0227	N	0.14661	0.345	0.23192	N	0.998149	P	0.36909	0.573	B	0.32342	0.144	T	0.08452	-1.0721	9	0.02654	T	1	1.9125	10.3339	0.43839	0.0:0.7991:0.2009:0.0	rs61052860	47	Q8WY54-2	.	S	47	ENSP00000312411:P47S	ENSP00000312411:P47S	P	+	1	0	PPM1E	54188496	0.741000	0.28217	1.000000	0.80357	0.229000	0.25112	1.208000	0.32345	2.017000	0.59298	0.462000	0.41574	CCC	C|0.900;T|0.100	0.100	weak		0.701	PPM1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445458.1	NM_014906		T	56833497	C	T	56833497	3	4	32	1	0	0	0	0	1	0	0	0	12350	739	26	2	141	2	PPM1E	17	56833497	Missense_Mutation	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10	7	56833497	24361713	53	14013	175	2	1	59		4	2	44	N	G_C	8.889429e-05
CD7	924	hgsc.bcm.edu	37	chr17	80274179	80274179	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctggcgggtcagggagggcAgaggctgtctgcgggtcagg	5	6	22	8	2	3	1	2	0	1	1	3	2	3	2	0	7	1	3	0	7	0	0	rs560319694		TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr17:80274179A>G	ENST00000312648.3	-	3	610	c.504T>C	c.(502-504)tcT>tcC	p.S168S	CD7_ENST00000584284.1_Silent_p.S168S|CD7_ENST00000578509.1_Silent_p.S68S|CD7_ENST00000583376.1_Silent_p.S68S	NM_006137.6	NP_006128.1	P09564	CD7_HUMAN	CD7 molecule	168	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)			CAGGGAGGGCAGAGGCTGTCT	0.716																																					p.S168S	Pancreas(45;804 1068 19702 28207 28798)	Atlas-SNP	.											CD7,rectum,carcinoma,0,1	CD7	25	1	0			c.T504C						scavenged	.						14	17	16					17																	80274179		2168	4265	6433	SO:0001819	synonymous_variant	924	exon3			GAGGGCAGAGGCT	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.504T>C	17.37:g.80274179A>G		85	1	0.0117647		48	13	0.270833	NM_006137		Silent	SNP	ENST00000312648.3	37	CCDS11807.1																																																																																			.	.	none		0.716	CD7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442826.1	NM_006137		G	80274179	A	G	80274179	2	3	32	1	0	0	0	0	0	0	0	1	3034	175	7	3		3	CD7	17	80274179	Silent	SNP	A	TCGA-GR-A4D5-01A-11D-A31X-10	23440682	80274179	921031	54	14014											
SLMO1	10650	hgsc.bcm.edu	37	chr18	12420448	12420448	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcggccgcctgcacagcttgCgcctgctcagcaccgagtgg	5	6	14	16	4	1	0	1	0	0	0	1	1	1	0	4	2	5	4	4	2	0	1			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr18:12420448C>T	ENST00000440960.1	+	2	237	c.157C>T	c.(157-159)Cgc>Tgc	p.R53C	SLMO1_ENST00000587735.1_5'Flank|SLMO1_ENST00000336990.4_Missense_Mutation_p.R53C|SLMO1_ENST00000592149.1_Missense_Mutation_p.R32C|SLMO1_ENST00000590956.1_Intron	NM_001142405.1	NP_001135877.1	Q96N28	SLMO1_HUMAN	slowmo homolog 1 (Drosophila)	53	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						GCACAGCTTGCGCCTGCTCAG	0.746																																					p.R53C		Atlas-SNP	.											.	SLMO1	11	.	0			c.C157T						PASS	.						8	9	9					18																	12420448		2149	4232	6381	SO:0001583	missense	10650	exon2			AGCTTGCGCCTGC	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.157C>T	18.37:g.12420448C>T	ENSP00000404700:p.Arg53Cys	63	0	0		68	6	0.0882353	NM_001142405	B0YJ10|B4E0C9|D3DUJ1|Q6AHX2	Missense_Mutation	SNP	ENST00000440960.1	37	CCDS11860.1	.	.	.	.	.	.	.	.	.	.	c	15.85	2.955021	0.53293	.	.	ENSG00000141391	ENST00000440960;ENST00000336990	T;T	0.37915	1.17;1.17	4.8	3.92	0.45320	PRELI/MSF1 (2);	0.000000	0.85682	D	0.000000	T	0.71719	0.3373	H	0.97340	3.985	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80686	-0.1272	10	0.87932	D	0	-6.8006	12.3369	0.55073	0.3069:0.693:0.0:0.0	.	53	Q96N28	SLMO1_HUMAN	C	53	ENSP00000404700:R53C;ENSP00000338988:R53C	ENSP00000338988:R53C	R	+	1	0	SLMO1	12410448	1.000000	0.71417	0.970000	0.41538	0.180000	0.23129	2.059000	0.41384	0.981000	0.38548	-0.329000	0.08387	CGC	.	.	none		0.746	SLMO1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254602.2	NM_006553		T	12420448	C	T	12420448	3	4	32	1	0	0	0	0	1	0	0	0	14765	768	27	1	163	1	SLMO1	18	12420448	Missense_Mutation	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10		12420448	65656800	55	14015											
CXXC1	30827	hgsc.bcm.edu	37	chr18	47812268	47812268	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	accacacatgcgggctgaccGtttgatctgctgctgctgct	6	11	11	13	2	1	2	0	2	1	0	1	2	1	2	2	1	5	6	2	1	0	1			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr18:47812268G>A	ENST00000285106.6	-	5	1204	c.490C>T	c.(490-492)Cgg>Tgg	p.R164W	CXXC1_ENST00000412036.2_Missense_Mutation_p.R164W|CXXC1_ENST00000589940.1_Missense_Mutation_p.R164W|CXXC1_ENST00000587396.1_5'Flank	NM_001101654.1|NM_014593.3	NP_001095124.1|NP_055408.2	Q9P0U4	CXXC1_HUMAN	CXXC finger protein 1	164					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)|histone H3-K4 methylation (GO:0051568)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	24						CGGGCTGACCGTTTGATctgc	0.577																																					p.R164W		Atlas-SNP	.											.	CXXC1	50	.	0			c.C490T						PASS	.						54	47	49					18																	47812268		2203	4300	6503	SO:0001583	missense	30827	exon5			CTGACCGTTTGAT	BC014940	CCDS11945.1, CCDS45866.1	18q12	2014-02-20	2014-02-20		ENSG00000154832	ENSG00000154832		"Zinc fingers, PHD-type"	24343	protein-coding gene	gene with protein product	"CpG binding protein", "DNA-binding protein with PHD finger and CXXC domain", "zinc finger, CpG binding-type containing 1"	609150	"CXXC finger 1 (PHD domain)"			10799292, 10688657	Standard	NM_014593		Approved	HsT2645, PCCX1, hCGBP, PHF18, CGBP, SPP1, CFP1, ZCGPC1	uc002ler.4	Q9P0U4	OTTHUMG00000132670	ENST00000285106.6:c.490C>T	18.37:g.47812268G>A	ENSP00000285106:p.Arg164Trp	67	0	0		65	5	0.0769231	NM_001101654	B2RC03|Q8N2W4|Q96BC8|Q9P2V7	Missense_Mutation	SNP	ENST00000285106.6	37	CCDS11945.1	.	.	.	.	.	.	.	.	.	.	G	17.46	3.395324	0.62066	.	.	ENSG00000154832	ENST00000285106;ENST00000412036	T;T	0.30182	1.54;1.56	3.99	3.08	0.35506	Zinc finger, CXXC-type (2);	0.062520	0.64402	D	0.000005	T	0.51363	0.1670	M	0.73217	2.22	0.54753	D	0.999989	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.999	D;D;D;D;D	0.91635	0.999;0.996;0.988;0.993;0.993	T	0.52548	-0.8561	10	0.72032	D	0.01	.	10.7306	0.46093	0.0:0.0:0.8078:0.1922	.	164;164;164;164;31	B4DGL1;B2RC03;Q9P0U4-2;Q9P0U4;Q59EC8	.;.;.;CXXC1_HUMAN;.	W	164	ENSP00000285106:R164W;ENSP00000390475:R164W	ENSP00000285106:R164W	R	-	1	2	CXXC1	46066266	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.810000	0.47979	0.772000	0.33382	0.542000	0.68232	CGG	.	.	none		0.577	CXXC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255927.2	NM_014593		A	47812268	G	A	47812268	3	1	32	1	0	0	0	0	1	0	0	0	4099	1144	40	1	1536	1	CXXC1	18	47812268	Missense_Mutation	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10	35391820	47812268	30264980	56	14016											
ALPK2	115701	hgsc.bcm.edu	37	chr18	56171335	56171335	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcctcctccactgtagcataCgggatattgttctcaggccg	7	12	9	13	2	1	0	1	0	1	0	5	1	4	1	4	2	2	3	4	2	3	5	rs199833082	byFrequency	TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr18:56171335C>T	ENST00000361673.3	-	11	6288	c.6075G>A	c.(6073-6075)ccG>ccA	p.P2025P		NM_052947.3	NP_443179.3	Q86TB3	ALPK2_HUMAN	alpha-kinase 2	2025	Alpha-type protein kinase. {ECO:0000255|PROSITE-ProRule:PRU00501}.					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						CTGTAGCATACGGGATATTGT	0.458													C|||	2	0.000399361	0.0	0.0	5008	,	,		20784	0.001		0.001	False		,,,				2504	0.0				p.P2025P		Atlas-SNP	.											ALPK2_ENST00000361673,NS,carcinoma,0,2	ALPK2	487	2	0			c.G6075A						PASS	.						151	147	148					18																	56171335		2203	4300	6503	SO:0001819	synonymous_variant	115701	exon11			AGCATACGGGATA	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.6075G>A	18.37:g.56171335C>T		121	0	0		88	7	0.0795455	NM_052947	Q6ZUX0|Q8NAT5|Q96L95	Silent	SNP	ENST00000361673.3	37	CCDS11966.2																																																																																			C|1.000;T|0.000	0.000	strong		0.458	ALPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256126.1	NM_052947		T	56171335	C	T	56171335	2	4	32	1	0	0	0	0	0	0	0	1	545	523	19	1		1	ALPK2	18	56171335	Silent	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10	8359067	56171335	21905913	57	14017											
SERPINB13	5275	hgsc.bcm.edu	37	chr18	61255917	61255917	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcatcatggattcacttggcGccgtcagcactcgacttggg	7	11	11	12	3	4	0	4	0	0	0	5	2	4	1	1	3	1	1	1	3	0	3	rs191405968	byFrequency	TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr18:61255917G>A	ENST00000344731.5	+	2	118	c.16G>A	c.(16-18)Gcc>Acc	p.A6T	SERPINB13_ENST00000269489.5_Missense_Mutation_p.A6T	NM_012397.3	NP_036529.1	Q9UIV8	SPB13_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 13	6					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						TTCACTTGGCGCCGTCAGCAC	0.423													G|||	2	0.000399361	0.0	0.0029	5008	,	,		19904	0.0		0.0	False		,,,				2504	0.0				p.A6T		Atlas-SNP	.											.	SERPINB13	51	.	0			c.G16A						PASS	.						92	89	90					18																	61255917		2203	4300	6503	SO:0001583	missense	5275	exon2			CTTGGCGCCGTCA	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.16G>A	18.37:g.61255917G>A	ENSP00000341584:p.Ala6Thr	105	0	0		88	6	0.0681818	NM_012397	A8K2Q8|Q3MII2|Q9HCX1|Q9UBW1|Q9UKG0	Missense_Mutation	SNP	ENST00000344731.5	37	CCDS11985.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	7.201	0.593433	0.13875	.	.	ENSG00000197641	ENST00000431153;ENST00000269489;ENST00000539341;ENST00000344731	T;T;D	0.82984	-0.88;2.75;-1.67	4.89	-0.0729	0.13737	Serpin domain (1);	0.665922	0.13840	N	0.359130	T	0.59878	0.2226	N	0.11313	0.125	0.09310	N	1	B;B	0.25105	0.118;0.004	B;B	0.21917	0.037;0.007	T	0.46062	-0.9218	10	0.11485	T	0.65	.	5.043	0.14469	0.4092:0.1437:0.4471:0.0	.	6;6	B7ZKV6;Q9UIV8	.;SPB13_HUMAN	T	36;6;6;6	ENSP00000388300:A36T;ENSP00000269489:A6T;ENSP00000341584:A6T	ENSP00000269489:A6T	A	+	1	0	SERPINB13	59406897	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.999000	0.03697	-0.219000	0.10003	-0.258000	0.10820	GCC	G|1.000;A|0.000	0.000	strong		0.423	SERPINB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133798.1	NM_012397		A	61255917	G	A	61255917	3	1	32	1	0	0	0	0	1	0	0	0	14115	1087	38	1	18	1	SERPINB13	18	61255917	Missense_Mutation	SNP	G	TCGA-GR-A4D5-01A-11D-A31X-10	5084582	61255917	16821331	58	14018											
POLR2E	5434	hgsc.bcm.edu	37	chr19	1089905	1089905	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcccacgctttatcccaaagTagcgcgccacagggtccccc	8	6	9	18	3	0	0	0	0	0	0	2	0	2	0	5	1	1	2	5	1	3	3			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr19:1089905T>C	ENST00000215587.7	-	6	828	c.545A>G	c.(544-546)tAc>tGc	p.Y182C	POLR2E_ENST00000586746.1_Missense_Mutation_p.Y182C|POLR2E_ENST00000585838.1_5'UTR			P19388	RPAB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide E, 25kDa	182					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 III transcription (GO:0006386)|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 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)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|skin(2)	11		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)		TATCCCAAAGTAGCGCGCCAC	0.657																																					p.Y182C		Atlas-SNP	.											.	POLR2E	22	.	0			c.A545G						PASS	.						25	30	28					19																	1089905		2203	4299	6502	SO:0001583	missense	5434	exon6			CCAAAGTAGCGCG		CCDS12056.1	19p13.3	2013-01-21	2002-08-29			ENSG00000099817		"RNA polymerase subunits"	9192	protein-coding gene	gene with protein product	"DNA directed RNA polymerase II 23 kda polypeptide"	180664	"polymerase (RNA) II (DNA directed) polypeptide E (25kD)"			8034326	Standard	NM_002695		Approved	RPB5, RPABC1, XAP4, hRPB25, hsRPB5	uc002lre.4	P19388		ENST00000215587.7:c.545A>G	19.37:g.1089905T>C	ENSP00000215587:p.Tyr182Cys	185	0	0		185	21	0.113514	NM_002695	B2R6L4|D6W5Y1|O43380|Q6PIH5|Q9BT06	Missense_Mutation	SNP	ENST00000215587.7	37	CCDS12056.1	.	.	.	.	.	.	.	.	.	.	T	17.53	3.412695	0.62511	.	.	ENSG00000099817	ENST00000215587	T	0.55052	0.54	3.95	3.95	0.45737	RNA polymerase, subunit H/Rpb5 C-terminal (4);	0.000000	0.85682	D	0.000000	T	0.81019	0.4736	H	0.98089	4.145	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	D	0.86577	0.1851	10	0.87932	D	0	0.1586	11.664	0.51363	0.0:0.0:0.0:1.0	.	182	P19388	RPAB1_HUMAN	C	182	ENSP00000215587:Y182C	ENSP00000215587:Y182C	Y	-	2	0	POLR2E	1040905	1.000000	0.71417	0.885000	0.34714	0.637000	0.38172	7.212000	0.77941	1.440000	0.47531	0.402000	0.26972	TAC	.	.	none		0.657	POLR2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458044.1	NM_002695		C	1089905	T	C	1089905	3	2	32	1	0	0	0	0	1	0	0	0	12227	1638	57	3	95	3	POLR2E	19	1089905	Missense_Mutation	SNP	T	TCGA-GR-A4D5-01A-11D-A31X-10		1089905	58039078	59	14019											
ZNF699	374879	hgsc.bcm.edu	37	chr19	9407194	9407194	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgtgaattcttttgtgttCtgtgagcgatgaggaacaac	10	14	11	6	1	2	3	0	3	2	0	2	5	2	4	0	1	3	1	0	1	3	4			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr19:9407194C>A	ENST00000591998.1	-	6	1114	c.886G>T	c.(886-888)Gaa>Taa	p.E296*	ZNF699_ENST00000308650.3_Nonsense_Mutation_p.E296*|CTC-325H20.4_ENST00000591336.1_RNA			Q32M78	ZN699_HUMAN	zinc finger protein 699	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)			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						CTTTTGTGTTCTGTGAGCGAT	0.393																																					p.E296X		Atlas-SNP	.											.	ZNF699	67	.	0			c.G886T						PASS	.						108	108	108					19																	9407194		2155	4272	6427	SO:0001587	stop_gained	374879	exon5			TGTGTTCTGTGAG	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.886G>T	19.37:g.9407194C>A	ENSP00000467723:p.Glu296*	88	0	0		69	6	0.0869565	NM_198535	Q8N9A1	Nonsense_Mutation	SNP	ENST00000591998.1	37	CCDS42495.1	.	.	.	.	.	.	.	.	.	.	c	13.38	2.220238	0.39201	.	.	ENSG00000196110	ENST00000308650	.	.	.	3.28	-2.43	0.06522	.	0.000000	0.36972	N	0.002303	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	.	0.656	0.00834	0.1756:0.2514:0.173:0.4	.	.	.	.	X	296	.	ENSP00000311596:E296X	E	-	1	0	ZNF699	9268194	0.382000	0.25148	0.000000	0.03702	0.002000	0.02628	0.028000	0.13644	-0.346000	0.08312	-0.273000	0.10243	GAA	.	.	none		0.393	ZNF699-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449010.1	NM_198535		A	9407194	C	A	9407194	4	1	32	1	0	0	0	0	0	1	0	0	18116	922	32	4	1046	4	ZNF699	19	9407194	Nonsense_Mutation	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10	8317289	9407194	49721789	60	14020											
CAPN12	147968	hgsc.bcm.edu	37	chr19	39227194	39227194	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	accccatcccagactcacctCctctggaatctgaaagaagc	12	7	6	16	0	3	3	1	1	2	2	5	4	5	4	5	1	1	0	5	1	3	0			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr19:39227194C>G	ENST00000328867.4	-	11	1680	c.1372G>C	c.(1372-1374)Gag>Cag	p.E458Q	CAPN12_ENST00000601953.1_Missense_Mutation_p.E309Q|CTD-2540F13.2_ENST00000602255.1_RNA	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	458	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)			AGACTCACCTCCTCTGGAATC	0.652																																					p.E458Q		Atlas-SNP	.											.	CAPN12	43	.	0			c.G1372C						PASS	.						22	24	23					19																	39227194		2198	4296	6494	SO:0001583	missense	147968	exon11			TCACCTCCTCTGG	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.1372G>C	19.37:g.39227194C>G	ENSP00000331636:p.Glu458Gln	337	0	0		313	25	0.0798722	NM_144691		Missense_Mutation	SNP	ENST00000328867.4	37	CCDS12519.1	.	.	.	.	.	.	.	.	.	.	c	13.68	2.308766	0.40895	.	.	ENSG00000182472	ENST00000328867	D	0.87809	-2.3	2.66	2.66	0.31614	Peptidase C2, calpain, large subunit, domain III (2);Peptidase C2, calpain, domain III (1);	0.845148	0.10500	N	0.667358	T	0.81692	0.4876	L	0.45228	1.405	0.32007	N	0.602555	B	0.06786	0.001	B	0.16722	0.016	T	0.78494	-0.2182	10	0.38643	T	0.18	.	8.9436	0.35745	0.0:1.0:0.0:0.0	.	458	Q6ZSI9	CAN12_HUMAN	Q	458	ENSP00000331636:E458Q	ENSP00000331636:E458Q	E	-	1	0	CAPN12	43919034	1.000000	0.71417	1.000000	0.80357	0.520000	0.34377	2.215000	0.42862	1.798000	0.52647	0.298000	0.19748	GAG	.	.	none		0.652	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1			G	39227194	C	G	39227194	3	3	32	1	0	0	0	0	1	0	0	0	2627	864	30	4	831	4	CAPN12	19	39227194	Missense_Mutation	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10	29820000	39227194	19901789	61	14021											
ZNF578	147660	hgsc.bcm.edu	37	chr19	53014878	53014878	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	taatcaacaatcacacctttCacgtcatcatagacttcata	15	12	2	12	1	6	1	6	0	0	1	6	1	6	1	1	0	1	0	1	0	5	5			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr19:53014878C>T	ENST00000421239.2	+	6	1488	c.1244C>T	c.(1243-1245)tCa>tTa	p.S415L	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	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)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		TCACACCTTTCACGTCATCAT	0.378																																					p.S415L		Atlas-SNP	.											.	.	.	.	0			c.C1244T						PASS	.						88	91	90					19																	53014878		2203	4300	6503	SO:0001583	missense	147660	exon6			ACCTTTCACGTCA	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.1244C>T	19.37:g.53014878C>T	ENSP00000459216:p.Ser415Leu	97	0	0		49	5	0.102041	NM_001099694	B4DR51|I3L1Y6	Missense_Mutation	SNP	ENST00000421239.2	37	CCDS54310.1	.	.	.	.	.	.	.	.	.	.	-	5.135	0.210440	0.09757	.	.	ENSG00000258405	ENST00000553364	.	.	.	1.48	-2.25	0.06888	.	.	.	.	.	T	0.17408	0.0418	N	0.17764	0.52	0.09310	N	1	B	0.12013	0.005	B	0.13407	0.009	T	0.24621	-1.0155	7	.	.	.	.	3.2313	0.06750	0.0:0.3277:0.2196:0.4527	.	415	G3V4F6	.	L	415	.	.	S	+	2	0	ZNF578	57706690	0.117000	0.22190	0.000000	0.03702	0.002000	0.02628	-0.265000	0.08644	-0.620000	0.05641	-0.734000	0.03567	TCA	.	.	none		0.378	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472		T	53014878	C	T	53014878	3	4	32	1	0	0	0	0	1	0	0	0	18025	838	29	2	1254	2	ZNF578	19	53014878	Missense_Mutation	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10	13787684	53014878	6114105	62	14022											
RAB36	9609	hgsc.bcm.edu	37	chr22	23495232	23495232	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccacaggttttgcaagaaTgtttttgatcgagactacaa	12	12	8	9	1	0	3	0	1	0	2	1	4	0	3	2	1	2	3	2	1	4	5			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr22:23495232T>G	ENST00000263116.2	+	5	478	c.438T>G	c.(436-438)aaT>aaG	p.N146K	RAB36_ENST00000341989.4_Missense_Mutation_p.N124K	NM_004914.2	NP_004905.2	O95755	RAB36_HUMAN	RAB36, member RAS oncogene family	146					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.155)		TTTGCAAGAATGTTTTTGATC	0.478																																					p.N146K		Atlas-SNP	.											.	RAB36	26	.	0			c.T438G						PASS	.						183	174	177					22																	23495232		2203	4300	6503	SO:0001583	missense	9609	exon5			CAAGAATGTTTTT	AB023061	CCDS13805.1	22q11.22	2008-06-11			ENSG00000100228	ENSG00000100228		"RAB, member RAS oncogene"	9775	protein-coding gene	gene with protein product		605662				9920784, 10591208	Standard	NM_004914		Approved		uc002zwv.1	O95755	OTTHUMG00000150601	ENST00000263116.2:c.438T>G	22.37:g.23495232T>G	ENSP00000263116:p.Asn146Lys	63	0	0		52	9	0.173077	NM_004914	Q2M390|Q7Z4A9|Q9UHP5	Missense_Mutation	SNP	ENST00000263116.2	37	CCDS13805.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.35|16.35	3.098812|3.098812	0.56183|0.56183	.|.	.|.	ENSG00000100228|ENSG00000100228	ENST00000420895|ENST00000263116;ENST00000341989	.|T;T	.|0.80214	.|-1.35;-1.35	5.53|5.53	-1.43|-1.43	0.08884|0.08884	.|Small GTP-binding protein domain (1);	.|0.059264	.|0.64402	.|D	.|0.000005	T|T	0.77505|0.77505	0.4140|0.4140	L|L	0.39514|0.39514	1.22|1.22	0.29904|0.29904	N|N	0.824138|0.824138	.|D;B	.|0.55605	.|0.972;0.118	.|P;B	.|0.53360	.|0.724;0.101	T|T	0.75665|0.75665	-0.3239|-0.3239	5|10	.|0.44086	.|T	.|0.13	-26.0893|-26.0893	11.9159|11.9159	0.52765|0.52765	0.0:0.4297:0.0:0.5703|0.0:0.4297:0.0:0.5703	.|.	.|124;146	.|O95755-2;O95755	.|.;RAB36_HUMAN	G|K	41|146;124	.|ENSP00000263116:N146K;ENSP00000343494:N124K	.|ENSP00000263116:N146K	C|N	+|+	1|3	0|2	RAB36|RAB36	21825232|21825232	0.355000|0.355000	0.24921|0.24921	0.226000|0.226000	0.23910|0.23910	0.816000|0.816000	0.46133|0.46133	0.251000|0.251000	0.18257|0.18257	-0.429000|-0.429000	0.07329|0.07329	-1.139000|-1.139000	0.01908|0.01908	TGT|AAT	.	.	none		0.478	RAB36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319046.1	NM_004914		G	23495232	T	G	23495232	3	3	32	1	0	0	0	0	1	0	0	0	12941	1461	51	5	456	5	RAB36	22	23495232	Missense_Mutation	SNP	T	TCGA-GR-A4D5-01A-11D-A31X-10		23495232	27809334	63	14023											
MKL1	57591	hgsc.bcm.edu	37	chr22	40816901	40816901	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttgtggtgctgctgctgctgCtggttgaggatctgcagctg	3	14	16	8	0	1	1	0	1	1	0	1	2	1	2	0	3	7	8	0	3	0	2			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chr22:40816901C>G	ENST00000355630.3	-	10	1421	c.831G>C	c.(829-831)caG>caC	p.Q277H	MKL1_ENST00000407029.1_Missense_Mutation_p.Q277H|MKL1_ENST00000402042.1_Missense_Mutation_p.Q227H|MKL1_ENST00000396617.3_Missense_Mutation_p.Q277H	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1	277	Gln-rich.				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						GCTGCTGCTGCTGGTTGAGGA	0.657			T	RBM15	acute megakaryocytic leukemia																																p.Q277H		Atlas-SNP	.		Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	.	MKL1	69	.	0			c.G831C						PASS	.						62	63	62					22																	40816901		2203	4300	6503	SO:0001583	missense	57591	exon10			CTGCTGCTGGTTG	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	ENST00000355630.3:c.831G>C	22.37:g.40816901C>G	ENSP00000347847:p.Gln277His	82	0	0		67	4	0.0597015	NM_020831	Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Missense_Mutation	SNP	ENST00000355630.3	37	CCDS14003.1	.	.	.	.	.	.	.	.	.	.	C	19.12	3.766193	0.69878	.	.	ENSG00000196588	ENST00000355630;ENST00000396617;ENST00000402042;ENST00000407029	T;T;T;T	0.61859	0.16;0.11;0.07;0.16	5.26	4.24	0.50183	.	0.000000	0.85682	D	0.000000	T	0.73353	0.3576	M	0.77616	2.38	0.48696	D	0.999692	P;D;P	0.67145	0.787;0.996;0.787	B;D;B	0.75484	0.294;0.986;0.294	T	0.75385	-0.3336	10	0.66056	D	0.02	-15.2355	9.9937	0.41887	0.0:0.8449:0.0:0.1551	.	227;277;277	B0QY83;E7ER32;Q969V6	.;.;MKL1_HUMAN	H	277;277;227;277	ENSP00000347847:Q277H;ENSP00000379861:Q277H;ENSP00000385584:Q227H;ENSP00000385835:Q277H	ENSP00000347847:Q277H	Q	-	3	2	MKL1	39146847	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.270000	0.51600	1.210000	0.43336	0.462000	0.41574	CAG	.	.	none		0.657	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321522.1	NM_020831		G	40816901	C	G	40816901	3	3	32	1	0	0	0	0	1	0	0	0	9610	796	28	4	1988	4	MKL1	22	40816901	Missense_Mutation	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10	17321669	40816901	10487665	64	14024											
MSN	4478	hgsc.bcm.edu	37	chrX	64951012	64951012	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acaaggaccagtgggaggagCggatccaggtgtggcatgag	11	5	18	7	1	0	1	0	1	0	0	1	5	1	5	2	6	1	1	2	6	1	0			TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chrX:64951012C>T	ENST00000360270.5	+	5	683	c.511C>T	c.(511-513)Cgg>Tgg	p.R171W		NM_002444.2	NP_002435.1	P26038	MOES_HUMAN	moesin	171	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						GTGGGAGGAGCGGATCCAGGT	0.532			T	ALK	ALCL																																p.R171W		Atlas-SNP	.		Dom	yes		X	Xq11.2-q12	4478	moesin		L	.	MSN	89	.	0			c.C511T						PASS	.						110	67	82					X																	64951012		2202	4300	6502	SO:0001583	missense	4478	exon5			GAGGAGCGGATCC	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.511C>T	X.37:g.64951012C>T	ENSP00000353408:p.Arg171Trp	330	0	0		270	24	0.0888889	NM_002444		Missense_Mutation	SNP	ENST00000360270.5	37	CCDS14382.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.223212	0.79464	.	.	ENSG00000147065	ENST00000360270	D	0.81739	-1.53	5.8	2.74	0.32292	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	0.92319	0.7563	H	0.97051	3.93	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93176	0.6570	10	0.87932	D	0	.	12.3315	0.55041	0.6829:0.3171:0.0:0.0	.	171	P26038	MOES_HUMAN	W	171	ENSP00000353408:R171W	ENSP00000353408:R171W	R	+	1	2	MSN	64867737	0.997000	0.39634	0.910000	0.35882	0.974000	0.67602	2.491000	0.45303	0.571000	0.29365	0.600000	0.82982	CGG	.	.	none		0.532	MSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056981.1	NM_002444		T	64951012	C	T	64951012	3	4	32	1	0	0	0	0	1	0	0	0	9894	759	27	1	529	1	MSN	23	64951012	Missense_Mutation	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10		64951012	90319548	65	14025											
AMOT	154796	hgsc.bcm.edu	37	chrX	112035109	112035109	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctccagtcgtgtccggagaCggtgctctagctgctcacgt	5	11	12	13	4	3	1	1	0	2	1	6	2	4	1	2	2	3	3	2	2	1	1	rs150900068		TCGA-GR-A4D5-01A-11D-A31X-10	TCGA-GR-A4D5-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	90533f5d-0761-4b4a-a1ee-91e10e9ba2c4	433ab22f-7d7f-4e86-86f3-0ab50681046c	g.chrX:112035109C>T	ENST00000524145.1	-	7	1951	c.1877G>A	c.(1876-1878)cGt>cAt	p.R626H	AMOT_ENST00000371962.1_Missense_Mutation_p.R394H|AMOT_ENST00000371959.3_Missense_Mutation_p.R626H|AMOT_ENST00000304758.1_Missense_Mutation_p.R217H|AMOT_ENST00000371958.1_Missense_Mutation_p.R394H			Q4VCS5	AMOT_HUMAN	angiomotin	626					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						TGTCCGGAGACGGTGCTCTAG	0.473																																					p.R626H		Atlas-SNP	.											.	AMOT	204	.	0			c.G1877A						PASS	.	C	HIS/ARG,HIS/ARG	0,3835		0,0,1632,571	154	132	140		1877,650	5.8	1	X	dbSNP_134	140	1,6727		0,1,2427,1872	no	missense,missense	AMOT	NM_001113490.1,NM_133265.2	29,29	0,1,4059,2443	TT,TC,CC,C		0.0149,0.0,0.0095	probably-damaging,probably-damaging	626/1085,217/676	112035109	1,10562	2203	4300	6503	SO:0001583	missense	154796	exon6			CGGAGACGGTGCT	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.1877G>A	X.37:g.112035109C>T	ENSP00000429013:p.Arg626His	88	0	0		83	8	0.0963855	NM_001113490	Q504X5|Q9HD27|Q9UPT1	Missense_Mutation	SNP	ENST00000524145.1	37	CCDS48154.1	.	.	.	.	.	.	.	.	.	.	C	35	5.460507	0.96240	0.0	1.49E-4	ENSG00000126016	ENST00000304758;ENST00000371959;ENST00000371962;ENST00000524145;ENST00000371958	T;T;T;T;T	0.35421	1.99;1.57;1.81;1.57;1.31	5.79	5.79	0.91817	Angiomotin, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.63522	0.2518	M	0.79123	2.44	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.66598	-0.5883	10	0.66056	D	0.02	-9.5449	17.8504	0.88746	0.0:1.0:0.0:0.0	.	626	Q4VCS5	AMOT_HUMAN	H	217;626;394;626;394	ENSP00000305557:R217H;ENSP00000361027:R626H;ENSP00000361030:R394H;ENSP00000429013:R626H;ENSP00000361026:R394H	ENSP00000305557:R217H	R	-	2	0	AMOT	111921765	1.000000	0.71417	0.987000	0.45799	0.926000	0.56050	7.818000	0.86416	2.435000	0.82474	0.600000	0.82982	CGT	C|1.000;T|0.000	0.000	weak		0.473	AMOT-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378570.1	NM_133265		T	112035109	C	T	112035109	3	4	32	1	0	0	0	0	1	0	0	0	582	536	19	1	1401	1	AMOT	23	112035109	Missense_Mutation	SNP	C	TCGA-GR-A4D5-01A-11D-A31X-10	47084097	112035109	43235451	66	14026											
PODN	127435	hgsc.bcm.edu	37	chr1	53544260	53544260	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggccttccagggcctcaagCggttgcacacggtgcacctg	6	8	13	14	2	1	0	1	0	0	0	2	0	2	0	4	4	3	3	4	4	1	2			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr1:53544260C>T	ENST00000312553.5	+	8	1229	c.1222C>T	c.(1222-1224)Cgg>Tgg	p.R408W	PODN_ENST00000371500.3_Missense_Mutation_p.R389W|RP11-334A14.5_ENST00000447867.1_RNA|PODN_ENST00000395871.2_Missense_Mutation_p.R266W	NM_001199081.1|NM_153703.4	NP_001186010.1|NP_714914.2	Q7Z5L7	PODN_HUMAN	podocan	360					negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						GGGCCTCAAGCGGTTGCACAC	0.652																																					p.R408W		Atlas-SNP	.											.	PODN	86	.	0			c.C1222T						PASS	.						57	54	55					1																	53544260		2203	4300	6503	SO:0001583	missense	127435	exon8			CTCAAGCGGTTGC	AY313607	CCDS573.1, CCDS55601.1, CCDS55602.1	1p32.3	2008-02-05			ENSG00000174348	ENSG00000174348		"Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"	23174	protein-coding gene	gene with protein product	"podocan proteoglycan"	608661					Standard	NM_153703		Approved	PCAN, PODOCAN, MGC24995, SLRR5A	uc010onr.2	Q7Z5L7	OTTHUMG00000008934	ENST00000312553.5:c.1222C>T	1.37:g.53544260C>T	ENSP00000308315:p.Arg408Trp	81	0	0		84	24	0.285714	NM_153703	B4DKN5|B4E373|Q5VVZ2|Q5VVZ3|Q6PIR3|Q6UXL8|Q8N641	Missense_Mutation	SNP	ENST00000312553.5	37	CCDS573.1	.	.	.	.	.	.	.	.	.	.	C	18.05	3.536732	0.65085	.	.	ENSG00000174348	ENST00000371500;ENST00000395871;ENST00000312553	T;T;T	0.58940	0.3;0.3;0.3	4.81	1.05	0.20165	.	0.456979	0.21202	N	0.078445	T	0.72630	0.3484	M	0.74467	2.265	0.32794	N	0.500809	D;D;D	0.76494	0.999;0.999;0.994	D;D;P	0.67103	0.949;0.946;0.877	T	0.80204	-0.1479	10	0.72032	D	0.01	.	14.7344	0.69406	0.8156:0.1844:0.0:0.0	.	266;389;408	Q7Z5L7-4;Q7Z5L7-2;Q7Z5L7-3	.;.;.	W	389;266;408	ENSP00000360555:R389W;ENSP00000379212:R266W;ENSP00000308315:R408W	ENSP00000308315:R408W	R	+	1	2	PODN	53316848	1.000000	0.71417	0.989000	0.46669	0.994000	0.84299	1.866000	0.39489	0.051000	0.15978	0.555000	0.69702	CGG	.	.	none		0.652	PODN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024735.1	NM_153703		T	53544260	C	T	53544260	3	4	33	1	0	0	0	0	1	0	0	0	12187	759	27	1	1252	1	PODN	1	53544260	Missense_Mutation	SNP	C	TCGA-GR-A4D6-01A-11D-A31X-10		53544260	195706361	1	14027											
COL24A1	255631	hgsc.bcm.edu	37	chr1	86249233	86249233	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccaacaatgccagcatccccTtcaggaccctagacatacaa	14	6	5	16	0	1	1	1	0	0	1	2	2	2	2	5	1	4	1	5	1	5	3			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr1:86249233T>G	ENST00000370571.2	-	51	4596	c.4230A>C	c.(4228-4230)gaA>gaC	p.E1410D	COL24A1_ENST00000436319.1_Missense_Mutation_p.E1410D	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	1410	Collagen-like 16.				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)	p.E1410D(1)		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)		CAGCATCCCCTTCAGGACCCT	0.353																																					p.E1410D		Atlas-SNP	.											COL24A1,colon,carcinoma,0,1	COL24A1	202	1	1	Substitution - Missense(1)	large_intestine(1)	c.A4230C						PASS	.						122	115	117					1																	86249233		1840	4085	5925	SO:0001583	missense	255631	exon51			ATCCCCTTCAGGA	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.4230A>C	1.37:g.86249233T>G	ENSP00000359603:p.Glu1410Asp	123	0	0		156	35	0.224359	NM_152890	C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	Missense_Mutation	SNP	ENST00000370571.2	37	CCDS41353.1	.	.	.	.	.	.	.	.	.	.	T	12.22	1.872250	0.33069	.	.	ENSG00000171502	ENST00000370571;ENST00000436319	D;D	0.93307	-3.2;-3.1	5.48	-3.93	0.04143	.	0.000000	0.39083	N	0.001464	T	0.65943	0.2740	N	0.11201	0.11	0.26770	N	0.969815	P;P	0.34977	0.478;0.458	B;B	0.38880	0.148;0.284	T	0.73672	-0.3909	10	0.13853	T	0.58	.	3.6705	0.08272	0.5974:0.1259:0.0997:0.177	.	1410;1410	Q17RW2;Q17RW2-2	COOA1_HUMAN;.	D	1410	ENSP00000359603:E1410D;ENSP00000392531:E1410D	ENSP00000359603:E1410D	E	-	3	2	COL24A1	86021821	0.021000	0.18746	0.961000	0.40146	0.883000	0.51084	-1.096000	0.03353	-0.281000	0.09141	-0.242000	0.12053	GAA	.	.	none		0.353	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890		G	86249233	T	G	86249233	3	3	33	1	0	0	0	0	1	0	0	0	3685	1606	56	5	954	5	COL24A1	1	86249233	Missense_Mutation	SNP	T	TCGA-GR-A4D6-01A-11D-A31X-10	32704973	86249233	163001388	2	14028											
FCRL3	115352	hgsc.bcm.edu	37	chr1	157670256	157670256	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cccatctactcactcaggatCagcagcagcagccacagaag	13	5	8	15	0	4	1	3	0	1	1	4	2	4	2	2	1	5	3	2	1	2	1			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr1:157670256C>T	ENST00000368184.3	-	2	315	c.24G>A	c.(22-24)ctG>ctA	p.L8L	FCRL3_ENST00000473231.1_5'Flank|FCRL3_ENST00000368186.5_Silent_p.L8L	NM_052939.3	NP_443171.2	Q96P31	FCRL3_HUMAN	Fc receptor-like 3	8						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(1)|large_intestine(13)|lung(31)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)	69	all_hematologic(112;0.0378)					CACTCAGGATCAGCAGCAGCA	0.547																																					p.L8L		Atlas-SNP	.											.	FCRL3	163	.	0			c.G24A						PASS	.						47	49	49					1																	157670256		2203	4300	6503	SO:0001819	synonymous_variant	115352	exon2			CAGGATCAGCAGC	AF459027	CCDS1167.1	1q21-q22	2013-01-11			ENSG00000160856	ENSG00000160856		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18506	protein-coding gene	gene with protein product		606510				11493702, 12014205	Standard	XR_241065		Approved	FCRH3, IRTA3, IFGP3, SPAP2a, SPAP2, SPAP2b, SPAP2c, SPAP2d, SPAP2e, CD307c	uc001frb.3	Q96P31	OTTHUMG00000019400	ENST00000368184.3:c.24G>A	1.37:g.157670256C>T		127	0	0		160	39	0.24375	NM_052939	A0N0M4|A8MTH7|D3DVD2|Q5VXZ8|Q8N6S2|Q96LA4|Q96P27|Q96P28|Q96P29|Q96P30	Silent	SNP	ENST00000368184.3	37	CCDS1167.1																																																																																			.	.	none		0.547	FCRL3-006	NOVEL	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051419.2	NM_052939		T	157670256	C	T	157670256	2	4	33	1	0	0	0	0	0	0	0	1	5804	813	29	2		2	FCRL3	1	157670256	Silent	SNP	C	TCGA-GR-A4D6-01A-11D-A31X-10	71421023	157670256	91580365	3	14029											
PAPPA2	60676	hgsc.bcm.edu	37	chr1	176671860	176671860	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gctccttattgtggagatggGaaggtgtcagagtgagtatt	9	13	15	4	0	1	3	1	1	0	2	2	5	2	4	1	3	0	2	1	3	3	4			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr1:176671860G>C	ENST00000367662.3	+	9	4518	c.3354G>C	c.(3352-3354)ggG>ggC	p.G1118G		NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	1118					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						GTGGAGATGGGAAGGTGTCAG	0.502																																					p.G1118G		Atlas-SNP	.											.	PAPPA2	665	.	0			c.G3354C						PASS	.						85	81	82					1																	176671860		1978	4164	6142	SO:0001819	synonymous_variant	60676	exon9			AGATGGGAAGGTG	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.3354G>C	1.37:g.176671860G>C		33	0	0		30	4	0.133333	NM_020318	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Silent	SNP	ENST00000367662.3	37	CCDS41438.1																																																																																			.	.	none		0.502	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1			C	176671860	G	C	176671860	2	2	33	1	0	0	0	0	0	0	0	1	11442	1161	41	4		4	PAPPA2	1	176671860	Silent	SNP	G	TCGA-GR-A4D6-01A-11D-A31X-10	19001604	176671860	72578761	4	14030											
PPP2R5A	5525	hgsc.bcm.edu	37	chr1	212532087	212532087	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatggaaatgaatggcaagcTtttcgatgaccttactagct	13	12	9	7	1	0	2	0	2	0	0	1	4	0	3	1	2	3	3	1	2	6	4			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr1:212532087T>G	ENST00000261461.2	+	12	1860	c.1286T>G	c.(1285-1287)cTt>cGt	p.L429R	RP11-384C4.2_ENST00000447949.1_RNA|PPP2R5A_ENST00000537030.3_Missense_Mutation_p.L372R	NM_006243.3	NP_006234.1	Q15172	2A5A_HUMAN	protein phosphatase 2, regulatory subunit B', alpha	429					negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of lipid kinase activity (GO:0090219)|positive regulation of protein dephosphorylation (GO:0035307)|signal transduction (GO:0007165)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|M band (GO:0031430)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)|Z disc (GO:0030018)	kinase binding (GO:0019900)|protein phosphatase type 2A regulator activity (GO:0008601)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)	16				OV - Ovarian serous cystadenocarcinoma(81;0.0125)|all cancers(67;0.029)|Epithelial(68;0.154)|GBM - Glioblastoma multiforme(131;0.155)		AATGGCAAGCTTTTCGATGAC	0.343																																					p.L429R		Atlas-SNP	.											.	PPP2R5A	48	.	0			c.T1286G						PASS	.						94	89	91					1																	212532087		2203	4300	6503	SO:0001583	missense	5525	exon12			GCAAGCTTTTCGA	BC022474	CCDS1503.1, CCDS55686.1	1q32.2-q32.3	2010-06-18	2010-04-14		ENSG00000066027	ENSG00000066027		"Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"	9309	protein-coding gene	gene with protein product		601643	"protein phosphatase 2, regulatory subunit B (B56), alpha isoform", "protein phosphatase 2, regulatory subunit B', alpha isoform"			7592815	Standard	NM_006243		Approved	PR61A, B56A	uc001hjb.3	Q15172	OTTHUMG00000036750	ENST00000261461.2:c.1286T>G	1.37:g.212532087T>G	ENSP00000261461:p.Leu429Arg	269	0	0		318	47	0.147799	NM_006243	B2R6D2|B7Z7L2|D3DT99|Q2NL72|Q5VVB2|Q8TBI9	Missense_Mutation	SNP	ENST00000261461.2	37	CCDS1503.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.736868	0.89482	.	.	ENSG00000066027	ENST00000542178;ENST00000261461;ENST00000537030	.	.	.	6.06	6.06	0.98353	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.87653	0.6231	H	0.97103	3.94	0.80722	D	1	D;D	0.57257	0.979;0.979	D;D	0.66084	0.941;0.941	D	0.91502	0.5220	9	0.72032	D	0.01	-16.7161	16.6154	0.84909	0.0:0.0:0.0:1.0	.	372;429	B7Z7L2;Q15172	.;2A5A_HUMAN	R	429;429;372	.	ENSP00000261461:L429R	L	+	2	0	PPP2R5A	210598710	1.000000	0.71417	0.994000	0.49952	0.997000	0.91878	7.678000	0.84035	2.315000	0.78130	0.533000	0.62120	CTT	.	.	none		0.343	PPP2R5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089302.1	NM_006243		G	212532087	T	G	212532087	3	3	33	1	0	0	0	0	1	0	0	0	12404	1609	56	5	1332	5	PPP2R5A	1	212532087	Missense_Mutation	SNP	T	TCGA-GR-A4D6-01A-11D-A31X-10	35860227	212532087	36718534	5	14031											
OR2L3	391192	hgsc.bcm.edu	37	chr1	248224739	248224739	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagtaactttctactatgcAccttttgtctacacttatct	9	18	4	10	0	3	0	0	0	3	0	3	0	3	0	1	0	4	3	1	0	6	9	rs113420317	byFrequency	TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr1:248224739A>G	ENST00000359959.3	+	1	756	c.756A>G	c.(754-756)gcA>gcG	p.A252A	OR2L13_ENST00000366478.2_Intron	NM_001004687.1	NP_001004687.1	Q8NG85	OR2L3_HUMAN	olfactory receptor, family 2, subfamily L, member 3	252						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)			TCTACTATGCACCTTTTGTCT	0.498													a|||	40	0.00798722	0.0287	0.0029	5008	,	,		20949	0.0		0.0	False		,,,				2504	0.0				p.A252A		Atlas-SNP	.											OR2L3,NS,carcinoma,0,2	OR2L3	97	2	0			c.A756G						scavenged	.	A	,	90,4316	73.1+/-111.1	2,86,2115	131	124	126		756,	-4	0	1	dbSNP_132	126	20,8576	3.0+/-9.4	0,20,4278	no	coding-synonymous,intron	OR2L13,OR2L3	NM_001004687.1,NM_175911.2	,	2,106,6393	GG,GA,AA		0.2327,2.0427,0.846	,	252/313,	248224739	110,12892	2203	4298	6501	SO:0001819	synonymous_variant	391192	exon1			CTATGCACCTTTT	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.756A>G	1.37:g.248224739A>G		115	1	0.00869565		60	4	0.0666667	NM_001004687	B9EH44	Silent	SNP	ENST00000359959.3	37	CCDS31104.1																																																																																			.	.	weak		0.498	OR2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096852.1	NM_001004687		G	248224739	A	G	248224739	2	3	33	1	0	0	0	0	0	0	0	1	11017	146	6	3		3	OR2L3	1	248224739	Silent	SNP	A	TCGA-GR-A4D6-01A-11D-A31X-10	35692652	248224739	1025882	6	14032											
LASS6	253782	hgsc.bcm.edu	37	chr2	169417787	169417787	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcgctggtttcgacaaagacGcaatcaggagaagccaagca	14	5	12	10	3	1	2	1	0	0	2	2	4	1	2	1	2	2	4	1	2	4	1			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr2:169417787G>A	ENST00000305747.6	+	3	949	c.362G>A	c.(361-363)cGc>cAc	p.R121H	CERS6_ENST00000392687.4_Missense_Mutation_p.R121H	NM_203463.2	NP_982288.1	Q6ZMG9	CERS6_HUMAN	ceramide synthase 6	121					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)										CGACAAAGACGCAATCAGGAG	0.458																																					p.R121H		Atlas-SNP	.											LASS6,colon,carcinoma,+1,1	.	.	1	0			c.G362A						PASS	.						151	143	145					2																	169417787		2203	4300	6503	SO:0001583	missense	253782	exon3			AAAGACGCAATCA	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.362G>A	2.37:g.169417787G>A	ENSP00000306579:p.Arg121His	96	0	0		73	20	0.273973	NM_001256126	Q32M63|Q8N617	Missense_Mutation	SNP	ENST00000305747.6	37	CCDS2228.1	.	.	.	.	.	.	.	.	.	.	G	34	5.405789	0.96051	.	.	ENSG00000172292	ENST00000305747;ENST00000392687	D;D	0.99158	-5.5;-5.5	5.31	5.31	0.75309	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.045720	0.85682	D	0.000000	D	0.99518	0.9828	H	0.94423	3.535	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.87578	0.995;0.998	D	0.98417	1.0575	10	0.52906	T	0.07	-28.4318	19.3447	0.94358	0.0:0.0:1.0:0.0	.	121;121	Q32M63;Q6ZMG9	.;CERS6_HUMAN	H	121	ENSP00000306579:R121H;ENSP00000376453:R121H	ENSP00000306579:R121H	R	+	2	0	CERS6	169126033	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	9.813000	0.99286	2.641000	0.89580	0.650000	0.86243	CGC	.	.	none		0.458	CERS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255235.2	NM_203463		A	169417787	G	A	169417787	3	1	33	1	0	0	0	0	1	0	0	0	8652	1087	38	1	372	1	LASS6	2	169417787	Missense_Mutation	SNP	G	TCGA-GR-A4D6-01A-11D-A31X-10		169417787	73781586	7	14033											
TTN	7273	hgsc.bcm.edu	37	chr2	179605902	179605902	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctctgctgcacaggtggActcacccaacatattctctg	9	10	8	14	0	3	0	1	0	2	0	4	1	3	1	1	2	4	3	1	2	2	2			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr2:179605902A>T	ENST00000591111.1	-	46	11331	c.11107T>A	c.(11107-11109)Tcc>Acc	p.S3703T	TTN_ENST00000342175.6_Missense_Mutation_p.S3849T|TTN_ENST00000589042.1_Missense_Mutation_p.S4020T|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.S3782T|TTN_ENST00000460472.2_Missense_Mutation_p.S3657T|TTN-AS1_ENST00000582847.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron			Q8WZ42	TITIN_HUMAN	titin	14005	Ig-like 22.				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)			GCACAGGTGGACTCACCCAAC	0.488																																					p.S4020T		Atlas-SNP	.											.	TTN	18412	.	0			c.T12058A						PASS	.						79	80	80					2																	179605902		1920	4138	6058	SO:0001583	missense	7273	exon48			AGGTGGACTCACC	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.11107T>A	2.37:g.179605902A>T	ENSP00000465570:p.Ser3703Thr	25	0	0		29	11	0.37931	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	37		.	.	.	.	.	.	.	.	.	.	A	9.788	1.177085	0.21787	.	.	ENSG00000155657	ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T	0.67345	-0.26;-0.26;-0.26	5.87	2.01	0.26516	.	.	.	.	.	T	0.51635	0.1686	N	0.21373	0.66	0.20638	N	0.99987	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.002;0.002;0.003	T	0.46247	-0.9205	9	0.87932	D	0	.	10.1952	0.43049	0.3712:0.524:0.0:0.1048	.	3657;3782;3849	D3DPF9;E7EQE6;E7ET18	.;.;.	T	3657;3849;3782;3657	ENSP00000434586:S3657T;ENSP00000340554:S3849T;ENSP00000352154:S3782T	ENSP00000340554:S3849T	S	-	1	0	TTN	179314147	1.000000	0.71417	0.717000	0.30585	0.415000	0.31203	1.705000	0.37867	0.157000	0.19338	-0.313000	0.08912	TCC	.	.	none		0.488	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		T	179605902	A	T	179605902	3	4	33	1	0	0	0	0	1	0	0	0	16750	275	10	5	92731	5	TTN	2	179605902	Missense_Mutation	SNP	A	TCGA-GR-A4D6-01A-11D-A31X-10	10188115	179605902	63593471	8	14034											
FN1	2335	hgsc.bcm.edu	37	chr2	216257886	216257886	+	Intron	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctcaggccgatgcttgaatcGgttatatcaacaaagcttag	12	11	9	9	2	2	1	2	1	0	0	3	2	2	1	1	2	3	3	1	2	6	4	rs61732520	byFrequency	TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr2:216257886G>T	ENST00000359671.1	-	25	4062				FN1_ENST00000356005.4_Intron|FN1_ENST00000346544.3_Intron|FN1_ENST00000443816.1_Intron|FN1_ENST00000354785.4_Silent_p.T1279T|FN1_ENST00000357009.2_Intron|FN1_ENST00000432072.2_Silent_p.T1279T|FN1_ENST00000323926.6_Silent_p.T1279T|FN1_ENST00000421182.1_Intron|FN1_ENST00000446046.1_Intron|FN1_ENST00000336916.4_Intron|FN1_ENST00000345488.5_Intron|FN1_ENST00000357867.4_Intron			P02751	FINC_HUMAN	fibronectin 1						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)	TGCTTGAATCGGTTATATCAA	0.473																																					p.T1279T		Atlas-SNP	.											.	FN1	521	.	0			c.C3837A						PASS	.						79	78	78					2																	216257886		1867	4095	5962	SO:0001627	intron_variant	2335	exon25			TGAATCGGTTATA		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.3797-1349C>A	2.37:g.216257886G>T		88	0	0		100	4	0.04	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	37																																																																																				G|0.994;A|0.006	.	alt		0.473	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476		T	216257886	G	T	216257886	1	4	33	0	1	0	0	0	0	0	0	0	5970	1103	39	4		4	FN1	2	216257886	Intron	SNP	G	TCGA-GR-A4D6-01A-11D-A31X-10	36651984	216257886	26941487	9	14035											
RARB	5915	hgsc.bcm.edu	37	chr3	25611289	25611289	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aagaaaaagaaggagacttcGaagcaagaatgcacagagag	21	3	12	5	1	0	5	0	0	0	5	1	8	0	5	0	1	2	2	0	1	7	1			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr3:25611289G>A	ENST00000404969.1	+	4	510	c.510G>A	c.(508-510)tcG>tcA	p.S170S	RARB_ENST00000458646.1_Silent_p.S51S|RARB_ENST00000330688.4_Silent_p.S163S|RARB_ENST00000462272.1_3'UTR|RARB_ENST00000437042.2_Silent_p.S51S			P10826	RARB_HUMAN	retinoic acid receptor, beta	170	Hinge.				embryonic digestive tract development (GO:0048566)|embryonic eye morphogenesis (GO:0048048)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|glandular epithelial cell development (GO:0002068)|growth plate cartilage development (GO:0003417)|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)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myelination (GO:0031641)|retinal pigment epithelium development (GO:0003406)|signal transduction (GO:0007165)|striatum development (GO:0021756)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ureteric bud development (GO:0001657)|ventricular cardiac muscle cell differentiation (GO:0055012)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|drug binding (GO:0008144)|retinoic acid receptor activity (GO:0003708)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|kidney(1)|large_intestine(10)|lung(11)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	28					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Tamibarotene(DB04942)|Tazarotene(DB00799)	AGGAGACTTCGAAGCAAGAAT	0.507																																					p.S163S		Atlas-SNP	.											RARB_ENST00000404969,rectum,carcinoma,+1,2	RARB	123	2	0			c.G489A						scavenged	.						118	114	115					3																	25611289		2203	4300	6503	SO:0001819	synonymous_variant	5915	exon4			GACTTCGAAGCAA	Y00291	CCDS2642.1, CCDS46775.1	3p24	2013-01-16			ENSG00000077092	ENSG00000077092		"Nuclear hormone receptors"	9865	protein-coding gene	gene with protein product		180220					Standard	NM_016152		Approved	HAP, NR1B2, RRB2	uc003cdh.3	P10826	OTTHUMG00000130480	ENST00000404969.1:c.510G>A	3.37:g.25611289G>A		102	1	0.00980392		82	20	0.243902	NM_000965	P12891|Q00989|Q15298|Q9UN48	Silent	SNP	ENST00000404969.1	37																																																																																				.	.	none		0.507	RARB-201	KNOWN	basic	protein_coding	protein_coding		NM_000965, NM_016152		A	25611289	G	A	25611289	2	1	33	1	0	0	0	0	0	0	0	1	13068	1045	37	1		1	RARB	3	25611289	Silent	SNP	G	TCGA-GR-A4D6-01A-11D-A31X-10		25611289	172411141	10	14036											
ROBO1	6091	hgsc.bcm.edu	37	chr3	78795978	78795978	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatggcctcgtggaggttggCattccattactgcaggctct	6	12	13	10	1	1	0	0	0	1	0	3	2	2	1	2	5	2	4	2	5	1	3			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr3:78795978C>A	ENST00000464233.1	-	5	685	c.572G>T	c.(571-573)tGc>tTc	p.C191F	ROBO1_ENST00000495273.1_Missense_Mutation_p.C152F|ROBO1_ENST00000467549.1_Missense_Mutation_p.C152F|ROBO1_ENST00000436010.2_Missense_Mutation_p.C152F	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	191	Ig-like C2-type 2.				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)		TGGAGGTTGGCATTCCATTAC	0.433																																					p.C191F		Atlas-SNP	.											.	ROBO1	833	.	0			c.G572T						PASS	.						124	123	123					3																	78795978		1923	4132	6055	SO:0001583	missense	6091	exon5			GGTTGGCATTCCA	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.572G>T	3.37:g.78795978C>A	ENSP00000420321:p.Cys191Phe	97	0	0		108	14	0.12963	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	37	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	C	18.63	3.664509	0.67700	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414	T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57	5.83	5.83	0.93111	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);	0.000000	0.85682	D	0.000000	D	0.90038	0.6889	H	0.96175	3.78	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	0.92395	0.5924	9	.	.	.	.	20.1133	0.97917	0.0:1.0:0.0:0.0	.	191;152;152;152	Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4	ROBO1_HUMAN;.;.;.	F	152;152;191;152;152;191	ENSP00000406043:C152F;ENSP00000420321:C191F;ENSP00000420637:C152F;ENSP00000417992:C152F	.	C	-	2	0	ROBO1	78878668	1.000000	0.71417	1.000000	0.80357	0.188000	0.23474	7.818000	0.86416	2.762000	0.94881	0.591000	0.81541	TGC	.	.	none		0.433	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941		A	78795978	C	A	78795978	3	1	33	1	0	0	0	0	1	0	0	0	13528	710	25	4	4504	4	ROBO1	3	78795978	Missense_Mutation	SNP	C	TCGA-GR-A4D6-01A-11D-A31X-10	53184689	78795978	119226452	11	14037											
CASR	846	hgsc.bcm.edu	37	chr3	122002948	122002948	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gatccccaccagcttccaccGcaagtggtgggggctcaacc	8	6	11	16	1	1	0	1	0	0	0	3	1	3	0	6	3	2	3	6	3	2	1	rs201670662		TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr3:122002948G>A	ENST00000490131.1	+	7	2519	c.2147G>A	c.(2146-2148)cGc>cAc	p.R716H	CASR_ENST00000296154.5_Missense_Mutation_p.R716H|AC068754.1_ENST00000408547.1_RNA|CASR_ENST00000498619.1_Missense_Mutation_p.R726H	NM_000388.3	NP_000379	P41180	CASR_HUMAN	calcium-sensing receptor	716					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)	AGCTTCCACCGCAAGTGGTGG	0.567																																					p.R726H		Atlas-SNP	.											.	CASR	190	.	0			c.G2177A						PASS	.	G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	55	51	52		2147,2177	6	1	3		52	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	CASR	NM_000388.3,NM_001178065.1	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	716/1079,726/1089	122002948	1,13005	2203	4300	6503	SO:0001583	missense	846	exon7			TCCACCGCAAGTG	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.2147G>A	3.37:g.122002948G>A	ENSP00000418685:p.Arg716His	53	0	0		29	7	0.241379	NM_001178065	Q13912|Q16108|Q16109|Q16110|Q16379|Q2M1T0|Q4PJ19	Missense_Mutation	SNP	ENST00000490131.1	37	CCDS3010.1	.	.	.	.	.	.	.	.	.	.	G	18.65	3.668983	0.67814	0.0	1.16E-4	ENSG00000036828	ENST00000490131;ENST00000498619;ENST00000296154	D;D;D	0.87729	-2.29;-2.29;-2.29	6.04	6.04	0.98038	GPCR, family 3, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.93304	0.7866	M	0.70595	2.14	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.98	D	0.92406	0.5933	10	0.51188	T	0.08	.	19.5674	0.95401	0.0:0.0:1.0:0.0	.	726;716	E7ENE0;P41180	.;CASR_HUMAN	H	716;726;716	ENSP00000418685:R716H;ENSP00000420194:R726H;ENSP00000296154:R716H	ENSP00000296154:R716H	R	+	2	0	CASR	123485638	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.928000	0.87587	2.873000	0.98535	0.561000	0.74099	CGC	.	.	weak		0.567	CASR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355761.1	NM_000388		A	122002948	G	A	122002948	3	1	33	1	0	0	0	0	1	0	0	0	2684	1087	38	1	2199	1	CASR	3	122002948	Missense_Mutation	SNP	G	TCGA-GR-A4D6-01A-11D-A31X-10	43206970	122002948	76019482	12	14038											
PLD1	5337	hgsc.bcm.edu	37	chr3	171455820	171455820	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtgcagaggtatttacccGtggctcgtttttcagtgaca	8	13	11	9	2	1	2	1	1	0	1	2	2	1	2	1	2	2	4	1	2	2	5			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr3:171455820G>A	ENST00000351298.4	-	2	148	c.22C>T	c.(22-24)Cgg>Tgg	p.R8W	PLD1_ENST00000356327.5_Missense_Mutation_p.R8W|PLD1_ENST00000342215.6_Missense_Mutation_p.R8W|PLD1_ENST00000340989.4_Missense_Mutation_p.R8W	NM_002662.4	NP_002653.1	Q13393	PLD1_HUMAN	phospholipase D1, phosphatidylcholine-specific	8					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)	p.R8W(1)		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)	GTATTTACCCGTGGCTCGTTT	0.418																																					p.R8W	NSCLC(149;2174 3517 34058)	Atlas-SNP	.											PLD1,NS,carcinoma,0,2	PLD1	134	2	1	Substitution - Missense(1)	endometrium(1)	c.C22T						scavenged	.						80	75	77					3																	171455820		2203	4300	6503	SO:0001583	missense	5337	exon2			TTACCCGTGGCTC	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.22C>T	3.37:g.171455820G>A	ENSP00000342793:p.Arg8Trp	130	1	0.00769231		172	27	0.156977	NM_002662		Missense_Mutation	SNP	ENST00000351298.4	37	CCDS3216.1	.	.	.	.	.	.	.	.	.	.	G	11.89	1.772291	0.31411	.	.	ENSG00000075651	ENST00000356327;ENST00000351298;ENST00000342215;ENST00000340989;ENST00000418087	T;T;T;T;T	0.46063	3.34;3.35;1.44;3.21;0.88	5.51	-5.02	0.02982	.	0.379407	0.22897	N	0.054316	T	0.29126	0.0724	L	0.29908	0.895	0.09310	N	1	D;D	0.69078	0.997;0.994	B;B	0.43783	0.409;0.431	T	0.48234	-0.9053	10	0.72032	D	0.01	-6.2871	14.8852	0.70564	0.0768:0.0:0.6076:0.3156	.	31;8	Q59EA4;Q13393	.;PLD1_HUMAN	W	8	ENSP00000348681:R8W;ENSP00000342793:R8W;ENSP00000339936:R8W;ENSP00000340326:R8W;ENSP00000400639:R8W	ENSP00000340326:R8W	R	-	1	2	PLD1	172938514	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.421000	0.07053	-0.550000	0.06183	-0.262000	0.10625	CGG	.	.	none		0.418	PLD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346730.2	NM_002662		A	171455820	G	A	171455820	3	1	33	1	0	0	0	0	1	0	0	0	12054	1144	40	1	3306	1	PLD1	3	171455820	Missense_Mutation	SNP	G	TCGA-GR-A4D6-01A-11D-A31X-10	49452872	171455820	26566610	13	14039											
KLHL6	89857	hgsc.bcm.edu	37	chr3	183212058	183212058	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttccaaacatcatgctgtgTttctttgccacctgcaagag	9	14	7	11	0	2	1	1	0	1	1	3	1	3	1	3	0	4	3	3	0	2	3	rs372112529		TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr3:183212058T>C	ENST00000341319.3	-	5	1194	c.1159A>G	c.(1159-1161)Aca>Gca	p.T387A		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	387					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)			TCATGCTGTGTTTCTTTGCCA	0.408																																					p.T387A		Atlas-SNP	.											.	KLHL6	100	.	0			c.A1159G						PASS	.						106	106	106					3																	183212058		2203	4300	6503	SO:0001583	missense	89857	exon5			GCTGTGTTTCTTT	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.1159A>G	3.37:g.183212058T>C	ENSP00000341342:p.Thr387Ala	69	0	0		78	19	0.24359	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Missense_Mutation	SNP	ENST00000341319.3	37	CCDS3245.2	.	.	.	.	.	.	.	.	.	.	T	18.48	3.633258	0.67015	.	.	ENSG00000172578	ENST00000341319	T	0.65549	-0.16	5.96	5.96	0.96718	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.65186	0.2667	M	0.64997	1.995	0.58432	D	0.999997	P	0.51449	0.945	P	0.44732	0.459	T	0.69558	-0.5113	10	0.59425	D	0.04	.	16.4338	0.83864	0.0:0.0:0.0:1.0	.	387	Q8WZ60	KLHL6_HUMAN	A	387	ENSP00000341342:T387A	ENSP00000341342:T387A	T	-	1	0	KLHL6	184694752	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.036000	0.88901	2.270000	0.75569	0.533000	0.62120	ACA	.	.	alt		0.408	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446		C	183212058	T	C	183212058	3	2	33	1	0	0	0	0	1	0	0	0	8402	1725	60	3	718	3	KLHL6	3	183212058	Missense_Mutation	SNP	T	TCGA-GR-A4D6-01A-11D-A31X-10	11756238	183212058	14810372	14	14040											
MAGEF1	64110	hgsc.bcm.edu	37	chr3	184429559	184429559	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tcatggccgccatccttctcCccctcggcctgcgggaccgg	3	8	11	19	4	2	0	1	0	1	0	5	1	3	1	7	4	1	0	7	4	0	1			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr3:184429559C>T	ENST00000317897.3	-	1	277	c.51G>A	c.(49-51)ggG>ggA	p.G17G		NM_022149.4	NP_071432.2	Q9HAY2	MAGF1_HUMAN	melanoma antigen family F, 1	17						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(2)|urinary_tract(1)	11	all_cancers(143;4.61e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;5.64e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.56e-22)			CATCCTTCTCCCCCTCGGCCT	0.721																																					p.G17G		Atlas-SNP	.											.	MAGEF1	27	.	0			c.G51A						PASS	.						8	10	9					3																	184429559		2097	4121	6218	SO:0001819	synonymous_variant	64110	exon1			CTTCTCCCCCTCG	AF295378	CCDS3269.1	3q13	2008-02-05			ENSG00000177383	ENSG00000177383			29639	protein-coding gene	gene with protein product		609267				11313144	Standard	NM_022149		Approved		uc003fpa.3	Q9HAY2	OTTHUMG00000156712	ENST00000317897.3:c.51G>A	3.37:g.184429559C>T		103	0	0		111	17	0.153153	NM_022149	Q9H215	Silent	SNP	ENST00000317897.3	37	CCDS3269.1																																																																																			.	.	none		0.721	MAGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345417.1	NM_022149		T	184429559	C	T	184429559	2	4	33	1	0	0	0	0	0	0	0	1	9196	610	22	2		2	MAGEF1	3	184429559	Silent	SNP	C	TCGA-GR-A4D6-01A-11D-A31X-10	1217501	184429559	13592871	15	14041											
TMEM44	93109	hgsc.bcm.edu	37	chr3	194338423	194338423	+	Missense_Mutation	SNP	C	C	T																															gccaatgtccgctgggagaaCgtgagggagactgggatggt																								rs12695036|rs386669926	byFrequency	TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr3:194338423C>T	ENST00000392432.2	-	6	900	c.695G>A	c.(694-696)cGt>cAt	p.R232H	TMEM44_ENST00000347147.4_Intron|TMEM44_ENST00000273580.7_Intron|TMEM44_ENST00000473092.1_Intron|TMEM44_ENST00000381975.3_Intron	NM_001166305.1	NP_001159777.1	Q2T9K0	TMM44_HUMAN	transmembrane protein 44	232			R -> H (in dbSNP:rs12695036). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			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)		gctgggagaacgTGAGGGAGA	0.622													C|||	2410	0.48123	0.3517	0.5331	5008	,	,		16125	0.75		0.2942	False		,,,				2504	0.5348				p.R232H		Atlas-SNP	.											.	TMEM44	42	.	0			c.G695A						PASS	.	C	,HIS/ARG,,	361,1023		75,211,406	60	69	66		,695,,	-2.8	0	3	dbSNP_121	66	912,2270		173,566,852	yes	intron,missense,intron,intron	TMEM44	NM_001011655.2,NM_001166305.1,NM_001166306.1,NM_138399.4	,29,,	248,777,1258	TT,TC,CC		28.6612,26.0838,27.88	,,,	,232/476,,	194338423	1273,3293	692	1591	2283	SO:0001583	missense	93109	exon6			GGAGAACGTGAGG	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.695G>A	3.37:g.194338423C>T	ENSP00000376227:p.Arg232His	0	0	.		4	4	1	NM_001166305	A1L3V7|B7ZLZ5|B7ZLZ6|C9JJ62|E9PGA9|Q0P6F7|Q6ZT47|Q8IXR1|Q8N4G3	Missense_Mutation	SNP	ENST00000392432.2	37	CCDS54699.1	1016	0.4652014652014652	176	0.35772357723577236	195	0.5386740331491713	431	0.7534965034965035	214	0.28232189973614774	C	6.123	0.390972	0.11581	0.260838	0.286612	ENSG00000145014	ENST00000392432	T	0.23950	1.88	2.03	-2.85	0.05734	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	.	.	.	.	.	.	T	0.32428	-0.9907	6	0.23302	T	0.38	.	0.4159	0.00448	0.1788:0.2613:0.2601:0.2998	rs12695036;rs59789853;rs12695036	.	.	.	H	232	ENSP00000376227:R232H	ENSP00000376227:R232H	R	-	2	0	TMEM44	195819712	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-1.678000	0.01942	-0.836000	0.04229	-1.270000	0.01421	CGT	C|0.567;T|0.433	0.433	strong		0.622	TMEM44-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000342750.1	NM_138399		T	194338423	C	T	194338423	3	4	33	1	0	0	0	0	1	0	0	0	16183	536	19	1	790	1	TMEM44	3	194338423	Missense_Mutation	SNP	C	TCGA-GR-A4D6-01A-11D-A31X-10	9908864	194338423	3684007	16	14042	176	2									
TMEM44	93109	hgsc.bcm.edu	37	chr3	194338424	194338424	+	Missense_Mutation	SNP	G	G	C																															ccaatgtccgctgggagaacGtgagggagactgggatggtt																								rs58679389|rs386669926	byFrequency	TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr3:194338424G>C	ENST00000392432.2	-	6	899	c.694C>G	c.(694-696)Cgt>Ggt	p.R232G	TMEM44_ENST00000347147.4_Intron|TMEM44_ENST00000273580.7_Intron|TMEM44_ENST00000473092.1_Intron|TMEM44_ENST00000381975.3_Intron	NM_001166305.1	NP_001159777.1	Q2T9K0	TMM44_HUMAN	transmembrane protein 44	232			R -> H (in dbSNP:rs12695036). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.			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)		ctgggagaacgTGAGGGAGAC	0.627													G|||	932	0.186102	0.1399	0.2003	5008	,	,		16153	0.3036		0.0666	False		,,,				2504	0.2403				p.R232G		Atlas-SNP	.											.	TMEM44	42	.	0			c.C694G						PASS	.						62	71	68					3																	194338424		692	1591	2283	SO:0001583	missense	93109	exon6			GAGAACGTGAGGG	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.694C>G	3.37:g.194338424G>C	ENSP00000376227:p.Arg232Gly	0	0	.		4	4	1	NM_001166305	A1L3V7|B7ZLZ5|B7ZLZ6|C9JJ62|E9PGA9|Q0P6F7|Q6ZT47|Q8IXR1|Q8N4G3	Missense_Mutation	SNP	ENST00000392432.2	37	CCDS54699.1	304	0.1391941391941392	64	0.13008130081300814	59	0.16298342541436464	148	0.25874125874125875	33	0.04353562005277045	G	3.222	-0.159324	0.06544	.	.	ENSG00000145014	ENST00000392432	T	0.23552	1.9	2.03	-2.52	0.06346	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	.	.	.	.	.	.	T	0.45101	-0.9284	6	0.30078	T	0.28	.	6.5849	0.22614	0.6181:0.0:0.3819:0.0	rs58679389	.	.	.	G	232	ENSP00000376227:R232G	ENSP00000376227:R232G	R	-	1	0	TMEM44	195819713	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-2.396000	0.01052	-0.762000	0.04664	-0.464000	0.05259	CGT	C|0.130;G|0.870	0.130	strong		0.627	TMEM44-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000342750.1	NM_138399		C	194338424	G	C	194338424	3	2	33	1	0	0	0	0	1	0	0	0	16183	1145	40	4	791	4	TMEM44	3	194338424	Missense_Mutation	SNP	G	TCGA-GR-A4D6-01A-11D-A31X-10	1	194338424	3684006	17	14043	176	2									
HIST1H2BG	8339	hgsc.bcm.edu	37	chr6	26216764	26216764	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tacacatacacggagtagctCtccttacgactgcgcttgcg	9	10	9	13	4	1	0	0	0	1	0	2	2	1	1	1	1	6	3	1	1	4	5			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr6:26216764C>T	ENST00000244601.3	-	1	108	c.108G>A	c.(106-108)gaG>gaA	p.E36E	HIST1H2AE_ENST00000303910.2_5'Flank	NM_003518.3	NP_003509.1	P62807	H2B1C_HUMAN	histone cluster 1, H2bg	36					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)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	8		all_hematologic(11;0.196)				CGGAGTAGCTCTCCTTACGAC	0.517																																					p.E36E		Atlas-SNP	.											.	HIST1H2BG	25	.	0			c.G108A						PASS	.						250	219	229					6																	26216764		2203	4300	6503	SO:0001819	synonymous_variant	8339	exon1			GTAGCTCTCCTTA	M60750	CCDS4594.1	6p21.3	2011-01-27	2006-10-11	2003-02-14	ENSG00000187990	ENSG00000273802		"Histones / Replication-dependent"	4746	protein-coding gene	gene with protein product		602798	"H2B histone family, member A", "histone 1, H2bg"	H2BFA		1916825, 12408966	Standard	NM_003518		Approved	H2B/a, H2B.1A	uc003ngz.2	P62807	OTTHUMG00000014446	ENST00000244601.3:c.108G>A	6.37:g.26216764C>T		105	0	0		88	19	0.215909	NM_003518	P02278|Q3B872|Q4VB69|Q93078|Q93080	Silent	SNP	ENST00000244601.3	37	CCDS4594.1																																																																																			.	.	none		0.517	HIST1H2BG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040109.2	NM_003518		T	26216764	C	T	26216764	2	4	33	1	0	0	0	0	0	0	0	1	7155	912	32	2		2	HIST1H2BG	6	26216764	Silent	SNP	C	TCGA-GR-A4D6-01A-11D-A31X-10		26216764	144898303	18	14044			1	60		2	2	64	N	G_C	8.547043e-05
HIST1H2BG	8339	hgsc.bcm.edu	37	chr6	26216827	26216827	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccttggtcacagccttcttGgaacccttcttcggagcagg	6	11	11	13	1	3	0	1	0	2	0	4	2	3	2	3	4	3	1	3	4	1	5	rs143774290		TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr6:26216827G>A	ENST00000244601.3	-	1	45	c.45C>T	c.(43-45)tcC>tcT	p.S15S	HIST1H2AE_ENST00000303910.2_5'Flank	NM_003518.3	NP_003509.1	P62807	H2B1C_HUMAN	histone cluster 1, H2bg	15					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)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	8		all_hematologic(11;0.196)				CAGCCTTCTTGGAACCCTTCT	0.493																																					p.S15S		Atlas-SNP	.											.	HIST1H2BG	25	.	0			c.C45T						PASS	.	G		0,4406		0,0,2203	138	125	129		45	2.2	1	6	dbSNP_134	129	2,8598		0,2,4298	no	coding-synonymous	HIST1H2BG	NM_003518.3		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		15/127	26216827	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	8339	exon1			CTTCTTGGAACCC	M60750	CCDS4594.1	6p21.3	2011-01-27	2006-10-11	2003-02-14	ENSG00000187990	ENSG00000273802		"Histones / Replication-dependent"	4746	protein-coding gene	gene with protein product		602798	"H2B histone family, member A", "histone 1, H2bg"	H2BFA		1916825, 12408966	Standard	NM_003518		Approved	H2B/a, H2B.1A	uc003ngz.2	P62807	OTTHUMG00000014446	ENST00000244601.3:c.45C>T	6.37:g.26216827G>A		96	0	0		74	16	0.216216	NM_003518	P02278|Q3B872|Q4VB69|Q93078|Q93080	Silent	SNP	ENST00000244601.3	37	CCDS4594.1																																																																																			G|1.000;A|0.000	0.000	weak		0.493	HIST1H2BG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040109.2	NM_003518		A	26216827	G	A	26216827	2	1	33	1	0	0	0	0	0	0	0	1	7155	1335	47	2		2	HIST1H2BG	6	26216827	Silent	SNP	G	TCGA-GR-A4D6-01A-11D-A31X-10	63	26216827	144898240	19	14045			1	60		2	2	64	N	G_C	8.547043e-05
HIST1H1D	3007	hgsc.bcm.edu	37	chr6	26234674	26234674	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcttggtcccagcagcggttGctggcttctttaccttctta	4	16	9	12	1	3	0	0	0	3	0	4	0	4	0	2	3	4	4	2	3	2	7			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr6:26234674G>C	ENST00000244534.5	-	1	542	c.488C>G	c.(487-489)gCa>gGa	p.A163G		NM_005320.2	NP_005311.1	P16402	H13_HUMAN	histone cluster 1, H1d	163					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				AGCAGCGGTTGCTGGCTTCTT	0.537																																					p.A163G		Atlas-SNP	.											.	HIST1H1D	40	.	0			c.C488G						PASS	.						95	103	100					6																	26234674		2203	4300	6503	SO:0001583	missense	3007	exon1			GCGGTTGCTGGCT	M60747	CCDS4597.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000124575	ENSG00000124575		"Histones / Replication-dependent"	4717	protein-coding gene	gene with protein product		142210	"H1 histone family, member 3", "histone 1, H1d"	H1F3		1916825, 12408966	Standard	NM_005320		Approved	H1.3, H1d, H1s-2	uc003nhd.3	P16402	OTTHUMG00000014432	ENST00000244534.5:c.488C>G	6.37:g.26234674G>C	ENSP00000244534:p.Ala163Gly	84	0	0		74	16	0.216216	NM_005320	B2R751|Q2M2I2	Missense_Mutation	SNP	ENST00000244534.5	37	CCDS4597.1	.	.	.	.	.	.	.	.	.	.	.	9.047	0.991113	0.18966	.	.	ENSG00000124575	ENST00000244534	T	0.25414	1.8	5.22	4.35	0.52113	.	0.316723	0.32444	N	0.006082	T	0.06280	0.0162	N	0.08118	0	0.53005	D	0.999965	B	0.27853	0.191	B	0.28465	0.09	T	0.16453	-1.0402	10	0.33940	T	0.23	-1.7269	13.338	0.60528	0.0768:0.0:0.9232:0.0	.	163	P16402	H13_HUMAN	G	163	ENSP00000244534:A163G	ENSP00000244534:A163G	A	-	2	0	HIST1H1D	26342653	0.437000	0.25593	0.009000	0.14445	0.105000	0.19272	2.513000	0.45494	1.351000	0.45789	0.650000	0.86243	GCA	.	.	none		0.537	HIST1H1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040095.1	NM_005320		C	26234674	G	C	26234674	3	2	33	1	0	0	0	0	1	0	0	0	7134	1319	46	4	181	4	HIST1H1D	6	26234674	Missense_Mutation	SNP	G	TCGA-GR-A4D6-01A-11D-A31X-10	17847	26234674	144880393	20	14046											
NFKBIE	4794	hgsc.bcm.edu	37	chr6	44227895	44227895	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccggccagctgccaggtgcAggggtgtgcacccgttcagc	5	6	15	15	2	1	0	1	0	0	0	1	0	1	0	4	4	5	4	4	4	0	1			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr6:44227895A>G	ENST00000275015.5	-	5	1321	c.1322T>C	c.(1321-1323)cTg>cCg	p.L441P	SLC35B2_ENST00000495706.1_5'Flank|SLC35B2_ENST00000393812.3_5'Flank|SLC35B2_ENST00000537814.1_5'Flank|SLC35B2_ENST00000538577.1_5'Flank|SLC35B2_ENST00000393810.1_5'Flank	NM_004556.2	NP_004547.2	O00221	IKBE_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, epsilon	441					cytoplasmic sequestering of transcription factor (GO:0042994)|D-serine transport (GO:0042942)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|urinary_tract(1)	10	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)			TGCCAGGTGCAGGGGTGTGCA	0.647																																					p.L441P		Atlas-SNP	.											.	NFKBIE	31	.	0			c.T1322C						PASS	.						49	51	50					6																	44227895		2203	4300	6503	SO:0001583	missense	4794	exon5			AGGTGCAGGGGTG	U91616	CCDS34463.1	6p21.1	2013-01-10			ENSG00000146232	ENSG00000146232		"Ankyrin repeat domain containing"	7799	protein-coding gene	gene with protein product		604548				9135156	Standard	NM_004556		Approved	IKBE	uc003oxe.1	O00221	OTTHUMG00000014762	ENST00000275015.5:c.1322T>C	6.37:g.44227895A>G	ENSP00000275015:p.Leu441Pro	42	0	0		45	17	0.377778	NM_004556	Q5T9V9	Missense_Mutation	SNP	ENST00000275015.5	37	CCDS34463.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.421610	0.83559	.	.	ENSG00000146232	ENST00000275015;ENST00000443607	D	0.82255	-1.59	5.05	5.05	0.67936	Ankyrin repeat-containing domain (3);	0.000000	0.64402	D	0.000007	D	0.94238	0.8150	H	0.98818	4.34	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96517	0.9383	10	0.87932	D	0	-42.6353	14.814	0.70017	1.0:0.0:0.0:0.0	.	441	O00221	IKBE_HUMAN	P	441;42	ENSP00000275015:L441P	ENSP00000275015:L441P	L	-	2	0	NFKBIE	44335873	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	9.297000	0.96120	1.895000	0.54865	0.533000	0.62120	CTG	.	.	none		0.647	NFKBIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040733.2			G	44227895	A	G	44227895	3	3	33	1	0	0	0	0	1	0	0	0	10389	188	7	3	188	3	NFKBIE	6	44227895	Missense_Mutation	SNP	A	TCGA-GR-A4D6-01A-11D-A31X-10	17993221	44227895	126887172	21	14047											
PTPRK	5796	hgsc.bcm.edu	37	chr6	128505735	128505735	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	catgggtttctgtccaggatCctgatgtcattcggtactct	6	15	10	10	1	3	1	1	1	2	0	6	2	5	2	2	3	1	2	2	3	1	3			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr6:128505735C>T	ENST00000368215.3	-	7	1003	c.1004G>A	c.(1003-1005)gGa>gAa	p.G335E	PTPRK_ENST00000368207.3_Missense_Mutation_p.G335E|PTPRK_ENST00000368210.3_Missense_Mutation_p.G335E|PTPRK_ENST00000368226.4_Missense_Mutation_p.G335E|PTPRK_ENST00000368227.3_Missense_Mutation_p.G335E|PTPRK_ENST00000524481.1_5'UTR|PTPRK_ENST00000532331.1_Missense_Mutation_p.G335E|PTPRK_ENST00000368213.5_Missense_Mutation_p.G335E			Q15262	PTPRK_HUMAN	protein tyrosine phosphatase, receptor type, K	335	Fibronectin type-III 1. {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)		TGTCCAGGATCCTGATGTCAT	0.433																																					p.G335E		Atlas-SNP	.											PTPRK_ENST00000368213,mucosal,malignant_melanoma,-1,2	PTPRK	330	2	0			c.G1004A						PASS	.						219	202	208					6																	128505735		2203	4300	6503	SO:0001583	missense	5796	exon7			CAGGATCCTGATG	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.1004G>A	6.37:g.128505735C>T	ENSP00000357198:p.Gly335Glu	137	0	0		127	10	0.0787402	NM_001135648	B2RTQ8|B7ZMG0|Q14763|Q5TG10|Q5TG11	Missense_Mutation	SNP	ENST00000368215.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	32|32	5.174795|5.174795	0.94807|0.94807	.|.	.|.	ENSG00000152894|ENSG00000152894	ENST00000490332|ENST00000368226;ENST00000368227;ENST00000532331;ENST00000368213;ENST00000368210;ENST00000368215;ENST00000368207;ENST00000427676	.|T;T;T;T;T;T;T	.|0.80480	.|-1.38;-1.38;-1.38;-1.38;-1.38;-1.38;-1.38	5.49|5.49	5.49|5.49	0.81192|0.81192	.|Fibronectin, type III (4);Immunoglobulin-like fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.85031|0.85031	0.5604|0.5604	L|L	0.48986|0.48986	1.54|1.54	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D	.|0.89917	.|1.0;0.995;0.993;0.988;1.0;1.0	.|D;D;P;P;D;D	.|0.91635	.|0.999;0.932;0.888;0.838;0.999;0.998	T|T	0.82764|0.82764	-0.0296|-0.0296	5|10	.|0.36615	.|T	.|0.2	.|.	19.3758|19.3758	0.94508|0.94508	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|335;335;335;192;335;335	.|B4DHC3;B7ZMG0;Q15262-3;F5GWP2;Q15262;Q15262-2	.|.;.;.;.;PTPRK_HUMAN;.	N|E	152|335;335;335;335;335;335;335;192	.|ENSP00000357209:G335E;ENSP00000357210:G335E;ENSP00000432973:G335E;ENSP00000357196:G335E;ENSP00000357193:G335E;ENSP00000357198:G335E;ENSP00000357190:G335E	.|ENSP00000357190:G335E	D|G	-|-	1|2	0|0	PTPRK|PTPRK	128547428|128547428	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.944000|0.944000	0.59088|0.59088	7.818000|7.818000	0.86416|0.86416	2.577000|2.577000	0.86979|0.86979	0.655000|0.655000	0.94253|0.94253	GAT|GGA	.	.	none		0.433	PTPRK-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000042163.1			T	128505735	C	T	128505735	3	4	33	1	0	0	0	0	1	0	0	0	12820	855	30	2	3436	2	PTPRK	6	128505735	Missense_Mutation	SNP	C	TCGA-GR-A4D6-01A-11D-A31X-10	84277840	128505735	42609332	22	14048											
ZKSCAN1	7586	hgsc.bcm.edu	37	chr7	99631550	99631550	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaggccttcagccagagctcGgacctcaccaagcatcagag	12	5	10	14	1	3	2	3	0	0	2	4	3	3	3	4	2	3	2	4	2	2	1			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr7:99631550G>T	ENST00000324306.6	+	6	1656	c.1422G>T	c.(1420-1422)tcG>tcT	p.S474S	ZKSCAN1_ENST00000426572.1_Silent_p.S438S|ZKSCAN1_ENST00000535170.1_Silent_p.S261S	NM_003439.1	NP_003430.1	P17029	ZKSC1_HUMAN	zinc finger with KRAB and SCAN domains 1	474					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)			GCCAGAGCTCGGACCTCACCA	0.483																																					p.S474S		Atlas-SNP	.											.	ZKSCAN1	59	.	0			c.G1422T						PASS	.						99	106	104					7																	99631550		2203	4300	6503	SO:0001819	synonymous_variant	7586	exon6			GAGCTCGGACCTC	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.1422G>T	7.37:g.99631550G>T		70	0	0		91	4	0.043956	NM_003439	A4D294|P52745|Q2M1U1|Q8TBW5|Q8TEK7	Silent	SNP	ENST00000324306.6	37	CCDS34698.1																																																																																			.	.	none		0.483	ZKSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344550.2	NM_003439		T	99631550	G	T	99631550	2	4	33	1	0	0	0	0	0	0	0	1	17701	1103	39	4		4	ZKSCAN1	7	99631550	Silent	SNP	G	TCGA-GR-A4D6-01A-11D-A31X-10		99631550	59507113	23	14049											
CRYGN	155051	hgsc.bcm.edu	37	chr7	151135158	151135158	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtcggggtagtcgccgtgcTccaagatgaactgctggccc	7	8	14	12	3	0	2	0	1	0	1	3	2	1	2	3	3	3	3	3	3	3	1			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr7:151135158T>G	ENST00000337323.2	-	2	320	c.194A>C	c.(193-195)gAg>gCg	p.E65A	CRYGN_ENST00000491928.1_Missense_Mutation_p.E65A|RP4-555L14.4_ENST00000465549.1_RNA|CRYGN_ENST00000476631.1_5'UTR	NM_144727.1	NP_653328.1	Q8WXF5	CRGN_HUMAN	crystallin, gamma N	65	Beta/gamma crystallin 'Greek key' 2. {ECO:0000255|PROSITE-ProRule:PRU00028}.									central_nervous_system(1)|kidney(1)|large_intestine(1)|liver(1)|lung(4)	8			OV - Ovarian serous cystadenocarcinoma(82;0.00358)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GTCGCCGTGCTCCAAGATGAA	0.617																																					p.E65A		Atlas-SNP	.											.	CRYGN	15	.	0			c.A194C						PASS	.						62	61	61					7																	151135158		2203	4300	6503	SO:0001583	missense	155051	exon2			CCGTGCTCCAAGA	AF445455	CCDS5926.1	7q36.1	2003-02-25			ENSG00000127377	ENSG00000127377			20458	protein-coding gene	gene with protein product		609603					Standard	NM_144727		Approved		uc003wke.3	Q8WXF5	OTTHUMG00000157353	ENST00000337323.2:c.194A>C	7.37:g.151135158T>G	ENSP00000338613:p.Glu65Ala	45	0	0		58	11	0.189655	NM_144727	Q496G6	Missense_Mutation	SNP	ENST00000337323.2	37	CCDS5926.1	.	.	.	.	.	.	.	.	.	.	T	25.6	4.655167	0.88056	.	.	ENSG00000127377	ENST00000337323	T	0.78364	-1.17	5.05	5.05	0.67936	Beta/gamma crystallin (5);Gamma-crystallin-related (1);	0.000000	0.85682	D	0.000000	D	0.90810	0.7114	H	0.94345	3.525	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.91635	0.998;0.999	D	0.92787	0.6245	10	0.56958	D	0.05	.	13.9762	0.64275	0.0:0.0:0.0:1.0	.	65;65	Q8WXF5-2;Q8WXF5	.;CRGN_HUMAN	A	65	ENSP00000338613:E65A	ENSP00000338613:E65A	E	-	2	0	CRYGN	150766091	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.602000	0.82796	1.894000	0.54839	0.379000	0.24179	GAG	.	.	none		0.617	CRYGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348553.1			G	151135158	T	G	151135158	3	3	33	1	0	0	0	0	1	0	0	0	3920	1551	54	5	366	5	CRYGN	7	151135158	Missense_Mutation	SNP	T	TCGA-GR-A4D6-01A-11D-A31X-10	51503608	151135158	8003505	24	14050											
CEP110	11064	hgsc.bcm.edu	37	chr9	123937296	123937296	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agtcttatcacacttttcagGcccaactccgacactgtatg	10	12	6	13	1	3	0	2	0	1	0	4	1	4	0	2	1	1	1	2	1	3	4			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr9:123937296G>A	ENST00000373855.1	+	43	7008	c.6748G>A	c.(6748-6750)Gcc>Acc	p.A2250T	CNTRL_ENST00000238341.5_Splice_Site_p.A2250T|CNTRL_ENST00000373850.1_Splice_Site_p.A1698T|CNTRL_ENST00000373845.2_3'UTR			Q7Z7A1	CNTRL_HUMAN	centriolin	2250	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						CACTTTTCAGGCCCAACTCCG	0.438																																					p.A2250T		Atlas-SNP	.											.	CNTRL	161	.	0			c.G6748A						PASS	.						115	122	120					9																	123937296		2203	4300	6503	SO:0001630	splice_region_variant	11064	exon41			TTTCAGGCCCAAC	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.6748-1G>A	9.37:g.123937296G>A		77	0	0		81	21	0.259259	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	37	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	G	33	5.277169	0.95459	.	.	ENSG00000119397	ENST00000373855;ENST00000238341;ENST00000454238;ENST00000394368;ENST00000373850;ENST00000373845	T;T;T	0.35421	1.48;1.48;1.31	5.59	5.59	0.84812	.	.	.	.	.	T	0.59169	0.2174	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.55108	-0.8192	8	.	.	.	.	18.5881	0.91197	0.0:0.0:1.0:0.0	.	2250	Q7Z7A1	CNTRL_HUMAN	T	2250;2250;2250;407;1698;932	ENSP00000362962:A2250T;ENSP00000238341:A2250T;ENSP00000362956:A1698T	.	A	+	1	0	CNTRL	122977117	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.810000	0.86072	2.629000	0.89072	0.555000	0.69702	GCC	.	.	none		0.438	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018	Missense_Mutation	A	123937296	G	A	123937296	5	1	33	1	0	0	0	0	0	0	1	0	3247	1217	42	2	6910	2	CEP110	9	123937296	Splice_Site	SNP	G	TCGA-GR-A4D6-01A-11D-A31X-10		123937296	17276135	25	14051											
PLXDC2	84898	hgsc.bcm.edu	37	chr10	20436808	20436808	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaccctgctcatggatggaCgaatcatctttggatacaaa	13	10	8	10	1	3	0	2	0	1	0	3	4	3	3	1	3	3	1	1	3	4	2	rs372842489		TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr10:20436808C>T	ENST00000377252.4	+	6	1601	c.760C>T	c.(760-762)Cga>Tga	p.R254*	PLXDC2_ENST00000377242.3_Nonsense_Mutation_p.R205*|PLXDC2_ENST00000377238.2_3'UTR	NM_001282736.1|NM_032812.7	NP_001269665.1|NP_116201.7	Q6UX71	PXDC2_HUMAN	plexin domain containing 2	254					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						CATGGATGGACGAATCATCTT	0.453																																					p.R254X		Atlas-SNP	.											.	PLXDC2	108	.	0			c.C760T						PASS	.						102	82	88					10																	20436808		2203	4300	6503	SO:0001587	stop_gained	84898	exon6			GATGGACGAATCA	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.760C>T	10.37:g.20436808C>T	ENSP00000366460:p.Arg254*	105	0	0		102	14	0.137255	NM_032812	Q96E59|Q96PD9|Q96SU9	Nonsense_Mutation	SNP	ENST00000377252.4	37	CCDS7132.1	.	.	.	.	.	.	.	.	.	.	C	44	11.271397	0.99539	.	.	ENSG00000120594	ENST00000377252;ENST00000377242;ENST00000377238;ENST00000536022	.	.	.	4.83	3.85	0.44370	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.1168	0.65159	0.1509:0.8491:0.0:0.0	.	.	.	.	X	254;205;117;240	.	ENSP00000366446:R117X	R	+	1	2	PLXDC2	20476814	1.000000	0.71417	1.000000	0.80357	0.900000	0.52787	3.792000	0.55476	2.392000	0.81423	0.557000	0.71058	CGA	.	.	none		0.453	PLXDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047101.2	NM_032812		T	20436808	C	T	20436808	4	4	33	1	0	0	0	0	0	1	0	0	12127	528	19	1	782	1	PLXDC2	10	20436808	Nonsense_Mutation	SNP	C	TCGA-GR-A4D6-01A-11D-A31X-10		20436808	115097939	26	14052											
OR4D6	219983	hgsc.bcm.edu	37	chr11	59225155	59225155	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaggccctctccacgtgcaCgtcccacatgctggtggtga	7	8	11	15	2	1	1	0	1	1	0	3	1	2	1	3	3	2	2	3	3	1	0	rs376910045	byFrequency	TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr11:59225155C>T	ENST00000300127.2	+	1	745	c.722C>T	c.(721-723)aCg>aTg	p.T241M		NM_001004708.1	NP_001004708.1	Q8NGJ1	OR4D6_HUMAN	olfactory receptor, family 4, subfamily D, member 6	241						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						TCCACGTGCACGTCCCACATG	0.562													C|||	2	0.000399361	0.0	0.0	5008	,	,		20259	0.0		0.0	False		,,,				2504	0.002				p.T241M		Atlas-SNP	.											OR4D6,colon,carcinoma,-1,1	OR4D6	65	1	0			c.C722T						PASS	.	C	MET/THR	0,4402		0,0,2201	120	107	112		722	5.1	1	11		112	1,8589	1.2+/-3.3	0,1,4294	no	missense	OR4D6	NM_001004708.1	81	0,1,6495	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	241/315	59225155	1,12991	2201	4295	6496	SO:0001583	missense	219983	exon1			CGTGCACGTCCCA	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.722C>T	11.37:g.59225155C>T	ENSP00000300127:p.Thr241Met	64	0	0		55	9	0.163636	NM_001004708	B2RNP7|Q6IFF5|Q96R74	Missense_Mutation	SNP	ENST00000300127.2	37	CCDS31562.1	.	.	.	.	.	.	.	.	.	.	C	13.59	2.281877	0.40394	0.0	1.16E-4	ENSG00000166884	ENST00000300127	T	0.40756	1.02	6.01	5.09	0.68999	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000039	T	0.65575	0.2704	M	0.77486	2.375	0.23831	N	0.996728	D	0.89917	1.0	D	0.77004	0.989	T	0.62581	-0.6824	10	0.62326	D	0.03	-21.1448	15.3738	0.74587	0.1406:0.8594:0.0:0.0	.	241	Q8NGJ1	OR4D6_HUMAN	M	241	ENSP00000300127:T241M	ENSP00000300127:T241M	T	+	2	0	OR4D6	58981731	0.000000	0.05858	0.983000	0.44433	0.227000	0.25037	0.628000	0.24522	1.516000	0.48900	0.655000	0.94253	ACG	.	.	weak		0.562	OR4D6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394234.1	NM_001004708		T	59225155	C	T	59225155	3	4	33	1	0	0	0	0	1	0	0	0	11067	536	19	1	724	1	OR4D6	11	59225155	Missense_Mutation	SNP	C	TCGA-GR-A4D6-01A-11D-A31X-10		59225155	75781361	27	14053											
VWF	7450	hgsc.bcm.edu	37	chr12	6085324	6085324	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgggagcactgggccacgcGgaggcccatcacggcatcct	7	5	14	15	3	1	0	1	0	0	0	2	2	2	2	3	5	1	2	3	5	0	0	rs61751286		TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr12:6085324G>A	ENST00000261405.5	-	43	7644	c.7390C>T	c.(7390-7392)Cgc>Tgc	p.R2464C		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	2464	VWFC 2. {ECO:0000255|PROSITE- ProRule:PRU00220}.				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)	TGGGCCACGCGGAGGCCCATC	0.642													G|||	1	0.000199681	0.0	0.0	5008	,	,		17555	0.0		0.001	False		,,,				2504	0.0				p.R2464C		Atlas-SNP	.											VWF,NS,lymphoid_neoplasm,+1,1	VWF	338	1	0			c.C7390T	GRCh37	CM070317	VWF	M	rs61751286	scavenged	.						70	63	65					12																	6085324		2203	4300	6503	SO:0001583	missense	7450	exon43			CCACGCGGAGGCC		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.7390C>T	12.37:g.6085324G>A	ENSP00000261405:p.Arg2464Cys	99	1	0.010101		68	16	0.235294	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	22.3	4.268417	0.80469	.	.	ENSG00000110799	ENST00000261405	T	0.65916	-0.18	5.19	5.19	0.71726	von Willebrand factor, type C (4);	0.185059	0.26631	N	0.023302	T	0.71779	0.3380	L	0.51422	1.61	0.80722	D	1	D	0.76494	0.999	P	0.60609	0.877	T	0.73563	-0.3943	10	0.56958	D	0.05	.	15.8551	0.78972	0.0:0.0:1.0:0.0	rs61751286	2464	P04275	VWF_HUMAN	C	2464	ENSP00000261405:R2464C	ENSP00000261405:R2464C	R	-	1	0	VWF	5955585	1.000000	0.71417	0.987000	0.45799	0.734000	0.41952	5.369000	0.66138	2.412000	0.81896	0.591000	0.81541	CGC	G|1.000;A|0.000	0.000	strong		0.642	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552		A	6085324	G	A	6085324	3	1	33	1	0	0	0	0	1	0	0	0	17261	1116	39	1	1091	1	VWF	12	6085324	Missense_Mutation	SNP	G	TCGA-GR-A4D6-01A-11D-A31X-10		6085324	127766571	28	14054											
KDM2B	84678	hgsc.bcm.edu	37	chr12	121891060	121891060	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggcatcgcgtccggcgccGccgagctcctgccgttgtcc	2	7	14	18	8	0	0	0	0	0	0	4	1	3	0	6	2	2	3	6	2	0	1			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr12:121891060G>A	ENST00000377071.4	-	13	1894	c.1822C>T	c.(1822-1824)Cgg>Tgg	p.R608W	KDM2B_ENST00000536437.1_Missense_Mutation_p.R491W|KDM2B_ENST00000542973.1_5'UTR|KDM2B_ENST00000377069.4_Missense_Mutation_p.R577W	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	608					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						GTCCGGCGCCGCCGAGCTCCT	0.706																																					p.R608W		Atlas-SNP	.											.	KDM2B	218	.	0			c.C1822T						PASS	.						10	13	12					12																	121891060		1945	4112	6057	SO:0001583	missense	84678	exon13			GGCGCCGCCGAGC	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.1822C>T	12.37:g.121891060G>A	ENSP00000366271:p.Arg608Trp	66	0	0		44	11	0.25	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Missense_Mutation	SNP	ENST00000377071.4	37	CCDS41850.1	.	.	.	.	.	.	.	.	.	.	G	19.83	3.900662	0.72754	.	.	ENSG00000089094	ENST00000397480;ENST00000377069;ENST00000377071;ENST00000536437;ENST00000397478;ENST00000540043;ENST00000261824	T;T;T	0.54675	1.97;1.38;0.56	5.18	0.934	0.19477	Zinc finger, CXXC-type (2);	0.000000	0.47852	D	0.000201	T	0.71134	0.3304	M	0.87547	2.89	0.47245	D	0.999366	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;0.971;0.999;0.971;0.999	T	0.72001	-0.4422	10	0.87932	D	0	-18.2694	9.0059	0.36111	0.0676:0.0:0.5518:0.3806	.	48;491;608;577;48	B7ZB05;Q1RLM7;Q8NHM5;A8MRS1;B4DSN4	.;.;KDM2B_HUMAN;.;.	W	608;577;608;491;608;48;608	ENSP00000366269:R577W;ENSP00000366271:R608W;ENSP00000445196:R491W	ENSP00000261824:R608W	R	-	1	2	KDM2B	120375443	1.000000	0.71417	1.000000	0.80357	0.862000	0.49288	1.788000	0.38714	0.298000	0.22638	-0.266000	0.10368	CGG	.	.	none		0.706	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590		A	121891060	G	A	121891060	3	1	33	1	0	0	0	0	1	0	0	0	8134	1086	38	1	2284	1	KDM2B	12	121891060	Missense_Mutation	SNP	G	TCGA-GR-A4D6-01A-11D-A31X-10	115805736	121891060	11960835	29	14055											
LRFN5	145581	hgsc.bcm.edu	37	chr14	42356300	42356300	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agctggatctgtcctataatAatctagaaaccattccttgg	12	13	7	9	0	2	1	0	0	2	1	4	2	4	2	3	2	2	1	3	2	5	6			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr14:42356300A>C	ENST00000298119.4	+	3	1661	c.472A>C	c.(472-474)Aat>Cat	p.N158H	LRFN5_ENST00000554120.1_Missense_Mutation_p.N158H|LRFN5_ENST00000554171.1_Missense_Mutation_p.N158H	NM_152447.3	NP_689660.2	Q96NI6	LRFN5_HUMAN	leucine rich repeat and fibronectin type III domain containing 5	158						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)		GTCCTATAATAATCTAGAAAC	0.398										HNSCC(30;0.082)																											p.N158H		Atlas-SNP	.											LRFN5,NS,carcinoma,0,1	LRFN5	269	1	0			c.A472C						scavenged	.						83	72	76					14																	42356300		2203	4300	6503	SO:0001583	missense	145581	exon3			TATAATAATCTAG	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.472A>C	14.37:g.42356300A>C	ENSP00000298119:p.Asn158His	67	1	0.0149254		55	15	0.272727	NM_152447	B3KU78|Q86XL2	Missense_Mutation	SNP	ENST00000298119.4	37	CCDS9678.1	.	.	.	.	.	.	.	.	.	.	A	17.04	3.288566	0.59976	.	.	ENSG00000165379	ENST00000298119;ENST00000554120;ENST00000554171	D;D;D	0.92249	-3.0;-3.0;-3.0	5.56	5.56	0.83823	.	0.000000	0.64402	D	0.000010	D	0.92251	0.7542	N	0.17800	0.525	0.58432	D	0.999995	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.993	D	0.92871	0.6314	10	0.51188	T	0.08	.	13.6661	0.62396	1.0:0.0:0.0:0.0	.	158;158	G3V364;Q96NI6	.;LRFN5_HUMAN	H	158	ENSP00000298119:N158H;ENSP00000451897:N158H;ENSP00000451067:N158H	ENSP00000298119:N158H	N	+	1	0	LRFN5	41426050	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.339000	0.96797	2.098000	0.63641	0.528000	0.53228	AAT	.	.	none		0.398	LRFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276786.1	NM_152447		C	42356300	A	C	42356300	3	2	33	1	0	0	0	0	1	0	0	0	8950	362	13	5	474	5	LRFN5	14	42356300	Missense_Mutation	SNP	A	TCGA-GR-A4D6-01A-11D-A31X-10		42356300	64993240	30	14056											
C16orf93	90835	hgsc.bcm.edu	37	chr16	30770512	30770512	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccttacccgtctcactctcTggccacagtttgggtggctg	4	12	10	15	1	2	0	1	0	2	0	4	0	2	0	3	3	1	2	3	3	1	2			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr16:30770512T>C	ENST00000543610.1	-	7	1675	c.714A>G	c.(712-714)ccA>ccG	p.P238P	PHKG2_ENST00000563588.1_3'UTR|RNF40_ENST00000324685.6_5'Flank|PHKG2_ENST00000424889.3_Intron|C16orf93_ENST00000541260.1_Silent_p.P303P	NM_001014979.2	NP_001014979.2	A1A4V9	CP093_HUMAN	chromosome 16 open reading frame 93	238										breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(6)	11						TCTCACTCTCTGGCCACAGTT	0.597																																					p.P238P		Atlas-SNP	.											.	C16orf93	33	.	0			c.A714G						PASS	.						68	70	70					16																	30770512		2197	4300	6497	SO:0001819	synonymous_variant	90835	exon7			ACTCTCTGGCCAC	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.714A>G	16.37:g.30770512T>C		38	0	0		51	12	0.235294	NM_001014979	A1A4V8|F5GX13|Q569G2	Silent	SNP	ENST00000543610.1	37	CCDS32434.2	.	.	.	.	.	.	.	.	.	.	T	5.075	0.199509	0.09652	.	.	ENSG00000196118	ENST00000535476	.	.	.	5.12	2.78	0.32641	.	.	.	.	.	T	0.51686	0.1689	.	.	.	0.51482	D	0.999921	.	.	.	.	.	.	T	0.39563	-0.9608	4	.	.	.	-0.303	4.4208	0.11479	0.1727:0.094:0.0:0.7333	.	.	.	.	R	135	.	.	Q	-	2	0	C16orf93	30678013	0.438000	0.25602	0.578000	0.28575	0.575000	0.36095	0.133000	0.15912	0.327000	0.23409	0.533000	0.62120	CAG	.	.	none		0.597	C16orf93-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397089.1	NM_001014979		C	30770512	T	C	30770512	2	2	33	1	0	0	0	0	0	0	0	1	1848	1567	55	3		3	C16orf93	16	30770512	Silent	SNP	T	TCGA-GR-A4D6-01A-11D-A31X-10		30770512	59584241	31	14057											
CNOT1	23019	hgsc.bcm.edu	37	chr16	58577327	58577327	+	Intron	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atataacagaaaaaaaaaaaAacacacagacatgatgcttt	24	7	4	6	0	0	3	0	1	0	2	0	3	0	3	0	0	3	1	0	0	8	3	rs556592424		TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr16:58577327A>C	ENST00000317147.5	-	31	4767				CNOT1_ENST00000441024.2_Missense_Mutation_p.F1540V|CNOT1_ENST00000569240.1_Intron|CNOT1_ENST00000245138.4_Intron	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)		aaaaaaaaaaaacacacagac	0.299													A|||	1	0.000199681	0.0	0.0	5008	,	,		18548	0.0		0.001	False		,,,				2504	0.0				p.F1540V		Atlas-SNP	.											CNOT1_ENST00000441024,caecum,carcinoma,0,1	CNOT1	359	1	0			c.T4618G						scavenged	.						20	20	20					16																	58577327		1013	2122	3135	SO:0001627	intron_variant	23019	exon31			AAAAAAAACACAC	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.4434+183T>G	16.37:g.58577327A>C		215	2	0.00930233		188	8	0.0425532	NM_206999	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	37	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	A	4.645	0.119968	0.08881	.	.	ENSG00000125107	ENST00000441024	T	0.44482	0.92	1.6	-3.2	0.05156	.	.	.	.	.	T	0.28499	0.0705	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.12400	-1.0549	8	0.87932	D	0	.	5.872	0.18809	0.2548:0.5872:0.158:0.0	.	1540	A5YKK6-4	.	V	1540	ENSP00000413113:F1540V	ENSP00000413113:F1540V	F	-	1	0	CNOT1	57134828	0.004000	0.15560	0.000000	0.03702	0.000000	0.00434	0.507000	0.22675	-2.105000	0.00842	-1.344000	0.01245	TTT	.	.	none		0.299	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284		C	58577327	A	C	58577327	1	2	33	0	1	0	0	0	0	0	0	0	3619	14	1	5		5	CNOT1	16	58577327	Intron	SNP	A	TCGA-GR-A4D6-01A-11D-A31X-10	27806815	58577327	31777426	32	14058											
ANKRD11	29123	hgsc.bcm.edu	37	chr16	89347228	89347228	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ggaggtgtccaggtccggggGaagggccccttcgagggaag	7	5	20	9	2	0	0	0	0	0	0	3	4	2	3	4	7	0	0	4	7	2	1			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr16:89347228G>A	ENST00000301030.4	-	9	6182	c.5722C>T	c.(5722-5724)Ccc>Tcc	p.P1908S	ANKRD11_ENST00000378330.2_Missense_Mutation_p.P1908S	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1908	Pro-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)		AGGTCCGGGGGAAGGGCCCCT	0.662																																					p.P1908S		Atlas-SNP	.											.	ANKRD11	195	.	0			c.C5722T						PASS	.						30	36	34					16																	89347228		2196	4296	6492	SO:0001583	missense	29123	exon9			CCGGGGGAAGGGC	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.5722C>T	16.37:g.89347228G>A	ENSP00000301030:p.Pro1908Ser	62	0	0		82	24	0.292683	NM_001256183	Q6NTG1|Q6QMF8	Missense_Mutation	SNP	ENST00000301030.4	37	CCDS32513.1	.	.	.	.	.	.	.	.	.	.	g	16.17	3.048706	0.55110	.	.	ENSG00000167522	ENST00000301030;ENST00000378330	T;T	0.43688	0.94;0.94	4.78	2.7	0.31948	.	0.169886	0.38111	N	0.001806	T	0.32224	0.0822	L	0.36672	1.1	0.80722	D	1	P	0.50066	0.931	B	0.41374	0.355	T	0.02743	-1.1116	10	0.24483	T	0.36	.	14.1122	0.65129	0.0:0.288:0.7119:0.0	.	1908	Q6UB99	ANR11_HUMAN	S	1908	ENSP00000301030:P1908S;ENSP00000367581:P1908S	ENSP00000301030:P1908S	P	-	1	0	ANKRD11	87874729	1.000000	0.71417	0.926000	0.36857	0.821000	0.46438	5.071000	0.64382	0.377000	0.24735	0.450000	0.29827	CCC	.	.	none		0.662	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		A	89347228	G	A	89347228	3	1	33	1	0	0	0	0	1	0	0	0	639	1174	41	2	2289	2	ANKRD11	16	89347228	Missense_Mutation	SNP	G	TCGA-GR-A4D6-01A-11D-A31X-10	30769901	89347228	1007525	33	14059											
SYNRG	11276	hgsc.bcm.edu	37	chr17	35913676	35913676	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggaacaggactggcttcctCtttaagggcatcatatttgt	10	13	10	8	0	2	0	1	0	1	0	3	2	3	2	1	4	1	2	1	4	3	5			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr17:35913676C>T	ENST00000339208.6	-	14	2289	c.2149G>A	c.(2149-2151)Gag>Aag	p.E717K	SYNRG_ENST00000591288.1_Missense_Mutation_p.E556K|SYNRG_ENST00000502449.2_Missense_Mutation_p.E639K|SYNRG_ENST00000585472.1_Missense_Mutation_p.E638K|SYNRG_ENST00000346661.4_Missense_Mutation_p.E717K|SYNRG_ENST00000345615.4_Missense_Mutation_p.E639K|SYNRG_ENST00000588194.1_5'UTR|SYNRG_ENST00000394378.2_Missense_Mutation_p.E639K	NM_001163544.1|NM_001163545.1|NM_007247.4	NP_001157016.1|NP_001157017.1|NP_009178.3	Q9UMZ2	SYNRG_HUMAN	synergin, gamma	717	Interaction with A1P1G1 and A1P1G2.				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						CTGGCTTCCTCTTTAAGGGCA	0.473																																					p.E717K		Atlas-SNP	.											.	SYNRG	101	.	0			c.G2149A						PASS	.						54	55	54					17																	35913676		2203	4300	6503	SO:0001583	missense	11276	exon14			CTTCCTCTTTAAG	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.2149G>A	17.37:g.35913676C>T	ENSP00000343610:p.Glu717Lys	88	0	0		73	7	0.0958904	NM_007247	A8MWU4|B7ZKZ2|B7ZKZ3|Q17RI2|Q5BKU5|Q6ZT17	Missense_Mutation	SNP	ENST00000339208.6	37	CCDS11321.1	.	.	.	.	.	.	.	.	.	.	C	18.34	3.603368	0.66445	.	.	ENSG00000006114	ENST00000346661;ENST00000339208;ENST00000345615;ENST00000502449;ENST00000394378	T;T;T;T;T	0.50548	1.48;1.15;0.74;0.9;0.9	6.17	6.17	0.99709	.	0.196730	0.53938	D	0.000058	T	0.38585	0.1046	L	0.54323	1.7	0.39716	D	0.971399	P;B;B;B;P;P	0.47762	0.57;0.317;0.317;0.317;0.9;0.9	B;B;B;B;B;B	0.39258	0.255;0.228;0.228;0.228;0.295;0.295	T	0.22591	-1.0212	10	0.16420	T	0.52	-12.6231	10.2468	0.43345	0.0:0.7921:0.1368:0.071	.	556;639;639;639;717;717	B7ZKZ2;Q9UMZ2-3;A8MWU4;Q9UMZ2-4;Q9UMZ2-5;Q9UMZ2	.;.;.;.;.;SYNRG_HUMAN	K	717;556;717;639;639	ENSP00000005279:E717K;ENSP00000343610:E556K;ENSP00000315722:E717K;ENSP00000424893:E639K;ENSP00000377903:E639K	ENSP00000343610:E556K	E	-	1	0	SYNRG	32987789	0.729000	0.28090	0.990000	0.47175	0.951000	0.60555	1.279000	0.33191	2.941000	0.99782	0.655000	0.94253	GAG	.	.	none		0.473	SYNRG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256811.2	NM_007247		T	35913676	C	T	35913676	3	4	33	1	0	0	0	0	1	0	0	0	15475	922	32	2	1904	2	SYNRG	17	35913676	Missense_Mutation	SNP	C	TCGA-GR-A4D6-01A-11D-A31X-10		35913676	45281534	34	14060											
CNN2	1265	hgsc.bcm.edu	37	chr19	1037764	1037764	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggccaggtcttcggcctgggCcggcagatatatgaccccaa	8	7	13	13	2	1	2	0	1	1	1	2	2	1	2	5	5	0	1	5	5	3	3			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr19:1037764C>G	ENST00000263097.4	+	7	1158	c.795C>G	c.(793-795)ggC>ggG	p.G265G	AC011558.5_ENST00000585757.1_RNA|CNN2_ENST00000565096.2_Silent_p.G254G|CNN2_ENST00000348419.3_Silent_p.G226G|CNN2_ENST00000562958.2_Silent_p.G286G|ABCA7_ENST00000263094.6_5'Flank|CNN2_ENST00000606983.1_3'UTR	NM_004368.2	NP_004359.1	Q99439	CNN2_HUMAN	calponin 2	265					actomyosin structure organization (GO:0031032)|cellular response to mechanical stimulus (GO:0071260)|cytoskeleton organization (GO:0007010)|hemopoiesis (GO:0030097)|negative regulation of cell migration (GO:0030336)|negative regulation of phagocytosis (GO:0050765)|positive regulation of gene expression (GO:0010628)|regulation of actin filament-based process (GO:0032970)|regulation of cell proliferation (GO:0042127)|wound healing (GO:0042060)	cell-cell junction (GO:0005911)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|stress fiber (GO:0001725)	actin binding (GO:0003779)			endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	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)		TCGGCCTGGGCCGGCAGATAT	0.652																																					p.G265G		Atlas-SNP	.											.	CNN2	26	.	0			c.C795G						PASS	.						70	81	77					19																	1037764		2200	4288	6488	SO:0001819	synonymous_variant	1265	exon7			CCTGGGCCGGCAG	D83735	CCDS12053.1, CCDS12054.1	19p13.3	2011-02-18			ENSG00000064666	ENSG00000064666			2156	protein-coding gene	gene with protein product		602373				8889829	Standard	NM_004368		Approved		uc002lqu.3	Q99439		ENST00000263097.4:c.795C>G	19.37:g.1037764C>G		137	0	0		108	26	0.240741	NM_004368	A5D8U8|A6NFI4|D6W5X9|Q92578	Silent	SNP	ENST00000263097.4	37	CCDS12053.1																																																																																			.	.	none		0.652	CNN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420293.3	NM_004368		G	1037764	C	G	1037764	2	3	33	1	0	0	0	0	0	0	0	1	3612	726	26	4		4	CNN2	19	1037764	Silent	SNP	C	TCGA-GR-A4D6-01A-11D-A31X-10		1037764	58091219	35	14061											
INSR	3643	hgsc.bcm.edu	37	chr19	7174667	7174667	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agctcctgggcagacgtcacCgagtcgatggtcttctcgcc	6	9	12	14	4	3	1	1	0	2	1	6	3	4	1	3	2	1	2	3	2	0	1			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr19:7174667C>T	ENST00000302850.5	-	4	1192	c.1050G>A	c.(1048-1050)tcG>tcA	p.S350S	INSR_ENST00000341500.5_Silent_p.S350S	NM_000208.2	NP_000199.2	P06213	INSR_HUMAN	insulin receptor	350			S -> L (in RMS and LEPRCH). {ECO:0000269|PubMed:12970295, ECO:0000269|PubMed:8314008}.		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)"	CAGACGTCACCGAGTCGATGG	0.602																																					p.S350S		Atlas-SNP	.											.	INSR	265	.	0			c.G1050A						PASS	.						109	80	90					19																	7174667		2203	4300	6503	SO:0001819	synonymous_variant	3643	exon4			CGTCACCGAGTCG	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.1050G>A	19.37:g.7174667C>T		67	0	0		75	13	0.173333	NM_000208	Q17RW0|Q59H98|Q9UCB7|Q9UCB8|Q9UCB9	Silent	SNP	ENST00000302850.5	37	CCDS12176.1																																																																																			.	.	none		0.602	INSR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458544.1			T	7174667	C	T	7174667	2	4	33	1	0	0	0	0	0	0	0	1	7782	639	23	1		1	INSR	19	7174667	Silent	SNP	C	TCGA-GR-A4D6-01A-11D-A31X-10	6136903	7174667	51954316	36	14062											
PRKCSH	5589	hgsc.bcm.edu	37	chr19	11558370	11558370	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggaggaggaggaggaggaGgaagaagaggctgaagaaga	17	1	22	1	0	0	5	0	1	0	4	0	13	0	12	0	8	0	1	0	8	4	0	rs77563879		TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr19:11558370G>A	ENST00000589838.1	+	10	966	c.966G>A	c.(964-966)gaG>gaA	p.E322E	PRKCSH_ENST00000587327.1_Silent_p.E322E|PRKCSH_ENST00000591462.1_Silent_p.E322E|PRKCSH_ENST00000592741.1_Silent_p.E322E|PRKCSH_ENST00000252455.2_Silent_p.E322E|PRKCSH_ENST00000412601.1_Silent_p.E322E			P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H	322	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						aggaggaggaggaagaagagg	0.632																																					p.E322E		Atlas-SNP	.											PRKCSH,caecum,carcinoma,0,1	PRKCSH	55	1	1	Deletion - In frame(1)	central_nervous_system(1)	c.G966A						PASS	.						27	27	27					19																	11558370		2200	4298	6498	SO:0001819	synonymous_variant	5589	exon11			GGAGGAGGAAGAA		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.966G>A	19.37:g.11558370G>A		60	0	0		71	5	0.0704225	NM_001001329	A8K318|Q96BU9|Q96D06|Q9P0W9	Silent	SNP	ENST00000589838.1	37	CCDS32911.1																																																																																			.	.	weak		0.632	PRKCSH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458817.1			A	11558370	G	A	11558370	2	1	33	1	0	0	0	0	0	0	0	1	12528	991	35	2		2	PRKCSH	19	11558370	Silent	SNP	G	TCGA-GR-A4D6-01A-11D-A31X-10	4383703	11558370	47570613	37	14063											
JUNB	3726	hgsc.bcm.edu	37	chr19	12902785	12902785	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agagggcggcggtggcggcaGctacttttctggtcagggct	5	9	18	9	3	2	1	1	0	1	1	2	1	2	1	0	7	2	3	0	7	1	3			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr19:12902785G>A	ENST00000302754.4	+	1	476	c.200G>A	c.(199-201)aGc>aAc	p.S67N		NM_002229.2	NP_002220.1	P17275	JUNB_HUMAN	jun B proto-oncogene	67					cellular response to calcium ion (GO:0071277)|cellular response to hormone stimulus (GO:0032870)|decidualization (GO:0046697)|embryonic process involved in female pregnancy (GO:0060136)|gene expression (GO:0010467)|labyrinthine layer blood vessel development (GO:0060716)|osteoblast differentiation (GO:0001649)|osteoblast proliferation (GO:0033687)|osteoclast differentiation (GO:0030316)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to corticosterone (GO:0051412)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to light stimulus (GO:0009416)|response to mechanical stimulus (GO:0009612)|response to peptide hormone (GO:0043434)|response to progesterone (GO:0032570)|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)|vasculogenesis (GO:0001570)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|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)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|cervix(1)|kidney(1)|lung(3)	6						GGTGGCGGCAGCTACTTTTCT	0.672																																					p.S67N		Atlas-SNP	.											.	JUNB	14	.	0			c.G200A						PASS	.						12	13	13					19																	12902785		2200	4293	6493	SO:0001583	missense	3726	exon1			GCGGCAGCTACTT	M29039	CCDS12280.1	19p13.13	2013-01-10				ENSG00000171223		"basic leucine zipper proteins"	6205	protein-coding gene	gene with protein product		165161				2513129	Standard	NM_002229		Approved		uc002mvc.3	P17275		ENST00000302754.4:c.200G>A	19.37:g.12902785G>A	ENSP00000303315:p.Ser67Asn	88	0	0		69	20	0.289855	NM_002229	Q96GH3	Missense_Mutation	SNP	ENST00000302754.4	37	CCDS12280.1	.	.	.	.	.	.	.	.	.	.	G	12.81	2.050854	0.36181	.	.	ENSG00000171223	ENST00000302754	T	0.29655	1.56	4.25	3.1	0.35709	Jun-like transcription factor (1);	.	.	.	.	T	0.20373	0.0490	N	0.25485	0.75	0.33704	D	0.614893	B	0.28820	0.224	B	0.26094	0.066	T	0.17107	-1.0380	9	0.17369	T	0.5	-16.9799	13.1068	0.59252	0.0:0.1633:0.8367:0.0	.	67	P17275	JUNB_HUMAN	N	67	ENSP00000303315:S67N	ENSP00000303315:S67N	S	+	2	0	JUNB	12763785	0.995000	0.38212	1.000000	0.80357	0.967000	0.64934	2.201000	0.42734	2.300000	0.77407	0.549000	0.68633	AGC	.	.	none		0.672	JUNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451015.1	NM_002229		A	12902785	G	A	12902785	3	1	33	1	0	0	0	0	1	0	0	0	7979	971	34	2	202	2	JUNB	19	12902785	Missense_Mutation	SNP	G	TCGA-GR-A4D6-01A-11D-A31X-10	1344415	12902785	46226198	38	14064											
TPRX1	284355	hgsc.bcm.edu	37	chr19	48305613	48305624	+	In_Frame_Del	DEL	TTGGGCCTGAGA	TTGGGCCTGAGA	-																															gcctgggatcgggcctgggtTtgggcctgagattgggcctg																								rs201007421		TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	TTGGGCCTGAGA	TTGGGCCTGAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr19:48305613_48305624delTTGGGCCTGAGA	ENST00000322175.3	-	2	799_810	c.644_655delTCTCAGGCCCAA	c.(643-657)atctcaggcccaaac>aac	p.ISGP215del	TPRX1_ENST00000535759.1_In_Frame_Del_p.ISGP312del|TPRX1_ENST00000543508.1_In_Frame_Del_p.ISGP205del	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)		gggcctgggtttgggcctgagattgggcctga	0.67																																					p.215_219del	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-Indel	.											TPRX1,NS,carcinoma,0,1	TPRX1	46	1	0			c.645_656del						PASS	.																																			SO:0001651	inframe_deletion	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.644_655delTCTCAGGCCCAA	19.37:g.48305613_48305624delTTGGGCCTGAGA	ENSP00000323455:p.Ile215_Pro218del	32	0	0		32	11	0.34375	NM_198479	A5D8Y3|B2RPL5	In_Frame_Del	DEL	ENST00000322175.3	37	CCDS33066.1																																																																																			.	.	none		0.67	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479		-	48305624	TTGGGCCTGAGA	-	48305613	7	5	33	1	0	1	0	1	0	0	0	0	16437	1841	64	0	584	0	TPRX1	19	48305613	In_Frame_Del	DEL	TTGGGCCTGAGA	TCGA-GR-A4D6-01A-11D-A31X-10	35402828	48305613	10823370	39	14065											
BIRC7	79444	hgsc.bcm.edu	37	chr20	61870941	61870941	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccccgtccgcagccgcgtgcGcaccttcctgtcctaggcca	4	7	10	20	5	0	0	0	0	0	0	3	0	3	0	8	1	2	2	8	1	1	2	rs142521563		TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr20:61870941G>A	ENST00000217169.3	+	6	1095	c.881G>A	c.(880-882)cGc>cAc	p.R294H	NKAIN4_ENST00000466885.1_5'Flank|BIRC7_ENST00000342412.6_Missense_Mutation_p.R276H|BIRC7_ENST00000395306.1_Missense_Mutation_p.R189H|MIR3196_ENST00000579556.1_RNA	NM_139317.1	NP_647478.1	Q96CA5	BIRC7_HUMAN	baculoviral IAP repeat containing 7	294					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)					AGCCGCGTGCGCACCTTCCTG	0.721																																					p.R294H		Atlas-SNP	.											BIRC7,colon,carcinoma,0,1	BIRC7	25	1	0			c.G881A						PASS	.	G	HIS/ARG,HIS/ARG	1,4385		0,1,2192	29	26	27		827,881	3.9	1	20	dbSNP_134	27	0,8582		0,0,4291	no	missense,missense	BIRC7	NM_022161.2,NM_139317.1	29,29	0,1,6483	AA,AG,GG		0.0,0.0228,0.0077	probably-damaging,probably-damaging	276/281,294/299	61870941	1,12967	2193	4291	6484	SO:0001583	missense	79444	exon6			GCGTGCGCACCTT	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.881G>A	20.37:g.61870941G>A	ENSP00000217169:p.Arg294His	30	0	0		32	11	0.34375	NM_139317	Q9BQV0|Q9H2A8|Q9HAP7	Missense_Mutation	SNP	ENST00000217169.3	37	CCDS13513.1	.	.	.	.	.	.	.	.	.	.	G	15.74	2.923510	0.52653	2.28E-4	0.0	ENSG00000101197	ENST00000342412;ENST00000217169;ENST00000395306	T;T;T	0.56776	0.64;0.44;1.65	4.89	3.94	0.45596	.	0.000000	0.40728	N	0.001031	T	0.51669	0.1688	M	0.70275	2.135	0.58432	D	0.999999	P;P	0.52842	0.943;0.956	B;B	0.42386	0.209;0.386	T	0.58188	-0.7680	10	0.87932	D	0	.	10.498	0.44789	0.162:0.0:0.838:0.0	.	294;276	Q96CA5;Q96CA5-2	BIRC7_HUMAN;.	H	276;294;189	ENSP00000345213:R276H;ENSP00000217169:R294H;ENSP00000378717:R189H	ENSP00000217169:R294H	R	+	2	0	BIRC7	61341386	1.000000	0.71417	0.998000	0.56505	0.136000	0.21042	4.069000	0.57541	1.038000	0.40049	0.467000	0.42956	CGC	G|1.000;A|0.000	0.000	weak		0.721	BIRC7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080114.2	NM_139317		A	61870941	G	A	61870941	3	1	33	1	0	0	0	0	1	0	0	0	1439	1087	38	1	903	1	BIRC7	20	61870941	Missense_Mutation	SNP	G	TCGA-GR-A4D6-01A-11D-A31X-10		61870941	1154579	40	14066											
TRPM2	7226	hgsc.bcm.edu	37	chr21	45825049	45825049	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctatgaccctgacgagtgcGggctgatgaagaaggcagcc	10	7	14	10	2	1	5	0	4	1	1	1	6	1	5	2	2	2	2	2	2	3	1	rs144022462		TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr21:45825049G>A	ENST00000397928.1	+	17	3008	c.2563G>A	c.(2563-2565)Ggg>Agg	p.G855R	TRPM2_ENST00000300482.5_Missense_Mutation_p.G855R|TRPM2_ENST00000397932.2_Missense_Mutation_p.G855R|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000300481.9_Missense_Mutation_p.G835R	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	855					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						TGACGAGTGCGGGCTGATGAA	0.537																																					p.G855R		Atlas-SNP	.											.	TRPM2	196	.	0			c.G2563A						PASS	.						200	156	171					21																	45825049		2202	4299	6501	SO:0001583	missense	7226	exon17			GAGTGCGGGCTGA	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.2563G>A	21.37:g.45825049G>A	ENSP00000381023:p.Gly855Arg	62	0	0		55	12	0.218182	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	37	CCDS13710.1	.	.	.	.	.	.	.	.	.	.	g	13.30	2.195886	0.38806	.	.	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932	T;T;T;T	0.62232	0.04;0.04;0.04;0.04	4.55	1.57	0.23409	Ion transport (1);	0.225132	0.36740	N	0.002438	T	0.52901	0.1763	M	0.70903	2.155	0.34092	D	0.660838	P;P;P	0.47106	0.731;0.89;0.604	B;B;B	0.39562	0.235;0.303;0.235	T	0.59182	-0.7502	10	0.33141	T	0.24	-18.79	6.0001	0.19515	0.0754:0.1359:0.6479:0.1408	.	855;641;855	E9PGK7;Q5KTC1;O94759	.;.;TRPM2_HUMAN	R	855;855;835;855	ENSP00000300482:G855R;ENSP00000381023:G855R;ENSP00000300481:G835R;ENSP00000381026:G855R	ENSP00000300481:G835R	G	+	1	0	TRPM2	44649477	1.000000	0.71417	0.005000	0.12908	0.850000	0.48378	4.013000	0.57138	0.096000	0.17463	0.465000	0.42564	GGG	G|1.000;T|0.000	.	alt		0.537	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307		A	45825049	G	A	45825049	3	1	33	1	0	0	0	0	1	0	0	0	16601	1116	39	1	2629	1	TRPM2	21	45825049	Missense_Mutation	SNP	G	TCGA-GR-A4D6-01A-11D-A31X-10		45825049	2304846	41	14067											
MYO18B	84700	hgsc.bcm.edu	37	chr22	26242205	26242205	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acctttgccagcagccttgcCgcggtgaggaggaaagcccc	8	6	13	14	2	0	1	0	1	0	0	0	3	0	3	6	3	5	1	6	3	1	2	rs375428629		TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr22:26242205C>T	ENST00000407587.2	+	19	3679	c.3510C>T	c.(3508-3510)gcC>gcT	p.A1170A	MYO18B_ENST00000335473.7_Silent_p.A1169A|MYO18B_ENST00000536101.1_Silent_p.A1169A			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1169	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						GCAGCCTTGCCGCGGTGAGGA	0.652																																					p.A1169A		Atlas-SNP	.											.	MYO18B	322	.	0			c.C3507T						PASS	.	C		1,4315		0,1,2157	71	84	80		3507	-8.6	0	22		80	0,8484		0,0,4242	no	coding-synonymous	MYO18B	NM_032608.5		0,1,6399	TT,TC,CC		0.0,0.0232,0.0078		1169/2568	26242205	1,12799	2158	4242	6400	SO:0001819	synonymous_variant	84700	exon19			CCTTGCCGCGGTG	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.3510C>T	22.37:g.26242205C>T		48	0	0		48	11	0.229167	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37																																																																																				.	.	weak		0.652	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		T	26242205	C	T	26242205	2	4	33	1	0	0	0	0	0	0	0	1	10075	639	23	1		1	MYO18B	22	26242205	Silent	SNP	C	TCGA-GR-A4D6-01A-11D-A31X-10		26242205	25062361	42	14068											
EP300	2033	hgsc.bcm.edu	37	chr22	41572795	41572795	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggattatgacttgtgtatcAcctgctataacactaaaaac	15	12	6	8	0	1	1	1	1	0	0	1	2	1	2	1	1	3	2	1	1	7	6			TCGA-GR-A4D6-01A-11D-A31X-10	TCGA-GR-A4D6-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	5a58bec0-67a8-4529-80d8-1042dfd8164a	5efebdb0-cfc1-42ae-be1d-e124289877a5	g.chr22:41572795A>G	ENST00000263253.7	+	31	6299	c.5080A>G	c.(5080-5082)Acc>Gcc	p.T1694A	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	1694	Binding region for E1A adenovirus.				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						CTTGTGTATCACCTGCTATAA	0.423			"T,  N, F, Mis, O"	"MLL, RUNXBP2"	"colorectal, breast, pancreatic, AML, ALL, DLBCL"				Rubinstein-Taybi syndrome																												p.T1694A		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"L, E"	.	EP300	367	.	0			c.A5080G						PASS	.						131	125	127					22																	41572795		2203	4300	6503	SO:0001583	missense	2033	exon31	Familial Cancer Database	Broad Thumb-Hallux syndrome	TGTATCACCTGCT	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.5080A>G	22.37:g.41572795A>G	ENSP00000263253:p.Thr1694Ala	69	0	0		93	25	0.268817	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	.	.	.	.	.	.	.	.	.	.	A	13.71	2.319613	0.41096	.	.	ENSG00000100393	ENST00000263253	D	0.91124	-2.79	5.45	5.45	0.79879	Zinc finger, ZZ-type (4);	0.000000	0.49916	D	0.000129	T	0.80727	0.4678	N	0.04655	-0.195	0.43032	D	0.994605	P	0.36616	0.561	B	0.40285	0.325	T	0.80016	-0.1559	10	0.08381	T	0.77	-9.5504	15.8114	0.78568	1.0:0.0:0.0:0.0	.	1694	Q09472	EP300_HUMAN	A	1694	ENSP00000263253:T1694A	ENSP00000263253:T1694A	T	+	1	0	EP300	39902741	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.576000	0.82467	2.191000	0.70037	0.528000	0.53228	ACC	.	.	none		0.423	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429		G	41572795	A	G	41572795	3	3	33	1	0	0	0	0	1	0	0	0	5150	159	6	3	5202	3	EP300	22	41572795	Missense_Mutation	SNP	A	TCGA-GR-A4D6-01A-11D-A31X-10	15330590	41572795	9731771	43	14069											
PRAMEF11	440560	hgsc.bcm.edu	37	chr1	12887686	12887686	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagcacttgaagtttccaTctcctgtgggaaaatagagg	11	11	10	9	0	1	2	0	1	1	1	4	3	3	3	3	2	1	2	3	2	4	3	rs59802947	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:12887686T>C	ENST00000535591.1	-	3	366	c.171A>G	c.(169-171)agA>agG	p.R57R		NM_001146344.1	NP_001139816.1	O60813	PRA11_HUMAN	PRAME family member 11	57					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)			p.R57R(1)		NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|lung(7)|pancreas(2)|skin(4)|urinary_tract(1)	27						GAAGTTTCCATCTCCTGTGGG	0.468													.|||	5	0.000998403	0.0008	0.0	5008	,	,		21622	0.001		0.0	False		,,,				2504	0.0031				p.R57R		Atlas-SNP	.											PRAMEF11,NS,carcinoma,0,1	PRAMEF11	72	1	1	Substitution - coding silent(1)	endometrium(1)	c.A171G						scavenged	.																																			SO:0001819	synonymous_variant	440560	exon3			TTTCCATCTCCTG	AL049680	CCDS53268.1	1p36.21	2013-01-17			ENSG00000204513	ENSG00000239810		"-"	14086	protein-coding gene	gene with protein product							Standard	XM_006710645		Approved		uc001auk.2	O60813	OTTHUMG00000001929	ENST00000535591.1:c.171A>G	1.37:g.12887686T>C		9	0	0		16	4	0.25	NM_001146344		Silent	SNP	ENST00000535591.1	37	CCDS53268.1																																																																																			T|0.986;C|0.014	0.014	strong		0.468	PRAMEF11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_496341		C	12887686	T	C	12887686	2	2	34	1	0	0	0	0	0	0	0	1	12439	1432	50	3		3	PRAMEF11	1	12887686	Silent	SNP	T	TCGA-GR-A4D9-01B-11D-A31X-10		12887686	236362935	1	14070											
ARID1A	8289	hgsc.bcm.edu	37	chr1	27102083	27102083	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcaggaaccccggaggcatGgcgggtaatgatgtccctca	9	8	13	11	2	2	1	2	1	0	0	3	3	3	3	3	5	1	2	3	5	2	2			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:27102083G>A	ENST00000324856.7	+	19	5380	c.5009G>A	c.(5008-5010)tGg>tAg	p.W1670*	ARID1A_ENST00000374152.2_Nonsense_Mutation_p.W1287*|ARID1A_ENST00000540690.1_5'UTR|ARID1A_ENST00000457599.2_Nonsense_Mutation_p.W1453*	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1670					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.W1670*(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)		CCGGAGGCATGGCGGGTAATG	0.542			"Mis, N, F, S, D"		"clear cell ovarian carcinoma, RCC"																																p.W1670X		Atlas-SNP	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	ARID1A,bladder,carcinoma,0,1	ARID1A	842	1	1	Substitution - Nonsense(1)	urinary_tract(1)	c.G5009A						PASS	.						80	67	71					1																	27102083		2203	4300	6503	SO:0001587	stop_gained	8289	exon19			AGGCATGGCGGGT	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.5009G>A	1.37:g.27102083G>A	ENSP00000320485:p.Trp1670*	44	0	0		43	17	0.395349	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Nonsense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	44|44	10.783098|10.783098	0.99467|0.99467	.|.	.|.	ENSG00000117713|ENSG00000117713	ENST00000430799|ENST00000324856;ENST00000457599;ENST00000374152	.|.	.|.	.|.	5.05|5.05	5.05|5.05	0.67936|0.67936	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.46560|.	0.1399|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.34825|.	-0.9813|.	4|.	.|0.02654	.|T	.|1	-4.3496|-4.3496	18.5907|18.5907	0.91210|0.91210	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	I|X	566|1670;1453;1287	.|.	.|ENSP00000320485:W1670X	M|W	+|+	3|2	0|0	ARID1A|ARID1A	26974670|26974670	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	9.657000|9.657000	0.98554|0.98554	2.634000|2.634000	0.89283|0.89283	0.655000|0.655000	0.94253|0.94253	ATG|TGG	.	.	none		0.542	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135		A	27102083	G	A	27102083	4	1	34	1	0	0	0	0	0	1	0	0	913	1357	47	2	5083	2	ARID1A	1	27102083	Nonsense_Mutation	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10	14214397	27102083	222148538	2	14071											
SFPQ	6421	hgsc.bcm.edu	37	chr1	35658418	35658432	+	In_Frame_Del	DEL	GGTGGCTGCTGCGGT	GGTGGCTGCTGCGGT	-																															gcggtggcggctgctgcggcGgtggctgctgcggtggtggc																										TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	GGTGGCTGCTGCGGT	GGTGGCTGCTGCGGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:35658418_35658432delGGTGGCTGCTGCGGT	ENST00000357214.5	-	1	317_331	c.219_233delACCGCAGCAGCCACC	c.(217-234)ccaccgcagcagccaccg>ccg	p.73_78PPQQPP>P		NM_005066.2	NP_005057.1	P23246	SFPQ_HUMAN	splicing factor proline/glutamine-rich	73	Gln/Glu/Pro-rich.				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)				ctgctgcggcggtggctgctgcggtggtggcTGTT	0.707			T	TFE3	papillary renal cell																																p.74_78del		Atlas-Indel	.		Dom	yes		1	1p34.3	6421	splicing factor proline/glutamine rich(polypyrimidine tract binding protein associated)		E	.	SFPQ	51	.	0			c.220_234del						PASS	.			136,3204		29,78,1563						1.2	0			4	216,6642		53,110,3266	no	coding	SFPQ	NM_005066.2		82,188,4829	A1A1,A1R,RR		3.1496,4.0719,3.4517				352,9846				SO:0001651	inframe_deletion	6421	exon1			.	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.219_233delACCGCAGCAGCCACC	1.37:g.35658418_35658432delGGTGGCTGCTGCGGT	ENSP00000349748:p.Pro78_Pro82del	27	0	0		29	13	0.448276	NM_005066	P30808|Q5SZ71	In_Frame_Del	DEL	ENST00000357214.5	37	CCDS388.1																																																																																			.	.	none		0.707	SFPQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011984.4	NM_005066		-	35658432	GGTGGCTGCTGCGGT	-	35658418	7	5	34	1	0	1	0	1	0	0	0	0	14175	1116	39	0	1930	0	SFPQ	1	35658418	In_Frame_Del	DEL	GGTGGCTGCTGCGGT	TCGA-GR-A4D9-01B-11D-A31X-10	8556335	35658418	213592203	3	14072											
BCL10	8915	hgsc.bcm.edu	37	chr1	85736460	85736460	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taacaattttccagccctttTtctacttgatgttcgacaag	10	16	5	10	1	1	1	0	1	1	0	3	2	2	1	2	0	3	1	2	0	4	8			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:85736460T>G	ENST00000370580.1	-	2	924	c.187A>C	c.(187-189)Aaa>Caa	p.K63Q		NM_003921.4	NP_003912.1	O95999	BCL10_HUMAN	B-cell CLL/lymphoma 10	63	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				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)		CCAGCCCTTTTTCTACTTGAT	0.373			T	IGH@	MALT																																p.K63Q	NSCLC(34;993 1034 12176 32621 50182)	Atlas-SNP	.		Dom	yes		1	1p22	8915	B-cell CLL/lymphoma 10		L	.	BCL10	39	.	0			c.A187C						PASS	.						110	114	113					1																	85736460		2203	4300	6503	SO:0001583	missense	8915	exon2			CCCTTTTTCTACT	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.187A>C	1.37:g.85736460T>G	ENSP00000359612:p.Lys63Gln	106	0	0		154	71	0.461039	NM_003921	Q5VUF1	Missense_Mutation	SNP	ENST00000370580.1	37	CCDS704.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.250050	0.80024	.	.	ENSG00000142867	ENST00000370580;ENST00000271015;ENST00000394761	T	0.20463	2.07	5.69	5.69	0.88448	DEATH-like (2);Caspase Recruitment (2);	0.048742	0.85682	D	0.000000	T	0.29620	0.0739	L	0.53249	1.67	0.42293	D	0.992143	D	0.76494	0.999	D	0.68483	0.958	T	0.04509	-1.0946	10	0.66056	D	0.02	-31.1976	12.1424	0.54005	0.0:0.0:0.1427:0.8573	.	63	O95999	BCL10_HUMAN	Q	63	ENSP00000359612:K63Q	ENSP00000271015:K63Q	K	-	1	0	BCL10	85509048	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.576000	0.60915	2.291000	0.77112	0.533000	0.62120	AAA	.	.	none		0.373	BCL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027612.1	NM_003921		G	85736460	T	G	85736460	3	3	34	1	0	0	0	0	1	0	0	0	1362	1850	64	5	522	5	BCL10	1	85736460	Missense_Mutation	SNP	T	TCGA-GR-A4D9-01B-11D-A31X-10	50078042	85736460	163514161	4	14073											
PTGFRN	5738	hgsc.bcm.edu	37	chr1	117491909	117491909	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaccgagccgatgacgtcCggcccgaggtgacgtggtcc	7	5	15	14	6	0	3	0	2	0	1	2	6	2	3	5	3	1	0	5	3	0	0	rs560392261	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:117491909C>T	ENST00000393203.2	+	4	1075	c.928C>T	c.(928-930)Cgg>Tgg	p.R310W		NM_020440.2	NP_065173.2	Q9P2B2	FPRP_HUMAN	prostaglandin F2 receptor inhibitor	310	Ig-like C2-type 3.				lipid particle organization (GO:0034389)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(4)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)	46	Lung SC(450;0.225)	all_cancers(81;0.00104)|all_lung(203;8.97e-05)|all_epithelial(167;0.000139)|Lung NSC(69;0.000446)		Lung(183;0.0704)|LUSC - Lung squamous cell carcinoma(189;0.227)|Colorectal(144;0.248)		CGATGACGTCCGGCCCGAGGT	0.597													C|||	2	0.000399361	0.0	0.0029	5008	,	,		18404	0.0		0.0	False		,,,				2504	0.0				p.R310W		Atlas-SNP	.											.	PTGFRN	91	.	0			c.C928T						PASS	.						115	99	105					1																	117491909		2203	4300	6503	SO:0001583	missense	5738	exon4			GACGTCCGGCCCG	AB014734	CCDS890.1	1p13.1	2013-01-29	2013-01-25		ENSG00000134247	ENSG00000134247		"CD molecules", "Immunoglobulin superfamily / V-set domain containing", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	9601	protein-coding gene	gene with protein product		601204	"prostaglandin F2 receptor negative regulator"			8655148	Standard	NM_020440		Approved	FPRP, EWI-F, CD9P-1, FLJ11001, KIAA1436, SMAP-6, CD315	uc001egv.1	Q9P2B2	OTTHUMG00000012028	ENST00000393203.2:c.928C>T	1.37:g.117491909C>T	ENSP00000376899:p.Arg310Trp	66	0	0		58	18	0.310345	NM_020440	Q5VVU9|Q8N2K6	Missense_Mutation	SNP	ENST00000393203.2	37	CCDS890.1	.	.	.	.	.	.	.	.	.	.	C	11.78	1.741688	0.30865	.	.	ENSG00000134247	ENST00000393203;ENST00000544471	T	0.65916	-0.18	5.77	2.78	0.32641	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.547984	0.19786	N	0.106117	T	0.43478	0.1249	L	0.27053	0.805	0.09310	N	1	D	0.89917	1.0	P	0.59703	0.862	T	0.28004	-1.0057	10	0.66056	D	0.02	-17.914	4.9405	0.13963	0.1512:0.6227:0.146:0.0801	.	310	Q9P2B2	FPRP_HUMAN	W	310;169	ENSP00000376899:R310W	ENSP00000376899:R310W	R	+	1	2	PTGFRN	117293432	0.445000	0.25657	0.005000	0.12908	0.012000	0.07955	2.573000	0.46007	0.781000	0.33589	-0.254000	0.11334	CGG	.	.	none		0.597	PTGFRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033271.1	NM_020440		T	117491909	C	T	117491909	3	4	34	1	0	0	0	0	1	0	0	0	12763	643	23	1	942	1	PTGFRN	1	117491909	Missense_Mutation	SNP	C	TCGA-GR-A4D9-01B-11D-A31X-10	31755449	117491909	131758712	5	14074											
ARHGEF2	9181	hgsc.bcm.edu	37	chr1	155920171	155920171	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtcactgctgtcttgcagccGctcttcggggctccccagtt	3	12	11	15	2	3	0	1	0	2	0	5	0	4	0	3	2	3	5	3	2	0	3			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:155920171G>A	ENST00000361247.4	-	21	2905	c.2806C>T	c.(2806-2808)Cgg>Tgg	p.R936W	ARHGEF2_ENST00000313695.7_Missense_Mutation_p.R908W|ARHGEF2_ENST00000477754.2_Intron|ARHGEF2_ENST00000368316.1_Missense_Mutation_p.R908W|ARHGEF2_ENST00000462460.2_Missense_Mutation_p.R981W|ARHGEF2_ENST00000368315.4_Missense_Mutation_p.R937W|ARHGEF2_ENST00000313667.4_Missense_Mutation_p.R935W	NM_001162383.1|NM_001162384.1	NP_001155855.1|NP_001155856.1	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 2	936					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)					TCTTGCAGCCGCTCTTCGGGG	0.627																																					p.R936W	Melanoma(178;35 2768 6610 28839)	Atlas-SNP	.											.	ARHGEF2	81	.	0			c.C2806T						PASS	.						58	55	56					1																	155920171		2203	4300	6503	SO:0001583	missense	9181	exon21			GCAGCCGCTCTTC	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.2806C>T	1.37:g.155920171G>A	ENSP00000354837:p.Arg936Trp	65	0	0		72	16	0.222222	NM_001162383	D3DVA6|O75142|Q15079|Q5VY92|Q8TDA3|Q8WUG4|Q9H023	Missense_Mutation	SNP	ENST00000361247.4	37	CCDS53376.1	.	.	.	.	.	.	.	.	.	.	G	13.65	2.300726	0.40694	.	.	ENSG00000116584	ENST00000313695;ENST00000361247;ENST00000368315;ENST00000368316;ENST00000313667	T;T;T;T;T	0.69561	-0.4;-0.28;-0.29;-0.4;-0.41	5.98	5.06	0.68205	.	0.177972	0.27319	N	0.019911	T	0.42877	0.1222	N	0.19112	0.55	0.33849	D	0.632384	D;P;P;D	0.60575	0.975;0.916;0.95;0.988	B;B;P;B	0.46275	0.312;0.312;0.51;0.386	T	0.54111	-0.8342	10	0.62326	D	0.03	-22.727	12.5577	0.56263	0.0:0.0:0.8335:0.1665	.	980;936;935;937	D3DVA5;Q92974;Q92974-2;Q5VY93	.;ARHG2_HUMAN;.;.	W	908;936;937;908;935	ENSP00000315325:R908W;ENSP00000354837:R936W;ENSP00000357298:R937W;ENSP00000357299:R908W;ENSP00000314787:R935W	ENSP00000314787:R935W	R	-	1	2	ARHGEF2	154186795	1.000000	0.71417	0.973000	0.42090	0.242000	0.25591	4.760000	0.62235	1.518000	0.48934	-0.181000	0.13052	CGG	.	.	none		0.627	ARHGEF2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046204.2	NM_004723		A	155920171	G	A	155920171	3	1	34	1	0	0	0	0	1	0	0	0	903	1086	38	1	162	1	ARHGEF2	1	155920171	Missense_Mutation	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10	38428262	155920171	93330450	6	14075											
USH2A	7399	hgsc.bcm.edu	37	chr1	216420482	216420482	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaatttgttcactgagccatGgaggttacactggcagggct	9	11	13	8	0	1	1	1	1	0	0	1	3	1	2	1	4	2	4	1	4	2	3			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr1:216420482G>T	ENST00000307340.3	-	13	2640	c.2254C>A	c.(2254-2256)Cat>Aat	p.H752N	USH2A_ENST00000366943.2_Missense_Mutation_p.H752N|USH2A_ENST00000366942.3_Missense_Mutation_p.H752N	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	752	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)		ACTGAGCCATGGAGGTTACAC	0.413										HNSCC(13;0.011)																											p.H752N		Atlas-SNP	.											.	USH2A	1168	.	0			c.C2254A						PASS	.						105	108	107					1																	216420482		2203	4300	6503	SO:0001583	missense	7399	exon13			AGCCATGGAGGTT	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.2254C>A	1.37:g.216420482G>T	ENSP00000305941:p.His752Asn	143	0	0		154	33	0.214286	NM_007123	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	12.25	1.880963	0.33255	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.61742	0.08;0.08;0.08	5.89	1.43	0.22495	EGF-like, laminin (3);	0.310145	0.22620	N	0.057702	T	0.45696	0.1355	L	0.34521	1.04	0.28645	N	0.906962	B;P	0.42584	0.041;0.784	B;P	0.45753	0.04;0.492	T	0.33624	-0.9861	10	0.28530	T	0.3	.	6.7169	0.23308	0.2729:0.0:0.6066:0.1205	.	752;752	O75445-2;O75445	.;USH2A_HUMAN	N	752	ENSP00000305941:H752N;ENSP00000355910:H752N;ENSP00000355909:H752N	ENSP00000305941:H752N	H	-	1	0	USH2A	214487105	0.529000	0.26322	0.945000	0.38365	0.997000	0.91878	-0.016000	0.12613	0.393000	0.25203	0.655000	0.94253	CAT	.	.	none		0.413	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216420482	G	T	216420482	3	4	34	1	0	0	0	0	1	0	0	0	17051	1348	47	4	13608	4	USH2A	1	216420482	Missense_Mutation	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10	60500311	216420482	32830139	7	14076											
TTN	7273	hgsc.bcm.edu	37	chr2	179604859	179604859	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctgtacctcctgcactttCtttattgccacgggctctct	4	15	6	16	1	2	0	0	0	2	0	4	0	3	0	4	1	3	3	4	1	2	5	rs367656813		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:179604859C>A	ENST00000591111.1	-	46	12374	c.12150G>T	c.(12148-12150)aaG>aaT	p.K4050N	TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.K4367N|TTN_ENST00000342175.6_Missense_Mutation_p.K4196N|TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342992.6_Intron|TTN_ENST00000359218.5_Missense_Mutation_p.K4129N|TTN_ENST00000460472.2_Missense_Mutation_p.K4004N			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)			CCTGCACTTTCTTTATTGCCA	0.443																																					p.K4367N		Atlas-SNP	.											.	TTN	18412	.	0			c.G13101T						PASS	.	C	ASN/LYS,,ASN/LYS,ASN/LYS	1,3693		0,1,1846	67	66	66		12012,,12387,12588	-3	0	2		66	0,8188		0,0,4094	no	missense,intron,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	94,,94,94	0,1,5940	AA,AC,CC		0.0,0.0271,0.0084	,,,	4004/26927,,4129/27052,4196/27119	179604859	1,11881	1847	4094	5941	SO:0001583	missense	7273	exon48			CACTTTCTTTATT	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.12150G>T	2.37:g.179604859C>A	ENSP00000465570:p.Lys4050Asn	107	0	0		109	29	0.266055	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	37		.	.	.	.	.	.	.	.	.	.	C	1.754	-0.488428	0.04352	2.71E-4	0.0	ENSG00000155657	ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T	0.61859	0.14;0.08;0.07	5.92	-3.05	0.05396	.	.	.	.	.	T	0.29190	0.0726	N	0.08118	0	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	0.12116	-1.0560	9	0.87932	D	0	.	1.5845	0.02641	0.2937:0.3519:0.1844:0.17	.	4004;4129;4196	D3DPF9;E7EQE6;E7ET18	.;.;.	N	4004;4196;4129;4004	ENSP00000434586:K4004N;ENSP00000340554:K4196N;ENSP00000352154:K4129N	ENSP00000340554:K4196N	K	-	3	2	TTN	179313104	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	0.294000	0.19047	-1.056000	0.03205	-0.182000	0.12963	AAG	.	.	weak		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378		A	179604859	C	A	179604859	3	1	34	1	0	0	0	0	1	0	0	0	16750	912	32	4	91688	4	TTN	2	179604859	Missense_Mutation	SNP	C	TCGA-GR-A4D9-01B-11D-A31X-10		179604859	63594514	8	14077											
SATB2	23314	hgsc.bcm.edu	37	chr2	200173610	200173610	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaagcgacggatggtacagAggttttcccagagggtgcgg	9	7	18	7	3	0	2	0	0	0	2	1	5	1	4	1	6	3	2	1	6	2	3			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:200173610A>G	ENST00000417098.1	-	10	2429	c.1613T>C	c.(1612-1614)cTc>cCc	p.L538P	SATB2_ENST00000260926.5_Missense_Mutation_p.L538P|SATB2_ENST00000443023.1_Missense_Mutation_p.L479P|SATB2_ENST00000428695.1_Missense_Mutation_p.L420P|SATB2_ENST00000457245.1_Missense_Mutation_p.L538P	NM_001172509.1	NP_001165980.1	Q9UPW6	SATB2_HUMAN	SATB homeobox 2	538					cartilage development (GO:0051216)|cellular response to organic substance (GO:0071310)|chromatin remodeling (GO:0006338)|embryonic pattern specification (GO:0009880)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|osteoblast development (GO:0002076)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(40)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						GATGGTACAGAGGTTTTCCCA	0.557																																					p.L538P	Colon(30;262 767 11040 24421 36230)	Atlas-SNP	.											.	SATB2	134	.	0			c.T1613C						PASS	.						132	106	115					2																	200173610		2203	4300	6503	SO:0001583	missense	23314	exon11			GTACAGAGGTTTT	AB028957	CCDS2327.1	2q33.1	2011-06-20	2007-02-15		ENSG00000119042	ENSG00000119042		"Homeoboxes / CUT class"	21637	protein-coding gene	gene with protein product		608148	"SATB family member 2"				Standard	NM_015265		Approved	KIAA1034, FLJ21474	uc002uva.2	Q9UPW6	OTTHUMG00000132767	ENST00000417098.1:c.1613T>C	2.37:g.200173610A>G	ENSP00000401112:p.Leu538Pro	140	0	0		119	47	0.394958	NM_015265	A8K5Z8|Q3ZB87|Q4V763	Missense_Mutation	SNP	ENST00000417098.1	37	CCDS2327.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.838366	0.91117	.	.	ENSG00000119042	ENST00000417098;ENST00000443023;ENST00000260926;ENST00000428695;ENST00000457245	T;T;T;T;T	0.61980	0.18;0.19;0.18;0.06;0.18	5.21	5.21	0.72293	Homeodomain protein CUT (2);Lambda repressor-like, DNA-binding (2);	0.000000	0.85682	D	0.000000	T	0.78188	0.4244	M	0.70275	2.135	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.999;1.0	T	0.80879	-0.1185	10	0.87932	D	0	-15.8414	15.5441	0.76081	1.0:0.0:0.0:0.0	.	420;538	Q3ZB87;Q9UPW6	.;SATB2_HUMAN	P	538;479;538;420;538	ENSP00000401112:L538P;ENSP00000388764:L479P;ENSP00000260926:L538P;ENSP00000388581:L420P;ENSP00000405420:L538P	ENSP00000260926:L538P	L	-	2	0	SATB2	199881855	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.087000	0.94110	2.317000	0.78254	0.459000	0.35465	CTC	.	.	none		0.557	SATB2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256140.1	NM_015265		G	200173610	A	G	200173610	3	3	34	1	0	0	0	0	1	0	0	0	13869	304	11	3	596	3	SATB2	2	200173610	Missense_Mutation	SNP	A	TCGA-GR-A4D9-01B-11D-A31X-10	20568751	200173610	43025763	9	14078											
ADAM23	8745	hgsc.bcm.edu	37	chr2	207425911	207425911	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctttggaggtgtctgttctcGcacaagaggagttggtgtga	7	13	15	6	1	2	2	0	1	2	1	3	4	2	4	0	4	0	3	0	4	1	3			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:207425911G>A	ENST00000264377.3	+	12	1557	c.1229G>A	c.(1228-1230)cGc>cAc	p.R410H	ADAM23_ENST00000374416.1_Missense_Mutation_p.R410H|ADAM23_ENST00000374415.3_Missense_Mutation_p.R410H	NM_003812.2	NP_003803.1	O75077	ADA23_HUMAN	ADAM metallopeptidase domain 23	410	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				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)	p.R410H(2)		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)		GTCTGTTCTCGCACAAGAGGA	0.413																																					p.R410H	Melanoma(194;1127 2130 19620 24042 27855)	Atlas-SNP	.											ADAM23_ENST00000374416,NS,carcinoma,0,2	ADAM23	239	2	2	Substitution - Missense(2)	prostate(2)	c.G1229A						PASS	.						155	160	158					2																	207425911		2203	4300	6503	SO:0001583	missense	8745	exon12			GTTCTCGCACAAG	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.1229G>A	2.37:g.207425911G>A	ENSP00000264377:p.Arg410His	199	0	0		139	6	0.0431655	NM_003812	A2RU59	Missense_Mutation	SNP	ENST00000264377.3	37	CCDS2369.1	.	.	.	.	.	.	.	.	.	.	G	14.01	2.409037	0.42715	.	.	ENSG00000114948	ENST00000264377;ENST00000374416;ENST00000431817;ENST00000374415	T;T;T	0.09630	2.96;2.96;2.96	5.92	3.8	0.43715	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.382911	0.21835	N	0.068402	T	0.06096	0.0158	N	0.17082	0.46	0.29434	N	0.859679	B	0.02656	0.0	B	0.04013	0.001	T	0.14420	-1.0473	10	0.34782	T	0.22	.	6.0539	0.19800	0.1747:0.0:0.6327:0.1926	.	410	O75077	ADA23_HUMAN	H	410;410;304;410	ENSP00000264377:R410H;ENSP00000363537:R410H;ENSP00000363536:R410H	ENSP00000264377:R410H	R	+	2	0	ADAM23	207134156	0.991000	0.36638	1.000000	0.80357	0.997000	0.91878	0.937000	0.28951	1.498000	0.48600	0.655000	0.94253	CGC	.	.	none		0.413	ADAM23-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256431.2	NM_003812		A	207425911	G	A	207425911	3	1	34	1	0	0	0	0	1	0	0	0	245	1087	38	1	1275	1	ADAM23	2	207425911	Missense_Mutation	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10	7252301	207425911	35773462	10	14079											
PPP1R7	5510	hgsc.bcm.edu	37	chr2	242097275	242097275	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcaacctggacagagatgcaGaggtaatgccgcctgctcag	11	7	12	11	1	2	2	2	0	0	2	2	4	2	3	3	2	4	3	3	2	2	1			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr2:242097275G>A	ENST00000234038.6	+	3	709	c.235G>A	c.(235-237)Gag>Aag	p.E79K	PPP1R7_ENST00000401987.1_Missense_Mutation_p.E36K|PPP1R7_ENST00000406106.3_Missense_Mutation_p.E79K|PPP1R7_ENST00000272983.8_Missense_Mutation_p.E36K|PPP1R7_ENST00000407025.1_Missense_Mutation_p.E79K|PPP1R7_ENST00000402734.1_Missense_Mutation_p.E20K|PPP1R7_ENST00000404405.3_Missense_Mutation_p.E79K|PPP1R7_ENST00000485630.1_3'UTR	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	79					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)		CAGAGATGCAGAGGTAATGCC	0.468																																					p.E79K	NSCLC(62;446 1299 5417 11238 27640)	Atlas-SNP	.											.	PPP1R7	35	.	0			c.G235A						PASS	.						83	73	76					2																	242097275		2203	4300	6503	SO:0001583	missense	5510	exon3			GATGCAGAGGTAA	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.235G>A	2.37:g.242097275G>A	ENSP00000234038:p.Glu79Lys	102	0	0		98	36	0.367347	NM_002712	B4DFD4|B5MCY6|Q9UQE5|Q9UQE6|Q9Y6K4	Missense_Mutation	SNP	ENST00000234038.6	37	CCDS2546.1	.	.	.	.	.	.	.	.	.	.	G	32	5.164816	0.94727	.	.	ENSG00000115685	ENST00000438799;ENST00000402734;ENST00000423280;ENST00000407025;ENST00000272983;ENST00000234038;ENST00000404405;ENST00000439916;ENST00000406106;ENST00000401987;ENST00000427172	T;T;T;T;T;T;T;T;T;T;T	0.47177	1.85;1.85;1.85;1.85;1.85;1.85;0.85;1.15;1.85;1.85;1.82	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.66167	0.2762	M	0.66506	2.035	0.80722	D	1	D;P;P;P;D;P	0.71674	0.996;0.947;0.902;0.893;0.998;0.956	P;P;B;P;D;P	0.80764	0.824;0.577;0.415;0.554;0.994;0.549	T	0.61917	-0.6964	10	0.27082	T	0.32	-26.0255	17.1348	0.86736	0.0:0.0:1.0:0.0	.	63;20;36;79;79;79	C9JD73;C9J177;Q15435-2;Q15435;Q15435-3;B5MBZ8	.;.;.;PP1R7_HUMAN;.;.	K	63;20;20;79;36;79;79;79;79;36;88	ENSP00000396376:E63K;ENSP00000385012:E20K;ENSP00000412092:E20K;ENSP00000385657:E79K;ENSP00000272983:E36K;ENSP00000234038:E79K;ENSP00000385498:E79K;ENSP00000409719:E79K;ENSP00000385022:E79K;ENSP00000385466:E36K;ENSP00000397985:E88K	ENSP00000234038:E79K	E	+	1	0	PPP1R7	241745948	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.281000	0.89905	2.490000	0.84030	0.655000	0.94253	GAG	.	.	none		0.468	PPP1R7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257244.4	NM_002712		A	242097275	G	A	242097275	3	1	34	1	0	0	0	0	1	0	0	0	12388	943	33	2	245	2	PPP1R7	2	242097275	Missense_Mutation	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10	34671364	242097275	1102098	11	14080											
CLASP2	23122	hgsc.bcm.edu	37	chr3	33552202	33552202	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aagcactttgatgcactgctCtggactaattgaagtggcca	11	11	10	9	0	1	2	0	2	1	0	1	3	1	3	1	2	3	3	1	2	3	3			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:33552202C>T	ENST00000468888.2	-	37	4235	c.4189G>A	c.(4189-4191)Gag>Aag	p.E1397K	CLASP2_ENST00000480013.1_Missense_Mutation_p.E1176K|CLASP2_ENST00000359576.5_Missense_Mutation_p.E1388K|CLASP2_ENST00000461133.3_Missense_Mutation_p.E1156K|CLASP2_ENST00000307312.7_Missense_Mutation_p.E878K|CLASP2_ENST00000399362.4_Missense_Mutation_p.E1396K|CLASP2_ENST00000539981.1_3'UTR			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	1177					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						ATGCACTGCTCTGGACTAATT	0.383																																					p.E1398K		Atlas-SNP	.											.	CLASP2	138	.	0			c.G4192A						PASS	.						97	84	88					3																	33552202		1950	4153	6103	SO:0001583	missense	23122	exon37			ACTGCTCTGGACT	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.4189G>A	3.37:g.33552202C>T	ENSP00000419974:p.Glu1397Lys	191	0	0		160	49	0.30625	NM_015097	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Missense_Mutation	SNP	ENST00000468888.2	37		.	.	.	.	.	.	.	.	.	.	C	29.9	5.044175	0.93685	.	.	ENSG00000163539	ENST00000468888;ENST00000399362;ENST00000359576;ENST00000307312;ENST00000480013;ENST00000461133	T;T;T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26;-0.26;-0.26	6.08	6.08	0.98989	.	0.099158	0.64402	D	0.000002	T	0.72653	0.3487	M	0.71581	2.175	0.58432	D	0.999999	B;P	0.35050	0.449;0.482	B;B	0.42593	0.107;0.392	T	0.65865	-0.6064	10	0.15952	T	0.53	-20.1545	20.6634	0.99662	0.0:1.0:0.0:0.0	.	1388;1396	F5H604;E7ERI8	.;.	K	1397;1396;1388;878;1176;1156	ENSP00000419974:E1397K;ENSP00000382297:E1396K;ENSP00000352581:E1388K;ENSP00000304743:E878K;ENSP00000417518:E1176K;ENSP00000419305:E1156K	ENSP00000304743:E878K	E	-	1	0	CLASP2	33527206	1.000000	0.71417	0.997000	0.53966	0.999000	0.98932	7.506000	0.81665	2.894000	0.99253	0.655000	0.94253	GAG	.	.	none		0.383	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044		T	33552202	C	T	33552202	3	4	34	1	0	0	0	0	1	0	0	0	3457	922	32	2	367	2	CLASP2	3	33552202	Missense_Mutation	SNP	C	TCGA-GR-A4D9-01B-11D-A31X-10		33552202	164470228	12	14081											
C3orf35	339883	hgsc.bcm.edu	37	chr3	37476379	37476379	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gggaggggactgactcaatcCcagctgctggcagatctggg	8	7	16	10	0	2	2	1	1	1	1	3	4	3	4	1	5	2	3	1	5	1	0			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:37476379C>T	ENST00000328376.5	+	6	1250	c.271C>T	c.(271-273)Cca>Tca	p.P91S	C3orf35_ENST00000481400.1_3'UTR	NM_178339.2	NP_848029.2	Q8IVJ8	APRG1_HUMAN	chromosome 3 open reading frame 35	91						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						tgactcaatcccagctgctgg	0.458																																					p.P91S		Atlas-SNP	.											.	C3orf35	21	.	0			c.C271T						PASS	.						34	33	34					3																	37476379		1889	4110	5999	SO:0001583	missense	339883	exon6			TCAATCCCAGCTG	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.271C>T	3.37:g.37476379C>T	ENSP00000331625:p.Pro91Ser	265	0	0		248	88	0.354839	NM_178339	B7ZMA0|Q8IVJ5|Q8IVJ9	Missense_Mutation	SNP	ENST00000328376.5	37	CCDS43065.1	.	.	.	.	.	.	.	.	.	.	c	4.256	0.046572	0.08243	.	.	ENSG00000198590	ENST00000328376	T	0.56611	0.45	0.565	-1.13	0.09775	.	.	.	.	.	T	0.26412	0.0645	N	0.08118	0	0.09310	N	1	B	0.15141	0.012	B	0.06405	0.002	T	0.12967	-1.0527	8	0.87932	D	0	.	.	.	.	.	91	Q8IVJ8	APRG1_HUMAN	S	91	ENSP00000331625:P91S	ENSP00000331625:P91S	P	+	1	0	C3orf35	37451383	0.027000	0.19231	0.004000	0.12327	0.004000	0.04260	-0.642000	0.05427	-0.979000	0.03529	-0.970000	0.02610	CCA	.	.	none		0.458	C3orf35-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342344.2	NM_178338		T	37476379	C	T	37476379	3	4	34	1	0	0	0	0	1	0	0	0	2227	623	22	2	411	2	C3orf35	3	37476379	Missense_Mutation	SNP	C	TCGA-GR-A4D9-01B-11D-A31X-10	3924177	37476379	160546051	13	14082											
CADPS	8618	hgsc.bcm.edu	37	chr3	62647994	62647994	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaatgtttccttaccctggCtatttggtctgccatttgta	7	17	7	10	0	1	0	0	0	1	0	2	0	2	0	3	2	2	3	3	2	4	6			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:62647994C>A	ENST00000383710.4	-	4	1313	c.964G>T	c.(964-966)Gcc>Tcc	p.A322S	CADPS_ENST00000283269.9_Missense_Mutation_p.A322S|CADPS_ENST00000357948.3_Missense_Mutation_p.A322S|CADPS_ENST00000490353.2_Missense_Mutation_p.A322S	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	322					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)		CTTACCCTGGCTATTTGGTCT	0.488																																					p.A322S		Atlas-SNP	.											.	CADPS	387	.	0			c.G964T						PASS	.						174	149	158					3																	62647994		2203	4300	6503	SO:0001583	missense	8618	exon4			CCCTGGCTATTTG	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.964G>T	3.37:g.62647994C>A	ENSP00000373215:p.Ala322Ser	31	0	0		36	18	0.5	NM_003716	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Missense_Mutation	SNP	ENST00000383710.4	37	CCDS46858.1	.	.	.	.	.	.	.	.	.	.	C	15.88	2.965064	0.53507	.	.	ENSG00000163618	ENST00000383709;ENST00000383710;ENST00000357948;ENST00000283269;ENST00000490353	D;D;D;D	0.85088	-1.94;-1.94;-1.94;-1.94	5.54	5.54	0.83059	.	0.111048	0.64402	D	0.000006	D	0.86389	0.5921	N	0.20845	0.615	0.58432	D	0.999993	B;D;P	0.61697	0.073;0.99;0.657	B;D;B	0.73380	0.074;0.98;0.138	D	0.83718	0.0191	10	0.21014	T	0.42	.	18.2515	0.90005	0.0:1.0:0.0:0.0	.	322;322;322	Q9ULU8-2;Q9ULU8-3;Q9ULU8	.;.;CAPS1_HUMAN	S	322	ENSP00000373215:A322S;ENSP00000350632:A322S;ENSP00000283269:A322S;ENSP00000418736:A322S	ENSP00000283269:A322S	A	-	1	0	CADPS	62623034	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.387000	0.66243	2.606000	0.88127	0.655000	0.94253	GCC	.	.	none		0.488	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394		A	62647994	C	A	62647994	3	1	34	1	0	0	0	0	1	0	0	0	2572	797	28	4	3278	4	CADPS	3	62647994	Missense_Mutation	SNP	C	TCGA-GR-A4D9-01B-11D-A31X-10	25171615	62647994	135374436	14	14083											
KLHL6	89857	hgsc.bcm.edu	37	chr3	183209942	183209942	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gataccgcagctggcccgctCgtggctgagctgggtcacca	6	7	14	14	3	1	1	1	1	0	0	2	2	1	1	3	3	3	5	3	3	1	1			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr3:183209942C>T	ENST00000341319.3	-	7	1674	c.1639G>A	c.(1639-1641)Gag>Aag	p.E547K		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	547					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)			CTGGCCCGCTCGTGGCTGAGC	0.657																																					p.E547K		Atlas-SNP	.											.	KLHL6	100	.	0			c.G1639A						PASS	.						39	39	39					3																	183209942		2202	4299	6501	SO:0001583	missense	89857	exon7			CCCGCTCGTGGCT	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.1639G>A	3.37:g.183209942C>T	ENSP00000341342:p.Glu547Lys	140	0	0		151	52	0.344371	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Missense_Mutation	SNP	ENST00000341319.3	37	CCDS3245.2	.	.	.	.	.	.	.	.	.	.	C	12.27	1.888221	0.33348	.	.	ENSG00000172578	ENST00000341319	T	0.65732	-0.17	5.8	5.8	0.92144	Kelch-type beta propeller (1);	0.000000	0.85682	D	0.000000	T	0.48295	0.1492	N	0.21194	0.64	0.53688	D	0.999972	P	0.37663	0.604	B	0.37508	0.252	T	0.48364	-0.9042	10	0.02654	T	1	.	20.029	0.97531	0.0:1.0:0.0:0.0	.	547	Q8WZ60	KLHL6_HUMAN	K	547	ENSP00000341342:E547K	ENSP00000341342:E547K	E	-	1	0	KLHL6	184692636	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.907000	0.69908	2.742000	0.94016	0.591000	0.81541	GAG	.	.	none		0.657	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446		T	183209942	C	T	183209942	3	4	34	1	0	0	0	0	1	0	0	0	8402	893	31	1	230	1	KLHL6	3	183209942	Missense_Mutation	SNP	C	TCGA-GR-A4D9-01B-11D-A31X-10	120561948	183209942	14812488	15	14084											
PRKG2	5593	hgsc.bcm.edu	37	chr4	82031675	82031675	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagtcatgtcccttgttgaGaatgacttcaggagctacat	11	12	10	8	0	2	2	2	2	0	1	3	5	3	3	1	1	2	2	1	1	3	4			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:82031675G>T	ENST00000395578.1	-	15	1983	c.1867C>A	c.(1867-1869)Ctc>Atc	p.L623I	PRKG2_ENST00000509169.1_5'UTR|PRKG2_ENST00000545647.1_Missense_Mutation_p.L203I|PRKG2_ENST00000264399.1_Missense_Mutation_p.L623I|PRKG2_ENST00000418486.2_Missense_Mutation_p.L594I			Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	623	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						CCCTTGTTGAGAATGACTTCA	0.438																																					p.L623I		Atlas-SNP	.											.	PRKG2	195	.	0			c.C1867A						PASS	.						124	121	122					4																	82031675		2203	4300	6503	SO:0001583	missense	5593	exon14			TGTTGAGAATGAC	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.1867C>A	4.37:g.82031675G>T	ENSP00000378945:p.Leu623Ile	119	0	0		98	4	0.0408163	NM_006259	B4DMX3|E7EPE6|O00125|O60916	Missense_Mutation	SNP	ENST00000395578.1	37	CCDS3589.1	.	.	.	.	.	.	.	.	.	.	G	17.55	3.417180	0.62511	.	.	ENSG00000138669	ENST00000395578;ENST00000264399;ENST00000418486;ENST00000545647	T;T;T;T	0.67171	-0.25;-0.25;-0.25;-0.25	5.23	4.39	0.52855	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.060084	0.64402	D	0.000002	T	0.77731	0.4174	M	0.66297	2.02	0.58432	D	0.999998	D;D	0.76494	0.999;0.993	D;D	0.77004	0.984;0.989	T	0.78730	-0.2090	10	0.72032	D	0.01	-12.3911	9.7878	0.40686	0.1593:0.0:0.8407:0.0	.	594;623	E7EPE6;Q13237	.;KGP2_HUMAN	I	623;623;594;203	ENSP00000378945:L623I;ENSP00000264399:L623I;ENSP00000389038:L594I;ENSP00000439967:L203I	ENSP00000264399:L623I	L	-	1	0	PRKG2	82250699	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	2.122000	0.41987	1.211000	0.43351	0.557000	0.71058	CTC	.	.	none		0.438	PRKG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252639.1	NM_006259		T	82031675	G	T	82031675	3	4	34	1	0	0	0	0	1	0	0	0	12535	942	33	4	441	4	PRKG2	4	82031675	Missense_Mutation	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10		82031675	109122601	16	14085											
ANP32C	55016	hgsc.bcm.edu	37	chr4	165118819	165118819	+	Intron	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttctttcacatcagagggCgccctgttccgcagctctga	7	11	10	13	2	4	2	2	1	2	1	5	2	5	2	2	1	1	4	2	1	0	3			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr4:165118819C>T	ENST00000503008.1	-	2	864				MARCH1_ENST00000508725.1_Intron|MARCH1_ENST00000514618.1_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)	p.A15A(1)		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)				CATCAGAGGGCGCCCTGTTCC	0.502																																					p.A15A		Atlas-SNP	.											ANP32C,NS,carcinoma,0,1	ANP32C	59	1	1	Substitution - coding silent(1)	endometrium(1)	c.G45A						PASS	.						121	123	123					4																	165118819		2203	4300	6503	SO:0001627	intron_variant	23520	exon1			AGAGGGCGCCCTG	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.113-86005G>A	4.37:g.165118819C>T		95	0	0		102	34	0.333333	NM_012403	D3DP29|Q9NWR0	Silent	SNP	ENST00000503008.1	37	CCDS54814.1																																																																																			.	.	none		0.502	MARCH1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364493.2	NM_017923		T	165118819	C	T	165118819	1	4	34	0	1	0	0	0	0	0	0	0	707	755	27	1		1	ANP32C	4	165118819	Intron	SNP	C	TCGA-GR-A4D9-01B-11D-A31X-10	83087144	165118819	26035457	17	14086											
KIAA0947	23379	hgsc.bcm.edu	37	chr5	5461621	5461621	+	Frame_Shift_Del	DEL	A	A	-																															gaagagcagtgggatagaatAtacaaaagtagtaaaaggct																										TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:5461621delA	ENST00000296564.7	+	13	2396	c.2174delA	c.(2173-2175)tatfs	p.Y725fs		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		725					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						GGGATAGAATATACAAAAGTA	0.383																																					p.Y725fs		Pindel,Atlas-Indel	.											KIAA0947_ENST00000296564,NS,carcinoma,-1,2	KIAA0947	301	2	0			c.2173delT						PASS	.						54	52	52					5																	5461621		1850	4094	5944	SO:0001589	frameshift_variant	23379	exon13			.																												ENST00000296564.7:c.2174delA	5.37:g.5461621delA	ENSP00000296564:p.Tyr725fs	173	0	.		158	30	0.19	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Frame_Shift_Del	DEL	ENST00000296564.7	37	CCDS47187.1																																																																																			.	.	none		0.383	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1			-	5461621	A	-	5461621	7	5	34	1	0	1	0	1	0	0	0	0	8211	449	16	0	2224	0	KIAA0947	5	5461621	Frame_Shift_Del	DEL	A	TCGA-GR-A4D9-01B-11D-A31X-10		5461621	175453639	18	14087											
SEMA5A	9037	hgsc.bcm.edu	37	chr5	9052036	9052036	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccggctctccgtggtgttccCggagcactggctgcccatgg	3	9	14	15	3	1	0	0	0	1	0	3	1	2	1	4	5	2	4	4	5	0	1	rs139882587		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:9052036C>T	ENST00000382496.5	-	20	3459	c.2794G>A	c.(2794-2796)Ggg>Agg	p.G932R	MIR4636_ENST00000582271.1_RNA	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	932	TSP type-1 7. {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						GTGGTGTTCCCGGAGCACTGG	0.552													C|||	1	0.000199681	0.0	0.0	5008	,	,		17425	0.0		0.0	False		,,,				2504	0.001				p.G932R		Atlas-SNP	.											SEMA5A,colon,carcinoma,+2,1	SEMA5A	236	1	0			c.G2794A						PASS	.	C	ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	46	48	47		2794	4.2	0.6	5	dbSNP_134	47	2,8598	2.2+/-6.3	0,2,4298	yes	missense	SEMA5A	NM_003966.2	125	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	probably-damaging	932/1075	9052036	3,13003	2203	4300	6503	SO:0001583	missense	9037	exon20			TGTTCCCGGAGCA	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.2794G>A	5.37:g.9052036C>T	ENSP00000371936:p.Gly932Arg	163	0	0		137	44	0.321168	NM_003966	D3DTC6|O60408|Q1RLL9	Missense_Mutation	SNP	ENST00000382496.5	37	CCDS3875.1	.	.	.	.	.	.	.	.	.	.	C	18.18	3.566959	0.65651	2.27E-4	2.33E-4	ENSG00000112902	ENST00000382496	T	0.22945	1.93	5.12	4.25	0.50352	.	0.000000	0.85682	D	0.000000	T	0.62233	0.2411	H	0.96301	3.8	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73360	-0.4007	10	0.87932	D	0	.	11.7168	0.51659	0.0:0.9131:0.0:0.0869	.	932	Q13591	SEM5A_HUMAN	R	932	ENSP00000371936:G932R	ENSP00000371936:G932R	G	-	1	0	SEMA5A	9105036	1.000000	0.71417	0.601000	0.28877	0.266000	0.26442	7.573000	0.82421	1.287000	0.44583	0.655000	0.94253	GGG	C|1.000;T|0.000	0.000	strong		0.552	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2			T	9052036	C	T	9052036	3	4	34	1	0	0	0	0	1	0	0	0	14052	652	23	1	446	1	SEMA5A	5	9052036	Missense_Mutation	SNP	C	TCGA-GR-A4D9-01B-11D-A31X-10	3590415	9052036	171863224	19	14088											
MSH3	4437	hgsc.bcm.edu	37	chr5	79950708	79950708	+	Silent	SNP	T	T	C																															gaccctggcgctgcagcggcTgcagcggccgcagcggccgc																								rs201874762|rs2405875	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:79950708T>C	ENST00000265081.6	+	1	242	c.162T>C	c.(160-162)gcT>gcC	p.A54A	DHFR_ENST00000504396.1_5'Flank|DHFR_ENST00000505337.1_5'Flank|DHFR_ENST00000511032.1_5'Flank|DHFR_ENST00000439211.2_5'UTR|DHFR_ENST00000513048.1_5'Flank	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	54	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)		CTgcagcggctgcagcggccg	0.687								Mismatch excision repair (MMR)					-|||	259	0.0517173	0.0499	0.0447	5008	,	,		6179	0.0754		0.0437	False		,,,				2504	0.0429				p.A54A	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											.	MSH3	129	.	0			c.T162C						PASS	.						9	9	9					5																	79950708		2150	4207	6357	SO:0001819	synonymous_variant	4437	exon1			AGCGGCTGCAGCG	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.162T>C	5.37:g.79950708T>C		11	0	0		29	22	0.758621	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Silent	SNP	ENST00000265081.6	37	CCDS34195.1																																																																																			T|0.781;C|0.219	0.219	strong		0.687	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		C	79950708	T	C	79950708	2	2	34	1	0	0	0	0	0	0	0	1	9880	1567	55	3		3	MSH3	5	79950708	Silent	SNP	T	TCGA-GR-A4D9-01B-11D-A31X-10	70898672	79950708	100964552	20	14089	177	2									
MSH3	4437	hgsc.bcm.edu	37	chr5	79950715	79950715	+	Missense_Mutation	SNP	G	G	C																															gcgctgcagcggctgcagcgGccgcagcggccgcagcgccc																								rs144776112|rs201874762		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:79950715G>C	ENST00000265081.6	+	1	249	c.169G>C	c.(169-171)Gcc>Ccc	p.A57P	DHFR_ENST00000504396.1_5'Flank|DHFR_ENST00000505337.1_5'Flank|DHFR_ENST00000511032.1_5'Flank|DHFR_ENST00000439211.2_5'UTR|DHFR_ENST00000513048.1_5'Flank	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	57	Poly-Ala.		Missing. {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:8942985}.		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)		ggctgcagcggccgcagcggc	0.692								Mismatch excision repair (MMR)																													p.A57P	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											MSH3_ENST00000265081,NS,carcinoma,0,1	MSH3	129	1	0			c.G169C						PASS	.						7	7	7					5																	79950715		2089	4077	6166	SO:0001583	missense	4437	exon1			GCAGCGGCCGCAG	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.169G>C	5.37:g.79950715G>C	ENSP00000265081:p.Ala57Pro	9	0	0		27	15	0.555556	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	37	CCDS34195.1	362	0.16575091575091574	115	0.23373983739837398	67	0.1850828729281768	32	0.055944055944055944	148	0.19525065963060687	-	0.222	-1.028222	0.02045	.	.	ENSG00000113318	ENST00000265081	D	0.87256	-2.23	.	.	.	.	.	.	.	.	T	0.00039	0.0001	N	0.03608	-0.345	0.80722	P	0.0	.	.	.	.	.	.	T	0.02983	-1.1086	3	.	.	.	.	.	.	.	.	57	P20585	MSH3_HUMAN	P	57	ENSP00000265081:A57P	.	A	+	1	0	MSH3	79986471	0.041000	0.20044	0.049000	0.19019	0.152000	0.21847	0.000000	0.12993	0.000000	0.14550	0.000000	0.15137	GCC	G|0.835;C|0.165	0.165	strong		0.692	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		C	79950715	G	C	79950715	3	2	34	1	0	0	0	0	1	0	0	0	9880	1203	42	4	171	4	MSH3	5	79950715	Missense_Mutation	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10	7	79950715	100964545	21	14090	177	2									
PCDHGA1	56114	hgsc.bcm.edu	37	chr5	140711241	140711241	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtgcggggctcatggctaaAgttaaggtactgatcaaagt	11	10	14	6	1	2	1	2	1	0	0	2	1	2	1	0	5	2	4	0	5	5	3			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr5:140711241A>C	ENST00000517417.1	+	1	990	c.990A>C	c.(988-990)aaA>aaC	p.K330N	PCDHGA1_ENST00000378105.3_Missense_Mutation_p.K330N|AC005618.6_ENST00000606901.1_lincRNA	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	330	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)			TCATGGCTAAAGTTAAGGTAC	0.418																																					p.K330N		Atlas-SNP	.											.	PCDHGA1	397	.	0			c.A990C						PASS	.						70	69	70					5																	140711241		2203	4300	6503	SO:0001583	missense	56114	exon1			GGCTAAAGTTAAG	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.990A>C	5.37:g.140711241A>C	ENSP00000431083:p.Lys330Asn	162	0	0		183	26	0.142077	NM_018912	Q2M273|Q9Y5D6	Missense_Mutation	SNP	ENST00000517417.1	37	CCDS54922.1	.	.	.	.	.	.	.	.	.	.	A	1.463	-0.561832	0.03939	.	.	ENSG00000204956	ENST00000517417;ENST00000378105	T;T	0.01838	4.61;4.61	3.99	2.81	0.32909	Cadherin (5);Cadherin-like (1);	0.118831	0.37348	N	0.002129	T	0.01222	0.0040	N	0.08118	0	0.09310	N	1	B;P	0.34815	0.061;0.47	B;B	0.33121	0.038;0.158	T	0.47873	-0.9083	10	0.72032	D	0.01	.	2.7623	0.05310	0.5109:0.0:0.1932:0.2958	.	330;330	Q9Y5H4-2;Q9Y5H4	.;PCDG1_HUMAN	N	330	ENSP00000431083:K330N;ENSP00000367345:K330N	ENSP00000367345:K330N	K	+	3	2	PCDHGA1	140691425	0.000000	0.05858	0.999000	0.59377	0.094000	0.18550	-1.649000	0.01993	0.698000	0.31739	-0.297000	0.09499	AAA	.	.	none		0.418	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912		C	140711241	A	C	140711241	3	2	34	1	0	0	0	0	1	0	0	0	11559	69	3	5	992	5	PCDHGA1	5	140711241	Missense_Mutation	SNP	A	TCGA-GR-A4D9-01B-11D-A31X-10	60760526	140711241	40204019	22	14091											
KIF13A	63971	hgsc.bcm.edu	37	chr6	17764996	17764996	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tactgctggtggtagggctaCgggacacttctttctccaag	7	12	12	10	1	2	0	0	0	2	0	3	1	2	1	1	4	3	3	1	4	4	5	rs184686655	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:17764996C>T	ENST00000259711.6	-	39	4868	c.4763G>A	c.(4762-4764)cGt>cAt	p.R1588H	KIF13A_ENST00000378843.2_Missense_Mutation_p.R1540H|KIF13A_ENST00000378816.5_Missense_Mutation_p.R1553H|KIF13A_ENST00000378814.5_Missense_Mutation_p.R1540H|KIF13A_ENST00000378826.2_Missense_Mutation_p.R1553H	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A	1588					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)			GGTAGGGCTACGGGACACTTC	0.502													C|||	2	0.000399361	0.0008	0.0014	5008	,	,		19335	0.0		0.0	False		,,,				2504	0.0				p.R1588H		Atlas-SNP	.											.	KIF13A	276	.	0			c.G4763A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,4005		0,1,2002	84	83	84		4658,4619,4619,4763	6.1	1	6		84	3,8327		0,3,4162	yes	missense,missense,missense,missense	KIF13A	NM_001105566.2,NM_001105567.2,NM_001105568.2,NM_022113.5	29,29,29,29	0,4,6164	TT,TC,CC		0.036,0.025,0.0324	probably-damaging,probably-damaging,probably-damaging,probably-damaging	1553/1771,1540/1758,1540/1750,1588/1806	17764996	4,12332	2003	4165	6168	SO:0001583	missense	63971	exon39			GGGCTACGGGACA	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.4763G>A	6.37:g.17764996C>T	ENSP00000259711:p.Arg1588His	97	0	0		86	28	0.325581	NM_022113	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Missense_Mutation	SNP	ENST00000259711.6	37	CCDS47381.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	31	5.074668	0.94000	2.5E-4	3.6E-4	ENSG00000137177	ENST00000378814;ENST00000502297;ENST00000259711;ENST00000378826;ENST00000378843;ENST00000378816	T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72;0.72	6.07	6.07	0.98685	.	0.275476	0.29280	N	0.012608	T	0.53126	0.1777	L	0.34521	1.04	0.58432	D	0.999994	D;D;D;D	0.89917	1.0;0.999;1.0;0.999	D;P;D;P	0.81914	0.995;0.897;0.951;0.897	T	0.41431	-0.9509	10	0.36615	T	0.2	.	20.6525	0.99598	0.0:1.0:0.0:0.0	.	1540;1553;1588;1540	Q9H1H9-4;Q9H1H9-2;Q9H1H9;Q9H1H9-3	.;.;KI13A_HUMAN;.	H	1540;592;1588;1553;1540;1553	ENSP00000368091:R1540H;ENSP00000425616:R592H;ENSP00000259711:R1588H;ENSP00000368103:R1553H;ENSP00000368120:R1540H;ENSP00000368093:R1553H	ENSP00000259711:R1588H	R	-	2	0	KIF13A	17872975	1.000000	0.71417	0.992000	0.48379	0.998000	0.95712	7.469000	0.80959	2.890000	0.99128	0.585000	0.79938	CGT	C|1.000;T|0.000	0.000	strong		0.502	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039954.4			T	17764996	C	T	17764996	3	4	34	1	0	0	0	0	1	0	0	0	8283	536	19	1	683	1	KIF13A	6	17764996	Missense_Mutation	SNP	C	TCGA-GR-A4D9-01B-11D-A31X-10		17764996	153350071	23	14092											
ANKS1A	23294	hgsc.bcm.edu	37	chr6	34857324	34857324	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcggcggcggcggcagcggcGgcggcggcggcggcctcggc	1	1	24	15	11	0	0	0	0	0	0	1	0	0	0	1	11	1	1	1	11	0	0			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:34857324G>A	ENST00000360359.3	+	1	283	c.145G>A	c.(145-147)Ggc>Agc	p.G49S	ANKS1A_ENST00000535627.1_Missense_Mutation_p.G49S|TAF11_ENST00000420584.2_5'Flank|TAF11_ENST00000361288.4_5'Flank	NM_015245.2	NP_056060.2	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1A	49	Gly-rich.				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						cggcagcggcggcggcggcgg	0.771																																					p.G49S		Atlas-SNP	.											ANKS1A,NS,carcinoma,0,1	ANKS1A	123	1	0			c.G145A						PASS	.						2	2	2					6																	34857324		382	1194	1576	SO:0001583	missense	23294	exon1			AGCGGCGGCGGCG	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.145G>A	6.37:g.34857324G>A	ENSP00000353518:p.Gly49Ser	4	0	0		8	4	0.5	NM_015245	A2RUC1|B4DQW8|Q5JYI9|Q5SYR2|Q86WQ7	Missense_Mutation	SNP	ENST00000360359.3	37	CCDS4798.1	.	.	.	.	.	.	.	.	.	.	G	16.03	3.008376	0.54361	.	.	ENSG00000064999	ENST00000544150;ENST00000360359;ENST00000535627	T;D	0.98649	1.19;-5.05	4.58	1.53	0.23141	Ankyrin repeat-containing domain (1);	1.264600	0.06451	N	0.727796	D	0.90783	0.7106	N	0.19112	0.55	0.25322	N	0.989108	P;B	0.49090	0.919;0.003	B;B	0.38655	0.278;0.002	D	0.88474	0.3064	10	0.17832	T	0.49	-4.009	8.7007	0.34323	0.0795:0.0:0.6816:0.2389	.	49;49	B4DQW8;Q92625	.;ANS1A_HUMAN	S	49	ENSP00000353518:G49S;ENSP00000438752:G49S	ENSP00000353518:G49S	G	+	1	0	ANKS1A	34965302	1.000000	0.71417	0.794000	0.32065	0.327000	0.28475	2.586000	0.46119	0.389000	0.25086	0.471000	0.43371	GGC	.	.	none		0.771	ANKS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040262.1	XM_166478		A	34857324	G	A	34857324	3	1	34	1	0	0	0	0	1	0	0	0	688	1116	39	1	147	1	ANKS1A	6	34857324	Missense_Mutation	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10	17092328	34857324	136257743	24	14093											
PRDM1	639	hgsc.bcm.edu	37	chr6	106552891	106552892	+	Frame_Shift_Ins	INS	-	-	GT																															cctcgatgactttagaagacINSgtgggagccccgaaatgccc																								rs17066588	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:106552891_106552892insGT	ENST00000369096.4	+	5	1090_1091	c.856_857insGT	c.(856-858)cgtfs	p.R286fs	PRDM1_ENST00000369091.2_Frame_Shift_Ins_p.R250fs|PRDM1_ENST00000369089.3_Frame_Shift_Ins_p.R152fs	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	286					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)		CTTTAGAAGACGTGGGAGCCCC	0.525			"D, N, Mis, F, S"		DLBCL																																p.R286fs		Pindel,Atlas-Indel	.		Rec	yes		6	6q21	639	"PR domain containing 1, with ZNF domain"		L	PRDM1,colon,carcinoma,0,1	PRDM1	195	1	0			c.856_857insGT						PASS	.																																			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.857_858dupGT	6.37:g.106552892_106552893dupGT	ENSP00000358092:p.Arg286fs	152	0	.		78	19	0.244	NM_001198	B2REA6|E1P5E0|Q86WM7	Frame_Shift_Ins	INS	ENST00000369096.4	37	CCDS5054.2																																																																																			.	.	none		0.525	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3			GT	106552892	-	GT	106552891	7	5	34	1	0	1	1	0	0	0	0	0	12462	536	19	0	887	0	PRDM1	6	106552891	Frame_Shift_Ins	INS	-	TCGA-GR-A4D9-01B-11D-A31X-10	71695567	106552891	64562176	25	14094											
FAM162B	221303	hgsc.bcm.edu	37	chr6	117086652	117086652	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggaagagccggtgcgggccGtcgcgtggcctcgagaggcg	5	4	20	12	8	0	2	0	0	0	2	2	4	0	3	3	5	2	0	3	5	1	0			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr6:117086652G>A	ENST00000368557.4	-	1	234	c.88C>T	c.(88-90)Cgg>Tgg	p.R30W		NM_001085480.2	NP_001078949.1	Q5T6X4	F162B_HUMAN	family with sequence similarity 162, member B	30						integral component of membrane (GO:0016021)				large_intestine(2)|lung(4)	6						GGTGCGGGCCGTCGCGTGGCC	0.746																																					p.R30W		Atlas-SNP	.											.	FAM162B	19	.	0			c.C88T						PASS	.						2	3	3					6																	117086652		1446	3410	4856	SO:0001583	missense	221303	exon1			CGGGCCGTCGCGT	BC038997	CCDS43497.1	6q22.31	2014-01-28	2008-06-05	2008-06-05	ENSG00000183807	ENSG00000183807			21549	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 189"	C6orf189			Standard	NM_001085480		Approved	bA86F4.2	uc003pxi.2	Q5T6X4	OTTHUMG00000015446	ENST00000368557.4:c.88C>T	6.37:g.117086652G>A	ENSP00000357545:p.Arg30Trp	23	0	0		13	7	0.538462	NM_001085480	Q8IXW8	Missense_Mutation	SNP	ENST00000368557.4	37	CCDS43497.1	.	.	.	.	.	.	.	.	.	.	G	9.606	1.129940	0.21041	.	.	ENSG00000183807	ENST00000368557	T	0.31769	1.48	2.93	-3.02	0.05446	.	0.936775	0.08728	N	0.902552	T	0.05135	0.0137	N	0.17474	0.49	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.39354	-0.9618	10	0.46703	T	0.11	0.0041	4.5061	0.11889	0.4972:0.2298:0.273:0.0	.	30	Q5T6X4	F162B_HUMAN	W	30	ENSP00000357545:R30W	ENSP00000357545:R30W	R	-	1	2	FAM162B	117193345	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.029000	0.12329	-0.773000	0.04596	-0.643000	0.03959	CGG	.	.	none		0.746	FAM162B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041965.1	XM_927381		A	117086652	G	A	117086652	3	1	34	1	0	0	0	0	1	0	0	0	5480	1144	40	1	416	1	FAM162B	6	117086652	Missense_Mutation	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10	10533761	117086652	54028415	26	14095											
CCDC132	55610	hgsc.bcm.edu	37	chr7	92887682	92887682	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttcagcaaagaacagatgTacggttaagtgaaatgctgg	14	11	11	5	1	1	3	1	1	0	2	1	3	1	3	0	2	4	4	0	2	5	4			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr7:92887682T>C	ENST00000305866.5	+	8	682	c.554T>C	c.(553-555)gTa>gCa	p.V185A	CCDC132_ENST00000251739.5_Missense_Mutation_p.V185A|CCDC132_ENST00000535481.1_Intron|CCDC132_ENST00000544910.1_Missense_Mutation_p.V155A|CCDC132_ENST00000317751.6_5'UTR|CCDC132_ENST00000541136.1_5'UTR	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	185						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)			AGAACAGATGTACGGTTAAGT	0.303																																					p.V185A		Atlas-SNP	.											.	CCDC132	136	.	0			c.T554C						PASS	.						117	121	120					7																	92887682		2203	4300	6503	SO:0001583	missense	55610	exon8			CAGATGTACGGTT	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.554T>C	7.37:g.92887682T>C	ENSP00000307666:p.Val185Ala	255	0	0		281	61	0.217082	NM_024553	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Missense_Mutation	SNP	ENST00000305866.5	37	CCDS43617.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.106232	0.77096	.	.	ENSG00000004766	ENST00000251739;ENST00000305866;ENST00000544910;ENST00000458530	.	.	.	5.5	5.5	0.81552	Vacuolar protein sorting-associated protein 54 (1);	0.061028	0.64402	D	0.000004	T	0.60327	0.2260	L	0.46157	1.445	0.80722	D	1	P;P;B	0.51147	0.541;0.942;0.2	B;P;B	0.53549	0.329;0.729;0.049	T	0.55237	-0.8172	9	0.08837	T	0.75	-16.6226	15.9126	0.79482	0.0:0.0:0.0:1.0	.	155;185;185	F5H5U7;Q96JG6;Q96JG6-2	.;CC132_HUMAN;.	A	185;185;155;184	.	ENSP00000251739:V185A	V	+	2	0	CCDC132	92725618	1.000000	0.71417	0.980000	0.43619	0.955000	0.61496	8.040000	0.89188	2.222000	0.72286	0.477000	0.44152	GTA	.	.	none		0.303	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667		C	92887682	T	C	92887682	3	2	34	1	0	0	0	0	1	0	0	0	2769	1638	57	3	584	3	CCDC132	7	92887682	Missense_Mutation	SNP	T	TCGA-GR-A4D9-01B-11D-A31X-10		92887682	66250981	27	14096											
IKBKB	3551	hgsc.bcm.edu	37	chr8	42176069	42176069	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgcttgtgtctctgtctccaGttcaagagcccaagaggaat	9	12	10	10	0	3	2	1	0	2	2	5	3	3	3	2	1	2	2	2	1	3	2			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr8:42176069G>T	ENST00000520810.1	+	13	1426		c.e13-1		IKBKB_ENST00000522147.1_Intron|IKBKB_ENST00000379708.3_Splice_Site|IKBKB_ENST00000520835.1_Splice_Site|IKBKB_ENST00000416505.2_Splice_Site	NM_001556.2	NP_001547.1	O14920	IKKB_HUMAN	inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase beta						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)	TCTGTCTCCAGTTCAAGAGCC	0.493																																					.		Atlas-SNP	.											.	IKBKB	88	.	0			c.1064-1G>T						PASS	.						89	86	87					8																	42176069		2203	4300	6503	SO:0001630	splice_region_variant	3551	exon12			TCTCCAGTTCAAG	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.1241-1G>T	8.37:g.42176069G>T		95	0	0		132	39	0.295455	NM_001242778	B4DZ30|B4E0U4|O75327	Splice_Site	SNP	ENST00000520810.1	37	CCDS6128.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.124132	0.77436	.	.	ENSG00000104365	ENST00000520810;ENST00000416505;ENST00000520835;ENST00000379708	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6681	0.95900	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	IKBKB	42295226	1.000000	0.71417	0.997000	0.53966	0.841000	0.47740	7.789000	0.85783	2.740000	0.93945	0.555000	0.69702	.	.	.	none		0.493	IKBKB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377214.1		Intron	T	42176069	G	T	42176069	5	4	34	1	0	0	0	0	0	0	1	0	7620	1043	36	4	1286	4	IKBKB	8	42176069	Splice_Site	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10		42176069	104187953	28	14097											
RIMS2	9699	hgsc.bcm.edu	37	chr8	104831794	104831794	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tttatctcattttcatggggTtttttcatccccaccaaata	9	18	4	10	0	3	0	3	0	1	0	5	0	4	0	3	2	0	1	3	2	3	8			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr8:104831794T>G	ENST00000507740.1	+	1	295	c.59T>G	c.(58-60)gTt>gGt	p.V20G	RIMS2_ENST00000406091.3_Intron|RIMS2_ENST00000522174.1_3'UTR|RIMS2_ENST00000262231.10_Missense_Mutation_p.V20G	NM_014677.4	NP_055492.3	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	0					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.S22fs*10(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)			TTTCATGGGGTTTTTTCATCC	0.343										HNSCC(12;0.0054)																											p.V20G		Atlas-SNP	.											RIMS2_ENST00000507740,colon,carcinoma,+1,1	RIMS2	1357	1	1	Insertion - Frameshift(1)	large_intestine(1)	c.T59G						scavenged	.						103	102	102					8																	104831794		1813	4086	5899	SO:0001583	missense	9699	exon1			ATGGGGTTTTTTC	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		ENST00000507740.1:c.59T>G	8.37:g.104831794T>G	ENSP00000423559:p.Val20Gly	114	1	0.00877193		84	22	0.261905	NM_014677	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Missense_Mutation	SNP	ENST00000507740.1	37	CCDS43761.1	.	.	.	.	.	.	.	.	.	.	T	15.55	2.865849	0.51588	.	.	ENSG00000176406	ENST00000515551;ENST00000262231;ENST00000507740;ENST00000408894	T;T;T;T	0.21932	1.98;2.04;2.05;1.99	5.71	5.71	0.89125	.	.	.	.	.	T	0.11879	0.0289	N	0.08118	0	0.80722	D	1	B;B	0.22683	0.073;0.073	B;B	0.24701	0.055;0.055	T	0.14587	-1.0467	9	0.39692	T	0.17	.	10.3403	0.43873	0.0:0.0731:0.0:0.9269	.	20;20	Q9UQ26-1;Q9UQ26-3	.;.	G	20	ENSP00000425205:V20G;ENSP00000262231:V20G;ENSP00000423559:V20G;ENSP00000386228:V20G	ENSP00000262231:V20G	V	+	2	0	RIMS2	104900970	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.646000	0.61411	2.168000	0.68352	0.477000	0.44152	GTT	.	.	none		0.343	RIMS2-005	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367215.1	NM_001100117		G	104831794	T	G	104831794	3	3	34	1	0	0	0	0	1	0	0	0	13383	1725	60	5	771	5	RIMS2	8	104831794	Missense_Mutation	SNP	T	TCGA-GR-A4D9-01B-11D-A31X-10	62655725	104831794	41532228	29	14098											
KIAA0196	9897	hgsc.bcm.edu	37	chr8	126069044	126069044	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	agatgtaaacatgctttctgGgatgatctgcaaaaccttca	13	12	8	8	0	3	2	1	1	2	1	3	3	3	3	1	1	4	3	1	1	4	3			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr8:126069044G>A	ENST00000318410.7	-	16	2240	c.1891C>T	c.(1891-1893)Cca>Tca	p.P631S	KIAA0196_ENST00000517845.1_Missense_Mutation_p.P483S	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	631					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)			ATGCTTTCTGGGATGATCTGC	0.408																																					p.P631S		Atlas-SNP	.											KIAA0196,NS,malignant_melanoma,0,1	KIAA0196	90	1	0			c.C1891T						PASS	.						156	146	149					8																	126069044		2203	4300	6503	SO:0001583	missense	9897	exon16			TTTCTGGGATGAT		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.1891C>T	8.37:g.126069044G>A	ENSP00000318016:p.Pro631Ser	70	0	0		73	23	0.315068	NM_014846	A8K4R7|Q3KQX5|Q8TBQ2	Missense_Mutation	SNP	ENST00000318410.7	37	CCDS6355.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.944848	0.92593	.	.	ENSG00000164961	ENST00000318410;ENST00000517845	D;D	0.96300	-3.97;-3.97	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	D	0.98457	0.9486	M	0.88310	2.945	0.80722	D	1	D;D	0.89917	1.0;0.997	D;D	0.97110	1.0;0.995	D	0.99289	1.0898	10	0.87932	D	0	-11.8017	19.4322	0.94775	0.0:0.0:1.0:0.0	.	483;631	E7EQI7;Q12768	.;STRUM_HUMAN	S	631;483	ENSP00000318016:P631S;ENSP00000429676:P483S	ENSP00000318016:P631S	P	-	1	0	KIAA0196	126138226	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.809000	0.99208	2.649000	0.89929	0.655000	0.94253	CCA	.	.	none		0.408	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846		A	126069044	G	A	126069044	3	1	34	1	0	0	0	0	1	0	0	0	8170	1232	43	2	1644	2	KIAA0196	8	126069044	Missense_Mutation	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10	21237250	126069044	20294978	30	14099											
MAN1B1	11253	hgsc.bcm.edu	37	chr9	139981546	139981546	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cggggccccttgggccgtcgCcaccactgtagtcatgtacc	5	8	12	16	3	1	0	1	0	0	0	2	0	1	0	6	3	1	2	6	3	2	3			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr9:139981546C>T	ENST00000371589.4	+	1	168	c.95C>T	c.(94-96)gCc>gTc	p.A32V	AL807752.1_ENST00000596585.1_5'Flank|MAN1B1_ENST00000474902.1_5'Flank	NM_016219.4	NP_057303.2	Q9UKM7	MA1B1_HUMAN	mannosidase, alpha, class 1B, member 1	32					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)		TGGGCCGTCGCCACCACTGTA	0.652																																					p.A32V		Atlas-SNP	.											.	MAN1B1	40	.	0			c.C95T						PASS	.						10	13	12					9																	139981546		2178	4265	6443	SO:0001583	missense	11253	exon1			CCGTCGCCACCAC	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.95C>T	9.37:g.139981546C>T	ENSP00000360645:p.Ala32Val	43	0	0		48	12	0.25	NM_016219	Q5VSG3|Q9BRS9|Q9Y5K7	Missense_Mutation	SNP	ENST00000371589.4	37	CCDS7029.1	.	.	.	.	.	.	.	.	.	.	C	10.55	1.382251	0.24944	.	.	ENSG00000177239	ENST00000371589	T	0.74106	-0.81	3.33	-0.544	0.11847	.	.	.	.	.	T	0.48660	0.1512	N	0.08118	0	0.09310	N	0.999995	B	0.02656	0.0	B	0.04013	0.001	T	0.36237	-0.9756	9	0.72032	D	0.01	.	2.3432	0.04265	0.404:0.2871:0.0:0.3089	.	32	Q9UKM7	MA1B1_HUMAN	V	32	ENSP00000360645:A32V	ENSP00000360645:A32V	A	+	2	0	MAN1B1	139101367	0.002000	0.14202	0.000000	0.03702	0.031000	0.12232	0.358000	0.20216	-0.242000	0.09667	0.462000	0.41574	GCC	.	.	none		0.652	MAN1B1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055294.2	NM_016219		T	139981546	C	T	139981546	3	4	34	1	0	0	0	0	1	0	0	0	9221	739	26	2	97	2	MAN1B1	9	139981546	Missense_Mutation	SNP	C	TCGA-GR-A4D9-01B-11D-A31X-10		139981546	1231885	31	14100											
FBXO18	84893	hgsc.bcm.edu	37	chr10	5960434	5960434	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacacccacgtcttctatcTcacgcaggtaagtgcgcact	9	9	7	16	3	3	0	1	0	3	0	4	0	3	0	2	1	1	3	2	1	2	3			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:5960434T>C	ENST00000362091.4	+	13	2208	c.2093T>C	c.(2092-2094)cTc>cCc	p.L698P	FBXO18_ENST00000397269.3_Missense_Mutation_p.L185P|FBXO18_ENST00000379999.5_Missense_Mutation_p.L749P	NM_001258453.1|NM_178150.2	NP_001245382.1|NP_835363.1	Q8NFZ0	FBX18_HUMAN	F-box protein, helicase, 18	698					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						GTCTTCTATCTCACGCAGGTA	0.567																																					p.L749P		Atlas-SNP	.											.	FBXO18	108	.	0			c.T2246C						PASS	.						129	107	114					10																	5960434		2203	4300	6503	SO:0001583	missense	84893	exon14			TCTATCTCACGCA	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.2093T>C	10.37:g.5960434T>C	ENSP00000355415:p.Leu698Pro	41	0	0		64	4	0.0625	NM_032807	Q5JVB0|Q5JVB1|Q7Z4Q6|Q7Z4R0|Q8N1P5|Q8N586|Q96E82|Q96K67|Q96SW7|Q9UFB2	Missense_Mutation	SNP	ENST00000362091.4	37	CCDS7072.1	.	.	.	.	.	.	.	.	.	.	T	26.4	4.736778	0.89482	.	.	ENSG00000134452	ENST00000397269;ENST00000362091;ENST00000379999	D;D;D	0.96685	-4.09;-4.09;-4.09	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	D	0.98131	0.9383	M	0.83953	2.67	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	0.99094	1.0841	10	0.87932	D	0	-22.7842	15.9978	0.80265	0.0:0.0:0.0:1.0	.	749;698;624	Q8NFZ0-2;Q8NFZ0;Q2TAK1	.;FBX18_HUMAN;.	P	185;698;749	ENSP00000380439:L185P;ENSP00000355415:L698P;ENSP00000369335:L749P	ENSP00000355415:L698P	L	+	2	0	FBXO18	6000440	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.130000	0.77235	2.252000	0.74401	0.529000	0.55759	CTC	.	.	none		0.567	FBXO18-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046596.1	NM_032807		C	5960434	T	C	5960434	3	2	34	1	0	0	0	0	1	0	0	0	5739	1551	54	3	2305	3	FBXO18	10	5960434	Missense_Mutation	SNP	T	TCGA-GR-A4D9-01B-11D-A31X-10		5960434	129574313	32	14101											
GATA3	2625	hgsc.bcm.edu	37	chr10	8100789	8100789	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gatgcaagtccaggcccaagGcccggtccagcacaggtagg	10	4	14	13	1	0	0	0	0	0	0	2	1	2	0	4	5	2	3	4	5	3	1			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr10:8100789G>A	ENST00000346208.3	+	3	1218	c.763G>A	c.(763-765)Gcc>Acc	p.A255T	GATA3_ENST00000379328.3_Missense_Mutation_p.A255T|GATA3_ENST00000461472.1_3'UTR			P23771	GATA3_HUMAN	GATA binding protein 3	255					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						CAGGCCCAAGGCCCGGTCCAG	0.672			"F, N, S"		breast		"HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE)"																														p.A255T		Atlas-SNP	.		Rec	yes		10	10p15	2625	GATA binding protein 3	yes	E	.	GATA3	182	.	0			c.G763A						PASS	.						22	26	25					10																	8100789		2200	4297	6497	SO:0001583	missense	2625	exon3			CCCAAGGCCCGGT	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.763G>A	10.37:g.8100789G>A	ENSP00000341619:p.Ala255Thr	13	0	0		13	4	0.307692	NM_002051	Q5VWG7|Q5VWG8|Q96J16	Missense_Mutation	SNP	ENST00000346208.3	37	CCDS7083.1	.	.	.	.	.	.	.	.	.	.	G	9.949	1.219508	0.22373	.	.	ENSG00000107485	ENST00000379328;ENST00000346208	D;D	0.99683	-4.03;-6.39	5.55	5.55	0.83447	.	0.114990	0.64402	D	0.000016	D	0.97108	0.9055	N	0.03983	-0.305	0.42059	D	0.991155	B;B	0.12630	0.001;0.006	B;B	0.13407	0.002;0.009	D	0.97432	1.0016	10	0.10377	T	0.69	-29.272	12.7969	0.57564	0.0747:0.0:0.9253:0.0	.	255;255	P23771;P23771-2	GATA3_HUMAN;.	T	255	ENSP00000368632:A255T;ENSP00000341619:A255T	ENSP00000341619:A255T	A	+	1	0	GATA3	8140795	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.681000	0.68175	2.607000	0.88179	0.561000	0.74099	GCC	.	.	none		0.672	GATA3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046719.1	NM_001002295		A	8100789	G	A	8100789	3	1	34	1	0	0	0	0	1	0	0	0	6263	1203	42	2	769	2	GATA3	10	8100789	Missense_Mutation	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10	2140355	8100789	127433958	33	14102											
RAB3IL1	5866	hgsc.bcm.edu	37	chr11	61675610	61675610	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagctgcgcaggcgcaacacGtccagctgggcggctgcggg	6	4	18	13	5	0	0	0	0	0	0	1	1	1	0	1	4	5	5	1	4	1	0			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:61675610G>A	ENST00000394836.2	-	2	337	c.180C>T	c.(178-180)gaC>gaT	p.D60D	RAB3IL1_ENST00000301773.5_Silent_p.D107D	NM_013401.2	NP_037533.2	Q8TBN0	R3GEF_HUMAN	RAB3A interacting protein (rabin3)-like 1	60					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						GGCGCAACACGTCCAGCTGGG	0.672																																					p.D107D		Atlas-SNP	.											.	RAB3IL1	39	.	0			c.C321T						PASS	.						13	14	14					11																	61675610		2200	4293	6493	SO:0001819	synonymous_variant	5866	exon2			CAACACGTCCAGC	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.180C>T	11.37:g.61675610G>A		42	0	0		46	11	0.23913	NM_001271686	Q86V32|Q9P1Q8	Silent	SNP	ENST00000394836.2	37	CCDS8014.1																																																																																			.	.	none		0.672	RAB3IL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394917.1	NM_013401		A	61675610	G	A	61675610	2	1	34	1	0	0	0	0	0	0	0	1	12952	1136	40	1		1	RAB3IL1	11	61675610	Silent	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10		61675610	73330906	34	14103											
TYR	7299	hgsc.bcm.edu	37	chr11	88911368	88911368	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accgggagtcgtggccttccGtcttttataataggacctgc	7	12	11	11	3	1	0	0	0	1	0	3	2	2	2	4	3	1	0	4	3	3	5	rs149684917		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:88911368G>A	ENST00000263321.5	+	1	749	c.247G>A	c.(247-249)Gtc>Atc	p.V83I	TYR_ENST00000526139.1_3'UTR	NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	83					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)	GTGGCCTTCCGTCTTTTATAA	0.512																																					p.V83I		Atlas-SNP	.											.	TYR	130	.	0			c.G247A						PASS	.	G	ILE/VAL	0,4402		0,0,2201	43	42	43		247	3.2	0.5	11	dbSNP_134	43	1,8597	1.2+/-3.3	0,1,4298	no	missense	TYR	NM_000372.4	29	0,1,6499	AA,AG,GG		0.0116,0.0,0.0077	benign	83/530	88911368	1,12999	2201	4299	6500	SO:0001583	missense	7299	exon1			CCTTCCGTCTTTT	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.247G>A	11.37:g.88911368G>A	ENSP00000263321:p.Val83Ile	63	0	0		64	24	0.375	NM_000372	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Missense_Mutation	SNP	ENST00000263321.5	37	CCDS8284.1	.	.	.	.	.	.	.	.	.	.	G	8.247	0.808214	0.16467	0.0	1.16E-4	ENSG00000077498	ENST00000263321	D	0.83591	-1.74	6.07	3.24	0.37175	Uncharacterised domain, di-copper centre (2);	0.232469	0.43919	N	0.000506	D	0.82834	0.5123	M	0.80508	2.5	0.35898	D	0.830158	B	0.21520	0.057	B	0.18561	0.022	T	0.80625	-0.1299	9	.	.	.	.	15.4391	0.75168	0.1263:0.0:0.8737:0.0	.	83	P14679	TYRO_HUMAN	I	83	ENSP00000263321:V83I	.	V	+	1	0	TYR	88551016	1.000000	0.71417	0.451000	0.26982	0.487000	0.33371	5.367000	0.66127	0.462000	0.27095	-0.940000	0.02684	GTC	G|1.000;A|0.000	0.000	weak		0.512	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	NM_000372		A	88911368	G	A	88911368	3	1	34	1	0	0	0	0	1	0	0	0	16828	1145	40	1	249	1	TYR	11	88911368	Missense_Mutation	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10	27235758	88911368	46095148	35	14104											
CD3D	915	hgsc.bcm.edu	37	chr11	118211113	118211113	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gataatgaacttgcacggtaGattctttgtccttgtatata	11	16	8	6	1	1	2	0	1	1	1	2	3	2	2	1	1	2	3	1	1	6	9			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:118211113G>A	ENST00000300692.4	-	2	387	c.251C>T	c.(250-252)tCt>tTt	p.S84F	CD3D_ENST00000392884.2_Missense_Mutation_p.S84F|CD3D_ENST00000529594.1_Intron	NM_000732.4	NP_000723.1	P04234	CD3D_HUMAN	CD3d molecule, delta (CD3-TCR complex)	84					cell surface receptor signaling pathway (GO:0007166)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive thymic T cell selection (GO:0045059)|regulation of immune response (GO:0050776)|T cell costimulation (GO:0031295)|T cell differentiation (GO:0030217)|T cell receptor signaling pathway (GO:0050852)	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)	protein heterodimerization activity (GO:0046982)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	9	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;3.04e-05)	Muromonab(DB00075)	TTGCACGGTAGATTCTTTGTC	0.458																																					p.S84F		Atlas-SNP	.											.	CD3D	21	.	0			c.C251T						PASS	.						224	173	191					11																	118211113		2200	4296	6496	SO:0001583	missense	915	exon2			ACGGTAGATTCTT	X01451	CCDS8394.1, CCDS41724.1	11q23	2014-09-17	2006-03-28		ENSG00000167286	ENSG00000167286		"CD molecules"	1673	protein-coding gene	gene with protein product		186790	"CD3d antigen, delta polypeptide (TiT3 complex)"	T3D			Standard	NM_000732		Approved		uc001pss.1	P04234	OTTHUMG00000166970	ENST00000300692.4:c.251C>T	11.37:g.118211113G>A	ENSP00000300692:p.Ser84Phe	108	0	0		102	25	0.245098	NM_000732	A8MVP6	Missense_Mutation	SNP	ENST00000300692.4	37	CCDS8394.1	.	.	.	.	.	.	.	.	.	.	G	11.19	1.566084	0.27915	.	.	ENSG00000167286	ENST00000300692;ENST00000392884	T;T	0.49720	2.09;0.77	5.15	-0.336	0.12658	Immunoglobulin-like fold (1);	1.180960	0.05785	N	0.609330	T	0.38054	0.1026	L	0.59436	1.845	0.09310	N	1	B;B	0.12630	0.006;0.006	B;B	0.08055	0.003;0.003	T	0.19745	-1.0296	10	0.10111	T	0.7	3.1627	4.787	0.13230	0.171:0.0:0.3239:0.5051	.	84;84	A8MVP6;P04234	.;CD3D_HUMAN	F	84	ENSP00000300692:S84F;ENSP00000376622:S84F	ENSP00000300692:S84F	S	-	2	0	CD3D	117716323	0.000000	0.05858	0.000000	0.03702	0.410000	0.31052	-0.767000	0.04720	-0.223000	0.09943	0.655000	0.94253	TCT	.	.	none		0.458	CD3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392128.1	NM_000732		A	118211113	G	A	118211113	3	1	34	1	0	0	0	0	1	0	0	0	3012	942	33	2	280	2	CD3D	11	118211113	Missense_Mutation	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10	29299745	118211113	16795403	36	14105											
OR6M1	390261	hgsc.bcm.edu	37	chr11	123676690	123676690	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgcagtgggtcgcagataGccatgtagcggtcaaaggac	11	7	15	8	2	1	1	1	0	0	1	2	2	1	2	1	3	3	3	1	3	3	2			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr11:123676690G>T	ENST00000309154.2	-	1	405	c.368C>A	c.(367-369)gCt>gAt	p.A123D		NM_001005325.1	NP_001005325.1	Q8NGM8	OR6M1_HUMAN	olfactory receptor, family 6, subfamily M, 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)			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)		GTCGCAGATAGCCATGTAGCG	0.507																																					p.A123D		Atlas-SNP	.											.	OR6M1	60	.	0			c.C368A						PASS	.						51	52	52					11																	123676690		2202	4299	6501	SO:0001583	missense	390261	exon1			CAGATAGCCATGT	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.368C>A	11.37:g.123676690G>T	ENSP00000311038:p.Ala123Asp	71	0	0		97	36	0.371134	NM_001005325	B2RNK0|Q6IEW9|Q96R37	Missense_Mutation	SNP	ENST00000309154.2	37	CCDS31696.1	.	.	.	.	.	.	.	.	.	.	G	16.13	3.035627	0.54896	.	.	ENSG00000196099	ENST00000309154	T	0.01234	5.13	3.68	2.73	0.32206	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33127	U	0.005259	T	0.13114	0.0318	H	0.98133	4.155	0.35910	D	0.831017	D	0.89917	1.0	D	0.80764	0.994	T	0.14392	-1.0474	10	0.87932	D	0	.	9.2511	0.37555	0.1145:0.0:0.8855:0.0	.	123	Q8NGM8	OR6M1_HUMAN	D	123	ENSP00000311038:A123D	ENSP00000311038:A123D	A	-	2	0	OR6M1	123181900	1.000000	0.71417	1.000000	0.80357	0.398000	0.30690	6.085000	0.71343	1.862000	0.54008	0.655000	0.94253	GCT	.	.	none		0.507	OR6M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387437.1	NM_001005325		T	123676690	G	T	123676690	3	4	34	1	0	0	0	0	1	0	0	0	11214	971	34	4	576	4	OR6M1	11	123676690	Missense_Mutation	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10	5465577	123676690	11329826	37	14106											
ITGA5	3678	hgsc.bcm.edu	37	chr12	54795600	54795600	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ctggatggttttcttagtgtCccggagatgagggactgtaa	8	13	14	6	1	1	2	0	1	1	1	2	5	2	4	1	4	0	2	1	4	2	4			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:54795600C>T	ENST00000293379.4	-	22	2527	c.2266G>A	c.(2266-2268)Gac>Aac	p.D756N	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)	756					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						TTCTTAGTGTCCCGGAGATGA	0.567																																					p.D756N		Atlas-SNP	.											.	ITGA5	99	.	0			c.G2266A						PASS	.						104	103	104					12																	54795600		2203	4300	6503	SO:0001583	missense	3678	exon22			TAGTGTCCCGGAG		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.2266G>A	12.37:g.54795600C>T	ENSP00000293379:p.Asp756Asn	94	0	0		106	42	0.396226	NM_002205	Q96HA5	Missense_Mutation	SNP	ENST00000293379.4	37	CCDS8880.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.906611	0.92107	.	.	ENSG00000161638	ENST00000293379	T	0.45668	0.89	5.15	5.15	0.70609	Integrin alpha-2 (1);	0.000000	0.85682	D	0.000000	T	0.58119	0.2100	L	0.45581	1.43	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.55477	-0.8135	10	0.44086	T	0.13	.	16.4804	0.84157	0.0:1.0:0.0:0.0	.	756	P08648	ITA5_HUMAN	N	756	ENSP00000293379:D756N	ENSP00000293379:D756N	D	-	1	0	ITGA5	53081867	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	6.874000	0.75546	2.567000	0.86603	0.655000	0.94253	GAC	.	.	none		0.567	ITGA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406174.1			T	54795600	C	T	54795600	3	4	34	1	0	0	0	0	1	0	0	0	7888	855	30	2	919	2	ITGA5	12	54795600	Missense_Mutation	SNP	C	TCGA-GR-A4D9-01B-11D-A31X-10		54795600	79056295	38	14107											
KCTD10	83892	hgsc.bcm.edu	37	chr12	109889615	109889615	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	aatccgggcttcgggaaactCcacctgtgttcccacagtat	9	10	9	13	2	0	0	0	0	0	0	4	1	3	1	4	2	1	3	4	2	3	3			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr12:109889615C>G	ENST00000228495.6	-	7	1008	c.727G>C	c.(727-729)Gag>Cag	p.E243Q	KCTD10_ENST00000540411.1_Missense_Mutation_p.E217Q|KCTD10_ENST00000424763.2_Missense_Mutation_p.E62Q|KCTD10_ENST00000538161.1_5'UTR|KCTD10_ENST00000540089.1_Missense_Mutation_p.E62Q	NM_031954.3	NP_114160.1	Q9H3F6	BACD3_HUMAN	potassium channel tetramerization domain containing 10	243					proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|TCTN-B9D complex (GO:0036038)				endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)	10						TCGGGAAACTCCACCTGTGTT	0.582																																					p.E243Q		Atlas-SNP	.											KCTD10,NS,carcinoma,0,1	KCTD10	24	1	0			c.G727C						PASS	.						25	28	27					12																	109889615		2203	4300	6503	SO:0001583	missense	83892	exon7			GAAACTCCACCTG	BC040062	CCDS9128.1	12q24.12	2013-06-20	2013-06-20		ENSG00000110906	ENSG00000110906		"BTB/POZ domain containing"	23236	protein-coding gene	gene with protein product		613421	"potassium channel tetramerisation domain containing 10"			12477932	Standard	XM_005253946		Approved	MSTP028, BTBD28	uc001toi.1	Q9H3F6	OTTHUMG00000169253	ENST00000228495.6:c.727G>C	12.37:g.109889615C>G	ENSP00000228495:p.Glu243Gln	47	0	0		71	24	0.338028	NM_031954	Q53HN2|Q59FV1|Q6PL47|Q96SU0	Missense_Mutation	SNP	ENST00000228495.6	37	CCDS9128.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.4|21.4	4.138586|4.138586	0.77775|0.77775	.|.	.|.	ENSG00000110906|ENSG00000110906	ENST00000228495;ENST00000540089;ENST00000545759;ENST00000424763;ENST00000540411;ENST00000542954;ENST00000535546;ENST00000540402;ENST00000540355|ENST00000538161	T;T|.	0.58060|.	0.51;0.36|.	4.97|4.97	4.97|4.97	0.65823|0.65823	.|.	0.051633|.	0.85682|.	D|.	0.000000|.	T|T	0.79275|0.79275	0.4418|0.4418	M|M	0.83953|0.83953	2.67|2.67	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	0.999;1.0;0.998|.	D;D;D|.	0.83275|.	0.988;0.996;0.974|.	T|T	0.80683|0.80683	-0.1273|-0.1273	10|5	0.87932|.	D|.	0|.	-31.0378|-31.0378	17.765|17.765	0.88475|0.88475	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	217;220;243|.	F5GWA4;Q9H3F6-2;Q9H3F6|.	.;.;BACD3_HUMAN|.	Q|C	243;62;85;62;217;62;62;62;62|208	ENSP00000228495:E243Q;ENSP00000441672:E217Q|.	ENSP00000228495:E243Q|.	E|W	-|-	1|3	0|0	KCTD10|KCTD10	108373998|108373998	1.000000|1.000000	0.71417|0.71417	0.988000|0.988000	0.46212|0.46212	0.476000|0.476000	0.33039|0.33039	7.622000|7.622000	0.83099|0.83099	2.757000|2.757000	0.94681|0.94681	0.655000|0.655000	0.94253|0.94253	GAG|TGG	.	.	none		0.582	KCTD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403099.1	NM_031954		G	109889615	C	G	109889615	3	3	34	1	0	0	0	0	1	0	0	0	8106	864	30	4	218	4	KCTD10	12	109889615	Missense_Mutation	SNP	C	TCGA-GR-A4D9-01B-11D-A31X-10	55094015	109889615	23962280	39	14108											
DAAM1	23002	hgsc.bcm.edu	37	chr14	59797397	59797397	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcacagcacagctccatgaGctcagcagggtgaggtcttc	9	8	11	13	0	3	2	2	2	1	0	5	2	4	2	1	2	4	4	1	2	0	1			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr14:59797397G>A	ENST00000395125.1	+	12	1574	c.1551G>A	c.(1549-1551)gaG>gaA	p.E517E	DAAM1_ENST00000351081.1_Silent_p.E517E|DAAM1_ENST00000360909.3_Silent_p.E517E	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	517					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)		AGCTCCATGAGCTCAGCAGGG	0.527																																					p.E517E		Atlas-SNP	.											.	DAAM1	95	.	0			c.G1551A						PASS	.						56	57	57					14																	59797397		2203	4300	6503	SO:0001819	synonymous_variant	23002	exon13			CCATGAGCTCAGC	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.1551G>A	14.37:g.59797397G>A		194	0	0		166	53	0.319277	NM_001270520	Q86U34|Q8N1Z8|Q8TB39	Silent	SNP	ENST00000395125.1	37	CCDS9737.1																																																																																			.	.	none		0.527	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992		A	59797397	G	A	59797397	2	1	34	1	0	0	0	0	0	0	0	1	4217	962	34	2		2	DAAM1	14	59797397	Silent	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10		59797397	47552143	40	14109											
B2M	567	hgsc.bcm.edu	37	chr15	45007689	45007690	+	Frame_Shift_Del	DEL	TA	TA	-																															agtcaaatttcctgaattgcTatgtgtctgggtttcatcca																										TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr15:45007689_45007690delTA	ENST00000558401.1	+	2	206_207	c.136_137delTA	c.(136-138)tatfs	p.Y46fs	B2M_ENST00000559916.1_Frame_Shift_Del_p.Y46fs|B2M_ENST00000559220.1_Intron|B2M_ENST00000544417.1_Frame_Shift_Del_p.Y46fs	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	46	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 exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|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 T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|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)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		CCTGAATTGCTATGTGTCTGGG	0.401																																					p.45_46del		Pindel,Atlas-Indel	.											B2M,NS,lymphoid_neoplasm,+2,1	B2M	99	1	0			c.135_136del						PASS	.																																			SO:0001589	frameshift_variant	567	exon2			.	AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"Immunoglobulin superfamily / C1-set domain containing"	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.136_137delTA	15.37:g.45007689_45007690delTA	ENSP00000452780:p.Tyr46fs	94	0	.		76	35	0.461	NM_004048	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Frame_Shift_Del	DEL	ENST00000558401.1	37	CCDS10113.1																																																																																			.	.	none		0.401	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048		-	45007690	TA	-	45007689	7	5	34	1	0	1	0	1	0	0	0	0	1244	1522	53	0	142	0	B2M	15	45007689	Frame_Shift_Del	DEL	TA	TCGA-GR-A4D9-01B-11D-A31X-10		45007689	57523703	41	14110											
CREBBP	1387	hgsc.bcm.edu	37	chr16	3789597	3789597	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctcgtgtttggaggggggCaatcagagccgtattcttgg	7	11	15	8	2	2	1	1	0	1	1	3	2	2	2	2	5	1	3	2	5	2	4	rs200616542		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:3789597C>A	ENST00000262367.5	-	25	5071	c.4262G>T	c.(4261-4263)tGc>tTc	p.C1421F	CREBBP_ENST00000382070.3_Missense_Mutation_p.C1383F	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1421	CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.|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)	p.C1421Y(1)		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)		TGGAGGGGGGCAATCAGAGCC	0.502			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.C1421F		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	CREBBP,NS,lymphoid_neoplasm,0,1	CREBBP	546	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G4262T						scavenged	.						75	70	71					16																	3789597		2197	4300	6497	SO:0001583	missense	1387	exon25			GGGGGGCAATCAG	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.4262G>T	16.37:g.3789597C>A	ENSP00000262367:p.Cys1421Phe	74	1	0.0135135		76	45	0.592105	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	c	19.94	3.920342	0.73098	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.93133	-3.17;-3.17	5.36	5.36	0.76844	.	0.128977	0.56097	D	0.000038	D	0.97813	0.9282	H	0.94222	3.51	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.98507	1.0617	10	0.72032	D	0.01	-14.7453	19.4402	0.94817	0.0:1.0:0.0:0.0	.	1451;1421	Q4LE28;Q92793	.;CBP_HUMAN	F	1421;1451;1383;10	ENSP00000262367:C1421F;ENSP00000371502:C1383F	ENSP00000262367:C1421F	C	-	2	0	CREBBP	3729598	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	7.713000	0.84693	2.665000	0.90641	0.561000	0.74099	TGC	.	.	alt		0.502	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		A	3789597	C	A	3789597	3	1	34	1	0	0	0	0	1	0	0	0	3863	710	25	4	3094	4	CREBBP	16	3789597	Missense_Mutation	SNP	C	TCGA-GR-A4D9-01B-11D-A31X-10		3789597	86565156	42	14111											
CIITA	4261	hgsc.bcm.edu	37	chr16	11001270	11001271	+	Frame_Shift_Del	DEL	TA	TA	-																															cctccacgctcacgggactcTatgtcggcctgctgggccgt																										TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:11001270_11001271delTA	ENST00000324288.8	+	11	2054_2055	c.1921_1922delTA	c.(1921-1923)tatfs	p.Y641fs	CIITA_ENST00000537380.1_Intron|CIITA_ENST00000381835.5_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	641	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						CACGGGACTCTATGTCGGCCTG	0.688			T	"FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"	"PMBL, Hodgkin Lymphona, "																																p.640_641del		Atlas-Indel	.		Dom	yes		16	16p13	4261	"class II, major histocompatibility complex, transactivator"		L	.	CIITA	92	.	0			c.1920_1921del						PASS	.																																			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.1921_1922delTA	16.37:g.11001270_11001271delTA	ENSP00000316328:p.Tyr641fs	71	0	0		97	19	0.195876	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Frame_Shift_Del	DEL	ENST00000324288.8	37	CCDS10544.1																																																																																			.	.	none		0.688	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246		-	11001271	TA	-	11001270	7	5	34	1	0	1	0	1	0	0	0	0	3430	1522	53	0	1963	0	CIITA	16	11001270	Frame_Shift_Del	DEL	TA	TCGA-GR-A4D9-01B-11D-A31X-10	7211673	11001270	79353483	43	14112											
HS3ST2	9956	hgsc.bcm.edu	37	chr16	22826243	22826243	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctccggttccaaccactcCggctcacccaagctgggtac	7	8	8	18	2	2	0	1	0	1	0	5	0	4	0	5	3	3	4	5	3	3	2			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:22826243C>T	ENST00000261374.3	+	1	746	c.312C>T	c.(310-312)tcC>tcT	p.S104S		NM_006043.1	NP_006034.1	Q9Y278	HS3S2_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 2	104					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)		CCAACCACTCCGGCTCACCCA	0.716																																					p.S104S		Atlas-SNP	.											.	HS3ST2	59	.	0			c.C312T						PASS	.						7	9	8					16																	22826243		2158	4266	6424	SO:0001819	synonymous_variant	9956	exon1			CCACTCCGGCTCA	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.312C>T	16.37:g.22826243C>T		47	0	0		66	21	0.318182	NM_006043	Q52LZ1	Silent	SNP	ENST00000261374.3	37	CCDS10606.1																																																																																			.	.	none		0.716	HS3ST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211598.1	NM_006043		T	22826243	C	T	22826243	2	4	34	1	0	0	0	0	0	0	0	1	7373	639	23	1		1	HS3ST2	16	22826243	Silent	SNP	C	TCGA-GR-A4D9-01B-11D-A31X-10	11824973	22826243	67528510	44	14113											
ARMC5	79798	hgsc.bcm.edu	37	chr16	31473872	31473872	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agatgagctccggcagcgccGggatcctaatggagctagcc	9	6	14	12	3	0	2	0	1	0	1	2	4	2	4	4	3	4	3	4	3	2	2			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:31473872G>A	ENST00000563544.1	+	4	1550	c.1004G>A	c.(1003-1005)cGg>cAg	p.R335Q	ARMC5_ENST00000408912.3_Missense_Mutation_p.R430Q|ARMC5_ENST00000538189.1_Missense_Mutation_p.R367Q|RP11-452L6.5_ENST00000564629.1_RNA|ARMC5_ENST00000457010.2_Missense_Mutation_p.R335Q|ARMC5_ENST00000268314.4_Missense_Mutation_p.R335Q|ARMC5_ENST00000412665.2_Intron			Q96C12	ARMC5_HUMAN	armadillo repeat containing 5	335										central_nervous_system(1)|endometrium(4)|large_intestine(3)|liver(2)|lung(12)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						CGGCAGCGCCGGGATCCTAAT	0.647																																					p.R335Q		Atlas-SNP	.											ARMC5_ENST00000457010,NS,carcinoma,+1,2	ARMC5	94	2	0			c.G1004A						PASS	.						36	41	39					16																	31473872		1998	4168	6166	SO:0001583	missense	79798	exon3			AGCGCCGGGATCC	AY217348	CCDS42155.1, CCDS45472.1, CCDS73874.1	16p11	2013-02-14			ENSG00000140691	ENSG00000140691		"Armadillo repeat containing"	25781	protein-coding gene	gene with protein product		615549					Standard	NM_024742		Approved	FLJ13063	uc002ecc.3	Q96C12	OTTHUMG00000176618	ENST00000563544.1:c.1004G>A	16.37:g.31473872G>A	ENSP00000456877:p.Arg335Gln	17	0	0		26	10	0.384615	NM_024742	Q86WM9|Q9H7P8|Q9H925	Missense_Mutation	SNP	ENST00000563544.1	37	CCDS45472.1	.	.	.	.	.	.	.	.	.	.	g	13.89	2.371251	0.42003	.	.	ENSG00000140691	ENST00000408912;ENST00000538189;ENST00000268314;ENST00000457010	T;T;T;T	0.22743	1.94;1.94;1.94;1.94	4.8	4.8	0.61643	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.53938	D	0.000055	T	0.31009	0.0783	L	0.34521	1.04	0.80722	D	1	D;D;D;D	0.71674	0.998;0.998;0.998;0.998	D;D;D;P	0.72982	0.979;0.979;0.979;0.895	T	0.02596	-1.1136	10	0.15066	T	0.55	-5.4148	13.3511	0.60603	0.0:0.0:1.0:0.0	.	367;430;335;335	F5H156;B4DIU9;Q96C12;Q96C12-4	.;.;ARMC5_HUMAN;.	Q	430;367;335;335	ENSP00000386125:R430Q;ENSP00000443995:R367Q;ENSP00000268314:R335Q;ENSP00000399561:R335Q	ENSP00000268314:R335Q	R	+	2	0	ARMC5	31381373	0.993000	0.37304	0.894000	0.35097	0.044000	0.14063	3.649000	0.54417	2.217000	0.71921	0.457000	0.33378	CGG	.	.	none		0.647	ARMC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432847.1	NM_024742		A	31473872	G	A	31473872	3	1	34	1	0	0	0	0	1	0	0	0	954	1116	39	1	1014	1	ARMC5	16	31473872	Missense_Mutation	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10	8647629	31473872	58880881	45	14114											
ZNF423	23090	hgsc.bcm.edu	37	chr16	49672444	49672444	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caggtggatcttgaggtggtCgctgcgggagaaggctgcct	6	9	18	8	2	1	2	0	1	1	1	2	4	1	3	1	6	2	2	1	6	1	1			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:49672444C>T	ENST00000561648.1	-	4	672	c.619G>A	c.(619-621)Gac>Aac	p.D207N	ZNF423_ENST00000262383.2_Missense_Mutation_p.D207N|ZNF423_ENST00000562520.1_Missense_Mutation_p.D147N|ZNF423_ENST00000562871.1_Missense_Mutation_p.D147N|ZNF423_ENST00000563137.2_Missense_Mutation_p.D147N|ZNF423_ENST00000567169.1_Missense_Mutation_p.D90N|ZNF423_ENST00000535559.1_Missense_Mutation_p.D90N	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	207					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)	p.D207Y(1)		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)				TTGAGGTGGTCGCTGCGGGAG	0.602																																					p.D207N		Atlas-SNP	.											ZNF423_ENST00000262383,NS,carcinoma,0,1	ZNF423	463	1	1	Substitution - Missense(1)	ovary(1)	c.G619A						PASS	.						67	48	55					16																	49672444		2198	4300	6498	SO:0001583	missense	23090	exon4			GGTGGTCGCTGCG	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.619G>A	16.37:g.49672444C>T	ENSP00000455426:p.Asp207Asn	53	0	0		64	21	0.328125	NM_015069	O94860|Q76N04|Q9NZ13	Missense_Mutation	SNP	ENST00000561648.1	37	CCDS32445.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.044496	0.75732	.	.	ENSG00000102935	ENST00000262383;ENST00000535559	T;T	0.07567	3.18;3.18	5.0	5.0	0.66597	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	0.21881	0.0527	L	0.41079	1.255	0.49483	D	0.999796	D	0.89917	1.0	D	0.91635	0.999	T	0.01099	-1.1452	9	.	.	.	.	18.3069	0.90185	0.0:1.0:0.0:0.0	.	207	Q2M1K9	ZN423_HUMAN	N	207;90	ENSP00000262383:D207N;ENSP00000442321:D90N	.	D	-	1	0	ZNF423	48229945	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.709000	0.84645	2.331000	0.79229	0.561000	0.74099	GAC	.	.	none		0.602	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069		T	49672444	C	T	49672444	3	4	34	1	0	0	0	0	1	0	0	0	17913	884	31	1	3255	1	ZNF423	16	49672444	Missense_Mutation	SNP	C	TCGA-GR-A4D9-01B-11D-A31X-10	18198572	49672444	40682309	46	14115											
DYNC1LI2	1783	hgsc.bcm.edu	37	chr16	66783159	66783159	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctaggcctcttccttttttgCcatgctcagctccttgtagt	4	17	7	13	0	2	0	1	0	1	0	4	0	4	0	4	1	3	3	4	1	2	7			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:66783159C>T	ENST00000258198.2	-	3	445	c.239G>A	c.(238-240)gGc>gAc	p.G80D	DYNC1LI2_ENST00000379482.2_Missense_Mutation_p.G80D|RP11-61A14.4_ENST00000501143.1_lincRNA|DYNC1LI2_ENST00000443351.2_Missense_Mutation_p.G80D|DYNC1LI2_ENST00000440564.2_Intron	NM_006141.2	NP_006132.1	O43237	DC1L2_HUMAN	dynein, cytoplasmic 1, light intermediate chain 2	80					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)		TCCTTTTTTGCCATGCTCAGC	0.458																																					p.G80D		Atlas-SNP	.											.	DYNC1LI2	37	.	0			c.G239A						PASS	.						246	213	224					16																	66783159		2200	4300	6500	SO:0001583	missense	1783	exon3			TTTTTGCCATGCT	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.239G>A	16.37:g.66783159C>T	ENSP00000258198:p.Gly80Asp	100	0	0		88	4	0.0454545	NM_006141	A8K6V1|B4DZP4|Q8TAT3	Missense_Mutation	SNP	ENST00000258198.2	37	CCDS10818.1	.	.	.	.	.	.	.	.	.	.	C	13.91	2.377507	0.42105	.	.	ENSG00000135720	ENST00000258198;ENST00000379482;ENST00000443351	T;T;T	0.28666	1.6;1.6;1.6	4.81	4.81	0.61882	.	0.164538	0.56097	D	0.000039	T	0.13286	0.0322	N	0.03608	-0.345	0.39621	D	0.97003	B;B;B	0.23735	0.0;0.09;0.022	B;B;B	0.29440	0.004;0.01;0.102	T	0.13442	-1.0509	10	0.07175	T	0.84	-23.9298	11.5313	0.50612	0.0:0.9183:0.0:0.0816	.	80;80;80	B4DHD8;B4DZP4;O43237	.;.;DC1L2_HUMAN	D	80	ENSP00000258198:G80D;ENSP00000368795:G80D;ENSP00000394289:G80D	ENSP00000258198:G80D	G	-	2	0	DYNC1LI2	65340660	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.649000	0.54417	2.494000	0.84150	0.455000	0.32223	GGC	.	.	none		0.458	DYNC1LI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268846.1	NM_006141		T	66783159	C	T	66783159	3	4	34	1	0	0	0	0	1	0	0	0	4847	739	26	2	1283	2	DYNC1LI2	16	66783159	Missense_Mutation	SNP	C	TCGA-GR-A4D9-01B-11D-A31X-10	17110715	66783159	23571594	47	14116											
ANKRD11	29123	hgsc.bcm.edu	37	chr16	89352567	89352567	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gttgctctgctgcgggttccCtccgtaccgcagcagcagct	4	10	12	15	3	1	0	0	0	1	0	3	0	3	0	3	1	7	9	3	1	1	3			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr16:89352567C>T	ENST00000301030.4	-	8	1232	c.772G>A	c.(772-774)Ggg>Agg	p.G258R	ANKRD11_ENST00000378330.2_Missense_Mutation_p.G258R	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	258					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)		TGCGGGTTCCCTCCGTACCGC	0.582																																					p.G258R		Atlas-SNP	.											.	ANKRD11	195	.	0			c.G772A						PASS	.						122	121	121					16																	89352567		2198	4300	6498	SO:0001583	missense	29123	exon8			GGTTCCCTCCGTA	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.772G>A	16.37:g.89352567C>T	ENSP00000301030:p.Gly258Arg	38	0	0		53	19	0.358491	NM_001256183	Q6NTG1|Q6QMF8	Missense_Mutation	SNP	ENST00000301030.4	37	CCDS32513.1	.	.	.	.	.	.	.	.	.	.	C	35	5.557873	0.96514	.	.	ENSG00000167522	ENST00000301030;ENST00000378330;ENST00000378332	T;T	0.65178	-0.14;-0.14	6.11	6.11	0.99139	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.75133	0.3808	L	0.41906	1.305	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75068	-0.3448	10	0.87932	D	0	.	20.7342	0.99715	0.0:1.0:0.0:0.0	.	258	Q6UB99	ANR11_HUMAN	R	258;258;272	ENSP00000301030:G258R;ENSP00000367581:G258R	ENSP00000301030:G258R	G	-	1	0	ANKRD11	87880068	1.000000	0.71417	0.756000	0.31282	0.773000	0.43773	7.527000	0.81931	2.906000	0.99361	0.655000	0.94253	GGG	.	.	none		0.582	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		T	89352567	C	T	89352567	3	4	34	1	0	0	0	0	1	0	0	0	639	681	24	2	7243	2	ANKRD11	16	89352567	Missense_Mutation	SNP	C	TCGA-GR-A4D9-01B-11D-A31X-10	22569408	89352567	1002186	48	14117											
MYO18A	399687	hgsc.bcm.edu	37	chr17	27448927	27448927	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcgtggtccagcttcacaCgcaccttcccctcaggcaag	8	8	8	17	2	2	0	2	0	0	0	5	0	4	0	4	2	1	3	4	2	1	2	rs201811476	byFrequency	TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:27448927C>T	ENST00000527372.1	-	4	1316	c.1136G>A	c.(1135-1137)cGt>cAt	p.R379H	MYO18A_ENST00000354329.4_Missense_Mutation_p.R379H|MYO18A_ENST00000533112.1_Missense_Mutation_p.R379H|MYO18A_ENST00000531253.1_Missense_Mutation_p.R379H	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	379	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)			CAGCTTCACACGCACCTTCCC	0.612													C|||	2	0.000399361	0.0	0.0014	5008	,	,		18179	0.0		0.001	False		,,,				2504	0.0				p.R379H	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.G1136A						PASS	.	C	HIS/ARG,HIS/ARG	1,4183		0,1,2091	112	113	113		1136,1136	5.6	1	17		113	0,8444		0,0,4222	no	missense,missense	MYO18A	NM_078471.3,NM_203318.1	29,29	0,1,6313	TT,TC,CC		0.0,0.0239,0.0079	probably-damaging,probably-damaging	379/2055,379/2040	27448927	1,12627	2092	4222	6314	SO:0001583	missense	399687	exon4			TTCACACGCACCT	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.1136G>A	17.37:g.27448927C>T	ENSP00000437073:p.Arg379His	58	0	0		49	17	0.346939	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Missense_Mutation	SNP	ENST00000527372.1	37	CCDS45642.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	21.6	4.171334	0.78452	2.39E-4	0.0	ENSG00000196535	ENST00000354329;ENST00000359450;ENST00000533112;ENST00000531253;ENST00000527372;ENST00000531686	T;T;T;T	0.72282	-0.64;-0.64;-0.64;-0.64	5.64	5.64	0.86602	.	0.054581	0.64402	D	0.000001	T	0.69160	0.3080	L	0.46157	1.445	0.37405	D	0.91299	P;D;D;D	0.63046	0.873;0.983;0.983;0.992	B;P;P;P	0.51582	0.26;0.674;0.584;0.477	T	0.74393	-0.3680	10	0.54805	T	0.06	.	7.7622	0.28959	0.0:0.8021:0.0:0.1979	.	48;379;379;379	Q92614-2;Q92614-3;Q92614-4;Q92614	.;.;.;MY18A_HUMAN	H	379;379;379;379;379;59	ENSP00000346291:R379H;ENSP00000435932:R379H;ENSP00000434228:R379H;ENSP00000437073:R379H	ENSP00000346291:R379H	R	-	2	0	MYO18A	24473053	0.999000	0.42202	0.963000	0.40424	0.991000	0.79684	3.661000	0.54503	2.655000	0.90218	0.655000	0.94253	CGT	C|0.999;T|0.001	0.001	strong		0.612	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471		T	27448927	C	T	27448927	3	4	34	1	0	0	0	0	1	0	0	0	10074	536	19	1	5184	1	MYO18A	17	27448927	Missense_Mutation	SNP	C	TCGA-GR-A4D9-01B-11D-A31X-10		27448927	53746283	49	14118											
KRTAP4-11	653240	hgsc.bcm.edu	37	chr17	39274172	39274172	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagctggggtggcagcaggtGggctggcagcacacagactg	8	5	18	10	0	0	1	0	0	0	1	0	1	0	1	0	6	3	6	0	6	0	0			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:39274172G>T	ENST00000391413.2	-	1	434	c.396C>A	c.(394-396)ccC>ccA	p.P132P		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	132	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)			ggcagcaggtgggctggcagc	0.672																																					p.P132P		Atlas-SNP	.											KRTAP4-11,NS,carcinoma,-2,2	KRTAP4-11	94	2	0			c.C396A						scavenged	.						7	12	11					17																	39274172		675	1578	2253	SO:0001819	synonymous_variant	653240	exon1			GCAGGTGGGCTGG	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.396C>A	17.37:g.39274172G>T		68	1	0.0147059		64	3	0.046875	NM_033059	A0AUY2	Silent	SNP	ENST00000391413.2	37	CCDS45675.1																																																																																			.	.	none		0.672	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1			T	39274172	G	T	39274172	2	4	34	1	0	0	0	0	0	0	0	1	8558	1335	47	4		4	KRTAP4-11	17	39274172	Silent	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10	11825245	39274172	41921038	50	14119											
MARCH10	162333	hgsc.bcm.edu	37	chr17	60821880	60821880	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttcttaataaaaccattggtGcttggtctgctgaaagatgc	11	14	9	7	0	2	2	0	1	2	1	2	2	2	2	1	2	4	2	1	2	4	5			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:60821880G>T	ENST00000311269.5	-	5	666	c.392C>A	c.(391-393)gCa>gAa	p.A131E	MARCH10_ENST00000544856.2_Missense_Mutation_p.A130E|MARCH10_ENST00000456609.2_Missense_Mutation_p.A131E|MARCH10_ENST00000583600.1_Missense_Mutation_p.A169E	NM_152598.2	NP_689811.2	Q8NA82	MARHA_HUMAN	membrane-associated ring finger (C3HC4) 10, E3 ubiquitin protein ligase	131					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						AACCATTGGTGCTTGGTCTGC	0.428																																					p.A131E		Atlas-SNP	.											.	MARCH10	102	.	0			c.C392A						PASS	.						93	86	89					17																	60821880		2203	4300	6503	SO:0001583	missense	162333	exon5			ATTGGTGCTTGGT	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.392C>A	17.37:g.60821880G>T	ENSP00000311496:p.Ala131Glu	65	0	0		52	14	0.269231	NM_001100875	D3DU09|Q8IYS7|Q8N7Z7	Missense_Mutation	SNP	ENST00000311269.5	37	CCDS11635.1	.	.	.	.	.	.	.	.	.	.	G	1.039	-0.679492	0.03353	.	.	ENSG00000173838	ENST00000456609;ENST00000311269;ENST00000544856	T;T;T	0.13089	2.66;2.66;2.62	4.02	-0.384	0.12474	.	1.015540	0.07895	N	0.971731	T	0.08980	0.0222	L	0.35723	1.085	0.09310	N	0.999999	B;B;B	0.18461	0.006;0.01;0.028	B;B;B	0.13407	0.004;0.009;0.009	T	0.42832	-0.9428	10	0.18710	T	0.47	-0.0502	3.2196	0.06711	0.205:0.0:0.4324:0.3626	.	130;130;131	B3KVK0;G3V1Q5;Q8NA82	.;.;MARHA_HUMAN	E	131;131;130	ENSP00000416177:A131E;ENSP00000311496:A131E;ENSP00000443746:A130E	ENSP00000311496:A131E	A	-	2	0	MARCH10	58175612	0.082000	0.21442	0.050000	0.19076	0.111000	0.19643	0.226000	0.17776	-0.006000	0.14370	0.561000	0.74099	GCA	.	.	none		0.428	MARCH10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445252.1	NM_152598		T	60821880	G	T	60821880	3	4	34	1	0	0	0	0	1	0	0	0	9308	1319	46	4	2062	4	MARCH10	17	60821880	Missense_Mutation	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10	21547708	60821880	20373330	51	14120											
EXOC7	23265	hgsc.bcm.edu	37	chr17	74080183	74080183	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggaatagcccaggccttcTggattttgcacagttcttcg	7	13	10	11	1	2	0	0	0	2	0	3	2	2	2	2	3	2	2	2	3	2	6			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:74080183T>C	ENST00000335146.7	-	19	2062	c.2009A>G	c.(2008-2010)cAg>cGg	p.Q670R	EXOC7_ENST00000405575.4_Missense_Mutation_p.Q628R|EXOC7_ENST00000607838.1_Missense_Mutation_p.Q642R|EXOC7_ENST00000589210.1_Missense_Mutation_p.Q619R|EXOC7_ENST00000411744.2_Missense_Mutation_p.Q611R|EXOC7_ENST00000467929.2_Missense_Mutation_p.Q591R|EXOC7_ENST00000591724.1_5'Flank|EXOC7_ENST00000332065.5_Missense_Mutation_p.Q588R			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7	670					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)			CCAGGCCTTCTGGATTTTGCA	0.522																																					p.Q670R		Atlas-SNP	.											.	EXOC7	47	.	0			c.A2009G						PASS	.						54	50	51					17																	74080183		2203	4300	6503	SO:0001583	missense	23265	exon19			GCCTTCTGGATTT	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.2009A>G	17.37:g.74080183T>C	ENSP00000334100:p.Gln670Arg	70	0	0		73	25	0.342466	NM_001145297	B5MC69|B8XXP2|Q8ND93|Q8WV91|Q96FF0|Q9H8C3|Q9H9X3|Q9HA32	Missense_Mutation	SNP	ENST00000335146.7	37	CCDS45782.1	.	.	.	.	.	.	.	.	.	.	t	25.0	4.593561	0.86953	.	.	ENSG00000182473	ENST00000332065;ENST00000351709;ENST00000405575;ENST00000335146;ENST00000357231;ENST00000425372;ENST00000411744	.	.	.	5.28	5.28	0.74379	Cullin repeat-like-containing domain (1);	0.136469	0.51477	D	0.000088	T	0.80019	0.4547	M	0.80422	2.495	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;0.999;0.987;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;0.999;0.932;1.0;1.0;0.983;1.0	T	0.83105	-0.0126	9	0.72032	D	0.01	-24.4938	15.2203	0.73306	0.0:0.0:0.0:1.0	.	611;642;591;556;670;588;619	Q9UPT5-5;Q9UPT5-6;B4DJ07;F5H1P1;Q9UPT5;Q9UPT5-2;Q9UPT5-1	.;.;.;.;EXOC7_HUMAN;.;.	R	588;508;642;670;619;556;611	.	ENSP00000333806:Q588R	Q	-	2	0	EXOC7	71591778	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.843000	0.86859	2.000000	0.58554	0.449000	0.29647	CAG	.	.	none		0.522	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	NM_015219		C	74080183	T	C	74080183	3	2	34	1	0	0	0	0	1	0	0	0	5312	1580	55	3	206	3	EXOC7	17	74080183	Missense_Mutation	SNP	T	TCGA-GR-A4D9-01B-11D-A31X-10	13258303	74080183	7115027	52	14121											
TNRC6C	57690	hgsc.bcm.edu	37	chr17	76063864	76063864	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	aatctatgcaagaaggctggGgcagtggtggggatgaaatg	12	8	17	4	0	1	2	0	1	1	1	1	3	1	3	0	6	1	3	0	6	5	1			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:76063864G>A	ENST00000588061.1	+	7	3365	c.2638G>A	c.(2638-2640)Ggc>Agc	p.G880S	RNU6-625P_ENST00000459412.1_RNA|TNRC6C_ENST00000335749.4_Missense_Mutation_p.G877S|TNRC6C_ENST00000541771.1_Missense_Mutation_p.G880S|TNRC6C_ENST00000544502.1_Missense_Mutation_p.G877S|TNRC6C_ENST00000588847.1_Missense_Mutation_p.G877S|TNRC6C_ENST00000301624.4_Missense_Mutation_p.G880S			Q9HCJ0	TNR6C_HUMAN	trinucleotide repeat containing 6C	880	Sufficient for interaction with argonaute family proteins.				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)			AGAAGGCTGGGGCAGTGGTGG	0.463																																					p.G880S		Atlas-SNP	.											.	TNRC6C	173	.	0			c.G2638A						PASS	.						127	129	128					17																	76063864		1937	4151	6088	SO:0001583	missense	57690	exon6			GGCTGGGGCAGTG	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.2638G>A	17.37:g.76063864G>A	ENSP00000468647:p.Gly880Ser	91	0	0		81	4	0.0493827	NM_018996	G3XAB8|Q86UE5|Q8N3D8|Q96MU9	Missense_Mutation	SNP	ENST00000588061.1	37	CCDS45798.1	.	.	.	.	.	.	.	.	.	.	G	35	5.459818	0.96240	.	.	ENSG00000078687	ENST00000455761;ENST00000395801;ENST00000335749;ENST00000301624;ENST00000541771;ENST00000544502	T;T;T;T	0.17054	2.3;2.33;2.33;2.3	5.84	5.84	0.93424	Argonaute hook domain (1);	0.000000	0.85682	D	0.000000	T	0.44932	0.1317	M	0.74647	2.275	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	0.07654	-1.0761	10	0.32370	T	0.25	-20.2912	20.1187	0.97949	0.0:0.0:1.0:0.0	.	877;880;880	G3XAB8;Q9HCJ0-2;Q9HCJ0	.;.;TNR6C_HUMAN	S	880;877;877;880;880;877	ENSP00000336783:G877S;ENSP00000301624:G880S;ENSP00000440310:G880S;ENSP00000442421:G877S	ENSP00000301624:G880S	G	+	1	0	TNRC6C	73575459	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.420000	0.97426	2.767000	0.95098	0.591000	0.81541	GGC	.	.	none		0.463	TNRC6C-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395947.1	NM_018996		A	76063864	G	A	76063864	3	1	34	1	0	0	0	0	1	0	0	0	16357	1232	43	2	2648	2	TNRC6C	17	76063864	Missense_Mutation	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10	1983681	76063864	5131346	53	14122											
AZI1	22994	hgsc.bcm.edu	37	chr17	79173545	79173545	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgctcgcctggcttggcGtgccttctcctcccgggcct	0	11	13	17	3	1	0	0	0	1	0	4	0	2	0	5	4	2	3	5	4	0	2			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr17:79173545G>T	ENST00000269392.4	-	9	1244	c.997C>A	c.(997-999)Cgc>Agc	p.R333S	AZI1_ENST00000450824.2_Missense_Mutation_p.R333S|AZI1_ENST00000570482.2_5'Flank|RP11-455O6.2_ENST00000571085.1_RNA|AZI1_ENST00000374782.3_Missense_Mutation_p.R333S|AZI1_ENST00000575907.1_Missense_Mutation_p.R333S	NM_014984.2	NP_055799.2	Q9UPN4	CP131_HUMAN		333					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)			CTGGCTTGGCGTGCCTTCTCC	0.692																																					p.R333S		Atlas-SNP	.											.	AZI1	145	.	0			c.C997A						PASS	.						63	56	58					17																	79173545		2201	4297	6498	SO:0001583	missense	22994	exon9			CTTGGCGTGCCTT																												ENST00000269392.4:c.997C>A	17.37:g.79173545G>T	ENSP00000269392:p.Arg333Ser	25	0	0		45	4	0.0888889	NM_014984	A6NHI8|B2RN11|Q96F50	Missense_Mutation	SNP	ENST00000269392.4	37		.	.	.	.	.	.	.	.	.	.	G	17.28	3.349810	0.61183	.	.	ENSG00000141577	ENST00000450824;ENST00000374782;ENST00000269392	T;T;T	0.26518	1.73;1.73;1.73	3.67	3.67	0.42095	.	0.060253	0.64402	D	0.000002	T	0.48732	0.1516	M	0.70275	2.135	0.51012	D	0.999904	D;D;D;D	0.76494	0.997;0.997;0.999;0.969	D;D;D;P	0.68765	0.917;0.917;0.96;0.806	T	0.56329	-0.7997	10	0.72032	D	0.01	-13.0848	15.5205	0.75862	0.0:0.0:1.0:0.0	.	333;333;333;333	B2RN10;Q9UPN4;Q9UPN4-3;Q9UPN4-2	.;AZI1_HUMAN;.;.	S	333	ENSP00000393583:R333S;ENSP00000363914:R333S;ENSP00000269392:R333S	ENSP00000269392:R333S	R	-	1	0	AZI1	76788140	1.000000	0.71417	0.916000	0.36221	0.034000	0.12701	5.139000	0.64801	2.038000	0.60285	0.313000	0.20887	CGC	.	.	none		0.692	AZI1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000256070.1			T	79173545	G	T	79173545	3	4	34	1	0	0	0	0	1	0	0	0	1240	1145	40	4	2317	4	AZI1	17	79173545	Missense_Mutation	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10	3109681	79173545	2021665	54	14123											
DLGAP1	9229	hgsc.bcm.edu	37	chr18	3814275	3814275	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tccattcatcttgtggaaccTattcagatagaaaacagata	15	12	6	8	0	3	3	2	0	1	3	4	4	4	4	2	1	2	0	2	1	6	6			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr18:3814275T>A	ENST00000315677.3	-	5	1553		c.e5-2		DLGAP1_ENST00000584874.1_Splice_Site|DLGAP1_ENST00000400147.2_Splice_Site|DLGAP1_ENST00000581699.1_Splice_Site|DLGAP1_ENST00000515196.2_Splice_Site|DLGAP1_ENST00000400150.3_Splice_Site|DLGAP1_ENST00000478161.1_Splice_Site|snoU13_ENST00000459060.1_RNA|DLGAP1_ENST00000539435.1_Splice_Site|DLGAP1_ENST00000400149.3_Splice_Site|DLGAP1_ENST00000400155.1_Splice_Site|DLGAP1_ENST00000400145.2_Splice_Site|DLGAP1_ENST00000534970.1_Splice_Site|DLGAP1_ENST00000581527.1_Splice_Site	NM_004746.3	NP_004737.2	O14490	DLGP1_HUMAN	discs, large (Drosophila) homolog-associated protein 1						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)				TTGTGGAACCTATTCAGATAG	0.338																																					.		Atlas-SNP	.											.	DLGAP1	201	.	0			c.958-2A>T						PASS	.						87	84	85					18																	3814275		2203	4300	6503	SO:0001630	splice_region_variant	9229	exon6			GGAACCTATTCAG	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.958-2A>T	18.37:g.3814275T>A		90	0	0		95	23	0.242105	NM_004746	A8MWN8|B2RMU8|B7WPA1|B7Z2H2|B7Z2I2|B7Z9Y4|O14489|P78335	Splice_Site	SNP	ENST00000315677.3	37	CCDS11836.1	.	.	.	.	.	.	.	.	.	.	T	17.08	3.297901	0.60086	.	.	ENSG00000170579	ENST00000315677;ENST00000400147;ENST00000400150;ENST00000400149;ENST00000400155;ENST00000534970;ENST00000539435;ENST00000400145;ENST00000515196	.	.	.	5.85	5.85	0.93711	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2416	0.82411	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	DLGAP1	3804275	1.000000	0.71417	0.959000	0.39883	0.990000	0.78478	7.942000	0.87708	2.229000	0.72834	0.533000	0.62120	.	.	.	none		0.338	DLGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254394.4		Intron	A	3814275	T	A	3814275	5	1	34	1	0	0	0	0	0	0	1	0	4561	1536	53	5	2013	5	DLGAP1	18	3814275	Splice_Site	SNP	T	TCGA-GR-A4D9-01B-11D-A31X-10		3814275	74262973	55	14124											
LAMA3	3909	hgsc.bcm.edu	37	chr18	21394444	21394444	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttatattggaatctggacaaAgaaaaccccagtggatgttc	14	11	9	7	0	1	1	0	0	1	1	2	4	1	4	2	3	1	1	2	3	6	4			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr18:21394444A>C	ENST00000313654.9	+	15	2107	c.1866A>C	c.(1864-1866)aaA>aaC	p.K622N	LAMA3_ENST00000399516.3_Missense_Mutation_p.K622N	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	622	Domain V.|Laminin EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00460}.				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)					ATCTGGACAAAGAAAACCCCA	0.363																																					p.K622N		Atlas-SNP	.											.	LAMA3	397	.	0			c.A1866C						PASS	.						140	129	132					18																	21394444		1812	4088	5900	SO:0001583	missense	3909	exon15			GGACAAAGAAAAC	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.1866A>C	18.37:g.21394444A>C	ENSP00000324532:p.Lys622Asn	152	0	0		139	52	0.374101	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	37	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	A	11.46	1.645160	0.29246	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000416669	T;T	0.54071	0.59;0.59	5.64	0.566	0.17317	EGF-like, laminin (3);	.	.	.	.	T	0.42381	0.1200	M	0.72118	2.19	0.80722	D	1	P;P	0.36392	0.551;0.551	B;B	0.31390	0.084;0.129	T	0.21484	-1.0244	9	0.21014	T	0.42	.	6.9004	0.24279	0.6634:0.1273:0.2093:0.0	.	622;622	Q6VU67;Q16787	.;LAMA3_HUMAN	N	622;622;620	ENSP00000324532:K622N;ENSP00000382432:K622N	ENSP00000324532:K622N	K	+	3	2	LAMA3	19648442	0.055000	0.20627	0.862000	0.33874	0.712000	0.41017	0.579000	0.23788	0.432000	0.26286	-0.256000	0.11100	AAA	.	.	none		0.363	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		C	21394444	A	C	21394444	3	2	34	1	0	0	0	0	1	0	0	0	8616	69	3	5	1924	5	LAMA3	18	21394444	Missense_Mutation	SNP	A	TCGA-GR-A4D9-01B-11D-A31X-10	17580169	21394444	56682804	56	14125											
SGTA	6449	hgsc.bcm.edu	37	chr19	2767594	2767594	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcaccttgcccgtggcagccGcttcaaatatctccggcaga	8	9	9	15	3	3	1	2	0	1	1	4	1	3	1	4	2	2	3	4	2	2	3	rs367983019		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:2767594G>T	ENST00000221566.2	-	3	352	c.191C>A	c.(190-192)gCg>gAg	p.A64E		NM_003021.3	NP_003012.1	O43765	SGTA_HUMAN	small glutamine-rich tetratricopeptide repeat (TPR)-containing, alpha	64					viral process (GO:0016032)	cytoplasm (GO:0005737)				endometrium(2)|large_intestine(2)|lung(2)|ovary(1)	7		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)		CGTGGCAGCCGCTTCAAATAT	0.622																																					p.A64E		Atlas-SNP	.											.	SGTA	19	.	0			c.C191A						PASS	.						42	37	39					19																	2767594		2203	4300	6503	SO:0001583	missense	6449	exon3			GCAGCCGCTTCAA	AJ223828	CCDS12094.1	19p13	2013-01-10	2003-11-24	2003-11-26		ENSG00000104969		"Tetratricopeptide (TTC) repeat domain containing"	10819	protein-coding gene	gene with protein product		603419	"small glutamine-rich tetratricopeptide repeat (TPR)-containing"	SGT		9740675, 12735788	Standard	NM_003021		Approved		uc002lwi.1	O43765		ENST00000221566.2:c.191C>A	19.37:g.2767594G>T	ENSP00000221566:p.Ala64Glu	99	0	0		82	4	0.0487805	NM_003021	D6W610|Q6FIA9|Q9BTZ9	Missense_Mutation	SNP	ENST00000221566.2	37	CCDS12094.1	.	.	.	.	.	.	.	.	.	.	G	1.436	-0.568915	0.03910	.	.	ENSG00000104969	ENST00000221566	T	0.35973	1.28	3.92	3.92	0.45320	.	3.510430	0.04959	U	0.461626	T	0.33469	0.0864	L	0.39245	1.2	0.35474	D	0.797628	B	0.11235	0.004	B	0.13407	0.009	T	0.15780	-1.0425	10	0.11485	T	0.65	-5.3653	13.7696	0.63018	0.0:0.0:1.0:0.0	.	64	O43765	SGTA_HUMAN	E	64	ENSP00000221566:A64E	ENSP00000221566:A64E	A	-	2	0	SGTA	2718594	0.999000	0.42202	0.930000	0.37139	0.102000	0.19082	2.917000	0.48821	1.893000	0.54813	0.491000	0.48974	GCG	.	.	alt		0.622	SGTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451448.2	NM_003021		T	2767594	G	T	2767594	3	4	34	1	0	0	0	0	1	0	0	0	14240	1087	38	4	786	4	SGTA	19	2767594	Missense_Mutation	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10		2767594	56361389	57	14126											
PTPRS	5802	hgsc.bcm.edu	37	chr19	5222916	5222916	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacggccaccgtgtatttgaCgatggccccgttgcgctcgg	5	9	13	14	6	0	1	0	1	0	0	1	2	0	1	4	3	1	3	4	3	1	3	rs62113240		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:5222916C>T	ENST00000587303.1	-	17	2986	c.2887G>A	c.(2887-2889)Gtc>Atc	p.V963I	PTPRS_ENST00000262963.6_Missense_Mutation_p.V959I|PTPRS_ENST00000588012.1_Missense_Mutation_p.V941I|PTPRS_ENST00000592099.1_Intron|PTPRS_ENST00000372412.4_Missense_Mutation_p.V964I|PTPRS_ENST00000348075.2_Missense_Mutation_p.V941I|PTPRS_ENST00000353284.2_Intron|PTPRS_ENST00000357368.4_Missense_Mutation_p.V963I|PTPRS_ENST00000588552.1_Intron			Q13332	PTPRS_HUMAN	protein tyrosine phosphatase, receptor type, S	963	Fibronectin type-III 7. {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)	GTGTATTTGACGATGGCCCCG	0.741																																					p.V963I		Atlas-SNP	.											.	PTPRS	169	.	0			c.G2887A						PASS	.						4	6	6					19																	5222916		1894	3710	5604	SO:0001583	missense	5802	exon18			ATTTGACGATGGC	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.2887G>A	19.37:g.5222916C>T	ENSP00000467537:p.Val963Ile	8	0	0		19	9	0.473684	NM_002850	O75255|O75870|Q15718|Q16341|Q2M3R7	Missense_Mutation	SNP	ENST00000587303.1	37	CCDS45930.1	.	.	.	.	.	.	.	.	.	.	C	9.675	1.147719	0.21288	.	.	ENSG00000105426	ENST00000372412;ENST00000357368;ENST00000355005;ENST00000356037;ENST00000262963;ENST00000348075	T;T;T;T	0.57752	0.38;0.38;0.38;0.38	4.01	0.642	0.17765	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.320832	0.23319	N	0.049473	T	0.26484	0.0647	N	0.11789	0.175	0.80722	D	1	B;B	0.12630	0.001;0.006	B;B	0.11329	0.002;0.006	T	0.06127	-1.0844	10	0.11794	T	0.64	.	7.107	0.25368	0.0:0.6232:0.0:0.3768	rs62113240	941;963	Q13332-6;Q13332	.;PTPRS_HUMAN	I	964;963;963;954;959;941	ENSP00000361489:V964I;ENSP00000349932:V963I;ENSP00000262963:V959I;ENSP00000269907:V941I	ENSP00000262963:V959I	V	-	1	0	PTPRS	5173916	0.966000	0.33281	0.984000	0.44739	0.983000	0.72400	0.897000	0.28390	0.039000	0.15632	0.557000	0.71058	GTC	.	.	weak		0.741	PTPRS-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450762.2			T	5222916	C	T	5222916	3	4	34	1	0	0	0	0	1	0	0	0	12826	536	19	1	3043	1	PTPRS	19	5222916	Missense_Mutation	SNP	C	TCGA-GR-A4D9-01B-11D-A31X-10	2455322	5222916	53906067	58	14127											
OR7A10	390892	hgsc.bcm.edu	37	chr19	14951929	14951929	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	taaggtacacccctaagcatGtaccataaaataaggagaca	18	7	7	9	0	0	1	0	0	0	1	0	2	0	1	3	2	3	3	3	2	7	6			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:14951929G>T	ENST00000248058.1	-	1	760	c.761C>A	c.(760-762)aCa>aAa	p.T254K		NM_001005190.1	NP_001005190.1	O76100	OR7AA_HUMAN	olfactory receptor, family 7, subfamily A, member 10	254						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)					CCCTAAGCATGTACCATAAAA	0.493																																					p.T254K		Atlas-SNP	.											OR7A10,NS,carcinoma,-1,1	OR7A10	33	1	0			c.C761A						PASS	.						103	88	93					19																	14951929		2203	4300	6503	SO:0001583	missense	390892	exon1			AAGCATGTACCAT		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.761C>A	19.37:g.14951929G>T	ENSP00000248058:p.Thr254Lys	112	0	0		92	30	0.326087	NM_001005190	Q6IFP0|Q96R97	Missense_Mutation	SNP	ENST00000248058.1	37	CCDS32936.1	.	.	.	.	.	.	.	.	.	.	g	14.39	2.519896	0.44866	.	.	ENSG00000127515	ENST00000248058	T	0.00287	8.29	2.75	1.65	0.23941	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40144	U	0.001177	T	0.01092	0.0036	H	0.98754	4.32	0.09310	N	1	D	0.64830	0.994	D	0.68943	0.961	T	0.24657	-1.0154	10	0.87932	D	0	.	9.5406	0.39248	0.0:0.2179:0.7821:0.0	.	254	O76100	OR7AA_HUMAN	K	254	ENSP00000248058:T254K	ENSP00000248058:T254K	T	-	2	0	OR7A10	14812929	0.008000	0.16893	0.001000	0.08648	0.236000	0.25371	1.536000	0.36072	0.499000	0.27970	0.134000	0.15878	ACA	.	.	none		0.493	OR7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466520.1	NM_001005190		T	14951929	G	T	14951929	3	4	34	1	0	0	0	0	1	0	0	0	11223	1377	48	4	172	4	OR7A10	19	14951929	Missense_Mutation	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10	9729013	14951929	44177054	59	14128											
ZNF100	163227	hgsc.bcm.edu	37	chr19	21948514	21948514	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accttttcaaaataagactgCaccagaagactcctctcagc	14	9	5	13	0	2	3	2	0	1	3	4	3	3	3	3	0	2	1	3	0	4	3	rs530281593		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:21948514C>A	ENST00000358296.6	-	2	276	c.78G>T	c.(76-78)gtG>gtT	p.V26V	ZNF100_ENST00000596452.1_5'UTR	NM_173531.3	NP_775802.2	Q8IYN0	ZN100_HUMAN	zinc finger protein 100	26					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						AATAAGACTGCACCAGAAGAC	0.478													C|||	1	0.000199681	0.0008	0.0	5008	,	,		15991	0.0		0.0	False		,,,				2504	0.0				p.V26V		Atlas-SNP	.											.	ZNF100	62	.	0			c.G78T						PASS	.						91	100	97					19																	21948514		2190	4297	6487	SO:0001819	synonymous_variant	163227	exon2			AGACTGCACCAGA	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.78G>T	19.37:g.21948514C>A		78	0	0		73	15	0.205479	NM_173531	Q7M4M0	Silent	SNP	ENST00000358296.6	37	CCDS42538.1																																																																																			.	.	none		0.478	ZNF100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464087.1	NM_173531		A	21948514	C	A	21948514	2	1	34	1	0	0	0	0	0	0	0	1	17728	697	25	4		4	ZNF100	19	21948514	Silent	SNP	C	TCGA-GR-A4D9-01B-11D-A31X-10	6996585	21948514	37180469	60	14129											
VN1R2	317701	hgsc.bcm.edu	37	chr19	53761881	53761881	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcacacggagagaaacccAccaaacctgtggggctggac	12	4	12	13	1	0	1	0	0	0	1	0	4	0	3	3	4	3	2	3	4	2	0			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:53761881A>C	ENST00000341702.3	+	1	337	c.253A>C	c.(253-255)Acc>Ccc	p.T85P		NM_173856.2	NP_776255.2	Q8NFZ6	VN1R2_HUMAN	vomeronasal 1 receptor 2	85					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)		agagaaacccaccaaacctgt	0.443																																					p.T85P		Atlas-SNP	.											.	VN1R2	71	.	0			c.A253C						PASS	.						43	44	44					19																	53761881		2193	4285	6478	SO:0001583	missense	317701	exon1			AAACCCACCAAAC	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.253A>C	19.37:g.53761881A>C	ENSP00000351244:p.Thr85Pro	109	0	0		114	35	0.307018	NM_173856	A1L411|Q8TDU4	Missense_Mutation	SNP	ENST00000341702.3	37	CCDS12862.1	.	.	.	.	.	.	.	.	.	.	A	3.624	-0.076953	0.07184	.	.	ENSG00000196131	ENST00000341702	T	0.10005	2.92	0.0465	0.0465	0.14256	.	.	.	.	.	T	0.04634	0.0126	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38757	-0.9646	9	0.62326	D	0.03	.	2.1718	0.03851	0.506:2.0E-4:1.0E-4:0.4937	.	85	Q8NFZ6	VN1R2_HUMAN	P	85	ENSP00000351244:T85P	ENSP00000351244:T85P	T	+	1	0	VN1R2	58453693	0.001000	0.12720	0.042000	0.18584	0.043000	0.13939	-0.066000	0.11598	0.115000	0.18071	0.113000	0.15668	ACC	.	.	none		0.443	VN1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464285.1	NM_173856		C	53761881	A	C	53761881	3	2	34	1	0	0	0	0	1	0	0	0	17194	159	6	5	255	5	VN1R2	19	53761881	Missense_Mutation	SNP	A	TCGA-GR-A4D9-01B-11D-A31X-10	31813367	53761881	5367102	61	14130											
NLRP9	338321	hgsc.bcm.edu	37	chr19	56249530	56249530	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tagaaacaggttcagtgttaCctcccatgcctgctttcctg	8	13	8	12	0	1	1	1	0	0	1	3	1	3	1	4	1	4	3	4	1	3	4			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:56249530C>A	ENST00000332836.2	-	1	238	c.211G>T	c.(211-213)Gta>Tta	p.V71L	RN7SKP109_ENST00000410592.1_RNA	NM_176820.2	NP_789790.2	Q7RTR0	NALP9_HUMAN	NLR family, pyrin domain containing 9	71	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.					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)		TTCAGTGTTACCTCCCATGCC	0.493																																					p.V71L		Atlas-SNP	.											.	NLRP9	163	.	0			c.G211T						PASS	.						444	438	440					19																	56249530		2203	4300	6503	SO:0001583	missense	338321	exon1			GTGTTACCTCCCA	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.211G>T	19.37:g.56249530C>A	ENSP00000331857:p.Val71Leu	130	0	0		166	46	0.277108	NM_176820	B2RN12|Q86W27	Missense_Mutation	SNP	ENST00000332836.2	37	CCDS12934.1	.	.	.	.	.	.	.	.	.	.	C	14.11	2.436550	0.43224	.	.	ENSG00000185792	ENST00000332836;ENST00000333452	T	0.57595	0.39	3.63	-3.39	0.04868	Pyrin (2);DEATH-like (2);	.	.	.	.	T	0.47581	0.1453	L	0.39020	1.185	0.09310	N	1	P	0.46395	0.877	P	0.51016	0.656	T	0.48647	-0.9017	9	0.33141	T	0.24	.	9.9981	0.41911	0.1498:0.2618:0.5884:0.0	.	71	Q7RTR0	NALP9_HUMAN	L	71	ENSP00000331857:V71L	ENSP00000331857:V71L	V	-	1	0	NLRP9	60941342	0.080000	0.21391	0.000000	0.03702	0.011000	0.07611	-0.007000	0.12810	-0.423000	0.07394	-0.175000	0.13238	GTA	.	.	none		0.493	NLRP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453653.1	NM_176820		A	56249530	C	A	56249530	3	1	34	1	0	0	0	0	1	0	0	0	10493	507	18	4	2800	4	NLRP9	19	56249530	Missense_Mutation	SNP	C	TCGA-GR-A4D9-01B-11D-A31X-10	2487649	56249530	2879453	62	14131											
NLRP5	126206	hgsc.bcm.edu	37	chr19	56552307	56552307	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gactggaggactgtggcatcAcagccacgggttgccagagt	9	7	15	10	1	1	1	1	0	0	1	1	4	1	3	2	4	2	2	2	4	0	1			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr19:56552307A>C	ENST00000390649.3	+	11	2806	c.2806A>C	c.(2806-2808)Aca>Cca	p.T936P		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	936					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)		CTGTGGCATCACAGCCACGGG	0.542																																					p.T936P		Atlas-SNP	.											.	NLRP5	217	.	0			c.A2806C						PASS	.						69	69	69					19																	56552307		2005	4191	6196	SO:0001583	missense	126206	exon11			GGCATCACAGCCA	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.2806A>C	19.37:g.56552307A>C	ENSP00000375063:p.Thr936Pro	62	0	0		58	6	0.103448	NM_153447	A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	37	CCDS12938.1	.	.	.	.	.	.	.	.	.	.	A	13.03	2.114132	0.37339	.	.	ENSG00000171487	ENST00000390649	T	0.57107	0.42	4.37	-2.11	0.07187	.	0.889887	0.09138	N	0.843342	T	0.59783	0.2219	M	0.90595	3.13	0.09310	N	0.999999	B	0.32543	0.375	B	0.42653	0.394	T	0.60712	-0.7209	10	0.66056	D	0.02	.	1.426	0.02323	0.3361:0.1463:0.0903:0.4272	.	936	P59047	NALP5_HUMAN	P	936	ENSP00000375063:T936P	ENSP00000375063:T936P	T	+	1	0	NLRP5	61244119	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-1.019000	0.03622	-0.685000	0.05177	-1.155000	0.01812	ACA	.	.	none		0.542	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447		C	56552307	A	C	56552307	3	2	34	1	0	0	0	0	1	0	0	0	10489	159	6	5	2848	5	NLRP5	19	56552307	Missense_Mutation	SNP	A	TCGA-GR-A4D9-01B-11D-A31X-10	302777	56552307	2576676	63	14132											
PYGB	5834	hgsc.bcm.edu	37	chr20	25264786	25264786	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggagaaggagtacaaggTgaagatcaacccctcctcca	13	6	10	12	0	1	3	1	1	0	2	3	5	3	4	5	3	2	1	5	3	5	1			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr20:25264786T>C	ENST00000216962.4	+	14	1777	c.1667T>C	c.(1666-1668)gTg>gCg	p.V556A		NM_002862.3	NP_002853.2	P11216	PYGB_HUMAN	phosphorylase, glycogen; brain	556					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						GAGTACAAGGTGAAGATCAAC	0.537																																					p.V556A		Atlas-SNP	.											.	PYGB	84	.	0			c.T1667C						PASS	.						216	150	173					20																	25264786		2203	4300	6503	SO:0001583	missense	5834	exon14			ACAAGGTGAAGAT		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.1667T>C	20.37:g.25264786T>C	ENSP00000216962:p.Val556Ala	114	0	0		87	25	0.287356	NM_002862	Q96AK1|Q9NPX8	Missense_Mutation	SNP	ENST00000216962.4	37	CCDS13171.1	.	.	.	.	.	.	.	.	.	.	T	17.89	3.498726	0.64298	.	.	ENSG00000100994	ENST00000216962	D	0.95069	-3.6	3.86	3.86	0.44501	.	0.060202	0.64402	D	0.000005	D	0.95802	0.8634	M	0.90870	3.155	0.80722	D	1	B	0.28208	0.203	B	0.37601	0.254	D	0.96223	0.9162	10	0.87932	D	0	-22.5788	12.7816	0.57480	0.0:0.0:0.0:1.0	.	556	P11216	PYGB_HUMAN	A	556	ENSP00000216962:V556A	ENSP00000216962:V556A	V	+	2	0	PYGB	25212786	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	7.626000	0.83164	1.761000	0.52028	0.379000	0.24179	GTG	.	.	none		0.537	PYGB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078415.2	NM_002862		C	25264786	T	C	25264786	3	2	34	1	0	0	0	0	1	0	0	0	12875	1696	59	3	1721	3	PYGB	20	25264786	Missense_Mutation	SNP	T	TCGA-GR-A4D9-01B-11D-A31X-10		25264786	37760734	64	14133											
CDH26	60437	hgsc.bcm.edu	37	chr20	58587641	58587641	+	Intron	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tacctacctcacgtctacagCgaggaaggggagtgtggagg	10	7	15	9	2	2	0	1	0	1	0	2	4	2	3	2	5	4	0	2	5	4	3	rs375717739		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr20:58587641C>T	ENST00000244047.5	+	15	2483				CDH26_ENST00000244049.3_Silent_p.S77S|CDH26_ENST00000348616.4_Silent_p.S785S|CDH26_ENST00000350849.6_Silent_p.S118S|CDH26_ENST00000497614.1_3'UTR			Q8IXH8	CAD26_HUMAN	cadherin 26						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)			ACGTCTACAGCGAGGAAGGGG	0.547																																					p.S785S		Atlas-SNP	.											.	CDH26	229	.	0			c.C2355T						PASS	.	C	,	0,4406		0,0,2203	99	92	94		354,2355	-7.6	0	20		94	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	CDH26	NM_021810.4,NM_177980.2	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	118/166,785/833	58587641	1,13005	2203	4300	6503	SO:0001627	intron_variant	60437	exon18			CTACAGCGAGGAA	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.2172+5799C>T	20.37:g.58587641C>T		84	0	0		78	24	0.307692	NM_177980	A2A2M5|B3KNX3|Q6P5Y6|Q8TCH3|Q9BQN4|Q9NRU1	Silent	SNP	ENST00000244047.5	37																																																																																				.	.	weak		0.547	CDH26-201	KNOWN	basic	protein_coding	protein_coding		NM_177980		T	58587641	C	T	58587641	1	4	34	0	1	0	0	0	0	0	0	0	3112	767	27	1		1	CDH26	20	58587641	Intron	SNP	C	TCGA-GR-A4D9-01B-11D-A31X-10	33322855	58587641	4437879	65	14134											
FBLN1	2192	hgsc.bcm.edu	37	chr22	45937241	45937241	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccatctcaacgaggagggaaCgcgctgtgttggttggtatt	8	11	14	8	3	1	0	1	0	1	0	2	3	1	2	1	4	2	4	1	4	3	4	rs540607391		TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chr22:45937241C>T	ENST00000327858.6	+	9	1150	c.1055C>T	c.(1054-1056)aCg>aTg	p.T352M	FBLN1_ENST00000442170.2_Missense_Mutation_p.T352M|FBLN1_ENST00000348697.2_Missense_Mutation_p.T352M|FBLN1_ENST00000340923.5_Missense_Mutation_p.T352M|FBLN1_ENST00000402984.3_Missense_Mutation_p.T390M|FBLN1_ENST00000476366.1_3'UTR|FBLN1_ENST00000262722.7_Missense_Mutation_p.T352M	NM_006486.2	NP_006477	P23142	FBLN1_HUMAN	fibulin 1	352	EGF-like 4; 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)		GAGGAGGGAACGCGCTGTGTT	0.522													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20118	0.0		0.0	False		,,,				2504	0.0				p.T352M		Atlas-SNP	.											.	FBLN1	143	.	0			c.C1055T						PASS	.						101	84	89					22																	45937241		2203	4300	6503	SO:0001583	missense	2192	exon9			AGGGAACGCGCTG		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.1055C>T	22.37:g.45937241C>T	ENSP00000331544:p.Thr352Met	76	0	0		83	28	0.337349	NM_006487	B0QY42|B1AHL4|P23143|P23144|P37888|Q5TIC4|Q8TBH8|Q9HBQ5|Q9UC21|Q9UGR4|Q9UH41	Missense_Mutation	SNP	ENST00000327858.6	37	CCDS14067.1	.	.	.	.	.	.	.	.	.	.	C	16.34	3.097040	0.56075	.	.	ENSG00000077942	ENST00000348697;ENST00000402984;ENST00000262722;ENST00000327858;ENST00000442170;ENST00000340923	D;D;D;D;D;D	0.92858	-3.12;-3.12;-3.12;-2.28;-3.12;-3.12	5.41	3.26	0.37387	EGF-like calcium-binding (2);	0.150392	0.64402	D	0.000014	D	0.93458	0.7913	L	0.45285	1.41	0.09310	N	0.99999	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.997;0.995;0.991;0.995	D	0.87244	0.2268	10	0.66056	D	0.02	.	11.9956	0.53201	0.1373:0.7308:0.1319:0.0	.	390;352;352;352	B1AHL2;P23142;B1AHL4;P23142-4	.;FBLN1_HUMAN;.;.	M	352;390;352;352;352;352	ENSP00000262723:T352M;ENSP00000385521:T390M;ENSP00000262722:T352M;ENSP00000331544:T352M;ENSP00000393812:T352M;ENSP00000342212:T352M	ENSP00000262722:T352M	T	+	2	0	FBLN1	44315905	0.909000	0.30893	0.017000	0.16124	0.824000	0.46624	1.899000	0.39818	0.627000	0.30340	0.655000	0.94253	ACG	.	.	none		0.522	FBLN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322287.1	NM_006486		T	45937241	C	T	45937241	3	4	34	1	0	0	0	0	1	0	0	0	5706	536	19	1	1089	1	FBLN1	22	45937241	Missense_Mutation	SNP	C	TCGA-GR-A4D9-01B-11D-A31X-10		45937241	5367325	66	14135											
BHLHB9	80823	hgsc.bcm.edu	37	chrX	102004884	102004884	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gcaaaatggaatgctatatgGattctgaggaatttgaaaaa	17	11	10	3	0	1	2	0	2	1	0	1	5	1	5	0	3	1	2	0	3	8	4			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chrX:102004884G>T	ENST00000372735.1	+	4	1546	c.961G>T	c.(961-963)Gat>Tat	p.D321Y	BHLHB9_ENST00000457056.1_Missense_Mutation_p.D321Y|BHLHB9_ENST00000361229.4_Missense_Mutation_p.D321Y|BHLHB9_ENST00000447531.1_Missense_Mutation_p.D321Y|BHLHB9_ENST00000448867.1_Missense_Mutation_p.D321Y			Q6PI77	BHLH9_HUMAN	basic helix-loop-helix domain containing, class B, 9	321					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						ATGCTATATGGATTCTGAGGA	0.383																																					p.D321Y		Atlas-SNP	.											.	BHLHB9	60	.	0			c.G961T						PASS	.						83	79	80					X																	102004884		2203	4300	6503	SO:0001583	missense	80823	exon2			TATATGGATTCTG	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.961G>T	X.37:g.102004884G>T	ENSP00000361820:p.Asp321Tyr	179	0	0		154	38	0.246753	NM_001142530	Q9C0G2	Missense_Mutation	SNP	ENST00000372735.1	37	CCDS14502.1	.	.	.	.	.	.	.	.	.	.	G	11.02	1.516286	0.27123	.	.	ENSG00000198908	ENST00000457056;ENST00000361229;ENST00000447531;ENST00000448867;ENST00000372735	T;T;T;T;T	0.33438	1.41;1.41;1.41;1.41;1.41	4.6	0.444	0.16592	Armadillo-type fold (1);	0.425883	0.20121	N	0.098805	T	0.28532	0.0706	L	0.38175	1.15	0.21445	N	0.999684	P	0.43231	0.801	P	0.49999	0.628	T	0.11421	-1.0588	9	.	.	.	-7.4256	6.7343	0.23401	0.5217:0.0:0.4783:0.0	.	321	Q6PI77	BHLH9_HUMAN	Y	321	ENSP00000403226:D321Y;ENSP00000354675:D321Y;ENSP00000405893:D321Y;ENSP00000391722:D321Y;ENSP00000361820:D321Y	.	D	+	1	0	BHLHB9	101891540	0.980000	0.34600	0.331000	0.25455	0.649000	0.38597	0.014000	0.13333	-0.059000	0.13154	-0.269000	0.10298	GAT	.	.	none		0.383	BHLHB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057630.1	NM_030639		T	102004884	G	T	102004884	3	4	34	1	0	0	0	0	1	0	0	0	1420	1174	41	4	963	4	BHLHB9	23	102004884	Missense_Mutation	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10		102004884	53265676	67	14136											
SLITRK2	84631	hgsc.bcm.edu	37	chrX	144905286	144905286	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tatgtttgatggactgcagaGcttgcaatatctctatttag	10	16	9	6	0	1	2	0	1	1	1	2	3	1	3	0	1	3	4	0	1	5	7			TCGA-GR-A4D9-01B-11D-A31X-10	TCGA-GR-A4D9-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	2628dbf8-af39-40c7-8cac-dc5f1d900038	a894d227-2be0-4820-b8b2-0e673e33fb95	g.chrX:144905286G>A	ENST00000370490.1	+	1	5598	c.1343G>A	c.(1342-1344)aGc>aAc	p.S448N	SLITRK2_ENST00000428560.2_Missense_Mutation_p.S448N|SLITRK2_ENST00000413937.2_Missense_Mutation_p.S448N|SLITRK2_ENST00000434188.2_Missense_Mutation_p.S448N|SLITRK2_ENST00000447897.2_Missense_Mutation_p.S448N			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	448					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)		p.S448I(1)		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)					GGACTGCAGAGCTTGCAATAT	0.393																																					p.S448N		Atlas-SNP	.											.	SLITRK2	221	.	1	Substitution - Missense(1)	lung(1)	c.G1343A						PASS	.						137	142	140					X																	144905286		2203	4300	6503	SO:0001583	missense	84631	exon5			TGCAGAGCTTGCA	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.1343G>A	X.37:g.144905286G>A	ENSP00000359521:p.Ser448Asn	133	0	0		120	37	0.308333	NM_001144005	A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Missense_Mutation	SNP	ENST00000370490.1	37	CCDS14680.1	.	.	.	.	.	.	.	.	.	.	G	10.42	1.344294	0.24339	.	.	ENSG00000185985	ENST00000335565;ENST00000447897;ENST00000370490;ENST00000434188;ENST00000413937;ENST00000428560	T;T;T;T;T;T	0.60672	0.17;0.17;0.17;0.17;0.17;0.17	5.5	5.5	0.81552	.	0.207561	0.46758	D	0.000261	T	0.39545	0.1082	N	0.05078	-0.115	0.50313	D	0.999865	P	0.40066	0.701	P	0.44946	0.465	T	0.39961	-0.9588	10	0.02654	T	1	-11.1755	15.6243	0.76840	0.0:0.0:1.0:0.0	.	448	Q9H156	SLIK2_HUMAN	N	448	ENSP00000334374:S448N;ENSP00000411681:S448N;ENSP00000359521:S448N;ENSP00000397015:S448N;ENSP00000407347:S448N;ENSP00000412010:S448N	ENSP00000334374:S448N	S	+	2	0	SLITRK2	144712978	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.233000	0.72320	2.285000	0.76669	0.600000	0.82982	AGC	.	.	none		0.393	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539		A	144905286	G	A	144905286	3	1	34	1	0	0	0	0	1	0	0	0	14758	971	34	2	1345	2	SLITRK2	23	144905286	Missense_Mutation	SNP	G	TCGA-GR-A4D9-01B-11D-A31X-10	42900402	144905286	10365274	68	14137											
DNAJC11	55735	hgsc.bcm.edu	37	chr1	6700045	6700045	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agaggccccacggtggcataGaacatggcgctgggcagaag	11	4	16	10	2	0	3	0	0	0	3	0	3	0	3	2	5	1	3	2	5	3	1			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr1:6700045G>A	ENST00000377577.5	-	11	1293	c.1170C>T	c.(1168-1170)ttC>ttT	p.F390F	DNAJC11_ENST00000349363.6_Intron|DNAJC11_ENST00000377573.5_Silent_p.F300F|DNAJC11_ENST00000294401.7_Intron|DNAJC11_ENST00000465508.1_5'UTR|DNAJC11_ENST00000542246.1_Silent_p.F352F	NM_018198.3	NP_060668.2	Q9NVH1	DJC11_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 11	390						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)		CGGTGGCATAGAACATGGCGC	0.483																																					p.F390F		Atlas-SNP	.											.	DNAJC11	93	.	0			c.C1170T						PASS	.						79	74	76					1																	6700045		2203	4300	6503	SO:0001819	synonymous_variant	55735	exon11			GGCATAGAACATG	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.1170C>T	1.37:g.6700045G>A		85	0	0		47	19	0.404255	NM_018198	Q4VWF5|Q5VZN0|Q6PK20|Q6PK70|Q8NDM2|Q96CL7	Silent	SNP	ENST00000377577.5	37	CCDS87.1																																																																																			.	.	none		0.483	DNAJC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004216.3	NM_018198		A	6700045	G	A	6700045	2	1	35	1	0	0	0	0	0	0	0	1	4632	933	33	2		2	DNAJC11	1	6700045	Silent	SNP	G	TCGA-GS-A9TQ-01A-11D-A382-10		6700045	242550576	1	14138											
SLC2A5	6518	hgsc.bcm.edu	37	chr1	9097845	9097845	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gaagctgtacgggccgaggcCctcctgcgggaagaggggca	8	4	18	11	3	0	1	0	0	0	1	1	4	1	2	3	5	3	3	3	5	3	1			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr1:9097845C>T	ENST00000377424.4	-	12	1485	c.1306G>A	c.(1306-1308)Ggc>Agc	p.G436S	SLC2A5_ENST00000536305.1_Missense_Mutation_p.G377S|SLC2A5_ENST00000535586.1_Missense_Mutation_p.G321S	NM_003039.2	NP_003030.1	P22732	GTR5_HUMAN	solute carrier family 2 (facilitated glucose/fructose transporter), member 5	436					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)		GGGCCGAGGCCCTCCTGCGGG	0.617																																					p.G436S		Atlas-SNP	.											.	SLC2A5	77	.	0			c.G1306A						PASS	.						62	66	65					1																	9097845		2203	4300	6503	SO:0001583	missense	6518	exon12			CGAGGCCCTCCTG	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.1306G>A	1.37:g.9097845C>T	ENSP00000366641:p.Gly436Ser	45	0	0		36	11	0.305556	NM_003039	Q14770|Q5T977|Q8IVB3	Missense_Mutation	SNP	ENST00000377424.4	37	CCDS99.1	.	.	.	.	.	.	.	.	.	.	C	12.40	1.926514	0.34002	.	.	ENSG00000142583	ENST00000377424;ENST00000456780;ENST00000536305;ENST00000535586	T;T;T	0.72835	-0.69;-0.69;-0.69	5.35	4.41	0.53225	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.103605	0.64402	D	0.000003	T	0.57989	0.2091	L	0.28014	0.82	0.54753	D	0.999985	B;P;B	0.34815	0.362;0.47;0.399	B;B;B	0.38755	0.11;0.11;0.281	T	0.52056	-0.8626	10	0.14252	T	0.57	.	12.5259	0.56085	0.167:0.833:0.0:0.0	.	392;377;436	B4DG19;B4DU31;P22732	.;.;GTR5_HUMAN	S	436;419;377;321	ENSP00000366641:G436S;ENSP00000440688:G377S;ENSP00000442744:G321S	ENSP00000366641:G436S	G	-	1	0	SLC2A5	9020432	0.001000	0.12720	0.380000	0.26093	0.103000	0.19146	1.019000	0.30014	1.311000	0.45024	0.655000	0.94253	GGC	.	.	none		0.617	SLC2A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004932.1	NM_003039		T	9097845	C	T	9097845	3	4	35	1	0	0	0	0	1	0	0	0	14563	623	22	2	203	2	SLC2A5	1	9097845	Missense_Mutation	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	2397800	9097845	240152776	2	14139											
UBR4	23352	hgsc.bcm.edu	37	chr1	19491323	19491323	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaacaatgtatgtggtcagtAactgcagcagctgccggttc	10	10	12	9	1	1	0	1	0	0	0	2	1	1	0	1	2	6	6	1	2	4	3			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr1:19491323A>T	ENST00000375254.3	-	32	4508	c.4481T>A	c.(4480-4482)tTa>tAa	p.L1494*	UBR4_ENST00000375226.2_Nonsense_Mutation_p.L1494*|UBR4_ENST00000375217.2_Nonsense_Mutation_p.L1494*|UBR4_ENST00000375267.2_Nonsense_Mutation_p.L1494*	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	1494					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)		TGTGGTCAGTAACTGCAGCAG	0.493																																					p.L1494X		Atlas-SNP	.											.	UBR4	415	.	0			c.T4481A						PASS	.						116	114	114					1																	19491323		2203	4300	6503	SO:0001587	stop_gained	23352	exon32			GTCAGTAACTGCA	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.4481T>A	1.37:g.19491323A>T	ENSP00000364403:p.Leu1494*	67	0	0		64	16	0.25	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Nonsense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	A	31	5.095569	0.94197	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000417040;ENST00000419533	.	.	.	5.99	5.99	0.97316	.	0.081308	0.49916	D	0.000127	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	.	16.1557	0.81666	1.0:0.0:0.0:0.0	.	.	.	.	X	1494;1494;1494;1494;204;710	.	ENSP00000364365:L1494X	L	-	2	0	UBR4	19363910	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	6.871000	0.75531	2.291000	0.77112	0.533000	0.62120	TTA	.	.	none		0.493	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		T	19491323	A	T	19491323	4	4	35	1	0	0	0	0	0	1	0	0	16919	372	13	5	11370	5	UBR4	1	19491323	Nonsense_Mutation	SNP	A	TCGA-GS-A9TQ-01A-11D-A382-10	10393478	19491323	229759298	3	14140											
KIAA0754	643314	hgsc.bcm.edu	37	chr1	39877011	39877011	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgagaagaacagcctggcAgatatttttgaagaaagaga	17	8	12	4	0	0	6	0	2	0	5	0	9	0	6	1	1	2	1	1	1	5	3			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr1:39877011A>C	ENST00000530275.1	+	1	861	c.666A>C	c.(664-666)gcA>gcC	p.A222A	MACF1_ENST00000289893.4_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000564288.1_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000539005.1_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	222										central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	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)			ACAGCCTGGCAGATATTTTTG	0.473											OREG0013393	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A358A		Atlas-SNP	.											.	KIAA0754	93	.	0			c.A1074C						PASS	.						123	126	125					1																	39877011		1964	4158	6122	SO:0001819	synonymous_variant	643314	exon1			CCTGGCAGATATT			1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.666A>C	1.37:g.39877011A>C		190	0	0	889	161	36	0.223602	NM_015038	E9PMC2|Q6ZSB2	Silent	SNP	ENST00000530275.1	37																																																																																				.	.	none		0.473	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038		C	39877011	A	C	39877011	2	2	35	1	0	0	0	0	0	0	0	1	8201	175	7	5		5	KIAA0754	1	39877011	Silent	SNP	A	TCGA-GS-A9TQ-01A-11D-A382-10	20385688	39877011	209373610	4	14141											
LPHN2	23266	hgsc.bcm.edu	37	chr1	82421682	82421682	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgatacattggaagaaggagCttttgtcctagctgacaatc	12	11	10	8	1	0	2	0	1	0	1	2	5	1	4	1	2	3	2	1	2	5	5			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr1:82421682C>A	ENST00000370728.1	+	13	2588	c.1943C>A	c.(1942-1944)gCt>gAt	p.A648D	LPHN2_ENST00000370725.1_Missense_Mutation_p.A648D|LPHN2_ENST00000469377.2_Intron|LPHN2_ENST00000271029.4_Missense_Mutation_p.A648D|LPHN2_ENST00000319517.6_Missense_Mutation_p.A635D|LPHN2_ENST00000335786.5_Missense_Mutation_p.A648D|LPHN2_ENST00000370721.1_Missense_Mutation_p.A573D|LPHN2_ENST00000370715.1_Missense_Mutation_p.A635D|LPHN2_ENST00000359929.3_Missense_Mutation_p.A635D|LPHN2_ENST00000370730.1_Missense_Mutation_p.A648D|LPHN2_ENST00000370717.2_Missense_Mutation_p.A648D|LPHN2_ENST00000370723.1_Missense_Mutation_p.A635D|LPHN2_ENST00000370713.1_Missense_Mutation_p.A635D|LPHN2_ENST00000370727.1_Missense_Mutation_p.A648D|LPHN2_ENST00000394879.1_Missense_Mutation_p.A635D			O95490	LPHN2_HUMAN	latrophilin 2	648					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)		GAAGAAGGAGCTTTTGTCCTA	0.378																																					p.A635D		Atlas-SNP	.											.	LPHN2	464	.	0			c.C1904A						PASS	.						114	106	109					1																	82421682		2203	4300	6503	SO:0001583	missense	23266	exon9			AAGGAGCTTTTGT	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.1943C>A	1.37:g.82421682C>A	ENSP00000359763:p.Ala648Asp	169	0	0		114	25	0.219298	NM_012302	A5XEI2|B1ALT8|B1ALT9|B1ALU0|B1ALU2|B1ALU4|B1ALU5|B1ALU6|O94882|Q5VX76|Q9UKY5|Q9UKY6	Missense_Mutation	SNP	ENST00000370728.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.6|28.6	4.936727|4.936727	0.92458|0.92458	.|.	.|.	ENSG00000117114|ENSG00000117114	ENST00000370721;ENST00000370728;ENST00000370730;ENST00000370727;ENST00000370725;ENST00000370723;ENST00000359929;ENST00000370715;ENST00000370713;ENST00000319517;ENST00000370717;ENST00000394879;ENST00000271029;ENST00000335786|ENST00000449420	T;T;T;T;T;T;T;T;T;T;T;T;T;T|.	0.14766|.	2.48;2.48;2.48;2.48;2.48;2.48;2.48;2.48;2.48;2.48;2.48;2.48;2.48;2.48|.	5.47|5.47	5.47|5.47	0.80525|0.80525	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.79493|0.79493	0.4455|0.4455	M|M	0.83953|0.83953	2.67|2.67	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	0.997;0.999;1.0|.	T|T	0.80214|0.80214	-0.1475|-0.1475	10|5	0.87932|.	D|.	0|.	.|.	19.3323|19.3323	0.94295|0.94295	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	635;635;635|.	O95490-3;O95490-4;O95490-2|.	.;.;.|.	D|I	573;648;648;648;648;635;635;635;635;635;648;635;648;648|516	ENSP00000359756:A573D;ENSP00000359763:A648D;ENSP00000359765:A648D;ENSP00000359762:A648D;ENSP00000359760:A648D;ENSP00000359758:A635D;ENSP00000353006:A635D;ENSP00000359750:A635D;ENSP00000359748:A635D;ENSP00000322270:A635D;ENSP00000359752:A648D;ENSP00000378344:A635D;ENSP00000271029:A648D;ENSP00000337306:A648D|.	ENSP00000271029:A648D|.	A|L	+|+	2|1	0|0	LPHN2|LPHN2	82194270|82194270	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.487000|7.487000	0.81328|0.81328	2.568000|2.568000	0.86640|0.86640	0.467000|0.467000	0.42956|0.42956	GCT|CTT	.	.	none		0.378	LPHN2-007	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000027188.1	NM_012302		A	82421682	C	A	82421682	3	1	35	1	0	0	0	0	1	0	0	0	8925	797	28	4	1934	4	LPHN2	1	82421682	Missense_Mutation	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	42544671	82421682	166828939	5	14142											
SNX27	81609	hgsc.bcm.edu	37	chr1	151630819	151630819	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttgccaactttacatttcctCgactcccagggaagtggcca	9	11	8	13	1	0	0	0	0	0	0	3	2	2	1	4	2	3	0	4	2	3	4			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr1:151630819C>T	ENST00000458013.2	+	3	772	c.652C>T	c.(652-654)Cga>Tga	p.R218*	SNX27_ENST00000368843.3_Nonsense_Mutation_p.R218*|SNX27_ENST00000368838.1_Nonsense_Mutation_p.R125*			Q96L92	SNX27_HUMAN	sorting nexin family member 27	218	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				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)			TACATTTCCTCGACTCCCAGG	0.458																																					p.R218X	Colon(46;291 966 40145 41237 41888)	Atlas-SNP	.											.	SNX27	44	.	0			c.C652T						PASS	.						145	141	143					1																	151630819		2203	4300	6503	SO:0001587	stop_gained	81609	exon3			TTTCCTCGACTCC	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.652C>T	1.37:g.151630819C>T	ENSP00000400333:p.Arg218*	124	0	0		147	24	0.163265	NM_030918	Q32Q36|Q4AEJ5|Q5VWB0|Q5VWB1|Q5VWB2|Q6IPP6|Q86UB1|Q96D79|Q9H3K8	Nonsense_Mutation	SNP	ENST00000458013.2	37		.	.	.	.	.	.	.	.	.	.	C	37	6.556807	0.97663	.	.	ENSG00000143376	ENST00000458013;ENST00000368843;ENST00000368838	.	.	.	5.81	5.81	0.92471	.	0.058920	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	.	18.6433	0.91402	0.0:1.0:0.0:0.0	.	.	.	.	X	218;218;125	.	ENSP00000357831:R125X	R	+	1	2	SNX27	149897443	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.816000	0.62642	2.747000	0.94245	0.650000	0.86243	CGA	.	.	none		0.458	SNX27-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000036624.3	NM_030918		T	151630819	C	T	151630819	4	4	35	1	0	0	0	0	0	1	0	0	14912	876	31	1	662	1	SNX27	1	151630819	Nonsense_Mutation	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	69209137	151630819	97619802	6	14143											
TCHH	7062	hgsc.bcm.edu	37	chr1	152084202	152084203	+	In_Frame_Ins	INS	-	-	CGCCTCTCCTGCTGCTCG																															cgcgcctctcctgctgctcgINScgcctctcctcctcctcgag																										TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr1:152084202_152084203insCGCCTCTCCTGCTGCTCG	ENST00000368804.1	-	2	1489_1490	c.1490_1491insCGAGCAGCAGGAGAGGCG	c.(1489-1491)cgc>cgCGAGCAGCAGGAGAGGCGc	p.497_497R>REQQERR		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	497	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)			CCTGCTGCTCGCGCCTCTCCTC	0.668																																					p.R497delinsREQQERR		Atlas-Indel	.											.	TCHH	275	.	0			c.1491_1492insCGAGCAGCAGGAGAGGCG						PASS	.																																			SO:0001652	inframe_insertion	7062	exon3			.	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.1473_1490dupCGAGCAGCAGGAGAGGCG	1.37:g.152084202_152084203insCGCCTCTCCTGCTGCTCG	Exception_encountered	103	0	0		94	11	0.117021	NM_007113	Q5VUI3	In_Frame_Ins	INS	ENST00000368804.1	37	CCDS41396.1																																																																																			.	.	none		0.668	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113		CGCCTCTCCTGCTGCTCG	152084203	-	CGCCTCTCCTGCTGCTCG	152084202	7	5	35	1	0	1	1	0	0	0	0	0	15715	1074	38	0	4344	0	TCHH	1	152084202	In_Frame_Ins	INS	-	TCGA-GS-A9TQ-01A-11D-A382-10	453383	152084202	97166419	7	14144											
FLG	2312	hgsc.bcm.edu	37	chr1	152285878	152285878	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctcgtgcctgctcgtggtgcGatccttgtcttcctccagtg	2	14	11	14	3	1	0	0	0	1	0	6	1	4	0	4	1	3	1	4	1	0	2	rs139321371		TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr1:152285878G>A	ENST00000368799.1	-	3	1519	c.1484C>T	c.(1483-1485)tCg>tTg	p.S495L	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	495	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)			CTCGTGGTGCGATCCTTGTCT	0.607									Ichthyosis																												p.S495L		Atlas-SNP	.											FLG,NS,carcinoma,0,1	FLG	900	1	0			c.C1484T						PASS	.	G	LEU/SER	0,4406		0,0,2203	278	260	266		1484	-2.5	0	1	dbSNP_134	266	1,8599		0,1,4299	no	missense	FLG	NM_002016.1	145	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	495/4062	152285878	1,13005	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGGTGCGATCCTT	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.1484C>T	1.37:g.152285878G>A	ENSP00000357789:p.Ser495Leu	233	0	0		180	21	0.116667	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	-	10.99	1.506078	0.26949	0.0	1.16E-4	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.03745	3.82	2.94	-2.49	0.06403	.	.	.	.	.	T	0.05364	0.0142	M	0.80028	2.48	0.09310	N	1	D	0.71674	0.998	D	0.79108	0.992	T	0.12528	-1.0544	9	0.31617	T	0.26	.	5.7028	0.17891	0.0:0.3484:0.2968:0.3548	.	495	P20930	FILA_HUMAN	L	495;27	ENSP00000357789:S495L	ENSP00000357789:S495L	S	-	2	0	FLG	150552502	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-2.842000	0.00737	-0.654000	0.05394	0.505000	0.49811	TCG	G|1.000;A|0.000	0.000	weak		0.607	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152285878	G	A	152285878	3	1	35	1	0	0	0	0	1	0	0	0	5930	1059	37	1	10705	1	FLG	1	152285878	Missense_Mutation	SNP	G	TCGA-GS-A9TQ-01A-11D-A382-10	201676	152285878	96964743	8	14145											
ARHGEF11	9826	hgsc.bcm.edu	37	chr1	156931508	156931508	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atattccagatgtctttcccCaagcttcgggaatccttggg	8	13	9	11	1	1	1	0	0	1	1	5	2	4	2	4	2	1	1	4	2	3	5			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr1:156931508C>T	ENST00000361409.2	-	13	1822	c.1080G>A	c.(1078-1080)ttG>ttA	p.L360L	ARHGEF11_ENST00000368194.3_Silent_p.L400L	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	360	RGSL. {ECO:0000255|PROSITE- ProRule:PRU00171}.				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)					TGTCTTTCCCCAAGCTTCGGG	0.443																																					p.L400L		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.G1200A						PASS	.						83	90	88					1																	156931508		2203	4300	6503	SO:0001819	synonymous_variant	9826	exon14			TTTCCCCAAGCTT	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.1080G>A	1.37:g.156931508C>T		91	0	0		102	26	0.254902	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Silent	SNP	ENST00000361409.2	37	CCDS1162.1																																																																																			.	.	none		0.443	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236		T	156931508	C	T	156931508	2	4	35	1	0	0	0	0	0	0	0	1	896	593	21	2		2	ARHGEF11	1	156931508	Silent	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	4645630	156931508	92319113	9	14146											
PLEKHA6	22874	hgsc.bcm.edu	37	chr1	204199657	204199657	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ccgcattcggtcaatctgctCctccacgctcatcttgacct	6	12	6	17	3	4	1	2	1	2	0	7	1	6	1	4	1	1	3	4	1	1	2			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr1:204199657C>T	ENST00000272203.3	-	18	2783	c.2467G>A	c.(2467-2469)Gag>Aag	p.E823K	PLEKHA6_ENST00000414478.1_Missense_Mutation_p.E843K	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	823										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)			TCAATCTGCTCCTCCACGCTC	0.647																																					p.E823K		Atlas-SNP	.											.	PLEKHA6	115	.	0			c.G2467A						PASS	.						40	33	35					1																	204199657		2203	4300	6503	SO:0001583	missense	22874	exon18			TCTGCTCCTCCAC	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.2467G>A	1.37:g.204199657C>T	ENSP00000272203:p.Glu823Lys	107	0	0		123	18	0.146341	NM_014935	A7MD51|Q5VTI6	Missense_Mutation	SNP	ENST00000272203.3	37	CCDS1444.1	.	.	.	.	.	.	.	.	.	.	C	32	5.119049	0.94385	.	.	ENSG00000143850	ENST00000272203;ENST00000414478	T;T	0.25912	1.77;2.24	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.55529	0.1926	M	0.82323	2.585	0.58432	D	0.999999	D	0.58268	0.982	D	0.67548	0.952	T	0.62229	-0.6898	10	0.87932	D	0	-30.4922	18.4131	0.90559	0.0:1.0:0.0:0.0	.	823	Q9Y2H5	PKHA6_HUMAN	K	823;843	ENSP00000272203:E823K;ENSP00000402046:E843K	ENSP00000272203:E823K	E	-	1	0	PLEKHA6	202466280	1.000000	0.71417	1.000000	0.80357	0.731000	0.41821	7.028000	0.76470	2.435000	0.82474	0.462000	0.41574	GAG	.	.	none		0.647	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935		T	204199657	C	T	204199657	3	4	35	1	0	0	0	0	1	0	0	0	12069	864	30	2	699	2	PLEKHA6	1	204199657	Missense_Mutation	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	47268149	204199657	45050964	10	14147											
FLVCR1	28982	hgsc.bcm.edu	37	chr1	213061854	213061854	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcatgactggttacctccCtttgggttttgaatttgctg	5	18	9	9	0	1	2	1	2	0	0	2	2	2	2	2	2	2	3	2	2	2	6			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr1:213061854C>A	ENST00000366971.4	+	7	1529	c.1331C>A	c.(1330-1332)cCt>cAt	p.P444H	FLVCR1_ENST00000483790.1_3'UTR	NM_014053.3	NP_054772.1	Q9Y5Y0	FLVC1_HUMAN	feline leukemia virus subgroup C cellular receptor 1	444					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)		GGTTACCTCCCTTTGGGTTTT	0.393																																					p.P444H	Esophageal Squamous(199;2235 2952 19233 26256)	Atlas-SNP	.											.	FLVCR1	31	.	0			c.C1331A						PASS	.						201	185	190					1																	213061854		2203	4300	6503	SO:0001583	missense	28982	exon7			ACCTCCCTTTGGG	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.1331C>A	1.37:g.213061854C>A	ENSP00000355938:p.Pro444His	210	0	0		248	38	0.153226	NM_014053	Q1HE16|Q86XY9|Q9NVR9	Missense_Mutation	SNP	ENST00000366971.4	37	CCDS1510.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.1|28.1	4.887770|4.887770	0.91814|0.91814	.|.	.|.	ENSG00000162769|ENSG00000162769	ENST00000419102|ENST00000366971	.|T	.|0.61627	.|0.09	5.78|5.78	5.78|5.78	0.91487|0.91487	.|Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.84261|0.84261	0.5433|0.5433	H|H	0.95151|0.95151	3.63|3.63	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.85130	.|0.997	D|D	0.88324|0.88324	0.2964|0.2964	5|10	.|0.87932	.|D	.|0	-24.5348|-24.5348	19.5996|19.5996	0.95554|0.95554	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|444	.|Q9Y5Y0	.|FLVC1_HUMAN	I|H	243|444	.|ENSP00000355938:P444H	.|ENSP00000355938:P444H	L|P	+|+	1|2	0|0	FLVCR1|FLVCR1	211128477|211128477	1.000000|1.000000	0.71417|0.71417	0.966000|0.966000	0.40874|0.40874	0.994000|0.994000	0.84299|0.84299	7.335000|7.335000	0.79234|0.79234	2.729000|2.729000	0.93468|0.93468	0.655000|0.655000	0.94253|0.94253	CTT|CCT	.	.	none		0.393	FLVCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089678.2	NM_014053		A	213061854	C	A	213061854	3	1	35	1	0	0	0	0	1	0	0	0	5953	681	24	4	1357	4	FLVCR1	1	213061854	Missense_Mutation	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	8862197	213061854	36188767	11	14148											
MIA3	375056	hgsc.bcm.edu	37	chr1	222805652	222805652	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcacagaagccaaatactgaGaaagacctggacccaggtaa	17	5	9	10	0	1	3	1	1	0	3	1	5	1	4	3	2	2	1	3	2	5	2			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr1:222805652G>A	ENST00000344922.5	+	5	3340	c.3315G>A	c.(3313-3315)gaG>gaA	p.E1105E	MIA3_ENST00000470521.1_3'UTR|MIA3_ENST00000344441.6_Silent_p.E1105E|MIA3_ENST00000344507.1_Intron	NM_198551.2	NP_940953.2	Q5JRA6	MIA3_HUMAN	melanoma inhibitory activity family, member 3	1105					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)		CAAATACTGAGAAAGACCTGG	0.453																																					p.E1105E		Atlas-SNP	.											.	MIA3	167	.	0			c.G3315A						PASS	.						90	86	87					1																	222805652		1864	4082	5946	SO:0001819	synonymous_variant	375056	exon5			TACTGAGAAAGAC		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.3315G>A	1.37:g.222805652G>A		96	0	0		108	20	0.185185	NM_198551	A8K2S0|A8MT05|A8MT13|B7Z430|Q14083|Q3S4X3|Q5JRA5|Q5JRB0|Q5JRB1|Q5JRB2|Q6UVY8|Q86Y60|Q8N8M5|Q92580	Silent	SNP	ENST00000344922.5	37	CCDS41470.1	.	.	.	.	.	.	.	.	.	.	G	3.427	-0.116990	0.06838	.	.	ENSG00000154305	ENST00000354906	T	0.19250	2.16	3.81	2.89	0.33648	.	.	.	.	.	T	0.21881	0.0527	.	.	.	0.22305	N	0.999213	.	.	.	.	.	.	T	0.13150	-1.0520	6	0.41790	T	0.15	.	8.8823	0.35382	0.0:0.0:0.7777:0.2223	.	.	.	.	K	688	ENSP00000355062:E688K	ENSP00000355062:E688K	E	+	1	0	MIA3	220872275	0.016000	0.18221	0.038000	0.18304	0.226000	0.24999	1.531000	0.36018	1.166000	0.42689	0.557000	0.71058	GAA	.	.	none		0.453	MIA3-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091489.4	NM_198551		A	222805652	G	A	222805652	2	1	35	1	0	0	0	0	0	0	0	1	9574	933	33	2		2	MIA3	1	222805652	Silent	SNP	G	TCGA-GS-A9TQ-01A-11D-A382-10	9743798	222805652	26444969	12	14149											
B3GALNT2	148789	hgsc.bcm.edu	37	chr1	235647809	235647809	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgtcttcggacagactgaaCgcttcaatttcctgattcaa	10	13	8	10	2	3	3	2	2	1	1	5	4	4	4	1	1	1	1	1	1	3	4			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr1:235647809C>T	ENST00000366600.3	-	4	612	c.384G>A	c.(382-384)gcG>gcA	p.A128A	B3GALNT2_ENST00000494378.1_5'UTR|B3GALNT2_ENST00000313984.3_Silent_p.A169A	NM_152490.2	NP_689703.1	Q8NCR0	B3GL2_HUMAN	beta-1,3-N-acetylgalactosaminyltransferase 2	128					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)			ACAGACTGAACGCTTCAATTT	0.423																																					p.A128A		Atlas-SNP	.											.	B3GALNT2	36	.	0			c.G384A						PASS	.						138	137	138					1																	235647809		2203	4300	6503	SO:0001819	synonymous_variant	148789	exon4			ACTGAACGCTTCA	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.384G>A	1.37:g.235647809C>T		79	0	0		61	14	0.229508	NM_152490	Q59GR3|Q5TCI3|Q96AL7	Silent	SNP	ENST00000366600.3	37	CCDS1606.1																																																																																			.	.	none		0.423	B3GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097376.1	NM_152490		T	235647809	C	T	235647809	2	4	35	1	0	0	0	0	0	0	0	1	1246	523	19	1		1	B3GALNT2	1	235647809	Silent	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	12842157	235647809	13602812	13	14150											
RYR2	6262	hgsc.bcm.edu	37	chr1	237819151	237819151	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaacttttcaaactggcaCtgccttgcctgagtgcagtt	10	12	9	10	0	1	2	1	1	0	1	1	2	1	2	2	1	5	3	2	1	3	4	rs370333448		TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr1:237819151C>A	ENST00000366574.2	+	53	8313	c.7996C>A	c.(7996-7998)Ctg>Atg	p.L2666M	RYR2_ENST00000542537.1_Missense_Mutation_p.L2650M|RYR2_ENST00000360064.6_Missense_Mutation_p.L2664M	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	2666	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)			CAAACTGGCACTGCCTTGCCT	0.408																																					p.L2666M		Atlas-SNP	.											.	RYR2	1273	.	0			c.C7996A						PASS	.						43	42	42					1																	237819151		1837	4092	5929	SO:0001583	missense	6262	exon53			CTGGCACTGCCTT	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.7996C>A	1.37:g.237819151C>A	ENSP00000355533:p.Leu2666Met	198	0	0		242	83	0.342975	NM_001035	Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	C	10.59	1.391987	0.25118	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.95069	-3.6;-3.6;-3.6	5.95	4.86	0.63082	.	0.000000	0.47093	D	0.000249	D	0.84995	0.5596	N	0.12527	0.23	0.80722	D	1	B	0.31599	0.33	B	0.28709	0.093	T	0.80443	-0.1380	10	0.32370	T	0.25	-11.7878	5.4522	0.16570	0.2052:0.6592:0.0:0.1356	.	2666	Q92736	RYR2_HUMAN	M	2666;2664;2650	ENSP00000355533:L2666M;ENSP00000353174:L2664M;ENSP00000443798:L2650M	ENSP00000353174:L2664M	L	+	1	2	RYR2	235885774	0.234000	0.23783	1.000000	0.80357	0.998000	0.95712	0.729000	0.26028	2.826000	0.97356	0.563000	0.77884	CTG	.	.	none		0.408	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035		A	237819151	C	A	237819151	3	1	35	1	0	0	0	0	1	0	0	0	13784	564	20	4	8206	4	RYR2	1	237819151	Missense_Mutation	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	2171342	237819151	11431470	14	14151											
WDR64	128025	hgsc.bcm.edu	37	chr1	241842832	241842832	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	attacctcttgcagctgaaaCgaatcgtagccacaaccgaa	14	8	7	12	3	1	1	0	1	1	0	2	3	1	1	3	0	6	3	3	0	6	3	rs41304038	byFrequency	TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr1:241842832C>T	ENST00000366552.2	+	5	736	c.529C>T	c.(529-531)Cga>Tga	p.R177*	WDR64_ENST00000461971.1_3'UTR|WDR64_ENST00000437684.2_Nonsense_Mutation_p.R177*	NM_144625.4	NP_653226.4	B1ANS9	WDR64_HUMAN	WD repeat domain 64	177										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)			GCAGCTGAAACGAATCGTAGC	0.438													C|||	4	0.000798722	0.0	0.0029	5008	,	,		19694	0.0		0.002	False		,,,				2504	0.0				p.R177X		Atlas-SNP	.											WDR64_ENST00000366552,NS,carcinoma,-1,1	WDR64	234	1	0			c.C529T						PASS	.	C	stop/ARG	0,1384		0,0,692	87	78	81		529	3.7	1	1	dbSNP_127	81	2,3180		0,2,1589	yes	stop-gained	WDR64	NM_144625.4		0,2,2281	TT,TC,CC		0.0629,0.0,0.0438		177/1082	241842832	2,4564	692	1591	2283	SO:0001587	stop_gained	128025	exon5			CTGAAACGAATCG	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.529C>T	1.37:g.241842832C>T	ENSP00000355510:p.Arg177*	161	0	0		164	21	0.128049	NM_144625	B1ANT0|Q7Z573|Q96LY9	Nonsense_Mutation	SNP	ENST00000366552.2	37		1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	38	6.963864	0.97967	0.0	6.29E-4	ENSG00000162843	ENST00000366552;ENST00000437684	.	.	.	5.72	3.72	0.42706	.	0.150508	0.30850	N	0.008744	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.4949	7.5122	0.27579	0.314:0.6081:0.0:0.0779	rs41304038	.	.	.	X	177	.	ENSP00000355510:R177X	R	+	1	2	WDR64	239909455	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.258000	0.32944	1.386000	0.46466	0.655000	0.94253	CGA	C|1.000;T|0.000	0.000	strong		0.438	WDR64-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_144625		T	241842832	C	T	241842832	4	4	35	1	0	0	0	0	0	1	0	0	17330	528	19	1	547	1	WDR64	1	241842832	Nonsense_Mutation	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	4023681	241842832	7407789	15	14152											
OR2T2	401992	hgsc.bcm.edu	37	chr1	248616329	248616329	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gataccatctacatctgtatCactgtccccaagatgctcca	11	11	5	14	0	3	1	1	0	2	1	5	2	5	1	4	0	3	2	4	0	4	3			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr1:248616329C>T	ENST00000342927.3	+	1	253	c.231C>T	c.(229-231)atC>atT	p.I77I		NM_001004136.1	NP_001004136.1	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T, member 2	77						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)			ACATCTGTATCACTGTCCCCA	0.522																																					p.I77I		Atlas-SNP	.											.	OR2T2	73	.	0			c.C231T						PASS	.						130	147	141					1																	248616329		2203	4297	6500	SO:0001819	synonymous_variant	401992	exon1			CTGTATCACTGTC	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.231C>T	1.37:g.248616329C>T		674	0	0		689	44	0.0638607	NM_001004136	B2RNM1|B9EH01	Silent	SNP	ENST00000342927.3	37	CCDS31116.1																																																																																			.	.	none		0.522	OR2T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097421.1	NM_001004136		T	248616329	C	T	248616329	2	4	35	1	0	0	0	0	0	0	0	1	11029	816	29	2		2	OR2T2	1	248616329	Silent	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	6773497	248616329	634292	16	14153											
MYT1L	23040	hgsc.bcm.edu	37	chr2	1796099	1796099	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctcagtcacttaccatgtgCggcagctggatgttagccag	8	10	12	11	1	2	0	2	0	0	0	2	1	2	1	2	2	4	4	2	2	2	2			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr2:1796099C>T	ENST00000399161.2	-	24	4161	c.3414G>A	c.(3412-3414)ccG>ccA	p.P1138P	MYT1L_ENST00000428368.2_Silent_p.P1136P|MYT1L_ENST00000407844.1_Silent_p.P136P	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	1138					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)		TTACCATGTGCGGCAGCTGGA	0.517																																					p.P1136P		Atlas-SNP	.											MYT1L,trunk,malignant_melanoma,-1,1	MYT1L	241	1	0			c.G3408A						PASS	.						59	61	61					2																	1796099		2086	4227	6313	SO:0001819	synonymous_variant	23040	exon24			CATGTGCGGCAGC	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.3414G>A	2.37:g.1796099C>T		104	0	0		83	19	0.228916	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Silent	SNP	ENST00000399161.2	37																																																																																				.	.	none		0.517	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		T	1796099	C	T	1796099	2	4	35	1	0	0	0	0	0	0	0	1	10116	755	27	1		1	MYT1L	2	1796099	Silent	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10		1796099	241403274	17	14154											
KIF3C	3797	hgsc.bcm.edu	37	chr2	26204558	26204558	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtctatcaggggcctcacggTttcgtcatacaggtcggcct	6	11	12	12	3	4	0	3	0	1	0	6	0	4	0	2	5	1	1	2	5	2	3			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr2:26204558T>A	ENST00000264712.3	-	1	808	c.229A>T	c.(229-231)Acc>Tcc	p.T77S	KIF3C_ENST00000405914.1_Missense_Mutation_p.T77S	NM_002254.6	NP_002245	O14782	KIF3C_HUMAN	kinesin family member 3C	77	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.			TVR -> RE (in Ref. 1; AAC05302). {ECO:0000305}.	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)					GGCCTCACGGTTTCGTCATAC	0.627																																					p.T77S		Atlas-SNP	.											.	KIF3C	79	.	0			c.A229T						PASS	.						81	79	80					2																	26204558		2203	4300	6503	SO:0001583	missense	3797	exon1			TCACGGTTTCGTC		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.229A>T	2.37:g.26204558T>A	ENSP00000264712:p.Thr77Ser	83	0	0		75	25	0.333333	NM_002254	O43544|Q4ZG18|Q53SX5|Q562F7	Missense_Mutation	SNP	ENST00000264712.3	37	CCDS1719.1	.	.	.	.	.	.	.	.	.	.	T	13.80	2.344081	0.41498	.	.	ENSG00000084731	ENST00000264712;ENST00000405914	T;T	0.44083	0.93;0.93	5.62	5.62	0.85841	Kinesin, motor domain (4);	0.150477	0.56097	D	0.000029	T	0.34483	0.0899	N	0.11255	0.115	0.50632	D	0.999887	P;B	0.34724	0.465;0.232	P;B	0.45232	0.474;0.145	T	0.32402	-0.9908	10	0.37606	T	0.19	.	13.7774	0.63062	0.0:0.0:0.0:1.0	.	77;77	B7ZM25;O14782	.;KIF3C_HUMAN	S	77	ENSP00000264712:T77S;ENSP00000385030:T77S	ENSP00000264712:T77S	T	-	1	0	KIF3C	26058062	1.000000	0.71417	0.983000	0.44433	0.983000	0.72400	3.312000	0.51927	2.131000	0.65755	0.460000	0.39030	ACC	.	.	none		0.627	KIF3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211611.1			A	26204558	T	A	26204558	3	1	35	1	0	0	0	0	1	0	0	0	8311	1725	60	5	2184	5	KIF3C	2	26204558	Missense_Mutation	SNP	T	TCGA-GS-A9TQ-01A-11D-A382-10	24408459	26204558	216994815	18	14155											
BIRC6	57448	hgsc.bcm.edu	37	chr2	32773075	32773075	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggaacatgttacctgcctTctgcaggtatatttgtaaac	11	13	9	8	0	1	0	0	0	1	0	1	2	1	1	2	2	5	4	2	2	6	6			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr2:32773075T>C	ENST00000421745.2	+	64	13103	c.12969T>C	c.(12967-12969)ctT>ctC	p.L4323L		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	4323					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)					TTACCTGCCTTCTGCAGGTAT	0.378																																					p.L4323L	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.T12969C						PASS	.						60	57	58					2																	32773075		2203	4300	6503	SO:0001819	synonymous_variant	57448	exon64			CTGCCTTCTGCAG	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.12969T>C	2.37:g.32773075T>C		81	0	0		115	47	0.408696	NM_016252	Q9ULD1	Silent	SNP	ENST00000421745.2	37	CCDS33175.2																																																																																			.	.	none		0.378	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252		C	32773075	T	C	32773075	2	2	35	1	0	0	0	0	0	0	0	1	1438	1770	62	3		3	BIRC6	2	32773075	Silent	SNP	T	TCGA-GS-A9TQ-01A-11D-A382-10	6568517	32773075	210426298	19	14156											
FANCD2	2177	hgsc.bcm.edu	37	chr3	10094085	10094085	+	Nonsense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacagggcattttagattaTctggataacatatcccctca	12	12	6	11	0	2	1	1	0	1	1	3	2	3	2	3	2	1	1	3	2	4	5			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr3:10094085T>G	ENST00000419585.1	+	18	1721	c.1560T>G	c.(1558-1560)taT>taG	p.Y520*	FANCD2_ENST00000383806.1_Nonsense_Mutation_p.Y520*|FANCD2_ENST00000287647.3_Nonsense_Mutation_p.Y520*|FANCD2_ENST00000383807.1_Nonsense_Mutation_p.Y520*			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	520					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)		TTTTAGATTATCTGGATAACA	0.378			"D, Mis, N, F"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.Y520X		Atlas-SNP	.	yes	Rec		Fanconi anaemia D2	3	3p26	2177	"Fanconi anemia, complementation group D2"		L	.	FANCD2	253	.	0			c.T1560G						PASS	.						69	66	67					3																	10094085		2203	4300	6503	SO:0001587	stop_gained	2177	exon18	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AGATTATCTGGAT	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.1560T>G	3.37:g.10094085T>G	ENSP00000398754:p.Tyr520*	91	0	0		80	25	0.3125	NM_001018115	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Nonsense_Mutation	SNP	ENST00000419585.1	37	CCDS33696.1	.	.	.	.	.	.	.	.	.	.	T	39	7.513557	0.98329	.	.	ENSG00000144554	ENST00000287647;ENST00000383807;ENST00000383806;ENST00000419585	.	.	.	5.55	-2.27	0.06846	.	0.196116	0.45606	D	0.000343	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.8243	0.52259	0.0:0.5994:0.0:0.4006	.	.	.	.	X	520	.	ENSP00000287647:Y520X	Y	+	3	2	FANCD2	10069085	0.995000	0.38212	0.991000	0.47740	0.970000	0.65996	0.342000	0.19926	-0.131000	0.11578	-0.440000	0.05779	TAT	.	.	none		0.378	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1			G	10094085	T	G	10094085	4	3	35	1	0	0	0	0	0	1	0	0	5673	1442	50	5	1626	5	FANCD2	3	10094085	Nonsense_Mutation	SNP	T	TCGA-GS-A9TQ-01A-11D-A382-10		10094085	187928345	20	14157											
RAF1	5894	hgsc.bcm.edu	37	chr3	12641240	12641240	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagagcctgacccaatccgaGtggacagcatcacttcactg	12	7	9	13	1	2	2	2	1	0	1	3	4	3	3	3	1	2	1	3	1	2	1			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr3:12641240G>A	ENST00000251849.4	-	10	1497	c.1058C>T	c.(1057-1059)aCt>aTt	p.T353I	RAF1_ENST00000542177.1_Missense_Mutation_p.T272I|RAF1_ENST00000442415.2_Missense_Mutation_p.T373I|RAF1_ENST00000534997.1_Missense_Mutation_p.T138I	NM_002880.3	NP_002871.1	P04049	RAF1_HUMAN	Raf-1 proto-oncogene, serine/threonine kinase	353	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		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)	CCCAATCCGAGTGGACAGCAT	0.458			T	SRGAP3	pilocytic astrocytoma				Noonan syndrome																												p.T353I		Atlas-SNP	.		Dom	yes		3	3p25	5894	v-raf-1 murine leukemia viral oncogene homolog 1		M	.	RAF1	66	.	0			c.C1058T						PASS	.						91	88	89					3																	12641240		2203	4300	6503	SO:0001583	missense	5894	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	ATCCGAGTGGACA	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.1058C>T	3.37:g.12641240G>A	ENSP00000251849:p.Thr353Ile	98	0	0		76	20	0.263158	NM_002880	B0LPH8|B2R5N3|Q15278|Q9UC20	Missense_Mutation	SNP	ENST00000251849.4	37	CCDS2612.1	.	.	.	.	.	.	.	.	.	.	G	18.63	3.665107	0.67700	.	.	ENSG00000132155	ENST00000251849;ENST00000442415;ENST00000432427;ENST00000534997;ENST00000542177	D;D;D;D;D	0.98947	-5.26;-5.26;-5.26;-5.26;-5.26	5.52	5.52	0.82312	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.201811	0.53938	D	0.000054	D	0.97517	0.9187	L	0.41492	1.28	0.52501	D	0.999959	B;B;B	0.23891	0.078;0.045;0.093	B;B;B	0.36534	0.227;0.151;0.214	D	0.95631	0.8689	10	0.49607	T	0.09	.	17.5749	0.87946	0.0:0.0:1.0:0.0	.	272;138;353	B4E0X2;B4E1N6;P04049	.;.;RAF1_HUMAN	I	353;373;232;138;272	ENSP00000251849:T353I;ENSP00000401888:T373I;ENSP00000398591:T232I;ENSP00000441186:T138I;ENSP00000443567:T272I	ENSP00000251849:T353I	T	-	2	0	RAF1	12616240	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.301000	0.65727	2.752000	0.94435	0.655000	0.94253	ACT	.	.	none		0.458	RAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252015.2	NM_002880		A	12641240	G	A	12641240	3	1	35	1	0	0	0	0	1	0	0	0	13017	1029	36	2	920	2	RAF1	3	12641240	Missense_Mutation	SNP	G	TCGA-GS-A9TQ-01A-11D-A382-10	2547155	12641240	185381190	21	14158											
ZNF385D	79750	hgsc.bcm.edu	37	chr3	21478509	21478509	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagagttgacagcaaccttgCatagcgaacagtaaagaagc	16	6	10	9	1	0	3	0	1	0	2	0	4	0	3	1	0	6	4	1	0	6	4			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr3:21478509C>A	ENST00000281523.2	-	5	1144	c.626G>T	c.(625-627)tGc>tTc	p.C209F	ZNF385D_ENST00000494118.1_5'UTR	NM_024697.2	NP_078973.1	Q9H6B1	Z385D_HUMAN	zinc finger protein 385D	209						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(1)|prostate(1)|skin(4)	46						AGCAACCTTGCATAGCGAACA	0.478																																					p.C209F		Atlas-SNP	.											.	ZNF385D	93	.	0			c.G626T						PASS	.						170	140	150					3																	21478509		2203	4300	6503	SO:0001583	missense	79750	exon5			ACCTTGCATAGCG	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.626G>T	3.37:g.21478509C>A	ENSP00000281523:p.Cys209Phe	145	0	0		85	21	0.247059	NM_024697		Missense_Mutation	SNP	ENST00000281523.2	37	CCDS2636.1	.	.	.	.	.	.	.	.	.	.	C	32	5.105674	0.94292	.	.	ENSG00000151789	ENST00000281523	D	0.99964	-9.97	6.09	6.09	0.99107	Zinc finger, C2H2-like (1);Zinc finger, U1-type (1);Zinc finger, C2H2 (1);	0.000000	0.85682	D	0.000000	D	0.99971	0.9990	M	0.81802	2.56	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.95511	0.8586	10	0.72032	D	0.01	-16.5546	20.6789	0.99705	0.0:1.0:0.0:0.0	.	209	Q9H6B1	Z385D_HUMAN	F	209	ENSP00000281523:C209F	ENSP00000281523:C209F	C	-	2	0	ZNF385D	21453513	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.742000	0.85008	2.891000	0.99171	0.655000	0.94253	TGC	.	.	none		0.478	ZNF385D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252884.1	NM_024697		A	21478509	C	A	21478509	3	1	35	1	0	0	0	0	1	0	0	0	17893	710	25	4	577	4	ZNF385D	3	21478509	Missense_Mutation	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	8837269	21478509	176543921	22	14159											
TRANK1	9881	hgsc.bcm.edu	37	chr3	36898455	36898455	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acacgtgttctgctccgtggCaatgatcttctcagggttct	6	14	10	11	2	4	1	1	1	4	0	6	1	5	1	1	2	1	4	1	2	1	3			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr3:36898455C>A	ENST00000429976.2	-	12	2873	c.2626G>T	c.(2626-2628)Gcc>Tcc	p.A876S	TRANK1_ENST00000301807.6_Missense_Mutation_p.A326S|TRANK1_ENST00000428977.2_Missense_Mutation_p.A326S	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	876							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						TGCTCCGTGGCAATGATCTTC	0.532																																					p.A876S		Atlas-SNP	.											.	TRANK1	398	.	0			c.G2626T						PASS	.						55	50	52					3																	36898455		1990	4175	6165	SO:0001583	missense	9881	exon12			CCGTGGCAATGAT	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.2626G>T	3.37:g.36898455C>A	ENSP00000416168:p.Ala876Ser	72	0	0		70	21	0.3	NM_014831	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	37	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	C	0.157	-1.085744	0.01873	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.29655	1.56;1.97;1.56	5.49	0.111	0.14619	.	0.642324	0.15186	N	0.275836	T	0.15305	0.0369	N	0.19112	0.55	0.09310	N	1	B	0.20887	0.049	B	0.22386	0.039	T	0.29058	-1.0024	10	0.17832	T	0.49	.	5.6844	0.17794	0.124:0.5867:0.0:0.2893	.	876	O15050	TRNK1_HUMAN	S	326;876;326	ENSP00000416826:A326S;ENSP00000416168:A876S;ENSP00000301807:A326S	ENSP00000301807:A326S	A	-	1	0	TRANK1	36873459	0.021000	0.18746	0.000000	0.03702	0.002000	0.02628	0.424000	0.21330	0.072000	0.16694	-0.275000	0.10095	GCC	.	.	none		0.532	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		A	36898455	C	A	36898455	3	1	35	1	0	0	0	0	1	0	0	0	16469	710	25	4	6199	4	TRANK1	3	36898455	Missense_Mutation	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	15419946	36898455	161123975	23	14160											
FBXW12	285231	hgsc.bcm.edu	37	chr3	48420937	48420937	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acatttacactgcctgggttAagagatgtttctaaagttac	12	14	8	7	0	1	1	0	0	1	1	1	2	1	1	1	1	3	3	1	1	5	6			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr3:48420937A>C	ENST00000296438.5	+	7	849	c.663A>C	c.(661-663)ttA>ttC	p.L221F	FBXW12_ENST00000415155.1_Missense_Mutation_p.L151F|FBXW12_ENST00000445170.1_Missense_Mutation_p.L202F|FBXW12_ENST00000436231.1_Missense_Mutation_p.L64F|RN7SL321P_ENST00000581742.1_RNA	NM_207102.2	NP_996985.2	Q6X9E4	FBW12_HUMAN	F-box and WD repeat domain containing 12	221										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		TGCCTGGGTTAAGAGATGTTT	0.413																																					p.L221F		Atlas-SNP	.											.	FBXW12	44	.	0			c.A663C						PASS	.						318	285	296					3																	48420937		2203	4300	6503	SO:0001583	missense	285231	exon7			TGGGTTAAGAGAT	AK097594, AY247969	CCDS2764.1, CCDS54577.1, CCDS54578.1	3p21.31	2011-07-01	2007-02-08	2004-07-21	ENSG00000164049	ENSG00000164049		"F-boxes / WD-40 domains", "WD repeat domain containing"	20729	protein-coding gene	gene with protein product		609075	"F-box only protein 35", "F-box and WD-40 domain protein 12"	FBXO35		15040455	Standard	NM_207102		Approved	Fbw12	uc010hjv.3	Q6X9E4	OTTHUMG00000133530	ENST00000296438.5:c.663A>C	3.37:g.48420937A>C	ENSP00000296438:p.Leu221Phe	175	0	0		156	40	0.25641	NM_207102	E9PG36|Q494Y9|Q494Z0	Missense_Mutation	SNP	ENST00000296438.5	37	CCDS2764.1	.	.	.	.	.	.	.	.	.	.	A	14.39	2.522619	0.44866	.	.	ENSG00000164049	ENST00000458736;ENST00000296438;ENST00000436231;ENST00000445170;ENST00000415155	T;T;T;T	0.63913	1.53;-0.07;1.53;3.4	3.64	-0.456	0.12190	WD40/YVTN repeat-like-containing domain (1);Quinoprotein amine dehydrogenase, beta chain-like (1);	0.000000	0.64402	D	0.000012	T	0.69097	0.3073	M	0.67397	2.05	0.09310	N	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.992;0.998;0.988;0.995	T	0.58070	-0.7701	10	0.66056	D	0.02	-0.3675	3.6866	0.08331	0.5915:0.1914:0.2171:0.0	.	120;202;151;221	E9PCA2;E9PG36;Q494Z0;Q6X9E4	.;.;.;FBW12_HUMAN	F	120;221;64;202;151	ENSP00000296438:L221F;ENSP00000413866:L64F;ENSP00000406139:L202F;ENSP00000414683:L151F	ENSP00000296438:L221F	L	+	3	2	FBXW12	48395941	0.002000	0.14202	0.000000	0.03702	0.003000	0.03518	0.092000	0.15066	-0.074000	0.12820	0.533000	0.62120	TTA	.	.	none		0.413	FBXW12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257505.1	NM_207102		C	48420937	A	C	48420937	3	2	35	1	0	0	0	0	1	0	0	0	5773	359	13	5	722	5	FBXW12	3	48420937	Missense_Mutation	SNP	A	TCGA-GS-A9TQ-01A-11D-A382-10	11522482	48420937	149601493	24	14161											
CSN3	1448	hgsc.bcm.edu	37	chr4	71110559	71110559	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagagttttcttctagttgTcaatgccctggcattaaccc	9	14	8	10	0	3	1	1	0	2	1	3	2	3	1	2	1	2	3	2	1	4	6			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr4:71110559T>C	ENST00000304954.3	+	2	109	c.23T>C	c.(22-24)gTc>gCc	p.V8A		NM_005212.2	NP_005203.2	Q9UNS2	CSN3_HUMAN	casein kappa	0					cullin deneddylation (GO:0010388)|in utero embryonic development (GO:0001701)|response to light stimulus (GO:0009416)|signal transduction (GO:0007165)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	18						CTTCTAGTTGTCAATGCCCTG	0.284																																					p.V8A		Atlas-SNP	.											.	CSN3	43	.	0			c.T23C						PASS	.						92	88	90					4																	71110559		2202	4296	6498	SO:0001583	missense	1448	exon2			TAGTTGTCAATGC	U51899	CCDS3538.1	4q21.1	2014-02-19	2003-01-24	2003-01-31	ENSG00000171209	ENSG00000171209			2446	protein-coding gene	gene with protein product		601695	"casein, kappa"	CSN10		8863730, 9050925	Standard	NM_005212		Approved		uc003hfe.4	P07498	OTTHUMG00000129399	ENST00000304954.3:c.23T>C	4.37:g.71110559T>C	ENSP00000304822:p.Val8Ala	85	0	0		72	22	0.305556	NM_005212	B2R683|B4DY81|O43191|Q7LDR6	Missense_Mutation	SNP	ENST00000304954.3	37	CCDS3538.1	.	.	.	.	.	.	.	.	.	.	T	14.25	2.479333	0.44044	.	.	ENSG00000171209	ENST00000304954	T	0.31247	1.5	4.08	4.08	0.47627	.	0.691470	0.12600	N	0.454752	T	0.41534	0.1163	L	0.59436	1.845	0.27033	N	0.964187	D	0.56968	0.978	P	0.53146	0.719	T	0.24548	-1.0157	10	0.66056	D	0.02	.	9.7345	0.40379	0.0:0.0:0.0:1.0	.	8	P07498	CASK_HUMAN	A	8	ENSP00000304822:V8A	ENSP00000304822:V8A	V	+	2	0	CSN3	71145148	0.978000	0.34361	0.952000	0.39060	0.866000	0.49608	1.903000	0.39858	2.078000	0.62432	0.455000	0.32223	GTC	.	.	none		0.284	CSN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251555.1	NM_005212		C	71110559	T	C	71110559	3	2	35	1	0	0	0	0	1	0	0	0	3951	1667	58	3	25	3	CSN3	4	71110559	Missense_Mutation	SNP	T	TCGA-GS-A9TQ-01A-11D-A382-10		71110559	120043717	25	14162											
ENAM	10117	hgsc.bcm.edu	37	chr4	71510318	71510318	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttctgcatttgccatgctttGgctccaaattagcaaagcat	10	14	7	10	0	1	0	0	0	1	0	2	0	2	0	2	1	5	5	2	1	3	4			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr4:71510318G>A	ENST00000396073.3	+	9	3456	c.3175G>A	c.(3175-3177)Ggc>Agc	p.G1059S	ENAM_ENST00000472903.1_Intron	NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	1059					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)			GCCATGCTTTGGCTCCAAATT	0.458																																					p.G1059S		Atlas-SNP	.											.	ENAM	140	.	0			c.G3175A						PASS	.						107	98	101					4																	71510318		2203	4300	6503	SO:0001583	missense	10117	exon9			TGCTTTGGCTCCA	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.3175G>A	4.37:g.71510318G>A	ENSP00000379383:p.Gly1059Ser	215	0	0		139	46	0.330935	NM_031889	Q17RI5|Q9H3D1	Missense_Mutation	SNP	ENST00000396073.3	37	CCDS3544.2	.	.	.	.	.	.	.	.	.	.	G	10.40	1.340890	0.24339	.	.	ENSG00000132464	ENST00000396073	T	0.34072	1.38	5.95	3.18	0.36537	.	0.357246	0.24557	N	0.037508	T	0.36166	0.0957	L	0.50333	1.59	0.29732	N	0.837785	B	0.20459	0.045	B	0.36030	0.216	T	0.40327	-0.9569	10	0.54805	T	0.06	-2.4743	7.769	0.28997	0.1511:0.1474:0.7015:0.0	.	1059	Q9NRM1	ENAM_HUMAN	S	1059	ENSP00000379383:G1059S	ENSP00000379383:G1059S	G	+	1	0	ENAM	71729182	1.000000	0.71417	1.000000	0.80357	0.490000	0.33462	1.006000	0.29847	0.872000	0.35775	-0.794000	0.03295	GGC	.	.	none		0.458	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3	NM_031889		A	71510318	G	A	71510318	3	1	35	1	0	0	0	0	1	0	0	0	5114	1348	47	2	3205	2	ENAM	4	71510318	Missense_Mutation	SNP	G	TCGA-GS-A9TQ-01A-11D-A382-10	399759	71510318	119643958	26	14163											
LARP1B	55132	hgsc.bcm.edu	37	chr4	129035899	129035899	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agccccagtgaaattgagggTaagttgttacagactgagtg	12	10	13	6	0	0	4	0	3	0	1	0	4	0	4	2	1	2	3	2	1	3	4			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr4:129035899T>C	ENST00000326639.6	+	10	1372		c.e10+2		LARP1B_ENST00000441387.1_Splice_Site|LARP1B_ENST00000427266.1_Splice_Site|LARP1B_ENST00000512292.1_Splice_Site|LARP1B_ENST00000354456.3_Splice_Site|LARP1B_ENST00000264584.5_Splice_Site	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						AAATTGAGGGTAAGTTGTTAC	0.408																																					.		Atlas-SNP	.											.	LARP1B	120	.	0			c.1161+2T>C						PASS	.						86	85	85					4																	129035899		2203	4300	6503	SO:0001630	splice_region_variant	55132	exon10			TGAGGGTAAGTTG		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.1161+2T>C	4.37:g.129035899T>C		149	0	0		68	17	0.25	NM_018078	Q2YDB6|Q4W599|Q4W5B2|Q659A0|Q6P5X2|Q7Z3F7|Q86VK7|Q8N6F4|Q8N7H4|Q8NAF2|Q9H5E7|Q9NW12	Splice_Site	SNP	ENST00000326639.6	37	CCDS3738.1	.	.	.	.	.	.	.	.	.	.	T	15.70	2.910818	0.52439	.	.	ENSG00000138709	ENST00000326639;ENST00000512292;ENST00000508819;ENST00000264584;ENST00000441387;ENST00000427266;ENST00000507377	.	.	.	4.42	4.42	0.53409	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.84	0.63432	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	LARP1B	129255349	1.000000	0.71417	0.986000	0.45419	0.668000	0.39293	5.211000	0.65219	1.840000	0.53500	0.482000	0.46254	.	.	.	none		0.408	LARP1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257173.2	NM_018078	Intron	C	129035899	T	C	129035899	5	2	35	1	0	0	0	0	0	0	1	0	8638	1652	57	3	1282	3	LARP1B	4	129035899	Splice_Site	SNP	T	TCGA-GS-A9TQ-01A-11D-A382-10	57525581	129035899	62118377	27	14164											
SH3D19	152503	hgsc.bcm.edu	37	chr4	152069110	152069110	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agagggtgtcctggtttgggAcgagggggtagcaccggatc	7	8	19	7	2	0	1	0	0	0	1	2	4	1	3	2	6	1	3	2	6	1	2			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr4:152069110A>C	ENST00000409252.2	-	10	1913	c.1206T>G	c.(1204-1206)cgT>cgG	p.R402R	SH3D19_ENST00000304527.4_Silent_p.R402R|SH3D19_ENST00000409598.4_Silent_p.R402R|SH3D19_ENST00000427414.2_Silent_p.R366R|SH3D19_ENST00000424281.1_Silent_p.R366R|SH3D19_ENST00000514152.1_Silent_p.R402R|SH3D19_ENST00000455740.1_Silent_p.R402R			Q5HYK7	SH319_HUMAN	SH3 domain containing 19	402					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)				CTGGTTTGGGACGAGGGGGTA	0.393																																					p.R402R		Atlas-SNP	.											.	SH3D19	54	.	0			c.T1206G						PASS	.						81	88	85					4																	152069110		2203	4300	6503	SO:0001819	synonymous_variant	152503	exon11			TTTGGGACGAGGG	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.1206T>G	4.37:g.152069110A>C		95	0	0		63	14	0.222222	NM_001128923	B7Z296|Q08EK1|Q32N10|Q5U3B8|Q86XB3|Q8N5E7|Q9UFC8	Silent	SNP	ENST00000409252.2	37	CCDS34077.2																																																																																			.	.	none		0.393	SH3D19-002	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000335132.3	NM_001009555		C	152069110	A	C	152069110	2	2	35	1	0	0	0	0	0	0	0	1	14264	262	10	5		5	SH3D19	4	152069110	Silent	SNP	A	TCGA-GS-A9TQ-01A-11D-A382-10	23033211	152069110	39085166	28	14165											
SH3RF1	57630	hgsc.bcm.edu	37	chr4	170043268	170043268	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tacacactggggcgagtctgCggccgtaaatgtgcaatctg	9	9	13	10	3	2	0	0	0	2	0	2	1	2	0	1	3	3	2	1	3	4	2	rs148721890		TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr4:170043268C>T	ENST00000284637.9	-	7	1670	c.1329G>A	c.(1327-1329)ccG>ccA	p.P443P	SH3RF1_ENST00000508685.1_5'UTR	NM_020870.3	NP_065921.2	Q7Z6J0	SH3R1_HUMAN	SH3 domain containing ring finger 1	443	Interaction with AKT2. {ECO:0000250}.				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)		GGCGAGTCTGCGGCCGTAAAT	0.552													C|||	1	0.000199681	0.0	0.0	5008	,	,		18539	0.0		0.001	False		,,,				2504	0.0				p.P443P		Atlas-SNP	.											.	SH3RF1	60	.	0			c.G1329A						PASS	.	C		4,4402	8.1+/-20.4	0,4,2199	88	78	81		1329	-10.6	0.8	4	dbSNP_134	81	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous	SH3RF1	NM_020870.3		0,15,6488	TT,TC,CC		0.1279,0.0908,0.1153		443/889	170043268	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	57630	exon7			AGTCTGCGGCCGT	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.1329G>A	4.37:g.170043268C>T		67	0	0		70	22	0.314286	NM_020870	Q05BT2|Q8IW46|Q9HAM2|Q9P234	Silent	SNP	ENST00000284637.9	37	CCDS34099.1																																																																																			C|0.999;T|0.001	0.001	strong		0.552	SH3RF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363382.3	NM_020870		T	170043268	C	T	170043268	2	4	35	1	0	0	0	0	0	0	0	1	14273	755	27	1		1	SH3RF1	4	170043268	Silent	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	17974158	170043268	21111008	29	14166											
MFAP3L	9848	hgsc.bcm.edu	37	chr4	170926948	170926948	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgttagtcacactcttagcGgtggctagagtggatactag	9	12	12	8	1	2	1	1	0	1	1	2	2	2	2	0	3	2	2	0	3	5	5			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr4:170926948G>A	ENST00000361618.3	-	2	388	c.81C>T	c.(79-81)acC>acT	p.T27T	MFAP3L_ENST00000393702.3_Silent_p.T27T|MFAP3L_ENST00000506110.1_Silent_p.T27T|MFAP3L_ENST00000393704.3_5'Flank	NM_021647.6	NP_067679.6	O75121	MFA3L_HUMAN	microfibrillar-associated protein 3-like	27						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0201)|LUSC - Lung squamous cell carcinoma(193;0.116)		CACTCTTAGCGGTGGCTAGAG	0.453																																					p.T27T		Atlas-SNP	.											.	MFAP3L	59	.	0			c.C81T						PASS	.						103	102	102					4																	170926948		2203	4300	6503	SO:0001819	synonymous_variant	9848	exon2			CTTAGCGGTGGCT	AB014526	CCDS34103.1, CCDS43281.1	4q33	2014-08-12			ENSG00000198948	ENSG00000198948		"Immunoglobulin superfamily / I-set domain containing"	29083	protein-coding gene	gene with protein product						9734811	Standard	XM_005263366		Approved	KIAA0626, NYD-sp9	uc003isp.4	O75121	OTTHUMG00000160942	ENST00000361618.3:c.81C>T	4.37:g.170926948G>A		81	0	0		69	19	0.275362	NM_021647	A8K1X6|D3DP35|Q4W5N7|Q4W5N9|Q6TNA8|Q9BVE1|Q9BXK0	Silent	SNP	ENST00000361618.3	37	CCDS34103.1																																																																																			.	.	none		0.453	MFAP3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363043.2	NM_021647		A	170926948	G	A	170926948	2	1	35	1	0	0	0	0	0	0	0	1	9525	1103	39	1		1	MFAP3L	4	170926948	Silent	SNP	G	TCGA-GS-A9TQ-01A-11D-A382-10	883680	170926948	20227328	30	14167											
FAT1	2195	hgsc.bcm.edu	37	chr4	187549438	187549438	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taggaggaagcggtgaaccaCggggcgtggtcattcgtgtc	8	8	17	8	4	1	1	1	1	0	0	3	3	1	3	1	6	2	0	1	6	3	2	rs370954148		TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr4:187549438C>T	ENST00000441802.2	-	9	4889	c.4680G>A	c.(4678-4680)ccG>ccA	p.P1560P		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1560	Cadherin 13. {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						CGGTGAACCACGGGGCGTGGT	0.498										HNSCC(5;0.00058)																											p.P1560P	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											FAT1,NS,carcinoma,0,2	FAT1	500	2	0			c.G4680A						PASS	.	C		0,4196		0,0,2098	54	57	56		4680	-1.7	1	4		56	1,8461		0,1,4230	no	coding-synonymous	FAT1	NM_005245.3		0,1,6328	TT,TC,CC		0.0118,0.0,0.0079		1560/4589	187549438	1,12657	2098	4231	6329	SO:0001819	synonymous_variant	2195	exon9			GAACCACGGGGCG	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.4680G>A	4.37:g.187549438C>T		159	0	0		82	21	0.256098	NM_005245		Silent	SNP	ENST00000441802.2	37	CCDS47177.1																																																																																			.	.	weak		0.498	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		T	187549438	C	T	187549438	2	4	35	1	0	0	0	0	0	0	0	1	5697	523	19	1		1	FAT1	4	187549438	Silent	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	16622490	187549438	3604838	31	14168											
ADCY2	108	hgsc.bcm.edu	37	chr5	7766914	7766914	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcgcagaatttatttttcCtcccggtaagaacattgcaa	11	13	8	9	2	0	2	0	0	0	2	2	2	2	2	2	1	3	3	2	1	5	6			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr5:7766914C>T	ENST00000338316.4	+	17	2298	c.2209C>T	c.(2209-2211)Ctc>Ttc	p.L737F	ADCY2_ENST00000537121.1_Missense_Mutation_p.L557F	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	737					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						TTTATTTTTCCTCCCGGTAAG	0.428																																					p.L737F		Atlas-SNP	.											.	ADCY2	337	.	0			c.C2209T						PASS	.						188	194	192					5																	7766914		2203	4300	6503	SO:0001583	missense	108	exon17			TTTTTCCTCCCGG	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.2209C>T	5.37:g.7766914C>T	ENSP00000342952:p.Leu737Phe	216	0	0		137	27	0.19708	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Missense_Mutation	SNP	ENST00000338316.4	37	CCDS3872.2	.	.	.	.	.	.	.	.	.	.	C	12.67	2.008322	0.35415	.	.	ENSG00000078295	ENST00000338316;ENST00000541993;ENST00000537121	T;D	0.81908	-1.08;-1.55	5.46	5.46	0.80206	.	0.068532	0.64402	N	0.000019	T	0.81064	0.4745	L	0.60455	1.87	0.49582	D	0.999802	B;B	0.14805	0.005;0.011	B;B	0.17979	0.019;0.02	T	0.76250	-0.3028	10	0.38643	T	0.18	.	16.0386	0.80648	0.0:1.0:0.0:0.0	.	557;737	B7Z2C1;Q08462	.;ADCY2_HUMAN	F	737;570;557	ENSP00000342952:L737F;ENSP00000444803:L557F	ENSP00000342952:L737F	L	+	1	0	ADCY2	7819914	1.000000	0.71417	0.999000	0.59377	0.978000	0.69477	3.754000	0.55189	2.559000	0.86315	0.655000	0.94253	CTC	.	.	none		0.428	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546		T	7766914	C	T	7766914	3	4	35	1	0	0	0	0	1	0	0	0	294	681	24	2	2275	2	ADCY2	5	7766914	Missense_Mutation	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10		7766914	173148346	32	14169											
CDH18	1016	hgsc.bcm.edu	37	chr5	19571926	19571926	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagggtatatgacttcttttTctcatagttcagtggctgtg	7	17	11	6	0	3	1	2	1	2	0	4	2	3	1	0	2	0	3	0	2	3	7			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr5:19571926T>A	ENST00000507958.1	-	10	2005	c.1015A>T	c.(1015-1017)Aaa>Taa	p.K339*	CDH18_ENST00000274170.4_Nonsense_Mutation_p.K339*|CDH18_ENST00000511273.1_Nonsense_Mutation_p.K339*|CDH18_ENST00000506372.1_Nonsense_Mutation_p.K339*|CDH18_ENST00000502796.1_Nonsense_Mutation_p.K339*|CDH18_ENST00000382275.1_Nonsense_Mutation_p.K339*			Q13634	CAD18_HUMAN	cadherin 18, type 2	339	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)					GACTTCTTTTTCTCATAGTTC	0.303																																					p.K339X		Atlas-SNP	.											.	CDH18	561	.	0			c.A1015T						PASS	.						62	65	64					5																	19571926		2203	4300	6503	SO:0001587	stop_gained	1016	exon8			TCTTTTTCTCATA	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.1015A>T	5.37:g.19571926T>A	ENSP00000425093:p.Lys339*	338	0	0		261	61	0.233716	NM_001167667	A8K0I2|B4DHG6|Q8N5Z2	Nonsense_Mutation	SNP	ENST00000507958.1	37	CCDS3889.1	.	.	.	.	.	.	.	.	.	.	T	47	13.320112	0.99734	.	.	ENSG00000145526	ENST00000382275;ENST00000507958;ENST00000542864;ENST00000274170;ENST00000506372;ENST00000502796;ENST00000515257;ENST00000511273	.	.	.	5.17	5.17	0.71159	.	0.048931	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.131	0.65253	0.0:0.0:0.0:1.0	.	.	.	.	X	339;339;339;339;339;339;285;339	.	.	K	-	1	0	CDH18	19607683	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.806000	0.69150	2.095000	0.63458	0.533000	0.62120	AAA	.	.	none		0.303	CDH18-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366747.1	NM_004934		A	19571926	T	A	19571926	4	1	35	1	0	0	0	0	0	1	0	0	3105	1792	62	5	1381	5	CDH18	5	19571926	Nonsense_Mutation	SNP	T	TCGA-GS-A9TQ-01A-11D-A382-10	11805012	19571926	161343334	33	14170											
IL6ST	3572	hgsc.bcm.edu	37	chr5	55237383	55237383	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgtagccactgtgtaccaCggtagaatactggacagtgc	10	10	11	10	1	1	1	0	0	1	1	1	2	1	2	2	2	4	3	2	2	5	4			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr5:55237383C>T	ENST00000381298.2	-	17	2596	c.2284G>A	c.(2284-2286)Gtg>Atg	p.V762M	IL6ST_ENST00000536319.1_3'UTR|IL6ST_ENST00000381287.4_3'UTR|IL6ST_ENST00000336909.5_Missense_Mutation_p.V762M|IL6ST_ENST00000502326.3_Missense_Mutation_p.V762M|CTD-2031P19.5_ENST00000576302.1_RNA|IL6ST_ENST00000381294.3_Missense_Mutation_p.V701M	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	762					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)				CTGTGTACCACGGTAGAATAC	0.483			O		hepatocellular ca																																p.V762M		Atlas-SNP	.		Dom	yes		5	5q11	3572	"interleukin 6 signal transducer (gp130, oncostatin M receptor)"		E	.	IL6ST	75	.	0			c.G2284A						PASS	.						145	144	144					5																	55237383		2203	4300	6503	SO:0001583	missense	3572	exon17			GTACCACGGTAGA	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.2284G>A	5.37:g.55237383C>T	ENSP00000370698:p.Val762Met	141	0	0		147	34	0.231293	NM_002184	A0N0L4|Q5FC04|Q9UQ41	Missense_Mutation	SNP	ENST00000381298.2	37	CCDS3971.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.376368	0.82682	.	.	ENSG00000134352	ENST00000381298;ENST00000336909;ENST00000381294	T;T;T	0.63580	0.3;0.3;-0.05	5.4	5.4	0.78164	.	0.000000	0.44688	D	0.000433	T	0.73481	0.3592	L	0.36672	1.1	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	0.75616	-0.3256	10	0.87932	D	0	.	19.5543	0.95335	0.0:1.0:0.0:0.0	.	762;701;762	Q17RA0;Q5FC04;P40189	.;.;IL6RB_HUMAN	M	762;762;701	ENSP00000370698:V762M;ENSP00000338799:V762M;ENSP00000370694:V701M	ENSP00000338799:V762M	V	-	1	0	IL6ST	55273140	1.000000	0.71417	0.961000	0.40146	0.713000	0.41058	5.413000	0.66399	2.687000	0.91594	0.557000	0.71058	GTG	.	.	none		0.483	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184		T	55237383	C	T	55237383	3	4	35	1	0	0	0	0	1	0	0	0	7712	536	19	1	476	1	IL6ST	5	55237383	Missense_Mutation	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	35665457	55237383	125677877	34	14171											
EGR1	1958	hgsc.bcm.edu	37	chr5	137801591	137801591	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgagcaacggggctccccaGttcctcggcgccgccggggc	4	5	15	17	5	0	1	0	1	0	0	3	1	2	1	5	5	2	3	5	5	1	1			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr5:137801591G>C	ENST00000239938.4	+	1	413	c.141G>C	c.(139-141)caG>caC	p.Q47H		NM_001964.2	NP_001955.1	P18146	EGR1_HUMAN	early growth response 1	47					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)			GGGCTCCCCAGTTCCTCGGCG	0.677																																					p.Q47H		Atlas-SNP	.											.	EGR1	52	.	0			c.G141C						PASS	.						52	49	50					5																	137801591		2203	4300	6503	SO:0001583	missense	1958	exon1			TCCCCAGTTCCTC	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.141G>C	5.37:g.137801591G>C	ENSP00000239938:p.Gln47His	130	0	0		83	22	0.26506	NM_001964		Missense_Mutation	SNP	ENST00000239938.4	37	CCDS4206.1	.	.	.	.	.	.	.	.	.	.	G	9.531	1.110797	0.20714	.	.	ENSG00000120738	ENST00000535792;ENST00000411801;ENST00000239938	T	0.09163	3.01	5.07	3.26	0.37387	.	0.120124	0.64402	D	0.000020	T	0.11410	0.0278	L	0.48642	1.525	0.36348	D	0.859902	B;B	0.21753	0.06;0.004	B;B	0.23275	0.045;0.002	T	0.07809	-1.0753	10	0.66056	D	0.02	-0.6163	11.2363	0.48942	0.0:0.2576:0.609:0.1334	.	47;47	B4DNX4;P18146	.;EGR1_HUMAN	H	47	ENSP00000239938:Q47H	ENSP00000239938:Q47H	Q	+	3	2	EGR1	137829490	1.000000	0.71417	1.000000	0.80357	0.389000	0.30415	1.087000	0.30865	0.700000	0.31782	-0.500000	0.04577	CAG	.	.	none		0.677	EGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251274.1	NM_001964		C	137801591	G	C	137801591	3	2	35	1	0	0	0	0	1	0	0	0	4973	1020	36	4	143	4	EGR1	5	137801591	Missense_Mutation	SNP	G	TCGA-GS-A9TQ-01A-11D-A382-10	82564208	137801591	43113669	35	14172											
PCDHA5	56143	hgsc.bcm.edu	37	chr5	140201632	140201632	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtgaattctcggatcgaccGggaggagctgtgccggcgga	7	8	17	9	5	1	1	0	1	1	0	3	6	1	5	2	5	2	1	2	5	1	1			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr5:140201632G>A	ENST00000529859.1	+	1	272	c.272G>A	c.(271-273)cGg>cAg	p.R91Q	PCDHA4_ENST00000512229.2_Intron|PCDHA5_ENST00000378126.3_Missense_Mutation_p.R91Q|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Missense_Mutation_p.R91Q|PCDHA1_ENST00000504120.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000530339.1_Intron	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	91	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)|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)			CGGATCGACCGGGAGGAGCTG	0.622																																					p.R91Q		Atlas-SNP	.											PCDHA5_ENST00000529859,NS,carcinoma,-1,2	PCDHA5	361	2	0			c.G272A						PASS	.						91	106	101					5																	140201632		2202	4300	6502	SO:0001583	missense	56143	exon1			TCGACCGGGAGGA	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.272G>A	5.37:g.140201632G>A	ENSP00000436557:p.Arg91Gln	99	0	0		90	14	0.155556	NM_018908	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	37	CCDS54917.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.765070	0.90020	.	.	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	T;T;T	0.53206	0.63;0.63;0.63	3.97	3.97	0.46021	Cadherin, N-terminal (1);Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.82185	0.4982	H	0.99565	4.63	0.37098	D	0.899752	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.992;0.989;0.989	D	0.92497	0.6005	9	0.87932	D	0	.	16.4728	0.84119	0.0:0.0:1.0:0.0	.	91;91;91	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	Q	91	ENSP00000433416:R91Q;ENSP00000436557:R91Q;ENSP00000367366:R91Q	ENSP00000367366:R91Q	R	+	2	0	PCDHA5	140181816	1.000000	0.71417	0.998000	0.56505	0.911000	0.54048	9.861000	0.99562	1.937000	0.56155	0.580000	0.79431	CGG	.	.	none		0.622	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908		A	140201632	G	A	140201632	3	1	35	1	0	0	0	0	1	0	0	0	11536	1116	39	1	274	1	PCDHA5	5	140201632	Missense_Mutation	SNP	G	TCGA-GS-A9TQ-01A-11D-A382-10	2400041	140201632	40713628	36	14173											
DSP	1832	hgsc.bcm.edu	37	chr6	7584954	7584954	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaggcctacaagaagggcCtaattgattatgaaaccttc	14	9	10	8	0	0	3	0	2	0	1	1	4	0	4	3	3	2	0	3	3	6	5			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr6:7584954C>T	ENST00000379802.3	+	24	7800	c.7459C>T	c.(7459-7461)Cta>Tta	p.L2487L	DSP_ENST00000418664.2_Silent_p.L1888L	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2487	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)		CAAGAAGGGCCTAATTGATTA	0.458																																					p.L2487L		Atlas-SNP	.											.	DSP	306	.	0			c.C7459T						PASS	.						105	111	109					6																	7584954		2203	4300	6503	SO:0001819	synonymous_variant	1832	exon24			AAGGGCCTAATTG	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.7459C>T	6.37:g.7584954C>T		65	0	0		90	66	0.733333	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Silent	SNP	ENST00000379802.3	37	CCDS4501.1																																																																																			.	.	none		0.458	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		T	7584954	C	T	7584954	2	4	35	1	0	0	0	0	0	0	0	1	4783	680	24	2		2	DSP	6	7584954	Silent	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10		7584954	163530113	37	14174											
KAAG1	353219	hgsc.bcm.edu	37	chr6	24358062	24358062	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcctcaccgcacccagggCgcgggatcgcctcctgaaac	7	4	12	18	5	1	1	1	1	0	0	3	2	2	2	5	3	1	1	5	3	1	0			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr6:24358062C>T	ENST00000274766.1	+	1	932	c.195C>T	c.(193-195)ggC>ggT	p.G65G	DCDC2_ENST00000378454.3_5'UTR	NM_181337.3	NP_851854.1	Q9UBP8	KAAG1_HUMAN	kidney associated antigen 1	65					immune response (GO:0006955)					central_nervous_system(1)|lung(1)|prostate(1)	3						GCACCCAGGGCGCGGGATCGC	0.667																																					p.G65G		Atlas-SNP	.											.	KAAG1	4	.	0			c.C195T						PASS	.						24	28	27					6																	24358062		2180	4266	6446	SO:0001819	synonymous_variant	353219	exon1			CCAGGGCGCGGGA	AF181722	CCDS4551.1	6p22.1	2010-11-23			ENSG00000146049	ENSG00000146049			21031	protein-coding gene	gene with protein product		608211				10601354	Standard	NM_181337		Approved	RU2, RU2AS	uc003ndz.1	Q9UBP8	OTTHUMG00000014354	ENST00000274766.1:c.195C>T	6.37:g.24358062C>T		75	0	0		99	13	0.131313	NM_181337		Silent	SNP	ENST00000274766.1	37	CCDS4551.1																																																																																			.	.	none		0.667	KAAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040001.1			T	24358062	C	T	24358062	2	4	35	1	0	0	0	0	0	0	0	1	7982	755	27	1		1	KAAG1	6	24358062	Silent	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	16773108	24358062	146757005	38	14175											
HIST1H1E	3008	hgsc.bcm.edu	37	chr6	26156745	26156745	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgggcccccggtgtccgagCtcattactaaagctgttgcc	6	10	11	14	2	1	0	1	0	0	0	2	1	2	0	4	2	4	3	4	2	3	3			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr6:26156745C>G	ENST00000304218.3	+	1	187	c.127C>G	c.(127-129)Ctc>Gtc	p.L43V	HIST1H2BD_ENST00000289316.2_5'Flank|HIST1H2BD_ENST00000377777.4_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	43	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						GGTGTCCGAGCTCATTACTAA	0.632																																					p.L43V		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.C127G						PASS	.						21	27	25					6																	26156745		2203	4299	6502	SO:0001583	missense	3008	exon1			TCCGAGCTCATTA	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.127C>G	6.37:g.26156745C>G	ENSP00000307705:p.Leu43Val	68	0	0		70	14	0.2	NM_005321	Q4VB25	Missense_Mutation	SNP	ENST00000304218.3	37	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	14.84	2.656485	0.47467	.	.	ENSG00000168298	ENST00000304218	T	0.26957	1.7	5.49	4.61	0.57282	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.065201	0.64402	D	0.000006	T	0.36880	0.0983	M	0.82433	2.59	0.58432	D	0.999999	P	0.37500	0.597	P	0.49953	0.627	T	0.38929	-0.9638	10	0.87932	D	0	-5.0498	15.0173	0.71597	0.1436:0.8564:0.0:0.0	.	43	P10412	H14_HUMAN	V	43	ENSP00000307705:L43V	ENSP00000307705:L43V	L	+	1	0	HIST1H1E	26264724	1.000000	0.71417	1.000000	0.80357	0.075000	0.17131	5.964000	0.70379	1.423000	0.47198	-0.181000	0.13052	CTC	.	.	none		0.632	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321		G	26156745	C	G	26156745	3	3	35	1	0	0	0	0	1	0	0	0	7135	797	28	4	129	4	HIST1H1E	6	26156745	Missense_Mutation	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	1798683	26156745	144958322	39	14176											
TFAP2B	7021	hgsc.bcm.edu	37	chr6	50803938	50803938	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtgggagaagttcagagaCggctgtcgccccctgaatgc	8	8	14	11	2	1	3	1	1	0	2	2	5	1	3	2	2	1	2	2	2	2	1			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr6:50803938C>T	ENST00000393655.3	+	4	935	c.766C>T	c.(766-768)Cgg>Tgg	p.R256W	TFAP2B_ENST00000263046.4_Missense_Mutation_p.R265W	NM_003221.3	NP_003212.2	Q92481	AP2B_HUMAN	transcription factor AP-2 beta (activating enhancer binding protein 2 beta)	256					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)	p.R256G(1)		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)					AGTTCAGAGACGGCTGTCGCC	0.498																																					p.R256W	Pancreas(116;1373 2332 5475 10752)	Atlas-SNP	.											TFAP2B,NS,carcinoma,0,1	TFAP2B	91	1	1	Substitution - Missense(1)	lung(1)	c.C766T						PASS	.						57	54	55					6																	50803938		2203	4300	6503	SO:0001583	missense	7021	exon4			CAGAGACGGCTGT	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.766C>T	6.37:g.50803938C>T	ENSP00000377265:p.Arg256Trp	59	0	0		67	10	0.149254	NM_003221	Q5JYX6|Q9NQ63|Q9NU99|Q9UJI7|Q9Y214|Q9Y3K3	Missense_Mutation	SNP	ENST00000393655.3	37	CCDS4934.2	.	.	.	.	.	.	.	.	.	.	C	15.72	2.917242	0.52546	.	.	ENSG00000008196	ENST00000393655;ENST00000263046	D;D	0.99051	-5.37;-5.37	5.44	3.61	0.41365	Transcription factor AP-2, C-terminal (1);	0.109437	0.64402	D	0.000016	D	0.99174	0.9714	M	0.92604	3.325	0.58432	D	0.999998	D	0.89917	1.0	D	0.83275	0.996	D	0.99690	1.1001	10	0.87932	D	0	-12.5531	8.0974	0.30837	0.2894:0.6377:0.0:0.0729	.	256	Q92481	AP2B_HUMAN	W	256;265	ENSP00000377265:R256W;ENSP00000263046:R265W	ENSP00000263046:R265W	R	+	1	2	TFAP2B	50911897	1.000000	0.71417	0.998000	0.56505	0.338000	0.28826	2.714000	0.47202	0.625000	0.30304	-0.157000	0.13467	CGG	.	.	none		0.498	TFAP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040886.3	NM_003221		T	50803938	C	T	50803938	3	4	35	1	0	0	0	0	1	0	0	0	15803	527	19	1	780	1	TFAP2B	6	50803938	Missense_Mutation	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	24647193	50803938	120311129	40	14177											
DST	667	hgsc.bcm.edu	37	chr6	56485371	56485371	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gttcttcctctactcgggacTtttgtttctttagttcagct	4	20	7	10	1	4	0	1	0	3	0	6	1	5	1	1	1	2	4	1	1	2	9			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr6:56485371T>G	ENST00000370765.6	-	23	3568	c.3461A>C	c.(3460-3462)aAg>aCg	p.K1154T	DST_ENST00000361203.3_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000244364.6_Intron|DST_ENST00000370788.2_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000370769.4_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000421834.2_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	0					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)			TACTCGGGACTTTTGTTTCTT	0.423																																					p.K1154T		Atlas-SNP	.											.	DST	1427	.	0			c.A3461C						PASS	.						184	178	180					6																	56485371		2203	4300	6503	SO:0001583	missense	667	exon23			CGGGACTTTTGTT	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.3461A>C	6.37:g.56485371T>G	ENSP00000359801:p.Lys1154Thr	190	0	0		226	32	0.141593	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	37	CCDS4959.1	.	.	.	.	.	.	.	.	.	.	T	14.77	2.635748	0.47049	.	.	ENSG00000151914	ENST00000370765	T	0.25250	1.81	4.46	4.46	0.54185	.	.	.	.	.	T	0.25644	0.0624	.	.	.	0.09310	N	0.999997	D	0.54964	0.969	P	0.55824	0.785	T	0.03157	-1.1066	7	0.27785	T	0.31	.	13.9147	0.63890	0.0:0.0:0.0:1.0	.	1154	Q03001-3	.	T	1154	ENSP00000359801:K1154T	ENSP00000359801:K1154T	K	-	2	0	DST	56593330	1.000000	0.71417	0.917000	0.36280	0.602000	0.36980	5.260000	0.65490	1.880000	0.54463	0.366000	0.22137	AAG	.	.	none		0.423	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2	NM_001723		G	56485371	T	G	56485371	3	3	35	1	0	0	0	0	1	0	0	0	4785	1609	56	5	16942	5	DST	6	56485371	Missense_Mutation	SNP	T	TCGA-GS-A9TQ-01A-11D-A382-10	5681433	56485371	114629696	41	14178											
TBX18	9096	hgsc.bcm.edu	37	chr6	85446869	85446869	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcccacataggagggagtcCtgggcggggcaaaggtctca	9	5	16	11	2	1	0	1	0	1	0	3	2	2	2	2	6	0	1	2	6	2	1			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr6:85446869C>T	ENST00000369663.5	-	8	1695	c.1358G>A	c.(1357-1359)aGg>aAg	p.R453K	TBX18_ENST00000606784.1_Intron	NM_001080508.1	NP_001073977.1	O95935	TBX18_HUMAN	T-box 18	453					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)	p.R453K(1)		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)		GGAGGGAGTCCTGGGCGGGGC	0.602																																					p.R453K		Atlas-SNP	.											TBX18,NS,carcinoma,0,1	TBX18	131	1	1	Substitution - Missense(1)	lung(1)	c.G1358A						PASS	.						98	89	92					6																	85446869		2203	4300	6503	SO:0001583	missense	9096	exon8			GGAGTCCTGGGCG	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.1358G>A	6.37:g.85446869C>T	ENSP00000358677:p.Arg453Lys	78	0	0		46	23	0.5	NM_001080508	A2RU13|Q7Z6U4|Q9UJI6	Missense_Mutation	SNP	ENST00000369663.5	37	CCDS34495.1	.	.	.	.	.	.	.	.	.	.	C	19.50	3.839155	0.71373	.	.	ENSG00000112837	ENST00000369663	D	0.87334	-2.24	5.48	4.59	0.56863	.	0.071026	0.64402	D	0.000017	D	0.86049	0.5840	L	0.32530	0.975	0.58432	D	0.999997	D	0.67145	0.996	D	0.75484	0.986	D	0.84996	0.0897	10	0.27082	T	0.32	.	16.1361	0.81490	0.0:0.866:0.134:0.0	.	453	O95935	TBX18_HUMAN	K	453	ENSP00000358677:R453K	ENSP00000358677:R453K	R	-	2	0	TBX18	85503588	1.000000	0.71417	1.000000	0.80357	0.741000	0.42261	6.367000	0.73099	1.277000	0.44412	0.585000	0.79938	AGG	.	.	none		0.602	TBX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041378.2	NM_001080508		T	85446869	C	T	85446869	3	4	35	1	0	0	0	0	1	0	0	0	15668	681	24	2	469	2	TBX18	6	85446869	Missense_Mutation	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	28961498	85446869	85668198	42	14179											
SYNE1	23345	hgsc.bcm.edu	37	chr6	152737628	152737629	+	Frame_Shift_Ins	INS	-	-	T																															tctttctggtcttggaatgcINSttttttcaacactgccagag																										TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr6:152737628_152737629insT	ENST00000367255.5	-	41	6544_6545	c.5943_5944insA	c.(5941-5946)aaagcafs	p.A1982fs	SYNE1_ENST00000341594.5_Frame_Shift_Ins_p.A2019fs|SYNE1_ENST00000265368.4_Frame_Shift_Ins_p.A1982fs|SYNE1_ENST00000423061.1_Frame_Shift_Ins_p.A1989fs|SYNE1_ENST00000448038.1_Frame_Shift_Ins_p.A1989fs	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1982					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)		TCTTGGAATGCTTTTTTCAACA	0.495										HNSCC(10;0.0054)																											p.A1989fs		Pindel,Atlas-Indel	.											.	SYNE1	3227	.	0			c.5965_5966insA						PASS	.																																			SO:0001589	frameshift_variant	23345	exon41			.	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.5944dupA	6.37:g.152737634_152737634dupT	ENSP00000356224:p.Ala1982fs	255	0	.		107	24	0.224	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Frame_Shift_Ins	INS	ENST00000367255.5	37	CCDS5236.2																																																																																			.	.	none		0.495	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961		T	152737629	-	T	152737628	7	5	35	1	0	1	1	0	0	0	0	0	15460	797	28	0	20946	0	SYNE1	6	152737628	Frame_Shift_Ins	INS	-	TCGA-GS-A9TQ-01A-11D-A382-10	67290759	152737628	18377439	43	14180											
CNPY4	245812	hgsc.bcm.edu	37	chr7	99720170	99720170	+	Frame_Shift_Del	DEL	T	T	-																															ctggactatagtgttcacgcTgagcgcaagggctcactgag																										TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr7:99720170delT	ENST00000262932.3	+	3	444	c.312delT	c.(310-312)gctfs	p.A104fs	CNPY4_ENST00000480692.1_3'UTR|TAF6_ENST00000437822.2_5'Flank|RP11-506M12.1_ENST00000494221.1_RNA	NM_152755.1	NP_689968.1	Q8N129	CNPY4_HUMAN	canopy FGF signaling regulator 4	104						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)					GTGTTCACGCTGAGCGCAAGG	0.522																																					p.A104fs		Atlas-Indel	.											.	CNPY4	18	.	0			c.311delC						PASS	.						101	106	105					7																	99720170		2203	4300	6503	SO:0001589	frameshift_variant	245812	exon3			.	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.312delT	7.37:g.99720170delT	ENSP00000262932:p.Ala104fs	47	0	0		87	17	0.195402	NM_152755	Q8WUN9	Frame_Shift_Del	DEL	ENST00000262932.3	37	CCDS34701.1																																																																																			.	.	none		0.522	CNPY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337224.4	NM_152755		-	99720170	T	-	99720170	7	5	35	1	0	1	0	1	0	0	0	0	3632	1567	55	0	322	0	CNPY4	7	99720170	Frame_Shift_Del	DEL	T	TCGA-GS-A9TQ-01A-11D-A382-10		99720170	59418493	44	14181											
PPP1R3A	5506	hgsc.bcm.edu	37	chr7	113518866	113518866	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcgatgggcctgtcacttcGtgctgtctcttgaggtagct	4	14	12	11	2	2	1	1	1	1	0	5	2	2	1	1	2	2	3	1	2	1	3			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr7:113518866G>A	ENST00000284601.3	-	4	2349	c.2281C>T	c.(2281-2283)Cga>Tga	p.R761*		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	761					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						CTGTCACTTCGTGCTGTCTCT	0.413																																					p.R761X		Atlas-SNP	.											PPP1R3A,trunk,malignant_melanoma,+1,1	PPP1R3A	317	1	0			c.C2281T						PASS	.						126	112	117					7																	113518866		2203	4299	6502	SO:0001587	stop_gained	5506	exon4			CACTTCGTGCTGT	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.2281C>T	7.37:g.113518866G>A	ENSP00000284601:p.Arg761*	183	0	0		127	37	0.291339	NM_002711	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Nonsense_Mutation	SNP	ENST00000284601.3	37	CCDS5759.1	.	.	.	.	.	.	.	.	.	.	G	37	6.149618	0.97324	.	.	ENSG00000154415	ENST00000284601	.	.	.	5.75	3.92	0.45320	.	0.606928	0.14573	N	0.311310	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	-7.4711	11.6747	0.51424	0.0:0.2503:0.6199:0.1298	.	.	.	.	X	761	.	ENSP00000284601:R761X	R	-	1	2	PPP1R3A	113306102	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	1.237000	0.32695	0.748000	0.32831	0.650000	0.86243	CGA	.	.	none		0.413	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711		A	113518866	G	A	113518866	4	1	35	1	0	0	0	0	0	1	0	0	12383	1153	40	1	1091	1	PPP1R3A	7	113518866	Nonsense_Mutation	SNP	G	TCGA-GS-A9TQ-01A-11D-A382-10	13798696	113518866	45619797	45	14182											
ABP1	26	hgsc.bcm.edu	37	chr7	150557673	150557673	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aacgacccctggcacccgccCgtggtctttgagcagtttct	6	10	10	15	3	2	1	0	1	2	0	2	2	2	1	4	2	2	3	4	2	1	2	rs375543270		TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr7:150557673C>T	ENST00000493429.1	+	6	2525	c.1941C>T	c.(1939-1941)ccC>ccT	p.P647P	AOC1_ENST00000467291.1_Silent_p.P647P|AOC1_ENST00000416793.2_Silent_p.P666P|AOC1_ENST00000480582.1_3'UTR|AOC1_ENST00000360937.4_Silent_p.P647P			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	647					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)	GGCACCCGCCCGTGGTCTTTG	0.617																																					p.P666P		Atlas-SNP	.											.	ABP1	92	.	0			c.C1998T						PASS	.						101	116	111					7																	150557673		2085	4217	6302	SO:0001819	synonymous_variant	26	exon4			CCCGCCCGTGGTC	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.1941C>T	7.37:g.150557673C>T		45	0	0		23	9	0.391304	NM_001272072	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Silent	SNP	ENST00000493429.1	37	CCDS43679.1	.	.	.	.	.	.	.	.	.	.	C	5.686	0.311190	0.10789	.	.	ENSG00000002726	ENST00000487631	.	.	.	5.05	-3.73	0.04398	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.2137	0.25947	0.1403:0.5182:0.0:0.3415	.	.	.	.	.	-1	.	.	.	+	.	.	ABP1	150188606	0.000000	0.05858	0.964000	0.40570	0.466000	0.32739	-3.706000	0.00388	-0.720000	0.04935	-0.339000	0.08088	.	.	.	weak		0.617	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091		T	150557673	C	T	150557673	2	4	35	1	0	0	0	0	0	0	0	1	98	639	23	1		1	ABP1	7	150557673	Silent	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	37038807	150557673	8580990	46	14183											
EXTL3	2137	hgsc.bcm.edu	37	chr8	28588800	28588800	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taccctggaatgaaattgagAcagaggccatcctgtccatt	12	10	9	10	0	0	3	0	2	0	2	2	5	2	4	4	2	1	0	4	2	3	3			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr8:28588800A>T	ENST00000220562.4	+	4	3111	c.2209A>T	c.(2209-2211)Aca>Tca	p.T737S	EXTL3_ENST00000523149.1_Missense_Mutation_p.T353S|EXTL3_ENST00000519886.1_Intron	NM_001440.2	NP_001431.1	O43909	EXTL3_HUMAN	exostosin-like glycosyltransferase 3	737					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)		TGAAATTGAGACAGAGGCCAT	0.433																																					p.T737S		Atlas-SNP	.											.	EXTL3	83	.	0			c.A2209T						PASS	.						133	121	125					8																	28588800		2203	4300	6503	SO:0001583	missense	2137	exon4			ATTGAGACAGAGG	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.2209A>T	8.37:g.28588800A>T	ENSP00000220562:p.Thr737Ser	82	0	0		76	40	0.526316	NM_001440	D3DST8|O00225|Q53XT3	Missense_Mutation	SNP	ENST00000220562.4	37	CCDS6070.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	28.5|28.5	4.928506|4.928506	0.92389|0.92389	.|.	.|.	ENSG00000012232|ENSG00000012232	ENST00000521473|ENST00000523149;ENST00000220562;ENST00000521532	.|D;D;D	.|0.92595	.|-3.07;-3.07;-3.07	5.13|5.13	5.13|5.13	0.70059|0.70059	.|EXTL2, alpha-1,4-N-acetylhexosaminyltransferase (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.96734|0.96734	0.8934|0.8934	M|M	0.91140|0.91140	3.18|3.18	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.97110	.|1.0	D|D	0.97429|0.97429	1.0014|1.0014	5|10	.|0.62326	.|D	.|0.03	-11.0701|-11.0701	15.1147|15.1147	0.72392|0.72392	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|737	.|O43909	.|EXTL3_HUMAN	V|S	70|353;737;35	.|ENSP00000428691:T353S;ENSP00000220562:T737S;ENSP00000431013:T35S	.|ENSP00000220562:T737S	D|T	+|+	2|1	0|0	EXTL3|EXTL3	28644719|28644719	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.922000|0.922000	0.55478|0.55478	8.989000|8.989000	0.93506|0.93506	2.150000|2.150000	0.67090|0.67090	0.477000|0.477000	0.44152|0.44152	GAC|ACA	.	.	none		0.433	EXTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219987.3	NM_001440		T	28588800	A	T	28588800	3	4	35	1	0	0	0	0	1	0	0	0	5329	275	10	5	2215	5	EXTL3	8	28588800	Missense_Mutation	SNP	A	TCGA-GS-A9TQ-01A-11D-A382-10		28588800	117775222	47	14184											
CYP11B1	1584	hgsc.bcm.edu	37	chr8	143958274	143958274	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtggccaaccaggcccagcCgctctccaaaaagagccaag	12	4	10	15	1	1	1	0	0	1	1	2	1	1	1	6	2	3	1	6	2	4	0	rs200559974		TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr8:143958274C>T	ENST00000292427.4	-	4	655	c.623G>A	c.(622-624)cGg>cAg	p.R208Q	CYP11B1_ENST00000517471.1_Missense_Mutation_p.R208Q|CYP11B1_ENST00000377675.3_Missense_Mutation_p.R279Q	NM_000497.3	NP_000488.3	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 1	208					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)	CAGGCCCAGCCGCTCTCCAAA	0.622									Familial Hyperaldosteronism type I				.|||	1	0.000199681	0.0	0.0	5008	,	,		19702	0.001		0.0	False		,,,				2504	0.0				p.R208Q		Atlas-SNP	.											CYP11B1,NS,carcinoma,+1,1	CYP11B1	128	1	0			c.G623A						PASS	.						31	33	33					8																	143958274		2203	4300	6503	SO:0001583	missense	1584	exon4	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	CCCAGCCGCTCTC	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.623G>A	8.37:g.143958274C>T	ENSP00000292427:p.Arg208Gln	105	0	0		150	66	0.44	NM_000497	Q14095|Q4VAQ8|Q4VAQ9|Q9UML2	Missense_Mutation	SNP	ENST00000292427.4	37	CCDS6392.1	.	.	.	.	.	.	.	.	.	.	.	26.2	4.714828	0.89112	.	.	ENSG00000160882	ENST00000292427;ENST00000517471;ENST00000377675	T;T;T	0.70631	-0.5;2.55;-0.5	4.3	4.3	0.51218	.	0.000000	0.47852	D	0.000205	D	0.85961	0.5819	M	0.90369	3.11	0.50313	D	0.999863	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.87885	0.2680	10	0.46703	T	0.11	.	14.6015	0.68445	0.0:1.0:0.0:0.0	.	279;208;208	Q4VAR0;Q4VAQ9;P15538	.;.;C11B1_HUMAN	Q	208;208;279	ENSP00000292427:R208Q;ENSP00000428043:R208Q;ENSP00000366903:R279Q	ENSP00000292427:R208Q	R	-	2	0	CYP11B1	143955276	0.993000	0.37304	1.000000	0.80357	0.754000	0.42855	2.707000	0.47143	2.086000	0.62901	0.650000	0.86243	CGG	C|0.999;T|0.001	0.001	weak		0.622	CYP11B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379475.2			T	143958274	C	T	143958274	3	4	35	1	0	0	0	0	1	0	0	0	4147	652	23	1	912	1	CYP11B1	8	143958274	Missense_Mutation	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	115369474	143958274	2405748	48	14185											
SETX	23064	hgsc.bcm.edu	37	chr9	135221697	135221698	+	Frame_Shift_Ins	INS	-	-	GGAACTC																															atttcagtatttcaagaagaINSggaactcgaagcttattttc																										TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr9:135221697_135221698insGGAACTC	ENST00000224140.5	-	4	520_521	c.338_339insGAGTTCC	c.(337-339)cctfs	p.-113fs	SETX_ENST00000372169.2_Frame_Shift_Ins_p.-113fs|SETX_ENST00000393220.1_Frame_Shift_Ins_p.-113fs	NM_015046.5	NP_055861.3	Q7Z333	SETX_HUMAN	senataxin						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)		TTTCAAGAAGAGGAACTCGAAG	0.342																																					p.P113fs		Pindel,Atlas-Indel	.											SETX,NS,carcinoma,-2,1	SETX	234	1	0			c.339_340insGAGTTCC						PASS	.																																			SO:0001589	frameshift_variant	23064	exon4			.	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.332_338dupGAGTTCC	9.37:g.135221698_135221704dupGGAACTC	ENSP00000224140:p.Pro113fs	144	0	.		85	27	0.318	NM_015046	A2A396|B2RPB2|B5ME16|C9JQ10|O75120|Q3KQX4|Q5JUJ1|Q68DW5|Q6AZD7|Q7Z3J6|Q8WX33|Q9H9D1|Q9NVP9	Frame_Shift_Ins	INS	ENST00000224140.5	37	CCDS6947.1																																																																																			.	.	none		0.342	SETX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054774.3	NM_015046		GGAACTC	135221698	-	GGAACTC	135221697	7	5	35	1	0	1	1	0	0	0	0	0	14156	291	11	0	7786	0	SETX	9	135221697	Frame_Shift_Ins	INS	-	TCGA-GS-A9TQ-01A-11D-A382-10		135221697	5991734	49	14186											
KIF5B	3799	hgsc.bcm.edu	37	chr10	32307310	32307310	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgtgtaaagtctgaagttcTtttgccttggattaagaaca	11	16	9	5	0	2	2	0	1	2	1	2	3	2	3	1	1	2	2	1	1	5	7			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr10:32307310T>C	ENST00000302418.4	-	22	2830	c.2373A>G	c.(2371-2373)aaA>aaG	p.K791K	KIF5B_ENST00000493889.1_Intron	NM_004521.2	NP_004512.1	P33176	KINH_HUMAN	kinesin family member 5B	791					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)				TCTGAAGTTCTTTTGCCTTGG	0.373			T	"RET, ALK"	NSCLC																																p.K791K		Atlas-SNP	.		Dom	yes		10	10p11.22	3799	kinesin family member 5B		E	.	KIF5B	81	.	0			c.A2373G						PASS	.						138	135	136					10																	32307310		2203	4300	6503	SO:0001819	synonymous_variant	3799	exon22			AAGTTCTTTTGCC	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.2373A>G	10.37:g.32307310T>C		187	0	0		200	43	0.215	NM_004521	A0AVB2|Q5VZ85	Silent	SNP	ENST00000302418.4	37	CCDS7171.1																																																																																			.	.	none		0.373	KIF5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047467.1	NM_004521		C	32307310	T	C	32307310	2	2	35	1	0	0	0	0	0	0	0	1	8315	1606	56	3		3	KIF5B	10	32307310	Silent	SNP	T	TCGA-GS-A9TQ-01A-11D-A382-10		32307310	103227437	50	14187											
JMJD1C	221037	hgsc.bcm.edu	37	chr10	64966940	64966940	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcagtctcactggcattacTacttttatactgagctgcag	9	15	7	10	0	2	1	2	1	1	0	3	1	2	1	0	1	5	3	0	1	4	6			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr10:64966940T>C	ENST00000399262.2	-	10	4707	c.4489A>G	c.(4489-4491)Agt>Ggt	p.S1497G	JMJD1C_ENST00000542921.1_Missense_Mutation_p.S1315G|JMJD1C_ENST00000402544.1_Missense_Mutation_p.S1278G|JMJD1C_ENST00000399251.1_Missense_Mutation_p.S1278G	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	1497					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)					CTGGCATTACTACTTTTATAC	0.408																																					p.S1497G		Atlas-SNP	.											.	JMJD1C	347	.	0			c.A4489G						PASS	.						105	100	102					10																	64966940		1886	4113	5999	SO:0001583	missense	221037	exon10			CATTACTACTTTT	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.4489A>G	10.37:g.64966940T>C	ENSP00000382204:p.Ser1497Gly	147	0	0		177	27	0.152542	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	37	CCDS41532.1	.	.	.	.	.	.	.	.	.	.	T	10.93	1.490177	0.26686	.	.	ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000399251;ENST00000542921	T;T;T;T	0.56275	0.84;0.47;2.38;0.82	5.75	4.6	0.57074	.	0.145674	0.64402	D	0.000008	T	0.40767	0.1130	L	0.29908	0.895	0.40990	D	0.984842	B;B;B	0.13145	0.007;0.007;0.007	B;B;B	0.11329	0.004;0.006;0.004	T	0.36792	-0.9733	10	0.52906	T	0.07	-16.6876	11.907	0.52717	0.0:0.0691:0.0:0.9309	.	1038;1497;1315	A6PW35;Q15652;A0T124	.;JHD2C_HUMAN;.	G	1497;1278;1278;1315	ENSP00000382204:S1497G;ENSP00000384990:S1278G;ENSP00000382195:S1278G;ENSP00000444682:S1315G	ENSP00000382195:S1278G	S	-	1	0	JMJD1C	64636946	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	3.239000	0.51360	2.194000	0.70268	0.482000	0.46254	AGT	.	.	none		0.408	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		C	64966940	T	C	64966940	3	2	35	1	0	0	0	0	1	0	0	0	7959	1522	53	3	3201	3	JMJD1C	10	64966940	Missense_Mutation	SNP	T	TCGA-GS-A9TQ-01A-11D-A382-10	32659630	64966940	70567807	51	14188											
GPR120	338557	hgsc.bcm.edu	37	chr10	95335856	95335856	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttgtaactaggaaatttcGatttgcacactgatttggcc	10	16	8	7	1	0	1	0	1	0	0	1	3	0	2	1	2	2	2	1	2	3	7	rs377477484		TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr10:95335856G>T	ENST00000371483.4	+	2	632	c.576G>T	c.(574-576)tcG>tcT	p.S192S	FFAR4_ENST00000371481.4_Silent_p.S192S|FFAR4_ENST00000604414.1_Silent_p.S192S	NM_181745.3	NP_859529.2	Q5NUL3	FFAR4_HUMAN	free fatty acid receptor 4	192					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)										AGGAAATTTCGATTTGCACAC	0.433																																					p.S192S		Atlas-SNP	.											O3FAR1,NS,malignant_melanoma,+1,2	.	.	2	0			c.G576T						PASS	.						259	227	238					10																	95335856		2203	4300	6503	SO:0001819	synonymous_variant	338557	exon2			AATTTCGATTTGC		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.576G>T	10.37:g.95335856G>T		320	0	0		353	42	0.11898	NM_001195755	Q495H1|Q5VY25|Q5VY26|Q7Z605|Q86SM7	Silent	SNP	ENST00000371483.4	37	CCDS31248.1																																																																																			.	.	none		0.433	FFAR4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000083179.1	NM_181745		T	95335856	G	T	95335856	2	4	35	1	0	0	0	0	0	0	0	1	6644	1045	37	4		4	GPR120	10	95335856	Silent	SNP	G	TCGA-GS-A9TQ-01A-11D-A382-10	30368916	95335856	40198891	52	14189											
HPSE2	60495	hgsc.bcm.edu	37	chr10	100995457	100995457	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcctgggaggaaagggagaGatggagcaacagagccaagt	15	3	17	6	0	0	2	0	0	0	2	0	7	0	6	2	4	4	1	2	4	3	0			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr10:100995457G>T	ENST00000370552.3	-	1	162	c.103C>A	c.(103-105)Ctc>Atc	p.L35I	HPSE2_ENST00000370546.1_Missense_Mutation_p.L35I|HPSE2_ENST00000404542.1_Missense_Mutation_p.L35I|HPSE2_ENST00000370549.1_Missense_Mutation_p.L35I	NM_021828.4	NP_068600.4	Q8WWQ2	HPSE2_HUMAN	heparanase 2 (inactive)	35					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)		GAAAGGGAGAGATGGAGCAAC	0.592																																					p.L35I		Atlas-SNP	.											.	HPSE2	203	.	0			c.C103A						PASS	.						86	90	88					10																	100995457		2203	4300	6503	SO:0001583	missense	60495	exon1			GGGAGAGATGGAG	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.103C>A	10.37:g.100995457G>T	ENSP00000359583:p.Leu35Ile	131	0	0		157	25	0.159236	NM_001166246	Q5VUH4|Q5VUH5|Q5VUH6|Q8WWQ1|Q9HB37|Q9HB38|Q9HB39	Missense_Mutation	SNP	ENST00000370552.3	37	CCDS7477.1	.	.	.	.	.	.	.	.	.	.	G	14.93	2.680987	0.47886	.	.	ENSG00000172987	ENST00000370552;ENST00000370549;ENST00000370546;ENST00000404542	T;T;T;T	0.00473	7.18;7.18;7.18;7.18	5.8	4.9	0.64082	.	0.447080	0.23696	N	0.045468	T	0.00328	0.0010	L	0.36672	1.1	0.20821	N	0.999848	B;B;B;B	0.26809	0.16;0.16;0.069;0.041	B;B;B;B	0.21917	0.037;0.037;0.037;0.016	T	0.44667	-0.9313	10	0.26408	T	0.33	-10.382	7.4123	0.27023	0.2518:0.0:0.7482:0.0	.	35;35;35;35	Q8WWQ2-4;Q8WWQ2-2;Q8WWQ2-3;Q8WWQ2	.;.;.;HPSE2_HUMAN	I	35	ENSP00000359583:L35I;ENSP00000359580:L35I;ENSP00000359577:L35I;ENSP00000384384:L35I	ENSP00000359577:L35I	L	-	1	0	HPSE2	100985447	0.990000	0.36364	1.000000	0.80357	0.994000	0.84299	1.007000	0.29860	1.474000	0.48178	0.561000	0.74099	CTC	.	.	none		0.592	HPSE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049789.1	NM_021828		T	100995457	G	T	100995457	3	4	35	1	0	0	0	0	1	0	0	0	7354	942	33	4	1761	4	HPSE2	10	100995457	Missense_Mutation	SNP	G	TCGA-GS-A9TQ-01A-11D-A382-10	5659601	100995457	34539290	53	14190											
PDCD11	22984	hgsc.bcm.edu	37	chr10	105184917	105184917	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cagggtgtctccctaaccctCaagaccacagaaccaggagt	12	6	9	14	0	2	2	1	0	1	2	3	3	2	3	4	2	2	0	4	2	3	1			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr10:105184917C>G	ENST00000369797.3	+	20	3034	c.2940C>G	c.(2938-2940)ctC>ctG	p.L980L		NM_014976.1	NP_055791.1	Q14690	RRP5_HUMAN	programmed cell death 11	980					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)		CCCTAACCCTCAAGACCACAG	0.587																																					p.L980L		Atlas-SNP	.											.	PDCD11	160	.	0			c.C2940G						PASS	.						86	75	79					10																	105184917		2203	4300	6503	SO:0001819	synonymous_variant	22984	exon20			AACCCTCAAGACC	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.2940C>G	10.37:g.105184917C>G		70	0	0		94	18	0.191489	NM_014976	Q2TA92|Q5W093|Q6P2J3|Q86VQ8|Q9H4P1	Silent	SNP	ENST00000369797.3	37	CCDS31276.1																																																																																			.	.	none		0.587	PDCD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050151.1			G	105184917	C	G	105184917	2	3	35	1	0	0	0	0	0	0	0	1	11626	813	29	4		4	PDCD11	10	105184917	Silent	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	4189460	105184917	30349830	54	14191											
INPP5F	22876	hgsc.bcm.edu	37	chr10	121556996	121556996	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcgctataaacgaagaggaGtggataaaaatggaaatgtt	17	9	12	3	2	0	1	0	0	0	1	0	5	0	4	0	3	2	2	0	3	8	4			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr10:121556996G>A	ENST00000361976.2	+	8	1058	c.892G>A	c.(892-894)Gtg>Atg	p.V298M	INPP5F_ENST00000369083.3_Missense_Mutation_p.V298M	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)		ACGAAGAGGAGTGGATAAAAA	0.353																																					p.V298M		Atlas-SNP	.											.	INPP5F	112	.	0			c.G892A						PASS	.						89	80	83					10																	121556996		2203	4300	6503	SO:0001583	missense	22876	exon8			AGAGGAGTGGATA	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.892G>A	10.37:g.121556996G>A	ENSP00000354519:p.Val298Met	123	0	0		174	26	0.149425	NM_014937	A6NKI1|A8KAP2|B7ZLX2|O60800|Q15684|Q15774|Q4VY09|Q4VY10|Q5JQF1|Q5JQF2|Q9UJG5|Q9UMA5	Missense_Mutation	SNP	ENST00000361976.2	37	CCDS7616.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.767250	0.90020	.	.	ENSG00000198825	ENST00000361976;ENST00000369083	T;T	0.60171	0.21;0.21	5.65	5.65	0.86999	Synaptojanin, N-terminal (2);	0.061078	0.64402	D	0.000003	T	0.79834	0.4514	M	0.85859	2.78	0.80722	D	1	D	0.76494	0.999	D	0.71184	0.972	T	0.81996	-0.0676	10	0.87932	D	0	-20.0928	20.0781	0.97751	0.0:0.0:1.0:0.0	.	298	Q9Y2H2	SAC2_HUMAN	M	298	ENSP00000354519:V298M;ENSP00000358079:V298M	ENSP00000354519:V298M	V	+	1	0	INPP5F	121546986	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.172000	0.77604	2.817000	0.96982	0.563000	0.77884	GTG	.	.	none		0.353	INPP5F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050679.1	NM_014937		A	121556996	G	A	121556996	3	1	35	1	0	0	0	0	1	0	0	0	7767	1029	36	2	922	2	INPP5F	10	121556996	Missense_Mutation	SNP	G	TCGA-GS-A9TQ-01A-11D-A382-10	16372079	121556996	13977751	55	14192											
OR5R1	219479	hgsc.bcm.edu	37	chr11	56184896	56184896	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taaaatacagaagccatcttGtctgtgtccaaggagtgatt	13	12	9	7	0	2	2	0	1	2	1	3	3	3	3	2	1	2	0	2	1	5	4			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr11:56184896G>T	ENST00000312253.1	-	1	812	c.813C>A	c.(811-813)gaC>gaA	p.D271E		NM_001004744.1	NP_001004744.1	Q8NH85	OR5R1_HUMAN	olfactory receptor, family 5, subfamily R, 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)|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)					AAGCCATCTTGTCTGTGTCCA	0.423																																					p.D271E		Atlas-SNP	.											.	OR5R1	83	.	0			c.C813A						PASS	.						177	166	170					11																	56184896		2201	4296	6497	SO:0001583	missense	219479	exon1			CATCTTGTCTGTG	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.813C>A	11.37:g.56184896G>T	ENSP00000308595:p.Asp271Glu	178	0	0		165	36	0.218182	NM_001004744		Missense_Mutation	SNP	ENST00000312253.1	37	CCDS31530.1	.	.	.	.	.	.	.	.	.	.	G	12.02	1.813840	0.32053	.	.	ENSG00000174942	ENST00000312253	T	0.00227	8.5	5.62	-2.82	0.05787	GPCR, rhodopsin-like superfamily (1);	0.000000	0.34507	U	0.003901	T	0.00300	0.0009	L	0.59912	1.85	0.09310	N	1	D	0.76494	0.999	D	0.75484	0.986	T	0.53549	-0.8423	10	0.51188	T	0.08	-16.7854	2.7811	0.05361	0.3173:0.1061:0.4679:0.1086	.	271	Q8NH85	OR5R1_HUMAN	E	271	ENSP00000308595:D271E	ENSP00000308595:D271E	D	-	3	2	OR5R1	55941472	0.792000	0.28813	0.480000	0.27341	0.008000	0.06430	-0.321000	0.08018	-0.445000	0.07159	-0.925000	0.02716	GAC	.	.	none		0.423	OR5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334444.1	NM_001004744		T	56184896	G	T	56184896	3	4	35	1	0	0	0	0	1	0	0	0	11189	1368	48	4	163	4	OR5R1	11	56184896	Missense_Mutation	SNP	G	TCGA-GS-A9TQ-01A-11D-A382-10		56184896	78821620	56	14193											
FAU	740	hgsc.bcm.edu	37	chr11	64889115	64889115	+	5'Flank	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctccagtgaggctacatgaGcctacagggaaagataaggc	13	6	12	10	0	0	3	0	2	0	1	1	4	1	4	3	3	3	1	3	3	4	3			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr11:64889115G>C	ENST00000279242.2	+	0	0				FAU_ENST00000529259.1_Splice_Site_p.A26G|MRPL49_ENST00000531705.1_5'Flank|FAU_ENST00000527548.1_Splice_Site_p.A26G|FAU_ENST00000525297.1_Intron|MRPL49_ENST00000534078.1_5'Flank|FAU_ENST00000531743.1_Splice_Site_p.A26G|FAU_ENST00000279259.3_Splice_Site_p.A26G|MRPL49_ENST00000526171.1_5'Flank|FAU_ENST00000434372.2_Splice_Site_p.A26G|FAU_ENST00000529639.1_Splice_Site_p.A26G	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						GGCTACATGAGCCTACAGGGA	0.612																																					p.A26G		Atlas-SNP	.											.	FAU	17	.	0			c.C77G						PASS	.						59	52	54					11																	64889115		2201	4297	6498	SO:0001631	upstream_gene_variant	2197	exon3			ACATGAGCCTACA		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		11.37:g.64889115G>C	Exception_encountered	57	0	0		76	14	0.184211	NM_001997	B2R4G6	Missense_Mutation	SNP	ENST00000279242.2	37	CCDS8096.1	.	.	.	.	.	.	.	.	.	.	G	14.16	2.452215	0.43531	.	.	ENSG00000149806	ENST00000529639;ENST00000531743;ENST00000527548;ENST00000279259;ENST00000529259;ENST00000526555;ENST00000434372	T;T;T;T;T;T;T	0.74526	-0.85;-0.85;-0.85;-0.85;-0.85;-0.85;-0.85	6.17	3.2	0.36748	Ubiquitin supergroup (1);Ubiquitin conserved site (1);Ubiquitin (2);	0.257041	0.44688	D	0.000439	T	0.78214	0.4248	M	0.78637	2.42	0.29175	N	0.876885	B;P	0.40000	0.015;0.698	B;P	0.46975	0.075;0.533	T	0.74372	-0.3687	10	0.72032	D	0.01	.	9.7529	0.40485	0.0:0.1301:0.4671:0.4028	.	26;26	E9PMS9;P35544	.;UBIM_HUMAN	G	26	ENSP00000435370:A26G;ENSP00000431822:A26G;ENSP00000434440:A26G;ENSP00000279259:A26G;ENSP00000434680:A26G;ENSP00000433139:A26G;ENSP00000413848:A26G	ENSP00000279259:A26G	A	-	2	0	FAU	64645691	1.000000	0.71417	0.997000	0.53966	0.191000	0.23601	3.507000	0.53371	0.425000	0.26087	-0.169000	0.13324	GCT	.	.	none		0.612	MRPL49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385293.1	NM_004927		C	64889115	G	C	64889115	1	2	35	0	1	0	0	0	0	0	0	0	5702	985	34	4		4	FAU	11	64889115	5'Flank	SNP	G	TCGA-GS-A9TQ-01A-11D-A382-10	8704219	64889115	70117401	57	14194											
ANO1	55107	hgsc.bcm.edu	37	chr11	70009435	70009435	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtacattttccgttccttcCgaatggaagaggtaaccgaa	11	12	9	9	3	0	1	0	0	0	1	3	4	3	2	4	2	2	3	4	2	5	6			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr11:70009435C>T	ENST00000355303.5	+	19	2244	c.1939C>T	c.(1939-1941)Cga>Tga	p.R647*	ANO1_ENST00000531349.1_Nonsense_Mutation_p.R356*|ANO1_ENST00000538023.1_Nonsense_Mutation_p.R647*|ANO1_ENST00000530676.1_Nonsense_Mutation_p.R501*|ANO1_ENST00000398543.2_Nonsense_Mutation_p.R501*|ANO1_ENST00000316296.5_Nonsense_Mutation_p.R589*	NM_018043.5	NP_060513.5	Q5XXA6	ANO1_HUMAN	anoctamin 1, calcium activated chloride channel	647					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)	CCGTTCCTTCCGAATGGAAGA	0.517																																					p.R647X		Atlas-SNP	.											ANO1_ENST00000355303,NS,carcinoma,-1,2	ANO1	156	2	0			c.C1939T						PASS	.						65	68	67					11																	70009435		1947	4128	6075	SO:0001587	stop_gained	55107	exon19			TCCTTCCGAATGG	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.1939C>T	11.37:g.70009435C>T	ENSP00000347454:p.Arg647*	88	0	0		100	17	0.17	NM_018043	A8KAM3|Q8IYY8|Q8N7V3	Nonsense_Mutation	SNP	ENST00000355303.5	37	CCDS44663.1	.	.	.	.	.	.	.	.	.	.	C	34	5.291684	0.95546	.	.	ENSG00000131620	ENST00000355303;ENST00000538023;ENST00000398543;ENST00000546327;ENST00000316296;ENST00000530676;ENST00000531349	.	.	.	5.08	5.08	0.68730	.	0.137550	0.48767	D	0.000162	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8074	0.63240	0.1531:0.8469:0.0:0.0	.	.	.	.	X	647;647;501;405;589;501;356	.	.	R	+	1	2	ANO1	69687083	1.000000	0.71417	0.999000	0.59377	0.440000	0.31957	2.470000	0.45119	2.535000	0.85469	0.655000	0.94253	CGA	.	.	none		0.517	ANO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393685.1	NM_018043		T	70009435	C	T	70009435	4	4	35	1	0	0	0	0	0	1	0	0	695	644	23	1	2013	1	ANO1	11	70009435	Nonsense_Mutation	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	5120320	70009435	64997081	58	14195											
MLL2	8085	hgsc.bcm.edu	37	chr12	49420424	49420424	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaatggtagacattggggcAacgcatgcgattgcagctgc	12	8	13	8	2	0	1	0	0	0	1	0	2	0	1	0	3	5	5	0	3	4	3			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr12:49420424A>G	ENST00000301067.7	-	48	15324	c.15325T>C	c.(15325-15327)Tgc>Cgc	p.C5109R		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	5109			C -> F (in KABUK1). {ECO:0000269|PubMed:20711175}.		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)										ACATTGGGGCAACGCATGCGA	0.552																																					p.C5109R		Atlas-SNP	.											MLL2_ENST00000301067,NS,carcinoma,+1,2	MLL2	1173	2	0			c.T15325C						PASS	.						66	67	67					12																	49420424		2159	4254	6413	SO:0001583	missense	8085	exon48			TGGGGCAACGCAT	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.15325T>C	12.37:g.49420424A>G	ENSP00000301067:p.Cys5109Arg	56	0	0		70	17	0.242857	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	A	11.76	1.735995	0.30774	.	.	ENSG00000167548	ENST00000301067	D	0.94330	-3.4	4.58	4.58	0.56647	Zinc finger, RING-type (1);Zinc finger, PHD-type (1);	0.000000	0.39909	N	0.001227	D	0.97623	0.9221	H	0.96269	3.795	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98595	1.0656	10	0.87932	D	0	.	13.246	0.60024	1.0:0.0:0.0:0.0	.	5109	O14686	MLL2_HUMAN	R	5109	ENSP00000301067:C5109R	ENSP00000301067:C5109R	C	-	1	0	MLL2	47706691	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.339000	0.96797	1.844000	0.53588	0.459000	0.35465	TGC	.	.	none		0.552	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			G	49420424	A	G	49420424	3	3	35	1	0	0	0	0	1	0	0	0	9630	130	5	3	1316	3	MLL2	12	49420424	Missense_Mutation	SNP	A	TCGA-GS-A9TQ-01A-11D-A382-10		49420424	84431471	59	14196											
MLL2	8085	hgsc.bcm.edu	37	chr12	49428192	49428192	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcccacgccccatactcaCtgatcactccctgagcaaaa	11	7	4	19	1	2	2	2	2	0	0	4	2	4	2	5	0	2	1	5	0	3	1			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr12:49428192C>T	ENST00000301067.7	-	37	10507		c.e37+1		KMT2D_ENST00000549743.1_5'Flank	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)										CCCATACTCACTGATCACTCC	0.572																																					.		Atlas-SNP	.											.	MLL2	1173	.	0			c.10507+1G>A						PASS	.						43	46	45					12																	49428192		1961	4160	6121	SO:0001630	splice_region_variant	8085	exon38			TACTCACTGATCA	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.10507+1G>A	12.37:g.49428192C>T		35	0	0		32	20	0.625	NM_003482	O14687	Splice_Site	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.011341	0.93346	.	.	ENSG00000167548	ENST00000301067	.	.	.	5.51	5.51	0.81932	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.5761	0.91155	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MLL2	47714459	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.305000	0.78891	2.779000	0.95612	0.655000	0.94253	.	.	.	none		0.572	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		Intron	T	49428192	C	T	49428192	5	4	35	1	0	0	0	0	0	0	1	0	9630	579	20	2	6177	2	MLL2	12	49428192	Splice_Site	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	7768	49428192	84423703	60	14197											
KRT3	3850	hgsc.bcm.edu	37	chr12	53183951	53183951	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagagatggagccaaagcCgctgccaccgctgaaaccgc	11	3	12	15	3	0	2	0	1	0	1	0	4	0	3	6	1	4	2	6	1	2	0	rs570613061|rs60125653	byFrequency	TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr12:53183951C>T	ENST00000417996.2	-	9	1836	c.1762G>A	c.(1762-1764)Ggc>Agc	p.G588S	KRT3_ENST00000309505.3_Missense_Mutation_p.G589S	NM_057088.2	NP_476429.2	P12035	K2C3_HUMAN	keratin 3	588	Gly-rich.|Tail.				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						GAGCCAAAgccgctgccaccg	0.697																																					p.G588S		Atlas-SNP	.											KRT3,rectum,carcinoma,0,1	KRT3	65	1	0			c.G1762A						PASS	.						14	31	25					12																	53183951		1574	3123	4697	SO:0001583	missense	3850	exon9			CAAAGCCGCTGCC		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.1762G>A	12.37:g.53183951C>T	ENSP00000413479:p.Gly588Ser	45	0	0		42	8	0.190476	NM_057088	A6NIS2|Q701L8	Missense_Mutation	SNP	ENST00000417996.2	37	CCDS44895.1	.	.	.	.	.	.	.	.	.	.	C	13.67	2.307617	0.40795	.	.	ENSG00000186442	ENST00000417996;ENST00000309505	D;D	0.91351	-2.83;-2.83	3.4	-1.34	0.09143	.	0.507655	0.14827	N	0.296110	T	0.80149	0.4570	N	0.22421	0.69	0.09310	N	1	B	0.18166	0.026	B	0.08055	0.003	T	0.65302	-0.6201	10	0.34782	T	0.22	.	7.4497	0.27231	0.0:0.4872:0.0:0.5128	.	588	P12035	K2C3_HUMAN	S	588;589	ENSP00000413479:G588S;ENSP00000312206:G589S	ENSP00000312206:G589S	G	-	1	0	KRT3	51470218	0.000000	0.05858	0.005000	0.12908	0.008000	0.06430	-1.682000	0.01935	-0.284000	0.09102	-0.258000	0.10820	GGC	.	.	none		0.697	KRT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405930.1	NM_057088		T	53183951	C	T	53183951	3	4	35	1	0	0	0	0	1	0	0	0	8475	652	23	1	128	1	KRT3	12	53183951	Missense_Mutation	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	3755759	53183951	80667944	61	14198											
BCL7A	605	hgsc.bcm.edu	37	chr12	122460029	122460029	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtcggttcgagccgagacgaGgagccgggccaaagatgata	11	5	16	9	5	0	3	0	1	0	2	2	7	0	4	3	3	2	1	3	3	2	2			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr12:122460029G>C	ENST00000261822.4	+	1	238	c.32G>C	c.(31-33)aGg>aCg	p.R11T	BCL7A_ENST00000538010.1_Missense_Mutation_p.R11T|RP11-87C12.5_ENST00000538710.1_lincRNA	NM_001024808.1	NP_001019979.1	Q4VC05	BCL7A_HUMAN	B-cell CLL/lymphoma 7A	11					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)		GCCGAGACGAGGAGCCGGGCC	0.721			T	MYC	BNHL																																p.R11T	GBM(17;197 467 16477 23242 44349)	Atlas-SNP	.		Dom	yes		12	12q24.1	605	B-cell CLL/lymphoma 7A		L	BCL7A,NS,lymphoid_neoplasm,+1,2	BCL7A	31	2	0			c.G32C						scavenged	.						22	22	22					12																	122460029		2199	4296	6495	SO:0001583	missense	605	exon1			AGACGAGGAGCCG	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.32G>C	12.37:g.122460029G>C	ENSP00000261822:p.Arg11Thr	45	1	0.0222222		44	26	0.590909	NM_020993	B4DJN6|B7ZB21|Q13843|Q14CT7	Missense_Mutation	SNP	ENST00000261822.4	37	CCDS53841.1	.	.	.	.	.	.	.	.	.	.	G	16.64	3.179630	0.57800	.	.	ENSG00000110987	ENST00000538010;ENST00000261822	T;T	0.79653	-1.29;-1.14	4.24	2.39	0.29439	.	0.000000	0.85682	U	0.000000	D	0.87549	0.6205	M	0.79926	2.475	0.58432	D	0.999999	B;D	0.61080	0.322;0.989	B;D	0.75020	0.192;0.985	D	0.85773	0.1356	10	0.87932	D	0	.	8.2255	0.31566	0.1964:0.0:0.8036:0.0	.	11;11	Q4VC05;Q4VC05-2	BCL7A_HUMAN;.	T	11	ENSP00000445868:R11T;ENSP00000261822:R11T	ENSP00000261822:R11T	R	+	2	0	BCL7A	120944412	1.000000	0.71417	1.000000	0.80357	0.300000	0.27592	7.291000	0.78721	0.271000	0.22005	0.460000	0.39030	AGG	.	.	none		0.721	BCL7A-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000401712.1			C	122460029	G	C	122460029	3	2	35	1	0	0	0	0	1	0	0	0	1378	1000	35	4	34	4	BCL7A	12	122460029	Missense_Mutation	SNP	G	TCGA-GS-A9TQ-01A-11D-A382-10	69276078	122460029	11391866	62	14199											
PRKD1	5587	hgsc.bcm.edu	37	chr14	30046638	30046638	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gattttgcattccagctctcGcaaatctaaccaggtctgat	10	13	7	11	1	3	1	0	1	3	0	5	2	4	1	2	1	3	3	2	1	2	4			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr14:30046638G>T	ENST00000331968.5	-	18	2774	c.2545C>A	c.(2545-2547)Cga>Aga	p.R849R	PRKD1_ENST00000415220.2_Silent_p.R857R	NM_002742.2	NP_002733.2	Q15139	KPCD1_HUMAN	protein kinase D1	849					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)		TCCAGCTCTCGCAAATCTAAC	0.453																																					p.R849R		Atlas-SNP	.											PRKD1_ENST00000331968,NS,carcinoma,0,2	PRKD1	316	2	0			c.C2545A						PASS	.						99	93	95					14																	30046638		2203	4300	6503	SO:0001819	synonymous_variant	5587	exon18			GCTCTCGCAAATC		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.2545C>A	14.37:g.30046638G>T		132	0	0		114	30	0.263158	NM_002742	A6NL64|B2RAF6	Silent	SNP	ENST00000331968.5	37	CCDS9637.1																																																																																			.	.	none		0.453	PRKD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276611.2	NM_002742		T	30046638	G	T	30046638	2	4	35	1	0	0	0	0	0	0	0	1	12530	1095	38	4		4	PRKD1	14	30046638	Silent	SNP	G	TCGA-GS-A9TQ-01A-11D-A382-10		30046638	77302902	63	14200											
SPTB	6710	hgsc.bcm.edu	37	chr14	65253667	65253667	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atccacacgggcctggatggCggccacgtcacgctccagcc	7	5	12	17	4	1	0	1	0	0	0	3	1	3	1	5	4	1	1	5	4	0	0	rs151112486	byFrequency	TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr14:65253667C>T	ENST00000389721.5	-	15	3048	c.3016G>A	c.(3016-3018)Gcc>Acc	p.A1006T	SPTB_ENST00000389722.3_Missense_Mutation_p.A1006T|SPTB_ENST00000389720.3_Missense_Mutation_p.A1006T|SPTB_ENST00000542895.1_Missense_Mutation_p.A1006T|SPTB_ENST00000556626.1_Missense_Mutation_p.A1006T	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1006					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)		GCCTGGATGGCGGCCACGTCA	0.592																																					p.A1006T		Atlas-SNP	.											.	SPTB	378	.	0			c.G3016A						PASS	.		THR/ALA,THR/ALA	4,4402	8.1+/-20.4	0,4,2199	85	79	81		3016,3016	4.9	0.9	14	dbSNP_134	81	11,8589	8.4+/-32.0	0,11,4289	yes	missense,missense	SPTB	NM_000347.5,NM_001024858.2	58,58	0,15,6488	TT,TC,CC		0.1279,0.0908,0.1153	probably-damaging,probably-damaging	1006/2138,1006/2329	65253667	15,12991	2203	4300	6503	SO:0001583	missense	6710	exon15			GGATGGCGGCCAC		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.3016G>A	14.37:g.65253667C>T	ENSP00000374371:p.Ala1006Thr	45	0	0		38	16	0.421053	NM_001024858	Q15510|Q15519	Missense_Mutation	SNP	ENST00000389721.5	37	CCDS32100.1	.	.	.	.	.	.	.	.	.	.	C	31	5.079450	0.94050	9.08E-4	0.001279	ENSG00000070182	ENST00000389723;ENST00000389722;ENST00000556626;ENST00000389721;ENST00000542895;ENST00000389720	T;T;T;T;T	0.55588	0.51;0.51;0.51;0.51;0.51	4.89	4.89	0.63831	.	0.000000	0.85682	D	0.000000	T	0.78059	0.4224	M	0.90309	3.105	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.988	D	0.83450	0.0048	10	0.87932	D	0	.	17.1796	0.86851	0.0:1.0:0.0:0.0	.	1006;1010	P11277;Q59FP5	SPTB1_HUMAN;.	T	1010;1006;1006;1006;1006;1006	ENSP00000374372:A1006T;ENSP00000451752:A1006T;ENSP00000374371:A1006T;ENSP00000443882:A1006T;ENSP00000374370:A1006T	ENSP00000374370:A1006T	A	-	1	0	SPTB	64323420	1.000000	0.71417	0.946000	0.38457	0.843000	0.47879	6.078000	0.71282	2.430000	0.82344	0.549000	0.68633	GCC	C|0.999;T|0.001	0.001	strong		0.592	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1			T	65253667	C	T	65253667	3	4	35	1	0	0	0	0	1	0	0	0	15133	768	27	1	4123	1	SPTB	14	65253667	Missense_Mutation	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	35207029	65253667	42095873	64	14201											
FAM161B	145483	hgsc.bcm.edu	37	chr14	74411424	74411424	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggccttcttccgggcctcgCgcagcgtcatgcggaatggc	4	8	14	15	6	2	0	1	0	1	0	4	1	3	1	3	4	2	1	3	4	1	2			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr14:74411424C>T	ENST00000534936.1	-	3	644	c.539G>A	c.(538-540)cGc>cAc	p.R180H	FAM161B_ENST00000286544.3_Missense_Mutation_p.R243H			Q96MY7	F161B_HUMAN	family with sequence similarity 161, member B	180										breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)	21						CCGGGCCTCGCGCAGCGTCAT	0.672																																					p.R243H		Atlas-SNP	.											.	FAM161B	67	.	0			c.G728A						PASS	.						26	27	26					14																	74411424		2203	4300	6503	SO:0001583	missense	145483	exon3			GCCTCGCGCAGCG	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.539G>A	14.37:g.74411424C>T	ENSP00000445326:p.Arg180His	68	0	0		89	19	0.213483	NM_152445	B7Z882|J3KNA2	Missense_Mutation	SNP	ENST00000534936.1	37		.	.	.	.	.	.	.	.	.	.	C	20.7	4.035056	0.75617	.	.	ENSG00000156050	ENST00000286544;ENST00000534936	T;T	0.76316	-1.01;-1.01	5.17	5.17	0.71159	.	0.000000	0.64402	D	0.000002	D	0.89935	0.6859	M	0.87682	2.9	0.58432	D	0.999993	D	0.89917	1.0	D	0.97110	1.0	D	0.91329	0.5088	10	0.87932	D	0	-7.9894	18.8556	0.92251	0.0:1.0:0.0:0.0	.	180	Q96MY7	F161B_HUMAN	H	243;180	ENSP00000286544:R243H;ENSP00000445326:R180H	ENSP00000286544:R243H	R	-	2	0	FAM161B	73481177	1.000000	0.71417	0.996000	0.52242	0.200000	0.23975	5.085000	0.64468	2.688000	0.91661	0.563000	0.77884	CGC	.	.	none		0.672	FAM161B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_152445		T	74411424	C	T	74411424	3	4	35	1	0	0	0	0	1	0	0	0	5478	768	27	1	1432	1	FAM161B	14	74411424	Missense_Mutation	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	9157757	74411424	32938116	65	14202											
ENTPD5	957	hgsc.bcm.edu	37	chr14	74449761	74449761	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctttgtgttctggcagtaagCgtagtcctgctgttgccttt	4	17	11	9	1	1	0	0	0	1	0	2	0	2	0	2	1	3	6	2	1	2	6			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr14:74449761C>T	ENST00000334696.6	-	6	720	c.401G>A	c.(400-402)cGc>cAc	p.R134H	ENTPD5_ENST00000557325.1_Missense_Mutation_p.R134H	NM_001249.2	NP_001240.1	O75356	ENTP5_HUMAN	ectonucleoside triphosphate diphosphohydrolase 5	134					'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)		TGGCAGTAAGCGTAGTCCTGC	0.473																																					p.R134H		Atlas-SNP	.											.	ENTPD5	26	.	0			c.G401A						PASS	.						237	220	226					14																	74449761		2203	4300	6503	SO:0001583	missense	957	exon6			AGTAAGCGTAGTC	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.401G>A	14.37:g.74449761C>T	ENSP00000335246:p.Arg134His	86	0	0		99	20	0.20202	NM_001249	A1L4C5|Q96RX0	Missense_Mutation	SNP	ENST00000334696.6	37	CCDS9825.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.621905	0.87460	.	.	ENSG00000187097	ENST00000557325;ENST00000334696;ENST00000553284	T;T;T	0.41065	1.01;1.01;1.01	4.99	4.99	0.66335	.	0.055041	0.85682	D	0.000000	T	0.77725	0.4173	H	0.97962	4.115	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.86237	0.1641	10	0.87932	D	0	-9.958	16.2422	0.82418	0.0:1.0:0.0:0.0	.	134;134	O75356;G3V4I0	ENTP5_HUMAN;.	H	134	ENSP00000451810:R134H;ENSP00000335246:R134H;ENSP00000451591:R134H	ENSP00000335246:R134H	R	-	2	0	ENTPD5	73519514	1.000000	0.71417	0.999000	0.59377	0.686000	0.39977	6.469000	0.73555	2.593000	0.87608	0.655000	0.94253	CGC	.	.	none		0.473	ENTPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412637.1	NM_001249		T	74449761	C	T	74449761	3	4	35	1	0	0	0	0	1	0	0	0	5144	768	27	1	929	1	ENTPD5	14	74449761	Missense_Mutation	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	38337	74449761	32899779	66	14203											
SPTBN5	51332	hgsc.bcm.edu	37	chr15	42172481	42172482	+	Frame_Shift_Ins	INS	-	-	ATGG																															tgcagaaaccgaacagggccINSatggcctcctccaaccgggc																										TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr15:42172481_42172482insATGG	ENST00000320955.6	-	14	2914_2915	c.2687_2688insCCAT	c.(2686-2688)atgfs	p.M896fs		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	896					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)		CGAACAGGGCCATGGCCTCCTC	0.668																																					p.M861fs		Pindel,Atlas-Indel	.											.	SPTBN5	171	.	0			c.2583_2584insCCAT						PASS	.																																			SO:0001589	frameshift_variant	51332	exon14			.	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.2684_2687dupCCAT	15.37:g.42172482_42172485dupATGG	ENSP00000317790:p.Met896fs	111	0	.		69	18	0.261	NM_016642		Frame_Shift_Ins	INS	ENST00000320955.6	37																																																																																				.	.	none		0.668	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642		ATGG	42172482	-	ATGG	42172481	7	5	35	1	0	1	1	0	0	0	0	0	15137	594	21	0	8556	0	SPTBN5	15	42172481	Frame_Shift_Ins	INS	-	TCGA-GS-A9TQ-01A-11D-A382-10		42172481	60358911	67	14204											
SPG11	80208	hgsc.bcm.edu	37	chr15	44914049	44914049	+	Missense_Mutation	SNP	T	T	G																															caattctatggtcctgtttgTtaaattcatctttacaatca																										TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr15:44914049T>G	ENST00000261866.7	-	14	2544	c.2528A>C	c.(2527-2529)aAc>aCc	p.N843T	SPG11_ENST00000558319.1_Missense_Mutation_p.N843T|SPG11_ENST00000535302.2_Missense_Mutation_p.N843T|SPG11_ENST00000427534.2_Missense_Mutation_p.N843T	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	843					cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		GTCCTGTTTGTTAAATTCATC	0.373																																					p.N843T		Atlas-SNP	.											.	SPG11	207	.	0			c.A2528C						PASS	.						101	91	94					15																	44914049		2198	4298	6496	SO:0001583	missense	80208	exon14			TGTTTGTTAAATT		CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"spatacsin"	610844	"KIAA1840"	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.2528A>C	15.37:g.44914049T>G	ENSP00000261866:p.Asn843Thr	153	0	0		121	31	0.256198	NM_025137	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Missense_Mutation	SNP	ENST00000261866.7	37	CCDS10112.1	.	.	.	.	.	.	.	.	.	.	T	7.050	0.564336	0.13498	.	.	ENSG00000104133	ENST00000261866;ENST00000535302;ENST00000427534	T;T;T	0.77098	-1.07;-0.81;-0.8	5.76	0.577	0.17385	.	1.017420	0.07812	N	0.958341	T	0.61652	0.2364	L	0.43152	1.355	0.09310	N	1	B;B;B	0.13594	0.005;0.008;0.008	B;B;B	0.09377	0.004;0.004;0.004	T	0.40270	-0.9572	10	0.09084	T	0.74	.	0.8387	0.01145	0.1525:0.2224:0.1583:0.4668	.	843;843;843	C4B7M2;F5H3N6;Q96JI7	.;.;SPTCS_HUMAN	T	843	ENSP00000261866:N843T;ENSP00000445278:N843T;ENSP00000396110:N843T	ENSP00000261866:N843T	N	-	2	0	SPG11	42701341	0.000000	0.05858	0.984000	0.44739	0.994000	0.84299	-0.031000	0.12287	0.422000	0.26005	0.533000	0.62120	AAC	.	.	none		0.373	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1			G	44914049	T	G	44914049	3	3	35	1	0	0	0	0	1	0	0	0	15056	1725	60	5	4911	5	SPG11	15	44914049	Missense_Mutation	SNP	T	TCGA-GS-A9TQ-01A-11D-A382-10	2741568	44914049	57617343	68	14205	178	2									
SPG11	80208	hgsc.bcm.edu	37	chr15	44914054	44914054	+	Missense_Mutation	SNP	T	T	A																															ctatggtcctgtttgttaaaTtcatctttacaatcatattt																										TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr15:44914054T>A	ENST00000261866.7	-	14	2539	c.2523A>T	c.(2521-2523)gaA>gaT	p.E841D	SPG11_ENST00000558319.1_Missense_Mutation_p.E841D|SPG11_ENST00000535302.2_Missense_Mutation_p.E841D|SPG11_ENST00000427534.2_Missense_Mutation_p.E841D	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	841					cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		GTTTGTTAAATTCATCTTTAC	0.363																																					p.E841D		Atlas-SNP	.											.	SPG11	207	.	0			c.A2523T						PASS	.						98	88	91					15																	44914054		2198	4298	6496	SO:0001583	missense	80208	exon14			GTTAAATTCATCT		CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"spatacsin"	610844	"KIAA1840"	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.2523A>T	15.37:g.44914054T>A	ENSP00000261866:p.Glu841Asp	153	0	0		126	30	0.238095	NM_025137	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Missense_Mutation	SNP	ENST00000261866.7	37	CCDS10112.1	.	.	.	.	.	.	.	.	.	.	T	15.83	2.950200	0.53186	.	.	ENSG00000104133	ENST00000261866;ENST00000535302;ENST00000427534	T;T;T	0.78595	-1.19;-0.94;-0.93	5.76	3.48	0.39840	.	0.413681	0.26432	N	0.024404	T	0.64472	0.2601	L	0.36672	1.1	0.47441	D	0.999429	B;B;B	0.20988	0.005;0.05;0.005	B;B;B	0.17722	0.008;0.019;0.008	T	0.52859	-0.8519	10	0.23302	T	0.38	.	7.7834	0.29078	0.0:0.1583:0.0:0.8417	.	841;841;841	C4B7M2;F5H3N6;Q96JI7	.;.;SPTCS_HUMAN	D	841	ENSP00000261866:E841D;ENSP00000445278:E841D;ENSP00000396110:E841D	ENSP00000261866:E841D	E	-	3	2	SPG11	42701346	0.022000	0.18835	0.992000	0.48379	0.993000	0.82548	0.240000	0.18042	0.472000	0.27344	0.533000	0.62120	GAA	.	.	none		0.363	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1			A	44914054	T	A	44914054	3	1	35	1	0	0	0	0	1	0	0	0	15056	1490	52	5	4916	5	SPG11	15	44914054	Missense_Mutation	SNP	T	TCGA-GS-A9TQ-01A-11D-A382-10	5	44914054	57617338	69	14206	178	2									
MYO9A	4649	hgsc.bcm.edu	37	chr15	72122636	72122636	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacctggatagtttcctcgaCgaatacgcccctttccctgc	7	11	8	15	3	0	0	0	0	0	0	3	4	2	1	5	1	2	1	5	1	3	4			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr15:72122636C>T	ENST00000356056.5	-	40	7326	c.6854G>A	c.(6853-6855)cGt>cAt	p.R2285H	MYO9A_ENST00000444904.1_Missense_Mutation_p.R2266H|MYO9A_ENST00000424560.1_Missense_Mutation_p.R2356H|MYO9A_ENST00000564571.1_Missense_Mutation_p.R2285H	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	2285	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						GTTTCCTCGACGAATACGCCC	0.443																																					p.R2285H		Atlas-SNP	.											MYO9A,colon,carcinoma,-1,2	MYO9A	203	2	0			c.G6854A						scavenged	.						92	92	92					15																	72122636		2199	4297	6496	SO:0001583	missense	4649	exon40			CCTCGACGAATAC	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.6854G>A	15.37:g.72122636C>T	ENSP00000348349:p.Arg2285His	83	1	0.0120482		58	17	0.293103	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	37	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	C	11.91	1.779952	0.31502	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	D;D;D	0.84730	-1.89;-1.89;-1.88	4.73	1.83	0.25207	.	.	.	.	.	T	0.73837	0.3638	N	0.25144	0.715	0.28282	N	0.923939	B;B	0.14012	0.009;0.0	B;B	0.04013	0.001;0.001	T	0.60372	-0.7276	9	0.30078	T	0.28	.	9.8686	0.41160	0.0:0.7822:0.0:0.2178	.	2285;2049	B2RTY4;B2RTY4-5	MYO9A_HUMAN;.	H	2285;2356;2266	ENSP00000348349:R2285H;ENSP00000399162:R2356H;ENSP00000398250:R2266H	ENSP00000348349:R2285H	R	-	2	0	MYO9A	69909690	0.020000	0.18652	0.797000	0.32132	0.997000	0.91878	0.416000	0.21198	0.319000	0.23209	0.655000	0.94253	CGT	.	.	none		0.443	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		T	72122636	C	T	72122636	3	4	35	1	0	0	0	0	1	0	0	0	10093	536	19	1	804	1	MYO9A	15	72122636	Missense_Mutation	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	27208582	72122636	30408756	70	14207											
ITFG1	81533	hgsc.bcm.edu	37	chr16	47494777	47494777	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcacgaagagatccgtctgCttgtcggagttgaggtcccc	8	9	13	11	3	1	2	0	1	1	1	4	5	3	3	3	2	2	3	3	2	1	2			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr16:47494777C>T	ENST00000320640.6	-	1	408	c.180G>A	c.(178-180)aaG>aaA	p.K60K	PHKB_ENST00000566044.1_5'Flank|PHKB_ENST00000455779.1_5'Flank|PHKB_ENST00000323584.5_5'Flank|PHKB_ENST00000299167.8_5'Flank|ITFG1_ENST00000544001.2_Intron	NM_030790.3	NP_110417.2	Q8TB96	TIP_HUMAN	integrin alpha FG-GAP repeat containing 1	60						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)				GATCCGTCTGCTTGTCGGAGT	0.672																																					p.K60K		Atlas-SNP	.											.	ITFG1	49	.	0			c.G180A						PASS	.						40	31	34					16																	47494777		2201	4300	6501	SO:0001819	synonymous_variant	81533	exon1			CGTCTGCTTGTCG	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.180G>A	16.37:g.47494777C>T		85	0	0		94	23	0.244681	NM_030790	Q96SR4|Q9BRE2|Q9H2V9	Silent	SNP	ENST00000320640.6	37	CCDS10728.1																																																																																			.	.	none		0.672	ITFG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256768.3	NM_030790		T	47494777	C	T	47494777	2	4	35	1	0	0	0	0	0	0	0	1	7878	796	28	2		2	ITFG1	16	47494777	Silent	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10		47494777	42859976	71	14208											
FANCA	2175	hgsc.bcm.edu	37	chr16	89880941	89880941	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aacttacctataaatgaactAgaatgattagcataggcctc	16	11	6	8	0	0	3	0	2	0	1	1	3	0	3	2	1	4	1	2	1	10	6			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr16:89880941A>T	ENST00000389301.3	-	3	300	c.270T>A	c.(268-270)tcT>tcA	p.S90S	FANCA_ENST00000568369.1_Silent_p.S90S|FANCA_ENST00000543736.1_Silent_p.S90S|FANCA_ENST00000389302.3_Silent_p.S90S|FANCA_ENST00000563673.1_Silent_p.S90S|FANCA_ENST00000534992.1_Silent_p.S90S	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	90					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)		TAAATGAACTAGAATGATTAG	0.328			"D, Mis, N, F, S"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.S90S		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"Fanconi anemia, complementation group A"		L	.	FANCA	99	.	0			c.T270A						PASS	.						90	88	89					16																	89880941		2198	4300	6498	SO:0001819	synonymous_variant	2175	exon3	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TGAACTAGAATGA	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.270T>A	16.37:g.89880941A>T		90	0	0		83	18	0.216867	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Silent	SNP	ENST00000389301.3	37	CCDS32515.1																																																																																			.	.	none		0.328	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1			T	89880941	A	T	89880941	2	4	35	1	0	0	0	0	0	0	0	1	5670	407	15	5		5	FANCA	16	89880941	Silent	SNP	A	TCGA-GS-A9TQ-01A-11D-A382-10	42386164	89880941	473812	72	14209											
ZNF286A	57335	hgsc.bcm.edu	37	chr17	15619433	15619433	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaagatttttccaaagcagAatcatgcaaagttgcaataa	17	10	7	7	0	1	2	1	0	0	2	2	2	2	2	1	0	3	5	1	0	6	4			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr17:15619433A>G	ENST00000464847.2	+	5	948	c.395A>G	c.(394-396)gAa>gGa	p.E132G	ZNF286A_ENST00000421016.1_Missense_Mutation_p.E132G|ZNF286A_ENST00000585171.1_Intron|ZNF286A_ENST00000593105.1_Missense_Mutation_p.E122G|ZNF286A_ENST00000395894.2_3'UTR|ZNF286A_ENST00000581529.1_3'UTR|ZNF286A_ENST00000413242.2_Missense_Mutation_p.E132G|ZNF286A_ENST00000583566.1_Missense_Mutation_p.E132G|ZNF286A_ENST00000472486.1_3'UTR			Q9HBT8	Z286A_HUMAN	zinc finger protein 286A	132					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)		TCCAAAGCAGAATCATGCAAA	0.393																																					p.E132G		Atlas-SNP	.											.	ZNF286A	58	.	0			c.A395G						PASS	.						49	49	49					17																	15619433		2201	4284	6485	SO:0001583	missense	57335	exon6			AAGCAGAATCATG	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.395A>G	17.37:g.15619433A>G	ENSP00000464218:p.Glu132Gly	342	0	0		237	51	0.21519	NM_020652	B4DKF9|Q96JF3	Missense_Mutation	SNP	ENST00000464847.2	37	CCDS11172.1	.	.	.	.	.	.	.	.	.	.	a	6.747	0.506566	0.12883	.	.	ENSG00000187607	ENST00000421016;ENST00000412988;ENST00000395894	T;T	0.08896	3.41;3.04	4.38	1.92	0.25849	.	0.867112	0.09338	N	0.815936	T	0.08088	0.0202	L	0.43152	1.355	0.09310	N	1	B	0.23377	0.084	B	0.21360	0.034	T	0.34129	-0.9841	10	0.46703	T	0.11	-2.0712	6.0049	0.19541	0.6718:0.1671:0.0:0.1611	.	132	Q9HBT8	Z286A_HUMAN	G	132;122;132	ENSP00000397163:E132G;ENSP00000408168:E122G	ENSP00000435872:E132G	E	+	2	0	ZNF286A	15560158	0.001000	0.12720	0.090000	0.20809	0.511000	0.34104	0.115000	0.15540	0.676000	0.31285	0.528000	0.53228	GAA	.	.	none		0.393	ZNF286A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130696.4	NM_020652		G	15619433	A	G	15619433	3	3	35	1	0	0	0	0	1	0	0	0	17838	246	9	3	413	3	ZNF286A	17	15619433	Missense_Mutation	SNP	A	TCGA-GS-A9TQ-01A-11D-A382-10		15619433	65575777	73	14210											
C17orf102	400591	hgsc.bcm.edu	37	chr17	32905908	32905908	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	acctgtaggaaagcactgtcCcctcctcttctccgtcttcc	6	12	6	17	1	3	0	0	0	3	0	7	1	6	1	6	1	1	2	6	1	2	3			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr17:32905908C>A	ENST00000357754.1	-	1	480	c.392G>T	c.(391-393)gGg>gTg	p.G131V	TMEM132E_ENST00000321639.5_5'Flank	NM_207454.2	NP_997337.2	A2RUQ5	CQ102_HUMAN	chromosome 17 open reading frame 102	131										central_nervous_system(1)|cervix(1)|large_intestine(3)|lung(3)|ovary(1)	9						AAGCACTGTCCCCTCCTCTTC	0.587																																					p.G131V		Atlas-SNP	.											.	C17orf102	24	.	0			c.G392T						PASS	.						175	185	182					17																	32905908		1946	4145	6091	SO:0001583	missense	400591	exon1			ACTGTCCCCTCCT		CCDS42297.1	17q12	2009-02-11			ENSG00000197322	ENSG00000197322			34412	protein-coding gene	gene with protein product							Standard	NM_207454		Approved	FLJ44815	uc002hie.1	A2RUQ5	OTTHUMG00000156883	ENST00000357754.1:c.392G>T	17.37:g.32905908C>A	ENSP00000350392:p.Gly131Val	64	0	0		93	22	0.236559	NM_207454	A5PKX0|Q6ZTB3	Missense_Mutation	SNP	ENST00000357754.1	37	CCDS42297.1	.	.	.	.	.	.	.	.	.	.	C	13.56	2.274858	0.40194	.	.	ENSG00000197322	ENST00000357754	T	0.46819	0.86	4.15	-0.222	0.13122	.	0.267652	0.20576	N	0.089625	T	0.33381	0.0861	N	0.19112	0.55	0.09310	N	1	P	0.49090	0.919	P	0.50082	0.63	T	0.17930	-1.0353	10	0.87932	D	0	.	2.7364	0.05241	0.2062:0.4407:0.0:0.3531	.	131	A2RUQ5	CQ102_HUMAN	V	131	ENSP00000350392:G131V	ENSP00000350392:G131V	G	-	2	0	C17orf102	29930021	0.000000	0.05858	0.000000	0.03702	0.653000	0.38743	-0.002000	0.12924	0.124000	0.18369	0.655000	0.94253	GGG	.	.	none		0.587	C17orf102-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346435.1	NM_207454		A	32905908	C	A	32905908	3	1	35	1	0	0	0	0	1	0	0	0	1851	623	22	4	119	4	C17orf102	17	32905908	Missense_Mutation	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	17286475	32905908	48289302	74	14211											
FKBP10	60681	hgsc.bcm.edu	37	chr17	39974646	39974646	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctgcagctacagtaagggCggcacttatgacacctacgt	10	10	10	11	2	1	1	0	1	1	0	1	1	1	1	1	2	4	4	1	2	4	5			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr17:39974646C>T	ENST00000321562.4	+	4	698	c.594C>T	c.(592-594)ggC>ggT	p.G198G	FKBP10_ENST00000544340.1_5'Flank	NM_021939.3	NP_068758.3	Q96AY3	FKB10_HUMAN	FK506 binding protein 10, 65 kDa	198	PPIase FKBP-type 2. {ECO:0000255|PROSITE- ProRule:PRU00277}.				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)		ACAGTAAGGGCGGCACTTATG	0.607																																					p.G198G		Atlas-SNP	.											FKBP10,NS,carcinoma,+2,1	FKBP10	57	1	0			c.C594T						PASS	.						86	76	79					17																	39974646		2203	4300	6503	SO:0001819	synonymous_variant	60681	exon4			TAAGGGCGGCACT	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.594C>T	17.37:g.39974646C>T		109	0	0		122	22	0.180328	NM_021939	Q7Z3R4|Q9H3N3|Q9H6J3|Q9H6N5|Q9UF89	Silent	SNP	ENST00000321562.4	37	CCDS11409.1																																																																																			.	.	none		0.607	FKBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257410.2	NM_021939		T	39974646	C	T	39974646	2	4	35	1	0	0	0	0	0	0	0	1	5910	755	27	1		1	FKBP10	17	39974646	Silent	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	7068738	39974646	41220564	75	14212											
BCL2	596	hgsc.bcm.edu	37	chr18	60985514	60985514	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctccaccaccgtggcaaagCgtccccgcgcggtgaagggc	7	4	13	17	5	0	1	0	1	0	0	2	1	2	1	6	3	1	1	6	3	2	0			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr18:60985514C>T	ENST00000398117.1	-	1	1847	c.386G>A	c.(385-387)cGc>cAc	p.R129H	BCL2_ENST00000444484.1_Missense_Mutation_p.R129H|BCL2_ENST00000589955.1_Missense_Mutation_p.R129H|BCL2_ENST00000333681.4_Missense_Mutation_p.R129H	NM_000633.2	NP_000624.2	P10415	BCL2_HUMAN	B-cell CLL/lymphoma 2	129				R -> C (in Ref. 4; CAA29778). {ECO:0000305}.	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)	p.R129H(1)		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)	CGTGGCAAAGCGTCCCCGCGC	0.667			T	IGH@	"NHL, CLL"																																p.R129H		Atlas-SNP	.		Dom	yes		18	18q21.3	596	B-cell CLL/lymphoma 2		L	BCL2,NS,lymphoid_neoplasm,0,1	BCL2	272	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G386A						PASS	.						100	116	111					18																	60985514		2203	4300	6503	SO:0001583	missense	596	exon2			GCAAAGCGTCCCC	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.386G>A	18.37:g.60985514C>T	ENSP00000381185:p.Arg129His	62	0	0		73	16	0.219178	NM_000633	C9JHD5|P10416|Q13842|Q16197	Missense_Mutation	SNP	ENST00000398117.1	37	CCDS11981.1	.	.	.	.	.	.	.	.	.	.	C	16.99	3.275064	0.59649	.	.	ENSG00000171791	ENST00000398117;ENST00000333681;ENST00000444484	T;T;T	0.11385	2.78;2.78;2.78	4.63	3.72	0.42706	Apoptosis regulator, Bcl2-like (1);Apoptosis regulator, Bcl-2, BH (2);	0.062950	0.64402	D	0.000003	T	0.27967	0.0689	L	0.55481	1.735	0.54753	D	0.999987	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.01966	-1.1238	10	0.72032	D	0.01	-20.1356	14.4183	0.67165	0.0:0.8513:0.1487:0.0	.	129;129	C9JHD5;P10415	.;BCL2_HUMAN	H	129	ENSP00000381185:R129H;ENSP00000329623:R129H;ENSP00000404214:R129H	ENSP00000329623:R129H	R	-	2	0	BCL2	59136494	1.000000	0.71417	0.959000	0.39883	0.138000	0.21146	5.728000	0.68531	1.092000	0.41356	0.655000	0.94253	CGC	.	.	none		0.667	BCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256199.1	NM_000633, NM_000657		T	60985514	C	T	60985514	3	4	35	1	0	0	0	0	1	0	0	0	1365	768	27	1	374	1	BCL2	18	60985514	Missense_Mutation	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10		60985514	17091734	76	14213											
BCL2	596	hgsc.bcm.edu	37	chr18	60985870	60985870	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcatcactatctcccggttAtcgtaccctgttctcccagc	6	14	5	16	2	4	0	2	0	2	0	7	0	4	0	3	1	2	3	3	1	3	5			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr18:60985870A>G	ENST00000398117.1	-	1	1491	c.30T>C	c.(28-30)gaT>gaC	p.D10D	BCL2_ENST00000444484.1_Silent_p.D10D|BCL2_ENST00000589955.1_Silent_p.D10D|BCL2_ENST00000333681.4_Silent_p.D10D	NM_000633.2	NP_000624.2	P10415	BCL2_HUMAN	B-cell CLL/lymphoma 2	10					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)	p.D10D(2)		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)	TCTCCCGGTTATCGTACCCTG	0.657			T	IGH@	"NHL, CLL"																																p.D10D		Atlas-SNP	.		Dom	yes		18	18q21.3	596	B-cell CLL/lymphoma 2		L	BCL2_ENST00000398117,NS,lymphoid_neoplasm,0,2	BCL2	272	2	2	Substitution - coding silent(2)	haematopoietic_and_lymphoid_tissue(2)	c.T30C						PASS	.						70	77	75					18																	60985870		1968	4072	6040	SO:0001819	synonymous_variant	596	exon2			CCGGTTATCGTAC	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.30T>C	18.37:g.60985870A>G		65	0	0		80	10	0.125	NM_000633	C9JHD5|P10416|Q13842|Q16197	Silent	SNP	ENST00000398117.1	37	CCDS11981.1																																																																																			.	.	none		0.657	BCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256199.1	NM_000633, NM_000657		G	60985870	A	G	60985870	2	3	35	1	0	0	0	0	0	0	0	1	1365	446	16	3		3	BCL2	18	60985870	Silent	SNP	A	TCGA-GS-A9TQ-01A-11D-A382-10	356	60985870	17091378	77	14214											
ZNF236	7776	hgsc.bcm.edu	37	chr18	74611013	74611013	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtcctcactgtgacaaaaaaTttcgaacctcaggccatagg	13	9	8	11	1	2	1	2	1	0	0	4	2	3	1	3	2	1	0	3	2	5	2			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr18:74611013T>A	ENST00000253159.8	+	11	1921	c.1723T>A	c.(1723-1725)Ttt>Att	p.F575I	ZNF236_ENST00000320610.9_Missense_Mutation_p.F577I	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	575					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)		TGACAAAAAATTTCGAACCTC	0.383																																					p.F575I		Atlas-SNP	.											.	ZNF236	325	.	0			c.T1723A						PASS	.						117	107	110					18																	74611013		1849	4096	5945	SO:0001583	missense	7776	exon11			AAAAAATTTCGAA	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.1723T>A	18.37:g.74611013T>A	ENSP00000253159:p.Phe575Ile	77	0	0		74	22	0.297297	NM_007345	B2RTX9|Q9UL37	Missense_Mutation	SNP	ENST00000253159.8	37	CCDS42447.1	.	.	.	.	.	.	.	.	.	.	T	32	5.149273	0.94645	.	.	ENSG00000130856	ENST00000253159;ENST00000543926;ENST00000320610	T;T	0.47528	0.84;0.84	5.09	5.09	0.68999	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	0.77698	0.4169	H	0.95611	3.695	0.58432	D	0.999991	D	0.89917	1.0	D	0.87578	0.998	D	0.85094	0.0953	10	0.87932	D	0	.	14.8972	0.70651	0.0:0.0:0.0:1.0	.	575	Q9UL36	ZN236_HUMAN	I	575	ENSP00000253159:F575I;ENSP00000444524:F575I	ENSP00000253159:F575I	F	+	1	0	ZNF236	72740001	1.000000	0.71417	0.849000	0.33467	0.989000	0.77384	7.751000	0.85126	1.928000	0.55862	0.482000	0.46254	TTT	.	.	none		0.383	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1			A	74611013	T	A	74611013	3	1	35	1	0	0	0	0	1	0	0	0	17804	1493	52	5	1765	5	ZNF236	18	74611013	Missense_Mutation	SNP	T	TCGA-GS-A9TQ-01A-11D-A382-10	13625143	74611013	3466235	78	14215											
RGL3	57139	hgsc.bcm.edu	37	chr19	11507932	11507932	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ctgctcaccccggtccccagGaaggacttgaaagagctgat	10	7	11	13	1	1	3	1	2	0	1	2	5	2	5	4	3	2	2	4	3	2	1			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr19:11507932G>A	ENST00000380456.3	-	18	2065	c.2002C>T	c.(2002-2004)Cct>Tct	p.P668S	RGL3_ENST00000393423.3_Missense_Mutation_p.P674S|RGL3_ENST00000568628.1_5'UTR	NM_001035223.2|NM_001161616.1	NP_001030300.2|NP_001155088.1	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation stimulator-like 3	668	Interaction with HRAS, MRAS and RIT1. {ECO:0000250}.|Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				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						CGGTCCCCAGGAAGGACTTGA	0.637																																					p.P674S	GBM(174;751 2067 17998 27979 33959)	Atlas-SNP	.											.	RGL3	100	.	0			c.C2020T						PASS	.						79	81	80					19																	11507932		2203	4300	6503	SO:0001583	missense	57139	exon18			CCCCAGGAAGGAC	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.2002C>T	19.37:g.11507932G>A	ENSP00000369823:p.Pro668Ser	46	0	0		33	13	0.393939	NM_001161616	B5ME84|B7ZL22|Q0P6G0	Missense_Mutation	SNP	ENST00000380456.3	37	CCDS32910.1	.	.	.	.	.	.	.	.	.	.	G	3.931	-0.016219	0.07681	.	.	ENSG00000205517	ENST00000342684;ENST00000393423;ENST00000380456	T;T	0.54479	0.57;0.57	4.7	2.56	0.30785	Ras-association (3);	0.301362	0.36374	N	0.002635	T	0.46151	0.1378	L	0.35723	1.085	0.42444	D	0.992721	B;B;B;D	0.57571	0.033;0.015;0.019;0.98	B;B;B;P	0.57244	0.084;0.023;0.012;0.816	T	0.54397	-0.8300	10	0.02654	T	1	.	6.4223	0.21750	0.2994:0.0:0.7005:0.0	.	668;674;674;465	Q3MIN7;B5ME84;B7ZL22;Q8TEP0	RGL3_HUMAN;.;.;.	S	465;674;668	ENSP00000377075:P674S;ENSP00000369823:P668S	ENSP00000344665:P465S	P	-	1	0	RGL3	11368932	0.980000	0.34600	0.991000	0.47740	0.984000	0.73092	1.078000	0.30754	0.694000	0.31654	0.555000	0.69702	CCT	.	.	none		0.637	RGL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421208.3	XM_290867		A	11507932	G	A	11507932	3	1	35	1	0	0	0	0	1	0	0	0	13293	1174	41	2	138	2	RGL3	19	11507932	Missense_Mutation	SNP	G	TCGA-GS-A9TQ-01A-11D-A382-10		11507932	47621051	79	14216											
KCNN1	3780	hgsc.bcm.edu	37	chr19	18108988	18108988	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtcatgtacgaccttgtaTcggagctgcacgctcagcac	8	9	10	14	4	2	0	2	0	0	0	3	2	2	1	2	1	4	6	2	1	2	3			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr19:18108988T>C	ENST00000222249.9	+	11	1724	c.1405T>C	c.(1405-1407)Tcg>Ccg	p.S469P	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	469					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)	CGACCTTGTATCGGAGCTGCA	0.642																																					p.S469P		Atlas-SNP	.											.	KCNN1	74	.	0			c.T1405C						PASS	.						14	17	16					19																	18108988		2163	4270	6433	SO:0001583	missense	3780	exon11			CTTGTATCGGAGC	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.1405T>C	19.37:g.18108988T>C	ENSP00000476519:p.Ser469Pro	46	0	0		44	13	0.295455	NM_002248	Q5KR10|Q6DJU4	Missense_Mutation	SNP	ENST00000222249.9	37		.	.	.	.	.	.	.	.	.	.	T	13.69	2.313548	0.40996	.	.	ENSG00000105642	ENST00000222249	.	.	.	4.19	1.79	0.24919	.	0.206931	0.42964	D	0.000639	T	0.45377	0.1339	L	0.55213	1.73	0.80722	D	1	P	0.44877	0.845	B	0.44044	0.439	T	0.32375	-0.9909	9	0.49607	T	0.09	-12.4163	5.103	0.14770	0.1427:0.0:0.2672:0.5901	.	469	Q92952	KCNN1_HUMAN	P	486	.	ENSP00000222249:S486P	S	+	1	0	KCNN1	17969988	0.961000	0.32948	0.965000	0.40720	0.134000	0.20937	0.750000	0.26334	0.486000	0.27676	0.397000	0.26171	TCG	.	.	none		0.642	KCNN1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471896.2	NM_002248		C	18108988	T	C	18108988	3	2	35	1	0	0	0	0	1	0	0	0	8087	1435	50	3	1439	3	KCNN1	19	18108988	Missense_Mutation	SNP	T	TCGA-GS-A9TQ-01A-11D-A382-10	6601056	18108988	41019995	80	14217											
B3GNT8	593	hgsc.bcm.edu	37	chr19	41932430	41932430	+	IGR	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtttcagtgctgtccccaCtgggcagggaccccagccgc	5	7	12	17	2	1	0	1	0	0	0	2	1	2	1	6	2	2	3	6	2	0	1			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr19:41932430C>G	ENST00000269980.2	+	0	2103				B3GNT8_ENST00000601379.1_Intron|B3GNT8_ENST00000321702.2_Missense_Mutation_p.S85T|CTC-435M10.6_ENST00000598887.1_RNA	NM_000709.3|NM_001164783.1	NP_000700.1|NP_001158255.1	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha polypeptide						branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity (GO:0003863)|alpha-ketoacid dehydrogenase activity (GO:0003826)|carboxy-lyase activity (GO:0016831)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	10						GCTGTCCCCACTGGGCAGGGA	0.692																																					p.S85T		Atlas-SNP	.											.	B3GNT8	20	.	0			c.G254C						PASS	.						11	11	11					19																	41932430		2174	4270	6444	SO:0001628	intergenic_variant	374907	exon3			TCCCCACTGGGCA	J04474	CCDS12581.1	19q13.1-q13.2	2008-07-09	2005-11-29		ENSG00000248098	ENSG00000248098			986	protein-coding gene	gene with protein product	"maple syrup urine disease"	608348	"branched chain keto acid dehydrogenase E1, alpha polypeptide (maple syrup urine disease)", "2-oxoisovalerate dehydrogenase (lipoamide)"	OVD1A			Standard	NM_000709		Approved	MSU	uc002oqq.3	P12694	OTTHUMG00000168128		19.37:g.41932430C>G		72	0	0		89	18	0.202247	NM_198540	B4DP47|E7EW46|Q16034|Q16472	Missense_Mutation	SNP	ENST00000269980.2	37	CCDS12581.1	.	.	.	.	.	.	.	.	.	.	C	10.21	1.288472	0.23478	.	.	ENSG00000177191	ENST00000321702	T	0.34859	1.34	4.21	1.79	0.24919	.	0.546871	0.16746	N	0.201230	T	0.21841	0.0526	N	0.25144	0.715	0.34090	D	0.660626	B	0.06786	0.001	B	0.04013	0.001	T	0.24333	-1.0163	10	0.14656	T	0.56	.	11.6491	0.51277	0.0:0.6581:0.3419:0.0	.	85	Q7Z7M8	B3GN8_HUMAN	T	85	ENSP00000312700:S85T	ENSP00000312700:S85T	S	-	2	0	B3GNT8	46624270	0.000000	0.05858	0.712000	0.30502	0.902000	0.53008	0.004000	0.13106	1.075000	0.40932	0.462000	0.41574	AGT	.	.	none		0.692	BCKDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398313.3	NM_000709		G	41932430	C	G	41932430	1	3	35	0	1	0	0	0	0	0	0	0	1263	565	20	4		4	B3GNT8	19	41932430	IGR	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	23823442	41932430	17196553	81	14218											
PSG6	5675	hgsc.bcm.edu	37	chr19	43420486	43420486	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taatgtaatggtagaggtccGtcatttgccctttgtaccag	9	14	10	8	1	1	1	1	0	0	1	2	1	2	1	3	2	2	3	3	2	4	6	rs140974685|rs386809478	byFrequency	TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr19:43420486G>A	ENST00000292125.2	-	2	262	c.218C>T	c.(217-219)aCg>aTg	p.T73M	PSG6_ENST00000187910.2_Missense_Mutation_p.T73M|PSG6_ENST00000601833.1_Missense_Mutation_p.T2M|PSG6_ENST00000402603.4_Missense_Mutation_p.T73M	NM_002782.4	NP_002773.1	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6	73	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)				GTAGAGGTCCGTCATTTGCCC	0.453																																					p.T73M		Atlas-SNP	.											.	PSG6	89	.	0			c.C218T						PASS	.						243	238	239					19																	43420486		2202	4299	6501	SO:0001583	missense	5675	exon2			AGGTCCGTCATTT		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.218C>T	19.37:g.43420486G>A	ENSP00000292125:p.Thr73Met	134	0	0		124	20	0.16129	NM_001031850	O75244|Q15224|Q15235|Q549K1	Missense_Mutation	SNP	ENST00000292125.2	37	CCDS12613.1	.	.	.	.	.	.	.	.	.	.	N	0.006	-2.086760	0.00367	.	.	ENSG00000170848	ENST00000187910;ENST00000402603;ENST00000292125;ENST00000402456	T;T;T	0.65916	-0.18;-0.18;-0.18	1.47	-2.95	0.05564	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.32882	0.0844	N	0.04724	-0.175	0.09310	N	1	B;B;B	0.22746	0.01;0.009;0.074	B;B;B	0.25987	0.028;0.01;0.065	T	0.15122	-1.0448	9	0.33141	T	0.24	.	1.1353	0.01754	0.2697:0.2892:0.2973:0.1438	.	73;73;73	Q00889;Q00889-2;B5MCE1	PSG6_HUMAN;.;.	M	73	ENSP00000187910:T73M;ENSP00000385736:T73M;ENSP00000292125:T73M	ENSP00000187910:T73M	T	-	2	0	PSG6	48112326	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.550000	0.02180	-5.346000	0.00016	-4.576000	0.00004	ACG	G|0.969;C|0.031	.	alt		0.453	PSG6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321436.1	NM_002782		A	43420486	G	A	43420486	3	1	35	1	0	0	0	0	1	0	0	0	12671	1145	40	1	1148	1	PSG6	19	43420486	Missense_Mutation	SNP	G	TCGA-GS-A9TQ-01A-11D-A382-10	1488056	43420486	15708497	82	14219											
PLCB1	23236	hgsc.bcm.edu	37	chr20	8352099	8352100	+	Splice_Site	INS	-	-	AGGATCCC																															cacgccaaagctcccaaggtINSaggaggttgagtgttgtgca																										TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr20:8352099_8352100insAGGATCCC	ENST00000338037.6	+	3	273		c.e3+2		PLCB1_ENST00000378641.3_Splice_Site|PLCB1_ENST00000378637.2_Splice_Site	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)						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						GCTCCCAAGGTAGGAGGTTGAG	0.446																																					.		Pindel,Atlas-Indel	.											.	PLCB1	394	.	0			c.246+2->AGGATCCC						PASS	.																																			SO:0001630	splice_region_variant	23236	exon3			.	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.246+2->AGGATCCC	20.37:g.8352099_8352100insAGGATCCC		71	0	.		62	19	0.306	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Splice_Site	INS	ENST00000338037.6	37	CCDS13102.1																																																																																			.	.	none		0.446	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3		Intron	AGGATCCC	8352100	-	AGGATCCC	8352099	8	5	35	1	0	1	1	0	0	0	1	0	12036	1652	57	0	258	0	PLCB1	20	8352099	Splice_Site	INS	-	TCGA-GS-A9TQ-01A-11D-A382-10		8352099	54673421	83	14220											
C20orf117	140710	hgsc.bcm.edu	37	chr20	35433301	35433301	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccagtgtcttgatgtactcaTtgggctgcagacaggaggca	9	10	13	9	0	2	2	1	1	1	1	2	3	2	3	1	3	2	4	1	3	1	3			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr20:35433301T>C	ENST00000357779.3	-	10	2536	c.2210A>G	c.(2209-2211)aAt>aGt	p.N737S	SOGA1_ENST00000456801.2_Missense_Mutation_p.N578S|SOGA1_ENST00000279034.6_Missense_Mutation_p.N737S|SOGA1_ENST00000237536.4_Missense_Mutation_p.N975S			O94964	SOGA1_HUMAN	suppressor of glucose, autophagy associated 1	737					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						GATGTACTCATTGGGCTGCAG	0.577																																					p.N975S		Atlas-SNP	.											SOGA1_ENST00000237536,NS,carcinoma,+1,4	SOGA1	136	4	0			c.A2924G						PASS	.						72	75	74					20																	35433301		2094	4240	6334	SO:0001583	missense	140710	exon10			TACTCATTGGGCT	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.2210A>G	20.37:g.35433301T>C	ENSP00000350424:p.Asn737Ser	38	0	0		38	10	0.263158	NM_080627	A6NK10|Q14DB2|Q5JW51|Q6ZTG8	Missense_Mutation	SNP	ENST00000357779.3	37		.	.	.	.	.	.	.	.	.	.	T	10.46	1.355804	0.24598	.	.	ENSG00000149639	ENST00000237536;ENST00000279034;ENST00000456801;ENST00000357779	T;T;T;T	0.16897	2.31;2.31;2.32;2.32	4.79	3.69	0.42338	.	0.175827	0.49916	D	0.000122	T	0.09468	0.0233	N	0.22421	0.69	0.28792	N	0.899245	B	0.30236	0.274	B	0.31751	0.135	T	0.28396	-1.0045	10	0.08599	T	0.76	-18.6184	7.0441	0.25037	0.0:0.1806:0.0:0.8194	.	737	O94964-4	.	S	975;737;578;737	ENSP00000237536:N975S;ENSP00000279034:N737S;ENSP00000413886:N578S;ENSP00000350424:N737S	ENSP00000237536:N975S	N	-	2	0	KIAA0889	34866715	0.998000	0.40836	0.901000	0.35422	0.935000	0.57460	3.290000	0.51755	0.858000	0.35431	0.455000	0.32223	AAT	.	.	none		0.577	SOGA1-201	KNOWN	basic	protein_coding	protein_coding		NM_199181		C	35433301	T	C	35433301	3	2	35	1	0	0	0	0	1	0	0	0	2085	1493	52	3	2147	3	C20orf117	20	35433301	Missense_Mutation	SNP	T	TCGA-GS-A9TQ-01A-11D-A382-10	27081202	35433301	27592219	84	14221											
ATP9A	10079	hgsc.bcm.edu	37	chr20	50310555	50310555	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagctactcacggcggccgTggggagcctctgcgtgcagg	7	6	16	12	4	2	0	1	0	1	0	2	1	2	1	2	5	5	2	2	5	2	1	rs566503519		TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr20:50310555T>C	ENST00000338821.5	-	7	898	c.634A>G	c.(634-636)Acg>Gcg	p.T212A	ATP9A_ENST00000402822.1_Intron|ATP9A_ENST00000311637.5_Intron	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	212					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						ACGGCGGCCGTGGGGAGCCTC	0.617																																					p.T212A		Atlas-SNP	.											ATP9A,rectum,carcinoma,+2,2	ATP9A	135	2	0			c.A634G						PASS	.						39	43	42					20																	50310555		2202	4299	6501	SO:0001583	missense	10079	exon7			CGGCCGTGGGGAG	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.634A>G	20.37:g.50310555T>C	ENSP00000342481:p.Thr212Ala	140	0	0		128	22	0.171875	NM_006045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Missense_Mutation	SNP	ENST00000338821.5	37	CCDS33489.1	.	.	.	.	.	.	.	.	.	.	T	11.73	1.726183	0.30593	.	.	ENSG00000054793	ENST00000338821	T	0.78364	-1.17	5.04	5.04	0.67666	ATPase, P-type, ATPase-associated domain (1);	0.000000	0.85682	D	0.000000	T	0.60894	0.2304	N	0.11818	0.18	0.80722	D	1	B	0.09022	0.002	B	0.15052	0.012	T	0.56517	-0.7966	10	0.15066	T	0.55	-28.3414	14.7939	0.69863	0.0:0.0:0.0:1.0	.	212	O75110	ATP9A_HUMAN	A	212	ENSP00000342481:T212A	ENSP00000342481:T212A	T	-	1	0	ATP9A	49743962	1.000000	0.71417	0.993000	0.49108	0.791000	0.44710	5.986000	0.70563	1.889000	0.54706	0.533000	0.62120	ACG	.	.	none		0.617	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045		C	50310555	T	C	50310555	3	2	35	1	0	0	0	0	1	0	0	0	1198	1696	59	3	2597	3	ATP9A	20	50310555	Missense_Mutation	SNP	T	TCGA-GS-A9TQ-01A-11D-A382-10	14877254	50310555	12714965	85	14222											
SPO11	23626	hgsc.bcm.edu	37	chr20	55910492	55910492	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aaggctgttgctgtgccatcGaatattcaaggaattcggag	11	11	12	7	2	1	0	1	0	0	0	3	3	1	2	1	3	2	3	1	3	5	4			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr20:55910492G>A	ENST00000371263.3	+	7	724	c.615G>A	c.(613-615)tcG>tcA	p.S205S	SPO11_ENST00000371260.4_Silent_p.S167S|SPO11_ENST00000345868.4_Silent_p.S167S	NM_012444.2	NP_036576.1	Q9Y5K1	SPO11_HUMAN	SPO11 meiotic protein covalently bound to DSB	205					DNA catabolic process, endonucleolytic (GO:0000737)|female gamete generation (GO:0007292)|male meiosis I (GO:0007141)|ovarian follicle development (GO:0001541)|protein localization to chromosome (GO:0034502)|reciprocal meiotic recombination (GO:0007131)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	chromosome, telomeric region (GO:0000781)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|hydrolase activity (GO:0016787)			autonomic_ganglia(1)|breast(3)|large_intestine(4)|lung(8)|skin(2)	18	Lung NSC(12;0.0066)|all_lung(29;0.0188)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;1.73e-14)|Epithelial(14;9.02e-10)|all cancers(14;9.31e-09)			CTGTGCCATCGAATATTCAAG	0.303								Editing and processing nucleases																													p.S205S		Atlas-SNP	.											.	SPO11	43	.	0			c.G615A						PASS	.						61	58	59					20																	55910492		2202	4300	6502	SO:0001819	synonymous_variant	23626	exon7			GCCATCGAATATT	AF169385	CCDS13456.1, CCDS13457.1	20q13.31	2013-06-05	2013-06-05		ENSG00000054796	ENSG00000054796			11250	protein-coding gene	gene with protein product	"cancer/testis antigen 35", "spermatogenesis associated 43"	605114	"SPO11, meiotic protein covalently bound to DSB (S. cerevisiae)-like", "SPO11 meiotic protein covalently bound to DSB-like (S. cerevisiae)", "SPO11 meiotic protein covalently bound to DSB homolog (S. cerevisiae)"			10534401	Standard	NM_012444		Approved	CT35, SPATA43, TOPVIA	uc002xye.3	Q9Y5K1	OTTHUMG00000032817	ENST00000371263.3:c.615G>A	20.37:g.55910492G>A		79	0	0		90	16	0.177778	NM_012444	Q5TCI1|Q8N4V0|Q9NQM7|Q9NQM8	Silent	SNP	ENST00000371263.3	37	CCDS13456.1																																																																																			.	.	none		0.303	SPO11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079836.2	NM_012444		A	55910492	G	A	55910492	2	1	35	1	0	0	0	0	0	0	0	1	15092	1045	37	1		1	SPO11	20	55910492	Silent	SNP	G	TCGA-GS-A9TQ-01A-11D-A382-10	5599937	55910492	7115028	86	14223											
PRIC285	85441	hgsc.bcm.edu	37	chr20	62194351	62194351	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatggttcccacacgcaggCgtactcatccacgtcgcggt	8	8	11	14	5	1	0	1	0	0	0	4	1	3	0	2	3	1	3	2	3	2	2	rs148162381		TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr20:62194351C>G	ENST00000467148.1	-	8	5893	c.5824G>C	c.(5824-5826)Gcc>Ccc	p.A1942P	HELZ2_ENST00000427522.2_Missense_Mutation_p.A1373P	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	1942					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)										CACACGCAGGCGTACTCATCC	0.667																																					p.A1942P		Atlas-SNP	.											.	.	.	.	0			c.G5824C						PASS	.						13	11	12					20																	62194351		2161	4264	6425	SO:0001583	missense	85441	exon9			CGCAGGCGTACTC	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.5824G>C	20.37:g.62194351C>G	ENSP00000417401:p.Ala1942Pro	77	0	0		79	21	0.265823	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	37	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	C	4.849	0.157913	0.09236	.	.	ENSG00000130589	ENST00000427522;ENST00000467148	T;T	0.80033	-1.33;-1.23	4.75	-9.5	0.00584	.	1.864240	0.02078	N	0.052103	T	0.66896	0.2836	N	0.22421	0.69	0.09310	N	1	P;P	0.46020	0.797;0.871	B;P	0.45406	0.286;0.479	T	0.70676	-0.4806	10	0.33141	T	0.24	-1.2872	4.4847	0.11783	0.1009:0.3812:0.1031:0.4149	.	1942;1373	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	P	1373;1942	ENSP00000393257:A1373P;ENSP00000417401:A1942P	ENSP00000393257:A1373P	A	-	1	0	RP4-697K14.7	61664795	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.460000	0.02368	-4.162000	0.00068	-1.185000	0.01705	GCC	C|1.000;T|0.000	.	alt		0.667	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		G	62194351	C	G	62194351	3	3	35	1	0	0	0	0	1	0	0	0	12497	768	27	4	2173	4	PRIC285	20	62194351	Missense_Mutation	SNP	C	TCGA-GS-A9TQ-01A-11D-A382-10	6283859	62194351	831169	87	14224											
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230400	23230400	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cccagaccctggagcctcagTtggaagcagccgatccagcc	9	5	11	16	1	1	1	1	0	0	1	2	4	2	3	6	2	4	2	6	2	1	1	rs189360394		TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr22:23230400T>C	ENST00000526893.1	+	1	441	c.167T>C	c.(166-168)gTt>gCt	p.V56A	IGLL5_ENST00000532223.2_Missense_Mutation_p.V56A|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000531372.1_Missense_Mutation_p.V56A	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	56						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GGAGCCTCAGTTGGAAGCAGC	0.667													T|||	1	0.000199681	0.0	0.0014	5008	,	,		10673	0.0		0.0	False		,,,				2504	0.0				p.V56A		Atlas-SNP	.											.	IGLL5	26	.	0			c.T167C						PASS	.																																			SO:0001583	missense	100423062	exon1			CCTCAGTTGGAAG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.167T>C	22.37:g.23230400T>C	ENSP00000431254:p.Val56Ala	137	0	0		112	21	0.1875	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	T	0.035	-1.312432	0.01331	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00571	6.5;6.5	3.92	-3.93	0.04143	.	.	.	.	.	T	0.00356	0.0011	L	0.27053	0.805	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.45071	-0.9286	9	0.54805	T	0.06	.	0.8497	0.01169	0.1514:0.2511:0.2977:0.2998	.	56	B9A064	IGLL5_HUMAN	A	56	ENSP00000436353:V56A;ENSP00000431254:V56A	ENSP00000431254:V56A	V	+	2	0	IGLL5	21560400	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.389000	0.02530	-0.629000	0.05575	-1.272000	0.01410	GTT	T|1.000;C|0.000	0.000	strong		0.667	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		C	23230400	T	C	23230400	3	2	35	1	0	0	0	0	1	0	0	0	7603	1725	60	3	169	3	IGLL5	22	23230400	Missense_Mutation	SNP	T	TCGA-GS-A9TQ-01A-11D-A382-10		23230400	28074166	88	14225											
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230440	23230440	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctgcggagcctgtggggcagGtaaggggcaagagattccag	9	6	18	8	1	0	1	0	0	0	1	1	3	1	2	2	6	2	3	2	6	2	2			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr22:23230440G>C	ENST00000526893.1	+	1	480		c.e1+1		IGLL5_ENST00000532223.2_Splice_Site|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000531372.1_Splice_Site	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5							extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						TGTGGGGCAGGTAAGGGGCAA	0.627																																					.		Atlas-SNP	.											.	IGLL5	26	.	0			c.100+1G>C						PASS	.																																			SO:0001630	splice_region_variant	100423062	exon1			GGGCAGGTAAGGG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.206+1G>C	22.37:g.23230440G>C		102	0	0		69	12	0.173913	NM_001256296		Splice_Site	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	9.687	1.150929	0.21371	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	.	.	.	3.92	3.92	0.45320	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.74	0.51788	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	IGLL5	21560440	1.000000	0.71417	1.000000	0.80357	0.199000	0.23934	1.700000	0.37815	2.481000	0.83766	0.643000	0.83706	.	.	.	none		0.627	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	Intron	C	23230440	G	C	23230440	5	2	35	1	0	0	0	0	0	0	1	0	7603	1275	44	4	209	4	IGLL5	22	23230440	Splice_Site	SNP	G	TCGA-GS-A9TQ-01A-11D-A382-10	40	23230440	28074126	89	14226											
ENTHD1	150350	hgsc.bcm.edu	37	chr22	40161596	40161599	+	Frame_Shift_Del	DEL	GAGA	GAGA	-																															gcccagaaggactattttctGagagagtaggcacagcatct																								rs140918120	byFrequency	TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	GAGA	GAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chr22:40161596_40161599delGAGA	ENST00000325157.6	-	6	1098_1101	c.848_851delTCTC	c.(847-852)ctctcafs	p.LS283fs		NM_152512.3	NP_689725.2	Q8IYW4	ENTD1_HUMAN	ENTH domain containing 1	283										breast(2)|endometrium(1)|kidney(6)|large_intestine(6)|lung(11)|ovary(3)|skin(3)	32	Melanoma(58;0.0749)					ACTATTTTCTGAGAGAGTAGGCAC	0.319																																					p.283_284del		Atlas-Indel	.											.	ENTHD1	83	.	0			c.849_852del						PASS	.																																			SO:0001589	frameshift_variant	150350	exon6			.	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.848_851delTCTC	22.37:g.40161596_40161599delGAGA	ENSP00000317431:p.Leu283fs	96	0	0		92	12	0.130435	NM_152512	B0QYD5|Q5H9F7|Q96LK3	Frame_Shift_Del	DEL	ENST00000325157.6	37	CCDS13998.1																																																																																			.	.	none		0.319	ENTHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321302.1	NM_152512		-	40161599	GAGA	-	40161596	7	5	35	1	0	1	0	1	0	0	0	0	5139	1294	45	0	980	0	ENTHD1	22	40161596	Frame_Shift_Del	DEL	GAGA	TCGA-GS-A9TQ-01A-11D-A382-10	16931156	40161596	11142970	90	14227											
BTK	695	hgsc.bcm.edu	37	chrX	100613634	100613634	+	Nonsense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttagcaaacacagacactgtAtatttgccagctttgctgga	12	12	8	9	0	0	1	0	0	0	1	0	2	0	2	1	1	5	4	1	1	4	5			TCGA-GS-A9TQ-01A-11D-A382-10	TCGA-GS-A9TQ-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	fed06f8b-2c24-4196-a3e5-4a6acea52761	e7763c46-3083-49b4-8739-24cb4ed05f3c	g.chrX:100613634A>C	ENST00000308731.7	-	11	1108	c.945T>G	c.(943-945)taT>taG	p.Y315*	BTK_ENST00000372880.1_Nonsense_Mutation_p.Y315*	NM_000061.2	NP_000052.1	Q06187	BTK_HUMAN	Bruton agammaglobulinemia tyrosine kinase	315	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				adaptive immune response (GO:0002250)|apoptotic signaling pathway (GO:0097190)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|calcium-mediated signaling (GO:0019722)|cell maturation (GO:0048469)|Fc-epsilon receptor signaling pathway (GO:0038095)|histamine secretion by mast cell (GO:0002553)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of B cell apoptotic process (GO:0002902)|regulation of B cell cytokine production (GO:0002721)|response to organic substance (GO:0010033)|response to reactive oxygen species (GO:0000302)|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)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein tyrosine kinase activity (GO:0004713)			breast(4)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(25)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						CAGACACTGTATATTTGCCAG	0.478									Agammaglobulinemia, X-linked																												p.Y315X		Atlas-SNP	.											.	BTK	87	.	0			c.T945G	GRCh37	CM980271	BTK	M		PASS	.						247	217	227					X																	100613634		2203	4300	6503	SO:0001587	stop_gained	695	exon11	Familial Cancer Database	Bruton Type Agammaglobulinemia	CACTGTATATTTG	AK057105	CCDS14482.1, CCDS76002.1, CCDS76003.1	Xq21.33-q22	2014-09-17			ENSG00000010671	ENSG00000010671	2.7.10.1	"Pleckstrin homology (PH) domain containing", "SH2 domain containing"	1133	protein-coding gene	gene with protein product		300300		AGMX1, IMD1		8380905	Standard	NM_000061		Approved	ATK, XLA, PSCTK1	uc004ehg.2	Q06187	OTTHUMG00000022022	ENST00000308731.7:c.945T>G	X.37:g.100613634A>C	ENSP00000308176:p.Tyr315*	304	0	0		134	34	0.253731	NM_000061	B2RAW1|Q32ML5	Nonsense_Mutation	SNP	ENST00000308731.7	37	CCDS14482.1	.	.	.	.	.	.	.	.	.	.	A	40	8.164449	0.98686	.	.	ENSG00000010671	ENST00000372880;ENST00000308731	.	.	.	5.88	-0.277	0.12898	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.0824	0.64932	0.2624:0.0:0.7376:0.0	.	.	.	.	X	315	.	ENSP00000308176:Y315X	Y	-	3	2	BTK	100500290	1.000000	0.71417	0.985000	0.45067	0.988000	0.76386	1.439000	0.35013	-0.260000	0.09418	0.486000	0.48141	TAT	.	.	none		0.478	BTK-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057532.2	NM_000061		C	100613634	A	C	100613634	4	2	35	1	0	0	0	0	0	1	0	0	1559	456	16	5	1070	5	BTK	23	100613634	Nonsense_Mutation	SNP	A	TCGA-GS-A9TQ-01A-11D-A382-10		100613634	54656926	91	14228											
KLHL21	9903	hgsc.bcm.edu	37	chr1	6662376	6662376	+	Silent	SNP	G	G	A																															ctccagctgctcggcgcccaGctcgcccacgtggcgcagaa																										TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr1:6662376G>A	ENST00000377658.4	-	1	553	c.502C>T	c.(502-504)Ctg>Ttg	p.L168L	KLHL21_ENST00000377663.3_Silent_p.L168L|KLHL21_ENST00000467612.1_Intron|KLHL21_ENST00000463043.1_Intron	NM_014851.2	NP_055666.2	Q9UJP4	KLH21_HUMAN	kelch-like family member 21	168	BACK.				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)		TCGGCGCCCAGCTCGCCCACG	0.706																																					p.L168L		Atlas-SNP	.											.	KLHL21	27	.	0			c.C502T						PASS	.						4	4	4					1																	6662376		1941	3902	5843	SO:0001819	synonymous_variant	9903	exon1			CGCCCAGCTCGCC	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.502C>T	1.37:g.6662376G>A		37	0	0		14	8	0.571429	NM_014851	B3KQP2|O75057|Q5SY26|Q5SY28|Q8N4I6|Q8NF10	Silent	SNP	ENST00000377658.4	37	CCDS30575.1																																																																																			.	.	none		0.706	KLHL21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004188.1	NM_014851		A	6662376	G	A	6662376	2	1	36	1	0	0	0	0	0	0	0	1	8385	962	34	2		2	KLHL21	1	6662376	Silent	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10		6662376	242588245	1	14229	179	2									
KLHL21	9903	hgsc.bcm.edu	37	chr1	6662386	6662386	+	Missense_Mutation	SNP	G	G	T																															tcggcgcccagctcgcccacGtggcgcagaatgaaccgctg																								rs531955371		TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr1:6662386G>T	ENST00000377658.4	-	1	543	c.492C>A	c.(490-492)caC>caA	p.H164Q	KLHL21_ENST00000377663.3_Missense_Mutation_p.H164Q|KLHL21_ENST00000467612.1_Intron|KLHL21_ENST00000463043.1_Intron	NM_014851.2	NP_055666.2	Q9UJP4	KLH21_HUMAN	kelch-like family member 21	164	BACK.				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)		GCTCGCCCACGTGGCGCAGAA	0.706																																					p.H164Q		Atlas-SNP	.											.	KLHL21	27	.	0			c.C492A						PASS	.						4	5	5					1																	6662386		2027	4033	6060	SO:0001583	missense	9903	exon1			GCCCACGTGGCGC	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.492C>A	1.37:g.6662386G>T	ENSP00000366886:p.His164Gln	41	0	0		16	8	0.5	NM_014851	B3KQP2|O75057|Q5SY26|Q5SY28|Q8N4I6|Q8NF10	Missense_Mutation	SNP	ENST00000377658.4	37	CCDS30575.1	.	.	.	.	.	.	.	.	.	.	G	36	5.617529	0.96649	.	.	ENSG00000162413	ENST00000377658;ENST00000377663	T;T	0.70045	-0.45;-0.45	4.05	4.05	0.47172	BTB/Kelch-associated (2);	0.050845	0.85682	D	0.000000	T	0.74030	0.3663	M	0.71920	2.185	0.80722	D	1	D;D	0.54397	0.966;0.958	P;P	0.51453	0.67;0.619	T	0.79685	-0.1700	10	0.72032	D	0.01	.	16.0713	0.80936	0.0:0.0:1.0:0.0	.	164;164	Q9UJP4;Q9UJP4-2	KLH21_HUMAN;.	Q	164	ENSP00000366886:H164Q;ENSP00000366891:H164Q	ENSP00000366886:H164Q	H	-	3	2	KLHL21	6584973	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.765000	0.62271	2.189000	0.69895	0.462000	0.41574	CAC	.	.	none		0.706	KLHL21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004188.1	NM_014851		T	6662386	G	T	6662386	3	4	36	1	0	0	0	0	1	0	0	0	8385	1136	40	4	1317	4	KLHL21	1	6662386	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	10	6662386	242588235	2	14230	179	2									
KIF17	57576	hgsc.bcm.edu	37	chr1	21031118	21031118	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctcatcgtagttgttgtcCgcaggcgacaggcaggccac	7	9	13	12	3	1	0	1	0	1	0	4	1	2	0	2	3	0	5	2	3	1	3	rs373442401		TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr1:21031118C>T	ENST00000247986.2	-	5	1255	c.945G>A	c.(943-945)gcG>gcA	p.A315A	KIF17_ENST00000375044.1_Silent_p.A215A|KIF17_ENST00000400463.3_Silent_p.A315A			Q9P2E2	KIF17_HUMAN	kinesin family member 17	315	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)		AGTTGTTGTCCGCAGGCGACA	0.617																																					p.A315A		Atlas-SNP	.											KIF17,NS,carcinoma,-2,1	KIF17	130	1	0			c.G945A						PASS	.	C	,	0,4406		0,0,2203	156	120	132		945,945	-10.2	0	1		132	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	KIF17	NM_001122819.1,NM_020816.2	,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,	315/1029,315/1030	21031118	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	57576	exon5			GTTGTCCGCAGGC	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.945G>A	1.37:g.21031118C>T		196	0	0		133	57	0.428571	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Silent	SNP	ENST00000247986.2	37	CCDS213.1																																																																																			.	.	none		0.617	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816		T	21031118	C	T	21031118	2	4	36	1	0	0	0	0	0	0	0	1	8288	639	23	1		1	KIF17	1	21031118	Silent	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	14368732	21031118	228219503	3	14231											
PTPRF	5792	hgsc.bcm.edu	37	chr1	44084821	44084821	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatcctggccttcctacgaCgggtcaaggcctgcaacccc	7	7	9	18	2	1	0	1	0	0	0	3	1	3	0	7	3	3	1	7	3	3	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr1:44084821C>T	ENST00000359947.4	+	27	4934	c.4594C>T	c.(4594-4596)Cgg>Tgg	p.R1532W	PTPRF_ENST00000496447.1_3'UTR|PTPRF_ENST00000438120.1_Missense_Mutation_p.R1523W|PTPRF_ENST00000422171.2_Missense_Mutation_p.R891W|PTPRF_ENST00000372414.3_Missense_Mutation_p.R1532W|PTPRF_ENST00000372413.3_Missense_Mutation_p.R1523W	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	1532	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				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)				CTTCCTACGACGGGTCAAGGC	0.632																																					p.R1532W		Atlas-SNP	.											.	PTPRF	172	.	0			c.C4594T						PASS	.						50	45	47					1																	44084821		2203	4300	6503	SO:0001583	missense	5792	exon27			CTACGACGGGTCA	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.4594C>T	1.37:g.44084821C>T	ENSP00000353030:p.Arg1532Trp	45	0	0		41	21	0.512195	NM_002840	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Missense_Mutation	SNP	ENST00000359947.4	37	CCDS489.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.47|15.47	2.842593|2.842593	0.51057|0.51057	.|.	.|.	ENSG00000142949|ENSG00000142949	ENST00000359947;ENST00000438120;ENST00000372414;ENST00000372413;ENST00000422171;ENST00000372407|ENST00000412568;ENST00000414879	D;D;D;D;D;D|.	0.84298|.	-1.83;-1.83;-1.83;-1.83;-1.83;-1.83|.	5.42|5.42	3.24|3.24	0.37175|0.37175	Protein-tyrosine phosphatase, receptor/non-receptor type (3);Protein-tyrosine/Dual-specificity phosphatase (1);|.	0.000000|.	0.31323|.	N|.	0.007859|.	D|D	0.85008|0.85008	0.5599|0.5599	H|H	0.94183|0.94183	3.505|3.505	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;0.999;0.998;0.997;1.0|.	D|D	0.89646|0.89646	0.3866|0.3866	10|5	0.87932|.	D|.	0|.	.|.	14.1802|14.1802	0.65568|0.65568	0.393:0.607:0.0:0.0|0.393:0.607:0.0:0.0	.|.	1177;891;1109;1523;1532|.	Q59FI2;F2Z3B8;Q5W9G3;P10586-2;P10586|.	.;.;.;.;PTPRF_HUMAN|.	W|M	1532;1523;1532;1523;891;604|915;956	ENSP00000353030:R1532W;ENSP00000398822:R1523W;ENSP00000361491:R1532W;ENSP00000361490:R1523W;ENSP00000387885:R891W;ENSP00000361484:R604W|.	ENSP00000353030:R1532W|.	R|T	+|+	1|2	2|0	PTPRF|PTPRF	43857408|43857408	0.005000|0.005000	0.15991|0.15991	1.000000|1.000000	0.80357|0.80357	0.709000|0.709000	0.40893|0.40893	0.051000|0.051000	0.14141|0.14141	1.389000|1.389000	0.46526|0.46526	0.561000|0.561000	0.74099|0.74099	CGG|ACG	.	.	none		0.632	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1			T	44084821	C	T	44084821	3	4	36	1	0	0	0	0	1	0	0	0	12816	527	19	1	4692	1	PTPRF	1	44084821	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	23053703	44084821	205165800	4	14232											
KANK4	163782	hgsc.bcm.edu	37	chr1	62739545	62739545	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	gtcagtgttcaccatcacgtCcgtctggccctgagtgtctt	5	13	10	13	2	5	1	3	1	2	0	6	1	6	1	3	1	0	1	3	1	0	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr1:62739545C>G	ENST00000371153.4	-	3	1609	c.1231G>C	c.(1231-1233)Gac>Cac	p.D411H	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	411						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						ACCATCACGTCCGTCTGGCCC	0.517																																					p.D411H		Atlas-SNP	.											KANK4,right_upper_lobe,carcinoma,+2,1	KANK4	135	1	0			c.G1231C						PASS	.						197	166	176					1																	62739545		2203	4300	6503	SO:0001583	missense	163782	exon3			TCACGTCCGTCTG	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.1231G>C	1.37:g.62739545C>G	ENSP00000360195:p.Asp411His	170	0	0		131	56	0.427481	NM_181712	B1ALP7|Q6P9A0|Q86T71|Q86VE6|Q8NAX3	Missense_Mutation	SNP	ENST00000371153.4	37	CCDS620.1	.	.	.	.	.	.	.	.	.	.	C	18.18	3.567050	0.65651	.	.	ENSG00000132854	ENST00000371153	T	0.62498	0.02	5.67	5.67	0.87782	.	0.000000	0.41097	D	0.000950	T	0.77598	0.4154	M	0.66939	2.045	0.80722	D	1	D	0.76494	0.999	D	0.64042	0.921	T	0.78848	-0.2042	10	0.72032	D	0.01	-16.8446	19.3774	0.94517	0.0:1.0:0.0:0.0	.	411	Q5T7N3	KANK4_HUMAN	H	411	ENSP00000360195:D411H	ENSP00000360195:D411H	D	-	1	0	KANK4	62512133	0.973000	0.33851	0.178000	0.23040	0.004000	0.04260	2.844000	0.48246	2.677000	0.91161	0.561000	0.74099	GAC	.	.	none		0.517	KANK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024877.1	NM_181712		G	62739545	C	G	62739545	3	3	36	1	0	0	0	0	1	0	0	0	7988	855	30	4	1788	4	KANK4	1	62739545	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	18654724	62739545	186511076	5	14233											
COL11A1	1301	hgsc.bcm.edu	37	chr1	103463891	103463891	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gcccatcagcaccaggaagtCcagcaagtcctggttttcct	9	9	9	14	0	1	0	1	0	0	0	4	1	4	1	5	2	2	3	5	2	2	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr1:103463891C>A	ENST00000370096.3	-	25	2483	c.2171G>T	c.(2170-2172)gGa>gTa	p.G724V	COL11A1_ENST00000358392.2_Missense_Mutation_p.G736V|COL11A1_ENST00000353414.4_Missense_Mutation_p.G685V|COL11A1_ENST00000512756.1_Missense_Mutation_p.G608V|COL11A1_ENST00000461720.1_5'Flank	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	724	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)	p.G736V(1)|p.G724V(1)		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)		ACCAGGAAGTCCAGCAAGTCC	0.303																																					p.G736V		Atlas-SNP	.											.	COL11A1	972	.	2	Substitution - Missense(2)	lung(2)	c.G2207T						PASS	.						38	40	39					1																	103463891		2202	4299	6501	SO:0001583	missense	1301	exon25			GGAAGTCCAGCAA	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.2171G>T	1.37:g.103463891C>A	ENSP00000359114:p.Gly724Val	567	1	0.00176367		401	166	0.413965	NM_080629	B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Missense_Mutation	SNP	ENST00000370096.3	37	CCDS778.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.521145	0.85600	.	.	ENSG00000060718	ENST00000370096;ENST00000358392;ENST00000353414;ENST00000512756	D;D;D;D	0.98807	-5.15;-5.15;-5.15;-5.15	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	D	0.99524	0.9830	H	0.97131	3.945	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.996;0.999;0.999;0.998	D	0.98152	1.0442	10	0.87932	D	0	.	18.9689	0.92707	0.0:1.0:0.0:0.0	.	608;685;736;724	E9PCU0;P12107-3;P12107-2;P12107	.;.;.;COBA1_HUMAN	V	724;736;685;608	ENSP00000359114:G724V;ENSP00000351163:G736V;ENSP00000302551:G685V;ENSP00000426533:G608V	ENSP00000302551:G685V	G	-	2	0	COL11A1	103236479	1.000000	0.71417	0.971000	0.41717	0.962000	0.63368	5.505000	0.66981	2.494000	0.84150	0.467000	0.42956	GGA	.	.	none		0.303	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630		A	103463891	C	A	103463891	3	1	36	1	0	0	0	0	1	0	0	0	3669	855	30	4	3421	4	COL11A1	1	103463891	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	40724346	103463891	145786730	6	14234											
KCNA3	3738	hgsc.bcm.edu	37	chr1	111216563	111216563	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgaagaagggatcggagaagCtggaggctcctgcgcgggac	10	4	18	9	4	0	2	0	0	0	2	2	7	1	5	1	5	2	2	1	5	3	0			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr1:111216563C>T	ENST00000369769.2	-	1	1092	c.869G>A	c.(868-870)aGc>aAc	p.S290N		NM_002232.3	NP_002223.3	P22001	KCNA3_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 3	290					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)	ATCGGAGAAGCTGGAGGCTCC	0.617																																					p.S290N		Atlas-SNP	.											.	KCNA3	91	.	0			c.G869A						PASS	.						63	66	65					1																	111216563		2203	4300	6503	SO:0001583	missense	3738	exon1			GAGAAGCTGGAGG	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.869G>A	1.37:g.111216563C>T	ENSP00000358784:p.Ser290Asn	58	0	0		56	25	0.446429	NM_002232	Q5VWN2	Missense_Mutation	SNP	ENST00000369769.2	37	CCDS828.2	.	.	.	.	.	.	.	.	.	.	C	7.305	0.613728	0.14066	.	.	ENSG00000177272	ENST00000369769	D	0.97404	-4.37	5.04	4.11	0.48088	.	0.311416	0.29861	U	0.011005	D	0.88983	0.6586	L	0.34521	1.04	0.39488	D	0.968005	B	0.14012	0.009	B	0.17433	0.018	D	0.84153	0.0424	10	0.17369	T	0.5	.	10.7352	0.46120	0.1908:0.8092:0.0:0.0	.	290	P22001	KCNA3_HUMAN	N	290	ENSP00000358784:S290N	ENSP00000358784:S290N	S	-	2	0	KCNA3	111018086	.	.	1.000000	0.80357	0.982000	0.71751	.	.	1.090000	0.41315	0.655000	0.94253	AGC	.	.	none		0.617	KCNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083391.1	NM_002232		T	111216563	C	T	111216563	3	4	36	1	0	0	0	0	1	0	0	0	8013	797	28	2	862	2	KCNA3	1	111216563	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	7752672	111216563	138034058	7	14235											
SEMA4A	64218	hgsc.bcm.edu	37	chr1	156146494	156146494	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgggagcatgtgaaggtcccGttgaccagggtcagtggtgg	7	8	18	8	2	1	2	1	2	0	0	2	3	2	3	2	5	1	2	2	5	1	1	rs185601992	byFrequency	TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr1:156146494G>A	ENST00000368285.3	+	15	2259	c.1992G>A	c.(1990-1992)ccG>ccA	p.P664P	SEMA4A_ENST00000355014.2_Silent_p.P664P|SEMA4A_ENST00000368286.2_Silent_p.P532P|SEMA4A_ENST00000368284.1_Silent_p.P532P|SEMA4A_ENST00000368282.1_Silent_p.P664P	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	664					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)					TGAAGGTCCCGTTGACCAGGG	0.607													G|||	3	0.000599042	0.0	0.0	5008	,	,		19484	0.003		0.0	False		,,,				2504	0.0				p.P664P		Atlas-SNP	.											.	SEMA4A	75	.	0			c.G1992A						PASS	.	G	,,,	0,4406		0,0,2203	66	62	63		1992,1992,1596,1992	-4.4	0.9	1		63	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEMA4A	NM_001193300.1,NM_001193301.1,NM_001193302.1,NM_022367.3	,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,	664/762,664/762,532/630,664/762	156146494	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	64218	exon15			GGTCCCGTTGACC	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.1992G>A	1.37:g.156146494G>A		73	0	0		119	65	0.546219	NM_001193300	B2RDH8|B3KR76|Q5TCI5|Q5TCJ6|Q8WUA9	Silent	SNP	ENST00000368285.3	37	CCDS1132.1																																																																																			G|0.999;A|0.001	0.001	strong		0.607	SEMA4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039484.2	NM_022367		A	156146494	G	A	156146494	2	1	36	1	0	0	0	0	0	0	0	1	14046	1132	40	1		1	SEMA4A	1	156146494	Silent	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	44929931	156146494	93104127	8	14236											
NUF2	83540	hgsc.bcm.edu	37	chr1	163318812	163318812	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taatcaagaaatccaaaaaaTtaaacttggaattcaacaac	22	9	3	7	0	2	1	2	0	0	1	3	2	3	2	1	1	3	0	1	1	11	4			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr1:163318812T>C	ENST00000271452.3	+	13	1481	c.1202T>C	c.(1201-1203)aTt>aCt	p.I401T	NUF2_ENST00000367900.3_Missense_Mutation_p.I401T|NUF2_ENST00000524800.1_Missense_Mutation_p.I354T	NM_145697.2	NP_663735.2	Q9BZD4	NUF2_HUMAN	NUF2, NDC80 kinetochore complex component	401	Interaction with the C-terminus of NDC80 and the SPBC24-SPBC25 subcomplex.				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)					ATCCAAAAAATTAAACTTGGA	0.338																																					p.I401T		Atlas-SNP	.											.	NUF2	138	.	0			c.T1202C						PASS	.						60	64	63					1																	163318812		2203	4299	6502	SO:0001583	missense	83540	exon13			AAAAAATTAAACT	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.1202T>C	1.37:g.163318812T>C	ENSP00000271452:p.Ile401Thr	369	0	0		276	124	0.449275	NM_145697	Q8WU69|Q96HJ4|Q96Q78	Missense_Mutation	SNP	ENST00000271452.3	37	CCDS1245.1	.	.	.	.	.	.	.	.	.	.	T	1.373	-0.585581	0.03827	.	.	ENSG00000143228	ENST00000524800;ENST00000367900;ENST00000271452	T;T;T	0.34072	1.45;1.38;1.38	5.5	3.13	0.36017	.	0.485095	0.24628	N	0.036908	T	0.09291	0.0229	L	0.34521	1.04	0.29837	N	0.829583	B;B	0.23058	0.079;0.079	B;B	0.21546	0.035;0.035	T	0.21793	-1.0235	9	0.17832	T	0.49	-1.6075	7.0329	0.24977	0.1477:0.0:0.1549:0.6974	.	354;401	E9PQC4;Q9BZD4	.;NUF2_HUMAN	T	354;401;401	ENSP00000436888:I354T;ENSP00000356875:I401T;ENSP00000271452:I401T	ENSP00000271452:I401T	I	+	2	0	NUF2	161585436	0.007000	0.16637	0.000000	0.03702	0.330000	0.28571	0.855000	0.27805	0.484000	0.27630	-0.301000	0.09380	ATT	.	.	none		0.338	NUF2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000082812.1	NM_145697		C	163318812	T	C	163318812	3	2	36	1	0	0	0	0	1	0	0	0	10756	1493	52	3	1248	3	NUF2	1	163318812	Missense_Mutation	SNP	T	TCGA-GS-A9TT-01A-11D-A382-10	7172318	163318812	85931809	9	14237											
FAM5B	57795	hgsc.bcm.edu	37	chr1	177250054	177250054	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ctgtctcaccaagaacagcaCcctggagcctgtcatggcca	10	7	9	15	0	2	1	2	0	1	1	3	2	2	2	4	2	3	1	4	2	2	0			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr1:177250054C>A	ENST00000361539.4	+	8	2054	c.1742C>A	c.(1741-1743)aCc>aAc	p.T581N	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	581					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)											AAGAACAGCACCCTGGAGCCT	0.562																																					p.T581N		Atlas-SNP	.											.	FAM5B	191	.	0			c.C1742A						PASS	.						59	54	56					1																	177250054		2203	4300	6503	SO:0001583	missense	57795	exon8			ACAGCACCCTGGA		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.1742C>A	1.37:g.177250054C>A	ENSP00000354481:p.Thr581Asn	104	0	0		89	45	0.505618	NM_021165	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	37	CCDS1320.1	.	.	.	.	.	.	.	.	.	.	C	18.01	3.528306	0.64860	.	.	ENSG00000198797	ENST00000536589;ENST00000361539	T	0.18174	2.23	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.45856	0.1363	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.91635	0.999;0.991	T	0.46119	-0.9214	10	0.62326	D	0.03	-26.8652	18.4386	0.90656	0.0:1.0:0.0:0.0	.	476;581	Q9C0B6-2;Q9C0B6	.;FAM5B_HUMAN	N	334;581	ENSP00000354481:T581N	ENSP00000354481:T581N	T	+	2	0	FAM5B	175516677	1.000000	0.71417	1.000000	0.80357	0.820000	0.46376	7.707000	0.84623	2.443000	0.82685	0.313000	0.20887	ACC	.	.	none		0.562	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165		A	177250054	C	A	177250054	3	1	36	1	0	0	0	0	1	0	0	0	5601	507	18	4	1768	4	FAM5B	1	177250054	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	13931242	177250054	72000567	10	14238											
PKP1	5317	hgsc.bcm.edu	37	chr1	201252908	201252908	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aactccacgttggctttgccGtcggaccaaaagatgaaaac	13	8	9	11	3	0	2	0	1	0	1	2	3	1	3	3	2	3	2	3	2	5	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr1:201252908G>A	ENST00000352845.3	+	1	78	c.78G>A	c.(76-78)ccG>ccA	p.P26P	PKP1_ENST00000263946.3_Silent_p.P26P|PKP1_ENST00000367324.3_Silent_p.P26P			Q13835	PKP1_HUMAN	plakophilin 1	26					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						TGGCTTTGCCGTCGGACCAAA	0.612																																					p.P26P		Atlas-SNP	.											.	PKP1	127	.	0			c.G78A						PASS	.						109	86	94					1																	201252908		2203	4300	6503	SO:0001819	synonymous_variant	5317	exon1			TTTGCCGTCGGAC	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.78G>A	1.37:g.201252908G>A		81	0	0		85	35	0.411765	NM_001005337	O00645|Q14CA0|Q15152	Silent	SNP	ENST00000352845.3	37	CCDS30966.1																																																																																			.	.	none		0.612	PKP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086897.1	NM_000299		A	201252908	G	A	201252908	2	1	36	1	0	0	0	0	0	0	0	1	11993	1132	40	1		1	PKP1	1	201252908	Silent	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	24002854	201252908	47997713	11	14239											
BTG2	7832	hgsc.bcm.edu	37	chr1	203274876	203274876	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgctccaggaggcactcacaGgtgagcgcatgccgaggggc	8	4	16	13	3	1	1	1	1	0	0	2	3	2	2	2	5	2	3	2	5	0	0			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr1:203274876G>T	ENST00000290551.4	+	1	213	c.142G>T	c.(142-144)Gag>Tag	p.E48*	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	48					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			GGCACTCACAGGTGAGCGCAT	0.706																																					p.E48X		Atlas-SNP	.											.	BTG2	16	.	0			c.G142T						PASS	.						10	12	12					1																	203274876		1996	3876	5872	SO:0001630	splice_region_variant	7832	exon1			CTCACAGGTGAGC		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.142+1G>T	1.37:g.203274876G>T		70	0	0		65	30	0.461538	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Nonsense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	g	37	6.127598	0.97305	.	.	ENSG00000159388	ENST00000290551	.	.	.	4.23	4.23	0.50019	.	0.072934	0.52532	D	0.000079	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-12.437	15.3407	0.74293	0.0:0.0:1.0:0.0	.	.	.	.	X	48	.	ENSP00000290551:E48X	E	+	1	0	BTG2	201541499	1.000000	0.71417	0.996000	0.52242	0.542000	0.35054	8.401000	0.90202	2.199000	0.70637	0.471000	0.43371	GAG	.	.	none		0.706	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763	Nonsense_Mutation	T	203274876	G	T	203274876	5	4	36	1	0	0	0	0	0	0	1	0	1556	1014	35	4	144	4	BTG2	1	203274876	Splice_Site	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	2021968	203274876	45975745	12	14240											
ESRRG	2104	hgsc.bcm.edu	37	chr1	216680418	216680418	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgtcatcagcatcttgccagCtcgacgagggtcttccatgt	7	12	10	12	2	4	0	2	0	2	0	6	2	5	0	2	1	3	2	2	1	0	2	rs200999094		TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr1:216680418C>G	ENST00000408911.3	-	7	1393	c.1240G>C	c.(1240-1242)Gct>Cct	p.A414P	ESRRG_ENST00000493748.1_Missense_Mutation_p.A391P|ESRRG_ENST00000360012.3_Missense_Mutation_p.A391P|ESRRG_ENST00000493603.1_Missense_Mutation_p.A391P|ESRRG_ENST00000366938.2_Missense_Mutation_p.A391P|ESRRG_ENST00000366937.1_Missense_Mutation_p.A426P|ESRRG_ENST00000359162.2_Missense_Mutation_p.A391P|ESRRG_ENST00000366940.2_Missense_Mutation_p.A391P|ESRRG_ENST00000361395.2_Missense_Mutation_p.A391P|ESRRG_ENST00000487276.1_Missense_Mutation_p.A391P|ESRRG_ENST00000463665.1_Missense_Mutation_p.A352P|ESRRG_ENST00000361525.3_Missense_Mutation_p.A391P|ESRRG_ENST00000391890.3_Missense_Mutation_p.A398P	NM_001438.3	NP_001429.2	P62508	ERR3_HUMAN	estrogen-related receptor gamma	414					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)	ATCTTGCCAGCTCGACGAGGG	0.507																																					p.A426P		Atlas-SNP	.											.	ESRRG	111	.	0			c.G1276C						PASS	.						122	107	112					1																	216680418		2203	4300	6503	SO:0001583	missense	2104	exon8			TGCCAGCTCGACG	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.1240G>C	1.37:g.216680418C>G	ENSP00000386171:p.Ala414Pro	205	0	0		150	69	0.46	NM_001243518	A8K4I0|A8K6I2|B3KY84|E9PGB7|F8W8J3|O75454|O96021|Q68DA0|Q6P274|Q6PK28|Q6TS38|Q9R1F3|Q9UNJ4	Missense_Mutation	SNP	ENST00000408911.3	37	CCDS41468.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.265011	0.80358	.	.	ENSG00000196482	ENST00000361525;ENST00000366940;ENST00000366937;ENST00000408911;ENST00000359162;ENST00000361395;ENST00000366938;ENST00000360012;ENST00000493603;ENST00000391890;ENST00000463665;ENST00000487276;ENST00000354407;ENST00000493748	D;D;D;D;D;D;D;D;D;D;D;D;D	0.96651	-4.08;-4.08;-4.08;-4.08;-4.08;-4.08;-4.08;-4.08;-4.08;-4.08;-4.08;-4.08;-4.08	5.14	5.14	0.70334	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.049439	0.85682	D	0.000000	D	0.97779	0.9271	M	0.70275	2.135	0.80722	D	1	B;P;D	0.56287	0.065;0.937;0.975	B;D;P	0.67725	0.083;0.953;0.654	D	0.98581	1.0650	10	0.72032	D	0.01	.	18.6137	0.91295	0.0:1.0:0.0:0.0	.	352;426;414	E9PGB7;F8W8J3;P62508	.;.;ERR3_HUMAN	P	391;391;426;414;391;391;391;391;391;398;352;391;391;391	ENSP00000355225:A391P;ENSP00000355907:A391P;ENSP00000355904:A426P;ENSP00000386171:A414P;ENSP00000352077:A391P;ENSP00000354584:A391P;ENSP00000355905:A391P;ENSP00000353108:A391P;ENSP00000419594:A391P;ENSP00000375761:A398P;ENSP00000418629:A352P;ENSP00000419155:A391P;ENSP00000417374:A391P	ENSP00000346386:A391P	A	-	1	0	ESRRG	214747041	1.000000	0.71417	0.261000	0.24466	0.984000	0.73092	7.818000	0.86416	2.395000	0.81488	0.561000	0.74099	GCT	C|0.999;T|0.001	.	alt		0.507	ESRRG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089882.2	NM_206595		G	216680418	C	G	216680418	3	3	36	1	0	0	0	0	1	0	0	0	5264	797	28	4	140	4	ESRRG	1	216680418	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	13405542	216680418	32570203	13	14241											
ITPKB	3707	hgsc.bcm.edu	37	chr1	226924565	226924565	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccaggactttgtcctccgttCctcgctccgggcgccctgaa	4	10	10	17	4	0	1	0	1	0	0	5	2	4	2	6	2	0	2	6	2	1	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr1:226924565C>A	ENST00000272117.3	-	1	594	c.595G>T	c.(595-597)Gaa>Taa	p.E199*	ITPKB_ENST00000366784.1_Nonsense_Mutation_p.E199*|ITPKB_ENST00000429204.1_Nonsense_Mutation_p.E199*			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	199					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)				GTCCTCCGTTCCTCGCTCCGG	0.667																																					p.E199X	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											.	ITPKB	158	.	0			c.G595T						PASS	.						30	36	34					1																	226924565		2198	4284	6482	SO:0001587	stop_gained	3707	exon2			TCCGTTCCTCGCT	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.595G>T	1.37:g.226924565C>A	ENSP00000272117:p.Glu199*	26	0	0		46	22	0.478261	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Nonsense_Mutation	SNP	ENST00000272117.3	37	CCDS1555.1	.	.	.	.	.	.	.	.	.	.	C	42	9.419618	0.99166	.	.	ENSG00000143772	ENST00000272117;ENST00000429204;ENST00000366784	.	.	.	4.6	4.6	0.57074	.	0.000000	0.51477	D	0.000083	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.18710	T	0.47	.	14.432	0.67257	0.0:1.0:0.0:0.0	.	.	.	.	X	199	.	ENSP00000272117:E199X	E	-	1	0	ITPKB	224991188	0.009000	0.17119	0.972000	0.41901	0.939000	0.58152	0.733000	0.26087	2.374000	0.81015	0.561000	0.74099	GAA	.	.	none		0.667	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221		A	226924565	C	A	226924565	4	1	36	1	0	0	0	0	0	1	0	0	7927	864	30	4	2273	4	ITPKB	1	226924565	Nonsense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	10244147	226924565	22326056	14	14242											
IRF2BP2	359948	hgsc.bcm.edu	37	chr1	234744253	234744253	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	caacctgcctgcagtcagggCcggctccttcttaaacttgc	7	10	9	15	1	2	0	1	0	1	0	3	0	3	0	4	2	5	2	4	2	3	3	rs565711940		TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr1:234744253C>T	ENST00000366609.3	-	1	1018	c.988G>A	c.(988-990)Gcc>Acc	p.A330T	RP4-781K5.2_ENST00000436039.1_RNA|IRF2BP2_ENST00000491430.1_5'Flank|IRF2BP2_ENST00000366610.3_Missense_Mutation_p.A330T	NM_182972.2	NP_892017.2	Q7Z5L9	I2BP2_HUMAN	interferon regulatory factor 2 binding protein 2	330					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)			GCAGTCAGGGCCGGCTCCTTC	0.637																																					p.A330T		Atlas-SNP	.											.	IRF2BP2	37	.	0			c.G988A						PASS	.						22	21	21					1																	234744253		2200	4300	6500	SO:0001583	missense	359948	exon1			TCAGGGCCGGCTC	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.988G>A	1.37:g.234744253C>T	ENSP00000355568:p.Ala330Thr	58	0	0		61	29	0.47541	NM_182972	B1AM35|B1AM36|Q6P083|Q7Z5L8|Q8N351|Q8WUH8	Missense_Mutation	SNP	ENST00000366609.3	37	CCDS1602.1	.	.	.	.	.	.	.	.	.	.	C	17.51	3.406532	0.62399	.	.	ENSG00000168264	ENST00000366610;ENST00000366609	T;T	0.32023	1.5;1.47	4.81	3.9	0.45041	.	0.264544	0.37053	N	0.002279	T	0.25121	0.0610	L	0.44542	1.39	0.35796	D	0.822801	B;B	0.19331	0.02;0.035	B;B	0.16289	0.007;0.015	T	0.19353	-1.0308	10	0.33940	T	0.23	-5.1635	10.9107	0.47108	0.0:0.9118:0.0:0.0882	.	330;330	Q7Z5L9;Q7Z5L9-2	I2BP2_HUMAN;.	T	330	ENSP00000355569:A330T;ENSP00000355568:A330T	ENSP00000355568:A330T	A	-	1	0	IRF2BP2	232810876	0.961000	0.32948	1.000000	0.80357	0.998000	0.95712	1.793000	0.38764	1.230000	0.43646	0.561000	0.74099	GCC	.	.	none		0.637	IRF2BP2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000092705.1	NM_182972		T	234744253	C	T	234744253	3	4	36	1	0	0	0	0	1	0	0	0	7839	739	26	2	783	2	IRF2BP2	1	234744253	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	7819688	234744253	14506368	15	14243											
MBOAT2	129642	hgsc.bcm.edu	37	chr2	9028160	9028160	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	attcttaccatcatgaatttCgcaagccaaactagtgatct	13	13	5	10	1	3	2	1	2	2	0	4	2	3	2	2	0	3	1	2	0	5	4			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr2:9028160C>T	ENST00000305997.3	-	5	637	c.439G>A	c.(439-441)Gaa>Aaa	p.E147K	MBOAT2_ENST00000486484.1_5'UTR	NM_138799.2	NP_620154.2	Q6ZWT7	MBOA2_HUMAN	membrane bound O-acyltransferase domain containing 2	147					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)	p.E147K(1)	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)					TCATGAATTTCGCAAGCCAAA	0.274																																					p.E147K	Ovarian(194;1699 3813 22401)	Atlas-SNP	.											MBOAT2,caecum,carcinoma,0,2	MBOAT2	36	2	1	Substitution - Missense(1)	large_intestine(1)	c.G439A						PASS	.						68	78	74					2																	9028160		2201	4292	6493	SO:0001583	missense	129642	exon5			GAATTTCGCAAGC	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.439G>A	2.37:g.9028160C>T	ENSP00000302177:p.Glu147Lys	531	1	0.00188324		456	218	0.47807	NM_138799	A9EDR2|Q8NCE7|Q96KY4	Missense_Mutation	SNP	ENST00000305997.3	37	CCDS1660.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.458328	0.84317	.	.	ENSG00000143797	ENST00000305997;ENST00000462696	T;T	0.74421	-0.84;-0.84	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	D	0.83046	0.5169	M	0.70595	2.14	0.58432	D	0.999992	D;D	0.62365	0.991;0.991	P;P	0.56612	0.802;0.802	D	0.83379	0.0011	10	0.52906	T	0.07	-24.9514	17.9261	0.88983	0.0:1.0:0.0:0.0	.	147;147	B7Z3I3;Q6ZWT7	.;MBOA2_HUMAN	K	147;124	ENSP00000302177:E147K;ENSP00000417409:E124K	ENSP00000302177:E147K	E	-	1	0	MBOAT2	8945611	1.000000	0.71417	0.967000	0.41034	0.919000	0.55068	5.638000	0.67861	2.767000	0.95098	0.655000	0.94253	GAA	.	.	none		0.274	MBOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206735.1	NM_138799		T	9028160	C	T	9028160	3	4	36	1	0	0	0	0	1	0	0	0	9366	893	31	1	1159	1	MBOAT2	2	9028160	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10		9028160	234171213	16	14244											
LRRTM4	80059	hgsc.bcm.edu	37	chr2	77746080	77746080	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atatttccagacaatgtgatGgatattaatgatatccacgc	14	13	7	7	1	0	3	0	2	0	1	2	4	2	4	2	1	0	0	2	1	5	5			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr2:77746080G>T	ENST00000409093.1	-	3	1251	c.915C>A	c.(913-915)tcC>tcA	p.S305S	LRRTM4_ENST00000409884.1_Silent_p.S305S|LRRTM4_ENST00000409088.3_Silent_p.S305S|LRRTM4_ENST00000409282.1_Silent_p.S306S|LRRTM4_ENST00000409911.1_Silent_p.S306S			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)		ACAATGTGATGGATATTAATG	0.353																																					p.S305S		Atlas-SNP	.											.	LRRTM4	334	.	0			c.C915A						PASS	.						45	40	42					2																	77746080		1858	4108	5966	SO:0001819	synonymous_variant	80059	exon3			TGTGATGGATATT	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.915C>A	2.37:g.77746080G>T		134	0	0		96	43	0.447917	NM_024993	Q4FZ98|Q6UXJ7	Silent	SNP	ENST00000409093.1	37	CCDS46346.1																																																																																			.	.	none		0.353	LRRTM4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328225.1	NM_024993		T	77746080	G	T	77746080	2	4	36	1	0	0	0	0	0	0	0	1	9051	1335	47	4		4	LRRTM4	2	77746080	Silent	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	68717920	77746080	165453293	17	14245											
POLR1A	25885	hgsc.bcm.edu	37	chr2	86302316	86302316	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cattagggccgttgatgaccGcttgcctaagttcctgaaca	9	11	10	11	2	0	3	0	3	0	0	1	3	1	3	4	1	2	3	4	1	3	5			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr2:86302316G>A	ENST00000263857.6	-	12	1826	c.1448C>T	c.(1447-1449)gCg>gTg	p.A483V	POLR1A_ENST00000409681.1_Missense_Mutation_p.A483V			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	483					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						GTTGATGACCGCTTGCCTAAG	0.552																																					p.A483V		Atlas-SNP	.											POLR1A,NS,carcinoma,0,1	POLR1A	137	1	0			c.C1448T						scavenged	.						36	38	37					2																	86302316		2009	4181	6190	SO:0001583	missense	25885	exon12			ATGACCGCTTGCC	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.1448C>T	2.37:g.86302316G>A	ENSP00000263857:p.Ala483Val	144	1	0.00694444		109	42	0.385321	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	ENST00000263857.6	37	CCDS42706.1	.	.	.	.	.	.	.	.	.	.	G	16.30	3.084366	0.55861	.	.	ENSG00000068654	ENST00000263857;ENST00000409681	T;T	0.68025	-0.3;-0.3	5.01	5.01	0.66863	RNA polymerase, alpha subunit (1);RNA polymerase, N-terminal (1);	0.101743	0.64402	D	0.000003	T	0.81375	0.4809	M	0.75777	2.31	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.80358	-0.1416	10	0.38643	T	0.18	-15.9554	18.1227	0.89577	0.0:0.0:1.0:0.0	.	483	O95602	RPA1_HUMAN	V	483	ENSP00000263857:A483V;ENSP00000386300:A483V	ENSP00000263857:A483V	A	-	2	0	POLR1A	86155827	1.000000	0.71417	1.000000	0.80357	0.425000	0.31504	9.165000	0.94761	2.606000	0.88127	0.655000	0.94253	GCG	.	.	none		0.552	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425		A	86302316	G	A	86302316	3	1	36	1	0	0	0	0	1	0	0	0	12218	1087	38	1	3806	1	POLR1A	2	86302316	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	8556236	86302316	156897057	18	14246											
PTPN18	26469	hgsc.bcm.edu	37	chr2	131130741	131130741	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttctcccaggtttcaacctgCgcattgggaggccgaagggt	7	10	13	11	2	2	0	1	0	1	0	3	2	2	1	3	4	2	2	3	4	2	3			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr2:131130741C>T	ENST00000175756.5	+	15	1428	c.1327C>T	c.(1327-1329)Cgc>Tgc	p.R443C	PTPN18_ENST00000347849.3_Missense_Mutation_p.R336C	NM_014369.3	NP_055184.2	Q99952	PTN18_HUMAN	protein tyrosine phosphatase, non-receptor type 18 (brain-derived)	443					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)			endometrium(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(3)|prostate(1)	15	Colorectal(110;0.1)					TTTCAACCTGCGCATTGGGAG	0.617																																					p.R443C		Atlas-SNP	.											PTPN18,colon,carcinoma,0,1	PTPN18	42	1	0			c.C1327T						PASS	.						41	38	39					2																	131130741		2203	4300	6503	SO:0001583	missense	26469	exon15			AACCTGCGCATTG	X79568	CCDS2161.1, CCDS46410.1	2q21	2011-06-09			ENSG00000072135	ENSG00000072135		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9649	protein-coding gene	gene with protein product		606587				8950995	Standard	NM_014369		Approved	BDP1	uc002trc.3	Q99952	OTTHUMG00000131630	ENST00000175756.5:c.1327C>T	2.37:g.131130741C>T	ENSP00000175756:p.Arg443Cys	87	0	0		56	23	0.410714	NM_014369	B4E1E6|Q53P42	Missense_Mutation	SNP	ENST00000175756.5	37	CCDS2161.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.083313	0.76642	.	.	ENSG00000072135	ENST00000175756;ENST00000347849;ENST00000409022	T;T	0.36699	2.13;1.24	5.29	5.29	0.74685	.	0.000000	0.39146	N	0.001451	T	0.56485	0.1988	L	0.59436	1.845	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.994;0.999;0.999	T	0.57974	-0.7718	10	0.87932	D	0	.	14.8028	0.69929	0.0:1.0:0.0:0.0	.	422;443;336	E7EMB8;Q99952;B4E1E6	.;PTN18_HUMAN;.	C	443;336;422	ENSP00000175756:R443C;ENSP00000310092:R336C	ENSP00000175756:R443C	R	+	1	0	PTPN18	130847211	0.996000	0.38824	1.000000	0.80357	0.449000	0.32228	3.714000	0.54889	2.634000	0.89283	0.655000	0.94253	CGC	.	.	none		0.617	PTPN18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254523.2			T	131130741	C	T	131130741	3	4	36	1	0	0	0	0	1	0	0	0	12797	768	27	1	1385	1	PTPN18	2	131130741	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	44828425	131130741	112068632	19	14247											
SCN2A	6326	hgsc.bcm.edu	37	chr2	166201313	166201313	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccttcctgatcgtgttccgCgtgctgtgtggagagtggat	4	14	14	9	3	0	2	0	1	0	1	4	4	3	3	3	2	1	2	3	2	0	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr2:166201313C>T	ENST00000375437.2	+	16	3101	c.2811C>T	c.(2809-2811)cgC>cgT	p.R937R	SCN2A_ENST00000357398.3_Silent_p.R937R|SCN2A_ENST00000283256.6_Silent_p.R937R|SCN2A_ENST00000375427.2_Silent_p.R937R	NM_001040142.1	NP_001035232.1	Q99250	SCN2A_HUMAN	sodium channel, voltage-gated, type II, alpha subunit	937					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)	TCGTGTTCCGCGTGCTGTGTG	0.488																																					p.R937R		Atlas-SNP	.											.	SCN2A	589	.	0			c.C2811T						PASS	.						254	221	232					2																	166201313		2203	4300	6503	SO:0001819	synonymous_variant	6326	exon15			GTTCCGCGTGCTG	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.2811C>T	2.37:g.166201313C>T		341	1	0.00293255		263	134	0.509506	NM_001040143	A6NC14|A6NIQ5|Q14472|Q53T77|Q9BZC9|Q9BZD0	Silent	SNP	ENST00000375437.2	37	CCDS33314.1																																																																																			.	.	none		0.488	SCN2A-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000102659.2	NM_021007		T	166201313	C	T	166201313	2	4	36	1	0	0	0	0	0	0	0	1	13931	755	27	1		1	SCN2A	2	166201313	Silent	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	35070572	166201313	76998060	20	14248											
DNAH7	56171	hgsc.bcm.edu	37	chr2	196852948	196852948	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaggttgttggtttagacttActttcctaaacaagggggta	11	14	11	5	0	0	1	0	0	0	1	1	1	1	1	1	4	2	4	1	4	7	8			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr2:196852948A>G	ENST00000312428.6	-	13	1459	c.1359T>C	c.(1357-1359)agT>agC	p.S453S		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	453	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						GTTTAGACTTACTTTCCTAAA	0.308																																					p.S453S		Atlas-SNP	.											.	DNAH7	512	.	0			c.T1359C						PASS	.						59	56	57					2																	196852948		1803	4063	5866	SO:0001819	synonymous_variant	56171	exon13			AGACTTACTTTCC	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.1359T>C	2.37:g.196852948A>G		273	0	0		202	79	0.391089	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	37	CCDS42794.1																																																																																			.	.	none		0.308	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		G	196852948	A	G	196852948	2	3	36	1	0	0	0	0	0	0	0	1	4608	388	14	3		3	DNAH7	2	196852948	Silent	SNP	A	TCGA-GS-A9TT-01A-11D-A382-10	30651635	196852948	46346425	21	14249											
FZD7	8324	hgsc.bcm.edu	37	chr2	202899479	202899479	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccggggcgcagccgtaccacGgagagaagggcatctccgtg	8	4	16	13	5	1	1	0	0	1	1	2	3	1	2	4	4	2	3	4	4	2	1			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr2:202899479G>A	ENST00000286201.1	+	1	170	c.109G>A	c.(109-111)Gga>Aga	p.G37R	RP11-107N15.1_ENST00000608741.1_lincRNA	NM_003507.1	NP_003498.1	O75084	FZD7_HUMAN	frizzled class receptor 7	37					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						GCCGTACCACGGAGAGAAGGG	0.711																																					p.G37R		Atlas-SNP	.											.	FZD7	70	.	0			c.G109A						PASS	.						69	62	65					2																	202899479		2203	4300	6503	SO:0001583	missense	8324	exon1			TACCACGGAGAGA	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.109G>A	2.37:g.202899479G>A	ENSP00000286201:p.Gly37Arg	46	0	0		56	28	0.5	NM_003507	O94816|Q53S59|Q96B74	Missense_Mutation	SNP	ENST00000286201.1	37	CCDS2351.1	.	.	.	.	.	.	.	.	.	.	G	14.06	2.423917	0.43020	.	.	ENSG00000155760	ENST00000286201	T	0.75704	-0.96	4.36	3.47	0.39725	.	0.211632	0.38492	U	0.001662	T	0.67202	0.2868	L	0.32530	0.975	0.52501	D	0.99995	P	0.48089	0.905	P	0.45913	0.497	T	0.66756	-0.5843	10	0.48119	T	0.1	.	11.8692	0.52511	0.0864:0.0:0.9136:0.0	.	37	O75084	FZD7_HUMAN	R	37	ENSP00000286201:G37R	ENSP00000286201:G37R	G	+	1	0	FZD7	202607724	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	6.093000	0.71422	0.799000	0.34018	0.313000	0.20887	GGA	.	.	none		0.711	FZD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256314.1	NM_003507		A	202899479	G	A	202899479	3	1	36	1	0	0	0	0	1	0	0	0	6143	1117	39	1	111	1	FZD7	2	202899479	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	6046531	202899479	40299894	22	14250											
SPHKAP	80309	hgsc.bcm.edu	37	chr2	228882550	228882550	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taagctcagggtgctcgtccGtcttcctcttgatctcactg	5	14	9	13	2	4	1	2	1	3	0	8	1	6	1	2	1	2	2	2	1	1	3			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr2:228882550G>A	ENST00000392056.3	-	7	3066	c.3020C>T	c.(3019-3021)aCg>aTg	p.T1007M	SPHKAP_ENST00000344657.5_Missense_Mutation_p.T1007M	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1007						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)	p.T1007M(4)		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)		GTGCTCGTCCGTCTTCCTCTT	0.517																																					p.T1007M		Atlas-SNP	.											SPHKAP_ENST00000392056,NS,carcinoma,0,4	SPHKAP	750	4	4	Substitution - Missense(4)	large_intestine(2)|prostate(2)	c.C3020T						scavenged	.						91	79	83					2																	228882550		2203	4300	6503	SO:0001583	missense	80309	exon7			TCGTCCGTCTTCC		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.3020C>T	2.37:g.228882550G>A	ENSP00000375909:p.Thr1007Met	149	1	0.00671141		131	59	0.450382	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.965491	0.74131	.	.	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.20738	2.06;2.05	6.08	6.08	0.98989	.	0.044434	0.85682	D	0.000000	T	0.38268	0.1034	L	0.29908	0.895	0.58432	D	0.999997	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79784	0.975;0.964;0.993	T	0.06826	-1.0805	10	0.87932	D	0	.	19.6516	0.95815	0.0:0.0:1.0:0.0	.	38;1007;1007	B3KR30;Q2M3C7;Q2M3C7-2	.;SPKAP_HUMAN;.	M	1007	ENSP00000375909:T1007M;ENSP00000339886:T1007M	ENSP00000339886:T1007M	T	-	2	0	SPHKAP	228590794	1.000000	0.71417	0.553000	0.28255	0.787000	0.44495	9.020000	0.93667	2.894000	0.99253	0.655000	0.94253	ACG	.	.	none		0.517	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623		A	228882550	G	A	228882550	3	1	36	1	0	0	0	0	1	0	0	0	15063	1145	40	1	2106	1	SPHKAP	2	228882550	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	25983071	228882550	14316823	23	14251											
PRRT3	285368	hgsc.bcm.edu	37	chr3	9991706	9991706	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcggagttttcaagtggccTgggaaagcccctccccaggg	7	9	13	12	1	1	0	1	0	0	0	3	2	2	2	5	4	1	1	5	4	2	3			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr3:9991706T>C	ENST00000412055.1	-	2	223	c.94A>G	c.(94-96)Agg>Ggg	p.R32G	PRRT3_ENST00000411976.2_Missense_Mutation_p.R32G|PRRT3-AS1_ENST00000431558.1_RNA	NM_207351.3	NP_997234.3	Q5FWE3	PRRT3_HUMAN	proline-rich transmembrane protein 3	32						integral component of membrane (GO:0016021)				NS(2)|breast(1)|endometrium(3)|large_intestine(3)|lung(1)|skin(1)|stomach(2)	13						TCAAGTGGCCTGGGAAAGCCC	0.632																																					p.R32G		Atlas-SNP	.											.	PRRT3	35	.	0			c.A94G						PASS	.						40	45	43					3																	9991706		1875	4109	5984	SO:0001583	missense	285368	exon2			GTGGCCTGGGAAA	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.94A>G	3.37:g.9991706T>C	ENSP00000392511:p.Arg32Gly	72	0	0		72	37	0.513889	NM_207351	Q49AD0|Q6UXY6|Q8NBC9	Missense_Mutation	SNP	ENST00000412055.1	37	CCDS43049.1	.	.	.	.	.	.	.	.	.	.	T	6.596	0.478299	0.12521	.	.	ENSG00000163704	ENST00000412055;ENST00000411976	T;T	0.22336	2.27;1.96	3.99	-0.116	0.13555	.	0.770020	0.11482	N	0.559607	T	0.11922	0.0290	L	0.32530	0.975	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.001	T	0.32295	-0.9912	9	.	.	.	-1.4593	2.4229	0.04453	0.208:0.2375:0.0:0.5545	.	32;32	Q5FWE3-3;Q5FWE3	.;PRRT3_HUMAN	G	32	ENSP00000392511:R32G;ENSP00000404512:R32G	.	R	-	1	2	PRRT3	9966706	0.099000	0.21834	0.007000	0.13788	0.098000	0.18820	0.390000	0.20768	0.198000	0.20407	0.455000	0.32223	AGG	.	.	none		0.632	PRRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339322.1	NM_207351		C	9991706	T	C	9991706	3	2	36	1	0	0	0	0	1	0	0	0	12623	1579	55	3	2863	3	PRRT3	3	9991706	Missense_Mutation	SNP	T	TCGA-GS-A9TT-01A-11D-A382-10		9991706	188030724	24	14252											
FANCD2	2177	hgsc.bcm.edu	37	chr3	10080992	10080992	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgatgaaatcaacatacctcGactcattgtcagtcaactaa	15	11	5	10	1	4	2	4	2	0	0	5	3	4	2	1	0	3	0	1	0	5	3	rs41291203		TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr3:10080992G>A	ENST00000419585.1	+	8	682	c.521G>A	c.(520-522)cGa>cAa	p.R174Q	FANCD2_ENST00000431693.1_Missense_Mutation_p.R174Q|FANCD2_ENST00000287647.3_Missense_Mutation_p.R174Q|FANCD2_ENST00000383807.1_Missense_Mutation_p.R174Q|RNU6-670P_ENST00000364312.1_RNA|FANCD2_ENST00000383806.1_Missense_Mutation_p.R174Q|FANCD2_ENST00000438741.1_3'UTR			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	174	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)		AACATACCTCGACTCATTGTC	0.378			"D, Mis, N, F"			"AML, leukemia"		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				g|||	1	0.000199681	0.0	0.0	5008	,	,		18397	0.0		0.001	False		,,,				2504	0.0				p.R174Q		Atlas-SNP	.	yes	Rec		Fanconi anaemia D2	3	3p26	2177	"Fanconi anemia, complementation group D2"		L	.	FANCD2	253	.	0			c.G521A						PASS	.	G	GLN/ARG,GLN/ARG	0,4406		0,0,2203	85	78	80		521,521	4.8	1	3	dbSNP_127	80	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	FANCD2	NM_001018115.1,NM_033084.3	43,43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	174/1452,174/1472	10080992	1,13005	2203	4300	6503	SO:0001583	missense	2177	exon8	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TACCTCGACTCAT	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.521G>A	3.37:g.10080992G>A	ENSP00000398754:p.Arg174Gln	193	0	0		129	58	0.449612	NM_001018115	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Missense_Mutation	SNP	ENST00000419585.1	37	CCDS33696.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	22.7	4.326378	0.81690	0.0	1.16E-4	ENSG00000144554	ENST00000287647;ENST00000383807;ENST00000383806;ENST00000419585;ENST00000431693	T;T;T;T;T	0.60424	0.19;0.19;0.19;0.19;0.19	5.68	4.81	0.61882	.	0.109676	0.64402	D	0.000010	T	0.62768	0.2455	M	0.81682	2.555	0.42202	D	0.991775	D;D;P	0.53462	0.96;0.96;0.848	B;P;B	0.47376	0.421;0.545;0.241	T	0.63056	-0.6722	10	0.27082	T	0.32	.	11.7293	0.51726	0.0845:0.0:0.9155:0.0	rs41291203	174;174;174	Q9BXW9-2;Q9BXW9;Q9BXW9-4	.;FACD2_HUMAN;.	Q	174	ENSP00000287647:R174Q;ENSP00000373318:R174Q;ENSP00000373317:R174Q;ENSP00000398754:R174Q;ENSP00000399354:R174Q	ENSP00000287647:R174Q	R	+	2	0	FANCD2	10055992	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	3.865000	0.56033	2.689000	0.91719	0.579000	0.79373	CGA	G|1.000;A|0.000	0.000	strong		0.378	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1			A	10080992	G	A	10080992	3	1	36	1	0	0	0	0	1	0	0	0	5673	1058	37	1	547	1	FANCD2	3	10080992	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	89286	10080992	187941438	25	14253											
OSBPL10	114884	hgsc.bcm.edu	37	chr3	32022391	32022391	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgggcggctggcgcgttacCtgttctgccagccctggagg	3	8	17	13	4	1	0	0	0	1	0	1	1	1	1	3	5	3	3	3	5	1	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr3:32022391C>T	ENST00000396556.2	-	1	403	c.281G>A	c.(280-282)aGg>aAg	p.R94K	OSBPL10_ENST00000438237.2_Splice_Site_p.R94K|ZNF860_ENST00000360311.4_5'Flank	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	94	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)		GGCGCGTTACCTGTTCTGCCA	0.687																																					p.R94K		Atlas-SNP	.											.	OSBPL10	160	.	0			c.G281A						PASS	.						18	19	18					3																	32022391		2198	4284	6482	SO:0001630	splice_region_variant	114884	exon1			CGTTACCTGTTCT	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.281+1G>A	3.37:g.32022391C>T		77	0	0		70	34	0.485714	NM_017784	B4E212|Q9BTU5	Missense_Mutation	SNP	ENST00000396556.2	37	CCDS2651.1	.	.	.	.	.	.	.	.	.	.	C	28.0	4.883001	0.91740	.	.	ENSG00000144645	ENST00000396556;ENST00000438237	T;T	0.72282	0.94;-0.64	3.84	3.84	0.44239	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	D	0.89065	0.6609	H	0.97918	4.105	0.38634	D	0.951444	D;P	0.57257	0.979;0.818	D;D	0.71414	0.973;0.93	D	0.93430	0.6784	9	.	.	.	-10.3747	13.6161	0.62108	0.0:1.0:0.0:0.0	.	94;94	B4E212;Q9BXB5	.;OSB10_HUMAN	K	94	ENSP00000379804:R94K;ENSP00000406124:R94K	.	R	-	2	0	OSBPL10	31997395	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	3.335000	0.52105	2.140000	0.66376	0.462000	0.41574	AGG	.	.	none		0.687	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2		Missense_Mutation	T	32022391	C	T	32022391	5	4	36	1	0	0	0	0	0	0	1	0	11284	695	24	2	2061	2	OSBPL10	3	32022391	Splice_Site	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	21941399	32022391	166000039	26	14254			1	61		8	5	229	N	G_C	1.144526e-13
OSBPL10	114884	hgsc.bcm.edu	37	chr3	32022420	32022420	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagccctggaggaggttggtGtatttgctgagcacgccctc	6	10	14	11	1	0	1	0	1	0	0	1	3	0	3	2	4	3	4	2	4	1	3			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr3:32022420G>T	ENST00000396556.2	-	1	374	c.252C>A	c.(250-252)taC>taA	p.Y84*	OSBPL10_ENST00000438237.2_Nonsense_Mutation_p.Y84*|ZNF860_ENST00000360311.4_5'Flank	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	84	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)		GGAGGTTGGTGTATTTGCTGA	0.716																																					p.Y84X		Atlas-SNP	.											.	OSBPL10	160	.	0			c.C252A						PASS	.						23	23	23					3																	32022420		2199	4294	6493	SO:0001587	stop_gained	114884	exon1			GTTGGTGTATTTG	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.252C>A	3.37:g.32022420G>T	ENSP00000379804:p.Tyr84*	89	0	0		78	33	0.423077	NM_017784	B4E212|Q9BTU5	Nonsense_Mutation	SNP	ENST00000396556.2	37	CCDS2651.1	.	.	.	.	.	.	.	.	.	.	G	39	7.644893	0.98409	.	.	ENSG00000144645	ENST00000396556;ENST00000438237	.	.	.	4.13	4.13	0.48395	.	0.088789	0.47093	D	0.000246	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12430	T	0.62	-10.6464	14.2571	0.66060	0.0:0.0:1.0:0.0	.	.	.	.	X	84	.	ENSP00000379804:Y84X	Y	-	3	2	OSBPL10	31997424	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.299000	0.78831	2.301000	0.77427	0.462000	0.41574	TAC	.	.	none		0.716	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2			T	32022420	G	T	32022420	4	4	36	1	0	0	0	0	0	1	0	0	11284	1372	48	4	2090	4	OSBPL10	3	32022420	Nonsense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	29	32022420	166000010	27	14255			1	61		8	5	229	N	G_C	1.144526e-13
OSBPL10	114884	hgsc.bcm.edu	37	chr3	32022431	32022431	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaggttggtgtatttgctgaGcacgccctcgagcgccggct	5	10	15	11	4	0	1	0	1	0	0	1	3	0	1	2	3	3	5	2	3	1	3			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr3:32022431G>A	ENST00000396556.2	-	1	363	c.241C>T	c.(241-243)Ctc>Ttc	p.L81F	OSBPL10_ENST00000438237.2_Missense_Mutation_p.L81F|ZNF860_ENST00000360311.4_5'Flank	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	81	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)		TATTTGCTGAGCACGCCCTCG	0.736																																					p.L81F		Atlas-SNP	.											.	OSBPL10	160	.	0			c.C241T						PASS	.						22	22	22					3																	32022431		2197	4295	6492	SO:0001583	missense	114884	exon1			TGCTGAGCACGCC	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.241C>T	3.37:g.32022431G>A	ENSP00000379804:p.Leu81Phe	89	0	0		76	37	0.486842	NM_017784	B4E212|Q9BTU5	Missense_Mutation	SNP	ENST00000396556.2	37	CCDS2651.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.001027	0.74818	.	.	ENSG00000144645	ENST00000396556;ENST00000438237	T;T	0.71341	-0.56;-0.23	4.13	4.13	0.48395	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.208621	0.31872	N	0.006927	D	0.89132	0.6628	H	0.97340	3.985	0.32435	N	0.547512	D;D	0.89917	0.997;1.0	D;D	0.97110	0.939;1.0	D	0.92912	0.6348	10	0.87932	D	0	-9.416	14.2571	0.66060	0.0:0.0:1.0:0.0	.	81;81	B4E212;Q9BXB5	.;OSB10_HUMAN	F	81	ENSP00000379804:L81F;ENSP00000406124:L81F	ENSP00000379804:L81F	L	-	1	0	OSBPL10	31997435	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	4.609000	0.61148	2.301000	0.77427	0.462000	0.41574	CTC	.	.	none		0.736	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2			A	32022431	G	A	32022431	3	1	36	1	0	0	0	0	1	0	0	0	11284	971	34	2	2101	2	OSBPL10	3	32022431	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	11	32022431	165999999	28	14256			1	61		8	5	229	N	G_C	1.144526e-13
OSBPL10	114884	hgsc.bcm.edu	37	chr3	32022569	32022569	+	Silent	SNP	G	G	A																															ggagaccccccggcccgccaGagagcaggagggcgaggagc																										TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr3:32022569G>A	ENST00000396556.2	-	1	225	c.103C>T	c.(103-105)Ctg>Ttg	p.L35L	OSBPL10_ENST00000438237.2_Silent_p.L35L|ZNF860_ENST00000360311.4_5'Flank	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	35					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)		CGGCCCGCCAGAGAGCAGGAG	0.781																																					p.L35L		Atlas-SNP	.											.	OSBPL10	160	.	0			c.C103T						PASS	.						1	2	2					3																	32022569		772	1638	2410	SO:0001819	synonymous_variant	114884	exon1			CCGCCAGAGAGCA	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.103C>T	3.37:g.32022569G>A		67	0	0		72	35	0.486111	NM_017784	B4E212|Q9BTU5	Silent	SNP	ENST00000396556.2	37	CCDS2651.1																																																																																			.	.	none		0.781	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2			A	32022569	G	A	32022569	2	1	36	1	0	0	0	0	0	0	0	1	11284	933	33	2		2	OSBPL10	3	32022569	Silent	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	138	32022569	165999861	29	14257	180	3	1	61		8	5	229	N	G_C	1.144526e-13
OSBPL10	114884	hgsc.bcm.edu	37	chr3	32022573	32022573	+	Silent	SNP	G	G	A																															accccccggcccgccagagaGcaggagggcgaggagcccgc																										TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr3:32022573G>A	ENST00000396556.2	-	1	221	c.99C>T	c.(97-99)tgC>tgT	p.C33C	OSBPL10_ENST00000438237.2_Silent_p.C33C|ZNF860_ENST00000360311.4_5'Flank	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	33					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)		CCGCCAGAGAGCAGGAGGGCG	0.771																																					p.C33C		Atlas-SNP	.											.	OSBPL10	160	.	0			c.C99T						PASS	.						1	2	2					3																	32022573		809	1712	2521	SO:0001819	synonymous_variant	114884	exon1			CAGAGAGCAGGAG	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.99C>T	3.37:g.32022573G>A		71	0	0		71	33	0.464789	NM_017784	B4E212|Q9BTU5	Silent	SNP	ENST00000396556.2	37	CCDS2651.1																																																																																			.	.	none		0.771	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2			A	32022573	G	A	32022573	2	1	36	1	0	0	0	0	0	0	0	1	11284	963	34	2		2	OSBPL10	3	32022573	Silent	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	4	32022573	165999857	30	14258	180	3	1	61		8	5	229	N	G_C	1.144526e-13
OSBPL10	114884	hgsc.bcm.edu	37	chr3	32022574	32022574	+	Missense_Mutation	SNP	C	C	T																															ccccccggcccgccagagagCaggagggcgaggagcccgcc																										TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr3:32022574C>T	ENST00000396556.2	-	1	220	c.98G>A	c.(97-99)tGc>tAc	p.C33Y	OSBPL10_ENST00000438237.2_Missense_Mutation_p.C33Y|ZNF860_ENST00000360311.4_5'Flank	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	33					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)		CGCCAGAGAGCAGGAGGGCGA	0.766																																					p.C33Y		Atlas-SNP	.											.	OSBPL10	160	.	0			c.G98A						PASS	.						1	2	2					3																	32022574		814	1720	2534	SO:0001583	missense	114884	exon1			AGAGAGCAGGAGG	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.98G>A	3.37:g.32022574C>T	ENSP00000379804:p.Cys33Tyr	72	0	0		70	35	0.5	NM_017784	B4E212|Q9BTU5	Missense_Mutation	SNP	ENST00000396556.2	37	CCDS2651.1	.	.	.	.	.	.	.	.	.	.	C	13.71	2.317836	0.40996	.	.	ENSG00000144645	ENST00000396556;ENST00000438237	T;T	0.21734	1.99;2.31	4.07	4.07	0.47477	.	0.908584	0.09077	N	0.851908	T	0.12561	0.0305	N	0.08118	0	0.27201	N	0.960169	B;B	0.18461	0.028;0.028	B;B	0.12156	0.007;0.007	T	0.07252	-1.0782	10	0.59425	D	0.04	-4.5991	10.0692	0.42322	0.0:0.7946:0.2054:0.0	.	33;33	B4E212;Q9BXB5	.;OSB10_HUMAN	Y	33	ENSP00000379804:C33Y;ENSP00000406124:C33Y	ENSP00000379804:C33Y	C	-	2	0	OSBPL10	31997578	0.942000	0.31987	1.000000	0.80357	0.923000	0.55619	0.426000	0.21363	2.271000	0.75665	0.313000	0.20887	TGC	.	.	none		0.766	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2			T	32022574	C	T	32022574	3	4	36	1	0	0	0	0	1	0	0	0	11284	710	25	2	2244	2	OSBPL10	3	32022574	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	1	32022574	165999856	31	14259	180	3	1	61		8	5	229	N	G_C	1.144526e-13
OSBPL10	114884	hgsc.bcm.edu	37	chr3	32022613	32022613	+	Missense_Mutation	SNP	C	C	T																															ccgaggtagcacggctgctgCtgcggctgctgctgttgcta																								rs549917934	byFrequency	TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr3:32022613C>T	ENST00000396556.2	-	1	181	c.59G>A	c.(58-60)aGc>aAc	p.S20N	OSBPL10_ENST00000438237.2_Missense_Mutation_p.S20N|ZNF860_ENST00000360311.4_5'Flank	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	20					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)		ACGgctgctgctgcggctgct	0.791																																					p.S20N		Atlas-SNP	.											.	OSBPL10	160	.	0			c.G59A						PASS	.						2	3	2					3																	32022613		709	1576	2285	SO:0001583	missense	114884	exon1			CTGCTGCTGCGGC	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.59G>A	3.37:g.32022613C>T	ENSP00000379804:p.Ser20Asn	85	0	0		113	48	0.424779	NM_017784	B4E212|Q9BTU5	Missense_Mutation	SNP	ENST00000396556.2	37	CCDS2651.1	.	.	.	.	.	.	.	.	.	.	C	14.96	2.691082	0.48097	.	.	ENSG00000144645	ENST00000396556;ENST00000438237	T;T	0.23552	1.9;2.19	4.02	4.02	0.46733	.	0.741172	0.11593	N	0.548529	T	0.18964	0.0455	N	0.14661	0.345	0.32706	N	0.512265	P;P	0.51791	0.9;0.948	B;B	0.43783	0.289;0.431	T	0.11616	-1.0580	10	0.35671	T	0.21	-3.7958	14.0918	0.64995	0.0:1.0:0.0:0.0	.	20;20	B4E212;Q9BXB5	.;OSB10_HUMAN	N	20	ENSP00000379804:S20N;ENSP00000406124:S20N	ENSP00000379804:S20N	S	-	2	0	OSBPL10	31997617	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	2.559000	0.45888	2.262000	0.75019	0.298000	0.19748	AGC	.	.	none		0.791	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2			T	32022613	C	T	32022613	3	4	36	1	0	0	0	0	1	0	0	0	11284	797	28	2	2283	2	OSBPL10	3	32022613	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	39	32022613	165999817	32	14260	181	2	1	61		8	5	229	N	G_C	1.144526e-13
OSBPL10	114884	hgsc.bcm.edu	37	chr3	32022619	32022619	+	Missense_Mutation	SNP	C	C	T																															tagcacggctgctgctgcggCtgctgctgttgctacccccg																										TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr3:32022619C>T	ENST00000396556.2	-	1	175	c.53G>A	c.(52-54)aGc>aAc	p.S18N	OSBPL10_ENST00000438237.2_Missense_Mutation_p.S18N|ZNF860_ENST00000360311.4_5'Flank	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	18					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)		gctgctgcggctgctgctgtt	0.796																																					p.S18N		Atlas-SNP	.											.	OSBPL10	160	.	0			c.G53A						PASS	.						2	3	2					3																	32022619		664	1482	2146	SO:0001583	missense	114884	exon1			CTGCGGCTGCTGC	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.53G>A	3.37:g.32022619C>T	ENSP00000379804:p.Ser18Asn	89	0	0		114	60	0.526316	NM_017784	B4E212|Q9BTU5	Missense_Mutation	SNP	ENST00000396556.2	37	CCDS2651.1	.	.	.	.	.	.	.	.	.	.	C	15.75	2.925701	0.52759	.	.	ENSG00000144645	ENST00000396556;ENST00000438237	T;T	0.23754	1.89;2.21	3.91	3.91	0.45181	.	1.365760	0.06023	N	0.651587	T	0.18964	0.0455	N	0.14661	0.345	0.32030	N	0.59962	B;B	0.27498	0.18;0.18	B;B	0.18871	0.023;0.023	T	0.08066	-1.0740	10	0.49607	T	0.09	.	13.8256	0.63348	0.0:1.0:0.0:0.0	.	18;18	B4E212;Q9BXB5	.;OSB10_HUMAN	N	18	ENSP00000379804:S18N;ENSP00000406124:S18N	ENSP00000379804:S18N	S	-	2	0	OSBPL10	31997623	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	2.935000	0.48963	2.196000	0.70406	0.298000	0.19748	AGC	.	.	none		0.796	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253165.2			T	32022619	C	T	32022619	3	4	36	1	0	0	0	0	1	0	0	0	11284	797	28	2	2289	2	OSBPL10	3	32022619	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	6	32022619	165999811	33	14261	181	2	1	61		8	5	229	N	G_C	1.144526e-13
MYD88	4615	hgsc.bcm.edu	37	chr3	38182641	38182641	+	Nonstop_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtgcccatcagaagcgacTgatccccatcaagtacaagg	13	6	10	12	1	2	2	2	1	0	1	3	3	3	2	3	2	3	1	3	2	4	1	rs387907272		TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr3:38182641T>C	ENST00000495303.1	+	3	483	c.478T>C	c.(478-480)Tga>Cga	p.*160R	MYD88_ENST00000481122.1_3'UTR|MYD88_ENST00000417037.2_Missense_Mutation_p.L273P|MYD88_ENST00000443433.2_Nonstop_Mutation_p.*205R|MYD88_ENST00000396334.3_Missense_Mutation_p.L265P|MYD88_ENST00000424893.1_Missense_Mutation_p.L220P	NM_001172566.1	NP_001166037.1	Q99836	MYD88_HUMAN	myeloid differentiation primary response 88	0	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|cell surface receptor signaling pathway (GO:0007166)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-positive bacterium (GO:0050830)|establishment of endothelial intestinal barrier (GO:0090557)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of apoptotic process (GO:0043066)|negative regulation of growth of symbiont in host (GO:0044130)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-23 production (GO:0032747)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of lymphocyte proliferation (GO:0050671)|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 tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)|response to molecule of fungal origin (GO:0002238)|response to peptidoglycan (GO:0032494)|response to virus (GO:0009615)|signal transduction (GO:0007165)|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)|type I interferon biosynthetic process (GO:0045351)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)	death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|TIR domain binding (GO:0070976)	p.L265P(188)		breast(1)|haematopoietic_and_lymphoid_tissue(226)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	237				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		CAGAAGCGACTGATCCCCATC	0.552			Mis		ABC-DLBCL								T|||	1	0.000199681	0.0	0.0	5008	,	,		22034	0.0		0.001	False		,,,				2504	0.0				p.X205R		Atlas-SNP	.		Dom	yes		3	3p22	4615	myeloid differentiation primary response gene (88)		L	MYD88,NS,lymphoid_neoplasm,0,828	MYD88	900	828	188	Substitution - Missense(188)	haematopoietic_and_lymphoid_tissue(188)	c.T613C						PASS	.						148	119	129					3																	38182641		2203	4300	6503	SO:0001578	stop_lost	4615	exon4			AGCGACTGATCCC	U84408	CCDS2674.2, CCDS54565.1, CCDS54566.1, CCDS54567.1, CCDS54568.1	3p22	2014-09-17	2012-11-15		ENSG00000172936	ENSG00000172936			7562	protein-coding gene	gene with protein product		602170	"myeloid differentiation primary response gene (88)"			9013863	Standard	NM_002468		Approved		uc003chx.3	Q99836	OTTHUMG00000131083	ENST00000495303.1:c.478T>C	3.37:g.38182641T>C	ENSP00000417848:p.*160Argext*8	65	0	0		55	27	0.490909	NM_001172569	B4DKH8|B4DKU4|B4DQ60|B4DQ72|J3KPU4|J3KQ87|J3KQJ6|P78397|Q53XS7	Missense_Mutation	SNP	ENST00000495303.1	37	CCDS54568.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.85|18.85	3.710754|3.710754	0.68730|0.68730	.|.	.|.	ENSG00000172936|ENSG00000172936	ENST00000417037;ENST00000396334;ENST00000424893;ENST00000421516;ENST00000415158|ENST00000495303;ENST00000443433	T;T;T;T|.	0.15487|.	2.42;2.42;2.42;2.42|.	5.74|5.74	5.74|5.74	0.90152|0.90152	Toll/interleukin-1 receptor homology (TIR) domain (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.71676|.	0.3368|.	.|.	.|.	.|.	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;0.999;0.999|.	T|.	0.70626|.	-0.4820|.	9|.	0.87932|.	D|.	0|.	-17.9268|-17.9268	15.535|15.535	0.75996|0.75996	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	207;252;241|.	Q99836-2;Q99836;B4E3D6|.	.;MYD88_HUMAN;.|.	P|R	273;265;220;272;241|160;205	ENSP00000401399:L273P;ENSP00000379625:L265P;ENSP00000389979:L220P;ENSP00000391753:L272P|.	ENSP00000379625:L265P|.	L|X	+|+	2|1	0|0	MYD88|MYD88	38157645|38157645	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.639000|7.639000	0.83342|0.83342	2.326000|2.326000	0.78906|0.78906	0.533000|0.533000	0.62120|0.62120	CTG|TGA	.	.	none		0.552	MYD88-008	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000342700.1	NM_002468		C	38182641	T	C	38182641	4	2	36	1	0	0	0	0	0	0	0	0	10032	1593	55	3	836	3	MYD88	3	38182641	Nonstop_Mutation	SNP	T	TCGA-GS-A9TT-01A-11D-A382-10	6160022	38182641	159839789	34	14262											
LIMD1	8994	hgsc.bcm.edu	37	chr3	45636456	45636456	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggcctctaaggatgggctcTtccgagtggacaagggtgca	9	8	15	9	1	2	0	0	0	2	0	3	3	3	2	2	5	1	2	2	5	2	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr3:45636456T>C	ENST00000273317.4	+	1	106	c.85T>C	c.(85-87)Ttc>Ctc	p.F29L	LIMD1_ENST00000440097.1_Missense_Mutation_p.F29L|AC099539.1_ENST00000516118.1_RNA|LIMD1_ENST00000465039.1_Intron	NM_014240.2	NP_055055.1	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1	29					cell migration (GO:0016477)|cytoplasmic mRNA processing body assembly (GO:0033962)|cytoskeleton organization (GO:0007010)|gene silencing by miRNA (GO:0035195)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of hippo signaling (GO:0035331)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|phosphorylation (GO:0016310)|positive regulation of gene silencing by miRNA (GO:2000637)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|RISC complex (GO:0016442)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)		GGATGGGCTCTTCCGAGTGGA	0.552																																					p.F29L		Atlas-SNP	.											.	LIMD1	34	.	0			c.T85C						PASS	.						69	69	69					3																	45636456		2203	4300	6503	SO:0001583	missense	8994	exon1			GGGCTCTTCCGAG	AJ132408	CCDS2729.1	3p21.31	2008-02-01			ENSG00000144791	ENSG00000144791			6612	protein-coding gene	gene with protein product		604543				10647888	Standard	NM_014240		Approved		uc003coq.3	Q9UGP4	OTTHUMG00000133453	ENST00000273317.4:c.85T>C	3.37:g.45636456T>C	ENSP00000273317:p.Phe29Leu	95	0	0		43	37	0.860465	NM_014240	Q17RQ1|Q9BQQ9|Q9NQ47	Missense_Mutation	SNP	ENST00000273317.4	37	CCDS2729.1	.	.	.	.	.	.	.	.	.	.	T	29.3	4.993146	0.93167	.	.	ENSG00000144791	ENST00000440097;ENST00000273317	T;T	0.73258	-0.73;-0.49	4.22	4.22	0.49857	.	0.140211	0.48286	D	0.000190	T	0.73140	0.3549	N	0.24115	0.695	0.50171	D	0.999852	D	0.69078	0.997	D	0.70716	0.97	T	0.76740	-0.2848	10	0.66056	D	0.02	.	13.3316	0.60490	0.0:0.0:0.0:1.0	.	29	Q9UGP4	LIMD1_HUMAN	L	29	ENSP00000394537:F29L;ENSP00000273317:F29L	ENSP00000273317:F29L	F	+	1	0	LIMD1	45611460	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.626000	0.83164	1.550000	0.49438	0.379000	0.24179	TTC	.	.	none		0.552	LIMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257327.1	NM_014240		C	45636456	T	C	45636456	3	2	36	1	0	0	0	0	1	0	0	0	8807	1609	56	3	87	3	LIMD1	3	45636456	Missense_Mutation	SNP	T	TCGA-GS-A9TT-01A-11D-A382-10	7453815	45636456	152385974	35	14263											
NISCH	11188	hgsc.bcm.edu	37	chr3	52521970	52521970	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcacatggccatgctgtgtaGccccatcctctacggcagcc	7	8	10	16	1	1	0	0	0	1	0	2	0	2	0	5	2	4	4	5	2	2	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr3:52521970G>T	ENST00000479054.1	+	17	2534	c.2462G>T	c.(2461-2463)aGc>aTc	p.S821I	NISCH_ENST00000345716.4_Missense_Mutation_p.S821I			Q9Y2I1	NISCH_HUMAN	nischarin	821	Interaction with LIMK. {ECO:0000250}.|Interaction with PAK1. {ECO:0000250}.				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)	ATGCTGTGTAGCCCCATCCTC	0.637																																					p.S821I		Atlas-SNP	.											.	NISCH	97	.	0			c.G2462T						PASS	.																																			SO:0001583	missense	11188	exon16			TGTGTAGCCCCAT	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.2462G>T	3.37:g.52521970G>T	ENSP00000418232:p.Ser821Ile	54	0	0		25	17	0.68	NM_007184	C9J245|Q6PGP3|Q6PIB4|Q7L8M3|Q7Z2X6|Q9UES6|Q9UEU4|Q9UFW3	Missense_Mutation	SNP	ENST00000479054.1	37	CCDS33767.1	.	.	.	.	.	.	.	.	.	.	G	13.16	2.154440	0.38021	.	.	ENSG00000010322	ENST00000479054;ENST00000345716;ENST00000414197	T;T	0.08008	3.14;3.14	5.04	3.91	0.45181	.	0.473507	0.24508	N	0.037909	T	0.04634	0.0126	N	0.19112	0.55	0.29426	N	0.860202	B	0.30824	0.296	B	0.23275	0.045	T	0.17837	-1.0356	10	0.32370	T	0.25	-32.2783	7.2654	0.26227	0.1185:0.0:0.7221:0.1594	.	821	Q9Y2I1	NISCH_HUMAN	I	821;821;165	ENSP00000418232:S821I;ENSP00000339958:S821I	ENSP00000339958:S821I	S	+	2	0	NISCH	52497010	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	1.986000	0.40677	2.504000	0.84457	0.561000	0.74099	AGC	.	.	none		0.637	NISCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351357.1	NM_007184		T	52521970	G	T	52521970	3	4	36	1	0	0	0	0	1	0	0	0	10441	971	34	4	2524	4	NISCH	3	52521970	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	6885514	52521970	145500460	36	14264											
ARHGEF3	50650	hgsc.bcm.edu	37	chr3	56763546	56763546	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aactgtttctttggcttgacGaatacagttaagccactgct	10	14	8	9	1	1	1	0	1	1	0	1	2	1	1	1	1	4	4	1	1	4	5			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr3:56763546G>A	ENST00000296315.3	-	10	1501	c.1333C>T	c.(1333-1335)Cgt>Tgt	p.R445C	ARHGEF3_ENST00000496106.1_Missense_Mutation_p.R451C|ARHGEF3_ENST00000497267.1_Missense_Mutation_p.R416C|ARHGEF3_ENST00000413728.2_Missense_Mutation_p.R451C|ARHGEF3_ENST00000338458.4_Missense_Mutation_p.R477C	NM_019555.2	NP_062455.1	Q9NR81	ARHG3_HUMAN	Rho guanine nucleotide exchange factor (GEF) 3	445	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|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)|intracellular (GO:0005622)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(1)	25				KIRC - Kidney renal clear cell carcinoma(284;0.0161)|Kidney(284;0.019)|OV - Ovarian serous cystadenocarcinoma(275;0.193)		TTGGCTTGACGAATACAGTTA	0.488																																					p.R477C		Atlas-SNP	.											ARHGEF3_ENST00000413728,NS,carcinoma,0,4	ARHGEF3	128	4	0			c.C1429T						scavenged	.						125	127	126					3																	56763546		2203	4300	6503	SO:0001583	missense	50650	exon13			CTTGACGAATACA	AB209661	CCDS2878.1, CCDS46854.1, CCDS46855.1, CCDS74948.1	3p14.3	2012-09-20			ENSG00000163947	ENSG00000163947		"Rho guanine nucleotide exchange factors"	683	protein-coding gene	gene with protein product	"exchange factor found in platelets and leukemic and neuronal tissues, XPLN", "RhoGEF protein"	612115				10873612	Standard	NM_019555		Approved	STA3, XPLN, GEF3, DKFZP434F2429	uc003dih.2	Q9NR81	OTTHUMG00000158857	ENST00000296315.3:c.1333C>T	3.37:g.56763546G>A	ENSP00000296315:p.Arg445Cys	292	2	0.00684932		260	122	0.469231	NM_001128615	A8K5U7|Q4FZB6|Q4QQI5|Q4QQQ0|Q59F00|Q6NUN3|Q7Z4U2|Q7Z5T2|Q9H7T4	Missense_Mutation	SNP	ENST00000296315.3	37	CCDS2878.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.226831	0.79576	.	.	ENSG00000163947	ENST00000296315;ENST00000338458;ENST00000413728;ENST00000496106;ENST00000497267	T;T;T;T;T	0.34072	1.38;1.38;1.38;1.38;1.38	5.95	5.95	0.96441	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	T	0.63212	0.2492	M	0.72118	2.19	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	0.987;0.992;0.999;0.994;0.987;0.997	T	0.63328	-0.6662	10	0.87932	D	0	-11.142	20.3789	0.98926	0.0:0.0:1.0:0.0	.	451;416;243;477;445;451	E9PG37;E7EU49;Q9NR81-4;Q9NR81-2;Q9NR81;Q9NR81-3	.;.;.;.;ARHG3_HUMAN;.	C	445;477;451;451;416	ENSP00000296315:R445C;ENSP00000341071:R477C;ENSP00000410922:R451C;ENSP00000420420:R451C;ENSP00000418826:R416C	ENSP00000296315:R445C	R	-	1	0	ARHGEF3	56738586	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	4.366000	0.59492	2.826000	0.97356	0.563000	0.77884	CGT	.	.	none		0.488	ARHGEF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352431.2	NM_019555		A	56763546	G	A	56763546	3	1	36	1	0	0	0	0	1	0	0	0	904	1058	37	1	251	1	ARHGEF3	3	56763546	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	4241576	56763546	141258884	37	14265											
PRICKLE2	166336	hgsc.bcm.edu	37	chr3	64085223	64085223	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctgtgaggtcggaaacggCggttgtcgtcgcgtgaagta	8	9	16	8	6	0	2	0	2	0	0	3	3	0	3	1	4	1	2	1	4	3	2	rs139750623		TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr3:64085223C>T	ENST00000295902.6	-	8	2624	c.2039G>A	c.(2038-2040)cGc>cAc	p.R680H	PRICKLE2_ENST00000564377.1_Missense_Mutation_p.R736H|RP11-129B22.1_ENST00000482609.1_RNA|PRICKLE2-AS1_ENST00000476308.1_RNA|PRICKLE2-AS1_ENST00000460946.1_RNA	NM_198859.3	NP_942559.1	Q7Z3G6	PRIC2_HUMAN	prickle homolog 2 (Drosophila)	680	Arg-rich.				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)		TCGGAAACGGCGGTTGTCGTC	0.647																																					p.R680H		Atlas-SNP	.											PRICKLE2,colon,carcinoma,-1,1	PRICKLE2	88	1	0			c.G2039A						PASS	.						44	47	46					3																	64085223		2203	4300	6503	SO:0001583	missense	166336	exon8			AAACGGCGGTTGT	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.2039G>A	3.37:g.64085223C>T	ENSP00000295902:p.Arg680His	55	0	0		53	25	0.471698	NM_198859	Q0VF44	Missense_Mutation	SNP	ENST00000295902.6	37	CCDS2902.1	.	.	.	.	.	.	.	.	.	.	C	12.40	1.926661	0.34002	.	.	ENSG00000163637	ENST00000295902	D	0.84944	-1.92	5.63	4.76	0.60689	.	0.082334	0.53938	D	0.000057	T	0.75250	0.3824	N	0.25647	0.755	0.58432	D	0.999994	B	0.10296	0.003	B	0.06405	0.002	T	0.68903	-0.5286	10	0.33141	T	0.24	-33.4654	10.4637	0.44594	0.0:0.8524:0.0:0.1476	.	680	Q7Z3G6	PRIC2_HUMAN	H	680	ENSP00000295902:R680H	ENSP00000295902:R680H	R	-	2	0	PRICKLE2	64060263	1.000000	0.71417	0.918000	0.36340	0.854000	0.48673	3.606000	0.54095	1.382000	0.46385	0.591000	0.81541	CGC	.	.	none		0.647	PRICKLE2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352219.1	NM_198859		T	64085223	C	T	64085223	3	4	36	1	0	0	0	0	1	0	0	0	12499	768	27	1	499	1	PRICKLE2	3	64085223	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	7321677	64085223	133937207	38	14266											
FNDC3B	64778	hgsc.bcm.edu	37	chr3	172025174	172025174	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgtatgccatgtacaattcCgtaaagggatcctgctccga	10	11	10	10	2	0	0	0	0	0	0	3	2	3	1	4	1	3	4	4	1	5	4			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr3:172025174C>T	ENST00000336824.4	+	10	1182	c.1083C>T	c.(1081-1083)tcC>tcT	p.S361S	FNDC3B_ENST00000416957.1_Silent_p.S361S|FNDC3B_ENST00000415807.2_Silent_p.S361S	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	361	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)			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)		TGTACAATTCCGTAAAGGGAT	0.493																																					p.S361S		Atlas-SNP	.											.	FNDC3B	118	.	0			c.C1083T						PASS	.						152	130	137					3																	172025174		2203	4300	6503	SO:0001819	synonymous_variant	64778	exon10			CAATTCCGTAAAG	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.1083C>T	3.37:g.172025174C>T		103	0	0		82	42	0.512195	NM_001135095	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Silent	SNP	ENST00000336824.4	37	CCDS3217.1																																																																																			.	.	none		0.493	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763		T	172025174	C	T	172025174	2	4	36	1	0	0	0	0	0	0	0	1	5978	639	23	1		1	FNDC3B	3	172025174	Silent	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	107939951	172025174	25997256	39	14267											
TBL1XR1	79718	hgsc.bcm.edu	37	chr3	176756174	176756174	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaatgcacatatctgtactaCaagaagcaaaggtgttgttg	14	11	10	6	0	1	1	0	0	1	1	1	2	1	1	0	1	4	5	0	1	7	5			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr3:176756174C>A	ENST00000430069.1	-	11	1233	c.974G>T	c.(973-975)tGt>tTt	p.C325F	TBL1XR1_ENST00000457928.2_Missense_Mutation_p.C325F			Q9BZK7	TBL1R_HUMAN	transducin (beta)-like 1 X-linked receptor 1	325					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)	p.C325S(1)		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)			ATCTGTACTACAAGAAGCAAA	0.373																																					p.C325F		Atlas-SNP	.											TBL1XR1,NS,carcinoma,0,1	TBL1XR1	87	1	1	Substitution - Missense(1)	lung(1)	c.G974T						PASS	.						110	98	102					3																	176756174		1878	4117	5995	SO:0001583	missense	79718	exon11			GTACTACAAGAAG	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.974G>T	3.37:g.176756174C>A	ENSP00000405574:p.Cys325Phe	128	0	0		104	99	0.951923	NM_024665	D3DNQ9|Q14DC3|Q9H2I1|Q9H9A1	Missense_Mutation	SNP	ENST00000430069.1	37	CCDS46961.1	.	.	.	.	.	.	.	.	.	.	C	26.6	4.753034	0.89753	.	.	ENSG00000177565	ENST00000430069;ENST00000457928;ENST00000536758	D;D	0.81996	-1.56;-1.56	5.82	5.82	0.92795	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	0.93074	0.7795	M	0.90425	3.115	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93618	0.6945	10	0.66056	D	0.02	-5.1506	19.0789	0.93173	0.0:1.0:0.0:0.0	.	325	Q9BZK7	TBL1R_HUMAN	F	325;325;187	ENSP00000405574:C325F;ENSP00000413251:C325F	ENSP00000405574:C325F	C	-	2	0	TBL1XR1	178238868	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.787000	0.85759	2.754000	0.94517	0.585000	0.79938	TGT	.	.	none		0.373	TBL1XR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347587.3	NM_024665		A	176756174	C	A	176756174	3	1	36	1	0	0	0	0	1	0	0	0	15655	478	17	4	594	4	TBL1XR1	3	176756174	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	4731000	176756174	21266256	40	14268											
GPR125	166647	hgsc.bcm.edu	37	chr4	22389666	22389666	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tccttcgttattgcccagccGgcttttaggtaagccgttct	5	15	9	12	3	1	0	0	0	1	0	3	0	2	0	4	2	3	4	4	2	3	7			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr4:22389666G>A	ENST00000334304.5	-	19	3897	c.3628C>T	c.(3628-3630)Cgg>Tgg	p.R1210W	GPR125_ENST00000282943.5_5'UTR	NM_145290.3	NP_660333.2	Q8IWK6	GP125_HUMAN	G protein-coupled receptor 125	1210					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)				TTGCCCAGCCGGCTTTTAGGT	0.542																																					p.R1210W		Atlas-SNP	.											.	GPR125	118	.	0			c.C3628T						PASS	.						93	86	89					4																	22389666		2203	4300	6503	SO:0001583	missense	166647	exon19			CCAGCCGGCTTTT	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.3628C>T	4.37:g.22389666G>A	ENSP00000334952:p.Arg1210Trp	271	0	0		196	88	0.44898	NM_145290	Q6UXK9|Q86SQ5|Q8TC55	Missense_Mutation	SNP	ENST00000334304.5	37	CCDS33964.1	.	.	.	.	.	.	.	.	.	.	G	12.86	2.065055	0.36470	.	.	ENSG00000152990	ENST00000334304	T	0.54675	0.56	5.9	5.05	0.67936	.	0.057434	0.64402	D	0.000002	T	0.65678	0.2714	L	0.56769	1.78	0.80722	D	1	D;D	0.89917	1.0;0.995	D;P	0.69142	0.962;0.609	T	0.64884	-0.6302	10	0.39692	T	0.17	-0.8166	11.9432	0.52913	0.0:0.132:0.7307:0.1373	.	1067;1210	Q8IWK6-3;Q8IWK6	.;GP125_HUMAN	W	1210	ENSP00000334952:R1210W	ENSP00000334952:R1210W	R	-	1	2	GPR125	21998764	1.000000	0.71417	0.037000	0.18230	0.260000	0.26232	6.194000	0.72082	1.471000	0.48121	0.650000	0.86243	CGG	.	.	none		0.542	GPR125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362960.3			A	22389666	G	A	22389666	3	1	36	1	0	0	0	0	1	0	0	0	6647	1115	39	1	341	1	GPR125	4	22389666	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10		22389666	168764610	41	14269											
CCDC109B	55013	hgsc.bcm.edu	37	chr4	110605694	110605699	+	In_Frame_Del	DEL	CTGGCT	CTGGCT	-																															attcagggtggggcactggcCtggctcacgtggtgggtgta																										TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	CTGGCT	CTGGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr4:110605694_110605699delCTGGCT	ENST00000394650.4	+	6	841_846	c.708_713delCTGGCT	c.(706-714)gcctggctc>gcc	p.WL237del		NM_017918.4	NP_060388.2	Q9NWR8	MCUB_HUMAN	coiled-coil domain containing 109B	237					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)		GGGCACTGGCCTGGCTCACGTGGTGG	0.49																																					p.236_238del		Pindel,Atlas-Indel	.											.	CCDC109B	47	.	0			c.707_712del						PASS	.																																			SO:0001651	inframe_deletion	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.708_713delCTGGCT	4.37:g.110605694_110605699delCTGGCT	ENSP00000378145:p.Trp237_Leu238del	228	0	.		203	43	0.212	NM_017918	A8K4Y3|Q6IAC1	In_Frame_Del	DEL	ENST00000394650.4	37	CCDS3683.2																																																																																			.	.	none		0.49	CCDC109B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254865.1	NM_017918		-	110605699	CTGGCT	-	110605694	7	5	36	1	0	1	0	1	0	0	0	0	2747	668	24	0	730	0	CCDC109B	4	110605694	In_Frame_Del	DEL	CTGGCT	TCGA-GS-A9TT-01A-11D-A382-10	88216028	110605694	80548582	42	14270											
ENPEP	2028	hgsc.bcm.edu	37	chr4	111398089	111398089	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagtacgtggtggtcgaggcGgaggaagagcttacccccag	9	6	17	9	3	0	1	0	0	0	1	1	5	0	3	2	5	3	2	2	5	3	2	rs373421438		TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr4:111398089G>A	ENST00000265162.5	+	1	861	c.519G>A	c.(517-519)gcG>gcA	p.A173A		NM_001977.3	NP_001968.3	Q07075	AMPE_HUMAN	glutamyl aminopeptidase (aminopeptidase A)	173					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)		TGGTCGAGGCGGAGGAAGAGC	0.597																																					p.A173A		Atlas-SNP	.											.	ENPEP	149	.	0			c.G519A						PASS	.						82	91	88					4																	111398089		2203	4300	6503	SO:0001819	synonymous_variant	2028	exon1			CGAGGCGGAGGAA	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.519G>A	4.37:g.111398089G>A		73	0	0		58	26	0.448276	NM_001977	Q504U2	Silent	SNP	ENST00000265162.5	37	CCDS3691.1																																																																																			.	.	alt		0.597	ENPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255747.2			A	111398089	G	A	111398089	2	1	36	1	0	0	0	0	0	0	0	1	5130	1103	39	1		1	ENPEP	4	111398089	Silent	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	792395	111398089	79756187	43	14271											
FAT4	79633	hgsc.bcm.edu	37	chr4	126241904	126241904	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	atttcagtgactgcacatgaCcctgatgcagacattaatgg	12	11	9	9	0	1	4	1	3	0	1	1	4	1	4	1	1	2	2	1	1	1	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr4:126241904C>G	ENST00000394329.3	+	1	4351	c.4338C>G	c.(4336-4338)gaC>gaG	p.D1446E		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1446	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						CTGCACATGACCCTGATGCAG	0.398																																					p.D1446E		Atlas-SNP	.											.	FAT4	1752	.	0			c.C4338G						PASS	.						147	135	139					4																	126241904		1910	4138	6048	SO:0001583	missense	79633	exon1			ACATGACCCTGAT	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.4338C>G	4.37:g.126241904C>G	ENSP00000377862:p.Asp1446Glu	155	0	0		96	45	0.46875	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	15.83	2.949004	0.53186	.	.	ENSG00000196159	ENST00000394329	T	0.73897	-0.79	4.8	1.91	0.25777	Cadherin (4);Cadherin-like (1);	0.000000	0.35585	U	0.003110	D	0.88175	0.6366	H	0.96430	3.82	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.85987	0.1486	10	0.87932	D	0	.	7.2653	0.26226	0.0:0.3824:0.0:0.6176	.	1446	Q6V0I7	FAT4_HUMAN	E	1446	ENSP00000377862:D1446E	ENSP00000377862:D1446E	D	+	3	2	FAT4	126461354	1.000000	0.71417	0.953000	0.39169	0.801000	0.45260	1.008000	0.29872	0.169000	0.19679	0.655000	0.94253	GAC	.	.	none		0.398	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		G	126241904	C	G	126241904	3	3	36	1	0	0	0	0	1	0	0	0	5700	506	18	4	4340	4	FAT4	4	126241904	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	14843815	126241904	64912372	44	14272											
FAM198B	51313	hgsc.bcm.edu	37	chr4	159092159	159092159	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcgcttgggcttcacggtGccacggatattggccggctt	4	11	14	12	4	1	0	1	0	0	0	1	1	1	1	2	5	2	3	2	5	1	5			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr4:159092159G>T	ENST00000296530.8	-	2	990	c.369C>A	c.(367-369)ggC>ggA	p.G123G	RP11-597D13.9_ENST00000514381.1_RNA|FAM198B_ENST00000393807.5_Silent_p.G123G|RP11-597D13.9_ENST00000509463.1_RNA|RP11-597D13.9_ENST00000505532.1_RNA|FAM198B_ENST00000585682.1_Silent_p.G123G|FAM198B_ENST00000592057.1_Silent_p.G123G|RP11-597D13.9_ENST00000503611.1_RNA|FAM198B_ENST00000589306.1_Intron	NM_016613.6	NP_057697.2	Q6UWH4	F198B_HUMAN	family with sequence similarity 198, member B	123						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						GCTTCACGGTGCCACGGATAT	0.622																																					p.G123G		Atlas-SNP	.											.	FAM198B	134	.	0			c.C369A						PASS	.						84	80	81					4																	159092159		2203	4300	6503	SO:0001819	synonymous_variant	51313	exon2			CACGGTGCCACGG		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.369C>A	4.37:g.159092159G>T		62	0	0		63	23	0.365079	NM_016613	Q498Z3|Q6IAF9|Q6ZMF2|Q86XL0	Silent	SNP	ENST00000296530.8	37	CCDS3798.1																																																																																			.	.	none		0.622	FAM198B-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365230.1	NM_001031700, NM_016613		T	159092159	G	T	159092159	2	4	36	1	0	0	0	0	0	0	0	1	5534	1306	46	4		4	FAM198B	4	159092159	Silent	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	32850255	159092159	32062117	45	14273											
F11	2160	hgsc.bcm.edu	37	chr4	187194287	187194287	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagagtgaataggacagcagCgatttctgggtattctttca	12	12	11	6	1	3	2	1	1	2	1	3	4	3	3	0	2	2	2	0	2	4	5	rs367856671		TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr4:187194287C>T	ENST00000403665.2	+	4	633	c.281C>T	c.(280-282)gCg>gTg	p.A94V	F11_ENST00000264692.4_Missense_Mutation_p.A94V|F11_ENST00000492972.2_Missense_Mutation_p.A94V	NM_000128.3	NP_000119.1	P03951	FA11_HUMAN	coagulation factor XI	94	Apple 1. {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)	AGGACAGCAGCGATTTCTGGG	0.368																																					p.A94V		Atlas-SNP	.											.	F11	65	.	0			c.C281T						PASS	.	C	VAL/ALA	1,4405	2.1+/-5.4	0,1,2202	96	90	92		281	5.4	1	4		92	0,8600		0,0,4300	no	missense	F11	NM_000128.3	64	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	94/626	187194287	1,13005	2203	4300	6503	SO:0001583	missense	2160	exon4			CAGCAGCGATTTC	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.281C>T	4.37:g.187194287C>T	ENSP00000384957:p.Ala94Val	334	1	0.00299401		221	84	0.380091	NM_000128	D3DP64|Q4W5C2|Q9Y495	Missense_Mutation	SNP	ENST00000403665.2	37	CCDS3847.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.765645	0.90020	2.27E-4	0.0	ENSG00000088926	ENST00000403665;ENST00000264692;ENST00000492972	D;D;D	0.89196	-2.48;-2.48;-2.48	5.45	5.45	0.79879	Apple domain (2);PAN-1 domain (1);Apple-like (1);	0.000000	0.85682	D	0.000000	D	0.94215	0.8143	M	0.76574	2.34	0.50467	D	0.999877	D	0.89917	1.0	D	0.97110	1.0	D	0.94070	0.7334	10	0.52906	T	0.07	.	17.8567	0.88765	0.0:1.0:0.0:0.0	.	94	P03951	FA11_HUMAN	V	94	ENSP00000384957:A94V;ENSP00000264692:A94V;ENSP00000424479:A94V	ENSP00000264692:A94V	A	+	2	0	F11	187431281	0.983000	0.35010	0.962000	0.40283	0.969000	0.65631	2.603000	0.46266	2.565000	0.86533	0.557000	0.71058	GCG	.	.	weak		0.368	F11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317519.4			T	187194287	C	T	187194287	3	4	36	1	0	0	0	0	1	0	0	0	5339	768	27	1	291	1	F11	4	187194287	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	28102128	187194287	3959989	46	14274											
SEMA5A	9037	hgsc.bcm.edu	37	chr5	9119196	9119196	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cgctgccgcacctggaagccGatcccacaggtagtgctgca	8	6	12	15	3	0	0	0	0	0	0	1	2	1	1	4	2	4	5	4	2	2	1			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr5:9119196G>A	ENST00000382496.5	-	15	2504	c.1839C>T	c.(1837-1839)atC>atT	p.I613I		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	613	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						CCTGGAAGCCGATCCCACAGG	0.657																																					p.I613I		Atlas-SNP	.											.	SEMA5A	236	.	0			c.C1839T						PASS	.						52	47	48					5																	9119196		2203	4300	6503	SO:0001819	synonymous_variant	9037	exon15			GAAGCCGATCCCA	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.1839C>T	5.37:g.9119196G>A		100	0	0		90	34	0.377778	NM_003966	D3DTC6|O60408|Q1RLL9	Silent	SNP	ENST00000382496.5	37	CCDS3875.1																																																																																			.	.	none		0.657	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2			A	9119196	G	A	9119196	2	1	36	1	0	0	0	0	0	0	0	1	14052	1048	37	1		1	SEMA5A	5	9119196	Silent	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10		9119196	171796064	47	14275											
ROPN1L	83853	hgsc.bcm.edu	37	chr5	10465050	10465050	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attgaaaactctgaagatgtAggccattaatacagagaaga	18	9	9	5	0	1	5	0	2	1	3	1	6	1	5	1	1	2	1	1	1	7	4			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr5:10465050A>C	ENST00000503804.1	+	6	1205	c.684A>C	c.(682-684)gtA>gtC	p.V228V	ROPN1L_ENST00000274134.4_Silent_p.V228V|ROPN1L_ENST00000510520.1_Intron			Q96C74	ROP1L_HUMAN	rhophilin associated tail protein 1-like	228					epithelial cilium movement (GO:0003351)|regulation of protein phosphorylation (GO:0001932)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)	14						CTGAAGATGTAGGCCATTAAT	0.363																																					p.V228V		Atlas-SNP	.											.	ROPN1L	33	.	0			c.A684C						PASS	.						66	74	71					5																	10465050		2203	4299	6502	SO:0001819	synonymous_variant	83853	exon5			AGATGTAGGCCAT	AF239723	CCDS3879.1	5p15	2011-01-20	2011-01-20		ENSG00000145491	ENSG00000145491			24060	protein-coding gene	gene with protein product	"radial spoke head 11 homolog (Chlamydomonas)"	611756	"ropporin 1-like"			11278869	Standard	NM_031916		Approved	ASP, FLJ25776, RSPH11	uc021xwo.1	Q96C74	OTTHUMG00000090507	ENST00000503804.1:c.684A>C	5.37:g.10465050A>C		382	0	0		296	132	0.445946	NM_031916	D3DTC9|Q9BZX0	Silent	SNP	ENST00000503804.1	37	CCDS3879.1																																																																																			.	.	none		0.363	ROPN1L-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367033.1	NM_031916		C	10465050	A	C	10465050	2	2	36	1	0	0	0	0	0	0	0	1	13540	407	15	5		5	ROPN1L	5	10465050	Silent	SNP	A	TCGA-GS-A9TT-01A-11D-A382-10	1345854	10465050	170450210	48	14276											
PRDM9	56979	hgsc.bcm.edu	37	chr5	23527377	23527377	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtctgcagggagtgtgggcGgggctttagcaataagtcac	8	10	16	7	1	2	0	1	0	1	0	2	1	2	1	0	4	2	3	0	4	3	3			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr5:23527377G>A	ENST00000296682.3	+	11	2362	c.2180G>A	c.(2179-2181)cGg>cAg	p.R727Q		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	727					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						GAGTGTGGGCGGGGCTTTAGC	0.597										HNSCC(3;0.000094)																											p.R727Q		Atlas-SNP	.											PRDM9,colon,carcinoma,+1,1	PRDM9	344	1	0			c.G2180A						PASS	.						20	22	21					5																	23527377		2038	4098	6136	SO:0001583	missense	56979	exon11			GTGGGCGGGGCTT	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.2180G>A	5.37:g.23527377G>A	ENSP00000296682:p.Arg727Gln	178	0	0		127	41	0.322835	NM_020227	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	G	3.932	-0.015891	0.07681	.	.	ENSG00000164256	ENST00000296682	T	0.18960	2.18	2.88	0.835	0.18886	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12135	0.0295	L	0.31157	0.91	0.09310	N	0.999999	P	0.38395	0.629	B	0.32805	0.153	T	0.17048	-1.0382	9	0.52906	T	0.07	.	5.2268	0.15399	0.4789:0.0:0.5211:0.0	.	727	Q9NQV7	PRDM9_HUMAN	Q	727	ENSP00000296682:R727Q	ENSP00000296682:R727Q	R	+	2	0	PRDM9	23563134	0.001000	0.12720	0.609000	0.28983	0.002000	0.02628	0.105000	0.15333	0.186000	0.20125	-0.378000	0.06908	CGG	.	.	none		0.597	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		A	23527377	G	A	23527377	3	1	36	1	0	0	0	0	1	0	0	0	12475	1116	39	1	2218	1	PRDM9	5	23527377	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	13062327	23527377	157387883	49	14277											
RNF180	285671	hgsc.bcm.edu	37	chr5	63626166	63626166	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tatttgaaaataaaacaaagCtttcagaaatccaactctgc	18	11	4	8	0	2	2	1	1	1	1	3	2	3	2	1	0	4	1	1	0	8	4			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr5:63626166C>T	ENST00000389100.4	+	7	1584	c.1512C>T	c.(1510-1512)agC>agT	p.S504S		NM_001113561.1	NP_001107033.1	Q86T96	RN180_HUMAN	ring finger protein 180	504					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)		TAAAACAAAGCTTTCAGAAAT	0.313																																					p.S504S		Atlas-SNP	.											.	RNF180	94	.	0			c.C1512T						PASS	.						52	47	48					5																	63626166		692	1591	2283	SO:0001819	synonymous_variant	285671	exon7			ACAAAGCTTTCAG	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.1512C>T	5.37:g.63626166C>T		327	0	0		258	105	0.406977	NM_001113561	Q0JSU3|Q495A8|Q8NBD1	Silent	SNP	ENST00000389100.4	37	CCDS47219.1																																																																																			.	.	none		0.313	RNF180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368394.1	NM_178532		T	63626166	C	T	63626166	2	4	36	1	0	0	0	0	0	0	0	1	13479	796	28	2		2	RNF180	5	63626166	Silent	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	40098789	63626166	117289094	50	14278											
SPATA9	83890	hgsc.bcm.edu	37	chr5	94994492	94994492	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaccttcagcaaacataggCtccgaaagcacaggctcaga	14	6	8	13	1	3	1	3	0	0	1	4	2	4	1	2	2	3	4	2	2	3	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr5:94994492C>T	ENST00000274432.8	-	5	741	c.600G>A	c.(598-600)gaG>gaA	p.E200E	RFESD_ENST00000508206.1_Intron|SPATA9_ENST00000477047.2_5'UTR	NM_031952.3	NP_114158.2	Q9BWV2	SPAT9_HUMAN	spermatogenesis associated 9	200					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)		CAAACATAGGCTCCGAAAGCA	0.418																																					p.E200E		Atlas-SNP	.											.	SPATA9	17	.	0			c.G600A						PASS	.						112	104	107					5																	94994492		2203	4299	6502	SO:0001819	synonymous_variant	83890	exon5			CATAGGCTCCGAA	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.600G>A	5.37:g.94994492C>T		190	0	0		207	91	0.439614	NM_031952	A8K8H3|Q4G122|Q86X33|Q8NA28	Silent	SNP	ENST00000274432.8	37	CCDS4076.1																																																																																			.	.	none		0.418	SPATA9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304036.1	NM_031952		T	94994492	C	T	94994492	2	4	36	1	0	0	0	0	0	0	0	1	15031	796	28	2		2	SPATA9	5	94994492	Silent	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	31368326	94994492	85920768	51	14279											
ZNF608	57507	hgsc.bcm.edu	37	chr5	124079845	124079845	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcttccttctttaccaacaTagagtttcccatgagccctg	8	14	5	14	0	2	2	0	1	2	1	4	2	4	2	4	0	3	1	4	0	3	6	rs371493737		TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr5:124079845T>A	ENST00000306315.5	-	1	1273	c.838A>T	c.(838-840)Atg>Ttg	p.M280L	ZNF608_ENST00000504926.1_Intron	NM_020747.2	NP_065798.2	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	280							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)		TTTACCAACATAGAGTTTCCC	0.557																																					p.M280L		Atlas-SNP	.											.	ZNF608	117	.	0			c.A838T						PASS	.						138	144	142					5																	124079845		2105	4156	6261	SO:0001583	missense	57507	exon1			CCAACATAGAGTT	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.838A>T	5.37:g.124079845T>A	ENSP00000307746:p.Met280Leu	171	0	0		142	61	0.429577	NM_020747	A7E2W9|Q3SYM6|Q68D12|Q8IY05|Q9Y5A1	Missense_Mutation	SNP	ENST00000306315.5	37	CCDS34219.1	.	.	.	.	.	.	.	.	.	.	T	4.006	-0.001568	0.07819	.	.	ENSG00000168916	ENST00000306315;ENST00000509799;ENST00000513986	T	0.37584	1.19	5.08	-3.65	0.04502	.	0.561470	0.17591	N	0.168770	T	0.12135	0.0295	N	0.08118	0	0.24410	N	0.994665	B	0.02656	0.0	B	0.01281	0.0	T	0.33954	-0.9848	10	0.02654	T	1	-3.1328	8.444	0.32830	0.1156:0.484:0.0:0.4004	.	280	Q9ULD9	ZN608_HUMAN	L	280	ENSP00000307746:M280L	ENSP00000307746:M280L	M	-	1	0	ZNF608	124107744	0.976000	0.34144	0.948000	0.38648	0.992000	0.81027	0.083000	0.14871	-0.868000	0.04058	-0.254000	0.11334	ATG	.	.	alt		0.557	ZNF608-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371300.1	XM_114432		A	124079845	T	A	124079845	3	1	36	1	0	0	0	0	1	0	0	0	18049	1406	49	5	3736	5	ZNF608	5	124079845	Missense_Mutation	SNP	T	TCGA-GS-A9TT-01A-11D-A382-10	29085353	124079845	56835415	52	14280											
PCDHA11	56138	hgsc.bcm.edu	37	chr5	140249903	140249903	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	accttcaagaattactactcGttggtgctggacagcgccct	9	11	9	12	2	1	1	1	0	0	1	2	2	1	2	2	2	4	2	2	2	4	4	rs372041974		TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr5:140249903G>A	ENST00000398640.2	+	1	1215	c.1215G>A	c.(1213-1215)tcG>tcA	p.S405S	PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA10_ENST00000307360.5_Intron	NM_018902.3	NP_061725.1	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11	405	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)			breast(1)|lung(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATTACTACTCGTTGGTGCTGG	0.617																																					p.S405S		Atlas-SNP	.											.	PCDHA11	209	.	0			c.G1215A						PASS	.	G	,,,,,,,,,,,,,,	1,4405	2.1+/-5.4	0,1,2202	156	146	149		,,1215,,,,,,,,,,,,1215	-11.4	0	5		149	0,8600		0,0,4300	no	intron,intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018902.3,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031861.1	,,,,,,,,,,,,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,,,,,,,,,,,,	,,405/950,,,,,,,,,,,,405/811	140249903	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	56138	exon1			CTACTCGTTGGTG	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.1215G>A	5.37:g.140249903G>A		178	0	0		140	60	0.428571	NM_018902	B2RN58|O75279	Silent	SNP	ENST00000398640.2	37	CCDS47284.1																																																																																			.	.	weak		0.617	PCDHA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372885.2	NM_018902		A	140249903	G	A	140249903	2	1	36	1	0	0	0	0	0	0	0	1	11530	1132	40	1		1	PCDHA11	5	140249903	Silent	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	16170058	140249903	40665357	53	14281											
PCDH1	5097	hgsc.bcm.edu	37	chr5	141244191	141244191	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgctgttcccgatccagagAtgtcttcacctggatctctc	6	12	8	15	2	3	1	1	0	2	1	7	4	5	2	4	1	0	2	4	1	0	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr5:141244191A>T	ENST00000394536.3	-	3	1844	c.1705T>A	c.(1705-1707)Tct>Act	p.S569T	PCDH1_ENST00000536585.1_Missense_Mutation_p.S547T|PCDH1_ENST00000511044.1_5'UTR|PCDH1_ENST00000503492.1_Intron|PCDH1_ENST00000287008.3_Missense_Mutation_p.S569T|PCDH1_ENST00000456271.1_Missense_Mutation_p.S557T	NM_001278613.1|NM_001278615.1	NP_001265542.1|NP_001265544.1	Q08174	PCDH1_HUMAN	protocadherin 1	569	Cadherin 5. {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)		CGATCCAGAGATGTCTTCACC	0.577																																					p.S569T	Ovarian(132;1609 1739 4190 14731 45037)	Atlas-SNP	.											.	PCDH1	119	.	0			c.T1705A						PASS	.						54	45	49					5																	141244191		2203	4300	6503	SO:0001583	missense	5097	exon3			CCAGAGATGTCTT	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.1705T>A	5.37:g.141244191A>T	ENSP00000378043:p.Ser569Thr	63	0	0		64	41	0.640625	NM_032420	Q8IUP2	Missense_Mutation	SNP	ENST00000394536.3	37	CCDS43375.1	.	.	.	.	.	.	.	.	.	.	a	8.695	0.908454	0.17833	.	.	ENSG00000156453	ENST00000287008;ENST00000394536;ENST00000456271;ENST00000357517;ENST00000536585	T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67	5.76	5.76	0.90799	Cadherin (4);Cadherin-like (1);	0.290510	0.24988	N	0.034015	T	0.30916	0.0780	N	0.17594	0.5	0.29962	N	0.819276	B;B	0.29085	0.232;0.115	B;B	0.29524	0.103;0.062	T	0.26258	-1.0108	10	0.29301	T	0.29	.	10.1435	0.42749	0.8323:0.1677:0.0:0.0	.	569;569	Q08174;Q08174-2	PCDH1_HUMAN;.	T	569;569;557;580;547	ENSP00000287008:S569T;ENSP00000378043:S569T;ENSP00000403497:S557T;ENSP00000350122:S580T;ENSP00000438825:S547T	ENSP00000287008:S569T	S	-	1	0	PCDH1	141224375	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	4.850000	0.62889	2.212000	0.71576	0.454000	0.30748	TCT	.	.	none		0.577	PCDH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251862.1	NM_032420		T	141244191	A	T	141244191	3	4	36	1	0	0	0	0	1	0	0	0	11515	333	12	5	2104	5	PCDH1	5	141244191	Missense_Mutation	SNP	A	TCGA-GS-A9TT-01A-11D-A382-10	994288	141244191	39671069	54	14282											
FAT2	2196	hgsc.bcm.edu	37	chr5	150922299	150922299	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttatatggatcagcctcaaAtacaggcctattgtcattga	12	13	7	9	0	3	1	3	1	0	0	3	2	3	2	2	2	2	0	2	2	5	6			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr5:150922299A>G	ENST00000261800.5	-	9	8401	c.8389T>C	c.(8389-8391)Ttt>Ctt	p.F2797L		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	2797	Cadherin 24. {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)			TCAGCCTCAAATACAGGCCTA	0.488																																					p.F2797L		Atlas-SNP	.											.	FAT2	465	.	0			c.T8389C						PASS	.						152	141	145					5																	150922299		2203	4300	6503	SO:0001583	missense	2196	exon9			CCTCAAATACAGG	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.8389T>C	5.37:g.150922299A>G	ENSP00000261800:p.Phe2797Leu	112	0	0		98	52	0.530612	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	A	17.89	3.499120	0.64298	.	.	ENSG00000086570	ENST00000261800	T	0.51325	0.71	5.79	5.79	0.91817	Cadherin (2);Cadherin-like (1);	0.000000	0.64402	D	0.000004	T	0.67401	0.2889	M	0.67625	2.065	0.80722	D	1	D	0.71674	0.998	D	0.77557	0.99	T	0.69224	-0.5201	10	0.56958	D	0.05	.	16.1296	0.81418	1.0:0.0:0.0:0.0	.	2797	Q9NYQ8	FAT2_HUMAN	L	2797	ENSP00000261800:F2797L	ENSP00000261800:F2797L	F	-	1	0	FAT2	150902492	1.000000	0.71417	0.939000	0.37840	0.888000	0.51559	9.262000	0.95591	2.216000	0.71823	0.379000	0.24179	TTT	.	.	none		0.488	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447		G	150922299	A	G	150922299	3	3	36	1	0	0	0	0	1	0	0	0	5698	101	4	3	4720	3	FAT2	5	150922299	Missense_Mutation	SNP	A	TCGA-GS-A9TT-01A-11D-A382-10	9678108	150922299	29992961	55	14283											
NUP153	9972	hgsc.bcm.edu	37	chr6	17629629	17629629	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagaatcggatgacacacctAttttgaatcctccctgatct	11	12	6	12	1	1	4	0	3	1	1	4	5	3	5	3	1	0	0	3	1	3	3	rs141169660	byFrequency	TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr6:17629629A>C	ENST00000262077.2	-	18	2800	c.2801T>G	c.(2800-2802)aTa>aGa	p.I934R	NUP153_ENST00000537253.1_Missense_Mutation_p.I965R	NM_005124.2	NP_005115.2	P49790	NU153_HUMAN	nucleoporin 153kDa	934					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)			TGACACACCTATTTTGAATCC	0.373																																					p.I934R		Atlas-SNP	.											.	NUP153	116	.	0			c.T2801G						PASS	.						74	81	79					6																	17629629		2203	4300	6503	SO:0001583	missense	9972	exon18			ACACCTATTTTGA	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.2801T>G	6.37:g.17629629A>C	ENSP00000262077:p.Ile934Arg	145	0	0		125	55	0.44	NM_005124	B4DIK2|E7EPX5|F6QR24|Q4LE47|Q5T9I7|Q7Z743	Missense_Mutation	SNP	ENST00000262077.2	37	CCDS4541.1	.	.	.	.	.	.	.	.	.	.	A	11.64	1.698550	0.30142	.	.	ENSG00000124789	ENST00000262077;ENST00000430136;ENST00000537253	T;T	0.07114	3.23;3.22	5.73	0.639	0.17747	.	0.539300	0.16784	N	0.199661	T	0.02688	0.0081	L	0.36672	1.1	0.32725	N	0.509803	P;B;B	0.43519	0.809;0.29;0.421	P;B;B	0.45232	0.474;0.095;0.095	T	0.47381	-0.9122	10	0.16896	T	0.51	-0.2277	8.855	0.35223	0.7261:0.0:0.2739:0.0	.	965;914;934	F6QR24;Q4LE47;P49790	.;.;NU153_HUMAN	R	934;914;965	ENSP00000262077:I934R;ENSP00000444029:I965R	ENSP00000262077:I934R	I	-	2	0	NUP153	17737608	1.000000	0.71417	0.412000	0.26496	0.483000	0.33249	3.701000	0.54793	-0.044000	0.13491	-0.912000	0.02778	ATA	A|0.999;G|0.001	.	alt		0.373	NUP153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039953.1			C	17629629	A	C	17629629	3	2	36	1	0	0	0	0	1	0	0	0	10764	449	16	5	1646	5	NUP153	6	17629629	Missense_Mutation	SNP	A	TCGA-GS-A9TT-01A-11D-A382-10		17629629	153485438	56	14284											
HIST1H2BD	3017	hgsc.bcm.edu	37	chr6	26158724	26158724	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttccgggggagctggccaaGcacgccgtgtcggagggcac	6	5	17	13	4	0	0	0	0	0	0	2	2	1	2	3	5	2	3	3	5	1	1			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr6:26158724G>A	ENST00000289316.2	+	1	351	c.327G>A	c.(325-327)aaG>aaA	p.K109K	HIST1H2BD_ENST00000377777.4_Silent_p.K109K	NM_138720.2	NP_619790.1	P58876	H2B1D_HUMAN	histone cluster 1, H2bd	109					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						AGCTGGCCAAGCACGCCGTGT	0.587																																					p.K109K		Atlas-SNP	.											.	HIST1H2BD	45	.	0			c.G327A						PASS	.						73	80	78					6																	26158724		2203	4300	6503	SO:0001819	synonymous_variant	3017	exon1			GGCCAAGCACGCC	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.327G>A	6.37:g.26158724G>A		127	0	0		110	48	0.436364	NM_021063		Silent	SNP	ENST00000289316.2	37	CCDS4587.1																																																																																			.	.	none		0.587	HIST1H2BD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040088.1	NM_021063		A	26158724	G	A	26158724	2	1	36	1	0	0	0	0	0	0	0	1	7152	962	34	2		2	HIST1H2BD	6	26158724	Silent	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	8529095	26158724	144956343	57	14285											
HIST1H2BJ	8970	hgsc.bcm.edu	37	chr6	27100220	27100220	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gtgcttggccaactccccagGcagcagcaggcgcacggccg	7	4	14	16	3	0	0	0	0	0	0	1	0	1	0	4	4	4	5	4	4	1	1			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr6:27100220G>T	ENST00000607124.1	-	1	309	c.310C>A	c.(310-312)Cct>Act	p.P104T	HIST1H2AG_ENST00000359193.2_5'Flank|HIST1H2BJ_ENST00000541790.1_Missense_Mutation_p.P104T|HIST1H2BJ_ENST00000339812.2_Missense_Mutation_p.P104T			P06899	H2B1J_HUMAN	histone cluster 1, H2bj	104					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						AACTCCCCAGGCAGCAGCAGG	0.602																																					p.P104T		Atlas-SNP	.											.	HIST1H2BJ	21	.	0			c.C310A						PASS	.						80	82	82					6																	27100220		2203	4300	6503	SO:0001583	missense	8970	exon1			CCCCAGGCAGCAG	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.310C>A	6.37:g.27100220G>T	ENSP00000476136:p.Pro104Thr	81	0	0		55	28	0.509091	NM_021058	B2R4J4|O60816	Missense_Mutation	SNP	ENST00000607124.1	37	CCDS4618.1	.	.	.	.	.	.	.	.	.	.	G	16.52	3.145750	0.57044	.	.	ENSG00000124635	ENST00000541790;ENST00000339812	T;T	0.60672	0.17;0.17	4.06	4.06	0.47325	Histone-fold (2);	0.000000	0.43747	U	0.000526	T	0.80696	0.4672	H	0.97077	3.935	0.53688	D	0.999973	D	0.89917	1.0	D	0.79108	0.992	D	0.87167	0.2218	10	0.87932	D	0	.	14.5496	0.68057	0.0:0.0:1.0:0.0	.	104	P06899	H2B1J_HUMAN	T	104	ENSP00000445633:P104T;ENSP00000342886:P104T	ENSP00000342886:P104T	P	-	1	0	HIST1H2BJ	27208199	1.000000	0.71417	1.000000	0.80357	0.219000	0.24729	6.815000	0.75242	2.210000	0.71456	0.585000	0.79938	CCT	.	.	none		0.602	HIST1H2BJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040138.2	NM_021058		T	27100220	G	T	27100220	3	4	36	1	0	0	0	0	1	0	0	0	7158	1203	42	4	74	4	HIST1H2BJ	6	27100220	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	941496	27100220	144014847	58	14286											
HIST1H2AM	8336	hgsc.bcm.edu	37	chr6	27860549	27860549	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagcccttacttgcccttagCtttgtggtggctctcagtct	4	15	9	13	0	2	0	1	0	2	0	3	0	2	0	2	2	4	2	2	2	2	4	rs191325870		TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr6:27860549C>G	ENST00000359611.2	-	1	414	c.379G>C	c.(379-381)Gct>Cct	p.A127P	HIST1H2BO_ENST00000303806.4_5'Flank|HIST1H3J_ENST00000359303.2_5'Flank|HIST1H3J_ENST00000479986.1_5'UTR	NM_003514.2	NP_003505.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2am	127						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						TTGCCCTTAGCTTTGTGGTGG	0.483																																					p.A127P		Atlas-SNP	.											.	HIST1H2AM	27	.	0			c.G379C						PASS	.						121	117	118					6																	27860549		2203	4300	6503	SO:0001583	missense	8336	exon1			CCTTAGCTTTGTG	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.379G>C	6.37:g.27860549C>G	ENSP00000352627:p.Ala127Pro	227	0	0		194	92	0.474227	NM_003514	P02261|Q2M1R2|Q76PA6	Missense_Mutation	SNP	ENST00000359611.2	37	CCDS4639.1	.	.	.	.	.	.	.	.	.	.	C	9.216	1.032045	0.19590	.	.	ENSG00000233224	ENST00000359611	T	0.44083	0.93	4.15	4.15	0.48705	.	0.000000	0.30068	U	0.010482	T	0.33059	0.0850	L	0.34521	1.04	0.34490	D	0.70489	.	.	.	.	.	.	T	0.16482	-1.0401	8	0.44086	T	0.13	.	16.2401	0.82402	0.0:1.0:0.0:0.0	.	.	.	.	P	127	ENSP00000352627:A127P	ENSP00000352627:A127P	A	-	1	0	HIST1H2AM	27968528	0.991000	0.36638	1.000000	0.80357	0.272000	0.26649	3.089000	0.50183	2.601000	0.87937	0.655000	0.94253	GCT	C|1.000;T|0.000	.	alt		0.483	HIST1H2AM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040162.1	NM_003514		G	27860549	C	G	27860549	3	3	36	1	0	0	0	0	1	0	0	0	7148	797	28	4	17	4	HIST1H2AM	6	27860549	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	760329	27860549	143254518	59	14287											
HSPA1L	3305	hgsc.bcm.edu	37	chr6	31778920	31778920	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggttggcctgggtgctggacGacagggtcctcttggccctc	3	10	16	12	1	1	0	0	0	1	0	3	2	2	1	3	6	1	2	3	6	0	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr6:31778920G>A	ENST00000375654.4	-	2	1019	c.830C>T	c.(829-831)tCg>tTg	p.S277L	HSPA1L_ENST00000417199.3_Missense_Mutation_p.S277L	NM_005527.3	NP_005518.3	P34931	HS71L_HUMAN	heat shock 70kDa protein 1-like	277					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						GGTGCTGGACGACAGGGTCCT	0.527																																					p.S277L		Atlas-SNP	.											.	HSPA1L	185	.	0			c.C830T						PASS	.						65	72	70					6																	31778920		2203	4300	6503	SO:0001583	missense	3305	exon2			CTGGACGACAGGG	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.830C>T	6.37:g.31778920G>A	ENSP00000364805:p.Ser277Leu	110	0	0		133	61	0.458647	NM_005527	A6NNB0|B0UXW8|O75634|Q2HXR3|Q8NE72|Q96QC9|Q9UQM1	Missense_Mutation	SNP	ENST00000375654.4	37	CCDS34413.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.408085	0.83340	.	.	ENSG00000204390	ENST00000375654;ENST00000417199;ENST00000375653;ENST00000424494	T;T	0.02525	4.26;4.26	5.4	5.4	0.78164	.	0.000000	0.30575	N	0.009335	T	0.29223	0.0727	H	0.99906	4.925	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.60717	-0.7208	10	0.87932	D	0	-13.5603	16.7131	0.85391	0.0:0.0:1.0:0.0	.	277	P34931	HS71L_HUMAN	L	277;277;222;167	ENSP00000364805:S277L;ENSP00000387691:S277L	ENSP00000364804:S222L	S	-	2	0	HSPA1L	31886899	1.000000	0.71417	0.988000	0.46212	0.967000	0.64934	5.202000	0.65169	2.810000	0.96702	0.585000	0.79938	TCG	.	.	none		0.527	HSPA1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076416.2			A	31778920	G	A	31778920	3	1	36	1	0	0	0	0	1	0	0	0	7419	1059	37	1	1099	1	HSPA1L	6	31778920	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	3918371	31778920	139336147	60	14288											
PIM1	5292	hgsc.bcm.edu	37	chr6	37138563	37138563	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tcctaggcaaggagaaggagCccctggagtcgcagtaccag	11	5	14	11	1	0	1	0	0	0	1	2	4	1	3	4	4	2	3	4	4	4	2	rs34095970		TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr6:37138563C>T	ENST00000373509.5	+	2	470	c.97C>T	c.(97-99)Ccc>Tcc	p.P33S		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	124					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)	GGAGAAGGAGCCCCTGGAGTC	0.701			T	BCL6	NHL																																p.P124S		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C370T						PASS	.						21	31	28					6																	37138563		2155	4262	6417	SO:0001583	missense	5292	exon2			AAGGAGCCCCTGG		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.97C>T	6.37:g.37138563C>T	ENSP00000362608:p.Pro33Ser	48	0	0		41	19	0.463415	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	12.64	1.997735	0.35226	.	.	ENSG00000137193	ENST00000373509	T	0.69040	-0.37	4.64	3.75	0.43078	Protein kinase-like domain (1);	0.000000	0.64402	D	0.000001	T	0.21267	0.0512	N	0.08118	0	0.48901	D	0.999723	B	0.12013	0.005	B	0.06405	0.002	T	0.22836	-1.0205	10	0.02654	T	1	.	12.1438	0.54012	0.0:0.9152:0.0:0.0848	.	124	P11309	PIM1_HUMAN	S	33	ENSP00000362608:P33S	ENSP00000362608:P33S	P	+	1	0	PIM1	37246541	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.980000	0.40618	2.294000	0.77228	0.549000	0.68633	CCC	.	.	none		0.701	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37138563	C	T	37138563	3	4	36	1	0	0	0	0	1	0	0	0	11936	739	26	2	103	2	PIM1	6	37138563	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	5359643	37138563	133976504	61	14289			2	62		11	9	647	N	G_C	7.836064e-25
PIM1	5292	hgsc.bcm.edu	37	chr6	37138577	37138577	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaggagcccctggagtcgcaGtaccaggtgggcccgctact	8	6	14	13	2	0	0	0	0	0	0	1	2	0	2	4	4	3	3	4	4	3	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr6:37138577G>T	ENST00000373509.5	+	2	484	c.111G>T	c.(109-111)caG>caT	p.Q37H		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	128					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)	p.Q37H(2)		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)	TGGAGTCGCAGTACCAGGTGG	0.706			T	BCL6	NHL																																p.Q128H		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,0,2	PIM1	71	2	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.G384T						PASS	.						22	32	28					6																	37138577		2167	4268	6435	SO:0001583	missense	5292	exon2			GTCGCAGTACCAG		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.111G>T	6.37:g.37138577G>T	ENSP00000362608:p.Gln37His	52	0	0		41	18	0.439024	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	G	12.20	1.866670	0.32977	.	.	ENSG00000137193	ENST00000373509	T	0.13901	2.55	4.64	0.515	0.17013	Protein kinase-like domain (1);	0.470425	0.18904	N	0.127947	T	0.01695	0.0054	N	0.08118	0	0.29021	N	0.886284	B	0.09022	0.002	B	0.04013	0.001	T	0.45056	-0.9287	10	0.41790	T	0.15	.	5.1594	0.15053	0.3201:0.2369:0.443:0.0	.	128	P11309	PIM1_HUMAN	H	37	ENSP00000362608:Q37H	ENSP00000362608:Q37H	Q	+	3	2	PIM1	37246555	0.171000	0.23029	0.997000	0.53966	0.994000	0.84299	-0.639000	0.05446	0.154000	0.19237	0.549000	0.68633	CAG	.	.	none		0.706	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37138577	G	T	37138577	3	4	36	1	0	0	0	0	1	0	0	0	11936	1020	36	4	117	4	PIM1	6	37138577	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	14	37138577	133976490	62	14290			2	62		11	9	647	N	G_C	7.836064e-25
PIM1	5292	hgsc.bcm.edu	37	chr6	37138591	37138591	+	Missense_Mutation	SNP	C	C	T																															gtcgcagtaccaggtgggccCgctactgggcagcggcggct																										TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr6:37138591C>T	ENST00000373509.5	+	2	498	c.125C>T	c.(124-126)cCg>cTg	p.P42L		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	133					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)	CAGGTGGGCCCGCTACTGGGC	0.721			T	BCL6	NHL																																p.P133L		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C398T						PASS	.						21	32	28					6																	37138591		2169	4265	6434	SO:0001583	missense	5292	exon2			TGGGCCCGCTACT		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.125C>T	6.37:g.37138591C>T	ENSP00000362608:p.Pro42Leu	59	0	0		53	23	0.433962	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	18.08	3.544320	0.65198	.	.	ENSG00000137193	ENST00000373509	T	0.13778	2.56	4.96	3.06	0.35304	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.260132	0.31415	N	0.007693	T	0.04407	0.0121	N	0.24115	0.695	0.49051	D	0.99974	P	0.37955	0.612	B	0.37422	0.249	T	0.29701	-1.0003	10	0.72032	D	0.01	.	10.5527	0.45099	0.0:0.7869:0.1356:0.0775	.	133	P11309	PIM1_HUMAN	L	42	ENSP00000362608:P42L	ENSP00000362608:P42L	P	+	2	0	PIM1	37246569	0.992000	0.36948	1.000000	0.80357	0.987000	0.75469	5.339000	0.65953	1.157000	0.42530	0.549000	0.68633	CCG	.	.	none		0.721	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37138591	C	T	37138591	3	4	36	1	0	0	0	0	1	0	0	0	11936	652	23	1	131	1	PIM1	6	37138591	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	14	37138591	133976476	63	14291	182	2	2	62		11	9	647	N	G_C	7.836064e-25
PIM1	5292	hgsc.bcm.edu	37	chr6	37138592	37138592	+	Silent	SNP	G	G	A																															tcgcagtaccaggtgggcccGctactgggcagcggcggctt																										TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr6:37138592G>A	ENST00000373509.5	+	2	499	c.126G>A	c.(124-126)ccG>ccA	p.P42P		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	133					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)	AGGTGGGCCCGCTACTGGGCA	0.721			T	BCL6	NHL																																p.P133P		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.G399A						PASS	.						21	32	28					6																	37138592		2169	4267	6436	SO:0001819	synonymous_variant	5292	exon2			GGGCCCGCTACTG		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.126G>A	6.37:g.37138592G>A		60	0	0		54	24	0.444444	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.721	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			A	37138592	G	A	37138592	2	1	36	1	0	0	0	0	0	0	0	1	11936	1074	38	1		1	PIM1	6	37138592	Silent	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	1	37138592	133976475	64	14292	182	2	2	62		11	9	647	N	G_C	7.836064e-25
PIM1	5292	hgsc.bcm.edu	37	chr6	37138804	37138804	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cggatttccgactggggagaGctggtgagtgccctgcagga	7	8	17	9	2	0	2	0	1	0	1	1	6	1	4	2	5	3	2	2	5	0	1			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr6:37138804G>C	ENST00000373509.5	+	3	610	c.237G>C	c.(235-237)gaG>gaC	p.E79D		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	170					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)	p.E79D(1)		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)	ACTGGGGAGAGCTGGTGAGTG	0.687			T	BCL6	NHL																																p.E170D		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,0,4	PIM1	71	4	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G510C						PASS	.						51	53	52					6																	37138804		2203	4300	6503	SO:0001583	missense	5292	exon3			GGGAGAGCTGGTG		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.237G>C	6.37:g.37138804G>C	ENSP00000362608:p.Glu79Asp	73	0	0		68	33	0.485294	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	G	12.44	1.939366	0.34189	.	.	ENSG00000137193	ENST00000373509	T	0.66280	-0.2	4.44	0.389	0.16269	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.068351	0.56097	D	0.000034	T	0.16938	0.0407	N	0.11023	0.085	0.34210	D	0.674133	B	0.15473	0.013	B	0.14578	0.011	T	0.02345	-1.1173	10	0.37606	T	0.19	.	4.6029	0.12363	0.4591:0.0:0.3935:0.1474	.	170	P11309	PIM1_HUMAN	D	79	ENSP00000362608:E79D	ENSP00000362608:E79D	E	+	3	2	PIM1	37246782	0.728000	0.28080	0.985000	0.45067	0.975000	0.68041	0.054000	0.14205	-0.042000	0.13535	0.549000	0.68633	GAG	.	.	none		0.687	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			C	37138804	G	C	37138804	3	2	36	1	0	0	0	0	1	0	0	0	11936	962	34	4	247	4	PIM1	6	37138804	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	212	37138804	133976263	65	14293			2	62		11	9	647	N	G_C	7.836064e-25
PIM1	5292	hgsc.bcm.edu	37	chr6	37138951	37138951	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtcctgctgaagaaggtgagCtcgggtttctccggcgtcat	6	11	14	10	3	2	3	1	2	1	1	5	3	3	3	2	3	2	3	2	3	2	1			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr6:37138951C>T	ENST00000373509.5	+	4	664	c.291C>T	c.(289-291)agC>agT	p.S97S		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	188					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)	AGAAGGTGAGCTCGGGTTTCT	0.647			T	BCL6	NHL																																p.S188S		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,+1,5	PIM1	71	5	0			c.C564T						PASS	.						82	92	89					6																	37138951		2203	4300	6503	SO:0001819	synonymous_variant	5292	exon4			GGTGAGCTCGGGT		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.291C>T	6.37:g.37138951C>T		53	0	0		48	24	0.5	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.647	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37138951	C	T	37138951	2	4	36	1	0	0	0	0	0	0	0	1	11936	796	28	2		2	PIM1	6	37138951	Silent	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	147	37138951	133976116	66	14294			2	62		11	9	647	N	G_C	7.836064e-25
PIM1	5292	hgsc.bcm.edu	37	chr6	37139045	37139045	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ggcccgagccggtgcaagatCtcttcgacttcatcacggaa	9	8	11	13	4	3	1	2	0	1	1	5	4	3	2	2	3	2	1	2	3	2	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr6:37139045C>G	ENST00000373509.5	+	4	758	c.385C>G	c.(385-387)Ctc>Gtc	p.L129V		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	220	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)	GGTGCAAGATCTCTTCGACTT	0.632			T	BCL6	NHL																																p.L220V		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C658G						PASS	.						82	96	91					6																	37139045		2203	4300	6503	SO:0001583	missense	5292	exon4			CAAGATCTCTTCG		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.385C>G	6.37:g.37139045C>G	ENSP00000362608:p.Leu129Val	97	0	0		76	30	0.394737	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.025243	0.75390	.	.	ENSG00000137193	ENST00000373509	T	0.42131	0.98	4.28	4.28	0.50868	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	0.64316	0.2587	M	0.86864	2.845	0.58432	D	0.999999	D	0.76494	0.999	D	0.85130	0.997	T	0.72597	-0.4245	10	0.87932	D	0	.	16.8746	0.86048	0.0:1.0:0.0:0.0	.	220	P11309	PIM1_HUMAN	V	129	ENSP00000362608:L129V	ENSP00000362608:L129V	L	+	1	0	PIM1	37247023	1.000000	0.71417	1.000000	0.80357	0.692000	0.40212	5.539000	0.67199	2.371000	0.80710	0.549000	0.68633	CTC	.	.	none		0.632	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			G	37139045	C	G	37139045	3	3	36	1	0	0	0	0	1	0	0	0	11936	913	32	4	399	4	PIM1	6	37139045	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	94	37139045	133976022	67	14295			2	62		11	9	647	N	G_C	7.836064e-25
PIM1	5292	hgsc.bcm.edu	37	chr6	37139097	37139097	+	Missense_Mutation	SNP	G	G	A																															gcaagaggagctggcccgcaGcttcttctggcaggtgctgg																										TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr6:37139097G>A	ENST00000373509.5	+	4	810	c.437G>A	c.(436-438)aGc>aAc	p.S146N		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	237	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)	CTGGCCCGCAGCTTCTTCTGG	0.612			T	BCL6	NHL																																p.S237N		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,carcinoma,+1,3	PIM1	71	3	0			c.G710A						scavenged	.						51	60	57					6																	37139097		2202	4300	6502	SO:0001583	missense	5292	exon4			CCCGCAGCTTCTT		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.437G>A	6.37:g.37139097G>A	ENSP00000362608:p.Ser146Asn	117	1	0.00854701		93	44	0.473118	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	G	11.20	1.567906	0.28003	.	.	ENSG00000137193	ENST00000373509	T	0.65364	-0.15	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);	0.376195	0.29355	N	0.012392	T	0.28599	0.0708	N	0.20304	0.555	0.31131	N	0.707701	B	0.06786	0.001	B	0.10450	0.005	T	0.05289	-1.0894	10	0.17832	T	0.49	.	15.8069	0.78520	0.0:0.0:1.0:0.0	.	237	P11309	PIM1_HUMAN	N	146	ENSP00000362608:S146N	ENSP00000362608:S146N	S	+	2	0	PIM1	37247075	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	4.004000	0.57068	2.254000	0.74563	0.448000	0.29417	AGC	.	.	none		0.612	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			A	37139097	G	A	37139097	3	1	36	1	0	0	0	0	1	0	0	0	11936	971	34	2	451	2	PIM1	6	37139097	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	52	37139097	133975970	68	14296	183	2	2	62		11	9	647	N	G_C	7.836064e-25
PIM1	5292	hgsc.bcm.edu	37	chr6	37139104	37139104	+	Silent	SNP	C	C	T																															gagctggcccgcagcttcttCtggcaggtgctggaggccgt																										TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr6:37139104C>T	ENST00000373509.5	+	4	817	c.444C>T	c.(442-444)ttC>ttT	p.F148F		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	239	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)	GCAGCTTCTTCTGGCAGGTGC	0.617			T	BCL6	NHL																																p.F239F		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C717T						PASS	.						47	56	53					6																	37139104		2202	4299	6501	SO:0001819	synonymous_variant	5292	exon4			CTTCTTCTGGCAG		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.444C>T	6.37:g.37139104C>T		110	0	0		95	46	0.484211	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.617	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37139104	C	T	37139104	2	4	36	1	0	0	0	0	0	0	0	1	11936	912	32	2		2	PIM1	6	37139104	Silent	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	7	37139104	133975963	69	14297	183	2	2	62		11	9	647	N	G_C	7.836064e-25
PIM1	5292	hgsc.bcm.edu	37	chr6	37139128	37139128	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	caggtgctggaggccgtgcgGcactgccacaactgcggggt	6	6	17	12	3	0	0	0	0	0	0	0	1	0	1	2	6	5	2	2	6	1	0			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr6:37139128G>A	ENST00000373509.5	+	4	841	c.468G>A	c.(466-468)cgG>cgA	p.R156R		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	247	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)	AGGCCGTGCGGCACTGCCACA	0.617			T	BCL6	NHL																																p.R247R		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.G741A						PASS	.						42	48	46					6																	37139128		2203	4300	6503	SO:0001819	synonymous_variant	5292	exon4			CGTGCGGCACTGC		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.468G>A	6.37:g.37139128G>A		109	0	0		98	48	0.489796	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.617	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			A	37139128	G	A	37139128	2	1	36	1	0	0	0	0	0	0	0	1	11936	1190	42	2		2	PIM1	6	37139128	Silent	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	24	37139128	133975939	70	14298			2	62		11	9	647	N	G_C	7.836064e-25
PIM1	5292	hgsc.bcm.edu	37	chr6	37139209	37139209	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcaatcgcggcgagctcaaGctcatcgacttcgggtcggg	7	8	13	13	6	3	0	3	0	0	0	7	2	3	0	0	3	2	2	0	3	2	1			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr6:37139209G>C	ENST00000373509.5	+	4	922	c.549G>C	c.(547-549)aaG>aaC	p.K183N		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	274	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)	GCGAGCTCAAGCTCATCGACT	0.647			T	BCL6	NHL																																p.K274N		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.G822C						PASS	.						31	32	32					6																	37139209		2203	4300	6503	SO:0001583	missense	5292	exon4			GCTCAAGCTCATC		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.549G>C	6.37:g.37139209G>C	ENSP00000362608:p.Lys183Asn	70	0	0		64	26	0.40625	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	G	18.97	3.735520	0.69189	.	.	ENSG00000137193	ENST00000373509	T	0.22336	1.96	4.36	3.47	0.39725	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.062020	0.64402	D	0.000006	T	0.48169	0.1485	H	0.98786	4.33	0.54753	D	0.999984	D	0.69078	0.997	D	0.71414	0.973	T	0.57642	-0.7776	10	0.66056	D	0.02	.	5.5129	0.16890	0.3296:0.0:0.6704:0.0	.	274	P11309	PIM1_HUMAN	N	183	ENSP00000362608:K183N	ENSP00000362608:K183N	K	+	3	2	PIM1	37247187	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.356000	0.44116	1.020000	0.39573	0.448000	0.29417	AAG	.	.	none		0.647	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			C	37139209	G	C	37139209	3	2	36	1	0	0	0	0	1	0	0	0	11936	962	34	4	563	4	PIM1	6	37139209	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	81	37139209	133975858	71	14299			2	62		11	9	647	N	G_C	7.836064e-25
COL21A1	81578	hgsc.bcm.edu	37	chr6	55924958	55924958	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atacccggggagccatgttgGgacaggcaatgatcacaatt	12	8	12	9	1	1	1	1	1	0	0	1	3	1	3	2	4	2	2	2	4	3	3			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr6:55924958G>A	ENST00000244728.5	-	28	2863	c.2466C>T	c.(2464-2466)tcC>tcT	p.S822S	COL21A1_ENST00000535941.1_Silent_p.S822S|COL21A1_ENST00000467045.1_5'UTR|COL21A1_ENST00000370819.1_Silent_p.S819S|COL21A1_ENST00000370808.2_Intron	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	822					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)			AGCCATGTTGGGACAGGCAAT	0.493																																					p.S822S		Atlas-SNP	.											.	COL21A1	201	.	0			c.C2466T						PASS	.						49	48	48					6																	55924958		1846	4088	5934	SO:0001819	synonymous_variant	81578	exon28			ATGTTGGGACAGG	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.2466C>T	6.37:g.55924958G>A		235	0	0		216	102	0.472222	NM_030820	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Silent	SNP	ENST00000244728.5	37	CCDS55025.1																																																																																			.	.	none		0.493	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2			A	55924958	G	A	55924958	2	1	36	1	0	0	0	0	0	0	0	1	3682	1219	43	2		2	COL21A1	6	55924958	Silent	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	18785749	55924958	115190109	72	14300											
COL12A1	1303	hgsc.bcm.edu	37	chr6	75890902	75890902	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taagaagtcacttctgaaaaActaagatcctttggagggac	15	10	9	7	0	2	3	1	1	1	2	3	5	3	5	1	2	1	0	1	2	5	4			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr6:75890902A>C	ENST00000322507.8	-	11	2226	c.1917T>G	c.(1915-1917)agT>agG	p.S639R	COL12A1_ENST00000483888.2_Missense_Mutation_p.S639R|COL12A1_ENST00000416123.2_Missense_Mutation_p.S639R|COL12A1_ENST00000345356.6_Intron	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	639	Fibronectin type-III 3. {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						CTTCTGAAAAACTAAGATCCT	0.343																																					p.S639R		Atlas-SNP	.											.	COL12A1	385	.	0			c.T1917G						PASS	.						53	54	54					6																	75890902		1854	4083	5937	SO:0001583	missense	1303	exon11			TGAAAAACTAAGA	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.1917T>G	6.37:g.75890902A>C	ENSP00000325146:p.Ser639Arg	117	0	0		100	44	0.44	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	.	.	.	.	.	.	.	.	.	.	A	4.453	0.083928	0.08583	.	.	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000416123;ENST00000483888	T;T;T	0.57907	0.37;0.37;0.37	5.68	-11.4	0.00090	Fibronectin, type III (4);	0.724585	0.13526	N	0.381263	T	0.06826	0.0174	N	0.11789	0.175	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.13953	-1.0490	10	0.16896	T	0.51	.	5.1045	0.14777	0.1741:0.0703:0.443:0.3126	.	639;639	D6RGG3;Q99715	.;COCA1_HUMAN	R	639	ENSP00000325146:S639R;ENSP00000412864:S639R;ENSP00000421216:S639R	ENSP00000325146:S639R	S	-	3	2	COL12A1	75947622	0.000000	0.05858	0.011000	0.14972	0.633000	0.38033	-1.183000	0.03079	-1.983000	0.00987	-0.341000	0.08007	AGT	.	.	none		0.343	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		C	75890902	A	C	75890902	3	2	36	1	0	0	0	0	1	0	0	0	3671	40	2	5	7498	5	COL12A1	6	75890902	Missense_Mutation	SNP	A	TCGA-GS-A9TT-01A-11D-A382-10	19965944	75890902	95224165	73	14301											
LIN28B	389421	hgsc.bcm.edu	37	chr6	105526426	105526426	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaatgttgcacagccacccgCgagttctcagggaagacagg	12	6	12	11	2	1	1	1	0	1	1	2	3	1	2	2	2	2	3	2	2	2	2	rs201716597		TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr6:105526426C>T	ENST00000345080.4	+	4	724	c.521C>T	c.(520-522)gCg>gTg	p.A174V		NM_001004317.3	NP_001004317.1	Q6ZN17	LN28B_HUMAN	lin-28 homolog B (C. elegans)	174					miRNA catabolic process (GO:0010587)|pre-miRNA processing (GO:0031054)|regulation of transcription, DNA-templated (GO:0006355)|RNA 3'-end processing (GO:0031123)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(10)|ovary(1)	12		all_cancers(87;0.00346)|Acute lymphoblastic leukemia(125;2.26e-08)|all_hematologic(75;2.79e-06)|all_epithelial(87;0.204)				CAGCCACCCGCGAGTTCTCAG	0.527													C|||	1	0.000199681	0.0	0.0	5008	,	,		20262	0.0		0.001	False		,,,				2504	0.0				p.A174V		Atlas-SNP	.											.	LIN28B	17	.	0			c.C521T						PASS	.						91	82	85					6																	105526426		2203	4300	6503	SO:0001583	missense	389421	exon4			CACCCGCGAGTTC	AK131411	CCDS34504.1	6q21	2010-04-06			ENSG00000187772	ENSG00000187772			32207	protein-coding gene	gene with protein product		611044					Standard	NM_001004317		Approved	FLJ16517, CSDD2	uc003pqv.2	Q6ZN17	OTTHUMG00000015290	ENST00000345080.4:c.521C>T	6.37:g.105526426C>T	ENSP00000344401:p.Ala174Val	58	0	0		34	30	0.882353	NM_001004317	A1L165|B2RPN6|Q5TCM4	Missense_Mutation	SNP	ENST00000345080.4	37	CCDS34504.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	5.567	0.289449	0.10567	.	.	ENSG00000187772	ENST00000345080	.	.	.	6.02	3.12	0.35913	.	0.509217	0.22018	N	0.065761	T	0.18841	0.0452	L	0.40543	1.245	0.09310	N	1	B	0.17852	0.024	B	0.08055	0.003	T	0.16276	-1.0408	9	0.31617	T	0.26	2.6381	13.409	0.60931	0.0:0.7984:0.0:0.2016	.	174	Q6ZN17	LN28B_HUMAN	V	174	.	ENSP00000344401:A174V	A	+	2	0	LIN28B	105633119	0.781000	0.28676	0.002000	0.10522	0.165000	0.22458	3.304000	0.51866	0.093000	0.17368	-0.797000	0.03246	GCG	C|1.000;T|0.000	0.000	strong		0.527	LIN28B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041646.2	NM_001004317		T	105526426	C	T	105526426	3	4	36	1	0	0	0	0	1	0	0	0	8815	768	27	1	535	1	LIN28B	6	105526426	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	29635524	105526426	65588641	74	14302											
ROS1	6098	hgsc.bcm.edu	37	chr6	117686814	117686814	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgcagggggaccattccacAggatttgaaaacttgaagca	13	7	11	10	1	0	2	0	2	0	0	1	4	1	4	3	3	2	2	3	3	3	3			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr6:117686814A>G	ENST00000368508.3	-	19	3101	c.2903T>C	c.(2902-2904)cTg>cCg	p.L968P	ROS1_ENST00000368507.3_Missense_Mutation_p.L963P|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	968	Fibronectin type-III 4. {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)		ACCATTCCACAGGATTTGAAA	0.403			T	"GOPC, SDC4, SLC34A2, EZR, LRIG3"	"glioblastoma, NSCLC"																																p.L968P		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"O, E"	.	ROS1	728	.	0			c.T2903C						PASS	.						62	58	59					6																	117686814		2203	4300	6503	SO:0001583	missense	6098	exon19			TTCCACAGGATTT	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.2903T>C	6.37:g.117686814A>G	ENSP00000357494:p.Leu968Pro	175	1	0.00571429		83	64	0.771084	NM_002944	Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	A	11.94	1.787844	0.31593	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	T;T	0.54675	0.56;0.56	4.98	0.875	0.19130	.	0.587883	0.14154	N	0.337834	T	0.19406	0.0466	N	0.19112	0.55	0.80722	D	1	B	0.26258	0.145	B	0.36608	0.229	T	0.12734	-1.0536	10	0.45353	T	0.12	.	3.3358	0.07101	0.5397:0.2614:0.0729:0.126	.	968	P08922	ROS1_HUMAN	P	968;963	ENSP00000357494:L968P;ENSP00000357493:L963P	ENSP00000357493:L963P	L	-	2	0	ROS1	117793507	0.989000	0.36119	0.945000	0.38365	0.870000	0.49936	0.937000	0.28951	-0.027000	0.13873	-0.299000	0.09455	CTG	.	.	none		0.403	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1			G	117686814	A	G	117686814	3	3	36	1	0	0	0	0	1	0	0	0	13546	188	7	3	4240	3	ROS1	6	117686814	Missense_Mutation	SNP	A	TCGA-GS-A9TT-01A-11D-A382-10	12160388	117686814	53428253	75	14303											
UTRN	7402	hgsc.bcm.edu	37	chr6	145148756	145148756	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcttttaaagcccctcacaAtctcctcaactgtttcatga	10	15	3	13	0	5	1	3	1	2	0	6	1	5	1	3	0	2	1	3	0	4	4			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr6:145148756A>G	ENST00000367545.3	+	67	9543	c.9543A>G	c.(9541-9543)caA>caG	p.Q3181Q	UTRN_ENST00000367526.4_Silent_p.Q736Q	NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	3181					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)		GCCCCTCACAATCTCCTCAAC	0.368																																					p.Q3181Q		Atlas-SNP	.											.	UTRN	327	.	0			c.A9543G						PASS	.						70	68	69					6																	145148756		2203	4300	6503	SO:0001819	synonymous_variant	7402	exon67			CTCACAATCTCCT	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.9543A>G	6.37:g.145148756A>G		146	0	0		59	45	0.762712	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Silent	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	A	3.934	-0.015659	0.07681	.	.	ENSG00000152818	ENST00000367524	.	.	.	5.78	2.9	0.33743	.	.	.	.	.	T	0.28732	0.0712	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.17137	-1.0379	4	.	.	.	.	2.5299	0.04700	0.209:0.1277:0.5314:0.1319	.	.	.	.	S	212	.	.	N	+	2	0	UTRN	145190449	1.000000	0.71417	0.995000	0.50966	0.674000	0.39518	1.026000	0.30103	0.337000	0.23665	-0.321000	0.08615	AAT	.	.	none		0.368	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1			G	145148756	A	G	145148756	2	3	36	1	0	0	0	0	0	0	0	1	17118	98	4	3		3	UTRN	6	145148756	Silent	SNP	A	TCGA-GS-A9TT-01A-11D-A382-10	27461942	145148756	25966311	76	14304											
OSBPL3	26031	hgsc.bcm.edu	37	chr7	24843988	24843991	+	Frame_Shift_Del	DEL	TCTC	TCTC	-																															cttctaagacccgccgccttTctctctgcagttgttcaatc																										TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	TCTC	TCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr7:24843988_24843991delTCTC	ENST00000313367.2	-	22	2961_2964	c.2510_2513delGAGA	c.(2509-2514)agagaafs	p.RE837fs	OSBPL3_ENST00000353930.1_Frame_Shift_Del_p.RE801fs|OSBPL3_ENST00000352860.1_Frame_Shift_Del_p.RE806fs|OSBPL3_ENST00000487020.1_5'UTR|OSBPL3_ENST00000409069.1_Frame_Shift_Del_p.RE770fs|OSBPL3_ENST00000431825.2_Frame_Shift_Del_p.RE770fs|OSBPL3_ENST00000396431.1_Frame_Shift_Del_p.RE806fs|OSBPL3_ENST00000396429.1_Frame_Shift_Del_p.RE801fs	NM_015550.2	NP_056365.1	Q9H4L5	OSBL3_HUMAN	oxysterol binding protein-like 3	837					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						CCGCCGCCTTTCTCTCTGCAGTTG	0.451																																					p.837_838del		Pindel,Atlas-Indel	.											.	OSBPL3	100	.	0			c.2511_2514del						PASS	.																																			SO:0001589	frameshift_variant	26031	exon22			.	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.2510_2513delGAGA	7.37:g.24843988_24843991delTCTC	ENSP00000315410:p.Arg837fs	266	0	.		187	62	0.332	NM_015550	A4D167|A4D168|A4D169|A4D170|A4D171|A4D172|B8ZZ79|B8ZZP0|O14591|O43357|O43358|Q8N702|Q8N703|Q8N704|Q8NFH0|Q8NFH1|Q8NI12|Q8NI13|Q9BZF4|Q9UED6	Frame_Shift_Del	DEL	ENST00000313367.2	37	CCDS5390.1																																																																																			.	.	none		0.451	OSBPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214085.2			-	24843991	TCTC	-	24843988	7	5	36	1	0	1	0	1	0	0	0	0	11288	1783	62	0	158	0	OSBPL3	7	24843988	Frame_Shift_Del	DEL	TCTC	TCGA-GS-A9TT-01A-11D-A382-10		24843988	134294675	77	14305											
MAGI2	9863	hgsc.bcm.edu	37	chr7	79082451	79082451	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acctccagcagcagctcctcCgacaccaatttgctgccgct	8	8	7	18	2	0	0	0	0	0	0	3	1	3	0	6	0	5	5	6	0	1	1			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr7:79082451C>T	ENST00000354212.4	-	1	439	c.186G>A	c.(184-186)tcG>tcA	p.S62S	MAGI2-AS3_ENST00000426835.1_RNA|MAGI2-AS3_ENST00000422093.1_RNA|MAGI2-AS3_ENST00000451809.1_RNA|MAGI2-AS3_ENST00000424477.1_RNA|MAGI2-AS3_ENST00000448195.1_RNA|MAGI2_ENST00000419488.1_Silent_p.S62S|MAGI2-AS3_ENST00000414797.1_RNA|MAGI2-AS3_ENST00000446159.1_RNA|MAGI2_ENST00000522391.1_Silent_p.S62S|MAGI2-AS3_ENST00000429408.1_RNA	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	62	PDZ 1. {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)				GCAGCTCCTCCGACACCAATT	0.637																																					p.S62S		Atlas-SNP	.											MAGI2,caecum,carcinoma,0,1	MAGI2	246	1	0			c.G186A						PASS	.						54	59	57					7																	79082451		2203	4300	6503	SO:0001819	synonymous_variant	9863	exon1			CTCCTCCGACACC	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.186G>A	7.37:g.79082451C>T		81	0	0		45	20	0.444444	NM_012301	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Silent	SNP	ENST00000354212.4	37	CCDS5594.1																																																																																			.	.	none		0.637	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301		T	79082451	C	T	79082451	2	4	36	1	0	0	0	0	0	0	0	1	9200	639	23	1		1	MAGI2	7	79082451	Silent	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	54238463	79082451	80056212	78	14306											
PTPRZ1	5803	hgsc.bcm.edu	37	chr7	121652288	121652288	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tccttctttcaatgagatggTttacccttctgaaagcacag	10	14	7	10	0	3	2	1	2	2	1	4	3	4	2	2	1	2	2	2	1	3	5			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr7:121652288T>G	ENST00000393386.2	+	12	3599	c.3188T>G	c.(3187-3189)gTt>gGt	p.V1063G	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	1063					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						AATGAGATGGTTTACCCTTCT	0.358																																					p.V1063G		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.T3188G						PASS	.						111	114	113					7																	121652288		2203	4300	6503	SO:0001583	missense	5803	exon12			AGATGGTTTACCC	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.3188T>G	7.37:g.121652288T>G	ENSP00000377047:p.Val1063Gly	146	0	0		109	55	0.504587	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	T	9.433	1.086036	0.20390	.	.	ENSG00000106278	ENST00000393386	T	0.42900	0.96	5.68	-1.26	0.09376	.	0.776615	0.11659	N	0.542035	T	0.31420	0.0796	L	0.51422	1.61	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.10636	-1.0621	10	0.33940	T	0.23	.	6.1933	0.20536	0.0:0.4622:0.2766:0.2612	.	1063	P23471	PTPRZ_HUMAN	G	1063	ENSP00000377047:V1063G	ENSP00000377047:V1063G	V	+	2	0	PTPRZ1	121439524	0.007000	0.16637	0.798000	0.32154	0.983000	0.72400	-0.397000	0.07269	-0.102000	0.12197	-0.299000	0.09455	GTT	.	.	none		0.358	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851		G	121652288	T	G	121652288	3	3	36	1	0	0	0	0	1	0	0	0	12829	1725	60	5	3234	5	PTPRZ1	7	121652288	Missense_Mutation	SNP	T	TCGA-GS-A9TT-01A-11D-A382-10	42569837	121652288	37486375	79	14307											
OR9A4	130075	hgsc.bcm.edu	37	chr7	141618791	141618791	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctacttggtgacattaaTgggaaacacagtcatcatca	13	13	7	8	0	4	1	3	1	1	0	4	2	4	2	0	2	2	0	0	2	3	4			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr7:141618791T>C	ENST00000548136.1	+	1	175	c.116T>C	c.(115-117)aTg>aCg	p.M39T	MGAM_ENST00000497554.1_Intron	NM_001001656.1	NP_001001656.1	Q8NGU2	OR9A4_HUMAN	olfactory receptor, family 9, subfamily A, member 4	39						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)					GTGACATTAATGGGAAACACA	0.443																																					p.M39T		Atlas-SNP	.											.	OR9A4	58	.	0			c.T116C						PASS	.						195	204	201					7																	141618791		2201	4300	6501	SO:0001583	missense	130075	exon1			CATTAATGGGAAA		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.116T>C	7.37:g.141618791T>C	ENSP00000448789:p.Met39Thr	225	0	0		195	91	0.466667	NM_001001656	B9EGV6|Q6IFI4	Missense_Mutation	SNP	ENST00000548136.1	37	CCDS43661.1	.	.	.	.	.	.	.	.	.	.	.	0.401	-0.918492	0.02396	.	.	ENSG00000258083	ENST00000548136	T	0.00457	7.29	3.88	2.71	0.32032	.	.	.	.	.	T	0.00210	0.0006	N	0.12611	0.24	0.21290	N	0.999731	B	0.06786	0.001	B	0.08055	0.003	T	0.31916	-0.9926	9	0.02654	T	1	-2.566	7.6507	0.28346	0.0:0.1051:0.0:0.8949	.	39	Q8NGU2	OR9A4_HUMAN	T	39	ENSP00000448789:M39T	ENSP00000386148:M39T	M	+	2	0	OR9A4	141265260	0.000000	0.05858	0.974000	0.42286	0.352000	0.29268	0.602000	0.24134	0.652000	0.30806	-0.288000	0.09946	ATG	.	.	none		0.443	OR9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350806.3	NM_001001656		C	141618791	T	C	141618791	3	2	36	1	0	0	0	0	1	0	0	0	11258	1464	51	3	118	3	OR9A4	7	141618791	Missense_Mutation	SNP	T	TCGA-GS-A9TT-01A-11D-A382-10	19966503	141618791	17519872	80	14308											
CUL1	8454	hgsc.bcm.edu	37	chr7	148454103	148454103	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agatttgatggatgagagtgTactgaaattctacactcaac	14	12	9	6	0	2	4	1	3	1	2	2	6	2	5	0	1	3	1	0	1	4	4			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr7:148454103T>C	ENST00000325222.4	+	4	623	c.344T>C	c.(343-345)gTa>gCa	p.V115A	CUL1_ENST00000409469.1_Missense_Mutation_p.V115A|CUL1_ENST00000602748.1_Missense_Mutation_p.V115A	NM_003592.2	NP_003583.2	Q13616	CUL1_HUMAN	cullin 1	115					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)			GATGAGAGTGTACTGAAATTC	0.338																																					p.V115A		Atlas-SNP	.											.	CUL1	80	.	0			c.T344C						PASS	.						134	136	135					7																	148454103		2203	4300	6503	SO:0001583	missense	8454	exon4			AGAGTGTACTGAA	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.344T>C	7.37:g.148454103T>C	ENSP00000326804:p.Val115Ala	104	0	0		131	48	0.366412	NM_003592	D3DWG3|O60719|Q08AL6|Q8IYW1	Missense_Mutation	SNP	ENST00000325222.4	37	CCDS34772.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.714714	0.89112	.	.	ENSG00000055130	ENST00000409469;ENST00000325222;ENST00000543583	T;T	0.30182	1.54;1.54	4.74	4.74	0.60224	Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.47210	0.1433	M	0.73598	2.24	0.80722	D	1	P	0.46020	0.871	P	0.51550	0.673	T	0.53401	-0.8444	10	0.72032	D	0.01	-16.5964	14.5335	0.67942	0.0:0.0:0.0:1.0	.	115	Q13616	CUL1_HUMAN	A	115;115;73	ENSP00000387160:V115A;ENSP00000326804:V115A	ENSP00000326804:V115A	V	+	2	0	CUL1	148085036	1.000000	0.71417	0.978000	0.43139	0.992000	0.81027	7.759000	0.85235	1.912000	0.55364	0.528000	0.53228	GTA	.	.	none		0.338	CUL1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467785.1	NM_003592		C	148454103	T	C	148454103	3	2	36	1	0	0	0	0	1	0	0	0	4056	1638	57	3	354	3	CUL1	7	148454103	Missense_Mutation	SNP	T	TCGA-GS-A9TT-01A-11D-A382-10	6835312	148454103	10684560	81	14309											
CSMD1	64478	hgsc.bcm.edu	37	chr8	2964161	2964161	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcactggtacttcacaaaatCtcctagaagagtcaatgcaa	15	9	7	10	0	3	2	2	0	1	2	4	2	3	2	1	1	2	3	1	1	7	3			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr8:2964161C>A	ENST00000520002.1	-	47	7396	c.6841G>T	c.(6841-6843)Gat>Tat	p.D2281Y	CSMD1_ENST00000542608.1_Missense_Mutation_p.D2280Y|CSMD1_ENST00000602557.1_Missense_Mutation_p.D2281Y|CSMD1_ENST00000537824.1_Missense_Mutation_p.D2280Y|CSMD1_ENST00000400186.3_Missense_Mutation_p.D2281Y|CSMD1_ENST00000602723.1_Missense_Mutation_p.D2281Y			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	2281	Sushi 13. {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)		TTCACAAAATCTCCTAGAAGA	0.468																																					p.D2280Y		Atlas-SNP	.											.	CSMD1	1469	.	0			c.G6838T						PASS	.						45	46	46					8																	2964161		1923	4128	6051	SO:0001583	missense	64478	exon46			CAAAATCTCCTAG			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.6841G>T	8.37:g.2964161C>A	ENSP00000430733:p.Asp2281Tyr	70	0	0		49	20	0.408163	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.42|17.42	3.385605|3.385605	0.61956|0.61956	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608|ENST00000335551	T;T;T;T|.	0.67171|.	-0.25;-0.25;-0.25;-0.25|.	5.31|5.31	5.31|5.31	0.75309|0.75309	Complement control module (2);Sushi/SCR/CCP (3);|.	0.062552|.	0.64402|.	D|.	0.000011|.	D|D	0.87446|0.87446	0.6179|0.6179	H|H	0.94264|0.94264	3.515|3.515	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	0.999;0.999;1.0|.	D|D	0.90900|0.90900	0.4768|0.4768	10|5	0.52906|.	T|.	0.07|.	.|.	18.9876|18.9876	0.92779|0.92779	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	2281;2281;2280|.	E5RIG2;Q96PZ7;F5H2I8|.	.;CSMD1_HUMAN;.|.	Y|I	2281;2281;2142;2280;2280|1760	ENSP00000383047:D2281Y;ENSP00000430733:D2281Y;ENSP00000441462:D2280Y;ENSP00000446243:D2280Y|.	ENSP00000320445:D2142Y|.	D|R	-|-	1|2	0|0	CSMD1|CSMD1	2951568|2951568	1.000000|1.000000	0.71417|0.71417	0.804000|0.804000	0.32291|0.32291	0.196000|0.196000	0.23810|0.23810	7.113000|7.113000	0.77095|0.77095	2.476000|2.476000	0.83614|0.83614	0.557000|0.557000	0.71058|0.71058	GAT|AGA	.	.	none		0.468	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		A	2964161	C	A	2964161	3	1	36	1	0	0	0	0	1	0	0	0	3946	913	32	4	3956	4	CSMD1	8	2964161	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10		2964161	143399861	82	14310											
RAB11FIP1	80223	hgsc.bcm.edu	37	chr8	37732263	37732263	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttaacccccatcagcatgccTtccttctccctccctgggac	6	11	5	19	0	2	0	1	0	1	0	5	1	4	1	6	1	3	1	6	1	1	3			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr8:37732263T>C	ENST00000330843.4	-	3	1404	c.1392A>G	c.(1390-1392)gaA>gaG	p.E464E	RAB11FIP1_ENST00000523182.1_5'Flank|RAB11FIP1_ENST00000522727.1_Silent_p.E316E|RAB11FIP1_ENST00000287263.4_Silent_p.E464E|RAB11FIP1_ENST00000524118.1_Silent_p.E316E	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	464					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)			TCAGCATGCCTTCCTTCTCCC	0.567																																					p.E464E		Atlas-SNP	.											.	RAB11FIP1	105	.	0			c.A1392G						PASS	.						175	171	172					8																	37732263		2203	4300	6503	SO:0001819	synonymous_variant	80223	exon3			CATGCCTTCCTTC	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.1392A>G	8.37:g.37732263T>C		133	0	0		137	60	0.437956	NM_025151	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Silent	SNP	ENST00000330843.4	37	CCDS34882.1																																																																																			.	.	none		0.567	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151		C	37732263	T	C	37732263	2	2	36	1	0	0	0	0	0	0	0	1	12908	1606	56	3		3	RAB11FIP1	8	37732263	Silent	SNP	T	TCGA-GS-A9TT-01A-11D-A382-10	34768102	37732263	108631759	83	14311											
IDO1	3620	hgsc.bcm.edu	37	chr8	39782769	39782769	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcaacccccagctatcagaCggtctggtgtatgaagggtt	9	9	13	10	1	2	2	1	1	1	1	2	2	2	2	2	4	2	4	2	4	4	3			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr8:39782769C>T	ENST00000518237.1	+	9	1374	c.735C>T	c.(733-735)gaC>gaT	p.D245D	IDO1_ENST00000522495.1_Silent_p.D245D|RP11-44K6.3_ENST00000517623.1_RNA	NM_002164.5	NP_002155.1	P14902	I23O1_HUMAN	indoleamine 2,3-dioxygenase 1	245					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)	AGCTATCAGACGGTCTGGTGT	0.463																																					p.D245D		Atlas-SNP	.											.	IDO1	43	.	0			c.C735T						PASS	.						39	41	40					8																	39782769		1880	4108	5988	SO:0001819	synonymous_variant	3620	exon9			ATCAGACGGTCTG	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.735C>T	8.37:g.39782769C>T		158	0	0		165	66	0.4	NM_002164	Q540B4	Silent	SNP	ENST00000518237.1	37	CCDS47847.1																																																																																			.	.	none		0.463	IDO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376987.1	NM_002164		T	39782769	C	T	39782769	2	4	36	1	0	0	0	0	0	0	0	1	7510	535	19	1		1	IDO1	8	39782769	Silent	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	2050506	39782769	106581253	84	14312											
MMP16	4325	hgsc.bcm.edu	37	chr8	89128762	89128762	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aacaaacatctcacgacgaaGaatagctagagtgttaaagt	18	8	8	7	2	1	2	1	0	1	2	2	4	1	2	0	0	3	2	0	0	8	3			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr8:89128762G>T	ENST00000286614.6	-	6	1338	c.1057C>A	c.(1057-1059)Ctt>Att	p.L353I	MMP16_ENST00000544227.1_5'UTR	NM_005941.4	NP_005932.2	P51512	MMP16_HUMAN	matrix metallopeptidase 16 (membrane-inserted)	353					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)	TCACGACGAAGAATAGCTAGA	0.428																																					p.L353I		Atlas-SNP	.											MMP16,NS,carcinoma,+1,1	MMP16	176	1	0			c.C1057A						PASS	.						100	98	99					8																	89128762		2203	4300	6503	SO:0001583	missense	4325	exon6			GACGAAGAATAGC	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.1057C>A	8.37:g.89128762G>T	ENSP00000286614:p.Leu353Ile	216	0	0		139	65	0.467626	NM_005941	B2RAN7|Q14824|Q52H48	Missense_Mutation	SNP	ENST00000286614.6	37	CCDS6246.1	.	.	.	.	.	.	.	.	.	.	G	18.97	3.736234	0.69189	.	.	ENSG00000156103	ENST00000286614	T	0.08193	3.12	5.73	5.73	0.89815	Hemopexin/matrixin (2);	0.000000	0.85682	D	0.000000	T	0.17238	0.0414	L	0.31845	0.965	0.80722	D	1	D;P	0.64830	0.994;0.543	P;P	0.60117	0.869;0.812	T	0.05517	-1.0880	10	0.16896	T	0.51	.	20.2786	0.98501	0.0:0.0:1.0:0.0	.	353;353	P51512-2;P51512	.;MMP16_HUMAN	I	353	ENSP00000286614:L353I	ENSP00000286614:L353I	L	-	1	0	MMP16	89197878	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.868000	0.98415	0.557000	0.71058	CTT	.	.	none		0.428	MMP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375304.2	NM_005941		T	89128762	G	T	89128762	3	4	36	1	0	0	0	0	1	0	0	0	9664	942	33	4	942	4	MMP16	8	89128762	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	49345993	89128762	57235260	85	14313											
CDKN2A	1029	hgsc.bcm.edu	37	chr9	21994305	21994305	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcacgcgcgccgaatccggAgggtcaccaagaacctgcgc	9	3	13	16	7	1	1	1	0	0	1	2	3	2	2	4	2	2	1	4	2	3	0			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr9:21994305A>G	ENST00000579755.1	-	1	318	c.26T>C	c.(25-27)cTc>cCc	p.L9P	RP11-145E5.5_ENST00000404796.2_Intron|CDKN2B-AS1_ENST00000468603.2_RNA|CDKN2A_ENST00000494262.1_Intron|CDKN2B-AS1_ENST00000583719.1_RNA|CDKN2B-AS1_ENST00000581051.1_RNA|CDKN2B-AS1_ENST00000455933.2_RNA|CDKN2B-AS1_ENST00000584816.1_RNA|CDKN2B-AS1_ENST00000584351.1_RNA|CDKN2B-AS1_ENST00000582072.1_RNA|CDKN2A_ENST00000498628.2_Intron|RP11-149I2.4_ENST00000578935.1_RNA|CDKN2B-AS1_ENST00000580467.1_RNA|CDKN2B-AS1_ENST00000580576.1_RNA|CDKN2B-AS1_ENST00000585267.1_RNA|CDKN2B-AS1_ENST00000584637.1_RNA|CDKN2A_ENST00000361570.3_Missense_Mutation_p.L50P|CDKN2B-AS1_ENST00000582301.1_RNA|CDKN2B-AS1_ENST00000428597.1_RNA|CDKN2B-AS1_ENST00000584020.1_RNA|CDKN2A_ENST00000470819.2_Intron|CDKN2A_ENST00000530628.2_Missense_Mutation_p.L9P|CDKN2B-AS1_ENST00000577551.1_RNA			P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	0					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)		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)		CCGAATCCGGAGGGTCACCAA	0.726		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																											p.L9P		Atlas-SNP	.											.	CDKN2A	4810	.	199	Whole gene deletion(199)	haematopoietic_and_lymphoid_tissue(34)|central_nervous_system(31)|lung(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.T26C						PASS	.						11	13	12					9																	21994305		2177	4270	6447	SO:0001583	missense	1029	exon1			ATCCGGAGGGTCA	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.26T>C	9.37:g.21994305A>G	ENSP00000462950:p.Leu9Pro	53	0	0		24	21	0.875	NM_058195	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Missense_Mutation	SNP	ENST00000579755.1	37	CCDS6511.2	.	.	.	.	.	.	.	.	.	.	A	14.39	2.522002	0.44866	.	.	ENSG00000147889	ENST00000361570;ENST00000530628	T;T	0.79141	-1.24;-1.24	4.23	4.23	0.50019	.	0.212553	0.23638	N	0.046047	T	0.65238	0.2672	N	0.08118	0	0.19775	N	0.999957	P	0.50710	0.938	P	0.48982	0.597	T	0.60616	-0.7228	10	0.72032	D	0.01	.	9.888	0.41272	1.0:0.0:0.0:0.0	.	50	Q8N726	CD2A2_HUMAN	P	50;9	ENSP00000355153:L50P;ENSP00000432664:L9P	ENSP00000355153:L50P	L	-	2	0	CDKN2A	21984305	0.982000	0.34865	0.153000	0.22517	0.221000	0.24807	2.190000	0.42630	1.917000	0.55516	0.454000	0.30748	CTC	.	.	none		0.726	CDKN2A-004	KNOWN	NMD_exception|upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051918.5	NM_000077		G	21994305	A	G	21994305	3	3	36	1	0	0	0	0	1	0	0	0	3163	304	11	3	854	3	CDKN2A	9	21994305	Missense_Mutation	SNP	A	TCGA-GS-A9TT-01A-11D-A382-10		21994305	119219126	86	14314											
FOXB2	442425	hgsc.bcm.edu	37	chr9	79635701	79635701	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcgctgccgcccgtgtccgcGctgcagccggggctcactgt	2	7	15	17	6	1	0	1	0	0	0	2	0	2	0	4	2	3	4	4	2	0	0			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr9:79635701G>A	ENST00000376708.1	+	1	1131	c.1131G>A	c.(1129-1131)gcG>gcA	p.A377A		NM_001013735.1	NP_001013757.1	Q5VYV0	FOXB2_HUMAN	forkhead box B2	377					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						CCGTGTCCGCGCTGCAGCCGG	0.741																																					p.A377A		Atlas-SNP	.											.	FOXB2	71	.	0			c.G1131A						PASS	.						5	7	6					9																	79635701		2097	4106	6203	SO:0001819	synonymous_variant	442425	exon1			GTCCGCGCTGCAG		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.1131G>A	9.37:g.79635701G>A		37	0	0		54	27	0.5	NM_001013735		Silent	SNP	ENST00000376708.1	37	CCDS35045.1																																																																																			.	.	none		0.741	FOXB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052745.1	NM_001013735		A	79635701	G	A	79635701	2	1	36	1	0	0	0	0	0	0	0	1	6001	1074	38	1		1	FOXB2	9	79635701	Silent	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	57641396	79635701	61577730	87	14315											
PHF2	5253	hgsc.bcm.edu	37	chr9	96416812	96416812	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgaccaggtcgacaaatgcTacaagtgcatcgtcaagcag	13	7	10	11	2	1	1	1	1	0	0	3	2	1	1	1	1	4	3	1	1	4	1			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr9:96416812T>A	ENST00000359246.4	+	7	1274	c.907T>A	c.(907-909)Tac>Aac	p.Y303N	PHF2_ENST00000375376.4_Intron	NM_005392.3	NP_005383.3	O75151	PHF2_HUMAN	PHD finger protein 2	303	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				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)		CGACAAATGCTACAAGTGCAT	0.587																																					p.Y303N		Atlas-SNP	.											.	PHF2	113	.	0			c.T907A						PASS	.						133	117	123					9																	96416812		2203	4300	6503	SO:0001583	missense	5253	exon7			AAATGCTACAAGT	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.907T>A	9.37:g.96416812T>A	ENSP00000352185:p.Tyr303Asn	64	0	0		42	15	0.357143	NM_005392	Q4VXG0|Q8N3K2|Q9Y6N4	Missense_Mutation	SNP	ENST00000359246.4	37	CCDS35069.1	.	.	.	.	.	.	.	.	.	.	T	28.1	4.888902	0.91814	.	.	ENSG00000197724	ENST00000359246	T	0.73258	-0.73	5.12	5.12	0.69794	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.000000	0.85682	D	0.000000	D	0.87047	0.6080	M	0.91140	3.18	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90098	0.4182	10	0.87932	D	0	-25.2923	15.0746	0.72066	0.0:0.0:0.0:1.0	.	303	O75151	PHF2_HUMAN	N	303	ENSP00000352185:Y303N	ENSP00000352185:Y303N	Y	+	1	0	PHF2	95456633	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.781000	0.85668	2.136000	0.66102	0.477000	0.44152	TAC	.	.	none		0.587	PHF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053162.1	NM_005392		A	96416812	T	A	96416812	3	1	36	1	0	0	0	0	1	0	0	0	11839	1522	53	5	933	5	PHF2	9	96416812	Missense_Mutation	SNP	T	TCGA-GS-A9TT-01A-11D-A382-10	16781111	96416812	44796619	88	14316											
ITIH2	3698	hgsc.bcm.edu	37	chr10	7780636	7780636	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gattccaccccgtcttgggcCaatccttcaccaacgcccgt	7	9	7	18	3	2	0	1	0	1	0	4	1	4	0	7	1	1	0	7	1	2	3			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr10:7780636C>A	ENST00000358415.4	+	16	2176	c.2010C>A	c.(2008-2010)gcC>gcA	p.A670A	ITIH2_ENST00000379587.4_Silent_p.A659A	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	670	O-glycosylated at three sites.				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						CGTCTTGGGCCAATCCTTCAC	0.532																																					p.A670A		Atlas-SNP	.											ITIH2,NS,neuroblastoma,0,1	ITIH2	144	1	0			c.C2010A						PASS	.						130	111	118					10																	7780636		2203	4300	6503	SO:0001819	synonymous_variant	3698	exon16			TTGGGCCAATCCT	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.2010C>A	10.37:g.7780636C>A		95	0	0		76	31	0.407895	NM_002216	Q14659|Q15484|Q5T986	Silent	SNP	ENST00000358415.4	37	CCDS31141.1																																																																																			.	.	none		0.532	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216		A	7780636	C	A	7780636	2	1	36	1	0	0	0	0	0	0	0	1	7913	581	21	4		4	ITIH2	10	7780636	Silent	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10		7780636	127754111	89	14317											
GATA3	2625	hgsc.bcm.edu	37	chr10	8100507	8100507	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcccaccccgccgaaggacGtctccccggacccatcgctg	6	4	10	21	6	1	0	0	0	1	0	3	3	1	2	7	2	0	1	7	2	1	0			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr10:8100507G>A	ENST00000346208.3	+	3	936	c.481G>A	c.(481-483)Gtc>Atc	p.V161I	GATA3_ENST00000461472.1_3'UTR|GATA3_ENST00000379328.3_Missense_Mutation_p.V161I			P23771	GATA3_HUMAN	GATA binding protein 3	161					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						GCCGAAGGACGTCTCCCCGGA	0.721			"F, N, S"		breast		"HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE)"																														p.V161I		Atlas-SNP	.		Rec	yes		10	10p15	2625	GATA binding protein 3	yes	E	.	GATA3	182	.	0			c.G481A						PASS	.						36	42	40					10																	8100507		2201	4297	6498	SO:0001583	missense	2625	exon3			AAGGACGTCTCCC	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.481G>A	10.37:g.8100507G>A	ENSP00000341619:p.Val161Ile	51	0	0		42	16	0.380952	NM_002051	Q5VWG7|Q5VWG8|Q96J16	Missense_Mutation	SNP	ENST00000346208.3	37	CCDS7083.1	.	.	.	.	.	.	.	.	.	.	G	18.16	3.563049	0.65538	.	.	ENSG00000107485	ENST00000379328;ENST00000346208	D;D	0.96491	-4.03;-4.01	5.55	5.55	0.83447	.	0.056766	0.64402	D	0.000001	D	0.96131	0.8739	M	0.83012	2.62	0.58432	D	0.999997	P;P	0.47302	0.7;0.893	B;B	0.39465	0.041;0.3	D	0.96314	0.9231	10	0.51188	T	0.08	-15.1001	19.5043	0.95108	0.0:0.0:1.0:0.0	.	161;161	P23771;P23771-2	GATA3_HUMAN;.	I	161	ENSP00000368632:V161I;ENSP00000341619:V161I	ENSP00000341619:V161I	V	+	1	0	GATA3	8140513	1.000000	0.71417	1.000000	0.80357	0.778000	0.44026	7.722000	0.84778	2.607000	0.88179	0.561000	0.74099	GTC	.	.	none		0.721	GATA3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046719.1	NM_001002295		A	8100507	G	A	8100507	3	1	36	1	0	0	0	0	1	0	0	0	6263	1145	40	1	487	1	GATA3	10	8100507	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	319871	8100507	127434240	90	14318											
ARHGAP21	57584	hgsc.bcm.edu	37	chr10	24909678	24909679	+	Frame_Shift_Ins	INS	-	-	G																															agtttttccagtctatgtgcINStgatgggaatttggcgaata																										TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr10:24909678_24909679insG	ENST00000396432.2	-	9	1631_1632	c.1145_1146insC	c.(1144-1146)cagfs	p.Q382fs	ARHGAP21_ENST00000320481.6_Frame_Shift_Ins_p.Q169fs	NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	381					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						AGTCTATGTGCTGATGGGAATT	0.381																																					p.Q382fs		Atlas-Indel	.											.	ARHGAP21	185	.	0			c.1146_1147insC						PASS	.																																			SO:0001589	frameshift_variant	57584	exon9			.	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.1145_1146insC	10.37:g.24909678_24909679insG	ENSP00000379709:p.Gln382fs	160	0	0		141	55	0.390071	NM_020824	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Frame_Shift_Ins	INS	ENST00000396432.2	37	CCDS7144.2																																																																																			.	.	none		0.381	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824		G	24909679	-	G	24909678	7	5	36	1	0	1	1	0	0	0	0	0	871	796	28	0	4802	0	ARHGAP21	10	24909678	Frame_Shift_Ins	INS	-	TCGA-GS-A9TT-01A-11D-A382-10	16809171	24909678	110625069	91	14319	184	2									
ARHGAP21	57584	hgsc.bcm.edu	37	chr10	24909679	24909679	+	Missense_Mutation	SNP	T	T	G																															agtttttccagtctatgtgcTgatgggaatttggcgaatag																										TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr10:24909679T>G	ENST00000396432.2	-	9	1631	c.1145A>C	c.(1144-1146)cAg>cCg	p.Q382P	ARHGAP21_ENST00000320481.6_Missense_Mutation_p.Q169P	NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	381					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						GTCTATGTGCTGATGGGAATT	0.383																																					p.Q382P		Atlas-SNP	.											.	ARHGAP21	185	.	0			c.A1145C						PASS	.						64	62	63					10																	24909679		2203	4300	6503	SO:0001583	missense	57584	exon9			ATGTGCTGATGGG	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.1145A>C	10.37:g.24909679T>G	ENSP00000379709:p.Gln382Pro	160	0	0		140	56	0.4	NM_020824	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000396432.2	37	CCDS7144.2	.	.	.	.	.	.	.	.	.	.	T	21.0	4.080051	0.76528	.	.	ENSG00000107863	ENST00000396432;ENST00000447364;ENST00000320481;ENST00000376410;ENST00000446003;ENST00000445703	T;T;T;T	0.58652	2.26;2.28;0.32;0.32	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.76227	0.3958	M	0.76002	2.32	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.79322	-0.1851	10	0.87932	D	0	.	16.0697	0.80914	0.0:0.0:0.0:1.0	.	372;381	F8W9U9;Q5T5U3	.;RHG21_HUMAN	P	382;371;169;372;382;217	ENSP00000379709:Q382P;ENSP00000365604:Q169P;ENSP00000365592:Q372P;ENSP00000405018:Q382P	ENSP00000365604:Q169P	Q	-	2	0	ARHGAP21	24949685	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.563000	0.82314	2.260000	0.74910	0.528000	0.53228	CAG	.	.	none		0.383	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824		G	24909679	T	G	24909679	3	3	36	1	0	0	0	0	1	0	0	0	871	1580	55	5	4803	5	ARHGAP21	10	24909679	Missense_Mutation	SNP	T	TCGA-GS-A9TT-01A-11D-A382-10	1	24909679	110625068	92	14320	184	2									
C10orf71	118461	hgsc.bcm.edu	37	chr10	50533936	50533937	+	Frame_Shift_Ins	INS	-	-	C																															gagggaggacctgacccacgINSccctcgtgtgggagggcggc																										TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr10:50533936_50533937insC	ENST00000374144.3	+	3	3634_3635	c.3346_3347insC	c.(3346-3348)gccfs	p.A1116fs	C10orf71_ENST00000323868.4_Intron			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	1116										endometrium(1)	1						CCTGACCCACGCCCTCGTGTGG	0.658																																					p.A1116fs		Atlas-Indel	.											.	C10orf71	179	.	0			c.3346_3347insC						PASS	.																																			SO:0001589	frameshift_variant	118461	exon3			.	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.3349dupC	10.37:g.50533939_50533939dupC	ENSP00000363259:p.Ala1116fs	73	0	0		34	11	0.323529	NM_001135196	A0AVL8	Frame_Shift_Ins	INS	ENST00000374144.3	37	CCDS44387.1																																																																																			.	.	none		0.658	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459		C	50533937	-	C	50533936	7	5	36	1	0	1	1	0	0	0	0	0	1616	1087	38	0	3348	0	C10orf71	10	50533936	Frame_Shift_Ins	INS	-	TCGA-GS-A9TT-01A-11D-A382-10	25624257	50533936	85000811	93	14321	185	3									
C10orf71	118461	hgsc.bcm.edu	37	chr10	50533940	50533940	+	Missense_Mutation	SNP	T	T	C																															ggaggacctgacccacgcccTcgtgtgggagggcggctctg																										TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr10:50533940T>C	ENST00000374144.3	+	3	3638	c.3350T>C	c.(3349-3351)cTc>cCc	p.L1117P	C10orf71_ENST00000323868.4_Intron			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	1117										endometrium(1)	1						ACCCACGCCCTCGTGTGGGAG	0.657																																					p.L1117P		Atlas-SNP	.											.	C10orf71	179	.	0			c.T3350C						PASS	.						20	24	23					10																	50533940		692	1591	2283	SO:0001583	missense	118461	exon3			ACGCCCTCGTGTG	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.3350T>C	10.37:g.50533940T>C	ENSP00000363259:p.Leu1117Pro	73	0	0		36	13	0.361111	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	37	CCDS44387.1	.	.	.	.	.	.	.	.	.	.	T	17.11	3.305585	0.60305	.	.	ENSG00000177354	ENST00000374144	T	0.05258	3.47	5.38	-0.584	0.11702	.	0.498207	0.15004	N	0.285973	T	0.04543	0.0124	L	0.32530	0.975	0.09310	N	1	.	.	.	.	.	.	T	0.37009	-0.9724	8	0.32370	T	0.25	.	1.3367	0.02146	0.1493:0.2989:0.1343:0.4176	.	.	.	.	P	1117	ENSP00000363259:L1117P	ENSP00000363259:L1117P	L	+	2	0	C10orf71	50203946	0.000000	0.05858	0.030000	0.17652	0.421000	0.31385	0.464000	0.21988	0.040000	0.15660	0.402000	0.26972	CTC	.	.	none		0.657	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459		C	50533940	T	C	50533940	3	2	36	1	0	0	0	0	1	0	0	0	1616	1551	54	3	3352	3	C10orf71	10	50533940	Missense_Mutation	SNP	T	TCGA-GS-A9TT-01A-11D-A382-10	4	50533940	85000807	94	14322	185	3									
C10orf71	118461	hgsc.bcm.edu	37	chr10	50533942	50533942	+	Missense_Mutation	SNP	G	G	C																															aggacctgacccacgccctcGtgtgggagggcggctctgac																										TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr10:50533942G>C	ENST00000374144.3	+	3	3640	c.3352G>C	c.(3352-3354)Gtg>Ctg	p.V1118L	C10orf71_ENST00000323868.4_Intron			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	1118										endometrium(1)	1						CCACGCCCTCGTGTGGGAGGG	0.657																																					p.V1118L		Atlas-SNP	.											.	C10orf71	179	.	0			c.G3352C						PASS	.						21	25	24					10																	50533942		692	1591	2283	SO:0001583	missense	118461	exon3			GCCCTCGTGTGGG	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.3352G>C	10.37:g.50533942G>C	ENSP00000363259:p.Val1118Leu	72	0	0		37	16	0.432432	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	37	CCDS44387.1	.	.	.	.	.	.	.	.	.	.	G	13.65	2.299071	0.40694	.	.	ENSG00000177354	ENST00000374144	T	0.04406	3.63	5.38	-4.86	0.03132	.	2.277970	0.02380	N	0.078691	T	0.02571	0.0078	N	0.14661	0.345	0.09310	N	1	.	.	.	.	.	.	T	0.41034	-0.9531	8	0.09084	T	0.74	.	5.7483	0.18132	0.4766:0.0:0.2649:0.2586	.	.	.	.	L	1118	ENSP00000363259:V1118L	ENSP00000363259:V1118L	V	+	1	0	C10orf71	50203948	0.000000	0.05858	0.000000	0.03702	0.391000	0.30476	-1.398000	0.02509	-1.114000	0.02977	-0.339000	0.08088	GTG	.	.	none		0.657	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459		C	50533942	G	C	50533942	3	2	36	1	0	0	0	0	1	0	0	0	1616	1145	40	4	3354	4	C10orf71	10	50533942	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	2	50533942	85000805	95	14323	185	3									
PIK3AP1	118788	hgsc.bcm.edu	37	chr10	98405403	98405403	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctctttaatgtgactcttgAgcatgtccaccgtttcctga	7	15	7	12	1	2	3	0	3	2	0	4	3	4	3	4	0	1	2	4	0	1	4			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr10:98405403A>C	ENST00000339364.5	-	8	1321	c.1202T>G	c.(1201-1203)cTc>cGc	p.L401R	PIK3AP1_ENST00000371110.2_Missense_Mutation_p.L223R|PIK3AP1_ENST00000468783.1_5'UTR	NM_152309.2	NP_689522.2	Q6ZUJ8	BCAP_HUMAN	phosphoinositide-3-kinase adaptor protein 1	401					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)		GTGACTCTTGAGCATGTCCAC	0.567																																					p.L401R		Atlas-SNP	.											.	PIK3AP1	111	.	0			c.T1202G						PASS	.						141	111	121					10																	98405403		2203	4300	6503	SO:0001583	missense	118788	exon8			CTCTTGAGCATGT	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.1202T>G	10.37:g.98405403A>C	ENSP00000339826:p.Leu401Arg	118	0	0		125	44	0.352	NM_152309	Q5TB56|Q5VXJ9|Q8N6J6|Q8NAC8	Missense_Mutation	SNP	ENST00000339364.5	37	CCDS31259.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.421619	0.83559	.	.	ENSG00000155629	ENST00000339364;ENST00000371110	T;T	0.26223	2.52;1.75	5.81	5.81	0.92471	Ankyrin repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.48077	0.1480	L	0.56769	1.78	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.42015	-0.9476	10	0.52906	T	0.07	-14.782	15.3374	0.74269	1.0:0.0:0.0:0.0	.	401	Q6ZUJ8	BCAP_HUMAN	R	401;223	ENSP00000339826:L401R;ENSP00000360151:L223R	ENSP00000339826:L401R	L	-	2	0	PIK3AP1	98395393	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.299000	0.89946	2.210000	0.71456	0.533000	0.62120	CTC	.	.	none		0.567	PIK3AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049619.2	NM_152309		C	98405403	A	C	98405403	3	2	36	1	0	0	0	0	1	0	0	0	11917	304	11	5	1255	5	PIK3AP1	10	98405403	Missense_Mutation	SNP	A	TCGA-GS-A9TT-01A-11D-A382-10	47871461	98405403	37129344	96	14324											
CALHM2	51063	hgsc.bcm.edu	37	chr10	105209154	105209154	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agctccttacctgggactcaTacctgagcctgcggctgacc	7	9	10	15	1	1	2	1	2	0	0	2	3	2	3	5	2	5	2	5	2	2	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr10:105209154T>A	ENST00000260743.5	-	3	1068	c.545A>T	c.(544-546)tAt>tTt	p.Y182F	CALHM2_ENST00000369788.3_Missense_Mutation_p.Y182F|CALHM2_ENST00000494180.1_5'Flank|CALHM2_ENST00000393235.1_Missense_Mutation_p.Y182F|RP11-225H22.7_ENST00000608063.1_RNA	NM_015916.4	NP_057000.2	Q9HA72	CAHM2_HUMAN	calcium homeostasis modulator 2	182					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						CTGGGACTCATACCTGAGCCT	0.602																																					p.Y182F		Atlas-SNP	.											.	CALHM2	30	.	0			c.A545T						PASS	.						67	70	69					10																	105209154		2194	4283	6477	SO:0001583	missense	51063	exon3			GACTCATACCTGA	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.545A>T	10.37:g.105209154T>A	ENSP00000260743:p.Tyr182Phe	25	0	0		41	14	0.341463	NM_015916	D3DR94|O95893|Q6ZUV9	Missense_Mutation	SNP	ENST00000260743.5	37	CCDS7549.1	.	.	.	.	.	.	.	.	.	.	T	25.2	4.617645	0.87359	.	.	ENSG00000138172	ENST00000369788;ENST00000260743;ENST00000393235	T;T;T	0.18502	2.21;2.21;2.21	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.39600	0.1084	M	0.80183	2.485	0.53005	D	0.999965	D;P	0.89917	1.0;0.86	D;P	0.83275	0.996;0.528	T	0.46693	-0.9173	10	0.02654	T	1	-3.6496	15.6983	0.77517	0.0:0.0:0.0:1.0	.	182;182	Q9HA72-2;Q9HA72	.;CAHM2_HUMAN	F	182	ENSP00000358803:Y182F;ENSP00000260743:Y182F;ENSP00000376927:Y182F	ENSP00000260743:Y182F	Y	-	2	0	CALHM2	105199144	1.000000	0.71417	0.997000	0.53966	0.977000	0.68977	6.980000	0.76160	2.112000	0.64535	0.459000	0.35465	TAT	.	.	none		0.602	CALHM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050159.1	NM_015916		A	105209154	T	A	105209154	3	1	36	1	0	0	0	0	1	0	0	0	2585	1406	49	5	434	5	CALHM2	10	105209154	Missense_Mutation	SNP	T	TCGA-GS-A9TT-01A-11D-A382-10	6803751	105209154	30325593	97	14325											
PNLIPRP3	119548	hgsc.bcm.edu	37	chr10	118220524	118220524	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacaacactccaaaggaagtCaggctagacccctcggatgc	13	5	9	14	1	1	1	1	0	0	1	3	3	2	3	3	3	2	1	3	3	4	1	rs199970109	byFrequency	TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr10:118220524C>A	ENST00000369230.3	+	6	758	c.612C>A	c.(610-612)gtC>gtA	p.V204V		NM_001011709.2	NP_001011709.2	Q17RR3	LIPR3_HUMAN	pancreatic lipase-related protein 3	204					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	triglyceride lipase activity (GO:0004806)	p.V204V(1)		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)		CAAAGGAAGTCAGGCTAGACC	0.438																																					p.V204V		Atlas-SNP	.											PNLIPRP3,NS,carcinoma,0,1	PNLIPRP3	101	1	1	Substitution - coding silent(1)	lung(1)	c.C612A						PASS	.						125	113	117					10																	118220524		2203	4300	6503	SO:0001819	synonymous_variant	119548	exon6			GGAAGTCAGGCTA	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.612C>A	10.37:g.118220524C>A		172	0	0		187	57	0.304813	NM_001011709		Silent	SNP	ENST00000369230.3	37	CCDS31292.1																																																																																			C|0.999;T|0.001	.	alt		0.438	PNLIPRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050520.1	XM_058404		A	118220524	C	A	118220524	2	1	36	1	0	0	0	0	0	0	0	1	12161	813	29	4		4	PNLIPRP3	10	118220524	Silent	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	13011370	118220524	17314223	98	14326											
NELL1	4745	hgsc.bcm.edu	37	chr11	20948897	20948897	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagtcaattggaaaactgtcAttgtgagaagacttgtcaag	14	12	10	5	0	3	2	3	1	0	2	3	4	3	3	0	1	1	0	0	1	6	4			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr11:20948897A>G	ENST00000357134.5	+	8	955	c.803A>G	c.(802-804)cAt>cGt	p.H268R	NELL1_ENST00000298925.5_Missense_Mutation_p.H296R|NELL1_ENST00000532434.1_Missense_Mutation_p.H268R|NELL1_ENST00000325319.5_Missense_Mutation_p.H211R	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	268					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						GAAAACTGTCATTGTGAGAAG	0.398																																					p.H268R		Atlas-SNP	.											.	NELL1	179	.	0			c.A803G						PASS	.						137	129	132					11																	20948897		2203	4300	6503	SO:0001583	missense	4745	exon8			ACTGTCATTGTGA	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.803A>G	11.37:g.20948897A>G	ENSP00000349654:p.His268Arg	83	0	0		65	30	0.461538	NM_006157	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Missense_Mutation	SNP	ENST00000357134.5	37	CCDS7855.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.081924	0.76528	.	.	ENSG00000165973	ENST00000298925;ENST00000357134;ENST00000325319;ENST00000532434	T;T;T;T	0.63913	-0.07;-0.07;-0.07;-0.07	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.70055	0.3180	L	0.36672	1.1	0.58432	D	0.999997	D;D;D;D	0.71674	0.996;0.993;0.998;0.985	D;D;D;P	0.77557	0.99;0.977;0.923;0.637	T	0.66052	-0.6019	10	0.23302	T	0.38	-19.4505	15.9803	0.80105	1.0:0.0:0.0:0.0	.	211;296;268;268	F5H6I3;B3KXR2;Q92832-2;Q92832	.;.;.;NELL1_HUMAN	R	296;268;211;268	ENSP00000298925:H296R;ENSP00000349654:H268R;ENSP00000317837:H211R;ENSP00000437170:H268R	ENSP00000298925:H296R	H	+	2	0	NELL1	20905473	1.000000	0.71417	0.993000	0.49108	0.998000	0.95712	8.701000	0.91331	2.170000	0.68504	0.455000	0.32223	CAT	.	.	none		0.398	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157		G	20948897	A	G	20948897	3	3	36	1	0	0	0	0	1	0	0	0	10342	217	8	3	833	3	NELL1	11	20948897	Missense_Mutation	SNP	A	TCGA-GS-A9TT-01A-11D-A382-10		20948897	114057619	99	14327											
OR5L1	219437	hgsc.bcm.edu	37	chr11	55579714	55579714	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccatggaacagtcctttccAtttattgcaggcccagttca	9	13	7	12	0	1	0	1	0	0	0	4	1	4	1	4	2	2	2	4	2	2	5			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr11:55579714A>G	ENST00000333973.2	+	1	861	c.772A>G	c.(772-774)Att>Gtt	p.I258V		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	258						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)				AGTCCTTTCCATTTATTGCAG	0.512																																					p.I258V		Atlas-SNP	.											.	OR5L1	145	.	0			c.A772G						PASS	.						120	104	109					11																	55579714		2200	4296	6496	SO:0001583	missense	219437	exon1			CTTTCCATTTATT	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.772A>G	11.37:g.55579714A>G	ENSP00000335529:p.Ile258Val	98	0	0		90	45	0.5	NM_001004738	B2RNK6|Q6IFD0	Missense_Mutation	SNP	ENST00000333973.2	37	CCDS31509.1	.	.	.	.	.	.	.	.	.	.	a	10.21	1.286627	0.23478	.	.	ENSG00000186117	ENST00000333973	T	0.00076	8.76	4.12	-2.28	0.06826	GPCR, rhodopsin-like superfamily (1);	0.509225	0.18083	N	0.152222	T	0.00073	0.0002	N	0.16130	0.375	0.09310	N	1	B	0.02656	0.0	B	0.12837	0.008	T	0.30909	-0.9962	10	0.72032	D	0.01	-12.5116	5.7752	0.18275	0.4031:0.4296:0.1673:0.0	.	258	Q8NGL2	OR5L1_HUMAN	V	258	ENSP00000335529:I258V	ENSP00000335529:I258V	I	+	1	0	OR5L1	55336290	0.000000	0.05858	0.000000	0.03702	0.078000	0.17371	0.358000	0.20216	-0.300000	0.08895	-0.815000	0.03128	ATT	.	.	none		0.512	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738		G	55579714	A	G	55579714	3	3	36	1	0	0	0	0	1	0	0	0	11179	217	8	3	774	3	OR5L1	11	55579714	Missense_Mutation	SNP	A	TCGA-GS-A9TT-01A-11D-A382-10	34630817	55579714	79426802	100	14328											
OR5M10	390167	hgsc.bcm.edu	37	chr11	56345145	56345145	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctctagcactgggtcgtctGtcagtcctaagagaatgaat	10	12	10	9	1	3	2	1	1	2	1	6	3	4	2	1	1	1	1	1	1	4	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr11:56345145G>C	ENST00000526812.2	-	1	118	c.53C>G	c.(52-54)aCa>aGa	p.T18R		NM_001004741.1	NP_001004741.1	Q6IEU7	OR5MA_HUMAN	olfactory receptor, family 5, subfamily M, member 10	18						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						TGGGTCGTCTGTCAGTCCTAA	0.463																																					p.T18R		Atlas-SNP	.											.	OR5M10	56	.	0			c.C53G						PASS	.						156	146	149					11																	56345145		1908	4132	6040	SO:0001583	missense	390167	exon1			TCGTCTGTCAGTC	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.53C>G	11.37:g.56345145G>C	ENSP00000436004:p.Thr18Arg	228	0	0		153	63	0.411765	NM_001004741	B9EIL9	Missense_Mutation	SNP	ENST00000526812.2	37	CCDS53630.1	.	.	.	.	.	.	.	.	.	.	G	12.13	1.845689	0.32606	.	.	ENSG00000254834	ENST00000526812	T	0.00438	7.42	4.04	4.04	0.47022	.	.	.	.	.	T	0.00998	0.0033	M	0.82716	2.605	0.09310	N	1	D	0.58268	0.982	P	0.59115	0.852	T	0.44452	-0.9327	9	0.72032	D	0.01	.	10.7138	0.46000	0.0:0.0:0.8092:0.1908	.	18	Q6IEU7	OR5MA_HUMAN	R	18	ENSP00000436004:T18R	ENSP00000436004:T18R	T	-	2	0	OR5M10	56101721	0.101000	0.21875	0.969000	0.41365	0.083000	0.17756	2.759000	0.47573	2.238000	0.73509	0.632000	0.83419	ACA	.	.	none		0.463	OR5M10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391609.1	NM_001004741		C	56345145	G	C	56345145	3	2	36	1	0	0	0	0	1	0	0	0	11182	1377	48	4	898	4	OR5M10	11	56345145	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	765431	56345145	78661371	101	14329											
ALG8	79053	hgsc.bcm.edu	37	chr11	77815052	77815052	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aaagtcttcagtgacgaaatActatatatggtgaatagtaa	17	12	8	4	1	2	2	1	2	1	0	2	3	2	2	0	1	1	1	0	1	9	7			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr11:77815052A>G	ENST00000299626.5	-	12	1394	c.1323T>C	c.(1321-1323)agT>agC	p.S441S	ALG8_ENST00000532552.2_5'UTR|ALG8_ENST00000376156.3_Silent_p.S441S	NM_024079.4	NP_076984.2	Q9BVK2	ALG8_HUMAN	ALG8, alpha-1,3-glucosyltransferase	441					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)			GTGACGAAATACTATATATGG	0.269																																					p.S441S		Atlas-SNP	.											.	ALG8	54	.	0			c.T1323C						PASS	.						25	29	28					11																	77815052		2166	4252	6418	SO:0001819	synonymous_variant	79053	exon12			CGAAATACTATAT	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.1323T>C	11.37:g.77815052A>G		217	0	0		228	117	0.513158	NM_024079	A6NDW6|O60860	Silent	SNP	ENST00000299626.5	37	CCDS8258.1	.	.	.	.	.	.	.	.	.	.	A	9.014	0.983159	0.18889	.	.	ENSG00000159063	ENST00000530608;ENST00000532306	.	.	.	5.66	4.54	0.55810	.	.	.	.	.	T	0.56673	0.2001	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54964	-0.8214	4	.	.	.	-10.9941	6.8814	0.24174	0.8312:0.0:0.1688:0.0	.	.	.	.	A	143;228	.	.	V	-	2	0	ALG8	77492700	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	2.624000	0.46444	2.147000	0.66899	0.533000	0.62120	GTA	.	.	none		0.269	ALG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390637.1	NM_024079		G	77815052	A	G	77815052	2	3	36	1	0	0	0	0	0	0	0	1	523	388	14	3		3	ALG8	11	77815052	Silent	SNP	A	TCGA-GS-A9TT-01A-11D-A382-10	21469907	77815052	57191464	102	14330											
CCDC89	220388	hgsc.bcm.edu	37	chr11	85396761	85396761	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcttgtattcatccttgaagCggagcatcaactcgtggttg	8	14	10	9	2	3	1	2	1	1	0	5	2	4	2	1	2	3	3	1	2	3	5			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr11:85396761C>T	ENST00000316398.3	-	1	559	c.413G>A	c.(412-414)cGc>cAc	p.R138H	CREBZF_ENST00000531515.1_5'Flank|CREBZF_ENST00000534224.1_5'Flank	NM_152723.1	NP_689936.1	Q8N998	CCD89_HUMAN	coiled-coil domain containing 89	138						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)				ATCCTTGAAGCGGAGCATCAA	0.517																																					p.R138H		Atlas-SNP	.											.	CCDC89	45	.	0			c.G413A						PASS	.						105	92	96					11																	85396761		2203	4299	6502	SO:0001583	missense	220388	exon1			TTGAAGCGGAGCA	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.413G>A	11.37:g.85396761C>T	ENSP00000320649:p.Arg138His	109	0	0		92	44	0.478261	NM_152723		Missense_Mutation	SNP	ENST00000316398.3	37	CCDS8270.1	.	.	.	.	.	.	.	.	.	.	c	16.35	3.099386	0.56183	.	.	ENSG00000179071	ENST00000316398	.	.	.	5.53	4.62	0.57501	.	0.712446	0.14115	N	0.340425	T	0.51007	0.1649	M	0.76002	2.32	0.32187	N	0.579655	B	0.22211	0.066	B	0.17098	0.017	T	0.56214	-0.8016	8	.	.	.	-8.569	9.1248	0.36807	0.0:0.7911:0.0:0.2089	.	138	Q8N998	CCD89_HUMAN	H	138	.	.	R	-	2	0	CCDC89	85074409	1.000000	0.71417	1.000000	0.80357	0.678000	0.39670	1.958000	0.40402	1.346000	0.45694	-0.141000	0.14075	CGC	.	.	none		0.517	CCDC89-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392182.1	NM_152723		T	85396761	C	T	85396761	3	4	36	1	0	0	0	0	1	0	0	0	2868	768	27	1	715	1	CCDC89	11	85396761	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	7581709	85396761	49609755	103	14331											
FAT3	120114	hgsc.bcm.edu	37	chr11	92577432	92577432	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttccaggtacccattgatgtGgtcgtgcatgtggagcagtt	7	13	13	8	1	0	1	0	1	0	0	2	2	1	2	2	3	3	4	2	3	1	4			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr11:92577432G>C	ENST00000298047.6	+	18	10916	c.10899G>C	c.(10897-10899)gtG>gtC	p.V3633V	FAT3_ENST00000533797.1_5'Flank|FAT3_ENST00000409404.2_Silent_p.V3633V|FAT3_ENST00000525166.1_Silent_p.V3483V			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3633	Cadherin 33. {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)				CCATTGATGTGGTCGTGCATG	0.547										TCGA Ovarian(4;0.039)																											p.V3633V		Atlas-SNP	.											.	FAT3	1822	.	0			c.G10899C						PASS	.						138	143	141					11																	92577432		2167	4274	6441	SO:0001819	synonymous_variant	120114	exon18			TGATGTGGTCGTG	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.10899G>C	11.37:g.92577432G>C		89	0	0		69	30	0.434783	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				.	.	none		0.547	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		C	92577432	G	C	92577432	2	2	36	1	0	0	0	0	0	0	0	1	5699	1335	47	4		4	FAT3	11	92577432	Silent	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	7180671	92577432	42429084	104	14332											
AMOTL1	154810	hgsc.bcm.edu	37	chr11	94554798	94554798	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgcactctgtctccctgccGcttccactcccgatggccct	3	11	7	20	2	2	0	0	0	2	0	5	1	4	0	5	1	2	2	5	1	0	1	rs370986721		TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr11:94554798G>A	ENST00000433060.2	+	4	1365	c.1224G>A	c.(1222-1224)ccG>ccA	p.P408P	AMOTL1_ENST00000317837.9_Intron|AMOTL1_ENST00000539727.1_3'UTR|AMOTL1_ENST00000317829.8_Silent_p.P358P	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	408					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)				TCTCCCTGCCGCTTCCACTCC	0.667																																					p.P408P		Atlas-SNP	.											.	AMOTL1	95	.	0			c.G1224A						PASS	.	A		0,4158		0,0,2079	26	32	30		1224	-10.5	0	11		30	1,8427		0,1,4213	no	coding-synonymous	AMOTL1	NM_130847.2		0,1,6292	AA,AG,GG		0.0119,0.0,0.0079		408/957	94554798	1,12585	2079	4214	6293	SO:0001819	synonymous_variant	154810	exon4			CCTGCCGCTTCCA	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.1224G>A	11.37:g.94554798G>A		58	0	0		71	33	0.464789	NM_130847	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Silent	SNP	ENST00000433060.2	37	CCDS44712.1																																																																																			.	.	weak		0.667	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847		A	94554798	G	A	94554798	2	1	36	1	0	0	0	0	0	0	0	1	583	1074	38	1		1	AMOTL1	11	94554798	Silent	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	1977366	94554798	40451718	105	14333											
AMOTL1	154810	hgsc.bcm.edu	37	chr11	94583365	94583365	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aggaccatcggagacacatcGagatcctggaccaggctttg	11	7	12	11	2	0	2	0	0	0	2	3	6	1	4	3	4	0	1	3	4	0	1	rs566138044		TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr11:94583365G>A	ENST00000433060.2	+	7	1876	c.1735G>A	c.(1735-1737)Gag>Aag	p.E579K	AMOTL1_ENST00000317837.9_Intron|AMOTL1_ENST00000317829.8_Missense_Mutation_p.E529K	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	579					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)				GAGACACATCGAGATCCTGGA	0.522													G|||	1	0.000199681	0.0	0.0	5008	,	,		19935	0.001		0.0	False		,,,				2504	0.0				p.E579K		Atlas-SNP	.											.	AMOTL1	95	.	0			c.G1735A						PASS	.						46	55	52					11																	94583365		2025	4179	6204	SO:0001583	missense	154810	exon7			CACATCGAGATCC	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.1735G>A	11.37:g.94583365G>A	ENSP00000387739:p.Glu579Lys	70	0	0		58	37	0.637931	NM_130847	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Missense_Mutation	SNP	ENST00000433060.2	37	CCDS44712.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.664939	0.88251	.	.	ENSG00000166025	ENST00000317829;ENST00000542840;ENST00000433060	T;T	0.25749	1.78;1.78	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.41050	0.1142	M	0.70275	2.135	0.80722	D	1	P;B	0.36183	0.542;0.111	B;B	0.43251	0.413;0.051	T	0.13656	-1.0501	10	0.46703	T	0.11	-34.7551	20.088	0.97803	0.0:0.0:1.0:0.0	.	529;579	Q8IY63-2;Q8IY63	.;AMOL1_HUMAN	K	529;585;579	ENSP00000320968:E529K;ENSP00000387739:E579K	ENSP00000320968:E529K	E	+	1	0	AMOTL1	94223013	1.000000	0.71417	0.989000	0.46669	0.980000	0.70556	9.578000	0.98200	2.739000	0.93911	0.655000	0.94253	GAG	.	.	none		0.522	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847		A	94583365	G	A	94583365	3	1	36	1	0	0	0	0	1	0	0	0	583	1059	37	1	1761	1	AMOTL1	11	94583365	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	28567	94583365	40423151	106	14334											
JAM3	83700	hgsc.bcm.edu	37	chr11	134019043	134019043	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgtgttggctttgcagggCgacttcagacacaagtcatc	8	12	12	9	1	2	1	2	0	0	1	3	2	2	1	0	2	1	3	0	2	1	3	rs200279211		TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr11:134019043C>T	ENST00000299106.4	+	9	1059	c.900C>T	c.(898-900)ggC>ggT	p.G300G	JAM3_ENST00000441717.3_Silent_p.G249G|NCAPD3_ENST00000526787.2_5'Flank|JAM3_ENST00000529443.2_Silent_p.G345G			Q9BX67	JAM3_HUMAN	junctional adhesion molecule 3	300					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)		CTTTGCAGGGCGACTTCAGAC	0.517													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18213	0.0		0.0	False		,,,				2504	0.0				p.G300G		Atlas-SNP	.											.	JAM3	41	.	0			c.C900T						PASS	.						138	122	127					11																	134019043		2201	4297	6498	SO:0001819	synonymous_variant	83700	exon9			GCAGGGCGACTTC	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.900C>T	11.37:g.134019043C>T		155	0	0		145	66	0.455172	NM_032801	B3KWG9|Q8WWL8|Q96FL1	Silent	SNP	ENST00000299106.4	37	CCDS8494.2	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	6.819	0.520209	0.13005	.	.	ENSG00000166086	ENST00000529443	.	.	.	6.04	-9.11	0.00711	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.1871	0.65612	0.0:0.2635:0.0769:0.6596	.	.	.	.	X	254	.	.	R	+	1	2	JAM3	133524253	0.021000	0.18746	0.743000	0.31040	0.986000	0.74619	-1.218000	0.02976	-1.497000	0.01826	-0.251000	0.11542	CGA	C|1.000;T|0.000	0.000	strong		0.517	JAM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393303.4	NM_032801		T	134019043	C	T	134019043	2	4	36	1	0	0	0	0	0	0	0	1	7953	755	27	1		1	JAM3	11	134019043	Silent	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	39435678	134019043	987473	107	14335											
C12orf59	120939	hgsc.bcm.edu	37	chr12	10339160	10339160	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accgtcattgctttcgatcaCgacagcactctccagagcac	10	9	7	15	3	3	1	2	0	1	1	5	3	3	1	2	0	3	3	2	0	0	2	rs145013082	byFrequency	TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr12:10339160C>T	ENST00000381923.2	+	5	683	c.279C>T	c.(277-279)caC>caT	p.H93H	TMEM52B_ENST00000536952.1_Silent_p.H93H|TMEM52B_ENST00000298530.3_Silent_p.H73H			Q4KMG9	TM52B_HUMAN	transmembrane protein 52B	93						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)											CTTTCGATCACGACAGCACTC	0.522																																					p.H73H		Atlas-SNP	.											.	.	.	.	0			c.C219T						PASS	.	C		0,4406		0,0,2203	97	87	91		219	-6.6	0.9	12	dbSNP_134	91	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	C12orf59	NM_153022.2		0,4,6499	TT,TC,CC		0.0465,0.0,0.0308		73/164	10339160	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	120939	exon3			CGATCACGACAGC	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.279C>T	12.37:g.10339160C>T		84	0	0		67	26	0.38806	NM_153022	Q96NA7	Silent	SNP	ENST00000381923.2	37																																																																																				C|1.000;T|0.000	0.000	strong		0.522	TMEM52B-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000399645.1	NM_153022		T	10339160	C	T	10339160	2	4	36	1	0	0	0	0	0	0	0	1	1704	535	19	1		1	C12orf59	12	10339160	Silent	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10		10339160	123512735	108	14336											
TAS2R19	259294	hgsc.bcm.edu	37	chr12	11174305	11174306	+	Frame_Shift_Del	DEL	GT	GT	-																															gccacaaaactgaaagaaagGtctgttttagcttcctactt																										TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr12:11174305_11174306delGT	ENST00000390673.2	-	1	913_914	c.865_866delAC	c.(865-867)accfs	p.T289fs	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_176888.1	NP_795369.1	P59542	T2R19_HUMAN	taste receptor, type 2, member 19	289					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)|cervix(1)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|stomach(1)	17						TGAAAGAAAGGTCTGTTTTAGC	0.441																																					p.289_289del		Pindel,Atlas-Indel	.											.	TAS2R19	30	.	0			c.866_867del						PASS	.																																			SO:0001589	frameshift_variant	259294	exon1			.	AX097730, AF494234	CCDS8640.1	12p13.2	2012-08-22			ENSG00000212124	ENSG00000212124		"Taste receptors / Type 2", "GPCR / Unclassified : Taste receptors"	19108	protein-coding gene	gene with protein product		613961	"taste receptor, type 2, member 48", "taste receptor, type 2, member 23"	TAS2R48, TAS2R23			Standard	NM_176888		Approved	T2R19, T2R23	uc010shj.2	P59542	OTTHUMG00000162687	ENST00000390673.2:c.865_866delAC	12.37:g.11174305_11174306delGT	ENSP00000375091:p.Thr289fs	116	0	.		81	35	0.432	NM_176888	Q3MIJ4|Q645X8	Frame_Shift_Del	DEL	ENST00000390673.2	37	CCDS8640.1																																																																																			.	.	none		0.441	TAS2R19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370080.1	NM_176888		-	11174306	GT	-	11174305	7	5	36	1	0	1	0	1	0	0	0	0	15585	1261	44	0	36	0	TAS2R19	12	11174305	Frame_Shift_Del	DEL	GT	TCGA-GS-A9TT-01A-11D-A382-10	835145	11174305	122677590	109	14337											
PDE3A	5139	hgsc.bcm.edu	37	chr12	20787920	20787920	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acagaatgaagatgaaacagAgtgcctgagagagcctctga	16	6	12	7	0	1	8	0	4	1	4	1	9	1	8	2	0	3	0	2	0	3	0			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr12:20787920A>G	ENST00000359062.3	+	8	1971	c.1931A>G	c.(1930-1932)gAg>gGg	p.E644G	PDE3A_ENST00000544307.1_3'UTR	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	644					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)	GATGAAACAGAGTGCCTGAGA	0.423																																					p.E644G		Atlas-SNP	.											.	PDE3A	184	.	0			c.A1931G						PASS	.						149	127	135					12																	20787920		2203	4300	6503	SO:0001583	missense	5139	exon8			AAACAGAGTGCCT		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.1931A>G	12.37:g.20787920A>G	ENSP00000351957:p.Glu644Gly	74	0	0		51	20	0.392157	NM_000921	O60865|Q13348|Q17RD1	Missense_Mutation	SNP	ENST00000359062.3	37	CCDS31754.1	.	.	.	.	.	.	.	.	.	.	A	15.91	2.971029	0.53614	.	.	ENSG00000172572	ENST00000359062	T	0.64991	-0.13	5.64	4.5	0.54988	.	3.679390	0.00550	N	0.000256	T	0.69895	0.3162	L	0.55481	1.735	0.45995	D	0.998804	P	0.50443	0.935	P	0.49528	0.614	T	0.50440	-0.8828	10	0.42905	T	0.14	.	11.0409	0.47831	0.9266:0.0:0.0734:0.0	.	644	Q14432	PDE3A_HUMAN	G	644	ENSP00000351957:E644G	ENSP00000351957:E644G	E	+	2	0	PDE3A	20679187	1.000000	0.71417	0.816000	0.32577	0.078000	0.17371	6.704000	0.74639	0.984000	0.38629	0.528000	0.53228	GAG	.	.	none		0.423	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2			G	20787920	A	G	20787920	3	3	36	1	0	0	0	0	1	0	0	0	11646	304	11	3	1961	3	PDE3A	12	20787920	Missense_Mutation	SNP	A	TCGA-GS-A9TT-01A-11D-A382-10	9613615	20787920	113063975	110	14338											
KRT1	3848	hgsc.bcm.edu	37	chr12	53069243	53069243	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acctccggagccgtagctgcTacctccggagccatagctgc	7	7	11	16	3	0	0	0	0	0	0	2	2	2	2	6	2	7	4	6	2	3	3	rs77846840|rs540699806|rs267607656	byFrequency	TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr12:53069243T>C	ENST00000252244.3	-	9	1727	c.1669A>G	c.(1669-1671)Agc>Ggc	p.S557G		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	557	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.S557_G563delSSYGSGG(3)		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						ccgtagctgctacctccggag	0.682																																					p.S557G		Atlas-SNP	.											.	KRT1	110	.	3	Deletion - In frame(3)	prostate(2)|central_nervous_system(1)	c.A1669G						PASS	.						4	4	4					12																	53069243		1805	3566	5371	SO:0001583	missense	3848	exon9			AGCTGCTACCTCC	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.1669A>G	12.37:g.53069243T>C	ENSP00000252244:p.Ser557Gly	11	0	0		26	12	0.461538	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Missense_Mutation	SNP	ENST00000252244.3	37	CCDS8836.1	.	.	.	.	.	.	.	.	.	.	t	12.77	2.037794	0.35989	.	.	ENSG00000167768	ENST00000252244	T	0.81247	-1.47	3.63	0.628	0.17681	.	.	.	.	.	T	0.54711	0.1875	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.48490	-0.9031	8	0.07644	T	0.81	.	5.639	0.17552	0.0:0.6406:0.1602:0.1993	.	557	P04264	K2C1_HUMAN	G	557	ENSP00000252244:S557G	ENSP00000252244:S557G	S	-	1	0	KRT1	51355510	0.000000	0.05858	0.034000	0.17996	0.201000	0.24016	-0.192000	0.09587	-0.104000	0.12154	-1.598000	0.00824	AGC	T|0.500;C|0.500	0.500	weak		0.682	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121		C	53069243	T	C	53069243	3	2	36	1	0	0	0	0	1	0	0	0	8456	1522	53	3	269	3	KRT1	12	53069243	Missense_Mutation	SNP	T	TCGA-GS-A9TT-01A-11D-A382-10	32281323	53069243	80782652	111	14339											
HNRNPA1	3178	hgsc.bcm.edu	37	chr12	54676988	54676988	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctatgacagctataacaacGgaggcggaggcggctttggc	10	7	15	9	3	0	1	0	1	0	0	0	3	0	3	0	6	3	3	0	6	4	4	rs367836050|rs539863165	byFrequency	TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr12:54676988G>T	ENST00000340913.6	+	8	930	c.877G>T	c.(877-879)Gga>Tga	p.G293*	RP11-968A15.8_ENST00000553061.1_RNA|HNRNPA1_ENST00000330752.8_Intron|HNRNPA1_ENST00000546500.1_Intron|HNRNPA1_ENST00000547276.1_Intron	NM_002136.2|NM_031157.2	NP_002127.1|NP_112420.1	P09651	ROA1_HUMAN	heterogeneous nuclear ribonucleoprotein A1	293	Gly-rich.				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						CTATAACAACGGAGGCGGAGG	0.537																																					p.G293X	Colon(83;502 1289 8436 16406 24870)	Atlas-SNP	.											.	HNRNPA1	72	.	0			c.G877T						PASS	.						46	66	59					12																	54676988		2040	4175	6215	SO:0001587	stop_gained	3178	exon8			AACAACGGAGGCG	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.877G>T	12.37:g.54676988G>T	ENSP00000341826:p.Gly293*	72	0	0		101	36	0.356436	NM_031157	A8K4Z8|Q3MIB7|Q6PJZ7	Nonsense_Mutation	SNP	ENST00000340913.6	37	CCDS44909.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.153932	0.78114	.	.	ENSG00000135486	ENST00000340913	.	.	.	2.8	1.89	0.25635	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.25106	T	0.35	.	9.9561	0.41668	0.0:0.2089:0.7911:0.0	.	.	.	.	X	293	.	ENSP00000341826:G293X	G	+	1	0	HNRNPA1	52963255	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.265000	0.58865	0.753000	0.32945	0.455000	0.32223	GGA	.	.	alt		0.537	HNRNPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000405480.1	NM_031157		T	54676988	G	T	54676988	4	4	36	1	0	0	0	0	0	1	0	0	7266	1117	39	4	907	4	HNRNPA1	12	54676988	Nonsense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	1607745	54676988	79174907	112	14340											
NUAK1	9891	hgsc.bcm.edu	37	chr12	106460866	106460866	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctgatgacactggaagggCggctgtagctccgggagagg	8	6	18	9	3	0	3	0	2	0	1	1	5	1	4	1	5	1	4	1	5	2	1			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr12:106460866C>T	ENST00000261402.2	-	7	3079	c.1700G>A	c.(1699-1701)cGc>cAc	p.R567H		NM_014840.2	NP_055655.1	O60285	NUAK1_HUMAN	NUAK family, SNF1-like kinase, 1	567					cell adhesion (GO:0007155)|cellular response to DNA damage stimulus (GO:0006974)|regulation of cell adhesion (GO:0030155)|regulation of cell proliferation (GO:0042127)|regulation of cellular senescence (GO:2000772)|regulation of myosin-light-chain-phosphatase activity (GO:0035507)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37						ACTGGAAGGGCGGCTGTAGCT	0.632																																					p.R567H		Atlas-SNP	.											NUAK1_ENST00000261402,NS,malignant_melanoma,-1,2	NUAK1	196	2	0			c.G1700A						scavenged	.						32	38	36					12																	106460866		2202	4300	6502	SO:0001583	missense	9891	exon7			GAAGGGCGGCTGT	AB011109	CCDS31892.1	12q23.3	2005-08-09				ENSG00000074590			14311	protein-coding gene	gene with protein product	"AMP-activated protein kinase family member 5"	608130				12409306, 13679856	Standard	NM_014840		Approved	ARK5, KIAA0537, NuaK1	uc001tlj.1	O60285	OTTHUMG00000169763	ENST00000261402.2:c.1700G>A	12.37:g.106460866C>T	ENSP00000261402:p.Arg567His	110	1	0.00909091		99	25	0.252525	NM_014840	A7MD39|Q96KA8	Missense_Mutation	SNP	ENST00000261402.2	37	CCDS31892.1	.	.	.	.	.	.	.	.	.	.	C	28.7	4.941751	0.92526	.	.	ENSG00000074590	ENST00000261402	D	0.82893	-1.66	5.66	5.66	0.87406	.	0.000000	0.64402	D	0.000014	D	0.90082	0.6902	M	0.61703	1.905	0.80722	D	1	D	0.89917	1.0	D	0.68621	0.959	D	0.90088	0.4175	10	0.62326	D	0.03	.	19.7554	0.96287	0.0:1.0:0.0:0.0	.	567	O60285	NUAK1_HUMAN	H	567	ENSP00000261402:R567H	ENSP00000261402:R567H	R	-	2	0	NUAK1	104984996	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	5.717000	0.68446	2.665000	0.90641	0.563000	0.77884	CGC	.	.	none		0.632	NUAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405767.2	NM_014840		T	106460866	C	T	106460866	3	4	36	1	0	0	0	0	1	0	0	0	10721	768	27	1	289	1	NUAK1	12	106460866	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	51783878	106460866	27391029	113	14341											
BTBD11	121551	hgsc.bcm.edu	37	chr12	108011111	108011111	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttagtttgctgttggagcGtggtgccgatcccctgatag	5	13	15	8	2	0	1	0	1	0	0	1	3	1	2	3	3	3	4	3	3	2	4	rs190270378	byFrequency	TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr12:108011111G>A	ENST00000280758.5	+	9	2657	c.2129G>A	c.(2128-2130)cGt>cAt	p.R710H	RP11-128P10.1_ENST00000548473.1_RNA|BTBD11_ENST00000420571.2_Intron|BTBD11_ENST00000490090.2_Missense_Mutation_p.R710H|BTBD11_ENST00000357167.4_Missense_Mutation_p.R247H	NM_001018072.1	NP_001018082.1	A6QL63	BTBDB_HUMAN	BTB (POZ) domain containing 11	710						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						CTGTTGGAGCGTGGTGCCGAT	0.483													G|||	3	0.000599042	0.0008	0.0	5008	,	,		21085	0.001		0.001	False		,,,				2504	0.0				p.R710H		Atlas-SNP	.											BTBD11,colon,carcinoma,+1,1	BTBD11	122	1	0			c.G2129A						scavenged	.						113	122	119					12																	108011111		2203	4300	6503	SO:0001583	missense	121551	exon9			TGGAGCGTGGTGC	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.2129G>A	12.37:g.108011111G>A	ENSP00000280758:p.Arg710His	193	2	0.0103627		210	121	0.57619	NM_001018072	A4FU41|B3KXG3|C9J019|C9JK80|E9PHS4|Q3ZTQ4|Q52M89|Q6ZV99|Q8N245	Missense_Mutation	SNP	ENST00000280758.5	37	CCDS31893.1	2	9.157509157509158E-4	0	0.0	0	0.0	1	0.0017482517482517483	1	0.0013192612137203166	G	18.33	3.599668	0.66332	.	.	ENSG00000151136	ENST00000280758;ENST00000490090;ENST00000357167	T;T;T	0.62498	0.02;0.02;0.02	5.49	5.49	0.81192	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.59810	0.2221	N	0.03177	-0.4	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;P	0.80764	0.975;0.994;0.795	T	0.63457	-0.6633	10	0.19590	T	0.45	.	19.3748	0.94503	0.0:0.0:1.0:0.0	.	247;710;710	E9PHS4;A6QL63;A6QL63-3	.;BTBDB_HUMAN;.	H	710;710;247	ENSP00000280758:R710H;ENSP00000447319:R710H;ENSP00000349690:R247H	ENSP00000280758:R710H	R	+	2	0	BTBD11	106535241	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.810000	0.75216	2.572000	0.86782	0.655000	0.94253	CGT	G|0.999;A|0.001	0.001	strong		0.483	BTBD11-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318003.1	NM_152322		A	108011111	G	A	108011111	3	1	36	1	0	0	0	0	1	0	0	0	1541	1145	40	1	2268	1	BTBD11	12	108011111	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	1550245	108011111	25840784	114	14342											
LHX5	64211	hgsc.bcm.edu	37	chr12	113901352	113901352	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcccggcgcgtagtagtcGccttggtagtctgcggaggg	4	10	16	11	5	1	0	0	0	1	0	3	1	2	1	2	4	1	3	2	4	3	5			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr12:113901352G>A	ENST00000261731.3	-	5	1425	c.852C>T	c.(850-852)ggC>ggT	p.G284G		NM_022363.2	NP_071758.1	Q9H2C1	LHX5_HUMAN	LIM homeobox 5	284					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						CGTAGTAGTCGCCTTGGTAGT	0.721																																					p.G284G		Atlas-SNP	.											.	LHX5	39	.	0			c.C852T						PASS	.						11	13	13					12																	113901352		2154	4167	6321	SO:0001819	synonymous_variant	64211	exon5			GTAGTCGCCTTGG	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.852C>T	12.37:g.113901352G>A		35	0	0		44	29	0.659091	NM_022363	Q32MA4	Silent	SNP	ENST00000261731.3	37	CCDS9171.1																																																																																			.	.	none		0.721	LHX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404788.3	NM_022363		A	113901352	G	A	113901352	2	1	36	1	0	0	0	0	0	0	0	1	8783	1074	38	1		1	LHX5	12	113901352	Silent	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	5890241	113901352	19950543	115	14343											
KDM2B	84678	hgsc.bcm.edu	37	chr12	121881588	121881588	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaaccgggggacgtttgaagCgatgaggcctaaaggggggt	10	6	19	6	3	0	2	0	2	0	0	0	5	0	3	2	6	2	1	2	6	4	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr12:121881588C>T	ENST00000377071.4	-	17	2532	c.2460G>A	c.(2458-2460)tcG>tcA	p.S820S	KDM2B_ENST00000377069.4_Intron|KDM2B_ENST00000542973.1_Silent_p.S188S|KDM2B_ENST00000536437.1_Intron	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	820					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						ACGTTTGAAGCGATGAGGCCT	0.607											OREG0022201	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S820S		Atlas-SNP	.											KDM2B_ENST00000377071,rectum,carcinoma,-1,2	KDM2B	218	2	0			c.G2460A						PASS	.						37	43	41					12																	121881588		1976	4158	6134	SO:0001819	synonymous_variant	84678	exon17			TTGAAGCGATGAG	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.2460G>A	12.37:g.121881588C>T		14	0	0	1514	14	13	0.928571	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Silent	SNP	ENST00000377071.4	37	CCDS41850.1																																																																																			.	.	none		0.607	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590		T	121881588	C	T	121881588	2	4	36	1	0	0	0	0	0	0	0	1	8134	755	27	1		1	KDM2B	12	121881588	Silent	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	7980236	121881588	11970307	116	14344											
ZCCHC8	55596	hgsc.bcm.edu	37	chr12	122958280	122958280	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctgatgtcacagtttggtaCgacactgccattatcaagaa	12	11	9	9	1	2	2	2	1	0	1	2	3	2	2	1	1	2	3	1	1	4	3			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr12:122958280C>T	ENST00000336229.4	-	14	2018	c.1888G>A	c.(1888-1890)Gta>Ata	p.V630I	ZCCHC8_ENST00000543897.1_Missense_Mutation_p.V392I|ZCCHC8_ENST00000536306.1_Missense_Mutation_p.V392I|ZCCHC8_ENST00000538116.1_Missense_Mutation_p.V241I	NM_017612.3	NP_060082.2	Q6NZY4	ZCHC8_HUMAN	zinc finger, CCHC domain containing 8	630					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)		CAGTTTGGTACGACACTGCCA	0.493																																					p.V630I		Atlas-SNP	.											.	ZCCHC8	56	.	0			c.G1888A						PASS	.						156	155	155					12																	122958280		1960	4140	6100	SO:0001583	missense	55596	exon14			TTGGTACGACACT	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.1888G>A	12.37:g.122958280C>T	ENSP00000337313:p.Val630Ile	159	0	0		267	161	0.602996	NM_017612	Q7L2P6|Q8N2K5|Q96SK7|Q9NSS2|Q9NSS3	Missense_Mutation	SNP	ENST00000336229.4	37		.	.	.	.	.	.	.	.	.	.	C	10.54	1.379058	0.24944	.	.	ENSG00000033030	ENST00000536306;ENST00000543897;ENST00000336229;ENST00000538116	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	5.78	-0.726	0.11170	.	0.855254	0.10528	N	0.664129	T	0.27629	0.0679	L	0.44542	1.39	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.26224	-1.0109	10	0.37606	T	0.19	0.0081	1.0127	0.01501	0.2262:0.3504:0.1053:0.318	.	630	Q6NZY4	ZCHC8_HUMAN	I	392;392;630;241	ENSP00000441423:V392I;ENSP00000438993:V392I;ENSP00000337313:V630I;ENSP00000440028:V241I	ENSP00000337313:V630I	V	-	1	0	ZCCHC8	121524233	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.257000	0.08745	-0.449000	0.07117	-0.827000	0.03088	GTA	.	.	none		0.493	ZCCHC8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017612		T	122958280	C	T	122958280	3	4	36	1	0	0	0	0	1	0	0	0	17609	536	19	1	239	1	ZCCHC8	12	122958280	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	1076692	122958280	10893615	117	14345											
KLHL1	57626	hgsc.bcm.edu	37	chr13	70370951	70370951	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtaacattcaacagtgttcaAtgtctttaagccatctcgac	12	13	6	10	1	4	0	2	0	2	0	5	1	4	0	1	0	3	2	1	0	4	5			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr13:70370951A>G	ENST00000377844.4	-	7	2317	c.1558T>C	c.(1558-1560)Ttg>Ctg	p.L520L	KLHL1_ENST00000545028.1_Silent_p.L327L	NM_020866.2	NP_065917.1	Q9NR64	KLHL1_HUMAN	kelch-like family member 1	520					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)		ACAGTGTTCAATGTCTTTAAG	0.423																																					p.L520L		Atlas-SNP	.											.	KLHL1	164	.	0			c.T1558C						PASS	.						208	177	188					13																	70370951		2203	4300	6503	SO:0001819	synonymous_variant	57626	exon7			TGTTCAATGTCTT	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.1558T>C	13.37:g.70370951A>G		209	0	0		152	69	0.453947	NM_020866	A8K5X0|Q5VZ64|Q9H4X4|Q9NR65|Q9P238	Silent	SNP	ENST00000377844.4	37	CCDS9445.1																																																																																			.	.	none		0.423	KLHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045231.3	NM_020866		G	70370951	A	G	70370951	2	3	36	1	0	0	0	0	0	0	0	1	8374	98	4	3		3	KLHL1	13	70370951	Silent	SNP	A	TCGA-GS-A9TT-01A-11D-A382-10		70370951	44798927	118	14346											
RNF113B	140432	hgsc.bcm.edu	37	chr13	98829048	98829048	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaggtagctgtggattcccCggtagatgtggtcgtgctcc	5	12	14	10	2	1	1	1	0	0	1	4	2	3	2	3	4	2	4	3	4	2	3			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr13:98829048C>T	ENST00000267291.6	-	1	471	c.443G>A	c.(442-444)cGg>cAg	p.R148Q	FARP1_ENST00000376586.2_Intron|FARP1_ENST00000595437.1_Intron|FARP1_ENST00000376581.5_Intron|FARP1_ENST00000319562.6_Intron	NM_178861.4	NP_849192.1	Q8IZP6	R113B_HUMAN	ring finger protein 113B	148							zinc ion binding (GO:0008270)	p.R148Q(1)		breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	18	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.13)			GTGGATTCCCCGGTAGATGTG	0.647																																					p.R148Q		Atlas-SNP	.											RNF113B,mouth,carcinoma,0,1	RNF113B	41	1	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.G443A						PASS	.						98	83	88					13																	98829048		2203	4300	6503	SO:0001583	missense	140432	exon1			ATTCCCCGGTAGA	AF539427	CCDS9486.1	13q32.2	2006-08-22	2005-03-22	2005-03-22	ENSG00000139797	ENSG00000139797		"RING-type (C3HC4) zinc fingers"	17267	protein-coding gene	gene with protein product			"zinc finger protein 183-like 1"	ZNF183L1			Standard	NM_178861		Approved	RNF161	uc001vnk.3	Q8IZP6	OTTHUMG00000017245	ENST00000267291.6:c.443G>A	13.37:g.98829048C>T	ENSP00000267291:p.Arg148Gln	49	0	0		59	26	0.440678	NM_178861	Q8WWF9|Q96QY9	Missense_Mutation	SNP	ENST00000267291.6	37	CCDS9486.1	.	.	.	.	.	.	.	.	.	.	C	14.65	2.597649	0.46318	.	.	ENSG00000139797	ENST00000267291	T	0.40476	1.03	1.16	1.16	0.20824	.	0.000000	0.85682	U	0.000000	T	0.48370	0.1496	M	0.83852	2.665	0.46901	D	0.999244	D	0.53151	0.958	P	0.47744	0.556	T	0.55879	-0.8071	10	0.72032	D	0.01	.	8.184	0.31328	0.0:1.0:0.0:0.0	.	148	Q8IZP6	R113B_HUMAN	Q	148	ENSP00000267291:R148Q	ENSP00000267291:R148Q	R	-	2	0	RNF113B	97627049	1.000000	0.71417	0.981000	0.43875	0.035000	0.12851	3.538000	0.53597	0.936000	0.37367	0.484000	0.47621	CGG	.	.	none		0.647	RNF113B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045536.3	NM_178861		T	98829048	C	T	98829048	3	4	36	1	0	0	0	0	1	0	0	0	13443	652	23	1	533	1	RNF113B	13	98829048	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	28458097	98829048	16340830	119	14347											
FLJ10357	55701	hgsc.bcm.edu	37	chr14	21550212	21550212	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggaacacgtgctgctgggccGggctagggggccagacggac	7	4	19	11	3	0	1	0	0	0	1	0	3	0	3	2	6	3	3	2	6	2	1	rs114591848	byFrequency	TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr14:21550212G>T	ENST00000298694.4	+	14	3312	c.3185G>T	c.(3184-3186)cGg>cTg	p.R1062L	ARHGEF40_ENST00000298693.3_Missense_Mutation_p.R1062L			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	1062						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						CTGCTGGGCCGGGCTAGGGGG	0.667																																					p.R1062L		Atlas-SNP	.											.	ARHGEF40	84	.	0			c.G3185T						PASS	.						11	11	11					14																	21550212		2177	4255	6432	SO:0001583	missense	55701	exon14			TGGGCCGGGCTAG		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.3185G>T	14.37:g.21550212G>T	ENSP00000298694:p.Arg1062Leu	41	0	0		20	16	0.8	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Missense_Mutation	SNP	ENST00000298694.4	37	CCDS32041.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.537891	0.85917	.	.	ENSG00000165801	ENST00000298694;ENST00000298693	T;T	0.02682	4.25;4.2	5.54	5.54	0.83059	.	0.000000	0.49305	D	0.000156	T	0.03959	0.0111	N	0.24115	0.695	0.39374	D	0.966145	B;B;D	0.56035	0.371;0.229;0.974	P;B;P	0.46629	0.461;0.174;0.522	T	0.51260	-0.8728	10	0.62326	D	0.03	.	14.8575	0.70351	0.0:0.0:1.0:0.0	.	1062;1062;348	Q8TER5-4;Q8TER5;Q8TER5-2	.;ARH40_HUMAN;.	L	1062	ENSP00000298694:R1062L;ENSP00000298693:R1062L	ENSP00000298693:R1062L	R	+	2	0	ARHGEF40	20620052	0.898000	0.30612	0.982000	0.44146	0.865000	0.49528	5.132000	0.64758	2.884000	0.98904	0.655000	0.94253	CGG	G|0.997;A|0.003	.	alt		0.667	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1			T	21550212	G	T	21550212	3	4	36	1	0	0	0	0	1	0	0	0	5934	1116	39	4	3239	4	FLJ10357	14	21550212	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10		21550212	85799328	120	14348											
OTX2	5015	hgsc.bcm.edu	37	chr14	57268664	57268664	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcattggtacccatgggaCtgagtgtggcccctggtccg	5	10	14	12	1	0	1	0	1	0	0	1	2	1	2	4	4	2	2	4	4	1	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr14:57268664C>G	ENST00000555006.1	-	4	1067	c.659G>C	c.(658-660)aGt>aCt	p.S220T	OTX2_ENST00000339475.5_Missense_Mutation_p.S228T|OTX2_ENST00000554788.1_3'UTR|RP11-1085N6.6_ENST00000602485.1_lincRNA|OTX2_ENST00000408990.3_Missense_Mutation_p.S220T			P32243	OTX2_HUMAN	orthodenticle homeobox 2	220					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)					ACCCATGGGACTGAGTGTGGC	0.527																																					p.S228T		Atlas-SNP	.											.	OTX2	47	.	0			c.G683C						PASS	.						128	116	120					14																	57268664		2203	4300	6503	SO:0001583	missense	5015	exon3			ATGGGACTGAGTG	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.659G>C	14.37:g.57268664C>G	ENSP00000452336:p.Ser220Thr	161	0	0		154	77	0.5	NM_001270525	B2RAN5|Q6GTV3|Q9HAW3|Q9P2R1	Missense_Mutation	SNP	ENST00000555006.1	37	CCDS41960.1	.	.	.	.	.	.	.	.	.	.	C	14.31	2.495794	0.44352	.	.	ENSG00000165588	ENST00000339475;ENST00000408990;ENST00000555006;ENST00000554845	D;D;D;D	0.88277	-2.36;-2.36;-2.36;-2.36	5.53	5.53	0.82687	Transcription factor Otx, C-terminal (1);	0.113525	0.39759	N	0.001270	D	0.94042	0.8091	M	0.80616	2.505	0.80722	D	1	B;D	0.56746	0.171;0.977	B;P	0.60886	0.364;0.88	D	0.93918	0.7203	10	0.59425	D	0.04	.	18.6325	0.91364	0.0:1.0:0.0:0.0	.	228;220	F1T0D1;P32243	.;OTX2_HUMAN	T	228;220;220;228	ENSP00000343819:S228T;ENSP00000386185:S220T;ENSP00000452336:S220T;ENSP00000451357:S228T	ENSP00000343819:S228T	S	-	2	0	OTX2	56338417	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.651000	0.83577	2.882000	0.98803	0.655000	0.94253	AGT	.	.	none		0.527	OTX2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411522.1	NM_021728.		G	57268664	C	G	57268664	3	3	36	1	0	0	0	0	1	0	0	0	11330	565	20	4	214	4	OTX2	14	57268664	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	35718452	57268664	50080876	121	14349											
SYNE2	23224	hgsc.bcm.edu	37	chr14	64593362	64593362	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttatttagcgctaagtgacaAgaagggtgatcttttgaaag	13	13	11	4	1	1	4	0	3	1	1	1	4	1	4	0	1	1	1	0	1	6	6			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr14:64593362A>G	ENST00000344113.4	+	73	13966	c.13754A>G	c.(13753-13755)aAg>aGg	p.K4585R	SYNE2_ENST00000394768.2_Missense_Mutation_p.K970R|SYNE2_ENST00000554584.1_Missense_Mutation_p.K4536R|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Missense_Mutation_p.K1219R|SYNE2_ENST00000358025.3_Missense_Mutation_p.K4585R|SYNE2_ENST00000357395.3_Missense_Mutation_p.K970R	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	4585					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)		CTAAGTGACAAGAAGGGTGAT	0.478																																					p.K4585R		Atlas-SNP	.											.	SYNE2	577	.	0			c.A13754G						PASS	.						144	142	143					14																	64593362		2203	4300	6503	SO:0001583	missense	23224	exon73			GTGACAAGAAGGG	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.13754A>G	14.37:g.64593362A>G	ENSP00000341781:p.Lys4585Arg	74	0	0		98	54	0.55102	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	A	9.978	1.227366	0.22542	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	T;T;T;T;T;T	0.65916	0.7;4.01;0.7;-0.18;4.06;4.01	5.87	4.62	0.57501	.	0.111585	0.38720	N	0.001585	T	0.64461	0.2600	L	0.32530	0.975	0.80722	D	1	D;D;P	0.60575	0.988;0.962;0.617	P;P;B	0.61201	0.885;0.767;0.221	T	0.62058	-0.6934	10	0.39692	T	0.17	.	10.0189	0.42031	0.903:0.0:0.097:0.0	.	970;4585;4585	Q8WXH0-7;Q8WXH0;Q8WXH0-2	.;SYNE2_HUMAN;.	R	4585;970;4585;4536;4536;1219;970	ENSP00000350719:K4585R;ENSP00000349969:K970R;ENSP00000341781:K4585R;ENSP00000452570:K4536R;ENSP00000450831:K1219R;ENSP00000378249:K970R	ENSP00000261678:K4536R	K	+	2	0	SYNE2	63663115	1.000000	0.71417	1.000000	0.80357	0.217000	0.24651	2.708000	0.47152	0.909000	0.36697	0.533000	0.62120	AAG	.	.	none		0.478	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914		G	64593362	A	G	64593362	3	3	36	1	0	0	0	0	1	0	0	0	15461	72	3	3	14040	3	SYNE2	14	64593362	Missense_Mutation	SNP	A	TCGA-GS-A9TT-01A-11D-A382-10	7324698	64593362	42756178	122	14350											
ESR2	2100	hgsc.bcm.edu	37	chr14	64749642	64749642	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cgtgctccaggggtaagatgGattgactgcagttgtaggag	9	10	16	6	1	0	2	0	1	0	1	1	4	1	4	1	4	2	5	1	4	2	4			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr14:64749642G>A	ENST00000341099.4	-	2	479	c.62C>T	c.(61-63)tCc>tTc	p.S21F	ESR2_ENST00000555483.1_5'Flank|ESR2_ENST00000353772.3_Missense_Mutation_p.S21F|ESR2_ENST00000554572.1_Missense_Mutation_p.S21F|ESR2_ENST00000555278.1_Missense_Mutation_p.S21F|ESR2_ENST00000542956.1_Missense_Mutation_p.S21F|ESR2_ENST00000557772.1_Missense_Mutation_p.S21F|ESR2_ENST00000267525.6_Missense_Mutation_p.S21F|ESR2_ENST00000358599.5_Missense_Mutation_p.S21F|ESR2_ENST00000357782.2_Missense_Mutation_p.S21F|ESR2_ENST00000553796.1_Missense_Mutation_p.S21F	NM_001437.2	NP_001428.1	Q92731	ESR2_HUMAN	estrogen receptor 2 (ER beta)	21	Modulating.				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)	GGGTAAGATGGATTGACTGCA	0.443																																					p.S21F		Atlas-SNP	.											.	ESR2	82	.	0			c.C62T						PASS	.						138	133	135					14																	64749642		2203	4300	6503	SO:0001583	missense	2100	exon1			AAGATGGATTGAC	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.62C>T	14.37:g.64749642G>A	ENSP00000343925:p.Ser21Phe	145	0	0		145	74	0.510345	NM_001214902	A8K8K5|G3V5M5|O60608|O60685|O60702|O60703|O75583|O75584|Q0MWT5|Q0MWT6|Q86Z31|Q9UEV6|Q9UHD3|Q9UQK9	Missense_Mutation	SNP	ENST00000341099.4	37	CCDS9762.1	.	.	.	.	.	.	.	.	.	.	G	12.86	2.065179	0.36470	.	.	ENSG00000140009	ENST00000556275;ENST00000542956;ENST00000554572;ENST00000353772;ENST00000358599;ENST00000555278;ENST00000553796;ENST00000357782;ENST00000557772;ENST00000341099;ENST00000267525	D;D;D;D;D;D;D;D;D;D;D	0.91894	-2.9;-2.89;-2.85;-2.85;-2.85;-2.93;-2.91;-2.93;-2.91;-2.76;-2.46	5.56	5.56	0.83823	Estrogen receptor beta, N-terminal (1);	0.421595	0.25701	N	0.028864	D	0.95316	0.8480	M	0.64997	1.995	0.09310	N	1	D;D;D;D;D	0.89917	0.998;1.0;0.999;0.999;0.999	D;D;D;D;D	0.91635	0.994;0.999;0.996;0.996;0.998	D	0.90007	0.4118	10	0.48119	T	0.1	.	17.708	0.88314	0.0:0.0:1.0:0.0	.	21;21;21;21;21	Q92731-7;Q92731;Q92731-6;Q92731-5;F1D8N3	.;ESR2_HUMAN;.;.;.	F	21	ENSP00000452485:S21F;ENSP00000441792:S21F;ENSP00000450699:S21F;ENSP00000335551:S21F;ENSP00000351412:S21F;ENSP00000450488:S21F;ENSP00000452426:S21F;ENSP00000350427:S21F;ENSP00000451582:S21F;ENSP00000343925:S21F;ENSP00000267525:S21F	ENSP00000267525:S21F	S	-	2	0	ESR2	63819395	0.923000	0.31300	0.019000	0.16419	0.047000	0.14425	5.705000	0.68355	2.616000	0.88540	0.563000	0.77884	TCC	.	.	none		0.443	ESR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280621.1			A	64749642	G	A	64749642	3	1	36	1	0	0	0	0	1	0	0	0	5259	1174	41	2	1648	2	ESR2	14	64749642	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	156280	64749642	42599898	123	14351											
NIPA2	81614	hgsc.bcm.edu	37	chr15	23006258	23006258	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttccatttcttcgggagacaTtttcaccagtgtgttgttcg	6	17	9	9	2	2	1	1	0	1	1	5	2	3	1	2	1	0	2	2	1	0	7			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr15:23006258T>C	ENST00000337451.3	-	8	1658	c.1046A>G	c.(1045-1047)aAt>aGt	p.N349S	NIPA2_ENST00000398013.3_Missense_Mutation_p.N349S|NIPA2_ENST00000398014.2_Missense_Mutation_p.N349S|NIPA2_ENST00000539711.2_Missense_Mutation_p.N330S|NIPA2_ENST00000359727.4_Missense_Mutation_p.N330S	NM_030922.6	NP_112184.4	Q8N8Q9	NIPA2_HUMAN	non imprinted in Prader-Willi/Angelman syndrome 2	349						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)		TCGGGAGACATTTTCACCAGT	0.333																																					p.N349S		Atlas-SNP	.											.	NIPA2	49	.	0			c.A1046G						PASS	.						67	69	69					15																	23006258		2203	4299	6502	SO:0001583	missense	81614	exon10			GAGACATTTTCAC	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.1046A>G	15.37:g.23006258T>C	ENSP00000337618:p.Asn349Ser	78	0	0		75	28	0.373333	NM_001184889	F8W7Y8|Q96F03|Q9BVS2	Missense_Mutation	SNP	ENST00000337451.3	37	CCDS10010.1	.	.	.	.	.	.	.	.	.	.	T	4.537	0.099732	0.08681	.	.	ENSG00000140157	ENST00000337451;ENST00000398014;ENST00000359727;ENST00000539711;ENST00000398013	D;D;D	0.89343	-2.5;-2.5;-2.5	5.76	3.47	0.39725	.	0.270973	0.41712	D	0.000834	T	0.69842	0.3156	N	0.08118	0	0.23138	N	0.998235	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.56420	-0.7982	10	0.02654	T	1	-7.2012	4.7	0.12822	0.0:0.2748:0.1546:0.5706	.	330;349	F8W7Y8;Q8N8Q9	.;NIPA2_HUMAN	S	349;349;330;349;330	ENSP00000337618:N349S;ENSP00000381096:N349S;ENSP00000352762:N330S	ENSP00000337618:N349S	N	-	2	0	NIPA2	20557699	0.849000	0.29639	0.375000	0.26029	0.637000	0.38172	1.381000	0.34362	0.537000	0.28751	-0.274000	0.10170	AAT	.	.	none		0.333	NIPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251137.1	NM_030922		C	23006258	T	C	23006258	3	2	36	1	0	0	0	0	1	0	0	0	10432	1493	52	3	40	3	NIPA2	15	23006258	Missense_Mutation	SNP	T	TCGA-GS-A9TT-01A-11D-A382-10		23006258	79525134	124	14352											
DUOX1	53905	hgsc.bcm.edu	37	chr15	45439820	45439820	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaatggctacctgtccttcCgagagttcctggacatcctg	7	11	10	13	1	0	1	0	0	0	1	4	3	4	2	5	2	1	3	5	2	2	3	rs143543011		TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr15:45439820C>T	ENST00000321429.4	+	20	2919	c.2512C>T	c.(2512-2514)Cga>Tga	p.R838*	DUOX1_ENST00000389037.3_Nonsense_Mutation_p.R838*|DUOX1_ENST00000561166.1_Nonsense_Mutation_p.R484*	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	838	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				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)		CCTGTCCTTCCGAGAGTTCCT	0.572																																					p.R838X		Atlas-SNP	.											.	DUOX1	125	.	0			c.C2512T						PASS	.	C	stop/ARG,stop/ARG	0,4396		0,0,2198	57	51	53		2512,2512	4.4	1	15	dbSNP_134	53	1,8593	1.2+/-3.3	0,1,4296	no	stop-gained,stop-gained	DUOX1	NM_017434.3,NM_175940.1	,	0,1,6494	TT,TC,CC		0.0116,0.0,0.0077	,	838/1552,838/1552	45439820	1,12989	2198	4297	6495	SO:0001587	stop_gained	53905	exon20			TCCTTCCGAGAGT	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.2512C>T	15.37:g.45439820C>T	ENSP00000317997:p.Arg838*	92	0	0		98	14	0.142857	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Nonsense_Mutation	SNP	ENST00000321429.4	37	CCDS32221.1	.	.	.	.	.	.	.	.	.	.	C	42	9.282840	0.99123	0.0	1.16E-4	ENSG00000137857	ENST00000431588;ENST00000321429;ENST00000389037	.	.	.	5.29	4.38	0.52667	.	0.119039	0.64402	D	0.000012	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-24.5202	6.7146	0.23296	0.175:0.7368:0.0:0.0882	.	.	.	.	X	838	.	ENSP00000317997:R838X	R	+	1	2	DUOX1	43227112	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	1.797000	0.38804	1.465000	0.48006	0.655000	0.94253	CGA	C|1.000;T|0.000	0.000	weak		0.572	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434		T	45439820	C	T	45439820	4	4	36	1	0	0	0	0	0	1	0	0	4802	644	23	1	2582	1	DUOX1	15	45439820	Nonsense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	22433562	45439820	57091572	125	14353											
SLC12A1	6557	hgsc.bcm.edu	37	chr15	48500287	48500287	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	caccggcagcatcagtgggcCcaaggtcaaccgacccagcc	10	3	11	17	2	2	0	2	0	0	0	2	1	2	0	5	3	3	2	5	3	2	0			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr15:48500287C>A	ENST00000558405.1	+	1	385	c.371C>A	c.(370-372)cCc>cAc	p.P124H	SLC12A1_ENST00000380993.3_Missense_Mutation_p.P124H|SLC12A1_ENST00000330289.6_Missense_Mutation_p.P124H|SLC12A1_ENST00000396577.3_Missense_Mutation_p.P124H|SLC12A1_ENST00000561031.1_Missense_Mutation_p.P124H			Q13621	S12A1_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 1	124					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)	ATCAGTGGGCCCAAGGTCAAC	0.478																																					p.P124H		Atlas-SNP	.											SLC12A1,NS,carcinoma,0,1	SLC12A1	243	1	0			c.C371A						PASS	.						89	85	86					15																	48500287		2198	4297	6495	SO:0001583	missense	6557	exon2			GTGGGCCCAAGGT		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.371C>A	15.37:g.48500287C>A	ENSP00000453409:p.Pro124His	47	0	0		46	40	0.869565	NM_001184832	A8JYA2|E9PDW4	Missense_Mutation	SNP	ENST00000558405.1	37	CCDS10129.2	.	.	.	.	.	.	.	.	.	.	C	12.73	2.024341	0.35701	.	.	ENSG00000074803	ENST00000380993;ENST00000396577;ENST00000330289	D;D;D	0.95756	-3.8;-3.8;-3.8	5.58	5.58	0.84498	Amino acid permease, N-terminal (1);	0.450963	0.26019	N	0.026831	D	0.86514	0.5951	N	0.02539	-0.55	0.32795	N	0.50066	P;B	0.39071	0.658;0.0	B;B	0.41894	0.369;0.003	D	0.86476	0.1788	10	0.39692	T	0.17	.	5.6925	0.17837	0.1763:0.6718:0.0:0.1519	.	124;124	Q8IUN5;Q13621	.;S12A1_HUMAN	H	124	ENSP00000370381:P124H;ENSP00000379822:P124H;ENSP00000331550:P124H	ENSP00000331550:P124H	P	+	2	0	SLC12A1	46287579	0.988000	0.35896	1.000000	0.80357	0.939000	0.58152	1.453000	0.35167	2.624000	0.88883	0.655000	0.94253	CCC	.	.	none		0.478	SLC12A1-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417131.1			A	48500287	C	A	48500287	3	1	36	1	0	0	0	0	1	0	0	0	14397	623	22	4	373	4	SLC12A1	15	48500287	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	3060467	48500287	54031105	126	14354											
KBTBD13	390594	hgsc.bcm.edu	37	chr15	65370255	65370255	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgacgacttcctgcactgcGccatcgactgtctcaacctg	7	9	8	17	4	1	0	1	0	1	0	4	3	2	0	4	0	3	1	4	0	1	1			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr15:65370255G>A	ENST00000432196.2	+	1	1102	c.1102G>A	c.(1102-1104)Gcc>Acc	p.A368T	RASL12_ENST00000434605.2_5'Flank	NM_001101362.2	NP_001094832.1	C9JR72	KBTBD_HUMAN	kelch repeat and BTB (POZ) domain containing 13	368					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)				lung(1)|prostate(1)|skin(1)	3						CCTGCACTGCGCCATCGACTG	0.672																																					p.A368T		Atlas-SNP	.											.	KBTBD13	9	.	0			c.G1102A						PASS	.						25	26	26					15																	65370255		1921	3918	5839	SO:0001583	missense	390594	exon1			CACTGCGCCATCG		CCDS45281.1	15q22.31	2014-09-17			ENSG00000234438	ENSG00000234438		"BTB/POZ domain containing"	37227	protein-coding gene	gene with protein product	"nemaline myopathy type 6"	613727				21109227, 22542517	Standard	NM_001101362		Approved	hCG_1645727, NEM6	uc010uis.2	C9JR72		ENST00000432196.2:c.1102G>A	15.37:g.65370255G>A	ENSP00000388723:p.Ala368Thr	62	0	0		90	30	0.333333	NM_001101362		Missense_Mutation	SNP	ENST00000432196.2	37	CCDS45281.1	.	.	.	.	.	.	.	.	.	.	G	6.881	0.532018	0.13127	.	.	ENSG00000234438	ENST00000432196	T	0.64991	-0.13	4.98	4.0	0.46444	Kelch-type beta propeller (1);	.	.	.	.	T	0.44767	0.1309	N	0.25647	0.755	0.26618	N	0.972717	B	0.13594	0.008	B	0.08055	0.003	T	0.17167	-1.0378	9	0.21540	T	0.41	.	7.5467	0.27770	0.0841:0.0:0.75:0.1659	.	368	C9JR72	KBTBD_HUMAN	T	368	ENSP00000388723:A368T	ENSP00000388723:A368T	A	+	1	0	KBTBD13	63157308	0.871000	0.30034	0.982000	0.44146	0.815000	0.46073	1.333000	0.33816	2.307000	0.77673	0.561000	0.74099	GCC	.	.	none		0.672	KBTBD13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418468.2	NM_001101362		A	65370255	G	A	65370255	3	1	36	1	0	0	0	0	1	0	0	0	8001	1087	38	1	1104	1	KBTBD13	15	65370255	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	16869968	65370255	37161137	127	14355											
LMF1	64788	hgsc.bcm.edu	37	chr16	919924	919924	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagccagtccaggcggtagtGgtacggggagatgaggcagg	9	5	19	8	2	0	2	0	1	0	1	1	3	1	2	2	7	2	3	2	7	2	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr16:919924G>A	ENST00000262301.11	-	9	1393	c.1375C>T	c.(1375-1377)Cac>Tac	p.H459Y	LMF1_ENST00000568897.1_Missense_Mutation_p.H242Y|LMF1_ENST00000399843.2_Missense_Mutation_p.H459Y|LMF1_ENST00000543238.1_Missense_Mutation_p.H222Y|LMF1_ENST00000568268.1_5'Flank	NM_022773.2	NP_073610.2	Q96S06	LMF1_HUMAN	lipase maturation factor 1	459					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)				AGGCGGTAGTGGTACGGGGAG	0.667																																					p.H459Y		Atlas-SNP	.											.	LMF1	42	.	0			c.C1375T						PASS	.						48	60	56					16																	919924		2134	4222	6356	SO:0001583	missense	64788	exon9			GGTAGTGGTACGG	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.1375C>T	16.37:g.919924G>A	ENSP00000262301:p.His459Tyr	82	0	0		67	37	0.552239	NM_022773	Q68CJ3|Q96FJ4|Q9H6G4|Q9H9K7	Missense_Mutation	SNP	ENST00000262301.11	37	CCDS45373.1	.	.	.	.	.	.	.	.	.	.	G	16.79	3.219622	0.58560	.	.	ENSG00000103227	ENST00000262301;ENST00000399843;ENST00000540070;ENST00000545827;ENST00000543238	T;T;T	0.25579	1.79;1.79;1.79	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.48370	0.1496	M	0.78285	2.405	0.80722	D	1	P	0.46859	0.885	P	0.55222	0.771	T	0.53012	-0.8498	10	0.87932	D	0	-7.2329	17.1986	0.86900	0.0:0.0:1.0:0.0	.	459	Q96S06	LMF1_HUMAN	Y	459;459;242;213;222	ENSP00000262301:H459Y;ENSP00000382737:H459Y;ENSP00000437418:H222Y	ENSP00000262301:H459Y	H	-	1	0	LMF1	859925	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	9.661000	0.98601	2.406000	0.81754	0.561000	0.74099	CAC	.	.	none		0.667	LMF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109071.3	NM_022773		A	919924	G	A	919924	3	1	36	1	0	0	0	0	1	0	0	0	8854	1348	47	2	340	2	LMF1	16	919924	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10		919924	89434829	128	14356											
CIITA	4261	hgsc.bcm.edu	37	chr16	11000690	11000691	+	Frame_Shift_Del	DEL	TG	TG	-																															cggcttccccagtacgacttTgtcttctctgtcccctgcca																										TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr16:11000690_11000691delTG	ENST00000324288.8	+	11	1474_1475	c.1341_1342delTG	c.(1339-1344)tttgtcfs	p.V448fs	CIITA_ENST00000537380.1_Intron|CIITA_ENST00000381835.5_Intron	NM_000246.3	NP_000237	P33076	C2TA_HUMAN	class II, major histocompatibility complex, transactivator	448	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						AGTACGACTTTGTCTTCTCTGT	0.634			T	"FLJ27352, CD274, CD273, RALGDS, RUNDC2A, C16orf75, BCL6"	"PMBL, Hodgkin Lymphona, "																																p.447_447del		Pindel,Atlas-Indel	.		Dom	yes		16	16p13	4261	"class II, major histocompatibility complex, transactivator"		L	.	CIITA	92	.	0			c.1340_1341del						PASS	.																																			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.1341_1342delTG	16.37:g.11000690_11000691delTG	ENSP00000316328:p.Val448fs	67	0	.		73	24	0.329	NM_000246	A0N0N9|D3DUG0|E9PFE0|Q29675|Q8SNB8|Q96KL4	Frame_Shift_Del	DEL	ENST00000324288.8	37	CCDS10544.1																																																																																			.	.	none		0.634	CIITA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251966.2	NM_000246		-	11000691	TG	-	11000690	7	5	36	1	0	1	0	1	0	0	0	0	3430	1809	63	0	1383	0	CIITA	16	11000690	Frame_Shift_Del	DEL	TG	TCGA-GS-A9TT-01A-11D-A382-10	10080766	11000690	79354063	129	14357											
TAOK2	9344	hgsc.bcm.edu	37	chr16	29996996	29996996	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caggagctccaggagaacccCagcactcccaagcgggagaa	13	2	12	14	1	0	2	0	0	0	2	2	5	2	3	4	3	4	2	4	3	3	0			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr16:29996996C>T	ENST00000308893.4	+	15	2849	c.1806C>T	c.(1804-1806)ccC>ccT	p.P602P	TAOK2_ENST00000279394.3_Silent_p.P602P|TAOK2_ENST00000416441.2_Silent_p.P429P|TAOK2_ENST00000543033.1_Silent_p.P602P	NM_001252043.1|NM_016151.3	NP_001238972.1|NP_057235.2	Q9UL54	TAOK2_HUMAN	TAO kinase 2	602					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						AGGAGAACCCCAGCACTCCCA	0.697																																					p.P602P		Atlas-SNP	.											TAOK2_ENST00000308893,NS,carcinoma,+2,2	TAOK2	142	2	0			c.C1806T						PASS	.						15	15	15					16																	29996996		2193	4294	6487	SO:0001819	synonymous_variant	9344	exon15			GAACCCCAGCACT	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.1806C>T	16.37:g.29996996C>T		43	0	0		27	14	0.518519	NM_004783	A5PKY1|A7MCZ2|B2RN35|B7ZM88|O94957|Q6UW73|Q7LC09|Q9NSW2	Silent	SNP	ENST00000308893.4	37	CCDS10663.1																																																																																			.	.	none		0.697	TAOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255152.2	NM_016151		T	29996996	C	T	29996996	2	4	36	1	0	0	0	0	0	0	0	1	15563	581	21	2		2	TAOK2	16	29996996	Silent	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	18996306	29996996	60357757	130	14358											
PLCG2	5336	hgsc.bcm.edu	37	chr16	81819709	81819709	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcttccgcaagtccacccccGagcggagaaccgtccaggtg	8	5	12	16	4	0	1	0	0	0	1	3	3	3	1	6	2	2	2	6	2	2	1			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr16:81819709G>A	ENST00000359376.3	+	2	329	c.115G>A	c.(115-117)Gag>Aag	p.E39K		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	39	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						GTCCACCCCCGAGCGGAGAAC	0.592																																					p.E39K		Atlas-SNP	.											.	PLCG2	276	.	0			c.G115A						PASS	.						56	63	61					16																	81819709		2048	4182	6230	SO:0001583	missense	5336	exon2			ACCCCCGAGCGGA		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.115G>A	16.37:g.81819709G>A	ENSP00000352336:p.Glu39Lys	61	0	0		59	29	0.491525	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	37	CCDS42204.1	.	.	.	.	.	.	.	.	.	.	G	35	5.583922	0.96578	.	.	ENSG00000197943	ENST00000359376	T	0.58797	0.31	5.14	5.14	0.70334	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.054632	0.64402	D	0.000001	T	0.68091	0.2963	M	0.79693	2.465	0.80722	D	1	D	0.62365	0.991	P	0.47402	0.546	T	0.75494	-0.3298	10	0.66056	D	0.02	.	18.5992	0.91242	0.0:0.0:1.0:0.0	.	39	P16885	PLCG2_HUMAN	K	39	ENSP00000352336:E39K	ENSP00000352336:E39K	E	+	1	0	PLCG2	80377210	1.000000	0.71417	0.989000	0.46669	0.993000	0.82548	9.443000	0.97568	2.388000	0.81334	0.655000	0.94253	GAG	.	.	none		0.592	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1			A	81819709	G	A	81819709	3	1	36	1	0	0	0	0	1	0	0	0	12045	1059	37	1	117	1	PLCG2	16	81819709	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	51822713	81819709	8535044	131	14359											
ANKRD11	29123	hgsc.bcm.edu	37	chr16	89348402	89348402	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggccctcgtccctggacttGtctttgagcacgcggggcgg	3	9	16	13	4	1	1	0	1	1	0	3	2	2	2	2	5	1	1	2	5	0	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr16:89348402G>A	ENST00000301030.4	-	9	5008	c.4548C>T	c.(4546-4548)gaC>gaT	p.D1516D	ANKRD11_ENST00000378330.2_Silent_p.D1516D	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	1516	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)		CCCTGGACTTGTCTTTGAGCA	0.622																																					p.D1516D		Atlas-SNP	.											.	ANKRD11	195	.	0			c.C4548T						PASS	.						71	68	69					16																	89348402		2198	4300	6498	SO:0001819	synonymous_variant	29123	exon9			GGACTTGTCTTTG	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.4548C>T	16.37:g.89348402G>A		132	0	0		156	58	0.371795	NM_001256183	Q6NTG1|Q6QMF8	Silent	SNP	ENST00000301030.4	37	CCDS32513.1																																																																																			.	.	none		0.622	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		A	89348402	G	A	89348402	2	1	36	1	0	0	0	0	0	0	0	1	639	1368	48	2		2	ANKRD11	16	89348402	Silent	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	7528693	89348402	1006351	132	14360											
TEKT1	83659	hgsc.bcm.edu	37	chr17	6719262	6719262	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgtgtcgtgcaccaggtCaatgccaatgcgcttctccc	7	10	9	15	2	2	0	1	0	1	0	4	0	2	0	3	1	3	2	3	1	2	1			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr17:6719262C>A	ENST00000338694.2	-	4	505	c.376G>T	c.(376-378)Gac>Tac	p.D126Y	TEKT1_ENST00000535086.1_5'UTR	NM_053285.1	NP_444515.1	Q969V4	TEKT1_HUMAN	tektin 1	126						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)				TGCACCAGGTCAATGCCAATG	0.557																																					p.D126Y		Atlas-SNP	.											.	TEKT1	49	.	0			c.G376T						PASS	.						148	93	112					17																	6719262		2203	4300	6503	SO:0001583	missense	83659	exon4			CCAGGTCAATGCC		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.376G>T	17.37:g.6719262C>A	ENSP00000341346:p.Asp126Tyr	69	0	0		32	16	0.5	NM_053285	D3DTM7	Missense_Mutation	SNP	ENST00000338694.2	37	CCDS11083.1	.	.	.	.	.	.	.	.	.	.	C	15.75	2.924476	0.52653	.	.	ENSG00000167858	ENST00000338694	T	0.05513	3.43	5.04	5.04	0.67666	.	0.048168	0.85682	D	0.000000	T	0.35393	0.0930	M	0.93720	3.45	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.47661	-0.9100	10	0.87932	D	0	.	16.2605	0.82541	0.0:1.0:0.0:0.0	.	126	Q969V4	TEKT1_HUMAN	Y	126	ENSP00000341346:D126Y	ENSP00000341346:D126Y	D	-	1	0	TEKT1	6659986	1.000000	0.71417	0.971000	0.41717	0.127000	0.20565	6.303000	0.72794	2.535000	0.85469	0.655000	0.94253	GAC	.	.	none		0.557	TEKT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219867.2	NM_053285		A	6719262	C	A	6719262	3	1	36	1	0	0	0	0	1	0	0	0	15767	826	29	4	900	4	TEKT1	17	6719262	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10		6719262	74475948	133	14361											
MYH2	4620	hgsc.bcm.edu	37	chr17	10430004	10430004	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcggtgttggccttggacaGtgctctctgcagctcggcct	3	12	13	13	2	1	0	0	0	1	0	4	1	1	1	2	4	3	4	2	4	0	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr17:10430004G>A	ENST00000245503.5	-	30	4483	c.4099C>T	c.(4099-4101)Ctg>Ttg	p.L1367L	RP11-799N11.1_ENST00000399342.2_RNA|MYH2_ENST00000397183.2_Silent_p.L1367L|RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|MYH2_ENST00000532183.2_Intron	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	1367					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						GCCTTGGACAGTGCTCTCTGC	0.617																																					p.L1367L		Atlas-SNP	.											.	MYH2	390	.	0			c.C4099T						PASS	.						185	168	174					17																	10430004		2203	4300	6503	SO:0001819	synonymous_variant	4620	exon30			TGGACAGTGCTCT		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.4099C>T	17.37:g.10430004G>A		215	0	0		179	76	0.424581	NM_017534	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Silent	SNP	ENST00000245503.5	37	CCDS11156.1																																																																																			.	.	none		0.617	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534		A	10430004	G	A	10430004	2	1	36	1	0	0	0	0	0	0	0	1	10044	1020	36	2		2	MYH2	17	10430004	Silent	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	3710742	10430004	70765206	134	14362											
VAT1	8153	hgsc.bcm.edu	37	chr17	41174312	41174312	+	5'Flank	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggcgtcttccccggtcgctgCctcggctacctctctctcgt	1	12	10	18	5	3	0	0	0	3	0	8	0	4	0	4	3	2	2	4	3	1	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr17:41174312C>T	ENST00000587250.2	+	0	0				RND2_ENST00000544533.1_5'Flank|VAT1_ENST00000587173.1_Missense_Mutation_p.A10T|VAT1_ENST00000420567.3_5'Flank|VAT1_ENST00000355653.3_Missense_Mutation_p.A10T			P52198	RND2_HUMAN	Rho family GTPase 2						GTP catabolic process (GO:0006184)|positive regulation of collateral sprouting (GO:0048672)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			large_intestine(1)|skin(1)	2		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.156)		CCGGTCGCTGCCTCGGCTACC	0.711																																					p.A10T		Atlas-SNP	.											.	VAT1	19	.	0			c.G28A						PASS	.						5	5	5					17																	41174312		1687	3256	4943	SO:0001631	upstream_gene_variant	10493	exon1			TCGCTGCCTCGGC	X95456	CCDS11452.1	17q21.31	2012-10-02	2005-01-24	2005-01-24	ENSG00000108830	ENSG00000108830			18315	protein-coding gene	gene with protein product		601555	"ras homolog gene family, member N"	ARHN			Standard	XM_005257706		Approved	Rho7, RhoN	uc002icn.3	P52198	OTTHUMG00000180817		17.37:g.41174312C>T	Exception_encountered	27	0	0		23	15	0.652174	NM_006373	A8K2D4|O00690|O00734|Q5U0P6|Q99535	Missense_Mutation	SNP	ENST00000587250.2	37	CCDS11452.1	.	.	.	.	.	.	.	.	.	.	C	10.52	1.372722	0.24857	.	.	ENSG00000108828	ENST00000355653;ENST00000315674	T	0.56103	0.48	3.74	3.74	0.42951	.	1.527300	0.03644	N	0.240005	T	0.35038	0.0918	N	0.08118	0	0.80722	D	1	B;B	0.33694	0.421;0.421	B;B	0.22386	0.039;0.039	T	0.04495	-1.0947	10	0.27082	T	0.32	.	14.4573	0.67425	0.0:1.0:0.0:0.0	.	10;10	B4DPX4;Q99536	.;VAT1_HUMAN	T	10	ENSP00000347872:A10T	ENSP00000326121:A10T	A	-	1	0	VAT1	38427838	0.993000	0.37304	0.963000	0.40424	0.142000	0.21351	1.476000	0.35420	1.913000	0.55393	0.555000	0.69702	GCA	.	.	none		0.711	RND2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453111.2	NM_005440		T	41174312	C	T	41174312	1	4	36	0	1	0	0	0	0	0	0	0	17144	739	26	2		2	VAT1	17	41174312	5'Flank	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	30744308	41174312	40020898	135	14363											
C17orf104	284071	hgsc.bcm.edu	37	chr17	42751550	42751550	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caatgaaccagagaggtgaaAcaaacaaacattaaggaaat	22	5	8	6	0	0	3	0	2	0	1	0	5	0	4	1	2	4	0	1	2	7	1			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr17:42751550A>G	ENST00000409122.2	+	8	2987	c.2845A>G	c.(2845-2847)Aca>Gca	p.T949A	RP11-1072C15.4_ENST00000591628.1_RNA	NM_001145080.2	NP_001138552.2	A2RUB1	CQ104_HUMAN	chromosome 17 open reading frame 104	949										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						GAGAGGTGAAACAAACAAACA	0.328																																					p.T949A		Atlas-SNP	.											.	C17orf104	75	.	0			c.A2845G						PASS	.						87	67	73					17																	42751550		692	1591	2283	SO:0001583	missense	284071	exon8			GGTGAAACAAACA		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.2845A>G	17.37:g.42751550A>G	ENSP00000386452:p.Thr949Ala	75	0	0		72	31	0.430556	NM_001145080	B4DXJ2|B5MD93|B9EGQ6|C4AM97|Q4G0Y1|Q8IVZ7|Q8NA45	Missense_Mutation	SNP	ENST00000409122.2	37	CCDS45703.2	.	.	.	.	.	.	.	.	.	.	A	0.210	-1.037054	0.02013	.	.	ENSG00000180336	ENST00000409122	T	0.29655	1.56	5.96	2.35	0.29111	.	.	.	.	.	T	0.16300	0.0392	N	0.22421	0.69	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.07966	-1.0745	9	0.25106	T	0.35	-11.6212	4.1762	0.10353	0.3833:0.0:0.4451:0.1716	.	949	A2RUB1	CQ104_HUMAN	A	949	ENSP00000386452:T949A	ENSP00000386452:T949A	T	+	1	0	C17orf104	40107076	0.371000	0.25056	1.000000	0.80357	0.990000	0.78478	0.306000	0.19279	0.714000	0.32081	-0.250000	0.11733	ACA	.	.	none		0.328	C17orf104-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329171.2	NM_001145080		G	42751550	A	G	42751550	3	3	36	1	0	0	0	0	1	0	0	0	1853	43	2	3	2875	3	C17orf104	17	42751550	Missense_Mutation	SNP	A	TCGA-GS-A9TT-01A-11D-A382-10	1577238	42751550	38443660	136	14364											
TOM1L1	10040	hgsc.bcm.edu	37	chr17	53007452	53007452	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaaactctataaaacaggtCgggagatgcaggagaggatc	16	6	13	6	1	1	3	0	0	1	3	3	6	1	4	0	4	3	1	0	4	4	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr17:53007452C>A	ENST00000575882.1	+	8	1092	c.739C>A	c.(739-741)Cgg>Agg	p.R247R	TOM1L1_ENST00000540336.1_Silent_p.R135R|TOM1L1_ENST00000572158.1_Silent_p.R240R|TOM1L1_ENST00000570371.1_Silent_p.R247R|TOM1L1_ENST00000575333.1_Silent_p.R247R|TOM1L1_ENST00000348161.4_Silent_p.R170R|TOM1L1_ENST00000536554.1_Silent_p.R170R|TOM1L1_ENST00000445275.2_Silent_p.R247R	NM_005486.2	NP_005477.2	O75674	TM1L1_HUMAN	target of myb1 (chicken)-like 1	247	GAT. {ECO:0000255|PROSITE- ProRule:PRU00373}.				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						TAAAACAGGTCGGGAGATGCA	0.423																																					p.R247R		Atlas-SNP	.											TOM1L1,caecum,carcinoma,-1,1	TOM1L1	33	1	0			c.C739A						scavenged	.						165	152	157					17																	53007452		2203	4300	6503	SO:0001819	synonymous_variant	10040	exon8			ACAGGTCGGGAGA	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.739C>A	17.37:g.53007452C>A		103	1	0.00970874		103	41	0.398058	NM_005486	Q53G06|Q8N749	Silent	SNP	ENST00000575882.1	37	CCDS11582.1																																																																																			.	.	none		0.423	TOM1L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439029.2	NM_005486		A	53007452	C	A	53007452	2	1	36	1	0	0	0	0	0	0	0	1	16367	875	31	4		4	TOM1L1	17	53007452	Silent	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	10255902	53007452	28187758	137	14365											
TMEM49	81671	hgsc.bcm.edu	37	chr17	57915672	57915672	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccagtgctgtccccggcataGgtccatctctgcagaagcca	8	8	10	15	1	1	1	0	0	1	1	4	1	3	1	5	2	3	3	5	2	2	1			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr17:57915672G>A	ENST00000262291.4	+	11	1301	c.991G>A	c.(991-993)Ggt>Agt	p.G331S	VMP1_ENST00000545362.1_Missense_Mutation_p.G275S|VMP1_ENST00000536180.1_Missense_Mutation_p.G234S|MIR21_ENST00000362134.1_RNA|VMP1_ENST00000539763.1_Missense_Mutation_p.G139S|VMP1_ENST00000588617.1_Splice_Site|VMP1_ENST00000537567.1_Missense_Mutation_p.G197S	NM_030938.3	NP_112200.2	Q96GC9	VMP1_HUMAN	vacuole membrane protein 1	331					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						CCCCGGCATAGGTCCATCTCT	0.468																																					p.G331S		Atlas-SNP	.											.	VMP1	49	.	0			c.G991A						PASS	.						83	80	81					17																	57915672		2203	4300	6503	SO:0001583	missense	81671	exon11			GGCATAGGTCCAT		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.991G>A	17.37:g.57915672G>A	ENSP00000262291:p.Gly331Ser	211	1	0.00473934		231	114	0.493506	NM_030938	B4DVV9|Q9H0P4|Q9P089	Missense_Mutation	SNP	ENST00000262291.4	37	CCDS11619.1	.	.	.	.	.	.	.	.	.	.	G	34	5.348786	0.95807	.	.	ENSG00000062716	ENST00000262291;ENST00000537567;ENST00000539763;ENST00000536180;ENST00000545362	.	.	.	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.73923	0.3649	L	0.56124	1.755	0.80722	D	1	P;P;P;D	0.56287	0.895;0.805;0.93;0.975	P;B;P;P	0.60173	0.839;0.333;0.54;0.87	T	0.67440	-0.5670	9	0.29301	T	0.29	-2.9829	20.422	0.99049	0.0:0.0:1.0:0.0	.	197;234;275;331	B4DED7;B4DGZ7;F5H2J3;Q96GC9	.;.;.;VMP1_HUMAN	S	331;197;139;234;275	.	ENSP00000262291:G331S	G	+	1	0	VMP1	55270454	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.624000	0.98398	2.832000	0.97577	0.655000	0.94253	GGT	.	.	none		0.468	VMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448793.1	NM_030938		A	57915672	G	A	57915672	3	1	36	1	0	0	0	0	1	0	0	0	16188	1000	35	2	1029	2	TMEM49	17	57915672	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	4908220	57915672	23279538	138	14366											
ACTG1	71	hgsc.bcm.edu	37	chr17	79479013	79479013	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcctccggggccacgcgcagCtcgttgtagaaggtgtggtg	5	9	16	11	4	0	1	0	0	0	1	3	1	2	1	3	4	1	4	3	4	2	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr17:79479013C>G	ENST00000575842.1	-	2	705	c.279G>C	c.(277-279)gaG>gaC	p.E93D	ACTG1_ENST00000331925.2_Missense_Mutation_p.E93D|RP13-766D20.2_ENST00000430912.1_RNA|AC139149.1_ENST00000584254.1_RNA|ACTG1_ENST00000573283.1_Missense_Mutation_p.E93D|ACTG1_ENST00000575087.1_Missense_Mutation_p.E93D			P63261	ACTG_HUMAN	actin, gamma 1	93					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)			CCACGCGCAGCTCGTTGTAGA	0.617																																					p.E93D		Atlas-SNP	.											.	ACTG1	55	.	0			c.G279C						PASS	.						56	60	59					17																	79479013		2202	4300	6502	SO:0001583	missense	71	exon3			GCGCAGCTCGTTG		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.279G>C	17.37:g.79479013C>G	ENSP00000458162:p.Glu93Asp	85	0	0		101	56	0.554455	NM_001614	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000575842.1	37	CCDS11782.1	.	.	.	.	.	.	.	.	.	.	C	10.57	1.388120	0.25118	.	.	ENSG00000184009	ENST00000331925;ENST00000447294	D	0.94897	-3.55	3.99	3.02	0.34903	.	0.000000	0.64402	D	0.000001	D	0.97554	0.9199	M	0.91354	3.2	0.46654	D	0.999145	P	0.39748	0.686	D	0.68353	0.957	D	0.97644	1.0150	10	0.87932	D	0	.	10.5389	0.45020	0.0:0.9026:0.0:0.0974	.	93	P63261	ACTG_HUMAN	D	93	ENSP00000331514:E93D	ENSP00000331514:E93D	E	-	3	2	ACTG1	77093608	1.000000	0.71417	0.984000	0.44739	0.011000	0.07611	4.453000	0.60061	0.903000	0.36546	-0.251000	0.11542	GAG	.	.	none		0.617	ACTG1-012	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439935.2	NM_001614		G	79479013	C	G	79479013	3	3	36	1	0	0	0	0	1	0	0	0	196	796	28	4	864	4	ACTG1	17	79479013	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	21563341	79479013	1716197	139	14367											
SIRT7	51547	hgsc.bcm.edu	37	chr17	79872227	79872227	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctggcagcctcggtcgcCgcttcccagttcaaaggctg	5	9	12	15	3	1	0	1	0	0	0	4	0	2	0	3	3	2	5	3	3	1	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr17:79872227C>T	ENST00000328666.6	-	7	821	c.759G>A	c.(757-759)gcG>gcA	p.A253A	PCYT2_ENST00000571105.1_5'Flank|PCYT2_ENST00000570388.1_5'Flank|PCYT2_ENST00000538721.2_5'Flank|PCYT2_ENST00000538936.2_5'Flank	NM_016538.2	NP_057622.1	Q9NRC8	SIR7_HUMAN	sirtuin 7	253	Deacetylase sirtuin-type. {ECO:0000255|PROSITE-ProRule:PRU00236}.				histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription on exit from mitosis (GO:0007072)|rRNA transcription (GO:0009303)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleolus organizer region (GO:0005731)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.0165)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)			CCTCGGTCGCCGCTTCCCAGT	0.627																																					p.A253A		Atlas-SNP	.											.	SIRT7	37	.	0			c.G759A						PASS	.						48	42	44					17																	79872227		2203	4299	6502	SO:0001819	synonymous_variant	51547	exon7			GGTCGCCGCTTCC	AF233395	CCDS11792.1	17q25.3	2010-06-25	2010-06-25			ENSG00000187531			14935	protein-coding gene	gene with protein product		606212	"sirtuin (silent mating type information regulation 2, S.cerevisiae, homolog) 7", "sirtuin (silent mating type information regulation 2 homolog) 7 (S. cerevisiae)"			10873683, 16618798	Standard	NM_016538		Approved		uc002kcj.2	Q9NRC8		ENST00000328666.6:c.759G>A	17.37:g.79872227C>T		54	0	0		67	27	0.402985	NM_016538	A8K2K0|B3KSU8|Q3MIK4|Q9NSZ6|Q9NUS6	Silent	SNP	ENST00000328666.6	37	CCDS11792.1																																																																																			.	.	none		0.627	SIRT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439961.1	NM_016538		T	79872227	C	T	79872227	2	4	36	1	0	0	0	0	0	0	0	1	14358	639	23	1		1	SIRT7	17	79872227	Silent	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	393214	79872227	1322983	140	14368											
ABHD3	171586	hgsc.bcm.edu	37	chr18	19283631	19283631	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagcaccagaccgtcgggtaGtacgtttctgtaaccacggg	9	8	12	12	4	1	1	0	0	1	1	2	1	1	1	3	2	3	5	3	2	3	4			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr18:19283631G>A	ENST00000289119.2	-	2	379	c.240C>T	c.(238-240)taC>taT	p.Y80Y	ABHD3_ENST00000580981.1_Silent_p.Y80Y|ABHD3_ENST00000578270.1_5'UTR|ABHD3_ENST00000579875.1_5'UTR	NM_138340.4	NP_612213.2	Q8WU67	ABHD3_HUMAN	abhydrolase domain containing 3	80						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						CCGTCGGGTAGTACGTTTCTG	0.537																																					p.Y80Y		Atlas-SNP	.											.	ABHD3	32	.	0			c.C240T						PASS	.						84	78	80					18																	19283631		2203	4300	6503	SO:0001819	synonymous_variant	171586	exon2			CGGGTAGTACGTT	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.240C>T	18.37:g.19283631G>A		91	0	0		105	34	0.32381	NM_138340	B0YIV0|B7Z5C2|O43411	Silent	SNP	ENST00000289119.2	37	CCDS32802.1																																																																																			.	.	none		0.537	ABHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444757.1			A	19283631	G	A	19283631	2	1	36	1	0	0	0	0	0	0	0	1	83	1024	36	2		2	ABHD3	18	19283631	Silent	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10		19283631	58793617	141	14369											
LAMA3	3909	hgsc.bcm.edu	37	chr18	21330979	21330979	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcaacaaacatccgcttgcGttttcttagaaccaatacgc	12	10	7	12	3	1	1	0	0	1	1	2	1	2	1	2	1	5	3	2	1	6	5			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr18:21330979G>A	ENST00000313654.9	+	5	1023	c.782G>A	c.(781-783)cGt>cAt	p.R261H	LAMA3_ENST00000399516.3_Missense_Mutation_p.R261H	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	261	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)					ATCCGCTTGCGTTTTCTTAGA	0.468																																					p.R261H		Atlas-SNP	.											.	LAMA3	397	.	0			c.G782A						PASS	.						116	114	115					18																	21330979		1887	4117	6004	SO:0001583	missense	3909	exon5			GCTTGCGTTTTCT	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.782G>A	18.37:g.21330979G>A	ENSP00000324532:p.Arg261His	210	0	0		267	86	0.322097	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	37	CCDS42419.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	13.63|13.63	2.294832|2.294832	0.40594|0.40594	.|.	.|.	ENSG00000053747|ENSG00000053747	ENST00000416669|ENST00000313654;ENST00000399516;ENST00000538801	.|T;T	.|0.76709	.|-1.04;-1.04	5.64|5.64	4.77|4.77	0.60923|0.60923	.|Laminin, N-terminal (3);	.|.	.|.	.|.	.|.	.|T	.|0.74921	.|0.3780	M|M	0.71920|0.71920	2.185|2.185	0.80722|0.80722	D|D	1|1	.|B;B;B	.|0.16396	.|0.017;0.011;0.008	.|B;B;B	.|0.15052	.|0.004;0.006;0.012	.|T	.|0.70901	.|-0.4746	.|9	.|0.37606	.|T	.|0.19	.|.	11.2504|11.2504	0.49022|0.49022	0.1911:0.0:0.8089:0.0|0.1911:0.0:0.8089:0.0	.|.	.|261;261;261	.|F5H8G3;Q6VU67;Q16787	.|.;.;LAMA3_HUMAN	.|H	-1|261	.|ENSP00000324532:R261H;ENSP00000382432:R261H	.|ENSP00000324532:R261H	.|R	+|+	.|2	.|0	LAMA3|LAMA3	19584977|19584977	0.991000|0.991000	0.36638|0.36638	1.000000|1.000000	0.80357|0.80357	0.724000|0.724000	0.41520|0.41520	1.510000|1.510000	0.35790|0.35790	1.390000|1.390000	0.46547|0.46547	-0.119000|-0.119000	0.15052|0.15052	.|CGT	.	.	none		0.468	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129		A	21330979	G	A	21330979	3	1	36	1	0	0	0	0	1	0	0	0	8616	1145	40	1	800	1	LAMA3	18	21330979	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	2047348	21330979	56746269	142	14370											
DSC3	1825	hgsc.bcm.edu	37	chr18	28587034	28587034	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctacatattcttgaagtattTctggtggattatcatttaca	11	18	6	6	0	3	1	1	1	2	0	3	2	3	2	0	2	2	1	0	2	6	9			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr18:28587034T>A	ENST00000360428.4	-	12	1807	c.1727A>T	c.(1726-1728)gAa>gTa	p.E576V	DSC3_ENST00000434452.1_Missense_Mutation_p.E576V	NM_001941.3	NP_001932.2	Q14574	DSC3_HUMAN	desmocollin 3	576	Cadherin 4. {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)			TTGAAGTATTTCTGGTGGATT	0.353																																					p.E576V		Atlas-SNP	.											.	DSC3	225	.	0			c.A1727T						PASS	.						113	104	107					18																	28587034		2203	4300	6503	SO:0001583	missense	1825	exon12			AGTATTTCTGGTG	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.1727A>T	18.37:g.28587034T>A	ENSP00000353608:p.Glu576Val	226	0	0		220	57	0.259091	NM_024423	A6NN35|Q14200|Q9HAZ9	Missense_Mutation	SNP	ENST00000360428.4	37	CCDS32810.1	.	.	.	.	.	.	.	.	.	.	t	5.327	0.245623	0.10077	.	.	ENSG00000134762	ENST00000360428;ENST00000434452	T;T	0.59772	0.24;0.24	5.26	-0.00853	0.14005	Cadherin (3);Cadherin-like (2);	0.240961	0.21231	N	0.077980	T	0.37100	0.0991	L	0.28740	0.885	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.13683	-1.0500	10	0.26408	T	0.33	.	6.246	0.20818	0.2308:0.0:0.4129:0.3563	.	576;576	Q14574;Q14574-2	DSC3_HUMAN;.	V	576	ENSP00000353608:E576V;ENSP00000392068:E576V	ENSP00000353608:E576V	E	-	2	0	DSC3	26841032	0.004000	0.15560	0.991000	0.47740	0.314000	0.28054	0.122000	0.15687	0.426000	0.26116	-0.363000	0.07495	GAA	.	.	none		0.353	DSC3-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447384.1	NM_001941, NM_024423		A	28587034	T	A	28587034	3	1	36	1	0	0	0	0	1	0	0	0	4769	1783	62	5	1014	5	DSC3	18	28587034	Missense_Mutation	SNP	T	TCGA-GS-A9TT-01A-11D-A382-10	7256055	28587034	49490214	143	14371											
MYO5B	4645	hgsc.bcm.edu	37	chr18	47518736	47518736	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtaccttttgtcaaagccAatctggatgtacttgccaaa	11	13	8	9	0	2	0	1	0	1	0	2	1	2	1	3	2	4	2	3	2	5	5			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr18:47518736A>C	ENST00000285039.7	-	6	977	c.678T>G	c.(676-678)atT>atG	p.I226M		NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	226	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)		TGTCAAAGCCAATCTGGATGT	0.502																																					p.I226M		Atlas-SNP	.											.	MYO5B	178	.	0			c.T678G						PASS	.						242	227	232					18																	47518736		1969	4160	6129	SO:0001583	missense	4645	exon6			AAAGCCAATCTGG	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.678T>G	18.37:g.47518736A>C	ENSP00000285039:p.Ile226Met	177	0	0		168	39	0.232143	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	Missense_Mutation	SNP	ENST00000285039.7	37	CCDS42436.1	.	.	.	.	.	.	.	.	.	.	A	17.97	3.517619	0.64634	.	.	ENSG00000167306	ENST00000285039;ENST00000356732	D	0.90563	-2.69	5.65	-10.9	0.00192	Myosin head, motor domain (3);	0.000000	0.85682	D	0.000000	D	0.94338	0.8180	M	0.87682	2.9	0.80722	D	1	D;D	0.57257	0.979;0.979	D;P	0.66084	0.941;0.83	D	0.94766	0.7940	10	0.87932	D	0	.	22.7498	0.99975	0.3171:0.0:0.6829:0.0	.	225;226	Q7Z7A5;Q9ULV0	.;MYO5B_HUMAN	M	226;225	ENSP00000285039:I226M	ENSP00000285039:I226M	I	-	3	3	MYO5B	45772734	0.552000	0.26505	0.251000	0.24312	0.946000	0.59487	-0.123000	0.10611	-2.356000	0.00613	-0.899000	0.02877	ATT	.	.	none		0.502	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2			C	47518736	A	C	47518736	3	2	36	1	0	0	0	0	1	0	0	0	10088	126	5	5	5008	5	MYO5B	18	47518736	Missense_Mutation	SNP	A	TCGA-GS-A9TT-01A-11D-A382-10	18931702	47518736	30558512	144	14372											
HMHA1	23526	hgsc.bcm.edu	37	chr19	1080926	1080926	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgacccccgagctgccggtgGccgtgcccagtggaccgttc	4	7	14	16	4	0	1	0	1	0	0	1	3	0	2	6	3	3	2	6	3	0	1			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr19:1080926G>T	ENST00000313093.2	+	17	2284	c.2053G>T	c.(2053-2055)Gcc>Tcc	p.A685S	HMHA1_ENST00000590214.1_Missense_Mutation_p.A712S|HMHA1_ENST00000586866.1_Missense_Mutation_p.A689S|HMHA1_ENST00000590577.1_Missense_Mutation_p.A320S|HMHA1_ENST00000543365.1_Missense_Mutation_p.A568S|HMHA1_ENST00000536472.1_Missense_Mutation_p.A553S|HMHA1_ENST00000539243.2_Missense_Mutation_p.A701S	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	685					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)		GCTGCCGGTGGCCGTGCCCAG	0.706																																					p.A701S		Atlas-SNP	.											.	HMHA1	78	.	0			c.G2101T						PASS	.						14	16	16					19																	1080926		2194	4289	6483	SO:0001583	missense	23526	exon17			CCGGTGGCCGTGC	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.2053G>T	19.37:g.1080926G>T	ENSP00000316772:p.Ala685Ser	81	0	0		92	41	0.445652	NM_001258328	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Missense_Mutation	SNP	ENST00000313093.2	37	CCDS32863.1	.	.	.	.	.	.	.	.	.	.	G	13.75	2.330792	0.41297	.	.	ENSG00000180448	ENST00000539243;ENST00000313093;ENST00000544746;ENST00000536472;ENST00000412039;ENST00000543365	T;T;T;T	0.22134	2.0;2.02;1.98;1.97	3.33	3.33	0.38152	.	0.213079	0.39759	N	0.001277	T	0.26159	0.0638	L	0.58101	1.795	0.35266	D	0.780041	D;P;P;P;P	0.56287	0.975;0.939;0.9;0.884;0.816	P;P;B;B;B	0.50659	0.647;0.554;0.351;0.4;0.225	T	0.26849	-1.0091	10	0.19147	T	0.46	-16.9373	10.0523	0.42223	0.0:0.207:0.793:0.0	.	553;701;320;568;685	F5H4A3;F6QP70;B3KVA9;F5H1R4;Q92619	.;.;.;.;HMHA1_HUMAN	S	701;685;685;553;679;568	ENSP00000439601:A701S;ENSP00000316772:A685S;ENSP00000445109:A553S;ENSP00000438979:A568S	ENSP00000316772:A685S	A	+	1	0	HMHA1	1031926	0.984000	0.35163	0.254000	0.24359	0.156000	0.22039	1.499000	0.35671	1.871000	0.54225	0.491000	0.48974	GCC	.	.	none		0.706	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1			T	1080926	G	T	1080926	3	4	36	1	0	0	0	0	1	0	0	0	7249	1203	42	4	2119	4	HMHA1	19	1080926	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10		1080926	58048057	145	14373											
OR1M1	125963	hgsc.bcm.edu	37	chr19	9204160	9204160	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccaccaacaccatccctaaGatgctggtgagccttcaaac	12	7	7	15	0	1	2	1	1	0	1	2	2	2	2	5	1	4	1	5	1	3	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr19:9204160G>T	ENST00000429566.3	+	1	306	c.240G>T	c.(238-240)aaG>aaT	p.K80N		NM_001004456.1	NP_001004456.1	Q8NGA1	OR1M1_HUMAN	olfactory receptor, family 1, subfamily M, 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)			breast(1)|endometrium(4)|large_intestine(3)|lung(17)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						CCATCCCTAAGATGCTGGTGA	0.537																																					p.K80N		Atlas-SNP	.											.	OR1M1	52	.	0			c.G240T						PASS	.						95	69	78					19																	9204160		2203	4300	6503	SO:0001583	missense	125963	exon1			CCCTAAGATGCTG		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.240G>T	19.37:g.9204160G>T	ENSP00000401966:p.Lys80Asn	160	0	0		147	71	0.482993	NM_001004456	B9EHA6|Q6IFJ3|Q96R91	Missense_Mutation	SNP	ENST00000429566.3	37	CCDS32896.1	.	.	.	.	.	.	.	.	.	.	g	11.79	1.744634	0.30865	.	.	ENSG00000170929	ENST00000305465;ENST00000429566	D	0.85861	-2.04	3.49	0.0484	0.14285	GPCR, rhodopsin-like superfamily (1);	0.204155	0.34223	N	0.004148	D	0.86184	0.5872	L	0.52266	1.64	0.09310	N	1	D	0.76494	0.999	D	0.78314	0.991	T	0.75479	-0.3303	10	0.72032	D	0.01	.	4.1085	0.10049	0.4185:0.1742:0.4073:0.0	.	80	Q8NGA1	OR1M1_HUMAN	N	83;80	ENSP00000401966:K80N	ENSP00000303195:K83N	K	+	3	2	OR1M1	9065160	0.000000	0.05858	0.927000	0.36925	0.440000	0.31957	-0.125000	0.10579	-0.000000	0.14550	0.400000	0.26472	AAG	.	.	none		0.537	OR1M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448993.1			T	9204160	G	T	9204160	3	4	36	1	0	0	0	0	1	0	0	0	10977	933	33	4	242	4	OR1M1	19	9204160	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	8123234	9204160	49924823	146	14374											
ZNF700	90592	hgsc.bcm.edu	37	chr19	12059331	12059331	+	Nonsense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaatatggaccaaagccataTaagtgtcaacaacctaaaaa	20	7	6	8	0	1	0	1	0	0	0	1	2	1	1	3	1	3	0	3	1	10	4			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr19:12059331T>G	ENST00000254321.5	+	4	635	c.492T>G	c.(490-492)taT>taG	p.Y164*	ZNF763_ENST00000538752.1_Intron|ZNF700_ENST00000482090.1_Nonsense_Mutation_p.Y146*|ZNF763_ENST00000591944.1_Intron|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	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)		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						CAAAGCCATATAAGTGTCAAC	0.413																																					p.Y167X		Atlas-SNP	.											.	ZNF700	81	.	0			c.T501G						PASS	.						140	136	137					19																	12059331		2203	4300	6503	SO:0001587	stop_gained	90592	exon4			GCCATATAAGTGT	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.492T>G	19.37:g.12059331T>G	ENSP00000254321:p.Tyr164*	137	0	0		128	65	0.507812	NM_001271848	B9EGU4	Nonsense_Mutation	SNP	ENST00000254321.5	37	CCDS32915.1	.	.	.	.	.	.	.	.	.	.	t	25.0	4.596718	0.86953	.	.	ENSG00000196757	ENST00000254321	.	.	.	0.554	0.554	0.17241	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.34	0.15979	0.0:1.0E-4:0.0:0.9999	.	.	.	.	X	164	.	ENSP00000254321:Y164X	Y	+	3	2	ZNF700	11920331	0.063000	0.20901	0.469000	0.27204	0.758000	0.43043	-0.370000	0.07523	0.450000	0.26774	0.254000	0.18369	TAT	.	.	none		0.413	ZNF700-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344126.2	NM_144566		G	12059331	T	G	12059331	4	3	36	1	0	0	0	0	0	1	0	0	18119	1413	49	5	506	5	ZNF700	19	12059331	Nonsense_Mutation	SNP	T	TCGA-GS-A9TT-01A-11D-A382-10	2855171	12059331	47069652	147	14375											
RFX1	5989	hgsc.bcm.edu	37	chr19	14076565	14076565	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaccaggatggctttgggCagtcgcttctcggcctcgtc	5	10	13	13	3	1	0	0	0	1	0	5	1	1	1	2	4	1	4	2	4	0	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr19:14076565C>G	ENST00000254325.4	-	15	2220	c.1986G>C	c.(1984-1986)ctG>ctC	p.L662L		NM_002918.4	NP_002909.4	P22670	RFX1_HUMAN	regulatory factor X, 1 (influences HLA class II expression)	662					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)			TGGCTTTGGGCAGTCGCTTCT	0.612																																					p.L662L		Atlas-SNP	.											.	RFX1	63	.	0			c.G1986C						PASS	.						139	121	127					19																	14076565		2203	4300	6503	SO:0001819	synonymous_variant	5989	exon15			TTTGGGCAGTCGC		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.1986G>C	19.37:g.14076565C>G		66	0	0		50	27	0.54	NM_002918		Silent	SNP	ENST00000254325.4	37	CCDS12301.1																																																																																			.	.	none		0.612	RFX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458510.1	NM_002918		G	14076565	C	G	14076565	2	3	36	1	0	0	0	0	0	0	0	1	13277	697	25	4		4	RFX1	19	14076565	Silent	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	2017234	14076565	45052418	148	14376											
MYO9B	4650	hgsc.bcm.edu	37	chr19	17308611	17308612	+	Frame_Shift_Ins	INS	-	-	CG																															atctcgcagggagaggcgcaINScctccttctccacgagcgac																										TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr19:17308611_17308612insCG	ENST00000594824.1	+	23	4204_4205	c.4057_4058insCG	c.(4057-4059)accfs	p.T1353fs	MYO9B_ENST00000397274.2_Frame_Shift_Ins_p.T1353fs|MYO9B_ENST00000595618.1_Frame_Shift_Ins_p.T1353fs			Q13459	MYO9B_HUMAN	myosin IXB	1353	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						GGAGAGGCGCACCTCCTTCTCC	0.515																																					p.T1353fs		Pindel,Atlas-Indel	.											.	MYO9B	264	.	0			c.4057_4058insCG						PASS	.																																			SO:0001589	frameshift_variant	4650	exon23			.		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		Exception_encountered	19.37:g.17308611_17308612insCG	ENSP00000471367:p.Thr1353fs	58	0	.		50	13	0.26	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Frame_Shift_Ins	INS	ENST00000594824.1	37																																																																																				.	.	none		0.515	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1			CG	17308612	-	CG	17308611	7	5	36	1	0	1	1	0	0	0	0	0	10094	159	6	0	4143	0	MYO9B	19	17308611	Frame_Shift_Ins	INS	-	TCGA-GS-A9TT-01A-11D-A382-10	3232046	17308611	41820372	149	14377											
CILP2	148113	hgsc.bcm.edu	37	chr19	19656250	19656250	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggcagccacccacgcaccCgcggccagctctacggactt	7	4	12	18	4	1	0	0	0	1	0	1	1	1	1	4	4	3	3	4	4	1	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr19:19656250C>T	ENST00000291495.5	+	8	2981	c.2896C>T	c.(2896-2898)Cgc>Tgc	p.R966C	CILP2_ENST00000586018.1_Missense_Mutation_p.R972C	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	966						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						CCCACGCACCCGCGGCCAGCT	0.677																																					p.R966C		Atlas-SNP	.											.	CILP2	84	.	0			c.C2896T						PASS	.						16	18	17					19																	19656250		2196	4294	6490	SO:0001583	missense	148113	exon8			CGCACCCGCGGCC	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.2896C>T	19.37:g.19656250C>T	ENSP00000291495:p.Arg966Cys	35	0	0		40	19	0.475	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Missense_Mutation	SNP	ENST00000291495.5	37	CCDS12405.1	.	.	.	.	.	.	.	.	.	.	C	10.26	1.300104	0.23650	.	.	ENSG00000160161	ENST00000291495	T	0.10192	2.9	5.79	4.73	0.59995	.	0.632272	0.16163	N	0.226641	T	0.11836	0.0288	L	0.46157	1.445	0.09310	N	0.999999	P;P	0.50819	0.939;0.939	B;B	0.42522	0.326;0.39	T	0.14282	-1.0478	10	0.54805	T	0.06	-8.0753	9.6471	0.39875	0.1599:0.6858:0.1543:0.0	.	966;966	B2RAJ0;Q8IUL8	.;CILP2_HUMAN	C	966	ENSP00000291495:R966C	ENSP00000291495:R966C	R	+	1	0	CILP2	19517250	0.000000	0.05858	0.006000	0.13384	0.010000	0.07245	0.965000	0.29319	1.419000	0.47118	0.555000	0.69702	CGC	.	.	none		0.677	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221		T	19656250	C	T	19656250	3	4	36	1	0	0	0	0	1	0	0	0	3432	652	23	1	2926	1	CILP2	19	19656250	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	2347639	19656250	39472733	150	14378											
ZNF493	284443	hgsc.bcm.edu	37	chr19	21607740	21607740	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttcacatcttagtagacataAgataattcatattggaattc	15	15	5	6	0	3	2	2	0	1	2	4	3	3	3	0	1	0	1	0	1	6	9			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr19:21607740A>C	ENST00000355504.4	+	2	2161	c.1895A>C	c.(1894-1896)aAg>aCg	p.K632T	CTD-2561J22.3_ENST00000600810.1_Intron|ZNF493_ENST00000392288.2_Missense_Mutation_p.K760T	NM_175910.6	NP_787106.4	Q6ZR52	ZN493_HUMAN	zinc finger protein 493	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)			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						AGTAGACATAAGATAATTCAT	0.368																																					p.K760T		Atlas-SNP	.											.	ZNF493	178	.	0			c.A2279C						PASS	.						46	49	48					19																	21607740		2203	4298	6501	SO:0001583	missense	284443	exon4			GACATAAGATAAT	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.1895A>C	19.37:g.21607740A>C	ENSP00000347691:p.Lys632Thr	178	0	0		143	65	0.454545	NM_001076678	G5E974|Q59GM3|Q6ZSF6|Q8N1Z6|Q8N965|Q9BR99	Missense_Mutation	SNP	ENST00000355504.4	37	CCDS12412.1	.	.	.	.	.	.	.	.	.	.	N	11.22	1.573663	0.28092	.	.	ENSG00000196268	ENST00000392288;ENST00000355504	T;T	0.28454	1.61;1.61	1.17	-0.519	0.11939	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.22666	0.0547	L	0.31476	0.935	0.20196	N	0.99993	P;B	0.39404	0.672;0.041	B;B	0.42495	0.389;0.031	T	0.22382	-1.0218	9	0.72032	D	0.01	.	5.2131	0.15329	0.7454:0.0:0.0:0.2546	.	632;760	Q6ZR52;Q6ZR52-2	ZN493_HUMAN;.	T	760;632	ENSP00000376110:K760T;ENSP00000347691:K632T	ENSP00000347691:K632T	K	+	2	0	ZNF493	21399580	0.000000	0.05858	0.008000	0.14137	0.048000	0.14542	0.259000	0.18405	0.474000	0.27392	0.332000	0.21555	AAG	.	.	none		0.368	ZNF493-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280563.1	NM_175910		C	21607740	A	C	21607740	3	2	36	1	0	0	0	0	1	0	0	0	17959	72	3	5	2356	5	ZNF493	19	21607740	Missense_Mutation	SNP	A	TCGA-GS-A9TT-01A-11D-A382-10	1951490	21607740	37521243	151	14379											
ZNF43	7594	hgsc.bcm.edu	37	chr19	21991819	21991819	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cattcttcacatgtgtagggTttctctccagtatgaattct	8	17	7	9	0	4	1	1	1	3	0	6	1	5	1	1	1	0	3	1	1	3	6			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr19:21991819T>G	ENST00000354959.4	-	4	1189	c.1020A>C	c.(1018-1020)aaA>aaC	p.K340N	ZNF43_ENST00000598381.1_Missense_Mutation_p.K334N|ZNF43_ENST00000595461.1_Missense_Mutation_p.K334N|ZNF43_ENST00000594012.1_Missense_Mutation_p.K334N	NM_003423.3	NP_003414.2	P17038	ZNF43_HUMAN	zinc finger protein 43	340					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)		ATGTGTAGGGTTTCTCTCCAG	0.383																																					p.K349N		Atlas-SNP	.											.	ZNF43	152	.	0			c.A1047C						PASS	.						51	54	53					19																	21991819		2203	4297	6500	SO:0001583	missense	7594	exon4			GTAGGGTTTCTCT	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.1020A>C	19.37:g.21991819T>G	ENSP00000347045:p.Lys340Asn	114	0	0		74	28	0.378378	NM_001256653	A8K5N8|P28160|Q53XQ2|Q5H9T3|Q96DG1	Missense_Mutation	SNP	ENST00000354959.4	37	CCDS12413.2	.	.	.	.	.	.	.	.	.	.	T	12.87	2.068339	0.36470	.	.	ENSG00000198521	ENST00000397148;ENST00000354959	T	0.26067	1.76	1.76	-1.03	0.10102	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.38480	0.1042	M	0.84511	2.7	0.28494	N	0.914327	P	0.45715	0.865	P	0.49665	0.618	T	0.35450	-0.9788	9	0.87932	D	0	.	6.1831	0.20482	0.0:0.4532:0.0:0.5468	.	340	P17038	ZNF43_HUMAN	N	339;340	ENSP00000347045:K340N	ENSP00000347045:K340N	K	-	3	2	ZNF43	21783659	0.187000	0.23238	0.000000	0.03702	0.039000	0.13416	-0.311000	0.08124	-0.521000	0.06426	0.254000	0.18369	AAA	.	.	none		0.383	ZNF43-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250380.2	NM_003423		G	21991819	T	G	21991819	3	3	36	1	0	0	0	0	1	0	0	0	17918	1722	60	5	1413	5	ZNF43	19	21991819	Missense_Mutation	SNP	T	TCGA-GS-A9TT-01A-11D-A382-10	384079	21991819	37137164	152	14380											
ADCK4	79934	hgsc.bcm.edu	37	chr19	41216028	41216028	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccagtactcctagccccaaGcccacagccagtcctggagt	9	6	9	17	0	0	0	0	0	0	0	2	1	2	1	7	1	4	1	7	1	3	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr19:41216028G>T	ENST00000324464.3	-	5	604	c.303C>A	c.(301-303)ggC>ggA	p.G101G	ADCK4_ENST00000243583.6_Silent_p.G101G|RNU6-195P_ENST00000411352.1_RNA|ADCK4_ENST00000450541.1_Silent_p.G101G	NM_024876.3	NP_079152.3	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4	101						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)			CTAGCCCCAAGCCCACAGCCA	0.577																																					p.G101G		Atlas-SNP	.											.	ADCK4	92	.	0			c.C303A						PASS	.						98	79	85					19																	41216028		2203	4300	6503	SO:0001819	synonymous_variant	79934	exon5			CCCCAAGCCCACA	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.303C>A	19.37:g.41216028G>T		74	0	0		117	75	0.641026	NM_001142555	Q8TAJ1|Q9HA52	Silent	SNP	ENST00000324464.3	37	CCDS12562.1																																																																																			.	.	none		0.577	ADCK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462731.1	NM_024876		T	41216028	G	T	41216028	2	4	36	1	0	0	0	0	0	0	0	1	290	958	34	4		4	ADCK4	19	41216028	Silent	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	19224209	41216028	17912955	153	14381											
POU2F2	5452	hgsc.bcm.edu	37	chr19	42600043	42600043	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atggtcgtctggctgaagtcGttgccgtagagcttgcccat	6	12	13	10	3	1	2	0	1	1	1	3	2	1	2	2	2	3	4	2	2	2	3			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr19:42600043G>A	ENST00000526816.2	-	9	717	c.702C>T	c.(700-702)aaC>aaT	p.N234N	POU2F2_ENST00000533720.1_Silent_p.N218N|POU2F2_ENST00000529952.1_Silent_p.N234N|POU2F2_ENST00000389341.5_Silent_p.N218N|POU2F2_ENST00000560558.1_Silent_p.N179N|POU2F2_ENST00000560398.1_Silent_p.N240N|POU2F2_ENST00000342301.4_Silent_p.N234N|POU2F2_ENST00000529067.1_Silent_p.N218N			P09086	PO2F2_HUMAN	POU class 2 homeobox 2	234	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				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)	GGCTGAAGTCGTTGCCGTAGA	0.637																																					p.N234N		Atlas-SNP	.											.	POU2F2	106	.	0			c.C702T						PASS	.						114	114	114					19																	42600043		2203	4300	6503	SO:0001819	synonymous_variant	5452	exon9			GAAGTCGTTGCCG		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.702C>T	19.37:g.42600043G>A		60	0	0		116	28	0.241379	NM_001207025	Q16648|Q7M4M8|Q9BRS4	Silent	SNP	ENST00000526816.2	37	CCDS56095.1																																																																																			.	.	none		0.637	POU2F2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387329.3			A	42600043	G	A	42600043	2	1	36	1	0	0	0	0	0	0	0	1	12281	1136	40	1		1	POU2F2	19	42600043	Silent	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	1384015	42600043	16528940	154	14382											
FOXA3	3171	hgsc.bcm.edu	37	chr19	46375993	46375993	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcctcgaccaccacccccGcggccacagtcacctccccg	6	4	7	24	4	1	0	1	0	0	0	3	1	2	0	9	1	1	0	9	1	0	0			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr19:46375993G>A	ENST00000302177.2	+	2	927	c.730G>A	c.(730-732)Gcg>Acg	p.A244T		NM_004497.2	NP_004488.2	P55318	FOXA3_HUMAN	forkhead box A3	244					cell differentiation (GO:0030154)|cellular glucose homeostasis (GO:0001678)|cellular response to starvation (GO:0009267)|chromatin modification (GO:0016568)|endocrine pancreas development (GO:0031018)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(2)|pancreas(1)|prostate(1)	13		Ovarian(192;0.0308)|all_neural(266;0.0476)		OV - Ovarian serous cystadenocarcinoma(262;0.00453)|GBM - Glioblastoma multiforme(486;0.0518)|Epithelial(262;0.236)		CACCACCCCCGCGGCCACAGT	0.697																																					p.A244T		Atlas-SNP	.											.	FOXA3	19	.	0			c.G730A						PASS	.						5	7	6					19																	46375993		2062	4117	6179	SO:0001583	missense	3171	exon2			ACCCCCGCGGCCA	L12141	CCDS12677.1	19q13.32	2014-09-11		2002-09-20	ENSG00000170608	ENSG00000170608		"Forkhead boxes"	5023	protein-coding gene	gene with protein product		602295	"hepatocyte nuclear factor 3, gamma"	HNF3G		9119385	Standard	NM_004497		Approved		uc002pdr.3	P55318	OTTHUMG00000182484	ENST00000302177.2:c.730G>A	19.37:g.46375993G>A	ENSP00000304004:p.Ala244Thr	25	0	0		36	23	0.638889	NM_004497	A9LYI5|Q53F16|Q9UMW9	Missense_Mutation	SNP	ENST00000302177.2	37	CCDS12677.1	.	.	.	.	.	.	.	.	.	.	G	0.470	-0.884804	0.02530	.	.	ENSG00000170608	ENST00000302177	D	0.91521	-2.86	3.31	-0.315	0.12746	.	1.202840	0.06199	N	0.682958	T	0.79845	0.4516	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.62973	-0.6740	10	0.13470	T	0.59	.	3.8218	0.08839	0.2781:0.3989:0.323:0.0	.	244	P55318	FOXA3_HUMAN	T	244	ENSP00000304004:A244T	ENSP00000304004:A244T	A	+	1	0	FOXA3	51067833	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.193000	0.09573	0.005000	0.14708	-0.476000	0.04901	GCG	.	.	none		0.697	FOXA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461682.1			A	46375993	G	A	46375993	3	1	36	1	0	0	0	0	1	0	0	0	5999	1087	38	1	736	1	FOXA3	19	46375993	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	3775950	46375993	12752990	155	14383											
PPP5C	5536	hgsc.bcm.edu	37	chr19	46878959	46878959	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgagcgggccatcgcgggCgacgagcacaagcgctccgt	7	6	15	13	7	0	1	0	1	0	0	2	3	1	1	2	2	3	2	2	2	1	1			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr19:46878959C>T	ENST00000012443.4	+	3	565	c.462C>T	c.(460-462)ggC>ggT	p.G154G	PPP5C_ENST00000391919.1_Silent_p.G48G	NM_006247.3	NP_006238.1	P53041	PPP5_HUMAN	protein phosphatase 5, catalytic subunit	154					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)		CCATCGCGGGCGACGAGCACA	0.582																																					p.G154G		Atlas-SNP	.											PPP5C,NS,carcinoma,0,1	PPP5C	44	1	0			c.C462T						PASS	.						60	49	53					19																	46878959		2203	4299	6502	SO:0001819	synonymous_variant	5536	exon3			CGCGGGCGACGAG		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.462C>T	19.37:g.46878959C>T		91	0	0		109	67	0.614679	NM_006247	Q16722|Q53XV2	Silent	SNP	ENST00000012443.4	37	CCDS12684.1																																																																																			.	.	none		0.582	PPP5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258969.2	NM_006247		T	46878959	C	T	46878959	2	4	36	1	0	0	0	0	0	0	0	1	12418	755	27	1		1	PPP5C	19	46878959	Silent	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	502966	46878959	12250024	156	14384											
FGF21	26291	hgsc.bcm.edu	37	chr19	49261218	49261218	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccctgaggcctgcagcttccGggagctgcttcttgaggacg	5	9	14	13	2	1	2	0	2	1	0	2	4	2	4	3	3	4	4	3	3	0	3	rs142980324		TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr19:49261218G>A	ENST00000593756.1	+	4	943	c.371G>A	c.(370-372)cGg>cAg	p.R124Q	FUT1_ENST00000310160.3_5'Flank|FGF21_ENST00000222157.3_Missense_Mutation_p.R124Q			Q9NSA1	FGF21_HUMAN	fibroblast growth factor 21	124					cell-cell signaling (GO:0007267)|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 low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|regulation of low-density lipoprotein particle clearance (GO:0010988)|signal transduction (GO:0007165)	extracellular region (GO:0005576)				breast(1)|cervix(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	8		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;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		TGCAGCTTCCGGGAGCTGCTT	0.582																																					p.R124Q		Atlas-SNP	.											.	FGF21	21	.	0			c.G371A						PASS	.	G	GLN/ARG	0,4402		0,0,2201	158	173	168		371	3.4	1	19	dbSNP_134	168	4,8592	3.7+/-12.6	0,4,4294	yes	missense	FGF21	NM_019113.2	43	0,4,6495	AA,AG,GG		0.0465,0.0,0.0308	probably-damaging	124/210	49261218	4,12994	2201	4298	6499	SO:0001583	missense	26291	exon3			GCTTCCGGGAGCT	AB021975	CCDS12734.1	19q13.33	2012-09-20			ENSG00000105550	ENSG00000105550			3678	protein-coding gene	gene with protein product		609436				10858549	Standard	XM_005258731		Approved		uc002pko.1	Q9NSA1		ENST00000593756.1:c.371G>A	19.37:g.49261218G>A	ENSP00000471477:p.Arg124Gln	96	0	0		151	94	0.622517	NM_019113	Q8N683	Missense_Mutation	SNP	ENST00000593756.1	37	CCDS12734.1	.	.	.	.	.	.	.	.	.	.	G	19.37	3.814192	0.70912	0.0	4.65E-4	ENSG00000105550	ENST00000222157	D	0.81579	-1.51	4.44	3.4	0.38934	.	0.076506	0.49916	D	0.000128	T	0.80969	0.4726	M	0.74258	2.255	0.37112	D	0.900381	D	0.53745	0.962	P	0.48270	0.572	T	0.82814	-0.0271	10	0.46703	T	0.11	-15.5157	8.3528	0.32312	0.1087:0.0:0.8913:0.0	.	124	Q9NSA1	FGF21_HUMAN	Q	124	ENSP00000222157:R124Q	ENSP00000222157:R124Q	R	+	2	0	FGF21	53953030	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	1.173000	0.31920	1.220000	0.43490	0.511000	0.50034	CGG	G|1.000;A|0.000	0.000	weak		0.582	FGF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466200.1			A	49261218	G	A	49261218	3	1	36	1	0	0	0	0	1	0	0	0	5858	1116	39	1	381	1	FGF21	19	49261218	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	2382259	49261218	9867765	157	14385											
LILRA2	11027	hgsc.bcm.edu	37	chr19	55086869	55086869	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgacttcctccagcgccctGgttggcagccccaggctggg	4	8	14	15	1	0	1	0	1	0	0	2	1	2	1	5	4	2	3	5	4	0	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr19:55086869G>T	ENST00000251377.3	+	6	935	c.802G>T	c.(802-804)Ggt>Tgt	p.G268C	LILRA2_ENST00000391737.1_Missense_Mutation_p.G256C|LILRA2_ENST00000251376.3_Missense_Mutation_p.G268C|LILRB1_ENST00000418536.2_Intron|LILRB1_ENST00000448689.1_Intron|LILRA2_ENST00000391738.3_Missense_Mutation_p.G268C|LILRB1_ENST00000396321.2_Intron			Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2	268	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)		CCAGCGCCCTGGTTGGCAGCC	0.627																																					p.G268C		Atlas-SNP	.											.	LILRA2	99	.	0			c.G802T						PASS	.						79	77	78					19																	55086869		2203	4300	6503	SO:0001583	missense	11027	exon5			CGCCCTGGTTGGC	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.802G>T	19.37:g.55086869G>T	ENSP00000251377:p.Gly268Cys	123	0	0		135	47	0.348148	NM_001130917	O75020	Missense_Mutation	SNP	ENST00000251377.3	37	CCDS46179.1	.	.	.	.	.	.	.	.	.	.	G	11.72	1.722701	0.30503	.	.	ENSG00000239998	ENST00000439534;ENST00000251377;ENST00000391738;ENST00000251376;ENST00000391737	T;T;T;T;T	0.00745	5.75;5.75;5.75;5.75;5.75	2.26	-0.112	0.13572	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	2.720370	0.01616	N	0.022766	T	0.06554	0.0168	H	0.95224	3.64	0.09310	N	1	B;D;D;D	0.89917	0.239;1.0;1.0;1.0	B;D;D;D	0.79108	0.2;0.992;0.992;0.987	T	0.27773	-1.0064	10	0.72032	D	0.01	.	2.6785	0.05087	0.1735:0.0:0.5315:0.295	.	268;256;268;268	E9PDF4;A8MZH0;Q8N149;Q8N149-2	.;.;LIRA2_HUMAN;.	C	268;268;268;268;256	ENSP00000388131:G268C;ENSP00000251377:G268C;ENSP00000375618:G268C;ENSP00000251376:G268C;ENSP00000375617:G256C	ENSP00000251376:G268C	G	+	1	0	LILRA2	59778681	.	.	0.000000	0.03702	0.012000	0.07955	.	.	0.034000	0.15491	0.400000	0.26472	GGT	.	.	none		0.627	LILRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140813.2			T	55086869	G	T	55086869	3	4	36	1	0	0	0	0	1	0	0	0	8794	1348	47	4	820	4	LILRA2	19	55086869	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	5825651	55086869	4042114	158	14386											
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385790	58385790	+	Missense_Mutation	SNP	G	G	T																															cacattctccacattcataaGgtcttttcccagtgtgaact																								rs111727691		TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr19:58385790G>T	ENST00000435989.2	-	3	1202	c.968C>A	c.(967-969)cCt>cAt	p.P323H	ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597832.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	323					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						ACATTCATAAGGTCTTTTCCC	0.358																																					p.P323H		Atlas-SNP	.											.	ZNF814	93	.	0			c.C968A						PASS	.						15	12	13					19																	58385790		688	1563	2251	SO:0001583	missense	730051	exon3			TCATAAGGTCTTT		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.968C>A	19.37:g.58385790G>T	ENSP00000410545:p.Pro323His	238	0	0		363	57	0.157025	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	8.139	0.784825	0.16189	.	.	ENSG00000204514	ENST00000435989	T	0.29397	1.57	2.27	1.18	0.20946	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.57080	0.2029	M	0.90019	3.08	0.20764	N	0.999853	D	0.89917	1.0	D	0.67231	0.95	T	0.46247	-0.9205	9	0.66056	D	0.02	.	9.258	0.37595	0.0:0.0:0.7811:0.2189	.	323	B7Z6K7	ZN814_HUMAN	H	323	ENSP00000410545:P323H	ENSP00000410545:P323H	P	-	2	0	ZNF814	63077602	0.000000	0.05858	0.028000	0.17463	0.016000	0.09150	-0.439000	0.06897	0.330000	0.23485	-1.407000	0.01130	CCT	G|0.500;T|0.500	0.500	weak		0.358	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		T	58385790	G	T	58385790	3	4	36	1	0	0	0	0	1	0	0	0	18191	1000	35	4	1603	4	ZNF814	19	58385790	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	3298921	58385790	743193	159	14387	186	2									
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385793	58385793	+	Missense_Mutation	SNP	C	C	T																															attctccacattcataaggtCttttcccagtgtgaactctc																								rs113623532		TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr19:58385793C>T	ENST00000435989.2	-	3	1199	c.965G>A	c.(964-966)aGa>aAa	p.R322K	ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597832.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	322					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						TTCATAAGGTCTTTTCCCAGT	0.358																																					p.R322K		Atlas-SNP	.											.	ZNF814	93	.	0			c.G965A						PASS	.						15	12	13					19																	58385793		687	1562	2249	SO:0001583	missense	730051	exon3			TAAGGTCTTTTCC		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.965G>A	19.37:g.58385793C>T	ENSP00000410545:p.Arg322Lys	229	0	0		348	54	0.155172	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	0.023	-1.395361	0.01175	.	.	ENSG00000204514	ENST00000435989	T	0.12361	2.69	2.27	9.47E-4	0.14044	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03608	0.0103	N	0.02225	-0.63	0.09310	N	0.999999	B	0.29301	0.241	B	0.28916	0.096	T	0.40534	-0.9558	9	0.02654	T	1	.	4.6969	0.12808	0.0:0.4166:0.0:0.5834	.	322	B7Z6K7	ZN814_HUMAN	K	322	ENSP00000410545:R322K	ENSP00000410545:R322K	R	-	2	0	ZNF814	63077605	0.000000	0.05858	0.024000	0.17045	0.009000	0.06853	-1.883000	0.01623	0.331000	0.23511	-1.381000	0.01174	AGA	C|0.500;T|0.500	0.500	weak		0.358	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		T	58385793	C	T	58385793	3	4	36	1	0	0	0	0	1	0	0	0	18191	913	32	2	1606	2	ZNF814	19	58385793	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	3	58385793	743190	160	14388	186	2									
C20orf194	25943	hgsc.bcm.edu	37	chr20	3302910	3302910	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgtccagcggtacaattCtaggaggggaaagagatgga	13	7	14	7	1	1	1	0	0	1	1	2	5	2	4	1	5	2	1	1	5	4	3			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr20:3302910C>A	ENST00000252032.9	-	16	1378		c.e16-1		C20orf194_ENST00000453730.2_Splice_Site	NM_001009984.2	NP_001009984.1	Q5TEA3	CT194_HUMAN	chromosome 20 open reading frame 194											NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	39						CGGTACAATTCTAGGAGGGGA	0.418																																					.		Atlas-SNP	.											.	C20orf194	83	.	0			c.1311-1G>T						PASS	.						80	74	76					20																	3302910		1877	4105	5982	SO:0001630	splice_region_variant	25943	exon17			ACAATTCTAGGAG	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.1311-1G>T	20.37:g.3302910C>A		59	0	0		44	17	0.386364	NM_001009984	Q66K86|Q6P2R9|Q9UFX9	Splice_Site	SNP	ENST00000252032.9	37	CCDS42851.1	.	.	.	.	.	.	.	.	.	.	C	17.43	3.387063	0.61956	.	.	ENSG00000088854	ENST00000252032;ENST00000453730	.	.	.	5.59	5.59	0.84812	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0876	0.72167	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C20orf194	3250910	1.000000	0.71417	1.000000	0.80357	0.773000	0.43773	4.403000	0.59729	2.622000	0.88805	0.655000	0.94253	.	.	.	none		0.418	C20orf194-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077734.1	NM_001009984	Intron	A	3302910	C	A	3302910	5	1	36	1	0	0	0	0	0	0	1	0	2101	927	32	4	2311	4	C20orf194	20	3302910	Splice_Site	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10		3302910	59722610	161	14389											
SEL1L2	80343	hgsc.bcm.edu	37	chr20	13866955	13866955	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtatctgaacatctcctctTtctgccaaaaatttatagta	12	16	4	9	0	4	1	0	1	4	0	5	1	4	1	2	0	2	2	2	0	7	6			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr20:13866955T>A	ENST00000284951.5	-	9	953	c.879A>T	c.(877-879)gaA>gaT	p.E293D	SEL1L2_ENST00000486903.1_5'UTR|SEL1L2_ENST00000378072.5_Missense_Mutation_p.E293D			Q5TEA6	SE1L2_HUMAN	sel-1 suppressor of lin-12-like 2 (C. elegans)	293						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						CATCTCCTCTTTCTGCCAAAA	0.358																																					p.E293D		Atlas-SNP	.											.	SEL1L2	103	.	0			c.A879T						PASS	.						138	126	130					20																	13866955		1826	4081	5907	SO:0001583	missense	80343	exon9			TCCTCTTTCTGCC	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.879A>T	20.37:g.13866955T>A	ENSP00000284951:p.Glu293Asp	233	0	0		197	89	0.451777	NM_001271539	B4DXX5	Missense_Mutation	SNP	ENST00000284951.5	37		.	.	.	.	.	.	.	.	.	.	T	13.98	2.397408	0.42512	.	.	ENSG00000101251	ENST00000378072;ENST00000284951	T;T	0.54479	0.57;0.57	5.78	5.78	0.91487	Tetratricopeptide-like helical (1);	0.000000	0.64402	D	0.000003	T	0.49372	0.1553	N	0.12637	0.245	0.37334	D	0.910102	B;D	0.64830	0.086;0.994	B;D	0.70716	0.05;0.97	T	0.48885	-0.8995	10	0.07813	T	0.8	-26.0605	12.5063	0.55984	0.0:0.0:0.0:1.0	.	293;293	B4DXX5;Q5TEA6	.;SE1L2_HUMAN	D	293	ENSP00000367312:E293D;ENSP00000284951:E293D	ENSP00000284951:E293D	E	-	3	2	SEL1L2	13814955	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.496000	0.35638	2.205000	0.71048	0.454000	0.30748	GAA	.	.	none		0.358	SEL1L2-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078067.3	NM_025229		A	13866955	T	A	13866955	3	1	36	1	0	0	0	0	1	0	0	0	14026	1838	64	5	1235	5	SEL1L2	20	13866955	Missense_Mutation	SNP	T	TCGA-GS-A9TT-01A-11D-A382-10	10564045	13866955	49158565	162	14390											
FOXS1	2307	hgsc.bcm.edu	37	chr20	30433068	30433068	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtggcagtcagggtccagcGtccagtagctgcccttgcct	5	9	13	14	2	1	0	1	0	0	0	3	0	3	0	4	2	4	3	4	2	1	2	rs140637242		TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr20:30433068G>A	ENST00000375978.3	-	1	352	c.278C>T	c.(277-279)aCg>aTg	p.T93M		NM_004118.3	NP_004109.1	O43638	FOXS1_HUMAN	forkhead box S1	93					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						AGGGTCCAGCGTCCAGTAGCT	0.667																																					p.T93M		Atlas-SNP	.											.	FOXS1	29	.	0			c.C278T						PASS	.	G	MET/THR	2,4404	4.2+/-10.8	0,2,2201	70	58	62		278	5	1	20	dbSNP_134	62	0,8600		0,0,4300	no	missense	FOXS1	NM_004118.3	81	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging	93/331	30433068	2,13004	2203	4300	6503	SO:0001583	missense	2307	exon1			TCCAGCGTCCAGT	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.278C>T	20.37:g.30433068G>A	ENSP00000365145:p.Thr93Met	47	0	0		44	18	0.409091	NM_004118	Q96D28	Missense_Mutation	SNP	ENST00000375978.3	37	CCDS13192.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.541894	0.85917	4.54E-4	0.0	ENSG00000179772	ENST00000375978	D	0.95788	-3.81	4.98	4.98	0.66077	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.49916	D	0.000130	D	0.95909	0.8668	L	0.53617	1.68	0.80722	D	1	D	0.61080	0.989	P	0.54312	0.748	D	0.96332	0.9244	10	0.87932	D	0	.	16.9787	0.86321	0.0:0.0:1.0:0.0	.	93	O43638	FOXS1_HUMAN	M	93	ENSP00000365145:T93M	ENSP00000365145:T93M	T	-	2	0	FOXS1	29896729	1.000000	0.71417	0.996000	0.52242	0.979000	0.70002	9.657000	0.98554	2.605000	0.88082	0.555000	0.69702	ACG	G|1.000;A|0.000	0.000	weak		0.667	FOXS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078560.2	NM_004118		A	30433068	G	A	30433068	3	1	36	1	0	0	0	0	1	0	0	0	6043	1145	40	1	718	1	FOXS1	20	30433068	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	16566113	30433068	32592452	163	14391											
NECAB3	63941	hgsc.bcm.edu	37	chr20	32246320	32246320	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atcctgccagaactcatacaGggtgaaggaggcaccgtcca	12	6	11	12	1	1	2	1	1	0	1	3	3	3	3	4	3	3	1	4	3	3	1			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr20:32246320G>T	ENST00000246190.6	-	10	1088	c.1033C>A	c.(1033-1035)Ctg>Atg	p.L345M	NECAB3_ENST00000375238.4_Missense_Mutation_p.L311M|RP1-63M2.6_ENST00000607224.1_RNA|NECAB3_ENST00000606525.1_5'UTR	NM_031232.3	NP_112509.3	Q96P71	NECA3_HUMAN	N-terminal EF-hand calcium binding protein 3	345	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						AACTCATACAGGGTGAAGGAG	0.627																																					p.L345M		Atlas-SNP	.											.	NECAB3	27	.	0			c.C1033A						PASS	.						158	168	165					20																	32246320		2078	4218	6296	SO:0001583	missense	63941	exon10			CATACAGGGTGAA	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.1033C>A	20.37:g.32246320G>T	ENSP00000246190:p.Leu345Met	91	0	0		69	39	0.565217	NM_031232	A8K780|E1P5N2|Q5JWF5|Q5JWF6|Q5JWF7|Q86VV1|Q9H433|Q9H8G8|Q9HBW7|Q9HCQ9	Missense_Mutation	SNP	ENST00000246190.6	37	CCDS42866.1	.	.	.	.	.	.	.	.	.	.	G	11.55	1.670715	0.29693	.	.	ENSG00000125967	ENST00000375238;ENST00000246190	T;T	0.31510	1.49;1.49	5.01	1.96	0.26148	Dimeric alpha-beta barrel (1);Antibiotic biosynthesis monooxygenase (1);	0.150264	0.45867	D	0.000337	T	0.38241	0.1033	L	0.41824	1.3	0.43787	D	0.996328	D;P;B	0.67145	0.996;0.688;0.348	D;P;B	0.74348	0.983;0.525;0.28	T	0.06534	-1.0821	10	0.32370	T	0.25	-16.9783	6.7897	0.23693	0.16:0.1438:0.6962:0.0	.	222;345;311	E1P5N3;Q96P71;Q96P71-2	.;NECA3_HUMAN;.	M	311;345	ENSP00000364386:L311M;ENSP00000246190:L345M	ENSP00000246190:L345M	L	-	1	2	NECAB3	31709981	1.000000	0.71417	0.739000	0.30968	0.373000	0.29922	1.387000	0.34430	0.157000	0.19338	0.561000	0.74099	CTG	.	.	none		0.627	NECAB3-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078724.2			T	32246320	G	T	32246320	3	4	36	1	0	0	0	0	1	0	0	0	10315	991	35	4	169	4	NECAB3	20	32246320	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	1813252	32246320	30779200	164	14392											
EIF2S2	8894	hgsc.bcm.edu	37	chr20	32677684	32677684	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcaggattgtgtccggtgatCggcatgtgtgacaagtgaca	9	10	15	7	2	0	3	0	3	0	0	2	4	1	4	1	3	0	2	1	3	1	1			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr20:32677684C>T	ENST00000374980.2	-	9	1075	c.854G>A	c.(853-855)cGa>cAa	p.R285Q		NM_003908.3	NP_003899.2	P20042	IF2B_HUMAN	eukaryotic translation initiation factor 2, subunit 2 beta, 38kDa	285					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						GTCCGGTGATCGGCATGTGTG	0.448																																					p.R285Q		Atlas-SNP	.											EIF2S2,NS,carcinoma,-1,3	EIF2S2	32	3	0			c.G854A						PASS	.						139	118	125					20																	32677684		2203	4300	6503	SO:0001583	missense	8894	exon9			GGTGATCGGCATG	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.854G>A	20.37:g.32677684C>T	ENSP00000364119:p.Arg285Gln	107	0	0		78	33	0.423077	NM_003908	Q9BVU0|Q9UJE4	Missense_Mutation	SNP	ENST00000374980.2	37	CCDS13231.1	.	.	.	.	.	.	.	.	.	.	C	35	5.436758	0.96168	.	.	ENSG00000125977	ENST00000374980	T	0.48201	0.82	6.07	6.07	0.98685	Translation initiation factor IF2/IF5, zinc-binding (1);Translation initiation factor IF2/IF5 (2);	0.000000	0.85682	D	0.000000	T	0.67107	0.2858	L	0.54965	1.715	0.80722	D	1	P;D;D	0.69078	0.784;0.997;0.997	B;D;D	0.72982	0.19;0.979;0.979	T	0.65479	-0.6158	10	0.66056	D	0.02	-8.2387	20.6439	0.99570	0.0:1.0:0.0:0.0	.	285;285;285	B5BU01;Q6IBR8;P20042	.;.;IF2B_HUMAN	Q	285	ENSP00000364119:R285Q	ENSP00000364119:R285Q	R	-	2	0	EIF2S2	32141345	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.786000	0.85741	2.884000	0.98904	0.655000	0.94253	CGA	.	.	none		0.448	EIF2S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078765.2	NM_003908		T	32677684	C	T	32677684	3	4	36	1	0	0	0	0	1	0	0	0	5012	884	31	1	151	1	EIF2S2	20	32677684	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	431364	32677684	30347836	165	14393											
STX16	8675	hgsc.bcm.edu	37	chr20	57227165	57227165	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagtagtcacatcacctccAgccctctgcattcacgtagc	9	10	7	15	1	4	1	3	1	1	0	5	1	5	1	3	0	3	3	3	0	2	3			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr20:57227165A>G	ENST00000371141.4	+	1	827	c.103A>G	c.(103-105)Agc>Ggc	p.S35G	STX16_ENST00000359617.4_5'UTR|STX16_ENST00000371132.4_Intron|STX16_ENST00000496003.1_3'UTR|STX16_ENST00000361830.3_Missense_Mutation_p.S35G|STX16_ENST00000361770.5_Intron|STX16_ENST00000355957.5_Intron|STX16-NPEPL1_ENST00000530122.1_Missense_Mutation_p.S35G|STX16_ENST00000358029.4_Missense_Mutation_p.S35G	NM_001001433.2	NP_001001433.1	O14662	STX16_HUMAN	syntaxin 16	35					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)			CATCACCTCCAGCCCTCTGCA	0.567																																					p.S35G		Atlas-SNP	.											.	STX16	36	.	0			c.A103G						PASS	.						100	82	88					20																	57227165		2203	4300	6503	SO:0001583	missense	8675	exon1			ACCTCCAGCCCTC	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.103A>G	20.37:g.57227165A>G	ENSP00000360183:p.Ser35Gly	44	0	0		32	18	0.5625	NM_001134772	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	37	CCDS13468.1	.	.	.	.	.	.	.	.	.	.	A	15.42	2.828198	0.50845	.	.	ENSG00000124222	ENST00000371141;ENST00000358029;ENST00000361830	T;T;T	0.47177	0.87;0.85;0.87	4.81	4.81	0.61882	.	0.097247	0.41396	U	0.000888	T	0.29749	0.0743	N	0.22421	0.69	0.80722	D	1	B;B	0.32620	0.063;0.378	B;B	0.29785	0.039;0.107	T	0.10019	-1.0648	10	0.19590	T	0.45	.	9.9808	0.41813	0.8301:0.1699:0.0:0.0	.	35;35	Q6GMS8;O14662	.;STX16_HUMAN	G	35	ENSP00000360183:S35G;ENSP00000350723:S35G;ENSP00000354445:S35G	ENSP00000432101:S35G	S	+	1	0	STX16	56660571	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.061000	0.71148	2.018000	0.59344	0.533000	0.62120	AGC	.	.	none		0.567	STX16-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080517.2	NM_001001433		G	57227165	A	G	57227165	3	3	36	1	0	0	0	0	1	0	0	0	15354	188	7	3	105	3	STX16	20	57227165	Missense_Mutation	SNP	A	TCGA-GS-A9TT-01A-11D-A382-10	24549481	57227165	5798355	166	14394											
PRIC285	85441	hgsc.bcm.edu	37	chr20	62195768	62195768	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcagctcacggccggcaccCgggtgctgcctgatcacctc	5	6	13	17	3	2	1	2	1	0	0	3	1	2	1	4	4	3	4	4	4	0	0			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr20:62195768C>T	ENST00000467148.1	-	8	4476	c.4407G>A	c.(4405-4407)ccG>ccA	p.P1469P	HELZ2_ENST00000427522.2_Silent_p.P900P	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	1469					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)										GGCCGGCACCCGGGTGCTGCC	0.711																																					p.P1469P		Atlas-SNP	.											.	.	.	.	0			c.G4407A						PASS	.						5	5	5					20																	62195768		2046	4119	6165	SO:0001819	synonymous_variant	85441	exon9			GGCACCCGGGTGC	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.4407G>A	20.37:g.62195768C>T		26	0	0		21	12	0.571429	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Silent	SNP	ENST00000467148.1	37	CCDS33508.1																																																																																			.	.	none		0.711	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335		T	62195768	C	T	62195768	2	4	36	1	0	0	0	0	0	0	0	1	12497	639	23	1		1	PRIC285	20	62195768	Silent	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	4968603	62195768	829752	167	14395											
NCAM2	4685	hgsc.bcm.edu	37	chr21	22656515	22656515	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tttccatggctctttgcagcGattggtgaacctgaaagtat	9	14	10	8	1	1	2	0	2	1	0	2	3	2	2	2	2	3	3	2	2	3	4			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr21:22656515G>A	ENST00000400546.1	+	3	381	c.132G>A	c.(130-132)gcG>gcA	p.A44A	NCAM2_ENST00000284894.7_Intron|NCAM2_ENST00000486367.1_3'UTR|NCAM2_ENST00000535285.1_Splice_Site_p.A69A	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	44	Ig-like C2-type 1.				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)		TCTTTGCAGCGATTGGTGAAC	0.328																																					p.A44A		Atlas-SNP	.											.	NCAM2	220	.	0			c.G132A						PASS	.						101	90	94					21																	22656515		1827	4072	5899	SO:0001630	splice_region_variant	4685	exon3			TGCAGCGATTGGT		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.131-1G>A	21.37:g.22656515G>A		109	0	0		81	43	0.530864	NM_004540	A8MQ06|B7Z841|Q7Z7F2	Silent	SNP	ENST00000400546.1	37	CCDS42910.1																																																																																			.	.	none		0.328	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540	Silent	A	22656515	G	A	22656515	5	1	36	1	0	0	0	0	0	0	1	0	10212	1072	37	1	142	1	NCAM2	21	22656515	Splice_Site	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10		22656515	25473380	168	14396											
TIAM1	7074	hgsc.bcm.edu	37	chr21	32617950	32617950	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtctatcccagacctgccgtCgctctcgtagaaaaatagcg	10	9	9	13	4	2	2	0	0	2	2	5	2	3	2	3	0	2	2	3	0	5	3			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr21:32617950C>T	ENST00000286827.3	-	7	1909	c.1438G>A	c.(1438-1440)Gac>Aac	p.D480N	TIAM1_ENST00000469412.1_5'UTR|TIAM1_ENST00000541036.1_Missense_Mutation_p.D480N	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	480	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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						GACCTGCCGTCGCTCTCGTAG	0.527																																					p.D480N		Atlas-SNP	.											.	TIAM1	522	.	0			c.G1438A						PASS	.						72	63	66					21																	32617950		2203	4300	6503	SO:0001583	missense	7074	exon7			TGCCGTCGCTCTC		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.1438G>A	21.37:g.32617950C>T	ENSP00000286827:p.Asp480Asn	90	0	0		99	51	0.515152	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	37	CCDS13609.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.376098	0.82682	.	.	ENSG00000156299	ENST00000286827;ENST00000399841;ENST00000541036	T;T	0.29655	1.56;1.56	5.22	5.22	0.72569	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.41396	0.1157	N	0.17474	0.49	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;0.994;0.994;0.994	T	0.32745	-0.9895	10	0.41790	T	0.15	.	18.9723	0.92719	0.0:1.0:0.0:0.0	.	480;480;321;480	F5GZ53;B7ZLR6;E9PD83;Q13009	.;.;.;TIAM1_HUMAN	N	480;321;480	ENSP00000286827:D480N;ENSP00000441570:D480N	ENSP00000286827:D480N	D	-	1	0	TIAM1	31539821	1.000000	0.71417	0.363000	0.25875	0.950000	0.60333	7.628000	0.83189	2.717000	0.92951	0.650000	0.86243	GAC	.	.	none		0.527	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253		T	32617950	C	T	32617950	3	4	36	1	0	0	0	0	1	0	0	0	15905	884	31	1	3429	1	TIAM1	21	32617950	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	9961435	32617950	15511945	169	14397											
DGCR8	54487	hgsc.bcm.edu	37	chr22	20079074	20079074	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atcgggaaatgaagcggaagCaggcggagtccgagaggccc	12	3	17	9	4	0	2	0	1	0	1	2	6	1	5	2	5	2	1	2	5	3	0			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr22:20079074C>T	ENST00000351989.3	+	6	1852	c.1423C>T	c.(1423-1425)Cag>Tag	p.Q475*	DGCR8_ENST00000407755.1_Nonsense_Mutation_p.Q475*|DGCR8_ENST00000383024.2_Nonsense_Mutation_p.Q475*	NM_022720.6	NP_073557.3	Q8WYQ5	DGCR8_HUMAN	DGCR8 microprocessor complex subunit	475	Necessary for heme-binding and pri-miRNA processing.				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)					GAAGCGGAAGCAGGCGGAGTC	0.478																																					p.Q475X		Atlas-SNP	.											.	DGCR8	53	.	0			c.C1423T						PASS	.						157	174	168					22																	20079074		2203	4300	6503	SO:0001587	stop_gained	54487	exon6			CGGAAGCAGGCGG	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.1423C>T	22.37:g.20079074C>T	ENSP00000263209:p.Gln475*	69	0	0		56	28	0.5	NM_001190326	B2R8G1|Q6DCB2|Q6MZE9|Q6Y2L0|Q96G39|Q96GP8|Q9H6L8|Q9H6T7|Q9NRW2	Nonsense_Mutation	SNP	ENST00000351989.3	37	CCDS13773.1	.	.	.	.	.	.	.	.	.	.	C	42	9.193922	0.99096	.	.	ENSG00000128191	ENST00000351989;ENST00000383024;ENST00000407755	.	.	.	4.62	4.62	0.57501	.	0.058892	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	-13.2898	17.2464	0.87029	0.0:1.0:0.0:0.0	.	.	.	.	X	475	.	ENSP00000263209:Q475X	Q	+	1	0	DGCR8	18459074	1.000000	0.71417	1.000000	0.80357	0.669000	0.39330	5.593000	0.67550	2.380000	0.81148	0.591000	0.81541	CAG	.	.	none		0.478	DGCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318654.1			T	20079074	C	T	20079074	4	4	36	1	0	0	0	0	0	1	0	0	4466	711	25	2	1441	2	DGCR8	22	20079074	Nonsense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10		20079074	31225492	170	14398											
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230309	23230310	+	In_Frame_Ins	INS	-	-	TTT																															tcccaggcagcgctggccccINStgctgctgctgggtctggcc																										TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr22:23230309_23230310insTTT	ENST00000526893.1	+	1	350_351	c.76_77insTTT	c.(76-78)ctg>cTTTtg	p.26_26L>LL	hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_In_Frame_Ins_p.26_26L>LL|IGLL5_ENST00000531372.1_In_Frame_Ins_p.26_26L>LL	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	26						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GCGCTGGCCCCTGCTGCTGCTG	0.663																																					p.L26delinsLL		Pindel,Atlas-Indel	.											.	IGLL5	26	.	0			c.76_77insTTT						PASS	.																																			SO:0001652	inframe_insertion	100423062	exon1			.	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	Exception_encountered	22.37:g.23230309_23230310insTTT	ENSP00000431254:p.Leu29dup	100	0	.		116	22	0.19	NM_001178126		In_Frame_Ins	INS	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.663	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		TTT	23230310	-	TTT	23230309	7	5	36	1	0	1	1	0	0	0	0	0	7603	680	24	0	78	0	IGLL5	22	23230309	In_Frame_Ins	INS	-	TCGA-GS-A9TT-01A-11D-A382-10	3151235	23230309	28074257	171	14399			3	63		4	4	95	N	T_G_-	2.46235e-11
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230323	23230323	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcccctgctgctgctgggTctggccatggtcgcccatgg	2	10	15	14	1	1	0	0	0	1	0	2	0	1	0	4	5	3	3	4	5	0	0			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr22:23230323T>C	ENST00000526893.1	+	1	364	c.90T>C	c.(88-90)ggT>ggC	p.G30G	hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Silent_p.G30G|IGLL5_ENST00000531372.1_Silent_p.G30G	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	30						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						TGCTGCTGGGTCTGGCCATGG	0.667																																					p.G30G		Atlas-SNP	.											.	IGLL5	26	.	0			c.T90C						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			GCTGGGTCTGGCC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.90T>C	22.37:g.23230323T>C		89	0	0		97	37	0.381443	NM_001178126		Silent	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.667	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		C	23230323	T	C	23230323	2	2	36	1	0	0	0	0	0	0	0	1	7603	1654	58	3		3	IGLL5	22	23230323	Silent	SNP	T	TCGA-GS-A9TT-01A-11D-A382-10	14	23230323	28074243	172	14400			3	63		4	4	95	N	T_G_-	2.46235e-11
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230360	23230360	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	atggcctgctgcgcccaatgGttgcaccgcaaagcggggac	8	6	14	13	3	0	0	0	0	0	0	0	1	0	1	3	4	4	4	3	4	2	1	rs6003368	byFrequency	TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr22:23230360G>A	ENST00000526893.1	+	1	401	c.127G>A	c.(127-129)Gtt>Att	p.V43I	hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Missense_Mutation_p.V43I|IGLL5_ENST00000531372.1_Missense_Mutation_p.V43I	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	43						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GCGCCCAATGGTTGCACCGCA	0.672																																					p.W7X		Atlas-SNP	.											.	IGLL5	26	.	0			c.G21A						PASS	.																																			SO:0001583	missense	100423062	exon1			CCAATGGTTGCAC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.127G>A	22.37:g.23230360G>A	ENSP00000431254:p.Val43Ile	104	0	0		101	47	0.465347	NM_001256296		Nonsense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	9.827	1.187440	0.21870	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00568	6.53;6.53	3.92	0.473	0.16763	.	.	.	.	.	T	0.00300	0.0009	N	0.08118	0	0.09310	N	1	B	0.16166	0.016	B	0.10450	0.005	T	0.44034	-0.9354	9	0.49607	T	0.09	.	2.3416	0.04261	0.1095:0.1927:0.4993:0.1985	rs6003368;rs6003368	43	B9A064	IGLL5_HUMAN	I	43	ENSP00000436353:V43I;ENSP00000431254:V43I	ENSP00000431254:V43I	V	+	1	0	IGLL5	21560360	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.128000	0.03247	0.192000	0.20272	0.643000	0.83706	GTT	G|1.000;|0.000	.	weak		0.672	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		A	23230360	G	A	23230360	3	1	36	1	0	0	0	0	1	0	0	0	7603	1261	44	2	129	2	IGLL5	22	23230360	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	37	23230360	28074206	173	14401			3	63		4	4	95	N	T_G_-	2.46235e-11
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230403	23230403	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	agaccctggagcctcagttgGaagcagccgatccagcctgc	9	6	12	14	1	1	1	1	0	0	1	2	4	2	3	5	2	5	2	5	2	1	1	rs530312149	byFrequency	TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr22:23230403G>A	ENST00000526893.1	+	1	444	c.170G>A	c.(169-171)gGa>gAa	p.G57E	hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Missense_Mutation_p.G57E|IGLL5_ENST00000531372.1_Missense_Mutation_p.G57E	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	57						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GCCTCAGTTGGAAGCAGCCGA	0.657													G|||	4	0.000798722	0.0	0.0	5008	,	,		10551	0.0		0.004	False		,,,				2504	0.0				p.G57E		Atlas-SNP	.											.	IGLL5	26	.	0			c.G170A						PASS	.																																			SO:0001583	missense	100423062	exon1			CAGTTGGAAGCAG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.170G>A	22.37:g.23230403G>A	ENSP00000431254:p.Gly57Glu	112	0	0		102	45	0.441176	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	14.68	2.608516	0.46527	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00581	6.43;6.42	3.92	0.609	0.17575	.	.	.	.	.	T	0.00468	0.0015	L	0.32530	0.975	0.09310	N	1	B	0.30584	0.286	B	0.23018	0.043	T	0.44190	-0.9344	9	0.29301	T	0.29	.	4.1265	0.10129	0.218:0.194:0.588:0.0	.	57	B9A064	IGLL5_HUMAN	E	57	ENSP00000436353:G57E;ENSP00000431254:G57E	ENSP00000431254:G57E	G	+	2	0	IGLL5	21560403	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.009000	0.12765	0.224000	0.20940	0.643000	0.83706	GGA	.	.	none		0.657	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		A	23230403	G	A	23230403	3	1	36	1	0	0	0	0	1	0	0	0	7603	1174	41	2	172	2	IGLL5	22	23230403	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	43	23230403	28074163	174	14402			3	63		4	4	95	N	T_G_-	2.46235e-11
BCR	613	hgsc.bcm.edu	37	chr22	23523318	23523318	+	Silent	SNP	C	C	T																															caggagcgcttccgcatgatCtacctgcagacgttgctggc																										TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr22:23523318C>T	ENST00000305877.8	+	1	922	c.171C>T	c.(169-171)atC>atT	p.I57I	BCR_ENST00000398512.5_Silent_p.I57I|BCR_ENST00000359540.3_Silent_p.I57I	NM_004327.3	NP_004318.3	P11274	BCR_HUMAN	breakpoint cluster region	57	Kinase.				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)	TCCGCATGATCTACCTGCAGA	0.677			T	"ABL1,  FGFR1, JAK2 "	"CML, ALL, AML"																																p.I57I		Atlas-SNP	.		Dom	yes		22	22q11.21	613	breakpoint cluster region		L	.	BCR	74	.	0			c.C171T						PASS	.						21	23	22					22																	23523318		2187	4281	6468	SO:0001819	synonymous_variant	613	exon1			CATGATCTACCTG		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.171C>T	22.37:g.23523318C>T		71	0	0		78	32	0.410256	NM_021574	P78501|Q12842|Q4LE80|Q6NZI3	Silent	SNP	ENST00000305877.8	37	CCDS13806.1																																																																																			.	.	none		0.677	BCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075819.1	NM_004327		T	23523318	C	T	23523318	2	4	36	1	0	0	0	0	0	0	0	1	1388	903	32	2		2	BCR	22	23523318	Silent	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	292915	23523318	27781248	175	14403	187	3									
BCR	613	hgsc.bcm.edu	37	chr22	23523322	23523322	+	Silent	SNP	C	C	T																															agcgcttccgcatgatctacCtgcagacgttgctggccaag																										TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr22:23523322C>T	ENST00000305877.8	+	1	926	c.175C>T	c.(175-177)Ctg>Ttg	p.L59L	BCR_ENST00000398512.5_Silent_p.L59L|BCR_ENST00000359540.3_Silent_p.L59L	NM_004327.3	NP_004318.3	P11274	BCR_HUMAN	breakpoint cluster region	59	Kinase.				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)	CATGATCTACCTGCAGACGTT	0.682			T	"ABL1,  FGFR1, JAK2 "	"CML, ALL, AML"																																p.L59L		Atlas-SNP	.		Dom	yes		22	22q11.21	613	breakpoint cluster region		L	.	BCR	74	.	0			c.C175T						PASS	.						21	22	22					22																	23523322		2186	4278	6464	SO:0001819	synonymous_variant	613	exon1			ATCTACCTGCAGA		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.175C>T	22.37:g.23523322C>T		69	0	0		78	31	0.397436	NM_021574	P78501|Q12842|Q4LE80|Q6NZI3	Silent	SNP	ENST00000305877.8	37	CCDS13806.1																																																																																			.	.	none		0.682	BCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075819.1	NM_004327		T	23523322	C	T	23523322	2	4	36	1	0	0	0	0	0	0	0	1	1388	680	24	2		2	BCR	22	23523322	Silent	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	4	23523322	27781244	176	14404	187	3									
BCR	613	hgsc.bcm.edu	37	chr22	23523331	23523331	+	Silent	SNP	T	T	C																															gcatgatctacctgcagacgTtgctggccaaggaaaagaag																										TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr22:23523331T>C	ENST00000305877.8	+	1	935	c.184T>C	c.(184-186)Ttg>Ctg	p.L62L	BCR_ENST00000398512.5_Silent_p.L62L|BCR_ENST00000359540.3_Silent_p.L62L	NM_004327.3	NP_004318.3	P11274	BCR_HUMAN	breakpoint cluster region	62	Kinase.				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)	CCTGCAGACGTTGCTGGCCAA	0.687			T	"ABL1,  FGFR1, JAK2 "	"CML, ALL, AML"																																p.L62L		Atlas-SNP	.		Dom	yes		22	22q11.21	613	breakpoint cluster region		L	.	BCR	74	.	0			c.T184C						PASS	.						22	22	22					22																	23523331		2186	4274	6460	SO:0001819	synonymous_variant	613	exon1			CAGACGTTGCTGG		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.184T>C	22.37:g.23523331T>C		73	0	0		78	41	0.525641	NM_021574	P78501|Q12842|Q4LE80|Q6NZI3	Silent	SNP	ENST00000305877.8	37	CCDS13806.1																																																																																			.	.	none		0.687	BCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075819.1	NM_004327		C	23523331	T	C	23523331	2	2	36	1	0	0	0	0	0	0	0	1	1388	1722	60	3		3	BCR	22	23523331	Silent	SNP	T	TCGA-GS-A9TT-01A-11D-A382-10	9	23523331	27781235	177	14405	187	3									
APOL2	23780	hgsc.bcm.edu	37	chr22	36623579	36623579	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccccctcaagcaagtgcttTgactcatatgcaaggctgac	10	9	9	13	0	2	2	2	2	0	0	2	2	2	2	2	1	3	4	2	1	4	2			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr22:36623579T>A	ENST00000249066.6	-	6	1361	c.885A>T	c.(883-885)tcA>tcT	p.S295S	APOL2_ENST00000451256.2_Silent_p.S407S|APOL2_ENST00000358502.5_Silent_p.S295S	NM_145637.1	NP_663612.1	Q9BQE5	APOL2_HUMAN	apolipoprotein L, 2	295					acute-phase response (GO:0006953)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|maternal process involved in female pregnancy (GO:0060135)|multicellular organismal development (GO:0007275)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|membrane (GO:0016020)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|skin(1)|urinary_tract(2)	9						GCAAGTGCTTTGACTCATATG	0.562																																					p.S295S		Atlas-SNP	.											.	APOL2	20	.	0			c.A885T						PASS	.						104	109	107					22																	36623579		2203	4300	6503	SO:0001819	synonymous_variant	23780	exon5			GTGCTTTGACTCA	AF324224	CCDS43014.1	22q12.3	2013-09-20			ENSG00000128335	ENSG00000128335		"Apolipoproteins"	619	protein-coding gene	gene with protein product	"apolipoprotein L-II"	607252				10591208, 11374903	Standard	NM_145637		Approved	APOL-II	uc003apa.3	Q9BQE5	OTTHUMG00000150634	ENST00000249066.6:c.885A>T	22.37:g.36623579T>A		140	0	0		163	79	0.484663	NM_030882	B0QYK7|O95915|Q59GW9|Q5TH96|Q969T6|Q9BT28|Q9UGT1|Q9UH10	Silent	SNP	ENST00000249066.6	37	CCDS43014.1																																																																																			.	.	none		0.562	APOL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000319279.1	NM_145637		A	36623579	T	A	36623579	2	1	36	1	0	0	0	0	0	0	0	1	806	1799	63	5		5	APOL2	22	36623579	Silent	SNP	T	TCGA-GS-A9TT-01A-11D-A382-10	13100248	36623579	14680987	178	14406											
TRIOBP	11078	hgsc.bcm.edu	37	chr22	38153834	38153834	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccagcccgcactcctgacCgcctggccaagcaggaggag	8	3	12	18	2	0	1	0	1	0	0	1	3	1	3	7	3	2	2	7	3	1	0			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr22:38153834C>T	ENST00000406386.3	+	16	6157	c.5902C>T	c.(5902-5904)Cgc>Tgc	p.R1968C	TRIOBP_ENST00000407319.2_Missense_Mutation_p.R255C|TRIOBP_ENST00000403663.2_Missense_Mutation_p.R255C	NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	1968					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)					CACTCCTGACCGCCTGGCCAA	0.716																																					p.R1968C		Atlas-SNP	.											.	TRIOBP	262	.	0			c.C5902T						PASS	.						5	7	6					22																	38153834		2074	4027	6101	SO:0001583	missense	11078	exon16			CCTGACCGCCTGG	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.5902C>T	22.37:g.38153834C>T	ENSP00000384312:p.Arg1968Cys	51	0	0		56	21	0.375	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.39|17.39	3.378678|3.378678	0.61735|0.61735	.|.	.|.	ENSG00000100106|ENSG00000100106	ENST00000428075|ENST00000406386;ENST00000407319;ENST00000403663;ENST00000418339;ENST00000417857	.|T	.|0.22743	.|1.94	5.19|5.19	5.19|5.19	0.71726|0.71726	.|.	.|.	.|.	.|.	.|.	T|T	0.39886|0.39886	0.1095|0.1095	M|M	0.61703|0.61703	1.905|1.905	0.22389|0.22389	N|N	0.999146|0.999146	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.68039	.|0.955;0.945;0.93	T|T	0.25502|0.25502	-1.0130|-1.0130	5|9	.|0.72032	.|D	.|0.01	.|.	8.7704|8.7704	0.34728|0.34728	0.0:0.7687:0.1523:0.079|0.0:0.7687:0.1523:0.079	.|.	.|255;255;1968	.|F8W6V6;F2Z2W0;Q9H2D6	.|.;.;TARA_HUMAN	L|C	208|1968;255;255;214;184	.|ENSP00000384312:R1968C	.|ENSP00000386026:R255C	P|R	+|+	2|1	0|0	TRIOBP|TRIOBP	36483780|36483780	0.632000|0.632000	0.27172|0.27172	0.974000|0.974000	0.42286|0.42286	0.895000|0.895000	0.52256|0.52256	1.766000|1.766000	0.38491|0.38491	2.413000|2.413000	0.81919|0.81919	0.561000|0.561000	0.74099|0.74099	CCG|CGC	.	.	none		0.716	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2			T	38153834	C	T	38153834	3	4	36	1	0	0	0	0	1	0	0	0	16568	652	23	1	6143	1	TRIOBP	22	38153834	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	1530255	38153834	13150732	179	14407											
CYB5R3	1727	hgsc.bcm.edu	37	chr22	43024249	43024249	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtactgagacatcttcccTccagcgggaaacttgggatg	10	9	12	10	1	1	1	0	1	1	1	3	4	3	3	2	3	3	1	2	3	2	3			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chr22:43024249T>C	ENST00000352397.5	-	5	624	c.372A>G	c.(370-372)ggA>ggG	p.G124G	CYB5R3_ENST00000361740.4_Silent_p.G157G|CYB5R3_ENST00000407623.3_Silent_p.G101G|CYB5R3_ENST00000396303.3_Silent_p.G101G|CYB5R3_ENST00000402438.1_Silent_p.G101G|CYB5R3_ENST00000407332.1_Silent_p.G101G	NM_000398.6	NP_000389.1	P00387	NB5R3_HUMAN	cytochrome b5 reductase 3	124	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)	ACATCTTCCCTCCAGCGGGAA	0.602																																					p.G157G		Atlas-SNP	.											.	CYB5R3	31	.	0			c.A471G						PASS	.						150	148	149					22																	43024249		2203	4300	6503	SO:0001819	synonymous_variant	1727	exon5			CTTCCCTCCAGCG	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.372A>G	22.37:g.43024249T>C		53	0	0		53	13	0.245283	NM_001171660	B1AHF2|B7Z7L3|O75675|Q8TDL8|Q8WTS8|Q9UEN4|Q9UEN5|Q9UL55|Q9UL56	Silent	SNP	ENST00000352397.5	37	CCDS33658.1																																																																																			.	.	none		0.602	CYB5R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320439.1			C	43024249	T	C	43024249	2	2	36	1	0	0	0	0	0	0	0	1	4130	1538	54	3		3	CYB5R3	22	43024249	Silent	SNP	T	TCGA-GS-A9TT-01A-11D-A382-10	4870415	43024249	8280317	180	14408											
ASB11	140456	hgsc.bcm.edu	37	chrX	15301725	15301725	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acacttccggacacacaggcGgcagagctgggaaagagcag	13	3	14	11	2	0	2	0	0	0	2	1	4	1	4	1	4	2	3	1	4	1	1			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chrX:15301725G>A	ENST00000480796.1	-	7	924	c.874C>T	c.(874-876)Cgc>Tgc	p.R292C	ASB11_ENST00000537676.1_Missense_Mutation_p.R271C|ASB11_ENST00000344384.4_Missense_Mutation_p.R271C|ASB11_ENST00000380470.3_Missense_Mutation_p.R275C			Q8WXH4	ASB11_HUMAN	ankyrin repeat and SOCS box containing 11, E3 ubiquitin protein ligase	292	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(2)|central_nervous_system(4)|endometrium(1)|large_intestine(1)|lung(5)|ovary(2)|skin(1)	16	Hepatocellular(33;0.183)					ACACACAGGCGGCAGAGCTGG	0.522																																					p.R292C		Atlas-SNP	.											.	ASB11	79	.	0			c.C874T						PASS	.						118	99	106					X																	15301725		2203	4300	6503	SO:0001583	missense	140456	exon7			ACAGGCGGCAGAG	AF425642	CCDS14164.1, CCDS35209.1, CCDS56596.1	Xp22.31	2014-02-10	2014-02-10		ENSG00000165192	ENSG00000165192		"Ankyrin repeat domain containing"	17186	protein-coding gene	gene with protein product		300626	"ankyrin repeat and SOCS box-containing 11", "ankyrin repeat and SOCS box containing 11"			24337577	Standard	NM_080873		Approved	DKFZp779E2460	uc004cwp.2	Q8WXH4	OTTHUMG00000021173	ENST00000480796.1:c.874C>T	X.37:g.15301725G>A	ENSP00000417914:p.Arg292Cys	56	0	0		67	65	0.970149	NM_080873	E9PEN1|Q3SYC4|Q7Z667	Missense_Mutation	SNP	ENST00000480796.1	37	CCDS14164.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.321100	0.81580	.	.	ENSG00000165192	ENST00000537676;ENST00000380470;ENST00000344384;ENST00000480796	D;D;D;D	0.85484	-1.99;-1.99;-1.99;-1.99	5.72	5.72	0.89469	SOCS protein, C-terminal (3);	0.000000	0.64402	D	0.000010	D	0.94321	0.8175	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	0.95462	0.8544	10	0.72032	D	0.01	-19.864	14.3095	0.66407	0.0:0.0:0.8516:0.1484	.	275;292;271	Q7Z667;Q8WXH4;E9PEN1	.;ASB11_HUMAN;.	C	271;275;271;292	ENSP00000445465:R271C;ENSP00000369837:R275C;ENSP00000343408:R271C;ENSP00000417914:R292C	ENSP00000343408:R271C	R	-	1	0	ASB11	15211646	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	6.183000	0.72002	2.398000	0.81561	0.544000	0.68410	CGC	.	.	none		0.522	ASB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055852.2			A	15301725	G	A	15301725	3	1	36	1	0	0	0	0	1	0	0	0	1015	1116	39	1	101	1	ASB11	23	15301725	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10		15301725	139968835	181	14409											
RBBP7	5931	hgsc.bcm.edu	37	chrX	16881137	16881137	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	catcatcattgggaatatgtActcgagcaaccaccagatga	14	9	8	10	1	2	2	2	1	0	1	3	4	2	3	2	1	3	2	2	1	4	3			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chrX:16881137A>C	ENST00000380087.2	-	3	608	c.248T>G	c.(247-249)gTa>gGa	p.V83G	RBBP7_ENST00000380084.4_Missense_Mutation_p.V127G|RBBP7_ENST00000404022.1_Missense_Mutation_p.V83G			Q16576	RBBP7_HUMAN	retinoblastoma binding protein 7	83					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)					GGGAATATGTACTCGAGCAAC	0.423																																					p.V127G		Atlas-SNP	.											.	RBBP7	58	.	0			c.T380G						PASS	.						162	133	143					X																	16881137		2203	4300	6503	SO:0001583	missense	5931	exon3			ATATGTACTCGAG	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.248T>G	X.37:g.16881137A>C	ENSP00000369427:p.Val83Gly	191	0	0		193	177	0.917098	NM_001198719	Q5JP00	Missense_Mutation	SNP	ENST00000380087.2	37	CCDS14179.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.617623	0.87359	.	.	ENSG00000102054	ENST00000380087;ENST00000380084;ENST00000404022;ENST00000416035;ENST00000468092	T;T;T;T	0.75260	-0.71;-0.92;-0.75;-0.77	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	D	0.90707	0.7084	H	0.96833	3.89	0.80722	D	1	P;D;D	0.63880	0.954;0.989;0.993	D;D;D	0.87578	0.995;0.998;0.997	D	0.93493	0.6837	10	0.87932	D	0	1.766	14.2069	0.65739	1.0:0.0:0.0:0.0	.	83;83;127	E9PC52;Q16576;Q5JP00	.;RBBP7_HUMAN;.	G	83;127;83;3;49	ENSP00000369427:V83G;ENSP00000369424:V127G;ENSP00000386068:V83G;ENSP00000392714:V3G	ENSP00000369424:V127G	V	-	2	0	RBBP7	16791058	1.000000	0.71417	0.973000	0.42090	0.998000	0.95712	9.283000	0.95860	1.954000	0.56735	0.481000	0.45027	GTA	.	.	none		0.423	RBBP7-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055920.2	NM_002893		C	16881137	A	C	16881137	3	2	36	1	0	0	0	0	1	0	0	0	13119	391	14	5	1069	5	RBBP7	23	16881137	Missense_Mutation	SNP	A	TCGA-GS-A9TT-01A-11D-A382-10	1579412	16881137	138389423	182	14410											
CXorf22	170063	hgsc.bcm.edu	37	chrX	35969413	35969413	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaacatgcacgtgtatacaaTaatagcccagagcccataaa	18	7	6	10	1	0	1	0	0	0	1	0	1	0	1	2	0	5	2	2	0	8	5			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chrX:35969413T>C	ENST00000297866.5	+	5	888	c.822T>C	c.(820-822)aaT>aaC	p.N274N		NM_152632.3	NP_689845.2	Q6ZTR5	CX022_HUMAN	chromosome X open reading frame 22	274										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						GTGTATACAATAATAGCCCAG	0.403																																					p.N274N		Atlas-SNP	.											.	CXorf22	272	.	0			c.T822C						PASS	.						64	57	59					X																	35969413		2202	4300	6502	SO:0001819	synonymous_variant	170063	exon5			ATACAATAATAGC	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.822T>C	X.37:g.35969413T>C		230	0	0		208	189	0.908654	NM_152632	Q5JRM8|Q8N6X8	Silent	SNP	ENST00000297866.5	37	CCDS14237.2																																																																																			.	.	none		0.403	CXorf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056216.2	NM_152632		C	35969413	T	C	35969413	2	2	36	1	0	0	0	0	0	0	0	1	4104	1403	49	3		3	CXorf22	23	35969413	Silent	SNP	T	TCGA-GS-A9TT-01A-11D-A382-10	19088276	35969413	119301147	183	14411											
BCOR	54880	hgsc.bcm.edu	37	chrX	39911471	39911471	+	Frame_Shift_Del	DEL	C	C	-																															ccagatctaacagctccttaCtttcagggttgaaggcttcc																										TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chrX:39911471delC	ENST00000378444.4	-	15	5387	c.5159delG	c.(5158-5160)agtfs	p.S1720fs	BCOR_ENST00000378455.4_Frame_Shift_Del_p.S1668fs|BCOR_ENST00000342274.4_Frame_Shift_Del_p.S1686fs|BCOR_ENST00000397354.3_Frame_Shift_Del_p.S1686fs|BCOR_ENST00000378463.1_Frame_Shift_Del_p.S563fs	NM_001123385.1	NP_001116857.1	Q6W2J9	BCOR_HUMAN	BCL6 corepressor	1720	Necessary and sufficient for interaction with PCGF1.				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						CAGCTCCTTACTTTCAGGGTT	0.493			"F, N, S, T"	RARA	"retinoblastoma, AML, APL(translocation)"		oculo-facio-cardio-dental genetic																														p.S1720fs		Pindel,Atlas-Indel	.		Rec	yes		X	Xp11.4	54880	BCL6 corepressor	yes		.	BCOR	351	.	0			c.5160delT						PASS	.						60	49	53					X																	39911471		2202	4300	6502	SO:0001589	frameshift_variant	54880	exon15			.	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.5159delG	X.37:g.39911471delC	ENSP00000367705:p.Ser1720fs	216	0	.		163	84	0.515	NM_001123385	D3DWB3|D3DWB4|Q29RF6|Q6P4B6|Q7Z2K7|Q8TEB4|Q96DB3|Q9H232|Q9H233|Q9HCJ7|Q9NXF2	Frame_Shift_Del	DEL	ENST00000378444.4	37	CCDS48093.1																																																																																			.	.	none		0.493	BCOR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060666.2	NM_017745		-	39911471	C	-	39911471	7	5	36	1	0	1	0	1	0	0	0	0	1386	565	20	0	112	0	BCOR	23	39911471	Frame_Shift_Del	DEL	C	TCGA-GS-A9TT-01A-11D-A382-10	3942058	39911471	115359089	184	14412											
PIM2	11040	hgsc.bcm.edu	37	chrX	48775918	48775918	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgaacgcttcccgatccttGcctcctacgcaggcggaggc	6	8	11	16	5	0	0	0	0	0	0	4	3	3	1	4	3	3	2	4	3	2	3			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chrX:48775918G>A	ENST00000376509.4	-	2	255	c.66C>T	c.(64-66)ggC>ggT	p.G22G		NM_006875.3	NP_006866.2	Q9P1W9	PIM2_HUMAN	Pim-2 proto-oncogene, serine/threonine kinase	22					apoptotic mitochondrial changes (GO:0008637)|cell proliferation (GO:0008283)|G1/S transition of mitotic cell cycle (GO:0000082)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|positive regulation of autophagy (GO:0010508)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|response to virus (GO:0009615)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			lung(3)|stomach(1)	4						CCCGATCCTTGCCTCCTACGC	0.677																																					p.G22G		Atlas-SNP	.											.	PIM2	31	.	0			c.C66T						PASS	.						27	25	26					X																	48775918		2203	4299	6502	SO:0001819	synonymous_variant	11040	exon2			ATCCTTGCCTCCT	U77735	CCDS14312.1	Xp11.23	2014-06-25	2014-06-25		ENSG00000102096	ENSG00000102096			8987	protein-coding gene	gene with protein product		300295	"pim-2 oncogene"			9804974	Standard	NM_006875		Approved		uc004dls.3	Q9P1W9	OTTHUMG00000024132	ENST00000376509.4:c.66C>T	X.37:g.48775918G>A		83	0	0		75	65	0.866667	NM_006875	A8K4G6|Q99739	Silent	SNP	ENST00000376509.4	37	CCDS14312.1																																																																																			.	.	none		0.677	PIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060805.1			A	48775918	G	A	48775918	2	1	36	1	0	0	0	0	0	0	0	1	11937	1306	46	2		2	PIM2	23	48775918	Silent	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	8864447	48775918	106494642	185	14413											
HDAC8	55869	hgsc.bcm.edu	37	chrX	71571612	71571612	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agttgaggatttgttggattCggtggggctcattgcggtct	5	15	16	5	2	2	1	1	1	1	0	3	3	2	3	0	6	1	3	0	6	0	5			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chrX:71571612C>T	ENST00000373573.3	-	10	1423	c.1082G>A	c.(1081-1083)cGa>cAa	p.R361Q	HDAC8_ENST00000373589.4_Missense_Mutation_p.R270Q|HDAC8_ENST00000429103.2_Missense_Mutation_p.R166Q|HDAC8_ENST00000373583.1_Intron	NM_018486.2	NP_060956.1	Q9BY41	HDAC8_HUMAN	histone deacetylase 8	361					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)	TTGTTGGATTCGGTGGGGCTC	0.547													C|||	1	0.000264901	0.0008	0.0	3775	,	,		14175	0.0		0.0	False		,,,				2504	0.0				p.R361Q		Atlas-SNP	.											.	HDAC8	18	.	0			c.G1082A						PASS	.						217	148	171					X																	71571612		2203	4300	6503	SO:0001583	missense	55869	exon10			TGGATTCGGTGGG	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.1082G>A	X.37:g.71571612C>T	ENSP00000362674:p.Arg361Gln	76	0	0		71	61	0.859155	NM_018486	A6ND12|A6ND61|A6NET3|A6NJR3|A8MQ62|B4DKN0|B4DV22|Q86VC8|Q9NP76|Q9NYH4	Missense_Mutation	SNP	ENST00000373573.3	37	CCDS14420.1	.	.	.	.	.	.	.	.	.	.	C	15.49	2.849435	0.51270	.	.	ENSG00000147099	ENST00000373573;ENST00000373589;ENST00000429103	T;T;T	0.80123	-1.34;-1.34;-1.34	4.79	3.0	0.34707	Histone deacetylase domain (1);	0.346769	0.32719	N	0.005733	T	0.55641	0.1933	N	0.03608	-0.345	0.80722	D	1	B;B	0.12013	0.005;0.0	B;B	0.01281	0.0;0.0	T	0.51718	-0.8670	10	0.54805	T	0.06	-1.3077	5.1597	0.15054	0.0:0.6597:0.0:0.3403	.	270;361	B4DKN0;Q9BY41	.;HDAC8_HUMAN	Q	361;270;166	ENSP00000362674:R361Q;ENSP00000362691:R270Q;ENSP00000388459:R166Q	ENSP00000362674:R361Q	R	-	2	0	HDAC8	71488337	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.434000	0.34958	1.105000	0.41606	0.436000	0.28706	CGA	.	.	none		0.547	HDAC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057193.2	NM_018486		T	71571612	C	T	71571612	3	4	36	1	0	0	0	0	1	0	0	0	7022	884	31	1	59	1	HDAC8	23	71571612	Missense_Mutation	SNP	C	TCGA-GS-A9TT-01A-11D-A382-10	22795694	71571612	83698948	186	14414											
CYLC1	1538	hgsc.bcm.edu	37	chrX	83127996	83127996	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggccacccatttacacagctGccagggaacagactccattc	11	7	8	15	0	0	1	0	0	0	1	2	2	1	2	4	2	4	1	4	2	2	3			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chrX:83127996G>T	ENST00000329312.4	+	4	317	c.280G>T	c.(280-282)Gcc>Tcc	p.A94S		NM_021118.1	NP_066941.1	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head cytoskeleton 1	94					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						TTACACAGCTGCCAGGGAACA	0.373																																					p.A94S		Atlas-SNP	.											.	CYLC1	272	.	0			c.G280T						PASS	.						39	37	38					X																	83127996		2201	4294	6495	SO:0001583	missense	1538	exon4			ACAGCTGCCAGGG	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.280G>T	X.37:g.83127996G>T	ENSP00000331556:p.Ala94Ser	214	0	0		157	143	0.910828	NM_021118	A0AVQ8|Q5JQQ9	Missense_Mutation	SNP	ENST00000329312.4	37	CCDS35341.1	.	.	.	.	.	.	.	.	.	.	g	13.83	2.353949	0.41700	.	.	ENSG00000183035	ENST00000329312;ENST00000544771	T	0.51817	0.69	4.58	-1.37	0.09056	.	.	.	.	.	T	0.33206	0.0855	L	0.49126	1.545	0.09310	N	1	B;B	0.28636	0.218;0.218	B;B	0.25140	0.058;0.058	T	0.30504	-0.9976	9	0.52906	T	0.07	4.0792	0.8651	0.01202	0.1939:0.1371:0.3069:0.3621	.	94;94	P35663;F5H4V5	CYLC1_HUMAN;.	S	94	ENSP00000331556:A94S	ENSP00000331556:A94S	A	+	1	0	CYLC1	83014652	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.925000	0.03992	-0.564000	0.06070	-0.191000	0.12829	GCC	.	.	none		0.373	CYLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057371.1	NM_021118		T	83127996	G	T	83127996	3	4	36	1	0	0	0	0	1	0	0	0	4143	1319	46	4	294	4	CYLC1	23	83127996	Missense_Mutation	SNP	G	TCGA-GS-A9TT-01A-11D-A382-10	11556384	83127996	72142564	187	14415											
AGTR2	186	hgsc.bcm.edu	37	chrX	115303934	115303934	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catgtttgcaagcattttttTtatcacctgcatgagtgttg	8	18	8	7	0	1	1	1	1	0	0	1	1	1	1	1	0	3	5	1	0	2	6			TCGA-GS-A9TT-01A-11D-A382-10	TCGA-GS-A9TT-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e6b849d0-569e-4f4a-aba6-25227d709267	ddddacd6-a277-4d16-bc20-4201b0fe2008	g.chrX:115303934T>G	ENST00000371906.4	+	3	591	c.401T>G	c.(400-402)tTt>tGt	p.F134C		NM_000686.4	NP_000677.2	P50052	AGTR2_HUMAN	angiotensin II receptor, type 2	134					aldosterone secretion (GO:0035932)|angiotensin-activated signaling pathway (GO:0038166)|blood vessel remodeling (GO:0001974)|brain development (GO:0007420)|brain renin-angiotensin system (GO:0002035)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell surface receptor signaling pathway (GO:0007166)|cellular response to dexamethasone stimulus (GO:0071549)|cellular sodium ion homeostasis (GO:0006883)|cerebellar cortex development (GO:0021695)|dopamine biosynthetic process (GO:0042416)|exploration behavior (GO:0035640)|extracellular negative regulation of signal transduction (GO:1900116)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell growth (GO:0030308)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of heart rate (GO:0010459)|negative regulation of icosanoid secretion (GO:0032304)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of norepinephrine secretion (GO:0010700)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasodilation (GO:0045909)|regulation of blood pressure (GO:0008217)|regulation of metanephros size (GO:0035566)|regulation of systemic arterial blood pressure by circulatory renin-angiotensin (GO:0001991)|regulation of transcription factor import into nucleus (GO:0042990)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to organonitrogen compound (GO:0010243)|vasodilation by angiotensin involved in regulation of systemic arterial blood pressure (GO:0002033)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	angiotensin type II receptor activity (GO:0004945)|peptide hormone binding (GO:0017046)|receptor antagonist activity (GO:0048019)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|skin(1)	24					Tasosartan(DB01349)	AGCATTTTTTTTATCACCTGC	0.388																																					p.F134C		Atlas-SNP	.											.	AGTR2	62	.	0			c.T401G						PASS	.						178	171	173					X																	115303934		2203	4300	6503	SO:0001583	missense	186	exon3			TTTTTTTTATCAC	AY324607	CCDS14569.1	Xq22-q23	2012-08-08			ENSG00000180772	ENSG00000180772		"GPCR / Class A : Angiotensin receptors"	338	protein-coding gene	gene with protein product		300034	"angiotensin receptor 2"			1550596	Standard	NM_000686		Approved	AT2, MRX88	uc004eqh.4	P50052	OTTHUMG00000022243	ENST00000371906.4:c.401T>G	X.37:g.115303934T>G	ENSP00000360973:p.Phe134Cys	345	0	0		249	228	0.915663	NM_000686	B2R9V1|Q13016|Q6FGY7	Missense_Mutation	SNP	ENST00000371906.4	37	CCDS14569.1	.	.	.	.	.	.	.	.	.	.	T	17.00	3.277816	0.59758	.	.	ENSG00000180772	ENST00000371906	T	0.39229	1.09	4.69	4.69	0.59074	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.58509	0.2127	L	0.59912	1.85	0.54753	D	0.999987	D	0.89917	1.0	D	0.85130	0.997	T	0.61753	-0.6998	10	0.87932	D	0	-12.1196	11.0559	0.47918	0.0:0.0:0.0:1.0	.	134	P50052	AGTR2_HUMAN	C	134	ENSP00000360973:F134C	ENSP00000360973:F134C	F	+	2	0	AGTR2	115217962	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.023000	0.70848	1.734000	0.51633	0.412000	0.27726	TTT	.	.	none		0.388	AGTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057984.1	NM_000686		G	115303934	T	G	115303934	3	3	36	1	0	0	0	0	1	0	0	0	402	1841	64	5	403	5	AGTR2	23	115303934	Missense_Mutation	SNP	T	TCGA-GS-A9TT-01A-11D-A382-10	32175938	115303934	39966626	188	14416											
PRAMEF4	400735	hgsc.bcm.edu	37	chr1	12943023	12943023	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagaggcctcagagggaggcGgcggaagggccaggactgca	10	2	19	10	2	1	2	1	0	0	2	1	5	1	5	2	7	1	1	2	7	1	0			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr1:12943023G>A	ENST00000235349.5	-	2	263	c.193C>T	c.(193-195)Cgc>Tgc	p.R65C		NM_001009611.2	NP_001009611.1	O60810	PRAM4_HUMAN	PRAME family member 4	65					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)		AGAGGGAGGCGGCGGAAGGGC	0.602																																					p.R65C		Atlas-SNP	.											.	PRAMEF4	62	.	0			c.C193T						PASS	.						39	45	43					1																	12943023		2186	4267	6453	SO:0001583	missense	400735	exon2			GGAGGCGGCGGAA		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.193C>T	1.37:g.12943023G>A	ENSP00000235349:p.Arg65Cys	203	0	0		195	49	0.251282	NM_001009611	Q5LJB5	Missense_Mutation	SNP	ENST00000235349.5	37	CCDS30592.1	.	.	.	.	.	.	.	.	.	.	g	3.809	-0.040112	0.07497	.	.	ENSG00000243073	ENST00000235349	T	0.05258	3.47	1.48	-0.647	0.11468	.	1.582610	0.03465	N	0.212854	T	0.03220	0.0094	N	0.05330	-0.07	0.09310	N	1	B	0.17038	0.02	B	0.13407	0.009	T	0.40664	-0.9551	10	0.14656	T	0.56	.	3.9166	0.09225	0.5068:0.0:0.4932:0.0	.	65	O60810	PRAM4_HUMAN	C	65	ENSP00000235349:R65C	ENSP00000235349:R65C	R	-	1	0	PRAMEF4	12865610	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.260000	0.02858	-0.198000	0.10333	-0.498000	0.04607	CGC	.	.	none		0.602	PRAMEF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005518.1	NM_001009611		A	12943023	G	A	12943023	3	1	37	1	0	0	0	0	1	0	0	0	12449	1116	39	1	1255	1	PRAMEF4	1	12943023	Missense_Mutation	SNP	G	TCGA-GS-A9TU-01A-11D-A382-10		12943023	236307598	1	14417											
ASAP3	55616	hgsc.bcm.edu	37	chr1	23779193	23779193	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagcatggagactcacctgTcgaccgtccctcagctgccc	7	7	9	18	2	2	1	2	0	0	1	4	3	3	1	5	1	3	2	5	1	0	0			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr1:23779193T>C	ENST00000336689.3	-	4	464	c.420A>G	c.(418-420)cgA>cgG	p.R140R	ASAP3_ENST00000437606.2_Silent_p.R140R	NM_017707.3	NP_060177.2	Q8TDY4	ASAP3_HUMAN	ArfGAP with SH3 domain, ankyrin repeat and PH domain 3	140					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						GACTCACCTGTCGACCGTCCC	0.577																																					p.R140R		Atlas-SNP	.											.	ASAP3	65	.	0			c.A420G						PASS	.						184	173	177					1																	23779193		2203	4300	6503	SO:0001819	synonymous_variant	55616	exon4			CACCTGTCGACCG	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.420A>G	1.37:g.23779193T>C		94	0	0		71	14	0.197183	NM_001143778	B3KRW0|B4DHH4|Q6P9F4|Q86UY1|Q9NXK2	Silent	SNP	ENST00000336689.3	37	CCDS235.1																																																																																			.	.	none		0.577	ASAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008916.2	NM_017707		C	23779193	T	C	23779193	2	2	37	1	0	0	0	0	0	0	0	1	1012	1654	58	3		3	ASAP3	1	23779193	Silent	SNP	T	TCGA-GS-A9TU-01A-11D-A382-10	10836170	23779193	225471428	2	14418											
ZC3H12A	80149	hgsc.bcm.edu	37	chr1	37947259	37947259	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cctggtgttcacaccatcacGacgcgtgggtggcaagcggg	7	7	15	12	4	2	0	2	0	0	0	2	1	2	0	2	4	1	2	2	4	1	1			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr1:37947259G>A	ENST00000373087.6	+	4	757	c.641G>A	c.(640-642)cGa>cAa	p.R214Q		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)				ACACCATCACGACGCGTGGGT	0.587																																					p.R214Q		Atlas-SNP	.											.	ZC3H12A	58	.	0			c.G641A						PASS	.						254	225	235					1																	37947259		2203	4300	6503	SO:0001583	missense	80149	exon4			CATCACGACGCGT		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.641G>A	1.37:g.37947259G>A	ENSP00000362179:p.Arg214Gln	95	0	0		74	12	0.162162	NM_025079		Missense_Mutation	SNP	ENST00000373087.6	37	CCDS417.1	.	.	.	.	.	.	.	.	.	.	G	35	5.518547	0.96416	.	.	ENSG00000163874	ENST00000373087;ENST00000373082	T	0.44482	0.92	5.65	5.65	0.86999	Ribonuclease Zc3h12a-like (1);	0.000000	0.85682	D	0.000000	T	0.68869	0.3048	M	0.80982	2.52	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.70637	-0.4817	10	0.56958	D	0.05	-36.0527	19.7405	0.96228	0.0:0.0:1.0:0.0	.	214	Q5D1E8	ZC12A_HUMAN	Q	214	ENSP00000362179:R214Q	ENSP00000362174:R214Q	R	+	2	0	ZC3H12A	37719846	1.000000	0.71417	0.478000	0.27316	0.805000	0.45488	9.807000	0.99171	2.655000	0.90218	0.655000	0.94253	CGA	.	.	none		0.587	ZC3H12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012154.2	NM_025079		A	37947259	G	A	37947259	3	1	37	1	0	0	0	0	1	0	0	0	17576	1058	37	1	651	1	ZC3H12A	1	37947259	Missense_Mutation	SNP	G	TCGA-GS-A9TU-01A-11D-A382-10	14168066	37947259	211303362	3	14419											
DCAF8	50717	hgsc.bcm.edu	37	chr1	160209665	160209665	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcccatgctgcaggcggaaaCgctgcacaaagactcttgcc	10	6	11	14	2	1	1	0	0	1	1	1	2	1	2	2	2	5	4	2	2	2	1			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr1:160209665C>T	ENST00000368073.3	-	4	979	c.545G>A	c.(544-546)cGt>cAt	p.R182H	DCAF8_ENST00000608310.1_Missense_Mutation_p.R336H|DCAF8_ENST00000556710.1_Missense_Mutation_p.R336H|DCAF8_ENST00000475733.1_Missense_Mutation_p.R182H|DCAF8_ENST00000610139.1_Missense_Mutation_p.R182H|DCAF8_ENST00000368074.1_Missense_Mutation_p.R182H|DCAF8_ENST00000326837.2_Missense_Mutation_p.R182H			Q5TAQ9	DCAF8_HUMAN	DDB1 and CUL4 associated factor 8	182				QR -> HG (in Ref. 1; AAA16607). {ECO:0000305}.	protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(16)|skin(3)|upper_aerodigestive_tract(1)	33						CAGGCGGAAACGCTGCACAAA	0.622																																					p.R182H		Atlas-SNP	.											.	DCAF8	64	.	0			c.G545A						PASS	.						60	59	60					1																	160209665		2203	4300	6503	SO:0001583	missense	50717	exon4			CGGAAACGCTGCA	AK093176	CCDS1200.1	1q22-q23	2013-01-09	2009-07-17	2009-07-17	ENSG00000132716	ENSG00000132716		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	24891	protein-coding gene	gene with protein product		615820	"WD repeat domain 42A"	WDR42A		11401431	Standard	NM_015726		Approved	H326, FLJ35857	uc010pjb.1	Q5TAQ9	OTTHUMG00000031604	ENST00000368073.3:c.545G>A	1.37:g.160209665C>T	ENSP00000357052:p.Arg182His	192	0	0		140	29	0.207143	NM_015726	D3DVE6|Q12839|Q4QQI6|Q53F14|Q66K50|Q68CS7|Q96E00	Missense_Mutation	SNP	ENST00000368073.3	37	CCDS1200.1	.	.	.	.	.	.	.	.	.	.	C	19.81	3.896809	0.72639	.	.	ENSG00000132716;ENSG00000132716;ENSG00000132716;ENSG00000132716;ENSG00000132716;ENSG00000132716;ENSG00000258465	ENST00000368073;ENST00000326837;ENST00000368074;ENST00000555195;ENST00000540855;ENST00000447377;ENST00000556710	D;D;D;D;D;D	0.81579	-1.51;-1.51;-1.51;-1.51;-1.51;-1.51	5.04	5.04	0.67666	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.64402	U	0.000001	D	0.82683	0.5090	L	0.39898	1.24	0.58432	D	0.999999	D;P;P	0.76494	0.999;0.934;0.742	D;B;B	0.78314	0.991;0.394;0.139	D	0.83516	0.0083	10	0.48119	T	0.1	-0.8097	17.1813	0.86856	0.0:1.0:0.0:0.0	.	336;182;182	G3V3G9;Q5TAQ9-2;Q5TAQ9	.;.;DCAF8_HUMAN	H	182;182;182;336;163;182;336	ENSP00000357052:R182H;ENSP00000318227:R182H;ENSP00000357053:R182H;ENSP00000451989:R336H;ENSP00000413688:R182H;ENSP00000451235:R336H	ENSP00000318227:R182H	R	-	2	0	RP11-574F21.3;DCAF8	158476289	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.125000	0.64715	2.333000	0.79357	0.655000	0.94253	CGT	.	.	none		0.622	DCAF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077402.2	NM_015726		T	160209665	C	T	160209665	3	4	37	1	0	0	0	0	1	0	0	0	4278	536	19	1	1292	1	DCAF8	1	160209665	Missense_Mutation	SNP	C	TCGA-GS-A9TU-01A-11D-A382-10	122262406	160209665	89040956	4	14420											
EIF2B4	8890	hgsc.bcm.edu	37	chr2	27587653	27587653	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtatgtttcacagcaaaccAgcactggtacattatgggct	11	12	9	9	0	1	0	1	0	0	0	1	0	1	0	1	2	4	6	1	2	4	4			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr2:27587653A>T	ENST00000347454.4	-	12	1475	c.1304T>A	c.(1303-1305)cTg>cAg	p.L435Q	EIF2B4_ENST00000451130.2_Missense_Mutation_p.L455Q|EIF2B4_ENST00000493344.2_Missense_Mutation_p.L456Q|EIF2B4_ENST00000445933.2_Missense_Mutation_p.L434Q|AC074117.10_ENST00000412749.1_RNA	NM_001034116.1|NM_015636.3	NP_001029288.1|NP_056451.3	Q9UI10	EI2BD_HUMAN	eukaryotic translation initiation factor 2B, subunit 4 delta, 67kDa	435					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)					ACAGCAAACCAGCACTGGTAC	0.522																																					p.L455Q		Atlas-SNP	.											.	EIF2B4	48	.	0			c.T1364A						PASS	.						106	94	98					2																	27587653		2203	4300	6503	SO:0001583	missense	8890	exon11			CAAACCAGCACTG	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.1304T>A	2.37:g.27587653A>T	ENSP00000233552:p.Leu435Gln	94	0	0		70	21	0.3	NM_172195	Q53RY7|Q5BJF4|Q9BUV9|Q9UBG4|Q9UIQ9|Q9UJ95	Missense_Mutation	SNP	ENST00000347454.4	37	CCDS33164.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.196658	0.79015	.	.	ENSG00000115211	ENST00000347454;ENST00000414437;ENST00000445933;ENST00000451130;ENST00000493344	D;D;D;D	0.94000	-3.33;-3.33;-3.33;-3.33	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	D	0.97145	0.9067	M	0.91510	3.215	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.997	D;D;D;D	0.87578	0.998;0.998;0.992;0.982	D	0.97934	1.0322	10	0.87932	D	0	-11.0063	13.5046	0.61477	1.0:0.0:0.0:0.0	.	432;434;435;455	F5H6W1;Q9UI10-3;Q9UI10;Q9UI10-2	.;.;EI2BD_HUMAN;.	Q	435;432;434;455;456	ENSP00000233552:L435Q;ENSP00000394397:L434Q;ENSP00000394869:L455Q;ENSP00000429323:L456Q	ENSP00000233552:L435Q	L	-	2	0	EIF2B4	27441157	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	9.081000	0.94049	2.058000	0.61347	0.533000	0.62120	CTG	.	.	none		0.522	EIF2B4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324448.1			T	27587653	A	T	27587653	3	4	37	1	0	0	0	0	1	0	0	0	5005	188	7	5	275	5	EIF2B4	2	27587653	Missense_Mutation	SNP	A	TCGA-GS-A9TU-01A-11D-A382-10		27587653	215611720	5	14421											
DYSF	8291	hgsc.bcm.edu	37	chr2	71778761	71778761	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggtgtggcttatcgtggcCggcttctgctctccctggag	4	12	14	11	2	2	0	0	0	2	0	4	1	2	1	2	5	1	3	2	5	2	2	rs377735262		TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr2:71778761C>T	ENST00000258104.3	+	19	1940	c.1663C>T	c.(1663-1665)Cgg>Tgg	p.R555W	DYSF_ENST00000409744.1_Missense_Mutation_p.R542W|DYSF_ENST00000409366.1_Missense_Mutation_p.R556W|DYSF_ENST00000409762.1_Missense_Mutation_p.R572W|DYSF_ENST00000394120.2_Missense_Mutation_p.R556W|DYSF_ENST00000410020.3_Missense_Mutation_p.R573W|DYSF_ENST00000409651.1_Missense_Mutation_p.R587W|DYSF_ENST00000410041.1_Missense_Mutation_p.R573W|DYSF_ENST00000409582.3_Missense_Mutation_p.R572W|DYSF_ENST00000429174.2_Missense_Mutation_p.R555W|DYSF_ENST00000413539.2_Missense_Mutation_p.R586W	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	555			R -> W (in isolated hyperCKemia, LGMD2B and MMD1). {ECO:0000269|PubMed:16010686, ECO:0000269|PubMed:18853459}.		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						TTATCGTGGCCGGCTTCTGCT	0.637																																					p.R587W		Atlas-SNP	.											.	DYSF	536	.	0			c.C1759T	GRCh37	CM053205	DYSF	M		PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	52	45	47		1666,1621,1621,1663,1756,1714,1714,1759,1666,1624,1717,1624,1717,1663	4.6	1	2		47	1,8593		0,1,4296	no	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	DYSF	NM_001130455.1,NM_001130976.1,NM_001130977.1,NM_001130978.1,NM_001130979.1,NM_001130980.1,NM_001130981.1,NM_001130982.1,NM_001130983.1,NM_001130984.1,NM_001130985.1,NM_001130986.1,NM_001130987.1,NM_003494.3	101,101,101,101,101,101,101,101,101,101,101,101,101,101	0,1,6499	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	556/2082,541/2067,541/2088,555/2102,586/2112,572/2098,572/2119,587/2113,556/2103,542/2089,573/2099,542/2068,573/2120,555/2081	71778761	1,12999	2203	4297	6500	SO:0001583	missense	8291	exon20			CGTGGCCGGCTTC	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.1663C>T	2.37:g.71778761C>T	ENSP00000258104:p.Arg555Trp	50	0	0		53	16	0.301887	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	37	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.228105	0.79576	0.0	1.16E-4	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	D;D;D;D;D;D;D;D;D;D;D	0.94232	-3.11;-3.38;-3.38;-3.06;-3.05;-3.11;-3.04;-3.32;-3.05;-3.38;-3.37	5.47	4.57	0.56435	.	0.000000	0.85682	D	0.000000	D	0.97002	0.9021	M	0.89534	3.04	0.58432	D	0.999996	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;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999	D	0.97395	0.9992	10	0.87932	D	0	-33.0299	12.9746	0.58531	0.1684:0.8316:0.0:0.0	.	587;573;556;542;573;542;572;541;586;572;555;541;556;555	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	W	586;572;572;555;555;587;556;542;556;573;573	ENSP00000407046:R586W;ENSP00000387137:R572W;ENSP00000386547:R572W;ENSP00000398305:R555W;ENSP00000258104:R555W;ENSP00000386683:R587W;ENSP00000377678:R556W;ENSP00000386285:R542W;ENSP00000386512:R556W;ENSP00000386881:R573W;ENSP00000386617:R573W	ENSP00000258104:R555W	R	+	1	2	DYSF	71632269	0.995000	0.38212	0.999000	0.59377	0.937000	0.57800	1.029000	0.30140	1.234000	0.43709	0.655000	0.94253	CGG	.	.	weak		0.637	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494		T	71778761	C	T	71778761	3	4	37	1	0	0	0	0	1	0	0	0	4861	643	23	1	1929	1	DYSF	2	71778761	Missense_Mutation	SNP	C	TCGA-GS-A9TU-01A-11D-A382-10	44191108	71778761	171420612	6	14422											
LRRTM4	80059	hgsc.bcm.edu	37	chr2	77746792	77746792	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctgaatgctgttgaaccttAatgataagccttgtgaccct	10	14	8	9	0	1	4	0	4	1	0	1	4	1	4	3	0	3	2	3	0	4	4			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr2:77746792A>G	ENST00000409093.1	-	3	539	c.203T>C	c.(202-204)tTa>tCa	p.L68S	LRRTM4_ENST00000409884.1_Missense_Mutation_p.L68S|LRRTM4_ENST00000409088.3_Missense_Mutation_p.L68S|LRRTM4_ENST00000409282.1_Missense_Mutation_p.L69S|LRRTM4_ENST00000409911.1_Missense_Mutation_p.L69S			Q86VH4	LRRT4_HUMAN	leucine rich repeat transmembrane neuronal 4	68					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)		GTTGAACCTTAATGATAAGCC	0.418																																					p.L68S		Atlas-SNP	.											LRRTM4_ENST00000409093,colon,carcinoma,+1,2	LRRTM4	334	2	0			c.T203C						PASS	.						130	123	125					2																	77746792		1926	4136	6062	SO:0001583	missense	80059	exon3			AACCTTAATGATA	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.203T>C	2.37:g.77746792A>G	ENSP00000386357:p.Leu68Ser	229	0	0		232	57	0.24569	NM_024993	Q4FZ98|Q6UXJ7	Missense_Mutation	SNP	ENST00000409093.1	37	CCDS46346.1	.	.	.	.	.	.	.	.	.	.	A	16.89	3.247695	0.59103	.	.	ENSG00000176204	ENST00000409911;ENST00000409884;ENST00000409093;ENST00000409088;ENST00000409282	T;T;T;T;T	0.75821	-0.97;-0.97;-0.97;-0.97;-0.97	5.72	5.72	0.89469	.	0.000000	0.64402	D	0.000001	D	0.90741	0.7094	H	0.96604	3.85	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.93611	0.6939	10	0.87932	D	0	.	14.8238	0.70094	1.0:0.0:0.0:0.0	.	69;68;68	Q4KMX1;Q86VH4-2;Q86VH4	.;.;LRRT4_HUMAN	S	69;68;68;68;69	ENSP00000387228:L69S;ENSP00000387297:L68S;ENSP00000386357:L68S;ENSP00000386236:L68S;ENSP00000386286:L69S	ENSP00000386236:L68S	L	-	2	0	LRRTM4	77600300	0.996000	0.38824	0.920000	0.36463	0.998000	0.95712	9.339000	0.96797	2.189000	0.69895	0.533000	0.62120	TTA	.	.	none		0.418	LRRTM4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328225.1	NM_024993		G	77746792	A	G	77746792	3	3	37	1	0	0	0	0	1	0	0	0	9051	372	13	3	1583	3	LRRTM4	2	77746792	Missense_Mutation	SNP	A	TCGA-GS-A9TU-01A-11D-A382-10	5968031	77746792	165452581	7	14423											
SCN3A	6328	hgsc.bcm.edu	37	chr2	165948871	165948871	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaattctccagtgaacagaAcaatgaacactaggttgatc	16	9	7	9	0	1	4	0	3	1	1	3	4	1	4	1	1	3	1	1	1	6	3			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr2:165948871A>C	ENST00000360093.3	-	27	5191	c.4700T>G	c.(4699-4701)gTt>gGt	p.V1567G	AC013463.2_ENST00000431341.1_RNA|SCN3A_ENST00000409101.3_Missense_Mutation_p.V1518G|SCN3A_ENST00000540861.1_Missense_Mutation_p.V50G|SCN3A_ENST00000283254.7_Missense_Mutation_p.V1567G|SCN3A_ENST00000465043.1_5'UTR	NM_001081677.1	NP_001075146.1	Q9NY46	SCN3A_HUMAN	sodium channel, voltage-gated, type III, alpha subunit	1567					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)	AGTGAACAGAACAATGAACAC	0.468																																					p.V1567G		Atlas-SNP	.											.	SCN3A	544	.	0			c.T4700G						PASS	.						168	135	146					2																	165948871		2203	4300	6503	SO:0001583	missense	6328	exon27			AACAGAACAATGA	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.4700T>G	2.37:g.165948871A>C	ENSP00000353206:p.Val1567Gly	160	0	0		125	27	0.216	NM_006922	Q16142|Q53SX0|Q9BZB3|Q9C006|Q9NYK2|Q9P2J1|Q9UPD1|Q9Y6P4	Missense_Mutation	SNP	ENST00000360093.3	37		.	.	.	.	.	.	.	.	.	.	A	15.82	2.945058	0.53079	.	.	ENSG00000153253	ENST00000360093;ENST00000283254;ENST00000409101;ENST00000540861	D;D;D;D	0.98493	-4.96;-4.96;-4.96;-4.96	5.78	5.78	0.91487	.	0.231242	0.33401	N	0.004958	D	0.97204	0.9086	L	0.37750	1.13	0.80722	D	1	P;B;B	0.41188	0.741;0.001;0.001	P;B;B	0.47744	0.556;0.003;0.015	D	0.97804	1.0246	10	0.56958	D	0.05	.	16.4053	0.83662	1.0:0.0:0.0:0.0	.	1518;1518;1567	Q9NY46-2;Q9NY46-4;Q9NY46-3	.;.;.	G	1567;1567;1518;50	ENSP00000353206:V1567G;ENSP00000283254:V1567G;ENSP00000386726:V1518G;ENSP00000439920:V50G	ENSP00000283254:V1567G	V	-	2	0	SCN3A	165657117	1.000000	0.71417	0.998000	0.56505	0.820000	0.46376	9.287000	0.95975	2.333000	0.79357	0.482000	0.46254	GTT	.	.	none		0.468	SCN3A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_006922		C	165948871	A	C	165948871	3	2	37	1	0	0	0	0	1	0	0	0	13933	43	2	5	1310	5	SCN3A	2	165948871	Missense_Mutation	SNP	A	TCGA-GS-A9TU-01A-11D-A382-10	88202079	165948871	77250502	8	14424											
SCN1A	6323	hgsc.bcm.edu	37	chr2	166930005	166930006	+	Frame_Shift_Ins	INS	-	-	T																															gggccattttcgtcgtcatcINSttttttgtctggtttgggat																										TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr2:166930005_166930006insT	ENST00000303395.4	-	1	125_126	c.126_127insA	c.(124-129)aaagatfs	p.D43fs	SCN1A_ENST00000375405.3_Frame_Shift_Ins_p.D43fs|AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000409050.1_Frame_Shift_Ins_p.D43fs|SCN1A_ENST00000423058.2_Frame_Shift_Ins_p.D43fs|AC010127.3_ENST00000599041.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	43					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)	p.K42N(4)		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)	TCGTCGTCATCTTTTTTGTCTG	0.446																																					p.D43fs		Pindel,Atlas-Indel	.											.	SCN1A	641	.	4	Substitution - Missense(4)	lung(4)	c.127_128insA						PASS	.																																			SO:0001589	frameshift_variant	6323	exon1			.	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.127dupA	2.37:g.166930011_166930011dupT	ENSP00000303540:p.Asp43fs	377	0	.		338	51	0.151	NM_001165964	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Frame_Shift_Ins	INS	ENST00000303395.4	37	CCDS54413.1																																																																																			.	.	none		0.446	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920		T	166930006	-	T	166930005	7	5	37	1	0	1	1	0	0	0	0	0	13929	913	32	0	6006	0	SCN1A	2	166930005	Frame_Shift_Ins	INS	-	TCGA-GS-A9TU-01A-11D-A382-10	981134	166930005	76269368	9	14425											
CPS1	1373	hgsc.bcm.edu	37	chr2	211464275	211464275	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcatgggtggccagacagcTctgaactgtggtgagttctt	7	11	15	8	0	2	3	0	2	2	1	2	3	2	3	1	4	2	3	1	4	1	2			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr2:211464275T>C	ENST00000233072.5	+	14	1735	c.1539T>C	c.(1537-1539)gcT>gcC	p.A513A	CPS1_ENST00000430249.2_Silent_p.A519A|CPS1_ENST00000451903.2_Silent_p.A62A	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	513					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)	GCCAGACAGCTCTGAACTGTG	0.428																																					p.A519A		Atlas-SNP	.											.	CPS1	485	.	0			c.T1557C						PASS	.						114	117	116					2																	211464275		2203	4300	6503	SO:0001819	synonymous_variant	1373	exon15			GACAGCTCTGAAC	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.1539T>C	2.37:g.211464275T>C		125	0	0		116	24	0.206897	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Silent	SNP	ENST00000233072.5	37	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	T	9.241	1.038216	0.19669	.	.	ENSG00000021826	ENST00000536125	.	.	.	5.17	3.93	0.45458	.	.	.	.	.	T	0.66703	0.2816	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.70539	-0.4844	5	0.87932	D	0	-26.7793	11.0084	0.47649	0.0:0.0:0.2859:0.7141	.	.	.	.	P	513	.	ENSP00000445539:L513P	L	+	2	0	CPS1	211172520	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	1.051000	0.30417	2.084000	0.62774	0.374000	0.22700	CTC	.	.	none		0.428	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5			C	211464275	T	C	211464275	2	2	37	1	0	0	0	0	0	0	0	1	3825	1538	54	3		3	CPS1	2	211464275	Silent	SNP	T	TCGA-GS-A9TU-01A-11D-A382-10	44534270	211464275	31735098	10	14426											
APEH	327	hgsc.bcm.edu	37	chr3	49718542	49718542	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tccccttggcagaaagttggGttcctgccttctgcagggaa	7	11	12	11	0	1	1	0	0	1	1	3	2	3	2	4	3	2	4	4	3	2	4			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr3:49718542G>A	ENST00000296456.5	+	15	1708	c.1308G>A	c.(1306-1308)ggG>ggA	p.G436G	APEH_ENST00000438011.1_Silent_p.G436G	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase	436					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)		AGAAAGTTGGGTTCCTGCCTT	0.597																																					p.G436G		Atlas-SNP	.											.	APEH	45	.	0			c.G1308A						PASS	.						113	105	108					3																	49718542		2203	4300	6503	SO:0001819	synonymous_variant	327	exon15			AGTTGGGTTCCTG	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.1308G>A	3.37:g.49718542G>A		94	0	0		65	20	0.307692	NM_001640	Q9BQ33|Q9P0Y2	Silent	SNP	ENST00000296456.5	37	CCDS2801.1																																																																																			.	.	none		0.597	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2			A	49718542	G	A	49718542	2	1	37	1	0	0	0	0	0	0	0	1	768	1248	44	2		2	APEH	3	49718542	Silent	SNP	G	TCGA-GS-A9TU-01A-11D-A382-10		49718542	148303888	11	14427											
MUC13	56667	hgsc.bcm.edu	37	chr3	124646710	124646710	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagtagctgttgggaaaggTgtatttgctgtggtgctagc	8	13	16	4	0	0	0	0	0	0	0	0	2	0	1	0	3	4	6	0	3	5	5	rs76825834		TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr3:124646710T>A	ENST00000311075.3	-	2	218	c.180A>T	c.(178-180)acA>acT	p.T60T	MUC13_ENST00000497378.1_5'Flank	NM_033049.3	NP_149038	Q9H3R2	MUC13_HUMAN	mucin 13, cell surface associated	60	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						TTGGGAAAGGTGTATTTGCTG	0.458																																					p.T60T		Atlas-SNP	.											.	MUC13	57	.	0			c.A180T						PASS	.						214	213	213					3																	124646710		2203	4300	6503	SO:0001819	synonymous_variant	56667	exon2			GAAAGGTGTATTT	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.180A>T	3.37:g.124646710T>A		123	0	0		121	7	0.0578512	NM_033049	Q6UWD9|Q9NXT5	Silent	SNP	ENST00000311075.3	37																																																																																				.	.	weak		0.458	MUC13-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000355714.1	NM_033049		A	124646710	T	A	124646710	2	1	37	1	0	0	0	0	0	0	0	1	9980	1683	59	5		5	MUC13	3	124646710	Silent	SNP	T	TCGA-GS-A9TU-01A-11D-A382-10	74928168	124646710	73375720	12	14428											
ZIC1	7545	hgsc.bcm.edu	37	chr3	147128808	147128808	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acgggcgagaagccctttccCtgccccttccctggctgtgg	4	9	12	16	2	0	1	0	0	0	1	2	2	2	1	5	3	2	1	5	3	1	2			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr3:147128808C>T	ENST00000282928.4	+	1	1638	c.909C>T	c.(907-909)ccC>ccT	p.P303P		NM_003412.3	NP_003403.2	Q15915	ZIC1_HUMAN	Zic family member 1	303					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						AGCCCTTTCCCTGCCCCTTCC	0.572																																					p.P303P		Atlas-SNP	.											.	ZIC1	141	.	0			c.C909T						PASS	.						83	87	86					3																	147128808		2203	4300	6503	SO:0001819	synonymous_variant	7545	exon1			CTTTCCCTGCCCC	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.909C>T	3.37:g.147128808C>T		71	0	0		74	13	0.175676	NM_003412	Q2M3N1	Silent	SNP	ENST00000282928.4	37	CCDS3136.1																																																																																			.	.	none		0.572	ZIC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355497.1	NM_003412		T	147128808	C	T	147128808	2	4	37	1	0	0	0	0	0	0	0	1	17693	668	24	2		2	ZIC1	3	147128808	Silent	SNP	C	TCGA-GS-A9TU-01A-11D-A382-10	22482098	147128808	50893622	13	14429											
AGTR1	185	hgsc.bcm.edu	37	chr3	148459567	148459567	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttatggcaattgtgcttttcTttttcttttcctggattccc	4	22	6	9	0	2	0	0	0	2	0	4	1	4	1	2	2	1	2	2	2	2	9			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr3:148459567T>G	ENST00000497524.1	+	2	1136	c.745T>G	c.(745-747)Ttt>Gtt	p.F249V	AGTR1_ENST00000542281.1_Missense_Mutation_p.F249V|AGTR1_ENST00000461609.1_Missense_Mutation_p.F249V|AGTR1_ENST00000418473.2_Missense_Mutation_p.F249V|AGTR1_ENST00000475347.1_Missense_Mutation_p.F249V|AGTR1_ENST00000474935.1_Missense_Mutation_p.F249V|AGTR1_ENST00000402260.1_Missense_Mutation_p.F249V|AGTR1_ENST00000349243.3_Missense_Mutation_p.F249V|AGTR1_ENST00000404754.2_Missense_Mutation_p.F249V	NM_009585.3	NP_033611.1	P30556	AGTR1_HUMAN	angiotensin II receptor, type 1	249					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)	TGTGCTTTTCTTTTTCTTTTC	0.343																																					p.F284V		Atlas-SNP	.											.	AGTR1	63	.	0			c.T850G						PASS	.						55	59	58					3																	148459567		2203	4300	6503	SO:0001583	missense	185	exon4			CTTTTCTTTTTCT	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.745T>G	3.37:g.148459567T>G	ENSP00000419422:p.Phe249Val	92	0	0		129	28	0.217054	NM_031850	Q13725|Q8TBK4	Missense_Mutation	SNP	ENST00000497524.1	37	CCDS3137.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.128394	0.77549	.	.	ENSG00000144891	ENST00000497524;ENST00000349243;ENST00000542281;ENST00000418473;ENST00000404754;ENST00000475347;ENST00000474935;ENST00000461609;ENST00000402260	T;T;T;T;T;T;T;T;T	0.22134	1.97;1.97;1.97;1.97;1.97;1.97;1.97;1.97;1.97	5.48	5.48	0.80851	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.66386	0.2784	H	0.99104	4.43	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.82151	-0.0599	10	0.87932	D	0	-19.2182	15.6059	0.76672	0.0:0.0:0.0:1.0	.	249	P30556	AGTR1_HUMAN	V	249	ENSP00000419422:F249V;ENSP00000273430:F249V;ENSP00000443186:F249V;ENSP00000398832:F249V;ENSP00000385612:F249V;ENSP00000419783:F249V;ENSP00000418084:F249V;ENSP00000418851:F249V;ENSP00000385641:F249V	ENSP00000273430:F249V	F	+	1	0	AGTR1	149942257	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.040000	0.89188	2.081000	0.62600	0.533000	0.62120	TTT	.	.	none		0.343	AGTR1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355807.1			G	148459567	T	G	148459567	3	3	37	1	0	0	0	0	1	0	0	0	401	1609	56	5	747	5	AGTR1	3	148459567	Missense_Mutation	SNP	T	TCGA-GS-A9TU-01A-11D-A382-10	1330759	148459567	49562863	14	14430											
PTX3	5806	hgsc.bcm.edu	37	chr3	157160548	157160548	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctgagggaggaatcctgcAgattggccaagaaaagaatg	14	7	13	7	0	0	4	0	1	0	3	2	6	2	6	3	3	1	1	3	3	5	1			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr3:157160548A>G	ENST00000295927.3	+	3	1071	c.926A>G	c.(925-927)cAg>cGg	p.Q309R	VEPH1_ENST00000362010.2_Intron|VEPH1_ENST00000392832.2_Intron|VEPH1_ENST00000543418.1_Intron|VEPH1_ENST00000392833.2_Intron	NM_002852.3	NP_002843.2	P26022	PTX3_HUMAN	pentraxin 3, long	309	Pentaxin.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of exo-alpha-sialidase activity (GO:1903016)|negative regulation of glycoprotein metabolic process (GO:1903019)|negative regulation of viral entry into host cell (GO:0046597)|opsonization (GO:0008228)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phagocytosis (GO:0050766)|response to yeast (GO:0001878)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	(1->3)-beta-D-glucan binding (GO:0001872)|complement component C1q binding (GO:0001849)|virion binding (GO:0046790)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|stomach(1)	10			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			GGAATCCTGCAGATTGGCCAA	0.502																																					p.Q309R		Atlas-SNP	.											.	PTX3	27	.	0			c.A926G						PASS	.						123	119	121					3																	157160548		2203	4300	6503	SO:0001583	missense	5806	exon3			TCCTGCAGATTGG	X63613	CCDS3180.1	3q25	2010-03-11	2010-03-11		ENSG00000163661	ENSG00000163661			9692	protein-coding gene	gene with protein product		602492	"pentaxin-related gene, rapidly induced by IL-1 beta", "tumor necrosis factor, alpha-induced protein 5", "pentraxin-related gene, rapidly induced by IL-1 beta"	TNFAIP5		1429570	Standard	NM_002852		Approved	TSG-14	uc003fbl.4	P26022	OTTHUMG00000158750	ENST00000295927.3:c.926A>G	3.37:g.157160548A>G	ENSP00000295927:p.Gln309Arg	203	0	0		230	43	0.186957	NM_002852	B2R6T6|Q38M82	Missense_Mutation	SNP	ENST00000295927.3	37	CCDS3180.1	.	.	.	.	.	.	.	.	.	.	A	18.74	3.688570	0.68271	.	.	ENSG00000163661	ENST00000295927	T	0.06294	3.32	5.97	3.59	0.41128	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.055526	0.85682	D	0.000000	T	0.19886	0.0478	M	0.70275	2.135	0.54753	D	0.999983	D	0.89917	1.0	D	0.79784	0.993	T	0.00158	-1.1975	10	0.62326	D	0.03	-23.4043	8.0147	0.30374	0.8124:0.0:0.0655:0.1221	.	309	P26022	PTX3_HUMAN	R	309	ENSP00000295927:Q309R	ENSP00000295927:Q309R	Q	+	2	0	PTX3	158643242	1.000000	0.71417	0.983000	0.44433	0.997000	0.91878	7.087000	0.76893	0.502000	0.28037	0.533000	0.62120	CAG	.	.	none		0.502	PTX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352028.1	NM_002852		G	157160548	A	G	157160548	3	3	37	1	0	0	0	0	1	0	0	0	12837	188	7	3	936	3	PTX3	3	157160548	Missense_Mutation	SNP	A	TCGA-GS-A9TU-01A-11D-A382-10	8700981	157160548	40861882	15	14431											
SI	6476	hgsc.bcm.edu	37	chr3	164730788	164730788	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attaacagcttcatcttccgTtagagttttatctattgtta	10	19	5	7	1	3	1	1	0	2	1	4	1	4	1	1	0	2	4	1	0	5	9			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr3:164730788T>C	ENST00000264382.3	-	34	4104	c.4042A>G	c.(4042-4044)Acg>Gcg	p.T1348A		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	1348	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)	TCATCTTCCGTTAGAGTTTTA	0.323										HNSCC(35;0.089)																											p.T1348A		Atlas-SNP	.											.	SI	500	.	0			c.A4042G						PASS	.						133	130	131					3																	164730788		2203	4300	6503	SO:0001583	missense	6476	exon34			CTTCCGTTAGAGT	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.4042A>G	3.37:g.164730788T>C	ENSP00000264382:p.Thr1348Ala	175	0	0		151	30	0.198675	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	37	CCDS3196.1	.	.	.	.	.	.	.	.	.	.	T	11.82	1.753476	0.31046	.	.	ENSG00000090402	ENST00000264382	D	0.88354	-2.37	4.54	4.54	0.55810	Glycoside hydrolase, superfamily (1);	0.278355	0.36234	N	0.002713	D	0.87055	0.6082	L	0.57536	1.79	0.09310	N	1	B	0.34290	0.447	B	0.44044	0.439	T	0.76386	-0.2978	10	0.25106	T	0.35	.	5.3666	0.16117	0.1734:0.0:0.1805:0.646	.	1348	P14410	SUIS_HUMAN	A	1348	ENSP00000264382:T1348A	ENSP00000264382:T1348A	T	-	1	0	SI	166213482	0.377000	0.25106	0.755000	0.31263	0.660000	0.38997	-0.129000	0.10515	1.876000	0.54355	0.477000	0.44152	ACG	.	.	none		0.323	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		C	164730788	T	C	164730788	3	2	37	1	0	0	0	0	1	0	0	0	14312	1725	60	3	1501	3	SI	3	164730788	Missense_Mutation	SNP	T	TCGA-GS-A9TU-01A-11D-A382-10	7570240	164730788	33291642	16	14432											
ZBBX	79740	hgsc.bcm.edu	37	chr3	167033615	167033615	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcttcaaattcctcttcataAgtcttattaaattaatgtta	13	19	2	7	0	5	0	2	0	3	0	6	0	6	0	1	0	0	1	1	0	7	8			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr3:167033615A>G	ENST00000392766.2	-	15	1537	c.1197T>C	c.(1195-1197)acT>acC	p.T399T	ZBBX_ENST00000307529.5_Silent_p.T399T|ZBBX_ENST00000392764.1_Silent_p.T370T|ZBBX_ENST00000392767.2_Silent_p.T399T|ZBBX_ENST00000455345.2_Silent_p.T399T|ZBBX_ENST00000469220.1_5'Flank	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	399						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						CCTCTTCATAAGTCttattaa	0.269																																					p.T399T		Atlas-SNP	.											.	ZBBX	299	.	0			c.T1197C						PASS	.						39	37	37					3																	167033615		1783	4053	5836	SO:0001819	synonymous_variant	79740	exon15			TTCATAAGTCTTA	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.1197T>C	3.37:g.167033615A>G		524	0	0		570	104	0.182456	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Silent	SNP	ENST00000392766.2	37	CCDS3199.2																																																																																			.	.	none		0.269	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687		G	167033615	A	G	167033615	2	3	37	1	0	0	0	0	0	0	0	1	17531	59	3	3		3	ZBBX	3	167033615	Silent	SNP	A	TCGA-GS-A9TU-01A-11D-A382-10	2302827	167033615	30988815	17	14433											
BMP3	651	hgsc.bcm.edu	37	chr4	81967644	81967644	+	Frame_Shift_Del	DEL	A	A	-																															aatttgatgagcagaccctgAaaaaggcaaggagaaagcag																										TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr4:81967644delA	ENST00000282701.2	+	2	1389	c.1069delA	c.(1069-1071)aaafs	p.K358fs		NM_001201.2	NP_001192.2	P12645	BMP3_HUMAN	bone morphogenetic protein 3	358					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						GCAGACCCTGAAAAAGGCAAG	0.478																																					p.L356fs		Atlas-Indel	.											.	BMP3	59	.	0			c.1068delG						PASS	.						74	71	72					4																	81967644		2203	4300	6503	SO:0001589	frameshift_variant	651	exon2			.	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.1069delA	4.37:g.81967644delA	ENSP00000282701:p.Lys358fs	135	0	0		115	19	0.165217	NM_001201	Q4VAS5	Frame_Shift_Del	DEL	ENST00000282701.2	37	CCDS3588.1																																																																																			.	.	none		0.478	BMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252634.1			-	81967644	A	-	81967644	7	5	37	1	0	1	0	1	0	0	0	0	1461	247	9	0	1075	0	BMP3	4	81967644	Frame_Shift_Del	DEL	A	TCGA-GS-A9TU-01A-11D-A382-10		81967644	109186632	18	14434											
FAT4	79633	hgsc.bcm.edu	37	chr4	126336502	126336502	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctaacagtggtggctacagaCaaaggtcaaccatctctctc	12	9	8	12	0	3	1	1	0	2	1	5	1	3	1	1	3	3	1	1	3	4	2			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr4:126336502C>T	ENST00000394329.3	+	5	6397	c.6384C>T	c.(6382-6384)gaC>gaT	p.D2128D	FAT4_ENST00000335110.5_Silent_p.D426D	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2128	Cadherin 20. {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						TGGCTACAGACAAAGGTCAAC	0.413																																					p.D2128D		Atlas-SNP	.											FAT4_ENST00000394329,NS,carcinoma,+2,2	FAT4	1752	2	0			c.C6384T						PASS	.						84	83	84					4																	126336502		2203	4300	6503	SO:0001819	synonymous_variant	79633	exon5			TACAGACAAAGGT	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.6384C>T	4.37:g.126336502C>T		100	0	0		85	23	0.270588	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Silent	SNP	ENST00000394329.3	37	CCDS3732.3																																																																																			.	.	none		0.413	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126336502	C	T	126336502	2	4	37	1	0	0	0	0	0	0	0	1	5700	477	17	2		2	FAT4	4	126336502	Silent	SNP	C	TCGA-GS-A9TU-01A-11D-A382-10	44368858	126336502	64817774	19	14435											
HMGB2	3148	hgsc.bcm.edu	37	chr4	174254780	174254780	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gacattttgccccgcggcttGttggggtctcctttacccat	4	14	10	13	2	1	0	0	0	1	0	2	1	1	0	4	3	2	2	4	3	1	6			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr4:174254780G>C	ENST00000296503.5	-	2	894	c.21C>G	c.(19-21)aaC>aaG	p.N7K	HMGB2_ENST00000438704.2_Missense_Mutation_p.N7K|HMGB2_ENST00000446922.2_Missense_Mutation_p.N7K			P26583	HMGB2_HUMAN	high mobility group box 2	7					apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|base-excision repair, DNA ligation (GO:0006288)|cell chemotaxis (GO:0060326)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to lipopolysaccharide (GO:0071222)|chromatin organization (GO:0006325)|DNA ligation involved in DNA repair (GO:0051103)|DNA topological change (GO:0006265)|male gonad development (GO:0008584)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive chemotaxis (GO:0050918)|positive regulation of DNA binding (GO:0043388)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of nuclease activity (GO:0032075)|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)|response to steroid hormone (GO:0048545)|spermatid nucleus differentiation (GO:0007289)|V(D)J recombination (GO:0033151)	condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)	chemoattractant activity (GO:0042056)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RAGE receptor binding (GO:0050786)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|urinary_tract(3)	14		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;9.58e-18)|Epithelial(43;3.75e-16)|OV - Ovarian serous cystadenocarcinoma(60;6.24e-09)|STAD - Stomach adenocarcinoma(60;0.00273)|GBM - Glioblastoma multiforme(59;0.0064)|LUSC - Lung squamous cell carcinoma(193;0.0903)|Kidney(143;0.249)		CCCGCGGCTTGTTGGGGTCTC	0.632																																					p.N7K		Atlas-SNP	.											.	HMGB2	24	.	0			c.C21G						PASS	.						66	69	68					4																	174254780		2203	4300	6503	SO:0001583	missense	3148	exon1			CGGCTTGTTGGGG		CCDS3816.1	4q31	2011-07-01	2011-04-05	2002-08-16	ENSG00000164104	ENSG00000164104		"High-mobility group / Canonical"	5000	protein-coding gene	gene with protein product		163906	"high-mobility group (nonhistone chromosomal) protein 2", "high-mobility group box 2"	HMG2		1754403	Standard	NM_002129		Approved		uc011ckc.1	P26583	OTTHUMG00000160799	ENST00000296503.5:c.21C>G	4.37:g.174254780G>C	ENSP00000296503:p.Asn7Lys	91	0	0		85	16	0.188235	NM_001130689	B2R4K8|D3DP37|Q5U072	Missense_Mutation	SNP	ENST00000296503.5	37	CCDS3816.1	.	.	.	.	.	.	.	.	.	.	G	0.105	-1.145864	0.01714	.	.	ENSG00000164104	ENST00000296503;ENST00000446922;ENST00000438704;ENST00000506267	T;T;T;T	0.13778	2.56;2.56;2.56;2.56	5.45	3.72	0.42706	High mobility group, superfamily (1);	0.000000	0.64402	D	0.000001	T	0.09423	0.0232	L	0.37800	1.135	0.48236	D	0.999614	B	0.02656	0.0	B	0.06405	0.002	T	0.11591	-1.0581	10	0.07030	T	0.85	.	10.0298	0.42094	0.0722:0.0:0.7896:0.1382	.	7	P26583	HMGB2_HUMAN	K	7	ENSP00000296503:N7K;ENSP00000393448:N7K;ENSP00000404912:N7K;ENSP00000423001:N7K	ENSP00000296503:N7K	N	-	3	2	HMGB2	174491355	1.000000	0.71417	1.000000	0.80357	0.077000	0.17291	0.752000	0.26362	0.672000	0.31204	-0.309000	0.09137	AAC	.	.	none		0.632	HMGB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362362.1	NM_001130688		C	174254780	G	C	174254780	3	2	37	1	0	0	0	0	1	0	0	0	7235	1368	48	4	624	4	HMGB2	4	174254780	Missense_Mutation	SNP	G	TCGA-GS-A9TU-01A-11D-A382-10	47918278	174254780	16899496	20	14436											
GCM2	9247	hgsc.bcm.edu	37	chr6	10875031	10875031	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtcacaggtagctttgtaaaCatcagactttgggaaggaag	13	10	12	6	0	2	1	2	0	0	1	2	3	2	3	0	3	2	3	0	3	5	4			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr6:10875031C>T	ENST00000379491.4	-	5	865	c.718G>A	c.(718-720)Gtt>Att	p.V240I	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)	240					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)				GCTTTGTAAACATCAGACTTT	0.463																																					p.V240I		Atlas-SNP	.											.	GCM2	81	.	0			c.G718A						PASS	.						135	127	130					6																	10875031		2203	4300	6503	SO:0001583	missense	9247	exon5			TGTAAACATCAGA	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.718G>A	6.37:g.10875031C>T	ENSP00000368805:p.Val240Ile	126	0	0		91	31	0.340659	NM_004752	D3GDV6|Q5THN5	Missense_Mutation	SNP	ENST00000379491.4	37	CCDS4517.1	.	.	.	.	.	.	.	.	.	.	C	9.809	1.182644	0.21870	.	.	ENSG00000124827	ENST00000379491	T	0.67865	-0.29	5.8	2.96	0.34315	.	0.437579	0.28125	N	0.016504	T	0.31949	0.0813	N	0.22421	0.69	0.80722	D	1	B	0.17038	0.02	B	0.14023	0.01	T	0.15150	-1.0447	10	0.37606	T	0.19	-1.735	9.5725	0.39436	0.1966:0.5631:0.2402:0.0	.	240	O75603	GCM2_HUMAN	I	240	ENSP00000368805:V240I	ENSP00000368805:V240I	V	-	1	0	GCM2	10983017	0.770000	0.28543	0.896000	0.35187	0.796000	0.44982	0.359000	0.20233	0.807000	0.34208	-0.824000	0.03097	GTT	.	.	none		0.463	GCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039844.1			T	10875031	C	T	10875031	3	4	37	1	0	0	0	0	1	0	0	0	6306	478	17	2	806	2	GCM2	6	10875031	Missense_Mutation	SNP	C	TCGA-GS-A9TU-01A-11D-A382-10		10875031	160240036	21	14437											
SLC17A4	10050	hgsc.bcm.edu	37	chr6	25771240	25771240	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cttacgtcttctatatctttGgtgagtgtgcttttcaaatc	7	19	7	8	1	4	1	1	1	3	0	5	1	4	1	0	1	2	1	0	1	4	7			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr6:25771240G>C	ENST00000377905.4	+	6	825	c.706G>C	c.(706-708)Gga>Cga	p.G236R	SLC17A4_ENST00000439485.2_Intron|SLC17A4_ENST00000397076.2_Intron	NM_005495.2	NP_005486.1	Q9Y2C5	S17A4_HUMAN	solute carrier family 17, member 4	236					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						CTATATCTTTGGTGAGTGTGC	0.403																																					p.G236R		Atlas-SNP	.											.	SLC17A4	79	.	0			c.G706C						PASS	.						235	222	226					6																	25771240		2203	4300	6503	SO:0001630	splice_region_variant	10050	exon6			ATCTTTGGTGAGT	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.706+1G>C	6.37:g.25771240G>C		246	0	0		209	53	0.253589	NM_005495	B4DDV9|E7EPE8|E7EU17|Q32MB7|Q32MB8	Missense_Mutation	SNP	ENST00000377905.4	37	CCDS4564.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.686492	0.88639	.	.	ENSG00000146039	ENST00000377905	T	0.63096	-0.02	5.56	5.56	0.83823	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.50627	D	0.000113	D	0.84777	0.5547	H	0.97415	4	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.89223	0.3572	10	0.87932	D	0	.	15.3921	0.74755	0.0:0.0:1.0:0.0	.	236	Q9Y2C5	S17A4_HUMAN	R	236	ENSP00000367137:G236R	ENSP00000367137:G236R	G	+	1	0	SLC17A4	25879219	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	6.752000	0.74898	2.791000	0.96007	0.563000	0.77884	GGA	.	.	none		0.403	SLC17A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040068.1		Missense_Mutation	C	25771240	G	C	25771240	5	2	37	1	0	0	0	0	0	0	1	0	14434	1362	47	4	724	4	SLC17A4	6	25771240	Splice_Site	SNP	G	TCGA-GS-A9TU-01A-11D-A382-10	14896209	25771240	145343827	22	14438											
CCND3	896	hgsc.bcm.edu	37	chr6	41903710	41903710	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggctgtgacatctgtaggagTgctggtctggctgggccctt	4	12	16	9	0	2	1	0	1	2	0	2	2	2	2	1	5	1	4	1	5	1	2			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr6:41903710T>C	ENST00000372991.4	-	5	1045	c.847A>G	c.(847-849)Act>Gct	p.T283A	CCND3_ENST00000511686.1_5'UTR|CCND3_ENST00000372987.4_Missense_Mutation_p.T233A|CCND3_ENST00000372988.4_Missense_Mutation_p.T202A|CCND3_ENST00000414200.2_Missense_Mutation_p.T211A|CCND3_ENST00000415497.2_Missense_Mutation_p.T87A|CCND3_ENST00000510503.1_Missense_Mutation_p.H156R|CCND3_ENST00000511642.1_Missense_Mutation_p.T202A	NM_001760.3	NP_001751.1	P30281	CCND3_HUMAN	cyclin D3	283					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)|signal transduction (GO:0007165)|T cell proliferation (GO:0042098)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase binding (GO:0019901)	p.T283P(1)|p.T283A(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(13)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	20	Colorectal(47;0.121)		Epithelial(12;0.000178)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TCTGTAGGAGTGCTGGTCTGG	0.667			T	IGH@	MM																																p.T283A		Atlas-SNP	.		Dom	yes		6	6p21	896	cyclin D3		L	CCND3,NS,lymphoid_neoplasm,0,2	CCND3	40	2	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.A847G						PASS	.						34	39	37					6																	41903710		2203	4300	6503	SO:0001583	missense	896	exon5			TAGGAGTGCTGGT		CCDS4863.1, CCDS47425.1, CCDS47426.1, CCDS47427.1, CCDS75452.1	6p21	2008-08-26			ENSG00000112576	ENSG00000112576			1585	protein-coding gene	gene with protein product		123834				1386335	Standard	NM_001136125		Approved		uc003orn.3	P30281	OTTHUMG00000014690	ENST00000372991.4:c.847A>G	6.37:g.41903710T>C	ENSP00000362082:p.Thr283Ala	82	0	0		69	15	0.217391	NM_001760	B2RD63|B3KQ22|E9PAS4|E9PB36|Q5T8J0|Q6FG62|Q96F49	Missense_Mutation	SNP	ENST00000372991.4	37	CCDS4863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	t|t	23.1|23.1	4.377335|4.377335	0.82682|0.82682	.|.	.|.	ENSG00000112576|ENSG00000112576	ENST00000510503|ENST00000372991;ENST00000511642;ENST00000372987;ENST00000372988;ENST00000415497;ENST00000414200	T|T;T;T;T;T;T	0.36878|0.54071	1.23|2.69;2.7;2.69;2.7;1.08;0.59	5.63|5.63	5.63|5.63	0.86233|0.86233	.|.	.|0.000000	.|0.64402	.|D	.|0.000011	T|T	0.63224|0.63224	0.2493|0.2493	M|M	0.73962|0.73962	2.25|2.25	0.31265|0.31265	N|N	0.692446|0.692446	.|D;D;D	.|0.69078	.|0.982;0.993;0.997	.|D;D;D	.|0.75020	.|0.952;0.978;0.985	T|T	0.66830|0.66830	-0.5824|-0.5824	7|10	0.23891|0.56958	T|D	0.37|0.05	.|.	14.0609|14.0609	0.64800|0.64800	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|211;283;233	.|E9PAS4;P30281;Q5T8J1	.|.;CCND3_HUMAN;.	R|A	156|283;202;233;202;87;211	ENSP00000425986:H156R|ENSP00000362082:T283A;ENSP00000426212:T202A;ENSP00000362078:T233A;ENSP00000362079:T202A;ENSP00000401595:T87A;ENSP00000397545:T211A	ENSP00000425986:H156R|ENSP00000362078:T233A	H|T	-|-	2|1	0|0	CCND3|CCND3	42011688|42011688	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.295000|7.295000	0.78780|0.78780	2.155000|2.155000	0.67459|0.67459	0.482000|0.482000	0.46254|0.46254	CAC|ACT	.	.	none		0.667	CCND3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040540.2	NM_001760		C	41903710	T	C	41903710	3	2	37	1	0	0	0	0	1	0	0	0	2920	1696	59	3	35	3	CCND3	6	41903710	Missense_Mutation	SNP	T	TCGA-GS-A9TU-01A-11D-A382-10	16132470	41903710	129211357	23	14439											
ZNF804B	219578	hgsc.bcm.edu	37	chr7	88963200	88963200	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccatctccataaactctaaaAttttgcaagacaaacacgac	17	9	3	12	1	2	1	0	0	2	1	3	2	2	1	2	0	3	1	2	0	6	4			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr7:88963200A>C	ENST00000333190.4	+	4	1513	c.904A>C	c.(904-906)Att>Ctt	p.I302L		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	302							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)			AAACTCTAAAATTTTGCAAGA	0.343										HNSCC(36;0.09)																											p.I302L		Atlas-SNP	.											ZNF804B,NS,carcinoma,0,1	ZNF804B	322	1	0			c.A904C						PASS	.						51	52	51					7																	88963200		2203	4299	6502	SO:0001583	missense	219578	exon4			TCTAAAATTTTGC	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.904A>C	7.37:g.88963200A>C	ENSP00000329638:p.Ile302Leu	132	0	0		160	37	0.23125	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	.	.	.	.	.	.	.	.	.	.	A	2.668	-0.278204	0.05679	.	.	ENSG00000182348	ENST00000333190	T	0.05081	3.5	5.14	-1.67	0.08238	.	0.708385	0.13164	N	0.408832	T	0.03959	0.0111	L	0.36672	1.1	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.42949	-0.9421	10	0.22706	T	0.39	-4.674	2.5809	0.04818	0.4096:0.3386:0.1418:0.11	.	302	A4D1E1	Z804B_HUMAN	L	302	ENSP00000329638:I302L	ENSP00000329638:I302L	I	+	1	0	ZNF804B	88801136	0.140000	0.22579	0.018000	0.16275	0.236000	0.25371	1.179000	0.31993	-0.158000	0.11040	0.533000	0.62120	ATT	.	.	none		0.343	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646		C	88963200	A	C	88963200	3	2	37	1	0	0	0	0	1	0	0	0	18186	101	4	5	918	5	ZNF804B	7	88963200	Missense_Mutation	SNP	A	TCGA-GS-A9TU-01A-11D-A382-10		88963200	70175463	24	14440											
LRRN3	54674	hgsc.bcm.edu	37	chr7	110763849	110763849	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccaagctggaatcactcatgCtgaacagcaatgctctcagt	12	9	8	12	0	3	1	3	1	1	0	4	2	3	2	1	1	5	4	1	1	4	0			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr7:110763849C>A	ENST00000422987.3	+	2	1852	c.1021C>A	c.(1021-1023)Ctg>Atg	p.L341M	IMMP2L_ENST00000405709.2_Intron|IMMP2L_ENST00000452895.1_Intron|IMMP2L_ENST00000489381.1_Intron|IMMP2L_ENST00000437687.1_Intron|IMMP2L_ENST00000447215.1_Intron|IMMP2L_ENST00000450877.1_Intron|LRRN3_ENST00000451085.1_Missense_Mutation_p.L341M|LRRN3_ENST00000308478.5_Missense_Mutation_p.L341M|IMMP2L_ENST00000415362.1_Intron|IMMP2L_ENST00000331762.3_Intron	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	341					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)		ATCACTCATGCTGAACAGCAA	0.453																																					p.L341M		Atlas-SNP	.											.	LRRN3	132	.	0			c.C1021A						PASS	.						106	100	102					7																	110763849		2203	4300	6503	SO:0001583	missense	54674	exon2			CTCATGCTGAACA	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.1021C>A	7.37:g.110763849C>A	ENSP00000412417:p.Leu341Met	134	0	0		149	56	0.375839	NM_018334	O43377|Q6I9V8|Q8IYQ6	Missense_Mutation	SNP	ENST00000422987.3	37	CCDS5754.1	.	.	.	.	.	.	.	.	.	.	C	14.85	2.659574	0.47467	.	.	ENSG00000173114	ENST00000308478;ENST00000451085;ENST00000422987	T;T;T	0.77229	-1.08;-1.08;-1.08	5.81	4.01	0.46588	.	0.000000	0.52532	D	0.000077	D	0.89480	0.6727	M	0.91717	3.235	0.48571	D	0.999679	D	0.89917	1.0	D	0.97110	1.0	D	0.90182	0.4243	10	0.59425	D	0.04	.	12.3926	0.55366	0.0:0.8648:0.0:0.1352	.	341	Q9H3W5	LRRN3_HUMAN	M	341	ENSP00000312001:L341M;ENSP00000397312:L341M;ENSP00000412417:L341M	ENSP00000312001:L341M	L	+	1	2	LRRN3	110551085	1.000000	0.71417	0.994000	0.49952	0.993000	0.82548	2.694000	0.47035	0.807000	0.34208	0.650000	0.86243	CTG	.	.	none		0.453	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334		A	110763849	C	A	110763849	3	1	37	1	0	0	0	0	1	0	0	0	9045	796	28	4	1023	4	LRRN3	7	110763849	Missense_Mutation	SNP	C	TCGA-GS-A9TU-01A-11D-A382-10	21800649	110763849	48374814	25	14441											
FLNC	2318	hgsc.bcm.edu	37	chr7	128475620	128475620	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcgccctggtggacaactGcgcccccggtgagtgggcca	5	5	17	14	3	0	1	0	1	0	0	0	2	0	2	4	5	2	0	4	5	1	0			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr7:128475620G>A	ENST00000325888.8	+	2	854	c.593G>A	c.(592-594)tGc>tAc	p.C198Y	FLNC_ENST00000346177.6_Missense_Mutation_p.C198Y	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	198	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				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						GTGGACAACTGCGCCCCCGGT	0.622																																					p.C198Y		Atlas-SNP	.											.	FLNC	339	.	0			c.G593A						PASS	.						33	38	37					7																	128475620		2072	4218	6290	SO:0001583	missense	2318	exon2			ACAACTGCGCCCC	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.593G>A	7.37:g.128475620G>A	ENSP00000327145:p.Cys198Tyr	23	0	0		40	19	0.475	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Missense_Mutation	SNP	ENST00000325888.8	37	CCDS43644.1	.	.	.	.	.	.	.	.	.	.	G	19.37	3.815232	0.70912	.	.	ENSG00000128591	ENST00000325888;ENST00000346177	D;D	0.93763	-3.28;-3.28	5.63	5.63	0.86233	Calponin homology domain (5);	0.000000	0.85682	D	0.000000	D	0.95085	0.8408	L	0.35854	1.095	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	D	0.95581	0.8646	10	0.87932	D	0	.	18.6585	0.91463	0.0:0.0:1.0:0.0	.	198;198	Q14315-2;Q14315	.;FLNC_HUMAN	Y	198	ENSP00000327145:C198Y;ENSP00000344002:C198Y	ENSP00000327145:C198Y	C	+	2	0	FLNC	128262856	1.000000	0.71417	1.000000	0.80357	0.310000	0.27922	9.869000	0.99810	2.659000	0.90383	0.561000	0.74099	TGC	.	.	none		0.622	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3			A	128475620	G	A	128475620	3	1	37	1	0	0	0	0	1	0	0	0	5943	1319	46	2	599	2	FLNC	7	128475620	Missense_Mutation	SNP	G	TCGA-GS-A9TU-01A-11D-A382-10	17711771	128475620	30663043	26	14442											
OR2A5	393046	hgsc.bcm.edu	37	chr7	143747902	143747902	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgcaatattctgtcatcatGagatggggagtgtgcacagt	10	12	12	7	0	3	1	2	1	1	1	3	3	3	2	0	2	2	2	0	2	2	2			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr7:143747902G>A	ENST00000408906.2	+	1	442	c.408G>A	c.(406-408)atG>atA	p.M136I		NM_012365.1	NP_036497.1	Q96R48	OR2A5_HUMAN	olfactory receptor, family 2, subfamily A, 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)	p.M136I(1)		cervix(1)|endometrium(3)|large_intestine(5)|lung(23)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	38	Melanoma(164;0.0783)					CTGTCATCATGAGATGGGGAG	0.512																																					p.M136I		Atlas-SNP	.											OR2A5,NS,carcinoma,0,1	OR2A5	78	1	1	Substitution - Missense(1)	prostate(1)	c.G408A						PASS	.						187	193	191					7																	143747902		2128	4247	6375	SO:0001583	missense	393046	exon1			CATCATGAGATGG	U86278	CCDS43668.1	7q35	2013-09-20	2003-11-24		ENSG00000221836	ENSG00000221836		"GPCR / Class A : Olfactory receptors"	8232	protein-coding gene	gene with protein product			"olfactory receptor, family 2, subfamily A, member 5"	OR2A8, OR2A26		9500546	Standard	NM_012365		Approved	OR7-138, OR7-141	uc011ktw.2	Q96R48	OTTHUMG00000158006	ENST00000408906.2:c.408G>A	7.37:g.143747902G>A	ENSP00000386208:p.Met136Ile	168	0	0		204	49	0.240196	NM_012365	B9EGX2|O43885|O43888	Missense_Mutation	SNP	ENST00000408906.2	37	CCDS43668.1	.	.	.	.	.	.	.	.	.	.	G	9.840	1.190889	0.21954	.	.	ENSG00000221836	ENST00000408906	T	0.00551	6.65	5.25	5.25	0.73442	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38436	U	0.001688	T	0.01156	0.0038	M	0.83223	2.63	0.29425	N	0.860251	B	0.20164	0.042	B	0.23852	0.049	T	0.07986	-1.0744	10	0.72032	D	0.01	.	16.3726	0.83370	0.0:0.0:1.0:0.0	.	136	Q96R48	OR2A5_HUMAN	I	136	ENSP00000386208:M136I	ENSP00000386208:M136I	M	+	3	0	OR2A5	143378835	1.000000	0.71417	1.000000	0.80357	0.202000	0.24057	4.248000	0.58760	2.728000	0.93425	0.557000	0.71058	ATG	.	.	none		0.512	OR2A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349986.1			A	143747902	G	A	143747902	3	1	37	1	0	0	0	0	1	0	0	0	10990	1290	45	2	410	2	OR2A5	7	143747902	Missense_Mutation	SNP	G	TCGA-GS-A9TU-01A-11D-A382-10	15272282	143747902	15390761	27	14443											
BAT2L1	84726	hgsc.bcm.edu	37	chr9	134357813	134357813	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgacttgagtgccgagtctcGggagtcgtctgcgacctcct	5	11	13	12	4	2	2	0	2	2	0	5	5	3	3	3	1	2	0	3	1	0	1			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr9:134357813G>A	ENST00000357304.4	+	20	5094	c.5039G>A	c.(5038-5040)cGg>cAg	p.R1680Q	PRRC2B_ENST00000405995.1_Missense_Mutation_p.R986Q|PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Missense_Mutation_p.R986Q	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	1680							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						GCCGAGTCTCGGGAGTCGTCT	0.602																																					p.R1680Q		Atlas-SNP	.											.	PRRC2B	266	.	0			c.G5039A						PASS	.						145	151	149					9																	134357813		1979	4166	6145	SO:0001583	missense	84726	exon20			AGTCTCGGGAGTC	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.5039G>A	9.37:g.134357813G>A	ENSP00000349856:p.Arg1680Gln	189	0	0		173	48	0.277457	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	37	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.004885	0.74932	.	.	ENSG00000130723	ENST00000405995;ENST00000357304;ENST00000458550	T;T;T	0.02280	4.36;4.71;4.36	4.92	4.92	0.64577	.	0.000000	0.37577	U	0.002038	T	0.05686	0.0149	N	0.21142	0.635	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.77557	0.99;0.956	T	0.62364	-0.6870	10	0.12103	T	0.63	-27.4773	17.105	0.86660	0.0:0.0:1.0:0.0	.	412;1680	Q5JSZ8;Q5JSZ5	.;PRC2B_HUMAN	Q	986;1680;986	ENSP00000384606:R986Q;ENSP00000349856:R1680Q;ENSP00000398853:R986Q	ENSP00000349856:R1680Q	R	+	2	0	PRRC2B	133347634	1.000000	0.71417	0.987000	0.45799	0.916000	0.54674	4.534000	0.60622	2.275000	0.75901	0.561000	0.74099	CGG	.	.	none		0.602	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	134357813	G	A	134357813	3	1	37	1	0	0	0	0	1	0	0	0	1320	1116	39	1	5117	1	BAT2L1	9	134357813	Missense_Mutation	SNP	G	TCGA-GS-A9TU-01A-11D-A382-10		134357813	6855618	28	14444											
MS4A8B	83661	hgsc.bcm.edu	37	chr11	60470906	60470906	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcggctccatcatggcgaCggttctcgtaggggaatacc	7	9	12	13	4	2	0	1	0	1	0	5	2	3	1	3	5	1	3	3	5	3	3			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr11:60470906C>T	ENST00000300226.2	+	3	478	c.275C>T	c.(274-276)aCg>aTg	p.T92M		NM_031457.1	NP_113645.1	Q9BY19	M4A8_HUMAN	membrane-spanning 4-domains, subfamily A, member 8	92						integral component of membrane (GO:0016021)											ATCATGGCGACGGTTCTCGTA	0.552																																					p.T92M		Atlas-SNP	.											.	.	.	.	0			c.C275T						PASS	.						151	139	143					11																	60470906		2203	4300	6503	SO:0001583	missense	83661	exon3			TGGCGACGGTTCT	AF237905	CCDS7990.1	11q12	2013-03-01	2013-03-01	2013-03-01	ENSG00000166959	ENSG00000166959			13380	protein-coding gene	gene with protein product		606549	"membrane-spanning 4-domains, subfamily A, member 8B"	MS4A8B		11245982, 11401424	Standard	NM_031457		Approved	MS4A4, CD20L5	uc001npv.3	Q9BY19	OTTHUMG00000167686	ENST00000300226.2:c.275C>T	11.37:g.60470906C>T	ENSP00000300226:p.Thr92Met	219	0	0		190	45	0.236842	NM_031457	Q8TCA5	Missense_Mutation	SNP	ENST00000300226.2	37	CCDS7990.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.36|11.36	1.615604|1.615604	0.28801|0.28801	.|.	.|.	ENSG00000166959|ENSG00000166959	ENST00000525458|ENST00000300226;ENST00000529752	.|T;T	.|0.02301	.|4.35;4.35	3.62|3.62	2.6|2.6	0.31112|0.31112	.|.	.|0.472817	.|0.19530	.|N	.|0.112065	T|T	0.03739|0.03739	0.0106|0.0106	L|L	0.41573|0.41573	1.285|1.285	0.09310|0.09310	N|N	1|1	.|D;D	.|0.69078	.|0.964;0.997	.|P;P	.|0.53102	.|0.557;0.718	T|T	0.45818|0.45818	-0.9235|-0.9235	5|10	.|0.31617	.|T	.|0.26	-14.2382|-14.2382	7.6502|7.6502	0.28344|0.28344	0.2522:0.7478:0.0:0.0|0.2522:0.7478:0.0:0.0	.|.	.|92;92	.|E9PQE1;Q9BY19	.|.;M4A8B_HUMAN	W|M	74|92	.|ENSP00000300226:T92M;ENSP00000436857:T92M	.|ENSP00000300226:T92M	R|T	+|+	1|2	2|0	MS4A8B|MS4A8B	60227482|60227482	0.001000|0.001000	0.12720|0.12720	0.011000|0.011000	0.14972|0.14972	0.004000|0.004000	0.04260|0.04260	0.804000|0.804000	0.27098|0.27098	1.745000|1.745000	0.51790|0.51790	0.491000|0.491000	0.48974|0.48974	CGG|ACG	.	.	none		0.552	MS4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395605.1			T	60470906	C	T	60470906	3	4	37	1	0	0	0	0	1	0	0	0	9876	536	19	1	281	1	MS4A8B	11	60470906	Missense_Mutation	SNP	C	TCGA-GS-A9TU-01A-11D-A382-10		60470906	74535610	29	14445											
CASC1	55259	hgsc.bcm.edu	37	chr12	25297343	25297343	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcctcctcaacttttatttCttcctcctgaattaagtgag	8	18	4	11	0	2	2	1	2	1	0	6	2	6	2	4	0	1	0	4	0	4	6			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr12:25297343C>A	ENST00000320267.9	-	8	1021	c.940G>T	c.(940-942)Gaa>Taa	p.E314*	CASC1_ENST00000557684.1_5'UTR|CASC1_ENST00000395987.3_Nonsense_Mutation_p.E320*|CASC1_ENST00000545133.1_Nonsense_Mutation_p.E255*|CASC1_ENST00000354189.5_Nonsense_Mutation_p.E378*|CASC1_ENST00000537577.1_Nonsense_Mutation_p.E202*|CASC1_ENST00000395990.2_Nonsense_Mutation_p.E274*	NM_001082973.1	NP_001076442	Q6TDU7	CASC1_HUMAN	cancer susceptibility candidate 1	314										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)			ACTTTTATTTCTTCCTCCTGA	0.348																																					p.E378X		Atlas-SNP	.											.	CASC1	146	.	0			c.G1132T						PASS	.						210	211	210					12																	25297343		2203	4300	6503	SO:0001587	stop_gained	55259	exon9			TTATTTCTTCCTC	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.940G>T	12.37:g.25297343C>A	ENSP00000313141:p.Glu314*	577	0	0		556	130	0.233813	NM_001082972	B4DNP2|F5H6T6|Q17RL2|Q4G171|Q5U5K5|Q9NV50	Nonsense_Mutation	SNP	ENST00000320267.9	37	CCDS41762.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.347205	0.82022	.	.	ENSG00000118307	ENST00000354189;ENST00000395987;ENST00000320267;ENST00000395990;ENST00000537577;ENST00000395992;ENST00000545133;ENST00000389246	.	.	.	4.25	2.36	0.29203	.	0.469935	0.22630	N	0.057588	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	-1.813	9.6523	0.39906	0.0:0.8066:0.0:0.1934	.	.	.	.	X	378;320;314;274;202;320;255;124	.	ENSP00000313141:E314X	E	-	1	0	CASC1	25188610	0.029000	0.19370	0.095000	0.20976	0.248000	0.25809	0.256000	0.18351	0.091000	0.17302	-1.161000	0.01788	GAA	.	.	none		0.348	CASC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316761.1	NM_018272		A	25297343	C	A	25297343	4	1	37	1	0	0	0	0	0	1	0	0	2662	922	32	4	1242	4	CASC1	12	25297343	Nonsense_Mutation	SNP	C	TCGA-GS-A9TU-01A-11D-A382-10		25297343	108554552	30	14446											
OR6C74	254783	hgsc.bcm.edu	37	chr12	55641766	55641767	+	Frame_Shift_Ins	INS	-	-	A																															ataccttcttctcaacagagINSaaaaaaagcattttctacat																										TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr12:55641766_55641767insA	ENST00000343870.4	+	1	785_786	c.695_696insA	c.(694-699)agaaaafs	p.RK232fs		NM_001005490.1	NP_001005490.1	A6NCV1	O6C74_HUMAN	olfactory receptor, family 6, subfamily C, member 74	232						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						TCTCAACAGAGAAAAAAAGCAT	0.401																																					p.R232fs		Atlas-Indel	.											.	OR6C74	52	.	0			c.695_696insA						PASS	.																																			SO:0001589	frameshift_variant	254783	exon1			.		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.702dupA	12.37:g.55641773_55641773dupA	ENSP00000342836:p.Arg232fs	172	0	0		178	35	0.196629	NM_001005490		Frame_Shift_Ins	INS	ENST00000343870.4	37	CCDS31816.1																																																																																			.	.	none		0.401	OR6C74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382312.1			A	55641767	-	A	55641766	7	5	37	1	0	1	1	0	0	0	0	0	11207	942	33	0	697	0	OR6C74	12	55641766	Frame_Shift_Ins	INS	-	TCGA-GS-A9TU-01A-11D-A382-10	30344423	55641766	78210129	31	14447											
CCDC60	160777	hgsc.bcm.edu	37	chr12	119942901	119942901	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aattcaaaattcccacaatgCgagtcaccaaccgcaaacca	17	6	4	14	2	2	0	2	0	0	0	3	1	3	0	4	0	3	1	4	0	6	2			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr12:119942901C>T	ENST00000327554.2	+	7	1141	c.676C>T	c.(676-678)Cga>Tga	p.R226*	RP11-768F21.1_ENST00000509470.2_lincRNA	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	226										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)		TCCCACAATGCGAGTCACCAA	0.517																																					p.R226X		Atlas-SNP	.											.	CCDC60	84	.	0			c.C676T						PASS	.						56	62	60					12																	119942901		2203	4300	6503	SO:0001587	stop_gained	160777	exon7			ACAATGCGAGTCA	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.676C>T	12.37:g.119942901C>T	ENSP00000333374:p.Arg226*	49	0	0		50	10	0.2	NM_178499		Nonsense_Mutation	SNP	ENST00000327554.2	37	CCDS9190.1	.	.	.	.	.	.	.	.	.	.	C	39	7.310390	0.98203	.	.	ENSG00000183273	ENST00000327554	.	.	.	5.07	5.07	0.68467	.	0.000000	0.45867	D	0.000322	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.7268	13.9816	0.64308	0.0:1.0:0.0:0.0	.	.	.	.	X	226	.	.	R	+	1	2	CCDC60	118427284	0.888000	0.30383	0.020000	0.16555	0.003000	0.03518	3.549000	0.53681	2.340000	0.79590	0.650000	0.86243	CGA	.	.	none		0.517	CCDC60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401680.1	NM_178499		T	119942901	C	T	119942901	4	4	37	1	0	0	0	0	0	1	0	0	2833	760	27	1	702	1	CCDC60	12	119942901	Nonsense_Mutation	SNP	C	TCGA-GS-A9TU-01A-11D-A382-10	64301135	119942901	13908994	32	14448											
DHRS12	79758	hgsc.bcm.edu	37	chr13	52346027	52346027	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcccttgggcccaccgctcCgtcagaaccacttgctgcct	5	9	9	18	2	1	1	1	0	0	1	2	1	2	1	6	1	4	2	6	1	1	2	rs151116008		TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr13:52346027C>T	ENST00000444610.2	-	8	649	c.636G>A	c.(634-636)acG>acA	p.T212T	DHRS12_ENST00000490949.1_5'UTR|DHRS12_ENST00000280056.2_Silent_p.T163T|DHRS12_ENST00000218981.1_Silent_p.T163T	NM_001270424.1	NP_001257353.1	A0PJE2	DHR12_HUMAN	dehydrogenase/reductase (SDR family) member 12	212							oxidoreductase activity (GO:0016491)			cervix(1)|large_intestine(1)|lung(2)|skin(2)|urinary_tract(1)	7		Breast(56;0.00173)|Prostate(109;0.00899)|Lung NSC(96;0.0199)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.81e-08)		CCCACCGCTCCGTCAGAACCA	0.607													C|||	1	0.000199681	0.0	0.0	5008	,	,		18842	0.001		0.0	False		,,,				2504	0.0				p.T212T		Atlas-SNP	.											.	DHRS12	28	.	0			c.G636A						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	70	74	73		489,489	-6.4	0	13	dbSNP_134	73	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	DHRS12	NM_001031719.1,NM_024705.1	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	163/272,163/243	52346027	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	79758	exon8			CCGCTCCGTCAGA	AK023701	CCDS9430.1, CCDS31976.1, CCDS58292.1	13q14.3	2013-10-11			ENSG00000102796	ENSG00000102796		"Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"	25832	protein-coding gene	gene with protein product	"short chain dehydrogenase/reductase family 40C, member 1"					19027726	Standard	NM_001031719		Approved	FLJ13639, SDR40C1	uc001vfq.4	A0PJE2	OTTHUMG00000016952	ENST00000444610.2:c.636G>A	13.37:g.52346027C>T		110	0	0		113	26	0.230089	NM_001270424	Q96GB2|Q9H8H1	Silent	SNP	ENST00000444610.2	37	CCDS58292.1																																																																																			C|1.000;T|0.000	0.000	strong		0.607	DHRS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045036.3	NM_024705		T	52346027	C	T	52346027	2	4	37	1	0	0	0	0	0	0	0	1	4490	639	23	1		1	DHRS12	13	52346027	Silent	SNP	C	TCGA-GS-A9TU-01A-11D-A382-10		52346027	62823851	33	14449											
CCDC33	80125	hgsc.bcm.edu	37	chr15	74623324	74623324	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tcctcccccatctcacagaaGaatgatcgagagaaggagct	13	7	9	12	1	1	4	1	1	1	3	5	7	3	5	3	1	1	1	3	1	3	0	rs370369621		TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr15:74623324G>A	ENST00000398814.3	+	14	1979	c.1548G>A	c.(1546-1548)aaG>aaA	p.K516K	CCDC33_ENST00000558821.1_Silent_p.K109K|CCDC33_ENST00000268082.4_Silent_p.K109K|CCDC33_ENST00000321288.5_Silent_p.K719K	NM_025055.3	NP_079331.3	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33	719										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						TCTCACAGAAGAATGATCGAG	0.607																																					p.K516K		Atlas-SNP	.											.	CCDC33	160	.	0			c.G1548A						PASS	.						17	20	19					15																	74623324		1994	4164	6158	SO:0001819	synonymous_variant	80125	exon14			ACAGAAGAATGAT	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.1548G>A	15.37:g.74623324G>A		49	0	0		47	12	0.255319	NM_025055	A8K3U4|A8MPQ6|A8MV61|A8MVU9|B3KQ49|Q8TAX6|Q9H5Q6	Silent	SNP	ENST00000398814.3	37	CCDS42058.1																																																																																			.	.	alt		0.607	CCDC33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419491.2	NM_182791		A	74623324	G	A	74623324	2	1	37	1	0	0	0	0	0	0	0	1	2808	933	33	2		2	CCDC33	15	74623324	Silent	SNP	G	TCGA-GS-A9TU-01A-11D-A382-10		74623324	27908068	34	14450											
MESP2	145873	hgsc.bcm.edu	37	chr15	90320149	90320149	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gggcaagggcaggggcagggGcaggggcaagggcaggggca	9	0	25	7	0	0	0	0	0	0	0	0	0	0	0	0	11	0	7	0	11	2	0			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr15:90320149G>A	ENST00000341735.3	+	1	561	c.561G>A	c.(559-561)ggG>ggA	p.G187G	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	187	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)			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)			aggggcaggggcaggggcaag	0.781																																					p.G187G		Atlas-SNP	.											.	MESP2	20	.	0			c.G561A						PASS	.						2	3	3					15																	90320149		1334	3199	4533	SO:0001819	synonymous_variant	145873	exon1			GCAGGGGCAGGGG		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.561G>A	15.37:g.90320149G>A		28	0	0		20	9	0.45	NM_001039958	Q7RTU2	Silent	SNP	ENST00000341735.3	37	CCDS42078.1																																																																																			.	.	none		0.781	MESP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416421.1	XM_085261		A	90320149	G	A	90320149	2	1	37	1	0	0	0	0	0	0	0	1	9492	1190	42	2		2	MESP2	15	90320149	Silent	SNP	G	TCGA-GS-A9TU-01A-11D-A382-10	15696825	90320149	12211243	35	14451											
PKMYT1	9088	hgsc.bcm.edu	37	chr16	3026927	3026927	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctgggcctcttgagggagAatccaggttctgcgtggcgg	5	9	16	11	2	2	2	0	1	2	1	3	3	3	2	3	5	1	1	3	5	1	2			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr16:3026927A>T	ENST00000262300.8	-	3	624	c.116T>A	c.(115-117)tTc>tAc	p.F39Y	PKMYT1_ENST00000573944.1_Missense_Mutation_p.F30Y|PKMYT1_ENST00000431515.2_Missense_Mutation_p.F39Y|PKMYT1_ENST00000574730.1_Intron|PKMYT1_ENST00000440027.2_Missense_Mutation_p.F39Y|PKMYT1_ENST00000574385.1_Missense_Mutation_p.F30Y	NM_001258450.1|NM_004203.4|NM_182687.2	NP_001245379.1|NP_004194.3|NP_872629.1	Q99640	PMYT1_HUMAN	protein kinase, membrane associated tyrosine/threonine 1	39	Pro-rich.				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)			NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	10						CTTGAGGGAGAATCCAGGTTC	0.692																																					p.F39Y		Atlas-SNP	.											.	PKMYT1	23	.	0			c.T116A						PASS	.						11	15	14					16																	3026927		2106	4183	6289	SO:0001583	missense	9088	exon3			AGGGAGAATCCAG	AK097642	CCDS10486.1, CCDS45391.1, CCDS58414.1, CCDS58415.1	16p13.3	2014-06-13			ENSG00000127564	ENSG00000127564			29650	protein-coding gene	gene with protein product	"membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase", "protein phosphatase 1, regulatory subunit 126"	602474				9001210, 12606722	Standard	NM_004203		Approved	MYT1, PPP1R126	uc002csn.3	Q99640	OTTHUMG00000128975	ENST00000262300.8:c.116T>A	16.37:g.3026927A>T	ENSP00000262300:p.Phe39Tyr	92	0	0		69	22	0.318841	NM_182687	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000262300.8	37	CCDS10486.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.472280	0.84533	.	.	ENSG00000127564	ENST00000431515;ENST00000262300;ENST00000440027;ENST00000402679;ENST00000382240	T;T;T;T	0.61274	0.12;0.2;0.25;0.29	5.68	4.57	0.56435	.	0.000000	0.85682	D	0.000000	T	0.69342	0.3100	M	0.63843	1.955	0.38873	D	0.956743	D;D;D	0.76494	0.999;0.996;0.998	D;P;D	0.63488	0.913;0.824;0.915	T	0.72906	-0.4150	10	0.72032	D	0.01	-19.7116	10.9777	0.47475	0.843:0.157:0.0:0.0	.	30;39;39	A6NHV6;Q99640;F8W164	.;PMYT1_HUMAN;.	Y	39;39;39;39;30	ENSP00000392855:F39Y;ENSP00000262300:F39Y;ENSP00000397739:F39Y;ENSP00000371675:F30Y	ENSP00000262300:F39Y	F	-	2	0	PKMYT1	2966928	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	5.755000	0.68750	0.938000	0.37419	0.533000	0.62120	TTC	.	.	none		0.692	PKMYT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250963.2	NM_004203		T	3026927	A	T	3026927	3	4	37	1	0	0	0	0	1	0	0	0	11987	246	9	5	1449	5	PKMYT1	16	3026927	Missense_Mutation	SNP	A	TCGA-GS-A9TU-01A-11D-A382-10		3026927	87327826	36	14452											
SRCAP	10847	hgsc.bcm.edu	37	chr16	30747922	30747922	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcactggaggaggtgagcCgagaggagctcaaacaggca	12	4	15	10	1	2	2	2	1	0	1	2	6	2	5	2	5	3	2	2	5	1	0			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr16:30747922C>T	ENST00000262518.4	+	33	7370	c.6985C>T	c.(6985-6987)Cga>Tga	p.R2329*	SRCAP_ENST00000344771.4_Nonsense_Mutation_p.R2171*|SRCAP_ENST00000395059.2_Nonsense_Mutation_p.R2267*	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	2329	Glu-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)			GGAGGTGAGCCGAGAGGAGCT	0.507																																					p.R2329X		Atlas-SNP	.											.	SRCAP	298	.	0			c.C6985T						PASS	.						40	42	41					16																	30747922		2197	4300	6497	SO:0001587	stop_gained	10847	exon33			GTGAGCCGAGAGG	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.6985C>T	16.37:g.30747922C>T	ENSP00000262518:p.Arg2329*	95	0	0		110	38	0.345455	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Nonsense_Mutation	SNP	ENST00000262518.4	37	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	C	46	12.453280	0.99669	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	.	.	.	4.99	4.02	0.46733	.	0.000000	0.38897	N	0.001525	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.2684	13.5265	0.61597	0.1574:0.8425:0.0:0.0	.	.	.	.	X	2329;2267;2171	.	ENSP00000262518:R2329X	R	+	1	2	SRCAP	30655423	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.623000	0.46435	1.292000	0.44672	0.563000	0.77884	CGA	.	.	none		0.507	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662		T	30747922	C	T	30747922	4	4	37	1	0	0	0	0	0	1	0	0	15150	644	23	1	7107	1	SRCAP	16	30747922	Nonsense_Mutation	SNP	C	TCGA-GS-A9TU-01A-11D-A382-10	27720995	30747922	59606831	37	14453											
ANKRD11	29123	hgsc.bcm.edu	37	chr16	89351721	89351722	+	Frame_Shift_Ins	INS	-	-	T																															cgcgtcctcctcgtccgacgINStgtctgacaggatacgatgg																										TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr16:89351721_89351722insT	ENST00000301030.4	-	9	1688_1689	c.1228_1229insA	c.(1228-1230)acgfs	p.T410fs	ANKRD11_ENST00000378330.2_Frame_Shift_Ins_p.T410fs	NM_001256183.1|NM_013275.5	NP_001243112.1|NP_037407.4	Q6UB99	ANR11_HUMAN	ankyrin repeat domain 11	410					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)		CTCGTCCGACGTGTCTGACAGG	0.47																																					p.T410fs		Pindel,Atlas-Indel	.											.	ANKRD11	195	.	0			c.1229_1230insA						PASS	.																																			SO:0001589	frameshift_variant	29123	exon9			.	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.1229dupA	16.37:g.89351722_89351722dupT	ENSP00000301030:p.Thr410fs	180	0	.		181	30	0.166	NM_001256183	Q6NTG1|Q6QMF8	Frame_Shift_Ins	INS	ENST00000301030.4	37	CCDS32513.1																																																																																			.	.	none		0.47	ANKRD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430462.3	NM_013275		T	89351722	-	T	89351721	7	5	37	1	0	1	1	0	0	0	0	0	639	1145	40	0	6782	0	ANKRD11	16	89351721	Frame_Shift_Ins	INS	-	TCGA-GS-A9TU-01A-11D-A382-10	58603799	89351721	1003032	38	14454											
DNAH9	1770	hgsc.bcm.edu	37	chr17	11666907	11666907	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tttgctgccatctgggctttCggcggagcaatggtccaaga	7	11	13	10	2	1	1	0	0	1	1	3	2	2	2	2	4	3	3	2	4	2	2			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr17:11666907C>T	ENST00000262442.4	+	36	7214	c.7146C>T	c.(7144-7146)ttC>ttT	p.F2382F	DNAH9_ENST00000454412.2_Silent_p.F2382F	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2382					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)		TCTGGGCTTTCGGCGGAGCAA	0.468																																					p.F2382F		Atlas-SNP	.											.	DNAH9	695	.	0			c.C7146T						PASS	.						71	65	67					17																	11666907		2203	4300	6503	SO:0001819	synonymous_variant	1770	exon36			GGCTTTCGGCGGA	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.7146C>T	17.37:g.11666907C>T		124	0	0		105	32	0.304762	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			.	.	none		0.468	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		T	11666907	C	T	11666907	2	4	37	1	0	0	0	0	0	0	0	1	4610	883	31	1		1	DNAH9	17	11666907	Silent	SNP	C	TCGA-GS-A9TU-01A-11D-A382-10		11666907	69528303	39	14455											
SUPT6H	6830	hgsc.bcm.edu	37	chr17	27016480	27016480	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaatacgatgaatcagccgaGgatgccaatcctgcaggagc	13	6	12	10	2	1	1	1	1	0	0	2	6	2	3	3	2	5	1	3	2	4	1			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr17:27016480G>T	ENST00000314616.6	+	25	3526	c.3243G>T	c.(3241-3243)gaG>gaT	p.E1081D	SUPT6H_ENST00000347486.4_Missense_Mutation_p.E1081D	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	1081	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)					AATCAGCCGAGGATGCCAATC	0.517																																					p.E1081D		Atlas-SNP	.											.	SUPT6H	165	.	0			c.G3243T						PASS	.						97	87	90					17																	27016480		2203	4300	6503	SO:0001583	missense	6830	exon25			AGCCGAGGATGCC	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.3243G>T	17.37:g.27016480G>T	ENSP00000319104:p.Glu1081Asp	80	0	0		88	4	0.0454545	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Missense_Mutation	SNP	ENST00000314616.6	37	CCDS32596.1	.	.	.	.	.	.	.	.	.	.	G	13.18	2.160282	0.38119	.	.	ENSG00000109111	ENST00000314616	.	.	.	5.61	1.4	0.22301	Tex RuvX-like domain (1);	0.000000	0.85682	D	0.000000	T	0.36717	0.0977	L	0.43554	1.36	0.80722	D	1	P	0.37688	0.605	B	0.30401	0.115	T	0.09357	-1.0678	9	0.30854	T	0.27	-23.0781	9.5962	0.39576	0.3447:0.0:0.6553:0.0	.	1081	Q7KZ85	SPT6H_HUMAN	D	1081	.	ENSP00000319104:E1081D	E	+	3	2	SUPT6H	24040607	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	0.535000	0.23114	0.314000	0.23086	0.655000	0.94253	GAG	.	.	none		0.517	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170		T	27016480	G	T	27016480	3	4	37	1	0	0	0	0	1	0	0	0	15415	991	35	4	3337	4	SUPT6H	17	27016480	Missense_Mutation	SNP	G	TCGA-GS-A9TU-01A-11D-A382-10	15349573	27016480	54178730	40	14456											
CWC25	54883	hgsc.bcm.edu	37	chr17	36959083	36959083	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gttttccatcatctcttgccGttttcgctctaattcctctg	4	19	5	13	2	4	0	1	0	3	0	8	0	6	0	3	0	1	3	3	0	1	7	rs199944848		TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr17:36959083G>A	ENST00000225428.5	-	9	1330	c.1033C>T	c.(1033-1035)Cgg>Tgg	p.R345W	CWC25_ENST00000536127.1_Missense_Mutation_p.R282W|PIP4K2B_ENST00000269554.3_5'Flank	NM_017748.3	NP_060218.1	Q9NXE8	CWC25_HUMAN	CWC25 spliceosome-associated protein homolog (S. cerevisiae)	345										central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	14						ATCTCTTGCCGTTTTCGCTCT	0.483																																					p.R345W		Atlas-SNP	.											.	CWC25	24	.	0			c.C1033T						PASS	.	G	TRP/ARG	0,3952		0,0,1976	195	192	193		1033	2.7	1	17		193	1,8315		0,1,4157	yes	missense	CWC25	NM_017748.3	101	0,1,6133	AA,AG,GG		0.012,0.0,0.0082	probably-damaging	345/426	36959083	1,12267	1976	4158	6134	SO:0001583	missense	54883	exon9			CTTGCCGTTTTCG	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.1033C>T	17.37:g.36959083G>A	ENSP00000225428:p.Arg345Trp	202	0	0		177	41	0.231638	NM_017748	A0JLM3|Q68DK5	Missense_Mutation	SNP	ENST00000225428.5	37	CCDS45663.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.058239	0.76074	0.0	1.2E-4	ENSG00000108296	ENST00000225428;ENST00000536127	.	.	.	5.88	2.74	0.32292	.	0.000000	0.85682	D	0.000000	T	0.71945	0.3400	M	0.78456	2.415	0.80722	D	1	P;D	0.89917	0.954;1.0	B;D	0.87578	0.429;0.998	T	0.70208	-0.4935	9	0.62326	D	0.03	.	7.9671	0.30104	0.0717:0.0:0.5191:0.4092	rs35783447	282;345	B4DJK2;Q9NXE8	.;CWC25_HUMAN	W	345;282	.	ENSP00000225428:R345W	R	-	1	2	CWC25	34212609	0.998000	0.40836	1.000000	0.80357	0.992000	0.81027	1.881000	0.39638	0.365000	0.24400	0.655000	0.94253	CGG	.	.	weak		0.483	CWC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442186.6	NM_017748		A	36959083	G	A	36959083	3	1	37	1	0	0	0	0	1	0	0	0	4071	1144	40	1	252	1	CWC25	17	36959083	Missense_Mutation	SNP	G	TCGA-GS-A9TU-01A-11D-A382-10	9942603	36959083	44236127	41	14457											
THRA	7067	hgsc.bcm.edu	37	chr17	38244519	38244519	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttgcgaagaccagatcatcCtcctgaaggggtgctgcatg	9	9	12	11	1	1	3	1	1	0	2	3	4	3	3	3	2	3	2	3	2	2	1			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr17:38244519C>T	ENST00000264637.4	+	8	1328	c.748C>T	c.(748-750)Ctc>Ttc	p.L250F	THRA_ENST00000450525.2_Missense_Mutation_p.L250F|THRA_ENST00000394121.4_Missense_Mutation_p.L250F|THRA_ENST00000584985.1_Missense_Mutation_p.L250F|THRA_ENST00000546243.1_Missense_Mutation_p.L250F	NM_003250.5	NP_003241.2	P10827	THA_HUMAN	thyroid hormone receptor, alpha	250	Ligand-binding.				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)	CCAGATCATCCTCCTGAAGGG	0.627																																					p.L250F		Atlas-SNP	.											.	THRA	88	.	0			c.C748T						PASS	.						77	64	68					17																	38244519		2203	4300	6503	SO:0001583	missense	7067	exon8			ATCATCCTCCTGA	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.748C>T	17.37:g.38244519C>T	ENSP00000264637:p.Leu250Phe	63	0	0		47	12	0.255319	NM_001190918	A8K3B5|P21205|Q8N6A1|Q96H73	Missense_Mutation	SNP	ENST00000264637.4	37	CCDS11360.1	.	.	.	.	.	.	.	.	.	.	c	21.8	4.208826	0.79240	.	.	ENSG00000126351	ENST00000394121;ENST00000264637;ENST00000450525;ENST00000546243	D;D;D;D	0.98437	-4.93;-4.93;-4.93;-4.93	4.97	3.78	0.43462	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.99137	0.9702	H	0.94886	3.595	0.51767	D	0.999938	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.87578	0.997;0.998;0.995	D	0.98698	1.0699	10	0.87932	D	0	.	13.2085	0.59811	0.0:0.9048:0.0:0.0952	.	250;250;250	P10827-3;P10827;Q6FH41	.;THA_HUMAN;.	F	250	ENSP00000377679:L250F;ENSP00000264637:L250F;ENSP00000395641:L250F;ENSP00000443972:L250F	ENSP00000264637:L250F	L	+	1	0	THRA	35498045	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.833000	0.62766	2.304000	0.77564	0.486000	0.48141	CTC	.	.	none		0.627	THRA-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257160.2			T	38244519	C	T	38244519	3	4	37	1	0	0	0	0	1	0	0	0	15888	681	24	2	774	2	THRA	17	38244519	Missense_Mutation	SNP	C	TCGA-GS-A9TU-01A-11D-A382-10	1285436	38244519	42950691	42	14458											
COASY	80347	hgsc.bcm.edu	37	chr17	40716134	40716134	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	acccctccctggagttcctgGtggtcagcgaggagacctat	7	9	12	13	1	1	1	1	0	0	1	3	4	3	2	5	4	1	1	5	4	1	2			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr17:40716134G>A	ENST00000393818.2	+	2	1312	c.856G>A	c.(856-858)Gtg>Atg	p.V286M	RP11-400F19.8_ENST00000585572.1_RNA|COASY_ENST00000590958.1_Missense_Mutation_p.V315M|MLX_ENST00000246912.4_5'Flank|MLX_ENST00000435881.2_5'Flank|COASY_ENST00000420359.1_Missense_Mutation_p.V286M|COASY_ENST00000421097.2_Missense_Mutation_p.V286M|MLX_ENST00000346833.4_5'Flank|COASY_ENST00000449624.1_5'UTR	NM_025233.6	NP_079509.5	Q13057	COASY_HUMAN	CoA synthase	286	Phosphopantetheine adenylyltransferase.				cell death (GO:0008219)|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)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)	ATP binding (GO:0005524)|dephospho-CoA kinase activity (GO:0004140)|pantetheine-phosphate adenylyltransferase activity (GO:0004595)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)	21		all_cancers(22;1.06e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)		GGAGTTCCTGGTGGTCAGCGA	0.602																																					p.V315M		Atlas-SNP	.											.	COASY	45	.	0			c.G943A						PASS	.						48	49	49					17																	40716134		2203	4300	6503	SO:0001583	missense	80347	exon4			TTCCTGGTGGTCA	AF453478	CCDS11429.1, CCDS45685.1	17q12-q21	2010-04-30	2010-04-30			ENSG00000068120	2.7.7.3		29932	protein-coding gene	gene with protein product		609855	"Coenzyme A synthase"			11923312, 11980892	Standard	NM_025233		Approved	DPCK, NBP, CoASY, PPAT	uc010cyj.4	Q13057		ENST00000393818.2:c.856G>A	17.37:g.40716134G>A	ENSP00000377406:p.Val286Met	140	0	0		123	28	0.227642	NM_001042532	B2RA78|B4DLU0|Q6GS23|Q8NBM7|Q8NEW1|Q8WXD4|Q9NRM3	Missense_Mutation	SNP	ENST00000393818.2	37	CCDS11429.1	.	.	.	.	.	.	.	.	.	.	G	31	5.070898	0.93950	.	.	ENSG00000068120	ENST00000421097;ENST00000420359;ENST00000393818	D;D	0.97575	-4.44;-4.44	5.23	5.23	0.72850	Cytidylyltransferase (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	D	0.98814	0.9600	M	0.93854	3.465	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.991;0.995	D	0.99289	1.0898	10	0.87932	D	0	-20.9887	16.6827	0.85297	0.0:0.0:1.0:0.0	.	315;286	Q13057-2;Q13057	.;COASY_HUMAN	M	315;286;286	ENSP00000413338:V286M;ENSP00000377406:V286M	ENSP00000377406:V286M	V	+	1	0	COASY	37969660	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.436000	0.97532	2.882000	0.98803	0.655000	0.94253	GTG	.	.	none		0.602	COASY-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450409.1	NM_025233		A	40716134	G	A	40716134	3	1	37	1	0	0	0	0	1	0	0	0	3654	1261	44	2	953	2	COASY	17	40716134	Missense_Mutation	SNP	G	TCGA-GS-A9TU-01A-11D-A382-10	2471615	40716134	40479076	43	14459											
ICT1	3396	hgsc.bcm.edu	37	chr17	73008803	73008803	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggcggccaccaggtgcctgCgctggggcctgagccgagcc	4	5	17	15	3	0	1	0	1	0	0	0	2	0	1	6	5	4	1	6	5	0	0			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr17:73008803C>G	ENST00000301585.5	+	1	35	c.22C>G	c.(22-24)Cgc>Ggc	p.R8G		NM_001545.1	NP_001536.1	Q14197	ICT1_HUMAN	immature colon carcinoma transcript 1	8			R -> P (in dbSNP:rs3744206).		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)					CAGGTGCCTGCGCTGGGGCCT	0.697											OREG0024724	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R8G		Atlas-SNP	.											ICT1,NS,carcinoma,-1,1	ICT1	17	1	0			c.C22G						PASS	.						10	9	9					17																	73008803		2150	4208	6358	SO:0001583	missense	3396	exon1			TGCCTGCGCTGGG	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.22C>G	17.37:g.73008803C>G	ENSP00000301585:p.Arg8Gly	40	0	0	1142	35	7	0.2	NM_001545	B2RAD1|Q53HM7|Q53Y11	Missense_Mutation	SNP	ENST00000301585.5	37	CCDS11711.1	.	.	.	.	.	.	.	.	.	.	C	10.16	1.274396	0.23307	.	.	ENSG00000167862	ENST00000301585	T	0.26810	1.71	5.58	4.33	0.51752	.	0.565130	0.17342	N	0.177719	T	0.17789	0.0427	N	0.24115	0.695	0.09310	N	0.999997	B	0.28055	0.199	B	0.24974	0.057	T	0.16158	-1.0412	10	0.62326	D	0.03	-4.1944	10.3113	0.43710	0.0:0.8818:0.0:0.1182	.	8	Q14197	ICT1_HUMAN	G	8	ENSP00000301585:R8G	ENSP00000301585:R8G	R	+	1	0	ICT1	70520398	0.002000	0.14202	0.649000	0.29536	0.023000	0.10783	0.523000	0.22925	0.962000	0.38057	0.655000	0.94253	CGC	.	.	none		0.697	ICT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445314.1	NM_001545		G	73008803	C	G	73008803	3	3	37	1	0	0	0	0	1	0	0	0	7497	768	27	4	24	4	ICT1	17	73008803	Missense_Mutation	SNP	C	TCGA-GS-A9TU-01A-11D-A382-10	32292669	73008803	8186407	44	14460											
ENPP7	339221	hgsc.bcm.edu	37	chr17	77704925	77704925	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agaggcctggccgtcctcctCactgtggctctggccacgct	4	9	12	16	2	2	1	1	0	1	1	4	1	4	1	5	4	0	2	5	4	0	0			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr17:77704925C>T	ENST00000328313.5	+	1	245	c.24C>T	c.(22-24)ctC>ctT	p.L8L		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)			CCGTCCTCCTCACTGTGGCTC	0.657																																					p.L8L		Atlas-SNP	.											.	ENPP7	63	.	0			c.C24T						PASS	.						15	16	16					17																	77704925		2173	4242	6415	SO:0001819	synonymous_variant	339221	exon1			CCTCCTCACTGTG	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.24C>T	17.37:g.77704925C>T		44	0	0		38	10	0.263158	NM_178543		Silent	SNP	ENST00000328313.5	37	CCDS11763.1																																																																																			.	.	none		0.657	ENPP7-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437038.1	NM_178543		T	77704925	C	T	77704925	2	4	37	1	0	0	0	0	0	0	0	1	5137	813	29	2		2	ENPP7	17	77704925	Silent	SNP	C	TCGA-GS-A9TU-01A-11D-A382-10	4696122	77704925	3490285	45	14461											
DSC2	1824	hgsc.bcm.edu	37	chr18	28662381	28662381	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actgtattttcttccactgaTgtcacatactaaaataataa	15	15	3	8	0	2	1	1	1	1	0	3	1	3	1	1	0	1	1	1	0	6	8			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr18:28662381T>G	ENST00000280904.6	-	9	1529	c.1086A>C	c.(1084-1086)acA>acC	p.T362T	DSC2_ENST00000251081.6_Silent_p.T362T	NM_024422.3	NP_077740.1	Q02487	DSC2_HUMAN	desmocollin 2	362	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)			CTTCCACTGATGTCACATACT	0.318																																					p.T362T		Atlas-SNP	.											DSC2_ENST00000251081,NS,carcinoma,0,2	DSC2	168	2	0			c.A1086C						PASS	.						69	66	67					18																	28662381		2200	4299	6499	SO:0001819	synonymous_variant	1824	exon9			CACTGATGTCACA	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.1086A>C	18.37:g.28662381T>G		140	0	0		221	27	0.122172	NM_024422		Silent	SNP	ENST00000280904.6	37	CCDS11892.1																																																																																			.	.	none		0.318	DSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254943.1	NM_004949		G	28662381	T	G	28662381	2	3	37	1	0	0	0	0	0	0	0	1	4768	1451	51	5		5	DSC2	18	28662381	Silent	SNP	T	TCGA-GS-A9TU-01A-11D-A382-10		28662381	49414867	46	14462											
DSG1	1828	hgsc.bcm.edu	37	chr18	28911696	28911696	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgatactcaatgctactgacGcagatgaaccgaacaatttg	14	10	8	9	2	1	4	1	3	0	1	1	5	1	4	1	0	5	2	1	0	6	3			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr18:28911696G>A	ENST00000257192.4	+	6	762	c.550G>A	c.(550-552)Gca>Aca	p.A184T		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	184	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				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)			TGCTACTGACGCAGATGAACC	0.333																																					p.A184T		Atlas-SNP	.											DSG1,colon,carcinoma,0,1	DSG1	176	1	0			c.G550A						PASS	.						74	68	70					18																	28911696		2203	4299	6502	SO:0001583	missense	1828	exon6			ACTGACGCAGATG	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.550G>A	18.37:g.28911696G>A	ENSP00000257192:p.Ala184Thr	127	0	0		299	31	0.103679	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	.	.	.	.	.	.	.	.	.	.	G	33	5.283521	0.95489	.	.	ENSG00000134760	ENST00000257192	T	0.61859	0.07	5.88	5.88	0.94601	Cadherin (5);Cadherin-like (1);	0.000000	0.64402	D	0.000016	T	0.82029	0.4948	M	0.90705	3.14	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84483	0.0606	10	0.72032	D	0.01	.	20.2187	0.98312	0.0:0.0:1.0:0.0	.	184	Q02413	DSG1_HUMAN	T	184	ENSP00000257192:A184T	ENSP00000257192:A184T	A	+	1	0	DSG1	27165694	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.063000	0.89482	2.780000	0.95670	0.655000	0.94253	GCA	.	.	none		0.333	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942		A	28911696	G	A	28911696	3	1	37	1	0	0	0	0	1	0	0	0	4778	1087	38	1	572	1	DSG1	18	28911696	Missense_Mutation	SNP	G	TCGA-GS-A9TU-01A-11D-A382-10	249315	28911696	49165552	47	14463											
SERPINB3	6317	hgsc.bcm.edu	37	chr18	61323022	61323022	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgatccgaatcctactacagCggtggcagctgcagcttctg	8	10	11	12	2	1	1	0	1	1	0	3	2	3	1	2	2	6	4	2	2	3	3	rs111442409		TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr18:61323022C>T	ENST00000283752.5	-	8	1185	c.1042G>A	c.(1042-1044)Gct>Act	p.A348T	SERPINB3_ENST00000332821.8_Missense_Mutation_p.A296T|SERPINB11_ENST00000489748.1_RNA	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	348					negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						CCTACTACAGCGGTGGCAGCT	0.498													c|||	1	0.000199681	0.0008	0.0	5008	,	,		19839	0.0		0.0	False		,,,				2504	0.0				p.A348T		Atlas-SNP	.											.	SERPINB3	90	.	0			c.G1042A						PASS	.						110	116	114					18																	61323022		2203	4300	6503	SO:0001583	missense	6317	exon8			CTACAGCGGTGGC	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"Serine (or cysteine) peptidase inhibitors"	10569	protein-coding gene	gene with protein product		600517	"serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.1042G>A	18.37:g.61323022C>T	ENSP00000283752:p.Ala348Thr	193	0	0		404	48	0.118812	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Missense_Mutation	SNP	ENST00000283752.5	37	CCDS11987.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	c	12.32	1.901744	0.33535	.	.	ENSG00000057149	ENST00000283752;ENST00000332821	D;D	0.83506	-1.73;-1.73	3.06	1.15	0.20763	Serpin domain (3);	0.530994	0.15710	N	0.248470	T	0.71813	0.3384	L	0.41710	1.295	0.09310	N	1	B;B	0.34264	0.446;0.002	B;B	0.29440	0.102;0.001	T	0.61407	-0.7069	10	0.52906	T	0.07	.	8.2078	0.31465	0.0:0.7806:0.0:0.2194	.	296;348	P29508-2;P29508	.;SPB3_HUMAN	T	348;296	ENSP00000283752:A348T;ENSP00000329498:A296T	ENSP00000283752:A348T	A	-	1	0	SERPINB3	59474002	0.000000	0.05858	0.003000	0.11579	0.025000	0.11179	-0.304000	0.08199	0.300000	0.22699	-0.384000	0.06662	GCT	C|0.999;T|0.001	0.001	strong		0.498	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919		T	61323022	C	T	61323022	3	4	37	1	0	0	0	0	1	0	0	0	14117	768	27	1	134	1	SERPINB3	18	61323022	Missense_Mutation	SNP	C	TCGA-GS-A9TU-01A-11D-A382-10	32411326	61323022	16754226	48	14464											
CYP4F12	66002	hgsc.bcm.edu	37	chr19	15794330	15794330	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtgaatatattgccaccatCttggagctcagtgcccttgt	9	13	9	10	0	2	1	1	1	1	0	2	2	2	2	3	1	3	1	3	1	3	5			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr19:15794330C>A	ENST00000550308.1	+	7	1055	c.675C>A	c.(673-675)atC>atA	p.I225I	CYP4F12_ENST00000324632.10_Silent_p.I225I	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	225					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)	TTGCCACCATCTTGGAGCTCA	0.542																																					p.I225I		Atlas-SNP	.											.	CYP4F12	89	.	0			c.C675A						PASS	.						71	71	71					19																	15794330		2201	4300	6501	SO:0001819	synonymous_variant	66002	exon7			CACCATCTTGGAG	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.675C>A	19.37:g.15794330C>A		111	0	0		96	20	0.208333	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	37	CCDS42517.1																																																																																			.	.	none		0.542	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9			A	15794330	C	A	15794330	2	1	37	1	0	0	0	0	0	0	0	1	4189	903	32	4		4	CYP4F12	19	15794330	Silent	SNP	C	TCGA-GS-A9TU-01A-11D-A382-10		15794330	43334653	49	14465											
UNC13A	23025	hgsc.bcm.edu	37	chr19	17751347	17751347	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttggaggcggcgaagcggtcGgaggcagacacgttggtgga	8	6	20	7	5	0	1	0	0	0	1	1	5	0	4	0	8	1	2	0	8	1	2	rs371816774		TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr19:17751347G>A	ENST00000519716.2	-	22	2759	c.2760C>T	c.(2758-2760)tcC>tcT	p.S920S	UNC13A_ENST00000551649.1_Silent_p.S920S|UNC13A_ENST00000252773.7_Silent_p.S920S|UNC13A_ENST00000550896.1_Silent_p.S918S|UNC13A_ENST00000552293.1_Silent_p.S920S|UNC13A_ENST00000428389.2_Silent_p.S1008S	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	920					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						CGAAGCGGTCGGAGGCAGACA	0.582																																					p.S920S		Atlas-SNP	.											.	UNC13A	299	.	0			c.C2760T						PASS	.	G		1,4327		0,1,2163	51	62	58		2760	-2.7	1	19		58	0,8492		0,0,4246	no	coding-synonymous	UNC13A	NM_001080421.2		0,1,6409	AA,AG,GG		0.0,0.0231,0.0078		920/1704	17751347	1,12819	2164	4246	6410	SO:0001819	synonymous_variant	23025	exon21			GCGGTCGGAGGCA	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.2760C>T	19.37:g.17751347G>A		124	0	0		89	19	0.213483	NM_001080421	E5RHY9	Silent	SNP	ENST00000519716.2	37	CCDS46013.2																																																																																			.	.	weak		0.582	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604		A	17751347	G	A	17751347	2	1	37	1	0	0	0	0	0	0	0	1	16999	1103	39	1		1	UNC13A	19	17751347	Silent	SNP	G	TCGA-GS-A9TU-01A-11D-A382-10	1957017	17751347	41377636	50	14466											
ISYNA1	51477	hgsc.bcm.edu	37	chr19	18546466	18546466	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgcttgctgtcacccacgtaCggcacatacttgatgaccac	9	9	8	15	3	1	2	1	2	0	0	1	2	1	2	2	1	3	4	2	1	2	4			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr19:18546466C>T	ENST00000338128.8	-	9	1378	c.1161G>A	c.(1159-1161)ccG>ccA	p.P387P	ISYNA1_ENST00000545187.1_Silent_p.P237P|ISYNA1_ENST00000578963.1_Silent_p.P259P|ISYNA1_ENST00000457269.4_Silent_p.P333P|ISYNA1_ENST00000317018.6_Silent_p.P185P	NM_001170938.1|NM_016368.4	NP_001164409.1|NP_057452.1	Q9NPH2	INO1_HUMAN	inositol-3-phosphate synthase 1	387					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						CACCCACGTACGGCACATACT	0.672																																					p.P387P		Atlas-SNP	.											.	ISYNA1	31	.	0			c.G1161A						PASS	.						60	46	51					19																	18546466		2201	4300	6501	SO:0001819	synonymous_variant	51477	exon9			CACGTACGGCACA		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.1161G>A	19.37:g.18546466C>T		63	0	0		60	17	0.283333	NM_016368	B3KRT1|G5E9U0|Q6NXT5|Q7Z525|Q9BT65|Q9H2Y2|Q9NSU0|Q9NVW7	Silent	SNP	ENST00000338128.8	37	CCDS12379.1																																																																																			.	.	none		0.672	ISYNA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444469.2	NM_016368		T	18546466	C	T	18546466	2	4	37	1	0	0	0	0	0	0	0	1	7876	523	19	1		1	ISYNA1	19	18546466	Silent	SNP	C	TCGA-GS-A9TU-01A-11D-A382-10	795119	18546466	40582517	51	14467											
RHPN2	85415	hgsc.bcm.edu	37	chr19	33517507	33517507	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagctcagctccagccgcaCttgctcccgcacctttgagt	7	9	9	16	2	1	1	1	1	0	0	3	2	3	1	4	0	4	5	4	0	1	2			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr19:33517507C>T	ENST00000254260.3	-	3	252	c.217G>A	c.(217-219)Gtg>Atg	p.V73M	RHPN2_ENST00000400226.4_De_novo_Start_OutOfFrame	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	73					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)		p.V73M(2)		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)					TCCAGCCGCACTTGCTCCCGC	0.552																																					p.V73M		Atlas-SNP	.											RHPN2,face,carcinoma,0,2	RHPN2	107	2	2	Substitution - Missense(2)	NS(1)|skin(1)	c.G217A						scavenged	.						84	83	83					19																	33517507		2203	4300	6503	SO:0001583	missense	85415	exon3			GCCGCACTTGCTC	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.217G>A	19.37:g.33517507C>T	ENSP00000254260:p.Val73Met	23	1	0.0434783		24	3	0.125	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	C	18.08	3.542997	0.65198	.	.	ENSG00000131941	ENST00000254260	T	0.39787	1.06	3.88	3.88	0.44766	.	0.000000	0.85682	D	0.000000	T	0.64853	0.2636	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.71984	-0.4427	10	0.87932	D	0	11.9954	16.025	0.80536	0.0:1.0:0.0:0.0	.	73	Q8IUC4	RHPN2_HUMAN	M	73	ENSP00000254260:V73M	ENSP00000254260:V73M	V	-	1	0	RHPN2	38209347	1.000000	0.71417	1.000000	0.80357	0.343000	0.28985	7.267000	0.78462	2.167000	0.68274	0.557000	0.71058	GTG	.	.	none		0.552	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103		T	33517507	C	T	33517507	3	4	37	1	0	0	0	0	1	0	0	0	13366	565	20	2	1895	2	RHPN2	19	33517507	Missense_Mutation	SNP	C	TCGA-GS-A9TU-01A-11D-A382-10	14971041	33517507	25611476	52	14468											
SLC6A16	28968	hgsc.bcm.edu	37	chr19	49812603	49812603	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ccaaattttgccccttccagGagtagagtccggatgaagaa	12	9	10	10	1	0	3	0	1	0	2	2	5	2	5	5	2	1	1	5	2	4	4			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr19:49812603G>A	ENST00000335875.4	-	6	1183	c.942C>T	c.(940-942)ctC>ctT	p.L314L	MIR4324_ENST00000584846.1_RNA|SLC6A16_ENST00000454748.3_Silent_p.L314L	NM_014037.2	NP_054756.2	Q9GZN6	S6A16_HUMAN	solute carrier family 6, member 16	314					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)		CCCCTTCCAGGAGTAGAGTCC	0.507																																					p.L314L		Atlas-SNP	.											.	SLC6A16	62	.	0			c.C942T						PASS	.						71	72	71					19																	49812603		1926	4128	6054	SO:0001819	synonymous_variant	28968	exon6			TTCCAGGAGTAGA	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.942C>T	19.37:g.49812603G>A		73	0	0		140	10	0.0714286	NM_014037	Q8IYV4|Q9Y5I9	Silent	SNP	ENST00000335875.4	37	CCDS42590.1																																																																																			.	.	none		0.507	SLC6A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465503.2	NM_014037		A	49812603	G	A	49812603	2	1	37	1	0	0	0	0	0	0	0	1	14694	1161	41	2		2	SLC6A16	19	49812603	Silent	SNP	G	TCGA-GS-A9TU-01A-11D-A382-10	16295096	49812603	9316380	53	14469											
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385793	58385793	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	attctccacattcataaggtCttttcccagtgtgaactctc	9	15	5	12	0	4	1	1	1	3	0	7	1	5	1	2	1	1	0	2	1	2	5	rs113623532		TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr19:58385793C>T	ENST00000435989.2	-	3	1199	c.965G>A	c.(964-966)aGa>aAa	p.R322K	ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597832.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	322					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						TTCATAAGGTCTTTTCCCAGT	0.358																																					p.R322K		Atlas-SNP	.											.	ZNF814	93	.	0			c.G965A						PASS	.						15	12	13					19																	58385793		687	1562	2249	SO:0001583	missense	730051	exon3			TAAGGTCTTTTCC		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.965G>A	19.37:g.58385793C>T	ENSP00000410545:p.Arg322Lys	202	0	0		272	38	0.139706	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	0.023	-1.395361	0.01175	.	.	ENSG00000204514	ENST00000435989	T	0.12361	2.69	2.27	9.47E-4	0.14044	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03608	0.0103	N	0.02225	-0.63	0.09310	N	0.999999	B	0.29301	0.241	B	0.28916	0.096	T	0.40534	-0.9558	9	0.02654	T	1	.	4.6969	0.12808	0.0:0.4166:0.0:0.5834	.	322	B7Z6K7	ZN814_HUMAN	K	322	ENSP00000410545:R322K	ENSP00000410545:R322K	R	-	2	0	ZNF814	63077605	0.000000	0.05858	0.024000	0.17045	0.009000	0.06853	-1.883000	0.01623	0.331000	0.23511	-1.381000	0.01174	AGA	C|0.500;T|0.500	0.500	weak		0.358	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		T	58385793	C	T	58385793	3	4	37	1	0	0	0	0	1	0	0	0	18191	913	32	2	1606	2	ZNF814	19	58385793	Missense_Mutation	SNP	C	TCGA-GS-A9TU-01A-11D-A382-10	8573190	58385793	743190	54	14470											
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385867	58385867	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatttcccacattctccacaTtcatgttttttttcagtgtg	7	19	5	10	0	3	0	2	0	1	0	5	1	4	0	2	0	0	1	2	0	0	7			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr19:58385867T>A	ENST00000435989.2	-	3	1125	c.891A>T	c.(889-891)gaA>gaT	p.E297D	ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597832.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	297					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						ATTCTCCACATTCATGTTTTT	0.363																																					p.E297D		Atlas-SNP	.											ZNF814,NS,carcinoma,-2,1	ZNF814	93	1	0			c.A891T						scavenged	.						5	4	4					19																	58385867		510	1081	1591	SO:0001583	missense	730051	exon3			TCCACATTCATGT		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.891A>T	19.37:g.58385867T>A	ENSP00000410545:p.Glu297Asp	70	0	0		104	11	0.105769	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	11.15	1.554325	0.27739	.	.	ENSG00000204514	ENST00000435989	T	0.22134	1.97	1.93	-3.87	0.04218	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.16214	0.0390	L	0.47078	1.49	0.09310	N	1	P	0.36048	0.534	B	0.39738	0.308	T	0.22208	-1.0223	9	0.40728	T	0.16	.	3.3223	0.07054	0.3234:0.181:0.0:0.4956	.	297	B7Z6K7	ZN814_HUMAN	D	297	ENSP00000410545:E297D	ENSP00000410545:E297D	E	-	3	2	ZNF814	63077679	0.000000	0.05858	0.000000	0.03702	0.378000	0.30076	-2.601000	0.00892	-0.795000	0.04462	0.102000	0.15555	GAA	.	.	none		0.363	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		A	58385867	T	A	58385867	3	1	37	1	0	0	0	0	1	0	0	0	18191	1490	52	5	1680	5	ZNF814	19	58385867	Missense_Mutation	SNP	T	TCGA-GS-A9TU-01A-11D-A382-10	74	58385867	743116	55	14471											
SNX21	90203	hgsc.bcm.edu	37	chr20	44469595	44469595	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agcctcacctgtactggcctCtatcgtgaggctctggcact	6	11	10	14	1	3	1	1	1	2	0	4	1	3	1	3	3	2	3	3	3	2	2			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr20:44469595C>T	ENST00000491381.1	+	4	833	c.765C>T	c.(763-765)ctC>ctT	p.L255L	SNX21_ENST00000344780.4_3'UTR|SNX21_ENST00000372542.1_Silent_p.L246L|SNX21_ENST00000342644.5_Intron|SNX21_ENST00000462307.1_3'UTR			Q969T3	SNX21_HUMAN	sorting nexin family member 21	255					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)				GTACTGGCCTCTATCGTGAGG	0.692																																					p.L255L		Atlas-SNP	.											.	SNX21	23	.	0			c.C765T						PASS	.						15	18	17					20																	44469595		2192	4258	6450	SO:0001819	synonymous_variant	90203	exon4			TGGCCTCTATCGT	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.765C>T	20.37:g.44469595C>T		68	0	0		64	17	0.265625	NM_033421	Q5JZH5|Q5JZH6|Q5JZH7|Q8WUR6|Q9BR16	Silent	SNP	ENST00000491381.1	37	CCDS13377.1																																																																																			.	.	none		0.692	SNX21-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079534.1	NM_033421		T	44469595	C	T	44469595	2	4	37	1	0	0	0	0	0	0	0	1	14908	900	32	2		2	SNX21	20	44469595	Silent	SNP	C	TCGA-GS-A9TU-01A-11D-A382-10		44469595	18555925	56	14472											
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230413	23230413	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctcagttggaagcagccgAtccagcctgcggagcctgtg	7	7	14	13	2	1	0	1	0	0	0	2	3	2	2	5	2	5	2	5	2	1	1			TCGA-GS-A9TU-01A-11D-A382-10	TCGA-GS-A9TU-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	a588279b-b306-445f-9584-61586da9887f	758b8554-5e4a-469e-92dd-c459fbcd4e0e	g.chr22:23230413A>G	ENST00000526893.1	+	1	454	c.180A>G	c.(178-180)cgA>cgG	p.R60R	hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000531372.1_Silent_p.R60R|IGLL5_ENST00000532223.2_Silent_p.R60R	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	60						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GAAGCAGCCGATCCAGCCTGC	0.647																																					p.D25G		Atlas-SNP	.											.	IGLL5	26	.	0			c.A74G						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			CAGCCGATCCAGC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.180A>G	22.37:g.23230413A>G		109	0	0		103	54	0.524272	NM_001256296		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.647	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		G	23230413	A	G	23230413	2	3	37	1	0	0	0	0	0	0	0	1	7603	320	12	3		3	IGLL5	22	23230413	Silent	SNP	A	TCGA-GS-A9TU-01A-11D-A382-10		23230413	28074153	57	14473											
FLG	2312	hgsc.bcm.edu	37	chr1	152280084	152280084	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtcccggtccgtccatgggcGgactcagactgttcatgagt	6	10	13	12	3	2	2	2	1	0	1	5	3	5	3	3	3	0	1	3	3	0	1	rs200015722		TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr1:152280084G>A	ENST00000368799.1	-	3	7313	c.7278C>T	c.(7276-7278)tcC>tcT	p.S2426S	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2426	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)			GTCCATGGGCGGACTCAGACT	0.602									Ichthyosis																												p.S2426S		Atlas-SNP	.											.	FLG	900	.	0			c.C7278T						PASS	.	A		3,4403	825.6+/-416.5	0,3,2200	245	231	236		7278	-9.1	0	1		236	3,8597	819.0+/-406.8	0,3,4297	no	coding-synonymous	FLG	NM_002016.1		0,6,6497	AA,AG,GG		0.0349,0.0681,0.0461		2426/4062	152280084	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	ATGGGCGGACTCA	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.7278C>T	1.37:g.152280084G>A		225	0	0		199	15	0.0753769	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			G|0.999;A|0.001	0.001	weak		0.602	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016		A	152280084	G	A	152280084	2	1	38	1	0	0	0	0	0	0	0	1	5930	1103	39	1		1	FLG	1	152280084	Silent	SNP	G	TCGA-GS-A9TV-01A-11D-A382-10		152280084	96970537	1	14474											
KPRP	448834	hgsc.bcm.edu	37	chr1	152733644	152733644	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acaccgcctagacaccgaagCtccctactgtggcccatcca	10	6	7	18	2	0	1	0	0	0	1	2	2	2	1	6	1	2	1	6	1	3	2			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr1:152733644C>G	ENST00000606109.1	+	1	1608	c.1580C>G	c.(1579-1581)gCt>gGt	p.A527G	KPRP_ENST00000368773.1_Missense_Mutation_p.A527G			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	527						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)			GACACCGAAGCTCCCTACTGT	0.602																																					p.A527G		Atlas-SNP	.											.	KPRP	152	.	0			c.C1580G						PASS	.						74	70	71					1																	152733644		2203	4300	6503	SO:0001583	missense	448834	exon2			CCGAAGCTCCCTA	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.1580C>G	1.37:g.152733644C>G	ENSP00000475216:p.Ala527Gly	93	0	0		83	6	0.0722892	NM_001025231		Missense_Mutation	SNP	ENST00000606109.1	37	CCDS30862.1	.	.	.	.	.	.	.	.	.	.	C	10.43	1.348734	0.24426	.	.	ENSG00000203786	ENST00000368773	T	0.12984	2.63	4.61	1.46	0.22682	.	0.519669	0.16240	N	0.223183	T	0.02083	0.0065	N	0.21194	0.64	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.46925	-0.9156	10	0.22706	T	0.39	-2.3812	4.8838	0.13692	0.0:0.5548:0.2368:0.2084	.	527	Q5T749	KPRP_HUMAN	G	527	ENSP00000357762:A527G	ENSP00000357762:A527G	A	+	2	0	KPRP	151000268	0.848000	0.29623	0.007000	0.13788	0.317000	0.28152	1.056000	0.30480	0.224000	0.20940	0.462000	0.41574	GCT	.	.	none		0.602	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231		G	152733644	C	G	152733644	3	3	38	1	0	0	0	0	1	0	0	0	8445	797	28	4	1582	4	KPRP	1	152733644	Missense_Mutation	SNP	C	TCGA-GS-A9TV-01A-11D-A382-10	453560	152733644	96516977	2	14475											
INTS3	65123	hgsc.bcm.edu	37	chr1	153741377	153741377	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttccatttagtttccagaTgaaaccttgaggagcggaga	11	13	10	7	1	0	4	0	2	0	2	2	6	2	5	3	2	2	1	3	2	2	6	rs372522734		TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr1:153741377T>G	ENST00000318967.2	+	22	2821	c.2253T>G	c.(2251-2253)gaT>gaG	p.D751E	INTS3_ENST00000476843.1_3'UTR|INTS3_ENST00000512605.1_Missense_Mutation_p.D545E|INTS3_ENST00000456435.1_Missense_Mutation_p.D545E|INTS3_ENST00000435409.2_Missense_Mutation_p.D751E	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	752					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)			AGTTTCCAGATGAAACCTTGA	0.488																																					p.D751E		Atlas-SNP	.											.	INTS3	83	.	0			c.T2253G						PASS	.						93	89	90					1																	153741377		2203	4300	6503	SO:0001583	missense	65123	exon22			TCCAGATGAAACC	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.2253T>G	1.37:g.153741377T>G	ENSP00000318641:p.Asp751Glu	70	0	0		84	4	0.047619	NM_023015	A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Missense_Mutation	SNP	ENST00000318967.2	37	CCDS1052.1	.	.	.	.	.	.	.	.	.	.	T	12.58	1.979299	0.34942	.	.	ENSG00000143624	ENST00000318967;ENST00000456435;ENST00000435409;ENST00000512605	.	.	.	5.46	4.33	0.51752	.	0.000000	0.85682	D	0.000000	T	0.34019	0.0883	N	0.10874	0.06	0.44085	D	0.996848	D;D;D	0.61697	0.99;0.984;0.99	D;D;D	0.75484	0.986;0.935;0.971	T	0.24728	-1.0152	9	0.19590	T	0.45	.	9.4306	0.38608	0.0:0.0845:0.0:0.9155	.	545;752;751	Q68E01-3;Q68E01;Q68E01-2	.;INT3_HUMAN;.	E	751;545;751;545	.	ENSP00000318641:D751E	D	+	3	2	INTS3	152008001	0.997000	0.39634	1.000000	0.80357	0.968000	0.65278	0.276000	0.18716	0.920000	0.36970	0.482000	0.46254	GAT	.	.	none		0.488	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015		G	153741377	T	G	153741377	3	3	38	1	0	0	0	0	1	0	0	0	7788	1461	51	5	2339	5	INTS3	1	153741377	Missense_Mutation	SNP	T	TCGA-GS-A9TV-01A-11D-A382-10	1007733	153741377	95509244	3	14476											
USH2A	7399	hgsc.bcm.edu	37	chr1	216424362	216424362	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccatcaggatccaactcttGtagattgtagaatccattct	11	13	7	10	0	3	2	1	0	2	2	5	3	5	3	3	1	1	2	3	1	4	5			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr1:216424362G>T	ENST00000307340.3	-	12	2436	c.2050C>A	c.(2050-2052)Caa>Aaa	p.Q684K	USH2A_ENST00000366943.2_Missense_Mutation_p.Q684K|USH2A_ENST00000366942.3_Missense_Mutation_p.Q684K	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	684	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)		TCCAACTCTTGTAGATTGTAG	0.458										HNSCC(13;0.011)																											p.Q684K		Atlas-SNP	.											.	USH2A	1168	.	0			c.C2050A						PASS	.						152	127	136					1																	216424362		2203	4300	6503	SO:0001583	missense	7399	exon12			ACTCTTGTAGATT	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.2050C>A	1.37:g.216424362G>T	ENSP00000305941:p.Gln684Lys	124	0	0		103	7	0.0679612	NM_007123	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	2.472	-0.321570	0.05386	.	.	ENSG00000042781	ENST00000307340;ENST00000366943;ENST00000366942	T;T;T	0.60548	0.18;0.18;0.18	5.26	4.34	0.51931	EGF-like, laminin (4);	0.000000	0.42172	D	0.000754	T	0.53222	0.1783	M	0.69248	2.105	0.09310	N	1	B;B	0.30146	0.061;0.27	B;B	0.34931	0.041;0.192	T	0.42565	-0.9444	10	0.18710	T	0.47	.	8.7337	0.34514	0.0764:0.0:0.7737:0.1499	.	684;684	O75445-2;O75445	.;USH2A_HUMAN	K	684	ENSP00000305941:Q684K;ENSP00000355910:Q684K;ENSP00000355909:Q684K	ENSP00000305941:Q684K	Q	-	1	0	USH2A	214490985	0.947000	0.32204	0.009000	0.14445	0.997000	0.91878	3.904000	0.56325	1.209000	0.43321	0.655000	0.94253	CAA	.	.	none		0.458	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		T	216424362	G	T	216424362	3	4	38	1	0	0	0	0	1	0	0	0	17051	1386	48	4	13816	4	USH2A	1	216424362	Missense_Mutation	SNP	G	TCGA-GS-A9TV-01A-11D-A382-10	62682985	216424362	32826259	4	14477											
VIT	5212	hgsc.bcm.edu	37	chr2	37035632	37035632	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	taggccgtgtgcagaacaaaCggcttctactcgctccacgt	9	9	10	13	4	1	1	0	0	1	1	3	1	2	1	2	2	4	3	2	2	4	3			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr2:37035632C>T	ENST00000389975.3	+	14	1664	c.1362C>T	c.(1360-1362)aaC>aaT	p.N454N	VIT_ENST00000497382.1_Silent_p.N123N|VIT_ENST00000401530.1_Silent_p.N433N|VIT_ENST00000404084.1_Silent_p.N406N|VIT_ENST00000379241.3_Silent_p.N432N|VIT_ENST00000379242.3_Silent_p.N469N	NM_001177969.1|NM_001177970.1	NP_001171440.1|NP_001171441.1	Q6UXI7	VITRN_HUMAN	vitrin	454	VWFA 1. {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)				GCAGAACAAACGGCTTCTACT	0.622																																					p.N469N		Atlas-SNP	.											.	VIT	138	.	0			c.C1407T						PASS	.						33	29	30					2																	37035632		2203	4300	6503	SO:0001819	synonymous_variant	5212	exon15			AACAAACGGCTTC	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.1362C>T	2.37:g.37035632C>T		94	0	0		95	8	0.0842105	NM_053276	A1A526|A6NKI9|A8K7Y4|E9PF47|Q6P7T3|Q96DM8|Q96DT1|Q9UDN0	Silent	SNP	ENST00000389975.3	37	CCDS54347.1																																																																																			.	.	none		0.622	VIT-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding				T	37035632	C	T	37035632	2	4	38	1	0	0	0	0	0	0	0	1	17186	535	19	1		1	VIT	2	37035632	Silent	SNP	C	TCGA-GS-A9TV-01A-11D-A382-10		37035632	206163741	5	14478											
PROKR1	10887	hgsc.bcm.edu	37	chr2	68882188	68882188	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatcttctgcggccagatctGgcctgtggaccagcagctct	6	10	12	13	1	4	1	0	0	4	1	4	3	4	2	3	3	3	2	3	3	0	1			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr2:68882188G>A	ENST00000303786.3	+	3	1082	c.662G>A	c.(661-663)tGg>tAg	p.W221*	PROKR1_ENST00000394342.2_Nonsense_Mutation_p.W221*			Q8TCW9	PKR1_HUMAN	prokineticin receptor 1	221					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						GGCCAGATCTGGCCTGTGGAC	0.552																																					p.W221X		Atlas-SNP	.											.	PROKR1	69	.	0			c.G662A						PASS	.						152	140	144					2																	68882188		2203	4300	6503	SO:0001587	stop_gained	10887	exon2			AGATCTGGCCTGT	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.662G>A	2.37:g.68882188G>A	ENSP00000303775:p.Trp221*	88	0	0		88	6	0.0681818	NM_138964	A5JUU2|Q53QT9|Q8NFJ7	Nonsense_Mutation	SNP	ENST00000303786.3	37	CCDS1889.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.765035	0.90020	.	.	ENSG00000169618	ENST00000303786;ENST00000394342	.	.	.	4.55	4.55	0.56014	.	0.050126	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.6333	0.76929	0.0:0.0:1.0:0.0	.	.	.	.	X	221	.	ENSP00000303775:W221X	W	+	2	0	PROKR1	68735692	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.297000	0.96120	2.816000	0.96949	0.563000	0.77884	TGG	.	.	none		0.552	PROKR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251760.2			A	68882188	G	A	68882188	4	1	38	1	0	0	0	0	0	1	0	0	12564	1357	47	2	668	2	PROKR1	2	68882188	Nonsense_Mutation	SNP	G	TCGA-GS-A9TV-01A-11D-A382-10	31846556	68882188	174317185	6	14479											
RANBP2	5903	hgsc.bcm.edu	37	chr2	109392255	109392255	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggtgggactgaagtgatggTaccttctttctgtaaatctg	9	14	12	6	0	3	2	0	2	3	0	3	3	3	3	1	3	1	2	1	3	4	4	rs367864778		TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr2:109392255T>G	ENST00000283195.6	+	24	8486	c.8360T>G	c.(8359-8361)gTa>gGa	p.V2787G		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	2787					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						GAAGTGATGGTACCTTCTTTC	0.383																																					p.V2787G		Atlas-SNP	.											.	RANBP2	488	.	0			c.T8360G						PASS	.	T	GLY/VAL	0,4406		0,0,2203	172	170	171		8360	-3.3	0	2		171	1,8599	1.2+/-3.3	0,1,4299	no	missense	RANBP2	NM_006267.4	109	0,1,6502	GG,GT,TT		0.0116,0.0,0.0077	benign	2787/3225	109392255	1,13005	2203	4300	6503	SO:0001583	missense	5903	exon24			TGATGGTACCTTC	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.8360T>G	2.37:g.109392255T>G	ENSP00000283195:p.Val2787Gly	138	0	0		100	5	0.05	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	T	12.33	1.904645	0.33628	0.0	1.16E-4	ENSG00000153201	ENST00000409491;ENST00000283195	T	0.27720	1.65	5.58	-3.34	0.04943	.	.	.	.	.	T	0.21590	0.0520	L	0.47716	1.5	0.09310	N	1	B	0.20887	0.049	B	0.14023	0.01	T	0.33929	-0.9849	9	0.17369	T	0.5	2.9813	9.2618	0.37616	0.1243:0.6276:0.0:0.248	.	2787	P49792	RBP2_HUMAN	G	1811;2787	ENSP00000283195:V2787G	ENSP00000283195:V2787G	V	+	2	0	RANBP2	108758687	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-2.045000	0.01410	-0.487000	0.06735	-0.250000	0.11733	GTA	.	.	weak		0.383	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267		G	109392255	T	G	109392255	3	3	38	1	0	0	0	0	1	0	0	0	13043	1638	57	5	8454	5	RANBP2	2	109392255	Missense_Mutation	SNP	T	TCGA-GS-A9TV-01A-11D-A382-10	40510067	109392255	133807118	7	14480											
GPD2	2820	hgsc.bcm.edu	37	chr2	157369859	157369859	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtaggtggtggcagttacCttactactgggtaggaatca	9	12	13	7	0	1	0	1	0	0	0	1	1	1	1	1	5	3	4	1	5	6	5	rs143467322		TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr2:157369859C>T	ENST00000310454.6	+	6	884	c.512C>T	c.(511-513)cCt>cTt	p.P171L	GPD2_ENST00000409674.1_Missense_Mutation_p.P171L|GPD2_ENST00000540309.1_Missense_Mutation_p.P171L|GPD2_ENST00000438166.2_Missense_Mutation_p.P171L|GPD2_ENST00000409125.4_Intron	NM_001083112.2	NP_001076581.2	P43304	GPDM_HUMAN	glycerol-3-phosphate dehydrogenase 2 (mitochondrial)	171					camera-type eye development (GO:0043010)|cellular lipid metabolic process (GO:0044255)|gluconeogenesis (GO:0006094)|glycerol catabolic process (GO:0019563)|glycerol-3-phosphate metabolic process (GO:0006072)|multicellular organism growth (GO:0035264)|small molecule metabolic process (GO:0044281)	glycerol-3-phosphate dehydrogenase complex (GO:0009331)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|glycerol-3-phosphate dehydrogenase activity (GO:0004368)|sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity (GO:0052591)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(1)|stomach(1)	22						TGGCAGTTACCTTACTACTGG	0.393																																					p.P171L		Atlas-SNP	.											.	GPD2	59	.	0			c.C512T						PASS	.	C	LEU/PRO,LEU/PRO	0,4406		0,0,2203	153	142	146		512,512	5	1	2	dbSNP_134	146	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	GPD2	NM_000408.4,NM_001083112.2	98,98	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	171/728,171/728	157369859	1,13005	2203	4300	6503	SO:0001583	missense	2820	exon6			AGTTACCTTACTA		CCDS2202.1	2q24.1	2013-01-10			ENSG00000115159	ENSG00000115159	1.1.1.8	"EF-hand domain containing"	4456	protein-coding gene	gene with protein product		138430					Standard	NM_001083112		Approved		uc002tzd.4	P43304	OTTHUMG00000131951	ENST00000310454.6:c.512C>T	2.37:g.157369859C>T	ENSP00000308610:p.Pro171Leu	170	0	0		166	7	0.0421687	NM_001083112	A8K4V0|B3KSA9|Q59FR1|Q9HAP9	Missense_Mutation	SNP	ENST00000310454.6	37	CCDS2202.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.385374	0.82792	0.0	1.16E-4	ENSG00000115159	ENST00000310454;ENST00000438166;ENST00000540309;ENST00000409674	D;D;D;D	0.81579	-1.51;-1.51;-1.51;-1.51	4.99	4.99	0.66335	FAD dependent oxidoreductase (1);	0.000000	0.85682	D	0.000000	D	0.87680	0.6238	M	0.71036	2.16	0.80722	D	1	B	0.27140	0.169	P	0.46885	0.53	D	0.87211	0.2247	10	0.66056	D	0.02	.	18.6714	0.91513	0.0:1.0:0.0:0.0	.	171	P43304	GPDM_HUMAN	L	171	ENSP00000308610:P171L;ENSP00000409708:P171L;ENSP00000440892:P171L;ENSP00000386425:P171L	ENSP00000308610:P171L	P	+	2	0	GPD2	157078105	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.818000	0.86416	2.489000	0.83994	0.655000	0.94253	CCT	C|1.000;T|0.000	0.000	weak		0.393	GPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254910.3			T	157369859	C	T	157369859	3	4	38	1	0	0	0	0	1	0	0	0	6614	681	24	2	530	2	GPD2	2	157369859	Missense_Mutation	SNP	C	TCGA-GS-A9TV-01A-11D-A382-10	47977604	157369859	85829514	8	14481											
FSIP2	401024	hgsc.bcm.edu	37	chr2	186671112	186671112	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatgttttagaactatcttcTtctccagaaccagcatatta	12	15	5	9	0	3	2	0	0	3	2	4	3	3	2	2	0	3	2	2	0	6	7			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr2:186671112T>G	ENST00000424728.1	+	17	17079	c.17079T>G	c.(17077-17079)tcT>tcG	p.S5693S	FSIP2_ENST00000343098.5_Silent_p.S5782S			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	5693										NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						AACTATCTTCTTCTCCAGAAC	0.373																																					p.S5782S		Atlas-SNP	.											.	FSIP2	251	.	0			c.T17346G						PASS	.						91	85	87					2																	186671112		1827	4088	5915	SO:0001819	synonymous_variant	401024	exon17			ATCTTCTTCTCCA	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.17079T>G	2.37:g.186671112T>G		206	0	0		195	8	0.0410256	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Silent	SNP	ENST00000424728.1	37																																																																																				.	.	none		0.373	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		G	186671112	T	G	186671112	2	3	38	1	0	0	0	0	0	0	0	1	6083	1596	56	5		5	FSIP2	2	186671112	Silent	SNP	T	TCGA-GS-A9TV-01A-11D-A382-10	29301253	186671112	56528261	9	14482											
PIKFYVE	200576	hgsc.bcm.edu	37	chr2	209218719	209218719	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctagatgaaaatctcctaaAgatggttcgagacaaccctc	14	9	8	10	1	1	4	0	1	1	3	4	5	1	4	2	1	1	2	2	1	6	3			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr2:209218719A>G	ENST00000264380.4	+	40	6100	c.5942A>G	c.(5941-5943)aAg>aGg	p.K1981R		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	1981	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						AATCTCCTAAAGATGGTTCGA	0.418																																					p.K1981R		Atlas-SNP	.											.	PIKFYVE	223	.	0			c.A5942G						PASS	.						142	145	144					2																	209218719		2203	4300	6503	SO:0001583	missense	200576	exon40			TCCTAAAGATGGT	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.5942A>G	2.37:g.209218719A>G	ENSP00000264380:p.Lys1981Arg	150	0	0		128	7	0.0546875	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Missense_Mutation	SNP	ENST00000264380.4	37	CCDS2382.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.651372	0.88056	.	.	ENSG00000115020	ENST00000264380	T	0.30182	1.54	6.17	6.17	0.99709	Phosphatidylinositol-4-phosphate 5-kinase, core (2);Phosphatidylinositol-4-phosphate 5-kinase, core, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.45617	0.1351	L	0.28458	0.855	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.39860	-0.9593	10	0.59425	D	0.04	-24.4674	16.8222	0.85835	1.0:0.0:0.0:0.0	.	1981	Q9Y2I7	FYV1_HUMAN	R	1981	ENSP00000264380:K1981R	ENSP00000264380:K1981R	K	+	2	0	PIKFYVE	208926964	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.401000	0.79962	2.371000	0.80710	0.533000	0.62120	AAG	.	.	none		0.418	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040		G	209218719	A	G	209218719	3	3	38	1	0	0	0	0	1	0	0	0	11933	72	3	3	6107	3	PIKFYVE	2	209218719	Missense_Mutation	SNP	A	TCGA-GS-A9TV-01A-11D-A382-10	22547607	209218719	33980654	10	14483											
ABCA12	26154	hgsc.bcm.edu	37	chr2	215855677	215855677	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatgatgaggatcacgatggTaaccagtaaaaatccaacac	18	7	8	8	1	1	2	1	2	0	0	2	4	2	3	2	2	2	2	2	2	6	2			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr2:215855677T>G	ENST00000272895.7	-	24	3592	c.3373A>C	c.(3373-3375)Acc>Ccc	p.T1125P	ABCA12_ENST00000389661.4_Missense_Mutation_p.T807P	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1125					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)		ATCACGATGGTAACCAGTAAA	0.388																																					p.T1125P	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.A3373C						PASS	.						100	102	101					2																	215855677		2203	4300	6503	SO:0001583	missense	26154	exon24			CGATGGTAACCAG	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.3373A>C	2.37:g.215855677T>G	ENSP00000272895:p.Thr1125Pro	92	0	0		87	4	0.045977	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Missense_Mutation	SNP	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	T	19.13	3.767808	0.69878	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.85773	-2.03;-2.03	5.39	5.39	0.77823	.	0.158061	0.45361	D	0.000373	D	0.92172	0.7518	M	0.80746	2.51	0.80722	D	1	D;D	0.76494	0.999;0.976	D;D	0.70487	0.969;0.937	D	0.93226	0.6613	10	0.87932	D	0	.	15.5646	0.76281	0.0:0.0:0.0:1.0	.	1125;807	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	P	1125;807	ENSP00000272895:T1125P;ENSP00000374312:T807P	ENSP00000272895:T1125P	T	-	1	0	ABCA12	215563922	1.000000	0.71417	0.998000	0.56505	0.655000	0.38815	7.832000	0.86757	2.263000	0.75096	0.528000	0.53228	ACC	.	.	none		0.388	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076		G	215855677	T	G	215855677	3	3	38	1	0	0	0	0	1	0	0	0	30	1638	57	5	4534	5	ABCA12	2	215855677	Missense_Mutation	SNP	T	TCGA-GS-A9TV-01A-11D-A382-10	6636958	215855677	27343696	11	14484											
GPR55	9290	hgsc.bcm.edu	37	chr2	231774792	231774792	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgggccctgatgttcatgcGgaattctttgatgacaaagt	9	13	12	7	1	2	3	1	3	1	0	2	4	2	4	1	2	1	1	1	2	2	3			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr2:231774792G>A	ENST00000392040.1	-	2	1078	c.886C>T	c.(886-888)Cgc>Tgc	p.R296C	AC012507.4_ENST00000454890.1_RNA|GPR55_ENST00000392039.2_Missense_Mutation_p.R296C	NM_005683.3	NP_005674.2	Q9Y2T6	GPR55_HUMAN	G protein-coupled receptor 55	296					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)		ATGTTCATGCGGAATTCTTTG	0.532																																					p.R296C		Atlas-SNP	.											GPR55,colon,carcinoma,+1,1	GPR55	46	1	0			c.C886T						PASS	.						83	85	84					2																	231774792		2203	4300	6503	SO:0001583	missense	9290	exon2			TCATGCGGAATTC	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.886C>T	2.37:g.231774792G>A	ENSP00000375894:p.Arg296Cys	80	0	0		80	4	0.05	NM_005683	Q8N580	Missense_Mutation	SNP	ENST00000392040.1	37	CCDS2480.1	.	.	.	.	.	.	.	.	.	.	G	18.56	3.650184	0.67472	.	.	ENSG00000135898	ENST00000392040;ENST00000392039	T;T	0.58358	0.34;0.34	4.6	3.65	0.41850	.	0.057515	0.64402	D	0.000002	T	0.49029	0.1533	N	0.08118	0	0.48975	D	0.999738	D	0.89917	1.0	D	0.65874	0.939	T	0.57516	-0.7798	10	0.87932	D	0	-42.499	11.8792	0.52564	0.0:0.0:0.8252:0.1748	.	296	Q9Y2T6	GPR55_HUMAN	C	296	ENSP00000375894:R296C;ENSP00000375893:R296C	ENSP00000375893:R296C	R	-	1	0	GPR55	231483036	0.999000	0.42202	0.980000	0.43619	0.953000	0.61014	2.382000	0.44345	2.522000	0.85027	0.561000	0.74099	CGC	.	.	none		0.532	GPR55-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332618.1	NM_005683		A	231774792	G	A	231774792	3	1	38	1	0	0	0	0	1	0	0	0	6707	1116	39	1	77	1	GPR55	2	231774792	Missense_Mutation	SNP	G	TCGA-GS-A9TV-01A-11D-A382-10	15919115	231774792	11424581	12	14485											
OGG1	4968	hgsc.bcm.edu	37	chr3	9792009	9792009	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcccaggcgcatggggcaTcgtactctagcctccactcc	6	8	10	17	2	1	0	0	0	1	0	4	0	3	0	4	3	3	3	4	3	2	2			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr3:9792009T>G	ENST00000344629.7	+	1	382	c.39T>G	c.(37-39)caT>caG	p.H13Q	OGG1_ENST00000349503.5_Missense_Mutation_p.H13Q|OGG1_ENST00000302003.7_Missense_Mutation_p.H13Q|OGG1_ENST00000449570.2_Missense_Mutation_p.H13Q|OGG1_ENST00000302008.8_Missense_Mutation_p.H13Q|OGG1_ENST00000436092.1_3'UTR|OGG1_ENST00000339511.5_Missense_Mutation_p.H13Q|OGG1_ENST00000383826.5_Missense_Mutation_p.H13Q|OGG1_ENST00000302036.7_Missense_Mutation_p.H13Q			O15527	OGG1_HUMAN	8-oxoguanine DNA glycosylase	13					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)					GCATGGGGCATCGTACTCTAG	0.667								Base excision repair (BER), DNA glycosylases																													p.H13Q		Atlas-SNP	.											.	OGG1	57	.	0			c.T39G						PASS	.						51	46	48					3																	9792009		2203	4300	6503	SO:0001583	missense	4968	exon1			GGGGCATCGTACT	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.39T>G	3.37:g.9792009T>G	ENSP00000342851:p.His13Gln	110	0	0		119	12	0.10084	NM_016819	A8K1E3|O00390|O00670|O00705|O14876|O95488|P78554|Q9BW42|Q9UIK0|Q9UIK1|Q9UIK2|Q9UL34|Q9Y2C0|Q9Y2C1|Q9Y6C3|Q9Y6C4	Missense_Mutation	SNP	ENST00000344629.7	37	CCDS2581.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.645755	0.87958	.	.	ENSG00000114026	ENST00000302003;ENST00000344629;ENST00000302036;ENST00000349503;ENST00000339511;ENST00000449570;ENST00000302008;ENST00000383826	T;T;T;T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58	5.85	-2.38	0.06622	Transcription factor TFIID, C-terminal/DNA glycosylase, N-terminal (1);	0.044063	0.85682	D	0.000000	T	0.62441	0.2428	M	0.61703	1.905	0.36706	D	0.88038	D;D;D;D;D;D;D;D	0.76494	0.999;0.999;0.999;0.997;0.993;0.996;0.994;0.996	D;D;P;P;P;P;P;P	0.65573	0.915;0.936;0.892;0.765;0.701;0.764;0.832;0.843	T	0.67776	-0.5583	10	0.72032	D	0.01	-25.825	12.1556	0.54074	0.0:0.6561:0.1289:0.215	.	13;13;13;13;13;13;13;13	E5KPM8;E5KPM6;E5KPM5;E5KPM7;E5KPM9;E5KPN0;O15527;O15527-2	.;.;.;.;.;.;OGG1_HUMAN;.	Q	13	ENSP00000305584:H13Q;ENSP00000342851:H13Q;ENSP00000306561:H13Q;ENSP00000303132:H13Q;ENSP00000345520:H13Q;ENSP00000403598:H13Q;ENSP00000305527:H13Q;ENSP00000373337:H13Q	ENSP00000305584:H13Q	H	+	3	2	OGG1	9767009	0.905000	0.30787	0.598000	0.28837	0.920000	0.55202	-0.374000	0.07484	-0.414000	0.07495	0.533000	0.62120	CAT	.	.	none		0.667	OGG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214223.2	NM_016821		G	9792009	T	G	9792009	3	3	38	1	0	0	0	0	1	0	0	0	10854	1432	50	5	41	5	OGG1	3	9792009	Missense_Mutation	SNP	T	TCGA-GS-A9TV-01A-11D-A382-10		9792009	188230421	13	14486											
KAT2B	8850	hgsc.bcm.edu	37	chr3	20178459	20178459	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggaacacacctgatgaatcAtttgaaagaatatcacataa	18	10	6	7	0	2	4	2	3	0	1	2	5	2	5	1	1	1	0	1	1	6	3			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr3:20178459A>G	ENST00000263754.4	+	12	2230	c.1775A>G	c.(1774-1776)cAt>cGt	p.H592R	MIR3135A_ENST00000578460.1_RNA	NM_003884.4	NP_003875.3	Q92831	KAT2B_HUMAN	K(lysine) acetyltransferase 2B	592	N-acetyltransferase. {ECO:0000250|UniProtKB:Q92830, ECO:0000255|PROSITE-ProRule:PRU00532}.				cell cycle arrest (GO:0007050)|cellular response to insulin stimulus (GO:0032869)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|histone H3-K9 acetylation (GO:0043970)|internal peptidyl-lysine acetylation (GO:0018393)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|Notch signaling pathway (GO:0007219)|peptidyl-lysine acetylation (GO:0018394)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein acetylation (GO:0006473)|regulation of protein ADP-ribosylation (GO:0010835)|rhythmic process (GO:0048511)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	A band (GO:0031672)|actomyosin (GO:0042641)|Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|I band (GO:0031674)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)	acetyltransferase activity (GO:0016407)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|histone acetyltransferase activity (GO:0004402)|histone deacetylase binding (GO:0042826)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	40						CTGATGAATCATTTGAAAGAA	0.353																																					p.H592R		Atlas-SNP	.											KAT2B,trunk,malignant_melanoma,+1,1	KAT2B	73	1	0			c.A1775G						PASS	.						129	112	118					3																	20178459		2203	4300	6503	SO:0001583	missense	8850	exon12			TGAATCATTTGAA	U57316	CCDS2634.1	3p24	2011-07-01	2008-07-04	2008-07-04	ENSG00000114166	ENSG00000114166		"Chromatin-modifying enzymes / K-acetyltransferases"	8638	protein-coding gene	gene with protein product		602303	"p300/CBP-associated factor"	PCAF		8684459, 9722949	Standard	NM_003884		Approved	P/CAF, GCN5, GCN5L	uc003cbq.3	Q92831	OTTHUMG00000130481	ENST00000263754.4:c.1775A>G	3.37:g.20178459A>G	ENSP00000263754:p.His592Arg	141	0	0		100	7	0.07	NM_003884	Q6NSK1	Missense_Mutation	SNP	ENST00000263754.4	37	CCDS2634.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.709027	0.89018	.	.	ENSG00000114166	ENST00000263754	T	0.24908	1.83	5.66	5.66	0.87406	GCN5-related N-acetyltransferase (GNAT) domain (2);Acyl-CoA N-acyltransferase (2);	0.000000	0.85682	D	0.000000	T	0.55194	0.1905	M	0.83852	2.665	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	T	0.61657	-0.7018	10	0.87932	D	0	-21.8842	16.2026	0.82095	1.0:0.0:0.0:0.0	.	592	Q92831	KAT2B_HUMAN	R	592	ENSP00000263754:H592R	ENSP00000263754:H592R	H	+	2	0	KAT2B	20153463	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.287000	0.95975	2.285000	0.76669	0.533000	0.62120	CAT	.	.	none		0.353	KAT2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252880.1	NM_003884		G	20178459	A	G	20178459	3	3	38	1	0	0	0	0	1	0	0	0	7991	217	8	3	1821	3	KAT2B	3	20178459	Missense_Mutation	SNP	A	TCGA-GS-A9TV-01A-11D-A382-10	10386450	20178459	177843971	14	14487											
MAGI1	9223	hgsc.bcm.edu	37	chr3	65425603	65425603	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgctgctgttgctgctgctgTtgctgctgctgctgctgctc	0	16	13	12	0	0	0	0	0	0	0	1	0	0	0	0	0	11	13	0	0	0	2	rs113562374|rs62642828	byFrequency	TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr3:65425603T>C	ENST00000497477.2	-	9	1220	c.1221A>G	c.(1219-1221)caA>caG	p.Q407Q	MAGI1_ENST00000470990.1_5'UTR|MAGI1_ENST00000483466.1_Silent_p.Q407Q|MAGI1_ENST00000402939.2_Silent_p.Q407Q|MAGI1_ENST00000330909.8_Silent_p.Q407Q			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	407	Poly-Gln.				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)		gctgctgctgttgctgctgct	0.532											OREG0015658	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q407Q		Atlas-SNP	.											.	MAGI1	481	.	0			c.A1221G						PASS	.						77	69	72					3																	65425603		2202	4299	6501	SO:0001819	synonymous_variant	9223	exon9			CTGCTGTTGCTGC	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.1221A>G	3.37:g.65425603T>C		122	0	0	1084	123	6	0.0487805	NM_001033057	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Silent	SNP	ENST00000497477.2	37		.	.	.	.	.	.	.	.	.	.	C	2.459	-0.324601	0.05350	.	.	ENSG00000151276	ENST00000460329	.	.	.	3.74	-1.34	0.09143	.	.	.	.	.	T	0.30665	0.0772	.	.	.	0.28889	N	0.893947	.	.	.	.	.	.	T	0.31668	-0.9935	4	.	.	.	2.613	7.1494	0.25601	0.123:0.2818:0.0:0.5952	.	.	.	.	S	288	.	.	N	-	2	0	MAGI1	65400643	0.949000	0.32298	0.008000	0.14137	0.009000	0.06853	-0.343000	0.07791	-1.060000	0.03189	-1.632000	0.00781	AAC	T|0.742;C|0.258	0.258	strong		0.532	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742		C	65425603	T	C	65425603	2	2	38	1	0	0	0	0	0	0	0	1	9199	1722	60	3		3	MAGI1	3	65425603	Silent	SNP	T	TCGA-GS-A9TV-01A-11D-A382-10	45247144	65425603	132596827	15	14488											
EIF2B5	8893	hgsc.bcm.edu	37	chr3	183853228	183853228	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggttagtcgggctaacaagCgcagcggcgcggggccggga	7	5	19	10	6	0	0	0	0	0	0	1	1	0	1	1	6	3	3	1	6	3	2			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr3:183853228C>T	ENST00000273783.3	+	1	177	c.55C>T	c.(55-57)Cgc>Tgc	p.R19C	EIF2B5_ENST00000432569.1_Missense_Mutation_p.R19C|RP11-778D9.12_ENST00000608232.1_RNA|RP11-778D9.13_ENST00000609288.1_lincRNA|EIF2B5_ENST00000444495.1_Missense_Mutation_p.R19C|RP11-778D9.12_ENST00000608135.1_RNA	NM_003907.2	NP_003898.2	Q13144	EI2BE_HUMAN	eukaryotic translation initiation factor 2B, subunit 5 epsilon, 82kDa	19					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)			GGCTAACAAGCGCAGCGGCGC	0.687											OREG0015363	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R19C		Atlas-SNP	.											.	EIF2B5	62	.	0			c.C55T						PASS	.						6	8	7					3																	183853228		2147	4220	6367	SO:0001583	missense	8893	exon1			AACAAGCGCAGCG	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.55C>T	3.37:g.183853228C>T	ENSP00000273783:p.Arg19Cys	171	0	0	1987	151	7	0.0463576	NM_003907	Q541Z1|Q96D04	Missense_Mutation	SNP	ENST00000273783.3	37	CCDS3252.1	.	.	.	.	.	.	.	.	.	.	c	15.18	2.756467	0.49362	.	.	ENSG00000145191	ENST00000273783;ENST00000432569;ENST00000444495	D;D;D	0.98150	-4.74;-4.08;-4.75	4.93	4.93	0.64822	.	0.270105	0.30959	N	0.008529	D	0.94666	0.8280	N	0.08118	0	0.54753	D	0.999983	D	0.76494	0.999	P	0.50754	0.649	D	0.95051	0.8187	10	0.66056	D	0.02	-12.6109	13.4835	0.61351	0.0:0.8436:0.1564:0.0	.	19	Q13144	EI2BE_HUMAN	C	19	ENSP00000273783:R19C;ENSP00000414775:R19C;ENSP00000409142:R19C	ENSP00000273783:R19C	R	+	1	0	EIF2B5	185335922	1.000000	0.71417	0.995000	0.50966	0.168000	0.22595	2.282000	0.43461	2.719000	0.93026	0.650000	0.86243	CGC	.	.	none		0.687	EIF2B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346168.1			T	183853228	C	T	183853228	3	4	38	1	0	0	0	0	1	0	0	0	5006	768	27	1	57	1	EIF2B5	3	183853228	Missense_Mutation	SNP	C	TCGA-GS-A9TV-01A-11D-A382-10	118427625	183853228	14169202	16	14489											
RFC4	5984	hgsc.bcm.edu	37	chr3	186507948	186507948	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tacggcaagtttttctgtgaTaatagacttctgtttatcag	10	17	8	6	1	3	2	1	1	2	1	3	2	3	2	0	1	1	3	0	1	5	8			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr3:186507948T>C	ENST00000392481.2	-	10	1260	c.979A>G	c.(979-981)Atc>Gtc	p.I327V	RFC4_ENST00000296273.2_Missense_Mutation_p.I327V|RFC4_ENST00000433496.1_Missense_Mutation_p.I300V|SNORA4_ENST00000584302.1_RNA|SNORA63_ENST00000363450.1_RNA	NM_181573.2	NP_853551.1	P35249	RFC4_HUMAN	replication factor C (activator 1) 4, 37kDa	327					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)		TTTTCTGTGATAATAGACTTC	0.353																																					p.I327V		Atlas-SNP	.											.	RFC4	54	.	0			c.A979G						PASS	.						107	103	105					3																	186507948		2203	4300	6503	SO:0001583	missense	5984	exon10			CTGTGATAATAGA		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.979A>G	3.37:g.186507948T>C	ENSP00000376272:p.Ile327Val	224	0	0		241	20	0.0829876	NM_181573	B4DM41|D3DNV2|Q6FHX7	Missense_Mutation	SNP	ENST00000392481.2	37	CCDS3283.1	.	.	.	.	.	.	.	.	.	.	T	15.89	2.966155	0.53507	.	.	ENSG00000163918	ENST00000433496;ENST00000392481;ENST00000296273;ENST00000417876	T;T;T;T	0.52526	0.66;0.66;0.66;0.66	5.85	5.85	0.93711	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	0.56292	0.1975	M	0.81802	2.56	0.80722	D	1	B	0.16802	0.019	B	0.31614	0.133	T	0.57516	-0.7798	10	0.59425	D	0.04	-17.5765	14.1937	0.65656	0.0:0.0:0.0:1.0	.	327	P35249	RFC4_HUMAN	V	300;327;327;102	ENSP00000399769:I300V;ENSP00000376272:I327V;ENSP00000296273:I327V;ENSP00000401429:I102V	ENSP00000296273:I327V	I	-	1	0	RFC4	187990642	1.000000	0.71417	0.268000	0.24571	0.954000	0.61252	5.725000	0.68507	2.229000	0.72834	0.533000	0.62120	ATC	.	.	none		0.353	RFC4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344471.1	NM_002916		C	186507948	T	C	186507948	3	2	38	1	0	0	0	0	1	0	0	0	13262	1406	49	3	120	3	RFC4	3	186507948	Missense_Mutation	SNP	T	TCGA-GS-A9TV-01A-11D-A382-10	2654720	186507948	11514482	17	14490											
WDR53	348793	hgsc.bcm.edu	37	chr3	196281315	196281315	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcctgtgggtacgttttgTgggactcttctgttttttct	2	21	10	8	1	3	0	0	0	3	0	4	1	4	1	1	2	1	3	1	2	1	8			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr3:196281315T>C	ENST00000332629.5	-	4	1411	c.844A>G	c.(844-846)Aca>Gca	p.T282A	WDR53_ENST00000433160.1_Missense_Mutation_p.T123A|WDR53_ENST00000429115.1_Missense_Mutation_p.T121A	NM_182627.1	NP_872433.1	Q7Z5U6	WDR53_HUMAN	WD repeat domain 53	282										breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)	13	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.6e-23)|all cancers(36;1.54e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.29e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00326)		GTACGTTTTGTGGGACTCTTC	0.443																																					p.T282A		Atlas-SNP	.											.	WDR53	26	.	0			c.A844G						PASS	.						244	210	221					3																	196281315		2203	4300	6503	SO:0001583	missense	348793	exon4			GTTTTGTGGGACT	BC054030	CCDS3318.1	3q29	2013-01-09			ENSG00000185798	ENSG00000185798		"WD repeat domain containing"	28786	protein-coding gene	gene with protein product		615110				12477932	Standard	NM_182627		Approved	MGC64882, MGC12928	uc003fwt.3	Q7Z5U6	OTTHUMG00000155572	ENST00000332629.5:c.844A>G	3.37:g.196281315T>C	ENSP00000328079:p.Thr282Ala	669	0	0		619	28	0.0452342	NM_182627	A0MNP1	Missense_Mutation	SNP	ENST00000332629.5	37	CCDS3318.1	.	.	.	.	.	.	.	.	.	.	T	0.841	-0.742019	0.03088	.	.	ENSG00000185798	ENST00000332629;ENST00000429115;ENST00000433160	T;T;T	0.72505	-0.66;1.24;1.24	5.67	1.29	0.21616	.	0.959404	0.08745	N	0.899979	T	0.47154	0.1430	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25012	-1.0144	10	0.14656	T	0.56	-7.5464	8.8373	0.35119	0.0:0.6094:0.0:0.3906	.	282	Q7Z5U6	WDR53_HUMAN	A	282;121;123	ENSP00000328079:T282A;ENSP00000396668:T121A;ENSP00000410677:T123A	ENSP00000328079:T282A	T	-	1	0	WDR53	197765712	0.000000	0.05858	0.008000	0.14137	0.027000	0.11550	0.693000	0.25497	0.229000	0.21039	0.528000	0.53228	ACA	.	.	none		0.443	WDR53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340689.1	NM_182627		C	196281315	T	C	196281315	3	2	38	1	0	0	0	0	1	0	0	0	17320	1696	59	3	236	3	WDR53	3	196281315	Missense_Mutation	SNP	T	TCGA-GS-A9TV-01A-11D-A382-10	9773367	196281315	1741115	18	14491											
PDLIM4	8572	hgsc.bcm.edu	37	chr5	131607911	131607911	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgtaccccaatgccaaggtgGaactcgtctgagctgggacc	9	8	12	12	1	1	1	0	1	1	0	2	3	1	3	4	3	4	2	4	3	4	1			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr5:131607911G>A	ENST00000253754.3	+	7	1046	c.982G>A	c.(982-984)Gaa>Aaa	p.E328K	P4HA2_ENST00000471826.1_Intron|PDLIM4_ENST00000379018.3_3'UTR	NM_001131027.1|NM_003687.3	NP_001124499.1|NP_003678.2	P50479	PDLI4_HUMAN	PDZ and LIM domain 4	328							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)			TGCCAAGGTGGAACTCGTCTG	0.607																																					p.E328K		Atlas-SNP	.											.	PDLIM4	22	.	0			c.G982A						PASS	.						44	45	45					5																	131607911		2203	4300	6503	SO:0001583	missense	8572	exon7			AAGGTGGAACTCG	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.982G>A	5.37:g.131607911G>A	ENSP00000253754:p.Glu328Lys	44	0	0		52	6	0.115385	NM_003687	B2R8U1|Q53Y39|Q96AT8|Q9BTW8|Q9Y292	Missense_Mutation	SNP	ENST00000253754.3	37	CCDS4152.1	.	.	.	.	.	.	.	.	.	.	G	32	5.192528	0.94960	.	.	ENSG00000131435	ENST00000253754	T	0.14516	2.5	5.05	4.16	0.48862	.	0.276256	0.34435	N	0.003965	T	0.28001	0.0690	L	0.36672	1.1	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.02526	-1.1146	10	0.87932	D	0	-8.9848	15.2133	0.73244	0.0:0.1416:0.8584:0.0	.	328	P50479	PDLI4_HUMAN	K	328	ENSP00000253754:E328K	ENSP00000253754:E328K	E	+	1	0	PDLIM4	131635810	1.000000	0.71417	1.000000	0.80357	0.799000	0.45148	9.617000	0.98361	1.068000	0.40764	0.655000	0.94253	GAA	.	.	none		0.607	PDLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132644.2	NM_003687		A	131607911	G	A	131607911	3	1	38	1	0	0	0	0	1	0	0	0	11691	1175	41	2	1008	2	PDLIM4	5	131607911	Missense_Mutation	SNP	G	TCGA-GS-A9TV-01A-11D-A382-10		131607911	49307349	19	14492											
FBXO38	81545	hgsc.bcm.edu	37	chr5	147813265	147813265	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtggaatcacagatctagTgctaaaagactgtccaaaga	15	10	9	7	0	2	3	1	0	1	3	3	4	3	4	1	1	1	1	1	1	5	3			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr5:147813265T>C	ENST00000340253.5	+	17	2990	c.2822T>C	c.(2821-2823)gTg>gCg	p.V941A	CTD-2283N19.1_ENST00000520980.2_RNA|FBXO38_ENST00000296701.6_Missense_Mutation_p.V696A|FBXO38_ENST00000394370.3_Missense_Mutation_p.V866A|FBXO38_ENST00000513826.1_Missense_Mutation_p.V696A			Q6PIJ6	FBX38_HUMAN	F-box protein 38	941					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)			ACAGATCTAGTGCTAAAAGAC	0.328																																					p.V866A		Atlas-SNP	.											.	FBXO38	115	.	0			c.T2597C						PASS	.						147	150	149					5																	147813265		2203	4300	6503	SO:0001583	missense	81545	exon17			ATCTAGTGCTAAA	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.2822T>C	5.37:g.147813265T>C	ENSP00000342023:p.Val941Ala	275	0	0		226	10	0.0442478	NM_030793	Q6PK72|Q7Z2U0|Q86VN3|Q9BXY6|Q9H837|Q9HC40	Missense_Mutation	SNP	ENST00000340253.5	37		.	.	.	.	.	.	.	.	.	.	T	23.5	4.426516	0.83667	.	.	ENSG00000145868	ENST00000340253;ENST00000296701;ENST00000394370;ENST00000513826	T;T;T;T	0.38240	1.15;1.24;1.21;1.24	5.16	5.16	0.70880	.	0.000000	0.85682	D	0.000000	T	0.48874	0.1524	L	0.34521	1.04	0.35153	D	0.769977	P;D;D	0.71674	0.954;0.998;0.998	D;D;D	0.77557	0.932;0.979;0.99	T	0.62431	-0.6856	10	0.87932	D	0	-14.1344	14.1172	0.65161	0.0:0.0:0.0:1.0	.	696;866;941	Q6PIJ6-3;Q6PIJ6-2;Q6PIJ6	.;.;FBX38_HUMAN	A	941;696;866;696	ENSP00000342023:V941A;ENSP00000296701:V696A;ENSP00000377895:V866A;ENSP00000426410:V696A	ENSP00000296701:V696A	V	+	2	0	FBXO38	147793458	1.000000	0.71417	0.997000	0.53966	0.937000	0.57800	7.679000	0.84048	2.069000	0.61940	0.460000	0.39030	GTG	.	.	none		0.328	FBXO38-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000252185.2	NM_030793		C	147813265	T	C	147813265	3	2	38	1	0	0	0	0	1	0	0	0	5754	1696	59	3	2884	3	FBXO38	5	147813265	Missense_Mutation	SNP	T	TCGA-GS-A9TV-01A-11D-A382-10	16205354	147813265	33101995	20	14493											
DSP	1832	hgsc.bcm.edu	37	chr6	7584037	7584037	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagtcaccaaaaagaaggTcagttacgtgcagctgaagg	14	7	11	9	1	2	2	2	1	0	1	3	2	3	2	2	2	3	3	2	2	5	1			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr6:7584037T>G	ENST00000379802.3	+	24	6883	c.6542T>G	c.(6541-6543)gTc>gGc	p.V2181G	DSP_ENST00000418664.2_Missense_Mutation_p.V1582G	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2181	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)		AAAAAGAAGGTCAGTTACGTG	0.478																																					p.V2181G		Atlas-SNP	.											.	DSP	306	.	0			c.T6542G						PASS	.						103	101	102					6																	7584037		2203	4300	6503	SO:0001583	missense	1832	exon24			AGAAGGTCAGTTA	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.6542T>G	6.37:g.7584037T>G	ENSP00000369129:p.Val2181Gly	69	0	0		57	6	0.105263	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	37	CCDS4501.1	.	.	.	.	.	.	.	.	.	.	T	13.57	2.275748	0.40294	.	.	ENSG00000096696	ENST00000379802;ENST00000418664	T;T	0.70749	-0.51;-0.51	5.37	5.37	0.77165	.	0.000000	0.53938	D	0.000058	T	0.62950	0.2470	L	0.55990	1.75	0.41567	D	0.988661	P;D	0.56521	0.925;0.976	P;B	0.46758	0.526;0.335	T	0.67078	-0.5761	10	0.46703	T	0.11	.	15.6695	0.77262	0.0:0.0:0.0:1.0	.	1629;2181	Q4LE79;P15924	.;DESP_HUMAN	G	2181;1582	ENSP00000369129:V2181G;ENSP00000396591:V1582G	ENSP00000369129:V2181G	V	+	2	0	DSP	7529036	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.250000	0.72435	2.178000	0.69098	0.533000	0.62120	GTC	.	.	none		0.478	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415		G	7584037	T	G	7584037	3	3	38	1	0	0	0	0	1	0	0	0	4783	1667	58	5	6636	5	DSP	6	7584037	Missense_Mutation	SNP	T	TCGA-GS-A9TV-01A-11D-A382-10		7584037	163531030	21	14494											
HIST1H1D	3007	hgsc.bcm.edu	37	chr6	26234939	26234939	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gatacggctgttgtttttttCtacatcgtagccagcagccg	7	14	10	10	3	1	0	0	0	1	0	2	1	1	0	2	1	5	5	2	1	3	7	rs2050949	byFrequency	TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr6:26234939C>T	ENST00000244534.5	-	1	277	c.223G>A	c.(223-225)Gaa>Aaa	p.E75K		NM_005320.2	NP_005311.1	P16402	H13_HUMAN	histone cluster 1, H1d	75	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.		E -> K (in dbSNP:rs2050949).		nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				TTGTTTTTTTCTACATCGTAG	0.532													C|||	439	0.0876597	0.0348	0.1037	5008	,	,		15763	0.2113		0.1004	False		,,,				2504	0.0072				p.E75K		Atlas-SNP	.											HIST1H1D,colon,carcinoma,+2,1	HIST1H1D	40	1	0			c.G223A						scavenged	.						71	80	77					6																	26234939		2203	4300	6503	SO:0001583	missense	3007	exon1			TTTTTTCTACATC	M60747	CCDS4597.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000124575	ENSG00000124575		"Histones / Replication-dependent"	4717	protein-coding gene	gene with protein product		142210	"H1 histone family, member 3", "histone 1, H1d"	H1F3		1916825, 12408966	Standard	NM_005320		Approved	H1.3, H1d, H1s-2	uc003nhd.3	P16402	OTTHUMG00000014432	ENST00000244534.5:c.223G>A	6.37:g.26234939C>T	ENSP00000244534:p.Glu75Lys	201	1	0.00497512		195	10	0.0512821	NM_005320	B2R751|Q2M2I2	Missense_Mutation	SNP	ENST00000244534.5	37	CCDS4597.1	.	.	.	.	.	.	.	.	.	.	.	22.3	4.269948	0.80469	.	.	ENSG00000124575	ENST00000244534	T	0.09255	3.0	5.23	5.23	0.72850	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.262738	0.43110	D	0.000603	T	0.17066	0.0410	L	0.54908	1.71	0.80722	D	1	B	0.29188	0.236	P	0.48304	0.573	T	0.02966	-1.1088	10	0.59425	D	0.04	-77.8298	18.1633	0.89717	0.0:1.0:0.0:0.0	rs2050949;rs2050949	75	P16402	H13_HUMAN	K	75	ENSP00000244534:E75K	ENSP00000244534:E75K	E	-	1	0	HIST1H1D	26342918	1.000000	0.71417	1.000000	0.80357	0.153000	0.21895	4.012000	0.57131	2.623000	0.88846	0.655000	0.94253	GAA	C|0.998;T|0.002	0.002	strong		0.532	HIST1H1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040095.1	NM_005320		T	26234939	C	T	26234939	3	4	38	1	0	0	0	0	1	0	0	0	7134	922	32	2	446	2	HIST1H1D	6	26234939	Missense_Mutation	SNP	C	TCGA-GS-A9TV-01A-11D-A382-10	18650902	26234939	144880128	22	14495											
LTB	4050	hgsc.bcm.edu	37	chr6	31548738	31548738	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccccccgcccggtacagagaGctgcgcagcgtgaccgagcg	7	3	14	17	6	0	2	0	1	0	1	0	4	0	2	5	1	5	3	5	1	1	1			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr6:31548738G>A	ENST00000429299.2	-	4	490	c.483C>T	c.(481-483)agC>agT	p.S161S	LTB_ENST00000446745.2_3'UTR|LTB_ENST00000483972.1_5'UTR	NM_002341.1	NP_002332.1	Q06643	TNFC_HUMAN	lymphotoxin beta (TNF superfamily, member 3)	161					cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|signal transduction (GO:0007165)|skin development (GO:0043588)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	9						GGTACAGAGAGCTGCGCAGCG	0.746																																					p.S161S		Atlas-SNP	.											.	LTB	19	.	0			c.C483T						PASS	.						4	4	4					6																	31548738		1367	2501	3868	SO:0001819	synonymous_variant	4050	exon4			CAGAGAGCTGCGC	L11015	CCDS4703.1, CCDS4704.1	6p21.3	2013-05-22			ENSG00000227507	ENSG00000227507		"Tumor necrosis factor (ligand) superfamily"	6711	protein-coding gene	gene with protein product		600978		TNFC		7916655, 1714477	Standard	NM_002341		Approved	p33, TNFSF3	uc003nuk.3	Q06643	OTTHUMG00000031136	ENST00000429299.2:c.483C>T	6.37:g.31548738G>A		58	0	0		51	4	0.0784314	NM_002341	P78370|Q52LU8|Q99761	Silent	SNP	ENST00000429299.2	37	CCDS4703.1																																																																																			.	.	none		0.746	LTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076239.3			A	31548738	G	A	31548738	2	1	38	1	0	0	0	0	0	0	0	1	9079	962	34	2		2	LTB	6	31548738	Silent	SNP	G	TCGA-GS-A9TV-01A-11D-A382-10	5313799	31548738	139566329	23	14496											
DOPEY1	23033	hgsc.bcm.edu	37	chr6	83849764	83849764	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaccagatatgattcttacTcttttggaagggattacagc	11	13	8	9	0	2	2	0	1	2	1	2	4	2	4	2	2	3	0	2	2	4	6			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr6:83849764T>C	ENST00000349129.2	+	22	5426	c.5166T>C	c.(5164-5166)acT>acC	p.T1722T	DOPEY1_ENST00000484282.1_3'UTR|DOPEY1_ENST00000369739.3_Silent_p.T1713T|DOPEY1_ENST00000237163.5_Silent_p.T1703T	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	1722					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)		TGATTCTTACTCTTTTGGAAG	0.338																																					p.T1722T		Atlas-SNP	.											.	DOPEY1	190	.	0			c.T5166C						PASS	.						141	130	134					6																	83849764		2203	4300	6503	SO:0001819	synonymous_variant	23033	exon22			TCTTACTCTTTTG	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.5166T>C	6.37:g.83849764T>C		208	0	0		169	8	0.0473373	NM_015018	Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Silent	SNP	ENST00000349129.2	37	CCDS4996.1																																																																																			.	.	none		0.338	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2	NM_015018		C	83849764	T	C	83849764	2	2	38	1	0	0	0	0	0	0	0	1	4709	1538	54	3		3	DOPEY1	6	83849764	Silent	SNP	T	TCGA-GS-A9TV-01A-11D-A382-10	52301026	83849764	87265303	24	14497											
SMPDL3A	10924	hgsc.bcm.edu	37	chr6	123116916	123116916	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttcatctaaaggtgcaaaTgcctccaaccctggcccttt	9	11	7	14	0	2	0	1	0	1	0	3	0	3	0	4	2	3	2	4	2	4	3			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr6:123116916T>C	ENST00000368440.4	+	2	384	c.207T>C	c.(205-207)aaT>aaC	p.N69N	SMPDL3A_ENST00000539041.1_Intron|SMPDL3A_ENST00000487215.1_3'UTR	NM_006714.3	NP_006705.1	Q92484	ASM3A_HUMAN	sphingomyelin phosphodiesterase, acid-like 3A	69					sphingomyelin catabolic process (GO:0006685)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|cervix(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	10				GBM - Glioblastoma multiforme(226;0.236)		AAGGTGCAAATGCCTCCAACC	0.403																																					p.N69N		Atlas-SNP	.											.	SMPDL3A	31	.	0			c.T207C						PASS	.						167	149	155					6																	123116916		2203	4300	6503	SO:0001819	synonymous_variant	10924	exon2			TGCAAATGCCTCC	AK000184	CCDS5128.1, CCDS69190.1	6q22.32	2006-04-12			ENSG00000172594	ENSG00000172594			17389	protein-coding gene	gene with protein product	"acid sphingomyelinase-like phosphodiesterase 3a"	610728				12442002	Standard	XM_005266798		Approved	FLJ20177, ASM3A, ASML3a, yR36GH4.1	uc003pzg.3	Q92484	OTTHUMG00000015490	ENST00000368440.4:c.207T>C	6.37:g.123116916T>C		265	0	0		242	10	0.0413223	NM_006714	B7Z729|Q8WV13	Silent	SNP	ENST00000368440.4	37	CCDS5128.1																																																																																			.	.	none		0.403	SMPDL3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042039.1	NM_006714		C	123116916	T	C	123116916	2	2	38	1	0	0	0	0	0	0	0	1	14823	1461	51	3		3	SMPDL3A	6	123116916	Silent	SNP	T	TCGA-GS-A9TV-01A-11D-A382-10	39267152	123116916	47998151	25	14498											
BCAP29	55973	hgsc.bcm.edu	37	chr7	107236323	107236323	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttttcttagagttttgagacGtctggttacgcttattactc	7	19	8	7	2	2	2	0	1	2	2	3	3	2	2	0	1	2	3	0	1	4	8	rs115169101		TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr7:107236323G>A	ENST00000005259.4	+	5	695	c.356G>A	c.(355-357)cGt>cAt	p.R119H	BCAP29_ENST00000494086.1_3'UTR|BCAP29_ENST00000379121.2_Missense_Mutation_p.R25H|BCAP29_ENST00000465919.1_Missense_Mutation_p.R25H|BCAP29_ENST00000445771.2_Missense_Mutation_p.R119H|BCAP29_ENST00000379119.2_Missense_Mutation_p.R119H|BCAP29_ENST00000379117.2_Missense_Mutation_p.R119H	NM_018844.3	NP_061332.2	Q9UHQ4	BAP29_HUMAN	B-cell receptor-associated protein 29	119					apoptotic process (GO:0006915)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|osteoblast differentiation (GO:0001649)|protein localization to endoplasmic reticulum exit site (GO:0070973)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				cervix(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)|skin(1)|urinary_tract(1)	14						GTTTTGAGACGTCTGGTTACG	0.338													G|||	1	0.000199681	0.0008	0.0	5008	,	,		15250	0.0		0.0	False		,,,				2504	0.0				p.R119H		Atlas-SNP	.											BCAP29,colon,carcinoma,+1,1	BCAP29	46	1	0			c.G356A						PASS	.	G	HIS/ARG,HIS/ARG	1,4403	2.1+/-5.4	0,1,2201	112	108	109		356,356	4.6	1	7	dbSNP_132	109	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	BCAP29	NM_001008405.2,NM_018844.3	29,29	0,2,6500	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging,probably-damaging	119/349,119/242	107236323	2,13002	2202	4300	6502	SO:0001583	missense	55973	exon5			TGAGACGTCTGGT		CCDS34730.1, CCDS34731.1	7q22.3	2012-09-20			ENSG00000075790	ENSG00000075790			24131	protein-coding gene	gene with protein product						12477932	Standard	NM_018844		Approved	BAP29, DKFZp686M2086	uc011kma.1	Q9UHQ4	OTTHUMG00000154770	ENST00000005259.4:c.356G>A	7.37:g.107236323G>A	ENSP00000005259:p.Arg119His	220	0	0		202	10	0.049505	NM_018844	G5E9L4|O95003	Missense_Mutation	SNP	ENST00000005259.4	37	CCDS34731.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.323123	0.81580	2.27E-4	1.16E-4	ENSG00000075790	ENST00000005259;ENST00000465919;ENST00000445771;ENST00000479917;ENST00000421217;ENST00000457837;ENST00000379117;ENST00000379119;ENST00000491150;ENST00000379121	.	.	.	5.45	4.57	0.56435	.	0.000000	0.85682	D	0.000000	D	0.84061	0.5389	M	0.90369	3.11	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	0.87335	0.2327	9	0.87932	D	0	0.1468	13.3198	0.60426	0.0778:0.0:0.9222:0.0	.	119;119;119	G5E9L4;C9JTE9;Q9UHQ4	.;.;BAP29_HUMAN	H	119;25;119;119;119;119;119;119;76;25	.	ENSP00000005259:R119H	R	+	2	0	BCAP29	107023559	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	6.256000	0.72473	1.444000	0.47605	0.650000	0.86243	CGT	G|1.000;A|0.000	0.000	strong		0.338	BCAP29-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337011.2	NM_018844		A	107236323	G	A	107236323	3	1	38	1	0	0	0	0	1	0	0	0	1346	1145	40	1	370	1	BCAP29	7	107236323	Missense_Mutation	SNP	G	TCGA-GS-A9TV-01A-11D-A382-10		107236323	51902340	26	14499											
RNF19A	25897	hgsc.bcm.edu	37	chr8	101276899	101276899	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acttttcagcattttcttacCtacagtcactgcagctacta	10	15	4	12	0	3	0	2	0	1	0	3	0	3	0	1	0	6	3	1	0	4	8			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr8:101276899C>T	ENST00000519449.1	-	7	1622	c.1306G>A	c.(1306-1308)Ggt>Agt	p.G436S	RNF19A_ENST00000523255.1_5'UTR|RNF19A_ENST00000341084.2_Splice_Site_p.G436S	NM_001280539.1|NM_015435.3	NP_001267468.1|NP_056250.3	Q9NV58	RN19A_HUMAN	ring finger protein 19A, RBR E3 ubiquitin protein ligase	436					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)			ATTTTCTTACCTACAGTCACT	0.353																																					p.G436S		Atlas-SNP	.											.	RNF19A	67	.	0			c.G1306A						PASS	.						175	155	162					8																	101276899		2203	4300	6503	SO:0001630	splice_region_variant	25897	exon7			TCTTACCTACAGT	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.1306+1G>A	8.37:g.101276899C>T		114	0	0		108	8	0.0740741	NM_015435	A3KCU9|Q52LG1|Q9H5H9|Q9H8M8|Q9UFG0|Q9UFX6|Q9Y4Y1	Missense_Mutation	SNP	ENST00000519449.1	37	CCDS6286.1	.	.	.	.	.	.	.	.	.	.	C	35	5.552861	0.96501	.	.	ENSG00000034677	ENST00000519449;ENST00000341084	D;D	0.86097	-2.07;-2.07	5.41	5.41	0.78517	.	0.046563	0.85682	D	0.000000	D	0.91112	0.7202	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.89895	0.4040	9	.	.	.	.	19.229	0.93829	0.0:1.0:0.0:0.0	.	436	Q9NV58	RN19A_HUMAN	S	436	ENSP00000428968:G436S;ENSP00000342667:G436S	.	G	-	1	0	RNF19A	101346075	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.776000	0.85560	2.699000	0.92147	0.650000	0.86243	GGT	.	.	none		0.353	RNF19A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380004.1	NM_015435	Missense_Mutation	T	101276899	C	T	101276899	5	4	38	1	0	0	0	0	0	0	1	0	13485	695	24	2	1230	2	RNF19A	8	101276899	Splice_Site	SNP	C	TCGA-GS-A9TV-01A-11D-A382-10		101276899	45087123	27	14500											
MYC	4609	hgsc.bcm.edu	37	chr8	128751013	128751013	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgaaccccgcccgcggccacAgcgtctgctccacctccagc	6	4	9	22	5	1	0	0	0	1	0	3	1	3	0	7	1	4	1	7	1	1	0			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr8:128751013A>T	ENST00000259523.6	+	2	1710	c.505A>T	c.(505-507)Agc>Tgc	p.S169C	MYC_ENST00000377970.2_Missense_Mutation_p.S184C|MYC_ENST00000524013.1_Missense_Mutation_p.S183C			P01106	MYC_HUMAN	v-myc avian myelocytomatosis viral oncogene homolog	169					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)	CCGCGGCCACAGCGTCTGCTC	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.S184C		Atlas-SNP	.		Dom	yes		8	8q24.12-q24.13	4609	v-myc myelocytomatosis viral oncogene homolog (avian)		"L, E"	.	MYC	168	.	0			c.A550T						PASS	.						20	22	21					8																	128751013		2203	4298	6501	SO:0001583	missense	4609	exon2			GGCCACAGCGTCT		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.505A>T	8.37:g.128751013A>T	ENSP00000259523:p.Ser169Cys	56	0	0	1567	53	4	0.0754717	NM_002467	A8WFE7|P01107|Q14026	Missense_Mutation	SNP	ENST00000259523.6	37		.	.	.	.	.	.	.	.	.	.	A	15.75	2.926604	0.52759	.	.	ENSG00000136997	ENST00000259523;ENST00000517291;ENST00000377970;ENST00000524013;ENST00000454617	T;T;T;T	0.25749	2.14;1.78;2.14;2.14	4.78	-3.13	0.05266	Transcription regulator Myc, N-terminal (1);	0.630931	0.16999	N	0.190997	T	0.28234	0.0697	L	0.52573	1.65	0.21020	N	0.99981	P	0.50156	0.932	P	0.55455	0.776	T	0.12863	-1.0531	10	0.62326	D	0.03	-9.1089	3.8255	0.08852	0.5346:0.1046:0.2554:0.1053	.	169	P01106	MYC_HUMAN	C	169;183;184;183;150	ENSP00000259523:S169C;ENSP00000429441:S183C;ENSP00000367207:S184C;ENSP00000430235:S183C	ENSP00000259523:S169C	S	+	1	0	MYC	128820195	0.000000	0.05858	0.819000	0.32651	0.693000	0.40251	-0.773000	0.04689	-0.571000	0.06014	0.459000	0.35465	AGC	.	.	none		0.677	MYC-002	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000250278.1			T	128751013	A	T	128751013	3	4	38	1	0	0	0	0	1	0	0	0	10025	188	7	5	556	5	MYC	8	128751013	Missense_Mutation	SNP	A	TCGA-GS-A9TV-01A-11D-A382-10	27474114	128751013	17613009	28	14501											
UNC13B	10497	hgsc.bcm.edu	37	chr9	35399645	35399645	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgctgatttctctgaacaGgatcacatggtacgagagga	11	10	12	8	1	2	3	1	2	1	1	3	6	2	5	0	3	3	3	0	3	2	2			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr9:35399645G>T	ENST00000378495.3	+	35	4230		c.e35-1		UNC13B_ENST00000396787.1_Splice_Site|UNC13B_ENST00000378496.4_Splice_Site	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)						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)			TCTCTGAACAGGATCACATGG	0.532																																					.		Atlas-SNP	.											.	UNC13B	153	.	0			c.4009-1G>T						PASS	.						249	228	235					9																	35399645		2203	4300	6503	SO:0001630	splice_region_variant	10497	exon35			TGAACAGGATCAC	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.4009-1G>T	9.37:g.35399645G>T		59	0	0		61	6	0.0983607	NM_006377	Q5VYM8	Splice_Site	SNP	ENST00000378495.3	37	CCDS6579.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.611073	0.87258	.	.	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496;ENST00000535471	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4471	0.94852	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UNC13B	35389645	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	9.267000	0.95665	2.824000	0.97209	0.655000	0.94253	.	.	.	none		0.532	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377	Intron	T	35399645	G	T	35399645	5	4	38	1	0	0	0	0	0	0	1	0	17000	1014	35	4	4146	4	UNC13B	9	35399645	Splice_Site	SNP	G	TCGA-GS-A9TV-01A-11D-A382-10		35399645	105813786	29	14502											
FAM120A	23196	hgsc.bcm.edu	37	chr9	96318697	96318697	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atccccgaggaattcagctaTcagctctcttcatgagtgga	10	11	9	11	1	4	1	3	1	1	0	6	4	5	3	2	2	2	2	2	2	2	3			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr9:96318697T>G	ENST00000277165.6	+	13	2502	c.2308T>G	c.(2308-2310)Tca>Gca	p.S770A	FAM120A_ENST00000333936.5_Missense_Mutation_p.S798A|FAM120A_ENST00000340893.4_Missense_Mutation_p.S770A	NM_014612.3	NP_055427.2	Q9NZB2	F120A_HUMAN	family with sequence similarity 120A	770						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						AATTCAGCTATCAGCTCTCTT	0.393																																					p.S770A		Atlas-SNP	.											.	FAM120A	105	.	0			c.T2308G						PASS	.						135	138	137					9																	96318697		2203	4300	6503	SO:0001583	missense	23196	exon13			CAGCTATCAGCTC	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.2308T>G	9.37:g.96318697T>G	ENSP00000277165:p.Ser770Ala	155	0	0		171	15	0.0877193	NM_014612	A6NGU0|C4AMC6|O60649|Q14688|Q4VXF4|Q4VXF5|Q4VXG2|Q86V69|Q96I21|Q9NZB1	Missense_Mutation	SNP	ENST00000277165.6	37	CCDS6706.1	.	.	.	.	.	.	.	.	.	.	T	11.45	1.643701	0.29246	.	.	ENSG00000048828	ENST00000277165;ENST00000333936;ENST00000340893;ENST00000427765	T;T;T;T	0.40225	1.04;1.04;1.04;1.04	5.68	5.68	0.88126	.	0.000000	0.64402	D	0.000010	T	0.12860	0.0312	N	0.00661	-1.28	0.40403	D	0.979668	B;B;B	0.09022	0.001;0.002;0.001	B;B;B	0.13407	0.004;0.007;0.009	T	0.27971	-1.0058	10	0.02654	T	1	-11.3047	11.8715	0.52523	0.0:0.0:0.1456:0.8543	.	770;798;770	Q9NZB2-4;Q9NZB2-6;Q9NZB2	.;.;F120A_HUMAN	A	770;798;770;192	ENSP00000277165:S770A;ENSP00000334918:S798A;ENSP00000344698:S770A;ENSP00000412440:S192A	ENSP00000277165:S770A	S	+	1	0	FAM120A	95358518	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.176000	0.65026	2.172000	0.68678	0.533000	0.62120	TCA	.	.	none		0.393	FAM120A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053160.2	NM_014612		G	96318697	T	G	96318697	3	3	38	1	0	0	0	0	1	0	0	0	5420	1435	50	5	2358	5	FAM120A	9	96318697	Missense_Mutation	SNP	T	TCGA-GS-A9TV-01A-11D-A382-10	60919052	96318697	44894734	30	14503											
FBP2	8789	hgsc.bcm.edu	37	chr9	97346890	97346890	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tggcaaagatggttccgatgGaggccaggcagtcaatattg	11	9	14	7	1	1	1	1	0	0	1	2	3	2	2	2	5	0	3	2	5	3	3			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr9:97346890G>C	ENST00000375337.3	-	3	461	c.395C>G	c.(394-396)tCc>tGc	p.S132C		NM_003837.2	NP_003828.2	O00757	F16P2_HUMAN	fructose-1,6-bisphosphatase 2	132					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)				GGTTCCGATGGAGGCCAGGCA	0.483																																					p.S132C		Atlas-SNP	.											.	FBP2	26	.	0			c.C395G						PASS	.						150	122	132					9																	97346890		2203	4300	6503	SO:0001583	missense	8789	exon3			CCGATGGAGGCCA	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.395C>G	9.37:g.97346890G>C	ENSP00000364486:p.Ser132Cys	64	0	0		78	8	0.102564	NM_003837	Q17R39|Q6FI53	Missense_Mutation	SNP	ENST00000375337.3	37	CCDS6711.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.555699	0.86231	.	.	ENSG00000130957	ENST00000375337	T	0.79454	-1.27	4.87	4.87	0.63330	.	0.169189	0.53938	D	0.000045	D	0.89543	0.6745	M	0.88640	2.97	0.80722	D	1	D	0.71674	0.998	D	0.66196	0.942	D	0.91770	0.5427	10	0.87932	D	0	-19.1055	18.3657	0.90390	0.0:0.0:1.0:0.0	.	132	O00757	F16P2_HUMAN	C	132	ENSP00000364486:S132C	ENSP00000364486:S132C	S	-	2	0	FBP2	96386711	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.542000	0.98086	2.397000	0.81536	0.655000	0.94253	TCC	.	.	none		0.483	FBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053189.1	NM_003837		C	97346890	G	C	97346890	3	2	38	1	0	0	0	0	1	0	0	0	5714	1174	41	4	644	4	FBP2	9	97346890	Missense_Mutation	SNP	G	TCGA-GS-A9TV-01A-11D-A382-10	1028193	97346890	43866541	31	14504											
GRIN3A	116443	hgsc.bcm.edu	37	chr9	104449271	104449271	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggaagctcaagaggtcctggGtggaggggaggttagcggtg	8	7	21	5	1	1	1	1	0	0	1	2	4	2	4	1	8	2	2	1	8	3	1			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr9:104449271G>A	ENST00000361820.3	-	2	1511	c.911C>T	c.(910-912)aCc>aTc	p.T304I		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	304					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)	GAGGTCCTGGGTGGAGGGGAG	0.507																																					p.T304I		Atlas-SNP	.											.	GRIN3A	186	.	0			c.C911T						PASS	.						125	114	118					9																	104449271		2203	4300	6503	SO:0001583	missense	116443	exon2			TCCTGGGTGGAGG		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.911C>T	9.37:g.104449271G>A	ENSP00000355155:p.Thr304Ile	169	0	0		172	12	0.0697674	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	37	CCDS6758.1	.	.	.	.	.	.	.	.	.	.	G	9.953	1.220762	0.22457	.	.	ENSG00000198785	ENST00000361820	D	0.86562	-2.14	5.82	3.79	0.43588	.	0.741427	0.13472	N	0.385327	T	0.81158	0.4764	L	0.36672	1.1	0.37462	D	0.915272	B	0.14012	0.009	B	0.10450	0.005	T	0.76830	-0.2814	10	0.34782	T	0.22	.	12.3574	0.55184	0.0:0.242:0.6501:0.108	.	304	Q8TCU5	NMD3A_HUMAN	I	304	ENSP00000355155:T304I	ENSP00000355155:T304I	T	-	2	0	GRIN3A	103489092	0.033000	0.19621	0.999000	0.59377	0.882000	0.50991	0.538000	0.23160	2.759000	0.94783	0.557000	0.71058	ACC	.	.	none		0.507	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1			A	104449271	G	A	104449271	3	1	38	1	0	0	0	0	1	0	0	0	6792	1261	44	2	2468	2	GRIN3A	9	104449271	Missense_Mutation	SNP	G	TCGA-GS-A9TV-01A-11D-A382-10	7102381	104449271	36764160	32	14505											
FAM13C	220965	hgsc.bcm.edu	37	chr10	61022354	61022354	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctcacacaacaggtttctaGgtggacctttgggagcactc	9	10	11	11	0	2	0	1	0	1	0	3	2	2	2	1	4	2	3	1	4	2	3			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr10:61022354G>A	ENST00000373868.2	-	10	1163	c.1076C>T	c.(1075-1077)cCt>cTt	p.P359L	FAM13C_ENST00000419214.2_Intron|FAM13C_ENST00000442566.3_Missense_Mutation_p.P380L|FAM13C_ENST00000422313.2_Missense_Mutation_p.P359L|FAM13C_ENST00000277705.6_Missense_Mutation_p.P380L|FAM13C_ENST00000373867.3_Missense_Mutation_p.P276L|FAM13C_ENST00000435852.2_Missense_Mutation_p.P359L|FAM13C_ENST00000468840.2_Missense_Mutation_p.P276L	NM_198215.3	NP_937858.2	Q8NE31	FA13C_HUMAN	family with sequence similarity 13, member C	359								p.P359R(1)		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						CAGGTTTCTAGGTGGACCTTT	0.493																																					p.P359L		Atlas-SNP	.											FAM13C_ENST00000422313,NS,carcinoma,0,2	FAM13C	124	2	1	Substitution - Missense(1)	lung(1)	c.C1076T						PASS	.						89	89	89					10																	61022354		2203	4300	6503	SO:0001583	missense	220965	exon10			TTTCTAGGTGGAC	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.1076C>T	10.37:g.61022354G>A	ENSP00000362975:p.Pro359Leu	190	0	0		159	10	0.0628931	NM_198215	B7ZB77|Q5T631|Q6P2M3|Q99787	Missense_Mutation	SNP	ENST00000373868.2	37	CCDS7255.1	.	.	.	.	.	.	.	.	.	.	G	8.792	0.930800	0.18131	.	.	ENSG00000148541	ENST00000373867;ENST00000373868;ENST00000442566;ENST00000277705;ENST00000468840;ENST00000435852;ENST00000422313	T;T;T;T;T;T;T	0.74947	-0.89;-0.89;-0.89;-0.89;-0.89;-0.89;-0.89	5.72	1.65	0.23941	.	0.704485	0.13552	N	0.379439	T	0.61035	0.2315	L	0.47716	1.5	0.09310	N	1	B;B;B;B	0.11235	0.003;0.001;0.004;0.001	B;B;B;B	0.14023	0.004;0.006;0.01;0.003	T	0.52719	-0.8538	10	0.48119	T	0.1	-0.0153	1.2001	0.01883	0.162:0.2361:0.3334:0.2684	.	359;276;359;359	B7Z2K3;B7ZB77;Q8NE31-2;Q8NE31	.;.;.;FA13C_HUMAN	L	276;359;380;380;276;359;359	ENSP00000362974:P276L;ENSP00000362975:P359L;ENSP00000395661:P380L;ENSP00000277705:P380L;ENSP00000423896:P276L;ENSP00000392302:P359L;ENSP00000400241:P359L	ENSP00000277705:P380L	P	-	2	0	FAM13C	60692360	0.287000	0.24315	0.110000	0.21437	0.648000	0.38561	0.848000	0.27710	0.306000	0.22856	0.563000	0.77884	CCT	.	.	none		0.493	FAM13C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048162.2			A	61022354	G	A	61022354	3	1	38	1	0	0	0	0	1	0	0	0	5459	1000	35	2	701	2	FAM13C	10	61022354	Missense_Mutation	SNP	G	TCGA-GS-A9TV-01A-11D-A382-10		61022354	74512393	33	14506											
TET1	80312	hgsc.bcm.edu	37	chr10	70405864	70405864	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagggcacaatacaacagaaAccaccttcaagtgtacacaa	19	5	6	11	0	1	1	1	0	0	1	1	1	1	1	2	1	4	2	2	1	8	3			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr10:70405864A>G	ENST00000373644.4	+	4	3587	c.3378A>G	c.(3376-3378)aaA>aaG	p.K1126K		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1126					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						TACAACAGAAACCACCTTCAA	0.388																																					p.K1126K		Atlas-SNP	.											.	TET1	255	.	0			c.A3378G						PASS	.						89	77	81					10																	70405864		2203	4300	6503	SO:0001819	synonymous_variant	80312	exon4			ACAGAAACCACCT	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.3378A>G	10.37:g.70405864A>G		115	0	0		121	14	0.115702	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Silent	SNP	ENST00000373644.4	37	CCDS7281.1																																																																																			.	.	none		0.388	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625		G	70405864	A	G	70405864	2	3	38	1	0	0	0	0	0	0	0	1	15784	40	2	3		3	TET1	10	70405864	Silent	SNP	A	TCGA-GS-A9TV-01A-11D-A382-10	9383510	70405864	65128883	34	14507											
SH3PXD2A	9644	hgsc.bcm.edu	37	chr10	105362350	105362350	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aacctcacataccaccacccGctctcctgcttctccagcac	9	8	3	21	1	3	0	1	0	2	0	5	0	3	0	6	0	4	3	6	0	2	2			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr10:105362350G>A	ENST00000369774.4	-	15	2901	c.2625C>T	c.(2623-2625)agC>agT	p.S875S	SH3PXD2A_ENST00000540321.1_Silent_p.S742S|SH3PXD2A_ENST00000315994.6_5'UTR|SH3PXD2A_ENST00000427662.2_Intron|SH3PXD2A_ENST00000538130.1_Silent_p.S710S|SH3PXD2A_ENST00000355946.2_Silent_p.S847S			Q5TCZ1	SPD2A_HUMAN	SH3 and PX domains 2A	875	SH3 4. {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)		ACCACCACCCGCTCTCCTGCT	0.617																																					p.S847S		Atlas-SNP	.											.	SH3PXD2A	90	.	0			c.C2541T						PASS	.						50	51	51					10																	105362350		2203	4300	6503	SO:0001819	synonymous_variant	9644	exon14			CCACCCGCTCTCC	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.2625C>T	10.37:g.105362350G>A		113	0	0		104	5	0.0480769	NM_014631	D3DR98|O43302|Q5TCZ2|Q5TDQ8	Silent	SNP	ENST00000369774.4	37		.	.	.	.	.	.	.	.	.	.	G	0.409	-0.914168	0.02415	.	.	ENSG00000107957	ENST00000420222	.	.	.	4.59	-2.81	0.05805	.	.	.	.	.	T	0.57169	0.2035	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55976	-0.8055	4	.	.	.	-16.5179	11.8174	0.52218	0.728:0.0:0.272:0.0	.	.	.	.	W	802	.	.	R	-	1	2	SH3PXD2A	105352340	0.038000	0.19896	0.854000	0.33618	0.429000	0.31625	-0.502000	0.06390	-0.468000	0.06922	-0.258000	0.10820	CGG	.	.	none		0.617	SH3PXD2A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050178.1	NM_014631		A	105362350	G	A	105362350	2	1	38	1	0	0	0	0	0	0	0	1	14271	1078	38	1		1	SH3PXD2A	10	105362350	Silent	SNP	G	TCGA-GS-A9TV-01A-11D-A382-10	34956486	105362350	30172397	35	14508											
OR4C13	283092	hgsc.bcm.edu	37	chr11	49974680	49974680	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcaaggcacgaagccctcTctacctgtgtctcccacatc	9	8	8	16	1	2	0	0	0	2	0	5	1	2	0	3	2	2	2	3	2	3	1			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr11:49974680T>A	ENST00000555099.1	+	1	738	c.706T>A	c.(706-708)Tct>Act	p.S236T		NM_001001955.2	NP_001001955.2	Q8NGP0	OR4CD_HUMAN	olfactory receptor, family 4, subfamily C, member 13	236						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)|kidney(1)|large_intestine(5)|lung(24)|ovary(2)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	43						CGAAGCCCTCTCTACCTGTGT	0.463																																					p.S236T		Atlas-SNP	.											.	OR4C13	96	.	0			c.T706A						PASS	.						181	155	164					11																	49974680		2201	4296	6497	SO:0001583	missense	283092	exon1			GCCCTCTCTACCT	AB065750	CCDS31495.1	11p11.12	2012-10-03			ENSG00000258817	ENSG00000258817		"GPCR / Class A : Olfactory receptors"	15169	protein-coding gene	gene with protein product							Standard	NM_001001955		Approved		uc010rhz.2	Q8NGP0	OTTHUMG00000166686	ENST00000555099.1:c.706T>A	11.37:g.49974680T>A	ENSP00000452277:p.Ser236Thr	227	0	0		185	9	0.0486486	NM_001001955	A6NJJ3|B9EH30|Q6IF48|Q96R68	Missense_Mutation	SNP	ENST00000555099.1	37	CCDS31495.1	.	.	.	.	.	.	.	.	.	.	.	9.238	1.037466	0.19669	.	.	ENSG00000258817	ENST00000555099	T	0.00295	8.25	2.91	2.91	0.33838	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46145	D	0.000319	T	0.00695	0.0023	M	0.88031	2.925	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.25222	-1.0138	9	.	.	.	.	9.2733	0.37684	0.0:0.0:0.0:1.0	.	236	Q8NGP0	OR4CD_HUMAN	T	236	ENSP00000452277:S236T	.	S	+	1	0	OR4C13	49931256	0.000000	0.05858	0.955000	0.39395	0.029000	0.11900	0.475000	0.22164	1.342000	0.45619	0.156000	0.16432	TCT	.	.	none		0.463	OR4C13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391103.1	NM_001001955		A	49974680	T	A	49974680	3	1	38	1	0	0	0	0	1	0	0	0	11056	1551	54	5	708	5	OR4C13	11	49974680	Missense_Mutation	SNP	T	TCGA-GS-A9TV-01A-11D-A382-10		49974680	85031836	36	14509											
OR4D10	390197	hgsc.bcm.edu	37	chr11	59244978	59244978	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaatcgggaagtgagcttaGtcttatttcttttcctactc	9	16	8	8	1	2	2	0	1	2	1	5	3	3	3	1	1	2	1	1	1	5	6			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr11:59244978G>C	ENST00000530162.1	+	1	133	c.76G>C	c.(76-78)Gtc>Ctc	p.V26L		NM_001004705.1	NP_001004705.1	Q8NGI6	OR4DA_HUMAN	olfactory receptor, family 4, subfamily D, member 10	26						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(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						AGTGAGCTTAGTCTTATTTCT	0.433																																					p.V26L		Atlas-SNP	.											.	OR4D10	120	.	0			c.G76C						PASS	.						107	110	109					11																	59244978		2053	4220	6273	SO:0001583	missense	390197	exon1			AGCTTAGTCTTAT	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.76G>C	11.37:g.59244978G>C	ENSP00000436424:p.Val26Leu	147	0	0		175	17	0.0971429	NM_001004705	B2RNH6	Missense_Mutation	SNP	ENST00000530162.1	37	CCDS53636.1	.	.	.	.	.	.	.	.	.	.	G	2.795	-0.250377	0.05867	.	.	ENSG00000254466	ENST00000530162	T	0.00063	8.78	4.2	-8.41	0.00961	.	.	.	.	.	T	0.00073	0.0002	N	0.02286	-0.61	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.18967	-1.0320	9	0.33940	T	0.23	.	8.643	0.33989	0.0831:0.1004:0.6209:0.1956	.	26	Q8NGI6	OR4DA_HUMAN	L	26	ENSP00000436424:V26L	ENSP00000436424:V26L	V	+	1	0	OR4D10	59001554	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-6.203000	0.00076	-1.731000	0.01360	-1.107000	0.02091	GTC	.	.	none		0.433	OR4D10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394235.1	NM_001004705		C	59244978	G	C	59244978	3	2	38	1	0	0	0	0	1	0	0	0	11063	1029	36	4	78	4	OR4D10	11	59244978	Missense_Mutation	SNP	G	TCGA-GS-A9TV-01A-11D-A382-10	9270298	59244978	75761538	37	14510											
PLCZ1	89869	hgsc.bcm.edu	37	chr12	18841114	18841114	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgaatcacctttgttagaTgatgaatgagtaagaggcaa	16	11	10	4	0	1	6	1	4	0	2	1	6	1	6	1	1	0	3	1	1	6	3			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr12:18841114T>C	ENST00000538330.1	-	9	1227	c.846A>G	c.(844-846)tcA>tcG	p.S282S	PLCZ1_ENST00000435379.1_Silent_p.S305S|PLCZ1_ENST00000534932.1_5'UTR|PLCZ1_ENST00000541695.1_Silent_p.S363S|PLCZ1_ENST00000539875.1_Silent_p.S307S|PLCZ1_ENST00000447925.2_Silent_p.S498S|PLCZ1_ENST00000266505.7_Silent_p.S500S					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)					CTTTGTTAGATGATGAATGAG	0.318																																					p.S500S		Atlas-SNP	.											.	PLCZ1	107	.	0			c.A1500G						PASS	.						94	103	100					12																	18841114		2203	4298	6501	SO:0001819	synonymous_variant	89869	exon13			GTTAGATGATGAA	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.846A>G	12.37:g.18841114T>C		94	0	0		93	7	0.0752688	NM_033123		Silent	SNP	ENST00000538330.1	37		.	.	.	.	.	.	.	.	.	.	T	1.226	-0.625562	0.03610	.	.	ENSG00000139151	ENST00000536023	.	.	.	5.39	0.37	0.16160	.	.	.	.	.	T	0.21718	0.0523	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.22977	-1.0201	4	.	.	.	.	2.5671	0.04785	0.1216:0.0984:0.3429:0.4371	.	.	.	.	V	70	.	.	I	-	1	0	PLCZ1	18732381	0.003000	0.15002	0.004000	0.12327	0.331000	0.28603	-0.103000	0.10940	0.407000	0.25591	0.260000	0.18958	ATC	.	.	none		0.318	PLCZ1-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000401666.3	NM_033123		C	18841114	T	C	18841114	2	2	38	1	0	0	0	0	0	0	0	1	12053	1451	51	3		3	PLCZ1	12	18841114	Silent	SNP	T	TCGA-GS-A9TV-01A-11D-A382-10		18841114	115010781	38	14511											
ERGIC2	51290	hgsc.bcm.edu	37	chr12	29514613	29514613	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgctgtggtgaaagatcaaaTactgtctgaaatgaaagaaa	17	10	10	4	0	2	5	1	3	1	2	2	5	2	5	0	1	2	1	0	1	6	1			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr12:29514613T>C	ENST00000360150.4	-	6	414	c.339A>G	c.(337-339)gtA>gtG	p.V113V		NM_016570.2	NP_057654.2	Q96RQ1	ERGI2_HUMAN	ERGIC and golgi 2	113					vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)				endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(2)|urinary_tract(1)	10	Lung NSC(12;2.02e-08)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)|Lung SC(9;0.184)					AAAGATCAAATACTGTCTGAA	0.308																																					p.V113V		Atlas-SNP	.											ERGIC2,NS,carcinoma,-2,1	ERGIC2	29	1	0			c.A339G						PASS	.						146	146	146					12																	29514613		1833	4083	5916	SO:0001819	synonymous_variant	51290	exon6			ATCAAATACTGTC	AF216751	CCDS41765.1	12p11.22	2006-02-08							30208	protein-coding gene	gene with protein product		612236				11445006, 12932305	Standard	NM_016570		Approved	PTX1, Erv41	uc001riv.3	Q96RQ1		ENST00000360150.4:c.339A>G	12.37:g.29514613T>C		131	0	0		143	8	0.0559441	NM_016570	A6NHH6|Q53GY2|Q8N2Q9|Q9BVV9|Q9NZA3	Silent	SNP	ENST00000360150.4	37	CCDS41765.1																																																																																			.	.	none		0.308	ERGIC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403489.1	NM_016570		C	29514613	T	C	29514613	2	2	38	1	0	0	0	0	0	0	0	1	5226	1393	49	3		3	ERGIC2	12	29514613	Silent	SNP	T	TCGA-GS-A9TV-01A-11D-A382-10	10673499	29514613	104337282	39	14512											
GNPTAB	79158	hgsc.bcm.edu	37	chr12	102158979	102158979	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcaccttcaactcctcttttGgctacttctgcaaagctgaa	9	13	6	13	0	3	1	1	1	2	0	4	1	4	1	2	1	4	4	2	1	4	5			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr12:102158979G>A	ENST00000299314.7	-	13	1978	c.1716C>T	c.(1714-1716)gcC>gcT	p.A572A	RNU6-101P_ENST00000410323.1_RNA	NM_024312.4	NP_077288.2	Q3T906	GNPTA_HUMAN	N-acetylglucosamine-1-phosphate transferase, alpha and beta subunits	572					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						CTCCTCTTTTGGCTACTTCTG	0.393																																					p.A572A		Atlas-SNP	.											GNPTAB,NS,carcinoma,-1,1	GNPTAB	120	1	0			c.C1716T						PASS	.						186	174	178					12																	102158979		2203	4300	6503	SO:0001819	synonymous_variant	79158	exon13			TCTTTTGGCTACT	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.1716C>T	12.37:g.102158979G>A		147	0	0		158	11	0.0696203	NM_024312	A2RRQ9|Q3ZQK2|Q6IPW5|Q86TQ2|Q96N13|Q9ULL2	Silent	SNP	ENST00000299314.7	37	CCDS9088.1																																																																																			.	.	none		0.393	GNPTAB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409182.1			A	102158979	G	A	102158979	2	1	38	1	0	0	0	0	0	0	0	1	6553	1335	47	2		2	GNPTAB	12	102158979	Silent	SNP	G	TCGA-GS-A9TV-01A-11D-A382-10	72644366	102158979	31692916	40	14513											
NUBPL	80224	hgsc.bcm.edu	37	chr14	32142594	32142594	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcctctcttgaattatggtaTtgcttggtgagcatatatat	9	17	9	6	0	1	2	0	2	1	0	2	2	1	2	1	2	2	3	1	2	6	8			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr14:32142594T>G	ENST00000281081.7	+	5	461	c.416T>G	c.(415-417)aTt>aGt	p.I139S	NUBPL_ENST00000536705.1_Missense_Mutation_p.I43S	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	139					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)		AATTATGGTATTGCTTGGTGA	0.279																																					p.I139S		Atlas-SNP	.											.	NUBPL	21	.	0			c.T416G						PASS	.						46	42	43					14																	32142594		1788	4062	5850	SO:0001583	missense	80224	exon5			ATGGTATTGCTTG	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.416T>G	14.37:g.32142594T>G	ENSP00000281081:p.Ile139Ser	382	0	0		353	17	0.0481586	NM_025152	B4DHZ1|Q86TZ4|Q9H9M2	Missense_Mutation	SNP	ENST00000281081.7	37	CCDS41940.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.132126	0.77662	.	.	ENSG00000151413	ENST00000281081;ENST00000551314;ENST00000536705	T;T;T	0.49432	0.78;0.87;0.78	5.53	5.53	0.82687	.	0.096119	0.64402	D	0.000001	T	0.67144	0.2862	H	0.96015	3.755	0.48135	D	0.99959	P;P	0.40578	0.586;0.722	B;B	0.43809	0.375;0.432	T	0.77395	-0.2604	10	0.87932	D	0	0.811	13.3964	0.60856	0.0:0.0:0.0:1.0	.	43;139	B4DWB0;Q8TB37	.;NUBPL_HUMAN	S	139;87;43	ENSP00000281081:I139S;ENSP00000447234:I87S;ENSP00000439286:I43S	ENSP00000281081:I139S	I	+	2	0	NUBPL	31212345	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	6.612000	0.74187	2.097000	0.63578	0.455000	0.32223	ATT	.	.	none		0.279	NUBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409519.1	NM_025152		G	32142594	T	G	32142594	3	3	38	1	0	0	0	0	1	0	0	0	10726	1493	52	5	434	5	NUBPL	14	32142594	Missense_Mutation	SNP	T	TCGA-GS-A9TV-01A-11D-A382-10		32142594	75206946	41	14514											
CCDC88C	440193	hgsc.bcm.edu	37	chr14	91883122	91883122	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caaaaagatgccgtccactaAatccatgtacatagtcaggt	15	9	7	10	1	1	1	1	0	0	1	3	1	3	1	3	1	2	1	3	1	6	3			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr14:91883122A>C	ENST00000389857.6	-	2	207	c.121T>G	c.(121-123)Tta>Gta	p.L41V	CCDC88C_ENST00000553403.1_Missense_Mutation_p.L41V|CCDC88C_ENST00000389856.5_Missense_Mutation_p.L33V|RP11-895M11.3_ENST00000557524.1_lincRNA|CCDC88C_ENST00000554165.1_5'UTR	NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	41					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)				CCGTCCACTAAATCCATGTAC	0.473																																					p.L41V		Atlas-SNP	.											.	CCDC88C	192	.	0			c.T121G						PASS	.						56	54	54					14																	91883122		1952	4139	6091	SO:0001583	missense	440193	exon2			CCACTAAATCCAT		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.121T>G	14.37:g.91883122A>C	ENSP00000374507:p.Leu41Val	87	0	0		88	6	0.0681818	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Missense_Mutation	SNP	ENST00000389857.6	37	CCDS45151.1	.	.	.	.	.	.	.	.	.	.	A	19.24	3.789352	0.70337	.	.	ENSG00000015133	ENST00000389857;ENST00000541408;ENST00000389856;ENST00000553403	T;T;T	0.65732	-0.17;-0.17;-0.17	5.18	1.39	0.22231	.	0.000000	0.30329	U	0.009879	T	0.73845	0.3639	M	0.86864	2.845	0.80722	D	1	D;D	0.65815	0.971;0.995	D;P	0.64506	0.926;0.894	T	0.70781	-0.4779	10	0.87932	D	0	-4.4737	2.9797	0.05949	0.4867:0.0:0.3289:0.1844	.	41;41	Q9P219;G3V3S0	DAPLE_HUMAN;.	V	41;5;33;41	ENSP00000374507:L41V;ENSP00000374506:L33V;ENSP00000451392:L41V	ENSP00000374506:L33V	L	-	1	2	CCDC88C	90952875	0.997000	0.39634	1.000000	0.80357	0.995000	0.86356	1.407000	0.34657	0.333000	0.23563	0.379000	0.24179	TTA	.	.	none		0.473	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353		C	91883122	A	C	91883122	3	2	38	1	0	0	0	0	1	0	0	0	2867	11	1	5	6081	5	CCDC88C	14	91883122	Missense_Mutation	SNP	A	TCGA-GS-A9TV-01A-11D-A382-10	59740528	91883122	15466418	42	14515											
TECPR2	9895	hgsc.bcm.edu	37	chr14	102894692	102894692	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggaacattataagaatttcaAgcaggcctgaaggattaaca	17	9	9	6	0	1	2	1	1	0	1	1	4	1	4	1	3	3	1	1	3	7	4			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr14:102894692A>G	ENST00000359520.7	+	7	1283	c.1057A>G	c.(1057-1059)Agc>Ggc	p.S353G	TECPR2_ENST00000558678.1_Missense_Mutation_p.S353G	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	353					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						AAGAATTTCAAGCAGGCCTGA	0.338																																					p.S353G		Atlas-SNP	.											.	TECPR2	114	.	0			c.A1057G						PASS	.						69	75	73					14																	102894692		2203	4300	6503	SO:0001583	missense	9895	exon7			ATTTCAAGCAGGC	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.1057A>G	14.37:g.102894692A>G	ENSP00000352510:p.Ser353Gly	305	0	0		297	14	0.047138	NM_001172631	A5PKY3|A6NFY9|A7E2X3|H0YMM9|Q9UEG6	Missense_Mutation	SNP	ENST00000359520.7	37	CCDS32162.1	.	.	.	.	.	.	.	.	.	.	a	19.19	3.779964	0.70222	.	.	ENSG00000196663	ENST00000359520;ENST00000380088	T	0.15487	2.42	5.31	5.31	0.75309	.	0.087074	0.85682	D	0.000000	T	0.22475	0.0542	L	0.51422	1.61	0.38609	D	0.950842	P;P	0.49447	0.86;0.924	B;P	0.45167	0.243;0.472	T	0.03933	-1.0991	10	0.56958	D	0.05	.	15.3084	0.74011	1.0:0.0:0.0:0.0	.	353;353	A5PKY3;O15040	.;TCPR2_HUMAN	G	353	ENSP00000352510:S353G	ENSP00000352510:S353G	S	+	1	0	TECPR2	101964445	1.000000	0.71417	0.940000	0.37924	0.997000	0.91878	8.560000	0.90712	2.029000	0.59856	0.472000	0.43445	AGC	.	.	none		0.338	TECPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415056.2	NM_014844		G	102894692	A	G	102894692	3	3	38	1	0	0	0	0	1	0	0	0	15759	72	3	3	1079	3	TECPR2	14	102894692	Missense_Mutation	SNP	A	TCGA-GS-A9TV-01A-11D-A382-10	11011570	102894692	4454848	43	14516											
B2M	567	hgsc.bcm.edu	37	chr15	45003779	45003779	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggccttagctgtgctcgcgcTactctctctttctggcctgg	2	14	11	14	2	3	0	0	0	3	0	5	0	3	0	2	3	3	3	2	3	2	3			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr15:45003779T>C	ENST00000558401.1	+	1	105	c.35T>C	c.(34-36)cTa>cCa	p.L12P	PATL2_ENST00000558573.1_5'Flank|B2M_ENST00000559916.1_Missense_Mutation_p.L12P|B2M_ENST00000544417.1_Missense_Mutation_p.L12P	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	12					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 exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|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 T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|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)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)	p.A11fs*42(1)|p.L12Q(1)		breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		GTGCTCGCGCTACTCTCTCTT	0.617																																					p.L12P		Atlas-SNP	.											B2M,colon,carcinoma,0,2	B2M	99	2	2	Substitution - Missense(1)|Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(2)	c.T35C						PASS	.						132	94	107					15																	45003779		2198	4298	6496	SO:0001583	missense	567	exon1			TCGCGCTACTCTC	AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"Immunoglobulin superfamily / C1-set domain containing"	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.35T>C	15.37:g.45003779T>C	ENSP00000452780:p.Leu12Pro	81	0	0		95	7	0.0736842	NM_004048	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Missense_Mutation	SNP	ENST00000558401.1	37	CCDS10113.1	.	.	.	.	.	.	.	.	.	.	T	17.66	3.443926	0.63067	.	.	ENSG00000166710	ENST00000349264;ENST00000544417;ENST00000396754	T	0.01388	4.95	5.35	5.35	0.76521	.	9.011740	0.00721	U	0.000881	T	0.10809	0.0264	M	0.74647	2.275	0.29321	N	0.867335	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	T	0.17107	-1.0380	10	0.87932	D	0	.	11.9001	0.52678	0.0:0.0:0.0:1.0	.	12;12;12	F5H6I0;A6XMH4;P61769	.;.;B2MG_HUMAN	P	12	ENSP00000437604:L12P	ENSP00000340858:L12P	L	+	2	0	B2M	42791071	0.253000	0.23982	0.051000	0.19133	0.007000	0.05969	3.556000	0.53734	2.371000	0.80710	0.533000	0.62120	CTA	.	.	none		0.617	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048		C	45003779	T	C	45003779	3	2	38	1	0	0	0	0	1	0	0	0	1244	1522	53	3	37	3	B2M	15	45003779	Missense_Mutation	SNP	T	TCGA-GS-A9TV-01A-11D-A382-10		45003779	57527613	44	14517											
UACA	55075	hgsc.bcm.edu	37	chr15	70976724	70976724	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caagcttatatcagcaccatTtttaattaagacttctactg	13	15	4	9	0	2	1	1	0	1	1	2	1	2	1	1	0	3	2	1	0	6	8			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr15:70976724T>C	ENST00000322954.6	-	8	849	c.664A>G	c.(664-666)Aat>Gat	p.N222D	UACA_ENST00000560441.1_Missense_Mutation_p.N209D|UACA_ENST00000559183.1_5'Flank|UACA_ENST00000539319.1_Intron|UACA_ENST00000379983.2_Missense_Mutation_p.N209D	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	222					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						TCAGCACCATTTTTAATTAAG	0.403																																					p.N222D		Atlas-SNP	.											UACA_ENST00000322954,colon,carcinoma,+1,2	UACA	235	2	0			c.A664G						PASS	.						180	172	175					15																	70976724		2199	4297	6496	SO:0001583	missense	55075	exon8			CACCATTTTTAAT	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.664A>G	15.37:g.70976724T>C	ENSP00000314556:p.Asn222Asp	182	0	0		140	7	0.05	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Missense_Mutation	SNP	ENST00000322954.6	37	CCDS10235.1	.	.	.	.	.	.	.	.	.	.	T	19.67	3.870855	0.72065	.	.	ENSG00000137831	ENST00000322954;ENST00000379983;ENST00000395362	T;T	0.64618	-0.11;-0.11	5.4	5.4	0.78164	Ankyrin repeat-containing domain (4);	0.000000	0.64402	D	0.000015	T	0.68604	0.3019	L	0.42744	1.35	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.85130	0.976;0.976;0.997	T	0.65356	-0.6188	10	0.25751	T	0.34	-31.1748	9.4231	0.38563	0.0:0.0794:0.0:0.9206	.	222;222;209	B7ZKM6;Q9BZF9;G3XAG2	.;UACA_HUMAN;.	D	222;209;209	ENSP00000314556:N222D;ENSP00000369319:N209D	ENSP00000314556:N222D	N	-	1	0	UACA	68763778	1.000000	0.71417	0.973000	0.42090	0.995000	0.86356	3.516000	0.53436	2.176000	0.68965	0.379000	0.24179	AAT	.	.	none		0.403	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			C	70976724	T	C	70976724	3	2	38	1	0	0	0	0	1	0	0	0	16839	1841	64	3	3634	3	UACA	15	70976724	Missense_Mutation	SNP	T	TCGA-GS-A9TV-01A-11D-A382-10	25972945	70976724	31554668	45	14518											
ZC3H18	124245	hgsc.bcm.edu	37	chr16	88675458	88675461	+	Splice_Site	DEL	GAGT	GAGT	-																															agagccgtatcataattaccGagtaagtatgacttcaatat																										TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	GAGT	GAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr16:88675458_88675461delGAGT	ENST00000301011.5	+	7	1405_1406	c.1205_1206delGAGT	c.(1204-1206)cga>c	p.R402fs	ZC3H18_ENST00000452588.2_Splice_Site_p.R426fs	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	402						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)		CATAATTACCGAGTAAGTATGACT	0.363																																					p.402_402del	Ovarian(121;375 2276 20373 38669)	Atlas-Indel	.											.	ZC3H18	90	.	0			c.1204_1206del						PASS	.																																			SO:0001630	splice_region_variant	124245	exon7			.	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.1206+1GAGT>-	16.37:g.88675458_88675461delGAGT		167	0	0		131	13	0.0992366	NM_144604	Q96DG4|Q96MP7	In_Frame_Del	DEL	ENST00000301011.5	37	CCDS10967.1																																																																																			.	.	none		0.363	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1	NM_144604	Frame_Shift_Del	-	88675461	GAGT	-	88675458	8	5	38	1	0	1	0	1	0	0	1	0	17583	1072	37	0	1227	0	ZC3H18	16	88675458	Splice_Site	DEL	GAGT	TCGA-GS-A9TV-01A-11D-A382-10		88675458	1679295	46	14519											
COPS3	8533	hgsc.bcm.edu	37	chr17	17163724	17163724	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgtgcttattcaccaggtttCggagttctgaggggttgttg	5	16	14	6	1	2	1	1	1	1	0	3	2	2	2	1	4	1	5	1	4	1	6			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr17:17163724C>T	ENST00000268717.5	-	8	933	c.827G>A	c.(826-828)cGa>cAa	p.R276Q	COPS3_ENST00000539941.2_Missense_Mutation_p.R256Q|COPS3_ENST00000439936.2_Intron	NM_003653.3	NP_003644.2	Q9UNS2	CSN3_HUMAN	COP9 signalosome subunit 3	276	PCI.				cullin deneddylation (GO:0010388)|in utero embryonic development (GO:0001701)|response to light stimulus (GO:0009416)|signal transduction (GO:0007165)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)				NS(1)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	13						CACCAGGTTTCGGAGTTCTGA	0.418																																					p.R276Q		Atlas-SNP	.											.	COPS3	41	.	0			c.G827A						PASS	.						223	186	198					17																	17163724		2203	4300	6503	SO:0001583	missense	8533	exon8			AGGTTTCGGAGTT	AF031647	CCDS11183.1, CCDS56022.1	17p11.2	2013-03-14	2013-03-14		ENSG00000141030	ENSG00000141030			2239	protein-coding gene	gene with protein product		604665	"COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 3", "COP9 constitutive photomorphogenic homolog subunit 3 (Arabidopsis)"			9535219, 10191102	Standard	NM_003653		Approved	SGN3, CSN3	uc002grd.3	Q9UNS2	OTTHUMG00000059281	ENST00000268717.5:c.827G>A	17.37:g.17163724C>T	ENSP00000268717:p.Arg276Gln	173	0	0		173	19	0.109827	NM_003653	B2R683|B4DY81|O43191|Q7LDR6	Missense_Mutation	SNP	ENST00000268717.5	37	CCDS11183.1	.	.	.	.	.	.	.	.	.	.	C	18.01	3.527788	0.64860	.	.	ENSG00000141030	ENST00000268717;ENST00000539941;ENST00000417352	T;T	0.29917	1.55;1.55	5.47	4.5	0.54988	Proteasome component (PCI) domain (1);	0.000000	0.85682	D	0.000000	T	0.22589	0.0545	L	0.35723	1.085	0.80722	D	1	B	0.27853	0.191	B	0.26416	0.069	T	0.03212	-1.1060	10	0.10377	T	0.69	-10.3403	13.1739	0.59615	0.0:0.9235:0.0:0.0765	.	276	Q9UNS2	CSN3_HUMAN	Q	276;256;307	ENSP00000268717:R276Q;ENSP00000437606:R256Q	ENSP00000268717:R276Q	R	-	2	0	COPS3	17104449	1.000000	0.71417	0.994000	0.49952	0.987000	0.75469	7.481000	0.81124	1.306000	0.44926	0.655000	0.94253	CGA	.	.	none		0.418	COPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131603.2			T	17163724	C	T	17163724	3	4	38	1	0	0	0	0	1	0	0	0	3736	884	31	1	464	1	COPS3	17	17163724	Missense_Mutation	SNP	C	TCGA-GS-A9TV-01A-11D-A382-10		17163724	64031486	47	14520											
KRTAP4-7	100132476	hgsc.bcm.edu	37	chr17	39240796	39240796	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcccacctgctgccgccccaGctgctgccgcccctgctgct	2	7	10	22	2	0	0	0	0	0	0	0	0	0	0	8	0	7	5	8	0	0	0	rs553572799|rs199957151	byFrequency	TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr17:39240796G>C	ENST00000391417.4	+	1	338	c.338G>C	c.(337-339)aGc>aCc	p.S113T		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	138	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].		Missing. {ECO:0000269|PubMed:15955084}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.R111_C115delRPSCC(1)|p.?(1)		NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						tgccgccccagctgctgccgc	0.667																																					p.S113T		Atlas-SNP	.											KRTAP4-7,NS,carcinoma,+1,1	KRTAP4-7	49	1	2	Unknown(1)|Deletion - In frame(1)	NS(2)	c.G338C						scavenged	.																																			SO:0001583	missense	100132476	exon1			GCCCCAGCTGCTG	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.338G>C	17.37:g.39240796G>C	ENSP00000375236:p.Ser113Thr	11	0	0		33	4	0.121212	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	0.047	-1.263726	0.01433	.	.	ENSG00000240871	ENST00000391417	T	0.00627	6.12	2.73	1.66	0.24008	.	2.038930	0.02697	N	0.111300	T	0.00552	0.0018	.	.	.	0.21290	N	0.999731	B	0.13145	0.007	B	0.12837	0.008	T	0.47222	-0.9134	9	0.17832	T	0.49	.	5.1702	0.15107	0.0:0.2319:0.5315:0.2367	.	168	Q9BYR0	KRA47_HUMAN	T	113	ENSP00000375236:S113T	ENSP00000375236:S113T	S	+	2	0	KRTAP4-7	36494322	0.010000	0.17322	0.067000	0.19924	0.024000	0.10985	-0.517000	0.06275	0.191000	0.20236	0.289000	0.19496	AGC	.	.	weak		0.667	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1			C	39240796	G	C	39240796	3	2	38	1	0	0	0	0	1	0	0	0	8564	971	34	4	340	4	KRTAP4-7	17	39240796	Missense_Mutation	SNP	G	TCGA-GS-A9TV-01A-11D-A382-10	22077072	39240796	41954414	48	14521											
ANKRD30B	374860	hgsc.bcm.edu	37	chr18	14797834	14797834	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagccttagaattaaaggaCagagaaacactcaaagcagg	20	5	9	7	0	1	2	1	0	0	2	1	4	1	3	1	2	3	1	1	2	7	2			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr18:14797834C>T	ENST00000358984.4	+	20	2190	c.2010C>T	c.(2008-2010)gaC>gaT	p.D670D	ANKRD30B_ENST00000579292.1_3'UTR	NM_001145029.1	NP_001138501.1	Q9BXX2	AN30B_HUMAN	ankyrin repeat domain 30B	670										breast(3)|endometrium(4)|kidney(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	22						AATTAAAGGACAGAGAAACAC	0.308																																					p.D670D		Atlas-SNP	.											.	ANKRD30B	237	.	0			c.C2010T						PASS	.						60	47	51					18																	14797834		692	1587	2279	SO:0001819	synonymous_variant	374860	exon20			AAAGGACAGAGAA	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.2010C>T	18.37:g.14797834C>T		281	0	0		258	19	0.0736434	NM_001145029	B4DGP1|F8WAG3|Q4G175	Silent	SNP	ENST00000358984.4	37	CCDS54182.1																																																																																			.	.	none		0.308	ANKRD30B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443557.1	NM_001145029		T	14797834	C	T	14797834	2	4	38	1	0	0	0	0	0	0	0	1	659	477	17	2		2	ANKRD30B	18	14797834	Silent	SNP	C	TCGA-GS-A9TV-01A-11D-A382-10		14797834	63279414	49	14522											
ASXL3	80816	hgsc.bcm.edu	37	chr18	31326209	31326209	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgctttctgagccacaaaagCcttttacccaattagctgct	10	13	6	12	0	1	1	0	1	1	0	1	1	1	1	3	0	6	3	3	0	5	4			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr18:31326209C>T	ENST00000269197.5	+	12	6397	c.6397C>T	c.(6397-6399)Cct>Tct	p.P2133S		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	2133					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						GCCACAAAAGCCTTTTACCCA	0.398																																					p.P2133S		Atlas-SNP	.											.	ASXL3	405	.	0			c.C6397T						PASS	.						82	87	85					18																	31326209		1892	4117	6009	SO:0001583	missense	80816	exon12			CAAAAGCCTTTTA	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.6397C>T	18.37:g.31326209C>T	ENSP00000269197:p.Pro2133Ser	164	0	0		110	7	0.0636364	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Missense_Mutation	SNP	ENST00000269197.5	37	CCDS45847.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.938029	0.73557	.	.	ENSG00000141431	ENST00000269197	T	0.15718	2.4	6.17	6.17	0.99709	.	.	.	.	.	T	0.23965	0.0580	N	0.24115	0.695	0.52501	D	0.999954	D	0.59767	0.986	P	0.55615	0.78	T	0.01363	-1.1374	9	0.17369	T	0.5	.	20.8794	0.99867	0.0:1.0:0.0:0.0	.	2133	Q9C0F0	ASXL3_HUMAN	S	2133	ENSP00000269197:P2133S	ENSP00000269197:P2133S	P	+	1	0	ASXL3	29580207	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.078000	0.57606	2.941000	0.99782	0.655000	0.94253	CCT	.	.	none		0.398	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2			T	31326209	C	T	31326209	3	4	38	1	0	0	0	0	1	0	0	0	1068	739	26	2	6443	2	ASXL3	18	31326209	Missense_Mutation	SNP	C	TCGA-GS-A9TV-01A-11D-A382-10	16528375	31326209	46751039	50	14523											
ZNF607	84775	hgsc.bcm.edu	37	chr19	38189064	38189064	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtatactaagttcatggctActattaaaagctttcccaca	13	14	5	9	0	1	0	1	0	0	0	2	0	2	0	1	1	3	4	1	1	7	8			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr19:38189064A>C	ENST00000355202.4	-	5	2563	c.1968T>G	c.(1966-1968)agT>agG	p.S656R	ZNF607_ENST00000395835.3_Missense_Mutation_p.S655R|CTD-2528L19.4_ENST00000586606.2_Intron	NM_032689.4	NP_116078.4	Q96SK3	ZN607_HUMAN	zinc finger protein 607	656					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)			GTTCATGGCTACTATTAAAAG	0.393																																					p.S656R		Atlas-SNP	.											.	ZNF607	82	.	0			c.T1968G						PASS	.						106	103	104					19																	38189064		2203	4300	6503	SO:0001583	missense	84775	exon5			ATGGCTACTATTA	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.1968T>G	19.37:g.38189064A>C	ENSP00000347338:p.Ser656Arg	206	0	0		188	8	0.0425532	NM_032689	F5H141|Q6ZMN2|Q6ZMN4|Q96C40	Missense_Mutation	SNP	ENST00000355202.4	37	CCDS33006.1	.	.	.	.	.	.	.	.	.	.	A	7.766	0.706483	0.15239	.	.	ENSG00000198182	ENST00000355202;ENST00000395835	T;T	0.28069	1.63;1.63	1.83	-3.66	0.04489	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11623	0.0283	N	0.11698	0.16	0.09310	N	1	B;B	0.26081	0.141;0.068	B;B	0.29077	0.098;0.062	T	0.26395	-1.0104	9	0.12430	T	0.62	.	0.6026	0.00747	0.2396:0.2281:0.3116:0.2206	.	656;655	Q96SK3;F5H141	ZN607_HUMAN;.	R	656;655	ENSP00000347338:S656R;ENSP00000438015:S655R	ENSP00000347338:S656R	S	-	3	2	ZNF607	42880904	0.000000	0.05858	0.000000	0.03702	0.929000	0.56500	-1.367000	0.02583	-2.253000	0.00698	0.260000	0.18958	AGT	.	.	none		0.393	ZNF607-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459502.2	NM_032689		C	38189064	A	C	38189064	3	2	38	1	0	0	0	0	1	0	0	0	18048	388	14	5	126	5	ZNF607	19	38189064	Missense_Mutation	SNP	A	TCGA-GS-A9TV-01A-11D-A382-10		38189064	20939919	51	14524											
PLCB1	23236	hgsc.bcm.edu	37	chr20	8352096	8352096	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagacacgccaaagctcccaAggtaggaggttgagtgttgt	11	8	14	8	1	0	2	0	1	0	1	1	4	1	3	2	3	1	4	2	3	3	3			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr20:8352096A>C	ENST00000338037.6	+	3	272	c.245A>C	c.(244-246)aAg>aCg	p.K82T	PLCB1_ENST00000378641.3_Splice_Site_p.K82T|PLCB1_ENST00000378637.2_Splice_Site_p.K82T	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	82					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.K82T(2)		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						AAAGCTCCCAAGGTAGGAGGT	0.448																																					p.E82A		Atlas-SNP	.											PLCB1_ENST00000378641,caecum,carcinoma,0,2	PLCB1	394	2	2	Substitution - Missense(2)	large_intestine(2)	c.A245C						PASS	.						157	127	137					20																	8352096		2203	4300	6503	SO:0001630	splice_region_variant	23236	exon3			CTCCCAAGGTAGG	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.246+1A>C	20.37:g.8352096A>C		82	0	0		86	5	0.0581395	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Missense_Mutation	SNP	ENST00000338037.6	37	CCDS13102.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.337731	0.81911	.	.	ENSG00000182621	ENST00000378641;ENST00000338037;ENST00000378637;ENST00000404098	T;T;T;T	0.55234	0.53;0.53;0.53;0.53	5.52	5.52	0.82312	.	0.058303	0.64402	D	0.000004	T	0.75774	0.3895	M	0.88979	2.995	0.80722	D	1	B;D;D	0.63880	0.048;0.993;0.993	B;P;D	0.74023	0.034;0.849;0.982	T	0.80830	-0.1207	10	0.87932	D	0	.	13.4657	0.61251	1.0:0.0:0.0:0.0	.	82;82;81	Q9NQ66;Q9NQ66-2;B1AK73	PLCB1_HUMAN;.;.	T	82;82;82;81	ENSP00000367908:K82T;ENSP00000338185:K82T;ENSP00000367904:K82T;ENSP00000384001:K81T	ENSP00000338185:K82T	K	+	2	0	PLCB1	8300096	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.240000	0.65378	2.216000	0.71823	0.533000	0.62120	AAG	.	.	none		0.448	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3		Missense_Mutation	C	8352096	A	C	8352096	5	2	38	1	0	0	0	0	0	0	1	0	12036	86	3	5	255	5	PLCB1	20	8352096	Splice_Site	SNP	A	TCGA-GS-A9TV-01A-11D-A382-10		8352096	54673424	52	14525											
ZNF217	7764	hgsc.bcm.edu	37	chr20	52193210	52193210	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttttactcaaagaaattgccGggcaattgtgaagagccccc	12	10	9	10	1	1	3	1	1	0	2	1	3	1	3	3	1	3	1	3	1	5	4	rs369074794		TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr20:52193210G>A	ENST00000371471.2	-	4	2518	c.2093C>T	c.(2092-2094)cCg>cTg	p.P698L	RP4-724E16.2_ENST00000424252.1_RNA|ZNF217_ENST00000302342.3_Missense_Mutation_p.P698L			O75362	ZN217_HUMAN	zinc finger protein 217	698					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)	p.P698Q(2)		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)			AGAAATTGCCGGGCAATTGTG	0.428																																					p.P698L		Atlas-SNP	.											.	ZNF217	227	.	2	Substitution - Missense(2)	lung(2)	c.C2093T						PASS	.	G	LEU/PRO	0,4406		0,0,2203	74	83	80		2093	4.2	0	20		80	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZNF217	NM_006526.2	98	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	698/1049	52193210	1,13005	2203	4300	6503	SO:0001583	missense	7764	exon3			ATTGCCGGGCAAT	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.2093C>T	20.37:g.52193210G>A	ENSP00000360526:p.Pro698Leu	174	0	0		160	18	0.1125	NM_006526	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	37	CCDS13443.1	.	.	.	.	.	.	.	.	.	.	G	10.50	1.366604	0.24771	0.0	1.16E-4	ENSG00000171940	ENST00000371471;ENST00000302342	T;T	0.08984	3.03;3.03	5.18	4.22	0.49857	.	0.790776	0.11324	N	0.575710	T	0.06735	0.0172	L	0.34521	1.04	0.20196	N	0.999922	B	0.18166	0.026	B	0.08055	0.003	T	0.34378	-0.9831	10	0.10636	T	0.68	-6.4731	10.3081	0.43693	0.1521:0.0:0.8479:0.0	.	698	O75362	ZN217_HUMAN	L	698	ENSP00000360526:P698L;ENSP00000304308:P698L	ENSP00000304308:P698L	P	-	2	0	ZNF217	51626617	0.963000	0.33076	0.029000	0.17559	0.089000	0.18198	3.870000	0.56070	2.411000	0.81874	0.555000	0.69702	CCG	.	.	weak		0.428	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		A	52193210	G	A	52193210	3	1	38	1	0	0	0	0	1	0	0	0	17787	1116	39	1	1061	1	ZNF217	20	52193210	Missense_Mutation	SNP	G	TCGA-GS-A9TV-01A-11D-A382-10	43841114	52193210	10832310	53	14526			1	64		3	3	5274	N	T_G	7.457772e-05
ZNF217	7764	hgsc.bcm.edu	37	chr20	52198348	52198348	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgcgagaggcctgcacaacTgcccttatttgtttctccaa	8	13	8	12	1	1	1	0	0	1	1	2	2	1	1	3	1	4	2	3	1	3	4			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr20:52198348T>A	ENST00000371471.2	-	2	1443	c.1018A>T	c.(1018-1020)Agt>Tgt	p.S340C	ZNF217_ENST00000540425.1_5'Flank|ZNF217_ENST00000302342.3_Missense_Mutation_p.S340C			O75362	ZN217_HUMAN	zinc finger protein 217	340					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)			CCTGCACAACTGCCCTTATTT	0.542																																					p.S340C		Atlas-SNP	.											.	ZNF217	227	.	0			c.A1018T						PASS	.						126	128	128					20																	52198348		2203	4300	6503	SO:0001583	missense	7764	exon1			CACAACTGCCCTT	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.1018A>T	20.37:g.52198348T>A	ENSP00000360526:p.Ser340Cys	221	0	0		259	24	0.0926641	NM_006526	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	37	CCDS13443.1	.	.	.	.	.	.	.	.	.	.	T	8.872	0.949551	0.18356	.	.	ENSG00000171940	ENST00000371471;ENST00000302342	T;T	0.10099	2.91;2.91	5.7	0.987	0.19790	.	0.778438	0.12010	N	0.507981	T	0.09686	0.0238	L	0.40543	1.245	0.09310	N	1	P	0.47106	0.89	B	0.40101	0.319	T	0.18935	-1.0321	10	0.66056	D	0.02	-9.5155	9.5173	0.39113	0.0:0.5469:0.0:0.4531	.	340	O75362	ZN217_HUMAN	C	340	ENSP00000360526:S340C;ENSP00000304308:S340C	ENSP00000304308:S340C	S	-	1	0	ZNF217	51631755	0.000000	0.05858	0.000000	0.03702	0.093000	0.18481	0.015000	0.13355	-0.056000	0.13221	-0.376000	0.06991	AGT	.	.	none		0.542	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		A	52198348	T	A	52198348	3	1	38	1	0	0	0	0	1	0	0	0	17787	1580	55	5	2144	5	ZNF217	20	52198348	Missense_Mutation	SNP	T	TCGA-GS-A9TV-01A-11D-A382-10	5138	52198348	10827172	54	14527			1	64		3	3	5274	N	T_G	7.457772e-05
ZNF217	7764	hgsc.bcm.edu	37	chr20	52198483	52198483	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagctgccaagcctggaaggTggtgaacggatcgagctgag	10	6	16	9	2	0	2	0	2	0	0	1	5	0	4	2	4	5	2	2	4	3	0			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr20:52198483T>G	ENST00000371471.2	-	2	1308	c.883A>C	c.(883-885)Acc>Ccc	p.T295P	ZNF217_ENST00000540425.1_5'Flank|ZNF217_ENST00000302342.3_Missense_Mutation_p.T295P			O75362	ZN217_HUMAN	zinc finger protein 217	295					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)			GCCTGGAAGGTGGTGAACGGA	0.532																																					p.T295P		Atlas-SNP	.											.	ZNF217	227	.	0			c.A883C						PASS	.						122	114	117					20																	52198483		2203	4300	6503	SO:0001583	missense	7764	exon1			GGAAGGTGGTGAA	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.883A>C	20.37:g.52198483T>G	ENSP00000360526:p.Thr295Pro	172	0	0		155	10	0.0645161	NM_006526	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	37	CCDS13443.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.386055	0.82902	.	.	ENSG00000171940	ENST00000371471;ENST00000302342	T;T	0.10382	2.88;2.88	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.35008	0.0917	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.06092	-1.0846	10	0.49607	T	0.09	-39.6624	15.6258	0.76855	0.0:0.0:0.0:1.0	.	295	O75362	ZN217_HUMAN	P	295	ENSP00000360526:T295P;ENSP00000304308:T295P	ENSP00000304308:T295P	T	-	1	0	ZNF217	51631890	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	7.585000	0.82584	2.170000	0.68504	0.482000	0.46254	ACC	.	.	none		0.532	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		G	52198483	T	G	52198483	3	3	38	1	0	0	0	0	1	0	0	0	17787	1696	59	5	2279	5	ZNF217	20	52198483	Missense_Mutation	SNP	T	TCGA-GS-A9TV-01A-11D-A382-10	135	52198483	10827037	55	14528			1	64		3	3	5274	N	T_G	7.457772e-05
ADRM1	11047	hgsc.bcm.edu	37	chr20	60878686	60878686	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctctcggggcgcctccaacaAgtacttggtggagtttcggg	6	10	14	11	3	1	0	0	0	1	0	4	1	2	1	2	5	2	2	2	5	3	3			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr20:60878686A>G	ENST00000253003.2	+	2	108	c.62A>G	c.(61-63)aAg>aGg	p.K21R	RP11-157P1.4_ENST00000414042.1_RNA|ADRM1_ENST00000462554.1_3'UTR	NM_007002.2|NM_175573.1	NP_008933.2|NP_783163.1	Q16186	ADRM1_HUMAN	adhesion regulating molecule 1	21	Interaction with PSMD1.				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)			GCCTCCAACAAGTACTTGGTG	0.622																																					p.K21R		Atlas-SNP	.											.	ADRM1	28	.	0			c.A62G						PASS	.						78	86	83					20																	60878686		2203	4299	6502	SO:0001583	missense	11047	exon2			CCAACAAGTACTT	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.62A>G	20.37:g.60878686A>G	ENSP00000253003:p.Lys21Arg	30	0	0		35	6	0.171429	NM_175573	A0PKB1|Q96FJ7|Q9H1P2	Missense_Mutation	SNP	ENST00000253003.2	37	CCDS13496.1	.	.	.	.	.	.	.	.	.	.	A	19.48	3.834980	0.71373	.	.	ENSG00000130706	ENST00000370744;ENST00000253003	.	.	.	4.62	4.62	0.57501	.	0.000000	0.85682	D	0.000000	T	0.65637	0.2710	L	0.41632	1.29	0.80722	D	1	B;P	0.48350	0.018;0.909	B;D	0.63957	0.046;0.92	T	0.64622	-0.6364	9	0.39692	T	0.17	-25.6551	13.6872	0.62524	1.0:0.0:0.0:0.0	.	21;21	B4DMP7;Q16186	.;ADRM1_HUMAN	R	21	.	ENSP00000253003:K21R	K	+	2	0	ADRM1	60312081	1.000000	0.71417	0.998000	0.56505	0.767000	0.43475	7.101000	0.76997	1.707000	0.51288	0.459000	0.35465	AAG	.	.	none		0.622	ADRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080007.1			G	60878686	A	G	60878686	3	3	38	1	0	0	0	0	1	0	0	0	345	72	3	3	64	3	ADRM1	20	60878686	Missense_Mutation	SNP	A	TCGA-GS-A9TV-01A-11D-A382-10	8680203	60878686	2146834	56	14529			2	65	8680203	2	2	31	N	T_A	6.977236e-05
ADRM1	11047	hgsc.bcm.edu	37	chr20	60878716	60878716	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagtttcgggcgggaaagaTgtccctgaaggggaccaccg	9	6	17	9	3	0	2	0	1	0	1	2	5	1	5	3	5	0	1	3	5	2	1			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr20:60878716T>G	ENST00000253003.2	+	2	138	c.92T>G	c.(91-93)aTg>aGg	p.M31R	RP11-157P1.4_ENST00000414042.1_RNA|ADRM1_ENST00000462554.1_3'UTR	NM_007002.2|NM_175573.1	NP_008933.2|NP_783163.1	Q16186	ADRM1_HUMAN	adhesion regulating molecule 1	31	Interaction with PSMD1.|PH.				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)			GCGGGAAAGATGTCCCTGAAG	0.587																																					p.M31R		Atlas-SNP	.											.	ADRM1	28	.	0			c.T92G						PASS	.						79	84	82					20																	60878716		2203	4300	6503	SO:0001583	missense	11047	exon2			GAAAGATGTCCCT	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.92T>G	20.37:g.60878716T>G	ENSP00000253003:p.Met31Arg	36	0	0		37	7	0.189189	NM_175573	A0PKB1|Q96FJ7|Q9H1P2	Missense_Mutation	SNP	ENST00000253003.2	37	CCDS13496.1	.	.	.	.	.	.	.	.	.	.	T	19.55	3.849175	0.71603	.	.	ENSG00000130706	ENST00000370744;ENST00000253003	.	.	.	4.62	4.62	0.57501	.	0.000000	0.85682	D	0.000000	D	0.84051	0.5387	M	0.90145	3.09	0.80722	D	1	D;P	0.65815	0.995;0.935	D;D	0.76575	0.988;0.971	D	0.87579	0.2483	9	0.87932	D	0	-22.7347	13.6872	0.62524	0.0:0.0:0.0:1.0	.	31;31	B4DMP7;Q16186	.;ADRM1_HUMAN	R	31	.	ENSP00000253003:M31R	M	+	2	0	ADRM1	60312111	1.000000	0.71417	0.999000	0.59377	0.825000	0.46686	7.676000	0.84012	1.707000	0.51288	0.459000	0.35465	ATG	.	.	none		0.587	ADRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080007.1			G	60878716	T	G	60878716	3	3	38	1	0	0	0	0	1	0	0	0	345	1464	51	5	94	5	ADRM1	20	60878716	Missense_Mutation	SNP	T	TCGA-GS-A9TV-01A-11D-A382-10	30	60878716	2146804	57	14530			2	65	8680203	2	2	31	N	T_A	6.977236e-05
SIM2	6493	hgsc.bcm.edu	37	chr21	38072069	38072069	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaaggagaagtccaagaatgCggccaagaccaggagggaga	16	2	16	7	1	0	4	0	0	0	4	1	8	1	5	3	4	1	0	3	4	5	0			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chr21:38072069C>T	ENST00000290399.6	+	1	636	c.23C>T	c.(22-24)gCg>gTg	p.A8V	SIM2_ENST00000430056.3_Missense_Mutation_p.A8V|SIM2_ENST00000460783.1_3'UTR|AP000697.6_ENST00000430607.1_RNA	NM_005069.3	NP_005060.1	Q14190	SIM2_HUMAN	single-minded family bHLH transcription factor 2	8	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				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						TCCAAGAATGCGGCCAAGACC	0.657																																					p.A8V		Atlas-SNP	.											.	SIM2	55	.	0			c.C23T						PASS	.						120	94	103					21																	38072069		2202	4300	6502	SO:0001583	missense	6493	exon1			AGAATGCGGCCAA		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.23C>T	21.37:g.38072069C>T	ENSP00000290399:p.Ala8Val	105	0	0		92	5	0.0543478	NM_005069	O60766|Q15470|Q15471|Q15472|Q15473|Q16532|Q2TBD8	Missense_Mutation	SNP	ENST00000290399.6	37	CCDS13646.1	.	.	.	.	.	.	.	.	.	.	C	33	5.244806	0.95272	.	.	ENSG00000159263	ENST00000290399;ENST00000430056	T;D	0.97850	2.88;-4.57	4.41	3.52	0.40303	Helix-loop-helix DNA-binding (4);	0.056007	0.64402	N	0.000001	D	0.98836	0.9607	M	0.92367	3.3	0.53688	D	0.999979	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.99449	1.0940	10	0.87932	D	0	.	12.3321	0.55046	0.0:0.9181:0.0:0.0819	.	8;8	Q14190;Q14190-2	SIM2_HUMAN;.	V	8	ENSP00000290399:A8V;ENSP00000404176:A8V	ENSP00000290399:A8V	A	+	2	0	SIM2	36993939	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.443000	0.80521	1.084000	0.41184	0.563000	0.77884	GCG	.	.	none		0.657	SIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194692.1	NM_009586		T	38072069	C	T	38072069	3	4	38	1	0	0	0	0	1	0	0	0	14339	768	27	1	25	1	SIM2	21	38072069	Missense_Mutation	SNP	C	TCGA-GS-A9TV-01A-11D-A382-10		38072069	10057826	58	14531											
TMSB4X	7114	hgsc.bcm.edu	37	chrX	12994394	12994394	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cgcaaccatgtctgacaaacCcgatatggctgagatcgaga	13	7	10	11	3	1	3	0	2	1	2	2	6	1	3	2	1	2	2	2	1	3	1			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:12994394C>G	ENST00000380635.1	+	2	230	c.14C>G	c.(13-15)cCc>cGc	p.P5R	TMSB4X_ENST00000380633.1_Missense_Mutation_p.P5R|TMSB4X_ENST00000380636.1_Missense_Mutation_p.P5R|TMSB4X_ENST00000451311.2_Missense_Mutation_p.P5R			P62328	TYB4_HUMAN	thymosin beta 4, X-linked	5					actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|sequestering of actin monomers (GO:0042989)	cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	poly(A) RNA binding (GO:0044822)			upper_aerodigestive_tract(1)	1						TCTGACAAACCCGATATGGCT	0.542																																					p.P5R		Atlas-SNP	.											.	TMSB4X	3	.	0			c.C14G						PASS	.						66	64	65					X																	12994394		2203	4300	6503	SO:0001583	missense	7114	exon2			ACAAACCCGATAT		CCDS35202.1	Xp22.2	2013-05-14	2008-02-25		ENSG00000205542	ENSG00000205542			11881	protein-coding gene	gene with protein product		300159	"thymosin, beta 4, X chromosome"	TMSB4		2677145, 9381176	Standard	NM_021109		Approved	TB4X	uc004cvf.3	P62328	OTTHUMG00000021144	ENST00000380635.1:c.14C>G	X.37:g.12994394C>G	ENSP00000370009:p.Pro5Arg	348	0	0		323	20	0.0619195	NM_021109	P01253|P01254|Q546P5|Q63576|Q9UE55	Missense_Mutation	SNP	ENST00000380635.1	37	CCDS35202.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.023167	0.75275	.	.	ENSG00000205542	ENST00000451311;ENST00000380636;ENST00000380635;ENST00000380633	T;T;T;T	0.61510	0.1;0.1;0.1;0.1	4.66	4.66	0.58398	.	0.000000	0.64402	U	0.000010	T	0.68476	0.3005	.	.	.	0.58432	D	0.99999	P	0.49307	0.922	P	0.51895	0.683	T	0.74685	-0.3582	9	0.87932	D	0	-6.1801	16.7451	0.85470	0.0:1.0:0.0:0.0	.	5	P62328	TYB4_HUMAN	R	5	ENSP00000414376:P5R;ENSP00000370010:P5R;ENSP00000370009:P5R;ENSP00000370007:P5R	ENSP00000370007:P5R	P	+	2	0	TMSB4X	12904315	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.929000	0.75852	2.064000	0.61679	0.600000	0.82982	CCC	.	.	none		0.542	TMSB4X-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000055779.1	NM_021109		G	12994394	C	G	12994394	3	3	38	1	0	0	0	0	1	0	0	0	16272	623	22	4	16	4	TMSB4X	23	12994394	Missense_Mutation	SNP	C	TCGA-GS-A9TV-01A-11D-A382-10		12994394	142276166	59	14532											
DCAF8L2	347442	hgsc.bcm.edu	37	chrX	27766417	27766417	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gatttaagggacacagaaatAataccacagtcaaaggtgtt	17	9	9	6	0	1	1	1	0	0	1	1	3	1	2	1	2	1	1	1	2	5	5			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:27766417A>G	ENST00000451261.2	+	5	1804	c.1405A>G	c.(1405-1407)Aat>Gat	p.N469D		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	469										central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						ACACAGAAATAATACCACAGT	0.443																																					p.N469D		Atlas-SNP	.											.	DCAF8L2	79	.	0			c.A1405G						PASS	.						84	56	65					X																	27766417		692	1591	2283	SO:0001583	missense	347442	exon1			AGAAATAATACCA		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.1405A>G	X.37:g.27766417A>G	ENSP00000462745:p.Asn469Asp	265	0	0		227	14	0.061674	NM_001136533	B2RXH9|J3KT06	Missense_Mutation	SNP	ENST00000451261.2	37	CCDS59162.1																																																																																			.	.	none		0.443	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354		G	27766417	A	G	27766417	3	3	38	1	0	0	0	0	1	0	0	0	4280	362	13	3	1407	3	DCAF8L2	23	27766417	Missense_Mutation	SNP	A	TCGA-GS-A9TV-01A-11D-A382-10	14772023	27766417	127504143	60	14533											
GPR82	27197	hgsc.bcm.edu	37	chrX	41586752	41586752	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgctagaaaactatgcatttAcatatggggagttgtactgg	12	13	11	5	0	0	1	0	0	0	1	0	2	0	2	0	3	5	4	0	3	7	7			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:41586752A>C	ENST00000302548.4	+	3	713	c.473A>C	c.(472-474)tAc>tCc	p.Y158S	CASK_ENST00000378163.1_Intron|CASK_ENST00000318588.9_Intron|CASK_ENST00000378166.4_Intron|CASK_ENST00000378158.1_Intron|CASK_ENST00000421587.2_Intron|CASK_ENST00000378154.1_Intron|CASK_ENST00000361962.4_Intron|CASK_ENST00000442742.2_Intron	NM_080817.4	NP_543007.1	Q96P67	GPR82_HUMAN	G protein-coupled receptor 82	158						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						CTATGCATTTACATATGGGGA	0.408																																					p.Y158S		Atlas-SNP	.											.	GPR82	52	.	0			c.A473C						PASS	.						59	58	58					X																	41586752		2202	4299	6501	SO:0001583	missense	27197	exon3			GCATTTACATATG	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.473A>C	X.37:g.41586752A>C	ENSP00000303549:p.Tyr158Ser	228	0	0		208	18	0.0865385	NM_080817	Q5VT13	Missense_Mutation	SNP	ENST00000302548.4	37	CCDS14259.1	.	.	.	.	.	.	.	.	.	.	A	4.819	0.152221	0.09185	.	.	ENSG00000171657	ENST00000302548	T	0.36340	1.26	5.73	2.98	0.34508	GPCR, rhodopsin-like superfamily (1);	0.469762	0.19219	N	0.119739	T	0.33411	0.0862	L	0.34521	1.04	0.09310	N	1	P	0.51933	0.949	P	0.54815	0.761	T	0.08289	-1.0729	10	0.22706	T	0.39	-4.4926	4.8507	0.13535	0.5399:0.0:0.0899:0.3702	.	158	Q96P67	GPR82_HUMAN	S	158	ENSP00000303549:Y158S	ENSP00000303549:Y158S	Y	+	2	0	GPR82	41471696	0.014000	0.17966	0.138000	0.22173	0.818000	0.46254	0.717000	0.25851	0.766000	0.33244	0.486000	0.48141	TAC	.	.	none		0.408	GPR82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056261.1	NM_080817		C	41586752	A	C	41586752	3	2	38	1	0	0	0	0	1	0	0	0	6720	391	14	5	475	5	GPR82	23	41586752	Missense_Mutation	SNP	A	TCGA-GS-A9TV-01A-11D-A382-10	13820335	41586752	113683808	61	14534			3	66		2	2	24	A		5.349258e-05
GPR82	27197	hgsc.bcm.edu	37	chrX	41586775	41586775	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatggggagttgtactgggcAtaatcattccagttaccgta	10	13	11	7	1	1	0	1	0	0	0	2	1	2	1	2	3	2	5	2	3	5	7			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:41586775A>G	ENST00000302548.4	+	3	736	c.496A>G	c.(496-498)Ata>Gta	p.I166V	CASK_ENST00000378163.1_Intron|CASK_ENST00000318588.9_Intron|CASK_ENST00000378166.4_Intron|CASK_ENST00000378158.1_Intron|CASK_ENST00000421587.2_Intron|CASK_ENST00000378154.1_Intron|CASK_ENST00000361962.4_Intron|CASK_ENST00000442742.2_Intron	NM_080817.4	NP_543007.1	Q96P67	GPR82_HUMAN	G protein-coupled receptor 82	166						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						TGTACTGGGCATAATCATTCC	0.408																																					p.I166V		Atlas-SNP	.											.	GPR82	52	.	0			c.A496G						PASS	.						69	67	67					X																	41586775		2203	4300	6503	SO:0001583	missense	27197	exon3			CTGGGCATAATCA	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.496A>G	X.37:g.41586775A>G	ENSP00000303549:p.Ile166Val	216	0	0		192	16	0.0833333	NM_080817	Q5VT13	Missense_Mutation	SNP	ENST00000302548.4	37	CCDS14259.1	.	.	.	.	.	.	.	.	.	.	A	0.372	-0.933289	0.02359	.	.	ENSG00000171657	ENST00000302548	T	0.72051	-0.62	5.62	-6.3	0.02007	GPCR, rhodopsin-like superfamily (1);	0.298098	0.25604	N	0.029527	T	0.35770	0.0943	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46965	-0.9153	10	0.02654	T	1	-6.7524	9.1887	0.37187	0.2148:0.3218:0.4634:0.0	.	166	Q96P67	GPR82_HUMAN	V	166	ENSP00000303549:I166V	ENSP00000303549:I166V	I	+	1	0	GPR82	41471719	0.000000	0.05858	0.015000	0.15790	0.245000	0.25701	-2.276000	0.01161	-1.138000	0.02884	-0.314000	0.08810	ATA	.	.	none		0.408	GPR82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056261.1	NM_080817		G	41586775	A	G	41586775	3	3	38	1	0	0	0	0	1	0	0	0	6720	217	8	3	498	3	GPR82	23	41586775	Missense_Mutation	SNP	A	TCGA-GS-A9TV-01A-11D-A382-10	23	41586775	113683785	62	14535			3	66		2	2	24	A		5.349258e-05
RBM10	8241	hgsc.bcm.edu	37	chrX	47045745	47045745	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgggctggaaagagggcagcGgcctgggccgcaagaagcag	10	3	19	9	2	0	2	0	0	0	2	0	3	0	3	2	5	2	4	2	5	3	0			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:47045745G>A	ENST00000377604.3	+	23	3368	c.2626G>A	c.(2626-2628)Ggc>Agc	p.G876S	RBM10_ENST00000329236.7_Missense_Mutation_p.G798S|RBM10_ENST00000345781.6_Missense_Mutation_p.G799S	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	876	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.				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						AGAGGGCAGCGGCCTGGGCCG	0.647																																					p.G941S	Melanoma(171;120 2705 19495 39241)	Atlas-SNP	.											.	RBM10	117	.	0			c.G2821A						PASS	.						56	53	54					X																	47045745		2199	4292	6491	SO:0001583	missense	8241	exon23			GGCAGCGGCCTGG	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.2626G>A	X.37:g.47045745G>A	ENSP00000366829:p.Gly876Ser	167	0	0		204	16	0.0784314	NM_001204468	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Missense_Mutation	SNP	ENST00000377604.3	37	CCDS14274.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.006668	0.93287	.	.	ENSG00000182872	ENST00000377604;ENST00000329236;ENST00000345781	T;T;T	0.80994	-1.44;-1.44;-1.44	5.53	5.53	0.82687	D111/G-patch (3);	0.000000	0.56097	D	0.000033	D	0.91442	0.7299	M	0.90425	3.115	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	0.999;1.0;1.0;0.999;0.998	D	0.93001	0.6423	10	0.87932	D	0	-22.4447	16.0209	0.80493	0.0:0.0:1.0:0.0	.	799;941;875;798;876	P98175-3;Q7Z3D7;P98175-2;P98175-4;P98175	.;.;.;.;RBM10_HUMAN	S	876;798;799	ENSP00000366829:G876S;ENSP00000328848:G798S;ENSP00000329659:G799S	ENSP00000328848:G798S	G	+	1	0	RBM10	46930689	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.359000	0.97115	2.471000	0.83476	0.600000	0.82982	GGC	.	.	none		0.647	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676		A	47045745	G	A	47045745	3	1	38	1	0	0	0	0	1	0	0	0	13126	1116	39	1	2712	1	RBM10	23	47045745	Missense_Mutation	SNP	G	TCGA-GS-A9TV-01A-11D-A382-10	5458970	47045745	108224815	63	14536											
FAM123B	139285	hgsc.bcm.edu	37	chrX	63412763	63412763	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tggagcctgtctccaaagccCcatgggcactctgagagctg	8	8	12	13	0	2	1	0	1	2	1	3	3	2	2	4	2	3	2	4	2	1	0			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:63412763C>A	ENST00000330258.3	-	2	676	c.404G>T	c.(403-405)gGg>gTg	p.G135V	AMER1_ENST00000374869.3_Missense_Mutation_p.G135V|AMER1_ENST00000403336.1_Missense_Mutation_p.G135V	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	135					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)									CTCCAAAGCCCCATGGGCACT	0.547																																					p.G135V		Atlas-SNP	.											.	.	.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.G404T						PASS	.						52	48	49					X																	63412763		2203	4300	6503	SO:0001583	missense	139285	exon2			AAAGCCCCATGGG	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.404G>T	X.37:g.63412763C>A	ENSP00000329117:p.Gly135Val	146	0	0		125	10	0.08	NM_152424	A2IB86|Q8N885	Missense_Mutation	SNP	ENST00000330258.3	37	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	C	9.805	1.181715	0.21787	.	.	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	T;T;T	0.18338	2.22;2.22;2.22	4.59	2.79	0.32731	.	0.360426	0.27807	N	0.017766	T	0.10637	0.0260	L	0.43152	1.355	0.20703	N	0.999866	B	0.23854	0.092	B	0.23574	0.047	T	0.26467	-1.0102	10	0.17369	T	0.5	-4.6723	1.1464	0.01776	0.1844:0.4399:0.1755:0.2003	.	135	Q5JTC6	F123B_HUMAN	V	135	ENSP00000364003:G135V;ENSP00000329117:G135V;ENSP00000384722:G135V	ENSP00000329117:G135V	G	-	2	0	FAM123B	63329488	0.000000	0.05858	0.010000	0.14722	0.766000	0.43426	0.351000	0.20096	0.641000	0.30601	0.600000	0.82982	GGG	.	.	none		0.547	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424		A	63412763	C	A	63412763	3	1	38	1	0	0	0	0	1	0	0	0	5428	623	22	4	3007	4	FAM123B	23	63412763	Missense_Mutation	SNP	C	TCGA-GS-A9TV-01A-11D-A382-10	16367018	63412763	91857797	64	14537											
ATRX	546	hgsc.bcm.edu	37	chrX	76907651	76907651	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctctcagcaatacgttttcGtctctcttcctcttccttaa	6	17	3	15	2	4	0	1	0	4	0	9	0	6	0	3	0	2	2	3	0	3	6			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:76907651G>A	ENST00000373344.5	-	15	4724	c.4510C>T	c.(4510-4512)Cga>Tga	p.R1504*	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Nonsense_Mutation_p.R1466*	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	1504					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						ATACGTTTTCGTCTCTCTTCC	0.388			"Mis, F, N"		"Pancreatic neuroendocrine tumors, paediatric GBM"		ATR-X (alpha thalassemia/mental retardation) syndrome																														p.R1504X		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.C4510T						PASS	.						346	308	321					X																	76907651		2203	4300	6503	SO:0001587	stop_gained	546	exon15			GTTTTCGTCTCTC	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.4510C>T	X.37:g.76907651G>A	ENSP00000362441:p.Arg1504*	303	0	0		255	15	0.0588235	NM_000489	D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Nonsense_Mutation	SNP	ENST00000373344.5	37	CCDS14434.1	.	.	.	.	.	.	.	.	.	.	G	46	12.165867	0.99642	.	.	ENSG00000085224	ENST00000373344;ENST00000395603	.	.	.	4.9	2.85	0.33270	.	0.066609	0.64402	D	0.000017	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.0156	10.5199	0.44912	0.0:0.0:0.3258:0.6742	.	.	.	.	X	1504;1466	.	ENSP00000362441:R1504X	R	-	1	2	ATRX	76794307	1.000000	0.71417	0.998000	0.56505	0.938000	0.57974	2.678000	0.46900	0.817000	0.34445	0.594000	0.82650	CGA	.	.	none		0.388	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489		A	76907651	G	A	76907651	4	1	38	1	0	0	0	0	0	1	0	0	1208	1153	40	1	3052	1	ATRX	23	76907651	Nonsense_Mutation	SNP	G	TCGA-GS-A9TV-01A-11D-A382-10	13494888	76907651	78362909	65	14538											
TBC1D8B	54885	hgsc.bcm.edu	37	chrX	106116883	106116883	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcattatatcaagccattgcTgttgtaaccagccttttact	10	16	5	10	0	2	0	2	0	0	0	2	0	2	0	3	0	5	3	3	0	5	7	rs140391999	byFrequency	TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:106116883T>A	ENST00000357242.5	+	21	3225	c.3051T>A	c.(3049-3051)gcT>gcA	p.A1017A	TBC1D8B_ENST00000276175.3_Silent_p.A1011A	NM_017752.2	NP_060222.2	Q0IIM8	TBC8B_HUMAN	TBC1 domain family, member 8B (with GRAM domain)	1017							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						AAGCCATTGCTGTTGTAACCA	0.403																																					p.A1017A		Atlas-SNP	.											.	TBC1D8B	181	.	0			c.T3051A						PASS	.						126	122	123					X																	106116883		2203	4300	6503	SO:0001819	synonymous_variant	54885	exon21			CATTGCTGTTGTA	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.3051T>A	X.37:g.106116883T>A		232	0	0		236	20	0.0847458	NM_017752	B9A6K5|B9A6K6|Q5JRB7|Q6ZVX5|Q9NXE3	Silent	SNP	ENST00000357242.5	37	CCDS14522.1																																																																																			T|0.999;C|0.001	.	alt		0.403	TBC1D8B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057807.2	NM_017752		A	106116883	T	A	106116883	2	1	38	1	0	0	0	0	0	0	0	1	15641	1567	55	5		5	TBC1D8B	23	106116883	Silent	SNP	T	TCGA-GS-A9TV-01A-11D-A382-10	29209232	106116883	49153677	66	14539											
ATG4A	115201	hgsc.bcm.edu	37	chrX	107396261	107396261	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	attagttcagaaacatccatCacactggcctccctttgtac	11	12	5	13	0	2	1	2	0	0	1	4	1	4	1	3	1	2	2	3	1	3	4			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:107396261C>T	ENST00000372232.3	+	12	1229	c.1070C>T	c.(1069-1071)tCa>tTa	p.S357L	ATG4A_ENST00000545696.1_Missense_Mutation_p.S218L|ATG4A_ENST00000489247.1_3'UTR|COL4A6_ENST00000418180.1_Intron|ATG4A_ENST00000372254.3_Missense_Mutation_p.S333L|ATG4A_ENST00000345734.3_Missense_Mutation_p.S295L	NM_052936.3	NP_443168.2	Q8WYN0	ATG4A_HUMAN	autophagy related 4A, cysteine peptidase	357					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						AAACATCCATCACACTGGCCT	0.428																																					p.S357L		Atlas-SNP	.											.	ATG4A	68	.	0			c.C1070T						PASS	.						72	58	63					X																	107396261		2203	4300	6503	SO:0001583	missense	115201	exon12			ATCCATCACACTG	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.1070C>T	X.37:g.107396261C>T	ENSP00000361306:p.Ser357Leu	565	0	0		469	33	0.0703625	NM_052936	A6NCH2|B2RAZ7|D3DUY0|O95534|Q5JYY9|Q5JYZ0|Q86VE5|Q96KQ0|Q96KQ1	Missense_Mutation	SNP	ENST00000372232.3	37	CCDS14538.1	.	.	.	.	.	.	.	.	.	.	C	17.18	3.323638	0.60634	.	.	ENSG00000101844	ENST00000372232;ENST00000345734;ENST00000372254;ENST00000545696	T;T;T;T	0.46819	0.86;0.88;0.87;0.89	5.88	5.88	0.94601	.	0.358447	0.29080	N	0.013207	T	0.42517	0.1206	L	0.41824	1.3	0.80722	D	1	B;B;B	0.25169	0.119;0.001;0.002	B;B;B	0.19666	0.026;0.002;0.002	T	0.17776	-1.0358	10	0.25751	T	0.34	-2.0371	19.2176	0.93783	0.0:1.0:0.0:0.0	.	218;295;357	F5H3G3;Q8WYN0-2;Q8WYN0	.;.;ATG4A_HUMAN	L	357;295;333;218	ENSP00000361306:S357L;ENSP00000298131:S295L;ENSP00000361328:S333L;ENSP00000438936:S218L	ENSP00000298131:S295L	S	+	2	0	ATG4A	107282917	0.998000	0.40836	0.986000	0.45419	0.985000	0.73830	6.135000	0.71696	2.489000	0.83994	0.600000	0.82982	TCA	.	.	none		0.428	ATG4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057860.1	NM_052936		T	107396261	C	T	107396261	3	4	38	1	0	0	0	0	1	0	0	0	1096	838	29	2	1116	2	ATG4A	23	107396261	Missense_Mutation	SNP	C	TCGA-GS-A9TV-01A-11D-A382-10	1279378	107396261	47874299	67	14540											
IL13RA1	3597	hgsc.bcm.edu	37	chrX	117907928	117907928	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caatcatagtactcctgcttTacctaaaaaggtaaggtagc	14	11	7	9	0	1	0	1	0	0	0	2	0	2	0	2	2	4	4	2	2	9	7			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:117907928T>A	ENST00000371666.3	+	9	1163	c.1096T>A	c.(1096-1098)Tac>Aac	p.Y366N	IL13RA1_ENST00000371637.3_Missense_Mutation_p.Y165N	NM_001560.2	NP_001551.1	P78552	I13R1_HUMAN	interleukin 13 receptor, alpha 1	366					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						ACTCCTGCTTTACCTAAAAAG	0.428																																					p.Y366N		Atlas-SNP	.											.	IL13RA1	41	.	0			c.T1096A						PASS	.						178	150	160					X																	117907928		2203	4300	6503	SO:0001583	missense	3597	exon9			CTGCTTTACCTAA	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.1096T>A	X.37:g.117907928T>A	ENSP00000360730:p.Tyr366Asn	89	0	0		92	6	0.0652174	NM_001560	O95646|Q5JSL4|Q99656|Q9UDY5	Missense_Mutation	SNP	ENST00000371666.3	37	CCDS14573.1	.	.	.	.	.	.	.	.	.	.	T	16.51	3.143297	0.57044	.	.	ENSG00000131724	ENST00000371666;ENST00000371637	D	0.90732	-2.72	5.54	4.37	0.52481	.	0.089367	0.49305	D	0.000160	D	0.93504	0.7927	M	0.72894	2.215	0.40981	D	0.984779	D;D	0.89917	1.0;1.0	D;D	0.73708	0.981;0.981	D	0.92830	0.6279	10	0.87932	D	0	-17.3933	7.6269	0.28218	0.0:0.0979:0.0:0.9021	.	366;366	Q5JSL4;P78552	.;I13R1_HUMAN	N	366;165	ENSP00000360730:Y366N	ENSP00000360700:Y165N	Y	+	1	0	IL13RA1	117791956	1.000000	0.71417	0.856000	0.33681	0.596000	0.36781	4.240000	0.58701	0.834000	0.34852	0.439000	0.28862	TAC	.	.	none		0.428	IL13RA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058009.1	NM_001560		A	117907928	T	A	117907928	3	1	38	1	0	0	0	0	1	0	0	0	7638	1754	61	5	1130	5	IL13RA1	23	117907928	Missense_Mutation	SNP	T	TCGA-GS-A9TV-01A-11D-A382-10	10511667	117907928	37362632	68	14541											
ELF4	2000	hgsc.bcm.edu	37	chrX	129201410	129201410	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggcccattggtcagcacCgtggtcagtgggatcgtctg	6	9	16	10	2	3	0	2	0	1	0	4	2	3	2	2	5	1	1	2	5	0	1	rs369363653		TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:129201410C>T	ENST00000308167.5	-	9	1657	c.1278G>A	c.(1276-1278)acG>acA	p.T426T	ELF4_ENST00000335997.7_Silent_p.T426T	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						TGGTCAGCACCGTGGTCAGTG	0.597			T	ERG	AML																																p.T426T		Atlas-SNP	.		Dom	yes		X	Xq26	2000	E74-like factor 4 (ets domain transcription factor)		L	.	ELF4	67	.	0			c.G1278A						PASS	.		,	1,3834		0,0,1,1632,570	66	62	63		1278,1278	-0.1	1	X		63	0,6728		0,0,0,2428,1872	no	coding-synonymous,coding-synonymous	ELF4	NM_001127197.1,NM_001421.3	,	0,0,1,4060,2442	TT,TC,T,CC,C		0.0,0.0261,0.0095	,	426/664,426/664	129201410	1,10562	2203	4300	6503	SO:0001819	synonymous_variant	2000	exon9			CAGCACCGTGGTC	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.1278G>A	X.37:g.129201410C>T		139	0	0		146	9	0.0616438	NM_001421		Silent	SNP	ENST00000308167.5	37	CCDS14617.1																																																																																			.	.	weak		0.597	ELF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058243.1	NM_001421		T	129201410	C	T	129201410	2	4	38	1	0	0	0	0	0	0	0	1	5058	639	23	1		1	ELF4	23	129201410	Silent	SNP	C	TCGA-GS-A9TV-01A-11D-A382-10	11293482	129201410	26069150	69	14542											
HTATSF1	27336	hgsc.bcm.edu	37	chrX	135593333	135593333	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gctgccccaaaagagggtttGaaggcagctgctcccaaaaa	13	6	11	11	0	0	2	0	1	0	1	1	2	1	2	3	2	3	5	3	2	5	1			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:135593333G>A	ENST00000218364.4	+	9	1603	c.1429G>A	c.(1429-1431)Gaa>Aaa	p.E477K	HTATSF1_ENST00000535601.1_Missense_Mutation_p.E477K	NM_014500.4	NP_055315.2	O43719	HTSF1_HUMAN	HIV-1 Tat specific factor 1	477	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)					AAGAGGGTTTGAAGGCAGCTG	0.443																																					p.E477K		Atlas-SNP	.											.	HTATSF1	66	.	0			c.G1429A						PASS	.						46	50	49					X																	135593333		2193	4279	6472	SO:0001583	missense	27336	exon10			GGGTTTGAAGGCA	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.1429G>A	X.37:g.135593333G>A	ENSP00000218364:p.Glu477Lys	124	0	0		139	10	0.0719424	NM_001163280	D3DWG9|Q59G06|Q99730	Missense_Mutation	SNP	ENST00000218364.4	37	CCDS14657.1	.	.	.	.	.	.	.	.	.	.	G	5.369	0.253360	0.10185	.	.	ENSG00000102241	ENST00000535601;ENST00000218364;ENST00000415377	T;T	0.04360	3.64;3.64	4.38	2.61	0.31194	.	0.642678	0.16646	N	0.205430	T	0.03477	0.0100	N	0.24115	0.695	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.40440	-0.9563	10	0.41790	T	0.15	-2.2713	5.8919	0.18917	0.3322:0.0:0.6678:0.0	.	477	O43719	HTSF1_HUMAN	K	477	ENSP00000442699:E477K;ENSP00000218364:E477K	ENSP00000218364:E477K	E	+	1	0	HTATSF1	135420999	0.007000	0.16637	0.001000	0.08648	0.006000	0.05464	1.430000	0.34914	0.607000	0.29982	0.523000	0.50628	GAA	.	.	none		0.443	HTATSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058497.1	NM_014500		A	135593333	G	A	135593333	3	1	38	1	0	0	0	0	1	0	0	0	7442	1291	45	2	1463	2	HTATSF1	23	135593333	Missense_Mutation	SNP	G	TCGA-GS-A9TV-01A-11D-A382-10	6391923	135593333	19677227	70	14543											
VMA21	203547	hgsc.bcm.edu	37	chrX	150573449	150573449	+	Silent	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctattgttgcagtggtcgcCgtccatgtggtgctggccct	3	13	14	11	2	0	0	0	0	0	0	2	0	1	0	3	3	2	4	3	3	1	3	rs139323488	byFrequency	TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:150573449C>G	ENST00000330374.6	+	3	330	c.225C>G	c.(223-225)gcC>gcG	p.A75A	VMA21_ENST00000370361.1_Silent_p.A130A|VMA21_ENST00000477649.1_3'UTR	NM_001017980.3	NP_001017980.1			VMA21 vacuolar H+-ATPase homolog (S. cerevisiae)											endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)	7						CAGTGGTCGCCGTCCATGTGG	0.458																																					p.A75A		Atlas-SNP	.											.	VMA21	17	.	0			c.C225G						PASS	.						137	108	118					X																	150573449		2203	4300	6503	SO:0001819	synonymous_variant	203547	exon3			GGTCGCCGTCCAT	AK096835	CCDS35430.1	Xq28	2014-09-17			ENSG00000160131	ENSG00000160131			22082	protein-coding gene	gene with protein product		300913	"myopathy with excessive autophagy"	MEAX		2892402, 10757644, 19379691	Standard	NM_001017980		Approved	XMEA	uc004feu.3	Q3ZAQ7	OTTHUMG00000024168	ENST00000330374.6:c.225C>G	X.37:g.150573449C>G		145	0	0		179	11	0.0614525	NM_001017980		Silent	SNP	ENST00000330374.6	37	CCDS35430.1																																																																																			C|0.996;T|0.004	.	alt		0.458	VMA21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060876.1	NM_001017980		G	150573449	C	G	150573449	2	3	38	1	0	0	0	0	0	0	0	1	17190	639	23	4		4	VMA21	23	150573449	Silent	SNP	C	TCGA-GS-A9TV-01A-11D-A382-10	14980116	150573449	4697111	71	14544											
F8	2157	hgsc.bcm.edu	37	chrX	154221377	154221377	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttccaccagggaagactttAtcatcttctttctccctttg	7	16	5	13	0	4	1	1	0	3	1	6	2	5	2	3	1	0	0	3	1	2	6			TCGA-GS-A9TV-01A-11D-A382-10	TCGA-GS-A9TV-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	856d7068-5d31-4bc0-b50c-e02ed89ced3f	a592e794-fb42-4d16-95b3-c2059390b14c	g.chrX:154221377A>T	ENST00000360256.4	-	4	635	c.435T>A	c.(433-435)gaT>gaA	p.D145E		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	145	F5/8 type A 1.|Plastocyanin-like 1.		D -> H (in HEMA; moderate). {ECO:0000269|PubMed:9886318}.		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)	p.D145D(2)		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)	GGAAGACTTTATCATCTTCTT	0.423																																					p.D145E		Atlas-SNP	.											.	F8	646	.	2	Substitution - coding silent(2)	endometrium(2)	c.T435A						PASS	.						228	210	217					X																	154221377		2203	4300	6503	SO:0001583	missense	2157	exon4			GACTTTATCATCT	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.435T>A	X.37:g.154221377A>T	ENSP00000353393:p.Asp145Glu	320	0	0		231	16	0.0692641	NM_000132	Q14286|Q5HY69	Missense_Mutation	SNP	ENST00000360256.4	37	CCDS35457.1	.	.	.	.	.	.	.	.	.	.	A	17.95	3.513344	0.64522	.	.	ENSG00000185010	ENST00000360256;ENST00000423959;ENST00000453950	D;D;D	0.99462	-5.43;-5.43;-5.94	5.35	-1.68	0.08212	Cupredoxin (2);Multicopper oxidase, type 3 (1);	0.145374	0.64402	D	0.000012	D	0.99290	0.9752	M	0.82433	2.59	0.23550	N	0.997433	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.99628	1.0985	10	0.87932	D	0	-6.3892	9.7796	0.40640	0.4251:0.0:0.5749:0.0	.	110;145	B1B0G8;P00451	.;FA8_HUMAN	E	145;110;139	ENSP00000353393:D145E;ENSP00000409446:D110E;ENSP00000389153:D139E	ENSP00000353393:D145E	D	-	3	2	F8	153874571	0.337000	0.24766	0.482000	0.27366	0.727000	0.41649	0.869000	0.27996	-0.449000	0.07117	-0.520000	0.04383	GAT	.	.	none		0.423	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4			T	154221377	A	T	154221377	3	4	38	1	0	0	0	0	1	0	0	0	5352	446	16	5	6740	5	F8	23	154221377	Missense_Mutation	SNP	A	TCGA-GS-A9TV-01A-11D-A382-10	3647928	154221377	1049183	72	14545											
SRM	6723	hgsc.bcm.edu	37	chr1	11115065	11115065	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	aggcggcgcggtgcacgtcgGagttgtagtacttcagctgc	6	9	16	10	5	1	0	1	0	0	0	2	1	1	1	0	4	4	5	0	4	2	4			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:11115065G>C	ENST00000376957.2	-	7	922	c.842C>G	c.(841-843)tCc>tGc	p.S281C		NM_003132.2	NP_003123.2	P19623	SPEE_HUMAN	spermidine synthase	281					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)	GTGCACGTCGGAGTTGTAGTA	0.682																																					p.S281C		Atlas-SNP	.											SRM,NS,carcinoma,+1,1	SRM	18	1	0			c.C842G						PASS	.						41	44	43					1																	11115065		2203	4300	6503	SO:0001583	missense	6723	exon7			ACGTCGGAGTTGT	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.842C>G	1.37:g.11115065G>C	ENSP00000366156:p.Ser281Cys	145	0	0		118	20	0.169492	NM_003132	B1AKP9|Q15511	Missense_Mutation	SNP	ENST00000376957.2	37	CCDS125.1	.	.	.	.	.	.	.	.	.	.	G	23.0	4.357565	0.82243	.	.	ENSG00000116649	ENST00000376957	T	0.77098	-1.07	5.29	4.38	0.52667	.	0.244273	0.42821	D	0.000659	D	0.87297	0.6142	M	0.90483	3.12	0.54753	D	0.99998	D	0.71674	0.998	P	0.57101	0.813	D	0.89582	0.3821	10	0.87932	D	0	.	12.9435	0.58359	0.0784:0.0:0.9216:0.0	.	281	P19623	SPEE_HUMAN	C	281	ENSP00000366156:S281C	ENSP00000366156:S281C	S	-	2	0	SRM	11037652	1.000000	0.71417	0.225000	0.23894	0.864000	0.49448	9.099000	0.94207	1.226000	0.43582	0.561000	0.74099	TCC	.	.	none		0.682	SRM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006056.1	NM_003132		C	11115065	G	C	11115065	3	2	39	1	0	0	0	0	1	0	0	0	15166	1174	41	4	74	4	SRM	1	11115065	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10		11115065	238135556	1	14546											
CTRC	11330	hgsc.bcm.edu	37	chr1	15771170	15771170	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggatcacgccacgtgctccaGgattgactggtggggcttca	7	9	14	11	2	2	1	2	1	0	0	3	3	3	3	2	5	1	2	2	5	0	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:15771170G>A	ENST00000375949.4	+	6	589	c.563G>A	c.(562-564)aGg>aAg	p.R188K	CTRC_ENST00000483406.1_Intron|CTRC_ENST00000375943.2_Intron	NM_007272.2	NP_009203.2	Q99895	CTRC_HUMAN	chymotrypsin C (caldecrin)	188	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)		peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)	13		Breast(348;0.000207)|all_lung(284;0.00021)|Colorectal(325;0.000257)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)|Hepatocellular(190;0.0634)		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)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		ACGTGCTCCAGGATTGACTGG	0.612																																					p.R188K		Atlas-SNP	.											.	CTRC	28	.	0			c.G563A						PASS	.						82	75	77					1																	15771170		2203	4300	6503	SO:0001583	missense	11330	exon6			GCTCCAGGATTGA	BC015118	CCDS156.1	1p36.21	2009-02-18			ENSG00000162438	ENSG00000162438	3.4.21.2		2523	protein-coding gene	gene with protein product	"elastase 4"	601405				8635596	Standard	NM_007272		Approved	CLCR, ELA4	uc001awi.1	Q99895	OTTHUMG00000002255	ENST00000375949.4:c.563G>A	1.37:g.15771170G>A	ENSP00000365116:p.Arg188Lys	108	0	0		101	10	0.0990099	NM_007272	A8K082|O00765|Q9NUH5	Missense_Mutation	SNP	ENST00000375949.4	37	CCDS156.1	.	.	.	.	.	.	.	.	.	.	G	0.477	-0.881497	0.02530	.	.	ENSG00000162438	ENST00000375949	D	0.88818	-2.43	5.13	-1.03	0.10102	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.672011	0.15148	N	0.277902	T	0.76666	0.4019	N	0.26162	0.8	0.09310	N	0.999999	B	0.06786	0.001	B	0.15484	0.013	T	0.59553	-0.7433	10	0.20519	T	0.43	-10.5099	5.303	0.15788	0.5736:0.0:0.2879:0.1384	.	188	Q99895	CTRC_HUMAN	K	188	ENSP00000365116:R188K	ENSP00000365116:R188K	R	+	2	0	CTRC	15643757	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.177000	0.16801	-0.046000	0.13446	-0.367000	0.07326	AGG	.	.	none		0.612	CTRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006435.1	NM_007272		A	15771170	G	A	15771170	3	1	39	1	0	0	0	0	1	0	0	0	4029	1000	35	2	585	2	CTRC	1	15771170	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	4656105	15771170	233479451	2	14547											
KIAA0090	23065	hgsc.bcm.edu	37	chr1	19559222	19559222	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tggcttgacattgggtagatActgtttccacaggatggtgc	8	13	13	7	0	0	2	0	1	0	1	1	3	1	3	1	4	2	3	1	4	2	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:19559222A>T	ENST00000477853.1	-	15	1720	c.1678T>A	c.(1678-1680)Tat>Aat	p.Y560N	EMC1_ENST00000375208.3_Missense_Mutation_p.Y538N|EMC1_ENST00000375199.3_Missense_Mutation_p.Y559N|RP1-43E13.2_ENST00000437898.1_RNA	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	560						ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)											TTGGGTAGATACTGTTTCCAC	0.473																																					p.Y560N		Atlas-SNP	.											.	.	.	.	0			c.T1678A						PASS	.						179	176	177					1																	19559222		2203	4300	6503	SO:0001583	missense	23065	exon15			GTAGATACTGTTT		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.1678T>A	1.37:g.19559222A>T	ENSP00000420608:p.Tyr560Asn	170	0	0		162	43	0.265432	NM_015047	A8K6F3|Q14700|Q5TG62|Q63HL0|Q63HL3|Q8NBH8	Missense_Mutation	SNP	ENST00000477853.1	37	CCDS190.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.9|22.9	4.347263|4.347263	0.82022|0.82022	.|.	.|.	ENSG00000127463|ENSG00000127463	ENST00000375197|ENST00000477853;ENST00000375199;ENST00000375208	.|T;T;T	.|0.24723	.|1.85;1.85;1.84	5.94|5.94	5.94|5.94	0.96194|0.96194	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.49660|0.49660	0.1570|0.1570	M|M	0.76574|0.76574	2.34|2.34	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.76494	.|0.981;0.991;0.999;0.999	.|D;D;D;D	.|0.71656	.|0.923;0.947;0.974;0.942	T|T	0.42515|0.42515	-0.9447|-0.9447	5|10	.|0.27785	.|T	.|0.31	-13.0003|-13.0003	15.2191|15.2191	0.73296|0.73296	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|538;559;559;560	.|Q8N766-4;Q8N766-2;Q8N766-3;Q8N766	.|.;.;.;K0090_HUMAN	E|N	293|560;559;538	.|ENSP00000420608:Y560N;ENSP00000364345:Y559N;ENSP00000364354:Y538N	.|ENSP00000364345:Y559N	V|Y	-|-	2|1	0|0	KIAA0090|KIAA0090	19431809|19431809	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.938000|0.938000	0.57974|0.57974	8.711000|8.711000	0.91396|0.91396	2.272000|2.272000	0.75746|0.75746	0.460000|0.460000	0.39030|0.39030	GTA|TAT	.	.	none		0.473	EMC1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007076.2	NM_015047		T	19559222	A	T	19559222	3	4	39	1	0	0	0	0	1	0	0	0	8162	391	14	5	1339	5	KIAA0090	1	19559222	Missense_Mutation	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	3788052	19559222	229691399	3	14548											
PINK1	65018	hgsc.bcm.edu	37	chr1	20975644	20975644	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gccgcagctaccaagaggctCagctacctgcactgcccgag	9	5	11	16	2	1	1	1	0	0	1	1	2	1	1	4	1	6	5	4	1	3	2	rs45499196		TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:20975644C>T	ENST00000321556.4	+	7	1502	c.1408C>T	c.(1408-1410)Cag>Tag	p.Q470*	PINK1_ENST00000492302.1_3'UTR|PINK1-AS_ENST00000451424.1_RNA	NM_032409.2	NP_115785.1	Q9BXM7	PINK1_HUMAN	PTEN induced putative kinase 1	470	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.				activation of protein kinase B activity (GO:0032148)|cell death (GO:0008219)|cellular response to hypoxia (GO:0071456)|cellular response to toxic substance (GO:0097237)|intracellular signal transduction (GO:0035556)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of gene expression (GO:0010629)|negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway (GO:1903384)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|peptidyl-serine autophosphorylation (GO:0036289)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial electron transport, NADH to ubiquinone (GO:1902958)|positive regulation of peptidase activity (GO:0010952)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of mitochondrion degradation (GO:1903146)|regulation of protein complex assembly (GO:0043254)|regulation of protein ubiquitination (GO:0031396)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|TORC2 signaling (GO:0038203)|ubiquitin-dependent protein catabolic process (GO:0006511)	astrocyte projection (GO:0097449)|axon (GO:0030424)|cell body (GO:0044297)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of mitochondrial outer membrane (GO:0031307)|Lewy body (GO:0097413)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|C3HC4-type RING finger domain binding (GO:0055131)|calcium-dependent protein kinase activity (GO:0010857)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)|protein kinase B binding (GO:0043422)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)	14		all_lung(284;2.72e-05)|Lung NSC(340;2.94e-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;0.0182)|COAD - Colon adenocarcinoma(152;1.21e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000146)|Kidney(64;0.000182)|GBM - Glioblastoma multiforme(114;0.000497)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		CCAAGAGGCTCAGCTACCTGC	0.617																																					p.Q470X	Esophageal Squamous(145;853 1803 8146 34412 35011)	Atlas-SNP	.											.	PINK1	37	.	0			c.C1408T						PASS	.						61	54	56					1																	20975644		2203	4300	6503	SO:0001587	stop_gained	65018	exon7			GAGGCTCAGCTAC	AB053323	CCDS211.1	1p36.12	2011-07-21			ENSG00000158828	ENSG00000158828		"Parkinson disease"	14581	protein-coding gene	gene with protein product		608309	"Parkinson disease (autosomal recessive) 6"	PARK6		11494141, 15349860	Standard	NM_032409		Approved		uc001bdm.3	Q9BXM7	OTTHUMG00000002841	ENST00000321556.4:c.1408C>T	1.37:g.20975644C>T	ENSP00000364204:p.Gln470*	145	0	0		148	40	0.27027	NM_032409	Q8N6T9|Q8NBU3|Q96DE4	Nonsense_Mutation	SNP	ENST00000321556.4	37	CCDS211.1	.	.	.	.	.	.	.	.	.	.	C	38	6.772314	0.97829	.	.	ENSG00000158828	ENST00000321556	.	.	.	6.17	6.17	0.99709	.	0.054055	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.23302	T	0.38	-12.4969	16.3795	0.83443	0.0:1.0:0.0:0.0	.	.	.	.	X	470	.	ENSP00000364204:Q470X	Q	+	1	0	PINK1	20848231	0.999000	0.42202	0.999000	0.59377	0.690000	0.40134	3.349000	0.52217	2.941000	0.99782	0.655000	0.94253	CAG	.	.	none		0.617	PINK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007954.1	NM_032409		T	20975644	C	T	20975644	4	4	39	1	0	0	0	0	0	1	0	0	11941	827	29	2	1434	2	PINK1	1	20975644	Nonsense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	1416422	20975644	228274977	4	14549											
ZBTB40	9923	hgsc.bcm.edu	37	chr1	22838349	22838349	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	agagaaagaggcttcagcctCcccagaccctgccaagaaga	14	4	10	13	0	1	5	1	0	0	5	2	6	2	5	5	1	2	1	5	1	3	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:22838349C>T	ENST00000375647.4	+	11	2390	c.2183C>T	c.(2182-2184)tCc>tTc	p.S728F	ZBTB40_ENST00000404138.1_Missense_Mutation_p.S728F|ZBTB40_ENST00000374651.4_Missense_Mutation_p.S616F	NM_014870.3	NP_055685.3	Q9NUA8	ZBT40_HUMAN	zinc finger and BTB domain containing 40	728					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)		GCTTCAGCCTCCCCAGACCCT	0.542																																					p.S728F		Atlas-SNP	.											.	ZBTB40	87	.	0			c.C2183T						PASS	.						62	57	59					1																	22838349		2203	4300	6503	SO:0001583	missense	9923	exon12			CAGCCTCCCCAGA	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.2183C>T	1.37:g.22838349C>T	ENSP00000364798:p.Ser728Phe	110	0	0		104	33	0.317308	NM_001083621	O75066|Q5TFU5|Q8N1R1	Missense_Mutation	SNP	ENST00000375647.4	37	CCDS224.1	.	.	.	.	.	.	.	.	.	.	C	14.63	2.591720	0.46214	.	.	ENSG00000184677	ENST00000404138;ENST00000375647;ENST00000374651	T;T;T	0.76060	-0.99;-0.99;-0.99	5.73	5.73	0.89815	.	0.117441	0.38720	N	0.001590	D	0.84488	0.5483	M	0.65677	2.01	0.35211	D	0.775199	D;D	0.76494	0.999;0.999	D;D	0.74023	0.982;0.96	D	0.88729	0.3235	10	0.66056	D	0.02	-19.9926	15.4065	0.74884	0.0:1.0:0.0:0.0	.	616;728	F8WAI8;Q9NUA8	.;ZBT40_HUMAN	F	728;728;616	ENSP00000384527:S728F;ENSP00000364798:S728F;ENSP00000363782:S616F	ENSP00000363782:S616F	S	+	2	0	ZBTB40	22710936	0.984000	0.35163	1.000000	0.80357	0.562000	0.35680	1.157000	0.31724	2.693000	0.91896	0.655000	0.94253	TCC	.	.	none		0.542	ZBTB40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008094.1	NM_014870		T	22838349	C	T	22838349	3	4	39	1	0	0	0	0	1	0	0	0	17557	855	30	2	2221	2	ZBTB40	1	22838349	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	1862705	22838349	226412272	5	14550											
RUNX3	864	hgsc.bcm.edu	37	chr1	25256143	25256143	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagcacggagcagaggaagtTggggctgtcggtgcgcacga	9	5	18	9	4	0	1	0	0	0	1	1	4	0	3	0	5	3	5	0	5	1	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:25256143T>A	ENST00000308873.6	-	1	225	c.217A>T	c.(217-219)Aac>Tac	p.N73Y	RUNX3_ENST00000338888.3_Missense_Mutation_p.N87Y|RUNX3_ENST00000399916.1_Missense_Mutation_p.N87Y|RUNX3_ENST00000540420.1_5'Flank|RUNX3_ENST00000496967.1_5'Flank	NM_004350.2	NP_004341.1	Q13761	RUNX3_HUMAN	runt-related transcription factor 3	73	Runt. {ECO:0000255|PROSITE- ProRule:PRU00399}.				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)		CAGAGGAAGTTGGGGCTGTCG	0.756																																					p.N87Y		Atlas-SNP	.											.	RUNX3	72	.	0			c.A259T						PASS	.						34	30	31					1																	25256143		2201	4298	6499	SO:0001583	missense	864	exon2			GGAAGTTGGGGCT	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.217A>T	1.37:g.25256143T>A	ENSP00000308051:p.Asn73Tyr	90	0	0		62	24	0.387097	NM_001031680	B1AJV5|Q12969|Q13760	Missense_Mutation	SNP	ENST00000308873.6	37	CCDS257.1	.	.	.	.	.	.	.	.	.	.	T	15.33	2.802911	0.50315	.	.	ENSG00000020633	ENST00000399916;ENST00000308873;ENST00000338888;ENST00000428150	D;D;D	0.99483	-5.99;-5.99;-5.99	3.37	2.2	0.27929	Acute myeloid leukemia 1 (AML 1)/Runt (2);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.184695	0.45361	N	0.000371	D	0.98979	0.9652	L	0.52126	1.63	0.80722	D	1	D;D;D;P	0.89917	0.983;1.0;1.0;0.719	P;D;D;P	0.78314	0.905;0.985;0.991;0.472	D	0.98235	1.0485	10	0.51188	T	0.08	-19.8886	7.7574	0.28932	0.1874:0.0:0.0:0.8126	.	73;87;87;73	E9PH34;Q13761-2;B1AJV5;Q13761	.;.;.;RUNX3_HUMAN	Y	87;73;87;73	ENSP00000382800:N87Y;ENSP00000308051:N73Y;ENSP00000343477:N87Y	ENSP00000308051:N73Y	N	-	1	0	RUNX3	25128730	1.000000	0.71417	1.000000	0.80357	0.238000	0.25445	5.566000	0.67372	0.376000	0.24707	0.402000	0.26972	AAC	.	.	none		0.756	RUNX3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000009284.1	NM_004350		A	25256143	T	A	25256143	3	1	39	1	0	0	0	0	1	0	0	0	13764	1812	63	5	1050	5	RUNX3	1	25256143	Missense_Mutation	SNP	T	TCGA-GS-A9TW-01A-11D-A382-10	2417794	25256143	223994478	6	14551											
CCDC21	64793	hgsc.bcm.edu	37	chr1	26601519	26601519	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgagagaggaggcccagcGaagggattcagccctgcagc	10	4	15	12	1	1	2	1	1	0	1	1	6	1	4	3	3	4	1	3	3	1	1	rs201784964		TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:26601519G>T	ENST00000252992.4	+	12	1990	c.1859G>T	c.(1858-1860)cGa>cTa	p.R620L	CEP85_ENST00000469609.1_3'UTR|CEP85_ENST00000451429.2_Missense_Mutation_p.R569L	NM_001281517.1|NM_022778.2	NP_001268446.1|NP_073615.2	Q6P2H3	CEP85_HUMAN	centrosomal protein 85kDa	620						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						GAGGCCCAGCGAAGGGATTCA	0.532																																					p.R620L		Atlas-SNP	.											.	CEP85	61	.	0			c.G1859T						PASS	.						51	47	48					1																	26601519		2188	4284	6472	SO:0001583	missense	64793	exon12			CCCAGCGAAGGGA	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.1859G>T	1.37:g.26601519G>T	ENSP00000252992:p.Arg620Leu	88	0	0		103	33	0.320388	NM_022778	B4DRL1|D3DPK4|F8W7K4|Q5VY68|Q5VY70|Q9H6Q1|Q9H828|Q9UF52	Missense_Mutation	SNP	ENST00000252992.4	37	CCDS277.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.30|17.30	3.355206|3.355206	0.61293|0.61293	.|.	.|.	ENSG00000130695|ENSG00000130695	ENST00000453146|ENST00000451429;ENST00000252992	.|T;T	.|0.11821	.|2.74;2.74	5.57|5.57	3.69|3.69	0.42338|0.42338	.|.	.|0.266541	.|0.43919	.|D	.|0.000505	.|T	.|0.14141	.|0.0342	L|L	0.54323|0.54323	1.7|1.7	0.42111|0.42111	D|D	0.991387|0.991387	.|B;B;P	.|0.36438	.|0.021;0.086;0.553	.|B;B;B	.|0.34418	.|0.014;0.058;0.182	.|T	.|0.04650	.|-1.0936	.|10	.|0.52906	.|T	.|0.07	-14.5059|-14.5059	11.5657|11.5657	0.50805|0.50805	0.144:0.0:0.856:0.0|0.144:0.0:0.856:0.0	.|.	.|569;620;620	.|F8W7K4;Q6P2H3;Q6P2H3-2	.|.;CEP85_HUMAN;.	X|L	294|569;620	.|ENSP00000417002:R569L;ENSP00000252992:R620L	.|ENSP00000252992:R620L	E|R	+|+	1|2	0|0	CEP85|CEP85	26474106|26474106	0.955000|0.955000	0.32602|0.32602	1.000000|1.000000	0.80357|0.80357	0.958000|0.958000	0.62258|0.62258	0.919000|0.919000	0.28692|0.28692	1.363000|1.363000	0.46019|0.46019	0.561000|0.561000	0.74099|0.74099	GAA|CGA	G|0.998;A|0.002	.	alt		0.532	CEP85-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009492.2	NM_022778		T	26601519	G	T	26601519	3	4	39	1	0	0	0	0	1	0	0	0	2798	1058	37	4	1901	4	CCDC21	1	26601519	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	1345376	26601519	222649102	7	14552											
IQCC	55721	hgsc.bcm.edu	37	chr1	32672879	32672879	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acactgagatccccagaggcGggcccgatcagagaggaacc	12	3	13	13	2	1	3	1	1	0	3	2	7	2	4	4	3	1	0	4	3	1	0	rs201910762		TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:32672879G>A	ENST00000291358.6	+	5	618	c.597G>A	c.(595-597)gcG>gcA	p.A199A	RP4-622L5.7_ENST00000373604.4_RNA|IQCC_ENST00000537469.1_Silent_p.A279A|DCDC2B_ENST00000409358.1_5'Flank|RP4-622L5.7_ENST00000421616.1_RNA	NM_018134.2	NP_060604.2	Q4KMZ1	IQCC_HUMAN	IQ motif containing C	199										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)				CCCCAGAGGCGGGCCCGATCA	0.567													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18496	0.0		0.0	False		,,,				2504	0.0				p.A279A		Atlas-SNP	.											.	IQCC	46	.	0			c.G837A						PASS	.						68	76	74					1																	32672879		2203	4300	6503	SO:0001819	synonymous_variant	55721	exon5			AGAGGCGGGCCCG	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.597G>A	1.37:g.32672879G>A		96	0	0		76	30	0.394737	NM_001160042	F5H7T8|Q4KMS3|Q4KMZ5|Q53FL2|Q5TFJ8|Q9NVS3	Silent	SNP	ENST00000291358.6	37	CCDS355.1																																																																																			G|1.000;A|0.000	0.000	strong		0.567	IQCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015731.3	NM_018134		A	32672879	G	A	32672879	2	1	39	1	0	0	0	0	0	0	0	1	7813	1103	39	1		1	IQCC	1	32672879	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	6071360	32672879	216577742	8	14553											
ZSCAN20	7579	hgsc.bcm.edu	37	chr1	33960285	33960285	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gctttagtgaccattctaatCtcatcactcaccagagaatt	12	13	5	11	0	4	2	3	1	2	1	5	3	4	2	2	0	0	1	2	0	3	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:33960285C>T	ENST00000361328.3	+	8	2494	c.2341C>T	c.(2341-2343)Ctc>Ttc	p.L781F		NM_145238.3	NP_660281	P17040	ZSC20_HUMAN	zinc finger and SCAN domain containing 20	781					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)				CCATTCTAATCTCATCACTCA	0.438																																					p.L781F		Atlas-SNP	.											.	ZSCAN20	107	.	0			c.C2341T						PASS	.						77	82	80					1																	33960285		2110	4257	6367	SO:0001583	missense	7579	exon8			TCTAATCTCATCA	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.2341C>T	1.37:g.33960285C>T	ENSP00000355053:p.Leu781Phe	95	0	0		90	32	0.355556	NM_145238	A8K2D0|B1ALI4|B1ALI5|B1ALI6|Q6ZN23|Q96FA9|Q96H84	Missense_Mutation	SNP	ENST00000361328.3	37	CCDS41300.1	.	.	.	.	.	.	.	.	.	.	C	13.61	2.287144	0.40494	.	.	ENSG00000121903	ENST00000326544;ENST00000361328;ENST00000401072	.	.	.	5.9	4.03	0.46877	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.168641	0.29403	N	0.012248	T	0.61110	0.2321	L	0.56280	1.765	0.28900	N	0.893326	P;D	0.89917	0.755;1.0	B;D	0.97110	0.31;1.0	T	0.57376	-0.7822	9	0.51188	T	0.08	-15.1702	10.8189	0.46593	0.0:0.8458:0.0:0.1542	.	780;781	P17040-3;P17040	.;ZSC20_HUMAN	F	781;715;715	.	ENSP00000324450:L781F	L	+	1	0	ZSCAN20	33732872	0.913000	0.31002	0.034000	0.17996	0.809000	0.45718	2.193000	0.42658	0.828000	0.34709	0.561000	0.74099	CTC	.	.	none		0.438	ZSCAN20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277003.2	NM_145238		T	33960285	C	T	33960285	3	4	39	1	0	0	0	0	1	0	0	0	18247	913	32	2	2367	2	ZSCAN20	1	33960285	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	1287406	33960285	215290336	9	14554											
USP24	23358	hgsc.bcm.edu	37	chr1	55549034	55549034	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aagatctccagccctaattcCttgctgtcacaagatattga	12	12	6	11	0	2	3	1	1	1	2	4	3	3	3	3	0	2	1	3	0	4	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:55549034C>T	ENST00000294383.6	-	58	6885	c.6886G>A	c.(6886-6888)Gga>Aga	p.G2296R	USP24_ENST00000407756.1_Missense_Mutation_p.G2136R	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	2296					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						GCCCTAATTCCTTGCTGTCAC	0.398																																					p.G2296R		Atlas-SNP	.											.	USP24	323	.	0			c.G6886A						PASS	.						74	70	71					1																	55549034		1903	4128	6031	SO:0001583	missense	23358	exon58			TAATTCCTTGCTG	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.6886G>A	1.37:g.55549034C>T	ENSP00000294383:p.Gly2296Arg	69	0	0		64	9	0.140625	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Missense_Mutation	SNP	ENST00000294383.6	37	CCDS44154.2	.	.	.	.	.	.	.	.	.	.	C	14.75	2.628881	0.46944	.	.	ENSG00000162402	ENST00000294383;ENST00000407756	T;T	0.03920	3.76;3.78	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.06142	0.0159	L	0.35341	1.055	0.58432	D	0.999996	P	0.36438	0.553	B	0.32465	0.146	T	0.34976	-0.9807	10	0.56958	D	0.05	.	19.6126	0.95616	0.0:1.0:0.0:0.0	.	2136	B7WPF4	.	R	2296;2136	ENSP00000294383:G2296R;ENSP00000385700:G2136R	ENSP00000294383:G2296R	G	-	1	0	USP24	55321622	1.000000	0.71417	0.993000	0.49108	0.502000	0.33828	5.981000	0.70524	2.647000	0.89833	0.650000	0.86243	GGA	.	.	none		0.398	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			T	55549034	C	T	55549034	3	4	39	1	0	0	0	0	1	0	0	0	17070	690	24	2	1020	2	USP24	1	55549034	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	21588749	55549034	193701587	10	14555											
USP24	23358	hgsc.bcm.edu	37	chr1	55587126	55587126	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tacctcagcacttggtgatcCgagcagaatatcaatgatga	13	10	9	9	1	2	4	2	3	0	1	3	5	3	4	2	1	3	2	2	1	4	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:55587126C>T	ENST00000294383.6	-	37	4329	c.4330G>A	c.(4330-4332)Gga>Aga	p.G1444R	USP24_ENST00000407756.1_Missense_Mutation_p.G1284R	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	1444					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						CTTGGTGATCCGAGCAGAATA	0.413																																					p.G1444R		Atlas-SNP	.											.	USP24	323	.	0			c.G4330A						PASS	.						104	102	102					1																	55587126		1910	4135	6045	SO:0001583	missense	23358	exon37			GTGATCCGAGCAG	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.4330G>A	1.37:g.55587126C>T	ENSP00000294383:p.Gly1444Arg	204	0	0		198	49	0.247475	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Missense_Mutation	SNP	ENST00000294383.6	37	CCDS44154.2	.	.	.	.	.	.	.	.	.	.	C	20.5	3.996122	0.74703	.	.	ENSG00000162402	ENST00000294383;ENST00000407756	T;T	0.02258	4.37;4.38	4.8	4.8	0.61643	.	0.000000	0.85682	D	0.000000	T	0.06325	0.0163	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.67231	0.95	T	0.59337	-0.7473	10	0.11794	T	0.64	.	18.0452	0.89330	0.0:1.0:0.0:0.0	.	1284	B7WPF4	.	R	1444;1284	ENSP00000294383:G1444R;ENSP00000385700:G1284R	ENSP00000294383:G1444R	G	-	1	0	USP24	55359714	1.000000	0.71417	0.984000	0.44739	0.962000	0.63368	6.971000	0.76105	2.499000	0.84300	0.650000	0.86243	GGA	.	.	none		0.413	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			T	55587126	C	T	55587126	3	4	39	1	0	0	0	0	1	0	0	0	17070	661	23	1	3660	1	USP24	1	55587126	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	38092	55587126	193663495	11	14556											
LEPR	3953	hgsc.bcm.edu	37	chr1	66101961	66101961	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agcctgaaacaatttcagaaGatatcagtgttgatacatca	16	11	7	7	0	3	4	3	2	0	2	3	4	3	4	1	0	3	1	1	0	5	4			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:66101961G>A	ENST00000349533.6	+	20	2946	c.2761G>A	c.(2761-2763)Gat>Aat	p.D921N	LEPR_ENST00000406510.3_5'UTR	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)	p.D921Y(1)		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)		AATTTCAGAAGATATCAGTGT	0.373																																					p.D921N		Atlas-SNP	.											LEPR_ENST00000349533,colon,carcinoma,0,1	LEPR	284	1	1	Substitution - Missense(1)	large_intestine(1)	c.G2761A						PASS	.						149	153	152					1																	66101961		2203	4300	6503	SO:0001583	missense	3953	exon20			TCAGAAGATATCA	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.2761G>A	1.37:g.66101961G>A	ENSP00000330393:p.Asp921Asn	236	0	0		239	43	0.179916	NM_002303	Q6FHL5	Missense_Mutation	SNP	ENST00000349533.6	37	CCDS631.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.888719	0.91814	.	.	ENSG00000116678	ENST00000349533	T	0.57273	0.41	5.79	5.79	0.91817	.	0.259962	0.42420	D	0.000718	T	0.67144	0.2862	M	0.76002	2.32	0.80722	D	1	D	0.71674	0.998	P	0.61800	0.894	T	0.69157	-0.5219	10	0.66056	D	0.02	-17.0787	20.0281	0.97530	0.0:0.0:1.0:0.0	.	921	P48357	LEPR_HUMAN	N	921	ENSP00000330393:D921N	ENSP00000330393:D921N	D	+	1	0	LEPR	65874549	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.681000	0.74523	2.727000	0.93392	0.655000	0.94253	GAT	.	.	none		0.373	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303		A	66101961	G	A	66101961	3	1	39	1	0	0	0	0	1	0	0	0	8737	942	33	2	3061	2	LEPR	1	66101961	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	10514835	66101961	183148660	12	14557											
DPYD	1806	hgsc.bcm.edu	37	chr1	98187169	98187169	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cagaggttggacataccattCcacaagtcagaccaagtggg	13	7	11	10	0	1	2	1	0	0	2	2	3	2	3	3	3	1	1	3	3	3	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:98187169C>T	ENST00000370192.3	-	5	480	c.380G>A	c.(379-381)gGa>gAa	p.G127E	DPYD_ENST00000306031.5_Missense_Mutation_p.G127E|DPYD_ENST00000423006.2_Missense_Mutation_p.G90E|DPYD_ENST00000474241.1_5'UTR	NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	127					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)	ACATACCATTCCACAAGTCAG	0.353																																					p.G127E		Atlas-SNP	.											.	DPYD	219	.	0			c.G380A						PASS	.						105	101	103					1																	98187169		2203	4299	6502	SO:0001583	missense	1806	exon5			ACCATTCCACAAG	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.380G>A	1.37:g.98187169C>T	ENSP00000359211:p.Gly127Glu	243	0	0		182	61	0.335165	NM_000110	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	37	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	C	31	5.090406	0.94149	.	.	ENSG00000188641	ENST00000370192;ENST00000423006;ENST00000306031	T;T;T	0.81163	-1.46;-1.46;-1.46	6.06	6.06	0.98353	Fumarate reductase, C-terminal (1);Alpha-helical ferredoxin (1);	0.000000	0.85682	D	0.000000	D	0.93585	0.7952	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	D	0.94584	0.7782	10	0.87932	D	0	-17.6068	20.6397	0.99537	0.0:1.0:0.0:0.0	.	127;127	E9PFN1;Q12882	.;DPYD_HUMAN	E	127;90;127	ENSP00000359211:G127E;ENSP00000398884:G90E;ENSP00000307107:G127E	ENSP00000307107:G127E	G	-	2	0	DPYD	97959757	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.433000	0.80362	2.880000	0.98712	0.650000	0.86243	GGA	.	.	none		0.353	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110		T	98187169	C	T	98187169	3	4	39	1	0	0	0	0	1	0	0	0	4747	855	30	2	2816	2	DPYD	1	98187169	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	32085208	98187169	151063452	13	14558											
CD1A	909	hgsc.bcm.edu	37	chr1	158226646	158226646	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctgcagcttgtgtgccatgtCtcaggattctacccaaagcc	8	11	9	13	0	2	0	1	0	2	0	3	1	2	1	3	1	5	2	3	1	2	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:158226646C>G	ENST00000289429.5	+	4	1208	c.675C>G	c.(673-675)gtC>gtG	p.V225V		NM_001763.2	NP_001754.2	P06126	CD1A_HUMAN	CD1a molecule	225	Ig-like.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)				NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(14)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	32	all_hematologic(112;0.0378)				Antithymocyte globulin(DB00098)	TGTGCCATGTCTCAGGATTCT	0.587																																					p.V225V		Atlas-SNP	.											.	CD1A	88	.	0			c.C675G						PASS	.						83	80	81					1																	158226646		2203	4300	6503	SO:0001819	synonymous_variant	909	exon4			CCATGTCTCAGGA	M28825	CCDS1174.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158477	ENSG00000158477		"CD molecules", "Immunoglobulin superfamily / C1-set domain containing"	1634	protein-coding gene	gene with protein product		188370	"CD1A antigen, a polypeptide", "CD1a antigen"	CD1		2447586, 2784820	Standard	NM_001763		Approved		uc001frt.3	P06126	OTTHUMG00000017512	ENST00000289429.5:c.675C>G	1.37:g.158226646C>G		242	0	0		245	71	0.289796	NM_001763	D3DVD7|Q13962|Q5TDJ8|Q9UMM4|Q9Y5M5	Silent	SNP	ENST00000289429.5	37	CCDS1174.1																																																																																			.	.	none		0.587	CD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046349.2	NM_001763		G	158226646	C	G	158226646	2	3	39	1	0	0	0	0	0	0	0	1	2976	900	32	4		4	CD1A	1	158226646	Silent	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	60039477	158226646	91023975	14	14559											
SPTA1	6708	hgsc.bcm.edu	37	chr1	158614070	158614070	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgattgctttgtccaaatcGtcccgtttcttcatcaaagc	8	15	7	11	2	3	1	2	1	1	0	6	1	5	1	2	0	2	2	2	0	2	4	rs189877287	byFrequency	TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:158614070G>A	ENST00000368147.4	-	30	4491	c.4311C>T	c.(4309-4311)gaC>gaT	p.D1437D		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1437					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.D1437D(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)					TGTCCAAATCGTCCCGTTTCT	0.403													g|||	4	0.000798722	0.0015	0.0	5008	,	,		17322	0.0		0.0	False		,,,				2504	0.002				p.D1437D		Atlas-SNP	.											SPTA1,NS,carcinoma,0,1	SPTA1	720	1	1	Substitution - coding silent(1)	endometrium(1)	c.C4311T						PASS	.	T		7,3797		0,7,1895	99	95	96		4311	-1	0.7	1		96	0,8222		0,0,4111	no	coding-synonymous	SPTA1	NM_003126.2		0,7,6006	AA,AG,GG		0.0,0.184,0.0582		1437/2420	158614070	7,12019	1902	4111	6013	SO:0001819	synonymous_variant	6708	exon30			CAAATCGTCCCGT	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.4311C>T	1.37:g.158614070G>A		186	0	0		145	17	0.117241	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	37	CCDS41423.1																																																																																			G|1.000;A|0.000	0.000	strong		0.403	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		A	158614070	G	A	158614070	2	1	39	1	0	0	0	0	0	0	0	1	15131	1136	40	1		1	SPTA1	1	158614070	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	387424	158614070	90636551	15	14560											
SPTA1	6708	hgsc.bcm.edu	37	chr1	158622386	158622386	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	taggccaataaaaattcattAtaacgttgcaatagacgacg	17	10	7	7	3	1	1	1	0	0	1	1	2	1	1	1	1	2	2	1	1	9	7			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:158622386A>T	ENST00000368147.4	-	23	3426	c.3246T>A	c.(3244-3246)taT>taA	p.Y1082*		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1082					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)					AAAATTCATTATAACGTTGCA	0.438																																					p.Y1082X		Atlas-SNP	.											.	SPTA1	720	.	0			c.T3246A						PASS	.						123	114	117					1																	158622386		1900	4119	6019	SO:0001587	stop_gained	6708	exon23			TTCATTATAACGT	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.3246T>A	1.37:g.158622386A>T	ENSP00000357129:p.Tyr1082*	179	0	0		161	23	0.142857	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Nonsense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	A	43	9.888015	0.99288	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	.	.	.	5.3	2.46	0.29980	.	0.000000	0.29699	N	0.011431	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.3384	0.38065	0.233:0.0:0.767:0.0	.	.	.	.	X	1082	.	ENSP00000357129:Y1082X	Y	-	3	2	SPTA1	156889010	1.000000	0.71417	0.994000	0.49952	0.821000	0.46438	2.557000	0.45871	0.403000	0.25479	-0.132000	0.14878	TAT	.	.	none		0.438	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126		T	158622386	A	T	158622386	4	4	39	1	0	0	0	0	0	1	0	0	15131	456	16	5	4133	5	SPTA1	1	158622386	Nonsense_Mutation	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	8316	158622386	90628235	16	14561											
SDHC	6391	hgsc.bcm.edu	37	chr1	161298187	161298187	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cggtctggttttattttagtGctgttcctttgggaaccacg	5	17	11	8	2	1	0	0	0	1	0	2	1	2	1	2	3	2	3	2	3	3	6			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:161298187G>A	ENST00000367975.2	+	3	228	c.79G>A	c.(79-81)Gct>Act	p.A27T	SDHC_ENST00000470743.3_3'UTR|SDHC_ENST00000432287.2_Intron|SDHC_ENST00000392169.2_Intron|SDHC_ENST00000513009.1_Intron|SDHC_ENST00000342751.4_Splice_Site_p.A27T	NM_003001.3	NP_002992.1	Q99643	C560_HUMAN	succinate dehydrogenase complex, subunit C, integral membrane protein, 15kDa	27					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|oxidation-reduction process (GO:0055114)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)|respiratory chain complex II (GO:0045273)	electron carrier activity (GO:0009055)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|succinate dehydrogenase activity (GO:0000104)			urinary_tract(1)	1	all_cancers(52;6.96e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Succinic acid(DB00139)	TTATTTTAGTGCTGTTCCTTT	0.368			"Mis, N, F"			"paraganglioma, pheochromocytoma"			Familial Paragangliomas;Carney-Stratakis syndrome																												p.A27T		Atlas-SNP	.	yes	Rec		Familial paraganglioma	1	1q21	6391	"succinate dehydrogenase complex, subunit C, integral membrane protein, 15kDa"		O	.	SDHC	19	.	0			c.G79A						PASS	.						114	119	117					1																	161298187		2203	4300	6503	SO:0001630	splice_region_variant	6391	exon3	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;Carney-Stratakis dyad, Paraganglioma-Gastric Stromal Sarcoma dyad	TTTAGTGCTGTTC	D49737	CCDS1230.1, CCDS41431.1, CCDS41432.1, CCDS44263.1, CCDS60330.1	1q23.3	2014-09-17	2002-08-29		ENSG00000143252	ENSG00000143252		"Mitochondrial respiratory chain complex / Complex II"	10682	protein-coding gene	gene with protein product		602413	"succinate dehydrogenase complex, subunit C, integral membrane protein, 15kD"	PGL3		9533030, 12658451	Standard	NM_001278172		Approved		uc001gag.3	Q99643	OTTHUMG00000034468	ENST00000367975.2:c.78-1G>A	1.37:g.161298187G>A		62	0	0		58	17	0.293103	NM_001035511	O75609|Q3C259|Q3C2D8|Q3C2H4|Q5VTH3	Missense_Mutation	SNP	ENST00000367975.2	37	CCDS1230.1	.	.	.	.	.	.	.	.	.	.	G	19.05	3.752903	0.69648	.	.	ENSG00000143252	ENST00000367975;ENST00000342751	D;D	0.97328	-4.34;-4.34	5.72	5.72	0.89469	.	0.211314	0.48767	D	0.000168	D	0.97133	0.9063	M	0.68952	2.095	.	.	.	D;P	0.57257	0.979;0.877	P;B	0.54270	0.747;0.417	D	0.97053	0.9765	9	0.56958	D	0.05	.	17.3691	0.87371	0.0:0.0:1.0:0.0	.	27;27	Q99643-2;Q99643	.;C560_HUMAN	T	27	ENSP00000356953:A27T;ENSP00000356952:A27T	ENSP00000356952:A27T	A	+	1	0	SDHC	159564811	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	1.880000	0.39628	2.699000	0.92147	0.591000	0.81541	GCT	.	.	none		0.368	SDHC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083316.2	NM_003001	Missense_Mutation	A	161298187	G	A	161298187	5	1	39	1	0	0	0	0	0	0	1	0	13981	1333	46	2	89	2	SDHC	1	161298187	Splice_Site	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	2675801	161298187	87952434	17	14562											
SELL	6402	hgsc.bcm.edu	37	chr1	169677562	169677562	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcttgtcactccctacctgtGtaacagagggctgcctttag	7	13	9	12	0	2	1	1	0	1	1	3	1	3	1	3	1	3	2	3	1	3	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:169677562G>A	ENST00000236147.4	-	3	667	c.507C>T	c.(505-507)taC>taT	p.Y169Y	C1orf112_ENST00000498289.1_Intron|SELL_ENST00000463108.1_5'UTR	NM_000655.4	NP_000646.2	P14151	LYAM1_HUMAN	selectin L	156	EGF-like. {ECO:0000255|PROSITE- ProRule:PRU00076}.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)|regulation of immune response (GO:0050776)|response to ATP (GO:0033198)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|glycosphingolipid binding (GO:0043208)|heparin binding (GO:0008201)|protease binding (GO:0002020)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|lung(5)|urinary_tract(1)	15	all_hematologic(923;0.208)					CCCTACCTGTGTAACAGAGGG	0.502																																					p.Y169Y		Atlas-SNP	.											.	SELL	43	.	0			c.C507T						PASS	.						98	93	95					1																	169677562		1975	4151	6126	SO:0001819	synonymous_variant	6402	exon3			ACCTGTGTAACAG	M25280	CCDS53427.1	1q23-q25	2008-07-31	2008-07-31		ENSG00000188404	ENSG00000188404		"CD molecules"	10720	protein-coding gene	gene with protein product		153240	"lymphocyte adhesion molecule 1"	LYAM1, LNHR		2664786, 1375831	Standard	NR_029467		Approved	LSEL, LAM1, LAM-1, hLHRc, Leu-8, Lyam-1, PLNHR, CD62L	uc001ggk.3	P14151	OTTHUMG00000034809	ENST00000236147.4:c.507C>T	1.37:g.169677562G>A		181	0	0		146	41	0.280822	NM_000655	B2R6Q8|P15023|Q9UJ43	Silent	SNP	ENST00000236147.4	37	CCDS53427.1																																																																																			.	.	none		0.502	SELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084233.1	NM_000655		A	169677562	G	A	169677562	2	1	39	1	0	0	0	0	0	0	0	1	14031	1372	48	2		2	SELL	1	169677562	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	8379375	169677562	79573059	18	14563											
C1orf112	55732	hgsc.bcm.edu	37	chr1	169821960	169821960	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	aaaagagctcgtcaggagttCccctgggaagaagagtacag	14	6	13	8	1	1	3	1	0	0	3	3	5	2	5	2	2	2	3	2	2	5	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:169821960C>A	ENST00000286031.6	+	24	3094	c.2394C>A	c.(2392-2394)ttC>ttA	p.F798L	C1orf112_ENST00000498289.1_3'UTR|C1orf112_ENST00000359326.4_Missense_Mutation_p.F798L|SCYL3_ENST00000367771.6_3'UTR|SCYL3_ENST00000367772.4_3'UTR	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	798										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)					GTCAGGAGTTCCCCTGGGAAG	0.443																																					p.F798L		Atlas-SNP	.											.	C1orf112	74	.	0			c.C2394A						PASS	.						85	96	92					1																	169821960		2203	4300	6503	SO:0001583	missense	55732	exon24			GGAGTTCCCCTGG	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.2394C>A	1.37:g.169821960C>A	ENSP00000286031:p.Phe798Leu	174	0	0		119	31	0.260504	NM_018186	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Missense_Mutation	SNP	ENST00000286031.6	37	CCDS1285.1	.	.	.	.	.	.	.	.	.	.	C	9.708	1.156280	0.21454	.	.	ENSG00000000460	ENST00000359326;ENST00000286031	T;T	0.40225	1.04;1.04	5.42	1.96	0.26148	.	1.278610	0.04710	N	0.417527	T	0.04998	0.0134	N	0.02736	-0.51	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.24905	-1.0147	10	0.06236	T	0.91	9.7704	6.7373	0.23417	0.0:0.5238:0.3553:0.1209	.	798	Q9NSG2	CA112_HUMAN	L	798	ENSP00000352276:F798L;ENSP00000286031:F798L	ENSP00000286031:F798L	F	+	3	2	C1orf112	168088584	0.000000	0.05858	0.002000	0.10522	0.469000	0.32828	-0.140000	0.10342	0.589000	0.29677	0.591000	0.81541	TTC	.	.	none		0.443	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186		A	169821960	C	A	169821960	3	1	39	1	0	0	0	0	1	0	0	0	1987	854	30	4	2480	4	C1orf112	1	169821960	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	144398	169821960	79428661	19	14564											
RGS8	85397	hgsc.bcm.edu	37	chr1	182640795	182640795	+	5'UTR	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaaaggcaatactcactgtCtttggccagtcctcatggcc	9	10	9	13	0	3	0	2	0	1	0	4	0	4	0	3	3	1	2	3	3	3	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:182640795C>A	ENST00000483095.2	-	0	151				RGS8_ENST00000367556.1_5'UTR|RGS8_ENST00000491420.2_5'UTR|RGS8_ENST00000258302.4_Missense_Mutation_p.R26I|RGS8_ENST00000367557.4_5'UTR			P57771	RGS8_HUMAN	regulator of G-protein signaling 8						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						TACTCACTGTCTTTGGCCAGT	0.448																																					p.R26I	Ovarian(189;1262 3804 41973)	Atlas-SNP	.											.	RGS8	51	.	0			c.G77T						PASS	.						153	155	154					1																	182640795		2203	4300	6503	SO:0001623	5_prime_UTR_variant	85397	exon2			CACTGTCTTTGGC	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.-107G>T	1.37:g.182640795C>A		279	0	0		223	73	0.327354	NM_033345	B4DGL9|Q3SYD2	Missense_Mutation	SNP	ENST00000483095.2	37	CCDS41443.1	.	.	.	.	.	.	.	.	.	.	C	16.60	3.168356	0.57584	.	.	ENSG00000135824	ENST00000258302	T	0.46063	0.88	5.28	2.37	0.29283	.	4.860240	0.00357	N	0.000025	T	0.34366	0.0895	.	.	.	0.80722	D	1	P	0.35982	0.531	B	0.31245	0.126	T	0.02829	-1.1105	9	0.40728	T	0.16	.	8.5475	0.33430	0.0:0.7619:0.0:0.238	.	26	P57771-2	.	I	26	ENSP00000258302:R26I	ENSP00000258302:R26I	R	-	2	0	RGS8	180907418	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	1.286000	0.33273	0.219000	0.20840	0.563000	0.77884	AGA	.	.	none		0.448	RGS8-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358979.1	NM_033345		A	182640795	C	A	182640795	1	1	39	0	1	0	0	0	0	0	0	0	13327	913	32	4		4	RGS8	1	182640795	5'UTR	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	12818835	182640795	66609826	20	14565											
HMCN1	83872	hgsc.bcm.edu	37	chr1	185953339	185953339	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	atcactgtgcgcagtgatggGagcctccatattgaaagagt	11	10	12	8	1	1	3	1	2	0	1	2	4	2	4	2	1	2	1	2	1	2	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:185953339G>A	ENST00000271588.4	+	19	3058	c.2829G>A	c.(2827-2829)ggG>ggA	p.G943G	HMCN1_ENST00000485744.1_3'UTR|HMCN1_ENST00000367492.2_Silent_p.G943G	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	943	Ig-like C2-type 6.				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						GCAGTGATGGGAGCCTCCATA	0.388																																					p.G943G		Atlas-SNP	.											.	HMCN1	797	.	0			c.G2829A						PASS	.						175	170	172					1																	185953339		2203	4300	6503	SO:0001819	synonymous_variant	83872	exon19			TGATGGGAGCCTC	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.2829G>A	1.37:g.185953339G>A		176	0	0		171	32	0.187135	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	37	CCDS30956.1																																																																																			.	.	none		0.388	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	185953339	G	A	185953339	2	1	39	1	0	0	0	0	0	0	0	1	7229	1161	41	2		2	HMCN1	1	185953339	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	3312544	185953339	63297282	21	14566											
TPR	7175	hgsc.bcm.edu	37	chr1	186313566	186313566	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctccaacaactgtgattctgCtttctgtgttgtttcttcca	6	18	6	11	0	3	1	0	1	3	0	5	1	5	1	2	0	3	3	2	0	2	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:186313566C>T	ENST00000367478.4	-	25	3654	c.3358G>A	c.(3358-3360)Gca>Aca	p.A1120T		NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	1120					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)		TGTGATTCTGCTTTCTGTGTT	0.403			T	NTRK1	papillary thyroid																																p.A1120T		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.G3358A						PASS	.						274	250	257					1																	186313566		1924	4146	6070	SO:0001583	missense	7175	exon25			ATTCTGCTTTCTG	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.3358G>A	1.37:g.186313566C>T	ENSP00000356448:p.Ala1120Thr	196	0	0		152	20	0.131579	NM_003292	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	37	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.274866	0.80580	.	.	ENSG00000047410	ENST00000367478	T	0.37235	1.21	5.22	5.22	0.72569	Tetratricopeptide, MLP1/MLP2-like (1);	0.109197	0.64402	D	0.000010	T	0.37571	0.1008	L	0.45470	1.425	0.49687	D	0.99981	B	0.30326	0.276	B	0.32393	0.145	T	0.20874	-1.0262	10	0.49607	T	0.09	.	18.7751	0.91908	0.0:1.0:0.0:0.0	.	1120	P12270	TPR_HUMAN	T	1120	ENSP00000356448:A1120T	ENSP00000356448:A1120T	A	-	1	0	TPR	184580189	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.108000	0.57817	2.447000	0.82792	0.561000	0.74099	GCA	.	.	none		0.403	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292		T	186313566	C	T	186313566	3	4	39	1	0	0	0	0	1	0	0	0	16431	797	28	2	3841	2	TPR	1	186313566	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	360227	186313566	62937055	22	14567											
PTPRC	5788	hgsc.bcm.edu	37	chr1	198685901	198685901	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	atatgttttatcattacatgCctacatcattgcaaaagtgc	13	15	5	8	0	2	0	2	0	0	0	2	0	2	0	1	0	5	2	1	0	6	6			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:198685901C>T	ENST00000367376.2	+	13	1547	c.1376C>T	c.(1375-1377)gCc>gTc	p.A459V	PTPRC_ENST00000442510.2_Missense_Mutation_p.A461V|PTPRC_ENST00000594404.1_Missense_Mutation_p.A298V|PTPRC_ENST00000352140.3_Missense_Mutation_p.A411V|PTPRC_ENST00000348564.6_Missense_Mutation_p.A300V	NM_002838.4	NP_002829.3	P08575	PTPRC_HUMAN	protein tyrosine phosphatase, receptor type, C	459	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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						TCATTACATGCCTACATCATT	0.313																																					p.A461V		Atlas-SNP	.											.	PTPRC	229	.	0			c.C1382T						PASS	.						81	83	82					1																	198685901		2202	4300	6502	SO:0001583	missense	5788	exon13			TACATGCCTACAT	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.1376C>T	1.37:g.198685901C>T	ENSP00000356346:p.Ala459Val	554	1	0.00180505		499	156	0.312625	NM_002838	A8K7W6|Q16614|Q9H0Y6	Missense_Mutation	SNP	ENST00000367376.2	37		.	.	.	.	.	.	.	.	.	.	C	18.56	3.650718	0.67472	.	.	ENSG00000081237	ENST00000367376;ENST00000367366;ENST00000352140;ENST00000535566;ENST00000530727;ENST00000442510;ENST00000367367;ENST00000348564	T	0.68624	-0.34	4.43	4.43	0.53597	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.49916	D	0.000129	T	0.77948	0.4207	M	0.64404	1.975	0.23628	N	0.997254	D;D;D;D;D	0.89917	0.984;0.997;1.0;1.0;1.0	D;D;D;D;D	0.80764	0.926;0.974;0.994;0.994;0.994	T	0.68899	-0.5287	10	0.87932	D	0	.	12.8585	0.57899	0.0:1.0:0.0:0.0	.	395;395;300;411;459	F5GXZ3;B4DSZ5;B1ALS3;E9PC28;P08575	.;.;.;.;PTPRC_HUMAN	V	461;395;411;411;345;459;393;298	ENSP00000193532:A411V	ENSP00000306782:A298V	A	+	2	0	PTPRC	196952524	0.391000	0.25221	0.192000	0.23308	0.044000	0.14063	2.994000	0.49433	2.741000	0.93983	0.650000	0.86243	GCC	.	.	none		0.313	PTPRC-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding				T	198685901	C	T	198685901	3	4	39	1	0	0	0	0	1	0	0	0	12812	739	26	2	1433	2	PTPRC	1	198685901	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	12372335	198685901	50564720	23	14568											
ITPKB	3707	hgsc.bcm.edu	37	chr1	226924346	226924346	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccttttgtcaatttccatagCtgtgggtgagccacagcggg	7	12	12	10	1	1	1	1	1	0	0	2	1	2	1	3	2	3	1	3	2	2	4			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:226924346C>T	ENST00000272117.3	-	1	813	c.814G>A	c.(814-816)Gct>Act	p.A272T	ITPKB_ENST00000429204.1_Missense_Mutation_p.A272T|ITPKB_ENST00000366784.1_Missense_Mutation_p.A272T			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	272					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)				ATTTCCATAGCTGTGGGTGAG	0.602																																					p.A272T	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											.	ITPKB	158	.	0			c.G814A						PASS	.						44	48	46					1																	226924346		2203	4300	6503	SO:0001583	missense	3707	exon2			CCATAGCTGTGGG	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.814G>A	1.37:g.226924346C>T	ENSP00000272117:p.Ala272Thr	78	0	0		67	25	0.373134	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Missense_Mutation	SNP	ENST00000272117.3	37	CCDS1555.1	.	.	.	.	.	.	.	.	.	.	C	12.19	1.864168	0.32977	.	.	ENSG00000143772	ENST00000272117;ENST00000429204;ENST00000366784	T;T;T	0.23147	1.95;1.95;1.92	4.6	-2.09	0.07232	.	1.387480	0.04488	N	0.378907	T	0.13927	0.0337	N	0.19112	0.55	0.09310	N	1	B	0.14438	0.01	B	0.13407	0.009	T	0.24621	-1.0155	10	0.11182	T	0.66	.	5.7879	0.18343	0.0:0.3502:0.3657:0.2841	.	272	P27987	IP3KB_HUMAN	T	272	ENSP00000272117:A272T;ENSP00000411152:A272T;ENSP00000355748:A272T	ENSP00000272117:A272T	A	-	1	0	ITPKB	224990969	0.000000	0.05858	0.000000	0.03702	0.443000	0.32047	-0.766000	0.04725	-0.214000	0.10078	0.561000	0.74099	GCT	.	.	none		0.602	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221		T	226924346	C	T	226924346	3	4	39	1	0	0	0	0	1	0	0	0	7927	797	28	2	2054	2	ITPKB	1	226924346	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	28238445	226924346	22326275	24	14569											
ITPKB	3707	hgsc.bcm.edu	37	chr1	226924770	226924770	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcgcgctgcaagatccgcagCttcctcttggcctcctccgg	4	10	10	17	4	1	1	0	0	1	1	6	1	5	1	5	2	2	4	5	2	1	2	rs144653273	byFrequency	TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:226924770C>T	ENST00000272117.3	-	1	389	c.390G>A	c.(388-390)aaG>aaA	p.K130K	ITPKB_ENST00000429204.1_Silent_p.K130K|ITPKB_ENST00000366784.1_Silent_p.K130K			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	130					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)				AGATCCGCAGCTTCCTCTTGG	0.652													C|||	4	0.000798722	0.0	0.0	5008	,	,		14921	0.004		0.0	False		,,,				2504	0.0				p.K130K	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											.	ITPKB	158	.	0			c.G390A						PASS	.						59	60	60					1																	226924770		2180	4279	6459	SO:0001819	synonymous_variant	3707	exon2			CCGCAGCTTCCTC	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.390G>A	1.37:g.226924770C>T		59	0	0		48	17	0.354167	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Silent	SNP	ENST00000272117.3	37	CCDS1555.1																																																																																			C|1.000;T|0.000	0.000	strong		0.652	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221		T	226924770	C	T	226924770	2	4	39	1	0	0	0	0	0	0	0	1	7927	796	28	2		2	ITPKB	1	226924770	Silent	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	424	226924770	22325851	25	14570											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228471339	228471339	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctcttggagctacgggcctCagggaagcaccagcccagcc	8	5	12	16	1	2	0	1	0	1	0	2	2	2	2	5	3	5	2	5	3	2	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr1:228471339C>T	ENST00000422127.1	+	33	8917	c.8873C>T	c.(8872-8874)tCa>tTa	p.S2958L	OBSCN_ENST00000359599.6_Missense_Mutation_p.S1805L|OBSCN_ENST00000284548.11_Missense_Mutation_p.S2958L|OBSCN_ENST00000366709.4_Missense_Mutation_p.S77L|OBSCN_ENST00000366707.4_Missense_Mutation_p.S77L|OBSCN_ENST00000570156.2_Missense_Mutation_p.S3387L	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	2958	Ig-like 29.				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)				CTACGGGCCTCAGGGAAGCAC	0.647																																					p.S3387L		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C10160T						PASS	.						32	38	36					1																	228471339		2129	4236	6365	SO:0001583	missense	84033	exon38			GGGCCTCAGGGAA	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.8873C>T	1.37:g.228471339C>T	ENSP00000409493:p.Ser2958Leu	105	0	0		77	23	0.298701	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	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	c	23.6	4.436810	0.83885	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599;ENST00000366706;ENST00000366704	T;T;T;T;T	0.06371	3.31;3.31;3.31;3.31;3.31	5.67	5.67	0.87782	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.302534	0.25613	N	0.029461	T	0.22282	0.0537	M	0.89030	3	0.26131	N	0.980411	P;P;P	0.49358	0.785;0.923;0.887	P;P;P	0.51582	0.674;0.56;0.511	T	0.14699	-1.0463	10	0.66056	D	0.02	.	14.2576	0.66062	0.0:0.7337:0.2663:0.0	.	2958;2958;2958	Q5VST9;Q5VST9-2;Q5VST9-3	OBSCN_HUMAN;.;.	L	2958;2958;77;77;1805;657;364	ENSP00000284548:S2958L;ENSP00000409493:S2958L;ENSP00000355668:S77L;ENSP00000355670:S77L;ENSP00000352613:S1805L	ENSP00000284548:S2958L	S	+	2	0	OBSCN	226537962	0.996000	0.38824	0.806000	0.32338	0.095000	0.18619	4.055000	0.57441	2.673000	0.90976	0.550000	0.68814	TCA	.	.	none		0.647	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228471339	C	T	228471339	3	4	39	1	0	0	0	0	1	0	0	0	10821	838	29	2	8999	2	OBSCN	1	228471339	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	1546569	228471339	20779282	26	14571											
MYT1L	23040	hgsc.bcm.edu	37	chr2	1926161	1926161	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcatatgacctcatattGtccctcctcccagcttccat	7	14	3	17	0	2	1	2	1	0	0	7	1	7	1	6	0	1	1	6	0	2	4			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr2:1926161G>C	ENST00000399161.2	-	10	2127	c.1380C>G	c.(1378-1380)gaC>gaG	p.D460E	MYT1L_ENST00000428368.2_Missense_Mutation_p.D460E	NM_015025.2	NP_055840.2	Q9UL68	MYT1L_HUMAN	myelin transcription factor 1-like	460					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)		ACCTCATATTGTCCCTCCTCC	0.522																																					p.D460E		Atlas-SNP	.											.	MYT1L	241	.	0			c.C1380G						PASS	.						186	179	181					2																	1926161		1995	4157	6152	SO:0001583	missense	23040	exon10			CATATTGTCCCTC	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.1380C>G	2.37:g.1926161G>C	ENSP00000382114:p.Asp460Glu	268	0	0		203	58	0.285714	NM_015025	A7E2C7|B2RP54|Q6IQ17|Q9UPP6	Missense_Mutation	SNP	ENST00000399161.2	37		.	.	.	.	.	.	.	.	.	.	G	4.141	0.024540	0.08054	.	.	ENSG00000186487	ENST00000399161;ENST00000295067;ENST00000428368	T;T	0.42900	0.96;0.97	5.91	-1.63	0.08345	.	0.204264	0.53938	N	0.000057	T	0.19446	0.0467	N	0.19112	0.55	0.28153	N	0.929329	B;B	0.15141	0.012;0.01	B;B	0.13407	0.006;0.009	T	0.07501	-1.0769	10	0.25106	T	0.35	-41.3752	3.7061	0.08401	0.4795:0.1027:0.3136:0.1041	.	460;460	Q9UL68;Q9UL68-4	MYT1L_HUMAN;.	E	460;408;460	ENSP00000382114:D460E;ENSP00000396103:D460E	ENSP00000295067:D408E	D	-	3	2	MYT1L	1905168	1.000000	0.71417	0.017000	0.16124	0.017000	0.09413	1.033000	0.30191	-0.339000	0.08401	0.655000	0.94253	GAC	.	.	none		0.522	MYT1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000322493.1	NM_015025		C	1926161	G	C	1926161	3	2	39	1	0	0	0	0	1	0	0	0	10116	1368	48	4	2238	4	MYT1L	2	1926161	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10		1926161	241273212	27	14572											
COLEC11	78989	hgsc.bcm.edu	37	chr2	3691387	3691387	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggagaagcgctacgcggaCgcccagctgtcctgccaggg	8	4	16	13	4	0	1	0	0	0	1	1	4	1	2	3	3	4	2	3	3	2	1	rs545129835		TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr2:3691387C>T	ENST00000349077.4	+	7	598	c.495C>T	c.(493-495)gaC>gaT	p.D165D	COLEC11_ENST00000487365.1_3'UTR|COLEC11_ENST00000402794.1_Silent_p.D115D|COLEC11_ENST00000403096.3_Silent_p.D139D|COLEC11_ENST00000404205.1_Silent_p.D91D|COLEC11_ENST00000236693.7_Silent_p.D162D|COLEC11_ENST00000418971.2_Silent_p.D179D|COLEC11_ENST00000402922.1_Silent_p.D115D|COLEC11_ENST00000382062.2_Silent_p.D141D	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						PASS	.						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	2.37:g.3691387C>T		94	0	0		70	16	0.228571	NM_001255985	A1IGE4|A1IGE5|A1IGE6|A7VJJ2|A7VJJ3|A7VJJ4|A7VJJ5|B2R9M5|B4E1G0|J3KQY9|Q5CZ85|Q7Z6N1	Silent	SNP	ENST00000349077.4	37	CCDS1649.1																																																																																			.	.	none		0.662	COLEC11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206666.1	NM_024027		T	3691387	C	T	3691387	2	4	39	1	0	0	0	0	0	0	0	1	3713	535	19	1		1	COLEC11	2	3691387	Silent	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	1765226	3691387	239507986	28	14573											
APOB	338	hgsc.bcm.edu	37	chr2	21241888	21241888	+	Frame_Shift_Del	DEL	G	G	-																															tgcttgagttacaaacttcaGggtatccaccaaggctctgt																										TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr2:21241888delG	ENST00000233242.1	-	20	3224	c.3097delC	c.(3097-3099)ctgfs	p.L1033fs		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1033					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)					ACAAACTTCAGGGTATCCACC	0.473																																					p.L1033fs		Atlas-Indel	.											APOB,caecum,carcinoma,+1,1	APOB	761	1	0			c.3098delT						PASS	.						133	123	127					2																	21241888		2203	4300	6503	SO:0001589	frameshift_variant	338	exon20			.	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.3097delC	2.37:g.21241888delG	ENSP00000233242:p.Leu1033fs	194	0	0		132	34	0.257576	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Frame_Shift_Del	DEL	ENST00000233242.1	37	CCDS1703.1																																																																																			.	.	none		0.473	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			-	21241888	G	-	21241888	7	5	39	1	0	1	0	1	0	0	0	0	785	991	35	0	10634	0	APOB	2	21241888	Frame_Shift_Del	DEL	G	TCGA-GS-A9TW-01A-11D-A382-10	17550501	21241888	221957485	29	14574	188	3									
APOB	338	hgsc.bcm.edu	37	chr2	21241889	21241890	+	Frame_Shift_Del	DEL	GG	GG	-																															gcttgagttacaaacttcagGgtatccaccaaggctctgtc																										TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr2:21241889_21241890delGG	ENST00000233242.1	-	20	3222_3223	c.3095_3096delCC	c.(3094-3096)accfs	p.T1032fs		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1032					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)					CAAACTTCAGGGTATCCACCAA	0.47																																					p.1032_1033del		Pindel	.											APOB,caecum,carcinoma,+2,1	APOB	761	1	0			c.3096_3097del						PASS	.																																			SO:0001589	frameshift_variant	338	exon20			.	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.3095_3096delCC	2.37:g.21241889_21241890delGG	ENSP00000233242:p.Thr1032fs	197	0	.		131	27	0.206	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Frame_Shift_Del	DEL	ENST00000233242.1	37	CCDS1703.1																																																																																			.	.	none		0.47	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			-	21241890	GG	-	21241889	7	5	39	1	0	1	0	1	0	0	0	0	785	1219	43	0	10635	0	APOB	2	21241889	Frame_Shift_Del	DEL	GG	TCGA-GS-A9TW-01A-11D-A382-10	1	21241889	221957484	30	14575	188	3									
APOB	338	hgsc.bcm.edu	37	chr2	21241890	21241890	+	Missense_Mutation	SNP	G	G	C																															cttgagttacaaacttcaggGtatccaccaaggctctgtcc																										TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr2:21241890G>C	ENST00000233242.1	-	20	3222	c.3095C>G	c.(3094-3096)aCc>aGc	p.T1032S		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	1032					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)					AAACTTCAGGGTATCCACCAA	0.473																																					p.T1032S		Atlas-SNP	.											.	APOB	761	.	0			c.C3095G						PASS	.						134	124	128					2																	21241890		2203	4300	6503	SO:0001583	missense	338	exon20			TTCAGGGTATCCA	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.3095C>G	2.37:g.21241890G>C	ENSP00000233242:p.Thr1032Ser	198	0	0		132	34	0.257576	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	14.34	2.507504	0.44558	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.00717	5.79	4.3	-0.221	0.13126	Lipid transport, open beta-sheet (1);Vitellinogen, open beta-sheet, subdomain 2 (1);	0.291638	0.24067	N	0.041848	T	0.00608	0.0020	N	0.26042	0.785	0.80722	D	1	B	0.24963	0.115	B	0.25140	0.058	T	0.62959	-0.6743	10	0.21014	T	0.42	.	6.8881	0.24214	0.1539:0.2639:0.5821:0.0	.	1032	P04114	APOB_HUMAN	S	1032	ENSP00000233242:T1032S	ENSP00000233242:T1032S	T	-	2	0	APOB	21095395	0.998000	0.40836	0.437000	0.26809	0.982000	0.71751	2.741000	0.47426	0.121000	0.18284	0.460000	0.39030	ACC	.	.	none		0.473	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			C	21241890	G	C	21241890	3	2	39	1	0	0	0	0	1	0	0	0	785	1261	44	4	10636	4	APOB	2	21241890	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	1	21241890	221957483	31	14576	188	3									
C2orf39	92749	hgsc.bcm.edu	37	chr2	26652610	26652610	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agaatgtgatgaaaacctttCgtgaggagctctataacatt	14	12	9	6	1	1	4	0	3	1	1	2	5	1	5	1	1	3	1	1	1	5	4	rs577516330	byFrequency	TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr2:26652610C>T	ENST00000288710.2	+	5	729	c.655C>T	c.(655-657)Cgt>Tgt	p.R219C		NM_145038.2	NP_659475.2	Q96MC2	DRC1_HUMAN	dynein regulatory complex subunit 1	219					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)											GAAAACCTTTCGTGAGGAGCT	0.473													C|||	6	0.00119808	0.0	0.0	5008	,	,		17363	0.0		0.0	False		,,,				2504	0.0061				p.R219C		Atlas-SNP	.											.	CCDC164	84	.	0			c.C655T						PASS	.						108	107	107					2																	26652610		2203	4300	6503	SO:0001583	missense	92749	exon5			ACCTTTCGTGAGG	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.655C>T	2.37:g.26652610C>T	ENSP00000288710:p.Arg219Cys	107	0	0		96	32	0.333333	NM_145038	A8K1N8|Q53R91|Q53TA3|Q8NDI5	Missense_Mutation	SNP	ENST00000288710.2	37	CCDS1723.1	.	.	.	.	.	.	.	.	.	.	C	15.96	2.987275	0.53934	.	.	ENSG00000157856	ENST00000288710	T	0.17528	2.27	5.35	5.35	0.76521	.	0.053346	0.64402	D	0.000001	T	0.41880	0.1178	M	0.83012	2.62	0.50313	D	0.99986	D	0.71674	0.998	P	0.62813	0.907	T	0.40979	-0.9534	10	0.87932	D	0	-10.8199	12.8901	0.58066	0.1629:0.8371:0.0:0.0	.	219	Q96MC2	CC164_HUMAN	C	219	ENSP00000288710:R219C	ENSP00000288710:R219C	R	+	1	0	CCDC164	26506114	0.848000	0.29623	0.782000	0.31804	0.377000	0.30045	1.849000	0.39318	2.506000	0.84524	0.563000	0.77884	CGT	.	.	none		0.473	DRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246862.1	NM_145038		T	26652610	C	T	26652610	3	4	39	1	0	0	0	0	1	0	0	0	2166	884	31	1	673	1	C2orf39	2	26652610	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	5410720	26652610	216546763	32	14577											
ZNF513	130557	hgsc.bcm.edu	37	chr2	27601207	27601207	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggcaccacctggtggcacAtggaggctcaaatctggaag	10	7	13	11	0	2	0	1	0	1	0	2	2	2	2	2	6	0	3	2	6	2	0			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr2:27601207A>G	ENST00000323703.6	-	4	1029	c.831T>C	c.(829-831)caT>caC	p.H277H	ZNF513_ENST00000491924.1_Intron|ZNF513_ENST00000407879.1_Silent_p.H215H	NM_144631.5	NP_653232.3	Q8N8E2	ZN513_HUMAN	zinc finger protein 513	277					regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transcription regulatory region DNA binding (GO:0044212)			endometrium(5)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)	17	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTGGTGGCACATGGAGGCTCA	0.592																																					p.H277H		Atlas-SNP	.											.	ZNF513	45	.	0			c.T831C						PASS	.						34	37	36					2																	27601207		2203	4300	6503	SO:0001819	synonymous_variant	130557	exon4			TGGCACATGGAGG	AL833946	CCDS1751.1, CCDS56114.1	2p23.3	2014-01-28			ENSG00000163795	ENSG00000163795		"Zinc fingers, C2H2-type"	26498	protein-coding gene	gene with protein product		613598				12477932	Standard	NM_001201459		Approved	FLJ32203, RP58	uc002rkk.3	Q8N8E2	OTTHUMG00000097783	ENST00000323703.6:c.831T>C	2.37:g.27601207A>G		12	0	0		22	7	0.318182	NM_144631	A8K3S5|B7WP71|Q3ZCU1|Q68CJ1|Q86UZ3|Q8NDL8|Q96ML3	Silent	SNP	ENST00000323703.6	37	CCDS1751.1																																																																																			.	.	none		0.592	ZNF513-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215026.2	NM_144631		G	27601207	A	G	27601207	2	3	39	1	0	0	0	0	0	0	0	1	17973	214	8	3		3	ZNF513	2	27601207	Silent	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	948597	27601207	215598166	33	14578											
SLC4A1AP	22950	hgsc.bcm.edu	37	chr2	27886844	27886844	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gacctcagtggggacttcaaGaagccagctctgccggtgtc	8	8	13	12	1	3	1	2	0	1	1	4	3	3	2	3	3	3	1	3	3	2	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr2:27886844G>A	ENST00000326019.6	+	1	507	c.225G>A	c.(223-225)aaG>aaA	p.K75K	SUPT7L_ENST00000337768.5_5'Flank|SUPT7L_ENST00000404798.2_5'Flank|SUPT7L_ENST00000464789.2_5'Flank|SUPT7L_ENST00000405491.1_5'Flank|SUPT7L_ENST00000406540.1_5'Flank	NM_018158.2	NP_060628.2	Q9BWU0	NADAP_HUMAN	solute carrier family 4 (anion exchanger), member 1, adaptor protein	75						cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(172;0.155)					GGGACTTCAAGAAGCCAGCTC	0.597																																					p.K75K		Atlas-SNP	.											.	SLC4A1AP	63	.	0			c.G225A						PASS	.						60	63	62					2																	27886844		2203	4300	6503	SO:0001819	synonymous_variant	22950	exon1			CTTCAAGAAGCCA		CCDS33166.1	2p23.3	2010-03-11	2001-11-28		ENSG00000163798	ENSG00000163798			13813	protein-coding gene	gene with protein product	"lung cancer oncogene 3"	602655	"solute carrier family 4 (anion exchanger), member 1, adapter protein"			9422766	Standard	NM_018158		Approved	kanadaptin, HLC3	uc002rlk.4	Q9BWU0	OTTHUMG00000151944	ENST00000326019.6:c.225G>A	2.37:g.27886844G>A		66	0	0		62	19	0.306452	NM_018158	A6NJ39|Q4KMT1|Q4KMX0|Q7Z5Q9|Q9NVN2	Silent	SNP	ENST00000326019.6	37	CCDS33166.1																																																																																			.	.	none		0.597	SLC4A1AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324550.1	NM_018158		A	27886844	G	A	27886844	2	1	39	1	0	0	0	0	0	0	0	1	14668	933	33	2		2	SLC4A1AP	2	27886844	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	285637	27886844	215312529	34	14579											
FANCL	55120	hgsc.bcm.edu	37	chr2	58459217	58459217	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cttcagttgtaaatcttcagGcaacactatcctaaggtgga	12	12	8	9	0	3	0	2	0	1	0	4	1	4	1	1	3	1	3	1	3	5	6			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr2:58459217G>A	ENST00000233741.4	-	2	163	c.127C>T	c.(127-129)Cct>Tct	p.P43S	FANCL_ENST00000402135.3_Missense_Mutation_p.P43S|FANCL_ENST00000403295.3_Missense_Mutation_p.P43S|FANCL_ENST00000403676.1_Intron|FANCL_ENST00000481670.1_5'Flank|FANCL_ENST00000540646.1_Missense_Mutation_p.P43S	NM_018062.3	NP_060532.2	Q9NW38	FANCL_HUMAN	Fanconi anemia, complementation group L	43					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|gamete generation (GO:0007276)|protein monoubiquitination (GO:0006513)|regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|Fanconi anaemia nuclear complex (GO:0043240)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	ligase activity (GO:0016874)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(1)|lung(4)|ovary(2)	8						AAATCTTCAGGCAACACTATC	0.348								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.P43S		Atlas-SNP	.											.	FANCL	35	.	0			c.C127T						PASS	.						122	105	111					2																	58459217		2201	4300	6501	SO:0001583	missense	55120	exon2	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CTTCAGGCAACAC	AK001197	CCDS1860.1, CCDS46294.1	2p16.1	2014-09-17	2003-10-14	2003-10-15	ENSG00000115392	ENSG00000115392		"Zinc fingers, PHD-type", "Fanconi anemia, complementation groups"	20748	protein-coding gene	gene with protein product		608111	"PHD finger protein 9"	PHF9			Standard	NM_018062		Approved	FLJ10335, FAAP43, Pog	uc002rzx.4	Q9NW38	OTTHUMG00000129349	ENST00000233741.4:c.127C>T	2.37:g.58459217G>A	ENSP00000233741:p.Pro43Ser	135	0	0		126	40	0.31746	NM_018062	Q6GU60	Missense_Mutation	SNP	ENST00000233741.4	37	CCDS1860.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.82|19.82	3.898417|3.898417	0.72639|0.72639	.|.	.|.	ENSG00000115392|ENSG00000115392	ENST00000427708|ENST00000403295;ENST00000233741;ENST00000402135;ENST00000540646	.|T;T;T;T	.|0.77489	.|-1.1;-1.1;-1.1;-1.1	6.01|6.01	6.01|6.01	0.97437|0.97437	.|Fanconi anemia complex, subunit FancL, WD-repeat containing domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.87034|0.87034	0.6077|0.6077	M|M	0.69248|0.69248	2.105|2.105	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D;D	.|0.89917	.|0.981;1.0;1.0	.|P;D;D	.|0.81914	.|0.869;0.991;0.995	D|D	0.86133|0.86133	0.1576|0.1576	5|10	.|0.49607	.|T	.|0.09	-21.5012|-21.5012	17.4309|17.4309	0.87539|0.87539	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|43;43;43	.|B5MC31;Q9NW38-2;Q9NW38	.|.;.;FANCL_HUMAN	V|S	42|43	.|ENSP00000386097:P43S;ENSP00000233741:P43S;ENSP00000385021:P43S;ENSP00000441431:P43S	.|ENSP00000233741:P43S	A|P	-|-	2|1	0|0	FANCL|FANCL	58312721|58312721	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.813000|0.813000	0.45954|0.45954	5.093000|5.093000	0.64517|0.64517	2.850000|2.850000	0.98022|0.98022	0.655000|0.655000	0.94253|0.94253	GCC|CCT	.	.	none		0.348	FANCL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251497.1	NM_018062		A	58459217	G	A	58459217	3	1	39	1	0	0	0	0	1	0	0	0	5678	1203	42	2	1067	2	FANCL	2	58459217	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	30572373	58459217	184740156	35	14580											
XPO1	7514	hgsc.bcm.edu	37	chr2	61719472	61719472	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agatttaccatgcatgaattCgaacagcttgttaactacag	14	12	7	8	1	0	2	0	1	0	1	1	3	0	2	1	0	6	3	1	0	5	6			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr2:61719472C>T	ENST00000401558.2	-	15	2438	c.1711G>A	c.(1711-1713)Gaa>Aaa	p.E571K	XPO1_ENST00000404992.2_Missense_Mutation_p.E571K|XPO1_ENST00000406957.1_Missense_Mutation_p.E571K	NM_003400.3	NP_003391.1	O14980	XPO1_HUMAN	exportin 1	571	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)	p.E571K(5)		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)			TGCATGAATTCGAACAGCTTG	0.313			Mis		CLL																																p.E571K		Atlas-SNP	.	-'	Dom	yes		2	2p15	7514	"exportin 1 (CRM1 homolog, yeast)"		L	XPO1,NS,carcinoma,0,17	XPO1	108	17	5	Substitution - Missense(5)	haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|prostate(1)|endometrium(1)	c.G1711A						PASS	.						66	63	64					2																	61719472		2203	4300	6503	SO:0001583	missense	7514	exon15			TGAATTCGAACAG	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.1711G>A	2.37:g.61719472C>T	ENSP00000384863:p.Glu571Lys	301	0	0		278	84	0.302158	NM_003400	A6NL14|A8K1K5|D6W5E2|Q63HP8|Q68CP3|Q99433	Missense_Mutation	SNP	ENST00000401558.2	37	CCDS33205.1	.	.	.	.	.	.	.	.	.	.	C	36	5.629400	0.96671	.	.	ENSG00000082898	ENST00000401558;ENST00000404992;ENST00000406957	T;T;T	0.66099	-0.19;-0.19;-0.19	5.63	5.63	0.86233	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.85856	0.5794	H	0.94734	3.575	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.88632	0.3170	10	0.66056	D	0.02	-19.4383	20.0572	0.97657	0.0:1.0:0.0:0.0	.	218;571	B3KWD0;O14980	.;XPO1_HUMAN	K	571	ENSP00000384863:E571K;ENSP00000385942:E571K;ENSP00000385559:E571K	ENSP00000384863:E571K	E	-	1	0	XPO1	61572976	1.000000	0.71417	0.996000	0.52242	0.987000	0.75469	7.722000	0.84778	2.826000	0.97356	0.655000	0.94253	GAA	.	.	none		0.313	XPO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325872.3	NM_003400		T	61719472	C	T	61719472	3	4	39	1	0	0	0	0	1	0	0	0	17460	893	31	1	1548	1	XPO1	2	61719472	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	3260255	61719472	181479901	36	14581											
SPRED2	200734	hgsc.bcm.edu	37	chr2	65561836	65561836	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaaacttcctattatcgacCttccagtgatgaaacgttgg	11	12	7	11	2	0	2	0	2	0	0	3	3	2	2	4	1	2	1	4	1	4	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr2:65561836C>G	ENST00000356388.4	-	3	465	c.276G>C	c.(274-276)aaG>aaC	p.K92N	SPRED2_ENST00000443619.2_Missense_Mutation_p.K89N|SPRED2_ENST00000474228.1_5'UTR	NM_181784.2	NP_861449.2	Q7Z698	SPRE2_HUMAN	sprouty-related, EVH1 domain containing 2	92	WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}.				inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|regulation of protein deacetylation (GO:0090311)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|stem cell factor receptor binding (GO:0005173)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(7)|ovary(2)|upper_aerodigestive_tract(3)	34						TATTATCGACCTTCCAGTGAT	0.453																																					p.K92N		Atlas-SNP	.											.	SPRED2	70	.	0			c.G276C						PASS	.						212	198	202					2																	65561836		2203	4300	6503	SO:0001583	missense	200734	exon3			ATCGACCTTCCAG	AF052178	CCDS33211.1, CCDS46308.1	2p14	2003-06-02			ENSG00000198369	ENSG00000198369			17722	protein-coding gene	gene with protein product		609292					Standard	NM_181784		Approved	Spred-2, FLJ21897, FLJ31917	uc002sdr.4	Q7Z698	OTTHUMG00000152737	ENST00000356388.4:c.276G>C	2.37:g.65561836C>G	ENSP00000348753:p.Lys92Asn	189	0	0		162	51	0.314815	NM_181784	A1L3V4|B7Z5K7|D6W5F7|E9PEP0|Q2NKX6	Missense_Mutation	SNP	ENST00000356388.4	37	CCDS33211.1	.	.	.	.	.	.	.	.	.	.	C	14.76	2.630623	0.46944	.	.	ENSG00000198369	ENST00000356388;ENST00000443619;ENST00000452315;ENST00000421087;ENST00000440972	D;D;D;D;D	0.98666	-5.06;-5.06;-5.06;-5.06;-5.06	5.28	-0.546	0.11840	EVH1 (2);Pleckstrin homology-type (1);	0.144353	0.64402	D	0.000010	D	0.97498	0.9181	M	0.73962	2.25	0.51482	D	0.999928	B;B	0.22146	0.065;0.049	B;B	0.34418	0.182;0.112	D	0.93945	0.7227	10	0.72032	D	0.01	-18.6884	9.8976	0.41329	0.0:0.329:0.0:0.671	.	89;92	E9PEP0;Q7Z698	.;SPRE2_HUMAN	N	92;89;107;24;92	ENSP00000348753:K92N;ENSP00000393697:K89N;ENSP00000390595:K107N;ENSP00000407627:K24N;ENSP00000406481:K92N	ENSP00000348753:K92N	K	-	3	2	SPRED2	65415340	0.976000	0.34144	0.998000	0.56505	0.993000	0.82548	0.200000	0.17257	-0.033000	0.13736	-0.136000	0.14681	AAG	.	.	none		0.453	SPRED2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000327632.1			G	65561836	C	G	65561836	3	3	39	1	0	0	0	0	1	0	0	0	15108	680	24	4	996	4	SPRED2	2	65561836	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	3842364	65561836	177637537	37	14582											
KDM3A	55818	hgsc.bcm.edu	37	chr2	86669185	86669185	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaaaccatggtgctcacgctCggagaaagttggccggtatt	10	9	13	9	3	1	1	1	0	0	1	2	3	1	1	2	4	2	4	2	4	3	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr2:86669185C>T	ENST00000409556.1	+	3	380	c.15C>T	c.(13-15)ctC>ctT	p.L5L	KDM3A_ENST00000542128.1_Silent_p.L5L|KDM3A_ENST00000312912.5_Silent_p.L5L|KDM3A_ENST00000409064.1_Silent_p.L5L			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	5					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						TGCTCACGCTCGGAGAAAGTT	0.642																																					p.L5L	NSCLC(96;1150 1523 6936 46253 49736)	Atlas-SNP	.											.	KDM3A	179	.	0			c.C15T						PASS	.						96	99	98					2																	86669185		2203	4300	6503	SO:0001819	synonymous_variant	55818	exon2			CACGCTCGGAGAA	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.15C>T	2.37:g.86669185C>T		71	0	0		51	20	0.392157	NM_001146688	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Silent	SNP	ENST00000409556.1	37	CCDS1990.1																																																																																			.	.	none		0.642	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433		T	86669185	C	T	86669185	2	4	39	1	0	0	0	0	0	0	0	1	8135	871	31	1		1	KDM3A	2	86669185	Silent	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	21107349	86669185	156530188	38	14583											
FAM178B	51252	hgsc.bcm.edu	37	chr2	97637661	97637661	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggggccgcagcctgctggcTcaggcctgacgtgttccaga	5	8	15	13	2	1	2	1	1	0	1	2	2	2	2	4	4	2	4	4	4	0	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr2:97637661T>C	ENST00000417561.3	-	7	984	c.985A>G	c.(985-987)Agc>Ggc	p.S329G	FAM178B_ENST00000327896.3_Missense_Mutation_p.S149G|FAM178B_ENST00000490605.2_Missense_Mutation_p.S181G			Q8IXR5	F178B_HUMAN	family with sequence similarity 178, member B	329										large_intestine(1)|ovary(1)	2						GCCTGCTGGCTCAGGCCTGAC	0.617																																					p.S181G		Atlas-SNP	.											.	FAM178B	35	.	0			c.A541G						PASS	.						16	26	23					2																	97637661		692	1590	2282	SO:0001583	missense	51252	exon3			GCTGGCTCAGGCC	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.985A>G	2.37:g.97637661T>C	ENSP00000413245:p.Ser329Gly	144	0	0		124	46	0.370968	NM_001122646	A8MXN2|E9PD86|Q8IUY0|Q9P0P4	Missense_Mutation	SNP	ENST00000417561.3	37		.	.	.	.	.	.	.	.	.	.	T	9.337	1.062118	0.19987	.	.	ENSG00000168754	ENST00000417561;ENST00000327896;ENST00000490605	T;T;T	0.51574	0.7;0.77;0.75	4.23	1.8	0.24995	.	1.317100	0.05971	U	0.642372	T	0.30727	0.0774	L	0.29908	0.895	0.09310	N	1	.	.	.	.	.	.	T	0.21793	-1.0235	8	0.11485	T	0.65	-1.5505	2.919	0.05762	0.212:0.1255:0.0:0.6625	.	.	.	.	G	329;149;181	ENSP00000413245:S329G;ENSP00000333553:S149G;ENSP00000429896:S181G	ENSP00000333553:S149G	S	-	1	0	FAM178B	97001388	0.007000	0.16637	0.002000	0.10522	0.008000	0.06430	1.048000	0.30379	0.393000	0.25203	-0.336000	0.08194	AGC	.	.	none		0.617	FAM178B-202	KNOWN	basic	protein_coding	protein_coding		NM_016490		C	97637661	T	C	97637661	3	2	39	1	0	0	0	0	1	0	0	0	5509	1551	54	3	1589	3	FAM178B	2	97637661	Missense_Mutation	SNP	T	TCGA-GS-A9TW-01A-11D-A382-10	10968476	97637661	145561712	39	14584											
SH3RF3	344558	hgsc.bcm.edu	37	chr2	110049003	110049003	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cccagaagagtgacgagctgGagctgcacaagggagagatg	13	4	16	8	1	0	4	0	1	0	3	0	8	0	6	1	2	3	3	1	2	2	0			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr2:110049003G>A	ENST00000309415.6	+	6	1450	c.1450G>A	c.(1450-1452)Gag>Aag	p.E484K		NM_001099289.1	NP_001092759.1	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3	484	SH3 3. {ECO:0000255|PROSITE- ProRule:PRU00192}.						zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(5)|ovary(2)	18						TGACGAGCTGGAGCTGCACAA	0.637																																					p.E484K		Atlas-SNP	.											.	SH3RF3	62	.	0			c.G1450A						PASS	.						39	45	43					2																	110049003		2020	4203	6223	SO:0001583	missense	344558	exon6			GAGCTGGAGCTGC	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.1450G>A	2.37:g.110049003G>A	ENSP00000309186:p.Glu484Lys	55	0	0		41	15	0.365854	NM_001099289	A0SDZ7|A8MPR1|Q8NDU1	Missense_Mutation	SNP	ENST00000309415.6	37		.	.	.	.	.	.	.	.	.	.	G	34	5.408357	0.96051	.	.	ENSG00000172985	ENST00000418513;ENST00000309415	T;T	0.29917	1.55;1.55	4.9	4.9	0.64082	Src homology-3 domain (4);	0.000000	0.85682	D	0.000000	T	0.58708	0.2141	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.61173	-0.7116	9	0.54805	T	0.06	-50.5295	18.6073	0.91271	0.0:0.0:1.0:0.0	.	484	Q8TEJ3	SH3R3_HUMAN	K	484	ENSP00000414997:E484K;ENSP00000309186:E484K	ENSP00000309186:E484K	E	+	1	0	SH3RF3	109415435	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.271000	0.95698	2.688000	0.91661	0.561000	0.74099	GAG	.	.	none		0.637	SH3RF3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001099289		A	110049003	G	A	110049003	3	1	39	1	0	0	0	0	1	0	0	0	14275	1175	41	2	1472	2	SH3RF3	2	110049003	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	12411342	110049003	133150370	40	14585											
SLC20A1	6574	hgsc.bcm.edu	37	chr2	113404650	113404650	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttactgggggccaaagtgaGcgaaaccatccggaagggct	11	6	14	10	2	0	1	0	1	0	0	1	3	1	2	3	4	3	1	3	4	4	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr2:113404650G>C	ENST00000272542.3	+	2	784	c.245G>C	c.(244-246)aGc>aCc	p.S82T	AC079922.3_ENST00000457336.1_lincRNA	NM_005415.4	NP_005406.3	Q8WUM9	S20A1_HUMAN	solute carrier family 20 (phosphate transporter), member 1	82					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						GCCAAAGTGAGCGAAACCATC	0.527																																					p.S82T		Atlas-SNP	.											.	SLC20A1	59	.	0			c.G245C						PASS	.						137	125	129					2																	113404650		2203	4300	6503	SO:0001583	missense	6574	exon2			AAGTGAGCGAAAC		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.245G>C	2.37:g.113404650G>C	ENSP00000272542:p.Ser82Thr	162	0	0		147	47	0.319728	NM_005415	Q08344|Q6DHX8|Q9UQ82	Missense_Mutation	SNP	ENST00000272542.3	37	CCDS2099.1	.	.	.	.	.	.	.	.	.	.	G	14.53	2.562548	0.45694	.	.	ENSG00000144136	ENST00000272542	D	0.90069	-2.61	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	D	0.83580	0.5285	N	0.17631	0.505	0.80722	D	1	B	0.25441	0.126	B	0.30316	0.114	T	0.80779	-0.1230	10	0.54805	T	0.06	-21.2441	17.2043	0.86914	0.0:0.0:1.0:0.0	.	82	Q8WUM9	S20A1_HUMAN	T	82	ENSP00000272542:S82T	ENSP00000272542:S82T	S	+	2	0	SLC20A1	113121121	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.806000	0.99153	2.733000	0.93635	0.591000	0.81541	AGC	.	.	none		0.527	SLC20A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254086.2	NM_005415		C	113404650	G	C	113404650	3	2	39	1	0	0	0	0	1	0	0	0	14453	971	34	4	247	4	SLC20A1	2	113404650	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	3355647	113404650	129794723	41	14586											
IFIH1	64135	hgsc.bcm.edu	37	chr2	163144683	163144684	+	Frame_Shift_Ins	INS	-	-	T																															acttttccaggctcagatgcINSttttttcttcttgtctaagt																										TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr2:163144683_163144684insT	ENST00000263642.2	-	5	1451_1452	c.1056_1057insA	c.(1054-1059)aaagcafs	p.A353fs		NM_022168.3	NP_071451.2	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	353	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)	p.A353T(1)|p.K352N(1)		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						GGCTCAGATGCTTTTTTCTTCT	0.366																																					p.A353fs		Pindel,Atlas-Indel	.											IFIH1,scalp,carcinoma,0,1	IFIH1	102	1	2	Substitution - Missense(2)	kidney(1)|skin(1)	c.1057_1058insA						PASS	.																																			SO:0001589	frameshift_variant	64135	exon5			.	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.1057dupA	2.37:g.163144689_163144689dupT	ENSP00000263642:p.Ala353fs	365	0	.		334	53	0.159	NM_022168	Q2NKL6|Q6DC96|Q86X56|Q96MX8|Q9H3G6	Frame_Shift_Ins	INS	ENST00000263642.2	37	CCDS2217.1																																																																																			.	.	none		0.366	IFIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255078.2	NM_022168		T	163144684	-	T	163144683	7	5	39	1	0	1	1	0	0	0	0	0	7529	797	28	0	2068	0	IFIH1	2	163144683	Frame_Shift_Ins	INS	-	TCGA-GS-A9TW-01A-11D-A382-10	49740033	163144683	80054690	42	14587											
SCN7A	6332	hgsc.bcm.edu	37	chr2	167298253	167298253	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccaatactttcccaacttgaAaattcttaactaatagagca	16	12	3	10	0	1	2	0	1	1	1	2	2	2	2	2	0	4	1	2	0	8	7			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr2:167298253A>T	ENST00000409855.1	-	14	1936	c.1810T>A	c.(1810-1812)Ttc>Atc	p.F604I		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	604					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)	CCCAACTTGAAAATTCTTAAC	0.353																																					p.F604I		Atlas-SNP	.											.	SCN7A	410	.	0			c.T1810A						PASS	.						72	69	70					2																	167298253		1889	4124	6013	SO:0001583	missense	6332	exon14			ACTTGAAAATTCT	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.1810T>A	2.37:g.167298253A>T	ENSP00000386796:p.Phe604Ile	224	0	0		172	47	0.273256	NM_002976		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.137203	0.77775	.	.	ENSG00000136546	ENST00000409855;ENST00000259060;ENST00000419992	D;D	0.98474	-4.95;-4.95	4.78	3.59	0.41128	Ion transport (1);	0.113989	0.40302	N	0.001126	D	0.95156	0.8430	L	0.34521	1.04	0.36641	D	0.876824	B	0.29162	0.235	B	0.29524	0.103	D	0.94194	0.7444	10	0.87932	D	0	.	8.9138	0.35570	0.827:0.0:0.0:0.173	.	604	Q01118	SCN7A_HUMAN	I	604	ENSP00000386796:F604I;ENSP00000413699:F604I	ENSP00000259060:F604I	F	-	1	0	SCN7A	167006499	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	7.203000	0.77864	0.917000	0.36895	0.477000	0.44152	TTC	.	.	none		0.353	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1			T	167298253	A	T	167298253	3	4	39	1	0	0	0	0	1	0	0	0	13938	14	1	5	3286	5	SCN7A	2	167298253	Missense_Mutation	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	4153570	167298253	75901120	43	14588											
CDCA7	83879	hgsc.bcm.edu	37	chr2	174224116	174224116	+	Intron	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccattgtggatttttacagaAaccaaggccagatgtcacta	13	11	8	9	0	1	2	1	0	0	2	1	3	1	3	3	2	2	0	3	2	4	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr2:174224116A>G	ENST00000347703.3	+	2	291				CDCA7_ENST00000306721.3_Missense_Mutation_p.K94R|CDCA7_ENST00000410101.3_Splice_Site_p.K50R|CDCA7_ENST00000392567.2_Intron|CDCA7_ENST00000410019.3_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)				breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.116)			TTTTTACAGAAACCAAGGCCA	0.413																																					p.K94R		Atlas-SNP	.											.	CDCA7	48	.	0			c.A281G						PASS	.						99	100	99					2																	174224116		2203	4300	6503	SO:0001627	intron_variant	83879	exon3			TACAGAAACCAAG	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+551A>G	2.37:g.174224116A>G		200	0	0		232	71	0.306034	NM_031942	B4DLP8|B4DV66|Q53EW5|Q580W9|Q658K4|Q658N4|Q8NBY9|Q96BV8|Q96SP5	Missense_Mutation	SNP	ENST00000347703.3	37	CCDS2253.1	.	.	.	.	.	.	.	.	.	.	A	14.22	2.470673	0.43942	.	.	ENSG00000144354	ENST00000306721;ENST00000410101	T;T	0.48522	0.81;0.81	6.06	6.06	0.98353	.	0.219733	0.31772	N	0.007090	T	0.49081	0.1536	.	.	.	0.80722	D	1	D;B	0.62365	0.991;0.2	P;B	0.47603	0.551;0.051	T	0.43310	-0.9399	9	0.31617	T	0.26	-21.9646	14.8662	0.70419	1.0:0.0:0.0:0.0	.	50;94	B4DV66;Q9BWT1-2	.;.	R	94;50	ENSP00000306968:K94R;ENSP00000386656:K50R	ENSP00000306968:K94R	K	+	2	0	CDCA7	173932362	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	5.236000	0.65354	2.323000	0.78572	0.528000	0.53228	AAA	.	.	none		0.413	CDCA7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255400.1	NM_031942		G	174224116	A	G	174224116	1	3	39	0	1	0	0	0	0	0	0	0	3092	14	1	3		3	CDCA7	2	174224116	Intron	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	6925863	174224116	68975257	44	14589											
SPATS2L	26010	hgsc.bcm.edu	37	chr2	201284179	201284179	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	cctcgtgagaaaaagatctcGatacttgaggaaccttcaaa	15	9	8	9	2	2	3	1	2	1	2	4	6	2	4	2	1	2	0	2	1	5	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr2:201284179G>C	ENST00000358677.5	+	6	652	c.405G>C	c.(403-405)tcG>tcC	p.S135S	SPATS2L_ENST00000409755.3_Silent_p.S165S|SPATS2L_ENST00000409151.1_Silent_p.S143S|SPATS2L_ENST00000409718.1_Silent_p.S135S|SPATS2L_ENST00000409988.3_Silent_p.S135S|SPATS2L_ENST00000451764.2_Silent_p.S135S|SPATS2L_ENST00000409385.1_Silent_p.S75S|SPATS2L_ENST00000360760.5_Silent_p.S135S|SPATS2L_ENST00000409140.3_Silent_p.S135S	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	135						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						AAAAGATCTCGATACTTGAGG	0.463																																					p.S135S		Atlas-SNP	.											.	SPATS2L	88	.	0			c.G405C						PASS	.						43	44	44					2																	201284179		1937	4129	6066	SO:0001819	synonymous_variant	26010	exon6			GATCTCGATACTT	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.405G>C	2.37:g.201284179G>C		147	0	0		90	31	0.344444	NM_001100423	A8K381|B4DRE6|B4DT67|B7WNZ7|Q53T22|Q8WV53|Q8WYG1|Q9NTW4	Silent	SNP	ENST00000358677.5	37	CCDS46483.1																																																																																			.	.	none		0.463	SPATS2L-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336208.3	NM_015535		C	201284179	G	C	201284179	2	2	39	1	0	0	0	0	0	0	0	1	15035	1045	37	4		4	SPATS2L	2	201284179	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	27060063	201284179	41915194	45	14590											
PARD3B	117583	hgsc.bcm.edu	37	chr2	206166288	206166288	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggacatggaaaataaagcCaggaaagtcaaaaaaacgaa	23	3	10	5	1	1	0	1	0	0	0	1	5	1	3	1	3	2	0	1	3	9	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr2:206166288C>A	ENST00000406610.2	+	18	2700	c.2493C>A	c.(2491-2493)gcC>gcA	p.A831A	PARD3B_ENST00000349953.3_Silent_p.A831A|PARD3B_ENST00000358768.2_Silent_p.A769A|PARD3B_ENST00000462231.1_Silent_p.A831A|PARD3B_ENST00000351153.1_Silent_p.A762A	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	831	Lys-rich.				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)		AAAATAAAGCCAGGAAAGTCA	0.443																																					p.A831A		Atlas-SNP	.											.	PARD3B	314	.	0			c.C2493A						PASS	.						78	76	77					2																	206166288		1813	4088	5901	SO:0001819	synonymous_variant	117583	exon18			TAAAGCCAGGAAA	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.2493C>A	2.37:g.206166288C>A		294	0	0		273	41	0.150183	NM_205863	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	Silent	SNP	ENST00000406610.2	37																																																																																				.	.	none		0.443	PARD3B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000335992.1	NM_057177		A	206166288	C	A	206166288	2	1	39	1	0	0	0	0	0	0	0	1	11453	581	21	4		4	PARD3B	2	206166288	Silent	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	4882109	206166288	37033085	46	14591											
ACSL3	2181	hgsc.bcm.edu	37	chr2	223787815	223787815	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gtcttcaaaaattaaaaaagGaagcaaaggggatacatcca	20	7	8	6	0	2	0	1	0	1	0	3	2	3	2	1	3	2	1	1	3	8	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr2:223787815G>A	ENST00000357430.3	+	10	1631	c.1100G>A	c.(1099-1101)gGa>gAa	p.G367E	ACSL3_ENST00000392066.3_Missense_Mutation_p.G367E	NM_004457.3	NP_004448.2	O95573	ACSL3_HUMAN	acyl-CoA synthetase long-chain family member 3	367					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)	ATTAAAAAAGGAAGCAAAGGG	0.318			T	ETV1	prostate																																p.G367E		Atlas-SNP	.		Dom	yes		2	2q36	2181	acyl-CoA synthetase long-chain family member 3		E	.	ACSL3	107	.	0			c.G1100A						PASS	.						47	50	49					2																	223787815		2200	4299	6499	SO:0001583	missense	2181	exon9			AAAAAGGAAGCAA	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.1100G>A	2.37:g.223787815G>A	ENSP00000350012:p.Gly367Glu	596	1	0.00167785		525	122	0.232381	NM_203372	Q60I92|Q8IUM9	Missense_Mutation	SNP	ENST00000357430.3	37	CCDS2455.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.746451	0.89663	.	.	ENSG00000123983	ENST00000357430;ENST00000392066;ENST00000421680	T;T;T	0.72835	1.32;1.32;-0.69	5.36	5.36	0.76844	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	D	0.83562	0.5281	M	0.75447	2.3	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80251	-0.1460	10	0.23302	T	0.38	-18.0091	19.0985	0.93265	0.0:0.0:1.0:0.0	.	367	O95573	ACSL3_HUMAN	E	367;367;137	ENSP00000350012:G367E;ENSP00000375918:G367E;ENSP00000404182:G137E	ENSP00000350012:G367E	G	+	2	0	ACSL3	223496059	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.325000	0.96381	2.524000	0.85096	0.655000	0.94253	GGA	.	.	none		0.318	ACSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256862.2	NM_004457		A	223787815	G	A	223787815	3	1	39	1	0	0	0	0	1	0	0	0	178	1174	41	2	1126	2	ACSL3	2	223787815	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	17621527	223787815	19411558	47	14592											
CXCR7	57007	hgsc.bcm.edu	37	chr2	237489798	237489798	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccttctccattatcgctgtCttctacttcctgctggccag	4	15	6	16	1	3	0	0	0	3	0	6	0	4	0	4	1	2	2	4	1	2	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr2:237489798C>A	ENST00000272928.3	+	2	1000	c.690C>A	c.(688-690)gtC>gtA	p.V230V		NM_020311.2	NP_064707.1	P25106	ACKR3_HUMAN	atypical chemokine receptor 3	230					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)										TTATCGCTGTCTTCTACTTCC	0.567																																					p.V230V		Atlas-SNP	.											.	CXCR7	72	.	0			c.C690A						PASS	.						102	86	92					2																	237489798		2203	4300	6503	SO:0001819	synonymous_variant	57007	exon2			CGCTGTCTTCTAC	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.690C>A	2.37:g.237489798C>A		139	0	0		115	24	0.208696	NM_020311	A8K6J4|Q53RV4|Q8NE10|Q92938|Q92986	Silent	SNP	ENST00000272928.3	37	CCDS2516.1																																																																																			.	.	none		0.567	ACKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257079.2	NM_020311		A	237489798	C	A	237489798	2	1	39	1	0	0	0	0	0	0	0	1	4098	900	32	4		4	CXCR7	2	237489798	Silent	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	13701983	237489798	5709575	48	14593											
LRRN1	57633	hgsc.bcm.edu	37	chr3	3888234	3888234	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cagcccttgctgcagtaatgGggtctatgtttgccgtcatt	6	14	11	10	1	2	0	1	0	1	0	2	0	2	0	2	2	4	4	2	2	2	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr3:3888234G>C	ENST00000319331.3	+	2	2670	c.1909G>C	c.(1909-1911)Ggg>Cgg	p.G637R	SUMF1_ENST00000534863.1_Intron	NM_020873.5	NP_065924.3	Q6UXK5	LRRN1_HUMAN	leucine rich repeat neuronal 1	637						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)		TGCAGTAATGGGGTCTATGTT	0.428																																					p.G637R		Atlas-SNP	.											.	LRRN1	82	.	0			c.G1909C						PASS	.						92	90	91					3																	3888234		2203	4300	6503	SO:0001583	missense	57633	exon2			GTAATGGGGTCTA	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.1909G>C	3.37:g.3888234G>C	ENSP00000314901:p.Gly637Arg	180	0	0		128	26	0.203125	NM_020873	Q3LID5|Q8IYV5|Q9H8V1|Q9P231	Missense_Mutation	SNP	ENST00000319331.3	37	CCDS33685.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.013600	0.75161	.	.	ENSG00000175928	ENST00000319331	T	0.43294	0.95	5.35	5.35	0.76521	.	0.101437	0.64402	D	0.000002	T	0.62429	0.2427	L	0.61218	1.895	0.80722	D	1	D	0.65815	0.995	D	0.63957	0.92	T	0.64618	-0.6365	10	0.87932	D	0	.	19.4437	0.94838	0.0:0.0:1.0:0.0	.	637	Q6UXK5	LRRN1_HUMAN	R	637	ENSP00000314901:G637R	ENSP00000314901:G637R	G	+	1	0	LRRN1	3863234	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.338000	0.96553	2.661000	0.90470	0.650000	0.86243	GGG	.	.	none		0.428	LRRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337704.2	NM_020873		C	3888234	G	C	3888234	3	2	39	1	0	0	0	0	1	0	0	0	9043	1232	43	4	1911	4	LRRN1	3	3888234	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10		3888234	194134196	49	14594											
KCNH8	131096	hgsc.bcm.edu	37	chr3	19322823	19322823	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccagaagataaaaaagaaggTttgtaccgttttcagaaaac	18	9	8	6	1	1	4	1	0	0	4	1	4	1	4	2	1	2	3	2	1	8	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr3:19322823T>C	ENST00000328405.2	+	3	708		c.e3+2			NM_144633.2	NP_653234.2	Q96L42	KCNH8_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 8						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						AAAAAGAAGGTTTGTACCGTT	0.308																																					.	NSCLC(124;1625 1765 8018 24930 42026)	Atlas-SNP	.											.	KCNH8	189	.	0			c.442+2T>C						PASS	.						65	72	69					3																	19322823		2203	4297	6500	SO:0001630	splice_region_variant	131096	exon3			AGAAGGTTTGTAC	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.442+2T>C	3.37:g.19322823T>C		150	0	0		129	39	0.302326	NM_144633	B7Z2I7|Q59GQ6	Splice_Site	SNP	ENST00000328405.2	37	CCDS2632.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.487429	0.84854	.	.	ENSG00000183960	ENST00000328405	.	.	.	6.17	6.17	0.99709	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	KCNH8	19297827	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	7.698000	0.84413	2.371000	0.80710	0.533000	0.62120	.	.	.	none		0.308	KCNH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252139.2	NM_144633	Intron	C	19322823	T	C	19322823	5	2	39	1	0	0	0	0	0	0	1	0	8047	1739	60	3	454	3	KCNH8	3	19322823	Splice_Site	SNP	T	TCGA-GS-A9TW-01A-11D-A382-10	15434589	19322823	178699607	50	14595											
ZNF445	353274	hgsc.bcm.edu	37	chr3	44488625	44488625	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cttttacgtgtaaaggttttCccacattcttgacaccaaaa	12	14	5	10	1	1	1	0	1	1	0	2	1	2	1	2	1	1	2	2	1	5	7			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr3:44488625C>A	ENST00000396077.2	-	8	2885	c.2538G>T	c.(2536-2538)ggG>ggT	p.G846G	ZNF445_ENST00000425708.2_Silent_p.G846G	NM_181489.5	NP_852466.1	P59923	ZN445_HUMAN	zinc finger protein 445	846					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)		TAAAGGTTTTCCCACATTCTT	0.373																																					p.G846G		Atlas-SNP	.											.	ZNF445	91	.	0			c.G2538T						PASS	.						126	131	129					3																	44488625		2203	4300	6503	SO:0001819	synonymous_variant	353274	exon8			GGTTTTCCCACAT	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.2538G>T	3.37:g.44488625C>A		245	0	0		235	75	0.319149	NM_181489	Q3MJD1	Silent	SNP	ENST00000396077.2	37	CCDS2713.1																																																																																			.	.	none		0.373	ZNF445-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256647.2	NM_181489		A	44488625	C	A	44488625	2	1	39	1	0	0	0	0	0	0	0	1	17933	842	30	4		4	ZNF445	3	44488625	Silent	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	25165802	44488625	153533805	51	14596											
ZNF501	115560	hgsc.bcm.edu	37	chr3	44776170	44776170	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	atgtaatgaatgtgagaaagCctttcaaacaaaagcaattc	18	10	7	6	0	1	2	1	2	0	1	2	3	1	2	1	0	3	2	1	0	7	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr3:44776170C>T	ENST00000396048.2	+	3	694	c.257C>T	c.(256-258)gCc>gTc	p.A86V	KIAA1143_ENST00000484437.1_5'Flank	NM_001258280.1|NM_145044.3	NP_001245209.1|NP_659481.2	Q96CX3	ZN501_HUMAN	zinc finger protein 501	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|large_intestine(4)|lung(3)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.00843)|KIRC - Kidney renal clear cell carcinoma(197;0.0463)|Kidney(197;0.0579)		TGTGAGAAAGCCTTTCAAACA	0.368																																					p.A86V		Atlas-SNP	.											.	ZNF501	27	.	0			c.C257T						PASS	.						81	94	90					3																	44776170		2194	4297	6491	SO:0001583	missense	115560	exon3			AGAAAGCCTTTCA	BC013762	CCDS2720.2	3p21.32	2013-01-08			ENSG00000186446	ENSG00000186446		"Zinc fingers, C2H2-type"	23717	protein-coding gene	gene with protein product			"zinc finger protein 52"	ZNF52		1505991	Standard	NM_145044		Approved	MGC21738	uc003cnu.2	Q96CX3	OTTHUMG00000133048	ENST00000396048.2:c.257C>T	3.37:g.44776170C>T	ENSP00000379363:p.Ala86Val	99	0	0		94	16	0.170213	NM_001258280	B4DLY7|Q96NU9	Missense_Mutation	SNP	ENST00000396048.2	37	CCDS2720.2	.	.	.	.	.	.	.	.	.	.	C	17.36	3.370854	0.61624	.	.	ENSG00000186446	ENST00000396048;ENST00000332489	T	0.01043	5.41	3.07	3.07	0.35406	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02418	0.0074	N	0.17312	0.475	0.26468	N	0.975336	D;D	0.71674	0.998;0.997	D;D	0.68483	0.948;0.958	T	0.55036	-0.8203	9	0.62326	D	0.03	.	10.2687	0.43470	0.0:0.7964:0.2036:0.0	.	86;86	Q96CX3-2;Q96CX3	.;ZN501_HUMAN	V	86	ENSP00000379363:A86V	ENSP00000330388:A86V	A	+	2	0	ZNF501	44751174	0.000000	0.05858	1.000000	0.80357	0.990000	0.78478	-0.075000	0.11431	1.717000	0.51406	0.563000	0.77884	GCC	.	.	none		0.368	ZNF501-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256654.4	NM_145044		T	44776170	C	T	44776170	3	4	39	1	0	0	0	0	1	0	0	0	17964	739	26	2	259	2	ZNF501	3	44776170	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	287545	44776170	153246260	52	14597											
CACNA2D2	9254	hgsc.bcm.edu	37	chr3	50405270	50405270	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatcctggtccctccacacaCgctctaccagctgctgcgtg	6	9	9	17	2	1	0	0	0	1	0	4	1	4	0	4	1	4	3	4	1	1	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr3:50405270C>T	ENST00000479441.1	-	26	2227	c.2228G>A	c.(2227-2229)cGt>cAt	p.R743H	XXcos-LUCA11.4_ENST00000606665.1_RNA|XXcos-LUCA11.4_ENST00000607088.1_RNA|CACNA2D2_ENST00000395083.1_Missense_Mutation_p.R736H|XXcos-LUCA11.4_ENST00000607362.1_RNA|CACNA2D2_ENST00000429770.1_Missense_Mutation_p.R736H|CACNA2D2_ENST00000435965.1_Missense_Mutation_p.R743H|CACNA2D2_ENST00000266039.3_Missense_Mutation_p.R736H|CACNA2D2_ENST00000360963.3_Missense_Mutation_p.R667H|CACNA2D2_ENST00000423994.2_Missense_Mutation_p.R743H|XXcos-LUCA11.4_ENST00000607121.1_RNA|XXcos-LUCA11.5_ENST00000606589.1_3'UTR|CACNA2D2_ENST00000424201.2_Missense_Mutation_p.R736H|XXcos-LUCA11.4_ENST00000606259.1_RNA|XXcos-LUCA11.4_ENST00000607583.1_RNA			Q9NY47	CA2D2_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 2	743					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)	CCTCCACACACGCTCTACCAG	0.627																																					p.R743H		Atlas-SNP	.											CACNA2D2,colon,carcinoma,-1,2	CACNA2D2	82	2	0			c.G2228A						scavenged	.						72	57	62					3																	50405270		2203	4299	6502	SO:0001583	missense	9254	exon26			CACACACGCTCTA	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.2228G>A	3.37:g.50405270C>T	ENSP00000418081:p.Arg743His	132	1	0.00757576		134	21	0.156716	NM_001174051	A7MD15|Q9NY48|Q9UEW0|Q9Y268	Missense_Mutation	SNP	ENST00000479441.1	37	CCDS54588.1	.	.	.	.	.	.	.	.	.	.	C	16.91	3.252687	0.59212	.	.	ENSG00000007402	ENST00000423994;ENST00000429770;ENST00000266039;ENST00000360963;ENST00000435965;ENST00000395083;ENST00000424201;ENST00000479441	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	5.12	4.11	0.48088	.	0.233753	0.28572	N	0.014878	T	0.68632	0.3022	L	0.51422	1.61	0.09310	N	0.999998	P;D	0.57571	0.944;0.98	B;P	0.49708	0.321;0.62	T	0.62172	-0.6910	10	0.45353	T	0.12	-7.0292	9.6929	0.40139	0.0:0.8325:0.0:0.1675	.	743;736	Q9NY47;Q9NY47-2	CA2D2_HUMAN;.	H	743;736;736;667;743;736;736;743	ENSP00000407393:R743H;ENSP00000404631:R736H;ENSP00000266039:R736H;ENSP00000354228:R667H;ENSP00000390526:R743H;ENSP00000378519:R736H;ENSP00000390329:R736H;ENSP00000418081:R743H	ENSP00000266039:R736H	R	-	2	0	CACNA2D2	50380274	0.938000	0.31826	0.971000	0.41717	0.961000	0.63080	2.318000	0.43779	2.399000	0.81585	0.462000	0.41574	CGT	.	.	none		0.627	CACNA2D2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346457.1	NM_006030		T	50405270	C	T	50405270	3	4	39	1	0	0	0	0	1	0	0	0	2551	536	19	1	1286	1	CACNA2D2	3	50405270	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	5629100	50405270	147617160	53	14598											
MAGI1	9223	hgsc.bcm.edu	37	chr3	65376868	65376868	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ccagattttaaaaggatctgGttttttctggccagagctgt	9	15	10	7	0	2	2	0	0	2	2	2	3	2	3	2	3	1	2	2	3	2	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr3:65376868G>T	ENST00000497477.2	-	14	2364	c.2365C>A	c.(2365-2367)Cca>Aca	p.P789T	MAGI1_ENST00000330909.8_Missense_Mutation_p.P789T|MAGI1_ENST00000483466.1_Missense_Mutation_p.P789T|MAGI1_ENST00000402939.2_Missense_Mutation_p.P789T			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	789					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)	p.P789T(2)		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)		AAAGGATCTGGTTTTTTCTGG	0.567																																					p.P789T		Atlas-SNP	.											MAGI1_ENST00000402939,NS,lymphoid_neoplasm,0,4	MAGI1	481	4	2	Substitution - Missense(2)	large_intestine(2)	c.C2365A						PASS	.						96	96	96					3																	65376868		2203	4300	6503	SO:0001583	missense	9223	exon14			GATCTGGTTTTTT	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.2365C>A	3.37:g.65376868G>T	ENSP00000424369:p.Pro789Thr	176	0	0		138	45	0.326087	NM_001033057	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Missense_Mutation	SNP	ENST00000497477.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.3|24.3	4.516730|4.516730	0.85495|0.85495	.|.	.|.	ENSG00000151276|ENSG00000151276	ENST00000460329|ENST00000402939;ENST00000330909;ENST00000422949;ENST00000463103;ENST00000483466;ENST00000497477;ENST00000472257	.|T;T;T;T;T;T	.|0.24908	.|2.42;2.21;2.21;2.22;1.83;2.02	6.02|6.02	6.02|6.02	0.97574|0.97574	.|.	.|0.103697	.|0.64402	.|D	.|0.000002	T|T	0.51278|0.51278	0.1665|0.1665	M|M	0.64997|0.64997	1.995|1.995	0.80722|0.80722	D|D	1|1	.|D;B;D;D;D	.|0.89917	.|0.998;0.033;1.0;1.0;0.998	.|D;B;D;D;D	.|0.87578	.|0.96;0.04;0.992;0.998;0.974	T|T	0.20472|0.20472	-1.0274|-1.0274	5|10	.|0.35671	.|T	.|0.21	-8.0913|-8.0913	20.5407|20.5407	0.99260|0.99260	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|789;789;789;789;789	.|A8K188;Q96QZ7-4;Q96QZ7-3;Q96QZ7-2;Q96QZ7-5	.|.;.;.;.;.	K|T	669|789;789;685;664;789;789;575	.|ENSP00000385450:P789T;ENSP00000331157:P789T;ENSP00000418177:P664T;ENSP00000420323:P789T;ENSP00000424369:P789T;ENSP00000420796:P575T	.|ENSP00000331157:P789T	N|P	-|-	3|1	2|0	MAGI1|MAGI1	65351908|65351908	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.979000|0.979000	0.70002|0.70002	9.476000|9.476000	0.97823|0.97823	2.865000|2.865000	0.98341|0.98341	0.655000|0.655000	0.94253|0.94253	AAC|CCA	.	.	none		0.567	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742		T	65376868	G	T	65376868	3	4	39	1	0	0	0	0	1	0	0	0	9199	1261	44	4	2297	4	MAGI1	3	65376868	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	14971598	65376868	132645562	54	14599											
FRMD4B	23150	hgsc.bcm.edu	37	chr3	69237039	69237039	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atgaggtactgaacttgatcGctgcccaggaaaagtgaagg	13	8	13	7	1	0	4	0	4	0	0	1	5	0	5	1	3	3	2	1	3	5	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr3:69237039G>A	ENST00000398540.3	-	19	1884	c.1801C>T	c.(1801-1803)Cga>Tga	p.R601*	FRMD4B_ENST00000478263.1_Nonsense_Mutation_p.R253*|FRMD4B_ENST00000542259.1_Nonsense_Mutation_p.R547*	NM_015123.1	NP_055938	Q9Y2L6	FRM4B_HUMAN	FERM domain containing 4B	601					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)		GAACTTGATCGCTGCCCAGGA	0.378																																					p.R601X		Atlas-SNP	.											.	FRMD4B	90	.	0			c.C1801T						PASS	.						43	41	42					3																	69237039		1860	4089	5949	SO:0001587	stop_gained	23150	exon19			TTGATCGCTGCCC	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.1801C>T	3.37:g.69237039G>A	ENSP00000381549:p.Arg601*	91	0	0		110	24	0.218182	NM_015123	Q8TAI3	Nonsense_Mutation	SNP	ENST00000398540.3	37	CCDS46863.1	.	.	.	.	.	.	.	.	.	.	G	37	6.631150	0.97718	.	.	ENSG00000114541	ENST00000398540;ENST00000542259;ENST00000478263	.	.	.	6.02	4.21	0.49690	.	0.064071	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.9519	8.9524	0.35796	0.0686:0.0:0.5937:0.3377	.	.	.	.	X	601;547;253	.	ENSP00000381549:R601X	R	-	1	2	FRMD4B	69319729	1.000000	0.71417	1.000000	0.80357	0.612000	0.37316	1.858000	0.39408	0.854000	0.35336	0.591000	0.81541	CGA	.	.	none		0.378	FRMD4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352111.1			A	69237039	G	A	69237039	4	1	39	1	0	0	0	0	0	1	0	0	6060	1095	38	1	1323	1	FRMD4B	3	69237039	Nonsense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	3860171	69237039	128785391	55	14600											
GTPBP8	29083	hgsc.bcm.edu	37	chr3	112719765	112719765	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtaacaggaagtcttgactAatggttcccggtttagctga	10	13	11	7	1	1	2	0	2	1	0	2	3	2	3	1	3	2	4	1	3	4	6			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr3:112719765A>G	ENST00000383678.2	+	6	936	c.854A>G	c.(853-855)tAa>tGa	p.*285*	GTPBP8_ENST00000467752.1_Silent_p.*174*|GTPBP8_ENST00000473129.1_Silent_p.*135*|GTPBP8_ENST00000383677.3_Silent_p.*252*	NM_014170.2	NP_054889.2	Q8N3Z3	GTPB8_HUMAN	GTP-binding protein 8 (putative)	0					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						AGTCTTGACTAATGGTTCCCG	0.338																																					p.X285X		Atlas-SNP	.											.	GTPBP8	22	.	0			c.A854G						PASS	.						97	94	95					3																	112719765		2203	4300	6503	SO:0001819	synonymous_variant	29083	exon6			TTGACTAATGGTT	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.854A>G	3.37:g.112719765A>G		98	0	0		99	32	0.323232	NM_014170	A6NE99|A6NN11|A8K0P6|Q5I0Y4	Silent	SNP	ENST00000383678.2	37	CCDS33820.1																																																																																			.	.	none		0.338	GTPBP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354260.2	NM_014170		G	112719765	A	G	112719765	2	3	39	1	0	0	0	0	0	0	0	1	6893	369	13	3		3	GTPBP8	3	112719765	Silent	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	43482726	112719765	85302665	56	14601											
DTX3L	151636	hgsc.bcm.edu	37	chr3	122288596	122288596	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gttctgaggcctcagaactgGacaagaaggaaaagggcatc	14	6	13	8	0	2	3	1	1	1	2	3	5	2	5	1	4	1	2	1	4	5	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr3:122288596G>C	ENST00000296161.4	+	3	1849	c.1660G>C	c.(1660-1662)Gac>Cac	p.D554H	DTX3L_ENST00000383661.3_Intron	NM_138287.3	NP_612144.1	Q8TDB6	DTX3L_HUMAN	deltex 3 like, E3 ubiquitin ligase	554					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)		CTCAGAACTGGACAAGAAGGA	0.468																																					p.D554H		Atlas-SNP	.											.	DTX3L	59	.	0			c.G1660C						PASS	.						76	79	78					3																	122288596		2203	4300	6503	SO:0001583	missense	151636	exon3			GAACTGGACAAGA		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.1660G>C	3.37:g.122288596G>C	ENSP00000296161:p.Asp554His	75	0	0		81	29	0.358025	NM_138287	B3KWH6|Q53ZZ3|Q5MJP7	Missense_Mutation	SNP	ENST00000296161.4	37	CCDS3015.1	.	.	.	.	.	.	.	.	.	.	G	6.614	0.481645	0.12581	.	.	ENSG00000163840	ENST00000296161	T	0.68765	-0.35	1.83	0.902	0.19290	.	0.659026	0.14112	N	0.340641	T	0.57036	0.2026	L	0.57536	1.79	0.21697	N	0.99958	B	0.26635	0.155	B	0.27887	0.084	T	0.46898	-0.9158	10	0.33940	T	0.23	-3.1283	6.0444	0.19752	0.0:0.3269:0.6731:0.0	.	554	Q8TDB6	DTX3L_HUMAN	H	554	ENSP00000296161:D554H	ENSP00000296161:D554H	D	+	1	0	DTX3L	123771286	0.175000	0.23083	0.031000	0.17742	0.128000	0.20619	0.852000	0.27764	0.304000	0.22809	-0.315000	0.08773	GAC	.	.	none		0.468	DTX3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355966.1	NM_138287		C	122288596	G	C	122288596	3	2	39	1	0	0	0	0	1	0	0	0	4798	1174	41	4	1670	4	DTX3L	3	122288596	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	9568831	122288596	75733834	57	14602											
RAB6B	51560	hgsc.bcm.edu	37	chr3	133557035	133557035	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcacgttgtagccagtcttcGcactggtctcaatgaacatg	9	12	9	11	2	3	1	2	1	2	0	5	1	3	1	1	1	2	3	1	1	3	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr3:133557035G>A	ENST00000285208.4	-	6	819	c.470C>T	c.(469-471)gCg>gTg	p.A157V	RAB6B_ENST00000486858.1_Missense_Mutation_p.A144V|RAB6B_ENST00000469959.1_Intron|RAB6B_ENST00000543906.1_Missense_Mutation_p.A157V	NM_016577.3	NP_057661.3	Q9NRW1	RAB6B_HUMAN	RAB6B, member RAS oncogene family	157					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						GCCAGTCTTCGCACTGGTCTC	0.617																																					p.A157V		Atlas-SNP	.											RAB6B,NS,carcinoma,+1,1	RAB6B	36	1	0			c.C470T						PASS	.						167	153	158					3																	133557035		2203	4300	6503	SO:0001583	missense	51560	exon6			GTCTTCGCACTGG	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.470C>T	3.37:g.133557035G>A	ENSP00000285208:p.Ala157Val	86	0	0		63	21	0.333333	NM_016577	B2R5Z9|B7Z337|D3DND3|Q92929	Missense_Mutation	SNP	ENST00000285208.4	37	CCDS3082.1	.	.	.	.	.	.	.	.	.	.	G	31	5.080334	0.94050	.	.	ENSG00000154917	ENST00000285208;ENST00000543906;ENST00000486858;ENST00000477759	D;D;D;D	0.88818	-2.43;-2.43;-2.43;-2.43	4.47	4.47	0.54385	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.95332	0.8485	M	0.90425	3.115	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.994;0.998	D	0.96189	0.9136	10	0.87932	D	0	-3.3637	16.4243	0.83809	0.0:0.0:1.0:0.0	.	144;157	B7Z337;Q9NRW1	.;RAB6B_HUMAN	V	157;157;144;124	ENSP00000285208:A157V;ENSP00000437797:A157V;ENSP00000419381:A144V;ENSP00000419941:A124V	ENSP00000285208:A157V	A	-	2	0	RAB6B	135039725	1.000000	0.71417	0.282000	0.24776	0.841000	0.47740	8.857000	0.92250	2.490000	0.84030	0.655000	0.94253	GCG	.	.	none		0.617	RAB6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357152.1			A	133557035	G	A	133557035	3	1	39	1	0	0	0	0	1	0	0	0	12967	1087	38	1	168	1	RAB6B	3	133557035	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	11268439	133557035	64465395	58	14603											
ATR	545	hgsc.bcm.edu	37	chr3	142281284	142281284	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acacagagtttttccagcagCatatttaaatagacaggttc	14	12	7	8	0	0	2	0	0	0	2	2	2	1	2	1	1	2	4	1	1	4	7			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr3:142281284C>A	ENST00000350721.4	-	4	1081	c.960G>T	c.(958-960)atG>atT	p.M320I	ATR_ENST00000383101.3_Missense_Mutation_p.M320I	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	320					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						TTTCCAGCAGCATATTTAAAT	0.373								Other conserved DNA damage response genes																													p.M320I		Atlas-SNP	.											.	ATR	285	.	0			c.G960T						PASS	.						83	90	88					3																	142281284		2203	4300	6503	SO:0001583	missense	545	exon4			CAGCAGCATATTT	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.960G>T	3.37:g.142281284C>A	ENSP00000343741:p.Met320Ile	162	0	0		177	61	0.344633	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	37	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	C	13.58	2.280953	0.40394	.	.	ENSG00000175054	ENST00000350721;ENST00000383101;ENST00000515149	T;T	0.66099	-0.19;-0.19	5.24	5.24	0.73138	Armadillo-like helical (1);Armadillo-type fold (1);	0.486681	0.24384	N	0.038987	T	0.48484	0.1502	L	0.29908	0.895	0.27328	N	0.956866	B	0.02656	0.0	B	0.04013	0.001	T	0.27773	-1.0064	10	0.20046	T	0.44	-8.2121	13.1607	0.59542	0.0:0.9229:0.0:0.0771	.	320	Q13535	ATR_HUMAN	I	320;320;1	ENSP00000343741:M320I;ENSP00000372581:M320I	ENSP00000343741:M320I	M	-	3	0	ATR	143763974	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.388000	0.52509	2.445000	0.82738	0.591000	0.81541	ATG	.	.	none		0.373	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		A	142281284	C	A	142281284	3	1	39	1	0	0	0	0	1	0	0	0	1204	710	25	4	7150	4	ATR	3	142281284	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	8724249	142281284	55741146	59	14604											
EVC	2121	hgsc.bcm.edu	37	chr4	5811258	5811258	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atttcaggaagctgaacagaActtcatctccgagctggcag	12	9	10	10	1	3	2	2	1	1	1	4	4	3	3	1	2	4	3	1	2	3	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr4:5811258A>C	ENST00000264956.6	+	19	2886	c.2702A>C	c.(2701-2703)aAc>aCc	p.N901T	EVC_ENST00000382674.2_Missense_Mutation_p.N901T	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	901					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)				GCTGAACAGAACTTCATCTCC	0.537																																					p.N901T		Atlas-SNP	.											.	EVC	90	.	0			c.A2702C						PASS	.						93	81	85					4																	5811258		2203	4300	6503	SO:0001583	missense	2121	exon19			AACAGAACTTCAT	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.2702A>C	4.37:g.5811258A>C	ENSP00000264956:p.Asn901Thr	65	0	0		55	18	0.327273	NM_153717		Missense_Mutation	SNP	ENST00000264956.6	37	CCDS3383.1	.	.	.	.	.	.	.	.	.	.	A	0.010	-1.766954	0.00645	.	.	ENSG00000072840	ENST00000264956;ENST00000382674	T;T	0.49432	0.78;0.78	4.78	-9.56	0.00566	.	0.707365	0.13224	N	0.404137	T	0.15825	0.0381	N	0.12182	0.205	0.18873	N	0.999988	B	0.02656	0.0	B	0.04013	0.001	T	0.13124	-1.0521	10	0.17832	T	0.49	.	1.2746	0.02027	0.3732:0.3068:0.1372:0.1828	.	901	P57679	EVC_HUMAN	T	901	ENSP00000264956:N901T;ENSP00000372120:N901T	ENSP00000264956:N901T	N	+	2	0	EVC	5862159	0.458000	0.25760	0.121000	0.21740	0.021000	0.10359	-0.389000	0.07342	-1.901000	0.01096	-1.151000	0.01829	AAC	.	.	none		0.537	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1			C	5811258	A	C	5811258	3	2	39	1	0	0	0	0	1	0	0	0	5287	43	2	5	2776	5	EVC	4	5811258	Missense_Mutation	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10		5811258	185343018	60	14605											
EVC	2121	hgsc.bcm.edu	37	chr4	5811337	5811337	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctgctaagcgtgggctgctAggtgagtcacagatgcttga	8	10	14	9	1	1	3	1	2	0	1	1	3	1	3	1	2	4	4	1	2	2	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr4:5811337A>G	ENST00000264956.6	+	19	2965	c.2781A>G	c.(2779-2781)ctA>ctG	p.L927L	EVC_ENST00000382674.2_Splice_Site_p.L927L	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	927					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)				GTGGGCTGCTAGGTGAGTCAc	0.542																																					p.L927L		Atlas-SNP	.											EVC,right_lower_lobe,carcinoma,0,1	EVC	90	1	0			c.A2781G						PASS	.						73	59	64					4																	5811337		2203	4300	6503	SO:0001630	splice_region_variant	2121	exon19			GCTGCTAGGTGAG	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.2782+1A>G	4.37:g.5811337A>G		60	0	0		53	16	0.301887	NM_153717		Silent	SNP	ENST00000264956.6	37	CCDS3383.1																																																																																			.	.	none		0.542	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1		Silent	G	5811337	A	G	5811337	5	3	39	1	0	0	0	0	0	0	1	0	5287	434	15	3	2855	3	EVC	4	5811337	Splice_Site	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	79	5811337	185342939	61	14606											
SULT1B1	27284	hgsc.bcm.edu	37	chr4	70615486	70615486	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggaagaagatcagtcggtaGatgtgttttcacaatccggg	12	10	13	6	2	2	3	2	0	0	3	4	4	3	4	1	3	0	2	1	3	4	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr4:70615486G>A	ENST00000310613.3	-	4	625	c.328C>T	c.(328-330)Cta>Tta	p.L110L		NM_014465.3	NP_055280.2	O43704	ST1B1_HUMAN	sulfotransferase family, cytosolic, 1B, member 1	110					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						TCAGTCGGTAGATGTGTTTTC	0.393																																					p.L110L		Atlas-SNP	.											.	SULT1B1	46	.	0			c.C328T						PASS	.						162	168	166					4																	70615486		2203	4300	6503	SO:0001819	synonymous_variant	27284	exon4			TCGGTAGATGTGT	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.328C>T	4.37:g.70615486G>A		274	0	0		231	38	0.164502	NM_014465	O15497|Q96FI1|Q9UK34	Silent	SNP	ENST00000310613.3	37	CCDS3530.1																																																																																			.	.	none		0.393	SULT1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251563.2	NM_014465		A	70615486	G	A	70615486	2	1	39	1	0	0	0	0	0	0	0	1	15391	933	33	2		2	SULT1B1	4	70615486	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	64804149	70615486	120538790	62	14607											
FAM190A	401145	hgsc.bcm.edu	37	chr4	91230610	91230610	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctggggacaaactccccaaGgaaacttggattttatgagc	12	9	11	9	0	0	1	0	1	0	0	1	4	1	4	2	4	3	1	2	4	4	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr4:91230610G>A	ENST00000509176.1	+	2	1463	c.1175G>A	c.(1174-1176)aGg>aAg	p.R392K	CCSER1_ENST00000333691.8_Missense_Mutation_p.R392K|CCSER1_ENST00000432775.2_Missense_Mutation_p.R392K	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	392																	AACTCCCCAAGGAAACTTGGA	0.393																																					p.R392K		Atlas-SNP	.											.	.	.	.	0			c.G1175A						PASS	.						124	120	121					4																	91230610		1849	4089	5938	SO:0001583	missense	401145	exon2			CCCCAAGGAAACT		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.1175G>A	4.37:g.91230610G>A	ENSP00000425040:p.Arg392Lys	185	0	0		145	21	0.144828	NM_001145065	Q4W5M0|Q86V57	Missense_Mutation	SNP	ENST00000509176.1	37	CCDS47099.1	.	.	.	.	.	.	.	.	.	.	G	7.084	0.570881	0.13623	.	.	ENSG00000184305	ENST00000509176;ENST00000432775;ENST00000333691;ENST00000458365	T;T;T	0.41065	1.55;1.01;1.55	4.96	3.24	0.37175	.	0.506740	0.20055	N	0.100219	T	0.21227	0.0511	N	0.25647	0.755	0.23126	N	0.998254	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.30679	-0.9970	10	0.02654	T	1	-11.0531	4.6727	0.12698	0.3615:0.1536:0.4849:0.0	.	392;392;392	Q9C0I3-2;Q9C0I3;E7EUW0	.;F190A_HUMAN;.	K	392	ENSP00000425040:R392K;ENSP00000389283:R392K;ENSP00000329482:R392K	ENSP00000329482:R392K	R	+	2	0	FAM190A	91449633	0.991000	0.36638	0.994000	0.49952	0.436000	0.31835	0.953000	0.29162	0.769000	0.33313	0.585000	0.79938	AGG	.	.	none		0.393	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065		A	91230610	G	A	91230610	3	1	39	1	0	0	0	0	1	0	0	0	5526	1000	35	2	1177	2	FAM190A	4	91230610	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	20615124	91230610	99923666	63	14608											
C4orf17	84103	hgsc.bcm.edu	37	chr4	100461611	100461618	+	Splice_Site	DEL	AGGTTAAG	AGGTTAAG	-																															gaaaacaaggaagtaccaaaAggttaagtacagtttttggt																										TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	AGGTTAAG	AGGTTAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr4:100461611_100461618delAGGTTAAG	ENST00000326581.4	+	8	1241_1242	c.879_880delAGGTTAAG	c.(877-882)aaaggt>aagt	p.G294fs	C4orf17_ENST00000514652.1_Stop_Codon_Del	NM_032149.2	NP_115525.2	Q53FE4	CD017_HUMAN	chromosome 4 open reading frame 17	294										central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|urinary_tract(3)	18				OV - Ovarian serous cystadenocarcinoma(123;2.08e-08)		AAGTACCAAAAGGTTAAGTACAGTTTTT	0.317																																					p.293_294del		Pindel,Atlas-Indel	.											.	C4orf17	42	.	0			c.878_880del						PASS	.																																			SO:0001630	splice_region_variant	84103	exon8			.	AL136838	CCDS3649.1	4q23	2008-02-05			ENSG00000138813	ENSG00000138813			25274	protein-coding gene	gene with protein product						11230166	Standard	NM_032149		Approved	DKFZP434G072	uc003huw.3	Q53FE4	OTTHUMG00000131027	ENST00000326581.4:c.880+1AGGTTAAG>-	4.37:g.100461611_100461618delAGGTTAAG		137	0	.		114	25	0.219	NM_032149	Q6FI84|Q6IS77|Q8NA78|Q9H0D9	In_Frame_Del	DEL	ENST00000326581.4	37	CCDS3649.1																																																																																			.	.	none		0.317	C4orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253670.2	NM_032149	Frame_Shift_Del	-	100461618	AGGTTAAG	-	100461611	8	5	39	1	0	1	0	1	0	0	1	0	2254	86	3	0	905	0	C4orf17	4	100461611	Splice_Site	DEL	AGGTTAAG	TCGA-GS-A9TW-01A-11D-A382-10	9231001	100461611	90692665	64	14609											
MANBA	4126	hgsc.bcm.edu	37	chr4	103585914	103585914	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atgtagattggccggtcagtGaaactgatatgataccaatt	13	12	10	6	1	1	4	1	3	0	1	1	4	1	4	2	2	2	1	2	2	5	5	rs547084645		TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr4:103585914G>A	ENST00000226578.4	-	11	1512	c.1413C>T	c.(1411-1413)ttC>ttT	p.F471F	MANBA_ENST00000505239.1_Silent_p.F414F	NM_005908.3	NP_005899.3	O00462	MANBA_HUMAN	mannosidase, beta A, lysosomal	471					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)		GCCGGTCAGTGAAACTGATAT	0.388													G|||	1	0.000199681	0.0	0.0	5008	,	,		16638	0.0		0.0	False		,,,				2504	0.001				p.F471F		Atlas-SNP	.											.	MANBA	78	.	0			c.C1413T						PASS	.						130	124	126					4																	103585914		2203	4300	6503	SO:0001819	synonymous_variant	4126	exon11			GTCAGTGAAACTG		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.1413C>T	4.37:g.103585914G>A		288	0	0		251	79	0.314741	NM_005908	Q96BC3|Q9NYX9	Silent	SNP	ENST00000226578.4	37	CCDS3658.1																																																																																			.	.	none		0.388	MANBA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253803.2			A	103585914	G	A	103585914	2	1	39	1	0	0	0	0	0	0	0	1	9228	1281	45	2		2	MANBA	4	103585914	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	3124303	103585914	87568362	65	14610											
QRFPR	84109	hgsc.bcm.edu	37	chr4	122250653	122250653	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggaaaactttgctttcttcCgcatcattgtaattcctgaa	10	15	7	9	1	2	1	1	1	1	0	4	2	4	2	2	1	2	3	2	1	4	6			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr4:122250653C>T	ENST00000394427.2	-	6	1523	c.1112G>A	c.(1111-1113)cGg>cAg	p.R371Q	Y_RNA_ENST00000384419.1_RNA|QRFPR_ENST00000334383.5_3'UTR	NM_198179.2	NP_937822.2	Q96P65	QRFPR_HUMAN	pyroglutamylated RFamide peptide receptor	371					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						TGCTTTCTTCCGCATCATTGT	0.378																																					p.R371Q		Atlas-SNP	.											QRFPR,NS,carcinoma,-1,1	QRFPR	65	1	0			c.G1112A						scavenged	.						192	190	191					4																	122250653		2203	4300	6503	SO:0001583	missense	84109	exon6			TTCTTCCGCATCA	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.1112G>A	4.37:g.122250653C>T	ENSP00000377948:p.Arg371Gln	385	1	0.0025974		298	28	0.0939597	NM_198179		Missense_Mutation	SNP	ENST00000394427.2	37	CCDS3719.1	.	.	.	.	.	.	.	.	.	.	C	1.400	-0.578442	0.03854	.	.	ENSG00000186867	ENST00000394427	T	0.72505	-0.66	5.0	-1.01	0.10169	.	0.634163	0.16362	N	0.217722	T	0.34774	0.0909	N	0.02539	-0.55	0.20196	N	0.999929	B	0.02656	0.0	B	0.01281	0.0	T	0.16188	-1.0411	10	0.25106	T	0.35	.	2.3119	0.04188	0.1146:0.2239:0.1177:0.5438	.	371	Q96P65	QRFPR_HUMAN	Q	371	ENSP00000377948:R371Q	ENSP00000377948:R371Q	R	-	2	0	QRFPR	122470103	0.949000	0.32298	0.157000	0.22605	0.088000	0.18126	0.537000	0.23144	0.018000	0.15052	-0.573000	0.04149	CGG	.	.	none		0.378	QRFPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256641.2	NM_198179		T	122250653	C	T	122250653	3	4	39	1	0	0	0	0	1	0	0	0	12893	652	23	1	187	1	QRFPR	4	122250653	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	18664739	122250653	68903623	66	14611											
KIAA0922	23240	hgsc.bcm.edu	37	chr4	154525477	154525477	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccgagttcaaggaacgggagCtctgtccactgaagacctcc	10	7	11	13	2	2	2	1	1	1	1	4	5	4	4	4	2	2	2	4	2	3	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr4:154525477C>A	ENST00000409663.3	+	25	3362	c.3310C>A	c.(3310-3312)Ctc>Atc	p.L1104I	KIAA0922_ENST00000440693.1_Missense_Mutation_p.L1021I|KIAA0922_ENST00000409959.3_Missense_Mutation_p.L1105I	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	1104						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)				GGAACGGGAGCTCTGTCCACT	0.428																																					p.L1105I		Atlas-SNP	.											.	KIAA0922	214	.	0			c.C3313A						PASS	.						52	53	52					4																	154525477		2203	4300	6503	SO:0001583	missense	23240	exon25			CGGGAGCTCTGTC	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.3310C>A	4.37:g.154525477C>A	ENSP00000386574:p.Leu1104Ile	215	0	0		204	55	0.269608	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	37	CCDS3783.2	.	.	.	.	.	.	.	.	.	.	C	9.236	1.037062	0.19669	.	.	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959;ENST00000240487	T;T;T;T	0.20069	2.38;2.1;2.37;2.11	5.79	4.95	0.65309	.	0.405134	0.27886	N	0.017441	T	0.20088	0.0483	L	0.44542	1.39	0.23238	N	0.998066	P;B;B	0.44281	0.831;0.136;0.083	P;B;B	0.45610	0.487;0.071;0.032	T	0.09684	-1.0663	10	0.22706	T	0.39	-4.7104	7.468	0.27332	0.0:0.6985:0.1573:0.1442	.	1021;1105;1104	A2VDJ0-3;A2VDJ0-5;A2VDJ0	.;.;T131L_HUMAN	I	1104;1021;1105;882	ENSP00000386574:L1104I;ENSP00000409663:L1021I;ENSP00000386787:L1105I;ENSP00000240487:L882I	ENSP00000240487:L882I	L	+	1	0	KIAA0922	154744927	1.000000	0.71417	0.997000	0.53966	0.662000	0.39071	0.619000	0.24388	1.434000	0.47414	0.655000	0.94253	CTC	.	.	none		0.428	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196		A	154525477	C	A	154525477	3	1	39	1	0	0	0	0	1	0	0	0	8210	797	28	4	3411	4	KIAA0922	4	154525477	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	32274824	154525477	36628799	67	14612											
ACCN5	51802	hgsc.bcm.edu	37	chr4	156757920	156757920	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggaaaagaggaataagaaaTagtggccgggtattctattt	15	11	12	3	1	1	2	0	0	1	2	1	4	1	4	1	4	0	1	1	4	8	6			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr4:156757920T>G	ENST00000537611.2	-	8	1202	c.1156A>C	c.(1156-1158)Att>Ctt	p.I386L		NM_017419.2	NP_059115.1	Q9NY37	ASIC5_HUMAN	acid-sensing (proton-gated) ion channel family member 5	386					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrogen ion channel activity (GO:0015252)|ligand-gated sodium channel activity (GO:0015280)										GAATAAGAAATAGTGGCCGGG	0.358																																					p.I386L		Atlas-SNP	.											.	.	.	.	0			c.A1156C						PASS	.						72	80	77					4																	156757920		2203	4300	6503	SO:0001583	missense	51802	exon8			AAGAAATAGTGGC	AJ252011	CCDS3793.1	4q32.1	2012-10-03	2012-03-02	2012-03-02	ENSG00000256394	ENSG00000256394			17537	protein-coding gene	gene with protein product			"amiloride-sensitive cation channel 5, intestinal"	ACCN5		10767424	Standard	NM_017419		Approved	INAC, HINAC	uc003ipe.1	Q9NY37	OTTHUMG00000161941	ENST00000537611.2:c.1156A>C	4.37:g.156757920T>G	ENSP00000442477:p.Ile386Leu	182	0	0		138	46	0.333333	NM_017419		Missense_Mutation	SNP	ENST00000537611.2	37	CCDS3793.1	.	.	.	.	.	.	.	.	.	.	T	10.44	1.350945	0.24512	.	.	ENSG00000256394	ENST00000537611	T	0.61742	0.08	4.8	-0.965	0.10323	.	0.519192	0.17888	N	0.158638	T	0.34193	0.0889	N	0.20483	0.58	0.09310	N	0.999997	B	0.09022	0.002	B	0.15484	0.013	T	0.14924	-1.0455	10	0.22706	T	0.39	-13.9873	6.8804	0.24170	0.0:0.2563:0.1169:0.6268	.	386	Q9NY37	ACCN5_HUMAN	L	386	ENSP00000442477:I386L	ENSP00000264432:I386L	I	-	1	0	ACCN5	156977370	0.013000	0.17824	0.049000	0.19019	0.972000	0.66771	-0.092000	0.11129	-0.199000	0.10317	0.533000	0.62120	ATT	.	.	none		0.358	ASIC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366464.1			G	156757920	T	G	156757920	3	3	39	1	0	0	0	0	1	0	0	0	132	1406	49	5	373	5	ACCN5	4	156757920	Missense_Mutation	SNP	T	TCGA-GS-A9TW-01A-11D-A382-10	2232443	156757920	34396356	68	14613											
IRX2	153572	hgsc.bcm.edu	37	chr5	2749795	2749795	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggcgtcccgcgtggcgttcTtgcggtacgcggggtcgttg	1	11	18	11	8	1	0	0	0	1	0	3	0	2	0	1	5	2	3	1	5	1	4			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr5:2749795T>C	ENST00000382611.6	-	2	604	c.356A>G	c.(355-357)aAg>aGg	p.K119R	C5orf38_ENST00000515640.1_5'Flank|C5orf38_ENST00000397835.4_5'Flank|C5orf38_ENST00000334000.3_5'Flank|IRX2_ENST00000502957.1_5'UTR|C5orf38_ENST00000505778.1_5'Flank|IRX2_ENST00000302057.5_Missense_Mutation_p.K119R|C5orf38_ENST00000457752.2_5'Flank	NM_001134222.1	NP_001127694.1	Q9BZI1	IRX2_HUMAN	iroquois homeobox 2	119					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)			breast(1)|central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2)	26				GBM - Glioblastoma multiforme(108;0.204)		CGTGGCGTTCTTGCGGTACGC	0.667																																					p.K119R		Atlas-SNP	.											.	IRX2	60	.	0			c.A356G						PASS	.						125	99	108					5																	2749795		2203	4300	6503	SO:0001583	missense	153572	exon2			GCGTTCTTGCGGT	AF319967	CCDS3868.1	5p15.33	2011-06-20	2007-07-13		ENSG00000170561	ENSG00000170561		"Homeoboxes / TALE class"	14359	protein-coding gene	gene with protein product		606198				11435706	Standard	NM_033267		Approved		uc003jdb.3	Q9BZI1	OTTHUMG00000090377	ENST00000382611.6:c.356A>G	5.37:g.2749795T>C	ENSP00000372056:p.Lys119Arg	172	0	0		137	28	0.20438	NM_001134222	Q68A19|Q7Z2I7	Missense_Mutation	SNP	ENST00000382611.6	37	CCDS3868.1	.	.	.	.	.	.	.	.	.	.	T	33	5.248878	0.95305	.	.	ENSG00000170561	ENST00000382611;ENST00000302057;ENST00000502957	D;D;D	0.83419	-1.72;-1.72;-1.72	4.85	4.85	0.62838	Homeodomain-related (1);Homeobox (2);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.88948	0.6576	M	0.82193	2.58	0.80722	D	1	P	0.44478	0.836	P	0.53490	0.727	D	0.88990	0.3414	10	0.40728	T	0.16	-25.838	14.441	0.67318	0.0:0.0:0.0:1.0	.	119	Q9BZI1	IRX2_HUMAN	R	119;119;26	ENSP00000372056:K119R;ENSP00000307006:K119R;ENSP00000426151:K26R	ENSP00000307006:K119R	K	-	2	0	IRX2	2802795	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.663000	0.83820	1.817000	0.53016	0.533000	0.62120	AAG	.	.	none		0.667	IRX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206749.2			C	2749795	T	C	2749795	3	2	39	1	0	0	0	0	1	0	0	0	7853	1609	56	3	1071	3	IRX2	5	2749795	Missense_Mutation	SNP	T	TCGA-GS-A9TW-01A-11D-A382-10		2749795	178165465	69	14614											
ISL1	3670	hgsc.bcm.edu	37	chr5	50683348	50683348	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacgggatcaaatgcgccaaGtgcagcatcggcttcagcaa	12	7	11	11	3	2	0	2	0	0	0	3	1	2	1	1	2	5	4	1	2	4	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr5:50683348G>A	ENST00000230658.7	+	3	828	c.243G>A	c.(241-243)aaG>aaA	p.K81K	ISL1_ENST00000505475.2_3'UTR|ISL1_ENST00000511384.1_Silent_p.K81K	NM_002202.2	NP_002193.2	P61371	ISL1_HUMAN	ISL LIM homeobox 1	81	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				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)				AATGCGCCAAGTGCAGCATCG	0.627																																					p.K81K		Atlas-SNP	.											.	ISL1	65	.	0			c.G243A						PASS	.						35	37	37					5																	50683348		2052	4189	6241	SO:0001819	synonymous_variant	3670	exon3			CGCCAAGTGCAGC	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.243G>A	5.37:g.50683348G>A		113	0	0		147	18	0.122449	NM_002202	P20663|P47894	Silent	SNP	ENST00000230658.7	37	CCDS43314.1	.	.	.	.	.	.	.	.	.	.	G	10.19	1.283104	0.23392	.	.	ENSG00000016082	ENST00000505475	T	0.56776	0.44	5.51	4.61	0.57282	.	.	.	.	.	T	0.60843	0.2300	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63616	-0.6597	6	0.87932	D	0	.	8.5384	0.33377	0.2478:0.0:0.7522:0.0	.	.	.	.	M	28	ENSP00000421737:V28M	ENSP00000421737:V28M	V	+	1	0	ISL1	50719105	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.379000	0.34340	1.272000	0.44329	0.505000	0.49811	GTG	.	.	none		0.627	ISL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368413.3	NM_002202		A	50683348	G	A	50683348	2	1	39	1	0	0	0	0	0	0	0	1	7865	1020	36	2		2	ISL1	5	50683348	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	47933553	50683348	130231912	70	14615											
ZNF366	167465	hgsc.bcm.edu	37	chr5	71756780	71756780	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gaaggggaacatgaggcccgGgtggactttggggtagtagg	9	7	20	5	1	0	1	0	1	0	0	0	4	0	3	1	8	1	2	1	8	4	3	rs140439481	byFrequency	TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr5:71756780G>C	ENST00000318442.5	-	2	1034	c.544C>G	c.(544-546)Ccg>Gcg	p.P182A		NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	182					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)		ATGAGGCCCGGGTGGACTTTG	0.672													G|||	4	0.000798722	0.003	0.0	5008	,	,		16364	0.0		0.0	False		,,,				2504	0.0				p.P182A		Atlas-SNP	.											.	ZNF366	108	.	0			c.C544G						PASS	.	G	ALA/PRO	5,4401	9.9+/-24.2	0,5,2198	99	107	104		544	4.1	0.8	5	dbSNP_134	104	0,8600		0,0,4300	yes	missense	ZNF366	NM_152625.1	27	0,5,6498	CC,CG,GG		0.0,0.1135,0.0384	possibly-damaging	182/745	71756780	5,13001	2203	4300	6503	SO:0001583	missense	167465	exon2			GGCCCGGGTGGAC	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.544C>G	5.37:g.71756780G>C	ENSP00000313158:p.Pro182Ala	80	0	0		73	40	0.547945	NM_152625	Q5HYI9|Q7RTV4	Missense_Mutation	SNP	ENST00000318442.5	37	CCDS4015.1	.	.	.	.	.	.	.	.	.	.	G	15.86	2.956642	0.53293	0.001135	0.0	ENSG00000178175	ENST00000318442	T	0.09445	2.98	5.92	4.06	0.47325	.	0.388965	0.25253	N	0.032014	T	0.10380	0.0254	L	0.34521	1.04	0.46927	D	0.999256	B	0.14012	0.009	B	0.12837	0.008	T	0.07121	-1.0789	10	0.27082	T	0.32	-27.0902	16.3517	0.83215	0.0:0.2494:0.7506:0.0	.	182	Q8N895	ZN366_HUMAN	A	182	ENSP00000313158:P182A	ENSP00000313158:P182A	P	-	1	0	ZNF366	71792536	1.000000	0.71417	0.812000	0.32479	0.962000	0.63368	6.566000	0.73978	0.769000	0.33313	0.561000	0.74099	CCG	G|1.000;C|0.000	0.000	strong		0.672	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3			C	71756780	G	C	71756780	3	2	39	1	0	0	0	0	1	0	0	0	17885	1232	43	4	1706	4	ZNF366	5	71756780	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	21073432	71756780	109158480	71	14616											
TNPO1	3842	hgsc.bcm.edu	37	chr5	72189245	72189245	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caatatgaagctccagataaAgattttatgatagtggctct	14	13	8	6	0	1	4	0	2	1	2	2	4	2	4	1	1	1	2	1	1	7	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr5:72189245A>C	ENST00000337273.5	+	17	2364	c.1938A>C	c.(1936-1938)aaA>aaC	p.K646N	TNPO1_ENST00000454282.1_Missense_Mutation_p.K596N|TNPO1_ENST00000523768.1_Missense_Mutation_p.K596N|TNPO1_ENST00000506351.2_Missense_Mutation_p.K638N	NM_002270.3	NP_002261.3	Q92973	TNPO1_HUMAN	transportin 1	646					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)		CTCCAGATAAAGATTTTATGA	0.373																																					p.K646N		Atlas-SNP	.											.	TNPO1	90	.	0			c.A1938C						PASS	.						56	59	58					5																	72189245		2203	4298	6501	SO:0001583	missense	3842	exon17			AGATAAAGATTTT	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.1938A>C	5.37:g.72189245A>C	ENSP00000336712:p.Lys646Asn	102	0	0		105	13	0.12381	NM_002270	B4DVC6|Q92957|Q92975	Missense_Mutation	SNP	ENST00000337273.5	37	CCDS43329.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.388130	0.82902	.	.	ENSG00000083312	ENST00000337273;ENST00000454282;ENST00000523768;ENST00000506351;ENST00000519220	T;T;T;T	0.39997	1.05;1.05;1.05;1.05	5.62	5.62	0.85841	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.70894	0.3276	H	0.95004	3.61	0.80722	D	1	D;D	0.67145	0.97;0.996	D;D	0.64776	0.92;0.929	T	0.79245	-0.1883	10	0.87932	D	0	-7.2071	12.0175	0.53321	0.9305:0.0:0.0695:0.0	.	596;646	Q92973-3;Q92973	.;TNPO1_HUMAN	N	646;596;596;638;157	ENSP00000336712:K646N;ENSP00000398524:K596N;ENSP00000428899:K596N;ENSP00000425118:K638N	ENSP00000336712:K646N	K	+	3	2	TNPO1	72225001	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.461000	0.53035	2.260000	0.74910	0.528000	0.53228	AAA	.	.	none		0.373	TNPO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000218577.3	NM_002270		C	72189245	A	C	72189245	3	2	39	1	0	0	0	0	1	0	0	0	16350	69	3	5	2004	5	TNPO1	5	72189245	Missense_Mutation	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	432465	72189245	108726015	72	14617											
AP3B1	8546	hgsc.bcm.edu	37	chr5	77412011	77412011	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gattcagaataaaacttcttAgcagaattctcttgctttgc	12	15	6	8	0	3	2	1	0	2	2	4	3	3	2	0	0	4	2	0	0	5	7	rs42360	byFrequency	TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr5:77412011A>T	ENST00000255194.6	-	18	2191	c.2016T>A	c.(2014-2016)gcT>gcA	p.A672A	AP3B1_ENST00000519295.1_Silent_p.A623A	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	672					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)		AAAACTTCTTAGCAGAATTCT	0.338									Hermansky-Pudlak syndrome																												p.A672A		Atlas-SNP	.											AP3B1,NS,carcinoma,0,1	AP3B1	94	1	0			c.T2016A						PASS	.						87	91	89					5																	77412011		2203	4300	6503	SO:0001819	synonymous_variant	8546	exon18	Familial Cancer Database	HPS, HPS1-8	CTTCTTAGCAGAA	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.2016T>A	5.37:g.77412011A>T		117	0	0		147	15	0.102041	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Silent	SNP	ENST00000255194.6	37	CCDS4041.1																																																																																			A|0.776;C|0.001	.	alt		0.338	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2			T	77412011	A	T	77412011	2	4	39	1	0	0	0	0	0	0	0	1	744	407	15	5		5	AP3B1	5	77412011	Silent	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	5222766	77412011	103503249	73	14618											
GPR98	84059	hgsc.bcm.edu	37	chr5	90052843	90052843	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaggtgcctccacccttgaaCgttcttcaagttcctgtagt	7	13	9	12	1	2	1	1	1	1	0	4	2	4	1	4	1	2	3	4	1	3	5	rs144269892	byFrequency	TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr5:90052843C>T	ENST00000405460.2	+	57	11901	c.11805C>T	c.(11803-11805)aaC>aaT	p.N3935N		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	3935	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)		CACCCTTGAACGTTCTTCAAG	0.443													C|||	6	0.00119808	0.0045	0.0	5008	,	,		15792	0.0		0.0	False		,,,				2504	0.0				p.N3935N		Atlas-SNP	.											.	GPR98	605	.	0			c.C11805T						PASS	.	C		10,3696		0,10,1843	101	98	99		11805	-9.8	0	5	dbSNP_134	99	0,8178		0,0,4089	no	coding-synonymous	GPR98	NM_032119.3		0,10,5932	TT,TC,CC		0.0,0.2698,0.0841		3935/6307	90052843	10,11874	1853	4089	5942	SO:0001819	synonymous_variant	84059	exon57			CTTGAACGTTCTT	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.11805C>T	5.37:g.90052843C>T		211	0	0		192	26	0.135417	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	37	CCDS47246.1	4	0.0018315018315018315	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	1.028	-0.682857	0.03353	0.002698	0.0	ENSG00000164199	ENST00000509621	.	.	.	5.3	-9.79	0.00494	.	.	.	.	.	T	0.63745	0.2537	.	.	.	0.35190	D	0.773244	.	.	.	.	.	.	T	0.71297	-0.4635	4	.	.	.	.	19.5309	0.95228	0.0:0.1654:0.0:0.8346	.	.	.	.	M	1501	.	.	T	+	2	0	GPR98	90088599	0.000000	0.05858	0.000000	0.03702	0.358000	0.29455	-0.645000	0.05409	-2.179000	0.00767	-0.670000	0.03821	ACG	C|0.998;T|0.002	0.002	strong		0.443	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		T	90052843	C	T	90052843	2	4	39	1	0	0	0	0	0	0	0	1	6730	535	19	1		1	GPR98	5	90052843	Silent	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	12640832	90052843	90862417	74	14619											
GPR98	84059	hgsc.bcm.edu	37	chr5	90151709	90151709	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttcacttctggatttataTgtatctcaggtcagtgacag	9	16	8	8	0	5	1	3	1	3	0	6	2	5	2	0	2	0	1	0	2	3	6			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr5:90151709T>C	ENST00000405460.2	+	82	17842	c.17746T>C	c.(17746-17748)Tgt>Cgt	p.C5916R	GPR98_ENST00000425867.2_Missense_Mutation_p.C1577R	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	5916					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)		TGGATTTATATGTATCTCAGG	0.363																																					p.C5916R		Atlas-SNP	.											.	GPR98	605	.	0			c.T17746C						PASS	.						158	146	150					5																	90151709		1888	4110	5998	SO:0001583	missense	84059	exon82			TTTATATGTATCT	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.17746T>C	5.37:g.90151709T>C	ENSP00000384582:p.Cys5916Arg	230	0	0		225	115	0.511111	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	T	19.38	3.817395	0.70912	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.43294	0.95;0.95	5.49	5.49	0.81192	GPCR, family 2-like (1);	0.041679	0.85682	D	0.000000	T	0.60117	0.2244	L	0.60455	1.87	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.998	D;D;D	0.71414	0.96;0.973;0.933	T	0.58858	-0.7562	9	.	.	.	.	15.8828	0.79216	0.0:0.0:0.0:1.0	.	1577;5916;1577	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	R	5916;5916;1577	ENSP00000384582:C5916R;ENSP00000392618:C1577R	.	C	+	1	0	GPR98	90187465	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.552000	0.67281	2.213000	0.71641	0.477000	0.44152	TGT	.	.	none		0.363	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119		C	90151709	T	C	90151709	3	2	39	1	0	0	0	0	1	0	0	0	6730	1464	51	3	18072	3	GPR98	5	90151709	Missense_Mutation	SNP	T	TCGA-GS-A9TW-01A-11D-A382-10	98866	90151709	90763551	75	14620											
SLC22A4	6583	hgsc.bcm.edu	37	chr5	131630330	131630330	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atgcgggactacgacgaggtGatcgccttcctgggcgagtg	7	8	16	10	5	0	1	0	1	0	0	2	5	1	2	2	3	2	0	2	3	1	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr5:131630330G>A	ENST00000200652.3	+	1	195	c.21G>A	c.(19-21)gtG>gtA	p.V7V	P4HA2_ENST00000471826.1_Intron	NM_003059.2	NP_003050.2	Q9H015	S22A4_HUMAN	solute carrier family 22 (organic cation/zwitterion transporter), member 4	7					body fluid secretion (GO:0007589)|carnitine metabolic process (GO:0009437)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cation transmembrane transport (GO:0098655)|organic cation transport (GO:0015695)|quaternary ammonium group transport (GO:0015697)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|triglyceride metabolic process (GO:0006641)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|carnitine transmembrane transporter activity (GO:0015226)|cation:cation antiporter activity (GO:0015491)|nucleotide binding (GO:0000166)|PDZ domain binding (GO:0030165)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|secondary active organic cation transmembrane transporter activity (GO:0008513)|symporter activity (GO:0015293)			endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|urinary_tract(1)	16		all_cancers(142;0.0752)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Amiloride(DB00594)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Desipramine(DB01151)|Guanidine(DB00536)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|L-Arginine(DB00125)|L-Carnitine(DB00583)|L-Lysine(DB00123)|Levofloxacin(DB01137)|Mepyramine(DB06691)|Nicotine(DB00184)|Ofloxacin(DB01165)|Procainamide(DB01035)|Quinidine(DB00908)|Quinine(DB00468)|Spermine(DB00127)|Testosterone(DB00624)|Tiotropium(DB01409)|Verapamil(DB00661)	ACGACGAGGTGATCGCCTTCC	0.592																																					p.V7V		Atlas-SNP	.											.	SLC22A4	45	.	0			c.G21A						PASS	.						78	84	82					5																	131630330		2203	4300	6503	SO:0001819	synonymous_variant	6583	exon1			CGAGGTGATCGCC	AB007448	CCDS4153.1	5q23.3	2013-07-18	2013-07-18		ENSG00000197208	ENSG00000197208		"Solute carriers"	10968	protein-coding gene	gene with protein product		604190	"solute carrier family 22 (organic cation/ergothioneine transporter), member 4"			9426230, 15795384	Standard	NM_003059		Approved	OCTN1, MGC34546	uc003kwq.3	Q9H015	OTTHUMG00000059648	ENST00000200652.3:c.21G>A	5.37:g.131630330G>A		95	0	0		107	15	0.140187	NM_003059	O14546	Silent	SNP	ENST00000200652.3	37	CCDS4153.1																																																																																			.	.	none		0.592	SLC22A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132661.1	NM_003059		A	131630330	G	A	131630330	2	1	39	1	0	0	0	0	0	0	0	1	14471	1277	45	2		2	SLC22A4	5	131630330	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	41478621	131630330	49284930	76	14621											
ABLIM3	22885	hgsc.bcm.edu	37	chr5	148620293	148620293	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	ccagttagatgtgaggtcctCcactccaacctcttaccagg	9	10	8	14	0	1	2	0	1	1	1	4	2	4	2	6	2	2	1	6	2	3	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr5:148620293C>G	ENST00000506113.1	+	13	1741	c.1259C>G	c.(1258-1260)tCc>tGc	p.S420C	ABLIM3_ENST00000508983.1_Intron|AC012613.2_ENST00000523176.1_RNA|RP11-331K21.1_ENST00000512647.2_RNA|ABLIM3_ENST00000504238.1_Intron|ABLIM3_ENST00000326685.7_Intron|RP11-331K21.1_ENST00000522685.1_RNA|ABLIM3_ENST00000356541.3_Intron|ABLIM3_ENST00000517451.1_5'Flank|ABLIM3_ENST00000309868.7_Missense_Mutation_p.S420C			O94929	ABLM3_HUMAN	actin binding LIM protein family, member 3	420					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|cilium assembly (GO:0042384)|lamellipodium assembly (GO:0030032)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGAGGTCCTCCACTCCAACC	0.577																																					p.S420C		Atlas-SNP	.											.	ABLIM3	91	.	0			c.C1259G						PASS	.						126	116	119					5																	148620293		2203	4300	6503	SO:0001583	missense	22885	exon14			GGTCCTCCACTCC	AB020650	CCDS4294.1	5q33.1	2008-02-05			ENSG00000173210	ENSG00000173210			29132	protein-coding gene	gene with protein product		611305					Standard	XM_005268392		Approved	KIAA0843	uc003lpy.2	O94929	OTTHUMG00000129932	ENST00000506113.1:c.1259C>G	5.37:g.148620293C>G	ENSP00000425394:p.Ser420Cys	72	0	0		71	43	0.605634	NM_014945	A8K121|Q19VH3|Q658S1|Q68CI5|Q9BV32	Missense_Mutation	SNP	ENST00000506113.1	37	CCDS4294.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.221000	0.79464	.	.	ENSG00000173210	ENST00000309868;ENST00000506113	T;T	0.45276	0.9;0.9	5.73	5.73	0.89815	.	0.304822	0.35970	N	0.002864	T	0.52996	0.1769	L	0.38175	1.15	0.80722	D	1	D	0.71674	0.998	P	0.58721	0.844	T	0.48833	-0.9000	10	0.52906	T	0.07	.	19.8552	0.96755	0.0:1.0:0.0:0.0	.	420	O94929	ABLM3_HUMAN	C	420	ENSP00000310309:S420C;ENSP00000425394:S420C	ENSP00000310309:S420C	S	+	2	0	ABLIM3	148600486	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.375000	0.52410	2.861000	0.98227	0.655000	0.94253	TCC	.	.	none		0.577	ABLIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373435.1	NM_014945		G	148620293	C	G	148620293	3	3	39	1	0	0	0	0	1	0	0	0	96	855	30	4	1309	4	ABLIM3	5	148620293	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	16989963	148620293	32294967	77	14622											
ATP10B	23120	hgsc.bcm.edu	37	chr5	160025799	160025799	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cagagttctggccactcttgTatagctcaggcaatgccagg	9	10	11	11	0	3	1	1	0	2	1	3	1	3	1	2	3	2	4	2	3	3	4			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr5:160025799T>G	ENST00000327245.5	-	22	4388	c.3542A>C	c.(3541-3543)tAc>tCc	p.Y1181S		NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	1181					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)			GCCACTCTTGTATAGCTCAGG	0.493																																					p.Y1181S		Atlas-SNP	.											.	ATP10B	201	.	0			c.A3542C						PASS	.						268	254	258					5																	160025799		1939	4133	6072	SO:0001583	missense	23120	exon22			CTCTTGTATAGCT	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.3542A>C	5.37:g.160025799T>G	ENSP00000313600:p.Tyr1181Ser	113	0	0		117	14	0.119658	NM_025153	Q9H725	Missense_Mutation	SNP	ENST00000327245.5	37	CCDS43394.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.698292	0.88830	.	.	ENSG00000118322	ENST00000327245	T	0.75821	-0.97	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.92622	0.7656	H	0.99770	4.765	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.95706	0.8753	9	.	.	.	.	14.8727	0.70471	0.0:0.0:0.0:1.0	.	1181	O94823	AT10B_HUMAN	S	1181	ENSP00000313600:Y1181S	.	Y	-	2	0	ATP10B	159958377	1.000000	0.71417	0.996000	0.52242	0.983000	0.72400	7.946000	0.87746	2.107000	0.64212	0.533000	0.62120	TAC	.	.	none		0.493	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153		G	160025799	T	G	160025799	3	3	39	1	0	0	0	0	1	0	0	0	1117	1638	57	5	863	5	ATP10B	5	160025799	Missense_Mutation	SNP	T	TCGA-GS-A9TW-01A-11D-A382-10	11405506	160025799	20889461	78	14623											
ATP10B	23120	hgsc.bcm.edu	37	chr5	160047422	160047422	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tggtgtagacaacaatctcgCcagtcagtgggtgcctcaca	10	9	11	11	1	3	1	2	0	1	1	4	1	3	1	2	2	2	1	2	2	3	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr5:160047422C>T	ENST00000327245.5	-	15	3194	c.2348G>A	c.(2347-2349)gGc>gAc	p.G783D	CTC-348L5.1_ENST00000523598.1_RNA	NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	783					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)			AACAATCTCGCCAGTCAGTGG	0.592																																					p.G783D		Atlas-SNP	.											.	ATP10B	201	.	0			c.G2348A						PASS	.						52	55	54					5																	160047422		2094	4205	6299	SO:0001583	missense	23120	exon15			ATCTCGCCAGTCA	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.2348G>A	5.37:g.160047422C>T	ENSP00000313600:p.Gly783Asp	167	0	0		141	15	0.106383	NM_025153	Q9H725	Missense_Mutation	SNP	ENST00000327245.5	37	CCDS43394.1	.	.	.	.	.	.	.	.	.	.	C	0.612	-0.824493	0.02755	.	.	ENSG00000118322	ENST00000327245;ENST00000520108	T;T	0.71934	-0.61;-0.61	5.48	1.49	0.22878	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	1.165400	0.05887	N	0.627584	T	0.56381	0.1981	L	0.31476	0.935	0.09310	N	1	B;B	0.14012	0.009;0.002	B;B	0.12156	0.007;0.005	T	0.39014	-0.9634	9	.	.	.	.	5.6592	0.17660	0.0:0.5569:0.1414:0.3017	.	391;783	Q2YDW8;O94823	.;AT10B_HUMAN	D	783;391	ENSP00000313600:G783D;ENSP00000431081:G391D	.	G	-	2	0	ATP10B	159980000	0.000000	0.05858	0.000000	0.03702	0.266000	0.26442	0.064000	0.14437	0.680000	0.31366	0.644000	0.83932	GGC	.	.	none		0.592	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153		T	160047422	C	T	160047422	3	4	39	1	0	0	0	0	1	0	0	0	1117	739	26	2	2085	2	ATP10B	5	160047422	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	21623	160047422	20867838	79	14624											
CLTB	1212	hgsc.bcm.edu	37	chr5	175824641	175824641	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttcttctctacttgttcaCtctggcgctggttccactcc	3	17	7	14	1	4	0	1	0	3	0	7	0	6	0	2	2	1	4	2	2	1	6			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr5:175824641C>T	ENST00000310418.4	-	4	636	c.431G>A	c.(430-432)aGt>aAt	p.S144N	CLTB_ENST00000345807.2_Missense_Mutation_p.S144N	NM_007097.3	NP_009028.1	P09497	CLCB_HUMAN	clathrin, light chain B	144	Involved in binding clathrin heavy chain.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	ciliary membrane (GO:0060170)|clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|trans-Golgi network (GO:0005802)	peptide binding (GO:0042277)|structural molecule activity (GO:0005198)			lung(1)	1	all_cancers(89;0.00522)|Renal(175;0.000269)|Lung NSC(126;0.0105)|all_lung(126;0.0168)	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;0.000178)	Kidney(146;0.098)		TACTTGTTCACTCTGGCGCTG	0.572																																					p.S144N		Atlas-SNP	.											.	CLTB	17	.	0			c.G431A						PASS	.						207	186	193					5																	175824641		2203	4300	6503	SO:0001583	missense	1212	exon4			TGTTCACTCTGGC	M20470	CCDS4402.1, CCDS4403.1	5q35.2	2010-05-11	2010-05-11		ENSG00000175416	ENSG00000175416			2091	protein-coding gene	gene with protein product		118970	"clathrin, light polypeptide (Lcb)"			7713494	Standard	NM_007097		Approved	Lcb	uc003meh.4	P09497	OTTHUMG00000130662	ENST00000310418.4:c.431G>A	5.37:g.175824641C>T	ENSP00000309415:p.Ser144Asn	129	0	0		133	15	0.112782	NM_001834	Q53Y37|Q6FHW1	Missense_Mutation	SNP	ENST00000310418.4	37	CCDS4403.1	.	.	.	.	.	.	.	.	.	.	c	8.653	0.898825	0.17686	.	.	ENSG00000175416	ENST00000310418;ENST00000345807	.	.	.	4.16	3.11	0.35812	.	0.215561	0.49916	D	0.000121	T	0.11707	0.0285	N	0.01515	-0.825	0.33890	D	0.637256	B;B	0.13145	0.001;0.007	B;B	0.16289	0.003;0.015	T	0.31752	-0.9932	9	0.02654	T	1	.	5.0552	0.14529	0.0:0.6844:0.0:0.3156	.	144;144	P09497-2;P09497	.;CLCB_HUMAN	N	144	.	ENSP00000309415:S144N	S	-	2	0	CLTB	175757247	0.306000	0.24490	0.999000	0.59377	0.974000	0.67602	0.716000	0.25836	1.850000	0.53721	0.298000	0.19748	AGT	.	.	none		0.572	CLTB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253153.1			T	175824641	C	T	175824641	3	4	39	1	0	0	0	0	1	0	0	0	3567	565	20	2	270	2	CLTB	5	175824641	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	15777219	175824641	5090619	80	14625											
FAF2	23197	hgsc.bcm.edu	37	chr5	175913491	175913491	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tctcaagacctcaaccaaggGcaagttatttcatagctggg	12	10	9	10	0	3	1	3	0	1	1	4	1	3	1	2	2	2	3	2	2	6	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr5:175913491G>A	ENST00000261942.6	+	3	320		c.e3+1		FAF2_ENST00000510446.1_Splice_Site	NM_014613.2	NP_055428.1	Q96CS3	FAF2_HUMAN	Fas associated factor family member 2						lipid particle organization (GO:0034389)|negative regulation of catalytic activity (GO:0043086)|response to unfolded protein (GO:0006986)	Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)	lipase binding (GO:0035473)|lipase inhibitor activity (GO:0055102)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	10						TCAACCAAGGGCAAGTTATTT	0.418																																					.		Atlas-SNP	.											.	FAF2	38	.	0			c.267+1G>A						PASS	.						114	99	104					5																	175913491		2203	4300	6503	SO:0001630	splice_region_variant	23197	exon3			CCAAGGGCAAGTT	BC015791	CCDS34296.1	5q35.2	2011-06-28	2008-07-25	2008-07-25	ENSG00000113194	ENSG00000113194		"UBX domain containing"	24666	protein-coding gene	gene with protein product	"expressed in T cells and eosinophils in atopic dermatitis", "UBX domain protein 3B"		"UBX domain containing 8"	UBXD8		10048485, 12372427	Standard	NM_014613		Approved	ETEA, KIAA0887, UBXN3B	uc003mej.4	Q96CS3	OTTHUMG00000163228	ENST00000261942.6:c.267+1G>A	5.37:g.175913491G>A		114	0	0		108	45	0.416667	NM_014613	O94963|Q8IUF2|Q9BRP2|Q9BVM7	Splice_Site	SNP	ENST00000261942.6	37	CCDS34296.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.961376	0.92791	.	.	ENSG00000113194	ENST00000261942;ENST00000540174	.	.	.	6.06	6.06	0.98353	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.6243	0.99512	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FAF2	175846097	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.313000	0.96297	2.879000	0.98667	0.650000	0.86243	.	.	.	none		0.418	FAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372194.1	NM_014613	Intron	A	175913491	G	A	175913491	5	1	39	1	0	0	0	0	0	0	1	0	5375	1217	42	2	278	2	FAF2	5	175913491	Splice_Site	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	88850	175913491	5001769	81	14626											
JARID2	3720	hgsc.bcm.edu	37	chr6	15504821	15504821	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agcctgccccagccgaaatcGaggtgagagaaggggcccct	10	4	14	13	2	0	2	0	1	0	1	1	5	0	2	6	3	3	0	6	3	2	0			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr6:15504821G>A	ENST00000341776.2	+	9	2783	c.2539G>A	c.(2539-2541)Gag>Aag	p.E847K	JARID2_ENST00000541660.1_Missense_Mutation_p.E809K|JARID2_ENST00000474854.1_3'UTR|JARID2_ENST00000397311.3_Missense_Mutation_p.E675K	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	847					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)				AGCCGAAATCGAGGTGAGAGA	0.557																																					p.E847K		Atlas-SNP	.											.	JARID2	135	.	0			c.G2539A						PASS	.						51	56	54					6																	15504821		2203	4300	6503	SO:0001583	missense	3720	exon9			GAAATCGAGGTGA	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.2539G>A	6.37:g.15504821G>A	ENSP00000341280:p.Glu847Lys	42	0	0		43	23	0.534884	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Missense_Mutation	SNP	ENST00000341776.2	37	CCDS4533.1	.	.	.	.	.	.	.	.	.	.	G	35	5.552389	0.96501	.	.	ENSG00000008083	ENST00000341776;ENST00000397311;ENST00000541660	D;D;D	0.96522	-3.28;-3.28;-4.04	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	D	0.98507	0.9502	M	0.91510	3.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.986	D	0.99624	1.0984	10	0.87932	D	0	-21.4897	18.8078	0.92045	0.0:0.0:1.0:0.0	.	809;847	F5H590;Q92833	.;JARD2_HUMAN	K	847;675;809	ENSP00000341280:E847K;ENSP00000380478:E675K;ENSP00000444623:E809K	ENSP00000341280:E847K	E	+	1	0	JARID2	15612800	1.000000	0.71417	0.985000	0.45067	0.750000	0.42670	9.544000	0.98092	2.435000	0.82474	0.561000	0.74099	GAG	.	.	none		0.557	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973		A	15504821	G	A	15504821	3	1	39	1	0	0	0	0	1	0	0	0	7954	1059	37	1	2573	1	JARID2	6	15504821	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10		15504821	155610246	82	14627											
HIST1H3D	8351	hgsc.bcm.edu	37	chr6	26197219	26197219	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcagcgccatcaccgccgagCtctgaaaacgcagatcagtc	11	5	10	15	4	3	2	2	1	1	1	4	3	3	2	3	0	3	3	3	0	2	0			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr6:26197219C>G	ENST00000356476.2	-	1	259	c.260G>C	c.(259-261)aGc>aCc	p.S87T	HIST1H2BF_ENST00000359985.1_5'Flank|HIST1H3D_ENST00000377831.5_Missense_Mutation_p.S87T			P68431	H31_HUMAN	histone cluster 1, H3d	87					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)			NS(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)	14		all_hematologic(11;0.196)				CACCGCCGAGCTCTGAAAACG	0.587																																					p.S87T	GBM(108;3816 4467)	Atlas-SNP	.											.	HIST1H3D	31	.	0			c.G260C						PASS	.						74	72	73					6																	26197219		2203	4300	6503	SO:0001583	missense	8351	exon2			GCCGAGCTCTGAA	Z80784	CCDS4590.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197409	ENSG00000197409		"Histones / Replication-dependent"	4767	protein-coding gene	gene with protein product		602811	"H3 histone family, member B", "histone 1, H3d"	H3FB		9119399, 12408966	Standard	NM_003530		Approved	H3/b	uc003ngv.4	P68431	OTTHUMG00000014433	ENST00000356476.2:c.260G>C	6.37:g.26197219C>G	ENSP00000366999:p.Ser87Thr	151	0	0		132	21	0.159091	NM_003530	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Missense_Mutation	SNP	ENST00000356476.2	37	CCDS4590.1	.	.	.	.	.	.	.	.	.	.	.	10.35	1.325234	0.24080	.	.	ENSG00000197409	ENST00000356476;ENST00000377831	T;T	0.71341	-0.56;-0.56	4.28	3.41	0.39046	.	.	.	.	.	T	0.63295	0.2499	.	.	.	0.31814	N	0.6269	.	.	.	.	.	.	T	0.63001	-0.6734	6	0.66056	D	0.02	.	11.3981	0.49854	0.0:0.9105:0.0:0.0895	.	.	.	.	T	87	ENSP00000366999:S87T;ENSP00000367062:S87T	ENSP00000366999:S87T	S	-	2	0	HIST1H3D	26305198	1.000000	0.71417	1.000000	0.80357	0.332000	0.28634	7.428000	0.80296	0.915000	0.36847	0.655000	0.94253	AGC	.	.	none		0.587	HIST1H3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040096.1	NM_003530		G	26197219	C	G	26197219	3	3	39	1	0	0	0	0	1	0	0	0	7167	797	28	4	154	4	HIST1H3D	6	26197219	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	10692398	26197219	144917848	83	14628											
ABT1	29777	hgsc.bcm.edu	37	chr6	26598677	26598677	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ccctgctcgcccagatggctCctggacatttgcccagcgtc	5	9	10	17	2	0	1	0	0	0	1	3	2	1	2	4	2	3	2	4	2	0	1	rs367868700		TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr6:26598677C>T	ENST00000274849.1	+	3	654	c.623C>T	c.(622-624)tCc>tTc	p.S208F		NM_013375.3	NP_037507.1	Q9ULW3	ABT1_HUMAN	activator of basal transcription 1	208					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						CCAGATGGCTCCTGGACATTT	0.617																																					p.S208F		Atlas-SNP	.											.	ABT1	39	.	0			c.C623T						PASS	.						37	39	38					6																	26598677		2203	4300	6503	SO:0001583	missense	29777	exon3			ATGGCTCCTGGAC	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.623C>T	6.37:g.26598677C>T	ENSP00000274849:p.Ser208Phe	105	0	0		116	51	0.439655	NM_013375		Missense_Mutation	SNP	ENST00000274849.1	37	CCDS4616.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.080257	0.76528	.	.	ENSG00000146109	ENST00000274849	.	.	.	5.49	5.49	0.81192	.	0.354787	0.30602	N	0.009280	T	0.61400	0.2344	L	0.57536	1.79	0.42957	D	0.994399	P	0.41569	0.755	P	0.48141	0.568	T	0.64812	-0.6319	9	0.59425	D	0.04	-9.8858	17.2409	0.87013	0.0:1.0:0.0:0.0	.	208	Q9ULW3	ABT1_HUMAN	F	208	.	ENSP00000274849:S208F	S	+	2	0	ABT1	26706656	0.982000	0.34865	0.938000	0.37757	0.698000	0.40448	1.381000	0.34362	2.741000	0.93983	0.655000	0.94253	TCC	.	.	alt		0.617	ABT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043698.1			T	26598677	C	T	26598677	3	4	39	1	0	0	0	0	1	0	0	0	101	855	30	2	633	2	ABT1	6	26598677	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	401458	26598677	144516390	84	14629											
KCTD20	222658	hgsc.bcm.edu	37	chr6	36447473	36447473	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	attttgacttcaacactatcCgatgtcaagatctgagtaag	13	13	7	8	1	3	3	2	2	1	1	4	4	4	3	1	0	1	1	1	0	4	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr6:36447473C>T	ENST00000373731.2	+	5	1034	c.643C>T	c.(643-645)Cga>Tga	p.R215*	KCTD20_ENST00000449081.2_Intron|KCTD20_ENST00000544295.1_Intron|KCTD20_ENST00000474988.1_Intron|KCTD20_ENST00000536244.1_Nonsense_Mutation_p.R70*	NM_173562.3	NP_775833.2	Q7Z5Y7	KCD20_HUMAN	potassium channel tetramerization domain containing 20	215					protein homooligomerization (GO:0051260)					central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|skin(1)	15						CAACACTATCCGATGTCAAGA	0.378																																					p.R215X		Atlas-SNP	.											KCTD20,rectum,carcinoma,-1,1	KCTD20	37	1	0			c.C643T						PASS	.						78	72	74					6																	36447473		2203	4300	6503	SO:0001587	stop_gained	222658	exon5			ACTATCCGATGTC	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.643C>T	6.37:g.36447473C>T	ENSP00000362836:p.Arg215*	63	0	0		64	29	0.453125	NM_173562	B4DZD3|B4E2Q3|F5H3T3|Q5W105|Q69YQ7|Q8IZ55	Nonsense_Mutation	SNP	ENST00000373731.2	37	CCDS4821.1	.	.	.	.	.	.	.	.	.	.	C	37	6.388762	0.97529	.	.	ENSG00000112078	ENST00000373731;ENST00000536244	.	.	.	4.72	2.74	0.32292	.	0.178769	0.34700	N	0.003742	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.09590	T	0.72	-9.9284	11.2051	0.48765	0.5758:0.4242:0.0:0.0	.	.	.	.	X	215;70	.	ENSP00000362836:R215X	R	+	1	2	KCTD20	36555451	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.532000	0.60608	1.189000	0.43028	0.591000	0.81541	CGA	.	.	none		0.378	KCTD20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040345.2	NM_173562		T	36447473	C	T	36447473	4	4	39	1	0	0	0	0	0	1	0	0	8117	644	23	1	657	1	KCTD20	6	36447473	Nonsense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	9848796	36447473	134667594	85	14630											
HSP90AB1	3326	hgsc.bcm.edu	37	chr6	44218144	44218144	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagatcgaagatgtgggttcAgatgaggaggatgacagcgg	13	7	17	4	2	1	5	1	2	0	3	2	8	1	7	0	4	1	1	0	4	2	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr6:44218144A>C	ENST00000371554.1	+	6	979	c.765A>C	c.(763-765)tcA>tcC	p.S255S	HSP90AB1_ENST00000353801.3_Silent_p.S255S|HSP90AB1_ENST00000371646.5_Silent_p.S255S			P08238	HS90B_HUMAN	heat shock protein 90kDa alpha (cytosolic), class B member 1	255					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)			atgtgggttcagatgaggagg	0.383																																					p.S255S		Atlas-SNP	.											.	HSP90AB1	83	.	0			c.A765C						PASS	.						52	52	52					6																	44218144		2203	4300	6503	SO:0001819	synonymous_variant	3326	exon6			GGGTTCAGATGAG	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.765A>C	6.37:g.44218144A>C		98	0	0		119	16	0.134454	NM_007355	B2R5P0|Q5T9W7|Q9NQW0|Q9NTK6	Silent	SNP	ENST00000371554.1	37	CCDS4909.1																																																																																			.	.	none		0.383	HSP90AB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040730.1	NM_007355		C	44218144	A	C	44218144	2	2	39	1	0	0	0	0	0	0	0	1	7411	175	7	5		5	HSP90AB1	6	44218144	Silent	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	7770671	44218144	126896923	86	14631											
AARS2	57505	hgsc.bcm.edu	37	chr6	44274068	44274068	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagtccgatcaatgatccGcctaccccgctccagggagg	9	6	11	15	3	1	2	1	1	0	1	4	4	4	3	6	2	1	1	6	2	2	1	rs143703625	byFrequency	TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr6:44274068G>A	ENST00000244571.4	-	9	1251	c.1249C>T	c.(1249-1251)Cgg>Tgg	p.R417W	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)			TCAATGATCCGCCTACCCCGC	0.597																																					p.R417W		Atlas-SNP	.											.	AARS2	77	.	0			c.C1249T						PASS	.						102	98	99					6																	44274068		2203	4300	6503	SO:0001583	missense	57505	exon9			TGATCCGCCTACC	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.1249C>T	6.37:g.44274068G>A	ENSP00000244571:p.Arg417Trp	75	0	0		72	12	0.166667	NM_020745		Missense_Mutation	SNP	ENST00000244571.4	37	CCDS34464.1	.	.	.	.	.	.	.	.	.	.	G	19.45	3.830210	0.71258	.	.	ENSG00000124608	ENST00000244571	T	0.58940	0.3	4.41	4.41	0.53225	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);	0.226724	0.43579	D	0.000545	T	0.74604	0.3738	M	0.91818	3.245	0.42141	D	0.991513	D	0.76494	0.999	P	0.59643	0.861	T	0.82458	-0.0447	10	0.87932	D	0	-10.4928	17.1894	0.86875	0.0:0.0:1.0:0.0	.	417	Q5JTZ9	SYAM_HUMAN	W	417	ENSP00000244571:R417W	ENSP00000244571:R417W	R	-	1	2	AARS2	44382046	0.993000	0.37304	0.997000	0.53966	0.846000	0.48090	4.028000	0.57246	2.301000	0.77427	0.655000	0.94253	CGG	G|0.999;T|0.001	.	alt		0.597	AARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040741.2	NM_020745		A	44274068	G	A	44274068	3	1	39	1	0	0	0	0	1	0	0	0	20	1086	38	1	1764	1	AARS2	6	44274068	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	55924	44274068	126840999	87	14632											
BAI3	577	hgsc.bcm.edu	37	chr6	70098685	70098685	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	caatcaatgtcttagacacaGaggcaaaggatgctttggaa	15	9	10	7	0	2	2	1	0	1	2	2	4	2	4	0	3	1	2	0	3	5	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr6:70098685G>A	ENST00000370598.1	+	32	5292	c.4471G>A	c.(4471-4473)Gag>Aag	p.E1491K	BAI3_ENST00000546190.1_Missense_Mutation_p.E455K|BAI3_ENST00000238918.8_Missense_Mutation_p.E697K	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1491					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)				CTTAGACACAGAGGCAAAGGA	0.453																																					p.E1491K		Atlas-SNP	.											BAI3,colon,carcinoma,0,1	BAI3	451	1	0			c.G4471A						PASS	.						112	96	101					6																	70098685		2203	4300	6503	SO:0001583	missense	577	exon32			GACACAGAGGCAA	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.4471G>A	6.37:g.70098685G>A	ENSP00000359630:p.Glu1491Lys	87	0	0		81	35	0.432099	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	37	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	G	15.25	2.778507	0.49786	.	.	ENSG00000135298	ENST00000370598;ENST00000238918;ENST00000546190	T;T;T	0.42513	2.13;2.73;0.97	5.94	5.94	0.96194	.	0.045450	0.85682	D	0.000000	T	0.16514	0.0397	N	0.19112	0.55	0.58432	D	0.999991	P;P	0.37781	0.608;0.608	B;B	0.29862	0.108;0.108	T	0.04427	-1.0952	10	0.21014	T	0.42	.	20.3812	0.98933	0.0:0.0:1.0:0.0	.	697;1491	B7Z356;O60242	.;BAI3_HUMAN	K	1491;697;455	ENSP00000359630:E1491K;ENSP00000238918:E697K;ENSP00000441821:E455K	ENSP00000238918:E697K	E	+	1	0	BAI3	70155406	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.220000	0.95180	2.823000	0.97156	0.643000	0.83706	GAG	.	.	none		0.453	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			A	70098685	G	A	70098685	3	1	39	1	0	0	0	0	1	0	0	0	1300	943	33	2	4589	2	BAI3	6	70098685	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	25824617	70098685	101016382	88	14633											
RIMS1	22999	hgsc.bcm.edu	37	chr6	72596832	72596832	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccgaagaggagaggaacattAtcatggcagtgatggaccgg	13	6	15	7	2	1	3	1	1	0	2	1	7	1	5	2	5	1	1	2	5	3	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr6:72596832A>G	ENST00000521978.1	+	1	106	c.106A>G	c.(106-108)Atc>Gtc	p.I36V	RIMS1_ENST00000491071.2_Missense_Mutation_p.I36V|RIMS1_ENST00000348717.5_Missense_Mutation_p.I36V|RIMS1_ENST00000264839.7_Missense_Mutation_p.I36V|RIMS1_ENST00000522291.1_Missense_Mutation_p.I36V|RIMS1_ENST00000520567.1_Missense_Mutation_p.I36V|RIMS1_ENST00000517960.1_Missense_Mutation_p.I36V|RIMS1_ENST00000518273.1_Missense_Mutation_p.I36V	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	36	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)				GAGGAACATTATCATGGCAGT	0.642																																					p.I36V		Atlas-SNP	.											.	RIMS1	278	.	0			c.A106G						PASS	.						40	51	48					6																	72596832		2097	4223	6320	SO:0001583	missense	22999	exon1			AACATTATCATGG	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.106A>G	6.37:g.72596832A>G	ENSP00000428417:p.Ile36Val	116	0	0		48	22	0.458333	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	37	CCDS47449.1	.	.	.	.	.	.	.	.	.	.	A	14.90	2.673997	0.47781	.	.	ENSG00000079841	ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978	T;T;T;T;T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18;-1.18;-1.18;-1.18;-1.18	5.05	3.85	0.44370	Zinc finger, RING/FYVE/PHD-type (1);Rab-binding domain (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.48767	D	0.000176	D	0.84238	0.5428	M	0.84948	2.725	0.80722	D	1	P	0.51351	0.944	D	0.68621	0.959	D	0.85939	0.1457	10	0.72032	D	0.01	-4.4049	11.053	0.47901	0.8441:0.1559:0.0:0.0	.	36	Q86UR5	RIMS1_HUMAN	V	36	ENSP00000430101:I36V;ENSP00000275037:I36V;ENSP00000264839:I36V;ENSP00000429959:I36V;ENSP00000430408:I36V;ENSP00000430502:I36V;ENSP00000430932:I36V;ENSP00000428417:I36V	ENSP00000264839:I36V	I	+	1	0	RIMS1	72653553	1.000000	0.71417	0.994000	0.49952	0.992000	0.81027	8.781000	0.91805	0.730000	0.32425	0.454000	0.30748	ATC	.	.	none		0.642	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1			G	72596832	A	G	72596832	3	3	39	1	0	0	0	0	1	0	0	0	13382	449	16	3	108	3	RIMS1	6	72596832	Missense_Mutation	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	2498147	72596832	98518235	89	14634											
NR2E1	7101	hgsc.bcm.edu	37	chr6	108499427	108499427	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agtgtgccagccttctccacGctgtctttgcaagaccaggt	7	11	10	13	1	2	1	0	0	2	1	3	1	2	1	4	1	3	2	4	1	1	2	rs561977068	byFrequency	TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr6:108499427G>A	ENST00000368986.4	+	5	1332	c.624G>A	c.(622-624)acG>acA	p.T208T	NR2E1_ENST00000368983.3_Silent_p.T245T	NM_003269.3	NP_003260.1	Q9Y466	NR2E1_HUMAN	nuclear receptor subfamily 2, group E, member 1	208	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)			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)		CCTTCTCCACGCTGTCTTTGC	0.507													G|||	8	0.00159744	0.0	0.0	5008	,	,		18263	0.0		0.0	False		,,,				2504	0.0082				p.T208T		Atlas-SNP	.											NR2E1,NS,carcinoma,0,1	NR2E1	57	1	0			c.G624A						PASS	.						98	81	87					6																	108499427		2203	4300	6503	SO:0001819	synonymous_variant	7101	exon5			CTCCACGCTGTCT	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.624G>A	6.37:g.108499427G>A		102	0	0		89	19	0.213483	NM_003269	Q6ZMP8	Silent	SNP	ENST00000368986.4	37	CCDS5063.1																																																																																			.	.	none		0.507	NR2E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041712.2			A	108499427	G	A	108499427	2	1	39	1	0	0	0	0	0	0	0	1	10634	1074	38	1		1	NR2E1	6	108499427	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	35902595	108499427	62615640	90	14635											
REV3L	5980	hgsc.bcm.edu	37	chr6	111685068	111685068	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agttttacctcatgtaaagcTtttgcctcctgtaagttttg	8	18	7	8	0	1	0	1	0	0	0	2	0	2	0	3	0	3	5	3	0	4	8			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr6:111685068T>C	ENST00000358835.3	-	17	7321	c.6867A>G	c.(6865-6867)aaA>aaG	p.K2289K	REV3L-IT1_ENST00000411895.1_RNA|REV3L_ENST00000368805.1_Silent_p.K2289K|REV3L_ENST00000368802.3_Silent_p.K2289K|REV3L_ENST00000435970.1_Silent_p.K2211K			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	2289					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)		CATGTAAAGCTTTTGCCTCCT	0.333								DNA polymerases (catalytic subunits)																													p.K2289K		Atlas-SNP	.											.	REV3L	386	.	0			c.A6867G						PASS	.						178	160	166					6																	111685068		2202	4299	6501	SO:0001819	synonymous_variant	5980	exon16			TAAAGCTTTTGCC	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.6867A>G	6.37:g.111685068T>C		197	0	0		190	25	0.131579	NM_002912	O43214|Q5TC33	Silent	SNP	ENST00000358835.3	37	CCDS5091.2																																																																																			.	.	none		0.333	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912		C	111685068	T	C	111685068	2	2	39	1	0	0	0	0	0	0	0	1	13255	1606	56	3		3	REV3L	6	111685068	Silent	SNP	T	TCGA-GS-A9TW-01A-11D-A382-10	3185641	111685068	59429999	91	14636											
FAM26E	254228	hgsc.bcm.edu	37	chr6	116836827	116836827	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctcaccacatgttatgctcGctgccgatctaaagttagct	9	12	8	12	2	2	0	1	0	1	0	3	1	2	0	2	0	3	6	2	0	4	3	rs571775020		TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr6:116836827G>A	ENST00000368599.3	+	2	656	c.605G>A	c.(604-606)cGc>cAc	p.R202H	TRAPPC3L_ENST00000368602.3_Intron	NM_153711.2	NP_714922.1	Q8N5C1	FA26E_HUMAN	family with sequence similarity 26, member E	202					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)	7		all_cancers(87;0.0608)|all_epithelial(87;0.05)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0242)|all cancers(137;0.0419)|OV - Ovarian serous cystadenocarcinoma(136;0.0671)|Epithelial(106;0.212)		TGTTATGCTCGCTGCCGATCT	0.413													G|||	1	0.000199681	0.0	0.0	5008	,	,		21409	0.0		0.0	False		,,,				2504	0.001				p.R202H		Atlas-SNP	.											FAM26E,NS,carcinoma,+1,1	FAM26E	26	1	0			c.G605A						PASS	.						154	155	155					6																	116836827		2203	4300	6503	SO:0001583	missense	254228	exon2			ATGCTCGCTGCCG	BC032556	CCDS5108.1	6q22.31	2008-02-05	2007-03-19	2007-03-19	ENSG00000178033	ENSG00000178033			21568	protein-coding gene	gene with protein product			"chromosome 6 open reading frame 188"	C6orf188			Standard	NM_153711		Approved	dJ493F7.3, MGC45451	uc003pwy.3	Q8N5C1	OTTHUMG00000015442	ENST00000368599.3:c.605G>A	6.37:g.116836827G>A	ENSP00000357588:p.Arg202His	285	0	0		224	62	0.276786	NM_153711	B2RDJ9|B3KSR3	Missense_Mutation	SNP	ENST00000368599.3	37	CCDS5108.1	.	.	.	.	.	.	.	.	.	.	G	16.56	3.158090	0.57368	.	.	ENSG00000178033	ENST00000368599	T	0.19250	2.16	6.03	6.03	0.97812	.	0.106321	0.64402	D	0.000002	T	0.23289	0.0563	L	0.43152	1.355	0.45464	D	0.99843	D	0.69078	0.997	P	0.58873	0.847	T	0.00436	-1.1740	10	0.46703	T	0.11	-4.565	12.8091	0.57629	0.0738:0.0:0.9262:0.0	.	202	Q8N5C1	FA26E_HUMAN	H	202	ENSP00000357588:R202H	ENSP00000357588:R202H	R	+	2	0	FAM26E	116943520	1.000000	0.71417	1.000000	0.80357	0.161000	0.22273	6.809000	0.75211	2.854000	0.98071	0.655000	0.94253	CGC	.	.	none		0.413	FAM26E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041956.1	NM_153711		A	116836827	G	A	116836827	3	1	39	1	0	0	0	0	1	0	0	0	5558	1087	38	1	611	1	FAM26E	6	116836827	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	5151759	116836827	54278240	92	14637											
OPRM1	4988	hgsc.bcm.edu	37	chr6	154411241	154411241	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaatgccaaaattatcaatGtctgcaactggatcctctct	13	12	6	10	0	3	0	1	0	2	0	5	2	4	1	2	1	3	1	2	1	6	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr6:154411241G>A	ENST00000330432.7	+	2	808	c.571G>A	c.(571-573)Gtc>Atc	p.V191I	OPRM1_ENST00000522555.1_Missense_Mutation_p.V91I|OPRM1_ENST00000414028.2_Missense_Mutation_p.V191I|OPRM1_ENST00000522236.1_Missense_Mutation_p.V91I|OPRM1_ENST00000428397.2_Missense_Mutation_p.V191I|OPRM1_ENST00000360422.4_Missense_Mutation_p.V191I|OPRM1_ENST00000435918.2_Missense_Mutation_p.V191I|OPRM1_ENST00000434900.2_Missense_Mutation_p.V284I|OPRM1_ENST00000520708.1_Missense_Mutation_p.V91I|OPRM1_ENST00000452687.2_Missense_Mutation_p.V191I|OPRM1_ENST00000518759.1_Missense_Mutation_p.V110I|OPRM1_ENST00000419506.2_Missense_Mutation_p.V191I|OPRM1_ENST00000337049.4_Missense_Mutation_p.V191I|OPRM1_ENST00000229768.5_Missense_Mutation_p.V191I|OPRM1_ENST00000524163.1_Missense_Mutation_p.V191I	NM_000914.3	NP_000905.3	P35372	OPRM_HUMAN	opioid receptor, mu 1	191					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)	AATTATCAATGTCTGCAACTG	0.468																																					p.V284I		Atlas-SNP	.											.	OPRM1	241	.	0			c.G850A						PASS	.						161	153	155					6																	154411241		2052	4235	6287	SO:0001583	missense	4988	exon4			ATCAATGTCTGCA	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.571G>A	6.37:g.154411241G>A	ENSP00000328264:p.Val191Ile	91	0	0		82	36	0.439024	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	37	CCDS55070.1	.	.	.	.	.	.	.	.	.	.	G	8.766	0.924735	0.18056	.	.	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	0.37915	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	5.8	2.95	0.34219	GPCR, rhodopsin-like superfamily (1);	0.108809	0.64402	N	0.000008	T	0.09642	0.0237	N	0.14661	0.345	0.41124	D	0.985834	B;B;B;B;B;B;B;B;B;B;B;B;B	0.19073	0.007;0.001;0.001;0.019;0.033;0.005;0.004;0.001;0.004;0.001;0.002;0.018;0.001	B;B;B;B;B;B;B;B;B;B;B;B;B	0.29353	0.013;0.027;0.014;0.034;0.101;0.074;0.027;0.045;0.044;0.024;0.019;0.071;0.014	T	0.10268	-1.0637	10	0.22109	T	0.4	.	10.791	0.46432	0.213:0.0:0.787:0.0	.	191;191;191;191;284;110;191;91;191;191;191;191;191	P35372-4;P35372-8;P35372-11;P35372-9;P35372-10;B8Q1L9;P35372-6;Q6UPP1;P35372-5;P35372;P35372-7;P35372-3;P35372-2	.;.;.;.;.;.;.;.;.;OPRM_HUMAN;.;.;.	I	284;91;110;191;191;191;191;191;191;191;191;191;191;91;91	ENSP00000394624:V284I;ENSP00000430876:V91I;ENSP00000430260:V110I;ENSP00000328264:V191I;ENSP00000353598:V191I;ENSP00000411903:V191I;ENSP00000410497:V191I;ENSP00000229768:V191I;ENSP00000403549:V191I;ENSP00000430097:V191I;ENSP00000399359:V191I;ENSP00000413752:V191I;ENSP00000338381:V191I;ENSP00000429719:V91I;ENSP00000429373:V91I	ENSP00000229768:V191I	V	+	1	0	OPRM1	154452934	1.000000	0.71417	0.938000	0.37757	0.998000	0.95712	2.492000	0.45311	0.317000	0.23160	0.655000	0.94253	GTC	.	.	none		0.468	OPRM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042786.2	NM_000914		A	154411241	G	A	154411241	3	1	39	1	0	0	0	0	1	0	0	0	10896	1377	48	2	911	2	OPRM1	6	154411241	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	37574414	154411241	16703826	93	14638											
KLHL7	55975	hgsc.bcm.edu	37	chr7	23165412	23165412	+	Intron	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aagttgatcagagccttccaGagtgtggtatgcttttcact	9	14	10	8	0	2	3	2	1	0	2	3	3	3	3	2	1	2	3	2	1	2	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr7:23165412G>A	ENST00000339077.5	+	4	685				KLHL7_ENST00000322231.7_Intron|KLHL7_ENST00000410047.1_Missense_Mutation_p.E137K|KLHL7_ENST00000545443.1_Intron|KLHL7_ENST00000542558.1_Intron|KLHL7_ENST00000409689.1_Intron|KLHL7_ENST00000322275.5_Missense_Mutation_p.E159K|KLHL7_ENST00000539124.1_Intron|KLHL7_ENST00000479288.1_Intron	NM_001031710.2	NP_001026880.2	Q8IXQ5	KLHL7_HUMAN	kelch-like family member 7						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						GAGCCTTCCAGAGTGTGGTAT	0.413																																					p.E159K		Atlas-SNP	.											.	KLHL7	102	.	0			c.G475A						PASS	.																																			SO:0001627	intron_variant	55975	exon5			CTTCCAGAGTGTG		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.442+621G>A	7.37:g.23165412G>A		152	0	0		84	42	0.5	NM_001172428	A4D144|B7Z5I9|G5E9G3|Q7Z765|Q96MV2|Q9BQF8|Q9UDQ9	Missense_Mutation	SNP	ENST00000339077.5	37	CCDS34609.1	.	.	.	.	.	.	.	.	.	.	G	7.947	0.743932	0.15642	.	.	ENSG00000122550	ENST00000322275;ENST00000410047	T;T	0.73897	-0.73;-0.79	2.26	0.299	0.15771	.	.	.	.	.	T	0.58807	0.2148	.	.	.	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.50030	-0.8875	8	0.59425	D	0.04	.	4.0126	0.09629	0.4137:0.0:0.5863:0.0	.	159;137	Q8IXQ5-3;Q8IXQ5-4	.;.	K	159;137	ENSP00000323270:E159K;ENSP00000386999:E137K	ENSP00000323270:E159K	E	+	1	0	KLHL7	23131937	0.000000	0.05858	0.001000	0.08648	0.204000	0.24138	-0.620000	0.05565	0.064000	0.16427	0.563000	0.77884	GAG	.	.	none		0.413	KLHL7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326860.3	NM_018846		A	23165412	G	A	23165412	1	1	39	0	1	0	0	0	0	0	0	0	8403	943	33	2		2	KLHL7	7	23165412	Intron	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10		23165412	135973251	94	14639											
PCLO	27445	hgsc.bcm.edu	37	chr7	82584908	82584908	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccctctgcttttcttgctcCtttaataattcttcttcctc	4	21	2	14	0	4	0	0	0	4	0	8	0	7	0	3	0	2	2	3	0	2	9			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr7:82584908C>G	ENST00000333891.9	-	5	5698	c.5361G>C	c.(5359-5361)aaG>aaC	p.K1787N	PCLO_ENST00000423517.2_Missense_Mutation_p.K1787N	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						TTTCTTGCTCCTTTAATAATT	0.403																																					p.K1787N		Atlas-SNP	.											.	PCLO	1506	.	0			c.G5361C						PASS	.						90	83	85					7																	82584908		1837	4081	5918	SO:0001583	missense	27445	exon5			TTGCTCCTTTAAT	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.5361G>C	7.37:g.82584908C>G	ENSP00000334319:p.Lys1787Asn	505	1	0.0019802		331	96	0.29003	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	5.765	0.325561	0.10900	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.19938	2.11;2.11	5.56	2.63	0.31362	.	.	.	.	.	T	0.13200	0.0320	N	0.08118	0	0.80722	D	1	P;P	0.41848	0.763;0.763	P;P	0.44897	0.463;0.463	T	0.09378	-1.0677	9	0.87932	D	0	.	8.1683	0.31239	0.0:0.5911:0.0:0.4089	.	1787;1787	Q9Y6V0-5;Q9Y6V0-6	.;.	N	1718;1787;1787	ENSP00000334319:K1787N;ENSP00000388393:K1787N	ENSP00000334319:K1787N	K	-	3	2	PCLO	82422844	0.989000	0.36119	0.956000	0.39512	0.996000	0.88848	0.330000	0.19715	0.238000	0.21222	0.650000	0.86243	AAG	.	.	none		0.403	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510		G	82584908	C	G	82584908	3	3	39	1	0	0	0	0	1	0	0	0	11592	680	24	4	10168	4	PCLO	7	82584908	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	59419496	82584908	76553755	95	14640											
BAIAP2L1	55971	hgsc.bcm.edu	37	chr7	97991678	97991678	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aacagacttaccgtttacagCtttctcataatttttcccca	11	15	3	12	1	1	1	1	0	1	1	3	1	2	1	3	0	4	2	3	0	4	7			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr7:97991678C>A	ENST00000005260.8	-	2	333	c.118G>T	c.(118-120)Gct>Tct	p.A40S	BAIAP2L1_ENST00000462558.1_5'UTR	NM_018842.4	NP_061330.2	Q9UHR4	BI2L1_HUMAN	BAI1-associated protein 2-like 1	40	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)			CCGTTTACAGCTTTCTCATAA	0.284																																					p.A40S		Atlas-SNP	.											BAIAP2L1,right_upper_lobe,carcinoma,0,1	BAIAP2L1	61	1	0			c.G118T						PASS	.						75	82	80					7																	97991678		2202	4300	6502	SO:0001583	missense	55971	exon2			TTACAGCTTTCTC	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.118G>T	7.37:g.97991678C>A	ENSP00000005260:p.Ala40Ser	411	0	0		351	59	0.168091	NM_018842	A4D268|Q75L21|Q75L22|Q96CV4|Q9H5F5|Q9Y2M8	Missense_Mutation	SNP	ENST00000005260.8	37	CCDS34687.1	.	.	.	.	.	.	.	.	.	.	C	18.13	3.556132	0.65425	.	.	ENSG00000006453	ENST00000005260	T	0.31247	1.5	5.45	5.45	0.79879	IRSp53/MIM homology domain (IMD) (3);	0.167136	0.53938	D	0.000051	T	0.42063	0.1186	L	0.43923	1.385	0.54753	D	0.999981	D	0.61080	0.989	P	0.57283	0.817	T	0.10064	-1.0646	10	0.42905	T	0.14	-18.9119	14.7855	0.69800	0.0:1.0:0.0:0.0	.	40	Q9UHR4	BI2L1_HUMAN	S	40	ENSP00000005260:A40S	ENSP00000005260:A40S	A	-	1	0	AC093799.1	97829614	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	1.770000	0.38532	2.575000	0.86900	0.591000	0.81541	GCT	.	.	none		0.284	BAIAP2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334681.1	NM_018842		A	97991678	C	A	97991678	3	1	39	1	0	0	0	0	1	0	0	0	1302	797	28	4	1469	4	BAIAP2L1	7	97991678	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	15406770	97991678	61146985	96	14641											
SMURF1	57154	hgsc.bcm.edu	37	chr7	98652487	98652487	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctgtctcgtgtctgtaaactGactaaaagagaaaagaacga	16	9	9	7	2	2	3	0	1	2	2	3	5	2	3	0	0	2	1	0	0	7	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr7:98652487G>C	ENST00000361125.1	-	6	724	c.405C>G	c.(403-405)gtC>gtG	p.V135V	SMURF1_ENST00000480055.1_5'UTR|SMURF1_ENST00000361368.2_Splice_Site_p.V135V	NM_020429.2	NP_065162.1	Q9HCE7	SMUF1_HUMAN	SMAD specific E3 ubiquitin protein ligase 1	135					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)			TCTGTAAACTGACTAAAAGAG	0.413																																					p.V135V		Atlas-SNP	.											.	SMURF1	58	.	0			c.C405G						PASS	.						96	99	98					7																	98652487		2203	4300	6503	SO:0001630	splice_region_variant	57154	exon6			TAAACTGACTAAA	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.404-1C>G	7.37:g.98652487G>C		59	0	0		60	16	0.266667	NM_020429	A4D279|B7ZMB6|B9EGV3|O75853|Q547Q3|Q9UJT8	Silent	SNP	ENST00000361125.1	37	CCDS34690.1																																																																																			.	.	none		0.413	SMURF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000335001.2	NM_020429	Silent	C	98652487	G	C	98652487	5	2	39	1	0	0	0	0	0	0	1	0	14834	1304	45	4	1924	4	SMURF1	7	98652487	Splice_Site	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	660809	98652487	60486176	97	14642											
MET	4233	hgsc.bcm.edu	37	chr7	116422095	116422095	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cttcaagtagccaaaggcatGaaatatcttgcaagcaaaaa	18	8	7	8	0	2	1	1	1	1	0	2	1	2	1	1	1	3	4	1	1	8	4			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr7:116422095G>A	ENST00000318493.6	+	18	3817	c.3630G>A	c.(3628-3630)atG>atA	p.M1210I	MET_ENST00000397752.3_Missense_Mutation_p.M1192I|MET_ENST00000539704.1_Missense_Mutation_p.M62I			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)			CCAAAGGCATGAAATATCTTG	0.373			Mis		"papillary renal, head-neck squamous cell "	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.M1210I		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.G3630A						PASS	.						60	58	58					7																	116422095		1831	4083	5914	SO:0001583	missense	4233	exon18	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	AGGCATGAAATAT	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.3630G>A	7.37:g.116422095G>A	ENSP00000317272:p.Met1210Ile	140	0	0		120	21	0.175	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	37	CCDS47689.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.799113	0.90538	.	.	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000539704	T;T;T	0.34072	1.38;1.38;1.38	5.87	5.87	0.94306	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	0.64159	0.2573	M	0.75615	2.305	0.80722	D	1	D;D	0.89917	1.0;0.995	D;D	0.91635	0.999;0.992	T	0.64292	-0.6442	10	0.87932	D	0	.	20.5827	0.99408	0.0:0.0:1.0:0.0	.	1210;1192	P08581-2;P08581	.;MET_HUMAN	I	1192;1210;62	ENSP00000380860:M1192I;ENSP00000317272:M1210I;ENSP00000445020:M62I	ENSP00000317272:M1210I	M	+	3	0	MET	116209331	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.781000	0.99029	2.941000	0.99782	0.655000	0.94253	ATG	.	.	none		0.373	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3			A	116422095	G	A	116422095	3	1	39	1	0	0	0	0	1	0	0	0	9494	1290	45	2	3696	2	MET	7	116422095	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	17769608	116422095	42716568	98	14643											
CTTNBP2	83992	hgsc.bcm.edu	37	chr7	117400606	117400606	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agagattgcctggaaatgatTtgtcagagcttgactcactg	11	12	11	7	0	2	4	2	2	0	2	2	6	2	5	1	1	2	1	1	1	1	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr7:117400606T>G	ENST00000160373.3	-	10	3146	c.3055A>C	c.(3055-3057)Aat>Cat	p.N1019H		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1019					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)		TGGAAATGATTTGTCAGAGCT	0.418																																					p.N1019H		Atlas-SNP	.											.	CTTNBP2	200	.	0			c.A3055C						PASS	.						235	213	220					7																	117400606		2203	4300	6503	SO:0001583	missense	83992	exon10			AATGATTTGTCAG		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.3055A>C	7.37:g.117400606T>G	ENSP00000160373:p.Asn1019His	313	0	0		191	74	0.387435	NM_033427	O43389|Q7LG11|Q9C0A5	Missense_Mutation	SNP	ENST00000160373.3	37	CCDS5774.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	20.2|20.2|20.2	3.957458|3.957458|3.957458	0.73902|0.73902|0.73902	.|.|.	.|.|.	ENSG00000077063|ENSG00000077063|ENSG00000077063	ENST00000446636|ENST00000160373|ENST00000435233;ENST00000416239	.|T|.	.|0.68479|.	.|-0.33|.	5.72|5.72|5.72	4.56|4.56|4.56	0.56223|0.56223|0.56223	.|.|.	.|0.312530|.	.|0.37906|.	.|N|.	.|0.001891|.	T|T|T	0.74831|0.74831|0.74831	0.3768|0.3768|0.3768	M|M|M	0.82630|0.82630|0.82630	2.6|2.6|2.6	0.37453|0.37453|0.37453	D|D|D	0.9149|0.9149|0.9149	.|D|.	.|0.53462|.	.|0.96|.	.|P|.	.|0.57204|.	.|0.815|.	T|T|T	0.79451|0.79451|0.79451	-0.1798|-0.1798|-0.1798	5|10|5	.|0.72032|.	.|D|.	.|0.01|.	-0.6073|-0.6073|-0.6073	11.8043|11.8043|11.8043	0.52145|0.52145|0.52145	0.0:0.0687:0.0:0.9313|0.0:0.0687:0.0:0.9313|0.0:0.0687:0.0:0.9313	.|.|.	.|1019|.	.|Q8WZ74|.	.|CTTB2_HUMAN|.	T|H|H	506|1019|32;14	.|ENSP00000160373:N1019H|.	.|ENSP00000160373:N1019H|.	K|N|Q	-|-|-	2|1|3	0|0|2	CTTNBP2|CTTNBP2|CTTNBP2	117187842|117187842|117187842	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	2.678000|2.678000|2.678000	0.46900|0.46900|0.46900	1.096000|1.096000|1.096000	0.41439|0.41439|0.41439	0.528000|0.528000|0.528000	0.53228|0.53228|0.53228	AAA|AAT|CAA	.	.	none		0.418	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427		G	117400606	T	G	117400606	3	3	39	1	0	0	0	0	1	0	0	0	4047	1841	64	5	1992	5	CTTNBP2	7	117400606	Missense_Mutation	SNP	T	TCGA-GS-A9TW-01A-11D-A382-10	978511	117400606	41738057	99	14644											
AASS	10157	hgsc.bcm.edu	37	chr7	121726174	121726174	+	Frame_Shift_Del	DEL	A	A	-																															ccttccaaatttaatcctggAaaaaaatccatggacgtaac																										TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr7:121726174delA	ENST00000393376.1	-	18	2171	c.2076delT	c.(2074-2076)tttfs	p.F692fs	AASS_ENST00000417368.2_Frame_Shift_Del_p.F692fs|AASS_ENST00000473553.1_5'UTR			Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase	692	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)	p.P693fs*3(1)		autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(6)|large_intestine(12)|lung(27)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	54						TTAATCCTGGAAAAAAATCCA	0.443																																					p.P693fs		Pindel,Atlas-Indel	.											.	AASS	123	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2077delC						PASS	.						81	79	80					7																	121726174		2203	4300	6503	SO:0001589	frameshift_variant	10157	exon19			.	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.2076delT	7.37:g.121726174delA	ENSP00000377040:p.Phe692fs	126	0	.		66	16	0.242	NM_005763	O95462	Frame_Shift_Del	DEL	ENST00000393376.1	37	CCDS5783.1																																																																																			.	.	none		0.443	AASS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347300.1	NM_005763		-	121726174	A	-	121726174	7	5	39	1	0	1	0	1	0	0	0	0	24	243	9	0	728	0	AASS	7	121726174	Frame_Shift_Del	DEL	A	TCGA-GS-A9TW-01A-11D-A382-10	4325568	121726174	37412489	100	14645											
EXOC4	60412	hgsc.bcm.edu	37	chr7	132959870	132959870	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cagaattgacgacagccattCgcacataccagagcatcaca	15	6	7	13	2	1	3	1	1	0	2	2	4	1	3	2	0	3	2	2	0	2	3	rs201300506		TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr7:132959870C>T	ENST00000253861.4	+	2	249	c.220C>T	c.(220-222)Cgc>Tgc	p.R74C	EXOC4_ENST00000539845.1_5'UTR|EXOC4_ENST00000393161.2_Missense_Mutation_p.R74C	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	74					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)				GACAGCCATTCGCACATACCA	0.468																																					p.R74C		Atlas-SNP	.											EXOC4,NS,carcinoma,-1,2	EXOC4	118	2	0			c.C220T						PASS	.	C	CYS/ARG,CYS/ARG	0,4406		0,0,2203	132	116	122		220,220	5.5	1	7		122	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	EXOC4	NM_001037126.1,NM_021807.3	180,180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	74/474,74/975	132959870	1,13005	2203	4300	6503	SO:0001583	missense	60412	exon2			GCCATTCGCACAT	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.220C>T	7.37:g.132959870C>T	ENSP00000253861:p.Arg74Cys	103	0	0		72	16	0.222222	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Missense_Mutation	SNP	ENST00000253861.4	37	CCDS5829.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.599554	0.87055	0.0	1.16E-4	ENSG00000131558	ENST00000253861;ENST00000393161	.	.	.	5.49	5.49	0.81192	Sec8 exocyst complex component specific domain (1);	0.000000	0.85682	D	0.000000	T	0.74215	0.3687	L	0.43152	1.355	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.73708	0.981;0.926	T	0.74396	-0.3679	9	0.52906	T	0.07	.	19.3733	0.94498	0.0:1.0:0.0:0.0	.	74;74	Q96A65;Q8TAR2	EXOC4_HUMAN;.	C	74	.	ENSP00000253861:R74C	R	+	1	0	EXOC4	132610410	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.534000	0.53568	2.579000	0.87056	0.650000	0.86243	CGC	C|0.999;T|0.001	0.001	weak		0.468	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807		T	132959870	C	T	132959870	3	4	39	1	0	0	0	0	1	0	0	0	5308	884	31	1	226	1	EXOC4	7	132959870	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	11233696	132959870	26178793	101	14646											
OR2A25	392138	hgsc.bcm.edu	37	chr7	143771336	143771336	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gggggaaatcagacttccatCacagagttcctcctactggg	10	9	11	11	0	2	2	2	0	0	2	5	3	5	3	3	3	1	1	3	3	2	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr7:143771336C>T	ENST00000408898.2	+	1	62	c.24C>T	c.(22-24)atC>atT	p.I8I		NM_001004488.1	NP_001004488.1	A4D2G3	O2A25_HUMAN	olfactory receptor, family 2, subfamily A, member 25	8						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(2)|lung(16)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	24	Melanoma(164;0.0783)					AGACTTCCATCACAGAGTTCC	0.468																																					p.I8I		Atlas-SNP	.											OR2A25,caecum,carcinoma,+2,1	OR2A25	66	1	0			c.C24T						PASS	.						75	83	80					7																	143771336		2201	4299	6500	SO:0001819	synonymous_variant	392138	exon1			TTCCATCACAGAG		CCDS43669.1	7q35	2012-08-09		2004-03-10	ENSG00000221933	ENSG00000221933		"GPCR / Class A : Olfactory receptors"	19562	protein-coding gene	gene with protein product				OR2A25P, OR2A27			Standard	NM_001004488		Approved		uc011ktx.2	A4D2G3	OTTHUMG00000158013	ENST00000408898.2:c.24C>T	7.37:g.143771336C>T		181	0	0		146	26	0.178082	NM_001004488	B2RNC9	Silent	SNP	ENST00000408898.2	37	CCDS43669.1																																																																																			.	.	none		0.468	OR2A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350000.1			T	143771336	C	T	143771336	2	4	39	1	0	0	0	0	0	0	0	1	10987	816	29	2		2	OR2A25	7	143771336	Silent	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	10811466	143771336	15367327	102	14647											
ABCB8	11194	hgsc.bcm.edu	37	chr7	150733637	150733637	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccctctcctgcaggcatggTcttgggtaccctatttattg	5	14	9	13	0	2	0	0	0	2	0	3	0	2	0	4	3	2	3	4	3	3	6			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr7:150733637T>G	ENST00000297504.6	+	10	1235	c.1169T>G	c.(1168-1170)gTc>gGc	p.V390G	ABCB8_ENST00000542328.1_Missense_Mutation_p.V285G|ABCB8_ENST00000356058.4_Missense_Mutation_p.V410G|ABCB8_ENST00000498578.1_Missense_Mutation_p.V373G|ABCB8_ENST00000477092.1_Missense_Mutation_p.V373G|ABCB8_ENST00000358849.4_Missense_Mutation_p.V373G|ABCB8_ENST00000477719.1_Missense_Mutation_p.V373G			Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 8	390	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)	GCAGGCATGGTCTTGGGTACC	0.617																																					p.V373G		Atlas-SNP	.											.	ABCB8	65	.	0			c.T1118G						PASS	.						108	98	101					7																	150733637		2203	4300	6503	SO:0001583	missense	11194	exon9			GCATGGTCTTGGG	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.1169T>G	7.37:g.150733637T>G	ENSP00000297504:p.Val390Gly	48	0	0		24	9	0.375	NM_007188	A5D8W3|B2RBL8|B3KND2|B4DG02|G3XAP3|O95787|Q53GM0	Missense_Mutation	SNP	ENST00000297504.6	37		.	.	.	.	.	.	.	.	.	.	T	20.6	4.020757	0.75275	.	.	ENSG00000197150	ENST00000358849;ENST00000360651;ENST00000297504;ENST00000542328;ENST00000498578;ENST00000356058;ENST00000477719;ENST00000477092	D;D;D;D;D;D;D	0.90197	-2.63;-2.63;-2.63;-2.63;-2.63;-2.63;-2.63	5.17	5.17	0.71159	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	0.95462	0.8526	M	0.86651	2.83	0.80722	D	1	D;D;D;D;D;D	0.89917	0.997;0.999;0.999;0.998;1.0;1.0	D;D;D;D;D;D	0.83275	0.958;0.991;0.991;0.984;0.996;0.996	D	0.95696	0.8745	10	0.56958	D	0.05	1.0E-4	12.955	0.58421	0.0:0.0:0.0:1.0	.	285;373;390;373;373;410	G3XAP3;A5D8W3;Q9NUT2;Q9NUT2-2;C9JTY4;E7ENE8	.;.;ABCB8_HUMAN;.;.;.	G	373;356;390;285;373;410;373;373	ENSP00000351717:V373G;ENSP00000297504:V390G;ENSP00000438776:V285G;ENSP00000418271:V373G;ENSP00000348353:V410G;ENSP00000419891:V373G;ENSP00000419558:V373G	ENSP00000297504:V390G	V	+	2	0	ABCB8	150364570	1.000000	0.71417	1.000000	0.80357	0.736000	0.42039	7.085000	0.76875	1.954000	0.56735	0.459000	0.35465	GTC	.	.	none		0.617	ABCB8-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351733.2	NM_007188		G	150733637	T	G	150733637	3	3	39	1	0	0	0	0	1	0	0	0	47	1667	58	5	1152	5	ABCB8	7	150733637	Missense_Mutation	SNP	T	TCGA-GS-A9TW-01A-11D-A382-10	6962301	150733637	8405026	103	14648											
MLL3	58508	hgsc.bcm.edu	37	chr7	151902302	151902302	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tctttgccgcaccataaatcCaccaatacctatccaaaaaa	16	9	2	14	1	1	0	0	0	1	0	3	0	3	0	6	0	2	1	6	0	8	4			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr7:151902302C>T	ENST00000262189.6	-	25	4068	c.3850G>A	c.(3850-3852)Gga>Aga	p.G1284R	KMT2C_ENST00000355193.2_Missense_Mutation_p.G1284R	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	1284					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.?(1)									ACCATAAATCCACCAATACCT	0.383																																					p.G1284R		Atlas-SNP	.											.	MLL3	1564	.	1	Unknown(1)	large_intestine(1)	c.G3850A						PASS	.						72	69	70					7																	151902302		2203	4300	6503	SO:0001583	missense	58508	exon25			TAAATCCACCAAT	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.3850G>A	7.37:g.151902302C>T	ENSP00000262189:p.Gly1284Arg	306	0	0		234	74	0.316239	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.944042	0.73672	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.86956	-2.19;-2.19	5.71	5.71	0.89125	.	0.000000	0.43260	D	0.000591	D	0.94291	0.8166	M	0.83774	2.66	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.94459	0.7674	10	0.87932	D	0	.	19.8604	0.96781	0.0:1.0:0.0:0.0	.	1284;345	Q8NEZ4;Q8NEZ4-2	MLL3_HUMAN;.	R	1284	ENSP00000262189:G1284R;ENSP00000347325:G1284R	ENSP00000262189:G1284R	G	-	1	0	MLL3	151533235	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.993000	0.76245	2.699000	0.92147	0.650000	0.86243	GGA	.	.	none		0.383	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			T	151902302	C	T	151902302	3	4	39	1	0	0	0	0	1	0	0	0	9631	603	21	2	11025	2	MLL3	7	151902302	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	1168665	151902302	7236361	104	14649											
REEP4	80346	hgsc.bcm.edu	37	chr8	21996529	21996529	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gtcagagatggagcgcaggtCctgcatggagaagctccgca	10	6	15	10	2	1	2	1	0	0	2	3	5	3	3	2	3	3	4	2	3	1	0			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr8:21996529C>T	ENST00000306306.3	-	6	931	c.463G>A	c.(463-465)Gac>Aac	p.D155N	REEP4_ENST00000334530.5_Intron|REEP4_ENST00000523293.1_Missense_Mutation_p.D155N	NM_025232.2	NP_079508.2	Q9H6H4	REEP4_HUMAN	receptor accessory protein 4	155					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)		GAGCGCAGGTCCTGCATGGAG	0.677																																					p.D155N		Atlas-SNP	.											.	REEP4	13	.	0			c.G463A						PASS	.						21	21	21					8																	21996529		2202	4296	6498	SO:0001583	missense	80346	exon6			GCAGGTCCTGCAT	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.463G>A	8.37:g.21996529C>T	ENSP00000303482:p.Asp155Asn	78	0	0		39	20	0.512821	NM_025232	D3DSQ9|Q86VL1|Q9H6I5|Q9HBP4	Missense_Mutation	SNP	ENST00000306306.3	37	CCDS6024.1	.	.	.	.	.	.	.	.	.	.	C	34	5.400018	0.96030	.	.	ENSG00000168476	ENST00000306306;ENST00000523293;ENST00000518664	D;D;D	0.90444	-2.25;-2.67;-2.64	4.69	4.69	0.59074	.	0.000000	0.64402	D	0.000019	D	0.95063	0.8401	M	0.80183	2.485	0.58432	D	0.999993	D	0.89917	1.0	D	0.80764	0.994	D	0.95497	0.8574	10	0.62326	D	0.03	-24.4594	15.1447	0.72641	0.0:1.0:0.0:0.0	.	155	Q9H6H4	REEP4_HUMAN	N	155	ENSP00000303482:D155N;ENSP00000428709:D155N;ENSP00000428160:D155N	ENSP00000303482:D155N	D	-	1	0	REEP4	22052474	1.000000	0.71417	1.000000	0.80357	0.846000	0.48090	7.547000	0.82146	2.156000	0.67533	0.655000	0.94253	GAC	.	.	none		0.677	REEP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254337.2	NM_025232		T	21996529	C	T	21996529	3	4	39	1	0	0	0	0	1	0	0	0	13222	855	30	2	322	2	REEP4	8	21996529	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10		21996529	124367493	105	14650											
RHOBTB2	23221	hgsc.bcm.edu	37	chr8	22865187	22865187	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	atgaggccttcatgaaccagGagatcaccaaggccttccac	12	7	9	13	0	2	3	2	2	0	1	3	4	3	3	5	3	1	0	5	3	2	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr8:22865187G>A	ENST00000251822.6	+	5	1966	c.1429G>A	c.(1429-1431)Gag>Aag	p.E477K	RHOBTB2_ENST00000519685.1_Missense_Mutation_p.E499K|RP11-875O11.1_ENST00000502083.2_RNA|RP11-875O11.1_ENST00000523884.1_RNA|RHOBTB2_ENST00000522948.1_Missense_Mutation_p.E484K	NM_015178.2	NP_055993.2	Q9BYZ6	RHBT2_HUMAN	Rho-related BTB domain containing 2	477					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)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	31		Prostate(55;0.0513)|Breast(100;0.214)		Colorectal(74;0.0157)|COAD - Colon adenocarcinoma(73;0.064)		CATGAACCAGGAGATCACCAA	0.542																																					p.E499K		Atlas-SNP	.											.	RHOBTB2	67	.	0			c.G1495A						PASS	.						106	103	104					8																	22865187		2203	4300	6503	SO:0001583	missense	23221	exon7			AACCAGGAGATCA	AF315385	CCDS6034.1, CCDS55210.1, CCDS55211.1	8p21.2	2013-01-08			ENSG00000008853	ENSG00000008853		"BTB/POZ domain containing"	18756	protein-coding gene	gene with protein product		607352				11222756	Standard	NM_001160036		Approved	KIAA0717, DBC2	uc011kzp.1	Q9BYZ6	OTTHUMG00000097827	ENST00000251822.6:c.1429G>A	8.37:g.22865187G>A	ENSP00000251822:p.Glu477Lys	32	0	0		47	12	0.255319	NM_001160036	A8K9Z8|D3DSR8|E9PBU2|E9PEI7|O94825|Q8N4A8|Q9BZK6	Missense_Mutation	SNP	ENST00000251822.6	37	CCDS6034.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.453804	0.84209	.	.	ENSG00000008853	ENST00000519685;ENST00000522948;ENST00000251822	T;T;T	0.10573	2.86;2.87;2.87	5.35	4.47	0.54385	BTB/POZ fold (1);	0.000000	0.85682	D	0.000000	T	0.34919	0.0914	M	0.82323	2.585	0.58432	D	0.999991	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.14448	-1.0472	10	0.72032	D	0.01	.	13.2086	0.59811	0.0797:0.0:0.9203:0.0	.	484;477;499	E9PEI7;Q9BYZ6;E9PBU2	.;RHBT2_HUMAN;.	K	499;484;477	ENSP00000427926:E499K;ENSP00000429141:E484K;ENSP00000251822:E477K	ENSP00000251822:E477K	E	+	1	0	RHOBTB2	22921132	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.781000	0.99029	2.476000	0.83614	0.655000	0.94253	GAG	.	.	none		0.542	RHOBTB2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000215101.2			A	22865187	G	A	22865187	3	1	39	1	0	0	0	0	1	0	0	0	13349	1175	41	2	1528	2	RHOBTB2	8	22865187	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	868658	22865187	123498835	106	14651											
TGS1	96764	hgsc.bcm.edu	37	chr8	56715141	56715141	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	acaggctcttctcccgttttGatgatgggattaagttggac	8	14	11	8	1	2	2	0	2	2	0	3	4	2	4	1	3	0	3	1	3	1	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr8:56715141G>C	ENST00000260129.5	+	9	2452	c.1975G>C	c.(1975-1977)Gat>Cat	p.D659H		NM_024831.6	NP_079107.6	Q96RS0	TGS1_HUMAN	trimethylguanosine synthase 1	659	Sufficient for catalytic activity.				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)			CTCCCGTTTTGATGATGGGAT	0.373																																					p.D659H	Esophageal Squamous(34;275 823 4842 34837 48447)	Atlas-SNP	.											.	TGS1	66	.	0			c.G1975C						PASS	.						100	94	96					8																	56715141		2203	4300	6503	SO:0001583	missense	96764	exon9			CGTTTTGATGATG	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.1975G>C	8.37:g.56715141G>C	ENSP00000260129:p.Asp659His	70	0	0		69	11	0.15942	NM_024831	A6NJQ5|Q5GH23|Q8TDG9|Q96QU3|Q9H5V3	Missense_Mutation	SNP	ENST00000260129.5	37	CCDS34894.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.947691	0.92593	.	.	ENSG00000137574	ENST00000260129	T	0.49139	0.79	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.79907	0.4527	H	0.95043	3.615	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.994	D	0.84845	0.0810	10	0.87932	D	0	-34.8829	20.4192	0.99033	0.0:0.0:1.0:0.0	.	659;659	B2RBJ7;Q96RS0	.;TGS1_HUMAN	H	659	ENSP00000260129:D659H	ENSP00000260129:D659H	D	+	1	0	TGS1	56877695	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.624000	0.98398	2.831000	0.97527	0.650000	0.86243	GAT	.	.	none		0.373	TGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378152.1	NM_024831		C	56715141	G	C	56715141	3	2	39	1	0	0	0	0	1	0	0	0	15852	1290	45	4	2009	4	TGS1	8	56715141	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	33849954	56715141	89648881	107	14652											
RPL7	6129	hgsc.bcm.edu	37	chr8	74204061	74204061	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atgttaatcgaagccttgttGagcttcacaaaggttccatt	11	14	8	8	1	1	1	1	1	0	0	3	2	2	1	2	1	2	4	2	1	3	6			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr8:74204061G>C	ENST00000352983.2	-	4	660	c.375C>G	c.(373-375)ctC>ctG	p.L125L	RPL7_ENST00000396465.1_Silent_p.L85L|RPL7_ENST00000396466.1_Silent_p.L85L|RPL7_ENST00000487500.1_5'Flank|RPL7_ENST00000396467.1_Silent_p.L85L|RDH10_ENST00000240285.5_5'Flank			P18124	RL7_HUMAN	ribosomal protein L7	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)|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)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|kidney(1)|large_intestine(2)|lung(1)	5	Breast(64;0.0954)		Epithelial(68;0.0193)|all cancers(69;0.0766)|BRCA - Breast invasive adenocarcinoma(89;0.134)			AAGCCTTGTTGAGCTTCACAA	0.413																																					p.L125L		Atlas-SNP	.											.	RPL7	20	.	0			c.C375G						PASS	.						91	90	90					8																	74204061		2203	4297	6500	SO:0001819	synonymous_variant	6129	exon4			CTTGTTGAGCTTC	L16557	CCDS6212.1	8q13.3	2011-04-06			ENSG00000147604	ENSG00000147604		"L ribosomal proteins"	10363	protein-coding gene	gene with protein product		604166				8360149, 8441630	Standard	XM_006716463		Approved	humL7-1, L7	uc003xzg.3	P18124	OTTHUMG00000134312	ENST00000352983.2:c.375C>G	8.37:g.74204061G>C		85	0	0		97	21	0.216495	NM_000971	A8K504|Q15289|Q3KQU0|Q5I0X1|Q6IBM9	Silent	SNP	ENST00000352983.2	37	CCDS6212.1																																																																																			.	.	none		0.413	RPL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259287.1	NM_000971		C	74204061	G	C	74204061	2	2	39	1	0	0	0	0	0	0	0	1	13614	1277	45	4		4	RPL7	8	74204061	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	17488920	74204061	72159961	108	14653											
SLC26A7	115111	hgsc.bcm.edu	37	chr8	92301369	92301369	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tagtcttcttcacaggattgGcctttgctgttctctcatct	5	18	7	11	0	6	0	2	0	4	0	7	1	6	1	1	2	1	2	1	2	1	6			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr8:92301369G>A	ENST00000276609.3	+	3	438	c.199G>A	c.(199-201)Gcc>Acc	p.A67T	SLC26A7_ENST00000309536.2_Missense_Mutation_p.A67T|SLC26A7_ENST00000523719.1_Missense_Mutation_p.A67T	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)			CACAGGATTGGCCTTTGCTGT	0.393																																					p.A67T		Atlas-SNP	.											SLC26A7_ENST00000309536,rectum,carcinoma,-1,2	SLC26A7	207	2	0			c.G199A						PASS	.						235	212	220					8																	92301369		2203	4300	6503	SO:0001583	missense	115111	exon3			GGATTGGCCTTTG	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.199G>A	8.37:g.92301369G>A	ENSP00000276609:p.Ala67Thr	425	1	0.00235294		466	124	0.266094	NM_134266		Missense_Mutation	SNP	ENST00000276609.3	37	CCDS6254.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.372351	0.82573	.	.	ENSG00000147606	ENST00000522862;ENST00000523719;ENST00000276609;ENST00000309536	D;D;D;D	0.95103	-3.61;-3.61;-3.61;-3.61	6.17	3.25	0.37280	.	0.338048	0.28198	N	0.016238	D	0.95332	0.8485	M	0.93106	3.38	0.27340	N	0.956538	P;P	0.40000	0.51;0.698	B;B	0.38803	0.154;0.282	D	0.89804	0.3977	10	0.72032	D	0.01	.	14.3597	0.66764	0.0:0.0:0.5817:0.4183	.	67;67	Q8TE54-2;Q8TE54	.;S26A7_HUMAN	T	67	ENSP00000428881:A67T;ENSP00000428849:A67T;ENSP00000276609:A67T;ENSP00000309504:A67T	ENSP00000276609:A67T	A	+	1	0	SLC26A7	92370545	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.242000	0.43106	0.380000	0.24823	0.655000	0.94253	GCC	.	.	none		0.393	SLC26A7-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377011.1			A	92301369	G	A	92301369	3	1	39	1	0	0	0	0	1	0	0	0	14537	1203	42	2	205	2	SLC26A7	8	92301369	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	18097308	92301369	54062653	109	14654											
PDP1	54704	hgsc.bcm.edu	37	chr8	94935821	94935821	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtcttcctgaagagcttgctCgaatgtacagagatgacatt	11	12	10	8	1	1	4	0	2	1	2	3	6	2	4	1	0	3	3	1	0	3	4	rs202225648		TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr8:94935821C>T	ENST00000297598.4	+	2	1803	c.1534C>T	c.(1534-1536)Cga>Tga	p.R512*	PDP1_ENST00000396200.3_Nonsense_Mutation_p.R537*|PDP1_ENST00000520728.1_Nonsense_Mutation_p.R512*|PDP1_ENST00000517764.1_Nonsense_Mutation_p.R512*	NM_001161781.1|NM_018444.3	NP_001155253.1|NP_060914.2	Q9P0J1	PDP1_HUMAN	pyruvate dehyrogenase phosphatase catalytic subunit 1	512					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						AGAGCTTGCTCGAATGTACAG	0.453																																					p.R537X		Atlas-SNP	.											PDP1,rectum,carcinoma,-1,1	PDP1	97	1	0			c.C1609T						PASS	.						106	96	99					8																	94935821		2203	4300	6503	SO:0001587	stop_gained	54704	exon3			CTTGCTCGAATGT	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.1534C>T	8.37:g.94935821C>T	ENSP00000297598:p.Arg512*	97	0	0		127	14	0.110236	NM_001161780	B3KX71|J3KPU0|Q5U5K1	Nonsense_Mutation	SNP	ENST00000297598.4	37	CCDS6259.1	.	.	.	.	.	.	.	.	.	.	C	38	6.810033	0.97853	.	.	ENSG00000164951	ENST00000297598;ENST00000520728;ENST00000396200;ENST00000517764	.	.	.	6.17	5.3	0.74995	.	0.058646	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.9484	17.1598	0.86801	0.1273:0.8727:0.0:0.0	.	.	.	.	X	512;512;537;512	.	ENSP00000297598:R512X	R	+	1	2	PDP1	95004997	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.804000	0.55568	1.623000	0.50342	0.655000	0.94253	CGA	C|0.999;T|0.001	0.001	weak		0.453	PDP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378415.2	NM_018444		T	94935821	C	T	94935821	4	4	39	1	0	0	0	0	0	1	0	0	11694	876	31	1	1717	1	PDP1	8	94935821	Nonsense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	2634452	94935821	51428201	110	14655											
ESRP1	54845	hgsc.bcm.edu	37	chr8	95676969	95676969	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	taacaccgtagtcagggcacGaggtttaccatggcagtctt	10	10	11	10	2	2	0	1	0	1	0	2	1	2	0	2	3	2	4	2	3	3	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr8:95676969G>A	ENST00000433389.2	+	7	879	c.689G>A	c.(688-690)cGa>cAa	p.R230Q	ESRP1_ENST00000423620.2_Missense_Mutation_p.R230Q|ESRP1_ENST00000358397.5_Missense_Mutation_p.R230Q|ESRP1_ENST00000454170.2_Missense_Mutation_p.R230Q	NM_001034915.2|NM_017697.3	NP_001030087.2|NP_060167.2	Q6NXG1	ESRP1_HUMAN	epithelial splicing regulatory protein 1	230	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				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						GTCAGGGCACGAGGTTTACCA	0.383																																					p.R230Q		Atlas-SNP	.											ESRP1_ENST00000433389,NS,carcinoma,+1,2	ESRP1	148	2	0			c.G689A						PASS	.						137	127	130					8																	95676969		1924	4146	6070	SO:0001583	missense	54845	exon7			GGGCACGAGGTTT	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.689G>A	8.37:g.95676969G>A	ENSP00000405738:p.Arg230Gln	171	0	0		145	59	0.406897	NM_001122827	A6NHA8|A8MPX1|E9PB47|Q2M2B0|Q499G3|Q6PJ86|Q9NXL8	Missense_Mutation	SNP	ENST00000433389.2	37	CCDS47897.1	.	.	.	.	.	.	.	.	.	.	G	36	5.754248	0.96890	.	.	ENSG00000104413	ENST00000423620;ENST00000433389;ENST00000358397;ENST00000454170;ENST00000522756;ENST00000517610	T;T;T;T;T;T	0.09723	2.95;3.31;3.31;2.95;2.95;3.31	5.68	5.68	0.88126	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.000000	0.85682	D	0.000000	T	0.40171	0.1106	M	0.83483	2.645	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	T	0.28138	-1.0053	10	0.87932	D	0	-9.7887	19.798	0.96494	0.0:0.0:1.0:0.0	.	230;230;230;230;230;230	D7PBN3;Q6NXG1-4;Q6NXG1-2;E9PB47;Q6NXG1-3;Q6NXG1	.;.;.;.;.;ESRP1_HUMAN	Q	230;230;230;230;13;89	ENSP00000407349:R230Q;ENSP00000405738:R230Q;ENSP00000351168:R230Q;ENSP00000402766:R230Q;ENSP00000428490:R13Q;ENSP00000429125:R89Q	ENSP00000351168:R230Q	R	+	2	0	ESRP1	95746145	1.000000	0.71417	0.992000	0.48379	0.987000	0.75469	9.869000	0.99810	2.677000	0.91161	0.563000	0.77884	CGA	.	.	none		0.383	ESRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379326.1	NM_017697		A	95676969	G	A	95676969	3	1	39	1	0	0	0	0	1	0	0	0	5260	1058	37	1	715	1	ESRP1	8	95676969	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	741148	95676969	50687053	111	14656											
STK3	6788	hgsc.bcm.edu	37	chr8	99591963	99591963	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agctttgatctccatagcttCtgtgatcaggtctcttaata	9	16	7	9	0	4	2	1	2	3	0	6	2	4	2	1	1	2	2	1	1	3	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr8:99591963C>T	ENST00000419617.2	-	8	1017	c.877G>A	c.(877-879)Gaa>Aaa	p.E293K	STK3_ENST00000523601.1_Missense_Mutation_p.E321K	NM_006281.3	NP_006272.2	Q13188	STK3_HUMAN	serine/threonine kinase 3	293					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)		TCCATAGCTTCTGTGATCAGG	0.318																																					p.E321K		Atlas-SNP	.											.	STK3	47	.	0			c.G961A						PASS	.						155	148	150					8																	99591963		1818	4093	5911	SO:0001583	missense	6788	exon10			TAGCTTCTGTGAT	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.877G>A	8.37:g.99591963C>T	ENSP00000390500:p.Glu293Lys	344	0	0		398	33	0.0829146	NM_001256312	A8K722|B3KYA7|Q15445|Q15801|Q96FM6	Missense_Mutation	SNP	ENST00000419617.2	37	CCDS47900.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.413500	0.83449	.	.	ENSG00000104375	ENST00000419617;ENST00000523601;ENST00000518165	T;T;T	0.72505	-0.66;-0.65;0.08	5.69	5.69	0.88448	Protein kinase-like domain (1);	0.054980	0.64402	D	0.000001	T	0.73393	0.3581	M	0.74467	2.265	0.80722	D	1	B;B;B	0.29862	0.155;0.035;0.259	B;B;B	0.28638	0.023;0.023;0.092	T	0.72814	-0.4179	10	0.54805	T	0.06	.	19.8097	0.96542	0.0:1.0:0.0:0.0	.	182;293;321	E5RFQ9;Q13188;B3KYA7	.;STK3_HUMAN;.	K	293;321;182	ENSP00000390500:E293K;ENSP00000429744:E321K;ENSP00000428014:E182K	ENSP00000390500:E293K	E	-	1	0	STK3	99661139	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.346000	0.79347	2.685000	0.91497	0.484000	0.47621	GAA	.	.	none		0.318	STK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379635.1	NM_006281		T	99591963	C	T	99591963	3	4	39	1	0	0	0	0	1	0	0	0	15310	922	32	2	614	2	STK3	8	99591963	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	3914994	99591963	46772059	112	14657											
TM7SF4	81501	hgsc.bcm.edu	37	chr8	105367391	105367391	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgggagaagtcaaaagacGgctgagtctctatcttacaa	13	9	11	8	1	3	3	1	1	2	2	4	4	3	3	0	2	1	2	0	2	6	2	rs139698540		TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr8:105367391G>A	ENST00000297581.2	+	3	1365	c.1316G>A	c.(1315-1317)cGg>cAg	p.R439Q	DCSTAMP_ENST00000517991.1_Intron|DCSTAMP_ENST00000520080.1_3'UTR|DPYS_ENST00000521601.1_Intron	NM_030788.3	NP_110415.1	Q9H295	DCSTP_HUMAN	dendrocyte expressed seven transmembrane protein	439					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)											GTCAAAAGACGGCTGAGTCTC	0.478																																					p.R439Q		Atlas-SNP	.											.	.	.	.	0			c.G1316A						PASS	.	G	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	47	49	49		1316	3.8	0	8	dbSNP_134	49	0,8600		0,0,4300	no	missense	TM7SF4	NM_030788.2	43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	439/471	105367391	1,13005	2203	4300	6503	SO:0001583	missense	81501	exon3			AAAGACGGCTGAG	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.1316G>A	8.37:g.105367391G>A	ENSP00000297581:p.Arg439Gln	94	0	0		109	10	0.0917431	NM_030788	B7ZVW2|E7ESG0|Q2M2D5	Missense_Mutation	SNP	ENST00000297581.2	37	CCDS6301.1	.	.	.	.	.	.	.	.	.	.	G	6.779	0.512749	0.12944	2.27E-4	0.0	ENSG00000164935	ENST00000297581	T	0.33654	1.4	5.04	3.81	0.43845	.	0.727973	0.14085	N	0.342420	T	0.17450	0.0419	N	0.08118	0	0.09310	N	0.999997	B	0.29671	0.254	B	0.17098	0.017	T	0.12192	-1.0557	10	0.39692	T	0.17	-1.5907	8.648	0.34018	0.9091:0.0:0.0909:0.0	.	439	Q9H295	TM7S4_HUMAN	Q	439	ENSP00000297581:R439Q	ENSP00000297581:R439Q	R	+	2	0	TM7SF4	105436567	0.002000	0.14202	0.001000	0.08648	0.005000	0.04900	1.796000	0.38794	0.865000	0.35603	-0.290000	0.09829	CGG	G|1.000;A|0.000	0.000	weak		0.478	DCSTAMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380810.1	NM_030788		A	105367391	G	A	105367391	3	1	39	1	0	0	0	0	1	0	0	0	15991	1116	39	1	1322	1	TM7SF4	8	105367391	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	5775428	105367391	40996631	113	14658											
COL14A1	7373	hgsc.bcm.edu	37	chr8	121219248	121219248	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgaagtcactgccagaagctTtatggttaactggactcatg	11	12	10	8	0	2	2	2	1	0	1	2	3	2	3	1	2	3	2	1	2	4	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr8:121219248T>G	ENST00000297848.3	+	10	1376	c.1106T>G	c.(1105-1107)tTt>tGt	p.F369C	COL14A1_ENST00000309791.4_Missense_Mutation_p.F369C|COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000537875.1_Missense_Mutation_p.F369C|COL14A1_ENST00000247781.3_Missense_Mutation_p.F274C	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)			GCCAGAAGCTTTATGGTTAAC	0.433																																					p.F369C		Atlas-SNP	.											.	COL14A1	292	.	0			c.T1106G						PASS	.						72	67	69					8																	121219248		2203	4300	6503	SO:0001583	missense	7373	exon10			GAAGCTTTATGGT		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.1106T>G	8.37:g.121219248T>G	ENSP00000297848:p.Phe369Cys	136	0	0		208	68	0.326923	NM_021110		Missense_Mutation	SNP	ENST00000297848.3	37	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.947976	0.73787	.	.	ENSG00000187955	ENST00000537875;ENST00000309791;ENST00000297848;ENST00000247781;ENST00000434620	T;T;T;T;T	0.58358	0.34;0.34;0.34;0.34;0.34	5.64	5.64	0.86602	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.77968	0.4210	M	0.89904	3.07	0.47819	D	0.999524	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.83146	-0.0106	10	0.87932	D	0	.	15.8462	0.78895	0.0:0.0:0.0:1.0	.	369;369	Q05707-2;Q05707	.;COEA1_HUMAN	C	369;369;369;274;182	ENSP00000443974:F369C;ENSP00000311809:F369C;ENSP00000297848:F369C;ENSP00000247781:F274C;ENSP00000409461:F182C	ENSP00000247781:F274C	F	+	2	0	COL14A1	121288429	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.881000	0.69706	2.143000	0.66587	0.482000	0.46254	TTT	.	.	none		0.433	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		G	121219248	T	G	121219248	3	3	39	1	0	0	0	0	1	0	0	0	3673	1841	64	5	1140	5	COL14A1	8	121219248	Missense_Mutation	SNP	T	TCGA-GS-A9TW-01A-11D-A382-10	15851857	121219248	25144774	114	14659											
COL14A1	7373	hgsc.bcm.edu	37	chr8	121219273	121219273	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttaactggactcatgccccAggaaatgtggaaaaatacag	15	8	10	8	0	1	0	1	0	0	0	1	3	1	3	2	3	3	1	2	3	5	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr8:121219273A>T	ENST00000297848.3	+	10	1401	c.1131A>T	c.(1129-1131)ccA>ccT	p.P377P	COL14A1_ENST00000309791.4_Silent_p.P377P|COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000537875.1_Silent_p.P377P|COL14A1_ENST00000247781.3_Silent_p.P282P	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)			CTCATGCCCCAGGAAATGTGG	0.433																																					p.P377P		Atlas-SNP	.											.	COL14A1	292	.	0			c.A1131T						PASS	.						66	62	63					8																	121219273		2203	4300	6503	SO:0001819	synonymous_variant	7373	exon10			TGCCCCAGGAAAT		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.1131A>T	8.37:g.121219273A>T		111	0	0		183	65	0.355191	NM_021110		Silent	SNP	ENST00000297848.3	37	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	A	10.15	1.271484	0.23221	.	.	ENSG00000187955	ENST00000523142	.	.	.	5.82	4.65	0.58169	.	.	.	.	.	T	0.58337	0.2115	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55173	-0.8182	4	.	.	.	.	7.6498	0.28342	0.788:0.1422:0.0698:0.0	.	.	.	.	W	134	.	.	R	+	1	2	COL14A1	121288454	0.996000	0.38824	1.000000	0.80357	0.929000	0.56500	0.568000	0.23623	1.013000	0.39391	0.482000	0.46254	AGG	.	.	none		0.433	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110		T	121219273	A	T	121219273	2	4	39	1	0	0	0	0	0	0	0	1	3673	175	7	5		5	COL14A1	8	121219273	Silent	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	25	121219273	25144749	115	14660											
FREM1	158326	hgsc.bcm.edu	37	chr9	14775791	14775791	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtttttcatacttgcctgaAtggtgaataaaacaggttct	11	16	8	6	0	2	2	1	2	1	0	2	2	2	2	1	2	3	2	1	2	5	6			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr9:14775791A>C	ENST00000380880.3	-	25	5636	c.4853T>G	c.(4852-4854)aTt>aGt	p.I1618S	FREM1_ENST00000422223.2_Missense_Mutation_p.I1618S|FREM1_ENST00000486223.1_5'UTR|FREM1_ENST00000380881.4_Missense_Mutation_p.I1619S|FREM1_ENST00000380894.1_Missense_Mutation_p.I154S			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1618					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)		ACTTGCCTGAATGGTGAATAA	0.393																																					p.I1618S		Atlas-SNP	.											.	FREM1	261	.	0			c.T4853G						PASS	.						59	55	56					9																	14775791		1885	4123	6008	SO:0001583	missense	158326	exon26			GCCTGAATGGTGA	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.4853T>G	9.37:g.14775791A>C	ENSP00000370262:p.Ile1618Ser	157	0	0		261	54	0.206897	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	.	.	.	.	.	.	.	.	.	.	A	19.12	3.765498	0.69878	.	.	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380894;ENST00000380880	T;T;T;T	0.56776	0.44;0.44;0.44;0.44	5.93	5.93	0.95920	.	0.262356	0.38272	N	0.001744	T	0.72614	0.3482	M	0.78801	2.425	0.54753	D	0.999982	D;D	0.67145	0.996;0.995	D;P	0.65874	0.939;0.878	T	0.76435	-0.2960	10	0.87932	D	0	-20.0105	16.3943	0.83563	1.0:0.0:0.0:0.0	.	1618;154	Q5H8C1;B7ZBX4	FREM1_HUMAN;.	S	1619;1618;154;1618	ENSP00000370263:I1619S;ENSP00000412940:I1618S;ENSP00000370278:I154S;ENSP00000370262:I1618S	ENSP00000370262:I1618S	I	-	2	0	FREM1	14765791	1.000000	0.71417	0.979000	0.43373	0.336000	0.28762	8.677000	0.91203	2.281000	0.76405	0.533000	0.62120	ATT	.	.	none		0.393	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		C	14775791	A	C	14775791	3	2	39	1	0	0	0	0	1	0	0	0	6052	101	4	5	1738	5	FREM1	9	14775791	Missense_Mutation	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10		14775791	126437640	116	14661											
IFNA14	3448	hgsc.bcm.edu	37	chr9	21239704	21239704	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atcatctcatggaggacagaGatggcttgagctttctggaa	11	11	12	7	0	3	2	2	1	2	1	4	6	3	5	0	4	1	2	0	4	1	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr9:21239704G>A	ENST00000380222.2	-	1	274	c.231C>T	c.(229-231)atC>atT	p.I77I		NM_002172.2	NP_002163.2	P01570	IFN14_HUMAN	interferon, alpha 14	77					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)		GGAGGACAGAGATGGCTTGAG	0.463																																					p.I77I		Atlas-SNP	.											.	IFNA14	29	.	0			c.C231T						PASS	.						115	113	114					9																	21239704		2203	4300	6503	SO:0001819	synonymous_variant	3448	exon1			GACAGAGATGGCT		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.231C>T	9.37:g.21239704G>A		154	0	0		178	41	0.230337	NM_002172	Q5VZ56|Q7M4S1	Silent	SNP	ENST00000380222.2	37	CCDS6501.1																																																																																			.	.	none		0.463	IFNA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051894.1	NM_002172		A	21239704	G	A	21239704	2	1	39	1	0	0	0	0	0	0	0	1	7543	932	33	2		2	IFNA14	9	21239704	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	6463913	21239704	119973727	117	14662											
TLN1	7094	hgsc.bcm.edu	37	chr9	35704399	35704399	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggcgaacatgatggtggtgtCgaggtcagcaatgataccag	11	8	15	7	2	1	2	1	2	0	0	2	4	1	2	1	4	3	1	1	4	3	1	rs149639715	byFrequency	TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr9:35704399C>T	ENST00000314888.9	-	45	6330	c.5977G>A	c.(5977-5979)Gac>Aac	p.D1993N	TLN1_ENST00000540444.1_Missense_Mutation_p.D1887N|TLN1_ENST00000464379.1_5'UTR	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1993					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)			ATGGTGGTGTCGAGGTCAGCA	0.602													C|||	6	0.00119808	0.0045	0.0	5008	,	,		21474	0.0		0.0	False		,,,				2504	0.0				p.D1993N		Atlas-SNP	.											.	TLN1	185	.	0			c.G5977A						PASS	.	C	ASN/ASP	32,4374	36.8+/-68.6	0,32,2171	154	134	141		5977	5	0.9	9	dbSNP_134	141	0,8600		0,0,4300	yes	missense	TLN1	NM_006289.3	23	0,32,6471	TT,TC,CC		0.0,0.7263,0.246	probably-damaging	1993/2542	35704399	32,12974	2203	4300	6503	SO:0001583	missense	7094	exon45			TGGTGTCGAGGTC	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.5977G>A	9.37:g.35704399C>T	ENSP00000316029:p.Asp1993Asn	82	0	0		148	15	0.101351	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Missense_Mutation	SNP	ENST00000314888.9	37	CCDS35009.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	32	5.139301	0.94560	0.007263	0.0	ENSG00000137076	ENST00000314888;ENST00000540444	T;T	0.81163	-1.46;-1.34	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	D	0.87795	0.6267	M	0.86028	2.79	0.80722	D	1	D	0.89917	1.0	D	0.69654	0.965	D	0.90568	0.4520	10	0.87932	D	0	-19.3792	18.2971	0.90150	0.0:1.0:0.0:0.0	.	1993	Q9Y490	TLN1_HUMAN	N	1993;1887	ENSP00000316029:D1993N;ENSP00000442981:D1887N	ENSP00000316029:D1993N	D	-	1	0	TLN1	35694399	1.000000	0.71417	0.932000	0.37286	0.965000	0.64279	7.795000	0.85887	2.319000	0.78375	0.561000	0.74099	GAC	C|0.998;T|0.002	0.002	strong		0.602	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289		T	35704399	C	T	35704399	3	4	39	1	0	0	0	0	1	0	0	0	15962	884	31	1	1700	1	TLN1	9	35704399	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	14464695	35704399	105509032	118	14663											
INVS	27130	hgsc.bcm.edu	37	chr9	103054777	103054777	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcttcgtgaagcagccctcCtgtatcagggtggctgggcc	5	9	15	12	1	1	1	1	1	0	0	3	1	2	1	3	4	2	4	3	4	2	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr9:103054777C>T	ENST00000262457.2	+	14	2423	c.2238C>T	c.(2236-2238)tcC>tcT	p.S746S	INVS_ENST00000262456.2_Intron|INVS_ENST00000541287.1_Silent_p.S650S	NM_014425.3	NP_055240.2	Q9Y283	INVS_HUMAN	inversin	746					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)				AGCAGCCCTCCTGTATCAGGG	0.612																																					p.S746S		Atlas-SNP	.											.	INVS	81	.	0			c.C2238T						PASS	.						56	50	52					9																	103054777		2203	4300	6503	SO:0001819	synonymous_variant	27130	exon14			GCCCTCCTGTATC	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.2238C>T	9.37:g.103054777C>T		122	0	0		174	47	0.270115	NM_014425	A2A2Y2|Q2NKL0|Q5W0T6|Q8IVX8|Q9BRB9|Q9Y488|Q9Y498	Silent	SNP	ENST00000262457.2	37	CCDS6746.1																																																																																			.	.	none		0.612	INVS-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053407.1	NM_014425		T	103054777	C	T	103054777	2	4	39	1	0	0	0	0	0	0	0	1	7796	668	24	2		2	INVS	9	103054777	Silent	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	67350378	103054777	38158654	119	14664											
SMC2	10592	hgsc.bcm.edu	37	chr9	106875690	106875690	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctacaggaaggatcaagaaGctctagaagctgtaaaaaga	18	6	11	6	0	2	3	1	0	1	3	2	5	2	5	0	2	3	4	0	2	9	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr9:106875690G>T	ENST00000286398.7	+	11	1636	c.1348G>T	c.(1348-1350)Gct>Tct	p.A450S	SMC2_ENST00000374787.3_Missense_Mutation_p.A450S|SMC2_ENST00000374793.3_Missense_Mutation_p.A450S|SMC2_ENST00000303219.8_Missense_Mutation_p.A450S	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	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)	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						GGATCAAGAAGCTCTAGAAGC	0.353																																					p.A450S		Atlas-SNP	.											.	SMC2	127	.	0			c.G1348T						PASS	.						68	70	69					9																	106875690		2203	4299	6502	SO:0001583	missense	10592	exon11			CAAGAAGCTCTAG	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.1348G>T	9.37:g.106875690G>T	ENSP00000286398:p.Ala450Ser	270	0	0		279	104	0.37276	NM_006444	Q6IEE0|Q9P1P2	Missense_Mutation	SNP	ENST00000286398.7	37	CCDS35086.1	.	.	.	.	.	.	.	.	.	.	G	8.759	0.923235	0.18056	.	.	ENSG00000136824	ENST00000286398;ENST00000374793;ENST00000303219;ENST00000374787	T;T;T;T	0.79653	-1.18;-1.18;-1.29;-1.18	4.86	3.96	0.45880	RecF/RecN/SMC (1);	0.210974	0.49916	D	0.000137	T	0.71213	0.3313	L	0.52011	1.625	0.32986	D	0.524259	B;B;B	0.22983	0.045;0.037;0.078	B;B;B	0.25759	0.055;0.021;0.063	T	0.66333	-0.5950	10	0.09590	T	0.72	-11.9229	9.247	0.37532	0.1751:0.0:0.8249:0.0	.	450;450;450	A8K984;O95347;Q2KQ72	.;SMC2_HUMAN;.	S	450	ENSP00000286398:A450S;ENSP00000363925:A450S;ENSP00000306152:A450S;ENSP00000363919:A450S	ENSP00000286398:A450S	A	+	1	0	SMC2	105915511	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	2.795000	0.47861	1.265000	0.44215	0.650000	0.86243	GCT	.	.	none		0.353	SMC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053470.1			T	106875690	G	T	106875690	3	4	39	1	0	0	0	0	1	0	0	0	14798	971	34	4	1386	4	SMC2	9	106875690	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	3820913	106875690	34337741	120	14665											
C9orf5	23731	hgsc.bcm.edu	37	chr9	111849490	111849490	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaagaattttccaagcccgAcaatgggccaaggcgcgaga	14	5	11	11	3	0	2	0	0	0	2	1	4	1	2	3	2	1	0	3	2	5	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr9:111849490A>C	ENST00000374586.3	-	6	1314	c.1283T>G	c.(1282-1284)gTc>gGc	p.V428G		NM_032012.3	NP_114401.2	Q9H330	TM245_HUMAN	transmembrane protein 245	428						integral component of membrane (GO:0016021)											TCCAAGCCCGACAATGGGCCA	0.443																																					p.V428G		Atlas-SNP	.											.	.	.	.	0			c.T1283G						PASS	.						93	92	92					9																	111849490		1829	4088	5917	SO:0001583	missense	23731	exon6			AGCCCGACAATGG	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.1283T>G	9.37:g.111849490A>C	ENSP00000363714:p.Val428Gly	94	0	0		129	45	0.348837	NM_032012	B4DSW7|Q5JTQ5|Q5SS43|Q6ZME3|Q8NDJ5|Q96CG6	Missense_Mutation	SNP	ENST00000374586.3	37	CCDS43858.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.382|9.382	1.073379|1.073379	0.20147|0.20147	.|.	.|.	ENSG00000106771|ENSG00000106771	ENST00000413712|ENST00000374587;ENST00000374586;ENST00000223608	.|T	.|0.21734	.|1.99	5.83|5.83	4.67|4.67	0.58626|0.58626	.|.	.|0.366676	.|0.33075	.|N	.|0.005301	T|T	0.09992|0.09992	0.0245|0.0245	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B;B	.|0.20459	.|0.045;0.039	.|B;B	.|0.18561	.|0.022;0.01	T|T	0.19257|0.19257	-1.0311|-1.0311	5|10	.|0.45353	.|T	.|0.12	-2.8289|-2.8289	5.8357|5.8357	0.18605|0.18605	0.6029:0.2488:0.1483:0.0|0.6029:0.2488:0.1483:0.0	.|.	.|428;428	.|Q9H330-2;Q9H330	.|.;CI005_HUMAN	W|G	28|428	.|ENSP00000363714:V428G	.|ENSP00000223608:V428G	C|V	-|-	3|2	2|0	C9orf5|C9orf5	110889311|110889311	0.233000|0.233000	0.23772|0.23772	0.003000|0.003000	0.11579|0.11579	0.793000|0.793000	0.44817|0.44817	2.435000|2.435000	0.44811|0.44811	0.991000|0.991000	0.38814|0.38814	0.460000|0.460000	0.39030|0.39030	TGT|GTC	.	.	none		0.443	TMEM245-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053587.2	NM_032012		C	111849490	A	C	111849490	3	2	39	1	0	0	0	0	1	0	0	0	2488	275	10	5	1408	5	C9orf5	9	111849490	Missense_Mutation	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	4973800	111849490	29363941	121	14666											
MUSK	4593	hgsc.bcm.edu	37	chr9	113538189	113538189	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtccgtgccagaatgcagcAagcttcccagcatgcattgg	9	9	11	12	1	0	1	0	0	0	1	2	1	2	1	3	1	6	5	3	1	2	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr9:113538189A>C	ENST00000374448.4	+	10	1440	c.1306A>C	c.(1306-1308)Aag>Cag	p.K436Q	MUSK_ENST00000374438.1_Missense_Mutation_p.Q27P|MUSK_ENST00000416899.2_Missense_Mutation_p.K436Q|MUSK_ENST00000189978.5_Missense_Mutation_p.K436Q	NM_001166281.1|NM_005592.3	NP_001159753.1|NP_005583.1	O15146	MUSK_HUMAN	muscle, skeletal, receptor tyrosine kinase	436	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				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						AGAATGCAGCAAGCTTCCCAG	0.512																																					p.K436Q		Atlas-SNP	.											.	MUSK	112	.	0			c.A1306C						PASS	.						134	131	132					9																	113538189		1935	4146	6081	SO:0001583	missense	4593	exon9			TGCAGCAAGCTTC	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.1306A>C	9.37:g.113538189A>C	ENSP00000363571:p.Lys436Gln	244	0	0		326	92	0.282209	NM_005592	Q32MJ8|Q32MJ9|Q5VZW7|Q5VZW8	Missense_Mutation	SNP	ENST00000374448.4	37	CCDS48005.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.18|14.18	2.458644|2.458644	0.43634|0.43634	.|.	.|.	ENSG00000030304|ENSG00000030304	ENST00000189978;ENST00000374448;ENST00000543335;ENST00000374447;ENST00000545907;ENST00000416899|ENST00000374441;ENST00000374438	T|D	0.76186|0.81579	-1.0|-1.51	5.74|5.74	5.74|5.74	0.90152|0.90152	Frizzled domain (2);|.	0.216683|.	0.49305|.	D|.	0.000156|.	D|D	0.84338|0.84338	0.5450|0.5450	L|L	0.56769|0.56769	1.78|1.78	0.80722|0.80722	D|D	1|1	B|.	0.29612|.	0.251|.	B|.	0.34931|.	0.192|.	T|T	0.83225|0.83225	-0.0066|-0.0066	10|7	0.27082|0.36615	T|T	0.32|0.2	.|.	15.2145|15.2145	0.73254|0.73254	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	436|.	O15146|.	MUSK_HUMAN|.	Q|P	442;436;436;358;358;442|27	ENSP00000363571:K436Q|ENSP00000363561:Q27P	ENSP00000189978:K442Q|ENSP00000363561:Q27P	K|Q	+|+	1|2	0|0	MUSK|MUSK	112578010|112578010	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	3.960000|3.960000	0.56752|0.56752	2.189000|2.189000	0.69895|0.69895	0.459000|0.459000	0.35465|0.35465	AAG|CAA	.	.	none		0.512	MUSK-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				C	113538189	A	C	113538189	3	2	39	1	0	0	0	0	1	0	0	0	9998	131	5	5	1376	5	MUSK	9	113538189	Missense_Mutation	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	1688699	113538189	27675242	122	14667											
TTF1	7270	hgsc.bcm.edu	37	chr9	135261984	135261984	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tcccagtctatttcattagtAtcttccacatttatttcata	10	19	2	10	0	4	0	2	0	2	0	6	0	6	0	2	0	0	1	2	0	5	9			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr9:135261984A>T	ENST00000334270.2	-	9	2376	c.2337T>A	c.(2335-2337)gaT>gaA	p.D779E		NM_001205296.1|NM_007344.3	NP_001192225.1|NP_031370.2	Q15361	TTF1_HUMAN	transcription termination factor, RNA polymerase I	779					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)		TTTCATTAGTATCTTCCACAT	0.299																																					p.D779E		Atlas-SNP	.											.	TTF1	82	.	0			c.T2337A						PASS	.						63	68	66					9																	135261984		2202	4300	6502	SO:0001583	missense	7270	exon9			ATTAGTATCTTCC	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.2337T>A	9.37:g.135261984A>T	ENSP00000333920:p.Asp779Glu	375	0	0		408	86	0.210784	NM_007344	A1L160|Q4VXF3|Q58EY2|Q6P5T5	Missense_Mutation	SNP	ENST00000334270.2	37	CCDS6948.1	.	.	.	.	.	.	.	.	.	.	A	13.16	2.155583	0.38021	.	.	ENSG00000125482	ENST00000334270;ENST00000245588	T	0.11063	2.81	5.81	-3.64	0.04515	.	0.207027	0.38164	N	0.001784	T	0.05090	0.0136	L	0.46741	1.465	0.22629	N	0.998911	P	0.43750	0.816	B	0.32762	0.152	T	0.34403	-0.9830	10	0.33940	T	0.23	.	2.1505	0.03798	0.4398:0.1188:0.313:0.1284	.	779	Q15361	TTF1_HUMAN	E	779	ENSP00000333920:D779E	ENSP00000245588:D779E	D	-	3	2	TTF1	134251805	0.800000	0.28916	0.174000	0.22961	0.833000	0.47200	0.086000	0.14935	-0.353000	0.08224	0.533000	0.62120	GAT	.	.	none		0.299	TTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054784.2	NM_007344		T	135261984	A	T	135261984	3	4	39	1	0	0	0	0	1	0	0	0	16733	446	16	5	392	5	TTF1	9	135261984	Missense_Mutation	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	21723795	135261984	5951447	123	14668											
OPTN	10133	hgsc.bcm.edu	37	chr10	13167997	13167997	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aacaagcttcttcaagaacaTaataatgcattgaaaacaat	20	10	4	7	0	2	2	1	1	1	1	2	2	2	2	0	0	5	2	0	0	9	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr10:13167997T>G	ENST00000378748.3	+	12	1562	c.1200T>G	c.(1198-1200)caT>caG	p.H400Q	OPTN_ENST00000378747.3_Missense_Mutation_p.H400Q|OPTN_ENST00000263036.5_Missense_Mutation_p.H400Q|OPTN_ENST00000378752.3_Missense_Mutation_p.H394Q|OPTN_ENST00000378757.2_Missense_Mutation_p.H400Q|OPTN_ENST00000378764.2_Missense_Mutation_p.H394Q	NM_001008211.1|NM_001008213.1	NP_001008212|NP_001008214	Q96CV9	OPTN_HUMAN	optineurin	400					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						TTCAAGAACATAATAATGCAT	0.313																																					p.H400Q		Atlas-SNP	.											OPTN,colon,carcinoma,+1,1	OPTN	57	1	0			c.T1200G						PASS	.						79	78	78					10																	13167997		2203	4299	6502	SO:0001583	missense	10133	exon11			AGAACATAATAAT	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.1200T>G	10.37:g.13167997T>G	ENSP00000368022:p.His400Gln	249	0	0		220	33	0.15	NM_001008212	B3KP00|D3DRS4|D3DRS8|Q5T672|Q5T673|Q5T674|Q5T675|Q7LDL9|Q8N562|Q9UET9|Q9UEV4|Q9Y218	Missense_Mutation	SNP	ENST00000378748.3	37	CCDS7094.1	.	.	.	.	.	.	.	.	.	.	T	7.760	0.705124	0.15172	.	.	ENSG00000123240	ENST00000263036;ENST00000378764;ENST00000378757;ENST00000378752;ENST00000378748;ENST00000378747	D;D;D;D;D;D	0.87103	-2.2;-2.21;-2.2;-2.21;-2.2;-2.2	5.57	-0.125	0.13519	.	0.329091	0.37809	N	0.001921	T	0.81192	0.4771	L	0.47716	1.5	0.09310	N	1	P;P	0.44195	0.828;0.736	B;B	0.43783	0.431;0.352	T	0.72727	-0.4206	10	0.51188	T	0.08	-3.8413	6.6495	0.22955	0.0:0.4744:0.1352:0.3903	.	394;400	Q96CV9-2;Q96CV9	.;OPTN_HUMAN	Q	400;394;400;394;400;400	ENSP00000263036:H400Q;ENSP00000368040:H394Q;ENSP00000368032:H400Q;ENSP00000368027:H394Q;ENSP00000368022:H400Q;ENSP00000368021:H400Q	ENSP00000263036:H400Q	H	+	3	2	OPTN	13208003	0.787000	0.28750	0.052000	0.19188	0.032000	0.12392	0.195000	0.17155	0.003000	0.14656	-0.280000	0.10049	CAT	.	.	none		0.313	OPTN-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046834.1	NM_021980		G	13167997	T	G	13167997	3	3	39	1	0	0	0	0	1	0	0	0	10898	1403	49	5	1234	5	OPTN	10	13167997	Missense_Mutation	SNP	T	TCGA-GS-A9TW-01A-11D-A382-10		13167997	122366750	124	14669											
HSPA14	51182	hgsc.bcm.edu	37	chr10	14893270	14893270	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcgattaattcacgaaccgTctgcagctcttcttgcttat	8	15	7	11	3	4	0	1	0	3	0	4	2	4	0	1	0	5	3	1	0	3	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr10:14893270T>C	ENST00000378372.3	+	7	759	c.520T>C	c.(520-522)Tct>Cct	p.S174P		NM_016299.2	NP_057383.2	Q0VDF9	HSP7E_HUMAN	heat shock 70kDa protein 14	174					'de novo' cotranslational protein folding (GO:0051083)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)			breast(4)|endometrium(2)|kidney(2)|large_intestine(3)|lung(4)|ovary(2)	17						TCACGAACCGTCTGCAGCTCT	0.358																																					p.S174P		Atlas-SNP	.											.	HSPA14	42	.	0			c.T520C						PASS	.						137	135	136					10																	14893270		2203	4300	6503	SO:0001583	missense	51182	exon7			GAACCGTCTGCAG	AF112210	CCDS7103.1, CCDS60487.1	10p13	2011-09-02			ENSG00000187522	ENSG00000187522		"Heat shock proteins / HSP70"	29526	protein-coding gene	gene with protein product		610369				12477932	Standard	NM_016299		Approved	HSP70-4, HSP70L1	uc001ind.4	Q0VDF9	OTTHUMG00000017712	ENST00000378372.3:c.520T>C	10.37:g.14893270T>C	ENSP00000367623:p.Ser174Pro	112	0	0		97	14	0.14433	NM_016299	A8K8F8|B0YIY9|Q9P0X2|Q9UI07	Missense_Mutation	SNP	ENST00000378372.3	37	CCDS7103.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.411879	0.83340	.	.	ENSG00000187522	ENST00000378372	T	0.01034	5.42	5.62	5.62	0.85841	.	0.052571	0.85682	D	0.000000	T	0.03434	0.0099	L	0.58101	1.795	0.80722	D	1	D	0.60575	0.988	P	0.56343	0.796	T	0.49916	-0.8888	10	0.87932	D	0	-17.0919	15.8307	0.78749	0.0:0.0:0.0:1.0	.	174	Q0VDF9	HSP7E_HUMAN	P	174	ENSP00000367623:S174P	ENSP00000367623:S174P	S	+	1	0	HSPA14	14933276	1.000000	0.71417	0.973000	0.42090	0.989000	0.77384	4.081000	0.57627	2.118000	0.64928	0.528000	0.53228	TCT	.	.	none		0.358	HSPA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046910.1	NM_016299		C	14893270	T	C	14893270	3	2	39	1	0	0	0	0	1	0	0	0	7416	1667	58	3	546	3	HSPA14	10	14893270	Missense_Mutation	SNP	T	TCGA-GS-A9TW-01A-11D-A382-10	1725273	14893270	120641477	125	14670											
NEBL	10529	hgsc.bcm.edu	37	chr10	21309114	21309114	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctgccaccgtggtgaaggActgcttcgggtagtgtctgt	6	12	14	9	2	2	1	0	1	2	0	3	2	2	2	2	3	2	2	2	3	2	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr10:21309114A>G	ENST00000417816.2	-	3	534	c.181T>C	c.(181-183)Tcc>Ccc	p.S61P	NEBL_ENST00000377159.4_Missense_Mutation_p.S27P	NM_001173484.1|NM_213569.2	NP_001166955.1|NP_998734.1	O76041	NEBL_HUMAN	nebulette	106					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						GTGGTGAAGGACTGCTTCGGG	0.413																																					p.S61P		Atlas-SNP	.											.	NEBL	199	.	0			c.T181C						PASS	.						102	96	98					10																	21309114		2203	4300	6503	SO:0001583	missense	10529	exon3			TGAAGGACTGCTT	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	ENST00000417816.2:c.181T>C	10.37:g.21309114A>G	ENSP00000393896:p.Ser61Pro	180	0	0		171	48	0.280702	NM_001173484	B0YJ45|Q2TBD0|Q70I54|Q9UIC4	Missense_Mutation	SNP	ENST00000417816.2	37	CCDS7133.1	.	.	.	.	.	.	.	.	.	.	a	14.03	2.414610	0.42817	.	.	ENSG00000078114	ENST00000417816;ENST00000377159	T;T	0.36157	1.27;1.73	5.24	4.11	0.48088	.	.	.	.	.	T	0.35828	0.0945	M	0.76838	2.35	0.29217	N	0.874206	P	0.36990	0.577	B	0.26310	0.068	T	0.37979	-0.9682	9	0.59425	D	0.04	.	10.3484	0.43920	0.9204:0.0:0.0796:0.0	.	61	Q70I54	.	P	61;27	ENSP00000393896:S61P;ENSP00000366364:S27P	ENSP00000366364:S27P	S	-	1	0	NEBL	21349120	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.287000	0.59001	0.932000	0.37266	0.529000	0.55759	TCC	.	.	none		0.413	NEBL-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047112.1	NM_006393		G	21309114	A	G	21309114	3	3	39	1	0	0	0	0	1	0	0	0	10312	275	10	3	3340	3	NEBL	10	21309114	Missense_Mutation	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	6415844	21309114	114225633	126	14671											
JMJD1C	221037	hgsc.bcm.edu	37	chr10	64967691	64967691	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agagttggaggcttctgtgaTtcttgaactttaccaccagc	9	13	10	9	0	2	3	0	2	2	1	2	4	2	4	2	2	3	2	2	2	2	6			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr10:64967691T>A	ENST00000399262.2	-	10	3956	c.3738A>T	c.(3736-3738)gaA>gaT	p.E1246D	JMJD1C_ENST00000542921.1_Missense_Mutation_p.E1064D|JMJD1C_ENST00000402544.1_Missense_Mutation_p.E1027D|JMJD1C_ENST00000399251.1_Missense_Mutation_p.E1027D	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	1246					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)					GCTTCTGTGATTCTTGAACTT	0.443																																					p.E1246D		Atlas-SNP	.											.	JMJD1C	347	.	0			c.A3738T						PASS	.						90	86	87					10																	64967691		1851	4104	5955	SO:0001583	missense	221037	exon10			CTGTGATTCTTGA	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.3738A>T	10.37:g.64967691T>A	ENSP00000382204:p.Glu1246Asp	182	0	0		193	48	0.248705	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	37	CCDS41532.1	.	.	.	.	.	.	.	.	.	.	T	12.35	1.912957	0.33815	.	.	ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000399251;ENST00000542921	T;T;T;T	0.60672	0.52;0.17;1.99;0.53	5.58	1.88	0.25563	.	0.000000	0.85682	D	0.000000	T	0.69797	0.3151	M	0.62723	1.935	0.43761	D	0.996277	D;D;D	0.89917	1.0;0.998;0.997	D;D;D	0.83275	0.996;0.942;0.92	T	0.65853	-0.6067	10	0.49607	T	0.09	-20.8338	11.4093	0.49917	0.0:0.3183:0.0:0.6817	.	787;1246;1064	A6PW35;Q15652;A0T124	.;JHD2C_HUMAN;.	D	1246;1027;1027;1064	ENSP00000382204:E1246D;ENSP00000384990:E1027D;ENSP00000382195:E1027D;ENSP00000444682:E1064D	ENSP00000382195:E1027D	E	-	3	2	JMJD1C	64637697	1.000000	0.71417	0.996000	0.52242	0.585000	0.36419	0.869000	0.27996	-0.168000	0.10853	-1.773000	0.00660	GAA	.	.	none		0.443	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241		A	64967691	T	A	64967691	3	1	39	1	0	0	0	0	1	0	0	0	7959	1490	52	5	3952	5	JMJD1C	10	64967691	Missense_Mutation	SNP	T	TCGA-GS-A9TW-01A-11D-A382-10	43658577	64967691	70567056	127	14672											
HKDC1	80201	hgsc.bcm.edu	37	chr10	70998835	70998835	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gacaaaaaagtttaaggcacGaggagttcaggacacggatg	16	6	13	6	2	1	0	1	0	0	0	1	5	1	3	0	4	0	3	0	4	4	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr10:70998835G>A	ENST00000354624.5	+	5	666	c.533G>A	c.(532-534)cGa>cAa	p.R178Q	HKDC1_ENST00000395086.2_Missense_Mutation_p.R178Q	NM_025130.3	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	178	Hexokinase type-1 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						TTTAAGGCACGAGGAGTTCAG	0.522																																					p.R178Q		Atlas-SNP	.											HKDC1,NS,carcinoma,+1,2	HKDC1	98	2	0			c.G533A						PASS	.						88	78	81					10																	70998835		2203	4300	6503	SO:0001583	missense	80201	exon5			AGGCACGAGGAGT		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.533G>A	10.37:g.70998835G>A	ENSP00000346643:p.Arg178Gln	96	0	0		88	28	0.318182	NM_025130	B5MDN9|Q2TB91|Q5VTC7|Q7Z373|Q8WU37|Q96EH2|Q9H5Y9	Missense_Mutation	SNP	ENST00000354624.5	37	CCDS7288.1	.	.	.	.	.	.	.	.	.	.	G	13.46	2.242803	0.39598	.	.	ENSG00000156510	ENST00000354624;ENST00000395087;ENST00000395086	D;D	0.98968	-5.28;-5.28	4.92	4.92	0.64577	Hexokinase, N-terminal (1);	0.060279	0.64402	D	0.000004	D	0.96476	0.8850	N	0.25789	0.76	0.19300	N	0.999972	B	0.14805	0.011	B	0.14023	0.01	D	0.90277	0.4312	10	0.72032	D	0.01	-15.4141	18.6753	0.91526	0.0:0.0:1.0:0.0	.	178	Q2TB90	HKDC1_HUMAN	Q	178	ENSP00000346643:R178Q;ENSP00000378521:R178Q	ENSP00000346643:R178Q	R	+	2	0	HKDC1	70668841	0.844000	0.29557	0.186000	0.23195	0.199000	0.23934	4.461000	0.60115	2.708000	0.92522	0.655000	0.94253	CGA	.	.	none		0.522	HKDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048389.1	NM_025130		A	70998835	G	A	70998835	3	1	39	1	0	0	0	0	1	0	0	0	7202	1058	37	1	551	1	HKDC1	10	70998835	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	6031144	70998835	64535912	128	14673											
SGPL1	8879	hgsc.bcm.edu	37	chr10	72633215	72633215	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cagggtggcatctatgcttcCccaaccatcgcaggctcacg	8	8	10	15	2	2	0	1	0	1	0	4	0	3	0	3	3	2	4	3	3	2	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr10:72633215C>T	ENST00000373202.3	+	12	1367	c.1167C>T	c.(1165-1167)tcC>tcT	p.S389S		NM_003901.3	NP_003892.2	O95470	SGPL1_HUMAN	sphingosine-1-phosphate lyase 1	389					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						TCTATGCTTCCCCAACCATCG	0.512																																					p.S389S	Colon(151;1054 2458 6676 40971)	Atlas-SNP	.											.	SGPL1	37	.	0			c.C1167T						PASS	.						151	130	137					10																	72633215		2203	4300	6503	SO:0001819	synonymous_variant	8879	exon12			TGCTTCCCCAACC	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.1167C>T	10.37:g.72633215C>T		139	0	0		113	13	0.115044	NM_003901	B2RBD4|Q7Z732|Q9ULG8|Q9UN89	Silent	SNP	ENST00000373202.3	37	CCDS31216.1																																																																																			.	.	none		0.512	SGPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048533.1	NM_003901		T	72633215	C	T	72633215	2	4	39	1	0	0	0	0	0	0	0	1	14233	610	22	2		2	SGPL1	10	72633215	Silent	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	1634380	72633215	62901532	129	14674											
CAMK2G	818	hgsc.bcm.edu	37	chr10	75608359	75608359	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacaagtaacctggggtgcCagcaaaacctgtagcaaaag	15	5	12	9	0	0	0	0	0	0	0	0	1	0	1	3	3	5	4	3	3	7	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr10:75608359C>T	ENST00000351293.3	-	8	583	c.526G>A	c.(526-528)Ggc>Agc	p.G176S	RP11-574K11.8_ENST00000446730.2_RNA|CAMK2G_ENST00000444854.2_Intron|CAMK2G_ENST00000423381.1_Missense_Mutation_p.G176S|CAMK2G_ENST00000372765.1_Missense_Mutation_p.G176S|CAMK2G_ENST00000394762.2_Missense_Mutation_p.G176S|CAMK2G_ENST00000322635.3_Missense_Mutation_p.G176S|CAMK2G_ENST00000322680.3_Missense_Mutation_p.G176S|CAMK2G_ENST00000472912.1_5'UTR|CAMK2G_ENST00000305762.7_Missense_Mutation_p.G176S	NM_001222.3|NM_172173.2	NP_001213.2|NP_751913.1	Q13555	KCC2G_HUMAN	calcium/calmodulin-dependent protein kinase II gamma	176	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)	CCTGGGGTGCCAGCAAAACCT	0.517											OREG0020267	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G176S		Atlas-SNP	.											.	CAMK2G	79	.	0			c.G526A						PASS	.						46	44	44					10																	75608359		2203	4300	6503	SO:0001583	missense	818	exon8			GGGTGCCAGCAAA	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.526G>A	10.37:g.75608359C>T	ENSP00000277853:p.Gly176Ser	71	0	0	1161	85	22	0.258824	NM_172170	O00561|O15378|Q13279|Q13282|Q13556|Q5SQZ3|Q5SQZ4|Q5SWX4|Q7KYX5|Q8N4I3|Q8NIA4	Missense_Mutation	SNP	ENST00000351293.3	37	CCDS7336.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.280223	0.80692	.	.	ENSG00000148660	ENST00000351293;ENST00000322635;ENST00000423381;ENST00000394763;ENST00000322680;ENST00000394762;ENST00000433289;ENST00000305762;ENST00000372765	T;T;T;T;T;T;T;T	0.40225	1.04;1.04;1.04;1.04;1.04;1.04;1.04;1.04	5.62	4.71	0.59529	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.127013	0.52532	D	0.000064	T	0.73682	0.3618	M	0.93594	3.435	0.80722	D	1	D;D;D;P;D;D;D;D	0.89917	0.993;0.997;0.968;0.863;0.974;1.0;0.998;0.999	D;D;P;P;D;D;D;D	0.97110	0.964;0.983;0.893;0.677;0.935;1.0;0.977;1.0	T	0.82559	-0.0397	10	0.87932	D	0	.	16.5573	0.84488	0.0:0.8693:0.1307:0.0	.	168;176;176;176;176;176;176;176	B3KY86;Q13555-4;Q13555-6;Q13555-10;A8K6N9;Q13555;Q13555-5;Q13555-8	.;.;.;.;.;KCC2G_HUMAN;.;.	S	176;176;176;176;176;176;111;176;176	ENSP00000277853:G176S;ENSP00000315599:G176S;ENSP00000410298:G176S;ENSP00000319060:G176S;ENSP00000378243:G176S;ENSP00000393784:G111S;ENSP00000307082:G176S;ENSP00000361851:G176S	ENSP00000307082:G176S	G	-	1	0	CAMK2G	75278365	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	7.818000	0.86416	1.351000	0.45789	-0.176000	0.13171	GGC	.	.	none		0.517	CAMK2G-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048715.1	NM_172169		T	75608359	C	T	75608359	3	4	39	1	0	0	0	0	1	0	0	0	2604	594	21	2	1300	2	CAMK2G	10	75608359	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	2975144	75608359	59926388	130	14675											
GRID1	2894	hgsc.bcm.edu	37	chr10	87898678	87898678	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tctgtcttcatcgtggtgaaGaggctggtgaatacgtggct	7	13	14	7	2	3	3	1	2	2	1	4	3	3	3	0	4	1	2	0	4	3	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr10:87898678G>A	ENST00000327946.7	-	4	709	c.624C>T	c.(622-624)ctC>ctT	p.L208L		NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	208					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						TCGTGGTGAAGAGGCTGGTGA	0.577										Multiple Myeloma(13;0.14)																											p.L208L		Atlas-SNP	.											.	GRID1	204	.	0			c.C624T						PASS	.						226	197	207					10																	87898678		2203	4300	6503	SO:0001819	synonymous_variant	2894	exon4			GGTGAAGAGGCTG	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.624C>T	10.37:g.87898678G>A		115	0	0		70	14	0.2	NM_017551	B3KXD5|B7Z7L0|Q8IXT3	Silent	SNP	ENST00000327946.7	37	CCDS31236.1																																																																																			.	.	none		0.577	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613		A	87898678	G	A	87898678	2	1	39	1	0	0	0	0	0	0	0	1	6780	929	33	2		2	GRID1	10	87898678	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	12290319	87898678	47636069	131	14676											
C10orf137	26098	hgsc.bcm.edu	37	chr10	127429569	127429569	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cttccctccctttctaaacaGatacttattgctgcctctgc	7	15	4	15	0	2	1	0	0	2	1	4	1	4	1	3	0	5	1	3	0	4	6			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr10:127429569G>A	ENST00000356792.4	+	17	2402		c.e17-1		C10orf137_ENST00000337623.3_Splice_Site	NM_001202438.1	NP_001189367.1	Q3B7T1	EDRF1_HUMAN							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)				TTTCTAAACAGATACTTATTG	0.378																																					.		Atlas-SNP	.											.	C10orf137	153	.	0			c.2171-1G>A						PASS	.						123	125	124					10																	127429569		2203	4300	6503	SO:0001630	splice_region_variant	26098	exon17			TAAACAGATACTT																												ENST00000356792.4:c.2171-1G>A	10.37:g.127429569G>A		254	0	0		209	50	0.239234	NM_001202438	B2RC65|Q3KR40|Q4G190|Q5VZQ4|Q8IZ74|Q9Y3W4	Splice_Site	SNP	ENST00000356792.4	37	CCDS55733.1	.	.	.	.	.	.	.	.	.	.	G	12.85	2.062592	0.36373	.	.	ENSG00000107938	ENST00000356792;ENST00000392732;ENST00000337623;ENST00000368813	.	.	.	5.5	5.5	0.81552	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4119	0.94677	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C10orf137	127419559	1.000000	0.71417	0.954000	0.39281	0.103000	0.19146	9.476000	0.97823	2.596000	0.87737	0.650000	0.86243	.	.	.	none		0.378	C10orf137-007	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388539.1		Intron	A	127429569	G	A	127429569	5	1	39	1	0	0	0	0	0	0	1	0	1596	956	33	2	2130	2	C10orf137	10	127429569	Splice_Site	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	39530891	127429569	8105178	132	14677											
OR56A3	390083	hgsc.bcm.edu	37	chr11	5968801	5968801	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	ctcctctccctgctggacatCgtgctctgcctcactgtcat	4	13	7	17	1	4	0	2	0	2	0	7	1	5	1	3	1	3	2	3	1	0	0	rs200944882		TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr11:5968801C>G	ENST00000329564.6	+	1	232	c.225C>G	c.(223-225)atC>atG	p.I75M	AC025016.1_ENST00000528915.1_lincRNA	NM_001003443.2	NP_001003443.2	Q8NH54	O56A3_HUMAN	olfactory receptor, family 56, subfamily A, member 3	75						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)		TGCTGGACATCGTGCTCTGCC	0.592																																					p.I75M		Atlas-SNP	.											.	OR56A3	81	.	0			c.C225G						PASS	.						143	138	140					11																	5968801		2201	4296	6497	SO:0001583	missense	390083	exon1			GGACATCGTGCTC		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.225C>G	11.37:g.5968801C>G	ENSP00000331572:p.Ile75Met	171	0	0		142	57	0.401408	NM_001003443	A6NN77|Q6IFF7	Missense_Mutation	SNP	ENST00000329564.6	37	CCDS41614.1	.	.	.	.	.	.	.	.	.	.	C	0	-2.606553	0.00121	.	.	ENSG00000184478	ENST00000329564	T	0.04809	3.55	5.13	-10.3	0.00346	GPCR, rhodopsin-like superfamily (1);	0.200388	0.34628	N	0.003816	T	0.02688	0.0081	L	0.31120	0.905	0.18873	N	0.999985	B	0.19073	0.033	B	0.23419	0.046	T	0.54788	-0.8241	10	0.72032	D	0.01	-6.3985	4.617	0.12432	0.1316:0.3919:0.315:0.1615	.	75	Q8NH54	O56A3_HUMAN	M	75	ENSP00000331572:I75M	ENSP00000331572:I75M	I	+	3	3	OR56A3	5925377	0.000000	0.05858	0.001000	0.08648	0.733000	0.41908	-7.065000	0.00045	-6.004000	0.00007	-1.847000	0.00572	ATC	C|1.000;T|0.000	.	alt		0.592	OR56A3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383753.1	NM_001003443		G	5968801	C	G	5968801	3	3	39	1	0	0	0	0	1	0	0	0	11143	874	31	4	227	4	OR56A3	11	5968801	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10		5968801	129037715	133	14678											
DNHD1	144132	hgsc.bcm.edu	37	chr11	6567484	6567484	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	actgtaccaggaggcttcccGaaacacaagcaccatagacc	14	5	8	14	1	0	1	0	0	0	1	1	3	1	2	4	2	3	3	4	2	4	3	rs553002964		TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr11:6567484G>A	ENST00000527990.2	+	19	5315	c.5315G>A	c.(5314-5316)cGa>cAa	p.R1772Q	DNHD1_ENST00000254579.6_Missense_Mutation_p.R1772Q			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	1772					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)		GAGGCTTCCCGAAACACAAGC	0.582													G|||	1	0.000199681	0.0	0.0	5008	,	,		20636	0.001		0.0	False		,,,				2504	0.0				p.R1772Q		Atlas-SNP	.											DNHD1,NS,carcinoma,+1,2	DNHD1	198	2	0			c.G5315A						PASS	.						41	38	39					11																	6567484		692	1591	2283	SO:0001583	missense	144132	exon21			CTTCCCGAAACAC	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.5315G>A	11.37:g.6567484G>A	ENSP00000436180:p.Arg1772Gln	103	0	0		107	53	0.495327	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	G	6.129	0.391949	0.11581	.	.	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000533649	T;T	0.56444	0.46;0.46	5.23	-1.78	0.07957	.	0.765678	0.12088	N	0.500700	T	0.39118	0.1066	L	0.46157	1.445	0.09310	N	0.999997	B	0.28512	0.214	B	0.22601	0.04	T	0.25779	-1.0122	10	0.16896	T	0.51	.	11.3716	0.49702	0.4825:0.0:0.5175:0.0	.	1772	Q96M86	DNHD1_HUMAN	Q	1772;1772;63	ENSP00000254579:R1772Q;ENSP00000436180:R1772Q	ENSP00000254579:R1772Q	R	+	2	0	DNHD1	6524060	0.055000	0.20627	0.403000	0.26384	0.455000	0.32408	-0.215000	0.09279	-0.191000	0.10448	-0.345000	0.07892	CGA	.	.	none		0.582	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666		A	6567484	G	A	6567484	3	1	39	1	0	0	0	0	1	0	0	0	4670	1058	37	1	5398	1	DNHD1	11	6567484	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	598683	6567484	128439032	134	14679											
ILK	3611	hgsc.bcm.edu	37	chr11	6629314	6629314	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccccttgcactgggcctgccGagagggccgctctgctgtgg	3	8	15	15	2	1	1	0	0	1	1	1	2	1	1	5	3	3	3	5	3	0	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr11:6629314G>A	ENST00000396751.2	+	2	584	c.128G>A	c.(127-129)cGa>cAa	p.R43Q	ILK_ENST00000528995.1_Missense_Mutation_p.R43Q|ILK_ENST00000420936.2_Missense_Mutation_p.R43Q|ILK_ENST00000537806.1_Intron|RP11-732A19.2_ENST00000527398.1_RNA|ILK_ENST00000299421.4_Missense_Mutation_p.R43Q	NM_001014795.1	NP_001014795.1	Q13418	ILK_HUMAN	integrin-linked kinase	43	Interaction with LIMS1.				branching involved in ureteric bud morphogenesis (GO:0001658)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell junction assembly (GO:0034329)|cell proliferation (GO:0008283)|cell-matrix adhesion (GO:0007160)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|extracellular fibril organization (GO:0043206)|fibroblast migration (GO:0010761)|integrin-mediated signaling pathway (GO:0007229)|myelin assembly (GO:0032288)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|peptidyl-serine phosphorylation (GO:0018105)|platelet aggregation (GO:0070527)|positive regulation of axon extension (GO:0045773)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|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 dendrite morphogenesis (GO:0050775)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			central_nervous_system(1)	1		Breast(177;7.61e-05)|Medulloblastoma(188;0.00263)|all_neural(188;0.026)|all_lung(207;0.152)		Epithelial(150;5.49e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00012)|Lung(200;0.00942)|LUSC - Lung squamous cell carcinoma(625;0.0163)		TGGGCCTGCCGAGAGGGCCGC	0.582																																					p.R43Q		Atlas-SNP	.											ILK_ENST00000299421,NS,malignant_melanoma,0,1	ILK	41	1	0			c.G128A						PASS	.						66	62	63					11																	6629314		2201	4296	6497	SO:0001583	missense	3611	exon3			CCTGCCGAGAGGG	U40282	CCDS7768.1, CCDS60712.1, CCDS60713.1	11p15.4	2014-09-17			ENSG00000166333	ENSG00000166333		"Ankyrin repeat domain containing"	6040	protein-coding gene	gene with protein product		602366				8538749	Standard	NM_004517		Approved		uc001mef.3	Q13418	OTTHUMG00000133407	ENST00000396751.2:c.128G>A	11.37:g.6629314G>A	ENSP00000379975:p.Arg43Gln	116	0	0		81	12	0.148148	NM_001014794	B7Z1I0|B7Z418|D3DQU0|P57043|Q68DZ3	Missense_Mutation	SNP	ENST00000396751.2	37	CCDS7768.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.633208	0.87660	.	.	ENSG00000166333	ENST00000299421;ENST00000420936;ENST00000528995;ENST00000396751	T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16	5.73	5.73	0.89815	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.53286	0.1787	N	0.25031	0.7	0.80722	D	1	B;P	0.38504	0.077;0.634	B;B	0.38428	0.273;0.038	T	0.56733	-0.7930	10	0.52906	T	0.07	.	18.8889	0.92391	0.0:0.0:1.0:0.0	.	43;43	B7Z418;Q13418	.;ILK_HUMAN	Q	43	ENSP00000299421:R43Q;ENSP00000403487:R43Q;ENSP00000435323:R43Q;ENSP00000379975:R43Q	ENSP00000299421:R43Q	R	+	2	0	ILK	6585890	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.415000	0.80131	2.714000	0.92807	0.561000	0.74099	CGA	.	.	none		0.582	ILK-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384519.1	NM_004517		A	6629314	G	A	6629314	3	1	39	1	0	0	0	0	1	0	0	0	7722	1058	37	1	134	1	ILK	11	6629314	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	61830	6629314	128377202	135	14680											
SWAP70	23075	hgsc.bcm.edu	37	chr11	9761816	9761816	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acgggagctggaagacatgtAcctaaagctgcaggaggctc	12	6	14	9	1	0	1	0	0	0	1	1	4	0	4	1	4	4	5	1	4	4	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr11:9761816A>G	ENST00000318950.6	+	9	1380	c.1277A>G	c.(1276-1278)tAc>tGc	p.Y426C	SWAP70_ENST00000447399.2_Missense_Mutation_p.Y368C	NM_015055.2	NP_055870.2	Q9UH65	SWP70_HUMAN	SWAP switching B-cell complex 70kDa subunit	426					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)		GAAGACATGTACCTAAAGCTG	0.493																																					p.Y426C		Atlas-SNP	.											.	SWAP70	40	.	0			c.A1277G						PASS	.						102	97	98					11																	9761816		2201	4294	6495	SO:0001583	missense	23075	exon9			ACATGTACCTAAA	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.1277A>G	11.37:g.9761816A>G	ENSP00000315630:p.Tyr426Cys	48	0	0		67	25	0.373134	NM_015055	D3DQV1|O75135|Q7LCY6|Q9P061|Q9P0Z8	Missense_Mutation	SNP	ENST00000318950.6	37	CCDS31426.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.948666	0.73787	.	.	ENSG00000133789	ENST00000447399;ENST00000318950	T;T	0.21734	1.99;1.99	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.43010	0.1228	L	0.56769	1.78	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	T	0.22173	-1.0224	10	0.45353	T	0.12	-10.3002	15.2595	0.73610	1.0:0.0:0.0:0.0	.	368;426;368	E7EMB1;Q9UH65;B3KUB9	.;SWP70_HUMAN;.	C	368;426	ENSP00000399056:Y368C;ENSP00000315630:Y426C	ENSP00000315630:Y426C	Y	+	2	0	SWAP70	9718392	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	8.962000	0.93254	2.006000	0.58801	0.402000	0.26972	TAC	.	.	none		0.493	SWAP70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386766.2	NM_015055		G	9761816	A	G	9761816	3	3	39	1	0	0	0	0	1	0	0	0	15440	391	14	3	1311	3	SWAP70	11	9761816	Missense_Mutation	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	3132502	9761816	125244700	136	14681											
ANO3	63982	hgsc.bcm.edu	37	chr11	26538445	26538445	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacacgctgtgcaagtatgcAgagaggctgaatatcaggat	13	8	13	7	1	1	2	1	1	0	1	1	5	1	3	0	2	2	5	0	2	4	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr11:26538445A>C	ENST00000256737.3	+	6	1515	c.663A>C	c.(661-663)gcA>gcC	p.A221A	ANO3_ENST00000525139.1_Silent_p.A205A|ANO3_ENST00000537978.1_Silent_p.A205A|ANO3_ENST00000531568.1_Silent_p.A75A	NM_031418.2	NP_113606.2	Q9BYT9	ANO3_HUMAN	anoctamin 3	221					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						GCAAGTATGCAGAGAGGCTGA	0.363																																					p.A221A		Atlas-SNP	.											.	ANO3	145	.	0			c.A663C						PASS	.						84	83	84					11																	26538445		2203	4299	6502	SO:0001819	synonymous_variant	63982	exon6			GTATGCAGAGAGG	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.663A>C	11.37:g.26538445A>C		218	0	0		182	55	0.302198	NM_031418	B7Z3F5	Silent	SNP	ENST00000256737.3	37	CCDS31447.1																																																																																			.	.	none		0.363	ANO3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387806.1	NM_031418		C	26538445	A	C	26538445	2	2	39	1	0	0	0	0	0	0	0	1	698	175	7	5		5	ANO3	11	26538445	Silent	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	16776629	26538445	108468071	137	14682											
C11orf87	399947	hgsc.bcm.edu	37	chr11	109294503	109294503	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcagcggcacctgcatcacGcaggtgggacagcagctctt	8	6	14	13	2	2	0	1	0	1	0	2	1	2	1	1	4	4	6	1	4	0	1	rs558968039		TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr11:109294503G>A	ENST00000327419.6	+	2	547	c.144G>A	c.(142-144)acG>acA	p.T48T	RP11-708B6.2_ENST00000532992.1_RNA|RP11-708B6.2_ENST00000532929.1_RNA	NM_207645.3	NP_997528.2	Q6NUJ2	CK087_HUMAN	chromosome 11 open reading frame 87	48						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|large_intestine(5)|lung(5)|ovary(2)|prostate(1)|urinary_tract(1)	17						CCTGCATCACGCAGGTGGGAC	0.637													G|||	1	0.000199681	0.0	0.0	5008	,	,		17890	0.001		0.0	False		,,,				2504	0.0				p.T48T		Atlas-SNP	.											C11orf87,NS,carcinoma,+1,1	C11orf87	37	1	0			c.G144A						scavenged	.						128	101	110					11																	109294503		2201	4298	6499	SO:0001819	synonymous_variant	399947	exon2			CATCACGCAGGTG	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.144G>A	11.37:g.109294503G>A		219	1	0.00456621		139	23	0.165468	NM_207645	B4E169	Silent	SNP	ENST00000327419.6	37	CCDS31672.1																																																																																			.	.	none		0.637	C11orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390403.1	NM_207645		A	109294503	G	A	109294503	2	1	39	1	0	0	0	0	0	0	0	1	1671	1074	38	1		1	C11orf87	11	109294503	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	82756058	109294503	25712013	138	14683											
ROBO3	64221	hgsc.bcm.edu	37	chr11	124748633	124748633	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccacagccactcttacaccCtcacctcctgaccctcccca	8	8	2	23	0	2	1	1	1	1	0	5	1	5	1	8	0	2	0	8	0	1	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr11:124748633C>T	ENST00000397801.1	+	23	3666	c.3474C>T	c.(3472-3474)ccC>ccT	p.P1158P	ROBO3_ENST00000543966.1_5'UTR|ROBO3_ENST00000525482.1_3'UTR|ROBO3_ENST00000538940.1_Silent_p.P1136P	NM_022370.3	NP_071765.2	Q96MS0	ROBO3_HUMAN	roundabout, axon guidance receptor, homolog 3 (Drosophila)	1158					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)		CTCTTACACCCTCACCTCCTG	0.592																																					p.P1158P		Atlas-SNP	.											.	ROBO3	199	.	0			c.C3474T						PASS	.						61	72	68					11																	124748633		2034	4171	6205	SO:0001819	synonymous_variant	64221	exon23			TACACCCTCACCT	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.3474C>T	11.37:g.124748633C>T		37	0	0		24	9	0.375	NM_022370		Silent	SNP	ENST00000397801.1	37	CCDS44755.1																																																																																			.	.	none		0.592	ROBO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387091.1	XM_370663		T	124748633	C	T	124748633	2	4	39	1	0	0	0	0	0	0	0	1	13530	668	24	2		2	ROBO3	11	124748633	Silent	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	15454130	124748633	10257883	139	14684											
LRRC23	10233	hgsc.bcm.edu	37	chr12	7016547	7016547	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcctgcacacagtggagcttCgggggaaccagctggaaagc	10	5	15	11	1	0	0	0	0	0	0	1	3	0	3	2	4	5	3	2	4	2	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr12:7016547C>T	ENST00000007969.8	+	5	779	c.559C>T	c.(559-561)Cgg>Tgg	p.R187W	LRRC23_ENST00000323702.5_Missense_Mutation_p.R187W|LRRC23_ENST00000443597.2_Missense_Mutation_p.R187W|LRRC23_ENST00000433346.1_Missense_Mutation_p.R187W|LRRC23_ENST00000429740.1_Intron|LRRC23_ENST00000436789.1_Missense_Mutation_p.R187W	NM_001135217.1|NM_201650.2	NP_001128689.1|NP_964013.1	Q53EV4	LRC23_HUMAN	leucine rich repeat containing 23	187										NS(1)|breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|stomach(1)	13						AGTGGAGCTTCGGGGGAACCA	0.572																																					p.R187W		Atlas-SNP	.											LRRC23,colon,carcinoma,0,2	LRRC23	46	2	0			c.C559T						PASS	.						123	119	120					12																	7016547		2203	4300	6503	SO:0001583	missense	10233	exon5			GAGCTTCGGGGGA	BC014450	CCDS8568.1, CCDS8569.1	12p13	2006-02-02			ENSG00000010626	ENSG00000010626			19138	protein-coding gene	gene with protein product						11830501, 11826754	Standard	NM_201650		Approved	B7, LRPB7	uc001qrp.3	Q53EV4	OTTHUMG00000156668	ENST00000007969.8:c.559C>T	12.37:g.7016547C>T	ENSP00000007969:p.Arg187Trp	101	0	0		85	28	0.329412	NM_001135217	A8K8C6|D3DUT1|Q8N6K6|Q92977|Q99620	Missense_Mutation	SNP	ENST00000007969.8	37	CCDS8569.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.291656	0.80914	.	.	ENSG00000010626	ENST00000433346;ENST00000007969;ENST00000323702;ENST00000443597;ENST00000436789	T;T;T;T;T	0.63096	1.88;-0.02;2.17;-0.02;2.18	5.59	5.59	0.84812	.	.	.	.	.	D	0.82953	0.5149	M	0.86805	2.84	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	0.87578	0.997;0.998;0.998;0.998;0.998	D	0.85330	0.1089	9	0.72032	D	0.01	-26.1317	19.586	0.95490	0.0:1.0:0.0:0.0	.	187;187;187;187;187	C9JEW3;A8K8K2;Q53EV4-2;Q53EV4;C9JKE8	.;.;.;LRC23_HUMAN;.	W	187	ENSP00000402554:R187W;ENSP00000007969:R187W;ENSP00000317464:R187W;ENSP00000390932:R187W;ENSP00000396049:R187W	ENSP00000007969:R187W	R	+	1	2	LRRC23	6886808	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	4.769000	0.62300	2.624000	0.88883	0.462000	0.41574	CGG	.	.	none		0.572	LRRC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345214.1	NM_006992		T	7016547	C	T	7016547	3	4	39	1	0	0	0	0	1	0	0	0	8987	875	31	1	573	1	LRRC23	12	7016547	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10		7016547	126835348	140	14685											
CLEC7A	64581	hgsc.bcm.edu	37	chr12	10278006	10278006	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatagataacagctcttctCatatataatccaattaggag	16	12	6	7	0	2	1	1	0	2	1	4	3	3	2	1	1	2	1	1	1	8	7			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr12:10278006C>A	ENST00000304084.8	-	4	536	c.382G>T	c.(382-384)Gag>Tag	p.E128*	CLEC7A_ENST00000298523.5_Nonsense_Mutation_p.E82*|CLEC7A_ENST00000533022.1_Nonsense_Mutation_p.E128*|CLEC7A_ENST00000353231.5_Nonsense_Mutation_p.E82*|CLEC7A_ENST00000396484.2_Nonsense_Mutation_p.E49*	NM_197947.2	NP_922938.1	Q9BXN2	CLC7A_HUMAN	C-type lectin domain family 7, member A	128	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				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						CAGCTCTTCTCATATATAATC	0.398																																					p.E128X		Atlas-SNP	.											.	CLEC7A	55	.	0			c.G382T						PASS	.						68	67	67					12																	10278006		2203	4300	6503	SO:0001587	stop_gained	64581	exon4			TCTTCTCATATAT	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.382G>T	12.37:g.10278006C>A	ENSP00000302569:p.Glu128*	74	0	0		56	20	0.357143	NM_197947	B2R861|B7Z494|B7Z5A9|B7Z5B9|Q6IPS7|Q96D32|Q96DR9|Q96LD3|Q96PA4|Q96PA5|Q96PA6|Q96PA7|Q96PA8|Q9H1K3	Nonsense_Mutation	SNP	ENST00000304084.8	37	CCDS41753.1	.	.	.	.	.	.	.	.	.	.	C	16.59	3.166740	0.57476	.	.	ENSG00000172243	ENST00000353231;ENST00000298523;ENST00000396484;ENST00000304084;ENST00000533022	.	.	.	4.68	1.88	0.25563	.	0.545935	0.16857	N	0.196677	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.13470	T	0.59	.	4.8851	0.13699	0.0:0.6358:0.1758:0.1884	.	.	.	.	X	82;82;49;128;128	.	ENSP00000298523:E82X	E	-	1	0	CLEC7A	10169273	0.004000	0.15560	0.001000	0.08648	0.738000	0.42128	0.694000	0.25512	0.452000	0.26830	0.650000	0.86243	GAG	.	.	none		0.398	CLEC7A-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390772.1	NM_197954		A	10278006	C	A	10278006	4	1	39	1	0	0	0	0	0	1	0	0	3523	835	29	4	373	4	CLEC7A	12	10278006	Nonsense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	3261459	10278006	123573889	141	14686											
PRB1	5542	hgsc.bcm.edu	37	chr12	11508468	11508468	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagggccagcaaggccactGacagcagaatcaacagcatc	14	4	10	13	0	2	2	2	1	0	1	3	2	2	2	2	2	4	3	2	2	3	0			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr12:11508468G>T	ENST00000500254.2	-	1	57	c.20C>A	c.(19-21)tCa>tAa	p.S7*	PRB1_ENST00000546254.1_Intron|PRB1_ENST00000545626.1_Nonsense_Mutation_p.S7*	NM_005039.3|NM_199353.2	NP_005030.2|NP_955385.1	P04280	PRP1_HUMAN	proline-rich protein BstNI subfamily 1	0						extracellular region (GO:0005576)				NS(1)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20			OV - Ovarian serous cystadenocarcinoma(49;0.185)			CAAGGCCACTGACAGCAGAAT	0.498																																					p.S7X		Atlas-SNP	.											.	PRB1	33	.	0			c.C20A						PASS	.						79	77	78					12																	11508468		2180	4276	6456	SO:0001587	stop_gained	5542	exon1			GCCACTGACAGCA		CCDS8642.1, CCDS55805.1	12p13.2	2012-10-02							9337	protein-coding gene	gene with protein product		180989				8317492	Standard	NM_199353		Approved	PM, PMF, PMS, PRB1M, PRB1L	uc001qzu.1	P04280		ENST00000500254.2:c.20C>A	12.37:g.11508468G>T	ENSP00000420826:p.Ser7*	134	0	0		138	27	0.195652	NM_199353	Q08805|Q15186|Q15187|Q15214|Q15215|Q16038	Nonsense_Mutation	SNP	ENST00000500254.2	37	CCDS8642.1	.	.	.	.	.	.	.	.	.	.	.	12.85	2.061179	0.36373	.	.	ENSG00000251655	ENST00000545626;ENST00000500254	.	.	.	1.39	-2.22	0.06952	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.4435	0.16521	0.6557:0.0:0.3443:0.0	.	.	.	.	X	7	.	ENSP00000420826:S7X	S	-	2	0	PRB1	11399735	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.518000	0.22847	-0.773000	0.04596	-0.259000	0.10710	TCA	.	.	none		0.498	PRB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402312.1	NM_005039		T	11508468	G	T	11508468	4	4	39	1	0	0	0	0	0	1	0	0	12454	1294	45	4	987	4	PRB1	12	11508468	Nonsense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	1230462	11508468	122343427	142	14687											
DUSP16	80824	hgsc.bcm.edu	37	chr12	12653527	12653527	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tggcccaatgttggcaacagGtaagcaaggctgagaaatgc	13	7	13	8	0	0	1	0	1	0	1	0	2	0	1	1	4	3	5	1	4	5	2	rs369986596		TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr12:12653527G>C	ENST00000228862.2	-	4	1088	c.457C>G	c.(457-459)Cct>Gct	p.P153A	DUSP16_ENST00000298573.4_Intron|DUSP16_ENST00000545864.1_5'UTR	NM_030640.2	NP_085143.1	Q9BY84	DUS16_HUMAN	dual specificity phosphatase 16	153					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)		TTGGCAACAGGTAAGCAAGGC	0.468																																					p.P153A	Ovarian(158;443 1896 15437 36069 46477)	Atlas-SNP	.											.	DUSP16	64	.	0			c.C457G						PASS	.	G	ALA/PRO	0,4406		0,0,2203	117	104	108		457	5.2	1	12		108	1,8599	1.2+/-3.3	0,1,4299	no	missense	DUSP16	NM_030640.2	27	0,1,6502	CC,CG,GG		0.0116,0.0,0.0077	probably-damaging	153/666	12653527	1,13005	2203	4300	6503	SO:0001583	missense	80824	exon4			CAACAGGTAAGCA	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.457C>G	12.37:g.12653527G>C	ENSP00000228862:p.Pro153Ala	110	0	0		114	38	0.333333	NM_030640	Q547C7|Q96QS2|Q9C0G3	Missense_Mutation	SNP	ENST00000228862.2	37	CCDS8650.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.622442	0.87460	0.0	1.16E-4	ENSG00000111266	ENST00000228862	T	0.59364	0.27	5.24	5.24	0.73138	.	0.260739	0.37393	N	0.002114	T	0.59985	0.2234	L	0.59436	1.845	0.80722	D	1	P	0.38455	0.632	B	0.39339	0.297	T	0.65352	-0.6189	10	0.72032	D	0.01	.	19.1583	0.93520	0.0:0.0:1.0:0.0	.	153	Q9BY84	DUS16_HUMAN	A	153	ENSP00000228862:P153A	ENSP00000228862:P153A	P	-	1	0	DUSP16	12544794	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	5.929000	0.70096	2.606000	0.88127	0.551000	0.68910	CCT	.	.	weak		0.468	DUSP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400311.1	NM_030640		C	12653527	G	C	12653527	3	2	39	1	0	0	0	0	1	0	0	0	4818	1261	44	4	1556	4	DUSP16	12	12653527	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	1145059	12653527	121198368	143	14688											
GRIN2B	2904	hgsc.bcm.edu	37	chr12	13717016	13717016	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcggagcggatcaagtcgtcGtggccactgtagcggtcgct	6	9	15	11	6	1	0	1	0	0	0	5	2	1	2	1	4	2	2	1	4	2	1	rs543452359		TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr12:13717016G>A	ENST00000609686.1	-	13	3365	c.3156C>T	c.(3154-3156)caC>caT	p.H1052H		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	1052					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)	TCAAGTCGTCGTGGCCACTGT	0.572													G|||	1	0.000199681	0.0	0.0	5008	,	,		17988	0.001		0.0	False		,,,				2504	0.0				p.H1052H		Atlas-SNP	.											.	GRIN2B	303	.	0			c.C3156T						PASS	.						61	52	55					12																	13717016		2203	4300	6503	SO:0001819	synonymous_variant	2904	exon13			GTCGTCGTGGCCA		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.3156C>T	12.37:g.13717016G>A		248	0	0		167	27	0.161677	NM_000834	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Silent	SNP	ENST00000609686.1	37	CCDS8662.1																																																																																			.	.	none		0.572	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2			A	13717016	G	A	13717016	2	1	39	1	0	0	0	0	0	0	0	1	6789	1136	40	1		1	GRIN2B	12	13717016	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	1063489	13717016	120134879	144	14689											
HIST4H4	121504	hgsc.bcm.edu	37	chr12	14923847	14923847	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccaggaagactttgaggaCtccccgggtctcctcgtaga	8	9	11	13	2	1	3	0	1	1	2	5	5	3	5	4	3	0	1	4	3	2	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr12:14923847C>G	ENST00000539745.1	-	1	218	c.172G>C	c.(172-174)Gtc>Ctc	p.V58L	RP11-174G6.5_ENST00000562691.2_RNA|HIST4H4_ENST00000541592.1_5'Flank	NM_175054.2	NP_778224.1	P62805	H4_HUMAN	histone cluster 4, H4	58					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)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)	6						ACTTTGAGGACTCCCCGGGTC	0.597											OREG0021698	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.V58L		Atlas-SNP	.											.	HIST4H4	13	.	0			c.G172C						PASS	.						83	70	74					12																	14923847		2203	4300	6503	SO:0001583	missense	121504	exon1			TGAGGACTCCCCG	AY128653	CCDS8665.1	12p12.3	2011-01-27	2006-10-11			ENSG00000197837		"Histones / Replication-dependent"	20510	protein-coding gene	gene with protein product		615069	"histone 4, H4"			12408966	Standard	NM_175054		Approved	MGC24116	uc001rcf.4	P62805		ENST00000539745.1:c.172G>C	12.37:g.14923847C>G	ENSP00000443017:p.Val58Leu	116	0	0	698	83	12	0.144578	NM_175054	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000539745.1	37	CCDS8665.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.442037	0.83993	.	.	ENSG00000197837	ENST00000539745	T	0.71222	-0.55	4.08	4.08	0.47627	.	0.000000	0.39407	U	0.001377	T	0.79551	0.4465	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.82265	-0.0543	7	0.66056	D	0.02	.	14.2139	0.65781	0.0:1.0:0.0:0.0	.	.	.	.	L	58	ENSP00000443017:V58L	ENSP00000350767:V58L	V	-	1	0	HIST4H4	14815114	1.000000	0.71417	0.694000	0.30210	0.948000	0.59901	5.385000	0.66231	2.285000	0.76669	0.585000	0.79938	GTC	.	.	none		0.597	HIST4H4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400844.1	NM_175054		G	14923847	C	G	14923847	3	3	39	1	0	0	0	0	1	0	0	0	7194	565	20	4	143	4	HIST4H4	12	14923847	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	1206831	14923847	118928048	145	14690											
HOXC13	3229	hgsc.bcm.edu	37	chr12	54339026	54339026	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcaaatcgaaagcgcctcatCtccactccacctgaccaccc	11	6	5	19	2	2	1	1	1	1	0	5	2	3	1	6	0	1	1	6	0	2	0			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr12:54339026C>T	ENST00000243056.3	+	2	1135	c.979C>T	c.(979-981)Ctc>Ttc	p.L327F		NM_017410.2	NP_059106.2	P31276	HXC13_HUMAN	homeobox C13	327					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						AGCGCCTCATCTCCACTCCAC	0.577			T	NUP98	AML																																p.L327F		Atlas-SNP	.		Dom	yes		12	12q13.3	3229	homeo box C13		L	.	HOXC13	24	.	0			c.C979T						PASS	.						70	71	71					12																	54339026		2203	4300	6503	SO:0001583	missense	3229	exon2			CCTCATCTCCACT		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.979C>T	12.37:g.54339026C>T	ENSP00000243056:p.Leu327Phe	55	0	0		42	13	0.309524	NM_017410	Q5BL02|Q96J32|Q9NR24|Q9NYD5	Missense_Mutation	SNP	ENST00000243056.3	37	CCDS8865.1	.	.	.	.	.	.	.	.	.	.	C	15.80	2.940705	0.52972	.	.	ENSG00000123364	ENST00000243056	D	0.93712	-3.27	4.57	3.68	0.42216	Homeodomain-like (1);	0.067197	0.56097	D	0.000026	D	0.90184	0.6932	L	0.54863	1.705	0.44694	D	0.997683	B	0.29432	0.244	B	0.26969	0.075	D	0.88725	0.3232	10	0.46703	T	0.11	.	12.2927	0.54827	0.0:0.9148:0.0:0.0851	.	327	P31276	HXC13_HUMAN	F	327	ENSP00000243056:L327F	ENSP00000243056:L327F	L	+	1	0	HOXC13	52625293	.	.	0.997000	0.53966	0.984000	0.73092	.	.	1.530000	0.49136	0.655000	0.94253	CTC	.	.	none		0.577	HOXC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358865.2			T	54339026	C	T	54339026	3	4	39	1	0	0	0	0	1	0	0	0	7321	913	32	2	985	2	HOXC13	12	54339026	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	39415179	54339026	79512869	146	14691											
PDE1B	5153	hgsc.bcm.edu	37	chr12	54963009	54963009	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgagctgcaggagctgcggtCagatgccgtgccttcggagg	6	7	17	11	4	1	1	1	0	0	1	2	4	1	3	2	4	6	3	2	4	0	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr12:54963009C>T	ENST00000243052.3	+	4	705	c.269C>T	c.(268-270)tCa>tTa	p.S90L	PDE1B_ENST00000394277.3_Intron|PDE1B_ENST00000550620.1_Missense_Mutation_p.S70L|PDE1B_ENST00000538346.1_Missense_Mutation_p.S49L	NM_000924.3	NP_000915.1	Q01064	PDE1B_HUMAN	phosphodiesterase 1B, calmodulin-dependent	90					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)	GAGCTGCGGTCAGATGCCGTG	0.637																																					p.S90L		Atlas-SNP	.											.	PDE1B	76	.	0			c.C269T						PASS	.						67	70	69					12																	54963009		2203	4300	6503	SO:0001583	missense	5153	exon4			TGCGGTCAGATGC	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.269C>T	12.37:g.54963009C>T	ENSP00000243052:p.Ser90Leu	105	0	0		79	38	0.481013	NM_000924	Q92825|Q96KP3	Missense_Mutation	SNP	ENST00000243052.3	37	CCDS8882.1	.	.	.	.	.	.	.	.	.	.	C	37	6.389836	0.97529	.	.	ENSG00000123360	ENST00000243052;ENST00000538346;ENST00000550620	T;T;T	0.70164	-0.46;-0.43;-0.44	4.97	4.97	0.65823	-cyclic nucleotide phosphodiesterase N-terminal (1);5&apos (1);3&apos (1);	0.162433	0.42682	D	0.000677	T	0.71074	0.3297	L	0.45581	1.43	0.58432	D	0.999992	P;P	0.43701	0.779;0.815	P;P	0.52189	0.484;0.692	T	0.70285	-0.4914	10	0.40728	T	0.16	.	16.096	0.81123	0.0:1.0:0.0:0.0	.	70;90	Q01064-2;Q01064	.;PDE1B_HUMAN	L	90;49;70	ENSP00000243052:S90L;ENSP00000442559:S49L;ENSP00000448519:S70L	ENSP00000243052:S90L	S	+	2	0	PDE1B	53249276	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	7.653000	0.83643	2.459000	0.83118	0.655000	0.94253	TCA	.	.	none		0.637	PDE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406203.1			T	54963009	C	T	54963009	3	4	39	1	0	0	0	0	1	0	0	0	11643	838	29	2	336	2	PDE1B	12	54963009	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	623983	54963009	78888886	147	14692											
AVIL	10677	hgsc.bcm.edu	37	chr12	58197374	58197374	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcggctggctcctggccctCggccacagtgttctcgctgc	2	10	12	17	3	1	0	0	0	1	0	5	0	2	0	3	4	1	4	3	4	0	1	rs143313987	byFrequency	TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr12:58197374C>A	ENST00000257861.3	-	14	2180	c.1750G>T	c.(1750-1752)Gag>Tag	p.E584*	AVIL_ENST00000537081.1_Nonsense_Mutation_p.E577*|AVIL_ENST00000550083.1_Intron|RNU6-1083P_ENST00000384022.1_RNA|TSFM_ENST00000548851.1_Intron|RP11-571M6.17_ENST00000602802.1_lincRNA	NM_006576.3	NP_006567.3	O75366	AVIL_HUMAN	advillin	584	Core. {ECO:0000250}.				actin filament capping (GO:0051693)|cilium morphogenesis (GO:0060271)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|positive regulation of neuron projection development (GO:0010976)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)	actin binding (GO:0003779)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(9)|ovary(1)|prostate(6)	32	Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)					TCCTGGCCCTCGGCCACAGTG	0.602											OREG0021955	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E584X		Atlas-SNP	.											.	AVIL	60	.	0			c.G1750T						PASS	.						44	40	41					12																	58197374		2203	4300	6503	SO:0001587	stop_gained	10677	exon14			GGCCCTCGGCCAC	AF041449	CCDS8959.1	12q13.11	2006-03-30				ENSG00000135407			14188	protein-coding gene	gene with protein product		613397				9664034, 12034507	Standard	NM_006576		Approved	p92, FLJ12386, ADVIL, DOC6	uc001sqj.2	O75366	OTTHUMG00000170461	ENST00000257861.3:c.1750G>T	12.37:g.58197374C>A	ENSP00000257861:p.Glu584*	101	0	0	1029	98	21	0.214286	NM_006576	B2RAU7|Q2NKM9	Nonsense_Mutation	SNP	ENST00000257861.3	37	CCDS8959.1	.	.	.	.	.	.	.	.	.	.	C	38	6.941279	0.97952	.	.	ENSG00000135407	ENST00000537081;ENST00000257861	.	.	.	4.86	3.95	0.45737	.	0.098954	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-25.788	13.9775	0.64282	0.0:0.8466:0.1534:0.0	.	.	.	.	X	577;584	.	ENSP00000257861:E584X	E	-	1	0	AVIL	56483641	1.000000	0.71417	0.982000	0.44146	0.197000	0.23852	5.839000	0.69395	1.216000	0.43427	0.561000	0.74099	GAG	C|1.000;T|0.000	.	alt		0.602	AVIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409276.1	NM_006576		A	58197374	C	A	58197374	4	1	39	1	0	0	0	0	0	1	0	0	1227	893	31	4	733	4	AVIL	12	58197374	Nonsense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	3234365	58197374	75654521	148	14693											
PTPRR	5801	hgsc.bcm.edu	37	chr12	71092083	71092083	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcgatttttagttccatgaCgcggaatatcaatttctttg	10	16	8	7	3	2	1	1	1	1	0	3	3	3	2	1	1	1	1	1	1	4	7			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr12:71092083C>T	ENST00000283228.2	-	8	1693	c.1241G>A	c.(1240-1242)cGt>cAt	p.R414H	PTPRR_ENST00000549308.1_Missense_Mutation_p.R169H|PTPRR_ENST00000378778.1_Missense_Mutation_p.R208H|PTPRR_ENST00000440835.2_Missense_Mutation_p.R169H|PTPRR_ENST00000342084.4_Missense_Mutation_p.R302H	NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	414	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				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)		AGTTCCATGACGCGGAATATC	0.348																																					p.R414H		Atlas-SNP	.											PTPRR,NS,carcinoma,0,1	PTPRR	109	1	0			c.G1241A						PASS	.						86	88	87					12																	71092083		2202	4300	6502	SO:0001583	missense	5801	exon8			CCATGACGCGGAA	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.1241G>A	12.37:g.71092083C>T	ENSP00000283228:p.Arg414His	81	0	0		84	25	0.297619	NM_002849	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Missense_Mutation	SNP	ENST00000283228.2	37	CCDS8998.1	.	.	.	.	.	.	.	.	.	.	C	17.10	3.303861	0.60305	.	.	ENSG00000153233	ENST00000440835;ENST00000283228;ENST00000378778;ENST00000342084;ENST00000549308;ENST00000550661	T;T;T;T;T;T	0.29917	1.55;1.55;1.55;1.55;1.55;1.55	5.79	5.79	0.91817	Protein-tyrosine phosphatase, receptor/non-receptor type (2);	0.245199	0.28940	N	0.013652	T	0.24812	0.0602	N	0.11756	0.17	0.34452	D	0.700805	P;P;D;P	0.58970	0.921;0.86;0.984;0.863	B;B;B;B	0.44044	0.092;0.136;0.439;0.094	T	0.21586	-1.0241	10	0.49607	T	0.09	-5.594	20.0341	0.97551	0.0:1.0:0.0:0.0	.	263;302;208;414	B7Z998;F5GXR7;Q15256-4;Q15256	.;.;.;PTPRR_HUMAN	H	169;414;208;302;169;169	ENSP00000391750:R169H;ENSP00000283228:R414H;ENSP00000368054:R208H;ENSP00000339605:R302H;ENSP00000446943:R169H;ENSP00000449616:R169H	ENSP00000283228:R414H	R	-	2	0	PTPRR	69378350	0.993000	0.37304	0.998000	0.56505	0.955000	0.61496	3.121000	0.50438	2.753000	0.94483	0.555000	0.69702	CGT	.	.	none		0.348	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849		T	71092083	C	T	71092083	3	4	39	1	0	0	0	0	1	0	0	0	12825	536	19	1	760	1	PTPRR	12	71092083	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	12894709	71092083	62759812	149	14694											
ZFC3H1	196441	hgsc.bcm.edu	37	chr12	72038798	72038798	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccattttttactggctgactGaagagccaaaaggcgaagct	12	10	10	9	1	0	3	0	2	0	1	0	4	0	3	2	2	3	2	2	2	5	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr12:72038798G>A	ENST00000378743.3	-	4	1496	c.1138C>T	c.(1138-1140)Cag>Tag	p.Q380*		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	380					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						CTGGCTGACTGAAGAGCCAAA	0.333																																					p.Q380X		Atlas-SNP	.											.	ZFC3H1	172	.	0			c.C1138T						PASS	.						100	87	91					12																	72038798		1825	4087	5912	SO:0001587	stop_gained	196441	exon4			CTGACTGAAGAGC	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.1138C>T	12.37:g.72038798G>A	ENSP00000368017:p.Gln380*	469	0	0		376	118	0.31383	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Nonsense_Mutation	SNP	ENST00000378743.3	37	CCDS41813.1	.	.	.	.	.	.	.	.	.	.	G	37	6.417400	0.97550	.	.	ENSG00000133858	ENST00000378743	.	.	.	5.58	5.58	0.84498	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	.	19.5809	0.95467	0.0:0.0:1.0:0.0	.	.	.	.	X	380	.	ENSP00000368017:Q380X	Q	-	1	0	ZFC3H1	70325065	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	8.519000	0.90563	2.629000	0.89072	0.650000	0.86243	CAG	.	.	none		0.333	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982		A	72038798	G	A	72038798	4	1	39	1	0	0	0	0	0	1	0	0	17648	1299	45	2	4959	2	ZFC3H1	12	72038798	Nonsense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	946715	72038798	61813097	150	14695											
LRRIQ1	84125	hgsc.bcm.edu	37	chr12	85449643	85449643	+	Frame_Shift_Del	DEL	A	A	-																															agcaaaaggaagaggaaaggAaaaggagagaaaaagaatat																										TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr12:85449643delA	ENST00000393217.2	+	8	1133	c.1072delA	c.(1072-1074)aaafs	p.K358fs		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	358	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)		agaggaaaggaaaaggagaga	0.318																																					p.R357fs		Pindel,Atlas-Indel	.											.	LRRIQ1	512	.	0			c.1071delG						PASS	.						19	21	20					12																	85449643		2186	4268	6454	SO:0001589	frameshift_variant	84125	exon8			.	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.1072delA	12.37:g.85449643delA	ENSP00000376910:p.Lys358fs	110	0	.		96	16	0.167	NM_001079910	Q567P4|Q9BS17|Q9HA36	Frame_Shift_Del	DEL	ENST00000393217.2	37	CCDS41816.1																																																																																			.	.	none		0.318	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		-	85449643	A	-	85449643	7	5	39	1	0	1	0	1	0	0	0	0	9038	247	9	0	1098	0	LRRIQ1	12	85449643	Frame_Shift_Del	DEL	A	TCGA-GS-A9TW-01A-11D-A382-10	13410845	85449643	48402252	151	14696											
ALX1	8092	hgsc.bcm.edu	37	chr12	85677538	85677538	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aacggaggcaccgaaccaccTtcaccagtttgcagctagag	12	6	10	13	2	1	1	1	0	0	1	1	3	1	2	4	2	4	4	4	2	3	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr12:85677538T>G	ENST00000316824.3	+	2	570	c.415T>G	c.(415-417)Ttc>Gtc	p.F139V		NM_006982.2	NP_008913.2	Q15699	ALX1_HUMAN	ALX homeobox 1	139					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)		CCGAACCACCTTCACCAGTTT	0.488																																					p.F139V		Atlas-SNP	.											.	ALX1	61	.	0			c.T415G						PASS	.						133	129	130					12																	85677538		2203	4300	6503	SO:0001583	missense	8092	exon2			ACCACCTTCACCA	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.415T>G	12.37:g.85677538T>G	ENSP00000315417:p.Phe139Val	143	0	0		118	27	0.228814	NM_006982	Q546C8|Q96FH4	Missense_Mutation	SNP	ENST00000316824.3	37	CCDS9028.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.509296	0.85282	.	.	ENSG00000180318	ENST00000316824	D	0.97186	-4.28	5.59	5.59	0.84812	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99093	0.9688	H	0.98629	4.285	0.80722	D	1	D	0.64830	0.994	D	0.68039	0.955	D	0.99097	1.0842	10	0.87932	D	0	.	16.1145	0.81295	0.0:0.0:0.0:1.0	.	139	Q15699	ALX1_HUMAN	V	139	ENSP00000315417:F139V	ENSP00000315417:F139V	F	+	1	0	ALX1	84201669	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.997000	0.88414	2.260000	0.74910	0.529000	0.55759	TTC	.	.	none		0.488	ALX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406072.1	NM_006982		G	85677538	T	G	85677538	3	3	39	1	0	0	0	0	1	0	0	0	556	1609	56	5	421	5	ALX1	12	85677538	Missense_Mutation	SNP	T	TCGA-GS-A9TW-01A-11D-A382-10	227895	85677538	48174357	152	14697											
NT5DC3	51559	hgsc.bcm.edu	37	chr12	104186994	104186994	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcctgaacaatgaccacatCgaacaggtccctccagtctt	12	8	7	14	1	1	2	0	2	1	0	4	3	3	2	4	1	3	0	4	1	3	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr12:104186994C>A	ENST00000392876.3	-	9	1007	c.967G>T	c.(967-969)Gat>Tat	p.D323Y		NM_001031701.2	NP_001026871.1	Q86UY8	NT5D3_HUMAN	5'-nucleotidase domain containing 3	323						cytosol (GO:0005829)|mitochondrion (GO:0005739)|receptor complex (GO:0043235)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.D248N(1)		NS(1)|breast(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|ovary(2)|skin(1)|stomach(2)	30						ATGACCACATCGAACAGGTCC	0.428																																					p.D323Y		Atlas-SNP	.											NT5DC3,rectum,carcinoma,0,1	NT5DC3	113	1	1	Substitution - Missense(1)	large_intestine(1)	c.G967T						PASS	.						194	204	200					12																	104186994		2203	4300	6503	SO:0001583	missense	51559	exon9			CCACATCGAACAG	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.967G>T	12.37:g.104186994C>A	ENSP00000376615:p.Asp323Tyr	176	0	0		154	42	0.272727	NM_001031701	Q9NUM7|Q9P2T2|Q9P2T3	Missense_Mutation	SNP	ENST00000392876.3	37	CCDS41824.1	.	.	.	.	.	.	.	.	.	.	C	31	5.058257	0.93846	.	.	ENSG00000111696	ENST00000392876	T	0.52057	0.68	5.99	5.99	0.97316	HAD-like domain (2);	0.000000	0.85682	D	0.000000	T	0.78898	0.4356	M	0.93638	3.44	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.83164	-0.0097	10	0.87932	D	0	-34.2755	20.4777	0.99188	0.0:1.0:0.0:0.0	.	323	Q86UY8	NT5D3_HUMAN	Y	323	ENSP00000376615:D323Y	ENSP00000376615:D323Y	D	-	1	0	NT5DC3	102711124	1.000000	0.71417	0.997000	0.53966	0.988000	0.76386	7.776000	0.85560	2.840000	0.97914	0.655000	0.94253	GAT	.	.	none		0.428	NT5DC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347118.2	NM_016575		A	104186994	C	A	104186994	3	1	39	1	0	0	0	0	1	0	0	0	10701	884	31	4	703	4	NT5DC3	12	104186994	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	18509456	104186994	29664901	153	14698											
ZCCHC8	55596	hgsc.bcm.edu	37	chr12	122962423	122962423	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgtcggcgggagatcccgctGagttgctttcattcttctgc	4	14	12	11	3	3	2	1	1	2	1	5	3	4	2	1	2	2	3	1	2	0	4			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr12:122962423G>A	ENST00000336229.4	-	13	1440	c.1310C>T	c.(1309-1311)tCa>tTa	p.S437L	ZCCHC8_ENST00000538116.1_Missense_Mutation_p.S48L|ZCCHC8_ENST00000543897.1_Missense_Mutation_p.S199L|ZCCHC8_ENST00000536306.1_Missense_Mutation_p.S199L	NM_017612.3	NP_060082.2	Q6NZY4	ZCHC8_HUMAN	zinc finger, CCHC domain containing 8	437					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)		AGATCCCGCTGAGTTGCTTTC	0.458																																					p.S437L		Atlas-SNP	.											.	ZCCHC8	56	.	0			c.C1310T						PASS	.						90	93	92					12																	122962423		1868	4103	5971	SO:0001583	missense	55596	exon13			CCCGCTGAGTTGC	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.1310C>T	12.37:g.122962423G>A	ENSP00000337313:p.Ser437Leu	130	0	0		119	31	0.260504	NM_017612	Q7L2P6|Q8N2K5|Q96SK7|Q9NSS2|Q9NSS3	Missense_Mutation	SNP	ENST00000336229.4	37		.	.	.	.	.	.	.	.	.	.	G	9.319	1.057609	0.19907	.	.	ENSG00000033030	ENST00000536306;ENST00000543897;ENST00000336229;ENST00000538116;ENST00000542892;ENST00000544054	T;T;T;T	0.47177	0.85;0.85;0.86;0.89	5.8	0.785	0.18584	.	0.920654	0.09181	N	0.837368	T	0.33206	0.0855	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.24048	-1.0171	10	0.42905	T	0.14	0.0801	8.1198	0.30965	0.2073:0.1097:0.683:0.0	.	437	Q6NZY4	ZCHC8_HUMAN	L	199;199;437;48;48;199	ENSP00000441423:S199L;ENSP00000438993:S199L;ENSP00000337313:S437L;ENSP00000440028:S48L	ENSP00000337313:S437L	S	-	2	0	ZCCHC8	121528376	0.000000	0.05858	0.000000	0.03702	0.575000	0.36095	0.208000	0.17415	-0.120000	0.11809	0.650000	0.86243	TCA	.	.	none		0.458	ZCCHC8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017612		A	122962423	G	A	122962423	3	1	39	1	0	0	0	0	1	0	0	0	17609	1294	45	2	821	2	ZCCHC8	12	122962423	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	18775429	122962423	10889472	154	14699											
KNTC1	9735	hgsc.bcm.edu	37	chr12	123107092	123107092	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaatactttcaaatgttgaaGatgcatgcgatgaataccaa	17	11	7	6	1	1	3	1	2	0	1	1	4	1	3	1	0	4	2	1	0	7	4			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr12:123107092G>A	ENST00000333479.7	+	62	6630	c.6453G>A	c.(6451-6453)aaG>aaA	p.K2151K	KNTC1_ENST00000534995.1_Silent_p.K72K|KNTC1_ENST00000436959.3_Silent_p.K72K|KNTC1_ENST00000450485.2_Silent_p.K1076K|HCAR1_ENST00000356987.2_Intron|KNTC1_ENST00000537348.1_3'UTR	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	2151					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)		AAATGTTGAAGATGCATGCGA	0.303																																					p.K2151K		Atlas-SNP	.											.	KNTC1	182	.	0			c.G6453A						PASS	.						48	45	46					12																	123107092		1849	4087	5936	SO:0001819	synonymous_variant	9735	exon62			GTTGAAGATGCAT		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.6453G>A	12.37:g.123107092G>A		187	0	0		192	58	0.302083	NM_014708	A7E2C4|B3KSG2	Silent	SNP	ENST00000333479.7	37	CCDS45002.1																																																																																			.	.	none		0.303	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2			A	123107092	G	A	123107092	2	1	39	1	0	0	0	0	0	0	0	1	8437	933	33	2		2	KNTC1	12	123107092	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	144669	123107092	10744803	155	14700											
DNAH10	196385	hgsc.bcm.edu	37	chr12	124272402	124272402	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttggaagccaggaacaccctCaggctgtggaaaaaggccta	13	6	12	10	0	1	0	1	0	0	0	1	3	1	3	3	5	2	1	3	5	5	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr12:124272402C>T	ENST00000409039.3	+	10	1315	c.1290C>T	c.(1288-1290)ctC>ctT	p.L430L		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	430	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)		GGAACACCCTCAGGCTGTGGA	0.582																																					p.L430L		Atlas-SNP	.											.	DNAH10	888	.	0			c.C1290T						PASS	.						53	52	52					12																	124272402		2203	4300	6503	SO:0001819	synonymous_variant	196385	exon10			CACCCTCAGGCTG	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.1290C>T	12.37:g.124272402C>T		70	0	0		61	11	0.180328	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																			.	.	none		0.582	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124272402	C	T	124272402	2	4	39	1	0	0	0	0	0	0	0	1	4600	813	29	2		2	DNAH10	12	124272402	Silent	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	1165310	124272402	9579493	156	14701											
DNAH10	196385	hgsc.bcm.edu	37	chr12	124359986	124359986	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cttcaatgtgccatttccttCagaggagtctctgcatttaa	9	15	7	10	0	3	1	2	0	1	1	5	2	4	2	2	1	2	1	2	1	2	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr12:124359986C>T	ENST00000409039.3	+	46	7818	c.7793C>T	c.(7792-7794)tCa>tTa	p.S2598L		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2598	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(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)		CCATTTCCTTCAGAGGAGTCT	0.443																																					p.S2598L		Atlas-SNP	.											.	DNAH10	888	.	0			c.C7793T						PASS	.						130	120	123					12																	124359986		1884	4112	5996	SO:0001583	missense	196385	exon46			TTCCTTCAGAGGA	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.7793C>T	12.37:g.124359986C>T	ENSP00000386770:p.Ser2598Leu	179	0	0		143	38	0.265734	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	C	25.6	4.652837	0.88056	.	.	ENSG00000197653	ENST00000409039	T	0.36157	1.27	5.41	5.41	0.78517	ATPase, AAA+ type, core (1);	0.314931	0.25839	U	0.027979	T	0.70254	0.3203	H	0.94847	3.59	0.47621	D	0.999473	D	0.57571	0.98	P	0.62184	0.899	T	0.78800	-0.2062	10	0.66056	D	0.02	.	19.6104	0.95604	0.0:1.0:0.0:0.0	.	2598	Q8IVF4	DYH10_HUMAN	L	2598	ENSP00000386770:S2598L	ENSP00000386770:S2598L	S	+	2	0	DNAH10	122925939	0.989000	0.36119	0.924000	0.36721	0.866000	0.49608	3.370000	0.52372	2.702000	0.92279	0.558000	0.71614	TCA	.	.	none		0.443	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3			T	124359986	C	T	124359986	3	4	39	1	0	0	0	0	1	0	0	0	4600	838	29	2	7975	2	DNAH10	12	124359986	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	87584	124359986	9491909	157	14702											
PABPC3	5042	hgsc.bcm.edu	37	chr13	25672209	25672209	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccagaaagcagttaacagtGctaccggtgttccaactgtt	11	10	9	11	1	0	1	0	0	0	1	1	1	1	1	3	1	5	5	3	1	4	4			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr13:25672209G>A	ENST00000281589.3	+	1	1910	c.1873G>A	c.(1873-1875)Gct>Act	p.A625T		NM_030979.2	NP_112241.2	Q9H361	PABP3_HUMAN	poly(A) binding protein, cytoplasmic 3	625					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)		AGTTAACAGTGCTACCGGTGT	0.428																																					p.A625T		Atlas-SNP	.											.	PABPC3	129	.	0			c.G1873A						PASS	.						99	106	104					13																	25672209		2203	4300	6503	SO:0001583	missense	5042	exon1			AACAGTGCTACCG	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.1873G>A	13.37:g.25672209G>A	ENSP00000281589:p.Ala625Thr	52	0	0		48	21	0.4375	NM_030979	Q8NHV0|Q9H086	Missense_Mutation	SNP	ENST00000281589.3	37	CCDS9311.1	.	.	.	.	.	.	.	.	.	.	G	9.328	1.059714	0.19987	.	.	ENSG00000151846	ENST00000281589	T	0.42131	0.98	0.875	0.875	0.19130	Polyadenylate-binding protein/Hyperplastic disc protein (1);	0.289642	0.23338	U	0.049266	T	0.19565	0.0470	N	0.08118	0	0.25795	N	0.984574	B	0.02656	0.0	B	0.04013	0.001	T	0.15983	-1.0418	10	0.42905	T	0.14	.	7.5489	0.27783	0.0:0.0:1.0:0.0	.	625	Q9H361	PABP3_HUMAN	T	625	ENSP00000281589:A625T	ENSP00000281589:A625T	A	+	1	0	PABPC3	24570209	0.671000	0.27521	0.772000	0.31596	0.202000	0.24057	2.323000	0.43823	0.759000	0.33084	0.313000	0.20887	GCT	.	.	none		0.428	PABPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044220.2	NM_030979		A	25672209	G	A	25672209	3	1	39	1	0	0	0	0	1	0	0	0	11374	1319	46	2	1875	2	PABPC3	13	25672209	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10		25672209	89497669	158	14703											
DCLK1	9201	hgsc.bcm.edu	37	chr13	36428729	36428729	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgactaccaggggttccattAactagaaatacaaagaatca	17	9	7	8	0	1	3	1	1	0	2	2	3	2	3	2	2	3	1	2	2	7	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr13:36428729A>G	ENST00000360631.3	-	6	1153	c.942T>C	c.(940-942)gtT>gtC	p.V314V	DCLK1_ENST00000460982.1_5'UTR|DCLK1_ENST00000255448.4_Splice_Site_p.V314V|DCLK1_ENST00000379892.4_Splice_Site_p.V314V|DCLK1_ENST00000379893.1_Splice_Site_p.V7V			O15075	DCLK1_HUMAN	doublecortin-like kinase 1	314	Pro/Ser-rich.				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)		GGGTTCCATTAACTAGAAATA	0.453																																					p.V314V		Atlas-SNP	.											.	DCLK1	350	.	0			c.T942C						PASS	.						74	74	74					13																	36428729		2203	4300	6503	SO:0001630	splice_region_variant	9201	exon6			TCCATTAACTAGA	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.941-1T>C	13.37:g.36428729A>G		111	0	0		82	21	0.256098	NM_004734	B7Z3E9|Q5VZY8|Q5VZZ0|Q5VZZ1	Silent	SNP	ENST00000360631.3	37																																																																																				.	.	none		0.453	DCLK1-010	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000044487.1	NM_004734	Silent	G	36428729	A	G	36428729	5	3	39	1	0	0	0	0	0	0	1	0	4293	376	13	3	1299	3	DCLK1	13	36428729	Splice_Site	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	10756520	36428729	78741149	159	14704											
FREM2	341640	hgsc.bcm.edu	37	chr13	39262600	39262600	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagggctacttggtgagcacCgatgatcgcagcctgcccct	7	8	12	14	2	0	2	0	2	0	0	1	3	0	2	4	2	4	3	4	2	1	2	rs558517957		TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr13:39262600C>T	ENST00000280481.7	+	1	1335	c.1119C>T	c.(1117-1119)acC>acT	p.T373T		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	373					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)		TGGTGAGCACCGATGATCGCA	0.582																																					p.T373T		Atlas-SNP	.											.	FREM2	385	.	0			c.C1119T						PASS	.						107	104	105					13																	39262600		2203	4300	6503	SO:0001819	synonymous_variant	341640	exon1			GAGCACCGATGAT	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.1119C>T	13.37:g.39262600C>T		61	0	0		56	11	0.196429	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																			.	.	none		0.582	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361		T	39262600	C	T	39262600	2	4	39	1	0	0	0	0	0	0	0	1	6053	639	23	1		1	FREM2	13	39262600	Silent	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	2833871	39262600	75907278	160	14705											
MYCBP2	23077	hgsc.bcm.edu	37	chr13	77754319	77754319	+	De_novo_Start_OutOfFrame	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgctggccagtaatccacaGgtgttagagacgaggtggga	11	8	15	7	1	0	1	0	0	0	1	1	4	1	2	2	4	1	3	2	4	2	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr13:77754319G>T	ENST00000360084.5	-	0	5054				MYCBP2_ENST00000407578.2_Silent_p.T1692T|MYCBP2_ENST00000357337.6_Silent_p.T1654T|MYCBP2_ENST00000544440.2_Silent_p.T1654T					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)		GTAATCCACAGGTGTTAGAGA	0.458																																					p.T1692T		Atlas-SNP	.											.	MYCBP2	1029	.	0			c.C5076A						PASS	.						140	136	137					13																	77754319		2203	4300	6503			23077	exon34			TCCACAGGTGTTA	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	ENST00000360084.5:c.-2650C>A	13.37:g.77754319G>T		182	0	0		206	62	0.300971	NM_015057		Silent	SNP	ENST00000360084.5	37																																																																																				.	.	none		0.458	MYCBP2-202	KNOWN	basic	protein_coding	protein_coding		NM_015057		T	77754319	G	T	77754319	1	4	39	1	0	1	0	0	0	0	0	0	10027	987	35	4		4	MYCBP2	13	77754319	De_novo_Start_OutOfFrame	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	38491719	77754319	37415559	161	14706											
SLITRK5	26050	hgsc.bcm.edu	37	chr13	88328058	88328058	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggagattgcatctaaacaatAataaactggaacttctgcga	16	10	8	7	1	2	1	0	0	2	1	2	4	2	2	0	2	5	1	0	2	7	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr13:88328058A>C	ENST00000325089.6	+	2	634	c.415A>C	c.(415-417)Aat>Cat	p.N139H	SLITRK5_ENST00000400028.3_Intron	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	139					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)					TCTAAACAATAATAAACTGGA	0.463																																					p.N139H		Atlas-SNP	.											.	SLITRK5	192	.	0			c.A415C						PASS	.						94	92	93					13																	88328058		2203	4300	6503	SO:0001583	missense	26050	exon2			AACAATAATAAAC	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.415A>C	13.37:g.88328058A>C	ENSP00000366283:p.Asn139His	149	0	0		148	29	0.195946	NM_015567	B3KNB8|B4DSH5|Q5VT81	Missense_Mutation	SNP	ENST00000325089.6	37	CCDS9465.1	.	.	.	.	.	.	.	.	.	.	A	14.76	2.630913	0.46944	.	.	ENSG00000165300	ENST00000325089	T	0.74526	-0.85	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	D	0.91216	0.7232	H	0.97896	4.1	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94065	0.7330	9	.	.	.	-10.4756	14.1162	0.65154	1.0:0.0:0.0:0.0	.	139	O94991	SLIK5_HUMAN	H	139	ENSP00000366283:N139H	.	N	+	1	0	SLITRK5	87126059	1.000000	0.71417	1.000000	0.80357	0.651000	0.38670	9.339000	0.96797	2.225000	0.72522	0.379000	0.24179	AAT	.	.	none		0.463	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3			C	88328058	A	C	88328058	3	2	39	1	0	0	0	0	1	0	0	0	14761	362	13	5	417	5	SLITRK5	13	88328058	Missense_Mutation	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	10573739	88328058	26841820	162	14707											
GPR183	1880	hgsc.bcm.edu	37	chr13	99948277	99948277	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cccacgagcccaatgatgaaGacgaggctgtaatgcagagg	13	5	13	10	2	0	4	0	2	0	2	0	6	0	4	2	2	2	3	2	2	3	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr13:99948277G>C	ENST00000376414.4	-	2	206	c.123C>G	c.(121-123)gtC>gtG	p.V41V	UBAC2_ENST00000376440.2_Intron|UBAC2_ENST00000403766.3_Intron	NM_004951.4	NP_004942.1	P32249	GP183_HUMAN	G protein-coupled receptor 183	41					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						CAATGATGAAGACGAGGCTGT	0.458																																					p.V41V		Atlas-SNP	.											GPR183,NS,carcinoma,-2,1	GPR183	38	1	0			c.C123G						scavenged	.						79	75	77					13																	99948277		2203	4300	6503	SO:0001819	synonymous_variant	1880	exon2			GATGAAGACGAGG	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.123C>G	13.37:g.99948277G>C		218	1	0.00458716		173	41	0.236994	NM_004951	B2R8N5|Q53F99|Q5JUH7	Silent	SNP	ENST00000376414.4	37	CCDS9492.1																																																																																			.	.	none		0.458	GPR183-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045582.2	NM_004951		C	99948277	G	C	99948277	2	2	39	1	0	0	0	0	0	0	0	1	6686	929	33	4		4	GPR183	13	99948277	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	11620219	99948277	15221601	163	14708											
RNASE3	6037	hgsc.bcm.edu	37	chr14	21360199	21360199	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctcataaatccaggtgcacaGaatatttcaaactgcacgta	15	10	6	10	1	2	1	2	0	0	1	3	1	3	1	1	1	3	3	1	1	6	4			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr14:21360199G>A	ENST00000304639.3	+	2	412	c.354G>A	c.(352-354)caG>caA	p.Q118Q		NM_002935.2	NP_002926.2	P12724	ECP_HUMAN	ribonuclease, RNase A family, 3	118					antibacterial humoral response (GO:0019731)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|RNA catabolic process (GO:0006401)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	endonuclease activity (GO:0004519)|nucleic acid binding (GO:0003676)|ribonuclease activity (GO:0004540)			endometrium(1)|large_intestine(1)|lung(6)|ovary(1)	9	all_cancers(95;0.00453)		OV - Ovarian serous cystadenocarcinoma(11;6.3e-09)|Epithelial(56;1.42e-07)|all cancers(55;5.48e-07)	GBM - Glioblastoma multiforme(265;0.0187)	Pranlukast(DB01411)	CAGGTGCACAGAATATTTCAA	0.468																																					p.Q118Q		Atlas-SNP	.											.	RNASE3	24	.	0			c.G354A						PASS	.						90	91	91					14																	21360199		2189	4300	6489	SO:0001819	synonymous_variant	6037	exon2			TGCACAGAATATT	X55990	CCDS9560.1	14q11.2	2014-03-13	2010-05-07		ENSG00000169397	ENSG00000169397	3.1.27.-	"Ribonucleases, RNase A"	10046	protein-coding gene	gene with protein product	"eosinophil cationic protein"	131398		RNS3		1577491	Standard	NM_002935		Approved	ECP	uc001vyj.3	P12724	OTTHUMG00000029604	ENST00000304639.3:c.354G>A	14.37:g.21360199G>A		144	0	0		129	42	0.325581	NM_002935	Q4VBC1|Q8WTP7|Q8WZ62|Q9GZN9	Silent	SNP	ENST00000304639.3	37	CCDS9560.1																																																																																			.	.	none		0.468	RNASE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073795.2	NM_002935		A	21360199	G	A	21360199	2	1	39	1	0	0	0	0	0	0	0	1	13420	933	33	2		2	RNASE3	14	21360199	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10		21360199	85989341	164	14709											
HECTD1	25831	hgsc.bcm.edu	37	chr14	31598245	31598247	+	In_Frame_Del	DEL	GGA	GGA	-																															aaggtgctggtgcttgcactGgaagatgaccctacttctgt																										TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr14:31598245_31598247delGGA	ENST00000399332.1	-	25	4818_4820	c.4330_4332delTCC	c.(4330-4332)tccdel	p.S1445del	HECTD1_ENST00000553700.1_In_Frame_Del_p.S1445del	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	1445	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)	p.S1444S(1)		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)		TGCTTGCACTGGAAGATGACCCT	0.458																																					p.1444_1445del		Atlas-Indel	.											.	HECTD1	159	.	1	Substitution - coding silent(1)	lung(1)	c.4331_4333del						PASS	.																																			SO:0001651	inframe_deletion	25831	exon25			.	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.4330_4332delTCC	14.37:g.31598245_31598247delGGA	ENSP00000382269:p.Ser1445del	282	0	0		208	27	0.129808	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	In_Frame_Del	DEL	ENST00000399332.1	37	CCDS41939.1																																																																																			.	.	none		0.458	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			-	31598247	GGA	-	31598245	7	5	39	1	0	1	0	1	0	0	0	0	7048	1335	47	0	3576	0	HECTD1	14	31598245	In_Frame_Del	DEL	GGA	TCGA-GS-A9TW-01A-11D-A382-10	10238046	31598245	75751295	165	14710	189	3									
HECTD1	25831	hgsc.bcm.edu	37	chr14	31598249	31598250	+	Frame_Shift_Ins	INS	-	-	C																															gctggtgcttgcactggaagINSatgaccctacttctgtttga																										TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr14:31598249_31598250insC	ENST00000399332.1	-	25	4815_4816	c.4327_4328insG	c.(4327-4329)tctfs	p.S1443fs	HECTD1_ENST00000553700.1_Frame_Shift_Ins_p.S1443fs	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	1443	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)		TGCACTGGAAGATGACCCTACT	0.45																																					p.S1443fs		Atlas-Indel	.											.	HECTD1	159	.	0			c.4328_4329insG						PASS	.																																			SO:0001589	frameshift_variant	25831	exon25			.	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.4327_4328insG	14.37:g.31598249_31598250insC	ENSP00000382269:p.Ser1443fs	290	0	0		206	28	0.135922	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Frame_Shift_Ins	INS	ENST00000399332.1	37	CCDS41939.1																																																																																			.	.	none		0.45	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			C	31598250	-	C	31598249	7	5	39	1	0	1	1	0	0	0	0	0	7048	942	33	0	3580	0	HECTD1	14	31598249	Frame_Shift_Ins	INS	-	TCGA-GS-A9TW-01A-11D-A382-10	4	31598249	75751291	166	14711	189	3									
HECTD1	25831	hgsc.bcm.edu	37	chr14	31598253	31598253	+	Missense_Mutation	SNP	A	A	T																															ggtgcttgcactggaagatgAccctacttctgtttgaggga																										TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr14:31598253A>T	ENST00000399332.1	-	25	4812	c.4324T>A	c.(4324-4326)Tca>Aca	p.S1442T	HECTD1_ENST00000553700.1_Missense_Mutation_p.S1442T	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	1442	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)		CTGGAAGATGACCCTACTTCT	0.448																																					p.S1442T		Atlas-SNP	.											.	HECTD1	159	.	0			c.T4324A						PASS	.						144	130	134					14																	31598253		1964	4151	6115	SO:0001583	missense	25831	exon25			AAGATGACCCTAC	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.4324T>A	14.37:g.31598253A>T	ENSP00000382269:p.Ser1442Thr	280	0	0		211	34	0.161137	NM_015382	D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	37	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	A	8.231	0.804577	0.16467	.	.	ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332;ENST00000553957	T;T;T	0.39997	1.05;1.05;1.15	5.86	5.86	0.93980	.	0.808994	0.10739	U	0.639730	T	0.28067	0.0692	N	0.08118	0	0.46356	D	0.999009	B;B	0.32620	0.378;0.378	B;B	0.32211	0.142;0.142	T	0.15350	-1.0440	10	0.23891	T	0.37	-9.1577	16.5602	0.84551	1.0:0.0:0.0:0.0	.	1442;1442	D3DS86;Q9ULT8	.;HECD1_HUMAN	T	1442;1444;1442;869	ENSP00000450697:S1442T;ENSP00000382269:S1442T;ENSP00000451860:S869T	ENSP00000261312:S1444T	S	-	1	0	HECTD1	30668004	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.678000	0.91211	2.367000	0.80283	0.528000	0.53228	TCA	.	.	none		0.448	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			T	31598253	A	T	31598253	3	4	39	1	0	0	0	0	1	0	0	0	7048	275	10	5	3584	5	HECTD1	14	31598253	Missense_Mutation	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	4	31598253	75751287	167	14712	189	3									
C14orf106	55320	hgsc.bcm.edu	37	chr14	45693171	45693171	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cattccttatcctgaattaaAccaggtaagcattctaaggg	13	12	7	9	0	1	1	0	1	1	0	3	1	3	1	3	2	2	2	3	2	6	6			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr14:45693171A>G	ENST00000310806.4	-	11	3077	c.2619T>C	c.(2617-2619)ggT>ggC	p.G873G		NM_018353.4	NP_060823.3	Q6P0N0	M18BP_HUMAN	MIS18 binding protein 1	873					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						CCTGAATTAAACCAGGTAAGC	0.383																																					p.G873G		Atlas-SNP	.											.	MIS18BP1	92	.	0			c.T2619C						PASS	.						87	83	84					14																	45693171		2203	4300	6503	SO:0001819	synonymous_variant	55320	exon11			AATTAAACCAGGT	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.2619T>C	14.37:g.45693171A>G		173	0	0		140	42	0.3	NM_018353	D3DSA7|Q86V14|Q96PY4|Q9NUR5|Q9Y4X9	Silent	SNP	ENST00000310806.4	37	CCDS9684.1																																																																																			.	.	none		0.383	MIS18BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276795.2			G	45693171	A	G	45693171	2	3	39	1	0	0	0	0	0	0	0	1	1740	30	2	3		3	C14orf106	14	45693171	Silent	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	14094918	45693171	61656369	168	14713											
RPL10L	140801	hgsc.bcm.edu	37	chr14	47120688	47120688	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccgcactcgcatgtgaaaGccatctctgccacaactttt	10	10	7	14	2	1	1	0	1	1	0	3	1	1	1	3	0	4	2	3	0	2	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr14:47120688G>C	ENST00000298283.3	-	1	340	c.252C>G	c.(250-252)ggC>ggG	p.G84G		NM_080746.2	NP_542784.1	Q96L21	RL10L_HUMAN	ribosomal protein L10-like	84					spermatogenesis (GO:0007283)|translation (GO:0006412)	cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)|nucleus (GO:0005634)|polysome (GO:0005844)	structural constituent of ribosome (GO:0003735)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(20)|ovary(1)	27						GCATGTGAAAGCCATCTCTGC	0.527																																					p.G84G		Atlas-SNP	.											.	RPL10L	64	.	0			c.C252G						PASS	.						71	69	70					14																	47120688		2203	4300	6503	SO:0001819	synonymous_variant	140801	exon1			GTGAAAGCCATCT	AB063608	CCDS32071.1	14q21.2	2011-09-15			ENSG00000165496	ENSG00000165496		"L ribosomal proteins"	17976	protein-coding gene	gene with protein product						19123937	Standard	NM_080746		Approved		uc001wwg.3	Q96L21	OTTHUMG00000157869	ENST00000298283.3:c.252C>G	14.37:g.47120688G>C		113	0	0		68	20	0.294118	NM_080746	Q8IUD1	Silent	SNP	ENST00000298283.3	37	CCDS32071.1																																																																																			.	.	none		0.527	RPL10L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349819.1			C	47120688	G	C	47120688	2	2	39	1	0	0	0	0	0	0	0	1	13571	958	34	4		4	RPL10L	14	47120688	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	1427517	47120688	60228852	169	14714											
CDKL1	8814	hgsc.bcm.edu	37	chr14	50808859	50808859	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcaatactcactcaaaagccGagcaaatccaaagtcacaaa	19	6	4	12	1	4	0	4	0	0	0	5	1	5	0	2	0	3	1	2	0	7	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr14:50808859G>A	ENST00000216378.2	-	5	1092	c.448C>T	c.(448-450)Cgg>Tgg	p.R150W	CDKL1_ENST00000395834.1_Missense_Mutation_p.R150W|CDKL1_ENST00000356146.1_5'UTR	NM_001282236.1	NP_001269165.1	Q00532	CDKL1_HUMAN	cyclin-dependent kinase-like 1 (CDC2-related kinase)	149	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)					CTCAAAAGCCGAGCAAATCCA	0.328																																					p.R150W		Atlas-SNP	.											CDKL1_ENST00000395834,NS,carcinoma,0,2	CDKL1	50	2	0			c.C448T						PASS	.						120	103	109					14																	50808859		2203	4300	6503	SO:0001583	missense	8814	exon4			AAAGCCGAGCAAA	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.448C>T	14.37:g.50808859G>A	ENSP00000216378:p.Arg150Trp	134	0	0		133	43	0.323308	NM_004196	Q2M3A4|Q6QUA0|Q8WXQ5	Missense_Mutation	SNP	ENST00000216378.2	37		.	.	.	.	.	.	.	.	.	.	G	19.86	3.904913	0.72868	.	.	ENSG00000100490	ENST00000395834;ENST00000216378	T;T	0.68025	-0.3;-0.3	5.04	5.04	0.67666	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.84723	0.5535	M	0.92026	3.265	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.87607	0.2501	9	0.87932	D	0	.	14.1742	0.65529	0.0:0.0:0.85:0.15	.	821;149	Q00532-2;Q00532	.;CDKL1_HUMAN	W	150	ENSP00000379176:R150W;ENSP00000216378:R150W	ENSP00000216378:R150W	R	-	1	2	CDKL1	49878609	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.593000	0.61034	2.723000	0.93209	0.655000	0.94253	CGG	.	.	none		0.328	CDKL1-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000382103.1			A	50808859	G	A	50808859	3	1	39	1	0	0	0	0	1	0	0	0	3155	1057	37	1	652	1	CDKL1	14	50808859	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	3688171	50808859	56540681	170	14715											
TRMT5	145389	hgsc.bcm.edu	37	chr14	61446275	61446275	+	5'Flank	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggcgctgcaatgctgcccttTttagggatcgcatcaattta	8	13	10	10	2	1	0	1	0	0	0	2	1	1	1	1	2	3	4	1	2	4	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr14:61446275T>C	ENST00000267488.4	+	0	0				TRMT5_ENST00000261249.6_Missense_Mutation_p.K114R|SLC38A6_ENST00000456840.2_5'Flank|SLC38A6_ENST00000354886.2_5'Flank|RP11-193F5.1_ENST00000553946.1_RNA	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)		TGCTGCCCTTTTTAGGGATCG	0.383																																					p.K114R		Atlas-SNP	.											.	TRMT5	44	.	0			c.A341G						PASS	.						178	180	179					14																	61446275		2203	4300	6503	SO:0001631	upstream_gene_variant	57570	exon2			GCCCTTTTTAGGG	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		14.37:g.61446275T>C	Exception_encountered	282	0	0		238	28	0.117647	NM_020810	C9JWA6|Q86SY5	Missense_Mutation	SNP	ENST00000267488.4	37	CCDS9751.1	.	.	.	.	.	.	.	.	.	.	T	9.300	1.052932	0.19907	.	.	ENSG00000126814	ENST00000261249;ENST00000553903;ENST00000555420	T	0.25250	1.81	4.54	2.16	0.27623	.	0.208180	0.49916	N	0.000135	T	0.19604	0.0471	L	0.41236	1.265	0.30390	N	0.781102	B	0.06786	0.001	B	0.12837	0.008	T	0.13282	-1.0515	10	0.30078	T	0.28	-15.4659	10.5438	0.45047	0.0:0.1521:0.0:0.8479	.	114	Q32P41	TRM5_HUMAN	R	114;142;141	ENSP00000261249:K114R	ENSP00000261249:K114R	K	-	2	0	TRMT5	60516028	1.000000	0.71417	0.945000	0.38365	0.511000	0.34104	1.923000	0.40055	0.039000	0.15632	-1.139000	0.01908	AAA	.	.	none		0.383	SLC38A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276957.1			C	61446275	T	C	61446275	1	2	39	0	1	0	0	0	0	0	0	0	16582	1841	64	3		3	TRMT5	14	61446275	5'Flank	SNP	T	TCGA-GS-A9TW-01A-11D-A382-10	10637416	61446275	45903265	171	14716											
SIPA1L1	26037	hgsc.bcm.edu	37	chr14	72152170	72152172	+	In_Frame_Del	DEL	AAC	AAC	-																															agtttcccttccgaaataatAacaagtggcagaggaacgcc																										TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr14:72152170_72152172delAAC	ENST00000555818.1	+	10	3544_3546	c.3196_3198delAAC	c.(3196-3198)aacdel	p.N1066del	SIPA1L1_ENST00000537413.1_In_Frame_Del_p.N541del|SIPA1L1_ENST00000358550.2_In_Frame_Del_p.N1066del|SIPA1L1_ENST00000381232.3_In_Frame_Del_p.N1066del	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	1066					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)		CCGAAATAATAACAAGTGGCAGA	0.498																																					p.1065_1066del		Pindel,Atlas-Indel	.											.	SIPA1L1	219	.	0			c.3195_3197del						PASS	.																																			SO:0001651	inframe_deletion	26037	exon10			.	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.3196_3198delAAC	14.37:g.72152170_72152172delAAC	ENSP00000450832:p.Asn1066del	81	0	.		94	28	0.298	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	In_Frame_Del	DEL	ENST00000555818.1	37	CCDS9807.1																																																																																			.	.	none		0.498	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556		-	72152172	AAC	-	72152170	7	5	39	1	0	1	0	1	0	0	0	0	14344	362	13	0	3230	0	SIPA1L1	14	72152170	In_Frame_Del	DEL	AAC	TCGA-GS-A9TW-01A-11D-A382-10	10705895	72152170	35197370	172	14717											
KCNK13	56659	hgsc.bcm.edu	37	chr14	90650648	90650648	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gccctgccccaggagagcctGaaggatgcggggcagtgtga	8	5	17	11	1	0	3	0	2	0	1	0	5	0	4	4	4	3	1	4	4	1	0			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr14:90650648G>A	ENST00000282146.4	+	2	969	c.528G>A	c.(526-528)ctG>ctA	p.L176L		NM_022054.2	NP_071337.2	Q9HB14	KCNKD_HUMAN	potassium channel, subfamily K, member 13	176					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)				AGGAGAGCCTGAAGGATGCGG	0.617																																					p.L176L		Atlas-SNP	.											.	KCNK13	76	.	0			c.G528A						PASS	.						81	78	79					14																	90650648		2203	4300	6503	SO:0001819	synonymous_variant	56659	exon2			GAGCCTGAAGGAT	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.528G>A	14.37:g.90650648G>A		108	0	0		88	26	0.295455	NM_022054	B5TJL8|Q96E79	Silent	SNP	ENST00000282146.4	37	CCDS9889.1																																																																																			.	.	none		0.617	KCNK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411251.1	NM_022054		A	90650648	G	A	90650648	2	1	39	1	0	0	0	0	0	0	0	1	8070	1277	45	2		2	KCNK13	14	90650648	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	18498478	90650648	16698892	173	14718											
C14orf68	283600	hgsc.bcm.edu	37	chr14	100795800	100795800	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agtcgagactgcaggcagacGggcagggccagaggcgctac	10	3	17	11	3	0	3	0	0	0	3	1	4	0	3	1	4	2	4	1	4	1	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr14:100795800G>A	ENST00000361529.3	+	6	823	c.745G>A	c.(745-747)Ggg>Agg	p.G249R	SLC25A47_ENST00000557052.1_Missense_Mutation_p.G103R	NM_207117.2	NP_997000.2	Q6Q0C1	S2547_HUMAN	solute carrier family 25, member 47	249					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|prostate(1)|skin(2)|urinary_tract(1)	13						GCAGGCAGACGGGCAGGGCCA	0.657																																					p.G249R	GBM(11;1289 1351)	Atlas-SNP	.											.	SLC25A47	36	.	0			c.G745A						PASS	.						52	55	54					14																	100795800		2203	4300	6503	SO:0001583	missense	283600	exon6			GCAGACGGGCAGG		CCDS9959.1	14q32.2	2013-05-22	2010-07-19	2010-07-19	ENSG00000140107	ENSG00000140107		"Solute carriers"	20115	protein-coding gene	gene with protein product		609911	"chromosome 14 open reading frame 68"	C14orf68			Standard	NM_207117		Approved		uc001yhc.3	Q6Q0C1	OTTHUMG00000171571	ENST00000361529.3:c.745G>A	14.37:g.100795800G>A	ENSP00000354886:p.Gly249Arg	75	0	0		56	12	0.214286	NM_207117	B2RP39|Q68CL2|Q6PZD8|Q86U14	Missense_Mutation	SNP	ENST00000361529.3	37	CCDS9959.1	.	.	.	.	.	.	.	.	.	.	G	17.31	3.357420	0.61293	.	.	ENSG00000140107	ENST00000361529;ENST00000557052	T;T	0.78816	-1.21;-1.21	5.39	4.5	0.54988	Mitochondrial carrier domain (2);	0.047683	0.85682	D	0.000000	D	0.85813	0.5784	M	0.63428	1.95	0.52501	D	0.999953	D	0.89917	1.0	D	0.87578	0.998	D	0.87017	0.2126	10	0.72032	D	0.01	-2.6913	14.0535	0.64751	0.0727:0.0:0.9273:0.0	.	249	Q6Q0C1	S2547_HUMAN	R	249;103	ENSP00000354886:G249R;ENSP00000451078:G103R	ENSP00000354886:G249R	G	+	1	0	SLC25A47	99865553	1.000000	0.71417	0.609000	0.28983	0.110000	0.19582	6.251000	0.72441	1.271000	0.44313	0.561000	0.74099	GGG	.	.	none		0.657	SLC25A47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414231.1			A	100795800	G	A	100795800	3	1	39	1	0	0	0	0	1	0	0	0	1780	1116	39	1	767	1	C14orf68	14	100795800	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	10145152	100795800	6553740	174	14719											
PGBD4	161779	hgsc.bcm.edu	37	chr15	34396402	34396402	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggatggcaagaagatccggaAagaaacgcgctatttttgtg	13	9	13	6	3	0	3	0	0	0	3	1	5	1	5	1	3	1	2	1	3	5	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr15:34396402A>G	ENST00000397766.2	+	1	2129	c.1670A>G	c.(1669-1671)aAa>aGa	p.K557R	EMC7_ENST00000256545.4_5'Flank|EMC7_ENST00000532113.1_5'Flank	NM_152595.4	NP_689808.2	Q96DM1	PGBD4_HUMAN	piggyBac transposable element derived 4	557										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)		AAGATCCGGAAAGAAACGCGC	0.438																																					p.K557R		Atlas-SNP	.											.	PGBD4	58	.	0			c.A1670G						PASS	.						137	115	122					15																	34396402		2201	4298	6499	SO:0001583	missense	161779	exon1			TCCGGAAAGAAAC	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.1670A>G	15.37:g.34396402A>G	ENSP00000380872:p.Lys557Arg	41	0	0		46	14	0.304348	NM_152595	A1L487|A8K0C6|Q8N9E8	Missense_Mutation	SNP	ENST00000397766.2	37	CCDS10033.1	.	.	.	.	.	.	.	.	.	.	a	0.042	-1.280633	0.01398	.	.	ENSG00000182405	ENST00000397766	T	0.19394	2.15	0.978	-0.492	0.12041	.	0.402218	0.14585	U	0.310592	T	0.06005	0.0156	N	0.11560	0.145	0.09310	N	1	P	0.40398	0.716	B	0.35039	0.194	T	0.24621	-1.0155	10	0.02654	T	1	.	3.1695	0.06548	0.7014:0.0:0.2986:0.0	.	557	Q96DM1	PGBD4_HUMAN	R	557	ENSP00000380872:K557R	ENSP00000380872:K557R	K	+	2	0	PGBD4	32183694	0.982000	0.34865	0.004000	0.12327	0.140000	0.21249	-0.042000	0.12063	-0.140000	0.11394	0.255000	0.18592	AAA	.	.	none		0.438	PGBD4-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251522.1			G	34396402	A	G	34396402	3	3	39	1	0	0	0	0	1	0	0	0	11792	14	1	3	1672	3	PGBD4	15	34396402	Missense_Mutation	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10		34396402	68134990	175	14720											
B2M	567	hgsc.bcm.edu	37	chr15	45003781	45003782	+	Frame_Shift_Del	DEL	CT	CT	-																															ccttagctgtgctcgcgctaCtctctctttctggcctggag																										TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr15:45003781_45003782delCT	ENST00000558401.1	+	1	107_108	c.37_38delCT	c.(37-39)ctcfs	p.L13fs	B2M_ENST00000559916.1_Frame_Shift_Del_p.L13fs|B2M_ENST00000544417.1_Frame_Shift_Del_p.L13fs|PATL2_ENST00000558573.1_5'Flank	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	13					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 exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|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 T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|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)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)	p.L15fs*41(4)|p.A11fs*42(1)|p.L13F(1)		breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		GCTCGCGCTACTCTCTCTTTCT	0.614																																					p.12_13del		Atlas-Indel	.											B2M,colon,carcinoma,+1,2	B2M	99	2	6	Deletion - Frameshift(5)|Substitution - Missense(1)	large_intestine(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|skin(1)	c.36_37del						PASS	.																																			SO:0001589	frameshift_variant	567	exon1			.	AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"Immunoglobulin superfamily / C1-set domain containing"	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.37_38delCT	15.37:g.45003787_45003788delCT	ENSP00000452780:p.Leu13fs	98	0	0		57	13	0.22807	NM_004048	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Frame_Shift_Del	DEL	ENST00000558401.1	37	CCDS10113.1																																																																																			.	.	none		0.614	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048		-	45003782	CT	-	45003781	7	5	39	1	0	1	0	1	0	0	0	0	1244	565	20	0	39	0	B2M	15	45003781	Frame_Shift_Del	DEL	CT	TCGA-GS-A9TW-01A-11D-A382-10	10607379	45003781	57527611	176	14721											
UACA	55075	hgsc.bcm.edu	37	chr15	70961075	70961076	+	Frame_Shift_Ins	INS	-	-	T																															tctctttccatttctactaaINStttttttgctttctcattca																										TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr15:70961075_70961076insT	ENST00000322954.6	-	16	2132_2133	c.1947_1948insA	c.(1945-1950)aaattafs	p.L650fs	UACA_ENST00000560441.1_Frame_Shift_Ins_p.L635fs|UACA_ENST00000379983.2_Frame_Shift_Ins_p.L637fs|UACA_ENST00000539319.1_Frame_Shift_Ins_p.L541fs	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	650					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						ATTTCTACTAATTTTTTTGCTT	0.351																																					p.L650fs		Pindel,Atlas-Indel	.											.	UACA	235	.	0			c.1948_1949insA						PASS	.																																			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.1948dupA	15.37:g.70961082_70961082dupT	ENSP00000314556:p.Leu650fs	504	0	.		424	80	0.189	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Frame_Shift_Ins	INS	ENST00000322954.6	37	CCDS10235.1																																																																																			.	.	none		0.351	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			T	70961076	-	T	70961075	7	5	39	1	0	1	1	0	0	0	0	0	16839	98	4	0	2318	0	UACA	15	70961075	Frame_Shift_Ins	INS	-	TCGA-GS-A9TW-01A-11D-A382-10	25957294	70961075	31570317	177	14722											
LMAN1L	79748	hgsc.bcm.edu	37	chr15	75108518	75108518	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	acgccatcctgggcctggagGaagtgcggctgacgccatcc	7	6	14	14	3	0	1	0	1	0	0	2	3	2	3	5	4	1	1	5	4	1	0			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr15:75108518G>A	ENST00000309664.5	+	2	335	c.196G>A	c.(196-198)Gaa>Aaa	p.E66K	LMAN1L_ENST00000379709.3_Missense_Mutation_p.E66K	NM_021819.2	NP_068591.2	Q9HAT1	LMA1L_HUMAN	lectin, mannose-binding, 1 like	66	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						GGGCCTGGAGGAAGTGCGGCT	0.647																																					p.E66K		Atlas-SNP	.											.	LMAN1L	43	.	0			c.G196A						PASS	.						30	26	27					15																	75108518		2147	4214	6361	SO:0001583	missense	79748	exon2			CTGGAGGAAGTGC	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.196G>A	15.37:g.75108518G>A	ENSP00000310431:p.Glu66Lys	44	0	0		31	15	0.483871	NM_021819	Q6UWN2	Missense_Mutation	SNP	ENST00000309664.5	37	CCDS10270.1	.	.	.	.	.	.	.	.	.	.	G	21.8	4.201208	0.79015	.	.	ENSG00000140506	ENST00000309664;ENST00000379709	T;T	0.62639	0.01;0.01	5.49	5.49	0.81192	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.073354	0.56097	D	0.000040	T	0.75975	0.3923	L	0.61218	1.895	0.42178	D	0.99167	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	T	0.75393	-0.3333	10	0.42905	T	0.14	.	14.8695	0.70444	0.0:0.0:1.0:0.0	.	66;66	Q9HAT1-3;Q9HAT1	.;LMA1L_HUMAN	K	66	ENSP00000310431:E66K;ENSP00000369031:E66K	ENSP00000310431:E66K	E	+	1	0	LMAN1L	72895571	1.000000	0.71417	0.993000	0.49108	0.978000	0.69477	2.160000	0.42348	2.596000	0.87737	0.484000	0.47621	GAA	.	.	none		0.647	LMAN1L-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286397.4			A	75108518	G	A	75108518	3	1	39	1	0	0	0	0	1	0	0	0	8846	1175	41	2	202	2	LMAN1L	15	75108518	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	4147443	75108518	27422874	178	14723											
KIAA1024	23251	hgsc.bcm.edu	37	chr15	79749276	79749276	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aaaggaatatcttcaaagagGattttcacaatttgatggca	16	12	8	5	0	3	2	2	1	1	1	3	4	3	4	0	3	0	1	0	3	5	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr15:79749276G>A	ENST00000305428.3	+	2	862	c.787G>A	c.(787-789)Gat>Aat	p.D263N		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	263						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						CTTCAAAGAGGATTTTCACAA	0.493																																					p.D263N		Atlas-SNP	.											KIAA1024,NS,carcinoma,0,1	KIAA1024	146	1	0			c.G787A						PASS	.						75	85	81					15																	79749276		2196	4293	6489	SO:0001583	missense	23251	exon2			AAAGAGGATTTTC	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.787G>A	15.37:g.79749276G>A	ENSP00000307461:p.Asp263Asn	190	0	0		138	18	0.130435	NM_015206	A7MD43	Missense_Mutation	SNP	ENST00000305428.3	37	CCDS32306.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.003181	0.74932	.	.	ENSG00000169330	ENST00000305428	T	0.38240	1.15	5.29	5.29	0.74685	.	0.049295	0.85682	D	0.000000	T	0.53417	0.1795	M	0.71581	2.175	0.58432	D	0.999997	D	0.59767	0.986	P	0.53954	0.738	T	0.54009	-0.8357	9	.	.	.	.	18.9224	0.92530	0.0:0.0:1.0:0.0	.	263	Q9UPX6	K1024_HUMAN	N	263	ENSP00000307461:D263N	.	D	+	1	0	KIAA1024	77536331	1.000000	0.71417	0.995000	0.50966	0.785000	0.44390	7.146000	0.77373	2.454000	0.82982	0.591000	0.81541	GAT	.	.	none		0.493	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206		A	79749276	G	A	79749276	3	1	39	1	0	0	0	0	1	0	0	0	8214	1174	41	2	789	2	KIAA1024	15	79749276	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	4640758	79749276	22782116	179	14724											
ABHD2	11057	hgsc.bcm.edu	37	chr15	89694933	89694933	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccaccgttgatctgggggAaaagtggacacatccagaca	12	8	11	10	1	1	2	0	1	1	1	3	4	3	4	3	3	0	1	3	3	2	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr15:89694933A>G	ENST00000352732.5	+	4	740	c.220A>G	c.(220-222)Aaa>Gaa	p.K74E	ABHD2_ENST00000565973.1_Missense_Mutation_p.K74E|ABHD2_ENST00000355100.3_Missense_Mutation_p.K74E	NM_152924.4	NP_690888.1	P08910	ABHD2_HUMAN	abhydrolase domain containing 2	74					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)					GATCTGGGGGAAAAGTGGACA	0.458																																					p.K74E	Colon(11;252 417 24570 33239 41878)	Atlas-SNP	.											.	ABHD2	55	.	0			c.A220G						PASS	.						147	133	138					15																	89694933		2200	4299	6499	SO:0001583	missense	11057	exon8			TGGGGGAAAAGTG	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.220A>G	15.37:g.89694933A>G	ENSP00000268129:p.Lys74Glu	146	0	0		123	46	0.373984	NM_007011	Q53G48|Q53GU0|Q5FVD9|Q8TC79	Missense_Mutation	SNP	ENST00000352732.5	37	CCDS10348.1	.	.	.	.	.	.	.	.	.	.	A	22.4	4.288792	0.80914	.	.	ENSG00000140526	ENST00000352732;ENST00000355100	T;T	0.14144	2.53;2.53	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.20088	0.0483	L	0.60455	1.87	0.80722	D	1	P	0.39326	0.668	B	0.42188	0.379	T	0.01670	-1.1299	10	0.25106	T	0.35	-0.2077	16.5655	0.84588	1.0:0.0:0.0:0.0	.	74	P08910	ABHD2_HUMAN	E	74	ENSP00000268129:K74E;ENSP00000347217:K74E	ENSP00000268129:K74E	K	+	1	0	ABHD2	87495937	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.937000	0.92936	2.302000	0.77476	0.533000	0.62120	AAA	.	.	none		0.458	ABHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309074.2			G	89694933	A	G	89694933	3	3	39	1	0	0	0	0	1	0	0	0	82	247	9	3	226	3	ABHD2	15	89694933	Missense_Mutation	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	9945657	89694933	12836459	180	14725											
NR2F2	7026	hgsc.bcm.edu	37	chr15	96877601	96877615	+	In_Frame_Del	DEL	CTCACCTGGAGCGAG	CTCACCTGGAGCGAG	-																															accaggtggccctgcttcgcCtcacctggagcgagctgttt																										TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	CTCACCTGGAGCGAG	CTCACCTGGAGCGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr15:96877601_96877615delCTCACCTGGAGCGAG	ENST00000394166.3	+	2	2128_2142	c.739_753delCTCACCTGGAGCGAG	c.(739-753)ctcacctggagcgagdel	p.LTWSE247del	MIR1469_ENST00000410719.1_RNA|NR2F2_ENST00000453270.2_In_Frame_Del_p.LTWSE94del|NR2F2_ENST00000394171.2_In_Frame_Del_p.LTWSE94del|NR2F2_ENST00000421109.2_In_Frame_Del_p.LTWSE114del	NM_021005.3	NP_066285.1	P24468	COT2_HUMAN	nuclear receptor subfamily 2, group F, member 2	247	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)			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)			CCTGCTTCGCCTCACCTGGAGCGAGCTGTTTGTGT	0.688																																					p.246_251del		Pindel,Atlas-Indel	.											.	NR2F2	35	.	0			c.738_752del						PASS	.																																			SO:0001651	inframe_deletion	7026	exon2			.	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.739_753delCTCACCTGGAGCGAG	15.37:g.96877601_96877615delCTCACCTGGAGCGAG	ENSP00000377721:p.Leu247_Glu251del	74	0	.		55	11	0.2	NM_021005	B4DQJ2|B6ZGU1|Q03754|Q3KQR7	In_Frame_Del	DEL	ENST00000394166.3	37	CCDS10375.1																																																																																			.	.	none		0.688	NR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313534.1			-	96877615	CTCACCTGGAGCGAG	-	96877601	7	5	39	1	0	1	0	1	0	0	0	0	10637	681	24	0	792	0	NR2F2	15	96877601	In_Frame_Del	DEL	CTCACCTGGAGCGAG	TCGA-GS-A9TW-01A-11D-A382-10	7182668	96877601	5653791	181	14726											
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1268451	1268451	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtgcacgccgggtggacgCggacaggcctcccttgcccc	5	5	15	16	4	0	0	0	0	0	0	1	3	1	2	5	4	2	1	5	4	0	1	rs35828403|rs139080716		TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr16:1268451C>T	ENST00000348261.5	+	33	5935	c.5687C>T	c.(5686-5688)gCg>gTg	p.A1896V	CACNA1H_ENST00000358590.4_Missense_Mutation_p.A1890V|CACNA1H_ENST00000565831.1_Missense_Mutation_p.A1890V	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1896					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)	CGGGTGGACGCGGACAGGCCT	0.692													C|||	1	0.000199681	0.0008	0.0	5008	,	,		14672	0.0		0.0	False		,,,				2504	0.0				p.A1896V		Atlas-SNP	.											.	CACNA1H	317	.	0			c.C5687T						PASS	.						28	36	33					16																	1268451		2040	4074	6114	SO:0001583	missense	8912	exon33			TGGACGCGGACAG	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.5687C>T	16.37:g.1268451C>T	ENSP00000334198:p.Ala1896Val	41	0	0		49	20	0.408163	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	5.801	0.332173	0.10956	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.96554	-4.05;-4.0	2.6	-0.801	0.10893	.	3.511550	0.00951	N	0.002976	D	0.89291	0.6673	N	0.22421	0.69	0.09310	N	1	B;B;B;B;P	0.36768	0.002;0.0;0.0;0.087;0.569	B;B;B;B;B	0.21708	0.001;0.001;0.001;0.006;0.036	D	0.83591	0.0123	10	0.49607	T	0.09	.	0.331	0.00318	0.2142:0.3259:0.193:0.2669	.	642;631;637;1890;1896	A2SX38;A2SX35;A2SX37;O95180-2;O95180	.;.;.;.;CAC1H_HUMAN	V	1896;1890	ENSP00000334198:A1896V;ENSP00000351401:A1890V	ENSP00000334198:A1896V	A	+	2	0	CACNA1H	1208452	.	.	0.000000	0.03702	0.002000	0.02628	.	.	-0.123000	0.11745	-0.643000	0.03959	GCG	C|0.999;T|0.001	0.001	strong		0.692	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		T	1268451	C	T	1268451	3	4	39	1	0	0	0	0	1	0	0	0	2547	768	27	1	5813	1	CACNA1H	16	1268451	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10		1268451	89086302	182	14727											
ZNF434	54925	hgsc.bcm.edu	37	chr16	3433530	3433530	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggatggggttttctcctcActctcccctggagaatttct	5	15	10	11	0	4	1	1	0	3	1	6	3	4	2	3	4	0	1	3	4	1	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr16:3433530A>G	ENST00000396852.4	-	7	1723	c.1416T>C	c.(1414-1416)agT>agC	p.S472S	ZSCAN32_ENST00000439568.2_Silent_p.S183S|ZSCAN32_ENST00000304926.3_Silent_p.S260S|ZSCAN32_ENST00000396846.3_Silent_p.S472S|NAA60_ENST00000576906.1_Intron	NM_001284527.1|NM_001284529.1	NP_001271456.1|NP_001271458.1	Q9NX65	ZSC32_HUMAN	zinc finger and SCAN domain containing 32	472					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)										TTTTCTCCTCACTCTCCCCTG	0.473																																					p.S260S		Atlas-SNP	.											.	.	.	.	0			c.T780C						PASS	.						108	102	104					16																	3433530		2197	4300	6497	SO:0001819	synonymous_variant	54925	exon6			CTCCTCACTCTCC	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.1416T>C	16.37:g.3433530A>G		158	0	0		124	22	0.177419	NM_017810	B4DWL5|C9JB03|Q6WMU8|Q7Z6G2|Q8NFX8|Q9BU74	Silent	SNP	ENST00000396852.4	37																																																																																				.	.	none		0.473	ZSCAN32-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000251509.2	NM_017810		G	3433530	A	G	3433530	2	3	39	1	0	0	0	0	0	0	0	1	17923	156	6	3		3	ZNF434	16	3433530	Silent	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	2165079	3433530	86921223	183	14728											
TNRC6A	27327	hgsc.bcm.edu	37	chr16	24804956	24804956	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagctctgttggtccacaagCattaagcaaatctggtaagt	12	11	9	9	0	2	0	0	0	2	0	3	0	3	0	1	2	3	5	1	2	4	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr16:24804956C>A	ENST00000395799.3	+	7	3467	c.3338C>A	c.(3337-3339)gCa>gAa	p.A1113E	TNRC6A_ENST00000315183.7_Missense_Mutation_p.A1113E	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	1113	Sufficient for interaction with AGO1 and AGO4.|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)		GGTCCACAAGCATTAAGCAAA	0.483																																					p.A1113E		Atlas-SNP	.											.	TNRC6A	171	.	0			c.C3338A						PASS	.						76	77	77					16																	24804956		2197	4300	6497	SO:0001583	missense	27327	exon7			CACAAGCATTAAG	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.3338C>A	16.37:g.24804956C>A	ENSP00000379144:p.Ala1113Glu	53	0	0		43	14	0.325581	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	37	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	C	12.98	2.099624	0.37048	.	.	ENSG00000090905	ENST00000315183;ENST00000395799	T;T	0.44083	0.93;0.93	6.06	3.07	0.35406	Argonaute hook domain (1);	0.704740	0.14503	N	0.315630	T	0.37598	0.1009	L	0.58810	1.83	0.45076	D	0.998093	B;B	0.27910	0.02;0.193	B;B	0.27608	0.06;0.081	T	0.06409	-1.0828	10	0.27082	T	0.32	0.0162	9.747	0.40453	0.0:0.7572:0.1163:0.1264	.	860;1113	Q8NDV7-2;Q8NDV7	.;TNR6A_HUMAN	E	1113	ENSP00000326900:A1113E;ENSP00000379144:A1113E	ENSP00000326900:A1113E	A	+	2	0	TNRC6A	24712457	0.103000	0.21917	0.092000	0.20876	0.896000	0.52359	0.835000	0.27531	0.444000	0.26612	0.650000	0.86243	GCA	.	.	none		0.483	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847		A	24804956	C	A	24804956	3	1	39	1	0	0	0	0	1	0	0	0	16355	710	25	4	3364	4	TNRC6A	16	24804956	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	21371426	24804956	65549797	184	14729											
NFATC2IP	84901	hgsc.bcm.edu	37	chr16	28962525	28962525	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttctggaggtcgccaccgctCgcggtgccgcggacgaggtt	4	8	16	13	7	1	0	0	0	1	0	3	3	1	2	3	5	1	2	3	5	0	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr16:28962525C>T	ENST00000320805.4	+	1	268	c.193C>T	c.(193-195)Cgc>Tgc	p.R65C	NFATC2IP_ENST00000564978.1_Intron|NFATC2IP_ENST00000562977.1_3'UTR	NM_032815.3	NP_116204.3	Q8NCF5	NF2IP_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2 interacting protein	65					cytokine production (GO:0001816)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(1)|lung(5)|ovary(2)	11						CGCCACCGCTCGCGGTGCCGC	0.687																																					p.R65C		Atlas-SNP	.											.	NFATC2IP	24	.	0			c.C193T						PASS	.						7	6	6					16																	28962525		1747	3277	5024	SO:0001583	missense	84901	exon1			ACCGCTCGCGGTG	AK074761	CCDS10645.1	16p11.2	2010-09-13			ENSG00000176953	ENSG00000176953			25906	protein-coding gene	gene with protein product		614525				15698469	Standard	NM_032815		Approved	FLJ14639, NIP45, RAD60, ESC2	uc002dru.3	Q8NCF5	OTTHUMG00000097763	ENST00000320805.4:c.193C>T	16.37:g.28962525C>T	ENSP00000324792:p.Arg65Cys	175	0	0		182	25	0.137363	NM_032815	B7Z4G5|Q66K34|Q6NVK1|Q8NFR2|Q96ST9	Missense_Mutation	SNP	ENST00000320805.4	37	CCDS10645.1	.	.	.	.	.	.	.	.	.	.	C	4.485	0.089866	0.08632	.	.	ENSG00000176953	ENST00000320805	T	0.21031	2.03	2.95	-3.58	0.04597	.	2.704170	0.02280	N	0.069349	T	0.11793	0.0287	N	0.17474	0.49	0.09310	N	0.999995	B;B	0.09022	0.002;0.002	B;B	0.04013	0.001;0.001	T	0.22173	-1.0224	10	0.39692	T	0.17	.	3.5809	0.07952	0.189:0.2928:0.0:0.5182	.	65;65	B7Z8Y9;Q8NCF5	.;NF2IP_HUMAN	C	65	ENSP00000324792:R65C	ENSP00000324792:R65C	R	+	1	0	NFATC2IP	28870026	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.829000	0.04415	-0.514000	0.06488	-0.459000	0.05422	CGC	.	.	none		0.687	NFATC2IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214999.2	NM_032815		T	28962525	C	T	28962525	3	4	39	1	0	0	0	0	1	0	0	0	10372	884	31	1	195	1	NFATC2IP	16	28962525	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	4157569	28962525	61392228	185	14730											
CX3CL1	6376	hgsc.bcm.edu	37	chr16	57416809	57416809	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gccttccttggcctcctcttCtgcctgggggtggccatgtt	1	14	12	14	0	2	0	0	0	2	0	4	0	4	0	6	4	1	1	6	4	0	4			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr16:57416809C>G	ENST00000006053.6	+	3	1170	c.1059C>G	c.(1057-1059)ttC>ttG	p.F353L	CX3CL1_ENST00000563383.1_Missense_Mutation_p.F359L|CX3CL1_ENST00000565912.1_Missense_Mutation_p.F315L	NM_002996.3	NP_002987.1	P78423	X3CL1_HUMAN	chemokine (C-X3-C motif) ligand 1	353					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						GCCTCCTCTTCTGCCTGGGGG	0.672																																					p.F353L		Atlas-SNP	.											.	CX3CL1	27	.	0			c.C1059G						PASS	.						51	55	53					16																	57416809		2198	4300	6498	SO:0001583	missense	6376	exon3			CCTCTTCTGCCTG	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.1059C>G	16.37:g.57416809C>G	ENSP00000006053:p.Phe353Leu	48	0	0		39	11	0.282051	NM_002996	O00672	Missense_Mutation	SNP	ENST00000006053.6	37	CCDS10779.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.380265	0.82682	.	.	ENSG00000006210	ENST00000006053	T	0.13778	2.56	5.19	4.14	0.48551	.	0.352416	0.20775	N	0.085910	T	0.22475	0.0542	L	0.36672	1.1	0.36879	D	0.889303	D	0.76494	0.999	D	0.78314	0.991	T	0.06534	-1.0821	10	0.87932	D	0	-9.3444	5.7989	0.18401	0.0:0.8319:0.0:0.1681	.	353	P78423	X3CL1_HUMAN	L	353	ENSP00000006053:F353L	ENSP00000006053:F353L	F	+	3	2	CX3CL1	55974310	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	0.420000	0.21263	2.412000	0.81896	0.558000	0.71614	TTC	.	.	none		0.672	CX3CL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257345.3	NM_002996		G	57416809	C	G	57416809	3	3	39	1	0	0	0	0	1	0	0	0	4076	912	32	4	1069	4	CX3CL1	16	57416809	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	28454284	57416809	32937944	186	14731											
BANP	54971	hgsc.bcm.edu	37	chr16	88039846	88039846	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagagcatcgggagcaacgtCacgctcatcaccctgaactc	11	6	9	15	3	3	2	3	1	0	1	5	3	3	3	1	1	4	3	1	1	2	0			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr16:88039846C>T	ENST00000393207.1	+	6	827	c.606C>T	c.(604-606)gtC>gtT	p.V202V	BANP_ENST00000538234.1_Silent_p.V210V|BANP_ENST00000355022.4_Silent_p.V171V|BANP_ENST00000393208.2_Silent_p.V171V|BANP_ENST00000355163.5_Silent_p.V177V|BANP_ENST00000479780.2_Silent_p.V171V|BANP_ENST00000286122.7_Silent_p.V202V	NM_001173543.1	NP_001167014.1	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein	202	Interaction with CUX1 and HDAC1. {ECO:0000250}.				cell cycle (GO:0007049)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of protein catabolic process (GO:0042177)|protein localization to nucleus (GO:0034504)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.00551)		GGAGCAACGTCACGCTCATCA	0.582																																					p.V210V		Atlas-SNP	.											.	BANP	67	.	0			c.C630T						PASS	.						78	78	78					16																	88039846		2198	4300	6498	SO:0001819	synonymous_variant	54971	exon6			CAACGTCACGCTC	AK094158	CCDS10966.2, CCDS42215.1, CCDS54052.1, CCDS54053.1, CCDS54054.1	16q24	2012-11-22			ENSG00000172530	ENSG00000172530		"BEN domain containing"	13450	protein-coding gene	gene with protein product	"BEN domain containing 1"	611564				10940556, 10950932	Standard	NM_017869		Approved	SMARBP1, SMAR1, FLJ20538, DKFZp761H172, FLJ10177, BEND1	uc010vow.2	Q8N9N5	OTTHUMG00000137678	ENST00000393207.1:c.606C>T	16.37:g.88039846C>T		57	0	0		58	15	0.258621	NM_001173542	A8MU25|A8MX25|B2RCF7|B4DNJ9|F5GZM0|Q96GJ7|Q9NWY1	Silent	SNP	ENST00000393207.1	37	CCDS54054.1																																																																																			.	.	none		0.582	BANP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269166.1	NM_017869		T	88039846	C	T	88039846	2	4	39	1	0	0	0	0	0	0	0	1	1310	813	29	2		2	BANP	16	88039846	Silent	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	30623037	88039846	2314907	187	14732											
CBFA2T3	863	hgsc.bcm.edu	37	chr16	89043112	89043112	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgcggagcagccggcagatGccaggaggccgctctccagc	7	4	16	14	3	1	1	0	0	1	1	2	3	1	3	4	4	5	3	4	4	0	0			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr16:89043112G>A	ENST00000268679.4	-	1	500	c.104C>T	c.(103-105)gCa>gTa	p.A35V	CBFA2T3_ENST00000436887.2_Missense_Mutation_p.A35V|CBFA2T3_ENST00000448839.1_Missense_Mutation_p.A35V|CBFA2T3_ENST00000360302.2_5'UTR	NM_005187.5	NP_005178.4	O75081	MTG16_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 3	35	Mediates interaction with PDE7A (in isoform 2).|Mediates localization to the nucleus. {ECO:0000250}.|Required for nucleolar targeting (in isoform 1).				cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	17				BRCA - Breast invasive adenocarcinoma(80;0.0275)		GCCGGCAGATGCCAGGAGGCC	0.697			T	RUNX1	AML																																p.A35V		Atlas-SNP	.		Dom	yes		16	16q24	863	"core-binding factor, runt domain, alpha subunit 2; translocated to, 3 (MTG-16)"		L	.	CBFA2T3	47	.	0			c.C104T						PASS	.						16	16	16					16																	89043112		2158	4249	6407	SO:0001583	missense	863	exon1			GCAGATGCCAGGA	AF052213	CCDS10972.1, CCDS10973.1	16q24	2013-10-16			ENSG00000129993	ENSG00000129993		"Zinc fingers, MYND-type", "A-kinase anchor proteins"	1537	protein-coding gene	gene with protein product	"myeloid translocation gene 8 and 16b"	603870				9790752, 20150326	Standard	NM_005187		Approved	MTGR2, ZMYND4, MTG16	uc002fmm.2	O75081	OTTHUMG00000137864	ENST00000268679.4:c.104C>T	16.37:g.89043112G>A	ENSP00000268679:p.Ala35Val	102	0	0		102	38	0.372549	NM_005187	D3DX78|O60615|O60616|O60617|O75082|O75107|O75108|Q0P5Z6|Q6P5W6	Missense_Mutation	SNP	ENST00000268679.4	37	CCDS10972.1	.	.	.	.	.	.	.	.	.	.	G	1.357	-0.589751	0.03799	.	.	ENSG00000129993	ENST00000268679;ENST00000436887;ENST00000448839	T;T;T	0.45668	0.96;0.89;1.22	2.41	0.253	0.15551	.	10.454500	0.01079	U	0.004953	T	0.20129	0.0484	N	0.08118	0	0.20196	N	0.999927	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.23833	-1.0177	10	0.02654	T	1	.	5.1646	0.15079	0.3359:0.0:0.6641:0.0	.	35;35	B2RBQ7;O75081	.;MTG16_HUMAN	V	35	ENSP00000268679:A35V;ENSP00000395739:A35V;ENSP00000401254:A35V	ENSP00000268679:A35V	A	-	2	0	CBFA2T3	87570613	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.173000	0.16724	-0.072000	0.12864	-0.657000	0.03884	GCA	.	.	none		0.697	CBFA2T3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269545.2	NM_005187		A	89043112	G	A	89043112	3	1	39	1	0	0	0	0	1	0	0	0	2700	1319	46	2	1905	2	CBFA2T3	16	89043112	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	1003266	89043112	1311641	188	14733											
GEMIN4	50628	hgsc.bcm.edu	37	chr17	648463	648463	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agactgccacagaggagtttGaccacgtggttccagccttc	9	9	11	12	1	0	3	0	1	0	2	2	4	1	4	4	2	2	2	4	2	0	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr17:648463G>C	ENST00000319004.5	-	2	2938	c.2820C>G	c.(2818-2820)gtC>gtG	p.V940V	GEMIN4_ENST00000576778.1_Silent_p.V929V	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	940					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		AGAGGAGTTTGACCACGTGGT	0.582																																					p.V940V		Atlas-SNP	.											.	GEMIN4	116	.	0			c.C2820G						PASS	.						16	17	17					17																	648463		1953	4136	6089	SO:0001819	synonymous_variant	50628	exon2			GAGTTTGACCACG	AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"HCC-associated protein 1", "component of gems 4"	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.2820C>G	17.37:g.648463G>C		62	0	0		32	11	0.34375	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Silent	SNP	ENST00000319004.5	37	CCDS45559.1																																																																																			.	.	none		0.582	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721		C	648463	G	C	648463	2	2	39	1	0	0	0	0	0	0	0	1	6338	1277	45	4		4	GEMIN4	17	648463	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10		648463	80546747	189	14734											
METT10D	79066	hgsc.bcm.edu	37	chr17	2371109	2371109	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttgcacatgcaaaagtcataGattatctcagattcttcttt	12	16	5	8	0	4	2	2	0	3	2	5	2	4	2	0	0	2	2	0	0	4	6			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr17:2371109G>C	ENST00000263092.6	-	5	658	c.531C>G	c.(529-531)atC>atG	p.I177M	METTL16_ENST00000571669.2_5'UTR|METTL16_ENST00000538844.1_Intron	NM_024086.3	NP_076991.3	Q86W50	MET16_HUMAN	methyltransferase like 16	177							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						AAAAGTCATAGATTATCTCAG	0.388																																					p.I177M		Atlas-SNP	.											.	METTL16	75	.	0			c.C531G						PASS	.						119	109	112					17																	2371109		1852	4093	5945	SO:0001583	missense	79066	exon5			GTCATAGATTATC	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.531C>G	17.37:g.2371109G>C	ENSP00000263092:p.Ile177Met	228	0	0		176	37	0.210227	NM_024086	D3DTI8|Q86TE5|Q96T16|Q9BVG7	Missense_Mutation	SNP	ENST00000263092.6	37	CCDS42232.1	.	.	.	.	.	.	.	.	.	.	G	11.58	1.680847	0.29872	.	.	ENSG00000127804	ENST00000263092;ENST00000399834	T	0.16897	2.31	5.45	0.758	0.18432	.	0.104656	0.64402	D	0.000004	T	0.08268	0.0206	N	0.10916	0.065	0.80722	D	1	B;B	0.27264	0.003;0.173	B;B	0.32022	0.005;0.139	T	0.26883	-1.0090	10	0.33141	T	0.24	-15.0476	6.5513	0.22436	0.5681:0.0:0.4319:0.0	.	177;177	Q86W50-2;Q86W50	.;MET16_HUMAN	M	177	ENSP00000263092:I177M	ENSP00000263092:I177M	I	-	3	3	METTL16	2317859	0.998000	0.40836	0.999000	0.59377	0.974000	0.67602	0.534000	0.23098	0.281000	0.22233	0.491000	0.48974	ATC	.	.	none		0.388	METTL16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437653.2	NM_024086		C	2371109	G	C	2371109	3	2	39	1	0	0	0	0	1	0	0	0	9499	932	33	4	1181	4	METT10D	17	2371109	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	1722646	2371109	78824101	190	14735											
UBB	7314	hgsc.bcm.edu	37	chr17	16285294	16285294	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcccagtgacaccatcgaaAatgtgaaggccaagatccag	15	5	10	11	1	0	3	0	2	0	1	2	4	1	3	4	1	1	0	4	1	4	0			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr17:16285294A>T	ENST00000395837.1	+	2	254	c.73A>T	c.(73-75)Aat>Tat	p.N25Y	RP11-138I1.4_ENST00000583934.1_RNA|UBB_ENST00000302182.3_Missense_Mutation_p.N25Y|UBB_ENST00000535788.1_Missense_Mutation_p.N25Y|UBB_ENST00000395839.1_Missense_Mutation_p.N25Y|UBB_ENST00000578649.1_Intron	NM_001281718.1|NM_001281720.1	NP_001268647.1|NP_001268649.1	P0CG47	UBB_HUMAN	ubiquitin B	25	Ubiquitin-like 1. {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)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		CACCATCGAAAATGTGAAGGC	0.488																																					p.N25Y	Melanoma(163;1126 3406 34901)	Atlas-SNP	.											.	UBB	30	.	0			c.A73T						PASS	.						91	89	90					17																	16285294		2203	4300	6503	SO:0001583	missense	7314	exon2			ATCGAAAATGTGA		CCDS11177.1	17p12-p11.2	2010-11-25			ENSG00000170315	ENSG00000170315			12463	protein-coding gene	gene with protein product	"polyubiquitin B"	191339				2154095	Standard	NM_018955		Approved	MGC8385, FLJ25987	uc002gpx.3	P0CG47	OTTHUMG00000058987	ENST00000395837.1:c.73A>T	17.37:g.16285294A>T	ENSP00000379178:p.Asn25Tyr	111	0	0		93	20	0.215054	NM_018955	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Missense_Mutation	SNP	ENST00000395837.1	37	CCDS11177.1	.	.	.	.	.	.	.	.	.	.	A	16.07	3.018466	0.54576	.	.	ENSG00000170315	ENST00000302182;ENST00000535788;ENST00000395839;ENST00000395837	T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83	4.05	4.05	0.47172	Ubiquitin supergroup (1);Ubiquitin (2);	0.000000	0.53938	U	0.000048	D	0.84497	0.5485	M	0.67517	2.055	0.80722	D	1	B	0.33413	0.411	P	0.58331	0.837	D	0.85769	0.1354	10	0.87932	D	0	.	12.5442	0.56190	1.0:0.0:0.0:0.0	.	25	P0CG47	UBB_HUMAN	Y	25	ENSP00000304697:N25Y;ENSP00000437475:N25Y;ENSP00000379180:N25Y;ENSP00000379178:N25Y	ENSP00000304697:N25Y	N	+	1	0	UBB	16226019	1.000000	0.71417	0.998000	0.56505	0.936000	0.57629	8.435000	0.90297	1.619000	0.50296	0.524000	0.50904	AAT	.	.	none		0.488	UBB-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130459.1	NM_018955		T	16285294	A	T	16285294	3	4	39	1	0	0	0	0	1	0	0	0	16856	14	1	5	75	5	UBB	17	16285294	Missense_Mutation	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	13914185	16285294	64909916	191	14736											
PHF12	57649	hgsc.bcm.edu	37	chr17	27248804	27248804	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tttttccctgtggtttcctcCtttcttctcctcttgctaga	2	21	5	13	0	3	1	0	0	3	1	7	1	6	1	4	1	1	2	4	1	1	7			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr17:27248804C>G	ENST00000332830.4	-	5	1548	c.738G>C	c.(736-738)aaG>aaC	p.K246N	PHF12_ENST00000268756.3_Missense_Mutation_p.K246N|PHF12_ENST00000577226.1_Missense_Mutation_p.K246N|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)			TGGTTTCCTCCTTTCTTCTCC	0.433																																					p.K246N		Atlas-SNP	.											.	PHF12	69	.	0			c.G738C						PASS	.						225	202	210					17																	27248804		2203	4300	6503	SO:0001583	missense	57649	exon5			TTCCTCCTTTCTT	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.738G>C	17.37:g.27248804C>G	ENSP00000329933:p.Lys246Asn	263	0	0		235	74	0.314894	NM_020889		Missense_Mutation	SNP	ENST00000332830.4	37	CCDS32598.1	.	.	.	.	.	.	.	.	.	.	C	16.41	3.114878	0.56505	.	.	ENSG00000109118	ENST00000332830;ENST00000378879;ENST00000268756	D;D;D	0.95238	-3.62;-3.65;-3.65	5.3	0.225	0.15325	.	0.094754	0.64402	D	0.000001	D	0.95030	0.8391	L	0.55481	1.735	0.58432	D	0.999999	D;D;D;P;D	0.76494	0.998;0.999;0.998;0.875;0.998	D;D;D;B;D	0.83275	0.991;0.996;0.991;0.357;0.991	D	0.92271	0.5825	10	0.40728	T	0.16	-22.7995	9.6823	0.40078	0.0:0.5558:0.0:0.4442	.	228;246;246;246;246	B4DFE2;Q96QT6-2;Q2TAK2;C9J9G2;Q96QT6	.;.;.;.;PHF12_HUMAN	N	246	ENSP00000329933:K246N;ENSP00000368157:K246N;ENSP00000268756:K246N	ENSP00000268756:K246N	K	-	3	2	PHF12	24272930	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	1.047000	0.30367	0.186000	0.20125	-0.345000	0.07892	AAG	.	.	none		0.433	PHF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255941.1	NM_020889		G	27248804	C	G	27248804	3	3	39	1	0	0	0	0	1	0	0	0	11832	680	24	4	2346	4	PHF12	17	27248804	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	10963510	27248804	53946406	192	14737											
DNAJC7	7266	hgsc.bcm.edu	37	chr17	40128785	40128785	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aaaagaaattccctggaccaGatgctgaaagagaaaagagg	19	5	11	6	0	0	5	0	1	0	4	1	7	1	6	2	2	1	1	2	2	6	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr17:40128785G>C	ENST00000457167.4	-	14	1687	c.1451C>G	c.(1450-1452)tCt>tGt	p.S484C	DNAJC7_ENST00000316603.7_Missense_Mutation_p.S428C|DNAJC7_ENST00000426588.3_Missense_Mutation_p.S428C|CNP_ENST00000393892.3_3'UTR	NM_003315.3	NP_003306.3	Q99615	DNJC7_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 7	484					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)				CCCTGGACCAGATGCTGAAAG	0.408																																					p.S484C	Colon(63;618 1117 8600 10857 19751)	Atlas-SNP	.											.	DNAJC7	51	.	0			c.C1451G						PASS	.						129	122	124					17																	40128785		1835	4091	5926	SO:0001583	missense	7266	exon14			GGACCAGATGCTG	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.1451C>G	17.37:g.40128785G>C	ENSP00000406463:p.Ser484Cys	57	0	0		58	21	0.362069	NM_003315	Q7Z784	Missense_Mutation	SNP	ENST00000457167.4	37	CCDS45677.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.941364	0.92526	.	.	ENSG00000168259	ENST00000457167;ENST00000426588;ENST00000316603	T;T;T	0.73363	-0.74;-0.74;-0.74	5.92	5.92	0.95590	Heat shock protein DnaJ, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.72028	0.3410	N	0.08118	0	0.80722	D	1	D;D	0.67145	0.985;0.996	P;P	0.56700	0.628;0.804	T	0.78031	-0.2363	10	0.72032	D	0.01	-12.1202	20.3248	0.98698	0.0:0.0:1.0:0.0	.	428;484	Q7Z784;Q99615	.;DNJC7_HUMAN	C	484;428;428	ENSP00000406463:S484C;ENSP00000394327:S428C;ENSP00000313311:S428C	ENSP00000313311:S428C	S	-	2	0	DNAJC7	37382311	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.447000	0.97595	2.818000	0.97014	0.655000	0.94253	TCT	.	.	none		0.408	DNAJC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453366.2			C	40128785	G	C	40128785	3	2	39	1	0	0	0	0	1	0	0	0	4656	942	33	4	37	4	DNAJC7	17	40128785	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	12879981	40128785	41066425	193	14738											
TRIM25	7706	hgsc.bcm.edu	37	chr17	54969281	54969281	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgttattgtgccaggcagagAtcttggtgttgaaccactcc	8	12	11	10	1	1	2	0	1	1	1	2	3	2	2	3	2	2	3	3	2	2	4			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr17:54969281A>T	ENST00000316881.4	-	9	1722	c.1673T>A	c.(1672-1674)aTc>aAc	p.I558N	MIR3614_ENST00000581261.1_RNA|TRIM25_ENST00000537230.1_Missense_Mutation_p.I558N|TRIM25_ENST00000573108.1_5'Flank|RP11-670E13.5_ENST00000574826.1_RNA	NM_005082.4	NP_005073.2	Q14258	TRI25_HUMAN	tripartite motif containing 25	558	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)					CCAGGCAGAGATCTTGGTGTT	0.602																																					p.I558N		Atlas-SNP	.											.	TRIM25	52	.	0			c.T1673A						PASS	.						86	76	79					17																	54969281		2203	4300	6503	SO:0001583	missense	7706	exon9			GCAGAGATCTTGG	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.1673T>A	17.37:g.54969281A>T	ENSP00000323889:p.Ile558Asn	101	0	0		82	29	0.353659	NM_005082		Missense_Mutation	SNP	ENST00000316881.4	37	CCDS11591.1	.	.	.	.	.	.	.	.	.	.	A	22.5	4.296090	0.81025	.	.	ENSG00000121060	ENST00000316881;ENST00000537230	T;T	0.70399	-0.48;-0.48	4.93	4.93	0.64822	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.102449	0.42821	D	0.000652	T	0.77980	0.4212	L	0.48642	1.525	0.38408	D	0.945854	D	0.67145	0.996	D	0.65323	0.934	T	0.80790	-0.1225	10	0.51188	T	0.08	.	14.5814	0.68295	1.0:0.0:0.0:0.0	.	558	Q14258	TRI25_HUMAN	N	558	ENSP00000323889:I558N;ENSP00000445961:I558N	ENSP00000323889:I558N	I	-	2	0	TRIM25	52324280	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.136000	0.77285	1.849000	0.53698	0.418000	0.28097	ATC	.	.	none		0.602	TRIM25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440609.1	NM_005082		T	54969281	A	T	54969281	3	4	39	1	0	0	0	0	1	0	0	0	16514	333	12	5	223	5	TRIM25	17	54969281	Missense_Mutation	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	14840496	54969281	26225929	194	14739											
RNFT1	51136	hgsc.bcm.edu	37	chr17	58034594	58034594	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atgttacctacttttaatatGaggtagagtaaagccagcag	14	12	9	6	0	0	2	0	1	0	1	0	2	0	2	2	1	4	4	2	1	7	7			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr17:58034594G>A	ENST00000305783.8	-	6	1051	c.996C>T	c.(994-996)ctC>ctT	p.L332L	RNFT1_ENST00000442346.2_3'UTR|RP11-178C3.1_ENST00000591035.1_Intron	NM_016125.3	NP_057209.3	Q5M7Z0	RNFT1_HUMAN	ring finger protein, transmembrane 1	332						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	9	all_cancers(5;1.58e-13)|Breast(5;2.91e-25)|all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;7.95e-12)|all cancers(12;1.34e-10)			CTTTTAATATGAGGTAGAGTA	0.358																																					p.L332L		Atlas-SNP	.											RNFT1_ENST00000305783,NS,carcinoma,0,1	RNFT1	30	1	0			c.C996T						PASS	.						93	84	87					17																	58034594		1890	4107	5997	SO:0001819	synonymous_variant	51136	exon6			TAATATGAGGTAG	BC006971	CCDS11622.2	17q23.2	2013-01-09			ENSG00000189050	ENSG00000189050		"RING-type (C3HC4) zinc fingers"	30206	protein-coding gene	gene with protein product		615172				12477932	Standard	NM_016125		Approved	PTD016	uc002iya.3	Q5M7Z0	OTTHUMG00000148658	ENST00000305783.8:c.996C>T	17.37:g.58034594G>A		135	0	0		142	61	0.429577	NM_016125	Q8N7D0|Q96IZ9|Q9Y686	Silent	SNP	ENST00000305783.8	37	CCDS11622.2																																																																																			.	.	none		0.358	RNFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308958.1	NM_016125		A	58034594	G	A	58034594	2	1	39	1	0	0	0	0	0	0	0	1	13516	1277	45	2		2	RNFT1	17	58034594	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	3065313	58034594	23160616	195	14740											
GRIN2C	2905	hgsc.bcm.edu	37	chr17	72846900	72846900	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taggacgccatgctcccagcGccccacctgtggagggtgac	7	6	13	15	2	0	1	0	1	0	0	1	3	1	3	5	3	2	1	5	3	1	1	rs539229067	byFrequency	TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr17:72846900G>A	ENST00000293190.5	-	5	1266	c.1120C>T	c.(1120-1122)Cgc>Tgc	p.R374C	GRIN2C_ENST00000347612.4_Missense_Mutation_p.R374C|GRIN2C_ENST00000578159.1_5'Flank	NM_000835.3	NP_000826.2	Q14957	NMDE3_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2C	374					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)	TGCTCCCAGCGCCCCACCTGT	0.652													G|||	2	0.000399361	0.0015	0.0	5008	,	,		19088	0.0		0.0	False		,,,				2504	0.0				p.R374C		Atlas-SNP	.											.	GRIN2C	144	.	0			c.C1120T						PASS	.						41	26	31					17																	72846900		2203	4298	6501	SO:0001583	missense	2905	exon5			CCCAGCGCCCCAC		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.1120C>T	17.37:g.72846900G>A	ENSP00000293190:p.Arg374Cys	87	0	0		58	18	0.310345	NM_000835	B2RTT1	Missense_Mutation	SNP	ENST00000293190.5	37	CCDS32724.1	.	.	.	.	.	.	.	.	.	.	G	11.80	1.745671	0.30955	.	.	ENSG00000161509	ENST00000293190;ENST00000347612	T	0.08634	3.07	4.3	4.3	0.51218	.	0.187992	0.44483	D	0.000450	T	0.15998	0.0385	L	0.48642	1.525	0.43054	D	0.994663	D;D	0.76494	0.989;0.999	P;P	0.55871	0.676;0.786	T	0.00357	-1.1792	10	0.66056	D	0.02	.	11.8257	0.52265	0.0:0.0:0.824:0.1759	.	408;374	Q8IW23;Q14957	.;NMDE3_HUMAN	C	374;408	ENSP00000293190:R374C	ENSP00000293190:R374C	R	-	1	0	GRIN2C	70358495	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	4.479000	0.60236	2.387000	0.81309	0.555000	0.69702	CGC	.	.	none		0.652	GRIN2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103824.1			A	72846900	G	A	72846900	3	1	39	1	0	0	0	0	1	0	0	0	6790	1087	38	1	2617	1	GRIN2C	17	72846900	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	14812306	72846900	8348310	196	14741											
ENOSF1	55556	hgsc.bcm.edu	37	chr18	697244	697244	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaataggtcccttacccatCtgagctgcccatcacttgtg	10	11	7	13	0	2	1	1	1	1	0	3	1	3	1	3	1	3	1	3	1	4	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr18:697244C>A	ENST00000251101.7	-	3	393	c.305G>T	c.(304-306)aGa>aTa	p.R102I	ENOSF1_ENST00000340116.7_Missense_Mutation_p.R123I|ENOSF1_ENST00000539164.1_Missense_Mutation_p.R102I|ENOSF1_ENST00000383578.3_Intron|ENOSF1_ENST00000580982.1_Intron	NM_017512.5	NP_059982.2	Q7L5Y1	ENOF1_HUMAN	enolase superfamily member 1	102					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						CCTTACCCATCTGAGCTGCCC	0.448																																					p.R123I		Atlas-SNP	.											.	ENOSF1	44	.	0			c.G368T						PASS	.						223	228	226					18																	697244		2203	4300	6503	SO:0001583	missense	55556	exon3			ACCCATCTGAGCT	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.305G>T	18.37:g.697244C>A	ENSP00000251101:p.Arg102Ile	112	0	0		141	50	0.35461	NM_202758	A6NMP3|A8K9R5|B3KSL6|B3KXE4|D3DUH0|Q15407|Q15594|Q15595|Q6ZS08|Q9HAS5|Q9HAS6	Missense_Mutation	SNP	ENST00000251101.7	37	CCDS11822.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.947632	0.92593	.	.	ENSG00000132199	ENST00000251101;ENST00000340116;ENST00000539164	T;T;T	0.50001	0.76;0.76;0.76	5.43	5.43	0.79202	Mandelate racemase/muconate lactonizing enzyme, N-terminal (1);	0.105878	0.64402	D	0.000001	T	0.79046	0.4380	H	0.95043	3.615	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.83275	0.996;0.99;0.996	D	0.85450	0.1160	10	0.87932	D	0	.	18.1826	0.89783	0.0:1.0:0.0:0.0	.	123;147;102	A6NMP3;Q6ZS08;Q7L5Y1	.;.;ENOF1_HUMAN	I	102;123;102	ENSP00000251101:R102I;ENSP00000345974:R123I;ENSP00000446321:R102I	ENSP00000251101:R102I	R	-	2	0	ENOSF1	687244	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.550000	0.60733	2.595000	0.87683	0.644000	0.83932	AGA	.	.	none		0.448	ENOSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254312.2	NM_017512		A	697244	C	A	697244	3	1	39	1	0	0	0	0	1	0	0	0	5127	913	32	4	1082	4	ENOSF1	18	697244	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10		697244	77380004	197	14742											
YES1	7525	hgsc.bcm.edu	37	chr18	743032	743032	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgagcttcttgaaggaaagCttctggcatcattgtacctg	9	13	10	9	0	3	2	1	2	2	0	3	3	3	3	1	2	3	4	1	2	3	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr18:743032C>T	ENST00000584307.1	-	8	1116	c.946G>A	c.(946-948)Gct>Act	p.A316T	YES1_ENST00000314574.4_Missense_Mutation_p.A316T|YES1_ENST00000577961.1_Missense_Mutation_p.A321T			P07947	YES_HUMAN	YES proto-oncogene 1, Src family tyrosine kinase	316	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)	TGAAGGAAAGCTTCTGGCATC	0.323																																					p.A316T		Atlas-SNP	.											.	YES1	50	.	0			c.G946A						PASS	.						117	112	114					18																	743032		2203	4299	6502	SO:0001583	missense	7525	exon8			GGAAAGCTTCTGG	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.946G>A	18.37:g.743032C>T	ENSP00000462468:p.Ala316Thr	258	0	0		293	25	0.0853242	NM_005433	A6NLB3|D3DUH1	Missense_Mutation	SNP	ENST00000584307.1	37	CCDS11824.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.903597	0.92035	.	.	ENSG00000176105	ENST00000359834;ENST00000314574	D	0.83419	-1.72	5.78	5.78	0.91487	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	0.88235	0.6382	L	0.45581	1.43	0.80722	D	1	D	0.58268	0.982	P	0.61533	0.89	D	0.88448	0.3047	10	0.72032	D	0.01	.	20.0216	0.97506	0.0:1.0:0.0:0.0	.	316	P07947	YES_HUMAN	T	316	ENSP00000324740:A316T	ENSP00000324740:A316T	A	-	1	0	YES1	733032	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.638000	0.83328	2.735000	0.93741	0.650000	0.86243	GCT	.	.	none		0.323	YES1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440827.2	NM_005433		T	743032	C	T	743032	3	4	39	1	0	0	0	0	1	0	0	0	17489	797	28	2	705	2	YES1	18	743032	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	45788	743032	77334216	198	14743											
CDH2	1000	hgsc.bcm.edu	37	chr18	25563042	25563042	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccataccacaaacatcagcaCaaggactaggtagaaaaata	20	5	6	10	0	1	1	1	0	0	1	1	2	1	2	2	2	3	2	2	2	8	4			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr18:25563042C>A	ENST00000269141.3	-	14	2638	c.2215G>T	c.(2215-2217)Gtg>Ttg	p.V739L	CDH2_ENST00000399380.3_Missense_Mutation_p.V708L	NM_001792.3	NP_001783.2	P19022	CADH2_HUMAN	cadherin 2, type 1, N-cadherin (neuronal)	739					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						AACATCAGCACAAGGACTAGG	0.313																																					p.V739L		Atlas-SNP	.											.	CDH2	194	.	0			c.G2215T						PASS	.						91	92	92					18																	25563042		2203	4300	6503	SO:0001583	missense	1000	exon14			TCAGCACAAGGAC	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.2215G>T	18.37:g.25563042C>A	ENSP00000269141:p.Val739Leu	172	0	0		177	20	0.112994	NM_001792	A8MWK3|B0YIY6|Q14923|Q8N173	Missense_Mutation	SNP	ENST00000269141.3	37	CCDS11891.1	.	.	.	.	.	.	.	.	.	.	C	13.64	2.297604	0.40694	.	.	ENSG00000170558	ENST00000269141;ENST00000399380	T;T	0.58506	0.37;0.33	5.82	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.71953	0.3401	M	0.67700	2.07	0.80722	D	1	B;D	0.89917	0.394;1.0	B;D	0.78314	0.228;0.991	T	0.68903	-0.5286	10	0.12103	T	0.63	.	17.0408	0.86489	0.0:0.8729:0.1271:0.0	.	708;739	A8MWK3;P19022	.;CADH2_HUMAN	L	739;708	ENSP00000269141:V739L;ENSP00000382312:V708L	ENSP00000269141:V739L	V	-	1	0	CDH2	23817040	1.000000	0.71417	0.975000	0.42487	0.958000	0.62258	7.487000	0.81328	1.453000	0.47775	0.655000	0.94253	GTG	.	.	none		0.313	CDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133246.3	NM_001792		A	25563042	C	A	25563042	3	1	39	1	0	0	0	0	1	0	0	0	3107	478	17	4	517	4	CDH2	18	25563042	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	24820010	25563042	52514206	199	14744											
C18orf54	162681	hgsc.bcm.edu	37	chr18	51904570	51904570	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gcaccatttatctcgcctgaGagacctggttgatgatacga	10	11	10	10	2	1	4	0	3	1	1	2	6	1	4	3	1	1	2	3	1	2	4			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr18:51904570G>C	ENST00000300091.5	+	8	1405	c.1073G>C	c.(1072-1074)aGa>aCa	p.R358T	C18orf54_ENST00000582188.1_3'UTR|C18orf54_ENST00000578138.1_Missense_Mutation_p.R137T|C18orf54_ENST00000382911.4_Missense_Mutation_p.R519T	NM_173529.4	NP_775800.3	Q8IYD9	LAS2_HUMAN	chromosome 18 open reading frame 54	358						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)		TCTCGCCTGAGAGACCTGGTT	0.378																																					p.R358T		Atlas-SNP	.											.	C18orf54	40	.	0			c.G1073C						PASS	.						76	70	72					18																	51904570		2203	4300	6503	SO:0001583	missense	162681	exon8			GCCTGAGAGACCT	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.1073G>C	18.37:g.51904570G>C	ENSP00000300091:p.Arg358Thr	145	0	0		172	40	0.232558	NM_173529	I7HFJ6|Q6MZU3|Q6ZTL6	Missense_Mutation	SNP	ENST00000300091.5	37	CCDS11956.1	.	.	.	.	.	.	.	.	.	.	G	12.34	1.908213	0.33721	.	.	ENSG00000166845	ENST00000300091;ENST00000382911	T;T	0.38077	1.19;1.16	5.55	5.55	0.83447	.	0.064020	0.64402	D	0.000010	T	0.54854	0.1884	M	0.72118	2.19	0.26124	N	0.980503	D;D	0.89917	0.999;1.0	D;D	0.71870	0.973;0.975	T	0.54146	-0.8337	10	0.72032	D	0.01	0.02	8.9048	0.35517	0.1603:0.0:0.8397:0.0	.	519;358	Q8IYD9-2;Q8IYD9	.;CR054_HUMAN	T	358;519	ENSP00000300091:R358T;ENSP00000372368:R519T	ENSP00000300091:R358T	R	+	2	0	C18orf54	50158568	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.933000	0.56545	2.755000	0.94549	0.655000	0.94253	AGA	.	.	none		0.378	C18orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256001.1	NM_173529		C	51904570	G	C	51904570	3	2	39	1	0	0	0	0	1	0	0	0	1906	942	33	4	1099	4	C18orf54	18	51904570	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	26341528	51904570	26172678	200	14745											
MUM1	84939	hgsc.bcm.edu	37	chr19	1357062	1357062	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	agagaagaaaggaatattttCtagctgtgcaaatcctctct	14	12	8	7	0	2	2	0	0	2	2	4	4	3	3	1	1	2	2	1	1	6	4			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr19:1357062C>G	ENST00000415183.3	+	2	141	c.115C>G	c.(115-117)Cta>Gta	p.L39V	MUM1_ENST00000311401.5_5'UTR|MUM1_ENST00000591806.1_Missense_Mutation_p.L39V|MUM1_ENST00000344663.3_Missense_Mutation_p.L39V			Q2TAK8	MUM1_HUMAN	melanoma associated antigen (mutated) 1	38					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)		GGAATATTTTCTAGCTGTGCA	0.358																																					p.L39V		Atlas-SNP	.											MUM1,colon,carcinoma,0,1	MUM1	54	1	0			c.C115G						PASS	.						143	145	144					19																	1357062		2203	4300	6503	SO:0001583	missense	84939	exon3			TATTTTCTAGCTG	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.115C>G	19.37:g.1357062C>G	ENSP00000394925:p.Leu39Val	232	0	0		240	70	0.291667	NM_032853	A1L489|B5ME02|B7ZLY8|J3KQD6|Q13109|Q5XKB9|Q8N2I4|Q96A67	Missense_Mutation	SNP	ENST00000415183.3	37		.	.	.	.	.	.	.	.	.	.	C	14.00	2.404734	0.42613	.	.	ENSG00000160953	ENST00000344663;ENST00000356765;ENST00000415183	T;T	0.33865	1.39;1.39	5.2	2.95	0.34219	.	0.135832	0.32655	N	0.005814	T	0.52075	0.1712	M	0.75085	2.285	0.80722	D	1	D;D	0.76494	0.991;0.999	P;D	0.80764	0.818;0.994	T	0.52335	-0.8589	10	0.54805	T	0.06	.	5.3523	0.16042	0.2025:0.6961:0.0:0.1014	.	39;38	B7ZLY8;Q2TAK8	.;MUM1_HUMAN	V	39;65;39	ENSP00000345789:L39V;ENSP00000394925:L39V	ENSP00000345789:L39V	L	+	1	2	MUM1	1308062	0.999000	0.42202	0.971000	0.41717	0.319000	0.28217	1.134000	0.31442	2.581000	0.87130	0.655000	0.94253	CTA	.	.	none		0.358	MUM1-016	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000449510.1	NM_032853		G	1357062	C	G	1357062	3	3	39	1	0	0	0	0	1	0	0	0	9994	912	32	4	121	4	MUM1	19	1357062	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10		1357062	57771921	201	14746											
STAP2	55620	hgsc.bcm.edu	37	chr19	4333777	4333777	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccagggaatctcatctgtgaGtttctcaaatgctcccaagt	10	12	8	11	0	3	1	2	1	3	0	6	2	4	2	2	1	1	2	2	1	3	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr19:4333777G>C	ENST00000594605.1	-	3	334	c.211C>G	c.(211-213)Ctc>Gtc	p.L71V	STAP2_ENST00000600324.1_Missense_Mutation_p.L71V	NM_001013841.1	NP_001013863.1	Q9UGK3	STAP2_HUMAN	signal transducing adaptor family member 2	71	PH.					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)		TCATCTGTGAGTTTCTCAAAT	0.567																																					p.L71V		Atlas-SNP	.											.	STAP2	38	.	0			c.C211G						PASS	.						96	88	91					19																	4333777		2203	4300	6503	SO:0001583	missense	55620	exon3			CTGTGAGTTTCTC	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.211C>G	19.37:g.4333777G>C	ENSP00000471052:p.Leu71Val	74	0	0		63	15	0.238095	NM_001013841	A6NKK3|Q9NXI2	Missense_Mutation	SNP	ENST00000594605.1	37	CCDS45926.1	.	.	.	.	.	.	.	.	.	.	G	2.350	-0.349058	0.05208	.	.	ENSG00000178078	ENST00000314714;ENST00000424810	.	.	.	5.02	1.66	0.24008	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.554688	0.18063	N	0.152891	T	0.39911	0.1096	L	0.58428	1.81	0.22610	N	0.998936	B;B	0.23891	0.093;0.015	B;B	0.23419	0.033;0.046	T	0.39840	-0.9594	9	0.87932	D	0	-2.2117	5.3364	0.15959	0.1854:0.1667:0.6479:0.0	.	71;71	Q9UGK3-2;Q9UGK3	.;STAP2_HUMAN	V	71	.	ENSP00000317912:L71V	L	-	1	0	STAP2	4284777	0.990000	0.36364	0.204000	0.23530	0.006000	0.05464	1.303000	0.33470	0.170000	0.19704	-0.294000	0.09567	CTC	.	.	none		0.567	STAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458114.2	NM_001013841		C	4333777	G	C	4333777	3	2	39	1	0	0	0	0	1	0	0	0	15268	1029	36	4	1182	4	STAP2	19	4333777	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	2976715	4333777	54795206	202	14747											
ZNF266	10781	hgsc.bcm.edu	37	chr19	9524292	9524292	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tttaccacattccaggcactCaaagggcttctctccagtgt	9	12	7	13	0	2	0	1	0	1	0	5	0	4	0	3	2	1	2	3	2	2	4			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr19:9524292C>G	ENST00000592904.1	-	5	3385	c.1309G>C	c.(1309-1311)Gag>Cag	p.E437Q	ZNF266_ENST00000588933.1_Missense_Mutation_p.E437Q|ZNF266_ENST00000590306.1_Missense_Mutation_p.E437Q|ZNF266_ENST00000361151.1_Missense_Mutation_p.E437Q|ZNF266_ENST00000592292.1_Missense_Mutation_p.E437Q|ZNF266_ENST00000588221.1_Missense_Mutation_p.E437Q|ZNF266_ENST00000361451.2_Missense_Mutation_p.E437Q			Q14584	ZN266_HUMAN	zinc finger protein 266	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)			NS(1)|breast(2)|endometrium(2)|large_intestine(11)|lung(8)|ovary(1)|skin(2)|stomach(1)	28						TCCAGGCACTCAAAGGGCTTC	0.433																																					p.E437Q		Atlas-SNP	.											.	ZNF266	65	.	0			c.G1309C						PASS	.						65	62	63					19																	9524292		2203	4300	6503	SO:0001583	missense	10781	exon11			GGCACTCAAAGGG	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.1309G>C	19.37:g.9524292C>G	ENSP00000466714:p.Glu437Gln	105	0	0		100	34	0.34	NM_001271314	A0AV90|A4FU85|Q6IQ07|Q6U8A5|Q8IVG3|Q8WVX1|Q96SX9	Missense_Mutation	SNP	ENST00000592904.1	37	CCDS12213.1	.	.	.	.	.	.	.	.	.	.	C	17.27	3.347587	0.61183	.	.	ENSG00000174652	ENST00000361451;ENST00000361151	T;T	0.07444	3.19;3.19	2.53	-1.76	0.08006	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02807	0.0084	N	0.04335	-0.225	0.09310	N	1	B	0.30634	0.288	B	0.25884	0.064	T	0.39840	-0.9594	9	0.45353	T	0.12	.	1.6977	0.02866	0.1866:0.3032:0.3688:0.1413	.	437	Q14584	ZN266_HUMAN	Q	437	ENSP00000354680:E437Q;ENSP00000355047:E437Q	ENSP00000355047:E437Q	E	-	1	0	ZNF266	9385292	0.000000	0.05858	0.001000	0.08648	0.894000	0.52154	-4.155000	0.00284	-0.243000	0.09653	0.555000	0.69702	GAG	.	.	none		0.433	ZNF266-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449033.1			G	9524292	C	G	9524292	3	3	39	1	0	0	0	0	1	0	0	0	17820	835	29	4	344	4	ZNF266	19	9524292	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	5190515	9524292	49604691	203	14748											
ZNF439	90594	hgsc.bcm.edu	37	chr19	11979140	11979140	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taagcaatgtgggaaagcctTcagatctgccccaaatcttc	12	10	8	11	0	3	1	1	0	2	1	4	2	3	2	3	1	3	1	3	1	4	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr19:11979140T>C	ENST00000304030.2	+	3	1456	c.1256T>C	c.(1255-1257)tTc>tCc	p.F419S	ZNF439_ENST00000592534.1_Intron|ZNF439_ENST00000455282.1_Missense_Mutation_p.F283S	NM_152262.2	NP_689475.1	Q8NDP4	ZN439_HUMAN	zinc finger protein 439	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)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(7)|pancreas(1)|skin(2)	27						GGGAAAGCCTTCAGATCTGCC	0.453																																					p.F419S		Atlas-SNP	.											.	ZNF439	67	.	0			c.T1256C						PASS	.						70	66	68					19																	11979140		2203	4300	6503	SO:0001583	missense	90594	exon3			AAGCCTTCAGATC	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.1256T>C	19.37:g.11979140T>C	ENSP00000305077:p.Phe419Ser	101	0	0		98	20	0.204082	NM_152262	Q8IYZ7|Q96SU1	Missense_Mutation	SNP	ENST00000304030.2	37	CCDS12268.1	.	.	.	.	.	.	.	.	.	.	t	14.29	2.490541	0.44249	.	.	ENSG00000171291	ENST00000455282;ENST00000304030	T;T	0.44482	0.92;0.92	0.575	0.575	0.17374	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.63954	0.2555	M	0.88906	2.99	0.33673	D	0.611198	D	0.89917	1.0	D	0.85130	0.997	T	0.70114	-0.4961	9	0.87932	D	0	.	6.7827	0.23654	0.0:0.0:0.0:1.0	.	419	Q8NDP4	ZN439_HUMAN	S	283;419	ENSP00000395632:F283S;ENSP00000305077:F419S	ENSP00000305077:F419S	F	+	2	0	ZNF439	11840140	1.000000	0.71417	0.016000	0.15963	0.049000	0.14656	4.420000	0.59841	0.485000	0.27652	0.163000	0.16589	TTC	.	.	none		0.453	ZNF439-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344513.1			C	11979140	T	C	11979140	3	2	39	1	0	0	0	0	1	0	0	0	17926	1783	62	3	1266	3	ZNF439	19	11979140	Missense_Mutation	SNP	T	TCGA-GS-A9TW-01A-11D-A382-10	2454848	11979140	47149843	204	14749											
MLL4	9757	hgsc.bcm.edu	37	chr19	36218067	36218067	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ctttctctaggaaactactgCccgatctgtacacgctgcta	9	12	7	13	2	2	0	0	0	2	0	3	2	2	1	1	1	5	3	1	1	5	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr19:36218067C>T	ENST00000222270.7	+	15	4014	c.4014C>T	c.(4012-4014)tgC>tgT	p.C1338C	KMT2B_ENST00000607650.1_RNA|KMT2B_ENST00000420124.1_Silent_p.C1338C	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1338					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)										GAAACTACTGCCCGATCTGTA	0.527																																					p.C1338C		Atlas-SNP	.											.	MLL4	229	.	0			c.C4014T						PASS	.						41	43	42					19																	36218067		2149	4270	6419	SO:0001819	synonymous_variant	8085	exon15			CTACTGCCCGATC	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.4014C>T	19.37:g.36218067C>T		106	0	0		65	17	0.261538	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Silent	SNP	ENST00000222270.7	37	CCDS46055.1																																																																																			.	.	none		0.527	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727		T	36218067	C	T	36218067	2	4	39	1	0	0	0	0	0	0	0	1	9632	747	26	2		2	MLL4	19	36218067	Silent	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	24238927	36218067	22910916	205	14750											
NUP62	23636	hgsc.bcm.edu	37	chr19	50412090	50412090	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgcgcgtaggtcatggcggaGctggcagccgcccctgcagc	5	6	16	14	4	1	0	1	0	0	0	1	1	1	1	3	4	5	4	3	4	1	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr19:50412090G>A	ENST00000596217.1	-	2	2862	c.975C>T	c.(973-975)agC>agT	p.S325S	NUP62_ENST00000597029.1_Silent_p.S325S|IL4I1_ENST00000595948.1_Intron|NUP62_ENST00000422090.2_Silent_p.S325S|NUP62_ENST00000413454.1_Silent_p.S325S|NUP62_ENST00000352066.3_Silent_p.S325S|NUP62_ENST00000600583.1_5'Flank|IL4I1_ENST00000341114.3_Intron|NUP62_ENST00000597723.1_Intron			P37198	NUP62_HUMAN	nucleoporin 62kDa	325	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)		TCATGGCGGAGCTGGCAGCCG	0.642																																					p.S325S		Atlas-SNP	.											.	NUP62	50	.	0			c.C975T						PASS	.						33	40	38					19																	50412090		2195	4296	6491	SO:0001819	synonymous_variant	23636	exon3			GGCGGAGCTGGCA	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.975C>T	19.37:g.50412090G>A		78	0	0		44	16	0.363636	NM_153719	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	Silent	SNP	ENST00000596217.1	37	CCDS12788.1																																																																																			.	.	none		0.642	NUP62-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464991.1	NM_153719		A	50412090	G	A	50412090	2	1	39	1	0	0	0	0	0	0	0	1	10777	962	34	2		2	NUP62	19	50412090	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	14194023	50412090	8716893	206	14751											
ZNF160	90338	hgsc.bcm.edu	37	chr19	53573446	53573446	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctttccaacaccactgtgTggaatactgcttctgtactg	8	14	8	11	0	2	0	0	0	2	0	3	1	3	1	2	1	4	2	2	1	4	4			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr19:53573446T>C	ENST00000429604.1	-	7	756	c.341A>G	c.(340-342)cAc>cGc	p.H114R	ZNF160_ENST00000599056.1_Missense_Mutation_p.H114R|ZNF160_ENST00000418871.1_Missense_Mutation_p.H114R|ZNF160_ENST00000601421.1_Missense_Mutation_p.H78R	NM_001102603.1|NM_198893.2	NP_001096073.1|NP_942596.1	Q9HCG1	ZN160_HUMAN	zinc finger protein 160	114					hemopoiesis (GO:0030097)|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)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(8)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	35				GBM - Glioblastoma multiforme(134;0.02)		CACCACTGTGTGGAATACTGC	0.393																																					p.H114R		Atlas-SNP	.											.	ZNF160	75	.	0			c.A341G						PASS	.						122	116	118					19																	53573446		2203	4300	6503	SO:0001583	missense	90338	exon7			ACTGTGTGGAATA	X78928	CCDS12859.1	19q13.42	2013-01-08				ENSG00000170949		"Zinc fingers, C2H2-type", "-"	12948	protein-coding gene	gene with protein product		600398				7774943, 7865130	Standard	NM_198893		Approved	HZF5, F11, KR18, HKr18, FLJ00032, KIAA1611	uc002qar.4	Q9HCG1		ENST00000429604.1:c.341A>G	19.37:g.53573446T>C	ENSP00000406201:p.His114Arg	221	0	0		181	28	0.154696	NM_001102603	Q14589|Q504Q8|Q96JC5|Q9BVY9|Q9H7N6	Missense_Mutation	SNP	ENST00000429604.1	37	CCDS12859.1	.	.	.	.	.	.	.	.	.	.	T	7.078	0.569697	0.13560	.	.	ENSG00000170949	ENST00000429604;ENST00000418871	T;T	0.06449	3.3;3.3	2.39	1.33	0.21861	.	.	.	.	.	T	0.05181	0.0138	L	0.38175	1.15	0.23758	N	0.996924	B	0.16396	0.017	B	0.14023	0.01	T	0.42032	-0.9475	9	0.30854	T	0.27	.	5.2183	0.15354	0.0:0.1543:0.0:0.8457	.	114	Q9HCG1	ZN160_HUMAN	R	114	ENSP00000406201:H114R;ENSP00000409597:H114R	ENSP00000409597:H114R	H	-	2	0	ZNF160	58265258	0.000000	0.05858	0.003000	0.11579	0.019000	0.09904	0.037000	0.13840	0.166000	0.19597	-0.379000	0.06801	CAC	.	.	none		0.393	ZNF160-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463994.2	NM_033288		C	53573446	T	C	53573446	3	2	39	1	0	0	0	0	1	0	0	0	17754	1696	59	3	2119	3	ZNF160	19	53573446	Missense_Mutation	SNP	T	TCGA-GS-A9TW-01A-11D-A382-10	3161356	53573446	5555537	207	14752											
ZFP28	140612	hgsc.bcm.edu	37	chr19	57065996	57065996	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttaaggattcatactggggaGaagccttttgaatgtgcgga	11	12	13	5	1	1	2	1	1	0	1	1	5	1	4	1	4	3	0	1	4	4	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr19:57065996G>A	ENST00000301318.3	+	8	1913	c.1842G>A	c.(1840-1842)gaG>gaA	p.E614E	AC007228.11_ENST00000596587.1_RNA	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	614					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)		ATACTGGGGAGAAGCCTTTTG	0.428																																					p.E614E	Ovarian(124;554 1662 19430 21141 52494)	Atlas-SNP	.											.	ZFP28	99	.	0			c.G1842A						PASS	.						97	108	104					19																	57065996		2203	4300	6503	SO:0001819	synonymous_variant	140612	exon8			TGGGGAGAAGCCT		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.1842G>A	19.37:g.57065996G>A		175	0	0		137	36	0.262774	NM_020828	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Silent	SNP	ENST00000301318.3	37	CCDS12946.1																																																																																			.	.	none		0.428	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828		A	57065996	G	A	57065996	2	1	39	1	0	0	0	0	0	0	0	1	17657	933	33	2		2	ZFP28	19	57065996	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	3492550	57065996	2062987	208	14753											
PEG3	5178	hgsc.bcm.edu	37	chr19	57325865	57325865	+	Frame_Shift_Del	DEL	A	A	-																															gtaagaaatgaggtgtgagtAtaggaggacccgtactcata																										TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr19:57325865delA	ENST00000326441.9	-	10	4308	c.3945delT	c.(3943-3945)tatfs	p.Y1315fs	ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000221722.5_Intron|PEG3_ENST00000423103.2_Frame_Shift_Del_p.Y1315fs|ZIM2_ENST00000593711.1_Intron|ZIM2_ENST00000601070.1_Intron|PEG3_ENST00000598410.1_Frame_Shift_Del_p.Y1191fs|ZIM2_ENST00000391708.3_Intron|PEG3_ENST00000593695.1_Frame_Shift_Del_p.Y1189fs	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	1315					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)		AGGTGTGAGTATAGGAGGACC	0.438																																					p.T1316fs		Atlas-Indel	.											.	PEG3	414	.	0			c.3946delA						PASS	.						103	99	101					19																	57325865		2203	4300	6503	SO:0001589	frameshift_variant	5178	exon9			.	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.3945delT	19.37:g.57325865delA	ENSP00000326581:p.Tyr1315fs	142	0	0		118	23	0.194915	NM_001146184	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Frame_Shift_Del	DEL	ENST00000326441.9	37	CCDS12948.1																																																																																			.	.	none		0.438	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			-	57325865	A	-	57325865	7	5	39	1	0	1	0	1	0	0	0	0	11729	456	16	0	825	0	PEG3	19	57325865	Frame_Shift_Del	DEL	A	TCGA-GS-A9TW-01A-11D-A382-10	259869	57325865	1803118	209	14754											
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385790	58385790	+	Missense_Mutation	SNP	G	G	T																															cacattctccacattcataaGgtcttttcccagtgtgaact																								rs111727691		TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr19:58385790G>T	ENST00000435989.2	-	3	1202	c.968C>A	c.(967-969)cCt>cAt	p.P323H	ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000595295.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	323					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						ACATTCATAAGGTCTTTTCCC	0.358																																					p.P323H		Atlas-SNP	.											.	ZNF814	93	.	0			c.C968A						PASS	.						15	12	13					19																	58385790		688	1563	2251	SO:0001583	missense	730051	exon3			TCATAAGGTCTTT		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.968C>A	19.37:g.58385790G>T	ENSP00000410545:p.Pro323His	221	0	0		211	20	0.0947867	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	8.139	0.784825	0.16189	.	.	ENSG00000204514	ENST00000435989	T	0.29397	1.57	2.27	1.18	0.20946	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.57080	0.2029	M	0.90019	3.08	0.20764	N	0.999853	D	0.89917	1.0	D	0.67231	0.95	T	0.46247	-0.9205	9	0.66056	D	0.02	.	9.258	0.37595	0.0:0.0:0.7811:0.2189	.	323	B7Z6K7	ZN814_HUMAN	H	323	ENSP00000410545:P323H	ENSP00000410545:P323H	P	-	2	0	ZNF814	63077602	0.000000	0.05858	0.028000	0.17463	0.016000	0.09150	-0.439000	0.06897	0.330000	0.23485	-1.407000	0.01130	CCT	G|0.500;T|0.500	0.500	weak		0.358	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		T	58385790	G	T	58385790	3	4	39	1	0	0	0	0	1	0	0	0	18191	1000	35	4	1603	4	ZNF814	19	58385790	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	1059925	58385790	743193	210	14755	190	2									
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385793	58385793	+	Missense_Mutation	SNP	C	C	T																															attctccacattcataaggtCttttcccagtgtgaactctc																								rs113623532		TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr19:58385793C>T	ENST00000435989.2	-	3	1199	c.965G>A	c.(964-966)aGa>aAa	p.R322K	ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000595295.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	322					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						TTCATAAGGTCTTTTCCCAGT	0.358																																					p.R322K		Atlas-SNP	.											.	ZNF814	93	.	0			c.G965A						PASS	.						15	12	13					19																	58385793		687	1562	2249	SO:0001583	missense	730051	exon3			TAAGGTCTTTTCC		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.965G>A	19.37:g.58385793C>T	ENSP00000410545:p.Arg322Lys	215	0	0		205	21	0.102439	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	0.023	-1.395361	0.01175	.	.	ENSG00000204514	ENST00000435989	T	0.12361	2.69	2.27	9.47E-4	0.14044	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03608	0.0103	N	0.02225	-0.63	0.09310	N	0.999999	B	0.29301	0.241	B	0.28916	0.096	T	0.40534	-0.9558	9	0.02654	T	1	.	4.6969	0.12808	0.0:0.4166:0.0:0.5834	.	322	B7Z6K7	ZN814_HUMAN	K	322	ENSP00000410545:R322K	ENSP00000410545:R322K	R	-	2	0	ZNF814	63077605	0.000000	0.05858	0.024000	0.17045	0.009000	0.06853	-1.883000	0.01623	0.331000	0.23511	-1.381000	0.01174	AGA	C|0.500;T|0.500	0.500	weak		0.358	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		T	58385793	C	T	58385793	3	4	39	1	0	0	0	0	1	0	0	0	18191	913	32	2	1606	2	ZNF814	19	58385793	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	3	58385793	743190	211	14756	190	2									
SLC32A1	140679	hgsc.bcm.edu	37	chr20	37356863	37356863	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccgtggtcaacatctttctgGtggccaaggcgctgttgtcc	5	12	12	12	2	3	0	1	0	2	0	4	0	4	0	3	4	1	2	3	4	2	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr20:37356863G>A	ENST00000217420.1	+	2	1422	c.1159G>A	c.(1159-1161)Gtg>Atg	p.V387M		NM_080552.2	NP_542119.1	Q9H598	VIAAT_HUMAN	solute carrier family 32 (GABA vesicular transporter), member 1	387					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)	CATCTTTCTGGTGGCCAAGGC	0.622																																					p.V387M		Atlas-SNP	.											.	SLC32A1	81	.	0			c.G1159A						PASS	.						79	77	78					20																	37356863		2203	4300	6503	SO:0001583	missense	140679	exon2			TTTCTGGTGGCCA	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.1159G>A	20.37:g.37356863G>A	ENSP00000217420:p.Val387Met	100	0	0		101	27	0.267327	NM_080552	Q8N489	Missense_Mutation	SNP	ENST00000217420.1	37	CCDS13307.1	.	.	.	.	.	.	.	.	.	.	G	17.49	3.402399	0.62288	.	.	ENSG00000101438	ENST00000217420	T	0.02837	4.14	4.45	4.45	0.53987	.	0.000000	0.85682	D	0.000000	T	0.13500	0.0327	M	0.71206	2.165	0.80722	D	1	D	0.67145	0.996	D	0.72982	0.979	T	0.00398	-1.1764	10	0.66056	D	0.02	-20.6777	14.9208	0.70835	0.0:0.0:1.0:0.0	.	387	Q9H598	VIAAT_HUMAN	M	387	ENSP00000217420:V387M	ENSP00000217420:V387M	V	+	1	0	SLC32A1	36790277	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.788000	0.99064	2.202000	0.70862	0.563000	0.77884	GTG	.	.	none		0.622	SLC32A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079206.1	NM_080552		A	37356863	G	A	37356863	3	1	39	1	0	0	0	0	1	0	0	0	14580	1261	44	2	1165	2	SLC32A1	20	37356863	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10		37356863	25668657	212	14757											
ZNF217	7764	hgsc.bcm.edu	37	chr20	52198236	52198236	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagctttgccgcactcggagCagtgagtgggcttctccttg	6	11	13	11	2	1	1	0	1	1	0	3	2	1	2	2	2	3	4	2	2	1	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr20:52198236C>T	ENST00000371471.2	-	2	1555	c.1130G>A	c.(1129-1131)tGc>tAc	p.C377Y	ZNF217_ENST00000302342.3_Missense_Mutation_p.C377Y|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)			GCACTCGGAGCAGTGAGTGGG	0.612																																					p.C377Y		Atlas-SNP	.											.	ZNF217	227	.	0			c.G1130A						PASS	.						96	99	98					20																	52198236		2203	4300	6503	SO:0001583	missense	7764	exon1			TCGGAGCAGTGAG	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.1130G>A	20.37:g.52198236C>T	ENSP00000360526:p.Cys377Tyr	131	0	0		132	50	0.378788	NM_006526	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	37	CCDS13443.1	.	.	.	.	.	.	.	.	.	.	C	18.74	3.689039	0.68271	.	.	ENSG00000171940	ENST00000371471;ENST00000302342	T;T	0.58358	0.34;0.34	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	0.75155	0.3811	M	0.79343	2.45	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.77308	-0.2636	10	0.87932	D	0	-29.0809	19.4277	0.94751	0.0:1.0:0.0:0.0	.	377	O75362	ZN217_HUMAN	Y	377	ENSP00000360526:C377Y;ENSP00000304308:C377Y	ENSP00000304308:C377Y	C	-	2	0	ZNF217	51631643	1.000000	0.71417	0.591000	0.28745	0.413000	0.31143	7.387000	0.79785	2.686000	0.91538	0.591000	0.81541	TGC	.	.	none		0.612	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526		T	52198236	C	T	52198236	3	4	39	1	0	0	0	0	1	0	0	0	17787	710	25	2	2032	2	ZNF217	20	52198236	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	14841373	52198236	10827284	213	14758											
LAMA5	3911	hgsc.bcm.edu	37	chr20	60909029	60909029	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacactcatggccccccggtTgacgtatcggaagacgagcc	9	6	11	15	4	1	2	1	1	0	1	2	4	1	3	4	3	1	2	4	3	2	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr20:60909029T>C	ENST00000252999.3	-	23	2872	c.2806A>G	c.(2806-2808)Aac>Gac	p.N936D	MIR4758_ENST00000577688.1_RNA	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	936	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)			GCCCCCCGGTTGACGTATCGG	0.672																																					p.N936D		Atlas-SNP	.											.	LAMA5	268	.	0			c.A2806G						PASS	.						37	32	34					20																	60909029		2201	4296	6497	SO:0001583	missense	3911	exon23			CCCGGTTGACGTA	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.2806A>G	20.37:g.60909029T>C	ENSP00000252999:p.Asn936Asp	122	0	0		97	35	0.360825	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	t	15.02	2.709053	0.48517	.	.	ENSG00000130702	ENST00000252999	T	0.20881	2.04	4.54	4.54	0.55810	.	0.047534	0.85682	U	0.000000	T	0.30854	0.0778	M	0.78456	2.415	0.80722	D	1	P	0.51791	0.948	P	0.46237	0.508	T	0.17623	-1.0363	10	0.66056	D	0.02	.	10.6683	0.45743	0.0:0.0:0.1605:0.8394	.	936	O15230	LAMA5_HUMAN	D	936	ENSP00000252999:N936D	ENSP00000252999:N936D	N	-	1	0	LAMA5	60342424	1.000000	0.71417	0.705000	0.30386	0.132000	0.20833	5.130000	0.64745	1.665000	0.50811	0.444000	0.29173	AAC	.	.	none		0.672	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560		C	60909029	T	C	60909029	3	2	39	1	0	0	0	0	1	0	0	0	8618	1812	63	3	8513	3	LAMA5	20	60909029	Missense_Mutation	SNP	T	TCGA-GS-A9TW-01A-11D-A382-10	8710793	60909029	2116491	214	14759											
NCAM2	4685	hgsc.bcm.edu	37	chr21	22881298	22881299	+	Frame_Shift_Ins	INS	-	-	C																															tgtgggttgctgatgtgcatINScactaggagaatgtgtggaa																										TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr21:22881298_22881299insC	ENST00000400546.1	+	16	2453_2454	c.2204_2205insC	c.(2203-2208)atcactfs	p.T736fs	NCAM2_ENST00000284894.7_Frame_Shift_Ins_p.T594fs	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	736					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)		CTGATGTGCATCACTAGGAGAA	0.465																																					p.I735fs		Atlas-Indel	.											.	NCAM2	220	.	0			c.2204_2205insC						PASS	.																																			SO:0001589	frameshift_variant	4685	exon16			.		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.2205dupC	21.37:g.22881299_22881299dupC	ENSP00000383392:p.Thr736fs	212	0	0		167	25	0.149701	NM_004540	A8MQ06|B7Z841|Q7Z7F2	Frame_Shift_Ins	INS	ENST00000400546.1	37	CCDS42910.1																																																																																			.	.	none		0.465	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		C	22881299	-	C	22881298	7	5	39	1	0	1	1	0	0	0	0	0	10212	1435	50	0	2266	0	NCAM2	21	22881298	Frame_Shift_Ins	INS	-	TCGA-GS-A9TW-01A-11D-A382-10		22881298	25248597	215	14760	191	2									
NCAM2	4685	hgsc.bcm.edu	37	chr21	22881305	22881306	+	Frame_Shift_Del	DEL	GA	GA	-																															ttgctgatgtgcatcactagGagaatgtgtggaaagaaaag																										TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr21:22881305_22881306delGA	ENST00000400546.1	+	16	2460_2461	c.2211_2212delGA	c.(2209-2214)aggagafs	p.RR737fs	NCAM2_ENST00000284894.7_Frame_Shift_Del_p.RR595fs	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	737					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)		GCATCACTAGGAGAATGTGTGG	0.45																																					p.737_737del		Atlas-Indel	.											NCAM2,NS,carcinoma,+1,1	NCAM2	220	1	0			c.2210_2211del						PASS	.																																			SO:0001589	frameshift_variant	4685	exon16			.		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.2211_2212delGA	21.37:g.22881307_22881308delGA	ENSP00000383392:p.Arg737fs	198	0	0		159	21	0.132075	NM_004540	A8MQ06|B7Z841|Q7Z7F2	Frame_Shift_Del	DEL	ENST00000400546.1	37	CCDS42910.1																																																																																			.	.	none		0.45	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		-	22881306	GA	-	22881305	7	5	39	1	0	1	0	1	0	0	0	0	10212	1165	41	0	2273	0	NCAM2	21	22881305	Frame_Shift_Del	DEL	GA	TCGA-GS-A9TW-01A-11D-A382-10	7	22881305	25248590	216	14761	191	2									
TTC3	7267	hgsc.bcm.edu	37	chr21	38520899	38520899	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aaaatagaatttcacatgaaTtgctggaagaagttaaaaac	20	10	7	4	0	1	3	1	1	0	2	1	4	1	4	0	1	2	2	0	1	10	4			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr21:38520899T>C	ENST00000399017.2	+	23	4817	c.2070T>C	c.(2068-2070)aaT>aaC	p.N690N	TTC3_ENST00000355666.1_Silent_p.N690N|TTC3_ENST00000540756.1_Silent_p.N380N|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000354749.2_Silent_p.N690N	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	690					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)				TTCACATGAATTGCTGGAAGA	0.299																																					p.N690N	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.T2070C						PASS	.						71	79	77					21																	38520899		2203	4296	6499	SO:0001819	synonymous_variant	7267	exon23			CATGAATTGCTGG	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.2070T>C	21.37:g.38520899T>C		331	0	0		353	89	0.252125	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Silent	SNP	ENST00000399017.2	37	CCDS13651.1																																																																																			.	.	none		0.299	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1			C	38520899	T	C	38520899	2	2	39	1	0	0	0	0	0	0	0	1	16712	1490	52	3		3	TTC3	21	38520899	Silent	SNP	T	TCGA-GS-A9TW-01A-11D-A382-10	15639594	38520899	9608996	217	14762											
DSCAM	1826	hgsc.bcm.edu	37	chr21	41648055	41648055	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtacatggacttgctgacGtctgcgcccacatcgttgct	7	11	11	12	3	1	1	0	1	1	0	2	2	1	2	1	2	4	4	1	2	1	3	rs372175757		TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr21:41648055G>A	ENST00000400454.1	-	11	2802	c.2325C>T	c.(2323-2325)gaC>gaT	p.D775D		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	775	Ig-like C2-type 8.				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)				ACTTGCTGACGTCTGCGCCCA	0.468																																					p.D775D	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											DSCAM,colon,carcinoma,0,1	DSCAM	347	1	0			c.C2325T						PASS	.	G		0,4152		0,0,2076	95	101	99		2325	4.7	1	21		99	1,8507		0,1,4253	no	coding-synonymous	DSCAM	NM_001389.3		0,1,6329	AA,AG,GG		0.0118,0.0,0.0079		775/2013	41648055	1,12659	2076	4254	6330	SO:0001819	synonymous_variant	1826	exon11			GCTGACGTCTGCG	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.2325C>T	21.37:g.41648055G>A		148	0	0		123	45	0.365854	NM_001271534	O60468	Silent	SNP	ENST00000400454.1	37	CCDS42929.1																																																																																			.	.	weak		0.468	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389		A	41648055	G	A	41648055	2	1	39	1	0	0	0	0	0	0	0	1	4770	1136	40	1		1	DSCAM	21	41648055	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	3127156	41648055	6481840	218	14763											
UMODL1	89766	hgsc.bcm.edu	37	chr21	43547122	43547122	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcttcctcttgcagggtttaCaccatcatcgaggacctcca	8	11	8	14	1	2	0	1	0	1	0	5	2	4	1	4	2	2	3	4	2	1	4			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr21:43547122C>T	ENST00000408910.2	+	19	3300	c.3300C>T	c.(3298-3300)taC>taT	p.Y1100Y	UMODL1_ENST00000400427.1_Silent_p.Y1156Y|UMODL1_ENST00000400424.2_Silent_p.Y1028Y|UMODL1_ENST00000408989.2_Silent_p.Y1228Y|UMODL1_ENST00000400423.2_3'UTR	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	1100	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				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						GCAGGGTTTACACCATCATCG	0.522																																					p.Y1228Y	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.C3684T						PASS	.						92	93	93					21																	43547122		1990	4164	6154	SO:0001819	synonymous_variant	89766	exon18			GGTTTACACCATC		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.3300C>T	21.37:g.43547122C>T		97	0	0		106	33	0.311321	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Silent	SNP	ENST00000408910.2	37	CCDS42936.1																																																																																			.	.	none		0.522	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2			T	43547122	C	T	43547122	2	4	39	1	0	0	0	0	0	0	0	1	16995	489	17	2		2	UMODL1	21	43547122	Silent	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	1899067	43547122	4582773	219	14764											
DGCR2	9993	hgsc.bcm.edu	37	chr22	19029399	19029399	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	atgaagagcagcagtgacagGatgaggaaggaggagatgca	16	4	17	4	0	0	5	0	3	0	2	0	9	0	8	0	4	3	3	0	4	2	0			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr22:19029399G>A	ENST00000263196.7	-	8	1327	c.1080C>T	c.(1078-1080)atC>atT	p.I360I	DGCR2_ENST00000545799.1_3'UTR|DGCR2_ENST00000537045.1_Silent_p.I319I	NM_001184781.1|NM_005137.2	NP_001171710.1|NP_005128.1	P98153	IDD_HUMAN	DiGeorge syndrome critical region gene 2	360					cell adhesion (GO:0007155)|cognition (GO:0050890)|organ morphogenesis (GO:0009887)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|skin(1)	18	Colorectal(54;0.0993)					GCAGTGACAGGATGAGGAAGG	0.627																																					p.I360I		Atlas-SNP	.											.	DGCR2	45	.	0			c.C1080T						PASS	.						90	72	78					22																	19029399		2203	4300	6503	SO:0001819	synonymous_variant	9993	exon8			TGACAGGATGAGG	D79985	CCDS33598.1, CCDS54496.1	22q11.21	2008-06-12			ENSG00000070413	ENSG00000070413			2845	protein-coding gene	gene with protein product	"integral membrane protein DGCR2"	600594				7655455, 8630060	Standard	NM_005137		Approved	KIAA0163, LAN, IDD, DGS-C, SEZ-12	uc002zoq.1	P98153	OTTHUMG00000150141	ENST00000263196.7:c.1080C>T	22.37:g.19029399G>A		79	0	0		64	21	0.328125	NM_005137	A6NIB5|A8K6K5|B5TY34|B7Z935	Silent	SNP	ENST00000263196.7	37	CCDS33598.1																																																																																			.	.	none		0.627	DGCR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316504.1	NM_005137		A	19029399	G	A	19029399	2	1	39	1	0	0	0	0	0	0	0	1	4463	1164	41	2		2	DGCR2	22	19029399	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10		19029399	32275167	220	14765											
SERPIND1	3053	hgsc.bcm.edu	37	chr22	21133944	21133944	+	Frame_Shift_Del	DEL	A	A	-																															gagtgctgggaacatcctccAgctttttcatggcaagagcc																										TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr22:21133944delA	ENST00000215727.5	+	2	627	c.344delA	c.(343-345)cagfs	p.Q115fs	SERPIND1_ENST00000406799.1_Frame_Shift_Del_p.Q115fs|PI4KA_ENST00000255882.6_Intron|PI4KA_ENST00000572273.1_Intron|PI4KA_ENST00000466162.1_Intron	NM_000185.3	NP_000176.2	P05546	HEP2_HUMAN	serpin peptidase inhibitor, clade D (heparin cofactor), member 1	115					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)	AACATCCTCCAGCTTTTTCAT	0.502																																					p.Q115fs		Pindel,Atlas-Indel	.											.	SERPIND1	92	.	0			c.343delC						PASS	.						75	67	69					22																	21133944		2203	4300	6503	SO:0001589	frameshift_variant	3053	exon2			.	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.344delA	22.37:g.21133944delA	ENSP00000215727:p.Gln115fs	95	0	.		114	27	0.237	NM_000185	B2RAI1|D3DX34|Q6IBZ5	Frame_Shift_Del	DEL	ENST00000215727.5	37	CCDS13783.1																																																																																			.	.	none		0.502	SERPIND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319961.1	NM_000185		-	21133944	A	-	21133944	7	5	39	1	0	1	0	1	0	0	0	0	14125	188	7	0	346	0	SERPIND1	22	21133944	Frame_Shift_Del	DEL	A	TCGA-GS-A9TW-01A-11D-A382-10	2104545	21133944	30170622	221	14766											
CHEK2	11200	hgsc.bcm.edu	37	chr22	29130412	29130412	+	Nonsense_Mutation	SNP	G	G	A																															aagattggcaaatccatcctGaagggcccataatcgagccc																										TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr22:29130412G>A	ENST00000405598.1	-	3	489	c.298C>T	c.(298-300)Cag>Tag	p.Q100*	CHEK2_ENST00000382565.1_Nonsense_Mutation_p.Q100*|CHEK2_ENST00000544772.1_5'UTR|CHEK2_ENST00000403642.1_Nonsense_Mutation_p.Q100*|CHEK2_ENST00000382580.2_Nonsense_Mutation_p.Q100*|CHEK2_ENST00000404276.1_Nonsense_Mutation_p.Q100*|CHEK2_ENST00000402731.1_Nonsense_Mutation_p.Q100*|CHEK2_ENST00000328354.6_Nonsense_Mutation_p.Q100*|CHEK2_ENST00000382566.1_Nonsense_Mutation_p.Q100*|CHEK2_ENST00000348295.3_Nonsense_Mutation_p.Q100*|CHEK2_ENST00000382578.1_Nonsense_Mutation_p.Q100*			O96017	CHK2_HUMAN	checkpoint kinase 2	100					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						AATCCATCCTGAAGGGCCCAT	0.473			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																													p.Q100X		Atlas-SNP	.	yes	Rec		familial breast cancer	22	22q12.1	11200	CHK2 checkpoint homolog (S. pombe)		E	.	CHEK2	438	.	0			c.C298T						PASS	.						42	47	45					22																	29130412		2203	4300	6503	SO:0001587	stop_gained	11200	exon2			CATCCTGAAGGGC	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.298C>T	22.37:g.29130412G>A	ENSP00000386087:p.Gln100*	65	0	0		78	20	0.25641	NM_145862	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Nonsense_Mutation	SNP	ENST00000405598.1	37	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	G	32	5.126742	0.94429	.	.	ENSG00000183765	ENST00000348295;ENST00000382578;ENST00000382565;ENST00000382566;ENST00000328354;ENST00000404276;ENST00000405598;ENST00000382580;ENST00000403642;ENST00000402731;ENST00000447421;ENST00000439200;ENST00000398017	.	.	.	5.42	4.35	0.52113	.	0.399138	0.30356	N	0.009817	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-2.7639	14.3897	0.66970	0.0:0.2582:0.7418:0.0	.	.	.	.	X	100;100;100;100;100;100;100;100;100;100;100;100;110	.	ENSP00000329178:Q100X	Q	-	1	0	CHEK2	27460412	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.141000	0.50593	2.704000	0.92352	0.655000	0.94253	CAG	.	.	none		0.473	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		A	29130412	G	A	29130412	4	1	39	1	0	0	0	0	0	1	0	0	3337	1299	45	2	1522	2	CHEK2	22	29130412	Nonsense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	7996468	29130412	22174154	222	14767	192	2									
CHEK2	11200	hgsc.bcm.edu	37	chr22	29130418	29130419	+	Frame_Shift_Ins	INS	-	-	AT																															gcaaatccatcctgaagggcINSccataatcgagcccaggggg																										TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr22:29130418_29130419insAT	ENST00000405598.1	-	3	482_483	c.291_292insAT	c.(289-294)tgggccfs	p.A98fs	CHEK2_ENST00000382565.1_Frame_Shift_Ins_p.A98fs|CHEK2_ENST00000544772.1_De_novo_Start_OutOfFrame|CHEK2_ENST00000403642.1_Frame_Shift_Ins_p.A98fs|CHEK2_ENST00000382580.2_Frame_Shift_Ins_p.A98fs|CHEK2_ENST00000404276.1_Frame_Shift_Ins_p.A98fs|CHEK2_ENST00000402731.1_Frame_Shift_Ins_p.A98fs|CHEK2_ENST00000328354.6_Frame_Shift_Ins_p.A98fs|CHEK2_ENST00000382566.1_Frame_Shift_Ins_p.A98fs|CHEK2_ENST00000348295.3_Frame_Shift_Ins_p.A98fs|CHEK2_ENST00000382578.1_Frame_Shift_Ins_p.A98fs			O96017	CHK2_HUMAN	checkpoint kinase 2	98					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						TCCTGAAGGGCCCATAATCGAG	0.47			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																													p.A98fs		Pindel,Atlas-Indel	.	yes	Rec		familial breast cancer	22	22q12.1	11200	CHK2 checkpoint homolog (S. pombe)		E	.	CHEK2	438	.	0			c.292_293insAT						PASS	.																																			SO:0001589	frameshift_variant	11200	exon2			.	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.291_292insAT	22.37:g.29130418_29130419insAT	ENSP00000386087:p.Ala98fs	71	0	.		84	15	0.179	NM_007194	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Frame_Shift_Ins	INS	ENST00000405598.1	37	CCDS13843.1																																																																																			.	.	none		0.47	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735		AT	29130419	-	AT	29130418	7	5	39	1	0	1	1	0	0	0	0	0	3337	739	26	0	1528	0	CHEK2	22	29130418	Frame_Shift_Ins	INS	-	TCGA-GS-A9TW-01A-11D-A382-10	6	29130418	22174148	223	14768	192	2									
FOXRED2	80020	hgsc.bcm.edu	37	chr22	36886232	36886232	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tgccaaaggctctcggtactCacgagtccctgcatcctcag	8	9	9	15	2	3	0	2	0	1	0	6	1	5	0	3	2	3	3	3	2	2	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr22:36886232C>G	ENST00000397224.4	-	9	1971	c.1878G>C	c.(1876-1878)gtG>gtC	p.V626V	FOXRED2_ENST00000397223.4_Silent_p.V626V|FOXRED2_ENST00000216187.6_Silent_p.V626V|FOXRED2_ENST00000366463.3_Silent_p.V178V	NM_001102371.1	NP_001095841.1	Q8IWF2	FXRD2_HUMAN	FAD-dependent oxidoreductase domain containing 2	626					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						TCTCGGTACTCACGAGTCCCT	0.612																																					p.V626V		Atlas-SNP	.											FOXRED2,right_upper_lobe,carcinoma,0,1	FOXRED2	48	1	0			c.G1878C						PASS	.						99	101	100					22																	36886232		2203	4300	6503	SO:0001819	synonymous_variant	80020	exon9			GGTACTCACGAGT	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.1878G>C	22.37:g.36886232C>G		49	0	0		49	14	0.285714	NM_001102371	B2RDI4|Q8N378|Q96BD1|Q9H5L5|Q9H6M8	Silent	SNP	ENST00000397224.4	37	CCDS13929.1																																																																																			.	.	none		0.612	FOXRED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104098.2	NM_024955		G	36886232	C	G	36886232	2	3	39	1	0	0	0	0	0	0	0	1	6042	813	29	4		4	FOXRED2	22	36886232	Silent	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	7755814	36886232	14418334	224	14769											
TMPRSS6	164656	hgsc.bcm.edu	37	chr22	37485626	37485626	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccagggactcacgaggtgatGagcctcttctccaggggccc	7	7	13	14	1	3	2	1	2	2	0	4	4	3	3	4	4	1	0	4	4	0	1			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr22:37485626G>A	ENST00000346753.3	-	7	971	c.855C>T	c.(853-855)ctC>ctT	p.L285L	TMPRSS6_ENST00000442782.2_Silent_p.L285L|TMPRSS6_ENST00000381792.2_Silent_p.L276L|TMPRSS6_ENST00000406856.1_Silent_p.L276L|TMPRSS6_ENST00000406725.1_Silent_p.L276L	NM_153609.2	NP_705837.1	Q8IU80	TMPS6_HUMAN	transmembrane protease, serine 6	285	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						ACGAGGTGATGAGCCTCTTCT	0.602																																					p.L285L		Atlas-SNP	.											.	TMPRSS6	99	.	0			c.C855T						PASS	.						21	20	21					22																	37485626		2201	4298	6499	SO:0001819	synonymous_variant	164656	exon7			GGTGATGAGCCTC	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.855C>T	22.37:g.37485626G>A		101	0	0		87	27	0.310345	NM_153609	B0QYB4|B0QYB7|B0QYB8|Q5TI06|Q6ICC2|Q6UXD8|Q8IUE2|Q8IXV8	Silent	SNP	ENST00000346753.3	37	CCDS13941.1																																																																																			.	.	none		0.602	TMPRSS6-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318822.1	NM_153609		A	37485626	G	A	37485626	2	1	39	1	0	0	0	0	0	0	0	1	16266	1277	45	2		2	TMPRSS6	22	37485626	Silent	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	599394	37485626	13818940	225	14770											
EIF3L	51386	hgsc.bcm.edu	37	chr22	38270414	38270414	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctggggagtatgggcggcaCtccctctacaaaatgcttgg	8	9	14	10	1	1	0	0	0	1	0	2	1	2	1	1	5	2	4	1	5	4	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr22:38270414C>A	ENST00000412331.2	+	9	1371	c.789C>A	c.(787-789)caC>caA	p.H263Q	EIF3L_ENST00000381683.6_Missense_Mutation_p.H215Q|EIF3L_ENST00000406934.1_Missense_Mutation_p.H165Q	NM_016091.3	NP_057175.1			eukaryotic translation initiation factor 3, subunit L											kidney(2)|large_intestine(3)|lung(4)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						ATGGGCGGCACTCCCTCTACA	0.552																																					p.H263Q		Atlas-SNP	.											.	EIF3L	35	.	0			c.C789A						PASS	.						216	170	186					22																	38270414		2203	4300	6503	SO:0001583	missense	51386	exon9			GCGGCACTCCCTC	AF083243	CCDS13960.1, CCDS56230.1	22q	2012-12-20	2009-01-07	2009-01-07	ENSG00000100129	ENSG00000100129			18138	protein-coding gene	gene with protein product			"eukaryotic translation initiation factor 3, subunit 6 interacting protein", "eukaryotic translation initiation factor 3, subunit E interacting protein"	EIF3S6IP, EIF3EIP		11042152, 11590142	Standard	NM_016091		Approved	HSPC021, HSPC025, EIF3S11	uc003auf.3	Q9Y262	OTTHUMG00000150671	ENST00000412331.2:c.789C>A	22.37:g.38270414C>A	ENSP00000416892:p.His263Gln	175	0	0		161	49	0.304348	NM_016091		Missense_Mutation	SNP	ENST00000412331.2	37	CCDS13960.1	.	.	.	.	.	.	.	.	.	.	C	17.51	3.406613	0.62399	.	.	ENSG00000100129	ENST00000412331;ENST00000425539;ENST00000381683;ENST00000262832;ENST00000406934	T;T;T	0.40476	1.03;1.03;1.03	5.57	4.54	0.55810	.	0.099918	0.64402	D	0.000001	T	0.58424	0.2121	M	0.78049	2.395	0.58432	D	0.999997	P;P;D;D	0.58620	0.539;0.748;0.966;0.983	P;P;P;D	0.63877	0.486;0.588;0.859;0.919	T	0.58493	-0.7627	10	0.14252	T	0.57	-33.9179	11.9022	0.52690	0.0:0.8588:0.0:0.1412	.	215;165;263;306	B4DYB2;B0QY90;Q9Y262;B0QY89	.;.;EIF3L_HUMAN;.	Q	263;306;215;230;165	ENSP00000416892:H263Q;ENSP00000371099:H215Q;ENSP00000384634:H165Q	ENSP00000262832:H230Q	H	+	3	2	EIF3L	36600360	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.779000	0.38624	1.368000	0.46115	0.573000	0.79308	CAC	.	.	none		0.552	EIF3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319551.2	NM_016091		A	38270414	C	A	38270414	3	1	39	1	0	0	0	0	1	0	0	0	5024	564	20	4	823	4	EIF3L	22	38270414	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	784788	38270414	13034152	226	14771											
PNPLA5	150379	hgsc.bcm.edu	37	chr22	44280171	44280171	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tcagcacctgtccaggccccGagtgccagaagcgggcccac	8	4	12	17	2	1	1	1	0	0	1	2	2	2	1	6	2	3	1	6	2	1	0			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chr22:44280171G>A	ENST00000597664.1	-	7	1133	c.1004C>T	c.(1003-1005)tCg>tTg	p.S335L	PNPLA5_ENST00000216177.4_Missense_Mutation_p.S335L|PNPLA5_ENST00000593866.1_Missense_Mutation_p.S221L|PNPLA5_ENST00000381198.2_Missense_Mutation_p.S221L			Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	335					lipid catabolic process (GO:0016042)		hydrolase activity (GO:0016787)	p.S335L(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)				TCCAGGCCCCGAGTGCCAGAA	0.627											OREG0026622	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S335L		Atlas-SNP	.											PNPLA5,NS,carcinoma,0,1	PNPLA5	46	1	1	Substitution - Missense(1)	endometrium(1)	c.C1004T						PASS	.						90	90	90					22																	44280171		2203	4300	6503	SO:0001583	missense	150379	exon7			GGCCCCGAGTGCC	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.1004C>T	22.37:g.44280171G>A	ENSP00000471069:p.Ser335Leu	78	0	0	922	52	17	0.326923	NM_138814	B1AHL8|B3KPR1|Q6ZST0	Missense_Mutation	SNP	ENST00000597664.1	37		.	.	.	.	.	.	.	.	.	.	G	4.655	0.121721	0.08931	.	.	ENSG00000100341	ENST00000216177;ENST00000381198;ENST00000438734	T;T;T	0.39056	1.56;1.1;1.94	3.9	1.76	0.24704	.	0.316936	0.21366	N	0.075714	T	0.38825	0.1055	L	0.31926	0.97	0.09310	N	1	D;D;D	0.76494	0.996;0.999;0.998	P;D;P	0.64687	0.823;0.928;0.688	T	0.31888	-0.9927	10	0.02654	T	1	-4.6125	6.2816	0.21011	0.2326:0.0:0.7674:0.0	.	243;221;335	E9PGS4;Q7Z6Z6-2;Q7Z6Z6	.;.;PLPL5_HUMAN	L	335;221;243	ENSP00000216177:S335L;ENSP00000370595:S221L;ENSP00000405732:S243L	ENSP00000216177:S335L	S	-	2	0	PNPLA5	42611504	0.075000	0.21258	0.001000	0.08648	0.010000	0.07245	1.941000	0.40233	0.427000	0.26145	0.313000	0.20887	TCG	.	.	none		0.627	PNPLA5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000075667.4	NM_138814		A	44280171	G	A	44280171	3	1	39	1	0	0	0	0	1	0	0	0	12177	1059	37	1	297	1	PNPLA5	22	44280171	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	6009757	44280171	7024395	227	14772											
P2RY8	286530	hgsc.bcm.edu	37	chrX	1584685	1584685	+	Missense_Mutation	SNP	A	A	G																															tcacgatgtgcgccaggagcAcgaagttgttgggggcgaag																										TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chrX:1584685A>G	ENST00000381297.4	-	2	977	c.767T>C	c.(766-768)gTg>gCg	p.V256A	P2RY8_ENST00000460672.1_5'Flank	NM_178129.4	NP_835230.1	Q86VZ1	P2RY8_HUMAN	purinergic receptor P2Y, G-protein coupled, 8	256						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(13)|prostate(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)				CGCCAGGAGCACGAAGTTGTT	0.647			T	CRLF2	"B-ALL, Downs associated ALL"																																p.V256A		Atlas-SNP	.		Dom	yes		"X,Y"	Xp22.3; Yp11.3	286530	"purinergic receptor P2Y, G-protein coupled, 8"		L	.	P2RY8	53	.	0			c.T767C						PASS	.						72	69	70					X																	1584685		2203	4296	6499	SO:0001583	missense	286530	exon2			AGGAGCACGAAGT	AA804531	CCDS14115.1	Xp22.33 and Yp11.3	2012-08-08			ENSG00000182162	ENSG00000182162		"Pseudoautosomal regions / PAR1", "Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	15524	protein-coding gene	gene with protein product		300525				11004484	Standard	NM_178129		Approved	P2Y8	uc004cpz.2	Q86VZ1	OTTHUMG00000021060	ENST00000381297.4:c.767T>C	X.37:g.1584685A>G	ENSP00000370697:p.Val256Ala	98	0	0		61	28	0.459016	NM_178129		Missense_Mutation	SNP	ENST00000381297.4	37	CCDS14115.1	.	.	.	.	.	.	.	.	.	.	a	15.47	2.841842	0.51057	.	.	ENSG00000182162	ENST00000381297	T	0.73152	-0.72	2.73	2.73	0.32206	GPCR, rhodopsin-like superfamily (1);	0.235347	0.27618	U	0.018564	T	0.61615	0.2361	L	0.38175	1.15	0.09310	N	1	P	0.44090	0.826	B	0.44315	0.446	T	0.52540	-0.8562	10	0.33141	T	0.24	.	10.658	0.45686	1.0:0.0:0.0:0.0	.	256	Q86VZ1	P2RY8_HUMAN	A	256	ENSP00000370697:V256A	ENSP00000370697:V256A	V	-	2	0	P2RY8	1544685	1.000000	0.71417	0.981000	0.43875	0.668000	0.39293	5.411000	0.66386	0.823000	0.34589	0.230000	0.17803	GTG	.	.	none		0.647	P2RY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055602.1	NM_178129		G	1584685	A	G	1584685	3	3	39	1	0	0	0	0	1	0	0	0	11364	159	6	3	316	3	P2RY8	23	1584685	Missense_Mutation	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10		1584685	153685875	228	14773	193	2									
P2RY8	286530	hgsc.bcm.edu	37	chrX	1584688	1584688	+	Missense_Mutation	SNP	A	A	G																															cgatgtgcgccaggagcacgAagttgttgggggcgaagcag																										TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chrX:1584688A>G	ENST00000381297.4	-	2	974	c.764T>C	c.(763-765)tTc>tCc	p.F255S	P2RY8_ENST00000460672.1_5'Flank	NM_178129.4	NP_835230.1	Q86VZ1	P2RY8_HUMAN	purinergic receptor P2Y, G-protein coupled, 8	255						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|lung(13)|prostate(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)				CAGGAGCACGAAGTTGTTGGG	0.652			T	CRLF2	"B-ALL, Downs associated ALL"																																p.F255S		Atlas-SNP	.		Dom	yes		"X,Y"	Xp22.3; Yp11.3	286530	"purinergic receptor P2Y, G-protein coupled, 8"		L	.	P2RY8	53	.	0			c.T764C						PASS	.						68	65	66					X																	1584688		2203	4296	6499	SO:0001583	missense	286530	exon2			AGCACGAAGTTGT	AA804531	CCDS14115.1	Xp22.33 and Yp11.3	2012-08-08			ENSG00000182162	ENSG00000182162		"Pseudoautosomal regions / PAR1", "Purinergic receptors", "GPCR / Class A : Purinergic receptors, P2Y"	15524	protein-coding gene	gene with protein product		300525				11004484	Standard	NM_178129		Approved	P2Y8	uc004cpz.2	Q86VZ1	OTTHUMG00000021060	ENST00000381297.4:c.764T>C	X.37:g.1584688A>G	ENSP00000370697:p.Phe255Ser	98	0	0		54	26	0.481481	NM_178129		Missense_Mutation	SNP	ENST00000381297.4	37	CCDS14115.1	.	.	.	.	.	.	.	.	.	.	a	15.15	2.746727	0.49257	.	.	ENSG00000182162	ENST00000381297	T	0.71698	-0.59	2.73	2.73	0.32206	GPCR, rhodopsin-like superfamily (1);	0.072053	0.49916	U	0.000127	T	0.63861	0.2547	N	0.20766	0.605	0.09310	N	1	D	0.53312	0.959	P	0.52343	0.696	T	0.58239	-0.7671	10	0.72032	D	0.01	.	10.658	0.45686	1.0:0.0:0.0:0.0	.	255	Q86VZ1	P2RY8_HUMAN	S	255	ENSP00000370697:F255S	ENSP00000370697:F255S	F	-	2	0	P2RY8	1544688	1.000000	0.71417	0.986000	0.45419	0.716000	0.41182	4.106000	0.57804	0.823000	0.34589	0.230000	0.17803	TTC	.	.	none		0.652	P2RY8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055602.1	NM_178129		G	1584688	A	G	1584688	3	3	39	1	0	0	0	0	1	0	0	0	11364	246	9	3	319	3	P2RY8	23	1584688	Missense_Mutation	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	3	1584688	153685872	229	14774	193	2									
SFRS17A	8227	hgsc.bcm.edu	37	chrX	1712439	1712439	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtacctgaagcccatcacCaagatgaccatcagcgtggc	11	8	9	13	1	2	3	2	2	0	1	2	3	2	3	4	1	3	1	4	1	3	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chrX:1712439C>T	ENST00000313871.3	+	2	280	c.84C>T	c.(82-84)acC>acT	p.T28T	AKAP17A_ENST00000381261.3_Silent_p.T28T	NM_005088.2	NP_005079.2	Q02040	AK17A_HUMAN	A kinase (PRKA) anchor protein 17A	28					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						AGCCCATCACCAAGATGACCA	0.617																																					p.T28T		Atlas-SNP	.											.	AKAP17A	46	.	0			c.C84T						PASS	.						129	113	118					X																	1712439		2203	4296	6499	SO:0001819	synonymous_variant	8227	exon2			CATCACCAAGATG	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.84C>T	X.37:g.1712439C>T		156	0	0		144	37	0.256944	NM_005088	Q02832|Q2TB98|Q5JQ74|Q5JQ76|Q8N6U9	Silent	SNP	ENST00000313871.3	37	CCDS14116.1																																																																																			.	.	none		0.617	AKAP17A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055609.2	NM_005088		T	1712439	C	T	1712439	2	4	39	1	0	0	0	0	0	0	0	1	14188	581	21	2		2	SFRS17A	23	1712439	Silent	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	127751	1712439	153558121	230	14775											
FAM9A	171482	hgsc.bcm.edu	37	chrX	8763298	8763298	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctcctcttcgtcttctactaCtattacttctgctgctgctg	4	18	5	14	1	4	0	0	0	4	0	6	0	5	0	1	0	6	3	1	0	4	7			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chrX:8763298C>G	ENST00000543214.1	-	7	787	c.652G>C	c.(652-654)Gta>Cta	p.V218L	FAM9A_ENST00000381003.3_Missense_Mutation_p.V218L	NM_001171186.1	NP_001164657.1	Q8IZU1	FAM9A_HUMAN	family with sequence similarity 9, member A	218	Glu-rich.					nucleus (GO:0005634)				endometrium(11)|kidney(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	18		Hepatocellular(5;0.219)				tcttctACTACTATTACTTct	0.517																																					p.V218L		Atlas-SNP	.											.	FAM9A	57	.	0			c.G652C						PASS	.						21	19	20					X																	8763298		2191	4281	6472	SO:0001583	missense	171482	exon7			CTACTACTATTAC		CCDS14131.1	Xp22.32	2012-11-29			ENSG00000183304	ENSG00000183304			18403	protein-coding gene	gene with protein product	"testis expressed 39A"	300477					Standard	NM_174951		Approved	TEX39A	uc004csg.3	Q8IZU1	OTTHUMG00000021110	ENST00000543214.1:c.652G>C	X.37:g.8763298C>G	ENSP00000440163:p.Val218Leu	84	0	0		75	30	0.4	NM_174951	B7ZLH5|Q2M2D1	Missense_Mutation	SNP	ENST00000543214.1	37	CCDS14131.1	.	.	.	.	.	.	.	.	.	.	c	1.212	-0.629328	0.03610	.	.	ENSG00000183304	ENST00000381003;ENST00000543214	.	.	.	0.392	-0.652	0.11450	.	.	.	.	.	T	0.15349	0.0370	N	0.08118	0	0.09310	N	1	B	0.26845	0.161	B	0.23852	0.049	T	0.18366	-1.0339	7	0.36615	T	0.2	.	.	.	.	.	218	Q8IZU1	FAM9A_HUMAN	L	218	.	ENSP00000370391:V218L	V	-	1	0	FAM9A	8723298	0.001000	0.12720	0.012000	0.15200	0.011000	0.07611	-0.729000	0.04920	-0.488000	0.06726	-0.481000	0.04817	GTA	.	.	none		0.517	FAM9A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055697.1	NM_174951		G	8763298	C	G	8763298	3	3	39	1	0	0	0	0	1	0	0	0	5667	565	20	4	358	4	FAM9A	23	8763298	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	7050859	8763298	146507262	231	14776											
TMSB4X	7114	hgsc.bcm.edu	37	chrX	12994405	12994410	+	In_Frame_Del	DEL	GAGATC	GAGATC	-																															ctgacaaacccgatatggctGagatcgagaaattcgataag																										TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	GAGATC	GAGATC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chrX:12994405_12994410delGAGATC	ENST00000380635.1	+	2	241_246	c.25_30delGAGATC	c.(25-30)gagatcdel	p.EI9del	TMSB4X_ENST00000380633.1_In_Frame_Del_p.EI9del|TMSB4X_ENST00000380636.1_In_Frame_Del_p.EI9del|TMSB4X_ENST00000451311.2_In_Frame_Del_p.EI9del			P62328	TYB4_HUMAN	thymosin beta 4, X-linked	9					actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|sequestering of actin monomers (GO:0042989)	cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	poly(A) RNA binding (GO:0044822)			upper_aerodigestive_tract(1)	1						CGATATGGCTGAGATCGAGAAATTCG	0.529																																					p.8_10del		Atlas-Indel	.											.	TMSB4X	3	.	0			c.24_29del						PASS	.																																			SO:0001651	inframe_deletion	7114	exon2			.		CCDS35202.1	Xp22.2	2013-05-14	2008-02-25		ENSG00000205542	ENSG00000205542			11881	protein-coding gene	gene with protein product		300159	"thymosin, beta 4, X chromosome"	TMSB4		2677145, 9381176	Standard	NM_021109		Approved	TB4X	uc004cvf.3	P62328	OTTHUMG00000021144	ENST00000380635.1:c.25_30delGAGATC	X.37:g.12994405_12994410delGAGATC	ENSP00000370009:p.Glu9_Ile10del	400	0	0		312	41	0.13141	NM_021109	P01253|P01254|Q546P5|Q63576|Q9UE55	In_Frame_Del	DEL	ENST00000380635.1	37	CCDS35202.1																																																																																			.	.	none		0.529	TMSB4X-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000055779.1	NM_021109		-	12994410	GAGATC	-	12994405	7	5	39	1	0	1	0	1	0	0	0	0	16272	1291	45	0	27	0	TMSB4X	23	12994405	In_Frame_Del	DEL	GAGATC	TCGA-GS-A9TW-01A-11D-A382-10	4231107	12994405	142276155	232	14777											
RAB9A	9367	hgsc.bcm.edu	37	chrX	13727323	13727323	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgactatccttattttgaaaCaagtgcaaaagatgccacaa	16	10	6	9	1	0	2	0	1	0	1	1	3	1	2	2	0	3	1	2	0	7	4			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chrX:13727323C>T	ENST00000464506.1	+	3	737	c.458C>T	c.(457-459)aCa>aTa	p.T153I	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	153					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						TATTTTGAAACAAGTGCAAAA	0.473																																					p.T153I		Atlas-SNP	.											.	RAB9A	17	.	0			c.C458T						PASS	.						93	94	93					X																	13727323		2203	4300	6503	SO:0001583	missense	9367	exon3			TTGAAACAAGTGC	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.458C>T	X.37:g.13727323C>T	ENSP00000420127:p.Thr153Ile	150	0	0		145	22	0.151724	NM_004251	A8K390|Q6ICN1	Missense_Mutation	SNP	ENST00000464506.1	37	CCDS14156.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.398162	0.83120	.	.	ENSG00000123595	ENST00000464506	T	0.80653	-1.4	5.51	5.51	0.81932	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90590	0.7050	M	0.82630	2.6	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91021	0.4857	9	.	.	.	-12.6253	18.4388	0.90656	0.0:1.0:0.0:0.0	.	153	P51151	RAB9A_HUMAN	I	153	ENSP00000420127:T153I	.	T	+	2	0	RAB9A	13637244	1.000000	0.71417	0.987000	0.45799	0.901000	0.52897	7.618000	0.83043	2.296000	0.77279	0.594000	0.82650	ACA	.	.	none		0.473	RAB9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055802.1	NM_004251		T	13727323	C	T	13727323	3	4	39	1	0	0	0	0	1	0	0	0	12973	478	17	2	460	2	RAB9A	23	13727323	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	732918	13727323	141543237	233	14778											
FAM120C	54954	hgsc.bcm.edu	37	chrX	54209068	54209068	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcgctgtctgccgctcggcCtggcaccgacggccccactc	3	7	12	19	5	1	0	0	0	1	0	3	1	1	0	5	3	2	3	5	3	0	0			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chrX:54209068C>T	ENST00000375180.2	-	1	620	c.564G>A	c.(562-564)caG>caA	p.Q188Q	FAM120C_ENST00000477084.1_Silent_p.Q188Q|FAM120C_ENST00000497680.1_5'UTR|FAM120C_ENST00000328235.4_Silent_p.Q188Q	NM_017848.4	NP_060318.3	Q9NX05	F120C_HUMAN	family with sequence similarity 120C	188							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						GCCGCTCGGCCTGGCACCGAC	0.711																																					p.Q188Q		Atlas-SNP	.											.	FAM120C	89	.	0			c.G564A						PASS	.						21	16	18					X																	54209068		2171	4260	6431	SO:0001819	synonymous_variant	54954	exon1			CTCGGCCTGGCAC	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.564G>A	X.37:g.54209068C>T		140	0	0		74	27	0.364865	NM_017848	B2RMT7	Silent	SNP	ENST00000375180.2	37	CCDS14356.1																																																																																			.	.	none		0.711	FAM120C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056795.2	NM_017848		T	54209068	C	T	54209068	2	4	39	1	0	0	0	0	0	0	0	1	5423	680	24	2		2	FAM120C	23	54209068	Silent	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	40481745	54209068	101061492	234	14779											
AR	367	hgsc.bcm.edu	37	chrX	66937418	66937418	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctggcgatccttcaccaatGtcaactccaggatgctctac	9	10	8	14	1	3	0	2	0	1	0	5	2	5	1	3	2	3	2	3	2	3	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chrX:66937418G>C	ENST00000374690.3	+	5	2796	c.2272G>C	c.(2272-2274)Gtc>Ctc	p.V758L	AR_ENST00000396043.2_Missense_Mutation_p.V226L|AR_ENST00000396044.3_Intron	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	757	Interaction with KAT7.|Interaction with LPXN.|Ligand-binding.		N -> T (in PAIS; 50% reduction in transactivation). {ECO:0000269|PubMed:9607727}.		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)	CTTCACCAATGTCAACTCCAG	0.537									Androgen Insensitivity Syndrome																												p.V758L		Atlas-SNP	.											.	AR	249	.	0			c.G2272C						PASS	.						141	99	113					X																	66937418		2203	4300	6503	SO:0001583	missense	367	exon5	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	ACCAATGTCAACT	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.2272G>C	X.37:g.66937418G>C	ENSP00000363822:p.Val758Leu	168	0	0		109	15	0.137615	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	37	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	g	16.67	3.187222	0.57909	.	.	ENSG00000169083	ENST00000544984;ENST00000374690;ENST00000396043	D;D	0.96136	-3.92;-3.92	5.09	5.09	0.68999	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.060824	0.64402	D	0.000003	D	0.95072	0.8404	M	0.63428	1.95	0.80722	D	1	B;D	0.54207	0.005;0.965	B;P	0.47673	0.02;0.554	D	0.95438	0.8523	10	0.72032	D	0.01	.	14.7147	0.69259	0.0:0.0:1.0:0.0	.	226;757	F1D8N5;P10275	.;ANDR_HUMAN	L	568;758;226	ENSP00000363822:V758L;ENSP00000379358:V226L	ENSP00000363822:V758L	V	+	1	0	AR	66854143	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	6.449000	0.73473	2.351000	0.79841	0.597000	0.82753	GTC	.	.	none		0.537	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044		C	66937418	G	C	66937418	3	2	39	1	0	0	0	0	1	0	0	0	836	1377	48	4	2314	4	AR	23	66937418	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	12728350	66937418	88333142	235	14780											
EDA	1896	hgsc.bcm.edu	37	chrX	69253328	69253328	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	agctacatccccgcagcgggGagctggaggtactggtggac	8	6	16	11	2	0	0	0	0	0	0	1	3	1	3	2	6	5	4	2	6	2	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chrX:69253328G>C	ENST00000374552.4	+	7	1116	c.874G>C	c.(874-876)Gag>Cag	p.E292Q	EDA_ENST00000374553.2_Missense_Mutation_p.E292Q|EDA_ENST00000524573.1_Missense_Mutation_p.E289Q	NM_001399.4	NP_001390.1	Q92838	EDA_HUMAN	ectodysplasin A	292					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)	p.E292K(2)		breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|ovary(2)|urinary_tract(1)	14						CCGCAGCGGGGAGCTGGAGGT	0.502											OREG0019847	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E292Q		Atlas-SNP	.											.	EDA	61	.	2	Substitution - Missense(2)	endometrium(2)	c.G874C						PASS	.						121	98	106					X																	69253328		2203	4300	6503	SO:0001583	missense	1896	exon7			AGCGGGGAGCTGG	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.874G>C	X.37:g.69253328G>C	ENSP00000363680:p.Glu292Gln	139	0	0	1113	74	21	0.283784	NM_001399	A0AUZ2|A2A337|B7ZLU2|B7ZLU4|O75910|Q5JS00|Q5JUM7|Q9UP77|Q9Y6L0|Q9Y6L1|Q9Y6L2|Q9Y6L3|Q9Y6L4	Missense_Mutation	SNP	ENST00000374552.4	37	CCDS14394.1	.	.	.	.	.	.	.	.	.	.	G	17.73	3.462303	0.63513	.	.	ENSG00000158813	ENST00000374552;ENST00000374553;ENST00000524573	D;D;D	0.94931	-3.56;-3.56;-3.56	5.48	5.48	0.80851	Tumour necrosis factor (3);Tumour necrosis factor-like (2);	0.062571	0.64402	D	0.000007	D	0.91798	0.7405	N	0.17723	0.515	0.80722	D	1	P;P;P	0.37466	0.541;0.596;0.541	B;B;B	0.43331	0.292;0.416;0.292	D	0.92537	0.6038	10	0.59425	D	0.04	-14.3379	17.2271	0.86973	0.0:0.0:1.0:0.0	.	289;292;292	Q92838-9;Q92838;Q92838-3	.;EDA_HUMAN;.	Q	292;292;289	ENSP00000363680:E292Q;ENSP00000363681:E292Q;ENSP00000432585:E289Q	ENSP00000363680:E292Q	E	+	1	0	EDA	69170053	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.062000	0.71155	2.279000	0.76181	0.600000	0.82982	GAG	.	.	none		0.502	EDA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057048.2	NM_001399		C	69253328	G	C	69253328	3	2	39	1	0	0	0	0	1	0	0	0	4905	1175	41	4	1036	4	EDA	23	69253328	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	2315910	69253328	86017232	236	14781											
ERCC6L	54821	hgsc.bcm.edu	37	chrX	71426262	71426262	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atactggagagatcttgtttCtcaccctctttgggcagatc	8	14	9	10	0	3	2	1	0	3	2	5	4	3	3	1	2	1	2	1	2	1	4			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chrX:71426262C>T	ENST00000334463.3	-	2	2490	c.2355G>A	c.(2353-2355)gaG>gaA	p.E785E	PIN4_ENST00000423432.2_Intron|ERCC6L_ENST00000373657.1_Silent_p.E662E	NM_017669.2	NP_060139.2	Q2NKX8	ERC6L_HUMAN	excision repair cross-complementation group 6-like	785					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)					GATCTTGTTTCTCACCCTCTT	0.423																																					p.E785E		Atlas-SNP	.											.	ERCC6L	98	.	0			c.G2355A						PASS	.						128	118	121					X																	71426262		2203	4299	6502	SO:0001819	synonymous_variant	54821	exon2			TTGTTTCTCACCC	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.2355G>A	X.37:g.71426262C>T		273	0	0		225	64	0.284444	NM_017669	Q8NCI1|Q96H93|Q9NXQ8	Silent	SNP	ENST00000334463.3	37	CCDS35329.1																																																																																			.	.	none		0.423	ERCC6L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057174.2	NM_017669		T	71426262	C	T	71426262	2	4	39	1	0	0	0	0	0	0	0	1	5220	912	32	2		2	ERCC6L	23	71426262	Silent	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	2172934	71426262	83844298	237	14782											
POU3F4	5456	hgsc.bcm.edu	37	chrX	82764220	82764220	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aagggcgtactggagacgcaTttcctcaagtgtcccaagcc	10	8	11	12	2	1	1	1	0	0	1	3	2	3	1	3	2	2	2	3	2	4	2			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chrX:82764220T>C	ENST00000373200.2	+	1	952	c.888T>C	c.(886-888)caT>caC	p.H296H	RP3-326L13.2_ENST00000607095.1_RNA|RP3-326L13.3_ENST00000607789.1_lincRNA	NM_000307.3	NP_000298	P49335	PO3F4_HUMAN	POU class 3 homeobox 4	296					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						TGGAGACGCATTTCCTCAAGT	0.592																																					p.H296H		Atlas-SNP	.											.	POU3F4	136	.	0			c.T888C						PASS	.						47	35	39					X																	82764220		2203	4300	6503	SO:0001819	synonymous_variant	5456	exon1			GACGCATTTCCTC	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.888T>C	X.37:g.82764220T>C		158	0	0		113	19	0.168142	NM_000307	B2RC71|Q5H9G9|Q99410	Silent	SNP	ENST00000373200.2	37	CCDS14450.1																																																																																			.	.	none		0.592	POU3F4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057368.2	NM_000307		C	82764220	T	C	82764220	2	2	39	1	0	0	0	0	0	0	0	1	12286	1490	52	3		3	POU3F4	23	82764220	Silent	SNP	T	TCGA-GS-A9TW-01A-11D-A382-10	11337958	82764220	72506340	238	14783											
PCDH11X	27328	hgsc.bcm.edu	37	chrX	91134203	91134203	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcaagcagttcagatccCtacagcgtttctgactgtgg	8	12	9	12	1	3	2	2	1	1	1	5	2	5	2	2	1	3	3	2	1	2	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chrX:91134203C>A	ENST00000373094.1	+	2	3809	c.2964C>A	c.(2962-2964)ccC>ccA	p.P988P	PCDH11X_ENST00000406881.1_Silent_p.P988P|PCDH11X_ENST00000504220.2_Silent_p.P988P|PCDH11X_ENST00000361655.2_Silent_p.P988P|PCDH11X_ENST00000395337.2_Silent_p.P988P|PCDH11X_ENST00000373097.1_Silent_p.P988P|PCDH11X_ENST00000373088.1_Silent_p.P988P|PCDH11X_ENST00000298274.8_Silent_p.P988P|PCDH11X_ENST00000361724.1_Silent_p.P988P	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	988					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						GTTCAGATCCCTACAGCGTTT	0.493																																					p.P988P	NSCLC(38;925 1092 2571 38200 45895)	Atlas-SNP	.											.	PCDH11X	714	.	0			c.C2964A						PASS	.						238	182	201					X																	91134203		2203	4300	6503	SO:0001819	synonymous_variant	27328	exon2			AGATCCCTACAGC	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.2964C>A	X.37:g.91134203C>A		251	0	0		175	27	0.154286	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	37	CCDS14461.1																																																																																			.	.	none		0.493	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969		A	91134203	C	A	91134203	2	1	39	1	0	0	0	0	0	0	0	1	11517	668	24	4		4	PCDH11X	23	91134203	Silent	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	8369983	91134203	64136357	239	14784											
PCDH11X	27328	hgsc.bcm.edu	37	chrX	91518117	91518117	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttttatcctaaatcagcggaAatctgaagggaaagtggcag	14	10	11	6	1	2	1	1	1	1	0	3	3	3	3	1	3	1	1	1	3	6	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chrX:91518117A>T	ENST00000373094.1	+	4	3964	c.3119A>T	c.(3118-3120)aAa>aTa	p.K1040I	PCDH11X_ENST00000406881.1_Missense_Mutation_p.K1040I|PCDH11X_ENST00000504220.2_Missense_Mutation_p.K1040I|PCDH11X_ENST00000361655.2_Intron|PCDH11X_ENST00000373097.1_Intron|PCDH11X_ENST00000373088.1_Intron|PCDH11X_ENST00000298274.8_Intron	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	1040					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						AATCAGCGGAAATCTGAAGGG	0.328																																					p.K1040I	NSCLC(38;925 1092 2571 38200 45895)	Atlas-SNP	.											.	PCDH11X	714	.	0			c.A3119T						PASS	.						45	40	42					X																	91518117		2200	4299	6499	SO:0001583	missense	27328	exon4			AGCGGAAATCTGA	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.3119A>T	X.37:g.91518117A>T	ENSP00000362186:p.Lys1040Ile	873	0	0		583	183	0.313894	NM_001168361	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	37	CCDS14461.1	.	.	.	.	.	.	.	.	.	.	A	3.420	-0.118458	0.06838	.	.	ENSG00000102290	ENST00000373094;ENST00000504220;ENST00000406881;ENST00000356934	T;T;T	0.55930	0.49;0.58;0.51	4.37	1.99	0.26369	.	2.689910	0.01979	U	0.044639	T	0.48429	0.1499	L	0.27053	0.805	0.18873	N	0.999984	P;P;P	0.48503	0.852;0.911;0.856	P;P;B	0.47705	0.555;0.555;0.352	T	0.31364	-0.9946	10	0.66056	D	0.02	.	5.1595	0.15054	0.735:0.0:0.265:0.0	.	1040;1040;1040	Q9BZA7-6;Q9BZA7-8;Q9BZA7	.;.;PC11X_HUMAN	I	1040	ENSP00000362186:K1040I;ENSP00000423762:K1040I;ENSP00000384758:K1040I	ENSP00000349408:K1040I	K	+	2	0	PCDH11X	91404773	0.968000	0.33430	0.142000	0.22268	0.048000	0.14542	0.914000	0.28624	0.034000	0.15491	0.339000	0.21740	AAA	.	.	none		0.328	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969		T	91518117	A	T	91518117	3	4	39	1	0	0	0	0	1	0	0	0	11517	14	1	5	3215	5	PCDH11X	23	91518117	Missense_Mutation	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	383914	91518117	63752443	240	14785											
NRK	203447	hgsc.bcm.edu	37	chrX	105153118	105153118	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aggcttctgcaggtacagtcCcaggtatccaaaaagcagca	13	7	10	11	0	1	0	0	0	1	0	3	0	3	0	2	3	4	6	2	3	4	3			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chrX:105153118C>T	ENST00000243300.9	+	13	1788	c.1485C>T	c.(1483-1485)tcC>tcT	p.S495S	NRK_ENST00000428173.2_Silent_p.S496S	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	495	Gln-rich.				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						AGGTACAGTCCCAGGTATCCA	0.542										HNSCC(51;0.14)																											p.S495S		Atlas-SNP	.											.	NRK	321	.	0			c.C1485T						PASS	.						53	54	53					X																	105153118		2025	4166	6191	SO:0001819	synonymous_variant	203447	exon13			ACAGTCCCAGGTA	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.1485C>T	X.37:g.105153118C>T		236	0	0		161	15	0.0931677	NM_198465	Q32ND6|Q5H9K2|Q6ZMP2	Silent	SNP	ENST00000243300.9	37																																																																																				.	.	none		0.542	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465		T	105153118	C	T	105153118	2	4	39	1	0	0	0	0	0	0	0	1	10664	610	22	2		2	NRK	23	105153118	Silent	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	13635001	105153118	50117442	241	14786											
GPC3	2719	hgsc.bcm.edu	37	chrX	132833966	132833966	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcatgttctacatgagcaaCttttaatactttcttgtcaa	11	18	4	8	0	4	1	2	1	2	0	4	1	4	1	0	0	4	2	0	0	5	8			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chrX:132833966C>A	ENST00000370818.3	-	4	1568	c.1123G>T	c.(1123-1125)Gtt>Ttt	p.V375F	GPC3_ENST00000394299.2_Missense_Mutation_p.V398F|GPC3_ENST00000543339.1_Missense_Mutation_p.V321F	NM_001164618.1|NM_004484.3	NP_001158090.1|NP_004475.1	P51654	GPC3_HUMAN	glypican 3	375					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)					ACATGAGCAACTTTTAATACT	0.333			"T, D, Mis, N, F, S"			Wilms tumour			Simpson-Golabi-Behmel syndrome																												p.V398F		Atlas-SNP	.	yes	Rec/X		Simpson-Golabi-Behmel syndrome	X	Xq26.1	2719	glypican 3		O	.	GPC3	88	.	0			c.G1192T						PASS	.						66	60	62					X																	132833966		2203	4298	6501	SO:0001583	missense	2719	exon5	Familial Cancer Database	SGBS	GAGCAACTTTTAA	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.1123G>T	X.37:g.132833966C>A	ENSP00000359854:p.Val375Phe	976	2	0.00204918		583	200	0.343053	NM_001164617	C9JLE3|G3V1R0|Q2L880|Q2L882	Missense_Mutation	SNP	ENST00000370818.3	37	CCDS14638.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.0|21.0	4.077701|4.077701	0.76528|0.76528	.|.	.|.	ENSG00000147257|ENSG00000147257	ENST00000406757|ENST00000370818;ENST00000394299;ENST00000543339	T|T;T;T	0.52526|0.51817	0.66|0.69;0.69;0.69	5.29|5.29	5.29|5.29	0.74685|0.74685	.|.	.|0.546935	.|0.17892	.|N	.|0.158471	T|T	0.59770|0.59770	0.2218|0.2218	L|L	0.47716|0.47716	1.5|1.5	0.39149|0.39149	D|D	0.962187|0.962187	.|D;D;P;P	.|0.67145	.|0.984;0.996;0.872;0.647	.|D;D;P;P	.|0.65140	.|0.932;0.93;0.593;0.593	T|T	0.57780|0.57780	-0.7752|-0.7752	7|10	0.29301|0.33141	T|T	0.29|0.24	.|.	15.0436|15.0436	0.71811|0.71811	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|359;321;398;375	.|B4DTD8;G3V1R0;C9JLE3;P51654	.|.;.;.;GPC3_HUMAN	N|F	104|375;398;321	ENSP00000385307:K104N|ENSP00000359854:V375F;ENSP00000377836:V398F;ENSP00000444222:V321F	ENSP00000385307:K104N|ENSP00000359854:V375F	K|V	-|-	3|1	2|0	GPC3|GPC3	132661632|132661632	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.957000|0.957000	0.61999|0.61999	2.376000|2.376000	0.44292|0.44292	2.194000|2.194000	0.70268|0.70268	0.429000|0.429000	0.28392|0.28392	AAG|GTT	.	.	none		0.333	GPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058356.1	NM_004484		A	132833966	C	A	132833966	3	1	39	1	0	0	0	0	1	0	0	0	6607	565	20	4	639	4	GPC3	23	132833966	Missense_Mutation	SNP	C	TCGA-GS-A9TW-01A-11D-A382-10	27680848	132833966	22436594	242	14787											
MTMR1	8776	hgsc.bcm.edu	37	chrX	149899968	149899968	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ccaaatgagagttggaaaatAtccaaaataaacagtaatta	21	9	6	5	0	0	1	0	1	0	1	1	3	1	2	2	1	1	2	2	1	10	5			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chrX:149899968A>G	ENST00000370390.3	+	8	901	c.744A>G	c.(742-744)atA>atG	p.I248M	MTMR1_ENST00000445323.2_Missense_Mutation_p.I256M|MTMR1_ENST00000544228.1_Missense_Mutation_p.I248M|MTMR1_ENST00000451863.2_Missense_Mutation_p.I248M|MTMR1_ENST00000542156.1_Missense_Mutation_p.I248M|MTMR1_ENST00000541925.1_Missense_Mutation_p.I154M|MTMR1_ENST00000538506.1_Missense_Mutation_p.I135M	NM_003828.2	NP_003819.1	Q13613	MTMR1_HUMAN	myotubularin related protein 1	248	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)					GTTGGAAAATATCCAAAATAA	0.388																																					p.I248M		Atlas-SNP	.											.	MTMR1	82	.	0			c.A744G						PASS	.						128	122	124					X																	149899968		2203	4300	6503	SO:0001583	missense	8776	exon8			GAAAATATCCAAA	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.744A>G	X.37:g.149899968A>G	ENSP00000359417:p.Ile248Met	317	0	0		219	74	0.3379	NM_003828	A0A024RC07|Q9UBX6|Q9UEM0|Q9UQD5	Missense_Mutation	SNP	ENST00000370390.3	37	CCDS14695.1	.	.	.	.	.	.	.	.	.	.	A	14.92	2.678394	0.47886	.	.	ENSG00000063601	ENST00000541925;ENST00000542156;ENST00000370390;ENST00000445323;ENST00000544228;ENST00000451863;ENST00000538506	D;D;D;D;D;D;D	0.94723	-3.5;-3.5;-3.5;-3.5;-3.5;-3.5;-2.85	5.78	1.79	0.24919	Myotubularin phosphatase domain (1);	0.038960	0.85682	D	0.000000	D	0.92996	0.7771	M	0.82433	2.59	0.51767	D	0.999939	B;P;B	0.40180	0.218;0.705;0.368	B;B;B	0.35510	0.09;0.186;0.204	D	0.89151	0.3523	9	.	.	.	.	12.7558	0.57335	0.613:0.387:0.0:0.0	.	248;256;248	Q13613;F8WA39;Q8NEC6	MTMR1_HUMAN;.;.	M	154;248;248;256;248;248;135	ENSP00000441879:I154M;ENSP00000445281:I248M;ENSP00000359417:I248M;ENSP00000414178:I256M;ENSP00000440534:I248M;ENSP00000387446:I248M;ENSP00000443444:I135M	.	I	+	3	3	MTMR1	149650626	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	1.089000	0.30890	0.013000	0.14918	0.441000	0.28932	ATA	.	.	none		0.388	MTMR1-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060863.2	NM_003828, NM_176789		G	149899968	A	G	149899968	3	3	39	1	0	0	0	0	1	0	0	0	9947	439	16	3	774	3	MTMR1	23	149899968	Missense_Mutation	SNP	A	TCGA-GS-A9TW-01A-11D-A382-10	17066002	149899968	5370592	243	14788											
GABRQ	55879	hgsc.bcm.edu	37	chrX	151817742	151817742	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ctacagcagcttgttccctgGatctgcataaattccctatg	9	13	7	12	0	1	0	0	0	1	0	3	1	3	1	2	1	4	4	2	1	4	6			TCGA-GS-A9TW-01A-11D-A382-10	TCGA-GS-A9TW-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	0c78bd1a-f7eb-4456-8210-f115aa079df5	e592ed1e-4fa3-459e-8256-01b5e2dc09ce	g.chrX:151817742G>C	ENST00000370306.2	+	5	576	c.556G>C	c.(556-558)Gat>Cat	p.D186H		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	186					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)	TTGTTCCCTGGATCTGCATAA	0.507																																					p.D186H		Atlas-SNP	.											.	GABRQ	131	.	0			c.G556C						PASS	.						188	147	161					X																	151817742		2203	4300	6503	SO:0001583	missense	55879	exon5			TCCCTGGATCTGC	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.556G>C	X.37:g.151817742G>C	ENSP00000359329:p.Asp186His	200	0	0		153	60	0.392157	NM_018558	A6NFN1|Q32MB4|Q9NZK8	Missense_Mutation	SNP	ENST00000370306.2	37	CCDS14707.1	.	.	.	.	.	.	.	.	.	.	G	14.91	2.676104	0.47886	.	.	ENSG00000147402	ENST00000370306	T	0.81415	-1.49	5.8	1.89	0.25635	Neurotransmitter-gated ion-channel ligand-binding (3);Neurotransmitter-gated ion-channel, conserved site (1);	0.399455	0.21498	N	0.073562	D	0.84656	0.5520	L	0.50847	1.595	0.35231	D	0.776932	D	0.76494	0.999	D	0.69824	0.966	D	0.85842	0.1398	10	0.66056	D	0.02	.	11.1219	0.48296	0.2236:0.0:0.7764:0.0	.	186	Q9UN88	GBRT_HUMAN	H	186	ENSP00000359329:D186H	ENSP00000359329:D186H	D	+	1	0	GABRQ	151568398	1.000000	0.71417	0.116000	0.21606	0.233000	0.25261	2.860000	0.48372	-0.063000	0.13065	0.600000	0.82982	GAT	.	.	none		0.507	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558		C	151817742	G	C	151817742	3	2	39	1	0	0	0	0	1	0	0	0	6183	1174	41	4	574	4	GABRQ	23	151817742	Missense_Mutation	SNP	G	TCGA-GS-A9TW-01A-11D-A382-10	1917774	151817742	3452818	244	14789											
NRD1	4898	hgsc.bcm.edu	37	chr1	52306075	52306075	+	Silent	SNP	T	T	C																															tcatcatcatcttcttcttcTtcctccacctcctcttcttc																								rs78724482	byFrequency	TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr1:52306075T>C	ENST00000354831.7	-	2	642	c.453A>G	c.(451-453)gaA>gaG	p.E151E	NRD1_ENST00000485608.1_5'UTR|NRD1_ENST00000352171.7_Silent_p.E151E|NRD1_ENST00000544028.1_Silent_p.E19E|NRD1_ENST00000539524.1_Silent_p.E19E	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						cttcttcttcttcctccacct	0.388																																					p.E151E		Atlas-SNP	.											.	NRD1	89	.	0			c.A453G						PASS	.						165	136	146					1																	52306075		2203	4300	6503	SO:0001819	synonymous_variant	4898	exon2			TTCTTCTTCCTCC	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.453A>G	1.37:g.52306075T>C		356	0	0		370	35	0.0945946	NM_001101662	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Silent	SNP	ENST00000354831.7	37	CCDS559.1																																																																																			T|0.952;C|0.048	0.048	strong		0.388	NRD1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000023045.1	NM_002525		C	52306075	T	C	52306075	2	2	40	1	0	0	0	0	0	0	0	1	10654	1606	56	3		3	NRD1	1	52306075	Silent	SNP	T	TCGA-GS-A9TX-01A-11D-A382-10		52306075	196944546	1	14790	194	2									
NRD1	4898	hgsc.bcm.edu	37	chr1	52306079	52306079	+	Missense_Mutation	SNP	T	T	A																															catcatcttcttcttcttccTccacctcctcttcttcttca																								rs62648104		TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	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						PASS	.						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	1.37:g.52306079T>A	ENSP00000346890:p.Glu150Val	354	0	0		366	26	0.0710383	NM_001101662	A6NI41|O15241|O15242|Q5VUL0|Q96HB2|Q9NU57	Missense_Mutation	SNP	ENST00000354831.7	37	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	0.976	weak		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	40	1	0	0	0	0	1	0	0	0	10654	1551	54	5	3338	5	NRD1	1	52306079	Missense_Mutation	SNP	T	TCGA-GS-A9TX-01A-11D-A382-10	4	52306079	196944542	2	14791	194	2									
OR2L2	26246	hgsc.bcm.edu	37	chr1	248202348	248202348	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttgcttatacctatgtacGtccaagatccctgcgatctc	8	14	6	13	2	1	1	0	0	1	1	4	2	3	1	3	0	4	2	3	0	5	5	rs138166879		TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr1:248202348G>A	ENST00000366479.2	+	1	875	c.779G>A	c.(778-780)cGt>cAt	p.R260H	OR2L13_ENST00000366478.2_Intron	NM_001004686.2	NP_001004686.1	Q8NH16	OR2L2_HUMAN	olfactory receptor, family 2, subfamily L, member 2	260						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)			ACCTATGTACGTCCAAGATCC	0.493																																					p.R260H		Atlas-SNP	.											OR2L2,right_upper_lobe,carcinoma,+1,2	OR2L2	115	2	0			c.G779A						PASS	.	G	HIS/ARG,	1,4405		0,1,2202	149	135	139		779,	-0.3	0	1	dbSNP_134	139	1,8599		0,1,4299	no	missense,intron	OR2L2,OR2L13	NM_001004686.2,NM_175911.2	29,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	benign,	260/313,	248202348	2,13004	2203	4300	6503	SO:0001583	missense	26246	exon1			ATGTACGTCCAAG	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.779G>A	1.37:g.248202348G>A	ENSP00000355435:p.Arg260His	149	0	0		116	18	0.155172	NM_001004686	Q2M3T5	Missense_Mutation	SNP	ENST00000366479.2	37	CCDS31103.1	.	.	.	.	.	.	.	.	.	.	.	7.027	0.559906	0.13436	2.27E-4	1.16E-4	ENSG00000203663	ENST00000366479	T	0.37752	1.18	1.9	-0.295	0.12828	GPCR, rhodopsin-like superfamily (1);	1.359230	0.05838	N	0.618748	T	0.15652	0.0377	N	0.02876	-0.465	0.09310	N	1	B	0.18741	0.03	B	0.20955	0.032	T	0.24728	-1.0152	10	0.27785	T	0.31	.	5.8101	0.18462	0.6147:0.0:0.3853:0.0	.	260	Q8NH16	OR2L2_HUMAN	H	260	ENSP00000355435:R260H	ENSP00000355435:R260H	R	+	2	0	OR2L2	246268971	0.000000	0.05858	0.001000	0.08648	0.129000	0.20672	-0.108000	0.10857	0.035000	0.15519	0.194000	0.17425	CGT	G|1.000;A|0.000	0.000	weak		0.493	OR2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096871.1	NM_001004686		A	248202348	G	A	248202348	3	1	40	1	0	0	0	0	1	0	0	0	11016	1145	40	1	781	1	OR2L2	1	248202348	Missense_Mutation	SNP	G	TCGA-GS-A9TX-01A-11D-A382-10	195896269	248202348	1048273	3	14792											
ASXL2	55252	hgsc.bcm.edu	37	chr2	25966225	25966225	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tttctgttgtgttggtagctAtgagcgctcccatccccctt	4	16	9	12	1	1	1	0	1	1	0	3	1	3	1	3	1	2	5	3	1	2	6			TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr2:25966225A>T	ENST00000435504.4	-	13	3274	c.2981T>A	c.(2980-2982)aTa>aAa	p.I994K	ASXL2_ENST00000404843.1_Intron|ASXL2_ENST00000336112.4_Missense_Mutation_p.I966K|ASXL2_ENST00000272341.4_Intron			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	994					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)					GTTGGTAGCTATGAGCGCTCC	0.478																																					p.I994K		Atlas-SNP	.											.	ASXL2	217	.	0			c.T2981A						PASS	.						69	71	70					2																	25966225		1942	4150	6092	SO:0001583	missense	55252	exon12			GTAGCTATGAGCG			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.2981T>A	2.37:g.25966225A>T	ENSP00000391447:p.Ile994Lys	67	0	0		74	14	0.189189	NM_018263	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Missense_Mutation	SNP	ENST00000435504.4	37		.	.	.	.	.	.	.	.	.	.	A	1.432	-0.570090	0.03910	.	.	ENSG00000143970	ENST00000435504;ENST00000336112	T;T	0.22134	1.97;1.97	5.94	2.99	0.34606	.	1.396170	0.03804	N	0.264897	T	0.16599	0.0399	N	0.22421	0.69	0.09310	N	0.999999	B	0.15473	0.013	B	0.12156	0.007	T	0.25779	-1.0122	10	0.87932	D	0	6.8419	5.2126	0.15325	0.2217:0.3059:0.4723:0.0	.	994	Q76L83	ASXL2_HUMAN	K	994;966	ENSP00000391447:I994K;ENSP00000337250:I966K	ENSP00000337250:I966K	I	-	2	0	ASXL2	25819729	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.088000	0.14979	0.775000	0.33450	0.460000	0.39030	ATA	.	.	none		0.478	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263		T	25966225	A	T	25966225	3	4	40	1	0	0	0	0	1	0	0	0	1067	449	16	5	1330	5	ASXL2	2	25966225	Missense_Mutation	SNP	A	TCGA-GS-A9TX-01A-11D-A382-10		25966225	217233148	4	14793			1	67		3	3	54	N	T_A	9.720131e-10
ASXL2	55252	hgsc.bcm.edu	37	chr2	25966254	25966254	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccatccccctttcctctttTgcagtcagtggaaccgtttt	5	15	6	15	1	2	0	1	0	1	0	4	1	4	1	5	1	2	2	5	1	1	5			TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr2:25966254T>C	ENST00000435504.4	-	13	3245	c.2952A>G	c.(2950-2952)gcA>gcG	p.A984A	ASXL2_ENST00000404843.1_Intron|ASXL2_ENST00000336112.4_Silent_p.A956A|ASXL2_ENST00000272341.4_Intron			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	984					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)					TTTCCTCTTTTGCAGTCAGTG	0.473																																					p.A984A		Atlas-SNP	.											.	ASXL2	217	.	0			c.A2952G						PASS	.						82	82	82					2																	25966254		1908	4135	6043	SO:0001819	synonymous_variant	55252	exon12			CTCTTTTGCAGTC			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.2952A>G	2.37:g.25966254T>C		76	0	0		77	16	0.207792	NM_018263	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Silent	SNP	ENST00000435504.4	37																																																																																				.	.	none		0.473	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263		C	25966254	T	C	25966254	2	2	40	1	0	0	0	0	0	0	0	1	1067	1799	63	3		3	ASXL2	2	25966254	Silent	SNP	T	TCGA-GS-A9TX-01A-11D-A382-10	29	25966254	217233119	5	14794			1	67		3	3	54	N	T_A	9.720131e-10
ASXL2	55252	hgsc.bcm.edu	37	chr2	25966278	25966278	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtcagtggaaccgttttcatTtcaactttggtgagaggttt	8	16	11	6	1	3	1	3	1	0	1	3	3	3	2	1	3	2	2	1	3	2	5			TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr2:25966278T>C	ENST00000435504.4	-	13	3221	c.2928A>G	c.(2926-2928)gaA>gaG	p.E976E	ASXL2_ENST00000404843.1_Intron|ASXL2_ENST00000336112.4_Silent_p.E948E|ASXL2_ENST00000272341.4_Intron			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	976					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)					CCGTTTTCATTTCAACTTTGG	0.448																																					p.E976E		Atlas-SNP	.											.	ASXL2	217	.	0			c.A2928G						PASS	.						108	107	107					2																	25966278		1893	4115	6008	SO:0001819	synonymous_variant	55252	exon12			TTTCATTTCAACT			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.2928A>G	2.37:g.25966278T>C		79	0	0		89	14	0.157303	NM_018263	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Silent	SNP	ENST00000435504.4	37																																																																																				.	.	none		0.448	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263		C	25966278	T	C	25966278	2	2	40	1	0	0	0	0	0	0	0	1	1067	1838	64	3		3	ASXL2	2	25966278	Silent	SNP	T	TCGA-GS-A9TX-01A-11D-A382-10	24	25966278	217233095	6	14795			1	67		3	3	54	N	T_A	9.720131e-10
USP39	10713	hgsc.bcm.edu	37	chr2	85857936	85857936	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccaggggatatcatgttcttGttggtccagcgttttggaga	7	14	13	7	1	2	1	1	0	1	1	3	3	3	2	2	4	1	3	2	4	1	6			TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr2:85857936G>C	ENST00000323701.6	+	6	826	c.816G>C	c.(814-816)ttG>ttC	p.L272F	USP39_ENST00000409025.1_Missense_Mutation_p.L272F|USP39_ENST00000409766.3_Missense_Mutation_p.L272F|USP39_ENST00000450066.2_Missense_Mutation_p.L169F|USP39_ENST00000409470.1_Missense_Mutation_p.L272F|USP39_ENST00000459775.1_3'UTR	NM_006590.3	NP_006581.2	Q53GS9	SNUT2_HUMAN	ubiquitin specific peptidase 39	272	USP.				cell cycle (GO:0007049)|cell division (GO:0051301)|mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|ubiquitin-dependent protein catabolic process (GO:0006511)	spliceosomal complex (GO:0005681)	ubiquitinyl hydrolase activity (GO:0036459)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	19						TCATGTTCTTGTTGGTCCAGC	0.438																																					p.L272F		Atlas-SNP	.											.	USP39	33	.	0			c.G816C						PASS	.						147	148	148					2																	85857936		2203	4300	6503	SO:0001583	missense	10713	exon6			GTTCTTGTTGGTC	AF132955	CCDS33234.1, CCDS58716.1, CCDS58717.1, CCDS74534.1	2p11.2	2009-01-06	2005-08-08		ENSG00000168883	ENSG00000168883		"Ubiquitin-specific peptidases"	20071	protein-coding gene	gene with protein product	"snRNP assembly defective 1 homolog (S.cerevisiae)", "small nuclear ribonucleoprotein 65kDa (U4/U6.U5)"	611594	"ubiquitin specific protease 39"			12838346	Standard	NM_006590		Approved	SAD1, CGI-21, SNRNP65	uc002sqg.4	Q53GS9	OTTHUMG00000153090	ENST00000323701.6:c.816G>C	2.37:g.85857936G>C	ENSP00000312981:p.Leu272Phe	212	0	0		258	67	0.25969	NM_001256725	A8K086|B3KM40|B4DHT4|D6W5L4|G5E9H0|Q6NX47|Q96RK9|Q9BV89|Q9H381|Q9P050|Q9Y310	Missense_Mutation	SNP	ENST00000323701.6	37	CCDS33234.1	.	.	.	.	.	.	.	.	.	.	G	17.97	3.518167	0.64634	.	.	ENSG00000168883	ENST00000450066;ENST00000409268;ENST00000409025;ENST00000409470;ENST00000323701;ENST00000409766	T;T;T;T;T	0.32272	1.46;4.1;1.46;1.46;1.46	5.97	0.741	0.18336	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.49932	0.1586	M	0.84219	2.685	0.49798	D	0.999825	D;P;D;D;D;D	0.71674	0.972;0.738;0.995;0.998;0.992;0.969	D;P;D;D;D;D	0.71414	0.924;0.738;0.918;0.973;0.933;0.924	T	0.47611	-0.9104	10	0.56958	D	0.05	-5.3478	6.4861	0.22089	0.2936:0.123:0.5834:0.0	.	169;194;272;272;272;272	B4DHT4;B7Z7L9;G5E9H0;B3KM40;B9A018;Q53GS9	.;.;.;.;.;SNUT2_HUMAN	F	169;272;272;272;272;272	ENSP00000396133:L169F;ENSP00000386572:L272F;ENSP00000386864:L272F;ENSP00000312981:L272F;ENSP00000386803:L272F	ENSP00000312981:L272F	L	+	3	2	USP39	85711447	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	0.904000	0.28491	0.421000	0.25980	-0.229000	0.12294	TTG	.	.	none		0.438	USP39-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329892.1	NM_006590		C	85857936	G	C	85857936	3	2	40	1	0	0	0	0	1	0	0	0	17085	1368	48	4	838	4	USP39	2	85857936	Missense_Mutation	SNP	G	TCGA-GS-A9TX-01A-11D-A382-10	59891658	85857936	157341437	7	14796											
REV1	51455	hgsc.bcm.edu	37	chr2	100065955	100065955	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cattagttttctcaattcctCagcggaaggatctgcaaaat	12	13	7	9	1	3	0	2	0	2	0	5	2	4	2	1	2	2	2	1	2	5	4			TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr2:100065955C>T	ENST00000258428.3	-	4	421	c.193G>A	c.(193-195)Gag>Aag	p.E65K	REV1_ENST00000465835.1_5'UTR|REV1_ENST00000393445.3_Missense_Mutation_p.E65K	NM_001037872.1|NM_016316.2	NP_001032961.1|NP_057400.1	Q9UBZ9	REV1_HUMAN	REV1, polymerase (DNA directed)	65	BRCT. {ECO:0000255|PROSITE- ProRule:PRU00033}.				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						CTCAATTCCTCAGCGGAAGGA	0.318								Direct reversal of damage																													p.E65K		Atlas-SNP	.											.	REV1	100	.	0			c.G193A						PASS	.						79	80	80					2																	100065955		2203	4300	6503	SO:0001583	missense	51455	exon4			ATTCCTCAGCGGA	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.193G>A	2.37:g.100065955C>T	ENSP00000258428:p.Glu65Lys	127	0	0		126	27	0.214286	NM_001037872	O95941|Q53SI7|Q9C0J4|Q9NUP2	Missense_Mutation	SNP	ENST00000258428.3	37	CCDS2045.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.794160	0.90453	.	.	ENSG00000135945	ENST00000393445;ENST00000258428	T;T	0.79940	-1.32;-1.32	6.07	6.07	0.98685	BRCT (4);	0.145050	0.64402	D	0.000009	T	0.79534	0.4462	L	0.52126	1.63	0.52501	D	0.999959	P;B;B	0.43352	0.804;0.389;0.029	B;B;B	0.39840	0.311;0.21;0.036	T	0.80538	-0.1338	10	0.59425	D	0.04	.	20.6593	0.99626	0.0:1.0:0.0:0.0	.	44;65;65	Q9UBZ9-3;Q9UBZ9;Q9UBZ9-2	.;REV1_HUMAN;.	K	65	ENSP00000377091:E65K;ENSP00000258428:E65K	ENSP00000258428:E65K	E	-	1	0	REV1	99432387	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.456000	0.80751	2.885000	0.99019	0.655000	0.94253	GAG	.	.	none		0.318	REV1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253123.2	NM_016316		T	100065955	C	T	100065955	3	4	40	1	0	0	0	0	1	0	0	0	13254	835	29	2	3642	2	REV1	2	100065955	Missense_Mutation	SNP	C	TCGA-GS-A9TX-01A-11D-A382-10	14208019	100065955	143133418	8	14797											
LRP1B	53353	hgsc.bcm.edu	37	chr2	141819775	141819775	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgaatcaattatccttgttcGgttcatcccatccatgtcac	9	15	5	12	1	3	1	3	1	0	0	7	1	6	1	3	1	0	2	3	1	3	4			TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr2:141819775G>T	ENST00000389484.3	-	8	2052	c.1081C>A	c.(1081-1083)Cga>Aga	p.R361R		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	361					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)		ATCCTTGTTCGGTTCATCCCA	0.413										TSP Lung(27;0.18)																											p.R361R	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											LRP1B,NS,carcinoma,+1,3	LRP1B	1315	3	0			c.C1081A						PASS	.						153	134	140					2																	141819775		2203	4300	6503	SO:0001819	synonymous_variant	53353	exon8			TTGTTCGGTTCAT	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.1081C>A	2.37:g.141819775G>T		181	0	0		141	26	0.184397	NM_018557	Q8WY29|Q8WY30|Q8WY31	Silent	SNP	ENST00000389484.3	37	CCDS2182.1																																																																																			.	.	none		0.413	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		T	141819775	G	T	141819775	2	4	40	1	0	0	0	0	0	0	0	1	8964	1124	39	4		4	LRP1B	2	141819775	Silent	SNP	G	TCGA-GS-A9TX-01A-11D-A382-10	41753820	141819775	101379598	9	14798											
SETMAR	6419	hgsc.bcm.edu	37	chr3	4354652	4354652	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aataacctttcccggatgcaTttgtgtcaaaactccctgcc	10	12	6	13	1	1	0	1	0	0	0	3	1	3	1	4	1	4	1	4	1	4	3			TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr3:4354652T>C	ENST00000358065.4	+	2	294	c.227T>C	c.(226-228)aTt>aCt	p.I76T	SETMAR_ENST00000425863.1_Missense_Mutation_p.I76T|SETMAR_ENST00000462115.1_3'UTR|SUMF1_ENST00000534863.1_Intron|SETMAR_ENST00000430981.1_Missense_Mutation_p.I76T	NM_006515.3	NP_006506.3	Q53H47	SETMR_HUMAN	SET domain and mariner transposase fusion gene	76	Histone-lysine N-methyltransferase.|Pre-SET. {ECO:0000255|PROSITE- ProRule:PRU00157}.				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)		CCCGGATGCATTTGTGTCAAA	0.458								Chromatin Structure																													p.I76T		Atlas-SNP	.											.	SETMAR	30	.	0			c.T227C						PASS	.						113	107	109					3																	4354652		2203	4300	6503	SO:0001583	missense	6419	exon2			GATGCATTTGTGT	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.227T>C	3.37:g.4354652T>C	ENSP00000373354:p.Ile76Thr	153	0	0		171	50	0.292398	NM_001243723	B4DY74|E7EN68|Q13579|Q1G668|Q96F41	Missense_Mutation	SNP	ENST00000358065.4	37	CCDS2563.2	.	.	.	.	.	.	.	.	.	.	T	8.760	0.923452	0.18056	.	.	ENSG00000170364	ENST00000358065;ENST00000430981;ENST00000425863	D;D;T	0.88354	-2.37;-2.37;-1.26	5.13	-7.57	0.01318	Pre-SET zinc-binding sub-group (1);Pre-SET domain (2);	.	.	.	.	T	0.75459	0.3852	N	0.20685	0.6	0.09310	N	1	B;B;B	0.16396	0.017;0.006;0.0	B;B;B	0.22753	0.031;0.041;0.008	T	0.60576	-0.7236	9	0.23302	T	0.38	.	7.2937	0.26380	0.0851:0.536:0.1722:0.2066	.	76;63;76	E7EN68;Q53H47;C9JHK2	.;SETMR_HUMAN;.	T	76	ENSP00000373354:I76T;ENSP00000403000:I76T;ENSP00000403145:I76T	ENSP00000373354:I76T	I	+	2	0	SETMAR	4329652	0.000000	0.05858	0.000000	0.03702	0.984000	0.73092	-2.058000	0.01394	-1.487000	0.01849	0.455000	0.32223	ATT	.	.	none		0.458	SETMAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206587.4	NM_006515		C	4354652	T	C	4354652	3	2	40	1	0	0	0	0	1	0	0	0	14155	1493	52	3	233	3	SETMAR	3	4354652	Missense_Mutation	SNP	T	TCGA-GS-A9TX-01A-11D-A382-10		4354652	193667778	10	14799											
CELSR3	1951	hgsc.bcm.edu	37	chr3	48698377	48698377	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtggccgtgacgcgcagcAcgactgtgtgggggcgcaca	7	5	17	12	5	0	1	0	1	0	0	0	2	0	1	1	3	1	3	1	3	0	0			TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr3:48698377A>C	ENST00000164024.4	-	1	1971	c.1691T>G	c.(1690-1692)gTg>gGg	p.V564G	RP11-148G20.1_ENST00000421275.1_RNA|CELSR3_ENST00000544264.1_Missense_Mutation_p.V564G	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	564	Cadherin 3. {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)		GACGCGCAGCACGACTGTGTG	0.587																																					p.V564G		Atlas-SNP	.											.	CELSR3	237	.	0			c.T1691G						PASS	.						69	49	56					3																	48698377		2203	4300	6503	SO:0001583	missense	1951	exon1			CGCAGCACGACTG	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.1691T>G	3.37:g.48698377A>C	ENSP00000164024:p.Val564Gly	107	0	0		81	15	0.185185	NM_001407	O75092	Missense_Mutation	SNP	ENST00000164024.4	37	CCDS2775.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.607092	0.87157	.	.	ENSG00000008300	ENST00000164024;ENST00000544264	T;T	0.02103	4.45;4.45	5.62	5.62	0.85841	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.18002	0.0432	M	0.92970	3.365	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.71656	0.974;0.939	T	0.02144	-1.1206	9	0.87932	D	0	.	15.8125	0.78576	1.0:0.0:0.0:0.0	.	564;634	Q9NYQ7;Q5Y190	CELR3_HUMAN;.	G	564	ENSP00000164024:V564G;ENSP00000445694:V564G	ENSP00000164024:V564G	V	-	2	0	CELSR3	48673381	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.277000	0.95755	2.134000	0.65973	0.533000	0.62120	GTG	.	.	none		0.587	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407		C	48698377	A	C	48698377	3	2	40	1	0	0	0	0	1	0	0	0	3225	159	6	5	8387	5	CELSR3	3	48698377	Missense_Mutation	SNP	A	TCGA-GS-A9TX-01A-11D-A382-10	44343725	48698377	149324053	11	14800											
SLC7A14	57709	hgsc.bcm.edu	37	chr3	170198934	170198934	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accactggtgtctctgtgtaGgagctgacgtgagccaggaa	9	9	14	9	1	1	2	0	2	1	0	2	4	1	4	2	3	2	2	2	3	2	1			TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr3:170198934G>A	ENST00000231706.5	-	7	1452	c.1137C>T	c.(1135-1137)tcC>tcT	p.S379S	CLDN11_ENST00000486975.1_Intron|CLDN11_ENST00000451576.1_Intron	NM_020949.2	NP_066000.2	Q8TBB6	S7A14_HUMAN	solute carrier family 7, member 14	379					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)			TCTCTGTGTAGGAGCTGACGT	0.572																																					p.S379S		Atlas-SNP	.											.	SLC7A14	110	.	0			c.C1137T						PASS	.						33	29	31					3																	170198934		2203	4300	6503	SO:0001819	synonymous_variant	57709	exon7			TGTGTAGGAGCTG	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.1137C>T	3.37:g.170198934G>A		39	0	0		49	7	0.142857	NM_020949	B3KV33|Q9HCF9	Silent	SNP	ENST00000231706.5	37	CCDS33892.1																																																																																			.	.	none		0.572	SLC7A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352598.2	NM_020949		A	170198934	G	A	170198934	2	1	40	1	0	0	0	0	0	0	0	1	14711	987	35	2		2	SLC7A14	3	170198934	Silent	SNP	G	TCGA-GS-A9TX-01A-11D-A382-10	121500557	170198934	27823496	12	14801											
KCNMB3	27094	hgsc.bcm.edu	37	chr3	178960904	178960904	+	Frame_Shift_Del	DEL	T	T	-																															ccaaaataaacagtggaagaTagccatttggtcatactttt																										TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr3:178960904delT	ENST00000314235.5	-	4	1139	c.628delA	c.(628-630)atcfs	p.I210fs	KCNMB3_ENST00000497599.1_Intron|KCNMB3_ENST00000392685.2_Frame_Shift_Del_p.I206fs|KCNMB3_ENST00000349697.2_Frame_Shift_Del_p.I208fs|KCNMB3_ENST00000485523.1_Frame_Shift_Del_p.I188fs|KCNMB3_ENST00000486944.1_Intron	NM_014407.3	NP_055222.3	Q9NPA1	KCMB3_HUMAN	potassium large conductance calcium-activated channel, subfamily M beta member 3	210					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)	CAGTGGAAGATAGCCATTTGG	0.418																																					p.I210fs		Atlas-Indel	.											.	KCNMB3	46	.	0			c.629delT						PASS	.						15	16	16					3																	178960904		2135	4244	6379	SO:0001589	frameshift_variant	27094	exon4			.	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.628delA	3.37:g.178960904delT	ENSP00000319370:p.Ile210fs	333	0	0		452	47	0.103982	NM_014407	B7Z9C9|D3DNR2|E9PER5|Q9NPG7|Q9NRM9|Q9UHN3	Frame_Shift_Del	DEL	ENST00000314235.5	37	CCDS3226.1																																																																																			.	.	none		0.418	KCNMB3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000348484.1			-	178960904	T	-	178960904	7	5	40	1	0	1	0	1	0	0	0	0	8085	1406	49	0	288	0	KCNMB3	3	178960904	Frame_Shift_Del	DEL	T	TCGA-GS-A9TX-01A-11D-A382-10	8761970	178960904	19061526	13	14802											
UBA6	55236	hgsc.bcm.edu	37	chr4	68530944	68530944	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagtcttaacttggacagctAtgcctccatgtaaatatggt	11	13	9	8	0	1	0	0	0	1	0	2	2	2	1	2	2	3	2	2	2	5	5			TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr4:68530944A>G	ENST00000322244.5	-	10	919	c.860T>C	c.(859-861)aTa>aCa	p.I287T	UBA6_ENST00000420827.2_Missense_Mutation_p.I287T	NM_018227.5	NP_060697.4	A0AVT1	UBA6_HUMAN	ubiquitin-like modifier activating enzyme 6	287					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						TTGGACAGCTATGCCTCCATG	0.308																																					p.I287T		Atlas-SNP	.											.	UBA6	98	.	0			c.T860C						PASS	.						77	83	81					4																	68530944		2203	4297	6500	SO:0001583	missense	55236	exon10			ACAGCTATGCCTC	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.860T>C	4.37:g.68530944A>G	ENSP00000313454:p.Ile287Thr	360	0	0		396	60	0.151515	NM_018227	A6N8M7|B2RAV3|Q4W5K0|Q6UV21|Q86T78|Q86TC7|Q8N5T3|Q8N9E4|Q9H3T7|Q9NVC9	Missense_Mutation	SNP	ENST00000322244.5	37	CCDS3516.1	.	.	.	.	.	.	.	.	.	.	A	15.64	2.892823	0.52121	.	.	ENSG00000033178	ENST00000322244;ENST00000420827	T;T	0.55760	0.5;0.5	5.37	5.37	0.77165	Molybdenum cofactor biosynthesis, MoeB (1);	0.046676	0.85682	D	0.000000	T	0.52613	0.1745	L	0.60957	1.885	0.50632	D	0.999888	P;P;P	0.43885	0.724;0.82;0.803	B;B;B	0.42062	0.259;0.374;0.232	T	0.56092	-0.8036	10	0.45353	T	0.12	-15.3972	15.3307	0.74208	1.0:0.0:0.0:0.0	.	287;287;287	A0AVT1-4;A0AVT1-3;A0AVT1	.;.;UBA6_HUMAN	T	287	ENSP00000313454:I287T;ENSP00000399234:I287T	ENSP00000313454:I287T	I	-	2	0	UBA6	68213539	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.799000	0.69101	2.173000	0.68751	0.377000	0.23210	ATA	.	.	none		0.308	UBA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251429.2	NM_018227		G	68530944	A	G	68530944	3	3	40	1	0	0	0	0	1	0	0	0	16847	449	16	3	2394	3	UBA6	4	68530944	Missense_Mutation	SNP	A	TCGA-GS-A9TX-01A-11D-A382-10		68530944	122623332	14	14803											
PTPN13	5783	hgsc.bcm.edu	37	chr4	87696720	87696720	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	atgtcatccattatgtgaacGgagtcagcacacaaggaatg	14	9	10	8	1	2	1	2	1	0	0	3	3	3	3	1	2	2	1	1	2	4	1			TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr4:87696720G>A	ENST00000411767.2	+	35	5869	c.5806G>A	c.(5806-5808)Gga>Aga	p.G1936R	PTPN13_ENST00000427191.2_Missense_Mutation_p.G1917R|PTPN13_ENST00000511467.1_Missense_Mutation_p.G1941R|PTPN13_ENST00000316707.6_Missense_Mutation_p.G1745R|PTPN13_ENST00000436978.1_Missense_Mutation_p.G1941R			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1936	PDZ 5. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)		TTATGTGAACGGAGTCAGCAC	0.408																																					p.G1941R		Atlas-SNP	.											.	PTPN13	203	.	0			c.G5821A						PASS	.						83	84	84					4																	87696720		2174	4282	6456	SO:0001583	missense	5783	exon35			GTGAACGGAGTCA		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.5806G>A	4.37:g.87696720G>A	ENSP00000407249:p.Gly1936Arg	126	0	0		132	22	0.166667	NM_080685	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Missense_Mutation	SNP	ENST00000411767.2	37	CCDS47094.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.981634	0.93044	.	.	ENSG00000163629	ENST00000427191;ENST00000436978;ENST00000316707;ENST00000411767;ENST00000511467;ENST00000357349	T;T;T;T;T	0.49720	0.77;0.77;0.77;0.77;0.77	5.45	5.45	0.79879	PDZ/DHR/GLGF (4);	0.000000	0.47852	D	0.000211	T	0.76835	0.4043	M	0.91510	3.215	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	0.82321	-0.0515	10	0.87932	D	0	.	19.2786	0.94042	0.0:0.0:1.0:0.0	.	1745;1917;1936;1941	Q12923-2;Q12923-3;Q12923;Q12923-4	.;.;PTN13_HUMAN;.	R	1917;1941;1745;1936;1941;1885	ENSP00000408368:G1917R;ENSP00000394794:G1941R;ENSP00000322675:G1745R;ENSP00000407249:G1936R;ENSP00000426626:G1941R	ENSP00000322675:G1745R	G	+	1	0	PTPN13	87915744	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	8.930000	0.92872	2.552000	0.86080	0.460000	0.39030	GGA	.	.	none		0.408	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1			A	87696720	G	A	87696720	3	1	40	1	0	0	0	0	1	0	0	0	12795	1117	39	1	5955	1	PTPN13	4	87696720	Missense_Mutation	SNP	G	TCGA-GS-A9TX-01A-11D-A382-10	19165776	87696720	103457556	15	14804											
SLC27A6	28965	hgsc.bcm.edu	37	chr5	128301873	128301873	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctaggggctggaatggtcGtcctgcacttcttgcagaaa	8	12	12	9	1	2	1	0	0	2	1	4	2	3	2	1	4	2	3	1	4	3	4			TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr5:128301873G>A	ENST00000262462.4	+	1	1053	c.43G>A	c.(43-45)Gtc>Atc	p.V15I	SLC27A6_ENST00000395266.1_Missense_Mutation_p.V15I|SLC27A6_ENST00000506176.1_Missense_Mutation_p.V15I			Q9Y2P4	S27A6_HUMAN	solute carrier family 27 (fatty acid transporter), member 6	15					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)		TGGAATGGTCGTCCTGCACTT	0.507																																					p.V15I		Atlas-SNP	.											.	SLC27A6	112	.	0			c.G43A						PASS	.						70	68	69					5																	128301873		2203	4300	6503	SO:0001583	missense	28965	exon1			ATGGTCGTCCTGC	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.43G>A	5.37:g.128301873G>A	ENSP00000262462:p.Val15Ile	195	0	0		234	31	0.132479	NM_001017372	Q6IAM5|Q7Z6E6|Q86YF6	Missense_Mutation	SNP	ENST00000262462.4	37	CCDS4145.1	.	.	.	.	.	.	.	.	.	.	G	0.021	-1.432019	0.01108	.	.	ENSG00000113396	ENST00000262462;ENST00000395266;ENST00000506176	T;T;T	0.52526	0.66;0.66;0.66	4.32	-1.02	0.10135	.	0.885476	0.10248	N	0.697577	T	0.18923	0.0454	N	0.02539	-0.55	0.09310	N	1	B	0.14805	0.011	B	0.12156	0.007	T	0.27468	-1.0073	10	0.07325	T	0.83	-9.4273	11.1007	0.48172	0.0:0.0714:0.6016:0.327	.	15	Q9Y2P4	S27A6_HUMAN	I	15	ENSP00000262462:V15I;ENSP00000378684:V15I;ENSP00000421024:V15I	ENSP00000262462:V15I	V	+	1	0	SLC27A6	128329772	0.000000	0.05858	0.026000	0.17262	0.533000	0.34776	-1.019000	0.03622	-0.143000	0.11334	-0.518000	0.04402	GTC	.	.	none		0.507	SLC27A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250980.1	NM_014031		A	128301873	G	A	128301873	3	1	40	1	0	0	0	0	1	0	0	0	14545	1145	40	1	45	1	SLC27A6	5	128301873	Missense_Mutation	SNP	G	TCGA-GS-A9TX-01A-11D-A382-10		128301873	52613387	16	14805											
HIST1H2BL	8340	hgsc.bcm.edu	37	chr6	27775319	27775319	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	agaatttacttggagctggtGtacttggtgacggccttggt	7	14	14	6	1	0	2	0	1	0	1	0	3	0	3	1	5	3	2	1	5	3	6	rs141178835	byFrequency	TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr6:27775319G>T	ENST00000377401.2	-	1	390	c.366C>A	c.(364-366)taC>taA	p.Y122*	HIST1H2AI_ENST00000358739.3_5'Flank|HIST1H3H_ENST00000369163.2_5'Flank	NM_003519.3	NP_003510.1	Q99880	H2B1L_HUMAN	histone cluster 1, H2bl	122					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						TGGAGCTGGTGTACTTGGTGA	0.562																																					p.Y122X		Atlas-SNP	.											HIST1H2BL,NS,carcinoma,0,2	HIST1H2BL	48	2	0			c.C366A						PASS	.						81	83	82					6																	27775319		2203	4300	6503	SO:0001587	stop_gained	8340	exon1			GCTGGTGTACTTG	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.366C>A	6.37:g.27775319G>T	ENSP00000366618:p.Tyr122*	128	0	0		139	17	0.122302	NM_003519	B2R5A3|Q52LW9	Nonsense_Mutation	SNP	ENST00000377401.2	37	CCDS4625.1	.	.	.	.	.	.	.	.	.	.	.	17.71	3.456850	0.63401	.	.	ENSG00000185130	ENST00000377401	.	.	.	4.35	1.58	0.23477	.	0.163302	0.23690	U	0.045538	.	.	.	.	.	.	0.33563	D	0.597642	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.4147	0.38514	0.2395:0.0:0.7605:0.0	.	.	.	.	X	122	.	ENSP00000366618:Y122X	Y	-	3	2	HIST1H2BL	27883298	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	2.813000	0.48002	0.180000	0.19960	-0.768000	0.03414	TAC	G|1.000;A|0.000	.	alt		0.562	HIST1H2BL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040153.1	NM_003519		T	27775319	G	T	27775319	4	4	40	1	0	0	0	0	0	1	0	0	7160	1372	48	4	18	4	HIST1H2BL	6	27775319	Nonsense_Mutation	SNP	G	TCGA-GS-A9TX-01A-11D-A382-10		27775319	143339748	17	14806											
LTB	4050	hgsc.bcm.edu	37	chr6	31549350	31549350	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccttacctatgaggtgggcaGctgggagcccggggctgaga	7	7	17	10	1	0	2	0	2	0	1	0	4	0	3	3	5	3	3	3	5	2	2			TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr6:31549350G>A	ENST00000429299.2	-	3	273	c.266C>T	c.(265-267)gCt>gTt	p.A89V	LTB_ENST00000483972.1_5'UTR|LTB_ENST00000446745.2_Silent_p.L74L	NM_002341.1	NP_002332.1	Q06643	TNFC_HUMAN	lymphotoxin beta (TNF superfamily, member 3)	89					cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|signal transduction (GO:0007165)|skin development (GO:0043588)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	9						GAGGTGGGCAGCTGGGAGCCC	0.567																																					p.A89V		Atlas-SNP	.											.	LTB	19	.	0			c.C266T						PASS	.						97	115	108					6																	31549350		1511	2708	4219	SO:0001583	missense	4050	exon3			TGGGCAGCTGGGA	L11015	CCDS4703.1, CCDS4704.1	6p21.3	2013-05-22			ENSG00000227507	ENSG00000227507		"Tumor necrosis factor (ligand) superfamily"	6711	protein-coding gene	gene with protein product		600978		TNFC		7916655, 1714477	Standard	NM_002341		Approved	p33, TNFSF3	uc003nuk.3	Q06643	OTTHUMG00000031136	ENST00000429299.2:c.266C>T	6.37:g.31549350G>A	ENSP00000410481:p.Ala89Val	120	0	0		123	19	0.154472	NM_002341	P78370|Q52LU8|Q99761	Missense_Mutation	SNP	ENST00000429299.2	37	CCDS4703.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.088790	0.76756	.	.	ENSG00000227507	ENST00000429299	T	0.24908	1.83	5.26	5.26	0.73747	Tumour necrosis factor (2);Tumour necrosis factor-like (2);	0.184906	0.37955	N	0.001867	T	0.33294	0.0858	.	.	.	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.03922	-1.0992	9	0.19147	T	0.46	-7.4596	14.3569	0.66742	0.0:0.0:1.0:0.0	.	89	Q06643	TNFC_HUMAN	V	89	ENSP00000410481:A89V	ENSP00000410481:A89V	A	-	2	0	LTB	31657329	1.000000	0.71417	0.995000	0.50966	0.871000	0.50021	3.084000	0.50143	2.434000	0.82447	0.655000	0.94253	GCT	.	.	none		0.567	LTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076239.3			A	31549350	G	A	31549350	3	1	40	1	0	0	0	0	1	0	0	0	9079	971	34	2	476	2	LTB	6	31549350	Missense_Mutation	SNP	G	TCGA-GS-A9TX-01A-11D-A382-10	3774031	31549350	139565717	18	14807											
TTBK1	84630	hgsc.bcm.edu	37	chr6	43250767	43250767	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaagaggaggaggaagaagaGgaggaggaggaagaggagga	18	0	23	0	0	0	4	0	0	0	4	0	14	0	13	0	9	0	0	0	9	4	0			TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr6:43250767G>A	ENST00000259750.4	+	14	2372	c.2289G>A	c.(2287-2289)gaG>gaA	p.E763E		NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	763	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)			aggaagaagaggaggaggagg	0.587																																					p.E763E		Atlas-SNP	.											.	TTBK1	124	.	0			c.G2289A						PASS	.						14	14	14					6																	43250767		2201	4297	6498	SO:0001819	synonymous_variant	84630	exon14			AGAAGAGGAGGAG	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.2289G>A	6.37:g.43250767G>A		21	0	0		32	7	0.21875	NM_032538	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Silent	SNP	ENST00000259750.4	37	CCDS34455.1																																																																																			.	.	none		0.587	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3			A	43250767	G	A	43250767	2	1	40	1	0	0	0	0	0	0	0	1	16691	991	35	2		2	TTBK1	6	43250767	Silent	SNP	G	TCGA-GS-A9TX-01A-11D-A382-10	11701417	43250767	127864300	19	14808											
B3GAT2	135152	hgsc.bcm.edu	37	chr6	71571677	71571677	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgacttgaagacttacagcAaatcctttgtgaaaaataaa	18	11	6	6	0	0	4	0	3	0	1	1	4	1	4	1	0	2	1	1	0	7	4			TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr6:71571677A>G	ENST00000230053.6	-	3	1349	c.741T>C	c.(739-741)ttT>ttC	p.F247F	SMAP1_ENST00000370455.3_3'UTR	NM_080742.2	NP_542780.1	Q9NPZ5	B3GA2_HUMAN	beta-1,3-glucuronyltransferase 2	247					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						GACTTACAGCAAATCCTTTGT	0.328																																					p.F247F		Atlas-SNP	.											.	B3GAT2	33	.	0			c.T741C						PASS	.						54	57	56					6																	71571677		2203	4300	6503	SO:0001819	synonymous_variant	135152	exon3			TACAGCAAATCCT	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.741T>C	6.37:g.71571677A>G		229	0	0		217	28	0.129032	NM_080742	Q5JS09|Q8TF38|Q96NK4	Silent	SNP	ENST00000230053.6	37	CCDS4974.1																																																																																			.	.	none		0.328	B3GAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041150.2	NM_080742		G	71571677	A	G	71571677	2	3	40	1	0	0	0	0	0	0	0	1	1254	127	5	3		3	B3GAT2	6	71571677	Silent	SNP	A	TCGA-GS-A9TX-01A-11D-A382-10	28320910	71571677	99543390	20	14809											
CACNA2D1	781	hgsc.bcm.edu	37	chr7	81642816	81642818	+	In_Frame_Del	DEL	ATA	ATA	-																															gcaccaatggaaggaatttcAtaataataacctgaaatata																										TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	ATA	ATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr7:81642816_81642818delATA	ENST00000356253.5	-	14	1486_1488	c.1231_1233delTAT	c.(1231-1233)tatdel	p.Y411del	MIR1255B1_ENST00000439234.1_RNA|CACNA2D1_ENST00000464354.1_5'UTR|MIR1255B1_ENST00000454066.1_RNA|CACNA2D1_ENST00000356860.3_In_Frame_Del_p.Y411del			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	411	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)	AAGGAATTTCATAATAATAACCT	0.197																																					p.411_412del		Atlas-Indel	.											.	CACNA2D1	191	.	0			c.1232_1234del						PASS	.																																			SO:0001651	inframe_deletion	781	exon14			.	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.1231_1233delTAT	7.37:g.81642822_81642824delATA	ENSP00000348589:p.Tyr411del	416	0	0		524	54	0.103053	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	In_Frame_Del	DEL	ENST00000356253.5	37																																																																																				.	.	none		0.197	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding				-	81642818	ATA	-	81642816	7	5	40	1	0	1	0	1	0	0	0	0	2550	224	8	0	2146	0	CACNA2D1	7	81642816	In_Frame_Del	DEL	ATA	TCGA-GS-A9TX-01A-11D-A382-10		81642816	77495847	21	14810											
ZDHHC6	64429	hgsc.bcm.edu	37	chr10	114200386	114200386	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgcagctaatccaaatggaAcaattggaagaggatctctc	15	9	9	8	0	1	1	0	0	1	1	4	4	2	4	1	3	3	2	1	3	5	2			TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr10:114200386A>C	ENST00000369405.3	-	5	1010	c.587T>G	c.(586-588)gTt>gGt	p.V196G	ZDHHC6_ENST00000369404.3_Missense_Mutation_p.V192G	NM_022494.1	NP_071939.1	Q9H6R6	ZDHC6_HUMAN	zinc finger, DHHC-type containing 6	196					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)			endometrium(4)|kidney(1)|large_intestine(2)|lung(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Colorectal(252;0.198)		Epithelial(162;0.0291)|all cancers(201;0.117)		TCCAAATGGAACAATTGGAAG	0.458																																					p.V196G		Atlas-SNP	.											.	ZDHHC6	32	.	0			c.T587G						PASS	.						172	155	161					10																	114200386		2203	4300	6503	SO:0001583	missense	64429	exon5			AATGGAACAATTG	AK025605	CCDS7574.1	10q26.11	2008-05-02			ENSG00000023041	ENSG00000023041		"Zinc fingers, DHHC-type"	19160	protein-coding gene	gene with protein product							Standard	NM_022494		Approved	ZNF376, FLJ21952	uc001kzv.3	Q9H6R6	OTTHUMG00000019062	ENST00000369405.3:c.587T>G	10.37:g.114200386A>C	ENSP00000358413:p.Val196Gly	117	0	0		96	17	0.177083	NM_022494	D3DRB6|Q53G45|Q96IV7|Q9H605	Missense_Mutation	SNP	ENST00000369405.3	37	CCDS7574.1	.	.	.	.	.	.	.	.	.	.	A	19.72	3.880428	0.72294	.	.	ENSG00000023041	ENST00000369405;ENST00000369404	T;T	0.66815	0.51;-0.23	5.92	5.92	0.95590	.	0.364419	0.32343	N	0.006237	T	0.65291	0.2677	L	0.49699	1.58	0.80722	D	1	B;B	0.26672	0.156;0.029	B;B	0.32805	0.153;0.11	T	0.62011	-0.6944	10	0.38643	T	0.18	-12.459	16.3492	0.83195	1.0:0.0:0.0:0.0	.	192;196	Q9H6R6-2;Q9H6R6	.;ZDHC6_HUMAN	G	196;192	ENSP00000358413:V196G;ENSP00000358412:V192G	ENSP00000358412:V192G	V	-	2	0	ZDHHC6	114190376	1.000000	0.71417	0.267000	0.24556	0.872000	0.50106	9.300000	0.96151	2.266000	0.75297	0.528000	0.53228	GTT	.	.	none		0.458	ZDHHC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050393.1	NM_022494		C	114200386	A	C	114200386	3	2	40	1	0	0	0	0	1	0	0	0	17634	43	2	5	682	5	ZDHHC6	10	114200386	Missense_Mutation	SNP	A	TCGA-GS-A9TX-01A-11D-A382-10		114200386	21334361	22	14811											
MUC2	4583	hgsc.bcm.edu	37	chr11	1092618	1092619	+	In_Frame_Ins	INS	-	-	CCA																															caaccaccactcccagccctINSccaaccaccactcccagccc																								rs201595190|rs201608750|rs547682241	byFrequency	TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr11:1092618_1092619insCCA	ENST00000441003.2	+	30	4464_4465	c.4437_4438insCCA	c.(4438-4440)cca>CCAcca	p.1480_1480P>PP	MUC2_ENST00000359061.5_In_Frame_Ins_p.1481_1481P>PP|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4215	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)	ctcccagccctccaaccaccac	0.639																																					p.P1479delinsPP		Atlas-Indel	.											.	MUC2	614	.	0			c.4437_4438insCCA						PASS	.																																			SO:0001652	inframe_insertion	4583	exon30			.	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.4438_4440dupCCA	11.37:g.1092619_1092621dupCCA	ENSP00000415183:p.Pro1480dup	66	0	0		58	19	0.327586	NM_002457	Q14878	In_Frame_Ins	INS	ENST00000441003.2	37																																																																																				.	.	none		0.639	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		CCA	1092619	-	CCA	1092618	7	5	40	1	0	1	1	0	0	0	0	0	9984	1538	54	0	4555	0	MUC2	11	1092618	In_Frame_Ins	INS	-	TCGA-GS-A9TX-01A-11D-A382-10		1092618	133913898	23	14812											
FAT3	120114	hgsc.bcm.edu	37	chr11	92533495	92533495	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cattttatctgggaatgaccGgacgagctttctgatggaca	10	12	11	8	2	2	2	0	2	2	0	2	6	2	5	1	3	1	1	1	3	2	3	rs149993900		TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr11:92533495G>A	ENST00000298047.6	+	9	7333	c.7316G>A	c.(7315-7317)cGg>cAg	p.R2439Q	FAT3_ENST00000409404.2_Missense_Mutation_p.R2439Q|FAT3_ENST00000525166.1_Missense_Mutation_p.R2289Q			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2439	Cadherin 22. {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)				GGGAATGACCGGACGAGCTTT	0.493										TCGA Ovarian(4;0.039)			G|||	1	0.000199681	0.0	0.0	5008	,	,		21024	0.0		0.001	False		,,,				2504	0.0				p.R2439Q		Atlas-SNP	.											.	FAT3	1822	.	0			c.G7316A						PASS	.	G	GLN/ARG	0,3892		0,0,1946	94	90	91		7316	4.9	0.9	11	dbSNP_134	91	5,8277		0,5,4136	yes	missense	FAT3	NM_001008781.2	43	0,5,6082	AA,AG,GG		0.0604,0.0,0.0411	possibly-damaging	2439/4558	92533495	5,12169	1946	4141	6087	SO:0001583	missense	120114	exon9			ATGACCGGACGAG	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.7316G>A	11.37:g.92533495G>A	ENSP00000298047:p.Arg2439Gln	123	0	0		96	12	0.125	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	11.46	1.644572	0.29246	0.0	6.04E-4	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.51325	0.71;0.71;0.71	5.82	4.91	0.64330	.	.	.	.	.	T	0.36608	0.0973	N	0.04162	-0.26	0.80722	D	1	D	0.69078	0.997	P	0.55545	0.778	T	0.20505	-1.0273	9	0.11182	T	0.66	.	14.4549	0.67409	0.0698:0.0:0.9302:0.0	.	2439	Q8TDW7-3	.	Q	2439;2439;2289	ENSP00000298047:R2439Q;ENSP00000387040:R2439Q;ENSP00000432586:R2289Q	ENSP00000298047:R2439Q	R	+	2	0	FAT3	92173143	1.000000	0.71417	0.925000	0.36789	0.967000	0.64934	5.115000	0.64655	1.468000	0.48064	0.561000	0.74099	CGG	G|1.000;A|0.000	0.000	strong		0.493	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781		A	92533495	G	A	92533495	3	1	40	1	0	0	0	0	1	0	0	0	5699	1116	39	1	7350	1	FAT3	11	92533495	Missense_Mutation	SNP	G	TCGA-GS-A9TX-01A-11D-A382-10	91440877	92533495	42473021	24	14813											
CREBBP	1387	hgsc.bcm.edu	37	chr16	3781324	3781326	+	In_Frame_Del	DEL	AGG	AGG	-																															ggaccacttggagcggcgcaAggaggagaactcccagtgct																										TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr16:3781324_3781326delAGG	ENST00000262367.5	-	30	5848_5850	c.5039_5041delCCT	c.(5038-5043)tccttg>ttg	p.S1680del	CREBBP_ENST00000382070.3_In_Frame_Del_p.S1642del	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1680	CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.|Interaction with TRERF1.				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)	p.S1680delS(1)		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)		GAGCGGCGCAAGGAGGAGAACTC	0.645			"T, N, F, Mis, O"	"MLL, MORF, RUNXBP2"	"ALL, AML, DLBCL, B-NHL "		Rubinstein-Taybi syndrome																														p.1680_1681del		Pindel,Atlas-Indel	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	1	Deletion - In frame(1)	large_intestine(1)	c.5040_5042del	GRCh37	CD084702	CREBBP	D		PASS	.																																			SO:0001651	inframe_deletion	1387	exon30			.	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.5039_5041delCCT	16.37:g.3781327_3781329delAGG	ENSP00000262367:p.Ser1680del	111	0	.		103	21	0.204	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	In_Frame_Del	DEL	ENST00000262367.5	37	CCDS10509.1																																																																																			.	.	none		0.645	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380		-	3781326	AGG	-	3781324	7	5	40	1	0	1	0	1	0	0	0	0	3863	69	3	0	2295	0	CREBBP	16	3781324	In_Frame_Del	DEL	AGG	TCGA-GS-A9TX-01A-11D-A382-10		3781324	86573429	25	14814											
LPCAT2	54947	hgsc.bcm.edu	37	chr16	55608567	55608567	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgatggcagcattgacttcCgagagtatgtgattggcctg	9	12	13	7	1	0	4	0	3	0	1	1	5	1	4	2	2	1	3	2	2	1	4			TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr16:55608567C>T	ENST00000262134.5	+	12	1424	c.1240C>T	c.(1240-1242)Cga>Tga	p.R414*	LPCAT2_ENST00000565056.1_3'UTR	NM_017839.4	NP_060309.2	Q7L5N7	PCAT2_HUMAN	lysophosphatidylcholine acyltransferase 2	414	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				glycerophospholipid biosynthetic process (GO:0046474)|membrane organization (GO:0061024)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)|1-acylglycerophosphocholine O-acyltransferase activity (GO:0047184)|1-alkylglycerophosphocholine O-acetyltransferase activity (GO:0047192)|calcium ion binding (GO:0005509)			endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	12						CATTGACTTCCGAGAGTATGT	0.448																																					p.R414X		Atlas-SNP	.											.	LPCAT2	35	.	0			c.C1240T						PASS	.						169	131	144					16																	55608567		2198	4300	6498	SO:0001587	stop_gained	54947	exon12			GACTTCCGAGAGT	AK000488	CCDS10753.1	16q12.2	2013-01-10	2007-12-17	2007-12-17	ENSG00000087253	ENSG00000087253		"EF-hand domain containing"	26032	protein-coding gene	gene with protein product		612040	"acyltransferase like 1"	AYTL1		16704971	Standard	NM_017839		Approved	FLJ20481	uc002eie.4	Q7L5N7	OTTHUMG00000133238	ENST00000262134.5:c.1240C>T	16.37:g.55608567C>T	ENSP00000262134:p.Arg414*	175	0	0		179	21	0.117318	NM_017839	A3KBM1|Q6MZJ6|Q9NX23	Nonsense_Mutation	SNP	ENST00000262134.5	37	CCDS10753.1	.	.	.	.	.	.	.	.	.	.	C	37	6.602750	0.97697	.	.	ENSG00000087253	ENST00000262134	.	.	.	5.84	3.74	0.42951	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-19.8774	12.3155	0.54953	0.5722:0.4278:0.0:0.0	.	.	.	.	X	414	.	ENSP00000262134:R414X	R	+	1	2	LPCAT2	54166068	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.870000	0.48451	1.463000	0.47967	0.655000	0.94253	CGA	.	.	none		0.448	LPCAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256977.2	NM_017839		T	55608567	C	T	55608567	4	4	40	1	0	0	0	0	0	1	0	0	8920	644	23	1	1286	1	LPCAT2	16	55608567	Nonsense_Mutation	SNP	C	TCGA-GS-A9TX-01A-11D-A382-10	51827243	55608567	34746186	26	14815											
PREX1	57580	hgsc.bcm.edu	37	chr20	47262400	47262400	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacacccacctgtaggagtcGcgataactcatggtgtcgtg	9	9	12	11	3	1	0	1	0	0	0	3	3	1	1	2	2	1	1	2	2	2	2	rs141398646	byFrequency	TCGA-GS-A9TX-01A-11D-A382-10	TCGA-GS-A9TX-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c4c499f3-91c4-400e-9d4c-34cc4ba25efd	5d6e6d97-dba3-4087-ba36-3840e5b33520	g.chr20:47262400G>A	ENST00000371941.3	-	26	3523	c.3501C>T	c.(3499-3501)cgC>cgT	p.R1167R	PREX1_ENST00000396220.1_Silent_p.R1167R	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	1167					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)			TGTAGGAGTCGCGATAACTCA	0.602													g|||	2	0.000399361	0.0008	0.0	5008	,	,		22326	0.001		0.0	False		,,,				2504	0.0				p.R1167R		Atlas-SNP	.											.	PREX1	441	.	0			c.C3501T						PASS	.	A		7,4399	11.4+/-27.6	0,7,2196	125	86	99		3501	-9.6	0.5	20	dbSNP_134	99	0,8600		0,0,4300	no	coding-synonymous	PREX1	NM_020820.3		0,7,6496	AA,AG,GG		0.0,0.1589,0.0538		1167/1660	47262400	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	57580	exon26			GGAGTCGCGATAA	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.3501C>T	20.37:g.47262400G>A		68	0	0		54	12	0.222222	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Silent	SNP	ENST00000371941.3	37	CCDS13410.1																																																																																			G|0.999;A|0.001	0.001	strong		0.602	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820		A	47262400	G	A	47262400	2	1	40	1	0	0	0	0	0	0	0	1	12488	1074	38	1		1	PREX1	20	47262400	Silent	SNP	G	TCGA-GS-A9TX-01A-11D-A382-10		47262400	15763120	27	14816											
CHD5	26038	hgsc.bcm.edu	37	chr1	6208928	6208928	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actcacagtacagcgcgggcAgagccattcaccgtttggga	10	7	12	12	3	2	1	2	0	0	1	2	2	2	2	2	2	3	3	2	2	1	3			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr1:6208928A>T	ENST00000262450.3	-	9	1468	c.1369T>A	c.(1369-1371)Tgc>Agc	p.C457S	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)		CAGCGCGGGCAGAGCCATTCA	0.721																																					p.C457S		Atlas-SNP	.											.	CHD5	267	.	0			c.T1369A						PASS	.						49	55	53					1																	6208928		2202	4300	6502	SO:0001583	missense	26038	exon9			GCGGGCAGAGCCA	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.1369T>A	1.37:g.6208928A>T	ENSP00000262450:p.Cys457Ser	100	0	0		77	51	0.662338	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Missense_Mutation	SNP	ENST00000262450.3	37	CCDS57.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.693706	0.88735	.	.	ENSG00000116254	ENST00000262450	D	0.99252	-5.63	3.56	3.56	0.40772	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, RING-type (1);Zinc finger, PHD-type (1);Chromo domain-like (1);	0.000000	0.85682	U	0.000000	D	0.99521	0.9829	H	0.98682	4.3	0.80722	D	1	D	0.63046	0.992	P	0.57244	0.816	D	0.98206	1.0470	10	0.87932	D	0	-21.3112	12.1231	0.53903	1.0:0.0:0.0:0.0	.	457	Q8TDI0	CHD5_HUMAN	S	457	ENSP00000262450:C457S	ENSP00000262450:C457S	C	-	1	0	CHD5	6131515	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.355000	0.79434	1.410000	0.46936	0.260000	0.18958	TGC	.	.	none		0.721	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557		T	6208928	A	T	6208928	3	4	41	1	0	0	0	0	1	0	0	0	3330	188	7	5	4627	5	CHD5	1	6208928	Missense_Mutation	SNP	A	TCGA-GS-A9TY-01A-11D-A38X-10		6208928	243041693	1	14817											
CHD5	26038	hgsc.bcm.edu	37	chr1	6208973	6208973	+	De_novo_Start_OutOfFrame	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcagcggcgggttgaggcAatgcaggtggtaggaggagg	8	5	23	5	2	0	1	0	1	0	0	0	3	0	3	0	9	2	5	0	9	2	2			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr1:6208973A>C	ENST00000378021.1	-	0	1423				CHD5_ENST00000262450.3_Missense_Mutation_p.C442G			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)		GGGTTGAGGCAATGCAGGTGG	0.697																																					p.C442G		Atlas-SNP	.											.	CHD5	267	.	0			c.T1324G						PASS	.						49	52	51					1																	6208973		2201	4300	6501			26038	exon9			TGAGGCAATGCAG	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	ENST00000378021.1:c.-2106T>G	1.37:g.6208973A>C		99	0	0		95	58	0.610526	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Missense_Mutation	SNP	ENST00000378021.1	37		.	.	.	.	.	.	.	.	.	.	A	18.99	3.738941	0.69304	.	.	ENSG00000116254	ENST00000262450	D	0.99252	-5.63	3.56	3.56	0.40772	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, RING-type (1);Zinc finger, PHD-type (1);Chromo domain-like (1);	0.000000	0.85682	U	0.000000	D	0.99687	0.9882	H	0.99609	4.655	0.80722	D	1	D	0.69078	0.997	D	0.79108	0.992	D	0.97244	0.9893	10	0.72032	D	0.01	-21.1597	12.1231	0.53903	1.0:0.0:0.0:0.0	.	442	Q8TDI0	CHD5_HUMAN	G	442	ENSP00000262450:C442G	ENSP00000262450:C442G	C	-	1	0	CHD5	6131560	1.000000	0.71417	1.000000	0.80357	0.562000	0.35680	9.157000	0.94714	1.410000	0.46936	0.260000	0.18958	TGC	.	.	none		0.697	CHD5-201	KNOWN	basic	protein_coding	protein_coding		NM_015557		C	6208973	A	C	6208973	1	2	41	1	0	1	0	0	0	0	0	0	3330	130	5	5		5	CHD5	1	6208973	De_novo_Start_OutOfFrame	SNP	A	TCGA-GS-A9TY-01A-11D-A38X-10	45	6208973	243041648	2	14818											
UBR4	23352	hgsc.bcm.edu	37	chr1	19403339	19403339	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatgggcatgtcgttgtggcGgatgtactcagcgagagagc	8	9	17	7	3	1	1	1	0	0	1	2	5	1	2	0	3	3	3	0	3	1	2			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr1:19403339G>A	ENST00000375254.3	-	105	15409	c.15382C>T	c.(15382-15384)Cgc>Tgc	p.R5128C	UBR4_ENST00000375226.2_Missense_Mutation_p.R5104C|UBR4_ENST00000429347.2_Missense_Mutation_p.R651C|UBR4_ENST00000375224.1_Missense_Mutation_p.R835C|UBR4_ENST00000375217.2_Missense_Mutation_p.R5121C|UBR4_ENST00000375267.2_Missense_Mutation_p.R5149C|UBR4_ENST00000375225.3_Missense_Mutation_p.R203C|RP5-1126H10.2_ENST00000606379.1_RNA|UBR4_ENST00000543981.1_Missense_Mutation_p.R792C	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	5128					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)		TCGTTGTGGCGGATGTACTCA	0.537																																					p.R5128C		Atlas-SNP	.											.	UBR4	415	.	0			c.C15382T						PASS	.						190	163	172					1																	19403339		2203	4300	6503	SO:0001583	missense	23352	exon105			TGTGGCGGATGTA	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.15382C>T	1.37:g.19403339G>A	ENSP00000364403:p.Arg5128Cys	132	0	0		97	22	0.226804	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	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	G	25.1	4.598627	0.87055	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000375225;ENST00000375224;ENST00000429347;ENST00000543981	T;T;T;T;T;T;T;T	0.33438	1.41;1.41;1.41;1.41;1.41;1.41;1.41;1.41	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.62527	0.2435	M	0.85542	2.76	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.81914	0.993;0.993;0.995;0.988	T	0.66448	-0.5921	10	0.87932	D	0	.	18.8623	0.92278	0.0:0.0:1.0:0.0	.	792;651;5128;5104	B4DYV5;B4DPF6;Q5T4S7;Q5T4S7-3	.;.;UBR4_HUMAN;.	C	5128;5149;5121;5104;203;835;651;792	ENSP00000364403:R5128C;ENSP00000364416:R5149C;ENSP00000364365:R5121C;ENSP00000364374:R5104C;ENSP00000364373:R203C;ENSP00000364372:R835C;ENSP00000394173:R651C;ENSP00000444070:R792C	ENSP00000364365:R5121C	R	-	1	0	UBR4	19275926	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.323000	0.65858	2.793000	0.96121	0.655000	0.94253	CGC	.	.	none		0.537	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765		A	19403339	G	A	19403339	3	1	41	1	0	0	0	0	1	0	0	0	16919	1116	39	1	177	1	UBR4	1	19403339	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	13194366	19403339	229847282	3	14819											
PSMB2	5690	hgsc.bcm.edu	37	chr1	36101985	36101986	+	Frame_Shift_Del	DEL	AC	AC	-																															cagtgtctccagcctctccaAcacacaggagtaatatcttt																								rs139138858		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr1:36101985_36101986delAC	ENST00000373237.3	-	2	550_551	c.139_140delGT	c.(139-141)gttfs	p.V47fs		NM_002794.4	NP_002785.1	P49721	PSB2_HUMAN	proteasome (prosome, macropain) subunit, beta type, 2	47					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)	AGCCTCTCCAACACACAGGAGT	0.381																																					p.47_47del		Pindel,Atlas-Indel	.											.	PSMB2	9	.	0			c.140_141del						PASS	.																																			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.139_140delGT	1.37:g.36101989_36101990delAC	ENSP00000362334:p.Val47fs	247	0	.		181	54	0.298	NM_002794	D3DPS0|P31145|Q9BWZ9	Frame_Shift_Del	DEL	ENST00000373237.3	37	CCDS394.1																																																																																			.	.	none		0.381	PSMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012016.1	NM_002794		-	36101986	AC	-	36101985	7	5	41	1	0	1	0	1	0	0	0	0	12689	43	2	0	485	0	PSMB2	1	36101985	Frame_Shift_Del	DEL	AC	TCGA-GS-A9TY-01A-11D-A38X-10	16698646	36101985	213148636	4	14820											
PDE4DIP	9659	hgsc.bcm.edu	37	chr1	145075675	145075675	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgcttcttcctcctcggccGctgctgcccagctcccggct	1	11	9	20	3	1	0	0	0	1	0	5	0	4	0	5	2	4	5	5	2	0	2			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr1:145075675G>A	ENST00000530740.1	-	1	226	c.188C>T	c.(187-189)gCg>gTg	p.A63V	PDE4DIP_ENST00000369345.4_Missense_Mutation_p.A63V|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.A63V|PDE4DIP_ENST00000369348.3_Missense_Mutation_p.A63V			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)		CTCCTCGGCCGCTGCTGCCCA	0.716			T	PDGFRB	MPD																																p.A63V		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C188T						PASS	.						38	48	45					1																	145075675		2192	4281	6473	SO:0001583	missense	9659	exon1			TCGGCCGCTGCTG	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.188C>T	1.37:g.145075675G>A	ENSP00000435654:p.Ala63Val	167	0	0		270	27	0.1	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	37		.	.	.	.	.	.	.	.	.	.	G	9.842	1.191237	0.21954	.	.	ENSG00000178104	ENST00000530740;ENST00000369359;ENST00000369348;ENST00000369345	T;T;T	0.15487	3.79;3.76;2.42	3.6	2.68	0.31781	.	.	.	.	.	T	0.04679	0.0127	N	0.24115	0.695	0.09310	N	1	D;P	0.65815	0.995;0.926	B;B	0.43155	0.41;0.117	T	0.23084	-1.0198	9	0.87932	D	0	.	6.8328	0.23919	0.1306:0.0:0.8694:0.0	.	63;63	Q5TB27;E9PJ64	.;.	V	63	ENSP00000435654:A63V;ENSP00000358366:A63V;ENSP00000358354:A63V	ENSP00000358351:A63V	A	-	2	0	PDE4DIP	143787032	0.056000	0.20664	0.012000	0.15200	0.095000	0.18619	0.881000	0.28173	0.849000	0.35215	0.561000	0.74099	GCG	.	.	none		0.716	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000384663.2	NM_022359		A	145075675	G	A	145075675	3	1	41	1	0	0	0	0	1	0	0	0	11652	1087	38	1	8624	1	PDE4DIP	1	145075675	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	108973690	145075675	104174946	5	14821											
ARHGEF2	9181	hgsc.bcm.edu	37	chr1	155928159	155928159	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttcctggagaaacaccagTacatctgtcatcagcagcac	12	10	7	12	0	3	1	2	0	1	1	4	2	4	1	2	1	4	3	2	1	2	3			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr1:155928159T>G	ENST00000361247.4	-	12	1596	c.1497A>C	c.(1495-1497)gtA>gtC	p.V499V	ARHGEF2_ENST00000368316.1_Silent_p.V471V|ARHGEF2_ENST00000462460.2_Silent_p.V544V|ARHGEF2_ENST00000313667.4_Silent_p.V498V|ARHGEF2_ENST00000313695.7_Silent_p.V471V|ARHGEF2_ENST00000368315.4_Silent_p.V500V|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	499	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)					GAAACACCAGTACATCTGTCA	0.488																																					p.V499V	Melanoma(178;35 2768 6610 28839)	Atlas-SNP	.											.	ARHGEF2	81	.	0			c.A1497C						PASS	.						126	101	110					1																	155928159		2203	4300	6503	SO:0001819	synonymous_variant	9181	exon12			CACCAGTACATCT	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.1497A>C	1.37:g.155928159T>G		89	0	0		106	25	0.235849	NM_001162383	D3DVA6|O75142|Q15079|Q5VY92|Q8TDA3|Q8WUG4|Q9H023	Silent	SNP	ENST00000361247.4	37	CCDS53376.1																																																																																			.	.	none		0.488	ARHGEF2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046204.2	NM_004723		G	155928159	T	G	155928159	2	3	41	1	0	0	0	0	0	0	0	1	903	1625	57	5		5	ARHGEF2	1	155928159	Silent	SNP	T	TCGA-GS-A9TY-01A-11D-A38X-10	10852484	155928159	93322462	6	14822											
SMG5	23381	hgsc.bcm.edu	37	chr1	156221239	156221239	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcttatgccgctcaaagctcTttcccacctctttctggcag	6	13	7	15	1	4	0	1	0	3	0	5	0	5	0	3	1	2	4	3	1	2	3			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr1:156221239T>C	ENST00000361813.5	-	20	2927	c.2783A>G	c.(2782-2784)aAg>aGg	p.K928R	SMG5_ENST00000368267.5_Intron	NM_015327.2	NP_056142.2	Q9UPR3	SMG5_HUMAN	SMG5 nonsense mediated mRNA decay factor	928	PINc.				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)					CTCAAAGCTCTTTCCCACCTC	0.557																																					p.K928R		Atlas-SNP	.											.	SMG5	98	.	0			c.A2783G						PASS	.						200	193	195					1																	156221239		2203	4300	6503	SO:0001583	missense	23381	exon20			AAGCTCTTTCCCA	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.2783A>G	1.37:g.156221239T>C	ENSP00000355261:p.Lys928Arg	118	0	0		128	24	0.1875	NM_015327	D3DVB7|Q5QJE7|Q659C7|Q8IXC0|Q8IY09|Q96IJ7	Missense_Mutation	SNP	ENST00000361813.5	37	CCDS1137.1	.	.	.	.	.	.	.	.	.	.	T	12.27	1.886395	0.33348	.	.	ENSG00000198952	ENST00000361813	T	0.29142	1.58	4.56	4.56	0.56223	Nucleotide binding protein, PINc (1);	0.065325	0.64402	D	0.000017	T	0.05364	0.0142	N	0.04508	-0.205	0.80722	D	1	B	0.21381	0.055	B	0.19391	0.025	T	0.19582	-1.0301	10	0.08381	T	0.77	-14.5089	13.2101	0.59819	0.0:0.0:0.0:1.0	.	928	Q9UPR3	SMG5_HUMAN	R	928	ENSP00000355261:K928R	ENSP00000355261:K928R	K	-	2	0	SMG5	154487863	1.000000	0.71417	0.999000	0.59377	0.986000	0.74619	2.513000	0.45494	2.062000	0.61559	0.459000	0.35465	AAG	.	.	none		0.557	SMG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046308.1	NM_015327		C	156221239	T	C	156221239	3	2	41	1	0	0	0	0	1	0	0	0	14811	1609	56	3	279	3	SMG5	1	156221239	Missense_Mutation	SNP	T	TCGA-GS-A9TY-01A-11D-A38X-10	293080	156221239	93029382	7	14823											
PEX19	5824	hgsc.bcm.edu	37	chr1	160252238	160252238	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcatttttggctaatccaCttagtgtttcctttaggcaa	8	17	8	8	0	0	0	0	0	0	0	2	0	2	0	2	3	0	4	2	3	4	7			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr1:160252238C>T	ENST00000368072.5	-	4	422	c.401G>A	c.(400-402)aGt>aAt	p.S134N	PEX19_ENST00000440949.3_Missense_Mutation_p.S44N|DCAF8_ENST00000608310.1_Intron|PEX19_ENST00000532508.1_5'UTR|DCAF8_ENST00000556710.1_Intron	NM_001193644.1|NM_002857.3	NP_001180573.1|NP_002848.1	P40855	PEX19_HUMAN	peroxisomal biogenesis factor 19	134					chaperone-mediated protein folding (GO:0061077)|chaperone-mediated protein transport (GO:0072321)|establishment of protein localization to peroxisome (GO:0072663)|negative regulation of lipid binding (GO:1900131)|peroxisome fission (GO:0016559)|peroxisome membrane biogenesis (GO:0016557)|peroxisome organization (GO:0007031)|protein import into peroxisome membrane (GO:0045046)|protein stabilization (GO:0050821)|protein targeting to peroxisome (GO:0006625)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	ATPase binding (GO:0051117)|peroxisome membrane class-1 targeting sequence binding (GO:0036105)|protein N-terminus binding (GO:0047485)			cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(2)	11	all_cancers(52;1.27e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			GGCTAATCCACTTAGTGTTTC	0.458																																					p.S134N		Atlas-SNP	.											.	PEX19	34	.	0			c.G401A						PASS	.						129	121	124					1																	160252238		2203	4300	6503	SO:0001583	missense	5824	exon4			AATCCACTTAGTG	Y09048	CCDS1201.1	1q22	2008-07-18	2004-03-17	2004-03-19	ENSG00000162735	ENSG00000162735			9713	protein-coding gene	gene with protein product	"housekeeping gene, 33kD"	600279	"peroxisomal farnesylated protein"	PXF		9339377, 10051604	Standard	NM_002857		Approved	HK33, D1S2223E, PMP1, PMPI, PXMP1		P40855	OTTHUMG00000033112	ENST00000368072.5:c.401G>A	1.37:g.160252238C>T	ENSP00000357051:p.Ser134Asn	255	0	0		287	57	0.198606	NM_002857	D3DVE7|Q5QNY4|Q8NI97	Missense_Mutation	SNP	ENST00000368072.5	37	CCDS1201.1	.	.	.	.	.	.	.	.	.	.	C	15.03	2.712935	0.48517	.	.	ENSG00000258465;ENSG00000162735;ENSG00000162735;ENSG00000162735;ENSG00000162735	ENST00000485079;ENST00000368072;ENST00000429425;ENST00000440949;ENST00000392220	.	.	.	5.5	5.5	0.81552	.	0.261768	0.45361	D	0.000379	T	0.25901	0.0631	N	0.16743	0.435	0.37882	D	0.930421	B	0.02656	0.0	B	0.11329	0.006	T	0.07849	-1.0751	9	0.26408	T	0.33	-7.953	13.885	0.63704	0.0:0.8471:0.1528:0.0	.	134	P40855	PEX19_HUMAN	N	4;134;114;44;114	.	ENSP00000357051:S134N	S	-	2	0	RP11-574F21.3;PEX19	158518862	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.956000	0.49129	2.584000	0.87258	0.563000	0.77884	AGT	.	.	none		0.458	PEX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080642.2	NM_002857		T	160252238	C	T	160252238	3	4	41	1	0	0	0	0	1	0	0	0	11753	565	20	2	518	2	PEX19	1	160252238	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	4030999	160252238	88998383	8	14824											
BTG2	7832	hgsc.bcm.edu	37	chr1	203274870	203274870	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggggcgctccaggaggcaCtcacaggtgagcgcatgccg	7	4	17	13	4	1	1	1	1	0	0	2	2	2	2	2	5	2	3	2	5	0	0			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr1:203274870C>G	ENST00000290551.4	+	1	207	c.136C>G	c.(136-138)Ctc>Gtc	p.L46V	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	46					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			CCAGGAGGCACTCACAGGTGA	0.706																																					p.L46V		Atlas-SNP	.											.	BTG2	16	.	0			c.C136G						PASS	.						11	13	12					1																	203274870		2008	3922	5930	SO:0001583	missense	7832	exon1			GAGGCACTCACAG		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.136C>G	1.37:g.203274870C>G	ENSP00000290551:p.Leu46Val	56	0	0		80	50	0.625	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	C	15.99	2.996025	0.54147	.	.	ENSG00000159388	ENST00000290551	T	0.38077	1.16	4.4	3.48	0.39840	Anti-proliferative protein (3);	0.000000	0.51477	D	0.000083	T	0.59514	0.2199	M	0.91818	3.245	0.39613	D	0.969913	D	0.55800	0.973	P	0.61275	0.886	T	0.64841	-0.6312	10	0.87932	D	0	-5.3352	6.4668	0.21985	0.1795:0.7256:0.0:0.0949	.	46	P78543	BTG2_HUMAN	V	46	ENSP00000290551:L46V	ENSP00000290551:L46V	L	+	1	0	BTG2	201541493	0.941000	0.31946	0.225000	0.23894	0.595000	0.36748	0.961000	0.29267	1.064000	0.40671	0.471000	0.43371	CTC	.	.	none		0.706	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		G	203274870	C	G	203274870	3	3	41	1	0	0	0	0	1	0	0	0	1556	565	20	4	138	4	BTG2	1	203274870	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	43022632	203274870	45975751	9	14825											
SLC41A1	254428	hgsc.bcm.edu	37	chr1	205768918	205768918	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatgttcccagtgatcatcCgccagagctccttgggtgtg	6	11	11	13	1	1	2	1	1	0	1	4	2	4	2	5	1	1	2	5	1	0	2			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr1:205768918C>T	ENST00000367137.3	-	4	1535	c.521G>A	c.(520-522)cGg>cAg	p.R174Q	SLC41A1_ENST00000468057.1_5'UTR	NM_173854.4	NP_776253.3	Q8IVJ1	S41A1_HUMAN	solute carrier family 41 (magnesium transporter), member 1	174					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)			AGTGATCATCCGCCAGAGCTC	0.572																																					p.R174Q		Atlas-SNP	.											.	SLC41A1	46	.	0			c.G521A						PASS	.						129	98	109					1																	205768918		2203	4300	6503	SO:0001583	missense	254428	exon4			ATCATCCGCCAGA	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.521G>A	1.37:g.205768918C>T	ENSP00000356105:p.Arg174Gln	122	0	0		167	38	0.227545	NM_173854	Q63HJ4|Q658Z5|Q659A4|Q6MZK2	Missense_Mutation	SNP	ENST00000367137.3	37	CCDS30988.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.539952	0.85917	.	.	ENSG00000133065	ENST00000367137	T	0.32753	1.44	5.99	4.9	0.64082	MgtE magnesium transporter, integral membrane (1);	0.213578	0.46145	D	0.000304	T	0.16769	0.0403	N	0.25286	0.73	0.34459	D	0.70156	B	0.33940	0.433	B	0.29862	0.108	T	0.14559	-1.0468	10	0.30854	T	0.27	-13.7793	6.4586	0.21944	0.0:0.6766:0.1902:0.1332	.	174	Q8IVJ1	S41A1_HUMAN	Q	174	ENSP00000356105:R174Q	ENSP00000356105:R174Q	R	-	2	0	SLC41A1	204035541	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.886000	0.39688	2.843000	0.97960	0.655000	0.94253	CGG	.	.	none		0.572	SLC41A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087731.1			T	205768918	C	T	205768918	3	4	41	1	0	0	0	0	1	0	0	0	14644	652	23	1	1052	1	SLC41A1	1	205768918	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	2494048	205768918	43481703	10	14826											
SPATA17	128153	hgsc.bcm.edu	37	chr1	217915347	217915347	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaggagtttgcagaaatgaaAgaaagagaagagaagaaggc	20	4	15	2	0	0	6	0	1	0	5	0	10	0	7	0	2	1	2	0	2	6	1			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr1:217915347A>T	ENST00000366933.4	+	6	481	c.426A>T	c.(424-426)aaA>aaT	p.K142N		NM_138796.2	NP_620151.1	Q96L03	SPT17_HUMAN	spermatogenesis associated 17	142						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)		CAGAAATGAAAGAAAGAGAAG	0.393																																					p.K142N		Atlas-SNP	.											.	SPATA17	59	.	0			c.A426T						PASS	.						122	113	116					1																	217915347		2203	4300	6503	SO:0001583	missense	128153	exon6			AATGAAAGAAAGA	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.426A>T	1.37:g.217915347A>T	ENSP00000355900:p.Lys142Asn	44	0	0		37	34	0.918919	NM_138796	A5D6N2	Missense_Mutation	SNP	ENST00000366933.4	37	CCDS1519.1	.	.	.	.	.	.	.	.	.	.	A	13.68	2.308373	0.40895	.	.	ENSG00000162814	ENST00000366933	T	0.47869	0.83	5.84	2.25	0.28309	.	0.498628	0.23552	N	0.046960	T	0.34308	0.0893	L	0.41027	1.25	0.30875	N	0.732086	B	0.14438	0.01	B	0.14578	0.011	T	0.26052	-1.0114	10	0.40728	T	0.16	-9.0478	6.8947	0.24249	0.6022:0.0:0.3978:0.0	.	142	Q96L03	SPT17_HUMAN	N	142	ENSP00000355900:K142N	ENSP00000355900:K142N	K	+	3	2	SPATA17	215981970	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	0.766000	0.26560	0.483000	0.27608	0.533000	0.62120	AAA	.	.	none		0.393	SPATA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092433.2	NM_138796		T	217915347	A	T	217915347	3	4	41	1	0	0	0	0	1	0	0	0	15017	69	3	5	448	5	SPATA17	1	217915347	Missense_Mutation	SNP	A	TCGA-GS-A9TY-01A-11D-A38X-10	12146429	217915347	31335274	11	14827											
OR14I1	401994	hgsc.bcm.edu	37	chr1	248845140	248845140	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaacatgttgccagtgtggaCggctgcgtaggaaaagcagc	12	7	14	8	2	0	0	0	0	0	0	0	2	0	2	1	3	5	4	1	3	4	2			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr1:248845140C>T	ENST00000342623.3	-	1	489	c.466G>A	c.(466-468)Gtc>Atc	p.V156I		NM_001004734.1	NP_001004734.1	A6ND48	O14I1_HUMAN	olfactory receptor, family 14, subfamily I, member 1	156						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						CCAGTGTGGACGGCTGCGTAG	0.547																																					p.V156I		Atlas-SNP	.											.	OR14I1	64	.	0			c.G466A						PASS	.						91	81	84					1																	248845140		2203	4300	6503	SO:0001583	missense	401994	exon1			TGTGGACGGCTGC		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.466G>A	1.37:g.248845140C>T	ENSP00000339726:p.Val156Ile	107	0	0		138	27	0.195652	NM_001004734		Missense_Mutation	SNP	ENST00000342623.3	37	CCDS31125.1	.	.	.	.	.	.	.	.	.	.	.	11.09	1.535424	0.27475	.	.	ENSG00000189181	ENST00000342623	T	0.37058	1.22	3.48	-2.84	0.05751	GPCR, rhodopsin-like superfamily (1);	0.376195	0.19197	N	0.120265	T	0.16085	0.0387	N	0.25201	0.72	0.09310	N	1	B	0.23937	0.094	B	0.22880	0.042	T	0.08229	-1.0732	10	0.32370	T	0.25	.	1.6843	0.02838	0.3234:0.2438:0.3194:0.1135	.	156	A6ND48	O14I1_HUMAN	I	156	ENSP00000339726:V156I	ENSP00000339726:V156I	V	-	1	0	OR14I1	246911763	0.000000	0.05858	0.000000	0.03702	0.166000	0.22503	-3.169000	0.00574	-0.144000	0.11314	0.536000	0.68110	GTC	.	.	none		0.547	OR14I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097128.1	NM_001004734		T	248845140	C	T	248845140	3	4	41	1	0	0	0	0	1	0	0	0	10956	536	19	1	473	1	OR14I1	1	248845140	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	30929793	248845140	405481	12	14828											
CD8B	926	hgsc.bcm.edu	37	chr2	87085358	87085358	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccgtggatagtcccttttgcGgaatcccagagggccaggaa	9	8	13	11	2	0	1	0	0	0	1	2	4	2	4	4	4	1	0	4	4	3	3	rs139740563		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr2:87085358G>A	ENST00000390655.6	-	2	283	c.225C>T	c.(223-225)tcC>tcT	p.S75S	CD8B_ENST00000393761.2_Silent_p.S75S|CD8B_ENST00000331469.2_Silent_p.S75S|CD8B_ENST00000431506.2_Intron|CD8B_ENST00000349455.3_Silent_p.S75S|CD8B_ENST00000393759.2_Silent_p.S75S	NM_004931.4	NP_004922.1	P10966	CD8B_HUMAN	CD8b molecule	75	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						TCCCTTTTGCGGAATCCCAGA	0.547																																					p.S75S		Atlas-SNP	.											.	CD8B	37	.	0			c.C225T						PASS	.						111	100	103					2																	87085358		2203	4300	6503	SO:0001819	synonymous_variant	926	exon2			TTTTGCGGAATCC		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.225C>T	2.37:g.87085358G>A		248	0	0		331	69	0.208459	NM_004931	P14860|P14861|Q15980|Q496E0|Q496E1|Q496E2|Q9UDB4|Q9UDB5|Q9UDB6|Q9UDB7|Q9UDB8|Q9UDB9|Q9UDC0|Q9UQ55	Silent	SNP	ENST00000390655.6	37	CCDS1997.1																																																																																			G|0.999;A|0.001	0.001	weak		0.547	CD8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330402.1	NM_172099		A	87085358	G	A	87085358	2	1	41	1	0	0	0	0	0	0	0	1	3047	1103	39	1		1	CD8B	2	87085358	Silent	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10		87085358	156114015	13	14829											
SMYD1	150572	hgsc.bcm.edu	37	chr2	88402591	88402591	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcccagccctctcaggaagtGgtgaaggagatgatacaatt	12	9	11	9	0	1	3	1	2	1	1	3	5	2	4	2	3	2	0	2	3	4	2			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr2:88402591G>T	ENST00000419482.2	+	7	988	c.903G>T	c.(901-903)gtG>gtT	p.V301V	SMYD1_ENST00000438570.1_Intron|SMYD1_ENST00000444564.2_Silent_p.V288V	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	301					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						CTCAGGAAGTGGTGAAGGAGA	0.428																																					p.V301V		Atlas-SNP	.											.	SMYD1	95	.	0			c.G903T						PASS	.						94	91	92					2																	88402591		2203	4300	6503	SO:0001819	synonymous_variant	150572	exon7			GGAAGTGGTGAAG	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.903G>T	2.37:g.88402591G>T		70	0	0		91	16	0.175824	NM_198274	A0AV30|A6NE13	Silent	SNP	ENST00000419482.2	37	CCDS33240.1																																																																																			.	.	none		0.428	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915		T	88402591	G	T	88402591	2	4	41	1	0	0	0	0	0	0	0	1	14836	1335	47	4		4	SMYD1	2	88402591	Silent	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	1317233	88402591	154796782	14	14830											
MARCO	8685	hgsc.bcm.edu	37	chr2	119739789	119739789	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgcagtgggacacccaggtgCcaagggtgagcctggcagtg	8	6	17	10	0	0	1	0	1	0	0	0	2	0	2	3	4	3	2	3	4	1	0			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr2:119739789C>A	ENST00000327097.4	+	11	1094	c.959C>A	c.(958-960)gCc>gAc	p.A320D	MARCO_ENST00000541757.1_Missense_Mutation_p.A242D	NM_006770.3	NP_006761.1	Q9UEW3	MARCO_HUMAN	macrophage receptor with collagenous structure	320	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						CACCCAGGTGCCAAGGGTGAG	0.622																																					p.A320D	GBM(8;18 374 7467 11269 32796)	Atlas-SNP	.											MARCO,pharynx,carcinoma,-1,1	MARCO	120	1	0			c.C959A						PASS	.						67	72	70					2																	119739789		2203	4300	6503	SO:0001583	missense	8685	exon11			CAGGTGCCAAGGG	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.959C>A	2.37:g.119739789C>A	ENSP00000318916:p.Ala320Asp	86	0	0		71	17	0.239437	NM_006770	B4DW79|Q9Y5S3	Missense_Mutation	SNP	ENST00000327097.4	37	CCDS2124.1	.	.	.	.	.	.	.	.	.	.	C	9.182	1.023855	0.19433	.	.	ENSG00000019169	ENST00000327097;ENST00000410021;ENST00000541757	D;D	0.83837	-1.77;-1.77	4.66	3.78	0.43462	.	0.966899	0.08556	N	0.928317	T	0.74321	0.3701	N	0.17278	0.47	0.33498	D	0.589607	P	0.52316	0.952	P	0.46585	0.521	T	0.70908	-0.4744	9	.	.	.	.	8.2489	0.31706	0.0:0.893:0.0:0.107	.	320	Q9UEW3	MARCO_HUMAN	D	320;320;242	ENSP00000318916:A320D;ENSP00000441769:A242D	.	A	+	2	0	MARCO	119456259	0.592000	0.26832	0.971000	0.41717	0.539000	0.34962	1.088000	0.30877	1.188000	0.43014	0.462000	0.41574	GCC	.	.	none		0.622	MARCO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254190.2	NM_006770		A	119739789	C	A	119739789	3	1	41	1	0	0	0	0	1	0	0	0	9320	739	26	4	1001	4	MARCO	2	119739789	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	31337198	119739789	123459584	15	14831											
GLS	2744	hgsc.bcm.edu	37	chr2	191746033	191746033	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgcgcggggcctgtccagcTctccttcggagatcttgcag	4	10	13	14	4	2	1	0	0	2	1	6	2	3	1	3	3	2	2	3	3	0	2			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr2:191746033T>G	ENST00000320717.3	+	1	481	c.223T>G	c.(223-225)Tct>Gct	p.S75A	AC005540.3_ENST00000413911.1_RNA|GLS_ENST00000338435.4_Missense_Mutation_p.S75A	NM_014905.4	NP_055720.3	O94925	GLSK_HUMAN	glutaminase	75					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)	ccTGTCCAGCTCTCCTTCGGA	0.806																																					p.S75A		Atlas-SNP	.											.	GLS	47	.	0			c.T223G						PASS	.						2	3	3					2																	191746033		1153	2110	3263	SO:0001583	missense	2744	exon1			TCCAGCTCTCCTT	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.223T>G	2.37:g.191746033T>G	ENSP00000317379:p.Ser75Ala	23	0	0		26	15	0.576923	NM_014905	Q9UL05|Q9UL06|Q9UL07|Q9UN40	Missense_Mutation	SNP	ENST00000320717.3	37	CCDS2308.1	.	.	.	.	.	.	.	.	.	.	T	14.48	2.549476	0.45383	.	.	ENSG00000115419	ENST00000320717;ENST00000338435	T;T	0.46451	0.98;0.87	3.58	3.58	0.41010	.	0.391203	0.18719	U	0.133071	T	0.26955	0.0660	N	0.24115	0.695	0.80722	D	1	B;B;P	0.35872	0.013;0.023;0.525	B;B;B	0.35353	0.006;0.07;0.201	T	0.05886	-1.0858	10	0.36615	T	0.2	-7.0459	8.6962	0.34298	0.0:0.0:0.0:1.0	.	75;75;75	O94925;O94925-3;O94925-2	GLSK_HUMAN;.;.	A	75	ENSP00000317379:S75A;ENSP00000340689:S75A	ENSP00000317379:S75A	S	+	1	0	GLS	191454278	0.983000	0.35010	0.645000	0.29479	0.495000	0.33615	2.600000	0.46240	1.623000	0.50342	0.402000	0.26972	TCT	.	.	none		0.806	GLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255999.2			G	191746033	T	G	191746033	3	3	41	1	0	0	0	0	1	0	0	0	6471	1551	54	5	225	5	GLS	2	191746033	Missense_Mutation	SNP	T	TCGA-GS-A9TY-01A-11D-A38X-10	72006244	191746033	51453340	16	14832											
RAPH1	65059	hgsc.bcm.edu	37	chr2	204304543	204304543	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctatcattccgtttgggtcGtgtgggtggaggggccttct	3	14	16	8	2	2	0	1	0	1	0	4	1	3	1	2	5	0	2	2	5	1	4			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr2:204304543G>A	ENST00000319170.5	-	14	3669	c.3370C>T	c.(3370-3372)Cga>Tga	p.R1124*	RAPH1_ENST00000374493.3_Nonsense_Mutation_p.R1176*|ABI2_ENST00000295851.5_3'UTR|RAPH1_ENST00000457812.1_Intron	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	1124					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						CGTTTGGGTCGTGTGGGTGGA	0.512																																					p.R1124X		Atlas-SNP	.											.	RAPH1	118	.	0			c.C3370T						PASS	.						119	106	110					2																	204304543		2203	4300	6503	SO:0001587	stop_gained	65059	exon14			TGGGTCGTGTGGG	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.3370C>T	2.37:g.204304543G>A	ENSP00000316543:p.Arg1124*	220	0	0		273	116	0.424908	NM_213589	Q96Q37|Q9C0I2	Nonsense_Mutation	SNP	ENST00000319170.5	37	CCDS2359.1	.	.	.	.	.	.	.	.	.	.	G	37	6.353621	0.97498	.	.	ENSG00000173166	ENST00000319170;ENST00000374493	.	.	.	4.94	4.02	0.46733	.	0.000000	0.31721	U	0.007163	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.2851	12.5109	0.56005	0.0:0.0:0.7007:0.2993	.	.	.	.	X	1124;1176	.	ENSP00000316543:R1124X	R	-	1	2	RAPH1	204012788	0.997000	0.39634	0.971000	0.41717	0.666000	0.39218	2.781000	0.47750	2.288000	0.76882	0.563000	0.77884	CGA	.	.	none		0.512	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2	NM_025252		A	204304543	G	A	204304543	4	1	41	1	0	0	0	0	0	1	0	0	13065	1153	40	1	386	1	RAPH1	2	204304543	Nonsense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	12558510	204304543	38894830	17	14833											
RAPH1	65059	hgsc.bcm.edu	37	chr2	204305402	204305402	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttgcttgggtaatgttggCgggggtactggaacaggagg	7	11	19	4	1	0	0	0	0	0	0	0	2	0	2	0	7	3	5	0	7	3	5	rs144494517	byFrequency	TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr2:204305402C>T	ENST00000319170.5	-	14	2810	c.2511G>A	c.(2509-2511)ccG>ccA	p.P837P	RAPH1_ENST00000374493.3_Silent_p.P889P|ABI2_ENST00000295851.5_3'UTR|RAPH1_ENST00000457812.1_Intron	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	837					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						GTAATGTTGGCGGGGGTACTG	0.582													C|||	4	0.000798722	0.0015	0.0014	5008	,	,		8603	0.0		0.001	False		,,,				2504	0.0				p.P837P		Atlas-SNP	.											.	RAPH1	118	.	0			c.G2511A						PASS	.	C		1,4403		0,1,2201	44	52	50		2511	-5.8	0	2	dbSNP_134	50	1,8599		0,1,4299	no	coding-synonymous	RAPH1	NM_213589.1		0,2,6500	TT,TC,CC		0.0116,0.0227,0.0154		837/1251	204305402	2,13002	2202	4300	6502	SO:0001819	synonymous_variant	65059	exon14			TGTTGGCGGGGGT	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.2511G>A	2.37:g.204305402C>T		40	0	0		78	15	0.192308	NM_213589	Q96Q37|Q9C0I2	Silent	SNP	ENST00000319170.5	37	CCDS2359.1																																																																																			C|0.999;T|0.001	0.001	strong		0.582	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2	NM_025252		T	204305402	C	T	204305402	2	4	41	1	0	0	0	0	0	0	0	1	13065	755	27	1		1	RAPH1	2	204305402	Silent	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	859	204305402	38893971	18	14834											
CPS1	1373	hgsc.bcm.edu	37	chr2	211481148	211481148	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tctcttctcctcttggcaggCcattgatgacaacatgtccc	7	13	7	14	0	3	2	0	2	3	0	6	2	4	2	3	2	1	1	3	2	1	3			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr2:211481148C>A	ENST00000233072.5	+	21	2766	c.2570C>A	c.(2569-2571)gCc>gAc	p.A857D	CPS1_ENST00000451903.2_Splice_Site_p.A406D|CPS1_ENST00000430249.2_Splice_Site_p.A863D	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	857					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)	TCTTGGCAGGCCATTGATGAC	0.353																																					p.A863D		Atlas-SNP	.											.	CPS1	485	.	0			c.C2588A						PASS	.						151	148	149					2																	211481148		2203	4300	6503	SO:0001630	splice_region_variant	1373	exon22			GGCAGGCCATTGA	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.2569-1C>A	2.37:g.211481148C>A		65	0	0		57	21	0.368421	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	37	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	C	18.57	3.653451	0.67472	.	.	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	D;D;D	0.99070	-5.39;-5.39;-5.39	5.41	5.41	0.78517	Carbamoyl-phosphate synthetase, large subunit, oligomerisation (3);	0.096332	0.64402	D	0.000001	D	0.99518	0.9828	H	0.97315	3.98	0.49051	D	0.999744	D;D	0.71674	0.998;0.998	D;D	0.66351	0.943;0.943	D	0.98128	1.0429	10	0.87932	D	0	-0.0201	15.0894	0.72180	0.0:0.8586:0.1414:0.0	.	867;857	Q59HF8;P31327	.;CPSM_HUMAN	D	863;865;857;406	ENSP00000402608:A863D;ENSP00000233072:A857D;ENSP00000406136:A406D	ENSP00000233072:A857D	A	+	2	0	CPS1	211189393	1.000000	0.71417	0.981000	0.43875	0.626000	0.37791	7.198000	0.77823	2.686000	0.91538	0.655000	0.94253	GCC	.	.	none		0.353	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5		Missense_Mutation	A	211481148	C	A	211481148	5	1	41	1	0	0	0	0	0	0	1	0	3825	753	26	4	2674	4	CPS1	2	211481148	Splice_Site	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	7175746	211481148	31718225	19	14835											
XRCC5	7520	hgsc.bcm.edu	37	chr2	216983663	216983769	+	Splice_Site	DEL	AGATCCATTTCTAAGCTTCTCTCCTCAGTGACCAAGTGTATTTGAATTTGTAGAAAAATAATTCAGGAGAATGATTTCTTAATATGATAACTCTCTCTTTTAGAGGA	AGATCCATTTCTAAGCTTCTCTCCTCAGTGACCAAGTGTATTTGAATTTGTAGAAAAATAATTCAGGAGAATGATTTCTTAATATGATAACTCTCTCTTTTAGAGGA	-																															taatcacatttattaactctAgatccatttctaagcttctc																								rs55885859|rs201183966|rs560904622|rs181615100|rs375440774|rs575986003		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	AGATCCATTTCTAAGCTTCTCTCCTCAGTGACCAAGTGTATTTGAATTTGTAGAAAAATAATTCAGGAGAATGATTTCTTAATATGATAACTCTCTCTTTTAGAGGA	AGATCCATTTCTAAGCTTCTCTCCTCAGTGACCAAGTGTATTTGAATTTGTAGAAAAATAATTCAGGAGAATGATTTCTTAATATGATAACTCTCTCTTTTAGAGGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr2:216983663_216983769delAGATCCATTTCTAAGCTTCTCTCCTCAGTGACCAAGTGTATTTGAATTTGTAGAAAAATAATTCAGGAGAATGATTTCTTAATATGATAACTCTCTCTTTTAGAGGA	ENST00000392133.3	+	7	829_833	c.368_372delAGATCCATTTCTAAGCTTCTCTCCTCAGTGACCAAGTGTATTTGAATTTGTAGAAAAATAATTCAGGAGAATGATTTCTTAATATGATAACTCTCTCTTTTAGAGGA	c.(367-372)aagatc>a	p.KI123fs	XRCC5_ENST00000392132.2_Splice_Site_p.KI123fs			P13010	XRCC5_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)	123					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)		TATTAACTCTAGATCCATTTCTAAGCTTCTCTCCTCAGTGACCAAGTGTATTTGAATTTGTAGAAAAATAATTCAGGAGAATGATTTCTTAATATGATAACTCTCTCTTTTAGAGGAAAGAAGTTTG	0.322								Non-homologous end-joining																													p.123_124del		Pindel	.											.	XRCC5	64	.	0			c.369_371del						PASS	.																																			SO:0001630	splice_region_variant	7520	exon5			.	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.369-1AGATCCATTTCTAAGCTTCTCTCCTCAGTGACCAAGTGTATTTGAATTTGTAGAAAAATAATTCAGGAGAATGATTTCTTAATATGATAACTCTCTCTTTTAGAGGA>-	2.37:g.216983663_216983769delAGATCCATTTCTAAGCTTCTCTCCTCAGTGACCAAGTGTATTTGAATTTGTAGAAAAATAATTCAGGAGAATGATTTCTTAATATGATAACTCTCTCTTTTAGAGGA		178	0	.		136	37	0.272	NM_021141	A8K3X5|Q0Z7V0|Q4VBQ5|Q53HH7|Q7M4N0|Q9UCQ0|Q9UCQ1	In_Frame_Del	DEL	ENST00000392133.3	37	CCDS2402.1																																																																																			.	.	none		0.322	XRCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256675.3	NM_021141	Frame_Shift_Del	-	216983769	AGATCCATTTCTAAGCTTCTCTCCTCAGTGACCAAGTGTATTTGAATTTGTAGAAAAATAATTCAGGAGAATGATTTCTTAATATGATAACTCTCTCTTTTAGAGGA	-	216983663	8	5	41	1	0	1	0	1	0	0	1	0	17471	435	15	0		0	XRCC5	2	216983663	Splice_Site	DEL	AGATCCATTTCTAAGCTTCTCTCCTCAGTGACCAAGTGTATTTGAATTTGTAGAAAAATAATTCAGGAGAATGATTTCTTAATATGATAACTCTCTCTTTTAGAGGA	TCGA-GS-A9TY-01A-11D-A38X-10	5502515	216983663	26215710	20	14836											
XRCC5	7520	hgsc.bcm.edu	37	chr2	216983862	216983862	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	attataattcatagcttgaaGaaatgtgacatctccctgca	14	13	6	8	0	2	3	1	2	1	1	3	3	2	3	1	0	2	2	1	0	5	5			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr2:216983862G>C	ENST00000392133.3	+	7	926	c.465G>C	c.(463-465)aaG>aaC	p.K155N	XRCC5_ENST00000392132.2_Missense_Mutation_p.K155N			P13010	XRCC5_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)	155	Leucine-zipper.				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)		ATAGCTTGAAGAAATGTGACA	0.368								Non-homologous end-joining																													p.K155N		Atlas-SNP	.											.	XRCC5	64	.	0			c.G465C						PASS	.						72	74	73					2																	216983862		2203	4300	6503	SO:0001583	missense	7520	exon5			CTTGAAGAAATGT	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.465G>C	2.37:g.216983862G>C	ENSP00000375978:p.Lys155Asn	243	1	0.00411523		222	99	0.445946	NM_021141	A8K3X5|Q0Z7V0|Q4VBQ5|Q53HH7|Q7M4N0|Q9UCQ0|Q9UCQ1	Missense_Mutation	SNP	ENST00000392133.3	37	CCDS2402.1	.	.	.	.	.	.	.	.	.	.	G	19.11	3.763741	0.69878	.	.	ENSG00000079246	ENST00000392133;ENST00000392132	T;T	0.34859	1.34;1.34	5.38	5.38	0.77491	Ku70/Ku80, N-terminal alpha/beta (1);von Willebrand factor, type A (1);	0.000000	0.85682	D	0.000000	T	0.51075	0.1653	M	0.64997	1.995	0.58432	D	0.999992	D	0.71674	0.998	D	0.64506	0.926	T	0.34650	-0.9820	10	0.23302	T	0.38	.	11.6821	0.51463	0.0793:0.0:0.9207:0.0	.	155	P13010	XRCC5_HUMAN	N	155	ENSP00000375978:K155N;ENSP00000375977:K155N	ENSP00000375977:K155N	K	+	3	2	XRCC5	216692107	1.000000	0.71417	0.998000	0.56505	0.847000	0.48162	2.124000	0.42006	2.793000	0.96121	0.655000	0.94253	AAG	.	.	none		0.368	XRCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256675.3	NM_021141		C	216983862	G	C	216983862	3	2	41	1	0	0	0	0	1	0	0	0	17471	933	33	4	483	4	XRCC5	2	216983862	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	199	216983862	26215511	21	14837											
CCDC108	255101	hgsc.bcm.edu	37	chr2	219883882	219883883	+	Frame_Shift_Ins	INS	-	-	G																															agccttaaaggggtgaggacINSgggggggatctggctcatgc																								rs568903495|rs189561241	byFrequency	TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr2:219883882_219883883insG	ENST00000341552.5	-	21	3575_3576	c.3492_3493insC	c.(3490-3495)cccgtcfs	p.V1165fs	CCDC108_ENST00000453220.1_Frame_Shift_Ins_p.V1165fs|CCDC108_ENST00000441968.1_Frame_Shift_Ins_p.V1165fs	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	1165						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)		GGGGTGAGGACGGGGGGGATCT	0.614																																					p.V1165fs		Pindel,Atlas-Indel	.											.	CCDC108	208	.	0			c.3493_3494insC						PASS	.			4,4248		0,4,2122						-2.8	0			53	5,8229		0,5,4112	no	frameshift	CCDC108	NM_194302.2		0,9,6234	A1A1,A1R,RR		0.0607,0.0941,0.0721				9,12477				SO:0001589	frameshift_variant	255101	exon21			.	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.3493dupC	2.37:g.219883889_219883889dupG	ENSP00000340776:p.Val1165fs	91	0	.		94	30	0.319	NM_194302	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Frame_Shift_Ins	INS	ENST00000341552.5	37	CCDS2430.2																																																																																			.	.	none		0.614	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302		G	219883883	-	G	219883882	7	5	41	1	0	1	1	0	0	0	0	0	2745	536	19	0	2344	0	CCDC108	2	219883882	Frame_Shift_Ins	INS	-	TCGA-GS-A9TY-01A-11D-A38X-10	2900020	219883882	23315491	22	14838											
DIS3L2	129563	hgsc.bcm.edu	37	chr2	233001289	233001289	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaatacgccctgttttctccCtcagaccaccgagtgcctag	9	10	7	15	2	2	1	1	0	1	1	3	2	2	1	5	0	2	1	5	0	3	4			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr2:233001289C>T	ENST00000360410.4	+	9	1145	c.869C>T	c.(868-870)cCt>cTt	p.P290L	DIS3L2_ENST00000273009.6_Silent_p.P270P|DIS3L2_ENST00000325385.7_Silent_p.P270P|DIS3L2_ENST00000409307.1_Silent_p.P270P					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)		TGTTTTCTCCCTCAGACCACC	0.483																																					p.P270P		Atlas-SNP	.											.	DIS3L2	77	.	0			c.C810T						PASS	.						196	181	186					2																	233001289		1890	4127	6017	SO:0001583	missense	129563	exon8			TTCTCCCTCAGAC	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	ENST00000360410.4:c.869C>T	2.37:g.233001289C>T	ENSP00000353584:p.Pro290Leu	139	0	0		160	61	0.38125	NM_152383		Silent	SNP	ENST00000360410.4	37		.	.	.	.	.	.	.	.	.	.	C	18.38	3.611078	0.66558	.	.	ENSG00000144535	ENST00000360410	T	0.41758	0.99	6.07	2.74	0.32292	.	0.000000	0.85682	D	0.000000	T	0.50394	0.1613	.	.	.	0.36177	D	0.849142	.	.	.	.	.	.	T	0.58346	-0.7652	7	0.87932	D	0	-18.9098	8.845	0.35164	0.0:0.5387:0.0:0.4613	.	.	.	.	L	290	ENSP00000353584:P290L	ENSP00000353584:P290L	P	+	2	0	DIS3L2	232709533	0.559000	0.26562	0.999000	0.59377	0.998000	0.95712	-0.207000	0.09384	0.234000	0.21139	0.585000	0.79938	CCT	.	.	none		0.483	DIS3L2-202	KNOWN	basic	protein_coding	protein_coding		NM_152383		T	233001289	C	T	233001289	3	4	41	1	0	0	0	0	1	0	0	0	4539	668	24	2	836	2	DIS3L2	2	233001289	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	13117407	233001289	10198084	23	14839											
NGEF	25791	hgsc.bcm.edu	37	chr2	233759514	233759514	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgttggagaagaggatgtgcGcctcggacgggtgcaggatc	8	7	18	8	4	0	2	0	0	0	2	2	6	0	5	1	5	2	2	1	5	1	1	rs183477550	byFrequency	TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr2:233759514G>A	ENST00000264051.3	-	6	1219	c.941C>T	c.(940-942)gCg>gTg	p.A314V	NGEF_ENST00000539537.1_Missense_Mutation_p.A37V|NGEF_ENST00000409079.1_Missense_Mutation_p.A222V|NGEF_ENST00000373552.4_Missense_Mutation_p.A222V	NM_019850.2	NP_062824.2	Q8N5V2	NGEF_HUMAN	neuronal guanine nucleotide exchange factor	314	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)		GAGGATGTGCGCCTCGGACGG	0.612													G|||	2	0.000399361	0.0008	0.0	5008	,	,		17319	0.001		0.0	False		,,,				2504	0.0				p.A314V		Atlas-SNP	.											.	NGEF	198	.	0			c.C941T						PASS	.						110	94	100					2																	233759514		2203	4299	6502	SO:0001583	missense	25791	exon6			ATGTGCGCCTCGG	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.941C>T	2.37:g.233759514G>A	ENSP00000264051:p.Ala314Val	81	0	0		115	12	0.104348	NM_019850	B4DMB8|B9A045|E9PC42|Q53QQ4|Q53ST7|Q6GMQ5|Q9NQD6	Missense_Mutation	SNP	ENST00000264051.3	37	CCDS2500.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	13.58	2.279274	0.40294	.	.	ENSG00000066248	ENST00000264051;ENST00000373552;ENST00000541023;ENST00000539537;ENST00000416114;ENST00000458735;ENST00000409079	T;T;T;T;T;T	0.61742	0.08;0.08;0.08;0.08;0.08;0.08	5.22	5.22	0.72569	Dbl homology (DH) domain (5);	0.479329	0.23496	N	0.047544	T	0.27524	0.0676	N	0.03608	-0.345	0.29453	N	0.858306	B;B;P	0.34800	0.045;0.044;0.469	B;B;B	0.19148	0.013;0.021;0.024	T	0.14364	-1.0475	10	0.18276	T	0.48	-26.6423	12.1758	0.54184	0.078:0.0:0.922:0.0	.	222;222;314	E9PC42;B4DMB8;Q8N5V2	.;.;NGEF_HUMAN	V	314;222;204;37;37;37;222	ENSP00000264051:A314V;ENSP00000362653:A222V;ENSP00000439035:A37V;ENSP00000401063:A37V;ENSP00000412614:A37V;ENSP00000387033:A222V	ENSP00000264051:A314V	A	-	2	0	NGEF	233467758	0.424000	0.25490	0.940000	0.37924	0.791000	0.44710	2.309000	0.43699	2.440000	0.82611	0.655000	0.94253	GCG	G|1.000;A|0.000	0.000	strong		0.612	NGEF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257051.2	XM_044799		A	233759514	G	A	233759514	3	1	41	1	0	0	0	0	1	0	0	0	10403	1087	38	1	1231	1	NGEF	2	233759514	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	758225	233759514	9439859	24	14840											
TRNT1	51095	hgsc.bcm.edu	37	chr3	3182323	3182323	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagatctcactataaattctAtgtttttaggtaatatttgc	12	18	6	5	0	2	1	1	0	2	1	3	2	2	1	0	1	1	2	0	1	7	10			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr3:3182323A>C	ENST00000251607.6	+	4	574	c.472A>C	c.(472-474)Atg>Ctg	p.M158L	TRNT1_ENST00000280591.6_Missense_Mutation_p.M158L	NM_182916.2	NP_886552	Q96Q11	TRNT1_HUMAN	tRNA nucleotidyl transferase, CCA-adding, 1	158					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)		TATAAATTCTATGTTTTTAGG	0.368																																					p.M158L		Atlas-SNP	.											.	TRNT1	34	.	0			c.A472C						PASS	.						75	77	76					3																	3182323		2203	4300	6503	SO:0001583	missense	51095	exon4			AATTCTATGTTTT	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.472A>C	3.37:g.3182323A>C	ENSP00000251607:p.Met158Leu	158	0	0		149	32	0.214765	NM_182916	A8K2Z6|B7WP13|C9JKA2|Q8ND57|Q9BS97|Q9Y362	Missense_Mutation	SNP	ENST00000251607.6	37	CCDS2561.2	.	.	.	.	.	.	.	.	.	.	A	18.65	3.670644	0.67814	.	.	ENSG00000072756	ENST00000251607;ENST00000280591	T;T	0.31247	1.53;1.5	5.71	5.71	0.89125	Poly A polymerase, head domain (1);	0.000000	0.85682	D	0.000000	T	0.20455	0.0492	N	0.17248	0.465	0.80722	D	1	B;B	0.18461	0.007;0.028	B;B	0.28385	0.028;0.089	T	0.05419	-1.0886	10	0.06099	T	0.92	0.0631	15.9869	0.80160	1.0:0.0:0.0:0.0	.	158;158	Q96Q11-2;Q96Q11	.;TRNT1_HUMAN	L	158	ENSP00000251607:M158L;ENSP00000280591:M158L	ENSP00000251607:M158L	M	+	1	0	TRNT1	3157323	1.000000	0.71417	0.990000	0.47175	0.994000	0.84299	9.125000	0.94402	2.171000	0.68590	0.533000	0.62120	ATG	.	.	none		0.368	TRNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337616.1			C	3182323	A	C	3182323	3	2	41	1	0	0	0	0	1	0	0	0	16588	449	16	5	482	5	TRNT1	3	3182323	Missense_Mutation	SNP	A	TCGA-GS-A9TY-01A-11D-A38X-10		3182323	194840107	25	14841											
QARS	5859	hgsc.bcm.edu	37	chr3	49136098	49136098	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gcccacaggctggccccaagCcaggcgcttaaatcctggct	8	6	11	16	1	0	0	0	0	0	0	1	0	1	0	5	4	1	3	5	4	3	1			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr3:49136098C>A	ENST00000306125.6	-	20	2228	c.1891G>T	c.(1891-1893)Gct>Tct	p.A631S	QARS_ENST00000470225.1_5'Flank|QARS_ENST00000414533.1_Missense_Mutation_p.A620S			P47897	SYQ_HUMAN	glutaminyl-tRNA synthetase	631					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)	TGGCCCCAAGCCAGGCGCTTA	0.582																																					p.A631S		Atlas-SNP	.											.	QARS	55	.	0			c.G1891T						PASS	.						17	19	18					3																	49136098		2202	4299	6501	SO:0001583	missense	5859	exon20			CCCAAGCCAGGCG	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.1891G>T	3.37:g.49136098C>A	ENSP00000307567:p.Ala631Ser	53	0	0		58	14	0.241379	NM_005051	B4DWJ2	Missense_Mutation	SNP	ENST00000306125.6	37	CCDS2788.1	.	.	.	.	.	.	.	.	.	.	C	12.62	1.992316	0.35131	.	.	ENSG00000172053	ENST00000453392;ENST00000306125;ENST00000414533	T;T	0.25250	1.81;1.81	5.74	3.95	0.45737	Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain (1);Ribosomal protein L25/Gln-tRNA synthetase, beta-barrel domain (1);Glutamyl/glutaminyl-tRNA synthetase, class Ib, anti-codon binding domain (1);	0.052310	0.85682	D	0.000000	T	0.21227	0.0511	L	0.46567	1.45	0.80722	D	1	B;B	0.27997	0.197;0.197	B;B	0.26614	0.071;0.071	T	0.04537	-1.0944	10	0.38643	T	0.18	-7.9256	8.9136	0.35568	0.0:0.7747:0.0:0.2253	.	620;631	B4DWJ2;P47897	.;SYQ_HUMAN	S	151;631;620	ENSP00000307567:A631S;ENSP00000390015:A620S	ENSP00000307567:A631S	A	-	1	0	QARS	49111102	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.822000	0.48073	1.429000	0.47314	0.561000	0.74099	GCT	.	.	none		0.582	QARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345689.2	NM_005051		A	49136098	C	A	49136098	3	1	41	1	0	0	0	0	1	0	0	0	12886	739	26	4	456	4	QARS	3	49136098	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	45953775	49136098	148886332	26	14842											
PBRM1	55193	hgsc.bcm.edu	37	chr3	52712591	52712591	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatagtctcggatggtattaTagagttcatggcacacggca	11	12	11	7	2	2	1	1	0	1	1	3	2	2	2	0	4	0	4	0	4	5	6			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr3:52712591T>C	ENST00000296302.7	-	2	162	c.161A>G	c.(160-162)tAt>tGt	p.Y54C	PBRM1_ENST00000356770.4_Missense_Mutation_p.Y54C|PBRM1_ENST00000337303.4_Missense_Mutation_p.Y54C|PBRM1_ENST00000409767.1_Missense_Mutation_p.Y54C|PBRM1_ENST00000409114.3_Missense_Mutation_p.Y54C|PBRM1_ENST00000409057.1_Missense_Mutation_p.Y54C|PBRM1_ENST00000394830.3_Missense_Mutation_p.Y54C|PBRM1_ENST00000410007.1_Missense_Mutation_p.Y54C			Q86U86	PB1_HUMAN	polybromo 1	54					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)		GATGGTATTATAGAGTTCATG	0.408			"Mis, N, F, S, D, O"		"clear cell renal carcinoma, breast"																																p.Y54C		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.A161G						PASS	.						122	110	114					3																	52712591		2203	4300	6503	SO:0001583	missense	55193	exon3			GTATTATAGAGTT	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.161A>G	3.37:g.52712591T>C	ENSP00000296302:p.Tyr54Cys	91	0	0		91	54	0.593407	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Missense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	T	19.44	3.827120	0.71143	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000431678;ENST00000420148;ENST00000449505;ENST00000450271	T;T;T;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;2.16;2.16;2.16	5.2	5.2	0.72013	Bromodomain (3);	0.000000	0.85682	D	0.000000	T	0.53351	0.1791	M	0.88906	2.99	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	0.992;0.999;0.992;0.969;0.99;0.997;0.974;1.0	T	0.63620	-0.6596	10	0.87932	D	0	.	15.0658	0.71992	0.0:0.0:0.0:1.0	.	54;54;54;54;54;54;54;54	Q86U86-9;Q86U86-4;Q86U86-2;Q86U86-8;Q86U86-7;Q86U86;Q86U86-3;Q86U86-5	.;.;.;.;.;PB1_HUMAN;.;.	C	54	ENSP00000349213:Y54C;ENSP00000378307:Y54C;ENSP00000296302:Y54C;ENSP00000338302:Y54C;ENSP00000386593:Y54C;ENSP00000386529:Y54C;ENSP00000386643:Y54C;ENSP00000386601:Y54C;ENSP00000387775:Y54C;ENSP00000409939:Y54C;ENSP00000389390:Y54C;ENSP00000412401:Y54C;ENSP00000416851:Y54C	ENSP00000296302:Y54C	Y	-	2	0	PBRM1	52687631	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	3.598000	0.54038	1.968000	0.57251	0.377000	0.23210	TAT	.	.	none		0.408	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165		C	52712591	T	C	52712591	3	2	41	1	0	0	0	0	1	0	0	0	11500	1406	49	3	4855	3	PBRM1	3	52712591	Missense_Mutation	SNP	T	TCGA-GS-A9TY-01A-11D-A38X-10	3576493	52712591	145309839	27	14843											
MSL2	55167	hgsc.bcm.edu	37	chr3	135871364	135871364	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagaacagtcaactgcttctAttatatcccgtgccagtgta	12	12	7	10	1	2	1	1	0	1	1	3	1	3	1	2	0	4	2	2	0	7	5			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr3:135871364A>G	ENST00000309993.2	-	2	1091	c.359T>C	c.(358-360)aTa>aCa	p.I120T	MSL2_ENST00000434835.2_Missense_Mutation_p.I46T	NM_018133.3	NP_060603.2	Q9HCI7	MSL2_HUMAN	male-specific lethal 2 homolog (Drosophila)	120					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						AACTGCTTCTATTATATCCCG	0.378																																					p.I120T		Atlas-SNP	.											.	MSL2	63	.	0			c.T359C						PASS	.						168	157	161					3																	135871364		2203	4300	6503	SO:0001583	missense	55167	exon2			GCTTCTATTATAT	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.359T>C	3.37:g.135871364A>G	ENSP00000311827:p.Ile120Thr	209	0	0		148	62	0.418919	NM_018133	B4DYL4|G5E9I1|Q0D2P1|Q8NDB4|Q9NVS4	Missense_Mutation	SNP	ENST00000309993.2	37	CCDS33861.1	.	.	.	.	.	.	.	.	.	.	A	3.117	-0.181422	0.06340	.	.	ENSG00000174579	ENST00000309993;ENST00000434835;ENST00000481989;ENST00000491050;ENST00000473093	.	.	.	6.17	5.01	0.66863	.	0.114979	0.64402	D	0.000013	T	0.37679	0.1012	N	0.24115	0.695	0.35088	D	0.764059	B	0.10296	0.003	B	0.09377	0.004	T	0.40701	-0.9549	9	0.29301	T	0.29	-11.1528	11.7296	0.51728	0.9316:0.0:0.0683:0.0	.	120	Q9HCI7	MSL2_HUMAN	T	120;46;46;46;46	.	ENSP00000311827:I120T	I	-	2	0	MSL2	137354054	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.691000	0.61738	1.146000	0.42352	0.533000	0.62120	ATA	.	.	none		0.378	MSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357347.1	NM_018133		G	135871364	A	G	135871364	3	3	41	1	0	0	0	0	1	0	0	0	9887	449	16	3	1378	3	MSL2	3	135871364	Missense_Mutation	SNP	A	TCGA-GS-A9TY-01A-11D-A38X-10	83158773	135871364	62151066	28	14844											
HS3ST1	9957	hgsc.bcm.edu	37	chr4	11401388	11401388	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacctcgttctccgcggccGccacgtcggggtgcaggctg	3	7	16	15	6	1	0	0	0	1	0	4	1	1	1	4	5	1	3	4	5	0	1			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr4:11401388G>A	ENST00000002596.5	-	2	1416	c.242C>T	c.(241-243)gCg>gTg	p.A81V		NM_005114.2	NP_005105.1	O14792	HS3S1_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 1	81					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						CTCCGCGGCCGCCACGTCGGG	0.657																																					p.A81V		Atlas-SNP	.											.	HS3ST1	41	.	0			c.C242T						PASS	.						61	52	55					4																	11401388		2203	4300	6503	SO:0001583	missense	9957	exon2			GCGGCCGCCACGT	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.242C>T	4.37:g.11401388G>A	ENSP00000002596:p.Ala81Val	68	0	0		64	28	0.4375	NM_005114	B3KUA6|Q6PEY8	Missense_Mutation	SNP	ENST00000002596.5	37	CCDS3408.1	.	.	.	.	.	.	.	.	.	.	G	16.34	3.096989	0.56075	.	.	ENSG00000002587	ENST00000002596;ENST00000514690;ENST00000510712	T;T;T	0.55234	0.53;0.53;0.53	5.81	5.81	0.92471	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	T	0.42381	0.1200	N	0.20610	0.595	0.80722	D	1	P	0.52692	0.955	P	0.44394	0.448	T	0.18840	-1.0324	10	0.13853	T	0.58	.	19.0707	0.93134	0.0:0.0:1.0:0.0	.	81	O14792	HS3S1_HUMAN	V	81	ENSP00000002596:A81V;ENSP00000425673:A81V;ENSP00000422629:A81V	ENSP00000002596:A81V	A	-	2	0	HS3ST1	11010486	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	8.006000	0.88564	2.746000	0.94184	0.655000	0.94253	GCG	.	.	none		0.657	HS3ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207073.3	NM_005114		A	11401388	G	A	11401388	3	1	41	1	0	0	0	0	1	0	0	0	7372	1087	38	1	685	1	HS3ST1	4	11401388	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10		11401388	179752888	29	14845											
PHOX2B	8929	hgsc.bcm.edu	37	chr4	41748171	41748171	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gggggtggggttgggattggGacctgggcccccagtgctgt	3	9	21	8	0	0	0	0	0	0	0	0	2	0	2	3	7	1	2	3	7	0	2			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr4:41748171G>A	ENST00000226382.2	-	3	957	c.598C>T	c.(598-600)Ccc>Tcc	p.P200S	RP11-227F19.1_ENST00000508038.1_RNA	NM_003924.3	NP_003915.2	Q99453	PHX2B_HUMAN	paired-like homeobox 2b	200					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						TTGGGATTGGGACCTGGGCCC	0.731			"Mis, F"		neuroblastoma	neuroblastoma	congenital central hypoventilation syndrome		Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.P200S		Atlas-SNP	.	yes	Rec	yes	familial neuroblastoma	4	4p12	8929	paired-like homeobox 2b	yes	O	.	PHOX2B	53	.	0			c.C598T						PASS	.						44	43	43					4																	41748171		2203	4300	6503	SO:0001583	missense	8929	exon3	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	GATTGGGACCTGG	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.598C>T	4.37:g.41748171G>A	ENSP00000226382:p.Pro200Ser	47	0	0		46	25	0.543478	NM_003924	Q6PJD9	Missense_Mutation	SNP	ENST00000226382.2	37	CCDS3463.1	.	.	.	.	.	.	.	.	.	.	G	7.728	0.698662	0.15106	.	.	ENSG00000109132	ENST00000226382	D	0.90563	-2.69	4.69	3.84	0.44239	.	0.000000	0.85682	D	0.000000	T	0.79423	0.4443	N	0.19112	0.55	0.42186	D	0.991702	B	0.26935	0.164	B	0.19946	0.027	T	0.71768	-0.4493	10	0.30078	T	0.28	.	4.8021	0.13301	0.0832:0.1498:0.6123:0.1547	.	200	Q99453	PHX2B_HUMAN	S	200	ENSP00000226382:P200S	ENSP00000226382:P200S	P	-	1	0	PHOX2B	41442928	1.000000	0.71417	0.114000	0.21550	0.004000	0.04260	6.516000	0.73755	1.173000	0.42796	-0.165000	0.13383	CCC	.	.	none		0.731	PHOX2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216832.2			A	41748171	G	A	41748171	3	1	41	1	0	0	0	0	1	0	0	0	11868	1174	41	2	350	2	PHOX2B	4	41748171	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	30346783	41748171	149406105	30	14846											
CLGN	1047	hgsc.bcm.edu	37	chr4	141313740	141313740	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaaatccattttctttacCtttacttttcttggccaaca	10	17	4	10	0	2	0	0	0	2	0	3	1	3	1	3	2	3	0	3	2	4	9			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr4:141313740C>T	ENST00000325617.5	-	12	1931	c.1491G>A	c.(1489-1491)aaG>aaA	p.K497K	CLGN_ENST00000414773.1_Splice_Site_p.K497K|CLGN_ENST00000537281.1_Splice_Site_p.K497K	NM_004362.2	NP_004353.1	O14967	CLGN_HUMAN	calmegin	497					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)					TTTTCTTTACCTTTACTTTTC	0.343																																					p.K497K		Atlas-SNP	.											.	CLGN	76	.	0			c.G1491A						PASS	.						60	58	59					4																	141313740		2203	4300	6503	SO:0001630	splice_region_variant	1047	exon13			CTTTACCTTTACT	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.1491+1G>A	4.37:g.141313740C>T		202	0	0		170	26	0.152941	NM_001130675	B3KS90|B4DXV8|D3DNY8	Silent	SNP	ENST00000325617.5	37	CCDS3751.1																																																																																			.	.	none		0.343	CLGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257272.2	NM_004362	Silent	T	141313740	C	T	141313740	5	4	41	1	0	0	0	0	0	0	1	0	3526	695	24	2	357	2	CLGN	4	141313740	Splice_Site	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	99565569	141313740	49840536	31	14847											
DDX60	55601	hgsc.bcm.edu	37	chr4	169212958	169212958	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agtgatgactctagcacaagCtctttgagaaagaggcagat	14	9	11	7	0	2	5	0	3	2	3	2	6	2	5	0	1	2	3	0	1	3	2			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr4:169212958C>G	ENST00000393743.3	-	8	1273	c.982G>C	c.(982-984)Gct>Cct	p.A328P		NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	328					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)		CTAGCACAAGCTCTTTGAGAA	0.388																																					p.A328P		Atlas-SNP	.											.	DDX60	304	.	0			c.G982C						PASS	.						97	97	97					4																	169212958		2203	4300	6503	SO:0001583	missense	55601	exon8			CACAAGCTCTTTG	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.982G>C	4.37:g.169212958C>G	ENSP00000377344:p.Ala328Pro	75	0	0		91	40	0.43956	NM_017631	Q6PK35|Q9NVE3	Missense_Mutation	SNP	ENST00000393743.3	37	CCDS34097.1	.	.	.	.	.	.	.	.	.	.	C	15.90	2.969121	0.53614	.	.	ENSG00000137628	ENST00000393743	T	0.23348	1.91	4.79	4.79	0.61399	.	0.000000	0.64402	D	0.000012	T	0.51210	0.1661	M	0.75264	2.295	0.39673	D	0.970785	D	0.89917	1.0	D	0.79108	0.992	T	0.56220	-0.8015	10	0.59425	D	0.04	.	15.7864	0.78306	0.0:1.0:0.0:0.0	.	328	Q8IY21	DDX60_HUMAN	P	328	ENSP00000377344:A328P	ENSP00000377344:A328P	A	-	1	0	DDX60	169449533	1.000000	0.71417	0.997000	0.53966	0.192000	0.23643	3.850000	0.55918	2.510000	0.84645	0.563000	0.77884	GCT	.	.	none		0.388	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631		G	169212958	C	G	169212958	3	3	41	1	0	0	0	0	1	0	0	0	4380	797	28	4	4280	4	DDX60	4	169212958	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	27899218	169212958	21941318	32	14848											
FST	10468	hgsc.bcm.edu	37	chr5	52778714	52778714	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	ccttgtctcttcacagctggGaactgctggctccgtcaagc	6	11	10	14	1	3	0	2	0	1	0	5	1	4	1	2	2	4	3	2	2	2	2	rs201482393	byFrequency	TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr5:52778714G>C	ENST00000256759.3	+	2	473	c.90G>C	c.(88-90)ggG>ggC	p.G30G	FST_ENST00000396947.3_Silent_p.G30G	NM_013409.2	NP_037541.1	P19883	FST_HUMAN	follistatin	30	TB.				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)				TCACAGCTGGGAACTGCTGGC	0.652											OREG0016608	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G30G		Atlas-SNP	.											.	FST	42	.	0			c.G90C						PASS	.						39	37	38					5																	52778714		2203	4300	6503	SO:0001819	synonymous_variant	10468	exon2			AGCTGGGAACTGC	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.90G>C	5.37:g.52778714G>C		150	0	0	987	127	34	0.267717	NM_013409	B5BU94|Q9BTH0	Silent	SNP	ENST00000256759.3	37	CCDS3959.1																																																																																			G|1.000;T|0.000	.	alt		0.652	FST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253906.1	NM_013409		C	52778714	G	C	52778714	2	2	41	1	0	0	0	0	0	0	0	1	6084	1161	41	4		4	FST	5	52778714	Silent	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10		52778714	128136546	33	14849											
SKIV2L2	23517	hgsc.bcm.edu	37	chr5	54635973	54635973	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgatgactggtgatgttacTattaatcctacggcatcttg	9	16	9	7	1	1	3	0	3	1	0	2	3	2	3	1	2	2	2	1	2	4	6			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr5:54635973T>G	ENST00000230640.5	+	6	905	c.651T>G	c.(649-651)acT>acG	p.T217T	SKIV2L2_ENST00000545714.1_Silent_p.T116T	NM_015360.4	NP_056175.3	P42285	SK2L2_HUMAN	superkiller viralicidic activity 2-like 2 (S. cerevisiae)	217	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)				GTGATGTTACTATTAATCCTA	0.348																																					p.T217T	Melanoma(2;92 134 23744 29976 33782)	Atlas-SNP	.											.	SKIV2L2	104	.	0			c.T651G						PASS	.						173	171	172					5																	54635973		2203	4300	6503	SO:0001819	synonymous_variant	23517	exon6			TGTTACTATTAAT	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.651T>G	5.37:g.54635973T>G		209	1	0.00478469		202	99	0.490099	NM_015360	Q2M386|Q6MZZ8|Q6P170|Q8N5R0|Q8TAG2	Silent	SNP	ENST00000230640.5	37	CCDS3967.1																																																																																			.	.	none		0.348	SKIV2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214108.1			G	54635973	T	G	54635973	2	3	41	1	0	0	0	0	0	0	0	1	14375	1509	53	5		5	SKIV2L2	5	54635973	Silent	SNP	T	TCGA-GS-A9TY-01A-11D-A38X-10	1857259	54635973	126279287	34	14850											
TRIM23	373	hgsc.bcm.edu	37	chr5	64905170	64905170	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgagccaaatcaatttttcaCgaacatgagcatcaacaaca	17	9	5	10	1	3	2	3	2	0	0	3	3	3	2	1	0	5	1	1	0	5	2			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr5:64905170C>T	ENST00000231524.9	-	6	1315	c.944G>A	c.(943-945)cGt>cAt	p.R315H	TRIM23_ENST00000381018.3_Missense_Mutation_p.R315H|TRIM23_ENST00000274327.7_Missense_Mutation_p.R315H|TRIM23_ENST00000508808.1_5'UTR	NM_001656.3	NP_001647.1	P36406	TRI23_HUMAN	tripartite motif containing 23	315					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)		CAATTTTTCACGAACATGAGC	0.418																																					p.R315H		Atlas-SNP	.											.	TRIM23	73	.	0			c.G944A						PASS	.						121	111	114					5																	64905170		2203	4300	6503	SO:0001583	missense	373	exon6			TTTTCACGAACAT	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.944G>A	5.37:g.64905170C>T	ENSP00000231524:p.Arg315His	291	0	0		265	82	0.309434	NM_033228	Q9BZY4|Q9BZY5	Missense_Mutation	SNP	ENST00000231524.9	37	CCDS3987.1	.	.	.	.	.	.	.	.	.	.	C	31	5.101218	0.94245	.	.	ENSG00000113595	ENST00000231524;ENST00000381018;ENST00000274327	T;T;T	0.75367	-0.84;-0.84;-0.93	5.39	5.39	0.77823	B-box, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.85270	0.5658	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	0.996;0.999;0.998	D	0.85178	0.1002	10	0.54805	T	0.06	.	19.5154	0.95162	0.0:1.0:0.0:0.0	.	315;315;315	P36406;P36406-2;P36406-3	TRI23_HUMAN;.;.	H	315	ENSP00000231524:R315H;ENSP00000370406:R315H;ENSP00000274327:R315H	ENSP00000231524:R315H	R	-	2	0	TRIM23	64940926	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.445000	0.80570	2.685000	0.91497	0.655000	0.94253	CGT	.	.	none		0.418	TRIM23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215058.2	NM_001656		T	64905170	C	T	64905170	3	4	41	1	0	0	0	0	1	0	0	0	16512	536	19	1	871	1	TRIM23	5	64905170	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	10269197	64905170	116010090	35	14851											
MAST4	375449	hgsc.bcm.edu	37	chr5	66350237	66350237	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctttctttttgatagttgccGaacaagcaaccggaaaagct	12	12	8	9	2	1	1	0	1	1	0	1	3	1	2	2	1	5	3	2	1	6	5			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr5:66350237G>A	ENST00000403625.2	+	5	975	c.680G>A	c.(679-681)cGa>cAa	p.R227Q	MAST4_ENST00000403666.1_Missense_Mutation_p.R38Q|MAST4_ENST00000490016.2_Missense_Mutation_p.R38Q|MAST4_ENST00000261569.7_Missense_Mutation_p.R33Q|MAST4_ENST00000405643.1_Missense_Mutation_p.R45Q|MAST4_ENST00000404260.3_Missense_Mutation_p.R227Q	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	227						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.R227Q(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)		GATAGTTGCCGAACAAGCAAC	0.423																																					p.R227Q		Atlas-SNP	.											MAST4_ENST00000404260,rectum,carcinoma,0,1	MAST4	218	1	1	Substitution - Missense(1)	large_intestine(1)	c.G680A						PASS	.						72	68	69					5																	66350237		1883	4100	5983	SO:0001583	missense	375449	exon5			GTTGCCGAACAAG	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.680G>A	5.37:g.66350237G>A	ENSP00000385727:p.Arg227Gln	194	1	0.00515464		140	117	0.835714	NM_001164664	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	37	CCDS54861.1	.	.	.	.	.	.	.	.	.	.	G	33	5.288148	0.95517	.	.	ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000490016;ENST00000403666;ENST00000405643;ENST00000432426;ENST00000380908;ENST00000261569;ENST00000436277;ENST00000432399	T;T;T;T;T;T	0.74106	-0.32;-0.32;1.26;-0.79;-0.81;-0.65	5.77	5.77	0.91146	.	0.225364	0.25089	U	0.033232	D	0.86012	0.5831	M	0.69358	2.11	0.32854	D	0.507104	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.991	D;D;D;D;P	0.78314	0.941;0.987;0.973;0.991;0.716	D	0.88093	0.2814	10	0.72032	D	0.01	-4.4909	19.9894	0.97361	0.0:0.0:1.0:0.0	.	45;227;33;38;38	E7EWQ5;O15021;O15021-2;O15021-3;D6RAK1	.;MAST4_HUMAN;.;.;.	Q	227;227;38;38;45;18;45;33;33;33	ENSP00000385048:R227Q;ENSP00000385727:R227Q;ENSP00000421739:R38Q;ENSP00000384313:R38Q;ENSP00000384099:R45Q;ENSP00000261569:R33Q	ENSP00000261569:R33Q	R	+	2	0	MAST4	66385993	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	8.398000	0.90195	2.726000	0.93360	0.561000	0.74099	CGA	.	.	none		0.423	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			A	66350237	G	A	66350237	3	1	41	1	0	0	0	0	1	0	0	0	9336	1058	37	1	828	1	MAST4	5	66350237	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	1445067	66350237	114565023	36	14852											
MAP1B	4131	hgsc.bcm.edu	37	chr5	71495764	71495764	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cccacagacaaaactgtcacGtacaaacacatggacccacc	16	4	5	16	1	1	1	1	0	0	1	1	2	1	2	3	1	3	1	3	1	4	1	rs368060624		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr5:71495764G>A	ENST00000296755.7	+	5	6880	c.6582G>A	c.(6580-6582)acG>acA	p.T2194T		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	2194					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)		AAACTGTCACGTACAAACACA	0.587																																					p.T2194T	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.G6582A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	142	128	133		6582	-11.9	0.1	5		133	0,8600		0,0,4300	no	coding-synonymous	MAP1B	NM_005909.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		2194/2469	71495764	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	4131	exon5			TGTCACGTACAAA	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.6582G>A	5.37:g.71495764G>A		53	0	0		56	23	0.410714	NM_005909	A2BDK5	Silent	SNP	ENST00000296755.7	37	CCDS4012.1																																																																																			.	.	weak		0.587	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		A	71495764	G	A	71495764	2	1	41	1	0	0	0	0	0	0	0	1	9237	1132	40	1		1	MAP1B	5	71495764	Silent	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	5145527	71495764	109419496	37	14853											
ZNF608	57507	hgsc.bcm.edu	37	chr5	124080282	124080282	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cttggacttcctgcctcttgCcagtgctgctgatctcggga	4	13	11	13	1	2	1	0	1	2	0	4	3	3	3	3	2	4	2	3	2	0	3			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr5:124080282C>T	ENST00000306315.5	-	1	836	c.401G>A	c.(400-402)gGc>gAc	p.G134D	ZNF608_ENST00000504926.1_5'Flank	NM_020747.2	NP_065798.2	Q9ULD9	ZN608_HUMAN	zinc finger protein 608	134							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)		CTGCCTCTTGCCAGTGCTGCT	0.527																																					p.G134D		Atlas-SNP	.											.	ZNF608	117	.	0			c.G401A						PASS	.						71	70	71					5																	124080282		2203	4300	6503	SO:0001583	missense	57507	exon1			CTCTTGCCAGTGC	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.401G>A	5.37:g.124080282C>T	ENSP00000307746:p.Gly134Asp	124	1	0.00806452		131	112	0.854962	NM_020747	A7E2W9|Q3SYM6|Q68D12|Q8IY05|Q9Y5A1	Missense_Mutation	SNP	ENST00000306315.5	37	CCDS34219.1	.	.	.	.	.	.	.	.	.	.	C	16.54	3.152626	0.57259	.	.	ENSG00000168916	ENST00000306315;ENST00000509799;ENST00000513986	T	0.55052	0.54	5.33	4.46	0.54185	.	0.287027	0.30446	N	0.009608	T	0.44244	0.1284	L	0.48642	1.525	0.80722	D	1	B	0.16802	0.019	B	0.19946	0.027	T	0.34825	-0.9813	10	0.37606	T	0.19	-16.5901	9.4407	0.38666	0.0:0.7796:0.1439:0.0765	.	134	Q9ULD9	ZN608_HUMAN	D	134	ENSP00000307746:G134D	ENSP00000307746:G134D	G	-	2	0	ZNF608	124108181	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.891000	0.48617	1.381000	0.46364	0.655000	0.94253	GGC	.	.	none		0.527	ZNF608-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371300.1	XM_114432		T	124080282	C	T	124080282	3	4	41	1	0	0	0	0	1	0	0	0	18049	739	26	2	4173	2	ZNF608	5	124080282	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	52584518	124080282	56834978	38	14854											
RGS14	10636	hgsc.bcm.edu	37	chr5	176795190	176795190	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcaaacgccgccttgcgcCgagagtctcagggctccctc	6	7	11	17	4	1	1	1	0	1	1	4	2	2	1	4	1	3	2	4	1	1	1			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr5:176795190C>T	ENST00000408923.3	+	8	960	c.772C>T	c.(772-774)Cga>Tga	p.R258*		NM_006480.4	NP_006471.2	O43566	RGS14_HUMAN	regulator of G-protein signaling 14	258					cell division (GO:0051301)|chromosome segregation (GO:0007059)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mitotic nuclear division (GO:0007067)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of synaptic plasticity (GO:0031914)|nucleocytoplasmic transport (GO:0006913)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of GTPase activity (GO:0043547)|positive regulation of neurogenesis (GO:0050769)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|response to oxidative stress (GO:0006979)|spindle organization (GO:0007051)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual learning (GO:0008542)|zygote asymmetric cell division (GO:0010070)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|microtubule (GO:0005874)|nuclear body (GO:0016604)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|spindle (GO:0005819)|spindle pole (GO:0000922)	GDP-dissociation inhibitor activity (GO:0005092)|GTPase activator activity (GO:0005096)|microtubule binding (GO:0008017)|receptor signaling complex scaffold activity (GO:0030159)|receptor signaling protein activity (GO:0005057)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(3)|upper_aerodigestive_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)			CGCCTTGCGCCGAGAGTCTCA	0.632																																					p.R258X	NSCLC(47;353 1896 28036)	Atlas-SNP	.											.	RGS14	34	.	0			c.C772T						PASS	.						56	61	60					5																	176795190		2014	4168	6182	SO:0001587	stop_gained	10636	exon8			TTGCGCCGAGAGT	AF037195	CCDS43405.1	5q35.3	2008-02-05	2007-08-14		ENSG00000169220	ENSG00000169220		"Regulators of G-protein signaling"	9996	protein-coding gene	gene with protein product		602513	"regulator of G-protein signalling 14"				Standard	NM_006480		Approved		uc003mgf.3	O43566	OTTHUMG00000163324	ENST00000408923.3:c.772C>T	5.37:g.176795190C>T	ENSP00000386229:p.Arg258*	33	0	0		65	10	0.153846	NM_006480	O43565|Q506M1|Q6ZWA4|Q8TD62	Nonsense_Mutation	SNP	ENST00000408923.3	37	CCDS43405.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.607138	0.87157	.	.	ENSG00000169220	ENST00000408923	.	.	.	4.14	1.12	0.20585	.	0.072462	0.53938	D	0.000042	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.6275	13.4062	0.60915	0.5852:0.4148:0.0:0.0	.	.	.	.	X	258	.	ENSP00000386229:R258X	R	+	1	2	RGS14	176727796	0.164000	0.22935	0.937000	0.37676	0.925000	0.55904	-0.314000	0.08092	0.010000	0.14839	0.491000	0.48974	CGA	.	.	none		0.632	RGS14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372676.1	NM_006480		T	176795190	C	T	176795190	4	4	41	1	0	0	0	0	0	1	0	0	13312	644	23	1	802	1	RGS14	5	176795190	Nonsense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	52714908	176795190	4120070	39	14855											
RREB1	6239	hgsc.bcm.edu	37	chr6	7230225	7230225	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccttcatgacagcgcccggCggcaagaagacgcccgccat	9	4	12	16	5	1	3	1	1	0	2	1	3	1	3	4	2	1	1	4	2	2	1			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr6:7230225C>T	ENST00000349384.6	+	10	2207	c.1893C>T	c.(1891-1893)ggC>ggT	p.G631G	RREB1_ENST00000379938.2_Silent_p.G631G|RREB1_ENST00000379933.3_Silent_p.G631G|RREB1_ENST00000334984.6_Silent_p.G631G	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	631					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)				CAGCGCCCGGCGGCAAGAAGA	0.637																																					p.G631G		Atlas-SNP	.											.	RREB1	242	.	0			c.C1893T						PASS	.						21	23	22					6																	7230225		2202	4297	6499	SO:0001819	synonymous_variant	6239	exon10			GCCCGGCGGCAAG	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.1893C>T	6.37:g.7230225C>T		63	0	0		68	41	0.602941	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Silent	SNP	ENST00000349384.6	37	CCDS34336.1																																																																																			.	.	none		0.637	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1			T	7230225	C	T	7230225	2	4	41	1	0	0	0	0	0	0	0	1	13694	755	27	1		1	RREB1	6	7230225	Silent	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10		7230225	163884842	40	14856											
ALDH5A1	7915	hgsc.bcm.edu	37	chr6	24522996	24523012	+	Splice_Site	DEL	CTTGTGTTTGCTCAAAC	CTTGTGTTTGCTCAAAC	-																															gtttttgtctcctgtccagaCttgtgtttgctcaaaccaat																								rs551402692		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	CTTGTGTTTGCTCAAAC	CTTGTGTTTGCTCAAAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr6:24522996_24523012delCTTGTGTTTGCTCAAAC	ENST00000357578.3	+	7	1161_1177	c.1016_1032delCTTGTGTTTGCTCAAAC	c.(1015-1032)acttgtgtttgctcaaac>a	p.TCVCSN339fs	ALDH5A1_ENST00000491546.1_Splice_Site_p.TCVCSN311fs|ALDH5A1_ENST00000348925.2_Splice_Site_p.TCVCSN352fs|ALDH5A1_ENST00000546278.1_Splice_Site_p.TCVCSN251fs	NM_001080.3	NP_001071.1	P51649	SSDH_HUMAN	aldehyde dehydrogenase 5 family, member A1	339					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)	CCTGTCCAGACTTGTGTTTGCTCAAACCAATTCTTGG	0.493																																					p.352_357del		Pindel,Atlas-Indel	.											.	ALDH5A1	42	.	0			c.1054_1070del						PASS	.																																			SO:0001630	splice_region_variant	7915	exon8			.	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.1015-1CTTGTGTTTGCTCAAAC>-	6.37:g.24522996_24523012delCTTGTGTTTGCTCAAAC		179	0	.		108	30	0.278	NM_170740	B2RD26|G5E949|Q546H9|Q8N3W6	Frame_Shift_Del	DEL	ENST00000357578.3	37	CCDS4555.1																																																																																			.	.	none		0.493	ALDH5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040007.2		Frame_Shift_Del	-	24523012	CTTGTGTTTGCTCAAAC	-	24522996	8	5	41	1	0	1	0	1	0	0	1	0	502	579	20	0	1085	0	ALDH5A1	6	24522996	Splice_Site	DEL	CTTGTGTTTGCTCAAAC	TCGA-GS-A9TY-01A-11D-A38X-10	17292771	24522996	146592071	41	14857											
HIST1H2BJ	8970	hgsc.bcm.edu	37	chr6	27100189	27100219	+	Frame_Shift_Del	DEL	TCGGACACGGCGTGCTTGGCCAACTCCCCAG	TCGGACACGGCGTGCTTGGCCAACTCCCCAG	-																															tggtgacggccttagtacccTcggacacggcgtgcttggcc																								rs2272811|rs145874703	byFrequency	TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	TCGGACACGGCGTGCTTGGCCAACTCCCCAG	TCGGACACGGCGTGCTTGGCCAACTCCCCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr6:27100189_27100219delTCGGACACGGCGTGCTTGGCCAACTCCCCAG	ENST00000607124.1	-	1	310_340	c.311_341delCTGGGGAGTTGGCCAAGCACGCCGTGTCCGA	c.(310-342)cctggggagttggccaagcacgccgtgtccgagfs	p.PGELAKHAVSE104fs	HIST1H2BJ_ENST00000541790.1_Frame_Shift_Del_p.PGELAKHAVSE104fs|HIST1H2AG_ENST00000359193.2_5'Flank|HIST1H2BJ_ENST00000339812.2_Frame_Shift_Del_p.PGELAKHAVSE104fs			P06899	H2B1J_HUMAN	histone cluster 1, H2bj	104					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)	p.E114K(1)		breast(1)|kidney(2)|lung(5)|ovary(1)|prostate(1)	10						CTTAGTACCCTCGGACACGGCGTGCTTGGCCAACTCCCCAGGCAGCAGCAG	0.584																																					p.104_114del		Pindel	.											HIST1H2BJ,NS,malignant_melanoma,-2,3	HIST1H2BJ	21	3	1	Substitution - Missense(1)	breast(1)	c.312_342del						PASS	.																																			SO:0001589	frameshift_variant	8970	exon1			.	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.311_341delCTGGGGAGTTGGCCAAGCACGCCGTGTCCGA	6.37:g.27100189_27100219delTCGGACACGGCGTGCTTGGCCAACTCCCCAG	ENSP00000476136:p.Pro104fs	99	0	.		72	13	0.181	NM_021058	B2R4J4|O60816	Frame_Shift_Del	DEL	ENST00000607124.1	37	CCDS4618.1																																																																																			.	.	none		0.584	HIST1H2BJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040138.2	NM_021058		-	27100219	TCGGACACGGCGTGCTTGGCCAACTCCCCAG	-	27100189	7	5	41	1	0	1	0	1	0	0	0	0	7158	1551	54	0	43	0	HIST1H2BJ	6	27100189	Frame_Shift_Del	DEL	TCGGACACGGCGTGCTTGGCCAACTCCCCAG	TCGA-GS-A9TY-01A-11D-A38X-10	2577193	27100189	144014878	42	14858											
PIM1	5292	hgsc.bcm.edu	37	chr6	37138571	37138571	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggagaaggagcccctggaGtcgcagtaccaggtgggccc	10	4	16	11	1	0	1	0	0	0	1	1	4	0	3	4	5	2	2	4	5	3	1			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr6:37138571G>A	ENST00000373509.5	+	2	478	c.105G>A	c.(103-105)gaG>gaA	p.E35E		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	126					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)	AGCCCCTGGAGTCGCAGTACC	0.711			T	BCL6	NHL																																p.E126E		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.G378A						PASS	.						21	31	28					6																	37138571		2163	4266	6429	SO:0001819	synonymous_variant	5292	exon2			CCTGGAGTCGCAG		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.105G>A	6.37:g.37138571G>A		51	0	0		75	19	0.253333	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.711	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			A	37138571	G	A	37138571	2	1	41	1	0	0	0	0	0	0	0	1	11936	1020	36	2		2	PIM1	6	37138571	Silent	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	10038382	37138571	133976496	43	14859											
PIM1	5292	hgsc.bcm.edu	37	chr6	37139092	37139092	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gccctgcaagaggagctggcCcgcagcttcttctggcaggt	6	8	14	13	1	2	1	0	0	2	1	2	2	2	2	2	4	3	5	2	4	1	2			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr6:37139092C>T	ENST00000373509.5	+	4	805	c.432C>T	c.(430-432)gcC>gcT	p.A144A		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	235	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		Y -> H (in a colorectal adenocarcinoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		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)	AGGAGCTGGCCCGCAGCTTCT	0.612			T	BCL6	NHL																																p.A235A		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C705T						PASS	.						54	65	61					6																	37139092		2203	4300	6503	SO:0001819	synonymous_variant	5292	exon4			GCTGGCCCGCAGC		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.432C>T	6.37:g.37139092C>T		93	0	0		129	27	0.209302	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.612	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37139092	C	T	37139092	2	4	41	1	0	0	0	0	0	0	0	1	11936	610	22	2		2	PIM1	6	37139092	Silent	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	521	37139092	133975975	44	14860											
COL21A1	81578	hgsc.bcm.edu	37	chr6	55939040	55939040	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcatatttaccttagatcccGgtgttccaggctggcctggt	6	14	10	11	1	1	1	1	0	0	1	3	1	3	1	4	4	1	2	4	4	3	5	rs368711091	byFrequency	TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr6:55939040G>T	ENST00000244728.5	-	20	2352	c.1955C>A	c.(1954-1956)cCg>cAg	p.P652Q	COL21A1_ENST00000535941.1_Missense_Mutation_p.P652Q|COL21A1_ENST00000370819.1_Missense_Mutation_p.P649Q|COL21A1_ENST00000370808.2_Missense_Mutation_p.P52Q|COL21A1_ENST00000467045.1_5'UTR	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	652					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)			CTTAGATCCCGGTGTTCCAGG	0.328																																					p.P652Q		Atlas-SNP	.											.	COL21A1	201	.	0			c.C1955A						PASS	.						87	86	86					6																	55939040		1810	4063	5873	SO:0001583	missense	81578	exon20			GATCCCGGTGTTC	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.1955C>A	6.37:g.55939040G>T	ENSP00000244728:p.Pro652Gln	123	0	0		204	69	0.338235	NM_030820	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Missense_Mutation	SNP	ENST00000244728.5	37	CCDS55025.1	.	.	.	.	.	.	.	.	.	.	G	11.26	1.585584	0.28268	.	.	ENSG00000124749	ENST00000244728;ENST00000370819;ENST00000535941;ENST00000370811;ENST00000370808	D;D;D;D	0.98684	-5.07;-4.1;-5.07;-5.07	4.56	3.66	0.41972	.	0.246146	0.28161	N	0.016380	D	0.97673	0.9237	M	0.66506	2.035	0.26532	N	0.974238	B;B;D	0.69078	0.102;0.062;0.997	B;B;P	0.59703	0.031;0.014;0.862	D	0.94533	0.7738	10	0.42905	T	0.14	.	9.9388	0.41567	0.0:0.0:0.7963:0.2037	.	52;652;652	Q96P44-2;B7ZLK3;Q96P44	.;.;COLA1_HUMAN	Q	652;649;652;649;52	ENSP00000244728:P652Q;ENSP00000359855:P649Q;ENSP00000444384:P652Q;ENSP00000359844:P52Q	ENSP00000244728:P652Q	P	-	2	0	COL21A1	56046999	0.999000	0.42202	0.516000	0.27786	0.808000	0.45660	2.261000	0.43276	0.962000	0.38057	0.655000	0.94253	CCG	.	.	alt		0.328	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2			T	55939040	G	T	55939040	3	4	41	1	0	0	0	0	1	0	0	0	3682	1116	39	4	962	4	COL21A1	6	55939040	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	18799948	55939040	115176027	45	14861											
DST	667	hgsc.bcm.edu	37	chr6	56505292	56505292	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctgagtttaaactttgagtGattcctgatatcatgagctt	10	16	8	7	0	1	5	1	5	0	0	2	5	2	5	2	0	2	2	2	0	3	6			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr6:56505292G>A	ENST00000361203.3	-	14	1513	c.1506C>T	c.(1504-1506)atC>atT	p.I502I	DST_ENST00000370754.5_Silent_p.I680I|DST_ENST00000370765.6_Silent_p.I176I|DST_ENST00000312431.6_Silent_p.I502I|DST_ENST00000370788.2_Silent_p.I502I|DST_ENST00000518935.1_Silent_p.I176I|DST_ENST00000244364.6_Silent_p.I176I|DST_ENST00000446842.2_Silent_p.I176I|DST_ENST00000421834.2_Silent_p.I502I|DST_ENST00000370769.4_Silent_p.I502I			Q03001	DYST_HUMAN	dystonin	502					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)			AACTTTGAGTGATTCCTGATA	0.438																																					p.I176I		Atlas-SNP	.											DST_ENST00000370769,NS,carcinoma,0,5	DST	1427	5	0			c.C528T						scavenged	.						122	122	122					6																	56505292		2203	4300	6503	SO:0001819	synonymous_variant	667	exon4			TTGAGTGATTCCT	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.1506C>T	6.37:g.56505292G>A		331	1	0.00302115		527	145	0.275142	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	37																																																																																				.	.	none		0.438	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		A	56505292	G	A	56505292	2	1	41	1	0	0	0	0	0	0	0	1	4785	1280	45	2		2	DST	6	56505292	Silent	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	566252	56505292	114609775	46	14862											
SMPD2	6610	hgsc.bcm.edu	37	chr6	109764547	109764547	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctcacaggggcacccccctCtctgatcatgaagccctgat	8	8	8	17	0	3	3	2	3	1	0	4	3	3	3	5	2	1	1	5	2	1	0			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr6:109764547C>T	ENST00000258052.3	+	9	1166	c.807C>T	c.(805-807)ctC>ctT	p.L269L	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)	269					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)		GCACCCCCCTCTCTGATCATG	0.542																																					p.L269L		Atlas-SNP	.											.	SMPD2	25	.	0			c.C807T						PASS	.						77	81	80					6																	109764547		2203	4300	6503	SO:0001819	synonymous_variant	6610	exon9			CCCCCTCTCTGAT	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.807C>T	6.37:g.109764547C>T		154	0	0		94	69	0.734043	NM_003080	Q5TED1|Q9BWR3	Silent	SNP	ENST00000258052.3	37	CCDS5075.1	.	.	.	.	.	.	.	.	.	.	C	3.719	-0.057929	0.07317	.	.	ENSG00000135587	ENST00000458487	.	.	.	5.95	0.892	0.19230	.	.	.	.	.	T	0.25568	0.0622	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.17440	-1.0369	4	.	.	.	-6.5899	1.8071	0.03083	0.1417:0.4848:0.1377:0.2358	.	.	.	.	F	166	.	.	S	+	2	0	SMPD2	109871240	0.987000	0.35691	0.922000	0.36590	0.668000	0.39293	0.475000	0.22164	0.089000	0.17243	-0.136000	0.14681	TCT	.	.	none		0.542	SMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041755.1			T	109764547	C	T	109764547	2	4	41	1	0	0	0	0	0	0	0	1	14820	900	32	2		2	SMPD2	6	109764547	Silent	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	53259255	109764547	61350520	47	14863											
SLC16A10	117247	hgsc.bcm.edu	37	chr6	111543327	111543327	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	catagtaagaagcaaagagaGatcagtaaaaccactggaaa	21	5	9	6	0	1	3	1	0	0	3	1	5	1	4	1	1	2	3	1	1	7	3			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr6:111543327G>A	ENST00000368851.5	+	6	1612	c.1437G>A	c.(1435-1437)gaG>gaA	p.E479E	SLC16A10_ENST00000368850.3_Silent_p.E165E	NM_018593.4	NP_061063.2	Q8TF71	MOT10_HUMAN	solute carrier family 16 (aromatic amino acid transporter), member 10	479					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)	AGCAAAGAGAGATCAGTAAAA	0.433																																					p.E479E		Atlas-SNP	.											SLC16A10,NS,carcinoma,+2,1	SLC16A10	33	1	0			c.G1437A						PASS	.						127	127	127					6																	111543327		2203	4300	6503	SO:0001819	synonymous_variant	117247	exon6			AAGAGAGATCAGT	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.1437G>A	6.37:g.111543327G>A		196	1	0.00510204		152	118	0.776316	NM_018593	B3KWY0|Q6ZMG0|Q8WVI5	Silent	SNP	ENST00000368851.5	37	CCDS5089.1																																																																																			.	.	none		0.433	SLC16A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041822.2			A	111543327	G	A	111543327	2	1	41	1	0	0	0	0	0	0	0	1	14418	933	33	2		2	SLC16A10	6	111543327	Silent	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	1778780	111543327	59571740	48	14864											
RNF217	154214	hgsc.bcm.edu	37	chr6	125397811	125397811	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ttgctgatacagatccacatCcagcgaactgaaggatgtga	13	9	10	9	1	0	4	0	3	0	1	2	6	2	5	2	1	4	1	2	1	3	2			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr6:125397811C>T	ENST00000521654.2	+	4	1290	c.1290C>T	c.(1288-1290)atC>atT	p.I430I	RNF217_ENST00000368414.2_5'UTR|RNF217_ENST00000359704.2_Silent_p.I138I|RNF217_ENST00000275184.6_Silent_p.I74I|RNF217_ENST00000560949.1_Silent_p.I195I			Q8TC41	RN217_HUMAN	ring finger protein 217	430					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)		AGATCCACATCCAGCGAACTG	0.408																																					p.I138I		Atlas-SNP	.											.	RNF217	64	.	0			c.C414T						PASS	.						115	100	105					6																	125397811		2203	4300	6503	SO:0001819	synonymous_variant	154214	exon6			CCACATCCAGCGA	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.1290C>T	6.37:g.125397811C>T		136	0	0		69	21	0.304348	NM_152553	H7C5V4|Q5TCA4|Q9BX48	Silent	SNP	ENST00000521654.2	37																																																																																				.	.	none		0.408	RNF217-002	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000042063.3	NM_152553		T	125397811	C	T	125397811	2	4	41	1	0	0	0	0	0	0	0	1	13496	845	30	2		2	RNF217	6	125397811	Silent	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	13854484	125397811	45717256	49	14865											
SASH1	23328	hgsc.bcm.edu	37	chr6	148865065	148865065	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cctcccagtttccatctgccGgagctgtgagaccctggagg	6	9	12	14	1	1	1	0	1	1	1	3	4	3	3	5	3	2	2	5	3	0	1	rs144633784	byFrequency	TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr6:148865065G>A	ENST00000367467.3	+	18	2934	c.2459G>A	c.(2458-2460)cGg>cAg	p.R820Q		NM_015278.3	NP_056093.3	O94885	SASH1_HUMAN	SAM and SH3 domain containing 1	820					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)		TCCATCTGCCGGAGCTGTGAG	0.592													G|||	11	0.00219649	0.0	0.0	5008	,	,		8739	0.0		0.004	False		,,,				2504	0.0072				p.R820Q		Atlas-SNP	.											SASH1,mouth,carcinoma,+1,1	SASH1	123	1	0			c.G2459A						PASS	.	G	GLN/ARG	0,4406		0,0,2203	106	120	116		2459	5.3	1	6	dbSNP_134	116	17,8583	11.9+/-42.8	0,17,4283	yes	missense	SASH1	NM_015278.3	43	0,17,6486	AA,AG,GG		0.1977,0.0,0.1307	probably-damaging	820/1248	148865065	17,12989	2203	4300	6503	SO:0001583	missense	23328	exon18			TCTGCCGGAGCTG	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.2459G>A	6.37:g.148865065G>A	ENSP00000356437:p.Arg820Gln	89	0	0		60	43	0.716667	NM_015278	Q5TGN5|Q8TAI0|Q9H7R7	Missense_Mutation	SNP	ENST00000367467.3	37	CCDS5212.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	34	5.322345	0.95708	0.0	0.001977	ENSG00000111961	ENST00000367467;ENST00000535767;ENST00000537769	T	0.42900	0.96	5.26	5.26	0.73747	.	0.053272	0.85682	D	0.000000	T	0.55784	0.1942	M	0.62723	1.935	0.49299	D	0.999772	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.994	T	0.59484	-0.7446	10	0.72032	D	0.01	-20.5504	17.0537	0.86527	0.0:0.0:1.0:0.0	.	801;820	Q6P4R9;O94885	.;SASH1_HUMAN	Q	820;581;230	ENSP00000356437:R820Q	ENSP00000356437:R820Q	R	+	2	0	SASH1	148906758	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.494000	0.66905	2.454000	0.82982	0.650000	0.86243	CGG	G|0.998;A|0.002	0.002	strong		0.592	SASH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042619.1	NM_015278		A	148865065	G	A	148865065	3	1	41	1	0	0	0	0	1	0	0	0	13863	1116	39	1	2529	1	SASH1	6	148865065	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	23467254	148865065	22250002	50	14866											
C6orf211	79624	hgsc.bcm.edu	37	chr6	151789707	151789707	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atttgagcttgttacagattTaatattagccgacttcttgt	10	18	7	6	1	1	2	0	1	1	1	1	3	1	2	1	0	3	2	1	0	4	9			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr6:151789707T>A	ENST00000367294.3	+	5	1047	c.788T>A	c.(787-789)tTa>tAa	p.L263*	C6orf211_ENST00000545879.1_Nonsense_Mutation_p.L144*	NM_024573.1	NP_078849.1	Q9H993	CF211_HUMAN	chromosome 6 open reading frame 211	263										breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(7)	15			BRCA - Breast invasive adenocarcinoma(37;0.183)	OV - Ovarian serous cystadenocarcinoma(155;5.27e-11)		GTTACAGATTTAATATTAGCC	0.348																																					p.L263X		Atlas-SNP	.											.	C6orf211	30	.	0			c.T788A						PASS	.						134	139	137					6																	151789707		2203	4300	6503	SO:0001587	stop_gained	79624	exon5			CAGATTTAATATT	AJ420548	CCDS5233.1, CCDS69224.1	6q25.1	2013-01-07			ENSG00000146476	ENSG00000146476			17872	protein-coding gene	gene with protein product							Standard	NM_001286562		Approved	FLJ12910	uc003qok.1	Q9H993	OTTHUMG00000015838	ENST00000367294.3:c.788T>A	6.37:g.151789707T>A	ENSP00000356263:p.Leu263*	353	0	0		194	154	0.793814	NM_024573	Q96FC6|Q9UFY5	Nonsense_Mutation	SNP	ENST00000367294.3	37	CCDS5233.1	.	.	.	.	.	.	.	.	.	.	T	37	6.256437	0.97417	.	.	ENSG00000146476	ENST00000367294;ENST00000545879	.	.	.	6.02	6.02	0.97574	.	0.264665	0.33075	N	0.005317	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.5494	0.84464	0.0:0.0:0.0:1.0	.	.	.	.	X	263;144	.	ENSP00000356263:L263X	L	+	2	0	C6orf211	151831400	1.000000	0.71417	0.593000	0.28771	0.819000	0.46315	7.963000	0.87922	2.299000	0.77371	0.528000	0.53228	TTA	.	.	none		0.348	C6orf211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042724.1	NM_024573		A	151789707	T	A	151789707	4	1	41	1	0	0	0	0	0	1	0	0	2356	1764	61	5	806	5	C6orf211	6	151789707	Nonsense_Mutation	SNP	T	TCGA-GS-A9TY-01A-11D-A38X-10	2924642	151789707	19325360	51	14867			1	68		2	2	22	T		9.225362e-05
C6orf211	79624	hgsc.bcm.edu	37	chr6	151789728	151789728	+	Nonsense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatattagccgacttcttgtTgtcctctgaactggctactg	8	15	8	10	1	2	1	0	1	2	0	3	2	3	1	2	1	3	2	2	1	5	6			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr6:151789728T>A	ENST00000367294.3	+	5	1068	c.809T>A	c.(808-810)tTg>tAg	p.L270*	C6orf211_ENST00000545879.1_Nonsense_Mutation_p.L151*	NM_024573.1	NP_078849.1	Q9H993	CF211_HUMAN	chromosome 6 open reading frame 211	270										breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(7)	15			BRCA - Breast invasive adenocarcinoma(37;0.183)	OV - Ovarian serous cystadenocarcinoma(155;5.27e-11)		GACTTCTTGTTGTCCTCTGAA	0.328																																					p.L270X		Atlas-SNP	.											.	C6orf211	30	.	0			c.T809A						PASS	.						131	137	135					6																	151789728		2203	4300	6503	SO:0001587	stop_gained	79624	exon5			TCTTGTTGTCCTC	AJ420548	CCDS5233.1, CCDS69224.1	6q25.1	2013-01-07			ENSG00000146476	ENSG00000146476			17872	protein-coding gene	gene with protein product							Standard	NM_001286562		Approved	FLJ12910	uc003qok.1	Q9H993	OTTHUMG00000015838	ENST00000367294.3:c.809T>A	6.37:g.151789728T>A	ENSP00000356263:p.Leu270*	335	0	0		179	136	0.759777	NM_024573	Q96FC6|Q9UFY5	Nonsense_Mutation	SNP	ENST00000367294.3	37	CCDS5233.1	.	.	.	.	.	.	.	.	.	.	T	38	6.806416	0.97853	.	.	ENSG00000146476	ENST00000367294;ENST00000545879	.	.	.	6.02	6.02	0.97574	.	0.324258	0.29791	N	0.011196	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.5494	0.84464	0.0:0.0:0.0:1.0	.	.	.	.	X	270;151	.	ENSP00000356263:L270X	L	+	2	0	C6orf211	151831421	1.000000	0.71417	0.774000	0.31636	0.994000	0.84299	6.221000	0.72243	2.299000	0.77371	0.528000	0.53228	TTG	.	.	none		0.328	C6orf211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042724.1	NM_024573		A	151789728	T	A	151789728	4	1	41	1	0	0	0	0	0	1	0	0	2356	1821	63	5	827	5	C6orf211	6	151789728	Nonsense_Mutation	SNP	T	TCGA-GS-A9TY-01A-11D-A38X-10	21	151789728	19325339	52	14868			1	68		2	2	22	T		9.225362e-05
EZR	7430	hgsc.bcm.edu	37	chr6	159188112	159188113	+	Splice_Site	DEL	TG	TG	-																															acagctcgctgctcagcgtcTgtaacattaagcagcattgg																										TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr6:159188112_159188113delTG	ENST00000367075.3	-	14	1765		c.e14-2		EZR_ENST00000392177.4_Splice_Site|MIR3918_ENST00000581555.1_RNA|EZR_ENST00000337147.7_Splice_Site	NM_001111077.1	NP_001104547.1	P15311	EZRI_HUMAN	ezrin						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)		GCTCAGCGTCTGTAACATTAAG	0.579			T	ROS1	NSCLC																																.		Pindel,Atlas-Indel	.		Dom	yes		6	6q25.3	7430	ezrin		E	.	EZR	44	.	0			.						PASS	.																																			SO:0001630	splice_region_variant	7430	.			.	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.1597-2CA>-	6.37:g.159188112_159188113delTG		191	0	.		111	52	0.468	.	E1P5A8|P23714|Q4VX75|Q96CU8|Q9NSJ4	Splice_Site	DEL	ENST00000367075.3	37	CCDS5258.1																																																																																			.	.	none		0.579	EZR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042878.1	NM_003379	Intron	-	159188113	TG	-	159188112	8	5	41	1	0	1	0	1	0	0	1	0	5337	1594	55	0	169	0	EZR	6	159188112	Splice_Site	DEL	TG	TCGA-GS-A9TY-01A-11D-A38X-10	7398384	159188112	11926955	53	14869											
CARD11	84433	hgsc.bcm.edu	37	chr7	2983971	2983971	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcgtcattgtagctgtcccGctcttccttcatcttgtagt	4	17	7	13	2	4	0	2	0	2	0	7	0	6	0	2	0	1	4	2	0	2	6			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr7:2983971G>A	ENST00000396946.4	-	5	962	c.559C>T	c.(559-561)Cgg>Tgg	p.R187W	AC004906.3_ENST00000423194.1_RNA	NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	187					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)		TAGCTGTCCCGCTCTTCCTTC	0.557			Mis		DLBCL																																p.R187W		Atlas-SNP	.		Dom	yes		7	7p22	84433	"caspase recruitment domain family, member 11"		L	CARD11,NS,carcinoma,0,1	CARD11	339	1	0			c.C559T						scavenged	.						248	154	186					7																	2983971		2203	4300	6503	SO:0001583	missense	84433	exon5			TGTCCCGCTCTTC	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.559C>T	7.37:g.2983971G>A	ENSP00000380150:p.Arg187Trp	190	1	0.00526316		260	106	0.407692	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	G	15.02	2.710363	0.48517	.	.	ENSG00000198286	ENST00000396946	T	0.36157	1.27	4.46	2.25	0.28309	.	0.000000	0.85682	D	0.000000	T	0.19765	0.0475	N	0.20881	0.62	0.52099	D	0.999945	B	0.27971	0.196	B	0.17722	0.019	T	0.05632	-1.0873	10	0.37606	T	0.19	-27.5118	7.2254	0.26012	0.0992:0.0:0.6097:0.2911	.	187	Q9BXL7	CAR11_HUMAN	W	187	ENSP00000380150:R187W	ENSP00000380150:R187W	R	-	1	2	CARD11	2950497	1.000000	0.71417	0.994000	0.49952	0.976000	0.68499	2.135000	0.42112	1.000000	0.39049	0.561000	0.74099	CGG	.	.	none		0.557	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415		A	2983971	G	A	2983971	3	1	41	1	0	0	0	0	1	0	0	0	2647	1086	38	1	2989	1	CARD11	7	2983971	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10		2983971	156154692	54	14870											
ABCB5	340273	hgsc.bcm.edu	37	chr7	20768004	20768004	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agccatgcctttatatatttTgcctatgcggcagggtttcg	7	15	10	9	2	0	0	0	0	0	0	1	0	0	0	3	2	4	2	3	2	4	8			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr7:20768004T>A	ENST00000404938.2	+	23	3445	c.2793T>A	c.(2791-2793)ttT>ttA	p.F931L	ABCB5_ENST00000258738.6_Missense_Mutation_p.F486L	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	931	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						TTATATATTTTGCCTATGCGG	0.418																																					p.F931L		Atlas-SNP	.											.	ABCB5	357	.	0			c.T2793A						PASS	.						131	134	133					7																	20768004		2203	4300	6503	SO:0001583	missense	340273	exon23			ATATTTTGCCTAT	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.2793T>A	7.37:g.20768004T>A	ENSP00000384881:p.Phe931Leu	175	0	0		181	67	0.370166	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	37	CCDS55090.1	.	.	.	.	.	.	.	.	.	.	T	19.42	3.824361	0.71143	.	.	ENSG00000004846	ENST00000404938;ENST00000258738	D;D	0.88664	-2.41;-2.41	3.91	-1.39	0.08997	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.102767	0.39544	N	0.001337	D	0.89153	0.6634	L	0.54965	1.715	0.41601	D	0.988854	B;D;P	0.65815	0.303;0.995;0.871	B;D;P	0.69654	0.282;0.965;0.714	D	0.84074	0.0381	10	0.39692	T	0.17	.	4.9214	0.13871	0.0:0.3962:0.176:0.4278	.	931;109;486	A7BKA4;A0ASV4;Q2M3G0	.;.;ABCB5_HUMAN	L	931;486	ENSP00000384881:F931L;ENSP00000258738:F486L	ENSP00000258738:F486L	F	+	3	2	ABCB5	20734529	0.992000	0.36948	0.995000	0.50966	0.967000	0.64934	0.073000	0.14640	-0.238000	0.09724	0.533000	0.62120	TTT	.	.	none		0.418	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559		A	20768004	T	A	20768004	3	1	41	1	0	0	0	0	1	0	0	0	44	1809	63	5	2920	5	ABCB5	7	20768004	Missense_Mutation	SNP	T	TCGA-GS-A9TY-01A-11D-A38X-10	17784033	20768004	138370659	55	14871											
IL6	3569	hgsc.bcm.edu	37	chr7	22767218	22767218	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaattgacaaacaaattcggTacatcctcgacggcatctca	14	9	7	11	3	1	1	1	1	1	0	5	3	2	1	1	2	2	2	1	2	4	3	rs201822486		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr7:22767218T>C	ENST00000404625.1	+	3	634	c.175T>C	c.(175-177)Tac>Cac	p.Y59H	AC073072.5_ENST00000325042.2_RNA|IL6_ENST00000407492.1_Intron|IL6_ENST00000420258.2_Missense_Mutation_p.Y113H|IL6_ENST00000406575.1_Missense_Mutation_p.Y59H|IL6_ENST00000258743.5_Missense_Mutation_p.Y59H|IL6_ENST00000401630.3_Missense_Mutation_p.Y36H|IL6_ENST00000401651.1_Intron			P05231	IL6_HUMAN	interleukin 6	59					acute-phase response (GO:0006953)|aging (GO:0007568)|bone remodeling (GO:0046849)|branching involved in salivary gland morphogenesis (GO:0060445)|cell growth (GO:0016049)|cell redox homeostasis (GO:0045454)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endocrine pancreas development (GO:0031018)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|glucagon secretion (GO:0070091)|hepatic immune response (GO:0002384)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|interleukin-6-mediated signaling pathway (GO:0070102)|monocyte chemotaxis (GO:0002548)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of hormone secretion (GO:0046888)|negative regulation of lipid storage (GO:0010888)|negative regulation of muscle organ development (GO:0048635)|negative regulation of neuron death (GO:1901215)|negative regulation of protein kinase activity (GO:0006469)|neuron projection development (GO:0031175)|neutrophil apoptotic process (GO:0001781)|neutrophil mediated immunity (GO:0002446)|platelet activation (GO:0030168)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell activation (GO:0050871)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine production (GO:0032722)|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 immunoglobulin secretion (GO:0051024)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of T cell proliferation (GO:0042102)|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)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of angiogenesis (GO:0045765)|regulation of cell shape (GO:0008360)|regulation of circadian sleep/wake cycle, non-REM sleep (GO:0045188)|regulation of vascular endothelial growth factor production (GO:0010574)|response to amino acid (GO:0043200)|response to antibiotic (GO:0046677)|response to caffeine (GO:0031000)|response to calcium ion (GO:0051592)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to glucocorticoid (GO:0051384)|response to heat (GO:0009408)|response to insulin (GO:0032868)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to peptidoglycan (GO:0032494)|T-helper 17 cell lineage commitment (GO:0072540)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-6 receptor complex (GO:0005896)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|interleukin-6 receptor binding (GO:0005138)			breast(1)|endometrium(2)|large_intestine(4)|lung(1)	8					Ginseng(DB01404)	ACAAATTCGGTACATCCTCGA	0.582																																					p.Y59H	Esophageal Squamous(47;342 1214 13936 33513)	Atlas-SNP	.											.	IL6	30	.	0			c.T175C						PASS	.						105	100	102					7																	22767218		2203	4300	6503	SO:0001583	missense	3569	exon2			ATTCGGTACATCC	M18403	CCDS5375.1	7p21-p15	2014-04-04	2014-04-04		ENSG00000136244	ENSG00000136244		"Interleukins and interleukin receptors", "Interferons"	6018	protein-coding gene	gene with protein product	"interferon, beta 2"	147620	"interleukin 6 (interferon, beta 2)"	IFNB2		3294161	Standard	NM_000600		Approved	IL-6, BSF2, HGF, HSF	uc003svj.4	P05231	OTTHUMG00000023178	ENST00000404625.1:c.175T>C	7.37:g.22767218T>C	ENSP00000385675:p.Tyr59His	53	0	0		132	80	0.606061	NM_000600	Q9UCU2|Q9UCU3|Q9UCU4	Missense_Mutation	SNP	ENST00000404625.1	37	CCDS5375.1	.	.	.	.	.	.	.	.	.	.	T	13.42	2.232174	0.39498	.	.	ENSG00000136244	ENST00000404625;ENST00000426291;ENST00000258743;ENST00000420258;ENST00000401630;ENST00000406575	T;T;T;T;T;T	0.17691	2.26;2.26;2.26;2.26;2.26;2.26	5.73	-5.7	0.02421	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	1.669760	0.02407	N	0.081299	T	0.11110	0.0271	N	0.16903	0.455	0.09310	N	1	B;B;B	0.27882	0.192;0.152;0.039	B;B;B	0.36719	0.231;0.133;0.037	T	0.28235	-1.0050	10	0.25751	T	0.34	-1.1849	5.1132	0.14821	0.2499:0.4044:0.0:0.3457	.	113;59;59	B4DNQ5;B5MC14;P05231	.;.;IL6_HUMAN	H	59;59;59;113;36;59	ENSP00000385675:Y59H;ENSP00000405150:Y59H;ENSP00000258743:Y59H;ENSP00000405994:Y113H;ENSP00000384928:Y36H;ENSP00000385227:Y59H	ENSP00000258743:Y59H	Y	+	1	0	IL6	22733743	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.787000	0.04618	-0.714000	0.04975	-0.375000	0.07067	TAC	.	.	weak		0.582	IL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250225.2	NM_000600		C	22767218	T	C	22767218	3	2	41	1	0	0	0	0	1	0	0	0	7710	1638	57	3	181	3	IL6	7	22767218	Missense_Mutation	SNP	T	TCGA-GS-A9TY-01A-11D-A38X-10	1999214	22767218	136371445	56	14872			2	69		2	2	13	N	T_G	5.27174e-05
IL6	3569	hgsc.bcm.edu	37	chr7	22767230	22767230	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaattcggtacatcctcgacGgcatctcagccctgagaaag	12	8	9	12	3	1	1	1	1	1	1	5	3	2	1	2	2	2	2	2	2	3	2			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr7:22767230G>A	ENST00000404625.1	+	3	646	c.187G>A	c.(187-189)Ggc>Agc	p.G63S	AC073072.5_ENST00000325042.2_RNA|IL6_ENST00000407492.1_Intron|IL6_ENST00000420258.2_Missense_Mutation_p.G117S|IL6_ENST00000406575.1_Missense_Mutation_p.G63S|IL6_ENST00000258743.5_Missense_Mutation_p.G63S|IL6_ENST00000401630.3_Missense_Mutation_p.G40S|IL6_ENST00000401651.1_Intron			P05231	IL6_HUMAN	interleukin 6	63					acute-phase response (GO:0006953)|aging (GO:0007568)|bone remodeling (GO:0046849)|branching involved in salivary gland morphogenesis (GO:0060445)|cell growth (GO:0016049)|cell redox homeostasis (GO:0045454)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endocrine pancreas development (GO:0031018)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|glucagon secretion (GO:0070091)|hepatic immune response (GO:0002384)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|interleukin-6-mediated signaling pathway (GO:0070102)|monocyte chemotaxis (GO:0002548)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine biosynthetic process (GO:0045079)|negative regulation of collagen biosynthetic process (GO:0032966)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of cytokine secretion (GO:0050710)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of hormone secretion (GO:0046888)|negative regulation of lipid storage (GO:0010888)|negative regulation of muscle organ development (GO:0048635)|negative regulation of neuron death (GO:1901215)|negative regulation of protein kinase activity (GO:0006469)|neuron projection development (GO:0031175)|neutrophil apoptotic process (GO:0001781)|neutrophil mediated immunity (GO:0002446)|platelet activation (GO:0030168)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell activation (GO:0050871)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine production (GO:0032722)|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 immunoglobulin secretion (GO:0051024)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of T cell proliferation (GO:0042102)|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)|positive regulation of translation (GO:0045727)|positive regulation of transmission of nerve impulse (GO:0051971)|positive regulation of type B pancreatic cell apoptotic process (GO:2000676)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of angiogenesis (GO:0045765)|regulation of cell shape (GO:0008360)|regulation of circadian sleep/wake cycle, non-REM sleep (GO:0045188)|regulation of vascular endothelial growth factor production (GO:0010574)|response to amino acid (GO:0043200)|response to antibiotic (GO:0046677)|response to caffeine (GO:0031000)|response to calcium ion (GO:0051592)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to glucocorticoid (GO:0051384)|response to heat (GO:0009408)|response to insulin (GO:0032868)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to peptidoglycan (GO:0032494)|T-helper 17 cell lineage commitment (GO:0072540)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|interleukin-6 receptor complex (GO:0005896)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|interleukin-6 receptor binding (GO:0005138)	p.G63S(1)		breast(1)|endometrium(2)|large_intestine(4)|lung(1)	8					Ginseng(DB01404)	CATCCTCGACGGCATCTCAGC	0.592																																					p.G63S	Esophageal Squamous(47;342 1214 13936 33513)	Atlas-SNP	.											IL6,colon,carcinoma,0,1	IL6	30	1	1	Substitution - Missense(1)	large_intestine(1)	c.G187A						PASS	.						93	88	90					7																	22767230		2203	4300	6503	SO:0001583	missense	3569	exon2			CTCGACGGCATCT	M18403	CCDS5375.1	7p21-p15	2014-04-04	2014-04-04		ENSG00000136244	ENSG00000136244		"Interleukins and interleukin receptors", "Interferons"	6018	protein-coding gene	gene with protein product	"interferon, beta 2"	147620	"interleukin 6 (interferon, beta 2)"	IFNB2		3294161	Standard	NM_000600		Approved	IL-6, BSF2, HGF, HSF	uc003svj.4	P05231	OTTHUMG00000023178	ENST00000404625.1:c.187G>A	7.37:g.22767230G>A	ENSP00000385675:p.Gly63Ser	52	0	0		125	35	0.28	NM_000600	Q9UCU2|Q9UCU3|Q9UCU4	Missense_Mutation	SNP	ENST00000404625.1	37	CCDS5375.1	.	.	.	.	.	.	.	.	.	.	G	18.44	3.624986	0.66901	.	.	ENSG00000136244	ENST00000404625;ENST00000426291;ENST00000258743;ENST00000420258;ENST00000401630;ENST00000406575	T;T;T;T;T;T	0.16073	2.37;2.37;2.37;2.37;2.37;2.37	5.73	-7.63	0.01290	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	1.051350	0.07276	N	0.869904	T	0.11623	0.0283	N	0.14661	0.345	0.09310	N	1	D;D;P	0.58970	0.983;0.984;0.933	P;P;B	0.52758	0.708;0.645;0.43	T	0.16689	-1.0394	10	0.22706	T	0.39	-0.2201	7.1005	0.25333	0.4851:0.2042:0.3107:0.0	.	117;63;63	B4DNQ5;B5MC14;P05231	.;.;IL6_HUMAN	S	63;63;63;117;40;63	ENSP00000385675:G63S;ENSP00000405150:G63S;ENSP00000258743:G63S;ENSP00000405994:G117S;ENSP00000384928:G40S;ENSP00000385227:G63S	ENSP00000258743:G63S	G	+	1	0	IL6	22733755	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.387000	0.07361	-1.013000	0.03383	-0.300000	0.09419	GGC	.	.	none		0.592	IL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250225.2	NM_000600		A	22767230	G	A	22767230	3	1	41	1	0	0	0	0	1	0	0	0	7710	1116	39	1	193	1	IL6	7	22767230	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	12	22767230	136371433	57	14873			2	69		2	2	13	N	T_G	5.27174e-05
SEMA3C	10512	hgsc.bcm.edu	37	chr7	80374533	80374533	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttgaaactattttctgtagCaatgcagtgataaagtcctt	12	15	7	7	0	1	2	0	2	1	0	2	2	2	2	1	0	3	3	1	0	6	7			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr7:80374533C>A	ENST00000265361.3	-	18	2494	c.1933G>T	c.(1933-1935)Gct>Tct	p.A645S	SEMA3C_ENST00000544525.1_Missense_Mutation_p.A663S|SEMA3C_ENST00000419255.2_Missense_Mutation_p.A645S	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	645	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						TTTTCTGTAGCAATGCAGTGA	0.433																																					p.A645S		Atlas-SNP	.											.	SEMA3C	106	.	0			c.G1933T						PASS	.						78	75	76					7																	80374533		2203	4300	6503	SO:0001583	missense	10512	exon18			CTGTAGCAATGCA	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.1933G>T	7.37:g.80374533C>A	ENSP00000265361:p.Ala645Ser	145	0	0		140	60	0.428571	NM_006379	B4DRL8	Missense_Mutation	SNP	ENST00000265361.3	37	CCDS5596.1	.	.	.	.	.	.	.	.	.	.	C	15.84	2.951421	0.53186	.	.	ENSG00000075223	ENST00000265361;ENST00000419255;ENST00000544525	T;T;T	0.76578	-1.03;-1.03;-1.03	5.56	5.56	0.83823	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.096714	0.64402	D	0.000001	T	0.74412	0.3713	L	0.39692	1.235	0.80722	D	1	B;P	0.39782	0.3;0.688	B;B	0.42625	0.106;0.393	T	0.69789	-0.5050	10	0.18710	T	0.47	.	19.5309	0.95228	0.0:1.0:0.0:0.0	.	663;645	F5H1Z7;Q99985	.;SEM3C_HUMAN	S	645;645;663	ENSP00000265361:A645S;ENSP00000411193:A645S;ENSP00000445649:A663S	ENSP00000265361:A645S	A	-	1	0	SEMA3C	80212469	1.000000	0.71417	0.998000	0.56505	0.863000	0.49368	5.641000	0.67881	2.636000	0.89361	0.650000	0.86243	GCT	.	.	none		0.433	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379		A	80374533	C	A	80374533	3	1	41	1	0	0	0	0	1	0	0	0	14041	710	25	4	326	4	SEMA3C	7	80374533	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	57607303	80374533	78764130	58	14874											
MUC17	140453	hgsc.bcm.edu	37	chr7	100695189	100695189	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tgagcctggcttcagtgtctCcaagaactgtaacctcggca	9	10	10	12	1	2	2	1	1	1	1	4	2	2	2	3	2	3	3	3	2	3	2			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr7:100695189C>A	ENST00000306151.4	+	9	13113	c.13049C>A	c.(13048-13050)tCc>tAc	p.S4350Y		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	4350					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)					TTCAGTGTCTCCAAGAACTGT	0.572																																					p.S4350Y		Atlas-SNP	.											.	MUC17	804	.	0			c.C13049A						PASS	.						188	167	174					7																	100695189		2203	4300	6503	SO:0001583	missense	140453	exon9			GTGTCTCCAAGAA	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.13049C>A	7.37:g.100695189C>A	ENSP00000302716:p.Ser4350Tyr	85	0	0		84	35	0.416667	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	5.810	0.333824	0.11013	.	.	ENSG00000169876	ENST00000306151	T	0.52057	0.68	4.26	3.34	0.38264	.	.	.	.	.	T	0.52158	0.1717	L	0.28556	0.865	0.09310	N	1	D	0.63046	0.992	D	0.64506	0.926	T	0.36261	-0.9755	9	0.66056	D	0.02	.	9.2479	0.37539	0.2158:0.7842:0.0:0.0	.	4350	Q685J3	MUC17_HUMAN	Y	4350	ENSP00000302716:S4350Y	ENSP00000302716:S4350Y	S	+	2	0	MUC17	100481909	0.058000	0.20735	0.004000	0.12327	0.003000	0.03518	3.104000	0.50306	1.079000	0.41038	0.561000	0.74099	TCC	.	.	none		0.572	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		A	100695189	C	A	100695189	3	1	41	1	0	0	0	0	1	0	0	0	9983	855	30	4	13083	4	MUC17	7	100695189	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	20320656	100695189	58443474	59	14875											
PIK3CG	5294	hgsc.bcm.edu	37	chr7	106523531	106523531	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgccaaaattcagcaaagcAcagtgggcaacacgggagca	15	5	11	10	1	1	0	1	0	0	0	1	1	1	1	1	2	5	4	1	2	4	2			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr7:106523531A>G	ENST00000359195.3	+	8	2993	c.2683A>G	c.(2683-2685)Aca>Gca	p.T895A	PIK3CG_ENST00000496166.1_Missense_Mutation_p.T895A|PIK3CG_ENST00000440650.2_Missense_Mutation_p.T895A	NM_001282427.1|NM_002649.2	NP_001269356.1|NP_002640.2	P48736	PK3CG_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma	895	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				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						TCAGCAAAGCACAGTGGGCAA	0.463																																					p.T895A		Atlas-SNP	.											.	PIK3CG	279	.	0			c.A2683G						PASS	.						159	155	156					7																	106523531		2203	4300	6503	SO:0001583	missense	5294	exon8			CAAAGCACAGTGG		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.2683A>G	7.37:g.106523531A>G	ENSP00000352121:p.Thr895Ala	80	0	0		70	30	0.428571	NM_002649	A4D0Q6|Q8IV23|Q9BZC8	Missense_Mutation	SNP	ENST00000359195.3	37	CCDS5739.1	.	.	.	.	.	.	.	.	.	.	A	10.43	1.348050	0.24426	.	.	ENSG00000105851	ENST00000440650;ENST00000496166;ENST00000473541;ENST00000359195	T;T;T;T	0.80994	-1.44;-1.44;-1.44;-1.44	5.1	5.1	0.69264	Protein kinase-like domain (1);Phosphatidylinositol 3-/4-kinase, catalytic (4);	0.097763	0.64402	D	0.000001	T	0.68430	0.3000	N	0.25890	0.77	0.54753	D	0.999984	B	0.11235	0.004	B	0.20384	0.029	T	0.62793	-0.6779	10	0.07325	T	0.83	-20.0097	15.0634	0.71973	1.0:0.0:0.0:0.0	.	895	P48736	PK3CG_HUMAN	A	895;895;168;895	ENSP00000392258:T895A;ENSP00000419260:T895A;ENSP00000417623:T168A;ENSP00000352121:T895A	ENSP00000352121:T895A	T	+	1	0	PIK3CG	106310767	1.000000	0.71417	0.995000	0.50966	0.872000	0.50106	6.652000	0.74377	2.131000	0.65755	0.459000	0.35465	ACA	.	.	none		0.463	PIK3CG-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349294.1			G	106523531	A	G	106523531	3	3	41	1	0	0	0	0	1	0	0	0	11925	159	6	3	2709	3	PIK3CG	7	106523531	Missense_Mutation	SNP	A	TCGA-GS-A9TY-01A-11D-A38X-10	5828342	106523531	52615132	60	14876											
AASS	10157	hgsc.bcm.edu	37	chr7	121738881	121738881	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagatccaagaaccaaaacCtttctcctggtgcccattga	12	9	6	14	0	1	3	0	1	1	2	3	3	2	3	6	1	3	0	6	1	4	2	rs549330560		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr7:121738881C>G	ENST00000393376.1	-	13	1541	c.1446G>C	c.(1444-1446)aaG>aaC	p.K482N	AASS_ENST00000473553.1_Intron|AASS_ENST00000417368.2_Missense_Mutation_p.K482N			Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase	482	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						GAACCAAAACCTTTCTCCTGG	0.313																																					p.K482N		Atlas-SNP	.											.	AASS	123	.	0			c.G1446C						PASS	.						62	67	66					7																	121738881		2203	4299	6502	SO:0001583	missense	10157	exon14			CAAAACCTTTCTC	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.1446G>C	7.37:g.121738881C>G	ENSP00000377040:p.Lys482Asn	158	0	0		137	49	0.357664	NM_005763	O95462	Missense_Mutation	SNP	ENST00000393376.1	37	CCDS5783.1	.	.	.	.	.	.	.	.	.	.	C	15.61	2.884697	0.51908	.	.	ENSG00000008311	ENST00000393376;ENST00000417368	.	.	.	5.96	4.9	0.64082	NAD(P)-binding domain (1);	0.189513	0.56097	D	0.000031	T	0.38639	0.1048	N	0.08118	0	0.45477	D	0.998446	B	0.06786	0.001	B	0.12837	0.008	T	0.20174	-1.0283	9	0.41790	T	0.15	-16.3813	14.9791	0.71299	0.0:0.9183:0.0:0.0817	.	482	Q9UDR5	AASS_HUMAN	N	482	.	ENSP00000351834:K482N	K	-	3	2	AASS	121526117	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	0.796000	0.26986	2.823000	0.97156	0.650000	0.86243	AAG	.	.	none		0.313	AASS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347300.1	NM_005763		G	121738881	C	G	121738881	3	3	41	1	0	0	0	0	1	0	0	0	24	680	24	4	1378	4	AASS	7	121738881	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	15215350	121738881	37399782	61	14877											
LUC7L2	100996928	hgsc.bcm.edu	37	chr7	139102385	139102385	+	Frame_Shift_Del	DEL	G	G	-																															ggagaaacgccatcgccacaGgtcccgctccagcagccgta																										TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr7:139102385delG	ENST00000354926.4	+	9	1265	c.911delG	c.(910-912)aggfs	p.R304fs	C7orf55-LUC7L2_ENST00000541170.3_Frame_Shift_Del_p.R301fs|LUC7L2_ENST00000541515.3_Frame_Shift_Del_p.R370fs|C7orf55-LUC7L2_ENST00000482860.1_3'UTR|C7orf55-LUC7L2_ENST00000263545.6_Frame_Shift_Del_p.R303fs	NM_001270643.1|NM_016019.4	NP_001257572.1|NP_057103.2			C7orf55-LUC7L2 readthrough																		CATCGCCACAGGTCCCGCTCC	0.562																																					p.R370fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.1108delA						PASS	.						56	67	63					7																	139102385		2127	4228	6355	SO:0001589	frameshift_variant	100996928	exon10			.		CCDS59084.1	7q34	2013-02-14			ENSG00000146963	ENSG00000146963			44671	other	readthrough							Standard	NM_001244584		Approved		uc011kqt.3		OTTHUMG00000151717	ENST00000354926.4:c.911delG	7.37:g.139102385delG	ENSP00000347005:p.Arg304fs	81	0	.		59	32	0.542	NM_001244584		Frame_Shift_Del	DEL	ENST00000354926.4	37	CCDS43656.1																																																																																			.	.	none		0.562	C7orf55-LUC7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323618.2			-	139102385	G	-	139102385	7	5	41	1	0	1	0	1	0	0	0	0	9092	1000	35	0	945	0	LUC7L2	7	139102385	Frame_Shift_Del	DEL	G	TCGA-GS-A9TY-01A-11D-A38X-10	17363504	139102385	20036278	62	14878											
PARP12	64761	hgsc.bcm.edu	37	chr7	139734083	139734083	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagacacgtatttgggtctgCggcaaacctttttagttgtg	8	14	12	7	2	1	1	0	0	1	1	1	2	1	1	1	2	2	3	1	2	3	6			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr7:139734083C>T	ENST00000263549.3	-	8	2246	c.1373G>A	c.(1372-1374)cGc>cAc	p.R458H	PARP12_ENST00000470515.1_5'UTR	NM_022750.2	NP_073587.1	Q9H0J9	PAR12_HUMAN	poly (ADP-ribose) polymerase family, member 12	458	WWE 2. {ECO:0000255|PROSITE- ProRule:PRU00248}.					nucleus (GO:0005634)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(1)	19	Melanoma(164;0.0142)					TTTGGGTCTGCGGCAAACCTT	0.443																																					p.R458H		Atlas-SNP	.											.	PARP12	59	.	0			c.G1373A						PASS	.						86	79	81					7																	139734083		2203	4300	6503	SO:0001583	missense	64761	exon8			GGTCTGCGGCAAA	AL136766	CCDS5857.1	7q34	2014-01-28	2005-06-02	2005-06-02	ENSG00000059378	ENSG00000059378		"Zinc fingers, CCCH-type domain containing", "Poly (ADP-ribose) polymerases"	21919	protein-coding gene	gene with protein product		612481	"zinc finger CCCH-type domain containing 1"	ZC3HDC1		11230166, 12851707	Standard	NM_022750		Approved	FLJ22693, PARP-12, ZC3H1	uc003vvl.1	Q9H0J9	OTTHUMG00000157315	ENST00000263549.3:c.1373G>A	7.37:g.139734083C>T	ENSP00000263549:p.Arg458His	116	0	0		100	36	0.36	NM_022750	Q9H610|Q9NP36|Q9NTI3	Missense_Mutation	SNP	ENST00000263549.3	37	CCDS5857.1	.	.	.	.	.	.	.	.	.	.	C	32	5.110229	0.94292	.	.	ENSG00000059378	ENST00000263549;ENST00000489809	T;T	0.72725	-0.25;-0.68	5.84	5.84	0.93424	WWE domain (1);	0.000000	0.85682	D	0.000000	D	0.86752	0.6008	M	0.87180	2.865	0.53688	D	0.999975	D	0.89917	1.0	D	0.87578	0.998	D	0.88096	0.2816	10	0.72032	D	0.01	.	18.3385	0.90297	0.0:1.0:0.0:0.0	.	458	Q9H0J9	PAR12_HUMAN	H	458;96	ENSP00000263549:R458H;ENSP00000417606:R96H	ENSP00000263549:R458H	R	-	2	0	PARP12	139380552	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.991000	0.70602	2.767000	0.95098	0.555000	0.69702	CGC	.	.	none		0.443	PARP12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348413.1	NM_022750		T	139734083	C	T	139734083	3	4	41	1	0	0	0	0	1	0	0	0	11466	768	27	1	752	1	PARP12	7	139734083	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	631698	139734083	19404580	63	14879											
MGAM	8972	hgsc.bcm.edu	37	chr7	141805676	141805676	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aattttacttcattgacgtgGataagcactctgtgaatttt	11	17	7	6	1	2	2	1	2	1	0	2	3	2	3	0	1	2	1	0	1	4	7			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr7:141805676G>T	ENST00000549489.2	+	48	5654	c.5559G>T	c.(5557-5559)tgG>tgT	p.W1853C	MGAM_ENST00000475668.2_Missense_Mutation_p.W2749C	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1853					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)	CATTGACGTGGATAAGCACTC	0.348																																					p.W1853C		Atlas-SNP	.											.	MGAM	767	.	0			c.G5559T						PASS	.						122	115	117					7																	141805676		1854	4099	5953	SO:0001583	missense	8972	exon48			GACGTGGATAAGC	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.5559G>T	7.37:g.141805676G>T	ENSP00000447378:p.Trp1853Cys	161	0	0		122	44	0.360656	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	37	CCDS47727.1	.	.	.	.	.	.	.	.	.	.	G	16.47	3.133003	0.56828	.	.	ENSG00000257335	ENST00000549489;ENST00000475668	D	0.90133	-2.62	5.43	4.56	0.56223	.	.	.	.	.	D	0.94420	0.8205	M	0.84683	2.71	0.45150	D	0.998161	D	0.67145	0.996	D	0.63033	0.91	D	0.94592	0.7788	9	0.87932	D	0	.	10.0176	0.42024	0.0904:0.0:0.9096:0.0	.	1853	O43451	MGA_HUMAN	C	1853;2750	ENSP00000447378:W1853C	ENSP00000373973:W1853C	W	+	3	0	MGAM	141452145	0.998000	0.40836	0.736000	0.30914	0.028000	0.11728	4.135000	0.57997	1.535000	0.49220	0.655000	0.94253	TGG	.	.	none		0.348	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3			T	141805676	G	T	141805676	3	4	41	1	0	0	0	0	1	0	0	0	9550	1183	41	4	5745	4	MGAM	7	141805676	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	2071593	141805676	17332987	64	14880											
TRIM55	84675	hgsc.bcm.edu	37	chr8	67067878	67067878	+	Intron	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagttagtaatctgcctagcGcttttggcttttcttattct	6	19	8	8	1	3	0	0	0	3	0	3	1	3	0	1	1	2	4	1	1	4	9	rs373183172		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr8:67067878G>A	ENST00000315962.4	+	9	1897				TRIM55_ENST00000276573.7_Silent_p.A515A|TRIM55_ENST00000353317.5_Intron|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)			TCTGCCTAGCGCTTTTGGCTT	0.318																																					p.A515A		Atlas-SNP	.											.	TRIM55	91	.	0			c.G1545A						PASS	.	G	,,,	0,4404		0,0,2202	164	155	158		1545,,,	1.8	1	8		158	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,intron,intron,intron	TRIM55	NM_033058.2,NM_184085.1,NM_184086.1,NM_184087.1	,,,	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	,,,	515/541,,,	67067878	1,13003	2202	4300	6502	SO:0001627	intron_variant	84675	exon10			CCTAGCGCTTTTG	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+1309G>A	8.37:g.67067878G>A		266	0	0		237	44	0.185654	NM_033058	B3KRC0|B3KRJ3|Q53XX3|Q8IUD9|Q8IUE4|Q96DV2|Q96DV3|Q9BYV5	Silent	SNP	ENST00000315962.4	37	CCDS6184.1																																																																																			.	.	weak		0.318	TRIM55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378921.1	NM_184085		A	67067878	G	A	67067878	1	1	41	0	1	0	0	0	0	0	0	0	16544	1074	38	1		1	TRIM55	8	67067878	Intron	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10		67067878	79296144	65	14881											
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77618778	77618778	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctcgccccggcggaagcaGagctttatcagtactaccta	9	8	10	14	3	1	1	1	0	0	1	2	2	1	2	4	2	4	3	4	2	5	5			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr8:77618778G>T	ENST00000521891.2	+	2	2903	c.2455G>T	c.(2455-2457)Gag>Tag	p.E819*	ZFHX4_ENST00000050961.6_Nonsense_Mutation_p.E819*|ZFHX4_ENST00000517683.1_Intron|ZFHX4_ENST00000455469.2_Nonsense_Mutation_p.E819*|ZFHX4_ENST00000518282.1_Nonsense_Mutation_p.E819*	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	819					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)			GGCGGAAGCAGAGCTTTATCA	0.507										HNSCC(33;0.089)																											p.E819X		Atlas-SNP	.											.	ZFHX4	878	.	0			c.G2455T						PASS	.						20	20	20					8																	77618778		2019	4178	6197	SO:0001587	stop_gained	79776	exon2			GAAGCAGAGCTTT		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.2455G>T	8.37:g.77618778G>T	ENSP00000430497:p.Glu819*	92	0	0		71	36	0.507042	NM_024721	G3V138|Q18PS0|Q6ZN20	Nonsense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	G	38	6.790914	0.97841	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	.	.	.	4.91	4.91	0.64330	.	0.000000	0.43579	U	0.000548	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	.	18.6385	0.91386	0.0:0.0:1.0:0.0	.	.	.	.	X	819	.	ENSP00000050961:E819X	E	+	1	0	ZFHX4	77781333	1.000000	0.71417	0.976000	0.42696	0.921000	0.55340	9.559000	0.98135	2.699000	0.92147	0.585000	0.79938	GAG	.	.	none		0.507	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77618778	G	T	77618778	4	4	41	1	0	0	0	0	0	1	0	0	17650	943	33	4	2457	4	ZFHX4	8	77618778	Nonsense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	10550900	77618778	68745244	66	14882											
RUNX1T1	862	hgsc.bcm.edu	37	chr8	93026977	93026977	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggaagaagaggaaggccCattgctgaagccattgggtg	12	6	17	6	0	0	3	0	1	0	2	0	6	0	6	2	5	2	1	2	5	4	2			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr8:93026977C>T	ENST00000523629.1	-	4	752	c.298G>A	c.(298-300)Ggg>Agg	p.G100R	RUNX1T1_ENST00000396218.1_Missense_Mutation_p.G73R|RUNX1T1_ENST00000522163.1_5'Flank|RUNX1T1_ENST00000360348.2_Missense_Mutation_p.G63R|RUNX1T1_ENST00000265814.3_Missense_Mutation_p.G100R|RUNX1T1_ENST00000436581.2_Missense_Mutation_p.G111R|RUNX1T1_ENST00000518844.1_Missense_Mutation_p.G73R|RUNX1T1_ENST00000422361.2_Missense_Mutation_p.G63R|RUNX1T1_ENST00000520724.1_Missense_Mutation_p.G63R|RUNX1T1_ENST00000521553.1_Missense_Mutation_p.G63R	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)	100					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)			GAGGAAGGCCCATTGCTGAAG	0.532																																					p.G159R		Atlas-SNP	.											.	RUNX1T1	516	.	0			c.G475A						PASS	.						58	60	59					8																	93026977		2203	4300	6503	SO:0001583	missense	862	exon4			AAGGCCCATTGCT	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.298G>A	8.37:g.93026977C>T	ENSP00000428543:p.Gly100Arg	79	0	0		52	22	0.423077	NM_001198679	B7Z4P4|E7EPN4|O14784|Q06456|Q14873|Q16239|Q16346|Q16347|Q6IBL1|Q6NXH1|Q7Z4J5|Q92479|Q9BRZ0	Missense_Mutation	SNP	ENST00000523629.1	37	CCDS6256.1	.	.	.	.	.	.	.	.	.	.	C	34	5.322905	0.95708	.	.	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	0.48836	1.36;1.37;1.36;1.38;1.38;1.38;1.36;1.37;0.82;0.8;1.42	6.05	6.05	0.98169	.	0.000000	0.85682	D	0.000000	T	0.68137	0.2968	L	0.57536	1.79	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	0.994;1.0;0.986;1.0;0.994	T	0.65071	-0.6257	10	0.52906	T	0.07	-18.8339	20.6013	0.99457	0.0:1.0:0.0:0.0	.	111;111;73;100;73	E7EPN4;B7Z4P4;B2R6I9;Q06455;Q06455-2	.;.;.;MTG8_HUMAN;.	R	100;73;100;63;63;63;111;73;63;100;63;100;63;100;100;73;63;63;100;100;73	ENSP00000428543:G100R;ENSP00000379520:G73R;ENSP00000265814:G100R;ENSP00000353504:G63R;ENSP00000390137:G63R;ENSP00000428742:G63R;ENSP00000402257:G111R;ENSP00000430728:G73R;ENSP00000429728:G63R;ENSP00000431094:G100R;ENSP00000427763:G63R	ENSP00000265814:G100R	G	-	1	0	RUNX1T1	93096153	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	7.783000	0.85696	2.878000	0.98634	0.650000	0.86243	GGG	.	.	none		0.532	RUNX1T1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377045.3	NM_004349, NM_175635		T	93026977	C	T	93026977	3	4	41	1	0	0	0	0	1	0	0	0	13762	594	21	2	1552	2	RUNX1T1	8	93026977	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	15408199	93026977	53337045	67	14883											
TMEM74	157753	hgsc.bcm.edu	37	chr8	109796609	109796609	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaggatgacgccccccagcGtgaggaggcagagccccgca	10	2	14	15	3	0	3	0	2	0	1	0	5	0	5	5	3	2	2	5	3	0	0			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr8:109796609G>A	ENST00000297459.3	-	2	897	c.719C>T	c.(718-720)aCg>aTg	p.T240M	TMEM74_ENST00000518838.1_Intron	NM_153015.1	NP_694560.1	Q96NL1	TMM74_HUMAN	transmembrane protein 74	240					autophagy (GO:0006914)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)		p.T240M(1)		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)			GCCCCCCAGCGTGAGGAGGCA	0.587																																					p.T240M		Atlas-SNP	.											TMEM74,NS,carcinoma,0,6	TMEM74	70	6	1	Substitution - Missense(1)	prostate(1)	c.C719T						PASS	.						64	62	63					8																	109796609		2203	4300	6503	SO:0001583	missense	157753	exon2			CCCAGCGTGAGGA	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.719C>T	8.37:g.109796609G>A	ENSP00000297459:p.Thr240Met	108	0	0		58	17	0.293103	NM_153015		Missense_Mutation	SNP	ENST00000297459.3	37	CCDS6310.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.318149	0.81469	.	.	ENSG00000164841	ENST00000297459	T	0.19394	2.15	5.42	5.42	0.78866	.	0.102142	0.64402	D	0.000003	T	0.48040	0.1478	M	0.69358	2.11	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.42447	-0.9451	10	0.87932	D	0	-17.0071	19.416	0.94700	0.0:0.0:1.0:0.0	.	240	Q96NL1	TMM74_HUMAN	M	240	ENSP00000297459:T240M	ENSP00000297459:T240M	T	-	2	0	TMEM74	109865785	1.000000	0.71417	0.973000	0.42090	0.826000	0.46750	9.657000	0.98554	2.821000	0.97095	0.650000	0.86243	ACG	.	.	none		0.587	TMEM74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380755.1	NM_153015		A	109796609	G	A	109796609	3	1	41	1	0	0	0	0	1	0	0	0	16217	1145	40	1	202	1	TMEM74	8	109796609	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	16769632	109796609	36567413	68	14884											
TSNARE1	203062	hgsc.bcm.edu	37	chr8	143356150	143356150	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acacggacttacttggtgccGgctggctccagccaggagct	7	8	13	13	2	0	0	0	0	0	0	1	2	1	2	3	5	4	3	3	5	1	2	rs546251254		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr8:143356150G>A	ENST00000307180.3	-	12	1555	c.1438C>T	c.(1438-1440)Cgg>Tgg	p.R480W	TSNARE1_ENST00000520166.1_Missense_Mutation_p.R480W|TSNARE1_ENST00000519651.1_Missense_Mutation_p.R261W|TSNARE1_ENST00000524325.1_Missense_Mutation_p.R479W	NM_145003.3	NP_659440.2	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	480					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)					ACTTGGTGCCGGCTGGCTCCA	0.652													G|||	1	0.000199681	0.0	0.0	5008	,	,		16768	0.0		0.001	False		,,,				2504	0.0				p.R480W		Atlas-SNP	.											.	TSNARE1	59	.	0			c.C1438T						PASS	.						11	15	14					8																	143356150		2174	4272	6446	SO:0001583	missense	203062	exon12			GGTGCCGGCTGGC			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.1438C>T	8.37:g.143356150G>A	ENSP00000303437:p.Arg480Trp	223	0	0		152	25	0.164474	NM_145003	B7ZLB0|Q14D03	Missense_Mutation	SNP	ENST00000307180.3	37	CCDS6384.1	.	.	.	.	.	.	.	.	.	.	G	13.27	2.188182	0.38609	.	.	ENSG00000171045	ENST00000524325;ENST00000307180;ENST00000520166;ENST00000519651	T;T;T;T	0.35236	2.61;2.61;2.61;1.32	2.4	2.4	0.29515	Target SNARE coiled-coil domain (1);	.	.	.	.	T	0.61375	0.2342	M	0.86502	2.82	0.27569	N	0.949932	D;D;D;D	0.89917	0.999;1.0;0.999;0.999	D;D;D;D	0.68483	0.958;0.925;0.958;0.958	T	0.53982	-0.8361	9	0.87932	D	0	.	10.9101	0.47103	0.0:0.0:1.0:0.0	.	479;261;480;481	B7ZLB0;E5RHT3;Q96NA8;A0AVG3	.;.;TSNA1_HUMAN;.	W	479;480;480;261	ENSP00000428763:R479W;ENSP00000303437:R480W;ENSP00000427770:R480W;ENSP00000429679:R261W	ENSP00000303437:R480W	R	-	1	2	TSNARE1	143354057	0.862000	0.29867	1.000000	0.80357	0.213000	0.24496	0.786000	0.26844	1.272000	0.44329	0.462000	0.41574	CGG	.	.	none		0.652	TSNARE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_145003		A	143356150	G	A	143356150	3	1	41	1	0	0	0	0	1	0	0	0	16645	1115	39	1	111	1	TSNARE1	8	143356150	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	33559541	143356150	3007872	69	14885											
FRMPD1	22844	hgsc.bcm.edu	37	chr9	37746410	37746410	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actttaccgaaagccggagcCgcctctgcatgggctcccag	8	7	11	15	3	1	0	0	0	1	0	2	2	2	1	5	2	4	2	5	2	2	2	rs199593687		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr9:37746410C>T	ENST00000539465.1	+	16	4974	c.4381C>T	c.(4381-4383)Cgc>Tgc	p.R1461C	RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000377765.3_Missense_Mutation_p.R1461C			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	1461						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)		AAGCCGGAGCCGCCTCTGCAT	0.572													C|||	1	0.000199681	0.0	0.0014	5008	,	,		16762	0.0		0.0	False		,,,				2504	0.0				p.R1461C		Atlas-SNP	.											.	FRMPD1	237	.	0			c.C4381T						PASS	.						20	23	22					9																	37746410		2202	4299	6501	SO:0001583	missense	22844	exon16			CGGAGCCGCCTCT	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.4381C>T	9.37:g.37746410C>T	ENSP00000444411:p.Arg1461Cys	32	0	0		22	14	0.636364	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	37	CCDS6612.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	17.19	3.325729	0.60743	.	.	ENSG00000070601	ENST00000377765;ENST00000539465	T;T	0.07444	3.19;3.19	5.67	3.13	0.36017	.	0.672742	0.15711	N	0.248395	T	0.06371	0.0164	L	0.29908	0.895	0.80722	D	1	B	0.16603	0.018	B	0.08055	0.003	T	0.21895	-1.0232	10	0.46703	T	0.11	-8.2395	7.7661	0.28980	0.23:0.6848:0.0:0.0852	.	1461	Q5SYB0	FRPD1_HUMAN	C	1461	ENSP00000366995:R1461C;ENSP00000444411:R1461C	ENSP00000366995:R1461C	R	+	1	0	FRMPD1	37736410	0.387000	0.25188	1.000000	0.80357	0.998000	0.95712	0.559000	0.23485	2.672000	0.90937	0.655000	0.94253	CGC	C|1.000;T|0.000	0.000	strong		0.572	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		T	37746410	C	T	37746410	3	4	41	1	0	0	0	0	1	0	0	0	6065	652	23	1	4439	1	FRMPD1	9	37746410	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10		37746410	103467021	70	14886											
PCSK5	5125	hgsc.bcm.edu	37	chr9	78796464	78796464	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttctgaatgaagaaaccaaCagctgtgttactcactgccc	12	11	7	11	0	2	3	1	2	1	1	2	3	2	3	2	0	5	2	2	0	5	2			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr9:78796464C>G	ENST00000545128.1	+	16	2692	c.2154C>G	c.(2152-2154)aaC>aaG	p.N718K	PCSK5_ENST00000376752.4_Missense_Mutation_p.N718K	NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	718	CRM (Cys-rich motif).				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						AAGAAACCAACAGCTGTGTTA	0.453																																					p.N718K		Atlas-SNP	.											.	PCSK5	329	.	0			c.C2154G						PASS	.						131	113	119					9																	78796464		2203	4300	6503	SO:0001583	missense	5125	exon16			AACCAACAGCTGT		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.2154C>G	9.37:g.78796464C>G	ENSP00000446280:p.Asn718Lys	93	0	0		127	34	0.267717	NM_006200	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	37	CCDS55320.1	.	.	.	.	.	.	.	.	.	.	C	13.29	2.193932	0.38707	.	.	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000376752;ENST00000424854	T;D;T	0.85484	-0.14;-1.99;-0.09	6.06	3.92	0.45320	.	0.166330	0.64402	D	0.000004	T	0.79969	0.4538	L	0.54908	1.71	0.37334	D	0.910111	B	0.21147	0.052	B	0.21917	0.037	T	0.78453	-0.2198	10	0.46703	T	0.11	-19.0967	7.7085	0.28663	0.0:0.6627:0.1411:0.1962	.	718	Q92824-2	.	K	718;421;718;391	ENSP00000446280:N718K;ENSP00000365943:N718K;ENSP00000411654:N391K	ENSP00000365943:N718K	N	+	3	2	PCSK5	77986284	1.000000	0.71417	0.992000	0.48379	0.966000	0.64601	0.911000	0.28584	1.581000	0.49865	0.655000	0.94253	AAC	.	.	none		0.453	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				G	78796464	C	G	78796464	3	3	41	1	0	0	0	0	1	0	0	0	11612	477	17	4	2216	4	PCSK5	9	78796464	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	41050054	78796464	62416967	71	14887											
MED22	6837	hgsc.bcm.edu	37	chr9	136213400	136213400	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaccccacccccaccttggCggtcttgatgatctcggtga	6	9	9	17	2	2	3	0	3	2	0	3	3	2	3	6	3	0	0	6	3	0	2			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr9:136213400C>T	ENST00000491289.1	-	2	699	c.118G>A	c.(118-120)Gcc>Acc	p.A40T	MED22_ENST00000344469.5_Missense_Mutation_p.A40T|RPL7A_ENST00000323345.6_5'Flank|MED22_ENST00000476080.1_Missense_Mutation_p.A40T|MED22_ENST00000471524.1_Intron|MED22_ENST00000371999.1_Missense_Mutation_p.A40T|SNORD24_ENST00000383884.1_RNA|MED22_ENST00000343730.5_Missense_Mutation_p.A40T|RPL7A_ENST00000315731.4_5'Flank			Q15528	MED22_HUMAN	mediator complex subunit 22	40						cytoplasm (GO:0005737)|mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			endometrium(1)|large_intestine(1)|ovary(1)|urinary_tract(1)	4				OV - Ovarian serous cystadenocarcinoma(145;1.14e-06)|Epithelial(140;8.2e-06)|all cancers(34;6.94e-05)		CCCACCTTGGCGGTCTTGATG	0.592																																					p.A40T		Atlas-SNP	.											.	MED22	13	.	0			c.G118A						PASS	.						140	123	129					9																	136213400		2203	4300	6503	SO:0001583	missense	6837	exon2			CCTTGGCGGTCTT		CCDS6963.1, CCDS6964.1	9q34.1	2008-02-05	2007-07-30	2007-07-30	ENSG00000148297	ENSG00000148297			11477	protein-coding gene	gene with protein product		185641	"surfeit 5"	SURF5		8499913, 15175163	Standard	NM_133640		Approved	Med24	uc004cdc.3	Q15528	OTTHUMG00000020869	ENST00000491289.1:c.118G>A	9.37:g.136213400C>T	ENSP00000420393:p.Ala40Thr	93	0	0		155	92	0.593548	NM_181491	B3KW83|B3KWX4|O76072|Q5T8U0	Missense_Mutation	SNP	ENST00000491289.1	37	CCDS6963.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.832980	0.91036	.	.	ENSG00000148297	ENST00000491289;ENST00000486395;ENST00000343730;ENST00000344469;ENST00000476080;ENST00000371999;ENST00000446777;ENST00000494177;ENST00000457204	.	.	.	5.01	3.17	0.36434	.	0.050283	0.85682	D	0.000000	T	0.62986	0.2473	M	0.70842	2.15	0.80722	D	1	P;D	0.57571	0.923;0.98	P;P	0.50490	0.563;0.642	T	0.65150	-0.6238	9	0.72032	D	0.01	-21.2717	10.5851	0.45278	0.0:0.8424:0.0:0.1576	.	40;40	Q15528-2;Q15528	.;MED22_HUMAN	T	40	.	ENSP00000342343:A40T	A	-	1	0	MED22	135203221	1.000000	0.71417	0.928000	0.36995	0.948000	0.59901	5.942000	0.70203	0.519000	0.28406	0.491000	0.48974	GCC	.	.	none		0.592	MED22-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054898.2	NM_133640		T	136213400	C	T	136213400	3	4	41	1	0	0	0	0	1	0	0	0	9449	768	27	1	510	1	MED22	9	136213400	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	57416936	136213400	5000031	72	14888											
C10orf18	54906	hgsc.bcm.edu	37	chr10	5790878	5790878	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aactctctggagattctgatCtagacctgcttggtgattgt	8	15	10	8	0	3	4	0	2	3	2	4	5	3	4	1	2	2	1	1	2	2	4			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr10:5790878C>G	ENST00000328090.5	+	15	6119	c.5494C>G	c.(5494-5496)Cta>Gta	p.L1832V		NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	1832																	AGATTCTGATCTAGACCTGCT	0.478																																					p.L1832V		Atlas-SNP	.											.	.	.	.	0			c.C5494G						PASS	.						67	66	66					10																	5790878		1873	4124	5997	SO:0001583	missense	54906	exon15			TCTGATCTAGACC	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.5494C>G	10.37:g.5790878C>G	ENSP00000328426:p.Leu1832Val	116	0	0		87	73	0.83908	NM_017782	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Missense_Mutation	SNP	ENST00000328090.5	37	CCDS41485.1	.	.	.	.	.	.	.	.	.	.	C	9.110	1.006421	0.19199	.	.	ENSG00000108021	ENST00000328090;ENST00000442808	T	0.04234	3.67	5.71	-3.08	0.05347	.	1.613740	0.03359	N	0.197302	T	0.03871	0.0109	N	0.22421	0.69	0.09310	N	1	B	0.22604	0.072	B	0.18871	0.023	T	0.45366	-0.9266	10	0.07813	T	0.8	.	11.99	0.53169	0.2271:0.2164:0.5565:0.0	.	1832	Q5VWN6	F208B_HUMAN	V	1832;1027	ENSP00000328426:L1832V	ENSP00000328426:L1832V	L	+	1	2	C10orf18	5830884	0.359000	0.24955	0.000000	0.03702	0.089000	0.18198	0.425000	0.21346	-0.953000	0.03645	0.563000	0.77884	CTA	.	.	none		0.478	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782		G	5790878	C	G	5790878	3	3	41	1	0	0	0	0	1	0	0	0	1598	912	32	4	5540	4	C10orf18	10	5790878	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10		5790878	129743869	73	14889											
OR10A4	283297	hgsc.bcm.edu	37	chr11	6898788	6898788	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagtgaaggctgcactgaagCggcttatccacaggaccctg	11	7	12	11	1	0	2	0	2	0	0	1	3	1	3	2	3	2	3	2	3	4	1	rs146085036	byFrequency	TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr11:6898788C>T	ENST00000379829.2	+	1	933	c.910C>T	c.(910-912)Cgg>Tgg	p.R304W		NM_207186.2	NP_997069.2	Q9H209	O10A4_HUMAN	olfactory receptor, family 10, subfamily A, member 4	304					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)			kidney(1)|large_intestine(2)|liver(2)|lung(20)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31		Medulloblastoma(188;0.0523)|all_neural(188;0.236)		Epithelial(150;4.78e-08)|BRCA - Breast invasive adenocarcinoma(625;0.129)		TGCACTGAAGCGGCTTATCCA	0.448													C|||	2	0.000399361	0.0	0.0	5008	,	,		19920	0.002		0.0	False		,,,				2504	0.0				p.R304W		Atlas-SNP	.											.	OR10A4	65	.	0			c.C910T						PASS	.		TRP/ARG	1,4401	2.1+/-5.4	0,1,2200	82	82	82		910	2	0.1	11	dbSNP_134	82	1,8591	1.2+/-3.3	0,1,4295	no	missense	OR10A4	NM_207186.2	101	0,2,6495	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging	304/316	6898788	2,12992	2201	4296	6497	SO:0001583	missense	283297	exon1			CTGAAGCGGCTTA	AF209506	CCDS7774.1	11p15.4	2012-08-09	2002-11-13	2004-03-10	ENSG00000170782	ENSG00000170782		"GPCR / Class A : Olfactory receptors"	15130	protein-coding gene	gene with protein product			"olfactory receptor, family 10, subfamily A, member 4 pseudogene"	OR10A4P			Standard	NM_207186		Approved		uc010rat.2	Q9H209	OTTHUMG00000165740	ENST00000379829.2:c.910C>T	11.37:g.6898788C>T	ENSP00000369157:p.Arg304Trp	75	0	0		44	26	0.590909	NM_207186	B2RNP5|B9EH36|Q96R20	Missense_Mutation	SNP	ENST00000379829.2	37	CCDS7774.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	c	11.99	1.802297	0.31869	2.27E-4	1.16E-4	ENSG00000170782	ENST00000379829	T	0.41758	0.99	3.99	2.01	0.26516	.	0.000000	0.40385	N	0.001120	T	0.39172	0.1068	M	0.65975	2.015	0.20563	N	0.999889	B	0.18968	0.032	B	0.20184	0.028	T	0.42599	-0.9442	10	0.87932	D	0	.	8.8618	0.35263	0.4398:0.5602:0.0:0.0	.	304	Q9H209	O10A4_HUMAN	W	304	ENSP00000369157:R304W	ENSP00000369157:R304W	R	+	1	2	OR10A4	6855364	0.001000	0.12720	0.064000	0.19789	0.163000	0.22366	1.026000	0.30103	0.580000	0.29522	0.651000	0.88453	CGG	C|1.000;T|0.000	0.000	strong		0.448	OR10A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385985.1	NM_207186		T	6898788	C	T	6898788	3	4	41	1	0	0	0	0	1	0	0	0	10901	759	27	1	912	1	OR10A4	11	6898788	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10		6898788	128107728	74	14890											
ANO5	203859	hgsc.bcm.edu	37	chr11	22249091	22249091	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagctcttcctcatcgaaGatcaggcaaccttctttcca	10	11	7	13	1	4	1	2	0	2	1	7	3	6	2	3	2	2	2	3	2	2	3			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr11:22249091G>T	ENST00000324559.8	+	7	924	c.607G>T	c.(607-609)Gat>Tat	p.D203Y		NM_001142649.1|NM_213599.2	NP_001136121.1|NP_998764.1	Q75V66	ANO5_HUMAN	anoctamin 5	203					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						CCTCATCGAAGATCAGGCAAC	0.458																																					p.D203Y		Atlas-SNP	.											.	ANO5	162	.	0			c.G607T						PASS	.						98	96	97					11																	22249091		2203	4300	6503	SO:0001583	missense	203859	exon7			ATCGAAGATCAGG	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.607G>T	11.37:g.22249091G>T	ENSP00000315371:p.Asp203Tyr	119	0	0		86	50	0.581395	NM_213599		Missense_Mutation	SNP	ENST00000324559.8	37	CCDS31444.1	.	.	.	.	.	.	.	.	.	.	G	18.57	3.651987	0.67472	.	.	ENSG00000171714	ENST00000324559	T	0.65916	-0.18	5.69	4.78	0.61160	.	0.174317	0.64402	D	0.000009	D	0.82388	0.5026	M	0.92317	3.295	0.58432	D	0.999994	D	0.71674	0.998	D	0.64506	0.926	D	0.87157	0.2212	10	0.87932	D	0	.	14.8589	0.70362	0.0693:0.0:0.9307:0.0	.	203	Q75V66	ANO5_HUMAN	Y	203	ENSP00000315371:D203Y	ENSP00000315371:D203Y	D	+	1	0	ANO5	22205667	1.000000	0.71417	0.390000	0.26220	0.843000	0.47879	3.119000	0.50422	1.409000	0.46915	0.650000	0.86243	GAT	.	.	none		0.458	ANO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387615.1	NM_213599		T	22249091	G	T	22249091	3	4	41	1	0	0	0	0	1	0	0	0	700	942	33	4	633	4	ANO5	11	22249091	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	15350303	22249091	112757425	75	14891											
HARBI1	283254	hgsc.bcm.edu	37	chr11	46637180	46637180	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tactgagggaagactgctgcAgcacagcacagtcctgtagg	11	7	13	10	0	0	2	0	1	0	1	1	3	1	3	1	2	5	5	1	2	3	2			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr11:46637180A>G	ENST00000326737.3	-	2	855	c.608T>C	c.(607-609)cTg>cCg	p.L203P	ATG13_ENST00000451945.1_5'Flank|ATG13_ENST00000434074.1_5'Flank|ATG13_ENST00000529655.1_5'Flank|ATG13_ENST00000530500.1_5'Flank|ATG13_ENST00000526508.1_5'Flank|ATG13_ENST00000312040.4_5'Flank|ATG13_ENST00000524625.1_5'Flank|ATG13_ENST00000528494.1_5'Flank|ATG13_ENST00000359513.4_5'Flank	NM_173811.3	NP_776172.1	Q96MB7	HARB1_HUMAN	harbinger transposase derived 1	203						centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nuclease activity (GO:0004518)			large_intestine(1)|prostate(1)|upper_aerodigestive_tract(1)	3						AGACTGCTGCAGCACAGCACA	0.493																																					p.L203P		Atlas-SNP	.											.	HARBI1	19	.	0			c.T608C						PASS	.						115	118	117					11																	46637180		2201	4299	6500	SO:0001583	missense	283254	exon2			TGCTGCAGCACAG	AK057237	CCDS7920.1	11p11.2	2008-07-10	2008-07-01	2008-07-01	ENSG00000180423	ENSG00000180423			26522	protein-coding gene	gene with protein product		615086	"chromosome 11 open reading frame 77"	C11orf77		15169610, 18339812	Standard	NM_173811		Approved	FLJ32675	uc001ncy.3	Q96MB7	OTTHUMG00000166537	ENST00000326737.3:c.608T>C	11.37:g.46637180A>G	ENSP00000317743:p.Leu203Pro	142	0	0		125	75	0.6	NM_173811	D3DQP9	Missense_Mutation	SNP	ENST00000326737.3	37	CCDS7920.1	.	.	.	.	.	.	.	.	.	.	A	21.5	4.158679	0.78226	.	.	ENSG00000180423	ENST00000326737	.	.	.	5.23	5.23	0.72850	.	0.141737	0.48767	D	0.000171	D	0.83663	0.5303	M	0.89601	3.045	0.80722	D	1	D	0.58970	0.984	D	0.64237	0.923	D	0.87380	0.2356	9	0.72032	D	0.01	-12.4836	15.1287	0.72503	1.0:0.0:0.0:0.0	.	203	Q96MB7	HARB1_HUMAN	P	203	.	ENSP00000317743:L203P	L	-	2	0	HARBI1	46593756	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	8.918000	0.92759	1.967000	0.57214	0.533000	0.62120	CTG	.	.	none		0.493	HARBI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390291.1	NM_173811		G	46637180	A	G	46637180	3	3	41	1	0	0	0	0	1	0	0	0	6967	188	7	3	449	3	HARBI1	11	46637180	Missense_Mutation	SNP	A	TCGA-GS-A9TY-01A-11D-A38X-10	24388089	46637180	88369336	76	14892											
FLRT1	28992	hgsc.bcm.edu	37	chr11	63884662	63884662	+	Intron	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccaacaacaacctgaccaCgctgccccgcggcctgttcg	8	6	9	18	4	0	1	0	1	0	0	2	1	1	1	6	1	4	2	6	1	3	1			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr11:63884662C>T	ENST00000255681.6	-	3	584				RP11-21A7A.3_ENST00000543817.1_RNA|FLRT1_ENST00000246841.3_Missense_Mutation_p.T308M	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						AACCTGACCACGCTGCCCCGC	0.617																																					p.T308M		Atlas-SNP	.											.	FLRT1	46	.	0			c.C923T						PASS	.						56	48	51					11																	63884662		2201	4297	6498	SO:0001627	intron_variant	23769	exon2			TGACCACGCTGCC	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+34048G>A	11.37:g.63884662C>T		85	0	0		65	34	0.523077	NM_013280	Q9UH96	Missense_Mutation	SNP	ENST00000255681.6	37	CCDS8056.1	.	.	.	.	.	.	.	.	.	.	C	12.14	1.848171	0.32699	.	.	ENSG00000126500	ENST00000246841	T	0.59906	0.23	5.07	3.14	0.36123	.	0.133754	0.49305	D	0.000152	T	0.60805	0.2297	L	0.57536	1.79	0.50039	D	0.99984	D	0.61697	0.99	P	0.56042	0.79	T	0.55425	-0.8143	10	0.20519	T	0.43	-19.8004	8.6572	0.34071	0.1515:0.767:0.0:0.0815	.	280	Q9NZU1	FLRT1_HUMAN	M	308	ENSP00000246841:T308M	ENSP00000246841:T308M	T	+	2	0	FLRT1	63641238	0.849000	0.29639	0.841000	0.33234	0.916000	0.54674	1.646000	0.37249	0.492000	0.27815	0.484000	0.47621	ACG	.	.	none		0.617	MACROD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396570.1	NM_014067		T	63884662	C	T	63884662	1	4	41	0	1	0	0	0	0	0	0	0	5946	536	19	1		1	FLRT1	11	63884662	Intron	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	17247482	63884662	71121854	77	14893											
ODZ4	26011	hgsc.bcm.edu	37	chr11	78369308	78369308	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tctgctgctcgcgggcccacGcttggcgcacggctctctgc	2	9	13	17	5	2	0	0	0	2	0	4	0	2	0	1	3	3	5	1	3	0	1			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr11:78369308G>A	ENST00000278550.7	-	34	8567	c.8105C>T	c.(8104-8106)gCg>gTg	p.A2702V		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	2702					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)										GCGGGCCCACGCTTGGCGCAC	0.672																																					p.A2702V		Atlas-SNP	.											ODZ4_ENST00000278550,colon,carcinoma,+1,2	.	.	2	0			c.C8105T						PASS	.						39	45	43					11																	78369308		2029	4182	6211	SO:0001583	missense	26011	exon34			GCCCACGCTTGGC	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.8105C>T	11.37:g.78369308G>A	ENSP00000278550:p.Ala2702Val	61	0	0		71	28	0.394366	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	37	CCDS44688.1	.	.	.	.	.	.	.	.	.	.	G	25.0	4.589110	0.86851	.	.	ENSG00000149256	ENST00000278550	D	0.92911	-3.13	5.54	5.54	0.83059	.	0.000000	0.85682	D	0.000000	D	0.95924	0.8673	M	0.74467	2.265	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	D	0.94982	0.8126	9	.	.	.	.	19.6787	0.95950	0.0:0.0:1.0:0.0	.	2702	Q6N022	TEN4_HUMAN	V	2702	ENSP00000278550:A2702V	.	A	-	2	0	ODZ4	78046956	1.000000	0.71417	0.972000	0.41901	0.607000	0.37147	9.601000	0.98297	2.884000	0.98904	0.655000	0.94253	GCG	.	.	none		0.672	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			A	78369308	G	A	78369308	3	1	41	1	0	0	0	0	1	0	0	0	10846	1087	38	1	208	1	ODZ4	11	78369308	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	14484646	78369308	56637208	78	14894											
SLC2A14	144195	hgsc.bcm.edu	37	chr12	7970447	7970447	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcagcagaggggaagagcaAtccgactaggaagttggagg	14	4	17	6	1	0	2	0	0	0	2	1	6	1	5	1	5	3	4	1	5	4	2			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr12:7970447A>C	ENST00000543909.1	-	15	2083	c.1324T>G	c.(1324-1326)Ttg>Gtg	p.L442V	SLC2A14_ENST00000542505.1_Missense_Mutation_p.L83V|SLC2A14_ENST00000396589.2_Missense_Mutation_p.L442V|SLC2A14_ENST00000535295.1_Missense_Mutation_p.L333V|SLC2A14_ENST00000542546.1_Missense_Mutation_p.L333V|SLC2A14_ENST00000340749.5_Missense_Mutation_p.L419V|SLC2A14_ENST00000431042.2_Missense_Mutation_p.L419V|SLC2A14_ENST00000539924.1_Missense_Mutation_p.L457V			Q8TDB8	GTR14_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 14	442					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)		GGGAAGAGCAATCCGACTAGG	0.483																																					p.L442V		Atlas-SNP	.											.	SLC2A14	78	.	0			c.T1324G						PASS	.						50	51	51					12																	7970447		2203	4300	6503	SO:0001583	missense	144195	exon11			AGAGCAATCCGAC	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.1324T>G	12.37:g.7970447A>C	ENSP00000440480:p.Leu442Val	158	1	0.00632911		96	80	0.833333	NM_153449	B3KVB5|B3KWW7|B7Z844|B7ZAC3|Q6UY84|Q8TDB9	Missense_Mutation	SNP	ENST00000543909.1	37	CCDS8585.1	.	.	.	.	.	.	.	.	.	.	A	13.73	2.325096	0.41197	.	.	ENSG00000173262	ENST00000340749;ENST00000543909;ENST00000431042;ENST00000542505;ENST00000396589;ENST00000535295;ENST00000542546;ENST00000539924	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	3.31	-2.39	0.06602	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.356645	0.29260	N	0.012680	T	0.73892	0.3645	M	0.76938	2.355	0.32386	N	0.553901	P;P;P;P	0.49358	0.923;0.866;0.545;0.549	P;P;B;B	0.52672	0.706;0.619;0.248;0.34	T	0.72090	-0.4395	10	0.66056	D	0.02	.	1.8486	0.03164	0.1194:0.1529:0.244:0.4836	.	457;333;419;442	B7ZAC3;B7Z844;Q8TDB8-2;Q8TDB8	.;.;.;GTR14_HUMAN	V	419;442;419;83;442;333;333;457	ENSP00000340450:L419V;ENSP00000440480:L442V;ENSP00000407287:L419V;ENSP00000438484:L83V;ENSP00000379834:L442V;ENSP00000440492:L333V;ENSP00000443903:L333V;ENSP00000445929:L457V	ENSP00000340450:L419V	L	-	1	2	SLC2A14	7861714	0.023000	0.18921	0.519000	0.27824	0.790000	0.44656	0.099000	0.15210	-0.335000	0.08451	0.164000	0.16699	TTG	.	.	none		0.483	SLC2A14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399836.2	NM_153449		C	7970447	A	C	7970447	3	2	41	1	0	0	0	0	1	0	0	0	14558	98	4	5	246	5	SLC2A14	12	7970447	Missense_Mutation	SNP	A	TCGA-GS-A9TY-01A-11D-A38X-10		7970447	125881448	79	14895											
MGP	4256	hgsc.bcm.edu	37	chr12	15035143	15035143	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atccataaaccatggcgtagCgttcgcaaagtctgtagtca	12	10	9	10	3	2	0	1	0	1	0	4	0	3	0	2	1	2	4	2	1	5	4	rs375828646		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr12:15035143C>T	ENST00000539261.1	-	4	376	c.242G>A	c.(241-243)cGc>cAc	p.R81H	C12orf60_ENST00000527783.1_Intron|MGP_ENST00000228938.5_Missense_Mutation_p.R106H	NM_000900.3	NP_000891.2	P08493	MGP_HUMAN	matrix Gla protein	81	Gla. {ECO:0000255|PROSITE- ProRule:PRU00463}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|ossification (GO:0001503)|regulation of bone mineralization (GO:0030500)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)|structural constituent of bone (GO:0008147)			large_intestine(1)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	7						CATGGCGTAGCGTTCGCAAAG	0.463																																					p.R106H		Atlas-SNP	.											MGP,colon,carcinoma,-1,3	MGP	16	3	0			c.G317A						PASS	.						156	148	151					12																	15035143		2203	4300	6503	SO:0001583	missense	4256	exon5			GCGTAGCGTTCGC	M58549	CCDS8669.1, CCDS53752.1	12p12.3	2006-12-15			ENSG00000111341	ENSG00000111341			7060	protein-coding gene	gene with protein product		154870				2394711	Standard	NM_000900		Approved		uc021qvr.1	P08493	OTTHUMG00000168740	ENST00000539261.1:c.242G>A	12.37:g.15035143C>T	ENSP00000445907:p.Arg81His	194	0	0		137	11	0.080292	NM_001190839	A0M8W5|B2R519|J3KMX7|Q2TU41|Q567P9|Q6ICN5	Missense_Mutation	SNP	ENST00000539261.1	37	CCDS8669.1	.	.	.	.	.	.	.	.	.	.	C	18.61	3.662123	0.67700	.	.	ENSG00000111341	ENST00000539261;ENST00000228938	D;D	0.99220	-5.58;-5.58	5.13	4.24	0.50183	Gamma-carboxyglutamic acid-rich (GLA) domain (5);	0.299010	0.32218	N	0.006413	D	0.98538	0.9512	L	0.61036	1.89	0.34062	D	0.657446	D	0.64830	0.994	P	0.55667	0.781	D	0.99940	1.1398	10	0.15066	T	0.55	-1.3297	9.507	0.39053	0.0:0.9048:0.0:0.0952	.	81	P08493	MGP_HUMAN	H	81;106	ENSP00000445907:R81H;ENSP00000228938:R106H	ENSP00000228938:R106H	R	-	2	0	MGP	14926410	1.000000	0.71417	1.000000	0.80357	0.674000	0.39518	0.727000	0.25999	1.532000	0.49169	0.655000	0.94253	CGC	.	.	alt		0.463	MGP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400864.1	NM_000900		T	15035143	C	T	15035143	3	4	41	1	0	0	0	0	1	0	0	0	9567	768	27	1	73	1	MGP	12	15035143	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	7064696	15035143	118816752	80	14896											
KCNJ8	3764	hgsc.bcm.edu	37	chr12	21918851	21918851	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaataaggatggaaggttTctcatccagctctcgggcac	10	10	11	10	1	2	1	1	1	2	0	5	3	3	3	1	4	1	3	1	4	3	2			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr12:21918851T>G	ENST00000240662.2	-	3	1426	c.1081A>C	c.(1081-1083)Aaa>Caa	p.K361Q	RP11-59N23.1_ENST00000542489.1_RNA	NM_004982.3	NP_004973.1	Q15842	KCNJ8_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 8	361					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)	ATGGAAGGTTTCTCATCCAGC	0.458																																					p.K361Q		Atlas-SNP	.											.	KCNJ8	59	.	0			c.A1081C						PASS	.						145	145	145					12																	21918851		2203	4300	6503	SO:0001583	missense	3764	exon3			AAGGTTTCTCATC	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.1081A>C	12.37:g.21918851T>G	ENSP00000240662:p.Lys361Gln	275	0	0		164	9	0.054878	NM_004982	O00657	Missense_Mutation	SNP	ENST00000240662.2	37	CCDS8692.1	.	.	.	.	.	.	.	.	.	.	T	19.90	3.913406	0.72983	.	.	ENSG00000121361	ENST00000240662;ENST00000539350	D	0.94138	-3.36	5.43	5.43	0.79202	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	0.94275	0.8161	L	0.48986	1.54	0.54753	D	0.99998	D	0.55800	0.973	P	0.58266	0.836	D	0.92996	0.6419	10	0.29301	T	0.29	.	15.6454	0.77046	0.0:0.0:0.0:1.0	.	361	Q15842	IRK8_HUMAN	Q	361	ENSP00000240662:K361Q	ENSP00000240662:K361Q	K	-	1	0	KCNJ8	21810118	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.010000	0.70753	2.279000	0.76181	0.533000	0.62120	AAA	.	.	none		0.458	KCNJ8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402226.1	NM_004982		G	21918851	T	G	21918851	3	3	41	1	0	0	0	0	1	0	0	0	8065	1792	62	5	197	5	KCNJ8	12	21918851	Missense_Mutation	SNP	T	TCGA-GS-A9TY-01A-11D-A38X-10	6883708	21918851	111933044	81	14897											
DENND5B	160518	hgsc.bcm.edu	37	chr12	31555505	31555505	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagctctcctgatacacagAtccaagggtttgatgtgatt	10	12	9	10	0	1	4	0	3	1	1	3	4	2	4	3	1	2	2	3	1	2	3			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr12:31555505A>T	ENST00000389082.5	-	15	3140	c.2876T>A	c.(2875-2877)aTc>aAc	p.I959N	DENND5B_ENST00000536562.1_Missense_Mutation_p.I994N|DENND5B_ENST00000306833.6_Missense_Mutation_p.I994N	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	959	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				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						TGATACACAGATCCAAGGGTT	0.403																																					p.I959N		Atlas-SNP	.											.	DENND5B	114	.	0			c.T2876A						PASS	.						168	165	166					12																	31555505		1882	4122	6004	SO:0001583	missense	160518	exon15			ACACAGATCCAAG	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.2876T>A	12.37:g.31555505A>T	ENSP00000373734:p.Ile959Asn	246	0	0		265	125	0.471698	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Missense_Mutation	SNP	ENST00000389082.5	37	CCDS44857.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.193138	0.78902	.	.	ENSG00000170456	ENST00000389082;ENST00000306833;ENST00000536562	T;T;T	0.69561	-0.41;-0.41;-0.41	4.2	4.2	0.49525	Lipoxygenase, LH2 (3);Lipase/lipooxygenase, PLAT/LH2 (1);	0.162227	0.43747	D	0.000534	D	0.83608	0.5291	M	0.90082	3.085	0.58432	D	0.999999	D;D	0.69078	0.997;0.996	D;D	0.72075	0.976;0.959	D	0.87352	0.2338	10	0.87932	D	0	-21.976	13.4458	0.61140	1.0:0.0:0.0:0.0	.	959;994	Q6ZUT9;G3V1S3	DEN5B_HUMAN;.	N	959;994;994	ENSP00000373734:I959N;ENSP00000306482:I994N;ENSP00000444889:I994N	ENSP00000306482:I994N	I	-	2	0	DENND5B	31446772	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.831000	0.92068	1.766000	0.52107	0.533000	0.62120	ATC	.	.	none		0.403	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973		T	31555505	A	T	31555505	3	4	41	1	0	0	0	0	1	0	0	0	4439	333	12	5	976	5	DENND5B	12	31555505	Missense_Mutation	SNP	A	TCGA-GS-A9TY-01A-11D-A38X-10	9636654	31555505	102296390	82	14898											
ADAMTS20	80070	hgsc.bcm.edu	37	chr12	43846488	43846488	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccacacagtaatttcctcCgtttcttggcctagtcaaat	9	13	6	13	1	2	0	1	0	1	0	4	0	4	0	4	1	0	2	4	1	3	5	rs375621283		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr12:43846488C>T	ENST00000389420.3	-	13	1770	c.1771G>A	c.(1771-1773)Gga>Aga	p.G591R	ADAMTS20_ENST00000553158.1_Missense_Mutation_p.G591R	NM_025003.3	NP_079279.3	P59510	ATS20_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 20	591	TSP type-1 1. {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)	p.G591R(2)		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)		TAATTTCCTCCGTTTCTTGGC	0.393																																					p.G591R		Atlas-SNP	.											ADAMTS20_ENST00000389420,NS,malignant_melanoma,0,4	ADAMTS20	635	4	2	Substitution - Missense(2)	skin(2)	c.G1771A						PASS	.	C	ARG/GLY	0,4406		0,0,2203	60	52	55		1771	4.7	1	12		55	1,8599	1.2+/-3.3	0,1,4299	no	missense	ADAMTS20	NM_025003.3	125	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	591/1911	43846488	1,13005	2203	4300	6503	SO:0001583	missense	80070	exon13			TTCCTCCGTTTCT	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.1771G>A	12.37:g.43846488C>T	ENSP00000374071:p.Gly591Arg	76	0	0		86	41	0.476744	NM_025003	A6NNC9|J3QT00	Missense_Mutation	SNP	ENST00000389420.3	37	CCDS31778.2	.	.	.	.	.	.	.	.	.	.	C	26.0	4.692176	0.88735	0.0	1.16E-4	ENSG00000173157	ENST00000389420;ENST00000553158;ENST00000389417	T;T	0.09163	3.01;3.01	4.7	4.7	0.59300	.	0.000000	0.49916	D	0.000124	T	0.47655	0.1457	H	0.95328	3.655	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.65516	-0.6149	10	0.87932	D	0	.	18.5382	0.91018	0.0:1.0:0.0:0.0	.	591	P59510	ATS20_HUMAN	R	591	ENSP00000374071:G591R;ENSP00000448341:G591R	ENSP00000374068:G591R	G	-	1	0	ADAMTS20	42132755	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.445000	0.80570	2.536000	0.85505	0.563000	0.77884	GGA	.	.	weak		0.393	ADAMTS20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403643.1	NM_025003		T	43846488	C	T	43846488	3	4	41	1	0	0	0	0	1	0	0	0	266	661	23	1	4068	1	ADAMTS20	12	43846488	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	12290983	43846488	90005407	83	14899											
MLL2	8085	hgsc.bcm.edu	37	chr12	49427324	49427324	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	catacgttgctgctgcagctGcagctgcctttcctgtaaaa	8	12	9	12	1	0	0	0	0	0	0	1	0	1	0	2	0	8	8	2	0	3	4			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr12:49427324G>A	ENST00000301067.7	-	39	11163	c.11164C>T	c.(11164-11166)Cag>Tag	p.Q3722*	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3722	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)										TGCTGCAGCTGCAGCTGCCTT	0.592																																					p.Q3722X		Atlas-SNP	.											.	MLL2	1173	.	0			c.C11164T						PASS	.						23	28	27					12																	49427324		2182	4289	6471	SO:0001587	stop_gained	8085	exon39			GCAGCTGCAGCTG	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.11164C>T	12.37:g.49427324G>A	ENSP00000301067:p.Gln3722*	42	0	0		38	25	0.657895	NM_003482	O14687	Nonsense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	51	18.529697	0.99906	.	.	ENSG00000167548	ENST00000301067	.	.	.	5.11	5.11	0.69529	.	0.000000	0.33180	N	0.005192	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	17.6784	0.88236	0.0:0.0:1.0:0.0	.	.	.	.	X	3722	.	ENSP00000301067:Q3722X	Q	-	1	0	MLL2	47713591	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	9.317000	0.96327	2.547000	0.85894	0.462000	0.41574	CAG	.	.	none		0.592	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2			A	49427324	G	A	49427324	4	1	41	1	0	0	0	0	0	1	0	0	9630	1328	46	2	5513	2	MLL2	12	49427324	Nonsense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	5580836	49427324	84424571	84	14900											
CELA1	1990	hgsc.bcm.edu	37	chr12	51736400	51736400	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttccagtatggatgcaccacGatcttctgcacactcacgta	10	11	7	13	2	3	0	1	0	2	0	4	2	4	1	2	1	2	4	2	1	2	4			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr12:51736400G>A	ENST00000293636.1	-	4	325	c.285C>T	c.(283-285)atC>atT	p.I95I		NM_001971.5	NP_001962.3	Q9UNI1	CELA1_HUMAN	chymotrypsin-like elastase family, member 1	95	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						GATGCACCACGATCTTCTGCA	0.582																																					p.I95I		Atlas-SNP	.											CELA1,NS,carcinoma,0,1	CELA1	39	1	0			c.C285T						PASS	.						197	146	163					12																	51736400		2203	4300	6503	SO:0001819	synonymous_variant	1990	exon4			CACCACGATCTTC		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.285C>T	12.37:g.51736400G>A		93	0	0		96	16	0.166667	NM_001971	Q5MLF0|Q6DJT0|Q6ISM6	Silent	SNP	ENST00000293636.1	37	CCDS8812.1																																																																																			.	.	none		0.582	CELA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394901.1	NM_001971		A	51736400	G	A	51736400	2	1	41	1	0	0	0	0	0	0	0	1	3212	1048	37	1		1	CELA1	12	51736400	Silent	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	2309076	51736400	82115495	85	14901											
TENC1	23371	hgsc.bcm.edu	37	chr12	53454755	53454756	+	Frame_Shift_Ins	INS	-	-	C																															ccctggcaaggccctcgaggINScccccccgacagcccagatg																								rs376940195|rs372006021		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr12:53454755_53454756insC	ENST00000314250.6	+	20	3355_3356	c.3065_3066insC	c.(3064-3069)ggccccfs	p.GP1022fs	TENC1_ENST00000379902.3_Frame_Shift_Ins_p.GP898fs|TENC1_ENST00000451358.1_Frame_Shift_Ins_p.GP1012fs|TENC1_ENST00000546602.1_Frame_Shift_Ins_p.GP925fs|TENC1_ENST00000552570.1_Frame_Shift_Ins_p.GP1022fs|TENC1_ENST00000314276.3_Frame_Shift_Ins_p.GP1032fs|TENC1_ENST00000549700.1_Frame_Shift_Ins_p.GP957fs	NM_170754.2	NP_736610.2	Q63HR2	TENC1_HUMAN	tensin like C1 domain containing phosphatase (tensin 2)	1022	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						GGCCCTCGAGGCCCCCCCGACA	0.688																																					p.G1032fs		Pindel,Atlas-Indel	.											.	TENC1	148	.	0			c.3095_3096insC						PASS	.																																			SO:0001589	frameshift_variant	23371	exon20			.	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.3072dupC	12.37:g.53454762_53454762dupC	ENSP00000319684:p.Gly1022fs	53	0	.		76	18	0.237	NM_015319	A2VDF2|A2VDF3|A2VDI8|A5PKY4|Q2NL80|Q76MW6|Q7Z5T9|Q8NFF9|Q8NFG0|Q96P25|Q9NT29|Q9UPS7	Frame_Shift_Ins	INS	ENST00000314250.6	37	CCDS8843.1																																																																																			.	.	none		0.688	TENC1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405779.1	NM_170754		C	53454756	-	C	53454755	7	5	41	1	0	1	1	0	0	0	0	0	15773	1203	42	0	3252	0	TENC1	12	53454755	Frame_Shift_Ins	INS	-	TCGA-GS-A9TY-01A-11D-A38X-10	1718355	53454755	80397140	86	14902											
MYL6B	140465	hgsc.bcm.edu	37	chr12	56548600	56548600	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcttttttcttccacagatcGagtttaacaaggaccagctg	10	13	8	10	1	1	1	0	0	1	1	3	3	2	2	2	1	2	3	2	1	2	6			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr12:56548600G>A	ENST00000553066.1	+	3	600	c.178G>A	c.(178-180)Gag>Aag	p.E60K	RP11-603J24.14_ENST00000548731.1_RNA|MYL6B_ENST00000550443.1_Missense_Mutation_p.E60K|MYL6B_ENST00000550152.1_3'UTR|MYL6B_ENST00000552568.1_Missense_Mutation_p.E60K|MYL6B_ENST00000207437.5_Missense_Mutation_p.E60K			P14649	MYL6B_HUMAN	myosin, light chain 6B, alkali, smooth muscle and non-muscle	60					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)|muscle myosin complex (GO:0005859)|myosin complex (GO:0016459)|unconventional myosin complex (GO:0016461)	calcium ion binding (GO:0005509)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			endometrium(2)|kidney(1)|large_intestine(4)	7			OV - Ovarian serous cystadenocarcinoma(18;0.0979)			TCCACAGATCGAGTTTAACAA	0.532																																					p.E60K		Atlas-SNP	.											.	MYL6B	12	.	0			c.G178A						PASS	.						196	194	195					12																	56548600		2203	4300	6503	SO:0001583	missense	140465	exon3			CAGATCGAGTTTA	M31211	CCDS8905.1	12q13.2	2013-01-10	2006-09-29			ENSG00000196465		"Myosins / Light chain", "EF-hand domain containing"	29823	protein-coding gene	gene with protein product	"myosin light chain 1 slow a"	609930	"myosin, light polypeptide 6B, alkali, smooth muscle and non-muscle"			2602161, 2304459	Standard	NM_002475		Approved	MLC1SA	uc001sjs.3	P14649		ENST00000553066.1:c.178G>A	12.37:g.56548600G>A	ENSP00000450385:p.Glu60Lys	114	0	0		151	61	0.403974	NM_001199629		Missense_Mutation	SNP	ENST00000553066.1	37	CCDS8905.1	.	.	.	.	.	.	.	.	.	.	G	14.48	2.549050	0.45383	.	.	ENSG00000196465	ENST00000553066;ENST00000550443;ENST00000207437;ENST00000552568	D;D;D;D	0.85955	-2.05;-2.05;-2.05;-2.05	4.08	3.16	0.36331	.	0.372052	0.29059	N	0.013270	T	0.78451	0.4285	L	0.49126	1.545	0.43907	D	0.996548	P;B	0.38922	0.651;0.256	B;B	0.31245	0.126;0.024	T	0.79067	-0.1955	10	0.72032	D	0.01	-19.8264	11.6215	0.51121	0.0:0.182:0.818:0.0	.	60;60	B4E368;P14649	.;MYL6B_HUMAN	K	60	ENSP00000450385:E60K;ENSP00000446643:E60K;ENSP00000207437:E60K;ENSP00000446965:E60K	ENSP00000207437:E60K	E	+	1	0	MYL6B	54834867	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.257000	0.72480	1.016000	0.39470	0.491000	0.48974	GAG	.	.	none		0.532	MYL6B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407920.2	NM_002475		A	56548600	G	A	56548600	3	1	41	1	0	0	0	0	1	0	0	0	10061	1059	37	1	184	1	MYL6B	12	56548600	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	3093845	56548600	77303295	87	14903											
PCDH17	27253	hgsc.bcm.edu	37	chr13	58208450	58208450	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtgctccccacgctgcagaaCgacaccgcggagctgcaggt	8	5	13	15	4	0	1	0	0	0	1	1	3	1	2	3	2	5	5	3	2	1	0			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr13:58208450C>T	ENST00000377918.3	+	1	1796	c.1770C>T	c.(1768-1770)aaC>aaT	p.N590N		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	590	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(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)		CGCTGCAGAACGACACCGCGG	0.672																																					p.N590N	Melanoma(72;952 1291 1619 12849 33676)	Atlas-SNP	.											.	PCDH17	304	.	0			c.C1770T						PASS	.						33	32	32					13																	58208450		2203	4300	6503	SO:0001819	synonymous_variant	27253	exon1			GCAGAACGACACC	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.1770C>T	13.37:g.58208450C>T		42	0	0		25	10	0.4	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Silent	SNP	ENST00000377918.3	37	CCDS31986.1																																																																																			.	.	none		0.672	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429		T	58208450	C	T	58208450	2	4	41	1	0	0	0	0	0	0	0	1	11521	535	19	1		1	PCDH17	13	58208450	Silent	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10		58208450	56961428	88	14904											
SIX4	51804	hgsc.bcm.edu	37	chr14	61186927	61186927	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgggtccctgaataaaagaaTttccattaaggaagacaggt	15	10	10	6	0	0	3	0	1	0	2	2	4	2	4	2	3	0	0	2	3	6	3			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr14:61186927T>C	ENST00000216513.4	-	2	1159	c.1100A>G	c.(1099-1101)aAt>aGt	p.N367S		NM_017420.4	NP_059116.3	Q9UIU6	SIX4_HUMAN	SIX homeobox 4	367					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)		AATAAAAGAATTTCCATTAAG	0.388																																					p.N367S		Atlas-SNP	.											.	SIX4	69	.	0			c.A1100G						PASS	.						83	80	81					14																	61186927		2203	4300	6503	SO:0001583	missense	51804	exon2			AAAGAATTTCCAT	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.1100A>G	14.37:g.61186927T>C	ENSP00000216513:p.Asn367Ser	154	0	0		142	40	0.28169	NM_017420	Q4QQH5|Q4V764	Missense_Mutation	SNP	ENST00000216513.4	37	CCDS9749.2	.	.	.	.	.	.	.	.	.	.	T	2.699	-0.271504	0.05716	.	.	ENSG00000100625	ENST00000216513;ENST00000554079;ENST00000556952	D;T	0.89746	-2.56;1.13	5.62	4.49	0.54785	.	0.333671	0.31624	N	0.007327	T	0.66587	0.2804	N	0.02916	-0.46	0.28150	N	0.929414	B;B	0.10296	0.003;0.002	B;B	0.08055	0.003;0.001	T	0.57429	-0.7813	10	0.06625	T	0.88	.	3.2835	0.06924	0.0:0.2058:0.2126:0.5816	.	359;367	G3V2N2;Q9UIU6	.;SIX4_HUMAN	S	367;40;359	ENSP00000216513:N367S;ENSP00000451537:N40S	ENSP00000216513:N367S	N	-	2	0	SIX4	60256680	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.575000	0.46025	2.150000	0.67090	0.533000	0.62120	AAT	.	.	none		0.388	SIX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072397.2			C	61186927	T	C	61186927	3	2	41	1	0	0	0	0	1	0	0	0	14364	1493	52	3	1253	3	SIX4	14	61186927	Missense_Mutation	SNP	T	TCGA-GS-A9TY-01A-11D-A38X-10		61186927	46162613	89	14905											
BCL11B	64919	hgsc.bcm.edu	37	chr14	99641823	99641823	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cacttgtagggcttctcgccCgtgtgactgcgccggtgcac	4	10	13	14	4	1	1	0	1	1	0	2	1	1	1	2	2	2	3	2	2	1	3	rs375880436		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr14:99641823C>T	ENST00000357195.3	-	4	1359	c.1350G>A	c.(1348-1350)acG>acA	p.T450T	BCL11B_ENST00000345514.2_Silent_p.T379T|BCL11B_ENST00000443726.2_Silent_p.T256T	NM_001282237.1|NM_138576.2	NP_001269166.1|NP_612808.1	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B (zinc finger protein)	450					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)		GCTTCTCGCCCGTGTGACTGC	0.647			T	TLX3	T-ALL																																p.T450T		Atlas-SNP	.		Dom	yes		14	14q32.1	64919	B-cell CLL/lymphoma 11B  (CTIP2)		L	.	BCL11B	108	.	0			c.G1350A						PASS	.	C	,	1,4403	2.1+/-5.4	0,1,2201	29	29	29		1137,1350	0.4	1	14		29	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	BCL11B	NM_022898.1,NM_138576.2	,	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	,	379/824,450/895	99641823	1,13003	2202	4300	6502	SO:0001819	synonymous_variant	64919	exon4			CTCGCCCGTGTGA	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.1350G>A	14.37:g.99641823C>T		91	0	0		58	38	0.655172	NM_138576	Q9H162	Silent	SNP	ENST00000357195.3	37	CCDS9950.1																																																																																			.	.	weak		0.647	BCL11B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000072332.2	NM_138576		T	99641823	C	T	99641823	2	4	41	1	0	0	0	0	0	0	0	1	1364	639	23	1		1	BCL11B	14	99641823	Silent	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	38454896	99641823	7707717	90	14906											
TJP1	7082	hgsc.bcm.edu	37	chr15	30011279	30011279	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgccctgggtgactaacggCtggctgtttcaaaacatggt	8	11	13	9	1	1	1	1	1	0	0	1	1	1	1	1	4	3	3	1	4	3	2			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr15:30011279C>G	ENST00000346128.6	-	21	3541	c.3067G>C	c.(3067-3069)Gcc>Ccc	p.A1023P	TJP1_ENST00000545208.2_Missense_Mutation_p.A943P|TJP1_ENST00000400011.2_Missense_Mutation_p.A947P|TJP1_ENST00000356107.6_Missense_Mutation_p.A1023P	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	1023					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)		TGACTAACGGCTGGCTGTTTC	0.458																																					p.A1023P	Melanoma(77;681 1843 6309 6570)	Atlas-SNP	.											TJP1,NS,NS,+2,1	TJP1	140	1	0			c.G3067C						PASS	.						194	196	195					15																	30011279		1987	4164	6151	SO:0001583	missense	7082	exon21			TAACGGCTGGCTG		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.3067G>C	15.37:g.30011279C>G	ENSP00000281537:p.Ala1023Pro	198	0	0		137	111	0.810219	NM_003257	B4E3K1|Q2NKP3|Q4ZGJ6	Missense_Mutation	SNP	ENST00000346128.6	37	CCDS42007.1	.	.	.	.	.	.	.	.	.	.	C	9.190	1.025747	0.19512	.	.	ENSG00000104067	ENST00000346128;ENST00000400011;ENST00000545208;ENST00000400007;ENST00000356107	T;T	0.07216	3.21;3.34	5.93	-0.696	0.11287	.	0.381382	0.27429	N	0.019405	T	0.06280	0.0162	L	0.45581	1.43	0.18873	N	0.999988	B;B;B;B	0.12013	0.005;0.001;0.002;0.0	B;B;B;B	0.09377	0.004;0.002;0.002;0.003	T	0.26950	-1.0088	10	0.40728	T	0.16	.	4.3747	0.11265	0.1004:0.5365:0.1958:0.1673	.	1016;943;1023;947	A9CQZ8;Q07157-2;Q07157;G5E9E7	.;.;ZO1_HUMAN;.	P	1023;947;1023;943;943	ENSP00000281537:A1023P;ENSP00000382890:A947P	ENSP00000281537:A1023P	A	-	1	0	TJP1	27798571	0.070000	0.21116	0.219000	0.23793	0.897000	0.52465	-0.263000	0.08670	0.126000	0.18424	0.563000	0.77884	GCC	.	.	none		0.458	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257		G	30011279	C	G	30011279	3	3	41	1	0	0	0	0	1	0	0	0	15944	797	28	4	2211	4	TJP1	15	30011279	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10		30011279	72520113	91	14907											
SEMA6D	80031	hgsc.bcm.edu	37	chr15	48062799	48062799	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tttgggggcattcattgcagGtgtggcagtatactgctatc	7	14	13	7	0	1	0	1	0	0	0	2	0	1	0	0	4	3	5	0	4	3	6			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr15:48062799G>C	ENST00000316364.5	+	19	2478	c.2039G>C	c.(2038-2040)gGt>gCt	p.G680A	SEMA6D_ENST00000354744.4_Missense_Mutation_p.G624A|SEMA6D_ENST00000389433.2_Missense_Mutation_p.G661A|SEMA6D_ENST00000355997.3_3'UTR|SEMA6D_ENST00000358066.4_Missense_Mutation_p.G618A|SEMA6D_ENST00000389432.2_Missense_Mutation_p.G637A|SEMA6D_ENST00000536845.2_Missense_Mutation_p.G680A|SEMA6D_ENST00000537942.1_Missense_Mutation_p.G618A|SEMA6D_ENST00000558816.1_3'UTR|SEMA6D_ENST00000389428.3_Missense_Mutation_p.G605A|SEMA6D_ENST00000558014.1_Missense_Mutation_p.G618A	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	680					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)		TTCATTGCAGGTGTGGCAGTA	0.483																																					p.G680A		Atlas-SNP	.											SEMA6D_ENST00000558014,NS,adenocarcinoma,0,2	SEMA6D	322	2	0			c.G2039C						PASS	.						140	134	136					15																	48062799		2198	4297	6495	SO:0001583	missense	80031	exon19			TTGCAGGTGTGGC	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.2039G>C	15.37:g.48062799G>C	ENSP00000324857:p.Gly680Ala	258	1	0.00387597		173	141	0.815029	NM_153618	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Missense_Mutation	SNP	ENST00000316364.5	37	CCDS32225.1	.	.	.	.	.	.	.	.	.	.	G	20.6	4.021097	0.75275	.	.	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428	T;T;T;T;T;T;T;T	0.72942	-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7;-0.7	6.01	6.01	0.97437	.	0.000000	0.85682	D	0.000000	D	0.84220	0.5424	M	0.65975	2.015	0.80722	D	1	D;D;D;D	0.89917	0.993;0.993;1.0;0.993	P;P;D;P	0.91635	0.822;0.822;0.999;0.822	D	0.83718	0.0191	10	0.62326	D	0.03	.	20.5141	0.99211	0.0:0.0:1.0:0.0	.	605;624;680;618	Q8NFY4-3;Q8NFY4-4;Q8NFY4;Q8NFY4-2	.;.;SEM6D_HUMAN;.	A	618;680;680;661;637;624;618;605	ENSP00000442040:G618A;ENSP00000446152:G680A;ENSP00000324857:G680A;ENSP00000374084:G661A;ENSP00000374083:G637A;ENSP00000346786:G624A;ENSP00000350770:G618A;ENSP00000374079:G605A	ENSP00000324857:G680A	G	+	2	0	SEMA6D	45850091	1.000000	0.71417	0.947000	0.38551	0.934000	0.57294	7.515000	0.81761	2.850000	0.98022	0.655000	0.94253	GGT	.	.	none		0.483	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966		C	48062799	G	C	48062799	3	2	41	1	0	0	0	0	1	0	0	0	14057	1261	44	4	2152	4	SEMA6D	15	48062799	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	18051520	48062799	54468593	92	14908											
IDH3A	3419	hgsc.bcm.edu	37	chr15	78453926	78453926	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tttcttctgtataacaggccCtttgaagaccccaatagcag	11	12	7	11	0	2	2	0	1	2	1	2	2	2	2	3	1	2	2	3	1	5	6			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr15:78453926C>T	ENST00000299518.2	+	5	376	c.293C>T	c.(292-294)cCt>cTt	p.P98L	IDH3A_ENST00000441490.2_5'UTR|IDH3A_ENST00000561366.1_5'Flank|IDH3A_ENST00000558535.1_3'UTR|IDH3A_ENST00000559205.1_Intron|IDH3A_ENST00000558554.1_Intron	NM_005530.2	NP_005521.1	P50213	IDH3A_HUMAN	isocitrate dehydrogenase 3 (NAD+) alpha	98					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						ATAACAGGCCCTTTGAAGACC	0.468																																					p.P98L		Atlas-SNP	.											.	IDH3A	24	.	0			c.C293T						PASS	.						94	86	89					15																	78453926		2196	4293	6489	SO:0001583	missense	3419	exon5			CAGGCCCTTTGAA		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.293C>T	15.37:g.78453926C>T	ENSP00000299518:p.Pro98Leu	63	0	0		45	15	0.333333	NM_005530	D3DW83|Q9H3X0	Missense_Mutation	SNP	ENST00000299518.2	37	CCDS10297.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.253008	0.80135	.	.	ENSG00000166411	ENST00000299518	T	0.71222	-0.55	6.02	6.02	0.97574	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.89646	0.6775	H	0.95539	3.685	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91725	0.5392	10	0.87932	D	0	-13.8159	19.5254	0.95203	0.0:1.0:0.0:0.0	.	98	P50213	IDH3A_HUMAN	L	98	ENSP00000299518:P98L	ENSP00000299518:P98L	P	+	2	0	IDH3A	76240981	1.000000	0.71417	0.997000	0.53966	0.990000	0.78478	7.608000	0.82898	2.857000	0.98124	0.650000	0.86243	CCT	.	.	none		0.468	IDH3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289799.4	NM_005530		T	78453926	C	T	78453926	3	4	41	1	0	0	0	0	1	0	0	0	7505	681	24	2	311	2	IDH3A	15	78453926	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	30391127	78453926	24077466	93	14909											
IFT140	9742	hgsc.bcm.edu	37	chr16	1652418	1652418	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actggggctccaacggagcaCggtgatgtcggctgtgtgtg	6	9	17	9	3	0	1	0	1	0	0	2	2	1	2	1	5	2	3	1	5	1	0	rs146128830	byFrequency	TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr16:1652418C>T	ENST00000426508.2	-	4	685	c.322G>A	c.(322-324)Gtg>Atg	p.V108M	LA16c-395F10.2_ENST00000563162.1_RNA|IFT140_ENST00000439987.2_5'UTR	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	108					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)				CAACGGAGCACGGTGATGTCG	0.582													C|||	14	0.00279553	0.0023	0.0029	5008	,	,		17970	0.0		0.007	False		,,,				2504	0.002				p.V108M		Atlas-SNP	.											IFT140,NS,carcinoma,0,1	IFT140	128	1	0			c.G322A						PASS	.	C	MET/VAL	12,4386	19.1+/-41.9	0,12,2187	110	80	90		322	-1.2	0	16	dbSNP_134	90	81,8519	47.6+/-106.9	0,81,4219	yes	missense	IFT140	NM_014714.3	21	0,93,6406	TT,TC,CC		0.9419,0.2729,0.7155	possibly-damaging	108/1463	1652418	93,12905	2199	4300	6499	SO:0001583	missense	9742	exon4			GGAGCACGGTGAT	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.322G>A	16.37:g.1652418C>T	ENSP00000406012:p.Val108Met	120	0	0		94	38	0.404255	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Missense_Mutation	SNP	ENST00000426508.2	37	CCDS10439.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	11.51	1.660137	0.29515	0.002729	0.009419	ENSG00000187535	ENST00000397417;ENST00000426508;ENST00000439987	T;T	0.60299	0.7;0.2	4.83	-1.19	0.09585	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.456706	0.22233	N	0.062786	T	0.56790	0.2009	M	0.78801	2.425	0.24640	N	0.993577	D	0.59357	0.985	P	0.56042	0.79	T	0.58126	-0.7691	10	0.32370	T	0.25	.	9.8005	0.40761	0.0:0.4051:0.0:0.5949	.	108	Q96RY7	IF140_HUMAN	M	108	ENSP00000380562:V108M;ENSP00000406012:V108M	ENSP00000380562:V108M	V	-	1	0	IFT140	1592419	0.004000	0.15560	0.008000	0.14137	0.004000	0.04260	-0.032000	0.12266	-0.555000	0.06142	0.561000	0.74099	GTG	C|0.993;T|0.007	0.007	strong		0.582	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714		T	1652418	C	T	1652418	3	4	41	1	0	0	0	0	1	0	0	0	7565	536	19	1	4178	1	IFT140	16	1652418	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10		1652418	88702335	94	14910											
CP110	9738	hgsc.bcm.edu	37	chr16	19554242	19554242	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caaaatttaacaaaataactGcagtggcaaaaggatttctt	18	11	6	6	0	1	0	0	0	1	0	1	1	1	1	0	2	3	2	0	2	8	5			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr16:19554242G>C	ENST00000381396.5	+	8	2657	c.2410G>C	c.(2410-2412)Gca>Cca	p.A804P	CCP110_ENST00000396212.2_Missense_Mutation_p.A804P|CCP110_ENST00000396208.2_Missense_Mutation_p.A804P	NM_001199022.1	NP_001185951	O43303	CP110_HUMAN	centriolar coiled coil protein 110kDa	804	Calmodulin-binding.				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						CAAAATAACTGCAGTGGCAAA	0.333																																					p.A804P		Atlas-SNP	.											.	CCP110	57	.	0			c.G2410C						PASS	.						96	97	97					16																	19554242		2197	4300	6497	SO:0001583	missense	9738	exon8			ATAACTGCAGTGG	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.2410G>C	16.37:g.19554242G>C	ENSP00000370803:p.Ala804Pro	163	0	0		183	10	0.0546448	NM_001199022	B7WP23|O43335|Q68DV9|Q8NE13	Missense_Mutation	SNP	ENST00000381396.5	37	CCDS55992.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.534605	0.85812	.	.	ENSG00000103540	ENST00000396212;ENST00000381396;ENST00000396208	T;T;T	0.46819	0.87;0.86;0.87	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	T	0.72684	0.3491	M	0.81497	2.545	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.75614	-0.3257	10	0.87932	D	0	-0.8444	19.7559	0.96291	0.0:0.0:1.0:0.0	.	804;804	O43303;O43303-2	CP110_HUMAN;.	P	804	ENSP00000379515:A804P;ENSP00000370803:A804P;ENSP00000379511:A804P	ENSP00000370803:A804P	A	+	1	0	CCP110	19461743	1.000000	0.71417	0.970000	0.41538	0.899000	0.52679	7.591000	0.82666	2.656000	0.90262	0.655000	0.94253	GCA	.	.	none		0.333	CCP110-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254284.2	NM_014711		C	19554242	G	C	19554242	3	2	41	1	0	0	0	0	1	0	0	0	3790	1319	46	4	2436	4	CP110	16	19554242	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	17901824	19554242	70800511	95	14911											
SCNN1G	6340	hgsc.bcm.edu	37	chr16	23200702	23200702	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	accttggcaggtacagcaccGttcgccaccttctagctgac	8	9	9	15	2	1	1	0	1	1	0	2	1	1	1	4	2	3	5	4	2	2	5	rs147276737	byFrequency	TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr16:23200702G>A	ENST00000300061.2	+	3	471	c.328G>A	c.(328-330)Gtt>Att	p.V110I		NM_001039.3	NP_001030.2	P51170	SCNNG_HUMAN	sodium channel, non-voltage-gated 1, gamma subunit	110					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)	GTACAGCACCGTTCGCCACCT	0.607													G|||	3	0.000599042	0.0	0.0	5008	,	,		17010	0.0		0.0	False		,,,				2504	0.0031				p.V110I		Atlas-SNP	.											.	SCNN1G	82	.	0			c.G328A						PASS	.	G	ILE/VAL	1,4393	2.1+/-5.4	0,1,2196	65	68	67		328	6	0.1	16	dbSNP_134	67	0,8600		0,0,4300	yes	missense	SCNN1G	NM_001039.3	29	0,1,6496	AA,AG,GG		0.0,0.0228,0.0077	benign	110/650	23200702	1,12993	2197	4300	6497	SO:0001583	missense	6340	exon3			AGCACCGTTCGCC	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.328G>A	16.37:g.23200702G>A	ENSP00000300061:p.Val110Ile	27	0	0		25	13	0.52	NM_001039	P78437|Q6PCC2|Q93023|Q93024|Q93025|Q93026|Q93027|Q96TD2	Missense_Mutation	SNP	ENST00000300061.2	37	CCDS10608.1	.	.	.	.	.	.	.	.	.	.	G	2.346	-0.349973	0.05173	2.28E-4	0.0	ENSG00000166828	ENST00000300061	T	0.63096	-0.02	6.04	6.04	0.98038	.	0.247869	0.34603	N	0.003824	T	0.39009	0.1062	N	0.11927	0.2	0.27873	N	0.939975	B	0.24882	0.113	B	0.15484	0.013	T	0.20472	-1.0274	10	0.11485	T	0.65	-2.2978	10.7521	0.46216	0.0889:0.0:0.9111:0.0	.	110	P51170	SCNNG_HUMAN	I	110	ENSP00000300061:V110I	ENSP00000300061:V110I	V	+	1	0	SCNN1G	23108203	0.998000	0.40836	0.088000	0.20740	0.251000	0.25915	3.219000	0.51200	2.873000	0.98535	0.561000	0.74099	GTT	G|1.000;A|0.000	0.000	weak		0.607	SCNN1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254496.1	NM_001039		A	23200702	G	A	23200702	3	1	41	1	0	0	0	0	1	0	0	0	13945	1145	40	1	334	1	SCNN1G	16	23200702	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	3646460	23200702	67154051	96	14912											
IRF8	3394	hgsc.bcm.edu	37	chr16	85942659	85942659	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaaccagccacttggaagAcgaggttacgctgtgctttg	9	10	12	10	2	0	2	0	1	0	1	0	4	0	3	2	2	4	3	2	2	3	3	rs397514711		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr16:85942659A>G	ENST00000268638.5	+	3	660	c.238A>G	c.(238-240)Acg>Gcg	p.T80A	IRF8_ENST00000563180.1_Missense_Mutation_p.T80A	NM_002163.2	NP_002154.1	Q02556	IRF8_HUMAN	interferon regulatory factor 8	80			T -> A (in IMD32A; impairs transcriptional activity by disrupting the interaction between IRF8 and DNA). {ECO:0000269|PubMed:21524210}.		cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	24		Prostate(104;0.0771)				CACTTGGAAGACGAGGTTACG	0.458																																					p.T80A		Atlas-SNP	.											IRF8,NS,neuroblastoma,-1,1	IRF8	65	1	0			c.A238G						scavenged	.						74	76	75					16																	85942659		2198	4300	6498	SO:0001583	missense	3394	exon3			TGGAAGACGAGGT	M91196	CCDS10956.1	16q24.1	2014-09-17	2004-11-12	2004-11-12	ENSG00000140968	ENSG00000140968			5358	protein-coding gene	gene with protein product		601565	"interferon consensus sequence binding protein 1"	ICSBP1		1460054, 11997525	Standard	NM_002163		Approved	IRF-8, ICSBP	uc002fjh.3	Q02556	OTTHUMG00000137648	ENST00000268638.5:c.238A>G	16.37:g.85942659A>G	ENSP00000268638:p.Thr80Ala	88	1	0.0113636		101	64	0.633663	NM_002163	A0AV82	Missense_Mutation	SNP	ENST00000268638.5	37	CCDS10956.1	.	.	.	.	.	.	.	.	.	.	A	19.11	3.763543	0.69878	.	.	ENSG00000140968	ENST00000268638	D	0.97688	-4.49	4.88	4.88	0.63580	Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (4);	0.046894	0.85682	D	0.000000	D	0.97791	0.9275	L	0.45470	1.425	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.91635	0.999;0.996	D	0.97383	0.9984	10	0.30854	T	0.27	-15.9347	14.7789	0.69751	1.0:0.0:0.0:0.0	.	80;80	B2R8V7;Q02556	.;IRF8_HUMAN	A	80	ENSP00000268638:T80A	ENSP00000268638:T80A	T	+	1	0	IRF8	84500160	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	8.780000	0.91799	1.973000	0.57446	0.397000	0.26171	ACG	.	.	none		0.458	IRF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269100.2	NM_002163		G	85942659	A	G	85942659	3	3	41	1	0	0	0	0	1	0	0	0	7845	275	10	3	244	3	IRF8	16	85942659	Missense_Mutation	SNP	A	TCGA-GS-A9TY-01A-11D-A38X-10	62741957	85942659	4412094	97	14913											
ANKFY1	51479	hgsc.bcm.edu	37	chr17	4071128	4071128	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aaatgttgcaaacccgcacaGgcttgttcagatcaaacttt	13	11	7	10	1	2	1	2	0	0	1	2	1	2	1	1	1	3	5	1	1	3	4			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr17:4071128G>A	ENST00000341657.4	-	25	3490	c.3455C>T	c.(3454-3456)cCt>cTt	p.P1152L	CYB5D2_ENST00000573984.1_Intron|ANKFY1_ENST00000574367.1_Missense_Mutation_p.P1153L|ANKFY1_ENST00000570535.1_Missense_Mutation_p.P1194L	NM_016376.3	NP_057460.3	Q9P2R3	ANFY1_HUMAN	ankyrin repeat and FYVE domain containing 1	1152					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						AACCCGCACAGGCTTGTTCAG	0.502																																					p.P1194L		Atlas-SNP	.											.	ANKFY1	81	.	0			c.C3581T						PASS	.						62	67	65					17																	4071128		1883	4107	5990	SO:0001583	missense	51479	exon25			CGCACAGGCTTGT	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.3455C>T	17.37:g.4071128G>A	ENSP00000343362:p.Pro1152Leu	50	0	0		37	27	0.72973	NM_001257999	A8KA65|Q5RKV4|Q9ULG5	Missense_Mutation	SNP	ENST00000341657.4	37		.	.	.	.	.	.	.	.	.	.	G	27.0	4.788564	0.90367	.	.	ENSG00000185722	ENST00000341657;ENST00000535427	.	.	.	4.88	4.88	0.63580	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	0.83737	0.5319	M	0.85542	2.76	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	0.86167	0.1597	9	0.72032	D	0.01	-14.4331	17.5598	0.87902	0.0:0.0:1.0:0.0	.	1094;1152;1153;1194	F5H754;Q9P2R3;Q9P2R3-2;Q9P2R3-4	.;ANFY1_HUMAN;.;.	L	1153;1094	.	ENSP00000343362:P1153L	P	-	2	0	ANKFY1	4017877	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	9.567000	0.98161	2.697000	0.92050	0.563000	0.77884	CCT	.	.	none		0.502	ANKFY1-008	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000438702.1	NM_016376		A	4071128	G	A	4071128	3	1	41	1	0	0	0	0	1	0	0	0	626	1000	35	2	58	2	ANKFY1	17	4071128	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10		4071128	77124082	98	14914											
TP53	7157	hgsc.bcm.edu	37	chr17	7577586	7577586	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tacacatgtagttgtagtggAtggtggtacagtcagagcca	11	11	13	6	0	1	1	1	0	0	1	1	2	1	2	1	3	3	4	1	3	4	5	rs587781589		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr17:7577586A>G	ENST00000269305.4	-	7	884	c.695T>C	c.(694-696)aTc>aCc	p.I232T	TP53_ENST00000413465.2_Missense_Mutation_p.I232T|TP53_ENST00000455263.2_Missense_Mutation_p.I232T|TP53_ENST00000359597.4_Missense_Mutation_p.I232T|TP53_ENST00000420246.2_Missense_Mutation_p.I232T|TP53_ENST00000445888.2_Missense_Mutation_p.I232T|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	232	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 sporadic cancers; somatic mutation).|I -> N (in sporadic cancers; somatic mutation).|I -> S (in sporadic cancers; somatic mutation; does not induce SNAI1 degradation).|I -> T (in sporadic cancers; somatic mutation).|I -> 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.I232T(8)|p.I232N(6)|p.?(5)|p.I232_H233insG(3)|p.I232S(2)|p.T230fs*6(2)|p.C229_H233delCTTIH(2)|p.I232_Y236delIHYNY(1)|p.T230_Y234delTTIHY(1)|p.C229_I232del(1)|p.I139T(1)|p.V225fs*23(1)|p.D228fs*12(1)|p.I139_H140insG(1)|p.I232fs*5(1)|p.S227_I232delSDCTTI(1)|p.I232fs*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)	GTTGTAGTGGATGGTGGTACA	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.I232T	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,0,67	TP53	33396	67	46	Substitution - Missense(17)|Whole gene deletion(8)|Deletion - In frame(6)|Deletion - Frameshift(5)|Unknown(5)|Insertion - In frame(4)|Insertion - Frameshift(1)	biliary_tract(5)|haematopoietic_and_lymphoid_tissue(5)|upper_aerodigestive_tract(4)|endometrium(4)|breast(4)|NS(4)|bone(4)|lung(3)|oesophagus(3)|liver(3)|stomach(2)|central_nervous_system(2)|ovary(2)|thymus(1)	c.T695C						PASS	.						113	90	98					17																	7577586		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;	TAGTGGATGGTGG	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.695T>C	17.37:g.7577586A>G	ENSP00000269305:p.Ile232Thr	76	0	0		40	34	0.85	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	37	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	A	23.1	4.370793	0.82573	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99807	-6.85;-6.85;-6.85;-6.85;-6.85;-6.85;-6.85;-6.85	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);	0.174276	0.51477	D	0.000096	D	0.99697	0.9885	M	0.85630	2.765	0.53005	D	0.99996	B;B;B;B;B;B	0.32781	0.327;0.032;0.106;0.12;0.21;0.384	P;B;B;P;P;B	0.53401	0.601;0.065;0.193;0.725;0.614;0.153	D	0.96603	0.9446	10	0.72032	D	0.01	-25.5076	12.3101	0.54924	1.0:0.0:0.0:0.0	.	232;232;139;232;232;232	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	T	232;232;232;232;232;232;221;139;100;139	ENSP00000410739:I232T;ENSP00000352610:I232T;ENSP00000269305:I232T;ENSP00000398846:I232T;ENSP00000391127:I232T;ENSP00000391478:I232T;ENSP00000425104:I100T;ENSP00000423862:I139T	ENSP00000269305:I232T	I	-	2	0	TP53	7518311	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	9.061000	0.93913	2.074000	0.62210	0.379000	0.24179	ATC	.	.	none		0.552	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		G	7577586	A	G	7577586	3	3	41	1	0	0	0	0	1	0	0	0	16396	333	12	3	595	3	TP53	17	7577586	Missense_Mutation	SNP	A	TCGA-GS-A9TY-01A-11D-A38X-10	3506458	7577586	73617624	99	14915											
CHD3	1107	hgsc.bcm.edu	37	chr17	7798425	7798425	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcattgtctaaaccctccccTgcctgacattcccaatggtg	8	12	6	15	0	2	1	1	1	1	0	4	1	4	1	5	1	2	0	5	1	3	3			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr17:7798425T>C	ENST00000330494.7	+	9	1610	c.1460T>C	c.(1459-1461)cTg>cCg	p.L487P	CHD3_ENST00000358181.4_Missense_Mutation_p.L487P|CHD3_ENST00000380358.4_Missense_Mutation_p.L546P	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	487					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)				AACCCTCCCCTGCCTGACATT	0.557																																					p.L546P		Atlas-SNP	.											.	CHD3	169	.	0			c.T1637C						PASS	.						257	184	209					17																	7798425		2203	4300	6503	SO:0001583	missense	1107	exon9			CTCCCCTGCCTGA	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.1460T>C	17.37:g.7798425T>C	ENSP00000332628:p.Leu487Pro	80	0	0		51	37	0.72549	NM_001005271	D3DTQ9|E9PG89|Q9Y4I0	Missense_Mutation	SNP	ENST00000330494.7	37	CCDS32554.1	.	.	.	.	.	.	.	.	.	.	T	12.90	2.077973	0.36662	.	.	ENSG00000170004	ENST00000380358;ENST00000358181;ENST00000330494	T;T;T	0.55930	0.49;0.49;0.49	5.01	5.01	0.66863	Zinc finger, PHD-finger (2);Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, PHD-type, conserved site (1);Zinc finger, RING-type (1);Zinc finger, PHD-type (1);Chromo domain-like (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.32231	N	0.006382	T	0.80844	0.4701	H	0.96365	3.81	0.80722	D	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.91635	0.998;0.999;0.999	D	0.87113	0.2186	10	0.87932	D	0	-13.9037	14.5551	0.68094	0.0:0.0:0.0:1.0	.	487;487;546	Q12873-2;Q12873;E9PG89	.;CHD3_HUMAN;.	P	546;487;487	ENSP00000369716:L546P;ENSP00000350907:L487P;ENSP00000332628:L487P	ENSP00000332628:L487P	L	+	2	0	CHD3	7739150	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.868000	0.87116	2.110000	0.64415	0.459000	0.35465	CTG	.	.	none		0.557	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273		C	7798425	T	C	7798425	3	2	41	1	0	0	0	0	1	0	0	0	3328	1580	55	3	1775	3	CHD3	17	7798425	Missense_Mutation	SNP	T	TCGA-GS-A9TY-01A-11D-A38X-10	220839	7798425	73396785	100	14916											
DRG2	1819	hgsc.bcm.edu	37	chr17	18003008	18003008	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctgacgtcatcatcatgatGctggatgccaccaagggaga	11	8	12	10	1	3	3	3	2	0	1	3	5	3	4	2	2	2	2	2	2	1	0			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr17:18003008G>A	ENST00000225729.3	+	5	576	c.438G>A	c.(436-438)atG>atA	p.M146I	DRG2_ENST00000395726.4_Missense_Mutation_p.M146I|DRG2_ENST00000583355.1_Intron	NM_001388.4	NP_001379.1	P55039	DRG2_HUMAN	developmentally regulated GTP binding protein 2	146	OBG-type G. {ECO:0000255|PROSITE- ProRule:PRU01047}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	14	all_neural(463;0.228)					TCATCATGATGCTGGATGCCA	0.617																																					p.M146I		Atlas-SNP	.											.	DRG2	27	.	0			c.G438A						PASS	.						56	41	46					17																	18003008		2203	4300	6503	SO:0001583	missense	1819	exon5			CATGATGCTGGAT	X80754	CCDS11191.1	17p13-p12	2008-07-18	2001-11-28		ENSG00000108591	ENSG00000108591			3030	protein-coding gene	gene with protein product		602986	"developmentally regulated GTP-binding protein 2"			9605870, 7929244	Standard	NM_001388		Approved		uc002gsh.2	P55039	OTTHUMG00000059399	ENST00000225729.3:c.438G>A	17.37:g.18003008G>A	ENSP00000225729:p.Met146Ile	146	0	0		67	52	0.776119	NM_001388	B2R8G5|Q53Y50|Q9BWB2	Missense_Mutation	SNP	ENST00000225729.3	37	CCDS11191.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.708499	0.68615	.	.	ENSG00000108591	ENST00000395726;ENST00000225729	T;T	0.15834	2.39;2.39	5.6	5.6	0.85130	Small GTP-binding protein domain (1);GTP1/OBG (1);GTP-binding domain, HSR1-related (1);	0.000000	0.85682	D	0.000000	T	0.15262	0.0368	N	0.13098	0.295	0.80722	D	1	B;B	0.16802	0.019;0.019	B;B	0.28709	0.093;0.056	T	0.10132	-1.0643	10	0.52906	T	0.07	-40.0835	19.5973	0.95546	0.0:0.0:1.0:0.0	.	146;146	A8MZF9;P55039	.;DRG2_HUMAN	I	146	ENSP00000379076:M146I;ENSP00000225729:M146I	ENSP00000225729:M146I	M	+	3	0	DRG2	17943733	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.744000	0.98853	2.640000	0.89533	0.467000	0.42956	ATG	.	.	none		0.617	DRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132075.3	NM_001388		A	18003008	G	A	18003008	3	1	41	1	0	0	0	0	1	0	0	0	4764	1319	46	2	456	2	DRG2	17	18003008	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	10204583	18003008	63192202	101	14917											
SMCR8	140775	hgsc.bcm.edu	37	chr17	18220580	18220580	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aatctgacagccaggcaagcCtcacagtaccattgagcccc	12	6	8	15	0	2	2	1	2	1	0	2	2	2	2	5	1	4	2	5	1	3	2	rs113043428		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr17:18220580C>T	ENST00000406438.3	+	1	1957	c.1477C>T	c.(1477-1479)Ctc>Ttc	p.L493F	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	493						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						CCAGGCAAGCCTCACAGTACC	0.517																																					p.L493F		Atlas-SNP	.											.	SMCR8	62	.	0			c.C1477T						PASS	.						58	61	60					17																	18220580		2203	4300	6503	SO:0001583	missense	140775	exon1			GCAAGCCTCACAG	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.1477C>T	17.37:g.18220580C>T	ENSP00000385025:p.Leu493Phe	53	0	0		29	24	0.827586	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Missense_Mutation	SNP	ENST00000406438.3	37	CCDS11195.2	.	.	.	.	.	.	.	.	.	.	C	15.01	2.705015	0.48412	.	.	ENSG00000176994	ENST00000406438	T	0.26223	1.75	5.73	4.68	0.58851	.	0.165285	0.39020	N	0.001492	T	0.30978	0.0782	L	0.32530	0.975	0.34570	D	0.713376	D	0.71674	0.998	P	0.61940	0.896	T	0.32824	-0.9892	10	0.44086	T	0.13	-37.0014	6.4655	0.21980	0.0:0.7155:0.0:0.2845	.	493	Q8TEV9	SMCR8_HUMAN	F	493	ENSP00000385025:L493F	ENSP00000385025:L493F	L	+	1	0	SMCR8	18161305	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	1.932000	0.40143	2.700000	0.92200	0.655000	0.94253	CTC	C|0.500;T|0.500	0.500	weak		0.517	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775		T	18220580	C	T	18220580	3	4	41	1	0	0	0	0	1	0	0	0	14807	681	24	2	1479	2	SMCR8	17	18220580	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	217572	18220580	62974630	102	14918											
CWC25	54883	hgsc.bcm.edu	37	chr17	36971290	36971290	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcgccccagcaggtactcGtcacggttcaccatcccacc	7	6	10	18	3	2	0	2	0	0	0	4	0	3	0	5	3	2	3	5	3	1	2	rs202146970		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr17:36971290G>A	ENST00000225428.5	-	3	549	c.252C>T	c.(250-252)gaC>gaT	p.D84D	CWC25_ENST00000536127.1_Silent_p.D21D	NM_017748.3	NP_060218.1	Q9NXE8	CWC25_HUMAN	CWC25 spliceosome-associated protein homolog (S. cerevisiae)	84										central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	14						GCAGGTACTCGTCACGGTTCA	0.463																																					p.D84D		Atlas-SNP	.											.	CWC25	24	.	0			c.C252T						PASS	.						134	135	135					17																	36971290		1907	4114	6021	SO:0001819	synonymous_variant	54883	exon3			GTACTCGTCACGG	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.252C>T	17.37:g.36971290G>A		72	0	0		112	93	0.830357	NM_017748	A0JLM3|Q68DK5	Silent	SNP	ENST00000225428.5	37	CCDS45663.1																																																																																			G|0.998;A|0.002	0.002	weak		0.463	CWC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442186.6	NM_017748		A	36971290	G	A	36971290	2	1	41	1	0	0	0	0	0	0	0	1	4071	1136	40	1		1	CWC25	17	36971290	Silent	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	18750710	36971290	44223920	103	14919											
BRCA1	672	hgsc.bcm.edu	37	chr17	41234477	41234477	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcaagggcagaagagtcaCttatgatggaagggtagctg	12	8	14	7	0	2	3	2	1	0	2	2	4	2	4	1	3	1	3	1	3	5	2	rs80357790		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr17:41234477C>T	ENST00000357654.3	-	12	4419	c.4301G>A	c.(4300-4302)aGt>aAt	p.S1434N	BRCA1_ENST00000309486.4_Missense_Mutation_p.S1138N|BRCA1_ENST00000352993.3_Missense_Mutation_p.S292N|BRCA1_ENST00000354071.3_Missense_Mutation_p.S1434N|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000471181.2_Missense_Mutation_p.S1434N|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000493795.1_Missense_Mutation_p.S1387N|BRCA1_ENST00000351666.3_Missense_Mutation_p.S251N|BRCA1_ENST00000468300.1_Missense_Mutation_p.S331N|BRCA1_ENST00000346315.3_Missense_Mutation_p.S1434N|BRCA1_ENST00000491747.2_Missense_Mutation_p.S331N	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	1434					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)		AGAAGAGTCACTTATGATGGA	0.438			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.S1434N		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	BRCA1,colon,carcinoma,+1,1	BRCA1	304	1	0			c.G4301A	GRCh37	CI992787	BRCA1	I	rs80357790	PASS	.						231	200	211					17																	41234477		2203	4300	6503	SO:0001583	missense	672	exon12	Familial Cancer Database		GAGTCACTTATGA	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.4301G>A	17.37:g.41234477C>T	ENSP00000350283:p.Ser1434Asn	135	0	0		113	67	0.59292	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	37	CCDS11453.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.24|13.24	2.177284|2.177284	0.38413|0.38413	.|.	.|.	ENSG00000012048|ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000354071;ENST00000352993;ENST00000346315;ENST00000351666;ENST00000309486;ENST00000468300;ENST00000393691;ENST00000471181;ENST00000493795;ENST00000491747;ENST00000478531;ENST00000484087;ENST00000493919;ENST00000487825|ENST00000461574	T;T;T;T;T;T;T;T;T;T;T;T;T;T|.	0.56444|.	0.46;0.46;0.46;0.46;0.46;0.46;0.46;0.46;0.46;0.46;0.46;0.46;0.46;0.46|.	5.36|5.36	-0.256|-0.256	0.12984|0.12984	.|.	1.181740|.	0.06245|.	N|.	0.691021|.	T|T	0.15046|0.15046	0.0363|0.0363	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	B;B;B;B;B;B;B;B|.	0.25007|.	0.023;0.026;0.007;0.116;0.007;0.003;0.007;0.005|.	B;B;B;B;B;B;B;B|.	0.26310|.	0.006;0.022;0.003;0.068;0.006;0.006;0.006;0.014|.	T|T	0.27297|0.27297	-1.0078|-1.0078	10|5	0.87932|.	D|.	0|.	0.1751|0.1751	4.5419|4.5419	0.12061|0.12061	0.0744:0.3923:0.3021:0.2313|0.0744:0.3923:0.3021:0.2313	.|.	330;284;330;331;331;1434;1434;1434|.	E7EUM2;B4DES0;E7ETR2;P38398-3;Q6IN79;E9PFC7;P38398;P38398-2|.	.;.;.;.;.;.;BRCA1_HUMAN;.|.	N|M	1434;1434;1434;292;1434;251;1138;331;284;1434;1387;330;330;205;284;206|199	ENSP00000350283:S1434N;ENSP00000326002:S1434N;ENSP00000312236:S292N;ENSP00000246907:S1434N;ENSP00000338007:S251N;ENSP00000310938:S1138N;ENSP00000417148:S331N;ENSP00000377294:S284N;ENSP00000418960:S1434N;ENSP00000418775:S1387N;ENSP00000420412:S330N;ENSP00000419481:S205N;ENSP00000418819:S284N;ENSP00000418212:S206N|.	ENSP00000310938:S1138N|.	S|V	-|-	2|1	0|0	BRCA1|BRCA1	38488003|38488003	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.169000|0.169000	0.22640|0.22640	-0.157000|-0.157000	0.10085|0.10085	-0.122000|-0.122000	0.11766|0.11766	-0.133000|-0.133000	0.14855|0.14855	AGT|GTG	.	.	none		0.438	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		T	41234477	C	T	41234477	3	4	41	1	0	0	0	0	1	0	0	0	1500	565	20	2	1408	2	BRCA1	17	41234477	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	4263187	41234477	39960733	104	14920											
HOXB5	3215	hgsc.bcm.edu	37	chr17	46669811	46669811	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcccttttcccgtccggcccGgtcatatctggagcagatag	6	10	11	14	3	2	1	1	0	1	1	4	2	4	2	4	3	1	1	4	3	2	4	rs201570571		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr17:46669811G>A	ENST00000239151.5	-	2	848	c.570C>T	c.(568-570)acC>acT	p.T190T	HOXB-AS3_ENST00000465846.2_RNA|HOXB-AS3_ENST00000474040.1_RNA|HOXB3_ENST00000476342.1_5'Flank|HOXB-AS3_ENST00000467155.2_RNA|HOXB-AS3_ENST00000487849.3_RNA|HOXB3_ENST00000460160.1_5'Flank|HOXB3_ENST00000552000.2_Intron|HOXB-AS3_ENST00000492897.3_RNA|HOXB-AS3_ENST00000480872.1_RNA|HOXB-AS3_ENST00000476204.1_RNA|HOXB-AS3_ENST00000429755.4_RNA|HOXB3_ENST00000498678.1_5'Flank|HOXB3_ENST00000472863.1_5'Flank	NM_002147.3	NP_002138.1	P09067	HXB5_HUMAN	homeobox B5	190					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						CGTCCGGCCCGGTCATATCTG	0.642																																					p.T190T		Atlas-SNP	.											.	HOXB5	20	.	0			c.C570T						PASS	.						37	38	37					17																	46669811		2203	4300	6503	SO:0001819	synonymous_variant	3215	exon2			CGGCCCGGTCATA		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.570C>T	17.37:g.46669811G>A		81	0	0		60	29	0.483333	NM_002147	B2RC69|P09069|Q17RP4	Silent	SNP	ENST00000239151.5	37	CCDS11530.1																																																																																			G|1.000;C|0.000	.	alt		0.642	HOXB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358148.2			A	46669811	G	A	46669811	2	1	41	1	0	0	0	0	0	0	0	1	7313	1103	39	1		1	HOXB5	17	46669811	Silent	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	5435334	46669811	34525399	105	14921											
EXOC7	23265	hgsc.bcm.edu	37	chr17	74093984	74093984	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcctgggcctccagatcaTcgtcaccactgatcagatcc	8	9	7	17	1	3	3	3	1	0	2	7	3	6	3	6	1	0	0	6	1	0	0			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr17:74093984T>A	ENST00000335146.7	-	5	586	c.533A>T	c.(532-534)gAt>gTt	p.D178V	EXOC7_ENST00000332065.5_Missense_Mutation_p.D178V|EXOC7_ENST00000589210.1_Missense_Mutation_p.D178V|EXOC7_ENST00000607838.1_Missense_Mutation_p.D178V|EXOC7_ENST00000467929.2_Missense_Mutation_p.D137V|EXOC7_ENST00000411744.2_Missense_Mutation_p.D178V|EXOC7_ENST00000405575.4_Missense_Mutation_p.D178V			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7	178					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)			CTCCAGATCATCGTCACCACT	0.622																																					p.D178V		Atlas-SNP	.											.	EXOC7	47	.	0			c.A533T						PASS	.						118	99	105					17																	74093984		2203	4300	6503	SO:0001583	missense	23265	exon5			AGATCATCGTCAC	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.533A>T	17.37:g.74093984T>A	ENSP00000334100:p.Asp178Val	77	0	0		120	45	0.375	NM_001145298	B5MC69|B8XXP2|Q8ND93|Q8WV91|Q96FF0|Q9H8C3|Q9H9X3|Q9HA32	Missense_Mutation	SNP	ENST00000335146.7	37	CCDS45782.1	.	.	.	.	.	.	.	.	.	.	T	18.99	3.739769	0.69304	.	.	ENSG00000182473	ENST00000332065;ENST00000351709;ENST00000405575;ENST00000335146;ENST00000357231;ENST00000425372;ENST00000411744;ENST00000405068;ENST00000420116	.	.	.	4.99	4.99	0.66335	Cullin repeat-like-containing domain (1);	0.157795	0.56097	D	0.000037	T	0.50956	0.1646	L	0.34521	1.04	0.80722	D	1	B;B;B;B;P;B;P;B	0.48089	0.04;0.001;0.007;0.244;0.675;0.043;0.905;0.073	B;B;B;B;B;B;P;B	0.50270	0.233;0.007;0.037;0.224;0.228;0.117;0.636;0.18	T	0.49123	-0.8972	9	0.38643	T	0.18	-16.317	13.4177	0.60979	0.0:0.0:0.0:1.0	.	178;178;137;137;178;178;178;178	Q9UPT5-5;Q9UPT5-6;B4DJ07;F5H1P1;Q9UPT5-4;Q9UPT5;Q9UPT5-2;Q9UPT5-1	.;.;.;.;.;EXOC7_HUMAN;.;.	V	178;98;178;178;178;137;178;178;63	.	ENSP00000333806:D178V	D	-	2	0	EXOC7	71605579	1.000000	0.71417	0.266000	0.24541	0.420000	0.31355	5.760000	0.68793	2.101000	0.63845	0.460000	0.39030	GAT	.	.	none		0.622	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	NM_015219		A	74093984	T	A	74093984	3	1	41	1	0	0	0	0	1	0	0	0	5312	1435	50	5	1738	5	EXOC7	17	74093984	Missense_Mutation	SNP	T	TCGA-GS-A9TY-01A-11D-A38X-10	27424173	74093984	7101226	106	14922											
FAM100B	283991	hgsc.bcm.edu	37	chr17	74262008	74262008	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	accgcgctgagcacgttcttCcaagaaaccaacattcccaa	13	7	6	15	3	1	2	0	1	1	1	3	2	3	2	4	0	3	3	4	0	4	3			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr17:74262008C>T	ENST00000327490.6	+	2	445	c.141C>T	c.(139-141)ttC>ttT	p.F47F	UBALD2_ENST00000589240.1_5'UTR	NM_182565.3	NP_872371.1	Q8IYN6	UBAD2_HUMAN	UBA-like domain containing 2	47																	GCACGTTCTTCCAAGAAACCA	0.701																																					p.F47F		Atlas-SNP	.											.	.	.	.	0			c.C141T						PASS	.						31	28	29					17																	74262008		2199	4297	6496	SO:0001819	synonymous_variant	283991	exon2			GTTCTTCCAAGAA		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.141C>T	17.37:g.74262008C>T		62	0	0		57	10	0.175439	NM_182565		Silent	SNP	ENST00000327490.6	37	CCDS11742.1																																																																																			.	.	none		0.701	UBALD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255920.1	NM_182565		T	74262008	C	T	74262008	2	4	41	1	0	0	0	0	0	0	0	1	5384	854	30	2		2	FAM100B	17	74262008	Silent	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	168024	74262008	6933202	107	14923											
CCDC40	55036	hgsc.bcm.edu	37	chr17	78032381	78032381	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacatgcgtgacgacatccgCgtgatgacacaagtggtaaa	13	7	12	9	4	0	3	0	3	0	0	1	5	1	3	1	1	1	1	1	1	3	1	rs375199947		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr17:78032381C>T	ENST00000397545.4	+	8	1275	c.1248C>T	c.(1246-1248)cgC>cgT	p.R416R	CCDC40_ENST00000269318.5_Silent_p.R416R|CCDC40_ENST00000374877.3_Silent_p.R416R|CCDC40_ENST00000374876.4_Silent_p.R416R	NM_017950.3	NP_060420.2	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	416					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)			ACGACATCCGCGTGATGACAC	0.532													C|||	1	0.000199681	0.0	0.0014	5008	,	,		21045	0.0		0.0	False		,,,				2504	0.0				p.R416R		Atlas-SNP	.											.	CCDC40	198	.	0			c.C1248T						PASS	.	C		1,4213		0,1,2106	67	71	70		1248	-7.1	0	17		70	4,8450		0,4,4223	no	coding-synonymous	CCDC40	NM_017950.3		0,5,6329	TT,TC,CC		0.0473,0.0237,0.0395		416/1143	78032381	5,12663	2107	4227	6334	SO:0001819	synonymous_variant	55036	exon8			CATCCGCGTGATG	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.1248C>T	17.37:g.78032381C>T		74	0	0		84	48	0.571429	NM_017950	A8MTD2|C9JTI9|C9JTJ0|C9JXW1|Q6PE47|Q9HCD2|Q9NWL5	Silent	SNP	ENST00000397545.4	37	CCDS42395.1																																																																																			.	.	weak		0.532	CCDC40-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256005.2	XM_371082		T	78032381	C	T	78032381	2	4	41	1	0	0	0	0	0	0	0	1	2814	755	27	1		1	CCDC40	17	78032381	Silent	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	3770373	78032381	3162829	108	14924											
KIAA1468	57614	hgsc.bcm.edu	37	chr18	59936160	59936160	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccccatttatgcaacaggAgtccttacgtgttatattca	10	14	7	10	1	1	0	1	0	0	0	3	1	3	1	3	1	3	2	3	1	5	6			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr18:59936160A>T	ENST00000398130.2	+	20	2971	c.2739A>T	c.(2737-2739)ggA>ggT	p.G913G	KIAA1468_ENST00000256858.6_Silent_p.G913G	NM_020854.3	NP_065905.2	Q9P260	K1468_HUMAN	KIAA1468	913										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)				ATGCAACAGGAGTCCTTACGT	0.318																																					p.G913G		Atlas-SNP	.											.	KIAA1468	93	.	0			c.A2739T						PASS	.						48	49	48					18																	59936160		2203	4298	6501	SO:0001819	synonymous_variant	57614	exon20			AACAGGAGTCCTT	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.2739A>T	18.37:g.59936160A>T		521	0	0		285	216	0.757895	NM_020854		Silent	SNP	ENST00000398130.2	37	CCDS11979.2																																																																																			.	.	none		0.318	KIAA1468-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256187.1	NM_020854		T	59936160	A	T	59936160	2	4	41	1	0	0	0	0	0	0	0	1	8245	291	11	5		5	KIAA1468	18	59936160	Silent	SNP	A	TCGA-GS-A9TY-01A-11D-A38X-10		59936160	18141088	109	14925											
ZADH2	284273	hgsc.bcm.edu	37	chr18	72914061	72914061	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accagcagggtaagatactcGggtttcactgagggcactgg	10	8	14	9	1	1	2	1	1	0	1	2	2	1	2	1	4	2	4	1	4	2	3	rs370732101		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr18:72914061G>A	ENST00000322342.3	-	2	733	c.444C>T	c.(442-444)ccC>ccT	p.P148P	ZADH2_ENST00000537114.2_Silent_p.P25P	NM_175907.4	NP_787103.1	Q8N4Q0	ZADH2_HUMAN	zinc binding alcohol dehydrogenase domain containing 2	148						mitochondrion (GO:0005739)|peroxisome (GO:0005777)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)	p.P148P(1)		endometrium(3)|large_intestine(3)|lung(8)|skin(1)	15		Esophageal squamous(42;0.131)|Prostate(75;0.155)		READ - Rectum adenocarcinoma(2;0.0276)|BRCA - Breast invasive adenocarcinoma(31;0.216)		TAAGATACTCGGGTTTCACTG	0.527													G|||	1	0.000199681	0.0	0.0014	5008	,	,		19496	0.0		0.0	False		,,,				2504	0.0				p.P148P		Atlas-SNP	.											.	ZADH2	25	.	1	Substitution - coding silent(1)	lung(1)	c.C444T						PASS	.	G		0,4406		0,0,2203	242	251	248		444	-10.9	0.3	18		248	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ZADH2	NM_175907.4		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		148/378	72914061	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	284273	exon2			ATACTCGGGTTTC	BC033780	CCDS12008.1	18q22.3	2008-05-29	2008-05-29		ENSG00000180011	ENSG00000180011			28697	protein-coding gene	gene with protein product						12477932	Standard	NM_175907		Approved	MGC45594	uc002llx.3	Q8N4Q0	OTTHUMG00000132858	ENST00000322342.3:c.444C>T	18.37:g.72914061G>A		104	0	0		50	16	0.32	NM_175907	A8KA15|B4DZ91	Silent	SNP	ENST00000322342.3	37	CCDS12008.1																																																																																			.	.	weak		0.527	ZADH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256332.1	NM_175907		A	72914061	G	A	72914061	2	1	41	1	0	0	0	0	0	0	0	1	17526	1103	39	1		1	ZADH2	18	72914061	Silent	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	12977901	72914061	5163187	110	14926											
CD320	51293	hgsc.bcm.edu	37	chr19	8369939	8369939	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	ctcctcctcatcgctgccatCgctgcagtccaagtccctgt	5	11	7	18	2	1	0	1	0	0	0	7	0	5	0	5	0	2	3	5	0	1	0			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr19:8369939C>G	ENST00000301458.5	-	2	308	c.244G>C	c.(244-246)Gat>Cat	p.D82H	CD320_ENST00000537716.2_Intron|CD320_ENST00000596246.1_5'Flank	NM_016579.3	NP_057663.1	Q9NPF0	CD320_HUMAN	CD320 molecule	82	LDL-receptor class A 1. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cobalamin metabolic process (GO:0009235)|regulation of cell growth (GO:0001558)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cobalamin binding (GO:0031419)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)	6						TCGCTGCCATCGCTGCAGTCC	0.687																																					p.D82H		Atlas-SNP	.											.	CD320	20	.	0			c.G244C						PASS	.						50	48	49					19																	8369939		2203	4300	6503	SO:0001583	missense	51293	exon2			TGCCATCGCTGCA	AF161254	CCDS12198.1, CCDS54210.1	19p13.3-p13.2	2008-02-05	2006-03-28			ENSG00000167775		"CD molecules"	16692	protein-coding gene	gene with protein product	"8D6 antigen"	606475	"CD320 antigen"			10727470	Standard	NM_016579		Approved	8D6, 8D6A	uc002mjj.2	Q9NPF0		ENST00000301458.5:c.244G>C	19.37:g.8369939C>G	ENSP00000301458:p.Asp82His	15	0	0		26	9	0.346154	NM_016579	B2RDS5|D6W668|F5H6D3|Q53HF7	Missense_Mutation	SNP	ENST00000301458.5	37	CCDS12198.1	.	.	.	.	.	.	.	.	.	.	C	15.53	2.860981	0.51482	.	.	ENSG00000167775	ENST00000301458	D	0.97620	-4.46	4.87	4.87	0.63330	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.136815	0.33591	N	0.004757	D	0.98741	0.9577	M	0.93550	3.43	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99184	1.0868	10	0.87932	D	0	-17.2415	14.2342	0.65913	0.0:1.0:0.0:0.0	.	82	Q9NPF0	CD320_HUMAN	H	82	ENSP00000301458:D82H	ENSP00000301458:D82H	D	-	1	0	CD320	8275939	0.938000	0.31826	0.648000	0.29521	0.001000	0.01503	2.947000	0.49058	2.644000	0.89710	0.655000	0.94253	GAT	.	.	none		0.687	CD320-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461366.1	NM_016579		G	8369939	C	G	8369939	3	3	41	1	0	0	0	0	1	0	0	0	3006	884	31	4	620	4	CD320	19	8369939	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10		8369939	50759044	111	14927											
MBD3L1	85509	hgsc.bcm.edu	37	chr19	8953842	8953845	+	Frame_Shift_Del	DEL	CAGT	CAGT	-																															acaggaagggaaagtgaagaCagtcagagagagactcgcaa																										TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	CAGT	CAGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr19:8953842_8953845delCAGT	ENST00000595891.1	+	3	719_722	c.488_491delCAGT	c.(487-492)acagtcfs	p.TV163fs	MBD3L1_ENST00000305625.2_Frame_Shift_Del_p.TV163fs			Q8WWY6	MB3L1_HUMAN	methyl-CpG binding domain protein 3-like 1	163					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						AAAGTGAAGACAGTCAGAGAGAGA	0.471																																					p.163_164del		Pindel,Atlas-Indel	.											.	MBD3L1	24	.	0			c.487_490del						PASS	.																																			SO:0001589	frameshift_variant	85509	exon1			.	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.488_491delCAGT	19.37:g.8953842_8953845delCAGT	ENSP00000471575:p.Thr163fs	58	0	.		70	16	0.229	NM_145208	B5BUM6|Q2M291	Frame_Shift_Del	DEL	ENST00000595891.1	37	CCDS12209.1																																																																																			.	.	none		0.471	MBD3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459973.1	NM_145208		-	8953845	CAGT	-	8953842	7	5	41	1	0	1	0	1	0	0	0	0	9354	478	17	0	490	0	MBD3L1	19	8953842	Frame_Shift_Del	DEL	CAGT	TCGA-GS-A9TY-01A-11D-A38X-10	583903	8953842	50175141	112	14928											
MUC16	94025	hgsc.bcm.edu	37	chr19	9033694	9033694	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcgtactgcaggttggtgatGgtgaagttgagggtgaatgg	8	12	18	3	1	0	4	0	4	0	0	1	4	0	4	0	5	2	4	0	5	3	3	rs200620444	byFrequency	TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr19:9033694G>A	ENST00000397910.4	-	9	36446	c.36243C>T	c.(36241-36243)acC>acT	p.T12081T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12083	SEA 1. {ECO:0000255|PROSITE- ProRule:PRU00188}.|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						GGTTGGTGATGGTGAAGTTGA	0.557																																					p.T12081T		Atlas-SNP	.											.	MUC16	4315	.	0			c.C36243T						PASS	.						136	133	134					19																	9033694		2107	4236	6343	SO:0001819	synonymous_variant	94025	exon9			GGTGATGGTGAAG	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.36243C>T	19.37:g.9033694G>A		103	0	0		99	43	0.434343	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			G|0.757;A|0.243	0.243	strong		0.557	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9033694	G	A	9033694	2	1	41	1	0	0	0	0	0	0	0	1	9982	1335	47	2		2	MUC16	19	9033694	Silent	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	79852	9033694	50095289	113	14929											
COL5A3	50509	hgsc.bcm.edu	37	chr19	10103700	10103700	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agggatccctgatactcaccGgctccccagcctggccagtg	7	7	11	16	1	1	1	1	1	0	0	3	2	3	2	6	3	2	1	6	3	1	1	rs147814824		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr19:10103700G>A	ENST00000264828.3	-	20	1878	c.1793C>T	c.(1792-1794)cCg>cTg	p.P598L	CTD-2553C6.1_ENST00000592332.1_RNA	NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3	598	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)			GATACTCACCGGCTCCCCAGC	0.632																																					p.P598L		Atlas-SNP	.											.	COL5A3	243	.	0			c.C1793T						PASS	.	G	LEU/PRO	1,4405		0,1,2202	21	23	22		1793	4.2	1	19	dbSNP_134	22	1,8599		0,1,4299	yes	missense-near-splice	COL5A3	NM_015719.3	98	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging	598/1746	10103700	2,13004	2203	4300	6503	SO:0001630	splice_region_variant	50509	exon20			CTCACCGGCTCCC	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.1794+1C>T	19.37:g.10103700G>A		78	0	0		68	23	0.338235	NM_015719	Q9NZQ6	Missense_Mutation	SNP	ENST00000264828.3	37	CCDS12222.1	.	.	.	.	.	.	.	.	.	.	G	13.18	2.160144	0.38119	2.27E-4	1.16E-4	ENSG00000080573	ENST00000264828	D	0.93488	-3.23	4.2	4.2	0.49525	.	0.075522	0.53938	D	0.000050	D	0.92080	0.7490	N	0.21240	0.645	0.51767	D	0.99993	D	0.76494	0.999	P	0.61800	0.894	D	0.91127	0.4934	10	0.38643	T	0.18	.	11.9061	0.52713	0.0:0.0:1.0:0.0	.	598	P25940	CO5A3_HUMAN	L	598	ENSP00000264828:P598L	ENSP00000264828:P598L	P	-	2	0	COL5A3	9964700	0.997000	0.39634	0.999000	0.59377	0.982000	0.71751	2.523000	0.45580	2.176000	0.68965	0.561000	0.74099	CCG	G|1.000;A|0.000	0.000	weak		0.632	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	Missense_Mutation	A	10103700	G	A	10103700	5	1	41	1	0	0	0	0	0	0	1	0	3700	1130	39	1	3636	1	COL5A3	19	10103700	Splice_Site	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	1070006	10103700	49025283	114	14930											
ZNF440	126070	hgsc.bcm.edu	37	chr19	11941439	11941439	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gtctgtattttaggaaaaagGtggaaagaccagaacattga	16	10	11	4	0	1	3	0	1	1	2	1	5	1	5	1	3	1	1	1	3	6	4			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr19:11941439G>T	ENST00000304060.5	+	3	302	c.138G>T	c.(136-138)agG>agT	p.R46S		NM_152357.2	NP_689570.2	Q8IYI8	ZN440_HUMAN	zinc finger protein 440	46	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(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(9)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27						TAGGAAAAAGGTGGAAAGACC	0.363																																					p.R46S		Atlas-SNP	.											.	ZNF440	56	.	0			c.G138T						PASS	.						85	85	85					19																	11941439		2203	4300	6503	SO:0001583	missense	126070	exon3			AAAAAGGTGGAAA	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.138G>T	19.37:g.11941439G>T	ENSP00000305373:p.Arg46Ser	434	1	0.00230415		452	207	0.457965	NM_152357	Q8N1R9	Missense_Mutation	SNP	ENST00000304060.5	37	CCDS42503.1	.	.	.	.	.	.	.	.	.	.	t	0.012	-1.686073	0.00738	.	.	ENSG00000171295	ENST00000304060;ENST00000427505;ENST00000414255	T;T;T	0.00776	5.71;5.71;5.71	1.15	-2.29	0.06805	Krueppel-associated box (3);	.	.	.	.	T	0.00384	0.0012	N	0.03268	-0.37	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42882	-0.9425	9	0.16896	T	0.51	.	0.5479	0.00657	0.1891:0.1734:0.3025:0.335	.	46	Q8IYI8	ZN440_HUMAN	S	46;49;48	ENSP00000305373:R46S;ENSP00000393489:R49S;ENSP00000411974:R48S	ENSP00000305373:R46S	R	+	3	2	ZNF440	11802439	0.000000	0.05858	0.000000	0.03702	0.075000	0.17131	-2.503000	0.00965	-2.524000	0.00495	-2.989000	0.00078	AGG	.	.	none		0.363	ZNF440-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344508.1	NM_152357		T	11941439	G	T	11941439	3	4	41	1	0	0	0	0	1	0	0	0	17928	1252	44	4	148	4	ZNF440	19	11941439	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	1837739	11941439	47187544	115	14931											
SLC27A1	376497	hgsc.bcm.edu	37	chr19	17615344	17615344	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cagaccggctcttcttcctgGacctgaagcagggccactac	8	8	10	15	1	2	2	0	1	2	1	3	3	3	3	4	3	2	2	4	3	2	3			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr19:17615344G>A	ENST00000252595.7	+	12	1961	c.1864G>A	c.(1864-1866)Gac>Aac	p.D622N	SLC27A1_ENST00000598424.1_Missense_Mutation_p.D443N|CTD-3131K8.2_ENST00000596643.1_lincRNA|SLC27A1_ENST00000598848.1_3'UTR|SLC27A1_ENST00000442725.1_Missense_Mutation_p.D622N	NM_198580.1	NP_940982.1	Q6PCB7	S27A1_HUMAN	solute carrier family 27 (fatty acid transporter), member 1	622					adiponectin-activated signaling pathway (GO:0033211)|cardiolipin biosynthetic process (GO:0032049)|cellular lipid metabolic process (GO:0044255)|fatty acid metabolic process (GO:0006631)|long-chain fatty acid transport (GO:0015909)|medium-chain fatty acid transport (GO:0001579)|negative regulation of phospholipid biosynthetic process (GO:0071072)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phosphatidylglycerol biosynthetic process (GO:0006655)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylserine biosynthetic process (GO:0006659)|positive regulation of heat generation (GO:0031652)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|response to cold (GO:0009409)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	fatty acid transporter activity (GO:0015245)|nucleotide binding (GO:0000166)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						CTTCTTCCTGGACCTGAAGCA	0.597																																					p.D622N		Atlas-SNP	.											.	SLC27A1	97	.	0			c.G1864A						PASS	.						84	71	75					19																	17615344		2203	4300	6503	SO:0001583	missense	376497	exon12			TTCCTGGACCTGA	BC059399	CCDS32953.1	19p13.11	2013-07-15			ENSG00000130304	ENSG00000130304		"Acyl-CoA synthetase family", "Solute carriers"	10995	protein-coding gene	gene with protein product		600691				10873384	Standard	NM_198580		Approved	FATP1, FATP, MGC71751, FLJ00336, ACSVL5	uc002ngu.1	Q6PCB7	OTTHUMG00000182878	ENST00000252595.7:c.1864G>A	19.37:g.17615344G>A	ENSP00000252595:p.Asp622Asn	62	0	0		67	15	0.223881	NM_198580	A6NIH2|B7Z662	Missense_Mutation	SNP	ENST00000252595.7	37	CCDS32953.1	.	.	.	.	.	.	.	.	.	.	G	12.97	2.097728	0.37048	.	.	ENSG00000130304	ENST00000442725;ENST00000252595	T;T	0.48201	0.82;0.82	4.13	4.13	0.48395	.	0.056406	0.64402	D	0.000001	T	0.31575	0.0801	N	0.17594	0.5	0.38800	D	0.955185	B;B	0.28667	0.008;0.219	B;B	0.27380	0.016;0.079	T	0.19712	-1.0297	10	0.30078	T	0.28	-8.2526	13.8877	0.63719	0.0:0.0:1.0:0.0	.	443;622	B7Z662;Q6PCB7	.;S27A1_HUMAN	N	622	ENSP00000413424:D622N;ENSP00000252595:D622N	ENSP00000252595:D622N	D	+	1	0	SLC27A1	17476344	1.000000	0.71417	1.000000	0.80357	0.894000	0.52154	5.864000	0.69575	1.831000	0.53308	0.561000	0.74099	GAC	.	.	none		0.597	SLC27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464145.1	NM_198580		A	17615344	G	A	17615344	3	1	41	1	0	0	0	0	1	0	0	0	14540	1174	41	2	1910	2	SLC27A1	19	17615344	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	5673905	17615344	41513639	116	14932											
ZNF536	9745	hgsc.bcm.edu	37	chr19	30934652	30934652	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aaccccgaggagaagcccccCgcatccctggaggagaaggc	11	2	13	15	2	0	2	0	0	0	2	1	6	1	3	6	4	2	1	6	4	3	0			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr19:30934652C>T	ENST00000355537.3	+	2	330	c.183C>T	c.(181-183)ccC>ccT	p.P61P		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	61					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.P61P(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)					AGAAGCCCCCCGCATCCCTGG	0.672																																					p.P61P		Atlas-SNP	.											.	ZNF536	424	.	1	Substitution - coding silent(1)	lung(1)	c.C183T						PASS	.						40	44	42					19																	30934652		2203	4300	6503	SO:0001819	synonymous_variant	9745	exon2			GCCCCCCGCATCC		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.183C>T	19.37:g.30934652C>T		33	0	0		45	11	0.244444	NM_014717	A2RU18	Silent	SNP	ENST00000355537.3	37	CCDS32984.1																																																																																			.	.	none		0.672	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717		T	30934652	C	T	30934652	2	4	41	1	0	0	0	0	0	0	0	1	17989	639	23	1		1	ZNF536	19	30934652	Silent	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	13319308	30934652	28194331	117	14933											
MEGF8	1954	hgsc.bcm.edu	37	chr19	42859915	42859915	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctctctcttcacagggctgCtcgtgctgcactgggaggcc	4	10	12	15	1	3	0	1	0	2	0	5	1	3	1	2	3	3	4	2	3	0	1			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr19:42859915C>T	ENST00000251268.6	+	24	4150	c.4150C>T	c.(4150-4152)Ctc>Ttc	p.L1384F	MEGF8_ENST00000334370.4_Missense_Mutation_p.L1317F	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	1384	CUB 2. {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)				CACAGGGCTGCTCGTGCTGCA	0.637																																					p.L1384F		Atlas-SNP	.											.	MEGF8	358	.	0			c.C4150T						PASS	.						18	13	15					19																	42859915		2201	4300	6501	SO:0001583	missense	1954	exon24			GGGCTGCTCGTGC	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.4150C>T	19.37:g.42859915C>T	ENSP00000251268:p.Leu1384Phe	97	0	0		66	53	0.80303	NM_001271938	A8KAY0|O75097	Missense_Mutation	SNP	ENST00000251268.6	37		.	.	.	.	.	.	.	.	.	.	C	13.61	2.288997	0.40494	.	.	ENSG00000105429	ENST00000334370;ENST00000251268	T;T	0.35789	1.29;1.29	4.74	4.74	0.60224	CUB (1);	0.172164	0.38897	N	0.001533	T	0.43523	0.1251	N	0.19112	0.55	0.80722	D	1	D;D	0.67145	0.995;0.996	P;D	0.63793	0.858;0.918	T	0.43605	-0.9381	10	0.52906	T	0.07	-20.7852	16.6455	0.85176	0.0:1.0:0.0:0.0	.	1384;1317	Q7Z7M0;Q7Z7M0-2	MEGF8_HUMAN;.	F	1317;1384	ENSP00000334219:L1317F;ENSP00000251268:L1384F	ENSP00000251268:L1384F	L	+	1	0	MEGF8	47551755	1.000000	0.71417	0.995000	0.50966	0.142000	0.21351	3.448000	0.52943	2.481000	0.83766	0.655000	0.94253	CTC	.	.	none		0.637	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410		T	42859915	C	T	42859915	3	4	41	1	0	0	0	0	1	0	0	0	9472	797	28	2	4039	2	MEGF8	19	42859915	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	11925263	42859915	16269068	118	14934											
RTN2	6253	hgsc.bcm.edu	37	chr19	45991939	45991939	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgaagatggcacccacgaagGtcaagatgtagaagaggagg	15	5	15	6	1	1	5	1	1	0	4	1	7	1	6	1	4	0	2	1	4	5	1	rs190900651		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr19:45991939G>T	ENST00000245923.4	-	8	1641	c.1406C>A	c.(1405-1407)aCc>aAc	p.T469N	PPM1N_ENST00000401705.1_5'Flank|RTN2_ENST00000430715.2_Missense_Mutation_p.T129N|RTN2_ENST00000590526.1_Missense_Mutation_p.T195N|RTN2_ENST00000344680.4_Missense_Mutation_p.T396N	NM_005619.4	NP_005610.1	O75298	RTN2_HUMAN	reticulon 2	469	Reticulon. {ECO:0000255|PROSITE- ProRule:PRU00170}.				cell death (GO:0008219)|intracellular protein transmembrane transport (GO:0065002)|regulation of glucose import (GO:0046324)	endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)				cervix(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(4)|skin(1)|urinary_tract(1)	20		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00829)|Epithelial(262;0.184)|GBM - Glioblastoma multiforme(486;0.246)		ACCCACGAAGGTCAAGATGTA	0.567													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18946	0.0		0.0	False		,,,				2504	0.0				p.T469N		Atlas-SNP	.											.	RTN2	45	.	0			c.C1406A						PASS	.						41	40	41					19																	45991939		2203	4300	6503	SO:0001583	missense	6253	exon8			ACGAAGGTCAAGA	AF038540	CCDS12665.1, CCDS12666.1, CCDS46114.1	19q13.2-q13.3	2012-03-30				ENSG00000125744			10468	protein-coding gene	gene with protein product	"NSP-like protein 1", "Neuroendocrine-specific protein-like 1"	603183	"spastic paraplegia 12 (autosomal dominant)"	SPG12		8812484, 9530622, 22232211	Standard	NM_005619		Approved	NSP2, NSPL1	uc002pcb.4	O75298		ENST00000245923.4:c.1406C>A	19.37:g.45991939G>T	ENSP00000245923:p.Thr469Asn	33	0	0		46	7	0.152174	NM_005619	O60509|Q7RTM6|Q7RTN1|Q7RTN2	Missense_Mutation	SNP	ENST00000245923.4	37	CCDS12665.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	26.3	4.722770	0.89298	.	.	ENSG00000125744	ENST00000344680;ENST00000245923;ENST00000430715	T;T;T	0.48201	0.82;0.82;0.82	5.58	5.58	0.84498	.	0.106863	0.64402	D	0.000006	T	0.67739	0.2925	M	0.72479	2.2	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.87578	0.973;0.998	T	0.69161	-0.5218	10	0.59425	D	0.04	-25.1144	15.1396	0.72601	0.0:0.0:1.0:0.0	.	396;469	O75298-2;O75298	.;RTN2_HUMAN	N	396;469;129	ENSP00000345127:T396N;ENSP00000245923:T469N;ENSP00000398178:T129N	ENSP00000245923:T469N	T	-	2	0	RTN2	50683779	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.591000	0.90824	2.649000	0.89929	0.650000	0.86243	ACC	G|1.000;T|0.000	0.000	strong		0.567	RTN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459574.1	NM_005619		T	45991939	G	T	45991939	3	4	41	1	0	0	0	0	1	0	0	0	13741	1261	44	4	247	4	RTN2	19	45991939	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	3132024	45991939	13137044	119	14935											
ZC3H4	23211	hgsc.bcm.edu	37	chr19	47575929	47575931	+	In_Frame_Del	DEL	CTT	CTT	-																															ttcttcagttcctccacctcCttctcatcctcggcacctgc																										TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr19:47575929_47575931delCTT	ENST00000253048.5	-	12	1517_1519	c.1480_1482delAAG	c.(1480-1482)aagdel	p.K494del	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	494							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)		CCTCCACCTCCTTCTCATCCTCG	0.631																																					p.494_495del		Atlas-Indel	.											.	ZC3H4	96	.	0			c.1481_1483del						PASS	.																																			SO:0001651	inframe_deletion	23211	exon12			.	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.1480_1482delAAG	19.37:g.47575929_47575931delCTT	ENSP00000253048:p.Lys494del	70	0	0		65	13	0.2	NM_015168	Q9Y420	In_Frame_Del	DEL	ENST00000253048.5	37	CCDS42582.1																																																																																			.	.	none		0.631	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1			-	47575931	CTT	-	47575929	7	5	41	1	0	1	0	1	0	0	0	0	17585	680	24	0	2445	0	ZC3H4	19	47575929	In_Frame_Del	DEL	CTT	TCGA-GS-A9TY-01A-11D-A38X-10	1583990	47575929	11553054	120	14936											
LAIR2	3904	hgsc.bcm.edu	37	chr19	55014155	55014155	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgtctccacacctcactgcTctcctgggcctaggtgagtc	6	11	9	15	0	3	1	1	1	2	0	6	1	3	1	4	2	1	1	4	2	1	1	rs143266047		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr19:55014155T>C	ENST00000301202.2	+	1	143	c.21T>C	c.(19-21)gcT>gcC	p.A7A	LAIR2_ENST00000351841.2_Silent_p.A7A	NM_002288.4	NP_002279.2	Q6ISS4	LAIR2_HUMAN	leukocyte-associated immunoglobulin-like receptor 2	7						extracellular region (GO:0005576)				central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)	18	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0967)		ACCTCACTGCTCTCCTGGGCC	0.627													T|||	1	0.000199681	0.0	0.0	5008	,	,		16035	0.0		0.0	False		,,,				2504	0.001				p.A7A		Atlas-SNP	.											LAIR2,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,1	LAIR2	30	1	0			c.T21C						scavenged	.	T	,	0,4406		0,0,2203	86	77	80		21,21	-0.2	0	19	dbSNP_134	80	3,8597	3.7+/-12.6	0,3,4297	no	coding-synonymous,coding-synonymous	LAIR2	NM_002288.4,NM_021270.3	,	0,3,6500	CC,CT,TT		0.0349,0.0,0.0231	,	7/153,7/136	55014155	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	3904	exon1			CACTGCTCTCCTG	AF013250	CCDS12897.1, CCDS12898.1	19q13.4	2013-01-29	2006-03-23		ENSG00000167618	ENSG00000167618		"Leukocyte-associated Ig like receptors", "CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	6478	protein-coding gene	gene with protein product		602993	"leukocyte-associated Ig-like receptor 2"			9285412	Standard	XM_005277264		Approved	CD306	uc002qgc.3	Q6ISS4	OTTHUMG00000065697	ENST00000301202.2:c.21T>C	19.37:g.55014155T>C		101	2	0.019802		108	8	0.0740741	NM_002288	Q6PEZ4	Silent	SNP	ENST00000301202.2	37	CCDS12897.1																																																																																			T|1.000;C|0.000	0.000	weak		0.627	LAIR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140801.1			C	55014155	T	C	55014155	2	2	41	1	0	0	0	0	0	0	0	1	8612	1538	54	3		3	LAIR2	19	55014155	Silent	SNP	T	TCGA-GS-A9TY-01A-11D-A38X-10	7438226	55014155	4114828	121	14937											
CDH26	60437	hgsc.bcm.edu	37	chr20	58558068	58558068	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcagtgatgtgaatgatcatGcaccccagtttccagagaag	12	10	10	9	0	2	4	2	3	0	1	3	5	3	4	3	0	1	2	3	0	2	1			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr20:58558068G>T	ENST00000244047.5	+	5	795	c.484G>T	c.(484-486)Gca>Tca	p.A162S	CDH26_ENST00000348616.4_Missense_Mutation_p.A162S			Q8IXH8	CAD26_HUMAN	cadherin 26	162	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)			GAATGATCATGCACCCCAGTT	0.463																																					p.A162S		Atlas-SNP	.											.	CDH26	229	.	0			c.G484T						PASS	.						156	161	160					20																	58558068		2203	4300	6503	SO:0001583	missense	60437	exon5			GATCATGCACCCC	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.484G>T	20.37:g.58558068G>T	ENSP00000244047:p.Ala162Ser	114	0	0		104	23	0.221154	NM_177980	A2A2M5|B3KNX3|Q6P5Y6|Q8TCH3|Q9BQN4|Q9NRU1	Missense_Mutation	SNP	ENST00000244047.5	37		.	.	.	.	.	.	.	.	.	.	G	17.28	3.350695	0.61183	.	.	ENSG00000124215	ENST00000244047;ENST00000348616	T;T	0.61742	0.08;0.08	4.91	3.97	0.46021	.	0.356242	0.29948	N	0.010794	T	0.71771	0.3379	M	0.73962	2.25	0.40699	D	0.982466	D	0.69078	0.997	D	0.73708	0.981	T	0.71623	-0.4537	10	0.38643	T	0.18	.	10.4423	0.44472	0.0927:0.0:0.9073:0.0	.	162	Q8IXH8-4	.	S	162	ENSP00000244047:A162S;ENSP00000339390:A162S	ENSP00000244047:A162S	A	+	1	0	CDH26	57991463	0.502000	0.26107	0.006000	0.13384	0.964000	0.63967	1.962000	0.40442	1.057000	0.40506	0.591000	0.81541	GCA	.	.	none		0.463	CDH26-201	KNOWN	basic	protein_coding	protein_coding		NM_177980		T	58558068	G	T	58558068	3	4	41	1	0	0	0	0	1	0	0	0	3112	1319	46	4	502	4	CDH26	20	58558068	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10		58558068	4467452	122	14938											
DIDO1	11083	hgsc.bcm.edu	37	chr20	61526223	61526223	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcctcctgcctgggggccGtcttcttgctttcattgtgc	1	15	12	13	1	3	0	1	0	2	0	4	0	4	0	4	3	3	1	4	3	0	4	rs139525718		TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr20:61526223G>T	ENST00000266070.4	-	10	2700	c.2375C>A	c.(2374-2376)aCg>aAg	p.T792K	DIDO1_ENST00000395340.1_Missense_Mutation_p.T792K|DIDO1_ENST00000395335.2_Missense_Mutation_p.T792K|DIDO1_ENST00000395343.1_Missense_Mutation_p.T792K	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	792					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)					CCTGGGGGCCGTCTTCTTGCT	0.498																																					p.T792K	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.C2375A						PASS	.						75	83	80					20																	61526223		2203	4300	6503	SO:0001583	missense	11083	exon10			GGGGCCGTCTTCT	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.2375C>A	20.37:g.61526223G>T	ENSP00000266070:p.Thr792Lys	105	0	0		83	47	0.566265	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	37	CCDS33506.1	.	.	.	.	.	.	.	.	.	.	G	14.64	2.594885	0.46318	.	.	ENSG00000101191	ENST00000266070;ENST00000395343;ENST00000395340;ENST00000395335	T;T;T;T	0.14640	2.91;2.91;2.49;2.49	5.5	2.33	0.28932	.	0.567818	0.14596	N	0.309931	T	0.08714	0.0216	L	0.44542	1.39	0.09310	N	0.999998	B;P	0.34724	0.302;0.465	B;B	0.23150	0.04;0.044	T	0.28964	-1.0027	10	0.34782	T	0.22	-2.3923	4.5074	0.11894	0.3162:0.0:0.5279:0.1559	.	792;792	Q9BTC0-1;Q9BTC0	.;DIDO1_HUMAN	K	792	ENSP00000266070:T792K;ENSP00000378752:T792K;ENSP00000378749:T792K;ENSP00000378744:T792K	ENSP00000266070:T792K	T	-	2	0	DIDO1	60996668	0.001000	0.12720	0.000000	0.03702	0.582000	0.36321	1.120000	0.31271	0.212000	0.20703	0.462000	0.41574	ACG	G|0.999;A|0.001	.	alt		0.498	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796		T	61526223	G	T	61526223	3	4	41	1	0	0	0	0	1	0	0	0	4524	1145	40	4	4404	4	DIDO1	20	61526223	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	2968155	61526223	1499297	123	14939											
RIPK4	54101	hgsc.bcm.edu	37	chr21	43161043	43161043	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtggcggcggggccatggccGccctggaacttgaggctctg	4	7	18	12	3	1	1	0	1	1	0	1	2	1	2	3	7	1	1	3	7	1	1			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr21:43161043G>A	ENST00000352483.2	-	9	2518	c.2454C>T	c.(2452-2454)ggC>ggT	p.G818G	RIPK4_ENST00000544709.1_Silent_p.G707G|RIPK4_ENST00000542057.1_Silent_p.G707G|RIPK4_ENST00000332512.3_Silent_p.G770G|AP001615.9_ENST00000423276.1_RNA			P57078	RIPK4_HUMAN	receptor-interacting serine-threonine kinase 4	818					morphogenesis of an epithelium (GO:0002009)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						GGCCATGGCCGCCCTGGAACT	0.697																																					p.G770G		Atlas-SNP	.											.	RIPK4	151	.	0			c.C2310T						PASS	.						31	31	31					21																	43161043		2200	4294	6494	SO:0001819	synonymous_variant	54101	exon8			ATGGCCGCCCTGG	AJ278016	CCDS13675.1	21q22.3	2013-01-10	2004-07-06	2004-07-06	ENSG00000183421	ENSG00000183421		"Ankyrin repeat domain containing"	496	protein-coding gene	gene with protein product	"protein kinase C-associated kinase", "PKC-delta-interacting protein kinase"	605706	"ankyrin repeat domain 3"	ANKRD3		10830953	Standard	NM_020639		Approved	DIK, ANKK2, RIP4, PKK	uc002yzn.1	P57078	OTTHUMG00000086770	ENST00000352483.2:c.2454C>T	21.37:g.43161043G>A		48	0	0		105	57	0.542857	NM_020639	Q96KH0	Silent	SNP	ENST00000352483.2	37																																																																																				.	.	none		0.697	RIPK4-201	KNOWN	basic	protein_coding	protein_coding		NM_020639		A	43161043	G	A	43161043	2	1	41	1	0	0	0	0	0	0	0	1	13398	1074	38	1		1	RIPK4	21	43161043	Silent	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10		43161043	4968852	124	14940											
MYO18B	84700	hgsc.bcm.edu	37	chr22	26291160	26291160	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgcttcgactgtgctcagatGgagaacgagttcctcagaaa	11	9	11	10	3	2	3	2	0	0	3	4	6	3	3	1	1	2	3	1	1	2	2			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr22:26291160G>A	ENST00000407587.2	+	28	4753	c.4584G>A	c.(4582-4584)atG>atA	p.M1528I	CTA-125H2.2_ENST00000599792.1_RNA|CTA-125H2.2_ENST00000593715.1_RNA|CTA-125H2.2_ENST00000608507.1_RNA|CTA-125H2.2_ENST00000594542.1_RNA|CTA-125H2.2_ENST00000608921.1_RNA|CTA-125H2.2_ENST00000607895.1_RNA|CTA-125H2.2_ENST00000608115.1_RNA|CTA-125H2.2_ENST00000599080.1_RNA|CTA-125H2.2_ENST00000600211.1_RNA|CTA-125H2.2_ENST00000609275.1_RNA|CTA-125H2.2_ENST00000597548.1_RNA|CTA-125H2.2_ENST00000600903.1_RNA|CTA-125H2.2_ENST00000596813.1_RNA|CTA-125H2.2_ENST00000609157.1_RNA|MYO18B_ENST00000335473.7_Missense_Mutation_p.M1527I|CTA-125H2.2_ENST00000609809.1_RNA|CTA-125H2.2_ENST00000609570.1_RNA|MYO18B_ENST00000536101.1_Missense_Mutation_p.M1527I|CTA-125H2.2_ENST00000600269.1_RNA|CTA-125H2.2_ENST00000609820.1_RNA|CTA-125H2.2_ENST00000608257.1_RNA|CTA-125H2.2_ENST00000595102.1_RNA|CTA-125H2.2_ENST00000453457.3_RNA|CTA-125H2.2_ENST00000597614.2_RNA|CTA-125H2.2_ENST00000609889.1_RNA|CTA-125H2.2_ENST00000594856.1_RNA|CTA-125H2.2_ENST00000597284.1_RNA|CTA-125H2.2_ENST00000594585.1_RNA|CTA-125H2.2_ENST00000609823.1_RNA			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1527	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						GTGCTCAGATGGAGAACGAGT	0.542																																					p.M1527I		Atlas-SNP	.											.	MYO18B	322	.	0			c.G4581A						PASS	.						40	44	43					22																	26291160		2180	4283	6463	SO:0001583	missense	84700	exon28			TCAGATGGAGAAC	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.4584G>A	22.37:g.26291160G>A	ENSP00000386096:p.Met1528Ile	50	0	0		32	11	0.34375	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		.	.	.	.	.	.	.	.	.	.	G	15.44	2.833067	0.50951	.	.	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;T	0.86297	-2.1;-2.1;-1.12	5.26	1.83	0.25207	.	0.303395	0.30704	N	0.009056	T	0.79868	0.4520	L	0.51422	1.61	0.30516	N	0.76893	B;B;P;P	0.35774	0.274;0.384;0.458;0.519	B;B;B;B	0.38264	0.112;0.138;0.194;0.269	T	0.73382	-0.4000	10	0.36615	T	0.2	.	2.7126	0.05179	0.173:0.1451:0.5328:0.1491	.	1040;1527;1528;1527	Q8IUG5-2;Q8IUG5;F5GXR6;F5GYU7	.;MY18B_HUMAN;.;.	I	1527;1527;1528	ENSP00000441229:M1527I;ENSP00000334563:M1527I;ENSP00000386096:M1528I	ENSP00000334563:M1527I	M	+	3	0	MYO18B	24621160	0.998000	0.40836	1.000000	0.80357	0.947000	0.59692	0.315000	0.19451	1.221000	0.43506	0.563000	0.77884	ATG	.	.	none		0.542	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608		A	26291160	G	A	26291160	3	1	41	1	0	0	0	0	1	0	0	0	10075	1348	47	2	4687	2	MYO18B	22	26291160	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10		26291160	25013406	125	14941											
NEFH	4744	hgsc.bcm.edu	37	chr22	29884844	29884844	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gatccatcctgcagaaaactCctggaaggtgaagagtgtcg	12	8	12	9	1	0	3	0	1	0	2	4	5	3	4	3	2	2	1	3	2	4	0			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chr22:29884844C>T	ENST00000310624.6	+	4	1248	c.1215C>T	c.(1213-1215)ctC>ctT	p.L405L		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	405	Coil 2B.|Rod.				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						GCAGAAAACTCCTGGAAGGTG	0.463																																					p.L405L		Atlas-SNP	.											.	NEFH	178	.	0			c.C1215T						PASS	.						71	74	73					22																	29884844		2203	4300	6503	SO:0001819	synonymous_variant	4744	exon4			AAAACTCCTGGAA		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.1215C>T	22.37:g.29884844C>T		75	0	0		57	22	0.385965	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Silent	SNP	ENST00000310624.6	37	CCDS13858.1																																																																																			.	.	none		0.463	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076		T	29884844	C	T	29884844	2	4	41	1	0	0	0	0	0	0	0	1	10323	842	30	2		2	NEFH	22	29884844	Silent	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	3593684	29884844	21419722	126	14942											
NHS	4810	hgsc.bcm.edu	37	chrX	17750129	17750129	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccaacagccagaggtctcctGgtctcatataccgaaatgcc	11	8	8	14	1	2	1	1	0	2	1	4	2	2	1	5	2	4	0	5	2	4	2			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chrX:17750129G>A	ENST00000380060.3	+	8	4776	c.4438G>A	c.(4438-4440)Ggt>Agt	p.G1480S	NHS_ENST00000398097.3_Missense_Mutation_p.G1324S	NM_198270.2	NP_938011.1	Q6T4R5	NHS_HUMAN	Nance-Horan syndrome (congenital cataracts and dental anomalies)	1501	Poly-Ser.				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)					GAGGTCTCCTGGTCTCATATA	0.493																																					p.G1480S		Atlas-SNP	.											.	NHS	302	.	0			c.G4438A						PASS	.						155	136	142					X																	17750129		2203	4300	6503	SO:0001583	missense	4810	exon8			TCTCCTGGTCTCA		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.4438G>A	X.37:g.17750129G>A	ENSP00000369400:p.Gly1480Ser	134	0	0		127	35	0.275591	NM_198270	B7ZVX8|E2DH69|Q5J7Q0|Q5J7Q1|Q68DR5	Missense_Mutation	SNP	ENST00000380060.3	37	CCDS14181.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.793800	0.90453	.	.	ENSG00000188158	ENST00000380060;ENST00000398097;ENST00000380057	T;T	0.61392	0.11;0.13	5.79	5.79	0.91817	.	0.102979	0.64402	D	0.000003	T	0.73651	0.3614	M	0.68952	2.095	0.58432	D	0.999999	D;D;D;D	0.69078	0.976;0.976;0.976;0.997	P;P;P;D	0.74348	0.698;0.698;0.698;0.983	T	0.68191	-0.5474	10	0.19147	T	0.46	-19.5354	18.9979	0.92821	0.0:0.0:1.0:0.0	.	1501;1322;1324;1480	B7ZVX8;C9IYM8;Q6T4R5-2;Q6T4R5	.;.;.;NHS_HUMAN	S	1480;1324;1322	ENSP00000369400:G1480S;ENSP00000381170:G1324S	ENSP00000369397:G1322S	G	+	1	0	NHS	17660050	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.404000	0.79996	2.435000	0.82474	0.600000	0.82982	GGT	.	.	none		0.493	NHS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059120.1	NM_198270		A	17750129	G	A	17750129	3	1	41	1	0	0	0	0	1	0	0	0	10420	1348	47	2	4573	2	NHS	23	17750129	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10		17750129	137520431	127	14943											
CXorf22	170063	hgsc.bcm.edu	37	chrX	35970007	35970007	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acatagatactactatcattAtctcctgtcttcctaatgaa	13	15	3	10	0	3	2	1	1	2	1	5	2	4	2	2	0	2	0	2	0	7	7			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chrX:35970007A>T	ENST00000297866.5	+	6	1039	c.973A>T	c.(973-975)Atc>Ttc	p.I325F		NM_152632.3	NP_689845.2	Q6ZTR5	CX022_HUMAN	chromosome X open reading frame 22	325										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						TACTATCATTATCTCCTGTCT	0.284																																					p.I325F		Atlas-SNP	.											.	CXorf22	272	.	0			c.A973T						PASS	.						56	54	55					X																	35970007		2194	4246	6440	SO:0001583	missense	170063	exon6			ATCATTATCTCCT	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.973A>T	X.37:g.35970007A>T	ENSP00000297866:p.Ile325Phe	876	0	0		782	311	0.397698	NM_152632	Q5JRM8|Q8N6X8	Missense_Mutation	SNP	ENST00000297866.5	37	CCDS14237.2	.	.	.	.	.	.	.	.	.	.	A	16.24	3.066679	0.55539	.	.	ENSG00000165164	ENST00000297866	T	0.60040	0.22	5.76	4.57	0.56435	.	0.189713	0.46758	N	0.000266	T	0.67050	0.2852	M	0.74258	2.255	0.32724	N	0.509944	D	0.64830	0.994	D	0.65010	0.931	T	0.68853	-0.5299	10	0.02654	T	1	-22.2371	10.4909	0.44750	0.8525:0.0:0.0:0.1475	.	325	Q6ZTR5	CX022_HUMAN	F	325	ENSP00000297866:I325F	ENSP00000297866:I325F	I	+	1	0	CXorf22	35879928	1.000000	0.71417	0.915000	0.36163	0.503000	0.33858	3.555000	0.53727	0.766000	0.33244	0.417000	0.27973	ATC	.	.	none		0.284	CXorf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056216.2	NM_152632		T	35970007	A	T	35970007	3	4	41	1	0	0	0	0	1	0	0	0	4104	449	16	5	995	5	CXorf22	23	35970007	Missense_Mutation	SNP	A	TCGA-GS-A9TY-01A-11D-A38X-10	18219878	35970007	119300553	128	14944											
AKAP4	8852	hgsc.bcm.edu	37	chrX	49961619	49961619	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acttcccaggtttaagttgcCttctgagctggaactagcag	9	12	10	10	0	1	1	0	1	1	0	2	2	2	2	2	2	4	4	2	2	3	6			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chrX:49961619C>T	ENST00000376056.2	-	4	322	c.172G>A	c.(172-174)Ggc>Agc	p.G58S	AKAP4_ENST00000358526.2_Missense_Mutation_p.G67S|AKAP4_ENST00000481402.1_5'UTR|AKAP4_ENST00000376058.2_Missense_Mutation_p.G58S|AKAP4_ENST00000376064.3_Missense_Mutation_p.G58S					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)					TTTAAGTTGCCTTCTGAGCTG	0.433																																					p.G67S		Atlas-SNP	.											.	AKAP4	131	.	0			c.G199A						PASS	.						174	144	154					X																	49961619		2203	4300	6503	SO:0001583	missense	8852	exon4			AGTTGCCTTCTGA	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.172G>A	X.37:g.49961619C>T	ENSP00000365224:p.Gly58Ser	221	0	0		283	108	0.381625	NM_003886		Missense_Mutation	SNP	ENST00000376056.2	37	CCDS14330.1	.	.	.	.	.	.	.	.	.	.	C	3.029	-0.200104	0.06219	.	.	ENSG00000147081	ENST00000376056;ENST00000376058;ENST00000358526;ENST00000376064;ENST00000448865;ENST00000437370	T;T;T;T;T	0.32272	2.7;1.46;2.7;2.7;1.46	4.35	2.5	0.30297	.	0.504572	0.16825	N	0.198005	T	0.25082	0.0609	L	0.57536	1.79	0.09310	N	1	B;B	0.17038	0.02;0.011	B;B	0.15052	0.006;0.012	T	0.23797	-1.0178	9	.	.	.	-0.9557	4.6452	0.12568	0.2165:0.6629:0.0:0.1206	.	67;58	Q5JQC9;A6ND82	AKAP4_HUMAN;.	S	58;58;67;58;58;58	ENSP00000365224:G58S;ENSP00000365226:G58S;ENSP00000351327:G67S;ENSP00000365232:G58S;ENSP00000412279:G58S	.	G	-	1	0	AKAP4	49848359	0.002000	0.14202	0.001000	0.08648	0.020000	0.10135	0.471000	0.22100	0.234000	0.21139	0.513000	0.50165	GGC	.	.	none		0.433	AKAP4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056552.1	NM_003886		T	49961619	C	T	49961619	3	4	41	1	0	0	0	0	1	0	0	0	453	681	24	2	2377	2	AKAP4	23	49961619	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	13991612	49961619	105308941	129	14945											
SPIN3	169981	hgsc.bcm.edu	37	chrX	57021350	57021350	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccgtcctggaccgctgccCtgcagctgcctttccaaacg	5	8	10	18	3	0	0	0	0	0	0	2	1	2	1	6	1	5	3	6	1	1	1			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chrX:57021350C>A	ENST00000374919.3	-	2	353	c.31G>T	c.(31-33)Ggg>Tgg	p.G11W		NM_001010862.2	NP_001010862.2	Q5JUX0	SPIN3_HUMAN	spindlin family, member 3	11					gamete generation (GO:0007276)					central_nervous_system(1)|large_intestine(1)|lung(1)|ovary(1)	4						GACCGCTGCCCTGCAGCTGCC	0.557																																					p.G11W		Atlas-SNP	.											.	SPIN3	33	.	0			c.G31T						PASS	.						37	37	37					X																	57021350		2059	4167	6226	SO:0001583	missense	169981	exon2			GCTGCCCTGCAGC	AL832091	CCDS43963.1	Xp11.22	2008-02-05			ENSG00000204271	ENSG00000204271			27272	protein-coding gene	gene with protein product							Standard	NM_001010862		Approved		uc004dux.1	Q5JUX0	OTTHUMG00000021677	ENST00000374919.3:c.31G>T	X.37:g.57021350C>A	ENSP00000364054:p.Gly11Trp	91	0	0		127	27	0.212598	NM_001010862	B2RUW3|B7Z8W2|Q8N5D9	Missense_Mutation	SNP	ENST00000374919.3	37	CCDS43963.1	.	.	.	.	.	.	.	.	.	.	C	17.15	3.315986	0.60524	.	.	ENSG00000204271	ENST00000374919;ENST00000374915	T	0.46063	0.88	2.32	2.32	0.28847	.	.	.	.	.	T	0.44329	0.1288	L	0.46157	1.445	0.24883	N	0.992217	D	0.61697	0.99	P	0.50659	0.647	T	0.29549	-1.0008	9	0.87932	D	0	-1.0721	9.9797	0.41806	0.0:1.0:0.0:0.0	.	11	Q5JUX0	SPIN3_HUMAN	W	11	ENSP00000364054:G11W	ENSP00000364050:G11W	G	-	1	0	SPIN3	57038075	0.171000	0.23029	0.509000	0.27700	0.071000	0.16799	1.058000	0.30504	1.449000	0.47699	0.513000	0.50165	GGG	.	.	none		0.557	SPIN3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056908.1	XM_093024		A	57021350	C	A	57021350	3	1	41	1	0	0	0	0	1	0	0	0	15070	681	24	4	749	4	SPIN3	23	57021350	Missense_Mutation	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	7059731	57021350	98249210	130	14946											
DGAT2L6	347516	hgsc.bcm.edu	37	chrX	69424307	69424307	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttctgtaccttccatggccGgggcttcactcgcggatcct	4	13	10	14	3	2	0	1	0	1	0	5	1	4	1	4	4	1	2	4	4	1	4			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chrX:69424307G>A	ENST00000333026.3	+	6	900	c.800G>A	c.(799-801)cGg>cAg	p.R267Q		NM_198512.1	NP_940914.1	Q6ZPD8	DG2L6_HUMAN	diacylglycerol O-acyltransferase 2-like 6	267					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						TTCCATGGCCGGGGCTTCACT	0.502																																					p.R267Q		Atlas-SNP	.											.	DGAT2L6	40	.	0			c.G800A						PASS	.						74	68	70					X																	69424307		2203	4300	6503	SO:0001583	missense	347516	exon6			ATGGCCGGGGCTT	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.800G>A	X.37:g.69424307G>A	ENSP00000328036:p.Arg267Gln	163	0	0		208	45	0.216346	NM_198512	Q6IEE2	Missense_Mutation	SNP	ENST00000333026.3	37	CCDS14397.1	.	.	.	.	.	.	.	.	.	.	G	10.62	1.402595	0.25291	.	.	ENSG00000184210	ENST00000333026	T	0.24723	1.84	4.98	1.19	0.21007	.	0.300803	0.27567	N	0.018792	T	0.36220	0.0959	M	0.88241	2.94	0.26196	N	0.979515	P	0.47191	0.891	P	0.45343	0.477	T	0.29761	-1.0001	10	0.49607	T	0.09	-17.6492	8.4724	0.32993	0.3533:0.0:0.6467:0.0	.	267	Q6ZPD8	DG2L6_HUMAN	Q	267	ENSP00000328036:R267Q	ENSP00000328036:R267Q	R	+	2	0	DGAT2L6	69341032	0.982000	0.34865	0.170000	0.22879	0.003000	0.03518	3.486000	0.53215	0.167000	0.19631	-0.208000	0.12717	CGG	.	.	none		0.502	DGAT2L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057067.1	NM_198512		A	69424307	G	A	69424307	3	1	41	1	0	0	0	0	1	0	0	0	4461	1116	39	1	822	1	DGAT2L6	23	69424307	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	12402957	69424307	85846253	131	14947											
MAGT1	84061	hgsc.bcm.edu	37	chrX	77112935	77112935	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgtaactcatatgtatcaccCcgtttgggtttcccttttgc	6	17	7	11	1	2	0	2	0	0	0	3	0	3	0	3	1	2	4	3	1	3	7			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chrX:77112935C>T	ENST00000358075.6	-	4	632	c.546G>A	c.(544-546)cgG>cgA	p.R182R		NM_032121.5	NP_115497.4	Q9H0U3	MAGT1_HUMAN	magnesium transporter 1	150					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)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	magnesium ion transmembrane transporter activity (GO:0015095)			cervix(1)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|upper_aerodigestive_tract(1)	17						ATGTATCACCCCGTTTGGGTT	0.423																																					p.R182R		Atlas-SNP	.											.	MAGT1	51	.	0			c.G546A						PASS	.						148	137	141					X																	77112935		2203	4296	6499	SO:0001819	synonymous_variant	84061	exon4			ATCACCCCGTTTG		CCDS14436.2	Xq21.1	2014-09-17			ENSG00000102158	ENSG00000102158			28880	protein-coding gene	gene with protein product	"oligosaccharyltransferase 3 homolog B (S. cerevisiae)"	300715				15804357	Standard	NM_032121		Approved	DKFZp564K142, IAP, OST3B, MRX95	uc004fof.3	Q9H0U3	OTTHUMG00000021882	ENST00000358075.6:c.546G>A	X.37:g.77112935C>T		182	0	0		146	16	0.109589	NM_032121	B2RAR4|D3DTE3|Q53G00|Q6P577|Q8NBN6	Silent	SNP	ENST00000358075.6	37	CCDS14436.2																																																																																			.	.	none		0.423	MAGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057301.2	NM_032121		T	77112935	C	T	77112935	2	4	41	1	0	0	0	0	0	0	0	1	9205	610	22	2		2	MAGT1	23	77112935	Silent	SNP	C	TCGA-GS-A9TY-01A-11D-A38X-10	7688628	77112935	78157625	132	14948											
DACH2	117154	hgsc.bcm.edu	37	chrX	85950135	85950135	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tggccagccaggcattggggGtgctccaaccctcaatccac	8	7	11	15	0	1	0	1	0	0	0	3	0	3	0	5	4	3	2	5	4	2	1			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chrX:85950135G>T	ENST00000373125.4	+	5	884	c.884G>T	c.(883-885)gGt>gTt	p.G295V	DACH2_ENST00000373131.1_Missense_Mutation_p.G282V|DACH2_ENST00000510272.1_Missense_Mutation_p.G76V|DACH2_ENST00000508860.1_Missense_Mutation_p.G128V	NM_053281.3	NP_444511.1	Q96NX9	DACH2_HUMAN	dachshund family transcription factor 2	295					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						GGCATTGGGGGTGCTCCAACC	0.498																																					p.G295V		Atlas-SNP	.											.	DACH2	263	.	0			c.G884T						PASS	.						64	47	53					X																	85950135		2203	4300	6503	SO:0001583	missense	117154	exon5			TTGGGGGTGCTCC	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.884G>T	X.37:g.85950135G>T	ENSP00000362217:p.Gly295Val	332	0	0		678	152	0.224189	NM_053281	B1AJV3|B4DQG3|Q8NAY3|Q8ND17|Q96N55	Missense_Mutation	SNP	ENST00000373125.4	37	CCDS14455.1	.	.	.	.	.	.	.	.	.	.	g	0.282	-0.985447	0.02180	.	.	ENSG00000126733	ENST00000344497;ENST00000373131;ENST00000373125;ENST00000508860;ENST00000510272;ENST00000400297	D;D	0.81996	-1.56;-1.56	4.99	3.16	0.36331	.	0.450888	0.22302	N	0.061844	T	0.64560	0.2609	N	0.11427	0.14	0.44780	D	0.997788	B;B;B	0.30236	0.085;0.274;0.091	B;B;B	0.27887	0.022;0.084;0.007	T	0.53739	-0.8396	10	0.27082	T	0.32	.	8.6822	0.34216	0.0813:0.0:0.767:0.1516	.	161;282;295	Q1RMF5;Q96NX9-2;Q96NX9	.;.;DACH2_HUMAN	V	295;282;295;128;76;128	ENSP00000362223:G282V;ENSP00000362217:G295V	ENSP00000345134:G295V	G	+	2	0	DACH2	85836791	1.000000	0.71417	0.012000	0.15200	0.005000	0.04900	3.040000	0.49799	0.320000	0.23234	0.509000	0.49947	GGT	.	.	none		0.498	DACH2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359266.1	NM_053281		T	85950135	G	T	85950135	3	4	41	1	0	0	0	0	1	0	0	0	4223	1261	44	4	902	4	DACH2	23	85950135	Missense_Mutation	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	8837200	85950135	69320425	133	14949											
GLUD2	2747	hgsc.bcm.edu	37	chrX	120182459	120182459	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gataaaacatttgttgttcaGggatttggtaatgtgggcct	10	15	12	4	0	1	0	1	0	0	0	1	2	1	1	1	3	1	3	1	3	3	6			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chrX:120182459G>A	ENST00000328078.1	+	1	998	c.921G>A	c.(919-921)caG>caA	p.Q307Q		NM_012084.3	NP_036216.2	P49448	DHE4_HUMAN	glutamate dehydrogenase 2	307					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						TTGTTGTTCAGGGATTTGGTA	0.393																																					p.Q307Q		Atlas-SNP	.											.	GLUD2	89	.	0			c.G921A						PASS	.						226	206	213					X																	120182459		2203	4300	6503	SO:0001819	synonymous_variant	2747	exon1			TGTTCAGGGATTT	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.921G>A	X.37:g.120182459G>A		472	0	0		409	235	0.574572	NM_012084	B2R8G0|Q9UDQ4	Silent	SNP	ENST00000328078.1	37	CCDS14603.1																																																																																			.	.	none		0.393	GLUD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058133.1	NM_012084		A	120182459	G	A	120182459	2	1	41	1	0	0	0	0	0	0	0	1	6485	991	35	2		2	GLUD2	23	120182459	Silent	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	34232324	120182459	35088101	134	14950											
TFDP3	51270	hgsc.bcm.edu	37	chrX	132351082	132351082	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaggacgtcagtcatcctcGtcattctcactgaggtcgtc	8	11	10	12	3	4	2	4	1	1	1	9	3	5	3	1	2	0	0	1	2	0	1			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chrX:132351082G>A	ENST00000310125.4	-	1	1294	c.1206C>T	c.(1204-1206)gaC>gaT	p.D402D		NM_016521.2	NP_057605.3	Q5H9I0	TFDP3_HUMAN	transcription factor Dp family, member 3	402	Asp/Glu-rich (acidic; NCB domain).				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)					AGTCATCCTCGTCATTCTCAC	0.468																																					p.D402D		Atlas-SNP	.											.	TFDP3	92	.	0			c.C1206T						PASS	.						86	85	85					X																	132351082		2198	4290	6488	SO:0001819	synonymous_variant	51270	exon1			ATCCTCGTCATTC	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.1206C>T	X.37:g.132351082G>A		115	0	0		52	41	0.788462	NM_016521	Q6DK49|Q9NZ54	Silent	SNP	ENST00000310125.4	37	CCDS14636.2																																																																																			.	.	none		0.468	TFDP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058337.1	NM_016521		A	132351082	G	A	132351082	2	1	41	1	0	0	0	0	0	0	0	1	15814	1136	40	1		1	TFDP3	23	132351082	Silent	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	12168623	132351082	22919478	135	14951											
MAGEC2	51438	hgsc.bcm.edu	37	chrX	141291747	141291747	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gagtcgttgtcaacgttgcgGaatggaacgcctggaacggg	9	8	16	8	5	1	0	1	0	0	0	2	4	1	3	1	4	4	2	1	4	4	2			TCGA-GS-A9TY-01A-11D-A38X-10	TCGA-GS-A9TY-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	efd48c02-60c4-4db1-9c40-8ffcac8b4991	9dba8651-a374-4e47-862f-f91f46c7bd4d	g.chrX:141291747G>A	ENST00000247452.3	-	3	374	c.27C>T	c.(25-27)ttC>ttT	p.F9F		NM_016249.3	NP_057333.1	Q9UBF1	MAGC2_HUMAN	melanoma antigen family C, 2	9					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)					CAACGTTGCGGAATGGAACGC	0.537										HNSCC(46;0.14)																											p.F9F		Atlas-SNP	.											.	MAGEC2	102	.	0			c.C27T						PASS	.						117	106	110					X																	141291747		2203	4300	6503	SO:0001819	synonymous_variant	51438	exon3			GTTGCGGAATGGA	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.27C>T	X.37:g.141291747G>A		102	0	0		54	43	0.796296	NM_016249	Q5JZ00|Q96D45|Q9P1M6|Q9P1M7	Silent	SNP	ENST00000247452.3	37	CCDS14678.1																																																																																			.	.	none		0.537	MAGEC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058611.1	NM_016249		A	141291747	G	A	141291747	2	1	41	1	0	0	0	0	0	0	0	1	9190	1165	41	2		2	MAGEC2	23	141291747	Silent	SNP	G	TCGA-GS-A9TY-01A-11D-A38X-10	8940665	141291747	13978813	136	14952											
DVL1	1855	hgsc.bcm.edu	37	chr1	1273785	1273785	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctccttgaagccctccacGtgtgtgtacagccagtccac	7	9	9	16	2	0	1	0	1	0	0	3	1	3	1	5	0	3	2	5	0	2	2	rs151161721		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:1273785G>A	ENST00000378888.5	-	13	1655	c.1371C>T	c.(1369-1371)caC>caT	p.H457H	DVL1_ENST00000378891.5_Silent_p.H432H			O14640	DVL1_HUMAN	dishevelled segment polarity protein 1	457	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)		AGCCCTCCACGTGTGTGTACA	0.682																																					p.H432H		Atlas-SNP	.											.	DVL1	36	.	0			c.C1296T						PASS	.	G		0,4404		0,0,2202	35	34	34		1296	-1.9	0.9	1	dbSNP_134	34	2,8586	2.2+/-6.3	0,2,4292	no	coding-synonymous	DVL1	NM_004421.2		0,2,6494	AA,AG,GG		0.0233,0.0,0.0154		432/671	1273785	2,12990	2202	4294	6496	SO:0001819	synonymous_variant	1855	exon13			CTCCACGTGTGTG	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.1371C>T	1.37:g.1273785G>A		72	0	0		64	21	0.328125	NM_004421	Q5TA33|Q5TA35	Silent	SNP	ENST00000378888.5	37																																																																																				G|1.000;A|0.000	0.000	weak		0.682	DVL1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000008490.1	NM_004421		A	1273785	G	A	1273785	2	1	42	1	0	0	0	0	0	0	0	1	4837	1136	40	1		1	DVL1	1	1273785	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10		1273785	247976836	1	14953											
MIB2	142678	hgsc.bcm.edu	37	chr1	1565043	1565043	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgcgcgcaggatgaagaagtGcatcaggtgccaggtggtcg	9	6	17	9	4	1	2	1	1	0	1	2	3	1	3	1	4	2	2	1	4	2	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:1565043G>A	ENST00000357210.4	+	19	2978	c.2762G>A	c.(2761-2763)tGc>tAc	p.C921Y	MIB2_ENST00000378712.1_Silent_p.V737V|MIB2_ENST00000504599.1_Missense_Mutation_p.C877Y|MMP23B_ENST00000378675.3_5'Flank|MIB2_ENST00000518681.1_Missense_Mutation_p.C913Y|MIB2_ENST00000355826.5_Missense_Mutation_p.C964Y|MMP23B_ENST00000356026.5_5'Flank|MIB2_ENST00000360522.4_Missense_Mutation_p.C886Y|MIB2_ENST00000378708.1_Missense_Mutation_p.C827Y|MIB2_ENST00000378710.3_Missense_Mutation_p.C885Y|MIB2_ENST00000520777.1_Missense_Mutation_p.C974Y|MIB2_ENST00000505820.2_Missense_Mutation_p.C978Y	NM_080875.2	NP_543151.2	Q96AX9	MIB2_HUMAN	mindbomb E3 ubiquitin protein ligase 2	921					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)		ATGAAGAAGTGCATCAGGTGC	0.701																																					p.C978Y		Atlas-SNP	.											MIB2,NS,carcinoma,-1,1	MIB2	62	1	0			c.G2933A						PASS	.						34	41	39					1																	1565043		2090	4210	6300	SO:0001583	missense	142678	exon19			AGAAGTGCATCAG	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.2762G>A	1.37:g.1565043G>A	ENSP00000349741:p.Cys921Tyr	148	0	0		139	16	0.115108	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	37		.	.	.	.	.	.	.	.	.	.	g	20.5	3.999930	0.74818	.	.	ENSG00000197530	ENST00000520777;ENST00000357210;ENST00000360522;ENST00000378710;ENST00000355826;ENST00000518681;ENST00000505820;ENST00000504599;ENST00000378708	D;D;D;D;D;D;D;D;D	0.99656	-6.31;-6.31;-6.31;-6.31;-6.31;-6.31;-6.31;-6.31;-6.31	3.25	3.25	0.37280	Zinc finger, RING-type (2);	0.051571	0.85682	U	0.000000	D	0.99704	0.9887	H	0.95712	3.71	0.80722	D	1	D;D;D;D;D;D	0.89917	0.997;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.976;0.999;1.0;0.999;0.999;1.0	D	0.97157	0.9835	10	0.87932	D	0	-6.0944	13.9945	0.64388	0.0:0.0:1.0:0.0	.	886;827;913;974;907;921	Q96AX9-5;F2Z2L2;E9PHQ1;E9PGU1;Q96AX9-2;Q96AX9	.;.;.;.;.;MIB2_HUMAN	Y	974;921;886;885;964;913;978;877;827	ENSP00000428660:C974Y;ENSP00000349741:C921Y;ENSP00000353713:C886Y;ENSP00000367982:C885Y;ENSP00000348081:C964Y;ENSP00000428264:C913Y;ENSP00000426103:C978Y;ENSP00000426128:C877Y;ENSP00000367980:C827Y	ENSP00000348081:C964Y	C	+	2	0	MIB2	1554906	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	8.562000	0.90719	1.802000	0.52723	0.450000	0.29827	TGC	.	.	none		0.701	MIB2-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_080875		A	1565043	G	A	1565043	3	1	42	1	0	0	0	0	1	0	0	0	9576	1319	46	2	3007	2	MIB2	1	1565043	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	291258	1565043	247685578	2	14954											
PRDM16	63976	hgsc.bcm.edu	37	chr1	3321441	3321441	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaacgcttcgaatgtgaaaaCtgcgtgaaggtaacctgcgg	13	8	12	8	4	0	2	0	2	0	0	1	3	0	2	1	2	5	2	1	2	6	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:3321441C>G	ENST00000270722.5	+	7	1072	c.1023C>G	c.(1021-1023)aaC>aaG	p.N341K	PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000442529.2_Missense_Mutation_p.N341K|PRDM16_ENST00000378398.3_Missense_Mutation_p.N342K|PRDM16_ENST00000378391.2_Missense_Mutation_p.N341K|PRDM16_ENST00000514189.1_Missense_Mutation_p.N342K|PRDM16_ENST00000511072.1_Missense_Mutation_p.N342K|PRDM16_ENST00000441472.2_Missense_Mutation_p.N341K			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	341					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)		AATGTGAAAACTGCGTGAAGG	0.642			T	EVI1	"MDS, AML"																																p.N341K		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.C1023G						PASS	.						61	66	64					1																	3321441		2145	4267	6412	SO:0001583	missense	63976	exon7			TGAAAACTGCGTG	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.1023C>G	1.37:g.3321441C>G	ENSP00000270722:p.Asn341Lys	39	0	0		44	11	0.25	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Missense_Mutation	SNP	ENST00000270722.5	37	CCDS41236.2	.	.	.	.	.	.	.	.	.	.	C	19.09	3.759552	0.69763	.	.	ENSG00000142611	ENST00000511072;ENST00000378398;ENST00000441472;ENST00000442529;ENST00000378391;ENST00000514189;ENST00000270722;ENST00000512462;ENST00000408992;ENST00000509860	T;T;T;T;T;T;T;T;T	0.07216	3.21;3.21;3.21;3.21;3.21;3.21;3.21;3.21;3.21	4.63	2.73	0.32206	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.988944	0.08186	U	0.984619	T	0.10551	0.0258	N	0.04655	-0.195	0.44194	D	0.997016	D;P;D;D	0.71674	0.998;0.952;0.996;0.988	D;P;D;P	0.69654	0.965;0.636;0.917;0.901	T	0.38993	-0.9635	10	0.52906	T	0.07	.	7.3185	0.26513	0.0:0.7186:0.0:0.2814	.	341;341;341;341	Q9HAZ2;Q9HAZ2-2;F8WEV3;D3YTA5	PRD16_HUMAN;.;.;.	K	342;342;341;341;341;342;341;157;157;150	ENSP00000426975:N342K;ENSP00000367651:N342K;ENSP00000407968:N341K;ENSP00000405253:N341K;ENSP00000367643:N341K;ENSP00000421400:N342K;ENSP00000270722:N341K;ENSP00000422504:N157K;ENSP00000425796:N150K	ENSP00000270722:N341K	N	+	3	2	PRDM16	3311301	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	1.212000	0.32394	0.928000	0.37168	0.467000	0.42956	AAC	.	.	none		0.642	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114		G	3321441	C	G	3321441	3	3	42	1	0	0	0	0	1	0	0	0	12469	564	20	4	1049	4	PRDM16	1	3321441	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	1756398	3321441	245929180	3	14955											
PRDM2	7799	hgsc.bcm.edu	37	chr1	14105995	14105995	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tctctgaaaacttaaattacTatattgatggtaaaattcaa	17	15	4	5	0	2	2	1	2	1	0	3	2	2	2	0	1	2	1	0	1	10	7			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:14105995T>C	ENST00000235372.7	+	8	2561	c.1705T>C	c.(1705-1707)Tat>Cat	p.Y569H	PRDM2_ENST00000343137.4_Missense_Mutation_p.Y368H|PRDM2_ENST00000311066.5_Missense_Mutation_p.Y569H|PRDM2_ENST00000376048.5_Intron|PRDM2_ENST00000505823.1_Intron|PRDM2_ENST00000413440.1_Missense_Mutation_p.Y368H|PRDM2_ENST00000503842.1_Intron	NM_012231.4	NP_036363.2	Q13029	PRDM2_HUMAN	PR domain containing 2, with ZNF domain	569					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)		CTTAAATTACTATATTGATGG	0.383																																					p.Y569H		Atlas-SNP	.											.	PRDM2	147	.	0			c.T1705C						PASS	.						51	55	53					1																	14105995		2203	4300	6503	SO:0001583	missense	7799	exon8			AATTACTATATTG	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.1705T>C	1.37:g.14105995T>C	ENSP00000235372:p.Tyr569His	95	0	0		74	12	0.162162	NM_015866	B1AJZ4|B5MC68|Q13149|Q14550|Q5THJ1|Q5VUL9	Missense_Mutation	SNP	ENST00000235372.7	37	CCDS150.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.963193	0.53507	.	.	ENSG00000116731	ENST00000235372;ENST00000311066;ENST00000400800;ENST00000413440;ENST00000343137	T;T;T;T	0.03181	4.16;4.05;4.02;4.02	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.18087	0.0434	M	0.74881	2.28	0.58432	D	0.999993	D;D;D;D	0.89917	0.968;1.0;0.985;0.981	P;D;P;D	0.87578	0.885;0.998;0.888;0.946	T	0.00116	-1.2037	10	0.87932	D	0	.	14.651	0.68797	0.0:0.0:0.0:1.0	.	569;427;569;569	A8MW16;Q5THJ0;Q13029;Q13029-2	.;.;PRDM2_HUMAN;.	H	569;569;569;368;368	ENSP00000235372:Y569H;ENSP00000312352:Y569H;ENSP00000411103:Y368H;ENSP00000341621:Y368H	ENSP00000235372:Y569H	Y	+	1	0	PRDM2	13978582	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.673000	0.83973	2.129000	0.65627	0.533000	0.62120	TAT	.	.	none		0.383	PRDM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021792.2	NM_012231		C	14105995	T	C	14105995	3	2	42	1	0	0	0	0	1	0	0	0	12470	1522	53	3	1731	3	PRDM2	1	14105995	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	10784554	14105995	235144626	4	14956											
HSPG2	3339	hgsc.bcm.edu	37	chr1	22183832	22183832	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gctccggggcgcacgctctgGctccgctgctcctccacagt	3	8	12	18	4	1	0	0	0	1	0	5	0	5	0	4	3	1	6	4	3	0	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:22183832G>A	ENST00000374695.3	-	43	5419	c.5340C>T	c.(5338-5340)agC>agT	p.S1780S	HSPG2_ENST00000430507.1_5'Flank	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	1780	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)	GCACGCTCTGGCTCCGCTGCT	0.647																																					p.S1780S		Atlas-SNP	.											.	HSPG2	311	.	0			c.C5340T						PASS	.						89	89	89					1																	22183832		2203	4300	6503	SO:0001819	synonymous_variant	3339	exon43			GCTCTGGCTCCGC	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.5340C>T	1.37:g.22183832G>A		86	0	0		60	18	0.3	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																			.	.	none		0.647	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529		A	22183832	G	A	22183832	2	1	42	1	0	0	0	0	0	0	0	1	7439	1194	42	2		2	HSPG2	1	22183832	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	8077837	22183832	227066789	5	14957											
ZBTB8OS	5928	hgsc.bcm.edu	37	chr1	33116071	33116071	+	5'Flank	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	actggcggatacttggccttGatcgccttctgttcttcagt	5	15	10	11	2	3	1	1	1	2	0	4	2	3	2	2	3	1	1	2	3	1	6			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:33116071G>A	ENST00000373493.5	+	0	0				ZBTB8OS_ENST00000373501.2_Silent_p.I20I|ZBTB8OS_ENST00000341885.5_Silent_p.I32I|RBBP4_ENST00000414241.3_5'Flank|RBBP4_ENST00000458695.2_5'Flank|ZBTB8OS_ENST00000492007.1_5'UTR|RBBP4_ENST00000373485.1_5'Flank|RBBP4_ENST00000544435.1_5'Flank|ZBTB8OS_ENST00000468695.1_Silent_p.I32I	NM_001135255.1|NM_005610.2	NP_001128727.1|NP_005601.1	Q09028	RBBP4_HUMAN	retinoblastoma binding protein 4						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)				ACTTGGCCTTGATCGCCTTCT	0.488																																					p.I32I		Atlas-SNP	.											.	ZBTB8OS	9	.	0			c.C96T						PASS	.						225	170	189					1																	33116071		2203	4300	6503	SO:0001631	upstream_gene_variant	339487	exon1			GGCCTTGATCGCC	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		1.37:g.33116071G>A	Exception_encountered	121	0	0		123	46	0.373984	NM_178547	B2R6G9|B4DRH0|D3DPQ3|P31149|Q53H02|Q96BV9	Silent	SNP	ENST00000373493.5	37	CCDS366.1	.	.	.	.	.	.	.	.	.	.	G	12.04	1.819270	0.32145	.	.	ENSG00000176261	ENST00000436661	.	.	.	5.66	4.75	0.60458	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-2.2676	10.2329	0.43266	0.0761:0.1463:0.7776:0.0	.	.	.	.	X	31	.	.	Q	-	1	0	ZBTB8OS	32888658	0.991000	0.36638	0.979000	0.43373	0.993000	0.82548	0.908000	0.28545	1.533000	0.49186	0.655000	0.94253	CAA	.	.	none		0.488	RBBP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021957.3	NM_005610		A	33116071	G	A	33116071	1	1	42	0	1	0	0	0	0	0	0	0	17572	1280	45	2		2	ZBTB8OS	1	33116071	5'Flank	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	10932239	33116071	216134550	6	14958											
RLF	6018	hgsc.bcm.edu	37	chr1	40697260	40697262	+	In_Frame_Del	DEL	GTC	GTC	-																															agatacttttttggagcgctGtcgtcagtttggtgtcatag																										TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	GTC	GTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:40697260_40697262delGTC	ENST00000372771.4	+	7	1046_1048	c.1019_1021delGTC	c.(1018-1023)tgtcgt>tgt	p.R341del		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	341					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)			TTGGAGCGCTGTCGTCAGTTTGG	0.365																																					p.340_340del		Pindel,Atlas-Indel	.											.	RLF	152	.	0			c.1018_1020del						PASS	.																																			SO:0001651	inframe_deletion	6018	exon7			.		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.1019_1021delGTC	1.37:g.40697263_40697265delGTC	ENSP00000361857:p.Arg341del	200	0	.		179	36	0.201	NM_012421	Q14CQ1|Q9NU60	In_Frame_Del	DEL	ENST00000372771.4	37	CCDS448.1																																																																																			.	.	none		0.365	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1	NM_012421		-	40697262	GTC	-	40697260	7	5	42	1	0	1	0	1	0	0	0	0	13404	1377	48	0	1045	0	RLF	1	40697260	In_Frame_Del	DEL	GTC	TCGA-GS-A9TZ-01A-11D-A38X-10	7581189	40697260	208553361	7	14959											
EBNA1BP2	10969	hgsc.bcm.edu	37	chr1	43637173	43637173	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctcatctctcgctggaagtcGtcttctggatcaacagcttt	7	14	8	12	2	5	0	2	0	3	0	8	2	5	2	0	2	2	2	0	2	2	2	rs367548162		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:43637173G>A	ENST00000236051.2	-	3	441	c.300C>T	c.(298-300)gaC>gaT	p.D100D	EBNA1BP2_ENST00000431635.2_Silent_p.D155D|EBNA1BP2_ENST00000472982.1_5'UTR|WDR65_ENST00000372492.4_5'Flank|WDR65_ENST00000528956.1_5'Flank	NM_006824.2	NP_006815.2	Q99848	EBP2_HUMAN	EBNA1 binding protein 2	100					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)				GCTGGAAGTCGTCTTCTGGAT	0.493													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19764	0.0		0.0	False		,,,				2504	0.0				p.D155D		Atlas-SNP	.											.	EBNA1BP2	37	.	0			c.C465T						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	135	130	132		465,300	-1.7	1	1		132	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	EBNA1BP2	NM_001159936.1,NM_006824.2	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	155/362,100/307	43637173	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	10969	exon4			GAAGTCGTCTTCT	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.300C>T	1.37:g.43637173G>A		145	0	0		125	37	0.296	NM_001159936	Q96A66	Silent	SNP	ENST00000236051.2	37	CCDS478.1																																																																																			.	.	none		0.493	EBNA1BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019015.1			A	43637173	G	A	43637173	2	1	42	1	0	0	0	0	0	0	0	1	4887	1136	40	1		1	EBNA1BP2	1	43637173	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	2939913	43637173	205613448	8	14960											
ATPAF1	64756	hgsc.bcm.edu	37	chr1	47110904	47110904	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tacaaaaaactcataaccttCccttcttggcagagcacata	15	10	4	12	0	2	1	1	0	1	1	3	1	3	1	2	1	4	2	2	1	6	6			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:47110904C>T	ENST00000371937.4	-	7	717	c.613G>A	c.(613-615)Gaa>Aaa	p.E205K	ATPAF1_ENST00000576409.1_Missense_Mutation_p.E228K|ATPAF1_ENST00000542495.1_Missense_Mutation_p.E54K|ATPAF1_ENST00000574428.1_Intron|ATPAF1_ENST00000532925.1_Missense_Mutation_p.E117K|ATPAF1_ENST00000329231.4_Intron	NM_022745.4	NP_073582.3	Q5TC12	ATPF1_HUMAN	ATP synthase mitochondrial F1 complex assembly factor 1	205					protein complex assembly (GO:0006461)	mitochondrion (GO:0005739)				endometrium(1)|kidney(1)|large_intestine(2)|lung(4)	8	Acute lymphoblastic leukemia(166;0.155)					TCATAACCTTCCCTTCTTGGC	0.393																																					p.E228K	Melanoma(138;107 1777 21672 30337 52312)	Atlas-SNP	.											.	ATPAF1	19	.	0			c.G682A						PASS	.						158	150	153					1																	47110904		2203	4300	6503	SO:0001583	missense	64756	exon7			AACCTTCCCTTCT	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.613G>A	1.37:g.47110904C>T	ENSP00000361005:p.Glu205Lys	64	0	0		54	19	0.351852	NM_022745	B1AQW7|B7Z7D6|B7Z7I6|Q9H6E3	Missense_Mutation	SNP	ENST00000371937.4	37		.	.	.	.	.	.	.	.	.	.	C	20.8	4.052768	0.75960	.	.	ENSG00000123472	ENST00000371937;ENST00000492233;ENST00000542495;ENST00000532925	T	0.49139	0.79	5.81	4.9	0.64082	.	0.088508	0.85682	N	0.000000	T	0.47248	0.1435	L	0.50333	1.59	0.58432	D	0.999992	P;P	0.40578	0.505;0.722	B;B	0.42625	0.158;0.393	T	0.42189	-0.9466	10	0.36615	T	0.2	-8.6794	14.9549	0.71104	0.0:0.9317:0.0:0.0683	.	117;205	B7Z7I6;Q5TC12	.;ATPF1_HUMAN	K	205;9;54;117	ENSP00000361005:E205K	ENSP00000361005:E205K	E	-	1	0	ATPAF1	46883491	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.021000	0.76425	1.470000	0.48102	0.650000	0.86243	GAA	.	.	none		0.393	ATPAF1-201	KNOWN	basic	protein_coding	protein_coding		NM_022745		T	47110904	C	T	47110904	3	4	42	1	0	0	0	0	1	0	0	0	1200	864	30	2	385	2	ATPAF1	1	47110904	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	3473731	47110904	202139717	9	14961											
HOOK1	51361	hgsc.bcm.edu	37	chr1	60325900	60325900	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aacatgaaaataagatgcttCgcttacagcaagaaggctct	16	9	8	8	1	1	3	0	1	1	2	2	3	1	3	0	1	4	4	0	1	7	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:60325900C>T	ENST00000371208.3	+	15	1689	c.1432C>T	c.(1432-1434)Cgc>Tgc	p.R478C	HOOK1_ENST00000395561.2_Missense_Mutation_p.R436C|HOOK1_ENST00000465876.1_3'UTR	NM_015888.4	NP_056972.1	Q9UJC3	HOOK1_HUMAN	hook microtubule-tethering protein 1	478	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)					TAAGATGCTTCGCTTACAGCA	0.353																																					p.R478C		Atlas-SNP	.											.	HOOK1	54	.	0			c.C1432T						PASS	.						108	112	111					1																	60325900		2203	4300	6503	SO:0001583	missense	51361	exon15			ATGCTTCGCTTAC	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.1432C>T	1.37:g.60325900C>T	ENSP00000360252:p.Arg478Cys	258	0	0		169	42	0.248521	NM_015888	A8K8E9|A8MU44|B4DX15|O60561|Q5TG44	Missense_Mutation	SNP	ENST00000371208.3	37	CCDS612.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.220105	0.79464	.	.	ENSG00000134709	ENST00000371208;ENST00000395561	T;T	0.23348	1.91;1.91	4.95	4.95	0.65309	.	0.171400	0.51477	D	0.000098	T	0.48259	0.1490	M	0.69823	2.125	0.80722	D	1	D	0.60575	0.988	P	0.58820	0.846	T	0.50242	-0.8851	10	0.72032	D	0.01	.	18.7375	0.91761	0.0:1.0:0.0:0.0	.	478	Q9UJC3	HOOK1_HUMAN	C	478;436	ENSP00000360252:R478C;ENSP00000378928:R436C	ENSP00000360252:R478C	R	+	1	0	HOOK1	60098488	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.167000	0.50793	2.733000	0.93635	0.655000	0.94253	CGC	.	.	none		0.353	HOOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024934.1	NM_015888		T	60325900	C	T	60325900	3	4	42	1	0	0	0	0	1	0	0	0	7291	884	31	1	1490	1	HOOK1	1	60325900	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	13214996	60325900	188924721	10	14962											
SGIP1	84251	hgsc.bcm.edu	37	chr1	67133214	67133214	+	Splice_Site	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcctttttgctgatcacagaGgcgcagcccggtaagaactc	9	10	10	12	2	1	3	1	1	0	2	3	3	2	3	2	2	3	3	2	2	2	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:67133214G>C	ENST00000371037.4	+	9	550	c.473G>C	c.(472-474)aGg>aCg	p.R158T	SGIP1_ENST00000237247.6_Splice_Site_p.R162T|AL139147.1_ENST00000502413.2_Intron|SGIP1_ENST00000371039.1_Intron|SGIP1_ENST00000371035.3_Splice_Site_p.R115T|SGIP1_ENST00000371036.3_Intron|SGIP1_ENST00000468286.1_Intron	NM_032291.2	NP_115667.2	Q9BQI5	SGIP1_HUMAN	SH3-domain GRB2-like (endophilin) interacting protein 1	158					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						TGATCACAGAGGCGCAGCCCG	0.423																																					p.R158T		Atlas-SNP	.											.	SGIP1	272	.	0			c.G473C						PASS	.						171	173	172					1																	67133214		2203	4300	6503	SO:0001630	splice_region_variant	84251	exon9			CACAGAGGCGCAG	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.472-1G>C	1.37:g.67133214G>C		110	0	0		90	20	0.222222	NM_032291	A6NL81|A6NLD1|Q4LE32|Q5VYE2|Q5VYE3|Q5VYE4|Q68D76|Q6MZY6|Q8IWC2	Missense_Mutation	SNP	ENST00000371037.4	37	CCDS30744.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.974426	0.74246	.	.	ENSG00000118473	ENST00000237247;ENST00000371035;ENST00000371037	T;T;T	0.17528	2.27;2.27;2.27	6.01	6.01	0.97437	.	1.194550	0.05982	N	0.644385	T	0.28928	0.0718	L	0.50333	1.59	0.80722	D	1	D	0.54601	0.967	D	0.63597	0.916	T	0.00484	-1.1712	10	0.29301	T	0.29	0.4172	18.015	0.89236	0.0:0.0:1.0:0.0	.	158	Q9BQI5	SGIP1_HUMAN	T	162;115;158	ENSP00000237247:R162T;ENSP00000360074:R115T;ENSP00000360076:R158T	ENSP00000237247:R162T	R	+	2	0	SGIP1	66905802	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.078000	0.76821	2.861000	0.98227	0.650000	0.86243	AGG	.	.	none		0.423	SGIP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025395.4	NM_032291	Missense_Mutation	C	67133214	G	C	67133214	5	2	42	1	0	0	0	0	0	0	1	0	14221	1014	35	4	507	4	SGIP1	1	67133214	Splice_Site	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	6807314	67133214	182117407	11	14963											
TGFBR3	7049	hgsc.bcm.edu	37	chr1	92161330	92161330	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttagggtgtccagaccatggAaaattgctataaaggagaga	15	9	12	5	0	0	2	0	0	0	2	1	5	1	4	2	3	1	1	2	3	6	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:92161330A>T	ENST00000525962.1	-	15	2397	c.2336T>A	c.(2335-2337)tTc>tAc	p.F779Y	TGFBR3_ENST00000370399.2_Missense_Mutation_p.F778Y|TGFBR3_ENST00000212355.4_Missense_Mutation_p.F779Y			Q03167	TGBR3_HUMAN	transforming growth factor, beta receptor III	779					blastocyst development (GO:0001824)|blood vessel development (GO:0001568)|BMP signaling pathway (GO:0030509)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell proliferation (GO:0060038)|cell growth (GO:0016049)|cell migration (GO:0016477)|definitive erythrocyte differentiation (GO:0060318)|definitive hemopoiesis (GO:0060216)|epithelial to mesenchymal transition (GO:0001837)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|negative regulation of cellular component movement (GO:0051271)|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 transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|palate development (GO:0060021)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of protein binding (GO:0043393)|response to follicle-stimulating hormone (GO:0032354)|response to hypoxia (GO:0001666)|response to luteinizing hormone (GO:0034699)|response to prostaglandin E (GO:0034695)|transforming growth factor beta receptor complex assembly (GO:0007181)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	coreceptor activity (GO:0015026)|glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|PDZ domain binding (GO:0030165)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type III (GO:0070123)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta-activated receptor activity (GO:0005024)|type II transforming growth factor beta receptor binding (GO:0005114)			endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(24)|ovary(3)|prostate(4)|skin(1)|stomach(1)|urinary_tract(3)	55		all_lung(203;0.00719)|Lung NSC(277;0.0268)		all cancers(265;0.0108)|Epithelial(280;0.0825)		CAGACCATGGAAAATTGCTAT	0.443																																					p.F779Y		Atlas-SNP	.											.	TGFBR3	103	.	0			c.T2336A						PASS	.						106	101	103					1																	92161330		2203	4300	6503	SO:0001583	missense	7049	exon16			CCATGGAAAATTG	L07594	CCDS30770.1, CCDS55614.1	1p33-p32	2008-02-05	2007-02-15		ENSG00000069702	ENSG00000069702		"Proteoglycans / Cell surface : Other"	11774	protein-coding gene	gene with protein product	"betaglycan proteoglycan"	600742	"transforming growth factor, beta receptor III (betaglycan, 300kDa)"			1333192, 1319842	Standard	NM_001195684		Approved	betaglycan, BGCAN	uc001doh.3	Q03167	OTTHUMG00000010097	ENST00000525962.1:c.2336T>A	1.37:g.92161330A>T	ENSP00000436127:p.Phe779Tyr	172	0	0		124	32	0.258065	NM_003243	A0AUW8|A8K5N0|B9EG88|Q5T2T4|Q5U731|Q9UGI2	Missense_Mutation	SNP	ENST00000525962.1	37	CCDS30770.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.923604	0.92319	.	.	ENSG00000069702	ENST00000212355;ENST00000370399;ENST00000525962;ENST00000465892	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	5.5	5.5	0.81552	.	0.171303	0.52532	D	0.000075	T	0.25005	0.0607	L	0.51422	1.61	0.45822	D	0.998696	P;P;P	0.51653	0.824;0.947;0.824	B;P;B	0.51550	0.258;0.673;0.258	T	0.03296	-1.1051	10	0.14656	T	0.56	-19.6117	15.6091	0.76699	1.0:0.0:0.0:0.0	.	779;778;779	A8K5N0;Q03167-2;Q03167	.;.;TGBR3_HUMAN	Y	779;778;779;778	ENSP00000212355:F779Y;ENSP00000359426:F778Y;ENSP00000436127:F779Y;ENSP00000432638:F778Y	ENSP00000212355:F779Y	F	-	2	0	TGFBR3	91933918	1.000000	0.71417	0.997000	0.53966	0.930000	0.56654	5.420000	0.66441	2.090000	0.63153	0.460000	0.39030	TTC	.	.	none		0.443	TGFBR3-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382308.1	NM_003243		T	92161330	A	T	92161330	3	4	42	1	0	0	0	0	1	0	0	0	15838	246	9	5	227	5	TGFBR3	1	92161330	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	25028116	92161330	157089291	12	14964											
LRRC39	127495	hgsc.bcm.edu	37	chr1	100623819	100623819	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atcacatatatctctgttaaCagccagttctagtttctcca	11	15	4	11	0	4	0	1	0	3	0	6	0	4	0	2	0	2	3	2	0	4	6			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:100623819C>A	ENST00000370137.1	-	6	679	c.481G>T	c.(481-483)Gtt>Ttt	p.V161F	LRRC39_ENST00000370138.1_Missense_Mutation_p.V161F|LRRC39_ENST00000342895.3_Missense_Mutation_p.V161F	NM_001256386.1|NM_144620.3	NP_001243315.1|NP_653221.1	Q96DD0	LRC39_HUMAN	leucine rich repeat containing 39	161										endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|skin(1)	13		all_epithelial(167;0.000542)|all_lung(203;0.0154)|Lung NSC(277;0.0155)		Epithelial(280;0.0826)|all cancers(265;0.135)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.195)		TCTCTGTTAACAGCCAGTTCT	0.398																																					p.V161F		Atlas-SNP	.											LRRC39,caecum,carcinoma,+1,1	LRRC39	37	1	0			c.G481T						PASS	.						180	186	184					1																	100623819		2203	4300	6503	SO:0001583	missense	127495	exon6			TGTTAACAGCCAG	AK096892	CCDS766.1, CCDS58014.1	1p21.3	2008-02-05			ENSG00000122477	ENSG00000122477			28228	protein-coding gene	gene with protein product						12975309	Standard	NM_001256385		Approved	MGC14816	uc001dsx.2	Q96DD0	OTTHUMG00000010839	ENST00000370137.1:c.481G>T	1.37:g.100623819C>A	ENSP00000359156:p.Val161Phe	231	0	0		179	44	0.24581	NM_144620	B3KUD2|D3DT56|Q5VVK7	Missense_Mutation	SNP	ENST00000370137.1	37	CCDS766.1	.	.	.	.	.	.	.	.	.	.	C	15.11	2.734973	0.48939	.	.	ENSG00000122477	ENST00000370137;ENST00000370138;ENST00000342895;ENST00000370136	T;T;T	0.17528	2.27;2.27;2.27	5.36	5.36	0.76844	.	0.000000	0.52532	D	0.000062	T	0.25269	0.0614	L	0.51422	1.61	0.54753	D	0.999989	D;D	0.76494	0.999;0.999	D;P	0.66979	0.948;0.888	T	0.00939	-1.1507	10	0.20046	T	0.44	.	19.4651	0.94934	0.0:1.0:0.0:0.0	.	161;161	Q96DD0-2;Q96DD0	.;LRC39_HUMAN	F	161	ENSP00000359156:V161F;ENSP00000359157:V161F;ENSP00000344470:V161F	ENSP00000344470:V161F	V	-	1	0	LRRC39	100396407	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	4.784000	0.62411	2.671000	0.90904	0.655000	0.94253	GTT	.	.	none		0.398	LRRC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029917.2	NM_144620		A	100623819	C	A	100623819	3	1	42	1	0	0	0	0	1	0	0	0	9004	478	17	4	546	4	LRRC39	1	100623819	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	8462489	100623819	148626802	13	14965											
FNDC7	163479	hgsc.bcm.edu	37	chr1	109265194	109265194	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tggatctagcaaatcatcttCagcaatgaccctgaaaactg	14	10	7	10	0	4	2	2	2	2	0	4	3	4	3	1	1	3	2	1	1	5	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:109265194C>T	ENST00000370017.3	+	5	1113	c.836C>T	c.(835-837)tCa>tTa	p.S279L	FNDC7_ENST00000271311.2_Missense_Mutation_p.S280L	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	279	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)		AAATCATCTTCAGCAATGACC	0.448																																					p.S279L		Atlas-SNP	.											.	FNDC7	113	.	0			c.C836T						PASS	.						72	63	66					1																	109265194		2203	4300	6503	SO:0001583	missense	163479	exon5			CATCTTCAGCAAT		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.836C>T	1.37:g.109265194C>T	ENSP00000359034:p.Ser279Leu	127	0	0		113	33	0.292035	NM_001144937	A1L468|E9PAZ5|Q6PF16|Q8NA51	Missense_Mutation	SNP	ENST00000370017.3	37	CCDS44185.1	.	.	.	.	.	.	.	.	.	.	C	13.57	2.277637	0.40294	.	.	ENSG00000143107	ENST00000370017;ENST00000271311	T;T	0.22134	1.97;1.97	5.91	4.94	0.65067	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.688360	0.15255	N	0.272122	T	0.06508	0.0167	L	0.44542	1.39	0.09310	N	1	B;P	0.40000	0.349;0.698	B;B	0.27380	0.079;0.079	T	0.16364	-1.0405	10	0.25751	T	0.34	-6.6208	12.3366	0.55071	0.3228:0.6772:0.0:0.0	.	280;279	Q5VTL7;E9PAZ5	FNDC7_HUMAN;.	L	279;280	ENSP00000359034:S279L;ENSP00000271311:S280L	ENSP00000271311:S280L	S	+	2	0	FNDC7	109066717	0.798000	0.28890	0.279000	0.24732	0.776000	0.43924	3.242000	0.51384	2.807000	0.96579	0.555000	0.69702	TCA	.	.	none		0.448	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532		T	109265194	C	T	109265194	3	4	42	1	0	0	0	0	1	0	0	0	5981	838	29	2	854	2	FNDC7	1	109265194	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	8641375	109265194	139985427	14	14966											
STXBP3	6814	hgsc.bcm.edu	37	chr1	109289364	109289364	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgcagtgtcgggaagatggCgccgccggtggcagagaggg	7	4	20	10	5	0	2	0	0	0	2	1	4	0	3	3	5	0	2	3	5	1	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:109289364C>T	ENST00000370008.3	+	1	55	c.5C>T	c.(4-6)gCg>gTg	p.A2V		NM_007269.2	NP_009200.2	O00186	STXB3_HUMAN	syntaxin binding protein 3	2	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)		GGGAAGATGGCGCCGCCGGTG	0.687											OREG0013625	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A2V		Atlas-SNP	.											.	STXBP3	44	.	0			c.C5T						PASS	.						22	28	26					1																	109289364		2035	3903	5938	SO:0001583	missense	6814	exon1			AGATGGCGCCGCC	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.5C>T	1.37:g.109289364C>T	ENSP00000359025:p.Ala2Val	138	0	0	1418	93	29	0.311828	NM_007269	A8K269|A8K5K7|Q53FW1|Q86YJ3|Q9UPD7	Missense_Mutation	SNP	ENST00000370008.3	37	CCDS790.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.549245	0.86127	.	.	ENSG00000116266	ENST00000370008	T	0.73469	-0.75	4.22	4.22	0.49857	.	0.230025	0.40064	N	0.001189	T	0.72366	0.3451	L	0.36672	1.1	0.39234	D	0.963721	D	0.76494	0.999	D	0.65874	0.939	T	0.77143	-0.2696	10	0.87932	D	0	-4.7439	11.9693	0.53055	0.0:1.0:0.0:0.0	.	2	O00186	STXB3_HUMAN	V	2	ENSP00000359025:A2V	ENSP00000359025:A2V	A	+	2	0	STXBP3	109090887	1.000000	0.71417	1.000000	0.80357	0.794000	0.44872	3.716000	0.54904	2.192000	0.70111	0.305000	0.20034	GCG	.	.	none		0.687	STXBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030591.1	NM_007269		T	109289364	C	T	109289364	3	4	42	1	0	0	0	0	1	0	0	0	15369	768	27	1	7	1	STXBP3	1	109289364	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	24170	109289364	139961257	15	14967											
ST7L	54879	hgsc.bcm.edu	37	chr1	113126634	113126634	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggactttggtgctggcactgCtgtgactgcctataaattgt	7	14	12	8	0	0	1	0	1	0	0	0	2	0	2	1	3	3	3	1	3	3	4	rs200595897		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:113126634C>A	ENST00000358039.4	-	7	1120	c.816G>T	c.(814-816)caG>caT	p.Q272H	ST7L_ENST00000369668.2_Missense_Mutation_p.Q272H|ST7L_ENST00000544629.1_Missense_Mutation_p.Q207H|ST7L_ENST00000543570.1_Missense_Mutation_p.Q255H|ST7L_ENST00000343210.7_Missense_Mutation_p.Q272H|ST7L_ENST00000369669.1_Missense_Mutation_p.Q89H|ST7L_ENST00000490067.1_Missense_Mutation_p.Q255H|ST7L_ENST00000369666.1_Missense_Mutation_p.Q255H|ST7L_ENST00000538187.1_Missense_Mutation_p.Q216H|ST7L_ENST00000360743.4_Missense_Mutation_p.Q272H|ST7L_ENST00000463235.1_5'UTR	NM_017744.4|NM_138727.3	NP_060214.2|NP_620055.1	Q8TDW4	ST7L_HUMAN	suppression of tumorigenicity 7 like	272					negative regulation of cell growth (GO:0030308)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(4)|large_intestine(3)|lung(1)|prostate(2)|stomach(1)|urinary_tract(3)	15	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)		GCTGGCACTGCTGTGACTGCC	0.408																																					p.Q272H		Atlas-SNP	.											.	ST7L	31	.	0			c.G816T						PASS	.						179	160	166					1																	113126634		2203	4300	6503	SO:0001583	missense	54879	exon7			GCACTGCTGTGAC	AB081317	CCDS848.1, CCDS849.1, CCDS850.1, CCDS852.1	1p13.1	2008-06-06			ENSG00000007341	ENSG00000007341			18441	protein-coding gene	gene with protein product						12012006	Standard	NM_138729		Approved	FLJ20284, STLR, ST7R, FAM4B	uc001ecd.3	Q8TDW4	OTTHUMG00000011753	ENST00000358039.4:c.816G>T	1.37:g.113126634C>A	ENSP00000350734:p.Gln272His	174	0	0		164	46	0.280488	NM_138729	A8K4S7|Q49AH6|Q5TEI4|Q5U5K6|Q6N067|Q7Z2Z0|Q7Z3C2|Q8N7P8|Q8TDW1|Q8TDW2|Q8TDW3|Q9NXF3	Missense_Mutation	SNP	ENST00000358039.4	37	CCDS848.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.90|14.90	2.673767|2.673767	0.47781|0.47781	.|.	.|.	ENSG00000007341|ENSG00000007341	ENST00000358039;ENST00000360743;ENST00000369673;ENST00000544629;ENST00000369669;ENST00000490067;ENST00000369668;ENST00000343210;ENST00000369666;ENST00000538187;ENST00000543570;ENST00000369665;ENST00000369664|ENST00000418497	T;T;T;T;T;T;T;T;T;T;T|.	0.75704|.	-0.96;2.18;-0.96;-0.96;2.18;2.18;2.18;2.18;2.18;-0.96;2.18|.	5.66|5.66	1.52|1.52	0.23074|0.23074	Tetratricopeptide-like helical (1);|.	0.475023|.	0.24191|.	N|.	0.040710|.	T|T	0.47507|0.47507	0.1449|0.1449	M|M	0.62723|0.62723	1.935|1.935	0.45946|0.45946	D|D	0.998775|0.998775	D;P;P;B;B;B;B;B|.	0.64830|.	0.994;0.882;0.593;0.14;0.14;0.14;0.14;0.169|.	P;P;B;B;B;B;B;B|.	0.62491|.	0.903;0.579;0.187;0.077;0.132;0.132;0.132;0.125|.	T|T	0.44159|0.44159	-0.9346|-0.9346	10|5	0.51188|.	T|.	0.08|.	-8.5894|-8.5894	9.5348|9.5348	0.39216|0.39216	0.0:0.6983:0.0:0.3017|0.0:0.6983:0.0:0.3017	.|.	255;216;207;272;255;255;272;272|.	B7Z8V6;B7Z7D4;F5H2P3;Q8TDW4-5;Q8TDW4-6;Q8TDW4-3;Q8TDW4-2;Q8TDW4|.	.;.;.;.;.;.;.;ST7L_HUMAN|.	H|I	272;272;150;207;89;255;272;272;255;216;255;150;216|144	ENSP00000350734:Q272H;ENSP00000353972:Q272H;ENSP00000445499:Q207H;ENSP00000358683:Q89H;ENSP00000417140:Q255H;ENSP00000358682:Q272H;ENSP00000345312:Q272H;ENSP00000358680:Q255H;ENSP00000444021:Q216H;ENSP00000444088:Q255H;ENSP00000358678:Q216H|.	ENSP00000345312:Q272H|.	Q|S	-|-	3|2	2|0	ST7L|ST7L	112928157|112928157	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.967000|0.967000	0.64934|0.64934	0.888000|0.888000	0.28268|0.28268	0.273000|0.273000	0.22049|0.22049	0.563000|0.563000	0.77884|0.77884	CAG|AGC	C|0.999;T|0.001	.	alt		0.408	ST7L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032504.3			A	113126634	C	A	113126634	3	1	42	1	0	0	0	0	1	0	0	0	15245	796	28	4	986	4	ST7L	1	113126634	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	3837270	113126634	136123987	16	14968											
ITGA10	8515	hgsc.bcm.edu	37	chr1	145537774	145537774	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggtggaatgtgccgccccttCtgctcatgcccggctctgca	4	10	12	15	2	3	0	1	0	2	0	3	1	3	1	4	3	4	3	4	3	1	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:145537774C>T	ENST00000369304.3	+	21	2787	c.2612C>T	c.(2611-2613)tCt>tTt	p.S871F	ITGA10_ENST00000539363.1_Missense_Mutation_p.S728F|ITGA10_ENST00000538811.1_Missense_Mutation_p.S740F	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	871					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)					GCCGCCCCTTCTGCTCATGCC	0.592																																					p.S871F		Atlas-SNP	.											.	ITGA10	131	.	0			c.C2612T						PASS	.						62	65	64					1																	145537774		2203	4300	6503	SO:0001583	missense	8515	exon21			CCCCTTCTGCTCA	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.2612C>T	1.37:g.145537774C>T	ENSP00000358310:p.Ser871Phe	81	0	0		80	18	0.225	NM_003637	B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Missense_Mutation	SNP	ENST00000369304.3	37	CCDS918.1	.	.	.	.	.	.	.	.	.	.	C	12.65	2.002323	0.35320	.	.	ENSG00000143127	ENST00000369304;ENST00000543043;ENST00000539363;ENST00000538811	T;T;T	0.48201	0.82;0.82;0.82	5.71	4.8	0.61643	Integrin alpha-2 (1);	0.906824	0.09669	N	0.771322	T	0.33933	0.0880	L	0.29908	0.895	0.09310	N	1	P;P;P;P	0.44877	0.708;0.708;0.845;0.752	P;P;P;P	0.51266	0.664;0.567;0.664;0.595	T	0.35375	-0.9791	10	0.59425	D	0.04	.	12.2744	0.54726	0.0:0.9179:0.0:0.0821	.	837;740;728;871	F5H3T9;F5GY13;B2RTV5;O75578	.;.;.;ITA10_HUMAN	F	871;837;728;740	ENSP00000358310:S871F;ENSP00000439894:S728F;ENSP00000440011:S740F	ENSP00000358310:S871F	S	+	2	0	ITGA10	144249131	0.018000	0.18449	0.006000	0.13384	0.468000	0.32798	2.425000	0.44723	1.423000	0.47198	0.655000	0.94253	TCT	.	.	none		0.592	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637		T	145537774	C	T	145537774	3	4	42	1	0	0	0	0	1	0	0	0	7882	913	32	2	2694	2	ITGA10	1	145537774	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	32411140	145537774	103712847	17	14969											
DCST1	149095	hgsc.bcm.edu	37	chr1	155013976	155013976	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	gggctacacgcctgaggataCcatggactcaggggagacag	11	5	15	10	1	1	2	1	1	0	1	1	5	1	4	2	5	2	1	2	5	2	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:155013976C>G	ENST00000295542.1	+	7	731	c.635C>G	c.(634-636)aCc>aGc	p.T212S	DCST1_ENST00000368419.2_Missense_Mutation_p.T212S|DCST1_ENST00000392480.1_Missense_Mutation_p.T212S|DCST1_ENST00000423025.2_Missense_Mutation_p.T187S	NM_152494.3	NP_689707.2	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1	212						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)			CCTGAGGATACCATGGACTCA	0.577																																					p.T212S		Atlas-SNP	.											.	DCST1	69	.	0			c.C635G						PASS	.						53	53	53					1																	155013976		2203	4300	6503	SO:0001583	missense	149095	exon7			AGGATACCATGGA	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.635C>G	1.37:g.155013976C>G	ENSP00000295542:p.Thr212Ser	73	0	0		76	25	0.328947	NM_152494	B4DXA0|E9PHV3|Q5T198|Q6P1W6|Q71S70|Q96M70	Missense_Mutation	SNP	ENST00000295542.1	37	CCDS1083.1	.	.	.	.	.	.	.	.	.	.	C	0.205	-1.041740	0.02013	.	.	ENSG00000163357	ENST00000295542;ENST00000392480;ENST00000423025;ENST00000368419	T;T;T;T	0.58940	0.3;0.3;0.3;0.3	4.27	-0.463	0.12164	.	3.667800	0.01104	N	0.005440	T	0.11922	0.0290	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;0.0	T	0.04229	-1.0967	10	0.17832	T	0.49	-0.0307	2.1458	0.03787	0.1423:0.455:0.2238:0.1789	.	187;237;212	E9PHV3;E9PJX3;Q5T197	.;.;DCST1_HUMAN	S	212;212;187;212	ENSP00000295542:T212S;ENSP00000376271:T212S;ENSP00000387369:T187S;ENSP00000357404:T212S	ENSP00000295542:T212S	T	+	2	0	DCST1	153280600	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.208000	0.09371	-0.171000	0.10797	-0.379000	0.06801	ACC	.	.	none		0.577	DCST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099006.1	NM_152494		G	155013976	C	G	155013976	3	3	42	1	0	0	0	0	1	0	0	0	4304	507	18	4	657	4	DCST1	1	155013976	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	9476202	155013976	94236645	18	14970											
IQGAP3	128239	hgsc.bcm.edu	37	chr1	156502774	156502774	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaggctggcatcacccacctCagaagcaggctacgggtgtt	9	7	13	12	1	2	1	2	0	0	1	2	2	2	1	2	4	2	5	2	4	2	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:156502774C>T	ENST00000361170.2	-	32	4111	c.4101G>A	c.(4099-4101)ctG>ctA	p.L1367L		NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	1367					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)					TCACCCACCTCAGAAGCAGGC	0.562																																					p.L1367L		Atlas-SNP	.											.	IQGAP3	146	.	0			c.G4101A						PASS	.						169	135	146					1																	156502774		2203	4300	6503	SO:0001819	synonymous_variant	128239	exon32			CCACCTCAGAAGC	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.4101G>A	1.37:g.156502774C>T		94	0	0		88	25	0.284091	NM_178229	Q5T3H8	Silent	SNP	ENST00000361170.2	37	CCDS1144.1																																																																																			.	.	none		0.562	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229		T	156502774	C	T	156502774	2	4	42	1	0	0	0	0	0	0	0	1	7825	813	29	2		2	IQGAP3	1	156502774	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	1488798	156502774	92747847	19	14971											
LY9	4063	hgsc.bcm.edu	37	chr1	160783595	160783595	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aatggaggctccattcttacCgtctcccgaacaccatgtga	10	10	8	13	2	2	1	0	1	2	0	4	3	3	2	4	2	2	1	4	2	3	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:160783595C>T	ENST00000263285.6	+	3	654	c.624C>T	c.(622-624)acC>acT	p.T208T	LY9_ENST00000341032.4_Silent_p.T208T|LY9_ENST00000368041.2_Silent_p.T168T|LY9_ENST00000368040.1_5'UTR|LY9_ENST00000368037.5_Silent_p.T208T|LY9_ENST00000392203.4_Silent_p.T208T|LY9_ENST00000471816.1_3'UTR			Q9HBG7	LY9_HUMAN	lymphocyte antigen 9	208	Ig-like C2-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)			CCATTCTTACCGTCTCCCGAA	0.562																																					p.T208T		Atlas-SNP	.											.	LY9	115	.	0			c.C624T						PASS	.						172	164	167					1																	160783595		2203	4300	6503	SO:0001819	synonymous_variant	4063	exon3			TCTTACCGTCTCC	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.624C>T	1.37:g.160783595C>T		59	0	0		58	11	0.189655	NM_001261457	A8K7N3|Q14775|Q5VYI3|Q6P2J4|Q9H4N5|Q9NQ24	Silent	SNP	ENST00000263285.6	37	CCDS30916.1																																																																																			.	.	none		0.562	LY9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060457.3	NM_002348		T	160783595	C	T	160783595	2	4	42	1	0	0	0	0	0	0	0	1	9110	639	23	1		1	LY9	1	160783595	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	4280821	160783595	88467026	20	14972											
HMCN1	83872	hgsc.bcm.edu	37	chr1	186077619	186077619	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctaatattgctggaactgatGagccccgggatatcactgtg	10	11	11	9	1	1	2	1	2	0	0	1	4	1	4	2	2	3	1	2	2	4	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:186077619G>A	ENST00000271588.4	+	71	11108	c.10879G>A	c.(10879-10881)Gag>Aag	p.E3627K	HMCN1_ENST00000367492.2_Missense_Mutation_p.E3627K	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3627	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						TGGAACTGATGAGCCCCGGGA	0.423																																					p.E3627K		Atlas-SNP	.											.	HMCN1	797	.	0			c.G10879A						PASS	.						117	107	110					1																	186077619		2203	4300	6503	SO:0001583	missense	83872	exon71			ACTGATGAGCCCC	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.10879G>A	1.37:g.186077619G>A	ENSP00000271588:p.Glu3627Lys	67	0	0		55	10	0.181818	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	14.84	2.654284	0.47467	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.65364	-0.15;-0.15	5.87	5.87	0.94306	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.398703	0.29508	N	0.011949	T	0.53786	0.1818	L	0.31752	0.955	0.09310	N	1	P	0.36837	0.571	P	0.44860	0.462	T	0.46247	-0.9205	10	0.05620	T	0.96	.	14.7159	0.69269	0.069:0.0:0.931:0.0	.	3627	Q96RW7	HMCN1_HUMAN	K	3627	ENSP00000271588:E3627K;ENSP00000356462:E3627K	ENSP00000271588:E3627K	E	+	1	0	HMCN1	184344242	1.000000	0.71417	0.787000	0.31911	0.930000	0.56654	4.165000	0.58196	2.941000	0.99782	0.655000	0.94253	GAG	.	.	none		0.423	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		A	186077619	G	A	186077619	3	1	42	1	0	0	0	0	1	0	0	0	7229	1291	45	2	11161	2	HMCN1	1	186077619	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	25294024	186077619	63173002	21	14973											
PTGS2	5743	hgsc.bcm.edu	37	chr1	186648465	186648465	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caaacttacgtgttgagcagTtttctccatagaatcctgtc	10	14	7	10	1	1	2	0	1	1	1	4	2	2	2	2	0	3	3	2	0	4	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:186648465T>A	ENST00000367468.5	-	2	294	c.158A>T	c.(157-159)aAc>aTc	p.N53I	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)	53	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)	TGTTGAGCAGTTTTCTCCATA	0.433																																					p.N53I		Atlas-SNP	.											.	PTGS2	144	.	0			c.A158T						PASS	.						137	115	122					1																	186648465		2203	4300	6503	SO:0001583	missense	5743	exon2			GAGCAGTTTTCTC	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.158A>T	1.37:g.186648465T>A	ENSP00000356438:p.Asn53Ile	182	0	0		152	26	0.171053	NM_000963	A8K802|Q16876	Missense_Mutation	SNP	ENST00000367468.5	37	CCDS1371.1	.	.	.	.	.	.	.	.	.	.	T	29.4	5.006720	0.93287	.	.	ENSG00000073756	ENST00000367468	T	0.69306	-0.39	5.27	5.27	0.74061	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	T	0.80808	0.4694	M	0.75777	2.31	0.80722	D	1	D	0.76494	0.999	D	0.71656	0.974	D	0.83543	0.0097	10	0.87932	D	0	-28.3851	14.879	0.70516	0.0:0.0:0.0:1.0	.	53	P35354	PGH2_HUMAN	I	53	ENSP00000356438:N53I	ENSP00000356438:N53I	N	-	2	0	PTGS2	184915088	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.807000	0.86032	1.979000	0.57680	0.533000	0.62120	AAC	.	.	none		0.433	PTGS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086157.2	NM_000963		A	186648465	T	A	186648465	3	1	42	1	0	0	0	0	1	0	0	0	12769	1725	60	5	1692	5	PTGS2	1	186648465	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	570846	186648465	62602156	22	14974											
ASPM	259266	hgsc.bcm.edu	37	chr1	197093397	197093397	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagatattgttttctttataCtctttgtgtgttttagaaag	9	21	8	3	0	2	2	0	0	2	2	2	3	2	2	0	0	1	2	0	0	5	10			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:197093397C>T	ENST00000367409.4	-	13	3489	c.3233G>A	c.(3232-3234)aGt>aAt	p.S1078N	ASPM_ENST00000367408.1_Missense_Mutation_p.S328N|ASPM_ENST00000294732.7_Missense_Mutation_p.S1078N	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	1078					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						TTTCTTTATACTCTTTGTGTG	0.289																																					p.S1078N		Atlas-SNP	.											.	ASPM	444	.	0			c.G3233A						PASS	.						79	81	80					1																	197093397		2202	4283	6485	SO:0001583	missense	259266	exon13			TTTATACTCTTTG	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.3233G>A	1.37:g.197093397C>T	ENSP00000356379:p.Ser1078Asn	765	0	0		579	154	0.265976	NM_001206846	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	37	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	C	3.744	-0.052963	0.07362	.	.	ENSG00000066279	ENST00000367409;ENST00000294732;ENST00000367408	T;T;T	0.58060	0.36;1.62;1.29	5.53	-0.305	0.12784	Calponin homology domain (1);	0.516189	0.20992	N	0.082012	T	0.15609	0.0376	N	0.01267	-0.92	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.17806	-1.0357	10	0.13853	T	0.58	.	2.2892	0.04134	0.1201:0.3525:0.1182:0.4092	.	1078;1078	Q4G1H1;Q8IZT6	.;ASPM_HUMAN	N	1078;1078;328	ENSP00000356379:S1078N;ENSP00000294732:S1078N;ENSP00000356378:S328N	ENSP00000294732:S1078N	S	-	2	0	ASPM	195360020	0.000000	0.05858	0.001000	0.08648	0.861000	0.49209	0.013000	0.13310	0.101000	0.17610	0.585000	0.79938	AGT	.	.	none		0.289	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136		T	197093397	C	T	197093397	3	4	42	1	0	0	0	0	1	0	0	0	1056	565	20	2	7264	2	ASPM	1	197093397	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	10444932	197093397	52157224	23	14975											
PLXNA2	5362	hgsc.bcm.edu	37	chr1	208216538	208216538	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcattgatatccgtctggagCtcagcaaaagctatgagaat	13	11	9	8	1	3	2	2	2	1	1	4	4	4	3	1	1	3	3	1	1	5	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:208216538C>T	ENST00000367033.3	-	21	4642	c.3885G>A	c.(3883-3885)gaG>gaA	p.E1295E		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	1295					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)		CCGTCTGGAGCTCAGCAAAAG	0.552																																					p.E1295E		Atlas-SNP	.											.	PLXNA2	178	.	0			c.G3885A						PASS	.						76	73	74					1																	208216538		2203	4300	6503	SO:0001819	synonymous_variant	5362	exon21			CTGGAGCTCAGCA	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.3885G>A	1.37:g.208216538C>T		87	0	0		70	10	0.142857	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Silent	SNP	ENST00000367033.3	37	CCDS31013.1																																																																																			.	.	none		0.552	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179		T	208216538	C	T	208216538	2	4	42	1	0	0	0	0	0	0	0	1	12129	796	28	2		2	PLXNA2	1	208216538	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	11123141	208216538	41034083	24	14976											
DTL	51514	hgsc.bcm.edu	37	chr1	212218054	212218054	+	Silent	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgaagaaggctttgttcgAttgtataacacagaatcaca	16	11	8	6	1	1	3	1	1	0	2	2	4	1	3	0	1	1	3	0	1	6	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:212218054A>C	ENST00000366991.4	+	3	545	c.231A>C	c.(229-231)cgA>cgC	p.R77R	DTL_ENST00000542077.1_Silent_p.R35R|DTL_ENST00000475419.1_3'UTR	NM_016448.2	NP_057532.2	Q9NZJ0	DTL_HUMAN	denticleless E3 ubiquitin protein ligase homolog (Drosophila)	77					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)		GCTTTGTTCGATTGTATAACA	0.303																																					p.R77R		Atlas-SNP	.											DTL,colon,carcinoma,+1,3	DTL	52	3	0			c.A231C						PASS	.						70	72	72					1																	212218054		2203	4300	6503	SO:0001819	synonymous_variant	51514	exon3			TGTTCGATTGTAT	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.231A>C	1.37:g.212218054A>C		724	0	0		584	66	0.113014	NM_016448	A8K8H8|D3DT98|Q5VT77|Q96SN0|Q9NW03|Q9NW34|Q9NWM5	Silent	SNP	ENST00000366991.4	37	CCDS1502.1																																																																																			.	.	none		0.303	DTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090182.1	NM_016448		C	212218054	A	C	212218054	2	2	42	1	0	0	0	0	0	0	0	1	4789	320	12	5		5	DTL	1	212218054	Silent	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	4001516	212218054	37032567	25	14977											
HHIPL2	79802	hgsc.bcm.edu	37	chr1	222721252	222721252	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aaagggggcccgtaatccagGcactgggggtgtccctgcag	8	6	16	11	1	0	0	0	0	0	0	2	0	2	0	3	5	1	3	3	5	2	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:222721252G>A	ENST00000343410.6	-	1	193	c.135C>T	c.(133-135)tgC>tgT	p.C45C		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	45					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)		CGTAATCCAGGCACTGGGGGT	0.607																																					p.C45C		Atlas-SNP	.											.	HHIPL2	122	.	0			c.C135T						PASS	.						31	35	34					1																	222721252		1918	4130	6048	SO:0001819	synonymous_variant	79802	exon1			ATCCAGGCACTGG	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.135C>T	1.37:g.222721252G>A		90	0	0		69	22	0.318841	NM_024746	Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Silent	SNP	ENST00000343410.6	37	CCDS1530.2																																																																																			.	.	none		0.607	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746		A	222721252	G	A	222721252	2	1	42	1	0	0	0	0	0	0	0	1	7103	1195	42	2		2	HHIPL2	1	222721252	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	10503198	222721252	26529369	26	14978											
ITPKB	3707	hgsc.bcm.edu	37	chr1	226924300	226924300	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccaatgagggagctaggcagCtccgagttcccggggtagga	9	6	16	10	2	0	1	0	1	0	0	2	4	2	3	3	5	2	5	3	5	3	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:226924300C>T	ENST00000272117.3	-	1	859	c.860G>A	c.(859-861)aGc>aAc	p.S287N	ITPKB_ENST00000429204.1_Missense_Mutation_p.S287N|ITPKB_ENST00000366784.1_Missense_Mutation_p.S287N			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	287					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)				AGCTAGGCAGCTCCGAGTTCC	0.577																																					p.S287N	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											.	ITPKB	158	.	0			c.G860A						PASS	.						47	52	50					1																	226924300		2203	4300	6503	SO:0001583	missense	3707	exon2			AGGCAGCTCCGAG	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.860G>A	1.37:g.226924300C>T	ENSP00000272117:p.Ser287Asn	65	0	0		47	11	0.234043	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Missense_Mutation	SNP	ENST00000272117.3	37	CCDS1555.1	.	.	.	.	.	.	.	.	.	.	C	12.10	1.837740	0.32513	.	.	ENSG00000143772	ENST00000272117;ENST00000429204;ENST00000366784	T;T;T	0.25250	1.82;1.82;1.81	4.21	2.28	0.28536	.	0.705821	0.13409	N	0.389999	T	0.10981	0.0268	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.37009	-0.9724	10	0.13853	T	0.58	.	7.0283	0.24952	0.0:0.7728:0.0:0.2272	.	287	P27987	IP3KB_HUMAN	N	287	ENSP00000272117:S287N;ENSP00000411152:S287N;ENSP00000355748:S287N	ENSP00000272117:S287N	S	-	2	0	ITPKB	224990923	0.021000	0.18746	0.002000	0.10522	0.102000	0.19082	1.392000	0.34486	0.387000	0.25024	0.561000	0.74099	AGC	.	.	none		0.577	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221		T	226924300	C	T	226924300	3	4	42	1	0	0	0	0	1	0	0	0	7927	797	28	2	2008	2	ITPKB	1	226924300	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	4203048	226924300	22326321	27	14979											
GGPS1	9453	hgsc.bcm.edu	37	chr1	235505867	235505867	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ttggtcaaggcctgaaagcaCccaggtgcagaatatcttgc	11	9	11	10	0	2	2	1	1	1	1	2	2	2	2	2	3	3	2	2	3	4	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:235505867C>G	ENST00000282841.5	+	4	915	c.683C>G	c.(682-684)aCc>aGc	p.T228S	GGPS1_ENST00000358966.2_Missense_Mutation_p.T228S|GGPS1_ENST00000488594.1_Missense_Mutation_p.T228S|GGPS1_ENST00000476121.1_Missense_Mutation_p.T228S|GGPS1_ENST00000391855.2_Missense_Mutation_p.T174S			O95749	GGPPS_HUMAN	geranylgeranyl diphosphate synthase 1	228					cholesterol biosynthetic process (GO:0006695)|farnesyl diphosphate biosynthetic process (GO:0045337)|geranyl diphosphate biosynthetic process (GO:0033384)|geranylgeranyl diphosphate biosynthetic process (GO:0033386)|isoprenoid metabolic process (GO:0006720)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	dimethylallyltranstransferase activity (GO:0004161)|farnesyltranstransferase activity (GO:0004311)|geranyltranstransferase activity (GO:0004337)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)	8	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;1.39e-05)		Zoledronate(DB00399)	CCTGAAAGCACCCAGGTGCAG	0.363																																					p.T228S		Atlas-SNP	.											.	GGPS1	23	.	0			c.C683G						PASS	.						70	74	73					1																	235505867		2203	4300	6503	SO:0001583	missense	9453	exon4			AAAGCACCCAGGT	AB016043	CCDS1604.1	1q43	2010-04-27			ENSG00000152904	ENSG00000152904	2.5.1.1, 2.5.1.10, 2.5.1.29		4249	protein-coding gene	gene with protein product		606982				9741684, 10101267	Standard	NR_036605		Approved	GGPPS1	uc001hwv.3	O95749	OTTHUMG00000037963	ENST00000282841.5:c.683C>G	1.37:g.235505867C>G	ENSP00000282841:p.Thr228Ser	121	0	0		106	34	0.320755	NM_001037277	A8MVQ8|Q5T2C8|Q6NW19	Missense_Mutation	SNP	ENST00000282841.5	37	CCDS1604.1	.	.	.	.	.	.	.	.	.	.	C	9.734	1.163108	0.21538	.	.	ENSG00000152904	ENST00000488594;ENST00000471812;ENST00000358966;ENST00000282841;ENST00000391855;ENST00000476121;ENST00000497327	T;T;T;T;T;T;T	0.76316	0.06;0.02;0.06;0.06;0.06;0.06;-1.01	6.17	6.17	0.99709	Terpenoid synthase (2);	0.000000	0.85682	D	0.000000	T	0.65238	0.2672	N	0.16098	0.37	0.80722	D	1	B	0.18741	0.03	B	0.23275	0.045	T	0.60591	-0.7233	10	0.09084	T	0.74	-11.438	20.8794	0.99867	0.0:1.0:0.0:0.0	.	228	O95749	GGPPS_HUMAN	S	228;228;228;228;174;228;228	ENSP00000418690:T228S;ENSP00000417772:T228S;ENSP00000351852:T228S;ENSP00000282841:T228S;ENSP00000375728:T174S;ENSP00000420183:T228S;ENSP00000417865:T228S	ENSP00000282841:T228S	T	+	2	0	GGPS1	233572490	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.932000	0.63476	2.941000	0.99782	0.655000	0.94253	ACC	.	.	none		0.363	GGPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092656.1	NM_004837		G	235505867	C	G	235505867	3	3	42	1	0	0	0	0	1	0	0	0	6368	507	18	4	693	4	GGPS1	1	235505867	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	8581567	235505867	13744754	28	14980											
LYST	1130	hgsc.bcm.edu	37	chr1	235966354	235966354	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gggatgacaattcttctgcaGattgatgactctataaatca	13	13	8	7	0	4	4	1	3	3	1	4	5	4	5	0	1	1	1	0	1	4	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:235966354G>C	ENST00000389794.3	-	8	3740	c.3566C>G	c.(3565-3567)tCt>tGt	p.S1189C	LYST_ENST00000389793.2_Missense_Mutation_p.S1189C|LYST_ENST00000536965.1_Missense_Mutation_p.S1189C			Q99698	LYST_HUMAN	lysosomal trafficking regulator	1189					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)			TTCTTCTGCAGATTGATGACT	0.328																																					p.S1189C		Atlas-SNP	.											.	LYST	370	.	0			c.C3566G						PASS	.						59	57	58					1																	235966354		2203	4300	6503	SO:0001583	missense	1130	exon8			TCTGCAGATTGAT	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.3566C>G	1.37:g.235966354G>C	ENSP00000374444:p.Ser1189Cys	96	0	0		92	35	0.380435	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	37	CCDS31062.1	.	.	.	.	.	.	.	.	.	.	G	15.08	2.727281	0.48833	.	.	ENSG00000143669	ENST00000389794;ENST00000389793;ENST00000536965	T;T;T	0.63417	-0.04;-0.04;1.13	5.2	5.2	0.72013	.	1.585600	0.03487	N	0.216015	T	0.67683	0.2919	N	0.22421	0.69	0.28915	N	0.892491	D;P	0.61697	0.99;0.77	P;P	0.52031	0.688;0.497	T	0.68281	-0.5450	10	0.59425	D	0.04	.	18.7355	0.91753	0.0:0.0:1.0:0.0	.	1189;1189	Q99698-3;Q99698	.;LYST_HUMAN	C	1189	ENSP00000374444:S1189C;ENSP00000374443:S1189C;ENSP00000438315:S1189C	ENSP00000374443:S1189C	S	-	2	0	LYST	234032977	0.699000	0.27786	0.992000	0.48379	0.504000	0.33889	1.100000	0.31025	2.452000	0.82932	0.655000	0.94253	TCT	.	.	none		0.328	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5			C	235966354	G	C	235966354	3	2	42	1	0	0	0	0	1	0	0	0	9137	942	33	4	8023	4	LYST	1	235966354	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	460487	235966354	13284267	29	14981											
CHRM3	1131	hgsc.bcm.edu	37	chr1	240071401	240071401	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttggaaagagaactgtgcCtccgggagagtgcttcattc	9	11	13	8	1	1	2	1	0	0	2	3	5	2	3	2	2	3	2	2	2	2	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:240071401C>A	ENST00000255380.4	+	5	1429	c.650C>A	c.(649-651)cCt>cAt	p.P217H		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	217					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)	AGAACTGTGCCTCCGGGAGAG	0.483																																					p.P217H		Atlas-SNP	.											CHRM3,NS,malignant_melanoma,0,2	CHRM3	118	2	0			c.C650A						PASS	.						156	161	160					1																	240071401		2203	4300	6503	SO:0001583	missense	1131	exon5			CTGTGCCTCCGGG	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.650C>A	1.37:g.240071401C>A	ENSP00000255380:p.Pro217His	208	0	0		160	22	0.1375	NM_000740	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Missense_Mutation	SNP	ENST00000255380.4	37	CCDS1616.1	.	.	.	.	.	.	.	.	.	.	C	18.82	3.704655	0.68615	.	.	ENSG00000133019	ENST00000255380	T	0.38560	1.13	5.79	5.79	0.91817	GPCR, rhodopsin-like superfamily (1);	0.182925	0.47852	D	0.000212	T	0.57829	0.2080	L	0.56280	1.765	0.80722	D	1	D	0.64830	0.994	P	0.62491	0.903	T	0.58272	-0.7665	10	0.72032	D	0.01	-22.6919	15.6263	0.76859	0.1379:0.8621:0.0:0.0	.	217	P20309	ACM3_HUMAN	H	217	ENSP00000255380:P217H	ENSP00000255380:P217H	P	+	2	0	CHRM3	238138024	1.000000	0.71417	0.977000	0.42913	0.912000	0.54170	4.831000	0.62752	2.731000	0.93534	0.650000	0.86243	CCT	.	.	none		0.483	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740		A	240071401	C	A	240071401	3	1	42	1	0	0	0	0	1	0	0	0	3380	681	24	4	652	4	CHRM3	1	240071401	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	4105047	240071401	9179220	30	14982											
OR2AK2	391191	hgsc.bcm.edu	37	chr1	248129487	248129487	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctccttgcgttccccttcacGggataaggcggtggcagtat	6	11	12	12	3	1	0	1	0	0	0	3	1	3	1	3	4	1	3	3	4	2	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:248129487G>A	ENST00000366480.3	+	1	953	c.854G>A	c.(853-855)cGg>cAg	p.R285Q	OR2L13_ENST00000366478.2_Intron	NM_001004491.1	NP_001004491.1	Q8NG84	O2AK2_HUMAN	olfactory receptor, family 2, subfamily AK, 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)			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)			TCCCCTTCACGGGATAAGGCG	0.502																																					p.R285Q	Melanoma(45;390 1181 23848 28461 41504)	Atlas-SNP	.											.	OR2AK2	90	.	0			c.G854A						PASS	.						144	115	124					1																	248129487		2203	4300	6503	SO:0001583	missense	391191	exon1			CTTCACGGGATAA	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.854G>A	1.37:g.248129487G>A	ENSP00000355436:p.Arg285Gln	215	0	0		167	27	0.161677	NM_001004491	B2RND1|Q6IF05	Missense_Mutation	SNP	ENST00000366480.3	37	CCDS31102.1	.	.	.	.	.	.	.	.	.	.	.	0.037	-1.303766	0.01353	.	.	ENSG00000187080	ENST00000366480	T	0.00044	8.83	3.04	-1.76	0.08006	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00039	0.0001	N	0.00446	-1.495	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.42616	-0.9441	9	0.02654	T	1	.	0.2301	0.00179	0.2893:0.1425:0.247:0.3211	.	285	Q8NG84	O2AK2_HUMAN	Q	285	ENSP00000355436:R285Q	ENSP00000355436:R285Q	R	+	2	0	OR2AK2	246196110	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.412000	0.01039	-0.016000	0.14127	-0.672000	0.03802	CGG	.	.	none		0.502	OR2AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096858.2	NM_001004491		A	248129487	G	A	248129487	3	1	42	1	0	0	0	0	1	0	0	0	10995	1116	39	1	856	1	OR2AK2	1	248129487	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	8058086	248129487	1121134	31	14983											
OR2M2	391194	hgsc.bcm.edu	37	chr1	248343746	248343746	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttctcctggatcctgggctcTacagatggaatcattgatgc	8	13	10	10	0	3	2	1	1	2	1	5	4	4	4	2	3	2	1	2	3	2	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr1:248343746T>C	ENST00000359682.2	+	1	459	c.459T>C	c.(457-459)tcT>tcC	p.S153S		NM_001004688.1	NP_001004688.1	Q96R28	OR2M2_HUMAN	olfactory receptor, family 2, subfamily M, member 2	153						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)			TCCTGGGCTCTACAGATGGAA	0.438																																					p.S153S		Atlas-SNP	.											.	OR2M2	149	.	0			c.T459C						PASS	.						183	187	185					1																	248343746		2203	4300	6503	SO:0001819	synonymous_variant	391194	exon1			GGGCTCTACAGAT	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.459T>C	1.37:g.248343746T>C		376	0	0		258	71	0.275194	NM_001004688	A3KFT4	Silent	SNP	ENST00000359682.2	37	CCDS31106.1																																																																																			.	.	none		0.438	OR2M2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097356.2	NM_001004688		C	248343746	T	C	248343746	2	2	42	1	0	0	0	0	0	0	0	1	11019	1509	53	3		3	OR2M2	1	248343746	Silent	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	214259	248343746	906875	32	14984											
TPO	7173	hgsc.bcm.edu	37	chr2	1440080	1440080	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acatgtctggatgtctccctTacatgctgcccccaaaatgc	9	11	7	14	0	2	0	0	0	2	0	3	1	2	1	3	1	4	1	3	1	3	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:1440080T>C	ENST00000345913.4	+	5	497	c.406T>C	c.(406-408)Tac>Cac	p.Y136H	TPO_ENST00000539820.1_Missense_Mutation_p.Y136H|TPO_ENST00000382198.1_Missense_Mutation_p.Y136H|TPO_ENST00000337415.3_Missense_Mutation_p.Y136H|TPO_ENST00000382201.3_Missense_Mutation_p.Y136H|TPO_ENST00000346956.3_Missense_Mutation_p.Y136H|TPO_ENST00000497517.2_Intron|TPO_ENST00000382269.3_Missense_Mutation_p.Y136H|TPO_ENST00000349624.3_Missense_Mutation_p.Y136H|TPO_ENST00000329066.4_Missense_Mutation_p.Y136H	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	136					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)	ATGTCTCCCTTACATGCTGCC	0.428																																					p.Y136H		Atlas-SNP	.											.	TPO	224	.	0			c.T406C						PASS	.						148	139	142					2																	1440080		2203	4300	6503	SO:0001583	missense	7173	exon5			CTCCCTTACATGC		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.406T>C	2.37:g.1440080T>C	ENSP00000318820:p.Tyr136His	150	0	0		107	34	0.317757	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	37	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	T	0.627	-0.818619	0.02776	.	.	ENSG00000115705	ENST00000382269;ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000539820;ENST00000329066;ENST00000382201;ENST00000423320;ENST00000382198;ENST00000422464	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	5.35	1.28	0.21552	.	1.077190	0.06972	N	0.818284	T	0.28267	0.0698	N	0.04018	-0.295	0.09310	N	1	B;B;B;B;B	0.16166	0.007;0.002;0.016;0.007;0.004	B;B;B;B;B	0.16722	0.009;0.004;0.016;0.005;0.002	T	0.22836	-1.0205	10	0.15952	T	0.53	-12.0061	7.5539	0.27812	0.0:0.2707:0.0:0.7293	.	136;136;136;136;136	P07202-4;P07202-5;E9PFM6;P07202-2;P07202	.;.;.;.;PERT_HUMAN	H	136;136;136;136;136;136;136;136;136;136;65	ENSP00000371704:Y136H;ENSP00000337263:Y136H;ENSP00000318820:Y136H;ENSP00000263886:Y136H;ENSP00000332044:Y136H;ENSP00000444840:Y136H;ENSP00000329869:Y136H;ENSP00000371636:Y136H;ENSP00000390994:Y136H;ENSP00000371633:Y136H;ENSP00000405788:Y65H	ENSP00000329869:Y136H	Y	+	1	0	TPO	1419087	0.007000	0.16637	0.078000	0.20375	0.040000	0.13550	-0.165000	0.09968	-0.013000	0.14199	0.260000	0.18958	TAC	.	.	none		0.428	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547		C	1440080	T	C	1440080	3	2	42	1	0	0	0	0	1	0	0	0	16425	1754	61	3	420	3	TPO	2	1440080	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10		1440080	241759293	33	14985											
PXDN	7837	hgsc.bcm.edu	37	chr2	1652954	1652954	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccccgctcctggcccgggaGtcattgggggggatcatgac	5	7	16	13	2	2	1	2	1	0	0	3	3	3	3	4	5	0	1	4	5	0	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:1652954G>T	ENST00000252804.4	-	17	2648	c.2598C>A	c.(2596-2598)gaC>gaA	p.D866E		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	866					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)		TGGCCCGGGAGTCATTGGGGG	0.657																																					p.D866E		Atlas-SNP	.											.	PXDN	255	.	0			c.C2598A						PASS	.						16	19	18					2																	1652954		2106	4209	6315	SO:0001583	missense	7837	exon17			CCGGGAGTCATTG	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.2598C>A	2.37:g.1652954G>T	ENSP00000252804:p.Asp866Glu	56	0	0		51	19	0.372549	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	37	CCDS46221.1	.	.	.	.	.	.	.	.	.	.	G	18.43	3.622388	0.66787	.	.	ENSG00000130508	ENST00000252804	D	0.84800	-1.9	5.36	4.47	0.54385	.	0.000000	0.85682	D	0.000000	D	0.93609	0.7959	H	0.94222	3.51	0.53005	D	0.999969	D	0.71674	0.998	D	0.75484	0.986	D	0.94094	0.7356	10	0.66056	D	0.02	-61.9551	10.546	0.45060	0.172:0.0:0.828:0.0	.	866	Q92626	PXDN_HUMAN	E	866	ENSP00000252804:D866E	ENSP00000252804:D866E	D	-	3	2	PXDN	1631961	1.000000	0.71417	1.000000	0.80357	0.705000	0.40729	4.692000	0.61746	1.376000	0.46267	0.558000	0.71614	GAC	.	.	none		0.657	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		T	1652954	G	T	1652954	3	4	42	1	0	0	0	0	1	0	0	0	12862	1020	36	4	1869	4	PXDN	2	1652954	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	212874	1652954	241546419	34	14986											
PXDN	7837	hgsc.bcm.edu	37	chr2	1653227	1653227	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttgatgccccgaggggtgttGaagccattctcgtacacgga	8	10	13	10	3	1	2	0	2	1	0	2	4	1	3	3	3	3	2	3	3	2	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:1653227G>A	ENST00000252804.4	-	17	2375	c.2325C>T	c.(2323-2325)ttC>ttT	p.F775F		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	775					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)		GAGGGGTGTTGAAGCCATTCT	0.652																																					p.F775F		Atlas-SNP	.											.	PXDN	255	.	0			c.C2325T						PASS	.						88	103	98					2																	1653227		2054	4195	6249	SO:0001819	synonymous_variant	7837	exon17			GGTGTTGAAGCCA	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.2325C>T	2.37:g.1653227G>A		119	0	0		101	25	0.247525	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Silent	SNP	ENST00000252804.4	37	CCDS46221.1																																																																																			.	.	none		0.652	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455		A	1653227	G	A	1653227	2	1	42	1	0	0	0	0	0	0	0	1	12862	1281	45	2		2	PXDN	2	1653227	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	273	1653227	241546146	35	14987											
CNRIP1	25927	hgsc.bcm.edu	37	chr2	68521067	68521067	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgcattcatactcaatgacaGagaaggggcttccccactgg	11	9	10	11	0	2	2	2	1	0	1	3	3	3	2	2	3	2	2	2	3	3	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:68521067G>A	ENST00000263655.3	-	3	1027	c.422C>T	c.(421-423)tCt>tTt	p.S141F	CNRIP1_ENST00000481714.1_5'UTR|CNRIP1_ENST00000409559.3_Intron	NM_015463.2	NP_056278.1	Q96F85	CNRP1_HUMAN	cannabinoid receptor interacting protein 1	141										kidney(1)|large_intestine(5)|liver(1)|lung(1)|skin(1)	9						CTCAATGACAGAGAAGGGGCT	0.507																																					p.S141F		Atlas-SNP	.											.	CNRIP1	45	.	0			c.C422T						PASS	.						145	117	126					2																	68521067		2203	4300	6503	SO:0001583	missense	25927	exon3			ATGACAGAGAAGG	AL110235	CCDS1886.1, CCDS46311.1	2p13	2008-02-05	2007-11-29	2007-11-29	ENSG00000119865	ENSG00000119865			24546	protein-coding gene	gene with protein product			"chromosome 2 open reading frame 32"	C2orf32		12477932	Standard	NM_015463		Approved	DKFZP566K1924, CRIP1, CRIP1a, CRIP1b	uc002sek.4	Q96F85	OTTHUMG00000129565	ENST00000263655.3:c.422C>T	2.37:g.68521067G>A	ENSP00000263655:p.Ser141Phe	159	0	0		131	34	0.259542	NM_015463	B2R4D0|Q49AN4|Q9UFZ0	Missense_Mutation	SNP	ENST00000263655.3	37	CCDS1886.1	.	.	.	.	.	.	.	.	.	.	G	14.33	2.504342	0.44558	.	.	ENSG00000119865	ENST00000263655	.	.	.	5.42	5.42	0.78866	.	0.327702	0.34959	N	0.003560	T	0.48857	0.1523	N	0.24115	0.695	0.80722	D	1	B	0.24963	0.115	B	0.34138	0.176	T	0.50189	-0.8857	9	0.56958	D	0.05	-7.1396	13.8208	0.63320	0.0:0.2784:0.7216:0.0	.	141	Q96F85	CNRP1_HUMAN	F	141	.	ENSP00000263655:S141F	S	-	2	0	CNRIP1	68374571	0.945000	0.32115	0.978000	0.43139	0.959000	0.62525	1.594000	0.36697	2.538000	0.85594	0.650000	0.86243	TCT	.	.	none		0.507	CNRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251758.1	NM_015463		A	68521067	G	A	68521067	3	1	42	1	0	0	0	0	1	0	0	0	3635	942	33	2	137	2	CNRIP1	2	68521067	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	66867840	68521067	174678306	36	14988											
LRRTM1	347730	hgsc.bcm.edu	37	chr2	80529909	80529909	+	Nonsense_Mutation	SNP	C	C	A																															gtcctcgccctgtgcgtactCcgggctggcgcactgcaagt																										TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:80529909C>A	ENST00000295057.3	-	2	1692	c.1036G>T	c.(1036-1038)Gag>Tag	p.E346*	CTNNA2_ENST00000496558.1_Intron|CTNNA2_ENST00000541047.1_Intron|CTNNA2_ENST00000402739.4_Intron|CTNNA2_ENST00000361291.4_Intron|LRRTM1_ENST00000409148.1_Nonsense_Mutation_p.E346*|CTNNA2_ENST00000466387.1_Intron|CTNNA2_ENST00000540488.1_Intron	NM_178839.4	NP_849161.2	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	346	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						TGTGCGTACTCCGGGCTGGCG	0.677										HNSCC(69;0.2)																											p.E346X		Atlas-SNP	.											.	LRRTM1	251	.	0			c.G1036T						PASS	.						23	22	22					2																	80529909		2203	4299	6502	SO:0001587	stop_gained	347730	exon2			CGTACTCCGGGCT	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.1036G>T	2.37:g.80529909C>A	ENSP00000295057:p.Glu346*	74	0	0		58	20	0.344828	NM_178839	A8K397|D6W5K1|Q96DN1	Nonsense_Mutation	SNP	ENST00000295057.3	37	CCDS1966.1	.	.	.	.	.	.	.	.	.	.	C	38	7.030314	0.98013	.	.	ENSG00000162951	ENST00000295057;ENST00000409148	.	.	.	5.32	5.32	0.75619	.	0.123786	0.52532	U	0.000064	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.995	0.92809	0.0:1.0:0.0:0.0	.	.	.	.	X	346	.	.	E	-	1	0	LRRTM1	80383420	1.000000	0.71417	0.984000	0.44739	0.995000	0.86356	4.909000	0.63314	2.452000	0.82932	0.655000	0.94253	GAG	.	.	none		0.677	LRRTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313614.1	NM_178839		A	80529909	C	A	80529909	4	1	42	1	0	0	0	0	0	1	0	0	9048	864	30	4	536	4	LRRTM1	2	80529909	Nonsense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	12008842	80529909	162669464	37	14989	195	2									
LRRTM1	347730	hgsc.bcm.edu	37	chr2	80529910	80529910	+	Silent	SNP	C	C	A																															tcctcgccctgtgcgtactcCgggctggcgcactgcaagtt																										TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:80529910C>A	ENST00000295057.3	-	2	1691	c.1035G>T	c.(1033-1035)ccG>ccT	p.P345P	CTNNA2_ENST00000496558.1_Intron|CTNNA2_ENST00000541047.1_Intron|CTNNA2_ENST00000402739.4_Intron|CTNNA2_ENST00000361291.4_Intron|LRRTM1_ENST00000409148.1_Silent_p.P345P|CTNNA2_ENST00000466387.1_Intron|CTNNA2_ENST00000540488.1_Intron	NM_178839.4	NP_849161.2	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	345	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						GTGCGTACTCCGGGCTGGCGC	0.677										HNSCC(69;0.2)																											p.P345P		Atlas-SNP	.											.	LRRTM1	251	.	0			c.G1035T						PASS	.						23	22	22					2																	80529910		2203	4299	6502	SO:0001819	synonymous_variant	347730	exon2			GTACTCCGGGCTG	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.1035G>T	2.37:g.80529910C>A		75	0	0		60	21	0.35	NM_178839	A8K397|D6W5K1|Q96DN1	Silent	SNP	ENST00000295057.3	37	CCDS1966.1																																																																																			.	.	none		0.677	LRRTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313614.1	NM_178839		A	80529910	C	A	80529910	2	1	42	1	0	0	0	0	0	0	0	1	9048	639	23	4		4	LRRTM1	2	80529910	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	1	80529910	162669463	38	14990	195	2									
ST6GAL2	84620	hgsc.bcm.edu	37	chr2	107460134	107460134	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	tcaaacccatcttgggactgGgcccatttctgcaggtctcc	7	11	9	14	0	4	0	1	0	3	0	5	1	4	1	3	3	2	1	3	3	1	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:107460134G>T	ENST00000409382.3	-	2	910	c.300C>A	c.(298-300)gcC>gcA	p.A100A	ST6GAL2_ENST00000409087.3_Silent_p.A100A|ST6GAL2_ENST00000361686.4_Silent_p.A100A|AC016994.2_ENST00000425419.1_RNA	NM_001142351.1	NP_001135823.1	Q96JF0	SIAT2_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 2	100					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						CTTGGGACTGGGCCCATTTCT	0.587																																					p.A100A		Atlas-SNP	.											.	ST6GAL2	159	.	0			c.C300A						PASS	.						41	50	47					2																	107460134		2190	4288	6478	SO:0001819	synonymous_variant	84620	exon2			GGACTGGGCCCAT	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.300C>A	2.37:g.107460134G>T		204	0	0		185	69	0.372973	NM_032528	D3DVK3|Q53QP4|Q86Y44|Q8IUG7|Q96HE4	Silent	SNP	ENST00000409382.3	37	CCDS2073.1																																																																																			.	.	none		0.587	ST6GAL2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330065.1	NM_032528		T	107460134	G	T	107460134	2	4	42	1	0	0	0	0	0	0	0	1	15237	1219	43	4		4	ST6GAL2	2	107460134	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	26930224	107460134	135739239	39	14991											
DBI	1622	hgsc.bcm.edu	37	chr2	120124666	120124666	+	Intron	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgcacagccaggctgcgaaGgtgcagcgggcgggaggccc	7	3	19	12	3	0	0	0	0	0	0	0	2	0	1	2	5	5	3	2	5	1	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:120124666G>T	ENST00000355857.3	+	1	140				C2orf76_ENST00000409466.2_5'Flank|C2orf76_ENST00000409523.1_5'Flank|DBI_ENST00000535617.1_Intron|C2orf76_ENST00000498049.1_5'Flank|DBI_ENST00000393103.2_5'Flank|DBI_ENST00000460901.1_3'UTR|C2orf76_ENST00000334816.7_5'Flank|DBI_ENST00000542275.1_5'Flank|C2orf76_ENST00000409877.1_5'Flank|DBI_ENST00000311521.4_5'UTR|DBI_ENST00000409094.1_Intron|DBI_ENST00000535757.1_5'UTR	NM_001079862.1|NM_001178043.1	NP_001073331.1|NP_001171514.1	P07108	ACBP_HUMAN	diazepam binding inhibitor (GABA receptor modulator, acyl-CoA binding protein)						hair follicle development (GO:0001942)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|transport (GO:0006810)|triglyceride metabolic process (GO:0006641)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|perinuclear endoplasmic reticulum (GO:0097038)	benzodiazepine receptor binding (GO:0030156)|lipid binding (GO:0008289)|long-chain fatty acyl-CoA binding (GO:0036042)|protein dimerization activity (GO:0046983)			kidney(1)|lung(4)|skin(1)	6						AGGCTGCGAAGGTGCAGCGGG	0.662																																					p.K13N		Atlas-SNP	.											.	DBI	10	.	0			c.G39T						PASS	.						21	24	23					2																	120124666		2055	4193	6248	SO:0001627	intron_variant	1622	exon1			TGCGAAGGTGCAG	L76366	CCDS2126.1, CCDS42740.1, CCDS42741.1, CCDS74568.1	2q12-q21	2010-10-20	2010-04-30		ENSG00000155368	ENSG00000155368			2690	protein-coding gene	gene with protein product	"endozepine"	125950	"diazepam binding inhibitor (GABA receptor modulator, acyl-Coenzyme A binding protein)"			1440058	Standard	NM_001079863		Approved	ACBP, ACBD1	uc021vnj.1	P07108	OTTHUMG00000131403	ENST00000355857.3:c.9+30G>T	2.37:g.120124666G>T		123	0	0		102	43	0.421569	NM_001178043	B8ZWD2|B8ZWD6|B8ZWD7|P08869|Q4VWZ6|Q53SQ7|Q6IB48|Q9UCI8	Missense_Mutation	SNP	ENST00000355857.3	37	CCDS42740.1																																																																																			.	.	none		0.662	DBI-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330590.1	NM_020548		T	120124666	G	T	120124666	1	4	42	0	1	0	0	0	0	0	0	0	4253	1014	35	4		4	DBI	2	120124666	Intron	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	12664532	120124666	123074707	40	14992											
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125530582	125530582	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcgactgcagctgaacagcCagttgtttgtaggtagggga	9	11	14	7	1	0	1	0	1	0	0	1	3	0	2	1	3	4	6	1	3	3	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:125530582C>A	ENST00000431078.1	+	17	3101	c.2737C>A	c.(2737-2739)Cag>Aag	p.Q913K		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	913	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)		GCTGAACAGCCAGTTGTTTGT	0.507																																					p.Q913K		Atlas-SNP	.											.	CNTNAP5	405	.	0			c.C2737A						PASS	.						100	95	97					2																	125530582		1909	4127	6036	SO:0001583	missense	129684	exon17			AACAGCCAGTTGT	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.2737C>A	2.37:g.125530582C>A	ENSP00000399013:p.Gln913Lys	250	0	0		230	49	0.213043	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	37	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	c	31	5.067704	0.93950	.	.	ENSG00000155052	ENST00000431078	T	0.48836	0.8	5.63	5.63	0.86233	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.151491	0.29868	N	0.010984	T	0.72922	0.3521	M	0.88842	2.985	0.58432	D	0.999999	D	0.69078	0.997	D	0.67231	0.95	T	0.72924	-0.4144	10	0.31617	T	0.26	.	18.7016	0.91621	0.0:1.0:0.0:0.0	.	913	Q8WYK1	CNTP5_HUMAN	K	913	ENSP00000399013:Q913K	ENSP00000399013:Q913K	Q	+	1	0	CNTNAP5	125247052	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	7.686000	0.84128	2.664000	0.90586	0.645000	0.84053	CAG	.	.	none		0.507	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3			A	125530582	C	A	125530582	3	1	42	1	0	0	0	0	1	0	0	0	3652	595	21	4	2803	4	CNTNAP5	2	125530582	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	5405916	125530582	117668791	41	14993											
CYP27C1	339761	hgsc.bcm.edu	37	chr2	127957076	127957076	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tccggcctcggtccatttggTactgtatgtccctcaacttg	5	14	9	13	2	1	0	1	0	0	0	5	0	4	0	4	3	2	2	4	3	3	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:127957076T>A	ENST00000335247.7	-	4	558	c.428A>T	c.(427-429)tAc>tTc	p.Y143F	CYP27C1_ENST00000409327.1_Missense_Mutation_p.Y143F	NM_001001665.3	NP_001001665.3	Q4G0S4	C27C1_HUMAN	cytochrome P450, family 27, subfamily C, polypeptide 1	143						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)		GTCCATTTGGTACTGTATGTC	0.483																																					p.Y143F		Atlas-SNP	.											.	CYP27C1	52	.	0			c.A428T						PASS	.						128	111	117					2																	127957076		2203	4300	6503	SO:0001583	missense	339761	exon4			ATTTGGTACTGTA	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.428A>T	2.37:g.127957076T>A	ENSP00000334128:p.Tyr143Phe	66	0	0		92	30	0.326087	NM_001001665	Q6ZNI7	Missense_Mutation	SNP	ENST00000335247.7	37	CCDS33285.1	.	.	.	.	.	.	.	.	.	.	T	11.48	1.652546	0.29336	.	.	ENSG00000186684	ENST00000335247;ENST00000409327	T;T	0.68624	-0.34;-0.34	4.27	1.04	0.20106	.	0.423021	0.24864	N	0.034983	T	0.40670	0.1126	N	0.08118	0	0.20403	N	0.9999	B	0.09022	0.002	B	0.10450	0.005	T	0.30090	-0.9990	10	0.59425	D	0.04	-25.285	5.7206	0.17985	0.0:0.2811:0.4352:0.2837	.	143	Q4G0S4	C27C1_HUMAN	F	143	ENSP00000334128:Y143F;ENSP00000387198:Y143F	ENSP00000334128:Y143F	Y	-	2	0	CYP27C1	127673546	1.000000	0.71417	0.865000	0.33974	0.468000	0.32798	1.167000	0.31847	0.201000	0.20466	0.460000	0.39030	TAC	.	.	none		0.483	CYP27C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331046.1	NM_001001665		A	127957076	T	A	127957076	3	1	42	1	0	0	0	0	1	0	0	0	4162	1638	57	5	710	5	CYP27C1	2	127957076	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	2426494	127957076	115242297	42	14994											
LRP1B	53353	hgsc.bcm.edu	37	chr2	141660530	141660530	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cgtctacatccagcttccaaCcttcataacatgagcacttg	11	11	5	14	1	2	1	1	1	1	0	4	1	4	1	3	0	5	2	3	0	3	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:141660530C>A	ENST00000389484.3	-	23	4696	c.3725G>T	c.(3724-3726)gGt>gTt	p.G1242V		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1242	EGF-like 6. {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)		CAGCTTCCAACCTTCATAACA	0.358										TSP Lung(27;0.18)																											p.G1242V	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											LRP1B,NS,carcinoma,-1,1	LRP1B	1315	1	0			c.G3725T						PASS	.						156	144	148					2																	141660530		2203	4300	6503	SO:0001583	missense	53353	exon23			TTCCAACCTTCAT	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.3725G>T	2.37:g.141660530C>A	ENSP00000374135:p.Gly1242Val	172	0	0		158	43	0.272152	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	C	33	5.203252	0.95033	.	.	ENSG00000168702	ENST00000389484;ENST00000544579;ENST00000434794	D;D	0.92752	-3.1;-3.1	5.44	5.44	0.79542	Epidermal growth factor-like (1);EGF-like region, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.98121	0.9380	H	0.99197	4.465	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.99368	1.0919	10	0.87932	D	0	.	19.6316	0.95708	0.0:1.0:0.0:0.0	.	425;1242	Q96NT6;Q9NZR2	.;LRP1B_HUMAN	V	1242;1180;387	ENSP00000374135:G1242V;ENSP00000413239:G387V	ENSP00000374135:G1242V	G	-	2	0	LRP1B	141377000	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	7.729000	0.84864	2.708000	0.92522	0.585000	0.79938	GGT	.	.	none		0.358	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557		A	141660530	C	A	141660530	3	1	42	1	0	0	0	0	1	0	0	0	8964	507	18	4	10350	4	LRP1B	2	141660530	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	13703454	141660530	101538843	43	14995											
TTC21B	79809	hgsc.bcm.edu	37	chr2	166770146	166770146	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccgagggttagccattctttCagcaatttctctggaaatca	10	13	8	10	1	4	0	2	0	2	0	5	2	4	1	2	2	2	2	2	2	3	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:166770146C>T	ENST00000243344.7	-	16	2286	c.2149G>A	c.(2149-2151)Gaa>Aaa	p.E717K		NM_024753.4	NP_079029.3	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	717					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						GCCATTCTTTCAGCAATTTCT	0.308																																					p.E717K		Atlas-SNP	.											.	TTC21B	130	.	0			c.G2149A						PASS	.						96	98	98					2																	166770146		2203	4300	6503	SO:0001583	missense	79809	exon16			TTCTTTCAGCAAT	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.2149G>A	2.37:g.166770146C>T	ENSP00000243344:p.Glu717Lys	381	0	0		295	54	0.183051	NM_024753	A8MUZ3|Q3LIE4|Q53T84|Q6P4A1|Q6PIF5|Q8NCN3|Q96MA4|Q9HAK8	Missense_Mutation	SNP	ENST00000243344.7	37	CCDS33315.1	.	.	.	.	.	.	.	.	.	.	C	33	5.216990	0.95104	.	.	ENSG00000123607	ENST00000243344	T	0.61158	0.13	5.39	5.39	0.77823	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.172662	0.56097	D	0.000029	T	0.62134	0.2403	M	0.71581	2.175	0.80722	D	1	P	0.48911	0.917	B	0.43950	0.437	T	0.62248	-0.6894	10	0.27785	T	0.31	-20.5549	19.1426	0.93451	0.0:1.0:0.0:0.0	.	717	Q7Z4L5	TT21B_HUMAN	K	717	ENSP00000243344:E717K	ENSP00000243344:E717K	E	-	1	0	TTC21B	166478392	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	7.487000	0.81328	2.512000	0.84698	0.591000	0.81541	GAA	.	.	none		0.308	TTC21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333770.1	NM_024753		T	166770146	C	T	166770146	3	4	42	1	0	0	0	0	1	0	0	0	16703	835	29	2	1857	2	TTC21B	2	166770146	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	25109616	166770146	76429227	44	14996											
SCN9A	6335	hgsc.bcm.edu	37	chr2	167145040	167145040	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcaatgtttgcctggttctgTtcttcatatgccatggcaac	7	16	8	10	0	4	0	2	0	2	0	4	0	4	0	2	2	3	4	2	2	3	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:167145040T>G	ENST00000409435.1	-	9	1220	c.1221A>C	c.(1219-1221)gaA>gaC	p.E407D	AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Missense_Mutation_p.E408D|SCN9A_ENST00000375387.4_Missense_Mutation_p.E408D|SCN9A_ENST00000409672.1_Missense_Mutation_p.E407D			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	407					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)	CCTGGTTCTGTTCTTCATATG	0.393																																					p.E407D		Atlas-SNP	.											SCN9A,colon,carcinoma,-2,1	SCN9A	296	1	0			c.A1221C						PASS	.						127	127	127					2																	167145040		1853	4113	5966	SO:0001583	missense	6335	exon10			GTTCTGTTCTTCA	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.1221A>C	2.37:g.167145040T>G	ENSP00000386330:p.Glu407Asp	242	0	0		199	44	0.221106	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Missense_Mutation	SNP	ENST00000409435.1	37	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.964450	0.74131	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435;ENST00000454569;ENST00000452182	D;D;D;D;D;D	0.98012	-4.66;-4.66;-4.66;-4.66;-4.66;-4.66	5.74	4.6	0.57074	.	0.087668	0.49305	N	0.000141	D	0.98492	0.9497	M	0.87971	2.92	0.45515	D	0.998479	D;D;D	0.89917	1.0;1.0;0.976	D;D;P	0.91635	0.989;0.999;0.881	D	0.98776	1.0730	10	0.62326	D	0.03	.	8.4814	0.33045	0.0:0.1451:0.0:0.8549	.	407;407;408	E7EUN6;Q15858;E9PF08	.;SCN9A_HUMAN;.	D	407;408;408;407;272;272	ENSP00000386306:E407D;ENSP00000364536:E408D;ENSP00000304748:E408D;ENSP00000386330:E407D;ENSP00000413212:E272D;ENSP00000393141:E272D	ENSP00000304748:E408D	E	-	3	2	SCN9A	166853286	0.997000	0.39634	1.000000	0.80357	0.995000	0.86356	0.437000	0.21543	2.190000	0.69967	0.528000	0.53228	GAA	.	.	none		0.393	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977		G	167145040	T	G	167145040	3	3	42	1	0	0	0	0	1	0	0	0	13940	1722	60	5	4784	5	SCN9A	2	167145040	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	374894	167145040	76054333	45	14997											
XIRP2	129446	hgsc.bcm.edu	37	chr2	168106466	168106466	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaccaaaggtcgtcaagcAaaaggttatcgatgcacatc	15	7	9	10	2	1	0	1	0	0	0	4	1	1	0	1	2	3	4	1	2	5	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:168106466A>G	ENST00000409195.1	+	9	8653	c.8564A>G	c.(8563-8565)cAa>cGa	p.Q2855R	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.Q2855R|XIRP2_ENST00000409273.1_Missense_Mutation_p.Q2633R|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2680					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						GTCGTCAAGCAAAAGGTTATC	0.378																																					p.Q2855R		Atlas-SNP	.											XIRP2,NS,carcinoma,0,1	XIRP2	914	1	0			c.A8564G						scavenged	.						118	114	116					2																	168106466		1885	4112	5997	SO:0001583	missense	129446	exon9			TCAAGCAAAAGGT	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.8564A>G	2.37:g.168106466A>G	ENSP00000386840:p.Gln2855Arg	340	2	0.00588235		352	114	0.323864	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	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	A	12.45	1.940991	0.34283	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.02763	4.17;4.17;4.17	5.82	4.64	0.57946	.	0.577929	0.18468	N	0.140332	T	0.07773	0.0195	M	0.67953	2.075	0.09310	N	0.999998	P;P;P	0.49090	0.868;0.919;0.919	B;P;P	0.48795	0.386;0.59;0.59	T	0.08166	-1.0735	10	0.66056	D	0.02	-5.8378	12.1135	0.53852	0.8561:0.1439:0.0:0.0	.	2680;2680;2633	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	R	2855;2855;2633;269	ENSP00000386840:Q2855R;ENSP00000295237:Q2855R;ENSP00000387255:Q2633R	ENSP00000295237:Q2855R	Q	+	2	0	XIRP2	167814712	0.995000	0.38212	0.041000	0.18516	0.307000	0.27823	1.995000	0.40767	1.001000	0.39076	0.533000	0.62120	CAA	.	.	none		0.378	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381		G	168106466	A	G	168106466	3	3	42	1	0	0	0	0	1	0	0	0	17445	130	5	3	8594	3	XIRP2	2	168106466	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	961426	168106466	75092907	46	14998											
LRP2	4036	hgsc.bcm.edu	37	chr2	170101220	170101220	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tactgcagttcttttcatcaGatccatccccacaatcattg	10	14	4	13	0	4	1	3	0	1	1	6	1	6	1	3	0	2	2	3	0	2	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:170101220G>A	ENST00000263816.3	-	22	3698	c.3413C>T	c.(3412-3414)tCt>tTt	p.S1138F	LRP2_ENST00000443831.1_Missense_Mutation_p.S1001F	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1138	LDL-receptor class A 10. {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)"	CTTTTCATCAGATCCATCCCC	0.453																																					p.S1138F		Atlas-SNP	.											.	LRP2	751	.	0			c.C3413T						PASS	.						158	147	151					2																	170101220		2203	4300	6503	SO:0001583	missense	4036	exon22			TCATCAGATCCAT		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.3413C>T	2.37:g.170101220G>A	ENSP00000263816:p.Ser1138Phe	136	0	0		137	44	0.321168	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	G	31	5.062054	0.93846	.	.	ENSG00000081479	ENST00000263816;ENST00000443831	D;D	0.97870	-4.58;-4.58	5.93	5.93	0.95920	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99318	0.9761	H	0.97707	4.06	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.98640	1.0675	10	0.87932	D	0	.	20.3368	0.98748	0.0:0.0:1.0:0.0	.	1001;1138	E9PC35;P98164	.;LRP2_HUMAN	F	1138;1001	ENSP00000263816:S1138F;ENSP00000409813:S1001F	ENSP00000263816:S1138F	S	-	2	0	LRP2	169809466	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.793000	0.99091	2.805000	0.96524	0.655000	0.94253	TCT	.	.	none		0.453	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		A	170101220	G	A	170101220	3	1	42	1	0	0	0	0	1	0	0	0	8965	942	33	2	10786	2	LRP2	2	170101220	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	1994754	170101220	73098153	47	14999											
HOXD1	3231	hgsc.bcm.edu	37	chr2	177053759	177053759	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggccgtccgtaccgcctcCggccgcgccccagtacgcgc	3	4	13	21	9	0	0	0	0	0	0	2	0	2	0	8	2	2	2	8	2	2	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:177053759C>T	ENST00000331462.4	+	1	453	c.230C>T	c.(229-231)cCg>cTg	p.P77L	HOXD-AS1_ENST00000436126.1_RNA|HOXD-AS1_ENST00000425005.1_RNA|HOXD-AS1_ENST00000413969.1_RNA|HOXD-AS1_ENST00000417086.1_RNA|HOXD-AS1_ENST00000452365.1_RNA	NM_024501.2	NP_078777.1	Q9GZZ0	HXD1_HUMAN	homeobox D1	77					embryonic skeletal system development (GO:0048706)|neuron differentiation (GO:0030182)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226)	Colorectal(32;0.0226)		gtaccgcctccggccgcgccc	0.786																																					p.P77L		Atlas-SNP	.											.	HOXD1	33	.	0			c.C230T						PASS	.						1	1	1					2																	177053759		653	1642	2295	SO:0001583	missense	3231	exon1			CGCCTCCGGCCGC		CCDS2271.1	2q31.1	2011-06-20	2005-12-22		ENSG00000128645	ENSG00000128645		"Homeoboxes / ANTP class : HOXL subclass"	5132	protein-coding gene	gene with protein product		142987	"homeo box D1"	HOX4, HOX4G		1973146, 1358459	Standard	NM_024501		Approved		uc002ukv.5	Q9GZZ0	OTTHUMG00000132512	ENST00000331462.4:c.230C>T	2.37:g.177053759C>T	ENSP00000328598:p.Pro77Leu	29	0	0		23	7	0.304348	NM_024501	B2RAB4	Missense_Mutation	SNP	ENST00000331462.4	37	CCDS2271.1	.	.	.	.	.	.	.	.	.	.	C	9.823	1.186401	0.21870	.	.	ENSG00000128645	ENST00000331462	D	0.92699	-3.09	3.21	1.19	0.21007	.	0.231155	0.22488	N	0.059410	T	0.80752	0.4683	N	0.24115	0.695	0.09310	N	0.999994	B;B	0.09022	0.002;0.002	B;B	0.04013	0.001;0.001	T	0.62263	-0.6891	10	0.10377	T	0.69	.	4.8389	0.13478	0.0:0.6184:0.176:0.2056	.	77;77	Q96CA4;Q9GZZ0	.;HXD1_HUMAN	L	77	ENSP00000328598:P77L	ENSP00000328598:P77L	P	+	2	0	HOXD1	176762005	0.000000	0.05858	0.030000	0.17652	0.267000	0.26476	-0.349000	0.07731	0.530000	0.28619	0.491000	0.48974	CCG	.	.	none		0.786	HOXD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255693.2			T	177053759	C	T	177053759	3	4	42	1	0	0	0	0	1	0	0	0	7327	652	23	1	232	1	HOXD1	2	177053759	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	6952539	177053759	66145614	48	15000											
NCKAP1	10787	hgsc.bcm.edu	37	chr2	183822287	183822287	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tttttgatttcttattcactGcttgactgatagttttggca	7	21	7	6	0	2	3	1	3	1	0	2	3	2	3	0	1	1	3	0	1	2	9			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:183822287G>A	ENST00000361354.4	-	19	2291	c.1919C>T	c.(1918-1920)gCa>gTa	p.A640V	NCKAP1_ENST00000360982.2_Missense_Mutation_p.A646V	NM_013436.3	NP_038464.1	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1	640					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)			CTTATTCACTGCTTGACTGAT	0.383																																					p.A646V		Atlas-SNP	.											.	NCKAP1	105	.	0			c.C1937T						PASS	.						161	141	148					2																	183822287		2203	4300	6503	SO:0001583	missense	10787	exon20			TTCACTGCTTGAC	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.1919C>T	2.37:g.183822287G>A	ENSP00000355348:p.Ala640Val	348	0	0		297	23	0.0774411	NM_205842	O60329|Q53QN5|Q53S94|Q53Y35	Missense_Mutation	SNP	ENST00000361354.4	37	CCDS2287.1	.	.	.	.	.	.	.	.	.	.	G	16.76	3.213566	0.58452	.	.	ENSG00000061676	ENST00000361354;ENST00000360982	T;T	0.31247	1.5;1.5	5.39	4.5	0.54988	.	0.046925	0.85682	D	0.000000	T	0.33498	0.0865	N	0.16656	0.425	0.80722	D	1	D;D	0.57899	0.981;0.976	P;P	0.60117	0.869;0.793	T	0.05886	-1.0858	10	0.17832	T	0.49	-15.0139	15.3439	0.74320	0.0:0.0:0.859:0.141	.	640;646	Q9Y2A7;Q9Y2A7-2	NCKP1_HUMAN;.	V	640;646	ENSP00000355348:A640V;ENSP00000354251:A646V	ENSP00000354251:A646V	A	-	2	0	NCKAP1	183530532	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.809000	0.99208	1.230000	0.43646	0.655000	0.94253	GCA	.	.	none		0.383	NCKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255867.2	NM_205842		A	183822287	G	A	183822287	3	1	42	1	0	0	0	0	1	0	0	0	10230	1319	46	2	1519	2	NCKAP1	2	183822287	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	6768528	183822287	59377086	49	15001											
NCKAP1	10787	hgsc.bcm.edu	37	chr2	183866768	183866768	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaaggcgtgggtattctctGtcacttaaaacagacatatc	12	11	8	10	1	2	1	1	0	1	1	4	1	2	1	1	2	1	1	1	2	5	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:183866768G>A	ENST00000361354.4	-	6	888	c.516C>T	c.(514-516)gaC>gaT	p.D172D	NCKAP1_ENST00000360982.2_Silent_p.D178D	NM_013436.3	NP_038464.1	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1	172					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)			GGTATTCTCTGTCACTTAAAA	0.368																																					p.D178D		Atlas-SNP	.											.	NCKAP1	105	.	0			c.C534T						PASS	.						142	142	142					2																	183866768		2203	4300	6503	SO:0001819	synonymous_variant	10787	exon7			TTCTCTGTCACTT	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.516C>T	2.37:g.183866768G>A		238	0	0		237	51	0.21519	NM_205842	O60329|Q53QN5|Q53S94|Q53Y35	Silent	SNP	ENST00000361354.4	37	CCDS2287.1																																																																																			.	.	none		0.368	NCKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255867.2	NM_205842		A	183866768	G	A	183866768	2	1	42	1	0	0	0	0	0	0	0	1	10230	1368	48	2		2	NCKAP1	2	183866768	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	44481	183866768	59332605	50	15002											
FSIP2	401024	hgsc.bcm.edu	37	chr2	186671505	186671505	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aagcaaaatcaagccaaactCtatgacactgctatgaaact	18	8	5	10	0	2	2	1	2	1	0	2	2	2	2	1	0	5	2	1	0	8	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:186671505C>G	ENST00000424728.1	+	17	17472	c.17472C>G	c.(17470-17472)ctC>ctG	p.L5824L	FSIP2_ENST00000343098.5_Silent_p.L5913L			Q5CZC0	FSIP2_HUMAN	fibrous sheath interacting protein 2	5824				L -> P (in Ref. 2; CAI46017). {ECO:0000305}.						NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(11)|lung(46)|pancreas(1)|urinary_tract(2)	69						AAGCCAAACTCTATGACACTG	0.358																																					p.L5913L		Atlas-SNP	.											FSIP2_ENST00000343098,NS,carcinoma,+2,2	FSIP2	251	2	0			c.C17739G						PASS	.						89	83	85					2																	186671505		1854	4092	5946	SO:0001819	synonymous_variant	401024	exon17			CAAACTCTATGAC	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.17472C>G	2.37:g.186671505C>G		249	0	0		201	57	0.283582	NM_173651	Q53TL3|Q53TN5|Q5HYH2|Q6ZTZ5|Q6ZU14|Q6ZU21	Silent	SNP	ENST00000424728.1	37																																																																																				.	.	none		0.358	FSIP2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000332778.3	NM_173651		G	186671505	C	G	186671505	2	3	42	1	0	0	0	0	0	0	0	1	6083	900	32	4		4	FSIP2	2	186671505	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	2804737	186671505	56527868	51	15003											
COL5A2	1290	hgsc.bcm.edu	37	chr2	189916123	189916123	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtcctcgatctcccacacGcccatgagagccagggtccc	7	7	10	17	2	1	1	0	1	1	1	5	3	3	1	5	2	1	0	5	2	0	0	rs199530997	byFrequency	TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:189916123G>A	ENST00000374866.3	-	42	3128	c.2854C>T	c.(2854-2856)Cgt>Tgt	p.R952C		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	952					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)			TCTCCCACACGCCCATGAGAG	0.617													G|||	3	0.000599042	0.0	0.0	5008	,	,		13494	0.003		0.0	False		,,,				2504	0.0				p.R952C		Atlas-SNP	.											.	COL5A2	230	.	0			c.C2854T						PASS	.						71	71	71					2																	189916123		2203	4300	6503	SO:0001583	missense	1290	exon42			CCACACGCCCATG	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.2854C>T	2.37:g.189916123G>A	ENSP00000364000:p.Arg952Cys	123	0	0		129	36	0.27907	NM_000393	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Missense_Mutation	SNP	ENST00000374866.3	37	CCDS33350.1	3	0.0013736263736263737	0	0.0	0	0.0	3	0.005244755244755245	0	0.0	G	18.93	3.728045	0.69074	.	.	ENSG00000204262	ENST00000374866;ENST00000452536	D	0.93604	-3.25	5.83	4.95	0.65309	.	0.319446	0.22337	N	0.061388	D	0.94331	0.8178	M	0.66939	2.045	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	P;D	0.66084	0.818;0.941	D	0.93512	0.6854	9	.	.	.	.	16.5704	0.84611	0.0:0.0:0.8688:0.1312	.	592;952	Q5PR22;P05997	.;CO5A2_HUMAN	C	952;592	ENSP00000364000:R952C	.	R	-	1	0	COL5A2	189624368	1.000000	0.71417	0.983000	0.44433	0.987000	0.75469	3.115000	0.50391	1.454000	0.47793	0.644000	0.83932	CGT	G|0.999;A|0.001	0.001	strong		0.617	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393		A	189916123	G	A	189916123	3	1	42	1	0	0	0	0	1	0	0	0	3699	1087	38	1	1697	1	COL5A2	2	189916123	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	3244618	189916123	53283250	52	15004											
STAT1	6772	hgsc.bcm.edu	37	chr2	191873810	191873810	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaaaacggatggtggcaaatGaaacatcattggcagcgtgc	14	7	13	7	2	1	1	1	1	0	0	1	3	1	2	0	4	4	2	0	4	4	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:191873810G>A	ENST00000361099.3	-	4	539	c.152C>T	c.(151-153)tCa>tTa	p.S51L	STAT1_ENST00000392322.3_Missense_Mutation_p.S51L|STAT1_ENST00000540176.1_Missense_Mutation_p.S51L|STAT1_ENST00000409465.1_Missense_Mutation_p.S51L|STAT1_ENST00000392323.2_Missense_Mutation_p.S53L	NM_007315.3	NP_009330.1	P42224	STAT1_HUMAN	signal transducer and activator of transcription 1, 91kDa	51					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)			GGTGGCAAATGAAACATCATT	0.378																																					p.S51L		Atlas-SNP	.											.	STAT1	93	.	0			c.C152T						PASS	.						113	106	108					2																	191873810		2203	4300	6503	SO:0001583	missense	6772	exon4			GCAAATGAAACAT		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.152C>T	2.37:g.191873810G>A	ENSP00000354394:p.Ser51Leu	118	0	0		118	22	0.186441	NM_007315	A8K989|B2RCA0|D2KFR8|D3DPI7|Q53S88|Q53XW4|Q68D00|Q9UDL5	Missense_Mutation	SNP	ENST00000361099.3	37	CCDS2309.1	.	.	.	.	.	.	.	.	.	.	G	35	5.469238	0.96274	.	.	ENSG00000115415	ENST00000361099;ENST00000409465;ENST00000540176;ENST00000392322;ENST00000392323;ENST00000424722;ENST00000454414;ENST00000432058	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	5.52	5.52	0.82312	STAT transcription factor, protein interaction (4);	0.000000	0.85682	D	0.000000	T	0.76004	0.3927	M	0.82630	2.6	0.80722	D	1	D;P	0.89917	1.0;0.883	D;P	0.91635	0.999;0.771	T	0.78934	-0.2008	10	0.66056	D	0.02	-14.2715	18.4444	0.90678	0.0:0.0:1.0:0.0	.	51;51	P42224-2;P42224	.;STAT1_HUMAN	L	51;51;51;51;53;51;51;51	ENSP00000354394:S51L;ENSP00000386244:S51L;ENSP00000438703:S51L;ENSP00000376136:S51L;ENSP00000376137:S53L;ENSP00000402548:S51L;ENSP00000411398:S51L;ENSP00000416019:S51L	ENSP00000354394:S51L	S	-	2	0	STAT1	191582055	1.000000	0.71417	0.909000	0.35828	0.913000	0.54294	9.869000	0.99810	2.602000	0.87976	0.557000	0.71058	TCA	.	.	none		0.378	STAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255997.3	NM_007315		A	191873810	G	A	191873810	3	1	42	1	0	0	0	0	1	0	0	0	15279	1294	45	2	2192	2	STAT1	2	191873810	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	1957687	191873810	51325563	53	15005											
PLCL1	5334	hgsc.bcm.edu	37	chr2	198950643	198950643	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgttttgttgttctggatgAtgactacattggggatgagt	7	16	13	5	1	1	3	0	3	1	0	1	5	1	5	1	3	1	3	1	3	1	6			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:198950643A>T	ENST00000428675.1	+	2	2800	c.2402A>T	c.(2401-2403)gAt>gTt	p.D801V	PLCL1_ENST00000437704.2_Missense_Mutation_p.D703V	NM_006226.3	NP_006217.3	Q15111	PLCL1_HUMAN	phospholipase C-like 1	801	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				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)	GTTCTGGATGATGACTACATT	0.418																																					p.D801V		Atlas-SNP	.											.	PLCL1	358	.	0			c.A2402T						PASS	.						181	168	173					2																	198950643		2203	4300	6503	SO:0001583	missense	5334	exon2			TGGATGATGACTA	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.2402A>T	2.37:g.198950643A>T	ENSP00000402861:p.Asp801Val	301	0	0		306	78	0.254902	NM_006226	Q3MJ90|Q53SD3|Q7Z3S3	Missense_Mutation	SNP	ENST00000428675.1	37	CCDS2326.2	.	.	.	.	.	.	.	.	.	.	A	17.06	3.292444	0.59976	.	.	ENSG00000115896	ENST00000428675;ENST00000437704	T;T	0.70164	-0.46;-0.46	5.5	5.5	0.81552	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.64402	D	0.000003	D	0.83362	0.5238	M	0.85099	2.735	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.85396	0.1128	9	.	.	.	.	15.7759	0.78214	1.0:0.0:0.0:0.0	.	801;727	Q15111;B4DYZ4	PLCL1_HUMAN;.	V	801;703	ENSP00000402861:D801V;ENSP00000414138:D703V	.	D	+	2	0	PLCL1	198658888	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.127000	0.94417	2.308000	0.77769	0.533000	0.62120	GAT	.	.	none		0.418	PLCL1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340210.1	NM_006226		T	198950643	A	T	198950643	3	4	42	1	0	0	0	0	1	0	0	0	12048	333	12	5	2408	5	PLCL1	2	198950643	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	7076833	198950643	44248730	54	15006											
PARD3B	117583	hgsc.bcm.edu	37	chr2	206041194	206041194	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	tgcagagtgtggggcattttCcaagccatgctttgagaact	9	12	12	8	0	0	2	0	1	0	2	1	3	1	2	2	2	4	3	2	2	2	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:206041194C>T	ENST00000406610.2	+	13	2024	c.1817C>T	c.(1816-1818)tCc>tTc	p.S606F	PARD3B_ENST00000462231.1_Missense_Mutation_p.S606F|PARD3B_ENST00000349953.3_Missense_Mutation_p.S606F|PARD3B_ENST00000358768.2_Missense_Mutation_p.S544F|PARD3B_ENST00000351153.1_Missense_Mutation_p.S606F	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	606					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)		GGGGCATTTTCCAAGCCATGC	0.393																																					p.S606F		Atlas-SNP	.											.	PARD3B	314	.	0			c.C1817T						PASS	.						82	75	77					2																	206041194		1855	4099	5954	SO:0001583	missense	117583	exon13			CATTTTCCAAGCC	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.1817C>T	2.37:g.206041194C>T	ENSP00000385848:p.Ser606Phe	360	0	0		302	61	0.201987	NM_205863	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	Missense_Mutation	SNP	ENST00000406610.2	37		.	.	.	.	.	.	.	.	.	.	C	18.46	3.628482	0.67015	.	.	ENSG00000116117	ENST00000406610;ENST00000358768;ENST00000351153;ENST00000349953	T;T;T;T	0.13089	2.85;2.62;2.85;2.85	6.03	5.11	0.69529	.	0.225498	0.32593	N	0.005900	T	0.24236	0.0587	L	0.44542	1.39	0.35016	D	0.757362	D;D;D;P;P	0.65815	0.995;0.991;0.967;0.941;0.941	P;P;P;P;P	0.59643	0.861;0.736;0.682;0.571;0.555	T	0.06643	-1.0815	10	0.59425	D	0.04	.	11.9098	0.52733	0.2451:0.7549:0.0:0.0	.	606;606;606;544;606	Q8TEW8-3;Q8TEW8;E9PE87;Q8TEW8-2;Q8TEW8-5	.;PAR3L_HUMAN;.;.;.	F	606;544;606;606	ENSP00000385848:S606F;ENSP00000351618:S544F;ENSP00000317261:S606F;ENSP00000340280:S606F	ENSP00000340280:S606F	S	+	2	0	PARD3B	205749439	0.997000	0.39634	1.000000	0.80357	0.977000	0.68977	1.791000	0.38744	2.854000	0.98071	0.655000	0.94253	TCC	.	.	none		0.393	PARD3B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000335992.1	NM_057177		T	206041194	C	T	206041194	3	4	42	1	0	0	0	0	1	0	0	0	11453	855	30	2	1867	2	PARD3B	2	206041194	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	7090551	206041194	37158179	55	15007											
INO80D	54891	hgsc.bcm.edu	37	chr2	206921607	206921607	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctcatctataggatcattCtttttcttcctctctttttt	6	22	2	11	0	6	0	2	0	4	0	8	1	7	1	2	1	0	0	2	1	2	9			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:206921607C>A	ENST00000403263.1	-	4	683	c.279G>T	c.(277-279)aaG>aaT	p.K93N		NM_017759.4	NP_060229.3	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	93					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						TAGGATCATTCTTTTTCTTCC	0.463																																					p.K93N		Atlas-SNP	.											.	INO80D	134	.	0			c.G279T						PASS	.						133	118	123					2																	206921607		1943	4138	6081	SO:0001583	missense	54891	exon4			ATCATTCTTTTTC		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.279G>T	2.37:g.206921607C>A	ENSP00000384198:p.Lys93Asn	172	0	0		184	60	0.326087	NM_017759	B3KU68|B9EG77|Q6PJC6|Q6PJU1|Q6PKA1|Q9NXD5	Missense_Mutation	SNP	ENST00000403263.1	37	CCDS46500.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.218033	0.79352	.	.	ENSG00000114933	ENST00000403263;ENST00000233270	T	0.36157	1.27	5.38	5.38	0.77491	.	0.000000	0.64402	D	0.000004	T	0.50120	0.1597	L	0.27053	0.805	0.58432	D	0.999997	D	0.76494	0.999	D	0.83275	0.996	T	0.53365	-0.8449	10	0.66056	D	0.02	.	19.1182	0.93351	0.0:1.0:0.0:0.0	.	93	Q53TQ3-2	.	N	93	ENSP00000384198:K93N	ENSP00000233270:K93N	K	-	3	2	INO80D	206629852	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.759000	0.62227	2.522000	0.85027	0.462000	0.41574	AAG	.	.	none		0.463	INO80D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336459.1	NM_017759		A	206921607	C	A	206921607	3	1	42	1	0	0	0	0	1	0	0	0	7758	912	32	4	2836	4	INO80D	2	206921607	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	880413	206921607	36277766	56	15008											
ERBB4	2066	hgsc.bcm.edu	37	chr2	213403208	213403208	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggctggacggtccccgccGccacgagaaggctcacccag	7	4	14	16	4	1	1	1	0	0	1	2	3	2	2	5	4	0	2	5	4	1	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:213403208G>A	ENST00000342788.4	-	1	357	c.47C>T	c.(46-48)gCg>gTg	p.A16V	ERBB4_ENST00000436443.1_Missense_Mutation_p.A16V|ERBB4_ENST00000402597.1_Missense_Mutation_p.A16V	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	16					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)	GGTCCCCGCCGCCACGAGAAG	0.612										TSP Lung(8;0.080)																											p.A16V		Atlas-SNP	.											ERBB4,NS,carcinoma,0,1	ERBB4	480	1	0			c.C47T						PASS	.						65	80	75					2																	213403208		2203	4300	6503	SO:0001583	missense	2066	exon1			CCCGCCGCCACGA	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.47C>T	2.37:g.213403208G>A	ENSP00000342235:p.Ala16Val	86	0	0		100	47	0.47	NM_001042599	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	37	CCDS2394.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	3.672|3.672	-0.067305|-0.067305	0.07273|0.07273	.|.	.|.	ENSG00000178568|ENSG00000178568	ENST00000342788;ENST00000436443;ENST00000402597|ENST00000260943	T;T;T|.	0.74526|.	-0.85;-0.85;-0.84|.	5.87|5.87	3.77|3.77	0.43336|0.43336	.|.	0.200683|.	0.32593|.	N|.	0.005888|.	T|T	0.19565|0.19565	0.0470|0.0470	N|N	0.08118|0.08118	0|0	0.26490|0.26490	N|N	0.974959|0.974959	B;B;B;B|.	0.25850|.	0.009;0.136;0.009;0.005|.	B;B;B;B|.	0.19148|.	0.008;0.024;0.008;0.003|.	T|T	0.17289|0.17289	-1.0374|-1.0374	10|5	0.02654|.	T|.	1|.	.|.	9.3157|9.3157	0.37932|0.37932	0.1874:0.0:0.8126:0.0|0.1874:0.0:0.8126:0.0	.|.	16;16;16;16|.	Q15303-4;Q15303-2;Q15303-3;Q15303|.	.;.;.;ERBB4_HUMAN|.	V|W	16|16	ENSP00000342235:A16V;ENSP00000403204:A16V;ENSP00000385565:A16V|.	ENSP00000342235:A16V|.	A|R	-|-	2|1	0|2	ERBB4|ERBB4	213111453|213111453	0.904000|0.904000	0.30761|0.30761	1.000000|1.000000	0.80357|0.80357	0.964000|0.964000	0.63967|0.63967	0.897000|0.897000	0.28390|0.28390	1.510000|1.510000	0.48803|0.48803	-0.467000|-0.467000	0.05162|0.05162	GCG|CGG	.	.	none		0.612	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		A	213403208	G	A	213403208	3	1	42	1	0	0	0	0	1	0	0	0	5211	1087	38	1	3991	1	ERBB4	2	213403208	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	6481601	213403208	29796165	57	15009											
DOCK10	55619	hgsc.bcm.edu	37	chr2	225637895	225637895	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttcacgctgacacttccttgCagtttgagctgcagtctgat	7	14	9	11	1	2	3	1	3	1	0	3	3	3	3	1	0	3	5	1	0	0	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:225637895C>T	ENST00000258390.7	-	53	6250	c.6183G>A	c.(6181-6183)ctG>ctA	p.L2061L	DOCK10_ENST00000409592.3_Silent_p.L2055L	NM_014689.2	NP_055504.2	Q96BY6	DOC10_HUMAN	dedicator of cytokinesis 10	2061	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)		CACTTCCTTGCAGTTTGAGCT	0.458																																					p.L2061L		Atlas-SNP	.											.	DOCK10	308	.	0			c.G6183A						PASS	.						87	85	86					2																	225637895		2176	4280	6456	SO:0001819	synonymous_variant	55619	exon53			TCCTTGCAGTTTG	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.6183G>A	2.37:g.225637895C>T		95	0	0		94	10	0.106383	NM_014689	B3FL70|O75178|Q9NW06|Q9NXI8	Silent	SNP	ENST00000258390.7	37	CCDS46528.1																																																																																			.	.	none		0.458	DOCK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331246.1			T	225637895	C	T	225637895	2	4	42	1	0	0	0	0	0	0	0	1	4687	697	25	2		2	DOCK10	2	225637895	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	12234687	225637895	17561478	58	15010											
AGFG1	3267	hgsc.bcm.edu	37	chr2	228401667	228401667	+	Missense_Mutation	SNP	T	T	G																															ctgctggtccttctgtggcaTcttctacaaacccatttcag																										TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:228401667T>G	ENST00000310078.8	+	10	1596	c.1336T>G	c.(1336-1338)Tct>Gct	p.S446A	AGFG1_ENST00000373671.3_Missense_Mutation_p.S406A|AGFG1_ENST00000409171.1_Missense_Mutation_p.S446A|AGFG1_ENST00000409315.1_Missense_Mutation_p.S425A|AGFG1_ENST00000409979.2_Missense_Mutation_p.S470A	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	446					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						TTCTGTGGCATCTTCTACAAA	0.368																																					p.S470A		Atlas-SNP	.											.	AGFG1	80	.	0			c.T1408G						PASS	.						95	98	97					2																	228401667		2203	4300	6503	SO:0001583	missense	3267	exon11			GTGGCATCTTCTA		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.1336T>G	2.37:g.228401667T>G	ENSP00000312059:p.Ser446Ala	293	0	0		261	61	0.233716	NM_001135187	B3KUL1|E9PHX7|Q15277|Q4VAS0|Q4VAS1|Q4VAS3|Q53QT8|Q53R11	Missense_Mutation	SNP	ENST00000310078.8	37	CCDS2467.1	.	.	.	.	.	.	.	.	.	.	T	13.24	2.179454	0.38511	.	.	ENSG00000173744	ENST00000409979;ENST00000542592;ENST00000310078;ENST00000409315;ENST00000373671;ENST00000409171	T;T;T;T;T	0.22539	2.0;2.02;2.02;1.95;2.03	6.06	6.06	0.98353	.	0.104141	0.64402	D	0.000004	T	0.09158	0.0226	N	0.08118	0	0.26605	N	0.972954	B;B;B;B	0.09022	0.002;0.0;0.0;0.001	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.34354	-0.9832	10	0.10111	T	0.7	-17.8795	7.4788	0.27393	0.0:0.1168:0.0:0.8832	.	406;446;470;446	P52594-2;P52594-3;E9PHX7;P52594	.;.;.;AGFG1_HUMAN	A	470;455;446;425;406;446	ENSP00000387282:S470A;ENSP00000312059:S446A;ENSP00000387154:S425A;ENSP00000362775:S406A;ENSP00000387218:S446A	ENSP00000312059:S446A	S	+	1	0	AGFG1	228109911	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.649000	0.37281	2.327000	0.79052	0.533000	0.62120	TCT	.	.	none		0.368	AGFG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256895.2	NM_004504		G	228401667	T	G	228401667	3	3	42	1	0	0	0	0	1	0	0	0	380	1435	50	5	1450	5	AGFG1	2	228401667	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	2763772	228401667	14797706	59	15011	196	2									
AGFG1	3267	hgsc.bcm.edu	37	chr2	228401669	228401669	+	Silent	SNP	T	T	C																															gctggtccttctgtggcatcTtctacaaacccatttcagac																								rs144069697	byFrequency	TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:228401669T>C	ENST00000310078.8	+	10	1598	c.1338T>C	c.(1336-1338)tcT>tcC	p.S446S	AGFG1_ENST00000373671.3_Silent_p.S406S|AGFG1_ENST00000409171.1_Silent_p.S446S|AGFG1_ENST00000409315.1_Silent_p.S425S|AGFG1_ENST00000409979.2_Silent_p.S470S	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	446					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						CTGTGGCATCTTCTACAAACC	0.373																																					p.S470S		Atlas-SNP	.											.	AGFG1	80	.	0			c.T1410C						PASS	.						94	96	96					2																	228401669		2203	4300	6503	SO:0001819	synonymous_variant	3267	exon11			GGCATCTTCTACA		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.1338T>C	2.37:g.228401669T>C		286	0	0		257	60	0.233463	NM_001135187	B3KUL1|E9PHX7|Q15277|Q4VAS0|Q4VAS1|Q4VAS3|Q53QT8|Q53R11	Silent	SNP	ENST00000310078.8	37	CCDS2467.1																																																																																			T|1.000;G|0.000	.	alt		0.373	AGFG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256895.2	NM_004504		C	228401669	T	C	228401669	2	2	42	1	0	0	0	0	0	0	0	1	380	1596	56	3		3	AGFG1	2	228401669	Silent	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	2	228401669	14797704	60	15012	196	2									
ALPPL2	251	hgsc.bcm.edu	37	chr2	233272600	233272600	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cacacgggtgcagcatgcctCgccagccggcgcctacgccc	6	4	12	19	5	0	0	0	0	0	0	1	0	0	0	5	2	5	2	5	2	1	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:233272600C>T	ENST00000295453.3	+	5	573	c.521C>T	c.(520-522)tCg>tTg	p.S174L		NM_031313.2	NP_112603.2	P10696	PPBN_HUMAN	alkaline phosphatase, placental-like 2	174					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(1)	13		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)	Amifostine(DB01143)	CAGCATGCCTCGCCAGCCGGC	0.647																																					p.S174L		Atlas-SNP	.											.	ALPPL2	36	.	0			c.C521T						PASS	.						61	64	63					2																	233272600		2203	4300	6503	SO:0001583	missense	251	exon5			ATGCCTCGCCAGC	J04948	CCDS2491.1	2q37	2008-05-20			ENSG00000163286	ENSG00000163286			441	protein-coding gene	gene with protein product		171810					Standard	NM_031313		Approved		uc002vss.4	P10696	OTTHUMG00000133257	ENST00000295453.3:c.521C>T	2.37:g.233272600C>T	ENSP00000295453:p.Ser174Leu	85	0	0		87	24	0.275862	NM_031313	A8KAF2|Q16727|Q53S81|Q96CM1	Missense_Mutation	SNP	ENST00000295453.3	37	CCDS2491.1	.	.	.	.	.	.	.	.	.	.	c	15.41	2.826270	0.50739	.	.	ENSG00000163286	ENST00000295453	D	0.96685	-4.09	2.71	2.71	0.32032	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	D	0.98520	0.9506	H	0.96208	3.785	0.58432	D	0.999998	D	0.76494	0.999	D	0.69824	0.966	D	0.99323	1.0907	10	0.87932	D	0	.	13.8099	0.63256	0.0:1.0:0.0:0.0	.	174	P10696	PPBN_HUMAN	L	174	ENSP00000295453:S174L	ENSP00000295453:S174L	S	+	2	0	ALPPL2	232980844	0.997000	0.39634	0.221000	0.23827	0.012000	0.07955	7.137000	0.77295	1.499000	0.48617	0.205000	0.17691	TCG	.	.	none		0.647	ALPPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257034.2	NM_031313		T	233272600	C	T	233272600	3	4	42	1	0	0	0	0	1	0	0	0	549	893	31	1	539	1	ALPPL2	2	233272600	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	4870931	233272600	9926773	61	15013											
OR6B3	150681	hgsc.bcm.edu	37	chr2	240984801	240984801	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctctccagcagccggtggccGaggggatgcgcaggacagcc	7	4	16	14	3	1	0	0	0	1	0	2	3	1	2	4	5	4	2	4	5	0	0	rs371957226		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr2:240984801G>A	ENST00000319423.4	-	1	688	c.689C>T	c.(688-690)tCg>tTg	p.S230L	PRR21_ENST00000408934.1_5'Flank	NM_173351.1	NP_775486.1	Q8NGW1	OR6B3_HUMAN	olfactory receptor, family 6, subfamily B, member 3	230						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)		GCCGGTGGCCGAGGGGATGCG	0.582																																					p.S230L		Atlas-SNP	.											.	OR6B3	37	.	0			c.C689T						PASS	.	G	LEU/SER	0,4234		0,0,2117	49	56	54		689	4.1	0.9	2		54	1,8477		0,1,4238	no	missense	OR6B3	NM_173351.1	145	0,1,6355	AA,AG,GG		0.0118,0.0,0.0079	benign	230/332	240984801	1,12711	2117	4239	6356	SO:0001583	missense	150681	exon1			GTGGCCGAGGGGA		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.689C>T	2.37:g.240984801G>A	ENSP00000322435:p.Ser230Leu	181	0	0		178	53	0.297753	NM_173351	Q6IFH3	Missense_Mutation	SNP	ENST00000319423.4	37	CCDS42837.1	.	.	.	.	.	.	.	.	.	.	g	10.43	1.347601	0.24426	0.0	1.18E-4	ENSG00000178586	ENST00000319423	T	0.00330	8.08	4.09	4.09	0.47781	GPCR, rhodopsin-like superfamily (1);	0.397274	0.18439	N	0.141189	T	0.00666	0.0022	M	0.93678	3.445	0.09310	N	1	P	0.34522	0.455	B	0.40285	0.325	T	0.05131	-1.0904	10	0.87932	D	0	.	14.6272	0.68629	0.0:0.0:1.0:0.0	.	230	Q8NGW1	OR6B3_HUMAN	L	230	ENSP00000322435:S230L	ENSP00000322435:S230L	S	-	2	0	OR6B3	240633474	0.415000	0.25416	0.900000	0.35374	0.073000	0.16967	1.832000	0.39151	2.540000	0.85666	0.603000	0.83216	TCG	.	.	weak		0.582	OR6B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326078.1			A	240984801	G	A	240984801	3	1	42	1	0	0	0	0	1	0	0	0	11198	1059	37	1	309	1	OR6B3	2	240984801	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	7712201	240984801	2214572	62	15014											
MTMR14	64419	hgsc.bcm.edu	37	chr3	9695364	9695364	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cgagactactgtttcagcgtGattccaaacacgaatgggga	12	9	11	9	3	1	2	1	1	0	1	2	5	2	3	1	2	3	1	1	2	3	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr3:9695364G>C	ENST00000296003.4	+	2	341	c.219G>C	c.(217-219)gtG>gtC	p.V73V	MTMR14_ENST00000420925.1_Intron|MTMR14_ENST00000353332.5_Silent_p.V73V|MTMR14_ENST00000351233.5_Silent_p.V73V	NM_001077525.2	NP_001070993.1	Q8NCE2	MTMRE_HUMAN	myotubularin related protein 14	73					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)					GTTTCAGCGTGATTCCAAACA	0.498																																					p.V73V		Atlas-SNP	.											.	MTMR14	43	.	0			c.G219C						PASS	.						168	163	164					3																	9695364		1990	4170	6160	SO:0001819	synonymous_variant	64419	exon2			CAGCGTGATTCCA	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.219G>C	3.37:g.9695364G>C		151	0	0		132	22	0.166667	NM_022485	Q0JTH5|Q0JU83|Q6PIZ4|Q6QE21|Q86VK9|Q8IYK1|Q8TCM7|Q9H6C0	Silent	SNP	ENST00000296003.4	37	CCDS43043.1																																																																																			.	.	none		0.498	MTMR14-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338435.1	NM_022485		C	9695364	G	C	9695364	2	2	42	1	0	0	0	0	0	0	0	1	9951	1277	45	4		4	MTMR14	3	9695364	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10		9695364	188327066	63	15015											
RPUSD3	285367	hgsc.bcm.edu	37	chr3	9885228	9885228	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttggcagcagccccgcgaaGggctggtccccgaggggccc	5	5	16	15	3	0	0	0	0	0	0	1	2	1	0	5	5	2	3	5	5	1	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr3:9885228G>T	ENST00000383820.5	-	2	184	c.183C>A	c.(181-183)ccC>ccA	p.P61P	RPUSD3_ENST00000485705.1_5'UTR|TTLL3_ENST00000455274.1_Intron|RPUSD3_ENST00000424438.1_Silent_p.P29P|RPUSD3_ENST00000433535.2_Silent_p.P61P	NM_173659.3	NP_775930.2	Q6P087	RUSD3_HUMAN	RNA pseudouridylate synthase domain containing 3	61					pseudouridine synthesis (GO:0001522)		poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)			central_nervous_system(2)|endometrium(3)|lung(2)	7	Medulloblastoma(99;0.227)					GCCCCGCGAAGGGCTGGTCCC	0.667																																					p.P61P		Atlas-SNP	.											.	RPUSD3	19	.	0			c.C183A						PASS	.						26	29	28					3																	9885228		2203	4298	6501	SO:0001819	synonymous_variant	285367	exon2			CGCGAAGGGCTGG	BC032135	CCDS2586.2, CCDS46744.1	3p25.3	2013-02-11			ENSG00000156990	ENSG00000156990		"RNA pseudouridylate synthase domain containing"	28437	protein-coding gene	gene with protein product						12477932	Standard	NM_173659		Approved	MGC29784	uc011atk.2	Q6P087	OTTHUMG00000128441	ENST00000383820.5:c.183C>A	3.37:g.9885228G>T		137	0	0		117	30	0.25641	NM_001142547	B4DS39|Q6P6A9|Q8N1B2|Q8NAV3	Silent	SNP	ENST00000383820.5	37	CCDS2586.2	.	.	.	.	.	.	.	.	.	.	G	14.80	2.644836	0.47258	.	.	ENSG00000156990	ENST00000427174	T	0.47528	0.84	4.77	-4.74	0.03249	.	0.288732	0.33959	N	0.004381	T	0.32615	0.0835	.	.	.	0.25345	N	0.988917	.	.	.	.	.	.	T	0.32455	-0.9906	7	0.87932	D	0	.	0.3873	0.00405	0.382:0.1558:0.2102:0.252	.	.	.	.	H	52	ENSP00000400397:P52H	ENSP00000400397:P52H	P	-	2	0	RPUSD3	9860228	0.045000	0.20229	0.031000	0.17742	0.805000	0.45488	-0.355000	0.07671	-1.117000	0.02965	0.655000	0.94253	CCT	.	.	none		0.667	RPUSD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250238.1	NM_173659		T	9885228	G	T	9885228	2	4	42	1	0	0	0	0	0	0	0	1	13683	987	35	4		4	RPUSD3	3	9885228	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	189864	9885228	188137202	64	15016											
STAC	6769	hgsc.bcm.edu	37	chr3	36422176	36422176	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ccgcgaggacggcgtggacgGgctgcccaaggaggcggtgg	6	3	21	11	6	0	0	0	0	0	0	0	4	0	3	2	8	1	1	2	8	1	0	rs143848363	byFrequency	TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr3:36422176G>A	ENST00000273183.3	+	1	341	c.41G>A	c.(40-42)gGg>gAg	p.G14E	STAC_ENST00000476388.1_3'UTR|STAC_ENST00000457375.2_Missense_Mutation_p.G14E	NM_003149.1	NP_003140.1	Q99469	STAC_HUMAN	SH3 and cysteine rich domain	14					cellular response to heat (GO:0034605)|intracellular signal transduction (GO:0035556)|signal transduction (GO:0007165)	cytosol (GO:0005829)	metal ion binding (GO:0046872)			endometrium(5)|large_intestine(9)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(5)	32						GGCGTGGACGGGCTGCCCAAG	0.692													G|||	7	0.00139776	0.0	0.0043	5008	,	,		13727	0.0		0.004	False		,,,				2504	0.0				p.G14E		Atlas-SNP	.											.	STAC	78	.	0			c.G41A						PASS	.	G	GLU/GLY	0,4384		0,0,2192	17	15	16		41	4.1	1	3	dbSNP_134	16	6,8552		0,6,4273	no	missense	STAC	NM_003149.1	98	0,6,6465	AA,AG,GG		0.0701,0.0,0.0464	possibly-damaging	14/403	36422176	6,12936	2192	4279	6471	SO:0001583	missense	6769	exon1			TGGACGGGCTGCC	D86640	CCDS2662.1	3p22.3	2007-06-08			ENSG00000144681	ENSG00000144681			11353	protein-coding gene	gene with protein product		602317	"src homology three (SH3) and cysteine rich domain"			8954993, 10393425	Standard	XM_006713308		Approved	STAC1	uc003cgh.1	Q99469	OTTHUMG00000130798	ENST00000273183.3:c.41G>A	3.37:g.36422176G>A	ENSP00000273183:p.Gly14Glu	57	0	0		42	9	0.214286	NM_003149	B2R8S8	Missense_Mutation	SNP	ENST00000273183.3	37	CCDS2662.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	G	18.22	3.574826	0.65878	0.0	7.01E-4	ENSG00000144681	ENST00000273183;ENST00000457375;ENST00000434649	T;T;T	0.77877	-1.13;0.62;0.32	4.96	4.08	0.47627	.	0.202960	0.40064	N	0.001190	T	0.69806	0.3152	L	0.44542	1.39	0.35585	D	0.806587	B;D	0.59767	0.006;0.986	B;P	0.50860	0.008;0.652	T	0.80973	-0.1143	10	0.72032	D	0.01	.	11.0518	0.47894	0.0898:0.0:0.9102:0.0	.	14;14	E9PEA7;Q99469	.;STAC_HUMAN	E	14	ENSP00000273183:G14E;ENSP00000393713:G14E;ENSP00000398403:G14E	ENSP00000273183:G14E	G	+	2	0	STAC	36397180	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.713000	0.47194	1.400000	0.46741	0.650000	0.86243	GGG	G|0.999;A|0.001	0.001	strong		0.692	STAC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253338.2	NM_003149		A	36422176	G	A	36422176	3	1	42	1	0	0	0	0	1	0	0	0	15254	1232	43	2	43	2	STAC	3	36422176	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	26536948	36422176	161600254	65	15017											
TRANK1	9881	hgsc.bcm.edu	37	chr3	36896835	36896835	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cgtgtcccccgtgaggaacaTagagttggggtcattgatgc	8	10	14	9	2	1	3	1	2	0	1	2	4	2	4	2	3	2	1	2	3	2	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr3:36896835T>A	ENST00000429976.2	-	12	4493	c.4246A>T	c.(4246-4248)Atg>Ttg	p.M1416L	TRANK1_ENST00000428977.2_Missense_Mutation_p.M866L|TRANK1_ENST00000301807.6_Missense_Mutation_p.M866L	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	1416							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						GTGAGGAACATAGAGTTGGGG	0.552																																					p.M1416L		Atlas-SNP	.											.	TRANK1	398	.	0			c.A4246T						PASS	.						134	131	132					3																	36896835		2076	4222	6298	SO:0001583	missense	9881	exon12			GGAACATAGAGTT	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.4246A>T	3.37:g.36896835T>A	ENSP00000416168:p.Met1416Leu	164	0	0		111	43	0.387387	NM_014831	Q8N8K0	Missense_Mutation	SNP	ENST00000429976.2	37	CCDS46789.2	.	.	.	.	.	.	.	.	.	.	T	12.18	1.861750	0.32884	.	.	ENSG00000168016	ENST00000428977;ENST00000429976;ENST00000301807	T;T;T	0.76968	-1.06;-1.06;-1.06	5.39	5.39	0.77823	.	0.000000	0.64402	D	0.000001	T	0.65154	0.2664	N	0.03177	-0.4	0.46203	D	0.99892	B	0.28178	0.202	B	0.40285	0.325	T	0.64833	-0.6314	10	0.27785	T	0.31	.	15.7204	0.77705	0.0:0.0:0.0:1.0	.	1416	O15050	TRNK1_HUMAN	L	866;1416;866	ENSP00000416826:M866L;ENSP00000416168:M1416L;ENSP00000301807:M866L	ENSP00000301807:M866L	M	-	1	0	TRANK1	36871839	1.000000	0.71417	1.000000	0.80357	0.389000	0.30415	6.193000	0.72075	2.180000	0.69256	0.459000	0.35465	ATG	.	.	none		0.552	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831		A	36896835	T	A	36896835	3	1	42	1	0	0	0	0	1	0	0	0	16469	1406	49	5	4579	5	TRANK1	3	36896835	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	474659	36896835	161125595	66	15018											
ZNF167	55888	hgsc.bcm.edu	37	chr3	44612048	44612048	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tttactcagagttcccgactCactgaccaccagagaaccca	12	8	6	15	1	2	3	2	1	0	2	3	5	3	3	4	0	2	1	4	0	2	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr3:44612048C>G	ENST00000273320.3	+	6	1875	c.1446C>G	c.(1444-1446)ctC>ctG	p.L482L	RP11-944L7.5_ENST00000419137.1_Intron|ZKSCAN7_ENST00000426540.1_Silent_p.L482L|ZKSCAN7_ENST00000341840.3_Intron|ZKSCAN7_ENST00000431636.1_Intron|RP11-944L7.4_ENST00000457331.1_RNA	NM_018651.2	NP_061121.2	Q9P0L1	ZKSC7_HUMAN	zinc finger with KRAB and SCAN domains 7	482					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)										GTTCCCGACTCACTGACCACC	0.468																																					p.L482L		Atlas-SNP	.											.	.	.	.	0			c.C1446G						PASS	.						94	96	95					3																	44612048		2203	4300	6503	SO:0001819	synonymous_variant	55888	exon6			CCGACTCACTGAC	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.1446C>G	3.37:g.44612048C>G		108	0	0		88	23	0.261364	NM_018651	A0PJV3|A8K5H0|Q6WL09|Q96FQ2	Silent	SNP	ENST00000273320.3	37	CCDS2715.1																																																																																			.	.	none		0.468	ZKSCAN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256752.4	NM_018651		G	44612048	C	G	44612048	2	3	42	1	0	0	0	0	0	0	0	1	17756	813	29	4		4	ZNF167	3	44612048	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	7715213	44612048	153410382	67	15019											
ATRIP	84126	hgsc.bcm.edu	37	chr3	48501189	48501189	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	catcttgtcttctgcaggttCcattttgataaacctgctcc	7	16	6	12	0	3	1	0	1	3	0	5	1	5	1	3	1	3	3	3	1	2	6			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr3:48501189C>T	ENST00000320211.3	+	7	1042	c.929C>T	c.(928-930)tCc>tTc	p.S310F	ATRIP_ENST00000346691.4_Missense_Mutation_p.S310F|ATRIP_ENST00000357105.6_Missense_Mutation_p.S183F|ATRIP_ENST00000412052.1_Missense_Mutation_p.S217F	NM_130384.2	NP_569055.1	Q8WXE1	ATRIP_HUMAN	ATR interacting protein	310					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)		TCTGCAGGTTCCATTTTGATA	0.483								Other conserved DNA damage response genes																													p.S310F		Atlas-SNP	.											ATRIP,upper_leg,malignant_melanoma,0,1	ATRIP	41	1	0			c.C929T						PASS	.						129	139	136					3																	48501189		2203	4300	6503	SO:0001583	missense	84126	exon7			CAGGTTCCATTTT	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.929C>T	3.37:g.48501189C>T	ENSP00000323099:p.Ser310Phe	69	0	0		67	24	0.358209	NM_130384	A8K6A3|A8K714|B2RCE7|B4DU92|B5MEB7|Q69YK9|Q8NHQ2|Q8WUG7|Q96CL3|Q9HA30	Missense_Mutation	SNP	ENST00000320211.3	37	CCDS2768.1	.	.	.	.	.	.	.	.	.	.	C	17.75	3.466426	0.63625	.	.	ENSG00000164053	ENST00000320211;ENST00000346691;ENST00000357105;ENST00000412052	T;T;T;T	0.54866	1.12;1.09;0.55;1.12	5.75	5.75	0.90469	.	0.221381	0.48286	D	0.000200	T	0.71779	0.3380	M	0.70275	2.135	0.47819	D	0.999525	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.73959	-0.3818	10	0.87932	D	0	-17.7002	15.4526	0.75285	0.0:1.0:0.0:0.0	.	310;310	Q8WXE1-2;Q8WXE1	.;ATRIP_HUMAN	F	310;310;183;217	ENSP00000323099:S310F;ENSP00000302338:S310F;ENSP00000349620:S183F;ENSP00000400930:S217F	ENSP00000323099:S310F	S	+	2	0	ATRIP	48476193	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	2.600000	0.46240	2.719000	0.93026	0.655000	0.94253	TCC	.	.	none		0.483	ATRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257507.2	NM_130384		T	48501189	C	T	48501189	3	4	42	1	0	0	0	0	1	0	0	0	1205	855	30	2	955	2	ATRIP	3	48501189	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	3889141	48501189	149521241	68	15020											
CISH	1154	hgsc.bcm.edu	37	chr3	50645816	50645816	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agactcaccagattcccgaaGgtaggagaaggtcttggcta	12	8	12	9	1	2	3	1	0	1	3	3	5	3	3	2	4	0	2	2	4	4	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr3:50645816G>T	ENST00000348721.3	-	2	409	c.229C>A	c.(229-231)Ctt>Att	p.L77I	CISH_ENST00000443053.2_Missense_Mutation_p.L94I	NM_145071.2	NP_659508.1	Q9NSE2	CISH_HUMAN	cytokine inducible SH2-containing protein	77					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)		GATTCCCGAAGGTAGGAGAAG	0.567																																					p.L94I		Atlas-SNP	.											.	CISH	27	.	0			c.C280A						PASS	.						71	62	65					3																	50645816		2203	4300	6503	SO:0001583	missense	1154	exon3			CCCGAAGGTAGGA	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.229C>A	3.37:g.50645816G>T	ENSP00000294173:p.Leu77Ile	66	0	0		35	12	0.342857	NM_013324	B2R9N1|G5E9R1|Q9NS38|Q9Y5R1	Missense_Mutation	SNP	ENST00000348721.3	37	CCDS2831.1	.	.	.	.	.	.	.	.	.	.	G	27.5	4.833132	0.91036	.	.	ENSG00000114737	ENST00000443053;ENST00000348721	T;T	0.65732	-0.17;-0.12	6.03	6.03	0.97812	SH2 motif (1);	0.066847	0.64402	N	0.000007	T	0.79997	0.4543	M	0.73962	2.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.991	T	0.75619	-0.3255	10	0.33141	T	0.24	-0.1319	20.177	0.98182	0.0:0.0:1.0:0.0	.	94;77	G5E9R1;Q9NSE2	.;CISH_HUMAN	I	94;77	ENSP00000409346:L94I;ENSP00000294173:L77I	ENSP00000294173:L77I	L	-	1	0	CISH	50620820	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.876000	0.87215	2.854000	0.98071	0.655000	0.94253	CTT	.	.	none		0.567	CISH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346245.1	NM_145071		T	50645816	G	T	50645816	3	4	42	1	0	0	0	0	1	0	0	0	3439	1000	35	4	555	4	CISH	3	50645816	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	2144627	50645816	147376614	69	15021											
ADAMTS9	56999	hgsc.bcm.edu	37	chr3	64606792	64606792	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gagaaaacagtggcccacctCaggtcacagtctgtaccaca	13	6	9	13	0	3	1	2	0	1	1	3	2	3	1	3	2	2	1	3	2	3	1	rs373590492		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr3:64606792C>T	ENST00000498707.1	-	19	3153	c.2811G>A	c.(2809-2811)ctG>ctA	p.L937L	ADAMTS9_ENST00000295903.4_Silent_p.L909L	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	937					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)		TGGCCCACCTCAGGTCACAGT	0.512																																					p.L937L		Atlas-SNP	.											.	ADAMTS9	206	.	0			c.G2811A						PASS	.	C		0,4406		0,0,2203	74	75	75		2811	-0.9	1	3		75	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ADAMTS9	NM_182920.1		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		937/1936	64606792	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	56999	exon19			CCACCTCAGGTCA	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.2811G>A	3.37:g.64606792C>T		133	0	0		68	10	0.147059	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Silent	SNP	ENST00000498707.1	37	CCDS2903.1																																																																																			.	.	weak		0.512	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1			T	64606792	C	T	64606792	2	4	42	1	0	0	0	0	0	0	0	1	273	813	29	2		2	ADAMTS9	3	64606792	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	13960976	64606792	133415638	70	15022											
MITF	4286	hgsc.bcm.edu	37	chr3	69915452	69915452	+	Intron	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aggaaaaaagatggaggcgcTtagagttcagatgttcatgc	14	9	13	5	1	2	3	2	0	0	3	2	5	2	5	0	3	1	3	0	3	4	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr3:69915452T>C	ENST00000448226.2	+	2	231				MITF_ENST00000328528.6_Intron|MITF_ENST00000352241.4_Intron|MITF_ENST00000472437.1_Intron|MITF_ENST00000314589.5_Missense_Mutation_p.L4P			O75030	MITF_HUMAN	microphthalmia-associated transcription factor						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)		ATGGAGGCGCTTAGAGTTCAG	0.453			A		melanoma		"Waardenburg syndrome type 2, Tietz syndrome"																														p.L4P	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.T11C						PASS	.						168	169	169					3																	69915452		1868	4113	5981	SO:0001627	intron_variant	4286	exon1			AGGCGCTTAGAGT		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.105-12833T>C	3.37:g.69915452T>C		128	0	0		90	9	0.1	NM_198177	B4DJL2|D3K197|E9PFN0|Q14841|Q9P2V0|Q9P2V1|Q9P2V2|Q9P2Y8	Missense_Mutation	SNP	ENST00000448226.2	37		.	.	.	.	.	.	.	.	.	.	T	19.91	3.913765	0.72983	.	.	ENSG00000187098	ENST00000451708;ENST00000314589	T;T	0.27720	1.65;2.46	5.93	5.93	0.95920	.	.	.	.	.	T	0.37892	0.1020	N	0.14661	0.345	0.80722	D	1	D	0.69078	0.997	D	0.78314	0.991	T	0.25082	-1.0142	8	.	.	.	.	15.3592	0.74457	0.0:0.0:0.0:1.0	.	4	O75030-8	.	P	4	ENSP00000398639:L4P;ENSP00000324443:L4P	.	L	+	2	0	MITF	69998142	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.555000	0.67301	2.263000	0.75096	0.533000	0.62120	CTT	.	.	none		0.453	MITF-007	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000313947.1	NM_198159		C	69915452	T	C	69915452	1	2	42	0	1	0	0	0	0	0	0	0	9605	1609	56	3		3	MITF	3	69915452	Intron	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	5308660	69915452	128106978	71	15023											
DTX3L	151636	hgsc.bcm.edu	37	chr3	122288257	122288257	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgcaagtttcatcgatgccTttcaacatgcctcatgtcag	10	13	7	11	1	4	0	4	0	0	0	5	1	4	0	2	0	4	2	2	0	2	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr3:122288257T>A	ENST00000296161.4	+	3	1510	c.1321T>A	c.(1321-1323)Ttt>Att	p.F441I	DTX3L_ENST00000383661.3_Intron	NM_138287.3	NP_612144.1	Q8TDB6	DTX3L_HUMAN	deltex 3 like, E3 ubiquitin ligase	441					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)		CATCGATGCCTTTCAACATGC	0.423																																					p.F441I		Atlas-SNP	.											.	DTX3L	59	.	0			c.T1321A						PASS	.						133	125	128					3																	122288257		2203	4300	6503	SO:0001583	missense	151636	exon3			GATGCCTTTCAAC		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.1321T>A	3.37:g.122288257T>A	ENSP00000296161:p.Phe441Ile	211	0	0		158	46	0.291139	NM_138287	B3KWH6|Q53ZZ3|Q5MJP7	Missense_Mutation	SNP	ENST00000296161.4	37	CCDS3015.1	.	.	.	.	.	.	.	.	.	.	T	17.37	3.371401	0.61624	.	.	ENSG00000163840	ENST00000296161	T	0.50548	0.74	5.65	3.26	0.37387	.	0.523151	0.17799	N	0.161628	T	0.35248	0.0925	L	0.39898	1.24	0.80722	D	1	P	0.46277	0.875	B	0.41440	0.357	T	0.04537	-1.0944	10	0.30854	T	0.27	-34.6537	6.3834	0.21548	0.0:0.08:0.1591:0.7609	.	441	Q8TDB6	DTX3L_HUMAN	I	441	ENSP00000296161:F441I	ENSP00000296161:F441I	F	+	1	0	DTX3L	123770947	1.000000	0.71417	0.983000	0.44433	0.710000	0.40934	1.590000	0.36654	0.553000	0.29044	0.533000	0.62120	TTT	.	.	none		0.423	DTX3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355966.1	NM_138287		A	122288257	T	A	122288257	3	1	42	1	0	0	0	0	1	0	0	0	4798	1609	56	5	1331	5	DTX3L	3	122288257	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	52372805	122288257	75734173	72	15024											
PRR23A	729627	hgsc.bcm.edu	37	chr3	138724565	138724565	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggctgaacatacttctggcGgaggagtagagcccagcggc	9	6	16	10	2	1	2	0	1	1	1	1	4	1	4	1	5	4	2	1	5	3	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr3:138724565G>A	ENST00000383163.2	-	1	545	c.546C>T	c.(544-546)tcC>tcT	p.S182S	MRPS22_ENST00000495075.1_5'Flank	NM_001134659.1	NP_001128131.1	A6NEV1	PR23A_HUMAN	proline rich 23A	182										endometrium(3)|kidney(1)|lung(7)	11						TACTTCTGGCGGAGGAGTAGA	0.667																																					p.S182S		Atlas-SNP	.											.	PRR23A	35	.	0			c.C546T						PASS	.						21	27	25					3																	138724565		692	1591	2283	SO:0001819	synonymous_variant	729627	exon1			TCTGGCGGAGGAG		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.546C>T	3.37:g.138724565G>A		128	0	0		130	17	0.130769	NM_001134659		Silent	SNP	ENST00000383163.2	37	CCDS46923.1																																																																																			.	.	none		0.667	PRR23A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361503.1	NM_001134659		A	138724565	G	A	138724565	2	1	42	1	0	0	0	0	0	0	0	1	12606	1103	39	1		1	PRR23A	3	138724565	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	16436308	138724565	59297865	73	15025											
ATR	545	hgsc.bcm.edu	37	chr3	142286975	142286975	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cttggcttctgtacaactgtAttatattcctctggtgtggc	6	17	9	9	0	2	0	0	0	2	0	3	0	3	0	1	3	2	3	1	3	5	7	rs545455583		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr3:142286975A>T	ENST00000350721.4	-	2	202	c.81T>A	c.(79-81)aaT>aaA	p.N27K	ATR_ENST00000383101.3_Missense_Mutation_p.N27K	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	27					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						GTACAACTGTATTATATTCCT	0.299								Other conserved DNA damage response genes																													p.N27K		Atlas-SNP	.											ATR,NS,carcinoma,-1,1	ATR	285	1	0			c.T81A						PASS	.						68	71	70					3																	142286975		2203	4293	6496	SO:0001583	missense	545	exon2			AACTGTATTATAT	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.81T>A	3.37:g.142286975A>T	ENSP00000343741:p.Asn27Lys	639	0	0		452	49	0.108407	NM_001184	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	37	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	A	17.80	3.477270	0.63849	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.35048	1.33;1.33	4.94	-1.9	0.07665	.	0.051950	0.85682	D	0.000000	T	0.39759	0.1090	L	0.57536	1.79	0.24160	N	0.995664	D	0.58268	0.982	P	0.50109	0.631	T	0.47898	-0.9081	10	0.59425	D	0.04	-16.858	13.1989	0.59756	0.4646:0.0:0.5354:0.0	.	27	Q13535	ATR_HUMAN	K	27	ENSP00000343741:N27K;ENSP00000372581:N27K	ENSP00000343741:N27K	N	-	3	2	ATR	143769665	1.000000	0.71417	0.920000	0.36463	0.854000	0.48673	1.322000	0.33689	-0.230000	0.09840	0.383000	0.25322	AAT	.	.	none		0.299	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184		T	142286975	A	T	142286975	3	4	42	1	0	0	0	0	1	0	0	0	1204	446	16	5	8037	5	ATR	3	142286975	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	3562410	142286975	55735455	74	15026											
SIAH2	6478	hgsc.bcm.edu	37	chr3	150480589	150480589	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggctgcggcggcggctgcttGctgcagggtttattagcgct	3	11	17	10	4	0	0	0	0	0	0	0	0	0	0	0	5	5	7	0	5	2	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr3:150480589G>A	ENST00000312960.3	-	1	575	c.48C>T	c.(46-48)agC>agT	p.S16S	SIAH2-AS1_ENST00000461943.1_RNA|SIAH2_ENST00000472885.1_Intron	NM_005067.5	NP_005058.3	O43255	SIAH2_HUMAN	siah E3 ubiquitin protein ligase 2	16					axon guidance (GO:0007411)|cell cycle (GO:0007049)|cellular protein catabolic process (GO:0044257)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|regulation of protein ubiquitination (GO:0031396)|regulation of RNA biosynthetic process (GO:2001141)|small GTPase mediated signal transduction (GO:0007264)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	ligase activity (GO:0016874)|transcription corepressor activity (GO:0003714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|pancreas(1)	16			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			GCGGCTGCTTGCTGCAGGGTT	0.771																																					p.S16S		Atlas-SNP	.											.	SIAH2	33	.	0			c.C48T						PASS	.						4	5	5					3																	150480589		1114	2511	3625	SO:0001819	synonymous_variant	6478	exon1			CTGCTTGCTGCAG	U76248	CCDS3152.1	3q25	2012-02-23	2012-02-23		ENSG00000181788	ENSG00000181788	6.3.2.1		10858	protein-coding gene	gene with protein product		602213	"seven in absentia (Drosophila) homolog 2", "seven in absentia homolog 2 (Drosophila)"			9334332	Standard	NM_005067		Approved		uc003eyi.3	O43255	OTTHUMG00000159847	ENST00000312960.3:c.48C>T	3.37:g.150480589G>A		118	0	0		88	30	0.340909	NM_005067	O43270	Silent	SNP	ENST00000312960.3	37	CCDS3152.1																																																																																			.	.	none		0.771	SIAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357697.1	NM_005067		A	150480589	G	A	150480589	2	1	42	1	0	0	0	0	0	0	0	1	14315	1310	46	2		2	SIAH2	3	150480589	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	8193614	150480589	47541841	75	15027											
MME	4311	hgsc.bcm.edu	37	chr3	154860063	154860063	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tgtcctggagattcataatgGatcttgtaagcagcctcagc	10	12	10	9	0	3	1	2	0	1	1	4	3	4	2	2	2	3	2	2	2	2	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr3:154860063G>A	ENST00000460393.1	+	12	1252	c.1132G>A	c.(1132-1134)Gat>Aat	p.D378N	MME_ENST00000492661.1_Missense_Mutation_p.D378N|MME_ENST00000493237.1_Missense_Mutation_p.D378N|MME_ENST00000360490.2_Missense_Mutation_p.D378N|MME_ENST00000462745.1_Missense_Mutation_p.D378N	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	378					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)	ATTCATAATGGATCTTGTAAG	0.398																																					p.D378N		Atlas-SNP	.											.	MME	133	.	0			c.G1132A						PASS	.						85	90	88					3																	154860063		2203	4300	6503	SO:0001583	missense	4311	exon12			ATAATGGATCTTG		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.1132G>A	3.37:g.154860063G>A	ENSP00000418525:p.Asp378Asn	179	0	0		133	39	0.293233	NM_007287	A8K6U6|D3DNJ9|Q3MIX4	Missense_Mutation	SNP	ENST00000460393.1	37	CCDS3172.1	.	.	.	.	.	.	.	.	.	.	G	17.04	3.287676	0.59976	.	.	ENSG00000196549	ENST00000492661;ENST00000460393;ENST00000462745;ENST00000493237;ENST00000360490	T;T;T;T;T	0.74106	-0.81;-0.81;-0.81;-0.81;-0.81	5.93	5.93	0.95920	Peptidase M13 (1);	0.217410	0.47455	D	0.000221	T	0.66954	0.2842	N	0.17564	0.495	0.45791	D	0.998674	B	0.23185	0.081	B	0.32928	0.155	T	0.60505	-0.7250	10	0.35671	T	0.21	-39.6187	20.3397	0.98756	0.0:0.0:1.0:0.0	.	378	P08473	NEP_HUMAN	N	378	ENSP00000420389:D378N;ENSP00000418525:D378N;ENSP00000419653:D378N;ENSP00000417079:D378N;ENSP00000353679:D378N	ENSP00000353679:D378N	D	+	1	0	MME	156342757	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.449000	0.73473	2.803000	0.96430	0.585000	0.79938	GAT	.	.	none		0.398	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902		A	154860063	G	A	154860063	3	1	42	1	0	0	0	0	1	0	0	0	9654	1174	41	2	1174	2	MME	3	154860063	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	4379474	154860063	43162367	76	15028											
LEKR1	389170	hgsc.bcm.edu	37	chr3	156742690	156742690	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	taatccaaaagtataagaaaGaacaagaggaactacaaatg	23	6	7	5	0	0	3	0	0	0	3	1	4	1	4	1	1	3	1	1	1	11	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr3:156742690G>A	ENST00000470811.1	+	12	1768	c.433G>A	c.(433-435)Gaa>Aaa	p.E145K	LEKR1_ENST00000356539.4_Missense_Mutation_p.E449K			Q6ZMV7	LEKR1_HUMAN	leucine, glutamate and lysine rich 1	145										breast(1)|large_intestine(5)|lung(3)|ovary(1)|skin(1)	11			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			GTATAAGAAAGAACAAGAGGA	0.303																																					p.E449K		Atlas-SNP	.											.	LEKR1	66	.	0			c.G1345A						PASS	.						55	57	57					3																	156742690		2203	4300	6503	SO:0001583	missense	389170	exon11			AAGAAAGAACAAG	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.433G>A	3.37:g.156742690G>A	ENSP00000418214:p.Glu145Lys	274	0	0		283	40	0.141343	NM_001004316		Missense_Mutation	SNP	ENST00000470811.1	37		.	.	.	.	.	.	.	.	.	.	G	18.14	3.558339	0.65538	.	.	ENSG00000178110	ENST00000470811;ENST00000356539	T;T	0.57107	0.47;0.42	5.63	5.63	0.86233	.	0.102632	0.43110	D	0.000612	T	0.68897	0.3051	M	0.69823	2.125	0.37085	D	0.899169	D	0.64830	0.994	D	0.65773	0.938	T	0.68089	-0.5501	10	0.21014	T	0.42	-10.1711	16.6082	0.84836	0.0:0.0:1.0:0.0	.	145	Q6ZMV7	LEKR1_HUMAN	K	145;449	ENSP00000418214:E145K;ENSP00000348936:E449K	ENSP00000348936:E449K	E	+	1	0	LEKR1	158225384	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.743000	0.68655	2.644000	0.89710	0.563000	0.77884	GAA	.	.	none		0.303	LEKR1-010	KNOWN	upstream_ATG|basic	protein_coding	protein_coding	OTTHUMT00000351625.3	NM_001004316		A	156742690	G	A	156742690	3	1	42	1	0	0	0	0	1	0	0	0	8726	943	33	2	1383	2	LEKR1	3	156742690	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	1882627	156742690	41279740	77	15029											
SI	6476	hgsc.bcm.edu	37	chr3	164733862	164733862	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagtcaatgtctgtgtactGaacatcctgaaatatccaaa	14	12	7	8	0	2	2	1	2	1	0	4	2	4	2	2	0	2	2	2	0	7	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr3:164733862G>T	ENST00000264382.3	-	32	3828	c.3766C>A	c.(3766-3768)Cag>Aag	p.Q1256K		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	1256	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)	p.Q1256E(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)	TCTGTGTACTGAACATCCTGA	0.333										HNSCC(35;0.089)																											p.Q1256K		Atlas-SNP	.											SI,NS,carcinoma,0,1	SI	500	1	2	Substitution - Missense(2)	lung(2)	c.C3766A						PASS	.						149	160	156					3																	164733862		2203	4300	6503	SO:0001583	missense	6476	exon32			TGTACTGAACATC	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.3766C>A	3.37:g.164733862G>T	ENSP00000264382:p.Gln1256Lys	152	0	0		95	26	0.273684	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Missense_Mutation	SNP	ENST00000264382.3	37	CCDS3196.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.279792	0.80692	.	.	ENSG00000090402	ENST00000264382	D	0.92752	-3.1	4.93	4.93	0.64822	Glycoside hydrolase, superfamily (1);	0.000000	0.85682	D	0.000000	D	0.97151	0.9069	M	0.94021	3.485	0.58432	D	0.999996	D	0.89917	1.0	D	0.80764	0.994	D	0.98111	1.0420	10	0.87932	D	0	.	18.3199	0.90234	0.0:0.0:1.0:0.0	.	1256	P14410	SUIS_HUMAN	K	1256	ENSP00000264382:Q1256K	ENSP00000264382:Q1256K	Q	-	1	0	SI	166216556	1.000000	0.71417	0.981000	0.43875	0.730000	0.41778	7.112000	0.77086	2.557000	0.86248	0.585000	0.79938	CAG	.	.	none		0.333	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041		T	164733862	G	T	164733862	3	4	42	1	0	0	0	0	1	0	0	0	14312	1299	45	4	1785	4	SI	3	164733862	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	7991172	164733862	33288568	78	15030											
CCDC39	339829	hgsc.bcm.edu	37	chr3	180334082	180334082	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcttaccttgctgatagtgAagtatgtgaaggagatctag	11	12	12	6	1	1	4	0	3	1	1	1	5	1	4	1	1	2	3	1	1	6	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr3:180334082A>G	ENST00000442201.2	-	19	2775	c.2656T>C	c.(2656-2658)Tca>Cca	p.S886P	CCDC39_ENST00000273654.4_3'UTR|TTC14_ENST00000382584.4_Intron	NM_181426.1	NP_852091.1	Q9UFE4	CCD39_HUMAN	coiled-coil domain containing 39	886	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)			GCTGATAGTGAAGTATGTGAA	0.428																																					p.S886P		Atlas-SNP	.											.	CCDC39	242	.	0			c.T2656C						PASS	.						124	114	117					3																	180334082		1901	4119	6020	SO:0001583	missense	339829	exon19			ATAGTGAAGTATG	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.2656T>C	3.37:g.180334082A>G	ENSP00000405708:p.Ser886Pro	208	0	0		118	31	0.262712	NM_181426	B4E2H1	Missense_Mutation	SNP	ENST00000442201.2	37	CCDS46964.1	.	.	.	.	.	.	.	.	.	.	A	10.62	1.401054	0.25291	.	.	ENSG00000145075	ENST00000489868;ENST00000442201	.	.	.	5.23	5.23	0.72850	.	.	.	.	.	T	0.79100	0.4389	M	0.80616	2.505	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.79909	-0.1604	8	0.41790	T	0.15	.	14.2533	0.66035	1.0:0.0:0.0:0.0	.	886	Q9UFE4	CCD39_HUMAN	P	58;886	.	ENSP00000405708:S886P	S	-	1	0	CCDC39	181816776	0.998000	0.40836	0.868000	0.34077	0.145000	0.21501	3.682000	0.54656	2.101000	0.63845	0.374000	0.22700	TCA	.	.	none		0.428	CCDC39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349783.3	XM_291028		G	180334082	A	G	180334082	3	3	42	1	0	0	0	0	1	0	0	0	2813	246	9	3	177	3	CCDC39	3	180334082	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	15600220	180334082	17688348	79	15031											
TAPT1	202018	hgsc.bcm.edu	37	chr4	16168278	16168278	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgagagggtttacatttgttCtgtgatttactggacggctt	7	17	12	5	1	1	2	0	2	1	1	1	4	1	3	0	3	2	3	0	3	2	7			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr4:16168278C>T	ENST00000405303.2	-	13	1535	c.1452G>A	c.(1450-1452)caG>caA	p.Q484Q	TAPT1_ENST00000399920.3_Silent_p.Q373Q|TAPT1_ENST00000304584.8_3'UTR	NM_153365.2	NP_699196.2	Q6NXT6	TAPT1_HUMAN	transmembrane anterior posterior transformation 1	484					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						TACATTTGTTCTGTGATTTAC	0.453																																					p.Q484Q		Atlas-SNP	.											.	TAPT1	31	.	0			c.G1452A						PASS	.						182	196	191					4																	16168278		1980	4169	6149	SO:0001819	synonymous_variant	202018	exon13			TTTGTTCTGTGAT	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.1452G>A	4.37:g.16168278C>T		200	0	0		146	64	0.438356	NM_153365	Q8N2S3|Q9NZK9	Silent	SNP	ENST00000405303.2	37	CCDS47030.1																																																																																			.	.	none		0.453	TAPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359568.1	NM_153365		T	16168278	C	T	16168278	2	4	42	1	0	0	0	0	0	0	0	1	15569	912	32	2		2	TAPT1	4	16168278	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10		16168278	174985998	80	15032											
NCAPG	64151	hgsc.bcm.edu	37	chr4	17843962	17843962	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtgacagtttcagctaggAcgaacaggaggtgtcagact	13	8	13	7	1	2	2	2	1	0	1	2	5	2	4	0	3	2	2	0	3	3	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr4:17843962A>C	ENST00000251496.2	+	20	3060	c.2884A>C	c.(2884-2886)Acg>Ccg	p.T962P	LCORL_ENST00000326877.4_3'UTR	NM_022346.4	NP_071741.2	Q9BPX3	CND3_HUMAN	non-SMC condensin I complex, subunit G	962					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)		TTCAGCTAGGACGAACAGGAG	0.368																																					p.T962P		Atlas-SNP	.											.	NCAPG	76	.	0			c.A2884C						PASS	.						85	82	83					4																	17843962		2203	4299	6502	SO:0001583	missense	64151	exon20			GCTAGGACGAACA	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.2884A>C	4.37:g.17843962A>C	ENSP00000251496:p.Thr962Pro	252	0	0		209	84	0.401914	NM_022346	Q3MJE0|Q96SV9|Q9BUR3|Q9BVY1|Q9H914|Q9H9Z6|Q9HBI9	Missense_Mutation	SNP	ENST00000251496.2	37	CCDS3424.1	.	.	.	.	.	.	.	.	.	.	A	4.242	0.043803	0.08196	.	.	ENSG00000109805	ENST00000251496	T	0.30981	1.51	5.35	3.2	0.36748	.	1.403140	0.04112	N	0.314705	T	0.26810	0.0656	L	0.43152	1.355	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20207	-1.0282	10	0.28530	T	0.3	1.9728	4.3865	0.11319	0.6264:0.0:0.3736:0.0	.	962	Q9BPX3	CND3_HUMAN	P	962	ENSP00000251496:T962P	ENSP00000251496:T962P	T	+	1	0	NCAPG	17453060	0.057000	0.20700	0.011000	0.14972	0.298000	0.27526	0.865000	0.27940	0.527000	0.28560	0.533000	0.62120	ACG	.	.	none		0.368	NCAPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250375.1	NM_022346		C	17843962	A	C	17843962	3	2	42	1	0	0	0	0	1	0	0	0	10216	275	10	5	2962	5	NCAPG	4	17843962	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	1675684	17843962	173310314	81	15033											
PHOX2B	8929	hgsc.bcm.edu	37	chr4	41747879	41747879	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caccgttgggtctttggagcGaagataggacgctggcgaag	9	8	16	8	4	1	1	0	0	1	1	1	5	1	3	1	4	1	2	1	4	3	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr4:41747879G>A	ENST00000226382.2	-	3	1249	c.890C>T	c.(889-891)tCg>tTg	p.S297L	RP11-227F19.1_ENST00000508038.1_RNA	NM_003924.3	NP_003915.2	Q99453	PHX2B_HUMAN	paired-like homeobox 2b	297					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						TCTTTGGAGCGAAGATAGGAC	0.682			"Mis, F"		neuroblastoma	neuroblastoma	congenital central hypoventilation syndrome		Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.S297L		Atlas-SNP	.	yes	Rec	yes	familial neuroblastoma	4	4p12	8929	paired-like homeobox 2b	yes	O	.	PHOX2B	53	.	0			c.C890T						PASS	.						24	34	31					4																	41747879		2203	4300	6503	SO:0001583	missense	8929	exon3	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	TGGAGCGAAGATA	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.890C>T	4.37:g.41747879G>A	ENSP00000226382:p.Ser297Leu	48	0	0		37	17	0.459459	NM_003924	Q6PJD9	Missense_Mutation	SNP	ENST00000226382.2	37	CCDS3463.1	.	.	.	.	.	.	.	.	.	.	G	17.99	3.522757	0.64747	.	.	ENSG00000109132	ENST00000226382	D	0.91631	-2.88	3.93	3.93	0.45458	.	0.065830	0.64402	D	0.000006	D	0.91815	0.7410	N	0.19112	0.55	0.58432	D	0.999999	D	0.69078	0.997	D	0.67725	0.953	D	0.93125	0.6528	10	0.66056	D	0.02	.	14.8458	0.70259	0.0:0.0:1.0:0.0	.	297	Q99453	PHX2B_HUMAN	L	297	ENSP00000226382:S297L	ENSP00000226382:S297L	S	-	2	0	PHOX2B	41442636	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.197000	0.65141	2.019000	0.59389	0.313000	0.20887	TCG	.	.	none		0.682	PHOX2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216832.2			A	41747879	G	A	41747879	3	1	42	1	0	0	0	0	1	0	0	0	11868	1059	37	1	58	1	PHOX2B	4	41747879	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	23903917	41747879	149406397	82	15034											
POLR2B	5431	hgsc.bcm.edu	37	chr4	57871515	57871515	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtgttactaaagagaaaaGaattaaatatgcaaaggaag	20	9	10	2	0	0	2	0	0	0	2	0	4	0	3	0	2	2	2	0	2	11	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr4:57871515G>T	ENST00000381227.1	+	9	1417	c.1004G>T	c.(1003-1005)aGa>aTa	p.R335I	POLR2B_ENST00000431623.2_Missense_Mutation_p.R260I|POLR2B_ENST00000441246.2_Missense_Mutation_p.R328I|RNU6-998P_ENST00000515894.1_RNA|POLR2B_ENST00000314595.5_Missense_Mutation_p.R335I			P30876	RPB2_HUMAN	polymerase (RNA) II (DNA directed) polypeptide B, 140kDa	335					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)	p.R335I(1)		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)					AAAGAGAAAAGAATTAAATAT	0.363																																					p.R335I		Atlas-SNP	.											POLR2B,NS,carcinoma,0,1	POLR2B	108	1	1	Substitution - Missense(1)	lung(1)	c.G1004T						PASS	.						93	95	94					4																	57871515		2203	4299	6502	SO:0001583	missense	5431	exon8			AGAAAAGAATTAA		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.1004G>T	4.37:g.57871515G>T	ENSP00000370625:p.Arg335Ile	474	0	0		326	155	0.47546	NM_000938	A8K1A8|Q8IZ61	Missense_Mutation	SNP	ENST00000381227.1	37	CCDS3511.1	.	.	.	.	.	.	.	.	.	.	G	34	5.294439	0.95546	.	.	ENSG00000047315	ENST00000381227;ENST00000431623;ENST00000441246;ENST00000314595	T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23	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	D	0.88811	0.6538	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	D	0.90815	0.4704	10	0.54805	T	0.06	.	20.3472	0.98799	0.0:0.0:1.0:0.0	.	260;335	C9J4M6;P30876	.;RPB2_HUMAN	I	335;260;328;335	ENSP00000370625:R335I;ENSP00000391096:R260I;ENSP00000391452:R328I;ENSP00000312735:R335I	ENSP00000312735:R335I	R	+	2	0	POLR2B	57566272	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.831000	0.86748	2.890000	0.99128	0.650000	0.86243	AGA	.	.	none		0.363	POLR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250692.1	NM_000938		T	57871515	G	T	57871515	3	4	42	1	0	0	0	0	1	0	0	0	12224	942	33	4	1034	4	POLR2B	4	57871515	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	16123636	57871515	133282761	83	15035											
PRDM8	56978	hgsc.bcm.edu	37	chr4	81123614	81123614	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgctggtctggtagggggccGgggccgcttcgtagagcggc	3	7	20	11	5	1	1	0	0	1	1	2	1	1	1	2	7	1	4	2	7	2	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr4:81123614G>A	ENST00000504452.1	+	8	1837	c.998G>A	c.(997-999)cGg>cAg	p.R333Q	PRDM8_ENST00000415738.2_Missense_Mutation_p.R333Q|PRDM8_ENST00000339711.4_Missense_Mutation_p.R333Q			Q9NQV8	PRDM8_HUMAN	PR domain containing 8	333	Gly-rich.				corpus callosum morphogenesis (GO:0021540)|corticospinal tract morphogenesis (GO:0021957)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(2)	10						GTAGGGGGCCGGGGCCGCTTC	0.701																																					p.R333Q		Atlas-SNP	.											.	PRDM8	44	.	0			c.G998A						PASS	.						2	2	2					4																	81123614		1024	2626	3650	SO:0001583	missense	56978	exon4			GGGGCCGGGGCCG	AF275815	CCDS43243.1	4q21	2008-08-21				ENSG00000152784			13993	protein-coding gene	gene with protein product							Standard	NM_020226		Approved		uc003hmc.4	Q9NQV8		ENST00000504452.1:c.998G>A	4.37:g.81123614G>A	ENSP00000423985:p.Arg333Gln	73	0	0		43	25	0.581395	NM_001099403	A8K7X2|Q6IQ36	Missense_Mutation	SNP	ENST00000504452.1	37	CCDS43243.1	.	.	.	.	.	.	.	.	.	.	G	10.94	1.494241	0.26774	.	.	ENSG00000152784	ENST00000504452;ENST00000515013;ENST00000339711;ENST00000415738	T;T;T;T	0.65549	-0.16;0.39;-0.16;-0.16	4.28	3.41	0.39046	.	0.462300	0.18430	N	0.141459	T	0.46580	0.1400	N	0.24115	0.695	0.29957	N	0.819696	B	0.23058	0.079	B	0.12156	0.007	T	0.49523	-0.8931	10	0.59425	D	0.04	.	11.106	0.48203	0.0:0.1879:0.8121:0.0	.	333	Q9NQV8	PRDM8_HUMAN	Q	333	ENSP00000423985:R333Q;ENSP00000425149:R333Q;ENSP00000339764:R333Q;ENSP00000406998:R333Q	ENSP00000339764:R333Q	R	+	2	0	PRDM8	81342638	0.971000	0.33674	0.998000	0.56505	0.274000	0.26718	-0.370000	0.07523	0.967000	0.38186	0.491000	0.48974	CGG	.	.	none		0.701	PRDM8-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362793.1			A	81123614	G	A	81123614	3	1	42	1	0	0	0	0	1	0	0	0	12474	1116	39	1	1008	1	PRDM8	4	81123614	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	23252099	81123614	110030662	84	15036											
UNC5C	8633	hgsc.bcm.edu	37	chr4	96222814	96222814	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acccgcggagctccaggccaCacactggcaccagtaatctt	10	6	9	16	2	1	0	0	0	1	0	2	1	2	1	4	3	1	3	4	3	1	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr4:96222814C>T	ENST00000453304.1	-	3	781	c.433G>A	c.(433-435)Gtg>Atg	p.V145M	UNC5C_ENST00000506749.1_Missense_Mutation_p.V145M|UNC5C_ENST00000504962.1_Missense_Mutation_p.V145M	NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	145	Ig-like.				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)		CTCCAGGCCACACACTGGCAC	0.507																																					p.V145M		Atlas-SNP	.											.	UNC5C	141	.	0			c.G433A						PASS	.						94	79	84					4																	96222814		2203	4300	6503	SO:0001583	missense	8633	exon3			AGGCCACACACTG	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.433G>A	4.37:g.96222814C>T	ENSP00000406022:p.Val145Met	93	0	0		50	20	0.4	NM_003728	Q8IUT0	Missense_Mutation	SNP	ENST00000453304.1	37	CCDS3643.1	.	.	.	.	.	.	.	.	.	.	C	33	5.289972	0.95546	.	.	ENSG00000182168	ENST00000453304;ENST00000331502;ENST00000513796;ENST00000506749;ENST00000504962	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	5.57	5.57	0.84162	Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.71151	0.3306	M	0.87269	2.87	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.99	D;D;D	0.80764	0.971;0.994;0.979	T	0.76119	-0.3076	10	0.87932	D	0	.	19.5525	0.95326	0.0:1.0:0.0:0.0	.	145;145;145	A8K385;E0CX15;O95185	.;.;UNC5C_HUMAN	M	145;104;145;145;145	ENSP00000406022:V145M;ENSP00000426924:V145M;ENSP00000426153:V145M;ENSP00000425117:V145M	ENSP00000328673:V104M	V	-	1	0	UNC5C	96441837	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.776000	0.85560	2.626000	0.88956	0.650000	0.86243	GTG	.	.	none		0.507	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728		T	96222814	C	T	96222814	3	4	42	1	0	0	0	0	1	0	0	0	17008	478	17	2	2418	2	UNC5C	4	96222814	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	15099200	96222814	94931462	85	15037											
SYNPO2	171024	hgsc.bcm.edu	37	chr4	119978995	119978995	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggcttcaagaaatgattctgCaatcatgtccatggaaacca	14	10	8	9	0	3	2	2	1	1	1	4	3	4	3	2	2	2	2	2	2	4	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr4:119978995C>T	ENST00000307142.4	+	5	3888	c.3692C>T	c.(3691-3693)gCa>gTa	p.A1231V	SYNPO2_ENST00000448416.2_3'UTR	NM_133477.2	NP_597734.2	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	0						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						AATGATTCTGCAATCATGTCC	0.423																																					p.A1231V		Atlas-SNP	.											.	SYNPO2	353	.	0			c.C3692T						PASS	.						83	77	79					4																	119978995		2203	4300	6503	SO:0001583	missense	171024	exon5			ATTCTGCAATCAT	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	ENST00000307142.4:c.3692C>T	4.37:g.119978995C>T	ENSP00000306015:p.Ala1231Val	148	0	0		119	14	0.117647	NM_133477	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000307142.4	37	CCDS34054.1	.	.	.	.	.	.	.	.	.	.	A	13.81	2.349191	0.41599	.	.	ENSG00000172403	ENST00000307142	T	0.08370	3.1	5.76	1.99	0.26369	.	0.491893	0.17073	N	0.188101	T	0.03783	0.0107	N	0.08118	0	0.09310	N	1	B;B	0.11235	0.002;0.004	B;B	0.06405	0.001;0.002	T	0.46857	-0.9161	9	.	.	.	-3.5532	7.5195	0.27620	0.6482:0.2283:0.1235:0.0	.	1231;1231	B9EG60;Q9UMS6-2	.;.	V	1231	ENSP00000306015:A1231V	.	A	+	2	0	SYNPO2	120198443	0.227000	0.23707	0.001000	0.08648	0.000000	0.00434	2.008000	0.40893	-0.094000	0.12374	-2.788000	0.00116	GCA	.	.	none		0.423	SYNPO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364018.1			T	119978995	C	T	119978995	3	4	42	1	0	0	0	0	1	0	0	0	15472	710	25	2	3822	2	SYNPO2	4	119978995	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	23756181	119978995	71175281	86	15038											
FAT4	79633	hgsc.bcm.edu	37	chr4	126240717	126240717	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttggcatattcccagatggtCaattgtatataaaaagtgaa	15	13	8	5	0	1	2	1	1	0	1	2	2	2	2	1	2	0	2	1	2	8	7			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr4:126240717C>T	ENST00000394329.3	+	1	3164	c.3151C>T	c.(3151-3153)Caa>Taa	p.Q1051*		NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1051	Cadherin 10. {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						CCCAGATGGTCAATTGTATAT	0.408																																					p.Q1051X		Atlas-SNP	.											FAT4_ENST00000394329,colon,carcinoma,0,2	FAT4	1752	2	0			c.C3151T						PASS	.						117	110	112					4																	126240717		1863	4101	5964	SO:0001587	stop_gained	79633	exon1			GATGGTCAATTGT	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.3151C>T	4.37:g.126240717C>T	ENSP00000377862:p.Gln1051*	164	0	0		148	23	0.155405	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Nonsense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	C	42	9.324994	0.99137	.	.	ENSG00000196159	ENST00000394329	.	.	.	4.56	4.56	0.56223	.	0.000000	0.32852	U	0.005574	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	.	17.5378	0.87837	0.0:1.0:0.0:0.0	.	.	.	.	X	1051	.	ENSP00000377862:Q1051X	Q	+	1	0	FAT4	126460167	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.495000	0.81514	2.354000	0.79902	0.462000	0.41574	CAA	.	.	none		0.408	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		T	126240717	C	T	126240717	4	4	42	1	0	0	0	0	0	1	0	0	5700	827	29	2	3153	2	FAT4	4	126240717	Nonsense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	6261722	126240717	64913559	87	15039											
TBC1D9	23158	hgsc.bcm.edu	37	chr4	141560570	141560570	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcaatcaaatctgcccggaTagttccgaatttctgtaaag	12	13	7	9	2	4	0	2	0	2	0	5	2	5	1	2	1	1	2	2	1	6	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr4:141560570T>G	ENST00000442267.2	-	14	2424	c.2350A>C	c.(2350-2352)Atc>Ctc	p.I784L		NM_015130.2	NP_055945.2	Q6ZT07	TBCD9_HUMAN	TBC1 domain family, member 9 (with GRAM domain)	784							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)				TCTGCCCGGATAGTTCCGAAT	0.433																																					p.I784L		Atlas-SNP	.											.	TBC1D9	198	.	0			c.A2350C						PASS	.						60	58	59					4																	141560570		1893	4113	6006	SO:0001583	missense	23158	exon14			CCCGGATAGTTCC	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.2350A>C	4.37:g.141560570T>G	ENSP00000411197:p.Ile784Leu	116	0	0		114	45	0.394737	NM_015130	A6H8U8|D3DNZ1|O94958	Missense_Mutation	SNP	ENST00000442267.2	37	CCDS47136.1	.	.	.	.	.	.	.	.	.	.	T	11.45	1.641600	0.29157	.	.	ENSG00000109436	ENST00000442267	T	0.08896	3.04	5.12	5.12	0.69794	Rab-GAP/TBC domain (1);	0.000000	0.85682	D	0.000000	T	0.05227	0.0139	N	0.05592	-0.015	0.80722	D	1	B	0.11235	0.004	B	0.11329	0.006	T	0.45145	-0.9281	10	0.20519	T	0.43	-10.5614	15.2296	0.73378	0.0:0.0:0.0:1.0	.	784	Q6ZT07	TBCD9_HUMAN	L	784	ENSP00000411197:I784L	ENSP00000411197:I784L	I	-	1	0	TBC1D9	141780020	1.000000	0.71417	0.964000	0.40570	0.998000	0.95712	7.897000	0.87356	2.052000	0.61016	0.533000	0.62120	ATC	.	.	none		0.433	TBC1D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364806.1	NM_015130		G	141560570	T	G	141560570	3	3	42	1	0	0	0	0	1	0	0	0	15642	1406	49	5	1482	5	TBC1D9	4	141560570	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	15319853	141560570	49593706	88	15040											
FAM198B	51313	hgsc.bcm.edu	37	chr4	159092202	159092202	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgcgcttggagcgtagggtaAtgtacaccacattgggctgc	8	10	14	9	2	0	0	0	0	0	0	0	1	0	1	1	3	4	5	1	3	3	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr4:159092202A>G	ENST00000296530.8	-	2	947	c.326T>C	c.(325-327)aTt>aCt	p.I109T	FAM198B_ENST00000592057.1_Missense_Mutation_p.I109T|RP11-597D13.9_ENST00000509463.1_RNA|FAM198B_ENST00000589306.1_Intron|RP11-597D13.9_ENST00000514381.1_RNA|FAM198B_ENST00000393807.5_Missense_Mutation_p.I109T|RP11-597D13.9_ENST00000505532.1_RNA|FAM198B_ENST00000585682.1_Missense_Mutation_p.I109T|RP11-597D13.9_ENST00000503611.1_RNA	NM_016613.6	NP_057697.2	Q6UWH4	F198B_HUMAN	family with sequence similarity 198, member B	109						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						GCGTAGGGTAATGTACACCAC	0.622																																					p.I109T		Atlas-SNP	.											.	FAM198B	134	.	0			c.T326C						PASS	.						80	78	79					4																	159092202		2203	4300	6503	SO:0001583	missense	51313	exon2			AGGGTAATGTACA		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.326T>C	4.37:g.159092202A>G	ENSP00000296530:p.Ile109Thr	84	0	0		60	23	0.383333	NM_016613	Q498Z3|Q6IAF9|Q6ZMF2|Q86XL0	Missense_Mutation	SNP	ENST00000296530.8	37	CCDS3798.1	.	.	.	.	.	.	.	.	.	.	A	22.0	4.223908	0.79576	.	.	ENSG00000164125	ENST00000337222;ENST00000296530;ENST00000393807;ENST00000417442	T;T	0.47869	0.88;0.83	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.66886	0.2835	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	0.70876	-0.4753	10	0.87932	D	0	-4.8854	15.0035	0.71492	1.0:0.0:0.0:0.0	.	109;109;109	Q6UWH4-3;Q6UWH4-2;Q6UWH4	.;.;F198B_HUMAN	T	109	ENSP00000296530:I109T;ENSP00000377396:I109T	ENSP00000296530:I109T	I	-	2	0	FAM198B	159311652	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	8.113000	0.89568	2.140000	0.66376	0.533000	0.62120	ATT	.	.	none		0.622	FAM198B-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365230.1	NM_001031700, NM_016613		G	159092202	A	G	159092202	3	3	42	1	0	0	0	0	1	0	0	0	5534	101	4	3	1354	3	FAM198B	4	159092202	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	17531632	159092202	32062074	89	15041											
FAT1	2195	hgsc.bcm.edu	37	chr4	187524408	187524408	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgctgtgtgttgacatcaCactttcatccacagacacct	9	13	7	12	0	2	2	2	1	0	1	3	2	3	2	2	0	1	2	2	0	0	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr4:187524408C>T	ENST00000441802.2	-	19	11481	c.11272G>A	c.(11272-11274)Gtg>Atg	p.V3758M		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	3758					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						GTTGACATCACACTTTCATCC	0.502										HNSCC(5;0.00058)																											p.V3758M	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.G11272A						PASS	.						69	66	67					4																	187524408		2030	4189	6219	SO:0001583	missense	2195	exon19			ACATCACACTTTC	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.11272G>A	4.37:g.187524408C>T	ENSP00000406229:p.Val3758Met	176	0	0		151	66	0.437086	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	12.05	1.822774	0.32237	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.30182	1.54	3.98	3.11	0.35812	.	0.268968	0.35805	N	0.002973	T	0.27349	0.0671	L	0.46157	1.445	0.28142	N	0.929741	P	0.36354	0.549	B	0.38880	0.284	T	0.11567	-1.0582	10	0.42905	T	0.14	.	9.5639	0.39387	0.0:0.8051:0.0:0.1949	.	3758	Q14517	FAT1_HUMAN	M	3758;3760	ENSP00000406229:V3758M	ENSP00000260147:V3760M	V	-	1	0	FAT1	187761402	0.035000	0.19736	0.009000	0.14445	0.913000	0.54294	0.593000	0.23999	0.992000	0.38840	0.557000	0.71058	GTG	.	.	none		0.502	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		T	187524408	C	T	187524408	3	4	42	1	0	0	0	0	1	0	0	0	5697	478	17	2	2530	2	FAT1	4	187524408	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	28432206	187524408	3629868	90	15042											
FAT1	2195	hgsc.bcm.edu	37	chr4	187542336	187542336	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tacaagcaaagcatttgagtCtttatcagcatcagctgctc	12	12	7	10	0	3	1	2	1	1	0	4	1	3	1	0	0	6	5	0	0	4	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr4:187542336C>G	ENST00000441802.2	-	10	5613	c.5404G>C	c.(5404-5406)Gac>Cac	p.D1802H		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1802	Cadherin 16. {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						GCATTTGAGTCTTTATCAGCA	0.398										HNSCC(5;0.00058)																											p.D1802H	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.G5404C						PASS	.						87	83	84					4																	187542336		1963	4160	6123	SO:0001583	missense	2195	exon10			TTGAGTCTTTATC	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.5404G>C	4.37:g.187542336C>G	ENSP00000406229:p.Asp1802His	127	0	0		108	18	0.166667	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	9.774	1.173534	0.21704	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.52526	0.66	5.5	5.5	0.81552	Cadherin (4);Cadherin-like (1);	0.145249	0.64402	D	0.000010	T	0.46560	0.1399	L	0.42529	1.33	0.58432	D	0.999999	B	0.17667	0.023	B	0.21708	0.036	T	0.37430	-0.9706	10	0.62326	D	0.03	.	19.5916	0.95514	0.0:1.0:0.0:0.0	.	1802	Q14517	FAT1_HUMAN	H	1802;1804	ENSP00000406229:D1802H	ENSP00000260147:D1804H	D	-	1	0	FAT1	187779330	1.000000	0.71417	0.693000	0.30195	0.030000	0.12068	7.651000	0.83577	2.861000	0.98227	0.655000	0.94253	GAC	.	.	none		0.398	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		G	187542336	C	G	187542336	3	3	42	1	0	0	0	0	1	0	0	0	5697	913	32	4	8434	4	FAT1	4	187542336	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	17928	187542336	3611940	91	15043											
CTNND2	1501	hgsc.bcm.edu	37	chr5	11364898	11364898	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catagggggcttctgatagaCgcggtcttcatagatgggat	9	11	14	7	2	3	3	1	1	2	2	3	4	3	4	0	4	0	1	0	4	3	5	rs148824970	byFrequency	TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr5:11364898C>T	ENST00000304623.8	-	8	1471	c.1282G>A	c.(1282-1284)Gtc>Atc	p.V428I	CTNND2_ENST00000503622.1_Missense_Mutation_p.V91I|CTNND2_ENST00000359640.2_Missense_Mutation_p.V428I|CTNND2_ENST00000495388.2_5'UTR|CTNND2_ENST00000458100.2_5'UTR|CTNND2_ENST00000511377.1_Missense_Mutation_p.V337I	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	428					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)		p.V428I(1)		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						TTCTGATAGACGCGGTCTTCA	0.617																																					p.V428I		Atlas-SNP	.											CTNND2,NS,carcinoma,0,1	CTNND2	289	1	1	Substitution - Missense(1)	lung(1)	c.G1282A						PASS	.	C	ILE/VAL	3,4403	6.2+/-15.9	0,3,2200	50	54	53		1282	4.6	1	5	dbSNP_134	53	1,8599	1.2+/-3.3	0,1,4299	yes	missense	CTNND2	NM_001332.2	29	0,4,6499	TT,TC,CC		0.0116,0.0681,0.0308	probably-damaging	428/1226	11364898	4,13002	2203	4300	6503	SO:0001583	missense	1501	exon8			GATAGACGCGGTC	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.1282G>A	5.37:g.11364898C>T	ENSP00000307134:p.Val428Ile	98	0	0		77	26	0.337662	NM_001332	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Missense_Mutation	SNP	ENST00000304623.8	37	CCDS3881.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.977602	0.92982	6.81E-4	1.16E-4	ENSG00000169862	ENST00000304623;ENST00000359640;ENST00000511377;ENST00000503622;ENST00000502551	T;T;T;T	0.78707	-1.08;-1.15;-1.09;-1.2	5.47	4.6	0.57074	.	0.086833	0.45361	N	0.000371	D	0.84129	0.5404	L	0.50333	1.59	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72982	0.959;0.979	D	0.85369	0.1112	10	0.66056	D	0.02	-16.9562	13.9713	0.64242	0.0:0.9272:0.0:0.0728	.	91;428	B4DRK2;Q9UQB3	.;CTND2_HUMAN	I	428;428;337;91;168	ENSP00000307134:V428I;ENSP00000352661:V428I;ENSP00000426510:V337I;ENSP00000426887:V91I	ENSP00000307134:V428I	V	-	1	0	CTNND2	11417898	1.000000	0.71417	0.995000	0.50966	0.997000	0.91878	5.748000	0.68697	1.313000	0.45069	0.655000	0.94253	GTC	C|0.999;T|0.001	0.001	strong		0.617	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332		T	11364898	C	T	11364898	3	4	42	1	0	0	0	0	1	0	0	0	4022	536	19	1	2455	1	CTNND2	5	11364898	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10		11364898	169550362	92	15044											
TRIO	7204	hgsc.bcm.edu	37	chr5	14397228	14397228	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gatgctcagcgtgccgaagcGagccaatgatgccatgcacc	10	6	12	13	3	1	1	1	1	0	0	1	4	1	1	4	0	7	2	4	0	2	0	rs373502206		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr5:14397228G>A	ENST00000344204.4	+	29	4412	c.4388G>A	c.(4387-4389)cGa>cAa	p.R1463Q	TRIO_ENST00000509967.2_Missense_Mutation_p.R1414Q|TRIO_ENST00000537187.1_Missense_Mutation_p.R1463Q	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	1463	DH 1. {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 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)					GTGCCGAAGCGAGCCAATGAT	0.493																																					p.R1463Q		Atlas-SNP	.											.	TRIO	305	.	0			c.G4388A						PASS	.	G	GLN/ARG	0,4406		0,0,2203	97	87	91		4388	5.7	1	5		91	1,8597	1.2+/-3.3	0,1,4298	no	missense	TRIO	NM_007118.2	43	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	1463/3098	14397228	1,13003	2203	4299	6502	SO:0001583	missense	7204	exon29			CGAAGCGAGCCAA	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.4388G>A	5.37:g.14397228G>A	ENSP00000339299:p.Arg1463Gln	126	0	0		118	11	0.0932203	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Missense_Mutation	SNP	ENST00000344204.4	37	CCDS3883.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.409928	0.83340	0.0	1.16E-4	ENSG00000038382	ENST00000344204;ENST00000537187;ENST00000509967;ENST00000513206	T;T;T	0.61980	0.06;0.06;0.06	5.65	5.65	0.86999	Dbl homology (DH) domain (5);	0.058548	0.64402	D	0.000002	T	0.65954	0.2741	L	0.48260	1.515	0.58432	D	0.999997	P;D;D	0.64830	0.931;0.979;0.994	P;B;P	0.48571	0.485;0.34;0.582	T	0.67906	-0.5549	10	0.59425	D	0.04	.	20.0965	0.97849	0.0:0.0:1.0:0.0	.	1414;1463;1463	F5H228;O75962-5;O75962	.;.;TRIO_HUMAN	Q	1463;1463;1414;1150	ENSP00000339299:R1463Q;ENSP00000446348:R1463Q;ENSP00000445592:R1414Q	ENSP00000339299:R1463Q	R	+	2	0	TRIO	14450228	1.000000	0.71417	1.000000	0.80357	0.788000	0.44548	4.018000	0.57174	2.824000	0.97209	0.655000	0.94253	CGA	.	.	weak		0.493	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118		A	14397228	G	A	14397228	3	1	42	1	0	0	0	0	1	0	0	0	16567	1058	37	1	4502	1	TRIO	5	14397228	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	3032330	14397228	166518032	93	15045											
OXCT1	5019	hgsc.bcm.edu	37	chr5	41870421	41870421	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatccgcgggcagaggcgcAgagccgaagcccggaggaga	11	1	18	11	5	0	4	0	0	0	4	1	7	1	5	3	4	2	2	3	4	1	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr5:41870421A>G	ENST00000196371.5	-	1	200	c.40T>C	c.(40-42)Tgc>Cgc	p.C14R	OXCT1-AS1_ENST00000508458.1_RNA	NM_000436.3	NP_000427.1	P55809	SCOT1_HUMAN	3-oxoacid CoA transferase 1	14					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)	GCAGAGGCGCAGAGCCGAAGC	0.652																																					p.C14R		Atlas-SNP	.											.	OXCT1	54	.	0			c.T40C						PASS	.						58	53	54					5																	41870421		2203	4300	6503	SO:0001583	missense	5019	exon1			AGGCGCAGAGCCG	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.40T>C	5.37:g.41870421A>G	ENSP00000196371:p.Cys14Arg	73	0	0		85	21	0.247059	NM_000436	B2R5V2|B7Z528	Missense_Mutation	SNP	ENST00000196371.5	37	CCDS3937.1	.	.	.	.	.	.	.	.	.	.	A	14.14	2.447431	0.43429	.	.	ENSG00000083720	ENST00000196371	D	0.84298	-1.83	4.71	-1.41	0.08941	.	0.617047	0.17164	N	0.184532	T	0.61173	0.2326	N	0.08118	0	0.39676	D	0.970823	B	0.02656	0.0	B	0.01281	0.0	T	0.36720	-0.9736	10	0.23302	T	0.38	2.3307	1.5265	0.02526	0.411:0.3174:0.0974:0.1742	.	14	P55809	SCOT1_HUMAN	R	14	ENSP00000196371:C14R	ENSP00000196371:C14R	C	-	1	0	OXCT1	41906178	0.941000	0.31946	0.426000	0.26672	0.821000	0.46438	0.003000	0.13083	-0.023000	0.13963	0.533000	0.62120	TGC	.	.	none		0.652	OXCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211594.2	NM_000436		G	41870421	A	G	41870421	3	3	42	1	0	0	0	0	1	0	0	0	11338	188	7	3	1590	3	OXCT1	5	41870421	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	27473193	41870421	139044839	94	15046											
HCN1	348980	hgsc.bcm.edu	37	chr5	45262330	45262330	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	catggggcagcgagggctgcGaggcggagagtggcctgact	7	5	20	9	3	0	2	0	1	0	1	0	5	0	2	1	6	2	2	1	6	0	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr5:45262330G>C	ENST00000303230.4	-	8	2423	c.2366C>G	c.(2365-2367)tCg>tGg	p.S789W		NM_021072.3	NP_066550.2	O60741	HCN1_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 1	789				S -> W (in Ref. 2; AAC39759). {ECO:0000305}.	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.S789L(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						CGAGGGCTGCGAGGCGGAGAG	0.627																																					p.S789W		Atlas-SNP	.											HCN1,NS,carcinoma,0,2	HCN1	298	2	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.C2366G						PASS	.						64	61	62					5																	45262330		2203	4300	6503	SO:0001583	missense	348980	exon8			GGCTGCGAGGCGG	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.2366C>G	5.37:g.45262330G>C	ENSP00000307342:p.Ser789Trp	85	0	0		88	28	0.318182	NM_021072		Missense_Mutation	SNP	ENST00000303230.4	37	CCDS3952.1	.	.	.	.	.	.	.	.	.	.	G	17.61	3.431846	0.62844	.	.	ENSG00000164588	ENST00000303230	T	0.77620	-1.11	5.02	5.02	0.67125	.	0.000000	0.56097	D	0.000034	D	0.82898	0.5137	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.70716	0.97	D	0.84674	0.0713	10	0.62326	D	0.03	.	18.7131	0.91666	0.0:0.0:1.0:0.0	.	789	O60741	HCN1_HUMAN	W	789	ENSP00000307342:S789W	ENSP00000307342:S789W	S	-	2	0	HCN1	45298087	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.689000	0.98673	2.491000	0.84063	0.655000	0.94253	TCG	.	.	none		0.627	HCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253847.1	NM_021072		C	45262330	G	C	45262330	3	2	42	1	0	0	0	0	1	0	0	0	7005	1059	37	4	310	4	HCN1	5	45262330	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	3391909	45262330	135652930	95	15047											
ITGA2	3673	hgsc.bcm.edu	37	chr5	52347391	52347391	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gagcaattcaatatgcaaggTaagttttggtgctaataggc	13	12	11	5	0	1	0	1	0	0	0	1	1	1	0	0	3	3	5	0	3	7	7			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr5:52347391T>A	ENST00000296585.5	+	7	922		c.e7+2			NM_002203.3	NP_002194.2	P17301	ITA2_HUMAN	integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor)						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)				ATATGCAAGGTAAGTTTTGGT	0.313																																					.		Atlas-SNP	.											.	ITGA2	211	.	0			c.779+2T>A						PASS	.						98	95	96					5																	52347391		2203	4300	6503	SO:0001630	splice_region_variant	3673	exon7			GCAAGGTAAGTTT		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.779+2T>A	5.37:g.52347391T>A		165	0	0		154	18	0.116883	NM_002203	Q14595	Splice_Site	SNP	ENST00000296585.5	37	CCDS3957.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.482598	0.84747	.	.	ENSG00000164171	ENST00000296585	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0828	0.81017	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	ITGA2	52383148	1.000000	0.71417	0.999000	0.59377	0.875000	0.50365	7.642000	0.83385	2.199000	0.70637	0.528000	0.53228	.	.	.	none		0.313	ITGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253857.2	NM_002203	Intron	A	52347391	T	A	52347391	5	1	42	1	0	0	0	0	0	0	1	0	7884	1652	57	5	807	5	ITGA2	5	52347391	Splice_Site	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	7085061	52347391	128567869	96	15048											
ERBB2IP	55914	hgsc.bcm.edu	37	chr5	65374285	65374285	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ttttataaatattgaacatgGacaagcagtgtccttgctaa	14	14	7	6	0	0	1	0	1	0	0	1	2	1	2	1	1	3	2	1	1	7	7			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr5:65374285G>A	ENST00000284037.5	+	26	4555	c.4166G>A	c.(4165-4167)gGa>gAa	p.G1389E	ERBB2IP_ENST00000511297.1_Missense_Mutation_p.G1344E|ERBB2IP_ENST00000380935.1_Missense_Mutation_p.G1279E|ERBB2IP_ENST00000380938.2_Missense_Mutation_p.G1323E|ERBB2IP_ENST00000506030.1_Missense_Mutation_p.G1396E|ERBB2IP_ENST00000380936.1_Missense_Mutation_p.G1317E|ERBB2IP_ENST00000503913.1_3'UTR|ERBB2IP_ENST00000380939.2_Missense_Mutation_p.G1337E|ERBB2IP_ENST00000380943.2_Missense_Mutation_p.G1348E|ERBB2IP_ENST00000416865.2_Missense_Mutation_p.G587E|ERBB2IP_ENST00000508515.1_Missense_Mutation_p.G1279E	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	1389	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)		ATTGAACATGGACAAGCAGTG	0.348																																					p.G1396E		Atlas-SNP	.											.	ERBB2IP	120	.	0			c.G4187A						PASS	.						66	68	67					5																	65374285		2203	4300	6503	SO:0001583	missense	55914	exon26			AACATGGACAAGC		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.4166G>A	5.37:g.65374285G>A	ENSP00000284037:p.Gly1389Glu	341	1	0.00293255		376	162	0.430851	NM_001253699	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Missense_Mutation	SNP	ENST00000284037.5	37	CCDS58953.1	.	.	.	.	.	.	.	.	.	.	G	6.208	0.406620	0.11754	.	.	ENSG00000112851	ENST00000284037;ENST00000380943;ENST00000416865;ENST00000380939;ENST00000380936;ENST00000380935;ENST00000380938;ENST00000511297;ENST00000506030;ENST00000508515	T;T;T;T;T;T;T;T;T;T	0.35605	2.0;2.0;2.0;2.0;2.0;2.0;1.3;2.0;2.0;2.0	5.63	5.63	0.86233	PDZ/DHR/GLGF (4);	0.131866	0.49916	D	0.000133	T	0.28067	0.0692	N	0.01522	-0.82	0.25967	N	0.982556	P;D;D;D;D;D;D;D	0.89917	0.78;0.997;0.998;0.996;1.0;0.993;0.992;1.0	P;D;D;D;D;D;P;D	0.97110	0.533;0.951;0.971;0.971;1.0;0.939;0.9;1.0	T	0.35351	-0.9792	10	0.02654	T	1	.	15.2084	0.73198	0.0:0.1401:0.8599:0.0	.	587;1323;1396;1396;1344;1389;1279;1348	B4DIP2;Q96RT1-4;E9PCR8;B7ZLV9;E7EQW9;Q96RT1;Q96RT1-7;Q96RT1-2	.;.;.;.;.;LAP2_HUMAN;.;.	E	1389;1348;587;1337;1317;1279;1323;1344;1396;1279	ENSP00000284037:G1389E;ENSP00000370330:G1348E;ENSP00000397833:G587E;ENSP00000370326:G1337E;ENSP00000370323:G1317E;ENSP00000370322:G1279E;ENSP00000370325:G1323E;ENSP00000422766:G1344E;ENSP00000426632:G1396E;ENSP00000422015:G1279E	ENSP00000284037:G1389E	G	+	2	0	ERBB2IP	65410041	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.464000	0.66719	2.650000	0.89964	0.655000	0.94253	GGA	.	.	none		0.348	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695		A	65374285	G	A	65374285	3	1	42	1	0	0	0	0	1	0	0	0	5209	1174	41	2	4133	2	ERBB2IP	5	65374285	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	13026894	65374285	115540975	97	15049											
MAST4	375449	hgsc.bcm.edu	37	chr5	66462503	66462503	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggagcttccagcccccagcaAcagggaccataggaaggctc	11	4	12	14	0	0	0	0	0	0	0	2	3	1	3	4	4	4	3	4	4	3	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr5:66462503A>T	ENST00000403625.2	+	29	7791	c.7496A>T	c.(7495-7497)aAc>aTc	p.N2499I	MAST4_ENST00000404260.3_Missense_Mutation_p.N2502I|MAST4_ENST00000405643.1_Missense_Mutation_p.N2320I|MAST4_ENST00000261569.7_Missense_Mutation_p.N2305I|MAST4_ENST00000403666.1_Missense_Mutation_p.N2310I	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	2502						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)		GCCCCCAGCAACAGGGACCAT	0.657											OREG0016638	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N2499I		Atlas-SNP	.											.	MAST4	218	.	0			c.A7496T						PASS	.						17	24	22					5																	66462503		1957	4169	6126	SO:0001583	missense	375449	exon29			CCAGCAACAGGGA	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.7496A>T	5.37:g.66462503A>T	ENSP00000385727:p.Asn2499Ile	108	0	0	1092	128	31	0.242188	NM_001164664	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	37	CCDS54861.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.02|15.02	2.708585|2.708585	0.48517|0.48517	.|.	.|.	ENSG00000069020|ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569|ENST00000443808	T;T;T;T;T|.	0.64260|.	-0.06;-0.06;-0.09;-0.08;-0.06|.	4.64|4.64	-8.76|-8.76	0.00830|0.00830	.|.	1.480450|.	0.03942|.	N|.	0.287123|.	T|T	0.25005|0.25005	0.0607|0.0607	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	B;B|.	0.26483|.	0.092;0.15|.	B;B|.	0.26614|.	0.032;0.071|.	T|T	0.34054|0.34054	-0.9844|-0.9844	10|5	0.36615|.	T|.	0.2|.	-1.2165|-1.2165	11.4774|11.4774	0.50306|0.50306	0.1289:0.3279:0.5432:0.0|0.1289:0.3279:0.5432:0.0	.|.	2502;2310|.	O15021;O15021-3|.	MAST4_HUMAN;.|.	I|H	2502;2499;2310;2320;2320;2305|1555	ENSP00000385048:N2502I;ENSP00000385727:N2499I;ENSP00000384313:N2310I;ENSP00000384099:N2320I;ENSP00000261569:N2305I|.	ENSP00000261569:N2305I|.	N|Q	+|+	2|3	0|2	MAST4|MAST4	66498259|66498259	0.000000|0.000000	0.05858|0.05858	0.138000|0.138000	0.22173|0.22173	0.228000|0.228000	0.25075|0.25075	-1.297000|-1.297000	0.02759|0.02759	-1.305000|-1.305000	0.02327|0.02327	0.379000|0.379000	0.24179|0.24179	AAC|CAA	.	.	none		0.657	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			T	66462503	A	T	66462503	3	4	42	1	0	0	0	0	1	0	0	0	9336	43	2	5	7740	5	MAST4	5	66462503	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	1088218	66462503	114452757	98	15050											
PAPD4	167153	hgsc.bcm.edu	37	chr5	78915498	78915498	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccaaactcaattttgggtcgCccacccttcactccaaatca	11	10	4	16	1	3	0	3	0	0	0	5	0	4	0	4	1	1	0	4	1	3	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr5:78915498C>A	ENST00000296783.3	+	3	326	c.27C>A	c.(25-27)cgC>cgA	p.R9R	PAPD4_ENST00000453514.1_Silent_p.R9R|PAPD4_ENST00000428308.2_Silent_p.R9R|PAPD4_ENST00000423041.2_Silent_p.R9R|PAPD4_ENST00000504233.1_Silent_p.R9R			Q6PIY7	GLD2_HUMAN	PAP associated domain containing 4	9				R -> H (in Ref. 1; BAC04629). {ECO:0000305}.	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)		TTTTGGGTCGCCCACCCTTCA	0.358																																					p.R9R		Atlas-SNP	.											.	PAPD4	51	.	0			c.C27A						PASS	.						104	101	102					5																	78915498		2203	4300	6503	SO:0001819	synonymous_variant	167153	exon3			GGGTCGCCCACCC	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.27C>A	5.37:g.78915498C>A		354	0	0		413	169	0.409201	NM_173797	Q86WZ2|Q8N927	Silent	SNP	ENST00000296783.3	37	CCDS4048.1																																																																																			.	.	none		0.358	PAPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226967.1	NM_173797		A	78915498	C	A	78915498	2	1	42	1	0	0	0	0	0	0	0	1	11433	726	26	4		4	PAPD4	5	78915498	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	12452995	78915498	101999762	99	15051											
CMYA5	202333	hgsc.bcm.edu	37	chr5	79028813	79028813	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactggtaacatctgcagatGaacattcagttcttgcagaa	13	11	8	9	0	3	3	1	1	2	2	3	3	3	3	0	1	4	4	0	1	3	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr5:79028813G>T	ENST00000446378.2	+	2	4256	c.4225G>T	c.(4225-4227)Gaa>Taa	p.E1409*		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	1409					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)		ATCTGCAGATGAACATTCAGT	0.418																																					p.E1409X		Atlas-SNP	.											CMYA5_ENST00000446378,colon,carcinoma,-1,2	CMYA5	643	2	0			c.G4225T						PASS	.						34	34	34					5																	79028813		1884	4105	5989	SO:0001587	stop_gained	202333	exon2			GCAGATGAACATT	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.4225G>T	5.37:g.79028813G>T	ENSP00000394770:p.Glu1409*	119	0	0		141	20	0.141844	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Nonsense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	.	.	.	.	.	.	.	.	.	.	G	39	7.514731	0.98332	.	.	ENSG00000164309	ENST00000446378	.	.	.	6.08	3.18	0.36537	.	0.675838	0.12870	N	0.432326	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	5.2941	0.15743	0.1919:0.165:0.6431:0.0	.	.	.	.	X	1409	.	ENSP00000394770:E1409X	E	+	1	0	CMYA5	79064569	0.126000	0.22350	0.005000	0.12908	0.228000	0.25075	1.662000	0.37418	0.364000	0.24374	0.650000	0.86243	GAA	.	.	none		0.418	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610		T	79028813	G	T	79028813	4	4	42	1	0	0	0	0	0	1	0	0	3592	1291	45	4	4231	4	CMYA5	5	79028813	Nonsense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	113315	79028813	101886447	100	15052											
CCNH	902	hgsc.bcm.edu	37	chr5	86708576	86708576	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agctgctcctcgctggagaaGgtccagtgccgcttctgact	6	10	12	13	2	1	2	0	1	1	1	4	3	3	2	3	2	3	4	3	2	1	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr5:86708576G>A	ENST00000256897.4	-	1	260	c.36C>T	c.(34-36)acC>acT	p.T12T	CCNH_ENST00000508855.1_5'Flank|CCNH_ENST00000513499.1_5'UTR|CCNH_ENST00000504878.1_5'UTR	NM_001239.3	NP_001230.1	P51946	CCNH_HUMAN	cyclin H	12					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)		CGCTGGAGAAGGTCCAGTGCC	0.577								Direct reversal of damage;Direct reversal of damage;Nucleotide excision repair (NER)																													p.T12T		Atlas-SNP	.											.	CCNH	40	.	0			c.C36T						PASS	.						96	74	82					5																	86708576		2203	4300	6503	SO:0001819	synonymous_variant	902	exon1			GGAGAAGGTCCAG	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.36C>T	5.37:g.86708576G>A		46	0	0		64	26	0.40625	NM_001239	Q53X72|Q8TBL9	Silent	SNP	ENST00000256897.4	37	CCDS4064.1																																																																																			.	.	none		0.577	CCNH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239291.3	NM_001239		A	86708576	G	A	86708576	2	1	42	1	0	0	0	0	0	0	0	1	2927	987	35	2		2	CCNH	5	86708576	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	7679763	86708576	94206684	101	15053											
LOX	4015	hgsc.bcm.edu	37	chr5	121412595	121412595	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tatcagcccgtacctggccaGacagttttcctccgccgcgc	6	9	9	17	4	1	1	1	0	0	1	3	1	3	1	6	1	2	2	6	1	2	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr5:121412595G>C	ENST00000231004.4	-	2	1032	c.733C>G	c.(733-735)Ctg>Gtg	p.L245V	LOX_ENST00000513319.1_Intron	NM_001178102.1|NM_002317.5	NP_001171573.1|NP_002308.2	P28300	LYOX_HUMAN	lysyl oxidase	245	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)		TACCTGGCCAGACAGTTTTCC	0.612											OREG0016741	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L245V		Atlas-SNP	.											LOX,NS,carcinoma,+1,1	LOX	29	1	0			c.C733G						PASS	.						108	104	105					5																	121412595		2203	4300	6503	SO:0001583	missense	4015	exon2			TGGCCAGACAGTT		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.733C>G	5.37:g.121412595G>C	ENSP00000231004:p.Leu245Val	24	0	0	1511	44	5	0.113636	NM_002317	B2R5Q3|Q5FWF0	Missense_Mutation	SNP	ENST00000231004.4	37	CCDS4129.1	.	.	.	.	.	.	.	.	.	.	G	15.34	2.804101	0.50315	.	.	ENSG00000113083	ENST00000231004;ENST00000543620	T	0.43688	0.94	5.45	3.54	0.40534	.	0.000000	0.85682	D	0.000000	T	0.53883	0.1824	L	0.58583	1.82	0.43724	D	0.996202	D	0.56287	0.975	D	0.67382	0.951	T	0.52563	-0.8559	10	0.87932	D	0	.	6.351	0.21375	0.5873:0.0:0.4127:0.0	.	245	P28300	LYOX_HUMAN	V	245;205	ENSP00000231004:L245V	ENSP00000231004:L245V	L	-	1	2	LOX	121440494	0.996000	0.38824	0.986000	0.45419	0.951000	0.60555	1.336000	0.33850	0.554000	0.29061	0.555000	0.69702	CTG	.	.	none		0.612	LOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250887.2			C	121412595	G	C	121412595	3	2	42	1	0	0	0	0	1	0	0	0	8907	933	33	4	544	4	LOX	5	121412595	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	34704019	121412595	59502665	102	15054											
CSNK1G3	1456	hgsc.bcm.edu	37	chr5	122881389	122881389	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aaagaaagacaaggacaaatCagatgatagaatggcacgac	21	4	10	6	1	1	5	1	1	0	4	1	7	1	6	0	2	0	1	0	2	6	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr5:122881389C>G	ENST00000361991.2	+	1	62	c.32C>G	c.(31-33)tCa>tGa	p.S11*	CSNK1G3_ENST00000512718.3_Intron|CSNK1G3_ENST00000511130.2_Intron|CSNK1G3_ENST00000360683.2_Nonsense_Mutation_p.S11*|CSNK1G3_ENST00000508708.1_3'UTR|CSNK1G3_ENST00000395412.1_Nonsense_Mutation_p.S11*|CSNK1G3_ENST00000395411.1_Nonsense_Mutation_p.S11*|CSNK1G3_ENST00000521364.1_Nonsense_Mutation_p.S11*|CSNK1G3_ENST00000510842.2_Nonsense_Mutation_p.S11*|CSNK1G3_ENST00000345990.4_Nonsense_Mutation_p.S11*			Q9Y6M4	KC1G3_HUMAN	casein kinase 1, gamma 3	11					cellular protein modification process (GO:0006464)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(3)|prostate(1)|skin(1)	15		all_cancers(142;0.0156)|Prostate(80;0.0322)|Lung NSC(810;0.245)	KIRC - Kidney renal clear cell carcinoma(527;0.165)|Kidney(363;0.229)	OV - Ovarian serous cystadenocarcinoma(64;0.000121)|Epithelial(69;0.000227)|all cancers(49;0.00176)		AAGGACAAATCAGATGATAGA	0.408																																					p.S11X	Pancreas(187;2868 2964 4353 6297)	Atlas-SNP	.											CSNK1G3,bladder,carcinoma,0,1	CSNK1G3	42	1	0			c.C32G						PASS	.						120	102	108					5																	122881389		2203	4300	6503	SO:0001587	stop_gained	1456	exon1			ACAAATCAGATGA	AF049090	CCDS4135.1, CCDS34218.1, CCDS43355.1, CCDS59491.1, CCDS59492.1, CCDS59493.1	5q23	2013-01-17			ENSG00000151292	ENSG00000151292			2456	protein-coding gene	gene with protein product		604253				9925945	Standard	NM_004384		Approved		uc031skv.1	Q9Y6M4	OTTHUMG00000128923	ENST00000361991.2:c.32C>G	5.37:g.122881389C>G	ENSP00000354942:p.Ser11*	159	0	0		184	30	0.163043	NM_001270572	A8K040|B4DSH2|B7Z9Q4|E7EVD0|Q86WZ7|Q9Y6M3	Nonsense_Mutation	SNP	ENST00000361991.2	37	CCDS4135.1	.	.	.	.	.	.	.	.	.	.	C	37	6.255040	0.97417	.	.	ENSG00000151292	ENST00000395412;ENST00000395411;ENST00000345990;ENST00000521364;ENST00000510842;ENST00000361991;ENST00000360683	.	.	.	5.2	4.32	0.51571	.	2.335320	0.01492	N	0.017111	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	.	13.6746	0.62447	0.0:0.9229:0.0:0.0771	.	.	.	.	X	11	.	ENSP00000334735:S11X	S	+	2	0	CSNK1G3	122909288	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	2.943000	0.49026	2.805000	0.96524	0.655000	0.94253	TCA	.	.	none		0.408	CSNK1G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000250900.1	NM_004384		G	122881389	C	G	122881389	4	3	42	1	0	0	0	0	0	1	0	0	3958	838	29	4	34	4	CSNK1G3	5	122881389	Nonsense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	1468794	122881389	58033871	103	15055											
PCBD2	84105	hgsc.bcm.edu	37	chr5	134296332	134296332	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgaccaaaaaagatgtgaaGctggccaagtttattgaaaa	17	9	9	6	0	0	4	0	3	0	1	0	4	0	4	2	1	1	2	2	1	8	3	rs144454290		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr5:134296332G>A	ENST00000512783.1	+	4	374	c.354G>A	c.(352-354)aaG>aaA	p.K118K	PCBD2_ENST00000254908.6_Silent_p.K118K			Q9H0N5	PHS2_HUMAN	pterin-4 alpha-carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 2	118					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)			AAGATGTGAAGCTGGCCAAGT	0.373													G|||	1	0.000199681	0.0	0.0	5008	,	,		19140	0.0		0.001	False		,,,				2504	0.0				p.K118K		Atlas-SNP	.											.	PCBD2	3	.	0			c.G354A						PASS	.	G		0,3672		0,0,1836	81	74	76		354	-4.9	0.7	5	dbSNP_134	76	2,8194		0,2,4096	no	coding-synonymous	PCBD2	NM_032151.4		0,2,5932	AA,AG,GG		0.0244,0.0,0.0169		118/131	134296332	2,11866	1836	4098	5934	SO:0001819	synonymous_variant	84105	exon4			TGTGAAGCTGGCC	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.354G>A	5.37:g.134296332G>A		182	0	0		219	10	0.0456621	NM_032151	Q8TD40	Silent	SNP	ENST00000512783.1	37	CCDS43364.1																																																																																			G|1.000;A|0.000	0.000	strong		0.373	PCBD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371578.1	NM_032151		A	134296332	G	A	134296332	2	1	42	1	0	0	0	0	0	0	0	1	11508	962	34	2		2	PCBD2	5	134296332	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	11414943	134296332	46618928	104	15056											
PCDHA4	56144	hgsc.bcm.edu	37	chr5	140186916	140186916	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggcaccttcgtgggccgcatCgcgcaggacctgggactgga	6	6	16	13	4	0	0	0	0	0	0	2	3	0	3	3	5	0	3	3	5	0	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr5:140186916C>T	ENST00000530339.1	+	1	144	c.144C>T	c.(142-144)atC>atT	p.I48I	PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA4_ENST00000356878.4_Silent_p.I48I|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Silent_p.I48I|PCDHA3_ENST00000522353.2_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	48	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)			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)			TGGGCCGCATCGCGCAGGACC	0.652																																					p.I48I		Atlas-SNP	.											.	PCDHA4	419	.	0			c.C144T						PASS	.						54	61	58					5																	140186916		2203	4300	6503	SO:0001819	synonymous_variant	56144	exon1			CCGCATCGCGCAG	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.144C>T	5.37:g.140186916C>T		104	0	0		117	41	0.350427	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			.	.	none		0.652	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		T	140186916	C	T	140186916	2	4	42	1	0	0	0	0	0	0	0	1	11535	874	31	1		1	PCDHA4	5	140186916	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	5890584	140186916	40728344	105	15057											
PCDHA5	56143	hgsc.bcm.edu	37	chr5	140201800	140201800	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cattttagagtcaagaatgcCagattcgcggtttccgctag	10	12	10	9	3	1	3	1	0	0	3	3	3	2	3	2	1	1	2	2	1	4	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr5:140201800C>T	ENST00000529859.1	+	1	440	c.440C>T	c.(439-441)cCa>cTa	p.P147L	PCDHA5_ENST00000378126.3_Missense_Mutation_p.P147L|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Missense_Mutation_p.P147L	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	147					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)			TCAAGAATGCCAGATTCGCGG	0.433																																					p.P147L		Atlas-SNP	.											.	PCDHA5	361	.	0			c.C440T						PASS	.						50	55	54					5																	140201800		2203	4300	6503	SO:0001583	missense	56143	exon1			GAATGCCAGATTC	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.440C>T	5.37:g.140201800C>T	ENSP00000436557:p.Pro147Leu	137	0	0		149	38	0.255034	NM_018908	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	37	CCDS54917.1	.	.	.	.	.	.	.	.	.	.	C	1.960	-0.439103	0.04636	.	.	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	T;T;T	0.21031	2.03;2.03;2.03	4.02	-0.26	0.12967	Cadherin (1);Cadherin-like (1);	.	.	.	.	T	0.14098	0.0341	L	0.35644	1.08	0.09310	N	1	B;B;B	0.16603	0.012;0.01;0.018	B;B;B	0.32289	0.143;0.008;0.008	T	0.44329	-0.9335	9	0.07813	T	0.8	.	5.1007	0.14759	0.1425:0.6129:0.0:0.2446	.	147;147;147	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	L	147	ENSP00000433416:P147L;ENSP00000436557:P147L;ENSP00000367366:P147L	ENSP00000367366:P147L	P	+	2	0	PCDHA5	140181984	0.000000	0.05858	0.826000	0.32828	0.990000	0.78478	-1.759000	0.01808	0.004000	0.14682	0.591000	0.81541	CCA	.	.	none		0.433	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908		T	140201800	C	T	140201800	3	4	42	1	0	0	0	0	1	0	0	0	11536	594	21	2	442	2	PCDHA5	5	140201800	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	14884	140201800	40713460	106	15058											
SH3RF2	153769	hgsc.bcm.edu	37	chr5	145428733	145428733	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cctggggaagtgccaggacgGctggctcaggggcgtctcct	5	7	17	12	2	2	0	1	0	1	0	3	2	2	2	3	7	1	2	3	7	1	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr5:145428733G>C	ENST00000511217.1	+	6	1299	c.1247G>C	c.(1246-1248)gGc>gCc	p.G416A	SH3RF2_ENST00000359120.4_Missense_Mutation_p.G416A			Q8TEC5	SH3R2_HUMAN	SH3 domain containing ring finger 2	416	SH3 3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				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)			TGCCAGGACGGCTGGCTCAGG	0.597											OREG0016895	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G416A		Atlas-SNP	.											.	SH3RF2	58	.	0			c.G1247C						PASS	.						65	66	65					5																	145428733		2203	4300	6503	SO:0001583	missense	153769	exon7			AGGACGGCTGGCT	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.1247G>C	5.37:g.145428733G>C	ENSP00000424497:p.Gly416Ala	101	0	0	1694	101	23	0.227723	NM_152550	A8K961|Q08AM9|Q6GMR9|Q8N5S8|Q96LP8	Missense_Mutation	SNP	ENST00000511217.1	37	CCDS4280.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.309463	0.81247	.	.	ENSG00000156463	ENST00000359120;ENST00000511217	T;T	0.42513	0.97;0.97	5.51	5.51	0.81932	Src homology-3 domain (4);	0.070489	0.64402	D	0.000018	T	0.58047	0.2095	M	0.91300	3.195	0.80722	D	1	P	0.36753	0.568	B	0.38225	0.268	T	0.68330	-0.5437	10	0.87932	D	0	-25.1307	18.1751	0.89759	0.0:0.0:1.0:0.0	.	416	Q8TEC5	SH3R2_HUMAN	A	416	ENSP00000352028:G416A;ENSP00000424497:G416A	ENSP00000352028:G416A	G	+	2	0	SH3RF2	145408926	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	9.687000	0.98667	2.587000	0.87381	0.484000	0.47621	GGC	.	.	none		0.597	SH3RF2-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372804.1	NM_152550		C	145428733	G	C	145428733	3	2	42	1	0	0	0	0	1	0	0	0	14274	1203	42	4	1269	4	SH3RF2	5	145428733	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	5226933	145428733	35486527	107	15059											
ATP10B	23120	hgsc.bcm.edu	37	chr5	160071166	160071166	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgcatagatgacaatgccaaCagccatctcggtgtttctga	11	11	9	10	1	2	3	0	2	2	1	3	3	2	3	2	1	4	2	2	1	3	2	rs369830205		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr5:160071166C>T	ENST00000327245.5	-	9	1693	c.847G>A	c.(847-849)Gtt>Att	p.V283I		NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	283					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)			ACAATGCCAACAGCCATCTCG	0.488																																					p.V283I		Atlas-SNP	.											.	ATP10B	201	.	0			c.G847A						PASS	.						129	131	131					5																	160071166		2003	4177	6180	SO:0001583	missense	23120	exon9			TGCCAACAGCCAT	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.847G>A	5.37:g.160071166C>T	ENSP00000313600:p.Val283Ile	62	0	0		77	33	0.428571	NM_025153	Q9H725	Missense_Mutation	SNP	ENST00000327245.5	37	CCDS43394.1	.	.	.	.	.	.	.	.	.	.	C	12.80	2.046598	0.36085	.	.	ENSG00000118322	ENST00000327245	T	0.72942	-0.7	4.9	2.14	0.27477	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.319926	0.29348	N	0.012417	T	0.47303	0.1438	N	0.11870	0.19	0.09310	N	1	B;B;B;B	0.31227	0.02;0.002;0.314;0.014	B;B;B;B	0.29077	0.044;0.012;0.098;0.028	T	0.28808	-1.0032	9	.	.	.	.	9.5577	0.39348	0.0:0.6982:0.0:0.3018	.	327;283;255;283	B4DHG1;O94823-2;O94823-3;O94823	.;.;.;AT10B_HUMAN	I	283	ENSP00000313600:V283I	.	V	-	1	0	ATP10B	160003744	0.000000	0.05858	0.723000	0.30687	0.996000	0.88848	-0.043000	0.12043	0.132000	0.18615	0.563000	0.77884	GTT	.	.	alt		0.488	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153		T	160071166	C	T	160071166	3	4	42	1	0	0	0	0	1	0	0	0	1117	478	17	2	3610	2	ATP10B	5	160071166	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	14642433	160071166	20844094	108	15060											
CPEB4	80315	hgsc.bcm.edu	37	chr5	173317237	173317237	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcgcatcgtctcttactggTttcagtaactggtcagcagc	8	12	10	11	2	3	0	2	0	1	0	5	0	3	0	0	2	5	4	0	2	2	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr5:173317237T>C	ENST00000265085.5	+	1	1955	c.501T>C	c.(499-501)ggT>ggC	p.G167G	CPEB4_ENST00000522336.1_5'Flank|CPEB4_ENST00000334035.5_Silent_p.G167G|CPEB4_ENST00000517880.1_5'Flank|CPEB4_ENST00000519835.1_Silent_p.G167G|CPEB4_ENST00000520867.1_Silent_p.G167G	NM_030627.2	NP_085130.2	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding protein 4	167					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)			CTCTTACTGGTTTCAGTAACT	0.493																																					p.G167G		Atlas-SNP	.											CPEB4,NS,carcinoma,+2,1	CPEB4	54	1	0			c.T501C						scavenged	.						89	93	92					5																	173317237		2203	4300	6503	SO:0001819	synonymous_variant	80315	exon1			TACTGGTTTCAGT	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.501T>C	5.37:g.173317237T>C		129	1	0.00775194		153	36	0.235294	NM_030627	B7ZLQ7|Q7Z310|Q8N405|Q9C0J0	Silent	SNP	ENST00000265085.5	37	CCDS4390.1																																																																																			.	.	none		0.493	CPEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252964.2	NM_030627		C	173317237	T	C	173317237	2	2	42	1	0	0	0	0	0	0	0	1	3805	1712	60	3		3	CPEB4	5	173317237	Silent	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	13246071	173317237	7598023	109	15061											
CPEB4	80315	hgsc.bcm.edu	37	chr5	173317293	173317293	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctctacaataatcaatgaagAtgcaagtttctttcaccagg	14	12	6	9	0	4	2	2	1	2	1	4	2	4	2	1	1	2	2	1	1	6	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr5:173317293A>C	ENST00000265085.5	+	1	2011	c.557A>C	c.(556-558)gAt>gCt	p.D186A	CPEB4_ENST00000522336.1_5'Flank|CPEB4_ENST00000334035.5_Missense_Mutation_p.D186A|CPEB4_ENST00000517880.1_5'Flank|CPEB4_ENST00000519835.1_Missense_Mutation_p.D186A|CPEB4_ENST00000520867.1_Missense_Mutation_p.D186A	NM_030627.2	NP_085130.2	Q17RY0	CPEB4_HUMAN	cytoplasmic polyadenylation element binding protein 4	186					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)			ATCAATGAAGATGCAAGTTTC	0.488																																					p.D186A		Atlas-SNP	.											.	CPEB4	54	.	0			c.A557C						PASS	.						70	75	73					5																	173317293		2203	4300	6503	SO:0001583	missense	80315	exon1			ATGAAGATGCAAG	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.557A>C	5.37:g.173317293A>C	ENSP00000265085:p.Asp186Ala	165	0	0		189	40	0.21164	NM_030627	B7ZLQ7|Q7Z310|Q8N405|Q9C0J0	Missense_Mutation	SNP	ENST00000265085.5	37	CCDS4390.1	.	.	.	.	.	.	.	.	.	.	A	15.50	2.851834	0.51270	.	.	ENSG00000113742	ENST00000265085;ENST00000520867;ENST00000334035;ENST00000519835	T;T;T;T	0.39997	1.05;1.05;1.05;1.05	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.41627	0.1167	L	0.29908	0.895	0.80722	D	1	P;P;B;P	0.52316	0.884;0.93;0.413;0.952	B;P;B;P	0.47827	0.355;0.558;0.214;0.449	T	0.38714	-0.9648	10	0.72032	D	0.01	-20.7982	16.1839	0.81934	1.0:0.0:0.0:0.0	.	186;186;186;186	B7ZLQ8;Q17RY0-2;E5RJM0;Q17RY0	.;.;.;CPEB4_HUMAN	A	186	ENSP00000265085:D186A;ENSP00000429092:D186A;ENSP00000334533:D186A;ENSP00000429048:D186A	ENSP00000265085:D186A	D	+	2	0	CPEB4	173249899	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.923000	0.92808	2.222000	0.72286	0.533000	0.62120	GAT	.	.	none		0.488	CPEB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252964.2	NM_030627		C	173317293	A	C	173317293	3	2	42	1	0	0	0	0	1	0	0	0	3805	333	12	5	559	5	CPEB4	5	173317293	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	56	173317293	7597967	110	15062											
FGFR4	2264	hgsc.bcm.edu	37	chr5	176516652	176516652	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tcctgctgagtgtgcctgggCctccagtcttgtccctggag	3	12	13	13	0	1	1	0	1	1	0	4	2	4	2	5	2	2	1	5	2	0	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr5:176516652C>T	ENST00000292408.4	+	2	294	c.49C>T	c.(49-51)Cct>Tct	p.P17S	FGFR4_ENST00000393648.2_Missense_Mutation_p.P17S|FGFR4_ENST00000502906.1_Missense_Mutation_p.P17S|FGFR4_ENST00000507708.1_3'UTR|FGFR4_ENST00000393637.1_Missense_Mutation_p.P17S|FGFR4_ENST00000292410.3_Missense_Mutation_p.P17S	NM_002011.3|NM_213647.1	NP_002002.3|NP_998812.1	P22455	FGFR4_HUMAN	fibroblast growth factor receptor 4	17					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)	TGTGCCTGGGCCTCCAGTCTT	0.632										TSP Lung(9;0.080)																											p.P17S		Atlas-SNP	.											.	FGFR4	174	.	0			c.C49T						PASS	.						62	57	58					5																	176516652		2203	4300	6503	SO:0001583	missense	2264	exon1			CCTGGGCCTCCAG	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.49C>T	5.37:g.176516652C>T	ENSP00000292408:p.Pro17Ser	139	0	0		159	76	0.477987	NM_022963	G3JVM2|G3JVM5|G3JVM7|G3JVM9|O43785|Q14309|Q71TW8|Q8TDA0|Q96KE5	Missense_Mutation	SNP	ENST00000292408.4	37	CCDS4410.1	.	.	.	.	.	.	.	.	.	.	C	0.067	-1.210794	0.01555	.	.	ENSG00000160867	ENST00000292408;ENST00000503708;ENST00000393648;ENST00000514472;ENST00000502906;ENST00000292410;ENST00000510911;ENST00000513166;ENST00000393637	T;T;T;D;T;T;T;D;T	0.87966	-1.06;-0.77;-1.02;-2.32;-1.06;-1.07;1.04;-2.25;-1.07	4.26	-0.824	0.10812	.	.	.	.	.	T	0.70954	0.3283	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	0.04013	0.0;0.0;0.0;0.001;0.0	T	0.57033	-0.7880	9	0.42905	T	0.14	.	1.7718	0.03013	0.1123:0.1673:0.312:0.4083	.	17;17;17;17;17	B5A965;B4DVP5;P22455-2;E7EWF4;P22455	.;.;.;.;FGFR4_HUMAN	S	17	ENSP00000292408:P17S;ENSP00000424905:P17S;ENSP00000377259:P17S;ENSP00000426492:P17S;ENSP00000424960:P17S;ENSP00000292410:P17S;ENSP00000427222:P17S;ENSP00000422889:P17S;ENSP00000377254:P17S	ENSP00000292408:P17S	P	+	1	0	FGFR4	176449258	0.462000	0.25791	0.417000	0.26559	0.235000	0.25334	0.500000	0.22562	0.049000	0.15920	-0.479000	0.04858	CCT	.	.	none		0.632	FGFR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253410.1			T	176516652	C	T	176516652	3	4	42	1	0	0	0	0	1	0	0	0	5876	739	26	2	51	2	FGFR4	5	176516652	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	3199359	176516652	4398608	111	15063											
LMAN2	10960	hgsc.bcm.edu	37	chr5	176778602	176778602	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaagcccaggccttcccaggCaccgccggccccagccccaa	8	2	10	21	2	0	0	0	0	0	0	1	1	1	0	9	3	2	1	9	3	2	1	rs143985896	byFrequency	TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr5:176778602C>T	ENST00000303127.7	-	1	251	c.47G>A	c.(46-48)tGc>tAc	p.C16Y	LMAN2_ENST00000515209.1_Missense_Mutation_p.C16Y|LMAN2_ENST00000506310.1_5'UTR	NM_006816.2	NP_006807.1	Q12907	LMAN2_HUMAN	lectin, mannose-binding 2	16					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)			CCTTCCCAGGCACCGCCGGCC	0.647													C|||	3	0.000599042	0.0023	0.0	5008	,	,		15298	0.0		0.0	False		,,,				2504	0.0				p.C16Y		Atlas-SNP	.											.	LMAN2	35	.	0			c.G47A						PASS	.	C	TYR/CYS	10,4396	15.5+/-35.6	0,10,2193	22	28	26		47	3.4	1	5	dbSNP_134	26	0,8600		0,0,4300	yes	missense	LMAN2	NM_006816.2	194	0,10,6493	TT,TC,CC		0.0,0.227,0.0769	benign	16/357	176778602	10,12996	2203	4300	6503	SO:0001583	missense	10960	exon1			CCCAGGCACCGCC	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.47G>A	5.37:g.176778602C>T	ENSP00000303366:p.Cys16Tyr	86	0	0		79	13	0.164557	NM_006816	Q53HH1	Missense_Mutation	SNP	ENST00000303127.7	37	CCDS4417.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	15.76	2.929099	0.52759	0.00227	0.0	ENSG00000169223	ENST00000303127;ENST00000515209;ENST00000514458;ENST00000502560	T;T;T;T	0.64085	-0.02;-0.04;-0.08;-0.02	5.25	3.44	0.39384	.	0.338095	0.32372	N	0.006186	T	0.36826	0.0981	N	0.08118	0	0.28596	N	0.909398	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.19353	-1.0308	10	0.38643	T	0.18	-16.1925	6.4711	0.22009	0.1786:0.7304:0.0:0.0909	.	16;16	Q12907;D6RBV2	LMAN2_HUMAN;.	Y	16	ENSP00000303366:C16Y;ENSP00000423998:C16Y;ENSP00000424132:C16Y;ENSP00000425229:C16Y	ENSP00000303366:C16Y	C	-	2	0	LMAN2	176711208	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.282000	0.33226	0.769000	0.33313	0.644000	0.83932	TGC	C|0.999;T|0.001	0.001	strong		0.647	LMAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253434.1	NM_006816		T	176778602	C	T	176778602	3	4	42	1	0	0	0	0	1	0	0	0	8847	710	25	2	1055	2	LMAN2	5	176778602	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	261950	176778602	4136658	112	15064											
COL23A1	91522	hgsc.bcm.edu	37	chr5	177695744	177695744	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacttaccttttcccctttcGggcctggaagtccctggaaa	7	12	8	14	1	0	0	0	0	0	0	3	2	2	2	5	3	1	0	5	3	3	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr5:177695744G>A	ENST00000390654.3	-	7	839	c.482C>T	c.(481-483)cCg>cTg	p.P161L	COL23A1_ENST00000407622.1_Missense_Mutation_p.P125L	NM_173465.3	NP_775736.2	Q86Y22	CONA1_HUMAN	collagen, type XXIII, alpha 1	161	Collagen-like 1.|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)		TTCCCCTTTCGGGCCTGGAAG	0.572																																					p.P161L		Atlas-SNP	.											.	COL23A1	47	.	0			c.C482T						PASS	.						66	69	68					5																	177695744		1960	4149	6109	SO:0001583	missense	91522	exon7			CCTTTCGGGCCTG	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.482C>T	5.37:g.177695744G>A	ENSP00000375069:p.Pro161Leu	58	0	0		54	8	0.148148	NM_173465	Q8IVR4|Q9NT93	Missense_Mutation	SNP	ENST00000390654.3	37	CCDS4436.1	.	.	.	.	.	.	.	.	.	.	G	14.99	2.700780	0.48307	.	.	ENSG00000050767	ENST00000390654;ENST00000407622	D;D	0.95885	-3.2;-3.84	4.9	4.9	0.64082	.	0.288677	0.27971	N	0.017120	D	0.91415	0.7291	L	0.41632	1.29	0.58432	D	0.999998	B	0.23128	0.08	B	0.04013	0.001	D	0.87953	0.2725	10	0.18276	T	0.48	1.1631	13.9866	0.64339	0.0:0.0:1.0:0.0	.	161	Q86Y22	CONA1_HUMAN	L	161;125	ENSP00000375069:P161L;ENSP00000385092:P125L	ENSP00000375069:P161L	P	-	2	0	COL23A1	177628350	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	3.625000	0.54238	2.442000	0.82660	0.555000	0.69702	CCG	.	.	none		0.572	COL23A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253475.1	NM_173465		A	177695744	G	A	177695744	3	1	42	1	0	0	0	0	1	0	0	0	3684	1116	39	1	1232	1	COL23A1	5	177695744	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	917142	177695744	3219516	113	15065											
ZNF454	285676	hgsc.bcm.edu	37	chr5	178373943	178373943	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gttttcccagctagaaaaaaGggaagtgtggatgccagagg	13	8	14	6	0	0	2	0	0	0	2	1	4	1	4	2	3	2	2	2	3	5	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr5:178373943G>A	ENST00000320129.3	+	4	509	c.206G>A	c.(205-207)aGg>aAg	p.R69K	ZNF454_ENST00000519564.1_Missense_Mutation_p.R69K	NM_001178090.1|NM_182594.2	NP_001171561.1|NP_872400.2	Q8N9F8	ZN454_HUMAN	zinc finger protein 454	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(11)|lung(18)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	46	all_cancers(89;0.000904)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.225)|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;0.234)		CTAGAAAAAAGGGAAGTGTGG	0.483																																					p.R69K		Atlas-SNP	.											.	ZNF454	99	.	0			c.G206A						PASS	.						123	123	123					5																	178373943		2203	4300	6503	SO:0001583	missense	285676	exon4			AAAAAAGGGAAGT	AK094763	CCDS4441.1	5q35.3	2013-01-08			ENSG00000178187	ENSG00000178187		"Zinc fingers, C2H2-type", "-"	21200	protein-coding gene	gene with protein product							Standard	NM_182594		Approved	FLJ37444	uc021yjc.1	Q8N9F8	OTTHUMG00000130891	ENST00000320129.3:c.206G>A	5.37:g.178373943G>A	ENSP00000326249:p.Arg69Lys	144	0	0		136	58	0.426471	NM_001178089	Q2M1P2|Q2M323	Missense_Mutation	SNP	ENST00000320129.3	37	CCDS4441.1	.	.	.	.	.	.	.	.	.	.	G	2.179	-0.387938	0.04932	.	.	ENSG00000178187	ENST00000320129;ENST00000519564	T;T	0.00801	5.68;5.68	4.15	1.23	0.21249	Krueppel-associated box (3);	0.848058	0.09606	U	0.779552	T	0.00784	0.0026	L	0.27975	0.815	0.09310	N	1	B	0.13594	0.008	B	0.12156	0.007	T	0.48625	-0.9019	10	0.21540	T	0.41	.	3.4847	0.07615	0.2209:0.0:0.5716:0.2075	.	69	Q8N9F8	ZN454_HUMAN	K	69	ENSP00000326249:R69K;ENSP00000430354:R69K	ENSP00000326249:R69K	R	+	2	0	ZNF454	178306549	0.016000	0.18221	0.003000	0.11579	0.013000	0.08279	0.214000	0.17541	0.128000	0.18479	0.563000	0.77884	AGG	.	.	none		0.483	ZNF454-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253476.2	XM_209718		A	178373943	G	A	178373943	3	1	42	1	0	0	0	0	1	0	0	0	17938	1000	35	2	216	2	ZNF454	5	178373943	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	678199	178373943	2541317	114	15066											
CD83	9308	hgsc.bcm.edu	37	chr6	14118269	14118269	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accgccccctgggatccgcaGgttccctacacggtctcctg	5	8	10	18	3	1	0	0	0	1	0	4	1	3	1	6	3	1	2	6	3	1	2	rs199841901		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:14118269G>C	ENST00000379153.3	+	2	297	c.126G>C	c.(124-126)caG>caC	p.Q42H		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)				GGGATCCGCAGGTTCCCTACA	0.617																																					p.Q42H		Atlas-SNP	.											CD83,NS,lymphoid_neoplasm,0,1	CD83	23	1	0			c.G126C						PASS	.						27	28	28					6																	14118269		2203	4300	6503	SO:0001583	missense	9308	exon2			TCCGCAGGTTCCC	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.126G>C	6.37:g.14118269G>C	ENSP00000368450:p.Gln42His	36	0	0		25	7	0.28	NM_004233	Q5THX9	Missense_Mutation	SNP	ENST00000379153.3	37	CCDS4532.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	7.529	0.658198	0.14645	.	.	ENSG00000112149	ENST00000379153	T	0.66280	-0.2	4.56	2.7	0.31948	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.543413	0.18136	N	0.150580	T	0.32133	0.0819	L	0.58101	1.795	0.09310	N	1	B	0.18013	0.025	B	0.19946	0.027	T	0.25710	-1.0124	10	0.27082	T	0.32	-2.8511	6.4298	0.21790	0.103:0.1834:0.7136:0.0	.	42	Q01151	CD83_HUMAN	H	42	ENSP00000368450:Q42H	ENSP00000368450:Q42H	Q	+	3	2	CD83	14226248	0.001000	0.12720	0.010000	0.14722	0.232000	0.25224	-0.028000	0.12350	0.324000	0.23333	0.491000	0.48974	CAG	G|1.000;C|0.000	0.000	strong		0.617	CD83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039916.1			C	14118269	G	C	14118269	3	2	42	1	0	0	0	0	1	0	0	0	3043	991	35	4	132	4	CD83	6	14118269	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10		14118269	156996798	115	15067											
C6orf62	81688	hgsc.bcm.edu	37	chr6	24718818	24718818	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cttgaagtcaaactggtcagCtagagattcttttttctttc	9	17	7	8	0	4	2	2	1	2	1	5	3	4	2	0	1	2	1	0	1	3	7			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:24718818C>T	ENST00000378119.4	-	1	2246	c.79G>A	c.(79-81)Gct>Act	p.A27T	C6orf62_ENST00000378102.3_Intron|C6orf62_ENST00000540769.1_Intron	NM_030939.4	NP_112201.1	Q9GZU0	CF062_HUMAN	chromosome 6 open reading frame 62	27						intracellular (GO:0005622)				endometrium(2)|kidney(3)|large_intestine(2)|lung(3)	10						AACTGGTCAGCTAGAGATTCT	0.373																																					p.A27T		Atlas-SNP	.											.	C6orf62	18	.	0			c.G79A						PASS	.						95	95	95					6																	24718818		2203	4300	6503	SO:0001583	missense	81688	exon1			GGTCAGCTAGAGA	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.79G>A	6.37:g.24718818C>T	ENSP00000367359:p.Ala27Thr	169	0	0		165	17	0.10303	NM_030939	Q3LIB6|Q5JVZ2|Q5JVZ3|Q6IA63|Q9H1Z2	Missense_Mutation	SNP	ENST00000378119.4	37	CCDS4559.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.037187	0.93630	.	.	ENSG00000112308	ENST00000378119	T	0.39592	1.07	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	T	0.23572	0.0570	N	0.24115	0.695	0.80722	D	1	P	0.40731	0.728	B	0.37888	0.26	T	0.13229	-1.0517	10	0.87932	D	0	-10.7654	19.8215	0.96599	0.0:1.0:0.0:0.0	.	27	Q9GZU0	CF062_HUMAN	T	27	ENSP00000367359:A27T	ENSP00000367359:A27T	A	-	1	0	C6orf62	24826797	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.251000	0.78297	2.679000	0.91253	0.650000	0.86243	GCT	.	.	none		0.373	C6orf62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040017.1	NM_030939		T	24718818	C	T	24718818	3	4	42	1	0	0	0	0	1	0	0	0	2370	797	28	2	630	2	C6orf62	6	24718818	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	10600549	24718818	146396249	116	15068											
HIST1H1E	3008	hgsc.bcm.edu	37	chr6	26156900	26156900	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgagcaagggcaccctggtGcagaccaagggcaccggcgc	9	3	16	13	2	0	2	0	1	0	1	0	2	0	2	3	4	2	4	3	4	2	0	rs549787183		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:26156900G>A	ENST00000304218.3	+	1	342	c.282G>A	c.(280-282)gtG>gtA	p.V94V	HIST1H2BD_ENST00000377777.4_5'Flank|HIST1H2BD_ENST00000289316.2_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	94	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						GCACCCTGGTGCAGACCAAGG	0.607													G|||	1	0.000199681	0.0	0.0	5008	,	,		15327	0.0		0.001	False		,,,				2504	0.0				p.V94V		Atlas-SNP	.											HIST1H1E,NS,carcinoma,+2,1	HIST1H1E	69	1	0			c.G282A						PASS	.						51	55	53					6																	26156900		2203	4300	6503	SO:0001819	synonymous_variant	3008	exon1			CCTGGTGCAGACC	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.282G>A	6.37:g.26156900G>A		144	0	0		91	22	0.241758	NM_005321	Q4VB25	Silent	SNP	ENST00000304218.3	37	CCDS4586.1																																																																																			.	.	none		0.607	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321		A	26156900	G	A	26156900	2	1	42	1	0	0	0	0	0	0	0	1	7135	1306	46	2		2	HIST1H1E	6	26156900	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	1438082	26156900	144958167	117	15069											
HIST1H2AD	3013	hgsc.bcm.edu	37	chr6	26199193	26199193	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttacccagcaacttgtttagCtcctcgtcgttgcggatggc	6	13	10	12	3	0	0	0	0	0	0	3	1	1	1	2	2	5	4	2	2	3	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:26199193C>T	ENST00000341023.1	-	1	278	c.279G>A	c.(277-279)gaG>gaA	p.E93E	HIST1H2BF_ENST00000359985.1_5'Flank|HIST1H3D_ENST00000377831.5_5'UTR|HIST1H3D_ENST00000356476.2_5'Flank	NM_021065.2	NP_066409.1	P20671	H2A1D_HUMAN	histone cluster 1, H2ad	93						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E93D(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6		all_hematologic(11;0.196)				ACTTGTTTAGCTCCTCGTCGT	0.602																																					p.E93E		Atlas-SNP	.											HIST1H2AD,NS,lymphoid_neoplasm,0,1	HIST1H2AD	20	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G279A						scavenged	.						128	121	123					6																	26199193		2203	4300	6503	SO:0001819	synonymous_variant	3013	exon1			GTTTAGCTCCTCG	Z80776	CCDS4591.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000196866	ENSG00000196866		"Histones / Replication-dependent"	4729	protein-coding gene	gene with protein product		602792	"H2A histone family, member G", "histone 1, H2ad"	H2AFG		9119399, 12408966	Standard	NM_021065		Approved	H2A/g, H2A.3	uc003ngw.4	P20671	OTTHUMG00000014437	ENST00000341023.1:c.279G>A	6.37:g.26199193C>T		259	1	0.003861		195	53	0.271795	NM_021065	A0PK91|P57754|Q6FGY6	Silent	SNP	ENST00000341023.1	37	CCDS4591.1																																																																																			.	.	none		0.602	HIST1H2AD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040100.1	NM_021065		T	26199193	C	T	26199193	2	4	42	1	0	0	0	0	0	0	0	1	7140	796	28	2		2	HIST1H2AD	6	26199193	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	42293	26199193	144915874	118	15070											
HIST1H2BJ	8970	hgsc.bcm.edu	37	chr6	27100437	27100437	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagctctccttgcggctgcgCttgcgcttcttgccgtcttt	1	16	10	14	4	3	0	0	0	3	0	4	0	3	0	2	1	5	4	2	1	1	6			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:27100437C>T	ENST00000607124.1	-	1	92	c.93G>A	c.(91-93)aaG>aaA	p.K31K	HIST1H2AG_ENST00000359193.2_5'Flank|HIST1H2BJ_ENST00000339812.2_Silent_p.K31K|HIST1H2BJ_ENST00000541790.1_Silent_p.K31K			P06899	H2B1J_HUMAN	histone cluster 1, H2bj	31				KRKRS -> SAAH (in Ref. 1; CAA24950). {ECO:0000305}.	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						TGCGGCTGCGCTTGCGCTTCT	0.557																																					p.K31K		Atlas-SNP	.											.	HIST1H2BJ	21	.	0			c.G93A						PASS	.						163	156	158					6																	27100437		2203	4300	6503	SO:0001819	synonymous_variant	8970	exon1			GCTGCGCTTGCGC	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.93G>A	6.37:g.27100437C>T		182	0	0		129	13	0.100775	NM_021058	B2R4J4|O60816	Silent	SNP	ENST00000607124.1	37	CCDS4618.1																																																																																			.	.	none		0.557	HIST1H2BJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040138.2	NM_021058		T	27100437	C	T	27100437	2	4	42	1	0	0	0	0	0	0	0	1	7158	796	28	2		2	HIST1H2BJ	6	27100437	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	901244	27100437	144014630	119	15071											
HIST1H2AK	8330	hgsc.bcm.edu	37	chr6	27805994	27805994	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctccggcaccgacccgctCagcgtagttgcccttgcgga	5	7	12	17	6	1	0	1	0	0	0	2	2	2	1	4	2	3	5	4	2	1	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:27805994C>A	ENST00000330180.2	-	1	123	c.124G>T	c.(124-126)Gag>Tag	p.E42*	HIST1H2BN_ENST00000396980.3_5'Flank|HIST1H2BN_ENST00000606613.1_5'Flank	NM_003510.2	NP_003501.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2ak	42						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						CCGACCCGCTCAGCGTAGTTG	0.657																																					p.E42X		Atlas-SNP	.											HIST1H2AK,bladder,carcinoma,0,1	HIST1H2AK	28	1	0			c.G124T						PASS	.						39	42	41					6																	27805994		2203	4300	6503	SO:0001587	stop_gained	8330	exon1			CCCGCTCAGCGTA	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.124G>T	6.37:g.27805994C>A	ENSP00000330307:p.Glu42*	114	0	0		120	38	0.316667	NM_003510	P02261|Q2M1R2|Q76PA6	Nonsense_Mutation	SNP	ENST00000330180.2	37	CCDS4632.1	.	.	.	.	.	.	.	.	.	.	.	14.23	2.474898	0.43942	.	.	ENSG00000184348	ENST00000330180	.	.	.	4.42	3.54	0.40534	.	0.000000	0.31381	U	0.007755	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	.	7.5482	0.27778	0.0:0.737:0.1708:0.0922	.	.	.	.	X	42	.	ENSP00000330307:E42X	E	-	1	0	HIST1H2AK	27913973	0.693000	0.27728	0.921000	0.36526	0.242000	0.25591	1.349000	0.33998	2.369000	0.80426	0.655000	0.94253	GAG	.	.	none		0.657	HIST1H2AK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043814.1	NM_003510		A	27805994	C	A	27805994	4	1	42	1	0	0	0	0	0	1	0	0	7146	835	29	4	272	4	HIST1H2AK	6	27805994	Nonsense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	705557	27805994	143309073	120	15072											
HIST1H1B	3009	hgsc.bcm.edu	37	chr6	27835055	27835055	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caccaagctcttgaggcccaGcttaatgcggctgttattct	8	12	9	12	1	2	1	0	1	2	0	2	1	2	1	2	2	3	4	2	2	3	4	rs116008322	byFrequency	TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:27835055G>A	ENST00000331442.3	-	1	304	c.253C>T	c.(253-255)Ctg>Ttg	p.L85L		NM_005322.2	NP_005313.1	P16401	H15_HUMAN	histone cluster 1, H1b	85	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				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						TTGAGGCCCAGCTTAATGCGG	0.577													G|||	45	0.00898562	0.0038	0.0101	5008	,	,		16701	0.004		0.0278	False		,,,				2504	0.001				p.L85L		Atlas-SNP	.											.	HIST1H1B	54	.	0			c.C253T						PASS	.	G		40,4366	43.8+/-77.6	0,40,2163	124	135	131		253	3.7	1	6	dbSNP_132	131	238,8362	96.6+/-158.3	4,230,4066	no	coding-synonymous	HIST1H1B	NM_005322.2		4,270,6229	AA,AG,GG		2.7674,0.9079,2.1375		85/227	27835055	278,12728	2203	4300	6503	SO:0001819	synonymous_variant	3009	exon1			GGCCCAGCTTAAT	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.253C>T	6.37:g.27835055G>A		176	0	0		149	15	0.100671	NM_005322	Q14529|Q3MJ42	Silent	SNP	ENST00000331442.3	37	CCDS4635.1																																																																																			G|0.982;A|0.018	0.018	strong		0.577	HIST1H1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043371.1	NM_005322		A	27835055	G	A	27835055	2	1	42	1	0	0	0	0	0	0	0	1	7132	962	34	2		2	HIST1H1B	6	27835055	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	29061	27835055	143280012	121	15073											
HLA-A	3105	hgsc.bcm.edu	37	chr6	29910559	29910565	+	Frame_Shift_Del	DEL	CACATCC	CACATCC	-																															cactccatgaggtatttcttCacatccgtgtcccggcccgg																								rs41562020|rs41543612|rs199474355|rs1059418|rs281864725|rs199474356	byFrequency	TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	CACATCC	CACATCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:29910559_29910565delCACATCC	ENST00000396634.1	+	4	440_446	c.99_105delCACATCC	c.(97-105)ttcacatccfs	p.FTS33fs	HLA-A_ENST00000376802.2_Frame_Shift_Del_p.FTS33fs|HLA-A_ENST00000376809.5_Frame_Shift_Del_p.FTS33fs|HLA-A_ENST00000376806.5_Frame_Shift_Del_p.FTS33fs			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	33	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)			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						GGTATTTCTTCACATCCGTGTCCCGGC	0.72									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.33_35del		Pindel,Atlas-Indel	.											HLA-A,NS,lymphoid_neoplasm,0,1	HLA-A	89	1	0			c.98_104del						PASS	.																																			SO:0001589	frameshift_variant	3105	exon2	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.99_105delCACATCC	6.37:g.29910559_29910565delCACATCC	ENSP00000379873:p.Phe33fs	83	0	.		52	14	0.269	NM_002116	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Frame_Shift_Del	DEL	ENST00000396634.1	37	CCDS34373.1																																																																																			.	.	none		0.72	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116		-	29910565	CACATCC	-	29910559	7	5	42	1	0	1	0	1	0	0	0	0	7204	825	29	0	105	0	HLA-A	6	29910559	Frame_Shift_Del	DEL	CACATCC	TCGA-GS-A9TZ-01A-11D-A38X-10	2075504	29910559	141204508	122	15074											
HLA-A	3105	hgsc.bcm.edu	37	chr6	29911109	29911109	+	Silent	SNP	G	G	A																															gacgggcgcttcctccgcggGtaccggcaggacgcctacga																								rs61760917		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:29911109G>A	ENST00000396634.1	+	5	749	c.408G>A	c.(406-408)ggG>ggA	p.G136G	HLA-A_ENST00000376802.2_Silent_p.G136G|HLA-A_ENST00000376809.5_Silent_p.G136G|HLA-A_ENST00000376806.5_Silent_p.G136G			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	136	Alpha-2.				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						TCCTCCGCGGGTACCGGCAGG	0.667									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.G136G		Atlas-SNP	.											HLA-A,colon,carcinoma,+2,1	HLA-A	89	1	0			c.G408A						PASS	.						33	25	28					6																	29911109		1500	2695	4195	SO:0001819	synonymous_variant	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CCGCGGGTACCGG	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.408G>A	6.37:g.29911109G>A		165	0	0		67	32	0.477612	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Silent	SNP	ENST00000396634.1	37	CCDS34373.1																																																																																			.	.	weak		0.667	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116		A	29911109	G	A	29911109	2	1	42	1	0	0	0	0	0	0	0	1	7204	1248	44	2		2	HLA-A	6	29911109	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	550	29911109	141203958	123	15075	197	2									
HLA-A	3105	hgsc.bcm.edu	37	chr6	29911113	29911115	+	In_Frame_Del	DEL	CGG	CGG	-																															ggcgcttcctccgcgggtacCggcaggacgcctacgacggc																								rs3173420|rs41540315|rs66488547|rs1059498|rs12721717	byFrequency	TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	CGG	CGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:29911113_29911115delCGG	ENST00000396634.1	+	5	753_755	c.412_414delCGG	c.(412-414)cggdel	p.R138del	HLA-A_ENST00000376802.2_In_Frame_Del_p.R138del|HLA-A_ENST00000376809.5_In_Frame_Del_p.R138del|HLA-A_ENST00000376806.5_In_Frame_Del_p.R138del			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	138	Alpha-2.		Q -> R (in allele A*31:03, allele A*31:04 and allele A*31:06).		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						CCGCGGGTACCGGCAGGACGCCT	0.665									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.137_138del		Pindel,Atlas-Indel	.											.	HLA-A	89	.	0			c.411_413del						PASS	.																																			SO:0001651	inframe_deletion	3105	exon3	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.412_414delCGG	6.37:g.29911113_29911115delCGG	ENSP00000379873:p.Arg138del	171	0	.		67	24	0.358	NM_002116	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	In_Frame_Del	DEL	ENST00000396634.1	37	CCDS34373.1																																																																																			.	.	none		0.665	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116		-	29911115	CGG	-	29911113	7	5	42	1	0	1	0	1	0	0	0	0	7204	643	23	0	422	0	HLA-A	6	29911113	In_Frame_Del	DEL	CGG	TCGA-GS-A9TZ-01A-11D-A38X-10	4	29911113	141203954	124	15076	197	2									
HLA-B	3106	hgsc.bcm.edu	37	chr6	31324195	31324201	+	Frame_Shift_Del	DEL	TACATGC	TACATGC	-																															ccggccccacgtcgcagccgTacatgctctggagggtgtga																								rs151341218|rs1071652|rs151341216|rs151341217|rs41545614|rs1140412|rs41547332|rs41562913	byFrequency	TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	TACATGC	TACATGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:31324195_31324201delTACATGC	ENST00000412585.2	-	3	390_396	c.362_368delGCATGTA	c.(361-369)agcatgtacfs	p.SMY121fs		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	121	Alpha-2.		S -> R (in allele B*48:03).		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						GTCGCAGCCGTACATGCTCTGGAGGGT	0.71									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.121_123del		Pindel,Atlas-Indel	.											.	HLA-B	54	.	0			c.363_369del						PASS	.																																			SO:0001589	frameshift_variant	3106	exon3	Familial Cancer Database	;Lichen Sclerosis, Familial	.	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.362_368delGCATGTA	6.37:g.31324195_31324201delTACATGC	ENSP00000399168:p.Ser121fs	55	0	.		36	13	0.361	NM_005514	Q29764	Frame_Shift_Del	DEL	ENST00000412585.2	37	CCDS34394.1																																																																																			.	.	alt		0.71	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514		-	31324201	TACATGC	-	31324195	7	5	42	1	0	1	0	1	0	0	0	0	7205	1638	57	0	740	0	HLA-B	6	31324195	Frame_Shift_Del	DEL	TACATGC	TCGA-GS-A9TZ-01A-11D-A38X-10	1413082	31324195	139790872	125	15077											
BAT2	7916	hgsc.bcm.edu	37	chr6	31602134	31602134	+	Nonsense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccctcacatctggaaccgttTacatactggtgagtaaagct	11	11	8	11	1	2	1	1	1	1	0	2	2	2	2	2	2	4	3	2	2	5	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:31602134T>G	ENST00000376033.2	+	19	5075	c.4841T>G	c.(4840-4842)tTa>tGa	p.L1614*	PRRC2A_ENST00000376007.4_Nonsense_Mutation_p.L1614*	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1614	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						TGGAACCGTTTACATACTGGT	0.522																																					p.L1614X		Atlas-SNP	.											.	PRRC2A	152	.	0			c.T4841G						PASS	.						156	182	173					6																	31602134		1511	2709	4220	SO:0001587	stop_gained	7916	exon19			ACCGTTTACATAC	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.4841T>G	6.37:g.31602134T>G	ENSP00000365201:p.Leu1614*	123	0	0		64	27	0.421875	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Nonsense_Mutation	SNP	ENST00000376033.2	37	CCDS4708.1	.	.	.	.	.	.	.	.	.	.	T	47	13.600033	0.99752	.	.	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033;ENST00000376010	.	.	.	5.31	5.31	0.75309	.	0.151859	0.30809	N	0.008826	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-0.4528	12.8775	0.57998	0.0:0.0:0.0:1.0	.	.	.	.	X	1608;1597;1614;1614;839	.	ENSP00000365175:L1614X	L	+	2	0	PRRC2A	31710113	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	3.955000	0.56715	2.234000	0.73211	0.459000	0.35465	TTA	.	.	none		0.522	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686		G	31602134	T	G	31602134	4	3	42	1	0	0	0	0	0	1	0	0	1319	1764	61	5	4911	5	BAT2	6	31602134	Nonsense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	277939	31602134	139512933	126	15078											
BRD2	6046	hgsc.bcm.edu	37	chr6	32948431	32948431	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tagcgcttccagctccagctCagattccagctcctcctctt	6	12	6	17	1	2	1	1	0	1	1	7	1	7	1	5	0	4	4	5	0	1	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:32948431C>G	ENST00000374825.4	+	13	4043	c.2342C>G	c.(2341-2343)tCa>tGa	p.S781*	BRD2_ENST00000374831.4_Nonsense_Mutation_p.S781*|BRD2_ENST00000395289.2_Nonsense_Mutation_p.S816*|BRD2_ENST00000449085.2_Nonsense_Mutation_p.S734*|BRD2_ENST00000395287.1_Nonsense_Mutation_p.S816*|BRD2_ENST00000443797.2_Nonsense_Mutation_p.S661*	NM_005104.3	NP_005095.1	P25440	BRD2_HUMAN	bromodomain containing 2	781	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						AGCTCCAGCTCAGATTCCAGC	0.537																																					p.S816X		Atlas-SNP	.											.	BRD2	70	.	0			c.C2447G						PASS	.						110	90	97					6																	32948431		1511	2709	4220	SO:0001587	stop_gained	6046	exon13			CCAGCTCAGATTC	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.2342C>G	6.37:g.32948431C>G	ENSP00000363958:p.Ser781*	80	0	0		56	17	0.303571	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	19.565009|19.565009	0.99921|0.99921	.|.	.|.	ENSG00000204256|ENSG00000204256	ENST00000449025|ENST00000374825;ENST00000374831;ENST00000395289;ENST00000443797;ENST00000395287;ENST00000449085	.|.	.|.	.|.	6.15|6.15	6.15|6.15	0.99193|0.99193	.|.	.|0.000000	.|0.42420	.|D	.|0.000718	T|.	0.68824|.	0.3043|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.64347|.	-0.6429|.	4|.	.|0.38643	.|T	.|0.18	-12.1118|-12.1118	18.3325|18.3325	0.90274|0.90274	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	E|X	787|781;781;816;661;816;734	.|.	.|ENSP00000363958:S781X	Q|S	+|+	1|2	0|0	BRD2|BRD2	33056409|33056409	1.000000|1.000000	0.71417|0.71417	0.978000|0.978000	0.43139|0.43139	0.967000|0.967000	0.64934|0.64934	6.781000|6.781000	0.75068|0.75068	2.932000|2.932000	0.99384|0.99384	0.643000|0.643000	0.83706|0.83706	CAG|TCA	.	.	none		0.537	BRD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076503.2			G	32948431	C	G	32948431	4	3	42	1	0	0	0	0	0	1	0	0	1504	838	29	4	2388	4	BRD2	6	32948431	Nonsense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	1346297	32948431	138166636	127	15079											
TBCC	6903	hgsc.bcm.edu	37	chr6	42713452	42713452	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cgctcggccaaggccgcctgCagccgcgccagcgcctcttg	4	5	13	19	6	1	0	0	0	1	0	2	0	1	0	6	2	3	2	6	2	1	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:42713452C>T	ENST00000372876.1	-	1	382	c.360G>A	c.(358-360)ctG>ctA	p.L120L	TBCC_ENST00000244625.2_Silent_p.L120L	NM_003192.2	NP_003183	Q15814	TBCC_HUMAN	tubulin folding cofactor C	120					'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)			AGGCCGCCTGCAGCCGCGCCA	0.627																																					p.L120L		Atlas-SNP	.											.	TBCC	31	.	0			c.G360A						PASS	.						18	24	22					6																	42713452		2172	4260	6432	SO:0001819	synonymous_variant	6903	exon1			CGCCTGCAGCCGC	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.360G>A	6.37:g.42713452C>T		39	0	0		41	13	0.317073	NM_003192	Q53Y43|Q5T787	Silent	SNP	ENST00000372876.1	37	CCDS4872.1																																																																																			.	.	none		0.627	TBCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040559.1	NM_003192		T	42713452	C	T	42713452	2	4	42	1	0	0	0	0	0	0	0	1	15646	697	25	2		2	TBCC	6	42713452	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	9765021	42713452	128401615	128	15080											
PGK2	5232	hgsc.bcm.edu	37	chr6	49754100	49754100	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgtgctttggccatgatatcTttaacgatcttggctccctc	6	16	8	11	1	2	1	0	1	2	0	4	2	3	1	2	2	2	2	2	2	2	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:49754100T>G	ENST00000304801.3	-	1	953	c.801A>C	c.(799-801)aaA>aaC	p.K267N		NM_138733.4	NP_620061.2	P07205	PGK2_HUMAN	phosphoglycerate kinase 2	267					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)					CCATGATATCTTTAACGATCT	0.418																																					p.K267N		Atlas-SNP	.											.	PGK2	87	.	0			c.A801C						PASS	.						135	128	130					6																	49754100		2203	4300	6503	SO:0001583	missense	5232	exon1			GATATCTTTAACG	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.801A>C	6.37:g.49754100T>G	ENSP00000305995:p.Lys267Asn	206	0	0		186	56	0.301075	NM_138733	B2R6Y8|Q9H107	Missense_Mutation	SNP	ENST00000304801.3	37	CCDS4930.1	.	.	.	.	.	.	.	.	.	.	T	2.954	-0.216024	0.06101	.	.	ENSG00000170950	ENST00000304801	D	0.92495	-3.05	4.09	-6.89	0.01660	Phosphoglycerate kinase, C-terminal (1);	0.232879	0.49916	N	0.000136	T	0.67841	0.2936	L	0.38531	1.155	0.38455	D	0.947053	B	0.06786	0.001	B	0.08055	0.003	T	0.39860	-0.9593	10	0.31617	T	0.26	-0.3183	1.399	0.02267	0.3607:0.3258:0.1225:0.1911	.	267	P07205	PGK2_HUMAN	N	267	ENSP00000305995:K267N	ENSP00000305995:K267N	K	-	3	2	PGK2	49862059	0.831000	0.29352	0.519000	0.27824	0.334000	0.28698	-0.119000	0.10676	-1.401000	0.02058	0.477000	0.44152	AAA	.	.	none		0.418	PGK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040872.1			G	49754100	T	G	49754100	3	3	42	1	0	0	0	0	1	0	0	0	11800	1606	56	5	456	5	PGK2	6	49754100	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	7040648	49754100	121360967	129	15081											
BAI3	577	hgsc.bcm.edu	37	chr6	70070955	70070955	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acatgcccatgagtatgaatGagcttagcaatccatgtttg	12	12	9	8	0	0	3	0	3	0	0	1	3	1	3	2	0	3	4	2	0	4	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:70070955G>A	ENST00000370598.1	+	29	4611	c.3790G>A	c.(3790-3792)Gag>Aag	p.E1264K	BAI3_ENST00000238918.8_Missense_Mutation_p.E470K|BAI3_ENST00000546190.1_Missense_Mutation_p.E228K	NM_001704.2	NP_001695	O60242	BAI3_HUMAN	brain-specific angiogenesis inhibitor 3	1264					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)				GAGTATGAATGAGCTTAGCAA	0.413																																					p.E1264K		Atlas-SNP	.											BAI3,right_upper_lobe,carcinoma,-2,1	BAI3	451	1	0			c.G3790A						PASS	.						92	85	87					6																	70070955		2203	4299	6502	SO:0001583	missense	577	exon29			ATGAATGAGCTTA	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.3790G>A	6.37:g.70070955G>A	ENSP00000359630:p.Glu1264Lys	99	0	0		95	25	0.263158	NM_001704	B7Z1K0|O60297|Q2NKN6|Q5VY37|Q9BX54	Missense_Mutation	SNP	ENST00000370598.1	37	CCDS4968.1	.	.	.	.	.	.	.	.	.	.	G	17.94	3.512258	0.64522	.	.	ENSG00000135298	ENST00000370598;ENST00000238918;ENST00000546190	T;T;T	0.48201	1.97;2.58;0.82	5.58	5.58	0.84498	.	0.052110	0.85682	D	0.000000	T	0.29491	0.0735	L	0.32530	0.975	0.47009	D	0.999288	B;P	0.46395	0.319;0.877	B;B	0.37731	0.055;0.257	T	0.27502	-1.0072	10	0.72032	D	0.01	.	19.9199	0.97084	0.0:0.0:1.0:0.0	.	470;1264	B7Z356;O60242	.;BAI3_HUMAN	K	1264;470;228	ENSP00000359630:E1264K;ENSP00000238918:E470K;ENSP00000441821:E228K	ENSP00000238918:E470K	E	+	1	0	BAI3	70127676	1.000000	0.71417	1.000000	0.80357	0.727000	0.41649	9.174000	0.94824	2.781000	0.95711	0.591000	0.81541	GAG	.	.	none		0.413	BAI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041120.1			A	70070955	G	A	70070955	3	1	42	1	0	0	0	0	1	0	0	0	1300	1291	45	2	3896	2	BAI3	6	70070955	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	20316855	70070955	101044112	130	15082											
TMEM30A	55754	hgsc.bcm.edu	37	chr6	75969173	75969173	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	aagcgataggtataggataaGaatcattgccaatgagaaac	18	8	10	5	1	1	2	1	1	0	2	1	5	1	3	1	2	3	1	1	2	8	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:75969173G>C	ENST00000230461.6	-	5	904	c.575C>G	c.(574-576)tCt>tGt	p.S192C	TMEM30A_ENST00000370050.5_Missense_Mutation_p.S73C|TMEM30A_ENST00000475111.2_Missense_Mutation_p.S156C	NM_018247.3	NP_060717.1	Q9NV96	CC50A_HUMAN	transmembrane protein 30A	192					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						TATAGGATAAGAATCATTGCC	0.353																																					p.S192C		Atlas-SNP	.											.	TMEM30A	40	.	0			c.C575G						PASS	.						81	81	81					6																	75969173		2203	4295	6498	SO:0001583	missense	55754	exon5			GGATAAGAATCAT	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.575C>G	6.37:g.75969173G>C	ENSP00000230461:p.Ser192Cys	348	0	0		262	59	0.225191	NM_018247	A8K9V8|E1P539|Q658Z3|Q96H09|Q9NSL9	Missense_Mutation	SNP	ENST00000230461.6	37	CCDS4983.1	.	.	.	.	.	.	.	.	.	.	G	19.56	3.850681	0.71719	.	.	ENSG00000112697	ENST00000230461;ENST00000545449;ENST00000370050;ENST00000475111;ENST00000518161	.	.	.	5.31	5.31	0.75309	.	0.374161	0.30565	N	0.009358	T	0.74966	0.3786	M	0.83012	2.62	0.38661	D	0.952079	D;D	0.63046	0.982;0.992	P;P	0.58520	0.753;0.84	T	0.78409	-0.2215	9	0.59425	D	0.04	.	19.3389	0.94334	0.0:0.0:1.0:0.0	.	156;192	Q9NV96-2;Q9NV96	.;CC50A_HUMAN	C	192;176;73;156;73	.	ENSP00000230461:S192C	S	-	2	0	TMEM30A	76025893	0.987000	0.35691	0.954000	0.39281	0.425000	0.31504	3.458000	0.53014	2.650000	0.89964	0.655000	0.94253	TCT	.	.	none		0.353	TMEM30A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041248.2	NM_018247		C	75969173	G	C	75969173	3	2	42	1	0	0	0	0	1	0	0	0	16168	942	33	4	522	4	TMEM30A	6	75969173	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	5898218	75969173	95145894	131	15083											
UBE2J1	51465	hgsc.bcm.edu	37	chr6	90062277	90062277	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccggactcttcaggttgtaGcgggtctccatggtgggtcg	4	11	15	11	3	3	0	1	0	2	0	5	1	3	1	2	5	1	2	2	5	1	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:90062277G>A	ENST00000435041.2	-	1	290	c.12C>T	c.(10-12)cgC>cgT	p.R4R		NM_016021.2	NP_057105.2	Q9Y385	UB2J1_HUMAN	ubiquitin-conjugating enzyme E2, J1	4					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)		TCAGGTTGTAGCGGGTCTCCA	0.761																																					p.R4R		Atlas-SNP	.											.	UBE2J1	28	.	0			c.C12T						PASS	.						17	18	17					6																	90062277		2192	4280	6472	SO:0001819	synonymous_variant	51465	exon1			GTTGTAGCGGGTC	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.12C>T	6.37:g.90062277G>A		52	0	0		48	16	0.333333	NM_016021	A8K3F9|Q53F25|Q5W0N4|Q9BZ32|Q9NQL3|Q9NY66|Q9P011|Q9P0S0|Q9UF10	Silent	SNP	ENST00000435041.2	37	CCDS5021.1																																																																																			.	.	none		0.761	UBE2J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043742.2	NM_016021		A	90062277	G	A	90062277	2	1	42	1	0	0	0	0	0	0	0	1	16875	958	34	2		2	UBE2J1	6	90062277	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	14093104	90062277	81052790	132	15084											
BACH2	60468	hgsc.bcm.edu	37	chr6	90660815	90660815	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gagaccttaagcaggagggcGaggccacgctcctggatctc	9	6	14	12	2	1	1	0	0	1	1	3	5	2	3	3	4	1	2	3	4	1	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:90660815G>A	ENST00000257749.4	-	7	1717	c.1010C>T	c.(1009-1011)tCg>tTg	p.S337L	RP3-512E2.2_ENST00000413986.1_RNA|BACH2_ENST00000537989.1_Missense_Mutation_p.S337L|BACH2_ENST00000343122.3_Missense_Mutation_p.S337L|RP3-512E2.2_ENST00000445838.1_RNA	NM_021813.2	NP_068585.1	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 2	337						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)		GCAGGAGGGCGAGGCCACGCT	0.642																																					p.S337L		Atlas-SNP	.											.	BACH2	224	.	0			c.C1010T						PASS	.						40	44	43					6																	90660815		2203	4299	6502	SO:0001583	missense	60468	exon5			GAGGGCGAGGCCA	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.1010C>T	6.37:g.90660815G>A	ENSP00000257749:p.Ser337Leu	65	0	0		77	21	0.272727	NM_001170794	E1P518|Q59H70|Q5T793|Q9NTS5	Missense_Mutation	SNP	ENST00000257749.4	37	CCDS5026.1	.	.	.	.	.	.	.	.	.	.	G	19.67	3.870621	0.72065	.	.	ENSG00000112182	ENST00000257749;ENST00000537989;ENST00000343122	T;T;T	0.55930	0.49;0.49;0.49	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.56366	0.1980	L	0.27053	0.805	0.51233	D	0.999915	D	0.89917	1.0	D	0.80764	0.994	T	0.62343	-0.6874	10	0.87932	D	0	-0.1721	19.5375	0.95260	0.0:0.0:1.0:0.0	.	337	Q9BYV9	BACH2_HUMAN	L	337	ENSP00000257749:S337L;ENSP00000437473:S337L;ENSP00000345642:S337L	ENSP00000257749:S337L	S	-	2	0	BACH2	90717536	1.000000	0.71417	0.921000	0.36526	0.606000	0.37113	9.230000	0.95299	2.620000	0.88729	0.655000	0.94253	TCG	.	.	none		0.642	BACH2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041522.2	NM_021813		A	90660815	G	A	90660815	3	1	42	1	0	0	0	0	1	0	0	0	1284	1059	37	1	1527	1	BACH2	6	90660815	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	598538	90660815	80454252	133	15085											
BACH2	60468	hgsc.bcm.edu	37	chr6	90718537	90718537	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	gactcatacacatacatgggGgagtcaggcttctcatccac	11	9	9	12	0	3	0	3	0	1	0	5	2	4	1	1	3	2	1	1	3	2	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:90718537G>A	ENST00000257749.4	-	6	734	c.27C>T	c.(25-27)tcC>tcT	p.S9S	BACH2_ENST00000537989.1_Silent_p.S9S|BACH2_ENST00000343122.3_Silent_p.S9S	NM_021813.2	NP_068585.1	Q9BYV9	BACH2_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 2	9						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)		CATACATGGGGGAGTCAGGCT	0.478																																					p.S9S		Atlas-SNP	.											.	BACH2	224	.	0			c.C27T						PASS	.						141	133	136					6																	90718537		2203	4300	6503	SO:0001819	synonymous_variant	60468	exon4			CATGGGGGAGTCA	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.27C>T	6.37:g.90718537G>A		69	0	0		67	15	0.223881	NM_001170794	E1P518|Q59H70|Q5T793|Q9NTS5	Silent	SNP	ENST00000257749.4	37	CCDS5026.1																																																																																			.	.	none		0.478	BACH2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041522.2	NM_021813		A	90718537	G	A	90718537	2	1	42	1	0	0	0	0	0	0	0	1	1284	1219	43	2		2	BACH2	6	90718537	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	57722	90718537	80396530	134	15086											
ASCC3	10973	hgsc.bcm.edu	37	chr6	101037846	101037846	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ctccaatttcaatacagtagGaaagttccaattcaatcagg	15	11	6	9	0	3	0	3	0	0	0	5	1	5	1	2	2	1	2	2	2	7	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:101037846G>A	ENST00000369162.2	-	35	5737	c.5393C>T	c.(5392-5394)tCc>tTc	p.S1798F		NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	1798					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)		AATACAGTAGGAAAGTTCCAA	0.358																																					p.S1798F		Atlas-SNP	.											.	ASCC3	205	.	0			c.C5393T						PASS	.						82	80	81					6																	101037846		2203	4300	6503	SO:0001583	missense	10973	exon35			CAGTAGGAAAGTT	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.5393C>T	6.37:g.101037846G>A	ENSP00000358159:p.Ser1798Phe	255	0	0		171	31	0.181287	NM_006828	E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	37	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	G	24.9	4.581274	0.86748	.	.	ENSG00000112249	ENST00000369162	T	0.42513	0.97	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.65709	0.2717	M	0.86502	2.82	0.80722	D	1	D	0.76494	0.999	D	0.70935	0.971	T	0.72327	-0.4327	10	0.87932	D	0	.	19.2468	0.93905	0.0:0.0:1.0:0.0	.	1798	Q8N3C0	HELC1_HUMAN	F	1798	ENSP00000358159:S1798F	ENSP00000358159:S1798F	S	-	2	0	ASCC3	101144567	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	8.802000	0.91910	2.558000	0.86282	0.579000	0.79373	TCC	.	.	none		0.358	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828		A	101037846	G	A	101037846	3	1	42	1	0	0	0	0	1	0	0	0	1033	1174	41	2	1247	2	ASCC3	6	101037846	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	10319309	101037846	70077221	135	15087											
POPDC3	64208	hgsc.bcm.edu	37	chr6	105607586	105607586	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgttctggtatcccttacCtgaaaaatgccttcctctgt	7	16	7	11	0	2	1	0	1	2	0	4	1	4	1	4	1	2	2	4	1	4	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:105607586C>T	ENST00000254765.3	-	3	872	c.594G>A	c.(592-594)caG>caA	p.Q198Q	BVES-AS1_ENST00000580511.1_RNA|BVES-AS1_ENST00000580854.1_RNA|POPDC3_ENST00000474760.1_5'UTR|BVES-AS1_ENST00000369122.3_RNA|BVES-AS1_ENST00000369120.2_RNA	NM_022361.4	NP_071756.2	Q9HBV1	POPD3_HUMAN	popeye domain containing 3	198					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)				TATCCCTTACCTGAAAAATGC	0.398																																					p.Q198Q		Atlas-SNP	.											.	POPDC3	47	.	0			c.G594A						PASS	.						82	78	80					6																	105607586		2203	4300	6503	SO:0001630	splice_region_variant	64208	exon3			CCTTACCTGAAAA	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.594+1G>A	6.37:g.105607586C>T		219	0	0		166	43	0.259036	NM_022361	B2RA98|Q5T3Y8|Q8TBW6	Silent	SNP	ENST00000254765.3	37	CCDS5052.1																																																																																			.	.	none		0.398	POPDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041651.1	NM_022361	Silent	T	105607586	C	T	105607586	5	4	42	1	0	0	0	0	0	0	1	0	12265	695	24	2	289	2	POPDC3	6	105607586	Splice_Site	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	4569740	105607586	65507481	136	15088											
AIM1	202	hgsc.bcm.edu	37	chr6	106968516	106968516	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ttgccatgcctcctattcacGaagaccatttagaaaaggtg	12	11	8	10	1	1	2	1	0	0	2	2	3	2	2	4	1	2	0	4	1	5	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:106968516G>A	ENST00000369066.3	+	2	2696	c.2209G>A	c.(2209-2211)Gaa>Aaa	p.E737K		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)		TCCTATTCACGAAGACCATTT	0.433																																					p.E737K		Atlas-SNP	.											.	AIM1	161	.	0			c.G2209A						PASS	.						62	66	64					6																	106968516		2203	4300	6503	SO:0001583	missense	202	exon2			ATTCACGAAGACC	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.2209G>A	6.37:g.106968516G>A	ENSP00000358062:p.Glu737Lys	84	0	0		81	17	0.209877	NM_001624	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	37	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.970040	0.92855	.	.	ENSG00000112297	ENST00000285105;ENST00000369066	D	0.83992	-1.79	6.16	6.16	0.99307	.	0.329901	0.30374	N	0.009768	D	0.91002	0.7170	M	0.78637	2.42	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.90292	0.4323	10	0.72032	D	0.01	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	737	Q9Y4K1	AIM1_HUMAN	K	1145;737	ENSP00000358062:E737K	ENSP00000285105:E1145K	E	+	1	0	AIM1	107075209	1.000000	0.71417	0.992000	0.48379	0.704000	0.40688	7.927000	0.87577	2.937000	0.99478	0.650000	0.86243	GAA	.	.	none		0.433	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			A	106968516	G	A	106968516	3	1	42	1	0	0	0	0	1	0	0	0	430	1059	37	1	2215	1	AIM1	6	106968516	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	1360930	106968516	64146551	137	15089											
OSTM1	28962	hgsc.bcm.edu	37	chr6	108370472	108370472	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttacgcagaatgagtttgcGtttcttttgctctgagtgaa	8	16	10	7	2	2	4	0	3	2	1	2	4	2	4	0	0	3	4	0	0	3	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:108370472G>A	ENST00000193322.3	-	5	1019	c.934C>T	c.(934-936)Cgc>Tgc	p.R312C		NM_014028.3	NP_054747.2	Q86WC4	OSTM1_HUMAN	osteopetrosis associated transmembrane protein 1	312					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)		ATGAGTTTGCGTTTCTTTTGC	0.338																																					p.R312C	Melanoma(162;1427 1909 3096 17430 21396)	Atlas-SNP	.											.	OSTM1	22	.	0			c.C934T						PASS	.						58	54	56					6																	108370472		2203	4300	6503	SO:0001583	missense	28962	exon5			GTTTGCGTTTCTT	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.934C>T	6.37:g.108370472G>A	ENSP00000193322:p.Arg312Cys	147	0	0		130	20	0.153846	NM_014028	E1P5E3|Q5R391|Q6PCA7|Q7RTW6|Q8NC29|Q8TC82|Q9Y2S9	Missense_Mutation	SNP	ENST00000193322.3	37	CCDS5062.1	.	.	.	.	.	.	.	.	.	.	G	19.83	3.899649	0.72754	.	.	ENSG00000081087	ENST00000193322;ENST00000440575	T	0.55234	0.53	5.59	4.64	0.57946	.	0.000000	0.85682	D	0.000000	T	0.69984	0.3172	M	0.81497	2.545	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.74466	-0.3656	10	0.87932	D	0	-10.502	17.1745	0.86838	0.0:0.0:0.8652:0.1348	.	312	Q86WC4	OSTM1_HUMAN	C	312;165	ENSP00000193322:R312C	ENSP00000193322:R312C	R	-	1	0	OSTM1	108477165	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.544000	0.82117	2.635000	0.89317	0.650000	0.86243	CGC	.	.	none		0.338	OSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041709.3	NM_014028		A	108370472	G	A	108370472	3	1	42	1	0	0	0	0	1	0	0	0	11307	1145	40	1	78	1	OSTM1	6	108370472	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	1401956	108370472	62744595	138	15090											
REV3L	5980	hgsc.bcm.edu	37	chr6	111656671	111656671	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gcaagaaaactgatttcccaCctgtgaaccccttgtcagta	12	10	7	12	0	1	3	1	2	0	1	2	3	2	3	4	0	2	2	4	0	5	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:111656671C>T	ENST00000358835.3	-	23	8135		c.e23+1		REV3L_ENST00000435970.1_Splice_Site|REV3L_ENST00000368805.1_Splice_Site|REV3L_ENST00000368802.3_Splice_Site			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit						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)		TGATTTCCCACCTGTGAACCC	0.388								DNA polymerases (catalytic subunits)																													.		Atlas-SNP	.											.	REV3L	386	.	0			c.7680+1G>A						PASS	.						128	125	126					6																	111656671		2203	4300	6503	SO:0001630	splice_region_variant	5980	exon23			TTCCCACCTGTGA	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.7680+1G>A	6.37:g.111656671C>T		88	0	0		84	20	0.238095	NM_002912	O43214|Q5TC33	Splice_Site	SNP	ENST00000358835.3	37	CCDS5091.2	.	.	.	.	.	.	.	.	.	.	C	27.9	4.872625	0.91587	.	.	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970;ENST00000543871	.	.	.	5.53	5.53	0.82687	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4635	0.94929	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	REV3L	111763364	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.814000	0.86154	2.585000	0.87301	0.460000	0.39030	.	.	.	none		0.388	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912	Intron	T	111656671	C	T	111656671	5	4	42	1	0	0	0	0	0	0	1	0	13255	521	18	2	1755	2	REV3L	6	111656671	Splice_Site	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	3286199	111656671	59458396	139	15091											
GOPC	57120	hgsc.bcm.edu	37	chr6	117894665	117894665	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgcattggtcgtttcaagtCattacgtcctctgcaggctc	6	15	9	11	2	3	0	2	0	1	0	6	0	4	0	1	2	3	4	1	2	2	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:117894665C>A	ENST00000368498.2	-	5	856	c.781G>T	c.(781-783)Gac>Tac	p.D261Y	GOPC_ENST00000467125.1_5'UTR|GOPC_ENST00000052569.6_Missense_Mutation_p.D253Y|GOPC_ENST00000535237.1_Missense_Mutation_p.D261Y	NM_020399.3	NP_065132.1	Q9HD26	GOPC_HUMAN	golgi-associated PDZ and coiled-coil motif containing	261					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)		CGTTTCAAGTCATTACGTCCT	0.448			O	ROS1	glioblastoma																																p.D261Y		Atlas-SNP	.		Dom	yes		6	6q21	57120	golgi associated PDZ and coiled-coil motif containing		O	.	GOPC	29	.	0			c.G781T						PASS	.						273	209	231					6																	117894665		2203	4300	6503	SO:0001583	missense	57120	exon5			TCAAGTCATTACG	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.781G>T	6.37:g.117894665C>A	ENSP00000357484:p.Asp261Tyr	209	0	0		164	50	0.304878	NM_020399	A6NM30|Q59FS4|Q969U8	Missense_Mutation	SNP	ENST00000368498.2	37	CCDS5117.1	.	.	.	.	.	.	.	.	.	.	C	29.3	4.998376	0.93227	.	.	ENSG00000047932	ENST00000052569;ENST00000368498;ENST00000535237	T;T;T	0.17691	2.26;2.27;2.27	6.06	6.06	0.98353	PDZ/DHR/GLGF (1);	0.098800	0.64402	D	0.000002	T	0.27663	0.0680	L	0.50333	1.59	0.80722	D	1	D;D;D	0.71674	0.998;0.997;0.993	P;P;P	0.59221	0.846;0.854;0.747	T	0.00494	-1.1706	10	0.72032	D	0.01	-13.5307	20.6208	0.99490	0.0:1.0:0.0:0.0	.	253;261;261	Q9HD26-2;Q9HD26;F5H1Y4	.;GOPC_HUMAN;.	Y	253;261;261	ENSP00000052569:D253Y;ENSP00000357484:D261Y;ENSP00000445690:D261Y	ENSP00000052569:D253Y	D	-	1	0	GOPC	118001358	1.000000	0.71417	0.995000	0.50966	0.986000	0.74619	6.089000	0.71384	2.882000	0.98803	0.655000	0.94253	GAC	.	.	none		0.448	GOPC-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041988.1	NM_020399		A	117894665	C	A	117894665	3	1	42	1	0	0	0	0	1	0	0	0	6581	826	29	4	627	4	GOPC	6	117894665	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	6237994	117894665	53220402	140	15092											
TNFAIP3	7128	hgsc.bcm.edu	37	chr6	138200319	138200319	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agcccctccccgcattcttgCcacagagctggaaacgacgc	9	6	9	17	3	1	1	0	0	1	1	2	3	2	2	5	1	4	2	5	1	1	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:138200319C>A	ENST00000237289.4	+	7	1803	c.1737C>A	c.(1735-1737)tgC>tgA	p.C579*		NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	579	Interaction with TNIP1. {ECO:0000250}.				apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|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 interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|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 protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		CGCATTCTTGCCACAGAGCTG	0.657			"D, N, F"		"marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"																																p.C579X	GBM(130;153 1739 22295 28918 47987)	Atlas-SNP	.		Rec	yes		6	6q23	7128	"tumor necrosis factor, alpha-induced protein 3"		L	.	TNFAIP3	340	.	25	Whole gene deletion(25)	haematopoietic_and_lymphoid_tissue(25)	c.C1737A						PASS	.						48	54	52					6																	138200319		2203	4300	6503	SO:0001587	stop_gained	7128	exon7			TTCTTGCCACAGA	M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"OTU domain containing"	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.1737C>A	6.37:g.138200319C>A	ENSP00000237289:p.Cys579*	53	0	0		40	11	0.275	NM_001270507	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Nonsense_Mutation	SNP	ENST00000237289.4	37	CCDS5187.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.062660	0.76187	.	.	ENSG00000118503	ENST00000237289;ENST00000535574;ENST00000544646	.	.	.	5.58	3.81	0.43845	.	0.307688	0.37053	N	0.002263	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.4105	10.5766	0.45231	0.0:0.8502:0.0:0.1498	.	.	.	.	X	579	.	ENSP00000237289:C579X	C	+	3	2	TNFAIP3	138242012	0.641000	0.27251	1.000000	0.80357	0.025000	0.11179	0.166000	0.16583	0.733000	0.32492	-0.254000	0.11334	TGC	.	.	none		0.657	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1			A	138200319	C	A	138200319	4	1	42	1	0	0	0	0	0	1	0	0	16289	747	26	4	1759	4	TNFAIP3	6	138200319	Nonsense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	20305654	138200319	32914748	141	15093											
TNFAIP3	7128	hgsc.bcm.edu	37	chr6	138202395	138202395	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ccccgcctgtgatcattttgGcaatgccaagtgcaacggct	8	10	10	13	2	1	1	1	1	0	0	1	1	1	1	4	2	3	3	4	2	3	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr6:138202395G>A	ENST00000237289.4	+	9	2378	c.2312G>A	c.(2311-2313)gGc>gAc	p.G771D		NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	771	Interaction with TNIP1. {ECO:0000250}.|Required for lysosomal localization and for TRAF2 lysosomal degradation.|Sufficient for inhibitory activity of TNF-induced NF-kappa-B activity. {ECO:0000250}.				apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|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 interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|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 protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		GATCATTTTGGCAATGCCAAG	0.617			"D, N, F"		"marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"																																p.G771D	GBM(130;153 1739 22295 28918 47987)	Atlas-SNP	.		Rec	yes		6	6q23	7128	"tumor necrosis factor, alpha-induced protein 3"		L	.	TNFAIP3	340	.	25	Whole gene deletion(25)	haematopoietic_and_lymphoid_tissue(25)	c.G2312A						PASS	.						71	78	76					6																	138202395		2202	4299	6501	SO:0001583	missense	7128	exon9			ATTTTGGCAATGC	M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"OTU domain containing"	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.2312G>A	6.37:g.138202395G>A	ENSP00000237289:p.Gly771Asp	146	0	0		116	37	0.318966	NM_001270507	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Missense_Mutation	SNP	ENST00000237289.4	37	CCDS5187.1	.	.	.	.	.	.	.	.	.	.	G	25.9	4.684692	0.88639	.	.	ENSG00000118503	ENST00000237289	T	0.69175	-0.38	5.66	5.66	0.87406	Zinc finger, A20-type (3);	0.050625	0.85682	D	0.000000	T	0.76751	0.4031	M	0.61703	1.905	0.54753	D	0.999986	D	0.89917	1.0	D	0.79784	0.993	T	0.77370	-0.2613	10	0.59425	D	0.04	-15.7251	17.9235	0.88975	0.0:0.0:1.0:0.0	.	771	P21580	TNAP3_HUMAN	D	771	ENSP00000237289:G771D	ENSP00000237289:G771D	G	+	2	0	TNFAIP3	138244088	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.625000	0.74248	2.668000	0.90789	0.557000	0.71058	GGC	.	.	none		0.617	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1			A	138202395	G	A	138202395	3	1	42	1	0	0	0	0	1	0	0	0	16289	1203	42	2	2342	2	TNFAIP3	6	138202395	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	2076	138202395	32912672	142	15094											
ACTB	60	hgsc.bcm.edu	37	chr7	5568300	5568300	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggcgtacagggatagcacAgcctggatagcaacgtacat	13	6	13	9	2	0	0	0	0	0	0	0	3	0	2	1	3	6	4	1	3	5	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr7:5568300A>T	ENST00000331789.5	-	4	605	c.414T>A	c.(412-414)gcT>gcA	p.A138A	AC006483.1_ENST00000579427.1_RNA|ACTB_ENST00000464611.1_5'Flank	NM_001101.3	NP_001092.1	P63261	ACTG_HUMAN	actin, beta	138					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)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(2)	8		Ovarian(82;0.0606)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)|OV - Ovarian serous cystadenocarcinoma(56;4.24e-37)		GGGATAGCACAGCCTGGATAG	0.577																																					p.A138A		Atlas-SNP	.											.	ACTB	45	.	0			c.T414A						PASS	.						106	107	107					7																	5568300		2203	4300	6503	SO:0001819	synonymous_variant	60	exon4			TAGCACAGCCTGG	M28424	CCDS5341.1	7p22	2014-09-17			ENSG00000075624	ENSG00000075624			132	protein-coding gene	gene with protein product		102630				1505215	Standard	NM_001101		Approved		uc003sot.4	P60709	OTTHUMG00000023268	ENST00000331789.5:c.414T>A	7.37:g.5568300A>T		101	0	0		69	18	0.26087	NM_001101	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Silent	SNP	ENST00000331789.5	37	CCDS5341.1																																																																																			.	.	none		0.577	ACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059589.4	NM_001101		T	5568300	A	T	5568300	2	4	42	1	0	0	0	0	0	0	0	1	193	175	7	5		5	ACTB	7	5568300	Silent	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10		5568300	153570363	143	15095			1	70		3	3	952	N	C_A	7.149037e-05
ACTB	60	hgsc.bcm.edu	37	chr7	5568897	5568897	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tcattgtagaaggtgtggtgCcagattttctccatgtcgtc	7	15	11	8	1	2	2	1	0	1	2	5	2	2	2	2	2	1	1	2	2	2	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr7:5568897C>G	ENST00000331789.5	-	3	449	c.258G>C	c.(256-258)tgG>tgC	p.W86C	AC006483.1_ENST00000579427.1_RNA|ACTB_ENST00000464611.1_5'Flank	NM_001101.3	NP_001092.1	P63261	ACTG_HUMAN	actin, beta	86					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)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(2)	8		Ovarian(82;0.0606)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)|OV - Ovarian serous cystadenocarcinoma(56;4.24e-37)		AGGTGTGGTGCCAGATTTTCT	0.612																																					p.W86C		Atlas-SNP	.											.	ACTB	45	.	0			c.G258C						PASS	.						66	65	66					7																	5568897		2203	4300	6503	SO:0001583	missense	60	exon3			GTGGTGCCAGATT	M28424	CCDS5341.1	7p22	2014-09-17			ENSG00000075624	ENSG00000075624			132	protein-coding gene	gene with protein product		102630				1505215	Standard	NM_001101		Approved		uc003sot.4	P60709	OTTHUMG00000023268	ENST00000331789.5:c.258G>C	7.37:g.5568897C>G	ENSP00000349960:p.Trp86Cys	86	0	0		72	16	0.222222	NM_001101	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000331789.5	37	CCDS5341.1	.	.	.	.	.	.	.	.	.	.	C	14.80	2.643886	0.47258	.	.	ENSG00000075624	ENST00000331789;ENST00000445914;ENST00000400179;ENST00000320713;ENST00000432588;ENST00000443528;ENST00000417101	D;D;D;D	0.96522	-4.04;-4.04;-4.04;-4.04	5.01	5.01	0.66863	.	0.316889	0.27375	N	0.019646	D	0.99105	0.9692	H	0.99726	4.73	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98789	1.0735	10	0.87932	D	0	.	15.8267	0.78711	0.0:1.0:0.0:0.0	.	86	P60709	ACTB_HUMAN	C	86;86;58;5;86;86;89	ENSP00000349960:W86C;ENSP00000407473:W86C;ENSP00000393951:W86C;ENSP00000399487:W89C	ENSP00000440549:W5C	W	-	3	0	ACTB	5535423	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.868000	0.69605	2.312000	0.78011	0.563000	0.77884	TGG	.	.	none		0.612	ACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059589.4	NM_001101		G	5568897	C	G	5568897	3	3	42	1	0	0	0	0	1	0	0	0	193	740	26	4	885	4	ACTB	7	5568897	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	597	5568897	153569766	144	15096			1	70		3	3	952	N	C_A	7.149037e-05
ACTB	60	hgsc.bcm.edu	37	chr7	5569251	5569251	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cggccttgcacatgccggagCcgttgtcgacgacgagcgcg	6	6	15	14	8	0	0	0	0	0	0	1	4	0	1	3	2	4	2	3	2	0	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr7:5569251C>G	ENST00000331789.5	-	2	229	c.38G>C	c.(37-39)gGc>gCc	p.G13A	AC006483.1_ENST00000579427.1_RNA|ACTB_ENST00000464611.1_5'Flank	NM_001101.3	NP_001092.1	P63261	ACTG_HUMAN	actin, beta	13					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)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(2)	8		Ovarian(82;0.0606)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)|OV - Ovarian serous cystadenocarcinoma(56;4.24e-37)		CATGCCGGAGCCGTTGTCGAC	0.706																																					p.G13A		Atlas-SNP	.											.	ACTB	45	.	0			c.G38C						PASS	.						19	22	21					7																	5569251		2164	4231	6395	SO:0001583	missense	60	exon2			CCGGAGCCGTTGT	M28424	CCDS5341.1	7p22	2014-09-17			ENSG00000075624	ENSG00000075624			132	protein-coding gene	gene with protein product		102630				1505215	Standard	NM_001101		Approved		uc003sot.4	P60709	OTTHUMG00000023268	ENST00000331789.5:c.38G>C	7.37:g.5569251C>G	ENSP00000349960:p.Gly13Ala	64	0	0		56	7	0.125	NM_001101	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000331789.5	37	CCDS5341.1	.	.	.	.	.	.	.	.	.	.	C	18.56	3.650746	0.67472	.	.	ENSG00000075624	ENST00000331789;ENST00000445914;ENST00000400179;ENST00000432588;ENST00000443528;ENST00000417101;ENST00000414620	D;D;D;D;D	0.99905	-7.72;-7.72;-6.54;-6.54;-6.54	4.69	3.79	0.43588	.	0.000000	0.64402	D	0.000008	D	0.99928	0.9967	H	0.98388	4.22	0.45205	D	0.998217	P	0.48503	0.911	P	0.61477	0.889	D	0.95933	0.8940	10	0.87932	D	0	.	11.9093	0.52729	0.1757:0.8243:0.0:0.0	.	13	P60709	ACTB_HUMAN	A	13;13;13;13;13;16;13	ENSP00000349960:G13A;ENSP00000407473:G13A;ENSP00000393951:G13A;ENSP00000399487:G16A;ENSP00000401032:G13A	ENSP00000349960:G13A	G	-	2	0	ACTB	5535777	1.000000	0.71417	1.000000	0.80357	0.696000	0.40369	5.726000	0.68515	0.945000	0.37605	0.557000	0.71058	GGC	.	.	none		0.706	ACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059589.4	NM_001101		G	5569251	C	G	5569251	3	3	42	1	0	0	0	0	1	0	0	0	193	739	26	4	1109	4	ACTB	7	5569251	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	354	5569251	153569412	145	15097			1	70		3	3	952	N	C_A	7.149037e-05
HDAC9	9734	hgsc.bcm.edu	37	chr7	18674253	18674253	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ttcacaatatttttcagaatCctcagtcagtagcagttctc	11	15	5	10	0	5	1	4	0	1	1	7	1	6	1	1	0	1	3	1	0	4	6			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr7:18674253C>T	ENST00000432645.2	+	7	791	c.791C>T	c.(790-792)tCc>tTc	p.S264F	HDAC9_ENST00000405010.3_Missense_Mutation_p.S264F|HDAC9_ENST00000406072.1_Missense_Mutation_p.S251F|HDAC9_ENST00000441542.2_Missense_Mutation_p.S267F|HDAC9_ENST00000456174.2_Missense_Mutation_p.S236F|HDAC9_ENST00000401921.1_Missense_Mutation_p.S223F|HDAC9_ENST00000406451.4_Missense_Mutation_p.S264F|HDAC9_ENST00000524023.1_Missense_Mutation_p.S187F|HDAC9_ENST00000417496.2_Missense_Mutation_p.S262F|HDAC9_ENST00000428307.2_Missense_Mutation_p.S220F	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	264	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)	TTTTCAGAATCCTCAGTCAGT	0.418																																					p.S267F		Atlas-SNP	.											.	HDAC9	560	.	0			c.C800T						PASS	.						75	70	71					7																	18674253		1872	4103	5975	SO:0001583	missense	9734	exon7			CAGAATCCTCAGT	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.791C>T	7.37:g.18674253C>T	ENSP00000410337:p.Ser264Phe	172	0	0		116	33	0.284483	NM_178425	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Missense_Mutation	SNP	ENST00000432645.2	37	CCDS47555.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.712624	0.89112	.	.	ENSG00000048052	ENST00000417496;ENST00000262069;ENST00000405010;ENST00000406451;ENST00000428307;ENST00000406072;ENST00000401921;ENST00000432645;ENST00000441542;ENST00000456174;ENST00000524023;ENST00000341009	T;T;T;T;T;T;T;T;T;T	0.68765	0.17;0.55;0.04;0.21;0.18;-0.35;0.04;0.04;0.55;0.22	5.51	5.51	0.81932	.	0.112732	0.40302	N	0.001132	D	0.82375	0.5023	M	0.82323	2.585	0.80722	D	1	D;D;D;P;D;D;P;D;D;D;P;D;D;D	0.71674	0.971;0.989;0.982;0.948;0.971;0.99;0.94;0.99;0.983;0.998;0.94;0.983;0.993;0.97	B;P;P;B;P;D;P;P;P;D;P;P;P;P	0.63488	0.446;0.768;0.875;0.446;0.548;0.912;0.641;0.875;0.735;0.915;0.641;0.735;0.884;0.754	D	0.84982	0.0889	10	0.87932	D	0	-29.5288	17.5956	0.88011	0.0:1.0:0.0:0.0	.	187;236;264;251;262;264;267;223;267;264;236;264;264;242	E7EX34;C9JS87;Q9UKV0-4;B5MCF1;B7Z917;Q9UKV0-2;Q68D71;Q9UKV0-6;Q9UKV0-7;Q9UKV0;B7Z928;Q9UKV0-5;Q9UKV0-3;Q8N879	.;.;.;.;.;.;.;.;.;HDAC9_HUMAN;.;.;.;.	F	262;265;264;264;220;251;223;264;267;236;187;264	ENSP00000401669:S262F;ENSP00000384382:S264F;ENSP00000384657:S264F;ENSP00000395655:S220F;ENSP00000384017:S251F;ENSP00000383912:S223F;ENSP00000410337:S264F;ENSP00000408617:S267F;ENSP00000388568:S236F;ENSP00000430036:S187F	ENSP00000262069:S265F	S	+	2	0	HDAC9	18640778	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.790000	0.75115	2.600000	0.87896	0.650000	0.86243	TCC	.	.	none		0.418	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1			T	18674253	C	T	18674253	3	4	42	1	0	0	0	0	1	0	0	0	7023	855	30	2	826	2	HDAC9	7	18674253	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	13105002	18674253	140464410	146	15098											
MACC1	346389	hgsc.bcm.edu	37	chr7	20199461	20199461	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agccattttataagcctcccGatcatttttaagccactcta	11	14	4	12	1	2	0	1	0	1	0	3	1	3	0	4	0	3	0	4	0	4	7	rs200826339	byFrequency	TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr7:20199461G>A	ENST00000400331.5	-	5	831	c.523C>T	c.(523-525)Cgg>Tgg	p.R175W	MACC1_ENST00000332878.4_Missense_Mutation_p.R175W|MACC1_ENST00000589011.1_Missense_Mutation_p.R175W	NM_182762.3	NP_877439.3	Q6ZN28	MACC1_HUMAN	metastasis associated in colon cancer 1	175					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						TAAGCCTCCCGATCATTTTTA	0.468													G|||	3	0.000599042	0.0	0.0043	5008	,	,		18694	0.0		0.0	False		,,,				2504	0.0				p.R175W		Atlas-SNP	.											MACC1,bladder,carcinoma,+2,1	MACC1	99	1	0			c.C523T						PASS	.						74	71	72					7																	20199461		2203	4300	6503	SO:0001583	missense	346389	exon5			CCTCCCGATCATT		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.523C>T	7.37:g.20199461G>A	ENSP00000383185:p.Arg175Trp	143	0	0		105	9	0.0857143	NM_182762	A8MUS5|B2RNR9|Q6ZQN8|Q7Z5A5	Missense_Mutation	SNP	ENST00000400331.5	37	CCDS5369.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	15.92	2.974997	0.53720	.	.	ENSG00000183742	ENST00000400331;ENST00000332878	T;T	0.25749	1.78;1.78	5.64	4.75	0.60458	.	0.000000	0.85682	D	0.000000	T	0.52240	0.1722	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.58584	-0.7611	10	0.87932	D	0	-14.655	15.8848	0.79238	0.0:0.0:0.8633:0.1367	.	175	Q6ZN28	MACC1_HUMAN	W	175	ENSP00000383185:R175W;ENSP00000328410:R175W	ENSP00000328410:R175W	R	-	1	2	MACC1	20165986	1.000000	0.71417	0.909000	0.35828	0.882000	0.50991	2.367000	0.44213	1.349000	0.45751	0.585000	0.79938	CGG	A|0.000;G|0.999;T|0.000	0.000	strong		0.468	MACC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250202.5	NM_182762		A	20199461	G	A	20199461	3	1	42	1	0	0	0	0	1	0	0	0	9152	1057	37	1	2047	1	MACC1	7	20199461	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	1525208	20199461	138939202	147	15099											
CCDC129	223075	hgsc.bcm.edu	37	chr7	31614238	31614238	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggtgctgatgagccagacatCtgcatgcaaatcccagccag	11	7	11	12	0	1	3	0	2	1	1	2	3	2	3	3	1	5	3	3	1	1	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr7:31614238C>T	ENST00000407970.3	+	7	518	c.480C>T	c.(478-480)atC>atT	p.I160I	CCDC129_ENST00000409210.1_Silent_p.I68I|CCDC129_ENST00000319386.3_Silent_p.I160I|CCDC129_ENST00000451887.2_Silent_p.I186I	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	160										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						AGCCAGACATCTGCATGCAAA	0.463																																					p.I186I		Atlas-SNP	.											.	CCDC129	127	.	0			c.C558T						PASS	.						130	136	134					7																	31614238		2203	4300	6503	SO:0001819	synonymous_variant	223075	exon7			AGACATCTGCATG	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.480C>T	7.37:g.31614238C>T		131	0	0		120	38	0.316667	NM_001257968	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Silent	SNP	ENST00000407970.3	37	CCDS5435.2																																																																																			.	.	none		0.463	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300		T	31614238	C	T	31614238	2	4	42	1	0	0	0	0	0	0	0	1	2766	903	32	2		2	CCDC129	7	31614238	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	11414777	31614238	127524425	148	15100											
FKBP9	11328	hgsc.bcm.edu	37	chr7	33044805	33044805	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agttctcagagtacattcacGcccaggtggcatctggcaaa	11	9	10	11	1	3	1	2	0	2	1	4	1	3	1	1	3	1	4	1	3	2	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr7:33044805G>A	ENST00000242209.4	+	10	1724	c.1555G>A	c.(1555-1557)Gcc>Acc	p.A519T	FKBP9_ENST00000538443.1_Missense_Mutation_p.A381T|FKBP9_ENST00000490776.2_Missense_Mutation_p.A287T|AVL9_ENST00000404479.1_Intron|FKBP9_ENST00000538336.1_Missense_Mutation_p.A572T	NM_001284343.1|NM_007270.3	NP_001271272.1|NP_009201.2	O95302	FKBP9_HUMAN	FK506 binding protein 9, 63 kDa	519	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				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)	p.A519T(2)|p.A287T(2)		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)			GTACATTCACGCCCAGGTGGC	0.537																																					p.A519T		Atlas-SNP	.											FKBP9_ENST00000490776,NS,carcinoma,0,4	FKBP9	335	4	4	Substitution - Missense(4)	lung(2)|endometrium(2)	c.G1555A						PASS	.						46	45	45					7																	33044805		2203	4297	6500	SO:0001583	missense	11328	exon10			ATTCACGCCCAGG	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.1555G>A	7.37:g.33044805G>A	ENSP00000242209:p.Ala519Thr	141	0	0		94	21	0.223404	NM_007270	B3KY35|B7Z1G9|B7Z6H3|Q2M2A1|Q3MIR7|Q6IN76|Q6P2N1|Q96EX5|Q96IJ9	Missense_Mutation	SNP	ENST00000242209.4	37	CCDS5439.1	.	.	.	.	.	.	.	.	.	.	G	13.35	2.210625	0.39102	.	.	ENSG00000122642	ENST00000242209;ENST00000538336;ENST00000538443;ENST00000490776	T;T;T;T	0.55234	0.53;0.53;0.53;2.25	5.07	5.07	0.68467	EF-hand-like domain (1);	0.271361	0.37348	N	0.002127	T	0.39410	0.1077	L	0.29908	0.895	0.32052	N	0.596862	B;B;B	0.26400	0.004;0.148;0.051	B;B;B	0.14578	0.001;0.011;0.006	T	0.46884	-0.9159	10	0.32370	T	0.25	-10.8601	13.7806	0.63081	0.0761:0.0:0.9239:0.0	.	287;572;519	B7Z1G9;B7Z6H3;O95302	.;.;FKBP9_HUMAN	T	519;572;381;287	ENSP00000242209:A519T;ENSP00000439250:A572T;ENSP00000437504:A381T;ENSP00000441317:A287T	ENSP00000242209:A519T	A	+	1	0	FKBP9	33011330	0.934000	0.31675	0.976000	0.42696	0.969000	0.65631	3.364000	0.52328	2.371000	0.80710	0.555000	0.69702	GCC	.	.	none		0.537	FKBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215137.1	NM_007270		A	33044805	G	A	33044805	3	1	42	1	0	0	0	0	1	0	0	0	5923	1087	38	1	1593	1	FKBP9	7	33044805	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	1430567	33044805	126093858	149	15101											
ABCA13	154664	hgsc.bcm.edu	37	chr7	48312478	48312478	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaacagctgctcataattgAtgaagattttcgtatttctt	12	16	6	7	1	2	3	1	2	1	1	3	3	2	3	0	0	3	3	0	0	4	7			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr7:48312478A>T	ENST00000435803.1	+	17	3239	c.3215A>T	c.(3214-3216)gAt>gTt	p.D1072V		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1072					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						CTCATAATTGATGAAGATTTT	0.378																																					p.D1072V		Atlas-SNP	.											.	ABCA13	1192	.	0			c.A3215T						PASS	.						37	34	35					7																	48312478		1822	4083	5905	SO:0001583	missense	154664	exon17			TAATTGATGAAGA	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.3215A>T	7.37:g.48312478A>T	ENSP00000411096:p.Asp1072Val	186	0	0		148	43	0.290541	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	A	13.55	2.271306	0.40194	.	.	ENSG00000179869	ENST00000435803	D	0.89810	-2.57	5.7	5.7	0.88788	.	0.124747	0.36200	N	0.002738	D	0.92466	0.7608	M	0.64997	1.995	0.29721	N	0.838639	D	0.76494	0.999	D	0.68765	0.96	D	0.89650	0.3869	10	0.87932	D	0	.	11.3534	0.49602	0.8491:0.1509:0.0:0.0	.	1072	Q86UQ4	ABCAD_HUMAN	V	1072	ENSP00000411096:D1072V	ENSP00000411096:D1072V	D	+	2	0	ABCA13	48283024	0.926000	0.31397	0.068000	0.19968	0.512000	0.34134	3.568000	0.53820	2.297000	0.77311	0.533000	0.62120	GAT	.	.	none		0.378	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701		T	48312478	A	T	48312478	3	4	42	1	0	0	0	0	1	0	0	0	31	333	12	5	3110	5	ABCA13	7	48312478	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	15267673	48312478	110826185	150	15102											
CASD1	64921	hgsc.bcm.edu	37	chr7	94173774	94173774	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tggttgctgcatatttatttCagacagggtatgggcatttc	8	16	11	6	0	1	1	1	0	0	1	2	1	1	1	0	3	2	5	0	3	3	7			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr7:94173774C>T	ENST00000297273.4	+	11	1695	c.1408C>T	c.(1408-1410)Cag>Tag	p.Q470*		NM_022900.4	NP_075051.4	Q96PB1	CASD1_HUMAN	CAS1 domain containing 1	470						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)			ATATTTATTTCAGACAGGGTA	0.368																																					p.Q470X		Atlas-SNP	.											.	CASD1	70	.	0			c.C1408T						PASS	.						152	143	146					7																	94173774		2203	4298	6501	SO:0001587	stop_gained	64921	exon11			TTATTTCAGACAG	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.1408C>T	7.37:g.94173774C>T	ENSP00000297273:p.Gln470*	384	0	0		313	81	0.258786	NM_022900	B3KW13|O14574|Q3LIE2|Q6P4R4|Q9H6T9|Q9H770	Nonsense_Mutation	SNP	ENST00000297273.4	37	CCDS5636.1	.	.	.	.	.	.	.	.	.	.	C	38	6.872998	0.97901	.	.	ENSG00000127995	ENST00000297273	.	.	.	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	18.1737	0.89754	0.0:1.0:0.0:0.0	.	.	.	.	X	470	.	ENSP00000297273:Q470X	Q	+	1	0	CASD1	94011710	1.000000	0.71417	1.000000	0.80357	0.419000	0.31324	7.782000	0.85680	2.377000	0.81083	0.455000	0.32223	CAG	.	.	none		0.368	CASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255216.1	NM_022900		T	94173774	C	T	94173774	4	4	42	1	0	0	0	0	0	1	0	0	2666	827	29	2	1450	2	CASD1	7	94173774	Nonsense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	45861296	94173774	64964889	151	15103											
SLC25A13	10165	hgsc.bcm.edu	37	chr7	95864216	95864216	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttcaaaggcaacaaattcttGaaaagatattaatctgcaac	18	11	5	7	0	3	2	1	1	2	1	3	2	3	2	0	1	3	2	0	1	8	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr7:95864216G>A	ENST00000265631.5	-	4	362	c.226C>T	c.(226-228)Caa>Taa	p.Q76*	SLC25A13_ENST00000416240.2_Nonsense_Mutation_p.Q76*|SLC25A13_ENST00000542654.1_Intron			Q9UJS0	CMC2_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 13	76	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				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)	ACAAATTCTTGAAAAGATATT	0.363																																					p.Q76X		Atlas-SNP	.											.	SLC25A13	131	.	0			c.C226T						PASS	.						74	70	71					7																	95864216		2203	4300	6503	SO:0001587	stop_gained	10165	exon4			ATTCTTGAAAAGA	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.226C>T	7.37:g.95864216G>A	ENSP00000265631:p.Gln76*	55	0	0		52	15	0.288462	NM_001160210	O14566|O14575|Q546F9|Q9NZW1|Q9UNI7	Nonsense_Mutation	SNP	ENST00000265631.5	37	CCDS5645.1	.	.	.	.	.	.	.	.	.	.	G	37	6.087648	0.97271	.	.	ENSG00000004864	ENST00000265631;ENST00000416240	.	.	.	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10636	T	0.68	-11.302	19.1939	0.93679	0.0:0.0:1.0:0.0	.	.	.	.	X	76	.	ENSP00000265631:Q76X	Q	-	1	0	SLC25A13	95702152	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	9.657000	0.98554	2.846000	0.97976	0.650000	0.86243	CAA	.	.	none		0.363	SLC25A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059395.2	NM_014251		A	95864216	G	A	95864216	4	1	42	1	0	0	0	0	0	1	0	0	14490	1299	45	2	1864	2	SLC25A13	7	95864216	Nonsense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	1690442	95864216	63274447	152	15104											
MEPCE	56257	hgsc.bcm.edu	37	chr7	100028402	100028402	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gggccatgtagttcttgcttCgccactcaagactggtcgga	7	11	12	11	2	2	1	1	0	1	1	4	2	2	2	2	3	1	3	2	3	2	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr7:100028402C>T	ENST00000310512.2	+	1	1149	c.761C>T	c.(760-762)tCg>tTg	p.S254L	ZCWPW1_ENST00000360951.4_5'Flank|ZCWPW1_ENST00000324725.6_5'Flank|MEPCE_ENST00000414441.1_5'UTR|ZCWPW1_ENST00000398027.2_5'Flank	NM_019606.5	NP_062552.2	Q7L2J0	MEPCE_HUMAN	methylphosphate capping enzyme	254					negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|RNA methylation (GO:0001510)|snRNA metabolic process (GO:0016073)|snRNA modification (GO:0040031)		poly(A) RNA binding (GO:0044822)|RNA methyltransferase activity (GO:0008173)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(2)|lung(9)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	24	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GTTCTTGCTTCGCCACTCAAG	0.592																																					p.S254L		Atlas-SNP	.											.	MEPCE	52	.	0			c.C761T						PASS	.						129	141	137					7																	100028402		2203	4300	6503	SO:0001583	missense	56257	exon1			TTGCTTCGCCACT	AF264752	CCDS5693.1, CCDS55136.1	7q22.1	2008-02-04	2007-07-26	2007-07-26	ENSG00000146834	ENSG00000146834			20247	protein-coding gene	gene with protein product		611478	"bin3, bicoid-interacting 3, homolog (Drosophila)"	BCDIN3		12358911, 17643375	Standard	NM_019606		Approved	FLJ20257, MePCE	uc003uuw.3	Q7L2J0	OTTHUMG00000155255	ENST00000310512.2:c.761C>T	7.37:g.100028402C>T	ENSP00000308546:p.Ser254Leu	48	0	0		32	8	0.25	NM_019606	B3KP86|D6W5V7|Q9NPD4	Missense_Mutation	SNP	ENST00000310512.2	37	CCDS5693.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.458824	0.84317	.	.	ENSG00000146834	ENST00000310512	.	.	.	4.17	4.17	0.49024	.	0.000000	0.64402	D	0.000001	T	0.69342	0.3100	L	0.49126	1.545	0.58432	D	0.999998	D	0.89917	1.0	D	0.78314	0.991	T	0.71679	-0.4520	9	0.56958	D	0.05	-2.8836	14.0318	0.64619	0.0:1.0:0.0:0.0	.	254	Q7L2J0	MEPCE_HUMAN	L	254	.	ENSP00000308546:S254L	S	+	2	0	MEPCE	99866338	1.000000	0.71417	0.987000	0.45799	0.987000	0.75469	6.607000	0.74163	2.164000	0.68074	0.313000	0.20887	TCG	.	.	none		0.592	MEPCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339135.1			T	100028402	C	T	100028402	3	4	42	1	0	0	0	0	1	0	0	0	9486	893	31	1	763	1	MEPCE	7	100028402	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	4164186	100028402	59110261	153	15105											
LRWD1	222229	hgsc.bcm.edu	37	chr7	102113388	102113388	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ccccagccctgggcccttggCcaggtggtgaccaagaccat	7	6	12	16	0	0	2	0	1	0	1	0	2	0	2	7	4	1	0	7	4	1	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr7:102113388C>A	ENST00000292616.5	+	15	1988	c.1836C>A	c.(1834-1836)ggC>ggA	p.G612G	MIR4467_ENST00000578629.1_RNA	NM_152892.1	NP_690852.1	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain containing 1	612					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						GGGCCCTTGGCCAGGTGGTGA	0.642																																					p.G612G		Atlas-SNP	.											.	LRWD1	41	.	0			c.C1836A						PASS	.						79	70	73					7																	102113388		2203	4300	6503	SO:0001819	synonymous_variant	222229	exon15			CCTTGGCCAGGTG	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.1836C>A	7.37:g.102113388C>A		41	0	0		66	20	0.30303	NM_152892	A8K4K2|B2R9G2|Q8N0T9|Q8WV43|Q96GJ2	Silent	SNP	ENST00000292616.5	37	CCDS34715.1	.	.	.	.	.	.	.	.	.	.	C	1.736	-0.493029	0.04322	.	.	ENSG00000161036	ENST00000468175	.	.	.	5.41	0.334	0.15948	.	.	.	.	.	T	0.39009	0.1062	.	.	.	0.23221	N	0.998094	.	.	.	.	.	.	T	0.33111	-0.9881	4	.	.	.	-17.3779	12.6444	0.56725	0.0:0.3065:0.6198:0.0737	.	.	.	.	D	207	.	.	A	+	2	0	LRWD1	101900393	0.697000	0.27767	0.046000	0.18839	0.325000	0.28411	-0.137000	0.10389	-0.100000	0.12241	0.561000	0.74099	GCC	.	.	none		0.642	LRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349493.1	NM_152892		A	102113388	C	A	102113388	2	1	42	1	0	0	0	0	0	0	0	1	9056	726	26	4		4	LRWD1	7	102113388	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	2084986	102113388	57025275	154	15106											
SLC26A4	5172	hgsc.bcm.edu	37	chr7	107330631	107330631	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctcttgttttgtggccacCactgctctttcccgcacggc	3	15	8	15	2	2	0	0	0	2	0	4	0	3	0	3	2	1	3	3	2	0	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr7:107330631C>A	ENST00000265715.3	+	10	1436	c.1212C>A	c.(1210-1212)acC>acA	p.T404T	SLC26A4_ENST00000541474.1_5'Flank|SLC26A4_ENST00000544569.1_5'Flank	NM_000441.1	NP_000432.1	O43511	S26A4_HUMAN	solute carrier family 26 (anion exchanger), member 4	404					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						TTGTGGCCACCACTGCTCTTT	0.478									Pendred syndrome																												p.T404T		Atlas-SNP	.											.	SLC26A4	117	.	0			c.C1212A						PASS	.						165	149	155					7																	107330631		2203	4300	6503	SO:0001819	synonymous_variant	5172	exon10	Familial Cancer Database	Goiter-Deafness syndrome	GGCCACCACTGCT	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.1212C>A	7.37:g.107330631C>A		258	0	0		244	22	0.0901639	NM_000441	B7Z266|O43170	Silent	SNP	ENST00000265715.3	37	CCDS5746.1																																																																																			.	.	none		0.478	SLC26A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337148.1	NM_000441		A	107330631	C	A	107330631	2	1	42	1	0	0	0	0	0	0	0	1	14534	581	21	4		4	SLC26A4	7	107330631	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	5217243	107330631	51808032	155	15107											
LRRN3	54674	hgsc.bcm.edu	37	chr7	110763595	110763595	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taaagtaccccatgttgctcTtcaaaaagttgtaaatctca	14	13	5	9	0	3	0	2	0	2	0	4	0	3	0	2	0	2	5	2	0	7	6			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr7:110763595T>C	ENST00000422987.3	+	2	1598	c.767T>C	c.(766-768)cTt>cCt	p.L256P	LRRN3_ENST00000308478.5_Missense_Mutation_p.L256P|IMMP2L_ENST00000489381.1_Intron|IMMP2L_ENST00000405709.2_Intron|IMMP2L_ENST00000437687.1_Intron|IMMP2L_ENST00000415362.1_Intron|IMMP2L_ENST00000450877.1_Intron|IMMP2L_ENST00000452895.1_Intron|IMMP2L_ENST00000447215.1_Intron|IMMP2L_ENST00000331762.3_Intron|LRRN3_ENST00000451085.1_Missense_Mutation_p.L256P	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	256					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)		CATGTTGCTCTTCAAAAAGTT	0.333																																					p.L256P		Atlas-SNP	.											.	LRRN3	132	.	0			c.T767C						PASS	.						44	49	47					7																	110763595		2203	4295	6498	SO:0001583	missense	54674	exon2			TTGCTCTTCAAAA	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.767T>C	7.37:g.110763595T>C	ENSP00000412417:p.Leu256Pro	207	0	0		148	38	0.256757	NM_018334	O43377|Q6I9V8|Q8IYQ6	Missense_Mutation	SNP	ENST00000422987.3	37	CCDS5754.1	.	.	.	.	.	.	.	.	.	.	T	16.81	3.227203	0.58668	.	.	ENSG00000173114	ENST00000308478;ENST00000451085;ENST00000422987;ENST00000421101	T;T;T;T	0.62639	0.01;0.01;0.01;0.01	5.87	5.87	0.94306	.	0.000000	0.52532	D	0.000069	D	0.85927	0.5811	H	0.96301	3.8	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90388	0.4393	10	0.87932	D	0	.	16.2662	0.82581	0.0:0.0:0.0:1.0	.	256	Q9H3W5	LRRN3_HUMAN	P	256	ENSP00000312001:L256P;ENSP00000397312:L256P;ENSP00000412417:L256P;ENSP00000407927:L256P	ENSP00000312001:L256P	L	+	2	0	LRRN3	110550831	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.040000	0.89188	2.247000	0.74100	0.528000	0.53228	CTT	.	.	none		0.333	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334		C	110763595	T	C	110763595	3	2	42	1	0	0	0	0	1	0	0	0	9045	1609	56	3	769	3	LRRN3	7	110763595	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	3432964	110763595	48375068	156	15108											
LRRN3	54674	hgsc.bcm.edu	37	chr7	110764124	110764124	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gagagctttccttctaatctAaatgtagaagctgggagcta	12	12	10	7	0	2	2	0	0	2	2	3	4	3	3	1	1	3	4	1	1	6	6			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr7:110764124A>G	ENST00000422987.3	+	2	2127	c.1296A>G	c.(1294-1296)ctA>ctG	p.L432L	LRRN3_ENST00000308478.5_Silent_p.L432L|IMMP2L_ENST00000489381.1_Intron|IMMP2L_ENST00000405709.2_Intron|IMMP2L_ENST00000437687.1_Intron|IMMP2L_ENST00000415362.1_Intron|IMMP2L_ENST00000450877.1_Intron|IMMP2L_ENST00000452895.1_Intron|IMMP2L_ENST00000447215.1_Intron|IMMP2L_ENST00000331762.3_Intron|LRRN3_ENST00000451085.1_Silent_p.L432L	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	432	Ig-like C2-type.				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)		CTTCTAATCTAAATGTAGAAG	0.438																																					p.L432L		Atlas-SNP	.											LRRN3,caecum,carcinoma,+2,2	LRRN3	132	2	0			c.A1296G						PASS	.						111	118	115					7																	110764124		2203	4300	6503	SO:0001819	synonymous_variant	54674	exon2			TAATCTAAATGTA	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.1296A>G	7.37:g.110764124A>G		56	0	0		54	13	0.240741	NM_018334	O43377|Q6I9V8|Q8IYQ6	Silent	SNP	ENST00000422987.3	37	CCDS5754.1																																																																																			.	.	none		0.438	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334		G	110764124	A	G	110764124	2	3	42	1	0	0	0	0	0	0	0	1	9045	349	13	3		3	LRRN3	7	110764124	Silent	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	529	110764124	48374539	157	15109											
NAA38	84316	hgsc.bcm.edu	37	chr7	117832025	117832025	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcttgatttggggaatattcGagcagaacctttaaattctg	11	14	10	6	1	1	2	0	1	1	1	2	4	1	3	1	2	2	2	1	2	5	7			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr7:117832025G>A	ENST00000249299.2	+	4	452	c.260G>A	c.(259-261)cGa>cAa	p.R87Q	NAA38_ENST00000424702.1_3'UTR|NAA38_ENST00000422760.1_Missense_Mutation_p.R66Q	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						GGGAATATTCGAGCAGAACCT	0.343																																					p.R87Q		Atlas-SNP	.											NAA38,NS,carcinoma,+1,1	NAA38	16	1	0			c.G260A						scavenged	.						96	99	98					7																	117832025		2203	4299	6502	SO:0001583	missense	51691	exon4			ATATTCGAGCAGA		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.260G>A	7.37:g.117832025G>A	ENSP00000249299:p.Arg87Gln	141	1	0.0070922		119	31	0.260504	NM_016200	Q8N4M0	Missense_Mutation	SNP	ENST00000249299.2	37	CCDS5775.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.575046	0.86542	.	.	ENSG00000128534	ENST00000249299;ENST00000422760	.	.	.	5.76	4.88	0.63580	.	0.000000	0.85682	D	0.000000	T	0.55433	0.1920	.	.	.	0.80722	D	1	P	0.51653	0.947	B	0.42771	0.397	T	0.60835	-0.7184	8	0.56958	D	0.05	-10.2314	14.6387	0.68708	0.0697:0.0:0.9303:0.0	.	87	O95777	NAA38_HUMAN	Q	87;66	.	ENSP00000249299:R87Q	R	+	2	0	NAA38	117619261	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	8.868000	0.92320	1.444000	0.47605	0.655000	0.94253	CGA	.	.	none		0.343	NAA38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346774.2	NM_032356		A	117832025	G	A	117832025	3	1	42	1	0	0	0	0	1	0	0	0	10133	1058	37	1	274	1	NAA38	7	117832025	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	7067901	117832025	41306638	158	15110											
FAM40B	57464	hgsc.bcm.edu	37	chr7	129104487	129104487	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agagcatgaagctgggcatcGatgtgaacaggcacaaggag	14	5	15	7	1	0	3	0	2	0	1	1	5	0	4	0	3	3	4	0	3	3	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr7:129104487G>A	ENST00000249344.2	+	16	1724	c.1684G>A	c.(1684-1686)Gat>Aat	p.D562N	STRIP2_ENST00000435494.2_Missense_Mutation_p.D562N	NM_020704.2	NP_065755.1	Q9ULQ0	STRP2_HUMAN	striatin interacting protein 2	562					cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)											GCTGGGCATCGATGTGAACAG	0.483																																					p.D562N		Atlas-SNP	.											.	.	.	.	0			c.G1684A						PASS	.						155	145	149					7																	129104487		2203	4300	6503	SO:0001583	missense	57464	exon16			GGCATCGATGTGA	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.1684G>A	7.37:g.129104487G>A	ENSP00000249344:p.Asp562Asn	81	0	0		93	27	0.290323	NM_020704	Q8WUZ4	Missense_Mutation	SNP	ENST00000249344.2	37	CCDS34752.1	.	.	.	.	.	.	.	.	.	.	G	36	5.625599	0.96671	.	.	ENSG00000128578	ENST00000249344;ENST00000435494	T;T	0.68331	-0.32;-0.32	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	D	0.86543	0.5958	M	0.92738	3.34	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.97110	0.996;1.0	D	0.89283	0.3613	10	0.87932	D	0	-20.2128	18.6487	0.91421	0.0:0.0:1.0:0.0	.	562;562	Q9ULQ0;Q9ULQ0-2	FA40B_HUMAN;.	N	562	ENSP00000249344:D562N;ENSP00000392393:D562N	ENSP00000249344:D562N	D	+	1	0	FAM40B	128891723	1.000000	0.71417	0.972000	0.41901	0.994000	0.84299	9.869000	0.99810	2.736000	0.93811	0.655000	0.94253	GAT	.	.	none		0.483	STRIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349418.1	NM_001134336		A	129104487	G	A	129104487	3	1	42	1	0	0	0	0	1	0	0	0	5569	1058	37	1	1746	1	FAM40B	7	129104487	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	11272462	129104487	30034176	159	15111											
SLC37A3	84255	hgsc.bcm.edu	37	chr7	140045717	140045717	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cagaagcagactcagggcaaGaaccggcgctctcttctgta	11	7	11	12	2	3	3	1	0	2	3	4	3	3	3	1	2	2	4	1	2	4	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr7:140045717G>A	ENST00000326232.9	-	11	1281	c.1078C>T	c.(1078-1080)Ctt>Ttt	p.L360F	SLC37A3_ENST00000447932.2_Missense_Mutation_p.L360F|SLC37A3_ENST00000340308.3_Intron	NM_207113.1	NP_996996.1	Q8NCC5	SPX3_HUMAN	solute carrier family 37, member 3	360					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)					CTCAGGGCAAGAACCGGCGCT	0.463																																					p.L360F	Esophageal Squamous(133;211 1716 4665 11387 37873)	Atlas-SNP	.											.	SLC37A3	80	.	0			c.C1078T						PASS	.						105	110	108					7																	140045717		2203	4300	6503	SO:0001583	missense	84255	exon11			GGGCAAGAACCGG	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.1078C>T	7.37:g.140045717G>A	ENSP00000321498:p.Leu360Phe	90	0	0		106	29	0.273585	NM_207113	Q6PIU7|Q86SS4|Q9BQG7	Missense_Mutation	SNP	ENST00000326232.9	37	CCDS5859.1	.	.	.	.	.	.	.	.	.	.	G	11.05	1.526203	0.27299	.	.	ENSG00000157800	ENST00000447932;ENST00000326232	T;T	0.62498	0.02;0.25	4.98	-2.26	0.06867	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.160257	0.38164	N	0.001783	T	0.66187	0.2764	L	0.43923	1.385	0.80722	D	1	P;D	0.57257	0.951;0.979	P;D	0.65573	0.802;0.936	T	0.65240	-0.6216	10	0.52906	T	0.07	-20.8561	12.608	0.56535	0.4046:0.0:0.5954:0.0	.	360;360	Q8NCC5-2;Q8NCC5	.;SPX3_HUMAN	F	360	ENSP00000397481:L360F;ENSP00000321498:L360F	ENSP00000321498:L360F	L	-	1	0	SLC37A3	139692186	0.004000	0.15560	0.064000	0.19789	0.046000	0.14306	-0.181000	0.09740	-0.309000	0.08779	-0.471000	0.05019	CTT	.	.	none		0.463	SLC37A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348492.1	NM_032295		A	140045717	G	A	140045717	3	1	42	1	0	0	0	0	1	0	0	0	14614	942	33	2	575	2	SLC37A3	7	140045717	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	10941230	140045717	19092946	160	15112											
ZNF425	155054	hgsc.bcm.edu	37	chr7	148801312	148801312	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gggacactggaagggctcctCgccactgtgaagcctcgtgt	7	8	14	12	2	0	1	0	1	0	0	3	3	1	3	3	3	1	1	3	3	2	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr7:148801312C>T	ENST00000378061.2	-	4	1783	c.1651G>A	c.(1651-1653)Gag>Aag	p.E551K		NM_001001661.2	NP_001001661.1	Q6IV72	ZN425_HUMAN	zinc finger protein 425	551					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(6)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	50	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			AAGGGCTCCTCGCCACTGTGA	0.632																																					p.E551K		Atlas-SNP	.											.	ZNF425	99	.	0			c.G1651A						PASS	.						33	33	33					7																	148801312		2202	4296	6498	SO:0001583	missense	155054	exon4			GCTCCTCGCCACT	AK056498	CCDS34773.1	7q36.1	2013-01-08			ENSG00000204947	ENSG00000204947		"Zinc fingers, C2H2-type", "-"	20690	protein-coding gene	gene with protein product							Standard	NM_001001661		Approved		uc003wfj.3	Q6IV72	OTTHUMG00000158971	ENST00000378061.2:c.1651G>A	7.37:g.148801312C>T	ENSP00000367300:p.Glu551Lys	48	0	0		65	22	0.338462	NM_001001661	B3KPM1|Q08AG3	Missense_Mutation	SNP	ENST00000378061.2	37	CCDS34773.1	.	.	.	.	.	.	.	.	.	.	C	12.21	1.870096	0.33069	.	.	ENSG00000204947	ENST00000378061	T	0.24350	1.86	3.15	3.15	0.36227	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.41305	0.1153	M	0.62266	1.93	0.30830	N	0.736807	D	0.63880	0.993	P	0.61397	0.888	T	0.40831	-0.9542	9	0.87932	D	0	.	8.417	0.32676	0.0:0.7575:0.2424:0.0	.	551	Q6IV72	ZN425_HUMAN	K	551	ENSP00000367300:E551K	ENSP00000367300:E551K	E	-	1	0	ZNF425	148432245	0.027000	0.19231	0.073000	0.20177	0.298000	0.27526	1.318000	0.33643	1.770000	0.52166	0.655000	0.94253	GAG	.	.	none		0.632	ZNF425-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352726.1	XM_088140		T	148801312	C	T	148801312	3	4	42	1	0	0	0	0	1	0	0	0	17914	893	31	1	611	1	ZNF425	7	148801312	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	8755595	148801312	10337351	161	15113											
GALNT11	63917	hgsc.bcm.edu	37	chr7	151818708	151818708	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgggtcagaagggctctgtCgccatggcgatctgcgatgg	6	9	16	10	3	3	1	1	0	2	1	4	3	3	1	1	4	1	1	1	4	1	0	rs368113531		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr7:151818708C>T	ENST00000434507.1	+	14	2210	c.1773C>T	c.(1771-1773)gtC>gtT	p.V591V	GALNT11_ENST00000430044.2_Silent_p.V591V|RP5-981O7.2_ENST00000424630.1_RNA|GALNT11_ENST00000320311.2_Silent_p.V591V|GALNT11_ENST00000452146.2_Silent_p.V510V			Q8NCW6	GLT11_HUMAN	polypeptide N-acetylgalactosaminyltransferase 11	591	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				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)	p.V591V(2)		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)		AGGGCTCTGTCGCCATGGCGA	0.532																																					p.V591V		Atlas-SNP	.											GALNT11,NS,carcinoma,0,1	GALNT11	59	1	2	Substitution - coding silent(2)	lung(2)	c.C1773T						PASS	.	T		1,4405	2.1+/-5.4	0,1,2202	126	101	110		1773	-10.4	0	7		110	0,8600		0,0,4300	no	coding-synonymous	GALNT11	NM_022087.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		591/609	151818708	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	63917	exon12			CTCTGTCGCCATG	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.1773C>T	7.37:g.151818708C>T		216	0	0		165	49	0.29697	NM_022087	B3KWF4|Q6PCD1|Q9H6C2|Q9H6Z5|Q9UDR8	Silent	SNP	ENST00000434507.1	37	CCDS5930.1																																																																																			.	.	weak		0.532	GALNT11-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348184.1	NM_022087		T	151818708	C	T	151818708	2	4	42	1	0	0	0	0	0	0	0	1	6217	871	31	1		1	GALNT11	7	151818708	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	3017396	151818708	7319955	162	15114											
CSMD1	64478	hgsc.bcm.edu	37	chr8	2966134	2966134	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatcaactgaccgtggaaatTgaggacaaagaagcctccat	16	7	9	9	1	1	3	1	2	0	1	2	5	2	5	3	2	2	0	3	2	5	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr8:2966134T>C	ENST00000520002.1	-	45	7303	c.6748A>G	c.(6748-6750)Aat>Gat	p.N2250D	CSMD1_ENST00000602723.1_Missense_Mutation_p.N2250D|CSMD1_ENST00000400186.3_Missense_Mutation_p.N2250D|CSMD1_ENST00000542608.1_Missense_Mutation_p.N2249D|CSMD1_ENST00000602557.1_Missense_Mutation_p.N2250D|CSMD1_ENST00000537824.1_Missense_Mutation_p.N2249D			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	2250	CUB 13. {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)		CCGTGGAAATTGAGGACAAAG	0.478																																					p.N2249D		Atlas-SNP	.											.	CSMD1	1469	.	0			c.A6745G						PASS	.						71	71	71					8																	2966134		1938	4145	6083	SO:0001583	missense	64478	exon44			GGAAATTGAGGAC			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.6748A>G	8.37:g.2966134T>C	ENSP00000430733:p.Asn2250Asp	78	0	0		45	20	0.444444	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.32|10.32	1.317341|1.317341	0.23908|0.23908	.|.	.|.	ENSG00000183117|ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608|ENST00000335551	T;T;T;T|.	0.59906|.	0.23;0.23;0.23;0.23|.	4.95|4.95	4.95|4.95	0.65309|0.65309	CUB (3);|.	0.127016|.	0.49916|.	D|.	0.000128|.	T|T	0.57388|0.57388	0.2050|0.2050	L|L	0.35854|0.35854	1.095|1.095	0.80722|0.80722	D|D	1|1	D;B;D|.	0.76494|.	0.992;0.012;0.999|.	D;B;D|.	0.85130|.	0.987;0.021;0.997|.	T|T	0.54516|0.54516	-0.8282|-0.8282	10|5	0.16420|.	T|.	0.52|.	.|.	14.8886|14.8886	0.70590|0.70590	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	2250;2250;2249|.	E5RIG2;Q96PZ7;F5H2I8|.	.;CSMD1_HUMAN;.|.	D|R	2250;2250;2111;2249;2249|1729	ENSP00000383047:N2250D;ENSP00000430733:N2250D;ENSP00000441462:N2249D;ENSP00000446243:N2249D|.	ENSP00000320445:N2111D|.	N|Q	-|-	1|2	0|0	CSMD1|CSMD1	2953541|2953541	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.184000|0.184000	0.23303|0.23303	4.667000|4.667000	0.61561|0.61561	1.971000|1.971000	0.57363|0.57363	0.472000|0.472000	0.43445|0.43445	AAT|CAA	.	.	none		0.478	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		C	2966134	T	C	2966134	3	2	42	1	0	0	0	0	1	0	0	0	3946	1812	63	3	4057	3	CSMD1	8	2966134	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10		2966134	143397888	163	15115											
XPO7	23039	hgsc.bcm.edu	37	chr8	21856273	21856273	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gctctctgctcaggtcccagCgactccagtttgatgtctct	5	13	9	14	1	3	1	1	1	2	0	7	2	5	1	2	1	2	3	2	1	0	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr8:21856273C>T	ENST00000252512.9	+	22	2453	c.2353C>T	c.(2353-2355)Cga>Tga	p.R785*	XPO7_ENST00000434536.1_Nonsense_Mutation_p.R794*|XPO7_ENST00000433566.4_Nonsense_Mutation_p.R786*	NM_015024.4	NP_055839.3	Q9UIA9	XPO7_HUMAN	exportin 7	785					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)		CAGGTCCCAGCGACTCCAGTT	0.478																																					p.R785X		Atlas-SNP	.											XPO7,NS,carcinoma,0,1	XPO7	79	1	0			c.C2353T						PASS	.						117	108	111					8																	21856273		1984	4183	6167	SO:0001587	stop_gained	23039	exon22			TCCCAGCGACTCC	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.2353C>T	8.37:g.21856273C>T	ENSP00000252512:p.Arg785*	115	0	0		74	24	0.324324	NM_015024	O94846|Q6PJK9|Q8NEK7	Nonsense_Mutation	SNP	ENST00000252512.9	37	CCDS47818.1	.	.	.	.	.	.	.	.	.	.	C	39	7.638127	0.98406	.	.	ENSG00000130227	ENST00000434536;ENST00000252512;ENST00000433566;ENST00000517551	.	.	.	5.95	4.07	0.47477	.	0.051284	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.1099	14.1003	0.65051	0.5454:0.4546:0.0:0.0	.	.	.	.	X	794;785;786;95	.	ENSP00000252512:R785X	R	+	1	2	XPO7	21912219	0.990000	0.36364	1.000000	0.80357	0.992000	0.81027	0.895000	0.28363	0.757000	0.33036	0.655000	0.94253	CGA	.	.	none		0.478	XPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375494.1	NM_015024		T	21856273	C	T	21856273	4	4	42	1	0	0	0	0	0	1	0	0	17464	760	27	1	2491	1	XPO7	8	21856273	Nonsense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	18890139	21856273	124507749	164	15116											
ASH2L	9070	hgsc.bcm.edu	37	chr8	37963905	37963905	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttatcttatagggaggcaaaCttggtcgatgtaagcggtgg	10	12	14	5	2	1	0	0	0	1	0	2	2	1	1	0	5	2	2	0	5	5	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr8:37963905C>G	ENST00000343823.6	+	2	507	c.198C>G	c.(196-198)aaC>aaG	p.N66K	ASH2L_ENST00000428278.2_5'UTR|ASH2L_ENST00000545394.1_5'UTR|ASH2L_ENST00000250635.7_5'UTR|ASH2L_ENST00000521652.1_5'UTR	NM_004674.4	NP_004665.2	Q9UBL3	ASH2L_HUMAN	ash2 (absent, small, or homeotic)-like (Drosophila)	66					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)				GGGAGGCAAACTTGGTCGATG	0.368																																					p.N66K		Atlas-SNP	.											.	ASH2L	62	.	0			c.C198G						PASS	.						170	173	172					8																	37963905		2203	4300	6503	SO:0001583	missense	9070	exon2			GGCAAACTTGGTC	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.198C>G	8.37:g.37963905C>G	ENSP00000340896:p.Asn66Lys	213	0	0		130	16	0.123077	NM_004674	A8K7C3|D3DSW9|O60659|O60660|Q96B62	Missense_Mutation	SNP	ENST00000343823.6	37	CCDS6101.1	.	.	.	.	.	.	.	.	.	.	C	13.73	2.325738	0.41197	.	.	ENSG00000129691	ENST00000343823	T	0.18174	2.23	5.99	2.1	0.27182	.	0.338836	0.35013	N	0.003507	T	0.07908	0.0198	N	0.08118	0	0.58432	D	0.999999	B	0.12013	0.005	B	0.08055	0.003	T	0.22452	-1.0216	10	0.38643	T	0.18	.	8.2691	0.31833	0.0:0.588:0.0:0.412	.	66	Q9UBL3	ASH2L_HUMAN	K	66	ENSP00000340896:N66K	ENSP00000340896:N66K	N	+	3	2	ASH2L	38083062	0.003000	0.15002	0.906000	0.35671	0.074000	0.17049	-0.047000	0.11963	0.389000	0.25086	0.655000	0.94253	AAC	.	.	none		0.368	ASH2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376749.4	NM_004674		G	37963905	C	G	37963905	3	3	42	1	0	0	0	0	1	0	0	0	1042	564	20	4	204	4	ASH2L	8	37963905	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	16107632	37963905	108400117	165	15117											
OPRK1	4986	hgsc.bcm.edu	37	chr8	54147398	54147398	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agccagatgcagatattgatGatctttgccttcaagggtgt	10	13	11	7	0	2	4	1	2	1	2	2	4	2	4	2	1	3	1	2	1	2	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr8:54147398G>A	ENST00000265572.3	-	3	828	c.531C>T	c.(529-531)atC>atT	p.I177I	RP11-162D9.3_ENST00000524425.1_RNA|OPRK1_ENST00000520287.1_Silent_p.I177I|OPRK1_ENST00000524278.1_Silent_p.I88I	NM_000912.3	NP_000903.2	P41145	OPRK_HUMAN	opioid receptor, kappa 1	177					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)	AGATATTGATGATCTTTGCCT	0.517																																					p.I177I		Atlas-SNP	.											.	OPRK1	90	.	0			c.C531T						PASS	.						117	102	107					8																	54147398		2203	4300	6503	SO:0001819	synonymous_variant	4986	exon3			ATTGATGATCTTT		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.531C>T	8.37:g.54147398G>A		83	0	0		85	20	0.235294	NM_000912	E5RHC9|Q499G4	Silent	SNP	ENST00000265572.3	37	CCDS6152.1																																																																																			.	.	none		0.517	OPRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378048.1			A	54147398	G	A	54147398	2	1	42	1	0	0	0	0	0	0	0	1	10894	1280	45	2		2	OPRK1	8	54147398	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	16183493	54147398	92216624	166	15118											
MYBL1	4603	hgsc.bcm.edu	37	chr8	67479124	67479124	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agattacctcttgtttgcagCttttgtaagcaggttcatct	8	17	8	8	0	3	1	1	0	2	1	3	1	3	1	1	1	4	6	1	1	2	7			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr8:67479124C>T	ENST00000522677.3	-	13	2242	c.1832G>A	c.(1831-1833)aGc>aAc	p.S611N	MYBL1_ENST00000522419.1_5'UTR|MYBL1_ENST00000517885.1_Missense_Mutation_p.S269N|MYBL1_ENST00000524176.2_Missense_Mutation_p.S611N	NM_001080416.2|NM_001144755.1	NP_001073885.1|NP_001138227.1	P10243	MYBA_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 1	611					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)			TTGTTTGCAGCTTTTGTAAGC	0.348																																					p.S611N		Atlas-SNP	.											.	MYBL1	73	.	0			c.G1832A						PASS	.						117	104	108					8																	67479124		1804	4076	5880	SO:0001583	missense	4603	exon13			TTGCAGCTTTTGT	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.1832G>A	8.37:g.67479124C>T	ENSP00000429633:p.Ser611Asn	275	0	0		328	138	0.420732	NM_001080416	E7EW29|Q495F9	Missense_Mutation	SNP	ENST00000522677.3	37	CCDS47867.1	.	.	.	.	.	.	.	.	.	.	C	10.89	1.477707	0.26511	.	.	ENSG00000185697	ENST00000522677;ENST00000517885;ENST00000524176	T;T;T	0.29142	1.58;1.58;1.58	5.48	3.69	0.42338	C-myb, C-terminal (1);	0.366974	0.34580	N	0.003860	T	0.21387	0.0515	L	0.34521	1.04	0.33887	D	0.636893	B;B;B	0.15930	0.015;0.005;0.015	B;B;B	0.18561	0.015;0.022;0.015	T	0.14671	-1.0464	10	0.46703	T	0.11	-0.9074	6.6436	0.22923	0.0:0.6574:0.1288:0.2137	.	611;610;611	Q495F9;Q495G0;P10243	.;.;MYBA_HUMAN	N	611;269;611	ENSP00000429633:S611N;ENSP00000428265:S269N;ENSP00000428011:S611N	ENSP00000428265:S269N	S	-	2	0	MYBL1	67641678	1.000000	0.71417	1.000000	0.80357	0.870000	0.49936	0.830000	0.27462	0.674000	0.31244	-0.142000	0.14014	AGC	.	.	none		0.348	MYBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379221.3	XM_034274		T	67479124	C	T	67479124	3	4	42	1	0	0	0	0	1	0	0	0	10018	797	28	2	442	2	MYBL1	8	67479124	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	13331726	67479124	78884898	167	15119											
VCPIP1	80124	hgsc.bcm.edu	37	chr8	67577327	67577327	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagtttcattgcaacatcgtAaacattactattcaaagatg	16	13	5	7	1	2	1	2	0	0	1	3	1	2	1	0	0	4	3	0	0	7	6			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr8:67577327A>T	ENST00000310421.4	-	1	2125	c.1867T>A	c.(1867-1869)Tac>Aac	p.Y623N	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	623					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)			GCAACATCGTAAACATTACTA	0.383																																					p.Y623N	NSCLC(179;265 2915 6144 43644)	Atlas-SNP	.											.	VCPIP1	110	.	0			c.T1867A						PASS	.						120	124	123					8																	67577327		2203	4300	6503	SO:0001583	missense	80124	exon1			CATCGTAAACATT	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.1867T>A	8.37:g.67577327A>T	ENSP00000309031:p.Tyr623Asn	168	0	0		180	76	0.422222	NM_025054	Q504T4|Q86T93|Q86W01|Q8N3A9|Q9H5R8	Missense_Mutation	SNP	ENST00000310421.4	37	CCDS6192.1	.	.	.	.	.	.	.	.	.	.	A	16.47	3.132876	0.56828	.	.	ENSG00000175073	ENST00000310421	T	0.39997	1.05	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.61400	0.2344	L	0.59436	1.845	0.80722	D	1	D	0.71674	0.998	D	0.78314	0.991	T	0.64728	-0.6339	10	0.87932	D	0	-11.2244	15.7082	0.77602	1.0:0.0:0.0:0.0	.	623	Q96JH7	VCIP1_HUMAN	N	623	ENSP00000309031:Y623N	ENSP00000309031:Y623N	Y	-	1	0	VCPIP1	67739881	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.287000	0.95975	2.163000	0.67991	0.533000	0.62120	TAC	.	.	none		0.383	VCPIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379227.1			T	67577327	A	T	67577327	3	4	42	1	0	0	0	0	1	0	0	0	17156	362	13	5	1813	5	VCPIP1	8	67577327	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	98203	67577327	78786695	168	15120											
VCPIP1	80124	hgsc.bcm.edu	37	chr8	67577531	67577531	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtctccatccaaatacacaaTagacccatctcctctgacct	12	10	3	16	0	3	2	0	1	3	1	6	2	4	2	5	0	1	0	5	0	4	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr8:67577531T>C	ENST00000310421.4	-	1	1921	c.1663A>G	c.(1663-1665)Att>Gtt	p.I555V	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	555					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)			AAATACACAATAGACCCATCT	0.433																																					p.I555V	NSCLC(179;265 2915 6144 43644)	Atlas-SNP	.											.	VCPIP1	110	.	0			c.A1663G						PASS	.						188	165	173					8																	67577531		2203	4300	6503	SO:0001583	missense	80124	exon1			ACACAATAGACCC	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.1663A>G	8.37:g.67577531T>C	ENSP00000309031:p.Ile555Val	152	0	0		158	76	0.481013	NM_025054	Q504T4|Q86T93|Q86W01|Q8N3A9|Q9H5R8	Missense_Mutation	SNP	ENST00000310421.4	37	CCDS6192.1	.	.	.	.	.	.	.	.	.	.	T	0.020	-1.447137	0.01089	.	.	ENSG00000175073	ENST00000310421	T	0.28255	1.62	4.98	3.65	0.41850	.	0.057027	0.64402	D	0.000001	T	0.09992	0.0245	N	0.02391	-0.57	0.43390	D	0.995508	B	0.02656	0.0	B	0.01281	0.0	T	0.15665	-1.0429	10	0.17369	T	0.5	-12.0027	5.1154	0.14831	0.0:0.2193:0.0:0.7807	.	555	Q96JH7	VCIP1_HUMAN	V	555	ENSP00000309031:I555V	ENSP00000309031:I555V	I	-	1	0	VCPIP1	67740085	1.000000	0.71417	1.000000	0.80357	0.803000	0.45373	2.772000	0.47678	1.988000	0.58038	0.528000	0.53228	ATT	.	.	none		0.433	VCPIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379227.1			C	67577531	T	C	67577531	3	2	42	1	0	0	0	0	1	0	0	0	17156	1406	49	3	2017	3	VCPIP1	8	67577531	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	204	67577531	78786491	169	15121											
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77616687	77616687	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatcagcgagttagaggacAgtgacgtggaaaatctaaca	16	7	12	6	2	2	3	1	1	1	2	2	6	2	5	0	2	2	1	0	2	4	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr8:77616687A>T	ENST00000521891.2	+	2	812	c.364A>T	c.(364-366)Agt>Tgt	p.S122C	ZFHX4_ENST00000517683.1_Intron|ZFHX4_ENST00000050961.6_Missense_Mutation_p.S122C|ZFHX4_ENST00000518282.1_Missense_Mutation_p.S122C|ZFHX4_ENST00000455469.2_Missense_Mutation_p.S122C	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	122					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)			GTTAGAGGACAGTGACGTGGA	0.483										HNSCC(33;0.089)																											p.S122C		Atlas-SNP	.											ZFHX4,colon,carcinoma,-1,1	ZFHX4	878	1	0			c.A364T						PASS	.						139	134	135					8																	77616687		1975	4171	6146	SO:0001583	missense	79776	exon2			GAGGACAGTGACG		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.364A>T	8.37:g.77616687A>T	ENSP00000430497:p.Ser122Cys	106	0	0		99	42	0.424242	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	A	18.06	3.538749	0.65085	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000520307;ENST00000517585;ENST00000523809;ENST00000518282	T;T;T;T;T;T;T	0.36157	1.27;1.27;1.27;1.27;1.27;1.27;1.27	5.42	5.42	0.78866	.	0.000000	0.52532	U	0.000073	T	0.60157	0.2247	M	0.71581	2.175	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.996;0.998;0.998;0.998	T	0.63808	-0.6553	10	0.72032	D	0.01	.	15.6293	0.76888	1.0:0.0:0.0:0.0	.	122;122;122;122	Q86UP3;Q86UP3-4;G3V138;Q86UP3-3	ZFHX4_HUMAN;.;.;.	C	122	ENSP00000430497:S122C;ENSP00000399605:S122C;ENSP00000050961:S122C;ENSP00000428525:S122C;ENSP00000427775:S122C;ENSP00000427739:S122C;ENSP00000430848:S122C	ENSP00000050961:S122C	S	+	1	0	ZFHX4	77779242	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.106000	0.94253	2.276000	0.75962	0.528000	0.53228	AGT	.	.	none		0.483	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		T	77616687	A	T	77616687	3	4	42	1	0	0	0	0	1	0	0	0	17650	188	7	5	366	5	ZFHX4	8	77616687	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	10039156	77616687	68747335	170	15122											
CA3	761	hgsc.bcm.edu	37	chr8	86352126	86352127	+	Frame_Shift_Ins	INS	-	-	A																															agttgtatttgatgatacttINSatgataggtcaagtaagtat																										TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr8:86352126_86352127insA	ENST00000285381.2	+	2	303_304	c.220_221insA	c.(220-222)tatfs	p.Y74fs	RP11-317J10.2_ENST00000517697.1_RNA|RP11-317J10.2_ENST00000521761.1_RNA	NM_005181.3	NP_005172.1	P07451	CAH3_HUMAN	carbonic anhydrase III, muscle specific	74					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|response to ethanol (GO:0045471)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	carbonate dehydratase activity (GO:0004089)|nickel cation binding (GO:0016151)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23					Acetazolamide(DB00819)|Zonisamide(DB00909)	TGATGATACTTATGATAGGTCA	0.411																																					p.Y74_D75delinsX		Pindel,Atlas-Indel	.											.	CA3	47	.	0			c.220_221insA						PASS	.																																			SO:0001589	frameshift_variant	761	exon2			.	AJ006473	CCDS6238.1	8q21.2	2012-10-02					4.2.1.1	"Carbonic anhydrases"	1374	protein-coding gene	gene with protein product		114750				6221502	Standard	NM_005181		Approved	Car3, CAIII	uc003ydj.3	P07451		ENST00000285381.2:c.221dupA	8.37:g.86352127_86352127dupA	ENSP00000285381:p.Tyr74fs	29	0	.		52	18	0.346	NM_005181	B2R867|B3KUC8|O60842	Frame_Shift_Ins	INS	ENST00000285381.2	37	CCDS6238.1																																																																																			.	.	none		0.411	CA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381090.1	NM_005181		A	86352127	-	A	86352126	7	5	42	1	0	1	1	0	0	0	0	0	2519	1754	61	0	226	0	CA3	8	86352126	Frame_Shift_Ins	INS	-	TCGA-GS-A9TZ-01A-11D-A38X-10	8735439	86352126	60011896	171	15123											
OXR1	55074	hgsc.bcm.edu	37	chr8	107695483	107695483	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagtttgatacaacacctaaCgaacttgttcaattaaataa	18	12	4	7	1	1	1	1	1	0	0	1	2	1	1	1	0	4	2	1	0	9	7	rs537961089		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr8:107695483C>T	ENST00000442977.2	+	4	462	c.363C>T	c.(361-363)aaC>aaT	p.N121N	OXR1_ENST00000517566.2_Silent_p.N120N|OXR1_ENST00000312046.6_Silent_p.N113N|OXR1_ENST00000452423.2_5'UTR|OXR1_ENST00000445937.1_Silent_p.N120N|OXR1_ENST00000531443.1_Silent_p.N120N|OXR1_ENST00000497705.1_Silent_p.N53N	NM_001198532.1	NP_001185461.1	Q8N573	OXR1_HUMAN	oxidation resistance 1	121					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)			CAACACCTAACGAACTTGTTC	0.299																																					p.N121N		Atlas-SNP	.											.	OXR1	190	.	0			c.C363T						PASS	.						80	82	81					8																	107695483		2203	4293	6496	SO:0001819	synonymous_variant	55074	exon4			ACCTAACGAACTT	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.363C>T	8.37:g.107695483C>T		185	0	0		186	41	0.22043	NM_001198532	A6NK11|A8KA34|B3KXL1|B7Z402|B7Z8N5|D3HIS6|Q3LIB5|Q6ZVK9|Q8N8V0|Q9H266|Q9NWC7	Silent	SNP	ENST00000442977.2	37	CCDS56548.1	.	.	.	.	.	.	.	.	.	.	C	9.200	1.028124	0.19512	.	.	ENSG00000164830	ENST00000517455	.	.	.	5.4	-4.2	0.03823	.	.	.	.	.	T	0.62539	0.2436	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61466	-0.7057	4	.	.	.	-10.1915	13.5748	0.61868	0.0:0.472:0.0:0.528	.	.	.	.	M	37	.	.	T	+	2	0	OXR1	107764659	0.752000	0.28338	0.927000	0.36925	0.971000	0.66376	-0.143000	0.10296	-0.951000	0.03654	-0.350000	0.07774	ACG	.	.	none		0.299	OXR1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_181354		T	107695483	C	T	107695483	2	4	42	1	0	0	0	0	0	0	0	1	11343	535	19	1		1	OXR1	8	107695483	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	21343357	107695483	38668539	172	15124											
PKHD1L1	93035	hgsc.bcm.edu	37	chr8	110535472	110535472	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttttttagggtaactgtgTatcagttggaattactgcac	9	18	9	5	0	1	0	1	0	0	0	1	1	1	1	0	2	3	4	0	2	5	8			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr8:110535472T>C	ENST00000378402.5	+	76	12445	c.12341T>C	c.(12340-12342)gTa>gCa	p.V4114A		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	4114					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)			GGTAACTGTGTATCAGTTGGA	0.313										HNSCC(38;0.096)																											p.V4114A		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.T12341C						PASS	.						81	73	76					8																	110535472		1834	4082	5916	SO:0001583	missense	93035	exon76			ACTGTGTATCAGT	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.12341T>C	8.37:g.110535472T>C	ENSP00000367655:p.Val4114Ala	78	0	0		80	17	0.2125	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	T	18.18	3.566189	0.65651	.	.	ENSG00000205038	ENST00000378402;ENST00000526472	D;D	0.89617	-2.54;-2.4	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	D	0.93350	0.7880	M	0.76574	2.34	0.35150	D	0.769649	D	0.71674	0.998	D	0.66196	0.942	D	0.96101	0.9069	10	0.54805	T	0.06	.	13.8903	0.63736	0.0:0.0:0.0:1.0	.	4114	Q86WI1	PKHL1_HUMAN	A	4114;1042	ENSP00000367655:V4114A;ENSP00000437376:V1042A	ENSP00000367655:V4114A	V	+	2	0	PKHD1L1	110604648	1.000000	0.71417	0.997000	0.53966	0.533000	0.34776	6.141000	0.71744	2.167000	0.68274	0.528000	0.53228	GTA	.	.	none		0.313	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531		C	110535472	T	C	110535472	3	2	42	1	0	0	0	0	1	0	0	0	11981	1638	57	3	12643	3	PKHD1L1	8	110535472	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	2839989	110535472	35828550	173	15125											
ZNF572	137209	hgsc.bcm.edu	37	chr8	125989683	125989683	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agatgttgtgaatgtgggaaGagttttggccttagctccca	9	13	13	6	0	0	3	0	1	0	2	1	4	1	4	2	2	1	3	2	2	3	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr8:125989683G>A	ENST00000319286.5	+	3	1327	c.1173G>A	c.(1171-1173)aaG>aaA	p.K391K		NM_152412.2	NP_689625.2	Q7Z3I7	ZN572_HUMAN	zinc finger protein 572	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(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)			AATGTGGGAAGAGTTTTGGCC	0.403										HNSCC(60;0.17)																											p.K391K		Atlas-SNP	.											ZNF572,parotid,carcinoma,+2,1	ZNF572	82	1	0			c.G1173A						PASS	.						96	91	93					8																	125989683		2203	4300	6503	SO:0001819	synonymous_variant	137209	exon3			TGGGAAGAGTTTT	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.1173G>A	8.37:g.125989683G>A		77	0	0		115	56	0.486957	NM_152412	A1L4F1|Q8N1Q0	Silent	SNP	ENST00000319286.5	37	CCDS6354.1																																																																																			.	.	none		0.403	ZNF572-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381359.1	NM_152412		A	125989683	G	A	125989683	2	1	42	1	0	0	0	0	0	0	0	1	18019	933	33	2		2	ZNF572	8	125989683	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	15454211	125989683	20374339	174	15126											
EPPK1	83481	hgsc.bcm.edu	37	chr8	144942991	144942991	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgccgcttgtcagcgccaacGtattcggagagcagcaggtc	8	7	13	13	5	1	1	1	0	0	1	3	2	1	1	2	2	4	4	2	2	2	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr8:144942991G>A	ENST00000525985.1	-	2	4502	c.4431C>T	c.(4429-4431)taC>taT	p.Y1477Y				P58107	EPIPL_HUMAN	epiplakin 1	1477						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)			CAGCGCCAACGTATTCGGAGA	0.662																																					p.Y1477Y		Atlas-SNP	.											.	EPPK1	199	.	0			c.C4431T						PASS	.						29	33	32					8																	144942991		2189	4283	6472	SO:0001819	synonymous_variant	83481	exon1			GCCAACGTATTCG	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.4431C>T	8.37:g.144942991G>A		29	0	0		37	20	0.540541	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				.	.	none		0.662	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308		A	144942991	G	A	144942991	2	1	42	1	0	0	0	0	0	0	0	1	5192	1140	40	1		1	EPPK1	8	144942991	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	18953308	144942991	1421031	175	15127											
PTPRD	5789	hgsc.bcm.edu	37	chr9	8504278	8504278	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tacttgactgcatggttctaGctgatatttctgcagtagaa	10	15	9	7	0	2	3	0	2	2	1	2	3	2	3	0	1	4	5	0	1	5	7			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr9:8504278G>A	ENST00000381196.4	-	20	2348	c.1805C>T	c.(1804-1806)gCt>gTt	p.A602V	PTPRD_ENST00000397617.3_Missense_Mutation_p.A592V|PTPRD_ENST00000486161.1_Missense_Mutation_p.A602V|PTPRD_ENST00000356435.5_Missense_Mutation_p.A602V|PTPRD_ENST00000540109.1_Missense_Mutation_p.A602V|PTPRD_ENST00000397611.3_Missense_Mutation_p.A599V|PTPRD_ENST00000537002.1_Missense_Mutation_p.A599V|PTPRD_ENST00000360074.4_Missense_Mutation_p.A589V|PTPRD_ENST00000358503.5_Missense_Mutation_p.A589V|PTPRD_ENST00000355233.5_Missense_Mutation_p.A602V|PTPRD_ENST00000397606.3_Missense_Mutation_p.A592V	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	602	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		CATGGTTCTAGCTGATATTTC	0.458										TSP Lung(15;0.13)																											p.A602V		Atlas-SNP	.											.	PTPRD	1348	.	0			c.C1805T						PASS	.						194	175	181					9																	8504278		2203	4300	6503	SO:0001583	missense	5789	exon12			GTTCTAGCTGATA	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.1805C>T	9.37:g.8504278G>A	ENSP00000370593:p.Ala602Val	177	0	0		192	12	0.0625	NM_130392	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	37	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	G	10.60	1.395997	0.25205	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606	T;T;T;T;T;T;T;T;T;T;T	0.52057	0.68;0.68;0.68;0.68;0.72;0.72;0.72;0.72;0.68;0.72;0.72	5.53	5.53	0.82687	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.35595	0.0937	N	0.16368	0.405	0.50171	D	0.999852	B;B;B;B;B;B;B;B;B	0.33212	0.01;0.029;0.402;0.104;0.022;0.041;0.073;0.047;0.02	B;B;B;B;B;B;B;B;B	0.33690	0.027;0.046;0.168;0.04;0.086;0.087;0.057;0.036;0.012	T	0.11012	-1.0605	9	.	.	.	.	19.4728	0.94969	0.0:0.0:1.0:0.0	.	592;596;602;602;599;599;589;602;602	Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;PTPRD_HUMAN	V	602;602;589;589;602;592;599;599;602;602;602;592	ENSP00000370593:A602V;ENSP00000348812:A602V;ENSP00000353187:A589V;ENSP00000351293:A589V;ENSP00000347373:A602V;ENSP00000380741:A592V;ENSP00000380735:A599V;ENSP00000440515:A599V;ENSP00000438164:A602V;ENSP00000417093:A602V;ENSP00000380731:A592V	.	A	-	2	0	PTPRD	8494278	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.324000	0.65863	2.602000	0.87976	0.467000	0.42956	GCT	.	.	none		0.458	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3			A	8504278	G	A	8504278	3	1	42	1	0	0	0	0	1	0	0	0	12814	971	34	2	4097	2	PTPRD	9	8504278	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10		8504278	132709153	176	15128											
TYRP1	7306	hgsc.bcm.edu	37	chr9	12702305	12702305	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaattaggagaaatccagcTggaaatgtggccagaccaat	15	7	10	9	0	0	2	0	0	0	2	1	4	1	3	4	3	1	1	4	3	5	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr9:12702305T>A	ENST00000388918.5	+	5	1077	c.948T>A	c.(946-948)gcT>gcA	p.A316A	TYRP1_ENST00000381136.2_Silent_p.A26A|TYRP1_ENST00000381137.2_Silent_p.A26A|RP11-3L8.3_ENST00000417638.1_RNA	NM_000550.2	NP_000541.1	P17643	TYRP1_HUMAN	tyrosinase-related protein 1	316					acetoacetic acid metabolic process (GO:0043438)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome organization (GO:0032438)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)|melanosome membrane (GO:0033162)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, another compound as one donor, and incorporation of one atom of oxygen (GO:0016716)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|stomach(1)	22		all_cancers(3;3.1e-05)|all_lung(3;1.7e-06)|Lung NSC(3;2.09e-06)|all_epithelial(3;0.000695)|all_hematologic(3;0.0033)|Acute lymphoblastic leukemia(23;0.0744)		GBM - Glioblastoma multiforme(50;9.85e-06)		GAAATCCAGCTGGAAATGTGG	0.448									Oculocutaneous Albinism																												p.A316A		Atlas-SNP	.											.	TYRP1	60	.	0			c.T948A						PASS	.						122	107	112					9																	12702305		2203	4300	6503	SO:0001819	synonymous_variant	7306	exon5	Familial Cancer Database		TCCAGCTGGAAAT	L33830	CCDS34990.1	9p23	2013-01-08			ENSG00000107165	ENSG00000107165			12450	protein-coding gene	gene with protein product		115501		TYRP, CAS2		9434945	Standard	NM_000550		Approved	GP75, CATB, TRP, b-PROTEIN, OCA3	uc003zkv.4	P17643	OTTHUMG00000021034	ENST00000388918.5:c.948T>A	9.37:g.12702305T>A		184	0	0		199	36	0.180905	NM_000550	P78468|P78469|Q13721|Q15679	Silent	SNP	ENST00000388918.5	37	CCDS34990.1																																																																																			.	.	none		0.448	TYRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055502.3	NM_000550		A	12702305	T	A	12702305	2	1	42	1	0	0	0	0	0	0	0	1	16831	1567	55	5		5	TYRP1	9	12702305	Silent	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	4198027	12702305	128511126	177	15129											
FREM1	158326	hgsc.bcm.edu	37	chr9	14750210	14750210	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagttcagaattacttcaaaGacctcatcatcttcctctaa	13	13	4	11	0	6	2	4	0	2	2	7	3	7	2	2	0	1	1	2	0	4	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr9:14750210G>T	ENST00000380880.3	-	30	6255	c.5472C>A	c.(5470-5472)gtC>gtA	p.V1824V	FREM1_ENST00000380894.1_Silent_p.V360V|FREM1_ENST00000380881.4_Silent_p.V1825V|FREM1_ENST00000422223.2_Silent_p.V1824V|FREM1_ENST00000486223.1_5'Flank			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	1824	Calx-beta.				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)		TTACTTCAAAGACCTCATCAT	0.358																																					p.V1824V		Atlas-SNP	.											FREM1_ENST00000380894,NS,carcinoma,0,2	FREM1	261	2	0			c.C5472A						PASS	.						147	137	140					9																	14750210		1858	4092	5950	SO:0001819	synonymous_variant	158326	exon31			TTCAAAGACCTCA	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.5472C>A	9.37:g.14750210G>T		225	0	0		277	17	0.0613718	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	37	CCDS47952.1																																																																																			.	.	none		0.358	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966		T	14750210	G	T	14750210	2	4	42	1	0	0	0	0	0	0	0	1	6052	929	33	4		4	FREM1	9	14750210	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	2047905	14750210	126463221	178	15130											
CNTLN	54875	hgsc.bcm.edu	37	chr9	17135148	17135148	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccccacgtgttgggcggggaGctgaagtacacgcaatgcgc	8	6	15	12	4	0	1	0	1	0	0	0	2	0	2	2	3	3	4	2	3	3	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr9:17135148G>A	ENST00000380647.3	+	1	169	c.85G>A	c.(85-87)Gct>Act	p.A29T	CNTLN_ENST00000484374.1_3'UTR|CNTLN_ENST00000262360.5_Missense_Mutation_p.A29T|CNTLN_ENST00000380641.4_Missense_Mutation_p.A29T|CNTLN_ENST00000425824.1_Missense_Mutation_p.A29T			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	29					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)		TGGGCGGGGAGCTGAAGTACA	0.677																																					p.A29T		Atlas-SNP	.											.	CNTLN	128	.	0			c.G85A						PASS	.						12	16	15					9																	17135148		1956	4128	6084	SO:0001583	missense	54875	exon1			CGGGGAGCTGAAG	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.85G>A	9.37:g.17135148G>A	ENSP00000370021:p.Ala29Thr	129	0	0		163	33	0.202454	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Missense_Mutation	SNP	ENST00000380647.3	37	CCDS43789.1	.	.	.	.	.	.	.	.	.	.	G	18.39	3.614003	0.66672	.	.	ENSG00000044459	ENST00000380647;ENST00000425824;ENST00000262360;ENST00000380641	T;T;T;T	0.14391	2.51;2.51;2.51;2.51	5.07	2.1	0.27182	.	.	.	.	.	T	0.11239	0.0274	L	0.36672	1.1	0.09310	N	1	B;B;B;B	0.20550	0.017;0.017;0.002;0.046	B;B;B;B	0.18871	0.005;0.005;0.002;0.023	T	0.26573	-1.0099	9	0.87932	D	0	.	7.3253	0.26551	0.0906:0.3251:0.5843:0.0	.	29;29;29;29	C9J1F9;Q9NXG0-2;Q9NXG0-3;B1AMC8	.;.;.;.	T	29	ENSP00000370021:A29T;ENSP00000392798:A29T;ENSP00000262360:A29T;ENSP00000370015:A29T	ENSP00000262360:A29T	A	+	1	0	CNTLN	17125148	0.188000	0.23250	0.014000	0.15608	0.985000	0.73830	0.310000	0.19356	0.217000	0.20800	-0.315000	0.08773	GCT	.	.	none		0.677	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738		A	17135148	G	A	17135148	3	1	42	1	0	0	0	0	1	0	0	0	3641	971	34	2	87	2	CNTLN	9	17135148	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	2384938	17135148	124078283	179	15131											
C9orf24	84688	hgsc.bcm.edu	37	chr9	34379662	34379662	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	acctaaggttcggatatgggTagtatgacggcgggggagtt	9	10	17	5	3	0	1	0	1	0	0	1	3	0	3	1	6	0	4	1	6	4	6			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr9:34379662T>A	ENST00000297623.2	-	6	969	c.771A>T	c.(769-771)ctA>ctT	p.L257L	C9orf24_ENST00000481295.1_5'UTR|C9orf24_ENST00000379127.1_Missense_Mutation_p.Y124F|C9orf24_ENST00000379124.1_Missense_Mutation_p.Y124F|C9orf24_ENST00000379133.3_Silent_p.L122L|C9orf24_ENST00000379126.3_Missense_Mutation_p.Y71F|KIAA1161_ENST00000297625.7_5'Flank	NM_032596.3	NP_115985.2	Q8NCR6	SMRP1_HUMAN	chromosome 9 open reading frame 24	257					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)		CGGATATGGGTAGTATGACGG	0.587											OREG0019150	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y124F		Atlas-SNP	.											.	C9orf24	15	.	0			c.A371T						PASS	.						134	125	128					9																	34379662		2203	4300	6503	SO:0001819	synonymous_variant	84688	exon4			TATGGGTAGTATG	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.771A>T	9.37:g.34379662T>A		96	0	0	847	128	30	0.234375	NM_001252195	Q5T598|Q5T599|Q5T5A0|Q8N9G4|Q96KD1|Q96LN1	Missense_Mutation	SNP	ENST00000297623.2	37	CCDS6554.1	.	.	.	.	.	.	.	.	.	.	T	15.41	2.826730	0.50739	.	.	ENSG00000164972	ENST00000379126;ENST00000379127;ENST00000379112;ENST00000379124	T;T	0.52057	0.68;0.68	4.73	0.955	0.19602	.	.	.	.	.	T	0.27731	0.0682	.	.	.	0.20403	N	0.999906	B	0.11235	0.004	B	0.12837	0.008	T	0.19614	-1.0300	8	0.25106	T	0.35	-7.9938	3.6798	0.08306	0.1602:0.1789:0.0:0.661	.	71	Q8NCR6-3	.	F	71;124;54;124	ENSP00000368422:Y124F;ENSP00000368419:Y124F	ENSP00000368407:Y54F	Y	-	2	0	C9orf24	34369662	0.975000	0.34042	0.730000	0.30809	0.465000	0.32709	-0.176000	0.09811	0.060000	0.16281	-0.411000	0.06167	TAC	.	.	none		0.587	C9orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001098.3	NM_147169		A	34379662	T	A	34379662	2	1	42	1	0	0	0	0	0	0	0	1	2477	1638	57	5		5	C9orf24	9	34379662	Silent	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	17244514	34379662	106833769	180	15132											
NPR2	4882	hgsc.bcm.edu	37	chr9	35792654	35792654	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagtacctggcaccgctgagCgctgtggacctcaagctgta	8	8	13	12	2	1	1	1	1	0	0	1	3	1	2	3	2	3	6	3	2	3	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr9:35792654C>A	ENST00000342694.2	+	1	504	c.249C>A	c.(247-249)agC>agA	p.S83R		NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2	83					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)	CACCGCTGAGCGCTGTGGACC	0.657																																					p.S83R		Atlas-SNP	.											.	NPR2	162	.	0			c.C249A						PASS	.						104	96	98					9																	35792654		2203	4300	6503	SO:0001583	missense	4882	exon1			GCTGAGCGCTGTG	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.249C>A	9.37:g.35792654C>A	ENSP00000341083:p.Ser83Arg	86	0	0		134	36	0.268657	NM_003995	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Missense_Mutation	SNP	ENST00000342694.2	37	CCDS6590.1	.	.	.	.	.	.	.	.	.	.	C	6.986	0.551947	0.13374	.	.	ENSG00000159899	ENST00000342694	D	0.83914	-1.78	3.93	1.05	0.20165	Extracellular ligand-binding receptor (1);	0.669254	0.13196	N	0.406396	T	0.65943	0.2740	N	0.24115	0.695	0.23972	N	0.996303	B;B	0.06786	0.0;0.001	B;B	0.11329	0.001;0.006	T	0.47169	-0.9138	10	0.13470	T	0.59	.	4.9576	0.14050	0.0:0.5488:0.1602:0.291	.	83;83	P20594-2;P20594	.;ANPRB_HUMAN	R	83	ENSP00000341083:S83R	ENSP00000341083:S83R	S	+	3	2	NPR2	35782654	0.011000	0.17503	1.000000	0.80357	0.976000	0.68499	-0.047000	0.11963	0.432000	0.26286	0.563000	0.77884	AGC	.	.	none		0.657	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1			A	35792654	C	A	35792654	3	1	42	1	0	0	0	0	1	0	0	0	10604	767	27	4	251	4	NPR2	9	35792654	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	1412992	35792654	105420777	181	15133											
FRMPD1	22844	hgsc.bcm.edu	37	chr9	37745741	37745741	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctaaccatgtgacagggcaaGatatagcccctagggacagc	13	6	11	11	0	0	2	0	1	0	1	0	3	0	3	3	2	3	1	3	2	5	4	rs62640014	byFrequency	TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr9:37745741G>C	ENST00000539465.1	+	16	4305	c.3712G>C	c.(3712-3714)Gat>Cat	p.D1238H	FRMPD1_ENST00000377765.3_Missense_Mutation_p.D1238H|RP11-613M10.9_ENST00000540557.1_Intron			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	1238						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.D1238Y(1)		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)		GACAGGGCAAGATATAGCCCC	0.522																																					p.D1238H		Atlas-SNP	.											FRMPD1,colon,carcinoma,-1,3	FRMPD1	237	3	1	Substitution - Missense(1)	ovary(1)	c.G3712C						PASS	.						82	82	82					9																	37745741		2203	4300	6503	SO:0001583	missense	22844	exon16			GGGCAAGATATAG	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.3712G>C	9.37:g.37745741G>C	ENSP00000444411:p.Asp1238His	69	0	0		91	18	0.197802	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	37	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	G	16.24	3.068314	0.55539	.	.	ENSG00000070601	ENST00000377765;ENST00000539465	T;T	0.09911	2.93;2.93	5.29	1.08	0.20341	.	0.978445	0.08425	N	0.947715	T	0.12518	0.0304	L	0.27053	0.805	0.09310	N	1	D	0.56968	0.978	P	0.54460	0.753	T	0.28681	-1.0036	10	0.48119	T	0.1	-1.2993	4.6247	0.12472	0.2747:0.1612:0.564:0.0	.	1238	Q5SYB0	FRPD1_HUMAN	H	1238	ENSP00000366995:D1238H;ENSP00000444411:D1238H	ENSP00000366995:D1238H	D	+	1	0	FRMPD1	37735741	0.091000	0.21658	0.001000	0.08648	0.113000	0.19764	1.983000	0.40648	0.641000	0.30601	0.556000	0.70494	GAT	G|0.998;T|0.002	.	alt		0.522	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907		C	37745741	G	C	37745741	3	2	42	1	0	0	0	0	1	0	0	0	6065	942	33	4	3770	4	FRMPD1	9	37745741	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	1953087	37745741	103467690	182	15134											
TMEM2	23670	hgsc.bcm.edu	37	chr9	74361164	74361164	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggtggcgtctgaggtcagaCggagcatatctccctccttg	6	10	13	12	3	3	2	1	1	2	1	5	3	4	3	2	4	1	1	2	4	1	2	rs200303233		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr9:74361164C>T	ENST00000377044.4	-	3	964	c.425G>A	c.(424-426)cGt>cAt	p.R142H	TMEM2_ENST00000377066.5_Missense_Mutation_p.R142H	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	142	G8. {ECO:0000255|PROSITE- ProRule:PRU00817}.				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)		TGAGGTCAGACGGAGCATATC	0.463																																					p.R142H		Atlas-SNP	.											.	TMEM2	112	.	0			c.G425A						PASS	.	C	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	157	143	148		425,425	4.5	1	9		148	0,8600		0,0,4300	no	missense,missense	TMEM2	NM_001135820.1,NM_013390.2	29,29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	142/1321,142/1384	74361164	1,13005	2203	4300	6503	SO:0001583	missense	23670	exon3			GTCAGACGGAGCA		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.425G>A	9.37:g.74361164C>T	ENSP00000366243:p.Arg142His	136	0	0		207	16	0.0772947	NM_001135820	A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Missense_Mutation	SNP	ENST00000377044.4	37	CCDS6638.1	.	.	.	.	.	.	.	.	.	.	C	20.5	3.994358	0.74703	2.27E-4	0.0	ENSG00000135048	ENST00000377044;ENST00000377066	D;D	0.89050	-2.46;-2.46	5.4	4.5	0.54988	G8 domain (2);	0.097616	0.64402	D	0.000001	D	0.92506	0.7620	L	0.59912	1.85	0.80722	D	1	D;D	0.89917	1.0;0.999	D;P	0.69479	0.964;0.884	D	0.92993	0.6416	10	0.72032	D	0.01	.	14.0641	0.64817	0.0:0.9271:0.0:0.0729	.	142;142	Q9UHN6;Q9UHN6-2	TMEM2_HUMAN;.	H	142	ENSP00000366243:R142H;ENSP00000366266:R142H	ENSP00000366243:R142H	R	-	2	0	TMEM2	73550984	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.481000	0.66826	1.288000	0.44600	-0.142000	0.14014	CGT	C|0.999;T|0.001	0.001	weak		0.463	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390		T	74361164	C	T	74361164	3	4	42	1	0	0	0	0	1	0	0	0	16136	536	19	1	3814	1	TMEM2	9	74361164	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	36615423	74361164	66852267	183	15135											
FAM108B1	51104	hgsc.bcm.edu	37	chr9	74489813	74489813	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	acactcaatagcatctttttCtctagaagaatactgccagt	13	13	5	10	0	3	2	1	0	2	2	4	2	3	2	1	0	3	1	1	0	6	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr9:74489813C>G	ENST00000333421.6	-	2	295	c.184G>C	c.(184-186)Gaa>Caa	p.E62Q	ABHD17B_ENST00000377041.2_Missense_Mutation_p.E62Q	NM_001025780.1	NP_001020951.1	Q5VST6	AB17B_HUMAN	abhydrolase domain containing 17B	62						extracellular region (GO:0005576)|membrane (GO:0016020)	hydrolase activity (GO:0016787)										GCATCTTTTTCTCTAGAAGAA	0.413																																					p.E62Q		Atlas-SNP	.											.	FAM108B1	24	.	0			c.G184C						PASS	.						154	142	146					9																	74489813		2203	4300	6503	SO:0001583	missense	51104	exon2			CTTTTTCTCTAGA	AF151825	CCDS35042.1, CCDS35043.1	9q21.2	2013-03-15	2013-03-15	2013-03-15	ENSG00000107362	ENSG00000107362		"Abhydrolase domain containing"	24278	protein-coding gene	gene with protein product			"chromosome 9 open reading frame 77", "family with sequence similarity 108, member B1"	C9orf77, FAM108B1		10810093	Standard	XM_006717134		Approved	CGI-67	uc004ail.3	Q5VST6	OTTHUMG00000020001	ENST00000333421.6:c.184G>C	9.37:g.74489813C>G	ENSP00000330222:p.Glu62Gln	175	0	0		222	45	0.202703	NM_016014	A8KAJ5|Q5VST7|Q86YB6|Q8IY03|Q9Y377	Missense_Mutation	SNP	ENST00000333421.6	37	CCDS35043.1	.	.	.	.	.	.	.	.	.	.	C	18.39	3.612627	0.66672	.	.	ENSG00000107362	ENST00000377041;ENST00000333421	T;T	0.43294	0.95;0.95	6.17	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.64305	0.2586	M	0.77103	2.36	0.80722	D	1	B;D	0.55800	0.312;0.973	B;P	0.61275	0.175;0.886	T	0.67515	-0.5651	10	0.48119	T	0.1	6.6998	17.7372	0.88397	0.0:0.8776:0.1223:0.0	.	62;62	Q5VST6;Q5VST6-2	F108B_HUMAN;.	Q	62	ENSP00000366240:E62Q;ENSP00000330222:E62Q	ENSP00000330222:E62Q	E	-	1	0	FAM108B1	73679633	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.959000	0.70339	1.611000	0.50210	0.655000	0.94253	GAA	.	.	none		0.413	ABHD17B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052625.1	NM_016014		G	74489813	C	G	74489813	3	3	42	1	0	0	0	0	1	0	0	0	5397	922	32	4	725	4	FAM108B1	9	74489813	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	128649	74489813	66723618	184	15136											
C9orf41	138199	hgsc.bcm.edu	37	chr9	77632226	77632226	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caatcattcacaatggtcagTagtatttcttgattatgatc	12	16	6	7	0	4	2	3	2	1	0	5	2	4	2	0	1	0	2	0	1	5	6	rs541125527		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr9:77632226T>C	ENST00000376834.3	-	2	521	c.369A>G	c.(367-369)ctA>ctG	p.L123L	RP11-197P3.5_ENST00000455336.2_RNA|C9orf41_ENST00000376830.3_Silent_p.L123L|C9orf41_ENST00000376837.3_Silent_p.L123L	NM_152420.1	NP_689633.1	Q8N4J0	CI041_HUMAN	chromosome 9 open reading frame 41	123										endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)|urinary_tract(2)	17						CAATGGTCAGTAGTATTTCTT	0.338																																					p.L123L		Atlas-SNP	.											.	C9orf41	57	.	0			c.A369G						PASS	.						127	116	120					9																	77632226		2203	4300	6503	SO:0001819	synonymous_variant	138199	exon2			GGTCAGTAGTATT	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.369A>G	9.37:g.77632226T>C		161	0	0		157	45	0.286624	NM_152420	Q7Z383|Q8N7C5	Silent	SNP	ENST00000376834.3	37	CCDS6649.1																																																																																			.	.	none		0.338	C9orf41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052703.1	NM_152420		C	77632226	T	C	77632226	2	2	42	1	0	0	0	0	0	0	0	1	2484	1625	57	3		3	C9orf41	9	77632226	Silent	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	3142413	77632226	63581205	185	15137											
ZNF189	7743	hgsc.bcm.edu	37	chr9	104170419	104170419	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaaataccaagggaatctttGacccaggaacagagaatgtt	16	8	10	7	0	1	2	0	1	1	1	1	6	1	4	2	2	2	1	2	2	6	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr9:104170419G>A	ENST00000339664.2	+	3	498	c.369G>A	c.(367-369)ttG>ttA	p.L123L	ZNF189_ENST00000374861.3_Silent_p.L109L|ZNF189_ENST00000259395.4_Silent_p.L81L	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	123					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)				GGGAATCTTTGACCCAGGAAC	0.383																																					p.L123L		Atlas-SNP	.											.	ZNF189	79	.	0			c.G369A						PASS	.						67	65	66					9																	104170419		2203	4300	6503	SO:0001819	synonymous_variant	7743	exon3			ATCTTTGACCCAG	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.369G>A	9.37:g.104170419G>A		178	0	0		165	12	0.0727273	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Silent	SNP	ENST00000339664.2	37	CCDS6754.1																																																																																			.	.	none		0.383	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452		A	104170419	G	A	104170419	2	1	42	1	0	0	0	0	0	0	0	1	17769	1281	45	2		2	ZNF189	9	104170419	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	26538193	104170419	37043012	186	15138											
OR13C9	286362	hgsc.bcm.edu	37	chr9	107380179	107380179	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtccccatggccaagccaaGgaacatctgcactgcacagc	11	6	9	15	0	1	0	0	0	1	0	2	1	2	1	4	2	5	2	4	2	3	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr9:107380179G>A	ENST00000259362.1	-	1	306	c.307C>T	c.(307-309)Ctt>Ttt	p.L103F		NM_001001956.1	NP_001001956.1	Q8NGT0	O13C9_HUMAN	olfactory receptor, family 13, subfamily C, member 9	103						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						GCCAAGCCAAGGAACATCTGC	0.502																																					p.L103F		Atlas-SNP	.											.	OR13C9	42	.	0			c.C307T						PASS	.						118	136	130					9																	107380179		2203	4300	6503	SO:0001583	missense	286362	exon1			AGCCAAGGAACAT		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.307C>T	9.37:g.107380179G>A	ENSP00000259362:p.Leu103Phe	319	0	0		361	168	0.465374	NM_001001956	Q6IFL2	Missense_Mutation	SNP	ENST00000259362.1	37	CCDS35093.1	.	.	.	.	.	.	.	.	.	.	G	6.495	0.459517	0.12342	.	.	ENSG00000136839	ENST00000259362	T	0.00307	8.17	4.64	1.65	0.23941	GPCR, rhodopsin-like superfamily (1);	0.338611	0.21256	N	0.077542	T	0.00073	0.0002	N	0.03967	-0.31	0.09310	N	1	B	0.09022	0.002	B	0.12837	0.008	T	0.12837	-1.0532	10	0.25106	T	0.35	.	4.164	0.10298	0.1843:0.0:0.5256:0.2901	.	103	Q8NGT0	O13C9_HUMAN	F	103	ENSP00000259362:L103F	ENSP00000259362:L103F	L	-	1	0	OR13C9	106420000	0.000000	0.05858	0.964000	0.40570	0.797000	0.45037	0.461000	0.21940	0.575000	0.29434	0.637000	0.83480	CTT	.	.	none		0.502	OR13C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053490.1			A	107380179	G	A	107380179	3	1	42	1	0	0	0	0	1	0	0	0	10948	1000	35	2	652	2	OR13C9	9	107380179	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	3209760	107380179	33833252	187	15139											
PAPPA	5069	hgsc.bcm.edu	37	chr9	119097230	119097230	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctaccacagccaggcggtacGtgtgagcttcagttcgcccc	7	8	11	15	3	1	1	1	1	0	0	2	1	1	1	4	2	4	3	4	2	2	4	rs138956040	byFrequency	TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr9:119097230G>A	ENST00000328252.3	+	13	3857	c.3488G>A	c.(3487-3489)cGt>cAt	p.R1163H	PAPPA_ENST00000534838.1_Missense_Mutation_p.R201H	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	1163					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						CAGGCGGTACGTGTGAGCTTC	0.622													G|||	4	0.000798722	0.0	0.0	5008	,	,		16541	0.004		0.0	False		,,,				2504	0.0				p.R1163H		Atlas-SNP	.											.	PAPPA	243	.	0			c.G3488A						PASS	.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	114	93	100		3488	1.6	1	9	dbSNP_134	100	0,8600		0,0,4300	yes	missense	PAPPA	NM_002581.3	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	1163/1628	119097230	1,13005	2203	4300	6503	SO:0001583	missense	5069	exon13			CGGTACGTGTGAG		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.3488G>A	9.37:g.119097230G>A	ENSP00000330658:p.Arg1163His	78	0	0		90	11	0.122222	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Missense_Mutation	SNP	ENST00000328252.3	37	CCDS6813.1	.	.	.	.	.	.	.	.	.	.	G	14.69	2.610298	0.46527	2.27E-4	0.0	ENSG00000182752	ENST00000328252;ENST00000534838	T;T	0.03717	4.62;3.83	5.86	1.59	0.23543	.	0.220749	0.48767	N	0.000178	T	0.02304	0.0071	N	0.19112	0.55	0.27531	N	0.951088	B;B	0.09022	0.001;0.002	B;B	0.04013	0.001;0.001	T	0.40156	-0.9578	10	0.37606	T	0.19	-8.6133	4.3967	0.11367	0.2709:0.0:0.4076:0.3215	.	201;1163	F5GZ19;Q13219	.;PAPP1_HUMAN	H	1163;201	ENSP00000330658:R1163H;ENSP00000441461:R201H	ENSP00000330658:R1163H	R	+	2	0	PAPPA	118137051	1.000000	0.71417	0.981000	0.43875	0.984000	0.73092	4.471000	0.60182	0.385000	0.24970	-0.137000	0.14449	CGT	G|1.000;A|0.000	0.000	weak		0.622	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581		A	119097230	G	A	119097230	3	1	42	1	0	0	0	0	1	0	0	0	11441	1145	40	1	3538	1	PAPPA	9	119097230	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	11717051	119097230	22116201	188	15140											
TLR4	7099	hgsc.bcm.edu	37	chr9	120476234	120476234	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aagttgaacgaatggaatgtGcaacaccttcagataagcag	16	8	10	7	1	1	2	1	1	0	1	1	4	1	3	1	1	4	3	1	1	6	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr9:120476234G>T	ENST00000355622.6	+	3	1929	c.1828G>T	c.(1828-1830)Gca>Tca	p.A610S	TLR4_ENST00000472304.1_3'UTR|TLR4_ENST00000394487.4_Missense_Mutation_p.A570S	NM_138554.4|NM_138557.2	NP_612564.1|NP_612567.1	O00206	TLR4_HUMAN	toll-like receptor 4	610	LRRCT.				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)	AATGGAATGTGCAACACCTTC	0.463																																					p.A610S		Atlas-SNP	.											.	TLR4	220	.	0			c.G1828T						PASS	.						154	131	139					9																	120476234		2203	4300	6503	SO:0001583	missense	7099	exon3			GAATGTGCAACAC	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.1828G>T	9.37:g.120476234G>T	ENSP00000363089:p.Ala610Ser	99	0	0		86	20	0.232558	NM_138554	A8K1Y8|A9XLP9|A9XLQ0|A9XLQ1|B4E194|D1CS52|D1CS53|Q5VZI8|Q5VZI9|Q9UK78|Q9UM57	Missense_Mutation	SNP	ENST00000355622.6	37	CCDS6818.1	.	.	.	.	.	.	.	.	.	.	G	5.591	0.293758	0.10567	.	.	ENSG00000136869	ENST00000394487;ENST00000355622	T;T	0.35421	1.58;1.31	6.02	-1.48	0.08745	Cysteine-rich flanking region, C-terminal (1);	1.168330	0.06040	N	0.654752	T	0.28699	0.0711	L	0.49350	1.555	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.32877	-0.9890	10	0.09084	T	0.74	.	8.608	0.33784	0.4529:0.1351:0.4121:0.0	.	610	O00206	TLR4_HUMAN	S	570;610	ENSP00000377997:A570S;ENSP00000363089:A610S	ENSP00000363089:A610S	A	+	1	0	TLR4	119516055	0.000000	0.05858	0.002000	0.10522	0.036000	0.12997	-0.510000	0.06328	-0.155000	0.11098	0.650000	0.86243	GCA	.	.	none		0.463	TLR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055549.3	NM_138554		T	120476234	G	T	120476234	3	4	42	1	0	0	0	0	1	0	0	0	15968	1319	46	4	1838	4	TLR4	9	120476234	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	1379004	120476234	20737197	189	15141											
PHF19	26147	hgsc.bcm.edu	37	chr9	123632173	123632173	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcagaaccaaggtgtgagcaGgggctggtcagcactgcccg	9	5	16	11	1	1	2	1	1	0	1	1	2	1	2	2	4	4	4	2	4	2	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr9:123632173G>A	ENST00000373896.3	-	5	667	c.415C>T	c.(415-417)Ctg>Ttg	p.L139L	PHF19_ENST00000419155.1_5'Flank|PHF19_ENST00000487555.1_5'Flank|PHF19_ENST00000312189.6_Silent_p.L139L	NM_015651.1	NP_056466.1	Q5T6S3	PHF19_HUMAN	PHD finger protein 19	139					chromatin modification (GO:0016568)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of histone H3-K27 methylation (GO:0061087)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(3)|large_intestine(1)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GGTGTGAGCAGGGGCTGGTCA	0.652																																					p.L139L		Atlas-SNP	.											.	PHF19	47	.	0			c.C415T						PASS	.						36	30	32					9																	123632173		2199	4299	6498	SO:0001819	synonymous_variant	26147	exon5			TGAGCAGGGGCTG	BX640713	CCDS35116.1, CCDS35117.1, CCDS69648.1, CCDS75889.1	9q34.11	2013-01-28			ENSG00000119403	ENSG00000119403		"Tudor domain containing", "Zinc fingers, PHD-type"	24566	protein-coding gene	gene with protein product	"polycomb-like 3", "tudor domain containing 19B"	609740				15563832	Standard	XM_005251906		Approved	DKFZP727G051, PCL3, MTF2L1, TDRD19B	uc004bks.1	Q5T6S3	OTTHUMG00000020577	ENST00000373896.3:c.415C>T	9.37:g.123632173G>A		69	0	0		57	9	0.157895	NM_015651	Q32NF2|Q5T6S4|Q6N038|Q8TBL6|Q9UFS9	Silent	SNP	ENST00000373896.3	37	CCDS35116.1																																																																																			.	.	none		0.652	PHF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053838.3	XM_045308		A	123632173	G	A	123632173	2	1	42	1	0	0	0	0	0	0	0	1	11838	991	35	2		2	PHF19	9	123632173	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	3155939	123632173	17581258	190	15142											
NUP188	23511	hgsc.bcm.edu	37	chr9	131768932	131768932	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgatccagttggtgcaggCgtttgtccggcatatgcaaa	8	12	12	9	2	1	1	0	1	1	0	3	1	3	1	2	3	2	5	2	3	2	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr9:131768932C>T	ENST00000372577.2	+	44	5246	c.5225C>T	c.(5224-5226)gCg>gTg	p.A1742V	RP11-167N5.5_ENST00000594418.1_lincRNA	NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	1742					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						TTGGTGCAGGCGTTTGTCCGG	0.627											OREG0019528	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A1742V		Atlas-SNP	.											.	NUP188	140	.	0			c.C5225T						PASS	.						117	109	112					9																	131768932		2203	4300	6503	SO:0001583	missense	23511	exon44			TGCAGGCGTTTGT	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.5225C>T	9.37:g.131768932C>T	ENSP00000361658:p.Ala1742Val	59	0	0	1590	51	14	0.27451	NM_015354	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Missense_Mutation	SNP	ENST00000372577.2	37	CCDS35156.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.101219	0.76983	.	.	ENSG00000095319	ENST00000356693;ENST00000372577	T	0.36340	1.26	5.22	5.22	0.72569	.	0.104805	0.64402	D	0.000004	T	0.56630	0.1998	L	0.54323	1.7	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.58521	-0.7622	10	0.66056	D	0.02	-4.3736	17.7677	0.88483	0.0:1.0:0.0:0.0	.	1742	Q5SRE5	NU188_HUMAN	V	1631;1742	ENSP00000361658:A1742V	ENSP00000349125:A1631V	A	+	2	0	NUP188	130808753	1.000000	0.71417	1.000000	0.80357	0.157000	0.22087	7.263000	0.78421	2.423000	0.82170	0.561000	0.74099	GCG	.	.	none		0.627	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2			T	131768932	C	T	131768932	3	4	42	1	0	0	0	0	1	0	0	0	10767	768	27	1	5399	1	NUP188	9	131768932	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	8136759	131768932	9444499	191	15143											
BAT2L1	84726	hgsc.bcm.edu	37	chr9	134319653	134319653	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctggagggcaggacaaggCtggcaaagaaaagggcgtct	13	4	17	7	1	1	1	0	0	1	1	1	3	1	3	0	6	1	4	0	6	4	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr9:134319653C>T	ENST00000357304.4	+	5	606	c.551C>T	c.(550-552)gCt>gTt	p.A184V	PRRC2B_ENST00000372249.1_5'Flank|PRRC2B_ENST00000458550.1_Missense_Mutation_p.A184V|PRRC2B_ENST00000405995.1_Missense_Mutation_p.A184V	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	184							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						CAGGACAAGGCTGGCAAAGAA	0.557																																					p.A184V		Atlas-SNP	.											.	PRRC2B	266	.	0			c.C551T						PASS	.						52	54	54					9																	134319653		2027	4190	6217	SO:0001583	missense	84726	exon5			ACAAGGCTGGCAA	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.551C>T	9.37:g.134319653C>T	ENSP00000349856:p.Ala184Val	53	0	0		52	18	0.346154	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	37	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	C	19.63	3.863201	0.71949	.	.	ENSG00000130723	ENST00000405995;ENST00000541684;ENST00000357304;ENST00000458550	T;T;T	0.27256	1.68;1.68;1.68	5.54	4.53	0.55603	BAT2, N-terminal (1);	0.190217	0.24359	U	0.039207	T	0.15046	0.0363	N	0.20401	0.57	0.80722	D	1	B	0.17038	0.02	B	0.20184	0.028	T	0.08269	-1.0730	10	0.30078	T	0.28	-32.5767	7.4546	0.27258	0.0:0.8271:0.0:0.1729	.	184	Q5JSZ5	PRC2B_HUMAN	V	184	ENSP00000384606:A184V;ENSP00000349856:A184V;ENSP00000398853:A184V	ENSP00000349856:A184V	A	+	2	0	PRRC2B	133309474	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.821000	0.39041	2.618000	0.88619	0.462000	0.41574	GCT	.	.	none		0.557	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				T	134319653	C	T	134319653	3	4	42	1	0	0	0	0	1	0	0	0	1320	797	28	2	569	2	BAT2L1	9	134319653	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	2550721	134319653	6893778	192	15144											
AGPAT2	10555	hgsc.bcm.edu	37	chr9	139568309	139568309	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcccggtggcaggtgtccacGagcgcagggacgtccgccgc	5	4	17	15	6	0	0	0	0	0	0	2	2	2	1	4	4	1	2	4	4	0	0	rs200288462		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr9:139568309G>A	ENST00000371696.2	-	6	797	c.732C>T	c.(730-732)ctC>ctT	p.L244L	AGPAT2_ENST00000538402.1_Silent_p.L244L|AGPAT2_ENST00000371694.3_Silent_p.L212L	NM_006412.3	NP_006403.2	O15120	PLCB_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 2	244					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)		AGGTGTCCACGAGCGCAGGGA	0.682																																					p.L244L		Atlas-SNP	.											.	AGPAT2	17	.	0			c.C732T						PASS	.	G	,	0,4388		0,0,2194	41	41	41		636,732	-6.7	0	9		41	3,8587		0,3,4292	no	coding-synonymous,coding-synonymous	AGPAT2	NM_001012727.1,NM_006412.3	,	0,3,6486	AA,AG,GG		0.0349,0.0,0.0231	,	212/247,244/279	139568309	3,12975	2194	4295	6489	SO:0001819	synonymous_variant	10555	exon6			GTCCACGAGCGCA	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.732C>T	9.37:g.139568309G>A		68	0	0		71	25	0.352113	NM_006412	O00516|O15106|Q5VUD3|Q5VUD4|Q9BSV7|Q9BWR7	Silent	SNP	ENST00000371696.2	37	CCDS7003.1																																																																																			G|0.997;A|0.003	0.003	weak		0.682	AGPAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055090.1	NM_006412		A	139568309	G	A	139568309	2	1	42	1	0	0	0	0	0	0	0	1	387	1045	37	1		1	AGPAT2	9	139568309	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	5248656	139568309	1645122	193	15145											
ABCA2	20	hgsc.bcm.edu	37	chr9	139909868	139909869	+	Frame_Shift_Ins	INS	-	-	G																															gcagcttcaacacagaccttINSgggggccccccggctcggcg																										TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr9:139909868_139909869insG	ENST00000371605.3	-	23	3838_3839	c.3691_3692insC	c.(3691-3693)caafs	p.Q1231fs	ABCA2_ENST00000492260.1_5'Flank|ABCA2_ENST00000341511.6_Frame_Shift_Ins_p.Q1232fs|ABCA2_ENST00000265662.5_Frame_Shift_Ins_p.Q1232fs			Q9BZC7	ABCA2_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 2	1231					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)		ACACAGACCTTGGGGGCCCCCC	0.678																																					p.Q1262fs		Atlas-Indel	.											.	ABCA2	113	.	0			c.3785_3786insC						PASS	.																																			SO:0001589	frameshift_variant	20	exon24			.	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.3692dupC	9.37:g.139909873_139909873dupG	ENSP00000360666:p.Gln1231fs	62	0	0		47	10	0.212766	NM_212533	A6NED5|Q5SPY5|Q5W9G5|Q76MW7|Q9HC28	Frame_Shift_Ins	INS	ENST00000371605.3	37																																																																																				.	.	none		0.678	ABCA2-202	KNOWN	basic	protein_coding	protein_coding		NM_001606		G	139909869	-	G	139909868	7	5	42	1	0	1	1	0	0	0	0	0	32	1812	63	0	3719	0	ABCA2	9	139909868	Frame_Shift_Ins	INS	-	TCGA-GS-A9TZ-01A-11D-A38X-10	341559	139909868	1303563	194	15146											
MCM10	55388	hgsc.bcm.edu	37	chr10	13222489	13222489	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaacaagaaaatgaccggccGaaaactgatcagactgtctc	16	6	9	10	2	2	4	1	2	1	2	3	6	2	4	2	1	2	0	2	1	6	0	rs556697001		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr10:13222489G>A	ENST00000484800.2	+	7	918	c.815G>A	c.(814-816)cGa>cAa	p.R272Q	MCM10_ENST00000378694.1_Missense_Mutation_p.R271Q|MCM10_ENST00000378714.3_Missense_Mutation_p.R271Q			Q7L590	MCM10_HUMAN	minichromosome maintenance complex component 10	272	OB-fold 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						ATGACCGGCCGAAAACTGATC	0.413													G|||	1	0.000199681	0.0	0.0	5008	,	,		16663	0.0		0.0	False		,,,				2504	0.001				p.R272Q		Atlas-SNP	.											.	MCM10	76	.	0			c.G815A						PASS	.						110	107	108					10																	13222489		2203	4300	6503	SO:0001583	missense	55388	exon7			CCGGCCGAAAACT	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.815G>A	10.37:g.13222489G>A	ENSP00000418268:p.Arg272Gln	138	0	0		106	15	0.141509	NM_182751	A8K9I6|B7ZKZ8|Q3MIR3|Q7LD55|Q96GX4|Q96NB6|Q9H0D7|Q9H3P9|Q9P177	Missense_Mutation	SNP	ENST00000484800.2	37	CCDS7096.1	.	.	.	.	.	.	.	.	.	.	G	36	5.892283	0.97074	.	.	ENSG00000065328	ENST00000378714;ENST00000361282;ENST00000484800;ENST00000378694	T;T;T	0.17370	2.29;2.3;2.28	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.51618	0.1685	M	0.88031	2.925	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.997;0.998;0.994	T	0.54022	-0.8355	10	0.48119	T	0.1	-24.3162	20.0953	0.97838	0.0:0.0:1.0:0.0	.	271;271;272	Q5T670;Q7L590-2;Q7L590	.;.;MCM10_HUMAN	Q	271;272;272;271	ENSP00000367986:R271Q;ENSP00000418268:R272Q;ENSP00000367966:R271Q	ENSP00000354945:R272Q	R	+	2	0	MCM10	13262495	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.236000	0.95360	2.767000	0.95098	0.655000	0.94253	CGA	.	.	none		0.413	MCM10-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356853.1	NM_182751		A	13222489	G	A	13222489	3	1	42	1	0	0	0	0	1	0	0	0	9394	1058	37	1	837	1	MCM10	10	13222489	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10		13222489	122312258	195	15147											
CUBN	8029	hgsc.bcm.edu	37	chr10	16967409	16967409	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagggtggagaacagatatcAggaccatttcttagctggaa	14	9	12	6	0	2	2	1	0	1	2	2	5	2	4	1	4	2	1	1	4	5	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr10:16967409A>G	ENST00000377833.4	-	43	6542	c.6477T>C	c.(6475-6477)ccT>ccC	p.P2159P		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	2159	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)	AACAGATATCAGGACCATTTC	0.408																																					p.P2159P		Atlas-SNP	.											CUBN,NS,carcinoma,0,1	CUBN	515	1	0			c.T6477C						scavenged	.						46	47	47					10																	16967409		2203	4300	6503	SO:0001819	synonymous_variant	8029	exon43			GATATCAGGACCA	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.6477T>C	10.37:g.16967409A>G		245	1	0.00408163		193	26	0.134715	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	37	CCDS7113.1																																																																																			.	.	none		0.408	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081		G	16967409	A	G	16967409	2	3	42	1	0	0	0	0	0	0	0	1	4053	175	7	3		3	CUBN	10	16967409	Silent	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	3744920	16967409	118567338	196	15148											
SVIL	6840	hgsc.bcm.edu	37	chr10	29751241	29751241	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	agcgatgtcctctctgtgctCccagctgggaaacatattgg	8	11	11	11	1	1	0	0	0	1	0	4	2	3	1	2	2	4	2	2	2	2	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr10:29751241C>G	ENST00000355867.4	-	36	7119	c.6367G>C	c.(6367-6369)Gag>Cag	p.E2123Q	PTCHD3P1_ENST00000413405.1_RNA|SVIL_ENST00000535393.1_Missense_Mutation_p.E1037Q|SVIL_ENST00000375398.2_Missense_Mutation_p.E2123Q|PTCHD3P1_ENST00000446807.1_RNA|PTCHD3P1_ENST00000414457.1_RNA|PTCHD3P1_ENST00000455774.1_RNA|PTCHD3P1_ENST00000445521.1_RNA|PTCHD3P1_ENST00000423223.1_RNA|SVIL_ENST00000375400.3_Missense_Mutation_p.E1697Q	NM_021738.2	NP_068506.2	O95425	SVIL_HUMAN	supervillin	2123					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)				TCTCTGTGCTCCCAGCTGGGA	0.502																																					p.E2123Q		Atlas-SNP	.											.	SVIL	226	.	0			c.G6367C						PASS	.						143	136	139					10																	29751241		2203	4300	6503	SO:0001583	missense	6840	exon36			TGTGCTCCCAGCT	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.6367G>C	10.37:g.29751241C>G	ENSP00000348128:p.Glu2123Gln	100	0	0		109	29	0.266055	NM_021738	D3DRW9|M1J557|O60611|O60612|Q5VZK5|Q5VZK6|Q9H1R7	Missense_Mutation	SNP	ENST00000355867.4	37	CCDS7164.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.908113	0.92107	.	.	ENSG00000197321	ENST00000375400;ENST00000375398;ENST00000355867;ENST00000535393	T;T;T;T	0.14391	2.63;2.65;2.65;2.51	4.54	4.54	0.55810	.	0.000000	0.85682	D	0.000000	T	0.35885	0.0947	M	0.62723	1.935	0.80722	D	1	D;P;P	0.76494	0.999;0.5;0.865	D;B;P	0.76071	0.987;0.336;0.594	T	0.14811	-1.0459	10	0.72032	D	0.01	-23.7608	17.4772	0.87662	0.0:1.0:0.0:0.0	.	1037;1697;2123	F5H2Q5;O95425-2;O95425	.;.;SVIL_HUMAN	Q	1697;2123;2123;1037	ENSP00000364549:E1697Q;ENSP00000364547:E2123Q;ENSP00000348128:E2123Q;ENSP00000445472:E1037Q	ENSP00000348128:E2123Q	E	-	1	0	SVIL	29791247	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.551000	0.82182	2.339000	0.79563	0.561000	0.74099	GAG	.	.	none		0.502	SVIL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047395.1			G	29751241	C	G	29751241	3	3	42	1	0	0	0	0	1	0	0	0	15436	864	30	4	289	4	SVIL	10	29751241	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	12783832	29751241	105783506	197	15149											
PARD3	56288	hgsc.bcm.edu	37	chr10	34648142	34648142	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ctcgtttattgccttcagtaGacatagaccttcttagggtt	8	16	8	9	1	2	2	1	0	1	2	3	2	2	2	2	1	1	3	2	1	4	9	rs142553947		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr10:34648142G>C	ENST00000374789.3	-	14	2325	c.2000C>G	c.(1999-2001)tCt>tGt	p.S667C	PARD3_ENST00000374788.3_Missense_Mutation_p.S667C|PARD3_ENST00000374776.1_Missense_Mutation_p.S654C|PARD3_ENST00000340077.5_Missense_Mutation_p.S667C|PARD3_ENST00000544292.1_Missense_Mutation_p.S384C|PARD3_ENST00000374768.1_Missense_Mutation_p.S105C|PARD3_ENST00000374790.3_Missense_Mutation_p.S610C|PARD3_ENST00000374794.3_Missense_Mutation_p.S610C|PARD3_ENST00000350537.4_Missense_Mutation_p.S654C|PARD3_ENST00000545260.1_Missense_Mutation_p.S610C|PARD3_ENST00000545693.1_Missense_Mutation_p.S654C|PARD3_ENST00000374773.1_Missense_Mutation_p.S667C|PARD3_ENST00000346874.4_Missense_Mutation_p.S667C	NM_019619.3	NP_062565.2	Q8TEW0	PARD3_HUMAN	par-3 family cell polarity regulator	667	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)				GCCTTCAGTAGACATAGACCT	0.413																																					p.S667C		Atlas-SNP	.											.	PARD3	131	.	0			c.C2000G						PASS	.						213	195	201					10																	34648142		2203	4300	6503	SO:0001583	missense	56288	exon14			TCAGTAGACATAG	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.2000C>G	10.37:g.34648142G>C	ENSP00000363921:p.Ser667Cys	372	0	0		290	69	0.237931	NM_001184792	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	37	CCDS7178.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.659053	0.88154	.	.	ENSG00000148498	ENST00000545693;ENST00000545260;ENST00000374789;ENST00000374788;ENST00000346874;ENST00000374794;ENST00000350537;ENST00000374790;ENST00000374776;ENST00000340077;ENST00000374773;ENST00000544292;ENST00000374768	T;T;T;T;T;T;T;T;T;T;T;T;T	0.17854	2.25;2.25;2.25;2.25;2.25;2.25;2.25;2.25;2.25;2.25;2.25;2.25;2.25	5.74	5.74	0.90152	PDZ/DHR/GLGF (2);	0.102934	0.64402	D	0.000001	T	0.52058	0.1711	M	0.88775	2.98	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;0.999;0.999;1.0;1.0;1.0;1.0;0.999;0.998;1.0;1.0;0.999;0.999;1.0;0.999	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.91635	0.997;0.984;0.996;0.997;0.996;0.998;0.998;0.972;0.955;0.998;0.999;0.989;0.954;0.999;0.989	T	0.58983	-0.7539	10	0.87932	D	0	.	19.9192	0.97079	0.0:0.0:1.0:0.0	.	610;610;654;654;654;667;667;667;610;654;667;667;654;667;384	Q8TEW0-5;Q8TEW0-3;Q8TEW0-7;Q8TEW0-6;F5H5T0;Q8TEW0-4;Q8TEW0-2;Q8TEW0;Q5VWV2;Q6IQ47;Q5VWU8;Q8TEW0-8;Q8TEW0-9;Q8TEW0-10;F5GZI3	.;.;.;.;.;.;.;PARD3_HUMAN;.;.;.;.;.;.;.	C	654;610;667;667;667;610;654;610;654;667;667;384;105	ENSP00000443147:S654C;ENSP00000440857:S610C;ENSP00000363921:S667C;ENSP00000363920:S667C;ENSP00000340591:S667C;ENSP00000363926:S610C;ENSP00000311986:S654C;ENSP00000363922:S610C;ENSP00000363908:S654C;ENSP00000341844:S667C;ENSP00000363905:S667C;ENSP00000444429:S384C;ENSP00000363900:S105C	ENSP00000341844:S667C	S	-	2	0	PARD3	34688148	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	9.869000	0.99810	2.719000	0.93026	0.655000	0.94253	TCT	G|1.000;C|0.000	0.000	weak		0.413	PARD3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047527.1	NM_019619		C	34648142	G	C	34648142	3	2	42	1	0	0	0	0	1	0	0	0	11452	942	33	4	2153	4	PARD3	10	34648142	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	4896901	34648142	100886605	198	15150											
PCDH15	65217	hgsc.bcm.edu	37	chr10	55782695	55782695	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagctggcaaattctcttcaAcaaggacagtgtatgttgaa	13	11	9	8	0	2	1	1	1	1	0	3	2	2	2	0	2	2	4	0	2	5	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr10:55782695A>G	ENST00000320301.6	-	19	2877	c.2483T>C	c.(2482-2484)gTt>gCt	p.V828A	PCDH15_ENST00000361849.3_Missense_Mutation_p.V828A|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000395445.1_Missense_Mutation_p.V835A|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395432.2_Missense_Mutation_p.V791A|PCDH15_ENST00000395433.1_Missense_Mutation_p.V806A|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000414778.1_Missense_Mutation_p.V833A|PCDH15_ENST00000437009.1_Missense_Mutation_p.V757A|PCDH15_ENST00000409834.1_Missense_Mutation_p.V439A|PCDH15_ENST00000373965.2_Missense_Mutation_p.V835A|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395438.1_Missense_Mutation_p.V828A|PCDH15_ENST00000373955.1_Missense_Mutation_p.V828A|PCDH15_ENST00000395430.1_Missense_Mutation_p.V828A	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	828	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)				ATTCTCTTCAACAAGGACAGT	0.413										HNSCC(58;0.16)																											p.V833A		Atlas-SNP	.											.	PCDH15	1715	.	0			c.T2498C						PASS	.						167	151	157					10																	55782695		2203	4300	6503	SO:0001583	missense	65217	exon20			TCTTCAACAAGGA	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.2483T>C	10.37:g.55782695A>G	ENSP00000322604:p.Val828Ala	190	0	0		165	42	0.254545	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	A	18.68	3.676898	0.67928	.	.	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	0.58210	0.35;0.35;0.35;0.35;0.35;0.35;0.35;0.35;0.35;0.35;0.35;0.35	5.52	5.52	0.82312	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.73690	0.3619	M	0.81614	2.55	0.58432	D	0.999998	D;D;D;P;D;D;D;P;D;D;D;P;P;D	0.69078	0.992;0.997;0.997;0.873;0.996;0.993;0.967;0.932;0.975;0.986;0.975;0.605;0.917;0.986	D;D;D;P;D;D;P;P;P;D;P;B;P;D	0.72075	0.944;0.957;0.976;0.846;0.973;0.963;0.901;0.717;0.858;0.932;0.734;0.257;0.539;0.932	T	0.78006	-0.2373	9	0.87932	D	0	.	15.5913	0.76530	1.0:0.0:0.0:0.0	.	806;828;828;833;757;791;828;828;835;835;828;833;828;828	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	A	835;833;828;828;439;835;791;828;806;828;828;833;757;828	ENSP00000363076:V835A;ENSP00000410304:V833A;ENSP00000378826:V828A;ENSP00000386693:V439A;ENSP00000378832:V835A;ENSP00000378820:V791A;ENSP00000354950:V828A;ENSP00000378821:V806A;ENSP00000322604:V828A;ENSP00000378818:V828A;ENSP00000412628:V757A;ENSP00000363066:V828A	ENSP00000322604:V828A	V	-	2	0	PCDH15	55452701	1.000000	0.71417	0.991000	0.47740	0.361000	0.29550	9.287000	0.95975	2.225000	0.72522	0.477000	0.44152	GTT	.	.	none		0.413	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		G	55782695	A	G	55782695	3	3	42	1	0	0	0	0	1	0	0	0	11520	43	2	3	5063	3	PCDH15	10	55782695	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	21134553	55782695	79752052	199	15151											
PCDH15	65217	hgsc.bcm.edu	37	chr10	55943228	55943228	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atgacactgtccccaggtctCatgtctgtataaacatacac	12	11	6	12	0	2	1	1	1	2	0	4	1	3	1	2	1	2	1	2	1	4	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr10:55943228C>T	ENST00000320301.6	-	13	1960	c.1566G>A	c.(1564-1566)atG>atA	p.M522I	PCDH15_ENST00000361849.3_Missense_Mutation_p.M522I|PCDH15_ENST00000395446.1_Missense_Mutation_p.M522I|PCDH15_ENST00000395445.1_Missense_Mutation_p.M529I|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000395432.2_Missense_Mutation_p.M485I|PCDH15_ENST00000395433.1_Missense_Mutation_p.M500I|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000414778.1_Missense_Mutation_p.M527I|PCDH15_ENST00000437009.1_Missense_Mutation_p.M522I|PCDH15_ENST00000409834.1_Missense_Mutation_p.M133I|PCDH15_ENST00000373965.2_Missense_Mutation_p.M529I|PCDH15_ENST00000373957.3_Missense_Mutation_p.M500I|PCDH15_ENST00000395438.1_Missense_Mutation_p.M522I|PCDH15_ENST00000373955.1_Missense_Mutation_p.M522I|PCDH15_ENST00000395430.1_Missense_Mutation_p.M522I	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	522	Cadherin 5. {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)				CCCCAGGTCTCATGTCTGTAT	0.378										HNSCC(58;0.16)																											p.M527I		Atlas-SNP	.											.	PCDH15	1715	.	0			c.G1581A						PASS	.						225	197	207					10																	55943228		2203	4300	6503	SO:0001583	missense	65217	exon14			AGGTCTCATGTCT	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.1566G>A	10.37:g.55943228C>T	ENSP00000322604:p.Met522Ile	144	0	0		128	32	0.25	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	C	11.74	1.727702	0.30593	.	.	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	0.50277	0.75;0.75;0.75;0.75;0.75;0.75;0.75;0.75;0.75;0.75;0.75;0.75;0.75;0.75	5.12	5.12	0.69794	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.45196	0.1330	L	0.31476	0.935	0.80722	D	1	P;B;B;B;P;P;P;B;B;B;B;B;B;B;B	0.43024	0.771;0.333;0.392;0.392;0.798;0.592;0.771;0.099;0.182;0.182;0.044;0.099;0.028;0.094;0.333	P;B;B;B;B;B;P;B;B;B;B;B;B;B;B	0.48334	0.574;0.241;0.173;0.348;0.326;0.241;0.574;0.085;0.241;0.173;0.101;0.058;0.03;0.05;0.241	T	0.42582	-0.9443	9	0.56958	D	0.05	.	12.7668	0.57396	0.1643:0.8357:0.0:0.0	.	500;522;522;527;522;485;522;522;529;529;522;527;522;500;522	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	I	529;527;522;522;133;529;522;485;522;500;500;522;522;527;522;522	ENSP00000363076:M529I;ENSP00000410304:M527I;ENSP00000378826:M522I;ENSP00000386693:M133I;ENSP00000378832:M529I;ENSP00000378833:M522I;ENSP00000378820:M485I;ENSP00000354950:M522I;ENSP00000378821:M500I;ENSP00000363068:M500I;ENSP00000322604:M522I;ENSP00000378818:M522I;ENSP00000412628:M522I;ENSP00000363066:M522I	ENSP00000322604:M522I	M	-	3	0	PCDH15	55613234	1.000000	0.71417	0.997000	0.53966	0.023000	0.10783	5.624000	0.67764	2.546000	0.85860	0.655000	0.94253	ATG	.	.	none		0.378	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056		T	55943228	C	T	55943228	3	4	42	1	0	0	0	0	1	0	0	0	11520	826	29	2	6004	2	PCDH15	10	55943228	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	160533	55943228	79591519	200	15152											
ARID5B	84159	hgsc.bcm.edu	37	chr10	63662068	63662068	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgatttgcatagcggagctcCagctgttgtgggaagagagg	9	9	16	7	2	0	1	0	0	0	1	1	5	1	3	1	3	4	4	1	3	2	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr10:63662068C>T	ENST00000279873.7	+	2	582	c.172C>T	c.(172-174)Cag>Tag	p.Q58*		NM_032199.2	NP_115575.1	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	58					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)					AGCGGAGCTCCAGCTGTTGTG	0.473																																					p.Q58X		Atlas-SNP	.											.	ARID5B	125	.	0			c.C172T						PASS	.						70	75	73					10																	63662068		2203	4300	6503	SO:0001587	stop_gained	84159	exon2			GAGCTCCAGCTGT	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.172C>T	10.37:g.63662068C>T	ENSP00000279873:p.Gln58*	123	0	0		117	18	0.153846	NM_032199	B4DLB3|Q05DG6|Q32Q59|Q5VST4|Q6NZ42|Q7Z3M4|Q8N421|Q9H786	Nonsense_Mutation	SNP	ENST00000279873.7	37	CCDS31208.1	.	.	.	.	.	.	.	.	.	.	C	41	8.590846	0.98877	.	.	ENSG00000150347	ENST00000279873	.	.	.	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-9.6758	18.7313	0.91736	0.0:1.0:0.0:0.0	.	.	.	.	X	58	.	ENSP00000279873:Q58X	Q	+	1	0	ARID5B	63332074	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.006000	0.63978	2.716000	0.92895	0.655000	0.94253	CAG	.	.	none		0.473	ARID5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048233.1	XM_084482		T	63662068	C	T	63662068	4	4	42	1	0	0	0	0	0	1	0	0	922	595	21	2	178	2	ARID5B	10	63662068	Nonsense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	7718840	63662068	71872679	201	15153											
EGR2	1959	hgsc.bcm.edu	37	chr10	64575715	64575715	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcgaggtcctccaccgggtaGatgttgtcagacagctggtg	7	9	15	10	2	1	2	1	0	0	2	3	3	3	2	3	3	1	3	3	3	1	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr10:64575715G>A	ENST00000242480.3	-	1	400	c.75C>T	c.(73-75)atC>atT	p.I25I	EGR2_ENST00000493899.2_5'UTR|EGR2_ENST00000411732.1_5'UTR|EGR2_ENST00000439032.1_Silent_p.I25I	NM_000399.3|NM_001136177.1	NP_000390.2|NP_001129649.1	P11161	EGR2_HUMAN	early growth response 2	25					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)					CCACCGGGTAGATGTTGTCAG	0.577																																					p.I25I		Atlas-SNP	.											EGR2,NS,carcinoma,-1,1	EGR2	77	1	0			c.C75T						scavenged	.						191	172	178					10																	64575715		2203	4300	6503	SO:0001819	synonymous_variant	1959	exon1			CGGGTAGATGTTG	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.75C>T	10.37:g.64575715G>A		73	2	0.0273973		63	18	0.285714	NM_000399	B2R724|B3KRD7|Q68CZ5|Q8IV26|Q9UNA6	Silent	SNP	ENST00000242480.3	37	CCDS7267.1																																																																																			.	.	none		0.577	EGR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048245.2	NM_000399		A	64575715	G	A	64575715	2	1	42	1	0	0	0	0	0	0	0	1	4974	932	33	2		2	EGR2	10	64575715	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	913647	64575715	70959032	202	15154											
HERC4	26091	hgsc.bcm.edu	37	chr10	69695935	69695935	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttgtttgttaacagctgtgtCtgcaccatttagaaccagct	9	15	8	9	0	1	1	0	0	1	1	1	1	1	1	2	0	5	5	2	0	3	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr10:69695935C>G	ENST00000395198.3	-	23	2900	c.2653G>C	c.(2653-2655)Gac>Cac	p.D885H	HERC4_ENST00000412272.2_Missense_Mutation_p.D807H|HERC4_ENST00000395187.2_3'UTR|HERC4_ENST00000277817.6_Missense_Mutation_p.D775H|HERC4_ENST00000373700.4_Missense_Mutation_p.D877H	NM_022079.2	NP_071362.1	Q5GLZ8	HERC4_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase 4	885	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				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						ACAGCTGTGTCTGCACCATTT	0.338																																					p.D885H		Atlas-SNP	.											.	HERC4	78	.	0			c.G2653C						PASS	.						181	169	173					10																	69695935		2203	4299	6502	SO:0001583	missense	26091	exon23			CTGTGTCTGCACC	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.2653G>C	10.37:g.69695935C>G	ENSP00000378624:p.Asp885His	267	0	0		188	49	0.260638	NM_022079	Q5GC98|Q5GC99|Q5GCA0|Q8IXP9|Q9HCH9	Missense_Mutation	SNP	ENST00000395198.3	37	CCDS41533.1	.	.	.	.	.	.	.	.	.	.	C	14.34	2.506093	0.44558	.	.	ENSG00000148634	ENST00000277817;ENST00000412272;ENST00000395198;ENST00000373700	T;T;T;T	0.47177	0.85;0.85;0.85;0.85	5.2	5.2	0.72013	HECT (4);	0.293542	0.41097	D	0.000954	T	0.48003	0.1476	L	0.39514	1.22	0.80722	D	1	B;B;B;B;B	0.24963	0.115;0.005;0.007;0.003;0.007	B;B;B;B;B	0.34779	0.189;0.008;0.021;0.012;0.021	T	0.43893	-0.9363	10	0.46703	T	0.11	.	19.1052	0.93291	0.0:1.0:0.0:0.0	.	807;775;735;877;885	Q5GLZ8-3;Q5GLZ8-6;Q5VXS9;Q5GLZ8-2;Q5GLZ8	.;.;.;.;HERC4_HUMAN	H	775;807;885;877	ENSP00000277817:D775H;ENSP00000416504:D807H;ENSP00000378624:D885H;ENSP00000362804:D877H	ENSP00000277817:D775H	D	-	1	0	HERC4	69365941	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.779000	0.47734	2.568000	0.86640	0.460000	0.39030	GAC	.	.	none		0.338	HERC4-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359262.1	NM_015601		G	69695935	C	G	69695935	3	3	42	1	0	0	0	0	1	0	0	0	7069	913	32	4	536	4	HERC4	10	69695935	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	5120220	69695935	65838812	203	15155											
AP3M1	26985	hgsc.bcm.edu	37	chr10	75896531	75896531	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatgaccacattatccttaaTtgcagcctctgaacactcac	12	12	4	13	0	2	2	1	2	1	0	3	2	3	2	3	0	3	1	3	0	4	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr10:75896531T>C	ENST00000355264.4	-	3	615	c.304A>G	c.(304-306)Att>Gtt	p.I102V	AP3M1_ENST00000487653.1_5'Flank|AP3M1_ENST00000372745.1_Missense_Mutation_p.I102V	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						PASS	.						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	10.37:g.75896531T>C	ENSP00000347408:p.Ile102Val	159	0	0		141	48	0.340426	NM_207012	Q5JQ12|Q9H5L2	Missense_Mutation	SNP	ENST00000355264.4	37	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	.	.	none		0.348	AP3M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048747.1			C	75896531	T	C	75896531	3	2	42	1	0	0	0	0	1	0	0	0	747	1493	52	3	980	3	AP3M1	10	75896531	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	6200596	75896531	59638216	204	15156											
FAM35A	54537	hgsc.bcm.edu	37	chr10	88939926	88939926	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctcacagttctctgaagagTattttttcttctcttcccaa	8	17	5	11	0	4	2	1	1	3	1	7	2	5	2	1	0	0	3	1	0	3	7			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr10:88939926T>G	ENST00000298784.1	+	7	2172	c.2058T>G	c.(2056-2058)agT>agG	p.S686R	FAM35A_ENST00000298786.4_Missense_Mutation_p.S755R	NM_019054.2	NP_061927.2	Q86V20	FA35A_HUMAN	family with sequence similarity 35, member A	686										endometrium(2)|kidney(2)|large_intestine(5)|lung(1)|ovary(2)|prostate(2)|skin(2)	16						CTCTGAAGAGTATTTTTTCTT	0.388																																					p.S686R	Ovarian(175;703 2004 25460 32514 43441)	Atlas-SNP	.											FAM35A,NS,carcinoma,+1,1	FAM35A	48	1	0			c.T2058G						scavenged	.						75	75	75					10																	88939926		2203	4300	6503	SO:0001583	missense	54537	exon7			GAAGAGTATTTTT	BC051863	CCDS7383.1	10q23.2	2010-06-02			ENSG00000122376	ENSG00000122376			28773	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_019054		Approved	MGC5560, bA163M19.1, FAM35A1	uc001kei.4	Q86V20	OTTHUMG00000018669	ENST00000298784.1:c.2058T>G	10.37:g.88939926T>G	ENSP00000298784:p.Ser686Arg	454	2	0.00440529		406	112	0.275862	NM_019054	O95885|Q9H991	Missense_Mutation	SNP	ENST00000298784.1	37	CCDS7383.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	6.059|6.059	0.379258|0.379258	0.11466|0.11466	.|.	.|.	ENSG00000122376|ENSG00000122376	ENST00000298786;ENST00000298784;ENST00000358313|ENST00000342900	T;T;T|.	0.64085|.	-0.08;-0.08;-0.08|.	2.87|2.87	-2.2|-2.2	0.06994|0.06994	.|.	0.554910|.	0.20762|.	N|.	0.086141|.	T|T	0.37652|0.37652	0.1011|0.1011	L|L	0.59436|0.59436	1.845|1.845	0.09310|0.09310	N|N	1|1	B;P|.	0.48016|.	0.001;0.904|.	B;P|.	0.46718|.	0.001;0.525|.	T|T	0.37865|0.37865	-0.9687|-0.9687	10|5	0.29301|.	T|.	0.29|.	-0.2296|-0.2296	3.8924|3.8924	0.09125|0.09125	0.0:0.2922:0.1808:0.527|0.0:0.2922:0.1808:0.527	.|.	409;686|.	Q5VSZ0;Q86V20|.	.;FA35A_HUMAN|.	R|D	755;686;686|410	ENSP00000298786:S755R;ENSP00000298784:S686R;ENSP00000351064:S686R|.	ENSP00000298784:S686R|.	S|Y	+|+	3|1	2|0	FAM35A|FAM35A	88929906|88929906	0.002000|0.002000	0.14202|0.14202	0.009000|0.009000	0.14445|0.14445	0.937000|0.937000	0.57800|0.57800	-0.235000|-0.235000	0.09016|0.09016	-0.554000|-0.554000	0.06150|0.06150	0.352000|0.352000	0.21897|0.21897	AGT|TAT	.	.	none		0.388	FAM35A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049196.2	NM_019054		G	88939926	T	G	88939926	3	3	42	1	0	0	0	0	1	0	0	0	5561	1635	57	5	2076	5	FAM35A	10	88939926	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	13043395	88939926	46594821	205	15157											
PLCE1	51196	hgsc.bcm.edu	37	chr10	96018781	96018781	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcattcagtgtcaggagcCgcaaggacctgaaggatctg	10	8	12	11	1	4	1	3	1	1	0	4	4	4	4	3	3	1	1	3	3	2	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr10:96018781C>T	ENST00000371380.3	+	12	3923	c.3688C>T	c.(3688-3690)Cgc>Tgc	p.R1230C	PLCE1_ENST00000260766.3_Missense_Mutation_p.R1230C|PLCE1_ENST00000371375.1_Missense_Mutation_p.R922C|PLCE1_ENST00000371385.3_Missense_Mutation_p.R922C			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	1230				SR -> QA (in Ref. 8; AAF22005). {ECO:0000305}.	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)				TGTCAGGAGCCGCAAGGACCT	0.463																																					p.R1230C		Atlas-SNP	.											PLCE1_ENST00000371375,NS,carcinoma,-1,3	PLCE1	543	3	0			c.C3688T						PASS	.						125	119	121					10																	96018781		1957	4149	6106	SO:0001583	missense	51196	exon13			AGGAGCCGCAAGG		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.3688C>T	10.37:g.96018781C>T	ENSP00000360431:p.Arg1230Cys	154	0	0		126	39	0.309524	NM_016341	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Missense_Mutation	SNP	ENST00000371380.3	37	CCDS41552.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.410254	0.83340	.	.	ENSG00000138193	ENST00000260766;ENST00000371380;ENST00000371385;ENST00000371375	T;T;T;T	0.60171	0.21;0.21;0.21;0.21	5.77	4.86	0.63082	.	0.000000	0.85682	D	0.000000	T	0.73900	0.3646	M	0.62723	1.935	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;0.999;1.0	T	0.77416	-0.2596	10	0.87932	D	0	.	16.238	0.82389	0.1339:0.8661:0.0:0.0	.	1214;922;1230	B7ZM61;Q9P212-2;Q9P212	.;.;PLCE1_HUMAN	C	1230;1230;922;922	ENSP00000260766:R1230C;ENSP00000360431:R1230C;ENSP00000360438:R922C;ENSP00000360426:R922C	ENSP00000260766:R1230C	R	+	1	0	PLCE1	96008771	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	4.002000	0.57053	1.420000	0.47138	0.555000	0.69702	CGC	.	.	none		0.463	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049469.3	NM_016341		T	96018781	C	T	96018781	3	4	42	1	0	0	0	0	1	0	0	0	12043	652	23	1	4020	1	PLCE1	10	96018781	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	7078855	96018781	39515966	206	15158											
HPSE2	60495	hgsc.bcm.edu	37	chr10	100249925	100249925	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agactttggggccgatcaggCgcttgtagaggagagagagc	10	7	17	7	2	1	4	1	0	0	4	1	7	1	4	1	4	1	2	1	4	1	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr10:100249925C>T	ENST00000370552.3	-	10	1408	c.1349G>A	c.(1348-1350)cGc>cAc	p.R450H	HPSE2_ENST00000404542.1_Missense_Mutation_p.R338H|HPSE2_ENST00000370546.1_Missense_Mutation_p.R450H|HPSE2_ENST00000370549.1_Missense_Mutation_p.R392H	NM_021828.4	NP_068600.4	Q8WWQ2	HPSE2_HUMAN	heparanase 2 (inactive)	450					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)		GCCGATCAGGCGCTTGTAGAG	0.557																																					p.R450H		Atlas-SNP	.											.	HPSE2	203	.	0			c.G1349A						PASS	.						81	82	82					10																	100249925		2203	4300	6503	SO:0001583	missense	60495	exon10			ATCAGGCGCTTGT	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.1349G>A	10.37:g.100249925C>T	ENSP00000359583:p.Arg450His	98	0	0		85	26	0.305882	NM_001166246	Q5VUH4|Q5VUH5|Q5VUH6|Q8WWQ1|Q9HB37|Q9HB38|Q9HB39	Missense_Mutation	SNP	ENST00000370552.3	37	CCDS7477.1	.	.	.	.	.	.	.	.	.	.	C	17.21	3.332532	0.60853	.	.	ENSG00000172987	ENST00000370552;ENST00000370549;ENST00000370546;ENST00000404542	T;T;T;T	0.34472	1.36;1.36;1.36;1.36	5.82	5.82	0.92795	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.065719	0.64402	D	0.000012	T	0.32102	0.0818	L	0.48935	1.535	0.42422	D	0.992648	B;B;B;B	0.28667	0.01;0.219;0.054;0.032	B;B;B;B	0.21360	0.005;0.034;0.017;0.007	T	0.09618	-1.0666	10	0.56958	D	0.05	-8.8517	13.3123	0.60386	0.0:0.9279:0.0:0.0721	.	338;450;392;450	Q8WWQ2-4;Q8WWQ2-2;Q8WWQ2-3;Q8WWQ2	.;.;.;HPSE2_HUMAN	H	450;392;450;338	ENSP00000359583:R450H;ENSP00000359580:R392H;ENSP00000359577:R450H;ENSP00000384384:R338H	ENSP00000359577:R450H	R	-	2	0	HPSE2	100239915	0.998000	0.40836	1.000000	0.80357	0.979000	0.70002	3.720000	0.54933	2.755000	0.94549	0.591000	0.81541	CGC	.	.	none		0.557	HPSE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049789.1	NM_021828		T	100249925	C	T	100249925	3	4	42	1	0	0	0	0	1	0	0	0	7354	768	27	1	479	1	HPSE2	10	100249925	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	4231144	100249925	35284822	207	15159											
SORCS1	114815	hgsc.bcm.edu	37	chr10	108389123	108389123	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ccatcgccaaagtccacttgGatgagtgtccgctgaacatc	10	9	9	13	2	0	2	0	2	0	0	4	3	2	3	4	1	1	1	4	1	2	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr10:108389123G>A	ENST00000263054.6	-	19	2506	c.2499C>T	c.(2497-2499)atC>atT	p.I833I	SORCS1_ENST00000369698.1_Silent_p.I368I|SORCS1_ENST00000344440.6_Silent_p.I833I	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	833	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)			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)		AGTCCACTTGGATGAGTGTCC	0.507																																					p.I833I		Atlas-SNP	.											.	SORCS1	534	.	0			c.C2499T						PASS	.						132	96	108					10																	108389123		2203	4300	6503	SO:0001819	synonymous_variant	114815	exon19			CACTTGGATGAGT	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.2499C>T	10.37:g.108389123G>A		63	0	0		63	18	0.285714	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Silent	SNP	ENST00000263054.6	37	CCDS7559.1																																																																																			.	.	none		0.507	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918		A	108389123	G	A	108389123	2	1	42	1	0	0	0	0	0	0	0	1	14945	1164	41	2		2	SORCS1	10	108389123	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	8139198	108389123	27145624	208	15160											
C10orf81	79949	hgsc.bcm.edu	37	chr10	115531832	115531832	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gaatcattatcttactcctcGaagtgttcttttagaggtaa	11	16	7	7	1	3	1	1	0	2	1	5	3	4	1	1	1	1	2	1	1	6	6	rs267602368		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr10:115531832G>A	ENST00000369310.3	+	7	1200	c.638G>A	c.(637-639)cGa>cAa	p.R213Q	PLEKHS1_ENST00000369309.1_Missense_Mutation_p.R33Q|PLEKHS1_ENST00000369312.4_Missense_Mutation_p.R131Q|PLEKHS1_ENST00000361048.1_Missense_Mutation_p.R219Q|PLEKHS1_ENST00000354462.3_5'UTR	NM_182601.1	NP_872407.1	Q5SXH7	PKHS1_HUMAN	pleckstrin homology domain containing, family S member 1	213																	CTTACTCCTCGAAGTGTTCTT	0.368																																					p.R219Q		Atlas-SNP	.											C10orf81_ENST00000369312,colon,carcinoma,0,2	PLEKHS1	19	2	0			c.G656A						PASS	.						155	142	147					10																	115531832		2203	4300	6503	SO:0001583	missense	79949	exon8			CTCCTCGAAGTGT	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.638G>A	10.37:g.115531832G>A	ENSP00000358316:p.Arg213Gln	136	0	0		99	29	0.292929	NM_024889	A8KA02|B3KX00|B6EDE1|Q5SXH8|Q5SXI0|Q6ZQR5|Q8NE42|Q9H5D9	Missense_Mutation	SNP	ENST00000369310.3	37	CCDS53580.1	.	.	.	.	.	.	.	.	.	.	G	17.56	3.420531	0.62622	.	.	ENSG00000148735	ENST00000361048;ENST00000369312;ENST00000369310;ENST00000369309	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	5.63	4.73	0.59995	.	0.148213	0.42964	N	0.000628	T	0.26376	0.0644	L	0.39397	1.21	0.35931	D	0.832512	D;D;P;P	0.57571	0.974;0.98;0.862;0.945	B;B;B;B	0.43867	0.286;0.372;0.322;0.434	T	0.29731	-1.0002	10	0.36615	T	0.2	-34.6782	10.4632	0.44592	0.0895:0.0:0.9105:0.0	.	213;213;213;219	Q5SXH7;Q5SXH7-5;Q5SXH7-2;Q5SXH7-4	CJ081_HUMAN;.;.;.	Q	219;131;213;33	ENSP00000354332:R219Q;ENSP00000358318:R131Q;ENSP00000358316:R213Q;ENSP00000358315:R33Q	ENSP00000354332:R219Q	R	+	2	0	C10orf81	115521822	0.999000	0.42202	0.879000	0.34478	0.678000	0.39670	1.486000	0.35530	1.389000	0.46526	0.650000	0.86243	CGA	.	.	none		0.368	PLEKHS1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050432.1	NM_024889		A	115531832	G	A	115531832	3	1	42	1	0	0	0	0	1	0	0	0	1621	1058	37	1	682	1	C10orf81	10	115531832	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	7142709	115531832	20002915	209	15161											
FGFR2	2263	hgsc.bcm.edu	37	chr10	123325112	123325112	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	aagtgcaccccatccttagtCcaactgatcacggcggcatc	10	8	8	15	2	1	1	1	1	0	0	4	1	3	1	4	2	2	2	4	2	3	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr10:123325112C>G	ENST00000358487.5	-	3	488	c.216G>C	c.(214-216)tgG>tgC	p.W72C	FGFR2_ENST00000369061.4_Missense_Mutation_p.W72C|FGFR2_ENST00000346997.2_Missense_Mutation_p.W72C|FGFR2_ENST00000369059.1_Intron|FGFR2_ENST00000359354.2_Missense_Mutation_p.W72C|FGFR2_ENST00000360144.3_Intron|FGFR2_ENST00000369060.4_Missense_Mutation_p.W72C|FGFR2_ENST00000457416.2_Missense_Mutation_p.W72C|FGFR2_ENST00000356226.4_Intron|FGFR2_ENST00000357555.5_Intron|FGFR2_ENST00000351936.6_Missense_Mutation_p.W72C|FGFR2_ENST00000490349.1_5'UTR|FGFR2_ENST00000369056.1_Missense_Mutation_p.W72C	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	72	Ig-like C2-type 1.				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)	CATCCTTAGTCCAACTGATCA	0.552		5	Mis		"gastric. NSCLC, endometrial"		"Crouzon, Pfeiffer, and Apert syndromes"		Saethre-Chotzen syndrome;Apert syndrome																												p.W72C		Atlas-SNP	.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	.	FGFR2	758	.	0			c.G216C						PASS	.						168	145	153					10																	123325112		2203	4300	6503	SO:0001583	missense	2263	exon3	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	CTTAGTCCAACTG	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.216G>C	10.37:g.123325112C>G	ENSP00000351276:p.Trp72Cys	185	0	0		146	47	0.321918	NM_022970	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	37	CCDS31298.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.182891	0.78677	.	.	ENSG00000066468	ENST00000369062;ENST00000369061;ENST00000358487;ENST00000369060;ENST00000346997;ENST00000457416;ENST00000351936;ENST00000369056;ENST00000369058;ENST00000359354	D;D;D;D;D;D;D;D;D	0.97161	-4.27;-4.27;-4.27;-4.27;-4.27;-4.27;-4.27;-4.27;-4.27	5.24	5.24	0.73138	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.99196	0.9721	H	0.98936	4.375	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;0.998;0.998;1.0;1.0;1.0	D	0.98786	1.0734	10	0.87932	D	0	.	17.3711	0.87377	0.0:1.0:0.0:0.0	.	91;91;72;91;72;72;91;72	D3DRD9;D3DRD4;B5A960;D3DRD5;P21802-18;P21802;D3DRE0;P21802-17	.;.;.;.;.;FGFR2_HUMAN;.;.	C	72	ENSP00000358057:W72C;ENSP00000351276:W72C;ENSP00000358056:W72C;ENSP00000263451:W72C;ENSP00000410294:W72C;ENSP00000309878:W72C;ENSP00000358052:W72C;ENSP00000358054:W72C;ENSP00000352309:W72C	ENSP00000263451:W72C	W	-	3	0	FGFR2	123315102	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.079000	0.76829	2.587000	0.87381	0.643000	0.83706	TGG	.	.	none		0.552	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141		G	123325112	C	G	123325112	3	3	42	1	0	0	0	0	1	0	0	0	5874	856	30	4	2569	4	FGFR2	10	123325112	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	7793280	123325112	12209635	210	15162											
TACC2	10579	hgsc.bcm.edu	37	chr10	124009153	124009153	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagcagctgcgagtggacGccctggaaaggacgctggag	10	4	18	9	3	0	0	0	0	0	0	0	6	0	5	1	5	3	3	1	5	1	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr10:124009153G>A	ENST00000369005.1	+	22	9095	c.8755G>A	c.(8755-8757)Gcc>Acc	p.A2919T	TACC2_ENST00000360561.3_Missense_Mutation_p.A967T|TACC2_ENST00000369000.1_Missense_Mutation_p.A542T|TACC2_ENST00000358010.1_Missense_Mutation_p.A1065T|TACC2_ENST00000368999.1_Missense_Mutation_p.A1009T|TACC2_ENST00000453444.2_Missense_Mutation_p.A2846T|TACC2_ENST00000515273.1_Missense_Mutation_p.A2846T|TACC2_ENST00000369004.3_Missense_Mutation_p.A979T|TACC2_ENST00000513429.1_Missense_Mutation_p.A1065T|TACC2_ENST00000515603.1_Missense_Mutation_p.A2797T|TACC2_ENST00000260733.3_Missense_Mutation_p.A997T|TACC2_ENST00000334433.3_Missense_Mutation_p.A2919T|TACC2_ENST00000369001.1_Missense_Mutation_p.A546T	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	2919					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)				GCGAGTGGACGCCCTGGAAAG	0.662																																					p.A2919T		Atlas-SNP	.											.	TACC2	271	.	0			c.G8755A						PASS	.						28	30	29					10																	124009153		2203	4300	6503	SO:0001583	missense	10579	exon22			GTGGACGCCCTGG	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.8755G>A	10.37:g.124009153G>A	ENSP00000358001:p.Ala2919Thr	154	0	0		128	33	0.257812	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	.	.	.	.	.	.	.	.	.	.	G	16.03	3.006134	0.54361	.	.	ENSG00000138162	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	0.53640	0.61;0.61;0.61;0.61;0.61;0.61;0.61;0.61;0.61;0.61;0.61;0.61;0.61	5.16	4.26	0.50523	.	0.000000	0.36703	N	0.002443	T	0.52289	0.1725	N	0.17474	0.49	0.46849	D	0.999228	D;D;D;D;D;P;B;P;D	0.89917	1.0;1.0;1.0;1.0;0.998;0.539;0.434;0.862;1.0	D;D;D;D;D;B;B;B;D	0.91635	0.994;0.999;0.994;0.996;0.921;0.237;0.151;0.39;0.997	T	0.58177	-0.7682	10	0.59425	D	0.04	-14.2358	13.9465	0.64089	0.0734:0.0:0.9265:0.0	.	2846;979;2797;2846;967;997;542;1065;2919	E9PBC6;D6RAA5;E7EMZ9;B7ZMJ9;O95359-6;O95359-1;O95359-2;O95359-5;O95359	.;.;.;.;.;.;.;.;TACC2_HUMAN	T	2919;1065;2846;2797;2919;1065;2846;2832;546;542;967;1009;979;997	ENSP00000358001:A2919T;ENSP00000425062:A1065T;ENSP00000424467:A2846T;ENSP00000427618:A2797T;ENSP00000334280:A2919T;ENSP00000350701:A1065T;ENSP00000395048:A2846T;ENSP00000357997:A546T;ENSP00000357996:A542T;ENSP00000353763:A967T;ENSP00000357995:A1009T;ENSP00000422815:A979T;ENSP00000260733:A997T	ENSP00000260733:A997T	A	+	1	0	TACC2	123999143	1.000000	0.71417	0.249000	0.24280	0.041000	0.13682	5.747000	0.68689	1.322000	0.45245	-0.136000	0.14681	GCC	.	.	none		0.662	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1			A	124009153	G	A	124009153	3	1	42	1	0	0	0	0	1	0	0	0	15517	1087	38	1	8909	1	TACC2	10	124009153	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	684041	124009153	11525594	211	15163											
ACADSB	36	hgsc.bcm.edu	37	chr10	124810591	124810591	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caacaccaagtggctcacgtGgccacccagctggaagctgc	10	5	11	15	1	1	0	1	0	0	0	1	1	1	1	3	3	4	3	3	3	3	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr10:124810591G>A	ENST00000358776.4	+	9	1031	c.1017G>A	c.(1015-1017)gtG>gtA	p.V339V	ACADSB_ENST00000368869.4_Silent_p.V237V	NM_001609.3	NP_001600.1	P45954	ACDSB_HUMAN	acyl-CoA dehydrogenase, short/branched chain	339					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|fatty acid metabolic process (GO:0006631)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(2)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	17		all_neural(114;0.0765)|Colorectal(57;0.102)|all_lung(145;0.11)|Lung NSC(174;0.163)		Colorectal(40;0.0811)|COAD - Colon adenocarcinoma(40;0.0835)	L-Isoleucine(DB00167)|Valproic Acid(DB00313)	TGGCTCACGTGGCCACCCAGC	0.458																																					p.V339V		Atlas-SNP	.											.	ACADSB	45	.	0			c.G1017A						PASS	.						41	41	41					10																	124810591		2203	4300	6503	SO:0001819	synonymous_variant	36	exon9			TCACGTGGCCACC	U12778	CCDS7634.1	10q25-q26	2014-09-17	2010-04-30		ENSG00000196177	ENSG00000196177	1.3.99.-		91	protein-coding gene	gene with protein product		600301	"acyl-Coenzyme A dehydrogenase, short/branched chain"			7698750, 7759115	Standard	NM_001609		Approved	SBCAD, ACAD7	uc001lhb.3	P45954	OTTHUMG00000019200	ENST00000358776.4:c.1017G>A	10.37:g.124810591G>A		98	0	0		75	27	0.36	NM_001609	B4DQ51|Q5SQN6|Q96CX7	Silent	SNP	ENST00000358776.4	37	CCDS7634.1																																																																																			.	.	none		0.458	ACADSB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050843.1	NM_001609		A	124810591	G	A	124810591	2	1	42	1	0	0	0	0	0	0	0	1	115	1335	47	2		2	ACADSB	10	124810591	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	801438	124810591	10724156	212	15164											
MUC5B	727897	hgsc.bcm.edu	37	chr11	1272843	1272843	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acccctgcagtgctccccagCagcctgccaaccttcagcgt	7	7	8	19	1	1	0	1	0	0	0	2	0	2	0	7	0	7	3	7	0	1	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr11:1272843C>T	ENST00000529681.1	+	31	14791	c.14733C>T	c.(14731-14733)agC>agT	p.S4911S	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Silent_p.S4914S	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4911	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)		TGCTCCCCAGCAGCCTGCCAA	0.637																																					p.S4911S		Atlas-SNP	.											.	MUC5B	473	.	0			c.C14733T						PASS	.						53	63	60					11																	1272843		2167	4248	6415	SO:0001819	synonymous_variant	727897	exon31			CCCCAGCAGCCTG	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.14733C>T	11.37:g.1272843C>T		38	0	0		33	16	0.484848	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			.	.	none		0.637	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		T	1272843	C	T	1272843	2	4	42	1	0	0	0	0	0	0	0	1	9988	709	25	2		2	MUC5B	11	1272843	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10		1272843	133733673	213	15165											
EIF3F	8665	hgsc.bcm.edu	37	chr11	8016899	8016899	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gatgactttgagaccatgctCaacagcaacatcaatgtgag	14	9	9	9	0	2	3	2	3	0	1	2	5	2	3	1	0	4	2	1	0	3	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr11:8016899C>G	ENST00000533626.1	+	9	1607	c.981C>G	c.(979-981)ctC>ctG	p.L327L	EIF3F_ENST00000309828.4_Silent_p.L327L|EIF3F_ENST00000449102.2_Silent_p.L178L|EIF3F_ENST00000537635.1_Silent_p.L342L					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)		AGACCATGCTCAACAGCAACA	0.498																																					p.L327L		Atlas-SNP	.											.	EIF3F	23	.	0			c.C981G						PASS	.						174	164	168					11																	8016899		2201	4296	6497	SO:0001819	synonymous_variant	8665	exon7			CATGCTCAACAGC	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.981C>G	11.37:g.8016899C>G		100	0	0		81	45	0.555556	NM_003754		Silent	SNP	ENST00000533626.1	37	CCDS7785.1																																																																																			.	.	none		0.498	EIF3F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385713.2	NM_003754		G	8016899	C	G	8016899	2	3	42	1	0	0	0	0	0	0	0	1	5018	813	29	4		4	EIF3F	11	8016899	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	6744056	8016899	126989617	214	15166											
CALCA	796	hgsc.bcm.edu	37	chr11	14989251	14989251	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attcagctgctcaggcttgaAggtccctgcggcgcctgcca	6	9	12	14	2	2	1	2	1	0	0	3	1	3	1	3	3	4	3	3	3	1	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr11:14989251A>C	ENST00000486207.1	-	3	385	c.377T>G	c.(376-378)cTt>cGt	p.L126R	CALCB_ENST00000523376.1_Intron|CALCA_ENST00000361010.3_Missense_Mutation_p.L126R			P06881	CALCA_HUMAN	calcitonin-related polypeptide alpha	126					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						TCAGGCTTGAAGGTCCCTGCG	0.537																																					p.L126R		Atlas-SNP	.											.	CALCA	30	.	0			c.T377G						PASS	.						61	58	59					11																	14989251		2200	4294	6494	SO:0001583	missense	796	exon4			GCTTGAAGGTCCC	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.377T>G	11.37:g.14989251A>C	ENSP00000417833:p.Leu126Arg	69	0	0		52	10	0.192308	NM_001033953	Q93048|Q9UCP0	Missense_Mutation	SNP	ENST00000486207.1	37	CCDS31432.1	.	.	.	.	.	.	.	.	.	.	A	18.40	3.615604	0.66672	.	.	ENSG00000110680	ENST00000486207;ENST00000361010	T;T	0.32515	1.45;1.45	4.65	3.5	0.40072	.	.	.	.	.	T	0.54240	0.1846	M	0.78916	2.43	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.58707	-0.7589	9	0.72032	D	0.01	.	11.7799	0.52008	0.8182:0.1818:0.0:0.0	.	126	P06881	CALCA_HUMAN	R	126	ENSP00000417833:L126R;ENSP00000354286:L126R	ENSP00000354286:L126R	L	-	2	0	CALCA	14945827	0.889000	0.30405	0.186000	0.23195	0.179000	0.23085	1.028000	0.30128	1.033000	0.39918	0.533000	0.62120	CTT	.	.	none		0.537	CALCA-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357068.1	NM_001741		C	14989251	A	C	14989251	3	2	42	1	0	0	0	0	1	0	0	0	2577	72	3	5	13	5	CALCA	11	14989251	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	6972352	14989251	120017265	215	15167											
PLEKHA7	144100	hgsc.bcm.edu	37	chr11	17035910	17035910	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cacaccccgtaggaccaatgCtcaggtaaagtgtcccgccc	10	6	9	16	2	1	0	1	0	0	0	2	1	2	1	5	2	1	3	5	2	4	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr11:17035910C>T	ENST00000355661.3	-	1	49	c.39G>A	c.(37-39)gaG>gaA	p.E13E	OR7E14P_ENST00000530490.1_RNA|PLEKHA7_ENST00000531066.1_Silent_p.E13E|PLEKHA7_ENST00000532079.1_5'UTR|PLEKHA7_ENST00000448080.2_Silent_p.E13E			Q6IQ23	PKHA7_HUMAN	pleckstrin homology domain containing, family A member 7	13	WW 1. {ECO:0000255|PROSITE- ProRule:PRU00224}.				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						AGGACCAATGCTCAGGTAAAG	0.781																																					p.E13E		Atlas-SNP	.											.	PLEKHA7	120	.	0			c.G39A						PASS	.						4	3	4					11																	17035910		1811	3701	5512	SO:0001819	synonymous_variant	144100	exon1			CCAATGCTCAGGT	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.39G>A	11.37:g.17035910C>T		52	0	0		29	15	0.517241	NM_175058	B4DK33|B4DWC3|Q86VZ7	Silent	SNP	ENST00000355661.3	37	CCDS31434.1																																																																																			.	.	none		0.781	PLEKHA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000387242.2	NM_175058		T	17035910	C	T	17035910	2	4	42	1	0	0	0	0	0	0	0	1	12070	796	28	2		2	PLEKHA7	11	17035910	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	2046659	17035910	117970606	216	15168											
MUC15	143662	hgsc.bcm.edu	37	chr11	26584710	26584710	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccgatgggaaaatgaatccGttttcctttttccacacaac	11	12	7	11	2	0	1	0	1	0	0	3	3	3	2	4	1	1	1	4	1	4	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr11:26584710G>A	ENST00000455601.2	-	3	915	c.797C>T	c.(796-798)aCg>aTg	p.T266M	ANO3_ENST00000531568.1_Intron|ANO3_ENST00000256737.3_Intron|MUC15_ENST00000527569.1_Intron|ANO3_ENST00000529242.1_3'UTR|MUC15_ENST00000436318.2_Missense_Mutation_p.T293M|MUC15_ENST00000529533.1_Missense_Mutation_p.T293M|MUC15_ENST00000281268.8_Intron|ANO3_ENST00000537978.1_Intron|ANO3_ENST00000525139.1_Intron	NM_145650.3	NP_663625.2	Q8N387	MUC15_HUMAN	mucin 15, cell surface associated	266					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)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	25						AAATGAATCCGTTTTCCTTTT	0.393																																					p.T293M		Atlas-SNP	.											MUC15,NS,carcinoma,0,1	MUC15	88	1	0			c.C878T						PASS	.						117	119	118					11																	26584710		2203	4300	6503	SO:0001583	missense	143662	exon4			GAATCCGTTTTCC	AJ417818	CCDS7859.1, CCDS44556.1, CCDS44557.1	11p14.3	2007-01-17	2006-03-14					"Mucins"	14956	protein-coding gene	gene with protein product		608566				12047385	Standard	NM_145650		Approved		uc001mqw.3	Q8N387		ENST00000455601.2:c.797C>T	11.37:g.26584710G>A	ENSP00000397339:p.Thr266Met	132	0	0		91	53	0.582418	NM_001135091	B3KY00|E9PII6|F8W945|Q6UWS3|Q8IXI8|Q8WW41	Missense_Mutation	SNP	ENST00000455601.2	37	CCDS7859.1	.	.	.	.	.	.	.	.	.	.	G	14.34	2.505843	0.44558	.	.	ENSG00000169550	ENST00000455601;ENST00000436318;ENST00000529533	T;T;T	0.26518	1.75;1.73;1.73	4.52	-0.183	0.13284	.	0.441624	0.19223	N	0.119636	T	0.11196	0.0273	L	0.27053	0.805	0.18873	N	0.999989	P;P	0.37398	0.593;0.593	B;B	0.24848	0.056;0.056	T	0.16988	-1.0384	10	0.66056	D	0.02	-1.4965	3.6308	0.08131	0.0809:0.2526:0.4092:0.2573	.	266;293	Q8N387;E9PII6	MUC15_HUMAN;.	M	266;293;293	ENSP00000397339:T266M;ENSP00000416753:T293M;ENSP00000431983:T293M	ENSP00000416753:T293M	T	-	2	0	MUC15	26541286	0.035000	0.19736	0.271000	0.24616	0.908000	0.53690	0.250000	0.18235	0.063000	0.16370	-0.898000	0.02899	ACG	.	.	none		0.393	MUC15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387866.1	NM_145650		A	26584710	G	A	26584710	3	1	42	1	0	0	0	0	1	0	0	0	9981	1145	40	1	215	1	MUC15	11	26584710	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	9548800	26584710	108421806	217	15169											
OR5M8	219484	hgsc.bcm.edu	37	chr11	56258097	56258097	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgaagaaaagggttgcataGaatatagtgacagctgtcag	16	9	12	4	0	1	4	1	2	0	2	1	4	1	4	0	1	2	3	0	1	7	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr11:56258097G>T	ENST00000327216.2	-	1	774	c.750C>A	c.(748-750)ttC>ttA	p.F250L		NM_001005282.1	NP_001005282.1	Q8NGP6	OR5M8_HUMAN	olfactory receptor, family 5, subfamily M, member 8	250						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)					GGGTTGCATAGAATATAGTGA	0.418																																					p.F250L		Atlas-SNP	.											.	OR5M8	74	.	0			c.C750A						PASS	.						37	40	39					11																	56258097		2201	4296	6497	SO:0001583	missense	219484	exon1			TGCATAGAATATA	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.750C>A	11.37:g.56258097G>T	ENSP00000323354:p.Phe250Leu	110	0	0		82	39	0.47561	NM_001005282	B2RNM5|Q6IEW3|Q96RB8	Missense_Mutation	SNP	ENST00000327216.2	37	CCDS31533.1	.	.	.	.	.	.	.	.	.	.	G	14.26	2.483308	0.44147	.	.	ENSG00000181371	ENST00000327216	T	0.00285	8.3	4.26	1.32	0.21799	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40385	U	0.001119	T	0.00496	0.0016	M	0.71581	2.175	0.33824	D	0.629419	D	0.89917	1.0	D	0.91635	0.999	T	0.63129	-0.6706	10	0.59425	D	0.04	-32.5199	7.1207	0.25442	0.375:0.0:0.625:0.0	.	250	Q8NGP6	OR5M8_HUMAN	L	250	ENSP00000323354:F250L	ENSP00000323354:F250L	F	-	3	2	OR5M8	56014673	0.001000	0.12720	0.978000	0.43139	0.568000	0.35870	-0.517000	0.06275	0.066000	0.16515	-1.079000	0.02226	TTC	.	.	none		0.418	OR5M8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391641.1	NM_001005282		T	56258097	G	T	56258097	3	4	42	1	0	0	0	0	1	0	0	0	11185	933	33	4	189	4	OR5M8	11	56258097	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	29673387	56258097	78748419	218	15170											
OR5M1	390168	hgsc.bcm.edu	37	chr11	56380719	56380719	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggagatggtcttctgttctGagaggaaattgtgcagcata	11	12	13	5	0	3	2	0	1	3	2	3	5	3	3	0	3	2	3	0	3	2	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr11:56380719G>A	ENST00000526538.1	-	1	259	c.260C>T	c.(259-261)tCa>tTa	p.S87L		NM_001004740.1	NP_001004740.1	Q8NGP8	OR5M1_HUMAN	olfactory receptor, family 5, subfamily M, 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)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(7)|upper_aerodigestive_tract(1)	12						CTTCTGTTCTGAGAGGAAATT	0.448																																					p.S87L		Atlas-SNP	.											.	OR5M1	92	.	0			c.C260T						PASS	.						145	136	139					11																	56380719		1908	4127	6035	SO:0001583	missense	390168	exon1			TGTTCTGAGAGGA	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.260C>T	11.37:g.56380719G>A	ENSP00000435416:p.Ser87Leu	228	0	0		174	100	0.574713	NM_001004740	Q6IF60|Q96RB6	Missense_Mutation	SNP	ENST00000526538.1	37	CCDS53631.1	.	.	.	.	.	.	.	.	.	.	G	10.36	1.328996	0.24167	.	.	ENSG00000255012	ENST00000526538	T	0.01335	5.0	3.71	2.77	0.32553	GPCR, rhodopsin-like superfamily (1);	0.244803	0.21257	N	0.077529	T	0.02012	0.0063	M	0.64630	1.985	0.09310	N	1	B	0.25850	0.136	B	0.30782	0.12	T	0.42430	-0.9452	10	0.22706	T	0.39	-28.6778	6.4532	0.21916	0.0:0.2037:0.5864:0.2099	.	87	Q8NGP8	OR5M1_HUMAN	L	87	ENSP00000435416:S87L	ENSP00000435416:S87L	S	-	2	0	OR5M1	56137295	0.000000	0.05858	0.617000	0.29091	0.796000	0.44982	0.694000	0.25512	0.775000	0.33450	0.280000	0.19369	TCA	.	.	none		0.448	OR5M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391610.1	NM_001004740		A	56380719	G	A	56380719	3	1	42	1	0	0	0	0	1	0	0	0	11181	1294	45	2	691	2	OR5M1	11	56380719	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	122622	56380719	78625797	219	15171											
AHNAK	79026	hgsc.bcm.edu	37	chr11	62284325	62284325	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcgggacttcttagaggccAgggacaccccactcccctgt	7	8	11	15	1	1	1	0	0	1	1	3	3	2	3	5	3	0	0	5	3	1	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr11:62284325A>T	ENST00000378024.4	-	5	17838	c.17564T>A	c.(17563-17565)cTg>cAg	p.L5855Q	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000525875.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	5855					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)				CTTAGAGGCCAGGGACACCCC	0.527																																					p.L5855Q		Atlas-SNP	.											.	AHNAK	532	.	0			c.T17564A						PASS	.						196	174	181					11																	62284325		2202	4299	6501	SO:0001583	missense	79026	exon5			GAGGCCAGGGACA	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.17564T>A	11.37:g.62284325A>T	ENSP00000367263:p.Leu5855Gln	140	0	0		138	78	0.565217	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	.	.	.	.	.	.	.	.	.	.	A	11.99	1.803170	0.31869	.	.	ENSG00000124942	ENST00000378024	T	0.03065	4.06	4.89	3.75	0.43078	.	.	.	.	.	T	0.02418	0.0074	N	0.12182	0.205	0.32889	D	0.511639	B	0.32753	0.383	B	0.27608	0.081	T	0.40887	-0.9539	9	0.38643	T	0.18	-0.5722	10.1511	0.42794	0.9194:0.0:0.0806:0.0	.	5855	Q09666	AHNK_HUMAN	Q	5855	ENSP00000367263:L5855Q	ENSP00000367263:L5855Q	L	-	2	0	AHNAK	62040901	0.979000	0.34478	0.998000	0.56505	0.991000	0.79684	2.803000	0.47924	0.711000	0.32018	0.448000	0.29417	CTG	.	.	none		0.527	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060		T	62284325	A	T	62284325	3	4	42	1	0	0	0	0	1	0	0	0	414	188	7	5	228	5	AHNAK	11	62284325	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	5903606	62284325	72722191	220	15172											
SLC22A9	114571	hgsc.bcm.edu	37	chr11	63137598	63137598	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agatccttcagactgtttttCtctcaatctttgctgttgct	6	19	6	10	0	4	2	2	0	2	2	6	2	5	2	1	0	2	4	1	0	1	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr11:63137598C>A	ENST00000279178.3	+	1	319	c.70C>A	c.(70-72)Ctc>Atc	p.L24I	SLC22A9_ENST00000310969.4_Missense_Mutation_p.L24I	NM_080866.2	NP_543142.2	Q8IVM8	S22A9_HUMAN	solute carrier family 22 (organic anion transporter), member 9	24					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						GACTGTTTTTCTCTCAATCTT	0.483																																					p.L24I		Atlas-SNP	.											SLC22A9,NS,carcinoma,0,1	SLC22A9	77	1	0			c.C70A						PASS	.						165	164	164					11																	63137598		2201	4298	6499	SO:0001583	missense	114571	exon1			GTTTTTCTCTCAA	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.70C>A	11.37:g.63137598C>A	ENSP00000279178:p.Leu24Ile	259	0	0		223	112	0.502242	NM_080866	A0AVB7|A4PB24|Q8TCC8|Q8TEC0|Q8WYN7	Missense_Mutation	SNP	ENST00000279178.3	37	CCDS8043.1	.	.	.	.	.	.	.	.	.	.	C	10.22	1.291568	0.23564	.	.	ENSG00000149742	ENST00000310969;ENST00000279178	T;T	0.38240	1.15;1.15	3.48	-3.73	0.04398	.	0.525769	0.17727	N	0.164008	T	0.22085	0.0532	L	0.41236	1.265	0.09310	N	1	B	0.14012	0.009	B	0.12837	0.008	T	0.11131	-1.0600	10	0.40728	T	0.16	.	6.0315	0.19683	0.0:0.3744:0.1409:0.4847	.	24	Q8IVM8	S22A9_HUMAN	I	24	ENSP00000311527:L24I;ENSP00000279178:L24I	ENSP00000279178:L24I	L	+	1	0	SLC22A9	62894174	0.000000	0.05858	0.000000	0.03702	0.196000	0.23810	-2.654000	0.00855	-0.613000	0.05694	0.134000	0.15878	CTC	.	.	none		0.483	SLC22A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396371.1	NM_080866		A	63137598	C	A	63137598	3	1	42	1	0	0	0	0	1	0	0	0	14476	913	32	4	72	4	SLC22A9	11	63137598	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	853273	63137598	71868918	221	15173											
CCDC88B	283234	hgsc.bcm.edu	37	chr11	64121559	64121559	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ccctggggggctgcgcctggGggccgatggggctggcagca	3	5	21	12	2	0	0	0	0	0	0	0	1	0	0	3	8	2	4	3	8	0	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr11:64121559G>A	ENST00000356786.5	+	24	4060	c.4016G>A	c.(4015-4017)gGg>gAg	p.G1339E	CCDC88B_ENST00000359902.2_Intron|CCDC88B_ENST00000463837.1_3'UTR|CCDC88B_ENST00000301897.4_Intron	NM_032251.5	NP_115627.6	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	1339						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						ctgcgcctgggggccgATGGG	0.741																																					p.G1339E		Atlas-SNP	.											.	CCDC88B	89	.	0			c.G4016A						PASS	.						5	6	6					11																	64121559		1975	3971	5946	SO:0001583	missense	283234	exon24			GCCTGGGGGCCGA	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.4016G>A	11.37:g.64121559G>A	ENSP00000349238:p.Gly1339Glu	79	0	0		73	38	0.520548	NM_032251	A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1	Missense_Mutation	SNP	ENST00000356786.5	37	CCDS8072.2	.	.	.	.	.	.	.	.	.	.	g	17.82	3.482314	0.63962	.	.	ENSG00000168071	ENST00000377638;ENST00000356786	T	0.22945	1.93	2.87	2.87	0.33458	.	.	.	.	.	T	0.33177	0.0854	L	0.36672	1.1	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.999;0.963;0.999	T	0.05435	-1.0885	9	0.12766	T	0.61	.	9.3241	0.37982	0.0:0.0:1.0:0.0	.	1339;1221;1339	B2RTU8;A6NC98-4;A6NC98	.;.;CC88B_HUMAN	E	1221;1339	ENSP00000349238:G1339E	ENSP00000349238:G1339E	G	+	2	0	CCDC88B	63878135	0.997000	0.39634	1.000000	0.80357	0.986000	0.74619	0.486000	0.22340	1.582000	0.49881	0.457000	0.33378	GGG	.	.	none		0.741	CCDC88B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104845.1	NM_032251		A	64121559	G	A	64121559	3	1	42	1	0	0	0	0	1	0	0	0	2866	1232	43	2	4110	2	CCDC88B	11	64121559	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	983961	64121559	70884957	222	15174											
PPP1CA	5499	hgsc.bcm.edu	37	chr11	67168324	67168324	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cccccagaaagaggtagttgCtctcgggagggaaaccgcca	11	5	13	12	2	1	2	0	0	1	2	2	4	1	4	4	3	2	3	4	3	3	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr11:67168324C>G	ENST00000376745.4	-	3	402	c.254G>C	c.(253-255)aGc>aCc	p.S85T	PPP1CA_ENST00000532446.1_5'UTR|PPP1CA_ENST00000358239.4_Missense_Mutation_p.S41T|PPP1CA_ENST00000312989.7_Missense_Mutation_p.S96T	NM_001008709.1|NM_002708.3	NP_001008709.1|NP_002699.1	P62136	PP1A_HUMAN	protein phosphatase 1, catalytic subunit, alpha isozyme	85					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)			GAGGTAGTTGCTCTCGGGAGG	0.542																																					p.S96T		Atlas-SNP	.											.	PPP1CA	83	.	0			c.G287C						PASS	.						109	105	106					11																	67168324		2200	4295	6495	SO:0001583	missense	5499	exon3			TAGTTGCTCTCGG		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.254G>C	11.37:g.67168324C>G	ENSP00000365936:p.Ser85Thr	87	0	0		82	17	0.207317	NM_001008709	A6NNR3|B2R908|P08129|P20653|P22802|Q07161	Missense_Mutation	SNP	ENST00000376745.4	37	CCDS8160.1	.	.	.	.	.	.	.	.	.	.	C	16.33	3.093159	0.56075	.	.	ENSG00000172531	ENST00000312989;ENST00000451458;ENST00000376745;ENST00000358239;ENST00000527663	T;T;T;T	0.80123	-1.34;-1.34;-1.34;-1.34	5.08	3.19	0.36642	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (2);Metallophosphoesterase domain (1);	0.000000	0.85682	D	0.000000	T	0.64757	0.2627	N	0.12569	0.235	0.52501	D	0.999958	B;B;B;B;B;B	0.18863	0.031;0.031;0.0;0.008;0.0;0.001	B;B;B;B;B;B	0.24269	0.052;0.03;0.006;0.014;0.006;0.01	T	0.58446	-0.7635	10	0.59425	D	0.04	.	9.3804	0.38311	0.0:0.7739:0.1456:0.0805	.	182;182;85;41;96;94	B3KXM2;E9PDP1;P62136;A6NNR3;Q07161;F8W0W8	.;.;PP1A_HUMAN;.;.;.	T	96;182;85;41;85	ENSP00000326031:S96T;ENSP00000365936:S85T;ENSP00000350974:S41T;ENSP00000431146:S85T	ENSP00000326031:S96T	S	-	2	0	PPP1CA	66924900	1.000000	0.71417	0.998000	0.56505	0.651000	0.38670	4.884000	0.63135	0.522000	0.28464	0.563000	0.77884	AGC	.	.	none		0.542	PPP1CA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395487.1	NM_002708		G	67168324	C	G	67168324	3	3	42	1	0	0	0	0	1	0	0	0	12361	797	28	4	758	4	PPP1CA	11	67168324	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	3046765	67168324	67838192	223	15175											
TBC1D10C	374403	hgsc.bcm.edu	37	chr11	67176563	67176563	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cactgggagcccttcgagccAtcccccccgcgcagctgcag	6	5	11	19	3	0	0	0	0	0	0	2	2	1	1	5	1	4	3	5	1	0	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr11:67176563A>G	ENST00000542590.1	+	8	966	c.952A>G	c.(952-954)Atc>Gtc	p.I318V	TBC1D10C_ENST00000312390.5_Missense_Mutation_p.I318V|TBC1D10C_ENST00000526387.1_Missense_Mutation_p.H253R			Q8IV04	TB10C_HUMAN	TBC1 domain family, member 10C	318					retrograde transport, endosome to Golgi (GO:0042147)	filopodium membrane (GO:0031527)|membrane (GO:0016020)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	16			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)			CCTTCGAGCCATCCCCCCCGC	0.687																																					p.I318V		Atlas-SNP	.											.	TBC1D10C	42	.	0			c.A952G						PASS	.						19	20	20					11																	67176563		2194	4291	6485	SO:0001583	missense	374403	exon9			CGAGCCATCCCCC	BC035630	CCDS8162.1, CCDS58150.1	11q13.1	2013-07-09			ENSG00000175463	ENSG00000175463			24702	protein-coding gene	gene with protein product		610831				17230191, 20404108	Standard	NM_001256508		Approved	FLJ00332, Carabin, EPI64C	uc001ola.4	Q8IV04	OTTHUMG00000167139	ENST00000542590.1:c.952A>G	11.37:g.67176563A>G	ENSP00000443654:p.Ile318Val	172	0	0		149	68	0.456376	NM_198517	G3V1D6	Missense_Mutation	SNP	ENST00000542590.1	37	CCDS8162.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.51|11.51	1.660112|1.660112	0.29515|0.29515	.|.	.|.	ENSG00000175463|ENSG00000175463	ENST00000526387|ENST00000312390;ENST00000542590	.|T;T	.|0.07114	.|3.22;3.22	4.94|4.94	3.69|3.69	0.42338|0.42338	.|Rab-GAP/TBC domain (1);	.|0.145274	.|0.31660	.|N	.|0.007262	T|T	0.07999|0.07999	0.0200|0.0200	L|L	0.55481|0.55481	1.735|1.735	0.31201|0.31201	N|N	0.69976|0.69976	B|B	0.21071|0.18610	0.051|0.029	B|B	0.16722|0.20184	0.016|0.028	T|T	0.12091|0.12091	-1.0561|-1.0561	8|10	0.87932|0.27785	D|T	0|0.31	.|.	4.707|4.707	0.12855|0.12855	0.6934:0.1811:0.1254:0.0|0.6934:0.1811:0.1254:0.0	.|.	253|318	G3V1D6|Q8IV04	.|TB10C_HUMAN	R|V	253|318	.|ENSP00000310193:I318V;ENSP00000443654:I318V	ENSP00000435543:H253R|ENSP00000310193:I318V	H|I	+|+	2|1	0|0	TBC1D10C|TBC1D10C	66933139|66933139	0.978000|0.978000	0.34361|0.34361	0.794000|0.794000	0.32065|0.32065	0.508000|0.508000	0.34012|0.34012	2.081000|2.081000	0.41596|0.41596	0.785000|0.785000	0.33685|0.33685	0.459000|0.459000	0.35465|0.35465	CAT|ATC	.	.	none		0.687	TBC1D10C-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395492.2	NM_198517		G	67176563	A	G	67176563	3	3	42	1	0	0	0	0	1	0	0	0	15615	217	8	3	982	3	TBC1D10C	11	67176563	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	8239	67176563	67829953	224	15176											
INPPL1	3636	hgsc.bcm.edu	37	chr11	71949157	71949157	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agtgcctggctgcgggccatCggcttggagcgctatgagga	6	8	17	10	3	0	1	0	1	0	0	1	3	0	3	2	5	3	3	2	5	1	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr11:71949157C>T	ENST00000298229.2	+	27	3828	c.3624C>T	c.(3622-3624)atC>atT	p.I1208I	PHOX2A_ENST00000544057.1_5'Flank|INPPL1_ENST00000541756.1_Silent_p.I966I|INPPL1_ENST00000538751.1_Silent_p.I966I	NM_001567.3	NP_001558.3	O15357	SHIP2_HUMAN	inositol polyphosphate phosphatase-like 1	1208	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				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						TGCGGGCCATCGGCTTGGAGC	0.711											OREG0021191	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.I1208I		Atlas-SNP	.											INPPL1,bladder,carcinoma,0,1	INPPL1	120	1	0			c.C3624T						scavenged	.						20	21	21					11																	71949157		2198	4289	6487	SO:0001819	synonymous_variant	3636	exon27			GGCCATCGGCTTG	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.3624C>T	11.37:g.71949157C>T		121	1	0.00826446	1133	95	51	0.536842	NM_001567	B2RTX5|Q13577|Q13578	Silent	SNP	ENST00000298229.2	37	CCDS8213.1	.	.	.	.	.	.	.	.	.	.	c	10.16	1.273590	0.23221	.	.	ENSG00000165458	ENST00000320683	.	.	.	4.84	-0.416	0.12351	.	.	.	.	.	T	0.44456	0.1294	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29243	-1.0018	4	.	.	.	.	4.3982	0.11374	0.0:0.3624:0.171:0.4666	.	.	.	.	L	70	.	.	S	+	2	0	INPPL1	71626805	0.980000	0.34600	1.000000	0.80357	0.975000	0.68041	0.085000	0.14912	0.257000	0.21650	-0.218000	0.12543	TCG	.	.	none		0.711	INPPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396789.1	NM_001567		T	71949157	C	T	71949157	2	4	42	1	0	0	0	0	0	0	0	1	7770	874	31	1		1	INPPL1	11	71949157	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	4772594	71949157	63057359	225	15177											
TMEM135	65084	hgsc.bcm.edu	37	chr11	86782566	86782566	+	Splice_Site	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccaaatttgaatttcaggAagatacttggaaaattctac	15	14	6	6	0	2	2	1	1	1	1	3	4	3	4	1	2	2	0	1	2	7	7			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr11:86782566A>T	ENST00000305494.5	+	3	310	c.271A>T	c.(271-273)Aag>Tag	p.K91*	TMEM135_ENST00000532959.1_Intron|TMEM135_ENST00000355734.4_Splice_Site_p.K91*|TMEM135_ENST00000340353.7_Splice_Site_p.K91*|TMEM135_ENST00000535167.1_De_novo_Start_OutOfFrame	NM_022918.3	NP_075069.3	Q86UB9	TM135_HUMAN	transmembrane protein 135	91					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)				GAATTTCAGGAAGATACTTGG	0.358																																					p.K91X		Atlas-SNP	.											.	TMEM135	40	.	0			c.A271T						PASS	.						62	65	64					11																	86782566		2201	4299	6500	SO:0001630	splice_region_variant	65084	exon3			TTCAGGAAGATAC	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.270-1A>T	11.37:g.86782566A>T		229	0	0		227	107	0.471366	NM_022918	Q6AW91|Q8ND01|Q9H6M3	Nonsense_Mutation	SNP	ENST00000305494.5	37	CCDS8280.1	.	.	.	.	.	.	.	.	.	.	A	40	8.079601	0.98643	.	.	ENSG00000166575	ENST00000340353;ENST00000525018;ENST00000355734;ENST00000305494	.	.	.	5.39	5.39	0.77823	.	0.270861	0.41712	D	0.000840	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-16.2891	14.5832	0.68305	1.0:0.0:0.0:0.0	.	.	.	.	X	91	.	.	K	+	1	0	TMEM135	86460214	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.369000	0.90118	2.048000	0.60808	0.533000	0.62120	AAG	.	.	none		0.358	TMEM135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393875.1	NM_022918	Nonsense_Mutation	T	86782566	A	T	86782566	5	4	42	1	0	0	0	0	0	0	1	0	16066	260	9	5	281	5	TMEM135	11	86782566	Splice_Site	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	14833409	86782566	48223950	226	15178											
CNTN5	53942	hgsc.bcm.edu	37	chr11	100211841	100211841	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcagctcctagtcaagcaccTagcaacctcaggtgggagca	11	6	11	13	0	2	0	2	0	0	0	3	1	3	1	3	2	5	5	3	2	4	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr11:100211841T>A	ENST00000524871.1	+	23	3224	c.2934T>A	c.(2932-2934)ccT>ccA	p.P978P	CNTN5_ENST00000418526.2_Silent_p.P904P|CNTN5_ENST00000524560.1_3'UTR|CNTN5_ENST00000279463.3_Silent_p.P978P|CNTN5_ENST00000528682.1_Silent_p.P978P	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	978	Fibronectin type-III 4. {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)		GTCAAGCACCTAGCAACCTCA	0.423																																					p.P978P		Atlas-SNP	.											.	CNTN5	324	.	0			c.T2934A						PASS	.						121	117	118					11																	100211841		1848	4097	5945	SO:0001819	synonymous_variant	53942	exon22			AGCACCTAGCAAC	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.2934T>A	11.37:g.100211841T>A		151	0	0		130	12	0.0923077	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Silent	SNP	ENST00000524871.1	37	CCDS53696.1																																																																																			.	.	none		0.423	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361		A	100211841	T	A	100211841	2	1	42	1	0	0	0	0	0	0	0	1	3646	1509	53	5		5	CNTN5	11	100211841	Silent	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	13429275	100211841	34794675	227	15179											
ZBTB16	7704	hgsc.bcm.edu	37	chr11	114027086	114027086	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cacagtgggatgaagacgtaCgggtgcgagctctgcgggaa	10	6	17	8	4	1	2	0	1	1	1	1	5	1	4	0	3	4	2	0	3	3	1	rs148436647	byFrequency	TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr11:114027086C>T	ENST00000335953.4	+	3	1676	c.1296C>T	c.(1294-1296)taC>taT	p.Y432Y	ZBTB16_ENST00000392996.2_Silent_p.Y432Y	NM_006006.4	NP_005997.2	Q05516	ZBT16_HUMAN	zinc finger and BTB domain containing 16	432					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)		TGAAGACGTACGGGTGCGAGC	0.572																																					p.Y432Y		Atlas-SNP	.											.	ZBTB16	101	.	0			c.C1296T						PASS	.	C	,	0,4402		0,0,2201	149	112	125		1296,1296	3.9	1	11	dbSNP_134	125	2,8590	2.2+/-6.3	0,2,4294	no	coding-synonymous,coding-synonymous	ZBTB16	NM_001018011.1,NM_006006.4	,	0,2,6495	TT,TC,CC		0.0233,0.0,0.0154	,	432/674,432/674	114027086	2,12992	2201	4296	6497	SO:0001819	synonymous_variant	7704	exon3			GACGTACGGGTGC	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.1296C>T	11.37:g.114027086C>T		71	0	0		69	13	0.188406	NM_006006	Q8TAL4	Silent	SNP	ENST00000335953.4	37	CCDS8367.1																																																																																			C|1.000;T|0.000	0.000	strong		0.572	ZBTB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398940.1	NM_006006		T	114027086	C	T	114027086	2	4	42	1	0	0	0	0	0	0	0	1	17541	547	19	1		1	ZBTB16	11	114027086	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	13815245	114027086	20979430	228	15180											
BCL9L	283149	hgsc.bcm.edu	37	chr11	118780644	118780644	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgtcttgttagccaggatcCtcatggctcccacacacagt	8	12	8	13	0	2	0	1	0	1	0	4	1	4	1	3	2	1	2	3	2	1	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr11:118780644C>T	ENST00000334801.3	-	1	969	c.5G>A	c.(4-6)aGg>aAg	p.R2K	BCL9L_ENST00000526143.1_Intron|MIR4492_ENST00000581627.1_RNA	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	2					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)		AGCCAGGATCCTCATGGCTCC	0.637																																					p.R2K		Atlas-SNP	.											.	BCL9L	254	.	0			c.G5A						PASS	.						213	128	157					11																	118780644		2200	4295	6495	SO:0001583	missense	283149	exon1			AGGATCCTCATGG	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.5G>A	11.37:g.118780644C>T	ENSP00000335320:p.Arg2Lys	46	0	0		63	29	0.460317	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Missense_Mutation	SNP	ENST00000334801.3	37	CCDS8403.1	.	.	.	.	.	.	.	.	.	.	C	18.55	3.648175	0.67358	.	.	ENSG00000186174	ENST00000334801;ENST00000392849;ENST00000431085;ENST00000532899	T	0.65916	-0.18	4.35	4.35	0.52113	.	0.000000	0.41712	D	0.000826	T	0.41604	0.1166	N	0.08118	0	0.26380	N	0.976745	B;B	0.24651	0.108;0.066	B;B	0.19391	0.025;0.011	T	0.46541	-0.9184	10	0.87932	D	0	-23.7519	12.56	0.56275	0.0:1.0:0.0:0.0	.	2;2	Q86UU0-2;Q86UU0	.;BCL9L_HUMAN	K	2	ENSP00000335320:R2K	ENSP00000335320:R2K	R	-	2	0	BCL9L	118285854	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.249000	0.32839	2.415000	0.81967	0.555000	0.69702	AGG	.	.	none		0.637	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557		T	118780644	C	T	118780644	3	4	42	1	0	0	0	0	1	0	0	0	1382	681	24	2	4526	2	BCL9L	11	118780644	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	4753558	118780644	16225872	229	15181											
PHC1	1911	hgsc.bcm.edu	37	chr12	9089488	9089488	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaatctcctgaagtgcgagtActgtgggaagtacgcccccg	9	8	13	11	3	1	1	0	1	1	0	2	4	1	2	3	1	3	2	3	1	5	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr12:9089488A>C	ENST00000543824.1	+	13	2737	c.2405A>C	c.(2404-2406)tAc>tCc	p.Y802S	PHC1_ENST00000544916.1_Missense_Mutation_p.Y802S|PHC1_ENST00000433083.2_Missense_Mutation_p.Y757S|PHC1_ENST00000536844.1_Missense_Mutation_p.Y408S			P78364	PHC1_HUMAN	polyhomeotic homolog 1 (Drosophila)	802					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						AAGTGCGAGTACTGTGGGAAG	0.522																																					p.Y802S		Atlas-SNP	.											.	PHC1	67	.	0			c.A2405C						PASS	.						97	83	88					12																	9089488		2203	4300	6503	SO:0001583	missense	1911	exon12			GCGAGTACTGTGG	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.2405A>C	12.37:g.9089488A>C	ENSP00000440674:p.Tyr802Ser	96	0	0		101	18	0.178218	NM_004426	D3DUV4|Q8WVM3|Q9BU63	Missense_Mutation	SNP	ENST00000543824.1	37	CCDS8597.1	.	.	.	.	.	.	.	.	.	.	A	17.29	3.353101	0.61293	.	.	ENSG00000111752	ENST00000543824;ENST00000251757;ENST00000433083;ENST00000544916;ENST00000536844	T;T;T;T;T	0.48201	1.78;1.78;1.75;1.78;0.82	5.03	5.03	0.67393	Zinc finger, FCS-type (1);Zinc finger, MYM-type (1);	0.181694	0.38897	N	0.001525	T	0.51261	0.1664	L	0.33485	1.01	0.80722	D	1	D	0.63046	0.992	P	0.59357	0.856	T	0.52786	-0.8529	10	0.56958	D	0.05	-11.3051	10.5323	0.44983	0.8553:0.0:0.0:0.1447	.	802	P78364	PHC1_HUMAN	S	802;802;757;802;408	ENSP00000440674:Y802S;ENSP00000251757:Y802S;ENSP00000399194:Y757S;ENSP00000437659:Y802S;ENSP00000440488:Y408S	ENSP00000251757:Y802S	Y	+	2	0	PHC1	8980755	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.484000	0.66844	2.114000	0.64651	0.459000	0.35465	TAC	.	.	none		0.522	PHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399115.1	NM_004426		C	9089488	A	C	9089488	3	2	42	1	0	0	0	0	1	0	0	0	11825	391	14	5	2447	5	PHC1	12	9089488	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10		9089488	124762407	230	15182											
KLRK1	22914	hgsc.bcm.edu	37	chr12	10539559	10539559	+	Frame_Shift_Del	DEL	A	A	-																															ttgcttttgccatcgtgttgAaaaatcactcttcttcagat																										TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr12:10539559delA	ENST00000240618.6	-	3	231	c.91delT	c.(91-93)tcafs	p.S31fs	KLRK1_ENST00000540818.1_Frame_Shift_Del_p.S31fs|RP11-277P12.20_ENST00000500682.1_RNA|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	31					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						CATCGTGTTGAAAAATCACTC	0.343																																					p.S31X		Atlas-Indel	.											.	.	.	.	0			c.92delC						PASS	.						173	161	165					12																	10539559		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.91delT	12.37:g.10539559delA	ENSP00000240618:p.Ser31fs	246	0	0		260	59	0.226923	NM_001199805	A8K7K5|A8K7P4|Q9NR41	Frame_Shift_Del	DEL	ENST00000240618.6	37	CCDS8623.1																																																																																			.	.	none		0.343	KLRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400269.1	NM_007360		-	10539559	A	-	10539559	7	5	42	1	0	1	0	1	0	0	0	0	8432	246	9	0	583	0	KLRK1	12	10539559	Frame_Shift_Del	DEL	A	TCGA-GS-A9TZ-01A-11D-A38X-10	1450071	10539559	123312336	231	15183											
DDX47	51202	hgsc.bcm.edu	37	chr12	12966365	12966365	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	agccgattgtggaagaggagGaaactaaaacatttaaagac	18	7	11	5	1	0	2	0	0	0	2	0	6	0	5	1	3	3	0	1	3	6	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr12:12966365G>C	ENST00000358007.3	+	1	86	c.64G>C	c.(64-66)Gaa>Caa	p.E22Q	DDX47_ENST00000352940.4_Missense_Mutation_p.E22Q	NM_016355.3	NP_057439.2	Q9H0S4	DDX47_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47	22					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)		GGAAGAGGAGGAAACTAAAAC	0.557											OREG0021680	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E22Q		Atlas-SNP	.											.	DDX47	37	.	0			c.G64C						PASS	.						66	64	65					12																	12966365		2203	4300	6503	SO:0001583	missense	51202	exon1			GAGGAGGAAACTA	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.64G>C	12.37:g.12966365G>C	ENSP00000350698:p.Glu22Gln	53	0	0	683	47	12	0.255319	NM_201224	B3KXP4|G5E955|Q96GM0|Q96NV8|Q9UI98	Missense_Mutation	SNP	ENST00000358007.3	37	CCDS8655.1	.	.	.	.	.	.	.	.	.	.	G	11.34	1.608805	0.28623	.	.	ENSG00000213782	ENST00000352940;ENST00000358007;ENST00000544400	T;T;T	0.43688	0.94;1.66;0.94	4.98	4.98	0.66077	.	0.054639	0.64402	D	0.000001	T	0.30603	0.0770	N	0.21545	0.675	0.43622	D	0.996008	B;B;B;B	0.15141	0.008;0.012;0.009;0.003	B;B;B;B	0.12837	0.008;0.007;0.007;0.002	T	0.06698	-1.0812	10	0.16420	T	0.52	-14.5554	17.5534	0.87884	0.0:0.0:1.0:0.0	.	22;22;22;22	B4DYP6;Q9H4E3;G5E955;Q9H0S4	.;.;.;DDX47_HUMAN	Q	22	ENSP00000319578:E22Q;ENSP00000350698:E22Q;ENSP00000444000:E22Q	ENSP00000319578:E22Q	E	+	1	0	DDX47	12857632	1.000000	0.71417	1.000000	0.80357	0.568000	0.35870	3.126000	0.50477	2.756000	0.94617	0.655000	0.94253	GAA	.	.	none		0.557	DDX47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400674.1	NM_016355		C	12966365	G	C	12966365	3	2	42	1	0	0	0	0	1	0	0	0	4367	1175	41	4	66	4	DDX47	12	12966365	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	2426806	12966365	120885530	232	15184											
PTPRO	5800	hgsc.bcm.edu	37	chr12	15677869	15677869	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgcttcactggatggtggtTgcagaaggaaaaaagaaaat	16	9	12	4	0	1	2	1	0	0	2	1	4	1	4	0	4	2	3	0	4	6	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr12:15677869T>C	ENST00000281171.4	+	11	2343	c.2013T>C	c.(2011-2013)gtT>gtC	p.V671V	PTPRO_ENST00000348962.2_Silent_p.V671V	NM_030667.2	NP_109592.1	Q16827	PTPRO_HUMAN	protein tyrosine phosphatase, receptor type, O	671	Fibronectin type-III 7. {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)				GGATGGTGGTTGCAGAAGGAA	0.353																																					p.V671V		Atlas-SNP	.											.	PTPRO	148	.	0			c.T2013C						PASS	.						84	85	84					12																	15677869		2203	4300	6503	SO:0001819	synonymous_variant	5800	exon11			GGTGGTTGCAGAA	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.2013T>C	12.37:g.15677869T>C		98	0	0		83	32	0.385542	NM_002848	A0AV39|Q13101|Q8IYG3|Q9UBF0|Q9UBT5	Silent	SNP	ENST00000281171.4	37	CCDS8675.1																																																																																			.	.	none		0.353	PTPRO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401079.1			C	15677869	T	C	15677869	2	2	42	1	0	0	0	0	0	0	0	1	12824	1799	63	3		3	PTPRO	12	15677869	Silent	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	2711504	15677869	118174026	233	15185											
KCNJ8	3764	hgsc.bcm.edu	37	chr12	21926491	21926491	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	atgcgcggcttgcgcaggttCtctgcggcgatgcgcgccag	4	8	16	13	7	1	0	0	0	1	0	2	1	1	0	1	3	4	3	1	3	0	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr12:21926491C>G	ENST00000240662.2	-	2	405	c.60G>C	c.(58-60)gaG>gaC	p.E20D		NM_004982.3	NP_004973.1	Q15842	KCNJ8_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 8	20					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)	TGCGCAGGTTCTCTGCGGCGA	0.617											OREG0021704	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E20D		Atlas-SNP	.											.	KCNJ8	59	.	0			c.G60C						PASS	.						74	76	76					12																	21926491		2203	4299	6502	SO:0001583	missense	3764	exon2			CAGGTTCTCTGCG	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.60G>C	12.37:g.21926491C>G	ENSP00000240662:p.Glu20Asp	72	0	0	752	73	15	0.205479	NM_004982	O00657	Missense_Mutation	SNP	ENST00000240662.2	37	CCDS8692.1	.	.	.	.	.	.	.	.	.	.	C	11.03	1.518644	0.27211	.	.	ENSG00000121361	ENST00000240662;ENST00000539350;ENST00000537950	D;D	0.91792	-2.39;-2.91	4.88	3.98	0.46160	.	0.202455	0.43919	D	0.000516	D	0.86326	0.5906	L	0.46157	1.445	0.33357	D	0.571788	B	0.06786	0.001	B	0.04013	0.001	T	0.80688	-0.1271	10	0.11485	T	0.65	.	9.2742	0.37690	0.0:0.7776:0.1447:0.0777	.	20	Q15842	IRK8_HUMAN	D	20	ENSP00000240662:E20D;ENSP00000440012:E20D	ENSP00000240662:E20D	E	-	3	2	KCNJ8	21817758	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	1.560000	0.36331	1.253000	0.44018	0.591000	0.81541	GAG	.	.	none		0.617	KCNJ8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402226.1	NM_004982		G	21926491	C	G	21926491	3	3	42	1	0	0	0	0	1	0	0	0	8065	912	32	4	1222	4	KCNJ8	12	21926491	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	6248622	21926491	111925404	234	15186											
ESPL1	9700	hgsc.bcm.edu	37	chr12	53683328	53683328	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tttggaatctggccacttccCccagcctgaaaaggagagtt	10	10	10	11	0	1	2	0	1	1	1	2	4	2	3	4	3	1	1	4	3	3	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr12:53683328C>T	ENST00000257934.4	+	22	5154	c.5063C>T	c.(5062-5064)cCc>cTc	p.P1688L	ESPL1_ENST00000552462.1_Missense_Mutation_p.P1688L	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	1688					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						GGCCACTTCCCCCAGCCTGAA	0.612																																					p.P1688L	Colon(53;1069 1201 2587 5382)	Atlas-SNP	.											.	ESPL1	158	.	0			c.C5063T						PASS	.						46	49	48					12																	53683328		2203	4300	6503	SO:0001583	missense	9700	exon22			ACTTCCCCCAGCC	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.5063C>T	12.37:g.53683328C>T	ENSP00000257934:p.Pro1688Leu	60	0	0		58	25	0.431034	NM_012291		Missense_Mutation	SNP	ENST00000257934.4	37	CCDS8852.1	.	.	.	.	.	.	.	.	.	.	C	18.15	3.559608	0.65538	.	.	ENSG00000135476	ENST00000257934;ENST00000552671;ENST00000552462	T;T	0.17370	2.28;2.28	5.26	5.26	0.73747	.	0.123552	0.53938	D	0.000041	T	0.30008	0.0751	L	0.34521	1.04	0.58432	D	0.999998	D	0.76494	0.999	D	0.68765	0.96	T	0.01143	-1.1438	10	0.87932	D	0	.	14.2504	0.66016	0.0:1.0:0.0:0.0	.	1688	Q14674	ESPL1_HUMAN	L	1688;1363;1688	ENSP00000257934:P1688L;ENSP00000449831:P1688L	ENSP00000257934:P1688L	P	+	2	0	ESPL1	51969595	0.950000	0.32346	1.000000	0.80357	0.345000	0.29048	1.549000	0.36212	2.735000	0.93741	0.563000	0.77884	CCC	.	.	none		0.612	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291		T	53683328	C	T	53683328	3	4	42	1	0	0	0	0	1	0	0	0	5255	623	22	2	5145	2	ESPL1	12	53683328	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	31756837	53683328	80168567	235	15187											
MYL6	4637	hgsc.bcm.edu	37	chr12	56554083	56554083	+	Frame_Shift_Del	DEL	A	A	-																															tggcagggcatgaggacagcAatggttgtatcaactatgaa																										TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr12:56554083delA	ENST00000550697.1	+	5	647	c.406delA	c.(406-408)aatfs	p.N136fs	MYL6_ENST00000548400.1_Frame_Shift_Del_p.N100fs|MYL6_ENST00000348108.4_Frame_Shift_Del_p.N137fs|MYL6_ENST00000549017.1_Frame_Shift_Del_p.N32fs|MYL6_ENST00000547649.1_Frame_Shift_Del_p.N136fs|MYL6_ENST00000536128.1_Frame_Shift_Del_p.N229fs|RP11-603J24.14_ENST00000548731.1_RNA|MYL6_ENST00000293422.5_Frame_Shift_Del_p.N137fs|MYL6_ENST00000548580.1_Frame_Shift_Del_p.N88fs|MYL6_ENST00000548293.1_Frame_Shift_Del_p.N136fs|MYL6_ENST00000547408.1_Frame_Shift_Del_p.N136fs|RP11-977G19.5_ENST00000553176.1_RNA|MYL6_ENST00000551589.1_Frame_Shift_Del_p.N136fs|MYL6_ENST00000549566.1_Frame_Shift_Del_p.N181fs	NM_021019.4	NP_066299.2	P60660	MYL6_HUMAN	myosin, light chain 6, alkali, smooth muscle and non-muscle	136	EF-hand 3. {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)			TGAGGACAGCAATGGTTGTAT	0.483																																					p.S135fs		Atlas-Indel	.											.	MYL6	16	.	0			c.405delC						PASS	.						79	71	74					12																	56554083		2203	4300	6503	SO:0001589	frameshift_variant	4637	exon5			.	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.406delA	12.37:g.56554083delA	ENSP00000446955:p.Asn136fs	60	0	0		77	12	0.155844	NM_079423	P16475|P24572|P24573|Q12790|Q561V9|Q6IAZ0|Q6IPY5	Frame_Shift_Del	DEL	ENST00000550697.1	37	CCDS8906.1																																																																																			.	.	none		0.483	MYL6-003	KNOWN	NAGNAG_splice_site|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000407928.3			-	56554083	A	-	56554083	7	5	42	1	0	1	0	1	0	0	0	0	10060	130	5	0	424	0	MYL6	12	56554083	Frame_Shift_Del	DEL	A	TCGA-GS-A9TZ-01A-11D-A38X-10	2870755	56554083	77297812	236	15188											
NACA	4666	hgsc.bcm.edu	37	chr12	57118252	57118252	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctacctgtctcagcctggggCtgcggcaactcctgctctgt	4	11	11	15	1	2	0	1	0	2	0	4	0	3	0	3	3	5	3	3	3	2	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr12:57118252C>T	ENST00000454682.1	-	2	335	c.54G>A	c.(52-54)caG>caA	p.Q18Q	NACA_ENST00000552540.1_Silent_p.Q18Q|NACA_ENST00000393891.4_Silent_p.Q18Q|NACA_ENST00000546392.1_Silent_p.Q18Q|NACA_ENST00000551793.1_5'UTR|NACA_ENST00000550952.1_Silent_p.Q18Q|NACA_ENST00000548563.1_5'UTR|NACA_ENST00000356769.3_Silent_p.Q18Q	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	18					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						CAGCCTGGGGCTGCGGCAACT	0.488			T	BCL6	NHL																																p.Q18Q		Atlas-SNP	.		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	NACA_ENST00000454682,NS,carcinoma,-1,2	NACA	131	2	0			c.G54A						PASS	.						34	31	32					12																	57118252		2203	4300	6503	SO:0001819	synonymous_variant	4666	exon2			CTGGGGCTGCGGC	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.54G>A	12.37:g.57118252C>T		61	0	0		68	31	0.455882	NM_001113202		Silent	SNP	ENST00000454682.1	37																																																																																				.	.	none		0.488	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594		T	57118252	C	T	57118252	2	4	42	1	0	0	0	0	0	0	0	1	10142	796	28	2		2	NACA	12	57118252	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	564169	57118252	76733643	237	15189											
TAC3	6866	hgsc.bcm.edu	37	chr12	57407443	57407443	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tctctggagcagctggtagaGatctggatccctctagggaa	9	10	13	9	0	3	1	0	0	3	1	5	5	4	4	1	4	2	3	1	4	3	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr12:57407443G>A	ENST00000458521.2	-	3	286	c.127C>T	c.(127-129)Ctc>Ttc	p.L43F	TAC3_ENST00000415231.1_Missense_Mutation_p.L43F|TAC3_ENST00000441881.1_Missense_Mutation_p.L43F	NM_013251.3	NP_037383.1	Q9UHF0	TKNK_HUMAN	tachykinin 3	43					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						AGCTGGTAGAGATCTGGATCC	0.567																																					p.L43F		Atlas-SNP	.											.	TAC3	11	.	0			c.C127T						PASS	.						40	42	41					12																	57407443		2203	4300	6503	SO:0001583	missense	6866	exon3			GGTAGAGATCTGG	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.127C>T	12.37:g.57407443G>A	ENSP00000404056:p.Leu43Phe	38	0	0		38	19	0.5	NM_013251	Q6IAG2|Q71BC6|Q71BC9	Missense_Mutation	SNP	ENST00000458521.2	37	CCDS8928.1	.	.	.	.	.	.	.	.	.	.	G	14.94	2.686261	0.47991	.	.	ENSG00000166863	ENST00000458521;ENST00000441881;ENST00000415231	D;D;D	0.86297	-2.1;-1.95;-2.1	6.02	2.15	0.27550	.	0.345998	0.26528	N	0.023870	T	0.76314	0.3970	L	0.34521	1.04	0.09310	N	1	P;P	0.39326	0.668;0.617	B;B	0.36808	0.233;0.15	T	0.66143	-0.5997	10	0.44086	T	0.13	-0.3145	5.0391	0.14449	0.1546:0.0:0.5513:0.2942	.	43;43	Q9UHF0;Q9UHF0-3	TKNK_HUMAN;.	F	43	ENSP00000404056:L43F;ENSP00000408208:L43F;ENSP00000402995:L43F	ENSP00000300108:L43F	L	-	1	0	TAC3	55693710	0.002000	0.14202	0.000000	0.03702	0.016000	0.09150	0.337000	0.19841	0.130000	0.18549	-0.181000	0.13052	CTC	.	.	none		0.567	TAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346793.1	NM_001006667		A	57407443	G	A	57407443	3	1	42	1	0	0	0	0	1	0	0	0	15514	942	33	2	254	2	TAC3	12	57407443	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	289191	57407443	76444452	238	15190											
STAT6	6778	hgsc.bcm.edu	37	chr12	57492825	57492825	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cggtcatcttgatggtagctGggacataacccctgccatcc	8	10	10	13	1	2	1	1	1	1	0	3	2	3	2	4	3	3	2	4	3	2	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr12:57492825G>A	ENST00000300134.3	-	17	2253	c.1928C>T	c.(1927-1929)cCa>cTa	p.P643L	STAT6_ENST00000538913.2_Missense_Mutation_p.P533L|STAT6_ENST00000454075.3_Missense_Mutation_p.P643L|STAT6_ENST00000537215.2_Missense_Mutation_p.P533L|STAT6_ENST00000543873.2_Missense_Mutation_p.P643L|STAT6_ENST00000556155.1_Missense_Mutation_p.P643L	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	643					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						GATGGTAGCTGGGACATAACC	0.537																																					p.P643L		Atlas-SNP	.											.	STAT6	69	.	0			c.C1928T						PASS	.						279	231	247					12																	57492825		2203	4300	6503	SO:0001583	missense	6778	exon17			GTAGCTGGGACAT	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.1928C>T	12.37:g.57492825G>A	ENSP00000300134:p.Pro643Leu	97	0	0		71	18	0.253521	NM_001178079	A8K316|B7ZA27|F5GXI9|Q5FBW5|Q71UP4	Missense_Mutation	SNP	ENST00000300134.3	37	CCDS8931.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.639707	0.87760	.	.	ENSG00000166888	ENST00000300134;ENST00000535201;ENST00000538913;ENST00000543873;ENST00000556155;ENST00000537215;ENST00000454075;ENST00000542721;ENST00000555318;ENST00000542516	D;D;D;D;D;D;D	0.96802	-4.13;-4.13;-4.13;-4.13;-4.13;-4.13;-4.13	5.77	5.77	0.91146	SH2 motif (1);	0.058012	0.64402	D	0.000002	D	0.95010	0.8385	N	0.24115	0.695	0.80722	D	1	P;P	0.52577	0.745;0.954	B;P	0.53450	0.351;0.726	D	0.95186	0.8304	10	0.56958	D	0.05	-3.6578	15.4962	0.75653	0.0:0.0:1.0:0.0	.	643;643	A8K4S9;P42226	.;STAT6_HUMAN	L	643;533;533;643;643;533;643;533;71;643	ENSP00000300134:P643L;ENSP00000445409:P533L;ENSP00000438451:P643L;ENSP00000451742:P643L;ENSP00000444530:P533L;ENSP00000401486:P643L;ENSP00000450428:P71L	ENSP00000300134:P643L	P	-	2	0	STAT6	55779092	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.807000	0.69157	2.744000	0.94065	0.561000	0.74099	CCA	.	.	none		0.537	STAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412248.3	NM_003153		A	57492825	G	A	57492825	3	1	42	1	0	0	0	0	1	0	0	0	15285	1348	47	2	639	2	STAT6	12	57492825	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	85382	57492825	76359070	239	15191											
STAT6	6778	hgsc.bcm.edu	37	chr12	57496658	57496658	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggatagtggctttggcattgTtgtcttggttgccatggacg	5	15	15	6	1	1	0	0	0	1	0	1	2	1	2	1	5	1	4	1	5	1	6			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr12:57496658T>C	ENST00000300134.3	-	12	1584	c.1259A>G	c.(1258-1260)aAc>aGc	p.N420S	STAT6_ENST00000538913.2_Missense_Mutation_p.N310S|STAT6_ENST00000454075.3_Missense_Mutation_p.N420S|STAT6_ENST00000537215.2_Missense_Mutation_p.N310S|STAT6_ENST00000543873.2_Missense_Mutation_p.N420S|STAT6_ENST00000556155.1_Missense_Mutation_p.N420S	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	420					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						TTTGGCATTGTTGTCTTGGTT	0.507																																					p.N420S		Atlas-SNP	.											.	STAT6	69	.	0			c.A1259G						PASS	.						144	116	125					12																	57496658		2203	4300	6503	SO:0001583	missense	6778	exon12			GCATTGTTGTCTT	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.1259A>G	12.37:g.57496658T>C	ENSP00000300134:p.Asn420Ser	94	0	0		84	11	0.130952	NM_001178079	A8K316|B7ZA27|F5GXI9|Q5FBW5|Q71UP4	Missense_Mutation	SNP	ENST00000300134.3	37	CCDS8931.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.159974	0.78226	.	.	ENSG00000166888	ENST00000300134;ENST00000535201;ENST00000538913;ENST00000543873;ENST00000556155;ENST00000537215;ENST00000454075;ENST00000542721;ENST00000542516	D;D;D;D;D;D	0.86769	-2.17;-2.17;-2.17;-2.17;-2.17;-2.17	5.44	5.44	0.79542	STAT transcription factor, DNA-binding (1);p53-like transcription factor, DNA-binding (1);EF-hand-like domain (1);	0.044809	0.85682	D	0.000000	D	0.87220	0.6123	N	0.17082	0.46	0.58432	D	0.999997	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.978	D	0.86277	0.1665	10	0.31617	T	0.26	-29.4754	13.4858	0.61364	0.0:0.0:0.0:1.0	.	420;420	A8K4S9;P42226	.;STAT6_HUMAN	S	420;310;310;420;420;310;420;310;420	ENSP00000300134:N420S;ENSP00000445409:N310S;ENSP00000438451:N420S;ENSP00000451742:N420S;ENSP00000444530:N310S;ENSP00000401486:N420S	ENSP00000300134:N420S	N	-	2	0	STAT6	55782925	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.728000	0.62000	2.285000	0.76669	0.528000	0.53228	AAC	.	.	none		0.507	STAT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412248.3	NM_003153		C	57496658	T	C	57496658	3	2	42	1	0	0	0	0	1	0	0	0	15285	1725	60	3	1328	3	STAT6	12	57496658	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	3833	57496658	76355237	240	15192											
TSPAN31	6302	hgsc.bcm.edu	37	chr12	58139640	58139640	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gggagtcttccttctccttaTtgcagtggctggactggtgg	4	14	14	9	0	2	0	0	0	2	0	4	2	3	2	2	5	1	2	2	5	1	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr12:58139640T>C	ENST00000257910.3	+	2	450	c.176T>C	c.(175-177)aTt>aCt	p.I59T	TSPAN31_ENST00000553221.1_3'UTR|TSPAN31_ENST00000547992.1_Missense_Mutation_p.I59T|TSPAN31_ENST00000547472.1_Intron	NM_005981.3	NP_005972.1	Q12999	TSN31_HUMAN	tetraspanin 31	59					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)			CTTCTCCTTATTGCAGTGGCT	0.582																																					p.I59T		Atlas-SNP	.											.	TSPAN31	20	.	0			c.T176C						PASS	.						105	94	98					12																	58139640		2203	4300	6503	SO:0001583	missense	6302	exon2			TCCTTATTGCAGT		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		ENST00000257910.3:c.176T>C	12.37:g.58139640T>C	ENSP00000257910:p.Ile59Thr	170	0	0		162	80	0.493827	NM_005981	O00577|Q53X76	Missense_Mutation	SNP	ENST00000257910.3	37	CCDS8952.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.566696	0.86439	.	.	ENSG00000135452	ENST00000257910;ENST00000547992	T	0.80653	-1.4	4.57	4.57	0.56435	.	0.000000	0.85682	D	0.000000	D	0.88829	0.6543	M	0.80616	2.505	0.80722	D	1	D;D	0.76494	0.989;0.999	D;D	0.85130	0.978;0.997	D	0.88313	0.2957	10	0.36615	T	0.2	-6.2344	13.35	0.60597	0.0:0.0:0.0:1.0	.	59;59	F8VS78;Q12999	.;TSN31_HUMAN	T	59	ENSP00000257910:I59T	ENSP00000257910:I59T	I	+	2	0	TSPAN31	56425907	1.000000	0.71417	0.934000	0.37439	0.960000	0.62799	7.506000	0.81665	2.053000	0.61076	0.377000	0.23210	ATT	.	.	none		0.582	TSPAN31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408778.1			C	58139640	T	C	58139640	3	2	42	1	0	0	0	0	1	0	0	0	16661	1493	52	3	182	3	TSPAN31	12	58139640	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	642982	58139640	75712255	241	15193											
C12orf66	144577	hgsc.bcm.edu	37	chr12	64587914	64587914	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtcgctgggcagagacactAcagctggatactggtccaca	10	8	12	11	1	0	1	0	0	0	1	2	3	1	2	1	3	3	3	1	3	2	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr12:64587914A>T	ENST00000398055.3	-	3	1099	c.1046T>A	c.(1045-1047)gTa>gAa	p.V349E	C12orf66_ENST00000311915.8_Missense_Mutation_p.V349E|C12orf66_ENST00000544871.1_Missense_Mutation_p.V296E	NM_152440.4	NP_689653	Q96MD2	CL066_HUMAN	chromosome 12 open reading frame 66	349										central_nervous_system(1)|large_intestine(1)|lung(2)|ovary(1)	5						CAGAGACACTACAGCTGGATA	0.522																																					p.V349E		Atlas-SNP	.											.	C12orf66	28	.	0			c.T1046A						PASS	.						83	81	81					12																	64587914		1984	4157	6141	SO:0001583	missense	144577	exon3			GACACTACAGCTG		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.1046T>A	12.37:g.64587914A>T	ENSP00000381132:p.Val349Glu	118	0	0		110	14	0.127273	NM_152440	C9JX54|Q8IYA0	Missense_Mutation	SNP	ENST00000398055.3	37	CCDS41803.1	.	.	.	.	.	.	.	.	.	.	A	16.72	3.200407	0.58126	.	.	ENSG00000174206	ENST00000311915;ENST00000544871;ENST00000398055	T;T;T	0.41065	1.01;1.01;1.01	6.07	6.07	0.98685	.	0.109673	0.64402	D	0.000006	T	0.56673	0.2001	M	0.63843	1.955	0.80722	D	1	P;P	0.49783	0.852;0.928	P;P	0.54965	0.555;0.765	T	0.54036	-0.8353	9	.	.	.	-18.644	16.6406	0.85098	1.0:0.0:0.0:0.0	.	296;349	F5H2Q3;Q96MD2	.;CL066_HUMAN	E	349;296;349	ENSP00000311486:V349E;ENSP00000445481:V296E;ENSP00000381132:V349E	.	V	-	2	0	C12orf66	62874181	1.000000	0.71417	0.996000	0.52242	0.011000	0.07611	9.262000	0.95591	2.326000	0.78906	0.533000	0.62120	GTA	.	.	none		0.522	C12orf66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400921.1	NM_152440		T	64587914	A	T	64587914	3	4	42	1	0	0	0	0	1	0	0	0	1711	391	14	5	295	5	C12orf66	12	64587914	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	6448274	64587914	69263981	242	15194											
LEMD3	23592	hgsc.bcm.edu	37	chr12	65564345	65564345	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcgatgaatgacagggcggcGgctgccgggagtctagacag	9	5	18	9	4	1	3	0	2	1	1	1	5	1	4	1	4	1	1	1	4	2	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr12:65564345G>T	ENST00000308330.2	+	1	995	c.969G>T	c.(967-969)gcG>gcT	p.A323A	LEMD3_ENST00000541171.1_Intron	NM_001167614.1|NM_014319.4	NP_001161086.1|NP_055134.2	Q9Y2U8	MAN1_HUMAN	LEM domain containing 3	323	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)		ACAGGGCGGCGGCTGCCGGGA	0.642																																					p.A323A		Atlas-SNP	.											.	LEMD3	68	.	0			c.G969T						PASS	.						22	26	25					12																	65564345		2203	4300	6503	SO:0001819	synonymous_variant	23592	exon1			GGCGGCGGCTGCC	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.969G>T	12.37:g.65564345G>T		31	0	0		32	16	0.5	NM_001167614	Q9NT47|Q9NYA5	Silent	SNP	ENST00000308330.2	37	CCDS8972.1																																																																																			.	.	none		0.642	LEMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401312.2			T	65564345	G	T	65564345	2	4	42	1	0	0	0	0	0	0	0	1	8730	1103	39	4		4	LEMD3	12	65564345	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	976431	65564345	68287550	243	15195											
CNOT2	4848	hgsc.bcm.edu	37	chr12	70724111	70724111	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatatgatgaaccactcccAggttggtcagggcattggaa	12	9	12	8	0	1	2	1	2	0	0	2	4	2	3	2	4	1	2	2	4	4	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr12:70724111A>G	ENST00000418359.3	+	7	882	c.431A>G	c.(430-432)cAg>cGg	p.Q144R	CNOT2_ENST00000548230.1_3'UTR|CNOT2_ENST00000229195.3_Missense_Mutation_p.Q144R	NM_001199302.1	NP_001186231.1	Q9NZN8	CNOT2_HUMAN	CCR4-NOT transcription complex, subunit 2	144					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)			AACCACTCCCAGGTTGGTCAG	0.418																																					p.Q144R		Atlas-SNP	.											CNOT2,colon,carcinoma,-1,1	CNOT2	53	1	0			c.A431G						PASS	.						112	106	108					12																	70724111		2203	4300	6503	SO:0001583	missense	4848	exon7			ACTCCCAGGTTGG	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.431A>G	12.37:g.70724111A>G	ENSP00000412091:p.Gln144Arg	168	0	0		163	64	0.392638	NM_001199302	Q9H3E0|Q9NSX5|Q9NWR6|Q9P028	Missense_Mutation	SNP	ENST00000418359.3	37	CCDS31857.1	.	.	.	.	.	.	.	.	.	.	A	17.42	3.385262	0.61956	.	.	ENSG00000111596	ENST00000552231;ENST00000229195;ENST00000418359;ENST00000550641;ENST00000548159;ENST00000549750;ENST00000551043;ENST00000551873;ENST00000550194	T;T;T;T	0.46063	0.88;0.88;0.89;0.88	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.44746	0.1308	L	0.32530	0.975	0.80722	D	1	D	0.58268	0.982	P	0.54270	0.747	T	0.17868	-1.0355	10	0.16896	T	0.51	-2.8571	15.9985	0.80270	1.0:0.0:0.0:0.0	.	144	Q9NZN8	CNOT2_HUMAN	R	144;144;144;124;135;144;144;59;144	ENSP00000229195:Q144R;ENSP00000412091:Q144R;ENSP00000449659:Q135R;ENSP00000449260:Q144R	ENSP00000229195:Q144R	Q	+	2	0	CNOT2	69010378	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.287000	0.95975	2.233000	0.73108	0.455000	0.32223	CAG	.	.	none		0.418	CNOT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404260.1			G	70724111	A	G	70724111	3	3	42	1	0	0	0	0	1	0	0	0	3621	188	7	3	449	3	CNOT2	12	70724111	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	5159766	70724111	63127784	244	15196											
TRHDE	29953	hgsc.bcm.edu	37	chr12	73046814	73046814	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggcttctaaatctgtcactGaattctgaggtggtgctgga	9	13	12	7	0	4	2	1	2	3	0	4	3	4	3	0	4	1	2	0	4	3	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr12:73046814G>A	ENST00000261180.4	+	17	2823	c.2727G>A	c.(2725-2727)ctG>ctA	p.L909L		NM_013381.2	NP_037513.1	Q9UKU6	TRHDE_HUMAN	thyrotropin-releasing hormone degrading enzyme	909					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						ATCTGTCACTGAATTCTGAGG	0.343																																					p.L909L		Atlas-SNP	.											.	TRHDE	194	.	0			c.G2727A						PASS	.						75	75	75					12																	73046814		2203	4300	6503	SO:0001819	synonymous_variant	29953	exon17			GTCACTGAATTCT	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.2727G>A	12.37:g.73046814G>A		158	0	0		134	60	0.447761	NM_013381	A5PL19|Q6UWJ4	Silent	SNP	ENST00000261180.4	37	CCDS9004.1																																																																																			.	.	none		0.343	TRHDE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405380.1	NM_013381		A	73046814	G	A	73046814	2	1	42	1	0	0	0	0	0	0	0	1	16494	1277	45	2		2	TRHDE	12	73046814	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	2322703	73046814	60805081	245	15197											
ZDHHC17	23390	hgsc.bcm.edu	37	chr12	77243231	77243231	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actttaaagtcacaacaacgTctattgaaagcccattcaag	16	10	5	10	1	3	1	2	1	1	0	3	1	3	1	1	0	3	0	1	0	7	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr12:77243231T>G	ENST00000426126.2	+	16	2390	c.1741T>G	c.(1741-1743)Tct>Gct	p.S581A	ZDHHC17_ENST00000334822.5_Missense_Mutation_p.S581A	NM_015336.2	NP_056151.2	Q8IUH5	ZDH17_HUMAN	zinc finger, DHHC-type containing 17	581					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						CACAACAACGTCTATTGAAAG	0.294																																					p.S581A		Atlas-SNP	.											.	ZDHHC17	45	.	0			c.T1741G						PASS	.						55	53	54					12																	77243231		1808	4057	5865	SO:0001583	missense	23390	exon16			ACAACGTCTATTG	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.1741T>G	12.37:g.77243231T>G	ENSP00000403397:p.Ser581Ala	342	0	0		328	38	0.115854	NM_015336	B4DR39|O75407|Q7Z2I0|Q86W89|Q86YK0|Q9P088|Q9UPZ8	Missense_Mutation	SNP	ENST00000426126.2	37	CCDS44946.1	.	.	.	.	.	.	.	.	.	.	T	13.24	2.178323	0.38511	.	.	ENSG00000186908	ENST00000426126;ENST00000334822	T;T	0.32515	1.45;1.45	5.62	5.62	0.85841	.	.	.	.	.	T	0.25827	0.0629	L	0.36672	1.1	0.80722	D	1	P	0.40931	0.733	B	0.39935	0.314	T	0.03354	-1.1045	9	0.11794	T	0.64	-13.0474	15.8846	0.79238	0.0:0.0:0.0:1.0	.	581	Q8IUH5	ZDH17_HUMAN	A	581	ENSP00000403397:S581A;ENSP00000334868:S581A	ENSP00000334868:S581A	S	+	1	0	ZDHHC17	75767362	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	6.082000	0.71318	2.159000	0.67721	0.373000	0.22412	TCT	.	.	none		0.294	ZDHHC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406555.1	NM_015336		G	77243231	T	G	77243231	3	3	42	1	0	0	0	0	1	0	0	0	17622	1667	58	5	1803	5	ZDHHC17	12	77243231	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	4196417	77243231	56608664	246	15198											
CCDC41	10154	hgsc.bcm.edu	37	chr12	94702622	94702622	+	IGR	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatccaagttcctctagttgTtttctttgtgttgtttccag	5	20	8	8	0	2	0	0	0	2	0	5	1	5	0	3	0	0	5	3	0	2	8			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr12:94702622T>C	ENST00000258526.4	+	0	7346				CCDC41_ENST00000397809.5_Silent_p.K691K|CCDC41_ENST00000339839.5_Silent_p.K691K	NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1						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)	p.K691K(1)		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						CCTCTAGTTGTTTTCTTTGTG	0.388																																					p.K691K		Atlas-SNP	.											CCDC41,NS,carcinoma,0,1	CCDC41	59	1	1	Substitution - coding silent(1)	kidney(1)	c.A2073G						PASS	.						218	195	202					12																	94702622		1864	4101	5965	SO:0001628	intergenic_variant	51134	exon17			TAGTTGTTTTCTT	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		12.37:g.94702622T>C		349	0	0		370	49	0.132432	NM_016122	Q59H25	Silent	SNP	ENST00000258526.4	37	CCDS9049.1																																																																																			.	.	none		0.388	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2			C	94702622	T	C	94702622	1	2	42	0	1	0	0	0	0	0	0	0	2815	1722	60	3		3	CCDC41	12	94702622	IGR	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	17459391	94702622	39149273	247	15199											
ACACB	32	hgsc.bcm.edu	37	chr12	109616950	109616950	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaagctggcccagcacgccCgtcacctggaagttcagatc	9	7	11	14	2	2	2	2	1	0	1	3	3	2	3	3	2	2	3	3	2	2	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr12:109616950C>T	ENST00000338432.7	+	10	1614	c.1495C>T	c.(1495-1497)Cgt>Tgt	p.R499C	ACACB_ENST00000377848.3_Missense_Mutation_p.R499C|ACACB_ENST00000377854.5_Missense_Mutation_p.R499C|ACACB_ENST00000543080.1_3'UTR			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	499	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)	CCAGCACGCCCGTCACCTGGA	0.572																																					p.R499C		Atlas-SNP	.											.	ACACB	330	.	0			c.C1495T						PASS	.						63	52	55					12																	109616950		2203	4300	6503	SO:0001583	missense	32	exon9			CACGCCCGTCACC	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.1495C>T	12.37:g.109616950C>T	ENSP00000341044:p.Arg499Cys	57	0	0		72	9	0.125	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.365697	0.82463	.	.	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854	D;D;D	0.97941	-4.62;-4.62;-4.62	5.2	5.2	0.72013	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);Biotin carboxylation domain (1);	0.106857	0.64402	D	0.000005	D	0.99369	0.9778	H	0.99650	4.68	0.80722	D	1	D	0.89917	1.0	D	0.74023	0.982	D	0.98128	1.0429	10	0.87932	D	0	.	15.1597	0.72775	0.1415:0.8585:0.0:0.0	.	499	O00763	ACACB_HUMAN	C	499	ENSP00000341044:R499C;ENSP00000367079:R499C;ENSP00000367085:R499C	ENSP00000341044:R499C	R	+	1	0	ACACB	108101333	0.998000	0.40836	0.970000	0.41538	0.999000	0.98932	4.030000	0.57260	2.428000	0.82296	0.643000	0.83706	CGT	.	.	none		0.572	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		T	109616950	C	T	109616950	3	4	42	1	0	0	0	0	1	0	0	0	107	652	23	1	1529	1	ACACB	12	109616950	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	14914328	109616950	24234945	248	15200											
MYO1H	283446	hgsc.bcm.edu	37	chr12	109858795	109858795	+	Frame_Shift_Del	DEL	A	A	-																															atgttttacaggattcttggAaaaaaacaatgatcttcttt																										TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr12:109858795delA	ENST00000431443.2	+	15	1589	c.1589delA	c.(1588-1590)gaafs	p.E530fs	MYO1H_ENST00000310903.5_Frame_Shift_Del_p.E520fs	NM_001101421.3	NP_001094891.3	Q8N1T3	MYO1H_HUMAN	myosin IH	530	Myosin motor.					myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.N522fs*9(1)		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						GGATTCTTGGAAAAAAACAAT	0.303																																					p.E520fs		Atlas-Indel	.											.	MYO1H	98	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.1558delG						PASS	.						66	64	64					12																	109858795		1793	4065	5858	SO:0001589	frameshift_variant	283446	exon15			.		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.1589delA	12.37:g.109858795delA	ENSP00000444076:p.Glu530fs	181	0	0		194	15	0.0773196	NM_001101421	F5H3C6	Frame_Shift_Del	DEL	ENST00000431443.2	37																																																																																				.	.	none		0.303	MYO1H-201	KNOWN	basic	protein_coding	protein_coding		NM_173597		-	109858795	A	-	109858795	7	5	42	1	0	1	0	1	0	0	0	0	10084	246	9	0	1617	0	MYO1H	12	109858795	Frame_Shift_Del	DEL	A	TCGA-GS-A9TZ-01A-11D-A38X-10	241845	109858795	23993100	249	15201											
EP400	57634	hgsc.bcm.edu	37	chr12	132498342	132498342	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtgacacagccatttattttGaggagaactaagagagatgt	14	11	11	5	0	0	5	0	2	0	3	0	7	0	5	1	1	2	0	1	1	3	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr12:132498342G>A	ENST00000333577.4	+	20	4024	c.3915G>A	c.(3913-3915)ttG>ttA	p.L1305L	EP400_ENST00000330386.6_Silent_p.L1269L|EP400_ENST00000389562.2_Silent_p.L1268L|EP400_ENST00000389561.2_Silent_p.L1269L|EP400_ENST00000332482.4_Silent_p.L1232L			Q96L91	EP400_HUMAN	E1A binding protein p400	1305	Interactions with RUVBL1 and RUVBL2.				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)		CATTTATTTTGAGGAGAACTA	0.363																																					p.L1269L		Atlas-SNP	.											.	EP400	370	.	0			c.G3807A						PASS	.						109	106	107					12																	132498342		2203	4300	6503	SO:0001819	synonymous_variant	57634	exon19			TATTTTGAGGAGA	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.3915G>A	12.37:g.132498342G>A		118	0	0		84	35	0.416667	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Silent	SNP	ENST00000333577.4	37																																																																																				.	.	none		0.363	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409		A	132498342	G	A	132498342	2	1	42	1	0	0	0	0	0	0	0	1	5151	1281	45	2		2	EP400	12	132498342	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	22639547	132498342	1353553	250	15202											
ATP12A	479	hgsc.bcm.edu	37	chr13	25285537	25285537	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cggaagctcttcatcaggctCtaccctggaagtgagtagcc	9	9	11	12	1	4	1	2	1	2	0	4	3	4	3	2	3	3	3	2	3	4	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr13:25285537C>T	ENST00000381946.3	+	22	3248	c.3081C>T	c.(3079-3081)ctC>ctT	p.L1027L	ATP12A_ENST00000218548.6_Silent_p.L1033L			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	1027					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)		TCATCAGGCTCTACCCTGGAA	0.498																																					p.L1033L	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.C3099T						PASS	.						109	97	101					13																	25285537		2203	4300	6503	SO:0001819	synonymous_variant	479	exon22			CAGGCTCTACCCT	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.3081C>T	13.37:g.25285537C>T		169	0	0		111	21	0.189189	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Silent	SNP	ENST00000381946.3	37	CCDS31948.1																																																																																			.	.	none		0.498	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676		T	25285537	C	T	25285537	2	4	42	1	0	0	0	0	0	0	0	1	1122	900	32	2		2	ATP12A	13	25285537	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10		25285537	89884341	251	15203											
FLT1	2321	hgsc.bcm.edu	37	chr13	28886173	28886173	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aatcacctagtttttccacaAgttctgcaaatcttggcctt	10	15	5	11	0	3	0	1	0	2	0	4	0	4	0	3	1	1	3	3	1	4	6			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr13:28886173A>C	ENST00000282397.4	-	26	3700	c.3449T>G	c.(3448-3450)cTt>cGt	p.L1150R	FLT1_ENST00000540678.1_Missense_Mutation_p.L368R|FLT1_ENST00000543394.1_Missense_Mutation_p.L173R	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	1150	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)	TTTTTCCACAAGTTCTGCAAA	0.413																																					p.L1150R		Atlas-SNP	.											.	FLT1	393	.	0			c.T3449G						PASS	.						109	106	107					13																	28886173		2203	4300	6503	SO:0001583	missense	2321	exon26			TCCACAAGTTCTG	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.3449T>G	13.37:g.28886173A>C	ENSP00000282397:p.Leu1150Arg	96	0	0		65	15	0.230769	NM_002019	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Missense_Mutation	SNP	ENST00000282397.4	37	CCDS9330.1	.	.	.	.	.	.	.	.	.	.	A	25.1	4.607815	0.87258	.	.	ENSG00000102755	ENST00000282397;ENST00000543394;ENST00000540678	D;D;D	0.91124	-2.79;-2.79;-2.79	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	0.64402	D	0.000001	D	0.96355	0.8811	M	0.91768	3.24	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97128	0.9816	10	0.87932	D	0	.	16.3797	0.83452	1.0:0.0:0.0:0.0	.	1150	P17948	VGFR1_HUMAN	R	1150;173;368	ENSP00000282397:L1150R;ENSP00000437841:L173R;ENSP00000443311:L368R	ENSP00000282397:L1150R	L	-	2	0	FLT1	27784173	1.000000	0.71417	0.994000	0.49952	0.924000	0.55760	9.310000	0.96267	2.271000	0.75665	0.533000	0.62120	CTT	.	.	none		0.413	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			C	28886173	A	C	28886173	3	2	42	1	0	0	0	0	1	0	0	0	5949	72	3	5	587	5	FLT1	13	28886173	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	3600636	28886173	86283705	252	15204											
BRCA2	675	hgsc.bcm.edu	37	chr13	32906689	32906689	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tactcatttgtatctgaagtGgaaccaaatgatactgatcc	13	13	7	8	0	2	3	1	3	1	0	3	4	3	4	2	1	3	1	2	1	6	4	rs276174805		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr13:32906689G>A	ENST00000380152.3	+	10	1307	c.1074G>A	c.(1072-1074)gtG>gtA	p.V358V	BRCA2_ENST00000544455.1_Silent_p.V358V			P51587	BRCA2_HUMAN	breast cancer 2, early onset	358					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)		TATCTGAAGTGGAACCAAATG	0.358			"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.V358V	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.G1074A						PASS	.						140	159	153					13																	32906689		2194	4296	6490	SO:0001819	synonymous_variant	675	exon10	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)	TGAAGTGGAACCA	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.1074G>A	13.37:g.32906689G>A		110	0	0		89	14	0.157303	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Silent	SNP	ENST00000380152.3	37	CCDS9344.1																																																																																			.	.	alt		0.358	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059		A	32906689	G	A	32906689	2	1	42	1	0	0	0	0	0	0	0	1	1501	1335	47	2		2	BRCA2	13	32906689	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	4020516	32906689	82263189	253	15205											
ENOX1	55068	hgsc.bcm.edu	37	chr13	43918835	43918835	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agcgccgattcacttcccctCgttcaatccaggaaagcagc	10	8	8	15	3	2	0	2	0	0	0	5	2	4	1	4	1	3	2	4	1	2	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr13:43918835C>T	ENST00000261488.6	-	9	1452	c.875G>A	c.(874-876)cGa>cAa	p.R292Q	ENOX1_ENST00000540032.1_Missense_Mutation_p.R105Q|ENOX1_ENST00000412891.1_Missense_Mutation_p.R292Q	NM_001242863.1|NM_017993.3	NP_001229792.1|NP_060463.2	Q8TC92	ENOX1_HUMAN	ecto-NOX disulfide-thiol exchanger 1	292					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)		CACTTCCCCTCGTTCAATCCA	0.478																																					p.R292Q		Atlas-SNP	.											ENOX1_ENST00000261488,NS,malignant_melanoma,0,2	ENOX1	158	2	0			c.G875A						PASS	.						120	110	113					13																	43918835		2203	4300	6503	SO:0001583	missense	55068	exon9			TCCCCTCGTTCAA	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.875G>A	13.37:g.43918835C>T	ENSP00000261488:p.Arg292Gln	210	0	0		128	42	0.328125	NM_017993	A4GU15|A6NMH9|B7Z5K1|Q2TU81|Q5VT11|Q9NWE0	Missense_Mutation	SNP	ENST00000261488.6	37	CCDS9389.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.827798	0.90955	.	.	ENSG00000120658	ENST00000261488;ENST00000412891;ENST00000540032	T;T	0.61040	0.14;0.14	5.92	5.08	0.68730	.	0.129804	0.51477	D	0.000083	T	0.76278	0.3965	M	0.78637	2.42	0.52501	D	0.999951	D;P	0.89917	1.0;0.725	D;B	0.87578	0.998;0.116	T	0.79792	-0.1654	10	0.72032	D	0.01	0.0067	14.8382	0.70201	0.0:0.9314:0.0:0.0686	.	105;292	B7Z5K1;Q8TC92	.;ENOX1_HUMAN	Q	292;292;105	ENSP00000261488:R292Q;ENSP00000415054:R292Q	ENSP00000261488:R292Q	R	-	2	0	ENOX1	42816835	1.000000	0.71417	0.382000	0.26119	0.968000	0.65278	7.487000	0.81328	1.502000	0.48669	0.655000	0.94253	CGA	.	.	none		0.478	ENOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044717.2	NM_017993		T	43918835	C	T	43918835	3	4	42	1	0	0	0	0	1	0	0	0	5128	884	31	1	1092	1	ENOX1	13	43918835	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	11012146	43918835	71251043	254	15206											
KLHL1	57626	hgsc.bcm.edu	37	chr13	70681527	70681527	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caggagccccttgctgcagcCtcgtggcaactggaagcagg	8	6	14	13	1	0	0	0	0	0	0	1	2	0	2	3	4	6	4	3	4	2	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr13:70681527C>G	ENST00000377844.4	-	1	1064	c.305G>C	c.(304-306)aGg>aCg	p.R102T	ATXN8OS_ENST00000424524.1_RNA|ATXN8OS_ENST00000414504.2_RNA|KLHL1_ENST00000545028.1_5'UTR	NM_020866.2	NP_065917.1	Q9NR64	KLHL1_HUMAN	kelch-like family member 1	102					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)		TTGCTGCAGCCTCGTGGCAAC	0.592																																					p.R102T		Atlas-SNP	.											.	KLHL1	164	.	0			c.G305C						PASS	.						51	52	52					13																	70681527		2203	4300	6503	SO:0001583	missense	57626	exon1			TGCAGCCTCGTGG	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.305G>C	13.37:g.70681527C>G	ENSP00000367075:p.Arg102Thr	151	0	0		90	14	0.155556	NM_020866	A8K5X0|Q5VZ64|Q9H4X4|Q9NR65|Q9P238	Missense_Mutation	SNP	ENST00000377844.4	37	CCDS9445.1	.	.	.	.	.	.	.	.	.	.	C	13.52	2.263076	0.39995	.	.	ENSG00000150361	ENST00000377844	T	0.74315	-0.83	5.45	4.6	0.57074	.	4.002300	0.00166	N	0.000008	T	0.68476	0.3005	L	0.36672	1.1	0.80722	D	1	B;B	0.32324	0.364;0.111	B;B	0.27170	0.077;0.026	T	0.32214	-0.9915	10	0.15952	T	0.53	.	13.6724	0.62434	0.1547:0.8452:0.0:0.0	.	102;102	Q8TBJ7;Q9NR64	.;KLHL1_HUMAN	T	102	ENSP00000367075:R102T	ENSP00000367075:R102T	R	-	2	0	KLHL1	69579528	0.999000	0.42202	0.901000	0.35422	0.991000	0.79684	3.513000	0.53414	1.279000	0.44446	0.655000	0.94253	AGG	.	.	none		0.592	KLHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045231.3	NM_020866		G	70681527	C	G	70681527	3	3	42	1	0	0	0	0	1	0	0	0	8374	681	24	4	1985	4	KLHL1	13	70681527	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	26762692	70681527	44488351	255	15207											
SPRY2	10253	hgsc.bcm.edu	37	chr13	80911241	80911241	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaaggcactgcttgtcgcaGatccagtctgatggcagagg	10	8	13	10	1	1	3	0	1	1	2	3	3	2	3	1	3	1	4	1	3	1	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr13:80911241G>T	ENST00000377102.1	-	2	1577	c.600C>A	c.(598-600)atC>atA	p.I200I	SPRY2_ENST00000540649.1_Silent_p.I200I|SPRY2_ENST00000377104.3_Silent_p.I200I			O43597	SPY2_HUMAN	sprouty homolog 2 (Drosophila)	200	Cys-rich.|SPR. {ECO:0000255|PROSITE- ProRule:PRU00572}.				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)		GCTTGTCGCAGATCCAGTCTG	0.512																																					p.I200I		Atlas-SNP	.											.	SPRY2	28	.	0			c.C600A						PASS	.						111	95	100					13																	80911241		2203	4300	6503	SO:0001819	synonymous_variant	10253	exon2			GTCGCAGATCCAG	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.600C>A	13.37:g.80911241G>T		88	0	0		65	12	0.184615	NM_005842	B2R9J9|Q5T6Z7	Silent	SNP	ENST00000377102.1	37	CCDS9463.1																																																																																			.	.	none		0.512	SPRY2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045387.1			T	80911241	G	T	80911241	2	4	42	1	0	0	0	0	0	0	0	1	15121	932	33	4		4	SPRY2	13	80911241	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	10229714	80911241	34258637	256	15208											
MCF2L	23263	hgsc.bcm.edu	37	chr13	113724398	113724398	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tggcccagctgaacgaaaccGaggctgccttcgatgagttc	9	8	12	12	3	0	2	0	2	0	0	2	5	0	2	3	2	4	3	3	2	2	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr13:113724398G>A	ENST00000375608.3	+	10	1055	c.997G>A	c.(997-999)Gag>Aag	p.E333K	MCF2L_ENST00000397030.1_Missense_Mutation_p.E336K|MCF2L_ENST00000375601.3_Missense_Mutation_p.E307K|MCF2L_ENST00000423482.2_Missense_Mutation_p.E301K|MCF2L_ENST00000434480.2_Missense_Mutation_p.E309K|MCF2L_ENST00000535094.2_Missense_Mutation_p.E303K|MCF2L_ENST00000375597.4_Missense_Mutation_p.E301K|MCF2L_ENST00000375604.2_Missense_Mutation_p.E360K|MCF2L_ENST00000442652.2_Missense_Mutation_p.E333K|MCF2L_ENST00000421756.1_Missense_Mutation_p.E307K			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	333					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)				GAACGAAACCGAGGCTGCCTT	0.622																																					p.E303K		Atlas-SNP	.											.	MCF2L	182	.	0			c.G907A						PASS	.						122	97	106					13																	113724398		2203	4300	6503	SO:0001583	missense	23263	exon9			GAAACCGAGGCTG	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.997G>A	13.37:g.113724398G>A	ENSP00000364758:p.Glu333Lys	54	0	0		31	12	0.387097	NM_001112732	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Missense_Mutation	SNP	ENST00000375608.3	37		.	.	.	.	.	.	.	.	.	.	G	24.6	4.551254	0.86127	.	.	ENSG00000126217	ENST00000375608;ENST00000442652;ENST00000375604;ENST00000397030;ENST00000535094;ENST00000421756;ENST00000375601;ENST00000434480;ENST00000423482;ENST00000375597;ENST00000440749	T;T;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;1.37;1.37	5.58	4.74	0.60224	.	0.053333	0.64402	N	0.000001	T	0.62816	0.2459	M	0.84511	2.7	0.47441	D	0.999425	D;D;D;D;D;D	0.76494	0.997;0.999;0.999;0.994;0.983;0.994	D;D;D;P;P;P	0.68943	0.916;0.961;0.916;0.711;0.78;0.827	T	0.70153	-0.4950	10	0.87932	D	0	.	14.1951	0.65664	0.0719:0.0:0.9281:0.0	.	301;303;360;265;301;333	E9PDN8;O15068-9;G5E9A1;E2QRA2;O15068-4;O15068	.;.;.;.;.;MCF2L_HUMAN	K	333;333;360;336;303;307;307;309;301;301;144	ENSP00000364758:E333K;ENSP00000401422:E333K;ENSP00000364754:E360K;ENSP00000380225:E336K;ENSP00000440374:E303K;ENSP00000397285:E307K;ENSP00000364751:E307K;ENSP00000407722:E309K;ENSP00000405639:E301K;ENSP00000364747:E301K	ENSP00000364747:E301K	E	+	1	0	MCF2L	112772399	1.000000	0.71417	0.871000	0.34182	0.522000	0.34438	9.180000	0.94867	1.356000	0.45884	0.655000	0.94253	GAG	.	.	none		0.622	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4			A	113724398	G	A	113724398	3	1	42	1	0	0	0	0	1	0	0	0	9388	1059	37	1	1207	1	MCF2L	13	113724398	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	32813157	113724398	1445480	257	15209											
OR6S1	341799	hgsc.bcm.edu	37	chr14	21109391	21109391	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	accaagcacagggacgagtcCccccacccagcaggccaagg	12	1	11	17	1	0	0	0	0	0	0	1	2	1	1	6	3	2	2	6	3	2	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr14:21109391C>T	ENST00000320704.3	-	1	459	c.460G>A	c.(460-462)Gga>Aga	p.G154R		NM_001001968.1	NP_001001968.1	Q8NH40	OR6S1_HUMAN	olfactory receptor, family 6, subfamily S, 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)			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)		GGGACGAGTCCCCCCACCCAG	0.607																																					p.G154R		Atlas-SNP	.											.	OR6S1	49	.	0			c.G460A						PASS	.						84	68	73					14																	21109391		2203	4300	6503	SO:0001583	missense	341799	exon1			CGAGTCCCCCCAC	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.460G>A	14.37:g.21109391C>T	ENSP00000313110:p.Gly154Arg	67	0	0		53	15	0.283019	NM_001001968	Q6IFJ9	Missense_Mutation	SNP	ENST00000320704.3	37	CCDS32038.1	.	.	.	.	.	.	.	.	.	.	C	14.50	2.554076	0.45487	.	.	ENSG00000181803	ENST00000320704	T	0.40476	1.03	5.76	4.87	0.63330	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000186	T	0.71031	0.3292	M	0.92268	3.29	0.35185	D	0.772818	D	0.89917	1.0	D	0.87578	0.998	D	0.83841	0.0257	10	0.87932	D	0	-6.6133	12.5635	0.56295	0.0:0.9197:0.0:0.0803	.	154	Q8NH40	OR6S1_HUMAN	R	154	ENSP00000313110:G154R	ENSP00000313110:G154R	G	-	1	0	OR6S1	20179231	0.032000	0.19561	0.995000	0.50966	0.276000	0.26787	1.890000	0.39728	1.443000	0.47586	-0.136000	0.14681	GGA	.	.	none		0.607	OR6S1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411227.1			T	21109391	C	T	21109391	3	4	42	1	0	0	0	0	1	0	0	0	11218	632	22	2	539	2	OR6S1	14	21109391	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10		21109391	86240149	258	15210											
CTAGE5	4253	hgsc.bcm.edu	37	chr14	39819363	39819363	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cccccaagacctggatttttCcccccacccccacattctga	8	9	4	20	0	1	2	0	1	1	1	2	3	2	3	8	1	0	0	8	1	1	3	rs529369922		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr14:39819363C>A	ENST00000280083.3	+	24	2624	c.2310C>A	c.(2308-2310)ttC>ttA	p.F770L	CTAGE5_ENST00000553352.1_Missense_Mutation_p.F741L|CTAGE5_ENST00000396158.2_Missense_Mutation_p.F775L|CTAGE5_ENST00000556148.1_Missense_Mutation_p.F695L|CTAGE5_ENST00000557038.1_Missense_Mutation_p.F690L|CTAGE5_ENST00000341502.5_Intron|CTAGE5_ENST00000348007.3_Missense_Mutation_p.F727L|RP11-407N17.3_ENST00000553728.1_Missense_Mutation_p.F1305L|CTAGE5_ENST00000553383.1_3'UTR|CTAGE5_ENST00000396165.4_Missense_Mutation_p.F741L|CTAGE5_ENST00000341749.3_Missense_Mutation_p.F758L|RP11-407N17.3_ENST00000603904.1_Missense_Mutation_p.F741L			O15320	CTGE5_HUMAN	CTAGE family, member 5	770	Pro-rich.				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)		CTGGATTTTTCCCCCCACCCC	0.448																																					p.F775L		Atlas-SNP	.											CTAGE5,colon,carcinoma,0,1	CTAGE5	75	1	0			c.C2325A						scavenged	.																																			SO:0001583	missense	4253	exon24			ATTTTTCCCCCCA	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.2310C>A	14.37:g.39819363C>A	ENSP00000280083:p.Phe770Leu	190	2	0.0105263		144	53	0.368056	NM_001247989	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Missense_Mutation	SNP	ENST00000280083.3	37	CCDS9674.1	.	.	.	.	.	.	.	.	.	.	C	10.03	1.238787	0.22711	.	.	ENSG00000258941;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527;ENSG00000150527	ENST00000553728;ENST00000341749;ENST00000557038;ENST00000382245;ENST00000396165;ENST00000396158;ENST00000280083;ENST00000556148;ENST00000348007;ENST00000553352	T;T;T;T;T;T;T;T;T	0.08102	3.29;3.13;3.13;3.15;3.43;3.43;3.14;3.45;3.15	5.24	0.284	0.15701	.	0.224065	0.22932	N	0.053900	T	0.04543	0.0124	L	0.31664	0.95	0.23076	N	0.998332	B;B;B;B;B	0.06786	0.0;0.001;0.0;0.001;0.0	B;B;B;B;B	0.09377	0.004;0.004;0.004;0.004;0.004	T	0.39251	-0.9623	9	.	.	.	.	2.0465	0.03561	0.1196:0.458:0.1299:0.2924	.	775;727;770;698;758	O15320-5;O15320-2;O15320;O15320-7;G3XAC5	.;.;CTGE5_HUMAN;.;.	L	1305;758;690;638;741;775;770;695;727;741	ENSP00000452252:F1305L;ENSP00000343897:F758L;ENSP00000450869:F690L;ENSP00000379468:F741L;ENSP00000379462:F775L;ENSP00000280083:F770L;ENSP00000452562:F695L;ENSP00000343912:F727L;ENSP00000450449:F741L	.	F	+	3	2	CTAGE5;RP11-407N17.3	38889114	0.007000	0.16637	0.137000	0.22149	0.838000	0.47535	-0.443000	0.06862	-0.253000	0.09514	-0.261000	0.10672	TTC	.	.	none		0.448	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930		A	39819363	C	A	39819363	3	1	42	1	0	0	0	0	1	0	0	0	3996	854	30	4	2435	4	CTAGE5	14	39819363	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	18709972	39819363	67530177	259	15211											
C14orf138	79609	hgsc.bcm.edu	37	chr14	50583173	50583173	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aacccacgccaccggagctaTactgctgtagtcgtagcact	10	8	9	14	3	0	0	0	0	0	0	1	1	0	1	3	1	5	5	3	1	5	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr14:50583173T>C	ENST00000395860.2	-	1	102	c.98A>G	c.(97-99)tAt>tGt	p.Y33C	VCPKMT_ENST00000395859.2_Missense_Mutation_p.Y33C	NM_024558.2	NP_078834.2	Q9H867	MT21D_HUMAN	valosin containing protein lysine (K) methyltransferase	33					peptidyl-lysine trimethylation (GO:0018023)	cytoplasm (GO:0005737)	protein-lysine N-methyltransferase activity (GO:0016279)										ACCGGAGCTATACTGCTGTAG	0.592																																					p.Y33C		Atlas-SNP	.											.	METTL21D	11	.	0			c.A98G						PASS	.						60	64	63					14																	50583173		2203	4300	6503	SO:0001583	missense	79609	exon1			GAGCTATACTGCT	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.98A>G	14.37:g.50583173T>C	ENSP00000379201:p.Tyr33Cys	59	0	0		40	14	0.35	NM_024558	B7ZLA3|B7ZLA4|Q2M2X3|Q86T12	Missense_Mutation	SNP	ENST00000395860.2	37	CCDS9696.2	.	.	.	.	.	.	.	.	.	.	T	14.64	2.595533	0.46318	.	.	ENSG00000100483	ENST00000395859;ENST00000395860	T;T	0.06528	3.29;3.29	6.06	6.06	0.98353	.	0.404301	0.27821	N	0.017709	T	0.03263	0.0095	N	0.05414	-0.055	0.35578	D	0.806016	B;B	0.11235	0.004;0.001	B;B	0.06405	0.002;0.002	T	0.39313	-0.9620	10	0.38643	T	0.18	-3.7456	4.4545	0.11637	0.1689:0.1059:0.0:0.7251	.	33;33	B7ZLA4;Q9H867	.;MT21D_HUMAN	C	33	ENSP00000379200:Y33C;ENSP00000379201:Y33C	ENSP00000379200:Y33C	Y	-	2	0	METTL21D	49652923	0.996000	0.38824	0.966000	0.40874	0.953000	0.61014	3.034000	0.49751	2.323000	0.78572	0.528000	0.53228	TAT	.	.	none		0.592	VCPKMT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276877.1	NM_024558		C	50583173	T	C	50583173	3	2	42	1	0	0	0	0	1	0	0	0	1748	1406	49	3	615	3	C14orf138	14	50583173	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	10763810	50583173	56766367	260	15212											
KCNH5	27133	hgsc.bcm.edu	37	chr14	63175121	63175121	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtcacctcattcttctgcCggaggcgctcctcctcctct	3	12	9	17	2	5	0	2	0	3	0	8	1	8	1	5	3	1	1	5	3	0	2	rs200737420		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr14:63175121C>T	ENST00000322893.7	-	11	2340	c.2072G>A	c.(2071-2073)cGg>cAg	p.R691Q	KCNH5_ENST00000420622.2_3'UTR	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	691					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)		ATTCTTCTGCCGGAGGCGCTC	0.512																																					p.R691Q		Atlas-SNP	.											KCNH5,NS,malignant_melanoma,-1,5	KCNH5	320	5	0			c.G2072A						PASS	.						91	97	95					14																	63175121		2203	4300	6503	SO:0001583	missense	27133	exon11			TTCTGCCGGAGGC	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.2072G>A	14.37:g.63175121C>T	ENSP00000321427:p.Arg691Gln	90	0	0		75	12	0.16	NM_139318	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	37	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	C	17.73	3.462267	0.63513	.	.	ENSG00000140015	ENST00000322893	T	0.16073	2.37	5.72	5.72	0.89469	.	0.061597	0.64402	D	0.000005	T	0.21841	0.0526	M	0.62723	1.935	0.80722	D	1	D	0.58620	0.983	B	0.39503	0.301	T	0.02603	-1.1135	10	0.37606	T	0.19	.	19.8965	0.96963	0.0:1.0:0.0:0.0	.	691	Q8NCM2	KCNH5_HUMAN	Q	691	ENSP00000321427:R691Q	ENSP00000321427:R691Q	R	-	2	0	KCNH5	62244874	1.000000	0.71417	0.943000	0.38184	0.992000	0.81027	5.970000	0.70431	2.717000	0.92951	0.655000	0.94253	CGG	C|0.999;T|0.001	0.001	weak		0.512	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318		T	63175121	C	T	63175121	3	4	42	1	0	0	0	0	1	0	0	0	8044	652	23	1	898	1	KCNH5	14	63175121	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	12591948	63175121	44174419	261	15213											
C14orf50	145376	hgsc.bcm.edu	37	chr14	65016722	65016722	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagggcgaggccatgtacCgggtgcccgagttttatgcg	6	9	15	11	4	0	0	0	0	0	0	1	2	1	0	4	3	3	2	4	3	2	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr14:65016722C>T	ENST00000298705.1	+	1	103	c.7C>T	c.(7-9)Cgg>Tgg	p.R3W	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	3					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										GGCCATGTACCGGGTGCCCGA	0.692																																					p.R3W		Atlas-SNP	.											C14orf50,NS,malignant_melanoma,0,1	.	.	1	0			c.C7T						PASS	.						36	27	30					14																	65016722		2185	4278	6463	SO:0001583	missense	145376	exon1			ATGTACCGGGTGC		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.7C>T	14.37:g.65016722C>T	ENSP00000298705:p.Arg3Trp	52	0	0		51	8	0.156863	NM_172365	Q6NTH6	Missense_Mutation	SNP	ENST00000298705.1	37	CCDS9767.1	.	.	.	.	.	.	.	.	.	.	C	11.03	1.517625	0.27123	.	.	ENSG00000165807	ENST00000298705	T	0.32753	1.44	3.21	-0.892	0.10570	.	4.411120	0.00859	N	0.001907	T	0.15349	0.0370	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.23119	-1.0197	10	0.66056	D	0.02	5.66	0.6167	0.00771	0.1968:0.3735:0.192:0.2377	.	3	Q96LQ0	PPR36_HUMAN	W	3	ENSP00000298705:R3W	ENSP00000298705:R3W	R	+	1	2	C14orf50	64086475	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.007000	0.12810	-0.198000	0.10333	-0.136000	0.14681	CGG	.	.	none		0.692	PPP1R36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280667.1	NM_172365		T	65016722	C	T	65016722	3	4	42	1	0	0	0	0	1	0	0	0	1779	643	23	1	9	1	C14orf50	14	65016722	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	1841601	65016722	42332818	262	15214											
YLPM1	56252	hgsc.bcm.edu	37	chr14	75248627	75248627	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcccaccattgtcttcagcTacacctcctccaggaatacc	9	10	4	18	0	2	0	1	0	1	0	5	1	5	1	6	1	3	1	6	1	3	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr14:75248627T>C	ENST00000238571.3	+	4	1420	c.1296T>C	c.(1294-1296)acT>acC	p.T432T	YLPM1_ENST00000325680.7_Silent_p.A627A|YLPM1_ENST00000552421.1_Silent_p.A627A			P49750	YLPM1_HUMAN	YLP motif containing 1	432					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)		TGTCTTCAGCTACACCTCCTC	0.577																																					p.A627A		Atlas-SNP	.											.	YLPM1	298	.	0			c.T1881C						PASS	.						93	97	96					14																	75248627		2023	4188	6211	SO:0001630	splice_region_variant	56252	exon4			TTCAGCTACACCT	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	ENST00000238571.3:c.1295-1T>C	14.37:g.75248627T>C		191	0	0		144	24	0.166667	NM_019589	P49752|Q96I64|Q9P1V7	Silent	SNP	ENST00000238571.3	37																																																																																				.	.	none		0.577	YLPM1-201	KNOWN	basic	protein_coding	protein_coding		NM_019589	Silent	C	75248627	T	C	75248627	5	2	42	1	0	0	0	0	0	0	1	0	17501	1509	53	3	1895	3	YLPM1	14	75248627	Splice_Site	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	10231905	75248627	32100913	263	15215											
RPS6KA5	9252	hgsc.bcm.edu	37	chr14	91367011	91367011	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggacgttcaactcccatgtGaaactgaagagggtctatga	13	9	11	8	1	2	4	1	3	1	1	3	5	3	5	1	2	2	1	1	2	4	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr14:91367011G>A	ENST00000261991.3	-	10	1362	c.1189C>T	c.(1189-1191)Cac>Tac	p.H397Y	RPS6KA5_ENST00000418736.2_Missense_Mutation_p.H397Y|RPS6KA5_ENST00000536315.2_Missense_Mutation_p.H318Y	NM_004755.2	NP_004746.2	O75582	KS6A5_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 5	397					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)		ACTCCCATGTGAAACTGAAGA	0.388																																					p.H397Y		Atlas-SNP	.											.	RPS6KA5	135	.	0			c.C1189T						PASS	.						80	75	77					14																	91367011		2203	4300	6503	SO:0001583	missense	9252	exon10			CCATGTGAAACTG	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.1189C>T	14.37:g.91367011G>A	ENSP00000261991:p.His397Tyr	92	0	0		42	13	0.309524	NM_182398	O95316|Q96AF7	Missense_Mutation	SNP	ENST00000261991.3	37	CCDS9893.1	.	.	.	.	.	.	.	.	.	.	G	5.167	0.216402	0.09810	.	.	ENSG00000100784	ENST00000261991;ENST00000536315;ENST00000418736	T;T;T	0.23754	1.89;1.89;1.89	4.9	4.9	0.64082	.	0.160682	0.64402	D	0.000020	T	0.12902	0.0313	N	0.12182	0.205	0.34711	D	0.727707	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.0	T	0.20840	-1.0263	10	0.15066	T	0.55	.	9.8505	0.41055	0.1294:0.0:0.8706:0.0	.	397;397	O75582-2;O75582	.;KS6A5_HUMAN	Y	397;318;397	ENSP00000261991:H397Y;ENSP00000442803:H318Y;ENSP00000402787:H397Y	ENSP00000261991:H397Y	H	-	1	0	RPS6KA5	90436764	0.982000	0.34865	0.518000	0.27811	0.650000	0.38633	3.427000	0.52785	2.424000	0.82194	0.655000	0.94253	CAC	.	.	none		0.388	RPS6KA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411442.2	NM_004755		A	91367011	G	A	91367011	3	1	42	1	0	0	0	0	1	0	0	0	13669	1290	45	2	1257	2	RPS6KA5	14	91367011	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	16118384	91367011	15982529	264	15216											
IFI27L2	83982	hgsc.bcm.edu	37	chr14	94594298	94594298	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gacccaacagaggccaggagGatgttggatgatgtggagag	12	6	17	6	0	0	3	0	1	0	2	0	8	0	6	2	5	1	1	2	5	1	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr14:94594298G>A	ENST00000238609.3	-	4	330	c.231C>T	c.(229-231)atC>atT	p.I77I	IFI27L2_ENST00000556727.1_Silent_p.I52I	NM_032036.2	NP_114425.1	Q9H2X8	I27L2_HUMAN	interferon, alpha-inducible protein 27-like 2	77						integral component of membrane (GO:0016021)				breast(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|skin(1)	8						AGGCCAGGAGGATGTTGGATG	0.582																																					p.I77I		Atlas-SNP	.											IFI27L2,NS,carcinoma,-2,1	IFI27L2	14	1	0			c.C231T						PASS	.						72	72	72					14																	94594298		2203	4300	6503	SO:0001819	synonymous_variant	83982	exon4			CAGGAGGATGTTG	AF208232	CCDS9920.1	14q32.13	2008-10-08	2008-10-08	2008-10-08		ENSG00000119632			19753	protein-coding gene	gene with protein product		611319	"family with sequence similarity 14, member A"	FAM14A			Standard	NM_032036		Approved	TLH29	uc001ycq.3	Q9H2X8		ENST00000238609.3:c.231C>T	14.37:g.94594298G>A		152	0	0		110	17	0.154545	NM_032036	Q8TBD7|Q9NYL0	Silent	SNP	ENST00000238609.3	37	CCDS9920.1																																																																																			.	.	none		0.582	IFI27L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412935.1	NM_032036		A	94594298	G	A	94594298	2	1	42	1	0	0	0	0	0	0	0	1	7523	1164	41	2		2	IFI27L2	14	94594298	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	3227287	94594298	12755242	265	15217											
BCL11B	64919	hgsc.bcm.edu	37	chr14	99641876	99641876	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggaacttgaaggtcttgcCgcagaactcgcacgacttgc	9	9	11	12	3	1	2	0	1	1	1	2	4	1	3	1	2	4	2	1	2	3	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr14:99641876C>T	ENST00000357195.3	-	4	1306	c.1297G>A	c.(1297-1299)Ggc>Agc	p.G433S	BCL11B_ENST00000345514.2_Missense_Mutation_p.G362S|BCL11B_ENST00000443726.2_Missense_Mutation_p.G239S	NM_001282237.1|NM_138576.2	NP_001269166.1|NP_612808.1	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B (zinc finger protein)	433					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)		AAGGTCTTGCCGCAGAACTCG	0.677			T	TLX3	T-ALL																																p.G433S		Atlas-SNP	.		Dom	yes		14	14q32.1	64919	B-cell CLL/lymphoma 11B  (CTIP2)		L	BCL11B,NS,carcinoma,+1,1	BCL11B	108	1	0			c.G1297A						PASS	.						24	26	26					14																	99641876		2201	4299	6500	SO:0001583	missense	64919	exon4			TCTTGCCGCAGAA	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.1297G>A	14.37:g.99641876C>T	ENSP00000349723:p.Gly433Ser	62	0	0		40	19	0.475	NM_138576	Q9H162	Missense_Mutation	SNP	ENST00000357195.3	37	CCDS9950.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.502207	0.85176	.	.	ENSG00000127152	ENST00000357195;ENST00000345514;ENST00000443726	T;T;T	0.01455	4.87;4.87;4.87	4.11	4.11	0.48088	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.075279	0.51477	D	0.000092	T	0.08670	0.0215	L	0.59436	1.845	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.994	T	0.07233	-1.0783	10	0.87932	D	0	-14.2957	16.7085	0.85378	0.0:1.0:0.0:0.0	.	362;433	Q9C0K0-2;Q9C0K0	.;BC11B_HUMAN	S	433;362;239	ENSP00000349723:G433S;ENSP00000280435:G362S;ENSP00000387419:G239S	ENSP00000280435:G362S	G	-	1	0	BCL11B	98711629	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.540000	0.82074	1.995000	0.58328	0.491000	0.48974	GGC	.	.	none		0.677	BCL11B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000072332.2	NM_138576		T	99641876	C	T	99641876	3	4	42	1	0	0	0	0	1	0	0	0	1364	652	23	1	1391	1	BCL11B	14	99641876	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	5047578	99641876	7707664	266	15218											
DYNC1H1	1778	hgsc.bcm.edu	37	chr14	102452967	102452967	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ggaggagcggaacaccatttCccttttggtggctggcttga	7	11	14	9	1	0	1	0	1	0	0	1	4	1	4	2	6	2	2	2	6	1	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr14:102452967C>T	ENST00000360184.4	+	8	2569	c.2405C>T	c.(2404-2406)tCc>tTc	p.S802F		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	802	Interaction with DYNC1LI2. {ECO:0000250}.|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						AACACCATTTCCCTTTTGGTG	0.527																																					p.S802F		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.C2405T						PASS	.						140	130	134					14																	102452967		2203	4300	6503	SO:0001583	missense	1778	exon8			CCATTTCCCTTTT	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.2405C>T	14.37:g.102452967C>T	ENSP00000348965:p.Ser802Phe	148	0	0		120	38	0.316667	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Missense_Mutation	SNP	ENST00000360184.4	37	CCDS9966.1	.	.	.	.	.	.	.	.	.	.	C	13.64	2.298198	0.40694	.	.	ENSG00000197102	ENST00000360184	T	0.55052	0.54	5.52	5.52	0.82312	Dynein heavy chain, domain-1 (1);	0.059633	0.64402	D	0.000001	T	0.56934	0.2019	M	0.61703	1.905	0.58432	D	0.999999	P	0.38195	0.622	B	0.42422	0.387	T	0.59963	-0.7355	10	0.59425	D	0.04	.	15.3008	0.73949	0.0:0.8606:0.1394:0.0	.	802	Q14204	DYHC1_HUMAN	F	802	ENSP00000348965:S802F	ENSP00000348965:S802F	S	+	2	0	DYNC1H1	101522720	1.000000	0.71417	0.837000	0.33122	0.405000	0.30901	5.618000	0.67722	2.767000	0.95098	0.655000	0.94253	TCC	.	.	none		0.527	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376		T	102452967	C	T	102452967	3	4	42	1	0	0	0	0	1	0	0	0	4843	855	30	2	2435	2	DYNC1H1	14	102452967	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	2811091	102452967	4896573	267	15219											
OR4N4	283694	hgsc.bcm.edu	37	chr15	22382649	22382649	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cctgggctcacagcccccctCtatttatttctgggcaactt	6	13	7	15	0	3	0	1	0	2	0	3	0	3	0	4	2	2	2	4	2	3	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr15:22382649C>G	ENST00000328795.4	+	1	268	c.177C>G	c.(175-177)ctC>ctG	p.L59L	RP11-69H14.6_ENST00000558896.1_RNA	NM_001005241.2	NP_001005241.2	Q8N0Y3	OR4N4_HUMAN	olfactory receptor, family 4, subfamily N, member 4	59						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)|kidney(3)|large_intestine(6)|lung(19)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	40		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)		CAGCCCCCCTCTATTTATTTC	0.453																																					p.L59L		Atlas-SNP	.											.	OR4N4	108	.	0			c.C177G						PASS	.						132	137	135					15																	22382649		2200	4292	6492	SO:0001819	synonymous_variant	283694	exon1			CCCCCTCTATTTA	AI018459	CCDS32173.1	15q11.2	2012-08-09				ENSG00000183706		"GPCR / Class A : Olfactory receptors"	15375	protein-coding gene	gene with protein product							Standard	NM_001005241		Approved		uc010tzv.2	Q8N0Y3		ENST00000328795.4:c.177C>G	15.37:g.22382649C>G		447	0	0		409	59	0.144254	NM_001005241	Q6IEY3|Q6IF56	Silent	SNP	ENST00000328795.4	37	CCDS32173.1																																																																																			.	.	none		0.453	OR4N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414922.1			G	22382649	C	G	22382649	2	3	42	1	0	0	0	0	0	0	0	1	11087	900	32	4		4	OR4N4	15	22382649	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10		22382649	80148743	268	15220											
ARHGAP11A	9824	hgsc.bcm.edu	37	chr15	32929606	32929606	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcaaatcagtgagctgtgacGgtgctctttcctcttgtata	8	15	9	9	1	4	2	2	2	2	0	5	2	5	2	1	1	2	3	1	1	3	4	rs144493501		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr15:32929606G>A	ENST00000361627.3	+	12	3354	c.2632G>A	c.(2632-2634)Ggt>Agt	p.G878S	ARHGAP11A_ENST00000543522.1_Missense_Mutation_p.G689S|ARHGAP11A_ENST00000565905.1_Missense_Mutation_p.G689S	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	878					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)		GAGCTGTGACGGTGCTCTTTC	0.413													G|||	1	0.000199681	0.0	0.0	5008	,	,		20692	0.0		0.001	False		,,,				2504	0.0				p.G878S	Colon(45;757 1134 30003 36652)	Atlas-SNP	.											.	ARHGAP11A	84	.	0			c.G2632A						PASS	.						129	135	133					15																	32929606		2201	4300	6501	SO:0001583	missense	9824	exon12			TGTGACGGTGCTC	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.2632G>A	15.37:g.32929606G>A	ENSP00000355090:p.Gly878Ser	149	0	0		140	24	0.171429	NM_014783	B4DZN9|Q6PI96|Q9Y3S6	Missense_Mutation	SNP	ENST00000361627.3	37	CCDS10028.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	0.014	-1.575382	0.00887	.	.	ENSG00000198826	ENST00000361627;ENST00000543522	T	0.04551	3.6	5.67	-0.974	0.10293	.	0.628015	0.15860	N	0.241064	T	0.01092	0.0036	N	0.01048	-1.04	0.20563	N	0.999884	B	0.20550	0.046	B	0.10450	0.005	T	0.45071	-0.9286	10	0.02654	T	1	.	3.1354	0.06437	0.5049:0.1006:0.2866:0.108	.	878	Q6P4F7	RHGBA_HUMAN	S	878;689	ENSP00000355090:G878S	ENSP00000355090:G878S	G	+	1	0	ARHGAP11A	30716898	0.224000	0.23674	0.980000	0.43619	0.254000	0.26022	0.774000	0.26675	0.099000	0.17552	-1.320000	0.01293	GGT	G|1.000;A|0.000	0.000	strong		0.413	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783		A	32929606	G	A	32929606	3	1	42	1	0	0	0	0	1	0	0	0	863	1116	39	1	2701	1	ARHGAP11A	15	32929606	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	10546957	32929606	69601786	269	15221											
CDAN1	146059	hgsc.bcm.edu	37	chr15	43022925	43022925	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cccggcgggcctgcagccctCgctgcagcagagtccgcaca	6	4	13	18	4	0	1	0	0	0	1	2	1	1	1	4	2	4	5	4	2	0	0	rs201057681	byFrequency	TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr15:43022925C>T	ENST00000356231.3	-	14	2068	c.2045G>A	c.(2044-2046)cGa>cAa	p.R682Q		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	682					chromatin assembly (GO:0031497)|chromatin organization (GO:0006325)|negative regulation of DNA replication (GO:0008156)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.R682Q(1)		endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	24		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		CTGCAGCCCTCGCTGCAGCAG	0.637													C|||	2	0.000399361	0.0008	0.0	5008	,	,		17535	0.001		0.0	False		,,,				2504	0.0				p.R682Q		Atlas-SNP	.											CDAN1,bladder,carcinoma,0,1	CDAN1	70	1	1	Substitution - Missense(1)	urinary_tract(1)	c.G2045A						scavenged	.	C	GLN/ARG	0,4396		0,0,2198	19	22	21		2045	4.7	1	15		21	1,8571		0,1,4285	no	missense	CDAN1	NM_138477.2	43	0,1,6483	TT,TC,CC		0.0117,0.0,0.0077	benign	682/1228	43022925	1,12967	2198	4286	6484	SO:0001583	missense	146059	exon14			AGCCCTCGCTGCA	AF525398	CCDS32209.1	15q15.2	2012-04-25	2012-04-25			ENSG00000140326			1713	protein-coding gene	gene with protein product		607465	"congenital dyserythropoietic anemia, type I"			8634422, 12434312	Standard	XM_005254177		Approved	CDA-I, CDAI	uc001zql.3	Q8IWY9		ENST00000356231.3:c.2045G>A	15.37:g.43022925C>T	ENSP00000348564:p.Arg682Gln	71	1	0.0140845		65	21	0.323077	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Missense_Mutation	SNP	ENST00000356231.3	37	CCDS32209.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	7.674	0.687680	0.14973	0.0	1.17E-4	ENSG00000140326	ENST00000356231;ENST00000267892	D	0.89343	-2.5	5.77	4.66	0.58398	.	0.414368	0.29053	N	0.013297	T	0.73087	0.3542	N	0.11651	0.15	0.27851	N	0.940738	B	0.06786	0.001	B	0.06405	0.002	T	0.57751	-0.7757	10	0.02654	T	1	-7.5903	8.3942	0.32546	0.0:0.2218:0.0:0.7782	.	682	Q8IWY9	CDAN1_HUMAN	Q	682;680	ENSP00000348564:R682Q	ENSP00000267892:R680Q	R	-	2	0	CDAN1	40810217	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	0.741000	0.26202	1.022000	0.39626	-0.302000	0.09304	CGA	C|1.000;T|0.000	0.000	strong		0.637	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300		T	43022925	C	T	43022925	3	4	42	1	0	0	0	0	1	0	0	0	3056	884	31	1	1698	1	CDAN1	15	43022925	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	10093319	43022925	59508467	270	15222											
SLC30A4	7782	hgsc.bcm.edu	37	chr15	45814162	45814162	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gagttggcaacacaactcacCtacaagttctccaatcatga	14	9	6	12	0	3	1	2	1	1	0	4	2	3	1	2	1	3	3	2	1	5	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr15:45814162C>G	ENST00000261867.4	-	2	705	c.391G>C	c.(391-393)Ggt>Cgt	p.G131R	SLC30A4_ENST00000559667.1_5'UTR|HMGN2P46_ENST00000409454.1_RNA	NM_013309.4	NP_037441.2	O14863	ZNT4_HUMAN	solute carrier family 30 (zinc transporter), member 4	131					regulation of sequestering of zinc ion (GO:0061088)|response to toxic substance (GO:0009636)|zinc ion homeostasis (GO:0055069)|zinc ion transmembrane transport (GO:0071577)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(3)|large_intestine(2)|lung(8)|prostate(1)|stomach(1)	15		Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.58e-16)|GBM - Glioblastoma multiforme(94;2.15e-06)		CACAACTCACCTACAAGTTCT	0.448																																					p.G131R		Atlas-SNP	.											.	SLC30A4	25	.	0			c.G391C						PASS	.						143	121	128					15																	45814162		2198	4298	6496	SO:0001630	splice_region_variant	7782	exon2			ACTCACCTACAAG		CCDS10125.1	15q21.1	2013-05-22			ENSG00000104154	ENSG00000104154		"Solute carriers"	11015	protein-coding gene	gene with protein product		602095		ZNT4			Standard	NM_013309		Approved		uc001zvj.3	O14863	OTTHUMG00000131439	ENST00000261867.4:c.391+1G>C	15.37:g.45814162C>G		146	0	0		142	43	0.302817	NM_013309	Q8TC39	Missense_Mutation	SNP	ENST00000261867.4	37	CCDS10125.1	.	.	.	.	.	.	.	.	.	.	C	32	5.116162	0.94339	.	.	ENSG00000104154	ENST00000261867	T	0.64260	-0.09	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	D	0.86723	0.6001	H	0.96861	3.895	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.90865	0.4741	9	.	.	.	-18.5553	18.2257	0.89916	0.0:1.0:0.0:0.0	.	131	O14863	ZNT4_HUMAN	R	131	ENSP00000261867:G131R	.	G	-	1	0	SLC30A4	43601454	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.307000	0.72815	2.653000	0.90120	0.655000	0.94253	GGT	.	.	none		0.448	SLC30A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254236.1		Missense_Mutation	G	45814162	C	G	45814162	5	3	42	1	0	0	0	0	0	0	1	0	14572	695	24	4	926	4	SLC30A4	15	45814162	Splice_Site	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	2791237	45814162	56717230	271	15223			2	71		6	5	332	N	T_G_C_A	1.245804e-11
SLC30A4	7782	hgsc.bcm.edu	37	chr15	45814226	45814226	+	Missense_Mutation	SNP	C	C	G																															atggtcaacctggctttcacCtttctctgcttcagtatctc																										TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr15:45814226C>G	ENST00000261867.4	-	2	641	c.327G>C	c.(325-327)aaG>aaC	p.K109N	SLC30A4_ENST00000559667.1_5'UTR|HMGN2P46_ENST00000409454.1_RNA	NM_013309.4	NP_037441.2	O14863	ZNT4_HUMAN	solute carrier family 30 (zinc transporter), member 4	109					regulation of sequestering of zinc ion (GO:0061088)|response to toxic substance (GO:0009636)|zinc ion homeostasis (GO:0055069)|zinc ion transmembrane transport (GO:0071577)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(3)|large_intestine(2)|lung(8)|prostate(1)|stomach(1)	15		Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.58e-16)|GBM - Glioblastoma multiforme(94;2.15e-06)		TGGCTTTCACCTTTCTCTGCT	0.458																																					p.K109N		Atlas-SNP	.											.	SLC30A4	25	.	0			c.G327C						PASS	.						210	177	188					15																	45814226		2198	4298	6496	SO:0001583	missense	7782	exon2			TTTCACCTTTCTC		CCDS10125.1	15q21.1	2013-05-22			ENSG00000104154	ENSG00000104154		"Solute carriers"	11015	protein-coding gene	gene with protein product		602095		ZNT4			Standard	NM_013309		Approved		uc001zvj.3	O14863	OTTHUMG00000131439	ENST00000261867.4:c.327G>C	15.37:g.45814226C>G	ENSP00000261867:p.Lys109Asn	160	0	0		155	32	0.206452	NM_013309	Q8TC39	Missense_Mutation	SNP	ENST00000261867.4	37	CCDS10125.1	.	.	.	.	.	.	.	.	.	.	C	19.18	3.776836	0.70107	.	.	ENSG00000104154	ENST00000261867	T	0.63913	-0.07	5.34	4.4	0.53042	.	0.239529	0.38005	N	0.001851	T	0.55369	0.1916	L	0.27053	0.805	0.50813	D	0.999898	P	0.50066	0.931	P	0.46629	0.522	T	0.59434	-0.7455	10	0.54805	T	0.06	-3.2851	14.5615	0.68140	0.0:0.8525:0.1474:0.0	.	109	O14863	ZNT4_HUMAN	N	109	ENSP00000261867:K109N	ENSP00000261867:K109N	K	-	3	2	SLC30A4	43601518	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.601000	0.36773	1.217000	0.43442	0.655000	0.94253	AAG	.	.	none		0.458	SLC30A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254236.1			G	45814226	C	G	45814226	3	3	42	1	0	0	0	0	1	0	0	0	14572	680	24	4	990	4	SLC30A4	15	45814226	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	64	45814226	56717166	272	15224	198	2	2	71		6	5	332	N	T_G_C_A	1.245804e-11
SLC30A4	7782	hgsc.bcm.edu	37	chr15	45814228	45814228	+	Missense_Mutation	SNP	T	T	C																															ggtcaacctggctttcacctTtctctgcttcagtatctctc																										TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr15:45814228T>C	ENST00000261867.4	-	2	639	c.325A>G	c.(325-327)Aag>Gag	p.K109E	SLC30A4_ENST00000559667.1_5'UTR|HMGN2P46_ENST00000409454.1_RNA	NM_013309.4	NP_037441.2	O14863	ZNT4_HUMAN	solute carrier family 30 (zinc transporter), member 4	109					regulation of sequestering of zinc ion (GO:0061088)|response to toxic substance (GO:0009636)|zinc ion homeostasis (GO:0055069)|zinc ion transmembrane transport (GO:0071577)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(3)|large_intestine(2)|lung(8)|prostate(1)|stomach(1)	15		Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.58e-16)|GBM - Glioblastoma multiforme(94;2.15e-06)		GCTTTCACCTTTCTCTGCTTC	0.463																																					p.K109E		Atlas-SNP	.											.	SLC30A4	25	.	0			c.A325G						PASS	.						211	178	189					15																	45814228		2198	4298	6496	SO:0001583	missense	7782	exon2			TCACCTTTCTCTG		CCDS10125.1	15q21.1	2013-05-22			ENSG00000104154	ENSG00000104154		"Solute carriers"	11015	protein-coding gene	gene with protein product		602095		ZNT4			Standard	NM_013309		Approved		uc001zvj.3	O14863	OTTHUMG00000131439	ENST00000261867.4:c.325A>G	15.37:g.45814228T>C	ENSP00000261867:p.Lys109Glu	163	0	0		153	32	0.20915	NM_013309	Q8TC39	Missense_Mutation	SNP	ENST00000261867.4	37	CCDS10125.1	.	.	.	.	.	.	.	.	.	.	T	17.03	3.283621	0.59867	.	.	ENSG00000104154	ENST00000261867	T	0.63417	-0.04	5.34	4.19	0.49359	.	0.239529	0.38005	N	0.001851	T	0.44993	0.1320	L	0.27053	0.805	0.40913	D	0.984245	P	0.42871	0.792	B	0.35182	0.197	T	0.43015	-0.9417	10	0.45353	T	0.12	-3.2851	11.2473	0.49004	0.0:0.0:0.1537:0.8463	.	109	O14863	ZNT4_HUMAN	E	109	ENSP00000261867:K109E	ENSP00000261867:K109E	K	-	1	0	SLC30A4	43601520	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	3.716000	0.54904	0.838000	0.34948	0.533000	0.62120	AAG	.	.	none		0.463	SLC30A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254236.1			C	45814228	T	C	45814228	3	2	42	1	0	0	0	0	1	0	0	0	14572	1850	64	3	992	3	SLC30A4	15	45814228	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	2	45814228	56717164	273	15225	198	2	2	71		6	5	332	N	T_G_C_A	1.245804e-11
SLC30A4	7782	hgsc.bcm.edu	37	chr15	45814252	45814252	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctgcttcagtatctctctctGtttgctgcagttgtcacagg	5	16	9	11	0	4	0	2	0	2	0	6	0	4	0	0	1	3	6	0	1	1	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr15:45814252G>T	ENST00000261867.4	-	2	615	c.301C>A	c.(301-303)Cag>Aag	p.Q101K	SLC30A4_ENST00000559667.1_5'UTR|HMGN2P46_ENST00000409454.1_RNA	NM_013309.4	NP_037441.2	O14863	ZNT4_HUMAN	solute carrier family 30 (zinc transporter), member 4	101					regulation of sequestering of zinc ion (GO:0061088)|response to toxic substance (GO:0009636)|zinc ion homeostasis (GO:0055069)|zinc ion transmembrane transport (GO:0071577)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(3)|large_intestine(2)|lung(8)|prostate(1)|stomach(1)	15		Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.58e-16)|GBM - Glioblastoma multiforme(94;2.15e-06)		ATCTCTCTCTGTTTGCTGCAG	0.483																																					p.Q101K		Atlas-SNP	.											SLC30A4,bladder,carcinoma,+2,1	SLC30A4	25	1	0			c.C301A						PASS	.						202	176	185					15																	45814252		2198	4298	6496	SO:0001583	missense	7782	exon2			CTCTCTGTTTGCT		CCDS10125.1	15q21.1	2013-05-22			ENSG00000104154	ENSG00000104154		"Solute carriers"	11015	protein-coding gene	gene with protein product		602095		ZNT4			Standard	NM_013309		Approved		uc001zvj.3	O14863	OTTHUMG00000131439	ENST00000261867.4:c.301C>A	15.37:g.45814252G>T	ENSP00000261867:p.Gln101Lys	148	0	0		143	30	0.20979	NM_013309	Q8TC39	Missense_Mutation	SNP	ENST00000261867.4	37	CCDS10125.1	.	.	.	.	.	.	.	.	.	.	G	10.30	1.312051	0.23821	.	.	ENSG00000104154	ENST00000261867	T	0.62364	0.03	5.23	5.23	0.72850	.	0.430782	0.27437	N	0.019367	T	0.44201	0.1282	N	0.12182	0.205	0.26034	N	0.981701	B	0.02656	0.0	B	0.01281	0.0	T	0.09058	-1.0692	10	0.13470	T	0.59	-0.0024	17.3837	0.87411	0.0:0.0:1.0:0.0	.	101	O14863	ZNT4_HUMAN	K	101	ENSP00000261867:Q101K	ENSP00000261867:Q101K	Q	-	1	0	SLC30A4	43601544	1.000000	0.71417	0.046000	0.18839	0.932000	0.56968	5.303000	0.65738	2.449000	0.82847	0.655000	0.94253	CAG	.	.	none		0.483	SLC30A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254236.1			T	45814252	G	T	45814252	3	4	42	1	0	0	0	0	1	0	0	0	14572	1386	48	4	1016	4	SLC30A4	15	45814252	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	24	45814252	56717140	274	15226			2	71		6	5	332	N	T_G_C_A	1.245804e-11
SLC30A4	7782	hgsc.bcm.edu	37	chr15	45814311	45814311	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gctgactgttggtcaaaggtAagtcttggtccagtaaggaa	11	11	13	6	0	2	1	1	1	1	0	3	2	3	2	1	4	0	4	1	4	4	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr15:45814311A>T	ENST00000261867.4	-	2	556	c.242T>A	c.(241-243)tTa>tAa	p.L81*	SLC30A4_ENST00000559667.1_5'UTR|HMGN2P46_ENST00000409454.1_RNA	NM_013309.4	NP_037441.2	O14863	ZNT4_HUMAN	solute carrier family 30 (zinc transporter), member 4	81	Asp-rich (acidic).				regulation of sequestering of zinc ion (GO:0061088)|response to toxic substance (GO:0009636)|zinc ion homeostasis (GO:0055069)|zinc ion transmembrane transport (GO:0071577)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(3)|large_intestine(2)|lung(8)|prostate(1)|stomach(1)	15		Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.58e-16)|GBM - Glioblastoma multiforme(94;2.15e-06)		GGTCAAAGGTAAGTCTTGGTC	0.547																																					p.L81X		Atlas-SNP	.											.	SLC30A4	25	.	0			c.T242A						PASS	.						158	150	152					15																	45814311		2198	4298	6496	SO:0001587	stop_gained	7782	exon2			AAAGGTAAGTCTT		CCDS10125.1	15q21.1	2013-05-22			ENSG00000104154	ENSG00000104154		"Solute carriers"	11015	protein-coding gene	gene with protein product		602095		ZNT4			Standard	NM_013309		Approved		uc001zvj.3	O14863	OTTHUMG00000131439	ENST00000261867.4:c.242T>A	15.37:g.45814311A>T	ENSP00000261867:p.Leu81*	102	0	0		97	27	0.278351	NM_013309	Q8TC39	Nonsense_Mutation	SNP	ENST00000261867.4	37	CCDS10125.1	.	.	.	.	.	.	.	.	.	.	A	38	7.239480	0.98157	.	.	ENSG00000104154	ENST00000261867	.	.	.	5.23	1.3	0.21679	.	0.228496	0.38217	N	0.001763	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.08381	T	0.77	-2.4494	7.0695	0.25171	0.6784:0.2421:0.0796:0.0	.	.	.	.	X	81	.	ENSP00000261867:L81X	L	-	2	0	SLC30A4	43601603	0.016000	0.18221	0.042000	0.18584	0.991000	0.79684	1.812000	0.38952	0.844000	0.35094	0.533000	0.62120	TTA	.	.	none		0.547	SLC30A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254236.1			T	45814311	A	T	45814311	4	4	42	1	0	0	0	0	0	1	0	0	14572	372	13	5	1075	5	SLC30A4	15	45814311	Nonsense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	59	45814311	56717081	275	15227			2	71		6	5	332	N	T_G_C_A	1.245804e-11
SLC30A4	7782	hgsc.bcm.edu	37	chr15	45814493	45814493	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctggtgtcatttaaaaacagCggcgcatcatccttccttag	10	12	8	11	2	2	0	2	0	0	0	4	0	4	0	2	2	2	1	2	2	4	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr15:45814493C>T	ENST00000261867.4	-	2	374	c.60G>A	c.(58-60)ccG>ccA	p.P20P	SLC30A4_ENST00000559667.1_5'Flank|HMGN2P46_ENST00000409454.1_RNA	NM_013309.4	NP_037441.2	O14863	ZNT4_HUMAN	solute carrier family 30 (zinc transporter), member 4	20	Asp-rich (acidic).				regulation of sequestering of zinc ion (GO:0061088)|response to toxic substance (GO:0009636)|zinc ion homeostasis (GO:0055069)|zinc ion transmembrane transport (GO:0071577)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(3)|large_intestine(2)|lung(8)|prostate(1)|stomach(1)	15		Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.58e-16)|GBM - Glioblastoma multiforme(94;2.15e-06)		TTAAAAACAGCGGCGCATCAT	0.602																																					p.P20P		Atlas-SNP	.											.	SLC30A4	25	.	0			c.G60A						PASS	.						32	38	36					15																	45814493		2197	4298	6495	SO:0001819	synonymous_variant	7782	exon2			AAACAGCGGCGCA		CCDS10125.1	15q21.1	2013-05-22			ENSG00000104154	ENSG00000104154		"Solute carriers"	11015	protein-coding gene	gene with protein product		602095		ZNT4			Standard	NM_013309		Approved		uc001zvj.3	O14863	OTTHUMG00000131439	ENST00000261867.4:c.60G>A	15.37:g.45814493C>T		59	0	0		50	20	0.4	NM_013309	Q8TC39	Silent	SNP	ENST00000261867.4	37	CCDS10125.1																																																																																			.	.	none		0.602	SLC30A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254236.1			T	45814493	C	T	45814493	2	4	42	1	0	0	0	0	0	0	0	1	14572	755	27	1		1	SLC30A4	15	45814493	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	182	45814493	56716899	276	15228			2	71		6	5	332	N	T_G_C_A	1.245804e-11
UNC13C	440279	hgsc.bcm.edu	37	chr15	54860103	54860103	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtctttatacccaaactactGatgccttgataaagaaattc	14	13	5	9	0	1	3	0	2	1	1	2	3	1	3	2	0	4	0	2	0	7	7			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr15:54860103G>A	ENST00000260323.11	+	29	6064	c.6064G>A	c.(6064-6066)Gat>Aat	p.D2022N	UNC13C_ENST00000537900.1_Missense_Mutation_p.D2020N|UNC13C_ENST00000545554.1_Missense_Mutation_p.D2022N	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	2022	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)		CCAAACTACTGATGCCTTGAT	0.358																																					p.D2022N		Atlas-SNP	.											.	UNC13C	674	.	0			c.G6064A						PASS	.						60	57	58					15																	54860103		1805	4071	5876	SO:0001583	missense	440279	exon28			ACTACTGATGCCT	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.6064G>A	15.37:g.54860103G>A	ENSP00000260323:p.Asp2022Asn	284	0	0		175	48	0.274286	NM_001080534	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	37	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	G	33	5.271380	0.95429	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	T;T;T	0.75938	-0.98;-0.98;-0.98	5.81	5.81	0.92471	Mammalian uncoordinated homology 13, domain 2 (1);Mammalian uncoordinated homology 13, subgroup, domain 2 (1);	0.000000	0.85682	D	0.000000	D	0.87842	0.6279	M	0.83774	2.66	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88178	0.2869	10	0.59425	D	0.04	.	19.0637	0.93101	0.0:0.0:1.0:0.0	.	2022	Q8NB66	UN13C_HUMAN	N	2022;2022;2020	ENSP00000260323:D2022N;ENSP00000438156:D2022N;ENSP00000442569:D2020N	ENSP00000260323:D2022N	D	+	1	0	UNC13C	52647395	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	9.799000	0.99117	2.749000	0.94314	0.460000	0.39030	GAT	.	.	none		0.358	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166		A	54860103	G	A	54860103	3	1	42	1	0	0	0	0	1	0	0	0	17001	1290	45	2	6174	2	UNC13C	15	54860103	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	9045610	54860103	47671289	277	15229											
UACA	55075	hgsc.bcm.edu	37	chr15	70959921	70959926	+	In_Frame_Del	DEL	CTTTAA	CTTTAA	-																															tgaagggtaaaaatctccttCtttaacttgtcattctcttg																										TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	CTTTAA	CTTTAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr15:70959921_70959926delCTTTAA	ENST00000322954.6	-	16	3282_3287	c.3097_3102delTTAAAG	c.(3097-3102)ttaaagdel	p.LK1033del	UACA_ENST00000539319.1_In_Frame_Del_p.LK924del|UACA_ENST00000560441.1_In_Frame_Del_p.LK1018del|UACA_ENST00000379983.2_In_Frame_Del_p.LK1020del	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	1033					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						AAATCTCCTTCTTTAACTTGTCATTC	0.364																																					p.1033_1035del		Pindel,Atlas-Indel	.											.	UACA	235	.	0			c.3098_3103del						PASS	.																																			SO:0001651	inframe_deletion	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.3097_3102delTTAAAG	15.37:g.70959921_70959926delCTTTAA	ENSP00000314556:p.Leu1033_Lys1034del	266	0	.		218	33	0.151	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	In_Frame_Del	DEL	ENST00000322954.6	37	CCDS10235.1																																																																																			.	.	none		0.364	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			-	70959926	CTTTAA	-	70959921	7	5	42	1	0	1	0	1	0	0	0	0	16839	912	32	0	1164	0	UACA	15	70959921	In_Frame_Del	DEL	CTTTAA	TCGA-GS-A9TZ-01A-11D-A38X-10	16099818	70959921	31571471	278	15230											
UACA	55075	hgsc.bcm.edu	37	chr15	70961044	70961044	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	actgtctaatttcactaagtGatttttcatgttctctttcc	8	20	4	9	0	4	1	2	1	2	0	6	1	5	1	1	0	0	1	1	0	2	7			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr15:70961044G>A	ENST00000322954.6	-	16	2164	c.1979C>T	c.(1978-1980)tCa>tTa	p.S660L	UACA_ENST00000539319.1_Missense_Mutation_p.S551L|UACA_ENST00000560441.1_Missense_Mutation_p.S645L|UACA_ENST00000379983.2_Missense_Mutation_p.S647L	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	660					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						TTCACTAAGTGATTTTTCATG	0.348																																					p.S660L		Atlas-SNP	.											.	UACA	235	.	0			c.C1979T						PASS	.						93	92	92					15																	70961044		2199	4297	6496	SO:0001583	missense	55075	exon16			CTAAGTGATTTTT	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.1979C>T	15.37:g.70961044G>A	ENSP00000314556:p.Ser660Leu	460	0	0		358	100	0.27933	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Missense_Mutation	SNP	ENST00000322954.6	37	CCDS10235.1	.	.	.	.	.	.	.	.	.	.	G	10.38	1.335587	0.24253	.	.	ENSG00000137831	ENST00000322954;ENST00000379983;ENST00000539319	T;T;T	0.31247	1.5;1.52;2.0	5.61	4.68	0.58851	.	0.467858	0.18621	N	0.135860	T	0.18593	0.0446	L	0.27053	0.805	0.09310	N	1	B;B;B;B	0.13145	0.007;0.007;0.007;0.006	B;B;B;B	0.15484	0.013;0.004;0.004;0.009	T	0.13818	-1.0495	10	0.42905	T	0.14	-4.9607	3.2938	0.06958	0.1074:0.1691:0.5488:0.1747	.	551;660;660;647	F5H2B9;B7ZKM6;Q9BZF9;G3XAG2	.;.;UACA_HUMAN;.	L	660;647;551	ENSP00000314556:S660L;ENSP00000369319:S647L;ENSP00000438667:S551L	ENSP00000314556:S660L	S	-	2	0	UACA	68748098	0.998000	0.40836	0.023000	0.16930	0.955000	0.61496	5.638000	0.67861	1.334000	0.45468	0.491000	0.48974	TCA	.	.	none		0.348	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2			A	70961044	G	A	70961044	3	1	42	1	0	0	0	0	1	0	0	0	16839	1294	45	2	2287	2	UACA	15	70961044	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	1123	70961044	31570348	279	15231											
MYO9A	4649	hgsc.bcm.edu	37	chr15	72338093	72338093	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ctggtccagctccaagaataAtctgttctactccactggca	10	11	7	13	0	2	1	0	0	2	1	5	1	5	1	3	2	2	3	3	2	4	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr15:72338093A>C	ENST00000356056.5	-	2	1284	c.812T>G	c.(811-813)aTt>aGt	p.I271S	MYO9A_ENST00000444904.1_Missense_Mutation_p.I271S|MYO9A_ENST00000564571.1_Missense_Mutation_p.I271S|RNU2-65P_ENST00000410162.1_RNA|MYO9A_ENST00000424560.1_Missense_Mutation_p.I271S|MYO9A_ENST00000563542.1_5'UTR|MYO9A_ENST00000566885.1_Intron	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	271	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						TCCAAGAATAATCTGTTCTAC	0.388																																					p.I271S		Atlas-SNP	.											.	MYO9A	203	.	0			c.T812G						PASS	.						69	68	69					15																	72338093		2199	4297	6496	SO:0001583	missense	4649	exon2			AGAATAATCTGTT	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.812T>G	15.37:g.72338093A>C	ENSP00000348349:p.Ile271Ser	109	0	0		62	25	0.403226	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	37	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	A	18.08	3.544760	0.65198	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904;ENST00000261864;ENST00000446448	D;D;D	0.86497	-2.13;-2.13;-2.13	5.92	5.92	0.95590	Myosin head, motor domain (2);	.	.	.	.	D	0.89726	0.6798	L	0.45051	1.395	0.80722	D	1	P;P;P	0.45957	0.575;0.753;0.869	B;B;P	0.56865	0.205;0.406;0.808	D	0.89772	0.3955	9	0.51188	T	0.08	.	16.4074	0.83684	1.0:0.0:0.0:0.0	.	271;271;271	B2RTY4-3;B7WP69;B2RTY4	.;.;MYO9A_HUMAN	S	271	ENSP00000348349:I271S;ENSP00000399162:I271S;ENSP00000398250:I271S	ENSP00000261864:I271S	I	-	2	0	MYO9A	70125147	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.489000	0.81451	2.275000	0.75901	0.529000	0.55759	ATT	.	.	none		0.388	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901		C	72338093	A	C	72338093	3	2	42	1	0	0	0	0	1	0	0	0	10093	101	4	5	6998	5	MYO9A	15	72338093	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	1377049	72338093	30193299	280	15232											
SEMA7A	8482	hgsc.bcm.edu	37	chr15	74708989	74708989	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caggattgtcctctcggaagAagtagtagatcttgtcatcg	10	12	11	8	2	3	2	1	0	2	2	6	4	4	4	1	2	0	2	1	2	4	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr15:74708989A>T	ENST00000261918.4	-	7	1276	c.728T>A	c.(727-729)tTc>tAc	p.F243Y	SEMA7A_ENST00000542748.1_Missense_Mutation_p.F78Y|SEMA7A_ENST00000543145.2_Missense_Mutation_p.F229Y	NM_003612.3	NP_003603.1	O75326	SEM7A_HUMAN	semaphorin 7A, GPI membrane anchor (John Milton Hagen blood group)	243	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						CTCTCGGAAGAAGTAGTAGAT	0.577																																					p.F243Y		Atlas-SNP	.											.	SEMA7A	58	.	0			c.T728A						PASS	.						327	280	295					15																	74708989		2197	4296	6493	SO:0001583	missense	8482	exon7			CGGAAGAAGTAGT	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.728T>A	15.37:g.74708989A>T	ENSP00000261918:p.Phe243Tyr	176	0	0		163	44	0.269939	NM_003612	B4DDP7|F5H1S0|Q1XE81|Q1XE82|Q1XE83|Q1XE84|Q3MIY5	Missense_Mutation	SNP	ENST00000261918.4	37	CCDS10262.1	.	.	.	.	.	.	.	.	.	.	A	29.2	4.985194	0.93044	.	.	ENSG00000138623	ENST00000261918;ENST00000543145;ENST00000542748	T;T;T	0.36157	1.27;1.27;1.27	5.39	5.39	0.77823	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.65637	0.2710	M	0.89030	3	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.73084	-0.4094	10	0.87932	D	0	-28.8004	13.6573	0.62346	1.0:0.0:0.0:0.0	.	229;243	F5H1S0;O75326	.;SEM7A_HUMAN	Y	243;229;78	ENSP00000261918:F243Y;ENSP00000438966:F229Y;ENSP00000441493:F78Y	ENSP00000261918:F243Y	F	-	2	0	SEMA7A	72496042	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.167000	0.77562	2.043000	0.60533	0.533000	0.62120	TTC	.	.	none		0.577	SEMA7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272904.3	NM_003612		T	74708989	A	T	74708989	3	4	42	1	0	0	0	0	1	0	0	0	14058	246	9	5	1304	5	SEMA7A	15	74708989	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	2370896	74708989	27822403	281	15233											
PTPN9	5780	hgsc.bcm.edu	37	chr15	75762326	75762326	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aactggaagtgggtcacctgGcgtttctgccgttccttaga	7	12	12	10	2	2	1	1	0	1	1	3	2	3	2	3	3	2	2	3	3	3	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr15:75762326G>T	ENST00000306726.2	-	12	1886	c.1374C>A	c.(1372-1374)cgC>cgA	p.R458R		NM_002833.2	NP_002824.1	P43378	PTN9_HUMAN	protein tyrosine phosphatase, non-receptor type 9	458	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						GGGTCACCTGGCGTTTCTGCC	0.488																																					p.R458R		Atlas-SNP	.											.	PTPN9	53	.	0			c.C1374A						PASS	.						93	73	79					15																	75762326		2197	4294	6491	SO:0001819	synonymous_variant	5780	exon12			CACCTGGCGTTTC		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.1374C>A	15.37:g.75762326G>T		102	0	0		100	25	0.25	NM_002833	Q53XR9	Silent	SNP	ENST00000306726.2	37	CCDS10280.1																																																																																			.	.	none		0.488	PTPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286474.1			T	75762326	G	T	75762326	2	4	42	1	0	0	0	0	0	0	0	1	12809	1190	42	4		4	PTPN9	15	75762326	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	1053337	75762326	26769066	282	15234											
BCL2A1	597	hgsc.bcm.edu	37	chr15	80263370	80263370	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtagcactctggacgttttgCttggacctgatccaggttgt	6	14	12	9	1	1	1	0	1	1	0	2	3	2	3	2	3	2	5	2	3	1	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr15:80263370C>T	ENST00000267953.3	-	1	418	c.92G>A	c.(91-93)aGc>aAc	p.S31N	BCL2A1_ENST00000335661.6_Missense_Mutation_p.S31N	NM_004049.3	NP_004040.1	Q16548	B2LA1_HUMAN	BCL2-related protein A1	31	Ala/Pro-rich.				extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)	mitochondrial outer membrane (GO:0005741)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	12						GGACGTTTTGCTTGGACCTGA	0.438																																					p.S31N		Atlas-SNP	.											.	BCL2A1	28	.	0			c.G92A						PASS	.						126	115	118					15																	80263370		2203	4300	6503	SO:0001583	missense	597	exon1			GTTTTGCTTGGAC		CCDS10312.1, CCDS45322.1	15q24.3	2014-05-20			ENSG00000140379	ENSG00000140379			991	protein-coding gene	gene with protein product		601056		HBPA1		8589678, 12771180	Standard	NM_004049		Approved	GRS, BFL1, BCL2L5, ACC-1, ACC-2	uc002bfc.4	Q16548	OTTHUMG00000144173	ENST00000267953.3:c.92G>A	15.37:g.80263370C>T	ENSP00000267953:p.Ser31Asn	222	0	0		212	35	0.165094	NM_001114735	Q6FGZ4|Q6FH19|Q86W13|Q99524	Missense_Mutation	SNP	ENST00000267953.3	37	CCDS10312.1	.	.	.	.	.	.	.	.	.	.	C	11.95	1.792023	0.31685	.	.	ENSG00000140379	ENST00000267953;ENST00000335661	T;T	0.19105	2.17;2.17	5.63	3.42	0.39159	.	0.384799	0.28016	N	0.016930	T	0.18045	0.0433	L	0.52364	1.645	0.09310	N	1	B;B	0.20261	0.019;0.043	B;B	0.11329	0.005;0.006	T	0.12785	-1.0534	10	0.40728	T	0.16	-9.7726	8.3084	0.32055	0.0:0.6889:0.1444:0.1667	.	31;31	Q86W13;Q16548	.;B2LA1_HUMAN	N	31	ENSP00000267953:S31N;ENSP00000335250:S31N	ENSP00000267953:S31N	S	-	2	0	BCL2A1	78050425	0.946000	0.32159	0.171000	0.22900	0.008000	0.06430	1.337000	0.33862	1.382000	0.46385	0.655000	0.94253	AGC	.	.	none		0.438	BCL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291372.1	NM_004049		T	80263370	C	T	80263370	3	4	42	1	0	0	0	0	1	0	0	0	1366	797	28	2	503	2	BCL2A1	15	80263370	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	4501044	80263370	22268022	283	15235											
MESDC2	23184	hgsc.bcm.edu	37	chr15	81271791	81271791	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctcccatcgcgaagcatgaaGatagcacggtctgatcccac	11	7	9	14	3	1	3	0	2	1	1	4	4	3	3	2	1	2	2	2	1	3	1	rs372944817		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr15:81271791G>A	ENST00000261758.4	-	3	560	c.474C>T	c.(472-474)atC>atT	p.I158I	MESDC2_ENST00000560244.1_5'Flank	NM_015154.1	NP_055969.1	Q14696	MESD_HUMAN	mesoderm development candidate 2	158	Chaperone domain. {ECO:0000250}.				mesoderm development (GO:0007498)|protein folding (GO:0006457)|protein localization to cell surface (GO:0034394)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)				cervix(1)|large_intestine(5)|ovary(1)|urinary_tract(1)	8						GAAGCATGAAGATAGCACGGT	0.537																																					p.I158I		Atlas-SNP	.											.	MESDC2	23	.	0			c.C474T						PASS	.						71	67	69					15																	81271791		2203	4300	6503	SO:0001819	synonymous_variant	23184	exon3			CATGAAGATAGCA	D42039	CCDS32308.1	15q13	2008-07-18							13520	protein-coding gene	gene with protein product		607783				7788527, 11247670	Standard	NM_015154		Approved	KIAA0081, BOCA, MESD	uc002bfy.1	Q14696		ENST00000261758.4:c.474C>T	15.37:g.81271791G>A		63	0	0		42	12	0.285714	NM_015154	B4DW84|D3DW96|Q969U1	Silent	SNP	ENST00000261758.4	37	CCDS32308.1																																																																																			.	.	weak		0.537	MESDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417673.2	NM_015154		A	81271791	G	A	81271791	2	1	42	1	0	0	0	0	0	0	0	1	9490	932	33	2		2	MESDC2	15	81271791	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	1008421	81271791	21259601	284	15236											
IQGAP1	8826	hgsc.bcm.edu	37	chr15	90976986	90976986	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	actacagatatctatgatcgAaagaacatgccaagatgtat	17	10	7	7	1	1	4	0	1	1	3	2	5	1	4	1	0	3	1	1	0	7	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr15:90976986A>G	ENST00000268182.5	+	5	550	c.426A>G	c.(424-426)cgA>cgG	p.R142R	IQGAP1_ENST00000560738.1_Intron	NM_003870.3	NP_003861.1	P46940	IQGA1_HUMAN	IQ motif containing GTPase activating protein 1	142	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)			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)			TCTATGATCGAAAGAACATGC	0.338																																					p.R142R		Atlas-SNP	.											.	IQGAP1	140	.	0			c.A426G						PASS	.						128	126	127					15																	90976986		2198	4298	6496	SO:0001819	synonymous_variant	8826	exon5			TGATCGAAAGAAC	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.426A>G	15.37:g.90976986A>G		196	0	0		175	49	0.28	NM_003870	A7MBM3	Silent	SNP	ENST00000268182.5	37	CCDS10362.1																																																																																			.	.	none		0.338	IQGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313493.1	NM_003870		G	90976986	A	G	90976986	2	3	42	1	0	0	0	0	0	0	0	1	7823	233	9	3		3	IQGAP1	15	90976986	Silent	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	9705195	90976986	11554406	285	15237											
CHD2	1106	hgsc.bcm.edu	37	chr15	93552523	93552523	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cgagtgccttaaagcctactCagatcaggagcacatcaaac	14	7	8	12	1	3	1	3	0	0	1	3	3	3	2	2	1	5	1	2	1	4	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr15:93552523C>G	ENST00000394196.4	+	35	5630	c.4562C>G	c.(4561-4563)tCa>tGa	p.S1521*	CHD2_ENST00000557381.1_Nonsense_Mutation_p.S1521*	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1521					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)			AAAGCCTACTCAGATCAGGAG	0.502																																					p.S1521X		Atlas-SNP	.											.	CHD2	280	.	0			c.C4562G						PASS	.						80	68	72					15																	93552523		2197	4298	6495	SO:0001587	stop_gained	1106	exon35			CCTACTCAGATCA	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.4562C>G	15.37:g.93552523C>G	ENSP00000377747:p.Ser1521*	55	0	0		47	17	0.361702	NM_001271	C6G482|Q96IP5	Nonsense_Mutation	SNP	ENST00000394196.4	37	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	C	50	16.405875	0.99862	.	.	ENSG00000173575	ENST00000394196;ENST00000557381;ENST00000557759	.	.	.	5.69	5.69	0.88448	.	0.313373	0.17353	U	0.177306	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.44086	T	0.13	-8.3814	16.1069	0.81230	0.1342:0.8658:0.0:0.0	.	.	.	.	X	1521;1521;46	.	ENSP00000377747:S1521X	S	+	2	0	CHD2	91353527	0.930000	0.31532	1.000000	0.80357	0.996000	0.88848	1.336000	0.33850	2.678000	0.91216	0.655000	0.94253	TCA	.	.	none		0.502	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271		G	93552523	C	G	93552523	4	3	42	1	0	0	0	0	0	1	0	0	3327	838	29	4	4700	4	CHD2	15	93552523	Nonsense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	2575537	93552523	8978869	286	15238											
WDR24	84219	hgsc.bcm.edu	37	chr16	735417	735417	+	Nonsense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ggctgtcgtagagcgcgtgtGagacagacaggagcgagaag	11	5	18	7	4	0	4	0	1	0	4	1	7	0	5	0	2	2	2	0	2	2	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:735417G>C	ENST00000248142.6	-	11	2248	c.2249C>G	c.(2248-2250)tCa>tGa	p.S750*	JMJD8_ENST00000562824.1_5'Flank|WDR24_ENST00000293883.4_Nonsense_Mutation_p.S620*|JMJD8_ENST00000454700.1_5'Flank|JMJD8_ENST00000412368.2_5'Flank|JMJD8_ENST00000293882.4_5'Flank|JMJD8_ENST00000609261.1_5'Flank|JMJD8_ENST00000562111.1_5'Flank			Q96S15	WDR24_HUMAN	WD repeat domain 24	750										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)				GAGCGCGTGTGAGACAGACAG	0.677																																					p.S620X		Atlas-SNP	.											.	WDR24	111	.	0			c.C1859G						PASS	.						36	46	43					16																	735417		2200	4298	6498	SO:0001587	stop_gained	84219	exon7			GCGTGTGAGACAG	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.2249C>G	16.37:g.735417G>C	ENSP00000248142:p.Ser750*	69	0	0		48	9	0.1875	NM_032259	A2IDB8|D3DU59|Q96GC7|Q9H0B7	Nonsense_Mutation	SNP	ENST00000248142.6	37		.	.	.	.	.	.	.	.	.	.	G	44	10.866820	0.99480	.	.	ENSG00000127580	ENST00000248142;ENST00000293883	.	.	.	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	-11.9116	16.9554	0.86258	0.0:0.0:1.0:0.0	.	.	.	.	X	750;620	.	ENSP00000248142:S750X	S	-	2	0	WDR24	675418	1.000000	0.71417	0.067000	0.19924	0.526000	0.34562	9.182000	0.94881	2.484000	0.83849	0.511000	0.50034	TCA	.	.	none		0.677	WDR24-201	KNOWN	basic	protein_coding	protein_coding		NM_032259		C	735417	G	C	735417	4	2	42	1	0	0	0	0	0	1	0	0	17296	1294	45	4	525	4	WDR24	16	735417	Nonsense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10		735417	89619336	287	15239											
NTHL1	7249	hgsc.bcm.edu	37	chr16	2094643	2094643	+	5'Flank	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gggctcaccctccagaaaccGacggggtagatgagcttgcc	9	6	13	13	2	1	3	1	1	0	2	2	4	2	3	4	3	3	3	4	3	2	2	rs140211154		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:2094643G>A	ENST00000219476.3	+	0	0				NTHL1_ENST00000562951.1_5'Flank|NTHL1_ENST00000219066.1_Silent_p.V179V	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2						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)				TCCAGAAACCGACGGGGTAGA	0.682			"D, Mis, N, F, S"			"hamartoma, renal cell"			Tuberous Sclerosis																												p.V179V		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"E, O"	.	NTHL1	24	.	0			c.C537T						PASS	.	G		0,4396		0,0,2198	53	47	49		537	-5.8	0.9	16	dbSNP_134	49	2,8596	2.2+/-6.3	0,2,4297	no	coding-synonymous	NTHL1	NM_002528.5		0,2,6495	AA,AG,GG		0.0233,0.0,0.0154		179/313	2094643	2,12992	2198	4299	6497	SO:0001631	upstream_gene_variant	4913	exon3	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	GAAACCGACGGGG	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		16.37:g.2094643G>A	Exception_encountered	29	0	0		39	14	0.358974	NM_002528	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Silent	SNP	ENST00000219476.3	37	CCDS10458.1																																																																																			G|1.000;A|0.000	0.000	weak		0.682	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548		A	2094643	G	A	2094643	1	1	42	0	1	0	0	0	0	0	0	0	10707	1045	37	1		1	NTHL1	16	2094643	5'Flank	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	1359226	2094643	88260110	288	15240											
PKD1	5310	hgsc.bcm.edu	37	chr16	2161349	2161349	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcggggctggccgcacccacGgtcactgtgcagttctgtgc	4	8	15	14	3	2	0	1	0	1	0	2	0	2	0	2	4	2	4	2	4	0	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:2161349G>A	ENST00000262304.4	-	15	4027	c.3819C>T	c.(3817-3819)acC>acT	p.T1273T	PKD1_ENST00000423118.1_Silent_p.T1273T|RP11-304L19.4_ENST00000568795.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1273	PKD 7. {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						CCGCACCCACGGTCACTGTGC	0.687																																					p.T1273T		Atlas-SNP	.											.	PKD1	184	.	0			c.C3819T						PASS	.						12	13	12					16																	2161349		2081	4116	6197	SO:0001819	synonymous_variant	5310	exon15			ACCCACGGTCACT	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.3819C>T	16.37:g.2161349G>A		54	0	0		46	17	0.369565	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1																																																																																			.	.	none		0.687	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1			A	2161349	G	A	2161349	2	1	42	1	0	0	0	0	0	0	0	1	11972	1103	39	1		1	PKD1	16	2161349	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	66706	2161349	88193404	289	15241											
CASKIN1	57524	hgsc.bcm.edu	37	chr16	2239543	2239543	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccttccggccctgccaggcCgcatagtgcagcggccgcat	5	7	12	17	4	0	0	0	0	0	0	2	0	2	0	6	3	3	3	6	3	1	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:2239543C>T	ENST00000343516.6	-	4	359	c.267G>A	c.(265-267)gcG>gcA	p.A89A		NM_020764.3	NP_065815.1	Q8WXD9	CSKI1_HUMAN	CASK interacting protein 1	89					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						CCTGCCAGGCCGCATAGTGCA	0.687																																					p.A89A		Atlas-SNP	.											.	CASKIN1	130	.	0			c.G267A						PASS	.						16	19	18					16																	2239543		1958	4121	6079	SO:0001819	synonymous_variant	57524	exon4			CCAGGCCGCATAG	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.267G>A	16.37:g.2239543C>T		54	0	0		47	16	0.340426	NM_020764	Q9P2P0	Silent	SNP	ENST00000343516.6	37	CCDS42103.1																																																																																			.	.	none		0.687	CASKIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435055.1	NM_020764		T	2239543	C	T	2239543	2	4	42	1	0	0	0	0	0	0	0	1	2668	639	23	1		1	CASKIN1	16	2239543	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	78194	2239543	88115210	290	15242											
FAM86A	196483	hgsc.bcm.edu	37	chr16	5141837	5141837	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgggtggactccttggccatCagggtctccgccagcgcttc	4	10	13	14	2	2	0	1	0	1	0	5	1	3	1	4	4	1	1	4	4	0	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:5141837C>T	ENST00000427587.4	-	4	368	c.300G>A	c.(298-300)ctG>ctA	p.L100L	FAM86A_ENST00000458008.4_Intron|FAM86A_ENST00000587133.1_Intron	NM_201400.2	NP_958802.1	Q96G04	FA86A_HUMAN	family with sequence similarity 86, member A	100						cytoplasm (GO:0005737)				endometrium(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	12						CCTTGGCCATCAGGGTCTCCG	0.587																																					p.L100L		Atlas-SNP	.											.	FAM86A	32	.	0			c.G300A						PASS	.						38	37	37					16																	5141837		2197	4300	6497	SO:0001819	synonymous_variant	196483	exon4			GGCCATCAGGGTC	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.300G>A	16.37:g.5141837C>T		201	0	0		156	54	0.346154	NM_201400	D3DUF0|Q96S85	Silent	SNP	ENST00000427587.4	37	CCDS10529.1																																																																																			.	.	none		0.587	FAM86A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251713.1	NM_201400		T	5141837	C	T	5141837	2	4	42	1	0	0	0	0	0	0	0	1	5651	813	29	2		2	FAM86A	16	5141837	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	2902294	5141837	85212916	291	15243											
SOCS1	8651	hgsc.bcm.edu	37	chr16	11348767	11348767	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgagggggatgcgagccaggTtctcgcggcccacggtggcc	5	6	18	12	4	1	1	0	1	1	0	2	3	1	2	3	6	2	1	3	6	0	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:11348767T>C	ENST00000332029.2	-	2	719	c.569A>G	c.(568-570)aAc>aGc	p.N190S	RMI2_ENST00000572173.1_Intron	NM_003745.1	NP_003736.1	O15524	SOCS1_HUMAN	suppressor of cytokine signaling 1	190	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				cellular response to amino acid stimulus (GO:0071230)|cytokine-mediated signaling pathway (GO:0019221)|fat cell differentiation (GO:0045444)|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 insulin receptor signaling pathway (GO:0046627)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of protein phosphorylation (GO:0001932)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)	insulin-like growth factor receptor binding (GO:0005159)|kinase inhibitor activity (GO:0019210)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)	p.A184_L191del(2)|p.R127_*212del(1)|p.0?(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(66)|lung(3)	71						GCGAGCCAGGTTCTCGCGGCC	0.726			"F, O"		"Hodgkin Lymphoma, PMBL"																																p.N190S	Colon(177;456 3548 27231)	Atlas-SNP	.		Rec	yes		16	16p13.13	8651	suppressor of cytokine signaling 1		L	.	SOCS1	84	.	4	Deletion - In frame(3)|Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(4)	c.A569G						PASS	.						11	11	11					16																	11348767		2173	4276	6449	SO:0001583	missense	8651	exon2			GCCAGGTTCTCGC	U88326	CCDS10546.1	16p13.13	2013-02-14			ENSG00000185338	ENSG00000185338		"Suppressors of cytokine signaling", "SH2 domain containing"	19383	protein-coding gene	gene with protein product		603597				7796808, 9266833	Standard	NM_003745		Approved	SOCS-1, SSI-1, JAB, TIP3, Cish1	uc002dar.1	O15524	OTTHUMG00000129792	ENST00000332029.2:c.569A>G	16.37:g.11348767T>C	ENSP00000329418:p.Asn190Ser	84	0	0		78	20	0.25641	NM_003745	O15097|Q9NSA7	Missense_Mutation	SNP	ENST00000332029.2	37	CCDS10546.1	.	.	.	.	.	.	.	.	.	.	T	14.18	2.459110	0.43634	.	.	ENSG00000185338	ENST00000332029	T	0.42900	0.96	4.25	3.14	0.36123	SOCS protein, C-terminal (4);	0.312361	0.34223	N	0.004146	T	0.24812	0.0602	N	0.19112	0.55	0.39165	D	0.962486	B	0.18310	0.027	B	0.26416	0.069	T	0.06752	-1.0809	10	0.07990	T	0.79	-4.2762	10.1694	0.42900	0.0:0.0:0.168:0.832	.	190	O15524	SOCS1_HUMAN	S	190	ENSP00000329418:N190S	ENSP00000329418:N190S	N	-	2	0	SOCS1	11256268	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	3.092000	0.50207	0.666000	0.31087	-0.466000	0.05196	AAC	.	.	none		0.726	SOCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252018.1			C	11348767	T	C	11348767	3	2	42	1	0	0	0	0	1	0	0	0	14928	1725	60	3	70	3	SOCS1	16	11348767	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	6206930	11348767	79005986	292	15244			3	72		7	6	336	N	TC_T_G_C	1.092993e-14
SOCS1	8651	hgsc.bcm.edu	37	chr16	11348807	11348807	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cacgatgcgctggcggcacaGctcctgcagcggccgcacgc	6	4	14	17	6	0	0	0	0	0	0	1	1	1	0	2	3	4	5	2	3	0	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:11348807G>A	ENST00000332029.2	-	2	679	c.529C>T	c.(529-531)Ctg>Ttg	p.L177L	RMI2_ENST00000572173.1_Intron	NM_003745.1	NP_003736.1	O15524	SOCS1_HUMAN	suppressor of cytokine signaling 1	177	Interaction with Elongin BC complex. {ECO:0000250}.|SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				cellular response to amino acid stimulus (GO:0071230)|cytokine-mediated signaling pathway (GO:0019221)|fat cell differentiation (GO:0045444)|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 insulin receptor signaling pathway (GO:0046627)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of protein phosphorylation (GO:0001932)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)	insulin-like growth factor receptor binding (GO:0005159)|kinase inhibitor activity (GO:0019210)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)	p.E176fs*35(3)|p.Y64fs*1(1)|p.R127_*212del(1)|p.V171_R179del(1)|p.0?(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(66)|lung(3)	71						TGGCGGCACAGCTCCTGCAGC	0.726			"F, O"		"Hodgkin Lymphoma, PMBL"																																p.L177L	Colon(177;456 3548 27231)	Atlas-SNP	.		Rec	yes		16	16p13.13	8651	suppressor of cytokine signaling 1		L	.	SOCS1	84	.	7	Deletion - Frameshift(4)|Deletion - In frame(2)|Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(7)	c.C529T						PASS	.						7	7	7					16																	11348807		2133	4196	6329	SO:0001819	synonymous_variant	8651	exon2			GGCACAGCTCCTG	U88326	CCDS10546.1	16p13.13	2013-02-14			ENSG00000185338	ENSG00000185338		"Suppressors of cytokine signaling", "SH2 domain containing"	19383	protein-coding gene	gene with protein product		603597				7796808, 9266833	Standard	NM_003745		Approved	SOCS-1, SSI-1, JAB, TIP3, Cish1	uc002dar.1	O15524	OTTHUMG00000129792	ENST00000332029.2:c.529C>T	16.37:g.11348807G>A		58	0	0		59	18	0.305085	NM_003745	O15097|Q9NSA7	Silent	SNP	ENST00000332029.2	37	CCDS10546.1																																																																																			.	.	none		0.726	SOCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252018.1			A	11348807	G	A	11348807	2	1	42	1	0	0	0	0	0	0	0	1	14928	962	34	2		2	SOCS1	16	11348807	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	40	11348807	79005946	293	15245			3	72		7	6	336	N	TC_T_G_C	1.092993e-14
SOCS1	8651	hgsc.bcm.edu	37	chr16	11348889	11348889	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gccacgtagtgctccagcagCtcgaagaggcagtcgaagct	10	6	13	12	3	0	1	0	0	0	1	3	3	1	1	2	1	4	6	2	1	3	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:11348889C>G	ENST00000332029.2	-	2	597	c.447G>C	c.(445-447)gaG>gaC	p.E149D	RMI2_ENST00000572173.1_Intron	NM_003745.1	NP_003736.1	O15524	SOCS1_HUMAN	suppressor of cytokine signaling 1	149	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cellular response to amino acid stimulus (GO:0071230)|cytokine-mediated signaling pathway (GO:0019221)|fat cell differentiation (GO:0045444)|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 insulin receptor signaling pathway (GO:0046627)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of protein phosphorylation (GO:0001932)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)	insulin-like growth factor receptor binding (GO:0005159)|kinase inhibitor activity (GO:0019210)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)	p.F144fs*34(1)|p.D145_L150>EV(1)|p.Y64fs*1(1)|p.R127_*212del(1)|p.0?(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(66)|lung(3)	71						GCTCCAGCAGCTCGAAGAGGC	0.721			"F, O"		"Hodgkin Lymphoma, PMBL"																																p.E149D	Colon(177;456 3548 27231)	Atlas-SNP	.		Rec	yes		16	16p13.13	8651	suppressor of cytokine signaling 1		L	.	SOCS1	84	.	5	Deletion - Frameshift(2)|Whole gene deletion(1)|Complex - deletion inframe(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(5)	c.G447C						PASS	.						11	13	12					16																	11348889		2160	4263	6423	SO:0001583	missense	8651	exon2			CAGCAGCTCGAAG	U88326	CCDS10546.1	16p13.13	2013-02-14			ENSG00000185338	ENSG00000185338		"Suppressors of cytokine signaling", "SH2 domain containing"	19383	protein-coding gene	gene with protein product		603597				7796808, 9266833	Standard	NM_003745		Approved	SOCS-1, SSI-1, JAB, TIP3, Cish1	uc002dar.1	O15524	OTTHUMG00000129792	ENST00000332029.2:c.447G>C	16.37:g.11348889C>G	ENSP00000329418:p.Glu149Asp	62	0	0		67	20	0.298507	NM_003745	O15097|Q9NSA7	Missense_Mutation	SNP	ENST00000332029.2	37	CCDS10546.1	.	.	.	.	.	.	.	.	.	.	C	9.253	1.041146	0.19669	.	.	ENSG00000185338	ENST00000332029	D	0.89050	-2.46	4.06	3.11	0.35812	SH2 motif (4);	0.549051	0.19105	U	0.122583	T	0.78175	0.4242	N	0.16862	0.45	0.28270	N	0.924431	B	0.21821	0.061	B	0.22152	0.038	T	0.63152	-0.6701	10	0.14252	T	0.57	-16.6032	11.0722	0.48010	0.0:0.9084:0.0:0.0916	.	149	O15524	SOCS1_HUMAN	D	149	ENSP00000329418:E149D	ENSP00000329418:E149D	E	-	3	2	SOCS1	11256390	0.998000	0.40836	1.000000	0.80357	0.838000	0.47535	1.217000	0.32455	0.930000	0.37217	-0.448000	0.05591	GAG	.	.	none		0.721	SOCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252018.1			G	11348889	C	G	11348889	3	3	42	1	0	0	0	0	1	0	0	0	14928	796	28	4	192	4	SOCS1	16	11348889	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	82	11348889	79005864	294	15246			3	72		7	6	336	N	TC_T_G_C	1.092993e-14
SOCS1	8651	hgsc.bcm.edu	37	chr16	11348920	11348920	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agtcgaagctctcgcggctgCcatccaggtgaaagcggccg	8	6	14	13	5	1	1	0	1	1	0	4	2	2	1	3	3	3	2	3	3	2	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:11348920C>T	ENST00000332029.2	-	2	566	c.416G>A	c.(415-417)gGc>gAc	p.G139D	RMI2_ENST00000572173.1_Intron	NM_003745.1	NP_003736.1	O15524	SOCS1_HUMAN	suppressor of cytokine signaling 1	139	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cellular response to amino acid stimulus (GO:0071230)|cytokine-mediated signaling pathway (GO:0019221)|fat cell differentiation (GO:0045444)|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 insulin receptor signaling pathway (GO:0046627)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of protein phosphorylation (GO:0001932)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)	insulin-like growth factor receptor binding (GO:0005159)|kinase inhibitor activity (GO:0019210)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)	p.Y64fs*1(1)|p.R127_*212del(1)|p.0?(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(66)|lung(3)	71						CTCGCGGCTGCCATCCAGGTG	0.697			"F, O"		"Hodgkin Lymphoma, PMBL"																																p.G139D	Colon(177;456 3548 27231)	Atlas-SNP	.		Rec	yes		16	16p13.13	8651	suppressor of cytokine signaling 1		L	.	SOCS1	84	.	3	Whole gene deletion(1)|Deletion - In frame(1)|Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(3)	c.G416A						PASS	.						14	16	15					16																	11348920		2182	4284	6466	SO:0001583	missense	8651	exon2			CGGCTGCCATCCA	U88326	CCDS10546.1	16p13.13	2013-02-14			ENSG00000185338	ENSG00000185338		"Suppressors of cytokine signaling", "SH2 domain containing"	19383	protein-coding gene	gene with protein product		603597				7796808, 9266833	Standard	NM_003745		Approved	SOCS-1, SSI-1, JAB, TIP3, Cish1	uc002dar.1	O15524	OTTHUMG00000129792	ENST00000332029.2:c.416G>A	16.37:g.11348920C>T	ENSP00000329418:p.Gly139Asp	57	0	0		64	20	0.3125	NM_003745	O15097|Q9NSA7	Missense_Mutation	SNP	ENST00000332029.2	37	CCDS10546.1	.	.	.	.	.	.	.	.	.	.	C	17.18	3.324652	0.60634	.	.	ENSG00000185338	ENST00000332029	D	0.88277	-2.36	4.19	3.22	0.36961	SH2 motif (4);	0.109277	0.64402	D	0.000007	D	0.89336	0.6686	L	0.52905	1.665	0.80722	D	1	P	0.37548	0.599	P	0.48189	0.57	D	0.87457	0.2405	10	0.41790	T	0.15	-29.8658	12.3946	0.55378	0.1695:0.8305:0.0:0.0	.	139	O15524	SOCS1_HUMAN	D	139	ENSP00000329418:G139D	ENSP00000329418:G139D	G	-	2	0	SOCS1	11256421	1.000000	0.71417	1.000000	0.80357	0.615000	0.37417	1.156000	0.31712	0.963000	0.38082	-0.314000	0.08810	GGC	.	.	none		0.697	SOCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252018.1			T	11348920	C	T	11348920	3	4	42	1	0	0	0	0	1	0	0	0	14928	739	26	2	223	2	SOCS1	16	11348920	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	31	11348920	79005833	295	15247			3	72		7	6	336	N	TC_T_G_C	1.092993e-14
SOCS1	8651	hgsc.bcm.edu	37	chr16	11348978	11348978	+	Missense_Mutation	SNP	C	C	T																															gatgctcgtgggtcccgaggCcatcttcacgctaagggcga																										TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:11348978C>T	ENST00000332029.2	-	2	508	c.358G>A	c.(358-360)Gcc>Acc	p.A120T	RMI2_ENST00000572173.1_Intron	NM_003745.1	NP_003736.1	O15524	SOCS1_HUMAN	suppressor of cytokine signaling 1	120	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cellular response to amino acid stimulus (GO:0071230)|cytokine-mediated signaling pathway (GO:0019221)|fat cell differentiation (GO:0045444)|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 insulin receptor signaling pathway (GO:0046627)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of protein phosphorylation (GO:0001932)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)	insulin-like growth factor receptor binding (GO:0005159)|kinase inhibitor activity (GO:0019210)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)	p.V117fs*93(2)|p.R107_I126del(1)|p.Y64fs*1(1)|p.K118_P123>T(1)|p.0?(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(66)|lung(3)	71						GGTCCCGAGGCCATCTTCACG	0.682			"F, O"		"Hodgkin Lymphoma, PMBL"																																p.A120T	Colon(177;456 3548 27231)	Atlas-SNP	.		Rec	yes		16	16p13.13	8651	suppressor of cytokine signaling 1		L	SOCS1,NS,lymphoid_neoplasm,+2,1	SOCS1	84	1	6	Deletion - Frameshift(3)|Whole gene deletion(1)|Complex - deletion inframe(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(6)	c.G358A						scavenged	.						17	19	18					16																	11348978		2190	4294	6484	SO:0001583	missense	8651	exon2			CCGAGGCCATCTT	U88326	CCDS10546.1	16p13.13	2013-02-14			ENSG00000185338	ENSG00000185338		"Suppressors of cytokine signaling", "SH2 domain containing"	19383	protein-coding gene	gene with protein product		603597				7796808, 9266833	Standard	NM_003745		Approved	SOCS-1, SSI-1, JAB, TIP3, Cish1	uc002dar.1	O15524	OTTHUMG00000129792	ENST00000332029.2:c.358G>A	16.37:g.11348978C>T	ENSP00000329418:p.Ala120Thr	38	1	0.0263158		40	8	0.2	NM_003745	O15097|Q9NSA7	Missense_Mutation	SNP	ENST00000332029.2	37	CCDS10546.1	.	.	.	.	.	.	.	.	.	.	C	19.56	3.851001	0.71719	.	.	ENSG00000185338	ENST00000332029	D	0.88509	-2.39	4.19	3.22	0.36961	SH2 motif (4);	0.585977	0.17953	N	0.156430	D	0.84474	0.5480	L	0.42686	1.345	0.44181	D	0.996992	B	0.32968	0.392	B	0.37989	0.262	T	0.77008	-0.2747	10	0.13108	T	0.6	-33.1096	12.3697	0.55248	0.1698:0.8302:0.0:0.0	.	120	O15524	SOCS1_HUMAN	T	120	ENSP00000329418:A120T	ENSP00000329418:A120T	A	-	1	0	SOCS1	11256479	1.000000	0.71417	1.000000	0.80357	0.638000	0.38207	1.808000	0.38912	0.952000	0.37798	0.561000	0.74099	GCC	.	.	none		0.682	SOCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252018.1			T	11348978	C	T	11348978	3	4	42	1	0	0	0	0	1	0	0	0	14928	739	26	2	281	2	SOCS1	16	11348978	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	58	11348978	79005775	296	15248	199	2	3	72		7	6	336	N	TC_T_G_C	1.092993e-14
SOCS1	8651	hgsc.bcm.edu	37	chr16	11348988	11348988	+	Silent	SNP	G	G	A																															ggtcccgaggccatcttcacGctaagggcgaaaaagcagtt																										TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:11348988G>A	ENST00000332029.2	-	2	498	c.348C>T	c.(346-348)agC>agT	p.S116S	RMI2_ENST00000572173.1_Intron	NM_003745.1	NP_003736.1	O15524	SOCS1_HUMAN	suppressor of cytokine signaling 1	116	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cellular response to amino acid stimulus (GO:0071230)|cytokine-mediated signaling pathway (GO:0019221)|fat cell differentiation (GO:0045444)|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 insulin receptor signaling pathway (GO:0046627)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of protein phosphorylation (GO:0001932)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)	insulin-like growth factor receptor binding (GO:0005159)|kinase inhibitor activity (GO:0019210)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)	p.R107_I126del(1)|p.Y64fs*1(1)|p.0?(1)|p.L115fs*1(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(66)|lung(3)	71						CCATCTTCACGCTAAGGGCGA	0.687			"F, O"		"Hodgkin Lymphoma, PMBL"																																p.S116S	Colon(177;456 3548 27231)	Atlas-SNP	.		Rec	yes		16	16p13.13	8651	suppressor of cytokine signaling 1		L	SOCS1,NS,lymphoid_neoplasm,0,2	SOCS1	84	2	4	Deletion - Frameshift(2)|Whole gene deletion(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(4)	c.C348T						PASS	.						16	17	17					16																	11348988		2188	4291	6479	SO:0001819	synonymous_variant	8651	exon2			CTTCACGCTAAGG	U88326	CCDS10546.1	16p13.13	2013-02-14			ENSG00000185338	ENSG00000185338		"Suppressors of cytokine signaling", "SH2 domain containing"	19383	protein-coding gene	gene with protein product		603597				7796808, 9266833	Standard	NM_003745		Approved	SOCS-1, SSI-1, JAB, TIP3, Cish1	uc002dar.1	O15524	OTTHUMG00000129792	ENST00000332029.2:c.348C>T	16.37:g.11348988G>A		33	0	0		40	11	0.275	NM_003745	O15097|Q9NSA7	Silent	SNP	ENST00000332029.2	37	CCDS10546.1																																																																																			.	.	none		0.687	SOCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252018.1			A	11348988	G	A	11348988	2	1	42	1	0	0	0	0	0	0	0	1	14928	1078	38	1		1	SOCS1	16	11348988	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	10	11348988	79005765	297	15249	199	2	3	72		7	6	336	N	TC_T_G_C	1.092993e-14
SOCS1	8651	hgsc.bcm.edu	37	chr16	11349102	11349103	+	Frame_Shift_Del	DEL	TC	TC	-																															ctcaggggcccccagtagaaTccgcaggcgtccaggagcgc																										TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	TC	TC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:11349102_11349103delTC	ENST00000332029.2	-	2	383_384	c.233_234delGA	c.(232-234)ggafs	p.G78fs	RMI2_ENST00000572173.1_Intron	NM_003745.1	NP_003736.1	O15524	SOCS1_HUMAN	suppressor of cytokine signaling 1	78	Extended SH2 subdomain (ESS).				cellular response to amino acid stimulus (GO:0071230)|cytokine-mediated signaling pathway (GO:0019221)|fat cell differentiation (GO:0045444)|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 insulin receptor signaling pathway (GO:0046627)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of protein phosphorylation (GO:0001932)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)	insulin-like growth factor receptor binding (GO:0005159)|kinase inhibitor activity (GO:0019210)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)	p.Y64fs*1(1)|p.0?(1)|p.D63_Q108del(1)|p.S71fs*29(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(66)|lung(3)	71						CCCAGTAGAATCCGCAGGCGTC	0.743			"F, O"		"Hodgkin Lymphoma, PMBL"																																p.78_79del	Colon(177;456 3548 27231)	Atlas-Indel	.		Rec	yes		16	16p13.13	8651	suppressor of cytokine signaling 1		L	SOCS1,lymph_node,lymphoid_neoplasm,+1,1	SOCS1	84	1	4	Deletion - Frameshift(2)|Whole gene deletion(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(4)	c.234_235del						PASS	.																																			SO:0001589	frameshift_variant	8651	exon2			.	U88326	CCDS10546.1	16p13.13	2013-02-14			ENSG00000185338	ENSG00000185338		"Suppressors of cytokine signaling", "SH2 domain containing"	19383	protein-coding gene	gene with protein product		603597				7796808, 9266833	Standard	NM_003745		Approved	SOCS-1, SSI-1, JAB, TIP3, Cish1	uc002dar.1	O15524	OTTHUMG00000129792	ENST00000332029.2:c.233_234delGA	16.37:g.11349102_11349103delTC	ENSP00000329418:p.Gly78fs	29	0	0		21	10	0.47619	NM_003745	O15097|Q9NSA7	Frame_Shift_Del	DEL	ENST00000332029.2	37	CCDS10546.1																																																																																			.	.	none		0.743	SOCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252018.1			-	11349103	TC	-	11349102	7	5	42	1	0	1	0	1	0	0	0	0	14928	1422	50	0	405	0	SOCS1	16	11349102	Frame_Shift_Del	DEL	TC	TCGA-GS-A9TZ-01A-11D-A38X-10	114	11349102	79005651	298	15250			3	72		7	6	336	N	TC_T_G_C	1.092993e-14
PALB2	79728	hgsc.bcm.edu	37	chr16	23614908	23614908	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaggagggcagtacactgacCgagaagtaagtcccaaatgg	14	5	14	8	1	0	2	0	1	0	1	1	5	1	3	2	3	1	3	2	3	4	2	rs180177137		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:23614908C>T	ENST00000261584.4	-	13	3585	c.3433G>A	c.(3433-3435)Ggt>Agt	p.G1145S	CTD-2196E14.3_ENST00000561764.1_RNA	NM_024675.3	NP_078951.2	Q86YC2	PALB2_HUMAN	partner and localizer of BRCA2	1145	Interaction with RAD51, BRCA2 and POLH.|Required for interaction with POLH and POLH DNA synthesis stimulation.				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)		GTACACTGACCGAGAAGTAAG	0.473			"F, N, Mis"			"Wilms tumor, medulloblastoma, AML ,breast"		Involved in tolerance or repair of DNA crosslinks																													p.G1145S		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.G3433A						PASS	.						112	96	102					16																	23614908		2197	4300	6497	SO:0001583	missense	79728	exon13			ACTGACCGAGAAG		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.3433G>A	16.37:g.23614908C>T	ENSP00000261584:p.Gly1145Ser	112	0	0		94	18	0.191489	NM_024675	A6NIE1|Q8N7Y6|Q8ND31|Q9H6W1	Missense_Mutation	SNP	ENST00000261584.4	37	CCDS32406.1	.	.	.	.	.	.	.	.	.	.	C	18.60	3.658675	0.67586	.	.	ENSG00000083093	ENST00000261584	T	0.34667	1.35	5.77	5.77	0.91146	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.134831	0.51477	D	0.000093	T	0.50360	0.1611	L	0.49126	1.545	0.41857	D	0.990202	D	0.89917	1.0	D	0.76575	0.988	T	0.38757	-0.9646	10	0.30854	T	0.27	-18.4454	10.8436	0.46730	0.0:0.9148:0.0:0.0852	.	1145	Q86YC2	PALB2_HUMAN	S	1145	ENSP00000261584:G1145S	ENSP00000261584:G1145S	G	-	1	0	PALB2	23522409	0.936000	0.31750	0.572000	0.28498	0.702000	0.40608	3.044000	0.49830	2.737000	0.93849	0.561000	0.74099	GGT	.	.	alt		0.473	PALB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435287.2	NM_024675		T	23614908	C	T	23614908	3	4	42	1	0	0	0	0	1	0	0	0	11415	652	23	1	131	1	PALB2	16	23614908	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	12265806	23614908	66739845	299	15251											
XPO6	23214	hgsc.bcm.edu	37	chr16	28187332	28187332	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtaaggtaaggttttatggtGagccaaaaggagtttgggca	12	11	15	3	0	0	1	0	1	0	0	0	2	0	2	1	5	1	5	1	5	5	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:28187332G>A	ENST00000304658.5	-	4	792	c.292C>T	c.(292-294)Cac>Tac	p.H98Y	XPO6_ENST00000565698.1_Missense_Mutation_p.H84Y	NM_015171.3	NP_055986.1	Q96QU8	XPO6_HUMAN	exportin 6	98					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						GTTTTATGGTGAGCCAAAAGG	0.408																																					p.H98Y		Atlas-SNP	.											.	XPO6	177	.	0			c.C292T						PASS	.						90	83	85					16																	28187332		1864	4102	5966	SO:0001583	missense	23214	exon4			TATGGTGAGCCAA	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.292C>T	16.37:g.28187332G>A	ENSP00000302790:p.His98Tyr	131	0	0		116	9	0.0775862	NM_015171	A1L3W4|D3DWF9|Q2YDX3|Q53G88|Q68G50|Q76N88|Q96CP8|Q9BT21	Missense_Mutation	SNP	ENST00000304658.5	37	CCDS42135.1	.	.	.	.	.	.	.	.	.	.	G	17.91	3.505413	0.64410	.	.	ENSG00000169180	ENST00000304658	T	0.44083	0.93	5.42	5.42	0.78866	Armadillo-like helical (1);Armadillo-type fold (1);	0.048798	0.85682	D	0.000000	T	0.27384	0.0672	N	0.14661	0.345	0.54753	D	0.999981	B;B	0.12630	0.006;0.006	B;B	0.16722	0.003;0.016	T	0.08994	-1.0695	10	0.11182	T	0.66	-18.2154	17.0597	0.86543	0.0:0.0:1.0:0.0	.	98;98	B7ZM10;Q96QU8	.;XPO6_HUMAN	Y	98	ENSP00000302790:H98Y	ENSP00000302790:H98Y	H	-	1	0	XPO6	28094833	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.842000	0.86851	2.698000	0.92095	0.655000	0.94253	CAC	.	.	none		0.408	XPO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433732.1	XM_055195		A	28187332	G	A	28187332	3	1	42	1	0	0	0	0	1	0	0	0	17463	1290	45	2	3169	2	XPO6	16	28187332	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	4572424	28187332	62167421	300	15252											
CORO1A	11151	hgsc.bcm.edu	37	chr16	30199792	30199792	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gggcccctcctcatctccctCaaggatggctacgtaccccc	6	8	8	19	1	3	0	2	0	1	0	5	1	4	1	6	3	2	2	6	3	3	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:30199792C>G	ENST00000219150.5	+	10	1481	c.1176C>G	c.(1174-1176)ctC>ctG	p.L392L	CORO1A_ENST00000570045.1_Silent_p.L392L|CORO1A_ENST00000565497.1_Intron	NM_001193333.2|NM_007074.3	NP_001180262.1|NP_009005.1	P31146	COR1A_HUMAN	coronin, actin binding protein, 1A	392					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						TCATCTCCCTCAAGGATGGCT	0.697																																					p.L392L		Atlas-SNP	.											.	CORO1A	36	.	0			c.C1176G						PASS	.						32	36	34					16																	30199792		2197	4299	6496	SO:0001819	synonymous_variant	11151	exon10			CTCCCTCAAGGAT	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.1176C>G	16.37:g.30199792C>G		90	0	0		80	32	0.4	NM_007074	B2RBL1|Q2YD73	Silent	SNP	ENST00000219150.5	37	CCDS10673.1																																																																																			.	.	none		0.697	CORO1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255195.2	NM_007074		G	30199792	C	G	30199792	2	3	42	1	0	0	0	0	0	0	0	1	3755	813	29	4		4	CORO1A	16	30199792	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	2012460	30199792	60154961	301	15253											
SETD1A	9739	hgsc.bcm.edu	37	chr16	30976634	30976634	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cagcatggtccttggggccaGagatacagggagtgaggtgc	9	7	17	8	0	0	2	0	1	0	1	1	4	1	3	2	5	3	1	2	5	1	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:30976634G>C	ENST00000262519.8	+	7	2257	c.1571G>C	c.(1570-1572)aGa>aCa	p.R524T		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	524	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						CTTGGGGCCAGAGATACAGGG	0.602																																					p.R524T		Atlas-SNP	.											.	SETD1A	143	.	0			c.G1571C						PASS	.						58	62	61					16																	30976634		2197	4300	6497	SO:0001583	missense	9739	exon7			GGGCCAGAGATAC	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.1571G>C	16.37:g.30976634G>C	ENSP00000262519:p.Arg524Thr	68	0	0		64	27	0.421875	NM_014712	A6NP62|Q6PIF3|Q8TAJ6	Missense_Mutation	SNP	ENST00000262519.8	37	CCDS32435.1	.	.	.	.	.	.	.	.	.	.	G	7.516	0.655738	0.14580	.	.	ENSG00000099381	ENST00000262519	D	0.94457	-3.43	5.69	4.73	0.59995	.	0.299822	0.30060	N	0.010511	D	0.88005	0.6321	L	0.29908	0.895	0.31246	N	0.694563	P	0.35433	0.501	B	0.22386	0.039	D	0.87028	0.2133	10	0.32370	T	0.25	.	12.9443	0.58364	0.081:0.0:0.919:0.0	.	524	O15047	SET1A_HUMAN	T	524	ENSP00000262519:R524T	ENSP00000262519:R524T	R	+	2	0	SETD1A	30884135	1.000000	0.71417	0.974000	0.42286	0.082000	0.17680	3.760000	0.55235	2.681000	0.91329	0.561000	0.74099	AGA	.	.	none		0.602	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712		C	30976634	G	C	30976634	3	2	42	1	0	0	0	0	1	0	0	0	14145	942	33	4	1593	4	SETD1A	16	30976634	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	776842	30976634	59378119	302	15254											
C16orf58	64755	hgsc.bcm.edu	37	chr16	31502228	31502228	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acctctagctggtgcttctcGgtcttccagccggcatcctg	4	12	10	15	2	3	0	0	0	3	0	6	0	5	0	4	3	3	3	4	3	1	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:31502228G>A	ENST00000327237.2	-	13	1374	c.1335C>T	c.(1333-1335)acC>acT	p.T445T	AC026471.6_ENST00000565137.1_RNA|C16orf58_ENST00000570164.1_Silent_p.T443T|C16orf58_ENST00000567994.1_Silent_p.T400T			Q96GQ5	RUS1_HUMAN	chromosome 16 open reading frame 58	445						integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)	14						GGTGCTTCTCGGTCTTCCAGC	0.622																																					p.G445G		Atlas-SNP	.											C16orf58,NS,carcinoma,0,1	C16orf58	28	1	0			c.G1335T						scavenged	.						79	67	71					16																	31502228		2197	4300	6497	SO:0001819	synonymous_variant	64755	exon13			CTTCTCGGTCTTC	AK023930	CCDS10715.1	16p11.2	2013-03-04			ENSG00000140688	ENSG00000140688			25848	protein-coding gene	gene with protein product							Standard	NM_022744		Approved	FLJ13868	uc002eci.3	Q96GQ5	OTTHUMG00000132466	ENST00000327237.2:c.1335C>T	16.37:g.31502228G>A		64	1	0.015625		55	15	0.272727	NM_022744	Q53GL8|Q8NAJ4|Q9BVY3|Q9H887	Silent	SNP	ENST00000327237.2	37	CCDS10715.1																																																																																			.	.	none		0.622	C16orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255629.2	NM_022744		A	31502228	G	A	31502228	2	1	42	1	0	0	0	0	0	0	0	1	1824	1103	39	1		1	C16orf58	16	31502228	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	525594	31502228	58852525	303	15255											
VPS35	55737	hgsc.bcm.edu	37	chr16	46706252	46706252	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caactcatgctctttctggaCtcgtagtcaaagtactcaaa	12	12	6	11	1	5	0	3	0	2	0	6	1	5	1	0	1	3	3	0	1	5	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:46706252C>T	ENST00000299138.7	-	11	1351	c.1293G>A	c.(1291-1293)gaG>gaA	p.E431E	VPS35_ENST00000568642.1_5'Flank	NM_018206.4	NP_060676.2	Q96QK1	VPS35_HUMAN	vacuolar protein sorting 35 homolog (S. cerevisiae)	431					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)				TCTTTCTGGACTCGTAGTCAA	0.348																																					p.E431E		Atlas-SNP	.											VPS35,NS,carcinoma,-2,1	VPS35	49	1	0			c.G1293A						PASS	.						82	82	82					16																	46706252		2203	4300	6503	SO:0001819	synonymous_variant	55737	exon11			TCTGGACTCGTAG	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.1293G>A	16.37:g.46706252C>T		169	0	0		165	15	0.0909091	NM_018206	Q561W2|Q9H016|Q9H096|Q9H4P3|Q9H8J0|Q9NRS7|Q9NVG2|Q9NX80|Q9NZK2	Silent	SNP	ENST00000299138.7	37	CCDS10721.1																																																																																			.	.	none		0.348	VPS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255742.3			T	46706252	C	T	46706252	2	4	42	1	0	0	0	0	0	0	0	1	17218	564	20	2		2	VPS35	16	46706252	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	15204024	46706252	43648501	304	15256											
SALL1	6299	hgsc.bcm.edu	37	chr16	51175656	51175664	+	In_Frame_Del	DEL	GCTGCTGCT	GCTGCTGCT	-																															gaggagctgccgccgccgccGctgctgctgctgctgctgct																								rs13336129|rs139646526|rs372299573	byFrequency	TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	GCTGCTGCT	GCTGCTGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:51175656_51175664delGCTGCTGCT	ENST00000251020.4	-	2	502_510	c.469_477delAGCAGCAGC	c.(469-477)agcagcagcdel	p.SSS157del	SALL1_ENST00000541611.1_Intron|SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_In_Frame_Del_p.SSS60del|SALL1_ENST00000562674.1_5'Flank	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	157	Poly-Ser.				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)	p.S159G(1)|p.S157G(1)		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)			cgccgccgccgctgctgctgctgctgctg	0.627																																					p.157_160del	GBM(103;1352 1446 1855 4775 8890)	Atlas-Indel	.											.	SALL1	301	.	2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	c.470_478del						PASS	.																																			SO:0001651	inframe_deletion	6299	exon2			.	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.469_477delAGCAGCAGC	16.37:g.51175665_51175673delGCTGCTGCT	ENSP00000251020:p.Ser157_Ser159del	137	0	0		125	25	0.2	NM_002968	Q99881|Q9NSC3|Q9P1R0	In_Frame_Del	DEL	ENST00000251020.4	37	CCDS10747.1																																																																																			-|0.500;GCC|0.250;GCT|0.250	0.500	strong		0.627	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968		-	51175664	GCTGCTGCT	-	51175656	7	5	42	1	0	1	0	1	0	0	0	0	13825	1078	38	0	3505	0	SALL1	16	51175656	In_Frame_Del	DEL	GCTGCTGCT	TCGA-GS-A9TZ-01A-11D-A38X-10	4469404	51175656	39179097	305	15257											
PHLPP2	23035	hgsc.bcm.edu	37	chr16	71683436	71683436	+	Nonsense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgctctggcctcggaagcAaggcagtgtccaggccccca	7	5	13	16	2	1	0	0	0	1	0	3	1	2	1	5	4	1	3	5	4	2	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:71683436A>T	ENST00000568954.1	-	19	3707	c.3329T>A	c.(3328-3330)tTg>tAg	p.L1110*	PHLPP2_ENST00000393524.2_Nonsense_Mutation_p.L1043*|PHLPP2_ENST00000540628.1_Intron|PHLPP2_ENST00000356272.3_Nonsense_Mutation_p.L1110*|PHLPP2_ENST00000360429.3_Intron|PHLPP2_ENST00000567016.1_Nonsense_Mutation_p.L1145*			Q6ZVD8	PHLP2_HUMAN	PH domain and leucine rich repeat protein phosphatase 2	1110					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						CCTCGGAAGCAAGGCAGTGTC	0.592																																					p.L1110X		Atlas-SNP	.											.	PHLPP2	96	.	0			c.T3329A						PASS	.						55	56	55					16																	71683436		2198	4300	6498	SO:0001587	stop_gained	23035	exon18			GGAAGCAAGGCAG	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.3329T>A	16.37:g.71683436A>T	ENSP00000457991:p.Leu1110*	72	0	0		64	15	0.234375	NM_015020	A1L374|Q9NV17|Q9Y2E3	Nonsense_Mutation	SNP	ENST00000568954.1	37	CCDS32479.1	.	.	.	.	.	.	.	.	.	.	A	38	6.724567	0.97792	.	.	ENSG00000040199	ENST00000356272;ENST00000393524	.	.	.	6.03	6.03	0.97812	.	0.000000	0.64402	D	0.000015	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	-7.6795	15.7393	0.77876	1.0:0.0:0.0:0.0	.	.	.	.	X	1110;1043	.	ENSP00000348611:L1110X	L	-	2	0	PHLPP2	70240937	0.999000	0.42202	0.996000	0.52242	0.565000	0.35776	3.591000	0.53986	2.308000	0.77769	0.533000	0.62120	TTG	.	.	none		0.592	PHLPP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000434139.1	NM_015020		T	71683436	A	T	71683436	4	4	42	1	0	0	0	0	0	1	0	0	11864	131	5	5	646	5	PHLPP2	16	71683436	Nonsense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	20507780	71683436	18671317	306	15258											
CHST6	4166	hgsc.bcm.edu	37	chr16	75512714	75512714	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cgcggcggatcttggcaaagGgcagcgcatggcgccaggcc	7	4	17	13	5	1	0	0	0	1	0	1	1	1	1	2	6	1	3	2	6	1	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:75512714G>A	ENST00000332272.4	-	3	1192	c.1013C>T	c.(1012-1014)cCc>cTc	p.P338L	RP11-77K12.4_ENST00000530512.3_RNA|CHST6_ENST00000390664.2_Missense_Mutation_p.P338L	NM_021615.4	NP_067628.1	Q9GZX3	CHST6_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 6	338					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						CTTGGCAAAGGGCAGCGCATG	0.652																																					p.P338L		Atlas-SNP	.											.	CHST6	57	.	0			c.C1013T						PASS	.						61	56	58					16																	75512714		2198	4300	6498	SO:0001583	missense	4166	exon3			GCAAAGGGCAGCG	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.1013C>T	16.37:g.75512714G>A	ENSP00000328983:p.Pro338Leu	85	0	0		72	25	0.347222	NM_021615	D3DUK3	Missense_Mutation	SNP	ENST00000332272.4	37	CCDS10918.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.064439	0.76187	.	.	ENSG00000183196	ENST00000332272;ENST00000390664	D;D	0.99766	-6.69;-6.69	4.9	4.9	0.64082	Sulfotransferase domain (1);	0.182083	0.49305	D	0.000151	D	0.99694	0.9884	M	0.83953	2.67	0.53005	D	0.999964	P	0.50710	0.938	P	0.62491	0.903	D	0.97282	0.9918	10	0.56958	D	0.05	.	15.563	0.76266	0.0:0.0:1.0:0.0	.	338	Q9GZX3	CHST6_HUMAN	L	338	ENSP00000328983:P338L;ENSP00000375079:P338L	ENSP00000328983:P338L	P	-	2	0	CHST6	74070215	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.425000	0.73370	2.278000	0.76064	0.591000	0.81541	CCC	.	.	none		0.652	CHST6-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435478.1	NM_021615		A	75512714	G	A	75512714	3	1	42	1	0	0	0	0	1	0	0	0	3410	1232	43	2	178	2	CHST6	16	75512714	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	3829278	75512714	14842039	307	15259											
CHST5	23563	hgsc.bcm.edu	37	chr16	75563924	75563924	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccatgtcgcacaaaaagataGagcgcatcaggtcgcgcacg	13	5	11	12	5	1	2	1	0	0	2	3	2	1	2	1	1	1	3	1	1	3	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:75563924G>A	ENST00000336257.3	-	3	1753	c.359C>T	c.(358-360)tCt>tTt	p.S120F	CHST5_ENST00000541075.1_Missense_Mutation_p.S126F|RP11-77K12.7_ENST00000460606.1_3'UTR	NM_024533.4	NP_078809.2	Q9GZS9	CHST5_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5	120					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						CAAAAAGATAGAGCGCATCAG	0.612																																					p.S120F		Atlas-SNP	.											.	CHST5	47	.	0			c.C359T						PASS	.						70	61	64					16																	75563924		2198	4300	6498	SO:0001583	missense	23563	exon3			AAGATAGAGCGCA	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.359C>T	16.37:g.75563924G>A	ENSP00000338783:p.Ser120Phe	83	0	0		78	32	0.410256	NM_024533	B2RV23|Q7LCN3|Q9UBY3	Missense_Mutation	SNP	ENST00000336257.3	37	CCDS10919.1	.	.	.	.	.	.	.	.	.	.	G	11.79	1.743665	0.30865	.	.	ENSG00000135702	ENST00000336257;ENST00000541075	T;T	0.81078	-1.45;-1.45	2.73	2.73	0.32206	Sulfotransferase domain (1);	0.115412	0.64402	D	0.000017	D	0.88239	0.6383	M	0.79123	2.44	0.51233	D	0.999917	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.89413	0.3704	10	0.72032	D	0.01	.	12.3965	0.55389	0.0:0.0:1.0:0.0	.	126;120	Q9GZS9-2;Q9GZS9	.;CHST5_HUMAN	F	120;126	ENSP00000338783:S120F;ENSP00000441220:S126F	ENSP00000338783:S120F	S	-	2	0	CHST5	74121425	1.000000	0.71417	0.769000	0.31535	0.031000	0.12232	6.803000	0.75180	1.514000	0.48869	0.313000	0.20887	TCT	.	.	none		0.612	CHST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269025.2	NM_012126		A	75563924	G	A	75563924	3	1	42	1	0	0	0	0	1	0	0	0	3409	942	33	2	880	2	CHST5	16	75563924	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	51210	75563924	14790829	308	15260											
CNTNAP4	85445	hgsc.bcm.edu	37	chr16	76389398	76389398	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaacaatatcgccaagaggAcagcatctgggtatgttctt	13	10	10	8	1	2	1	0	0	2	1	3	3	2	2	1	2	2	3	1	2	5	4	rs139740249		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:76389398A>C	ENST00000476707.1	+	2	528	c.389A>C	c.(388-390)gAc>gCc	p.D130A	CNTNAP4_ENST00000469589.1_3'UTR|CNTNAP4_ENST00000377504.4_Missense_Mutation_p.D126A|CNTNAP4_ENST00000307431.8_Missense_Mutation_p.D126A|CNTNAP4_ENST00000478060.1_Missense_Mutation_p.D102A			Q9C0A0	CNTP4_HUMAN	contactin associated protein-like 4	127	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				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						CGCCAAGAGGACAGCATCTGG	0.438																																					p.D102A		Atlas-SNP	.											.	CNTNAP4	600	.	0			c.A305C						PASS	.						86	82	84					16																	76389398		2198	4300	6498	SO:0001583	missense	85445	exon3			AAGAGGACAGCAT	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.389A>C	16.37:g.76389398A>C	ENSP00000417628:p.Asp130Ala	98	0	0		83	24	0.289157	NM_138994	E9PFZ6|Q86YZ7	Missense_Mutation	SNP	ENST00000476707.1	37		.	.	.	.	.	.	.	.	.	.	A	17.37	3.373308	0.61624	.	.	ENSG00000152910	ENST00000307431;ENST00000377504;ENST00000478060;ENST00000476707	D;D;D;D	0.97328	-4.34;-4.34;-4.34;-4.34	4.8	4.8	0.61643	Coagulation factor 5/8 C-terminal type domain (3);Galactose-binding domain-like (1);	0.335067	0.21454	N	0.074283	D	0.97860	0.9297	.	.	.	0.37784	D	0.927109	D;D;P;P	0.56521	0.976;0.961;0.767;0.88	P;P;P;P	0.62560	0.904;0.85;0.752;0.685	D	0.99632	1.0986	9	0.54805	T	0.06	.	12.6038	0.56511	1.0:0.0:0.0:0.0	.	102;130;102;127	E9PFZ6;E9PDN6;Q96M80;Q9C0A0	.;.;.;CNTP4_HUMAN	A	126;126;102;130	ENSP00000306893:D126A;ENSP00000439733:D126A;ENSP00000418741:D102A;ENSP00000417628:D130A	ENSP00000306893:D126A	D	+	2	0	CNTNAP4	74946899	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.028000	0.70889	2.145000	0.66743	0.482000	0.46254	GAC	A|1.000;G|0.000	.	alt		0.438	CNTNAP4-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000348216.1	NM_033401		C	76389398	A	C	76389398	3	2	42	1	0	0	0	0	1	0	0	0	3651	275	10	5	403	5	CNTNAP4	16	76389398	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	825474	76389398	13965355	309	15261											
ADAD2	161931	hgsc.bcm.edu	37	chr16	84228066	84228066	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aggtccctgcttccccttctCggtgagcgcggaactggatg	5	10	13	13	3	1	1	0	1	1	0	4	3	3	3	3	4	3	1	3	4	1	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:84228066C>T	ENST00000315906.5	+	2	489	c.437C>T	c.(436-438)tCg>tTg	p.S146L	RP11-486L19.2_ENST00000565643.1_RNA|RP11-486L19.2_ENST00000569834.1_RNA|RP11-486L19.2_ENST00000561900.1_RNA|ADAD2_ENST00000268624.3_Missense_Mutation_p.S218L|RP11-486L19.2_ENST00000536986.1_RNA	NM_001145400.1	NP_001138872.1	Q8NCV1	ADAD2_HUMAN	adenosine deaminase domain containing 2	146	DRBM. {ECO:0000255|PROSITE- ProRule:PRU00266}.				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						TTCCCCTTCTCGGTGAGCGCG	0.647																																					p.S218L		Atlas-SNP	.											.	ADAD2	46	.	0			c.C653T						PASS	.						27	29	28					16																	84228066		2200	4300	6500	SO:0001583	missense	161931	exon3			CCTTCTCGGTGAG	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.437C>T	16.37:g.84228066C>T	ENSP00000325153:p.Ser146Leu	33	0	0		43	9	0.209302	NM_139174	B2RCL6|Q8NA94	Missense_Mutation	SNP	ENST00000315906.5	37	CCDS45536.1	.	.	.	.	.	.	.	.	.	.	C	12.39	1.923087	0.33908	.	.	ENSG00000140955	ENST00000315906;ENST00000268624	T;T	0.78003	-1.14;-1.14	4.33	3.36	0.38483	Double-stranded RNA-binding (3);Double-stranded RNA-binding-like (1);	0.000000	0.50627	D	0.000113	T	0.62901	0.2466	L	0.34521	1.04	0.30049	N	0.811913	P;P	0.49862	0.929;0.733	B;B	0.37267	0.245;0.154	T	0.64837	-0.6313	10	0.49607	T	0.09	-16.5901	10.2642	0.43445	0.0:0.7989:0.2011:0.0	.	146;218	Q8NCV1;Q8NCV1-2	ADAD2_HUMAN;.	L	146;218	ENSP00000325153:S146L;ENSP00000268624:S218L	ENSP00000268624:S218L	S	+	2	0	ADAD2	82785567	0.985000	0.35326	0.771000	0.31576	0.338000	0.28826	3.491000	0.53252	1.141000	0.42275	0.511000	0.50034	TCG	.	.	none		0.647	ADAD2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433385.1	NM_139174		T	84228066	C	T	84228066	3	4	42	1	0	0	0	0	1	0	0	0	232	893	31	1	663	1	ADAD2	16	84228066	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	7838668	84228066	6126687	310	15262											
IRF8	3394	hgsc.bcm.edu	37	chr16	85942692	85942692	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtgctttgaataagagcccaGattttgaggaagtgacggac	12	10	13	6	1	0	5	0	3	0	2	0	7	0	7	1	2	2	1	1	2	3	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:85942692G>A	ENST00000268638.5	+	3	693	c.271G>A	c.(271-273)Gat>Aat	p.D91N	IRF8_ENST00000563180.1_Missense_Mutation_p.D91N	NM_002163.2	NP_002154.1	Q02556	IRF8_HUMAN	interferon regulatory factor 8	91					cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	24		Prostate(104;0.0771)				TAAGAGCCCAGATTTTGAGGA	0.458																																					p.D91N		Atlas-SNP	.											.	IRF8	65	.	0			c.G271A						PASS	.						75	74	74					16																	85942692		2198	4300	6498	SO:0001583	missense	3394	exon3			AGCCCAGATTTTG	M91196	CCDS10956.1	16q24.1	2014-09-17	2004-11-12	2004-11-12	ENSG00000140968	ENSG00000140968			5358	protein-coding gene	gene with protein product		601565	"interferon consensus sequence binding protein 1"	ICSBP1		1460054, 11997525	Standard	NM_002163		Approved	IRF-8, ICSBP	uc002fjh.3	Q02556	OTTHUMG00000137648	ENST00000268638.5:c.271G>A	16.37:g.85942692G>A	ENSP00000268638:p.Asp91Asn	113	0	0		90	33	0.366667	NM_002163	A0AV82	Missense_Mutation	SNP	ENST00000268638.5	37	CCDS10956.1	.	.	.	.	.	.	.	.	.	.	G	34	5.339716	0.95783	.	.	ENSG00000140968	ENST00000268638	D	0.98090	-4.71	4.88	4.88	0.63580	Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (4);	0.000000	0.85682	D	0.000000	D	0.98419	0.9474	M	0.65498	2.005	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.85130	0.997;0.996	D	0.98988	1.0807	10	0.49607	T	0.09	-19.2746	18.3888	0.90475	0.0:0.0:1.0:0.0	.	91;91	B2R8V7;Q02556	.;IRF8_HUMAN	N	91	ENSP00000268638:D91N	ENSP00000268638:D91N	D	+	1	0	IRF8	84500193	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.282000	0.95840	2.438000	0.82558	0.484000	0.47621	GAT	.	.	none		0.458	IRF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269100.2	NM_002163		A	85942692	G	A	85942692	3	1	42	1	0	0	0	0	1	0	0	0	7845	942	33	2	277	2	IRF8	16	85942692	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	1714626	85942692	4412061	311	15263											
IRF8	3394	hgsc.bcm.edu	37	chr16	85942775	85942775	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attgttcctgaggaagagcaAaaatgtaactatcctttatg	14	13	8	6	0	0	2	0	1	0	1	2	3	2	3	2	1	2	3	2	1	6	6			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr16:85942775A>G	ENST00000268638.5	+	3	776	c.354A>G	c.(352-354)caA>caG	p.Q118Q	IRF8_ENST00000563180.1_Silent_p.Q118Q	NM_002163.2	NP_002154.1	Q02556	IRF8_HUMAN	interferon regulatory factor 8	118					cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	24		Prostate(104;0.0771)				AGGAAGAGCAAAAATGTAACT	0.493																																					p.Q118Q		Atlas-SNP	.											.	IRF8	65	.	0			c.A354G						PASS	.						48	47	47					16																	85942775		2198	4300	6498	SO:0001819	synonymous_variant	3394	exon3			AGAGCAAAAATGT	M91196	CCDS10956.1	16q24.1	2014-09-17	2004-11-12	2004-11-12	ENSG00000140968	ENSG00000140968			5358	protein-coding gene	gene with protein product		601565	"interferon consensus sequence binding protein 1"	ICSBP1		1460054, 11997525	Standard	NM_002163		Approved	IRF-8, ICSBP	uc002fjh.3	Q02556	OTTHUMG00000137648	ENST00000268638.5:c.354A>G	16.37:g.85942775A>G		79	0	0		75	27	0.36	NM_002163	A0AV82	Silent	SNP	ENST00000268638.5	37	CCDS10956.1																																																																																			.	.	none		0.493	IRF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269100.2	NM_002163		G	85942775	A	G	85942775	2	3	42	1	0	0	0	0	0	0	0	1	7845	11	1	3		3	IRF8	16	85942775	Silent	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	83	85942775	4411978	312	15264											
SLC16A13	201232	hgsc.bcm.edu	37	chr17	6941796	6941796	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctccgttacactgttgccctCaccctgatcaacactggcta	8	11	6	16	1	2	1	2	1	0	0	3	1	3	1	3	1	3	3	3	1	3	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr17:6941796C>T	ENST00000308027.6	+	3	977	c.669C>T	c.(667-669)ctC>ctT	p.L223L		NM_201566.2	NP_963860.1	Q7RTY0	MOT13_HUMAN	solute carrier family 16, member 13	223						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|skin(1)|stomach(1)	10						CTGTTGCCCTCACCCTGATCA	0.612																																					p.L223L		Atlas-SNP	.											.	SLC16A13	28	.	0			c.C669T						PASS	.						159	139	146					17																	6941796		2203	4300	6503	SO:0001819	synonymous_variant	201232	exon3			TGCCCTCACCCTG	BN000145	CCDS11085.1	17p13.1	2013-07-18	2013-07-18		ENSG00000174327	ENSG00000174327		"Solute carriers"	31037	protein-coding gene	gene with protein product	"monocarboxylic acid transporter 13"		"solute carrier family 16 (monocarboxylic acid transporters), member 13"				Standard	NM_201566		Approved	MCT13	uc002geh.3	Q7RTY0	OTTHUMG00000102089	ENST00000308027.6:c.669C>T	17.37:g.6941796C>T		156	0	0		97	41	0.42268	NM_201566	A3KMG3|A5PKU5|Q2VP92	Silent	SNP	ENST00000308027.6	37	CCDS11085.1																																																																																			.	.	none		0.612	SLC16A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219923.2			T	6941796	C	T	6941796	2	4	42	1	0	0	0	0	0	0	0	1	14421	813	29	2		2	SLC16A13	17	6941796	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10		6941796	74253414	313	15265											
DNAH2	146754	hgsc.bcm.edu	37	chr17	7662326	7662326	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tatacagggacctggaatttGaagaggaccaaagagagcat	16	7	12	6	0	0	3	0	1	0	2	0	7	0	6	2	3	2	1	2	3	5	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr17:7662326G>A	ENST00000572933.1	+	15	3792	c.2332G>A	c.(2332-2334)Gaa>Aaa	p.E778K	DNAH2_ENST00000389173.2_Missense_Mutation_p.E778K			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	778	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)				CCTGGAATTTGAAGAGGACCA	0.512																																					p.E778K		Atlas-SNP	.											.	DNAH2	498	.	0			c.G2332A						PASS	.						97	86	90					17																	7662326		2203	4300	6503	SO:0001583	missense	146754	exon14			GAATTTGAAGAGG	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.2332G>A	17.37:g.7662326G>A	ENSP00000458355:p.Glu778Lys	75	0	0		56	17	0.303571	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	CCDS32551.1	.	.	.	.	.	.	.	.	.	.	G	14.59	2.582224	0.46006	.	.	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.23348	1.91	5.42	5.42	0.78866	.	0.228580	0.35936	N	0.002888	T	0.24160	0.0585	L	0.46157	1.445	0.80722	D	1	B	0.17268	0.021	B	0.19148	0.024	T	0.02893	-1.1097	10	0.27082	T	0.32	.	13.709	0.62656	0.0:0.1549:0.8451:0.0	.	778	Q9P225	DYH2_HUMAN	K	778	ENSP00000373825:E778K	ENSP00000353818:E778K	E	+	1	0	DNAH2	7603051	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.091000	0.64505	2.535000	0.85469	0.555000	0.69702	GAA	.	.	none		0.512	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877		A	7662326	G	A	7662326	3	1	42	1	0	0	0	0	1	0	0	0	4604	1291	45	2	2386	2	DNAH2	17	7662326	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	720530	7662326	73532884	314	15266											
KCNAB3	9196	hgsc.bcm.edu	37	chr17	7832622	7832622	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggccagaccctccacccccCggaggattcccgtgcccccc	5	4	10	22	2	0	1	0	0	0	1	2	3	2	3	10	3	1	0	10	3	0	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr17:7832622C>T	ENST00000303790.2	-	1	131	c.132G>A	c.(130-132)ccG>ccA	p.P44P	CNTROB_ENST00000380262.3_5'Flank|CNTROB_ENST00000563694.1_5'Flank|CNTROB_ENST00000380255.3_5'Flank|RP11-1099M24.7_ENST00000573621.1_Intron	NM_004732.3	NP_004723.2	O43448	KCAB3_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 3	44					potassium ion transport (GO:0006813)|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(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)	8		Prostate(122;0.157)				CTCCACCCCCCGGAGGATTCC	0.761																																					p.P44P		Atlas-SNP	.											.	KCNAB3	30	.	0			c.G132A						PASS	.						3	5	4					17																	7832622		1903	3833	5736	SO:0001819	synonymous_variant	9196	exon1			ACCCCCCGGAGGA	AF016411	CCDS11124.1	17p13.1	2006-11-29			ENSG00000170049	ENSG00000170049		"Potassium channels", "Aldo-keto reductases"	6230	protein-coding gene	gene with protein product		604111				9857044	Standard	NM_004732		Approved	AKR6A9, KCNA3B	uc002gjm.2	O43448	OTTHUMG00000108170	ENST00000303790.2:c.132G>A	17.37:g.7832622C>T		59	0	0		68	28	0.411765	NM_004732	Q4VAW0	Silent	SNP	ENST00000303790.2	37	CCDS11124.1																																																																																			.	.	none		0.761	KCNAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226974.1	NM_004732		T	7832622	C	T	7832622	2	4	42	1	0	0	0	0	0	0	0	1	8020	639	23	1		1	KCNAB3	17	7832622	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	170296	7832622	73362588	315	15267											
WDR16	146845	hgsc.bcm.edu	37	chr17	9515643	9515643	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aaggaagattcagttacaagGcggcatcacttctatcacac	14	9	8	10	1	4	1	3	0	1	1	4	2	4	2	0	3	1	2	0	3	5	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr17:9515643G>A	ENST00000352665.5	+	8	941	c.872G>A	c.(871-873)gGc>gAc	p.G291D	WDR16_ENST00000299764.5_Missense_Mutation_p.G301D|WDR16_ENST00000396219.3_Missense_Mutation_p.G223D	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						CAGTTACAAGGCGGCATCACT	0.428																																					p.G291D		Atlas-SNP	.											.	WDR16	67	.	0			c.G872A						PASS	.						123	108	113					17																	9515643		2203	4300	6503	SO:0001583	missense	146845	exon8			TACAAGGCGGCAT	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.872G>A	17.37:g.9515643G>A	ENSP00000339449:p.Gly291Asp	66	0	0		61	19	0.311475	NM_145054		Missense_Mutation	SNP	ENST00000352665.5	37	CCDS11149.2	.	.	.	.	.	.	.	.	.	.	G	20.2	3.944743	0.73672	.	.	ENSG00000166596	ENST00000352665;ENST00000396219;ENST00000299764	T;T;T	0.18016	2.47;2.84;2.24	5.53	5.53	0.82687	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (2);	0.097447	0.64402	D	0.000001	T	0.31451	0.0797	M	0.83603	2.65	0.80722	D	1	P;P;D	0.53885	0.79;0.87;0.963	B;P;P	0.45558	0.377;0.453;0.485	T	0.16041	-1.0416	10	0.37606	T	0.19	-21.2963	18.2327	0.89939	0.0:0.0:1.0:0.0	.	301;223;291	Q8N1V2-2;Q8N1V2-3;Q8N1V2	.;.;WDR16_HUMAN	D	291;223;301	ENSP00000339449:G291D;ENSP00000379521:G223D;ENSP00000299764:G301D	ENSP00000299764:G301D	G	+	2	0	WDR16	9456368	1.000000	0.71417	0.993000	0.49108	0.591000	0.36615	7.220000	0.78008	2.585000	0.87301	0.557000	0.71058	GGC	.	.	none		0.428	WDR16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316569.2	NM_145054		A	9515643	G	A	9515643	3	1	42	1	0	0	0	0	1	0	0	0	17291	1203	42	2	902	2	WDR16	17	9515643	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	1683021	9515643	71679567	316	15268											
DNAH9	1770	hgsc.bcm.edu	37	chr17	11608409	11608409	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgggatgacgaggtcaaacActgctttgccaacatctgtg	10	11	11	9	1	2	1	1	1	1	0	2	3	2	2	1	2	4	1	1	2	2	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr17:11608409A>C	ENST00000262442.4	+	26	5527	c.5459A>C	c.(5458-5460)cAc>cCc	p.H1820P	DNAH9_ENST00000454412.2_Missense_Mutation_p.H1820P	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	1820	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)		GAGGTCAAACACTGCTTTGCC	0.502																																					p.H1820P		Atlas-SNP	.											.	DNAH9	695	.	0			c.A5459C						PASS	.						222	171	188					17																	11608409		2203	4300	6503	SO:0001583	missense	1770	exon26			TCAAACACTGCTT	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.5459A>C	17.37:g.11608409A>C	ENSP00000262442:p.His1820Pro	246	0	0		172	45	0.261628	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.413784	0.83449	.	.	ENSG00000007174	ENST00000262442;ENST00000454412;ENST00000413703	T;T	0.26373	1.78;1.74	5.73	5.73	0.89815	.	0.817102	0.11759	N	0.532278	T	0.58264	0.2110	M	0.89840	3.065	0.80722	D	1	D	0.59357	0.985	P	0.61070	0.883	T	0.61584	-0.7033	10	0.59425	D	0.04	.	16.0174	0.80450	1.0:0.0:0.0:0.0	.	1820	Q9NYC9	DYH9_HUMAN	P	1820;1820;402	ENSP00000262442:H1820P;ENSP00000414874:H1820P	ENSP00000262442:H1820P	H	+	2	0	DNAH9	11549134	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	9.287000	0.95975	2.186000	0.69663	0.533000	0.62120	CAC	.	.	none		0.502	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372		C	11608409	A	C	11608409	3	2	42	1	0	0	0	0	1	0	0	0	4610	159	6	5	5561	5	DNAH9	17	11608409	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	2092766	11608409	69586801	317	15269											
SHMT1	6470	hgsc.bcm.edu	37	chr17	18259246	18259246	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gtgccagcatcttgtcatgtGaggaccacaggtcagcatcc	9	9	11	12	0	3	1	2	1	1	0	4	2	4	2	3	2	3	2	3	2	0	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr17:18259246G>A	ENST00000316694.3	-	2	184	c.50C>T	c.(49-51)tCa>tTa	p.S17L	SHMT1_ENST00000352886.6_Missense_Mutation_p.S17L|SHMT1_ENST00000539052.1_5'UTR|SHMT1_ENST00000354098.3_Missense_Mutation_p.S17L	NM_004169.3	NP_004160.3	P34896	GLYC_HUMAN	serine hydroxymethyltransferase 1 (soluble)	17					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)	CTTGTCATGTGAGGACCACAG	0.463																																					p.S17L		Atlas-SNP	.											.	SHMT1	36	.	0			c.C50T						PASS	.						104	88	94					17																	18259246		2203	4300	6503	SO:0001583	missense	6470	exon2			TCATGTGAGGACC		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.50C>T	17.37:g.18259246G>A	ENSP00000318868:p.Ser17Leu	91	0	0		70	10	0.142857	NM_148918	B4DPM9|D3DXD0|Q96HY0|Q9UMD1|Q9UMD2	Missense_Mutation	SNP	ENST00000316694.3	37	CCDS11196.1	.	.	.	.	.	.	.	.	.	.	G	15.12	2.738814	0.49045	.	.	ENSG00000176974	ENST00000316694;ENST00000352886;ENST00000354098;ENST00000395685;ENST00000395682	T;T;T	0.28454	1.61;1.61;1.61	5.13	4.15	0.48705	Pyridoxal phosphate-dependent transferase, major domain (1);	0.055757	0.64402	N	0.000001	T	0.31638	0.0803	L	0.57536	1.79	0.80722	D	1	B;B;B;B	0.10296	0.003;0.001;0.002;0.001	B;B;B;B	0.15052	0.002;0.002;0.012;0.001	T	0.12604	-1.0541	10	0.54805	T	0.06	-34.6932	13.0663	0.59036	0.0785:0.0:0.9215:0.0	.	17;17;17;17	B4DZB5;A8MYA6;P34896-2;P34896	.;.;.;GLYC_HUMAN	L	17	ENSP00000318868:S17L;ENSP00000345881:S17L;ENSP00000318805:S17L	ENSP00000318868:S17L	S	-	2	0	SHMT1	18199971	1.000000	0.71417	0.735000	0.30896	0.974000	0.67602	3.637000	0.54324	1.288000	0.44600	0.650000	0.86243	TCA	.	.	none		0.463	SHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130831.2	NM_004169		A	18259246	G	A	18259246	3	1	42	1	0	0	0	0	1	0	0	0	14300	1294	45	2	1445	2	SHMT1	17	18259246	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	6650837	18259246	62935964	318	15270											
SPAG5	10615	hgsc.bcm.edu	37	chr17	26919738	26919738	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acctgtctcccatgcagggtGccacctcctctctcaccaga	7	9	7	18	0	3	1	1	0	2	1	6	1	4	1	6	1	2	1	6	1	0	0	rs149403082		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr17:26919738G>A	ENST00000321765.5	-	3	856	c.524C>T	c.(523-525)gCa>gTa	p.A175V		NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	175					chromosome segregation (GO:0007059)|mitotic sister chromatid segregation (GO:0000070)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|microtubule plus-end (GO:0035371)|mitotic spindle (GO:0072686)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43	Lung NSC(42;0.00431)					CATGCAGGGTGCCACCTCCTC	0.463													G|||	1	0.000199681	0.0008	0.0	5008	,	,		21845	0.0		0.0	False		,,,				2504	0.0				p.A175V		Atlas-SNP	.											.	SPAG5	92	.	0			c.C524T						PASS	.	G	VAL/ALA	4,4402	8.1+/-20.4	0,4,2199	128	127	128		524	1.6	0	17	dbSNP_134	128	0,8600		0,0,4300	no	missense	SPAG5	NM_006461.3	64	0,4,6499	AA,AG,GG		0.0,0.0908,0.0308	possibly-damaging	175/1194	26919738	4,13002	2203	4300	6503	SO:0001583	missense	10615	exon3			CAGGGTGCCACCT	AF063308	CCDS32594.1	17q11.2	2008-07-18			ENSG00000076382	ENSG00000076382			13452	protein-coding gene	gene with protein product	"mitotic spindle coiled-coil related protein", "astrin", "mitotic spindle associated protein p126"	615562				11549262	Standard	NM_006461		Approved	DEEPEST, MAP126, hMAP126	uc002hbq.3	Q96R06	OTTHUMG00000166586	ENST00000321765.5:c.524C>T	17.37:g.26919738G>A	ENSP00000323300:p.Ala175Val	161	0	0		103	37	0.359223	NM_006461	O95213|Q9BWE8|Q9NT17|Q9UFE6	Missense_Mutation	SNP	ENST00000321765.5	37	CCDS32594.1	.	.	.	.	.	.	.	.	.	.	G	3.453	-0.111589	0.06881	9.08E-4	0.0	ENSG00000076382	ENST00000321765	T	0.25414	1.8	5.89	1.63	0.23807	.	0.635159	0.14929	N	0.290200	T	0.23054	0.0557	M	0.62723	1.935	0.09310	N	1	B	0.23377	0.084	B	0.18561	0.022	T	0.25117	-1.0141	10	0.72032	D	0.01	-0.0103	5.0763	0.14632	0.2345:0.0:0.6218:0.1437	.	175	Q96R06	SPAG5_HUMAN	V	175	ENSP00000323300:A175V	ENSP00000323300:A175V	A	-	2	0	SPAG5	23943865	0.000000	0.05858	0.001000	0.08648	0.048000	0.14542	0.541000	0.23207	0.383000	0.24910	0.655000	0.94253	GCA	G|1.000;A|0.000	0.000	strong		0.463	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461		A	26919738	G	A	26919738	3	1	42	1	0	0	0	0	1	0	0	0	14996	1319	46	2	3145	2	SPAG5	17	26919738	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	8660492	26919738	54275472	319	15271											
FBXL20	84961	hgsc.bcm.edu	37	chr17	37557627	37557627	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctcacacctcaaacctgctcTtggtcactccgttcacgtcc	7	11	5	18	2	5	0	4	0	1	0	7	0	7	0	4	1	2	2	4	1	1	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr17:37557627T>G	ENST00000264658.6	-	1	289	c.29A>C	c.(28-30)aAg>aCg	p.K10T	CTB-131K11.1_ENST00000582842.1_RNA|FBXL20_ENST00000394294.3_Missense_Mutation_p.K10T|FBXL20_ENST00000583610.1_Missense_Mutation_p.K10T|FBXL20_ENST00000577399.1_Intron	NM_032875.2	NP_116264.2	Q96IG2	FXL20_HUMAN	F-box and leucine-rich repeat protein 20	10					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)			AAACCTGCTCTTGGTCACTCC	0.726																																					p.K10T		Atlas-SNP	.											.	FBXL20	36	.	0			c.A29C						PASS	.						48	32	38					17																	37557627		2201	4297	6498	SO:0001583	missense	84961	exon1			CTGCTCTTGGTCA	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.29A>C	17.37:g.37557627T>G	ENSP00000264658:p.Lys10Thr	180	0	0		107	33	0.308411	NM_001184906	A8K729|Q38J52	Missense_Mutation	SNP	ENST00000264658.6	37	CCDS32640.1	.	.	.	.	.	.	.	.	.	.	T	14.84	2.655110	0.47467	.	.	ENSG00000108306	ENST00000264658;ENST00000394294	T;T	0.12147	2.72;2.71	3.8	3.8	0.43715	.	0.421938	0.23213	U	0.050657	T	0.09113	0.0225	L	0.34521	1.04	0.80722	D	1	B;B	0.13145	0.007;0.003	B;B	0.14023	0.01;0.004	T	0.15723	-1.0427	10	0.15066	T	0.55	.	7.424	0.27088	0.0:0.1063:0.0:0.8937	.	10;10	Q96IG2-2;Q96IG2	.;FXL20_HUMAN	T	10	ENSP00000264658:K10T;ENSP00000377832:K10T	ENSP00000264658:K10T	K	-	2	0	FBXL20	34811153	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.098000	0.41757	1.703000	0.51240	0.397000	0.26171	AAG	.	.	none		0.726	FBXL20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444315.2	NM_032875		G	37557627	T	G	37557627	3	3	42	1	0	0	0	0	1	0	0	0	5725	1609	56	5	1341	5	FBXL20	17	37557627	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	10637889	37557627	43637583	320	15272											
CDK12	51755	hgsc.bcm.edu	37	chr17	37627743	37627743	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcagacaccccctttgccacCtttgcctccaataccagctc	8	10	4	19	0	1	1	1	0	0	1	3	1	2	1	7	0	4	1	7	0	2	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr17:37627743C>T	ENST00000447079.4	+	2	1691	c.1658C>T	c.(1657-1659)cCt>cTt	p.P553L	CDK12_ENST00000430627.2_Missense_Mutation_p.P553L	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	553					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						CCTTTGCCACCTTTGCCTCCA	0.547			"Mis, N, F"		serous ovarian					TCGA Ovarian(9;0.13)																											p.P553L		Atlas-SNP	.		Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	.	CDK12	161	.	0			c.C1658T						PASS	.						211	198	203					17																	37627743		2203	4300	6503	SO:0001583	missense	51755	exon2			TGCCACCTTTGCC	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.1658C>T	17.37:g.37627743C>T	ENSP00000398880:p.Pro553Leu	212	0	0		166	60	0.361446	NM_016507	A7E2B2|B4DYX4|B9EIQ6|O94978	Missense_Mutation	SNP	ENST00000447079.4	37	CCDS11337.1	.	.	.	.	.	.	.	.	.	.	C	16.05	3.013687	0.54468	.	.	ENSG00000167258	ENST00000430627;ENST00000447079	T;T	0.72615	-0.64;-0.67	5.89	5.89	0.94794	.	0.000000	0.48767	D	0.000165	T	0.72779	0.3503	N	0.24115	0.695	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.997;0.999	T	0.63906	-0.6531	10	0.02654	T	1	-10.7187	19.2499	0.93919	0.0:1.0:0.0:0.0	.	552;553;553	E7EUM9;Q9NYV4;Q9NYV4-2	.;CDK12_HUMAN;.	L	553	ENSP00000407720:P553L;ENSP00000398880:P553L	ENSP00000407720:P553L	P	+	2	0	CDK12	34881269	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.871000	0.69628	2.793000	0.96121	0.655000	0.94253	CCT	.	.	none		0.547	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507		T	37627743	C	T	37627743	3	4	42	1	0	0	0	0	1	0	0	0	3130	681	24	2	1664	2	CDK12	17	37627743	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	70116	37627743	43567467	321	15273											
KRT23	25984	hgsc.bcm.edu	37	chr17	39092714	39092714	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtgggcagctccgcgtggTgaaggacagggagatgcggg	7	5	22	7	3	0	2	0	1	0	1	1	4	1	3	1	6	2	2	1	6	1	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr17:39092714T>C	ENST00000209718.3	-	2	566	c.142A>G	c.(142-144)Acc>Gcc	p.T48A	KRT23_ENST00000582283.1_5'Flank|KRT23_ENST00000436344.3_Intron|AC004231.2_ENST00000418393.1_RNA	NM_015515.3	NP_056330.3	Q9C075	K1C23_HUMAN	keratin 23 (histone deacetylase inducible)	48	Head.					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)				CTCCGCGTGGTGAAGGACAGG	0.677																																					p.T48A		Atlas-SNP	.											.	KRT23	59	.	0			c.A142G						PASS	.						42	48	46					17																	39092714		2203	4300	6503	SO:0001583	missense	25984	exon2			GCGTGGTGAAGGA	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.142A>G	17.37:g.39092714T>C	ENSP00000209718:p.Thr48Ala	94	0	0		69	9	0.130435	NM_015515	A8K084|B7Z7J2|I3L3Q6|Q9NUR6	Missense_Mutation	SNP	ENST00000209718.3	37	CCDS11380.1	.	.	.	.	.	.	.	.	.	.	T	4.039	0.004794	0.07866	.	.	ENSG00000108244	ENST00000209718	D	0.81579	-1.51	5.73	0.828	0.18841	.	0.380192	0.22341	N	0.061323	T	0.53916	0.1826	N	0.08118	0	0.37959	D	0.932911	B	0.06786	0.001	B	0.04013	0.001	T	0.22626	-1.0211	10	0.14252	T	0.57	.	3.9587	0.09401	0.3632:0.2514:0.0:0.3854	.	48	Q9C075	K1C23_HUMAN	A	48	ENSP00000209718:T48A	ENSP00000209718:T48A	T	-	1	0	KRT23	36346240	0.023000	0.18921	0.806000	0.32338	0.292000	0.27327	-0.784000	0.04633	-0.152000	0.11156	0.455000	0.32223	ACC	.	.	none		0.677	KRT23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257223.1			C	39092714	T	C	39092714	3	2	42	1	0	0	0	0	1	0	0	0	8469	1696	59	3	1158	3	KRT23	17	39092714	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	1464971	39092714	42102496	322	15274											
ATP6V0A1	535	hgsc.bcm.edu	37	chr17	40666448	40666448	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cctgatcatggagggcctctCggcctttctccacgcactgc	5	10	10	16	2	3	1	1	1	2	0	5	2	3	2	4	3	1	1	4	3	0	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr17:40666448C>T	ENST00000343619.4	+	21	2513	c.2390C>T	c.(2389-2391)tCg>tTg	p.S797L	RP11-400F19.18_ENST00000591237.1_RNA|ATP6V0A1_ENST00000585525.1_Missense_Mutation_p.S754L|MIR5010_ENST00000582846.1_RNA|ATP6V0A1_ENST00000264649.6_Missense_Mutation_p.S798L|ATP6V0A1_ENST00000544137.1_Missense_Mutation_p.S443L|ATP6V0A1_ENST00000537728.1_Missense_Mutation_p.S748L|ATP6V0A1_ENST00000546249.1_Missense_Mutation_p.S797L|ATP6V0A1_ENST00000393829.2_Missense_Mutation_p.S791L	NM_001130021.1	NP_001123493.1	Q93050	VPP1_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a1	797					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)		GAGGGCCTCTCGGCCTTTCTC	0.612																																					p.S798L		Atlas-SNP	.											.	ATP6V0A1	67	.	0			c.C2393T						PASS	.						143	121	128					17																	40666448		2203	4300	6503	SO:0001583	missense	535	exon20			GCCTCTCGGCCTT	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.2390C>T	17.37:g.40666448C>T	ENSP00000342951:p.Ser797Leu	170	0	0		80	11	0.1375	NM_001130020	B7Z3B7|Q8N5G7|Q9NSX0	Missense_Mutation	SNP	ENST00000343619.4	37	CCDS45684.1	.	.	.	.	.	.	.	.	.	.	C	34	5.303011	0.95601	.	.	ENSG00000033627	ENST00000343619;ENST00000546249;ENST00000393829;ENST00000264649;ENST00000537728;ENST00000544137	D;D;D;D;D;D	0.90732	-2.72;-2.72;-2.72;-2.72;-2.72;-2.72	4.57	4.57	0.56435	.	0.000000	0.85682	D	0.000000	D	0.97275	0.9109	H	0.97829	4.085	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;0.999;0.998;0.999;1.0	D	0.99013	1.0815	10	0.87932	D	0	-9.722	17.5259	0.87800	0.0:1.0:0.0:0.0	.	748;754;798;797;791	B7Z641;B7Z2A9;B7Z3B7;Q93050;Q93050-1	.;.;.;VPP1_HUMAN;.	L	797;797;791;798;748;443	ENSP00000342951:S797L;ENSP00000444676:S797L;ENSP00000377415:S791L;ENSP00000264649:S798L;ENSP00000443991:S748L;ENSP00000446377:S443L	ENSP00000264649:S798L	S	+	2	0	ATP6V0A1	37919974	1.000000	0.71417	0.953000	0.39169	0.939000	0.58152	7.643000	0.83403	2.390000	0.81377	0.561000	0.74099	TCG	.	.	none		0.612	ATP6V0A1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450364.1	NM_001130020		T	40666448	C	T	40666448	3	4	42	1	0	0	0	0	1	0	0	0	1168	893	31	1	2489	1	ATP6V0A1	17	40666448	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	1573734	40666448	40528762	323	15275											
BRCA1	672	hgsc.bcm.edu	37	chr17	41245531	41245531	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cttggctccagttgcaggttCtttaccttccatgagttgta	6	16	9	10	0	1	1	0	1	1	0	3	1	3	1	3	2	2	6	3	2	2	8	rs80357638|rs80357391		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr17:41245531C>T	ENST00000357654.3	-	10	2135	c.2017G>A	c.(2017-2019)Gaa>Aaa	p.E673K	BRCA1_ENST00000309486.4_Missense_Mutation_p.E377K|BRCA1_ENST00000493795.1_Missense_Mutation_p.E626K|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000346315.3_Missense_Mutation_p.E673K|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000354071.3_Missense_Mutation_p.E673K|BRCA1_ENST00000471181.2_Missense_Mutation_p.E673K|BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000591534.1_Intron	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	673					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)		GTTGCAGGTTCTTTACCTTCC	0.408			"D, Mis, N, F, S"		ovarian	"breast, ovarian"		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.E673K		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	BRCA1,NS,carcinoma,0,1	BRCA1	304	1	0			c.G2017A						PASS	.						111	98	103					17																	41245531		2202	4300	6502	SO:0001583	missense	672	exon10	Familial Cancer Database		CAGGTTCTTTACC	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.2017G>A	17.37:g.41245531C>T	ENSP00000350283:p.Glu673Lys	323	0	0		223	40	0.179372	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	37	CCDS11453.1	.	.	.	.	.	.	.	.	.	.	C	15.75	2.925121	0.52759	.	.	ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000354071;ENST00000346315;ENST00000309486;ENST00000471181;ENST00000493795	D;D;D;D;D;D	0.83419	-1.72;-1.72;-1.72;-1.72;-1.72;-1.72	4.95	4.95	0.65309	.	0.000000	0.56097	D	0.000028	D	0.93054	0.7789	M	0.92555	3.32	0.36954	D	0.893016	D;D;D;P;P;P	0.89917	1.0;1.0;0.987;0.877;0.707;0.851	D;D;D;P;P;P	0.97110	1.0;1.0;0.963;0.627;0.838;0.55	D	0.95953	0.8956	10	0.87932	D	0	.	16.5462	0.84446	0.0:1.0:0.0:0.0	.	673;632;673;673;673;673	E7EMP0;E7ERL4;Q5YLB2;E9PFC7;P38398;P38398-2	.;.;.;.;BRCA1_HUMAN;.	K	673;673;673;673;377;673;626	ENSP00000350283:E673K;ENSP00000326002:E673K;ENSP00000246907:E673K;ENSP00000310938:E377K;ENSP00000418960:E673K;ENSP00000418775:E626K	ENSP00000310938:E377K	E	-	1	0	BRCA1	38499057	0.991000	0.36638	0.596000	0.28811	0.097000	0.18754	3.270000	0.51600	2.581000	0.87130	0.561000	0.74099	GAA	.	.	alt		0.408	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		T	41245531	C	T	41245531	3	4	42	1	0	0	0	0	1	0	0	0	1500	922	32	2	3700	2	BRCA1	17	41245531	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	579083	41245531	39949679	324	15276											
NPEPPS	9520	hgsc.bcm.edu	37	chr17	45699275	45699275	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ttcagcggaaggcctcaccaCccacagtgtgaatcctgagg	10	7	11	13	1	2	2	2	2	0	0	3	3	3	3	4	3	1	0	4	3	2	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr17:45699275C>G	ENST00000322157.4	+	23	2986	c.2749C>G	c.(2749-2751)Ccc>Gcc	p.P917A	RP11-580I16.2_ENST00000582066.1_RNA|RP11-580I16.2_ENST00000584391.1_RNA|RP11-580I16.2_ENST00000582389.1_RNA|NPEPPS_ENST00000530173.1_Missense_Mutation_p.P913A|NPEPPS_ENST00000544660.1_Missense_Mutation_p.P837A	NM_006310.3	NP_006301.3	P55786	PSA_HUMAN	aminopeptidase puromycin sensitive	917					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						GGCCTCACCACCCACAGTGTG	0.527																																					p.P917A		Atlas-SNP	.											.	NPEPPS	59	.	0			c.C2749G						PASS	.						35	35	35					17																	45699275		1964	4166	6130	SO:0001583	missense	9520	exon23			TCACCACCCACAG	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.2749C>G	17.37:g.45699275C>G	ENSP00000320324:p.Pro917Ala	59	0	0		62	14	0.225806	NM_006310	B7Z463|Q6P145|Q9NP16|Q9UEM2	Missense_Mutation	SNP	ENST00000322157.4	37	CCDS45721.1	.	.	.	.	.	.	.	.	.	.	C	5.074	0.199356	0.09652	.	.	ENSG00000141279	ENST00000530173;ENST00000322157;ENST00000544660;ENST00000528565	T;T;T;T	0.45668	5.14;5.15;5.03;0.89	5.8	3.78	0.43462	.	0.259526	0.39020	N	0.001489	T	0.24774	0.0601	N	0.22421	0.69	0.21527	N	0.999656	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.13388	-1.0511	10	0.34782	T	0.22	.	5.2014	0.15267	0.1937:0.3949:0.3422:0.0692	.	913;917	E9PLK3;P55786	.;PSA_HUMAN	A	913;917;837;167	ENSP00000433287:P913A;ENSP00000320324:P917A;ENSP00000442461:P837A;ENSP00000433549:P167A	ENSP00000320324:P917A	P	+	1	0	NPEPPS	43054274	0.798000	0.28890	0.059000	0.19551	0.487000	0.33371	1.145000	0.31577	0.761000	0.33130	0.561000	0.74099	CCC	.	.	none		0.527	NPEPPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384269.1	NM_006310		G	45699275	C	G	45699275	3	3	42	1	0	0	0	0	1	0	0	0	10584	507	18	4	2839	4	NPEPPS	17	45699275	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	4453744	45699275	35495935	325	15277											
KIF2B	84643	hgsc.bcm.edu	37	chr17	51900705	51900705	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cttggctctggcgccctcttCggccatcagggaccagcgta	5	9	12	15	3	3	0	1	0	2	0	4	1	3	1	3	4	1	2	3	4	1	3	rs371085430		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr17:51900705C>T	ENST00000268919.4	+	1	467	c.311C>T	c.(310-312)tCg>tTg	p.S104L		NM_032559.4	NP_115948.4	Q8N4N8	KIF2B_HUMAN	kinesin family member 2B	104					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						GCGCCCTCTTCGGCCATCAGG	0.612													C|||	1	0.000199681	0.0	0.0	5008	,	,		15275	0.001		0.0	False		,,,				2504	0.0				p.S104L		Atlas-SNP	.											KIF2B,NS,carcinoma,-1,2	KIF2B	254	2	0			c.C311T						scavenged	.	C	LEU/SER	0,4406		0,0,2203	89	98	95		311	2.9	0	17		95	1,8599	1.2+/-3.3	0,1,4299	no	missense	KIF2B	NM_032559.4	145	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	104/674	51900705	1,13005	2203	4300	6503	SO:0001583	missense	84643	exon1			CCTCTTCGGCCAT	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.311C>T	17.37:g.51900705C>T	ENSP00000268919:p.Ser104Leu	62	1	0.016129		47	12	0.255319	NM_032559	Q96MA2|Q9BXG6	Missense_Mutation	SNP	ENST00000268919.4	37	CCDS32685.1	.	.	.	.	.	.	.	.	.	.	C	2.386	-0.340855	0.05243	0.0	1.16E-4	ENSG00000141200	ENST00000268919;ENST00000416491	T	0.74106	-0.81	4.96	2.93	0.34026	.	1.236910	0.06126	U	0.669728	T	0.64605	0.2613	L	0.49778	1.585	0.09310	N	1	P	0.37731	0.607	B	0.29785	0.107	T	0.49844	-0.8896	10	0.23891	T	0.37	.	7.475	0.27371	0.1646:0.7497:0.0:0.0857	.	104	Q8N4N8	KIF2B_HUMAN	L	104;27	ENSP00000268919:S104L	ENSP00000268919:S104L	S	+	2	0	KIF2B	49255704	0.004000	0.15560	0.001000	0.08648	0.003000	0.03518	1.901000	0.39838	0.763000	0.33175	0.655000	0.94253	TCG	.	.	weak		0.612	KIF2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438854.1	NM_032559		T	51900705	C	T	51900705	3	4	42	1	0	0	0	0	1	0	0	0	8307	893	31	1	313	1	KIF2B	17	51900705	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	6201430	51900705	29294505	326	15278											
GH1	2688	hgsc.bcm.edu	37	chr17	61995272	61995272	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagcagcagggagatgcggaGcagctctaggttctgcaggg	9	6	18	8	1	2	1	0	0	2	1	2	4	2	2	0	4	6	6	0	4	1	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr17:61995272G>A	ENST00000323322.5	-	4	346	c.304C>T	c.(304-306)Ctc>Ttc	p.L102F	GH1_ENST00000351388.4_Missense_Mutation_p.L62F|GH1_ENST00000342364.4_Intron|CSHL1_ENST00000392824.4_Intron|GH1_ENST00000458650.2_Missense_Mutation_p.L87F	NM_000515.3	NP_000506.2	P01241	SOMA_HUMAN	growth hormone 1	102					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						GAGATGCGGAGCAGCTCTAGG	0.642																																					p.L102F		Atlas-SNP	.											.	GH1	39	.	0			c.C304T						PASS	.						71	73	72					17																	61995272		2203	4300	6503	SO:0001583	missense	2688	exon4			TGCGGAGCAGCTC	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.304C>T	17.37:g.61995272G>A	ENSP00000312673:p.Leu102Phe	76	0	0		75	20	0.266667	NM_000515	A6NEF6|Q14405|Q16631|Q5EB53|Q9HBZ1|Q9UMJ7|Q9UNL5	Missense_Mutation	SNP	ENST00000323322.5	37	CCDS11653.1	.	.	.	.	.	.	.	.	.	.	g	13.50	2.255074	0.39896	.	.	ENSG00000204414	ENST00000323322;ENST00000458650;ENST00000351388	D;D;D	0.92752	-3.1;-3.1;-3.1	2.86	2.86	0.33363	Somatotropin hormone, conserved site (1);Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.000000	0.64402	D	0.000001	D	0.96466	0.8847	H	0.95850	3.73	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.997;1.0;1.0;1.0	D	0.95291	0.8395	10	0.87932	D	0	.	5.8888	0.18896	0.151:0.0:0.849:0.0	.	102;62;102;87	C9JYZ1;A6NEF6;P01241;B1A4G7	.;.;SOMA_HUMAN;.	F	102;87;62	ENSP00000312673:L102F;ENSP00000408486:L87F;ENSP00000343791:L62F	ENSP00000312673:L102F	L	-	1	0	GH1	59349004	1.000000	0.71417	0.991000	0.47740	0.430000	0.31655	4.851000	0.62896	1.594000	0.50039	0.298000	0.19748	CTC	.	.	none		0.642	GH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417708.1	NM_000515		A	61995272	G	A	61995272	3	1	42	1	0	0	0	0	1	0	0	0	6375	971	34	2	357	2	GH1	17	61995272	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	10094567	61995272	19199938	327	15279											
FAM104A	84923	hgsc.bcm.edu	37	chr17	71228291	71228291	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcggcgccgctccgcgaagaGagggaacagagggggttgtg	8	4	20	9	5	0	2	0	0	0	2	1	5	1	3	2	4	1	2	2	4	2	1	rs569512877		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr17:71228291G>A	ENST00000403627.3	-	1	215	c.155C>T	c.(154-156)tCt>tTt	p.S52F	C17orf80_ENST00000359042.2_5'Flank|C17orf80_ENST00000268942.8_5'Flank|C17orf80_ENST00000577615.1_5'Flank|FAM104A_ENST00000581110.1_Missense_Mutation_p.S52F|FAM104A_ENST00000583024.1_Missense_Mutation_p.S52F|FAM104A_ENST00000583178.1_Intron|FAM104A_ENST00000405159.3_Missense_Mutation_p.S52F|C17orf80_ENST00000255557.4_5'Flank|C17orf80_ENST00000535032.2_5'Flank|C17orf80_ENST00000582793.1_5'Flank|C17orf80_ENST00000426147.2_5'Flank	NM_032837.2	NP_116226.2	Q969W3	F104A_HUMAN	family with sequence similarity 104, member A	52										endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6			LUSC - Lung squamous cell carcinoma(166;0.197)			TCCGCGAAGAGAGGGAACAGA	0.706																																					p.S52F		Atlas-SNP	.											.	FAM104A	15	.	0			c.C155T						PASS	.						18	22	20					17																	71228291		2200	4297	6497	SO:0001583	missense	84923	exon1			CGAAGAGAGGGAA	AK027681	CCDS11693.2, CCDS45766.1, CCDS74143.1, CCDS74144.1	17q25.1	2005-12-16			ENSG00000133193	ENSG00000133193			25918	protein-coding gene	gene with protein product							Standard	NM_032837		Approved	FLJ14775	uc002jjj.4	Q969W3	OTTHUMG00000150564	ENST00000403627.3:c.155C>T	17.37:g.71228291G>A	ENSP00000384648:p.Ser52Phe	98	0	0		93	29	0.311828	NM_032837	B4E339	Missense_Mutation	SNP	ENST00000403627.3	37	CCDS11693.2	.	.	.	.	.	.	.	.	.	.	G	12.53	1.965297	0.34659	.	.	ENSG00000133193	ENST00000403627;ENST00000405159	T;T	0.50813	0.76;0.73	4.75	1.61	0.23674	.	.	.	.	.	T	0.24928	0.0605	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.10450	0.005;0.005	T	0.19484	-1.0304	9	0.62326	D	0.03	.	4.6392	0.12540	0.2012:0.1899:0.609:0.0	.	52;52	Q969W3-2;Q969W3	.;F104A_HUMAN	F	52	ENSP00000384648:S52F;ENSP00000384832:S52F	ENSP00000384648:S52F	S	-	2	0	FAM104A	68739886	0.671000	0.27521	0.000000	0.03702	0.019000	0.09904	2.392000	0.44433	0.209000	0.20645	0.655000	0.94253	TCT	.	.	none		0.706	FAM104A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318935.1	NM_032837		A	71228291	G	A	71228291	3	1	42	1	0	0	0	0	1	0	0	0	5390	942	33	2	484	2	FAM104A	17	71228291	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	9233019	71228291	9966919	328	15280											
C1QTNF1	114897	hgsc.bcm.edu	37	chr17	77043849	77043849	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acggagttcgtgaacctctaCgaccacttcaacatgttcac	11	10	7	13	3	3	1	2	1	1	0	4	3	3	2	2	1	3	2	2	1	3	4	rs566729160		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr17:77043849C>T	ENST00000339142.2	+	5	1080	c.525C>T	c.(523-525)taC>taT	p.Y175Y	C1QTNF1_ENST00000580474.1_Silent_p.Y175Y|C1QTNF1_ENST00000392445.2_Silent_p.Y175Y|C1QTNF1_ENST00000582625.1_3'UTR|C1QTNF1_ENST00000311661.4_Silent_p.Y93Y|C1QTNF1_ENST00000578229.1_Silent_p.Y93Y|C1QTNF1_ENST00000354124.3_Silent_p.Y185Y|C1QTNF1_ENST00000583904.1_Silent_p.Y175Y|C1QTNF1_ENST00000580454.1_Silent_p.Y175Y|C1QTNF1_ENST00000581774.1_Silent_p.Y175Y|C1QTNF1_ENST00000579760.1_Silent_p.Y175Y	NM_198593.3	NP_940995.1	Q9BXJ1	C1QT1_HUMAN	C1q and tumor necrosis factor related protein 1	175	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				negative regulation of platelet activation (GO:0010544)|negative regulation of platelet aggregation (GO:0090331)|positive regulation of aldosterone secretion (GO:2000860)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of gene expression (GO:0010628)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase B signaling (GO:0051897)|protein heterotrimerization (GO:0070208)|protein homooligomerization (GO:0051260)|regulation of glucose metabolic process (GO:0010906)	collagen trimer (GO:0005581)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	collagen binding (GO:0005518)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(5)|ovary(2)	14			BRCA - Breast invasive adenocarcinoma(99;0.0294)|OV - Ovarian serous cystadenocarcinoma(97;0.201)			TGAACCTCTACGACCACTTCA	0.562													C|||	1	0.000199681	0.0	0.0	5008	,	,		19992	0.0		0.001	False		,,,				2504	0.0				p.Y175Y		Atlas-SNP	.											.	C1QTNF1	62	.	0			c.C525T						PASS	.						161	146	151					17																	77043849		2203	4300	6503	SO:0001819	synonymous_variant	114897	exon4			CCTCTACGACCAC	AF329840	CCDS11761.1, CCDS11762.1	17q25	2012-07-02			ENSG00000173918	ENSG00000173918			14324	protein-coding gene	gene with protein product	"G protein coupled receptor interacting protein"	610365				12409230	Standard	NM_198593		Approved	CTRP1, ZSIG37, GIP, FLJ90694	uc002jwp.4	Q9BXJ1	OTTHUMG00000177533	ENST00000339142.2:c.525C>T	17.37:g.77043849C>T		80	0	0		60	24	0.4	NM_030968	Q6ZMH6|Q96NF2|Q9GZR4	Silent	SNP	ENST00000339142.2	37	CCDS11761.1																																																																																			.	.	none		0.562	C1QTNF1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437388.2	NM_030968		T	77043849	C	T	77043849	2	4	42	1	0	0	0	0	0	0	0	1	1964	547	19	1		1	C1QTNF1	17	77043849	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	5815558	77043849	4151361	329	15281											
ACTG1	71	hgsc.bcm.edu	37	chr17	79479257	79479257	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cccgcggcgccatccactcaCctggtgtctggggcgcccga	4	6	13	18	5	2	0	1	0	1	0	3	1	3	0	5	4	0	0	5	4	0	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr17:79479257C>T	ENST00000575842.1	-	1	550		c.e1+1		ACTG1_ENST00000575087.1_Splice_Site|AC139149.1_ENST00000584254.1_RNA|ACTG1_ENST00000331925.2_Splice_Site|ACTG1_ENST00000573283.1_Splice_Site|RP13-766D20.2_ENST00000430912.1_RNA			P63261	ACTG_HUMAN	actin, gamma 1						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)			CATCCACTCACCTGGTGTCTG	0.672																																					.		Atlas-SNP	.											.	ACTG1	55	.	0			c.123+1G>A						PASS	.						41	50	47					17																	79479257		2202	4300	6502	SO:0001630	splice_region_variant	71	exon3			CACTCACCTGGTG		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.123+1G>A	17.37:g.79479257C>T		100	0	0		97	10	0.103093	NM_001199954	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Splice_Site	SNP	ENST00000575842.1	37	CCDS11782.1	.	.	.	.	.	.	.	.	.	.	C	13.22	2.172931	0.38413	.	.	ENSG00000184009	ENST00000331925;ENST00000447294	.	.	.	3.66	3.66	0.41972	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3213	0.66489	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ACTG1	77093852	1.000000	0.71417	0.965000	0.40720	0.234000	0.25298	5.468000	0.66743	1.871000	0.54225	0.563000	0.77884	.	.	.	none		0.672	ACTG1-012	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439935.2	NM_001614	Intron	T	79479257	C	T	79479257	5	4	42	1	0	0	0	0	0	0	1	0	196	521	18	2	1023	2	ACTG1	17	79479257	Splice_Site	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	2435408	79479257	1715953	330	15282											
HGS	9146	hgsc.bcm.edu	37	chr17	79663744	79663744	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagacggtccagatgcgcgcGcagatgcccgccttccccct	6	6	11	18	5	0	3	0	0	0	3	2	3	2	3	5	1	2	1	5	1	0	1	rs190451033	byFrequency	TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr17:79663744G>A	ENST00000329138.4	+	17	1809	c.1674G>A	c.(1672-1674)gcG>gcA	p.A558A		NM_004712.4	NP_004703.1	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine kinase substrate	558	Gln-rich.|Interaction with NF2.|Interaction with STAM1. {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)			AGATGCGCGCGCAGATGCCCG	0.662													G|||	2	0.000399361	0.0	0.0	5008	,	,		14915	0.0		0.001	False		,,,				2504	0.001				p.A558A		Atlas-SNP	.											.	HGS	54	.	0			c.G1674A						PASS	.	G		0,4406		0,0,2203	44	55	51		1674	-2.9	0.9	17		51	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	HGS	NM_004712.4		0,1,6501	AA,AG,GG		0.0116,0.0,0.0077		558/778	79663744	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	9146	exon17			GCGCGCGCAGATG	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.1674G>A	17.37:g.79663744G>A		39	0	0		40	14	0.35	NM_004712	Q9NR36	Silent	SNP	ENST00000329138.4	37	CCDS11784.1																																																																																			G|1.000;A|0.000	0.000	strong		0.662	HGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440541.1	NM_004712		A	79663744	G	A	79663744	2	1	42	1	0	0	0	0	0	0	0	1	7096	1074	38	1		1	HGS	17	79663744	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	184487	79663744	1531466	331	15283											
DYSFIP1	116729	hgsc.bcm.edu	37	chr17	79791648	79791648	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agagctccaccagctccttgTagtccgggtcgatgaggtcg	7	9	13	12	3	0	2	0	1	0	1	5	3	3	2	4	2	2	3	4	2	1	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr17:79791648T>C	ENST00000330261.4	-	3	501	c.422A>G	c.(421-423)tAc>tGc	p.Y141C	PPP1R27_ENST00000573182.1_5'UTR|FAM195B_ENST00000455127.2_5'Flank|FAM195B_ENST00000538396.1_5'Flank|FAM195B_ENST00000572645.1_5'Flank|PPP1R27_ENST00000570394.1_3'UTR|FAM195B_ENST00000575061.1_5'Flank|FAM195B_ENST00000576431.1_5'Flank|FAM195B_ENST00000573478.1_5'Flank	NM_001007533.3	NP_001007534.1	Q86WC6	PPR27_HUMAN	protein phosphatase 1, regulatory subunit 27	141					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										CAGCTCCTTGTAGTCCGGGTC	0.662																																					p.Y141C		Atlas-SNP	.											.	.	.	.	0			c.A422G						PASS	.						73	50	58					17																	79791648		2174	4259	6433	SO:0001583	missense	116729	exon3			TCCTTGTAGTCCG	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.422A>G	17.37:g.79791648T>C	ENSP00000331065:p.Tyr141Cys	60	0	0		54	17	0.314815	NM_001007533		Missense_Mutation	SNP	ENST00000330261.4	37	CCDS32767.1	.	.	.	.	.	.	.	.	.	.	t	10.85	1.466188	0.26335	.	.	ENSG00000182676	ENST00000330261	T	0.61859	0.07	4.6	2.22	0.28083	.	0.335152	0.31601	N	0.007361	T	0.31606	0.0802	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.04373	-1.0956	10	0.27785	T	0.31	.	7.7153	0.28700	0.4418:0.0:0.0:0.5582	.	141	Q86WC6	PPR27_HUMAN	C	141	ENSP00000331065:Y141C	ENSP00000331065:Y141C	Y	-	2	0	DYSFIP1	77384937	0.885000	0.30320	0.999000	0.59377	0.615000	0.37417	0.378000	0.20569	0.601000	0.29879	-0.425000	0.05940	TAC	.	.	none		0.662	PPP1R27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439692.1	NM_001007533		C	79791648	T	C	79791648	3	2	42	1	0	0	0	0	1	0	0	0	4862	1638	57	3	46	3	DYSFIP1	17	79791648	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	127904	79791648	1403562	332	15284											
FASN	2194	hgsc.bcm.edu	37	chr17	80046669	80046669	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agcctgccgatgccggccagGaagaactccaggttgtccct	8	7	12	14	2	0	1	0	0	0	1	2	3	2	2	6	3	4	1	6	3	2	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr17:80046669G>T	ENST00000306749.2	-	15	2606	c.2388C>A	c.(2386-2388)ttC>ttA	p.F796L		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	796	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)	TGCCGGCCAGGAAGAACTCCA	0.682																																					p.F796L	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.C2388A						PASS	.						41	43	42					17																	80046669		2202	4296	6498	SO:0001583	missense	2194	exon15			GGCCAGGAAGAAC	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.2388C>A	17.37:g.80046669G>T	ENSP00000304592:p.Phe796Leu	76	0	0		51	19	0.372549	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	37	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	G	15.46	2.841118	0.51057	.	.	ENSG00000169710	ENST00000306749	T	0.47869	0.83	4.16	1.42	0.22433	Acyl transferase (1);	0.000000	0.85682	D	0.000000	T	0.45418	0.1341	N	0.21448	0.665	0.80722	D	1	D	0.76494	0.999	D	0.72982	0.979	T	0.27054	-1.0085	10	0.17832	T	0.49	-23.5367	7.5118	0.27577	0.1229:0.1518:0.7253:0.0	.	796	P49327	FAS_HUMAN	L	796	ENSP00000304592:F796L	ENSP00000304592:F796L	F	-	3	2	FASN	77639958	1.000000	0.71417	0.958000	0.39756	0.212000	0.24457	4.590000	0.61013	0.100000	0.17581	0.462000	0.41574	TTC	.	.	none		0.682	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104		T	80046669	G	T	80046669	3	4	42	1	0	0	0	0	1	0	0	0	5691	1165	41	4	5263	4	FASN	17	80046669	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	255021	80046669	1148541	333	15285											
LRRC30	339291	hgsc.bcm.edu	37	chr18	7231257	7231257	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgctctcgggaagggacccgCggtccctgctgaagcggggc	5	6	17	13	4	1	1	0	1	1	0	3	3	2	3	2	5	3	2	2	5	2	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr18:7231257C>T	ENST00000383467.2	+	1	135	c.121C>T	c.(121-123)Cgg>Tgg	p.R41W		NM_001105581.1	NP_001099051.1	A6NM36	LRC30_HUMAN	leucine rich repeat containing 30	41										central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(13)|ovary(1)|prostate(1)|skin(3)	31						AAGGGACCCGCGGTCCCTGCT	0.617																																					p.R41W		Atlas-SNP	.											.	LRRC30	68	.	0			c.C121T						PASS	.						69	74	72					18																	7231257		1973	4153	6126	SO:0001583	missense	339291	exon1			GACCCGCGGTCCC		CCDS42409.1	18p11.23	2005-01-06				ENSG00000206422			30219	protein-coding gene	gene with protein product							Standard	NM_001105581		Approved		uc010wzk.2	A6NM36		ENST00000383467.2:c.121C>T	18.37:g.7231257C>T	ENSP00000372959:p.Arg41Trp	51	0	0		39	10	0.25641	NM_001105581		Missense_Mutation	SNP	ENST00000383467.2	37	CCDS42409.1	.	.	.	.	.	.	.	.	.	.	C	14.92	2.678390	0.47886	.	.	ENSG00000206422	ENST00000383467	T	0.47528	0.84	5.65	0.876	0.19138	.	0.050447	0.64402	D	0.000001	T	0.50735	0.1633	L	0.29908	0.895	0.09310	N	1	D	0.76494	0.999	P	0.61722	0.893	T	0.52087	-0.8622	10	0.66056	D	0.02	.	13.9302	0.63991	0.7158:0.2841:0.0:0.0	.	41	A6NM36	LRC30_HUMAN	W	41	ENSP00000372959:R41W	ENSP00000372959:R41W	R	+	1	2	LRRC30	7221257	0.337000	0.24766	0.022000	0.16811	0.671000	0.39405	0.831000	0.27476	0.343000	0.23821	0.650000	0.86243	CGG	.	.	none		0.617	LRRC30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442140.1	XM_292678		T	7231257	C	T	7231257	3	4	42	1	0	0	0	0	1	0	0	0	8994	759	27	1	123	1	LRRC30	18	7231257	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10		7231257	70845991	334	15286											
PSMG2	56984	hgsc.bcm.edu	37	chr18	12720538	12720538	+	Frame_Shift_Del	DEL	C	C	-																															ccggtacctacttacaccttCcatgcaaaaaagtgttcaaa																										TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr18:12720538delC	ENST00000317615.6	+	5	1119	c.437delC	c.(436-438)tccfs	p.S146fs	PSMG2_ENST00000590217.1_Frame_Shift_Del_p.S146fs|PSMG2_ENST00000585331.2_Frame_Shift_Del_p.S115fs	NM_020232.4	NP_064617.2			proteasome (prosome, macropain) assembly chaperone 2											lung(1)|prostate(2)|skin(1)	4						CTTACACCTTCCATGCAAAAA	0.338																																					p.S146fs		Atlas-Indel	.											.	PSMG2	17	.	0			c.436delT						PASS	.						55	55	55					18																	12720538		2203	4300	6503	SO:0001589	frameshift_variant	56984	exon5			.	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.437delC	18.37:g.12720538delC	ENSP00000325919:p.Ser146fs	201	0	0		144	17	0.118056	NM_020232		Frame_Shift_Del	DEL	ENST00000317615.6	37	CCDS11862.1																																																																																			.	.	none		0.338	PSMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254615.1	NM_020232		-	12720538	C	-	12720538	7	5	42	1	0	1	0	1	0	0	0	0	12724	855	30	0	455	0	PSMG2	18	12720538	Frame_Shift_Del	DEL	C	TCGA-GS-A9TZ-01A-11D-A38X-10	5489281	12720538	65356710	335	15287											
PTPN2	5771	hgsc.bcm.edu	37	chr18	12884137	12884137	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ctcccgctcgatggtggtggGcatggctgcgggagcgagct	4	8	18	11	4	0	0	0	0	0	0	2	3	1	1	1	5	3	4	1	5	0	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr18:12884137G>A	ENST00000309660.5	-	1	97	c.4C>T	c.(4-6)Ccc>Tcc	p.P2S	PTPN2_ENST00000327283.3_Missense_Mutation_p.P2S|PTPN2_ENST00000353319.4_Missense_Mutation_p.P2S|PTPN2_ENST00000591115.1_Missense_Mutation_p.P2S	NM_002828.3	NP_002819.2	P17706	PTN2_HUMAN	protein tyrosine phosphatase, non-receptor type 2	2					B cell differentiation (GO:0030183)|cytokine-mediated signaling pathway (GO:0019221)|erythrocyte differentiation (GO:0030218)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemotaxis (GO:0050922)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of inflammatory response (GO:0050728)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of interleukin-2-mediated signaling pathway (GO:1902206)|negative regulation of interleukin-4-mediated signaling pathway (GO:1902215)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|negative regulation of lipid storage (GO:0010888)|negative regulation of macrophage colony-stimulating factor signaling pathway (GO:1902227)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of positive thymic T cell selection (GO:1902233)|negative regulation of prolactin signaling pathway (GO:1902212)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|negative regulation of tyrosine phosphorylation of Stat1 protein (GO:0042512)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|negative regulation of tyrosine phosphorylation of Stat6 protein (GO:0042527)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of gluconeogenesis (GO:0045722)|regulation of hepatocyte growth factor receptor signaling pathway (GO:1902202)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|T cell differentiation (GO:0030217)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|syntaxin binding (GO:0019905)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|prostate(1)|skin(3)	13		Lung NSC(161;8.94e-06)				ATGGTGGTGGGCATGGCTGCG	0.711																																					p.P2S		Atlas-SNP	.											.	PTPN2	37	.	0			c.C4T						PASS	.						17	15	15					18																	12884137		2178	4288	6466	SO:0001583	missense	5771	exon1			TGGTGGGCATGGC	M25393	CCDS11863.1, CCDS11864.1, CCDS11865.1, CCDS59306.1	18p11.3-p11.2	2011-06-09			ENSG00000175354	ENSG00000175354		"Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"	9650	protein-coding gene	gene with protein product		176887		PTPT		2164224	Standard	NM_002828		Approved	TCELLPTP, TC-PTP, TCPTP	uc002krp.3	P17706	OTTHUMG00000131702	ENST00000309660.5:c.4C>T	18.37:g.12884137G>A	ENSP00000311857:p.Pro2Ser	97	0	0		80	15	0.1875	NM_001207013	A8K955|A8MXU3|K7ENG3|Q96AU5|Q96HR2	Missense_Mutation	SNP	ENST00000309660.5	37	CCDS11865.1	.	.	.	.	.	.	.	.	.	.	G	0.012	-1.685979	0.00738	.	.	ENSG00000175354	ENST00000327283;ENST00000353319;ENST00000309660	T;T;T	0.04049	3.73;3.74;3.72	3.74	0.301	0.15781	.	0.171955	0.27577	N	0.018760	T	0.01254	0.0041	N	0.02011	-0.69	0.20975	N	0.999813	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	0.44605	-0.9317	10	0.02654	T	1	.	3.1224	0.06396	0.5705:0.2244:0.2051:0.0	.	2;2;2;2	P17706;P17706-2;Q96AU5;A8K3N4	PTN2_HUMAN;.;.;.	S	2	ENSP00000320298:P2S;ENSP00000320546:P2S;ENSP00000311857:P2S	ENSP00000311857:P2S	P	-	1	0	PTPN2	12874137	0.989000	0.36119	0.526000	0.27913	0.038000	0.13279	0.352000	0.20113	-0.103000	0.12175	0.306000	0.20318	CCC	.	.	none		0.711	PTPN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254613.3	NM_002828, NM_080422, NM_080423		A	12884137	G	A	12884137	3	1	42	1	0	0	0	0	1	0	0	0	12798	1203	42	2	1305	2	PTPN2	18	12884137	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	163599	12884137	65193111	336	15288											
HCN2	610	hgsc.bcm.edu	37	chr19	608077	608077	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgacggacatctggctgacCatgctcagcatgattgtggg	9	10	13	9	1	2	3	1	3	1	0	2	4	2	4	1	3	2	3	1	3	0	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:608077C>T	ENST00000251287.2	+	4	1385	c.1332C>T	c.(1330-1332)acC>acT	p.T444T		NM_001194.3	NP_001185.3	Q9UL51	HCN2_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 2	444					cell-cell signaling (GO:0007267)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|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)|voltage-gated potassium channel complex (GO:0008076)	cAMP binding (GO:0030552)|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)			endometrium(5)|lung(4)	9		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)		TCTGGCTGACCATGCTCAGCA	0.622																																					p.T444T	Melanoma(145;1175 2427 8056 36306)	Atlas-SNP	.											HCN2,NS,carcinoma,+1,1	HCN2	36	1	0			c.C1332T						PASS	.						99	80	87					19																	608077		2203	4300	6503	SO:0001819	synonymous_variant	610	exon4			GCTGACCATGCTC	AF064877	CCDS12035.1	19p13	2011-07-05				ENSG00000099822		"Voltage-gated ion channels / Cyclic nucleotide-regulated channels"	4846	protein-coding gene	gene with protein product		602781		BCNG2		9405696, 9630217, 16382102	Standard	NM_001194		Approved	BCNG-2, HAC-1	uc002lpe.3	Q9UL51		ENST00000251287.2:c.1332C>T	19.37:g.608077C>T		63	0	0		49	16	0.326531	NM_001194	O60742|O60743|O75267|Q9UBS2	Silent	SNP	ENST00000251287.2	37	CCDS12035.1																																																																																			.	.	none		0.622	HCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452100.1	NM_001194		T	608077	C	T	608077	2	4	42	1	0	0	0	0	0	0	0	1	7006	581	21	2		2	HCN2	19	608077	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10		608077	58520906	337	15289											
HMHA1	23526	hgsc.bcm.edu	37	chr19	1081892	1081892	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aggccttcgagaacggcaagGagctggtcgagctgtcgcag	9	6	16	10	4	0	1	0	0	0	1	3	4	0	2	1	4	3	4	1	4	2	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:1081892G>A	ENST00000313093.2	+	19	2680	c.2449G>A	c.(2449-2451)Gag>Aag	p.E817K	HMHA1_ENST00000539243.2_Missense_Mutation_p.E833K|HMHA1_ENST00000586866.1_Missense_Mutation_p.E821K|HMHA1_ENST00000590577.1_Missense_Mutation_p.E452K|HMHA1_ENST00000543365.1_Missense_Mutation_p.E700K|HMHA1_ENST00000590214.1_Missense_Mutation_p.E844K|HMHA1_ENST00000536472.1_Missense_Mutation_p.E685K	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	817	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)|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)		GAACGGCAAGGAGCTGGTCGA	0.662																																					p.E833K		Atlas-SNP	.											.	HMHA1	78	.	0			c.G2497A						PASS	.						74	54	61					19																	1081892		2203	4300	6503	SO:0001583	missense	23526	exon19			GGCAAGGAGCTGG	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.2449G>A	19.37:g.1081892G>A	ENSP00000316772:p.Glu817Lys	25	0	0		29	9	0.310345	NM_001258328	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Missense_Mutation	SNP	ENST00000313093.2	37	CCDS32863.1	.	.	.	.	.	.	.	.	.	.	g	35	5.582067	0.96578	.	.	ENSG00000180448	ENST00000539243;ENST00000313093;ENST00000544746;ENST00000536472;ENST00000412039;ENST00000543365	T;T;T;T	0.18810	2.19;2.19;2.19;2.19	4.73	4.73	0.59995	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.41834	0.1176	L	0.50993	1.605	0.58432	D	0.999999	D;D;D;D;D	0.89917	1.0;1.0;0.974;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.932;0.998;0.999	T	0.28396	-1.0045	10	0.56958	D	0.05	-33.2846	16.7261	0.85422	0.0:0.0:1.0:0.0	.	685;833;452;700;817	F5H4A3;F6QP70;B3KVA9;F5H1R4;Q92619	.;.;.;.;HMHA1_HUMAN	K	833;817;817;685;811;700	ENSP00000439601:E833K;ENSP00000316772:E817K;ENSP00000445109:E685K;ENSP00000438979:E700K	ENSP00000316772:E817K	E	+	1	0	HMHA1	1032892	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	9.247000	0.95444	2.175000	0.68902	0.550000	0.68814	GAG	.	.	none		0.662	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1			A	1081892	G	A	1081892	3	1	42	1	0	0	0	0	1	0	0	0	7249	1175	41	2	2523	2	HMHA1	19	1081892	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	473815	1081892	58047091	338	15290											
C19orf26	255057	hgsc.bcm.edu	37	chr19	1235089	1235089	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cccgtggagctggtggacagGaagcgttcggtctccgcatc	6	8	15	12	4	1	0	0	0	1	0	4	3	1	3	2	5	2	3	2	5	1	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:1235089G>T	ENST00000382477.2	-	5	622	c.348C>A	c.(346-348)ttC>ttA	p.F116L	C19orf26_ENST00000590083.1_Missense_Mutation_p.F122L|C19orf26_ENST00000215376.6_Missense_Mutation_p.F116L			Q8N350	DOS_HUMAN	chromosome 19 open reading frame 26	116						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)		TGGTGGACAGGAAGCGTTCGG	0.706										HNSCC(14;0.022)																											p.F122L		Atlas-SNP	.											.	C19orf26	31	.	0			c.C366A						PASS	.						25	27	26					19																	1235089		2197	4294	6491	SO:0001583	missense	255057	exon5			GGACAGGAAGCGT	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.348C>A	19.37:g.1235089G>T	ENSP00000371917:p.Phe116Leu	94	0	0		91	21	0.230769	NM_152769	O43385	Missense_Mutation	SNP	ENST00000382477.2	37		.	.	.	.	.	.	.	.	.	.	G	13.90	2.373884	0.42105	.	.	ENSG00000099625	ENST00000382477;ENST00000215376	.	.	.	3.64	3.64	0.41730	.	0.062767	0.64402	D	0.000004	T	0.64316	0.2587	L	0.29908	0.895	0.58432	D	0.999994	D	0.67145	0.996	D	0.77557	0.99	T	0.68591	-0.5368	9	0.62326	D	0.03	.	14.4186	0.67168	0.0:0.0:1.0:0.0	.	116	Q8N350-2	.	L	116	.	ENSP00000215376:F116L	F	-	3	2	C19orf26	1186089	1.000000	0.71417	1.000000	0.80357	0.118000	0.20060	4.074000	0.57577	2.026000	0.59711	0.561000	0.74099	TTC	.	.	none		0.706	C19orf26-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_152769		T	1235089	G	T	1235089	3	4	42	1	0	0	0	0	1	0	0	0	1918	1165	41	4	1015	4	C19orf26	19	1235089	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	153197	1235089	57893894	339	15291											
LINGO3	645191	hgsc.bcm.edu	37	chr19	2290848	2290848	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gcccaggaaggcctgcggctCcaccacagccagcagggccc	8	2	13	18	1	0	0	0	0	0	0	1	1	1	1	6	4	3	2	6	4	1	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:2290848C>T	ENST00000585527.1	-	1	1175	c.928G>A	c.(928-930)Gag>Aag	p.E310K	LINGO3_ENST00000404279.1_Missense_Mutation_p.E310K			P0C6S8	LIGO3_HUMAN	leucine rich repeat and Ig domain containing 3	310						integral component of membrane (GO:0016021)				lung(1)|urinary_tract(1)	2						GCCTGCGGCTCCACCACAGCC	0.682																																					p.E310K		Atlas-SNP	.											.	LINGO3	19	.	0			c.G928A						PASS	.						13	17	16					19																	2290848		1958	4125	6083	SO:0001583	missense	645191	exon2			GCGGCTCCACCAC	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.928G>A	19.37:g.2290848C>T	ENSP00000467753:p.Glu310Lys	155	0	0		128	39	0.304688	NM_001101391		Missense_Mutation	SNP	ENST00000585527.1	37	CCDS45905.1	.	.	.	.	.	.	.	.	.	.	c	25.3	4.624090	0.87560	.	.	ENSG00000220008	ENST00000404279	T	0.79940	-1.32	4.62	4.62	0.57501	.	.	.	.	.	D	0.86464	0.5939	L	0.54965	1.715	0.80722	D	1	D	0.76494	0.999	D	0.68943	0.961	D	0.86507	0.1807	9	0.44086	T	0.13	.	16.0085	0.80380	0.0:1.0:0.0:0.0	.	310	P0C6S8	LIGO3_HUMAN	K	310	ENSP00000384979:E310K	ENSP00000384979:E310K	E	-	1	0	LINGO3	2241848	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.841000	0.55850	2.102000	0.63906	0.462000	0.41574	GAG	.	.	none		0.682	LINGO3-001	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451291.2	NM_001101391		T	2290848	C	T	2290848	3	4	42	1	0	0	0	0	1	0	0	0	8825	864	30	2	854	2	LINGO3	19	2290848	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	1055759	2290848	56838135	340	15292											
SMARCA4	6597	hgsc.bcm.edu	37	chr19	11134230	11134230	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaaaccattctcatcatcCggcgtctccacaaagtgctg	11	9	8	13	2	3	0	2	0	2	0	6	1	4	1	3	2	2	1	3	2	2	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:11134230C>T	ENST00000429416.3	+	21	3177	c.2896C>T	c.(2896-2898)Cgg>Tgg	p.R966W	SMARCA4_ENST00000450717.3_Missense_Mutation_p.R966W|SMARCA4_ENST00000444061.3_Missense_Mutation_p.R966W|SMARCA4_ENST00000358026.2_Missense_Mutation_p.R966W|SMARCA4_ENST00000541122.2_Missense_Mutation_p.R966W|SMARCA4_ENST00000413806.3_Missense_Mutation_p.R966W|SMARCA4_ENST00000589677.1_Missense_Mutation_p.R966W|SMARCA4_ENST00000590574.1_Missense_Mutation_p.R966W|SMARCA4_ENST00000344626.4_Missense_Mutation_p.R966W	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	966					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.R966W(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)				TCTCATCATCCGGCGTCTCCA	0.567			"F, N, Mis"		NSCLC																																p.R966W		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,caecum,carcinoma,-1,7	SMARCA4	502	7	2	Substitution - Missense(1)|Unknown(1)	ovary(1)|lung(1)	c.C2896T						PASS	.						68	61	63					19																	11134230		2203	4300	6503	SO:0001583	missense	6597	exon20			ATCATCCGGCGTC	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.2896C>T	19.37:g.11134230C>T	ENSP00000395654:p.Arg966Trp	45	0	0		50	10	0.2	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.649626	0.87958	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.93426	-3.22;-3.22;-3.22;-3.22;-3.22;-3.22;-3.22	4.9	4.9	0.64082	SNF2-related (1);	0.000000	0.85682	D	0.000000	D	0.97145	0.9067	M	0.88906	2.99	0.58432	D	0.999998	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;0.994;0.965;0.999;0.999	D	0.97864	1.0282	10	0.87932	D	0	-18.8931	16.9975	0.86372	0.0:1.0:0.0:0.0	.	966;966;966;966;966;186;966;966	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;A7E2E1;P51532	.;.;.;.;.;.;.;SMCA4_HUMAN	W	966;966;1030;966;966;966;966;966	ENSP00000395654:R966W;ENSP00000350720:R966W;ENSP00000343896:R966W;ENSP00000445036:R966W;ENSP00000392837:R966W;ENSP00000397783:R966W;ENSP00000414727:R966W	ENSP00000343896:R966W	R	+	1	2	SMARCA4	10995230	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	4.576000	0.60915	2.542000	0.85734	0.655000	0.94253	CGG	.	.	none		0.567	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		T	11134230	C	T	11134230	3	4	42	1	0	0	0	0	1	0	0	0	14785	643	23	1	2970	1	SMARCA4	19	11134230	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	8843382	11134230	47994753	341	15293											
DOCK6	57572	hgsc.bcm.edu	37	chr19	11325005	11325005	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgctgcaagaagagggcactCtgggcactgcccaggctgta	9	7	14	11	0	1	2	0	0	1	2	1	2	1	2	1	3	3	6	1	3	3	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:11325005C>T	ENST00000294618.7	-	34	4295	c.4284G>A	c.(4282-4284)caG>caA	p.Q1428Q	DOCK6_ENST00000319867.7_Silent_p.Q767Q|CTC-510F12.2_ENST00000588634.1_RNA	NM_020812.3	NP_065863.2	Q96HP0	DOCK6_HUMAN	dedicator of cytokinesis 6	1428					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						AGAGGGCACTCTGGGCACTGC	0.582																																					p.Q1428Q		Atlas-SNP	.											.	DOCK6	104	.	0			c.G4284A						PASS	.						42	44	43					19																	11325005		1986	4158	6144	SO:0001819	synonymous_variant	57572	exon34			GGCACTCTGGGCA		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.4284G>A	19.37:g.11325005C>T		74	0	0		60	19	0.316667	NM_020812	A6H8X5|Q7Z7P4|Q9P2F2	Silent	SNP	ENST00000294618.7	37	CCDS45975.1																																																																																			.	.	none		0.582	DOCK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453155.1	NM_020812		T	11325005	C	T	11325005	2	4	42	1	0	0	0	0	0	0	0	1	4693	912	32	2		2	DOCK6	19	11325005	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	190775	11325005	47803978	342	15294											
ZNF490	57474	hgsc.bcm.edu	37	chr19	12692409	12692409	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcatgaagacttccccacaCacactgcagtcacatggttt	11	10	7	13	0	1	2	1	1	0	1	2	2	2	2	2	1	2	3	2	1	1	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:12692409C>T	ENST00000311437.6	-	5	602	c.480G>A	c.(478-480)gtG>gtA	p.V160V	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	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V160V(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	18						CTTCCCCACACACACTGCAGT	0.433																																					p.V160V		Atlas-SNP	.											ZNF490,NS,carcinoma,0,1	ZNF490	42	1	1	Substitution - coding silent(1)	lung(1)	c.G480A						PASS	.						195	169	178					19																	12692409		2203	4300	6503	SO:0001819	synonymous_variant	57474	exon5			CCCACACACACTG	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.480G>A	19.37:g.12692409C>T		340	0	0		288	74	0.256944	NM_020714		Silent	SNP	ENST00000311437.6	37	CCDS12272.1																																																																																			.	.	none		0.433	ZNF490-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344073.1	NM_020714		T	12692409	C	T	12692409	2	4	42	1	0	0	0	0	0	0	0	1	17956	465	17	2		2	ZNF490	19	12692409	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	1367404	12692409	46436574	343	15295											
BRD4	23476	hgsc.bcm.edu	37	chr19	15366921	15366921	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	tttcttcgtctttttaggagGaggttccttggctttgcttt	3	21	10	7	1	2	0	0	0	2	0	4	2	3	2	1	4	1	3	1	4	1	9	rs201937726		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:15366921G>A	ENST00000263377.2	-	9	1926	c.1705C>T	c.(1705-1707)Cct>Tct	p.P569S	BRD4_ENST00000602230.1_5'Flank|BRD4_ENST00000360016.5_Missense_Mutation_p.P569S|BRD4_ENST00000371835.4_Missense_Mutation_p.P569S	NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	569	BID region.|Lys-rich.				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)			tttttaggaggaggttccttg	0.428			T	C15orf55	lethal midline carcinoma of young people																																p.P569S		Atlas-SNP	.		Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	BRD4_ENST00000263377,NS,carcinoma,+2,2	BRD4	172	2	0			c.C1705T						PASS	.						288	255	266					19																	15366921		2203	4300	6503	SO:0001583	missense	23476	exon9			TAGGAGGAGGTTC	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.1705C>T	19.37:g.15366921G>A	ENSP00000263377:p.Pro569Ser	648	0	0		541	133	0.245841	NM_058243	O60433|Q4G0X8|Q86YS8|Q96PD3	Missense_Mutation	SNP	ENST00000263377.2	37	CCDS12328.1	.	.	.	.	.	.	.	.	.	.	G	13.90	2.375762	0.42105	.	.	ENSG00000141867	ENST00000263377;ENST00000371835;ENST00000360016	T;T;T	0.10477	2.87;4.39;4.39	5.05	3.98	0.46160	.	0.202174	0.35320	N	0.003284	T	0.13756	0.0333	M	0.75615	2.305	0.35607	D	0.808345	B;B;B	0.34103	0.437;0.16;0.267	B;B;B	0.30401	0.115;0.06;0.055	T	0.15321	-1.0441	10	0.16896	T	0.51	-8.0525	14.2679	0.66133	0.0:0.1503:0.8497:0.0	.	569;569;569	Q4G0X8;O60885-2;O60885	.;.;BRD4_HUMAN	S	569	ENSP00000263377:P569S;ENSP00000360901:P569S;ENSP00000353112:P569S	ENSP00000263377:P569S	P	-	1	0	BRD4	15227921	1.000000	0.71417	0.984000	0.44739	0.813000	0.45954	6.325000	0.72901	1.088000	0.41272	0.561000	0.74099	CCT	.	.	weak		0.428	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243		A	15366921	G	A	15366921	3	1	42	1	0	0	0	0	1	0	0	0	1506	1174	41	2	2446	2	BRD4	19	15366921	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	2674512	15366921	43762062	344	15296											
IL12RB1	3594	hgsc.bcm.edu	37	chr19	18174694	18174694	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctccactcaccgatgctgAagcgctggggctggctccag	6	7	12	16	2	1	1	1	1	0	0	3	2	3	1	4	3	2	4	4	3	1	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:18174694A>T	ENST00000600835.2	-	14	1908	c.1610T>A	c.(1609-1611)tTc>tAc	p.F537Y	IL12RB1_ENST00000593993.2_Missense_Mutation_p.F537Y			P42701	I12R1_HUMAN	interleukin 12 receptor, beta 1	537	Fibronectin type-III 5. {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						ACCGATGCTGAAGCGCTGGGG	0.612																																					p.F537Y		Atlas-SNP	.											.	IL12RB1	92	.	0			c.T1610A						PASS	.						28	32	31					19																	18174694		2091	4228	6319	SO:0001583	missense	3594	exon13			ATGCTGAAGCGCT	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.1610T>A	19.37:g.18174694A>T	ENSP00000470788:p.Phe537Tyr	43	0	0		43	12	0.27907	NM_005535	A8K308|B2RPF1|B7ZKK3|Q8N6Q7	Missense_Mutation	SNP	ENST00000600835.2	37	CCDS54232.1	.	.	.	.	.	.	.	.	.	.	A	17.05	3.291175	0.59976	.	.	ENSG00000096996	ENST00000430026	T	0.55930	0.49	3.21	3.21	0.36854	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.000000	0.51477	D	0.000093	T	0.63977	0.2557	M	0.77103	2.36	0.80722	D	1	D;D	0.71674	0.998;0.997	D;D	0.81914	0.995;0.989	T	0.66027	-0.6025	10	0.07325	T	0.83	-29.046	8.1692	0.31245	1.0:0.0:0.0:0.0	.	537;537	P42701-2;P42701	.;I12R1_HUMAN	Y	537	ENSP00000403103:F537Y	ENSP00000403103:F537Y	F	-	2	0	IL12RB1	18035694	0.927000	0.31430	0.630000	0.29268	0.790000	0.44656	3.390000	0.52523	1.697000	0.51169	0.402000	0.26972	TTC	.	.	none		0.612	IL12RB1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466525.3			T	18174694	A	T	18174694	3	4	42	1	0	0	0	0	1	0	0	0	7635	246	9	5	398	5	IL12RB1	19	18174694	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	2807773	18174694	40954289	345	15297											
UPF1	5976	hgsc.bcm.edu	37	chr19	18965440	18965440	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgagatcgccattgagctgcGgagcagcgtgggtgcacctg	7	8	16	10	3	0	2	0	2	0	1	1	4	0	3	2	2	5	3	2	2	0	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:18965440G>A	ENST00000599848.1	+	9	1429	c.1220G>A	c.(1219-1221)cGg>cAg	p.R407Q	UPF1_ENST00000262803.5_Missense_Mutation_p.R396Q			Q92900	RENT1_HUMAN	UPF1 regulator of nonsense transcripts homolog (yeast)	407	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						ATTGAGCTGCGGAGCAGCGTG	0.537																																					p.R396Q		Atlas-SNP	.											.	UPF1	88	.	0			c.G1187A						PASS	.						197	195	196					19																	18965440		2203	4300	6503	SO:0001583	missense	5976	exon9			AGCTGCGGAGCAG	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.1220G>A	19.37:g.18965440G>A	ENSP00000470142:p.Arg407Gln	103	0	0		82	23	0.280488	NM_002911	O00239|O43343|Q86Z25|Q92842	Missense_Mutation	SNP	ENST00000599848.1	37		.	.	.	.	.	.	.	.	.	.	G	19.55	3.847933	0.71603	.	.	ENSG00000005007	ENST00000262803	D	0.90197	-2.63	5.02	3.98	0.46160	.	0.052869	0.64402	D	0.000001	D	0.86838	0.6029	L	0.49126	1.545	0.80722	D	1	B;B	0.27229	0.108;0.172	B;B	0.16722	0.011;0.016	D	0.84750	0.0756	10	0.72032	D	0.01	-42.4753	12.6337	0.56671	0.0813:0.0:0.9187:0.0	.	407;396	Q92900;Q92900-2	RENT1_HUMAN;.	Q	396	ENSP00000262803:R396Q	ENSP00000262803:R396Q	R	+	2	0	UPF1	18826440	1.000000	0.71417	0.959000	0.39883	0.846000	0.48090	9.429000	0.97481	1.117000	0.41842	0.655000	0.94253	CGG	.	.	none		0.537	UPF1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464684.1	NM_002911		A	18965440	G	A	18965440	3	1	42	1	0	0	0	0	1	0	0	0	17018	1116	39	1	1221	1	UPF1	19	18965440	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	790746	18965440	40163543	346	15298											
ZNF708	7562	hgsc.bcm.edu	37	chr19	21477477	21477477	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccatatcttctcagtatcacTtgttggaaagaattttttat	11	18	5	7	0	3	1	2	0	2	1	4	2	3	2	1	1	0	2	1	1	5	8			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:21477477T>G	ENST00000356929.3	-	4	488	c.291A>C	c.(289-291)caA>caC	p.Q97H		NM_021269.2	NP_067092.2	P17019	ZN708_HUMAN	zinc finger protein 708	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)			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						TCAGTATCACTTGTTGGAAAG	0.353																																					p.Q97H		Atlas-SNP	.											.	ZNF708	66	.	0			c.A291C						PASS	.						80	80	80					19																	21477477		2203	4299	6502	SO:0001583	missense	7562	exon4			TATCACTTGTTGG	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.291A>C	19.37:g.21477477T>G	ENSP00000349401:p.Gln97His	215	0	0		182	42	0.230769	NM_021269	Q6ZMR0	Missense_Mutation	SNP	ENST00000356929.3	37	CCDS32980.1	.	.	.	.	.	.	.	.	.	.	.	5.752	0.323255	0.10900	.	.	ENSG00000182141	ENST00000356929	T	0.06528	3.29	0.449	-0.676	0.11361	.	.	.	.	.	T	0.09113	0.0225	L	0.43152	1.355	0.09310	N	1	B	0.27351	0.176	B	0.42738	0.396	T	0.48399	-0.9039	8	0.54805	T	0.06	.	.	.	.	.	97	P17019	ZN708_HUMAN	H	97	ENSP00000349401:Q97H	ENSP00000349401:Q97H	Q	-	3	2	ZNF708	21269317	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.386000	0.07370	-0.428000	0.07339	-0.436000	0.05848	CAA	.	.	none		0.353	ZNF708-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463953.1	NM_021269		G	21477477	T	G	21477477	3	3	42	1	0	0	0	0	1	0	0	0	18127	1606	56	5	1404	5	ZNF708	19	21477477	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	2512037	21477477	37651506	347	15299											
ZNF208	7757	hgsc.bcm.edu	37	chr19	22155873	22155873	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccagcatgaattgccttatGtgtagtaagggttgagacct	10	13	11	7	0	0	2	0	2	0	1	1	3	1	2	3	1	2	4	3	1	4	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:22155873G>T	ENST00000397126.4	-	4	2111	c.1963C>A	c.(1963-1965)Cat>Aat	p.H655N	ZNF208_ENST00000601773.1_Intron|ZNF208_ENST00000599916.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	655					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)				ATTGCCTTATGTGTAGTAAGG	0.383																																					p.H655N		Atlas-SNP	.											.	ZNF208	817	.	0			c.C1963A						PASS	.						84	90	88					19																	22155873		2099	4256	6355	SO:0001583	missense	7757	exon4			CCTTATGTGTAGT	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.1963C>A	19.37:g.22155873G>T	ENSP00000380315:p.His655Asn	152	0	0		120	29	0.241667	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	G	9.493	1.101239	0.20632	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	D	0.86865	-2.18	2.49	2.49	0.30216	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.92299	0.7557	.	.	.	0.24812	N	0.992636	D	0.89917	1.0	D	0.91635	0.999	D	0.83937	0.0309	8	0.87932	D	0	.	11.6277	0.51156	0.0:0.0:1.0:0.0	.	555	O43345	ZN208_HUMAN	N	655;555	ENSP00000380315:H655N	ENSP00000380315:H655N	H	-	1	0	ZNF208	21947713	0.987000	0.35691	0.002000	0.10522	0.002000	0.02628	3.980000	0.56895	0.923000	0.37045	0.289000	0.19496	CAT	.	.	none		0.383	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		T	22155873	G	T	22155873	3	4	42	1	0	0	0	0	1	0	0	0	17781	1377	48	4	1883	4	ZNF208	19	22155873	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	678396	22155873	36973110	348	15300											
ZNF257	113835	hgsc.bcm.edu	37	chr19	22271296	22271296	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcacaccttactcaacataaGgtaattcatactagagagaa	17	10	5	9	0	3	2	3	0	0	2	3	3	3	2	1	1	3	1	1	1	7	6			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:22271296G>A	ENST00000594947.1	+	4	888	c.744G>A	c.(742-744)aaG>aaA	p.K248K		NM_033468.2	NP_258429.2	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	248					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|lung(4)	6		all_lung(12;0.0961)|Lung NSC(12;0.103)				CTCAACATAAGGTAATTCATA	0.388																																					p.K248K		Atlas-SNP	.											.	ZNF257	156	.	0			c.G744A						PASS	.						37	40	39					19																	22271296		2124	4259	6383	SO:0001819	synonymous_variant	113835	exon4			ACATAAGGTAATT	AF070651	CCDS46030.1	19p12	2014-02-14			ENSG00000197134	ENSG00000197134		"Zinc fingers, C2H2-type", "-"	13498	protein-coding gene	gene with protein product		606957				10585455	Standard	NM_033468		Approved	BMZF-4	uc010ecx.3	Q9Y2Q1	OTTHUMG00000182927	ENST00000594947.1:c.744G>A	19.37:g.22271296G>A		219	0	0		197	52	0.263959	NM_033468	B3KPS4|E9PG34|Q8NE34	Silent	SNP	ENST00000594947.1	37	CCDS46030.1																																																																																			.	.	none		0.388	ZNF257-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464382.1			A	22271296	G	A	22271296	2	1	42	1	0	0	0	0	0	0	0	1	17815	991	35	2		2	ZNF257	19	22271296	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	115423	22271296	36857687	349	15301											
PAK4	10298	hgsc.bcm.edu	37	chr19	39660292	39660292	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagcacgagcagaagttcacGgggctgccccgccagtggca	9	4	14	14	3	1	1	1	0	0	1	1	2	1	1	3	3	3	5	3	3	1	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:39660292G>A	ENST00000593690.1	+	4	526	c.99G>A	c.(97-99)acG>acA	p.T33T	PAK4_ENST00000599386.1_Silent_p.T33T|PAK4_ENST00000360442.3_Silent_p.T33T|PAK4_ENST00000358301.3_Silent_p.T33T|PAK4_ENST00000599470.1_Silent_p.T33T|PAK4_ENST00000435673.2_Silent_p.T33T|PAK4_ENST00000321944.4_Silent_p.T33T	NM_001014831.2	NP_001014831.1	O96013	PAK4_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 4	33	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)			AGAAGTTCACGGGGCTGCCCC	0.682																																					p.T33T		Atlas-SNP	.											.	PAK4	40	.	0			c.G99A						PASS	.						37	40	39					19																	39660292		2202	4300	6502	SO:0001819	synonymous_variant	10298	exon2			GTTCACGGGGCTG	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.99G>A	19.37:g.39660292G>A		88	0	0		73	18	0.246575	NM_001014832	B4DGG6|Q8N4E1|Q8NCH5|Q8NDE3|Q9BU33|Q9ULS8	Silent	SNP	ENST00000593690.1	37	CCDS12528.1																																																																																			.	.	none		0.682	PAK4-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463823.1			A	39660292	G	A	39660292	2	1	42	1	0	0	0	0	0	0	0	1	11412	1103	39	1		1	PAK4	19	39660292	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	17388996	39660292	19468691	350	15302											
DYRK1B	9149	hgsc.bcm.edu	37	chr19	40317311	40317311	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	tttgggcacctgggcacccaCcagaactggagatggagctg	9	7	14	11	0	0	2	0	0	0	2	0	4	0	3	3	4	2	3	3	4	1	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:40317311C>T	ENST00000593685.1	-	9	1880		c.e9+1		DYRK1B_ENST00000323039.5_Splice_Site|DYRK1B_ENST00000430012.2_Splice_Site|DYRK1B_ENST00000348817.3_Splice_Site|DYRK1B_ENST00000597639.1_Splice_Site			Q9Y463	DYR1B_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1B						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)			TGGGCACCCACCAGAACTGGA	0.672																																					.		Atlas-SNP	.											.	DYRK1B	114	.	0			c.1291+1G>A						PASS	.						12	9	10					19																	40317311		2001	3978	5979	SO:0001630	splice_region_variant	9149	exon10			CACCCACCAGAAC	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.1411+1G>A	19.37:g.40317311C>T		76	0	0		74	20	0.27027	NM_006483	O75258|O75788|O75789	Splice_Site	SNP	ENST00000593685.1	37	CCDS12543.1	.	.	.	.	.	.	.	.	.	.	C	19.00	3.742056	0.69418	.	.	ENSG00000105204	ENST00000323039;ENST00000348817;ENST00000430012	.	.	.	4.64	4.64	0.57946	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9869	0.71356	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DYRK1B	45009151	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.413000	0.80104	2.096000	0.63516	0.563000	0.77884	.	.	.	none		0.672	DYRK1B-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462874.2	NM_004714	Intron	T	40317311	C	T	40317311	5	4	42	1	0	0	0	0	0	0	1	0	4857	521	18	2	489	2	DYRK1B	19	40317311	Splice_Site	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	657019	40317311	18811672	351	15303											
CD79A	973	hgsc.bcm.edu	37	chr19	42381447	42381447	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tcttcctgctgtctgctgtcTacctgggtatgtggccaaag	5	14	11	11	0	3	0	0	0	3	0	4	0	4	0	3	2	3	3	3	2	3	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:42381447T>A	ENST00000221972.3	+	1	258	c.73T>A	c.(73-75)Tac>Aac	p.Y25N	CD79A_ENST00000444740.2_Missense_Mutation_p.Y25N	NM_001783.3|NM_021601.3	NP_001774.1|NP_067612.1	P11912	CD79A_HUMAN	CD79a molecule, immunoglobulin-associated alpha	25					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						GTCTGCTGTCTACCTGGGTAT	0.612			"O, S"		DLBCL																																p.Y25N		Atlas-SNP	.		Dom	yes		19	19q13.2	973	"CD79a molecule, immunoglobulin-associated alpha"		L	.	CD79A	25	.	0			c.T73A						PASS	.						145	109	121					19																	42381447		2203	4300	6503	SO:0001583	missense	973	exon1			GCTGTCTACCTGG	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.73T>A	19.37:g.42381447T>A	ENSP00000221972:p.Tyr25Asn	93	0	0		87	19	0.218391	NM_021601	A0N775|Q53FB8	Missense_Mutation	SNP	ENST00000221972.3	37	CCDS12589.1	.	.	.	.	.	.	.	.	.	.	T	5.787	0.329487	0.10956	.	.	ENSG00000105369	ENST00000221972;ENST00000444740	T	0.76186	-1.0	3.61	-1.13	0.09775	.	0.545236	0.15449	N	0.261790	T	0.45875	0.1364	N	0.08118	0	0.09310	N	1	B;B	0.27068	0.003;0.167	B;B	0.20767	0.002;0.031	T	0.27157	-1.0082	10	0.27785	T	0.31	-1.8651	5.5865	0.17277	0.1758:0.0:0.596:0.2282	.	25;25	P11912;A0N775	CD79A_HUMAN;.	N	25	ENSP00000221972:Y25N	ENSP00000221972:Y25N	Y	+	1	0	CD79A	47073287	0.002000	0.14202	0.008000	0.14137	0.816000	0.46133	0.755000	0.26405	-0.168000	0.10853	0.449000	0.29647	TAC	.	.	none		0.612	CD79A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463058.1			A	42381447	T	A	42381447	3	1	42	1	0	0	0	0	1	0	0	0	3038	1522	53	5	75	5	CD79A	19	42381447	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	2064136	42381447	16747536	352	15304											
ZNF234	10780	hgsc.bcm.edu	37	chr19	44661323	44661323	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	taagggtttcatttacagttCaagttttcaggcccatcagg	10	14	9	8	0	4	0	4	0	0	0	4	0	4	0	1	3	1	3	1	3	3	7	rs191045580		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:44661323C>T	ENST00000426739.2	+	6	1412	c.1154C>T	c.(1153-1155)tCa>tTa	p.S385L	ZNF234_ENST00000592437.1_Missense_Mutation_p.S385L	NM_006630.2	NP_006621.1	Q14588	ZN234_HUMAN	zinc finger protein 234	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)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)	23		Prostate(69;0.0435)				ATTTACAGTTCAAGTTTTCAG	0.428																																					p.S385L		Atlas-SNP	.											.	ZNF234	132	.	0			c.C1154T						PASS	.						59	62	61					19																	44661323		2149	4280	6429	SO:0001583	missense	10780	exon6			ACAGTTCAAGTTT	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.1154C>T	19.37:g.44661323C>T	ENSP00000400878:p.Ser385Leu	105	0	0		119	27	0.226891	NM_006630	A8K1C8|Q96IR4|Q9NS45|Q9NYT7	Missense_Mutation	SNP	ENST00000426739.2	37	CCDS46101.1	.	.	.	.	.	.	.	.	.	.	C	15.97	2.990174	0.54041	.	.	ENSG00000167380	ENST00000426739	T	0.36520	1.25	3.93	3.93	0.45458	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.55417	0.1919	M	0.62088	1.915	0.09310	N	1	D	0.63880	0.993	D	0.72338	0.977	T	0.41945	-0.9480	9	0.72032	D	0.01	.	11.8477	0.52393	0.0:0.8215:0.1785:0.0	.	385	Q14588	ZN234_HUMAN	L	385	ENSP00000400878:S385L	ENSP00000400878:S385L	S	+	2	0	ZNF226	49353163	0.000000	0.05858	0.125000	0.21846	0.988000	0.76386	0.053000	0.14184	2.175000	0.68902	0.591000	0.81541	TCA	C|0.999;A|0.001	.	alt		0.428	ZNF234-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460586.2			T	44661323	C	T	44661323	3	4	42	1	0	0	0	0	1	0	0	0	17802	838	29	2	1168	2	ZNF234	19	44661323	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	2279876	44661323	14467660	353	15305											
ZNF234	10780	hgsc.bcm.edu	37	chr19	44661732	44661732	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gaggagtgtgggaaggtcttCagtcaggcctcgcatcttct	7	11	14	9	1	5	0	2	0	3	0	6	3	5	2	1	4	0	1	1	4	1	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:44661732C>T	ENST00000426739.2	+	6	1821	c.1563C>T	c.(1561-1563)ttC>ttT	p.F521F	ZNF234_ENST00000592437.1_Silent_p.F521F	NM_006630.2	NP_006621.1	Q14588	ZN234_HUMAN	zinc finger protein 234	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)|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)				GGAAGGTCTTCAGTCAGGCCT	0.463																																					p.F521F		Atlas-SNP	.											.	ZNF234	132	.	0			c.C1563T						PASS	.						84	90	88					19																	44661732		2181	4285	6466	SO:0001819	synonymous_variant	10780	exon6			GGTCTTCAGTCAG	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.1563C>T	19.37:g.44661732C>T		101	0	0		95	22	0.231579	NM_006630	A8K1C8|Q96IR4|Q9NS45|Q9NYT7	Silent	SNP	ENST00000426739.2	37	CCDS46101.1																																																																																			.	.	none		0.463	ZNF234-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460586.2			T	44661732	C	T	44661732	2	4	42	1	0	0	0	0	0	0	0	1	17802	825	29	2		2	ZNF234	19	44661732	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	409	44661732	14467251	354	15306											
SHANK1	50944	hgsc.bcm.edu	37	chr19	51169477	51169477	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgcagggaggaggtcctctCggggacatagctggctcccc	6	7	15	13	1	1	0	0	0	1	0	4	3	3	3	3	6	2	3	3	6	1	1	rs549051295		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:51169477C>T	ENST00000293441.1	-	22	5758	c.5740G>A	c.(5740-5742)Gag>Aag	p.E1914K	SHANK1_ENST00000391813.1_Missense_Mutation_p.E1301K|SHANK1_ENST00000359082.3_Missense_Mutation_p.E1905K|SHANK1_ENST00000391814.1_Missense_Mutation_p.E1922K|SYT3_ENST00000544769.1_Intron	NM_016148.2	NP_057232.2	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	1914					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)		GAGGTCCTCTCGGGGACATAG	0.687																																					p.E1914K		Atlas-SNP	.											SHANK1,caecum,carcinoma,0,1	SHANK1	210	1	0			c.G5740A						scavenged	.						14	12	13					19																	51169477		2197	4289	6486	SO:0001583	missense	50944	exon22			TCCTCTCGGGGAC	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.5740G>A	19.37:g.51169477C>T	ENSP00000293441:p.Glu1914Lys	66	1	0.0151515		49	14	0.285714	NM_016148	A8MXP5|B7WNY6|Q9NYW9	Missense_Mutation	SNP	ENST00000293441.1	37	CCDS12799.1	.	.	.	.	.	.	.	.	.	.	C	9.758	1.169414	0.21621	.	.	ENSG00000161681	ENST00000293441;ENST00000391813;ENST00000359082;ENST00000391814	T;T;T;T	0.39229	1.21;1.67;1.2;1.09	2.46	2.46	0.29980	.	0.963048	0.08427	U	0.947541	T	0.38746	0.1052	L	0.46157	1.445	0.35068	D	0.762213	D;D	0.67145	0.993;0.996	B;P	0.48030	0.361;0.564	T	0.42310	-0.9459	10	0.07175	T	0.84	.	10.6653	0.45726	0.0:1.0:0.0:0.0	.	1914;1301	Q9Y566;Q9Y566-2	SHAN1_HUMAN;.	K	1914;1301;1905;1922	ENSP00000293441:E1914K;ENSP00000375689:E1301K;ENSP00000351984:E1905K;ENSP00000375690:E1922K	ENSP00000293441:E1914K	E	-	1	0	SHANK1	55861289	0.997000	0.39634	0.872000	0.34217	0.521000	0.34408	4.778000	0.62368	1.682000	0.51000	0.195000	0.17529	GAG	.	.	none		0.687	SHANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268071.1	NM_016148		T	51169477	C	T	51169477	3	4	42	1	0	0	0	0	1	0	0	0	14279	893	31	1	753	1	SHANK1	19	51169477	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	6507745	51169477	7959506	355	15307											
ZNF649	65251	hgsc.bcm.edu	37	chr19	52394595	52394595	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaaggctttcccacattcaCtgcacccgtatggtttctct	7	13	8	13	1	2	0	1	0	1	0	4	1	3	1	2	3	1	4	2	3	2	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:52394595C>G	ENST00000354957.3	-	5	1078	c.794G>C	c.(793-795)aGt>aCt	p.S265T	ZNF649_ENST00000600738.1_Missense_Mutation_p.S237T|CTC-429C10.2_ENST00000600329.1_RNA	NM_023074.3	NP_075562.2	Q9BS31	ZN649_HUMAN	zinc finger protein 649	265					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular space (GO:0005615)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	29		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00152)|OV - Ovarian serous cystadenocarcinoma(262;0.0185)		CCCACATTCACTGCACCCGTA	0.502																																					p.S265T		Atlas-SNP	.											.	ZNF649	72	.	0			c.G794C						PASS	.						116	117	116					19																	52394595		2203	4300	6503	SO:0001583	missense	65251	exon5			CATTCACTGCACC	BC005368	CCDS12843.1	19q13.41	2013-01-08				ENSG00000198093		"Zinc fingers, C2H2-type", "-"	25741	protein-coding gene	gene with protein product		611903				15950191	Standard	NM_023074		Approved	FLJ12644	uc002pxy.3	Q9BS31		ENST00000354957.3:c.794G>C	19.37:g.52394595C>G	ENSP00000347043:p.Ser265Thr	316	0	0		273	76	0.278388	NM_023074	A8MYJ5|B2RDC4|Q9H9N2	Missense_Mutation	SNP	ENST00000354957.3	37	CCDS12843.1	.	.	.	.	.	.	.	.	.	.	C	2.723	-0.266213	0.05754	.	.	ENSG00000198093	ENST00000354957	T	0.07567	3.18	2.25	-4.49	0.03504	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03915	0.0110	N	0.20845	0.615	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.42515	-0.9447	9	0.33141	T	0.24	.	1.7035	0.02877	0.2242:0.4224:0.1926:0.1609	.	265	Q9BS31	ZN649_HUMAN	T	265	ENSP00000347043:S265T	ENSP00000347043:S265T	S	-	2	0	ZNF649	57086407	0.000000	0.05858	0.002000	0.10522	0.009000	0.06853	-12.841000	0.00001	-0.804000	0.04410	-0.714000	0.03626	AGT	.	.	none		0.502	ZNF649-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461097.1	NM_023074		G	52394595	C	G	52394595	3	3	42	1	0	0	0	0	1	0	0	0	18079	565	20	4	727	4	ZNF649	19	52394595	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	1225118	52394595	6734388	356	15308											
ZNF615	284370	hgsc.bcm.edu	37	chr19	52497677	52497677	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	tctctgatgatcaataaactGagacaacttgaggaaggctt	14	11	9	7	0	2	4	1	4	1	1	3	6	2	5	0	2	2	1	0	2	5	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:52497677G>C	ENST00000602063.1	-	6	1001	c.652C>G	c.(652-654)Cag>Gag	p.Q218E	ZNF615_ENST00000376716.5_Missense_Mutation_p.Q218E|ZNF615_ENST00000594083.1_Missense_Mutation_p.Q229E|ZNF615_ENST00000391795.3_Missense_Mutation_p.Q223E|ZNF615_ENST00000598071.1_Missense_Mutation_p.Q229E			Q8N8J6	ZN615_HUMAN	zinc finger protein 615	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)|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)		TCAATAAACTGAGACAACTTG	0.408																																					p.Q229E		Atlas-SNP	.											.	ZNF615	111	.	0			c.C685G						PASS	.						190	183	185					19																	52497677		2203	4300	6503	SO:0001583	missense	284370	exon7			TAAACTGAGACAA	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.652C>G	19.37:g.52497677G>C	ENSP00000473089:p.Gln218Glu	257	0	0		252	66	0.261905	NM_001199324	B7ZKW9|Q2M2Y6|Q5CZB0|Q6ZMT7|Q6ZRB3	Missense_Mutation	SNP	ENST00000602063.1	37	CCDS12846.1	.	.	.	.	.	.	.	.	.	.	G	0.017	-1.511184	0.00984	.	.	ENSG00000197619	ENST00000376716;ENST00000354939;ENST00000391795;ENST00000391793	T;T	0.27720	1.65;1.65	3.2	-1.87	0.07737	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.14442	0.0349	L	0.27053	0.805	0.09310	N	1	B;B;B;B	0.27732	0.118;0.187;0.187;0.118	B;B;B;B	0.24155	0.023;0.051;0.051;0.023	T	0.32824	-0.9892	9	0.08599	T	0.76	.	4.8415	0.13492	0.5616:0.1784:0.26:0.0	.	223;225;229;218	B4DH87;Q8N8J6-3;Q8N8J6-2;Q8N8J6	.;.;.;ZN615_HUMAN	E	218;228;223;228	ENSP00000365906:Q218E;ENSP00000375672:Q223E	ENSP00000347019:Q228E	Q	-	1	0	ZNF615	57189489	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.995000	0.01472	-0.067000	0.12976	0.655000	0.94253	CAG	.	.	none		0.408	ZNF615-009	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462391.1	NM_198480		C	52497677	G	C	52497677	3	2	42	1	0	0	0	0	1	0	0	0	18055	1299	45	4	1547	4	ZNF615	19	52497677	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	103082	52497677	6631306	357	15309											
ZNF616	90317	hgsc.bcm.edu	37	chr19	52618943	52618943	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	acattcattgcatttgtaagGtttctctccagtatgaattc	10	17	6	8	0	2	1	1	1	1	0	5	1	3	1	1	1	1	4	1	1	3	7			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:52618943G>A	ENST00000600228.1	-	4	1735	c.1474C>T	c.(1474-1476)Cct>Tct	p.P492S	ZNF616_ENST00000330123.5_3'UTR	NM_178523.3	NP_848618.2	Q08AN1	ZN616_HUMAN	zinc finger protein 616	492					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)		CATTTGTAAGGTTTCTCTCCA	0.408																																					p.P492S		Atlas-SNP	.											.	ZNF616	109	.	0			c.C1474T						PASS	.						106	99	102					19																	52618943		2203	4300	6503	SO:0001583	missense	90317	exon4			TGTAAGGTTTCTC	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.1474C>T	19.37:g.52618943G>A	ENSP00000471000:p.Pro492Ser	124	0	0		128	38	0.296875	NM_178523	B3KRV1|Q0P658|Q658V7	Missense_Mutation	SNP	ENST00000600228.1	37	CCDS33090.1	.	.	.	.	.	.	.	.	.	.	G	16.43	3.120924	0.56613	.	.	ENSG00000204611	ENST00000330123	.	.	.	1.08	-0.00954	0.14000	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.49304	0.1549	L	0.59912	1.85	0.20196	N	0.999921	D	0.65815	0.995	P	0.59357	0.856	T	0.35076	-0.9803	8	0.59425	D	0.04	.	5.0165	0.14339	0.2201:0.0:0.7799:0.0	.	492	Q08AN1	ZN616_HUMAN	S	492	.	ENSP00000328722:P492S	P	-	1	0	ZNF616	57310755	0.995000	0.38212	0.008000	0.14137	0.900000	0.52787	3.357000	0.52277	0.031000	0.15407	0.305000	0.20034	CCT	.	.	none		0.408	ZNF616-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462451.1	XM_030892		A	52618943	G	A	52618943	3	1	42	1	0	0	0	0	1	0	0	0	18056	1261	44	2	875	2	ZNF616	19	52618943	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	121266	52618943	6510040	358	15310											
ZNF836	162962	hgsc.bcm.edu	37	chr19	52659320	52659320	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ttaaatgtcttacaaggcatGaattttcactaaagaccttt	14	15	5	7	0	2	2	1	1	1	1	2	2	2	2	1	1	1	1	1	1	7	6			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:52659320G>A	ENST00000322146.8	-	5	2137	c.1616C>T	c.(1615-1617)tCa>tTa	p.S539L	CTC-471J1.8_ENST00000594362.1_RNA|ZNF836_ENST00000597252.1_Missense_Mutation_p.S539L	NM_001102657.1	NP_001096127.1	Q6ZNA1	ZN836_HUMAN	zinc finger protein 836	539					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						TACAAGGCATGAATTTTCACT	0.383																																					p.S539L		Atlas-SNP	.											.	ZNF836	158	.	0			c.C1616T						PASS	.						116	127	123					19																	52659320		2080	4245	6325	SO:0001583	missense	162962	exon5			AGGCATGAATTTT	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.1616C>T	19.37:g.52659320G>A	ENSP00000325038:p.Ser539Leu	215	0	0		164	55	0.335366	NM_001102657		Missense_Mutation	SNP	ENST00000322146.8	37	CCDS46162.1	.	.	.	.	.	.	.	.	.	.	G	13.55	2.270902	0.40194	.	.	ENSG00000196267	ENST00000322146	T	0.07444	3.19	2.09	-0.172	0.13327	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17152	0.0412	L	0.54863	1.705	0.09310	N	1	D	0.63880	0.993	D	0.72338	0.977	T	0.14337	-1.0476	9	0.66056	D	0.02	.	2.8352	0.05512	0.4341:0.2455:0.3204:0.0	.	539	Q6ZNA1	ZN836_HUMAN	L	539	ENSP00000325038:S539L	ENSP00000325038:S539L	S	-	2	0	ZNF836	57351132	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.484000	0.06528	0.207000	0.20607	0.484000	0.47621	TCA	.	.	none		0.383	ZNF836-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462456.1	NM_001102657		A	52659320	G	A	52659320	3	1	42	1	0	0	0	0	1	0	0	0	18202	1294	45	2	1196	2	ZNF836	19	52659320	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	40377	52659320	6469663	359	15311											
NCR1	9437	hgsc.bcm.edu	37	chr19	55423582	55423582	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	accacagagacgggactccaGaaaggtaagtagacagctgg	15	4	13	9	1	0	3	0	0	0	3	1	5	1	4	2	3	1	3	2	3	3	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:55423582G>A	ENST00000291890.4	+	6	767	c.729G>A	c.(727-729)caG>caA	p.Q243Q	NCR1_ENST00000338835.5_Intron|NCR1_ENST00000447255.1_Silent_p.Q242Q|NCR1_ENST00000350790.5_Silent_p.Q148Q|NCR1_ENST00000594765.1_Silent_p.Q242Q|NCR1_ENST00000598576.1_Silent_p.Q230Q|NCR1_ENST00000357397.5_Silent_p.Q136Q	NM_004829.5	NP_004820.2	O76036	NCTR1_HUMAN	natural cytotoxicity triggering receptor 1	243					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)		CGGGACTCCAGAAAGGTAAGT	0.512																																					p.Q243Q		Atlas-SNP	.											.	NCR1	60	.	0			c.G729A						PASS	.						118	110	113					19																	55423582		2203	4300	6503	SO:0001819	synonymous_variant	9437	exon6			ACTCCAGAAAGGT	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.729G>A	19.37:g.55423582G>A		96	0	0		84	34	0.404762	NM_004829	B0V3L2|B0V3L3|B0V3L4|B0V3L5|B8JL03|O76016|O76017|O76018	Silent	SNP	ENST00000291890.4	37	CCDS12911.1																																																																																			.	.	none		0.512	NCR1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465680.1			A	55423582	G	A	55423582	2	1	42	1	0	0	0	0	0	0	0	1	10246	933	33	2		2	NCR1	19	55423582	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	2764262	55423582	3705401	360	15312											
ZIM3	114026	hgsc.bcm.edu	37	chr19	57646662	57646662	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	tctcatgatcgatgacattgGatttctgggaaaaggccttc	10	13	10	8	1	2	2	1	2	2	0	5	5	2	4	1	3	0	0	1	3	2	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:57646662G>C	ENST00000269834.1	-	5	1428	c.1043C>G	c.(1042-1044)tCc>tGc	p.S348C	U3_ENST00000516874.1_RNA	NM_052882.1	NP_443114.1	Q96PE6	ZIM3_HUMAN	zinc finger, imprinted 3	348					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)		GATGACATTGGATTTCTGGGA	0.388																																					p.S348C		Atlas-SNP	.											.	ZIM3	107	.	0			c.C1043G						PASS	.						168	164	165					19																	57646662		2203	4300	6503	SO:0001583	missense	114026	exon5			ACATTGGATTTCT	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.1043C>G	19.37:g.57646662G>C	ENSP00000269834:p.Ser348Cys	322	0	0		285	79	0.277193	NM_052882	Q14CA6	Missense_Mutation	SNP	ENST00000269834.1	37	CCDS33125.1	.	.	.	.	.	.	.	.	.	.	G	9.453	1.090990	0.20471	.	.	ENSG00000141946	ENST00000269834	T	0.08008	3.14	2.29	2.29	0.28610	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.25158	0.0611	M	0.71206	2.165	0.09310	N	1	D	0.89917	1.0	D	0.81914	0.995	T	0.02144	-1.1206	9	0.87932	D	0	.	10.2276	0.43236	0.0:0.0:1.0:0.0	.	348	Q96PE6	ZIM3_HUMAN	C	348	ENSP00000269834:S348C	ENSP00000269834:S348C	S	-	2	0	ZIM3	62338474	0.000000	0.05858	0.774000	0.31636	0.297000	0.27493	-1.288000	0.02783	1.266000	0.44231	0.313000	0.20887	TCC	.	.	none		0.388	ZIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465078.1			C	57646662	G	C	57646662	3	2	42	1	0	0	0	0	1	0	0	0	17700	1174	41	4	379	4	ZIM3	19	57646662	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	2223080	57646662	1482321	361	15313											
VN1R1	57191	hgsc.bcm.edu	37	chr19	57967400	57967400	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ccatccacctgcatatactgGggttgagcttaatggcttgg	8	12	11	10	0	0	1	0	1	0	0	1	1	1	1	3	4	3	4	3	4	3	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr19:57967400G>T	ENST00000321039.3	-	1	454	c.455C>A	c.(454-456)cCc>cAc	p.P152H	AC004076.9_ENST00000596831.1_Intron|AC004076.9_ENST00000415705.3_Intron	NM_020633.3	NP_065684.1	Q9GZP7	VN1R1_HUMAN	vomeronasal 1 receptor 1	152					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)		GCATATACTGGGGTTGAGCTT	0.463																																					p.P152H		Atlas-SNP	.											.	VN1R1	48	.	0			c.C455A						PASS	.						99	91	94					19																	57967400		2203	4300	6503	SO:0001583	missense	57191	exon1			ATACTGGGGTTGA	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.455C>A	19.37:g.57967400G>T	ENSP00000322339:p.Pro152His	214	0	0		171	43	0.251462	NM_020633	B3KSV5|Q7Z5H8|Q7Z5H9	Missense_Mutation	SNP	ENST00000321039.3	37	CCDS12951.1	.	.	.	.	.	.	.	.	.	.	G	14.66	2.602874	0.46423	.	.	ENSG00000178201	ENST00000321039	T	0.10763	2.84	4.24	3.19	0.36642	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.39937	0.1097	H	0.94503	3.545	0.09310	N	1	D	0.55172	0.97	D	0.64042	0.921	T	0.28138	-1.0053	9	0.66056	D	0.02	.	10.4287	0.44393	0.0977:0.0:0.9023:0.0	.	152	Q9GZP7	VN1R1_HUMAN	H	152	ENSP00000322339:P152H	ENSP00000322339:P152H	P	-	2	0	VN1R1	62659212	0.904000	0.30761	0.002000	0.10522	0.008000	0.06430	1.682000	0.37628	1.140000	0.42260	0.644000	0.83932	CCC	.	.	none		0.463	VN1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466464.1	NM_020633		T	57967400	G	T	57967400	3	4	42	1	0	0	0	0	1	0	0	0	17193	1232	43	4	610	4	VN1R1	19	57967400	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	320738	57967400	1161583	362	15314											
CSNK2A1	1457	hgsc.bcm.edu	37	chr20	472918	472918	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ctgatagtctacaagtagctCaggacctttgaagtatcggg	11	11	11	8	1	2	2	1	2	1	0	3	3	2	3	1	2	2	3	1	2	6	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr20:472918C>T	ENST00000217244.3	-	9	976	c.601G>A	c.(601-603)Gag>Aag	p.E201K	CSNK2A1_ENST00000400217.2_Missense_Mutation_p.E65K|CSNK2A1_ENST00000400227.3_Missense_Mutation_p.E201K|CSNK2A1_ENST00000349736.5_Missense_Mutation_p.E201K	NM_177559.2	NP_808227.1	P68400	CSK21_HUMAN	casein kinase 2, alpha 1 polypeptide	201	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)			ACAAGTAGCTCAGGACCTTTG	0.388																																					p.E201K		Atlas-SNP	.											.	CSNK2A1	36	.	0			c.G601A						PASS	.						88	81	83					20																	472918		2203	4300	6503	SO:0001583	missense	1457	exon8			GTAGCTCAGGACC	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.601G>A	20.37:g.472918C>T	ENSP00000217244:p.Glu201Lys	94	0	0		59	13	0.220339	NM_001895	B4DYS6|D3DVV8|P19138|P20426|Q14013|Q5U065	Missense_Mutation	SNP	ENST00000217244.3	37	CCDS13003.1	.	.	.	.	.	.	.	.	.	.	C	35	5.500490	0.96355	.	.	ENSG00000101266	ENST00000400227;ENST00000349736;ENST00000217244;ENST00000381973;ENST00000400217	T;T;T;T	0.71103	1.52;1.52;1.52;-0.54	4.83	4.83	0.62350	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	0.86615	0.5975	H	0.98295	4.195	0.80722	D	1	P	0.48089	0.905	P	0.49085	0.6	D	0.91949	0.5569	10	0.87932	D	0	-5.5019	17.4514	0.87593	0.0:1.0:0.0:0.0	.	201	P68400	CSK21_HUMAN	K	201;201;201;201;65	ENSP00000383086:E201K;ENSP00000339247:E201K;ENSP00000217244:E201K;ENSP00000383076:E65K	ENSP00000217244:E201K	E	-	1	0	CSNK2A1	420918	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.580000	0.82523	2.674000	0.91012	0.650000	0.86243	GAG	.	.	none		0.388	CSNK2A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077466.1	NM_001895		T	472918	C	T	472918	3	4	42	1	0	0	0	0	1	0	0	0	3959	835	29	2	598	2	CSNK2A1	20	472918	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10		472918	62552602	363	15315											
CSNK2A1	1457	hgsc.bcm.edu	37	chr20	485848	485848	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tttacctcggcctaattttcGaaccagctggtagtcatctt	8	15	7	11	2	2	0	1	0	1	0	4	1	2	0	3	2	3	2	3	2	4	7			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr20:485848G>A	ENST00000217244.3	-	4	502	c.127C>T	c.(127-129)Cga>Tga	p.R43*	CSNK2A1_ENST00000400217.2_5'UTR|CSNK2A1_ENST00000400227.3_Nonsense_Mutation_p.R43*|CSNK2A1_ENST00000349736.5_Nonsense_Mutation_p.R43*	NM_177559.2	NP_808227.1	P68400	CSK21_HUMAN	casein kinase 2, alpha 1 polypeptide	43	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)			CCTAATTTTCGAACCAGCTGG	0.338																																					p.R43X		Atlas-SNP	.											.	CSNK2A1	36	.	0			c.C127T						PASS	.						79	66	70					20																	485848		2203	4299	6502	SO:0001587	stop_gained	1457	exon3			ATTTTCGAACCAG	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.127C>T	20.37:g.485848G>A	ENSP00000217244:p.Arg43*	567	1	0.00176367		421	105	0.249406	NM_001895	B4DYS6|D3DVV8|P19138|P20426|Q14013|Q5U065	Nonsense_Mutation	SNP	ENST00000217244.3	37	CCDS13003.1	.	.	.	.	.	.	.	.	.	.	G	37	6.022125	0.97211	.	.	ENSG00000101266	ENST00000400227;ENST00000349736;ENST00000217244;ENST00000381973	.	.	.	4.56	1.35	0.21983	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.2591	13.1247	0.59346	0.0:0.0:0.4164:0.5836	.	.	.	.	X	43	.	ENSP00000217244:R43X	R	-	1	2	CSNK2A1	433848	1.000000	0.71417	0.997000	0.53966	0.974000	0.67602	1.156000	0.31712	0.210000	0.20664	0.555000	0.69702	CGA	.	.	none		0.338	CSNK2A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077466.1	NM_001895		A	485848	G	A	485848	4	1	42	1	0	0	0	0	0	1	0	0	3959	1066	37	1	1092	1	CSNK2A1	20	485848	Nonsense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	12930	485848	62539672	364	15316											
HAO1	54363	hgsc.bcm.edu	37	chr20	7920952	7920952	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cctggaaaatgctgcaatatTatcagccaaagtttcttcat	13	13	6	9	0	3	0	2	0	1	0	3	1	3	1	2	1	3	3	2	1	6	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr20:7920952T>G	ENST00000378789.3	-	1	169	c.118A>C	c.(118-120)Aat>Cat	p.N40H		NM_017545.2	NP_060015.1	Q9UJM8	HAOX1_HUMAN	hydroxyacid oxidase (glycolate oxidase) 1	40	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)			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						GCTGCAATATTATCAGCCAAA	0.303																																					p.N40H		Atlas-SNP	.											.	HAO1	71	.	0			c.A118C						PASS	.						58	56	57					20																	7920952		2203	4300	6503	SO:0001583	missense	54363	exon1			CAATATTATCAGC	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.118A>C	20.37:g.7920952T>G	ENSP00000368066:p.Asn40His	109	0	0		87	14	0.16092	NM_017545	Q14CQ0|Q9UPZ0|Q9Y3I7	Missense_Mutation	SNP	ENST00000378789.3	37	CCDS13100.1	.	.	.	.	.	.	.	.	.	.	T	17.53	3.412595	0.62511	.	.	ENSG00000101323	ENST00000378789	T	0.51574	0.7	5.16	5.16	0.70880	Aldolase-type TIM barrel (1);FMN-dependent dehydrogenase (1);	0.043429	0.85682	D	0.000000	T	0.79393	0.4438	H	0.97707	4.06	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.86768	0.1971	10	0.87932	D	0	0.3185	14.2604	0.66080	0.0:0.0:0.0:1.0	.	40;40	A8K058;Q9UJM8	.;HAOX1_HUMAN	H	40	ENSP00000368066:N40H	ENSP00000368066:N40H	N	-	1	0	HAO1	7868952	1.000000	0.71417	0.992000	0.48379	0.745000	0.42441	6.312000	0.72840	2.060000	0.61445	0.459000	0.35465	AAT	.	.	none		0.303	HAO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077926.2			G	7920952	T	G	7920952	3	3	42	1	0	0	0	0	1	0	0	0	6960	1754	61	5	1026	5	HAO1	20	7920952	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	7435104	7920952	55104568	365	15317											
CSRP2BP	57325	hgsc.bcm.edu	37	chr20	18131484	18131484	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtcgtcatgttggcaatgtAcaacttgtctctggaaggaa	10	12	12	7	1	2	0	1	0	1	0	4	2	2	2	0	4	2	3	0	4	5	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr20:18131484A>T	ENST00000435364.3	+	3	739	c.398A>T	c.(397-399)tAc>tTc	p.Y133F	CSRP2BP_ENST00000489634.2_Missense_Mutation_p.Y5F|CSRP2BP_ENST00000377681.3_Missense_Mutation_p.Y133F	NM_020536.4	NP_065397	Q9H8E8	CSR2B_HUMAN	CSRP2 binding protein	133					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						TTGGCAATGTACAACTTGTCT	0.413																																					p.Y133F		Atlas-SNP	.											.	CSRP2BP	80	.	0			c.A398T						PASS	.						264	246	252					20																	18131484		2203	4300	6503	SO:0001583	missense	57325	exon3			CAATGTACAACTT	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.398A>T	20.37:g.18131484A>T	ENSP00000392318:p.Tyr133Phe	213	0	0		186	54	0.290323	NM_020536	A2A2I5|Q96GW6|Q96IH3|Q9HBF0|Q9UIY5	Missense_Mutation	SNP	ENST00000435364.3	37	CCDS13133.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.737051	0.89482	.	.	ENSG00000149474	ENST00000278816;ENST00000377681;ENST00000435364;ENST00000489634	T;T;T;T	0.36878	1.84;1.84;1.84;1.23	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	T	0.55752	0.1940	L	0.58510	1.815	0.80722	D	1	D;D	0.67145	0.996;0.993	D;D	0.70935	0.971;0.956	T	0.58962	-0.7543	10	0.66056	D	0.02	-6.9195	15.1792	0.72941	1.0:0.0:0.0:0.0	.	5;133	Q9H8E8-2;Q9H8E8	.;CSR2B_HUMAN	F	133;133;133;5	ENSP00000278816:Y133F;ENSP00000366909:Y133F;ENSP00000392318:Y133F;ENSP00000425909:Y5F	ENSP00000278816:Y133F	Y	+	2	0	CSRP2BP	18079484	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.564000	0.90726	2.044000	0.60594	0.455000	0.32223	TAC	.	.	none		0.413	CSRP2BP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078152.5	NM_020536		T	18131484	A	T	18131484	3	4	42	1	0	0	0	0	1	0	0	0	3970	391	14	5	408	5	CSRP2BP	20	18131484	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	10210532	18131484	44894036	366	15318											
CSRP2BP	57325	hgsc.bcm.edu	37	chr20	18131517	18131517	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggaaggaagtggacgtcaagGttatttcaggtggaaagaag	14	8	16	3	1	2	1	2	0	0	1	2	5	2	5	0	6	0	1	0	6	6	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr20:18131517G>C	ENST00000435364.3	+	3	772	c.431G>C	c.(430-432)gGt>gCt	p.G144A	CSRP2BP_ENST00000489634.2_Missense_Mutation_p.G16A|CSRP2BP_ENST00000377681.3_Missense_Mutation_p.G144A	NM_020536.4	NP_065397	Q9H8E8	CSR2B_HUMAN	CSRP2 binding protein	144					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						GGACGTCAAGGTTATTTCAGG	0.378																																					p.G144A		Atlas-SNP	.											.	CSRP2BP	80	.	0			c.G431C						PASS	.						250	233	239					20																	18131517		2203	4300	6503	SO:0001583	missense	57325	exon3			GTCAAGGTTATTT	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.431G>C	20.37:g.18131517G>C	ENSP00000392318:p.Gly144Ala	209	0	0		186	55	0.295699	NM_020536	A2A2I5|Q96GW6|Q96IH3|Q9HBF0|Q9UIY5	Missense_Mutation	SNP	ENST00000435364.3	37	CCDS13133.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.738635	0.89573	.	.	ENSG00000149474	ENST00000278816;ENST00000377681;ENST00000435364;ENST00000489634	T;T;T;T	0.20069	2.38;2.37;2.38;2.1	5.1	5.1	0.69264	.	0.000000	0.85682	D	0.000000	T	0.46308	0.1386	M	0.64997	1.995	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.995	T	0.38887	-0.9640	10	0.56958	D	0.05	-8.237	18.8794	0.92351	0.0:0.0:1.0:0.0	.	16;144	Q9H8E8-2;Q9H8E8	.;CSR2B_HUMAN	A	144;144;144;16	ENSP00000278816:G144A;ENSP00000366909:G144A;ENSP00000392318:G144A;ENSP00000425909:G16A	ENSP00000278816:G144A	G	+	2	0	CSRP2BP	18079517	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	9.052000	0.93855	2.527000	0.85204	0.557000	0.71058	GGT	.	.	none		0.378	CSRP2BP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078152.5	NM_020536		C	18131517	G	C	18131517	3	2	42	1	0	0	0	0	1	0	0	0	3970	1261	44	4	441	4	CSRP2BP	20	18131517	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	33	18131517	44894003	367	15319											
SEC23B	10483	hgsc.bcm.edu	37	chr20	18492908	18492908	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaactttgggcctgtaatttCtgttttcaaagaaatcaggt	12	15	8	6	0	3	1	2	0	1	1	3	1	3	1	1	2	1	2	1	2	4	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr20:18492908C>T	ENST00000336714.3	+	3	693	c.261C>T	c.(259-261)ttC>ttT	p.F87F	SEC23B_ENST00000494645.1_3'UTR|SEC23B_ENST00000377465.1_Silent_p.F87F|SEC23B_ENST00000377475.3_Silent_p.F87F|SEC23B_ENST00000262544.2_Silent_p.F87F	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)	87					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						CCTGTAATTTCTGTTTTCAAA	0.229																																					p.F87F		Atlas-SNP	.											.	SEC23B	70	.	0			c.C261T						PASS	.						28	30	29					20																	18492908		2198	4287	6485	SO:0001819	synonymous_variant	10483	exon3			TAATTTCTGTTTT	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.261C>T	20.37:g.18492908C>T		866	1	0.00115473		700	82	0.117143	NM_032985	D3DW33|Q503A9|Q5W183|Q9BS15|Q9BSI2|Q9H1D7	Silent	SNP	ENST00000336714.3	37	CCDS13137.1																																																																																			.	.	none		0.229	SEC23B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078184.5			T	18492908	C	T	18492908	2	4	42	1	0	0	0	0	0	0	0	1	14007	912	32	2		2	SEC23B	20	18492908	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	361391	18492908	44532612	368	15320											
RIN2	54453	hgsc.bcm.edu	37	chr20	19977369	19977369	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagcactttctctgataaaGaatttccaagaagaacaagc	16	9	8	8	0	1	4	0	1	1	3	3	5	2	5	1	1	3	1	1	1	7	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr20:19977369G>T	ENST00000255006.6	+	11	2543	c.2394G>T	c.(2392-2394)aaG>aaT	p.K798N	RIN2_ENST00000484638.1_3'UTR|RIN2_ENST00000440354.2_Missense_Mutation_p.K316N	NM_001242581.1|NM_018993.3	NP_001229510.1|NP_061866.1	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	749	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						CTCTGATAAAGAATTTCCAAG	0.532																																					p.K798N		Atlas-SNP	.											.	RIN2	126	.	0			c.G2394T						PASS	.						72	77	75					20																	19977369		1969	4164	6133	SO:0001583	missense	54453	exon11			GATAAAGAATTTC	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.2394G>T	20.37:g.19977369G>T	ENSP00000255006:p.Lys798Asn	155	0	0		118	34	0.288136	NM_001242581	Q00425|Q5TFT8|Q9BQL3|Q9H071	Missense_Mutation	SNP	ENST00000255006.6	37	CCDS56182.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.677559	0.88445	.	.	ENSG00000132669	ENST00000255006;ENST00000440354	T;T	0.32515	1.45;1.45	5.69	5.69	0.88448	Vacuolar sorting protein 9, subgroup (1);Vacuolar sorting protein 9 (2);	0.052451	0.85682	D	0.000000	T	0.60248	0.2254	M	0.80508	2.5	0.80722	D	1	P;D	0.89917	0.883;1.0	B;D	0.79784	0.444;0.993	T	0.60301	-0.7290	9	.	.	.	-35.8035	19.4007	0.94629	0.0:0.0:1.0:0.0	.	316;749	E7EPJ1;Q8WYP3	.;RIN2_HUMAN	N	798;316	ENSP00000255006:K798N;ENSP00000391239:K316N	.	K	+	3	2	RIN2	19925369	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	4.072000	0.57563	2.682000	0.91365	0.655000	0.94253	AAG	.	.	none		0.532	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1			T	19977369	G	T	19977369	3	4	42	1	0	0	0	0	1	0	0	0	13387	933	33	4	2285	4	RIN2	20	19977369	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	1484461	19977369	43048151	369	15321											
C20orf186	149954	hgsc.bcm.edu	37	chr20	31671452	31671452	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgtgggcaggcttcaccggcGagagctgcagcctggagaaa	9	6	16	10	2	1	2	1	0	0	2	1	4	1	2	2	4	3	4	2	4	1	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr20:31671452G>A	ENST00000375483.3	+	3	449	c.449G>A	c.(448-450)cGa>cAa	p.R150Q		NM_182519.2	NP_872325.2	P59827	BPIB4_HUMAN	BPI fold containing family B, member 4	150	Gly-rich.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										CTTCACCGGCGAGAGCTGCAG	0.642																																					p.R150Q		Atlas-SNP	.											C20orf186,NS,carcinoma,+1,1	.	.	1	0			c.G449A						scavenged	.						43	44	44					20																	31671452		2203	4300	6503	SO:0001583	missense	149954	exon3			ACCGGCGAGAGCT	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.449G>A	20.37:g.31671452G>A	ENSP00000364632:p.Arg150Gln	138	2	0.0144928		100	27	0.27	NM_182519	Q5TDX6	Missense_Mutation	SNP	ENST00000375483.3	37	CCDS13213.2	.	.	.	.	.	.	.	.	.	.	G	11.88	1.769766	0.31320	.	.	ENSG00000186191	ENST00000375483	T	0.01495	4.83	3.28	2.32	0.28847	.	0.230809	0.28883	N	0.013835	T	0.01661	0.0053	L	0.32530	0.975	0.18873	N	0.999989	B	0.21147	0.052	B	0.08055	0.003	T	0.44421	-0.9329	10	0.87932	D	0	-7.3415	6.7308	0.23383	0.1358:0.0:0.8642:0.0	.	150	P59827	BPIB4_HUMAN	Q	150	ENSP00000364632:R150Q	ENSP00000364632:R150Q	R	+	2	0	BPIFB4	31135113	0.088000	0.21588	0.762000	0.31397	0.036000	0.12997	1.645000	0.37238	0.715000	0.32103	-0.369000	0.07265	CGA	.	.	none		0.642	BPIFB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078655.5	NM_182519		A	31671452	G	A	31671452	3	1	42	1	0	0	0	0	1	0	0	0	2100	1058	37	1	459	1	C20orf186	20	31671452	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	11694083	31671452	31354068	370	15322											
TGIF2	60436	hgsc.bcm.edu	37	chr20	35219312	35219312	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtcttgtatattcattccaGatatgtaactggttcatcaa	11	16	7	7	0	4	1	3	0	1	1	5	1	5	1	1	2	1	3	1	2	5	8			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr20:35219312G>T	ENST00000373874.2	+	3	391		c.e3-1		TGIF2-C20orf24_ENST00000558530.1_Intron|RP5-977B1.11_ENST00000561134.1_RNA|TGIF2_ENST00000373872.4_Splice_Site	NM_001199514.1|NM_001199515.1	NP_001186443.1|NP_001186444.1	Q9GZN2	TGIF2_HUMAN	TGFB-induced factor homeobox 2						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)				ATTCATTCCAGATATGTAACT	0.502																																					.		Atlas-SNP	.											.	TGIF2	26	.	0			c.193-1G>T						PASS	.						137	153	148					20																	35219312		2203	4300	6503	SO:0001630	splice_region_variant	60436	exon3			ATTCCAGATATGT	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.193-1G>T	20.37:g.35219312G>T		100	0	0		84	19	0.22619	NM_001199513	B2R9U3|E1P5T9|H0YNI0	Splice_Site	SNP	ENST00000373874.2	37	CCDS13278.1	.	.	.	.	.	.	.	.	.	.	G	18.97	3.736257	0.69189	.	.	ENSG00000118707	ENST00000373874;ENST00000373872	.	.	.	5.61	4.66	0.58398	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3415	0.60547	0.0756:0.0:0.9244:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TGIF2	34652726	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.414000	0.97362	1.366000	0.46076	0.561000	0.74099	.	.	.	none		0.502	TGIF2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079004.2	NM_021809	Intron	T	35219312	G	T	35219312	5	4	42	1	0	0	0	0	0	0	1	0	15841	956	33	4	198	4	TGIF2	20	35219312	Splice_Site	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	3547860	35219312	27806208	371	15323											
NFATC2	4773	hgsc.bcm.edu	37	chr20	50048903	50048903	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtgagtagtggatcacaggcGaggcctgctggttggtcgga	7	9	18	7	2	1	1	1	1	0	0	2	4	1	3	1	6	1	3	1	6	1	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr20:50048903G>A	ENST00000396009.3	-	9	2642	c.2423C>T	c.(2422-2424)tCg>tTg	p.S808L	NFATC2_ENST00000609943.1_Missense_Mutation_p.S788L|NFATC2_ENST00000414705.1_Missense_Mutation_p.S788L|NFATC2_ENST00000371564.3_Missense_Mutation_p.S808L|NFATC2_ENST00000609507.1_Missense_Mutation_p.S589L|NFATC2_ENST00000610033.1_Missense_Mutation_p.S589L	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	808					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)	p.S808L(2)	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)					GATCACAGGCGAGGCCTGCTG	0.647																																					p.S808L		Atlas-SNP	.											NFATC2,NS,carcinoma,0,2	NFATC2	112	2	2	Substitution - Missense(2)	lung(2)	c.C2423T						PASS	.						47	50	49					20																	50048903		2203	4300	6503	SO:0001583	missense	4773	exon9			ACAGGCGAGGCCT	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.2423C>T	20.37:g.50048903G>A	ENSP00000379330:p.Ser808Leu	112	0	0		65	22	0.338462	NM_012340	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Missense_Mutation	SNP	ENST00000396009.3	37	CCDS13437.1	.	.	.	.	.	.	.	.	.	.	G	15.26	2.780159	0.49891	.	.	ENSG00000101096	ENST00000371564;ENST00000396009;ENST00000414705	T;T;T	0.18960	2.19;2.18;2.21	5.45	5.45	0.79879	.	0.135690	0.50627	D	0.000108	T	0.15003	0.0362	L	0.36672	1.1	0.48901	D	0.999727	P;P;D;P	0.54601	0.931;0.913;0.967;0.931	B;B;B;B	0.34489	0.081;0.17;0.173;0.184	T	0.12400	-1.0549	10	0.11794	T	0.64	-4.4372	19.296	0.94122	0.0:0.0:1.0:0.0	.	788;788;808;808	B5B2N9;B5B2P2;Q13469;B5B2N8	.;.;NFAC2_HUMAN;.	L	808;808;788	ENSP00000360619:S808L;ENSP00000379330:S808L;ENSP00000396471:S788L	ENSP00000360619:S808L	S	-	2	0	NFATC2	49482310	1.000000	0.71417	0.903000	0.35520	0.152000	0.21847	9.452000	0.97615	2.563000	0.86464	0.650000	0.86243	TCG	.	.	none		0.647	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340		A	50048903	G	A	50048903	3	1	42	1	0	0	0	0	1	0	0	0	10371	1059	37	1	410	1	NFATC2	20	50048903	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	14829591	50048903	12976617	372	15324											
BMP7	655	hgsc.bcm.edu	37	chr20	55748291	55748291	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgtggttggtggcgttcaTgtaggagttcagagggaagg	7	10	20	4	2	2	1	2	0	0	1	2	3	2	3	0	7	0	4	0	7	2	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr20:55748291T>C	ENST00000395863.3	-	6	1616	c.1111A>G	c.(1111-1113)Atg>Gtg	p.M371V	BMP7_ENST00000460817.1_5'UTR|BMP7_ENST00000395864.3_Missense_Mutation_p.M305V|BMP7_ENST00000450594.2_Missense_Mutation_p.M371V	NM_001719.2	NP_001710.1	P18075	BMP7_HUMAN	bone morphogenetic protein 7	371					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)			GTGGCGTTCATGTAGGAGTTC	0.632																																					p.M371V		Atlas-SNP	.											.	BMP7	60	.	0			c.A1111G						PASS	.						214	132	160					20																	55748291		2203	4300	6503	SO:0001583	missense	655	exon6			CGTTCATGTAGGA		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.1111A>G	20.37:g.55748291T>C	ENSP00000379204:p.Met371Val	63	0	0		39	15	0.384615	NM_001719	Q9H512|Q9NTQ7	Missense_Mutation	SNP	ENST00000395863.3	37	CCDS13455.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.7|24.7	4.564597|4.564597	0.86439|0.86439	.|.	.|.	ENSG00000101144|ENSG00000101144	ENST00000433911|ENST00000395863;ENST00000395864;ENST00000450594	.|D;D;D	.|0.88124	.|-2.34;-2.34;-2.34	4.84|4.84	4.84|4.84	0.62591|0.62591	.|Transforming growth factor-beta, C-terminal (3);	.|0.034872	.|0.85682	.|D	.|0.000000	D|D	0.90338|0.90338	0.6977|0.6977	L|L	0.40543|0.40543	1.245|1.245	0.80722|0.80722	D|D	1|1	.|P;D;D	.|0.76494	.|0.902;0.994;0.999	.|P;D;D	.|0.91635	.|0.795;0.913;0.999	D|D	0.91561|0.91561	0.5264|0.5264	5|10	.|0.87932	.|D	.|0	.|.	14.7165|14.7165	0.69272|0.69272	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|305;371;371	.|B1AKZ9;P18075;B1AL00	.|.;BMP7_HUMAN;.	R|V	292|371;305;371	.|ENSP00000379204:M371V;ENSP00000379205:M305V;ENSP00000398687:M371V	.|ENSP00000379204:M371V	H|M	-|-	2|1	0|0	BMP7|BMP7	55181698|55181698	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.930000|7.930000	0.87610|0.87610	1.946000|1.946000	0.56461|0.56461	0.482000|0.482000	0.46254|0.46254	CAT|ATG	.	.	none		0.632	BMP7-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079831.2			C	55748291	T	C	55748291	3	2	42	1	0	0	0	0	1	0	0	0	1465	1464	51	3	192	3	BMP7	20	55748291	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	5699388	55748291	7277229	373	15325											
RAB22A	57403	hgsc.bcm.edu	37	chr20	56929269	56929269	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctattcatgcaatttttgtAgagaccagcgcaaaaaacgc	14	11	7	9	2	2	1	1	0	1	1	2	2	2	1	1	0	3	3	1	0	6	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr20:56929269A>G	ENST00000244040.3	+	6	716	c.435A>G	c.(433-435)gtA>gtG	p.V145V		NM_020673.2	NP_065724.1	Q9UL26	RB22A_HUMAN	RAB22A, member RAS oncogene family	145					endocytosis (GO:0006897)|endosome organization (GO:0007032)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|kidney(1)|large_intestine(2)|pancreas(1)	6	all_epithelial(3;5.09e-14)|Lung NSC(12;0.000122)|all_lung(29;0.00042)		BRCA - Breast invasive adenocarcinoma(13;6.2e-12)|Epithelial(14;4.73e-08)|all cancers(14;4.83e-07)			CAATTTTTGTAGAGACCAGCG	0.393																																					p.V145V		Atlas-SNP	.											.	RAB22A	15	.	0			c.A435G						PASS	.						93	92	93					20																	56929269		2203	4300	6503	SO:0001819	synonymous_variant	57403	exon6			TTTTGTAGAGACC	AF091034	CCDS33497.1	20q13	2008-07-03			ENSG00000124209	ENSG00000124209		"RAB, member RAS oncogene"	9764	protein-coding gene	gene with protein product		612966					Standard	NM_020673		Approved		uc002xyz.3	Q9UL26	OTTHUMG00000032844	ENST00000244040.3:c.435A>G	20.37:g.56929269A>G		79	0	0		73	14	0.191781	NM_020673	B3KR86|E1P605|Q8TF12|Q9H4E6	Silent	SNP	ENST00000244040.3	37	CCDS33497.1																																																																																			.	.	none		0.393	RAB22A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079880.2			G	56929269	A	G	56929269	2	3	42	1	0	0	0	0	0	0	0	1	12924	407	15	3		3	RAB22A	20	56929269	Silent	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	1180978	56929269	6096251	374	15326											
STX16	8675	hgsc.bcm.edu	37	chr20	57227077	57227077	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgagacatggccaccaggcgTttaaccgacgctttcttgtt	8	12	10	11	3	1	1	0	1	1	1	1	3	1	1	3	2	1	3	3	2	1	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr20:57227077T>C	ENST00000371141.4	+	1	739	c.15T>C	c.(13-15)cgT>cgC	p.R5R	STX16-NPEPL1_ENST00000530122.1_Silent_p.R5R|STX16_ENST00000371132.4_Silent_p.R5R|STX16_ENST00000361770.5_Silent_p.R5R|STX16_ENST00000358029.4_Silent_p.R5R|STX16_ENST00000355957.5_Silent_p.R5R|STX16_ENST00000361830.3_Silent_p.R5R|STX16_ENST00000496003.1_3'UTR|STX16_ENST00000359617.4_Intron	NM_001001433.2	NP_001001433.1	O14662	STX16_HUMAN	syntaxin 16	5					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)			CCACCAGGCGTTTAACCGACG	0.542																																					p.R5R		Atlas-SNP	.											.	STX16	36	.	0			c.T15C						PASS	.						104	100	101					20																	57227077		2203	4300	6503	SO:0001819	synonymous_variant	8675	exon1			CAGGCGTTTAACC	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.15T>C	20.37:g.57227077T>C		68	0	0		42	10	0.238095	NM_001134772	A6NK32|A6NN69|A8MPP0|B7ZBN1|B7ZBN2|B7ZBN3|E1P5M0|E1P607|O14661|O14663|O60517|Q5W084|Q5W086|Q5W087|Q5XKI6|Q6GMS8|Q9H0Z0|Q9H1T7|Q9H1T8|Q9UIX5	Silent	SNP	ENST00000371141.4	37	CCDS13468.1																																																																																			.	.	none		0.542	STX16-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080517.2	NM_001001433		C	57227077	T	C	57227077	2	2	42	1	0	0	0	0	0	0	0	1	15354	1712	60	3		3	STX16	20	57227077	Silent	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10	297808	57227077	5798443	375	15327											
OGFR	11054	hgsc.bcm.edu	37	chr20	61443664	61443664	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agcacttccaggcgccgctgGtccgcttcttcctggaggag	5	9	13	14	3	1	0	0	0	1	0	4	2	4	2	4	4	1	3	4	4	0	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr20:61443664G>A	ENST00000290291.6	+	7	722	c.697G>A	c.(697-699)Gtc>Atc	p.V233I	OGFR_ENST00000370461.1_Missense_Mutation_p.V181I	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	233					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)					GGCGCCGCTGGTCCGCTTCTT	0.672																																					p.V233I		Atlas-SNP	.											.	OGFR	63	.	0			c.G697A						PASS	.						20	17	18					20																	61443664		2123	4194	6317	SO:0001583	missense	11054	exon7			CCGCTGGTCCGCT	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.697G>A	20.37:g.61443664G>A	ENSP00000290291:p.Val233Ile	112	0	0		73	22	0.30137	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Missense_Mutation	SNP	ENST00000290291.6	37	CCDS13504.1	.	.	.	.	.	.	.	.	.	.	G	13.56	2.272510	0.40194	.	.	ENSG00000060491	ENST00000290291;ENST00000370468;ENST00000357163;ENST00000370469;ENST00000370461	T;T;T	0.53857	1.49;0.6;1.18	4.72	3.53	0.40419	Opioid growth factor receptor (OGFr) conserved domain (1);	0.250853	0.38778	N	0.001574	T	0.46946	0.1419	L	0.37750	1.13	0.28516	N	0.913283	P;B;B	0.42908	0.793;0.029;0.029	P;B;B	0.45449	0.481;0.037;0.037	T	0.41734	-0.9492	10	0.29301	T	0.29	-15.2161	13.7306	0.62785	0.0901:0.0:0.9099:0.0	.	233;216;233	B3KMQ6;Q05BV5;Q9NZT2	.;.;OGFR_HUMAN	I	233;233;233;88;181	ENSP00000290291:V233I;ENSP00000359499:V233I;ENSP00000359491:V181I	ENSP00000290291:V233I	V	+	1	0	OGFR	60914109	1.000000	0.71417	0.308000	0.25141	0.523000	0.34469	7.454000	0.80714	2.129000	0.65627	0.561000	0.74099	GTC	.	.	none		0.672	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1			A	61443664	G	A	61443664	3	1	42	1	0	0	0	0	1	0	0	0	10852	1261	44	2	723	2	OGFR	20	61443664	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	4216587	61443664	1581856	376	15328											
ZNF512B	57473	hgsc.bcm.edu	37	chr20	62597525	62597525	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	actgttcctccctgtggcacGaggtgctttgttctccgacc	4	13	10	14	2	1	0	0	0	1	0	4	2	3	0	4	2	1	4	4	2	0	3	rs371234637		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr20:62597525G>A	ENST00000450537.1	-	5	1063	c.1003C>T	c.(1003-1005)Cgt>Tgt	p.R335C	ZNF512B_ENST00000369888.1_Missense_Mutation_p.R335C|ZNF512B_ENST00000217130.3_Missense_Mutation_p.R335C			Q96KM6	Z512B_HUMAN	zinc finger protein 512B	335					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)					CCTGTGGCACGAGGTGCTTTG	0.582																																					p.R335C		Atlas-SNP	.											ZNF512B,NS,lymphoid_neoplasm,+1,1	ZNF512B	72	1	0			c.C1003T						PASS	.	G	CYS/ARG	2,4402	6.2+/-15.9	0,2,2200	76	72	73		1003	4.4	0.1	20		73	0,8600		0,0,4300	no	missense	ZNF512B	NM_020713.1	180	0,2,6500	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging	335/893	62597525	2,13002	2202	4300	6502	SO:0001583	missense	57473	exon5			TGGCACGAGGTGC	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.1003C>T	20.37:g.62597525G>A	ENSP00000393795:p.Arg335Cys	182	0	0		133	25	0.18797	NM_020713	Q08AK9|Q9ULM4	Missense_Mutation	SNP	ENST00000450537.1	37	CCDS13548.1	.	.	.	.	.	.	.	.	.	.	G	11.14	1.551719	0.27739	4.54E-4	0.0	ENSG00000196700	ENST00000369888;ENST00000450537;ENST00000217130	T;T;T	0.26810	1.71;1.71;1.71	5.43	4.42	0.53409	.	0.669254	0.14337	N	0.325977	T	0.34832	0.0911	L	0.47716	1.5	0.09310	N	0.999999	D	0.76494	0.999	P	0.54924	0.764	T	0.11227	-1.0596	10	0.87932	D	0	-18.6947	10.2751	0.43506	0.0:0.0:0.6755:0.3245	.	335	Q96KM6	Z512B_HUMAN	C	335	ENSP00000358904:R335C;ENSP00000393795:R335C;ENSP00000217130:R335C	ENSP00000217130:R335C	R	-	1	0	ZNF512B	62067969	0.026000	0.19158	0.119000	0.21687	0.022000	0.10575	2.040000	0.41203	2.532000	0.85374	0.585000	0.79938	CGT	.	.	weak		0.582	ZNF512B-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080246.1	NM_020713		A	62597525	G	A	62597525	3	1	42	1	0	0	0	0	1	0	0	0	17972	1058	37	1	1727	1	ZNF512B	20	62597525	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	1153861	62597525	427995	377	15329											
NCAM2	4685	hgsc.bcm.edu	37	chr21	22710786	22710786	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cactcgtatgtgatgcggaaGgggagcctattccagaaatc	11	9	12	9	2	0	2	0	1	0	1	3	4	1	4	2	3	2	1	2	3	4	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr21:22710786G>A	ENST00000400546.1	+	8	1225	c.976G>A	c.(976-978)Ggg>Agg	p.G326R	NCAM2_ENST00000535285.1_Missense_Mutation_p.G351R|NCAM2_ENST00000284894.7_Missense_Mutation_p.G184R	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	326	Ig-like C2-type 4.				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)		TGATGCGGAAGGGGAGCCTAT	0.388																																					p.G326R		Atlas-SNP	.											.	NCAM2	220	.	0			c.G976A						PASS	.						69	66	67					21																	22710786		1894	4116	6010	SO:0001583	missense	4685	exon8			GCGGAAGGGGAGC		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.976G>A	21.37:g.22710786G>A	ENSP00000383392:p.Gly326Arg	163	0	0		156	39	0.25	NM_004540	A8MQ06|B7Z841|Q7Z7F2	Missense_Mutation	SNP	ENST00000400546.1	37	CCDS42910.1	.	.	.	.	.	.	.	.	.	.	G	27.7	4.852909	0.91355	.	.	ENSG00000154654	ENST00000400546;ENST00000284894;ENST00000535285	T;T;T	0.79940	-1.32;-1.32;-1.32	5.8	5.8	0.92144	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.046370	0.85682	D	0.000000	D	0.93835	0.8028	H	0.97635	4.045	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	0.95498	0.8575	10	0.87932	D	0	-16.7196	18.6141	0.91296	0.0:0.0:1.0:0.0	.	351;184;326	B7Z841;B7Z5K2;O15394	.;.;NCAM2_HUMAN	R	326;184;351	ENSP00000383392:G326R;ENSP00000284894:G184R;ENSP00000441887:G351R	ENSP00000284894:G184R	G	+	1	0	NCAM2	21632657	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	6.717000	0.74707	2.736000	0.93811	0.591000	0.81541	GGG	.	.	none		0.388	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540		A	22710786	G	A	22710786	3	1	42	1	0	0	0	0	1	0	0	0	10212	1000	35	2	1006	2	NCAM2	21	22710786	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10		22710786	25419109	378	15330											
SON	6651	hgsc.bcm.edu	37	chr21	34924682	34924682	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgtcagcctacgagcgctctAtgatgtcccctatggctgag	7	11	11	12	2	2	2	1	2	1	0	3	3	3	2	3	1	3	2	3	1	3	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr21:34924682A>C	ENST00000356577.4	+	3	3620	c.3145A>C	c.(3145-3147)Atg>Ctg	p.M1049L	SON_ENST00000381692.2_Intron|SON_ENST00000300278.4_Missense_Mutation_p.M1049L|SON_ENST00000290239.6_Missense_Mutation_p.M1049L|SON_ENST00000381679.4_Missense_Mutation_p.M1049L	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	1049	14 X 6 AA repeats of [ED]-R-S-M-M-S.				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						CGAGCGCTCTATGATGTCCCC	0.502																																					p.M1049L		Atlas-SNP	.											.	SON	343	.	0			c.A3145C						PASS	.						103	96	99					21																	34924682		2203	4300	6503	SO:0001583	missense	6651	exon3			CGCTCTATGATGT	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.3145A>C	21.37:g.34924682A>C	ENSP00000348984:p.Met1049Leu	145	0	0		129	46	0.356589	NM_032195	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	37	CCDS13629.1	.	.	.	.	.	.	.	.	.	.	A	17.86	3.493740	0.64186	.	.	ENSG00000159140	ENST00000356577;ENST00000290239;ENST00000300278;ENST00000381679	T;T;T;T	0.27720	1.65;1.65;1.65;1.65	6.06	6.06	0.98353	.	0.000000	0.64402	D	0.000003	T	0.51534	0.1680	M	0.68593	2.085	0.33298	D	0.564499	P;P;P;P;P	0.52577	0.93;0.885;0.954;0.93;0.93	P;P;P;P;P	0.62435	0.902;0.801;0.711;0.902;0.902	T	0.64630	-0.6362	10	0.51188	T	0.08	.	14.5614	0.68140	1.0:0.0:0.0:0.0	.	1049;1049;730;1049;1049	P18583-10;P18583;P18583-2;P18583-3;P18583-6	.;SON_HUMAN;.;.;.	L	1049	ENSP00000348984:M1049L;ENSP00000290239:M1049L;ENSP00000300278:M1049L;ENSP00000371095:M1049L	ENSP00000290239:M1049L	M	+	1	0	SON	33846552	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.024000	0.64090	2.324000	0.78689	0.533000	0.62120	ATG	.	.	none		0.502	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		C	34924682	A	C	34924682	3	2	42	1	0	0	0	0	1	0	0	0	14941	449	16	5	3155	5	SON	21	34924682	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	12213896	34924682	13205213	379	15331											
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230415	23230416	+	In_Frame_Ins	INS	-	-	CAG																															tcagttggaagcagccgatcINScagcctgcggagcctgtggg																								rs180844836	byFrequency	TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr22:23230415_23230416insCAG	ENST00000526893.1	+	1	456_457	c.182_183insCAG	c.(181-186)tccagc>tcCAGcagc	p.61_62SS>SSS	IGLL5_ENST00000531372.1_In_Frame_Ins_p.61_62SS>SSS|IGLL5_ENST00000532223.2_In_Frame_Ins_p.61_62SS>SSS|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	61						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						AGCAGCCGATCCAGCCTGCGGA	0.653																																					p.S61delinsSS		Pindel,Atlas-Indel	.											.	IGLL5	26	.	0			c.182_183insCAG						PASS	.																																			SO:0001652	inframe_insertion	100423062	exon1			.	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.183_185dupCAG	22.37:g.23230416_23230418dupCAG	ENSP00000431254:p.Ser61_Ser61dup	113	0	.		65	14	0.215	NM_001178126		In_Frame_Ins	INS	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.653	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		CAG	23230416	-	CAG	23230415	7	5	42	1	0	1	1	0	0	0	0	0	7603	855	30	0	184	0	IGLL5	22	23230415	In_Frame_Ins	INS	-	TCGA-GS-A9TZ-01A-11D-A38X-10		23230415	28074151	380	15332											
RHBDD3	25807	hgsc.bcm.edu	37	chr22	29660104	29660104	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcaggaatctcagcgtgccCaggtggcactcctgctgcca	7	8	12	14	1	1	0	1	0	1	0	3	1	2	1	3	3	5	3	3	3	1	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr22:29660104C>T	ENST00000216085.7	-	4	676	c.252G>A	c.(250-252)ctG>ctA	p.L84L	CTA-984G1.5_ENST00000433125.1_RNA	NM_012265.1	NP_036397.1	Q9Y3P4	RHBD3_HUMAN	rhomboid domain containing 3	84					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						TCAGCGTGCCCAGGTGGCACT	0.697																																					p.L84L		Atlas-SNP	.											.	RHBDD3	17	.	0			c.G252A						PASS	.						10	10	10					22																	29660104		2180	4269	6449	SO:0001819	synonymous_variant	25807	exon4			CGTGCCCAGGTGG	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.252G>A	22.37:g.29660104C>T		87	0	0		73	27	0.369863	NM_012265	Q6I9X3|Q9UGQ7	Silent	SNP	ENST00000216085.7	37	CCDS13850.1																																																																																			.	.	none		0.697	RHBDD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321085.1	NM_012265		T	29660104	C	T	29660104	2	4	42	1	0	0	0	0	0	0	0	1	13333	581	21	2		2	RHBDD3	22	29660104	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	6429689	29660104	21644462	381	15333											
THOC5	8563	hgsc.bcm.edu	37	chr22	29938874	29938876	+	In_Frame_Del	DEL	CTT	CTT	-																															tccaaacatttggtgatctcCttctgtaggtgcatcacctc																										TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr22:29938874_29938876delCTT	ENST00000490103.1	-	5	546_548	c.424_426delAAG	c.(424-426)aagdel	p.K142del	THOC5_ENST00000397872.1_In_Frame_Del_p.K142del|THOC5_ENST00000397873.2_In_Frame_Del_p.K142del|THOC5_ENST00000397871.1_In_Frame_Del_p.K142del	NM_003678.4	NP_003669.4	Q13769	THOC5_HUMAN	THO complex 5	142	Interaction with CSF1R. {ECO:0000250}.|Interaction with THOC7.				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						TGGTGATCTCCTTCTGTAGGTGC	0.453																																					p.142_143del		Atlas-Indel	.											.	THOC5	58	.	0			c.425_427del						PASS	.																																			SO:0001651	inframe_deletion	8563	exon5			.	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.424_426delAAG	22.37:g.29938874_29938876delCTT	ENSP00000420306:p.Lys142del	59	0	0		64	15	0.234375	NM_001002879	O60839|Q9UPZ5	In_Frame_Del	DEL	ENST00000490103.1	37	CCDS13859.1																																																																																			.	.	none		0.453	THOC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322097.1	NM_003678		-	29938876	CTT	-	29938874	7	5	42	1	0	1	0	1	0	0	0	0	15883	680	24	0	1689	0	THOC5	22	29938874	In_Frame_Del	DEL	CTT	TCGA-GS-A9TZ-01A-11D-A38X-10	278770	29938874	21365692	382	15334											
PNPLA5	150379	hgsc.bcm.edu	37	chr22	44287689	44287689	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcattcggtggcgcccacGtggtgggcgcccaggtagcc	5	6	17	13	4	0	0	0	0	0	0	1	0	0	0	3	6	1	2	3	6	1	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr22:44287689G>A	ENST00000597664.1	-	1	201	c.72C>T	c.(70-72)caC>caT	p.H24H	PNPLA5_ENST00000216177.4_Silent_p.H24H|PNPLA5_ENST00000593866.1_Silent_p.H24H|PNPLA5_ENST00000381198.2_Silent_p.H24H			Q7Z6Z6	PLPL5_HUMAN	patatin-like phospholipase domain containing 5	24	Patatin.				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)				TGGCGCCCACGTGGTGGGCGC	0.711																																					p.H24H		Atlas-SNP	.											.	PNPLA5	46	.	0			c.C72T						PASS	.						4	5	5					22																	44287689		1620	3066	4686	SO:0001819	synonymous_variant	150379	exon1			GCCCACGTGGTGG	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.72C>T	22.37:g.44287689G>A		111	0	0		83	21	0.253012	NM_138814	B1AHL8|B3KPR1|Q6ZST0	Silent	SNP	ENST00000597664.1	37																																																																																				.	.	none		0.711	PNPLA5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000075667.4	NM_138814		A	44287689	G	A	44287689	2	1	42	1	0	0	0	0	0	0	0	1	12177	1136	40	1		1	PNPLA5	22	44287689	Silent	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	14348815	44287689	7016877	383	15335											
SMC1B	27127	hgsc.bcm.edu	37	chr22	45789587	45789587	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gctgacgttttccctcatggGtatcaatcccagcattctgc	7	13	8	13	1	3	1	2	1	1	0	5	1	5	1	2	1	2	4	2	1	2	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr22:45789587G>A	ENST00000357450.4	-	9	1471	c.1472C>T	c.(1471-1473)aCc>aTc	p.T491I	SMC1B_ENST00000404354.3_Missense_Mutation_p.T491I	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	491	Flexible hinge.				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)		TCCCTCATGGGTATCAATCCC	0.348																																					p.T491I		Atlas-SNP	.											.	SMC1B	215	.	0			c.C1472T						PASS	.						134	119	124					22																	45789587		1849	4099	5948	SO:0001583	missense	27127	exon9			TCATGGGTATCAA	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.1472C>T	22.37:g.45789587G>A	ENSP00000350036:p.Thr491Ile	315	0	0		270	76	0.281481	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Missense_Mutation	SNP	ENST00000357450.4	37	CCDS43027.1	.	.	.	.	.	.	.	.	.	.	G	11.86	1.764130	0.31228	.	.	ENSG00000077935	ENST00000357450;ENST00000404354	D;D	0.85013	-1.93;-1.93	6.07	-11.8	0.00035	SMCs flexible hinge (1);RecF/RecN/SMC (1);	0.886598	0.09782	N	0.756484	T	0.67702	0.2921	N	0.19112	0.55	0.09310	N	1	B;B;B	0.19445	0.019;0.036;0.036	B;B;B	0.18871	0.006;0.023;0.023	T	0.54925	-0.8220	10	0.45353	T	0.12	.	10.1489	0.42780	0.1425:0.0951:0.6149:0.1475	.	491;491;491	Q8NDV3;Q8NDV3-2;Q8NDV3-3	SMC1B_HUMAN;.;.	I	491	ENSP00000350036:T491I;ENSP00000385902:T491I	ENSP00000350036:T491I	T	-	2	0	SMC1B	44168251	0.000000	0.05858	0.001000	0.08648	0.680000	0.39746	-1.271000	0.02828	-2.950000	0.00293	-0.375000	0.07067	ACC	.	.	none		0.348	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674		A	45789587	G	A	45789587	3	1	42	1	0	0	0	0	1	0	0	0	14797	1261	44	2	2303	2	SMC1B	22	45789587	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	1501898	45789587	5514979	384	15336											
FBLN1	2192	hgsc.bcm.edu	37	chr22	45958992	45958992	+	Intron	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggagggctttttcaccacccGgaaggtgagcccccacagtg	8	7	13	13	1	1	1	1	1	0	0	1	3	1	3	4	4	1	1	4	4	1	2	rs11551		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chr22:45958992G>A	ENST00000327858.6	+	15	1792				FBLN1_ENST00000402984.3_Missense_Mutation_p.R671Q|FBLN1_ENST00000348697.2_Intron|FBLN1_ENST00000442170.2_Intron|FBLN1_ENST00000262722.7_Missense_Mutation_p.R633Q	NM_006486.2	NP_006477	P23142	FBLN1_HUMAN	fibulin 1						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)		TTCACCACCCGGAAGGTGAGC	0.667													G|||	1	0.000199681	0.0008	0.0	5008	,	,		13832	0.0		0.0	False		,,,				2504	0.0				p.R633Q		Atlas-SNP	.											.	FBLN1	143	.	0			c.G1898A						PASS	.	G	GLN/ARG,,	1,4405	2.1+/-5.4	0,1,2202	43	48	46		1898,,	-3	1	22	dbSNP_52	46	0,8600		0,0,4300	no	missense,intron,intron	FBLN1	NM_001996.3,NM_006485.3,NM_006486.2	43,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,	633/684,,	45958992	1,13005	2203	4300	6503	SO:0001627	intron_variant	2192	exon15			CCACCCGGAAGGT		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.1698-11399G>A	22.37:g.45958992G>A		92	0	0		81	26	0.320988	NM_001996	B0QY42|B1AHL4|P23143|P23144|P37888|Q5TIC4|Q8TBH8|Q9HBQ5|Q9UC21|Q9UGR4|Q9UH41	Missense_Mutation	SNP	ENST00000327858.6	37	CCDS14067.1	.	.	.	.	.	.	.	.	.	.	G	12.58	1.981906	0.34942	2.27E-4	0.0	ENSG00000077942	ENST00000402984;ENST00000262722	D;D	0.86030	-2.06;-1.93	4.72	-3.03	0.05429	.	.	.	.	.	T	0.69806	0.3152	N	0.17248	0.465	0.58432	D	0.999998	B;B	0.20052	0.041;0.038	B;B	0.08055	0.002;0.003	T	0.48387	-0.9040	9	0.25751	T	0.34	.	11.7537	0.51863	0.8271:0.0:0.1729:0.0	.	671;633	B1AHL2;P23142-4	.;.	Q	671;633	ENSP00000385521:R671Q;ENSP00000262722:R633Q	ENSP00000262722:R633Q	R	+	2	0	FBLN1	44337656	0.998000	0.40836	0.977000	0.42913	0.972000	0.66771	1.151000	0.31651	-0.447000	0.07138	-0.444000	0.05651	CGG	G|1.000	.	weak		0.667	FBLN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322287.1	NM_006486		A	45958992	G	A	45958992	1	1	42	0	1	0	0	0	0	0	0	0	5706	1116	39	1		1	FBLN1	22	45958992	Intron	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	169405	45958992	5345574	385	15337											
FRMPD4	9758	hgsc.bcm.edu	37	chrX	12728588	12728588	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacggctggatactaccggcTgcttgttgattccaggaggt	7	11	14	9	2	0	1	0	1	0	0	1	4	1	3	2	5	3	4	2	5	2	5			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chrX:12728588T>A	ENST00000380682.1	+	14	2047	c.1541T>A	c.(1540-1542)cTg>cAg	p.L514Q		NM_014728.3	NP_055543.2	Q14CM0	FRPD4_HUMAN	FERM and PDZ domain containing 4	514	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						TACTACCGGCTGCTTGTTGAT	0.473																																					p.L514Q		Atlas-SNP	.											.	FRMPD4	214	.	0			c.T1541A						PASS	.						166	154	158					X																	12728588		2203	4300	6503	SO:0001583	missense	9758	exon14			ACCGGCTGCTTGT	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.1541T>A	X.37:g.12728588T>A	ENSP00000370057:p.Leu514Gln	59	0	0		67	47	0.701493	NM_014728	A8K0X9|O15032	Missense_Mutation	SNP	ENST00000380682.1	37	CCDS35201.1	.	.	.	.	.	.	.	.	.	.	T	15.98	2.993601	0.54041	.	.	ENSG00000169933	ENST00000380682;ENST00000429478;ENST00000304087	T	0.26957	1.7	5.47	5.47	0.80525	FERM domain (1);	0.000000	0.64402	D	0.000015	T	0.53786	0.1818	M	0.80422	2.495	0.45097	D	0.998116	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.993	T	0.60316	-0.7287	10	0.87932	D	0	.	14.5914	0.68368	0.0:0.0:0.0:1.0	.	506;514	B7ZLE1;Q14CM0	.;FRPD4_HUMAN	Q	514;505;503	ENSP00000370057:L514Q	ENSP00000304583:L503Q	L	+	2	0	FRMPD4	12638509	1.000000	0.71417	0.086000	0.20670	0.057000	0.15508	7.621000	0.83083	1.825000	0.53177	0.486000	0.48141	CTG	.	.	none		0.473	FRMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055771.1	XM_045712		A	12728588	T	A	12728588	3	1	42	1	0	0	0	0	1	0	0	0	6067	1580	55	5	1595	5	FRMPD4	23	12728588	Missense_Mutation	SNP	T	TCGA-GS-A9TZ-01A-11D-A38X-10		12728588	142541972	386	15338											
PDHA1	5160	hgsc.bcm.edu	37	chrX	19369482	19369482	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgggctcacggctttactttCacccggggcctttccgtccg	3	11	11	16	5	2	0	2	0	0	0	4	0	4	0	4	4	1	2	4	4	1	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chrX:19369482C>T	ENST00000422285.2	+	4	480	c.375C>T	c.(373-375)ttC>ttT	p.F125F	PDHA1_ENST00000379806.5_Silent_p.F163F|PDHA1_ENST00000540249.1_Silent_p.F125F|PDHA1_ENST00000545074.1_Silent_p.F132F|PDHA1_ENST00000379805.3_Silent_p.F125F			P08559	ODPA_HUMAN	pyruvate dehydrogenase (lipoamide) alpha 1	125					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)					GCTTTACTTTCACCCGGGGCC	0.502																																					p.F163F		Atlas-SNP	.											.	PDHA1	85	.	0			c.C489T						PASS	.						104	97	99					X																	19369482		2203	4300	6503	SO:0001819	synonymous_variant	5160	exon5			TACTTTCACCCGG		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.375C>T	X.37:g.19369482C>T		245	0	0		273	181	0.663004	NM_001173454	A5YVE9|B2R5P7|B7Z3T7|B7Z3X5|Q53H41|Q5JPT8|Q9NP12|Q9UBJ8|Q9UBU0|Q9UNG4|Q9UNG5	Silent	SNP	ENST00000422285.2	37	CCDS14192.1																																																																																			.	.	none		0.502	PDHA1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055977.1			T	19369482	C	T	19369482	2	4	42	1	0	0	0	0	0	0	0	1	11673	825	29	2		2	PDHA1	23	19369482	Silent	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	6640894	19369482	135901078	387	15339											
MAP7D2	256714	hgsc.bcm.edu	37	chrX	20074801	20074801	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ggcaaccctacactcaccatCatgtcctccgggtccaatgg	9	8	8	16	1	2	0	2	0	0	0	5	0	5	0	5	3	2	1	5	3	3	1			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chrX:20074801C>T	ENST00000379651.3	-	4	499	c.481G>A	c.(481-483)Gat>Aat	p.D161N	MAP7D2_ENST00000379643.5_Missense_Mutation_p.D161N|MAP7D2_ENST00000543767.1_Missense_Mutation_p.D32N|MAP7D2_ENST00000443379.3_Missense_Mutation_p.D161N|MAP7D2_ENST00000452324.3_Missense_Mutation_p.D117N	NM_152780.3	NP_689993.2	Q96T17	MA7D2_HUMAN	MAP7 domain containing 2	161					microtubule cytoskeleton organization (GO:0000226)	microtubule (GO:0005874)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	37						CACTCACCATCATGTCCTCCG	0.587																																					p.D161N		Atlas-SNP	.											.	MAP7D2	165	.	0			c.G481A						PASS	.						115	74	88					X																	20074801		2203	4300	6503	SO:0001583	missense	256714	exon4			CACCATCATGTCC	BC089400	CCDS14195.1, CCDS55384.1, CCDS55385.1, CCDS55386.1	Xp22.12	2008-02-05			ENSG00000184368	ENSG00000184368			25899	protein-coding gene	gene with protein product						12477932	Standard	NM_152780		Approved	FLJ14503	uc010nfo.2	Q96T17	OTTHUMG00000021228	ENST00000379651.3:c.481G>A	X.37:g.20074801C>T	ENSP00000368972:p.Asp161Asn	34	0	0		44	30	0.681818	NM_001168466	B7Z2J8|B7Z3S7|B9EGC7|C9JMA4|C9JYW0|Q5EBN1|Q5JPS7|Q6PIC7|Q8N792	Missense_Mutation	SNP	ENST00000379651.3	37	CCDS14195.1	.	.	.	.	.	.	.	.	.	.	C	13.63	2.295847	0.40594	.	.	ENSG00000184368	ENST00000379651;ENST00000379643;ENST00000543767;ENST00000443379;ENST00000452324;ENST00000330274	T;T;T;T;T	0.11930	2.73;2.73;2.73;2.73;2.73	5.03	5.03	0.67393	.	0.081663	0.49916	D	0.000125	T	0.16685	0.0401	L	0.32530	0.975	0.42193	D	0.991732	P;P;P;P;P;P	0.51351	0.906;0.835;0.944;0.734;0.906;0.9	B;P;P;P;B;P	0.47645	0.444;0.553;0.553;0.549;0.351;0.553	T	0.03025	-1.1081	10	0.29301	T	0.29	.	17.726	0.88365	0.0:1.0:0.0:0.0	.	161;117;161;161;161;32	B7Z3S7;C9JYW0;Q96T17-2;B5ME62;Q96T17;F5GYC2	.;.;.;.;MA7D2_HUMAN;.	N	161;161;32;161;117;161	ENSP00000368972:D161N;ENSP00000368964:D161N;ENSP00000440691:D32N;ENSP00000388239:D161N;ENSP00000413301:D117N	ENSP00000332677:D161N	D	-	1	0	MAP7D2	19984722	0.992000	0.36948	0.623000	0.29173	0.295000	0.27426	3.135000	0.50546	2.204000	0.70986	0.506000	0.49869	GAT	.	.	none		0.587	MAP7D2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056001.1	NM_152780		T	20074801	C	T	20074801	3	4	42	1	0	0	0	0	1	0	0	0	9277	826	29	2	1892	2	MAP7D2	23	20074801	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	705319	20074801	135195759	388	15340											
DMD	1756	hgsc.bcm.edu	37	chrX	33146262	33146262	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttatctgcagcttttactcAccagatgagacctcagacat	11	13	6	11	0	3	3	2	1	1	3	3	4	3	3	2	0	3	2	2	0	2	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chrX:33146262A>G	ENST00000378677.2	-	1	214		c.e1+1		DMD_ENST00000357033.4_Intron|DMD_ENST00000288447.4_Intron	NM_004009.3|NM_004010.3|NM_004011.3|NM_004012.3|NM_004014.2	NP_004000|NP_004001.1|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)				GCTTTTACTCACCAGATGAGA	0.418																																					.		Atlas-SNP	.											.	DMD	2127	.	0			c.19+2T>C						PASS	.						112	90	97					X																	33146262		1857	4091	5948	SO:0001630	splice_region_variant	1756	exon2			TTACTCACCAGAT	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	ENST00000378677.2:c.19+1T>C	X.37:g.33146262A>G		87	0	0		99	63	0.636364	NM_004009	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Splice_Site	SNP	ENST00000378677.2	37	CCDS55395.1	.	.	.	.	.	.	.	.	.	.	A	15.17	2.754929	0.49362	.	.	ENSG00000198947	ENST00000378677	.	.	.	5.25	5.25	0.73442	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.0527	0.53515	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DMD	33056183	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	5.789000	0.69029	2.056000	0.61249	0.441000	0.28932	.	.	.	none		0.418	DMD-006	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056187.2	NM_004006	Intron	G	33146262	A	G	33146262	5	3	42	1	0	0	0	0	0	0	1	0	4582	173	6	3	11583	3	DMD	23	33146262	Splice_Site	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	13071461	33146262	122124298	389	15341											
DDX3X	1654	hgsc.bcm.edu	37	chrX	41206603	41206603	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gtttggtgccagagactaccGacaaagtagcggtgccagca	11	7	13	10	2	0	1	0	0	0	1	0	3	0	1	3	2	5	3	3	2	3	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chrX:41206603G>A	ENST00000399959.2	+	16	2663	c.1808G>A	c.(1807-1809)cGa>cAa	p.R603Q	DDX3X_ENST00000478993.1_3'UTR|DDX3X_ENST00000441189.2_Intron|DDX3X_ENST00000457138.2_Missense_Mutation_p.R587Q|RN7SL15P_ENST00000582825.1_RNA	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	603	Gly/Ser-rich.|Interaction with GSK3B.				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						AGAGACTACCGACAAagtagc	0.502										HNSCC(61;0.18)																											p.R603Q		Atlas-SNP	.											.	DDX3X	138	.	0			c.G1808A						PASS	.						66	73	70					X																	41206603		2188	4289	6477	SO:0001583	missense	1654	exon16			ACTACCGACAAAG	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.1808G>A	X.37:g.41206603G>A	ENSP00000382840:p.Arg603Gln	101	0	0		126	83	0.65873	NM_001356	A8K538|B4E3E8|O15536	Missense_Mutation	SNP	ENST00000399959.2	37	CCDS43931.1	.	.	.	.	.	.	.	.	.	.	g	24.2	4.505398	0.85282	.	.	ENSG00000215301	ENST00000399959;ENST00000457138	T;T	0.24538	1.85;1.87	5.48	5.48	0.80851	.	0.055112	0.85682	D	0.000000	T	0.58906	0.2155	M	0.91717	3.235	0.80722	D	1	D;D;D;D	0.64830	0.994;0.994;0.994;0.994	P;P;P;P	0.61201	0.885;0.885;0.885;0.885	T	0.70055	-0.4977	10	0.87932	D	0	-29.9248	18.4946	0.90860	0.0:0.0:1.0:0.0	.	473;587;615;603	B4DLU5;B4E3E8;Q59GX6;O00571	.;.;.;DDX3X_HUMAN	Q	603;587	ENSP00000382840:R603Q;ENSP00000392494:R587Q	ENSP00000382840:R603Q	R	+	2	0	DDX3X	41091547	1.000000	0.71417	0.978000	0.43139	0.970000	0.65996	9.431000	0.97494	2.309000	0.77851	0.591000	0.81541	CGA	.	.	none		0.502	DDX3X-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056253.1	NM_024005		A	41206603	G	A	41206603	3	1	42	1	0	0	0	0	1	0	0	0	4360	1058	37	1	1870	1	DDX3X	23	41206603	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	8060341	41206603	114063957	390	15342											
PIM2	11040	hgsc.bcm.edu	37	chrX	48775891	48775891	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggagggggccgagtcgataCtcggcctcgaacgcttcccg	7	6	15	13	6	0	0	0	0	0	0	4	4	1	1	3	4	2	1	3	4	2	2			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chrX:48775891C>G	ENST00000376509.4	-	2	282	c.93G>C	c.(91-93)gaG>gaC	p.E31D		NM_006875.3	NP_006866.2	Q9P1W9	PIM2_HUMAN	Pim-2 proto-oncogene, serine/threonine kinase	31					apoptotic mitochondrial changes (GO:0008637)|cell proliferation (GO:0008283)|G1/S transition of mitotic cell cycle (GO:0000082)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|positive regulation of autophagy (GO:0010508)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|response to virus (GO:0009615)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			lung(3)|stomach(1)	4						CGAGTCGATACTCGGCCTCGA	0.667																																					p.E31D		Atlas-SNP	.											.	PIM2	31	.	0			c.G93C						PASS	.						35	32	33					X																	48775891		2202	4300	6502	SO:0001583	missense	11040	exon2			TCGATACTCGGCC	U77735	CCDS14312.1	Xp11.23	2014-06-25	2014-06-25		ENSG00000102096	ENSG00000102096			8987	protein-coding gene	gene with protein product		300295	"pim-2 oncogene"			9804974	Standard	NM_006875		Approved		uc004dls.3	Q9P1W9	OTTHUMG00000024132	ENST00000376509.4:c.93G>C	X.37:g.48775891C>G	ENSP00000365692:p.Glu31Asp	71	0	0		109	85	0.779817	NM_006875	A8K4G6|Q99739	Missense_Mutation	SNP	ENST00000376509.4	37	CCDS14312.1	.	.	.	.	.	.	.	.	.	.	C	8.849	0.944106	0.18281	.	.	ENSG00000102096	ENST00000376509	T	0.12569	2.67	3.9	-1.03	0.10102	Protein kinase-like domain (1);	0.277470	0.28989	N	0.013499	T	0.06645	0.0170	N	0.19112	0.55	0.28880	N	0.894448	B	0.18968	0.032	B	0.15484	0.013	T	0.39292	-0.9621	10	0.15952	T	0.53	.	8.1126	0.30924	0.0:0.4588:0.0:0.5412	.	31	Q9P1W9	PIM2_HUMAN	D	31	ENSP00000365692:E31D	ENSP00000365692:E31D	E	-	3	2	PIM2	48660835	0.001000	0.12720	0.982000	0.44146	0.965000	0.64279	-1.883000	0.01623	-0.398000	0.07679	0.544000	0.68410	GAG	.	.	none		0.667	PIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060805.1			G	48775891	C	G	48775891	3	3	42	1	0	0	0	0	1	0	0	0	11937	564	20	4	862	4	PIM2	23	48775891	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	7569288	48775891	106494669	391	15343											
FGF16	8823	hgsc.bcm.edu	37	chrX	76709750	76709750	+	Splice_Site	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcgaggagaactctatgggtCggtaagtttaaggttttttt	9	15	13	4	2	1	1	0	0	1	1	2	3	1	1	0	4	1	3	0	4	4	7	rs376876932		TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chrX:76709750C>T	ENST00000439435.1	+	1	103	c.103C>T	c.(103-105)Cga>Tga	p.R35*				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						CTCTATGGGTCGGTAAGTTTA	0.393																																					p.S35L		Atlas-SNP	.											.	FGF16	16	.	0			c.C104T						PASS	.	C	LEU/SER	0,3122		0,0,1276,570	72	61	64		106	4.3	1	X		64	1,6376		0,1,2302,1771	no	missense-near-splice	FGF16	NM_003868.1	145	0,1,3578,2341	TT,TC,CC,C		0.0157,0.0,0.0105	probably-damaging	126/208	76709750	1,9498	1846	4074	5920	SO:0001630	splice_region_variant	8823	exon1			ATGGGTCGGTAAG	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.104+1C>T	X.37:g.76709750C>T		95	0	0		130	81	0.623077	NM_003868		Missense_Mutation	SNP	ENST00000439435.1	37		.	.	.	.	.	.	.	.	.	.	C	26.3	4.727957	0.89390	0.0	1.57E-4	ENSG00000196468	ENST00000439435	.	.	.	4.3	4.3	0.51218	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3197	0.82945	0.0:1.0:0.0:0.0	.	.	.	.	X	35	.	.	R	+	1	2	FGF16	76596406	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.567000	0.82357	2.107000	0.64212	0.600000	0.82982	CGA	.	.	weak		0.393	FGF16-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000036814.1	NM_003868	Nonsense_Mutation	T	76709750	C	T	76709750	5	4	42	1	0	0	0	0	0	0	1	0	5852	898	31	1	106	1	FGF16	23	76709750	Splice_Site	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	27933859	76709750	78560810	392	15344											
KCNE1L	23630	hgsc.bcm.edu	37	chrX	108867913	108867913	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagcccgcggcagcctcggCgtcggcggtcagggcgcctc	3	4	18	16	7	1	0	1	0	0	0	4	1	1	1	3	6	2	1	3	6	0	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chrX:108867913C>T	ENST00000372101.2	-	1	480	c.337G>A	c.(337-339)Gcc>Acc	p.A113T		NM_012282.2	NP_036414.1	Q9UJ90	KCE1L_HUMAN	KCNE1-like	113					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						GCAGCCTCGGCGTCGGCGGTC	0.746																																					p.A113T		Atlas-SNP	.											.	KCNE1L	8	.	0			c.G337A						PASS	.						4	4	4					X																	108867913		1938	3803	5741	SO:0001583	missense	23630	exon1			CCTCGGCGTCGGC	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.337G>A	X.37:g.108867913C>T	ENSP00000361173:p.Ala113Thr	38	0	0		50	36	0.72	NM_012282		Missense_Mutation	SNP	ENST00000372101.2	37	CCDS14547.1	.	.	.	.	.	.	.	.	.	.	c	9.703	1.154965	0.21371	.	.	ENSG00000176076	ENST00000372101	T	0.70399	-0.48	4.31	2.5	0.30297	.	0.407802	0.20787	N	0.085687	T	0.50667	0.1629	L	0.27053	0.805	0.20074	N	0.999935	B	0.31125	0.309	B	0.23852	0.049	T	0.42899	-0.9424	10	0.52906	T	0.07	-10.0695	5.8092	0.18457	0.0:0.651:0.1631:0.1859	.	113	Q9UJ90	KCE1L_HUMAN	T	113	ENSP00000361173:A113T	ENSP00000361173:A113T	A	-	1	0	KCNE1L	108754569	0.083000	0.21467	0.399000	0.26333	0.231000	0.25187	0.510000	0.22723	0.546000	0.28920	0.597000	0.82753	GCC	.	.	none		0.746	KCNE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057892.1	NM_012282		T	108867913	C	T	108867913	3	4	42	1	0	0	0	0	1	0	0	0	8031	768	27	1	95	1	KCNE1L	23	108867913	Missense_Mutation	SNP	C	TCGA-GS-A9TZ-01A-11D-A38X-10	32158163	108867913	46402647	393	15345											
AFF2	2334	hgsc.bcm.edu	37	chrX	147743486	147743486	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acacgcttggaaactatgatGaaatgaagaatttgctaact	16	11	8	6	1	0	4	0	3	0	1	0	5	0	5	0	1	3	2	0	1	6	4			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chrX:147743486G>A	ENST00000370460.2	+	3	717	c.238G>A	c.(238-240)Gaa>Aaa	p.E80K	AFF2_ENST00000370458.1_Missense_Mutation_p.E76K|AFF2_ENST00000370457.5_Missense_Mutation_p.E76K|AFF2_ENST00000342251.3_Missense_Mutation_p.E76K	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	80					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)					AAACTATGATGAAATGAAGAA	0.403																																					p.E80K		Atlas-SNP	.											.	AFF2	679	.	0			c.G238A						PASS	.						124	124	124					X																	147743486		2203	4300	6503	SO:0001583	missense	2334	exon3			TATGATGAAATGA	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.238G>A	X.37:g.147743486G>A	ENSP00000359489:p.Glu80Lys	213	0	0		272	193	0.709559	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	ENST00000370460.2	37	CCDS14684.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.513184	0.85389	.	.	ENSG00000155966	ENST00000370460;ENST00000370457;ENST00000342251;ENST00000370458	T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05	5.49	5.49	0.81192	.	0.057352	0.64402	D	0.000003	D	0.86740	0.6005	L	0.58583	1.82	0.80722	D	1	D;D;D;D;D;D	0.89917	0.971;0.971;0.971;0.971;0.977;1.0	P;P;P;P;P;D	0.87578	0.783;0.783;0.783;0.783;0.862;0.998	D	0.87917	0.2701	10	0.87932	D	0	.	18.4456	0.90682	0.0:0.0:1.0:0.0	.	80;76;76;76;80;76	P51816-6;P51816-3;P51816-2;P51816-5;P51816;P51816-4	.;.;.;.;AFF2_HUMAN;.	K	80;76;76;76	ENSP00000359489:E80K;ENSP00000359486:E76K;ENSP00000345459:E76K;ENSP00000359487:E76K	ENSP00000345459:E76K	E	+	1	0	AFF2	147551178	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.490000	0.97952	2.297000	0.77311	0.600000	0.82982	GAA	.	.	none		0.403	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025		A	147743486	G	A	147743486	3	1	42	1	0	0	0	0	1	0	0	0	357	1291	45	2	248	2	AFF2	23	147743486	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	38875573	147743486	7527074	394	15346											
NSDHL	50814	hgsc.bcm.edu	37	chrX	152034408	152034408	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agaagaatttcttaaccacaGccatccgccctcatggcatt	12	10	6	13	1	2	2	1	0	1	2	3	2	3	2	4	1	2	1	4	1	3	3			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chrX:152034408G>A	ENST00000370274.3	+	6	783	c.589G>A	c.(589-591)Gcc>Acc	p.A197T	NSDHL_ENST00000440023.1_Missense_Mutation_p.A197T	NM_015922.2	NP_057006.1	Q15738	NSDHL_HUMAN	NAD(P) dependent steroid dehydrogenase-like	197					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)					CTTAACCACAGCCATCCGCCC	0.567																																					p.A197T		Atlas-SNP	.											.	NSDHL	33	.	0			c.G589A						PASS	.						123	112	116					X																	152034408		2203	4300	6503	SO:0001583	missense	50814	exon6			ACCACAGCCATCC	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.589G>A	X.37:g.152034408G>A	ENSP00000359297:p.Ala197Thr	25	0	0		43	27	0.627907	NM_015922	D3DWT6|O00344	Missense_Mutation	SNP	ENST00000370274.3	37	CCDS14717.1	.	.	.	.	.	.	.	.	.	.	G	26.2	4.711312	0.89112	.	.	ENSG00000147383	ENST00000370274;ENST00000440023;ENST00000432467	D;D;D	0.90955	-2.76;-2.76;-2.76	5.89	5.02	0.67125	3-beta hydroxysteroid dehydrogenase/isomerase (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.95027	0.8390	M	0.79926	2.475	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.95132	0.8256	10	0.66056	D	0.02	-0.1274	13.7626	0.62975	0.0:0.1506:0.8494:0.0	.	197	Q15738	NSDHL_HUMAN	T	197	ENSP00000359297:A197T;ENSP00000391854:A197T;ENSP00000396266:A197T	ENSP00000359297:A197T	A	+	1	0	NSDHL	151785064	1.000000	0.71417	0.832000	0.32986	0.674000	0.39518	9.869000	0.99810	1.239000	0.43787	0.529000	0.55759	GCC	.	.	none		0.567	NSDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060927.1	NM_015922		A	152034408	G	A	152034408	3	1	42	1	0	0	0	0	1	0	0	0	10679	971	34	2	607	2	NSDHL	23	152034408	Missense_Mutation	SNP	G	TCGA-GS-A9TZ-01A-11D-A38X-10	4290922	152034408	3236152	395	15347											
FAM50A	9130	hgsc.bcm.edu	37	chrX	153674051	153674051	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cgcggtggaggcagagctcaAgtccagcaccgtgggtgagc	8	5	17	11	3	1	2	1	1	0	1	2	3	2	3	2	4	3	3	2	4	1	0			TCGA-GS-A9TZ-01A-11D-A38X-10	TCGA-GS-A9TZ-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	93217755-b79d-4e32-8e97-76bcd262bae8	96fefcbd-9bc5-4473-be47-0f4c19aa6e57	g.chrX:153674051A>G	ENST00000393600.3	+	2	292	c.182A>G	c.(181-183)aAg>aGg	p.K61R		NM_004699.3	NP_004690.1	Q14320	FA50A_HUMAN	family with sequence similarity 50, member A	61					spermatogenesis (GO:0007283)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|lung(9)|ovary(2)|skin(1)	15	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)					GCAGAGCTCAAGTCCAGCACC	0.627																																					p.K61R		Atlas-SNP	.											.	FAM50A	32	.	0			c.A182G						PASS	.						67	53	57					X																	153674051		2203	4300	6503	SO:0001583	missense	9130	exon2			AGCTCAAGTCCAG	BC000028	CCDS14751.1	Xq28	2008-02-05			ENSG00000071859	ENSG00000071859			18786	protein-coding gene	gene with protein product	"DNA segment on chromosome X (unique) 9928 expressed sequence"	300453				9339379, 9039504	Standard	NM_004699		Approved	DXS9928E, XAP5, HXC-26, 9F	uc004fll.4	Q14320	OTTHUMG00000033292	ENST00000393600.3:c.182A>G	X.37:g.153674051A>G	ENSP00000377225:p.Lys61Arg	84	0	0		95	67	0.705263	NM_004699	A8KAQ4|B2R997|Q5HY37|Q6PJH5	Missense_Mutation	SNP	ENST00000393600.3	37	CCDS14751.1	.	.	.	.	.	.	.	.	.	.	A	19.06	3.754495	0.69648	.	.	ENSG00000071859	ENST00000393600;ENST00000158526	.	.	.	4.71	3.45	0.39498	.	0.000000	0.85682	D	0.000000	T	0.49115	0.1538	M	0.62154	1.92	0.51012	D	0.999904	B	0.31548	0.328	B	0.25506	0.061	T	0.51044	-0.8755	9	0.38643	T	0.18	-43.1027	9.473	0.38853	0.8403:0.0:0.0:0.1597	.	61	Q14320	FA50A_HUMAN	R	61;21	.	ENSP00000158526:K21R	K	+	2	0	FAM50A	153327245	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	5.688000	0.68227	1.658000	0.50742	0.430000	0.28490	AAG	.	.	none		0.627	FAM50A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081643.2	NM_004699		G	153674051	A	G	153674051	3	3	42	1	0	0	0	0	1	0	0	0	5585	72	3	3	188	3	FAM50A	23	153674051	Missense_Mutation	SNP	A	TCGA-GS-A9TZ-01A-11D-A38X-10	1639643	153674051	1596509	396	15348											
PTCHD2	57540	hgsc.bcm.edu	37	chr1	11595630	11595630	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatcctcgttggctcctccGtggattactgcgtccacctg	4	12	9	16	3	0	0	0	0	0	0	5	1	4	1	6	2	2	2	6	2	1	2			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr1:11595630G>A	ENST00000294484.6	+	20	3883	c.3745G>A	c.(3745-3747)Gtg>Atg	p.V1249M	PTCHD2_ENST00000304391.6_Missense_Mutation_p.R135H|PTCHD2_ENST00000389575.3_Missense_Mutation_p.V1249M	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	1249					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)		TGGCTCCTCCGTGGATTACTG	0.647																																					p.V1249M		Atlas-SNP	.											PTCHD2,NS,carcinoma,-2,1	PTCHD2	193	1	0			c.G3745A						PASS	.						68	80	76					1																	11595630		2133	4230	6363	SO:0001583	missense	57540	exon20			TCCTCCGTGGATT	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.3745G>A	1.37:g.11595630G>A	ENSP00000294484:p.Val1249Met	44	0	0		48	5	0.104167	NM_020780	Q5VTU9|Q9UJD6	Missense_Mutation	SNP	ENST00000294484.6	37	CCDS41247.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.12|18.12	3.552516|3.552516	0.65425|0.65425	.|.	.|.	ENSG00000204624|ENSG00000204624	ENST00000304391|ENST00000294484;ENST00000389575	.|D;D	.|0.94457	.|-3.43;-2.84	5.54|5.54	5.54|5.54	0.83059|0.83059	.|Membrane transport protein, MMPL type (1);	.|0.000000	.|0.64402	.|D	.|0.000003	D|D	0.97334|0.97334	0.9128|0.9128	M|M	0.81802|0.81802	2.56|2.56	0.48185|0.48185	D|D	0.999605|0.999605	.|D	.|0.89917	.|1.0	.|D	.|0.91635	.|0.999	D|D	0.97740|0.97740	1.0208|1.0208	6|10	0.87932|0.72032	D|D	0|0.01	-24.6787|-24.6787	18.4583|18.4583	0.90729|0.90729	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1249	.|Q9P2K9	.|PTHD2_HUMAN	H|M	135|1249	.|ENSP00000294484:V1249M;ENSP00000374226:V1249M	ENSP00000303400:R135H|ENSP00000294484:V1249M	R|V	+|+	2|1	0|0	PTCHD2|PTCHD2	11518217|11518217	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.766000|0.766000	0.43426|0.43426	7.578000|7.578000	0.82498|0.82498	2.604000|2.604000	0.88044|0.88044	0.655000|0.655000	0.94253|0.94253	CGT|GTG	.	.	none		0.647	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561		A	11595630	G	A	11595630	3	1	43	1	0	0	0	0	1	0	0	0	12745	1145	40	1	3819	1	PTCHD2	1	11595630	Missense_Mutation	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10		11595630	237654991	1	15349											
CCDC21	64793	hgsc.bcm.edu	37	chr1	26584680	26584680	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agcagaaagtgcgagagagcGaactgcaagtccacagtgcc	14	4	13	10	2	0	2	0	0	0	2	1	5	1	2	2	0	6	2	2	0	3	0			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr1:26584680G>A	ENST00000252992.4	+	6	1215	c.1084G>A	c.(1084-1086)Gaa>Aaa	p.E362K	CEP85_ENST00000451429.2_Missense_Mutation_p.E311K	NM_001281517.1|NM_022778.2	NP_001268446.1|NP_073615.2	Q6P2H3	CEP85_HUMAN	centrosomal protein 85kDa	362						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						GCGAGAGAGCGAACTGCAAGT	0.547																																					p.E362K		Atlas-SNP	.											.	CEP85	61	.	0			c.G1084A						PASS	.						127	114	118					1																	26584680		2203	4300	6503	SO:0001583	missense	64793	exon6			GAGAGCGAACTGC	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.1084G>A	1.37:g.26584680G>A	ENSP00000252992:p.Glu362Lys	73	0	0		85	17	0.2	NM_022778	B4DRL1|D3DPK4|F8W7K4|Q5VY68|Q5VY70|Q9H6Q1|Q9H828|Q9UF52	Missense_Mutation	SNP	ENST00000252992.4	37	CCDS277.1	.	.	.	.	.	.	.	.	.	.	G	36	5.790414	0.96945	.	.	ENSG00000130695	ENST00000451429;ENST00000252992	T;T	0.11604	2.76;2.76	6.04	6.04	0.98038	.	0.047882	0.85682	D	0.000000	T	0.34542	0.0901	M	0.66939	2.045	0.80722	D	1	D;D;D	0.89917	0.981;0.991;1.0	P;P;D	0.77557	0.572;0.653;0.99	T	0.00166	-1.1965	10	0.44086	T	0.13	-16.1413	20.5948	0.99439	0.0:0.0:1.0:0.0	.	311;362;362	F8W7K4;Q6P2H3;Q6P2H3-2	.;CEP85_HUMAN;.	K	311;362	ENSP00000417002:E311K;ENSP00000252992:E362K	ENSP00000252992:E362K	E	+	1	0	CEP85	26457267	1.000000	0.71417	1.000000	0.80357	0.903000	0.53119	9.476000	0.97823	2.873000	0.98535	0.563000	0.77884	GAA	.	.	none		0.547	CEP85-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009492.2	NM_022778		A	26584680	G	A	26584680	3	1	43	1	0	0	0	0	1	0	0	0	2798	1059	37	1	1102	1	CCDC21	1	26584680	Missense_Mutation	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10	14989050	26584680	222665941	2	15350											
SPOCD1	90853	hgsc.bcm.edu	37	chr1	32258931	32258931	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgggccctggcccggaacCgcttgatggagaacatgtcc	7	7	14	13	2	0	2	0	1	0	1	1	4	1	3	4	4	2	2	4	4	2	1			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr1:32258931C>T	ENST00000360482.2	-	13	2762	c.2633G>A	c.(2632-2634)cGg>cAg	p.R878Q	SPOCD1_ENST00000257100.3_Missense_Mutation_p.R371Q|SPOCD1_ENST00000533231.1_Missense_Mutation_p.R878Q|RP11-84A19.3_ENST00000527035.1_RNA|SPOCD1_ENST00000373648.2_3'UTR	NM_144569.4	NP_653170.3	Q6ZMY3	SPOC1_HUMAN	SPOC domain containing 1	878	SPOC.				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)		GGCCCGGAACCGCTTGATGGA	0.647																																					p.R878Q		Atlas-SNP	.											.	SPOCD1	109	.	0			c.G2633A						PASS	.						33	29	30					1																	32258931		2199	4298	6497	SO:0001583	missense	90853	exon13			CGGAACCGCTTGA	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.2633G>A	1.37:g.32258931C>T	ENSP00000353670:p.Arg878Gln	124	0	0		150	28	0.186667	NM_144569	Q24JU3|Q6PI90|Q8N869|Q8N8U0|Q8NBC6|Q96LN6	Missense_Mutation	SNP	ENST00000360482.2	37	CCDS347.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.45|15.45	2.837206|2.837206	0.50951|0.50951	.|.	.|.	ENSG00000134668|ENSG00000134668	ENST00000528579|ENST00000257100;ENST00000360482;ENST00000294514;ENST00000452755;ENST00000533231	.|T;T;T;T	.|0.43688	.|0.94;1.94;0.95;1.95	5.73|5.73	-0.674|-0.674	0.11369|0.11369	.|Spen paralogue and orthologue SPOC, C-terminal (1);	.|.	.|.	.|.	.|.	T|T	0.22003|0.22003	0.0530|0.0530	L|L	0.39633|0.39633	1.23|1.23	0.80722|0.80722	D|D	1|1	.|P;P;P	.|0.40398	.|0.669;0.515;0.716	.|B;B;B	.|0.25405	.|0.053;0.06;0.06	T|T	0.05767|0.05767	-1.0865|-1.0865	5|9	.|0.37606	.|T	.|0.19	-11.3723|-11.3723	5.2404|5.2404	0.15469|0.15469	0.0:0.4735:0.1415:0.385|0.0:0.4735:0.1415:0.385	.|.	.|878;314;878	.|Q6ZMY3-2;E9PPM7;Q6ZMY3	.|.;.;SPOC1_HUMAN	S|Q	252|371;878;238;314;878	.|ENSP00000257100:R371Q;ENSP00000353670:R878Q;ENSP00000399778:R314Q;ENSP00000435851:R878Q	.|ENSP00000257100:R371Q	G|R	-|-	1|2	0|0	SPOCD1|SPOCD1	32031518|32031518	0.006000|0.006000	0.16342|0.16342	0.935000|0.935000	0.37517|0.37517	0.999000|0.999000	0.98932|0.98932	-0.937000|-0.937000	0.03942|0.03942	-0.063000|-0.063000	0.13065|0.13065	0.655000|0.655000	0.94253|0.94253	GGT|CGG	.	.	none		0.647	SPOCD1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000381912.1	NM_144569		T	32258931	C	T	32258931	3	4	43	1	0	0	0	0	1	0	0	0	15093	652	23	1	1033	1	SPOCD1	1	32258931	Missense_Mutation	SNP	C	TCGA-GS-A9U3-01A-11D-A38X-10	5674251	32258931	216991690	3	15351											
C1orf173	127254	hgsc.bcm.edu	37	chr1	75038599	75038599	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagccaccccaccctcagccTctccctcctccgatgtcgct	5	8	5	23	2	2	0	1	0	1	0	6	1	4	0	8	0	2	1	8	0	0	0			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr1:75038599T>C	ENST00000326665.5	-	14	3013	c.2795A>G	c.(2794-2796)gAg>gGg	p.E932G	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		932	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						ACCCTCAGCCTCTCCCTCCTC	0.542																																					p.E932G		Atlas-SNP	.											.	C1orf173	380	.	0			c.A2795G						PASS	.						133	136	135					1																	75038599		2203	4300	6503	SO:0001583	missense	127254	exon14			TCAGCCTCTCCCT																												ENST00000326665.5:c.2795A>G	1.37:g.75038599T>C	ENSP00000322609:p.Glu932Gly	84	0	0		79	16	0.202532	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	37	CCDS30755.1	.	.	.	.	.	.	.	.	.	.	T	15.28	2.786245	0.49997	.	.	ENSG00000178965	ENST00000326665	T	0.18174	2.23	4.73	0.749	0.18381	.	.	.	.	.	T	0.03695	0.0105	L	0.36672	1.1	0.09310	N	1	B	0.21225	0.053	B	0.21917	0.037	T	0.42241	-0.9463	9	0.44086	T	0.13	-6.2511	2.33	0.04233	0.1433:0.085:0.2952:0.4765	.	932	Q5RHP9	CA173_HUMAN	G	932	ENSP00000322609:E932G	ENSP00000322609:E932G	E	-	2	0	C1orf173	74811187	0.000000	0.05858	0.063000	0.19743	0.011000	0.07611	0.421000	0.21280	0.174000	0.19809	-0.460000	0.05396	GAG	.	.	none		0.542	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1			C	75038599	T	C	75038599	3	2	43	1	0	0	0	0	1	0	0	0	2016	1551	54	3	1801	3	C1orf173	1	75038599	Missense_Mutation	SNP	T	TCGA-GS-A9U3-01A-11D-A38X-10	42779668	75038599	174212022	4	15352											
PIP5K1A	8394	hgsc.bcm.edu	37	chr1	151206713	151206713	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gactttgctgcctaaattctAtggactgtactgtgtgcagg	8	14	11	8	0	1	0	0	0	1	0	1	2	1	1	1	2	4	3	1	2	4	5			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr1:151206713A>G	ENST00000368888.4	+	8	1102	c.680A>G	c.(679-681)tAt>tGt	p.Y227C	PIP5K1A_ENST00000409426.1_Missense_Mutation_p.Y215C|PIP5K1A_ENST00000441902.2_Missense_Mutation_p.Y215C|PIP5K1A_ENST00000414290.2_5'Flank|PIP5K1A_ENST00000368890.4_Missense_Mutation_p.Y214C|PIP5K1A_ENST00000464105.1_3'UTR	NM_001135638.1	NP_001129110.1	Q99755	PI51A_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, alpha	227	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				actin cytoskeleton reorganization (GO:0031532)|activation of Rac GTPase activity (GO:0032863)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|fibroblast migration (GO:0010761)|focal adhesion assembly (GO:0048041)|glycerophospholipid metabolic process (GO:0006650)|keratinocyte differentiation (GO:0030216)|phagocytosis (GO:0006909)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|protein targeting to plasma membrane (GO:0072661)|ruffle assembly (GO:0097178)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|kinase binding (GO:0019900)			breast(1)|central_nervous_system(1)|ovary(1)|skin(1)|stomach(1)	5	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;0.181)			CCTAAATTCTATGGACTGTAC	0.418																																					p.Y227C	Pancreas(80;36 1443 2325 16095 21302)	Atlas-SNP	.											.	PIP5K1A	61	.	0			c.A680G						PASS	.						108	99	102					1																	151206713		2203	4300	6503	SO:0001583	missense	8394	exon8			AATTCTATGGACT	U78575	CCDS990.1, CCDS44219.1, CCDS44220.1, CCDS44221.1	1q21.3	2010-04-08			ENSG00000143398	ENSG00000143398			8994	protein-coding gene	gene with protein product		603275				8955136, 10828584	Standard	NM_003557		Approved		uc001exj.3	Q99755	OTTHUMG00000012351	ENST00000368888.4:c.680A>G	1.37:g.151206713A>G	ENSP00000357883:p.Tyr227Cys	193	0	0		218	70	0.321101	NM_001135638	A8K4Q0|B4DIN0|Q99754|Q99756	Missense_Mutation	SNP	ENST00000368888.4	37	CCDS44219.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.358986	0.82353	.	.	ENSG00000143398	ENST00000349792;ENST00000409426;ENST00000441902;ENST00000368890;ENST00000368888	T;T;T;T;T	0.39592	1.07;1.07;1.07;1.07;1.07	4.88	4.88	0.63580	Phosphatidylinositol-4-phosphate 5-kinase, core (2);Phosphatidylinositol-4-phosphate 5-kinase, core, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.60676	0.2287	M	0.84773	2.715	0.80722	D	1	B;D;P;D	0.89917	0.152;1.0;0.881;1.0	P;D;P;D	0.71414	0.511;0.957;0.745;0.973	T	0.68834	-0.5304	10	0.87932	D	0	.	14.6488	0.68780	1.0:0.0:0.0:0.0	.	215;214;227;214	Q99755-4;Q99755-2;Q99755;Q99755-3	.;.;PI51A_HUMAN;.	C	214;215;215;214;227	ENSP00000271663:Y214C;ENSP00000386432:Y215C;ENSP00000415648:Y215C;ENSP00000357885:Y214C;ENSP00000357883:Y227C	ENSP00000271663:Y214C	Y	+	2	0	PIP5K1A	149473337	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.051000	0.93849	2.196000	0.70406	0.473000	0.43528	TAT	.	.	none		0.418	PIP5K1A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034425.2	NM_003557		G	151206713	A	G	151206713	3	3	43	1	0	0	0	0	1	0	0	0	11948	449	16	3	710	3	PIP5K1A	1	151206713	Missense_Mutation	SNP	A	TCGA-GS-A9U3-01A-11D-A38X-10	76168114	151206713	98043908	5	15353											
LY9	4063	hgsc.bcm.edu	37	chr1	160794028	160794028	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccacaatctactgctccataCggaaacctcaggtggtgaga	12	8	9	12	1	2	1	1	1	1	1	3	3	3	2	3	3	4	1	3	3	4	2	rs374075565		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr1:160794028C>T	ENST00000263285.6	+	9	1918	c.1888C>T	c.(1888-1890)Cgg>Tgg	p.R630W	LY9_ENST00000341032.4_Missense_Mutation_p.R496W|LY9_ENST00000392203.4_Missense_Mutation_p.R540W|LY9_ENST00000368041.2_Missense_Mutation_p.R500W|LY9_ENST00000368040.1_Intron|LY9_ENST00000368037.5_Missense_Mutation_p.R616W			Q9HBG7	LY9_HUMAN	lymphocyte antigen 9	630					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)			CTGCTCCATACGGAAACCTCA	0.488																																					p.R630W		Atlas-SNP	.											.	LY9	115	.	0			c.C1888T						PASS	.	C	TRP/ARG	0,4406		0,0,2203	168	161	163		1888	1.7	0	1		163	1,8599	1.2+/-3.3	0,1,4299	no	missense	LY9	NM_002348.2	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	630/656	160794028	1,13005	2203	4300	6503	SO:0001583	missense	4063	exon9			TCCATACGGAAAC	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.1888C>T	1.37:g.160794028C>T	ENSP00000263285:p.Arg630Trp	54	0	0		84	26	0.309524	NM_002348	A8K7N3|Q14775|Q5VYI3|Q6P2J4|Q9H4N5|Q9NQ24	Missense_Mutation	SNP	ENST00000263285.6	37	CCDS30916.1	.	.	.	.	.	.	.	.	.	.	C	8.482	0.859951	0.17178	0.0	1.16E-4	ENSG00000122224	ENST00000368041;ENST00000341032;ENST00000263285;ENST00000392203;ENST00000368037;ENST00000368036	T;T	0.35973	1.34;1.28	3.57	1.66	0.24008	.	1.958810	0.03098	N	0.160758	T	0.13072	0.0317	N	0.08118	0	0.09310	N	1	B;D;D	0.65815	0.0;0.995;0.991	B;P;B	0.50708	0.0;0.648;0.446	T	0.15350	-1.0440	10	0.87932	D	0	-6.4141	5.0343	0.14426	0.0:0.6336:0.2444:0.122	.	496;616;630	E7EME5;Q9HBG7-2;Q9HBG7	.;.;LY9_HUMAN	W	630;496;630;500;576;398	ENSP00000342921:R496W;ENSP00000263285:R630W	ENSP00000263285:R630W	R	+	1	2	LY9	159060652	0.013000	0.17824	0.011000	0.14972	0.006000	0.05464	0.283000	0.18846	0.467000	0.27218	-0.214000	0.12660	CGG	.	.	none		0.488	LY9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060457.3	NM_002348		T	160794028	C	T	160794028	3	4	43	1	0	0	0	0	1	0	0	0	9110	527	19	1	2054	1	LY9	1	160794028	Missense_Mutation	SNP	C	TCGA-GS-A9U3-01A-11D-A38X-10	9587315	160794028	88456593	6	15354											
POGK	57645	hgsc.bcm.edu	37	chr1	166818482	166818482	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aacaactgccaggctgccaaGcagtttggagtattggaaaa	14	8	11	8	0	0	0	0	0	0	0	0	2	0	2	2	3	5	4	2	3	6	3			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr1:166818482G>A	ENST00000367875.1	+	5	1026	c.666G>A	c.(664-666)aaG>aaA	p.K222K	POGK_ENST00000536514.1_Silent_p.K137K|POGK_ENST00000537173.1_Silent_p.K104K|POGK_ENST00000367876.4_Silent_p.K222K			Q9P215	POGK_HUMAN	pogo transposable element with KRAB domain	222					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						AGGCTGCCAAGCAGTTTGGAG	0.552																																					p.K222K	GBM(76;192 1530 30153 48742)	Atlas-SNP	.											.	POGK	54	.	0			c.G666A						PASS	.						49	51	50					1																	166818482		2203	4300	6503	SO:0001819	synonymous_variant	57645	exon5			TGCCAAGCAGTTT	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.666G>A	1.37:g.166818482G>A		75	0	0		95	9	0.0947368	NM_017542	Q5TIJ1|Q8TE07	Silent	SNP	ENST00000367875.1	37	CCDS1254.1																																																																																			.	.	none		0.552	POGK-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000082888.1	NM_017542		A	166818482	G	A	166818482	2	1	43	1	0	0	0	0	0	0	0	1	12194	962	34	2		2	POGK	1	166818482	Silent	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10	6024454	166818482	82432139	7	15355											
OR2T4	127074	hgsc.bcm.edu	37	chr1	248525640	248525640	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcaagctcctatttactcaTcctcctcaccatccacggga	9	12	4	16	1	3	0	3	0	0	0	7	1	7	1	5	1	2	1	5	1	3	4			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr1:248525640T>C	ENST00000366475.1	+	1	758	c.758T>C	c.(757-759)aTc>aCc	p.I253T		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	253						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)			TATTTACTCATCCTCCTCACC	0.517																																					p.I253T		Atlas-SNP	.											OR2T4,brain,glioma,+1,1	OR2T4	126	1	0			c.T758C						PASS	.						135	130	132					1																	248525640		2203	4300	6503	SO:0001583	missense	127074	exon1			TACTCATCCTCCT	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.758T>C	1.37:g.248525640T>C	ENSP00000355431:p.Ile253Thr	13	0	0		47	24	0.510638	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	37	CCDS31113.1	.	.	.	.	.	.	.	.	.	.	T	10.31	1.315398	0.23908	.	.	ENSG00000196944	ENST00000366475	T	0.00402	7.56	3.09	1.94	0.25998	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	D	0.000219	T	0.01523	0.0049	H	0.95151	3.63	0.33277	D	0.561816	D	0.89917	1.0	D	0.85130	0.997	T	0.11299	-1.0593	10	0.87932	D	0	.	7.6506	0.28346	0.0:0.1075:0.0:0.8925	.	253	Q8NH00	OR2T4_HUMAN	T	253	ENSP00000355431:I253T	ENSP00000355431:I253T	I	+	2	0	OR2T4	246592263	1.000000	0.71417	0.061000	0.19648	0.014000	0.08584	4.666000	0.61554	0.295000	0.22570	-0.361000	0.07541	ATC	.	.	none		0.517	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696		C	248525640	T	C	248525640	3	2	43	1	0	0	0	0	1	0	0	0	11036	1435	50	3	760	3	OR2T4	1	248525640	Missense_Mutation	SNP	T	TCGA-GS-A9U3-01A-11D-A38X-10	81707158	248525640	724981	8	15356											
GPR113	165082	hgsc.bcm.edu	37	chr2	26534617	26534617	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcagaaggtggtccagttttCgcagcaccaggctagtaata	11	9	12	9	1	0	1	0	0	0	1	2	1	1	1	2	3	1	6	2	3	4	5	rs201936475	byFrequency	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr2:26534617C>T	ENST00000311519.1	-	11	1978	c.1979G>A	c.(1978-1980)cGa>cAa	p.R660Q	GPR113_ENST00000459892.1_5'UTR|GPR113_ENST00000421160.2_Missense_Mutation_p.R591Q|GPR113_ENST00000541401.1_Missense_Mutation_p.R263Q|GPR113_ENST00000333478.6_Missense_Mutation_p.R461Q	NM_001145168.1	NP_001138640.1	Q8IZF5	GP113_HUMAN	G protein-coupled receptor 113	660					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)					GTCCAGTTTTCGCAGCACCAG	0.547													C|||	4	0.000798722	0.0	0.0043	5008	,	,		21134	0.0		0.0	False		,,,				2504	0.001				p.R660Q		Atlas-SNP	.											GPR113_ENST00000311519,NS,malignant_melanoma,0,5	GPR113	134	5	0			c.G1979A						PASS	.						49	49	49					2																	26534617		2203	4300	6503	SO:0001583	missense	165082	exon11			AGTTTTCGCAGCA	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.1979G>A	2.37:g.26534617C>T	ENSP00000307831:p.Arg660Gln	31	0	0		41	12	0.292683	NM_001145168	B4DF15|E9PEV1|Q53TA5|Q6UXT7|Q6UXX3|Q86SL7|Q8IXD8|Q8TDT3	Missense_Mutation	SNP	ENST00000311519.1	37	CCDS46239.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	0.197	-1.048092	0.01981	.	.	ENSG00000173567	ENST00000541401;ENST00000333478;ENST00000421160;ENST00000311519	T;T;T;T	0.11604	2.76;2.76;2.76;2.76	5.84	-0.949	0.10376	Domain of unknown function DUF3497 (1);	.	.	.	.	T	0.02727	0.0082	N	0.00554	-1.385	0.09310	N	0.999999	B;B;B;B	0.18013	0.025;0.02;0.025;0.02	B;B;B;B	0.19148	0.01;0.024;0.019;0.006	T	0.47824	-0.9087	9	0.15499	T	0.54	-0.1341	10.2306	0.43253	0.0:0.4465:0.0:0.5535	.	591;461;660;263	E9PEV1;Q8IZF5-2;Q8IZF5;F5H1E4	.;.;GP113_HUMAN;.	Q	263;461;591;660	ENSP00000445729:R263Q;ENSP00000327396:R461Q;ENSP00000388537:R591Q;ENSP00000307831:R660Q	ENSP00000307831:R660Q	R	-	2	0	GPR113	26388121	0.000000	0.05858	0.032000	0.17829	0.051000	0.14879	-1.851000	0.01669	-0.127000	0.11661	-1.110000	0.02074	CGA	C|1.000;T|0.000	0.000	strong		0.547	GPR113-004	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316892.1	NM_153835		T	26534617	C	T	26534617	3	4	43	1	0	0	0	0	1	0	0	0	6638	884	31	1	1361	1	GPR113	2	26534617	Missense_Mutation	SNP	C	TCGA-GS-A9U3-01A-11D-A38X-10		26534617	216664756	9	15357											
PLEKHH2	130271	hgsc.bcm.edu	37	chr2	43919728	43919728	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agacaagattatataataagTgtcaagatctggagtcgcta	16	11	9	5	1	2	3	1	0	1	3	3	4	2	4	0	1	0	1	0	1	7	5			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr2:43919728T>C	ENST00000282406.4	+	4	372	c.262T>C	c.(262-264)Tgt>Cgt	p.C88R		NM_172069.3	NP_742066.2	Q8IVE3	PKHH2_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 2	88					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)				ATATAATAAGTGTCAAGATCT	0.313																																					p.C88R		Atlas-SNP	.											.	PLEKHH2	156	.	0			c.T262C						PASS	.						82	88	86					2																	43919728		2203	4300	6503	SO:0001583	missense	130271	exon4			AATAAGTGTCAAG	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.262T>C	2.37:g.43919728T>C	ENSP00000282406:p.Cys88Arg	180	0	0		217	41	0.18894	NM_172069	Q5JPJ6|Q6P4Q1|Q8N3Q3	Missense_Mutation	SNP	ENST00000282406.4	37	CCDS1812.1	.	.	.	.	.	.	.	.	.	.	T	7.732	0.699411	0.15106	.	.	ENSG00000152527	ENST00000282406	T	0.28895	1.59	5.48	5.48	0.80851	.	0.053195	0.85682	D	0.000000	T	0.38081	0.1027	L	0.48642	1.525	0.80722	D	1	B;P	0.48640	0.437;0.913	B;P	0.53593	0.201;0.73	T	0.08046	-1.0741	10	0.31617	T	0.26	-15.4001	10.7541	0.46225	0.1418:0.0:0.0:0.8582	.	88;88	Q8IVE3;Q8IVE3-3	PKHH2_HUMAN;.	R	88	ENSP00000282406:C88R	ENSP00000282406:C88R	C	+	1	0	PLEKHH2	43773232	1.000000	0.71417	1.000000	0.80357	0.502000	0.33828	4.392000	0.59659	2.077000	0.62373	0.460000	0.39030	TGT	.	.	none		0.313	PLEKHH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250537.1	NM_172069		C	43919728	T	C	43919728	3	2	43	1	0	0	0	0	1	0	0	0	12086	1696	59	3	272	3	PLEKHH2	2	43919728	Missense_Mutation	SNP	T	TCGA-GS-A9U3-01A-11D-A38X-10	17385111	43919728	199279645	10	15358											
MRPL19	9801	hgsc.bcm.edu	37	chr2	75879766	75879766	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agctactttcatccttaggaAtgttatcgaaggacaaggta	13	12	9	7	1	1	0	1	0	0	0	3	3	2	2	1	3	2	3	1	3	7	5			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr2:75879766A>T	ENST00000393909.2	+	4	483	c.458A>T	c.(457-459)aAt>aTt	p.N153I	MRPL19_ENST00000358788.6_Missense_Mutation_p.N153I|MRPL19_ENST00000409374.1_Missense_Mutation_p.N153I	NM_014763.3	NP_055578.2	P49406	RM19_HUMAN	mitochondrial ribosomal protein L19	153					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						ATCCTTAGGAATGTTATCGAA	0.388																																					p.N153I		Atlas-SNP	.											.	MRPL19	21	.	0			c.A458T						PASS	.						131	117	121					2																	75879766		1846	4091	5937	SO:0001583	missense	9801	exon4			TTAGGAATGTTAT	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.458A>T	2.37:g.75879766A>T	ENSP00000377486:p.Asn153Ile	266	0	0		229	32	0.139738	NM_014763	Q53TX9|Q96Q52	Missense_Mutation	SNP	ENST00000393909.2	37	CCDS1960.2	.	.	.	.	.	.	.	.	.	.	A	16.85	3.237813	0.58886	.	.	ENSG00000115364	ENST00000393909;ENST00000409374	.	.	.	5.39	5.39	0.77823	Translation protein SH3-like (1);	0.000000	0.85682	D	0.000000	D	0.85265	0.5657	M	0.92507	3.315	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88718	0.3227	9	0.87932	D	0	-33.2818	13.6754	0.62451	1.0:0.0:0.0:0.0	.	153	P49406	RM19_HUMAN	I	153	.	ENSP00000377486:N153I	N	+	2	0	MRPL19	75733274	1.000000	0.71417	1.000000	0.80357	0.267000	0.26476	8.779000	0.91792	2.187000	0.69744	0.528000	0.53228	AAT	.	.	none		0.388	MRPL19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252256.1	NM_014763		T	75879766	A	T	75879766	3	4	43	1	0	0	0	0	1	0	0	0	9793	101	4	5	472	5	MRPL19	2	75879766	Missense_Mutation	SNP	A	TCGA-GS-A9U3-01A-11D-A38X-10	31960038	75879766	167319607	11	15359											
DNAH7	56171	hgsc.bcm.edu	37	chr2	196651835	196651835	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctaggggtccaaatttccGtctttcttgtaccaaagcat	9	13	7	12	1	2	0	0	0	2	0	4	0	4	0	4	2	2	2	4	2	4	5	rs200008102	byFrequency	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr2:196651835G>A	ENST00000312428.6	-	58	10877	c.10777C>T	c.(10777-10779)Cgg>Tgg	p.R3593W	DNAH7_ENST00000409063.1_Missense_Mutation_p.R76W	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	3593	AAA 6. {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						CCAAATTTCCGTCTTTCTTGT	0.413													G|||	2	0.000399361	0.0008	0.0014	5008	,	,		18598	0.0		0.0	False		,,,				2504	0.0				p.R3593W		Atlas-SNP	.											.	DNAH7	512	.	0			c.C10777T						PASS	.						110	103	105					2																	196651835		1906	4145	6051	SO:0001583	missense	56171	exon58			ATTTCCGTCTTTC	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.10777C>T	2.37:g.196651835G>A	ENSP00000311273:p.Arg3593Trp	200	0	0		198	29	0.146465	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	19.54	3.846185	0.71603	.	.	ENSG00000118997	ENST00000312428;ENST00000409063	T;T	0.11604	2.76;2.76	4.34	3.43	0.39272	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.51873	0.1700	H	0.99565	4.63	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73369	-0.4004	10	0.87932	D	0	.	13.35	0.60597	0.0:0.0:0.8406:0.1594	.	3593	Q8WXX0	DYH7_HUMAN	W	3593;76	ENSP00000311273:R3593W;ENSP00000386912:R76W	ENSP00000311273:R3593W	R	-	1	2	DNAH7	196360080	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.696000	0.47052	1.120000	0.41904	0.555000	0.69702	CGG	G|1.000;A|0.000	0.000	strong		0.413	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897		A	196651835	G	A	196651835	3	1	43	1	0	0	0	0	1	0	0	0	4608	1144	40	1	1329	1	DNAH7	2	196651835	Missense_Mutation	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10	120772069	196651835	46547538	12	15360											
TNS1	7145	hgsc.bcm.edu	37	chr2	218712997	218712997	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcagctggggttcagcttccGaaaaggattgagagcggaac	11	7	15	8	2	1	1	1	1	0	1	2	5	2	3	1	4	4	4	1	4	3	3			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr2:218712997G>A	ENST00000171887.4	-	17	2320	c.1868C>T	c.(1867-1869)tCg>tTg	p.S623L	TNS1_ENST00000480665.1_5'Flank|TNS1_ENST00000430930.1_Missense_Mutation_p.S623L|TNS1_ENST00000419504.1_Missense_Mutation_p.S623L	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	623					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)		TTCAGCTTCCGAAAAGGATTG	0.652																																					p.S623L		Atlas-SNP	.											.	TNS1	251	.	0			c.C1868T						PASS	.						53	45	47					2																	218712997		2202	4300	6502	SO:0001583	missense	7145	exon17			GCTTCCGAAAAGG	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.1868C>T	2.37:g.218712997G>A	ENSP00000171887:p.Ser623Leu	78	0	0		61	9	0.147541	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	.	.	.	.	.	.	.	.	.	.	G	12.82	2.053240	0.36181	.	.	ENSG00000079308	ENST00000171887;ENST00000419504;ENST00000430930;ENST00000446903	D;D;D;D	0.93859	-2.81;-2.82;-2.82;-3.3	4.57	4.57	0.56435	.	0.441217	0.24465	N	0.038288	D	0.86070	0.5845	N	0.08118	0	0.80722	D	1	B;B;B;B;B	0.23891	0.036;0.0;0.093;0.059;0.059	B;B;B;B;B	0.15870	0.009;0.001;0.014;0.01;0.006	T	0.82955	-0.0200	10	0.48119	T	0.1	.	17.539	0.87842	0.0:0.0:1.0:0.0	.	623;677;623;623;623	B2RU35;A1L0S7;Q9HBL0;E9PGF5;E9PF55	.;.;TENS1_HUMAN;.;.	L	623;623;623;748	ENSP00000171887:S623L;ENSP00000408724:S623L;ENSP00000406016:S623L;ENSP00000405460:S748L	ENSP00000171887:S623L	S	-	2	0	TNS1	218421242	0.980000	0.34600	0.937000	0.37676	0.979000	0.70002	1.802000	0.38853	2.370000	0.80446	0.561000	0.74099	TCG	.	.	none		0.652	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648		A	218712997	G	A	218712997	3	1	43	1	0	0	0	0	1	0	0	0	16358	1059	37	1	3407	1	TNS1	2	218712997	Missense_Mutation	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10	22061162	218712997	24486376	13	15361											
PLCL2	23228	hgsc.bcm.edu	37	chr3	17051505	17051505	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgcgttttccgtcatatatGgagagaattatgagtcactg	10	14	11	6	2	2	2	2	1	0	1	3	4	3	3	1	1	1	1	1	1	4	5			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr3:17051505G>A	ENST00000418129.2	+	2	754	c.289G>A	c.(289-291)Gga>Aga	p.G97R	PLCL2_ENST00000460467.1_3'UTR|PLCL2_ENST00000432376.1_Missense_Mutation_p.G97R|PLCL2_ENST00000396755.2_Missense_Mutation_p.G97R	NM_001144382.1	NP_001137854.1	Q9UPR0	PLCL2_HUMAN	phospholipase C-like 2	223					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						CGTCATATATGGAGAGAATTA	0.418																																					p.G97R		Atlas-SNP	.											.	PLCL2	145	.	0			c.G289A						PASS	.						123	123	123					3																	17051505		2203	4300	6503	SO:0001583	missense	23228	exon2			ATATATGGAGAGA	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.289G>A	3.37:g.17051505G>A	ENSP00000409637:p.Gly97Arg	49	0	0		107	11	0.102804	NM_015184	A8K5V4|Q8N498|Q9H8L0|Q9UFP9	Missense_Mutation	SNP	ENST00000418129.2	37	CCDS33713.1	.	.	.	.	.	.	.	.	.	.	G	17.03	3.283509	0.59867	.	.	ENSG00000154822	ENST00000418129;ENST00000285094;ENST00000396755;ENST00000432376	T;T;T	0.66099	-0.19;-0.19;-0.19	5.33	4.45	0.53987	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.045302	0.85682	D	0.000000	T	0.79782	0.4505	.	.	.	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.82520	-0.0416	9	0.59425	D	0.04	.	15.4192	0.74997	0.0:0.0:0.8598:0.1402	.	223;97	Q9UPR0;Q9UPR0-2	PLCL2_HUMAN;.	R	97;224;97;97	ENSP00000409637:G97R;ENSP00000379979:G97R;ENSP00000412836:G97R	ENSP00000285094:G224R	G	+	1	0	PLCL2	17026509	1.000000	0.71417	1.000000	0.80357	0.860000	0.49131	9.869000	0.99810	1.240000	0.43803	0.561000	0.74099	GGA	.	.	none		0.418	PLCL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340250.3			A	17051505	G	A	17051505	3	1	43	1	0	0	0	0	1	0	0	0	12049	1349	47	2	667	2	PLCL2	3	17051505	Missense_Mutation	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10		17051505	180970925	14	15362											
LIMD1	8994	hgsc.bcm.edu	37	chr3	45636379	45636379	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acctgtctgcagcatggataAgtatgacgacctgggcctgg	9	9	13	10	1	1	1	0	1	1	0	1	3	1	2	3	3	2	3	3	3	2	2			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr3:45636379A>T	ENST00000273317.4	+	1	29	c.8A>T	c.(7-9)aAg>aTg	p.K3M	AC099539.1_ENST00000516118.1_RNA|LIMD1_ENST00000440097.1_Missense_Mutation_p.K3M|LIMD1_ENST00000465039.1_Intron	NM_014240.2	NP_055055.1	Q9UGP4	LIMD1_HUMAN	LIM domains containing 1	3					cell migration (GO:0016477)|cytoplasmic mRNA processing body assembly (GO:0033962)|cytoskeleton organization (GO:0007010)|gene silencing by miRNA (GO:0035195)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of hippo signaling (GO:0035331)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|phosphorylation (GO:0016310)|positive regulation of gene silencing by miRNA (GO:2000637)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|RISC complex (GO:0016442)	transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(193;0.011)|KIRC - Kidney renal clear cell carcinoma(197;0.0264)|Kidney(197;0.0315)		AGCATGGATAAGTATGACGAC	0.557																																					p.K3M		Atlas-SNP	.											.	LIMD1	34	.	0			c.A8T						PASS	.						68	71	70					3																	45636379		2203	4300	6503	SO:0001583	missense	8994	exon1			TGGATAAGTATGA	AJ132408	CCDS2729.1	3p21.31	2008-02-01			ENSG00000144791	ENSG00000144791			6612	protein-coding gene	gene with protein product		604543				10647888	Standard	NM_014240		Approved		uc003coq.3	Q9UGP4	OTTHUMG00000133453	ENST00000273317.4:c.8A>T	3.37:g.45636379A>T	ENSP00000273317:p.Lys3Met	50	0	0		73	8	0.109589	NM_014240	Q17RQ1|Q9BQQ9|Q9NQ47	Missense_Mutation	SNP	ENST00000273317.4	37	CCDS2729.1	.	.	.	.	.	.	.	.	.	.	A	18.47	3.630201	0.67015	.	.	ENSG00000144791	ENST00000440097;ENST00000273317	T;T	0.71103	-0.54;-0.3	4.16	4.16	0.48862	.	0.000000	0.85682	D	0.000000	T	0.71074	0.3297	N	0.19112	0.55	0.43936	D	0.996592	D	0.71674	0.998	D	0.77557	0.99	T	0.74003	-0.3804	10	0.87932	D	0	.	9.5521	0.39317	0.8229:0.177:0.0:0.0	.	3	Q9UGP4	LIMD1_HUMAN	M	3	ENSP00000394537:K3M;ENSP00000273317:K3M	ENSP00000273317:K3M	K	+	2	0	LIMD1	45611383	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	6.879000	0.75572	1.520000	0.48965	0.379000	0.24179	AAG	.	.	none		0.557	LIMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257327.1	NM_014240		T	45636379	A	T	45636379	3	4	43	1	0	0	0	0	1	0	0	0	8807	72	3	5	10	5	LIMD1	3	45636379	Missense_Mutation	SNP	A	TCGA-GS-A9U3-01A-11D-A38X-10	28584874	45636379	152386051	15	15363											
MST1R	4486	hgsc.bcm.edu	37	chr3	49940010	49940010	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cacaaagaccccaaatagtaCttcctggccctcggcgatgc	11	7	8	15	2	0	1	0	0	0	1	2	2	1	1	4	2	2	1	4	2	4	3	rs367549694		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr3:49940010C>T	ENST00000296474.3	-	1	1060	c.1033G>A	c.(1033-1035)Gta>Ata	p.V345I	CTD-2330K9.2_ENST00000435478.1_RNA|MST1R_ENST00000344206.4_Missense_Mutation_p.V345I|CTD-2330K9.3_ENST00000419183.1_5'Flank	NM_002447.2	NP_002438	Q04912	RON_HUMAN	macrophage stimulating 1 receptor (c-met-related tyrosine kinase)	345	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)		CCAAATAGTACTTCCTGGCCC	0.617																																					p.V345I		Atlas-SNP	.											.	MST1R	205	.	0			c.G1033A						PASS	.	C	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	146	143	144		1033	4.9	1	3		144	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	345/1401	49940010	1,13005	2203	4300	6503	SO:0001583	missense	4486	exon1			ATAGTACTTCCTG	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.1033G>A	3.37:g.49940010C>T	ENSP00000296474:p.Val345Ile	90	0	0		112	18	0.160714	NM_001244937	B5A944|B5A945|B5A946|B5A947	Missense_Mutation	SNP	ENST00000296474.3	37	CCDS2807.1	.	.	.	.	.	.	.	.	.	.	C	15.44	2.834437	0.50951	2.27E-4	0.0	ENSG00000164078	ENST00000296474;ENST00000344206	T;T	0.13420	2.59;2.59	4.92	4.92	0.64577	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.057844	0.64402	D	0.000002	T	0.23410	0.0566	L	0.32530	0.975	0.43439	D	0.995613	P;D;P;P;D	0.76494	0.867;0.996;0.867;0.867;0.999	P;D;P;P;D	0.85130	0.47;0.99;0.47;0.673;0.997	T	0.01545	-1.1328	10	0.02654	T	1	-18.159	17.7272	0.88368	0.0:1.0:0.0:0.0	.	345;345;345;345;345	Q04912-3;Q04912-4;Q04912-6;Q04912-5;Q04912	.;.;.;.;RON_HUMAN	I	345	ENSP00000296474:V345I;ENSP00000341325:V345I	ENSP00000296474:V345I	V	-	1	0	MST1R	49915014	0.976000	0.34144	0.994000	0.49952	0.660000	0.38997	2.258000	0.43249	2.268000	0.75426	0.561000	0.74099	GTA	.	.	weak		0.617	MST1R-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345403.1			T	49940010	C	T	49940010	3	4	43	1	0	0	0	0	1	0	0	0	9900	565	20	2	3249	2	MST1R	3	49940010	Missense_Mutation	SNP	C	TCGA-GS-A9U3-01A-11D-A38X-10	4303631	49940010	148082420	16	15364											
EPHA6	285220	hgsc.bcm.edu	37	chr3	96706499	96706499	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccagatggatttgggtgatcGcatcctcaaactcaacactg	11	10	9	11	1	2	2	2	1	0	1	4	3	3	3	2	2	2	1	2	2	2	1			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr3:96706499G>A	ENST00000389672.5	+	3	814	c.776G>A	c.(775-777)cGc>cAc	p.R259H	EPHA6_ENST00000542517.1_Missense_Mutation_p.R165H|EPHA6_ENST00000470610.2_Missense_Mutation_p.R259H	NM_001080448.2	NP_001073917.2	Q9UF33	EPHA6_HUMAN	EPH receptor A6	165						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						TTGGGTGATCGCATCCTCAAA	0.443																																					p.R259H		Atlas-SNP	.											EPHA6_ENST00000389672,colon,carcinoma,+1,9	EPHA6	439	9	0			c.G776A						PASS	.						203	209	207					3																	96706499		1900	4141	6041	SO:0001583	missense	285220	exon3			GTGATCGCATCCT	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.776G>A	3.37:g.96706499G>A	ENSP00000374323:p.Arg259His	126	0	0		155	28	0.180645	NM_001080448	D6RAL5	Missense_Mutation	SNP	ENST00000389672.5	37	CCDS46876.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.677321	0.88445	.	.	ENSG00000080224	ENST00000470610;ENST00000389672;ENST00000542517	T;T;T	0.03920	3.76;3.76;3.76	5.48	5.48	0.80851	.	0.000000	0.64402	U	0.000013	T	0.30665	0.0772	M	0.90977	3.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.24476	-1.0159	10	0.87932	D	0	.	18.3424	0.90309	0.0:0.0:1.0:0.0	.	259;259	B3KS12;E7EU71	.;.	H	259;259;165	ENSP00000420598:R259H;ENSP00000374323:R259H;ENSP00000439758:R165H	ENSP00000374323:R259H	R	+	2	0	EPHA6	98189189	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.869000	0.99810	2.554000	0.86153	0.655000	0.94253	CGC	.	.	none		0.443	EPHA6-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353845.3	NM_001080448		A	96706499	G	A	96706499	3	1	43	1	0	0	0	0	1	0	0	0	5173	1087	38	1	786	1	EPHA6	3	96706499	Missense_Mutation	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10	46766489	96706499	101315931	17	15365											
ANKRD50	57182	hgsc.bcm.edu	37	chr4	125590963	125590963	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	agaactaaaagcatgagtagGcccattaggtaaaccacgta	17	7	9	8	1	0	2	0	1	0	1	0	2	0	2	2	2	3	4	2	2	8	5			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr4:125590963G>A	ENST00000504087.1	-	4	4506	c.3469C>T	c.(3469-3471)Cct>Tct	p.P1157S	ANKRD50_ENST00000515641.1_Missense_Mutation_p.P978S	NM_020337.2	NP_065070.1	Q9ULJ7	ANR50_HUMAN	ankyrin repeat domain 50	1157	Ser-rich.									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						GCATGAGTAGGCCCATTAGGT	0.403																																					p.P1157S		Atlas-SNP	.											.	ANKRD50	136	.	0			c.C3469T						PASS	.						128	125	126					4																	125590963		2203	4300	6503	SO:0001583	missense	57182	exon4			GAGTAGGCCCATT	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.3469C>T	4.37:g.125590963G>A	ENSP00000425658:p.Pro1157Ser	78	0	0		72	11	0.152778	NM_020337	A8K4V3|B4DHJ6|E9PDW0|Q6N064|Q6ZSE6	Missense_Mutation	SNP	ENST00000504087.1	37	CCDS34060.1	.	.	.	.	.	.	.	.	.	.	G	14.07	2.425738	0.43020	.	.	ENSG00000151458	ENST00000504087;ENST00000515641	T;T	0.66638	-0.22;-0.2	5.19	5.19	0.71726	.	0.052846	0.85682	D	0.000000	T	0.69833	0.3155	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.79108	0.992	T	0.61192	-0.7112	10	0.06757	T	0.87	.	18.8923	0.92410	0.0:0.0:1.0:0.0	.	1157	Q9ULJ7	ANR50_HUMAN	S	1157;978	ENSP00000425658:P1157S;ENSP00000425355:P978S	ENSP00000425658:P1157S	P	-	1	0	ANKRD50	125810413	1.000000	0.71417	0.987000	0.45799	0.947000	0.59692	9.060000	0.93907	2.698000	0.92095	0.561000	0.74099	CCT	.	.	none		0.403	ANKRD50-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364775.1	NM_020337		A	125590963	G	A	125590963	3	1	43	1	0	0	0	0	1	0	0	0	677	1203	42	2	824	2	ANKRD50	4	125590963	Missense_Mutation	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10		125590963	65563313	18	15366											
AGA	175	hgsc.bcm.edu	37	chr4	178355570	178355570	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	catcaatatatcaccattccCagtggctgcggctgcccctg	8	10	8	15	1	2	0	2	0	0	0	3	0	3	0	4	2	2	2	4	2	3	3			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr4:178355570C>T	ENST00000264595.2	-	7	899	c.772G>A	c.(772-774)Ggg>Agg	p.G258R	AGA_ENST00000506853.1_5'UTR	NM_000027.3|NM_001171988.1	NP_000018.2|NP_001165459.1	P20933	ASPG_HUMAN	aspartylglucosaminidase	258	Substrate binding.				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)		TCACCATTCCCAGTGGCTGCG	0.443																																					p.G258R		Atlas-SNP	.											.	AGA	39	.	0			c.G772A						PASS	.						118	116	117					4																	178355570		2203	4300	6503	SO:0001583	missense	175	exon7			CATTCCCAGTGGC	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.772G>A	4.37:g.178355570C>T	ENSP00000264595:p.Gly258Arg	259	0	0		213	18	0.084507	NM_000027	B2R7H2|D3DP47|Q4W5Q2|Q6FHN6|Q9UCK6|Q9UCK7|Q9UCK8	Missense_Mutation	SNP	ENST00000264595.2	37	CCDS3829.1	.	.	.	.	.	.	.	.	.	.	C	19.07	3.756271	0.69648	.	.	ENSG00000038002	ENST00000264595;ENST00000502310	D;D	0.98822	-5.16;-5.16	5.68	5.68	0.88126	.	0.048505	0.85682	D	0.000000	D	0.99603	0.9856	H	0.99156	4.45	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97590	1.0116	10	0.87932	D	0	-28.7267	19.3909	0.94583	0.0:1.0:0.0:0.0	.	258	P20933	ASPG_HUMAN	R	258;115	ENSP00000264595:G258R;ENSP00000423798:G115R	ENSP00000264595:G258R	G	-	1	0	AGA	178592564	1.000000	0.71417	0.483000	0.27378	0.099000	0.18886	7.350000	0.79385	2.695000	0.91970	0.650000	0.86243	GGG	.	.	none		0.443	AGA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361916.1	NM_000027		T	178355570	C	T	178355570	3	4	43	1	0	0	0	0	1	0	0	0	365	594	21	2	280	2	AGA	4	178355570	Missense_Mutation	SNP	C	TCGA-GS-A9U3-01A-11D-A38X-10	52764607	178355570	12798706	19	15367											
AHRR	57491	hgsc.bcm.edu	37	chr5	427978	427978	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggacagaagaagaaggcgccGtcaggagccatgctcccgcc	11	3	14	13	3	1	3	1	0	0	3	2	5	2	5	4	3	2	1	4	3	3	0	rs371473301		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr5:427978G>A	ENST00000505113.1	+	8	821	c.777G>A	c.(775-777)ccG>ccA	p.P259P	AHRR_ENST00000316418.5_Silent_p.P277P|AHRR_ENST00000512529.1_Silent_p.P105P|AHRR_ENST00000506456.1_Silent_p.P115P	NM_001242412.1	NP_001229341.1	A9YTQ3	AHRR_HUMAN	aryl-hydrocarbon receptor repressor	259					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein sumoylation (GO:0033235)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|endometrium(4)|large_intestine(1)|lung(12)|prostate(1)	20			Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)			AGAAGGCGCCGTCAGGAGCCA	0.557																																					p.P277P		Atlas-SNP	.											.	AHRR	67	.	0			c.G831A						PASS	.		,	0,3748		0,0,1874	25	29	27		777,831	-9.8	0	5		27	2,8210		0,2,4104	no	coding-synonymous,coding-synonymous	AHRR	NM_001242412.1,NM_020731.4	,	0,2,5978	AA,AG,GG		0.0244,0.0,0.0167	,	259/702,277/720	427978	2,11958	1874	4106	5980	SO:0001819	synonymous_variant	57491	exon9			GGCGCCGTCAGGA	AB033060	CCDS43297.1, CCDS56355.1	5p15.33	2013-05-21	2003-09-11	2003-09-12	ENSG00000063438	ENSG00000063438		"Basic helix-loop-helix proteins"	346	protein-coding gene	gene with protein product		606517	"aryl hydrocarbon receptor regulator"	AHH, AHHR		1070014, 11423533	Standard	NM_020731		Approved	KIAA1234, bHLHe77	uc003jaw.3	A9YTQ3	OTTHUMG00000162171	ENST00000505113.1:c.777G>A	5.37:g.427978G>A		72	0	0		93	22	0.236559	NM_020731	A7MBN5|D6RAZ1|Q9HAZ3|Q9ULI6	Silent	SNP	ENST00000505113.1	37	CCDS56355.1																																																																																			.	.	weak		0.557	AHRR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367720.1	NM_020731		A	427978	G	A	427978	2	1	43	1	0	0	0	0	0	0	0	1	417	1132	40	1		1	AHRR	5	427978	Silent	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10		427978	180487282	20	15368											
ADAMTS19	171019	hgsc.bcm.edu	37	chr5	128863470	128863470	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cttttccaacacaagagtctGagtgtgcaggtcaatcttcg	10	12	9	10	1	3	2	1	1	2	1	5	2	4	2	1	1	2	1	1	1	3	3			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr5:128863470G>C	ENST00000274487.4	+	5	1243	c.1098G>C	c.(1096-1098)ctG>ctC	p.L366L	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	366	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)		ACAAGAGTCTGAGTGTGCAGG	0.308																																					p.L366L		Atlas-SNP	.											ADAMTS19,NS,carcinoma,+2,1	ADAMTS19	216	1	0			c.G1098C						PASS	.						86	91	89					5																	128863470		2203	4300	6503	SO:0001819	synonymous_variant	171019	exon5			GAGTCTGAGTGTG	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.1098G>C	5.37:g.128863470G>C		369	0	0		399	18	0.0451128	NM_133638		Silent	SNP	ENST00000274487.4	37	CCDS4146.1																																																																																			.	.	none		0.308	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638		C	128863470	G	C	128863470	2	2	43	1	0	0	0	0	0	0	0	1	264	1277	45	4		4	ADAMTS19	5	128863470	Silent	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10	128435492	128863470	52051790	21	15369											
PCDHA2	56146	hgsc.bcm.edu	37	chr5	140174824	140174824	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgtgaattctcggatcgaccGggaggagctgtgcgggcgga	7	8	18	8	5	1	1	0	1	1	0	3	6	1	5	1	5	2	1	1	5	1	1			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr5:140174824G>A	ENST00000526136.1	+	1	275	c.275G>A	c.(274-276)cGg>cAg	p.R92Q	PCDHA2_ENST00000378132.1_Missense_Mutation_p.R92Q|PCDHA2_ENST00000520672.2_Missense_Mutation_p.R92Q|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018905.2	NP_061728.1	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2	92	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(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)			CGGATCGACCGGGAGGAGCTG	0.587																																					p.R92Q		Atlas-SNP	.											.	PCDHA2	404	.	0			c.G275A						PASS	.						103	119	114					5																	140174824		2203	4300	6503	SO:0001583	missense	56146	exon1			TCGACCGGGAGGA	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.275G>A	5.37:g.140174824G>A	ENSP00000431748:p.Arg92Gln	82	0	0		86	13	0.151163	NM_031495	O75287|Q9BTV3	Missense_Mutation	SNP	ENST00000526136.1	37	CCDS54914.1	.	.	.	.	.	.	.	.	.	.	g	26.6	4.752294	0.89753	.	.	ENSG00000204969	ENST00000520672;ENST00000378132;ENST00000526136	T;T;T	0.53206	0.63;0.63;0.63	3.98	3.02	0.34903	Cadherin, N-terminal (1);Cadherin (4);Cadherin-like (1);	0.000000	0.38381	U	0.001708	T	0.81716	0.4881	H	0.99740	4.74	0.32371	N	0.555858	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	D	0.89310	0.3632	10	0.87932	D	0	.	14.2561	0.66053	0.0:0.1501:0.8499:0.0	.	92;92;92	Q9Y5H9-3;Q9Y5H9;Q9Y5H9-2	.;PCDA2_HUMAN;.	Q	92	ENSP00000430584:R92Q;ENSP00000367372:R92Q;ENSP00000431748:R92Q	ENSP00000367372:R92Q	R	+	2	0	PCDHA2	140155008	1.000000	0.71417	0.995000	0.50966	0.984000	0.73092	7.604000	0.82830	2.234000	0.73211	0.644000	0.83932	CGG	.	.	none		0.587	PCDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372877.3	NM_018905		A	140174824	G	A	140174824	3	1	43	1	0	0	0	0	1	0	0	0	11533	1116	39	1	277	1	PCDHA2	5	140174824	Missense_Mutation	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10	11311354	140174824	40740436	22	15370											
PCDHA10	56139	hgsc.bcm.edu	37	chr5	140236219	140236219	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aattcccagtgcttgttctgCggaagctgctggatcgtgaa	8	12	12	9	2	1	1	0	1	1	0	3	3	2	3	1	2	4	4	1	2	3	3			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr5:140236219C>T	ENST00000307360.5	+	1	586	c.586C>T	c.(586-588)Cgg>Tgg	p.R196W	PCDHA9_ENST00000532602.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000506939.2_Missense_Mutation_p.R196W|PCDHA4_ENST00000512229.2_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	196	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)			GCTTGTTCTGCGGAAGCTGCT	0.393																																					p.R196W		Atlas-SNP	.											.	PCDHA10	358	.	0			c.C586T						PASS	.						88	90	90					5																	140236219		2196	4267	6463	SO:0001583	missense	56139	exon1			GTTCTGCGGAAGC	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.586C>T	5.37:g.140236219C>T	ENSP00000304234:p.Arg196Trp	153	0	0		171	26	0.152047	NM_031859	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	37	CCDS54921.1	.	.	.	.	.	.	.	.	.	.	C	10.85	1.465536	0.26335	.	.	ENSG00000250120	ENST00000506939;ENST00000307360	T;T	0.21031	2.03;2.03	4.45	-3.91	0.04168	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.25938	0.0632	M	0.85197	2.74	0.09310	N	1	B;B;B	0.33919	0.432;0.137;0.111	B;B;B	0.31290	0.127;0.015;0.03	T	0.34825	-0.9813	9	0.72032	D	0.01	.	10.9471	0.47306	0.6677:0.1603:0.1719:0.0	.	196;196;196	Q9Y5I2-3;Q9Y5I2;Q9Y5I2-2	.;PCDAA_HUMAN;.	W	196	ENSP00000421030:R196W;ENSP00000304234:R196W	ENSP00000304234:R196W	R	+	1	2	PCDHA10	140216403	0.000000	0.05858	0.336000	0.25522	0.972000	0.66771	-1.579000	0.02123	-0.500000	0.06614	0.561000	0.74099	CGG	.	.	none		0.393	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901		T	140236219	C	T	140236219	3	4	43	1	0	0	0	0	1	0	0	0	11529	759	27	1	588	1	PCDHA10	5	140236219	Missense_Mutation	SNP	C	TCGA-GS-A9U3-01A-11D-A38X-10	61395	140236219	40679041	23	15371											
PCDHB1	29930	hgsc.bcm.edu	37	chr5	140431538	140431538	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagcgcccaggatctggaCgtgggccttaacggtctcca	8	7	13	13	3	2	1	0	0	2	1	3	3	2	3	3	4	2	0	3	4	1	1			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr5:140431538C>T	ENST00000306549.3	+	1	560	c.483C>T	c.(481-483)gaC>gaT	p.D161D		NM_013340.2	NP_037472.2	Q9Y5F3	PCDB1_HUMAN	protocadherin beta 1	161	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)|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)			AGGATCTGGACGTGGGCCTTA	0.547																																					p.D161D		Atlas-SNP	.											.	PCDHB1	148	.	0			c.C483T						PASS	.						47	49	48					5																	140431538		2203	4300	6503	SO:0001819	synonymous_variant	29930	exon1			TCTGGACGTGGGC	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.483C>T	5.37:g.140431538C>T		90	0	0		96	18	0.1875	NM_013340	Q2M257	Silent	SNP	ENST00000306549.3	37	CCDS4243.1																																																																																			.	.	none		0.547	PCDHB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251822.2	NM_013340		T	140431538	C	T	140431538	2	4	43	1	0	0	0	0	0	0	0	1	11543	535	19	1		1	PCDHB1	5	140431538	Silent	SNP	C	TCGA-GS-A9U3-01A-11D-A38X-10	195319	140431538	40483722	24	15372											
C1QTNF2	114898	hgsc.bcm.edu	37	chr5	159781844	159781844	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgccaggaaagcccattcGtcccatcattcctgagggcc	8	10	9	14	1	1	1	1	1	0	0	4	2	3	2	5	2	2	0	5	2	1	3	rs144600396		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr5:159781844G>A	ENST00000393975.3	-	2	313	c.310C>T	c.(310-312)Cga>Tga	p.R104*		NM_031908.4	NP_114114.2	Q9BXJ5	C1QT2_HUMAN	C1q and tumor necrosis factor related protein 2	59	Collagen-like.				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)			AAGCCCATTCGTCCCATCATT	0.662													G|||	1	0.000199681	0.0	0.0	5008	,	,		9581	0.0		0.0	False		,,,				2504	0.001				p.R104X		Atlas-SNP	.											.	C1QTNF2	33	.	0			c.C310T						PASS	.	G	stop/ARG	0,4406		0,0,2203	28	25	26		310	2.6	1	5	dbSNP_134	26	1,8599	1.2+/-3.3	0,1,4299	yes	stop-gained	C1QTNF2	NM_031908.4		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		104/331	159781844	1,13005	2203	4300	6503	SO:0001587	stop_gained	114898	exon2			CCATTCGTCCCAT	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.310C>T	5.37:g.159781844G>A	ENSP00000377545:p.Arg104*	61	0	0		68	10	0.147059	NM_031908		Nonsense_Mutation	SNP	ENST00000393975.3	37	CCDS4351.2	.	.	.	.	.	.	.	.	.	.	G	27.8	4.860499	0.91433	0.0	1.16E-4	ENSG00000145861	ENST00000393975	.	.	.	5.16	2.62	0.31277	.	0.300113	0.33515	N	0.004835	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.7246	0.46061	0.0:0.0:0.3199:0.6801	.	.	.	.	X	104	.	ENSP00000377545:R104X	R	-	1	2	C1QTNF2	159714422	0.998000	0.40836	1.000000	0.80357	0.961000	0.63080	1.207000	0.32333	0.802000	0.34089	0.313000	0.20887	CGA	G|1.000;A|0.000	0.000	strong		0.662	C1QTNF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252672.2			A	159781844	G	A	159781844	4	1	43	1	0	0	0	0	0	1	0	0	1965	1153	40	1	690	1	C1QTNF2	5	159781844	Nonsense_Mutation	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10	19350306	159781844	21133416	25	15373											
HIST1H1B	3009	hgsc.bcm.edu	37	chr6	27835042	27835042	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gggtgcccttgctcaccaagCtcttgaggcccagcttaatg	7	10	11	13	0	2	1	1	1	1	0	2	1	2	1	3	2	4	3	3	2	2	3			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr6:27835042C>T	ENST00000331442.3	-	1	317	c.266G>A	c.(265-267)aGc>aAc	p.S89N		NM_005322.2	NP_005313.1	P16401	H15_HUMAN	histone cluster 1, H1b	89	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				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						GCTCACCAAGCTCTTGAGGCC	0.577																																					p.S89N		Atlas-SNP	.											.	HIST1H1B	54	.	0			c.G266A						PASS	.						130	141	138					6																	27835042		2203	4300	6503	SO:0001583	missense	3009	exon1			ACCAAGCTCTTGA	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.266G>A	6.37:g.27835042C>T	ENSP00000330074:p.Ser89Asn	120	0	0		151	27	0.178808	NM_005322	Q14529|Q3MJ42	Missense_Mutation	SNP	ENST00000331442.3	37	CCDS4635.1	.	.	.	.	.	.	.	.	.	.	C	18.11	3.550368	0.65311	.	.	ENSG00000184357	ENST00000331442	T	0.09630	2.96	5.43	5.43	0.79202	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.352440	0.35615	N	0.003089	T	0.12518	0.0304	L	0.45422	1.42	0.37742	D	0.925646	P	0.38048	0.616	P	0.51355	0.667	T	0.00855	-1.1539	10	0.54805	T	0.06	-25.9517	14.2524	0.66028	0.0:0.8513:0.1487:0.0	.	89	P16401	H15_HUMAN	N	89	ENSP00000330074:S89N	ENSP00000330074:S89N	S	-	2	0	HIST1H1B	27943021	1.000000	0.71417	1.000000	0.80357	0.293000	0.27360	1.955000	0.40372	2.716000	0.92895	0.655000	0.94253	AGC	.	.	none		0.577	HIST1H1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043371.1	NM_005322		T	27835042	C	T	27835042	3	4	43	1	0	0	0	0	1	0	0	0	7132	797	28	2	418	2	HIST1H1B	6	27835042	Missense_Mutation	SNP	C	TCGA-GS-A9U3-01A-11D-A38X-10		27835042	143280025	26	15374											
ABCF1	23	hgsc.bcm.edu	37	chr6	30553108	30553108	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctggacctcaacgctgtcaTctggcttaataagtgcgtta	9	12	9	11	2	3	0	2	0	1	0	3	1	3	1	2	2	2	3	2	2	4	3			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr6:30553108T>A	ENST00000326195.8	+	15	1575	c.1463T>A	c.(1462-1464)aTc>aAc	p.I488N	ABCF1_ENST00000376545.3_Missense_Mutation_p.I450N|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	488	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						AACGCTGTCATCTGGCTTAAT	0.557																																					p.I488N		Atlas-SNP	.											.	ABCF1	61	.	0			c.T1463A						PASS	.						210	153	173					6																	30553108		1511	2709	4220	SO:0001583	missense	23	exon15			CTGTCATCTGGCT	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.1463T>A	6.37:g.30553108T>A	ENSP00000313603:p.Ile488Asn	100	0	0		109	24	0.220183	NM_001025091	A2BF75|O14897|Q69YP6	Missense_Mutation	SNP	ENST00000326195.8	37	CCDS34380.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.337644	0.81911	.	.	ENSG00000204574	ENST00000326195;ENST00000376545	D;D	0.90620	-2.5;-2.7	5.01	5.01	0.66863	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.053150	0.85682	D	0.000000	D	0.90748	0.7096	L	0.36672	1.1	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.74674	0.984;0.961;0.961	D	0.92519	0.6023	10	0.87932	D	0	-18.381	13.843	0.63451	0.0:0.0:0.0:1.0	.	450;488;488	Q2L6I2;Q8NE71;A2BF75	.;ABCF1_HUMAN;.	N	488;450	ENSP00000313603:I488N;ENSP00000365728:I450N	ENSP00000313603:I488N	I	+	2	0	ABCF1	30661087	1.000000	0.71417	0.994000	0.49952	0.886000	0.51366	7.367000	0.79558	2.107000	0.64212	0.379000	0.24179	ATC	.	.	none		0.557	ABCF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076137.3			A	30553108	T	A	30553108	3	1	43	1	0	0	0	0	1	0	0	0	65	1435	50	5	1521	5	ABCF1	6	30553108	Missense_Mutation	SNP	T	TCGA-GS-A9U3-01A-11D-A38X-10	2718066	30553108	140561959	27	15375											
COL9A1	1297	hgsc.bcm.edu	37	chr6	70991128	70991128	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	gcctggaactccaggggggcCcggaggcccgggaggaccct	6	3	18	14	2	0	0	0	0	0	0	1	4	1	4	5	8	1	0	5	8	1	0			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr6:70991128C>A	ENST00000357250.6	-	8	999	c.841G>T	c.(841-843)Ggc>Tgc	p.G281C	COL9A1_ENST00000370499.4_Missense_Mutation_p.G38C|COL9A1_ENST00000370496.3_Missense_Mutation_p.G281C|COL9A1_ENST00000320755.7_Missense_Mutation_p.G38C|COL9A1_ENST00000489611.1_5'Flank	NM_001851.4	NP_001842.3	P20849	CO9A1_HUMAN	collagen, type IX, alpha 1	281	Collagen-like 1.|Triple-helical region (COL3).				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						CCAGGGGGGCCCGGAGGCCCG	0.597																																					p.G281C		Atlas-SNP	.											COL9A1_ENST00000320755,NS,carcinoma,+1,2	COL9A1	228	2	0			c.G841T						PASS	.						22	26	25					6																	70991128		2203	4300	6503	SO:0001583	missense	1297	exon8			GGGGGCCCGGAGG		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.841G>T	6.37:g.70991128C>A	ENSP00000349790:p.Gly281Cys	52	0	0		72	12	0.166667	NM_001851	Q13699|Q13700|Q5TF52|Q6P467|Q96BM8|Q99225|Q9H151|Q9H152|Q9Y6P2|Q9Y6P3	Missense_Mutation	SNP	ENST00000357250.6	37	CCDS4971.1	.	.	.	.	.	.	.	.	.	.	C	12.39	1.923575	0.33908	.	.	ENSG00000112280	ENST00000357250;ENST00000320755;ENST00000370499;ENST00000370496	D;D;D;D	0.99369	-5.78;-5.78;-5.78;-5.78	5.74	5.74	0.90152	.	0.095514	0.64402	D	0.000001	D	0.99802	0.9915	H	0.99464	4.58	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96865	0.9635	10	0.87932	D	0	.	18.8993	0.92435	0.0:1.0:0.0:0.0	.	281;38	P20849;P20849-2	CO9A1_HUMAN;.	C	281;38;38;281	ENSP00000349790:G281C;ENSP00000315252:G38C;ENSP00000359530:G38C;ENSP00000359527:G281C	ENSP00000315252:G38C	G	-	1	0	COL9A1	71047849	0.997000	0.39634	0.196000	0.23383	0.014000	0.08584	5.631000	0.67812	2.722000	0.93159	0.591000	0.81541	GGC	.	.	none		0.597	COL9A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041131.2			A	70991128	C	A	70991128	3	1	43	1	0	0	0	0	1	0	0	0	3709	623	22	4	2048	4	COL9A1	6	70991128	Missense_Mutation	SNP	C	TCGA-GS-A9U3-01A-11D-A38X-10	40438020	70991128	100123939	28	15376											
NMBR	4829	hgsc.bcm.edu	37	chr6	142400028	142400028	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcatgtccatggggttaacGatggctctgtacctgggaaa	9	11	13	8	1	1	0	0	0	1	0	2	2	2	1	2	4	3	4	2	4	3	2	rs147371910		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr6:142400028G>T	ENST00000258042.1	-	2	575	c.435C>A	c.(433-435)atC>atA	p.I145I	NMBR_ENST00000480652.1_5'Flank	NM_002511.2	NP_002502.2	P28336	NMBR_HUMAN	neuromedin B receptor	145					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)		TGGGGTTAACGATGGCTCTGT	0.458																																					p.I145I		Atlas-SNP	.											.	NMBR	62	.	0			c.C435A						PASS	.						51	43	46					6																	142400028		2203	4300	6503	SO:0001819	synonymous_variant	4829	exon2			GTTAACGATGGCT		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.435C>A	6.37:g.142400028G>T		63	0	0		88	21	0.238636	NM_002511	E9KL38|Q5VUK8	Silent	SNP	ENST00000258042.1	37	CCDS5196.1																																																																																			G|1.000;A|0.000	.	alt		0.458	NMBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042479.1			T	142400028	G	T	142400028	2	4	43	1	0	0	0	0	0	0	0	1	10496	1048	37	4		4	NMBR	6	142400028	Silent	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10	71408900	142400028	28715039	29	15377											
SEC61G	23480	hgsc.bcm.edu	37	chr7	54823513	54823513	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atatggatcaatttcacaaaGaagccaatgaatcccattat	17	11	5	8	0	2	2	2	1	0	1	3	3	3	3	2	1	1	0	2	1	7	3			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr7:54823513G>A	ENST00000415949.1	-	4	522	c.156C>T	c.(154-156)ttC>ttT	p.F52F	SEC61G_ENST00000352861.4_Silent_p.F52F|SEC61G_ENST00000450622.1_Silent_p.F52F|SEC61G_ENST00000395535.3_Silent_p.F52F			P60059	SC61G_HUMAN	Sec61 gamma subunit	52					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 protein metabolic process (GO:0044267)|gene expression (GO:0010467)|protein targeting to ER (GO:0045047)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	P-P-bond-hydrolysis-driven protein transmembrane transporter activity (GO:0015450)|protein transporter activity (GO:0008565)			kidney(1)|lung(5)	6	Esophageal squamous(2;7.55e-08)|Breast(14;0.0654)		Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)			ATTTCACAAAGAAGCCAATGA	0.313																																					p.F52F		Atlas-SNP	.											.	SEC61G	10	.	0			c.C156T						PASS	.						98	97	98					7																	54823513		2203	4300	6503	SO:0001819	synonymous_variant	23480	exon3			CACAAAGAAGCCA	AF086539	CCDS5513.1	7p11.2	2014-05-19			ENSG00000132432	ENSG00000132432			18277	protein-coding gene	gene with protein product		609215				8107851, 10212142	Standard	NM_014302		Approved	SSS1	uc003tqg.3	P60059	OTTHUMG00000023430	ENST00000415949.1:c.156C>T	7.37:g.54823513G>A		51	0	0		80	9	0.1125	NM_001012456	B2R4J0|P38384|Q6IB25	Silent	SNP	ENST00000415949.1	37	CCDS5513.1																																																																																			.	.	none		0.313	SEC61G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251384.2	NM_014302		A	54823513	G	A	54823513	2	1	43	1	0	0	0	0	0	0	0	1	14018	933	33	2		2	SEC61G	7	54823513	Silent	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10		54823513	104315150	30	15378											
RSBN1L	222194	hgsc.bcm.edu	37	chr7	77378893	77378893	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tctgctcaggattgctaactGatgttgaagatcaagcagcc	11	11	10	9	0	3	3	2	2	1	1	3	4	3	4	1	1	5	4	1	1	3	3			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr7:77378893G>A	ENST00000334955.8	+	3	883	c.856G>A	c.(856-858)Gat>Aat	p.D286N	RSBN1L_ENST00000445288.1_Missense_Mutation_p.D16N	NM_198467.2	NP_940869.2	Q6PCB5	RSBNL_HUMAN	round spermatid basic protein 1-like	286						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						ATTGCTAACTGATGTTGAAGA	0.353																																					p.D286N		Atlas-SNP	.											.	RSBN1L	74	.	0			c.G856A						PASS	.						107	98	101					7																	77378893		1854	4109	5963	SO:0001583	missense	222194	exon3			CTAACTGATGTTG	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.856G>A	7.37:g.77378893G>A	ENSP00000334040:p.Asp286Asn	98	0	0		87	16	0.183908	NM_198467	C9K0P1|Q6ZS58|Q6ZVI9|Q86X48	Missense_Mutation	SNP	ENST00000334955.8	37	CCDS43607.1	.	.	.	.	.	.	.	.	.	.	G	21.4	4.147805	0.78001	.	.	ENSG00000187257	ENST00000334955;ENST00000445288	T	0.08193	3.12	5.58	5.58	0.84498	.	0.052712	0.85682	D	0.000000	T	0.20495	0.0493	L	0.43152	1.355	0.33216	D	0.554005	D	0.56968	0.978	D	0.63488	0.915	T	0.05273	-1.0895	10	0.18710	T	0.47	-19.8707	19.578	0.95452	0.0:0.0:1.0:0.0	.	286	Q6PCB5	RSBNL_HUMAN	N	286;16	ENSP00000334040:D286N	ENSP00000334040:D286N	D	+	1	0	RSBN1L	77216829	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.973000	0.76116	2.628000	0.89032	0.655000	0.94253	GAT	.	.	none		0.353	RSBN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340455.3	NM_198467		A	77378893	G	A	77378893	3	1	43	1	0	0	0	0	1	0	0	0	13712	1290	45	2	866	2	RSBN1L	7	77378893	Missense_Mutation	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10	22555380	77378893	81759770	31	15379											
DOCK5	80005	hgsc.bcm.edu	37	chr8	25230091	25230091	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccaggctcctagaacattgcCggaaacacaaatacctctcc	13	7	6	15	1	1	1	0	0	1	1	3	2	2	2	5	2	4	1	5	2	5	3			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr8:25230091C>T	ENST00000276440.7	+	35	3585	c.3541C>T	c.(3541-3543)Cgg>Tgg	p.R1181W		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	1181					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)		AGAACATTGCCGGAAACACAA	0.552																																					p.R1181W	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											.	DOCK5	167	.	0			c.C3541T						PASS	.						68	65	66					8																	25230091		2203	4300	6503	SO:0001583	missense	80005	exon35			CATTGCCGGAAAC		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.3541C>T	8.37:g.25230091C>T	ENSP00000276440:p.Arg1181Trp	53	0	0		64	9	0.140625	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Missense_Mutation	SNP	ENST00000276440.7	37	CCDS6047.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.4|20.4	3.987709|3.987709	0.74589|0.74589	.|.	.|.	ENSG00000147459|ENSG00000147459	ENST00000444569|ENST00000276440	.|T	.|0.67523	.|-0.27	5.56|5.56	5.56|5.56	0.83823|0.83823	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.80025|0.80025	0.4548|0.4548	M|M	0.70595|0.70595	2.14|2.14	0.58432|0.58432	D|D	0.999995|0.999995	.|D;D;D	.|0.76494	.|0.999;0.999;0.999	.|D;P;D	.|0.65684	.|0.937;0.889;0.937	T|T	0.81722|0.81722	-0.0803|-0.0803	5|10	.|0.72032	.|D	.|0.01	.|.	15.8389|15.8389	0.78824|0.78824	0.1362:0.8638:0.0:0.0|0.1362:0.8638:0.0:0.0	.|.	.|1171;956;1181	.|D3DSS6;Q68DL4;Q9H7D0	.|.;.;DOCK5_HUMAN	L|W	952|1181	.|ENSP00000276440:R1181W	.|ENSP00000276440:R1181W	P|R	+|+	2|1	0|2	DOCK5|DOCK5	25286008|25286008	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	1.952000|1.952000	0.40343|0.40343	2.633000|2.633000	0.89246|0.89246	0.655000|0.655000	0.94253|0.94253	CCG|CGG	.	.	none		0.552	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940		T	25230091	C	T	25230091	3	4	43	1	0	0	0	0	1	0	0	0	4692	643	23	1	3679	1	DOCK5	8	25230091	Missense_Mutation	SNP	C	TCGA-GS-A9U3-01A-11D-A38X-10		25230091	121133931	32	15380											
PXDNL	137902	hgsc.bcm.edu	37	chr8	52252217	52252217	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctgtgatggtttcctgaatTtccgctgcaaacgtgctgaa	8	13	11	9	2	0	3	0	3	0	0	2	3	2	3	2	1	3	5	2	1	3	2			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr8:52252217T>A	ENST00000356297.4	-	21	4213	c.4113A>T	c.(4111-4113)gaA>gaT	p.E1371D	PXDNL_ENST00000543296.1_Intron	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	1371					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)				TTTCCTGAATTTCCGCTGCAA	0.373																																					p.E1371D		Atlas-SNP	.											.	PXDNL	414	.	0			c.A4113T						PASS	.						139	136	137					8																	52252217		1879	4103	5982	SO:0001583	missense	137902	exon21			CTGAATTTCCGCT		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.4113A>T	8.37:g.52252217T>A	ENSP00000348645:p.Glu1371Asp	150	0	0		138	19	0.137681	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	8.130|8.130	0.782774|0.782774	0.16189|0.16189	.|.	.|.	ENSG00000147485|ENSG00000147485	ENST00000356297|ENST00000522933	T|.	0.64803|.	-0.12|.	5.0|5.0	2.54|2.54	0.30619|0.30619	.|.	.|.	.|.	.|.	.|.	T|T	0.35068|0.35068	0.0919|0.0919	N|N	0.19112|0.19112	0.55|0.55	0.80722|0.80722	D|D	1|1	B|.	0.06786|.	0.001|.	B|.	0.08055|.	0.003|.	T|T	0.05517|0.05517	-1.0880|-1.0880	9|5	0.45353|.	T|.	0.12|.	.|.	4.3388|4.3388	0.11099|0.11099	0.174:0.0969:0.0:0.7291|0.174:0.0969:0.0:0.7291	.|.	1371|.	A1KZ92|.	PXDNL_HUMAN|.	D|I	1371|445	ENSP00000348645:E1371D|.	ENSP00000348645:E1371D|.	E|K	-|-	3|2	2|0	PXDNL|PXDNL	52414770|52414770	0.998000|0.998000	0.40836|0.40836	0.935000|0.935000	0.37517|0.37517	0.044000|0.044000	0.14063|0.14063	1.971000|1.971000	0.40530|0.40530	0.224000|0.224000	0.20940|0.20940	0.482000|0.482000	0.46254|0.46254	GAA|AAA	.	.	none		0.373	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		A	52252217	T	A	52252217	3	1	43	1	0	0	0	0	1	0	0	0	12863	1838	64	5	290	5	PXDNL	8	52252217	Missense_Mutation	SNP	T	TCGA-GS-A9U3-01A-11D-A38X-10	27022126	52252217	94111805	33	15381											
RP1	6101	hgsc.bcm.edu	37	chr8	55533908	55533908	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtcggcgcccgcggccctggCtcagcagccgggccattagc	4	5	15	17	5	1	0	1	0	0	0	2	0	1	0	4	4	3	2	4	4	1	1	rs147116231	byFrequency	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr8:55533908C>T	ENST00000220676.1	+	2	530	c.382C>T	c.(382-384)Ctc>Ttc	p.L128F		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	128					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)			GCGGCCCTGGCTCAGCAGCCG	0.697																																					p.L128F	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.C382T						PASS	.						26	33	30					8																	55533908		2194	4294	6488	SO:0001583	missense	6101	exon2			CCCTGGCTCAGCA	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.382C>T	8.37:g.55533908C>T	ENSP00000220676:p.Leu128Phe	42	0	0		62	14	0.225806	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	37	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	C	13.35	2.211455	0.39102	.	.	ENSG00000104237	ENST00000220676	D	0.87650	-2.28	4.9	4.9	0.64082	Doublecortin domain (1);	0.532611	0.16143	N	0.227643	D	0.88518	0.6458	M	0.63428	1.95	0.42132	D	0.991472	P	0.49961	0.93	P	0.48030	0.564	D	0.86910	0.2060	10	0.27082	T	0.32	0.1336	18.0907	0.89475	0.0:1.0:0.0:0.0	.	128	P56715	RP1_HUMAN	F	128	ENSP00000220676:L128F	ENSP00000220676:L128F	L	+	1	0	RP1	55696461	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	2.568000	0.45965	2.273000	0.75805	0.650000	0.86243	CTC	C|0.998;A|0.002	.	alt		0.697	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269		T	55533908	C	T	55533908	3	4	43	1	0	0	0	0	1	0	0	0	13547	797	28	2	384	2	RP1	8	55533908	Missense_Mutation	SNP	C	TCGA-GS-A9U3-01A-11D-A38X-10	3281691	55533908	90830114	34	15382											
TMEM70	54968	hgsc.bcm.edu	37	chr8	74893545	74893545	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttacggtgatcaccccagtgCtgcttcactttattacaaaa	11	13	6	11	1	2	1	2	1	0	0	2	1	2	1	2	1	4	2	2	1	5	5			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr8:74893545C>T	ENST00000312184.5	+	3	545	c.472C>T	c.(472-474)Ctg>Ttg	p.L158L	Y_RNA_ENST00000365350.1_RNA|TMEM70_ENST00000517439.1_3'UTR	NM_001040613.2|NM_017866.5	NP_001035703.1|NP_060336.3	Q9BUB7	TMM70_HUMAN	transmembrane protein 70	158					mitochondrial proton-transporting ATP synthase complex assembly (GO:0033615)	integral component of mitochondrial membrane (GO:0032592)|mitochondrial inner membrane (GO:0005743)				breast(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|skin(1)	8	Breast(64;0.0311)		Epithelial(68;0.0186)|BRCA - Breast invasive adenocarcinoma(89;0.0499)|all cancers(69;0.0564)			CACCCCAGTGCTGCTTCACTT	0.393																																					p.L158L		Atlas-SNP	.											.	TMEM70	12	.	0			c.C472T						PASS	.						166	155	158					8																	74893545		2203	4300	6503	SO:0001819	synonymous_variant	54968	exon3			CCAGTGCTGCTTC	BC002748	CCDS6215.1, CCDS47876.1	8q21.11	2013-05-23				ENSG00000175606			26050	protein-coding gene	gene with protein product		612418				21945727, 22986587	Standard	NM_017866		Approved	FLJ20533	uc003yab.3	Q9BUB7		ENST00000312184.5:c.472C>T	8.37:g.74893545C>T		125	0	0		180	19	0.105556	NM_017866	E9PDY9|Q9NWY5	Silent	SNP	ENST00000312184.5	37	CCDS6215.1																																																																																			.	.	none		0.393	TMEM70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379028.1	NM_017866		T	74893545	C	T	74893545	2	4	43	1	0	0	0	0	0	0	0	1	16214	796	28	2		2	TMEM70	8	74893545	Silent	SNP	C	TCGA-GS-A9U3-01A-11D-A38X-10	19359637	74893545	71470477	35	15383											
ZFHX4	79776	hgsc.bcm.edu	37	chr8	77767750	77767750	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtctgcgatgacaaatttCtcttttctctcacaagccca	10	13	6	12	1	4	1	1	1	3	0	6	2	4	1	1	1	2	0	1	1	2	3			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr8:77767750C>A	ENST00000521891.2	+	10	9041	c.8593C>A	c.(8593-8595)Ctc>Atc	p.L2865I	ZFHX4_ENST00000518282.1_Missense_Mutation_p.L2839I|ZFHX4_ENST00000050961.6_Missense_Mutation_p.L2820I|ZFHX4_ENST00000455469.2_Missense_Mutation_p.L2820I	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2820					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.L2849I(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)			TGACAAATTTCTCTTTTCTCT	0.488										HNSCC(33;0.089)																											p.L2865I		Atlas-SNP	.											ZFHX4,caecum,carcinoma,0,2	ZFHX4	878	2	1	Substitution - Missense(1)	large_intestine(1)	c.C8593A						PASS	.						94	96	95					8																	77767750		1969	4146	6115	SO:0001583	missense	79776	exon10			AAATTTCTCTTTT		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.8593C>A	8.37:g.77767750C>A	ENSP00000430497:p.Leu2865Ile	37	0	0		41	8	0.195122	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	C	7.948	0.744269	0.15710	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.49139	0.79;0.84;0.81;0.8	5.25	4.35	0.52113	.	0.000000	0.40144	U	0.001178	T	0.31734	0.0806	N	0.22421	0.69	0.25788	N	0.984655	B;B;B	0.22080	0.038;0.064;0.064	B;B;B	0.30251	0.032;0.07;0.113	T	0.20505	-1.0273	10	0.18276	T	0.48	.	8.0132	0.30365	0.2859:0.641:0.0:0.0731	.	2820;2820;2865	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	I	2865;2849;2820;2820;2839	ENSP00000430497:L2865I;ENSP00000399605:L2820I;ENSP00000050961:L2820I;ENSP00000430848:L2839I	ENSP00000050961:L2820I	L	+	1	0	ZFHX4	77930305	1.000000	0.71417	1.000000	0.80357	0.741000	0.42261	3.209000	0.51122	1.397000	0.46682	0.561000	0.74099	CTC	.	.	none		0.488	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721		A	77767750	C	A	77767750	3	1	43	1	0	0	0	0	1	0	0	0	17650	913	32	4	8627	4	ZFHX4	8	77767750	Missense_Mutation	SNP	C	TCGA-GS-A9U3-01A-11D-A38X-10	2874205	77767750	68596272	36	15384											
TJP2	9414	hgsc.bcm.edu	37	chr9	71836110	71836110	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgcacccgagaccgcagccGtggccggagcctggagcggg	6	2	18	15	6	0	1	0	0	0	1	0	4	0	3	5	4	3	2	5	4	0	0			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr9:71836110G>A	ENST00000377245.4	+	5	858	c.650G>A	c.(649-651)cGt>cAt	p.R217H	TJP2_ENST00000348208.4_Missense_Mutation_p.R217H|TJP2_ENST00000265384.7_Missense_Mutation_p.R217H|TJP2_ENST00000539225.1_Missense_Mutation_p.R248H|TJP2_ENST00000453658.2_Missense_Mutation_p.R194H|TJP2_ENST00000535702.1_Missense_Mutation_p.R221H	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	217					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						GACCGCAGCCGTGGCCGGAGC	0.751																																					p.R248H		Atlas-SNP	.											.	TJP2	120	.	0			c.G743A						PASS	.						10	16	14					9																	71836110		2154	4213	6367	SO:0001583	missense	9414	exon5			GCAGCCGTGGCCG	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.650G>A	9.37:g.71836110G>A	ENSP00000366453:p.Arg217His	56	0	0		59	9	0.152542	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Missense_Mutation	SNP	ENST00000377245.4	37	CCDS6627.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.249862	0.80024	.	.	ENSG00000119139	ENST00000453658;ENST00000377245;ENST00000348208;ENST00000265384;ENST00000535702;ENST00000539225	T;T;T;T;T;T	0.54479	0.57;0.57;0.57;0.57;0.57;0.57	5.11	4.19	0.49359	.	0.100863	0.64402	D	0.000005	T	0.68128	0.2967	M	0.72894	2.215	0.51482	D	0.99992	D;D;D;D;D	0.89917	0.997;1.0;0.988;1.0;0.989	P;D;P;P;P	0.64877	0.892;0.93;0.742;0.891;0.682	T	0.69487	-0.5132	9	.	.	.	.	14.4752	0.67541	0.075:0.0:0.925:0.0	.	248;221;217;217;217	F5H301;F5H886;Q9UDY2-2;Q9UDY2;Q9UDY2-5	.;.;.;ZO2_HUMAN;.	H	194;217;217;217;221;248	ENSP00000392178:R194H;ENSP00000366453:R217H;ENSP00000345893:R217H;ENSP00000265384:R217H;ENSP00000442090:R221H;ENSP00000438262:R248H	.	R	+	2	0	TJP2	71025930	0.885000	0.30320	0.508000	0.27688	0.547000	0.35210	2.779000	0.47734	2.531000	0.85337	0.591000	0.81541	CGT	.	.	none		0.751	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629		A	71836110	G	A	71836110	3	1	43	1	0	0	0	0	1	0	0	0	15945	1145	40	1	825	1	TJP2	9	71836110	Missense_Mutation	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10		71836110	69377321	37	15385											
PAPPA	5069	hgsc.bcm.edu	37	chr9	119097144	119097144	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ctgtctcccctgacaggcctCcatgtcctgagctgcaggaa	7	9	10	15	0	1	2	0	2	1	0	4	3	3	3	5	2	2	2	5	2	1	0			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr9:119097144C>T	ENST00000328252.3	+	13	3771	c.3402C>T	c.(3400-3402)ctC>ctT	p.L1134L	PAPPA_ENST00000534838.1_Silent_p.L172L	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	1134					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						TGACAGGCCTCCATGTCCTGA	0.622																																					p.L1134L		Atlas-SNP	.											.	PAPPA	243	.	0			c.C3402T						PASS	.						51	45	47					9																	119097144		2203	4300	6503	SO:0001819	synonymous_variant	5069	exon13			AGGCCTCCATGTC		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.3402C>T	9.37:g.119097144C>T		42	0	0		53	11	0.207547	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Silent	SNP	ENST00000328252.3	37	CCDS6813.1																																																																																			.	.	none		0.622	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581		T	119097144	C	T	119097144	2	4	43	1	0	0	0	0	0	0	0	1	11441	842	30	2		2	PAPPA	9	119097144	Silent	SNP	C	TCGA-GS-A9U3-01A-11D-A38X-10	47261034	119097144	22116287	38	15386											
FAS	355	hgsc.bcm.edu	37	chr10	90773975	90773975	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tggtgtcaatgaagccaaaaTagatgagatcaagaatgaca	18	8	10	5	0	2	5	2	3	0	3	2	6	2	5	1	1	1	0	1	1	7	1			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr10:90773975T>C	ENST00000355740.2	+	9	996	c.776T>C	c.(775-777)aTa>aCa	p.I259T	FAS_ENST00000352159.4_3'UTR|FAS_ENST00000355279.2_3'UTR|FAS_ENST00000357339.2_Missense_Mutation_p.I238T|RP11-399O19.9_ENST00000562983.1_RNA	NM_000043.4|NM_152871.2|NM_152872.2	NP_000034.1|NP_690610.1|NP_690611.1	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)	GAAGCCAAAATAGATGAGATC	0.383																																					p.I259T		Atlas-SNP	.											.	FAS	47	.	0			c.T776C	GRCh37	CM033041|CM994522	FAS	M		PASS	.						121	114	116					10																	90773975		2203	4300	6503	SO:0001583	missense	355	exon9			CCAAAATAGATGA	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	ENST00000355740.2:c.776T>C	10.37:g.90773975T>C	ENSP00000347979:p.Ile259Thr	49	0	0		66	15	0.227273	NM_000043	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000355740.2	37	CCDS7393.1	.	.	.	.	.	.	.	.	.	.	T	18.88	3.717060	0.68844	.	.	ENSG00000026103	ENST00000540197;ENST00000355740;ENST00000357339	D;D	0.97378	-4.36;-4.36	4.65	4.65	0.58169	Death (3);DEATH-like (2);	0.172999	0.47093	D	0.000242	D	0.98093	0.9371	M	0.81497	2.545	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98611	1.0663	10	0.87932	D	0	-24.7594	11.0512	0.47893	0.0:0.0:0.0:1.0	.	238;259	P25445-6;P25445	.;TNR6_HUMAN	T	286;259;238	ENSP00000347979:I259T;ENSP00000349896:I238T	ENSP00000347979:I259T	I	+	2	0	FAS	90763955	0.993000	0.37304	0.956000	0.39512	0.989000	0.77384	3.843000	0.55865	2.042000	0.60477	0.528000	0.53228	ATA	.	.	none		0.383	FAS-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049274.3			C	90773975	T	C	90773975	3	2	43	1	0	0	0	0	1	0	0	0	5689	1406	49	3	810	3	FAS	10	90773975	Missense_Mutation	SNP	T	TCGA-GS-A9U3-01A-11D-A38X-10		90773975	44760772	39	15387											
SLC16A12	387700	hgsc.bcm.edu	37	chr10	91195994	91195994	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cacgagcagagggagactttGaagcattgggaggcagagat	13	6	16	6	1	0	4	0	1	0	3	0	8	0	5	0	3	2	3	0	3	1	2			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr10:91195994G>A	ENST00000341233.4	-	7	1411	c.1021C>T	c.(1021-1023)Caa>Taa	p.Q341*	SLC16A12_ENST00000371790.4_Nonsense_Mutation_p.Q371*	NM_213606.3	NP_998771.3	Q6ZSM3	MOT12_HUMAN	solute carrier family 16, member 12	341						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						GGGAGACTTTGAAGCATTGGG	0.478																																					p.Q371X		Atlas-SNP	.											.	SLC16A12	40	.	0			c.C1111T						PASS	.						134	112	119					10																	91195994		2203	4300	6503	SO:0001587	stop_gained	387700	exon7			GACTTTGAAGCAT		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.1021C>T	10.37:g.91195994G>A	ENSP00000343022:p.Gln341*	76	0	0		69	12	0.173913	NM_213606	Q5M9M9|Q5T7J2|Q6ZV76	Nonsense_Mutation	SNP	ENST00000341233.4	37		.	.	.	.	.	.	.	.	.	.	G	39	7.589363	0.98374	.	.	ENSG00000152779	ENST00000341233;ENST00000371790	.	.	.	5.91	5.91	0.95273	.	0.434509	0.27362	N	0.019717	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05436	T	0.98	.	19.2867	0.94077	0.0:0.0:1.0:0.0	.	.	.	.	X	341;371	.	ENSP00000343022:Q341X	Q	-	1	0	SLC16A12	91185974	0.979000	0.34478	0.987000	0.45799	0.729000	0.41735	3.908000	0.56355	2.793000	0.96121	0.655000	0.94253	CAA	.	.	none		0.478	SLC16A12-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_213606		A	91195994	G	A	91195994	4	1	43	1	0	0	0	0	0	1	0	0	14420	1299	45	2	447	2	SLC16A12	10	91195994	Nonsense_Mutation	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10	422019	91195994	44338753	40	15388											
TLL2	7093	hgsc.bcm.edu	37	chr10	98170201	98170201	+	Frame_Shift_Del	DEL	C	C	-																															aaccaggtgcagaaaagtttCccgttgtgtcctgcagggtc																										TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr10:98170201delC	ENST00000357947.3	-	9	1304	c.1079delG	c.(1078-1080)ggafs	p.G360fs	TLL2_ENST00000469598.1_5'UTR	NM_012465.3	NP_036597.1	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	360	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)		AGAAAAGTTTCCCGTTGTGTC	0.582																																					p.G360fs		Atlas-Indel	.											TLL2,NS,malignant_melanoma,-2,1	TLL2	122	1	0			c.1080delA						PASS	.						96	85	88					10																	98170201		2203	4300	6503	SO:0001589	frameshift_variant	7093	exon9			.	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.1079delG	10.37:g.98170201delC	ENSP00000350630:p.Gly360fs	63	0	0		77	13	0.168831	NM_012465	A6NDK0|Q2M1H1|Q6PJN5|Q9UQ00	Frame_Shift_Del	DEL	ENST00000357947.3	37	CCDS7449.1																																																																																			.	.	none		0.582	TLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049608.1			-	98170201	C	-	98170201	7	5	43	1	0	1	0	1	0	0	0	0	15961	855	30	0	2020	0	TLL2	10	98170201	Frame_Shift_Del	DEL	C	TCGA-GS-A9U3-01A-11D-A38X-10	6974207	98170201	37364546	41	15389											
CNNM2	54805	hgsc.bcm.edu	37	chr10	104679785	104679785	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cccctgaaaaccatcaccaaAttttataaccaccccttgca	14	9	2	16	0	1	1	1	1	0	0	1	1	1	1	7	0	3	1	7	0	5	4			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr10:104679785A>G	ENST00000369878.4	+	1	1736	c.1548A>G	c.(1546-1548)aaA>aaG	p.K516K	CNNM2_ENST00000369875.3_Silent_p.K516K|CNNM2_ENST00000433628.2_Silent_p.K516K	NM_017649.4	NP_060119.3	Q9H8M5	CNNM2_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 2	516					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)		CCATCACCAAATTTTATAACC	0.453																																					p.K516K		Atlas-SNP	.											.	CNNM2	119	.	0			c.A1548G						PASS	.						121	131	128					10																	104679785		2203	4300	6503	SO:0001819	synonymous_variant	54805	exon1			CACCAAATTTTAT	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.1548A>G	10.37:g.104679785A>G		133	0	0		167	9	0.0538922	NM_199076	Q5T569|Q5T570|Q8WU59|Q9H952|Q9NRK5|Q9NXT4	Silent	SNP	ENST00000369878.4	37	CCDS44474.1																																																																																			.	.	none		0.453	CNNM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050113.3	NM_017649		G	104679785	A	G	104679785	2	3	43	1	0	0	0	0	0	0	0	1	3615	98	4	3		3	CNNM2	10	104679785	Silent	SNP	A	TCGA-GS-A9U3-01A-11D-A38X-10	6509584	104679785	30854962	42	15390											
OR52L1	338751	hgsc.bcm.edu	37	chr11	6007398	6007398	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	agagccacatgtgctaaacgCcttaagtcgggcctcactcc	10	8	9	14	2	1	1	1	0	0	1	3	1	2	1	4	1	3	1	4	1	3	2			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr11:6007398C>T	ENST00000332249.4	-	1	817	c.763G>A	c.(763-765)Gcg>Acg	p.A255T		NM_001005173.2	NP_001005173.2	Q8NGH7	O52L1_HUMAN	olfactory receptor, family 52, subfamily L, 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)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|pancreas(1)|skin(3)|soft_tissue(1)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.98e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GTGCTAAACGCCTTAAGTCGG	0.512																																					p.A255T	Melanoma(121;653 1666 10547 22796 51255)	Atlas-SNP	.											.	OR52L1	100	.	0			c.G763A						PASS	.						160	156	157					11																	6007398		2072	4222	6294	SO:0001583	missense	338751	exon1			TAAACGCCTTAAG	AB065819	CCDS44529.1	11p15.4	2012-08-09			ENSG00000183313	ENSG00000183313		"GPCR / Class A : Olfactory receptors"	14785	protein-coding gene	gene with protein product							Standard	NM_001005173		Approved		uc001mcd.2	Q8NGH7	OTTHUMG00000165374	ENST00000332249.4:c.763G>A	11.37:g.6007398C>T	ENSP00000330338:p.Ala255Thr	58	0	0		77	13	0.168831	NM_001005173	B2RPA6|Q6IFK9	Missense_Mutation	SNP	ENST00000332249.4	37	CCDS44529.1	.	.	.	.	.	.	.	.	.	.	C	6.616	0.482107	0.12581	.	.	ENSG00000183313	ENST00000332249	T	0.00357	7.89	3.95	3.95	0.45737	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43579	D	0.000558	T	0.00412	0.0013	M	0.79123	2.44	0.31266	N	0.692361	P	0.34955	0.477	B	0.37888	0.26	T	0.25117	-1.0141	10	0.42905	T	0.14	.	14.9281	0.70896	0.0:1.0:0.0:0.0	.	255	Q8NGH7	O52L1_HUMAN	T	255	ENSP00000330338:A255T	ENSP00000330338:A255T	A	-	1	0	OR52L1	5963974	0.522000	0.26266	0.997000	0.53966	0.072000	0.16883	1.327000	0.33746	1.914000	0.55421	0.313000	0.20887	GCG	.	.	none		0.512	OR52L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383754.1	NM_001005173		T	6007398	C	T	6007398	3	4	43	1	0	0	0	0	1	0	0	0	11134	739	26	2	230	2	OR52L1	11	6007398	Missense_Mutation	SNP	C	TCGA-GS-A9U3-01A-11D-A38X-10		6007398	128999118	43	15391											
RBMXL2	27288	hgsc.bcm.edu	37	chr11	7111164	7111164	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ggtcgcgaccgtgactacggGgatcatctgagcagaggctc	8	7	15	11	4	2	3	1	2	1	1	4	5	2	4	1	4	2	2	1	4	1	1	rs138708788		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr11:7111164G>A	ENST00000306904.5	+	1	1000	c.813G>A	c.(811-813)ggG>ggA	p.G271G		NM_014469.4	NP_055284.3	O75526	RMXL2_HUMAN	RNA binding motif protein, X-linked-like 2	271	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)		GTGACTACGGGGATCATCTGA	0.657																																					p.G271G		Atlas-SNP	.											.	RBMXL2	47	.	0			c.G813A						PASS	.	G		2,4390		0,2,2194	26	30	29		813	-1.5	0	11	dbSNP_134	29	0,8582		0,0,4291	no	coding-synonymous	RBMXL2	NM_014469.4		0,2,6485	AA,AG,GG		0.0,0.0455,0.0154		271/393	7111164	2,12972	2196	4291	6487	SO:0001819	synonymous_variant	27288	exon1			CTACGGGGATCAT	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.813G>A	11.37:g.7111164G>A		50	0	0		68	14	0.205882	NM_014469	Q6PEZ2|Q9NQU0	Silent	SNP	ENST00000306904.5	37	CCDS7777.1																																																																																			G|1.000;A|0.000	0.000	weak		0.657	RBMXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384552.1	NM_014469		A	7111164	G	A	7111164	2	1	43	1	0	0	0	0	0	0	0	1	13169	1219	43	2		2	RBMXL2	11	7111164	Silent	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10	1103766	7111164	127895352	44	15392											
OR4A15	81328	hgsc.bcm.edu	37	chr11	55135959	55135959	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccctttctgtggacccaaTgtcattgacaacttcctgtg	7	14	7	13	0	2	1	1	1	1	0	4	2	4	2	3	1	1	0	3	1	2	3			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr11:55135959T>C	ENST00000314706.3	+	1	600	c.600T>C	c.(598-600)aaT>aaC	p.N200N		NM_001005275.1	NP_001005275.1	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A, member 15	200						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						GTGGACCCAATGTCATTGACA	0.433																																					p.N200N		Atlas-SNP	.											.	OR4A15	161	.	0			c.T600C						PASS	.						139	128	132					11																	55135959		2200	4276	6476	SO:0001819	synonymous_variant	81328	exon1			ACCCAATGTCATT	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.600T>C	11.37:g.55135959T>C		315	0	0		314	49	0.156051	NM_001005275	Q6IFL4|Q96R65	Silent	SNP	ENST00000314706.3	37	CCDS31500.1																																																																																			.	.	none		0.433	OR4A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391161.1	NM_001005275		C	55135959	T	C	55135959	2	2	43	1	0	0	0	0	0	0	0	1	11049	1461	51	3		3	OR4A15	11	55135959	Silent	SNP	T	TCGA-GS-A9U3-01A-11D-A38X-10	48024795	55135959	79870557	45	15393											
OR5L1	219437	hgsc.bcm.edu	37	chr11	55579056	55579056	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cttctcatctatggagtcacGttgttagccaacctgggcat	8	13	9	11	1	3	0	2	0	2	0	4	1	3	1	2	2	2	3	2	2	3	4	rs147224918		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr11:55579056G>A	ENST00000333973.2	+	1	203	c.114G>A	c.(112-114)acG>acA	p.T38T		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, 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)	p.T38T(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)				ATGGAGTCACGTTGTTAGCCA	0.502													N|||	1	0.000199681	0.0008	0.0	5008	,	,		18448	0.0		0.0	False		,,,				2504	0.0				p.T38T		Atlas-SNP	.											OR5L1,colon,carcinoma,+2,2	OR5L1	145	2	1	Substitution - coding silent(1)	ovary(1)	c.G114A						scavenged	.	G		1,4399	2.1+/-5.4	0,1,2199	304	268	280		114	-8.6	0	11	dbSNP_134	280	4,8588	3.7+/-12.6	0,4,4292	no	coding-synonymous	OR5L1	NM_001004738.1		0,5,6491	AA,AG,GG		0.0466,0.0227,0.0385		38/312	55579056	5,12987	2200	4296	6496	SO:0001819	synonymous_variant	219437	exon1			AGTCACGTTGTTA	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.114G>A	11.37:g.55579056G>A		136	1	0.00735294		155	28	0.180645	NM_001004738	B2RNK6|Q6IFD0	Silent	SNP	ENST00000333973.2	37	CCDS31509.1																																																																																			G|1.000;A|0.000	0.000	weak		0.502	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738		A	55579056	G	A	55579056	2	1	43	1	0	0	0	0	0	0	0	1	11179	1132	40	1		1	OR5L1	11	55579056	Silent	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10	443097	55579056	79427460	46	15394											
PCNXL3	399909	hgsc.bcm.edu	37	chr11	65388334	65388334	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gcattcctccagcttccactCggctgatgtccctgaggcta	6	11	9	15	1	0	2	0	2	0	0	5	2	4	2	4	2	1	4	4	2	1	3			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr11:65388334C>T	ENST00000355703.3	+	10	2671	c.2132C>T	c.(2131-2133)tCg>tTg	p.S711L		NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	711						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						AGCTTCCACTCGGCTGATGTC	0.682																																					p.S711L		Atlas-SNP	.											.	PCNXL3	140	.	0			c.C2132T						PASS	.						16	20	18					11																	65388334		2029	4170	6199	SO:0001583	missense	399909	exon10			TCCACTCGGCTGA	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.2132C>T	11.37:g.65388334C>T	ENSP00000347931:p.Ser711Leu	50	0	0		66	12	0.181818	NM_032223	Q6MZN8	Missense_Mutation	SNP	ENST00000355703.3	37	CCDS44650.1	.	.	.	.	.	.	.	.	.	.	C	18.22	3.576123	0.65878	.	.	ENSG00000197136	ENST00000355703	T	0.27557	1.66	5.41	4.49	0.54785	.	.	.	.	.	T	0.29524	0.0736	M	0.64404	1.975	0.38704	D	0.953055	B	0.18310	0.027	B	0.06405	0.002	T	0.10405	-1.0631	9	0.31617	T	0.26	.	10.5747	0.45221	0.0:0.9076:0.0:0.0924	.	711	Q9H6A9	PCX3_HUMAN	L	711	ENSP00000347931:S711L	ENSP00000347931:S711L	S	+	2	0	PCNXL3	65144910	1.000000	0.71417	0.952000	0.39060	0.988000	0.76386	6.243000	0.72384	2.536000	0.85505	0.555000	0.69702	TCG	.	.	none		0.682	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223		T	65388334	C	T	65388334	3	4	43	1	0	0	0	0	1	0	0	0	11602	893	31	1	2170	1	PCNXL3	11	65388334	Missense_Mutation	SNP	C	TCGA-GS-A9U3-01A-11D-A38X-10	9809278	65388334	69618182	47	15395											
BBS1	582	hgsc.bcm.edu	37	chr11	66299440	66299440	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggtgctggtgcttcgagaaGgccaaagtgcacccctgctg	8	8	14	11	1	0	1	0	0	0	1	1	2	0	1	3	3	4	4	3	3	2	1			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr11:66299440G>A	ENST00000318312.7	+	17	1765	c.1714G>A	c.(1714-1716)Ggc>Agc	p.G572S	ZDHHC24_ENST00000526986.1_Intron|CTD-3074O7.11_ENST00000419755.3_Missense_Mutation_p.G609S|BBS1_ENST00000393994.2_3'UTR|BBS1_ENST00000455748.2_Missense_Mutation_p.G475S	NM_024649.4	NP_078925.3	Q8NFJ9	BBS1_HUMAN	Bardet-Biedl syndrome 1	572					cilium assembly (GO:0042384)|Golgi to plasma membrane protein transport (GO:0043001)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	patched binding (GO:0005113)|RNA polymerase II repressing transcription factor binding (GO:0001103)|smoothened binding (GO:0005119)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|kidney(5)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(2)|urinary_tract(1)	28						GCTTCGAGAAGGCCAAAGTGC	0.642									Bardet-Biedl syndrome																												p.G572S	GBM(152;173 2612 9770 10137)	Atlas-SNP	.											.	BBS1	58	.	0			c.G1714A						PASS	.						45	39	41					11																	66299440		2196	4293	6489	SO:0001583	missense	582	exon17	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	CGAGAAGGCCAAA	AF503941	CCDS8142.1	11q13	2013-01-08			ENSG00000174483	ENSG00000174483			966	protein-coding gene	gene with protein product		209901				9039982, 12567324	Standard	NM_024649		Approved	FLJ23590	uc001oij.1	Q8NFJ9	OTTHUMG00000167110	ENST00000318312.7:c.1714G>A	11.37:g.66299440G>A	ENSP00000317469:p.Gly572Ser	62	0	0		46	10	0.217391	NM_024649	Q32MM9|Q32MN0|Q96SN4	Missense_Mutation	SNP	ENST00000318312.7	37	CCDS8142.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.828530	0.90955	.	.	ENSG00000256349;ENSG00000174483;ENSG00000174483	ENST00000419755;ENST00000318312;ENST00000455748	D;D;D	0.96856	-4.08;-4.15;-3.97	5.14	5.14	0.70334	.	.	.	.	.	D	0.95671	0.8592	L	0.43152	1.355	0.80722	D	1	D;D;D	0.56521	0.976;0.976;0.976	P;P;P	0.54060	0.741;0.629;0.741	D	0.93872	0.7163	9	0.22109	T	0.4	.	16.1961	0.82025	0.0:0.0:1.0:0.0	.	475;572;609	E7EQH1;Q8NFJ9;Q8NFJ9-2	.;BBS1_HUMAN;.	S	609;572;475	ENSP00000398526:G609S;ENSP00000317469:G572S;ENSP00000405764:G475S	ENSP00000317469:G572S	G	+	1	0	BBS1;CTD-3074O7.11	66056016	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.211000	0.89754	2.682000	0.91365	0.585000	0.79938	GGC	.	.	none		0.642	BBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393235.2			A	66299440	G	A	66299440	3	1	43	1	0	0	0	0	1	0	0	0	1335	1000	35	2	1780	2	BBS1	11	66299440	Missense_Mutation	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10	911106	66299440	68707076	48	15396											
P4HA3	283208	hgsc.bcm.edu	37	chr11	73997431	73997431	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctggccatcctcttattatCtgggcctggaagaaatcaga	10	11	9	11	0	3	2	1	0	2	2	4	3	4	3	4	3	0	0	4	3	4	2			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr11:73997431C>T	ENST00000331597.4	-	6	820	c.775G>A	c.(775-777)Gat>Aat	p.D259N	P4HA3_ENST00000427714.2_Missense_Mutation_p.D259N	NM_182904.3	NP_878907.1	Q7Z4N8	P4HA3_HUMAN	prolyl 4-hydroxylase, alpha polypeptide III	259						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)					CTCTTATTATCTGGGCCTGGA	0.498																																					p.D259N		Atlas-SNP	.											.	P4HA3	43	.	0			c.G775A						PASS	.						83	90	88					11																	73997431		2200	4293	6493	SO:0001583	missense	283208	exon6			TATTATCTGGGCC	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.775G>A	11.37:g.73997431C>T	ENSP00000332170:p.Asp259Asn	81	0	0		112	28	0.25	NM_182904	A0AV13|B4DUD3|Q5EBL3|Q5JPA9	Missense_Mutation	SNP	ENST00000331597.4	37	CCDS8230.1	.	.	.	.	.	.	.	.	.	.	C	11.45	1.642375	0.29246	.	.	ENSG00000149380	ENST00000331597;ENST00000427714	T;T	0.60920	0.15;0.15	5.56	3.67	0.42095	Tetratricopeptide-like helical (1);	0.972834	0.08531	N	0.932012	T	0.43366	0.1244	L	0.28344	0.845	0.30401	N	0.779985	B;B	0.10296	0.003;0.0	B;B	0.08055	0.003;0.001	T	0.33828	-0.9853	10	0.13108	T	0.6	-9.1567	10.8359	0.46688	0.0:0.842:0.0:0.158	.	259;259	B4DUD3;Q7Z4N8	.;P4HA3_HUMAN	N	259	ENSP00000332170:D259N;ENSP00000401749:D259N	ENSP00000332170:D259N	D	-	1	0	P4HA3	73675079	0.177000	0.23109	0.998000	0.56505	0.982000	0.71751	0.753000	0.26376	1.379000	0.46325	0.644000	0.83932	GAT	.	.	none		0.498	P4HA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382988.1	NM_182904		T	73997431	C	T	73997431	3	4	43	1	0	0	0	0	1	0	0	0	11367	913	32	2	891	2	P4HA3	11	73997431	Missense_Mutation	SNP	C	TCGA-GS-A9U3-01A-11D-A38X-10	7697991	73997431	61009085	49	15397											
CARD17	440068	hgsc.bcm.edu	37	chr11	104970112	104970112	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aggaaggaagtactatttgaGaatcttgtgtagtaaggtga	14	12	13	2	0	1	2	0	2	1	1	1	5	1	4	0	3	1	3	0	3	7	6			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr11:104970112G>A	ENST00000375707.1	-	3	327	c.311C>T	c.(310-312)tCt>tTt	p.S104F	CASP1_ENST00000594519.1_Intron|CARD16_ENST00000525374.1_Intron|CASP1_ENST00000415981.2_Intron|CASP1_ENST00000598974.1_Intron|CASP1_ENST00000593315.1_Intron	NM_001007232.1	NP_001007233.1	Q5XLA6	CAR17_HUMAN	caspase recruitment domain family, member 17	104					regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|large_intestine(1)|lung(2)|ovary(1)|stomach(1)	6						TACTATTTGAGAATCTTGTGT	0.383																																					p.S104F		Atlas-SNP	.											.	CARD17	15	.	0			c.C311T						PASS	.						124	119	121					11																	104970112		2202	4299	6501	SO:0001583	missense	440068	exon3			ATTTGAGAATCTT		CCDS31662.1	11q22.3	2009-01-13				ENSG00000255221			33827	protein-coding gene	gene with protein product	"Inhibitory CARD"	609490				15383541	Standard	NM_001007232		Approved	INCA	uc001pir.1	Q5XLA6		ENST00000375707.1:c.311C>T	11.37:g.104970112G>A	ENSP00000364859:p.Ser104Phe	43	0	0		34	8	0.235294	NM_001007232		Missense_Mutation	SNP	ENST00000375707.1	37	CCDS31662.1	.	.	.	.	.	.	.	.	.	.	.	2.868	-0.234690	0.05983	.	.	ENSG00000255221	ENST00000375707	T	0.19394	2.15	1.6	0.655	0.17839	.	.	.	.	.	T	0.16128	0.0388	M	0.64567	1.98	0.09310	N	1	B	0.19706	0.038	B	0.14023	0.01	T	0.39099	-0.9630	9	0.10111	T	0.7	.	3.8812	0.09079	0.2387:0.0:0.7613:0.0	.	104	Q5XLA6	CAR17_HUMAN	F	104	ENSP00000364859:S104F	ENSP00000364859:S104F	S	-	2	0	CARD17	104475322	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.215000	0.17562	0.225000	0.20959	0.430000	0.28490	TCT	.	.	none		0.383	CARD17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388181.1	NM_001007232		A	104970112	G	A	104970112	3	1	43	1	0	0	0	0	1	0	0	0	2650	942	33	2	25	2	CARD17	11	104970112	Missense_Mutation	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10	30972681	104970112	30036404	50	15398											
GLIPR1L2	144321	hgsc.bcm.edu	37	chr12	75816842	75816843	+	Intron	INS	-	-	T																															aataagcgattgaacactagINSttttttatggtcatgttaat																										TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr12:75816842_75816843insT	ENST00000550916.1	+	4	717				GLIPR1L2_ENST00000435775.1_Intron|GLIPR1L2_ENST00000441218.1_Intron|GLIPR1L2_ENST00000320460.4_Frame_Shift_Ins_p.SF248fs|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						TTGAACACTAGTTTTTTATGGT	0.292																																					p.S248fs		Atlas-Indel	.											.	GLIPR1L2	54	.	0			c.743_744insT						PASS	.																																			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+73->T	12.37:g.75816848_75816848dupT		67	0	0		88	11	0.125	NM_152436	Q6MZS1|Q8N6N0|Q8NA43	Frame_Shift_Ins	INS	ENST00000550916.1	37	CCDS58258.1																																																																																			.	.	none		0.292	GLIPR1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405718.1	NM_152436		T	75816843	-	T	75816842	6	5	43	0	1	1	1	0	0	0	0	0	6451	1029	36	0		0	GLIPR1L2	12	75816842	Intron	INS	-	TCGA-GS-A9U3-01A-11D-A38X-10		75816842	58035053	51	15399											
SETD8	387893	hgsc.bcm.edu	37	chr12	123892235	123892235	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcttccattgaagcccacccGtggctgaagcattaaccggt	9	9	10	13	2	0	2	0	2	0	0	1	2	1	2	4	2	3	3	4	2	3	3	rs61955128	byFrequency	TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr12:123892235G>A	ENST00000402868.3	+	8	1470	c.1044G>A	c.(1042-1044)ccG>ccA	p.P348P	SETD8_ENST00000330479.4_Silent_p.P348P			Q9NQR1	SETD8_HUMAN	SET domain containing (lysine methyltransferase) 8	389	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				histone lysine methylation (GO:0034968)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|urinary_tract(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		AAGCCCACCCGTGGCTGAAGC	0.562													G|||	26	0.00519169	0.0083	0.0014	5008	,	,		14479	0.003		0.003	False		,,,				2504	0.0082				p.P348P		Atlas-SNP	.											SETD8,NS,neuroblastoma,0,1	SETD8	35	1	0			c.G1044A						scavenged	.						15	15	15					12																	123892235		2194	4279	6473	SO:0001819	synonymous_variant	387893	exon8			CCACCCGTGGCTG	AY102937	CCDS9247.1	12q24.31	2011-07-01			ENSG00000183955	ENSG00000183955		"Chromatin-modifying enzymes / K-methyltransferases"	29489	protein-coding gene	gene with protein product		607240				15933070, 12086618, 12121615	Standard	NM_020382		Approved	SET8, SET07, PR-Set7, KMT5A	uc001uew.3	Q9NQR1	OTTHUMG00000150477	ENST00000402868.3:c.1044G>A	12.37:g.123892235G>A		41	0	0		61	5	0.0819672	NM_020382	A8K9D0|Q86W83|Q8TD09	Silent	SNP	ENST00000402868.3	37	CCDS9247.1																																																																																			G|0.999;A|0.001	0.001	strong		0.562	SETD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318263.1	NM_020382		A	123892235	G	A	123892235	2	1	43	1	0	0	0	0	0	0	0	1	14152	1132	40	1		1	SETD8	12	123892235	Silent	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10	48075393	123892235	9959660	52	15400											
FZD10	11211	hgsc.bcm.edu	37	chr12	130649024	130649024	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgaagatctttatgctgctgGtggtggggatcaccagcggg	7	11	16	7	1	2	2	1	1	1	1	2	3	2	3	1	5	3	2	1	5	2	2	rs369465643		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr12:130649024G>C	ENST00000229030.4	+	1	2021	c.1537G>C	c.(1537-1539)Gtg>Ctg	p.V513L	FZD10_ENST00000539839.1_3'UTR|FZD10-AS1_ENST00000505807.2_RNA			Q9ULW2	FZD10_HUMAN	frizzled class receptor 10	513					brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|gonad development (GO:0008406)|negative regulation of Rho GTPase activity (GO:0034259)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of actin cytoskeleton organization (GO:0032956)|vasculature development (GO:0001944)	cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|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)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|pancreas(1)|prostate(3)|urinary_tract(1)	35	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.3e-06)|Epithelial(86;1.66e-05)|all cancers(50;5.18e-05)		TATGCTGCTGGTGGTGGGGAT	0.542																																					p.V513L		Atlas-SNP	.											.	FZD10	95	.	0			c.G1537C						PASS	.						42	43	42					12																	130649024		2203	4300	6503	SO:0001583	missense	11211	exon1			CTGCTGGTGGTGG	AB027464	CCDS9267.1	12q24.33	2014-01-29	2014-01-29			ENSG00000111432		"GPCR / Class F : Frizzled receptors", "CD molecules"	4039	protein-coding gene	gene with protein product		606147	"frizzled (Drosophila) homolog 10", "frizzled homolog 10 (Drosophila)", "frizzled 10, seven transmembrane spanning receptor", "frizzled family receptor 10"			10448064	Standard	NM_007197		Approved	CD350	uc001uii.3	Q9ULW2		ENST00000229030.4:c.1537G>C	12.37:g.130649024G>C	ENSP00000229030:p.Val513Leu	37	0	0		40	7	0.175	NM_007197		Missense_Mutation	SNP	ENST00000229030.4	37	CCDS9267.1	.	.	.	.	.	.	.	.	.	.	G	13.54	2.266811	0.40095	.	.	ENSG00000111432	ENST00000229030	D	0.82081	-1.57	4.87	3.97	0.46021	GPCR, family 2-like (1);	0.000000	0.64402	U	0.000002	T	0.75034	0.3795	L	0.28556	0.865	0.54753	D	0.999985	P	0.35107	0.484	B	0.38225	0.268	T	0.70066	-0.4974	10	0.25751	T	0.34	.	13.0162	0.58759	0.0787:0.0:0.9213:0.0	.	513	Q9ULW2	FZD10_HUMAN	L	513	ENSP00000229030:V513L	ENSP00000229030:V513L	V	+	1	0	FZD10	129214977	1.000000	0.71417	0.996000	0.52242	0.835000	0.47333	4.761000	0.62243	1.027000	0.39758	0.561000	0.74099	GTG	.	.	alt		0.542	FZD10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				C	130649024	G	C	130649024	3	2	43	1	0	0	0	0	1	0	0	0	6137	1261	44	4	1539	4	FZD10	12	130649024	Missense_Mutation	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10	6756789	130649024	3202871	53	15401											
SACS	26278	hgsc.bcm.edu	37	chr13	23908091	23908091	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatttggaaaaactgcaatGtgcataaggctgagaggaag	15	8	13	5	0	0	1	0	1	0	1	0	4	0	3	0	3	3	4	0	3	5	2			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr13:23908091G>A	ENST00000382292.3	-	9	10197	c.9924C>T	c.(9922-9924)caC>caT	p.H3308H	SACS_ENST00000402364.1_Silent_p.H2558H|SACS_ENST00000382298.3_Silent_p.H3308H			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3308					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)		AAACTGCAATGTGCATAAGGC	0.418																																					p.H3308H		Atlas-SNP	.											.	SACS	871	.	0			c.C9924T						PASS	.						79	71	74					13																	23908091		2203	4299	6502	SO:0001819	synonymous_variant	26278	exon10			TGCAATGTGCATA	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.9924C>T	13.37:g.23908091G>A		89	0	0		107	20	0.186916	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2																																																																																			.	.	none		0.418	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		A	23908091	G	A	23908091	2	1	43	1	0	0	0	0	0	0	0	1	13819	1368	48	2		2	SACS	13	23908091	Silent	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10		23908091	91261787	54	15402											
CSNK1A1L	122011	hgsc.bcm.edu	37	chr13	37679015	37679015	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tagaaaattctttgtatgcaCgtattcaattctgctgatca	12	16	6	7	1	4	2	2	1	2	1	4	2	4	2	0	0	2	4	0	0	6	7	rs558439842		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr13:37679015C>T	ENST00000379800.3	-	1	788	c.379G>A	c.(379-381)Gtg>Atg	p.V127M		NM_145203.5	NP_660204.2	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like	127	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)		TTTGTATGCACGTATTCAATT	0.403																																					p.V127M		Atlas-SNP	.											.	CSNK1A1L	69	.	0			c.G379A						PASS	.						184	168	173					13																	37679015		2203	4300	6503	SO:0001583	missense	122011	exon1			TATGCACGTATTC	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.379G>A	13.37:g.37679015C>T	ENSP00000369126:p.Val127Met	134	0	0		165	27	0.163636	NM_145203	Q5T2N2	Missense_Mutation	SNP	ENST00000379800.3	37	CCDS9363.1	.	.	.	.	.	.	.	.	.	.	C	10.50	1.368569	0.24771	.	.	ENSG00000180138	ENST00000379800	T	0.19105	2.17	1.01	1.01	0.19927	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.130073	0.51477	D	0.000098	T	0.19046	0.0457	L	0.37561	1.115	0.37424	D	0.913758	D	0.61080	0.989	P	0.50405	0.64	T	0.11518	-1.0584	10	0.27785	T	0.31	.	7.8591	0.29499	0.0:1.0:0.0:0.0	.	127	Q8N752	KC1AL_HUMAN	M	127	ENSP00000369126:V127M	ENSP00000369126:V127M	V	-	1	0	CSNK1A1L	36577015	1.000000	0.71417	0.490000	0.27465	0.493000	0.33554	1.450000	0.35134	0.825000	0.34637	0.561000	0.74099	GTG	.	.	none		0.403	CSNK1A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044563.1	NM_145203		T	37679015	C	T	37679015	3	4	43	1	0	0	0	0	1	0	0	0	3953	536	19	1	638	1	CSNK1A1L	13	37679015	Missense_Mutation	SNP	C	TCGA-GS-A9U3-01A-11D-A38X-10	13770924	37679015	77490863	55	15403											
HTR2A	3356	hgsc.bcm.edu	37	chr13	47409701	47409701	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggacaaagttatcatcggcGagtaagcaactcccctcctt	12	9	8	12	2	1	0	1	0	0	0	4	2	3	1	3	2	2	3	3	2	4	3	rs141413930		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr13:47409701G>T	ENST00000378688.4	-	3	818	c.687C>A	c.(685-687)ctC>ctA	p.L229L	HTR2A_ENST00000542664.1_Silent_p.L229L|HTR2A_ENST00000543956.1_Silent_p.L145L			P28223	5HT2A_HUMAN	5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupled	229					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)	TATCATCGGCGAGTAAGCAAC	0.428																																					p.L229L		Atlas-SNP	.											.	HTR2A	98	.	0			c.C687A						PASS	.						76	74	75					13																	47409701		2203	4300	6503	SO:0001819	synonymous_variant	3356	exon4			ATCGGCGAGTAAG	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.687C>A	13.37:g.47409701G>T		63	0	0		85	22	0.258824	NM_000621	B2RAC5|B4DZ79|F5GWE8|Q5T8C0	Silent	SNP	ENST00000378688.4	37	CCDS9405.1																																																																																			G|0.999;A|0.001	.	alt		0.428	HTR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044835.3	NM_000621		T	47409701	G	T	47409701	2	4	43	1	0	0	0	0	0	0	0	1	7450	1045	37	4		4	HTR2A	13	47409701	Silent	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10	9730686	47409701	67760177	56	15404											
GABRG3	2567	hgsc.bcm.edu	37	chr15	27772692	27772692	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgaccgtgtgcttcctgtttGtcttcgccgcgctgatggag	3	14	13	11	4	1	2	0	2	1	0	3	3	2	3	3	1	1	3	3	1	0	3			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr15:27772692G>A	ENST00000333743.6	+	8	1233	c.979G>A	c.(979-981)Gtc>Atc	p.V327I	RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	327					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)	CTTCCTGTTTGTCTTCGCCGC	0.547																																					p.V327I	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											.	GABRG3	115	.	0			c.G979A						PASS	.						130	119	123					15																	27772692		2165	4275	6440	SO:0001583	missense	2567	exon8			CTGTTTGTCTTCG		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.979G>A	15.37:g.27772692G>A	ENSP00000331912:p.Val327Ile	78	0	0		74	8	0.108108	NM_033223	G3V594|Q9HD46|Q9NYT2	Missense_Mutation	SNP	ENST00000333743.6	37	CCDS45195.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.738335	0.89573	.	.	ENSG00000182256	ENST00000333743	D	0.88354	-2.37	5.48	4.57	0.56435	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.90431	0.7004	L	0.39020	1.185	0.80722	D	1	D	0.55385	0.971	D	0.63033	0.91	D	0.91243	0.5023	10	0.87932	D	0	.	13.4198	0.60989	0.0754:0.0:0.9246:0.0	.	327	Q99928	GBRG3_HUMAN	I	327	ENSP00000331912:V327I	ENSP00000331912:V327I	V	+	1	0	GABRG3	25446287	1.000000	0.71417	0.977000	0.42913	0.838000	0.47535	9.402000	0.97298	1.312000	0.45043	0.563000	0.77884	GTC	.	.	none		0.547	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2			A	27772692	G	A	27772692	3	1	43	1	0	0	0	0	1	0	0	0	6181	1377	48	2	1009	2	GABRG3	15	27772692	Missense_Mutation	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10		27772692	74758700	57	15405											
UBE2Q2	92912	hgsc.bcm.edu	37	chr15	76161328	76161330	+	In_Frame_Del	DEL	GAA	GAA	-																															aagtgacttcagaagaagagGaagaagaagaagagatggct																										TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	GAA	GAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr15:76161328_76161330delGAA	ENST00000267938.4	+	4	806_808	c.424_426delGAA	c.(424-426)gaadel	p.E146del	UBE2Q2_ENST00000561851.1_In_Frame_Del_p.E130del|UBE2Q2_ENST00000569423.1_In_Frame_Del_p.E111del|UBE2Q2_ENST00000338677.4_In_Frame_Del_p.E146del	NM_173469.2	NP_775740.1	Q8WVN8	UB2Q2_HUMAN	ubiquitin-conjugating enzyme E2Q family member 2	146	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						agaagaagaggaagaagaagaag	0.335																																					p.141_142del		Atlas-Indel	.											.	UBE2Q2	26	.	0			c.423_425del						PASS	.																																			SO:0001651	inframe_deletion	92912	exon4			.	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.424_426delGAA	15.37:g.76161337_76161339delGAA	ENSP00000267938:p.Glu146del	142	0	0		194	38	0.195876	NM_173469	B7Z3Q2|H3BRG2|Q8N4G6|Q96J08	In_Frame_Del	DEL	ENST00000267938.4	37	CCDS10286.1																																																																																			.	.	none		0.335	UBE2Q2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286475.1	NM_173469		-	76161330	GAA	-	76161328	7	5	43	1	0	1	0	1	0	0	0	0	16885	1175	41	0	574	0	UBE2Q2	15	76161328	In_Frame_Del	DEL	GAA	TCGA-GS-A9U3-01A-11D-A38X-10	48388636	76161328	26370064	58	15406											
PPP4C	5531	hgsc.bcm.edu	37	chr16	30093814	30093814	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgttccccaggtgtgcggcGacatccatggacaattctat	8	11	10	12	2	1	0	0	0	1	0	3	2	3	1	3	3	1	1	3	3	2	3			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr16:30093814G>A	ENST00000279387.7	+	4	328	c.160G>A	c.(160-162)Gac>Aac	p.D54N	PPP4C_ENST00000561610.1_Missense_Mutation_p.D54N	NM_002720.1	NP_002711.1	P60510	PP4C_HUMAN	protein phosphatase 4, catalytic subunit	54					dephosphorylation (GO:0016311)|NIK/NF-kappaB signaling (GO:0038061)|regulation of double-strand break repair via homologous recombination (GO:0010569)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein phosphatase 4 complex (GO:0030289)	metal ion binding (GO:0046872)|NF-kappaB-inducing kinase activity (GO:0004704)|protein serine/threonine phosphatase activity (GO:0004722)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|liver(2)|lung(2)|pancreas(1)|skin(1)|urinary_tract(1)	9						GGTGTGCGGCGACATCCATGG	0.522																																					p.D54N		Atlas-SNP	.											.	PPP4C	25	.	0			c.G160A						PASS	.						104	89	94					16																	30093814		2197	4300	6497	SO:0001583	missense	5531	exon4			TGCGGCGACATCC		CCDS10669.1	16p11.2	2010-03-17	2010-03-05		ENSG00000149923	ENSG00000149923	3.1.3.16	"Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"	9319	protein-coding gene	gene with protein product	"protein phosphatase X, catalytic subunit"	602035	"protein phosphatase 4 (formerly X), catalytic subunit"			9177794	Standard	NM_002720		Approved	PP4, PPX	uc002dwf.3	P60510	OTTHUMG00000132113	ENST00000279387.7:c.160G>A	16.37:g.30093814G>A	ENSP00000279387:p.Asp54Asn	41	0	0		60	8	0.133333	NM_002720	P33172	Missense_Mutation	SNP	ENST00000279387.7	37	CCDS10669.1	.	.	.	.	.	.	.	.	.	.	G	17.69	3.450968	0.63290	.	.	ENSG00000149923	ENST00000279387	D	0.99842	-7.1	5.88	4.93	0.64822	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (2);Metallophosphoesterase domain (1);	0.000000	0.85682	D	0.000000	D	0.99837	0.9926	H	0.97783	4.075	0.80722	D	1	D	0.55385	0.971	P	0.51657	0.676	D	0.96754	0.9556	10	0.66056	D	0.02	-1.226	15.362	0.74483	0.0:0.0:0.8591:0.1409	.	54	P60510	PP4C_HUMAN	N	54	ENSP00000279387:D54N	ENSP00000279387:D54N	D	+	1	0	PPP4C	30001315	1.000000	0.71417	0.849000	0.33467	0.366000	0.29705	9.363000	0.97131	1.489000	0.48450	0.561000	0.74099	GAC	.	.	none		0.522	PPP4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255155.2	NM_002720		A	30093814	G	A	30093814	3	1	43	1	0	0	0	0	1	0	0	0	12414	1058	37	1	170	1	PPP4C	16	30093814	Missense_Mutation	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10		30093814	60260939	59	15407											
FAM117A	81558	hgsc.bcm.edu	37	chr17	47799869	47799869	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgggtagctacctcttttcGgtggtctgtgctgccccagg	3	13	14	11	1	2	0	0	0	2	0	3	0	2	0	3	4	4	3	3	4	2	4			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr17:47799869G>A	ENST00000240364.2	-	3	533	c.454C>T	c.(454-456)Cga>Tga	p.R152*	FAM117A_ENST00000513602.1_5'UTR|FAM117A_ENST00000514018.1_5'UTR|RP11-613C6.2_ENST00000512720.1_RNA	NM_030802.3	NP_110429.1	Q9C073	F117A_HUMAN	family with sequence similarity 117, member A	152										haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	17						ACCTCTTTTCGGTGGTCTGTG	0.582																																					p.R152X		Atlas-SNP	.											.	FAM117A	45	.	0			c.C454T						PASS	.						129	95	106					17																	47799869		2203	4300	6503	SO:0001587	stop_gained	81558	exon3			CTTTTCGGTGGTC	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.454C>T	17.37:g.47799869G>A	ENSP00000240364:p.Arg152*	59	0	0		63	9	0.142857	NM_030802	B7Z7Q3	Nonsense_Mutation	SNP	ENST00000240364.2	37	CCDS11553.1	.	.	.	.	.	.	.	.	.	.	G	19.67	3.870750	0.72065	.	.	ENSG00000121104	ENST00000240364;ENST00000511743	.	.	.	5.22	4.24	0.50183	.	0.096296	0.44688	D	0.000421	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	-13.8172	13.1594	0.59537	0.0:0.0:0.8398:0.1602	.	.	.	.	X	152;42	.	ENSP00000240364:R152X	R	-	1	2	FAM117A	45154868	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	4.596000	0.61055	1.400000	0.46741	0.655000	0.94253	CGA	.	.	none		0.582	FAM117A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365736.1	NM_030802		A	47799869	G	A	47799869	4	1	43	1	0	0	0	0	0	1	0	0	5414	1124	39	1	931	1	FAM117A	17	47799869	Nonsense_Mutation	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10		47799869	33395341	60	15408											
SSTR2	6752	hgsc.bcm.edu	37	chr17	71166537	71166537	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacggagacccagaggacccTcctcaatggagacctccaaa	13	4	9	15	1	1	3	1	0	0	3	3	6	3	4	5	3	0	0	5	3	2	0			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr17:71166537T>C	ENST00000357585.2	+	2	1448	c.1079T>C	c.(1078-1080)cTc>cCc	p.L360P	SSTR2_ENST00000315332.2_Intron|RP11-143K11.5_ENST00000580671.1_RNA	NM_001050.2	NP_001041.1	P30874	SSR2_HUMAN	somatostatin receptor 2	360					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucocorticoid stimulus (GO:0071385)|cerebellum development (GO:0021549)|digestion (GO:0007586)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cell proliferation (GO:0008285)|peristalsis (GO:0030432)|regulation of muscle contraction (GO:0006937)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|somatostatin receptor activity (GO:0004994)			endometrium(2)|large_intestine(5)|lung(2)|prostate(2)	11			LUSC - Lung squamous cell carcinoma(166;0.197)		Octreotide(DB00104)|Pasireotide(DB06663)|Vapreotide(DB04894)	CAGAGGACCCTCCTCAATGGA	0.567																																					p.L360P		Atlas-SNP	.											.	SSTR2	27	.	0			c.T1079C						PASS	.						48	46	47					17																	71166537		2203	4300	6503	SO:0001583	missense	6752	exon2			GGACCCTCCTCAA		CCDS11691.1	17q24	2012-08-08				ENSG00000180616		"GPCR / Class A : Somatostatin receptors"	11331	protein-coding gene	gene with protein product		182452				8449518	Standard	NM_001050		Approved		uc002jje.3	P30874		ENST00000357585.2:c.1079T>C	17.37:g.71166537T>C	ENSP00000350198:p.Leu360Pro	48	0	0		49	12	0.244898	NM_001050	A8K3Y0|B2R9P7|Q4VBP0|Q96GE0|Q96TF2|Q9BWH1	Missense_Mutation	SNP	ENST00000357585.2	37	CCDS11691.1	.	.	.	.	.	.	.	.	.	.	T	12.50	1.956312	0.34565	.	.	ENSG00000180616	ENST00000357585	T	0.73575	-0.76	5.19	5.19	0.71726	.	0.000000	0.64402	D	0.000001	T	0.68007	0.2954	L	0.46157	1.445	0.80722	D	1	B	0.14012	0.009	B	0.13407	0.009	T	0.63287	-0.6671	10	0.27082	T	0.32	.	15.0092	0.71536	0.0:0.0:0.0:1.0	.	360	P30874	SSR2_HUMAN	P	360	ENSP00000350198:L360P	ENSP00000350198:L360P	L	+	2	0	SSTR2	68678132	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.940000	0.70187	2.084000	0.62774	0.533000	0.62120	CTC	.	.	none		0.567	SSTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441633.1			C	71166537	T	C	71166537	3	2	43	1	0	0	0	0	1	0	0	0	15213	1551	54	3	1081	3	SSTR2	17	71166537	Missense_Mutation	SNP	T	TCGA-GS-A9U3-01A-11D-A38X-10	23366668	71166537	10028673	61	15409											
POTEC	388468	hgsc.bcm.edu	37	chr18	14542891	14542891	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ttcataaaggagttgtcatgGtctccagaagtgcccacgtt	10	12	10	9	1	3	1	2	0	1	1	4	2	3	2	2	2	1	2	2	2	3	4			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr18:14542891G>A	ENST00000358970.5	-	1	254	c.255C>T	c.(253-255)gaC>gaT	p.D85D	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	85										NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						AGTTGTCATGGTCTCCAGAAG	0.592																																					p.D85D		Atlas-SNP	.											POTEC,NS,carcinoma,0,1	POTEC	129	1	0			c.C255T						PASS	.						48	53	52					18																	14542891		692	1591	2283	SO:0001819	synonymous_variant	388468	exon1			GTCATGGTCTCCA	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.255C>T	18.37:g.14542891G>A		298	0	0		275	28	0.101818	NM_001137671		Silent	SNP	ENST00000358970.5	37	CCDS45835.1																																																																																			.	.	none		0.592	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269		A	14542891	G	A	14542891	2	1	43	1	0	0	0	0	0	0	0	1	12271	1252	44	2		2	POTEC	18	14542891	Silent	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10		14542891	63534357	62	15410											
DSG3	1830	hgsc.bcm.edu	37	chr18	29039873	29039873	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accacttgaattctaaaattGccttcaaaattgtctctcag	13	14	4	10	0	4	1	2	1	2	0	5	1	4	1	2	0	1	0	2	0	5	6			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr18:29039873G>T	ENST00000257189.4	+	6	666	c.583G>T	c.(583-585)Gcc>Tcc	p.A195S		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	195	Cadherin 2. {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)			TTCTAAAATTGCCTTCAAAAT	0.418																																					p.A195S		Atlas-SNP	.											DSG3,colon,carcinoma,0,1	DSG3	172	1	0			c.G583T						scavenged	.						87	82	84					18																	29039873		2203	4300	6503	SO:0001583	missense	1830	exon6			AAAATTGCCTTCA	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.583G>T	18.37:g.29039873G>T	ENSP00000257189:p.Ala195Ser	60	2	0.0333333		90	12	0.133333	NM_001944	A8K2V2	Missense_Mutation	SNP	ENST00000257189.4	37	CCDS11898.1	.	.	.	.	.	.	.	.	.	.	G	16.08	3.021035	0.54576	.	.	ENSG00000134757	ENST00000257189	T	0.49432	0.78	5.38	5.38	0.77491	Cadherin (4);Cadherin-like (1);	0.000000	0.46758	D	0.000263	T	0.54515	0.1863	L	0.37466	1.105	0.39402	D	0.966605	P	0.50710	0.938	P	0.61397	0.888	T	0.44236	-0.9341	10	0.20046	T	0.44	.	15.4834	0.75545	0.0:0.1389:0.8611:0.0	.	195	P32926	DSG3_HUMAN	S	195	ENSP00000257189:A195S	ENSP00000257189:A195S	A	+	1	0	DSG3	27293871	1.000000	0.71417	1.000000	0.80357	0.793000	0.44817	4.366000	0.59492	2.698000	0.92095	0.561000	0.74099	GCC	.	.	none		0.418	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944		T	29039873	G	T	29039873	3	4	43	1	0	0	0	0	1	0	0	0	4780	1319	46	4	605	4	DSG3	18	29039873	Missense_Mutation	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10	14496982	29039873	49037375	63	15411											
SHANK1	50944	hgsc.bcm.edu	37	chr19	51165532	51165532	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgagccccccggatatccccGggtgtggcggcacaaagact	8	5	13	15	4	0	1	0	0	0	1	1	3	1	2	5	4	1	1	5	4	2	1	rs571797572		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr19:51165532G>A	ENST00000293441.1	-	23	6194	c.6176C>T	c.(6175-6177)cCg>cTg	p.P2059L	SHANK1_ENST00000359082.3_Missense_Mutation_p.P2050L|SHANK1_ENST00000391814.1_Missense_Mutation_p.P2067L|SYT3_ENST00000544769.1_Intron|SHANK1_ENST00000391813.1_Missense_Mutation_p.P1446L|SHANK1_ENST00000483981.2_5'Flank	NM_016148.2	NP_057232.2	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	2059					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)		GGATATCCCCGGGTGTGGCGG	0.701													g|||	1	0.000199681	0.0	0.0	5008	,	,		12621	0.001		0.0	False		,,,				2504	0.0				p.P2059L		Atlas-SNP	.											.	SHANK1	210	.	0			c.C6176T						PASS	.																																			SO:0001583	missense	50944	exon23			ATCCCCGGGTGTG	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.6176C>T	19.37:g.51165532G>A	ENSP00000293441:p.Pro2059Leu	81	0	0		68	15	0.220588	NM_016148	A8MXP5|B7WNY6|Q9NYW9	Missense_Mutation	SNP	ENST00000293441.1	37	CCDS12799.1	.	.	.	.	.	.	.	.	.	.	g	9.125	1.010036	0.19277	.	.	ENSG00000161681	ENST00000293441;ENST00000391813;ENST00000359082;ENST00000391814	T;T;T;T	0.37584	1.31;1.76;1.3;1.19	3.55	2.5	0.30297	.	0.169189	0.38436	U	0.001681	T	0.28366	0.0701	L	0.52573	1.65	0.43485	D	0.995716	B;B	0.23490	0.052;0.086	B;B	0.10450	0.002;0.005	T	0.10660	-1.0620	10	0.52906	T	0.07	.	7.0697	0.25171	0.1295:0.0:0.8705:0.0	.	2059;1446	Q9Y566;Q9Y566-2	SHAN1_HUMAN;.	L	2059;1446;2050;2067	ENSP00000293441:P2059L;ENSP00000375689:P1446L;ENSP00000351984:P2050L;ENSP00000375690:P2067L	ENSP00000293441:P2059L	P	-	2	0	SHANK1	55857344	0.985000	0.35326	0.735000	0.30896	0.825000	0.46686	0.923000	0.28757	0.845000	0.35118	0.450000	0.29827	CCG	.	.	none		0.701	SHANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268071.1	NM_016148		A	51165532	G	A	51165532	3	1	43	1	0	0	0	0	1	0	0	0	14279	1116	39	1	313	1	SHANK1	19	51165532	Missense_Mutation	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10		51165532	7963451	64	15412											
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385790	58385790	+	Missense_Mutation	SNP	G	G	T																															cacattctccacattcataaGgtcttttcccagtgtgaact																								rs111727691		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr19:58385790G>T	ENST00000435989.2	-	3	1202	c.968C>A	c.(967-969)cCt>cAt	p.P323H	ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000600634.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	323					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						ACATTCATAAGGTCTTTTCCC	0.358																																					p.P323H		Atlas-SNP	.											.	ZNF814	93	.	0			c.C968A						PASS	.						15	12	13					19																	58385790		688	1563	2251	SO:0001583	missense	730051	exon3			TCATAAGGTCTTT		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.968C>A	19.37:g.58385790G>T	ENSP00000410545:p.Pro323His	170	0	0		189	28	0.148148	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	8.139	0.784825	0.16189	.	.	ENSG00000204514	ENST00000435989	T	0.29397	1.57	2.27	1.18	0.20946	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.57080	0.2029	M	0.90019	3.08	0.20764	N	0.999853	D	0.89917	1.0	D	0.67231	0.95	T	0.46247	-0.9205	9	0.66056	D	0.02	.	9.258	0.37595	0.0:0.0:0.7811:0.2189	.	323	B7Z6K7	ZN814_HUMAN	H	323	ENSP00000410545:P323H	ENSP00000410545:P323H	P	-	2	0	ZNF814	63077602	0.000000	0.05858	0.028000	0.17463	0.016000	0.09150	-0.439000	0.06897	0.330000	0.23485	-1.407000	0.01130	CCT	G|0.500;T|0.500	0.500	weak		0.358	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		T	58385790	G	T	58385790	3	4	43	1	0	0	0	0	1	0	0	0	18191	1000	35	4	1603	4	ZNF814	19	58385790	Missense_Mutation	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10	7220258	58385790	743193	65	15413	200	2									
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385793	58385793	+	Missense_Mutation	SNP	C	C	T																															attctccacattcataaggtCttttcccagtgtgaactctc																								rs113623532		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr19:58385793C>T	ENST00000435989.2	-	3	1199	c.965G>A	c.(964-966)aGa>aAa	p.R322K	ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000600634.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	322					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						TTCATAAGGTCTTTTCCCAGT	0.358																																					p.R322K		Atlas-SNP	.											.	ZNF814	93	.	0			c.G965A						PASS	.						15	12	13					19																	58385793		687	1562	2249	SO:0001583	missense	730051	exon3			TAAGGTCTTTTCC		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.965G>A	19.37:g.58385793C>T	ENSP00000410545:p.Arg322Lys	161	0	0		179	25	0.139665	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	0.023	-1.395361	0.01175	.	.	ENSG00000204514	ENST00000435989	T	0.12361	2.69	2.27	9.47E-4	0.14044	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03608	0.0103	N	0.02225	-0.63	0.09310	N	0.999999	B	0.29301	0.241	B	0.28916	0.096	T	0.40534	-0.9558	9	0.02654	T	1	.	4.6969	0.12808	0.0:0.4166:0.0:0.5834	.	322	B7Z6K7	ZN814_HUMAN	K	322	ENSP00000410545:R322K	ENSP00000410545:R322K	R	-	2	0	ZNF814	63077605	0.000000	0.05858	0.024000	0.17045	0.009000	0.06853	-1.883000	0.01623	0.331000	0.23511	-1.381000	0.01174	AGA	C|0.500;T|0.500	0.500	weak		0.358	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		T	58385793	C	T	58385793	3	4	43	1	0	0	0	0	1	0	0	0	18191	913	32	2	1606	2	ZNF814	19	58385793	Missense_Mutation	SNP	C	TCGA-GS-A9U3-01A-11D-A38X-10	3	58385793	743190	66	15414	200	2									
ZNF814	730051	hgsc.bcm.edu	37	chr19	58385867	58385867	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gatttcccacattctccacaTtcatgttttttttcagtgtg	7	19	5	10	0	3	0	2	0	1	0	5	1	4	0	2	0	0	1	2	0	0	7			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr19:58385867T>A	ENST00000435989.2	-	3	1125	c.891A>T	c.(889-891)gaA>gaT	p.E297D	ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000600634.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	297					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						ATTCTCCACATTCATGTTTTT	0.363																																					p.E297D		Atlas-SNP	.											ZNF814,NS,carcinoma,-2,1	ZNF814	93	1	0			c.A891T						scavenged	.						5	4	4					19																	58385867		510	1081	1591	SO:0001583	missense	730051	exon3			TCCACATTCATGT		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.891A>T	19.37:g.58385867T>A	ENSP00000410545:p.Glu297Asp	58	1	0.0172414		79	11	0.139241	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	11.15	1.554325	0.27739	.	.	ENSG00000204514	ENST00000435989	T	0.22134	1.97	1.93	-3.87	0.04218	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.16214	0.0390	L	0.47078	1.49	0.09310	N	1	P	0.36048	0.534	B	0.39738	0.308	T	0.22208	-1.0223	9	0.40728	T	0.16	.	3.3223	0.07054	0.3234:0.181:0.0:0.4956	.	297	B7Z6K7	ZN814_HUMAN	D	297	ENSP00000410545:E297D	ENSP00000410545:E297D	E	-	3	2	ZNF814	63077679	0.000000	0.05858	0.000000	0.03702	0.378000	0.30076	-2.601000	0.00892	-0.795000	0.04462	0.102000	0.15555	GAA	.	.	none		0.363	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		A	58385867	T	A	58385867	3	1	43	1	0	0	0	0	1	0	0	0	18191	1490	52	5	1680	5	ZNF814	19	58385867	Missense_Mutation	SNP	T	TCGA-GS-A9U3-01A-11D-A38X-10	74	58385867	743116	67	15415											
THBD	7056	hgsc.bcm.edu	37	chr20	23028813	23028813	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagccgccgttttcgcactcGtcgatgtccgtgcagatgaa	8	10	11	12	6	0	2	0	1	0	1	4	3	1	2	3	0	2	3	3	0	2	2			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr20:23028813G>A	ENST00000377103.2	-	1	1565	c.1329C>T	c.(1327-1329)gaC>gaT	p.D443D		NM_000361.2	NP_000352.1	P07204	TRBM_HUMAN	thrombomodulin	443	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)	TTTCGCACTCGTCGATGTCCG	0.637																																					p.D443D		Atlas-SNP	.											.	THBD	26	.	0			c.C1329T						PASS	.						51	47	49					20																	23028813		2203	4300	6503	SO:0001819	synonymous_variant	7056	exon1			GCACTCGTCGATG		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.1329C>T	20.37:g.23028813G>A		72	0	0		72	9	0.125	NM_000361	Q8IV29|Q9UC32	Silent	SNP	ENST00000377103.2	37	CCDS13148.1																																																																																			.	.	none		0.637	THBD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078307.2			A	23028813	G	A	23028813	2	1	43	1	0	0	0	0	0	0	0	1	15867	1136	40	1		1	THBD	20	23028813	Silent	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10		23028813	39996707	68	15416											
KRTAP11-1	337880	hgsc.bcm.edu	37	chr21	32253665	32253665	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggcaagcagtgggctcacagCaggtctcttgacagtggtcc	8	8	14	11	0	2	1	1	1	1	0	4	1	3	1	1	4	2	4	1	4	1	1			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr21:32253665C>A	ENST00000332378.4	-	1	209	c.179G>T	c.(178-180)tGc>tTc	p.C60F		NM_175858.2	NP_787054.1	Q8IUC1	KR111_HUMAN	keratin associated protein 11-1	60						keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(12)|pancreas(1)	18						GGGCTCACAGCAGGTCTCTTG	0.562																																					p.C60F		Atlas-SNP	.											KRTAP11-1,NS,carcinoma,+1,1	KRTAP11-1	46	1	0			c.G179T						PASS	.						74	69	71					21																	32253665		2203	4300	6503	SO:0001583	missense	337880	exon1			TCACAGCAGGTCT	AJ457065	CCDS13608.1	21q22.1	2003-03-11			ENSG00000182591	ENSG00000182591		"Keratin associated proteins"	18922	protein-coding gene	gene with protein product		600064				12359730	Standard	NM_175858		Approved	KAP11.1	uc002yov.3	Q8IUC1	OTTHUMG00000057773	ENST00000332378.4:c.179G>T	21.37:g.32253665C>A	ENSP00000330720:p.Cys60Phe	45	0	0		74	27	0.364865	NM_175858	A1L4I8	Missense_Mutation	SNP	ENST00000332378.4	37	CCDS13608.1	.	.	.	.	.	.	.	.	.	.	C	6.705	0.498771	0.12762	.	.	ENSG00000182591	ENST00000332378	T	0.04015	3.73	5.4	0.0314	0.14171	.	1.043570	0.07461	N	0.900691	T	0.07143	0.0181	M	0.71581	2.175	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.41716	-0.9493	10	0.59425	D	0.04	3.1197	3.5867	0.07973	0.1227:0.3415:0.3867:0.1491	.	60	Q8IUC1	KR111_HUMAN	F	60	ENSP00000330720:C60F	ENSP00000330720:C60F	C	-	2	0	KRTAP11-1	31175536	0.064000	0.20934	0.001000	0.08648	0.538000	0.34931	-0.002000	0.12924	-0.184000	0.10567	0.650000	0.86243	TGC	.	.	none		0.562	KRTAP11-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128225.1			A	32253665	C	A	32253665	3	1	43	1	0	0	0	0	1	0	0	0	8526	710	25	4	316	4	KRTAP11-1	21	32253665	Missense_Mutation	SNP	C	TCGA-GS-A9U3-01A-11D-A38X-10		32253665	15876230	69	15417											
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23237676	23237677	+	Frame_Shift_Ins	INS	-	-	T																															cgggagctgtgacagtggccINStggaaggcagatggcagccc																										TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr22:23237676_23237677insT	ENST00000526893.1	+	3	721_722	c.447_448insT	c.(448-450)tggfs	p.W150fs	IGLC1_ENST00000390321.2_RNA|IGLJ1_ENST00000390320.2_RNA|IGLL5_ENST00000532223.2_Frame_Shift_Ins_p.W151fs|IGLL5_ENST00000531372.1_3'UTR	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	150	C region (By similarity to lambda light- chain).|Ig-like C1-type.					extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						TGACAGTGGCCTGGAAGGCAGA	0.594																																					p.A149fs		Atlas-Indel	.											.	IGLL5	26	.	0			c.447_448insT						PASS	.																																			SO:0001589	frameshift_variant	100423062	exon3			.	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.448dupT	22.37:g.23237677_23237677dupT	ENSP00000431254:p.Trp150fs	151	0	0		171	28	0.163743	NM_001178126		Frame_Shift_Ins	INS	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.594	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		T	23237677	-	T	23237676	7	5	43	1	0	1	1	0	0	0	0	0	7603	668	24	0	457	0	IGLL5	22	23237676	Frame_Shift_Ins	INS	-	TCGA-GS-A9U3-01A-11D-A38X-10		23237676	28066890	70	15418											
KIAA1644	85352	hgsc.bcm.edu	37	chr22	44681413	44681413	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcgggcctgggggaggctgcGgctgtggggcccgctgaccc	2	5	21	13	3	0	1	0	1	0	0	0	2	0	2	3	7	1	3	3	7	0	0	rs372785890		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr22:44681413G>A	ENST00000381176.4	-	4	626	c.494C>T	c.(493-495)cCg>cTg	p.P165L		NM_001099294.1	NP_001092764.1	Q3SXP7	K1644_HUMAN	KIAA1644	165						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)				GGGAGGCTGCGGCTGTGGGGC	0.701													G|||	1	0.000199681	0.0	0.0014	5008	,	,		11290	0.0		0.0	False		,,,				2504	0.0				p.P165L		Atlas-SNP	.											.	KIAA1644	39	.	0			c.C494T						PASS	.	G	LEU/PRO	0,3994		0,0,1997	34	40	38		494	5.1	1	22		38	1,8323		0,1,4161	no	missense	KIAA1644	NM_001099294.1	98	0,1,6158	AA,AG,GG		0.012,0.0,0.0081	benign	165/200	44681413	1,12317	1997	4162	6159	SO:0001583	missense	85352	exon4			GGCTGCGGCTGTG	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.494C>T	22.37:g.44681413G>A	ENSP00000370568:p.Pro165Leu	90	0	0		81	11	0.135802	NM_001099294	A6NHP0|A9Z1Z0|Q3SXP8|Q5JZ71|Q9BYB5	Missense_Mutation	SNP	ENST00000381176.4	37	CCDS43025.1	.	.	.	.	.	.	.	.	.	.	G	16.80	3.223504	0.58668	0.0	1.2E-4	ENSG00000138944	ENST00000381176	.	.	.	5.06	5.06	0.68205	.	0.127367	0.53938	D	0.000058	T	0.39172	0.1068	N	0.19112	0.55	0.30929	N	0.727169	B	0.26708	0.157	B	0.22386	0.039	T	0.50759	-0.8790	8	0.46703	T	0.11	-21.0547	15.5806	0.76432	0.0:0.0:1.0:0.0	.	165	Q3SXP7	K1644_HUMAN	L	165	.	ENSP00000370568:P165L	P	-	2	0	KIAA1644	43012746	1.000000	0.71417	1.000000	0.80357	0.813000	0.45954	3.558000	0.53749	2.345000	0.79718	0.561000	0.74099	CCG	.	.	weak		0.701	KIAA1644-006	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000075879.2	NM_001099294		A	44681413	G	A	44681413	3	1	43	1	0	0	0	0	1	0	0	0	8259	1116	39	1	113	1	KIAA1644	22	44681413	Missense_Mutation	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10	21443737	44681413	6623153	71	15419											
CELSR1	9620	hgsc.bcm.edu	37	chr22	46860090	46860090	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttggtggtggacagcacggCggccaccccctccacgaaga	8	5	13	15	3	0	1	0	0	0	1	1	3	1	2	4	5	1	1	4	5	1	1	rs200980049		TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chr22:46860090C>T	ENST00000262738.3	-	2	3696	c.3697G>A	c.(3697-3699)Gcc>Acc	p.A1233T	CELSR1_ENST00000395964.1_Missense_Mutation_p.A1233T	NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1233					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)		GACAGCACGGCGGCCACCCCC	0.612																																					p.A1233T		Atlas-SNP	.											CELSR1,NS,carcinoma,+2,1	CELSR1	242	1	0			c.G3697A						PASS	.	C	THR/ALA	0,4406		0,0,2203	72	65	67		3697	-2.1	0.9	22		67	1,8599	1.2+/-3.3	0,1,4299	yes	missense	CELSR1	NM_014246.1	58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	1233/3015	46860090	1,13005	2203	4300	6503	SO:0001583	missense	9620	exon2			GCACGGCGGCCAC	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.3697G>A	22.37:g.46860090C>T	ENSP00000262738:p.Ala1233Thr	45	0	0		58	8	0.137931	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	C	12.69	2.013015	0.35511	0.0	1.16E-4	ENSG00000075275	ENST00000262738;ENST00000395964	T;T	0.68025	-0.3;0.02	4.75	-2.12	0.07165	.	0.352176	0.25214	N	0.032288	T	0.50905	0.1643	L	0.47716	1.5	0.09310	N	1	B	0.27656	0.184	B	0.15870	0.014	T	0.36432	-0.9748	10	0.26408	T	0.33	.	11.2292	0.48901	0.0:0.4283:0.0:0.5717	.	1233	Q9NYQ6	CELR1_HUMAN	T	1233	ENSP00000262738:A1233T;ENSP00000379293:A1233T	ENSP00000262738:A1233T	A	-	1	0	CELSR1	45238754	0.657000	0.27393	0.930000	0.37139	0.954000	0.61252	0.849000	0.27723	-0.358000	0.08162	-0.302000	0.09304	GCC	.	.	weak		0.612	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246		T	46860090	C	T	46860090	3	4	43	1	0	0	0	0	1	0	0	0	3223	768	27	1	5483	1	CELSR1	22	46860090	Missense_Mutation	SNP	C	TCGA-GS-A9U3-01A-11D-A38X-10	2178677	46860090	4444476	72	15420											
USP9X	8239	hgsc.bcm.edu	37	chrX	41075218	41075218	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttgctatacaactaaagcgaTttgactatgactgggaaaga	15	11	9	6	1	0	3	0	2	0	1	0	5	0	4	0	1	4	1	0	1	7	6			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chrX:41075218T>G	ENST00000324545.8	+	35	6031	c.5398T>G	c.(5398-5400)Ttt>Gtt	p.F1800V	USP9X_ENST00000378308.2_Missense_Mutation_p.F1800V	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	1800	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						ACTAAAGCGATTTGACTATGA	0.383																																					p.F1800V	Ovarian(172;1807 2695 35459 49286)	Atlas-SNP	.											.	USP9X	385	.	0			c.T5398G						PASS	.						82	78	79					X																	41075218		2067	4244	6311	SO:0001583	missense	8239	exon35			AAGCGATTTGACT	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.5398T>G	X.37:g.41075218T>G	ENSP00000316357:p.Phe1800Val	357	0	0		289	62	0.214533	NM_001039591	O75550|Q8WWT3|Q8WX12	Missense_Mutation	SNP	ENST00000324545.8	37	CCDS43930.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.129933	0.77549	.	.	ENSG00000124486	ENST00000378308;ENST00000324545	T;T	0.41400	1.0;1.0	5.67	5.67	0.87782	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.71609	0.3360	M	0.92923	3.36	0.80722	D	1	D;D	0.69078	0.989;0.997	P;D	0.69479	0.818;0.964	T	0.79804	-0.1649	10	0.87932	D	0	.	14.935	0.70948	0.0:0.0:0.0:1.0	.	1800;1800	Q93008-1;Q93008	.;USP9X_HUMAN	V	1800	ENSP00000367558:F1800V;ENSP00000316357:F1800V	ENSP00000316357:F1800V	F	+	1	0	USP9X	40960162	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.651000	0.83577	1.909000	0.55274	0.486000	0.48141	TTT	.	.	none		0.383	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652		G	41075218	T	G	41075218	3	3	43	1	0	0	0	0	1	0	0	0	17105	1493	52	5	5532	5	USP9X	23	41075218	Missense_Mutation	SNP	T	TCGA-GS-A9U3-01A-11D-A38X-10		41075218	114195342	73	15421											
ZC4H2	55906	hgsc.bcm.edu	37	chrX	64141833	64141833	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctcaaactcagccttcaaaCgagccttgatcttctccatc	10	11	4	16	1	5	1	3	1	2	0	7	2	5	1	4	0	4	0	4	0	2	3			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chrX:64141833C>T	ENST00000374839.3	-	2	195	c.89G>A	c.(88-90)cGt>cAt	p.R30H	ZC4H2_ENST00000337990.2_Missense_Mutation_p.R7H|ZC4H2_ENST00000545618.1_Missense_Mutation_p.R25H|ZC4H2_ENST00000447788.2_Missense_Mutation_p.R30H|ZC4H2_ENST00000488608.1_5'UTR	NM_018684.3	NP_061154.1	Q9NQZ6	ZC4H2_HUMAN	zinc finger, C4H2 domain containing	30					nervous system development (GO:0007399)|neuromuscular junction development (GO:0007528)|spinal cord motor neuron differentiation (GO:0021522)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	metal ion binding (GO:0046872)			endometrium(2)|large_intestine(4)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						AGCCTTCAAACGAGCCTTGAT	0.488													C|||	1	0.000264901	0.0	0.0	3775	,	,		14356	0.001		0.0	False		,,,				2504	0.0				p.R30H		Atlas-SNP	.											.	ZC4H2	64	.	0			c.G89A						PASS	.						129	94	106					X																	64141833		2203	4300	6503	SO:0001583	missense	55906	exon2			TTCAAACGAGCCT	AF270491	CCDS14380.1, CCDS55431.1, CCDS55432.1	Xq11.1	2013-07-23	2008-10-01	2008-10-01	ENSG00000126970	ENSG00000126970		"Zinc fingers"	24931	protein-coding gene	gene with protein product		300897	"KIAA1166", "Wieacker-Wolff syndrome"	KIAA1166, WWS		10574461, 12097419, 23623388	Standard	NM_018684		Approved	HCA127	uc004dvu.3	Q9NQZ6	OTTHUMG00000021712	ENST00000374839.3:c.89G>A	X.37:g.64141833C>T	ENSP00000363972:p.Arg30His	382	0	0		438	76	0.173516	NM_018684	B2RDC2|B3KVZ5|B4DED0|E7EM74|G3V1L3|Q53H73|Q5JTF9|Q9H9C3|Q9H9H7|Q9ULQ4	Missense_Mutation	SNP	ENST00000374839.3	37	CCDS14380.1	.	.	.	.	.	.	.	.	.	.	C	32	5.151734	0.94645	.	.	ENSG00000126970	ENST00000447788;ENST00000545618;ENST00000374839;ENST00000337990	.	.	.	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	T	0.76884	0.4050	L	0.61218	1.895	0.80722	D	1	D;D	0.89917	1.0;0.997	D;P	0.85130	0.997;0.856	T	0.79047	-0.1963	9	0.72032	D	0.01	.	15.669	0.77258	0.0:1.0:0.0:0.0	.	30;30	B4DED0;Q9NQZ6	.;ZC4H2_HUMAN	H	30;25;30;7	.	ENSP00000338650:R7H	R	-	2	0	ZC4H2	64058558	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	7.555000	0.82223	2.384000	0.81235	0.529000	0.55759	CGT	.	.	none		0.488	ZC4H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056958.1	NM_018684		T	64141833	C	T	64141833	3	4	43	1	0	0	0	0	1	0	0	0	17593	536	19	1	620	1	ZC4H2	23	64141833	Missense_Mutation	SNP	C	TCGA-GS-A9U3-01A-11D-A38X-10	23066615	64141833	91128727	74	15422											
POF1B	79983	hgsc.bcm.edu	37	chrX	84586065	84586065	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ctggggtccaatttttcaggGccatcatcctgaattatcac	9	13	8	11	0	3	1	3	1	0	0	5	1	5	1	3	3	0	0	3	3	3	3			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chrX:84586065G>T	ENST00000262753.4	-	7	889	c.744C>A	c.(742-744)ggC>ggA	p.G248G	POF1B_ENST00000373145.3_Silent_p.G248G	NM_024921.3	NP_079197.3	Q8WVV4	POF1B_HUMAN	premature ovarian failure, 1B	248						tight junction (GO:0005923)				central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|liver(2)|lung(17)|ovary(1)|prostate(1)	35						ATTTTTCAGGGCCATCATCCT	0.353																																					p.G248G		Atlas-SNP	.											.	POF1B	77	.	0			c.C744A						PASS	.						92	77	82					X																	84586065		2203	4300	6503	SO:0001819	synonymous_variant	79983	exon7			TTCAGGGCCATCA	BC017500	CCDS14452.1	Xq21.2	2008-02-05			ENSG00000124429	ENSG00000124429			13711	protein-coding gene	gene with protein product		300603				11299520	Standard	NM_024921		Approved	POF, FLJ22792	uc004eer.2	Q8WVV4	OTTHUMG00000021934	ENST00000262753.4:c.744C>A	X.37:g.84586065G>T		287	0	0		357	58	0.162465	NM_024921	A8K2U5|Q5H9E9|Q5H9F0|Q8NG12|Q9H5Y2|Q9H738|Q9H744	Silent	SNP	ENST00000262753.4	37	CCDS14452.1																																																																																			.	.	none		0.353	POF1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057391.2	NM_024921		T	84586065	G	T	84586065	2	4	43	1	0	0	0	0	0	0	0	1	12191	1190	42	4		4	POF1B	23	84586065	Silent	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10	20444232	84586065	70684495	75	15423											
CHM	1121	hgsc.bcm.edu	37	chrX	85119697	85119697	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	cttgaaagtctccgagttagCctctggtatggcactggatt	8	13	11	9	1	2	1	0	1	2	0	3	3	2	2	2	3	1	3	2	3	3	4			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chrX:85119697C>A	ENST00000357749.2	-	15	1929	c.1900G>T	c.(1900-1902)Gct>Tct	p.A634S	CHM_ENST00000537751.1_Missense_Mutation_p.A486S|CHM_ENST00000467744.2_Intron	NM_000390.2	NP_000381.1	P24386	RAE1_HUMAN	choroideremia (Rab escort protein 1)	634					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)				TCCGAGTTAGCCTCTGGTATG	0.443																																					p.A634S		Atlas-SNP	.											.	CHM	57	.	0			c.G1900T						PASS	.						79	66	71					X																	85119697		2203	4300	6503	SO:0001583	missense	1121	exon15			AGTTAGCCTCTGG	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.1900G>T	X.37:g.85119697C>A	ENSP00000350386:p.Ala634Ser	184	0	0		210	16	0.0761905	NM_000390	A1L4D2|O43732	Missense_Mutation	SNP	ENST00000357749.2	37	CCDS14454.1	.	.	.	.	.	.	.	.	.	.	C	2.408	-0.336006	0.05278	.	.	ENSG00000188419	ENST00000357749;ENST00000537751	D;D	0.88509	-2.39;-2.07	4.13	-3.43	0.04810	.	1.119830	0.06565	N	0.747470	T	0.80003	0.4544	L	0.42245	1.32	0.09310	N	1	B	0.18166	0.026	B	0.18263	0.021	T	0.60510	-0.7249	10	0.20519	T	0.43	0.7097	2.0276	0.03523	0.1101:0.2218:0.3252:0.3429	.	634	P24386	RAE1_HUMAN	S	634;486	ENSP00000350386:A634S;ENSP00000441728:A486S	ENSP00000350386:A634S	A	-	1	0	CHM	85006353	0.000000	0.05858	0.005000	0.12908	0.230000	0.25150	-0.820000	0.04457	-0.680000	0.05211	-0.366000	0.07423	GCT	.	.	none		0.443	CHM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057396.3	NM_000390		A	85119697	C	A	85119697	3	1	43	1	0	0	0	0	1	0	0	0	3352	739	26	4	65	4	CHM	23	85119697	Missense_Mutation	SNP	C	TCGA-GS-A9U3-01A-11D-A38X-10	533632	85119697	70150863	76	15424											
MID2	11043	hgsc.bcm.edu	37	chrX	107147248	107147248	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtgacgagttggtagagatcAtccagcagaggaagcaaatg	14	7	14	6	1	1	3	1	1	0	2	2	6	2	4	1	2	2	4	1	2	3	2			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chrX:107147248A>G	ENST00000262843.6	+	4	1425	c.877A>G	c.(877-879)Atc>Gtc	p.I293V	MID2_ENST00000443968.2_Missense_Mutation_p.I293V|Y_RNA_ENST00000384633.1_RNA|RP6-191P20.4_ENST00000430140.1_RNA	NM_012216.3|NM_052817.2	NP_036348.2|NP_438112.2	Q9UJV3	TRIM1_HUMAN	midline 2	293					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 localization to microtubule (GO:0035372)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	ligase activity (GO:0016874)|microtubule binding (GO:0008017)|phosphoprotein binding (GO:0051219)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(1)|prostate(2)	19						GGTAGAGATCATCCAGCAGAG	0.413																																					p.I293V		Atlas-SNP	.											.	MID2	122	.	0			c.A877G						PASS	.						139	115	123					X																	107147248		2203	4300	6503	SO:0001583	missense	11043	exon4			GAGATCATCCAGC		CCDS14532.2, CCDS14533.2	Xq22.1-q22.2	2013-02-11			ENSG00000080561	ENSG00000080561		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers", "Fibronectin type III domain containing"	7096	protein-coding gene	gene with protein product		300204				10400986	Standard	NM_012216		Approved	FXY2, TRIM1, RNF60	uc004enl.3	Q9UJV3	OTTHUMG00000022171	ENST00000262843.6:c.877A>G	X.37:g.107147248A>G	ENSP00000262843:p.Ile293Val	194	0	0		240	39	0.1625	NM_012216	A6NEL8|A6PVI5|Q5JYF5|Q8WWK1|Q9UJR9	Missense_Mutation	SNP	ENST00000262843.6	37	CCDS14532.2	.	.	.	.	.	.	.	.	.	.	A	14.90	2.674540	0.47781	.	.	ENSG00000080561	ENST00000262843;ENST00000443968	T;T	0.60299	0.2;0.22	5.23	5.23	0.72850	B-box, C-terminal (1);	0.119673	0.56097	N	0.000025	T	0.45296	0.1335	L	0.31664	0.95	0.53688	D	0.999972	B;P	0.39480	0.303;0.675	B;B	0.37346	0.085;0.247	T	0.46665	-0.9175	10	0.46703	T	0.11	.	12.0069	0.53265	1.0:0.0:0.0:0.0	.	293;293	Q9UJV3;Q9UJV3-2	TRIM1_HUMAN;.	V	293	ENSP00000262843:I293V;ENSP00000413976:I293V	ENSP00000262843:I293V	I	+	1	0	MID2	107033904	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.700000	0.91322	1.738000	0.51689	0.486000	0.48141	ATC	.	.	none		0.413	MID2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057852.2	NM_012216		G	107147248	A	G	107147248	3	3	43	1	0	0	0	0	1	0	0	0	9587	217	8	3	891	3	MID2	23	107147248	Missense_Mutation	SNP	A	TCGA-GS-A9U3-01A-11D-A38X-10	22027551	107147248	48123312	77	15425											
GPR50	9248	hgsc.bcm.edu	37	chrX	150348455	150348455	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	actgctacatctgccacagcCtccagtacgaacggatcttc	10	9	7	15	2	2	0	0	0	2	0	4	2	3	1	3	1	6	2	3	1	3	3			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chrX:150348455C>T	ENST00000218316.3	+	2	469	c.400C>T	c.(400-402)Ctc>Ttc	p.L134F	AF003625.3_ENST00000602313.1_lincRNA|GPR50-AS1_ENST00000454196.1_RNA	NM_004224.3	NP_004215.2	Q13585	MTR1L_HUMAN	G protein-coupled receptor 50	134					cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)|identical protein binding (GO:0042802)|melatonin receptor activity (GO:0008502)			breast(4)|central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	38	Acute lymphoblastic leukemia(192;6.56e-05)					CTGCCACAGCCTCCAGTACGA	0.542																																					p.L134F		Atlas-SNP	.											.	GPR50	195	.	0			c.C400T						PASS	.						122	122	122					X																	150348455		2203	4300	6503	SO:0001583	missense	9248	exon2			CACAGCCTCCAGT	U52219	CCDS44012.1	Xq28	2012-08-21			ENSG00000102195	ENSG00000102195		"GPCR / Class A : Orphans"	4506	protein-coding gene	gene with protein product		300207				9933574, 18400093	Standard	NM_004224		Approved	H9, Mel1c	uc010ntg.2	Q13585	OTTHUMG00000024166	ENST00000218316.3:c.400C>T	X.37:g.150348455C>T	ENSP00000218316:p.Leu134Phe	147	0	0		152	27	0.177632	NM_004224	Q0VGG3|Q3ZAR0	Missense_Mutation	SNP	ENST00000218316.3	37	CCDS44012.1	.	.	.	.	.	.	.	.	.	.	C	13.71	2.318460	0.40996	.	.	ENSG00000102195	ENST00000535473;ENST00000218316	T	0.51071	0.72	4.21	4.21	0.49690	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.36276	0.0961	L	0.35249	1.045	0.45852	D	0.998714	B;P	0.37423	0.026;0.594	B;B	0.40940	0.064;0.344	T	0.11891	-1.0569	10	0.29301	T	0.29	-19.0452	7.6173	0.28165	0.0:0.8782:0.0:0.1218	.	87;134	F5H1S3;Q13585	.;MTR1L_HUMAN	F	87;134	ENSP00000218316:L134F	ENSP00000218316:L134F	L	+	1	0	GPR50	150099113	1.000000	0.71417	0.999000	0.59377	0.720000	0.41350	2.687000	0.46976	1.838000	0.53458	0.523000	0.50628	CTC	.	.	none		0.542	GPR50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060874.1	NM_004224		T	150348455	C	T	150348455	3	4	43	1	0	0	0	0	1	0	0	0	6705	681	24	2	406	2	GPR50	23	150348455	Missense_Mutation	SNP	C	TCGA-GS-A9U3-01A-11D-A38X-10	43201207	150348455	4922105	78	15426											
VMA21	203547	hgsc.bcm.edu	37	chrX	150573426	150573426	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atagggacagctatttttacGctgctattgttgcagtggtc	8	15	11	7	1	0	0	0	0	0	0	1	1	0	1	0	2	4	5	0	2	4	8			TCGA-GS-A9U3-01A-11D-A38X-10	TCGA-GS-A9U3-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	50af794e-c494-4546-be75-32392cfe1183	112ae0ce-a64e-4c94-92bc-27be6b47b249	g.chrX:150573426G>A	ENST00000330374.6	+	3	307	c.202G>A	c.(202-204)Gct>Act	p.A68T	VMA21_ENST00000477649.1_3'UTR|VMA21_ENST00000370361.1_Missense_Mutation_p.A123T	NM_001017980.3	NP_001017980.1			VMA21 vacuolar H+-ATPase homolog (S. cerevisiae)									p.A68T(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)	7						CTATTTTTACGCTGCTATTGT	0.448																																					p.A68T		Atlas-SNP	.											.	VMA21	17	.	1	Substitution - Missense(1)	endometrium(1)	c.G202A						PASS	.						143	114	124					X																	150573426		2203	4300	6503	SO:0001583	missense	203547	exon3			TTTTACGCTGCTA	AK096835	CCDS35430.1	Xq28	2014-09-17			ENSG00000160131	ENSG00000160131			22082	protein-coding gene	gene with protein product		300913	"myopathy with excessive autophagy"	MEAX		2892402, 10757644, 19379691	Standard	NM_001017980		Approved	XMEA	uc004feu.3	Q3ZAQ7	OTTHUMG00000024168	ENST00000330374.6:c.202G>A	X.37:g.150573426G>A	ENSP00000333255:p.Ala68Thr	134	0	0		146	35	0.239726	NM_001017980		Missense_Mutation	SNP	ENST00000330374.6	37	CCDS35430.1	.	.	.	.	.	.	.	.	.	.	.	35	5.500966	0.96371	.	.	ENSG00000160131	ENST00000370361;ENST00000330374	.	.	.	5.8	5.8	0.92144	Vacuolar ATPase assembly integral membrane protein VMA21-like domain (1);	0.000000	0.85682	D	0.000000	D	0.83585	0.5286	M	0.85630	2.765	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.86029	0.1512	9	0.72032	D	0.01	-6.2343	16.2228	0.82267	0.0:0.0:1.0:0.0	.	68	Q3ZAQ7	VMA21_HUMAN	T	123;68	.	ENSP00000333255:A68T	A	+	1	0	VMA21	150324084	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.823000	0.99369	2.434000	0.82447	0.600000	0.82982	GCT	.	.	none		0.448	VMA21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060876.1	NM_001017980		A	150573426	G	A	150573426	3	1	43	1	0	0	0	0	1	0	0	0	17190	1087	38	1	212	1	VMA21	23	150573426	Missense_Mutation	SNP	G	TCGA-GS-A9U3-01A-11D-A38X-10	224971	150573426	4697134	79	15427											
CAMTA1	23261	hgsc.bcm.edu	37	chr1	7796527	7796527	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatccactcaaagactttcCgcggaatgaccctactccac	11	9	6	15	2	1	3	1	2	0	1	4	4	4	4	4	1	1	0	4	1	3	2			TCGA-GS-A9U4-01A-11D-A38X-10	TCGA-GS-A9U4-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4b7512d6-8e65-47d9-98ca-1fe4bd7c455f	22fb535e-5b36-4add-ba3f-997cb70efcff	g.chr1:7796527C>G	ENST00000303635.7	+	13	3397	c.3190C>G	c.(3190-3192)Cgc>Ggc	p.R1064G	CAMTA1_ENST00000439411.2_Missense_Mutation_p.R1064G	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	1064					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)		AAAGACTTTCCGCGGAATGAC	0.597			T	WWTR1	epitheliod hemangioendothelioma																																p.R1064G		Atlas-SNP	.		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	.	CAMTA1	226	.	0			c.C3190G						PASS	.						136	122	127					1																	7796527		2203	4300	6503	SO:0001583	missense	23261	exon13			ACTTTCCGCGGAA	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.3190C>G	1.37:g.7796527C>G	ENSP00000306522:p.Arg1064Gly	96	0	0		92	9	0.0978261	NM_015215	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Missense_Mutation	SNP	ENST00000303635.7	37	CCDS30576.1	.	.	.	.	.	.	.	.	.	.	C	18.41	3.617775	0.66787	.	.	ENSG00000171735	ENST00000303635;ENST00000439411;ENST00000414738;ENST00000303646	T;T	0.42900	0.96;0.96	5.58	5.58	0.84498	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.55305	0.1912	L	0.41824	1.3	0.58432	D	0.999992	D;D;D;D	0.89917	1.0;1.0;1.0;0.998	D;D;D;D	0.91635	0.999;0.995;0.998;0.991	T	0.52741	-0.8535	10	0.48119	T	0.1	-10.5237	14.4254	0.67212	0.1473:0.8526:0.0:0.0	.	1064;151;20;1064	Q9Y6Y1-2;B4DXR3;Q7Z7P1;Q9Y6Y1	.;.;.;CMTA1_HUMAN	G	1064;1064;151;20	ENSP00000306522:R1064G;ENSP00000402561:R1064G	ENSP00000306522:R1064G	R	+	1	0	CAMTA1	7719114	1.000000	0.71417	0.998000	0.56505	0.704000	0.40688	4.842000	0.62831	2.624000	0.88883	0.655000	0.94253	CGC	.	.	none		0.597	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215		G	7796527	C	G	7796527	3	3	44	1	0	0	0	0	1	0	0	0	2615	652	23	4	3240	4	CAMTA1	1	7796527	Missense_Mutation	SNP	C	TCGA-GS-A9U4-01A-11D-A38X-10		7796527	241454094	1	15428											
DLGAP3	58512	hgsc.bcm.edu	37	chr1	35370945	35370945	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ttggtcagcaaagcgggctgGgcggggatggctgcctcggt	5	8	19	9	3	1	0	1	0	0	0	2	1	1	1	1	7	3	3	1	7	1	1			TCGA-GS-A9U4-01A-11D-A38X-10	TCGA-GS-A9U4-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4b7512d6-8e65-47d9-98ca-1fe4bd7c455f	22fb535e-5b36-4add-ba3f-997cb70efcff	g.chr1:35370945G>A	ENST00000373347.1	-	3	308	c.40C>T	c.(40-42)Cca>Tca	p.P14S	DLGAP3_ENST00000495979.1_5'UTR|DLGAP3_ENST00000235180.4_Missense_Mutation_p.P14S			O95886	DLGP3_HUMAN	discs, large (Drosophila) homolog-associated protein 3	14					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)				AAGCGGGCTGGGCGGGGATGG	0.642																																					p.P14S		Atlas-SNP	.											.	DLGAP3	107	.	0			c.C40T						PASS	.						4	4	4					1																	35370945		2095	4128	6223	SO:0001583	missense	58512	exon1			GGGCTGGGCGGGG	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.40C>T	1.37:g.35370945G>A	ENSP00000362444:p.Pro14Ser	88	0	0		63	8	0.126984	NM_001080418	Q5TDD5|Q9H3X7	Missense_Mutation	SNP	ENST00000373347.1	37	CCDS30670.1	.	.	.	.	.	.	.	.	.	.	g	7.354	0.623400	0.14193	.	.	ENSG00000116544	ENST00000373347;ENST00000235180	T;T	0.25579	1.79;1.79	4.49	3.57	0.40892	.	0.177561	0.37483	N	0.002071	T	0.16342	0.0393	L	0.27053	0.805	0.33953	D	0.644702	B	0.26081	0.141	B	0.20955	0.032	T	0.17379	-1.0371	10	0.28530	T	0.3	-3.2976	10.9404	0.47270	0.0919:0.0:0.9081:0.0	.	14	O95886	DLGP3_HUMAN	S	14	ENSP00000362444:P14S;ENSP00000235180:P14S	ENSP00000235180:P14S	P	-	1	0	DLGAP3	35143532	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.279000	0.51670	2.054000	0.61138	0.457000	0.33378	CCA	.	.	none		0.642	DLGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011554.1	NM_021234		A	35370945	G	A	35370945	3	1	44	1	0	0	0	0	1	0	0	0	4563	1232	43	2	2939	2	DLGAP3	1	35370945	Missense_Mutation	SNP	G	TCGA-GS-A9U4-01A-11D-A38X-10	27574418	35370945	213879676	2	15429											
HHLA3	11147	hgsc.bcm.edu	37	chr1	70832174	70832174	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ccagaccccaagagagcattCttggatctcttgcaagaaag	13	8	9	11	0	2	3	0	0	2	3	3	5	2	4	3	1	2	2	3	1	3	3	rs143161214		TCGA-GS-A9U4-01A-11D-A38X-10	TCGA-GS-A9U4-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4b7512d6-8e65-47d9-98ca-1fe4bd7c455f	22fb535e-5b36-4add-ba3f-997cb70efcff	g.chr1:70832174C>G	ENST00000359875.5	+	2	445	c.305C>G	c.(304-306)tCt>tGt	p.S102C	HHLA3_ENST00000361764.4_Missense_Mutation_p.F68L|HHLA3_ENST00000370940.5_Missense_Mutation_p.L70V|HHLA3_ENST00000531950.1_Missense_Mutation_p.S102C|HHLA3_ENST00000432224.1_Missense_Mutation_p.L103V	NM_001036645.1	NP_001031722.1	Q9XRX5	HHLA3_HUMAN	HERV-H LTR-associating 3	102										large_intestine(3)|lung(1)	4						agagagcattcttggatctct	0.368																																					p.S102C		Atlas-SNP	.											.	HHLA3	11	.	0			c.C305G						PASS	.						13	15	14					1																	70832174		2182	4265	6447	SO:0001583	missense	11147	exon2			AGCATTCTTGGAT	AF126164	CCDS649.1, CCDS30752.1, CCDS30753.1	1p31.1	2008-02-05			ENSG00000197568	ENSG00000197568			4906	protein-coding gene	gene with protein product		604372				10444326	Standard	NR_027404		Approved		uc001dfa.3	Q9XRX5	OTTHUMG00000009346	ENST00000359875.5:c.305C>G	1.37:g.70832174C>G	ENSP00000352938:p.Ser102Cys	152	0	0		140	8	0.0571429	NM_001036645	D3DQ74|Q5VZP2|Q96FH5|Q9XRX4	Missense_Mutation	SNP	ENST00000359875.5	37	CCDS30753.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	3.184|3.184|3.184	-0.167279|-0.167279|-0.167279	0.06461|0.06461|0.06461	.|.|.	.|.|.	ENSG00000197568|ENSG00000197568|ENSG00000197568	ENST00000361764|ENST00000370940;ENST00000432224|ENST00000359875;ENST00000531950	.|.|.	.|.|.	.|.|.	0.137|0.137|0.137	0.137|0.137|0.137	0.14787|0.14787|0.14787	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	0.37019|0.37019|0.37019	0.0988|0.0988|0.0988	.|.|.	.|.|.	.|.|.	0.09310|0.09310|0.09310	N|N|N	1|1|1	B|P|P	0.28667|0.37398|0.49696	0.219|0.593|0.927	B|P|P	0.39217|0.48114|0.58660	0.294|0.567|0.843	T|T|T	0.14559|0.14559|0.14559	-1.0468|-1.0468|-1.0468	6|6|6	0.02654|0.87932|0.87932	T|D|D	1|0|0	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	68|70|102	Q9XRX5-3|Q9XRX5-2|Q9XRX5	.|.|HHLA3_HUMAN	L|V|C	68|70;103|102	.|.|.	ENSP00000354815:F68L|ENSP00000359978:L70V|ENSP00000352938:S102C	F|L|S	+|+|+	3|1|2	2|0|0	HHLA3|HHLA3|HHLA3	70604762|70604762|70604762	0.005000|0.005000|0.005000	0.15991|0.15991|0.15991	0.015000|0.015000|0.015000	0.15790|0.15790|0.15790	0.016000|0.016000|0.016000	0.09150|0.09150|0.09150	-0.771000|-0.771000|-0.771000	0.04699|0.04699|0.04699	0.291000|0.291000|0.291000	0.22468|0.22468|0.22468	0.297000|0.297000|0.297000	0.19635|0.19635|0.19635	TTC|CTT|TCT	C|1.000;A|0.000	.	alt		0.368	HHLA3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000025911.2	NM_007071		G	70832174	C	G	70832174	3	3	44	1	0	0	0	0	1	0	0	0	7105	913	32	4	311	4	HHLA3	1	70832174	Missense_Mutation	SNP	C	TCGA-GS-A9U4-01A-11D-A38X-10	35461229	70832174	178418447	3	15430											
PKN2	5586	hgsc.bcm.edu	37	chr1	89271287	89271287	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	attctggcaccttcagccctCaagctcctgtgcctactaca	8	11	6	16	0	3	0	2	0	1	0	4	0	4	0	4	1	5	2	4	1	3	4			TCGA-GS-A9U4-01A-11D-A38X-10	TCGA-GS-A9U4-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4b7512d6-8e65-47d9-98ca-1fe4bd7c455f	22fb535e-5b36-4add-ba3f-997cb70efcff	g.chr1:89271287C>G	ENST00000370521.3	+	11	1968	c.1609C>G	c.(1609-1611)Caa>Gaa	p.Q537E	PKN2_ENST00000316005.7_Missense_Mutation_p.Q537E|PKN2_ENST00000370513.5_Missense_Mutation_p.Q489E|PKN2_ENST00000544045.1_Missense_Mutation_p.Q211E|PKN2_ENST00000370505.3_Missense_Mutation_p.Q380E	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	537					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)		CTTCAGCCCTCAAGCTCCTGT	0.443																																					p.Q537E		Atlas-SNP	.											.	PKN2	109	.	0			c.C1609G						PASS	.						67	66	67					1																	89271287		1960	4158	6118	SO:0001583	missense	5586	exon11			AGCCCTCAAGCTC	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.1609C>G	1.37:g.89271287C>G	ENSP00000359552:p.Gln537Glu	148	0	0		122	8	0.0655738	NM_006256	B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	Missense_Mutation	SNP	ENST00000370521.3	37	CCDS714.1	.	.	.	.	.	.	.	.	.	.	C	4.487	0.090208	0.08632	.	.	ENSG00000065243	ENST00000370521;ENST00000316005;ENST00000370505;ENST00000370513;ENST00000544045	T;T;T;T;T	0.35236	1.32;1.32;1.32;1.32;1.32	6.02	6.02	0.97574	.	0.000000	0.43260	U	0.000595	T	0.15219	0.0367	L	0.38175	1.15	0.48632	D	0.999685	B;B;B;B	0.20368	0.002;0.001;0.044;0.025	B;B;B;B	0.18561	0.002;0.002;0.022;0.02	T	0.19160	-1.0314	10	0.02654	T	1	.	20.5269	0.99230	0.0:1.0:0.0:0.0	.	521;489;537;537	B4DTP5;E7ESL7;Q16513;B1AL79	.;.;PKN2_HUMAN;.	E	537;537;380;489;211	ENSP00000359552:Q537E;ENSP00000317851:Q537E;ENSP00000359536:Q380E;ENSP00000359544:Q489E;ENSP00000439643:Q211E	ENSP00000317851:Q537E	Q	+	1	0	PKN2	89043875	1.000000	0.71417	0.998000	0.56505	0.995000	0.86356	7.144000	0.77357	2.859000	0.98148	0.591000	0.81541	CAA	.	.	none		0.443	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027828.3	NM_006256		G	89271287	C	G	89271287	3	3	44	1	0	0	0	0	1	0	0	0	11989	827	29	4	1651	4	PKN2	1	89271287	Missense_Mutation	SNP	C	TCGA-GS-A9U4-01A-11D-A38X-10	18439113	89271287	159979334	4	15431											
NEK1	4750	hgsc.bcm.edu	37	chr4	170509869	170509869	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	atggggtccctatgcaagttCgagccagctctacagtacta	10	10	10	11	1	1	0	0	0	1	0	3	1	2	0	2	2	5	4	2	2	5	5			TCGA-GS-A9U4-01A-11D-A38X-10	TCGA-GS-A9U4-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4b7512d6-8e65-47d9-98ca-1fe4bd7c455f	22fb535e-5b36-4add-ba3f-997cb70efcff	g.chr4:170509869C>T	ENST00000439128.2	-	7	1122	c.482G>A	c.(481-483)cGa>cAa	p.R161Q	NEK1_ENST00000510533.1_Missense_Mutation_p.R161Q|NEK1_ENST00000512193.1_Missense_Mutation_p.R161Q|NEK1_ENST00000511633.1_Missense_Mutation_p.R161Q|NEK1_ENST00000507142.1_Missense_Mutation_p.R161Q	NM_012224.2	NP_036356.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	161	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|stomach(1)	45		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		TATGCAAGTTCGAGCCAGCTC	0.343																																					p.R161Q		Atlas-SNP	.											.	NEK1	203	.	0			c.G482A						PASS	.						43	42	42					4																	170509869		1718	3745	5463	SO:0001583	missense	4750	exon8			CAAGTTCGAGCCA	AB067488	CCDS47162.1, CCDS56348.1, CCDS56349.1, CCDS56350.1, CCDS56351.1	4q32.3	2012-11-15	2012-11-15		ENSG00000137601	ENSG00000137601			7744	protein-coding gene	gene with protein product		604588	"NIMA (never in mitosis gene a)-related kinase 1"			1382974, 8274451	Standard	NM_012224		Approved	NY-REN-55, KIAA1901	uc003isd.2	Q96PY6	OTTHUMG00000160963	ENST00000439128.2:c.482G>A	4.37:g.170509869C>T	ENSP00000408020:p.Arg161Gln	275	0	0		176	23	0.130682	NM_001199399	G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	Missense_Mutation	SNP	ENST00000439128.2	37	CCDS47162.1	.	.	.	.	.	.	.	.	.	.	C	36	5.684701	0.96784	.	.	ENSG00000137601	ENST00000439128;ENST00000511633;ENST00000510533;ENST00000507142;ENST00000512193	T;T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12;-0.12	6.02	6.02	0.97574	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	0.66636	0.2809	N	0.11255	0.115	0.80722	D	1	D;D;D;D;D;D	0.89917	0.97;1.0;1.0;1.0;1.0;1.0	P;D;D;D;D;D	0.91635	0.637;0.998;0.999;0.999;0.999;0.999	T	0.70594	-0.4829	10	0.48119	T	0.1	.	20.5373	0.99239	0.0:1.0:0.0:0.0	.	161;161;161;161;161;161	Q96PY6-5;Q96PY6-4;G5E9Z3;Q96PY6-3;Q96PY6-2;Q96PY6	.;.;.;.;.;NEK1_HUMAN	Q	161	ENSP00000408020:R161Q;ENSP00000423332:R161Q;ENSP00000427653:R161Q;ENSP00000424757:R161Q;ENSP00000424938:R161Q	ENSP00000408020:R161Q	R	-	2	0	NEK1	170746444	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.492000	0.81482	2.857000	0.98124	0.650000	0.86243	CGA	.	.	none		0.343	NEK1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363157.3			T	170509869	C	T	170509869	3	4	44	1	0	0	0	0	1	0	0	0	10330	884	31	1	3406	1	NEK1	4	170509869	Missense_Mutation	SNP	C	TCGA-GS-A9U4-01A-11D-A38X-10		170509869	20644407	5	15432											
RPL37	6167	hgsc.bcm.edu	37	chr5	40832665	40832665	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttaggtgttgttccttcacGgaatccatgcctgcaggatg	7	14	11	9	1	1	0	1	0	0	0	3	2	3	2	3	3	2	3	3	3	2	5	rs368304251		TCGA-GS-A9U4-01A-11D-A38X-10	TCGA-GS-A9U4-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4b7512d6-8e65-47d9-98ca-1fe4bd7c455f	22fb535e-5b36-4add-ba3f-997cb70efcff	g.chr5:40832665G>A	ENST00000274242.5	-	4	384	c.235C>T	c.(235-237)Cgt>Tgt	p.R79C	SNORD72_ENST00000390994.1_RNA|RPL37_ENST00000504562.1_5'UTR|RPL37_ENST00000509877.1_Silent_p.S50S	NM_000997.4	NP_000988.1	P61927	RL37_HUMAN	ribosomal protein L37	79					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)				GTTCCTTCACGGAATCCATGC	0.383																																					p.R79C	Colon(188;1411 2035 4978 19588 31462)	Atlas-SNP	.											RPL37,NS,carcinoma,0,1	RPL37	7	1	0			c.C235T						PASS	.	G	CYS/ARG	0,4406		0,0,2203	180	184	183		235	3.9	1	5		183	1,8599	1.2+/-3.3	0,1,4299	no	missense	RPL37	NM_000997.4	180	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	79/98	40832665	1,13005	2203	4300	6503	SO:0001583	missense	6167	exon4			CTTCACGGAATCC	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.235C>T	5.37:g.40832665G>A	ENSP00000274242:p.Arg79Cys	193	0	0		145	8	0.0551724	NM_000997	B2R4H2|P02403|Q6IBB4|Q99883	Missense_Mutation	SNP	ENST00000274242.5	37	CCDS3934.1	.	.	.	.	.	.	.	.	.	.	G	15.73	2.919716	0.52653	0.0	1.16E-4	ENSG00000145592	ENST00000274242	T	0.53423	0.62	4.81	3.94	0.45596	.	0.000000	0.85682	U	0.000000	T	0.39253	0.1071	.	.	.	0.80722	D	1	B	0.12013	0.005	B	0.08055	0.003	T	0.20672	-1.0268	9	0.46703	T	0.11	.	12.9052	0.58147	0.0788:0.0:0.9212:0.0	.	79	P61927	RL37_HUMAN	C	79	ENSP00000274242:R79C	ENSP00000274242:R79C	R	-	1	0	RPL37	40868422	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.595000	0.82710	1.023000	0.39654	0.563000	0.77884	CGT	.	.	weak		0.383	RPL37-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000211583.2	NM_000997		A	40832665	G	A	40832665	3	1	44	1	0	0	0	0	1	0	0	0	13604	1116	39	1	62	1	RPL37	5	40832665	Missense_Mutation	SNP	G	TCGA-GS-A9U4-01A-11D-A38X-10		40832665	140082595	6	15433											
MAP1B	4131	hgsc.bcm.edu	37	chr5	71495880	71495880	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cattgagcagaacctgggcaAagctctaaagaaagatctga	16	7	10	8	0	2	5	0	2	2	3	2	5	2	5	1	1	3	3	1	1	5	2			TCGA-GS-A9U4-01A-11D-A38X-10	TCGA-GS-A9U4-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4b7512d6-8e65-47d9-98ca-1fe4bd7c455f	22fb535e-5b36-4add-ba3f-997cb70efcff	g.chr5:71495880A>C	ENST00000296755.7	+	5	6996	c.6698A>C	c.(6697-6699)aAa>aCa	p.K2233T		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	2233					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)		AACCTGGGCAAAGCTCTAAAG	0.522																																					p.K2233T	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.A6698C						PASS	.						101	102	101					5																	71495880		2203	4300	6503	SO:0001583	missense	4131	exon5			TGGGCAAAGCTCT	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.6698A>C	5.37:g.71495880A>C	ENSP00000296755:p.Lys2233Thr	61	0	0		50	5	0.1	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	A	16.32	3.089024	0.55968	.	.	ENSG00000131711	ENST00000296755	T	0.03920	3.76	5.79	5.79	0.91817	.	0.000000	0.64402	D	0.000001	T	0.15696	0.0378	L	0.52364	1.645	0.51767	D	0.999934	D;D	0.61697	0.99;0.979	D;P	0.63957	0.92;0.702	T	0.00303	-1.1833	10	0.48119	T	0.1	-23.3459	16.1303	0.81428	1.0:0.0:0.0:0.0	.	2107;2233	A2BDK6;P46821	.;MAP1B_HUMAN	T	2233	ENSP00000296755:K2233T	ENSP00000296755:K2233T	K	+	2	0	MAP1B	71531636	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.846000	0.92159	2.218000	0.71995	0.533000	0.62120	AAA	.	.	none		0.522	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		C	71495880	A	C	71495880	3	2	44	1	0	0	0	0	1	0	0	0	9237	14	1	5	6716	5	MAP1B	5	71495880	Missense_Mutation	SNP	A	TCGA-GS-A9U4-01A-11D-A38X-10	30663215	71495880	109419380	7	15434											
GAL3ST4	79690	hgsc.bcm.edu	37	chr7	99757593	99757593	+	Silent	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtcttgaggggcagtgagacGgtaggggggaactgcttggc	7	8	20	6	1	1	2	0	2	1	1	1	4	1	3	0	7	2	3	0	7	2	3			TCGA-GS-A9U4-01A-11D-A38X-10	TCGA-GS-A9U4-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4b7512d6-8e65-47d9-98ca-1fe4bd7c455f	22fb535e-5b36-4add-ba3f-997cb70efcff	g.chr7:99757593G>C	ENST00000360039.4	-	4	1811	c.1419C>G	c.(1417-1419)acC>acG	p.T473T	C7orf43_ENST00000419841.1_5'Flank|C7orf43_ENST00000498638.1_5'Flank|GAL3ST4_ENST00000426974.2_Silent_p.T411T|C7orf43_ENST00000316937.3_5'Flank|C7orf43_ENST00000457641.1_5'Flank|GAL3ST4_ENST00000411994.1_3'UTR|GAL3ST4_ENST00000413800.1_Silent_p.T473T|GAL3ST4_ENST00000423751.1_3'UTR	NM_024637.4	NP_078913.3	Q96RP7	G3ST4_HUMAN	galactose-3-O-sulfotransferase 4	473					cell-cell signaling (GO:0007267)|glycoprotein metabolic process (GO:0009100)|oligosaccharide metabolic process (GO:0009311)|proteoglycan biosynthetic process (GO:0030166)|sulfur compound metabolic process (GO:0006790)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|galactose 3-O-sulfotransferase activity (GO:0050694)|galactosylceramide sulfotransferase activity (GO:0001733)|proteoglycan sulfotransferase activity (GO:0050698)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(8)|ovary(5)|prostate(1)|upper_aerodigestive_tract(1)	26	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GCAGTGAGACGGTAGGGGGGA	0.537																																					p.T473T		Atlas-SNP	.											.	GAL3ST4	59	.	0			c.C1419G						PASS	.						94	81	85					7																	99757593		2203	4300	6503	SO:0001819	synonymous_variant	79690	exon4			TGAGACGGTAGGG	AF316113	CCDS5688.1	7q22.1	2007-04-02			ENSG00000197093	ENSG00000197093		"Sulfotransferases, membrane-bound"	24145	protein-coding gene	gene with protein product		608235				11333265	Standard	NM_024637		Approved	FLJ12116	uc003utu.3	Q96RP7	OTTHUMG00000154885	ENST00000360039.4:c.1419C>G	7.37:g.99757593G>C		76	0	0		63	6	0.0952381	NM_024637	A4D2A8|B4DWL8|D6W5U5|Q8N3P7|Q8WZ17|Q96E33|Q9HA78	Silent	SNP	ENST00000360039.4	37	CCDS5688.1																																																																																			.	.	none		0.537	GAL3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337495.2	NM_024637		C	99757593	G	C	99757593	2	2	44	1	0	0	0	0	0	0	0	1	6208	1103	39	4		4	GAL3ST4	7	99757593	Silent	SNP	G	TCGA-GS-A9U4-01A-11D-A38X-10		99757593	59381070	8	15435											
UBE2R2	54926	hgsc.bcm.edu	37	chr9	33900200	33900200	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtatgcatttcgattcttcAtccgcctgtagatgacccac	8	14	7	12	2	2	2	1	1	1	1	4	3	3	2	3	0	1	3	3	0	2	5			TCGA-GS-A9U4-01A-11D-A38X-10	TCGA-GS-A9U4-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4b7512d6-8e65-47d9-98ca-1fe4bd7c455f	22fb535e-5b36-4add-ba3f-997cb70efcff	g.chr9:33900200A>T	ENST00000263228.3	+	3	484	c.293A>T	c.(292-294)cAt>cTt	p.H98L		NM_017811.3	NP_060281.2	Q712K3	UB2R2_HUMAN	ubiquitin-conjugating enzyme E2R 2	98					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)		TCGATTCTTCATCCGCCTGTA	0.403																																					p.H98L		Atlas-SNP	.											UBE2R2,NS,carcinoma,+1,1	UBE2R2	19	1	0			c.A293T						PASS	.						154	146	149					9																	33900200		2203	4300	6503	SO:0001583	missense	54926	exon3			TTCTTCATCCGCC	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	ENST00000263228.3:c.293A>T	9.37:g.33900200A>T	ENSP00000263228:p.His98Leu	141	0	0		153	11	0.0718954	NM_017811	D3DRL5|Q9NX64	Missense_Mutation	SNP	ENST00000263228.3	37	CCDS6546.1	.	.	.	.	.	.	.	.	.	.	A	32	5.129742	0.94473	.	.	ENSG00000107341	ENST00000263228	T	0.37915	1.17	5.73	5.73	0.89815	Ubiquitin-conjugating enzyme, E2 (2);Ubiquitin-conjugating enzyme/RWD-like (2);	0.000000	0.85682	D	0.000000	T	0.64638	0.2616	M	0.85462	2.755	0.80722	D	1	D	0.89917	1.0	D	0.73380	0.98	T	0.71048	-0.4705	10	0.87932	D	0	-12.1031	15.6837	0.77393	1.0:0.0:0.0:0.0	.	98	Q712K3	UB2R2_HUMAN	L	98	ENSP00000263228:H98L	ENSP00000263228:H98L	H	+	2	0	UBE2R2	33890200	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.770000	0.91746	2.182000	0.69389	0.528000	0.53228	CAT	.	.	none		0.403	UBE2R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052118.1	NM_017811		T	33900200	A	T	33900200	3	4	44	1	0	0	0	0	1	0	0	0	16886	217	8	5	303	5	UBE2R2	9	33900200	Missense_Mutation	SNP	A	TCGA-GS-A9U4-01A-11D-A38X-10		33900200	107313231	9	15436											
TRPM3	80036	hgsc.bcm.edu	37	chr9	73225579	73225579	+	Silent	SNP	G	G	T																															tagaattcatagatttttctGccgagggggattaaccggtg																										TCGA-GS-A9U4-01A-11D-A38X-10	TCGA-GS-A9U4-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4b7512d6-8e65-47d9-98ca-1fe4bd7c455f	22fb535e-5b36-4add-ba3f-997cb70efcff	g.chr9:73225579G>T	ENST00000377111.2	-	18	2820	c.2577C>A	c.(2575-2577)ggC>ggA	p.G859G	TRPM3_ENST00000377105.1_Silent_p.G718G|TRPM3_ENST00000377106.1_Silent_p.G731G|TRPM3_ENST00000358082.3_Silent_p.G721G|TRPM3_ENST00000396280.5_Silent_p.G708G|TRPM3_ENST00000377110.3_Silent_p.G859G|TRPM3_ENST00000357533.2_Silent_p.G863G|TRPM3_ENST00000396285.1_Silent_p.G706G|TRPM3_ENST00000408909.2_Silent_p.G718G|TRPM3_ENST00000423814.3_Silent_p.G886G|TRPM3_ENST00000360823.2_Silent_p.G721G|TRPM3_ENST00000396292.4_Silent_p.G731G	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	884					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						AGATTTTTCTGCCGAGGGGGA	0.478																																					p.G859G		Atlas-SNP	.											TRPM3_ENST00000423814,NS,carcinoma,-2,3	TRPM3	700	3	0			c.C2577A						PASS	.						212	190	197					9																	73225579		2203	4300	6503	SO:0001819	synonymous_variant	80036	exon18			TTTTCTGCCGAGG	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.2577C>A	9.37:g.73225579G>T		112	0	0		99	9	0.0909091	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Silent	SNP	ENST00000377111.2	37		.	.	.	.	.	.	.	.	.	.	G	9.856	1.195023	0.22037	.	.	ENSG00000083067	ENST00000396280	.	.	.	6.17	4.21	0.49690	.	.	.	.	.	T	0.53706	0.1813	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51942	-0.8641	4	.	.	.	-26.6526	5.2178	0.15352	0.1719:0.0:0.5664:0.2617	.	.	.	.	K	708	.	.	Q	-	1	0	TRPM3	72415399	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.191000	0.32138	1.631000	0.50456	0.655000	0.94253	CAG	.	.	none		0.478	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945		T	73225579	G	T	73225579	2	4	44	1	0	0	0	0	0	0	0	1	16602	1306	46	4		4	TRPM3	9	73225579	Silent	SNP	G	TCGA-GS-A9U4-01A-11D-A38X-10	39325379	73225579	67987852	10	15437	201	2									
TRPM3	80036	hgsc.bcm.edu	37	chr9	73225580	73225580	+	Missense_Mutation	SNP	C	C	G																															agaattcatagatttttctgCcgagggggattaaccggtgc																										TCGA-GS-A9U4-01A-11D-A38X-10	TCGA-GS-A9U4-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4b7512d6-8e65-47d9-98ca-1fe4bd7c455f	22fb535e-5b36-4add-ba3f-997cb70efcff	g.chr9:73225580C>G	ENST00000377111.2	-	18	2819	c.2576G>C	c.(2575-2577)gGc>gCc	p.G859A	TRPM3_ENST00000377105.1_Missense_Mutation_p.G718A|TRPM3_ENST00000377106.1_Missense_Mutation_p.G731A|TRPM3_ENST00000358082.3_Missense_Mutation_p.G721A|TRPM3_ENST00000396280.5_Missense_Mutation_p.G708A|TRPM3_ENST00000377110.3_Missense_Mutation_p.G859A|TRPM3_ENST00000357533.2_Missense_Mutation_p.G863A|TRPM3_ENST00000396285.1_Missense_Mutation_p.G706A|TRPM3_ENST00000408909.2_Missense_Mutation_p.G718A|TRPM3_ENST00000423814.3_Missense_Mutation_p.G886A|TRPM3_ENST00000360823.2_Missense_Mutation_p.G721A|TRPM3_ENST00000396292.4_Missense_Mutation_p.G731A	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	884					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						GATTTTTCTGCCGAGGGGGAT	0.473																																					p.G859A		Atlas-SNP	.											TRPM3_ENST00000423814,NS,carcinoma,-1,3	TRPM3	700	3	0			c.G2576C						PASS	.						211	190	197					9																	73225580		2203	4300	6503	SO:0001583	missense	80036	exon18			TTTCTGCCGAGGG	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.2576G>C	9.37:g.73225580C>G	ENSP00000366315:p.Gly859Ala	114	0	0		100	9	0.09	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	ENST00000377111.2	37		.	.	.	.	.	.	.	.	.	.	C	16.76	3.211406	0.58343	.	.	ENSG00000083067	ENST00000377111;ENST00000377110;ENST00000377106;ENST00000360823;ENST00000377105;ENST00000357533;ENST00000408909;ENST00000396285;ENST00000396292;ENST00000358082;ENST00000423814	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	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	D	0.88310	0.6402	M	0.69823	2.125	0.80722	D	1	B;B;D;B;B;D;B;B	0.64830	0.049;0.021;0.994;0.066;0.066;0.981;0.336;0.354	B;B;D;B;B;P;B;B	0.64687	0.061;0.022;0.928;0.046;0.016;0.742;0.17;0.138	T	0.82682	-0.0336	10	0.15499	T	0.54	-26.6526	20.8794	0.99867	0.0:1.0:0.0:0.0	.	859;859;849;863;721;718;831;706	Q9HCF6-2;Q9HCF6-10;Q9HCF6-4;A2A3F7;A2A3F4;G5E9G1;Q9HCF6-8;A2A3F3	.;.;.;.;.;.;.;.	A	859;859;731;721;718;863;718;706;731;721;886	ENSP00000366315:G859A;ENSP00000366314:G859A;ENSP00000366310:G731A;ENSP00000354066:G721A;ENSP00000366309:G718A;ENSP00000350140:G863A;ENSP00000386127:G718A;ENSP00000379581:G706A;ENSP00000379587:G731A;ENSP00000350791:G721A;ENSP00000389542:G886A	ENSP00000350140:G863A	G	-	2	0	TRPM3	72415400	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.818000	0.86416	2.941000	0.99782	0.655000	0.94253	GGC	.	.	none		0.473	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945		G	73225580	C	G	73225580	3	3	44	1	0	0	0	0	1	0	0	0	16602	739	26	4	2579	4	TRPM3	9	73225580	Missense_Mutation	SNP	C	TCGA-GS-A9U4-01A-11D-A38X-10	1	73225580	67987851	11	15438	201	2									
TRIM22	10346	hgsc.bcm.edu	37	chr11	5730437	5730437	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggctgccaatatttctcttcGgggaaatattactgggaagt	10	13	11	7	1	1	0	0	0	1	0	3	2	1	2	1	4	2	1	1	4	6	5	rs140700337	byFrequency	TCGA-GS-A9U4-01A-11D-A38X-10	TCGA-GS-A9U4-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4b7512d6-8e65-47d9-98ca-1fe4bd7c455f	22fb535e-5b36-4add-ba3f-997cb70efcff	g.chr11:5730437G>A	ENST00000379965.3	+	8	1333	c.1056G>A	c.(1054-1056)tcG>tcA	p.S352S	TRIM5_ENST00000380027.1_Intron	NM_001199573.1|NM_006074.4	NP_001186502.1|NP_006065.2	Q8IYM9	TRI22_HUMAN	tripartite motif containing 22	352	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				defense response to virus (GO:0051607)|immune response (GO:0006955)|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 trimerization (GO:0070206)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			kidney(3)|large_intestine(8)|lung(9)|prostate(1)|stomach(2)	23		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;7.54e-09)|BRCA - Breast invasive adenocarcinoma(625;0.14)		ATTTCTCTTCGGGGAAATATT	0.413													G|||	19	0.00379393	0.0136	0.0014	5008	,	,		19088	0.0		0.0	False		,,,				2504	0.0				p.S352S	GBM(104;491 2336 5222)	Atlas-SNP	.											.	TRIM22	66	.	0			c.G1056A						PASS	.	G	,	17,3647		0,17,1815	131	123	126		1044,1056	2.5	0.6	11	dbSNP_134	126	0,8182		0,0,4091	no	coding-synonymous,coding-synonymous	TRIM22	NM_001199573.1,NM_006074.4	,	0,17,5906	AA,AG,GG		0.0,0.464,0.1435	,	348/495,352/499	5730437	17,11829	1832	4091	5923	SO:0001819	synonymous_variant	10346	exon8			CTCTTCGGGGAAA	X82200	CCDS41612.1	11p15	2013-01-09	2011-01-25		ENSG00000132274	ENSG00000132274		"Tripartite motif containing / Tripartite motif containing", "RING-type (C3HC4) zinc fingers"	16379	protein-coding gene	gene with protein product		606559	"tripartite motif-containing 22"			11331580, 11096452	Standard	NM_006074		Approved	STAF50, GPSTAF50, RNF94	uc001mbr.3	Q8IYM9	OTTHUMG00000066904	ENST00000379965.3:c.1056G>A	11.37:g.5730437G>A		132	0	0		116	11	0.0948276	NM_006074	Q05CQ0|Q15521	Silent	SNP	ENST00000379965.3	37	CCDS41612.1																																																																																			G|0.993;A|0.007	0.007	strong		0.413	TRIM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143387.2	NM_006074		A	5730437	G	A	5730437	2	1	44	1	0	0	0	0	0	0	0	1	16511	1103	39	1		1	TRIM22	11	5730437	Silent	SNP	G	TCGA-GS-A9U4-01A-11D-A38X-10		5730437	129276079	12	15439											
C11orf41	25758	hgsc.bcm.edu	37	chr11	33581343	33581343	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtcaccttggtgtacgtcGtgggcaatcagagcacattc	9	10	11	11	2	2	1	2	0	0	1	4	1	2	1	1	2	2	3	1	2	2	3	rs369439478		TCGA-GS-A9U4-01A-11D-A38X-10	TCGA-GS-A9U4-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4b7512d6-8e65-47d9-98ca-1fe4bd7c455f	22fb535e-5b36-4add-ba3f-997cb70efcff	g.chr11:33581343G>A	ENST00000321505.4	+	6	3193	c.3013G>A	c.(3013-3015)Gtg>Atg	p.V1005M	KIAA1549L_ENST00000389726.3_Missense_Mutation_p.V1011M|KIAA1549L_ENST00000265654.5_Missense_Mutation_p.V1011M			Q6ZVL6	K154L_HUMAN	KIAA1549-like	1005						integral component of membrane (GO:0016021)											GGTGTACGTCGTGGGCAATCA	0.582																																					p.V1005M		Atlas-SNP	.											.	.	.	.	0			c.G3013A						PASS	.	G	MET/VAL	0,4294		0,0,2147	102	102	102		3013	4.5	1	11		102	1,8491		0,1,4245	no	missense	C11orf41	NM_012194.2	21	0,1,6392	AA,AG,GG		0.0118,0.0,0.0078	probably-damaging	1005/1850	33581343	1,12785	2147	4246	6393	SO:0001583	missense	25758	exon6			TACGTCGTGGGCA	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.3013G>A	11.37:g.33581343G>A	ENSP00000315295:p.Val1005Met	73	0	0		53	9	0.169811	NM_012194	B0QYU0	Missense_Mutation	SNP	ENST00000321505.4	37	CCDS44565.2	.	.	.	.	.	.	.	.	.	.	G	22.4	4.291386	0.80914	0.0	1.18E-4	ENSG00000110427	ENST00000321505;ENST00000389726;ENST00000265654;ENST00000536568	.	.	.	5.42	4.49	0.54785	.	0.119417	0.56097	D	0.000022	T	0.73590	0.3606	M	0.80847	2.515	0.29328	N	0.866907	D;D	0.89917	1.0;0.999	D;P	0.78314	0.991;0.814	T	0.73984	-0.3810	9	0.87932	D	0	-9.1816	15.7714	0.78173	0.0:0.0:0.8626:0.1374	.	1011;1011	E9PAT2;Q6ZVL6-2	.;.	M	1005;1011;1011;844	.	ENSP00000265654:V1011M	V	+	1	0	C11orf41	33537919	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.357000	0.73051	1.389000	0.46526	0.573000	0.79308	GTG	.	.	weak		0.582	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194		A	33581343	G	A	33581343	3	1	44	1	0	0	0	0	1	0	0	0	1642	1145	40	1	3053	1	C11orf41	11	33581343	Missense_Mutation	SNP	G	TCGA-GS-A9U4-01A-11D-A38X-10	27850906	33581343	101425173	13	15440											
TNKS1BP1	85456	hgsc.bcm.edu	37	chr11	57081004	57081004	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcgatcaggggccggggtgaGgtggcagggggctgatccag	6	6	21	8	2	1	2	1	2	0	0	3	3	2	2	2	8	0	2	2	8	0	0			TCGA-GS-A9U4-01A-11D-A38X-10	TCGA-GS-A9U4-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4b7512d6-8e65-47d9-98ca-1fe4bd7c455f	22fb535e-5b36-4add-ba3f-997cb70efcff	g.chr11:57081004G>A	ENST00000532437.1	-	4	1469	c.1158C>T	c.(1156-1158)acC>acT	p.T386T	TNKS1BP1_ENST00000358252.3_Silent_p.T386T|TNKS1BP1_ENST00000530920.1_5'Flank			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	386	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)				GCCGGGGTGAGGTGGCAGGGG	0.701																																					p.T386T		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.C1158T						PASS	.						14	16	15					11																	57081004		2187	4268	6455	SO:0001819	synonymous_variant	85456	exon5			GGGTGAGGTGGCA	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.1158C>T	11.37:g.57081004G>A		35	0	0		50	13	0.26	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Silent	SNP	ENST00000532437.1	37	CCDS7951.1																																																																																			.	.	none		0.701	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396		A	57081004	G	A	57081004	2	1	44	1	0	0	0	0	0	0	0	1	16335	987	35	2		2	TNKS1BP1	11	57081004	Silent	SNP	G	TCGA-GS-A9U4-01A-11D-A38X-10	23499661	57081004	77925512	14	15441											
C12orf64	283310	hgsc.bcm.edu	37	chr12	80714313	80714313	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggcgaattcagcctttcatcGgagagcaacatttttccacc	10	11	8	12	2	2	1	2	0	0	1	4	3	3	1	3	2	3	1	3	2	2	4	rs369089877		TCGA-GS-A9U4-01A-11D-A38X-10	TCGA-GS-A9U4-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4b7512d6-8e65-47d9-98ca-1fe4bd7c455f	22fb535e-5b36-4add-ba3f-997cb70efcff	g.chr12:80714313G>A	ENST00000547103.1	+	33	3893	c.3887G>A	c.(3886-3888)cGg>cAg	p.R1296Q	OTOGL_ENST00000458043.2_Missense_Mutation_p.R1296Q			Q3ZCN5	OTOGL_HUMAN	otogelin-like	1296					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						GCCTTTCATCGGAGAGCAACA	0.433																																					p.R1296Q		Atlas-SNP	.											OTOGL_ENST00000458043,NS,carcinoma,+1,1	OTOGL	235	1	0			c.G3887A						PASS	.	G	GLN/ARG	1,3779		0,1,1889	80	76	78		3887	-4.1	0.3	12		78	0,8246		0,0,4123	no	missense	OTOGL	NM_173591.3	43	0,1,6012	AA,AG,GG		0.0,0.0265,0.0083		1296/2345	80714313	1,12025	1890	4123	6013	SO:0001583	missense	283310	exon33			TTCATCGGAGAGC	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.3887G>A	12.37:g.80714313G>A	ENSP00000447211:p.Arg1296Gln	127	0	0		93	9	0.0967742	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	37		.	.	.	.	.	.	.	.	.	.	G	5.435	0.265401	0.10294	2.65E-4	0.0	ENSG00000165899	ENST00000547103;ENST00000458043	T;T	0.15718	2.4;2.4	5.53	-4.09	0.03951	.	.	.	.	.	T	0.05686	0.0149	N	0.08118	0	0.09310	N	1	.	.	.	.	.	.	T	0.42396	-0.9454	7	0.07175	T	0.84	.	6.9939	0.24772	0.5056:0.0:0.3838:0.1106	.	.	.	.	Q	1296	ENSP00000447211:R1296Q;ENSP00000400895:R1296Q	ENSP00000400895:R1296Q	R	+	2	0	OTOGL	79238444	0.029000	0.19370	0.264000	0.24511	0.877000	0.50540	0.314000	0.19432	-0.957000	0.03627	-0.755000	0.03482	CGG	.	.	weak		0.433	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591		A	80714313	G	A	80714313	3	1	44	1	0	0	0	0	1	0	0	0	1709	1116	39	1	4017	1	C12orf64	12	80714313	Missense_Mutation	SNP	G	TCGA-GS-A9U4-01A-11D-A38X-10		80714313	53137582	15	15442											
KTN1	3895	hgsc.bcm.edu	37	chr14	56079010	56079010	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccgactctgagagtgtacctCgagactttaaattatcagat	12	12	8	9	2	2	3	1	1	1	3	3	6	2	3	2	0	1	1	2	0	4	4			TCGA-GS-A9U4-01A-11D-A38X-10	TCGA-GS-A9U4-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4b7512d6-8e65-47d9-98ca-1fe4bd7c455f	22fb535e-5b36-4add-ba3f-997cb70efcff	g.chr14:56079010C>T	ENST00000395314.3	+	2	312	c.244C>T	c.(244-246)Cga>Tga	p.R82*	KTN1_ENST00000395308.1_Nonsense_Mutation_p.R82*|KTN1_ENST00000395311.1_Nonsense_Mutation_p.R82*|KTN1_ENST00000413890.2_Nonsense_Mutation_p.R82*|KTN1_ENST00000438792.2_Nonsense_Mutation_p.R82*|KTN1_ENST00000416613.1_Nonsense_Mutation_p.R82*|KTN1_ENST00000395309.3_Nonsense_Mutation_p.R82*	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	82					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						GAGTGTACCTCGAGACTTTAA	0.363			T	RET	papillary thryoid																																p.R82X		Atlas-SNP	.		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	KTN1	147	.	0			c.C244T						PASS	.						74	78	77					14																	56079010		2203	4300	6503	SO:0001587	stop_gained	3895	exon2			GTACCTCGAGACT		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.244C>T	14.37:g.56079010C>T	ENSP00000378725:p.Arg82*	188	0	0		145	19	0.131034	NM_004986	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Nonsense_Mutation	SNP	ENST00000395314.3	37	CCDS41957.1	.	.	.	.	.	.	.	.	.	.	C	35	5.445114	0.96187	.	.	ENSG00000126777	ENST00000413890;ENST00000395309;ENST00000438792;ENST00000395314;ENST00000395308;ENST00000395311;ENST00000416613	.	.	.	5.63	4.75	0.60458	.	0.296616	0.24176	N	0.040855	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-3.098	14.4179	0.67163	0.0:0.9292:0.0:0.0708	.	.	.	.	X	82	.	ENSP00000378719:R82X	R	+	1	2	KTN1	55148763	0.999000	0.42202	1.000000	0.80357	0.991000	0.79684	2.425000	0.44723	1.379000	0.46325	0.591000	0.81541	CGA	.	.	none		0.363	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2			T	56079010	C	T	56079010	4	4	44	1	0	0	0	0	0	1	0	0	8594	876	31	1	246	1	KTN1	14	56079010	Nonsense_Mutation	SNP	C	TCGA-GS-A9U4-01A-11D-A38X-10		56079010	51270530	16	15443											
MESP2	145873	hgsc.bcm.edu	37	chr15	90320149	90320149	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gggcaagggcaggggcagggGcaggggcaagggcaggggca	9	0	25	7	0	0	0	0	0	0	0	0	0	0	0	0	11	0	7	0	11	2	0			TCGA-GS-A9U4-01A-11D-A38X-10	TCGA-GS-A9U4-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4b7512d6-8e65-47d9-98ca-1fe4bd7c455f	22fb535e-5b36-4add-ba3f-997cb70efcff	g.chr15:90320149G>A	ENST00000341735.3	+	1	561	c.561G>A	c.(559-561)ggG>ggA	p.G187G	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	187	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)			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)			aggggcaggggcaggggcaag	0.781																																					p.G187G		Atlas-SNP	.											.	MESP2	20	.	0			c.G561A						PASS	.						2	3	3					15																	90320149		1334	3199	4533	SO:0001819	synonymous_variant	145873	exon1			GCAGGGGCAGGGG		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.561G>A	15.37:g.90320149G>A		23	0	0		22	8	0.363636	NM_001039958	Q7RTU2	Silent	SNP	ENST00000341735.3	37	CCDS42078.1																																																																																			.	.	none		0.781	MESP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416421.1	XM_085261		A	90320149	G	A	90320149	2	1	44	1	0	0	0	0	0	0	0	1	9492	1190	42	2		2	MESP2	15	90320149	Silent	SNP	G	TCGA-GS-A9U4-01A-11D-A38X-10		90320149	12211243	17	15444											
GRIN2A	2903	hgsc.bcm.edu	37	chr16	9916205	9916205	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcatgtagggatagttattcCgaatgtttctctccgtgctt	7	16	10	8	2	1	0	0	0	1	0	4	2	3	1	2	1	1	5	2	1	4	6			TCGA-GS-A9U4-01A-11D-A38X-10	TCGA-GS-A9U4-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4b7512d6-8e65-47d9-98ca-1fe4bd7c455f	22fb535e-5b36-4add-ba3f-997cb70efcff	g.chr16:9916205C>T	ENST00000396573.2	-	11	2393	c.2084G>A	c.(2083-2085)cGg>cAg	p.R695Q	GRIN2A_ENST00000396575.2_Missense_Mutation_p.R695Q|GRIN2A_ENST00000330684.3_Missense_Mutation_p.R695Q|GRIN2A_ENST00000562109.1_Missense_Mutation_p.R695Q|GRIN2A_ENST00000404927.2_Missense_Mutation_p.R695Q|GRIN2A_ENST00000535259.1_Missense_Mutation_p.R538Q	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	695					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)	ATAGTTATTCCGAATGTTTCT	0.458																																					p.R695Q		Atlas-SNP	.											.	GRIN2A	366	.	0			c.G2084A						PASS	.						167	142	150					16																	9916205		2197	4300	6497	SO:0001583	missense	2903	exon11			TTATTCCGAATGT		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.2084G>A	16.37:g.9916205C>T	ENSP00000379818:p.Arg695Gln	177	0	0		127	7	0.0551181	NM_000833	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	37	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	C	36	5.757827	0.96898	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000535259;ENST00000330684;ENST00000396575	T;T;T;T;T	0.28069	1.63;1.63;1.63;1.63;1.63	5.65	5.65	0.86999	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.000000	0.85682	D	0.000000	T	0.51278	0.1665	L	0.52266	1.64	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.921;0.953;0.992	T	0.34950	-0.9808	9	.	.	.	.	18.7287	0.91726	0.0:1.0:0.0:0.0	.	538;695;695	F5GZ52;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	Q	695;695;538;695;695	ENSP00000379818:R695Q;ENSP00000385872:R695Q;ENSP00000441572:R538Q;ENSP00000332549:R695Q;ENSP00000379820:R695Q	.	R	-	2	0	GRIN2A	9823706	1.000000	0.71417	0.999000	0.59377	0.997000	0.91878	5.943000	0.70211	2.655000	0.90218	0.655000	0.94253	CGG	.	.	none		0.458	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3			T	9916205	C	T	9916205	3	4	44	1	0	0	0	0	1	0	0	0	6788	652	23	1	2326	1	GRIN2A	16	9916205	Missense_Mutation	SNP	C	TCGA-GS-A9U4-01A-11D-A38X-10		9916205	80438548	18	15445											
CNGB1	1258	hgsc.bcm.edu	37	chr16	57918303	57918303	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcggcctcctttgggtgcGtgtgctggtctggggcggcg	0	11	20	10	4	1	0	0	0	1	0	2	0	2	0	2	7	2	1	2	7	0	1			TCGA-GS-A9U4-01A-11D-A38X-10	TCGA-GS-A9U4-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4b7512d6-8e65-47d9-98ca-1fe4bd7c455f	22fb535e-5b36-4add-ba3f-997cb70efcff	g.chr16:57918303G>A	ENST00000251102.8	-	33	3581	c.3521C>T	c.(3520-3522)aCg>aTg	p.T1174M	CNGB1_ENST00000564448.1_Missense_Mutation_p.T1168M	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	1174					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						CTTTGGGTGCGTGTGCTGGTC	0.701																																					p.T1174M	Colon(156;1293 1853 16336 28962 38659)	Atlas-SNP	.											.	CNGB1	105	.	0			c.C3521T						PASS	.						21	23	23					16																	57918303		1970	4139	6109	SO:0001583	missense	1258	exon33			GGGTGCGTGTGCT	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.3521C>T	16.37:g.57918303G>A	ENSP00000251102:p.Thr1174Met	72	0	0		64	16	0.25	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Missense_Mutation	SNP	ENST00000251102.8	37	CCDS42169.1	.	.	.	.	.	.	.	.	.	.	G	11.97	1.798004	0.31777	.	.	ENSG00000070729	ENST00000251102	D	0.96716	-4.1	4.33	-1.25	0.09405	.	1.568360	0.04324	N	0.351159	D	0.88444	0.6438	N	0.08118	0	0.09310	N	1	B;B	0.12013	0.005;0.003	B;B	0.09377	0.004;0.002	T	0.79167	-0.1915	10	0.45353	T	0.12	.	0.7321	0.00959	0.292:0.1654:0.3729:0.1697	.	546;1174	Q14028-2;Q14028	.;CNGB1_HUMAN	M	1174	ENSP00000251102:T1174M	ENSP00000251102:T1174M	T	-	2	0	CNGB1	56475804	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.110000	0.15437	-0.050000	0.13356	-0.982000	0.02568	ACG	.	.	none		0.701	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297		A	57918303	G	A	57918303	3	1	44	1	0	0	0	0	1	0	0	0	3602	1145	40	1	238	1	CNGB1	16	57918303	Missense_Mutation	SNP	G	TCGA-GS-A9U4-01A-11D-A38X-10	48002098	57918303	32436450	19	15446											
CDH3	1001	hgsc.bcm.edu	37	chr16	68712537	68712537	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gttgaataagccactggaccGggaggagattgccaagtatg	12	8	14	7	1	0	2	0	1	0	1	0	5	0	4	3	3	2	2	3	3	4	4			TCGA-GS-A9U4-01A-11D-A38X-10	TCGA-GS-A9U4-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4b7512d6-8e65-47d9-98ca-1fe4bd7c455f	22fb535e-5b36-4add-ba3f-997cb70efcff	g.chr16:68712537G>A	ENST00000264012.4	+	5	1068	c.524G>A	c.(523-525)cGg>cAg	p.R175Q	CDH3_ENST00000429102.2_Missense_Mutation_p.R175Q|CDH3_ENST00000581171.1_Missense_Mutation_p.R120Q	NM_001793.4	NP_001784.2	P22223	CADH3_HUMAN	cadherin 3, type 1, P-cadherin (placental)	175	Cadherin 1. {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)		CCACTGGACCGGGAGGAGATT	0.572																																					p.R175Q		Atlas-SNP	.											.	CDH3	68	.	2	Unknown(2)	breast(2)	c.G524A						PASS	.						89	92	91					16																	68712537		2198	4300	6498	SO:0001583	missense	1001	exon5			TGGACCGGGAGGA	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.524G>A	16.37:g.68712537G>A	ENSP00000264012:p.Arg175Gln	56	0	0		35	6	0.171429	NM_001793	B2R6F4|Q05DI6	Missense_Mutation	SNP	ENST00000264012.4	37	CCDS10868.1	.	.	.	.	.	.	.	.	.	.	G	35	5.512360	0.96402	.	.	ENSG00000062038	ENST00000429102;ENST00000264012;ENST00000542274	T;T	0.59364	0.27;0.27	5.64	5.64	0.86602	Cadherin (5);Cadherin-like (1);	0.000000	0.38837	N	0.001542	D	0.84424	0.5469	H	0.97051	3.93	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.88804	0.3287	10	0.87932	D	0	.	17.243	0.87019	0.0:0.0:1.0:0.0	.	175	P22223	CADH3_HUMAN	Q	175;175;120	ENSP00000398485:R175Q;ENSP00000264012:R175Q	ENSP00000264012:R175Q	R	+	2	0	CDH3	67270038	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.625000	0.98406	2.937000	0.99478	0.650000	0.86243	CGG	.	.	none		0.572	CDH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268896.2	NM_001793		A	68712537	G	A	68712537	3	1	44	1	0	0	0	0	1	0	0	0	3113	1116	39	1	542	1	CDH3	16	68712537	Missense_Mutation	SNP	G	TCGA-GS-A9U4-01A-11D-A38X-10	10794234	68712537	21642216	20	15447											
PMFBP1	83449	hgsc.bcm.edu	37	chr16	72198813	72198813	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acttctctgtctctctccccCgcctaggcagccagaaaaac	9	9	6	17	1	3	1	0	0	3	1	6	1	3	1	4	1	2	1	4	1	3	2	rs550862432	byFrequency	TCGA-GS-A9U4-01A-11D-A38X-10	TCGA-GS-A9U4-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4b7512d6-8e65-47d9-98ca-1fe4bd7c455f	22fb535e-5b36-4add-ba3f-997cb70efcff	g.chr16:72198813C>T	ENST00000237353.10	-	3	276	c.15G>A	c.(13-15)gcG>gcA	p.A5A	PMFBP1_ENST00000355636.6_5'UTR|PMFBP1_ENST00000543746.1_5'UTR|PMFBP1_ENST00000537465.1_Silent_p.A5A	NM_031293.2	NP_112583.2	Q8TBY8	PMFBP_HUMAN	polyamine modulated factor 1 binding protein 1	5						cytoplasm (GO:0005737)		p.A5A(1)		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)				CTCTCTCCCCCGCCTAGGCAG	0.443													C|||	2	0.000399361	0.0	0.0	5008	,	,		20548	0.0		0.0	False		,,,				2504	0.002				p.A5A		Atlas-SNP	.											PMFBP1,NS,carcinoma,-1,2	PMFBP1	101	2	1	Substitution - coding silent(1)	endometrium(1)	c.G15A						PASS	.						51	48	49					16																	72198813		2198	4300	6498	SO:0001819	synonymous_variant	83449	exon3			CTCCCCCGCCTAG	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.15G>A	16.37:g.72198813C>T		45	0	0		33	6	0.181818	NM_031293	B3KVI9|H7BY07|Q8NA09|Q9BY16|Q9H0H4	Silent	SNP	ENST00000237353.10	37	CCDS32483.1																																																																																			.	.	none		0.443	PMFBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396473.2	NM_031293		T	72198813	C	T	72198813	2	4	44	1	0	0	0	0	0	0	0	1	12143	639	23	1		1	PMFBP1	16	72198813	Silent	SNP	C	TCGA-GS-A9U4-01A-11D-A38X-10	3486276	72198813	18155940	21	15448											
MYH10	4628	hgsc.bcm.edu	37	chr17	8455392	8455392	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tgttctcctgctccagataaCaactggtaaaagatatgaaa	15	11	7	8	0	1	3	0	1	1	2	3	3	2	3	2	1	3	3	2	1	6	4			TCGA-GS-A9U4-01A-11D-A38X-10	TCGA-GS-A9U4-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4b7512d6-8e65-47d9-98ca-1fe4bd7c455f	22fb535e-5b36-4add-ba3f-997cb70efcff	g.chr17:8455392C>T	ENST00000269243.4	-	8	999	c.861G>A	c.(859-861)ttG>ttA	p.L287L	MYH10_ENST00000379980.4_Silent_p.L303L|MYH10_ENST00000396239.1_Silent_p.L287L|MYH10_ENST00000360416.3_Silent_p.L297L	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	287	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						CTCCAGATAACAACTGGTAAA	0.313																																					p.L297L		Atlas-SNP	.											.	MYH10	148	.	0			c.G891A						PASS	.						46	48	47					17																	8455392		2203	4300	6503	SO:0001819	synonymous_variant	4628	exon9			AGATAACAACTGG	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.861G>A	17.37:g.8455392C>T		168	0	0		161	15	0.0931677	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	37	CCDS11144.1																																																																																			.	.	none		0.313	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2			T	8455392	C	T	8455392	2	4	44	1	0	0	0	0	0	0	0	1	10039	477	17	2		2	MYH10	17	8455392	Silent	SNP	C	TCGA-GS-A9U4-01A-11D-A38X-10		8455392	72739818	22	15449											
MYH7B	26133	hgsc.bcm.edu	37	chr20	33588659	33588659	+	IGR	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggaggctgcacaggagaggcGggaggctgaggagaaggcca	11	2	21	7	1	0	3	0	1	0	2	0	7	0	5	1	8	1	3	1	8	1	0			TCGA-GS-A9U4-01A-11D-A38X-10	TCGA-GS-A9U4-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4b7512d6-8e65-47d9-98ca-1fe4bd7c455f	22fb535e-5b36-4add-ba3f-997cb70efcff	g.chr20:33588659G>A	ENST00000252015.2	-	0	3226				MYH7B_ENST00000262873.7_Missense_Mutation_p.R1798Q			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)			CAGGAGAGGCGGGAGGCTGAG	0.612																																					p.R1798Q		Atlas-SNP	.											MYH7B,NS,carcinoma,+1,1	MYH7B	145	1	0			c.G5393A						PASS	.						45	64	58					20																	33588659		2134	4257	6391	SO:0001628	intergenic_variant	57644	exon40			AGAGGCGGGAGGC	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		20.37:g.33588659G>A		40	0	0		42	6	0.142857	NM_020884	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Missense_Mutation	SNP	ENST00000252015.2	37	CCDS13246.1	.	.	.	.	.	.	.	.	.	.	G	18.76	3.692707	0.68271	.	.	ENSG00000078814	ENST00000262873	T	0.78246	-1.16	4.65	4.65	0.58169	Myosin tail (1);	0.000000	0.34580	N	0.003843	D	0.88779	0.6529	M	0.85859	2.78	0.49389	D	0.999786	D	0.76494	0.999	D	0.80764	0.994	D	0.88397	0.3012	10	0.35671	T	0.21	.	17.7847	0.88534	0.0:0.0:1.0:0.0	.	1756	A7E2Y1	MYH7B_HUMAN	Q	1798	ENSP00000262873:R1798Q	ENSP00000262873:R1798Q	R	+	2	0	MYH7B	33052320	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.797000	0.85911	2.433000	0.82419	0.558000	0.71614	CGG	.	.	none		0.612	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638		A	33588659	G	A	33588659	1	1	44	0	1	0	0	0	0	0	0	0	10049	1116	39	1		1	MYH7B	20	33588659	IGR	SNP	G	TCGA-GS-A9U4-01A-11D-A38X-10		33588659	29436861	23	15450											
MED12	9968	hgsc.bcm.edu	37	chrX	70352367	70352367	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcctcttcacgcaaagaacGtgatcgacaaaagcagaaga	16	7	8	10	3	2	4	1	1	1	3	4	5	3	4	1	0	2	2	1	0	5	2			TCGA-GS-A9U4-01A-11D-A38X-10	TCGA-GS-A9U4-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4b7512d6-8e65-47d9-98ca-1fe4bd7c455f	22fb535e-5b36-4add-ba3f-997cb70efcff	g.chrX:70352367G>A	ENST00000374080.3	+	31	4426	c.4394G>A	c.(4393-4395)cGt>cAt	p.R1465H	MED12_ENST00000374102.1_Missense_Mutation_p.R1465H|MED12_ENST00000333646.6_Missense_Mutation_p.R1465H			Q93074	MED12_HUMAN	mediator complex subunit 12	1465					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)					CGCAAAGAACGTGATCGACAA	0.522			"M, S"		uterine leiomyoma		Opitz-Kaveggia Syndrome																														p.R1465H		Atlas-SNP	.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12	984	.	0			c.G4394A						PASS	.						50	46	47					X																	70352367		1904	4122	6026	SO:0001583	missense	9968	exon31			AAGAACGTGATCG	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.4394G>A	X.37:g.70352367G>A	ENSP00000363193:p.Arg1465His	94	0	0		106	11	0.103774	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Missense_Mutation	SNP	ENST00000374080.3	37	CCDS43970.1	.	.	.	.	.	.	.	.	.	.	G	25.8	4.673341	0.88445	.	.	ENSG00000184634	ENST00000333646;ENST00000536756;ENST00000374102;ENST00000374080;ENST00000430072;ENST00000439750	D;D;D;D;T	0.84873	-1.91;-1.91;-1.91;-1.91;1.26	4.15	4.15	0.48705	.	0.000000	0.85682	D	0.000000	D	0.91287	0.7253	M	0.71581	2.175	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;1.0;0.999	D;D;D;D	0.74348	0.983;0.968;0.977;0.961	D	0.92570	0.6065	10	0.72032	D	0.01	-10.5615	16.1804	0.81895	0.0:0.0:1.0:0.0	.	1465;1312;1465;1465	F5H3Y1;Q7Z3Z5;Q93074-3;Q93074	.;.;.;MED12_HUMAN	H	1465;1465;1465;1465;1433;210	ENSP00000333125:R1465H;ENSP00000363215:R1465H;ENSP00000363193:R1465H;ENSP00000414203:R1433H;ENSP00000408388:R210H	ENSP00000333125:R1465H	R	+	2	0	MED12	70269092	1.000000	0.71417	0.993000	0.49108	0.987000	0.75469	8.933000	0.92911	2.071000	0.62044	0.523000	0.50628	CGT	.	.	none		0.522	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120		A	70352367	G	A	70352367	3	1	44	1	0	0	0	0	1	0	0	0	9437	1145	40	1	4516	1	MED12	23	70352367	Missense_Mutation	SNP	G	TCGA-GS-A9U4-01A-11D-A38X-10		70352367	84918193	24	15451											
RAB40A	142684	hgsc.bcm.edu	37	chrX	102755451	102755451	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgagagtaggagcggaatatGgtacaaaatcttccctgccc	12	8	11	10	2	1	1	0	0	1	1	2	4	2	3	2	3	3	2	2	3	6	4			TCGA-GS-A9U4-01A-11D-A38X-10	TCGA-GS-A9U4-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	4b7512d6-8e65-47d9-98ca-1fe4bd7c455f	22fb535e-5b36-4add-ba3f-997cb70efcff	g.chrX:102755451G>A	ENST00000372633.1	-	1	2352	c.234C>T	c.(232-234)acC>acT	p.T78T	LL0XNC01-250H12.3_ENST00000445990.1_RNA|RAB40A_ENST00000304236.1_Silent_p.T78T			Q8WXH6	RB40A_HUMAN	RAB40A, member RAS oncogene family	78					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						AGCGGAATATGGTACAAAATC	0.542																																					p.T78T		Atlas-SNP	.											.	RAB40A	30	.	0			c.C234T						PASS	.						67	60	62					X																	102755451		2202	4279	6481	SO:0001819	synonymous_variant	142684	exon3			GAATATGGTACAA	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.234C>T	X.37:g.102755451G>A		461	0	0		350	25	0.0714286	NM_080879	O00407|Q17RQ5|Q6DK06|Q8TF06	Silent	SNP	ENST00000372633.1	37	CCDS35357.1																																																																																			.	.	none		0.542	RAB40A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057714.1			A	102755451	G	A	102755451	2	1	44	1	0	0	0	0	0	0	0	1	12954	1335	47	2		2	RAB40A	23	102755451	Silent	SNP	G	TCGA-GS-A9U4-01A-11D-A38X-10	32403084	102755451	52515109	25	15452											
SLC45A1	50651	hgsc.bcm.edu	37	chr1	8390800	8390800	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggcttctaccgccaggaccGtggacttctggagggcagag	7	7	15	12	3	2	1	0	0	2	1	2	4	2	4	3	5	1	2	3	5	1	3	rs370439504		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr1:8390800G>A	ENST00000471889.1	+	5	1632	c.1247G>A	c.(1246-1248)cGt>cAt	p.R416H	Y_RNA_ENST00000516445.1_RNA|SLC45A1_ENST00000481265.1_3'UTR|SLC45A1_ENST00000377479.2_Missense_Mutation_p.R450H|SLC45A1_ENST00000289877.8_Missense_Mutation_p.R416H			Q9Y2W3	S45A1_HUMAN	solute carrier family 45, member 1	416					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)		CGCCAGGACCGTGGACTTCTG	0.687																																					p.R416H		Atlas-SNP	.											.	SLC45A1	85	.	0			c.G1247A						PASS	.	G	HIS/ARG	0,4404		0,0,2202	30	32	32		1247	-0.2	0.1	1		32	1,8599	1.2+/-3.3	0,1,4299	no	missense	SLC45A1	NM_001080397.1	29	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	416/749	8390800	1,13003	2202	4300	6502	SO:0001583	missense	50651	exon4			AGGACCGTGGACT	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.1247G>A	1.37:g.8390800G>A	ENSP00000418096:p.Arg416His	77	0	0		59	34	0.576271	NM_001080397	Q5VY46|Q5VY49	Missense_Mutation	SNP	ENST00000471889.1	37	CCDS30577.1	.	.	.	.	.	.	.	.	.	.	G	10.44	1.349538	0.24426	0.0	1.16E-4	ENSG00000162426	ENST00000471889;ENST00000377479;ENST00000289877	T;T;T	0.18174	2.24;2.23;2.24	4.8	-0.234	0.13074	.	1.040590	0.07531	N	0.912288	T	0.14570	0.0352	L	0.36672	1.1	0.19775	N	0.999954	B	0.06786	0.001	B	0.01281	0.0	T	0.34725	-0.9817	10	0.45353	T	0.12	-10.1951	9.9895	0.41863	0.8358:0.0:0.1642:0.0	.	416	Q9Y2W3	S45A1_HUMAN	H	416;450;416	ENSP00000418096:R416H;ENSP00000366699:R450H;ENSP00000289877:R416H	ENSP00000289877:R416H	R	+	2	0	SLC45A1	8313387	0.006000	0.16342	0.068000	0.19968	0.535000	0.34838	0.743000	0.26231	-0.196000	0.10366	0.561000	0.74099	CGT	.	.	none		0.687	SLC45A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001245.5			A	8390800	G	A	8390800	3	1	45	1	0	0	0	0	1	0	0	0	14655	1145	40	1	1261	1	SLC45A1	1	8390800	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10		8390800	240859821	1	15453											
SLC45A1	50651	hgsc.bcm.edu	37	chr1	8399646	8399646	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggaccgggcttgccacccTctccaggaacctctacgtgg	6	7	13	15	2	2	0	0	0	2	0	3	2	2	2	5	5	3	1	5	5	2	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr1:8399646T>C	ENST00000471889.1	+	8	2253	c.1868T>C	c.(1867-1869)cTc>cCc	p.L623P	SLC45A1_ENST00000377479.2_Missense_Mutation_p.L657P|SLC45A1_ENST00000289877.8_Missense_Mutation_p.L623P			Q9Y2W3	S45A1_HUMAN	solute carrier family 45, member 1	623					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)		CTTGCCACCCTCTCCAGGAAC	0.577																																					p.L623P		Atlas-SNP	.											.	SLC45A1	85	.	0			c.T1868C						PASS	.						176	158	164					1																	8399646		2203	4300	6503	SO:0001583	missense	50651	exon7			CCACCCTCTCCAG	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.1868T>C	1.37:g.8399646T>C	ENSP00000418096:p.Leu623Pro	99	0	0		95	4	0.0421053	NM_001080397	Q5VY46|Q5VY49	Missense_Mutation	SNP	ENST00000471889.1	37	CCDS30577.1	.	.	.	.	.	.	.	.	.	.	T	17.77	3.471360	0.63737	.	.	ENSG00000162426	ENST00000471889;ENST00000377479;ENST00000289877	D;D;D	0.92858	-3.12;-3.12;-3.12	5.11	5.11	0.69529	Major facilitator superfamily domain, general substrate transporter (1);	0.075695	0.64402	D	0.000012	D	0.96005	0.8699	M	0.82823	2.61	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.96576	0.9427	10	0.87932	D	0	-36.5672	14.0943	0.65010	0.0:0.0:0.0:1.0	.	623	Q9Y2W3	S45A1_HUMAN	P	623;657;623	ENSP00000418096:L623P;ENSP00000366699:L657P;ENSP00000289877:L623P	ENSP00000289877:L623P	L	+	2	0	SLC45A1	8322233	1.000000	0.71417	0.841000	0.33234	0.417000	0.31264	7.574000	0.82434	1.908000	0.55244	0.454000	0.30748	CTC	.	.	none		0.577	SLC45A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001245.5			C	8399646	T	C	8399646	3	2	45	1	0	0	0	0	1	0	0	0	14655	1551	54	3	1894	3	SLC45A1	1	8399646	Missense_Mutation	SNP	T	TCGA-RQ-A68N-01A-11D-A31X-10	8846	8399646	240850975	2	15454											
TIE1	7075	hgsc.bcm.edu	37	chr1	43779453	43779453	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctctcactgtgtccagggctGcaggctgagggcccagtcca	6	8	13	14	0	1	1	1	1	1	0	4	1	3	1	3	3	1	3	3	3	0	0			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr1:43779453G>T	ENST00000372476.3	+	14	2302	c.2223G>T	c.(2221-2223)ctG>ctT	p.L741L	TIE1_ENST00000473014.1_3'UTR|TIE1_ENST00000433781.2_Silent_p.L386L	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	741					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)				GTCCAGGGCTGCAGGCTGAGG	0.637																																					p.L741L		Atlas-SNP	.											.	TIE1	132	.	0			c.G2223T						PASS	.						22	25	24					1																	43779453		2203	4300	6503	SO:0001819	synonymous_variant	7075	exon14			AGGGCTGCAGGCT	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.2223G>T	1.37:g.43779453G>T		53	0	0		49	31	0.632653	NM_005424	B5A949|B5A950	Silent	SNP	ENST00000372476.3	37	CCDS482.1																																																																																			.	.	none		0.637	TIE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019011.1	NM_005424		T	43779453	G	T	43779453	2	4	45	1	0	0	0	0	0	0	0	1	15908	1306	46	4		4	TIE1	1	43779453	Silent	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	35379807	43779453	205471168	3	15455											
USP24	23358	hgsc.bcm.edu	37	chr1	55622939	55622939	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaacttaccttccagtgcAatcgacagaactgagttttc	12	11	7	11	1	0	2	0	1	0	1	3	3	1	2	2	0	5	3	2	0	4	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr1:55622939A>C	ENST00000294383.6	-	11	1331	c.1332T>G	c.(1330-1332)atT>atG	p.I444M	USP24_ENST00000407756.1_Missense_Mutation_p.I332M	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	444					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						CTTCCAGTGCAATCGACAGAA	0.289																																					p.I444M		Atlas-SNP	.											.	USP24	323	.	0			c.T1332G						PASS	.						74	68	70					1																	55622939		1813	4073	5886	SO:0001583	missense	23358	exon11			CAGTGCAATCGAC	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.1332T>G	1.37:g.55622939A>C	ENSP00000294383:p.Ile444Met	183	0	0		159	97	0.610063	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Missense_Mutation	SNP	ENST00000294383.6	37	CCDS44154.2	.	.	.	.	.	.	.	.	.	.	A	13.78	2.340683	0.41498	.	.	ENSG00000162402	ENST00000294383;ENST00000407756	T;T	0.80033	-1.33;-1.33	5.93	0.863	0.19062	.	0.057109	0.64402	D	0.000003	T	0.71005	0.3289	L	0.49126	1.545	0.35414	D	0.792651	P	0.44578	0.838	B	0.42422	0.387	T	0.69632	-0.5093	10	0.46703	T	0.11	.	4.0534	0.09806	0.5186:0.0:0.2415:0.2399	.	332	B7WPF4	.	M	444;332	ENSP00000294383:I444M;ENSP00000385700:I332M	ENSP00000294383:I444M	I	-	3	3	USP24	55395527	1.000000	0.71417	1.000000	0.80357	0.575000	0.36095	2.338000	0.43957	0.140000	0.18849	-1.518000	0.00936	ATT	.	.	none		0.289	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2			C	55622939	A	C	55622939	3	2	45	1	0	0	0	0	1	0	0	0	17070	126	5	5	6762	5	USP24	1	55622939	Missense_Mutation	SNP	A	TCGA-RQ-A68N-01A-11D-A31X-10	11843486	55622939	193627682	4	15456											
C8A	731	hgsc.bcm.edu	37	chr1	57378088	57378088	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcccacagatgcagcctatcCacgaggtgctgcggcacaca	10	5	11	15	2	0	1	0	0	0	1	1	2	1	1	3	2	4	3	3	2	1	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr1:57378088C>T	ENST00000361249.3	+	10	1489	c.1393C>T	c.(1393-1395)Cac>Tac	p.H465Y		NM_000562.2	NP_000553.1	P07357	CO8A_HUMAN	complement component 8, alpha polypeptide	465	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						GCAGCCTATCCACGAGGTGCT	0.617																																					p.H465Y		Atlas-SNP	.											.	C8A	103	.	0			c.C1393T						PASS	.						38	40	39					1																	57378088		2203	4299	6502	SO:0001583	missense	731	exon10			CCTATCCACGAGG	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.1393C>T	1.37:g.57378088C>T	ENSP00000354458:p.His465Tyr	111	0	0		79	47	0.594937	NM_000562	A2RUI4|A2RUI5|Q13668|Q9H130	Missense_Mutation	SNP	ENST00000361249.3	37	CCDS606.1	.	.	.	.	.	.	.	.	.	.	C	0.288	-0.981797	0.02197	.	.	ENSG00000157131	ENST00000361249	D	0.83837	-1.77	5.55	-5.79	0.02354	Membrane attack complex component/perforin (MACPF) domain (3);	0.486260	0.24917	N	0.034574	T	0.54127	0.1839	N	0.05383	-0.06	0.09310	N	1	B	0.12013	0.005	B	0.12156	0.007	T	0.56829	-0.7914	10	0.02654	T	1	-3.2246	9.1379	0.36886	0.0:0.3531:0.1005:0.5464	.	465	P07357	CO8A_HUMAN	Y	465	ENSP00000354458:H465Y	ENSP00000354458:H465Y	H	+	1	0	C8A	57150676	0.000000	0.05858	0.012000	0.15200	0.003000	0.03518	-0.562000	0.05950	-0.689000	0.05149	-0.748000	0.03510	CAC	.	.	none		0.617	C8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022890.1	NM_000562		T	57378088	C	T	57378088	3	4	45	1	0	0	0	0	1	0	0	0	2418	594	21	2	1431	2	C8A	1	57378088	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	1755149	57378088	191872533	5	15457											
GPR88	54112	hgsc.bcm.edu	37	chr1	101004706	101004706	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcgtgtcgtccttccgaaagCtgcagaccaccagcaacgcc	9	7	9	16	4	0	1	0	0	0	1	4	2	2	1	5	0	4	3	5	0	2	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr1:101004706C>T	ENST00000315033.4	+	2	623	c.184C>T	c.(184-186)Ctg>Ttg	p.L62L		NM_022049.2	NP_071332.2	Q9GZN0	GPR88_HUMAN	G protein-coupled receptor 88	62					G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuronal action potential (GO:0019228)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			large_intestine(2)|skin(1)	3		all_epithelial(167;1.19e-05)|all_lung(203;0.00159)|Lung NSC(277;0.00171)		Epithelial(280;0.0372)|all cancers(265;0.0558)|COAD - Colon adenocarcinoma(174;0.141)|Colorectal(144;0.156)|Lung(183;0.189)		CTTCCGAAAGCTGCAGACCAC	0.677																																					p.L62L		Atlas-SNP	.											.	GPR88	17	.	0			c.C184T						PASS	.						40	37	38					1																	101004706		2203	4300	6503	SO:0001819	synonymous_variant	54112	exon2			CGAAAGCTGCAGA	AB042411	CCDS772.1	1p21.3	2012-08-21	2006-02-15		ENSG00000181656	ENSG00000181656		"GPCR / Class A : Orphans"	4539	protein-coding gene	gene with protein product		607468	"G-protein coupled receptor 88", "G protein coupled receptor 88"				Standard	NM_022049		Approved		uc001dth.3	Q9GZN0	OTTHUMG00000010981	ENST00000315033.4:c.184C>T	1.37:g.101004706C>T		127	0	0		94	40	0.425532	NM_022049	Q29S24|Q6VN48	Silent	SNP	ENST00000315033.4	37	CCDS772.1																																																																																			.	.	none		0.677	GPR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030212.1	NM_022049		T	101004706	C	T	101004706	2	4	45	1	0	0	0	0	0	0	0	1	6725	796	28	2		2	GPR88	1	101004706	Silent	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	43626618	101004706	148245915	6	15458											
C1orf183	55924	hgsc.bcm.edu	37	chr1	112269753	112269753	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcttcttgaccttctgtgagCggccggttcgggactcaggg	4	11	15	11	3	3	2	1	2	2	0	4	3	3	3	2	4	1	2	2	4	0	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr1:112269753C>T	ENST00000357260.5	-	2	912	c.731G>A	c.(730-732)cGc>cAc	p.R244H	FAM212B_ENST00000534365.1_Intron|FAM212B_ENST00000444059.2_Missense_Mutation_p.R229H	NM_019099.4	NP_061972.1	Q9NTI7	F212B_HUMAN	family with sequence similarity 212, member B	244										cervix(1)|endometrium(1)	2						CTTCTGTGAGCGGCCGGTTCG	0.617																																					p.R244H		Atlas-SNP	.											.	FAM212B	17	.	0			c.G731A						PASS	.						61	66	64					1																	112269753		2203	4300	6503	SO:0001583	missense	55924	exon2			TGTGAGCGGCCGG	AK055667	CCDS841.1, CCDS44195.1	1p13.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000197852	ENSG00000197852			28045	protein-coding gene	gene with protein product			"chromosome 1 open reading frame 183"	C1orf183			Standard	NM_019099		Approved	FLJ31105	uc001ebo.2	Q9NTI7	OTTHUMG00000011953	ENST00000357260.5:c.731G>A	1.37:g.112269753C>T	ENSP00000349805:p.Arg244His	88	0	0		56	39	0.696429	NM_019099	B3KP38|B4DF94|Q9NTI6	Missense_Mutation	SNP	ENST00000357260.5	37	CCDS841.1	.	.	.	.	.	.	.	.	.	.	C	14.98	2.696087	0.48202	.	.	ENSG00000197852	ENST00000357260;ENST00000444059	.	.	.	4.93	4.93	0.64822	.	0.061291	0.64402	D	0.000012	T	0.51092	0.1654	L	0.32530	0.975	0.34183	D	0.671209	D;D	0.89917	1.0;1.0	D;D	0.72338	0.977;0.977	T	0.56823	-0.7915	9	0.51188	T	0.08	-18.9743	13.6697	0.62418	0.0:1.0:0.0:0.0	.	229;244	Q9NTI7-2;Q9NTI7	.;CA183_HUMAN	H	244;229	.	ENSP00000349805:R244H	R	-	2	0	C1orf183	112071276	1.000000	0.71417	0.569000	0.28460	0.039000	0.13416	6.056000	0.71111	2.287000	0.76781	0.555000	0.69702	CGC	.	.	none		0.617	FAM212B-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033060.2	NM_019099		T	112269753	C	T	112269753	3	4	45	1	0	0	0	0	1	0	0	0	2021	768	27	1	166	1	C1orf183	1	112269753	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	11265047	112269753	136980868	7	15459											
UBAP2L	9898	hgsc.bcm.edu	37	chr1	154209612	154209612	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgaaccagatgatgggacgAgtgagtgaccatttatcatt	12	12	11	6	1	1	5	1	4	0	1	1	7	1	6	2	1	1	0	2	1	2	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr1:154209612A>G	ENST00000361546.2	+	7	745	c.703A>G	c.(703-705)Agt>Ggt	p.S235G	UBAP2L_ENST00000428931.1_Splice_Site_p.S235G|UBAP2L_ENST00000343815.6_Splice_Site_p.S235G|UBAP2L_ENST00000271877.7_Splice_Site_p.S246G			Q14157	UBP2L_HUMAN	ubiquitin associated protein 2-like	235					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)			TGATGGGACGAGTGAGTGACC	0.398																																					p.S235G		Atlas-SNP	.											.	UBAP2L	197	.	0			c.A703G						PASS	.						125	102	110					1																	154209612		2203	4300	6503	SO:0001630	splice_region_variant	9898	exon8			GGGACGAGTGAGT	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.703+1A>G	1.37:g.154209612A>G		273	1	0.003663		183	98	0.535519	NM_001127320	B4E0U8|Q5VU75|Q5VU76|Q9BTU3|Q9UGL2|Q9UGL3|Q9UGL4|Q9UGL5	Missense_Mutation	SNP	ENST00000361546.2	37	CCDS1063.1	.	.	.	.	.	.	.	.	.	.	A	7.104	0.574611	0.13623	.	.	ENSG00000143569	ENST00000343815;ENST00000428931;ENST00000271877;ENST00000412596;ENST00000368504;ENST00000437652;ENST00000361546	T;T;T;T;T;T;T	0.41400	2.87;2.87;2.84;1.01;1.02;1.0;2.87	5.68	5.68	0.88126	.	0.281854	0.44285	D	0.000464	T	0.08088	0.0202	N	0.01242	-0.935	0.31470	N	0.668466	P;B;P;P;P	0.49783	0.882;0.008;0.928;0.928;0.788	B;B;P;P;B	0.46975	0.332;0.004;0.533;0.533;0.287	T	0.10894	-1.0610	10	0.02654	T	1	0.5595	15.1058	0.72322	1.0:0.0:0.0:0.0	.	149;246;228;235;235	B4DZJ6;F8W726;Q14157-4;Q14157-1;Q14157	.;.;.;.;UBP2L_HUMAN	G	235;235;246;235;246;228;235	ENSP00000345308:S235G;ENSP00000389445:S235G;ENSP00000271877:S246G;ENSP00000389052:S235G;ENSP00000357490:S246G;ENSP00000389717:S228G;ENSP00000355343:S235G	ENSP00000271877:S246G	S	+	1	0	UBAP2L	152476236	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.569000	0.60865	2.161000	0.67846	0.482000	0.46254	AGT	.	.	none		0.398	UBAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087673.1	NM_014847	Missense_Mutation	G	154209612	A	G	154209612	5	3	45	1	0	0	0	0	0	0	1	0	16853	318	11	3	729	3	UBAP2L	1	154209612	Splice_Site	SNP	A	TCGA-RQ-A68N-01A-11D-A31X-10	41939859	154209612	95041009	8	15460											
FCRL3	115352	hgsc.bcm.edu	37	chr1	157665375	157665375	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gccctgggagccctgaaggtGaggacagggtgagataccgg	9	5	18	9	1	0	3	0	3	0	1	0	6	0	5	3	5	2	0	3	5	2	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr1:157665375G>A	ENST00000368184.3	-	8	1446	c.1155C>T	c.(1153-1155)ctC>ctT	p.L385L	RP11-367J7.3_ENST00000453692.1_RNA|FCRL3_ENST00000473231.1_5'UTR|FCRL3_ENST00000368186.5_Silent_p.L385L	NM_052939.3	NP_443171.2	Q96P31	FCRL3_HUMAN	Fc receptor-like 3	385	Ig-like C2-type 5.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(1)|large_intestine(13)|lung(31)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)	69	all_hematologic(112;0.0378)					CCCTGAAGGTGAGGACAGGGT	0.562																																					p.L385L		Atlas-SNP	.											.	FCRL3	163	.	0			c.C1155T						PASS	.						38	39	39					1																	157665375		2203	4300	6503	SO:0001819	synonymous_variant	115352	exon8			GAAGGTGAGGACA	AF459027	CCDS1167.1	1q21-q22	2013-01-11			ENSG00000160856	ENSG00000160856		"CD molecules", "Immunoglobulin superfamily / Immunoglobulin-like domain containing"	18506	protein-coding gene	gene with protein product		606510				11493702, 12014205	Standard	XR_241065		Approved	FCRH3, IRTA3, IFGP3, SPAP2a, SPAP2, SPAP2b, SPAP2c, SPAP2d, SPAP2e, CD307c	uc001frb.3	Q96P31	OTTHUMG00000019400	ENST00000368184.3:c.1155C>T	1.37:g.157665375G>A		139	0	0		100	56	0.56	NM_052939	A0N0M4|A8MTH7|D3DVD2|Q5VXZ8|Q8N6S2|Q96LA4|Q96P27|Q96P28|Q96P29|Q96P30	Silent	SNP	ENST00000368184.3	37	CCDS1167.1																																																																																			.	.	none		0.562	FCRL3-006	NOVEL	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051419.2	NM_052939		A	157665375	G	A	157665375	2	1	45	1	0	0	0	0	0	0	0	1	5804	1277	45	2		2	FCRL3	1	157665375	Silent	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	3455763	157665375	91585246	9	15461											
IGSF8	93185	hgsc.bcm.edu	37	chr1	160063649	160063649	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cccctactaccatgcggtacCgatcggtcccttccttgccc	5	10	7	19	3	0	0	0	0	0	0	3	1	2	0	7	2	5	1	7	2	3	5			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr1:160063649C>T	ENST00000368086.1	-	3	971	c.755G>A	c.(754-756)cGg>cAg	p.R252Q	IGSF8_ENST00000460351.1_5'UTR|IGSF8_ENST00000314485.7_Missense_Mutation_p.R252Q			Q969P0	IGSF8_HUMAN	immunoglobulin superfamily, member 8	252	Ig-like C2-type 2.				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)			CATGCGGTACCGATCGGTCCC	0.642																																					p.R252Q		Atlas-SNP	.											.	IGSF8	59	.	0			c.G755A						PASS	.						65	54	58					1																	160063649		2203	4300	6503	SO:0001583	missense	93185	exon3			CGGTACCGATCGG	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.755G>A	1.37:g.160063649C>T	ENSP00000357065:p.Arg252Gln	71	0	0		58	33	0.568965	NM_052868	Q8NG09|Q96DP4|Q9BTG9	Missense_Mutation	SNP	ENST00000368086.1	37	CCDS1195.1	.	.	.	.	.	.	.	.	.	.	C	8.668	0.902158	0.17760	.	.	ENSG00000162729	ENST00000314485;ENST00000368086;ENST00000358475;ENST00000448417	T;T;T	0.21191	2.02;2.02;2.02	3.74	1.85	0.25348	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.515891	0.17879	N	0.158924	T	0.02119	0.0066	N	0.08118	0	0.24433	N	0.994565	B	0.20164	0.042	B	0.08055	0.003	T	0.44236	-0.9341	10	0.15499	T	0.54	-16.8689	3.1886	0.06609	0.0:0.4775:0.2166:0.3059	.	252	Q969P0	IGSF8_HUMAN	Q	252	ENSP00000316664:R252Q;ENSP00000357065:R252Q;ENSP00000397464:R252Q	ENSP00000316664:R252Q	R	-	2	0	IGSF8	158330273	0.001000	0.12720	0.694000	0.30210	0.499000	0.33736	0.560000	0.23500	0.930000	0.37217	0.491000	0.48974	CGG	.	.	none		0.642	IGSF8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060636.1	NM_052868		T	160063649	C	T	160063649	3	4	45	1	0	0	0	0	1	0	0	0	7613	652	23	1	1102	1	IGSF8	1	160063649	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	2398274	160063649	89186972	10	15462											
CRB1	23418	hgsc.bcm.edu	37	chr1	197390429	197390429	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccacactttcatttgagggcGatggcttcctgtgggtcaaa	8	12	11	10	1	2	1	2	1	0	0	3	2	3	1	2	3	0	1	2	3	1	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr1:197390429G>A	ENST00000367400.3	+	6	1606	c.1471G>A	c.(1471-1473)Gat>Aat	p.D491N	CRB1_ENST00000476483.1_3'UTR|CRB1_ENST00000543483.1_Missense_Mutation_p.D190N|CRB1_ENST00000538660.1_Missense_Mutation_p.D491N|CRB1_ENST00000544212.1_De_novo_Start_OutOfFrame|CRB1_ENST00000535699.1_Missense_Mutation_p.D422N|CRB1_ENST00000367399.2_Missense_Mutation_p.D379N|CRB1_ENST00000367397.1_De_novo_Start_OutOfFrame	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	491	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.		D -> V (found in a patient with early- onset retinal dystrophy; unknown pathological significance). {ECO:0000269|PubMed:20683928}.		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)	p.D491N(1)		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						ATTTGAGGGCGATGGCTTCCT	0.517																																					p.D491N		Atlas-SNP	.											CRB1,bladder,carcinoma,0,1	CRB1	284	1	1	Substitution - Missense(1)	urinary_tract(1)	c.G1471A						PASS	.						108	97	101					1																	197390429		2203	4300	6503	SO:0001583	missense	23418	exon6			GAGGGCGATGGCT		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.1471G>A	1.37:g.197390429G>A	ENSP00000356370:p.Asp491Asn	87	0	0		69	40	0.57971	NM_001257966	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Missense_Mutation	SNP	ENST00000367400.3	37	CCDS1390.1	.	.	.	.	.	.	.	.	.	.	G	0.010	-1.762289	0.00651	.	.	ENSG00000134376	ENST00000535699;ENST00000538660;ENST00000367400;ENST00000367399;ENST00000543483;ENST00000367401	T;T;T;T;T	0.78924	-1.22;-1.22;-1.22;-1.22;-1.22	5.82	-0.494	0.12034	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	.	.	.	.	T	0.35828	0.0945	N	0.00193	-1.875	0.28017	N	0.934662	B;B;B;B;B	0.10296	0.002;0.0;0.003;0.001;0.001	B;B;B;B;B	0.06405	0.001;0.0;0.002;0.0;0.0	T	0.40701	-0.9549	9	0.11182	T	0.66	.	7.0169	0.24892	0.6755:0.112:0.2124:0.0	.	491;422;379;140;491	B7Z5T2;F5H0L2;P82279-3;P82279-4;P82279	.;.;.;.;CRUM1_HUMAN	N	422;491;491;379;190;140	ENSP00000438786:D422N;ENSP00000438091:D491N;ENSP00000356370:D491N;ENSP00000356369:D379N;ENSP00000439579:D190N	ENSP00000356369:D379N	D	+	1	0	CRB1	195657052	0.013000	0.17824	0.007000	0.13788	0.001000	0.01503	0.490000	0.22403	-0.339000	0.08401	-1.283000	0.01379	GAT	.	.	none		0.517	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	NM_201253		A	197390429	G	A	197390429	3	1	45	1	0	0	0	0	1	0	0	0	3850	1058	37	1	1493	1	CRB1	1	197390429	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	37326780	197390429	51860192	11	15463											
BTG2	7832	hgsc.bcm.edu	37	chr1	203274836	203274836	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ggctgcgtgagcgagcagagGcttaaggtcttcagcggggc	7	7	18	9	3	2	2	1	1	1	1	2	3	2	2	0	5	4	3	0	5	1	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr1:203274836G>A	ENST00000290551.4	+	1	173	c.102G>A	c.(100-102)agG>agA	p.R34R	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	34					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			GCGAGCAGAGGCTTAAGGTCT	0.716																																					p.R34R		Atlas-SNP	.											.	BTG2	16	.	0			c.G102A						PASS	.						15	16	15					1																	203274836		2144	4202	6346	SO:0001819	synonymous_variant	7832	exon1			GCAGAGGCTTAAG		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.102G>A	1.37:g.203274836G>A		123	0	0		78	27	0.346154	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Silent	SNP	ENST00000290551.4	37	CCDS1437.1																																																																																			.	.	none		0.716	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		A	203274836	G	A	203274836	2	1	45	1	0	0	0	0	0	0	0	1	1556	1194	42	2		2	BTG2	1	203274836	Silent	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	5884407	203274836	45975785	12	15464											
PLB1	151056	hgsc.bcm.edu	37	chr2	28772953	28772953	+	Splice_Site	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	accccaagacaagcttgaggTaaggaaaggttttctgtaat	14	10	10	7	0	1	2	0	1	1	1	1	3	1	3	2	3	1	4	2	3	5	5			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr2:28772953T>G	ENST00000327757.5	+	16	1127		c.e16+2		PLB1_ENST00000422425.2_Splice_Site|PLB1_ENST00000329020.6_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)					AAGCTTGAGGTAAGGAAAGGT	0.448																																					.		Atlas-SNP	.											.	PLB1	255	.	0			c.1083+2T>G						PASS	.						76	67	70					2																	28772953		2203	4300	6503	SO:0001630	splice_region_variant	151056	exon16			TTGAGGTAAGGAA		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.1083+2T>G	2.37:g.28772953T>G		121	0	0		87	26	0.298851	NM_153021	A8KAX2|Q53S03|Q8IUP7|Q96DP9	Splice_Site	SNP	ENST00000327757.5	37	CCDS33168.1	.	.	.	.	.	.	.	.	.	.	T	12.05	1.822878	0.32237	.	.	ENSG00000163803	ENST00000327757;ENST00000422425;ENST00000404858;ENST00000436544;ENST00000329020	.	.	.	4.97	3.81	0.43845	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.8203	0.23852	0.0:0.1043:0.0:0.8957	.	.	.	.	.	-1	.	.	.	+	.	.	PLB1	28626457	1.000000	0.71417	0.997000	0.53966	0.069000	0.16628	2.145000	0.42207	1.997000	0.58415	0.459000	0.35465	.	.	.	none		0.448	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2		Intron	G	28772953	T	G	28772953	5	3	45	1	0	0	0	0	0	0	1	0	12033	1652	57	5	1180	5	PLB1	2	28772953	Splice_Site	SNP	T	TCGA-RQ-A68N-01A-11D-A31X-10		28772953	214426420	13	15465											
ALMS1	7840	hgsc.bcm.edu	37	chr2	73646370	73646370	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgacagacttcccctctctGgaggagggcatattgacgca	9	9	12	11	1	1	3	0	2	1	1	3	5	2	5	2	3	0	2	2	3	1	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr2:73646370G>A	ENST00000264448.6	+	3	681	c.570G>A	c.(568-570)ctG>ctA	p.L190L	ALMS1_ENST00000409009.1_Silent_p.L148L|ALMS1_ENST00000377715.1_Silent_p.L190L	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	190					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						TCCCCTCTCTGGAGGAGGGCA	0.433																																					p.L190L		Atlas-SNP	.											.	ALMS1	384	.	0			c.G570A						PASS	.						131	124	126					2																	73646370		1849	4096	5945	SO:0001819	synonymous_variant	7840	exon3			CTCTCTGGAGGAG	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.570G>A	2.37:g.73646370G>A		98	0	0		92	28	0.304348	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	37	CCDS42697.1																																																																																			.	.	none		0.433	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120		A	73646370	G	A	73646370	2	1	45	1	0	0	0	0	0	0	0	1	535	1335	47	2		2	ALMS1	2	73646370	Silent	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	44873417	73646370	169553003	14	15466											
REEP1	65055	hgsc.bcm.edu	37	chr2	86459825	86459825	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgctggcccgcccagaccccGgtggtggggggcccgaggga	4	3	19	15	4	0	1	0	0	0	1	0	3	0	2	5	7	0	1	5	7	0	0			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr2:86459825G>A	ENST00000165698.5	-	6	661	c.518C>T	c.(517-519)cCg>cTg	p.P173L	REEP1_ENST00000540790.1_Missense_Mutation_p.P152L|REEP1_ENST00000538924.1_Missense_Mutation_p.P180L|REEP1_ENST00000535845.1_Missense_Mutation_p.P146L|REEP1_ENST00000541910.1_Missense_Mutation_p.R95W|REEP1_ENST00000473407.1_5'Flank	NM_022912.2	NP_075063.1	Q9H902	REEP1_HUMAN	receptor accessory protein 1	173	Poly-Pro.				cell death (GO:0008219)|endoplasmic reticulum tubular network organization (GO:0071786)|protein insertion into membrane (GO:0051205)|regulation of intracellular transport (GO:0032386)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)	microtubule binding (GO:0008017)|olfactory receptor binding (GO:0031849)			breast(1)|endometrium(2)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	13						CCCAGACCCCGGTGGTGGGGG	0.647																																					p.P180L		Atlas-SNP	.											.	REEP1	22	.	0			c.C539T						PASS	.						34	33	33					2																	86459825		2203	4300	6503	SO:0001583	missense	65055	exon6			GACCCCGGTGGTG	AK023172	CCDS1989.1, CCDS54372.1, CCDS54373.1, CCDS54374.1	2p11.2	2014-09-17	2006-02-07	2006-02-07	ENSG00000068615	ENSG00000068615		"Receptor accessory proteins"	25786	protein-coding gene	gene with protein product	"receptor expression enhancing protein 1"	609139	"chromosome 2 open reading frame 23"	C2orf23		16271481, 15550249	Standard	NM_022912		Approved	FLJ13110, SPG31	uc002srh.4	Q9H902	OTTHUMG00000130205	ENST00000165698.5:c.518C>T	2.37:g.86459825G>A	ENSP00000165698:p.Pro173Leu	34	0	0		33	9	0.272727	NM_001164730	B7Z4D7|B7Z4F2|B7Z5R9|D6W5M2|Q53TI0	Missense_Mutation	SNP	ENST00000165698.5	37	CCDS1989.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.09|15.09	2.729874|2.729874	0.48833|0.48833	.|.	.|.	ENSG00000068615|ENSG00000068615	ENST00000165698;ENST00000538924;ENST00000535845;ENST00000540790;ENST00000453231|ENST00000541910;ENST00000437769	D;D;D;D;D|D;D	0.88354|0.95001	-2.35;-2.37;-1.53;-1.53;-2.32|-3.58;-3.52	5.48|5.48	4.6|4.6	0.57074|0.57074	.|.	0.302480|.	0.28760|.	N|.	0.014224|.	D|D	0.90356|0.90356	0.6982|0.6982	N|N	0.22421|0.22421	0.69|0.69	0.21290|0.21290	N|N	0.999732|0.999732	B;B;B|D	0.20887|0.56968	0.012;0.049;0.012|0.978	B;B;B|B	0.19148|0.43623	0.003;0.024;0.003|0.425	D|D	0.83759|0.83759	0.0213|0.0213	10|9	0.17369|0.62326	T|D	0.5|0.03	.|.	13.2924|13.2924	0.60278|0.60278	0.0:0.0:0.8413:0.1587|0.0:0.0:0.8413:0.1587	.|.	146;152;173|95	B7Z5R9;F5H7Z9;Q9H902|B7Z4D7	.;.;REEP1_HUMAN|.	L|W	173;180;146;152;180|95	ENSP00000165698:P173L;ENSP00000438346:P180L;ENSP00000437567:P146L;ENSP00000443831:P152L;ENSP00000392197:P180L|ENSP00000442681:R95W;ENSP00000401140:R95W	ENSP00000165698:P173L|ENSP00000401140:R95W	P|R	-|-	2|1	0|2	REEP1|REEP1	86313336|86313336	0.994000|0.994000	0.37717|0.37717	0.134000|0.134000	0.22075|0.22075	0.187000|0.187000	0.23431|0.23431	5.056000|5.056000	0.64287|0.64287	1.430000|1.430000	0.47334|0.47334	0.655000|0.655000	0.94253|0.94253	CCG|CGG	.	.	none		0.647	REEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252523.2	NM_022912		A	86459825	G	A	86459825	3	1	45	1	0	0	0	0	1	0	0	0	13219	1116	39	1	156	1	REEP1	2	86459825	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	12813455	86459825	156739548	15	15467											
GLI2	2736	hgsc.bcm.edu	37	chr2	121708912	121708912	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cctggggagtcccccttcaaCgccccccacccgtacgtgaa	7	6	9	19	3	1	1	1	1	0	0	2	2	2	2	7	2	2	1	7	2	3	2	rs140711756		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr2:121708912C>T	ENST00000452319.1	+	4	408	c.348C>T	c.(346-348)aaC>aaT	p.N116N	GLI2_ENST00000361492.4_Silent_p.N116N|GLI2_ENST00000435313.2_3'UTR|GLI2_ENST00000314490.11_5'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)				CCCCCTTCAACGCCCCCCACC	0.667																																					p.N116N		Atlas-SNP	.											GLI2,NS,adenocarcinoma,0,1	GLI2	187	1	0			c.C348T						PASS	.	C		6,4400	12.9+/-30.5	0,6,2197	61	66	64		348	-5	0.2	2	dbSNP_134	64	0,8600		0,0,4300	no	coding-synonymous	GLI2	NM_005270.4		0,6,6497	TT,TC,CC		0.0,0.1362,0.0461		116/1587	121708912	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	2736	exon3			CTTCAACGCCCCC		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.348C>T	2.37:g.121708912C>T		159	0	0		111	21	0.189189	NM_005270		Silent	SNP	ENST00000452319.1	37	CCDS33283.1																																																																																			C|1.000;T|0.000	0.000	weak		0.667	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270		T	121708912	C	T	121708912	2	4	45	1	0	0	0	0	0	0	0	1	6446	535	19	1		1	GLI2	2	121708912	Silent	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	35249087	121708912	121490461	16	15468											
CNTNAP5	129684	hgsc.bcm.edu	37	chr2	125627339	125627339	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcaccttgggcaaagtcacaGgtatgttgttctagttcata	10	14	9	8	0	4	0	3	0	1	0	4	0	4	0	1	2	0	5	1	2	4	7			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr2:125627339G>T	ENST00000431078.1	+	21	3797	c.3433G>T	c.(3433-3435)Gag>Tag	p.E1145*		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	1145	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)		CAAAGTCACAGGTATGTTGTT	0.403																																					p.E1145X		Atlas-SNP	.											.	CNTNAP5	405	.	0			c.G3433T						PASS	.						72	69	70					2																	125627339		1870	4105	5975	SO:0001630	splice_region_variant	129684	exon21			GTCACAGGTATGT	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.3433+1G>T	2.37:g.125627339G>T		201	0	0		150	15	0.1	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Nonsense_Mutation	SNP	ENST00000431078.1	37	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	G	45	11.607466	0.99582	.	.	ENSG00000155052	ENST00000431078	.	.	.	5.57	5.57	0.84162	.	0.270733	0.25535	N	0.030011	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.39692	T	0.17	.	15.1209	0.72441	0.0:0.0:1.0:0.0	.	.	.	.	X	1145	.	ENSP00000399013:E1145X	E	+	1	0	CNTNAP5	125343809	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	5.395000	0.66291	2.610000	0.88304	0.558000	0.71614	GAG	.	.	none		0.403	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3		Nonsense_Mutation	T	125627339	G	T	125627339	5	4	45	1	0	0	0	0	0	0	1	0	3652	1014	35	4	3515	4	CNTNAP5	2	125627339	Splice_Site	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	3918427	125627339	117572034	17	15469											
NEB	4703	hgsc.bcm.edu	37	chr2	152420390	152420390	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aacaatgggaatgtagcgctCatccagggtgtagccatagg	12	8	13	8	1	1	0	1	0	0	0	2	1	2	1	2	3	3	3	2	3	6	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr2:152420390C>T	ENST00000172853.10	-	90	13570	c.13423G>A	c.(13423-13425)Gag>Aag	p.E4475K	NEB_ENST00000409198.1_Missense_Mutation_p.E4475K|NEB_ENST00000427231.2_Missense_Mutation_p.E6176K|NEB_ENST00000604864.1_Missense_Mutation_p.E6176K|NEB_ENST00000603639.1_Missense_Mutation_p.E6176K|NEB_ENST00000397345.3_Missense_Mutation_p.E6176K			P20929	NEBU_HUMAN	nebulin	4475					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)		ATGTAGCGCTCATCCAGGGTG	0.463																																					p.E6176K		Atlas-SNP	.											.	NEB	1697	.	0			c.G18526A						PASS	.						71	71	71					2																	152420390		1965	4171	6136	SO:0001583	missense	4703	exon118			AGCGCTCATCCAG	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.13423G>A	2.37:g.152420390C>T	ENSP00000172853:p.Glu4475Lys	163	0	0		129	23	0.178295	NM_001271208	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	C	16.23	3.064033	0.55432	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000397342;ENST00000413693;ENST00000172853	T;T;T;T;T	0.06528	3.4;3.39;3.39;3.29;3.4	5.67	5.67	0.87782	.	0.178823	0.50627	D	0.000102	T	0.06508	0.0167	N	0.25647	0.755	0.80722	D	1	B;P	0.37573	0.043;0.6	B;B	0.42625	0.179;0.393	T	0.29610	-1.0006	10	0.06625	T	0.88	.	14.9243	0.70866	0.0:0.7397:0.2603:0.0	.	4475;906	P20929;Q14215	NEBU_HUMAN;.	K	4475;6176;6176;524;906;4475	ENSP00000386259:E4475K;ENSP00000380505:E6176K;ENSP00000416578:E6176K;ENSP00000410961:E906K;ENSP00000172853:E4475K	ENSP00000172853:E4475K	E	-	1	0	NEB	152128636	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.020000	0.49643	2.834000	0.97654	0.650000	0.86243	GAG	.	.	none		0.463	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543		T	152420390	C	T	152420390	3	4	45	1	0	0	0	0	1	0	0	0	10311	835	29	2	7420	2	NEB	2	152420390	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	26793051	152420390	90778983	18	15470											
RAPGEF4	11069	hgsc.bcm.edu	37	chr2	173882186	173882186	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttgcaacagttcaatacgggCgatgagagagcccagaagcg	13	6	13	9	3	1	3	1	1	0	2	1	5	1	3	1	1	5	2	1	1	4	3	rs549829112		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr2:173882186C>T	ENST00000397081.3	+	21	2105	c.1962C>T	c.(1960-1962)ggC>ggT	p.G654G	RAPGEF4_ENST00000538974.1_Silent_p.G483G|RAPGEF4_ENST00000540783.1_Silent_p.G501G|RAPGEF4_ENST00000264111.6_Silent_p.G653G|RAPGEF4_ENST00000535187.1_Silent_p.G434G|RAPGEF4_ENST00000409036.1_Silent_p.G654G|RAPGEF4_ENST00000539331.1_Silent_p.G501G|RAPGEF4_ENST00000397087.3_Silent_p.G510G	NM_007023.3	NP_008954.2	Q8WZA2	RPGF4_HUMAN	Rap guanine nucleotide exchange factor (GEF) 4	654					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)	p.G654G(1)		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)			TCAATACGGGCGATGAGAGAG	0.468													c|||	1	0.000199681	0.0008	0.0	5008	,	,		17335	0.0		0.0	False		,,,				2504	0.0				p.G654G		Atlas-SNP	.											RAPGEF4,NS,carcinoma,0,2	RAPGEF4	103	2	1	Substitution - coding silent(1)	large_intestine(1)	c.C1962T						PASS	.						72	70	71					2																	173882186		1905	4124	6029	SO:0001819	synonymous_variant	11069	exon21			TACGGGCGATGAG	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.1962C>T	2.37:g.173882186C>T		60	0	0		50	10	0.2	NM_007023	B2R7R3|B7Z283|B7Z3T6|B7Z912|O95636|Q8IXK6|Q8TAA4	Silent	SNP	ENST00000397081.3	37	CCDS42775.1																																																																																			.	.	none		0.468	RAPGEF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257864.2	NM_007023		T	173882186	C	T	173882186	2	4	45	1	0	0	0	0	0	0	0	1	13061	755	27	1		1	RAPGEF4	2	173882186	Silent	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	21461796	173882186	69317187	19	15471											
NMUR1	10316	hgsc.bcm.edu	37	chr2	232393132	232393132	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgtgcagctgccggatgccGtgcaggctggtgttgggcag	5	8	18	10	3	0	0	0	0	0	0	0	1	0	1	2	4	5	6	2	4	0	1	rs370312738		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr2:232393132G>A	ENST00000305141.4	-	2	733	c.600C>T	c.(598-600)caC>caT	p.H200H		NM_006056.4	NP_006047.3	Q9HB89	NMUR1_HUMAN	neuromedin U receptor 1	200					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)		GCCGGATGCCGTGCAGGCTGG	0.672																																					p.H200H		Atlas-SNP	.											.	NMUR1	46	.	0			c.C600T						PASS	.	G		0,4404		0,0,2202	30	29	29		600	-2.6	0.8	2		29	1,8595		0,1,4297	no	coding-synonymous	NMUR1	NM_006056.4		0,1,6499	AA,AG,GG		0.0116,0.0,0.0077		200/427	232393132	1,12999	2202	4298	6500	SO:0001819	synonymous_variant	10316	exon2			GATGCCGTGCAGG	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.600C>T	2.37:g.232393132G>A		51	0	0		48	14	0.291667	NM_006056	O43664|Q7LDP6|Q8NE20	Silent	SNP	ENST00000305141.4	37	CCDS2486.1																																																																																			.	.	weak		0.672	NMUR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256961.1	NM_006056		A	232393132	G	A	232393132	2	1	45	1	0	0	0	0	0	0	0	1	10515	1136	40	1		1	NMUR1	2	232393132	Silent	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	58510946	232393132	10806241	20	15472											
COL6A3	1293	hgsc.bcm.edu	37	chr2	238253001	238253001	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagagcacagacctgcaaagCgttgatgagctgccggtctt	10	8	12	11	2	1	4	0	2	1	2	1	4	1	4	2	1	5	4	2	1	1	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr2:238253001C>T	ENST00000295550.4	-	36	8112	c.7660G>A	c.(7660-7662)Gct>Act	p.A2554T	COL6A3_ENST00000346358.4_Missense_Mutation_p.A2354T|COL6A3_ENST00000347401.3_Missense_Mutation_p.A2353T|COL6A3_ENST00000472056.1_Missense_Mutation_p.A1947T|COL6A3_ENST00000353578.4_Missense_Mutation_p.A2348T|COL6A3_ENST00000409809.1_Missense_Mutation_p.A2348T	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2554	Nonhelical region.|VWFA 11. {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)		ACCTGCAAAGCGTTGATGAGC	0.557																																					p.A2554T		Atlas-SNP	.											COL6A3,NS,carcinoma,0,1	COL6A3	608	1	0			c.G7660A						PASS	.						151	155	154					2																	238253001		2203	4300	6503	SO:0001583	missense	1293	exon36			GCAAAGCGTTGAT	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.7660G>A	2.37:g.238253001C>T	ENSP00000295550:p.Ala2554Thr	90	0	0		47	7	0.148936	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	15.60	2.881687	0.51908	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	D;D;D;D;D;D	0.82984	-1.67;-1.67;-1.67;-1.67;-1.67;-1.67	5.08	5.08	0.68730	von Willebrand factor, type A (3);	0.000000	0.52532	D	0.000069	D	0.90335	0.6976	M	0.71581	2.175	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;0.999	D	0.88468	0.3060	10	0.30854	T	0.27	.	18.8647	0.92287	0.0:1.0:0.0:0.0	.	1947;1947;2348;2554	E9PFQ6;B7ZMJ7;P12111-2;P12111	.;.;.;CO6A3_HUMAN	T	2554;2353;2348;1947;2348;2354	ENSP00000295550:A2554T;ENSP00000315609:A2353T;ENSP00000315873:A2348T;ENSP00000418285:A1947T;ENSP00000386844:A2348T;ENSP00000295546:A2354T	ENSP00000295550:A2554T	A	-	1	0	COL6A3	237917740	1.000000	0.71417	0.210000	0.23637	0.878000	0.50629	7.308000	0.78929	2.507000	0.84556	0.655000	0.94253	GCT	.	.	none		0.557	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		T	238253001	C	T	238253001	3	4	45	1	0	0	0	0	1	0	0	0	3703	768	27	1	1909	1	COL6A3	2	238253001	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	5859869	238253001	4946372	21	15473											
PER2	8864	hgsc.bcm.edu	37	chr2	239162025	239162025	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctggaggtccacgggcacaGcaggcactgtgaagctggcg	8	5	17	11	2	0	1	0	1	0	0	1	2	1	2	1	5	2	5	1	5	1	0			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr2:239162025G>A	ENST00000254657.3	-	19	2918	c.2639C>T	c.(2638-2640)gCt>gTt	p.A880V	PER2_ENST00000254658.3_3'UTR|AC096574.4_ENST00000456601.1_RNA	NM_022817.2	NP_073728.1	O15055	PER2_HUMAN	period circadian clock 2	880	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)		CACGGGCACAGCAGGCACTGT	0.637																																					p.A880V		Atlas-SNP	.											.	PER2	85	.	0			c.C2639T						PASS	.						30	31	31					2																	239162025		2203	4299	6502	SO:0001583	missense	8864	exon19			GGCACAGCAGGCA	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.2639C>T	2.37:g.239162025G>A	ENSP00000254657:p.Ala880Val	64	0	0		53	22	0.415094	NM_022817	A2I2P7|Q4ZG49|Q6DT41|Q9UQ45	Missense_Mutation	SNP	ENST00000254657.3	37	CCDS2528.1	.	.	.	.	.	.	.	.	.	.	G	1.276	-0.611740	0.03690	.	.	ENSG00000132326	ENST00000254657	T	0.11169	2.8	2.97	0.428	0.16499	.	1.738710	0.03244	N	0.180882	T	0.04952	0.0133	N	0.03115	-0.41	0.09310	N	0.999999	B;B	0.09022	0.002;0.001	B;B	0.06405	0.002;0.002	T	0.35624	-0.9781	10	0.15952	T	0.53	.	6.0569	0.19816	0.397:0.0:0.603:0.0	.	880;880	B4DH14;O15055	.;PER2_HUMAN	V	880	ENSP00000254657:A880V	ENSP00000254657:A880V	A	-	2	0	PER2	238826764	0.001000	0.12720	0.000000	0.03702	0.010000	0.07245	0.969000	0.29370	0.299000	0.22661	0.561000	0.74099	GCT	.	.	none		0.637	PER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257167.1	NM_022817		A	239162025	G	A	239162025	3	1	45	1	0	0	0	0	1	0	0	0	11739	971	34	2	1148	2	PER2	2	239162025	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	909024	239162025	4037348	22	15474											
MYD88	4615	hgsc.bcm.edu	37	chr3	38182641	38182641	+	Nonstop_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtgcccatcagaagcgacTgatccccatcaagtacaagg	13	6	10	12	1	2	2	2	1	0	1	3	3	3	2	3	2	3	1	3	2	4	1	rs387907272		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr3:38182641T>C	ENST00000495303.1	+	3	483	c.478T>C	c.(478-480)Tga>Cga	p.*160R	MYD88_ENST00000417037.2_Missense_Mutation_p.L273P|MYD88_ENST00000424893.1_Missense_Mutation_p.L220P|MYD88_ENST00000481122.1_3'UTR|MYD88_ENST00000443433.2_Nonstop_Mutation_p.*205R|MYD88_ENST00000396334.3_Missense_Mutation_p.L265P	NM_001172566.1	NP_001166037.1	Q99836	MYD88_HUMAN	myeloid differentiation primary response 88	0	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|cell surface receptor signaling pathway (GO:0007166)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-positive bacterium (GO:0050830)|establishment of endothelial intestinal barrier (GO:0090557)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of apoptotic process (GO:0043066)|negative regulation of growth of symbiont in host (GO:0044130)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-23 production (GO:0032747)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of lymphocyte proliferation (GO:0050671)|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 tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)|response to molecule of fungal origin (GO:0002238)|response to peptidoglycan (GO:0032494)|response to virus (GO:0009615)|signal transduction (GO:0007165)|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)|type I interferon biosynthetic process (GO:0045351)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)	death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|TIR domain binding (GO:0070976)	p.L265P(188)		breast(1)|haematopoietic_and_lymphoid_tissue(226)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	237				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		CAGAAGCGACTGATCCCCATC	0.552			Mis		ABC-DLBCL								T|||	1	0.000199681	0.0	0.0	5008	,	,		22034	0.0		0.001	False		,,,				2504	0.0				p.X205R		Atlas-SNP	.		Dom	yes		3	3p22	4615	myeloid differentiation primary response gene (88)		L	MYD88,NS,lymphoid_neoplasm,0,828	MYD88	900	828	188	Substitution - Missense(188)	haematopoietic_and_lymphoid_tissue(188)	c.T613C						PASS	.						148	119	129					3																	38182641		2203	4300	6503	SO:0001578	stop_lost	4615	exon4			AGCGACTGATCCC	U84408	CCDS2674.2, CCDS54565.1, CCDS54566.1, CCDS54567.1, CCDS54568.1	3p22	2014-09-17	2012-11-15		ENSG00000172936	ENSG00000172936			7562	protein-coding gene	gene with protein product		602170	"myeloid differentiation primary response gene (88)"			9013863	Standard	NM_002468		Approved		uc003chx.3	Q99836	OTTHUMG00000131083	ENST00000495303.1:c.478T>C	3.37:g.38182641T>C	ENSP00000417848:p.*160Argext*8	83	0	0		80	30	0.375	NM_001172569	B4DKH8|B4DKU4|B4DQ60|B4DQ72|J3KPU4|J3KQ87|J3KQJ6|P78397|Q53XS7	Missense_Mutation	SNP	ENST00000495303.1	37	CCDS54568.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.85|18.85	3.710754|3.710754	0.68730|0.68730	.|.	.|.	ENSG00000172936|ENSG00000172936	ENST00000417037;ENST00000396334;ENST00000424893;ENST00000421516;ENST00000415158|ENST00000495303;ENST00000443433	T;T;T;T|.	0.15487|.	2.42;2.42;2.42;2.42|.	5.74|5.74	5.74|5.74	0.90152|0.90152	Toll/interleukin-1 receptor homology (TIR) domain (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.71676|.	0.3368|.	.|.	.|.	.|.	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;0.999;0.999|.	T|.	0.70626|.	-0.4820|.	9|.	0.87932|.	D|.	0|.	-17.9268|-17.9268	15.535|15.535	0.75996|0.75996	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	207;252;241|.	Q99836-2;Q99836;B4E3D6|.	.;MYD88_HUMAN;.|.	P|R	273;265;220;272;241|160;205	ENSP00000401399:L273P;ENSP00000379625:L265P;ENSP00000389979:L220P;ENSP00000391753:L272P|.	ENSP00000379625:L265P|.	L|X	+|+	2|1	0|0	MYD88|MYD88	38157645|38157645	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.639000|7.639000	0.83342|0.83342	2.326000|2.326000	0.78906|0.78906	0.533000|0.533000	0.62120|0.62120	CTG|TGA	.	.	none		0.552	MYD88-008	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000342700.1	NM_002468		C	38182641	T	C	38182641	4	2	45	1	0	0	0	0	0	0	0	0	10032	1593	55	3	836	3	MYD88	3	38182641	Nonstop_Mutation	SNP	T	TCGA-RQ-A68N-01A-11D-A31X-10		38182641	159839789	23	15475											
ITIH1	3697	hgsc.bcm.edu	37	chr3	52817273	52817273	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctccggggaattgagatcttGaaccaagttcaggaaagcct	12	9	11	9	1	2	2	1	2	1	1	3	5	3	4	3	3	2	1	3	3	4	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr3:52817273G>T	ENST00000273283.2	+	10	1167	c.1143G>T	c.(1141-1143)ttG>ttT	p.L381F	ITIH1_ENST00000540715.1_Missense_Mutation_p.L239F|ITIH1_ENST00000542827.1_Missense_Mutation_p.L381F|ITIH1_ENST00000537050.1_Missense_Mutation_p.L93F	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	381	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				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)		TTGAGATCTTGAACCAAGTTC	0.517																																					p.L381F		Atlas-SNP	.											.	ITIH1	108	.	0			c.G1143T						PASS	.						95	81	86					3																	52817273		2203	4300	6503	SO:0001583	missense	3697	exon10			GATCTTGAACCAA		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.1143G>T	3.37:g.52817273G>T	ENSP00000273283:p.Leu381Phe	136	0	0		113	50	0.442478	NM_002215	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Missense_Mutation	SNP	ENST00000273283.2	37	CCDS2864.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.003520	0.74932	.	.	ENSG00000055957	ENST00000542827;ENST00000273283;ENST00000540715;ENST00000537050	D;D;D;D	0.86366	-2.11;-2.11;-2.11;-2.11	5.8	4.92	0.64577	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	D	0.91216	0.7232	M	0.63169	1.94	0.40406	D	0.979707	D	0.89917	1.0	D	0.87578	0.998	D	0.91687	0.5363	10	0.87932	D	0	-18.3723	9.4229	0.38561	0.0769:0.1441:0.779:0.0	.	381	P19827	ITIH1_HUMAN	F	381;381;239;93	ENSP00000442584:L381F;ENSP00000273283:L381F;ENSP00000443973:L239F;ENSP00000443847:L93F	ENSP00000273283:L381F	L	+	3	2	ITIH1	52792313	1.000000	0.71417	0.999000	0.59377	0.969000	0.65631	3.777000	0.55364	1.456000	0.47831	0.650000	0.86243	TTG	.	.	none		0.517	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215		T	52817273	G	T	52817273	3	4	45	1	0	0	0	0	1	0	0	0	7912	1281	45	4	1181	4	ITIH1	3	52817273	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	14634632	52817273	145205157	24	15476											
ROBO2	6092	hgsc.bcm.edu	37	chr3	77693936	77693936	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aggaacagcttcttctaaggGatccactggacctaggaaaa	14	8	10	9	0	2	0	0	0	2	0	3	4	3	4	2	4	2	1	2	4	5	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr3:77693936G>T	ENST00000461745.1	+	25	4916	c.4016G>T	c.(4015-4017)gGa>gTa	p.G1339V	ROBO2_ENST00000487694.3_Missense_Mutation_p.G1355V|ROBO2_ENST00000332191.8_Missense_Mutation_p.G1400V	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	1339					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)		TCTTCTAAGGGATCCACTGGA	0.517																																					p.G1339V		Atlas-SNP	.											ROBO2_ENST00000487694,colon,carcinoma,-1,3	ROBO2	527	3	0			c.G4016T						scavenged	.						85	87	87					3																	77693936		2017	4172	6189	SO:0001583	missense	6092	exon25			CTAAGGGATCCAC	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.4016G>T	3.37:g.77693936G>T	ENSP00000417164:p.Gly1339Val	84	1	0.0119048		58	23	0.396552	NM_002942	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	37	CCDS43109.1	.	.	.	.	.	.	.	.	.	.	G	17.41	3.382918	0.61845	.	.	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000461745;ENST00000332191	T;T;T	0.70516	-0.27;-0.23;-0.49	5.85	5.85	0.93711	.	0.000000	0.45126	D	0.000396	T	0.71962	0.3402	L	0.49778	1.585	0.34784	D	0.735015	P;P;P	0.41131	0.622;0.739;0.622	B;P;B	0.46917	0.33;0.531;0.33	T	0.79822	-0.1641	9	0.66056	D	0.02	.	13.3754	0.60736	0.0716:0.0:0.9284:0.0	.	1355;1400;1339	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	V	1355;1355;1339;1400	ENSP00000417335:G1355V;ENSP00000417164:G1339V;ENSP00000327536:G1400V	ENSP00000327536:G1400V	G	+	2	0	ROBO2	77776626	1.000000	0.71417	1.000000	0.80357	0.308000	0.27856	7.394000	0.79862	2.775000	0.95449	0.655000	0.94253	GGA	.	.	none		0.517	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246		T	77693936	G	T	77693936	3	4	45	1	0	0	0	0	1	0	0	0	13529	1174	41	4	4116	4	ROBO2	3	77693936	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	24876663	77693936	120328494	25	15477											
H1FOO	132243	hgsc.bcm.edu	37	chr3	129266464	129266464	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctggccactggcatgcgcCgtggcctcctcgccaggccc	3	6	13	19	4	0	0	0	0	0	0	2	0	1	0	6	4	1	2	6	4	0	0			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr3:129266464C>T	ENST00000324382.2	+	2	324	c.319C>T	c.(319-321)Cgt>Tgt	p.R107C	H1FOO_ENST00000503977.1_5'Flank	NM_153833.1	NP_722575.1	Q8IZA3	H1FOO_HUMAN	H1 histone family, member O, oocyte-specific	107	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				meiotic nuclear division (GO:0007126)|negative regulation of stem cell differentiation (GO:2000737)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of DNA methylation (GO:0044030)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|female germ cell nucleus (GO:0001674)|nucleosome (GO:0000786)|nucleus (GO:0005634)	nucleosomal DNA binding (GO:0031492)			endometrium(1)|lung(4)|skin(1)	6						TGGCATGCGCCGTGGCCTCCT	0.622																																					p.R107C		Atlas-SNP	.											.	H1FOO	20	.	0			c.C319T						PASS	.						12	8	9					3																	129266464		1984	3937	5921	SO:0001583	missense	132243	exon2			ATGCGCCGTGGCC	AY158091	CCDS3064.1	3q21.3	2011-01-27			ENSG00000178804	ENSG00000178804		"Histones / Replication-independent"	18463	protein-coding gene	gene with protein product						12408966	Standard	NM_153833		Approved		uc003emu.3	Q8IZA3	OTTHUMG00000159541	ENST00000324382.2:c.319C>T	3.37:g.129266464C>T	ENSP00000319799:p.Arg107Cys	44	0	0		47	24	0.510638	NM_153833	Q86WT7	Missense_Mutation	SNP	ENST00000324382.2	37	CCDS3064.1	.	.	.	.	.	.	.	.	.	.	C	11.20	1.569113	0.28003	.	.	ENSG00000178804	ENST00000324382	T	0.22743	1.94	5.56	3.63	0.41609	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.569731	0.17640	N	0.167052	T	0.25382	0.0617	M	0.64404	1.975	0.09310	N	1	P	0.52061	0.95	P	0.47206	0.541	T	0.16482	-1.0401	10	0.87932	D	0	-3.2272	5.9767	0.19385	0.2261:0.5766:0.1234:0.074	.	107	Q8IZA3	H1FOO_HUMAN	C	107	ENSP00000319799:R107C	ENSP00000319799:R107C	R	+	1	0	H1FOO	130749154	0.000000	0.05858	0.015000	0.15790	0.063000	0.16089	0.176000	0.16782	1.323000	0.45263	0.655000	0.94253	CGT	.	.	none		0.622	H1FOO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356100.3	NM_153833		T	129266464	C	T	129266464	3	4	45	1	0	0	0	0	1	0	0	0	6931	652	23	1	325	1	H1FOO	3	129266464	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	51572528	129266464	68755966	26	15478											
XRN1	54464	hgsc.bcm.edu	37	chr3	142123761	142123761	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aacattaccttgtacaacatCgttctatggcagggaacttt	12	13	7	9	1	1	0	0	0	1	0	2	1	1	1	1	2	5	3	1	2	6	6	rs150688965		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr3:142123761C>T	ENST00000264951.4	-	16	1988	c.1871G>A	c.(1870-1872)cGa>cAa	p.R624Q	XRN1_ENST00000392981.2_Missense_Mutation_p.R624Q|RNU6-1294P_ENST00000515995.1_RNA	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	624					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						TGTACAACATCGTTCTATGGC	0.418																																					p.R624Q		Atlas-SNP	.											.	XRN1	138	.	0			c.G1871A						PASS	.	C	GLN/ARG,GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	98	85	89		1871,1871	3.4	0.8	3	dbSNP_134	89	0,8600		0,0,4300	no	missense,missense	XRN1	NM_001042604.1,NM_019001.3	43,43	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign,benign	624/1694,624/1707	142123761	2,13004	2203	4300	6503	SO:0001583	missense	54464	exon16			CAACATCGTTCTA	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.1871G>A	3.37:g.142123761C>T	ENSP00000264951:p.Arg624Gln	146	0	0		157	32	0.203822	NM_001042604	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Missense_Mutation	SNP	ENST00000264951.4	37	CCDS3123.1	.	.	.	.	.	.	.	.	.	.	C	14.45	2.538979	0.45176	4.54E-4	0.0	ENSG00000114127	ENST00000264951;ENST00000392981	T;T	0.22945	1.93;1.93	5.53	3.41	0.39046	.	0.475762	0.20827	N	0.084957	T	0.19248	0.0462	L	0.39397	1.21	0.19945	N	0.999948	B;B;B	0.21905	0.021;0.062;0.037	B;B;B	0.19946	0.002;0.027;0.012	T	0.18587	-1.0332	10	0.13470	T	0.59	-1.414	11.6559	0.51318	0.0:0.7832:0.0:0.2168	.	485;624;624	B3KW17;Q8IZH2-2;Q8IZH2	.;.;XRN1_HUMAN	Q	624	ENSP00000264951:R624Q;ENSP00000376707:R624Q	ENSP00000264951:R624Q	R	-	2	0	XRN1	143606451	0.041000	0.20044	0.845000	0.33349	0.932000	0.56968	0.215000	0.17562	1.332000	0.45431	0.650000	0.86243	CGA	C|1.000;T|0.000	0.000	weak		0.418	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001		T	142123761	C	T	142123761	3	4	45	1	0	0	0	0	1	0	0	0	17474	884	31	1	3357	1	XRN1	3	142123761	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	12857297	142123761	55898669	27	15479											
P2RY1	5028	hgsc.bcm.edu	37	chr3	152553954	152553954	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgccatgtgtaaactgcagaGgttcatctttcatgtgaacc	10	13	9	9	0	3	2	2	1	1	1	3	2	3	2	2	1	4	3	2	1	3	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr3:152553954G>A	ENST00000305097.3	+	1	1219	c.383G>A	c.(382-384)aGg>aAg	p.R128K		NM_002563.3	NP_002554.1	P47900	P2RY1_HUMAN	purinergic receptor P2Y, G-protein coupled, 1	128					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)			AAACTGCAGAGGTTCATCTTT	0.517																																					p.R128K		Atlas-SNP	.											.	P2RY1	49	.	0			c.G383A						PASS	.						80	78	78					3																	152553954		2203	4300	6503	SO:0001583	missense	5028	exon1			TGCAGAGGTTCAT	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.383G>A	3.37:g.152553954G>A	ENSP00000304767:p.Arg128Lys	72	0	0		83	37	0.445783	NM_002563		Missense_Mutation	SNP	ENST00000305097.3	37	CCDS3169.1	.	.	.	.	.	.	.	.	.	.	G	35	5.443803	0.96187	.	.	ENSG00000169860	ENST00000305097	T	0.37058	1.22	5.76	5.76	0.90799	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.61615	0.2361	M	0.78801	2.425	0.58432	D	0.999999	D	0.63046	0.992	D	0.77004	0.989	T	0.55036	-0.8203	10	0.21014	T	0.42	.	18.9739	0.92728	0.0:0.0:1.0:0.0	.	128	P47900	P2RY1_HUMAN	K	128	ENSP00000304767:R128K	ENSP00000304767:R128K	R	+	2	0	P2RY1	154036644	1.000000	0.71417	0.878000	0.34440	0.992000	0.81027	7.731000	0.84895	2.706000	0.92434	0.655000	0.94253	AGG	.	.	none		0.517	P2RY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356943.1	NM_002563		A	152553954	G	A	152553954	3	1	45	1	0	0	0	0	1	0	0	0	11355	1000	35	2	385	2	P2RY1	3	152553954	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	10430193	152553954	45468476	28	15480											
TBL1XR1	79718	hgsc.bcm.edu	37	chr3	176750838	176750838	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	caggactgaaagctacactgTacacaggctcttggtgtttt	10	12	10	9	0	1	1	0	1	1	0	1	2	1	2	0	3	3	4	0	3	3	5			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr3:176750838T>C	ENST00000430069.1	-	14	1596	c.1337A>G	c.(1336-1338)tAc>tGc	p.Y446C	TBL1XR1_ENST00000457928.2_Missense_Mutation_p.Y446C			Q9BZK7	TBL1R_HUMAN	transducin (beta)-like 1 X-linked receptor 1	446					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)			AGCTACACTGTACACAGGCTC	0.423																																					p.Y446C		Atlas-SNP	.											.	TBL1XR1	87	.	0			c.A1337G						PASS	.						119	117	118					3																	176750838		1942	4178	6120	SO:0001583	missense	79718	exon14			ACACTGTACACAG	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.1337A>G	3.37:g.176750838T>C	ENSP00000405574:p.Tyr446Cys	278	0	0		316	124	0.392405	NM_024665	D3DNQ9|Q14DC3|Q9H2I1|Q9H9A1	Missense_Mutation	SNP	ENST00000430069.1	37	CCDS46961.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.339487	0.81911	.	.	ENSG00000177565	ENST00000430069;ENST00000457928;ENST00000536758	T;T	0.60299	0.2;0.2	5.51	5.51	0.81932	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.202715	0.44483	D	0.000449	T	0.72550	0.3474	M	0.71581	2.175	0.80722	D	1	P	0.50943	0.94	P	0.61070	0.883	T	0.75439	-0.3317	10	0.62326	D	0.03	-3.9263	14.8126	0.70006	0.0:0.0:0.0:1.0	.	446	Q9BZK7	TBL1R_HUMAN	C	446;446;308	ENSP00000405574:Y446C;ENSP00000413251:Y446C	ENSP00000405574:Y446C	Y	-	2	0	TBL1XR1	178233532	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.098000	0.63641	0.533000	0.62120	TAC	.	.	none		0.423	TBL1XR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347587.3	NM_024665		C	176750838	T	C	176750838	3	2	45	1	0	0	0	0	1	0	0	0	15655	1638	57	3	219	3	TBL1XR1	3	176750838	Missense_Mutation	SNP	T	TCGA-RQ-A68N-01A-11D-A31X-10	24196884	176750838	21271592	29	15481											
ZBTB49	166793	hgsc.bcm.edu	37	chr4	4322555	4322555	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aggagctcagccaagccatcGagacctccgacctcgagaaa	13	4	10	14	3	1	2	1	0	0	2	4	6	2	3	5	1	3	1	5	1	2	0			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr4:4322555G>A	ENST00000337872.4	+	8	1931	c.1810G>A	c.(1810-1812)Gag>Aag	p.E604K	ZBTB49_ENST00000538529.1_Missense_Mutation_p.E87K|RP11-265O12.1_ENST00000509015.1_lincRNA|ZBTB49_ENST00000355834.3_Missense_Mutation_p.E482K	NM_145291.3	NP_660334.3	Q6ZSB9	ZBT49_HUMAN	zinc finger and BTB domain containing 49	604					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						CCAAGCCATCGAGACCTCCGA	0.577																																					p.E604K		Atlas-SNP	.											.	ZBTB49	63	.	0			c.G1810A						PASS	.						59	54	56					4																	4322555		2203	4300	6503	SO:0001583	missense	166793	exon8			GCCATCGAGACCT	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.1810G>A	4.37:g.4322555G>A	ENSP00000338807:p.Glu604Lys	83	0	0		74	14	0.189189	NM_145291	Q59FJ4|Q5EBN0|Q8TB80	Missense_Mutation	SNP	ENST00000337872.4	37	CCDS3375.1	.	.	.	.	.	.	.	.	.	.	G	14.67	2.604935	0.46423	.	.	ENSG00000168826	ENST00000355834;ENST00000337872;ENST00000538529	T;T;T	0.14516	2.5;2.89;3.13	4.57	2.62	0.31277	.	0.279254	0.25197	N	0.032418	T	0.10809	0.0264	M	0.62723	1.935	0.09310	N	1	P;P	0.49862	0.601;0.929	B;B	0.33392	0.07;0.163	T	0.28839	-1.0031	10	0.21014	T	0.42	.	10.6094	0.45412	0.0:0.1439:0.7069:0.1491	.	482;604	Q6ZSB9-2;Q6ZSB9	.;ZBT49_HUMAN	K	482;604;87	ENSP00000348091:E482K;ENSP00000338807:E604K;ENSP00000445653:E87K	ENSP00000338807:E604K	E	+	1	0	ZBTB49	4373456	0.202000	0.23423	0.003000	0.11579	0.269000	0.26545	1.500000	0.35682	1.016000	0.39470	0.455000	0.32223	GAG	.	.	none		0.577	ZBTB49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206688.3	NM_145291		A	4322555	G	A	4322555	3	1	45	1	0	0	0	0	1	0	0	0	17565	1059	37	1	1836	1	ZBTB49	4	4322555	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10		4322555	186831721	30	15482											
KDR	3791	hgsc.bcm.edu	37	chr4	55961059	55961059	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggtgatgctgtccaagcgccGtttcagatccacagggattg	8	10	13	10	2	1	2	1	1	0	1	3	3	3	3	3	2	2	2	3	2	1	2	rs530419081		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr4:55961059G>A	ENST00000263923.4	-	21	3176	c.2881C>T	c.(2881-2883)Cgg>Tgg	p.R961W	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)	961	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)	p.R961W(1)		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)	TCCAAGCGCCGTTTCAGATCC	0.488			Mis		"NSCLC, angiosarcoma"					TSP Lung(20;0.16)			G|||	1	0.000199681	0.0	0.0	5008	,	,		18407	0.0		0.0	False		,,,				2504	0.001				p.R961W		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	KDR,NS,carcinoma,0,1	KDR	307	1	1	Substitution - Missense(1)	breast(1)	c.C2881T						PASS	.						122	112	115					4																	55961059		2203	4300	6503	SO:0001583	missense	3791	exon21			AGCGCCGTTTCAG	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.2881C>T	4.37:g.55961059G>A	ENSP00000263923:p.Arg961Trp	137	0	0		105	23	0.219048	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Missense_Mutation	SNP	ENST00000263923.4	37	CCDS3497.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.111932	0.77210	.	.	ENSG00000128052	ENST00000263923	T	0.77620	-1.11	5.87	4.08	0.47627	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.331135	0.32258	N	0.006349	T	0.77011	0.4068	L	0.42245	1.32	0.38997	D	0.959262	D	0.76494	0.999	P	0.53185	0.72	T	0.78303	-0.2256	10	0.72032	D	0.01	.	9.5094	0.39067	0.0669:0.0:0.679:0.2541	.	961	P35968	VGFR2_HUMAN	W	961	ENSP00000263923:R961W	ENSP00000263923:R961W	R	-	1	2	KDR	55655816	1.000000	0.71417	0.974000	0.42286	0.668000	0.39293	3.418000	0.52721	0.755000	0.32990	0.655000	0.94253	CGG	.	.	none		0.488	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1			A	55961059	G	A	55961059	3	1	45	1	0	0	0	0	1	0	0	0	8148	1144	40	1	1229	1	KDR	4	55961059	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	51638504	55961059	135193217	31	15483											
GC	2638	hgsc.bcm.edu	37	chr4	72620785	72620785	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agtaccttactgaggaatacTtccggaagatgagtccttct	11	12	9	9	1	1	3	0	2	1	1	3	5	3	5	3	2	3	1	3	2	5	5			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr4:72620785T>G	ENST00000273951.8	-	9	1417	c.1074A>C	c.(1072-1074)gaA>gaC	p.E358D	GC_ENST00000513476.1_Missense_Mutation_p.E358D|GC_ENST00000503472.1_5'UTR|GC_ENST00000504199.1_Missense_Mutation_p.E377D	NM_000583.3|NM_001204306.1	NP_000574.2|NP_001191235.1	P02774	VTDB_HUMAN	group-specific component (vitamin D binding protein)	358	Albumin 2. {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)	TGAGGAATACTTCCGGAAGAT	0.348																																					p.E377D		Atlas-SNP	.											.	GC	132	.	0			c.A1131C						PASS	.						123	115	118					4																	72620785		2203	4300	6503	SO:0001583	missense	2638	exon10			GAATACTTCCGGA	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.1074A>C	4.37:g.72620785T>G	ENSP00000273951:p.Glu358Asp	314	0	0		279	93	0.333333	NM_001204307	B4DPP2|D6RAK8|Q16309|Q16310|Q53F31|Q6GTG1	Missense_Mutation	SNP	ENST00000273951.8	37	CCDS3550.1	.	.	.	.	.	.	.	.	.	.	T	9.556	1.117265	0.20795	.	.	ENSG00000145321	ENST00000273951;ENST00000504199;ENST00000513476	T;T;T	0.73152	-0.72;-0.72;-0.72	4.81	3.65	0.41850	.	0.246243	0.36066	N	0.002815	T	0.64659	0.2618	L	0.61036	1.89	0.31742	N	0.635658	P;P	0.40476	0.718;0.513	B;B	0.42771	0.255;0.397	T	0.63994	-0.6511	10	0.20519	T	0.43	.	5.9139	0.19043	0.0:0.13:0.0:0.87	.	377;358	D6RAK8;D6RF35	.;.	D	358;377;358	ENSP00000273951:E358D;ENSP00000421725:E377D;ENSP00000426683:E358D	ENSP00000273951:E358D	E	-	3	2	GC	72839649	1.000000	0.71417	1.000000	0.80357	0.357000	0.29423	0.421000	0.21280	0.953000	0.37825	0.459000	0.35465	GAA	.	.	none		0.348	GC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252167.2			G	72620785	T	G	72620785	3	3	45	1	0	0	0	0	1	0	0	0	6290	1606	56	5	366	5	GC	4	72620785	Missense_Mutation	SNP	T	TCGA-RQ-A68N-01A-11D-A31X-10	16659726	72620785	118533491	32	15484											
FAT4	79633	hgsc.bcm.edu	37	chr4	126329648	126329648	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatgatgactctggtgtgaaTggagaaattacatatattgt	13	14	11	3	0	1	4	0	3	1	1	1	6	1	4	0	2	1	0	0	2	5	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr4:126329648T>A	ENST00000394329.3	+	4	5632	c.5619T>A	c.(5617-5619)aaT>aaA	p.N1873K	FAT4_ENST00000335110.5_Missense_Mutation_p.N171K	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	1873	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)			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						CTGGTGTGAATGGAGAAATTA	0.323																																					p.N1873K		Atlas-SNP	.											.	FAT4	1752	.	0			c.T5619A						PASS	.						114	117	116					4																	126329648		2203	4300	6503	SO:0001583	missense	79633	exon4			TGTGAATGGAGAA	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.5619T>A	4.37:g.126329648T>A	ENSP00000377862:p.Asn1873Lys	143	0	0		118	14	0.118644	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	T	18.43	3.621835	0.66787	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.59906	0.23;0.23	5.03	2.62	0.31277	Cadherin (4);Cadherin-like (1);	0.000000	0.36519	U	0.002554	T	0.79828	0.4513	H	0.95187	3.635	0.58432	D	0.999995	D;D	0.76494	0.995;0.999	D;D	0.80764	0.98;0.994	T	0.81389	-0.0955	10	0.72032	D	0.01	.	8.8314	0.35087	0.0:0.1539:0.0:0.8461	.	171;1873	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	K	1873;171	ENSP00000377862:N1873K;ENSP00000335169:N171K	ENSP00000335169:N171K	N	+	3	2	FAT4	126549098	0.989000	0.36119	1.000000	0.80357	0.969000	0.65631	0.128000	0.15810	0.761000	0.33130	0.482000	0.46254	AAT	.	.	none		0.323	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126329648	T	A	126329648	3	1	45	1	0	0	0	0	1	0	0	0	5700	1461	51	5	5633	5	FAT4	4	126329648	Missense_Mutation	SNP	T	TCGA-RQ-A68N-01A-11D-A31X-10	53708863	126329648	64824628	33	15485											
FAT4	79633	hgsc.bcm.edu	37	chr4	126384754	126384754	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttcagtcaattactgtgaatGcaacccctgctttaatggtg	10	14	8	9	0	2	1	2	1	0	0	2	1	2	1	2	1	4	2	2	1	5	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr4:126384754G>A	ENST00000394329.3	+	10	11844	c.11831G>A	c.(11830-11832)tGc>tAc	p.C3944Y	FAT4_ENST00000335110.5_Intron	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	3944	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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						TACTGTGAATGCAACCCCTGC	0.308																																					p.C3944Y		Atlas-SNP	.											.	FAT4	1752	.	0			c.G11831A						PASS	.						142	121	127					4																	126384754		1568	3582	5150	SO:0001583	missense	79633	exon10			GTGAATGCAACCC	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.11831G>A	4.37:g.126384754G>A	ENSP00000377862:p.Cys3944Tyr	243	0	0		189	57	0.301587	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	20.1	3.933600	0.73442	.	.	ENSG00000196159	ENST00000394329	T	0.74002	-0.8	5.34	5.34	0.76211	Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.37857	U	0.001912	T	0.71617	0.3361	N	0.04746	-0.17	0.80722	D	1	D;D	0.67145	0.996;0.987	P;P	0.59703	0.862;0.773	T	0.78708	-0.2099	10	0.56958	D	0.05	.	19.0682	0.93122	0.0:0.0:1.0:0.0	.	3944;3944	Q6V0I7;Q6V0I7-3	FAT4_HUMAN;.	Y	3944	ENSP00000377862:C3944Y	ENSP00000377862:C3944Y	C	+	2	0	FAT4	126604204	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.460000	0.80816	2.489000	0.83994	0.650000	0.86243	TGC	.	.	none		0.308	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582		A	126384754	G	A	126384754	3	1	45	1	0	0	0	0	1	0	0	0	5700	1319	46	2	11869	2	FAT4	4	126384754	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	55106	126384754	64769522	34	15486											
FHDC1	85462	hgsc.bcm.edu	37	chr4	153875426	153875426	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaagtgagcattatggatcAgagaccttgcgagaatttct	14	11	10	6	1	2	3	1	1	1	2	2	6	2	4	1	1	2	1	1	1	4	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr4:153875426A>G	ENST00000511601.1	+	4	806	c.618A>G	c.(616-618)tcA>tcG	p.S206S	FHDC1_ENST00000260008.3_Silent_p.S206S			Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	206	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)					ATTATGGATCAGAGACCTTGC	0.383																																					p.S206S		Atlas-SNP	.											.	FHDC1	102	.	0			c.A618G						PASS	.						113	117	116					4																	153875426		2203	4300	6503	SO:0001819	synonymous_variant	85462	exon3			TGGATCAGAGACC	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.618A>G	4.37:g.153875426A>G		105	0	0		93	18	0.193548	NM_033393		Silent	SNP	ENST00000511601.1	37	CCDS34081.1																																																																																			.	.	none		0.383	FHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364981.2	NM_033393		G	153875426	A	G	153875426	2	3	45	1	0	0	0	0	0	0	0	1	5884	175	7	3		3	FHDC1	4	153875426	Silent	SNP	A	TCGA-RQ-A68N-01A-11D-A31X-10	27490672	153875426	37278850	35	15487											
IRF2	3660	hgsc.bcm.edu	37	chr4	185309962	185309962	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atccgatgttttcttgatgaCgctggcccgggtctcccggt	4	13	12	12	4	2	2	0	2	2	0	4	3	3	2	3	3	0	2	3	3	0	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr4:185309962C>T	ENST00000393593.3	-	9	1207	c.1000G>A	c.(1000-1002)Gtc>Atc	p.V334I		NM_002199.3	NP_002190.2	P14316	IRF2_HUMAN	interferon regulatory factor 2	334					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)		TTCTTGATGACGCTGGCCCGG	0.572																																					p.V334I		Atlas-SNP	.											IRF2,caecum,carcinoma,0,1	IRF2	53	1	0			c.G1000A						PASS	.						65	76	72					4																	185309962		2203	4300	6503	SO:0001583	missense	3660	exon9			TGATGACGCTGGC		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.1000G>A	4.37:g.185309962C>T	ENSP00000377218:p.Val334Ile	64	0	0		70	19	0.271429	NM_002199	D6RCK5|H0Y8S3|Q6IAS7|Q96B99	Missense_Mutation	SNP	ENST00000393593.3	37	CCDS3835.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.664083	0.88251	.	.	ENSG00000168310	ENST00000393593	D	0.98822	-5.16	5.08	5.08	0.68730	.	0.615176	0.15998	N	0.234496	D	0.98937	0.9639	L	0.61218	1.895	0.54753	D	0.999988	D	0.89917	1.0	D	0.79108	0.992	D	0.99911	1.1201	10	0.87932	D	0	-14.8728	18.6427	0.91400	0.0:1.0:0.0:0.0	.	334	P14316	IRF2_HUMAN	I	334	ENSP00000377218:V334I	ENSP00000377218:V334I	V	-	1	0	IRF2	185546956	1.000000	0.71417	0.989000	0.46669	0.979000	0.70002	5.799000	0.69101	2.646000	0.89796	0.561000	0.74099	GTC	.	.	none		0.572	IRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361393.1			T	185309962	C	T	185309962	3	4	45	1	0	0	0	0	1	0	0	0	7837	536	19	1	53	1	IRF2	4	185309962	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	31434536	185309962	5844314	36	15488											
FAT1	2195	hgsc.bcm.edu	37	chr4	187530476	187530476	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cggcatcatcggccataaccTagaacacaccacactcctgt	12	7	6	16	2	1	1	1	0	0	1	3	1	2	1	4	2	2	1	4	2	3	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr4:187530476T>C	ENST00000441802.2	-	16	10278		c.e16-2			NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1						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						GGCCATAACCTAGAACACACC	0.433										HNSCC(5;0.00058)																											.	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.10069-2A>G						PASS	.						92	85	87					4																	187530476		1938	4155	6093	SO:0001630	splice_region_variant	2195	exon17			ATAACCTAGAACA	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.10069-2A>G	4.37:g.187530476T>C		93	0	0		106	37	0.349057	NM_005245		Splice_Site	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	T	12.67	2.008466	0.35415	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	.	.	.	5.35	5.35	0.76521	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3319	0.74219	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	FAT1	187767470	1.000000	0.71417	0.998000	0.56505	0.160000	0.22226	7.977000	0.88081	2.030000	0.59900	0.533000	0.62120	.	.	.	none		0.433	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	Intron	C	187530476	T	C	187530476	5	2	45	1	0	0	0	0	0	0	1	0	5697	1536	53	3	3747	3	FAT1	4	187530476	Splice_Site	SNP	T	TCGA-RQ-A68N-01A-11D-A31X-10	2220514	187530476	3623800	37	15489											
FAT1	2195	hgsc.bcm.edu	37	chr4	187539926	187539926	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttagcagcactggacccgAtattcacttcgtatttggtt	8	15	8	10	2	1	0	1	0	0	0	2	2	1	1	1	2	2	4	1	2	3	8			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr4:187539926A>T	ENST00000441802.2	-	10	8023	c.7814T>A	c.(7813-7815)aTc>aAc	p.I2605N		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2605	Cadherin 24. {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						ACTGGACCCGATATTCACTTC	0.468										HNSCC(5;0.00058)																											p.I2605N	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T7814A						PASS	.						56	55	56					4																	187539926		1986	4156	6142	SO:0001583	missense	2195	exon10			GACCCGATATTCA	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.7814T>A	4.37:g.187539926A>T	ENSP00000406229:p.Ile2605Asn	117	0	0		101	26	0.257426	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	A	14.05	2.420334	0.42918	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.01854	4.6	5.1	5.1	0.69264	Cadherin (3);Cadherin-like (1);	0.158326	0.56097	D	0.000030	T	0.19327	0.0464	H	0.95539	3.685	0.58432	D	0.999999	D	0.64830	0.994	D	0.66716	0.946	T	0.09465	-1.0673	10	0.87932	D	0	.	15.3444	0.74324	1.0:0.0:0.0:0.0	.	2605	Q14517	FAT1_HUMAN	N	2605;2607	ENSP00000406229:I2605N	ENSP00000260147:I2607N	I	-	2	0	FAT1	187776920	1.000000	0.71417	0.445000	0.26908	0.015000	0.08874	9.139000	0.94554	2.263000	0.75096	0.533000	0.62120	ATC	.	.	none		0.468	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245		T	187539926	A	T	187539926	3	4	45	1	0	0	0	0	1	0	0	0	5697	333	12	5	6024	5	FAT1	4	187539926	Missense_Mutation	SNP	A	TCGA-RQ-A68N-01A-11D-A31X-10	9450	187539926	3614350	38	15490											
MTRR	4552	hgsc.bcm.edu	37	chr5	7875473	7875473	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttctatgacactggacatgCagatgactgtgtagggtaag	11	12	12	6	0	1	3	0	2	1	1	1	4	1	4	0	2	1	3	0	2	3	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr5:7875473C>T	ENST00000264668.2	+	4	497	c.467C>T	c.(466-468)gCa>gTa	p.A156V	MTRR_ENST00000341013.6_3'UTR|MTRR_ENST00000440940.2_Missense_Mutation_p.A129V|MTRR_ENST00000502509.1_3'UTR	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	156	Flavodoxin-like. {ECO:0000255|PROSITE- ProRule:PRU00088}.		A -> T (in HMAE). {ECO:0000269|PubMed:10484769}.		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)	ACTGGACATGCAGATGACTGT	0.423																																					p.A156V		Atlas-SNP	.											.	MTRR	74	.	0			c.C467T						PASS	.						138	146	143					5																	7875473		2203	4300	6503	SO:0001583	missense	4552	exon4			GACATGCAGATGA	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.467C>T	5.37:g.7875473C>T	ENSP00000264668:p.Ala156Val	142	0	0		105	35	0.333333	NM_024010	O60471|Q32MA9|Q7Z4M8	Missense_Mutation	SNP	ENST00000264668.2	37	CCDS3874.1	.	.	.	.	.	.	.	.	.	.	C	32	5.174970	0.94807	.	.	ENSG00000124275	ENST00000264668;ENST00000440940;ENST00000502550	T;T;T	0.71817	-0.6;-0.6;-0.6	5.37	5.37	0.77165	Flavodoxin/nitric oxide synthase (2);	0.051018	0.85682	N	0.000000	T	0.81987	0.4939	L	0.55213	1.73	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80872	-0.1188	10	0.45353	T	0.12	-31.5321	19.4731	0.94971	0.0:1.0:0.0:0.0	.	156	Q9UBK8	MTRR_HUMAN	V	156;129;129	ENSP00000264668:A156V;ENSP00000402510:A129V;ENSP00000424599:A129V	ENSP00000264668:A156V	A	+	2	0	MTRR	7928473	1.000000	0.71417	0.592000	0.28758	0.990000	0.78478	6.576000	0.74023	2.659000	0.90383	0.655000	0.94253	GCA	.	.	none		0.423	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1			T	7875473	C	T	7875473	3	4	45	1	0	0	0	0	1	0	0	0	9970	710	25	2	481	2	MTRR	5	7875473	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10		7875473	173039787	39	15491											
MARCH11	441061	hgsc.bcm.edu	37	chr5	16091041	16091041	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	ccatacattccatagcagatCtgaaaaaggatgtccttcct	13	11	6	11	0	1	2	0	1	1	1	4	3	4	3	4	1	2	1	4	1	4	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr5:16091041C>T	ENST00000332432.8	-	3	1042	c.843G>A	c.(841-843)caG>caA	p.Q281Q	MARCH11_ENST00000505509.1_5'UTR	NM_001102562.1	NP_001096032.1	A6NNE9	MARHB_HUMAN	membrane-associated ring finger (C3HC4) 11	281					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						CATAGCAGATCTGAAAAAGGA	0.448																																					p.Q281Q		Atlas-SNP	.											.	MARCH11	50	.	0			c.G843A						PASS	.						99	97	98					5																	16091041		2004	4181	6185	SO:0001819	synonymous_variant	441061	exon3			GCAGATCTGAAAA	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.843G>A	5.37:g.16091041C>T		106	0	0		95	10	0.105263	NM_001102562	A7E2S6	Silent	SNP	ENST00000332432.8	37	CCDS47192.1																																																																																			.	.	none		0.448	MARCH11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000366096.2	NM_001102562		T	16091041	C	T	16091041	2	4	45	1	0	0	0	0	0	0	0	1	9309	912	32	2		2	MARCH11	5	16091041	Silent	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	8215568	16091041	164824219	40	15492											
PRDM9	56979	hgsc.bcm.edu	37	chr5	23523413	23523413	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aactcagatcaccaaggggaGaaactgctatgagtatgtgg	14	8	12	7	0	2	3	2	1	0	2	2	4	2	3	1	3	3	2	1	3	5	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr5:23523413G>T	ENST00000296682.3	+	9	1078	c.896G>T	c.(895-897)aGa>aTa	p.R299I		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	299	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				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						ACCAAGGGGAGAAACTGCTAT	0.433										HNSCC(3;0.000094)																											p.R299I		Atlas-SNP	.											.	PRDM9	344	.	0			c.G896T						PASS	.						129	125	126					5																	23523413		2203	4300	6503	SO:0001583	missense	56979	exon9			AGGGGAGAAACTG	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.896G>T	5.37:g.23523413G>T	ENSP00000296682:p.Arg299Ile	127	0	0		140	45	0.321429	NM_020227	B4DX22|Q27Q50	Missense_Mutation	SNP	ENST00000296682.3	37	CCDS43307.1	.	.	.	.	.	.	.	.	.	.	g	15.01	2.707568	0.48412	.	.	ENSG00000164256	ENST00000296682;ENST00000253473	T	0.38722	1.12	3.72	2.82	0.32997	SET domain (2);	0.189395	0.26045	N	0.026680	T	0.41558	0.1164	L	0.51853	1.615	0.45227	D	0.998238	D	0.61080	0.989	P	0.50708	0.648	T	0.37820	-0.9689	10	0.72032	D	0.01	-20.6175	6.2592	0.20891	0.1394:0.0:0.8606:0.0	.	299	Q9NQV7	PRDM9_HUMAN	I	299;93	ENSP00000296682:R299I	ENSP00000253473:R93I	R	+	2	0	PRDM9	23559170	0.996000	0.38824	1.000000	0.80357	0.992000	0.81027	2.460000	0.45031	2.009000	0.58944	0.592000	0.82586	AGA	.	.	none		0.433	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227		T	23523413	G	T	23523413	3	4	45	1	0	0	0	0	1	0	0	0	12475	942	33	4	926	4	PRDM9	5	23523413	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	7432372	23523413	157391847	41	15493											
C7	730	hgsc.bcm.edu	37	chr5	40936442	40936442	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gatttctctggtgttcaggtCagtgcatcagcaaatcattg	9	14	10	8	0	5	0	4	0	1	0	6	1	5	0	0	2	2	3	0	2	1	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr5:40936442C>T	ENST00000313164.9	+	5	642	c.283C>T	c.(283-285)Cag>Tag	p.Q95*		NM_000587.2	NP_000578.2	P10643	CO7_HUMAN	complement component 7	95	LDL-receptor class A. {ECO:0000255|PROSITE-ProRule:PRU00124}.				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)				GTGTTCAGGTCAGTGCATCAG	0.463																																					p.Q95X		Atlas-SNP	.											.	C7	136	.	0			c.C283T						PASS	.						104	101	102					5																	40936442		1993	4174	6167	SO:0001587	stop_gained	730	exon5			TCAGGTCAGTGCA	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.283C>T	5.37:g.40936442C>T	ENSP00000322061:p.Gln95*	130	0	0		124	34	0.274194	NM_000587	Q6P3T5|Q92489	Nonsense_Mutation	SNP	ENST00000313164.9	37	CCDS47201.1	.	.	.	.	.	.	.	.	.	.	C	37	6.596583	0.97692	.	.	ENSG00000112936	ENST00000313164;ENST00000440677;ENST00000515157	.	.	.	5.02	5.02	0.67125	.	0.058459	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	-15.7368	18.483	0.90819	0.0:1.0:0.0:0.0	.	.	.	.	X	95	.	ENSP00000322061:Q95X	Q	+	1	0	C7	40972199	1.000000	0.71417	1.000000	0.80357	0.124000	0.20399	5.560000	0.67332	2.779000	0.95612	0.491000	0.48974	CAG	.	.	none		0.463	C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317680.1			T	40936442	C	T	40936442	4	4	45	1	0	0	0	0	0	1	0	0	2377	827	29	2	301	2	C7	5	40936442	Nonsense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	17413029	40936442	139978818	42	15494											
MSH3	4437	hgsc.bcm.edu	37	chr5	79950750	79950750	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgcccccagcgcccccagcTcccgccttcccgccccagct	3	4	8	26	4	0	0	0	0	0	0	2	0	2	0	9	0	3	2	9	0	0	1	rs144629981|rs3045983|rs1047489	byFrequency	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr5:79950750T>G	ENST00000265081.6	+	1	284	c.204T>G	c.(202-204)gcT>gcG	p.A68A	DHFR_ENST00000511032.1_5'Flank|DHFR_ENST00000513048.1_5'Flank|DHFR_ENST00000505337.1_5'Flank|DHFR_ENST00000439211.2_5'UTR|DHFR_ENST00000504396.1_5'Flank	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	68					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)		CGCCCCCAGCTCCCGCCTTCC	0.741								Mismatch excision repair (MMR)																													p.A68A	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											.	MSH3	129	.	0			c.T204G						PASS	.						3	3	3					5																	79950750		1568	3264	4832	SO:0001819	synonymous_variant	4437	exon1			CCCAGCTCCCGCC	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.204T>G	5.37:g.79950750T>G		2	0	0		18	15	0.833333	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Silent	SNP	ENST00000265081.6	37	CCDS34195.1																																																																																			.	.	weak		0.741	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		G	79950750	T	G	79950750	2	3	45	1	0	0	0	0	0	0	0	1	9880	1538	54	5		5	MSH3	5	79950750	Silent	SNP	T	TCGA-RQ-A68N-01A-11D-A31X-10	39014308	79950750	100964510	43	15495											
CAST	831	hgsc.bcm.edu	37	chr5	96073629	96073629	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aactgaagaagaaaatacaaCgtatactggaccagaagttt	19	8	8	6	1	0	4	0	1	0	3	0	5	0	5	1	1	4	2	1	1	10	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr5:96073629C>T	ENST00000341926.3	+	9	689	c.527C>T	c.(526-528)aCg>aTg	p.T176M	CAST_ENST00000325674.7_Missense_Mutation_p.T237M|CAST_ENST00000395812.2_Missense_Mutation_p.T218M|CAST_ENST00000511049.1_Missense_Mutation_p.T162M|CAST_ENST00000348386.3_3'UTR|CAST_ENST00000309190.5_Missense_Mutation_p.T154M|CAST_ENST00000510756.1_Missense_Mutation_p.T237M|CAST_ENST00000508608.1_Missense_Mutation_p.T222M|CAST_ENST00000338252.3_Missense_Mutation_p.T176M|CAST_ENST00000511782.1_Missense_Mutation_p.T162M|CAST_ENST00000504465.1_Missense_Mutation_p.T104M|CAST_ENST00000508830.1_Missense_Mutation_p.T259M|CAST_ENST00000359176.4_Missense_Mutation_p.T240M|CAST_ENST00000509903.1_Missense_Mutation_p.T154M|CAST_ENST00000395813.1_Missense_Mutation_p.T259M			P20810	ICAL_HUMAN	calpastatin	176					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)	p.T154M(1)		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)		GAAAATACAACGTATACTGGA	0.373																																					p.T218M		Atlas-SNP	.											CAST,NS,carcinoma,0,2	CAST	58	2	1	Substitution - Missense(1)	endometrium(1)	c.C653T						PASS	.						119	126	123					5																	96073629		2203	4300	6503	SO:0001583	missense	831	exon9			ATACAACGTATAC	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.527C>T	5.37:g.96073629C>T	ENSP00000339914:p.Thr176Met	50	0	0		61	17	0.278689	NM_001042440	B7Z468|G5E946|G5E9D3|O95360|Q05DE8|Q7Z4K0|Q96D08|Q9H1Z5	Missense_Mutation	SNP	ENST00000341926.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.531|9.531	1.110739|1.110739	0.20714|0.20714	.|.	.|.	ENSG00000153113|ENSG00000153113	ENST00000512620|ENST00000505143;ENST00000338252;ENST00000508830;ENST00000511097;ENST00000395813;ENST00000359176;ENST00000325674;ENST00000395812;ENST00000421689;ENST00000510756;ENST00000508608;ENST00000341926;ENST00000511049;ENST00000309190;ENST00000510156;ENST00000504465;ENST00000509903;ENST00000511782;ENST00000508197	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.17370	.|2.28;2.28;2.28;2.28;2.28;2.28;2.28;2.28;2.28;2.28;2.28;2.28;2.28;2.28;2.28;2.28;2.28;2.28;2.28	5.4|5.4	2.27|2.27	0.28462|0.28462	.|.	.|1.563230	.|0.03377	.|N	.|0.199788	T|T	0.28034|0.28034	0.0691|0.0691	L|L	0.44542|0.44542	1.39|1.39	0.09310|0.09310	N|N	1|1	.|D;P;B;D;P;D;D;D;D;D;D;D;D;D	.|0.64830	.|0.988;0.905;0.04;0.994;0.942;0.99;0.988;0.971;0.988;0.989;0.994;0.985;0.98;0.982	.|P;P;B;P;P;P;P;P;P;P;P;P;P;P	.|0.58013	.|0.727;0.607;0.017;0.787;0.714;0.686;0.682;0.714;0.76;0.747;0.831;0.599;0.747;0.686	T|T	0.07233|0.07233	-1.0783|-1.0783	5|10	.|0.46703	.|T	.|0.11	1.6995|1.6995	4.6011|4.6011	0.12354|0.12354	0.1838:0.5991:0.1273:0.0898|0.1838:0.5991:0.1273:0.0898	.|.	.|104;24;154;222;154;154;135;176;237;218;240;237;259;176	.|E9PDE4;B7Z8S8;B7Z5T6;B7Z468;E9PCH5;G5E946;P20810-4;P20810;P20810-5;G5E9D3;P20810-7;E7ESM9;P20810-6;P20810-2	.|.;.;.;.;.;.;.;ICAL_HUMAN;.;.;.;.;.;.	C|M	193|254;176;259;237;259;240;237;218;240;237;222;176;162;154;176;104;154;162;127	.|ENSP00000422957:T254M;ENSP00000343421:T176M;ENSP00000425721:T259M;ENSP00000422951:T237M;ENSP00000379158:T259M;ENSP00000352098:T240M;ENSP00000320319:T237M;ENSP00000379157:T218M;ENSP00000396558:T240M;ENSP00000422176:T237M;ENSP00000422677:T222M;ENSP00000339914:T176M;ENSP00000421130:T162M;ENSP00000312523:T154M;ENSP00000422325:T176M;ENSP00000425670:T104M;ENSP00000426946:T154M;ENSP00000423638:T162M;ENSP00000422831:T127M	.|ENSP00000312523:T154M	R|T	+|+	1|2	0|0	CAST|CAST	96099385|96099385	0.000000|0.000000	0.05858|0.05858	0.037000|0.037000	0.18230|0.18230	0.049000|0.049000	0.14656|0.14656	-1.415000|-1.415000	0.02469|0.02469	0.641000|0.641000	0.30601|0.30601	0.655000|0.655000	0.94253|0.94253	CGT|ACG	.	.	none		0.373	CAST-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000250199.2	NM_173062		T	96073629	C	T	96073629	3	4	45	1	0	0	0	0	1	0	0	0	2686	536	19	1	818	1	CAST	5	96073629	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	16122879	96073629	84841631	44	15496											
PCDHAC2	56134	hgsc.bcm.edu	37	chr5	140346765	140346765	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agcgccgttgaggtggaaatAttggacatcaacgacaactc	13	8	11	9	3	1	1	1	1	0	0	2	4	1	3	1	3	3	1	1	3	4	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr5:140346765A>T	ENST00000289269.5	+	1	946	c.414A>T	c.(412-414)atA>atT	p.I138I	PCDHA2_ENST00000526136.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA4_ENST00000530339.1_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	138	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(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)			AGGTGGAAATATTGGACATCA	0.612																																					p.I138I	Melanoma(190;638 2083 3390 11909 52360)	Atlas-SNP	.											.	PCDHAC2	142	.	0			c.A414T						PASS	.						39	42	41					5																	140346765		2203	4300	6503	SO:0001819	synonymous_variant	56134	exon1			GGAAATATTGGAC	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.414A>T	5.37:g.140346765A>T		162	0	0		155	47	0.303226	NM_031883	Q2M3V1|Q9Y5F4	Silent	SNP	ENST00000289269.5	37	CCDS4242.1																																																																																			.	.	none		0.612	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899		T	140346765	A	T	140346765	2	4	45	1	0	0	0	0	0	0	0	1	11542	439	16	5		5	PCDHAC2	5	140346765	Silent	SNP	A	TCGA-RQ-A68N-01A-11D-A31X-10	44273136	140346765	40568495	45	15497											
GABRA1	2554	hgsc.bcm.edu	37	chr5	161300240	161300240	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	caagtaaaatctggactccgGacacatttttccacaatgga	14	10	7	10	1	1	0	0	0	1	0	3	3	3	3	2	3	0	1	2	3	4	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr5:161300240G>A	ENST00000428797.2	+	6	728	c.373G>A	c.(373-375)Gac>Aac	p.D125N	GABRA1_ENST00000023897.6_Missense_Mutation_p.D125N|GABRA1_ENST00000437025.2_Missense_Mutation_p.D125N|GABRA1_ENST00000393943.4_Missense_Mutation_p.D125N|GABRA1_ENST00000444819.1_Missense_Mutation_p.D125N|GABRA1_ENST00000420560.1_Missense_Mutation_p.D125N	NM_001127643.1	NP_001121115.1	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 1	125					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)	CTGGACTCCGGACACATTTTT	0.443																																					p.D125N		Atlas-SNP	.											.	GABRA1	132	.	0			c.G373A						PASS	.						74	71	72					5																	161300240		2203	4300	6503	SO:0001583	missense	2554	exon6			ACTCCGGACACAT		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.373G>A	5.37:g.161300240G>A	ENSP00000393097:p.Asp125Asn	163	0	0		139	25	0.179856	NM_001127643	D3DQK6|Q8N629	Missense_Mutation	SNP	ENST00000428797.2	37	CCDS4357.1	.	.	.	.	.	.	.	.	.	.	G	36	5.667549	0.96745	.	.	ENSG00000022355	ENST00000023897;ENST00000428797;ENST00000393943;ENST00000437025;ENST00000420560;ENST00000444819	D;D;D;D;D;D	0.84370	-1.84;-1.84;-1.84;-1.84;-1.84;-1.84	5.85	5.85	0.93711	Neurotransmitter-gated ion-channel ligand-binding (3);	0.107767	0.64402	D	0.000006	D	0.94735	0.8301	M	0.93939	3.475	0.80722	D	1	D	0.76494	0.999	D	0.72625	0.978	D	0.95296	0.8399	10	0.87932	D	0	.	20.1663	0.98152	0.0:0.0:1.0:0.0	.	125	P14867	GBRA1_HUMAN	N	125	ENSP00000023897:D125N;ENSP00000393097:D125N;ENSP00000377517:D125N;ENSP00000415441:D125N;ENSP00000408041:D125N;ENSP00000414232:D125N	ENSP00000023897:D125N	D	+	1	0	GABRA1	161232818	1.000000	0.71417	0.947000	0.38551	0.873000	0.50193	9.751000	0.98889	2.773000	0.95371	0.585000	0.79938	GAC	.	.	none		0.443	GABRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252702.2	NM_000806.5		A	161300240	G	A	161300240	3	1	45	1	0	0	0	0	1	0	0	0	6168	1174	41	2	387	2	GABRA1	5	161300240	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	20953475	161300240	19615020	46	15498											
GABRP	2568	hgsc.bcm.edu	37	chr5	170235620	170235620	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcaggaaattacactagattGgtcttacagtttgagcttcg	11	14	9	7	1	2	2	1	1	1	1	3	3	2	3	0	2	3	2	0	2	4	6			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr5:170235620G>A	ENST00000518525.1	+	9	1160	c.696G>A	c.(694-696)ttG>ttA	p.L232L	GABRP_ENST00000519385.1_Silent_p.L232L|GABRP_ENST00000265294.4_Silent_p.L232L|GABRP_ENST00000519598.1_Silent_p.L232L			O00591	GBRP_HUMAN	gamma-aminobutyric acid (GABA) A receptor, pi	232					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)	ACACTAGATTGGTCTTACAGT	0.398																																					p.L232L		Atlas-SNP	.											.	GABRP	65	.	0			c.G696A						PASS	.						184	164	170					5																	170235620		2203	4300	6503	SO:0001819	synonymous_variant	2568	exon8			TAGATTGGTCTTA	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.696G>A	5.37:g.170235620G>A		101	0	0		87	13	0.149425	NM_014211	A8KA36|D3DQL2|Q32MJ1	Silent	SNP	ENST00000518525.1	37	CCDS4375.1																																																																																			.	.	none		0.398	GABRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252834.3	NM_014211		A	170235620	G	A	170235620	2	1	45	1	0	0	0	0	0	0	0	1	6182	1339	47	2		2	GABRP	5	170235620	Silent	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	8935380	170235620	10679640	47	15499											
IRF4	3662	hgsc.bcm.edu	37	chr6	393159	393159	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acggcacgcggggcatgaacCtggagggcggcggccgaggc	7	2	20	12	6	0	1	0	1	0	0	0	3	0	2	2	8	1	2	2	8	1	0			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr6:393159C>G	ENST00000380956.4	+	2	133	c.7C>G	c.(7-9)Ctg>Gtg	p.L3V	IRF4_ENST00000495137.1_Intron	NM_001195286.1|NM_002460.3	NP_001182215.1|NP_002451.2	Q15306	IRF4_HUMAN	interferon regulatory factor 4	3					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)		GGGCATGAACCTGGAGGGCGG	0.721			T	IGH@	MM																																p.L3V		Atlas-SNP	.		Dom	yes		6	6p25-p23	3662	interferon regulatory factor 4		L	.	IRF4	65	.	0			c.C7G						PASS	.						13	17	16					6																	393159		2057	4045	6102	SO:0001583	missense	3662	exon2			ATGAACCTGGAGG	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.7C>G	6.37:g.393159C>G	ENSP00000370343:p.Leu3Val	62	0	0		74	17	0.22973	NM_001195286	Q5VUI7|Q99660	Missense_Mutation	SNP	ENST00000380956.4	37	CCDS4469.1	.	.	.	.	.	.	.	.	.	.	C	15.67	2.903550	0.52333	.	.	ENSG00000137265	ENST00000380956;ENST00000412334	D	0.97430	-4.38	5.0	-4.42	0.03579	.	2.154200	0.02356	N	0.076424	D	0.90212	0.6940	L	0.36672	1.1	0.42989	D	0.994487	P;P;P	0.40731	0.608;0.728;0.608	B;B;B	0.38500	0.142;0.275;0.142	T	0.81324	-0.0984	10	0.51188	T	0.08	-13.6896	8.239	0.31650	0.0:0.1841:0.1273:0.6886	.	3;3;3	F2Z3D5;Q15306-2;Q15306	.;.;IRF4_HUMAN	V	3;33	ENSP00000370343:L3V	ENSP00000370343:L3V	L	+	1	2	IRF4	338159	0.419000	0.25449	0.985000	0.45067	0.673000	0.39480	-0.471000	0.06631	-0.533000	0.06323	-0.683000	0.03753	CTG	.	.	none		0.721	IRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043638.1			G	393159	C	G	393159	3	3	45	1	0	0	0	0	1	0	0	0	7841	680	24	4	9	4	IRF4	6	393159	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10		393159	170721908	48	15500											
SSR1	6745	hgsc.bcm.edu	37	chr6	7295651	7295651	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gattcaatgtttcctgaggaAtccaactcatgtcaacatca	13	12	6	10	0	4	1	4	1	0	0	6	3	6	2	2	1	2	1	2	1	4	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr6:7295651A>G	ENST00000244763.4	-	7	853	c.767T>C	c.(766-768)aTt>aCt	p.I256T	RP11-69L16.4_ENST00000379928.4_RNA|SSR1_ENST00000479365.1_Missense_Mutation_p.I256T|SSR1_ENST00000397511.2_Missense_Mutation_p.I256T|SSR1_ENST00000474597.1_Missense_Mutation_p.I256T|SSR1_ENST00000534851.1_Missense_Mutation_p.I229T|SSR1_ENST00000489567.1_Missense_Mutation_p.I188T	NM_003144.3	NP_003135.2	P43307	SSRA_HUMAN	signal sequence receptor, alpha	256					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)					TTCCTGAGGAATCCAACTCAT	0.333																																					p.I256T		Atlas-SNP	.											.	SSR1	21	.	0			c.T767C						PASS	.						128	115	119					6																	7295651		2202	4300	6502	SO:0001583	missense	6745	exon7			TGAGGAATCCAAC		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.767T>C	6.37:g.7295651A>G	ENSP00000244763:p.Ile256Thr	106	0	0		103	11	0.106796	NM_003144	A8K685|Q53GX2|Q53H19|Q5TAM3|Q6IB43|Q8NBH9|Q96IA2|Q9TNQ8|Q9UN49	Missense_Mutation	SNP	ENST00000244763.4	37	CCDS4499.1	.	.	.	.	.	.	.	.	.	.	A	24.1	4.495748	0.85069	.	.	ENSG00000124783	ENST00000474597;ENST00000244763;ENST00000397511;ENST00000534851;ENST00000489567;ENST00000479365;ENST00000479485	T;T;T;T;T;T;T	0.56103	0.48;0.48;0.48;0.48;0.48;0.48;0.48	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.69369	0.3103	M	0.85945	2.785	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.74674	0.98;0.937;0.984	T	0.76323	-0.3001	10	0.87932	D	0	.	14.6236	0.68605	1.0:0.0:0.0:0.0	.	256;188;256	C9J5W0;C9JBX5;P43307	.;.;SSRA_HUMAN	T	256;256;256;229;188;256;93	ENSP00000418617:I256T;ENSP00000244763:I256T;ENSP00000380647:I256T;ENSP00000443020:I229T;ENSP00000420730:I188T;ENSP00000417911:I256T;ENSP00000419953:I93T	ENSP00000244763:I256T	I	-	2	0	SSR1	7240650	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.747000	0.91610	2.055000	0.61198	0.528000	0.53228	ATT	.	.	none		0.333	SSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039775.2			G	7295651	A	G	7295651	3	3	45	1	0	0	0	0	1	0	0	0	15205	101	4	3	101	3	SSR1	6	7295651	Missense_Mutation	SNP	A	TCGA-RQ-A68N-01A-11D-A31X-10	6902492	7295651	163819416	49	15501											
HIST1H1E	3008	hgsc.bcm.edu	37	chr6	26156757	26156757	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgtccgagctcattactaaaGctgttgccgcctccaaggag	9	10	10	12	2	1	0	1	0	0	0	3	2	3	1	4	1	4	3	4	1	4	3	rs547695315		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr6:26156757G>C	ENST00000304218.3	+	1	199	c.139G>C	c.(139-141)Gct>Cct	p.A47P	HIST1H2BD_ENST00000289316.2_5'Flank|HIST1H2BD_ENST00000377777.4_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	47	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						CATTACTAAAGCTGTTGCCGC	0.617													G|||	1	0.000199681	0.0008	0.0	5008	,	,		14468	0.0		0.0	False		,,,				2504	0.0				p.A47P		Atlas-SNP	.											HIST1H1E,NS,lymphoid_neoplasm,-1,1	HIST1H1E	69	1	0			c.G139C						PASS	.						22	27	25					6																	26156757		2203	4300	6503	SO:0001583	missense	3008	exon1			ACTAAAGCTGTTG	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.139G>C	6.37:g.26156757G>C	ENSP00000307705:p.Ala47Pro	66	0	0		60	8	0.133333	NM_005321	Q4VB25	Missense_Mutation	SNP	ENST00000304218.3	37	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	15.85	2.954554	0.53293	.	.	ENSG00000168298	ENST00000304218	T	0.55760	0.5	5.49	5.49	0.81192	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.170654	0.52532	D	0.000080	D	0.83436	0.5254	H	0.99156	4.45	0.51482	D	0.999923	D	0.76494	0.999	D	0.79784	0.993	D	0.90132	0.4207	10	0.87932	D	0	-2.8941	18.7044	0.91632	0.0:0.0:1.0:0.0	.	47	P10412	H14_HUMAN	P	47	ENSP00000307705:A47P	ENSP00000307705:A47P	A	+	1	0	HIST1H1E	26264736	1.000000	0.71417	0.980000	0.43619	0.175000	0.22909	4.733000	0.62036	2.727000	0.93392	0.655000	0.94253	GCT	.	.	none		0.617	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321		C	26156757	G	C	26156757	3	2	45	1	0	0	0	0	1	0	0	0	7135	971	34	4	141	4	HIST1H1E	6	26156757	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	18861106	26156757	144958310	50	15502			1	73		3	3	221	N	G_C	1.024746e-06
HIST1H1E	3008	hgsc.bcm.edu	37	chr6	26156929	26156929	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	gggcaccggcgcgtcgggttCcttcaaactcaacaagaagg	10	6	13	12	4	2	1	2	0	0	1	4	1	3	1	2	4	2	2	2	4	4	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr6:26156929C>G	ENST00000304218.3	+	1	371	c.311C>G	c.(310-312)tCc>tGc	p.S104C	HIST1H2BD_ENST00000289316.2_5'Flank|HIST1H2BD_ENST00000377777.4_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	104	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						GCGTCGGGTTCCTTCAAACTC	0.602																																					p.S104C		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.C311G						PASS	.						39	45	43					6																	26156929		2203	4300	6503	SO:0001583	missense	3008	exon1			CGGGTTCCTTCAA	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.311C>G	6.37:g.26156929C>G	ENSP00000307705:p.Ser104Cys	157	0	0		127	43	0.338583	NM_005321	Q4VB25	Missense_Mutation	SNP	ENST00000304218.3	37	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	19.18	3.777704	0.70107	.	.	ENSG00000168298	ENST00000304218	T	0.10960	2.82	5.35	5.35	0.76521	Histone H1/H5 (2);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.40522	0.1120	H	0.95850	3.73	0.80722	D	1	D	0.56287	0.975	D	0.64410	0.925	T	0.58725	-0.7586	10	0.87932	D	0	-5.7108	18.4042	0.90528	0.0:1.0:0.0:0.0	.	104	P10412	H14_HUMAN	C	104	ENSP00000307705:S104C	ENSP00000307705:S104C	S	+	2	0	HIST1H1E	26264908	1.000000	0.71417	0.711000	0.30485	0.551000	0.35334	7.751000	0.85126	2.658000	0.90341	0.561000	0.74099	TCC	.	.	none		0.602	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321		G	26156929	C	G	26156929	3	3	45	1	0	0	0	0	1	0	0	0	7135	855	30	4	313	4	HIST1H1E	6	26156929	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	172	26156929	144958138	51	15503			1	73		3	3	221	N	G_C	1.024746e-06
HIST1H1E	3008	hgsc.bcm.edu	37	chr6	26156977	26156977	+	Frame_Shift_Del	DEL	C	C	-																															tggggaagccaagcctaaggCtaaaaaggcaggcgcggcca																										TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr6:26156977delC	ENST00000304218.3	+	1	419	c.359delC	c.(358-360)gctfs	p.A120fs	HIST1H2BD_ENST00000289316.2_5'Flank|HIST1H2BD_ENST00000377777.4_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	120					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						AAGCCTAAGGCTAAAAAGGCA	0.642																																					p.A120fs		Pindel,Atlas-Indel	.											.	HIST1H1E	69	.	0			c.358delG						PASS	.						21	28	26					6																	26156977		2203	4300	6503	SO:0001589	frameshift_variant	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.359delC	6.37:g.26156977delC	ENSP00000307705:p.Ala120fs	0	0	.		11	11	1	NM_005321	Q4VB25	Frame_Shift_Del	DEL	ENST00000304218.3	37	CCDS4586.1																																																																																			.	.	none		0.642	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321		-	26156977	C	-	26156977	7	5	45	1	0	1	0	1	0	0	0	0	7135	797	28	0	361	0	HIST1H1E	6	26156977	Frame_Shift_Del	DEL	C	TCGA-RQ-A68N-01A-11D-A31X-10	48	26156977	144958090	52	15504			1	73		3	3	221	N	G_C	1.024746e-06
HIST1H2AE	3012	hgsc.bcm.edu	37	chr6	26217410	26217410	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttagagctagctggcaacGcggctcgcgacaataagaag	12	7	12	10	4	1	2	0	0	1	2	2	3	1	2	0	2	3	4	0	2	6	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr6:26217410G>A	ENST00000303910.2	+	1	246	c.208G>A	c.(208-210)Gcg>Acg	p.A70T	HIST1H2BG_ENST00000244601.3_5'Flank	NM_021052.2	NP_066390.1	P04908	H2A1B_HUMAN	histone cluster 1, H2ae	70						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)				AGCTGGCAACGCGGCTCGCGA	0.592																																					p.A70T		Atlas-SNP	.											.	HIST1H2AE	25	.	0			c.G208A						PASS	.						60	61	61					6																	26217410		2203	4300	6503	SO:0001583	missense	3012	exon1			GGCAACGCGGCTC	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.208G>A	6.37:g.26217410G>A	ENSP00000303373:p.Ala70Thr	138	0	0		106	13	0.122642	NM_021052	P28001|Q76P63	Missense_Mutation	SNP	ENST00000303910.2	37	CCDS4595.1	.	.	.	.	.	.	.	.	.	.	.	19.05	3.751476	0.69533	.	.	ENSG00000168274	ENST00000303910	T	0.69685	-0.42	4.07	4.07	0.47477	.	0.000000	0.33732	U	0.004605	T	0.80670	0.4667	M	0.89658	3.05	0.52099	D	0.999946	.	.	.	.	.	.	D	0.85308	0.1077	8	0.72032	D	0.01	.	15.7762	0.78220	0.0:0.0:1.0:0.0	.	.	.	.	T	70	ENSP00000303373:A70T	ENSP00000303373:A70T	A	+	1	0	HIST1H2AE	26325389	1.000000	0.71417	1.000000	0.80357	0.577000	0.36160	7.549000	0.82163	2.263000	0.75096	0.650000	0.86243	GCG	.	.	none		0.592	HIST1H2AE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040103.1	NM_021052		A	26217410	G	A	26217410	3	1	45	1	0	0	0	0	1	0	0	0	7141	1087	38	1	210	1	HIST1H2AE	6	26217410	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	60433	26217410	144897657	53	15505											
HIST1H2BM	8342	hgsc.bcm.edu	37	chr6	27782969	27782969	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acaaggtgctgaagcaggtcCaccccgacaccggcatctct	10	6	10	15	2	1	1	0	1	1	0	3	2	2	1	4	3	2	3	4	3	2	0			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr6:27782969C>T	ENST00000359465.4	+	1	148	c.148C>T	c.(148-150)Cac>Tac	p.H50Y	HIST1H2AJ_ENST00000333151.3_5'Flank	NM_003521.2	NP_003512.1	Q99879	H2B1M_HUMAN	histone cluster 1, H2bm	50					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)	p.H50Y(1)		NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)	12						GAAGCAGGTCCACCCCGACAC	0.542																																					p.H50Y		Atlas-SNP	.											HIST1H2BM,NS,malignant_melanoma,0,1	HIST1H2BM	36	1	1	Substitution - Missense(1)	NS(1)	c.C148T						PASS	.						198	187	191					6																	27782969		2203	4300	6503	SO:0001583	missense	8342	exon1			CAGGTCCACCCCG	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.148C>T	6.37:g.27782969C>T	ENSP00000352442:p.His50Tyr	108	0	0		65	17	0.261538	NM_003521	Q6NWQ3	Missense_Mutation	SNP	ENST00000359465.4	37	CCDS4629.1	.	.	.	.	.	.	.	.	.	.	.	5.665	0.307325	0.10733	.	.	ENSG00000196374	ENST00000359465	T	0.23754	1.89	4.29	2.43	0.29744	Histone-fold (2);Histone core (1);	0.000000	0.64402	U	0.000009	T	0.29850	0.0746	M	0.94021	3.485	0.51482	D	0.999929	P	0.36535	0.557	B	0.41917	0.37	T	0.23404	-1.0189	10	0.66056	D	0.02	.	10.2104	0.43136	0.1534:0.6988:0.1478:0.0	.	50	Q99879	H2B1M_HUMAN	Y	50	ENSP00000352442:H50Y	ENSP00000352442:H50Y	H	+	1	0	HIST1H2BM	27890948	1.000000	0.71417	0.954000	0.39281	0.007000	0.05969	5.538000	0.67193	0.512000	0.28257	-0.309000	0.09137	CAC	.	.	none		0.542	HIST1H2BM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040157.1	NM_003521		T	27782969	C	T	27782969	3	4	45	1	0	0	0	0	1	0	0	0	7161	594	21	2	150	2	HIST1H2BM	6	27782969	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	1565559	27782969	143332098	54	15506											
HIST1H4K	8362	hgsc.bcm.edu	37	chr6	27799131	27799131	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gttctccaggaacaccttcaGcaccccgcgagtctcctcgt	7	9	8	17	3	3	0	1	0	2	0	6	2	3	1	5	1	2	2	5	1	1	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr6:27799131G>A	ENST00000357549.2	-	1	174	c.175C>T	c.(175-177)Ctg>Ttg	p.L59L		NM_003541.2	NP_003532.1	P62805	H4_HUMAN	histone cluster 1, H4k	59					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(1)|endometrium(1)|lung(3)|ovary(1)|prostate(1)	7						AACACCTTCAGCACCCCGCGA	0.637																																					p.L59L		Atlas-SNP	.											HIST1H4K,NS,carcinoma,+2,1	HIST1H4K	15	1	0			c.C175T						scavenged	.						10	12	11					6																	27799131		2147	4241	6388	SO:0001819	synonymous_variant	8362	exon1			CCTTCAGCACCCC	X60483	CCDS4631.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197914	ENSG00000273542		"Histones / Replication-dependent"	4784	protein-coding gene	gene with protein product		602825	"H4 histone family, member D", "histone 1, H4k"	H4FD		9439656, 12408966	Standard	NM_003541		Approved	H4/d, H4F2iii, dJ160A22.1	uc003njr.3	P62805	OTTHUMG00000014488	ENST00000357549.2:c.175C>T	6.37:g.27799131G>A		358	0	0		292	23	0.0787671	NM_003541	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Silent	SNP	ENST00000357549.2	37	CCDS4631.1																																																																																			.	.	none		0.637	HIST1H4K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040156.1	NM_003541		A	27799131	G	A	27799131	2	1	45	1	0	0	0	0	0	0	0	1	7184	962	34	2		2	HIST1H4K	6	27799131	Silent	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	16162	27799131	143315936	55	15507											
HIST1H2AM	8336	hgsc.bcm.edu	37	chr6	27860580	27860580	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctctcagtcttcttggggagCagtacggcctggatgttagg	6	12	14	9	1	3	0	1	0	3	0	4	2	3	2	1	5	2	3	1	5	2	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr6:27860580C>T	ENST00000359611.2	-	1	383	c.348G>A	c.(346-348)ctG>ctA	p.L116L	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	116						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						TCTTGGGGAGCAGTACGGCCT	0.502																																					p.L116L		Atlas-SNP	.											.	HIST1H2AM	27	.	0			c.G348A						PASS	.						131	126	128					6																	27860580		2203	4300	6503	SO:0001819	synonymous_variant	8336	exon1			GGGGAGCAGTACG	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.348G>A	6.37:g.27860580C>T		172	0	0		182	25	0.137363	NM_003514	P02261|Q2M1R2|Q76PA6	Silent	SNP	ENST00000359611.2	37	CCDS4639.1																																																																																			.	.	none		0.502	HIST1H2AM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040162.1	NM_003514		T	27860580	C	T	27860580	2	4	45	1	0	0	0	0	0	0	0	1	7148	697	25	2		2	HIST1H2AM	6	27860580	Silent	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	61449	27860580	143254487	56	15508											
OR12D2	26529	hgsc.bcm.edu	37	chr6	29365028	29365028	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gatattaagccattgctaaaGctggcctgtgggaacactga	12	10	11	8	0	0	1	0	1	0	0	0	3	0	2	2	2	4	2	2	2	5	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr6:29365028G>A	ENST00000383555.2	+	1	613	c.552G>A	c.(550-552)aaG>aaA	p.K184K	OR5V1_ENST00000377154.1_Intron	NM_013936.3	NP_039224.2	P58182	O12D2_HUMAN	olfactory receptor, family 12, subfamily D, member 2 (gene/pseudogene)	184						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						CATTGCTAAAGCTGGCCTGTG	0.473																																					p.K184K		Atlas-SNP	.											.	OR12D2	42	.	0			c.G552A						PASS	.						165	168	167					6																	29365028		1511	2709	4220	SO:0001819	synonymous_variant	26529	exon1			GCTAAAGCTGGCC		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.552G>A	6.37:g.29365028G>A		99	0	0		101	17	0.168317	NM_013936	B0S862|Q5SUN9|Q6IET9	Silent	SNP	ENST00000383555.2	37	CCDS4659.1																																																																																			.	.	none		0.473	OR12D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076054.2			A	29365028	G	A	29365028	2	1	45	1	0	0	0	0	0	0	0	1	10940	962	34	2		2	OR12D2	6	29365028	Silent	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	1504448	29365028	141750039	57	15509											
RNF39	80352	hgsc.bcm.edu	37	chr6	30039324	30039324	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggccggccccgaagccctgcGcacccagcacagctgggagc	7	2	14	18	3	0	0	0	0	0	0	0	2	0	1	5	3	5	3	5	3	1	0			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr6:30039324G>A	ENST00000244360.6	-	4	924	c.827C>T	c.(826-828)gCg>gTg	p.A276V	RNF39_ENST00000376751.3_Missense_Mutation_p.A276V	NM_025236.3	NP_079512.2	Q9H2S5	RNF39_HUMAN	ring finger protein 39	276	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)										GAAGCCCTGCGCACCCAGCAC	0.716																																					p.A276V	NSCLC(8;188 360 1520 20207 31481)	Atlas-SNP	.											.	RNF39	27	.	0			c.C827T						PASS	.						3	3	3					6																	30039324		1332	2321	3653	SO:0001583	missense	80352	exon4			CCCTGCGCACCCA	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.827C>T	6.37:g.30039324G>A	ENSP00000244360:p.Ala276Val	12	0	0		16	6	0.375	NM_025236	A2BEK3|A6NCD6|B0S858|Q5SPM8|Q5SPM9|Q5SPN0|Q5SRJ9|Q5SRK1|Q5SS29|Q9H2S3|Q9H2S4	Missense_Mutation	SNP	ENST00000244360.6	37	CCDS4673.1	.	.	.	.	.	.	.	.	.	.	g	24.3	4.518055	0.85495	.	.	ENSG00000204618	ENST00000376751;ENST00000244360	T;T	0.10860	2.83;2.83	4.54	4.54	0.55810	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	0.000000	0.43919	D	0.000520	T	0.15955	0.0384	L	0.47716	1.5	0.41952	D	0.990666	D;D	0.69078	0.996;0.997	P;D	0.63488	0.853;0.915	T	0.00857	-1.1538	10	0.56958	D	0.05	-16.6616	15.217	0.73277	0.0:0.0:1.0:0.0	.	276;276	Q9H2S5;Q9H2S5-2	RNF39_HUMAN;.	V	276	ENSP00000365942:A276V;ENSP00000244360:A276V	ENSP00000244360:A276V	A	-	2	0	RNF39	30147303	0.000000	0.05858	0.882000	0.34594	0.806000	0.45545	0.239000	0.18023	2.252000	0.74401	0.282000	0.19409	GCG	.	.	none		0.716	RNF39-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076625.3	NM_170769		A	30039324	G	A	30039324	3	1	45	1	0	0	0	0	1	0	0	0	13506	1087	38	1	439	1	RNF39	6	30039324	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	674296	30039324	141075743	58	15510											
SPDEF	25803	hgsc.bcm.edu	37	chr6	34511927	34511927	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcaccaagtccaggctgccCgctggggcttggctgtcaat	6	8	14	13	1	1	0	1	0	0	0	2	0	2	0	3	5	1	5	3	5	2	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr6:34511927C>T	ENST00000374037.3	-	2	720	c.306G>A	c.(304-306)gcG>gcA	p.A102A	SPDEF_ENST00000544425.1_Silent_p.A102A	NM_012391.2	NP_036523.1	O95238	SPDEF_HUMAN	SAM pointed domain containing ETS transcription factor	102					cell differentiation (GO:0030154)|intestinal epithelial cell development (GO:0060576)|lung goblet cell differentiation (GO:0060480)|multicellular organismal development (GO:0007275)|negative regulation of cell fate commitment (GO:0010454)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell fate commitment (GO:0010455)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|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)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|skin(3)	15						CCAGGCTGCCCGCTGGGGCTT	0.672																																					p.A102A		Atlas-SNP	.											SPDEF,colon,carcinoma,0,1	SPDEF	34	1	0			c.G306A						PASS	.						36	37	37					6																	34511927		2203	4300	6503	SO:0001819	synonymous_variant	25803	exon2			GCTGCCCGCTGGG	AF071538	CCDS4794.1, CCDS59013.1	6p21.3	2013-08-07	2013-08-07		ENSG00000124664	ENSG00000124664			17257	protein-coding gene	gene with protein product		608144	"SAM pointed domain containing ets transcription factor"			10625666, 6857767	Standard	NM_012391		Approved	PDEF, bA375E1.3	uc003ojq.2	O95238	OTTHUMG00000014548	ENST00000374037.3:c.306G>A	6.37:g.34511927C>T		76	0	0		43	9	0.209302	NM_001252294	B4DWH8|F5H778	Silent	SNP	ENST00000374037.3	37	CCDS4794.1																																																																																			.	.	none		0.672	SPDEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040246.1	NM_012391		T	34511927	C	T	34511927	2	4	45	1	0	0	0	0	0	0	0	1	15041	639	23	1		1	SPDEF	6	34511927	Silent	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	4472603	34511927	136603140	59	15511											
PIM1	5292	hgsc.bcm.edu	37	chr6	37138355	37138355	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acatcctggaggttgggatgCtcttgtccaaaatcaactcg	10	11	10	10	1	2	0	1	0	1	0	5	2	4	2	2	3	2	2	2	3	3	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr6:37138355C>G	ENST00000373509.5	+	1	377	c.4C>G	c.(4-6)Ctc>Gtc	p.L2V		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	93					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)	p.L2V(1)|p.L2F(1)		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)	GGTTGGGATGCTCTTGTCCAA	0.701			T	BCL6	NHL																																p.L93V		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,0,3	PIM1	71	3	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.C277G						scavenged	.						30	30	30					6																	37138355		2201	4298	6499	SO:0001583	missense	5292	exon1			GGGATGCTCTTGT		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.4C>G	6.37:g.37138355C>G	ENSP00000362608:p.Leu2Val	48	0	0		44	7	0.159091	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.688054	0.88639	.	.	ENSG00000137193	ENST00000373509	T	0.70164	-0.46	4.05	4.05	0.47172	.	0.000000	0.32147	N	0.006517	T	0.36468	0.0968	N	0.08118	0	0.45390	D	0.998372	P	0.38020	0.615	B	0.37091	0.241	T	0.55198	-0.8178	10	0.72032	D	0.01	.	16.7252	0.85419	0.0:1.0:0.0:0.0	.	93	P11309	PIM1_HUMAN	V	2	ENSP00000362608:L2V	ENSP00000362608:L2V	L	+	1	0	PIM1	37246333	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.672000	0.61597	2.211000	0.71520	0.542000	0.68232	CTC	.	.	none		0.701	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			G	37138355	C	G	37138355	3	3	45	1	0	0	0	0	1	0	0	0	11936	797	28	4	6	4	PIM1	6	37138355	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	2626428	37138355	133976712	60	15512			2	74	10981378	4	4	599	N	G_C	9.824106e-09
PIM1	5292	hgsc.bcm.edu	37	chr6	37138549	37138549	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	cgtgcttccccctttcctagGcaaggagaaggagcccctgg	7	8	12	14	1	0	1	0	0	0	1	2	3	2	2	5	4	2	2	5	4	3	3	rs377274719		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr6:37138549G>A	ENST00000373509.5	+	2	456	c.83G>A	c.(82-84)gGc>gAc	p.G28D		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	119					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)	CCTTTCCTAGGCAAGGAGAAG	0.721			T	BCL6	NHL																																p.G119D		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,0,3	PIM1	71	3	0			c.G356A						scavenged	.	G	ASP/GLY	1,4257		0,1,2128	18	26	23		83	3.8	1	6		23	0,8506		0,0,4253	no	missense-near-splice	PIM1	NM_002648.3	94	0,1,6381	AA,AG,GG		0.0,0.0235,0.0078	probably-damaging	28/314	37138549	1,12763	2129	4253	6382	SO:0001630	splice_region_variant	5292	exon2			TCCTAGGCAAGGA		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.83-1G>A	6.37:g.37138549G>A		53	1	0.0188679		56	6	0.107143	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	G	13.37	2.215565	0.39102	2.35E-4	0.0	ENSG00000137193	ENST00000373509	T	0.69306	-0.39	3.83	3.83	0.44106	Protein kinase-like domain (1);	0.187844	0.33772	N	0.004562	T	0.23330	0.0564	N	0.08118	0	0.30455	N	0.774827	P	0.42827	0.791	B	0.36719	0.231	T	0.07083	-1.0791	9	.	.	.	.	9.7286	0.40348	0.0983:0.0:0.9017:0.0	.	119	P11309	PIM1_HUMAN	D	28	ENSP00000362608:G28D	.	G	+	2	0	PIM1	37246527	0.119000	0.22226	0.998000	0.56505	0.963000	0.63663	-0.036000	0.12185	2.138000	0.66242	0.549000	0.68633	GGC	.	.	weak		0.721	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1		Missense_Mutation	A	37138549	G	A	37138549	5	1	45	1	0	0	0	0	0	0	1	0	11936	1217	42	2	89	2	PIM1	6	37138549	Splice_Site	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	194	37138549	133976518	61	15513			2	74	10981378	4	4	599	N	G_C	9.824106e-09
PIM1	5292	hgsc.bcm.edu	37	chr6	37138791	37138791	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	cgtggagaaggaccggatttCcgactggggagagctggtga	9	7	18	7	3	0	3	0	1	0	2	1	8	1	5	2	6	1	1	2	6	1	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr6:37138791C>T	ENST00000373509.5	+	3	597	c.224C>T	c.(223-225)tCc>tTc	p.S75F		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	166					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)	p.S75F(1)		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)	GACCGGATTTCCGACTGGGGA	0.701			T	BCL6	NHL																																p.S166F		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,carcinoma,0,1	PIM1	71	1	1	Substitution - Missense(1)	lung(1)	c.C497T						PASS	.						53	55	55					6																	37138791		2203	4300	6503	SO:0001583	missense	5292	exon3			GGATTTCCGACTG		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.224C>T	6.37:g.37138791C>T	ENSP00000362608:p.Ser75Phe	160	0	0		143	28	0.195804	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	11.19	1.566693	0.28003	.	.	ENSG00000137193	ENST00000373509	T	0.67171	-0.25	4.44	4.44	0.53790	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.073980	0.53938	D	0.000044	T	0.47764	0.1463	L	0.47716	1.5	0.47621	D	0.999477	B	0.29270	0.24	B	0.29663	0.105	T	0.48747	-0.9008	10	0.25751	T	0.34	.	17.2083	0.86924	0.0:1.0:0.0:0.0	.	166	P11309	PIM1_HUMAN	F	75	ENSP00000362608:S75F	ENSP00000362608:S75F	S	+	2	0	PIM1	37246769	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.030000	0.76484	2.468000	0.83385	0.549000	0.68633	TCC	.	.	none		0.701	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37138791	C	T	37138791	3	4	45	1	0	0	0	0	1	0	0	0	11936	855	30	2	234	2	PIM1	6	37138791	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	242	37138791	133976276	62	15514			2	74	10981378	4	4	599	N	G_C	9.824106e-09
PIM1	5292	hgsc.bcm.edu	37	chr6	37138953	37138953	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgctgaagaaggtgagctCgggtttctccggcgtcatta	7	11	13	10	3	2	3	1	2	1	1	4	3	2	3	2	3	2	3	2	3	3	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr6:37138953C>A	ENST00000373509.5	+	4	666	c.293C>A	c.(292-294)tCg>tAg	p.S98*		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	189					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)	AAGGTGAGCTCGGGTTTCTCC	0.647			T	BCL6	NHL																																p.S189X		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C566A						PASS	.						84	94	90					6																	37138953		2203	4300	6503	SO:0001587	stop_gained	5292	exon4			TGAGCTCGGGTTT		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.293C>A	6.37:g.37138953C>A	ENSP00000362608:p.Ser98*	97	0	0		87	23	0.264368	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Nonsense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	40	8.002206	0.98605	.	.	ENSG00000137193	ENST00000373509	.	.	.	4.28	4.28	0.50868	.	0.237529	0.32769	N	0.005670	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.8746	0.86048	0.0:1.0:0.0:0.0	.	.	.	.	X	98	.	ENSP00000362608:S98X	S	+	2	0	PIM1	37246931	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.684000	0.61686	2.371000	0.80710	0.549000	0.68633	TCG	.	.	none		0.647	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			A	37138953	C	A	37138953	4	1	45	1	0	0	0	0	0	1	0	0	11936	893	31	4	307	4	PIM1	6	37138953	Nonsense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	162	37138953	133976114	63	15515			2	74	10981378	4	4	599	N	G_C	9.824106e-09
GPR116	221395	hgsc.bcm.edu	37	chr6	46845956	46845956	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cacctggaatatttatttttCcttcctgcttccattctact	7	19	3	12	0	1	0	0	0	1	0	4	1	4	1	4	1	2	1	4	1	4	9			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr6:46845956C>A	ENST00000283296.7	-	10	1511	c.1223G>T	c.(1222-1224)gGa>gTa	p.G408V	GPR116_ENST00000362015.4_Missense_Mutation_p.G408V|GPR116_ENST00000265417.7_Missense_Mutation_p.G408V|GPR116_ENST00000456426.2_Intron	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	408	Ig-like 2.				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)			ATTTATTTTTCCTTCCTGCTT	0.408																																					p.G408V	NSCLC(59;410 1274 8751 36715 50546)	Atlas-SNP	.											GPR116,NS,malignant_melanoma,-1,1	GPR116	133	1	0			c.G1223T						PASS	.						153	147	149					6																	46845956		2203	4300	6503	SO:0001583	missense	221395	exon10			ATTTTTCCTTCCT	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.1223G>T	6.37:g.46845956C>A	ENSP00000283296:p.Gly408Val	171	0	0		171	29	0.169591	NM_015234	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Missense_Mutation	SNP	ENST00000283296.7	37	CCDS4919.1	.	.	.	.	.	.	.	.	.	.	C	17.88	3.497890	0.64186	.	.	ENSG00000069122	ENST00000452370;ENST00000283296;ENST00000362015;ENST00000265417	T;T;T	0.43688	0.94;1.39;0.94	6.02	6.02	0.97574	Immunoglobulin-like (1);	0.000000	0.64402	D	0.000007	T	0.58409	0.2120	M	0.71581	2.175	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	0.59225	-0.7494	10	0.66056	D	0.02	-21.2525	16.0408	0.80680	0.0:1.0:0.0:0.0	.	408;408;408	E9PBS6;A8K0D8;Q8IZF2	.;.;GP116_HUMAN	V	408	ENSP00000283296:G408V;ENSP00000354563:G408V;ENSP00000265417:G408V	ENSP00000265417:G408V	G	-	2	0	GPR116	46953915	0.275000	0.24201	0.316000	0.25252	0.830000	0.47004	2.146000	0.42216	2.865000	0.98341	0.655000	0.94253	GGA	.	.	none		0.408	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234		A	46845956	C	A	46845956	3	1	45	1	0	0	0	0	1	0	0	0	6641	855	30	4	2865	4	GPR116	6	46845956	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	9707003	46845956	124269111	64	15516											
DST	667	hgsc.bcm.edu	37	chr6	56350230	56350230	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gcctgtagggcatctgtgaaTtgtccagaaaataacagggc	12	9	12	8	0	1	2	0	1	1	1	2	2	2	2	2	2	1	2	2	2	5	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr6:56350230T>G	ENST00000361203.3	-	83	20134	c.20127A>C	c.(20125-20127)caA>caC	p.Q6709H	DST_ENST00000244364.6_Missense_Mutation_p.Q4406H|DST_ENST00000370754.5_Missense_Mutation_p.Q6998H|DST_ENST00000312431.6_3'UTR|DST_ENST00000370769.4_Missense_Mutation_p.Q6820H|DST_ENST00000446842.2_Missense_Mutation_p.Q6494H|DST_ENST00000421834.2_Missense_Mutation_p.Q4732H|DST_ENST00000370788.2_Missense_Mutation_p.Q4623H			Q03001	DYST_HUMAN	dystonin	6708					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)			CATCTGTGAATTGTCCAGAAA	0.408																																					p.Q4406H		Atlas-SNP	.											.	DST	1427	.	0			c.A13218C						PASS	.						60	58	59					6																	56350230		1822	4072	5894	SO:0001583	missense	667	exon69			TGTGAATTGTCCA	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.20127A>C	6.37:g.56350230T>G	ENSP00000354508:p.Gln6709His	105	0	0		103	21	0.203883	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	37		.	.	.	.	.	.	.	.	.	.	T	14.11	2.438295	0.43326	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.55413	0.52;0.52;0.52;0.52;0.52;0.52;0.52	5.76	0.0736	0.14391	.	0.000000	0.52532	D	0.000071	T	0.59088	0.2168	M	0.78456	2.415	0.32844	D	0.505733	D;D;D;D;D;D	0.89917	0.998;1.0;1.0;0.999;1.0;1.0	D;D;D;D;D;D	0.97110	0.998;1.0;0.998;0.94;0.999;0.998	T	0.64993	-0.6276	9	0.62326	D	0.03	.	11.513	0.50504	0.0:0.4674:0.0:0.5326	.	4732;6820;6998;102;6818;4406	Q5TBT1;E7ERU2;E9PEB9;Q9H722;Q03001;Q03001-8	.;.;.;.;DYST_HUMAN;.	H	4406;6998;6820;4732;6494;4623;6709	ENSP00000244364:Q4406H;ENSP00000359790:Q6998H;ENSP00000359805:Q6820H;ENSP00000400883:Q4732H;ENSP00000393645:Q6494H;ENSP00000359824:Q4623H;ENSP00000354508:Q6709H	ENSP00000244364:Q4406H	Q	-	3	2	DST	56458189	0.986000	0.35501	0.997000	0.53966	0.669000	0.39330	0.216000	0.17585	-0.125000	0.11703	-0.263000	0.10527	CAA	.	.	none		0.408	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723		G	56350230	T	G	56350230	3	3	45	1	0	0	0	0	1	0	0	0	4785	1490	52	5	2361	5	DST	6	56350230	Missense_Mutation	SNP	T	TCGA-RQ-A68N-01A-11D-A31X-10	9504274	56350230	114764837	65	15517											
MDN1	23195	hgsc.bcm.edu	37	chr6	90423000	90423000	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tctggattagagttgatacaGaagatgttggagaacctatt	13	13	11	4	0	1	5	0	1	1	4	1	7	1	6	1	2	2	2	1	2	5	6			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr6:90423000G>A	ENST00000369393.3	-	47	7200	c.7085C>T	c.(7084-7086)tCt>tTt	p.S2362F	MDN1_ENST00000428876.1_Missense_Mutation_p.S2362F			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	2362					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)		AGTTGATACAGAAGATGTTGG	0.383																																					p.S2362F		Atlas-SNP	.											.	MDN1	478	.	0			c.C7085T						PASS	.						122	132	129					6																	90423000		2203	4300	6503	SO:0001583	missense	23195	exon47			GATACAGAAGATG	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.7085C>T	6.37:g.90423000G>A	ENSP00000358400:p.Ser2362Phe	70	0	0		54	25	0.462963	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	G	10.01	1.234635	0.22626	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03580	3.88;3.88	5.94	4.12	0.48240	.	0.137285	0.51477	D	0.000097	T	0.06325	0.0163	M	0.68952	2.095	0.47476	D	0.999437	D	0.60575	0.988	P	0.57679	0.825	T	0.04268	-1.0964	10	0.87932	D	0	.	11.7102	0.51620	0.0665:0.1243:0.8092:0.0	.	2362	Q9NU22	MDN1_HUMAN	F	2362	ENSP00000358400:S2362F;ENSP00000413970:S2362F	ENSP00000358400:S2362F	S	-	2	0	MDN1	90479721	0.999000	0.42202	0.218000	0.23776	0.721000	0.41392	4.186000	0.58337	0.809000	0.34255	-0.262000	0.10625	TCT	.	.	none		0.383	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			A	90423000	G	A	90423000	3	1	45	1	0	0	0	0	1	0	0	0	9424	942	33	2	9929	2	MDN1	6	90423000	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	34072770	90423000	80692067	66	15518											
PRDM1	639	hgsc.bcm.edu	37	chr6	106553289	106553289	+	Nonsense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aagttcctcttgcccccctaCggcatgaattgtaatggcct	8	12	8	13	1	1	1	0	1	1	0	2	1	2	1	5	2	2	3	5	2	4	5			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr6:106553289C>G	ENST00000369096.4	+	5	1488	c.1254C>G	c.(1252-1254)taC>taG	p.Y418*	PRDM1_ENST00000369089.3_Nonsense_Mutation_p.Y284*|PRDM1_ENST00000369091.2_Nonsense_Mutation_p.Y382*	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	418					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)		TGCCCCCCTACGGCATGAATT	0.587			"D, N, Mis, F, S"		DLBCL																																p.Y418X		Atlas-SNP	.		Rec	yes		6	6q21	639	"PR domain containing 1, with ZNF domain"		L	.	PRDM1	195	.	0			c.C1254G						PASS	.						77	58	65					6																	106553289		2203	4300	6503	SO:0001587	stop_gained	639	exon5			CCCCTACGGCATG		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.1254C>G	6.37:g.106553289C>G	ENSP00000358092:p.Tyr418*	46	0	0		33	21	0.636364	NM_001198	B2REA6|E1P5E0|Q86WM7	Nonsense_Mutation	SNP	ENST00000369096.4	37	CCDS5054.2	.	.	.	.	.	.	.	.	.	.	C	35	5.568123	0.96540	.	.	ENSG00000057657	ENST00000369091;ENST00000369096;ENST00000456278;ENST00000369089	.	.	.	5.32	-4.24	0.03777	.	0.055914	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-20.8074	15.6863	0.77411	0.0:0.3976:0.0:0.6024	.	.	.	.	X	382;418;382;284	.	ENSP00000358085:Y284X	Y	+	3	2	PRDM1	106659982	0.001000	0.12720	0.465000	0.27155	0.971000	0.66376	-1.479000	0.02327	-0.847000	0.04168	-0.150000	0.13652	TAC	.	.	none		0.587	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3			G	106553289	C	G	106553289	4	3	45	1	0	0	0	0	0	1	0	0	12462	547	19	4	1285	4	PRDM1	6	106553289	Nonsense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	16130289	106553289	64561778	67	15519											
SERINC1	57515	hgsc.bcm.edu	37	chr6	122766211	122766211	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	agtcaaaatcacgatttgtaAgaacaagtggtgccacgagt	15	9	10	7	2	2	1	2	0	0	1	2	3	2	1	1	1	2	1	1	1	5	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr6:122766211A>C	ENST00000339697.4	-	10	1424	c.1340T>G	c.(1339-1341)cTt>cGt	p.L447R		NM_020755.2	NP_065806.1	Q9NRX5	SERC1_HUMAN	serine incorporator 1	447					L-serine transport (GO:0015825)|phosphatidylserine metabolic process (GO:0006658)|phospholipid biosynthetic process (GO:0008654)|positive regulation of transferase activity (GO:0051347)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-serine transmembrane transporter activity (GO:0015194)			endometrium(2)|kidney(2)|large_intestine(4)|liver(1)|lung(2)|ovary(1)|skin(1)	13				GBM - Glioblastoma multiforme(226;0.126)		ACGATTTGTAAGAACAAGTGG	0.413																																					p.L447R		Atlas-SNP	.											.	SERINC1	39	.	0			c.T1340G						PASS	.						97	86	89					6																	122766211		2203	4300	6503	SO:0001583	missense	57515	exon10			TTTGTAAGAACAA	AF087902	CCDS5125.1	6q22.32	2006-02-09	2005-10-14	2005-10-14	ENSG00000111897	ENSG00000111897			13464	protein-coding gene	gene with protein product		614548	"tumor differentially expressed 2"	TDE2		10637174	Standard	NM_020755		Approved	TMS-2, TDE1L, KIAA1253	uc003pyy.1	Q9NRX5	OTTHUMG00000015487	ENST00000339697.4:c.1340T>G	6.37:g.122766211A>C	ENSP00000342962:p.Leu447Arg	89	0	0		43	24	0.55814	NM_020755	B3KY69|E1P565|O75655|Q7Z2F5|Q8TAG1|Q9NTH8|Q9ULG7	Missense_Mutation	SNP	ENST00000339697.4	37	CCDS5125.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.722297	0.89298	.	.	ENSG00000111897	ENST00000339697;ENST00000368454	T;T	0.19250	2.16;2.16	5.59	5.59	0.84812	.	0.125021	0.56097	D	0.000040	T	0.44912	0.1316	M	0.86864	2.845	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	T	0.55457	-0.8138	10	0.87932	D	0	-16.0237	15.7663	0.78128	1.0:0.0:0.0:0.0	.	447	Q9NRX5	SERC1_HUMAN	R	447	ENSP00000342962:L447R;ENSP00000357439:L447R	ENSP00000342962:L447R	L	-	2	0	SERINC1	122807910	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.315000	0.96313	2.124000	0.65301	0.533000	0.62120	CTT	.	.	none		0.413	SERINC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042031.2	NM_020755		C	122766211	A	C	122766211	3	2	45	1	0	0	0	0	1	0	0	0	14094	72	3	5	25	5	SERINC1	6	122766211	Missense_Mutation	SNP	A	TCGA-RQ-A68N-01A-11D-A31X-10	16212922	122766211	48348856	68	15520											
KIAA1244	57221	hgsc.bcm.edu	37	chr6	138645253	138645253	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cgtcctcctccccaagtgccGaggccgagtactggcgcatc	6	7	11	17	4	0	0	0	0	0	0	4	2	3	0	6	2	2	2	6	2	2	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr6:138645253G>A	ENST00000251691.4	+	31	5129	c.4963G>A	c.(4963-4965)Gag>Aag	p.E1655K		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)		CCCAAGTGCCGAGGCCGAGTA	0.647																																					p.E1655K		Atlas-SNP	.											.	KIAA1244	236	.	0			c.G4963A						PASS	.						37	42	40					6																	138645253		2203	4299	6502	SO:0001583	missense	57221	exon31			AGTGCCGAGGCCG	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.4963G>A	6.37:g.138645253G>A	ENSP00000251691:p.Glu1655Lys	80	0	0		43	7	0.162791	NM_020340		Missense_Mutation	SNP	ENST00000251691.4	37	CCDS5189.2	.	.	.	.	.	.	.	.	.	.	G	28.2	4.898200	0.91962	.	.	ENSG00000112379	ENST00000251691	T	0.19669	2.13	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.36468	0.0968	L	0.55481	1.735	0.80722	D	1	D	0.89917	1.0	D	0.73708	0.981	T	0.07233	-1.0783	10	0.66056	D	0.02	-15.4417	19.6229	0.95667	0.0:0.0:1.0:0.0	.	1655	Q5TH69	BIG3_HUMAN	K	1655	ENSP00000251691:E1655K	ENSP00000251691:E1655K	E	+	1	0	KIAA1244	138686946	1.000000	0.71417	0.993000	0.49108	0.985000	0.73830	9.388000	0.97237	2.708000	0.92522	0.650000	0.86243	GAG	.	.	none		0.647	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340		A	138645253	G	A	138645253	3	1	45	1	0	0	0	0	1	0	0	0	8226	1059	37	1	5085	1	KIAA1244	6	138645253	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	15879042	138645253	32469814	69	15521											
TBP	6908	hgsc.bcm.edu	37	chr6	170871044	170871046	+	In_Frame_Del	DEL	CAA	CAA	-																															agcagcagcagcagcaacagCaacagcagcagcagcagcag																								rs369312237|rs62430309	byFrequency	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr6:170871044_170871046delCAA	ENST00000392092.2	+	3	499_501	c.220_222delCAA	c.(220-222)caadel	p.Q95del	TBP_ENST00000230354.6_In_Frame_Del_p.Q95del|TBP_ENST00000540980.1_In_Frame_Del_p.Q75del	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	95	Poly-Gln.		Missing. {ECO:0000269|PubMed:2374612}.	Missing (in Ref. 4; BAG65425). {ECO:0000305}.	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)		gcagcaacagcaacagcagcagc	0.567																																					p.73_74del		Atlas-Indel	.											TBP,NS,carcinoma,0,1	TBP	58	1	0			c.219_221del						PASS	.																																			SO:0001651	inframe_deletion	6908	exon3			.	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.220_222delCAA	6.37:g.170871044_170871046delCAA	ENSP00000375942:p.Gln95del	31	0	0		22	14	0.636364	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	In_Frame_Del	DEL	ENST00000392092.2	37	CCDS5315.1																																																																																			.	.	none		0.567	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		-	170871046	CAA	-	170871044	7	5	45	1	0	1	0	1	0	0	0	0	15659	711	25	0	226	0	TBP	6	170871044	In_Frame_Del	DEL	CAA	TCGA-RQ-A68N-01A-11D-A31X-10	32225791	170871044	244023	70	15522											
AMZ1	155185	hgsc.bcm.edu	37	chr7	2748854	2748854	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgggccctgtgcttcagtgcCctggggatggttcagtgctg	3	12	16	10	0	2	0	2	0	0	0	2	1	2	1	2	4	3	3	2	4	0	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr7:2748854C>T	ENST00000312371.4	+	5	1115	c.747C>T	c.(745-747)gcC>gcT	p.A249A	AMZ1_ENST00000489665.1_Intron|AMZ1_ENST00000407112.1_Intron	NM_133463.1	NP_597720.1	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1	249							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)		GCTTCAGTGCCCTGGGGATGG	0.682																																					p.A249A		Atlas-SNP	.											.	AMZ1	41	.	0			c.C747T						PASS	.						16	20	18					7																	2748854		2196	4292	6488	SO:0001819	synonymous_variant	155185	exon5			CAGTGCCCTGGGG	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.747C>T	7.37:g.2748854C>T		62	0	0		37	9	0.243243	NM_133463	B3KRS0|Q8TF51	Silent	SNP	ENST00000312371.4	37	CCDS34589.1																																																																																			.	.	none		0.682	AMZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325244.1	NM_133463		T	2748854	C	T	2748854	2	4	45	1	0	0	0	0	0	0	0	1	596	610	22	2		2	AMZ1	7	2748854	Silent	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10		2748854	156389809	71	15523											
PEX1	5189	hgsc.bcm.edu	37	chr7	92146905	92146905	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	aatacatgaatggcacagtgTttatgaaaaacagaggttgc	16	10	10	5	0	0	3	0	2	0	1	0	3	0	3	0	2	3	3	0	2	6	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr7:92146905T>C	ENST00000248633.4	-	5	1019	c.924A>G	c.(922-924)aaA>aaG	p.K308K	PEX1_ENST00000428214.1_Silent_p.K308K|PEX1_ENST00000438045.1_Intron|PEX1_ENST00000541751.1_5'Flank	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1	308					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)			TGGCACAGTGTTTATGAAAAA	0.383																																					p.K308K		Atlas-SNP	.											.	PEX1	102	.	0			c.A924G						PASS	.						73	68	69					7																	92146905		2203	4300	6503	SO:0001819	synonymous_variant	5189	exon5			ACAGTGTTTATGA	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.924A>G	7.37:g.92146905T>C		129	0	0		119	76	0.638655	NM_000466	A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Silent	SNP	ENST00000248633.4	37	CCDS5627.1																																																																																			.	.	none		0.383	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466		C	92146905	T	C	92146905	2	2	45	1	0	0	0	0	0	0	0	1	11744	1722	60	3		3	PEX1	7	92146905	Silent	SNP	T	TCGA-RQ-A68N-01A-11D-A31X-10	89398051	92146905	66991758	72	15524											
DGKI	9162	hgsc.bcm.edu	37	chr7	137092719	137092719	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	cctgaattagcagactgcctCcatttttatagctttctatt	9	17	5	10	0	1	2	0	1	1	1	2	2	2	2	3	0	3	2	3	0	5	8			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr7:137092719C>G	ENST00000288490.5	-	31	2846	c.2846G>C	c.(2845-2847)gGa>gCa	p.G949A	DGKI_ENST00000453654.2_Missense_Mutation_p.G618A|DGKI_ENST00000494390.1_5'UTR|DGKI_ENST00000446122.1_Missense_Mutation_p.G931A|DGKI_ENST00000424189.2_Missense_Mutation_p.G962A	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	949					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						CAGACTGCCTCCATTTTTATA	0.433																																					p.G949A		Atlas-SNP	.											.	DGKI	335	.	0			c.G2846C						PASS	.						151	139	143					7																	137092719		2203	4300	6503	SO:0001583	missense	9162	exon31			CTGCCTCCATTTT	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.2846G>C	7.37:g.137092719C>G	ENSP00000288490:p.Gly949Ala	149	0	0		113	62	0.548673	NM_004717	A4D1Q9|Q9NZ49	Missense_Mutation	SNP	ENST00000288490.5	37	CCDS5845.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.252341	0.80135	.	.	ENSG00000157680	ENST00000453654;ENST00000540376;ENST00000424189;ENST00000288490;ENST00000446122	T;T;T	0.49720	0.77;0.77;0.77	5.6	5.6	0.85130	Ankyrin repeat-containing domain (2);	0.000000	0.85682	D	0.000000	T	0.47746	0.1462	N	0.08118	0	0.80722	D	1	D;D	0.59357	0.969;0.985	P;P	0.59948	0.776;0.866	T	0.57900	-0.7731	10	0.66056	D	0.02	.	17.8057	0.88600	0.0:1.0:0.0:0.0	.	618;949	E9PFX6;O75912	.;DGKI_HUMAN	A	618;866;952;949;931	ENSP00000392161:G618A;ENSP00000288490:G949A;ENSP00000399131:G931A	ENSP00000288490:G949A	G	-	2	0	DGKI	136743259	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.019000	0.64060	2.636000	0.89361	0.655000	0.94253	GGA	.	.	none		0.433	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717		G	137092719	C	G	137092719	3	3	45	1	0	0	0	0	1	0	0	0	4473	855	30	4	367	4	DGKI	7	137092719	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	44945814	137092719	22045944	73	15525											
TAS2R39	259285	hgsc.bcm.edu	37	chr7	142881334	142881334	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcattctctacattttcaatGcagttgctctgtttatctac	8	19	4	10	0	5	0	2	0	3	0	6	0	5	0	0	0	4	4	0	0	4	8			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr7:142881334G>A	ENST00000446620.1	+	1	823	c.823G>A	c.(823-825)Gca>Aca	p.A275T		NM_176881.2	NP_795362.2	P59534	T2R39_HUMAN	taste receptor, type 2, member 39	275					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)					CATTTTCAATGCAGTTGCTCT	0.488																																					p.A275T		Atlas-SNP	.											.	TAS2R39	42	.	0			c.G823A						PASS	.						147	136	139					7																	142881334		1923	4142	6065	SO:0001583	missense	259285	exon1			TTCAATGCAGTTG	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.823G>A	7.37:g.142881334G>A	ENSP00000405095:p.Ala275Thr	117	0	0		82	57	0.695122	NM_176881	A4FUI7|Q3ZCN6|Q645W4	Missense_Mutation	SNP	ENST00000446620.1	37	CCDS47729.1	.	.	.	.	.	.	.	.	.	.	G	8.428	0.847872	0.17034	.	.	ENSG00000236398	ENST00000446620	T	0.37584	1.19	4.62	1.55	0.23275	.	.	.	.	.	T	0.35451	0.0932	L	0.55481	1.735	0.21064	N	0.999792	P	0.39883	0.693	B	0.41619	0.361	T	0.15292	-1.0442	9	0.27785	T	0.31	.	12.1023	0.53792	0.0:0.0:0.3507:0.6493	.	275	P59534	T2R39_HUMAN	T	275	ENSP00000405095:A275T	ENSP00000405095:A275T	A	+	1	0	TAS2R39	142591456	0.450000	0.25697	0.353000	0.25747	0.529000	0.34654	1.145000	0.31577	0.656000	0.30886	0.650000	0.86243	GCA	.	.	none		0.488	TAS2R39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327090.2	NM_176881		A	142881334	G	A	142881334	3	1	45	1	0	0	0	0	1	0	0	0	15591	1319	46	2	825	2	TAS2R39	7	142881334	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	5788615	142881334	16257329	74	15526											
LRRC61	65999	hgsc.bcm.edu	37	chr7	150034703	150034703	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gagcaggtactcagctctgcGggccccacctcttccttcgt	5	10	10	16	2	3	0	1	0	2	0	5	1	4	0	4	2	4	3	4	2	1	3	rs149223172	byFrequency	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr7:150034703G>A	ENST00000359623.4	+	3	1341	c.753G>A	c.(751-753)gcG>gcA	p.A251A	LRRC61_ENST00000493307.1_Silent_p.A251A|LRRC61_ENST00000323078.7_Silent_p.A251A	NM_001142928.1	NP_001136400.1	Q9BV99	LRC61_HUMAN	leucine rich repeat containing 61	251										endometrium(2)|large_intestine(1)|skin(1)|upper_aerodigestive_tract(1)	5			OV - Ovarian serous cystadenocarcinoma(82;0.011)			TCAGCTCTGCGGGCCCCACCT	0.682													G|||	12	0.00239617	0.0	0.0014	5008	,	,		17182	0.0		0.001	False		,,,				2504	0.0102				p.A251A		Atlas-SNP	.											.	LRRC61	17	.	0			c.G753A						PASS	.	G	,	0,4224		0,0,2112	15	15	15		753,753	-7.9	0	7	dbSNP_134	15	18,8284		0,18,4133	no	coding-synonymous,coding-synonymous	LRRC61	NM_001142928.1,NM_023942.2	,	0,18,6245	AA,AG,GG		0.2168,0.0,0.1437	,	251/260,251/260	150034703	18,12508	2112	4151	6263	SO:0001819	synonymous_variant	65999	exon2			CTCTGCGGGCCCC	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	ENST00000359623.4:c.753G>A	7.37:g.150034703G>A		39	0	0		33	16	0.484848	NM_023942	B3KUW0|D3DWY8	Silent	SNP	ENST00000359623.4	37	CCDS5901.1																																																																																			G|0.998;A|0.002	0.002	strong		0.682	LRRC61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350696.1	NM_023942		A	150034703	G	A	150034703	2	1	45	1	0	0	0	0	0	0	0	1	9026	1103	39	1		1	LRRC61	7	150034703	Silent	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	7153369	150034703	9103960	75	15527											
PTPRN2	5799	hgsc.bcm.edu	37	chr7	157931091	157931091	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcgagctactccatggtccaCgccttgcatcaggccagcca	8	8	9	16	2	1	0	1	0	0	0	4	1	3	0	5	2	4	2	5	2	1	2	rs3752368	byFrequency	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr7:157931091C>G	ENST00000389418.4	-	7	1036	c.1027G>C	c.(1027-1029)Gtg>Ctg	p.V343L	PTPRN2_ENST00000409483.1_Missense_Mutation_p.V305L|PTPRN2_ENST00000389413.3_Missense_Mutation_p.V343L|PTPRN2_ENST00000389416.4_Missense_Mutation_p.V326L|PTPRN2_ENST00000404321.2_Missense_Mutation_p.V366L	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	343			V -> M (in dbSNP:rs3752368).		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)		CCATGGTCCACGCCTTGCATC	0.667																																					p.V343L		Atlas-SNP	.											.	PTPRN2	243	.	0			c.G1027C						PASS	.						68	70	69					7																	157931091		2203	4300	6503	SO:0001583	missense	5799	exon7			GGTCCACGCCTTG	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.1027G>C	7.37:g.157931091C>G	ENSP00000374069:p.Val343Leu	61	0	0		41	28	0.682927	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	.	.	.	.	.	.	.	.	.	.	C	8.901	0.956399	0.18507	.	.	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.03124	4.04;4.04;4.05;4.05;4.04	4.15	2.14	0.27477	.	5.222610	0.01476	N	0.016495	T	0.03651	0.0104	N	0.19112	0.55	0.09310	N	1	B;B;B;B;B	0.18741	0.03;0.007;0.012;0.007;0.007	B;B;B;B;B	0.16289	0.015;0.007;0.015;0.007;0.007	T	0.46162	-0.9211	10	0.17369	T	0.5	.	9.3148	0.37928	0.1426:0.7662:0.0:0.0912	.	366;305;343;326;343	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	L	305;343;326;343;366	ENSP00000387114:V305L;ENSP00000374064:V343L;ENSP00000374067:V326L;ENSP00000374069:V343L;ENSP00000385464:V366L	ENSP00000374064:V343L	V	-	1	0	PTPRN2	157623852	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.799000	0.27028	0.316000	0.23135	-0.797000	0.03246	GTG	C|0.987;T|0.013	.	alt		0.667	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1			G	157931091	C	G	157931091	3	3	45	1	0	0	0	0	1	0	0	0	12823	536	19	4	2088	4	PTPRN2	7	157931091	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	7896388	157931091	1207572	76	15528											
DLGAP2	9228	hgsc.bcm.edu	37	chr8	1624701	1624701	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgttctctgttgaattaggtGgaaacggccacagattctga	10	12	11	8	2	2	3	0	2	2	1	3	4	2	4	1	3	1	2	1	3	3	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr8:1624701G>A	ENST00000421627.2	+	8	2099	c.1965G>A	c.(1963-1965)gtG>gtA	p.V655V		NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	734					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)		TGAATTAGGTGGAAACGGCCA	0.493																																					p.V655V		Atlas-SNP	.											.	DLGAP2	292	.	0			c.G1965A						PASS	.						32	35	34					8																	1624701		1887	4107	5994	SO:0001819	synonymous_variant	9228	exon8			TTAGGTGGAAACG	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.1965G>A	8.37:g.1624701G>A		107	0	0		91	37	0.406593	NM_004745	A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	Silent	SNP	ENST00000421627.2	37	CCDS47760.1	.	.	.	.	.	.	.	.	.	.	G	8.829	0.939412	0.18281	.	.	ENSG00000198010	ENST00000520901	.	.	.	5.51	4.62	0.57501	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.356	13.4157	0.60968	0.0769:0.0:0.9231:0.0	.	.	.	.	X	658	.	.	W	+	2	0	DLGAP2	1612108	1.000000	0.71417	1.000000	0.80357	0.095000	0.18619	4.906000	0.63293	1.292000	0.44672	0.563000	0.77884	TGG	.	.	none		0.493	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374478.1	NM_004745		A	1624701	G	A	1624701	2	1	45	1	0	0	0	0	0	0	0	1	4562	1335	47	2		2	DLGAP2	8	1624701	Silent	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10		1624701	144739321	77	15529											
NEFL	4747	hgsc.bcm.edu	37	chr8	24813640	24813640	+	RNA	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcccggaagcgggatggctcGgagtgcttctggcgcagcac	6	6	17	12	4	1	0	0	0	1	0	2	3	1	3	1	5	3	4	1	5	1	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr8:24813640G>A	ENST00000221169.5	-	0	984				CTD-2168K21.2_ENST00000607735.1_RNA			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)		GGGATGGCTCGGAGTGCTTCT	0.662																																					p.S130S		Atlas-SNP	.											.	NEFL	47	.	0			c.C390T						PASS	.						12	13	13					8																	24813640		2075	4213	6288			4747	exon1			TGGCTCGGAGTGC		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		8.37:g.24813640G>A		34	0	0		37	15	0.405405	NM_006158	B9ZVN2|Q16154|Q8IU72	Silent	SNP	ENST00000221169.5	37																																																																																				.	.	none		0.662	NEFL-001	KNOWN	sequence_error|basic	processed_transcript	processed_transcript	OTTHUMT00000258943.4	NM_006158		A	24813640	G	A	24813640	1	1	45	0	1	0	0	0	0	0	0	0	10324	1103	39	1		1	NEFL	8	24813640	RNA	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	23188939	24813640	121550382	78	15530											
ANK1	286	hgsc.bcm.edu	37	chr8	41577226	41577226	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tttatccagaaggaccttagCcaccctgtggtgtccacagt	9	11	9	12	0	0	1	0	0	0	1	2	2	2	2	5	2	1	0	5	2	3	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr8:41577226C>T	ENST00000347528.4	-	10	1143	c.1060G>A	c.(1060-1062)Gct>Act	p.A354T	ANK1_ENST00000265709.8_Missense_Mutation_p.A387T|ANK1_ENST00000289734.7_Missense_Mutation_p.A354T|ANK1_ENST00000396942.1_Missense_Mutation_p.A354T|ANK1_ENST00000396945.1_Missense_Mutation_p.A354T|ANK1_ENST00000352337.4_Missense_Mutation_p.A354T|ANK1_ENST00000379758.2_Missense_Mutation_p.A354T	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	354	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)			AGGACCTTAGCCACCCTGTGG	0.622																																					p.A387T		Atlas-SNP	.											.	ANK1	497	.	0			c.G1159A						PASS	.						196	180	186					8																	41577226		2203	4300	6503	SO:0001583	missense	286	exon10			CCTTAGCCACCCT	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.1060G>A	8.37:g.41577226C>T	ENSP00000339620:p.Ala354Thr	86	0	0		68	38	0.558824	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Missense_Mutation	SNP	ENST00000347528.4	37	CCDS6119.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.470456	0.84533	.	.	ENSG00000029534	ENST00000347528;ENST00000289734;ENST00000379758;ENST00000396945;ENST00000396942;ENST00000352337;ENST00000265709;ENST00000358820	T;T;T;T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09;-0.09;-0.09;-0.09	5.76	4.89	0.63831	Ankyrin repeat-containing domain (3);	0.107603	0.64402	D	0.000006	T	0.67496	0.2899	L	0.31845	0.965	0.80722	D	1	D;D;P;D;D	0.67145	0.996;0.982;0.794;0.994;0.996	D;P;B;P;D	0.70016	0.967;0.883;0.363;0.837;0.967	T	0.63211	-0.6688	10	0.20046	T	0.44	.	14.6541	0.68820	0.0:0.9304:0.0:0.0696	.	387;354;354;354;354	P16157-21;P16157-4;P16157;P16157-5;P16157-3	.;.;ANK1_HUMAN;.;.	T	354;354;354;354;354;354;387;354	ENSP00000339620:A354T;ENSP00000289734:A354T;ENSP00000369082:A354T;ENSP00000380149:A354T;ENSP00000380147:A354T;ENSP00000309131:A354T;ENSP00000265709:A387T	ENSP00000265709:A387T	A	-	1	0	ANK1	41696383	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	6.086000	0.71352	1.460000	0.47911	0.555000	0.69702	GCT	.	.	none		0.622	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475		T	41577226	C	T	41577226	3	4	45	1	0	0	0	0	1	0	0	0	620	739	26	2	5071	2	ANK1	8	41577226	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	16763586	41577226	104786796	79	15531											
PXDNL	137902	hgsc.bcm.edu	37	chr8	52321593	52321593	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggcacacgcggggctggagCgcgcgaagagcatgcagggc	8	3	19	11	5	0	1	0	0	0	1	0	3	0	2	0	5	3	4	0	5	1	0			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr8:52321593C>T	ENST00000356297.4	-	17	2691	c.2591G>A	c.(2590-2592)cGc>cAc	p.R864H	PXDNL_ENST00000543296.1_Missense_Mutation_p.R864H	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	864					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.R63L(1)|p.R864L(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)				GGGGCTGGAGCGCGCGAAGAG	0.662																																					p.R864H		Atlas-SNP	.											PXDNL_ENST00000356297,colon,carcinoma,-1,3	PXDNL	414	3	2	Substitution - Missense(2)	lung(2)	c.G2591A						PASS	.						23	27	25					8																	52321593		2024	4155	6179	SO:0001583	missense	137902	exon17			CTGGAGCGCGCGA		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.2591G>A	8.37:g.52321593C>T	ENSP00000348645:p.Arg864His	74	0	0		54	24	0.444444	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	C	14.05	2.420939	0.42918	.	.	ENSG00000147485	ENST00000356297;ENST00000543296	D;D	0.84660	-1.88;-1.88	3.31	2.41	0.29592	.	0.272281	0.26156	N	0.026002	D	0.94991	0.8379	H	0.99286	4.5	0.35901	D	0.830399	D	0.89917	1.0	D	0.87578	0.998	D	0.95258	0.8366	10	0.87932	D	0	.	9.6539	0.39914	0.2105:0.7895:0.0:0.0	.	864	A1KZ92	PXDNL_HUMAN	H	864	ENSP00000348645:R864H;ENSP00000444865:R864H	ENSP00000348645:R864H	R	-	2	0	PXDNL	52484146	1.000000	0.71417	0.249000	0.24280	0.019000	0.09904	5.019000	0.64060	0.487000	0.27698	0.650000	0.86243	CGC	.	.	none		0.662	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651		T	52321593	C	T	52321593	3	4	45	1	0	0	0	0	1	0	0	0	12863	768	27	1	1828	1	PXDNL	8	52321593	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	10744367	52321593	94042429	80	15532											
SLC7A13	157724	hgsc.bcm.edu	37	chr8	87235201	87235201	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ttagccatttgcatacaaacCtgaagagagaatttccctgg	13	11	8	9	0	0	3	0	1	0	2	1	4	1	3	3	1	4	1	3	1	5	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr8:87235201C>A	ENST00000297524.3	-	2	920	c.817G>T	c.(817-819)Gat>Tat	p.D273Y	SLC7A13_ENST00000419776.2_Splice_Site_p.D264Y|SLC7A13_ENST00000520624.1_5'UTR	NM_138817.2	NP_620172.2	Q8TCU3	S7A13_HUMAN	solute carrier family 7 (anionic amino acid transporter), member 13	273						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						GCATACAAACCTGAAGAGAGA	0.373																																					p.D273Y		Atlas-SNP	.											.	SLC7A13	97	.	0			c.G817T						PASS	.						114	117	116					8																	87235201		2203	4300	6503	SO:0001630	splice_region_variant	157724	exon2			ACAAACCTGAAGA	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.817+1G>T	8.37:g.87235201C>A		122	0	0		86	16	0.186047	NM_138817	Q05C37|Q08AH9|Q96N84	Missense_Mutation	SNP	ENST00000297524.3	37	CCDS34917.1	.	.	.	.	.	.	.	.	.	.	C	16.75	3.209895	0.58343	.	.	ENSG00000164893	ENST00000297524;ENST00000419776	D;D	0.90620	-2.7;-2.7	4.36	4.36	0.52297	Amino acid permease domain (1);	0.363429	0.26019	N	0.026835	D	0.95089	0.8409	M	0.83774	2.66	0.36861	D	0.888401	D;D	0.89917	0.989;1.0	D;D	0.79108	0.947;0.992	D	0.96707	0.9522	9	.	.	.	.	14.4409	0.67318	0.0:1.0:0.0:0.0	.	264;273	Q8TCU3-2;Q8TCU3	.;S7A13_HUMAN	Y	273;264	ENSP00000297524:D273Y;ENSP00000410982:D264Y	.	D	-	1	0	SLC7A13	87304317	1.000000	0.71417	0.998000	0.56505	0.714000	0.41099	3.140000	0.50585	2.266000	0.75297	0.650000	0.86243	GAT	.	.	none		0.373	SLC7A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374704.1	NM_138817	Missense_Mutation	A	87235201	C	A	87235201	5	1	45	1	0	0	0	0	0	0	1	0	14710	695	24	4	607	4	SLC7A13	8	87235201	Splice_Site	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	34913608	87235201	59128821	81	15533											
CNGB3	54714	hgsc.bcm.edu	37	chr8	87638258	87638258	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgaagttcacatcaatggCgagggctaactggaccgtag	11	8	13	9	2	2	1	2	1	0	0	2	3	2	2	1	3	1	4	1	3	4	3	rs150642676	byFrequency	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr8:87638258C>A	ENST00000320005.5	-	13	1578	c.1531G>T	c.(1531-1533)Gcc>Tcc	p.A511S		NM_019098.4	NP_061971.3	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	511					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						ACATCAATGGCGAGGGCTAAC	0.373																																					p.A511S		Atlas-SNP	.											.	CNGB3	176	.	0			c.G1531T						PASS	.						123	112	115					8																	87638258		2203	4300	6503	SO:0001583	missense	54714	exon13			CAATGGCGAGGGC	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.1531G>T	8.37:g.87638258C>A	ENSP00000316605:p.Ala511Ser	144	0	0		98	17	0.173469	NM_019098	C9JA51|Q9NRE9	Missense_Mutation	SNP	ENST00000320005.5	37	CCDS6244.1	.	.	.	.	.	.	.	.	.	.	C	17.27	3.346934	0.61183	.	.	ENSG00000170289	ENST00000320005	D	0.96745	-4.11	5.37	2.47	0.30058	Cyclic nucleotide-binding-like (1);	0.202097	0.41194	D	0.000925	D	0.98204	0.9406	M	0.92268	3.29	0.80722	D	1	D;D	0.59357	0.985;0.975	D;P	0.63597	0.916;0.826	D	0.98338	1.0537	10	0.72032	D	0.01	.	14.4978	0.67700	0.0:0.9177:0.0:0.0823	.	511;511	Q9NQW8-2;Q9NQW8	.;CNGB3_HUMAN	S	511	ENSP00000316605:A511S	ENSP00000316605:A511S	A	-	1	0	CNGB3	87707374	0.999000	0.42202	0.003000	0.11579	0.482000	0.33219	3.118000	0.50414	0.198000	0.20407	0.650000	0.86243	GCC	C|0.999;T|0.001	.	alt		0.373	CNGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375107.1	NM_019098		A	87638258	C	A	87638258	3	1	45	1	0	0	0	0	1	0	0	0	3603	768	27	4	922	4	CNGB3	8	87638258	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	403057	87638258	58725764	82	15534											
VPS13B	157680	hgsc.bcm.edu	37	chr8	100829995	100829995	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggtcaagagatgtgtgcctGgaatccaaagcccctgagta	11	9	12	9	0	1	2	1	1	0	1	2	4	2	3	4	2	2	1	4	2	4	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr8:100829995G>A	ENST00000358544.2	+	45	8511	c.8400G>A	c.(8398-8400)ctG>ctA	p.L2800L	VPS13B_ENST00000357162.2_Silent_p.L2775L|VPS13B_ENST00000395996.1_3'UTR	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	2800					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)			ATGTGTGCCTGGAATCCAAAG	0.413																																					p.L2800L	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.G8400A						PASS	.						139	130	133					8																	100829995		2203	4300	6503	SO:0001819	synonymous_variant	157680	exon45			GTGCCTGGAATCC	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.8400G>A	8.37:g.100829995G>A		115	0	0		90	21	0.233333	NM_017890	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Silent	SNP	ENST00000358544.2	37	CCDS6280.1																																																																																			.	.	none		0.413	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042		A	100829995	G	A	100829995	2	1	45	1	0	0	0	0	0	0	0	1	17205	1335	47	2		2	VPS13B	8	100829995	Silent	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	13191737	100829995	45534027	83	15535											
RGS22	26166	hgsc.bcm.edu	37	chr8	101016183	101016183	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tgagtctcaagaaactgacgGaaatgttcaaactccagttt	14	11	8	8	1	2	3	2	2	1	1	4	4	3	4	1	1	2	2	1	1	4	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr8:101016183G>T	ENST00000360863.6	-	17	2792	c.2598C>A	c.(2596-2598)ttC>ttA	p.F866L	SNORD77_ENST00000391112.1_RNA|RGS22_ENST00000519421.1_5'UTR|RGS22_ENST00000523437.1_Missense_Mutation_p.F854L|RGS22_ENST00000523287.1_Missense_Mutation_p.F685L	NM_015668.3	NP_056483.3	Q8NE09	RGS22_HUMAN	regulator of G-protein signaling 22	866	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)			GAAACTGACGGAAATGTTCAA	0.333																																					p.F866L		Atlas-SNP	.											.	RGS22	319	.	0			c.C2598A						PASS	.						132	122	125					8																	101016183		1850	4091	5941	SO:0001583	missense	26166	exon17			CTGACGGAAATGT	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.2598C>A	8.37:g.101016183G>T	ENSP00000354109:p.Phe866Leu	117	0	0		91	12	0.131868	NM_015668	A8K944|Q569L2|Q86Y71|Q9BYZ4|Q9UFN6	Missense_Mutation	SNP	ENST00000360863.6	37	CCDS43758.1	.	.	.	.	.	.	.	.	.	.	G	19.04	3.749832	0.69533	.	.	ENSG00000132554	ENST00000360863;ENST00000427793;ENST00000523287;ENST00000523437;ENST00000517828	T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14	5.49	0.68	0.17980	Regulator of G protein signalling (3);Regulator of G protein signalling superfamily (1);	0.000000	0.85682	D	0.000000	T	0.71256	0.3318	M	0.62723	1.935	0.33255	D	0.558978	D;D;P	0.76494	0.999;0.999;0.734	D;D;B	0.83275	0.996;0.996;0.391	T	0.73538	-0.3951	10	0.40728	T	0.16	.	9.3926	0.38383	0.358:0.0:0.642:0.0	.	854;866;685	A8K944;Q8NE09;G3V112	.;RGS22_HUMAN;.	L	866;854;685;854;181	ENSP00000354109:F866L;ENSP00000429382:F685L;ENSP00000428212:F854L;ENSP00000427754:F181L	ENSP00000354109:F866L	F	-	3	2	RGS22	101085359	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	0.755000	0.26405	-0.163000	0.10946	0.655000	0.94253	TTC	.	.	none		0.333	RGS22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380365.1	NM_015668		T	101016183	G	T	101016183	3	4	45	1	0	0	0	0	1	0	0	0	13320	1165	41	4	1240	4	RGS22	8	101016183	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	186188	101016183	45347839	84	15536											
EXT1	2131	hgsc.bcm.edu	37	chr8	118830723	118830723	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcacagcagtggcaggccagCggtgtttggctggtaggggc	6	7	19	9	1	0	0	0	0	0	0	0	0	0	0	1	7	2	6	1	7	1	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr8:118830723C>G	ENST00000378204.2	-	7	2389	c.1583G>C	c.(1582-1584)cGc>cCc	p.R528P		NM_000127.2	NP_000118.2	Q16394	EXT1_HUMAN	exostosin glycosyltransferase 1	528					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)			GGCAGGCCAGCGGTGTTTGGC	0.512			"Mis, N, F, S"			"exostoses, osteosarcoma"			Langer-Giedion syndrome;Hereditary Multiple Exostoses																												p.R528P		Atlas-SNP	.	yes	Rec		Multiple Exostoses Type 1	8	8q24.11-q24.13	2131	multiple exostoses type 1 gene		M	.	EXT1	98	.	0			c.G1583C						PASS	.						131	131	131					8																	118830723		2203	4300	6503	SO:0001583	missense	2131	exon7	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II;HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	GGCCAGCGGTGTT	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.1583G>C	8.37:g.118830723C>G	ENSP00000367446:p.Arg528Pro	105	0	0		56	15	0.267857	NM_000127	B2R7V2|Q9BVI9	Missense_Mutation	SNP	ENST00000378204.2	37	CCDS6324.1	.	.	.	.	.	.	.	.	.	.	c	32	5.188410	0.94923	.	.	ENSG00000182197	ENST00000378204	T	0.77750	-1.12	5.44	5.44	0.79542	EXTL2, alpha-1,4-N-acetylhexosaminyltransferase (1);	0.000000	0.85682	D	0.000000	D	0.88955	0.6578	M	0.82517	2.595	0.80722	D	1	D	0.62365	0.991	D	0.69479	0.964	D	0.88651	0.3182	10	0.48119	T	0.1	1.1966	19.6267	0.95680	0.0:1.0:0.0:0.0	.	528	Q16394	EXT1_HUMAN	P	528	ENSP00000367446:R528P	ENSP00000367446:R528P	R	-	2	0	EXT1	118899904	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.442000	0.80503	2.712000	0.92718	0.563000	0.77884	CGC	.	.	none		0.512	EXT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132768.3	NM_000127		G	118830723	C	G	118830723	3	3	45	1	0	0	0	0	1	0	0	0	5325	768	27	4	677	4	EXT1	8	118830723	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	17814540	118830723	27533299	85	15537											
WISP1	8840	hgsc.bcm.edu	37	chr8	134225357	134225357	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgtgactacagcggggaccGcccgaggtacgcaataggag	10	5	15	11	4	0	1	0	1	0	0	0	4	0	3	2	4	3	2	2	4	4	3	rs536884015		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr8:134225357G>A	ENST00000250160.6	+	2	426	c.320G>A	c.(319-321)cGc>cAc	p.R107H	WISP1_ENST00000220856.6_Missense_Mutation_p.R107H|WISP1_ENST00000377863.2_Intron|WISP1_ENST00000517423.1_Missense_Mutation_p.R107H|WISP1_ENST00000519433.1_Intron	NM_003882.3	NP_003873.1	O95388	WISP1_HUMAN	WNT1 inducible signaling pathway protein 1	107	IGFBP N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00653}.				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)			AGCGGGGACCGCCCGAGGTAC	0.617													G|||	1	0.000199681	0.0	0.0	5008	,	,		15051	0.0		0.0	False		,,,				2504	0.001				p.R107H		Atlas-SNP	.											.	WISP1	64	.	0			c.G320A						PASS	.						63	62	62					8																	134225357		2203	4300	6503	SO:0001583	missense	8840	exon2			GGGACCGCCCGAG	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.320G>A	8.37:g.134225357G>A	ENSP00000250160:p.Arg107His	137	0	0		104	18	0.173077	NM_003882	A8KAG6|E7EMM5|Q5JBS6|Q5JBS7|Q5JBS8|Q9HCS3	Missense_Mutation	SNP	ENST00000250160.6	37	CCDS6371.1	.	.	.	.	.	.	.	.	.	.	G	15.62	2.886789	0.51908	.	.	ENSG00000104415	ENST00000250160;ENST00000517423;ENST00000220856	T;T;T	0.63417	-0.04;-0.04;-0.04	5.27	3.36	0.38483	Insulin-like growth factor-binding protein, IGFBP (2);	0.480222	0.24615	N	0.037015	T	0.71333	0.3327	L	0.59436	1.845	0.80722	D	1	B;D;B	0.89917	0.01;1.0;0.018	B;D;B	0.71870	0.003;0.975;0.002	T	0.70004	-0.4991	10	0.44086	T	0.13	-31.2725	9.5448	0.39273	0.0784:0.1429:0.7787:0.0	.	107;107;107	E7EMM5;O95388-2;O95388	.;.;WISP1_HUMAN	H	107	ENSP00000250160:R107H;ENSP00000427744:R107H;ENSP00000220856:R107H	ENSP00000220856:R107H	R	+	2	0	WISP1	134294539	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.732000	0.62029	1.221000	0.43506	0.542000	0.68232	CGC	.	.	none		0.617	WISP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378794.2	NM_003882		A	134225357	G	A	134225357	3	1	45	1	0	0	0	0	1	0	0	0	17387	1087	38	1	326	1	WISP1	8	134225357	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	15394634	134225357	12138665	86	15538											
PLEC	5339	hgsc.bcm.edu	37	chr8	144994192	144994192	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacgcaacagctcctgccgcTgctccgcagtgaagtactca	9	7	10	15	3	1	1	1	1	0	0	3	2	3	1	3	0	5	6	3	0	3	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr8:144994192T>C	ENST00000322810.4	-	32	10377	c.10208A>G	c.(10207-10209)cAg>cGg	p.Q3403R	PLEC_ENST00000357649.2_Missense_Mutation_p.Q3270R|PLEC_ENST00000436759.2_Missense_Mutation_p.Q3293R|PLEC_ENST00000356346.3_Missense_Mutation_p.Q3252R|PLEC_ENST00000354958.2_Missense_Mutation_p.Q3244R|PLEC_ENST00000345136.3_Missense_Mutation_p.Q3266R|PLEC_ENST00000527096.1_Missense_Mutation_p.Q3289R|PLEC_ENST00000398774.2_Missense_Mutation_p.Q3234R|PLEC_ENST00000354589.3_Missense_Mutation_p.Q3266R	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3403	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						CTCCTGCCGCTGCTCCGCAGT	0.597																																					p.Q3403R		Atlas-SNP	.											.	PLEC	1144	.	0			c.A10208G						PASS	.						57	65	62					8																	144994192		2176	4269	6445	SO:0001583	missense	5339	exon32			TGCCGCTGCTCCG	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.10208A>G	8.37:g.144994192T>C	ENSP00000323856:p.Gln3403Arg	65	0	0		58	12	0.206897	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	T	7.769	0.707022	0.15239	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.76709	-1.01;-1.01;-1.04;-1.04;-1.02;-1.01;-1.01;-1.01;-1.01	4.76	1.01	0.19927	.	0.000000	0.64402	U	0.000010	T	0.63367	0.2505	L	0.41356	1.27	0.42614	D	0.993327	B;B;B;B;B;B;B;B	0.12630	0.005;0.005;0.005;0.006;0.005;0.005;0.005;0.005	B;B;B;B;B;B;B;B	0.09377	0.004;0.004;0.004;0.002;0.004;0.004;0.004;0.004	T	0.53851	-0.8380	10	0.48119	T	0.1	.	4.852	0.13542	0.1389:0.1579:0.0:0.7033	.	3293;3252;3244;3403;3234;3266;3270;3266	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	R	3266;3270;3266;3234;3403;3244;3252;3293;3289	ENSP00000344848:Q3266R;ENSP00000350277:Q3270R;ENSP00000346602:Q3266R;ENSP00000381756:Q3234R;ENSP00000323856:Q3403R;ENSP00000347044:Q3244R;ENSP00000348702:Q3252R;ENSP00000388180:Q3293R;ENSP00000434583:Q3289R	ENSP00000323856:Q3403R	Q	-	2	0	PLEC	145066180	1.000000	0.71417	0.988000	0.46212	0.551000	0.35334	4.721000	0.61951	0.252000	0.21531	0.368000	0.22195	CAG	.	.	none		0.597	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		C	144994192	T	C	144994192	3	2	45	1	0	0	0	0	1	0	0	0	12061	1580	55	3	3850	3	PLEC	8	144994192	Missense_Mutation	SNP	T	TCGA-RQ-A68N-01A-11D-A31X-10	10768835	144994192	1369830	87	15539											
PLEC	5339	hgsc.bcm.edu	37	chr8	145010055	145010055	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cattgaagaggcggccgtctCtccagctggaggtgaagttg	8	9	15	9	2	1	3	0	2	1	1	3	4	2	4	2	4	1	2	2	4	2	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr8:145010055C>T	ENST00000322810.4	-	6	1143	c.974G>A	c.(973-975)aGa>aAa	p.R325K	PLEC_ENST00000357649.2_Missense_Mutation_p.R192K|PLEC_ENST00000436759.2_Missense_Mutation_p.R215K|PLEC_ENST00000356346.3_Missense_Mutation_p.R174K|PLEC_ENST00000354958.2_Missense_Mutation_p.R166K|PLEC_ENST00000345136.3_Missense_Mutation_p.R188K|PLEC_ENST00000527096.1_Missense_Mutation_p.R215K|PLEC_ENST00000398774.2_Missense_Mutation_p.R156K|PLEC_ENST00000354589.3_Missense_Mutation_p.R188K	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	325	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.|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						GCGGCCGTCTCTCCAGCTGGA	0.657																																					p.R325K		Atlas-SNP	.											.	PLEC	1144	.	0			c.G974A						PASS	.						53	65	61					8																	145010055		2088	4210	6298	SO:0001583	missense	5339	exon6			CCGTCTCTCCAGC	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.974G>A	8.37:g.145010055C>T	ENSP00000323856:p.Arg325Lys	71	0	0		68	13	0.191176	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	C	18.90	3.721462	0.68959	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096;ENST00000528025;ENST00000526416	D;D;D;D;D;D;D;D;D;D;D	0.94828	-3.53;-3.53;-3.53;-3.53;-3.53;-3.53;-3.53;-3.53;-3.53;-3.53;-3.53	4.39	4.39	0.52855	Calponin homology domain (5);	0.000000	0.64402	U	0.000012	D	0.94850	0.8336	L	0.35249	1.045	0.53688	D	0.99997	D;P;P;D;P;P;D;D	0.56968	0.971;0.949;0.949;0.958;0.949;0.949;0.978;0.978	D;D;D;D;D;D;D;D	0.69307	0.963;0.927;0.927;0.957;0.927;0.927;0.946;0.946	D	0.95054	0.8189	10	0.52906	T	0.07	.	14.4611	0.67450	0.0:1.0:0.0:0.0	.	215;174;166;325;156;188;192;188	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	K	188;192;188;156;325;166;174;215;215;232;165	ENSP00000344848:R188K;ENSP00000350277:R192K;ENSP00000346602:R188K;ENSP00000381756:R156K;ENSP00000323856:R325K;ENSP00000347044:R166K;ENSP00000348702:R174K;ENSP00000388180:R215K;ENSP00000434583:R215K;ENSP00000437303:R232K;ENSP00000433557:R165K	ENSP00000323856:R325K	R	-	2	0	PLEC	145082043	1.000000	0.71417	0.909000	0.35828	0.884000	0.51177	4.835000	0.62781	1.995000	0.58328	0.462000	0.41574	AGA	.	.	none		0.657	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		T	145010055	C	T	145010055	3	4	45	1	0	0	0	0	1	0	0	0	12061	913	32	2	13188	2	PLEC	8	145010055	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	15863	145010055	1353967	88	15540											
CNTLN	54875	hgsc.bcm.edu	37	chr9	17135258	17135258	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggtgaagaagggtcagggggCcggcgagggcctgggggggc	6	3	25	7	2	1	2	1	1	0	1	1	3	1	2	2	9	0	0	2	9	2	0			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr9:17135258C>A	ENST00000380647.3	+	1	279	c.195C>A	c.(193-195)ggC>ggA	p.G65G	CNTLN_ENST00000380641.4_Silent_p.G65G|CNTLN_ENST00000262360.5_Silent_p.G65G|CNTLN_ENST00000425824.1_Silent_p.G65G|CNTLN_ENST00000484374.1_3'UTR			Q9NXG0	CNTLN_HUMAN	centlein, centrosomal protein	65					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)		GGTCAGGGGGCCGGCGAGGGC	0.682																																					p.G65G		Atlas-SNP	.											.	CNTLN	128	.	0			c.C195A						PASS	.						12	17	16					9																	17135258		1913	4098	6011	SO:0001819	synonymous_variant	54875	exon1			AGGGGGCCGGCGA	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.195C>A	9.37:g.17135258C>A		102	0	0		83	25	0.301205	NM_017738	A5Z2X6|Q5VYJ0|Q8N1G9|Q9HAJ5	Silent	SNP	ENST00000380647.3	37	CCDS43789.1																																																																																			.	.	none		0.682	CNTLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051793.3	NM_017738		A	17135258	C	A	17135258	2	1	45	1	0	0	0	0	0	0	0	1	3641	726	26	4		4	CNTLN	9	17135258	Silent	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10		17135258	124078173	89	15541											
TRPM3	80036	hgsc.bcm.edu	37	chr9	73461506	73461506	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tatcaaaagatactcgcacaTactggaagaagaaaggacat	19	7	8	7	1	1	3	1	0	0	3	2	5	1	5	0	2	2	1	0	2	8	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr9:73461506T>C	ENST00000377111.2	-	4	707	c.464A>G	c.(463-465)tAt>tGt	p.Y155C	TRPM3_ENST00000408909.2_Splice_Site_p.Y2C|TRPM3_ENST00000396285.1_Splice_Site_p.Y2C|TRPM3_ENST00000360823.2_Splice_Site_p.Y2C|TRPM3_ENST00000377106.1_Splice_Site_p.Y2C|TRPM3_ENST00000377097.3_Splice_Site_p.Y2C|TRPM3_ENST00000358082.3_Splice_Site_p.Y2C|TRPM3_ENST00000377110.3_Splice_Site_p.Y155C|TRPM3_ENST00000357533.2_Splice_Site_p.Y157C|TRPM3_ENST00000396292.4_Splice_Site_p.Y2C|TRPM3_ENST00000361823.5_Splice_Site_p.Y2C|TRPM3_ENST00000423814.3_Splice_Site_p.Y157C|TRPM3_ENST00000377105.1_Splice_Site_p.Y2C|TRPM3_ENST00000377101.1_Splice_Site_p.Y2C|TRPM3_ENST00000396283.1_Splice_Site_p.Y2C|TRPM3_ENST00000396280.5_Splice_Site_p.Y2C	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	155					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						TACTCGCACATACTGGAAGAA	0.433																																					p.Y155C		Atlas-SNP	.											.	TRPM3	700	.	0			c.A464G						PASS	.						64	59	60					9																	73461506		2203	4300	6503	SO:0001630	splice_region_variant	80036	exon4			CGCACATACTGGA	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.463-1A>G	9.37:g.73461506T>C		101	0	0		79	58	0.734177	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Missense_Mutation	SNP	ENST00000377111.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	22.3|22.3	4.276497|4.276497	0.80580|0.80580	.|.	.|.	ENSG00000083067|ENSG00000083067	ENST00000377097|ENST00000377111;ENST00000377110;ENST00000377106;ENST00000360823;ENST00000377105;ENST00000357533;ENST00000408909;ENST00000396285;ENST00000396292;ENST00000358082;ENST00000423814;ENST00000377101;ENST00000396283;ENST00000361823;ENST00000455451	.|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	6.01|6.01	6.01|6.01	0.97437|0.97437	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.86234|0.86234	0.5884|0.5884	M|M	0.93016|0.93016	3.37|3.37	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D;D;D;D	.|0.89917	.|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	.|0.85130	.|0.954;0.981;0.996;0.996;0.992;0.997;0.994;0.995;0.997	D|D	0.89433|0.89433	0.3718|0.3718	5|10	.|0.87932	.|D	.|0	-6.475|-6.475	16.5285|16.5285	0.84344|0.84344	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|155;157;2;155;155;155;157;2;2	.|Q9HCF6;Q4VXD2;Q504Y1;Q9HCF6-2;Q9HCF6-10;Q9HCF6-4;A2A3F7;A2A3F4;G5E9G1	.|TRPM3_HUMAN;.;.;.;.;.;.;.;.	V|C	45|155;155;2;2;2;157;2;2;2;2;157;2;2;2;2	.|ENSP00000366315:Y155C;ENSP00000366314:Y155C;ENSP00000366310:Y2C;ENSP00000354066:Y2C;ENSP00000366309:Y2C;ENSP00000350140:Y157C;ENSP00000386127:Y2C;ENSP00000379581:Y2C;ENSP00000379587:Y2C;ENSP00000350791:Y2C;ENSP00000389542:Y157C;ENSP00000366305:Y2C;ENSP00000379579:Y2C;ENSP00000355395:Y2C	.|ENSP00000350140:Y157C	M|Y	-|-	1|2	0|0	TRPM3|TRPM3	72651326|72651326	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.899000|0.899000	0.52679|0.52679	7.960000|7.960000	0.87893|0.87893	2.307000|2.307000	0.77673|0.77673	0.528000|0.528000	0.53228|0.53228	ATG|TAT	.	.	none		0.433	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945	Missense_Mutation	C	73461506	T	C	73461506	5	2	45	1	0	0	0	0	0	0	1	0	16602	1420	49	3	4870	3	TRPM3	9	73461506	Splice_Site	SNP	T	TCGA-RQ-A68N-01A-11D-A31X-10	56326248	73461506	67751925	90	15542											
TRPM3	80036	hgsc.bcm.edu	37	chr9	73477848	73477848	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctttgttggaatggccaccTccttggaactcaatggtccc	7	12	10	12	0	1	0	1	0	0	0	3	2	3	2	4	4	1	2	4	4	3	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr9:73477848T>A	ENST00000377111.2	-	3	681	c.438A>T	c.(436-438)ggA>ggT	p.G146G	TRPM3_ENST00000408909.2_5'Flank|TRPM3_ENST00000396285.1_5'Flank|TRPM3_ENST00000360823.2_5'UTR|TRPM3_ENST00000377106.1_5'UTR|TRPM3_ENST00000377097.3_5'UTR|TRPM3_ENST00000358082.3_5'Flank|TRPM3_ENST00000377110.3_Silent_p.G146G|TRPM3_ENST00000357533.2_Silent_p.G148G|TRPM3_ENST00000396292.4_5'Flank|TRPM3_ENST00000361823.5_5'UTR|TRPM3_ENST00000423814.3_Silent_p.G148G|TRPM3_ENST00000377105.1_5'UTR|TRPM3_ENST00000377101.1_5'UTR|TRPM3_ENST00000396283.1_5'UTR|TRPM3_ENST00000437699.3_5'UTR|TRPM3_ENST00000396280.5_5'Flank	NM_001007471.2	NP_001007472.2	Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	146					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						AATGGCCACCTCCTTGGAACT	0.488																																					p.G146G		Atlas-SNP	.											TRPM3_ENST00000423814,NS,carcinoma,-2,2	TRPM3	700	2	0			c.A438T						PASS	.						210	198	202					9																	73477848		2203	4300	6503	SO:0001819	synonymous_variant	80036	exon3			GCCACCTCCTTGG	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.438A>T	9.37:g.73477848T>A		254	0	0		181	123	0.679558	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Silent	SNP	ENST00000377111.2	37		.	.	.	.	.	.	.	.	.	.	T	11.19	1.566901	0.28003	.	.	ENSG00000083067	ENST00000377097	.	.	.	5.95	3.44	0.39384	.	.	.	.	.	T	0.60431	0.2268	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57165	-0.7858	4	.	.	.	-14.1673	10.6299	0.45530	0.3559:0.0:0.0:0.6441	.	.	.	.	V	36	.	.	E	-	2	0	TRPM3	72667668	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.519000	0.35888	1.034000	0.39945	0.533000	0.62120	GAG	.	.	none		0.488	TRPM3-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000214157.5	NM_206945		A	73477848	T	A	73477848	2	1	45	1	0	0	0	0	0	0	0	1	16602	1538	54	5		5	TRPM3	9	73477848	Silent	SNP	T	TCGA-RQ-A68N-01A-11D-A31X-10	16342	73477848	67735583	91	15543											
C9orf41	138199	hgsc.bcm.edu	37	chr9	77614780	77614780	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	accagaatatttactttagaAggatccctgaaatgaaataa	18	11	6	6	0	0	4	0	2	0	2	1	5	1	5	2	1	1	0	2	1	8	6			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr9:77614780A>G	ENST00000376834.3	-	4	749	c.597T>C	c.(595-597)ccT>ccC	p.P199P	C9orf41_ENST00000376837.3_Intron	NM_152420.1	NP_689633.1	Q8N4J0	CI041_HUMAN	chromosome 9 open reading frame 41	199										endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|skin(1)|urinary_tract(2)	17						TTACTTTAGAAGGATCCCTGA	0.368																																					p.P199P		Atlas-SNP	.											.	C9orf41	57	.	0			c.T597C						PASS	.						83	83	83					9																	77614780		2203	4300	6503	SO:0001819	synonymous_variant	138199	exon4			TTTAGAAGGATCC	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.597T>C	9.37:g.77614780A>G		159	0	0		108	32	0.296296	NM_152420	Q7Z383|Q8N7C5	Silent	SNP	ENST00000376834.3	37	CCDS6649.1																																																																																			.	.	none		0.368	C9orf41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052703.1	NM_152420		G	77614780	A	G	77614780	2	3	45	1	0	0	0	0	0	0	0	1	2484	59	3	3		3	C9orf41	9	77614780	Silent	SNP	A	TCGA-RQ-A68N-01A-11D-A31X-10	4136932	77614780	63598651	92	15544											
UBQLN1	29979	hgsc.bcm.edu	37	chr9	86322427	86322427	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggcctcacctgctggacggaGctattctcgggcacggcgaa	7	7	14	13	4	2	0	1	0	1	0	3	3	2	2	2	5	2	3	2	5	2	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr9:86322427G>C	ENST00000376395.4	-	1	691	c.168C>G	c.(166-168)agC>agG	p.S56R	UBQLN1_ENST00000257468.7_Missense_Mutation_p.S56R|RP11-522I20.3_ENST00000531661.1_RNA|RP11-522I20.3_ENST00000524818.1_RNA	NM_013438.4|NM_053067.2	NP_038466.2|NP_444295.1	Q9UMX0	UBQL1_HUMAN	ubiquilin 1	56	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				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						GCTGGACGGAGCTATTCTCGG	0.692																																					p.S56R	Melanoma(186;1284 2073 12755 14558 18426)	Atlas-SNP	.											.	UBQLN1	49	.	0			c.C168G						PASS	.						21	22	21					9																	86322427		2201	4298	6499	SO:0001583	missense	29979	exon1			GACGGAGCTATTC	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.168C>G	9.37:g.86322427G>C	ENSP00000365576:p.Ser56Arg	103	0	0		79	12	0.151899	NM_053067	Q5T6J5|Q5T6J9|Q8IXS9|Q8N2Q3|Q9H0T8|Q9H3R4|Q9HAZ5	Missense_Mutation	SNP	ENST00000376395.4	37	CCDS6663.1	.	.	.	.	.	.	.	.	.	.	G	19.47	3.833689	0.71258	.	.	ENSG00000135018	ENST00000376395;ENST00000257468;ENST00000529923	T;T;T	0.80123	-0.8;-0.8;-1.34	3.88	2.97	0.34412	Ubiquitin supergroup (1);Ubiquitin (2);	0.000000	0.64402	D	0.000001	D	0.84224	0.5425	L	0.51853	1.615	0.46586	D	0.999117	D;D	0.76494	0.993;0.999	D;D	0.79108	0.949;0.992	T	0.83041	-0.0157	10	0.54805	T	0.06	.	8.8201	0.35020	0.1097:0.0:0.8903:0.0	.	56;56	Q9UMX0-2;Q9UMX0	.;UBQL1_HUMAN	R	56;56;30	ENSP00000365576:S56R;ENSP00000257468:S56R;ENSP00000434194:S30R	ENSP00000257468:S56R	S	-	3	2	UBQLN1	85512247	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	2.822000	0.48073	0.956000	0.37904	0.561000	0.74099	AGC	.	.	none		0.692	UBQLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000052834.1	NM_013438		C	86322427	G	C	86322427	3	2	45	1	0	0	0	0	1	0	0	0	16911	962	34	4	1645	4	UBQLN1	9	86322427	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	8707647	86322427	54891004	93	15545											
ANKS6	203286	hgsc.bcm.edu	37	chr9	101498863	101498863	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	actgctctcaaaggaagagtGaaagttgtgaatggtttcct	12	12	11	6	0	1	3	1	2	1	1	3	4	2	4	1	2	1	3	1	2	4	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr9:101498863G>A	ENST00000353234.4	-	15	2601	c.2554C>T	c.(2554-2556)Cac>Tac	p.H852Y	ANKS6_ENST00000375019.2_Missense_Mutation_p.H551Y|ANKS6_ENST00000540940.1_Missense_Mutation_p.H657Y|ANKS6_ENST00000375018.1_Missense_Mutation_p.H853Y			Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain containing 6	852						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)				AAGGAAGAGTGAAAGTTGTGA	0.483																																					p.H852Y		Atlas-SNP	.											.	ANKS6	59	.	0			c.C2554T						PASS	.						84	87	86					9																	101498863		1936	4135	6071	SO:0001583	missense	203286	exon15			AAGAGTGAAAGTT	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.2554C>T	9.37:g.101498863G>A	ENSP00000297837:p.His852Tyr	85	0	0		102	28	0.27451	NM_173551	A0SE62|Q5VSL0|Q5VSL2|Q5VSL3|Q5VSL4|Q68DB8|Q6P2R2|Q8N9L6|Q96D62	Missense_Mutation	SNP	ENST00000353234.4	37	CCDS43856.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	27.6|27.6	4.850167|4.850167	0.91277|0.91277	.|.	.|.	ENSG00000165138|ENSG00000165138	ENST00000375019;ENST00000375018;ENST00000353234;ENST00000540940|ENST00000444472	T;T;T;T|.	0.69435|.	1.78;-0.4;-0.4;2.03|.	5.31|5.31	5.31|5.31	0.75309|0.75309	.|.	0.049154|.	0.85682|.	D|.	0.000000|.	T|T	0.52273|0.52273	0.1724|0.1724	N|N	0.19112|0.19112	0.55|0.55	0.45439|0.45439	D|D	0.998416|0.998416	D;D|.	0.63880|.	0.993;0.988|.	D;D|.	0.73708|.	0.981;0.957|.	T|T	0.46512|0.46512	-0.9186|-0.9186	10|5	0.87932|.	D|.	0|.	-21.0365|-21.0365	16.8343|16.8343	0.85953|0.85953	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	853;852|.	Q68DC2-4;Q68DC2|.	.;ANKS6_HUMAN|.	Y|L	551;853;852;657|321	ENSP00000364159:H551Y;ENSP00000364158:H853Y;ENSP00000297837:H852Y;ENSP00000442189:H657Y|.	ENSP00000297837:H852Y|.	H|S	-|-	1|2	0|0	ANKS6|ANKS6	100538684|100538684	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	8.692000|8.692000	0.91284|0.91284	2.640000|2.640000	0.89533|0.89533	0.655000|0.655000	0.94253|0.94253	CAC|TCA	.	.	none		0.483	ANKS6-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277053.1	NM_173551		A	101498863	G	A	101498863	3	1	45	1	0	0	0	0	1	0	0	0	692	1290	45	2	65	2	ANKS6	9	101498863	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	15176436	101498863	39714568	94	15546											
OLFM1	10439	hgsc.bcm.edu	37	chr9	138011665	138011665	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgagagcgggctgtgggccGtgtacgccaccaaccagaac	10	4	14	13	4	0	2	0	0	0	2	0	3	0	2	4	2	4	2	4	2	3	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr9:138011665G>A	ENST00000371793.3	+	6	1350	c.1099G>A	c.(1099-1101)Gtg>Atg	p.V367M	OLFM1_ENST00000371796.3_Missense_Mutation_p.V340M|OLFM1_ENST00000252854.4_Missense_Mutation_p.V349M	NM_001282611.1	NP_001269540.1	Q99784	NOE1_HUMAN	olfactomedin 1	367	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)		GCTGTGGGCCGTGTACGCCAC	0.627																																					p.V349M		Atlas-SNP	.											.	OLFM1	57	.	0			c.G1045A						PASS	.						77	60	66					9																	138011665		2203	4300	6503	SO:0001583	missense	10439	exon6			TGGGCCGTGTACG	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.1099G>A	9.37:g.138011665G>A	ENSP00000360858:p.Val367Met	88	0	0		85	59	0.694118	NM_014279	Q53XZ8|Q6IMJ4|Q6IMJ5|Q8N8R0|Q969S7|Q99452	Missense_Mutation	SNP	ENST00000371793.3	37		.	.	.	.	.	.	.	.	.	.	G	21.7	4.190584	0.78789	.	.	ENSG00000130558	ENST00000252854;ENST00000371796;ENST00000371793	D;D;D	0.90676	-2.71;-2.71;-2.71	5.07	5.07	0.68467	Olfactomedin-like (3);Quinonprotein alcohol dehydrogenase-like (1);	0.061993	0.64402	D	0.000004	D	0.95089	0.8409	M	0.75447	2.3	0.58432	D	0.999999	D;D	0.89917	0.989;1.0	P;D	0.74348	0.874;0.983	D	0.95612	0.8673	10	0.87932	D	0	.	18.4324	0.90630	0.0:0.0:1.0:0.0	.	367;349	Q99784;Q6IMJ8	NOE1_HUMAN;.	M	349;340;367	ENSP00000252854:V349M;ENSP00000360861:V340M;ENSP00000360858:V367M	ENSP00000252854:V349M	V	+	1	0	OLFM1	137151486	1.000000	0.71417	1.000000	0.80357	0.833000	0.47200	9.571000	0.98176	2.357000	0.79964	0.561000	0.74099	GTG	.	.	none		0.627	OLFM1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000054974.1	NM_014279		A	138011665	G	A	138011665	3	1	45	1	0	0	0	0	1	0	0	0	10861	1145	40	1	1077	1	OLFM1	9	138011665	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	36512802	138011665	3201766	95	15547											
SOHLH1	402381	hgsc.bcm.edu	37	chr9	138590933	138590933	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggcgggcccgagccccgggcCgagtcctcgcagcaggagag	6	2	18	15	5	0	1	0	0	0	1	2	4	1	1	5	4	2	2	5	4	0	0			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr9:138590933C>T	ENST00000298466.5	-	2	165	c.105G>A	c.(103-105)tcG>tcA	p.S35S	SOHLH1_ENST00000425225.1_Silent_p.S35S	NM_001012415.2	NP_001012415	Q5JUK2	SOLH1_HUMAN	spermatogenesis and oogenesis specific basic helix-loop-helix 1	35					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)		AGCCCCGGGCCGAGTCCTCGC	0.701																																					p.S35S		Atlas-SNP	.											.	SOHLH1	70	.	0			c.G105A						PASS	.						12	14	13					9																	138590933		2184	4273	6457	SO:0001819	synonymous_variant	402381	exon2			CCGGGCCGAGTCC	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.105G>A	9.37:g.138590933C>T		69	0	0		52	38	0.730769	NM_001012415	C9JG81|Q5EE14|Q5EGC2|Q8NEE3	Silent	SNP	ENST00000298466.5	37	CCDS35174.1																																																																																			.	.	none		0.701	SOHLH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055018.2	NM_001012415		T	138590933	C	T	138590933	2	4	45	1	0	0	0	0	0	0	0	1	14938	639	23	1		1	SOHLH1	9	138590933	Silent	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	579268	138590933	2622498	96	15548											
DPP7	29952	hgsc.bcm.edu	37	chr9	140009157	140009157	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggaccggggcccagggagcGgagcccatgtcgccttccgc	6	4	16	15	4	0	0	0	0	0	0	2	3	1	3	5	5	2	0	5	5	0	1	rs557666825	byFrequency	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr9:140009157G>T	ENST00000371579.2	-	1	13	c.9C>A	c.(7-9)tcC>tcA	p.S3S		NM_013379.2	NP_037511.2	Q9UHL4	DPP2_HUMAN	dipeptidyl-peptidase 7	3						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)		CCCAGGGAGCGGAGCCCATGT	0.811													G|||	3	0.000599042	0.0	0.0	5008	,	,		6530	0.0		0.001	False		,,,				2504	0.002				p.S3S		Atlas-SNP	.											.	DPP7	22	.	0			c.C9A						PASS	.						1	1	1					9																	140009157		671	1474	2145	SO:0001819	synonymous_variant	29952	exon1			GGGAGCGGAGCCC	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.9C>A	9.37:g.140009157G>T		3	0	0		6	6	1	NM_013379	A8K7U7|Q5VSF1|Q969X4	Silent	SNP	ENST00000371579.2	37	CCDS7030.1																																																																																			.	.	none		0.811	DPP7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055279.1	NM_013379		T	140009157	G	T	140009157	2	4	45	1	0	0	0	0	0	0	0	1	4733	1103	39	4		4	DPP7	9	140009157	Silent	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	1418224	140009157	1204274	97	15549											
COBRA1	25920	hgsc.bcm.edu	37	chr9	140158730	140158730	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggacgcctgcatccgagagCggttcgtggacagcaagagg	9	6	16	10	4	0	2	0	0	0	2	2	5	1	4	2	4	3	3	2	4	1	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr9:140158730C>T	ENST00000343053.4	+	6	1154	c.817C>T	c.(817-819)Cgg>Tgg	p.R273W		NM_015456.3	NP_056271.2	Q8WX92	NELFB_HUMAN	negative elongation factor complex member B	273					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)											CATCCGAGAGCGGTTCGTGGA	0.657																																					p.R273W		Atlas-SNP	.											.	.	.	.	0			c.C817T						PASS	.						51	48	49					9																	140158730		2200	4299	6499	SO:0001583	missense	25920	exon6			CGAGAGCGGTTCG	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.817C>T	9.37:g.140158730C>T	ENSP00000339495:p.Arg273Trp	38	0	0		33	10	0.30303	NM_015456	A2BFA3|Q96EW5|Q9H9R4|Q9ULN8|Q9Y3W0	Missense_Mutation	SNP	ENST00000343053.4	37	CCDS7040.1	.	.	.	.	.	.	.	.	.	.	C	19.93	3.917586	0.73098	.	.	ENSG00000188986	ENST00000343053	.	.	.	4.85	2.75	0.32379	.	0.107079	0.64402	D	0.000008	T	0.55657	0.1934	L	0.38175	1.15	0.35791	D	0.822412	D	0.65815	0.995	P	0.59889	0.865	T	0.66232	-0.5975	9	0.87932	D	0	-52.3267	10.4259	0.44378	0.5916:0.4084:0.0:0.0	.	273	Q8WX92	NELFB_HUMAN	W	273	.	ENSP00000339495:R273W	R	+	1	2	COBRA1	139278551	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	4.438000	0.59961	1.001000	0.39076	0.313000	0.20887	CGG	.	.	none		0.657	NELFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254710.1	NM_015456		T	140158730	C	T	140158730	3	4	45	1	0	0	0	0	1	0	0	0	3657	759	27	1	839	1	COBRA1	9	140158730	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	149573	140158730	1054701	98	15550											
ARHGAP21	57584	hgsc.bcm.edu	37	chr10	24880821	24880821	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaagcatgaacttacgtgctGgatgagcgtttctacaatct	11	12	10	8	2	2	2	0	2	2	0	2	4	2	3	0	1	6	3	0	1	5	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr10:24880821G>A	ENST00000396432.2	-	22	4483	c.3997C>T	c.(3997-3999)Cag>Tag	p.Q1333*	ARHGAP21_ENST00000320481.6_Nonsense_Mutation_p.Q1120*	NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	1332	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				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						CTTACGTGCTGGATGAGCGTT	0.458																																					p.Q1333X		Atlas-SNP	.											.	ARHGAP21	185	.	0			c.C3997T						PASS	.						235	192	207					10																	24880821		2203	4300	6503	SO:0001587	stop_gained	57584	exon22			CGTGCTGGATGAG	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.3997C>T	10.37:g.24880821G>A	ENSP00000379709:p.Gln1333*	119	0	0		72	9	0.125	NM_020824	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Nonsense_Mutation	SNP	ENST00000396432.2	37	CCDS7144.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	43|43	10.326684|10.326684	0.99383|0.99383	.|.	.|.	ENSG00000107863|ENSG00000107863	ENST00000418033|ENST00000396432;ENST00000447364;ENST00000320481	.|.	.|.	.|.	5.29|5.29	5.29|5.29	0.74685|0.74685	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|.	0.76586|.	0.4008|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.76727|.	-0.2853|.	3|.	.|0.49607	.|T	.|0.09	.|.	19.294|19.294	0.94115|0.94115	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|.	.|.	.|.	L|X	146|1333;782;1120	.|.	.|ENSP00000365604:Q1120X	P|Q	-|-	2|1	0|0	ARHGAP21|ARHGAP21	24920827|24920827	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.913000|0.913000	0.54294|0.54294	9.805000|9.805000	0.99149|0.99149	2.642000|2.642000	0.89623|0.89623	0.563000|0.563000	0.77884|0.77884	CCA|CAG	.	.	none		0.458	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824		A	24880821	G	A	24880821	4	1	45	1	0	0	0	0	0	1	0	0	871	1357	47	2	1899	2	ARHGAP21	10	24880821	Nonsense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10		24880821	110653926	99	15551											
MYO3A	53904	hgsc.bcm.edu	37	chr10	26446318	26446318	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcaaaccaaatagtgagcGtcaggcaagaaaatatgaca	19	6	8	8	1	2	3	2	2	0	1	2	3	2	3	1	1	2	1	1	1	7	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr10:26446318G>A	ENST00000265944.5	+	26	3039	c.2873G>A	c.(2872-2874)cGt>cAt	p.R958H	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.R958H		Atlas-SNP	.											MYO3A,caecum,carcinoma,0,3	MYO3A	371	3	1	Substitution - Missense(1)	breast(1)	c.G2873A						PASS	.						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>A	10.37:g.26446318G>A	ENSP00000265944:p.Arg958His	169	0	0		153	71	0.464052	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	G	34	5.320239	0.95682	.	.	ENSG00000095777	ENST00000265944	D	0.87887	-2.31	5.31	5.31	0.75309	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.93713	0.7991	M	0.78223	2.4	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.94022	0.7293	10	0.72032	D	0.01	.	19.3468	0.94367	0.0:0.0:1.0:0.0	.	958	Q8NEV4	MYO3A_HUMAN	H	958	ENSP00000265944:R958H	ENSP00000265944:R958H	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	.	.	none		0.408	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433		A	26446318	G	A	26446318	3	1	45	1	0	0	0	0	1	0	0	0	10085	1145	40	1	2967	1	MYO3A	10	26446318	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	1565497	26446318	109088429	100	15552											
FAM13C	220965	hgsc.bcm.edu	37	chr10	61028362	61028362	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcaaatttccgaattttcCgcttgaggctctggatgtgc	7	15	9	10	2	2	1	1	1	1	0	4	3	4	2	2	2	1	2	2	2	2	5	rs534813877		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr10:61028362C>T	ENST00000373868.2	-	8	980	c.893G>A	c.(892-894)cGg>cAg	p.R298Q	FAM13C_ENST00000419214.2_Missense_Mutation_p.R298Q|FAM13C_ENST00000422313.2_Missense_Mutation_p.R298Q|FAM13C_ENST00000373867.3_Missense_Mutation_p.R215Q|FAM13C_ENST00000442566.3_Missense_Mutation_p.R319Q|FAM13C_ENST00000277705.6_Missense_Mutation_p.R319Q|FAM13C_ENST00000435852.2_Missense_Mutation_p.R298Q|FAM13C_ENST00000468840.2_Missense_Mutation_p.R215Q	NM_198215.3	NP_937858.2	Q8NE31	FA13C_HUMAN	family with sequence similarity 13, member C	298								p.R298L(1)		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						CCGAATTTTCCGCTTGAGGCT	0.502													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18151	0.0		0.0	False		,,,				2504	0.0				p.R298Q		Atlas-SNP	.											FAM13C,mouth,carcinoma,0,1	FAM13C	124	1	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.G893A						PASS	.						70	69	69					10																	61028362		2203	4300	6503	SO:0001583	missense	220965	exon8			ATTTTCCGCTTGA	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.893G>A	10.37:g.61028362C>T	ENSP00000362975:p.Arg298Gln	71	0	0		50	11	0.22	NM_198215	B7ZB77|Q5T631|Q6P2M3|Q99787	Missense_Mutation	SNP	ENST00000373868.2	37	CCDS7255.1	.	.	.	.	.	.	.	.	.	.	C	32	5.178996	0.94846	.	.	ENSG00000148541	ENST00000373867;ENST00000373868;ENST00000442566;ENST00000277705;ENST00000419214;ENST00000468840;ENST00000435852;ENST00000422313;ENST00000468696	T;T;T;T;T;T;T;T;T	0.77750	-1.12;-1.12;-1.12;-1.12;0.9;-1.12;-1.12;-1.12;-1.12	6.17	6.17	0.99709	.	0.000000	0.64402	D	0.000001	D	0.86768	0.6012	L	0.55834	1.745	0.39444	D	0.967292	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.998;0.978;0.993;0.984;0.998	D	0.84996	0.0897	10	0.45353	T	0.12	-9.5074	20.8794	0.99867	0.0:1.0:0.0:0.0	.	298;215;298;298;298	B7Z2K3;B7ZB77;Q8NE31-2;Q8NE31-3;Q8NE31	.;.;.;.;FA13C_HUMAN	Q	215;298;319;319;298;215;298;298;76	ENSP00000362974:R215Q;ENSP00000362975:R298Q;ENSP00000395661:R319Q;ENSP00000277705:R319Q;ENSP00000391993:R298Q;ENSP00000423896:R215Q;ENSP00000392302:R298Q;ENSP00000400241:R298Q;ENSP00000445068:R76Q	ENSP00000277705:R319Q	R	-	2	0	FAM13C	60698368	1.000000	0.71417	0.997000	0.53966	0.986000	0.74619	3.452000	0.52971	2.941000	0.99782	0.655000	0.94253	CGG	.	.	none		0.502	FAM13C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048162.2			T	61028362	C	T	61028362	3	4	45	1	0	0	0	0	1	0	0	0	5459	652	23	1	892	1	FAM13C	10	61028362	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	34582044	61028362	74506385	101	15553											
CTNNA3	29119	hgsc.bcm.edu	37	chr10	68940122	68940122	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgaagagcctggcgaatggCgttgcattctgcgataatcc	9	10	12	10	3	1	2	0	1	1	1	2	4	2	2	2	2	3	2	2	2	3	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr10:68940122C>T	ENST00000433211.2	-	7	1174	c.1000G>A	c.(1000-1002)Gcc>Acc	p.A334T	CTNNA3_ENST00000545309.1_Missense_Mutation_p.A334T|CTNNA3_ENST00000373744.4_Missense_Mutation_p.A334T	NM_013266.2	NP_037398.2			catenin (cadherin-associated protein), alpha 3									p.A334T(2)		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						TGGCGAATGGCGTTGCATTCT	0.517																																					p.A334T		Atlas-SNP	.											CTNNA3_ENST00000433211,colon,carcinoma,0,2	CTNNA3	401	2	2	Substitution - Missense(2)	large_intestine(2)	c.G1000A						PASS	.						133	114	120					10																	68940122		2203	4300	6503	SO:0001583	missense	29119	exon7			GAATGGCGTTGCA	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.1000G>A	10.37:g.68940122C>T	ENSP00000389714:p.Ala334Thr	74	0	0		78	11	0.141026	NM_013266		Missense_Mutation	SNP	ENST00000433211.2	37	CCDS7269.1	.	.	.	.	.	.	.	.	.	.	C	17.46	3.396049	0.62177	.	.	ENSG00000183230	ENST00000433211;ENST00000373744;ENST00000545309	T;T;T	0.38401	1.14;1.14;1.23	5.83	4.85	0.62838	.	0.000000	0.50627	D	0.000112	T	0.59128	0.2171	M	0.86573	2.825	0.36848	D	0.887738	D;D;D;P	0.56746	0.977;0.977;0.965;0.74	P;P;P;B	0.56343	0.604;0.604;0.796;0.157	T	0.71111	-0.4687	10	0.62326	D	0.03	-9.5472	14.885	0.70560	0.2138:0.7862:0.0:0.0	.	334;334;334;334	A8K141;F2Z2R0;Q9UI47-2;Q9UI47	.;.;.;CTNA3_HUMAN	T	334	ENSP00000389714:A334T;ENSP00000362849:A334T;ENSP00000441444:A334T	ENSP00000362849:A334T	A	-	1	0	CTNNA3	68610128	0.937000	0.31787	0.885000	0.34714	0.939000	0.58152	2.034000	0.41145	2.753000	0.94483	0.585000	0.79938	GCC	.	.	none		0.517	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048282.2	NM_013266		T	68940122	C	T	68940122	3	4	45	1	0	0	0	0	1	0	0	0	4016	768	27	1	1735	1	CTNNA3	10	68940122	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	7911760	68940122	66594625	102	15554											
CDH23	414152	hgsc.bcm.edu	37	chr10	73498388	73498388	+	5'Flank	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	caaggcctgggaccctgatgCtggcagcaatgggcaggtgg	8	6	17	10	0	0	1	0	1	0	0	0	2	0	2	2	6	2	4	2	6	2	0			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr10:73498388C>T	ENST00000398786.2	-	0	0				CDH23_ENST00000224721.6_Missense_Mutation_p.A1453V	NM_001168390.1	NP_001161862.1	Q8TEF2	CJ105_HUMAN	chromosome 10 open reading frame 105							integral component of membrane (GO:0016021)											GACCCTGATGCTGGCAGCAAT	0.647																																					p.A1448V		Atlas-SNP	.											.	CDH23	365	.	0			c.C4343T						PASS	.						40	46	44					10																	73498388		2075	4228	6303	SO:0001631	upstream_gene_variant	64072	exon33			CTGATGCTGGCAG	AK074172	CCDS44430.1	10q22.1	2012-06-01			ENSG00000214688	ENSG00000214688			20304	protein-coding gene	gene with protein product							Standard	NM_001164375		Approved	FLJ00245	uc001jsa.2	Q8TEF2	OTTHUMG00000018427		10.37:g.73498388C>T	Exception_encountered	41	0	0		33	7	0.212121	NM_022124		Missense_Mutation	SNP	ENST00000398786.2	37	CCDS44430.1	.	.	.	.	.	.	.	.	.	.	C	16.04	3.011477	0.54468	.	.	ENSG00000107736	ENST00000398860;ENST00000398855;ENST00000224721;ENST00000398792	.	.	.	5.38	4.46	0.54185	Cadherin (4);Cadherin-like (1);	0.198265	0.42420	D	0.000712	T	0.47414	0.1444	N	0.25094	0.71	0.80722	D	1	B;B	0.28026	0.009;0.198	B;B	0.39152	0.022;0.292	T	0.45352	-0.9267	9	0.40728	T	0.16	.	9.8858	0.41260	0.1395:0.7872:0.0:0.0733	.	268;1448	E7ERT0;Q9H251	.;CAD23_HUMAN	V	1453;1448;1451;268	.	ENSP00000224721:A1453V	A	+	2	0	CDH23	73168394	0.998000	0.40836	0.076000	0.20297	0.710000	0.40934	4.206000	0.58473	2.683000	0.91414	0.561000	0.74099	GCT	.	.	none		0.647	C10orf105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048551.2	NM_001164375		T	73498388	C	T	73498388	1	4	45	0	1	0	0	0	0	0	0	0	3110	797	28	2		2	CDH23	10	73498388	5'Flank	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	4558266	73498388	62036359	103	15555											
NFKB2	4791	hgsc.bcm.edu	37	chr10	104160708	104160708	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctgctcgcacccccagctccGggccaacgtgaacgctcgca	7	5	10	19	5	0	1	0	1	0	0	3	1	1	1	4	1	4	5	4	1	2	0	rs574309302		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr10:104160708G>A	ENST00000369966.3	+	18	2223	c.1973G>A	c.(1972-1974)cGg>cAg	p.R658Q	NFKB2_ENST00000428099.1_Missense_Mutation_p.R658Q|NFKB2_ENST00000189444.6_Missense_Mutation_p.R658Q	NM_001077494.2	NP_001070962.1	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)	658			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)	CCCCAGCTCCGGGCCAACGTG	0.667			T	IGH@	B-NHL								g|||	1	0.000199681	0.0008	0.0	5008	,	,		16003	0.0		0.0	False		,,,				2504	0.0				p.R658Q		Atlas-SNP	.		Dom	yes		10	10q24	4791	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)		L	NFKB2,NS,carcinoma,+1,1	NFKB2	48	1	0			c.G1973A						scavenged	.						28	35	33					10																	104160708		2129	4229	6358	SO:0001583	missense	4791	exon18			AGCTCCGGGCCAA	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.1973G>A	10.37:g.104160708G>A	ENSP00000358983:p.Arg658Gln	97	2	0.0206186		90	27	0.3	NM_001077494	A8K9D9|D3DR83|Q04860|Q9BU75|Q9H471|Q9H472	Missense_Mutation	SNP	ENST00000369966.3	37	CCDS41564.1	.	.	.	.	.	.	.	.	.	.	g	11.98	1.801863	0.31869	.	.	ENSG00000077150	ENST00000428099;ENST00000369966;ENST00000336486;ENST00000189444	T;T;T	0.63913	-0.07;-0.07;-0.07	4.52	-0.74	0.11115	Ankyrin repeat-containing domain (4);	0.547844	0.19667	N	0.108844	T	0.34250	0.0891	N	0.08118	0	0.20489	N	0.999895	B;B	0.28820	0.224;0.224	B;B	0.21546	0.035;0.035	T	0.15954	-1.0419	10	0.35671	T	0.21	.	8.7763	0.34765	0.6305:0.0:0.3695:0.0	.	658;658	Q00653;A8K9D9	NFKB2_HUMAN;.	Q	658	ENSP00000410256:R658Q;ENSP00000358983:R658Q;ENSP00000189444:R658Q	ENSP00000189444:R658Q	R	+	2	0	NFKB2	104150698	0.989000	0.36119	0.926000	0.36857	0.560000	0.35617	1.729000	0.38115	-0.235000	0.09767	-0.330000	0.08379	CGG	.	.	none		0.667	NFKB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050080.2			A	104160708	G	A	104160708	3	1	45	1	0	0	0	0	1	0	0	0	10385	1116	39	1	2039	1	NFKB2	10	104160708	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	30662320	104160708	31374039	104	15556											
NRAP	4892	hgsc.bcm.edu	37	chr10	115412746	115412746	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttgataagcaggtgtgatcAtggctggaaagctccccttg	9	12	12	8	0	1	2	1	2	0	0	2	3	2	3	2	3	2	3	2	3	2	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr10:115412746A>G	ENST00000359988.3	-	6	762	c.518T>C	c.(517-519)aTg>aCg	p.M173T	NRAP_ENST00000369358.4_Missense_Mutation_p.M173T|NRAP_ENST00000369360.3_Missense_Mutation_p.M173T|NRAP_ENST00000360478.3_Missense_Mutation_p.M173T	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)		AGGTGTGATCATGGCTGGAAA	0.463																																					p.M173T		Atlas-SNP	.											.	NRAP	208	.	0			c.T518C						PASS	.						179	156	164					10																	115412746		2203	4300	6503	SO:0001583	missense	4892	exon6			GTGATCATGGCTG		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.518T>C	10.37:g.115412746A>G	ENSP00000353078:p.Met173Thr	76	0	0		77	28	0.363636	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	37	CCDS7579.1	.	.	.	.	.	.	.	.	.	.	A	6.482	0.457167	0.12283	.	.	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	T;T;T;T	0.16897	2.56;2.52;2.44;2.31	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.16085	0.0387	L	0.42245	1.32	0.49483	D	0.999797	B;B;B	0.19706	0.038;0.02;0.017	B;B;B	0.21708	0.024;0.036;0.016	T	0.06391	-1.0829	10	0.07813	T	0.8	.	16.3782	0.83418	1.0:0.0:0.0:0.0	.	173;173;173	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	T	173	ENSP00000358365:M173T;ENSP00000358367:M173T;ENSP00000353078:M173T;ENSP00000353666:M173T	ENSP00000353078:M173T	M	-	2	0	NRAP	115402736	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.287000	0.72671	2.277000	0.76020	0.528000	0.53228	ATG	.	.	none		0.463	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175		G	115412746	A	G	115412746	3	3	45	1	0	0	0	0	1	0	0	0	10647	217	8	3	4822	3	NRAP	10	115412746	Missense_Mutation	SNP	A	TCGA-RQ-A68N-01A-11D-A31X-10	11252038	115412746	20122001	105	15557											
TCERG1L	256536	hgsc.bcm.edu	37	chr10	132896590	132896590	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggagacactttagattccTctagaagtttcttgaattct	10	16	8	7	0	3	4	0	1	3	3	4	5	4	4	1	1	0	1	1	1	4	7			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr10:132896590T>G	ENST00000368642.4	-	11	1668	c.1583A>C	c.(1582-1584)gAg>gCg	p.E528A	RP11-462G8.3_ENST00000436942.1_RNA	NM_174937.3	NP_777597.2	Q5VWI1	TCRGL_HUMAN	transcription elongation regulator 1-like	528	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)		TTTAGATTCCTCTAGAAGTTT	0.368																																					p.E528A		Atlas-SNP	.											.	TCERG1L	91	.	0			c.A1583C						PASS	.						75	65	69					10																	132896590		2157	4224	6381	SO:0001583	missense	256536	exon11			GATTCCTCTAGAA	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.1583A>C	10.37:g.132896590T>G	ENSP00000357631:p.Glu528Ala	46	0	0		45	14	0.311111	NM_174937	Q5VWI2|Q86XM8	Missense_Mutation	SNP	ENST00000368642.4	37	CCDS7662.2	.	.	.	.	.	.	.	.	.	.	T	20.6	4.022569	0.75275	.	.	ENSG00000176769	ENST00000368642	T	0.32753	1.44	4.83	4.83	0.62350	FF domain (4);	0.000000	0.64402	D	0.000003	T	0.47691	0.1459	L	0.53671	1.685	0.80722	D	1	D	0.61697	0.99	D	0.64410	0.925	T	0.45906	-0.9229	10	0.54805	T	0.06	-8.1045	13.2339	0.59958	0.0:0.0:0.0:1.0	.	528	Q5VWI1	TCRGL_HUMAN	A	528	ENSP00000357631:E528A	ENSP00000357631:E528A	E	-	2	0	TCERG1L	132786580	1.000000	0.71417	0.997000	0.53966	0.985000	0.73830	6.505000	0.73708	1.806000	0.52798	0.460000	0.39030	GAG	.	.	none		0.368	TCERG1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091619.2	NM_174937		G	132896590	T	G	132896590	3	3	45	1	0	0	0	0	1	0	0	0	15701	1551	54	5	185	5	TCERG1L	10	132896590	Missense_Mutation	SNP	T	TCGA-RQ-A68N-01A-11D-A31X-10	17483844	132896590	2638157	106	15558											
OR52W1	120787	hgsc.bcm.edu	37	chr11	6221264	6221264	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	acctcacacaccgctttggtCatcacactgtcccaaagcct	10	9	5	17	1	3	0	3	0	0	0	4	0	4	0	4	1	1	1	4	1	1	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr11:6221264C>T	ENST00000311352.2	+	1	889	c.811C>T	c.(811-813)Cat>Tat	p.H271Y	RP11-290F24.6_ENST00000600308.1_lincRNA	NM_001005178.1	NP_001005178.1	Q6IF63	O52W1_HUMAN	olfactory receptor, family 52, subfamily W, 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)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)	11		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;2.13e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCGCTTTGGTCATCACACTGT	0.542																																					p.H271Y		Atlas-SNP	.											.	OR52W1	33	.	0			c.C811T						PASS	.						446	414	425					11																	6221264		2201	4296	6497	SO:0001583	missense	120787	exon1			TTTGGTCATCACA	AB065511	CCDS31407.1	11p15.4	2012-08-09		2004-03-10	ENSG00000175485	ENSG00000175485		"GPCR / Class A : Olfactory receptors"	15239	protein-coding gene	gene with protein product				OR52W1P			Standard	NM_001005178		Approved		uc010qzz.2	Q6IF63	OTTHUMG00000165378	ENST00000311352.2:c.811C>T	11.37:g.6221264C>T	ENSP00000309673:p.His271Tyr	51	0	0		50	8	0.16	NM_001005178	Q8NH78	Missense_Mutation	SNP	ENST00000311352.2	37	CCDS31407.1	.	.	.	.	.	.	.	.	.	.	C	6.164	0.398365	0.11696	.	.	ENSG00000175485	ENST00000311352	T	0.37058	1.22	4.59	4.59	0.56863	GPCR, rhodopsin-like superfamily (1);	0.392383	0.18710	N	0.133340	T	0.19366	0.0465	N	0.08118	0	0.22811	N	0.998706	P	0.41313	0.745	B	0.38428	0.273	T	0.08027	-1.0742	10	0.48119	T	0.1	.	10.3227	0.43775	0.1965:0.8035:0.0:0.0	.	271	Q6IF63	O52W1_HUMAN	Y	271	ENSP00000309673:H271Y	ENSP00000309673:H271Y	H	+	1	0	OR52W1	6177840	0.023000	0.18921	0.991000	0.47740	0.037000	0.13140	3.010000	0.49559	2.518000	0.84900	0.563000	0.77884	CAT	.	.	none		0.542	OR52W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383758.1	NM_001005178		T	6221264	C	T	6221264	3	4	45	1	0	0	0	0	1	0	0	0	11141	826	29	2	813	2	OR52W1	11	6221264	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10		6221264	128785252	107	15559											
SLC5A12	159963	hgsc.bcm.edu	37	chr11	26700336	26700336	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tgtagtaaaggtaggagatcGagtaccaggtatcagctatt	13	11	12	5	1	1	1	1	0	0	1	2	3	1	1	1	3	2	6	1	3	7	7			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr11:26700336G>A	ENST00000396005.3	-	13	1811	c.1502C>T	c.(1501-1503)tCg>tTg	p.S501L		NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	501					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						GTAGGAGATCGAGTACCAGGT	0.468																																					p.S501L		Atlas-SNP	.											.	SLC5A12	134	.	0			c.C1502T						PASS	.						122	121	121					11																	26700336		1978	4171	6149	SO:0001583	missense	159963	exon13			GAGATCGAGTACC	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.1502C>T	11.37:g.26700336G>A	ENSP00000379326:p.Ser501Leu	117	0	0		107	7	0.0654206	NM_178498	Q86UC7	Missense_Mutation	SNP	ENST00000396005.3	37	CCDS7860.2	.	.	.	.	.	.	.	.	.	.	G	21.1	4.102821	0.76983	.	.	ENSG00000148942	ENST00000396005	T	0.77750	-1.12	5.95	5.95	0.96441	.	0.451885	0.21540	N	0.072906	D	0.84406	0.5465	M	0.72576	2.205	0.80722	D	1	D	0.56035	0.974	P	0.55391	0.775	D	0.85350	0.1101	10	0.72032	D	0.01	.	14.7327	0.69393	0.0:0.1448:0.8552:0.0	.	501	Q1EHB4	SC5AC_HUMAN	L	501	ENSP00000379326:S501L	ENSP00000379326:S501L	S	-	2	0	SLC5A12	26656912	1.000000	0.71417	0.842000	0.33263	0.625000	0.37756	5.509000	0.67012	2.825000	0.97269	0.655000	0.94253	TCG	.	.	none		0.468	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498		A	26700336	G	A	26700336	3	1	45	1	0	0	0	0	1	0	0	0	14679	1059	37	1	366	1	SLC5A12	11	26700336	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	20479072	26700336	108306180	108	15560											
SLC5A12	159963	hgsc.bcm.edu	37	chr11	26743090	26743090	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agctgacatgaagctggctgTcagagacaagccgacagggc	12	5	14	10	1	1	3	1	2	0	1	1	5	1	3	1	2	3	3	1	2	2	0			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr11:26743090T>C	ENST00000396005.3	-	1	481	c.172A>G	c.(172-174)Aca>Gca	p.T58A	SLC5A12_ENST00000280467.6_Missense_Mutation_p.T58A	NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	58					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						AAGCTGGCTGTCAGAGACAAG	0.517																																					p.T58A		Atlas-SNP	.											.	SLC5A12	134	.	0			c.A172G						PASS	.						68	68	68					11																	26743090		2203	4299	6502	SO:0001583	missense	159963	exon1			TGGCTGTCAGAGA	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.172A>G	11.37:g.26743090T>C	ENSP00000379326:p.Thr58Ala	207	1	0.00483092		218	107	0.490826	NM_178498	Q86UC7	Missense_Mutation	SNP	ENST00000396005.3	37	CCDS7860.2	.	.	.	.	.	.	.	.	.	.	T	15.48	2.845233	0.51164	.	.	ENSG00000148942	ENST00000396005;ENST00000280467	D;D	0.86497	-2.13;-2.13	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	D	0.88115	0.6350	L	0.39514	1.22	0.58432	D	0.999997	B;P	0.43701	0.074;0.815	B;P	0.54706	0.043;0.759	D	0.85149	0.0985	10	0.19147	T	0.46	.	15.7638	0.78110	0.0:0.0:0.0:1.0	.	58;58	Q1EHB4-2;Q1EHB4	.;SC5AC_HUMAN	A	58	ENSP00000379326:T58A;ENSP00000280467:T58A	ENSP00000280467:T58A	T	-	1	0	SLC5A12	26699666	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.066000	0.64351	2.135000	0.66039	0.477000	0.44152	ACA	.	.	none		0.517	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498		C	26743090	T	C	26743090	3	2	45	1	0	0	0	0	1	0	0	0	14679	1667	58	3	1744	3	SLC5A12	11	26743090	Missense_Mutation	SNP	T	TCGA-RQ-A68N-01A-11D-A31X-10	42754	26743090	108263426	109	15561											
OR4C3	256144	hgsc.bcm.edu	37	chr11	48346815	48346815	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tatggctcctaaactcattgCtgactcattgtatgagggga	10	13	10	8	0	2	2	2	2	0	0	3	3	3	3	1	3	2	3	1	3	4	5			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr11:48346815C>A	ENST00000319856.4	+	1	344	c.323C>A	c.(322-324)gCt>gAt	p.A108D		NM_001004702.1	NP_001004702.1	Q8NH37	OR4C3_HUMAN	olfactory receptor, family 4, subfamily C, member 3	81						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A108V(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(18)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	32						AAACTCATTGCTGACTCATTG	0.463																																					p.A108D		Atlas-SNP	.											OR4C3,mouth,carcinoma,0,1	OR4C3	75	1	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.C323A						PASS	.						210	199	202					11																	48346815		2201	4298	6499	SO:0001583	missense	256144	exon1			TCATTGCTGACTC	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.323C>A	11.37:g.48346815C>A	ENSP00000321419:p.Ala108Asp	103	0	0		109	9	0.0825688	NM_001004702	B2RNF2|Q6IFB3	Missense_Mutation	SNP	ENST00000319856.4	37	CCDS31489.1	.	.	.	.	.	.	.	.	.	.	C	14.09	2.431927	0.43122	.	.	ENSG00000176547	ENST00000319856	T	0.00912	5.55	5.78	2.81	0.32909	GPCR, rhodopsin-like superfamily (1);	0.123186	0.37219	N	0.002190	T	0.01421	0.0046	L	0.51914	1.62	0.09310	N	1	P	0.43857	0.819	B	0.43867	0.434	T	0.46555	-0.9183	10	0.72032	D	0.01	.	7.969	0.30117	0.0:0.6612:0.0:0.3388	.	81	Q8NH37	OR4C3_HUMAN	D	108	ENSP00000321419:A108D	ENSP00000321419:A108D	A	+	2	0	OR4C3	48303391	0.000000	0.05858	0.987000	0.45799	0.357000	0.29423	-0.501000	0.06398	0.778000	0.33520	0.478000	0.44815	GCT	.	.	none		0.463	OR4C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390557.1	NM_001004702		A	48346815	C	A	48346815	3	1	45	1	0	0	0	0	1	0	0	0	11059	797	28	4	325	4	OR4C3	11	48346815	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	21603725	48346815	86659701	110	15562											
OR8I2	120586	hgsc.bcm.edu	37	chr11	55860964	55860964	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agcttcacacccctatgtacTttttcctgagcaatttagca	10	14	5	12	0	1	1	1	1	0	0	2	1	2	1	3	0	4	4	3	0	4	7			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr11:55860964T>C	ENST00000302124.2	+	1	212	c.181T>C	c.(181-183)Ttt>Ctt	p.F61L		NM_001003750.1	NP_001003750.1	Q8N0Y5	OR8I2_HUMAN	olfactory receptor, family 8, subfamily I, member 2	61						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)					CCCTATGTACTTTTTCCTGAG	0.378																																					p.F61L		Atlas-SNP	.											.	OR8I2	119	.	0			c.T181C						PASS	.						242	232	236					11																	55860964		2201	4296	6497	SO:0001583	missense	120586	exon1			ATGTACTTTTTCC	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.181T>C	11.37:g.55860964T>C	ENSP00000303864:p.Phe61Leu	101	0	0		104	29	0.278846	NM_001003750	B2RNN4|Q6IFC0|Q96RC5	Missense_Mutation	SNP	ENST00000302124.2	37	CCDS31517.1	.	.	.	.	.	.	.	.	.	.	T	11.98	1.801602	0.31869	.	.	ENSG00000172154	ENST00000302124	T	0.00551	6.65	4.5	4.5	0.54988	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41500	U	0.000876	T	0.00754	0.0025	M	0.71036	2.16	0.09310	N	1	B	0.19073	0.033	B	0.14023	0.01	T	0.39014	-0.9634	10	0.66056	D	0.02	-19.7083	9.6379	0.39822	0.0:0.0:0.1757:0.8243	.	61	Q8N0Y5	OR8I2_HUMAN	L	61	ENSP00000303864:F61L	ENSP00000303864:F61L	F	+	1	0	OR8I2	55617540	0.014000	0.17966	0.905000	0.35620	0.031000	0.12232	1.570000	0.36439	1.803000	0.52742	0.362000	0.22060	TTT	.	.	none		0.378	OR8I2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001003750		C	55860964	T	C	55860964	3	2	45	1	0	0	0	0	1	0	0	0	11249	1609	56	3	183	3	OR8I2	11	55860964	Missense_Mutation	SNP	T	TCGA-RQ-A68N-01A-11D-A31X-10	7514149	55860964	79145552	111	15563											
NUDT22	84304	hgsc.bcm.edu	37	chr11	63994599	63994599	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tacctggtgggcaccctgagCctcaggtgagattccaggct	7	9	13	12	0	1	2	1	2	0	1	2	3	2	2	4	4	2	2	4	4	1	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr11:63994599C>A	ENST00000279206.3	+	2	631	c.475C>A	c.(475-477)Cct>Act	p.P159T	TRPT1_ENST00000546133.1_5'Flank|TRPT1_ENST00000546089.1_5'Flank|RP11-783K16.14_ENST00000534988.1_RNA|TRPT1_ENST00000540472.1_5'Flank|NUDT22_ENST00000441250.2_Missense_Mutation_p.P159T|TRPT1_ENST00000394546.2_5'Flank|TRPT1_ENST00000541278.1_5'Flank|TRPT1_ENST00000317459.6_5'Flank|TRPT1_ENST00000394547.3_5'Flank	NM_001128612.2|NM_032344.2	NP_001122084.1|NP_115720	Q9BRQ3	NUD22_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 22	159	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.						hydrolase activity (GO:0016787)			breast(1)|endometrium(1)|large_intestine(2)|lung(4)	8						GCACCCTGAGCCTCAGGTGAG	0.622																																					p.P159T		Atlas-SNP	.											.	NUDT22	24	.	0			c.C475A						PASS	.						8	10	9					11																	63994599		2097	4232	6329	SO:0001583	missense	84304	exon2			CCTGAGCCTCAGG	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.475C>A	11.37:g.63994599C>A	ENSP00000279206:p.Pro159Thr	31	0	0		42	14	0.333333	NM_001128613	C9JY06|Q71RD5	Missense_Mutation	SNP	ENST00000279206.3	37	CCDS8061.1	.	.	.	.	.	.	.	.	.	.	C	31	5.098505	0.94197	.	.	ENSG00000149761	ENST00000279206;ENST00000441250;ENST00000428347;ENST00000536237	T;T;T	0.49139	0.79;0.79;0.79	4.55	4.55	0.56014	NUDIX hydrolase domain (1);	0.052647	0.85682	D	0.000000	T	0.70491	0.3230	M	0.80982	2.52	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	0.75654	-0.3243	10	0.87932	D	0	-5.8406	16.6018	0.84817	0.0:1.0:0.0:0.0	.	159;159;159	Q9BRQ3-2;C9JY06;Q9BRQ3	.;.;NUD22_HUMAN	T	159	ENSP00000279206:P159T;ENSP00000407970:P159T;ENSP00000401085:P159T	ENSP00000279206:P159T	P	+	1	0	NUDT22	63751175	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.990000	0.76225	2.528000	0.85240	0.491000	0.48974	CCT	.	.	none		0.622	NUDT22-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396304.2	NM_032344		A	63994599	C	A	63994599	3	1	45	1	0	0	0	0	1	0	0	0	10748	739	26	4	477	4	NUDT22	11	63994599	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	8133635	63994599	71011917	112	15564											
ATG2A	23130	hgsc.bcm.edu	37	chr11	64662599	64662599	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	ggggcagctggcggatcacgCcccccacggcgcccgtcagc	5	3	15	18	5	2	0	2	0	0	0	2	1	2	1	4	5	2	2	4	5	0	0			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr11:64662599C>G	ENST00000377264.3	-	41	5775	c.5663G>C	c.(5662-5664)gGc>gCc	p.G1888A	ATG2A_ENST00000421419.2_Missense_Mutation_p.G1890A	NM_015104.2	NP_055919.2	Q2TAZ0	ATG2A_HUMAN	autophagy related 2A	1888					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						GCGGATCACGCCCCCCACGGC	0.672																																					p.G1888A		Atlas-SNP	.											.	ATG2A	133	.	0			c.G5663C						PASS	.						39	38	39					11																	64662599		2200	4295	6495	SO:0001583	missense	23130	exon41			ATCACGCCCCCCA		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.5663G>C	11.37:g.64662599C>G	ENSP00000366475:p.Gly1888Ala	48	0	0		51	14	0.27451	NM_015104	O43154|Q14DM2|Q6ZTV2|Q7Z6K8|Q8IVY5|Q8TAI8|Q96HH7	Missense_Mutation	SNP	ENST00000377264.3	37	CCDS31602.1	.	.	.	.	.	.	.	.	.	.	C	14.40	2.524797	0.44969	.	.	ENSG00000110046	ENST00000421419;ENST00000377262;ENST00000377264	T;T	0.05996	3.36;3.36	3.99	3.06	0.35304	Autophagy-related, C-terminal (1);	0.000000	0.64402	D	0.000001	T	0.14227	0.0344	L	0.47078	1.49	0.53005	D	0.999966	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.14811	-1.0459	10	0.12103	T	0.63	.	10.8388	0.46702	0.1905:0.8095:0.0:0.0	.	1888;1890	Q2TAZ0;Q2TAZ0-3	ATG2A_HUMAN;.	A	1890;281;1888	ENSP00000410522:G1890A;ENSP00000366475:G1888A	ENSP00000366473:G281A	G	-	2	0	ATG2A	64419175	1.000000	0.71417	0.846000	0.33378	0.094000	0.18550	5.489000	0.66875	0.999000	0.39023	0.561000	0.74099	GGC	.	.	none		0.672	ATG2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000143224.1	NM_015104		G	64662599	C	G	64662599	3	3	45	1	0	0	0	0	1	0	0	0	1093	739	26	4	157	4	ATG2A	11	64662599	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	668000	64662599	70343917	113	15565											
CTTN	2017	hgsc.bcm.edu	37	chr11	70265880	70265880	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaaggtttcggcggcaaataCggtatcgacaaggacaaagt	15	7	12	7	4	0	0	0	0	0	0	2	2	0	1	0	5	1	3	0	5	6	3	rs35414621	byFrequency	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr11:70265880C>T	ENST00000301843.8	+	9	803	c.597C>T	c.(595-597)taC>taT	p.Y199Y	CTTN_ENST00000538675.1_5'Flank|CTTN_ENST00000376561.3_Silent_p.Y199Y|CTTN_ENST00000346329.3_Silent_p.Y199Y	NM_005231.3	NP_005222.2	Q14247	SRC8_HUMAN	cortactin	199					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)		GCGGCAAATACGGTATCGACA	0.413													C|||	49	0.00978435	0.0	0.0086	5008	,	,		18676	0.0		0.0119	False		,,,				2504	0.0317				p.Y199Y		Atlas-SNP	.											.	CTTN	162	.	0			c.C597T						PASS	.	C	,,	8,4392	14.3+/-33.2	0,8,2192	74	70	71		597,597,597	-7.3	0.2	11	dbSNP_126	71	113,8475	60.6+/-122.4	1,111,4182	no	coding-synonymous,coding-synonymous,coding-synonymous	CTTN	NM_001184740.1,NM_005231.3,NM_138565.2	,,	1,119,6374	TT,TC,CC		1.3158,0.1818,0.9316	,,	199/635,199/551,199/514	70265880	121,12867	2200	4294	6494	SO:0001819	synonymous_variant	2017	exon9			CAAATACGGTATC	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.597C>T	11.37:g.70265880C>T		136	0	0		150	31	0.206667	NM_001184740	Q8N707|Q96H99	Silent	SNP	ENST00000301843.8	37	CCDS41680.1	11	0.005036630036630037	0	0.0	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	C	0.906	-0.720787	0.03182	0.001818	0.013158	ENSG00000085733	ENST00000415461	.	.	.	4.92	-7.32	0.01436	.	.	.	.	.	T	0.55752	0.1940	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.67345	-0.5694	4	.	.	.	-15.9401	17.09	0.86619	0.0:0.2583:0.0:0.7417	rs35414621;rs61749188	.	.	.	M	181	.	.	T	+	2	0	CTTN	69943528	0.004000	0.15560	0.164000	0.22755	0.079000	0.17450	-1.423000	0.02450	-1.404000	0.02050	-0.971000	0.02607	ACG	C|0.993;T|0.007	0.007	strong		0.413	CTTN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259233.2	NM_138565		T	70265880	C	T	70265880	2	4	45	1	0	0	0	0	0	0	0	1	4046	547	19	1		1	CTTN	11	70265880	Silent	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	5603281	70265880	64740636	114	15566											
CASP1	834	hgsc.bcm.edu	37	chr11	104899975	104899975	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	actcctactgaatctttaaaCcacaccacaccagggctgtc	12	9	5	15	0	1	1	0	1	1	0	3	1	2	1	4	1	2	1	4	1	4	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr11:104899975C>T	ENST00000533400.1	-	7	917	c.882G>A	c.(880-882)tgG>tgA	p.W294*	CASP1_ENST00000415981.2_Intron|CASP1_ENST00000353247.5_Intron|CASP1_ENST00000534497.1_Intron|CASP1_ENST00000393136.4_Nonsense_Mutation_p.W273*|CASP1_ENST00000594519.1_Intron|CASP1_ENST00000446369.1_Intron|CASP1_ENST00000528974.1_Nonsense_Mutation_p.W255*|CASP1_ENST00000436863.3_Nonsense_Mutation_p.W294*|CASP1_ENST00000525825.1_Nonsense_Mutation_p.W273*|CASP1_ENST00000526568.1_Nonsense_Mutation_p.W201*|CASP1_ENST00000531166.1_Intron|CASP1_ENST00000598974.1_Nonsense_Mutation_p.W294*|CASP1_ENST00000527979.1_Nonsense_Mutation_p.W257*|CASP1_ENST00000593315.1_Nonsense_Mutation_p.W273*	NM_001257118.1	NP_001244047.1	P29466	CASP1_HUMAN	caspase 1, apoptosis-related cysteine peptidase	294					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic substance (GO:0071310)|execution phase of apoptosis (GO:0097194)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|membrane hyperpolarization (GO:0060081)|mitochondrial depolarization (GO:0051882)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 alpha secretion (GO:0050717)|positive regulation of interleukin-1 beta secretion (GO:0050718)|programmed necrotic cell death (GO:0097300)|proteolysis (GO:0006508)|pyroptosis (GO:0070269)|regulation of inflammatory response (GO:0050727)|response to ATP (GO:0033198)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|IPAF inflammasome complex (GO:0072557)|NLRP1 inflammasome complex (GO:0072558)|NLRP3 inflammasome complex (GO:0072559)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|cysteine-type endopeptidase activity (GO:0004197)|endopeptidase activity (GO:0004175)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)	5		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000525)|Epithelial(105;0.0128)|all cancers(92;0.0482)	Minocycline(DB01017)	AATCTTTAAACCACACCACAC	0.393																																					p.W294X	NSCLC(41;1246 1743 4934)	Atlas-SNP	.											.	CASP1	53	.	0			c.G882A						PASS	.						65	59	61					11																	104899975		2202	4299	6501	SO:0001587	stop_gained	834	exon7			TTTAAACCACACC	U13697	CCDS8329.1, CCDS8330.1, CCDS8331.1, CCDS8332.1, CCDS53704.1	11q23	2012-02-29	2012-02-29		ENSG00000137752	ENSG00000137752		"Caspases"	1499	protein-coding gene	gene with protein product	"caspase-1", "interleukin 1, beta, convertase"	147678	"caspase 1, apoptosis-related cysteine protease (interleukin 1, beta, convertase)", "caspase 1, apoptosis-related cysteine peptidase (interleukin 1, beta, convertase)"	IL1BC		1373520, 9250871	Standard	NM_033292		Approved	ICE	uc001pim.5	P29466	OTTHUMG00000048072	ENST00000533400.1:c.882G>A	11.37:g.104899975C>T	ENSP00000433138:p.Trp294*	75	0	0		89	15	0.168539	NM_001257118	B5MDZ1|Q53EY6|Q6DMQ1|Q6GSS3|Q6PI75|Q9UCN3	Nonsense_Mutation	SNP	ENST00000533400.1	37	CCDS8330.1	.	.	.	.	.	.	.	.	.	.	.	24.2	4.503509	0.85176	.	.	ENSG00000137752	ENST00000532439;ENST00000526568;ENST00000527979;ENST00000533400;ENST00000436863;ENST00000393136;ENST00000525825;ENST00000528974	.	.	.	4.25	4.25	0.50352	.	0.813732	0.11570	N	0.550882	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11485	T	0.65	.	12.3575	0.55184	0.0:1.0:0.0:0.0	.	.	.	.	X	143;201;257;294;294;273;273;255	.	ENSP00000376844:W273X	W	-	3	0	CASP1	104405185	0.002000	0.14202	0.067000	0.19924	0.030000	0.12068	0.280000	0.18790	2.370000	0.80446	0.557000	0.71058	TGG	.	.	none		0.393	CASP1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388116.1	NM_033292		T	104899975	C	T	104899975	4	4	45	1	0	0	0	0	0	1	0	0	2670	508	18	2	344	2	CASP1	11	104899975	Nonsense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	34634095	104899975	30106541	115	15567											
EXPH5	23086	hgsc.bcm.edu	37	chr11	108380629	108380629	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cctgggacctgtttttgtccCgctgcgataagcccaacttt	6	13	9	13	2	0	0	0	0	0	0	1	2	1	1	4	1	3	2	4	1	2	4	rs181581015		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr11:108380629C>T	ENST00000265843.4	-	6	5715	c.5605G>A	c.(5605-5607)Ggg>Agg	p.G1869R	EXPH5_ENST00000428840.1_Missense_Mutation_p.G1793R|EXPH5_ENST00000525344.1_Missense_Mutation_p.G1862R|EXPH5_ENST00000443411.1_Missense_Mutation_p.G1681R	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1869					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)		GTTTTTGTCCCGCTGCGATAA	0.413													C|||	1	0.000199681	0.0	0.0014	5008	,	,		19294	0.0		0.0	False		,,,				2504	0.0				p.G1869R		Atlas-SNP	.											.	EXPH5	193	.	0			c.G5605A						PASS	.	C	ARG/GLY	2,4400	4.2+/-10.8	0,2,2199	60	59	60		5605	-0.9	0	11		60	0,8596		0,0,4298	no	missense	EXPH5	NM_015065.2	125	0,2,6497	TT,TC,CC		0.0,0.0454,0.0154	benign	1869/1990	108380629	2,12996	2201	4298	6499	SO:0001583	missense	23086	exon6			TTGTCCCGCTGCG		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.5605G>A	11.37:g.108380629C>T	ENSP00000265843:p.Gly1869Arg	152	0	0		180	47	0.261111	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	0.005	-2.195634	0.00299	4.54E-4	0.0	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000439956	T;T;T;T	0.02737	4.4;4.33;4.18;4.4	5.95	-0.868	0.10652	.	0.272209	0.32372	N	0.006197	T	0.00580	0.0019	N	0.00104	-2.125	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.45818	-0.9235	10	0.05351	T	0.99	-1.6345	8.4291	0.32746	0.0:0.177:0.1025:0.7206	.	1869	Q8NEV8	EXPH5_HUMAN	R	1869;1793;1681;1862;699	ENSP00000265843:G1869R;ENSP00000391966:G1793R;ENSP00000411390:G1681R;ENSP00000432546:G1862R	ENSP00000265843:G1869R	G	-	1	0	EXPH5	107885839	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.794000	0.26958	-0.340000	0.08388	-1.090000	0.02178	GGG	C|1.000;T|0.000	0.000	strong		0.413	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065		T	108380629	C	T	108380629	3	4	45	1	0	0	0	0	1	0	0	0	5324	652	23	1	368	1	EXPH5	11	108380629	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	3480654	108380629	26625887	116	15568											
CADM1	23705	hgsc.bcm.edu	37	chr11	115110994	115110994	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctatagagatggaaacttacGcctgaagtccctgaaataaa	16	9	8	8	1	0	3	0	2	0	1	1	5	1	4	2	1	2	0	2	1	8	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr11:115110994G>A	ENST00000452722.3	-	2	291	c.271C>T	c.(271-273)Cct>Tct	p.P91S	CADM1_ENST00000542447.2_Splice_Site_p.P91S|CADM1_ENST00000536727.1_Splice_Site_p.P91S|CADM1_ENST00000331581.6_Splice_Site_p.P91S|CADM1_ENST00000537058.1_Splice_Site_p.P91S|CADM1_ENST00000537140.1_5'UTR	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)		GGAAACTTACGCCTGAAGTCC	0.398																																					p.P91S		Atlas-SNP	.											.	CADM1	74	.	0			c.C271T						PASS	.						79	73	75					11																	115110994		2201	4296	6497	SO:0001630	splice_region_variant	23705	exon2			ACTTACGCCTGAA	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.271+1C>T	11.37:g.115110994G>A		85	0	0		85	30	0.352941	NM_014333		Missense_Mutation	SNP	ENST00000452722.3	37	CCDS8373.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.4|20.4	3.981333|3.981333	0.74474|0.74474	.|.	.|.	ENSG00000182985|ENSG00000182985	ENST00000545380|ENST00000542447;ENST00000452722;ENST00000537058;ENST00000536727;ENST00000404468;ENST00000331581;ENST00000545094	.|T;T;T;T;T;T	.|0.67171	.|-0.25;-0.25;-0.25;-0.25;-0.25;-0.25	5.97|5.97	5.97|5.97	0.96955|0.96955	.|Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.78253|0.78253	0.4254|0.4254	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	D|D	1|1	.|D;D;D;P;D	.|0.89917	.|1.0;1.0;1.0;0.635;0.995	.|D;D;D;B;P	.|0.91635	.|0.998;0.998;0.999;0.364;0.691	T|T	0.75703|0.75703	-0.3225|-0.3225	5|9	.|.	.|.	.|.	.|.	15.856|15.856	0.78977|0.78977	0.0:0.1349:0.8651:0.0|0.0:0.1349:0.8651:0.0	.|.	.|91;91;92;91;91	.|Q9BY67-2;F5H0J4;A4FVB5;Q9BY67;A0A4Z1	.|.;.;.;CADM1_HUMAN;.	V|S	89|91;91;91;91;50;91;58	.|ENSP00000439176:P91S;ENSP00000395359:P91S;ENSP00000439817:P91S;ENSP00000440322:P91S;ENSP00000329797:P91S;ENSP00000439696:P58S	.|.	A|P	-|-	2|1	0|0	CADM1|CADM1	114616204|114616204	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	9.434000|9.434000	0.97515|0.97515	2.834000|2.834000	0.97654|0.97654	0.650000|0.650000	0.86243|0.86243	GCC|CCT	.	.	none		0.398	CADM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398753.2	NM_014333	Missense_Mutation	A	115110994	G	A	115110994	5	1	45	1	0	0	0	0	0	0	1	0	2568	1101	38	1	1093	1	CADM1	11	115110994	Splice_Site	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	6730365	115110994	19895522	117	15569											
ARCN1	372	hgsc.bcm.edu	37	chr11	118463477	118463477	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gcagagtctctaattggcctGaagaatccagagaagtcatt	13	10	10	8	0	2	4	1	1	1	3	4	5	3	4	2	1	0	1	2	1	4	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr11:118463477G>A	ENST00000264028.4	+	7	1133	c.1038G>A	c.(1036-1038)ctG>ctA	p.L346L	ARCN1_ENST00000534182.2_Intron|ARCN1_ENST00000359415.4_Silent_p.L387L|RNU6-1157P_ENST00000384456.1_RNA|ARCN1_ENST00000392859.3_Silent_p.L258L	NM_001655.4	NP_001646.2	P48444	COPD_HUMAN	archain 1	346	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer maturation (GO:0021691)|COPI coating of Golgi vesicle (GO:0048205)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|pigmentation (GO:0043473)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	clathrin adaptor complex (GO:0030131)|COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(3)|lung(4)|ovary(2)|urinary_tract(1)	13	all_hematologic(175;0.0349)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		TAATTGGCCTGAAGAATCCAG	0.423																																					p.L346L		Atlas-SNP	.											.	ARCN1	33	.	0			c.G1038A						PASS	.						179	186	184					11																	118463477		2200	4295	6495	SO:0001819	synonymous_variant	372	exon7			TGGCCTGAAGAAT	X81197	CCDS8400.1, CCDS44749.1	11q23.3	2010-04-21	2003-01-29		ENSG00000095139	ENSG00000095139			649	protein-coding gene	gene with protein product		600820	"coatomer protein complex, subunit delta"	COPD		7782067, 8854871	Standard	NM_001655		Approved		uc001ptq.3	P48444	OTTHUMG00000166340	ENST00000264028.4:c.1038G>A	11.37:g.118463477G>A		106	0	0		140	42	0.3	NM_001655	B4E1X2|E9PEU4|Q52M80	Silent	SNP	ENST00000264028.4	37	CCDS8400.1																																																																																			.	.	none		0.423	ARCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389278.1			A	118463477	G	A	118463477	2	1	45	1	0	0	0	0	0	0	0	1	842	1277	45	2		2	ARCN1	11	118463477	Silent	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	3352483	118463477	16543039	118	15570											
TECTA	7007	hgsc.bcm.edu	37	chr11	121008699	121008699	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgtgtttggctacagcatcGtgatccaccgagcttacaag	9	10	10	12	3	0	1	0	1	0	0	2	2	1	1	3	1	4	4	3	1	3	3	rs186780639	byFrequency	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr11:121008699G>A	ENST00000392793.1	+	11	3782	c.3511G>A	c.(3511-3513)Gtg>Atg	p.V1171M	TECTA_ENST00000264037.2_Missense_Mutation_p.V1171M			O75443	TECTA_HUMAN	tectorin alpha	1171	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)		CTACAGCATCGTGATCCACCG	0.562													G|||	4	0.000798722	0.0	0.0	5008	,	,		20826	0.004		0.0	False		,,,				2504	0.0				p.V1171M		Atlas-SNP	.											.	TECTA	329	.	0			c.G3511A						PASS	.						58	47	51					11																	121008699		2203	4299	6502	SO:0001583	missense	7007	exon10			AGCATCGTGATCC	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.3511G>A	11.37:g.121008699G>A	ENSP00000376543:p.Val1171Met	102	0	0		123	28	0.227642	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	37	CCDS8434.1	4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	G	15.87	2.959524	0.53400	.	.	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.59906	0.23;0.23	4.63	4.63	0.57726	von Willebrand factor, type D domain (3);	0.143107	0.47455	D	0.000237	T	0.50803	0.1637	L	0.55213	1.73	0.36863	D	0.888532	D	0.55800	0.973	P	0.50270	0.636	T	0.62077	-0.6930	10	0.35671	T	0.21	.	11.3966	0.49845	0.0837:0.0:0.9163:0.0	.	1171	O75443	TECTA_HUMAN	M	1171	ENSP00000376543:V1171M;ENSP00000264037:V1171M	ENSP00000264037:V1171M	V	+	1	0	TECTA	120513909	0.998000	0.40836	0.967000	0.41034	0.957000	0.61999	2.702000	0.47102	2.267000	0.75376	0.655000	0.94253	GTG	G|0.998;A|0.002	0.002	strong		0.562	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422		A	121008699	G	A	121008699	3	1	45	1	0	0	0	0	1	0	0	0	15762	1145	40	1	3549	1	TECTA	11	121008699	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	2545222	121008699	13997817	119	15571											
KLRC4	8302	hgsc.bcm.edu	37	chr12	10560927	10560927	+	Splice_Site	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	acattgacaatcataatgtaCctttctgcattcttctattc	11	17	3	10	0	4	1	1	1	3	0	5	1	4	1	1	0	2	2	1	0	4	8			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr12:10560927C>G	ENST00000309384.1	-	3	522		c.e3+1		KLRC4-KLRK1_ENST00000539300.1_Splice_Site	NM_013431.2	NP_038459.1	O43908	NKG2F_HUMAN	killer cell lectin-like receptor subfamily C, member 4						cellular defense response (GO:0006968)	integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(1)	5						TCATAATGTACCTTTCTGCAT	0.279																																					.		Atlas-SNP	.											.	KLRC4	23	.	0			c.340+1G>C						PASS	.						71	68	69					12																	10560927		2200	4280	6480	SO:0001630	splice_region_variant	8302	exon4			AATGTACCTTTCT	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.340+1G>C	12.37:g.10560927C>G		239	0	0		189	53	0.280423	NM_013431	O60851	Splice_Site	SNP	ENST00000309384.1	37	CCDS8624.1	.	.	.	.	.	.	.	.	.	.	C	4.834	0.155014	0.09236	.	.	ENSG00000183542	ENST00000309384	.	.	.	3.2	2.28	0.28536	.	.	.	.	.	.	.	.	.	.	.	0.25354	N	0.988846	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.5561	0.27824	0.2554:0.7445:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KLRC4	10452194	0.098000	0.21812	0.116000	0.21606	0.016000	0.09150	1.254000	0.32897	0.878000	0.35920	0.585000	0.79938	.	.	.	none		0.279	KLRC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400108.1	NM_013431	Intron	G	10560927	C	G	10560927	5	3	45	1	0	0	0	0	0	0	1	0	8427	521	18	4	143	4	KLRC4	12	10560927	Splice_Site	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10		10560927	123290968	120	15572											
CPNE8	144402	hgsc.bcm.edu	37	chr12	39299291	39299291	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cgggatggcagcgctcagctGgttcaagtccccgatgcccg	6	7	14	14	4	2	0	2	0	0	0	3	2	3	1	3	3	3	4	3	3	1	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr12:39299291G>T	ENST00000331366.5	-	1	142	c.46C>A	c.(46-48)Cag>Aag	p.Q16K	RP11-396F22.1_ENST00000551152.1_RNA|CPNE8_ENST00000360449.3_Intron	NM_153634.2	NP_705898.1	Q86YQ8	CPNE8_HUMAN	copine VIII	16	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.					extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(1)|large_intestine(6)|lung(6)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	21	Esophageal squamous(101;0.187)	Lung NSC(34;0.137)|Melanoma(24;0.152)|all_lung(34;0.157)				GCGCTCAGCTGGTTCAAGTCC	0.662																																					p.Q16K		Atlas-SNP	.											.	CPNE8	66	.	0			c.C46A						PASS	.						59	50	53					12																	39299291		2200	4295	6495	SO:0001583	missense	144402	exon1			TCAGCTGGTTCAA	AY177785	CCDS8733.1	12q12	2008-02-05				ENSG00000139117			23498	protein-coding gene	gene with protein product						12670487	Standard	NM_153634		Approved		uc001rls.1	Q86YQ8	OTTHUMG00000169396	ENST00000331366.5:c.46C>A	12.37:g.39299291G>T	ENSP00000329748:p.Gln16Lys	49	0	0		32	11	0.34375	NM_153634	Q2TB41|Q86VY2	Missense_Mutation	SNP	ENST00000331366.5	37	CCDS8733.1	.	.	.	.	.	.	.	.	.	.	G	15.15	2.748722	0.49257	.	.	ENSG00000139117	ENST00000331366	T	0.23348	1.91	4.73	4.73	0.59995	C2 calcium/lipid-binding domain, CaLB (1);	1.034400	0.07657	N	0.932936	T	0.13970	0.0338	N	0.03608	-0.345	0.80722	D	1	B	0.09022	0.002	B	0.10450	0.005	T	0.10823	-1.0613	10	0.49607	T	0.09	-3.0068	9.6428	0.39850	0.098:0.0:0.902:0.0	.	16	Q86YQ8	CPNE8_HUMAN	K	16	ENSP00000329748:Q16K	ENSP00000329748:Q16K	Q	-	1	0	CPNE8	37585558	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.799000	0.38824	2.555000	0.86185	0.563000	0.77884	CAG	.	.	none		0.662	CPNE8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403856.1	NM_153634		T	39299291	G	T	39299291	3	4	45	1	0	0	0	0	1	0	0	0	3820	1357	47	4	1728	4	CPNE8	12	39299291	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	28738364	39299291	94552604	121	15573											
KRT81	3887	hgsc.bcm.edu	37	chr12	52684932	52684934	+	In_Frame_Del	DEL	CTC	CTC	-																															agggacttgatctgctccttCtcctcctgcttcacgcactg																										TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr12:52684932_52684934delCTC	ENST00000327741.5	-	1	384_386	c.316_318delGAG	c.(316-318)gagdel	p.E106del	KRT86_ENST00000544024.1_Intron|KRT86_ENST00000423955.2_Intron	NM_002281.3	NP_002272.2	Q14533	KRT81_HUMAN	keratin 81	106	Head.					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)		TCTGCTCCTTCTCCTCCTGCTTC	0.616																																					p.106_107del		Atlas-Indel	.											.	KRT81	46	.	0			c.317_319del						PASS	.																																			SO:0001651	inframe_deletion	3887	exon1			.	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.316_318delGAG	12.37:g.52684935_52684937delCTC	ENSP00000369349:p.Glu106del	461	0	0		527	44	0.0834915	NM_002281	Q14846|Q16274|Q17R48|Q8WU52|Q9BR74	In_Frame_Del	DEL	ENST00000327741.5	37	CCDS31805.1																																																																																			.	.	none		0.616	KRT81-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395128.2	NM_002281		-	52684934	CTC	-	52684932	7	5	45	1	0	1	0	1	0	0	0	0	8504	912	32	0	1235	0	KRT81	12	52684932	In_Frame_Del	DEL	CTC	TCGA-RQ-A68N-01A-11D-A31X-10	13385641	52684932	81166963	122	15574											
KRT86	3892	hgsc.bcm.edu	37	chr12	52696011	52696013	+	In_Frame_Del	DEL	AGG	AGG	-																															caacgcgcagtgcgtgaagcAggaggagaaggagcagatca																										TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr12:52696011_52696013delAGG	ENST00000423955.2	+	3	489_491	c.311_313delAGG	c.(310-315)caggag>cag	p.E106del	KRT86_ENST00000544024.1_In_Frame_Del_p.E106del|KRT86_ENST00000293525.5_In_Frame_Del_p.E106del			O43790	KRT86_HUMAN	keratin 86	106	Head.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(357;0.189)		TGCGTGAAGCAGGAGGAGAAGGA	0.621																																					p.104_104del		Atlas-Indel	.											.	KRT86	33	.	0			c.310_312del						PASS	.																																			SO:0001651	inframe_deletion	3892	exon1			.	X99142	CCDS41785.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000170442		"-", "Intermediate filaments type II, keratins (basic)"	6463	protein-coding gene	gene with protein product	"hard keratin type II 6"	601928	"keratin, hair, basic, 6 (monilethrix)"	KRTHB6		9241275, 16831889	Standard	NM_002284		Approved	MNX, Hb6	uc001sad.3	O43790		ENST00000423955.2:c.311_313delAGG	12.37:g.52696014_52696016delAGG	ENSP00000444533:p.Glu106del	483	0	0		526	55	0.104563	NM_002284	P78387	In_Frame_Del	DEL	ENST00000423955.2	37	CCDS41785.1																																																																																			.	.	none		0.621	KRT86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404911.1	NM_002284		-	52696013	AGG	-	52696011	7	5	45	1	0	1	0	1	0	0	0	0	8509	188	7	0	313	0	KRT86	12	52696011	In_Frame_Del	DEL	AGG	TCGA-RQ-A68N-01A-11D-A31X-10	11079	52696011	81155884	123	15575											
KRT85	3891	hgsc.bcm.edu	37	chr12	52761179	52761179	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctgagctgatcctgtaggagCggcacgacatcgtgtgaggc	8	8	15	10	3	0	3	0	3	0	0	2	5	1	4	1	3	2	3	1	3	1	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr12:52761179C>T	ENST00000257901.3	-	1	86	c.11G>A	c.(10-12)cGc>cAc	p.R4H	KRT85_ENST00000544265.1_5'Flank	NM_002283.3	NP_002274.1	P78386	KRT85_HUMAN	keratin 85	4	Head.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(7)|liver(1)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	36	Myeloproliferative disorder(4;0.0484)|all_hematologic(5;0.088)			BRCA - Breast invasive adenocarcinoma(357;0.189)		CCTGTAGGAGCGGCACGACAT	0.632																																					p.R4H		Atlas-SNP	.											.	KRT85	78	.	0			c.G11A						PASS	.						32	31	32					12																	52761179		2203	4300	6503	SO:0001583	missense	3891	exon1			TAGGAGCGGCACG	X99140	CCDS8824.1, CCDS73472.1	12q13.13	2013-06-20	2006-07-17	2006-07-17	ENSG00000135443	ENSG00000135443		"-", "Intermediate filaments type II, keratins (basic)"	6462	protein-coding gene	gene with protein product	"hard keratin type II"	602767	"keratin, hair, basic, 5"	KRTHB5		9084137, 16831889	Standard	NM_002283		Approved	Hb-5	uc001sag.3	P78386	OTTHUMG00000169633	ENST00000257901.3:c.11G>A	12.37:g.52761179C>T	ENSP00000257901:p.Arg4His	91	0	0		99	26	0.262626	NM_002283	Q9NSB1	Missense_Mutation	SNP	ENST00000257901.3	37	CCDS8824.1	.	.	.	.	.	.	.	.	.	.	C	12.05	1.823096	0.32237	.	.	ENSG00000135443	ENST00000257901	D	0.83506	-1.73	4.63	1.68	0.24146	.	0.354724	0.24647	N	0.036744	T	0.73992	0.3658	L	0.50333	1.59	0.80722	D	1	B	0.21905	0.062	B	0.15870	0.014	T	0.67558	-0.5640	10	0.51188	T	0.08	.	5.8657	0.18773	0.4318:0.4532:0.0:0.1149	.	4	P78386	KRT85_HUMAN	H	4	ENSP00000257901:R4H	ENSP00000257901:R4H	R	-	2	0	KRT85	51047446	0.838000	0.29461	0.998000	0.56505	0.906000	0.53458	0.695000	0.25527	0.611000	0.30052	0.561000	0.74099	CGC	.	.	none		0.632	KRT85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405184.1	NM_002283		T	52761179	C	T	52761179	3	4	45	1	0	0	0	0	1	0	0	0	8508	768	27	1	1548	1	KRT85	12	52761179	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	65168	52761179	81090716	124	15576											
AGAP2	116986	hgsc.bcm.edu	37	chr12	58131511	58131511	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accttgagcctccggctgccGgtgccagggtgcggagagga	6	6	17	12	3	0	2	0	1	0	1	1	4	1	3	5	5	4	1	5	5	0	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr12:58131511G>A	ENST00000547588.1	-	1	518	c.519C>T	c.(517-519)acC>acT	p.T173T	AGAP2_ENST00000257897.3_Intron	NM_001122772.2	NP_001116244.1	Q99490	AGAP2_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 2	173					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						TCCGGCTGCCGGTGCCAGGGT	0.766																																					p.T173T		Atlas-SNP	.											.	AGAP2	167	.	0			c.C519T						PASS	.						2	2	2					12																	58131511		1052	2723	3775	SO:0001819	synonymous_variant	116986	exon1			GCTGCCGGTGCCA	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.519C>T	12.37:g.58131511G>A		33	0	0		50	7	0.14	NM_001122772	A8K9F7|O00578|Q548E0|Q8IWU3	Silent	SNP	ENST00000547588.1	37	CCDS44932.1	.	.	.	.	.	.	.	.	.	.	g	3.978	-0.007039	0.07773	.	.	ENSG00000135439	ENST00000328568	.	.	.	4.07	-0.962	0.10333	.	.	.	.	.	T	0.54159	0.1841	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47446	-0.9117	4	.	.	.	.	8.364	0.32376	0.5943:0.0:0.4057:0.0	.	.	.	.	W	37	.	.	R	-	1	2	AGAP2	56417778	0.000000	0.05858	0.991000	0.47740	0.624000	0.37722	-3.808000	0.00361	-0.164000	0.10927	-0.372000	0.07161	CGG	.	.	none		0.766	AGAP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408367.1	NM_014770		A	58131511	G	A	58131511	2	1	45	1	0	0	0	0	0	0	0	1	368	1103	39	1		1	AGAP2	12	58131511	Silent	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	5370332	58131511	75720384	125	15577											
C12orf12	196477	hgsc.bcm.edu	37	chr12	91348068	91348068	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggagtggcgagggtggtggCgcaggccgcggcctctgcgg	4	5	22	10	5	1	0	0	0	1	0	1	2	1	1	2	8	1	1	2	8	0	0			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr12:91348068C>T	ENST00000358859.2	-	1	885	c.452G>A	c.(451-453)cGc>cAc	p.R151H	CCER1_ENST00000548187.1_Intron	NM_152638.2	NP_689851.1	Q8TC90	CCER1_HUMAN	coiled-coil glutamate-rich protein 1	151																	AGGGTGGTGGCGCAGGCCGCG	0.697																																					p.R151H		Atlas-SNP	.											.	.	.	.	0			c.G452A						PASS	.						16	19	18					12																	91348068		2195	4288	6483	SO:0001583	missense	196477	exon1			TGGTGGCGCAGGC	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.452G>A	12.37:g.91348068C>T	ENSP00000351727:p.Arg151His	18	0	0		19	6	0.315789	NM_152638	Q8TC47	Missense_Mutation	SNP	ENST00000358859.2	37	CCDS9036.1	.	.	.	.	.	.	.	.	.	.	C	19.93	3.917602	0.73098	.	.	ENSG00000197651	ENST00000358859	T	0.38240	1.15	4.49	4.49	0.54785	.	0.000000	0.35040	N	0.003499	T	0.45054	0.1323	L	0.27053	0.805	0.33723	D	0.617254	D	0.89917	1.0	D	0.74348	0.983	T	0.59048	-0.7527	10	0.87932	D	0	-16.1942	12.5539	0.56242	0.0:1.0:0.0:0.0	.	151	Q8TC90	CL012_HUMAN	H	151	ENSP00000351727:R151H	ENSP00000351727:R151H	R	-	2	0	C12orf12	89872199	0.987000	0.35691	1.000000	0.80357	0.598000	0.36846	1.586000	0.36611	2.311000	0.77944	0.313000	0.20887	CGC	.	.	none		0.697	CCER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407142.2	NM_152638		T	91348068	C	T	91348068	3	4	45	1	0	0	0	0	1	0	0	0	1678	768	27	1	772	1	C12orf12	12	91348068	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	33216557	91348068	42503827	126	15578											
BTG1	694	hgsc.bcm.edu	37	chr12	92539171	92539171	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcgccctgctcacctgccagCagctcctgcaggctctggct	4	9	10	18	1	2	0	1	0	1	0	4	0	3	0	4	2	5	6	4	2	0	0			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr12:92539171C>T	ENST00000256015.3	-	1	502	c.141G>A	c.(139-141)ctG>ctA	p.L47L	C12orf79_ENST00000549802.1_5'Flank|C12orf79_ENST00000546975.1_5'Flank|C12orf79_ENST00000551563.2_5'Flank|RP11-796E2.4_ENST00000499685.2_RNA|RP11-796E2.4_ENST00000501008.2_RNA	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	47					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)			haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				CACCTGCCAGCAGCTCCTGCA	0.701			T	MYC	BCLL																																p.L47L		Atlas-SNP	.		Dom	yes		12	12q22	694	"B-cell translocation gene 1, anti-proliferative"		L	.	BTG1	30	.	0			c.G141A						PASS	.						28	30	30					12																	92539171		2201	4299	6500	SO:0001819	synonymous_variant	694	exon1			TGCCAGCAGCTCC		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.141G>A	12.37:g.92539171C>T		91	0	0		110	48	0.436364	NM_001731	P31607	Silent	SNP	ENST00000256015.3	37	CCDS9043.1																																																																																			.	.	none		0.701	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1			T	92539171	C	T	92539171	2	4	45	1	0	0	0	0	0	0	0	1	1555	697	25	2		2	BTG1	12	92539171	Silent	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	1191103	92539171	41312724	127	15579											
ACACB	32	hgsc.bcm.edu	37	chr12	109625822	109625822	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agggttttaagccgagctccGggactgtccaggaactgaat	10	9	13	9	2	0	1	0	1	0	0	2	4	2	3	3	3	3	2	3	3	3	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr12:109625822G>A	ENST00000338432.7	+	13	2118	c.1999G>A	c.(1999-2001)Ggg>Agg	p.G667R	ACACB_ENST00000377854.5_Missense_Mutation_p.G667R|ACACB_ENST00000377848.3_Missense_Mutation_p.G667R			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	667	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)	GCCGAGCTCCGGGACTGTCCA	0.493																																					p.G667R		Atlas-SNP	.											.	ACACB	330	.	0			c.G1999A						PASS	.						76	78	77					12																	109625822		2203	4300	6503	SO:0001583	missense	32	exon12			AGCTCCGGGACTG	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.1999G>A	12.37:g.109625822G>A	ENSP00000341044:p.Gly667Arg	136	0	0		135	17	0.125926	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	.	.	.	.	.	.	.	.	.	.	g	20.5	3.997239	0.74818	.	.	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854	D;D;D	0.81499	-1.5;-1.5;-1.5	5.27	5.27	0.74061	Rudiment single hybrid motif (1);ATP-grasp fold, subdomain 2 (1);Biotin carboxylation domain (1);Biotin carboxylase, C-terminal (2);	0.049617	0.85682	D	0.000000	D	0.88862	0.6552	H	0.95043	3.615	0.80722	D	1	P	0.45672	0.864	P	0.44696	0.458	D	0.92298	0.5847	10	0.87932	D	0	.	18.6174	0.91308	0.0:0.0:1.0:0.0	.	667	O00763	ACACB_HUMAN	R	667	ENSP00000341044:G667R;ENSP00000367079:G667R;ENSP00000367085:G667R	ENSP00000341044:G667R	G	+	1	0	ACACB	108110205	1.000000	0.71417	0.448000	0.26945	0.454000	0.32378	9.778000	0.99011	2.509000	0.84616	0.531000	0.56144	GGG	.	.	none		0.493	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093		A	109625822	G	A	109625822	3	1	45	1	0	0	0	0	1	0	0	0	107	1116	39	1	2045	1	ACACB	12	109625822	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	17086651	109625822	24226073	128	15580											
FZD10	11211	hgsc.bcm.edu	37	chr12	130648918	130648918	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tactggaagatcctggcggcGcagcacaagtgcaaaatgaa	14	6	12	9	2	0	2	0	1	0	1	1	3	1	3	1	3	3	3	1	3	6	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr12:130648918G>A	ENST00000229030.4	+	1	1915	c.1431G>A	c.(1429-1431)gcG>gcA	p.A477A	FZD10_ENST00000539839.1_Missense_Mutation_p.A445T|FZD10-AS1_ENST00000505807.2_RNA			Q9ULW2	FZD10_HUMAN	frizzled class receptor 10	477					brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|gonad development (GO:0008406)|negative regulation of Rho GTPase activity (GO:0034259)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of actin cytoskeleton organization (GO:0032956)|vasculature development (GO:0001944)	cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|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)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|pancreas(1)|prostate(3)|urinary_tract(1)	35	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.3e-06)|Epithelial(86;1.66e-05)|all cancers(50;5.18e-05)		TCCTGGCGGCGCAGCACAAGT	0.547																																					p.A477A		Atlas-SNP	.											.	FZD10	95	.	0			c.G1431A						PASS	.						80	79	79					12																	130648918		2203	4300	6503	SO:0001819	synonymous_variant	11211	exon1			GGCGGCGCAGCAC	AB027464	CCDS9267.1	12q24.33	2014-01-29	2014-01-29			ENSG00000111432		"GPCR / Class F : Frizzled receptors", "CD molecules"	4039	protein-coding gene	gene with protein product		606147	"frizzled (Drosophila) homolog 10", "frizzled homolog 10 (Drosophila)", "frizzled 10, seven transmembrane spanning receptor", "frizzled family receptor 10"			10448064	Standard	NM_007197		Approved	CD350	uc001uii.3	Q9ULW2		ENST00000229030.4:c.1431G>A	12.37:g.130648918G>A		100	0	0		77	10	0.12987	NM_007197		Silent	SNP	ENST00000229030.4	37	CCDS9267.1	.	.	.	.	.	.	.	.	.	.	G	7.448	0.642158	0.14451	.	.	ENSG00000111432	ENST00000539839	.	.	.	4.98	1.95	0.26073	.	3.678390	0.02114	N	0.055040	T	0.59183	0.2175	.	.	.	0.43439	D	0.995613	.	.	.	.	.	.	T	0.53415	-0.8442	6	0.87932	D	0	.	3.0754	0.06245	0.1715:0.2875:0.4239:0.1172	.	.	.	.	T	445	.	ENSP00000438460:A445T	A	+	1	0	FZD10	129214871	0.000000	0.05858	0.884000	0.34674	0.978000	0.69477	-0.874000	0.04210	0.468000	0.27243	-0.254000	0.11334	GCA	.	.	none		0.547	FZD10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				A	130648918	G	A	130648918	2	1	45	1	0	0	0	0	0	0	0	1	6137	1074	38	1		1	FZD10	12	130648918	Silent	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	21023096	130648918	3202977	129	15581											
FLT1	2321	hgsc.bcm.edu	37	chr13	28971155	28971155	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	actttattggaagctatgcaAatgtagattccagaaattct	14	14	7	6	0	1	2	0	0	1	2	2	3	2	3	1	1	2	3	1	1	6	7			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr13:28971155A>C	ENST00000282397.4	-	12	1853	c.1602T>G	c.(1600-1602)atT>atG	p.I534M	FLT1_ENST00000541932.1_Missense_Mutation_p.I534M	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	534	Ig-like C2-type 5.				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)	AAGCTATGCAAATGTAGATTC	0.408																																					p.I534M		Atlas-SNP	.											.	FLT1	393	.	0			c.T1602G						PASS	.						125	115	118					13																	28971155		2203	4300	6503	SO:0001583	missense	2321	exon12			TATGCAAATGTAG	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.1602T>G	13.37:g.28971155A>C	ENSP00000282397:p.Ile534Met	87	0	0		90	16	0.177778	NM_002019	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Missense_Mutation	SNP	ENST00000282397.4	37	CCDS9330.1	.	.	.	.	.	.	.	.	.	.	A	14.57	2.575330	0.45902	.	.	ENSG00000102755	ENST00000282397;ENST00000541932	T;T	0.36157	1.27;2.7	5.87	2.26	0.28386	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.367956	0.33272	N	0.005099	T	0.18551	0.0445	N	0.17474	0.49	0.80722	D	1	B;B;B	0.23249	0.082;0.01;0.025	B;B;B	0.15870	0.014;0.005;0.009	T	0.05533	-1.0879	10	0.29301	T	0.29	.	6.7504	0.23483	0.5627:0.0:0.4373:0.0	.	534;534;534	P17948-3;P17948-2;P17948	.;.;VGFR1_HUMAN	M	534	ENSP00000282397:I534M;ENSP00000437631:I534M	ENSP00000282397:I534M	I	-	3	3	FLT1	27869155	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	1.203000	0.32284	0.497000	0.27926	0.533000	0.62120	ATT	.	.	none		0.408	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1			C	28971155	A	C	28971155	3	2	45	1	0	0	0	0	1	0	0	0	5949	10	1	5	2675	5	FLT1	13	28971155	Missense_Mutation	SNP	A	TCGA-RQ-A68N-01A-11D-A31X-10		28971155	86198723	130	15582											
ZC3H13	23091	hgsc.bcm.edu	37	chr13	46543189	46543189	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtctctactttttctactcGtgttctgtggcattttctgt	3	21	7	10	2	4	0	0	0	4	0	6	0	4	0	0	1	2	2	0	1	2	7			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr13:46543189G>A	ENST00000242848.4	-	14	3838	c.3490C>T	c.(3490-3492)Cga>Tga	p.R1164*	ZC3H13_ENST00000282007.3_Nonsense_Mutation_p.R1164*|ZC3H13_ENST00000378921.2_Nonsense_Mutation_p.R120*			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	1164							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.R1164*(1)		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)		TTTTCTACTCGTGTTCTGTGG	0.488																																					p.R1164X	Esophageal Squamous(187;747 2077 11056 31291 44172)	Atlas-SNP	.											ZC3H13,colon,carcinoma,0,1	ZC3H13	197	1	1	Substitution - Nonsense(1)	large_intestine(1)	c.C3490T						PASS	.						187	181	183					13																	46543189		2203	4300	6503	SO:0001587	stop_gained	23091	exon14			CTACTCGTGTTCT	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.3490C>T	13.37:g.46543189G>A	ENSP00000242848:p.Arg1164*	120	0	0		94	11	0.117021	NM_015070	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Nonsense_Mutation	SNP	ENST00000242848.4	37		.	.	.	.	.	.	.	.	.	.	G	43	10.293987	0.99377	.	.	ENSG00000123200	ENST00000242848;ENST00000378921;ENST00000282007	.	.	.	5.52	4.56	0.56223	.	0.000000	0.52532	D	0.000074	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.3895	0.49806	0.0:0.0:0.6178:0.3821	.	.	.	.	X	1164;120;1164	.	ENSP00000242848:R1164X	R	-	1	2	ZC3H13	45441190	0.999000	0.42202	0.964000	0.40570	0.505000	0.33919	3.399000	0.52586	2.756000	0.94617	0.655000	0.94253	CGA	.	.	none		0.488	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070		A	46543189	G	A	46543189	4	1	45	1	0	0	0	0	0	1	0	0	17580	1153	40	1	1220	1	ZC3H13	13	46543189	Nonsense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	17572034	46543189	68626689	131	15583											
LRCH1	23143	hgsc.bcm.edu	37	chr13	47224430	47224430	+	Silent	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tatcacaactgtatcagagtCattcctgaggccatcgttaa	12	12	7	10	1	3	2	3	1	0	1	5	2	4	2	2	1	1	2	2	1	4	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr13:47224430C>A	ENST00000389798.3	+	2	599	c.402C>A	c.(400-402)gtC>gtA	p.V134V	LRCH1_ENST00000389797.3_Silent_p.V134V|LRCH1_ENST00000311191.6_Silent_p.V134V	NM_015116.2	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 1	134										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)		GTATCAGAGTCATTCCTGAGG	0.338																																					p.V134V		Atlas-SNP	.											.	LRCH1	104	.	0			c.C402A						PASS	.						90	82	85					13																	47224430		2203	4300	6503	SO:0001819	synonymous_variant	23143	exon2			CAGAGTCATTCCT	AB023233	CCDS31972.1, CCDS53865.1, CCDS53866.1	13q14.11	2008-02-05	2004-05-27	2004-05-28	ENSG00000136141	ENSG00000136141			20309	protein-coding gene	gene with protein product		610368	"calponin homology (CH) domain containing 1"	CHDC1		10231032	Standard	NM_015116		Approved	KIAA1016	uc001vbk.3	Q9Y2L9	OTTHUMG00000016877	ENST00000389798.3:c.402C>A	13.37:g.47224430C>A		92	0	0		98	18	0.183673	NM_015116	B7ZLL5|F8W6F0|Q17R43|Q2KHR1|Q5TBU9|Q7Z5F6|Q7Z5F7	Silent	SNP	ENST00000389798.3	37	CCDS31972.1																																																																																			.	.	none		0.338	LRCH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044824.2	NM_015116		A	47224430	C	A	47224430	2	1	45	1	0	0	0	0	0	0	0	1	8941	813	29	4		4	LRCH1	13	47224430	Silent	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	681241	47224430	67945448	132	15584											
HTR2A	3356	hgsc.bcm.edu	37	chr13	47409325	47409325	+	Nonsense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagggccccaatgacatcctCattgcaggactctttgcaga	10	9	9	13	0	2	2	1	1	1	1	3	3	3	3	3	2	2	2	3	2	1	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr13:47409325C>A	ENST00000378688.4	-	3	1194	c.1063G>T	c.(1063-1065)Gag>Tag	p.E355*	HTR2A_ENST00000543956.1_Nonsense_Mutation_p.E271*|HTR2A_ENST00000542664.1_Nonsense_Mutation_p.E355*			P28223	5HT2A_HUMAN	5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupled	355					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)	ATGACATCCTCATTGCAGGAC	0.478																																					p.E355X		Atlas-SNP	.											.	HTR2A	98	.	0			c.G1063T						PASS	.						128	114	118					13																	47409325		2203	4300	6503	SO:0001587	stop_gained	3356	exon4			CATCCTCATTGCA	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.1063G>T	13.37:g.47409325C>A	ENSP00000367959:p.Glu355*	109	0	0		113	17	0.150442	NM_000621	B2RAC5|B4DZ79|F5GWE8|Q5T8C0	Nonsense_Mutation	SNP	ENST00000378688.4	37	CCDS9405.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.708347	0.89018	.	.	ENSG00000102468	ENST00000378688;ENST00000543956;ENST00000542664	.	.	.	5.86	5.02	0.67125	.	0.164517	0.52532	D	0.000067	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06625	T	0.88	.	14.4486	0.67370	0.0:0.9297:0.0:0.0703	.	.	.	.	X	355;271;355	.	ENSP00000367959:E355X	E	-	1	0	HTR2A	46307326	0.002000	0.14202	0.220000	0.23810	0.682000	0.39822	0.639000	0.24690	1.630000	0.50440	0.650000	0.86243	GAG	.	.	none		0.478	HTR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044835.3	NM_000621		A	47409325	C	A	47409325	4	1	45	1	0	0	0	0	0	1	0	0	7450	835	29	4	356	4	HTR2A	13	47409325	Nonsense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	184895	47409325	67760553	133	15585											
PCDH9	5101	hgsc.bcm.edu	37	chr13	67205459	67205459	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	tgagatcagggttccactacCcaccggctcatggtctccta	8	10	9	14	1	3	1	2	1	1	1	5	2	4	1	4	3	1	2	4	3	2	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr13:67205459C>A	ENST00000377865.2	-	3	3357	c.3223G>T	c.(3223-3225)Ggt>Tgt	p.G1075C	PCDH9_ENST00000328454.5_Missense_Mutation_p.G1041C|RNU7-87P_ENST00000459343.1_RNA|PCDH9_ENST00000544246.1_Missense_Mutation_p.G1075C|PCDH9_ENST00000456367.1_Missense_Mutation_p.G1041C			Q9HC56	PCDH9_HUMAN	protocadherin 9	1075					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)		GTTCCACTACCCACCGGCTCA	0.552																																					p.G1075C		Atlas-SNP	.											PCDH9,NS,carcinoma,+1,1	PCDH9	252	1	0			c.G3223T						PASS	.						129	111	117					13																	67205459		2203	4300	6503	SO:0001583	missense	5101	exon4			CACTACCCACCGG	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.3223G>T	13.37:g.67205459C>A	ENSP00000367096:p.Gly1075Cys	88	0	0		70	25	0.357143	NM_203487	A2A6U1|Q5VT83|Q7Z3U0|Q8N3K7	Missense_Mutation	SNP	ENST00000377865.2	37	CCDS9444.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.857443	0.91433	.	.	ENSG00000184226	ENST00000544246;ENST00000377865;ENST00000456367;ENST00000328454	T;T;T;T	0.56776	0.54;0.54;0.44;0.44	5.63	5.63	0.86233	.	0.175226	0.28403	N	0.015463	T	0.68293	0.2985	L	0.47190	1.495	0.54753	D	0.999984	D;D	0.89917	1.0;1.0	D;D	0.71656	0.974;0.947	T	0.69277	-0.5187	10	0.72032	D	0.01	.	19.6801	0.95958	0.0:1.0:0.0:0.0	.	1041;1075	Q9HC56-2;Q9HC56	.;PCDH9_HUMAN	C	1075;1075;1041;1041	ENSP00000442186:G1075C;ENSP00000367096:G1075C;ENSP00000401699:G1041C;ENSP00000332060:G1041C	ENSP00000332060:G1041C	G	-	1	0	PCDH9	66103460	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.259000	0.78381	2.652000	0.90054	0.655000	0.94253	GGT	.	.	none		0.552	PCDH9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276387.1	NM_203487		A	67205459	C	A	67205459	3	1	45	1	0	0	0	0	1	0	0	0	11527	623	22	4	498	4	PCDH9	13	67205459	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	19796134	67205459	47964419	134	15586											
SLITRK1	114798	hgsc.bcm.edu	37	chr13	84454325	84454325	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cagccccgcgaatttctcccGggacagcgtgtccaggtaat	8	8	11	14	4	1	0	0	0	1	0	3	2	2	1	4	2	2	1	4	2	2	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr13:84454325G>A	ENST00000377084.2	-	1	2203	c.1318C>T	c.(1318-1320)Cgg>Tgg	p.R440W		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	440					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|homeostatic process (GO:0042592)|multicellular organism growth (GO:0035264)	integral component of membrane (GO:0016021)		p.R440R(1)		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)		AATTTCTCCCGGGACAGCGTG	0.502																																					p.R440W		Atlas-SNP	.											SLITRK1,NS,carcinoma,0,1	SLITRK1	196	1	1	Substitution - coding silent(1)	lung(1)	c.C1318T						scavenged	.						122	115	118					13																	84454325		2203	4300	6503	SO:0001583	missense	114798	exon1			TCTCCCGGGACAG	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.1318C>T	13.37:g.84454325G>A	ENSP00000366288:p.Arg440Trp	107	1	0.00934579		84	32	0.380952	NM_052910	Q5U5I6|Q96SF9	Missense_Mutation	SNP	ENST00000377084.2	37	CCDS9464.1	.	.	.	.	.	.	.	.	.	.	G	14.30	2.493804	0.44352	.	.	ENSG00000178235	ENST00000377084	T	0.57436	0.4	5.22	5.22	0.72569	.	0.138450	0.49305	D	0.000152	T	0.61502	0.2352	L	0.45581	1.43	0.51482	D	0.99992	D	0.57899	0.981	P	0.54629	0.757	T	0.64875	-0.6304	10	0.87932	D	0	-11.4904	17.693	0.88273	0.0:0.0:1.0:0.0	.	440	Q96PX8	SLIK1_HUMAN	W	440	ENSP00000366288:R440W	ENSP00000366288:R440W	R	-	1	2	SLITRK1	83352326	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.086000	0.64474	2.603000	0.88011	0.655000	0.94253	CGG	.	.	none		0.502	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910		A	84454325	G	A	84454325	3	1	45	1	0	0	0	0	1	0	0	0	14757	1115	39	1	776	1	SLITRK1	13	84454325	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	17248866	84454325	30715553	135	15587											
FARP1	10160	hgsc.bcm.edu	37	chr13	99091388	99091388	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acgtcctgctatacacgagcCgggggctgacggcctccaat	8	7	12	14	4	0	1	0	1	0	0	2	2	2	1	4	3	3	2	4	3	3	2	rs142251812		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr13:99091388C>T	ENST00000319562.6	+	21	2636	c.2371C>T	c.(2371-2373)Cgg>Tgg	p.R791W	FARP1_ENST00000595437.1_Missense_Mutation_p.R822W|FARP1_ENST00000376586.2_Missense_Mutation_p.R822W	NM_005766.2	NP_005757.1	Q9Y4F1	FARP1_HUMAN	FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)	791	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				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)	p.R791W(1)		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)			ATACACGAGCCGGGGGCTGAC	0.592																																					p.R791W		Atlas-SNP	.											FARP1,scalp,carcinoma,0,1	FARP1	207	1	1	Substitution - Missense(1)	skin(1)	c.C2371T						PASS	.	C	TRP/ARG	2,4404	4.2+/-10.8	0,2,2201	163	158	160		2371	-3.3	0.9	13	dbSNP_134	160	0,8600		0,0,4300	no	missense	FARP1	NM_005766.2	101	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging	791/1046	99091388	2,13004	2203	4300	6503	SO:0001583	missense	10160	exon21			ACGAGCCGGGGGC	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.2371C>T	13.37:g.99091388C>T	ENSP00000322926:p.Arg791Trp	120	0	0		89	32	0.359551	NM_005766	Q5JVI9|Q6IQ29	Missense_Mutation	SNP	ENST00000319562.6	37	CCDS9487.1	.	.	.	.	.	.	.	.	.	.	C	15.00	2.703907	0.48412	4.54E-4	0.0	ENSG00000152767	ENST00000376586;ENST00000319562	T;T	0.75821	-0.97;-0.97	5.57	-3.34	0.04943	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.067341	0.64402	D	0.000018	D	0.84933	0.5582	M	0.80746	2.51	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.995;0.997	D	0.86106	0.1559	10	0.87932	D	0	.	18.5771	0.91159	0.7275:0.2725:0.0:0.0	.	791;822	Q9Y4F1;C9JME2	FARP1_HUMAN;.	W	822;791	ENSP00000365771:R822W;ENSP00000322926:R791W	ENSP00000322926:R791W	R	+	1	2	FARP1	97889389	1.000000	0.71417	0.857000	0.33713	0.044000	0.14063	1.152000	0.31663	-0.545000	0.06224	-0.262000	0.10625	CGG	C|1.000;T|0.000	0.000	weak		0.592	FARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045541.3	NM_005766		T	99091388	C	T	99091388	3	4	45	1	0	0	0	0	1	0	0	0	5684	643	23	1	2672	1	FARP1	13	99091388	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	14637063	99091388	16078490	136	15588											
CDC16	8881	hgsc.bcm.edu	37	chr13	115004951	115004951	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atccttccagcgactgggaaAtgtcacagtcttcagtaagt	11	11	9	10	1	3	0	2	0	1	0	5	2	5	1	2	1	1	1	2	1	2	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr13:115004951A>T	ENST00000356221.3	+	5	475	c.367A>T	c.(367-369)Atg>Ttg	p.M123L	CDC16_ENST00000252457.5_Missense_Mutation_p.M122L|CDC16_ENST00000375310.1_Missense_Mutation_p.M29L|CDC16_ENST00000375308.1_Missense_Mutation_p.M29L|CDC16_ENST00000375312.3_Missense_Mutation_p.M29L|CDC16_ENST00000360383.3_Missense_Mutation_p.M123L|CDC16_ENST00000252458.6_Missense_Mutation_p.M29L			Q13042	CDC16_HUMAN	cell division cycle 16	123					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|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 mitosis (GO:0007088)|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)|spindle (GO:0005819)				endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22	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)			CGACTGGGAAATGTCACAGTC	0.418																																					p.M123L		Atlas-SNP	.											.	CDC16	50	.	0			c.A367T						PASS	.						39	43	42					13																	115004951		2203	4300	6503	SO:0001583	missense	8881	exon5			TGGGAAATGTCAC	U18291	CCDS9542.2	13q34	2013-01-17	2013-01-17		ENSG00000130177	ENSG00000130177		"Anaphase promoting complex subunits", "Tetratricopeptide (TTC) repeat domain containing"	1720	protein-coding gene	gene with protein product	"anaphase-promoting complex, subunit 6"	603461	"CDC16 (cell division cycle 16, S. cerevisiae, homolog)", "CDC16 cell division cycle 16 homolog (S. cerevisiae)", "cell division cycle 16 homolog (S. cerevisiae)"			7736578	Standard	NM_001078645		Approved	APC6, ANAPC6, CUT9	uc001vul.1	Q13042	OTTHUMG00000017402	ENST00000356221.3:c.367A>T	13.37:g.115004951A>T	ENSP00000348554:p.Met123Leu	95	0	0		106	19	0.179245	NM_003903	A2A365|Q5T8C8|Q96AE6|Q9Y564	Missense_Mutation	SNP	ENST00000356221.3	37	CCDS9542.2	.	.	.	.	.	.	.	.	.	.	A	6.976	0.550066	0.13374	.	.	ENSG00000130177	ENST00000360383;ENST00000375312;ENST00000356221;ENST00000375310;ENST00000252457;ENST00000375308;ENST00000252458	.	.	.	5.73	3.32	0.38043	Tetratricopeptide-like helical (1);	0.110567	0.85682	D	0.000000	T	0.37461	0.1004	N	0.19112	0.55	0.43168	D	0.994969	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.0;0.0	T	0.09058	-1.0692	8	.	.	.	-28.7507	9.0916	0.36614	0.7929:0.0:0.2071:0.0	.	123;122;122;123	B4DK74;Q13042-3;Q13042-2;Q13042	.;.;.;CDC16_HUMAN	L	123;29;123;29;122;29;29	.	.	M	+	1	0	CDC16	114023053	1.000000	0.71417	0.801000	0.32222	0.154000	0.21943	5.567000	0.67378	0.457000	0.26962	-0.376000	0.06991	ATG	.	.	none		0.418	CDC16-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276737.1	NM_003903		T	115004951	A	T	115004951	3	4	45	1	0	0	0	0	1	0	0	0	3060	101	4	5	385	5	CDC16	13	115004951	Missense_Mutation	SNP	A	TCGA-RQ-A68N-01A-11D-A31X-10	15913563	115004951	164927	137	15589											
C14orf21	161424	hgsc.bcm.edu	37	chr14	24771450	24771450	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtccctagtcccctactgctAtttctccgagatcagacgag	8	11	8	14	2	2	2	1	0	1	2	5	4	4	2	4	0	2	1	4	0	3	4	rs182491838		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr14:24771450A>G	ENST00000267425.3	+	5	1056	c.963A>G	c.(961-963)ctA>ctG	p.L321L	NOP9_ENST00000396802.3_Silent_p.L321L|DHRS1_ENST00000288111.7_5'Flank|DHRS1_ENST00000396813.1_5'Flank	NM_174913.1	NP_777573.1	Q86U38	NOP9_HUMAN	NOP9 nucleolar protein	321							poly(A) RNA binding (GO:0044822)										CCCTACTGCTATTTCTCCGAG	0.522													A|||	1	0.000199681	0.0	0.0	5008	,	,		21836	0.0		0.001	False		,,,				2504	0.0				p.L321L		Atlas-SNP	.											.	.	.	.	0			c.A963G						PASS	.						278	276	277					14																	24771450		2203	4300	6503	SO:0001819	synonymous_variant	161424	exon5			ACTGCTATTTCTC		CCDS9624.1, CCDS66616.1	14q12	2012-12-10	2012-12-10	2012-06-06	ENSG00000196943	ENSG00000196943			19826	protein-coding gene	gene with protein product			"chromosome 14 open reading frame 21", "NOP9 nucleolar protein homolog (yeast)"	C14orf21		21653694	Standard	XM_005267385		Approved		uc001wol.1	Q86U38	OTTHUMG00000029342	ENST00000267425.3:c.963A>G	14.37:g.24771450A>G		50	0	0		47	18	0.382979	NM_174913	A8MY76|Q8IVF0|Q8TBS6	Silent	SNP	ENST00000267425.3	37	CCDS9624.1																																																																																			A|1.000;G|0.000	0.000	strong		0.522	NOP9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073186.2			G	24771450	A	G	24771450	2	3	45	1	0	0	0	0	0	0	0	1	1771	436	16	3		3	C14orf21	14	24771450	Silent	SNP	A	TCGA-RQ-A68N-01A-11D-A31X-10		24771450	82578090	138	15590											
FUT8	2530	hgsc.bcm.edu	37	chr14	66209049	66209049	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caacaggaaattgggaaggaCgggcctatatccctcctaca	13	7	10	11	1	0	0	0	0	0	0	2	3	2	3	3	4	2	0	3	4	6	4	rs149328619	byFrequency	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr14:66209049C>A	ENST00000360689.5	+	11	3376	c.1649C>A	c.(1648-1650)aCg>aAg	p.T550K	FUT8_ENST00000557164.1_Missense_Mutation_p.T387K|FUT8_ENST00000394585.1_Missense_Mutation_p.T550K|FUT8_ENST00000358307.2_Missense_Mutation_p.T421K|FUT8_ENST00000394586.2_Missense_Mutation_p.T550K|FUT8_ENST00000417683.1_Missense_Mutation_p.T144K	NM_004480.4|NM_178155.2	NP_004471.4|NP_835368.1	Q9BYC5	FUT8_HUMAN	fucosyltransferase 8 (alpha (1,6) fucosyltransferase)	550	SH3.				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)		TTGGGAAGGACGGGCCTATAT	0.443																																					p.T550K		Atlas-SNP	.											.	FUT8	101	.	0			c.C1649A						PASS	.						77	77	77					14																	66209049		2203	4300	6503	SO:0001583	missense	2530	exon11			GAAGGACGGGCCT	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	ENST00000360689.5:c.1649C>A	14.37:g.66209049C>A	ENSP00000353910:p.Thr550Lys	134	0	0		147	6	0.0408163	NM_178155	B4DFS7|G3V5N0|O00235|Q8IUA5|Q9BYC6|Q9P2U5|Q9P2U6	Missense_Mutation	SNP	ENST00000360689.5	37	CCDS9775.1	.	.	.	.	.	.	.	.	.	.	C	10.64	1.406205	0.25378	.	.	ENSG00000033170	ENST00000360689;ENST00000394586;ENST00000557164;ENST00000394585;ENST00000358307;ENST00000417683	T;T;T;T;T;T	0.50277	0.75;0.75;0.75;0.75;0.75;0.75	6.04	5.16	0.70880	Src homology-3 domain (2);	0.043935	0.85682	D	0.000000	T	0.31263	0.0791	L	0.31157	0.91	0.80722	D	1	P;P;P	0.38420	0.595;0.587;0.63	B;B;B	0.34931	0.122;0.051;0.192	T	0.10590	-1.0623	10	0.07175	T	0.84	-5.1746	13.1167	0.59303	0.0:0.9232:0.0:0.0768	.	144;421;550	Q8IUA5;G3XAD2;Q9BYC5	.;.;FUT8_HUMAN	K	550;550;387;550;421;144	ENSP00000353910:T550K;ENSP00000378087:T550K;ENSP00000452433:T387K;ENSP00000378086:T550K;ENSP00000351057:T421K;ENSP00000396770:T144K	ENSP00000351057:T421K	T	+	2	0	FUT8	65278802	1.000000	0.71417	1.000000	0.80357	0.773000	0.43773	6.089000	0.71384	1.578000	0.49821	-0.253000	0.11424	ACG	C|0.999;T|0.001	.	alt		0.443	FUT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286406.1	NM_004480		A	66209049	C	A	66209049	3	1	45	1	0	0	0	0	1	0	0	0	6118	536	19	4	1782	4	FUT8	14	66209049	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	41437599	66209049	41140491	139	15591											
GPHN	10243	hgsc.bcm.edu	37	chr14	67147830	67147830	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccatttctatttagtgagtGatagttgcttcaggaatctt	9	17	8	7	0	3	2	1	2	2	0	3	3	3	3	1	1	1	2	1	1	4	8			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr14:67147830G>T	ENST00000315266.5	+	2	1191	c.70G>T	c.(70-72)Gat>Tat	p.D24Y	GPHN_ENST00000459628.1_Missense_Mutation_p.D24Y|GPHN_ENST00000543237.1_Missense_Mutation_p.D24Y|GPHN_ENST00000478722.1_Missense_Mutation_p.D24Y|GPHN_ENST00000305960.9_Missense_Mutation_p.D24Y	NM_001024218.1	NP_001019389.1	Q9NQX3	GEPH_HUMAN	gephyrin	24	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)		TTTAGTGAGTGATAGTTGCTT	0.323			T	MLL	AL																																p.D24Y		Atlas-SNP	.		Dom	yes		14	14q24	10243	gephyrin (GPH)		L	.	GPHN	79	.	0			c.G70T						PASS	.						74	76	75					14																	67147830		2203	4300	6503	SO:0001583	missense	10243	exon2			GTGAGTGATAGTT	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.70G>T	14.37:g.67147830G>T	ENSP00000312771:p.Asp24Tyr	101	0	0		114	18	0.157895	NM_001024218	Q9H4E9|Q9P2G2	Missense_Mutation	SNP	ENST00000315266.5	37	CCDS32103.1	.	.	.	.	.	.	.	.	.	.	G	15.63	2.890906	0.52014	.	.	ENSG00000171723	ENST00000315266;ENST00000478722;ENST00000459628;ENST00000543237;ENST00000305960	D;D;D;D;D	0.82526	-1.62;-1.62;-1.62;-1.62;-1.62	5.11	5.11	0.69529	Molybdenum cofactor synthesis (1);Molybdopterin binding (4);	0.000000	0.85682	D	0.000000	D	0.94149	0.8123	H	0.96748	3.875	0.58432	D	0.999999	D;D;D;D;D	0.89917	0.994;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.986;1.0;0.997;0.999;1.0	D	0.95993	0.8987	10	0.87932	D	0	-7.1651	16.0118	0.80409	0.0:0.0:1.0:0.0	.	24;24;24;24;24	F8W7D6;F5H039;Q9NQX3;Q9NQX3-2;G3V582	.;.;GEPH_HUMAN;.;.	Y	24	ENSP00000312771:D24Y;ENSP00000417901:D24Y;ENSP00000452220:D24Y;ENSP00000438404:D24Y;ENSP00000303019:D24Y	ENSP00000303019:D24Y	D	+	1	0	GPHN	66217583	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.659000	0.91116	2.374000	0.81015	0.579000	0.79373	GAT	.	.	none		0.323	GPHN-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000074299.2	NM_020806		T	67147830	G	T	67147830	3	4	45	1	0	0	0	0	1	0	0	0	6618	1290	45	4	76	4	GPHN	14	67147830	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	938781	67147830	40201710	140	15592											
PCNX	22990	hgsc.bcm.edu	37	chr14	71500228	71500228	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	agtgtcttaccatctcagccGacaaagcagtgatccatctg	11	10	8	12	1	3	1	1	1	3	0	5	2	4	1	3	0	3	1	3	0	2	1	rs201430424		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr14:71500228G>A	ENST00000304743.2	+	17	4087	c.3641G>A	c.(3640-3642)cGa>cAa	p.R1214Q	PCNX_ENST00000238570.5_Missense_Mutation_p.R1214Q|PCNX_ENST00000439984.3_Missense_Mutation_p.R1103Q	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1214						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)		CATCTCAGCCGACAAAGCAGT	0.348													G|||	1	0.000199681	0.0	0.0	5008	,	,		15772	0.001		0.0	False		,,,				2504	0.0				p.R1214Q		Atlas-SNP	.											.	PCNX	198	.	0			c.G3641A						PASS	.						149	132	138					14																	71500228		2203	4300	6503	SO:0001583	missense	22990	exon17			TCAGCCGACAAAG	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.3641G>A	14.37:g.71500228G>A	ENSP00000304192:p.Arg1214Gln	141	0	0		154	38	0.246753	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	37	CCDS9806.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0017482517482517483|0.0017482517482517483	0|0	0.0|0.0	G|G	34|34	5.349420|5.349420	0.95830|0.95830	.|.	.|.	ENSG00000100731|ENSG00000100731	ENST00000554691|ENST00000304743;ENST00000238570;ENST00000439984	.|T;T;T	.|0.21361	.|2.3;2.18;2.01	5.72|5.72	5.72|5.72	0.89469|0.89469	.|.	.|0.057498	.|0.64402	.|D	.|0.000001	T|T	0.55146|0.55146	0.1902|0.1902	M|M	0.86502|0.86502	2.82|2.82	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.76494	.|0.998;0.987;0.999	.|D;P;D	.|0.75484	.|0.986;0.746;0.978	T|T	0.60747|0.60747	-0.7202|-0.7202	5|10	.|0.72032	.|D	.|0.01	.|.	19.8731|19.8731	0.96858|0.96858	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1214;1103;1214	.|Q96RV3-3;B2RTR6;Q96RV3	.|.;.;PCX1_HUMAN	N|Q	273|1214;1214;1103	.|ENSP00000304192:R1214Q;ENSP00000238570:R1214Q;ENSP00000396617:R1103Q	.|ENSP00000238570:R1214Q	D|R	+|+	1|2	0|0	PCNX|PCNX	70569981|70569981	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	9.148000|9.148000	0.94652|0.94652	2.707000|2.707000	0.92482|0.92482	0.650000|0.650000	0.86243|0.86243	GAC|CGA	G|1.000;A|0.000	0.000	strong		0.348	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982		A	71500228	G	A	71500228	3	1	45	1	0	0	0	0	1	0	0	0	11600	1058	37	1	3707	1	PCNX	14	71500228	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	4352398	71500228	35849312	141	15593											
ACOT1	641371	hgsc.bcm.edu	37	chr14	74008216	74008216	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaacctgggccctttcctggCattgtggacatgttcggaac	7	11	12	11	1	0	0	0	0	0	0	2	3	1	2	3	4	2	2	3	4	2	3	rs201966235	byFrequency	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr14:74008216C>G	ENST00000311148.4	+	2	785	c.477C>G	c.(475-477)ggC>ggG	p.G159G	HEATR4_ENST00000560393.1_Intron|HEATR4_ENST00000334988.2_Intron|ACOT1_ENST00000557556.1_Silent_p.G159G|HEATR4_ENST00000553558.1_Intron	NM_001037161.1	NP_001032238.1	Q86TX2	ACOT1_HUMAN	acyl-CoA thioesterase 1	159					acyl-CoA metabolic process (GO:0006637)|long-chain fatty acid metabolic process (GO:0001676)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)	p.G159G(1)		endometrium(1)|large_intestine(1)|lung(2)	4				OV - Ovarian serous cystadenocarcinoma(108;1.37e-45)|BRCA - Breast invasive adenocarcinoma(234;0.0033)		CCTTTCCTGGCATTGTGGACA	0.463													-|||	62	0.0123802	0.0257	0.0115	5008	,	,		11074	0.002		0.0139	False		,,,				2504	0.0041				p.G159G		Atlas-SNP	.											ACOT1,NS,carcinoma,0,1	ACOT1	12	1	1	Substitution - coding silent(1)	endometrium(1)	c.C477G						scavenged	.						170	130	144					14																	74008216		1974	3593	5567	SO:0001819	synonymous_variant	641371	exon2			TCCTGGCATTGTG	DQ082754	CCDS32117.1	14q24.3	2013-09-20			ENSG00000184227	ENSG00000184227		"Acyl CoA thioesterases"	33128	protein-coding gene	gene with protein product		614313				16103133, 16940157	Standard	NM_001037161		Approved	ACH2, CTE-1, LACH2		Q86TX2	OTTHUMG00000171607	ENST00000311148.4:c.477C>G	14.37:g.74008216C>G		3	1	0.333333		5	5	1	NM_001037161	A1L173|Q3I5F9	Silent	SNP	ENST00000311148.4	37	CCDS32117.1																																																																																			C|0.785;G|0.215	0.215	strong		0.463	ACOT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414432.1	NM_001037161		G	74008216	C	G	74008216	2	3	45	1	0	0	0	0	0	0	0	1	148	697	25	4		4	ACOT1	14	74008216	Silent	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	2507988	74008216	33341324	142	15594											
LTBP2	4053	hgsc.bcm.edu	37	chr14	74970174	74970174	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acgctcaggcccactcacccGtgctgctggtgctgttcatg	5	10	11	15	2	3	0	3	0	0	0	3	0	3	0	2	2	3	5	2	2	0	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr14:74970174G>A	ENST00000261978.4	-	32	5104	c.4718C>T	c.(4717-4719)aCg>aTg	p.T1573M	LTBP2_ENST00000556690.1_Missense_Mutation_p.T1529M	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	1573					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)		CCACTCACCCGTGCTGCTGGT	0.677																																					p.T1573M		Atlas-SNP	.											.	LTBP2	158	.	0			c.C4718T						PASS	.						42	36	38					14																	74970174		2202	4300	6502	SO:0001583	missense	4053	exon32			TCACCCGTGCTGC		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.4718C>T	14.37:g.74970174G>A	ENSP00000261978:p.Thr1573Met	43	0	0		43	9	0.209302	NM_000428	Q99907|Q9NS51	Missense_Mutation	SNP	ENST00000261978.4	37	CCDS9831.1	.	.	.	.	.	.	.	.	.	.	G	5.194	0.221357	0.09863	.	.	ENSG00000119681	ENST00000261978;ENST00000556690	T;T	0.78924	-1.22;-1.22	4.86	-6.15	0.02105	.	2.988510	0.01279	N	0.009675	T	0.68961	0.3058	L	0.34521	1.04	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.57015	-0.7883	10	0.45353	T	0.12	.	14.329	0.66541	0.6899:0.0:0.3101:0.0	.	1573	Q14767	LTBP2_HUMAN	M	1573;1529	ENSP00000261978:T1573M;ENSP00000451477:T1529M	ENSP00000261978:T1573M	T	-	2	0	LTBP2	74039927	0.000000	0.05858	0.000000	0.03702	0.340000	0.28889	-0.517000	0.06275	-1.200000	0.02662	-0.224000	0.12420	ACG	.	.	none		0.677	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428		A	74970174	G	A	74970174	3	1	45	1	0	0	0	0	1	0	0	0	9083	1145	40	1	767	1	LTBP2	14	74970174	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	961958	74970174	32379366	143	15595											
POMT2	29954	hgsc.bcm.edu	37	chr14	77762563	77762563	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtgcctgtgggagtgcagatAgccgatggccatccggaggt	7	8	17	9	2	0	1	0	0	0	1	1	4	1	3	4	4	3	1	4	4	1	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr14:77762563A>G	ENST00000261534.4	-	9	1262	c.1060T>C	c.(1060-1062)Tat>Cat	p.Y354H		NM_013382.5	NP_037514.2	Q9UKY4	POMT2_HUMAN	protein-O-mannosyltransferase 2	354	MIR 1. {ECO:0000255|PROSITE- ProRule:PRU00131}.					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)		GAGTGCAGATAGCCGATGGCC	0.602																																					p.Y354H		Atlas-SNP	.											.	POMT2	47	.	0			c.T1060C						PASS	.						99	67	78					14																	77762563		2203	4300	6503	SO:0001583	missense	29954	exon9			GCAGATAGCCGAT	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.1060T>C	14.37:g.77762563A>G	ENSP00000261534:p.Tyr354His	34	0	0		51	7	0.137255	NM_013382	Q9NSG6|Q9P1W0|Q9P1W2	Missense_Mutation	SNP	ENST00000261534.4	37	CCDS9857.1	.	.	.	.	.	.	.	.	.	.	A	19.06	3.753167	0.69648	.	.	ENSG00000009830	ENST00000261534	D	0.88509	-2.39	4.98	4.98	0.66077	MIR motif (2);MIR (2);	0.000000	0.85682	D	0.000000	D	0.95014	0.8386	M	0.88842	2.985	0.80722	D	1	D	0.76494	0.999	D	0.79108	0.992	D	0.95884	0.8901	10	0.87932	D	0	-7.1602	14.6543	0.68823	1.0:0.0:0.0:0.0	.	354	Q9UKY4	POMT2_HUMAN	H	354	ENSP00000261534:Y354H	ENSP00000261534:Y354H	Y	-	1	0	POMT2	76832316	1.000000	0.71417	1.000000	0.80357	0.278000	0.26855	9.179000	0.94861	1.859000	0.53934	0.379000	0.24179	TAT	.	.	none		0.602	POMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414155.1	NM_013382		G	77762563	A	G	77762563	3	3	45	1	0	0	0	0	1	0	0	0	12255	420	15	3	1244	3	POMT2	14	77762563	Missense_Mutation	SNP	A	TCGA-RQ-A68N-01A-11D-A31X-10	2792389	77762563	29586977	144	15596											
NRXN3	9369	hgsc.bcm.edu	37	chr14	79432416	79432416	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggagttccacaacattgaaaCgggaatcatgactgagaaac	16	7	10	8	1	1	3	1	3	0	1	2	6	2	5	1	2	3	1	1	2	4	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr14:79432416C>T	ENST00000554719.1	+	9	1816	c.1325C>T	c.(1324-1326)aCg>aTg	p.T442M	NRXN3_ENST00000335750.5_Missense_Mutation_p.T442M	NM_004796.4	NP_004787.2	Q9HDB5	NRX3B_HUMAN	neurexin 3	211					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)		AACATTGAAACGGGAATCATG	0.433																																					p.T442M		Atlas-SNP	.											.	NRXN3	342	.	0			c.C1325T						PASS	.						117	104	108					14																	79432416		2203	4300	6503	SO:0001583	missense	9369	exon9			TTGAAACGGGAAT	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.1325C>T	14.37:g.79432416C>T	ENSP00000451648:p.Thr442Met	87	0	0		87	17	0.195402	NM_004796	A5PKW8|A8MPU5|B3KPM7|Q6NUR0|Q8IUD8	Missense_Mutation	SNP	ENST00000554719.1	37	CCDS9870.1	.	.	.	.	.	.	.	.	.	.	C	19.05	3.752562	0.69533	.	.	ENSG00000021645	ENST00000330071;ENST00000332068;ENST00000554719;ENST00000335750	T;T	0.78246	-1.16;-1.16	5.22	5.22	0.72569	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	0.88496	0.6452	.	.	.	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	D	0.87752	0.2592	8	.	.	.	.	19.3296	0.94280	0.0:1.0:0.0:0.0	.	815;442	Q9Y4C0;Q9Y4C0-3	NRX3A_HUMAN;.	M	815;804;442;442	ENSP00000451648:T442M;ENSP00000338349:T442M	.	T	+	2	0	NRXN3	78502169	1.000000	0.71417	0.951000	0.38953	0.381000	0.30169	7.609000	0.82925	2.873000	0.98535	0.563000	0.77884	ACG	.	.	none		0.433	NRXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413787.1	NM_001105250		T	79432416	C	T	79432416	3	4	45	1	0	0	0	0	1	0	0	0	10676	536	19	1	1351	1	NRXN3	14	79432416	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	1669853	79432416	27917124	145	15597											
BCL11B	64919	hgsc.bcm.edu	37	chr14	99640652	99640652	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cccgtgcgtcttcatgtggcGcgtgagcttgctgctctgcg	2	12	14	13	5	3	1	1	1	2	0	3	1	3	1	1	1	5	3	1	1	0	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr14:99640652G>A	ENST00000357195.3	-	4	2530	c.2521C>T	c.(2521-2523)Cgc>Tgc	p.R841C	BCL11B_ENST00000443726.2_Missense_Mutation_p.R647C|BCL11B_ENST00000345514.2_Missense_Mutation_p.R770C	NM_001282237.1|NM_138576.2	NP_001269166.1|NP_612808.1	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B (zinc finger protein)	841					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)		TTCATGTGGCGCGTGAGCTTG	0.622			T	TLX3	T-ALL																																p.R841C		Atlas-SNP	.		Dom	yes		14	14q32.1	64919	B-cell CLL/lymphoma 11B  (CTIP2)		L	BCL11B,NS,carcinoma,+1,2	BCL11B	108	2	0			c.C2521T						PASS	.						78	62	68					14																	99640652		2203	4300	6503	SO:0001583	missense	64919	exon4			TGTGGCGCGTGAG	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.2521C>T	14.37:g.99640652G>A	ENSP00000349723:p.Arg841Cys	24	0	0		25	6	0.24	NM_138576	Q9H162	Missense_Mutation	SNP	ENST00000357195.3	37	CCDS9950.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.343578	0.82022	.	.	ENSG00000127152	ENST00000357195;ENST00000345514;ENST00000443726	T;T;T	0.07688	3.17;3.17;3.17	4.7	4.7	0.59300	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.318118	0.23997	N	0.042508	T	0.24431	0.0592	L	0.46741	1.465	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.01033	-1.1474	10	0.72032	D	0.01	-19.448	17.9731	0.89119	0.0:0.0:1.0:0.0	.	770;841	Q9C0K0-2;Q9C0K0	.;BC11B_HUMAN	C	841;770;647	ENSP00000349723:R841C;ENSP00000280435:R770C;ENSP00000387419:R647C	ENSP00000280435:R770C	R	-	1	0	BCL11B	98710405	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.352000	0.97076	2.331000	0.79229	0.462000	0.41574	CGC	.	.	none		0.622	BCL11B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000072332.2	NM_138576		A	99640652	G	A	99640652	3	1	45	1	0	0	0	0	1	0	0	0	1364	1087	38	1	167	1	BCL11B	14	99640652	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	20208236	99640652	7708888	146	15598											
USP3	9960	hgsc.bcm.edu	37	chr15	63829314	63829314	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaaaagcaagataaagttcaGcacacagtatgtatggattg	17	9	10	5	0	1	1	1	0	0	1	1	3	1	2	0	1	2	5	0	1	7	5	rs567231691	byFrequency	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr15:63829314G>T	ENST00000380324.3	+	3	372	c.243G>T	c.(241-243)caG>caT	p.Q81H	USP3_ENST00000539772.1_Intron|USP3_ENST00000540797.1_Intron|USP3_ENST00000558285.1_Missense_Mutation_p.Q64H|USP3_ENST00000268049.7_Missense_Mutation_p.Q59H|USP3_ENST00000536001.1_Missense_Mutation_p.Q81H	NM_006537.3	NP_006528.2	Q9Y6I4	UBP3_HUMAN	ubiquitin specific peptidase 3	81					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)		ATAAAGTTCAGCACACAGTAT	0.368																																					p.Q81H		Atlas-SNP	.											.	USP3	37	.	0			c.G243T						PASS	.						121	93	102					15																	63829314		2203	4300	6503	SO:0001583	missense	9960	exon3			AGTTCAGCACACA	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.243G>T	15.37:g.63829314G>T	ENSP00000369681:p.Gln81His	311	0	0		278	97	0.348921	NM_006537	B4DVU5|F5H1A6|Q8WVD0	Missense_Mutation	SNP	ENST00000380324.3	37	CCDS32265.1	.	.	.	.	.	.	.	.	.	.	G	11.91	1.780649	0.31502	.	.	ENSG00000140455	ENST00000380324;ENST00000268049;ENST00000536001	T;T;T	0.30448	1.53;1.53;1.53	5.73	2.82	0.32997	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, UBP-type (2);	0.051593	0.85682	D	0.000000	T	0.23965	0.0580	L	0.37507	1.11	0.80722	D	1	B;B	0.24258	0.026;0.1	B;B	0.23419	0.037;0.046	T	0.07065	-1.0792	10	0.51188	T	0.08	.	10.8979	0.47034	0.2634:0.0:0.7366:0.0	.	59;81	Q6JHV3;Q9Y6I4	.;UBP3_HUMAN	H	81;59;81	ENSP00000369681:Q81H;ENSP00000268049:Q59H;ENSP00000445615:Q81H	ENSP00000268049:Q59H	Q	+	3	2	USP3	61616367	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	1.505000	0.35736	0.891000	0.36235	-0.150000	0.13652	CAG	.	.	none		0.368	USP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417773.1			T	63829314	G	T	63829314	3	4	45	1	0	0	0	0	1	0	0	0	17075	962	34	4	253	4	USP3	15	63829314	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10		63829314	38702078	147	15599											
C15orf39	56905	hgsc.bcm.edu	37	chr15	75500343	75500343	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctctgtggccttcatgttcCgaaagttcaagatcctccgt	7	13	9	12	2	3	1	2	0	1	1	6	2	6	1	4	1	0	3	4	1	2	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr15:75500343C>T	ENST00000360639.2	+	2	2274	c.1954C>T	c.(1954-1956)Cga>Tga	p.R652*	C15orf39_ENST00000394987.4_Nonsense_Mutation_p.R652*|C15orf39_ENST00000567617.1_Nonsense_Mutation_p.R652*			Q6ZRI6	CO039_HUMAN	chromosome 15 open reading frame 39	652						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(2)|endometrium(3)|large_intestine(4)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	16						CTTCATGTTCCGAAAGTTCAA	0.602																																					p.R652X		Atlas-SNP	.											.	C15orf39	64	.	0			c.C1954T						PASS	.						99	85	90					15																	75500343		2197	4295	6492	SO:0001587	stop_gained	56905	exon2			ATGTTCCGAAAGT	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.1954C>T	15.37:g.75500343C>T	ENSP00000353854:p.Arg652*	59	0	0		60	19	0.316667	NM_015492	B3KWI3|C9J888|Q71JB1|Q7L3S0|Q8N3F2|Q96FB6|Q9NTU5	Nonsense_Mutation	SNP	ENST00000360639.2	37	CCDS10276.1	.	.	.	.	.	.	.	.	.	.	C	42	9.497434	0.99187	.	.	ENSG00000167173	ENST00000360639;ENST00000394987;ENST00000446981	.	.	.	5.64	3.67	0.42095	.	0.378991	0.25701	N	0.028880	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.1494	8.5421	0.33399	0.3109:0.5386:0.1506:0.0	.	.	.	.	X	652;652;50	.	ENSP00000353854:R652X	R	+	1	2	C15orf39	73287396	0.996000	0.38824	0.974000	0.42286	0.996000	0.88848	1.192000	0.32150	0.667000	0.31107	0.655000	0.94253	CGA	.	.	none		0.602	C15orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286410.1	NM_015492		T	75500343	C	T	75500343	4	4	45	1	0	0	0	0	0	1	0	0	1795	644	23	1	1956	1	C15orf39	15	75500343	Nonsense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	11671029	75500343	27031049	148	15600											
KIAA1199	57214	hgsc.bcm.edu	37	chr15	81188310	81188310	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaacctggagataccctggtCattgccagtactgattactc	11	11	8	11	0	1	2	1	1	0	1	2	3	1	2	3	2	5	1	3	2	4	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr15:81188310C>T	ENST00000394685.3	+	12	1739	c.1320C>T	c.(1318-1320)gtC>gtT	p.V440V	KIAA1199_ENST00000220244.3_Silent_p.V440V|RP11-351M8.2_ENST00000560873.1_RNA|KIAA1199_ENST00000356249.5_Silent_p.V440V			Q8WUJ3	CEMIP_HUMAN		440	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						ATACCCTGGTCATTGCCAGTA	0.507																																					p.V440V		Atlas-SNP	.											.	KIAA1199	118	.	0			c.C1320T						PASS	.						164	138	147					15																	81188310		2203	4300	6503	SO:0001819	synonymous_variant	57214	exon11			CCTGGTCATTGCC																												ENST00000394685.3:c.1320C>T	15.37:g.81188310C>T		110	0	0		118	30	0.254237	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Silent	SNP	ENST00000394685.3	37	CCDS10315.1																																																																																			.	.	none		0.507	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1			T	81188310	C	T	81188310	2	4	45	1	0	0	0	0	0	0	0	1	8222	813	29	2		2	KIAA1199	15	81188310	Silent	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	5687967	81188310	21343082	149	15601											
WHAMM	123720	hgsc.bcm.edu	37	chr15	83499809	83499809	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gctgagcgaccacgtgactcCttggaaagtttttcatgtcc	8	12	10	11	2	1	2	1	2	0	0	3	4	3	3	3	1	1	2	3	1	1	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr15:83499809C>T	ENST00000286760.4	+	9	2199	c.2100C>T	c.(2098-2100)tcC>tcT	p.S700S		NM_001080435.1	NP_001073904.1	Q8TF30	WHAMM_HUMAN	WAS protein homolog associated with actin, golgi membranes and microtubules	700	Mediates actin nucleation. {ECO:0000269|PubMed:18614018}.				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						CACGTGACTCCTTGGAAAGTT	0.498																																					p.S700S		Atlas-SNP	.											.	WHAMM	63	.	0			c.C2100T						PASS	.						113	119	117					15																	83499809		2165	4279	6444	SO:0001819	synonymous_variant	123720	exon9			TGACTCCTTGGAA	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.2100C>T	15.37:g.83499809C>T		8	0	0		17	7	0.411765	NM_001080435	Q8N1J9	Silent	SNP	ENST00000286760.4	37	CCDS45333.1																																																																																			.	.	none		0.498	WHAMM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418463.1			T	83499809	C	T	83499809	2	4	45	1	0	0	0	0	0	0	0	1	17376	668	24	2		2	WHAMM	15	83499809	Silent	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	2311499	83499809	19031583	150	15602											
BNC1	646	hgsc.bcm.edu	37	chr15	83932823	83932823	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttagggagctgaacaccaTgttacacccttcgatggtgc	9	10	10	12	1	0	1	0	1	0	0	1	3	0	2	3	2	4	2	3	2	3	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr15:83932823T>A	ENST00000345382.2	-	4	1265	c.1180A>T	c.(1180-1182)Atg>Ttg	p.M394L	RP11-382A20.4_ENST00000565495.1_RNA|BNC1_ENST00000569704.1_Missense_Mutation_p.M387L	NM_001717.3	NP_001708.3	Q01954	BNC1_HUMAN	basonuclin 1	394					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						CTGAACACCATGTTACACCCT	0.507																																					p.M394L		Atlas-SNP	.											.	BNC1	149	.	0			c.A1180T						PASS	.						156	142	147					15																	83932823		2203	4300	6503	SO:0001583	missense	646	exon4			ACACCATGTTACA	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.1180A>T	15.37:g.83932823T>A	ENSP00000307041:p.Met394Leu	159	0	0		124	33	0.266129	NM_001717	Q15840	Missense_Mutation	SNP	ENST00000345382.2	37	CCDS10324.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.455053	0.84209	.	.	ENSG00000169594	ENST00000345382;ENST00000541809	T	0.26810	1.71	5.75	5.75	0.90469	Zinc finger, C2H2-like (1);	0.078751	0.85682	D	0.000000	T	0.54431	0.1858	M	0.80183	2.485	0.80722	D	1	D;P	0.59357	0.985;0.882	D;P	0.74674	0.984;0.858	T	0.59878	-0.7371	10	0.87932	D	0	-37.7656	16.0707	0.80928	0.0:0.0:0.0:1.0	.	387;394	F5GY04;Q01954	.;BNC1_HUMAN	L	394;387	ENSP00000307041:M394L	ENSP00000307041:M394L	M	-	1	0	BNC1	81723827	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.975000	0.88055	2.194000	0.70268	0.533000	0.62120	ATG	.	.	none		0.507	BNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304006.1	NM_001717		A	83932823	T	A	83932823	3	1	45	1	0	0	0	0	1	0	0	0	1474	1464	51	5	1812	5	BNC1	15	83932823	Missense_Mutation	SNP	T	TCGA-RQ-A68N-01A-11D-A31X-10	433014	83932823	18598569	151	15603											
NARFL	64428	hgsc.bcm.edu	37	chr16	787323	787323	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cttctccagcctccgggtccCgccgtcctacaagggagaag	7	7	11	16	3	1	1	0	0	1	1	5	2	4	1	6	2	2	0	6	2	3	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr16:787323C>G	ENST00000251588.2	-	3	185	c.169G>C	c.(169-171)Ggg>Cgg	p.G57R	NARFL_ENST00000301694.5_Missense_Mutation_p.G57R|NARFL_ENST00000568545.1_5'UTR|NARFL_ENST00000540986.1_5'UTR	NM_022493.1	NP_071938.1	Q9H6Q4	NARFL_HUMAN	nuclear prelamin A recognition factor-like	57					hematopoietic progenitor cell differentiation (GO:0002244)|iron-sulfur cluster assembly (GO:0016226)|oxygen homeostasis (GO:0032364)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)	CIA complex (GO:0097361)	4 iron, 4 sulfur cluster binding (GO:0051539)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|large_intestine(1)|lung(7)	9		Hepatocellular(780;0.0218)				CTCCGGGTCCCGCCGTCCTAC	0.617																																					p.G57R		Atlas-SNP	.											NARFL,NS,carcinoma,0,1	NARFL	31	1	0			c.G169C						PASS	.						63	64	63					16																	787323		2200	4299	6499	SO:0001583	missense	64428	exon3			GGGTCCCGCCGTC	AY129231	CCDS10425.1	16p13.3	2009-12-17			ENSG00000103245	ENSG00000103245			14179	protein-coding gene	gene with protein product	"iron-only hydrogenase-like protein 1"	611118				16956324	Standard	NM_022493		Approved	FLJ21988, PRN, HPRN, IOP1	uc002cjr.3	Q9H6Q4	OTTHUMG00000122093	ENST00000251588.2:c.169G>C	16.37:g.787323C>G	ENSP00000251588:p.Gly57Arg	77	0	0		67	32	0.477612	NM_022493	A1L385|B3KTJ3|Q53GC6|Q96S10|Q9H6J8	Missense_Mutation	SNP	ENST00000251588.2	37	CCDS10425.1	.	.	.	.	.	.	.	.	.	.	C	8.934	0.964176	0.18583	.	.	ENSG00000103245	ENST00000251588;ENST00000301694	T;T	0.25912	1.77;1.77	4.29	2.31	0.28768	.	0.195215	0.43919	N	0.000519	T	0.15262	0.0368	L	0.28694	0.88	0.09310	N	0.999999	B;B;B	0.31174	0.311;0.311;0.002	B;B;B	0.30251	0.113;0.113;0.002	T	0.23368	-1.0190	10	0.16896	T	0.51	-28.7067	8.6826	0.34218	0.0:0.8105:0.0:0.1895	.	57;57;57	B4DT78;B4DEE7;Q9H6Q4	.;.;NARFL_HUMAN	R	57	ENSP00000251588:G57R;ENSP00000301694:G57R	ENSP00000251588:G57R	G	-	1	0	NARFL	727324	0.475000	0.25894	0.026000	0.17262	0.467000	0.32768	3.402000	0.52608	0.455000	0.26910	-0.192000	0.12808	GGG	.	.	none		0.617	NARFL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242855.1	NM_022493		G	787323	C	G	787323	3	3	45	1	0	0	0	0	1	0	0	0	10177	652	23	4	1297	4	NARFL	16	787323	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10		787323	89567430	152	15604											
GGA2	23062	hgsc.bcm.edu	37	chr16	23498055	23498055	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ttgaccaaattcttgattaaCcggtttgcagcctgaaggtc	10	13	9	9	1	1	3	0	3	1	0	2	3	1	3	3	2	3	2	3	2	3	5			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr16:23498055C>T	ENST00000309859.4	-	7	718	c.636G>A	c.(634-636)cgG>cgA	p.R212R	GGA2_ENST00000567468.1_Intron	NM_015044.4	NP_055859.1	Q9UJY4	GGA2_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 2	212	GAT. {ECO:0000255|PROSITE- ProRule:PRU00373}.				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)		TCTTGATTAACCGGTTTGCAG	0.493																																					p.R212R		Atlas-SNP	.											.	GGA2	49	.	0			c.G636A						PASS	.						288	275	279					16																	23498055		2197	4300	6497	SO:0001819	synonymous_variant	23062	exon7			GATTAACCGGTTT	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.636G>A	16.37:g.23498055C>T		104	0	0		102	25	0.245098	NM_015044	D3DWF0|O14564|Q9NYN2|Q9UPS2	Silent	SNP	ENST00000309859.4	37	CCDS10611.1																																																																																			.	.	none		0.493	GGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214019.1			T	23498055	C	T	23498055	2	4	45	1	0	0	0	0	0	0	0	1	6361	494	18	2		2	GGA2	16	23498055	Silent	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	22710732	23498055	66856698	153	15605											
ZNF785	146540	hgsc.bcm.edu	37	chr16	30594344	30594344	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	agcacgcgtaaggcttctccCcggtgtgagcccgcctgtgg	5	8	14	14	4	1	1	0	1	1	0	2	1	1	1	4	3	2	3	4	3	1	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr16:30594344C>T	ENST00000395216.2	-	3	914	c.755G>A	c.(754-756)gGg>gAg	p.G252E	RP11-146F11.5_ENST00000563540.1_RNA|AC002310.7_ENST00000486926.1_RNA|ZNF785_ENST00000470110.1_Missense_Mutation_p.G237E|AC002310.7_ENST00000492040.1_RNA	NM_152458.6	NP_689671.2	A8K8V0	ZN785_HUMAN	zinc finger protein 785	252					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						AGGCTTCTCCCCGGTGTGAGC	0.657																																					p.G252E		Atlas-SNP	.											ZNF785,NS,carcinoma,+1,1	ZNF785	30	1	0			c.G755A						PASS	.						43	39	40					16																	30594344		2197	4300	6497	SO:0001583	missense	146540	exon3			TTCTCCCCGGTGT	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.755G>A	16.37:g.30594344C>T	ENSP00000378642:p.Gly252Glu	87	0	0		87	12	0.137931	NM_152458	O75701|Q8IW91|Q8WV14|Q96MN0	Missense_Mutation	SNP	ENST00000395216.2	37	CCDS10685.1	.	.	.	.	.	.	.	.	.	.	c	22.8	4.333110	0.81801	.	.	ENSG00000197162	ENST00000470110;ENST00000395222;ENST00000395216	T;T	0.25749	1.78;1.78	3.48	2.53	0.30540	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.37972	0.1023	L	0.38531	1.155	0.25695	N	0.985645	D;D;D	0.89917	0.981;1.0;0.977	P;D;B	0.91635	0.51;0.999;0.376	T	0.09207	-1.0685	9	0.87932	D	0	.	9.2692	0.37661	0.0:0.8899:0.0:0.1101	.	217;252;237	B4DQL1;A8K8V0;A8K8V0-2	.;ZN785_HUMAN;.	E	237;217;252	ENSP00000420340:G237E;ENSP00000378642:G252E	ENSP00000378642:G252E	G	-	2	0	ZNF785	30501845	0.938000	0.31826	0.229000	0.23960	0.537000	0.34900	3.507000	0.53371	1.077000	0.40990	-0.152000	0.13540	GGG	.	.	none		0.657	ZNF785-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255529.2	NM_152458		T	30594344	C	T	30594344	3	4	45	1	0	0	0	0	1	0	0	0	18172	623	22	2	466	2	ZNF785	16	30594344	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	7096289	30594344	59760409	154	15606											
ZNF319	57567	hgsc.bcm.edu	37	chr16	58030541	58030541	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctccccgcaccatacacaCttgaactgctgctcgcgggc	7	7	9	18	4	0	1	0	1	0	0	2	1	1	1	3	1	4	4	3	1	2	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr16:58030541C>T	ENST00000299237.2	-	2	2251	c.1629G>A	c.(1627-1629)aaG>aaA	p.K543K	USB1_ENST00000561743.1_5'Flank	NM_020807.1	NP_065858.1	Q9P2F9	ZN319_HUMAN	zinc finger protein 319	543					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(2)|lung(4)|ovary(1)|urinary_tract(1)	8						ACCATACACACTTGAACTGCT	0.662																																					p.K543K		Atlas-SNP	.											.	ZNF319	42	.	0			c.G1629A						PASS	.						42	35	37					16																	58030541		2198	4300	6498	SO:0001819	synonymous_variant	57567	exon2			TACACACTTGAAC	AB037809	CCDS32462.1	16q21	2013-01-08				ENSG00000166188		"Zinc fingers, C2H2-type"	13644	protein-coding gene	gene with protein product						10718198, 11161788	Standard	XM_005256069		Approved	KIAA1388, Zfp319	uc002emx.1	Q9P2F9		ENST00000299237.2:c.1629G>A	16.37:g.58030541C>T		42	0	0		60	7	0.116667	NM_020807	Q52LH8	Silent	SNP	ENST00000299237.2	37	CCDS32462.1																																																																																			.	.	none		0.662	ZNF319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430317.1			T	58030541	C	T	58030541	2	4	45	1	0	0	0	0	0	0	0	1	17852	564	20	2		2	ZNF319	16	58030541	Silent	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	27436197	58030541	32324212	155	15607											
ZDHHC7	55625	hgsc.bcm.edu	37	chr16	85024162	85024162	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gacgatgaagagtcatagttGtcattttcagccaggagagg	12	10	13	6	1	3	3	3	1	0	2	3	6	3	3	1	2	1	1	1	2	2	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr16:85024162G>A	ENST00000313732.4	-	3	415	c.63C>T	c.(61-63)gaC>gaT	p.D21D	ZDHHC7_ENST00000564466.1_Silent_p.D21D|ZDHHC7_ENST00000569488.1_5'UTR	NM_017740.2	NP_060210.2	Q9NXF8	ZDHC7_HUMAN	zinc finger, DHHC-type containing 7	21					peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein palmitoylation (GO:0018345)	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)			large_intestine(6)|lung(4)	10						AGTCATAGTTGTCATTTTCAG	0.592																																					p.D21D		Atlas-SNP	.											.	ZDHHC7	55	.	0			c.C63T						PASS	.						103	82	89					16																	85024162		2199	4300	6499	SO:0001819	synonymous_variant	55625	exon3			ATAGTTGTCATTT	AK000286	CCDS10950.1, CCDS45538.1	16q23.1	2010-02-09			ENSG00000153786	ENSG00000153786		"Zinc fingers, DHHC-type"	18459	protein-coding gene	gene with protein product	"Sertoli cell gene with zinc finger domain-&#946;"	614604					Standard	NM_017740		Approved	FLJ10792, ZNF370, FLJ20279, SERZ-B, SERZ1	uc002fiq.2	Q9NXF8	OTTHUMG00000137645	ENST00000313732.4:c.63C>T	16.37:g.85024162G>A		74	0	0		62	27	0.435484	NM_001145548	D3DUM1|Q8WV42|Q9NVD8	Silent	SNP	ENST00000313732.4	37	CCDS10950.1																																																																																			.	.	none		0.592	ZDHHC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269087.1	NM_017740		A	85024162	G	A	85024162	2	1	45	1	0	0	0	0	0	0	0	1	17635	1368	48	2		2	ZDHHC7	16	85024162	Silent	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	26993621	85024162	5330591	156	15608											
ACADVL	37	hgsc.bcm.edu	37	chr17	7124102	7124103	+	Frame_Shift_Del	DEL	AC	AC	-																															cagtgctcaacgaagagcagAcacagtttcttaaagagctg																										TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr17:7124102_7124103delAC	ENST00000356839.5	+	5	474_475	c.295_296delAC	c.(295-297)acafs	p.T99fs	ACADVL_ENST00000350303.5_Frame_Shift_Del_p.T77fs|ACADVL_ENST00000581562.1_3'UTR|DLG4_ENST00000399510.2_5'Flank|ACADVL_ENST00000543245.2_Frame_Shift_Del_p.T122fs|MIR324_ENST00000362183.1_RNA	NM_000018.3|NM_001270448.1	NP_000009.1|NP_001257377.1	P49748	ACADV_HUMAN	acyl-CoA dehydrogenase, very long chain	99	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						CGAAGAGCAGACACAGTTTCTT	0.574																																					p.121_122del		Pindel,Atlas-Indel	.											ACADVL,NS,carcinoma,0,1	ACADVL	43	1	0			c.363_364del						PASS	.																																			SO:0001589	frameshift_variant	37	exon6			.	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.295_296delAC	17.37:g.7124104_7124105delAC	ENSP00000349297:p.Thr99fs	0	0	.		13	13	1	NM_001270447	B4DEB6|F5H2A9|O76056|Q8WUL0	Frame_Shift_Del	DEL	ENST00000356839.5	37	CCDS11090.1																																																																																			.	.	none		0.574	ACADVL-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220001.5	NM_000018		-	7124103	AC	-	7124102	7	5	45	1	0	1	0	1	0	0	0	0	116	275	10	0	313	0	ACADVL	17	7124102	Frame_Shift_Del	DEL	AC	TCGA-RQ-A68N-01A-11D-A31X-10		7124102	74071108	157	15609											
NEURL4	84461	hgsc.bcm.edu	37	chr17	7221436	7221436	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caaagggcatggtactcgcaGctctttagaggactagcggc	10	8	13	10	2	1	1	0	0	1	1	2	2	1	2	0	4	3	4	0	4	4	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr17:7221436G>C	ENST00000399464.2	-	25	4023	c.4008C>G	c.(4006-4008)agC>agG	p.S1336R	RP11-542C16.2_ENST00000575474.1_Missense_Mutation_p.A150G|NEURL4_ENST00000570460.1_Missense_Mutation_p.S1312R|NEURL4_ENST00000574120.1_5'UTR|GPS2_ENST00000380728.2_5'Flank|GPS2_ENST00000391950.3_5'Flank|GPS2_ENST00000389167.5_5'Flank|NEURL4_ENST00000315614.7_Missense_Mutation_p.S1334R	NM_032442.2	NP_115818.2	Q96JN8	NEUL4_HUMAN	neuralized E3 ubiquitin protein ligase 4	1336						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						GGTACTCGCAGCTCTTTAGAG	0.597																																					p.S1336R		Atlas-SNP	.											.	NEURL4	192	.	0			c.C4008G						PASS	.						97	108	105					17																	7221436		2064	4205	6269	SO:0001583	missense	84461	exon25			CTCGCAGCTCTTT		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.4008C>G	17.37:g.7221436G>C	ENSP00000382390:p.Ser1336Arg	54	0	0		46	5	0.108696	NM_032442	Q6GPI8|Q96IU9|Q9H0B0	Missense_Mutation	SNP	ENST00000399464.2	37	CCDS42251.1	.	.	.	.	.	.	.	.	.	.	G	13.83	2.355021	0.41700	.	.	ENSG00000215041	ENST00000315614;ENST00000399464	T;T	0.32515	1.45;1.45	5.03	1.81	0.25067	.	0.098701	0.64402	D	0.000002	T	0.26774	0.0655	L	0.59436	1.845	0.30519	N	0.768615	P;P	0.47677	0.899;0.838	B;B	0.39258	0.295;0.154	T	0.33854	-0.9852	10	0.66056	D	0.02	-29.3741	9.9785	0.41800	0.2648:0.0:0.7352:0.0	.	1334;1336	Q96JN8-2;Q96JN8	.;NEUL4_HUMAN	R	1334;1336	ENSP00000319826:S1334R;ENSP00000382390:S1336R	ENSP00000319826:S1334R	S	-	3	2	NEURL4	7162160	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	1.751000	0.38339	0.727000	0.32360	0.305000	0.20034	AGC	.	.	none		0.597	NEURL4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255434.2	NM_032442		C	7221436	G	C	7221436	3	2	45	1	0	0	0	0	1	0	0	0	10356	962	34	4	700	4	NEURL4	17	7221436	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	97334	7221436	73973774	158	15610											
C17orf48	56985	hgsc.bcm.edu	37	chr17	10608524	10608524	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagtccctagaacttgttaTggacatgttcaagaggctta	13	12	9	7	0	1	2	1	0	0	2	2	3	2	3	1	2	1	3	1	2	6	5			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr17:10608524T>C	ENST00000379774.4	+	2	372	c.281T>C	c.(280-282)aTg>aCg	p.M94T	ADPRM_ENST00000609540.1_Missense_Mutation_p.M94T	NM_020233.4	NP_064618.3	Q3LIE5	ADPRM_HUMAN	ADP-ribose/CDP-alcohol diphosphatase, manganese-dependent	94							ADP-ribose diphosphatase activity (GO:0047631)|CDP-glycerol diphosphatase activity (GO:0047734)|metal ion binding (GO:0046872)										GAACTTGTTATGGACATGTTC	0.378																																					p.M94T		Atlas-SNP	.											.	.	.	.	0			c.T281C						PASS	.						102	96	98					17																	10608524		2203	4300	6503	SO:0001583	missense	56985	exon2			TTGTTATGGACAT	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.281T>C	17.37:g.10608524T>C	ENSP00000369099:p.Met94Thr	157	0	0		100	6	0.06	NM_020233	A8K9B4|D3DTS4|Q9BVD4|Q9NRU8	Missense_Mutation	SNP	ENST00000379774.4	37	CCDS11159.2	.	.	.	.	.	.	.	.	.	.	T	13.94	2.387844	0.42308	.	.	ENSG00000170222	ENST00000379774	D	0.84589	-1.87	5.65	5.65	0.86999	Metallophosphoesterase domain (1);	0.252882	0.47093	D	0.000257	D	0.87450	0.6180	L	0.37561	1.115	0.80722	D	1	B	0.30634	0.288	P	0.52424	0.698	T	0.82339	-0.0506	10	0.16420	T	0.52	-16.4474	15.7104	0.77623	0.0:0.0:0.0:1.0	.	94	Q3LIE5	ADPRM_HUMAN	T	94	ENSP00000369099:M94T	ENSP00000369099:M94T	M	+	2	0	C17orf48	10549249	1.000000	0.71417	0.815000	0.32552	0.716000	0.41182	7.127000	0.77210	2.371000	0.80710	0.533000	0.62120	ATG	.	.	none		0.378	ADPRM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252732.2	NM_020233		C	10608524	T	C	10608524	3	2	45	1	0	0	0	0	1	0	0	0	1861	1464	51	3	283	3	C17orf48	17	10608524	Missense_Mutation	SNP	T	TCGA-RQ-A68N-01A-11D-A31X-10	3387088	10608524	70586686	159	15611											
MAP2K4	6416	hgsc.bcm.edu	37	chr17	12044515	12044515	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgccgttgaggtcgcatgcTatgtttgtaaaatcctggat	8	14	12	7	2	0	1	0	1	0	0	2	2	1	2	2	2	2	5	2	2	3	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr17:12044515T>C	ENST00000353533.5	+	11	1201	c.1138T>C	c.(1138-1140)Tat>Cat	p.Y380H	MAP2K4_ENST00000415385.3_Missense_Mutation_p.Y391H	NM_003010.2	NP_003001.1	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4	380	DVD domain.				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.?(2)		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)		GGTCGCATGCTATGTTTGTAA	0.408			"D, Mis, N"		"pancreatic, breast, colorectal"																																p.Y380H		Atlas-SNP	.		Rec	yes		17	17p11.2	6416	mitogen-activated protein kinase kinase 4		E	.	MAP2K4	176	.	12	Whole gene deletion(10)|Unknown(2)	ovary(4)|breast(4)|pancreas(2)|biliary_tract(1)|lung(1)	c.T1138C						PASS	.						151	131	138					17																	12044515		2203	4300	6503	SO:0001583	missense	6416	exon11			GCATGCTATGTTT	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.1138T>C	17.37:g.12044515T>C	ENSP00000262445:p.Tyr380His	94	0	0		78	4	0.0512821	NM_003010	B2R7N7|B3KYB2|D3DTS5|Q5U0B8|Q6FHX4|Q6P9H2|Q6PIE6	Missense_Mutation	SNP	ENST00000353533.5	37	CCDS11162.1	.	.	.	.	.	.	.	.	.	.	T	23.9	4.467476	0.84533	.	.	ENSG00000065559	ENST00000353533;ENST00000415385;ENST00000538465;ENST00000536413	T;T	0.20200	2.09;2.09	5.53	5.53	0.82687	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	T	0.45196	0.1330	M	0.67953	2.075	0.80722	D	1	D;D;D	0.76494	0.999;0.998;0.997	D;D;D	0.76071	0.909;0.987;0.971	T	0.41395	-0.9511	10	0.87932	D	0	.	14.7836	0.69784	0.0:0.0:0.0:1.0	.	252;391;380	B7ZA62;P45985-2;P45985	.;.;MP2K4_HUMAN	H	380;391;357;252	ENSP00000262445:Y380H;ENSP00000410402:Y391H	ENSP00000262445:Y380H	Y	+	1	0	MAP2K4	11985240	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.864000	0.87037	2.322000	0.78497	0.528000	0.53228	TAT	.	.	none		0.408	MAP2K4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441226.1			C	12044515	T	C	12044515	3	2	45	1	0	0	0	0	1	0	0	0	9248	1522	53	3	1180	3	MAP2K4	17	12044515	Missense_Mutation	SNP	T	TCGA-RQ-A68N-01A-11D-A31X-10	1435991	12044515	69150695	160	15612											
ACCN1	40	hgsc.bcm.edu	37	chr17	31618815	31618815	+	Intron	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gctgagccagtagagcaagcGgttcgaggaccaggacagca	12	4	15	10	2	0	2	0	1	0	1	1	5	0	4	2	3	4	5	2	3	2	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr17:31618815G>A	ENST00000359872.6	-	2	1317				ASIC2_ENST00000448983.1_5'Flank|ASIC2_ENST00000225823.2_Missense_Mutation_p.R107C	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)	TAGAGCAAGCGGTTCGAGGAC	0.672																																					p.R107C		Atlas-SNP	.											.	.	.	.	0			c.C319T						PASS	.						36	36	36					17																	31618815		2203	4297	6500	SO:0001627	intron_variant	40	exon1			GCAAGCGGTTCGA	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.556-179730C>T	17.37:g.31618815G>A		48	0	0		36	4	0.111111	NM_183377	E9PBX2|Q13553|Q6DJU1|Q8N3E2	Missense_Mutation	SNP	ENST00000359872.6	37	CCDS42296.1	.	.	.	.	.	.	.	.	.	.	G	16.21	3.058468	0.55325	.	.	ENSG00000108684	ENST00000225823	T	0.65916	-0.18	4.73	3.74	0.42951	.	0.065766	0.56097	D	0.000040	T	0.65647	0.2711	M	0.79258	2.445	0.80722	D	1	P	0.50369	0.934	P	0.47044	0.535	T	0.65533	-0.6145	10	0.38643	T	0.18	-3.7744	10.0793	0.42379	0.0:0.0:0.635:0.365	.	107	E9PBX2	.	C	107	ENSP00000225823:R107C	ENSP00000225823:R107C	R	-	1	0	ACCN1	28642928	1.000000	0.71417	1.000000	0.80357	0.806000	0.45545	5.203000	0.65174	0.937000	0.37394	0.313000	0.20887	CGC	.	.	none		0.672	ASIC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447552.1	NM_183377, NM_001094		A	31618815	G	A	31618815	1	1	45	0	1	0	0	0	0	0	0	0	128	1116	39	1		1	ACCN1	17	31618815	Intron	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	19574300	31618815	49576395	161	15613											
ACACA	31	hgsc.bcm.edu	37	chr17	35609904	35609904	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	taacaatttgatcaggtattCaactgtagttcgaaagtcac	14	13	7	7	1	3	1	3	1	0	0	4	2	3	1	0	1	2	3	0	1	6	6			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr17:35609904C>T	ENST00000394406.2	-	15	1964	c.1774G>A	c.(1774-1776)Gaa>Aaa	p.E592K	ACACA_ENST00000335166.5_Missense_Mutation_p.E514K|ACACA_ENST00000360679.3_Missense_Mutation_p.E534K|ACACA_ENST00000353139.5_Missense_Mutation_p.E629K	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	592	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)	ATCAGGTATTCAACTGTAGTT	0.423																																					p.E629K	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-SNP	.											.	ACACA	395	.	0			c.G1885A						PASS	.						159	155	156					17																	35609904		2203	4300	6503	SO:0001583	missense	31	exon15			GGTATTCAACTGT	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.1774G>A	17.37:g.35609904C>T	ENSP00000377928:p.Glu592Lys	95	0	0		91	17	0.186813	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Missense_Mutation	SNP	ENST00000394406.2	37	CCDS11317.1	.	.	.	.	.	.	.	.	.	.	C	36	5.896819	0.97081	.	.	ENSG00000132142	ENST00000353139;ENST00000360679;ENST00000394406;ENST00000452074;ENST00000335166	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	6.04	6.04	0.98038	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	0.68366	0.2993	M	0.82056	2.57	0.80722	D	1	D;D;D	0.60575	0.984;0.988;0.984	D;D;P	0.71414	0.973;0.934;0.891	T	0.68808	-0.5311	10	0.59425	D	0.04	-18.994	19.5674	0.95401	0.0:1.0:0.0:0.0	.	629;592;534	Q13085-4;Q13085;Q13085-2	.;ACACA_HUMAN;.	K	629;534;592;616;514	ENSP00000344789:E629K;ENSP00000353898:E534K;ENSP00000377928:E592K;ENSP00000335323:E514K	ENSP00000335323:E514K	E	-	1	0	ACACA	32684017	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	7.818000	0.86416	2.873000	0.98535	0.561000	0.74099	GAA	.	.	none		0.423	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836		T	35609904	C	T	35609904	3	4	45	1	0	0	0	0	1	0	0	0	106	835	29	2	5434	2	ACACA	17	35609904	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	3991089	35609904	45585306	162	15614											
STAT3	6774	hgsc.bcm.edu	37	chr17	40485746	40485746	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gacgaggggccggtcaggatGcatgggcatgcagggctgcc	7	5	19	10	2	1	0	1	0	0	0	1	3	1	1	2	6	3	4	2	6	0	0			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr17:40485746G>A	ENST00000264657.5	-	10	1306	c.994C>T	c.(994-996)Cat>Tat	p.H332Y	STAT3_ENST00000389272.3_Missense_Mutation_p.H234Y|STAT3_ENST00000404395.3_Missense_Mutation_p.H332Y|STAT3_ENST00000585517.1_Missense_Mutation_p.H332Y|STAT3_ENST00000588969.1_Missense_Mutation_p.H332Y	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)	332					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)		CGGTCAGGATGCATGGGCATG	0.577									Hyperimmunoglobulin E Recurrent Infection Syndrome																												p.H332Y		Atlas-SNP	.											.	STAT3	268	.	0			c.C994T	GRCh37	CM085729	STAT3	M		PASS	.						72	65	67					17																	40485746		2203	4300	6503	SO:0001583	missense	6774	exon10	Familial Cancer Database	HIES, Hyper IgE syndrome, autosomal dominant (Job syndrome) / recessive	CAGGATGCATGGG	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.994C>T	17.37:g.40485746G>A	ENSP00000264657:p.His332Tyr	66	0	0		71	24	0.338028	NM_003150	A8K7B8|K7ENL3|O14916|Q9BW54	Missense_Mutation	SNP	ENST00000264657.5	37	CCDS32656.1	.	.	.	.	.	.	.	.	.	.	G	34	5.310461	0.95629	.	.	ENSG00000168610	ENST00000264657;ENST00000389272;ENST00000404395	D;D;D	0.88586	-2.4;-2.4;-2.4	5.41	5.41	0.78517	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	0.92639	0.7661	L	0.48362	1.52	0.80722	D	1	D;D;D	0.58268	0.978;0.982;0.982	D;D;D	0.71414	0.955;0.973;0.973	D	0.92482	0.5993	10	0.51188	T	0.08	-37.9112	19.1988	0.93701	0.0:0.0:1.0:0.0	.	332;332;332	P40763-2;P40763;B5BTZ6	.;STAT3_HUMAN;.	Y	332;234;332	ENSP00000264657:H332Y;ENSP00000373923:H234Y;ENSP00000384943:H332Y	ENSP00000264657:H332Y	H	-	1	0	STAT3	37739272	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.869000	0.99810	2.531000	0.85337	0.655000	0.94253	CAT	.	.	none		0.577	STAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319353.3	NM_139276, NM_003150		A	40485746	G	A	40485746	3	1	45	1	0	0	0	0	1	0	0	0	15281	1319	46	2	1378	2	STAT3	17	40485746	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	4875842	40485746	40709464	163	15615											
KCNH6	81033	hgsc.bcm.edu	37	chr17	61622590	61622590	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	cggagacgacgagtccagggCccaggctgccccagggcttt	7	5	15	14	3	0	1	0	0	0	1	1	4	1	1	4	4	1	2	4	4	0	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr17:61622590C>G	ENST00000583023.1	+	13	2667	c.2656C>G	c.(2656-2658)Ccc>Gcc	p.P886A	KCNH6_ENST00000456941.2_Missense_Mutation_p.P797A|KCNH6_ENST00000314672.5_Missense_Mutation_p.P850A|KCNH6_ENST00000581784.1_Missense_Mutation_p.P797A	NM_030779.2	NP_110406.1	Q9H252	KCNH6_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 6	886					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)	GAGTCCAGGGCCCAGGCTGCC	0.632																																					p.P886A		Atlas-SNP	.											.	KCNH6	122	.	0			c.C2656G						PASS	.						53	54	54					17																	61622590		2203	4300	6503	SO:0001583	missense	81033	exon13			CCAGGGCCCAGGC	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.2656C>G	17.37:g.61622590C>G	ENSP00000463533:p.Pro886Ala	67	0	0		45	22	0.488889	NM_030779	Q9BRD7	Missense_Mutation	SNP	ENST00000583023.1	37	CCDS11638.1	.	.	.	.	.	.	.	.	.	.	C	7.956	0.745821	0.15710	.	.	ENSG00000173826	ENST00000314672;ENST00000456941	D	0.99220	-5.58	4.82	1.64	0.23874	.	1.794330	0.02752	N	0.117564	D	0.96759	0.8942	L	0.29908	0.895	0.09310	N	0.999998	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	D	0.93664	0.6984	10	0.10377	T	0.69	.	4.0312	0.09710	0.1928:0.5845:0.1298:0.0929	.	727;850;797;886	B4DPJ3;B4DKC0;Q9H252-2;Q9H252	.;.;.;KCNH6_HUMAN	A	886;797	ENSP00000396900:P797A	ENSP00000318212:P886A	P	+	1	0	KCNH6	58976322	0.000000	0.05858	0.005000	0.12908	0.035000	0.12851	0.146000	0.16180	0.253000	0.21552	0.655000	0.94253	CCC	.	.	none		0.632	KCNH6-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443853.1	NM_030779		G	61622590	C	G	61622590	3	3	45	1	0	0	0	0	1	0	0	0	8045	739	26	4	2706	4	KCNH6	17	61622590	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	21136844	61622590	19572620	164	15616											
CD79B	974	hgsc.bcm.edu	37	chr17	62006799	62006799	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tgcccctctccttacctcgtAggtgtgatcttcctccatgc	4	14	7	16	1	2	1	0	1	2	0	6	1	4	1	6	1	3	1	6	1	2	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr17:62006799A>T	ENST00000006750.3	-	5	678	c.586T>A	c.(586-588)Tac>Aac	p.Y196N	CD79B_ENST00000392795.3_Missense_Mutation_p.Y197N|CD79B_ENST00000349817.2_Missense_Mutation_p.Y92N	NM_000626.2|NM_021602.2	NP_000617.1|NP_067613.1	P40259	CD79B_HUMAN	CD79b molecule, immunoglobulin-associated beta	196	ITAM. {ECO:0000255|PROSITE- ProRule:PRU00379}.				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)	p.Y196H(2)|p.Y196N(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	15						CTTACCTCGTAGGTGTGATCT	0.632			"Mis, O"		DLBCL																																p.Y197N		Atlas-SNP	.		Dom	yes		17	17q23	974	"CD79b molecule, immunoglobulin-associated beta"		L	CD79B,NS,lymphoid_neoplasm,0,13	CD79B	38	13	3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	c.T589A						PASS	.						94	74	81					17																	62006799		2203	4300	6503	SO:0001583	missense	974	exon5			CCTCGTAGGTGTG	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.586T>A	17.37:g.62006799A>T	ENSP00000006750:p.Tyr196Asn	85	0	0		72	29	0.402778	NM_001039933	Q53FS2|Q9BU06	Missense_Mutation	SNP	ENST00000006750.3	37	CCDS11655.1	.	.	.	.	.	.	.	.	.	.	A	14.45	2.539798	0.45176	.	.	ENSG00000007312	ENST00000349817;ENST00000392795;ENST00000006750	D;D;D	0.96651	-4.08;-4.08;-4.08	4.2	4.2	0.49525	.	0.000000	0.64402	D	0.000002	D	0.95601	0.8570	N	0.24115	0.695	0.49915	D	0.999838	D;D	0.89917	0.999;1.0	D;D	0.91635	0.996;0.999	D	0.95387	0.8478	10	0.87932	D	0	-12.4743	9.5967	0.39578	1.0:0.0:0.0:0.0	.	92;196	P40259-2;P40259	.;CD79B_HUMAN	N	92;197;196	ENSP00000245862:Y92N;ENSP00000376544:Y197N;ENSP00000006750:Y196N	ENSP00000006750:Y196N	Y	-	1	0	CD79B	59360531	1.000000	0.71417	0.995000	0.50966	0.298000	0.27526	4.559000	0.60796	1.782000	0.52362	0.358000	0.22013	TAC	.	.	none		0.632	CD79B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417711.1			T	62006799	A	T	62006799	3	4	45	1	0	0	0	0	1	0	0	0	3039	420	15	5	111	5	CD79B	17	62006799	Missense_Mutation	SNP	A	TCGA-RQ-A68N-01A-11D-A31X-10	384209	62006799	19188411	165	15617											
CD79B	974	hgsc.bcm.edu	37	chr17	62006833	62006833	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccatgccagccttgctgtcAtcctgggggcggagagggat	6	9	15	11	1	1	1	1	0	0	1	3	3	3	2	4	4	3	1	4	4	0	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr17:62006833A>G	ENST00000006750.3	-	5	644	c.552T>C	c.(550-552)gaT>gaC	p.D184D	CD79B_ENST00000392795.3_Silent_p.D185D|CD79B_ENST00000349817.2_Silent_p.D80D	NM_000626.2|NM_021602.2	NP_000617.1|NP_067613.1	P40259	CD79B_HUMAN	CD79b molecule, immunoglobulin-associated beta	184					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						CCTTGCTGTCATCCTGGGGGC	0.647			"Mis, O"		DLBCL																																p.D185D		Atlas-SNP	.		Dom	yes		17	17q23	974	"CD79b molecule, immunoglobulin-associated beta"		L	.	CD79B	38	.	0			c.T555C						PASS	.						77	59	65					17																	62006833		2203	4300	6503	SO:0001819	synonymous_variant	974	exon5			GCTGTCATCCTGG	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.552T>C	17.37:g.62006833A>G		80	0	0		69	27	0.391304	NM_001039933	Q53FS2|Q9BU06	Silent	SNP	ENST00000006750.3	37	CCDS11655.1																																																																																			.	.	none		0.647	CD79B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417711.1			G	62006833	A	G	62006833	2	3	45	1	0	0	0	0	0	0	0	1	3039	214	8	3		3	CD79B	17	62006833	Silent	SNP	A	TCGA-RQ-A68N-01A-11D-A31X-10	34	62006833	19188377	166	15618											
CCDC57	284001	hgsc.bcm.edu	37	chr17	80121138	80121138	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgtccccgagcttcctgaGtgccagtccagaggatactg	7	10	11	13	1	1	2	0	1	1	1	4	4	4	3	5	1	3	1	5	1	1	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr17:80121138G>A	ENST00000389641.4	-	13	2014	c.1978C>T	c.(1978-1980)Ctc>Ttc	p.L660F	CCDC57_ENST00000327026.3_5'UTR|RP11-1376P16.1_ENST00000582774.1_RNA|CCDC57_ENST00000392347.1_Missense_Mutation_p.L660F|CCDC57_ENST00000392343.3_Missense_Mutation_p.L660F			Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	660										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)			AGCTTCCTGAGTGCCAGTCCA	0.582																																					p.L660F		Atlas-SNP	.											.	CCDC57	102	.	0			c.C1978T						PASS	.						124	129	127					17																	80121138		2022	4182	6204	SO:0001583	missense	284001	exon13			TCCTGAGTGCCAG	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.1978C>T	17.37:g.80121138G>A	ENSP00000374292:p.Leu660Phe	95	0	0		84	30	0.357143	NM_198082	A6NP51|A8MQC7|Q8IWG2|Q8TER3	Missense_Mutation	SNP	ENST00000389641.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.19|10.19	1.281031|1.281031	0.23392|0.23392	.|.	.|.	ENSG00000176155|ENSG00000176155	ENST00000389641;ENST00000392347;ENST00000327026;ENST00000392343|ENST00000419322	T;T;T|.	0.54071|.	1.93;1.93;0.59|.	2.86|2.86	-0.301|-0.301	0.12800|0.12800	.|.	0.893166|.	0.09083|.	N|.	0.851066|.	T|T	0.43010|0.43010	0.1228|0.1228	M|M	0.67953|0.67953	2.075|2.075	0.09310|0.09310	N|N	1|1	B;B|.	0.27498|.	0.18;0.09|.	B;B|.	0.31442|.	0.13;0.046|.	T|T	0.38972|0.38972	-0.9636|-0.9636	10|5	0.66056|.	D|.	0.02|.	-0.0705|-0.0705	5.0858|5.0858	0.14680|0.14680	0.4431:0.0:0.5569:0.0|0.4431:0.0:0.5569:0.0	.|.	660;660|.	Q2TAC2-2;Q2TAC2|.	.;CCD57_HUMAN|.	F|I	660;660;168;660|5	ENSP00000374292:L660F;ENSP00000376158:L660F;ENSP00000376154:L660F|.	ENSP00000315967:L168F|.	L|T	-|-	1|2	0|0	CCDC57|CCDC57	77714427|77714427	0.115000|0.115000	0.22152|0.22152	0.001000|0.001000	0.08648|0.08648	0.047000|0.047000	0.14425|0.14425	1.267000|1.267000	0.33050|0.33050	-0.017000|-0.017000	0.14103|0.14103	-0.262000|-0.262000	0.10625|0.10625	CTC|ACT	.	.	none		0.582	CCDC57-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000277182.3	NM_198082		A	80121138	G	A	80121138	3	1	45	1	0	0	0	0	1	0	0	0	2829	1029	36	2	789	2	CCDC57	17	80121138	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	18114305	80121138	1074072	167	15619											
L3MBTL4	91133	hgsc.bcm.edu	37	chr18	6138191	6138191	+	Splice_Site	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acttaaataagaaaaatgttAcctgtgatgtcccgaataac	17	11	6	7	1	0	2	0	1	0	1	1	3	1	2	2	0	2	1	2	0	8	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr18:6138191A>G	ENST00000284898.6	-	14	1400		c.e14+1		L3MBTL4_ENST00000317931.7_Splice_Site|L3MBTL4_ENST00000400104.3_Splice_Site|L3MBTL4_ENST00000535782.1_Splice_Site|L3MBTL4_ENST00000400105.2_Splice_Site	NM_173464.3	NP_775735.2	Q8NA19	LMBL4_HUMAN	l(3)mbt-like 4 (Drosophila)						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)				GAAAAATGTTACCTGTGATGT	0.463																																					.	Esophageal Squamous(41;748 902 17366 28959 43175)	Atlas-SNP	.											.	L3MBTL4	87	.	0			c.1199+2T>C						PASS	.						53	47	49					18																	6138191		2203	4300	6503	SO:0001630	splice_region_variant	91133	exon15			AATGTTACCTGTG	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.1199+1T>C	18.37:g.6138191A>G		39	0	0		43	14	0.325581	NM_173464	A8MTL8|Q8IXS3	Splice_Site	SNP	ENST00000284898.6	37	CCDS11839.2	.	.	.	.	.	.	.	.	.	.	A	15.63	2.889732	0.52014	.	.	ENSG00000154655	ENST00000400105;ENST00000317931;ENST00000284898;ENST00000535782;ENST00000400104	.	.	.	4.72	4.72	0.59763	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.5945	0.45329	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	L3MBTL4	6128191	1.000000	0.71417	0.999000	0.59377	0.620000	0.37586	4.228000	0.58619	1.773000	0.52216	0.528000	0.53228	.	.	.	none		0.463	L3MBTL4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254448.2	NM_173464	Intron	G	6138191	A	G	6138191	5	3	45	1	0	0	0	0	0	0	1	0	8603	405	14	3	698	3	L3MBTL4	18	6138191	Splice_Site	SNP	A	TCGA-RQ-A68N-01A-11D-A31X-10		6138191	71939057	168	15620											
DSC3	1825	hgsc.bcm.edu	37	chr18	28576767	28576767	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaaactcacttcaccgagaCggggttgagtaaaactgtgc	12	8	12	9	2	2	2	2	1	0	1	2	4	2	3	1	3	3	2	1	3	3	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr18:28576767C>T	ENST00000360428.4	-	15	2563	c.2483G>A	c.(2482-2484)cGt>cAt	p.R828H	DSC3_ENST00000434452.1_Missense_Mutation_p.R828H	NM_001941.3	NP_001932.2	Q14574	DSC3_HUMAN	desmocollin 3	828					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)			TTCACCGAGACGGGGTTGAGT	0.433																																					p.R828H		Atlas-SNP	.											DSC3_ENST00000434452,colon,carcinoma,-1,2	DSC3	225	2	0			c.G2483A						PASS	.						80	71	74					18																	28576767		2203	4300	6503	SO:0001583	missense	1825	exon15			CCGAGACGGGGTT	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.2483G>A	18.37:g.28576767C>T	ENSP00000353608:p.Arg828His	94	0	0		65	16	0.246154	NM_024423	A6NN35|Q14200|Q9HAZ9	Missense_Mutation	SNP	ENST00000360428.4	37	CCDS32810.1	.	.	.	.	.	.	.	.	.	.	C	9.912	1.209685	0.22289	.	.	ENSG00000134762	ENST00000360428;ENST00000434452	T;T	0.76448	-1.02;0.28	4.64	3.77	0.43336	Cadherin, cytoplasmic domain (1);	0.000000	0.32287	N	0.006305	T	0.65780	0.2724	L	0.39898	1.24	0.39448	D	0.967356	P;P	0.45634	0.616;0.863	B;B	0.37888	0.167;0.26	T	0.67647	-0.5617	10	0.45353	T	0.12	.	9.6501	0.39892	0.0:0.8391:0.0:0.1609	.	828;828	Q14574;Q14574-2	DSC3_HUMAN;.	H	828	ENSP00000353608:R828H;ENSP00000392068:R828H	ENSP00000353608:R828H	R	-	2	0	DSC3	26830765	0.994000	0.37717	0.965000	0.40720	0.627000	0.37826	2.519000	0.45546	1.296000	0.44742	-0.150000	0.13652	CGT	.	.	none		0.433	DSC3-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447384.1	NM_001941, NM_024423		T	28576767	C	T	28576767	3	4	45	1	0	0	0	0	1	0	0	0	4769	536	19	1	246	1	DSC3	18	28576767	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	22438576	28576767	49500481	169	15621											
C3	718	hgsc.bcm.edu	37	chr19	6696418	6696418	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agaattctggtctcagactcGgtgtccgggacttggtcact	7	12	12	10	2	3	2	2	0	2	2	6	3	4	3	1	4	0	0	1	4	1	2	rs139152390		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr19:6696418G>A	ENST00000245907.6	-	23	3014	c.2922C>T	c.(2920-2922)acC>acT	p.T974T		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	974					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)	TCTCAGACTCGGTGTCCGGGA	0.572																																					p.T974T		Atlas-SNP	.											.	C3	192	.	0			c.C2922T						PASS	.	A		1,4405	2.1+/-5.4	0,1,2202	167	124	138		2922	-11.9	0	19	dbSNP_134	138	0,8600		0,0,4300	no	coding-synonymous	C3	NM_000064.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		974/1664	6696418	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	718	exon23			AGACTCGGTGTCC	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.2922C>T	19.37:g.6696418G>A		97	0	0		77	6	0.0779221	NM_000064	A7E236	Silent	SNP	ENST00000245907.6	37	CCDS32883.1																																																																																			G|1.000;A|0.000	0.000	weak		0.572	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064		A	6696418	G	A	6696418	2	1	45	1	0	0	0	0	0	0	0	1	2206	1103	39	1		1	C3	19	6696418	Silent	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10		6696418	52432565	170	15622											
MUC16	94025	hgsc.bcm.edu	37	chr19	9070331	9070331	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcatgcatggcttctgtgtgCgcagtgtctttgtaagtggt	5	15	14	7	1	2	0	0	0	2	0	2	0	2	0	0	2	2	5	0	2	1	3	rs186109841	byFrequency	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr19:9070331C>T	ENST00000397910.4	-	3	17318	c.17115G>A	c.(17113-17115)gcG>gcA	p.A5705A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5707	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						CTTCTGTGTGCGCAGTGTCTT	0.507													a|||	2	0.000399361	0.0008	0.0	5008	,	,		21807	0.001		0.0	False		,,,				2504	0.0				p.A5705A		Atlas-SNP	.											.	MUC16	4315	.	0			c.G17115A						PASS	.	C		5,4193		0,5,2094	166	161	163		17115	-3.1	0	19		163	7,8421		0,7,4207	no	coding-synonymous	MUC16	NM_024690.2		0,12,6301	TT,TC,CC		0.0831,0.1191,0.095		5705/14508	9070331	12,12614	2099	4214	6313	SO:0001819	synonymous_variant	94025	exon3			TGTGTGCGCAGTG	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.17115G>A	19.37:g.9070331C>T		168	0	0		136	82	0.602941	NM_024690	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																			C|1.000;T|0.000	0.000	strong		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		T	9070331	C	T	9070331	2	4	45	1	0	0	0	0	0	0	0	1	9982	755	27	1		1	MUC16	19	9070331	Silent	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	2373913	9070331	50058652	171	15623											
FCHO1	23149	hgsc.bcm.edu	37	chr19	17897428	17897428	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggaggcttccagatgtgtcCgaggcaggcggtgagctgtg	6	9	18	8	2	0	2	0	1	0	1	2	4	2	3	2	5	1	3	2	5	0	1	rs370950809		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr19:17897428C>T	ENST00000596536.1	+	27	2755	c.2472C>T	c.(2470-2472)tcC>tcT	p.S824S	FCHO1_ENST00000539407.1_Silent_p.S824S|FCHO1_ENST00000389133.4_Silent_p.S824S|FCHO1_ENST00000595033.1_Silent_p.S774S|FCHO1_ENST00000594202.1_Silent_p.S824S|FCHO1_ENST00000597512.1_Silent_p.S831S|FCHO1_ENST00000252771.7_Silent_p.S824S|FCHO1_ENST00000596951.1_Silent_p.S824S|FCHO1_ENST00000600676.1_Silent_p.S824S	NM_015122.2	NP_055937.1	O14526	FCHO1_HUMAN	FCH domain only 1	824	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						CAGATGTGTCCGAGGCAGGCG	0.562																																					p.S824S		Atlas-SNP	.											.	FCHO1	69	.	0			c.C2472T						PASS	.	C	,,,	0,4406		0,0,2203	59	61	60		2472,2472,2322,2472	-4.7	1	19		60	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FCHO1	NM_001161357.1,NM_001161358.1,NM_001161359.1,NM_015122.2	,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,	824/892,824/890,774/840,824/890	17897428	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23149	exon26			TGTGTCCGAGGCA	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.2472C>T	19.37:g.17897428C>T		39	0	0		35	27	0.771429	NM_001161358	A6NHE6|A8K5U5|B4E120|Q05C93|Q8IW22	Silent	SNP	ENST00000596536.1	37	CCDS32955.1																																																																																			.	.	weak		0.562	FCHO1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466946.2	NM_015122		T	17897428	C	T	17897428	2	4	45	1	0	0	0	0	0	0	0	1	5795	639	23	1		1	FCHO1	19	17897428	Silent	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	8827097	17897428	41231555	172	15624											
ZNF208	7757	hgsc.bcm.edu	37	chr19	22156967	22156967	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttactaaaggctttgccaCattcttcacatttgttgggt	8	16	7	10	0	2	0	1	0	1	0	2	0	2	0	2	2	2	2	2	2	3	7			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr19:22156967C>T	ENST00000397126.4	-	4	1017	c.869G>A	c.(868-870)tGt>tAt	p.C290Y	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	290					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)				GGCTTTGCCACATTCTTCACA	0.388																																					p.C290Y		Atlas-SNP	.											.	ZNF208	817	.	0			c.G869A						PASS	.						48	52	51					19																	22156967		2144	4264	6408	SO:0001583	missense	7757	exon4			TTGCCACATTCTT	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.869G>A	19.37:g.22156967C>T	ENSP00000380315:p.Cys290Tyr	45	0	0		38	21	0.552632	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	C	14.64	2.596455	0.46318	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	D	0.85861	-2.04	2.89	1.79	0.24919	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.90689	0.7079	.	.	.	0.34667	D	0.723249	D	0.89917	1.0	D	0.78314	0.991	D	0.91372	0.5120	8	0.62326	D	0.03	.	10.3364	0.43852	0.0:0.7964:0.2036:0.0	.	290	O43345	ZN208_HUMAN	Y	290	ENSP00000380315:C290Y	ENSP00000380315:C290Y	C	-	2	0	ZNF208	21948807	0.925000	0.31364	0.001000	0.08648	0.023000	0.10783	2.741000	0.47426	0.187000	0.20147	0.306000	0.20318	TGT	.	.	none		0.388	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		T	22156967	C	T	22156967	3	4	45	1	0	0	0	0	1	0	0	0	17781	478	17	2	2977	2	ZNF208	19	22156967	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	4259539	22156967	36972016	173	15625											
WDR88	126248	hgsc.bcm.edu	37	chr19	33642122	33642122	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatcacgtcatgctgctttGaccccgacagccagagggtg	8	8	11	14	2	2	2	2	1	0	1	2	3	2	2	4	1	3	2	4	1	0	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr19:33642122G>T	ENST00000355868.3	+	6	791	c.715G>T	c.(715-717)Gac>Tac	p.D239Y	WDR88_ENST00000361680.2_Missense_Mutation_p.D239Y	NM_173479.3	NP_775750.3	Q6ZMY6	WDR88_HUMAN	WD repeat domain 88	239										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)					ATGCTGCTTTGACCCCGACAG	0.557																																					p.D239Y		Atlas-SNP	.											.	WDR88	50	.	0			c.G715T						PASS	.						149	90	110					19																	33642122		2203	4300	6503	SO:0001583	missense	126248	exon6			TGCTTTGACCCCG	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.715G>T	19.37:g.33642122G>T	ENSP00000348129:p.Asp239Tyr	37	0	0		61	39	0.639344	NM_173479	Q8NEF8	Missense_Mutation	SNP	ENST00000355868.3	37	CCDS12429.1	.	.	.	.	.	.	.	.	.	.	G	19.01	3.744689	0.69418	.	.	ENSG00000166359	ENST00000355868;ENST00000361680	T;T	0.60920	0.15;0.15	5.89	4.67	0.58626	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	3.304740	0.00998	N	0.003621	T	0.77485	0.4137	L	0.59436	1.845	0.32073	N	0.594173	D	0.89917	1.0	D	0.85130	0.997	T	0.63554	-0.6611	10	0.66056	D	0.02	.	14.6624	0.68882	0.0826:0.0:0.9174:0.0	.	239	Q6ZMY6	WDR88_HUMAN	Y	239	ENSP00000348129:D239Y;ENSP00000355148:D239Y	ENSP00000348129:D239Y	D	+	1	0	WDR88	38333962	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	4.586000	0.60984	2.783000	0.95769	0.655000	0.94253	GAC	.	.	none		0.557	WDR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450840.1	NM_173479		T	33642122	G	T	33642122	3	4	45	1	0	0	0	0	1	0	0	0	17350	1290	45	4	737	4	WDR88	19	33642122	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	11485155	33642122	25486861	174	15626											
KIAA0355	9710	hgsc.bcm.edu	37	chr19	34791796	34791796	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggccataaagcctgagatcGccaagatgctaatggaactt	13	8	10	10	2	0	2	0	1	0	2	1	4	0	3	3	2	3	1	3	2	5	3			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr19:34791796G>A	ENST00000299505.6	+	2	1291	c.418G>A	c.(418-420)Gcc>Acc	p.A140T		NM_014686.3	NP_055501.2	O15063	K0355_HUMAN	KIAA0355	140								p.A140T(1)		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)					GCCTGAGATCGCCAAGATGCT	0.488																																					p.A140T		Atlas-SNP	.											KIAA0355,NS,carcinoma,0,1	KIAA0355	105	1	1	Substitution - Missense(1)	endometrium(1)	c.G418A						scavenged	.						56	46	49					19																	34791796		2203	4300	6503	SO:0001583	missense	9710	exon2			GAGATCGCCAAGA		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.418G>A	19.37:g.34791796G>A	ENSP00000299505:p.Ala140Thr	34	0	0		29	5	0.172414	NM_014686	Q2M3W4	Missense_Mutation	SNP	ENST00000299505.6	37	CCDS12436.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.905079	0.92035	.	.	ENSG00000166398	ENST00000299505	.	.	.	5.25	5.25	0.73442	.	0.055990	0.64402	D	0.000001	T	0.61060	0.2317	N	0.24115	0.695	0.80722	D	1	D	0.64830	0.994	P	0.56343	0.796	T	0.66292	-0.5960	9	0.87932	D	0	-14.461	19.2076	0.93739	0.0:0.0:1.0:0.0	.	140	O15063	K0355_HUMAN	T	140	.	ENSP00000299505:A140T	A	+	1	0	KIAA0355	39483636	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	9.420000	0.97426	2.607000	0.88179	0.561000	0.74099	GCC	.	.	none		0.488	KIAA0355-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451678.4	NM_014686		A	34791796	G	A	34791796	3	1	45	1	0	0	0	0	1	0	0	0	8179	1087	38	1	420	1	KIAA0355	19	34791796	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	1149674	34791796	24337187	175	15627											
PLA2G4C	8605	hgsc.bcm.edu	37	chr19	48609797	48609797	+	5'UTR	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accttcccatggtgcactgcGgtcagaaaattctcagtcct	9	11	8	13	1	2	1	2	0	1	1	5	1	4	1	3	2	2	1	3	2	2	2	rs570635333		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr19:48609797G>A	ENST00000599921.1	-	0	347				PLA2G4C_ENST00000599111.1_Silent_p.T17T|PLA2G4C_ENST00000354276.3_5'UTR|PLA2G4C_ENST00000413144.2_5'Flank			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)						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)		GGTGCACTGCGGTCAGAAAAT	0.517																																					p.T17T		Atlas-SNP	.											.	PLA2G4C	76	.	0			c.C51T						PASS	.						157	130	140					19																	48609797		2203	4300	6503	SO:0001623	5_prime_UTR_variant	8605	exon2			CACTGCGGTCAGA	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.-11C>T	19.37:g.48609797G>A		82	0	0		65	41	0.630769	NM_001159322	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Silent	SNP	ENST00000599921.1	37	CCDS12710.1																																																																																			.	.	none		0.517	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1			A	48609797	G	A	48609797	1	1	45	0	1	0	0	0	0	0	0	0	12012	1103	39	1		1	PLA2G4C	19	48609797	5'UTR	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	13818001	48609797	10519186	176	15628											
PRKCG	5582	hgsc.bcm.edu	37	chr19	54392899	54392899	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tctctgcccccaggacccccGgaacaaacacaagttccgcc	10	5	7	19	2	1	0	0	0	1	0	3	2	2	2	6	2	3	1	6	2	3	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr19:54392899G>A	ENST00000263431.3	+	4	575	c.293G>A	c.(292-294)cGg>cAg	p.R98Q	PRKCG_ENST00000536044.1_Missense_Mutation_p.R98Q|PRKCG_ENST00000540413.1_Missense_Mutation_p.R98Q|PRKCG_ENST00000542049.1_Intron	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	98					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)	CAGGACCCCCGGAACAAACAC	0.602																																					p.R98Q		Atlas-SNP	.											.	PRKCG	246	.	0			c.G293A						PASS	.						57	50	52					19																	54392899		2203	4300	6503	SO:0001583	missense	5582	exon4			ACCCCCGGAACAA	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.293G>A	19.37:g.54392899G>A	ENSP00000263431:p.Arg98Gln	88	0	0		84	60	0.714286	NM_002739	B7Z8Q0	Missense_Mutation	SNP	ENST00000263431.3	37	CCDS12867.1	.	.	.	.	.	.	.	.	.	.	G	18.21	3.574096	0.65765	.	.	ENSG00000126583	ENST00000536044;ENST00000540413;ENST00000263431;ENST00000419486	D;D;D	0.84370	-1.84;-1.84;-1.84	4.54	4.54	0.55810	.	.	.	.	.	D	0.82499	0.5050	M	0.74881	2.28	0.80722	D	1	P;B;P;P	0.43701	0.769;0.425;0.815;0.679	B;B;B;B	0.33121	0.149;0.066;0.111;0.158	D	0.84896	0.0839	9	0.45353	T	0.12	.	15.2147	0.73254	0.0:0.0:1.0:0.0	.	98;98;98;98	F5H5C4;B7Z870;B7Z3W6;P05129	.;.;.;KPCG_HUMAN	Q	98;98;98;121	ENSP00000440541:R98Q;ENSP00000443493:R98Q;ENSP00000263431:R98Q	ENSP00000263431:R98Q	R	+	2	0	PRKCG	59084711	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.634000	0.61325	2.260000	0.74910	0.644000	0.83932	CGG	.	.	none		0.602	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739		A	54392899	G	A	54392899	3	1	45	1	0	0	0	0	1	0	0	0	12524	1116	39	1	307	1	PRKCG	19	54392899	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	5783102	54392899	4736084	177	15629											
CNOT3	4849	hgsc.bcm.edu	37	chr19	54648016	54648016	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaggtggaccagtttgagaGtgaagtggagtcactgtcag	10	9	16	6	0	2	2	2	2	0	1	2	5	2	4	1	3	0	2	1	3	1	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr19:54648016G>A	ENST00000406403.1	+	6	2034	c.431G>A	c.(430-432)aGt>aAt	p.S144N	CNOT3_ENST00000221232.5_Missense_Mutation_p.S144N|CNOT3_ENST00000358389.3_5'UTR			O75175	CNOT3_HUMAN	CCR4-NOT transcription complex, subunit 3	144					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)					CAGTTTGAGAGTGAAGTGGAG	0.567																																					p.S144N		Atlas-SNP	.											.	CNOT3	133	.	0			c.G431A						PASS	.						149	111	124					19																	54648016		2203	4300	6503	SO:0001583	missense	4849	exon7			TTGAGAGTGAAGT	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.431G>A	19.37:g.54648016G>A	ENSP00000383954:p.Ser144Asn	165	0	0		166	35	0.210843	NM_014516	Q9NZN7|Q9UF76	Missense_Mutation	SNP	ENST00000406403.1	37	CCDS12880.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	35|35	5.452152|5.452152	0.96223|0.96223	.|.	.|.	ENSG00000088038|ENSG00000088038	ENST00000221232;ENST00000406403|ENST00000440571	T;T|.	0.46063|.	0.88;0.88|.	5.38|5.38	5.38|5.38	0.77491|0.77491	Not CCR4-Not complex component, N-terminal (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.74512|0.74512	0.3726|0.3726	M|M	0.67397|0.67397	2.05|2.05	0.80722|0.80722	D|D	1|1	D;D;D|.	0.76494|.	0.999;0.997;0.999|.	D;D;D|.	0.83275|.	0.996;0.992;0.996|.	T|T	0.72686|0.72686	-0.4218|-0.4218	10|5	0.51188|.	T|.	0.08|.	-14.3079|-14.3079	18.2928|18.2928	0.90136|0.90136	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	144;144;68|.	B7Z6J7;O75175;Q6ZMJ6|.	.;CNOT3_HUMAN;.|.	N|M	144|65	ENSP00000221232:S144N;ENSP00000383954:S144N|.	ENSP00000221232:S144N|.	S|V	+|+	2|1	0|0	CNOT3|CNOT3	59339828|59339828	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	9.224000|9.224000	0.95209|0.95209	2.697000|2.697000	0.92050|0.92050	0.655000|0.655000	0.94253|0.94253	AGT|GTG	.	.	none		0.567	CNOT3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142130.3	NM_014516		A	54648016	G	A	54648016	3	1	45	1	0	0	0	0	1	0	0	0	3622	1029	36	2	453	2	CNOT3	19	54648016	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	255117	54648016	4480967	178	15630											
TGM3	7053	hgsc.bcm.edu	37	chr20	2312744	2312744	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttcaatgggtttggaaacagAggaacaggagcccagcatca	14	7	12	8	0	2	1	2	0	0	1	2	4	2	4	1	4	4	2	1	4	3	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr20:2312744A>G	ENST00000381458.5	+	10	1493	c.1430A>G	c.(1429-1431)gAg>gGg	p.E477G		NM_003245.3	NP_003236.3	Q08188	TGM3_HUMAN	transglutaminase 3	477					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)	TTGGAAACAGAGGAACAGGAG	0.522																																					p.E477G		Atlas-SNP	.											.	TGM3	105	.	0			c.A1430G						PASS	.						77	67	71					20																	2312744		2203	4300	6503	SO:0001583	missense	7053	exon10			AAACAGAGGAACA	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.1430A>G	20.37:g.2312744A>G	ENSP00000370867:p.Glu477Gly	183	0	0		169	64	0.378698	NM_003245	A8K5N6|B2RCR6|D3DVX1|O95933|Q32ML9|Q32MM0	Missense_Mutation	SNP	ENST00000381458.5	37	CCDS33435.1	.	.	.	.	.	.	.	.	.	.	A	10.47	1.360470	0.24598	.	.	ENSG00000125780	ENST00000381458;ENST00000420960	T	0.80393	-1.37	5.14	1.38	0.22167	.	1.225800	0.05291	N	0.521192	T	0.65228	0.2671	N	0.22421	0.69	0.09310	N	1	B	0.23128	0.08	B	0.15484	0.013	T	0.49234	-0.8961	10	0.25106	T	0.35	-13.1893	2.8138	0.05450	0.6238:0.1494:0.0829:0.1439	.	477	Q08188	TGM3_HUMAN	G	477	ENSP00000370867:E477G	ENSP00000370867:E477G	E	+	2	0	TGM3	2260744	0.002000	0.14202	0.003000	0.11579	0.016000	0.09150	0.221000	0.17680	0.403000	0.25479	0.533000	0.62120	GAG	.	.	none		0.522	TGM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077579.2	NM_003245		G	2312744	A	G	2312744	3	3	45	1	0	0	0	0	1	0	0	0	15846	304	11	3	1468	3	TGM3	20	2312744	Missense_Mutation	SNP	A	TCGA-RQ-A68N-01A-11D-A31X-10		2312744	60712776	179	15631											
TMX4	56255	hgsc.bcm.edu	37	chr20	7967957	7967957	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gacccataaaaaggccaaaaAccaaggtggctatgacgaaa	19	4	9	9	1	0	1	0	1	0	0	0	3	0	1	3	3	1	1	3	3	8	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr20:7967957A>G	ENST00000246024.2	-	6	808	c.593T>C	c.(592-594)gTt>gCt	p.V198A	TMX4_ENST00000530935.1_5'Flank	NM_021156.2	NP_066979.2	Q9H1E5	TMX4_HUMAN	thioredoxin-related transmembrane protein 4	198					cell redox homeostasis (GO:0045454)|oxidation-reduction process (GO:0055114)|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(2)|lung(11)|skin(1)	17						AAGGCCAAAAACCAAGGTGGC	0.353																																					p.V198A		Atlas-SNP	.											.	TMX4	39	.	0			c.T593C						PASS	.						75	73	73					20																	7967957		2203	4300	6503	SO:0001583	missense	56255	exon6			CCAAAAACCAAGG		CCDS13101.1	20p12	2011-10-19	2009-02-23	2009-02-23	ENSG00000125827	ENSG00000125827		"Protein disulfide isomerases"	25237	protein-coding gene	gene with protein product	"protein disulfide isomerase family A, member 14"		"thioredoxin domain containing 13"	TXNDC13			Standard	NM_021156		Approved	DJ971N18.2, KIAA1162, PDIA14	uc002wmx.1	Q9H1E5	OTTHUMG00000031843	ENST00000246024.2:c.593T>C	20.37:g.7967957A>G	ENSP00000246024:p.Val198Ala	540	0	0		445	120	0.269663	NM_021156	Q8N4P7|Q8NCC1|Q9UJA1|Q9ULQ8	Missense_Mutation	SNP	ENST00000246024.2	37	CCDS13101.1	.	.	.	.	.	.	.	.	.	.	A	13.68	2.309628	0.40895	.	.	ENSG00000125827	ENST00000246024;ENST00000527925	T;T	0.41400	1.0;1.0	6.16	5.07	0.68467	.	0.500444	0.20258	N	0.095924	T	0.30916	0.0780	L	0.34521	1.04	0.25773	N	0.984812	B	0.21147	0.052	B	0.15870	0.014	T	0.18178	-1.0345	10	0.39692	T	0.17	-5.7309	9.0628	0.36444	0.9179:0.0:0.0821:0.0	.	198	Q9H1E5	TMX4_HUMAN	A	198;170	ENSP00000246024:V198A;ENSP00000435735:V170A	ENSP00000246024:V198A	V	-	2	0	TMX4	7915957	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.750000	0.62162	1.148000	0.42385	0.528000	0.53228	GTT	.	.	none		0.353	TMX4-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000077928.2	NM_021156		G	7967957	A	G	7967957	3	3	45	1	0	0	0	0	1	0	0	0	16284	43	2	3	468	3	TMX4	20	7967957	Missense_Mutation	SNP	A	TCGA-RQ-A68N-01A-11D-A31X-10	5655213	7967957	55057563	180	15632											
PLCB1	23236	hgsc.bcm.edu	37	chr20	8741074	8741074	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttctgtaaaggcacctgccAaaacagaagatcttattcag	14	10	8	9	0	3	2	1	0	2	2	3	2	3	2	2	1	2	3	2	1	6	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr20:8741074A>C	ENST00000338037.6	+	25	2704	c.2677A>C	c.(2677-2679)Aaa>Caa	p.K893Q	PLCB1_ENST00000494924.1_3'UTR|PLCB1_ENST00000378641.3_Missense_Mutation_p.K893Q|PLCB1_ENST00000378637.2_Missense_Mutation_p.K893Q	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	893					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						GGCACCTGCCAAAACAGAAGA	0.353																																					p.Q893Q		Atlas-SNP	.											.	PLCB1	394	.	0			c.C2677C						PASS	.						52	51	52					20																	8741074		2203	4300	6503	SO:0001583	missense	23236	exon25			CCTGCCAAAACAG	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.2677A>C	20.37:g.8741074A>C	ENSP00000338185:p.Lys893Gln	521	0	0		461	75	0.16269	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Silent	SNP	ENST00000338037.6	37	CCDS13102.1	.	.	.	.	.	.	.	.	.	.	A	12.27	1.887080	0.33348	.	.	ENSG00000182621	ENST00000378641;ENST00000338037;ENST00000378637;ENST00000441163;ENST00000535719	T;T;T	0.18960	2.18;2.18;2.18	6.07	6.07	0.98685	.	0.054036	0.64402	D	0.000001	T	0.15003	0.0362	N	0.25144	0.715	0.53688	D	0.999978	B;B	0.28378	0.209;0.02	B;B	0.24394	0.031;0.053	T	0.10847	-1.0612	10	0.13470	T	0.59	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	893;893	Q9NQ66;Q9NQ66-2	PLCB1_HUMAN;.	Q	893;893;893;813;813	ENSP00000367908:K893Q;ENSP00000338185:K893Q;ENSP00000367904:K893Q	ENSP00000338185:K893Q	K	+	1	0	PLCB1	8689074	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.476000	0.90421	2.326000	0.78906	0.533000	0.62120	AAA	.	.	none		0.353	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3			C	8741074	A	C	8741074	3	2	45	1	0	0	0	0	1	0	0	0	12036	131	5	5	2775	5	PLCB1	20	8741074	Missense_Mutation	SNP	A	TCGA-RQ-A68N-01A-11D-A31X-10	773117	8741074	54284446	181	15633											
PLCB4	5332	hgsc.bcm.edu	37	chr20	9288481	9288481	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	catggccaaaccttatgaatTtaactggcagaaggaagttc	14	10	9	8	0	0	2	0	1	0	1	1	3	0	3	2	3	2	2	2	3	6	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr20:9288481T>G	ENST00000378493.1	+	1	35	c.20T>G	c.(19-21)tTt>tGt	p.F7C	PLCB4_ENST00000414679.2_Missense_Mutation_p.F7C|PLCB4_ENST00000378473.3_Missense_Mutation_p.F7C|PLCB4_ENST00000492632.1_3'UTR|PLCB4_ENST00000378501.2_Missense_Mutation_p.F7C|PLCB4_ENST00000278655.4_Missense_Mutation_p.F7C|PLCB4_ENST00000334005.3_Missense_Mutation_p.F7C			Q15147	PLCB4_HUMAN	phospholipase C, beta 4	7					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						CCTTATGAATTTAACTGGCAG	0.328																																					p.F7C		Atlas-SNP	.											.	PLCB4	204	.	0			c.T20G						PASS	.						61	57	59					20																	9288481		2203	4299	6502	SO:0001583	missense	5332	exon2			ATGAATTTAACTG		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.20T>G	20.37:g.9288481T>G	ENSP00000367754:p.Phe7Cys	135	0	0		78	20	0.25641	NM_182797	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	Missense_Mutation	SNP	ENST00000378493.1	37	CCDS13105.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.041460	0.75732	.	.	ENSG00000101333	ENST00000407043;ENST00000441846;ENST00000334005;ENST00000378473;ENST00000437503;ENST00000416836;ENST00000278655;ENST00000378493;ENST00000378501	T;T;T;T;T;T;T;T;T	0.68765	0.5;0.51;1.84;1.87;0.37;-0.35;1.85;1.85;1.84	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	T	0.81583	0.4853	M	0.75615	2.305	0.58432	D	0.999995	D;D;D	0.89917	1.0;0.997;1.0	D;D;D	0.97110	0.998;0.971;1.0	D	0.83766	0.0217	10	0.87932	D	0	.	15.2632	0.73640	0.0:0.0:0.0:1.0	.	7;7;7	E2QRH8;Q15147;Q15147-4	.;PLCB4_HUMAN;.	C	7	ENSP00000385805:F7C;ENSP00000412982:F7C;ENSP00000334105:F7C;ENSP00000367734:F7C;ENSP00000391614:F7C;ENSP00000395753:F7C;ENSP00000278655:F7C;ENSP00000367754:F7C;ENSP00000367762:F7C	ENSP00000278655:F7C	F	+	2	0	PLCB4	9236481	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.792000	0.69052	2.248000	0.74166	0.533000	0.62120	TTT	.	.	none		0.328	PLCB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077948.2			G	9288481	T	G	9288481	3	3	45	1	0	0	0	0	1	0	0	0	12039	1841	64	5	22	5	PLCB4	20	9288481	Missense_Mutation	SNP	T	TCGA-RQ-A68N-01A-11D-A31X-10	547407	9288481	53737039	182	15634											
NINL	22981	hgsc.bcm.edu	37	chr20	25457204	25457204	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccactccacagggctgcatgCgtgaccacctctctgagggg	7	7	12	15	1	1	2	0	2	1	0	3	2	2	2	4	3	2	2	4	3	0	0			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr20:25457204C>T	ENST00000278886.6	-	17	2796	c.2723G>A	c.(2722-2724)cGc>cAc	p.R908H	NINL_ENST00000422516.1_Intron	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	908					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						GGGCTGCATGCGTGACCACCT	0.711																																					p.R908H		Atlas-SNP	.											.	NINL	148	.	0			c.G2723A						PASS	.						10	13	12					20																	25457204		2045	4077	6122	SO:0001583	missense	22981	exon17			TGCATGCGTGACC		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.2723G>A	20.37:g.25457204C>T	ENSP00000278886:p.Arg908His	18	0	0		27	8	0.296296	NM_025176	A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Missense_Mutation	SNP	ENST00000278886.6	37	CCDS33452.1	.	.	.	.	.	.	.	.	.	.	C	3.161	-0.172044	0.06421	.	.	ENSG00000101004	ENST00000278886	T	0.23754	1.89	2.27	-4.54	0.03452	.	7.030270	0.00166	N	0.000001	T	0.11024	0.0269	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18524	-1.0334	10	0.33141	T	0.24	6.6904	5.9106	0.19027	0.0:0.5264:0.1852:0.2884	.	908	Q9Y2I6	NINL_HUMAN	H	908	ENSP00000278886:R908H	ENSP00000278886:R908H	R	-	2	0	NINL	25405204	.	.	0.000000	0.03702	0.000000	0.00434	.	.	-1.476000	0.01874	-2.579000	0.00168	CGC	.	.	none		0.711	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176		T	25457204	C	T	25457204	3	4	45	1	0	0	0	0	1	0	0	0	10429	768	27	1	1457	1	NINL	20	25457204	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	16168723	25457204	37568316	183	15635											
EPB41L1	2036	hgsc.bcm.edu	37	chr20	34775618	34775618	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggggatgaccccgggagaagCagaaatccacttcttagaga	13	6	13	9	1	1	4	0	1	1	3	2	7	2	5	3	3	1	1	3	3	3	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr20:34775618C>T	ENST00000338074.2	+	8	967	c.806C>T	c.(805-807)gCa>gTa	p.A269V	EPB41L1_ENST00000373941.1_Missense_Mutation_p.A269V|EPB41L1_ENST00000202028.5_Missense_Mutation_p.A207V|EPB41L1_ENST00000441639.1_Missense_Mutation_p.A207V|EPB41L1_ENST00000373946.3_Missense_Mutation_p.A238V|EPB41L1_ENST00000373950.2_Missense_Mutation_p.A172V	NM_001258329.1|NM_012156.2	NP_001245258.1|NP_036288.2	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	269	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				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)			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)					CCGGGAGAAGCAGAAATCCAC	0.537																																					p.A269V		Atlas-SNP	.											.	EPB41L1	111	.	0			c.C806T						PASS	.						64	57	59					20																	34775618		2203	4300	6503	SO:0001583	missense	2036	exon9			GAGAAGCAGAAAT	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.806C>T	20.37:g.34775618C>T	ENSP00000337168:p.Ala269Val	81	0	0		78	18	0.230769	NM_001258329	O15046|Q4VXM6|Q4VXM7|Q4VXM8|Q4VXN4|Q6ZT61|Q8IUU7|Q96CV5|Q96L65	Missense_Mutation	SNP	ENST00000338074.2	37	CCDS13271.1	.	.	.	.	.	.	.	.	.	.	C	36	5.903422	0.97087	.	.	ENSG00000088367	ENST00000202028;ENST00000430276;ENST00000373950;ENST00000397315;ENST00000373951;ENST00000441639;ENST00000373946;ENST00000338074;ENST00000373941	D;D;D;D;D;D;D	0.83992	-1.79;-1.79;-1.79;-1.79;-1.79;-1.79;-1.79	6.17	6.17	0.99709	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);FERM conserved site (1);	.	.	.	.	D	0.93877	0.8041	M	0.94021	3.485	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;1.0;0.996;1.0;0.999;0.999	D;D;D;D;D;D	0.91635	0.969;0.999;0.914;0.998;0.996;0.955	D	0.94417	0.7637	9	0.87932	D	0	.	19.4432	0.94831	0.0:1.0:0.0:0.0	.	269;269;238;172;172;207	B7Z653;Q9H4G0;Q9H4G0-4;Q9H4G0-3;B3KUB6;Q9H4G0-2	.;E41L1_HUMAN;.;.;.;.	V	207;207;172;269;172;207;238;269;269	ENSP00000202028:A207V;ENSP00000404341:A207V;ENSP00000363061:A172V;ENSP00000399214:A207V;ENSP00000363057:A238V;ENSP00000337168:A269V;ENSP00000363052:A269V	ENSP00000202028:A207V	A	+	2	0	EPB41L1	34239032	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.941000	0.99782	0.655000	0.94253	GCA	.	.	none		0.537	EPB41L1-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078978.3	NM_012156		T	34775618	C	T	34775618	3	4	45	1	0	0	0	0	1	0	0	0	5154	710	25	2	832	2	EPB41L1	20	34775618	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	9318414	34775618	28249902	184	15636											
TNFRSF6B	8771	hgsc.bcm.edu	37	chr20	62328311	62328311	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgtgcagcggccgtgccgccGagacagccccacgacgtgtg	6	5	15	15	6	0	1	0	0	0	1	0	3	0	1	5	1	4	1	5	1	0	0	rs61760056		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr20:62328311G>T	ENST00000369996.1	+	1	291	c.191G>T	c.(190-192)cGa>cTa	p.R64L	ARFRP1_ENST00000485858.1_5'Flank|RTEL1-TNFRSF6B_ENST00000482936.1_Silent_p.P1366P|RTEL1_ENST00000318100.4_Silent_p.P1366P	NM_003823.3	NP_003814.1	O95407	TNF6B_HUMAN	tumor necrosis factor receptor superfamily, member 6b, decoy	64					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)	extracellular space (GO:0005615)	receptor activity (GO:0004872)			central_nervous_system(1)|lung(2)|skin(1)	4	all_cancers(38;4.66e-12)|all_epithelial(29;2.56e-13)|Lung NSC(23;1.06e-08)|all_lung(23;3.34e-08)		Epithelial(9;1.78e-08)|all cancers(9;7.89e-08)|OV - Ovarian serous cystadenocarcinoma(5;0.00504)			CCGTGCCGCCGAGACAGCCCC	0.687																																					p.R64L		Atlas-SNP	.											.	TNFRSF6B	22	.	0			c.G191T						PASS	.						19	22	21					20																	62328311		2180	4277	6457	SO:0001583	missense	8771	exon1			GCCGCCGAGACAG	AF104419	CCDS13532.1	20q13.33	2012-06-27						"Tumor necrosis factor receptor superfamily"	11921	protein-coding gene	gene with protein product		603361				9872321, 10318773	Standard	NM_003823		Approved	DcR3, DCR3, TR6, M68	uc002yfz.3	O95407	OTTHUMG00000143724	ENST00000369996.1:c.191G>T	20.37:g.62328311G>T	ENSP00000359013:p.Arg64Leu	75	0	0		62	20	0.322581	NM_003823		Missense_Mutation	SNP	ENST00000369996.1	37	CCDS13532.1	.	.	.	.	.	.	.	.	.	.	G	8.280	0.815343	0.16607	.	.	ENSG00000243509	ENST00000370006;ENST00000369996;ENST00000342852	T	0.75704	-0.96	3.89	-1.07	0.09968	TNFR/CD27/30/40/95 cysteine-rich region (1);	.	.	.	.	T	0.56790	0.2009	L	0.38531	1.155	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.43877	-0.9364	9	0.40728	T	0.16	-8.2878	1.7996	0.03068	0.2662:0.2449:0.3654:0.1235	.	64	O95407	TNF6B_HUMAN	L	64	ENSP00000359013:R64L	ENSP00000342328:R64L	R	+	2	0	TNFRSF6B	61798755	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.243000	0.08915	0.132000	0.18615	0.561000	0.74099	CGA	.	.	alt		0.687	TNFRSF6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080182.1			T	62328311	G	T	62328311	3	4	45	1	0	0	0	0	1	0	0	0	16313	1058	37	4	193	4	TNFRSF6B	20	62328311	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	27552693	62328311	697209	185	15637											
HUNK	30811	hgsc.bcm.edu	37	chr21	33318469	33318469	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aagaaatacggccccaaaatCgatgtctggtccatgtgagt	13	9	10	9	2	1	2	0	1	1	1	3	3	2	2	3	2	1	0	3	2	5	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr21:33318469C>T	ENST00000270112.2	+	4	1092	c.732C>T	c.(730-732)atC>atT	p.I244I		NM_014586.1	NP_055401.1	P57058	HUNK_HUMAN	hormonally up-regulated Neu-associated kinase	244	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						GCCCCAAAATCGATGTCTGGT	0.527																																					p.I244I		Atlas-SNP	.											.	HUNK	74	.	0			c.C732T						PASS	.						89	76	80					21																	33318469		2203	4300	6503	SO:0001819	synonymous_variant	30811	exon4			CAAAATCGATGTC	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.732C>T	21.37:g.33318469C>T		77	0	0		62	11	0.177419	NM_014586		Silent	SNP	ENST00000270112.2	37	CCDS13610.1																																																																																			.	.	none		0.527	HUNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192782.1	NM_014586		T	33318469	C	T	33318469	2	4	45	1	0	0	0	0	0	0	0	1	7467	874	31	1		1	HUNK	21	33318469	Silent	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10		33318469	14811426	186	15638											
RIPK4	54101	hgsc.bcm.edu	37	chr21	43161063	43161063	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccctggaacttgaggctctGcaggttgatgtgggccccat	6	10	14	11	0	1	2	0	2	1	0	1	3	1	3	3	4	2	3	3	4	1	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr21:43161063G>T	ENST00000352483.2	-	9	2498	c.2434C>A	c.(2434-2436)Cag>Aag	p.Q812K	AP001615.9_ENST00000423276.1_RNA|RIPK4_ENST00000332512.3_Missense_Mutation_p.Q764K|RIPK4_ENST00000542057.1_Missense_Mutation_p.Q701K|RIPK4_ENST00000544709.1_Missense_Mutation_p.Q701K			P57078	RIPK4_HUMAN	receptor-interacting serine-threonine kinase 4	812					morphogenesis of an epithelium (GO:0002009)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						TTGAGGCTCTGCAGGTTGATG	0.711																																					p.Q764K		Atlas-SNP	.											.	RIPK4	151	.	0			c.C2290A						PASS	.						41	40	40					21																	43161063		2202	4298	6500	SO:0001583	missense	54101	exon8			GGCTCTGCAGGTT	AJ278016	CCDS13675.1	21q22.3	2013-01-10	2004-07-06	2004-07-06	ENSG00000183421	ENSG00000183421		"Ankyrin repeat domain containing"	496	protein-coding gene	gene with protein product	"protein kinase C-associated kinase", "PKC-delta-interacting protein kinase"	605706	"ankyrin repeat domain 3"	ANKRD3		10830953	Standard	NM_020639		Approved	DIK, ANKK2, RIP4, PKK	uc002yzn.1	P57078	OTTHUMG00000086770	ENST00000352483.2:c.2434C>A	21.37:g.43161063G>T	ENSP00000330161:p.Gln812Lys	47	0	0		45	18	0.4	NM_020639	Q96KH0	Missense_Mutation	SNP	ENST00000352483.2	37		.	.	.	.	.	.	.	.	.	.	G	14.76	2.631833	0.46944	.	.	ENSG00000183421	ENST00000332512;ENST00000352483;ENST00000544709;ENST00000542057	T;T;T;T	0.62364	0.03;0.03;0.03;0.03	4.8	4.8	0.61643	.	0.000000	0.49916	D	0.000129	T	0.46889	0.1416	N	0.12471	0.22	0.29208	N	0.874744	P	0.36837	0.571	B	0.39027	0.288	T	0.43163	-0.9408	10	0.22109	T	0.4	-41.9581	16.842	0.85971	0.0:0.0:1.0:0.0	.	764	P57078-2	.	K	764;812;701;701	ENSP00000332454:Q764K;ENSP00000330161:Q812K;ENSP00000441754:Q701K;ENSP00000442901:Q701K	ENSP00000332454:Q764K	Q	-	1	0	RIPK4	42034132	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.765000	0.85310	2.202000	0.70862	0.655000	0.94253	CAG	.	.	none		0.711	RIPK4-201	KNOWN	basic	protein_coding	protein_coding		NM_020639		T	43161063	G	T	43161063	3	4	45	1	0	0	0	0	1	0	0	0	13398	1328	46	4	68	4	RIPK4	21	43161063	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	9842594	43161063	4968832	187	15639											
PRDM15	63977	hgsc.bcm.edu	37	chr21	43256244	43256244	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cgttcctgctgtgcttgtagGaaacgtgctgctttaggctc	5	14	12	10	2	0	0	0	0	0	0	2	1	1	1	1	2	5	7	1	2	3	5			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr21:43256244G>A	ENST00000269844.3	-	17	2464	c.2354C>T	c.(2353-2355)tCc>tTc	p.S785F	PRDM15_ENST00000538201.1_Missense_Mutation_p.S419F|PRDM15_ENST00000447207.2_Missense_Mutation_p.S419F|PRDM15_ENST00000422911.1_Missense_Mutation_p.S456F|PRDM15_ENST00000398548.1_Missense_Mutation_p.S456F	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	785					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						GTGCTTGTAGGAAACGTGCTG	0.488																																					p.S785F		Atlas-SNP	.											.	PRDM15	110	.	0			c.C2354T						PASS	.						254	186	209					21																	43256244		2203	4300	6503	SO:0001583	missense	63977	exon17			TTGTAGGAAACGT	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.2354C>T	21.37:g.43256244G>A	ENSP00000269844:p.Ser785Phe	159	0	0		133	28	0.210526	NM_022115	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Missense_Mutation	SNP	ENST00000269844.3	37	CCDS13676.1	.	.	.	.	.	.	.	.	.	.	g	17.29	3.353248	0.61293	.	.	ENSG00000141956	ENST00000422911;ENST00000398548;ENST00000538201;ENST00000447207;ENST00000269844;ENST00000380489	T;T;T;T;T	0.76709	-1.04;-1.04;-1.04;-1.04;3.06	4.41	4.41	0.53225	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.86585	0.5968	M	0.69248	2.105	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.999;0.998;0.999	D	0.88273	0.2931	9	0.66056	D	0.02	-23.6982	15.9984	0.80268	0.0:0.0:1.0:0.0	.	785;456;456	P57071;E9PDJ6;E9PF37	PRD15_HUMAN;.;.	F	456;456;419;419;785;419	ENSP00000408592:S456F;ENSP00000381556:S456F;ENSP00000444044:S419F;ENSP00000390245:S419F;ENSP00000269844:S785F	ENSP00000269844:S785F	S	-	2	0	PRDM15	42129313	1.000000	0.71417	0.737000	0.30932	0.077000	0.17291	9.586000	0.98226	1.998000	0.58463	0.651000	0.88453	TCC	.	.	none		0.488	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115		A	43256244	G	A	43256244	3	1	45	1	0	0	0	0	1	0	0	0	12468	1174	41	2	2229	2	PRDM15	21	43256244	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	95181	43256244	4873651	188	15640											
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230302	23230302	+	Silent	SNP	C	C	T																															ggccctggtcccaggcagcgCtggcccctgctgctgctggg																								rs546631945		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr22:23230302C>T	ENST00000526893.1	+	1	343	c.69C>T	c.(67-69)cgC>cgT	p.R23R	IGLL5_ENST00000531372.1_Silent_p.R23R|IGLL5_ENST00000532223.2_Silent_p.R23R|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	23						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CCAGGCAGCGCTGGCCCCTGC	0.672																																					p.R23R		Atlas-SNP	.											.	IGLL5	26	.	0			c.C69T						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			GCAGCGCTGGCCC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.69C>T	22.37:g.23230302C>T		190	0	0		155	51	0.329032	NM_001178126		Silent	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.672	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		T	23230302	C	T	23230302	2	4	45	1	0	0	0	0	0	0	0	1	7603	784	28	2		2	IGLL5	22	23230302	Silent	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10		23230302	28074264	189	15641	202	2	3	75		8	5	108	N	T_G_C	9.350831e-15
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230311	23230311	+	Silent	SNP	G	G	A																															cccaggcagcgctggcccctGctgctgctgggtctggccat																								rs551962377	byFrequency	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr22:23230311G>A	ENST00000526893.1	+	1	352	c.78G>A	c.(76-78)ctG>ctA	p.L26L	IGLL5_ENST00000531372.1_Silent_p.L26L|IGLL5_ENST00000532223.2_Silent_p.L26L|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	26						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GCTGGCCCCTGCTGCTGCTGG	0.667																																					p.L26L		Atlas-SNP	.											.	IGLL5	26	.	0			c.G78A						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			GCCCCTGCTGCTG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.78G>A	22.37:g.23230311G>A		182	0	0		146	49	0.335616	NM_001178126		Silent	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.667	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		A	23230311	G	A	23230311	2	1	45	1	0	0	0	0	0	0	0	1	7603	1306	46	2		2	IGLL5	22	23230311	Silent	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	9	23230311	28074255	190	15642	202	2	3	75		8	5	108	N	T_G_C	9.350831e-15
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230326	23230326	+	Silent	SNP	G	G	A																															cccctgctgctgctgggtctGgccatggtcgcccatggcct																										TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr22:23230326G>A	ENST00000526893.1	+	1	367	c.93G>A	c.(91-93)ctG>ctA	p.L31L	IGLL5_ENST00000531372.1_Silent_p.L31L|IGLL5_ENST00000532223.2_Silent_p.L31L|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	31						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						TGCTGGGTCTGGCCATGGTCG	0.667																																					p.L31L		Atlas-SNP	.											.	IGLL5	26	.	0			c.G93A						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			GGGTCTGGCCATG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.93G>A	22.37:g.23230326G>A		180	0	0		139	31	0.223022	NM_001178126		Silent	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.667	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		A	23230326	G	A	23230326	2	1	45	1	0	0	0	0	0	0	0	1	7603	1335	47	2		2	IGLL5	22	23230326	Silent	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	15	23230326	28074240	191	15643	203	2	3	75		8	5	108	N	T_G_C	9.350831e-15
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230328	23230328	+	Missense_Mutation	SNP	C	C	T																															cctgctgctgctgggtctggCcatggtcgcccatggcctgc																								rs545109780	byFrequency	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr22:23230328C>T	ENST00000526893.1	+	1	369	c.95C>T	c.(94-96)gCc>gTc	p.A32V	IGLL5_ENST00000531372.1_Missense_Mutation_p.A32V|IGLL5_ENST00000532223.2_Missense_Mutation_p.A32V|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	32						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CTGGGTCTGGCCATGGTCGCC	0.672													C|||	3	0.000599042	0.0015	0.0014	5008	,	,		12180	0.0		0.0	False		,,,				2504	0.0				p.A32V		Atlas-SNP	.											.	IGLL5	26	.	0			c.C95T						PASS	.																																			SO:0001583	missense	100423062	exon1			GTCTGGCCATGGT	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.95C>T	22.37:g.23230328C>T	ENSP00000431254:p.Ala32Val	176	0	0		134	30	0.223881	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	C	10.84	1.463570	0.26248	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00569	6.52;6.52	3.92	-1.21	0.09524	.	.	.	.	.	T	0.00271	0.0008	N	0.08118	0	0.09310	N	1	B	0.25235	0.121	B	0.17722	0.019	T	0.42155	-0.9468	9	0.46703	T	0.11	.	0.7979	0.01069	0.1873:0.383:0.2094:0.2203	.	32	B9A064	IGLL5_HUMAN	V	32	ENSP00000436353:A32V;ENSP00000431254:A32V	ENSP00000431254:A32V	A	+	2	0	IGLL5	21560328	0.000000	0.05858	0.004000	0.12327	0.013000	0.08279	-0.047000	0.11963	-0.086000	0.12550	0.643000	0.83706	GCC	.	.	none		0.672	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		T	23230328	C	T	23230328	3	4	45	1	0	0	0	0	1	0	0	0	7603	739	26	2	97	2	IGLL5	22	23230328	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	2	23230328	28074238	192	15644	203	2	3	75		8	5	108	N	T_G_C	9.350831e-15
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230359	23230359	+	Missense_Mutation	SNP	G	G	A																															catggcctgctgcgcccaatGgttgcaccgcaaagcgggga																								rs536568891	byFrequency	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr22:23230359G>A	ENST00000526893.1	+	1	400	c.126G>A	c.(124-126)atG>atA	p.M42I	IGLL5_ENST00000531372.1_Missense_Mutation_p.M42I|IGLL5_ENST00000532223.2_Missense_Mutation_p.M42I|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	42						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						TGCGCCCAATGGTTGCACCGC	0.672													G|||	2	0.000399361	0.0008	0.0	5008	,	,		11398	0.001		0.0	False		,,,				2504	0.0				p.W7X		Atlas-SNP	.											.	IGLL5	26	.	0			c.G20A						PASS	.																																			SO:0001583	missense	100423062	exon1			CCCAATGGTTGCA	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.126G>A	22.37:g.23230359G>A	ENSP00000431254:p.Met42Ile	167	0	0		124	29	0.233871	NM_001256296		Nonsense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	10.98	1.503640	0.26949	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00558	6.61;6.61	3.81	-7.61	0.01299	.	.	.	.	.	T	0.00328	0.0010	N	0.14661	0.345	0.09310	N	1	B	0.14012	0.009	B	0.08055	0.003	T	0.43956	-0.9359	9	0.52906	T	0.07	.	6.9861	0.24729	0.6223:0.0:0.1512:0.2265	.	42	B9A064	IGLL5_HUMAN	I	42	ENSP00000436353:M42I;ENSP00000431254:M42I	ENSP00000431254:M42I	M	+	3	0	IGLL5	21560359	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-3.041000	0.00632	-2.254000	0.00697	0.643000	0.83706	ATG	.	.	none		0.672	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		A	23230359	G	A	23230359	3	1	45	1	0	0	0	0	1	0	0	0	7603	1348	47	2	128	2	IGLL5	22	23230359	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	31	23230359	28074207	193	15645	204	2	3	75		8	5	108	N	T_G_C	9.350831e-15
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230360	23230360	+	Missense_Mutation	SNP	G	G	A																															atggcctgctgcgcccaatgGttgcaccgcaaagcggggac																								rs6003368	byFrequency	TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr22:23230360G>A	ENST00000526893.1	+	1	401	c.127G>A	c.(127-129)Gtt>Att	p.V43I	IGLL5_ENST00000531372.1_Missense_Mutation_p.V43I|IGLL5_ENST00000532223.2_Missense_Mutation_p.V43I|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	43						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GCGCCCAATGGTTGCACCGCA	0.672																																					p.W7X		Atlas-SNP	.											.	IGLL5	26	.	0			c.G21A						PASS	.																																			SO:0001583	missense	100423062	exon1			CCAATGGTTGCAC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.127G>A	22.37:g.23230360G>A	ENSP00000431254:p.Val43Ile	170	0	0		121	28	0.231405	NM_001256296		Nonsense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	9.827	1.187440	0.21870	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00568	6.53;6.53	3.92	0.473	0.16763	.	.	.	.	.	T	0.00300	0.0009	N	0.08118	0	0.09310	N	1	B	0.16166	0.016	B	0.10450	0.005	T	0.44034	-0.9354	9	0.49607	T	0.09	.	2.3416	0.04261	0.1095:0.1927:0.4993:0.1985	rs6003368;rs6003368	43	B9A064	IGLL5_HUMAN	I	43	ENSP00000436353:V43I;ENSP00000431254:V43I	ENSP00000431254:V43I	V	+	1	0	IGLL5	21560360	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.128000	0.03247	0.192000	0.20272	0.643000	0.83706	GTT	G|1.000;|0.000	.	weak		0.672	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		A	23230360	G	A	23230360	3	1	45	1	0	0	0	0	1	0	0	0	7603	1261	44	2	129	2	IGLL5	22	23230360	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	1	23230360	28074206	194	15646	204	2	3	75		8	5	108	N	T_G_C	9.350831e-15
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230389	23230389	+	Silent	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caaagcggggacccagacccTggagcctcagttggaagcag	11	4	14	12	1	1	1	1	0	0	1	1	4	1	4	3	4	3	2	3	4	2	1	rs576960332		TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr22:23230389T>A	ENST00000526893.1	+	1	430	c.156T>A	c.(154-156)ccT>ccA	p.P52P	IGLL5_ENST00000531372.1_Silent_p.P52P|IGLL5_ENST00000532223.2_Silent_p.P52P|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	52						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						ACCCAGACCCTGGAGCCTCAG	0.677																																					p.L17Q		Atlas-SNP	.											.	IGLL5	26	.	0			c.T50A						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			AGACCCTGGAGCC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.156T>A	22.37:g.23230389T>A		163	0	0		115	22	0.191304	NM_001256296		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.677	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		A	23230389	T	A	23230389	2	1	45	1	0	0	0	0	0	0	0	1	7603	1567	55	5		5	IGLL5	22	23230389	Silent	SNP	T	TCGA-RQ-A68N-01A-11D-A31X-10	29	23230389	28074177	195	15647			3	75		8	5	108	N	T_G_C	9.350831e-15
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230409	23230409	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggagcctcagttggaagcaGccgatccagcctgcggagcc	8	6	14	13	2	1	0	1	0	0	0	2	4	2	3	5	3	6	2	5	3	1	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr22:23230409G>A	ENST00000526893.1	+	1	450	c.176G>A	c.(175-177)aGc>aAc	p.S59N	IGLL5_ENST00000531372.1_Missense_Mutation_p.S59N|IGLL5_ENST00000532223.2_Missense_Mutation_p.S59N|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	59						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GTTGGAAGCAGCCGATCCAGC	0.657																																					p.S59N		Atlas-SNP	.											.	IGLL5	26	.	0			c.G176A						PASS	.																																			SO:0001583	missense	100423062	exon1			GAAGCAGCCGATC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.176G>A	22.37:g.23230409G>A	ENSP00000431254:p.Ser59Asn	153	0	0		98	36	0.367347	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	10.14	1.267343	0.23136	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00583	6.41;6.41	3.92	-0.797	0.10909	.	.	.	.	.	T	0.00440	0.0014	N	0.19112	0.55	0.09310	N	1	B	0.21821	0.061	B	0.17098	0.017	T	0.45056	-0.9287	9	0.59425	D	0.04	.	3.0635	0.06207	0.2132:0.0:0.4153:0.3715	.	59	B9A064	IGLL5_HUMAN	N	59	ENSP00000436353:S59N;ENSP00000431254:S59N	ENSP00000431254:S59N	S	+	2	0	IGLL5	21560409	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.100000	0.10990	-0.036000	0.13669	-0.196000	0.12772	AGC	.	.	none		0.657	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		A	23230409	G	A	23230409	3	1	45	1	0	0	0	0	1	0	0	0	7603	971	34	2	178	2	IGLL5	22	23230409	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	20	23230409	28074157	196	15648			3	75		8	5	108	N	T_G_C	9.350831e-15
SUSD2	56241	hgsc.bcm.edu	37	chr22	24583607	24583607	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tggtccacaacttcctgtacCaacccaagcacgaccccacc	11	6	5	19	1	0	0	0	0	0	0	2	1	2	0	7	1	4	2	7	1	4	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr22:24583607C>T	ENST00000358321.3	+	12	2221	c.1960C>T	c.(1960-1962)Caa>Taa	p.Q654*		NM_019601.3	NP_062547.1	Q9UGT4	SUSD2_HUMAN	sushi domain containing 2	654	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						CTTCCTGTACCAACCCAAGCA	0.607																																					p.Q654X		Atlas-SNP	.											.	SUSD2	68	.	0			c.C1960T						PASS	.						170	136	148					22																	24583607		2203	4300	6503	SO:0001587	stop_gained	56241	exon12			CTGTACCAACCCA	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.1960C>T	22.37:g.24583607C>T	ENSP00000351075:p.Gln654*	125	0	0		92	30	0.326087	NM_019601	Q9H5Y6	Nonsense_Mutation	SNP	ENST00000358321.3	37	CCDS13824.1	.	.	.	.	.	.	.	.	.	.	C	38	6.727593	0.97792	.	.	ENSG00000099994	ENST00000358321	.	.	.	4.52	-4.27	0.03744	.	0.879590	0.09795	N	0.754864	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06236	T	0.91	-0.0961	12.2189	0.54423	0.1287:0.2034:0.6679:0.0	.	.	.	.	X	654	.	ENSP00000351075:Q654X	Q	+	1	0	SUSD2	22913607	0.000000	0.05858	0.000000	0.03702	0.884000	0.51177	0.100000	0.15231	-0.175000	0.10725	0.505000	0.49811	CAA	.	.	none		0.607	SUSD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320088.1	NM_019601		T	24583607	C	T	24583607	4	4	45	1	0	0	0	0	0	1	0	0	15423	595	21	2	2006	2	SUSD2	22	24583607	Nonsense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	1353198	24583607	26720959	197	15649											
BPIL2	254240	hgsc.bcm.edu	37	chr22	32841910	32841910	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagggtaggatgaccaaagtCatttcgggttaggataatga	13	10	13	5	1	1	2	1	2	0	0	2	4	1	4	1	4	0	2	1	4	4	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr22:32841910C>A	ENST00000397452.1	-	5	558	c.448G>T	c.(448-450)Gac>Tac	p.D150Y	BPIFC_ENST00000432451.2_5'UTR|BPIFC_ENST00000534972.1_Intron|BPIFC_ENST00000300399.3_Missense_Mutation_p.D150Y			Q8NFQ6	BPIFC_HUMAN	BPI fold containing family C	150						extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)|phospholipid binding (GO:0005543)										TGACCAAAGTCATTTCGGGTT	0.498																																					p.D150Y		Atlas-SNP	.											BPIL2,NS,carcinoma,0,1	.	.	1	0			c.G448T						PASS	.						88	91	90					22																	32841910		2203	4300	6503	SO:0001583	missense	254240	exon4			CAAAGTCATTTCG	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.448G>T	22.37:g.32841910C>A	ENSP00000380594:p.Asp150Tyr	108	0	0		113	15	0.132743	NM_174932	A2RRF1	Missense_Mutation	SNP	ENST00000397452.1	37	CCDS13906.1	.	.	.	.	.	.	.	.	.	.	C	12.69	2.013664	0.35511	.	.	ENSG00000184459	ENST00000397452;ENST00000300399	T;T	0.05855	3.38;3.38	5.71	2.48	0.30137	.	0.908340	0.09747	N	0.761146	T	0.13670	0.0331	M	0.75447	2.3	0.09310	N	0.999999	P	0.48589	0.912	P	0.47528	0.549	T	0.14924	-1.0455	10	0.66056	D	0.02	-2.0646	8.4699	0.32980	0.0:0.7511:0.0:0.2489	.	150	Q8NFQ6	BPIFC_HUMAN	Y	150	ENSP00000380594:D150Y;ENSP00000300399:D150Y	ENSP00000300399:D150Y	D	-	1	0	BPIFC	31171910	0.000000	0.05858	0.506000	0.27664	0.169000	0.22640	-0.863000	0.04259	0.792000	0.33850	0.650000	0.86243	GAC	.	.	none		0.498	BPIFC-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129029.2	NM_174932		A	32841910	C	A	32841910	3	1	45	1	0	0	0	0	1	0	0	0	1494	826	29	4	1123	4	BPIL2	22	32841910	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	8258303	32841910	18462656	198	15650											
TYMP	1890	hgsc.bcm.edu	37	chr22	50966942	50966942	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gatccgtggcgccccgtaccTgctctgggctctggatgaca	5	9	13	14	3	2	1	0	1	2	0	3	3	3	2	4	3	2	3	4	3	1	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chr22:50966942T>A	ENST00000252029.3	-	4	677	c.515A>T	c.(514-516)cAg>cTg	p.Q172L	SCO2_ENST00000543927.1_5'Flank|SCO2_ENST00000252785.3_5'Flank|TYMP_ENST00000395680.1_Splice_Site_p.Q172L|SCO2_ENST00000535425.1_5'Flank|TYMP_ENST00000395681.1_Splice_Site_p.Q172L|SCO2_ENST00000395693.3_5'Flank|TYMP_ENST00000395678.3_Splice_Site_p.Q172L	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	172					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)	GCCCCGTACCTGCTCTGGGCT	0.527																																					p.Q172L		Atlas-SNP	.											TYMP,NS,carcinoma,-1,1	TYMP	25	1	0			c.A515T						PASS	.						108	81	90					22																	50966942		2203	4300	6503	SO:0001630	splice_region_variant	1890	exon4			CGTACCTGCTCTG	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.516+1A>T	22.37:g.50966942T>A		45	0	0		44	14	0.318182	NM_001257989	A8MW15|H9KVA0|Q13390|Q8WVB7	Missense_Mutation	SNP	ENST00000252029.3	37	CCDS14096.1	.	.	.	.	.	.	.	.	.	.	T	18.08	3.544117	0.65198	.	.	ENSG00000025708	ENST00000395680;ENST00000395681;ENST00000252029;ENST00000395678	D;D;D;D	0.98345	-4.88;-4.88;-4.88;-4.88	4.66	4.66	0.58398	Glycosyl transferase, family 3 (3);	0.068178	0.64402	D	0.000011	D	0.96172	0.8752	L	0.57536	1.79	0.54753	D	0.999983	P;P;P	0.45531	0.86;0.563;0.563	B;B;B	0.37015	0.239;0.159;0.159	D	0.96009	0.9000	10	0.72032	D	0.01	-6.6403	12.0967	0.53758	0.0:0.0:0.0:1.0	.	172;172;172	B4DVR2;E5KRG5;P19971	.;.;TYPH_HUMAN	L	172	ENSP00000379037:Q172L;ENSP00000379038:Q172L;ENSP00000252029:Q172L;ENSP00000379036:Q172L	ENSP00000252029:Q172L	Q	-	2	0	TYMP	49313808	1.000000	0.71417	1.000000	0.80357	0.693000	0.40251	6.408000	0.73285	1.961000	0.56991	0.454000	0.30748	CAG	.	.	none		0.527	TYMP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317081.1	NM_001953	Missense_Mutation	A	50966942	T	A	50966942	5	1	45	1	0	0	0	0	0	0	1	0	16826	1594	55	5	961	5	TYMP	22	50966942	Splice_Site	SNP	T	TCGA-RQ-A68N-01A-11D-A31X-10	18125032	50966942	337624	199	15651											
NR0B1	190	hgsc.bcm.edu	37	chrX	30326889	30326889	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttcaccgcaaaagcagcagcGgtacagaagcgccgtggccc	11	4	12	14	4	1	1	1	0	0	1	1	1	1	1	3	2	5	4	3	2	4	2			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chrX:30326889G>A	ENST00000378970.4	-	1	826	c.592C>T	c.(592-594)Cgc>Tgc	p.R198C	NR0B1_ENST00000378963.1_5'Flank|NR0B1_ENST00000453287.1_Missense_Mutation_p.R198C	NM_000475.4	NP_000466.2	P51843	NR0B1_HUMAN	nuclear receptor subfamily 0, group B, member 1	198	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)	AAGCAGCAGCGGTACAGAAGC	0.701											OREG0019719	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R198C		Atlas-SNP	.											.	NR0B1	61	.	0			c.C592T						PASS	.						10	8	8					X																	30326889		2170	4233	6403	SO:0001583	missense	190	exon1			AGCAGCGGTACAG	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.592C>T	X.37:g.30326889G>A	ENSP00000368253:p.Arg198Cys	86	0	0	816	128	99	0.773438	NM_000475	Q96F69	Missense_Mutation	SNP	ENST00000378970.4	37	CCDS14223.1	.	.	.	.	.	.	.	.	.	.	G	11.43	1.636797	0.29068	.	.	ENSG00000169297	ENST00000378970;ENST00000453287	D;D	0.98207	-3.84;-4.79	3.84	1.96	0.26148	.	0.363841	0.22773	N	0.055806	D	0.98419	0.9474	M	0.71581	2.175	0.19775	N	0.999955	D	0.89917	1.0	D	0.73708	0.981	D	0.95009	0.8150	10	0.87932	D	0	-22.9197	11.7993	0.52118	0.0:0.3317:0.6683:0.0	.	198	P51843	NR0B1_HUMAN	C	198	ENSP00000368253:R198C;ENSP00000396403:R198C	ENSP00000368253:R198C	R	-	1	0	NR0B1	30236810	.	.	0.104000	0.21259	0.483000	0.33249	.	.	0.381000	0.24851	0.466000	0.42574	CGC	.	.	none		0.701	NR0B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056161.1	NM_000475		A	30326889	G	A	30326889	3	1	45	1	0	0	0	0	1	0	0	0	10622	1116	39	1	828	1	NR0B1	23	30326889	Missense_Mutation	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10		30326889	124943671	200	15652											
LANCL3	347404	hgsc.bcm.edu	37	chrX	37431669	37431669	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggttacctgtgtgccgcgctGgtgctcaagcagaaactcgc	7	9	13	12	3	1	1	1	0	0	1	2	1	1	1	2	2	5	4	2	2	3	1			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chrX:37431669G>A	ENST00000378619.3	+	1	765	c.546G>A	c.(544-546)ctG>ctA	p.L182L	LANCL3_ENST00000378621.3_Silent_p.L182L|TM4SF2_ENST00000465127.1_Intron	NM_001170331.1	NP_001163802.1	Q6ZV70	LANC3_HUMAN	LanC lantibiotic synthetase component C-like 3 (bacterial)	182							catalytic activity (GO:0003824)			lung(4)|pancreas(1)	5						GTGCCGCGCTGGTGCTCAAGC	0.711																																					p.L182L		Atlas-SNP	.											.	LANCL3	42	.	0			c.G546A						PASS	.						4	5	5					X																	37431669		2102	4096	6198	SO:0001819	synonymous_variant	347404	exon1			CGCGCTGGTGCTC	AK124915	CCDS14240.1, CCDS55398.1	Xp21.1	2008-02-05			ENSG00000147036	ENSG00000147036			24767	protein-coding gene	gene with protein product							Standard	NM_198511		Approved	FLJ42925	uc011mkd.2	Q6ZV70	OTTHUMG00000033177	ENST00000378619.3:c.546G>A	X.37:g.37431669G>A		45	0	0		75	61	0.813333	NM_001170331	A6NHE3	Silent	SNP	ENST00000378619.3	37	CCDS55398.1																																																																																			.	.	none		0.711	LANCL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080885.1	NM_198511		A	37431669	G	A	37431669	2	1	45	1	0	0	0	0	0	0	0	1	8631	1335	47	2		2	LANCL3	23	37431669	Silent	SNP	G	TCGA-RQ-A68N-01A-11D-A31X-10	7104780	37431669	117838891	201	15653											
FAM104B	90736	hgsc.bcm.edu	37	chrX	55187411	55187411	+	Intron	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccggccaacactgtcacctgCaggtcatgagagccgagcgc	9	5	12	15	3	2	1	2	1	0	1	2	3	2	1	4	2	4	1	4	2	1	0			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chrX:55187411C>T	ENST00000358460.4	-	1	174				FAM104B_ENST00000472571.2_Intron|FAM104B_ENST00000489298.1_5'UTR|FAM104B_ENST00000477847.2_Missense_Mutation_p.C3Y|FAM104B_ENST00000425133.2_Intron|FAM104B_ENST00000478918.1_5'Flank|FAM104B_ENST00000332132.4_Intron			Q5XKR9	F104B_HUMAN	family with sequence similarity 104, member B											endometrium(3)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	8						CTGTCACCTGCAGGTCATGAG	0.592																																					p.C3Y		Atlas-SNP	.											.	FAM104B	28	.	0			c.G8A						PASS	.						44	44	44					X																	55187411		692	1591	2283	SO:0001627	intron_variant	90736	exon1			CACCTGCAGGTCA	BC000919	CCDS35305.1, CCDS35305.2, CCDS55422.1, CCDS55423.1, CCDS55424.1, CCDS55425.1, CCDS55426.1	Xp11.22	2008-02-05	2006-05-16	2006-05-16	ENSG00000182518	ENSG00000182518			25085	protein-coding gene	gene with protein product			"chromosome X open reading frame 44"	CXorf44		12477932	Standard	NM_138362		Approved	FLJ20434	uc004dug.2	Q5XKR9	OTTHUMG00000021646	ENST00000358460.4:c.20+158G>A	X.37:g.55187411C>T		24	0	0		32	25	0.78125	NM_001166702	A6NEH1|B4DSV6|D6R9S5|D6RDJ5|E9PH40|Q8WVU5|Q9BRA1	Missense_Mutation	SNP	ENST00000358460.4	37	CCDS35305.2	.	.	.	.	.	.	.	.	.	.	c	6.691	0.496119	0.12762	.	.	ENSG00000182518	ENST00000477847	T	0.41400	1.0	1.76	-0.296	0.12824	.	.	.	.	.	T	0.19805	0.0476	N	0.08118	0	0.09310	N	0.999992	.	.	.	.	.	.	T	0.27706	-1.0066	6	.	.	.	.	7.3096	0.26467	0.0:0.4049:0.5951:0.0	.	.	.	.	Y	3	ENSP00000421161:C3Y	.	C	-	2	0	FAM104B	55204136	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-2.057000	0.01395	-0.167000	0.10871	0.292000	0.19580	TGC	.	.	none		0.592	FAM104B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056851.1	NM_138362		T	55187411	C	T	55187411	1	4	45	0	1	0	0	0	0	0	0	0	5391	710	25	2		2	FAM104B	23	55187411	Intron	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	17755742	55187411	100083149	202	15654											
CPXCR1	53336	hgsc.bcm.edu	37	chrX	88009293	88009293	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacttactctgaattaagacAacattcatgcagctcttctg	12	13	5	11	0	4	2	1	1	3	1	4	2	4	2	0	0	4	2	0	0	4	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chrX:88009293A>T	ENST00000276127.4	+	3	1137	c.878A>T	c.(877-879)cAa>cTa	p.Q293L	CPXCR1_ENST00000373111.1_Missense_Mutation_p.Q293L	NM_033048.5	NP_149037	Q8N123	CPXCR_HUMAN	CPX chromosome region, candidate 1	293							metal ion binding (GO:0046872)			NS(1)|cervix(1)|kidney(1)|large_intestine(11)|liver(1)|lung(20)|ovary(3)|upper_aerodigestive_tract(2)	40						GAATTAAGACAACATTCATGC	0.299																																					p.Q293L		Atlas-SNP	.											.	CPXCR1	83	.	0			c.A878T						PASS	.						40	40	40					X																	88009293		2198	4294	6492	SO:0001583	missense	53336	exon3			TAAGACAACATTC	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.878A>T	X.37:g.88009293A>T	ENSP00000276127:p.Gln293Leu	166	0	0		170	51	0.3	NM_001184771	B2R9F9|D3DTE7|Q96RS3	Missense_Mutation	SNP	ENST00000276127.4	37	CCDS14458.1	.	.	.	.	.	.	.	.	.	.	A	0.749	-0.773453	0.02951	.	.	ENSG00000147183	ENST00000276127;ENST00000373111	T;T	0.01527	4.8;4.8	3.42	0.89	0.19218	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	1.490400	0.04667	N	0.409900	T	0.01523	0.0049	N	0.19112	0.55	0.09310	N	1	B	0.15141	0.012	B	0.10450	0.005	T	0.49588	-0.8924	9	.	.	.	2.5471	4.0038	0.09592	0.695:0.0:0.1198:0.1852	.	293	Q8N123	CPXCR_HUMAN	L	293	ENSP00000276127:Q293L;ENSP00000362203:Q293L	.	Q	+	2	0	CPXCR1	87895949	0.028000	0.19301	0.002000	0.10522	0.000000	0.00434	0.297000	0.19101	-0.207000	0.10187	-1.278000	0.01390	CAA	.	.	none		0.299	CPXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057418.1	NM_033048		T	88009293	A	T	88009293	3	4	45	1	0	0	0	0	1	0	0	0	3838	130	5	5	880	5	CPXCR1	23	88009293	Missense_Mutation	SNP	A	TCGA-RQ-A68N-01A-11D-A31X-10	32821882	88009293	67261267	203	15655											
COL4A5	1287	hgsc.bcm.edu	37	chrX	107816878	107816878	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggatatccaggtcctcctggAatacaagtaagtatccagtg	12	10	10	9	0	0	0	0	0	0	0	4	2	4	2	4	3	1	2	4	3	6	4			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chrX:107816878A>G	ENST00000361603.2	+	9	784	c.540A>G	c.(538-540)ggA>ggG	p.G180G	COL4A5_ENST00000328300.6_Silent_p.G180G	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	180	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						GTCCTCCTGGAATACAAGTAA	0.378									Alport syndrome with Diffuse Leiomyomatosis																												p.G180G		Atlas-SNP	.											.	COL4A5	262	.	0			c.A540G						PASS	.						111	105	107					X																	107816878		2203	4300	6503	SO:0001819	synonymous_variant	1287	exon9	Familial Cancer Database		TCCTGGAATACAA	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.540A>G	X.37:g.107816878A>G		129	0	0		142	12	0.084507	NM_000495	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Silent	SNP	ENST00000361603.2	37	CCDS14543.1																																																																																			.	.	none		0.378	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2			G	107816878	A	G	107816878	2	3	45	1	0	0	0	0	0	0	0	1	3696	233	9	3		3	COL4A5	23	107816878	Silent	SNP	A	TCGA-RQ-A68N-01A-11D-A31X-10	19807585	107816878	47453682	204	15656											
GPR101	83550	hgsc.bcm.edu	37	chrX	136113230	136113230	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgacaatcagtggaatgaCgatgaaggacaccacgctga	15	6	11	9	2	1	4	1	4	0	0	1	7	1	6	1	2	0	1	1	2	3	0			TCGA-RQ-A68N-01A-11D-A31X-10	TCGA-RQ-A68N-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	f0f86783-1a4a-4b9c-a8aa-6b06f57ab5c9	8e299ec1-c619-4564-80cd-223c3c960027	g.chrX:136113230C>T	ENST00000298110.1	-	1	603	c.604G>A	c.(604-606)Gtc>Atc	p.V202I		NM_054021.1	NP_473362.1	Q96P66	GP101_HUMAN	G protein-coupled receptor 101	202						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)					AGTGGAATGACGATGAAGGAC	0.567																																					p.V202I		Atlas-SNP	.											.	GPR101	96	.	0			c.G604A						PASS	.						78	66	70					X																	136113230		2203	4300	6503	SO:0001583	missense	83550	exon1			GAATGACGATGAA	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.604G>A	X.37:g.136113230C>T	ENSP00000298110:p.Val202Ile	20	0	0		46	38	0.826087	NM_054021	Q5JSM8|Q8NG93	Missense_Mutation	SNP	ENST00000298110.1	37	CCDS14662.1	.	.	.	.	.	.	.	.	.	.	C	0.017	-1.499489	0.01001	.	.	ENSG00000165370	ENST00000298110	T	0.73152	-0.72	5.13	-1.89	0.07689	GPCR, rhodopsin-like superfamily (1);	0.589703	0.12687	N	0.447441	T	0.51907	0.1702	N	0.26042	0.785	0.19300	N	0.99997	B	0.11235	0.004	B	0.06405	0.002	T	0.37686	-0.9695	10	0.54805	T	0.06	-6.8495	6.9808	0.24702	0.0:0.3125:0.1519:0.5356	.	202	Q96P66	GP101_HUMAN	I	202	ENSP00000298110:V202I	ENSP00000298110:V202I	V	-	1	0	GPR101	135940896	0.594000	0.26849	0.042000	0.18584	0.676000	0.39594	-0.176000	0.09811	-0.530000	0.06349	-0.208000	0.12717	GTC	.	.	none		0.567	GPR101-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058519.1			T	136113230	C	T	136113230	3	4	45	1	0	0	0	0	1	0	0	0	6630	536	19	1	925	1	GPR101	23	136113230	Missense_Mutation	SNP	C	TCGA-RQ-A68N-01A-11D-A31X-10	28296352	136113230	19157330	205	15657											
MARCKSL1	65108	hgsc.bcm.edu	37	chr1	32800454	32800454	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagaagaatcacccccacccTccttccgatttctcttgaag	10	10	5	16	1	2	3	1	1	1	2	5	4	4	3	5	0	0	0	5	0	3	3			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr1:32800454T>A	ENST00000329421.7	-	2	677	c.332A>T	c.(331-333)gAg>gTg	p.E111V		NM_023009.6	NP_075385.1	P49006	MRP_HUMAN	MARCKS-like 1	111					positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				breast(1)|large_intestine(3)|lung(1)|ovary(1)	6		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				ACCCCCACCCTCCTTCCGATT	0.572																																					p.E111V		Atlas-SNP	.											.	MARCKSL1	17	.	0			c.A332T						PASS	.						45	45	45					1																	32800454		2203	4300	6503	SO:0001583	missense	65108	exon2			CCACCCTCCTTCC	AF031640	CCDS361.1	1p35.1	2008-02-05	2004-11-17	2004-11-17	ENSG00000175130	ENSG00000175130			7142	protein-coding gene	gene with protein product		602940	"MARCKS-like protein"	MLP		9598313	Standard	NM_023009		Approved	F52, MacMARCKS, MLP1	uc001bvd.4	P49006	OTTHUMG00000007589	ENST00000329421.7:c.332A>T	1.37:g.32800454T>A	ENSP00000362638:p.Glu111Val	42	0	0		48	13	0.270833	NM_023009	D3DPQ0|Q5TEE6|Q6NXS5	Missense_Mutation	SNP	ENST00000329421.7	37	CCDS361.1	.	.	.	.	.	.	.	.	.	.	T	19.60	3.858221	0.71834	.	.	ENSG00000175130	ENST00000329421	T	0.47528	0.84	5.17	4.04	0.47022	.	0.310671	0.35805	N	0.002978	T	0.52041	0.1710	L	0.52011	1.625	0.41063	D	0.985396	D	0.53462	0.96	P	0.52386	0.697	T	0.55250	-0.8170	10	0.87932	D	0	-5.9678	11.0117	0.47667	0.0:0.0745:0.0:0.9254	.	111	P49006	MRP_HUMAN	V	111	ENSP00000362638:E111V	ENSP00000362638:E111V	E	-	2	0	MARCKSL1	32573041	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.764000	0.55264	0.923000	0.37045	0.459000	0.35465	GAG	.	.	none		0.572	MARCKSL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020059.3	NM_023009		A	32800454	T	A	32800454	3	1	46	1	0	0	0	0	1	0	0	0	9319	1551	54	5	259	5	MARCKSL1	1	32800454	Missense_Mutation	SNP	T	TCGA-RQ-A6JB-01A-11D-A31X-10		32800454	216450167	1	15658											
ZSCAN20	7579	hgsc.bcm.edu	37	chr1	33956948	33956948	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atcgggccattgcagagcagCtaagggcaaggggcttcctg	9	7	15	10	1	0	1	0	0	0	1	2	1	1	1	2	4	3	5	2	4	2	3			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr1:33956948C>T	ENST00000361328.3	+	6	1243	c.1090C>T	c.(1090-1092)Cta>Tta	p.L364L	ZSCAN20_ENST00000373413.2_Silent_p.L310L	NM_145238.3	NP_660281	P17040	ZSC20_HUMAN	zinc finger and SCAN domain containing 20	364					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)				TGCAGAGCAGCTAAGGGCAAG	0.532																																					p.L364L		Atlas-SNP	.											.	ZSCAN20	107	.	0			c.C1090T						PASS	.						94	98	97					1																	33956948		1957	4167	6124	SO:0001819	synonymous_variant	7579	exon6			GAGCAGCTAAGGG	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.1090C>T	1.37:g.33956948C>T		135	0	0		107	42	0.392523	NM_145238	A8K2D0|B1ALI4|B1ALI5|B1ALI6|Q6ZN23|Q96FA9|Q96H84	Silent	SNP	ENST00000361328.3	37	CCDS41300.1																																																																																			.	.	none		0.532	ZSCAN20-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277003.2	NM_145238		T	33956948	C	T	33956948	2	4	46	1	0	0	0	0	0	0	0	1	18247	796	28	2		2	ZSCAN20	1	33956948	Silent	SNP	C	TCGA-RQ-A6JB-01A-11D-A31X-10	1156494	33956948	215293673	2	15659											
FCER1G	2207	hgsc.bcm.edu	37	chr1	161187859	161187859	+	Silent	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcctcaccctcctctactgtCgactgaaggtagcgctgggc	6	10	10	15	2	2	1	1	1	1	0	5	2	4	1	3	2	2	2	3	2	3	2			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr1:161187859C>A	ENST00000289902.1	+	2	158	c.133C>A	c.(133-135)Cga>Aga	p.R45R	AL590714.1_ENST00000594609.1_5'Flank|FCER1G_ENST00000490414.1_Intron|FCER1G_ENST00000367992.3_Silent_p.R45R	NM_004106.1	NP_004097.1	P30273	FCERG_HUMAN	Fc fragment of IgE, high affinity I, receptor for; gamma polypeptide	45					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)|blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|Fc receptor mediated stimulatory signaling pathway (GO:0002431)|Fc-epsilon receptor signaling pathway (GO:0038095)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mast cell activation (GO:0045576)|negative regulation of mast cell apoptotic process (GO:0033026)|neutrophil activation involved in immune response (GO:0002283)|neutrophil chemotaxis (GO:0030593)|phagocytosis, engulfment (GO:0006911)|platelet activation (GO:0030168)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of mast cell cytokine production (GO:0032765)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of phagocytosis (GO:0050766)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I hypersensitivity (GO:0001812)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation of type III hypersensitivity (GO:0001805)|protein localization to plasma membrane (GO:0072659)|regulation of platelet activation (GO:0010543)|serotonin secretion by platelet (GO:0002554)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|Fc-epsilon receptor I complex (GO:0032998)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	IgE receptor activity (GO:0019767)			endometrium(1)|lung(5)	6	all_cancers(52;1.35e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Benzylpenicilloyl Polylysine(DB00895)	CCTCTACTGTCGACTGAAGGT	0.562																																					p.R45R		Atlas-SNP	.											FCER1G,NS,carcinoma,-1,2	FCER1G	11	2	0			c.C133A						PASS	.						145	133	137					1																	161187859		2203	4300	6503	SO:0001819	synonymous_variant	2207	exon2			TACTGTCGACTGA		CCDS1225.1	1q23	2008-02-05			ENSG00000158869	ENSG00000158869			3611	protein-coding gene	gene with protein product		147139				2138619	Standard	NM_004106		Approved		uc001fyz.1	P30273	OTTHUMG00000034343	ENST00000289902.1:c.133C>A	1.37:g.161187859C>A		52	0	0		74	24	0.324324	NM_004106	Q5VTW4	Silent	SNP	ENST00000289902.1	37	CCDS1225.1																																																																																			.	.	none		0.562	FCER1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083012.1	NM_004106		A	161187859	C	A	161187859	2	1	46	1	0	0	0	0	0	0	0	1	5783	876	31	4		4	FCER1G	1	161187859	Silent	SNP	C	TCGA-RQ-A6JB-01A-11D-A31X-10	127230911	161187859	88062762	3	15660											
TNN	63923	hgsc.bcm.edu	37	chr1	175049323	175049323	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	caccccacagggcctgcagcTgctcaagaacacggaggatt	11	5	11	14	1	1	1	1	0	0	1	1	3	1	3	3	3	4	3	3	3	2	1			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr1:175049323T>C	ENST00000239462.4	+	4	922	c.809T>C	c.(808-810)cTg>cCg	p.L270P		NM_022093.1	NP_071376.1	Q9UQP3	TENN_HUMAN	tenascin N	270	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)		GGCCTGCAGCTGCTCAAGAAC	0.607																																					p.L270P		Atlas-SNP	.											.	TNN	297	.	0			c.T809C						PASS	.						49	51	50					1																	175049323		2203	4300	6503	SO:0001583	missense	63923	exon4			TGCAGCTGCTCAA	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.809T>C	1.37:g.175049323T>C	ENSP00000239462:p.Leu270Pro	32	0	0		40	14	0.35	NM_022093	B9EGP3|Q5R360	Missense_Mutation	SNP	ENST00000239462.4	37	CCDS30943.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.159759	0.78226	.	.	ENSG00000120332	ENST00000239462;ENST00000539081	T	0.58940	0.3	5.58	5.58	0.84498	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.146450	0.47455	D	0.000233	T	0.76884	0.4050	M	0.81802	2.56	0.80722	D	1	D;B	0.76494	0.999;0.118	D;B	0.73708	0.981;0.118	T	0.80246	-0.1462	10	0.66056	D	0.02	.	15.4264	0.75055	0.0:0.0:0.0:1.0	.	270;270	B3KXB6;Q9UQP3	.;TENN_HUMAN	P	270	ENSP00000239462:L270P	ENSP00000239462:L270P	L	+	2	0	TNN	173315946	1.000000	0.71417	1.000000	0.80357	0.844000	0.47949	3.954000	0.56708	2.119000	0.64992	0.528000	0.53228	CTG	.	.	none		0.607	TNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084422.1	XM_040527		C	175049323	T	C	175049323	3	2	46	1	0	0	0	0	1	0	0	0	16338	1580	55	3	819	3	TNN	1	175049323	Missense_Mutation	SNP	T	TCGA-RQ-A6JB-01A-11D-A31X-10	13861464	175049323	74201298	4	15661											
USH2A	7399	hgsc.bcm.edu	37	chr1	216251568	216251568	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gtccattcacacttgctgatAtgaaagagccttccttttta	10	15	6	10	0	1	3	1	2	0	1	3	3	3	3	3	0	2	1	3	0	3	7			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr1:216251568A>C	ENST00000307340.3	-	27	5821	c.5435T>G	c.(5434-5436)aTa>aGa	p.I1812R	USH2A_ENST00000366943.2_Missense_Mutation_p.I1812R|RP11-22M7.2_ENST00000430890.1_RNA|RP11-22M7.2_ENST00000442606.1_RNA|RP11-22M7.2_ENST00000446411.1_RNA|RP11-22M7.2_ENST00000445619.1_RNA	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1812	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				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)		ACTTGCTGATATGAAAGAGCC	0.438										HNSCC(13;0.011)																											p.I1812R		Atlas-SNP	.											.	USH2A	1168	.	0			c.T5435G						PASS	.						156	158	158					1																	216251568		2203	4300	6503	SO:0001583	missense	7399	exon27			GCTGATATGAAAG	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.5435T>G	1.37:g.216251568A>C	ENSP00000305941:p.Ile1812Arg	130	0	0		114	39	0.342105	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	A	18.27	3.586819	0.66105	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.79141	-1.24;-1.24	5.01	3.88	0.44766	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Fibronectin, type III (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	0.468184	0.17640	N	0.167065	D	0.82706	0.5095	M	0.66939	2.045	0.09310	N	1	P	0.47484	0.896	P	0.55455	0.776	T	0.73858	-0.3850	10	0.72032	D	0.01	.	10.3204	0.43762	0.922:0.0:0.078:0.0	.	1812	O75445	USH2A_HUMAN	R	1812	ENSP00000305941:I1812R;ENSP00000355910:I1812R	ENSP00000305941:I1812R	I	-	2	0	USH2A	214318191	0.191000	0.23288	0.001000	0.08648	0.523000	0.34469	4.275000	0.58927	0.772000	0.33382	0.528000	0.53228	ATA	.	.	none		0.438	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123		C	216251568	A	C	216251568	3	2	46	1	0	0	0	0	1	0	0	0	17051	449	16	5	10357	5	USH2A	1	216251568	Missense_Mutation	SNP	A	TCGA-RQ-A6JB-01A-11D-A31X-10	41202245	216251568	32999053	5	15662											
FMN2	56776	hgsc.bcm.edu	37	chr1	240370997	240370997	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tccgccccctcttcccggggCaggcataccccttcctcccc	3	8	7	23	2	1	0	0	0	1	0	5	0	5	0	9	3	1	2	9	3	1	3			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr1:240370997C>A	ENST00000319653.9	+	5	3115	c.2885C>A	c.(2884-2886)gCa>gAa	p.A962E		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	962	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)			CTTCCCGGGGCAGGCATACCC	0.697																																					p.A962E		Atlas-SNP	.											FMN2,NS,carcinoma,-1,2	FMN2	451	2	0			c.C2885A						scavenged	.						20	23	22					1																	240370997		2200	4297	6497	SO:0001583	missense	56776	exon5			CCGGGGCAGGCAT	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.2885C>A	1.37:g.240370997C>A	ENSP00000318884:p.Ala962Glu	93	1	0.0107527		96	64	0.666667	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	C	7.783	0.709962	0.15239	.	.	ENSG00000155816	ENST00000319653	T	0.56941	0.43	3.8	-3.7	0.04437	Actin-binding FH2/DRF autoregulatory (1);Formin Homology 1 (1);	.	.	.	.	T	0.31295	0.0792	L	0.38175	1.15	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.22173	-1.0224	8	.	.	.	.	0.4251	0.00462	0.2272:0.1627:0.2561:0.3541	.	962	Q9NZ56	FMN2_HUMAN	E	962	ENSP00000318884:A962E	.	A	+	2	0	FMN2	238437620	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-6.269000	0.00073	-0.532000	0.06332	-0.878000	0.02970	GCA	.	.	none		0.697	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		A	240370997	C	A	240370997	3	1	46	1	0	0	0	0	1	0	0	0	5958	710	25	4	2903	4	FMN2	1	240370997	Missense_Mutation	SNP	C	TCGA-RQ-A6JB-01A-11D-A31X-10	24119429	240370997	8879624	6	15663											
TMEM177	80775	hgsc.bcm.edu	37	chr2	120438454	120438454	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	caggtcccctgtggcggaccGcagcatttgtgcagagacac	8	7	13	13	2	0	1	0	0	0	1	1	3	1	2	3	3	2	3	3	3	0	1			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr2:120438454G>A	ENST00000424086.1	+	2	498	c.25G>A	c.(25-27)Gca>Aca	p.A9T	TMEM177_ENST00000409951.1_Missense_Mutation_p.A9T|TMEM177_ENST00000401466.1_Missense_Mutation_p.A9T|TMEM177_ENST00000496203.1_Intron|TMEM177_ENST00000272521.6_Missense_Mutation_p.A9T	NM_001105198.1	NP_001098668.1	Q53S58	TM177_HUMAN	transmembrane protein 177	9						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)					GTGGCGGACCGCAGCATTTGT	0.577																																					p.A9T		Atlas-SNP	.											.	TMEM177	26	.	0			c.G25A						PASS	.						31	32	32					2																	120438454		2203	4300	6503	SO:0001583	missense	80775	exon2			CGGACCGCAGCAT	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.25G>A	2.37:g.120438454G>A	ENSP00000402661:p.Ala9Thr	97	0	0		98	37	0.377551	NM_030577	Q9BT20	Missense_Mutation	SNP	ENST00000424086.1	37	CCDS2128.1	.	.	.	.	.	.	.	.	.	.	G	3.212	-0.161456	0.06502	.	.	ENSG00000144120	ENST00000401466;ENST00000424086;ENST00000272521;ENST00000445518;ENST00000409951;ENST00000415646	T;T;T;T;T	0.17691	2.26;2.26;2.26;2.26;2.26	4.05	-1.07	0.09968	.	0.587988	0.18617	N	0.135983	T	0.10380	0.0254	L	0.47716	1.5	0.09310	N	1	B;B	0.14012	0.009;0.005	B;B	0.10450	0.005;0.003	T	0.25257	-1.0137	10	0.26408	T	0.33	.	0.9877	0.01450	0.3926:0.1542:0.296:0.1572	.	9;9	B8ZZT5;Q53S58	.;TM177_HUMAN	T	9	ENSP00000385966:A9T;ENSP00000402661:A9T;ENSP00000272521:A9T;ENSP00000405898:A9T;ENSP00000386430:A9T	ENSP00000272521:A9T	A	+	1	0	TMEM177	120154924	0.001000	0.12720	0.000000	0.03702	0.267000	0.26476	-0.011000	0.12721	-0.221000	0.09973	0.549000	0.68633	GCA	.	.	none		0.577	TMEM177-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330673.1	NM_030577		A	120438454	G	A	120438454	3	1	46	1	0	0	0	0	1	0	0	0	16109	1087	38	1	27	1	TMEM177	2	120438454	Missense_Mutation	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10		120438454	122760919	7	15664											
ITGAV	3685	hgsc.bcm.edu	37	chr2	187533626	187533626	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aactgcacttcagatatggaGatcaaccctttgagaattaa	15	11	7	8	0	2	3	2	1	0	3	2	5	2	3	1	1	3	1	1	1	5	4			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr2:187533626G>A	ENST00000261023.3	+	25	2845	c.2571G>A	c.(2569-2571)gaG>gaA	p.E857E	ITGAV_ENST00000474571.1_3'UTR|ITGAV_ENST00000433736.2_Silent_p.E811E|AC017101.10_ENST00000453665.1_RNA|ITGAV_ENST00000374907.3_Silent_p.E821E	NM_002210.3	NP_002201	P06756	ITAV_HUMAN	integrin, alpha V	857					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)	CAGATATGGAGATCAACCCTT	0.323																																					p.E857E	Melanoma(58;108 1995 6081)	Atlas-SNP	.											.	ITGAV	124	.	0			c.G2571A						PASS	.						116	114	115					2																	187533626		2203	4300	6503	SO:0001819	synonymous_variant	3685	exon25			TATGGAGATCAAC		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.2571G>A	2.37:g.187533626G>A		187	0	0		174	60	0.344828	NM_002210	A0AV67|B0LPF4|B7Z883|B7ZLX0|D3DPG8|E7EWZ6|Q53SK4|Q59EB7|Q6LD15	Silent	SNP	ENST00000261023.3	37	CCDS2292.1	.	.	.	.	.	.	.	.	.	.	G	8.464	0.856071	0.17106	.	.	ENSG00000138448	ENST00000430709	.	.	.	5.54	3.75	0.43078	.	.	.	.	.	T	0.59321	0.2185	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54302	-0.8314	4	.	.	.	.	9.257	0.37590	0.2825:0.0:0.7175:0.0	.	.	.	.	K	8	.	.	R	+	2	0	ITGAV	187241871	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	1.129000	0.31381	0.716000	0.32124	-0.143000	0.13931	AGA	.	.	none		0.323	ITGAV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255882.2	NM_002210		A	187533626	G	A	187533626	2	1	46	1	0	0	0	0	0	0	0	1	7897	933	33	2		2	ITGAV	2	187533626	Silent	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10	67095172	187533626	55665747	8	15665											
EFHD1	80303	hgsc.bcm.edu	37	chr2	233546429	233546429	+	Nonstop_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaggccaacttcaatacataGtcctgctgaccttgccctct	10	11	6	14	0	2	1	1	1	1	0	3	1	3	1	4	1	4	1	4	1	5	4			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr2:233546429G>T	ENST00000264059.3	+	4	1197	c.720G>T	c.(718-720)taG>taT	p.*240Y	EFHD1_ENST00000410095.1_Nonstop_Mutation_p.*128Y|EFHD1_ENST00000409708.1_Nonstop_Mutation_p.*128Y|EFHD1_ENST00000409613.1_Nonstop_Mutation_p.*144Y|snoU13_ENST00000459149.1_RNA	NM_025202.3	NP_079478.1	Q9BUP0	EFHD1_HUMAN	EF-hand domain family, member D1	0					neuron projection development (GO:0031175)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|large_intestine(2)|lung(3)	7		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Breast(86;0.0199)|Renal(207;0.025)		Epithelial(121;2.08e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00825)|Lung(119;0.0101)		TCAATACATAGTCCTGCTGAC	0.582																																					p.X240Y		Atlas-SNP	.											.	EFHD1	28	.	0			c.G720T						PASS	.						71	61	64					2																	233546429		2203	4300	6503	SO:0001578	stop_lost	80303	exon4			TACATAGTCCTGC		CCDS2497.1, CCDS58755.1	2q37.1	2014-07-01	2005-01-25		ENSG00000115468	ENSG00000115468		"EF-hand domain containing"	29556	protein-coding gene	gene with protein product	"swiprosin-2"	611617	"EF hand domain containing 1"			21244694	Standard	NM_025202		Approved	FLJ13612	uc002vtc.3	Q9BUP0	OTTHUMG00000133263	ENST00000264059.3:c.720G>T	2.37:g.233546429G>T	ENSP00000264059:p.*240Tyrext*3	42	0	0		45	13	0.288889	NM_025202	B2RD83|E9PFH3|Q9BTF8|Q9H8I2|Q9HBQ0	Missense_Mutation	SNP	ENST00000264059.3	37	CCDS2497.1	.	.	.	.	.	.	.	.	.	.	G	19.83	3.899836	0.72754	.	.	ENSG00000115468	ENST00000409613;ENST00000264059;ENST00000540187;ENST00000409708;ENST00000410095	.	.	.	5.59	3.77	0.43336	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.0595	0.25117	0.0907:0.1752:0.7341:0.0	.	.	.	.	Y	144;240;143;128;128	.	.	X	+	3	2	EFHD1	233254673	0.965000	0.33210	0.119000	0.21687	0.759000	0.43091	2.287000	0.43505	1.345000	0.45676	0.591000	0.81541	TAG	.	.	none		0.582	EFHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257040.2	NM_025202		T	233546429	G	T	233546429	4	4	46	1	0	0	0	0	0	0	0	0	4950	1024	36	4	734	4	EFHD1	2	233546429	Nonstop_Mutation	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10	46012803	233546429	9652944	9	15666											
MYD88	4615	hgsc.bcm.edu	37	chr3	38181908	38181908	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgagcgtttcgatgccttcAtctgctattgccccagcgac	6	12	9	14	3	2	1	1	1	1	0	3	3	2	1	3	0	5	2	3	0	1	4			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr3:38181908A>G	ENST00000396334.3	+	3	716	c.532A>G	c.(532-534)Atc>Gtc	p.I178V	MYD88_ENST00000443433.2_Intron|MYD88_ENST00000417037.2_Missense_Mutation_p.I178V|MYD88_ENST00000424893.1_Missense_Mutation_p.I133V|MYD88_ENST00000481122.1_3'UTR|MYD88_ENST00000495303.1_Intron	NM_002468.4	NP_002459.2	Q99836	MYD88_HUMAN	myeloid differentiation primary response 88	165	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|cell surface receptor signaling pathway (GO:0007166)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-positive bacterium (GO:0050830)|establishment of endothelial intestinal barrier (GO:0090557)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of apoptotic process (GO:0043066)|negative regulation of growth of symbiont in host (GO:0044130)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-23 production (GO:0032747)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of lymphocyte proliferation (GO:0050671)|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 tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)|response to molecule of fungal origin (GO:0002238)|response to peptidoglycan (GO:0032494)|response to virus (GO:0009615)|signal transduction (GO:0007165)|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)|type I interferon biosynthetic process (GO:0045351)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)	death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|TIR domain binding (GO:0070976)			breast(1)|haematopoietic_and_lymphoid_tissue(226)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	237				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		CGATGCCTTCATCTGCTATTG	0.552			Mis		ABC-DLBCL																																p.I178V		Atlas-SNP	.		Dom	yes		3	3p22	4615	myeloid differentiation primary response gene (88)		L	.	MYD88	900	.	0			c.A532G						PASS	.						118	91	100					3																	38181908		2203	4300	6503	SO:0001583	missense	4615	exon3			GCCTTCATCTGCT	U84408	CCDS2674.2, CCDS54565.1, CCDS54566.1, CCDS54567.1, CCDS54568.1	3p22	2014-09-17	2012-11-15		ENSG00000172936	ENSG00000172936			7562	protein-coding gene	gene with protein product		602170	"myeloid differentiation primary response gene (88)"			9013863	Standard	NM_002468		Approved		uc003chx.3	Q99836	OTTHUMG00000131083	ENST00000396334.3:c.532A>G	3.37:g.38181908A>G	ENSP00000379625:p.Ile178Val	37	0	0		40	27	0.675	NM_002468	B4DKH8|B4DKU4|B4DQ60|B4DQ72|J3KPU4|J3KQ87|J3KQJ6|P78397|Q53XS7	Missense_Mutation	SNP	ENST00000396334.3	37	CCDS2674.2	.	.	.	.	.	.	.	.	.	.	A	15.34	2.805447	0.50315	.	.	ENSG00000172936	ENST00000417037;ENST00000396334;ENST00000424893;ENST00000421516;ENST00000415158	T;T;T;T	0.25579	1.79;1.79;1.79;1.79	5.61	5.61	0.85477	Toll/interleukin-1 receptor homology (TIR) domain (4);	0.000000	0.85682	D	0.000000	T	0.24586	0.0596	L	0.43701	1.375	0.80722	D	1	B;B;B	0.22909	0.077;0.031;0.031	B;B;B	0.29077	0.086;0.098;0.098	T	0.05550	-1.0878	10	0.14252	T	0.57	.	15.3005	0.73945	1.0:0.0:0.0:0.0	.	120;165;154	Q99836-2;Q99836;B4E3D6	.;MYD88_HUMAN;.	V	178;178;133;177;154	ENSP00000401399:I178V;ENSP00000379625:I178V;ENSP00000389979:I133V;ENSP00000391753:I177V	ENSP00000379625:I178V	I	+	1	0	MYD88	38156912	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.964000	0.76061	2.281000	0.76405	0.533000	0.62120	ATC	.	.	none		0.552	MYD88-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253743.4	NM_002468		G	38181908	A	G	38181908	3	3	46	1	0	0	0	0	1	0	0	0	10032	217	8	3	542	3	MYD88	3	38181908	Missense_Mutation	SNP	A	TCGA-RQ-A6JB-01A-11D-A31X-10		38181908	159840522	10	15667											
XIRP1	165904	hgsc.bcm.edu	37	chr3	39230658	39230658	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttctcaaagatccagcgcatGcactgaacgtcaccctcggt	10	9	8	14	3	2	2	2	1	1	1	5	2	3	2	2	1	3	2	2	1	2	1			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr3:39230658G>A	ENST00000340369.3	-	2	507	c.279C>T	c.(277-279)tgC>tgT	p.C93C	XIRP1_ENST00000421646.1_Intron|XIRP1_ENST00000396251.1_Silent_p.C93C	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	93					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)		TCCAGCGCATGCACTGAACGT	0.607																																					p.C93C		Atlas-SNP	.											.	XIRP1	173	.	0			c.C279T						PASS	.						72	70	71					3																	39230658		2203	4300	6503	SO:0001819	synonymous_variant	165904	exon2			GCGCATGCACTGA	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.279C>T	3.37:g.39230658G>A		63	0	0		63	6	0.0952381	NM_001198621	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Silent	SNP	ENST00000340369.3	37	CCDS2683.1																																																																																			.	.	none		0.607	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522		A	39230658	G	A	39230658	2	1	46	1	0	0	0	0	0	0	0	1	17444	1311	46	2		2	XIRP1	3	39230658	Silent	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10	1048750	39230658	158791772	11	15668											
VPRBP	9730	hgsc.bcm.edu	37	chr3	51497147	51497147	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taccttttcttgaaagacgaCagcagtttccagccctggca	10	11	8	12	1	1	2	0	1	1	1	2	3	2	2	3	1	3	3	3	1	2	5			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr3:51497147C>T	ENST00000335891.5	-	4	367	c.358G>A	c.(358-360)Gtc>Atc	p.V120I				Q9Y4B6	VPRBP_HUMAN	Vpr (HIV-1) binding protein	120					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)		TGAAAGACGACAGCAGTTTCC	0.373																																					p.V120I		Atlas-SNP	.											VPRBP,colon,carcinoma,+1,1	VPRBP	107	1	0			c.G358A						scavenged	.						56	52	53					3																	51497147		1903	4142	6045	SO:0001583	missense	9730	exon6			AGACGACAGCAGT	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.358G>A	3.37:g.51497147C>T	ENSP00000338857:p.Val120Ile	83	1	0.0120482		100	38	0.38	NM_014703	Q2YD74|Q8TBD9|Q9HCA1|Q9UG37	Missense_Mutation	SNP	ENST00000335891.5	37		.	.	.	.	.	.	.	.	.	.	C	27.4	4.825197	0.90955	.	.	ENSG00000145041	ENST00000335891;ENST00000504652	T;T	0.57595	0.39;0.81	5.51	5.51	0.81932	Armadillo-type fold (1);	0.057232	0.64402	D	0.000002	T	0.54711	0.1875	M	0.65975	2.015	0.30565	N	0.764119	P	0.41784	0.762	B	0.38327	0.271	T	0.63506	-0.6622	10	0.51188	T	0.08	-11.4123	19.0105	0.92871	0.0:1.0:0.0:0.0	.	120	Q9Y4B6	VPRBP_HUMAN	I	120	ENSP00000338857:V120I;ENSP00000421724:V120I	ENSP00000338857:V120I	V	-	1	0	VPRBP	51472187	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.332000	0.79203	2.589000	0.87451	0.561000	0.74099	GTC	.	.	none		0.373	VPRBP-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014703		T	51497147	C	T	51497147	3	4	46	1	0	0	0	0	1	0	0	0	17200	478	17	2	4082	2	VPRBP	3	51497147	Missense_Mutation	SNP	C	TCGA-RQ-A6JB-01A-11D-A31X-10	12266489	51497147	146525283	12	15669											
KALRN	8997	hgsc.bcm.edu	37	chr3	124175525	124175525	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgggaggtcaagctgcgggaCgccaaccacgaagtcaatga	12	4	14	11	4	2	1	2	1	0	0	2	4	2	3	2	3	3	1	2	3	4	0			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr3:124175525C>T	ENST00000240874.3	+	23	3955	c.3798C>T	c.(3796-3798)gaC>gaT	p.D1266D	KALRN_ENST00000460856.1_Silent_p.D1257D|KALRN_ENST00000360013.3_Silent_p.D1266D	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1266					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						AGCTGCGGGACGCCAACCACG	0.557																																					p.D1266D		Atlas-SNP	.											.	KALRN	556	.	0			c.C3798T						PASS	.						105	100	102					3																	124175525		2203	4300	6503	SO:0001819	synonymous_variant	8997	exon23			GCGGGACGCCAAC	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.3798C>T	3.37:g.124175525C>T		174	0	0		174	51	0.293103	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	37	CCDS3027.1	.	.	.	.	.	.	.	.	.	.	C	9.785	1.176432	0.21704	.	.	ENSG00000160145	ENST00000354186	.	.	.	4.88	-9.12	0.00707	.	.	.	.	.	T	0.59972	0.2233	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68401	-0.5418	4	.	.	.	.	15.3034	0.73972	0.0:0.5754:0.0:0.4246	.	.	.	.	M	1235	.	.	T	+	2	0	KALRN	125658215	0.014000	0.17966	0.808000	0.32385	0.960000	0.62799	-0.945000	0.03909	-1.767000	0.01300	-0.966000	0.02617	ACG	.	.	none		0.557	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		T	124175525	C	T	124175525	2	4	46	1	0	0	0	0	0	0	0	1	7984	535	19	1		1	KALRN	3	124175525	Silent	SNP	C	TCGA-RQ-A6JB-01A-11D-A31X-10	72678378	124175525	73846905	13	15670											
ATOH1	474	hgsc.bcm.edu	37	chr4	94751127	94751127	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cattcccattacagtgactcGgatgaggcaagttaggaagg	12	9	12	8	1	0	2	0	2	0	0	2	4	1	4	1	4	1	2	1	4	4	3			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr4:94751127G>A	ENST00000306011.3	+	1	1086	c.1050G>A	c.(1048-1050)tcG>tcA	p.S350S		NM_005172.1	NP_005163.1	Q92858	ATOH1_HUMAN	atonal homolog 1 (Drosophila)	350					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)		ACAGTGACTCGGATGAGGCAA	0.547																																					p.S350S		Atlas-SNP	.											.	ATOH1	40	.	0			c.G1050A						PASS	.						53	57	56					4																	94751127		2203	4294	6497	SO:0001819	synonymous_variant	474	exon1			TGACTCGGATGAG	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.1050G>A	4.37:g.94751127G>A		74	0	0		83	23	0.277108	NM_005172	Q14CT9	Silent	SNP	ENST00000306011.3	37	CCDS3638.1																																																																																			.	.	none		0.547	ATOH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253585.1	NM_005172		A	94751127	G	A	94751127	2	1	46	1	0	0	0	0	0	0	0	1	1112	1103	39	1		1	ATOH1	4	94751127	Silent	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10		94751127	96403149	14	15671											
PDHA2	5161	hgsc.bcm.edu	37	chr4	96761963	96761963	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	accttgtgttttcatctgtgAgaataacctatatggaatgg	11	15	9	6	0	2	1	1	1	1	1	2	3	2	2	2	2	1	1	2	2	5	6			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr4:96761963A>G	ENST00000295266.4	+	1	725	c.662A>G	c.(661-663)gAg>gGg	p.E221G		NM_005390.4	NP_005381.1	P29803	ODPAT_HUMAN	pyruvate dehydrogenase (lipoamide) alpha 2	221					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)		TTCATCTGTGAGAATAACCTA	0.453																																					p.E221G		Atlas-SNP	.											.	PDHA2	118	.	0			c.A662G						PASS	.						80	83	82					4																	96761963		2203	4300	6503	SO:0001583	missense	5161	exon1			TCTGTGAGAATAA		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.662A>G	4.37:g.96761963A>G	ENSP00000295266:p.Glu221Gly	69	0	0		47	19	0.404255	NM_005390	B2R9Q3|Q0VDI5|Q4VC02|Q6NXQ1	Missense_Mutation	SNP	ENST00000295266.4	37	CCDS3644.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.145730	0.77888	.	.	ENSG00000163114	ENST00000295266	D	0.96522	-4.04	4.7	4.7	0.59300	Dehydrogenase, E1 component (1);	0.000000	0.85682	D	0.000000	D	0.98918	0.9633	H	0.99249	4.485	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98794	1.0737	10	0.87932	D	0	-26.8347	12.4398	0.55619	1.0:0.0:0.0:0.0	.	221	P29803	ODPAT_HUMAN	G	221	ENSP00000295266:E221G	ENSP00000295266:E221G	E	+	2	0	PDHA2	96980986	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	8.369000	0.90118	2.103000	0.63969	0.383000	0.25322	GAG	.	.	none		0.453	PDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253608.1			G	96761963	A	G	96761963	3	3	46	1	0	0	0	0	1	0	0	0	11674	304	11	3	664	3	PDHA2	4	96761963	Missense_Mutation	SNP	A	TCGA-RQ-A6JB-01A-11D-A31X-10	2010836	96761963	94392313	15	15672											
CISD2	493856	hgsc.bcm.edu	37	chr4	103806567	103806567	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttactaaagcagcttattgtAggtgttggcgttctaaaacg	11	14	10	6	2	1	0	0	0	1	0	1	0	1	0	0	2	4	5	0	2	7	8			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr4:103806567A>T	ENST00000273986.4	+	2	405	c.298A>T	c.(298-300)Agg>Tgg	p.R100W	SLC9B1_ENST00000394789.3_Intron|CISD2_ENST00000503643.1_Missense_Mutation_p.R110W	NM_001008388.4	NP_001008389.1	Q8N5K1	CISD2_HUMAN	CDGSH iron sulfur domain 2	100					mitochondrion degradation (GO:0000422)|multicellular organismal aging (GO:0010259)|regulation of autophagy (GO:0010506)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|protein complex (GO:0043234)	2 iron, 2 sulfur cluster binding (GO:0051537)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			endometrium(1)|lung(3)	4				OV - Ovarian serous cystadenocarcinoma(123;1.97e-08)		AGCTTATTGTAGGTGTTGGCG	0.343																																					p.R100W		Atlas-SNP	.											.	CISD2	9	.	0			c.A298T						PASS	.						53	51	52					4																	103806567		2203	4300	6503	SO:0001583	missense	493856	exon2			TATTGTAGGTGTT	BX537971	CCDS34040.1	4q24	2009-03-25	2007-08-10	2007-08-10	ENSG00000145354	ENSG00000145354		"CDGSH iron sulfur domain containing"	24212	protein-coding gene	gene with protein product	"mitoNEET related 1", "endoplasmic reticulum intermembrane small protein"	611507	"zinc finger, CDGSH-type domain 2", "Wolfram syndrome 2"	ZCD2, WFS2		17376863, 17584744, 17846994	Standard	NM_001008388		Approved	Miner1, ERIS	uc003hwt.4	Q8N5K1	OTTHUMG00000161014	ENST00000273986.4:c.298A>T	4.37:g.103806567A>T	ENSP00000273986:p.Arg100Trp	96	0	0		97	34	0.350515	NM_001008388	Q7Z3D5	Missense_Mutation	SNP	ENST00000273986.4	37	CCDS34040.1	.	.	.	.	.	.	.	.	.	.	A	23.8	4.460468	0.84317	.	.	ENSG00000145354	ENST00000273986;ENST00000503643	.	.	.	6.17	2.16	0.27623	Iron sulphur-containing domain, CDGSH-type, subfamily (1);Iron sulphur-containing domain, CDGSH-type (1);	0.000000	0.85682	D	0.000000	D	0.83691	0.5309	M	0.89904	3.07	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.85812	0.1380	9	0.87932	D	0	-30.1136	14.2849	0.66240	0.4988:0.5012:0.0:0.0	.	100	Q8N5K1	CISD2_HUMAN	W	100;110	.	ENSP00000273986:R100W	R	+	1	2	CISD2	104026002	0.999000	0.42202	0.964000	0.40570	0.979000	0.70002	1.460000	0.35244	0.142000	0.18901	0.533000	0.62120	AGG	.	.	none		0.343	CISD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363417.2	NM_001008388		T	103806567	A	T	103806567	3	4	46	1	0	0	0	0	1	0	0	0	3438	411	15	5	304	5	CISD2	4	103806567	Missense_Mutation	SNP	A	TCGA-RQ-A6JB-01A-11D-A31X-10	7044604	103806567	87347709	16	15673											
HELT	391723	hgsc.bcm.edu	37	chr4	185941741	185941741	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttcccctggccgcctggcGcggcccgcagccccgcgctg	1	6	13	21	6	0	0	0	0	0	0	1	0	1	0	7	3	1	2	7	3	0	1			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr4:185941741G>A	ENST00000515777.1	+	4	632	c.544G>A	c.(544-546)Gcg>Acg	p.A182T	HELT_ENST00000505610.1_Missense_Mutation_p.A181T|HELT_ENST00000338875.4_Missense_Mutation_p.A267T			A6NFD8	HELT_HUMAN	helt bHLH transcription factor	182	Pro-rich.				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)		GCCGCCTGGCGCGGCCCGCAG	0.756																																					p.A267T		Atlas-SNP	.											.	HELT	34	.	0			c.G799A						PASS	.						7	9	8					4																	185941741		2021	4009	6030	SO:0001583	missense	391723	exon4			CCTGGCGCGGCCC	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.544G>A	4.37:g.185941741G>A	ENSP00000426033:p.Ala182Thr	31	0	0		21	11	0.52381	NM_001029887	B2RTS5|B7ZMI7|B7ZMI8	Missense_Mutation	SNP	ENST00000515777.1	37		.	.	.	.	.	.	.	.	.	.	G	5.378	0.255065	0.10185	.	.	ENSG00000187821	ENST00000505610;ENST00000515777;ENST00000338875	T;T;T	0.64260	-0.08;-0.09;1.92	4.96	1.05	0.20165	.	0.293161	0.33916	N	0.004423	T	0.31796	0.0808	N	0.12182	0.205	0.28373	N	0.919909	B;B;B	0.10296	0.003;0.0;0.0	B;B;B	0.06405	0.002;0.0;0.001	T	0.06588	-1.0818	10	0.13853	T	0.58	.	1.5726	0.02618	0.3402:0.3161:0.2239:0.1198	.	267;182;181	A6NFD8;B7ZMI7;A6NFD8-2	HELT_HUMAN;.;.	T	181;182;267	ENSP00000422140:A181T;ENSP00000426033:A182T;ENSP00000343464:A267T	ENSP00000343464:A267T	A	+	1	0	HELT	186178735	0.996000	0.38824	0.101000	0.21167	0.038000	0.13279	0.539000	0.23175	0.138000	0.18790	0.561000	0.74099	GCG	.	.	none		0.756	HELT-002	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000360792.1	NM_001300781		A	185941741	G	A	185941741	3	1	46	1	0	0	0	0	1	0	0	0	7057	1087	38	1	813	1	HELT	4	185941741	Missense_Mutation	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10	82135174	185941741	5212535	17	15674											
C5orf42	65250	hgsc.bcm.edu	37	chr5	37224369	37224369	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttacctttctcttcgattTcttgtagagcttttttccac	5	21	4	11	1	3	1	0	0	3	1	6	2	4	1	2	0	2	2	2	0	2	9			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr5:37224369T>C	ENST00000508244.1	-	13	2660	c.2567A>G	c.(2566-2568)gAa>gGa	p.E856G	C5orf42_ENST00000425232.2_Missense_Mutation_p.E856G|C5orf42_ENST00000274258.7_5'UTR			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	856						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)			CTCTTCGATTTCTTGTAGAGC	0.328																																					p.E856G		Atlas-SNP	.											.	C5orf42	422	.	0			c.A2567G						PASS	.						266	193	215					5																	37224369		692	1588	2280	SO:0001583	missense	65250	exon14			TCGATTTCTTGTA		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.2567A>G	5.37:g.37224369T>C	ENSP00000421690:p.Glu856Gly	156	0	0		123	39	0.317073	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	T	18.35	3.603999	0.66445	.	.	ENSG00000197603	ENST00000508244;ENST00000425232	T;T	0.27402	1.67;1.67	5.38	5.38	0.77491	.	0.192036	0.31821	U	0.007004	T	0.55081	0.1898	M	0.72118	2.19	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.58335	-0.7654	10	0.62326	D	0.03	-11.8602	15.3477	0.74355	0.0:0.0:0.0:1.0	.	856	E9PH94	.	G	856	ENSP00000421690:E856G;ENSP00000389014:E856G	ENSP00000389014:E856G	E	-	2	0	C5orf42	37260126	1.000000	0.71417	0.986000	0.45419	0.706000	0.40770	3.584000	0.53936	2.175000	0.68902	0.533000	0.62120	GAA	.	.	none		0.328	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		C	37224369	T	C	37224369	3	2	46	1	0	0	0	0	1	0	0	0	2303	1783	62	3	7182	3	C5orf42	5	37224369	Missense_Mutation	SNP	T	TCGA-RQ-A6JB-01A-11D-A31X-10		37224369	143690891	18	15675											
FAM81B	153643	hgsc.bcm.edu	37	chr5	94764428	94764428	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	aaactctttccaagaacttgGacatgaaggtaattgaaaat	17	11	7	6	0	1	3	0	2	1	1	2	4	2	4	1	2	2	1	1	2	7	4			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr5:94764428G>A	ENST00000283357.5	+	6	824	c.778G>A	c.(778-780)Gac>Aac	p.D260N		NM_152548.2	NP_689761	Q96LP2	FA81B_HUMAN	family with sequence similarity 81, member B	260						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)		CAAGAACTTGGACATGAAGGT	0.408																																					p.D260N		Atlas-SNP	.											FAM81B,NS,carcinoma,0,1	FAM81B	51	1	0			c.G778A						scavenged	.						115	106	109					5																	94764428		1844	4088	5932	SO:0001583	missense	153643	exon6			AACTTGGACATGA		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.778G>A	5.37:g.94764428G>A	ENSP00000283357:p.Asp260Asn	180	1	0.00555556		195	67	0.34359	NM_152548		Missense_Mutation	SNP	ENST00000283357.5	37	CCDS43341.1	.	.	.	.	.	.	.	.	.	.	G	19.61	3.860601	0.71834	.	.	ENSG00000153347	ENST00000283357;ENST00000512365	T	0.21361	2.01	5.87	5.87	0.94306	.	0.251835	0.40469	N	0.001099	T	0.47266	0.1436	M	0.69823	2.125	0.36848	D	0.887755	D	0.76494	0.999	D	0.69479	0.964	T	0.46679	-0.9174	10	0.46703	T	0.11	-11.1539	18.9772	0.92742	0.0:0.0:1.0:0.0	.	260	Q96LP2	FA81B_HUMAN	N	260;16	ENSP00000283357:D260N	ENSP00000283357:D260N	D	+	1	0	FAM81B	94790184	1.000000	0.71417	1.000000	0.80357	0.721000	0.41392	5.789000	0.69029	2.780000	0.95670	0.655000	0.94253	GAC	.	.	none		0.408	FAM81B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370690.1	NM_152548		A	94764428	G	A	94764428	3	1	46	1	0	0	0	0	1	0	0	0	5637	1174	41	2	800	2	FAM81B	5	94764428	Missense_Mutation	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10	57540059	94764428	86150832	19	15676											
PPP2CA	5515	hgsc.bcm.edu	37	chr5	133561476	133561476	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cgcagaggctcttgacctggGactcggacagctgcttgcac	7	8	13	13	2	1	2	0	1	1	1	2	4	1	4	1	3	3	5	1	3	0	2			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr5:133561476G>A	ENST00000481195.1	-	1	357	c.77C>T	c.(76-78)tCc>tTc	p.S26F	CTD-2410N18.4_ENST00000518409.1_RNA|CDKL3_ENST00000609654.1_Intron|CDKL3_ENST00000609383.1_Intron|CTD-2410N18.3_ENST00000602919.1_lincRNA|MIR3661_ENST00000577394.1_RNA|PPP2CA_ENST00000231504.5_5'UTR|CTD-2410N18.5_ENST00000519718.1_Missense_Mutation_p.S26F	NM_002715.2	NP_002706.1	P67775	PP2AA_HUMAN	protein phosphatase 2, catalytic subunit, alpha isozyme	26					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)	CTTGACCTGGGACTCGGACAG	0.662																																					p.S26F		Atlas-SNP	.											.	PPP2CA	29	.	0			c.C77T						PASS	.						76	68	71					5																	133561476		2203	4300	6503	SO:0001583	missense	5515	exon1			ACCTGGGACTCGG		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.77C>T	5.37:g.133561476G>A	ENSP00000418447:p.Ser26Phe	15	0	0		37	17	0.459459	NM_002715	P05323|P13197	Missense_Mutation	SNP	ENST00000481195.1	37	CCDS4173.1	.	.	.	.	.	.	.	.	.	.	G	17.70	3.453473	0.63290	.	.	ENSG00000113558;ENSG00000113575	ENST00000519718;ENST00000481195	T;T	0.46819	0.86;0.95	5.1	5.1	0.69264	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (1);	0.390870	0.24755	N	0.035880	T	0.47967	0.1474	M	0.79011	2.435	0.80722	D	1	B	0.11235	0.004	B	0.09377	0.004	T	0.52704	-0.8540	10	0.72032	D	0.01	-1.9595	8.9806	0.35964	0.0:0.205:0.6547:0.1403	.	26	P67775	PP2AA_HUMAN	F	26	ENSP00000430774:S26F;ENSP00000418447:S26F	ENSP00000418447:S26F	S	-	2	0	PPP2CA;SKP1	133589375	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.051000	0.49885	2.653000	0.90120	0.655000	0.94253	TCC	.	.	none		0.662	PPP2CA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251165.1	NM_002715		A	133561476	G	A	133561476	3	1	46	1	0	0	0	0	1	0	0	0	12392	1174	41	2	880	2	PPP2CA	5	133561476	Missense_Mutation	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10	38797048	133561476	47353784	20	15677											
OR10C1	442194	hgsc.bcm.edu	37	chr6	29407999	29407999	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cgcaccctctcggccttggaGattggctatacgtctgtcac	6	11	10	14	3	3	1	1	0	2	1	4	2	3	1	2	3	1	2	2	3	2	4			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr6:29407999G>C	ENST00000444197.2	+	1	917	c.207G>C	c.(205-207)gaG>gaC	p.E69D	OR11A1_ENST00000377149.1_Intron	NM_013941.3	NP_039229.3	Q96KK4	O10C1_HUMAN	olfactory receptor, family 10, subfamily C, member 1 (gene/pseudogene)	69						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						CGGCCTTGGAGATTGGCTATA	0.572																																					p.E69D		Atlas-SNP	.											.	OR10C1	58	.	0			c.G207C						PASS	.						176	154	161					6																	29407999		1511	2708	4219	SO:0001583	missense	442194	exon1			CTTGGAGATTGGC		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.207G>C	6.37:g.29407999G>C	ENSP00000419119:p.Glu69Asp	58	0	0		74	28	0.378378	NM_013941	Q5SUN7|Q96R18	Missense_Mutation	SNP	ENST00000444197.2	37	CCDS34364.1	.	.	.	.	.	.	.	.	.	.	G	3.194	-0.165267	0.06461	.	.	ENSG00000206474	ENST00000444197	T	0.00008	9.61	3.6	3.6	0.41247	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39615	N	0.001313	T	0.00012	0.0000	N	0.21240	0.645	0.22975	N	0.998488	B	0.18461	0.028	B	0.24394	0.053	T	0.49835	-0.8897	10	0.15499	T	0.54	.	2.6706	0.05066	0.1058:0.1827:0.5232:0.1884	.	69	Q96KK4	O10C1_HUMAN	D	69	ENSP00000419119:E69D	ENSP00000419119:E69D	E	+	3	2	OR10C1	29515978	0.000000	0.05858	0.633000	0.29310	0.011000	0.07611	-0.801000	0.04550	2.008000	0.58898	0.430000	0.28490	GAG	.	.	none		0.572	OR10C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076415.2			C	29407999	G	C	29407999	3	2	46	1	0	0	0	0	1	0	0	0	10907	933	33	4	209	4	OR10C1	6	29407999	Missense_Mutation	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10		29407999	141707068	21	15678											
HLA-A	3105	hgsc.bcm.edu	37	chr6	29910609	29910609	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	gccccgcttcatcgccgtggGctacgtggacgacacgcagt	6	7	13	15	6	1	0	1	0	0	0	2	2	1	1	3	2	1	3	3	2	1	2	rs199474372		TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr6:29910609G>T	ENST00000396634.1	+	4	490	c.149G>T	c.(148-150)gGc>gTc	p.G50V	HLA-A_ENST00000376809.5_Missense_Mutation_p.G50V|HLA-A_ENST00000376802.2_Missense_Mutation_p.G50V|HLA-A_ENST00000376806.5_Missense_Mutation_p.G50V			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	50	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)			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						ATCGCCGTGGGCTACGTGGAC	0.687									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.G50V		Atlas-SNP	.											.	HLA-A	89	.	0			c.G149T						PASS	.						38	33	35					6																	29910609		2202	4299	6501	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CCGTGGGCTACGT	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.149G>T	6.37:g.29910609G>T	ENSP00000379873:p.Gly50Val	174	0	0		200	107	0.535	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	.	.	.	.	.	.	.	.	.	.	.	15.22	2.768304	0.49680	.	.	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.01438	4.89;4.89;4.89;4.89	3.72	3.72	0.42706	MHC class I, alpha chain, alpha1/alpha2 (3);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	0.000000	0.34110	U	0.004248	T	0.12817	0.0311	H	0.99859	4.855	0.48975	D	0.999735	D;D;D;D;D	0.89917	0.998;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.985;1.0;0.999;1.0;0.999	T	0.14727	-1.0462	10	0.87932	D	0	.	11.3314	0.49479	0.0:0.0:1.0:0.0	.	50;50;50;50;50	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	V	50	ENSP00000379873:G50V;ENSP00000366002:G50V;ENSP00000366005:G50V;ENSP00000365998:G50V	ENSP00000348012:G50V	G	+	2	0	HLA-A	30018588	0.997000	0.39634	0.992000	0.48379	0.629000	0.37895	2.884000	0.48562	2.112000	0.64535	0.478000	0.44815	GGC	.	.	alt		0.687	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116		T	29910609	G	T	29910609	3	4	46	1	0	0	0	0	1	0	0	0	7204	1203	42	4	155	4	HLA-A	6	29910609	Missense_Mutation	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10	502610	29910609	141204458	22	15679											
RUNX2	860	hgsc.bcm.edu	37	chr6	45390482	45390482	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agcaacagcagcagcagcagCaggaggcggcggcggcggct	10	1	18	12	4	0	0	0	0	0	0	0	1	0	1	0	6	7	7	0	6	1	0			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr6:45390482C>G	ENST00000371438.1	+	2	569	c.211C>G	c.(211-213)Cag>Gag	p.Q71E	RUNX2_ENST00000465038.2_Missense_Mutation_p.Q71E|RP1-244F24.1_ENST00000606796.1_RNA|RUNX2_ENST00000371436.6_Missense_Mutation_p.Q71E|RUNX2_ENST00000576263.1_Missense_Mutation_p.Q71E|RUNX2_ENST00000352853.5_Missense_Mutation_p.Q139E|RUNX2_ENST00000371432.3_Missense_Mutation_p.Q57E|RUNX2_ENST00000541979.1_Missense_Mutation_p.Q139E|RUNX2_ENST00000359524.5_Missense_Mutation_p.Q57E	NM_001024630.3	NP_001019801.3	Q13950	RUNX2_HUMAN	runt-related transcription factor 2	71	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						gcagcagcagcaggaggcggc	0.716																																					p.Q71E		Atlas-SNP	.											RUNX2_ENST00000352853,NS,carcinoma,0,2	RUNX2	128	2	0			c.C211G						scavenged	.						6	10	9					6																	45390482		1279	2789	4068	SO:0001583	missense	860	exon3			CAGCAGCAGGAGG	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.211C>G	6.37:g.45390482C>G	ENSP00000360493:p.Gln71Glu	17	1	0.0588235		24	2	0.0833333	NM_001024630	O14614|O14615|O95181	Missense_Mutation	SNP	ENST00000371438.1	37	CCDS43467.2	.	.	.	.	.	.	.	.	.	.	C	12.60	1.985548	0.35036	.	.	ENSG00000124813	ENST00000465038;ENST00000352853;ENST00000541979;ENST00000371438;ENST00000371436;ENST00000359524;ENST00000371432	T;T;T;T;T;T;T	0.61742	0.08;0.08;0.08;0.08;0.08;0.08;0.08	3.45	3.45	0.39498	.	1.972660	0.03402	N	0.203449	T	0.19248	0.0462	N	0.14661	0.345	0.27094	N	0.962779	B;B;B	0.23806	0.033;0.055;0.091	B;B;B	0.20384	0.029;0.013;0.029	T	0.13818	-1.0495	10	0.02654	T	1	.	14.8379	0.70197	0.0:1.0:0.0:0.0	.	139;71;57	F6RGB9;Q13950;Q13950-2	.;RUNX2_HUMAN;.	E	71;139;139;71;71;57;57	ENSP00000420707:Q71E;ENSP00000319087:Q139E;ENSP00000446290:Q139E;ENSP00000360493:Q71E;ENSP00000360491:Q71E;ENSP00000352514:Q57E;ENSP00000360486:Q57E	ENSP00000319087:Q139E	Q	+	1	0	RUNX2	45498460	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	1.268000	0.33062	1.622000	0.50330	0.407000	0.27541	CAG	.	.	none		0.716	RUNX2-003	KNOWN	not_organism_supported|upstream_ATG|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040755.2	NM_004348		G	45390482	C	G	45390482	3	3	46	1	0	0	0	0	1	0	0	0	13763	711	25	4	233	4	RUNX2	6	45390482	Missense_Mutation	SNP	C	TCGA-RQ-A6JB-01A-11D-A31X-10	15479873	45390482	125724585	23	15680											
CRISP3	10321	hgsc.bcm.edu	37	chr6	49704124	49704124	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catcttcagcatgtttctggCagggggagatactgctctcc	7	12	11	11	0	4	1	1	0	3	1	5	2	4	1	1	3	3	4	1	3	1	3			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr6:49704124C>A	ENST00000393666.1	-	2	175	c.169G>T	c.(169-171)Gcc>Tcc	p.A57S	CRISP3_ENST00000433368.2_Missense_Mutation_p.A80S|CRISP3_ENST00000371159.4_Missense_Mutation_p.A88S|CRISP3_ENST00000423399.2_Intron|CRISP3_ENST00000263045.4_Missense_Mutation_p.A70S			P54108	CRIS3_HUMAN	cysteine-rich secretory protein 3	57	SCP.				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)			ATGTTTCTGGCAGGGGGAGAT	0.458																																					p.A80S		Atlas-SNP	.											.	CRISP3	67	.	0			c.G238T						PASS	.						183	163	170					6																	49704124		2203	4300	6503	SO:0001583	missense	10321	exon3			TTCTGGCAGGGGG	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.169G>T	6.37:g.49704124C>A	ENSP00000377274:p.Ala57Ser	125	0	0		107	37	0.345794	NM_001190986	A8K9S1|B2R8I8|Q15512|Q3MJ82|Q53FA9|Q5JW83|Q9H108	Missense_Mutation	SNP	ENST00000393666.1	37		.	.	.	.	.	.	.	.	.	.	C	17.17	3.321590	0.60634	.	.	ENSG00000096006	ENST00000263045;ENST00000433368;ENST00000393666;ENST00000371159;ENST00000354620	T;T;T;T;T	0.27557	1.66;1.66;1.66;1.66;1.66	4.9	4.02	0.46733	CAP domain (3);	0.000000	0.64402	U	0.000005	T	0.54565	0.1866	H	0.94222	3.51	0.80722	D	1	P	0.50943	0.94	D	0.66602	0.945	T	0.67059	-0.5766	10	0.87932	D	0	.	11.4692	0.50257	0.0:0.8177:0.1823:0.0	.	57	P54108	CRIS3_HUMAN	S	70;80;57;88;80	ENSP00000263045:A70S;ENSP00000389026:A80S;ENSP00000377274:A57S;ENSP00000360201:A88S;ENSP00000346636:A80S	ENSP00000263045:A70S	A	-	1	0	CRISP3	49812083	0.735000	0.28153	0.754000	0.31244	0.652000	0.38707	1.138000	0.31491	1.179000	0.42884	0.561000	0.74099	GCC	.	.	none		0.458	CRISP3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_006061		A	49704124	C	A	49704124	3	1	46	1	0	0	0	0	1	0	0	0	3883	710	25	4	592	4	CRISP3	6	49704124	Missense_Mutation	SNP	C	TCGA-RQ-A6JB-01A-11D-A31X-10	4313642	49704124	121410943	24	15681											
CTGF	1490	hgsc.bcm.edu	37	chr6	132271952	132271952	+	Missense_Mutation	SNP	G	G	C																															gttggccggggagccgaagtGacagaataggcccttgtgcg																								rs7451102		TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr6:132271952G>C	ENST00000367976.3	-	2	447	c.247C>G	c.(247-249)Cac>Gac	p.H83D	RP11-69I8.3_ENST00000435287.1_RNA	NM_001901.2	NP_001892	P29279	CTGF_HUMAN	connective tissue growth factor	83	IGFBP N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00653}.		H -> D (in dbSNP:rs7451102). {ECO:0000269|PubMed:1293144, ECO:0000269|PubMed:1654338, ECO:0000269|PubMed:9054739, ECO:0000269|Ref.12, ECO:0000269|Ref.4, ECO:0000269|Ref.5, ECO:0000269|Ref.6, ECO:0000269|Ref.7}.		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)		GAGCCGAAGTGACAGAATAGG	0.711													C|||	5007	0.9998	1.0	1.0	5008	,	,		8487	1.0		0.999	False		,,,				2504	1.0				p.H83D	Esophageal Squamous(127;510 1660 12817 24400 38449)	Atlas-SNP	.											.	CTGF	36	.	0			c.C247G						PASS	.						7	8	7					6																	132271952		2119	4187	6306	SO:0001583	missense	1490	exon2			CGAAGTGACAGAA	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.247C>G	6.37:g.132271952G>C	ENSP00000356954:p.His83Asp	0	0	.		6	6	1	NM_001901	E1P578|Q6LCY0|Q96A79|Q96QX2|Q9UDL6	Missense_Mutation	SNP	ENST00000367976.3	37	CCDS5151.1	2184	1.0	492	1.0	362	1.0	572	1.0	758	1.0	C	8.018	0.758919	0.15846	.	.	ENSG00000118523	ENST00000367976	T	0.62232	0.04	5.28	5.28	0.74379	Insulin-like growth factor-binding protein, IGFBP (2);	0.048665	0.85682	N	0.000000	T	0.06781	0.0173	N	0.00042	-2.475	0.40675	P	0.017750000000000044	B	0.02656	0.0	B	0.01281	0.0	T	0.27739	-1.0065	9	0.02654	T	1	.	15.7931	0.78384	0.0:0.863:0.137:0.0	rs7451102;rs59294435	83	P29279	CTGF_HUMAN	D	83	ENSP00000356954:H83D	ENSP00000356954:H83D	H	-	1	0	CTGF	132313645	1.000000	0.71417	0.923000	0.36655	0.645000	0.38454	4.000000	0.57039	1.236000	0.43740	-0.293000	0.09583	CAC	G|0.000;C|1.000	1.000	strong		0.711	CTGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042239.2	NM_001901		C	132271952	G	C	132271952	3	2	46	1	0	0	0	0	1	0	0	0	4010	1290	45	4	818	4	CTGF	6	132271952	Missense_Mutation	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10	82567828	132271952	38843115	25	15682	205	2									
CTGF	1490	hgsc.bcm.edu	37	chr6	132271959	132271959	+	Silent	SNP	T	T	G																															ggggagccgaagtgacagaaTaggcccttgtgcgggtcgca																								rs12206231		TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr6:132271959T>G	ENST00000367976.3	-	2	440	c.240A>C	c.(238-240)ctA>ctC	p.L80L	RP11-69I8.3_ENST00000435287.1_RNA	NM_001901.2	NP_001892	P29279	CTGF_HUMAN	connective tissue growth factor	80	IGFBP N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00653}.				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)		AGTGACAGAATAGGCCCTTGT	0.701													G|||	5008	1.0	1.0	1.0	5008	,	,		8368	1.0		1.0	False		,,,				2504	1.0				p.L80L	Esophageal Squamous(127;510 1660 12817 24400 38449)	Atlas-SNP	.											.	CTGF	36	.	0			c.A240C						PASS	.						7	8	7					6																	132271959		2127	4192	6319	SO:0001819	synonymous_variant	1490	exon2			ACAGAATAGGCCC	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.240A>C	6.37:g.132271959T>G		0	0	.		5	5	1	NM_001901	E1P578|Q6LCY0|Q96A79|Q96QX2|Q9UDL6	Silent	SNP	ENST00000367976.3	37	CCDS5151.1																																																																																			T|0.000;G|1.000	1.000	strong		0.701	CTGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042239.2	NM_001901		G	132271959	T	G	132271959	2	3	46	1	0	0	0	0	0	0	0	1	4010	1393	49	5		5	CTGF	6	132271959	Silent	SNP	T	TCGA-RQ-A6JB-01A-11D-A31X-10	7	132271959	38843108	26	15683	205	2									
ADAM22	53616	hgsc.bcm.edu	37	chr7	87765308	87765308	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctcttaggtgaatgtaaatgCgaggacacgtggtccgggtg	9	10	15	7	3	1	1	0	1	1	0	2	3	2	2	1	4	1	1	1	4	4	2			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr7:87765308C>T	ENST00000265727.7	+	14	1261	c.1182C>T	c.(1180-1182)tgC>tgT	p.C394C	ADAM22_ENST00000398209.3_Silent_p.C394C|ADAM22_ENST00000315984.7_Silent_p.C394C|ADAM22_ENST00000398201.4_Silent_p.C394C|ADAM22_ENST00000398204.4_Silent_p.C394C			Q9P0K1	ADA22_HUMAN	ADAM metallopeptidase domain 22	394	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				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)			AATGTAAATGCGAGGACACGT	0.383																																					p.C394C		Atlas-SNP	.											.	ADAM22	280	.	0			c.C1182T						PASS	.						177	167	170					7																	87765308		1890	4107	5997	SO:0001819	synonymous_variant	53616	exon14			TAAATGCGAGGAC	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.1182C>T	7.37:g.87765308C>T		79	0	0		72	19	0.263889	NM_021722	O75075|O75076|Q9P0K2|Q9UIA1|Q9UKK2	Silent	SNP	ENST00000265727.7	37	CCDS47637.1																																																																																			.	.	none		0.383	ADAM22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268370.2	NM_021723		T	87765308	C	T	87765308	2	4	46	1	0	0	0	0	0	0	0	1	244	776	27	1		1	ADAM22	7	87765308	Silent	SNP	C	TCGA-RQ-A6JB-01A-11D-A31X-10		87765308	71373355	27	15684											
AHCYL2	23382	hgsc.bcm.edu	37	chr7	129028933	129028933	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tagctctgatgatgagacatCgcccagggacaagcagcaaa	14	6	11	10	1	1	3	0	3	1	1	2	5	1	4	1	1	3	3	1	1	3	1			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr7:129028933C>T	ENST00000325006.3	+	3	566	c.512C>T	c.(511-513)tCg>tTg	p.S171L	AHCYL2_ENST00000446544.2_Missense_Mutation_p.S170L|AHCYL2_ENST00000474594.1_Missense_Mutation_p.S68L|AHCYL2_ENST00000531335.2_Missense_Mutation_p.S90L|AHCYL2_ENST00000472554.1_3'UTR|AHCYL2_ENST00000446212.1_Missense_Mutation_p.S69L|AHCYL2_ENST00000490911.1_Missense_Mutation_p.S68L	NM_001130720.2|NM_015328.3	NP_001124192.1|NP_056143.1	Q96HN2	SAHH3_HUMAN	adenosylhomocysteinase-like 2	171					one-carbon metabolic process (GO:0006730)		adenosylhomocysteinase activity (GO:0004013)			breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	22						GATGAGACATCGCCCAGGGAC	0.398																																					p.S171L	Pancreas(160;1736 1964 29875 40941 45605)	Atlas-SNP	.											AHCYL2,caecum,carcinoma,-1,1	AHCYL2	79	1	0			c.C512T						scavenged	.						100	94	96					7																	129028933		2203	4300	6503	SO:0001583	missense	23382	exon3			AGACATCGCCCAG	AB020635	CCDS5812.1, CCDS47706.1, CCDS47707.1, CCDS47708.1, CCDS47707.2	7q32.1	2009-06-12	2009-06-12		ENSG00000158467	ENSG00000158467			22204	protein-coding gene	gene with protein product			"S-adenosylhomocysteine hydrolase-like 2"				Standard	NM_001130720		Approved	KIAA0828	uc011kov.2	Q96HN2	OTTHUMG00000157677	ENST00000325006.3:c.512C>T	7.37:g.129028933C>T	ENSP00000315931:p.Ser171Leu	175	1	0.00571429		180	77	0.427778	NM_015328	B4DIZ5|D9N155|O94917	Missense_Mutation	SNP	ENST00000325006.3	37	CCDS5812.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	31|31	5.086009|5.086009	0.94100|0.94100	.|.	.|.	ENSG00000158467|ENSG00000158467	ENST00000466924|ENST00000325006;ENST00000446544;ENST00000531335;ENST00000460109;ENST00000474594;ENST00000446212;ENST00000490911;ENST00000466993	.|T;T;T;T;T;T;T	.|0.78595	.|-1.19;-1.19;-1.15;-1.14;-1.14;-1.14;-0.96	5.62|5.62	5.62|5.62	0.85841|0.85841	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.85039|0.85039	0.5606|0.5606	L|L	0.45352|0.45352	1.415|1.415	0.58432|0.58432	D|D	0.999999|0.999999	.|D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D	.|0.87578	.|0.996;0.996;0.996;0.996;0.998	D|D	0.86023|0.86023	0.1508|0.1508	5|10	.|0.87932	.|D	.|0	-15.2176|-15.2176	18.6782|18.6782	0.91537|0.91537	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|68;69;171;68;170	.|B4DIZ5;D7UEQ7;Q96HN2;D9N155;Q96HN2-2	.|.;.;SAHH3_HUMAN;.;.	C|L	78|171;170;90;69;68;69;68;69	.|ENSP00000315931:S171L;ENSP00000413639:S170L;ENSP00000431787:S90L;ENSP00000420459:S68L;ENSP00000405267:S69L;ENSP00000420801:S68L;ENSP00000419608:S69L	.|ENSP00000315931:S171L	R|S	+|+	1|2	0|0	AHCYL2|AHCYL2	128816169|128816169	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.991000|0.991000	0.79684|0.79684	7.776000|7.776000	0.85560|0.85560	2.648000|2.648000	0.89879|0.89879	0.650000|0.650000	0.86243|0.86243	CGC|TCG	.	.	none		0.398	AHCYL2-012	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354065.1			T	129028933	C	T	129028933	3	4	46	1	0	0	0	0	1	0	0	0	411	893	31	1	644	1	AHCYL2	7	129028933	Missense_Mutation	SNP	C	TCGA-RQ-A6JB-01A-11D-A31X-10	41263625	129028933	30109730	28	15685											
SLC25A37	51312	hgsc.bcm.edu	37	chr8	23429084	23429084	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tcatctcaggcgggctggccGgggccctcgccgcggccgcc	2	5	16	18	6	2	0	2	0	1	0	4	0	2	0	5	6	0	1	5	6	0	0			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr8:23429084G>A	ENST00000519973.1	+	4	931	c.733G>A	c.(733-735)Ggg>Agg	p.G245R	FP15737_ENST00000399967.3_5'Flank	NM_016612.2	NP_057696.2	Q9NYZ2	MFRN1_HUMAN	solute carrier family 25 (mitochondrial iron transporter), member 37	245					iron ion homeostasis (GO:0055072)|mitochondrial iron ion transport (GO:0048250)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	iron ion transmembrane transporter activity (GO:0005381)	p.G245W(1)		NS(1)|endometrium(3)|large_intestine(2)|lung(8)|urinary_tract(1)	15		Prostate(55;0.114)		Colorectal(74;0.0198)|COAD - Colon adenocarcinoma(73;0.0751)		CGGGCTGGCCGGGGCCCTCGC	0.652																																					p.G245R		Atlas-SNP	.											SLC25A37,NS,carcinoma,0,1	SLC25A37	27	1	1	Substitution - Missense(1)	lung(1)	c.G733A						PASS	.						25	29	28					8																	23429084		1907	4113	6020	SO:0001583	missense	51312	exon4			CTGGCCGGGGCCC	AF495725	CCDS47828.1	8p21.2	2013-05-22	2012-03-29		ENSG00000147454	ENSG00000147454		"Solute carriers"	29786	protein-coding gene	gene with protein product	"mitoferrin"	610387	"solute carrier family 25, member 37"			16511496	Standard	XM_006716352		Approved	MSCP, MFRN, MFRN1	uc003xdo.3	Q9NYZ2	OTTHUMG00000163865	ENST00000519973.1:c.733G>A	8.37:g.23429084G>A	ENSP00000429200:p.Gly245Arg	87	0	0		86	35	0.406977	NM_016612	A2RU93|Q53FT7|Q69YJ8|Q969S1|Q9P0J2	Missense_Mutation	SNP	ENST00000519973.1	37	CCDS47828.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.004468	0.93287	.	.	ENSG00000147454	ENST00000519973	D	0.85339	-1.97	5.8	5.8	0.92144	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.94984	0.8377	H	0.95114	3.625	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	D	0.95928	0.8936	10	0.87932	D	0	-3.0931	18.6148	0.91299	0.0:0.0:1.0:0.0	.	245	Q9NYZ2	MFRN1_HUMAN	R	245	ENSP00000429200:G245R	ENSP00000429200:G245R	G	+	1	0	SLC25A37	23485029	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.460000	0.97641	2.740000	0.93945	0.650000	0.86243	GGG	.	.	none		0.652	SLC25A37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376039.1	NM_016612		A	23429084	G	A	23429084	3	1	46	1	0	0	0	0	1	0	0	0	14516	1116	39	1	747	1	SLC25A37	8	23429084	Missense_Mutation	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10		23429084	122934938	29	15686											
EPHX2	2053	hgsc.bcm.edu	37	chr8	27382956	27382956	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagagtatcaaagccaaccCagtatttgattaccagctct	13	10	8	10	0	2	2	1	1	1	1	2	3	2	2	3	1	4	3	3	1	5	4			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr8:27382956C>T	ENST00000521400.1	+	12	1566	c.1136C>T	c.(1135-1137)cCa>cTa	p.P379L	EPHX2_ENST00000521780.1_Missense_Mutation_p.P313L|EPHX2_ENST00000517536.1_Missense_Mutation_p.P196L|EPHX2_ENST00000380476.3_Missense_Mutation_p.P326L|EPHX2_ENST00000518379.1_Missense_Mutation_p.P347L	NM_001979.5	NP_001970.2	P34913	HYES_HUMAN	epoxide hydrolase 2, cytoplasmic	379	Epoxide hydrolase.				arachidonic acid metabolic process (GO:0019369)|cellular calcium ion homeostasis (GO:0006874)|cholesterol homeostasis (GO:0042632)|dephosphorylation (GO:0016311)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|inflammatory response (GO:0006954)|phospholipid dephosphorylation (GO:0046839)|positive regulation of gene expression (GO:0010628)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|regulation of blood pressure (GO:0008217)|regulation of cholesterol metabolic process (GO:0090181)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|stilbene catabolic process (GO:0046272)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity (GO:0033885)|epoxide hydrolase activity (GO:0004301)|lipid phosphatase activity (GO:0042577)|magnesium ion binding (GO:0000287)|phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxic substance binding (GO:0015643)			cervix(1)|endometrium(8)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	27		Ovarian(32;2.61e-05)|all_epithelial(46;0.207)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0226)|Epithelial(17;1.12e-09)|Colorectal(74;0.157)		AAAGCCAACCCAGTATTTGAT	0.478																																					p.P379L		Atlas-SNP	.											EPHX2,NS,carcinoma,-1,1	EPHX2	57	1	0			c.C1136T						PASS	.						161	143	149					8																	27382956		2203	4300	6503	SO:0001583	missense	2053	exon12			CCAACCCAGTATT	L05779	CCDS6060.1, CCDS59097.1, CCDS59098.1	8p21	2010-04-23			ENSG00000120915	ENSG00000120915	3.3.2.10		3402	protein-coding gene	gene with protein product		132811					Standard	NM_001979		Approved		uc003xfu.4	P34913	OTTHUMG00000102115	ENST00000521400.1:c.1136C>T	8.37:g.27382956C>T	ENSP00000430269:p.Pro379Leu	115	0	0		154	55	0.357143	NM_001979	B2Z3B1|B3KTU8|B3KUA0|G3V134|J3KPH7|Q16764|Q9HBJ1|Q9HBJ2	Missense_Mutation	SNP	ENST00000521400.1	37	CCDS6060.1	.	.	.	.	.	.	.	.	.	.	C	17.77	3.470626	0.63625	.	.	ENSG00000120915	ENST00000521400;ENST00000517536;ENST00000521780;ENST00000380476;ENST00000415449;ENST00000518379	T;T;T;T;T	0.03441	3.93;3.93;3.93;3.93;3.93	5.24	4.35	0.52113	Alpha/beta hydrolase fold-1 (1);	2.166600	0.01505	N	0.017652	T	0.21347	0.0514	M	0.81802	2.56	0.49582	D	0.999806	D;D;D	0.89917	0.993;0.998;1.0	D;D;D	0.74023	0.978;0.944;0.982	T	0.02868	-1.1100	10	0.24483	T	0.36	-1.3552	12.0912	0.53728	0.0:0.9128:0.0:0.0872	.	347;379;379	E5RFU2;E7ETW9;P34913	.;.;HYES_HUMAN	L	379;196;313;326;326;347	ENSP00000430269:P379L;ENSP00000428875:P196L;ENSP00000430302:P313L;ENSP00000369843:P326L;ENSP00000427956:P347L	ENSP00000369843:P326L	P	+	2	0	EPHX2	27438873	0.977000	0.34250	0.428000	0.26697	0.035000	0.12851	3.791000	0.55469	2.421000	0.82119	0.563000	0.77884	CCA	.	.	none		0.478	EPHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219954.4			T	27382956	C	T	27382956	3	4	46	1	0	0	0	0	1	0	0	0	5182	594	21	2	1182	2	EPHX2	8	27382956	Missense_Mutation	SNP	C	TCGA-RQ-A6JB-01A-11D-A31X-10	3953872	27382956	118981066	30	15687											
KIAA0146	23514	hgsc.bcm.edu	37	chr8	48614293	48614293	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atttaaacagataaaaactcAtctgcctcctccagccttgt	13	12	4	12	0	2	1	1	0	1	1	4	1	4	1	4	0	4	0	4	0	5	4			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr8:48614293A>C	ENST00000297423.4	+	13	2168	c.1784A>C	c.(1783-1785)cAt>cCt	p.H595P	SPIDR_ENST00000517693.1_Missense_Mutation_p.H70P|SPIDR_ENST00000518074.1_Missense_Mutation_p.H535P|SPIDR_ENST00000541342.1_Missense_Mutation_p.H525P|SPIDR_ENST00000521214.1_3'UTR	NM_001080394.2|NM_001282916.1	NP_001073863.1|NP_001269845.1	Q14159	SPIDR_HUMAN	scaffolding protein involved in DNA repair	595					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)											ATAAAAACTCATCTGCCTCCT	0.348																																					p.H595P		Atlas-SNP	.											KIAA0146,bladder,carcinoma,+1,1	KIAA0146	64	1	0			c.A1784C						PASS	.						129	121	124					8																	48614293		1882	4119	6001	SO:0001583	missense	23514	exon13			AAACTCATCTGCC	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.1784A>C	8.37:g.48614293A>C	ENSP00000297423:p.His595Pro	126	0	0		111	40	0.36036	NM_001080394	B4DFV2|B4E0Y6|Q96BI5	Missense_Mutation	SNP	ENST00000297423.4	37	CCDS43737.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	9.029|9.029	0.986713|0.986713	0.18889|0.18889	.|.	.|.	ENSG00000164808|ENSG00000164808	ENST00000297423;ENST00000518074;ENST00000541342;ENST00000519141;ENST00000517693;ENST00000519362|ENST00000519401	.|.	.|.	.|.	5.4|5.4	2.96|2.96	0.34315|0.34315	.|.	0.536026|.	0.20846|.	N|.	0.084612|.	T|T	0.35740|0.35740	0.0942|0.0942	L|L	0.40543|0.40543	1.245|1.245	0.09310|0.09310	N|N	1|1	B;B;B;B;B;B;B;B|.	0.23442|.	0.001;0.001;0.013;0.011;0.085;0.009;0.001;0.05|.	B;B;B;B;B;B;B;B|.	0.18561|.	0.001;0.001;0.014;0.012;0.014;0.007;0.001;0.022|.	T|T	0.21861|0.21861	-1.0233|-1.0233	9|5	0.48119|.	T|.	0.1|.	.|.	6.9387|6.9387	0.24481|0.24481	0.7729:0.1496:0.0775:0.0|0.7729:0.1496:0.0775:0.0	.|.	85;100;535;525;595;284;70;595|.	B4DZY2;B4DWT8;B4E0Y6;B4DFV2;B4DEV5;B4DFT3;B3KP42;Q14159|.	.;.;.;.;.;.;.;K0146_HUMAN|.	P|L	595;535;525;100;70;70|277	.|.	ENSP00000297423:H595P|.	H|I	+|+	2|1	0|0	KIAA0146|KIAA0146	48776846|48776846	0.000000|0.000000	0.05858|0.05858	0.056000|0.056000	0.19401|0.19401	0.921000|0.921000	0.55340|0.55340	0.966000|0.966000	0.29331|0.29331	0.336000|0.336000	0.23639|0.23639	0.528000|0.528000	0.53228|0.53228	CAT|ATC	.	.	none		0.348	SPIDR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377611.1	NM_001080394		C	48614293	A	C	48614293	3	2	46	1	0	0	0	0	1	0	0	0	8166	217	8	5	1834	5	KIAA0146	8	48614293	Missense_Mutation	SNP	A	TCGA-RQ-A6JB-01A-11D-A31X-10	21231337	48614293	97749729	31	15688											
MOS	4342	hgsc.bcm.edu	37	chr8	57026520	57026520	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcgctccggaggtaggggcGtagggccaggggcgagggca	6	4	21	10	4	0	0	0	0	0	0	2	2	1	1	2	8	0	4	2	8	2	2			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr8:57026520G>A	ENST00000311923.1	-	1	21	c.22C>T	c.(22-24)Cgc>Tgc	p.R8C		NM_005372.1	NP_005363.1	P00540	MOS_HUMAN	v-mos Moloney murine sarcoma viral oncogene homolog	8					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)			AGGTAGGGGCGTAGGGCCAGG	0.642																																					p.R8C	Esophageal Squamous(124;373 2870 4778)	Atlas-SNP	.											.	MOS	63	.	0			c.C22T						PASS	.						14	17	16					8																	57026520		2187	4271	6458	SO:0001583	missense	4342	exon1			AGGGGCGTAGGGC		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.22C>T	8.37:g.57026520G>A	ENSP00000310722:p.Arg8Cys	144	0	0		112	33	0.294643	NM_005372	Q3KPG9|Q3KPH0	Missense_Mutation	SNP	ENST00000311923.1	37	CCDS6164.1	.	.	.	.	.	.	.	.	.	.	G	11.86	1.763732	0.31228	.	.	ENSG00000172680	ENST00000311923	D	0.81739	-1.53	5.14	0.608	0.17569	.	0.727768	0.12172	N	0.492935	T	0.53254	0.1785	N	0.03115	-0.41	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.46219	-0.9207	10	0.62326	D	0.03	.	0.6283	0.00789	0.1882:0.23:0.3053:0.2765	.	8	P00540	MOS_HUMAN	C	8	ENSP00000310722:R8C	ENSP00000310722:R8C	R	-	1	0	MOS	57189074	0.028000	0.19301	0.000000	0.03702	0.008000	0.06430	2.093000	0.41710	0.541000	0.28827	0.557000	0.71058	CGC	.	.	none		0.642	MOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378174.1	NM_005372		A	57026520	G	A	57026520	3	1	46	1	0	0	0	0	1	0	0	0	9721	1145	40	1	1021	1	MOS	8	57026520	Missense_Mutation	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10	8412227	57026520	89337502	32	15689											
C8orf84	157869	hgsc.bcm.edu	37	chr8	73993379	73993379	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaccgagcgcctccgcacaCgggttgtaggcttgcactgg	6	7	14	14	4	0	0	0	0	0	0	1	1	1	0	3	3	2	6	3	3	1	3	rs34728970		TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr8:73993379C>T	ENST00000297354.6	-	2	488	c.284G>A	c.(283-285)cGt>cAt	p.R95H	RP11-956J14.1_ENST00000442274.1_RNA|SBSPON_ENST00000519697.1_5'UTR	NM_153225.3	NP_694957.3	Q8IVN8	SBSPO_HUMAN	somatomedin B and thrombospondin, type 1 domain containing	95	TSP type-1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				immune response (GO:0006955)	proteinaceous extracellular matrix (GO:0005578)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)										CCTCCGCACACGGGTTGTAGG	0.652																																					p.R95H		Atlas-SNP	.											C8orf84,NS,carcinoma,-1,1	.	.	1	0			c.G284A						scavenged	.						65	72	70					8																	73993379		2021	4174	6195	SO:0001583	missense	157869	exon2			CGCACACGGGTTG		CCDS43747.2	8q21.11	2013-08-07	2012-05-15	2012-05-15	ENSG00000164764	ENSG00000164764			30362	protein-coding gene	gene with protein product	"RPE spondin", "rpe-spondin"		"chromosome 8 open reading frame 84"	C8orf84		12107410	Standard	NM_153225		Approved	RPESP	uc003xzf.3	Q8IVN8	OTTHUMG00000157144	ENST00000297354.6:c.284G>A	8.37:g.73993379C>T	ENSP00000297354:p.Arg95His	151	1	0.00662252		170	59	0.347059	NM_153225	A8KAA5|Q96J64	Missense_Mutation	SNP	ENST00000297354.6	37	CCDS43747.2	.	.	.	.	.	.	.	.	.	.	C	28.1	4.888198	0.91814	.	.	ENSG00000164764	ENST00000297354	T	0.21191	2.02	5.29	4.4	0.53042	.	0.118037	0.56097	D	0.000031	T	0.44117	0.1278	M	0.80982	2.52	0.80722	D	1	D	0.67145	0.996	P	0.58077	0.832	T	0.52026	-0.8630	10	0.66056	D	0.02	-5.0986	15.3079	0.74008	0.1412:0.8588:0.0:0.0	.	95	Q8IVN8	RPESP_HUMAN	H	95	ENSP00000297354:R95H	ENSP00000297354:R95H	R	-	2	0	C8orf84	74155933	1.000000	0.71417	0.971000	0.41717	0.926000	0.56050	5.388000	0.66249	1.204000	0.43247	0.591000	0.81541	CGT	.	.	none		0.652	SBSPON-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347584.2	NM_153225		T	73993379	C	T	73993379	3	4	46	1	0	0	0	0	1	0	0	0	2442	536	19	1	526	1	C8orf84	8	73993379	Missense_Mutation	SNP	C	TCGA-RQ-A6JB-01A-11D-A31X-10	16966859	73993379	72370643	33	15690											
ZHX2	22882	hgsc.bcm.edu	37	chr8	123966206	123966206	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcaggctgcggcagaaggtgTgtcggaactggctgaatcag	9	8	16	8	2	2	2	2	1	0	1	3	3	2	3	0	5	2	3	0	5	3	0			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr8:123966206T>C	ENST00000314393.4	+	3	3291	c.2456T>C	c.(2455-2457)gTg>gCg	p.V819A		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	819					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)			GCAGAAGGTGTGTCGGAACTG	0.597																																					p.V819A	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											.	ZHX2	106	.	0			c.T2456C						PASS	.						101	73	82					8																	123966206		2203	4300	6503	SO:0001583	missense	22882	exon3			AAGGTGTGTCGGA	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.2456T>C	8.37:g.123966206T>C	ENSP00000314709:p.Val819Ala	87	0	0		98	50	0.510204	NM_014943		Missense_Mutation	SNP	ENST00000314393.4	37	CCDS6336.1	.	.	.	.	.	.	.	.	.	.	T	0.004	-2.328921	0.00229	.	.	ENSG00000178764	ENST00000314393	T	0.16073	2.37	6.04	-2.28	0.06826	.	2.219640	0.01526	N	0.018567	T	0.06554	0.0168	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.17258	-1.0375	10	0.08179	T	0.78	0.1412	0.4746	0.00538	0.2626:0.3085:0.1678:0.2611	.	819	Q9Y6X8	ZHX2_HUMAN	A	819	ENSP00000314709:V819A	ENSP00000314709:V819A	V	+	2	0	ZHX2	124035387	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.290000	0.18975	-0.298000	0.08921	-2.109000	0.00356	GTG	.	.	none		0.597	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943		C	123966206	T	C	123966206	3	2	46	1	0	0	0	0	1	0	0	0	17691	1696	59	3	2458	3	ZHX2	8	123966206	Missense_Mutation	SNP	T	TCGA-RQ-A6JB-01A-11D-A31X-10	49972827	123966206	22397816	34	15691											
MURC	347273	hgsc.bcm.edu	37	chr9	103348299	103348299	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgacaagaaagtgaacagaAttagaactagaatagtgacc	19	8	9	5	0	0	7	0	3	0	4	0	7	0	7	1	0	2	0	1	0	9	4			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr9:103348299A>T	ENST00000307584.5	+	2	726	c.661A>T	c.(661-663)Att>Ttt	p.I221F		NM_001018116.1	NP_001018126.1	Q5BKX8	MURC_HUMAN	muscle-related coiled-coil protein	221					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)				AGTGAACAGAATTAGAACTAG	0.478																																					p.I221F		Atlas-SNP	.											.	MURC	43	.	0			c.A661T						PASS	.						110	118	115					9																	103348299		2203	4300	6503	SO:0001583	missense	347273	exon2			AACAGAATTAGAA	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.661A>T	9.37:g.103348299A>T	ENSP00000418668:p.Ile221Phe	111	0	0		115	38	0.330435	NM_001018116	B1PRL3|B4DT88	Missense_Mutation	SNP	ENST00000307584.5	37	CCDS35083.1	.	.	.	.	.	.	.	.	.	.	A	15.85	2.955464	0.53293	.	.	ENSG00000170681	ENST00000307584	T	0.61274	0.12	5.27	4.09	0.47781	.	0.186907	0.46758	D	0.000270	T	0.51466	0.1676	L	0.49126	1.545	0.44603	D	0.997578	P	0.41131	0.739	B	0.40066	0.318	T	0.52548	-0.8561	10	0.56958	D	0.05	-8.7658	10.5979	0.45349	0.838:0.162:0.0:0.0	.	221	Q5BKX8	MURC_HUMAN	F	221	ENSP00000418668:I221F	ENSP00000418668:I221F	I	+	1	0	MURC	102388120	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	2.488000	0.45276	0.905000	0.36596	0.459000	0.35465	ATT	.	.	none		0.478	MURC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053419.2	NM_001018116		T	103348299	A	T	103348299	3	4	46	1	0	0	0	0	1	0	0	0	9996	101	4	5	667	5	MURC	9	103348299	Missense_Mutation	SNP	A	TCGA-RQ-A6JB-01A-11D-A31X-10		103348299	37865132	35	15692											
PTPN3	5774	hgsc.bcm.edu	37	chr9	112225710	112225710	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ccaacgcacgtaaccgggagGtcataactatcgctgaataa	14	7	9	11	4	1	1	1	1	0	0	2	2	1	2	2	2	3	3	2	2	6	4			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr9:112225710G>C	ENST00000374541.2	-	2	109	c.5C>G	c.(4-6)aCc>aGc	p.T2S	PTPN3_ENST00000262539.3_5'UTR	NM_001145368.1|NM_002829.3	NP_001138840.1|NP_002820.3	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type 3	2					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						TAACCGGGAGGTCATAACTAT	0.408																																					p.T2S		Atlas-SNP	.											.	PTPN3	106	.	0			c.C5G						PASS	.						100	99	100					9																	112225710		2203	4300	6503	SO:0001583	missense	5774	exon2			CGGGAGGTCATAA		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.5C>G	9.37:g.112225710G>C	ENSP00000363667:p.Thr2Ser	99	0	0		103	36	0.349515	NM_001145368	A0AUW9|E7EN99|E9PGU7	Missense_Mutation	SNP	ENST00000374541.2	37	CCDS6776.1	.	.	.	.	.	.	.	.	.	.	G	15.32	2.799131	0.50208	.	.	ENSG00000070159	ENST00000394831;ENST00000374541	T	0.70749	-0.51	5.25	4.23	0.50019	.	0.157695	0.41396	D	0.000896	T	0.49932	0.1586	N	0.17082	0.46	0.80722	D	1	B;P;B	0.35612	0.172;0.512;0.067	B;B;B	0.31442	0.058;0.13;0.034	T	0.50363	-0.8837	10	0.29301	T	0.29	.	10.8355	0.46685	0.0:0.0:0.6104:0.3896	.	2;2;2	B7Z9V1;Q45VJ3;P26045	.;.;PTN3_HUMAN	S	2	ENSP00000363667:T2S	ENSP00000363667:T2S	T	-	2	0	PTPN3	111265531	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.591000	0.53986	2.604000	0.88044	0.557000	0.71058	ACC	.	.	none		0.408	PTPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053598.4			C	112225710	G	C	112225710	3	2	46	1	0	0	0	0	1	0	0	0	12804	1261	44	4	2836	4	PTPN3	9	112225710	Missense_Mutation	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10	8877411	112225710	28987721	36	15693											
MEGF9	1955	hgsc.bcm.edu	37	chr9	123367753	123367753	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgttaaattgggtccatgaTacatcagctaaagctgaagt	14	12	9	6	0	1	2	1	2	0	0	2	2	2	2	1	1	3	3	1	1	6	4			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr9:123367753T>C	ENST00000373930.3	-	6	1635	c.1524A>G	c.(1522-1524)gtA>gtG	p.V508V	MEGF9_ENST00000426959.1_Silent_p.V545V	NM_001080497.2	NP_001073966.2	Q9H1U4	MEGF9_HUMAN	multiple EGF-like-domains 9	508						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						GGGTCCATGATACATCAGCTA	0.423																																					p.V508V		Atlas-SNP	.											.	MEGF9	33	.	0			c.A1524G						PASS	.						95	90	92					9																	123367753		1927	4140	6067	SO:0001819	synonymous_variant	1955	exon6			CCATGATACATCA	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.1524A>G	9.37:g.123367753T>C		205	0	0		202	74	0.366337	NM_001080497	B7Z315|O75098	Silent	SNP	ENST00000373930.3	37	CCDS48010.2																																																																																			.	.	none		0.423	MEGF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055513.1	NM_001080497		C	123367753	T	C	123367753	2	2	46	1	0	0	0	0	0	0	0	1	9473	1393	49	3		3	MEGF9	9	123367753	Silent	SNP	T	TCGA-RQ-A6JB-01A-11D-A31X-10	11142043	123367753	17845678	37	15694											
NUDT5	11164	hgsc.bcm.edu	37	chr10	12215729	12215729	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ataccaacctggagaacattCggcaatgtcccctttgtagc	11	10	8	12	1	0	1	0	0	0	1	2	2	1	1	4	2	4	2	4	2	5	4			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr10:12215729C>T	ENST00000491614.1	-	6	768	c.373G>A	c.(373-375)Gaa>Aaa	p.E125K	NUDT5_ENST00000378927.3_Missense_Mutation_p.E125K|NUDT5_ENST00000378940.3_Missense_Mutation_p.E125K|NUDT5_ENST00000378937.3_Missense_Mutation_p.E138K|NUDT5_ENST00000537776.1_Missense_Mutation_p.E125K|NUDT5_ENST00000378952.3_5'UTR			Q9UKK9	NUDT5_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 5	125	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				D-ribose catabolic process (GO:0019303)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide metabolic process (GO:0009117)|ribonucleoside diphosphate catabolic process (GO:0009191)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)|magnesium ion binding (GO:0000287)|nucleoside-diphosphatase activity (GO:0017110)|snoRNA binding (GO:0030515)			breast(1)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)	8		Renal(717;0.228)				GGAGAACATTCGGCAATGTCC	0.463																																					p.E125K		Atlas-SNP	.											.	NUDT5	10	.	0			c.G373A						PASS	.						180	176	178					10																	12215729		2203	4300	6503	SO:0001583	missense	11164	exon6			AACATTCGGCAAT	AF155832	CCDS7089.1	10p14	2008-05-14			ENSG00000165609	ENSG00000165609		"Nudix motif containing"	8052	protein-coding gene	gene with protein product		609230				10373642	Standard	NM_014142		Approved	hYSAH1, YSA1H	uc001ilj.3	Q9UKK9	OTTHUMG00000017682	ENST00000491614.1:c.373G>A	10.37:g.12215729C>T	ENSP00000419628:p.Glu125Lys	77	0	0		60	21	0.35	NM_014142	A8K516|Q6IAG0|Q9UH49	Missense_Mutation	SNP	ENST00000491614.1	37	CCDS7089.1	.	.	.	.	.	.	.	.	.	.	C	22.4	4.279041	0.80692	.	.	ENSG00000165609	ENST00000491614;ENST00000378929;ENST00000378937;ENST00000537776;ENST00000378940;ENST00000378927	T;T;T;T;T	0.07800	3.16;3.16;3.16;3.16;3.16	5.76	5.76	0.90799	NUDIX hydrolase domain (3);NUDIX hydrolase domain-like (1);	0.047168	0.85682	D	0.000000	T	0.18002	0.0432	L	0.28776	0.89	0.58432	D	0.999999	D;D	0.76494	0.999;0.998	P;P	0.62491	0.903;0.707	T	0.01557	-1.1325	10	0.28530	T	0.3	-33.9397	20.3242	0.98691	0.0:1.0:0.0:0.0	.	125;125	A6NCQ0;Q9UKK9	.;NUDT5_HUMAN	K	125;125;138;125;125;125	ENSP00000419628:E125K;ENSP00000368219:E138K;ENSP00000445116:E125K;ENSP00000368222:E125K;ENSP00000368209:E125K	ENSP00000368209:E125K	E	-	1	0	NUDT5	12255735	1.000000	0.71417	0.984000	0.44739	0.547000	0.35210	6.507000	0.73717	2.882000	0.98803	0.655000	0.94253	GAA	.	.	none		0.463	NUDT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046811.1			T	12215729	C	T	12215729	3	4	46	1	0	0	0	0	1	0	0	0	10751	893	31	1	306	1	NUDT5	10	12215729	Missense_Mutation	SNP	C	TCGA-RQ-A6JB-01A-11D-A31X-10		12215729	123319018	38	15695											
C10orf71	118461	hgsc.bcm.edu	37	chr10	50534484	50534486	+	In_Frame_Del	DEL	CTT	CTT	-																															ctccaggtgaaaatcaagacCttctatgacccagagacggg																										TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr10:50534484_50534486delCTT	ENST00000374144.3	+	3	4182_4184	c.3894_3896delCTT	c.(3892-3897)accttc>acc	p.F1299del	C10orf71_ENST00000323868.4_Intron			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	1299										endometrium(1)	1						AAATCAAGACCTTCTATGACCCA	0.64																																					p.1298_1299del		Pindel,Atlas-Indel	.											.	C10orf71	179	.	0			c.3893_3895del						PASS	.																																			SO:0001651	inframe_deletion	118461	exon3			.	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.3894_3896delCTT	10.37:g.50534484_50534486delCTT	ENSP00000363259:p.Phe1299del	0	0	.		19	19	1	NM_001135196	A0AVL8	In_Frame_Del	DEL	ENST00000374144.3	37	CCDS44387.1																																																																																			.	.	none		0.64	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459		-	50534486	CTT	-	50534484	7	5	46	1	0	1	0	1	0	0	0	0	1616	668	24	0	3896	0	C10orf71	10	50534484	In_Frame_Del	DEL	CTT	TCGA-RQ-A6JB-01A-11D-A31X-10	38318755	50534484	85000263	39	15696											
ZWINT	11130	hgsc.bcm.edu	37	chr10	58120984	58120984	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcagcttccgcctctgtcTccgctgcctccatctttcca	3	13	6	19	2	3	0	0	0	3	0	7	0	6	0	6	0	3	3	6	0	0	2			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr10:58120984T>C	ENST00000373944.3	-	1	52	c.14A>G	c.(13-15)gAg>gGg	p.E5G	ZWINT_ENST00000460654.1_5'Flank|ZWINT_ENST00000361148.6_Missense_Mutation_p.E5G|ZWINT_ENST00000395405.1_Missense_Mutation_p.E5G|ZWINT_ENST00000318387.2_5'Flank			O95229	ZWINT_HUMAN	ZW10 interacting kinetochore protein	5					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						CGCCTCTGTCTCCGCTGCCTC	0.587																																					p.E5G		Atlas-SNP	.											.	ZWINT	39	.	0			c.A14G						PASS	.						37	35	36					10																	58120984		2203	4300	6503	SO:0001583	missense	11130	exon1			TCTGTCTCCGCTG	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.14A>G	10.37:g.58120984T>C	ENSP00000363055:p.Glu5Gly	26	0	0		27	16	0.592593	NM_007057	A6NNV6|Q0D2I3|Q9BWD0	Missense_Mutation	SNP	ENST00000373944.3	37	CCDS7249.1	.	.	.	.	.	.	.	.	.	.	T	11.77	1.737651	0.30774	.	.	ENSG00000122952	ENST00000373944;ENST00000395405;ENST00000373940;ENST00000361148	T;T;T	0.38401	1.14;1.14;1.17	4.03	-2.36	0.06663	.	0.931407	0.08897	N	0.877771	T	0.25754	0.0627	L	0.44542	1.39	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.002	T	0.27123	-1.0083	10	0.38643	T	0.18	0.0641	5.5396	0.17031	0.0:0.4279:0.1986:0.3735	.	5;5	A6NNV6;O95229	.;ZWINT_HUMAN	G	5	ENSP00000363055:E5G;ENSP00000378801:E5G;ENSP00000354921:E5G	ENSP00000354921:E5G	E	-	2	0	ZWINT	57790990	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.057000	0.14279	-0.452000	0.07087	-0.256000	0.11100	GAG	.	.	none		0.587	ZWINT-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048132.1			C	58120984	T	C	58120984	3	2	46	1	0	0	0	0	1	0	0	0	18264	1551	54	3	851	3	ZWINT	10	58120984	Missense_Mutation	SNP	T	TCGA-RQ-A6JB-01A-11D-A31X-10	7586500	58120984	77413763	40	15697											
CYP2C8	1558	hgsc.bcm.edu	37	chr10	96802724	96802724	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ggtggggacaaggtcactgtAtctctggatctcgtgcacta	8	11	13	9	1	3	0	1	0	2	0	5	2	3	2	0	5	1	2	0	5	3	2			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr10:96802724A>G	ENST00000371270.3	-	7	1166	c.1072T>C	c.(1072-1074)Tac>Cac	p.Y358H	CYP2C8_ENST00000539050.1_Missense_Mutation_p.Y272H|CYP2C8_ENST00000535898.1_Missense_Mutation_p.Y256H	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	358					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)	AGGTCACTGTATCTCTGGATC	0.498																																					p.Y358H		Atlas-SNP	.											.	CYP2C8	73	.	0			c.T1072C						PASS	.						273	218	236					10																	96802724		2203	4300	6503	SO:0001583	missense	1558	exon7			CACTGTATCTCTG	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.1072T>C	10.37:g.96802724A>G	ENSP00000360317:p.Tyr358His	111	0	0		133	49	0.368421	NM_000770	A8K9N8|B0AZN2|B7Z1F6|Q5VX93|Q8WWB1|Q9UCZ9	Missense_Mutation	SNP	ENST00000371270.3	37	CCDS7438.1	.	.	.	.	.	.	.	.	.	.	A	11.07	1.531632	0.27387	.	.	ENSG00000138115	ENST00000371270;ENST00000535868;ENST00000535898;ENST00000539050	T;T;T	0.69806	-0.43;-0.43;-0.43	4.49	3.32	0.38043	.	0.348041	0.24856	U	0.035053	T	0.58352	0.2116	L	0.31845	0.965	0.25918	N	0.983155	B;P;P;B	0.45594	0.426;0.862;0.554;0.303	B;P;P;B	0.46237	0.282;0.508;0.462;0.329	T	0.53330	-0.8454	10	0.72032	D	0.01	.	8.5378	0.33373	0.8271:0.0:0.0:0.1729	.	272;256;326;358	F5H7Q9;B7Z1F6;B7Z8S1;P10632	.;.;.;CP2C8_HUMAN	H	358;325;256;272	ENSP00000360317:Y358H;ENSP00000445062:Y256H;ENSP00000442343:Y272H	ENSP00000360317:Y358H	Y	-	1	0	CYP2C8	96792714	1.000000	0.71417	0.923000	0.36655	0.130000	0.20726	4.231000	0.58639	0.725000	0.32318	0.477000	0.44152	TAC	.	.	none		0.498	CYP2C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049499.2	NM_000770		G	96802724	A	G	96802724	3	3	46	1	0	0	0	0	1	0	0	0	4169	449	16	3	412	3	CYP2C8	10	96802724	Missense_Mutation	SNP	A	TCGA-RQ-A6JB-01A-11D-A31X-10	38681740	96802724	38732023	41	15698											
CTSD	1509	hgsc.bcm.edu	37	chr11	1780809	1780809	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caggttggaggagcccgtgtCgaagacgactgtgaagcact	10	7	15	9	3	0	2	0	1	0	1	1	6	0	4	1	3	2	2	1	3	2	1			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr11:1780809C>T	ENST00000236671.2	-	3	421	c.289G>A	c.(289-291)Gac>Aac	p.D97N	RP11-295K3.1_ENST00000427721.1_5'Flank|AC068580.6_ENST00000449248.1_RNA	NM_001909.4	NP_001900.1	P07339	CATD_HUMAN	cathepsin D	97					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)"	GAGCCCGTGTCGAAGACGACT	0.657																																					p.D97N		Atlas-SNP	.											.	CTSD	26	.	0			c.G289A						PASS	.						65	63	64					11																	1780809		2202	4299	6501	SO:0001583	missense	1509	exon3			CCGTGTCGAAGAC	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.289G>A	11.37:g.1780809C>T	ENSP00000236671:p.Asp97Asn	29	0	0		23	7	0.304348	NM_001909	Q6IB57	Missense_Mutation	SNP	ENST00000236671.2	37	CCDS7725.1	.	.	.	.	.	.	.	.	.	.	c	29.3	4.994971	0.93167	.	.	ENSG00000117984	ENST00000236671;ENST00000438213;ENST00000367196	D;T;D	0.84944	-1.92;-1.39;-1.83	4.2	4.2	0.49525	Peptidase aspartic (1);Peptidase aspartic, catalytic (1);	0.052549	0.64402	D	0.000001	D	0.96027	0.8706	H	0.99498	4.595	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98537	1.0630	10	0.87932	D	0	.	16.9432	0.86224	0.0:1.0:0.0:0.0	.	97	P07339	CATD_HUMAN	N	97;82;62	ENSP00000236671:D97N;ENSP00000415036:D82N;ENSP00000356164:D62N	ENSP00000236671:D97N	D	-	1	0	CTSD	1737385	1.000000	0.71417	1.000000	0.80357	0.714000	0.41099	6.980000	0.76160	2.061000	0.61500	0.486000	0.48141	GAC	.	.	none		0.657	CTSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104272.5	NM_001909		T	1780809	C	T	1780809	3	4	46	1	0	0	0	0	1	0	0	0	4034	884	31	1	977	1	CTSD	11	1780809	Missense_Mutation	SNP	C	TCGA-RQ-A6JB-01A-11D-A31X-10		1780809	133225707	42	15699											
APOA1	335	hgsc.bcm.edu	37	chr11	116707093	116707093	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgcagcttgctgaaggtggAggtcacgctgtcccagttgt	6	10	15	10	2	1	1	1	1	0	0	2	2	2	2	1	3	2	5	1	3	1	2			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr11:116707093A>G	ENST00000236850.4	-	4	600	c.235T>C	c.(235-237)Tcc>Ccc	p.S79P	APOA1_ENST00000375320.1_Missense_Mutation_p.S79P|APOA1_ENST00000375323.1_Missense_Mutation_p.S79P|AP006216.12_ENST00000444200.1_RNA|APOA1_ENST00000375329.2_Missense_Mutation_p.S57P|APOA1_ENST00000359492.2_Missense_Mutation_p.S79P	NM_000039.1	NP_000030.1	P02647	APOA1_HUMAN	apolipoprotein A-I	79	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)		CTGAAGGTGGAGGTCACGCTG	0.612																																					p.S79P		Atlas-SNP	.											.	APOA1	19	.	0			c.T235C						PASS	.						50	48	48					11																	116707093		2201	4292	6493	SO:0001583	missense	335	exon4			AGGTGGAGGTCAC	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.235T>C	11.37:g.116707093A>G	ENSP00000236850:p.Ser79Pro	66	0	0		78	32	0.410256	NM_000039	A8K866|Q6LDN9|Q6Q785|Q9UCS8|Q9UCT8	Missense_Mutation	SNP	ENST00000236850.4	37	CCDS8378.1	.	.	.	.	.	.	.	.	.	.	A	13.91	2.378823	0.42207	.	.	ENSG00000118137	ENST00000375320;ENST00000359492;ENST00000375329;ENST00000375323;ENST00000236850	T;T;T;T;T	0.75050	-0.9;-0.9;-0.9;-0.9;-0.9	5.38	-7.41	0.01392	Apolipoprotein/apolipophorin (1);	0.971554	0.08387	N	0.953551	T	0.58878	0.2153	L	0.55743	1.74	0.09310	N	1	B	0.14805	0.011	B	0.17979	0.02	T	0.51301	-0.8723	10	0.45353	T	0.12	-4.2027	1.3102	0.02096	0.4455:0.194:0.0931:0.2674	.	79	P02647	APOA1_HUMAN	P	79;79;57;79;79	ENSP00000364469:S79P;ENSP00000352471:S79P;ENSP00000364478:S57P;ENSP00000364472:S79P;ENSP00000236850:S79P	ENSP00000236850:S79P	S	-	1	0	APOA1	116212303	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-1.029000	0.03585	-0.810000	0.04375	-0.379000	0.06801	TCC	.	.	none		0.612	APOA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106281.2	NM_000039		G	116707093	A	G	116707093	3	3	46	1	0	0	0	0	1	0	0	0	780	304	11	3	572	3	APOA1	11	116707093	Missense_Mutation	SNP	A	TCGA-RQ-A6JB-01A-11D-A31X-10	114926284	116707093	18299423	43	15700											
NTM	50863	hgsc.bcm.edu	37	chr11	132016345	132016345	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atgtgtatgacgagggccctTacacctgctcggtgcagaca	9	9	12	11	2	0	2	0	1	0	1	1	3	0	2	2	2	3	3	2	2	2	2			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr11:132016345T>A	ENST00000374786.1	+	2	816	c.337T>A	c.(337-339)Tac>Aac	p.Y113N	NTM_ENST00000374791.3_Missense_Mutation_p.Y113N|NTM_ENST00000427481.2_Missense_Mutation_p.Y104N|NTM_ENST00000374784.1_Missense_Mutation_p.Y113N|NTM_ENST00000425719.2_Missense_Mutation_p.Y113N|NTM_ENST00000539799.1_Missense_Mutation_p.Y113N	NM_001144058.1|NM_016522.2	NP_001137530.1|NP_057606.1	Q9P121	NTRI_HUMAN	neurotrimin	113	Ig-like C2-type 1.				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						CGAGGGCCCTTACACCTGCTC	0.587																																					p.Y113N		Atlas-SNP	.											.	NTM	253	.	0			c.T337A						PASS	.						162	112	129					11																	132016345		2201	4297	6498	SO:0001583	missense	50863	exon2			GGCCCTTACACCT	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.337T>A	11.37:g.132016345T>A	ENSP00000363918:p.Tyr113Asn	110	0	0		116	41	0.353448	NM_001144059	A0MTT2|Q6UXJ3|Q86VJ9	Missense_Mutation	SNP	ENST00000374786.1	37	CCDS8491.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.301473	0.81136	.	.	ENSG00000182667	ENST00000374791;ENST00000539799;ENST00000550167;ENST00000427481;ENST00000374786;ENST00000425719;ENST00000374784	T;T;T;T;T;T;T	0.73469	-0.75;-0.75;-0.75;-0.75;-0.75;-0.75;-0.75	5.58	5.58	0.84498	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.305913	0.36268	N	0.002692	D	0.90191	0.6934	H	0.96633	3.855	0.52501	D	0.999958	D;D;D;D;D;D	0.89917	1.0;0.997;1.0;0.997;0.999;1.0	D;D;D;D;D;D	0.85130	0.997;0.993;0.995;0.997;0.982;0.995	D	0.92723	0.6193	10	0.87932	D	0	-20.7387	12.0456	0.53477	0.1289:0.0:0.0:0.8711	.	113;104;113;113;113;113	B7Z1Z5;B7Z1I4;Q9P121-4;Q9P121;Q9P121-3;Q9P121-2	.;.;.;NTRI_HUMAN;.;.	N	113;113;104;104;113;113;113	ENSP00000363923:Y113N;ENSP00000437668:Y113N;ENSP00000448104:Y104N;ENSP00000416320:Y104N;ENSP00000363918:Y113N;ENSP00000396722:Y113N;ENSP00000363916:Y113N	ENSP00000363916:Y113N	Y	+	1	0	NTM	131521555	1.000000	0.71417	0.916000	0.36221	0.950000	0.60333	8.026000	0.88783	2.126000	0.65437	0.533000	0.62120	TAC	.	.	none		0.587	NTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141937.1	NM_016522		A	132016345	T	A	132016345	3	1	46	1	0	0	0	0	1	0	0	0	10708	1754	61	5	429	5	NTM	11	132016345	Missense_Mutation	SNP	T	TCGA-RQ-A6JB-01A-11D-A31X-10	15309252	132016345	2990171	44	15701											
CACNA2D4	93589	hgsc.bcm.edu	37	chr12	1993483	1993483	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	caatgaggtaagtgaaaactCggacctaacccacaagacac	17	5	8	11	1	0	3	0	2	0	1	1	4	0	4	2	2	2	1	2	2	6	2			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr12:1993483C>T	ENST00000382722.5	-	12	1639	c.1277G>A	c.(1276-1278)cGa>cAa	p.R426Q	CACNA2D4_ENST00000588077.1_Missense_Mutation_p.R362Q|CACNA2D4_ENST00000586184.1_Missense_Mutation_p.R426Q|CACNA2D4_ENST00000587995.1_Missense_Mutation_p.R426Q|CACNA2D4_ENST00000585708.1_Missense_Mutation_p.R362Q|CACNA2D4_ENST00000585732.1_Intron	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	426	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)		AGTGAAAACTCGGACCTAACC	0.478																																					p.R426Q	Colon(2;101 179 21030 23310 28141)	Atlas-SNP	.											.	CACNA2D4	220	.	0			c.G1277A						PASS	.						78	85	82					12																	1993483		2017	4193	6210	SO:0001583	missense	93589	exon12			AAAACTCGGACCT	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.1277G>A	12.37:g.1993483C>T	ENSP00000372169:p.Arg426Gln	71	0	0		78	28	0.358974	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Missense_Mutation	SNP	ENST00000382722.5	37	CCDS44785.1	.	.	.	.	.	.	.	.	.	.	C	33	5.206269	0.95033	.	.	ENSG00000151062	ENST00000456077;ENST00000280663;ENST00000382722	T	0.09163	3.01	5.27	5.27	0.74061	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	T	0.38772	0.1053	M	0.90082	3.085	0.80722	D	1	D	0.69078	0.997	P	0.59424	0.857	T	0.50118	-0.8865	10	0.87932	D	0	.	18.4934	0.90855	0.0:1.0:0.0:0.0	.	426	Q7Z3S7	CA2D4_HUMAN	Q	362;426;426	ENSP00000372169:R426Q	ENSP00000280663:R426Q	R	-	2	0	CACNA2D4	1863744	1.000000	0.71417	0.834000	0.33040	0.831000	0.47069	7.780000	0.85658	2.463000	0.83235	0.603000	0.83216	CGA	.	.	none		0.478	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2			T	1993483	C	T	1993483	3	4	46	1	0	0	0	0	1	0	0	0	2553	884	31	1	2244	1	CACNA2D4	12	1993483	Missense_Mutation	SNP	C	TCGA-RQ-A6JB-01A-11D-A31X-10		1993483	131858412	45	15702											
SCNN1A	6337	hgsc.bcm.edu	37	chr12	6471387	6471387	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtatgtctggtagaagcaGtccgatttgttctggttgca	8	14	13	6	1	2	1	0	0	2	1	3	3	3	1	1	2	2	6	1	2	3	5			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr12:6471387G>A	ENST00000228916.2	-	4	803	c.705C>T	c.(703-705)gaC>gaT	p.D235D	SCNN1A_ENST00000360168.3_Silent_p.D294D|SCNN1A_ENST00000540037.1_5'UTR|SCNN1A_ENST00000538979.1_Intron|SCNN1A_ENST00000358945.3_Silent_p.D235D|SCNN1A_ENST00000543768.1_Silent_p.D258D|SCNN1A_ENST00000396966.2_Silent_p.D235D	NM_001038.5	NP_001029.1	P37088	SCNNA_HUMAN	sodium channel, non-voltage-gated 1 alpha subunit	235					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)	apical plasma membrane (GO:0016324)|ciliary membrane (GO:0060170)|cortical actin cytoskeleton (GO:0030864)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(2)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Amiloride(DB00594)|Triamterene(DB00384)	GGTAGAAGCAGTCCGATTTGT	0.562																																					p.D294D		Atlas-SNP	.											SCNN1A,NS,adenocarcinoma,-2,1	SCNN1A	54	1	0			c.C882T						PASS	.						158	112	128					12																	6471387		2203	4300	6503	SO:0001819	synonymous_variant	6337	exon3			GAAGCAGTCCGAT	Z92978	CCDS8543.1, CCDS53738.1, CCDS53739.1	12p13	2012-02-28	2012-02-28		ENSG00000111319	ENSG00000111319		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10599	protein-coding gene	gene with protein product		600228	"sodium channel, nonvoltage-gated 1 alpha", "sodium channel, non-voltage-gated 1 alpha"	SCNN1		7896277	Standard	NM_001038		Approved	ENaCalpha	uc001qnw.3	P37088	OTTHUMG00000168268	ENST00000228916.2:c.705C>T	12.37:g.6471387G>A		97	0	0		97	24	0.247423	NM_001159576	A5X2U9|B4E2Q5|C5HTZ0|O43271|Q6GSQ6|Q9UM64	Silent	SNP	ENST00000228916.2	37	CCDS8543.1																																																																																			.	.	none		0.562	SCNN1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399055.1			A	6471387	G	A	6471387	2	1	46	1	0	0	0	0	0	0	0	1	13942	1020	36	2		2	SCNN1A	12	6471387	Silent	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10	4477904	6471387	127380508	46	15703											
TSPAN31	6302	hgsc.bcm.edu	37	chr12	58140844	58140844	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atgccagatgtgtggagaaaAgtttcttaagcattcagacg	13	11	11	6	1	2	3	1	0	1	3	2	4	2	3	1	1	2	2	1	1	3	3			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr12:58140844A>C	ENST00000257910.3	+	5	762	c.488A>C	c.(487-489)aAg>aCg	p.K163T	TSPAN31_ENST00000547472.1_Missense_Mutation_p.K80T|TSPAN31_ENST00000547992.1_Missense_Mutation_p.K79T|TSPAN31_ENST00000553221.1_3'UTR|CDK4_ENST00000551888.1_5'Flank	NM_005981.3	NP_005972.1	Q12999	TSN31_HUMAN	tetraspanin 31	163					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)			TGTGGAGAAAAGTTTCTTAAG	0.438																																					p.K163T		Atlas-SNP	.											.	TSPAN31	20	.	0			c.A488C						PASS	.						128	133	131					12																	58140844		2203	4300	6503	SO:0001583	missense	6302	exon5			GAGAAAAGTTTCT		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		ENST00000257910.3:c.488A>C	12.37:g.58140844A>C	ENSP00000257910:p.Lys163Thr	130	0	0		164	64	0.390244	NM_005981	O00577|Q53X76	Missense_Mutation	SNP	ENST00000257910.3	37	CCDS8952.1	.	.	.	.	.	.	.	.	.	.	A	13.64	2.296104	0.40594	.	.	ENSG00000135452	ENST00000257910;ENST00000547992;ENST00000547472;ENST00000548167	T;T	0.80566	-1.39;-1.39	5.03	2.65	0.31530	.	0.157358	0.53938	N	0.000054	T	0.72326	0.3446	M	0.73962	2.25	0.46028	D	0.99882	B;B	0.06786	0.0;0.001	B;B	0.08055	0.001;0.003	T	0.58244	-0.7670	10	0.13853	T	0.58	-5.5034	3.0344	0.06117	0.6323:0.1468:0.0797:0.1412	.	79;163	F8VS78;Q12999	.;TSN31_HUMAN	T	163;79;80;85	ENSP00000257910:K163T;ENSP00000449199:K80T	ENSP00000257910:K163T	K	+	2	0	TSPAN31	56427111	0.931000	0.31567	0.895000	0.35142	0.995000	0.86356	1.087000	0.30865	0.483000	0.27608	0.459000	0.35465	AAG	.	.	none		0.438	TSPAN31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408778.1			C	58140844	A	C	58140844	3	2	46	1	0	0	0	0	1	0	0	0	16661	72	3	5	506	5	TSPAN31	12	58140844	Missense_Mutation	SNP	A	TCGA-RQ-A6JB-01A-11D-A31X-10	51669457	58140844	75711051	47	15704											
RASSF9	9182	hgsc.bcm.edu	37	chr12	86198771	86198771	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	ctgtatttaatctctttctgGatgccactcaaatgagagtg	10	15	8	8	0	3	1	1	1	2	1	4	3	3	2	1	1	1	1	1	1	3	4			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr12:86198771G>A	ENST00000361228.3	-	2	1385	c.1017C>T	c.(1015-1017)atC>atT	p.I339I		NM_005447.3	NP_005438.2	O75901	RASF9_HUMAN	Ras association (RalGDS/AF-6) domain family (N-terminal) member 9	339					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						TCTCTTTCTGGATGCCACTCA	0.373																																					p.I339I		Atlas-SNP	.											.	RASSF9	100	.	0			c.C1017T						PASS	.						179	182	181					12																	86198771		1854	4089	5943	SO:0001819	synonymous_variant	9182	exon2			TTTCTGGATGCCA		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.1017C>T	12.37:g.86198771G>A		133	0	0		113	45	0.39823	NM_005447	B3KMQ4|Q8N5U8	Silent	SNP	ENST00000361228.3	37	CCDS44950.1																																																																																			.	.	none		0.373	RASSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406109.1			A	86198771	G	A	86198771	2	1	46	1	0	0	0	0	0	0	0	1	13108	1164	41	2		2	RASSF9	12	86198771	Silent	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10	28057927	86198771	47653124	48	15705											
GPN3	51184	hgsc.bcm.edu	37	chr12	110902947	110902947	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	gttgaagtgttctgctgctgGatccaggtttacaacttgga	8	14	12	7	0	1	1	0	1	1	0	2	3	2	3	1	3	4	5	1	3	3	5			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr12:110902947G>A	ENST00000228827.3	-	2	183	c.121C>T	c.(121-123)Cca>Tca	p.P41S	GPN3_ENST00000537466.2_Missense_Mutation_p.P51S|GPN3_ENST00000552180.1_5'UTR|GPN3_ENST00000543199.1_Missense_Mutation_p.P80S	NM_016301.3	NP_057385.3			GPN-loop GTPase 3											endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|urinary_tract(1)	8						TCTGCTGCTGGATCCAGGTTT	0.537																																					p.P80S		Atlas-SNP	.											.	GPN3	37	.	0			c.C238T						PASS	.						197	157	170					12																	110902947		2203	4300	6503	SO:0001583	missense	51184	exon2			CTGCTGGATCCAG	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.121C>T	12.37:g.110902947G>A	ENSP00000228827:p.Pro41Ser	94	0	0		87	37	0.425287	NM_001164372		Missense_Mutation	SNP	ENST00000228827.3	37	CCDS9147.1	.	.	.	.	.	.	.	.	.	.	G	35	5.541728	0.96474	.	.	ENSG00000111231	ENST00000228827;ENST00000543199;ENST00000537466;ENST00000550974	T;T;T;T	0.47177	0.85;0.85;0.85;0.85	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.77987	0.4213	M	0.92738	3.34	0.80722	D	1	D;D	0.71674	0.996;0.998	D;D	0.79108	0.987;0.992	T	0.82172	-0.0589	10	0.87932	D	0	-14.8795	20.3789	0.98926	0.0:0.0:1.0:0.0	.	51;41	Q9UHW5-2;Q9UHW5	.;GPN3_HUMAN	S	41;80;51;19	ENSP00000228827:P41S;ENSP00000442770:P80S;ENSP00000443068:P51S;ENSP00000447480:P19S	ENSP00000228827:P41S	P	-	1	0	GPN3	109387330	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.221000	0.95188	2.826000	0.97356	0.563000	0.77884	CCA	.	.	none		0.537	GPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404607.1	NM_016301		A	110902947	G	A	110902947	3	1	46	1	0	0	0	0	1	0	0	0	6627	1174	41	2	761	2	GPN3	12	110902947	Missense_Mutation	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10	24704176	110902947	22948948	49	15706											
STARD13	90627	hgsc.bcm.edu	37	chr13	33684064	33684064	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccatgctgttcagcacatacTggtagatctctgtttgcctg	7	14	9	11	0	2	1	1	0	1	1	3	1	2	1	2	1	4	5	2	1	2	4			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr13:33684064T>A	ENST00000336934.5	-	12	3109	c.2993A>T	c.(2992-2994)cAg>cTg	p.Q998L	STARD13_ENST00000399365.3_Missense_Mutation_p.Q880L|STARD13_ENST00000255486.4_Missense_Mutation_p.Q990L	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	998	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)		CAGCACATACTGGTAGATCTC	0.527											OREG0022359	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q998L		Atlas-SNP	.											.	STARD13	100	.	0			c.A2993T						PASS	.						233	186	202					13																	33684064		2203	4300	6503	SO:0001583	missense	90627	exon12			ACATACTGGTAGA	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.2993A>T	13.37:g.33684064T>A	ENSP00000338785:p.Gln998Leu	81	0	0	841	81	32	0.395062	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Missense_Mutation	SNP	ENST00000336934.5	37	CCDS9348.1	.	.	.	.	.	.	.	.	.	.	T	19.36	3.812965	0.70912	.	.	ENSG00000133121	ENST00000399365;ENST00000255486;ENST00000336934	T;T;T	0.29397	1.57;1.57;1.57	5.86	5.86	0.93980	Lipid-binding START (3);START-like domain (1);	0.053876	0.85682	D	0.000000	T	0.48677	0.1513	M	0.84683	2.71	0.80722	D	1	B;B;B	0.32653	0.107;0.379;0.215	B;B;B	0.40901	0.11;0.343;0.139	T	0.54070	-0.8348	10	0.87932	D	0	.	16.255	0.82510	0.0:0.0:0.0:1.0	.	963;998;990	Q9Y3M8-4;Q9Y3M8;Q9Y3M8-2	.;STA13_HUMAN;.	L	880;990;998	ENSP00000382300:Q880L;ENSP00000255486:Q990L;ENSP00000338785:Q998L	ENSP00000255486:Q990L	Q	-	2	0	STARD13	32582064	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	7.950000	0.87804	2.240000	0.73641	0.533000	0.62120	CAG	.	.	none		0.527	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466		A	33684064	T	A	33684064	3	1	46	1	0	0	0	0	1	0	0	0	15271	1580	55	5	360	5	STARD13	13	33684064	Missense_Mutation	SNP	T	TCGA-RQ-A6JB-01A-11D-A31X-10		33684064	81485814	50	15707											
RNASE4	6038	hgsc.bcm.edu	37	chr14	21167775	21167775	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgaagatatctggaacattcGtagtatctgcagcaccacca	13	10	8	10	1	2	2	0	1	2	1	3	3	2	3	2	1	3	4	2	1	5	4			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr14:21167775G>A	ENST00000555835.1	+	2	921	c.245G>A	c.(244-246)cGt>cAt	p.R82H	AL163636.6_ENST00000553909.1_3'UTR|RNASE4_ENST00000304704.4_Missense_Mutation_p.R82H|RNASE4_ENST00000397995.2_Missense_Mutation_p.R82H|RP11-903H12.3_ENST00000554286.1_RNA|RNASE4_ENST00000555597.1_Missense_Mutation_p.R82H	NM_002937.3	NP_002928.1	P34096	RNAS4_HUMAN	ribonuclease, RNase A family, 4	82					cellular response to starvation (GO:0009267)|mRNA cleavage (GO:0006379)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	nucleic acid binding (GO:0003676)|pancreatic ribonuclease activity (GO:0004522)			central_nervous_system(1)|large_intestine(1)|lung(3)|skin(1)	6	all_cancers(95;0.00304)		Epithelial(56;5.13e-07)|all cancers(55;4.73e-06)	GBM - Glioblastoma multiforme(265;0.0133)		TGGAACATTCGTAGTATCTGC	0.463																																					p.R82H	Esophageal Squamous(59;1059 1362 26290 51151)	Atlas-SNP	.											RNASE4,caecum,carcinoma,+1,2	RNASE4	18	2	0			c.G245A						PASS	.						165	134	145					14																	21167775		2203	4300	6503	SO:0001583	missense	6038	exon2			ACATTCGTAGTAT	U36775	CCDS9555.1	14q11	2014-07-16			ENSG00000258818	ENSG00000258818		"Ribonucleases, RNase A"	10047	protein-coding gene	gene with protein product		601030				7501448	Standard	NM_002937		Approved		uc001vxy.4	P34096	OTTHUMG00000029575	ENST00000555835.1:c.245G>A	14.37:g.21167775G>A	ENSP00000452245:p.Arg82His	36	0	0		34	8	0.235294	NM_002937		Missense_Mutation	SNP	ENST00000555835.1	37	CCDS9555.1	.	.	.	.	.	.	.	.	.	.	G	12.72	2.021831	0.35701	.	.	ENSG00000258818;ENSG00000258818;ENSG00000258818;ENSG00000181784;ENSG00000181784;ENSG00000181784	ENST00000555835;ENST00000397995;ENST00000555597;ENST00000398001;ENST00000304704;ENST00000397999	T;T;T;T;T;T	0.73469	-0.75;-0.75;-0.75;-0.75;-0.75;-0.75	5.81	-3.72	0.04411	Ribonuclease A, domain (4);	0.988640	0.08242	N	0.975881	T	0.61689	0.2367	L	0.48877	1.53	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.52193	-0.8608	10	0.56958	D	0.05	-2.1766	4.7289	0.12955	0.4995:0.0:0.2424:0.2581	.	82	P34096	RNAS4_HUMAN	H	82	ENSP00000452245:R82H;ENSP00000381081:R82H;ENSP00000451624:R82H;ENSP00000381087:R82H;ENSP00000307096:R82H;ENSP00000381085:R82H	ENSP00000307096:R82H	R	+	2	0	AL163636.2;RNASE4	20237615	0.000000	0.05858	0.001000	0.08648	0.915000	0.54546	-0.828000	0.04419	-0.537000	0.06290	-0.899000	0.02877	CGT	.	.	none		0.463	RNASE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073729.3			A	21167775	G	A	21167775	3	1	46	1	0	0	0	0	1	0	0	0	13421	1145	40	1	247	1	RNASE4	14	21167775	Missense_Mutation	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10		21167775	86181765	51	15708											
CIDEB	27141	hgsc.bcm.edu	37	chr14	24775219	24775219	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	agtagagcccgtagaatgtgGctttgacattcaggctgcca	10	10	12	9	1	1	3	1	1	0	2	1	3	1	3	2	2	2	4	2	2	3	4			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr14:24775219G>A	ENST00000336557.5	-	7	1763	c.461C>T	c.(460-462)gCc>gTc	p.A154V	LTB4R2_ENST00000528054.1_5'Flank|CIDEB_ENST00000258807.5_Missense_Mutation_p.A154V|NOP9_ENST00000267425.3_3'UTR|CIDEB_ENST00000554411.1_Missense_Mutation_p.A154V			Q9UHD4	CIDEB_HUMAN	cell death-inducing DFFA-like effector b	154					apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|regulation of apoptotic process (GO:0042981)	cytosol (GO:0005829)|lipid particle (GO:0005811)	identical protein binding (GO:0042802)			NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|urinary_tract(1)	7				GBM - Glioblastoma multiforme(265;0.0181)		GTAGAATGTGGCTTTGACATT	0.512																																					p.A154V		Atlas-SNP	.											.	CIDEB	17	.	0			c.C461T						PASS	.						160	146	151					14																	24775219		2203	4300	6503	SO:0001583	missense	27141	exon6			AATGTGGCTTTGA	AF190901	CCDS32056.1	14q12	2012-09-20			ENSG00000136305	ENSG00000136305			1977	protein-coding gene	gene with protein product		604441				10619428, 10837461	Standard	XM_005267540		Approved		uc001woo.3	Q9UHD4	OTTHUMG00000171555	ENST00000336557.5:c.461C>T	14.37:g.24775219G>A	ENSP00000337731:p.Ala154Val	60	0	0		65	23	0.353846	NM_014430	D3DS73|Q546V8|Q9NNW9	Missense_Mutation	SNP	ENST00000336557.5	37	CCDS32056.1	.	.	.	.	.	.	.	.	.	.	G	34	5.325029	0.95708	.	.	ENSG00000136305	ENST00000554411;ENST00000336557;ENST00000258807;ENST00000541830	D;D;D	0.84516	-1.86;-1.86;-1.86	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	D	0.92838	0.7722	M	0.84082	2.675	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.93644	0.6967	10	0.87932	D	0	-23.741	17.4084	0.87480	0.0:0.0:1.0:0.0	.	154	Q9UHD4	CIDEB_HUMAN	V	154	ENSP00000451089:A154V;ENSP00000337731:A154V;ENSP00000258807:A154V	ENSP00000258807:A154V	A	-	2	0	CIDEB	23845059	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.787000	0.75099	2.654000	0.90174	0.563000	0.77884	GCC	.	.	none		0.512	CIDEB-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414120.1			A	24775219	G	A	24775219	3	1	46	1	0	0	0	0	1	0	0	0	3428	1203	42	2	206	2	CIDEB	14	24775219	Missense_Mutation	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10	3607444	24775219	82574321	52	15709											
B2M	567	hgsc.bcm.edu	37	chr15	45007714	45007714	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtctgggtttcatccatccgAcattgaagttgacttactga	9	14	9	9	1	2	3	1	3	1	0	4	4	4	3	2	1	1	2	2	1	2	4			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr15:45007714A>T	ENST00000558401.1	+	2	231	c.161A>T	c.(160-162)gAc>gTc	p.D54V	B2M_ENST00000544417.1_Missense_Mutation_p.D54V|B2M_ENST00000559220.1_Intron|B2M_ENST00000559916.1_Missense_Mutation_p.D54V	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	54	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 exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|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 T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|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)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		CATCCATCCGACATTGAAGTT	0.413																																					p.D54V		Atlas-SNP	.											B2M,bladder,carcinoma,+1,1	B2M	99	1	0			c.A161T						scavenged	.						183	188	186					15																	45007714		2198	4298	6496	SO:0001583	missense	567	exon2			CATCCGACATTGA	AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"Immunoglobulin superfamily / C1-set domain containing"	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.161A>T	15.37:g.45007714A>T	ENSP00000452780:p.Asp54Val	106	1	0.00943396		67	35	0.522388	NM_004048	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Missense_Mutation	SNP	ENST00000558401.1	37	CCDS10113.1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.124893	0.77436	.	.	ENSG00000166710	ENST00000349264;ENST00000544417;ENST00000396754	T	0.03212	4.01	6.03	6.03	0.97812	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.936939	0.09208	N	0.833609	T	0.08891	0.0220	N	0.20328	0.56	0.20307	N	0.999913	P;P;P	0.50369	0.821;0.781;0.934	P;P;P	0.58331	0.6;0.721;0.837	T	0.49234	-0.8961	10	0.87932	D	0	.	12.95	0.58394	1.0:0.0:0.0:0.0	.	54;54;54	F5H6I0;A6XMH4;P61769	.;.;B2MG_HUMAN	V	54	ENSP00000437604:D54V	ENSP00000340858:D54V	D	+	2	0	B2M	42795006	0.302000	0.24454	0.009000	0.14445	0.002000	0.02628	5.095000	0.64529	2.308000	0.77769	0.533000	0.62120	GAC	.	.	none		0.413	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048		T	45007714	A	T	45007714	3	4	46	1	0	0	0	0	1	0	0	0	1244	275	10	5	167	5	B2M	15	45007714	Missense_Mutation	SNP	A	TCGA-RQ-A6JB-01A-11D-A31X-10		45007714	57523678	53	15710											
B2M	567	hgsc.bcm.edu	37	chr15	45007809	45007809	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actggtctttctatctcttgTactacactgaattcaccccc	8	15	4	14	0	4	1	1	1	3	0	5	1	4	1	2	1	2	1	2	1	4	6			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr15:45007809T>G	ENST00000558401.1	+	2	326	c.256T>G	c.(256-258)Tac>Gac	p.Y86D	B2M_ENST00000544417.1_Missense_Mutation_p.Y86D|B2M_ENST00000559220.1_Intron|B2M_ENST00000559916.1_Missense_Mutation_p.Y86D	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	86	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 exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|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 T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|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)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)	p.Y86N(1)		breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		CTATCTCTTGTACTACACTGA	0.423																																					p.Y86D		Atlas-SNP	.											B2M,NS,lymphoid_neoplasm,-2,2	B2M	99	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.T256G						scavenged	.						172	169	170					15																	45007809		2198	4298	6496	SO:0001583	missense	567	exon2			CTCTTGTACTACA	AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"Immunoglobulin superfamily / C1-set domain containing"	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.256T>G	15.37:g.45007809T>G	ENSP00000452780:p.Tyr86Asp	147	1	0.00680272		98	56	0.571429	NM_004048	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Missense_Mutation	SNP	ENST00000558401.1	37	CCDS10113.1	.	.	.	.	.	.	.	.	.	.	T	15.60	2.880536	0.51801	.	.	ENSG00000166710	ENST00000349264;ENST00000544417;ENST00000396754	T	0.02709	4.19	6.03	0.942	0.19525	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.726338	0.14242	N	0.332034	T	0.02970	0.0088	N	0.08118	0	0.09310	N	0.999997	P;P	0.51537	0.946;0.57	P;P	0.56042	0.79;0.708	T	0.45920	-0.9228	10	0.59425	D	0.04	.	4.1475	0.10222	0.222:0.0:0.486:0.292	.	86;86	F5H6I0;P61769	.;B2MG_HUMAN	D	86	ENSP00000437604:Y86D	ENSP00000340858:Y86D	Y	+	1	0	B2M	42795101	0.992000	0.36948	0.077000	0.20336	0.001000	0.01503	2.183000	0.42565	-0.061000	0.13110	-1.392000	0.01152	TAC	.	.	none		0.423	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048		G	45007809	T	G	45007809	3	3	46	1	0	0	0	0	1	0	0	0	1244	1638	57	5	262	5	B2M	15	45007809	Missense_Mutation	SNP	T	TCGA-RQ-A6JB-01A-11D-A31X-10	95	45007809	57523583	54	15711											
RASL12	51285	hgsc.bcm.edu	37	chr15	65347441	65347441	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggggcagggccctctcctcGgagatgaagaggggccgggt	6	6	19	10	2	1	3	0	1	1	2	3	4	1	3	3	7	0	1	3	7	1	0			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr15:65347441G>A	ENST00000220062.4	-	5	873	c.597C>T	c.(595-597)tcC>tcT	p.S199S	RASL12_ENST00000434605.2_Silent_p.S188S|RASL12_ENST00000421977.3_Silent_p.S180S	NM_016563.2	NP_057647.1	Q9NYN1	RASLC_HUMAN	RAS-like, family 12	199					GTP catabolic process (GO:0006184)|small GTPase mediated signal transduction (GO:0007264)	membrane (GO:0016020)	GTP binding (GO:0005525)			lung(1)|ovary(1)|skin(1)|urinary_tract(1)	4						CCCTCTCCTCGGAGATGAAGA	0.662																																					p.S199S		Atlas-SNP	.											.	RASL12	32	.	0			c.C597T						PASS	.						15	16	16					15																	65347441		2200	4298	6498	SO:0001819	synonymous_variant	51285	exon5			CTCCTCGGAGATG	AF233588	CCDS10200.1	15q11.2-q22.33	2014-05-09			ENSG00000103710	ENSG00000103710			30289	protein-coding gene	gene with protein product	"Ras family member Ris"					12107412	Standard	NM_016563		Approved	RIS	uc002aoi.1	Q9NYN1	OTTHUMG00000133115	ENST00000220062.4:c.597C>T	15.37:g.65347441G>A		33	0	0		49	16	0.326531	NM_016563	B2RC29|B4DJW2|B4DU82	Silent	SNP	ENST00000220062.4	37	CCDS10200.1																																																																																			.	.	none		0.662	RASL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256782.2	NM_016563		A	65347441	G	A	65347441	2	1	46	1	0	0	0	0	0	0	0	1	13098	1103	39	1		1	RASL12	15	65347441	Silent	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10	20339632	65347441	37183951	55	15712											
HYDIN	54768	hgsc.bcm.edu	37	chr16	70989411	70989411	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tcgatgctcaggcaggctgcGttgtagtacttggccacgct	6	11	13	11	3	1	0	1	0	0	0	2	1	1	0	1	3	3	7	1	3	2	4	rs375756894	byFrequency	TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr16:70989411G>A	ENST00000393567.2	-	40	6333	c.6183C>T	c.(6181-6183)aaC>aaT	p.N2061N		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2061					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)				GGCAGGCTGCGTTGTAGTACT	0.552													G|||	2	0.000399361	0.0008	0.0	5008	,	,		19316	0.0		0.001	False		,,,				2504	0.0				p.N2061N		Atlas-SNP	.											.	HYDIN	788	.	0			c.C6183T						PASS	.	G		2,3706		0,2,1852	24	22	23		6180	-8	0	16		23	2,8124		0,2,4061	no	coding-synonymous	HYDIN	NM_032821.2		0,4,5913	AA,AG,GG		0.0246,0.0539,0.0338		2060/5121	70989411	4,11830	1854	4063	5917	SO:0001819	synonymous_variant	54768	exon40			GGCTGCGTTGTAG	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.6183C>T	16.37:g.70989411G>A		47	0	0		39	12	0.307692	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Silent	SNP	ENST00000393567.2	37	CCDS59269.1																																																																																			.	.	weak		0.552	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			A	70989411	G	A	70989411	2	1	46	1	0	0	0	0	0	0	0	1	7476	1136	40	1		1	HYDIN	16	70989411	Silent	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10		70989411	19365342	56	15713											
IRF8	3394	hgsc.bcm.edu	37	chr16	85936784	85936784	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataatcaggaagtggatgccTccatttttaaggtaaagagc	14	11	10	6	0	1	1	1	0	0	1	2	3	2	3	2	3	2	1	2	3	5	5			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr16:85936784T>G	ENST00000268638.5	+	2	585	c.163T>G	c.(163-165)Tcc>Gcc	p.S55A	IRF8_ENST00000563180.1_Missense_Mutation_p.S55A	NM_002163.2	NP_002154.1	Q02556	IRF8_HUMAN	interferon regulatory factor 8	55					cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)	p.S55A(1)		breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	24		Prostate(104;0.0771)				AGTGGATGCCTCCATTTTTAA	0.483																																					p.S55A		Atlas-SNP	.											IRF8,lymph_node,lymphoid_neoplasm,0,1	IRF8	65	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.T163G						PASS	.						74	70	71					16																	85936784		2198	4300	6498	SO:0001583	missense	3394	exon2			GATGCCTCCATTT	M91196	CCDS10956.1	16q24.1	2014-09-17	2004-11-12	2004-11-12	ENSG00000140968	ENSG00000140968			5358	protein-coding gene	gene with protein product		601565	"interferon consensus sequence binding protein 1"	ICSBP1		1460054, 11997525	Standard	NM_002163		Approved	IRF-8, ICSBP	uc002fjh.3	Q02556	OTTHUMG00000137648	ENST00000268638.5:c.163T>G	16.37:g.85936784T>G	ENSP00000268638:p.Ser55Ala	75	0	0		88	69	0.784091	NM_002163	A0AV82	Missense_Mutation	SNP	ENST00000268638.5	37	CCDS10956.1	.	.	.	.	.	.	.	.	.	.	T	4.129	0.022168	0.08006	.	.	ENSG00000140968	ENST00000268638	D	0.97598	-4.45	5.58	5.58	0.84498	Interferon regulatory factor, conserved site (1);Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (4);	0.112568	0.64402	D	0.000006	D	0.89378	0.6698	N	0.00738	-1.235	0.80722	D	1	B;B	0.30973	0.302;0.041	B;B	0.43728	0.429;0.023	D	0.87510	0.2439	10	0.02654	T	1	-37.9646	11.4255	0.50007	0.0:0.0:0.1508:0.8491	.	55;55	B2R8V7;Q02556	.;IRF8_HUMAN	A	55	ENSP00000268638:S55A	ENSP00000268638:S55A	S	+	1	0	IRF8	84494285	1.000000	0.71417	0.997000	0.53966	0.596000	0.36781	3.823000	0.55715	2.122000	0.65172	0.454000	0.30748	TCC	.	.	none		0.483	IRF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269100.2	NM_002163		G	85936784	T	G	85936784	3	3	46	1	0	0	0	0	1	0	0	0	7845	1551	54	5	165	5	IRF8	16	85936784	Missense_Mutation	SNP	T	TCGA-RQ-A6JB-01A-11D-A31X-10	14947373	85936784	4417969	57	15714											
KRTAP4-5	85289	hgsc.bcm.edu	37	chr17	39305774	39305775	+	In_Frame_Ins	INS	-	-	TGGCAGCAGCTGGGG																															tggtcctgcagcaggtggtcINStggcagcagcaggggcggca																								rs137947981|rs535144703|rs141265645|rs58117746	byFrequency	TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	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	1	Substitution - Missense(1)	lung(1)	c.246_247insCCCCAGCTGCTGCCA						PASS	.																																			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	17.37:g.39305774_39305775insTGGCAGCAGCTGGGG	ENSP00000340546:p.Cys81_Gln82insHisProSerCysCys	46	0	0		45	25	0.555556	NM_033188		In_Frame_Ins	INS	ENST00000343246.4	37	CCDS32650.1																																																																																			.	.	none		0.653	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1			TGGCAGCAGCTGGGG	39305775	-	TGGCAGCAGCTGGGG	39305774	7	5	46	1	0	1	1	0	0	0	0	0	8563	912	32	0	303	0	KRTAP4-5	17	39305774	In_Frame_Ins	INS	-	TCGA-RQ-A6JB-01A-11D-A31X-10		39305774	41889436	58	15715											
STAT3	6774	hgsc.bcm.edu	37	chr17	40475061	40475063	+	In_Frame_Del	DEL	CTT	CTT	-																															ccaagtgaaagtgacgcctcCttctttgctgctttcactga																										TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr17:40475061_40475063delCTT	ENST00000264657.5	-	20	2159_2161	c.1847_1849delAAG	c.(1846-1851)gaagga>gga	p.E616del	STAT3_ENST00000588969.1_In_Frame_Del_p.E616del|STAT3_ENST00000389272.3_In_Frame_Del_p.E518del|STAT3_ENST00000404395.3_In_Frame_Del_p.E616del|STAT3_ENST00000585517.1_In_Frame_Del_p.E616del	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)	616	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)		GTGACGCCTCCTTCTTTGCTGCT	0.562									Hyperimmunoglobulin E Recurrent Infection Syndrome		OREG0024421	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.616_617del		Pindel,Atlas-Indel	.											.	STAT3	268	.	0			c.1848_1850del						PASS	.																																			SO:0001651	inframe_deletion	6774	exon20	Familial Cancer Database	HIES, Hyper IgE syndrome, autosomal dominant (Job syndrome) / recessive	.	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.1847_1849delAAG	17.37:g.40475064_40475066delCTT	ENSP00000264657:p.Glu616del	0	0	.	893	16	16	1	NM_003150	A8K7B8|K7ENL3|O14916|Q9BW54	In_Frame_Del	DEL	ENST00000264657.5	37	CCDS32656.1																																																																																			.	.	none		0.562	STAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319353.3	NM_139276, NM_003150		-	40475063	CTT	-	40475061	7	5	46	1	0	1	0	1	0	0	0	0	15281	690	24	0	483	0	STAT3	17	40475061	In_Frame_Del	DEL	CTT	TCGA-RQ-A6JB-01A-11D-A31X-10	1169287	40475061	40720149	59	15716											
DNAH17	8632	hgsc.bcm.edu	37	chr17	76567366	76567366	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtcacaggctcaccttcaGtgacgttggtgtaaacgttt	8	12	12	9	2	3	1	3	1	0	0	3	1	3	1	1	3	1	4	1	3	2	4			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr17:76567366G>A	ENST00000585328.1	-	5	951	c.827C>T	c.(826-828)aCt>aTt	p.T276I	DNAH17_ENST00000389840.5_Missense_Mutation_p.T276I	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	276	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)			CTCACCTTCAGTGACGTTGGT	0.517																																					p.T276I		Atlas-SNP	.											.	DNAH17	347	.	0			c.C827T						PASS	.						80	82	82					17																	76567366		2151	4244	6395	SO:0001583	missense	8632	exon5			CCTTCAGTGACGT	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.827C>T	17.37:g.76567366G>A	ENSP00000465516:p.Thr276Ile	127	0	0		157	64	0.407643	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	37		.	.	.	.	.	.	.	.	.	.	G	10.10	1.258295	0.23051	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.57107	0.42	4.31	2.14	0.27477	.	.	.	.	.	T	0.38746	0.1052	N	0.24115	0.695	0.23371	N	0.997811	.	.	.	.	.	.	T	0.21621	-1.0240	7	0.35671	T	0.21	.	6.7434	0.23449	0.0:0.3411:0.4984:0.1605	.	.	.	.	I	276	ENSP00000374490:T276I	ENSP00000300671:T276I	T	-	2	0	DNAH17	74078961	0.326000	0.24669	0.376000	0.26042	0.015000	0.08874	0.724000	0.25954	2.115000	0.64714	0.561000	0.74099	ACT	.	.	none		0.517	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		A	76567366	G	A	76567366	3	1	46	1	0	0	0	0	1	0	0	0	4603	1029	36	2	12869	2	DNAH17	17	76567366	Missense_Mutation	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10	36092305	76567366	4627844	60	15717											
CDH2	1000	hgsc.bcm.edu	37	chr18	25583075	25583075	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	acgattctgtacctcaacatCccattgagggcattgggatc	10	11	9	11	1	2	1	1	1	1	0	4	3	3	2	2	2	2	2	2	2	2	4			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr18:25583075C>T	ENST00000269141.3	-	7	1329	c.906G>A	c.(904-906)ggG>ggA	p.G302G	CDH2_ENST00000399380.3_Silent_p.G271G	NM_001792.3	NP_001783.2	P19022	CADH2_HUMAN	cadherin 2, type 1, N-cadherin (neuronal)	302	Cadherin 2. {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						ACCTCAACATCCCATTGAGGG	0.458																																					p.G302G		Atlas-SNP	.											CDH2,right_upper_lobe,carcinoma,-1,2	CDH2	194	2	0			c.G906A						scavenged	.						235	171	193					18																	25583075		2203	4300	6503	SO:0001819	synonymous_variant	1000	exon7			CAACATCCCATTG	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.906G>A	18.37:g.25583075C>T		148	1	0.00675676		107	41	0.383178	NM_001792	A8MWK3|B0YIY6|Q14923|Q8N173	Silent	SNP	ENST00000269141.3	37	CCDS11891.1																																																																																			.	.	none		0.458	CDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133246.3	NM_001792		T	25583075	C	T	25583075	2	4	46	1	0	0	0	0	0	0	0	1	3107	842	30	2		2	CDH2	18	25583075	Silent	SNP	C	TCGA-RQ-A6JB-01A-11D-A31X-10		25583075	52494173	61	15718											
APBA3	9546	hgsc.bcm.edu	37	chr19	3751204	3751204	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacctcgccataggcctcggTgagcagctcgatgatgcggg	7	7	14	13	4	0	2	0	2	0	0	3	3	0	2	3	3	3	2	3	3	1	1			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr19:3751204T>G	ENST00000316757.3	-	10	1839	c.1639A>C	c.(1639-1641)Acc>Ccc	p.T547P	AC005954.4_ENST00000586503.1_RNA	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	547	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)		TAGGCCTCGGTGAGCAGCTCG	0.706																																					p.T547P		Atlas-SNP	.											.	APBA3	28	.	0			c.A1639C						PASS	.						15	14	14					19																	3751204		2142	4234	6376	SO:0001583	missense	9546	exon10			CCTCGGTGAGCAG	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.1639A>C	19.37:g.3751204T>G	ENSP00000315136:p.Thr547Pro	55	0	0		33	10	0.30303	NM_004886	O60483|Q9UPZ2	Missense_Mutation	SNP	ENST00000316757.3	37	CCDS12110.1	.	.	.	.	.	.	.	.	.	.	T	11.98	1.801049	0.31869	.	.	ENSG00000011132	ENST00000316757	T	0.28069	1.63	4.68	3.66	0.41972	PDZ/DHR/GLGF (4);	0.126503	0.52532	D	0.000076	T	0.45558	0.1348	M	0.64997	1.995	0.47009	D	0.999282	D	0.76494	0.999	D	0.69824	0.966	T	0.37709	-0.9694	10	0.66056	D	0.02	.	5.0977	0.14742	0.1586:0.0873:0.0:0.7542	.	547	O96018	APBA3_HUMAN	P	547	ENSP00000315136:T547P	ENSP00000315136:T547P	T	-	1	0	APBA3	3702204	1.000000	0.71417	0.838000	0.33150	0.015000	0.08874	3.472000	0.53114	0.637000	0.30526	-0.441000	0.05720	ACC	.	.	none		0.706	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2			G	3751204	T	G	3751204	3	3	46	1	0	0	0	0	1	0	0	0	758	1696	59	5	96	5	APBA3	19	3751204	Missense_Mutation	SNP	T	TCGA-RQ-A6JB-01A-11D-A31X-10		3751204	55377779	62	15719											
PNPLA6	10908	hgsc.bcm.edu	37	chr19	7620541	7620541	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	gcattagaggaggcgggggtCcccgtggacctggtgggcgg	5	6	21	9	3	0	1	0	0	0	1	1	3	1	3	3	8	0	1	3	8	1	1	rs572115607		TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr19:7620541C>T	ENST00000221249.6	+	27	3302	c.2871C>T	c.(2869-2871)gtC>gtT	p.V957V	PNPLA6_ENST00000450331.3_Silent_p.V957V|PNPLA6_ENST00000414982.3_Silent_p.V1005V|PNPLA6_ENST00000545201.2_Silent_p.V930V|PNPLA6_ENST00000600737.1_Silent_p.V995V	NM_006702.4	NP_006693.3	Q8IY17	PLPL6_HUMAN	patatin-like phospholipase domain containing 6	996					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						AGGCGGGGGTCCCCGTGGACC	0.672													C|||	1	0.000199681	0.0008	0.0	5008	,	,		10953	0.0		0.0	False		,,,				2504	0.0				p.V1005V		Atlas-SNP	.											.	PNPLA6	163	.	0			c.C3015T						PASS	.						33	33	33					19																	7620541		2203	4300	6503	SO:0001819	synonymous_variant	10908	exon26			GGGGGTCCCCGTG	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.2871C>T	19.37:g.7620541C>T		70	0	0		84	36	0.428571	NM_001166111	A6NGQ0|B4DFB9|B7Z7T2|F5H5K9|J3KQS3|O60859|Q86W58|Q9UG58	Silent	SNP	ENST00000221249.6	37	CCDS32891.1																																																																																			.	.	none		0.672	PNPLA6-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459275.1	NM_006702		T	7620541	C	T	7620541	2	4	46	1	0	0	0	0	0	0	0	1	12178	842	30	2		2	PNPLA6	19	7620541	Silent	SNP	C	TCGA-RQ-A6JB-01A-11D-A31X-10	3869337	7620541	51508442	63	15720											
S1PR2	9294	hgsc.bcm.edu	37	chr19	10334795	10334795	+	Missense_Mutation	SNP	A	A	G																															tttgtagaggatcgggcaggAgtggacgggacaggcatagt																										TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr19:10334795A>G	ENST00000590320.1	-	2	897	c.787T>C	c.(787-789)Tcc>Ccc	p.S263P	CTD-2369P2.2_ENST00000317726.4_lincRNA	NM_004230.3	NP_004221.3	O95136	S1PR2_HUMAN	sphingosine-1-phosphate receptor 2	263					activation of MAPK activity (GO:0000187)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|positive regulation of cell proliferation (GO:0008284)|positive regulation of establishment of endothelial barrier (GO:1903142)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|G-protein coupled receptor binding (GO:0001664)|integrin binding (GO:0005178)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15						ATCGGGCAGGAGTGGACGGGA	0.602																																					p.S263P	Pancreas(194;229 3020 15179 45747)	Atlas-SNP	.											.	S1PR2	36	.	0			c.T787C						PASS	.						79	67	71					19																	10334795		2203	4300	6503	SO:0001583	missense	9294	exon2			GGCAGGAGTGGAC	AF034780	CCDS12229.1	19q13	2013-03-13	2008-04-30	2008-04-30	ENSG00000267534	ENSG00000267534		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"	3169	protein-coding gene	gene with protein product		605111	"endothelial differentiation, sphingolipid G-protein-coupled receptor, 5"	EDG5		8087418, 8878560	Standard	NM_004230		Approved	Gpcr13, H218, AGR16	uc002mnl.2	O95136	OTTHUMG00000180399	ENST00000590320.1:c.787T>C	19.37:g.10334795A>G	ENSP00000466933:p.Ser263Pro	40	0	0		18	8	0.444444	NM_004230	Q86UN8	Missense_Mutation	SNP	ENST00000590320.1	37	CCDS12229.1	.	.	.	.	.	.	.	.	.	.	A	7.551	0.662679	0.14645	.	.	ENSG00000175898	ENST00000317726	.	.	.	5.63	-11.3	0.00108	GPCR, rhodopsin-like superfamily (1);	0.999489	0.08097	N	0.998495	T	0.23289	0.0563	N	0.13352	0.335	0.19775	N	0.999952	B	0.27316	0.175	B	0.31869	0.137	T	0.40136	-0.9579	9	0.12766	T	0.61	.	17.8161	0.88634	0.8127:0.1317:0.0:0.0557	.	263	O95136	S1PR2_HUMAN	P	263	.	ENSP00000322049:S263P	S	-	1	0	S1PR2	10195795	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-3.435000	0.00472	-2.793000	0.00355	-0.319000	0.08680	TCC	.	.	none		0.602	S1PR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451194.1	NM_004230		G	10334795	A	G	10334795	3	3	46	1	0	0	0	0	1	0	0	0	13809	304	11	3	278	3	S1PR2	19	10334795	Missense_Mutation	SNP	A	TCGA-RQ-A6JB-01A-11D-A31X-10	2714254	10334795	48794188	64	15721	206	2									
S1PR2	9294	hgsc.bcm.edu	37	chr19	10334796	10334796	+	Missense_Mutation	SNP	G	G	T																															ttgtagaggatcgggcaggaGtggacgggacaggcatagtc																										TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr19:10334796G>T	ENST00000590320.1	-	2	896	c.786C>A	c.(784-786)caC>caA	p.H262Q	CTD-2369P2.2_ENST00000317726.4_lincRNA	NM_004230.3	NP_004221.3	O95136	S1PR2_HUMAN	sphingosine-1-phosphate receptor 2	262					activation of MAPK activity (GO:0000187)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|positive regulation of cell proliferation (GO:0008284)|positive regulation of establishment of endothelial barrier (GO:1903142)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|G-protein coupled receptor binding (GO:0001664)|integrin binding (GO:0005178)|lipid binding (GO:0008289)|sphingosine-1-phosphate receptor activity (GO:0038036)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15						TCGGGCAGGAGTGGACGGGAC	0.597																																					p.H262Q	Pancreas(194;229 3020 15179 45747)	Atlas-SNP	.											.	S1PR2	36	.	0			c.C786A						PASS	.						79	67	71					19																	10334796		2203	4300	6503	SO:0001583	missense	9294	exon2			GCAGGAGTGGACG	AF034780	CCDS12229.1	19q13	2013-03-13	2008-04-30	2008-04-30	ENSG00000267534	ENSG00000267534		"GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"	3169	protein-coding gene	gene with protein product		605111	"endothelial differentiation, sphingolipid G-protein-coupled receptor, 5"	EDG5		8087418, 8878560	Standard	NM_004230		Approved	Gpcr13, H218, AGR16	uc002mnl.2	O95136	OTTHUMG00000180399	ENST00000590320.1:c.786C>A	19.37:g.10334796G>T	ENSP00000466933:p.His262Gln	40	0	0		18	8	0.444444	NM_004230	Q86UN8	Missense_Mutation	SNP	ENST00000590320.1	37	CCDS12229.1	.	.	.	.	.	.	.	.	.	.	G	5.422	0.263065	0.10294	.	.	ENSG00000175898	ENST00000317726	.	.	.	5.63	-9.3	0.00649	GPCR, rhodopsin-like superfamily (1);	0.279293	0.32068	N	0.006628	T	0.15176	0.0366	N	0.11673	0.155	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.12811	-1.0533	9	0.36615	T	0.2	.	8.6306	0.33917	0.1406:0.6179:0.1056:0.136	.	262	O95136	S1PR2_HUMAN	Q	262	.	ENSP00000322049:H262Q	H	-	3	2	S1PR2	10195796	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	-2.194000	0.01243	-0.667000	0.05303	-0.141000	0.14075	CAC	.	.	none		0.597	S1PR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451194.1	NM_004230		T	10334796	G	T	10334796	3	4	46	1	0	0	0	0	1	0	0	0	13809	1020	36	4	279	4	S1PR2	19	10334796	Missense_Mutation	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10	1	10334796	48794187	65	15722	206	2									
ZNF709	163051	hgsc.bcm.edu	37	chr19	12577645	12577645	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggtgaagttcacagccacaTcctcaaagaccactgagtcc	12	7	9	13	0	2	3	2	2	0	1	4	3	4	3	4	1	1	1	4	1	2	1			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr19:12577645T>C	ENST00000397732.3	-	2	194	c.23A>G	c.(22-24)gAt>gGt	p.D8G	CTD-3105H18.18_ENST00000598753.1_Missense_Mutation_p.D8G|ZNF709_ENST00000428311.1_Missense_Mutation_p.D8G	NM_152601.3	NP_689814.1	Q8N972	ZN709_HUMAN	zinc finger protein 709	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)			large_intestine(3)|upper_aerodigestive_tract(3)	6						CACAGCCACATCCTCAAAGAC	0.473																																					p.D8G	GBM(33;565 669 12371 29134 51667)	Atlas-SNP	.											.	ZNF709	80	.	0			c.A23G						PASS	.						92	93	93					19																	12577645		2203	4300	6503	SO:0001583	missense	163051	exon2			GCCACATCCTCAA	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.23A>G	19.37:g.12577645T>C	ENSP00000380840:p.Asp8Gly	78	0	0		50	11	0.22	NM_152601	A8K4E6	Missense_Mutation	SNP	ENST00000397732.3	37	CCDS42504.1	.	.	.	.	.	.	.	.	.	.	T	18.00	3.525627	0.64860	.	.	ENSG00000242852;ENSG00000242852;ENSG00000196826	ENST00000397732;ENST00000455490;ENST00000428311	T;T;T	0.11930	2.73;2.73;2.73	3.09	3.09	0.35607	Krueppel-associated box (4);	0.000000	0.34828	N	0.003641	T	0.48624	0.1510	H	0.97465	4.01	0.34327	D	0.687282	D	0.89917	1.0	D	0.97110	1.0	T	0.70608	-0.4825	10	0.87932	D	0	.	9.6307	0.39778	0.0:0.0:0.0:1.0	.	8	Q8N972	ZN709_HUMAN	G	8;37;8	ENSP00000380840:D8G;ENSP00000398085:D37G;ENSP00000404127:D8G	ENSP00000404127:D8G	D	-	2	0	ZNF709;CTD-2192J16.17	12438645	0.989000	0.36119	1.000000	0.80357	0.994000	0.84299	1.442000	0.35046	1.660000	0.50760	0.402000	0.26972	GAT	.	.	none		0.473	ZNF709-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344088.1	NM_152601		C	12577645	T	C	12577645	3	2	46	1	0	0	0	0	1	0	0	0	18128	1435	50	3	1914	3	ZNF709	19	12577645	Missense_Mutation	SNP	T	TCGA-RQ-A6JB-01A-11D-A31X-10	2242849	12577645	46551338	66	15723											
DMKN	93099	hgsc.bcm.edu	37	chr19	36002421	36002422	+	In_Frame_Ins	INS	-	-	CTGCTGCTG																															tgctgccactgctgctgccaINSccactgctgctgccattgtt																								rs72334573	byFrequency	TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr19:36002421_36002422insCTGCTGCTG	ENST00000339686.3	-	5	985_986	c.809_810insCAGCAGCAG	c.(808-810)ggt>ggCAGCAGCAGt	p.270_271insSSS	DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000418261.1_In_Frame_Ins_p.270_271insSSS|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000451297.2_In_Frame_Ins_p.270_271insSSS|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000440396.1_In_Frame_Ins_p.270_271insSSS|DMKN_ENST00000447113.2_In_Frame_Ins_p.270_271insSSS|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000424570.2_In_Frame_Ins_p.270_271insSSS|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000443640.1_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	270	Gly-rich.			Missing (in Ref. 3; ABN11273/ABN11274). {ECO:0000305}.		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)			tgctgctgccaccactgctgct	0.653																																					p.G270delinsGSSS		Atlas-Indel	.											DMKN,colon,carcinoma,0,1	DMKN	116	1	0			c.810_811insCAGCAGCAG						PASS	.																																			SO:0001652	inframe_insertion	93099	exon5			.	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.809_810insCAGCAGCAG	19.37:g.36002421_36002422insCTGCTGCTG	ENSP00000342012:p.Gly270_Gly271insSerSerSer	51	0	0		47	14	0.297872	NM_033317	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	In_Frame_Ins	INS	ENST00000339686.3	37	CCDS12463.1																																																																																			.	.	alt		0.653	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317		CTGCTGCTG	36002422	-	CTGCTGCTG	36002421	7	5	46	1	0	1	1	0	0	0	0	0	4584	146	6	0	985	0	DMKN	19	36002421	In_Frame_Ins	INS	-	TCGA-RQ-A6JB-01A-11D-A31X-10	23424776	36002421	23126562	67	15724											
ZC3H4	23211	hgsc.bcm.edu	37	chr19	47572412	47572412	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	cctcgctctctcctcctcctCctgctgcttctgctggatcc	1	14	6	20	1	2	0	0	0	2	0	9	1	7	1	6	1	3	4	6	1	0	1			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr19:47572412C>G	ENST00000253048.5	-	14	2372	c.2335G>C	c.(2335-2337)Gag>Cag	p.E779Q	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	779							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)		TCCTCCTCCTCCTGCTGCTTC	0.701																																					p.E779Q		Atlas-SNP	.											ZC3H4,colon,carcinoma,0,1	ZC3H4	96	1	0			c.G2335C						scavenged	.						60	69	66					19																	47572412		2082	4205	6287	SO:0001583	missense	23211	exon14			CCTCCTCCTGCTG	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.2335G>C	19.37:g.47572412C>G	ENSP00000253048:p.Glu779Gln	45	0	0		35	2	0.0571429	NM_015168	Q9Y420	Missense_Mutation	SNP	ENST00000253048.5	37	CCDS42582.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.765923	0.90020	.	.	ENSG00000130749	ENST00000253048	T	0.21361	2.01	5.03	5.03	0.67393	.	0.259884	0.30043	N	0.010552	T	0.41305	0.1153	L	0.48642	1.525	0.54753	D	0.999986	D	0.89917	1.0	D	0.83275	0.996	T	0.13202	-1.0518	10	0.56958	D	0.05	.	17.2939	0.87164	0.0:1.0:0.0:0.0	.	779	Q9UPT8	ZC3H4_HUMAN	Q	779	ENSP00000253048:E779Q	ENSP00000253048:E779Q	E	-	1	0	ZC3H4	52264252	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.347000	0.59373	2.619000	0.88677	0.491000	0.48974	GAG	.	.	none		0.701	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1			G	47572412	C	G	47572412	3	3	46	1	0	0	0	0	1	0	0	0	17585	864	30	4	1584	4	ZC3H4	19	47572412	Missense_Mutation	SNP	C	TCGA-RQ-A6JB-01A-11D-A31X-10	11569991	47572412	11556571	68	15725											
PEG3	5178	hgsc.bcm.edu	37	chr19	57327786	57327786	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttattgtaagttttctgaCgccttttaagggactgacca	9	15	8	9	1	1	2	0	2	1	0	1	3	1	3	3	1	0	2	3	1	3	7	rs371769465		TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr19:57327786C>G	ENST00000326441.9	-	10	2387	c.2024G>C	c.(2023-2025)cGt>cCt	p.R675P	ZIM2_ENST00000221722.5_Intron|ZIM2_ENST00000601070.1_Intron|ZIM2_ENST00000599935.1_Intron|ZIM2_ENST00000391708.3_Intron|ZIM2_ENST00000593711.1_Intron|PEG3_ENST00000423103.2_Missense_Mutation_p.R675P|PEG3_ENST00000598410.1_Missense_Mutation_p.R551P|PEG3_ENST00000593695.1_Missense_Mutation_p.R549P	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	675					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)		AGTTTTCTGACGCCTTTTAAG	0.423																																					p.R675P		Atlas-SNP	.											ZIM2_ENST00000326441,NS,carcinoma,0,4	PEG3	414	4	0			c.G2024C						PASS	.						106	108	107					19																	57327786		2203	4300	6503	SO:0001583	missense	5178	exon9			TTCTGACGCCTTT	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.2024G>C	19.37:g.57327786C>G	ENSP00000326581:p.Arg675Pro	198	0	0		181	8	0.0441989	NM_001146184	A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	37	CCDS12948.1	.	.	.	.	.	.	.	.	.	.	C	15.57	2.872774	0.51695	.	.	ENSG00000198300	ENST00000326441;ENST00000423103	T;T	0.02682	4.2;4.2	4.05	0.0115	0.14087	Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.662273	0.13428	N	0.388633	T	0.10165	0.0249	M	0.73962	2.25	.	.	.	D;D;D	0.71674	0.976;0.997;0.998	P;P;D	0.65323	0.706;0.902;0.934	T	0.10847	-1.0612	9	0.72032	D	0.01	-9.8771	6.8386	0.23951	0.0:0.4257:0.0:0.5743	.	551;675;610	A7E2B8;Q9GZU2;Q96Q96	.;PEG3_HUMAN;.	P	675	ENSP00000326581:R675P;ENSP00000403051:R675P	ENSP00000326581:R675P	R	-	2	0	ZIM2	62019598	0.746000	0.28272	0.080000	0.20451	0.673000	0.39480	0.972000	0.29409	0.072000	0.16694	0.585000	0.79938	CGT	.	.	alt		0.423	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			G	57327786	C	G	57327786	3	3	46	1	0	0	0	0	1	0	0	0	11729	536	19	4	2746	4	PEG3	19	57327786	Missense_Mutation	SNP	C	TCGA-RQ-A6JB-01A-11D-A31X-10	9755374	57327786	1801197	69	15726											
ZNF547	284306	hgsc.bcm.edu	37	chr19	57889497	57889497	+	Missense_Mutation	SNP	A	A	G																															agcagtgcagtgaatgtgggAaattctttaggtataactct																										TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr19:57889497A>G	ENST00000282282.3	+	4	1303	c.1153A>G	c.(1153-1155)Aaa>Gaa	p.K385E	AC003002.4_ENST00000597658.1_Intron	NM_173631.2	NP_775902.2	Q8IVP9	ZN547_HUMAN	zinc finger protein 547	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)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	12		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TGAATGTGGGAAATTCTTTAG	0.448																																					p.K385E		Atlas-SNP	.											ZNF547,NS,carcinoma,-1,1	ZNF547	45	1	0			c.A1153G						PASS	.						75	68	70					19																	57889497		2203	4300	6503	SO:0001583	missense	284306	exon4			TGTGGGAAATTCT	AK055662	CCDS33131.1	19q13.43	2013-01-08				ENSG00000152433		"Zinc fingers, C2H2-type", "-"	26432	protein-coding gene	gene with protein product							Standard	NM_173631		Approved	FLJ31100	uc002qol.3	Q8IVP9		ENST00000282282.3:c.1153A>G	19.37:g.57889497A>G	ENSP00000282282:p.Lys385Glu	63	0	0		73	20	0.273973	NM_173631	A8K5Z9|Q96NC4	Missense_Mutation	SNP	ENST00000282282.3	37	CCDS33131.1	.	.	.	.	.	.	.	.	.	.	A	15.64	2.893684	0.52121	.	.	ENSG00000152433	ENST00000282282	T	0.60040	0.22	1.81	1.81	0.25067	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.59128	0.2171	M	0.75447	2.3	0.22354	N	0.999175	P	0.50369	0.934	P	0.45660	0.489	T	0.51973	-0.8637	8	.	.	.	.	8.9234	0.35625	1.0:0.0:0.0:0.0	.	385	Q8IVP9	ZN547_HUMAN	E	385	ENSP00000282282:K385E	.	K	+	1	0	ZNF547	62581309	0.987000	0.35691	0.383000	0.26132	0.685000	0.39939	0.230000	0.17852	1.088000	0.41272	0.397000	0.26171	AAA	.	.	none		0.448	ZNF547-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465787.1	NM_173631		G	57889497	A	G	57889497	3	3	46	1	0	0	0	0	1	0	0	0	17994	247	9	3	1163	3	ZNF547	19	57889497	Missense_Mutation	SNP	A	TCGA-RQ-A6JB-01A-11D-A31X-10	561711	57889497	1239486	70	15727	207	2									
ZNF547	284306	hgsc.bcm.edu	37	chr19	57889498	57889498	+	Missense_Mutation	SNP	A	A	C																															gcagtgcagtgaatgtgggaAattctttaggtataactcta																										TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr19:57889498A>C	ENST00000282282.3	+	4	1304	c.1154A>C	c.(1153-1155)aAa>aCa	p.K385T	AC003002.4_ENST00000597658.1_Intron	NM_173631.2	NP_775902.2	Q8IVP9	ZN547_HUMAN	zinc finger protein 547	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)	p.K385R(1)		central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	12		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GAATGTGGGAAATTCTTTAGG	0.448																																					p.K385T		Atlas-SNP	.											ZNF547,NS,carcinoma,0,1	ZNF547	45	1	1	Substitution - Missense(1)	endometrium(1)	c.A1154C						PASS	.						75	68	70					19																	57889498		2203	4300	6503	SO:0001583	missense	284306	exon4			GTGGGAAATTCTT	AK055662	CCDS33131.1	19q13.43	2013-01-08				ENSG00000152433		"Zinc fingers, C2H2-type", "-"	26432	protein-coding gene	gene with protein product							Standard	NM_173631		Approved	FLJ31100	uc002qol.3	Q8IVP9		ENST00000282282.3:c.1154A>C	19.37:g.57889498A>C	ENSP00000282282:p.Lys385Thr	63	0	0		73	19	0.260274	NM_173631	A8K5Z9|Q96NC4	Missense_Mutation	SNP	ENST00000282282.3	37	CCDS33131.1	.	.	.	.	.	.	.	.	.	.	A	17.43	3.387608	0.61956	.	.	ENSG00000152433	ENST00000282282	T	0.60299	0.2	1.81	1.81	0.25067	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.75398	0.3844	M	0.92459	3.31	0.23144	N	0.998222	D	0.61697	0.99	P	0.58577	0.841	T	0.64300	-0.6440	8	.	.	.	.	8.9234	0.35625	1.0:0.0:0.0:0.0	.	385	Q8IVP9	ZN547_HUMAN	T	385	ENSP00000282282:K385T	.	K	+	2	0	ZNF547	62581310	0.988000	0.35896	0.327000	0.25402	0.678000	0.39670	0.685000	0.25378	1.088000	0.41272	0.397000	0.26171	AAA	.	.	none		0.448	ZNF547-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465787.1	NM_173631		C	57889498	A	C	57889498	3	2	46	1	0	0	0	0	1	0	0	0	17994	14	1	5	1164	5	ZNF547	19	57889498	Missense_Mutation	SNP	A	TCGA-RQ-A6JB-01A-11D-A31X-10	1	57889498	1239485	71	15728	207	2									
SALL4	57167	hgsc.bcm.edu	37	chr20	50408196	50408196	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttggcttccagctttctggcTgagcaaagccacagctgcag	8	10	11	12	0	1	1	0	1	1	0	2	1	2	1	2	2	5	6	2	2	1	3			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr20:50408196T>G	ENST00000217086.4	-	2	937	c.826A>C	c.(826-828)Agc>Cgc	p.S276R	SALL4_ENST00000395997.3_Missense_Mutation_p.S276R|SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000371539.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	276					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						GCTTTCTGGCTGAGCAAAGCC	0.607																																					p.S276R		Atlas-SNP	.											.	SALL4	168	.	0			c.A826C						PASS	.						53	44	47					20																	50408196		2203	4300	6503	SO:0001583	missense	57167	exon2			TCTGGCTGAGCAA	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.826A>C	20.37:g.50408196T>G	ENSP00000217086:p.Ser276Arg	41	0	0		29	8	0.275862	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Missense_Mutation	SNP	ENST00000217086.4	37	CCDS13438.1	.	.	.	.	.	.	.	.	.	.	T	17.81	3.481871	0.63849	.	.	ENSG00000101115	ENST00000217086;ENST00000395997	T;T	0.70631	-0.5;-0.5	5.29	4.17	0.49024	.	0.116249	0.39759	N	0.001276	T	0.65302	0.2678	M	0.80028	2.48	0.80722	D	1	P;P	0.47302	0.893;0.744	B;B	0.39068	0.289;0.289	T	0.71199	-0.4663	10	0.87932	D	0	-37.3797	3.3042	0.06993	0.0:0.3594:0.0:0.6406	.	276;276	A2A2D8;Q9UJQ4	.;SALL4_HUMAN	R	276	ENSP00000217086:S276R;ENSP00000379319:S276R	ENSP00000217086:S276R	S	-	1	0	SALL4	49841603	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.877000	0.63086	1.996000	0.58369	0.533000	0.62120	AGC	.	.	none		0.607	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3			G	50408196	T	G	50408196	3	3	46	1	0	0	0	0	1	0	0	0	13828	1580	55	5	2347	5	SALL4	20	50408196	Missense_Mutation	SNP	T	TCGA-RQ-A6JB-01A-11D-A31X-10		50408196	12617324	72	15729											
RNF160	26046	hgsc.bcm.edu	37	chr21	30365143	30365143	+	5'UTR	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccatggtcgcggttgcagctGtactctgagcactcagaccc	7	9	11	14	2	2	2	1	1	1	1	3	2	2	2	2	2	4	5	2	2	1	2			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chr21:30365143G>A	ENST00000361371.5	-	0	63				LTN1_ENST00000389194.2_Missense_Mutation_p.T41I|LTN1_ENST00000389195.2_Missense_Mutation_p.T41I			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1						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						GGTTGCAGCTGTACTCTGAGC	0.637																																					p.T41I		Atlas-SNP	.											.	LTN1	141	.	0			c.C122T						PASS	.						71	56	61					21																	30365143		2203	4300	6503	SO:0001623	5_prime_UTR_variant	26046	exon1			GCAGCTGTACTCT	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.-17C>T	21.37:g.30365143G>A		85	0	0		84	27	0.321429	NM_015565	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Missense_Mutation	SNP	ENST00000361371.5	37		.	.	.	.	.	.	.	.	.	.	G	11.79	1.744234	0.30865	.	.	ENSG00000198862	ENST00000389194;ENST00000389195	T;T	0.23950	2.24;1.88	4.49	-1.12	0.09808	.	.	.	.	.	T	0.11324	0.0276	N	0.14661	0.345	0.20196	N	0.999928	.	.	.	.	.	.	T	0.29852	-0.9998	7	0.26408	T	0.33	.	2.0606	0.03591	0.314:0.1198:0.4439:0.1224	.	.	.	.	I	41	ENSP00000373846:T41I;ENSP00000373847:T41I	ENSP00000373846:T41I	T	-	2	0	LTN1	29287014	0.000000	0.05858	0.004000	0.12327	0.011000	0.07611	-0.194000	0.09559	-0.140000	0.11394	-0.345000	0.07892	ACA	.	.	none		0.637	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000472108.1	NM_015565		A	30365143	G	A	30365143	1	1	46	0	1	0	0	0	0	0	0	0	13470	1377	48	2		2	RNF160	21	30365143	5'UTR	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10		30365143	17764752	73	15730											
CDKL5	6792	hgsc.bcm.edu	37	chrX	18671625	18671625	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	caggtaaaccaagctgcgctCctgacataccatgagaatgc	13	7	9	12	1	0	2	0	2	0	1	1	3	1	2	3	1	5	3	3	1	5	2			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chrX:18671625C>G	ENST00000379989.3	+	22	3339	c.3054C>G	c.(3052-3054)ctC>ctG	p.L1018L	RS1_ENST00000379984.3_Intron|CDKL5_ENST00000379996.3_Silent_p.L1018L|RS1_ENST00000476595.1_5'Flank	NM_001037343.1	NP_001032420.1	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	1018					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)					AAGCTGCGCTCCTGACATACC	0.547																																					p.L1018L		Atlas-SNP	.											.	CDKL5	124	.	0			c.C3054G						PASS	.						70	52	58					X																	18671625		2203	4300	6503	SO:0001819	synonymous_variant	6792	exon21			TGCGCTCCTGACA	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.3054C>G	X.37:g.18671625C>G		44	0	0		46	13	0.282609	NM_003159	G9B9X4|Q14198|Q5H985|Q8IYC7|Q9UJL6	Silent	SNP	ENST00000379989.3	37	CCDS14186.1																																																																																			.	.	none		0.547	CDKL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055945.2	NM_003159		G	18671625	C	G	18671625	2	3	46	1	0	0	0	0	0	0	0	1	3159	842	30	4		4	CDKL5	23	18671625	Silent	SNP	C	TCGA-RQ-A6JB-01A-11D-A31X-10		18671625	136598935	74	15731											
FAAH2	158584	hgsc.bcm.edu	37	chrX	57515299	57515299	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaccctttaatgatcatctGaccctggctgtggcccagta	8	11	10	12	0	2	2	1	2	1	0	2	3	2	3	3	3	0	2	3	3	2	3			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chrX:57515299G>T	ENST00000374900.4	+	11	1653	c.1533G>T	c.(1531-1533)ctG>ctT	p.L511L	FAAH2_ENST00000491179.1_3'UTR	NM_174912.3	NP_777572.2	Q6GMR7	FAAH2_HUMAN	fatty acid amide hydrolase 2	511						integral component of membrane (GO:0016021)	carbon-nitrogen ligase activity, with glutamine as amido-N-donor (GO:0016884)|hydrolase activity (GO:0016787)			endometrium(2)|large_intestine(4)|lung(10)|ovary(3)|upper_aerodigestive_tract(3)	22						ATGATCATCTGACCCTGGCTG	0.527										HNSCC(52;0.14)																											p.L511L		Atlas-SNP	.											.	FAAH2	66	.	0			c.G1533T						PASS	.						85	74	78					X																	57515299		2203	4300	6503	SO:0001819	synonymous_variant	158584	exon11			TCATCTGACCCTG	AK055766	CCDS14375.1	Xp11.1	2008-02-05	2006-11-24	2006-11-24	ENSG00000165591	ENSG00000165591			26440	protein-coding gene	gene with protein product		300654	"amidase domain containing"	AMDD		17015445	Standard	NM_174912		Approved	RP11-479E16.1, FLJ31204, FAAH-2	uc004dvc.3	Q6GMR7	OTTHUMG00000021684	ENST00000374900.4:c.1533G>T	X.37:g.57515299G>T		131	0	0		130	34	0.261538	NM_174912	Q86VT2|Q96N98	Silent	SNP	ENST00000374900.4	37	CCDS14375.1																																																																																			.	.	none		0.527	FAAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056919.1	NM_174912		T	57515299	G	T	57515299	2	4	46	1	0	0	0	0	0	0	0	1	5359	1277	45	4		4	FAAH2	23	57515299	Silent	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10	38843674	57515299	97755261	75	15732											
DACH2	117154	hgsc.bcm.edu	37	chrX	85403679	85403679	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cttccagcggcgccggcgtcCcggggggcttattccgggcc	2	7	16	16	6	0	0	0	0	0	0	3	0	3	0	5	6	1	1	5	6	1	3			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chrX:85403679C>T	ENST00000373125.4	+	1	55	c.55C>T	c.(55-57)Ccg>Tcg	p.P19S	DACH2_ENST00000373131.1_Missense_Mutation_p.P19S	NM_053281.3	NP_444511.1	Q96NX9	DACH2_HUMAN	dachshund family transcription factor 2	19					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						CGCCGGCGTCCCGGGGGGCTT	0.582																																					p.P19S		Atlas-SNP	.											.	DACH2	263	.	0			c.C55T						PASS	.						17	17	17					X																	85403679		2201	4291	6492	SO:0001583	missense	117154	exon1			GGCGTCCCGGGGG	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.55C>T	X.37:g.85403679C>T	ENSP00000362217:p.Pro19Ser	164	0	0		121	41	0.338843	NM_001139514	B1AJV3|B4DQG3|Q8NAY3|Q8ND17|Q96N55	Missense_Mutation	SNP	ENST00000373125.4	37	CCDS14455.1	.	.	.	.	.	.	.	.	.	.	C	1.400	-0.578490	0.03854	.	.	ENSG00000126733	ENST00000344497;ENST00000373131;ENST00000373125	D;T	0.81499	-1.5;-1.49	4.64	2.87	0.33458	.	0.669254	0.13433	N	0.388254	T	0.55337	0.1914	N	0.08118	0	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.001	T	0.37572	-0.9700	10	0.10377	T	0.69	.	3.1449	0.06468	0.0:0.4362:0.2055:0.3583	.	19;19	Q96NX9-2;Q96NX9	.;DACH2_HUMAN	S	19	ENSP00000362223:P19S;ENSP00000362217:P19S	ENSP00000345134:P19S	P	+	1	0	DACH2	85290335	0.011000	0.17503	0.888000	0.34837	0.009000	0.06853	0.048000	0.14078	0.409000	0.25649	-0.276000	0.10085	CCG	.	.	none		0.582	DACH2-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359266.1	NM_053281		T	85403679	C	T	85403679	3	4	46	1	0	0	0	0	1	0	0	0	4223	623	22	2	57	2	DACH2	23	85403679	Missense_Mutation	SNP	C	TCGA-RQ-A6JB-01A-11D-A31X-10	27888380	85403679	69866881	76	15733											
MAGEC1	9947	hgsc.bcm.edu	37	chrX	140995449	140995449	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tgctcctcctccacttctttGagtcttccccagagtttccc	4	15	5	17	0	2	2	0	1	2	1	7	2	7	2	6	0	1	2	6	0	0	4			TCGA-RQ-A6JB-01A-11D-A31X-10	TCGA-RQ-A6JB-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	820fd611-7c08-4a0a-8884-6d25954b28f4	47b47ec9-ab7b-47f1-b2f6-e76b3584891f	g.chrX:140995449G>A	ENST00000285879.4	+	4	2545	c.2259G>A	c.(2257-2259)ttG>ttA	p.L753L	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	753										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)					CCACTTCTTTGAGTCTTCCCC	0.552										HNSCC(15;0.026)																											p.L753L		Atlas-SNP	.											.	MAGEC1	317	.	0			c.G2259A						PASS	.						133	145	141					X																	140995449		2203	4300	6503	SO:0001819	synonymous_variant	9947	exon4			TTCTTTGAGTCTT	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.2259G>A	X.37:g.140995449G>A		52	0	0		49	17	0.346939	NM_005462	A0PK03|O75451|Q8TCV4	Silent	SNP	ENST00000285879.4	37	CCDS35417.1																																																																																			.	.	none		0.552	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462		A	140995449	G	A	140995449	2	1	46	1	0	0	0	0	0	0	0	1	9189	1281	45	2		2	MAGEC1	23	140995449	Silent	SNP	G	TCGA-RQ-A6JB-01A-11D-A31X-10	55591770	140995449	14275111	77	15734											
PLCH2	9651	hgsc.bcm.edu	37	chr1	2422698	2422698	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggattccctcatcaaagagtCgaagattcgggactgtgagg	11	9	13	8	2	2	3	2	1	0	2	5	6	3	5	1	3	0	0	1	3	2	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:2422698C>T	ENST00000419816.2	+	11	1857	c.1583C>T	c.(1582-1584)tCg>tTg	p.S528L	PLCH2_ENST00000378486.3_Missense_Mutation_p.S528L|PLCH2_ENST00000449969.1_Missense_Mutation_p.S501L|RP3-395M20.2_ENST00000424657.1_RNA|RP3-395M20.3_ENST00000442305.1_RNA|PLCH2_ENST00000288766.5_Intron|PLCH2_ENST00000378488.3_Missense_Mutation_p.S528L			O75038	PLCH2_HUMAN	phospholipase C, eta 2	528					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)		ATCAAAGAGTCGAAGATTCGG	0.542																																					p.S528L		Atlas-SNP	.											.	PLCH2	131	.	0			c.C1583T						PASS	.						83	91	88					1																	2422698		1982	4152	6134	SO:0001583	missense	9651	exon11			AAGAGTCGAAGAT	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.1583C>T	1.37:g.2422698C>T	ENSP00000389803:p.Ser528Leu	50	0	0		39	7	0.179487	NM_014638	A2VCM3|B9DI80|Q3LUA8|Q86XJ2|Q86XU1|Q86YU7|Q8TEH5|Q8WUS6	Missense_Mutation	SNP	ENST00000419816.2	37		.	.	.	.	.	.	.	.	.	.	C	18.90	3.722431	0.68959	.	.	ENSG00000149527	ENST00000449969;ENST00000378486;ENST00000378488;ENST00000343889;ENST00000278878	T;T;T	0.46451	0.87;0.87;0.87	5.03	4.1	0.47936	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (1);	0.329188	0.28871	N	0.013871	T	0.63177	0.2489	M	0.81341	2.54	0.80722	D	1	D;P;D;P	0.71674	0.998;0.949;0.996;0.865	P;B;P;B	0.62184	0.899;0.275;0.819;0.233	T	0.69139	-0.5224	10	0.66056	D	0.02	.	14.474	0.67535	0.0:0.8518:0.1482:0.0	.	375;316;501;528	B9DI81;B9DI82;O75038-2;O75038	.;.;.;PLCH2_HUMAN	L	501;528;528;375;316	ENSP00000397289:S501L;ENSP00000367747:S528L;ENSP00000367749:S528L	ENSP00000278878:S316L	S	+	2	0	PLCH2	2412558	1.000000	0.71417	0.958000	0.39756	0.901000	0.52897	5.514000	0.67043	1.083000	0.41159	0.561000	0.74099	TCG	.	.	none		0.542	PLCH2-009	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467514.1	NM_014638		T	2422698	C	T	2422698	3	4	47	1	0	0	0	0	1	0	0	0	12047	893	31	1	1625	1	PLCH2	1	2422698	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10		2422698	246827923	1	15735											
TGFBR3	7049	hgsc.bcm.edu	37	chr1	92262875	92262875	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctggccaggcccctggcctGcagtgcggagattcaggaca	7	6	15	13	1	1	1	1	0	0	1	1	3	1	2	4	5	2	2	4	5	0	1			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:92262875G>A	ENST00000525962.1	-	2	276	c.215C>T	c.(214-216)gCa>gTa	p.A72V	TGFBR3_ENST00000212355.4_Missense_Mutation_p.A72V|TGFBR3_ENST00000370399.2_Missense_Mutation_p.A72V			Q03167	TGBR3_HUMAN	transforming growth factor, beta receptor III	72					blastocyst development (GO:0001824)|blood vessel development (GO:0001568)|BMP signaling pathway (GO:0030509)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell proliferation (GO:0060038)|cell growth (GO:0016049)|cell migration (GO:0016477)|definitive erythrocyte differentiation (GO:0060318)|definitive hemopoiesis (GO:0060216)|epithelial to mesenchymal transition (GO:0001837)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|negative regulation of cellular component movement (GO:0051271)|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 transforming growth factor beta receptor signaling pathway (GO:0030512)|organ regeneration (GO:0031100)|palate development (GO:0060021)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of protein binding (GO:0043393)|response to follicle-stimulating hormone (GO:0032354)|response to hypoxia (GO:0001666)|response to luteinizing hormone (GO:0034699)|response to prostaglandin E (GO:0034695)|transforming growth factor beta receptor complex assembly (GO:0007181)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	coreceptor activity (GO:0015026)|glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|PDZ domain binding (GO:0030165)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type III (GO:0070123)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta-activated receptor activity (GO:0005024)|type II transforming growth factor beta receptor binding (GO:0005114)			endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(24)|ovary(3)|prostate(4)|skin(1)|stomach(1)|urinary_tract(3)	55		all_lung(203;0.00719)|Lung NSC(277;0.0268)		all cancers(265;0.0108)|Epithelial(280;0.0825)		CCCCTGGCCTGCAGTGCGGAG	0.582																																					p.A72V		Atlas-SNP	.											.	TGFBR3	103	.	0			c.C215T						PASS	.						129	135	133					1																	92262875		2203	4300	6503	SO:0001583	missense	7049	exon4			TGGCCTGCAGTGC	L07594	CCDS30770.1, CCDS55614.1	1p33-p32	2008-02-05	2007-02-15		ENSG00000069702	ENSG00000069702		"Proteoglycans / Cell surface : Other"	11774	protein-coding gene	gene with protein product	"betaglycan proteoglycan"	600742	"transforming growth factor, beta receptor III (betaglycan, 300kDa)"			1333192, 1319842	Standard	NM_001195684		Approved	betaglycan, BGCAN	uc001doh.3	Q03167	OTTHUMG00000010097	ENST00000525962.1:c.215C>T	1.37:g.92262875G>A	ENSP00000436127:p.Ala72Val	143	0	0		147	63	0.428571	NM_001195684	A0AUW8|A8K5N0|B9EG88|Q5T2T4|Q5U731|Q9UGI2	Missense_Mutation	SNP	ENST00000525962.1	37	CCDS30770.1	.	.	.	.	.	.	.	.	.	.	G	12.56	1.973422	0.34848	.	.	ENSG00000069702	ENST00000212355;ENST00000370399;ENST00000525962;ENST00000465892	T;T;T;T	0.31247	1.5;1.5;1.5;1.5	5.57	0.33	0.15929	.	1.116350	0.06529	N	0.741131	T	0.09730	0.0239	L	0.36672	1.1	0.09310	N	1	B;B	0.23249	0.082;0.037	B;B	0.28011	0.085;0.025	T	0.43475	-0.9389	10	0.59425	D	0.04	0.0	4.6991	0.12818	0.0674:0.2453:0.4336:0.2537	.	72;72	Q03167-2;Q03167	.;TGBR3_HUMAN	V	72	ENSP00000212355:A72V;ENSP00000359426:A72V;ENSP00000436127:A72V;ENSP00000432638:A72V	ENSP00000212355:A72V	A	-	2	0	TGFBR3	92035463	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	0.743000	0.26231	-0.177000	0.10690	-0.182000	0.12963	GCA	.	.	none		0.582	TGFBR3-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382308.1	NM_003243		A	92262875	G	A	92262875	3	1	47	1	0	0	0	0	1	0	0	0	15838	1319	46	2	2400	2	TGFBR3	1	92262875	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	89840177	92262875	156987746	2	15736											
VANGL1	81839	hgsc.bcm.edu	37	chr1	116206843	116206843	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgttcacgctgcaggtggtcCgctccaccgatggcgagtcc	5	9	13	14	4	1	0	1	0	0	0	4	2	4	0	4	3	1	4	4	3	0	1	rs199932833		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:116206843C>T	ENST00000355485.2	+	4	1037	c.766C>T	c.(766-768)Cgc>Tgc	p.R256C	VANGL1_ENST00000369510.4_Missense_Mutation_p.R254C|VANGL1_ENST00000310260.3_Missense_Mutation_p.R256C|VANGL1_ENST00000369509.1_Missense_Mutation_p.R256C	NM_001172411.1|NM_138959.2	NP_001165882.1|NP_620409.1	Q8TAA9	VANG1_HUMAN	VANGL planar cell polarity protein 1	256					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)		GCAGGTGGTCCGCTCCACCGA	0.597																																					p.R256C		Atlas-SNP	.											.	VANGL1	65	.	0			c.C766T						PASS	.						53	50	51					1																	116206843		2203	4300	6503	SO:0001583	missense	81839	exon4			GTGGTCCGCTCCA	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.766C>T	1.37:g.116206843C>T	ENSP00000347672:p.Arg256Cys	115	0	0		96	34	0.354167	NM_138959	Q5T1D3|Q5T1D4|Q86WG8|Q8N559	Missense_Mutation	SNP	ENST00000355485.2	37	CCDS883.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.631358	0.87660	.	.	ENSG00000173218	ENST00000355485;ENST00000369510;ENST00000310260;ENST00000369509	D;D;D;D	0.87334	-2.24;-2.24;-2.24;-2.24	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	D	0.93969	0.8069	M	0.90198	3.095	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.94379	0.7603	10	0.87932	D	0	-0.3431	15.0586	0.71933	0.1419:0.8581:0.0:0.0	.	254;256	Q8TAA9-2;Q8TAA9	.;VANG1_HUMAN	C	256;254;256;256	ENSP00000347672:R256C;ENSP00000358523:R254C;ENSP00000310800:R256C;ENSP00000358522:R256C	ENSP00000310800:R256C	R	+	1	0	VANGL1	116008366	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.621000	0.67743	2.879000	0.98667	0.650000	0.86243	CGC	.	.	weak		0.597	VANGL1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033096.1			T	116206843	C	T	116206843	3	4	47	1	0	0	0	0	1	0	0	0	17134	652	23	1	776	1	VANGL1	1	116206843	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	23943968	116206843	133043778	3	15737											
HIST2H2BE	8349	hgsc.bcm.edu	37	chr1	149857872	149857872	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggacacggcgtgcttggccaGctcgccgggcagcagcaggc	6	4	17	14	4	0	0	0	0	0	0	1	1	0	1	2	5	4	5	2	5	0	1	rs587684290		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:149857872G>C	ENST00000369155.2	-	1	360	c.319C>G	c.(319-321)Ctg>Gtg	p.L107V	BOLA1_ENST00000369153.2_5'Flank|HIST2H2AC_ENST00000331380.2_5'Flank	NM_003528.2	NP_003519.1	Q16778	H2B2E_HUMAN	histone cluster 2, H2be	107					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)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	14	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			TGCTTGGCCAGCTCGCCGGGC	0.687																																					p.L107V		Atlas-SNP	.											.	HIST2H2BE	33	.	0			c.C319G						PASS	.						23	28	26					1																	149857872		2197	4277	6474	SO:0001583	missense	8349	exon1			TGGCCAGCTCGCC	AY131979	CCDS936.1	1q21.2	2011-01-27	2006-10-11	2003-03-07	ENSG00000184678	ENSG00000184678		"Histones / Replication-dependent"	4760	protein-coding gene	gene with protein product		601831	"H2B histone family, member Q", "histone 2, H2be"	H2B, H2BFQ		1469070, 12408966	Standard	NM_003528		Approved	H2B/q, H2B.1	uc001etc.3	Q16778	OTTHUMG00000012095	ENST00000369155.2:c.319C>G	1.37:g.149857872G>C	ENSP00000358151:p.Leu107Val	125	0	0		116	51	0.439655	NM_003528	A3KMC7|A8K110|Q4KMY1|Q5QNX0|Q9UE88	Missense_Mutation	SNP	ENST00000369155.2	37	CCDS936.1	.	.	.	.	.	.	.	.	.	.	G	18.18	3.565889	0.65651	.	.	ENSG00000184678	ENST00000369155	T	0.50813	0.73	5.92	5.02	0.67125	Histone-fold (2);	0.000000	0.64402	D	0.000017	T	0.53674	0.1811	H	0.97940	4.11	0.34129	D	0.665045	B	0.34226	0.443	B	0.33295	0.161	T	0.69548	-0.5116	10	0.66056	D	0.02	.	13.8428	0.63449	0.0738:0.0:0.9262:0.0	.	107	Q16778	H2B2E_HUMAN	V	107	ENSP00000358151:L107V	ENSP00000358151:L107V	L	-	1	2	HIST2H2BE	148124496	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.648000	0.67930	1.519000	0.48950	0.585000	0.79938	CTG	.	.	none		0.687	HIST2H2BE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033455.1	NM_003528		C	149857872	G	C	149857872	3	2	47	1	0	0	0	0	1	0	0	0	7188	962	34	4	65	4	HIST2H2BE	1	149857872	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	33651029	149857872	99392749	4	15738											
RFX5	5993	hgsc.bcm.edu	37	chr1	151318690	151318690	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tgagtacttacgaaatggtaCctcggagcctctgaagaagg	12	9	12	8	2	1	3	0	2	1	1	2	5	1	4	2	3	4	2	2	3	6	3			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:151318690C>T	ENST00000290524.4	-	3	285	c.107G>A	c.(106-108)gGt>gAt	p.G36D	RFX5_ENST00000478564.1_5'UTR|RP11-126K1.6_ENST00000455503.1_RNA|RFX5_ENST00000452671.2_Missense_Mutation_p.G36D|RFX5_ENST00000368870.2_Missense_Mutation_p.G36D|RFX5_ENST00000452513.2_Missense_Mutation_p.G36D	NM_000449.3|NM_001025603.1	NP_000440.1|NP_001020774.1	P48382	RFX5_HUMAN	regulatory factor X, 5 (influences HLA class II expression)	36	N-terminal domain.				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)			CGAAATGGTACCTCGGAGCCT	0.547																																					p.G36D		Atlas-SNP	.											.	RFX5	69	.	0			c.G107A						PASS	.						119	120	120					1																	151318690		2203	4300	6503	SO:0001583	missense	5993	exon3			ATGGTACCTCGGA		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.107G>A	1.37:g.151318690C>T	ENSP00000290524:p.Gly36Asp	98	0	0		89	16	0.179775	NM_000449	B7Z848|D3DV19|E9PFU4|Q5VWC3	Missense_Mutation	SNP	ENST00000290524.4	37	CCDS994.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.383663	0.82792	.	.	ENSG00000143390	ENST00000290524;ENST00000368870;ENST00000452671;ENST00000452513;ENST00000392746;ENST00000422595;ENST00000450506;ENST00000458484;ENST00000430227;ENST00000412774;ENST00000437327;ENST00000436271	T;T;T;T;T;T;D;D	0.82167	0.31;0.31;0.31;0.28;0.32;-0.58;-1.58;-1.58	4.98	4.98	0.66077	.	0.118290	0.56097	D	0.000027	D	0.85561	0.5725	L	0.51422	1.61	0.47547	D	0.999453	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.96	D	0.85596	0.1249	10	0.49607	T	0.09	-8.8161	13.6052	0.62044	0.0:1.0:0.0:0.0	.	36;36	B7Z848;P48382	.;RFX5_HUMAN	D	36	ENSP00000290524:G36D;ENSP00000357864:G36D;ENSP00000389130:G36D;ENSP00000398388:G36D;ENSP00000376502:G36D;ENSP00000399095:G36D;ENSP00000398666:G36D;ENSP00000409187:G36D	ENSP00000290524:G36D	G	-	2	0	RFX5	149585314	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.461000	0.66699	2.591000	0.87537	0.491000	0.48974	GGT	.	.	none		0.547	RFX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034892.6	NM_000449		T	151318690	C	T	151318690	3	4	47	1	0	0	0	0	1	0	0	0	13281	507	18	2	1779	2	RFX5	1	151318690	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	1460818	151318690	97931931	5	15739											
CGN	57530	hgsc.bcm.edu	37	chr1	151508789	151508789	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tatccatccagattgaagacGagcggcagcatgtcaatgac	13	8	10	10	2	1	4	1	2	0	2	3	5	3	4	2	1	2	2	2	1	3	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:151508789G>A	ENST00000271636.7	+	19	3407	c.3274G>A	c.(3274-3276)Gag>Aag	p.E1092K		NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	1086					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)			GATTGAAGACGAGCGGCAGCA	0.473																																					p.E1092K		Atlas-SNP	.											.	CGN	106	.	0			c.G3274A						PASS	.						64	65	64					1																	151508789		2203	4300	6503	SO:0001583	missense	57530	exon19			GAAGACGAGCGGC	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.3274G>A	1.37:g.151508789G>A	ENSP00000271636:p.Glu1092Lys	215	0	0		179	37	0.206704	NM_020770	A6H8L3|A7MD22|Q5T386|Q9NR25	Missense_Mutation	SNP	ENST00000271636.7	37	CCDS999.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.793437	0.90453	.	.	ENSG00000143375	ENST00000271636	T	0.80738	-1.41	5.65	5.65	0.86999	Myosin tail (1);	0.000000	0.85682	D	0.000000	D	0.89955	0.6865	M	0.85197	2.74	0.58432	D	0.999991	D	0.89917	1.0	D	0.91635	0.999	D	0.90900	0.4768	10	0.87932	D	0	-26.5062	18.2859	0.90114	0.0:0.0:1.0:0.0	.	1086	Q9P2M7	CING_HUMAN	K	1092	ENSP00000271636:E1092K	ENSP00000271636:E1092K	E	+	1	0	CGN	149775413	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	9.054000	0.93866	2.679000	0.91253	0.655000	0.94253	GAG	.	.	none		0.473	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770		A	151508789	G	A	151508789	3	1	47	1	0	0	0	0	1	0	0	0	3305	1059	37	1	3344	1	CGN	1	151508789	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	190099	151508789	97741832	6	15740											
RPTN	126638	hgsc.bcm.edu	37	chr1	152128973	152128973	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taccagagctggagtcttgaCtttgtctctctgactgatca	8	14	9	10	0	4	4	1	3	3	1	5	5	4	5	1	1	2	1	1	1	1	3			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:152128973C>A	ENST00000316073.3	-	3	666	c.602G>T	c.(601-603)aGt>aTt	p.S201I		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	201	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						GGAGTCTTGACTTTGTCTCTC	0.453																																					p.S201I		Atlas-SNP	.											.	RPTN	123	.	0			c.G602T						PASS	.						288	250	262					1																	152128973		1568	3582	5150	SO:0001583	missense	126638	exon3			TCTTGACTTTGTC	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.602G>T	1.37:g.152128973C>A	ENSP00000317895:p.Ser201Ile	284	0	0		270	124	0.459259	NM_001122965	B7ZBZ3	Missense_Mutation	SNP	ENST00000316073.3	37	CCDS41397.1	.	.	.	.	.	.	.	.	.	.	C	11.68	1.710731	0.30322	.	.	ENSG00000215853	ENST00000316073	T	0.14022	2.54	4.43	-0.543	0.11851	.	.	.	.	.	T	0.05135	0.0137	N	0.22421	0.69	0.09310	N	1	D	0.62365	0.991	P	0.53593	0.73	T	0.31280	-0.9949	9	0.35671	T	0.21	0.1604	6.4478	0.21885	0.0:0.4361:0.0:0.5639	.	201	Q6XPR3	RPTN_HUMAN	I	201	ENSP00000317895:S201I	ENSP00000317895:S201I	S	-	2	0	RPTN	150395597	0.048000	0.20356	0.000000	0.03702	0.024000	0.10985	0.878000	0.28126	0.008000	0.14787	0.442000	0.29010	AGT	.	.	none		0.453	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312		A	152128973	C	A	152128973	3	1	47	1	0	0	0	0	1	0	0	0	13679	565	20	4	1756	4	RPTN	1	152128973	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	620184	152128973	97121648	7	15741											
FAM189B	10712	hgsc.bcm.edu	37	chr1	155220451	155220451	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	caggccacagtccaggctgaGgcagtagccggcacggctgc	8	4	15	14	2	0	1	0	1	0	0	1	1	1	1	3	5	2	5	3	5	1	1			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:155220451G>A	ENST00000361361.2	-	9	1635	c.1126C>T	c.(1126-1128)Ctc>Ttc	p.L376F	FAM189B_ENST00000368368.3_Missense_Mutation_p.L358F|FAM189B_ENST00000472550.1_5'Flank|FAM189B_ENST00000350210.2_Missense_Mutation_p.L280F	NM_006589.2	NP_006580.2	P81408	F189B_HUMAN	family with sequence similarity 189, member B	376						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						TCCAGGCTGAGGCAGTAGCCG	0.701																																					p.L376F		Atlas-SNP	.											.	FAM189B	51	.	0			c.C1126T						PASS	.						14	17	16					1																	155220451		2171	4254	6425	SO:0001583	missense	10712	exon9			GGCTGAGGCAGTA	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.1126C>T	1.37:g.155220451G>A	ENSP00000354958:p.Leu376Phe	63	0	0		37	18	0.486486	NM_006589	B1AVS5|Q8IXL3|Q9BR66	Missense_Mutation	SNP	ENST00000361361.2	37	CCDS1103.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.397776	0.83120	.	.	ENSG00000160767	ENST00000350210;ENST00000368368;ENST00000361361;ENST00000323361	T;T;T	0.19669	2.13;2.41;2.41	4.21	4.21	0.49690	.	0.237014	0.27319	N	0.019901	T	0.16811	0.0404	N	0.08118	0	0.35127	D	0.767568	D;D;D;D	0.89917	1.0;0.995;0.997;0.995	D;D;D;D	0.85130	0.997;0.979;0.986;0.969	T	0.21552	-1.0242	10	0.59425	D	0.04	.	14.442	0.67323	0.0:0.0:1.0:0.0	.	141;358;280;376	B1AVS2;B1AVS5;P81408-2;P81408	.;.;.;F189B_HUMAN	F	280;358;376;86	ENSP00000307128:L280F;ENSP00000357352:L358F;ENSP00000354958:L376F	ENSP00000323164:L86F	L	-	1	0	FAM189B	153487075	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.426000	0.66476	2.351000	0.79841	0.563000	0.77884	CTC	.	.	none		0.701	FAM189B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087224.1	NM_006589		A	155220451	G	A	155220451	3	1	47	1	0	0	0	0	1	0	0	0	5522	1000	35	2	896	2	FAM189B	1	155220451	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	3091478	155220451	94030170	8	15742											
PMF1	9673	hgsc.bcm.edu	37	chr1	156182902	156182902	+	IGR	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgccacccggcactaccatTtcgagggtgaagctcctcga	8	8	11	14	3	0	1	0	1	0	0	3	3	1	1	4	2	3	2	4	2	2	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:156182902T>C	ENST00000359511.4	+	0	3482				PMF1_ENST00000567140.1_Silent_p.I32I|PMF1_ENST00000368277.3_Silent_p.I32I|PMF1_ENST00000368279.3_Silent_p.I32I|PMF1-BGLAP_ENST00000320139.5_Silent_p.I32I|PMF1_ENST00000565805.1_Silent_p.I32I|PMF1_ENST00000368273.4_Silent_p.I32I|PMF1-BGLAP_ENST00000368276.4_Silent_p.I32I|PMF1-BGLAP_ENST00000490491.1_Silent_p.I32I	NM_014655.2	NP_055470.1	Q96H78	S2544_HUMAN	solute carrier family 25, member 44						transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				breast(3)|kidney(2)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14	Hepatocellular(266;0.158)					GCACTACCATTTCGAGGGTGA	0.572																																					p.I32I		Atlas-SNP	.											.	.	.	.	0			c.T96C						PASS	.						91	84	86					1																	156182902		2203	4300	6503	SO:0001628	intergenic_variant	100527963	exon1			TACCATTTCGAGG	AB007915	CCDS1133.1, CCDS72943.1	1q22	2013-05-22			ENSG00000160785	ENSG00000160785		"Solute carriers"	29036	protein-coding gene	gene with protein product		610824				16949250	Standard	NM_001286184		Approved	FLJ90431, KIAA0446	uc001fnp.3	Q96H78	OTTHUMG00000014816		1.37:g.156182902T>C		127	0	0		97	44	0.453608	NM_001199664	O75034	Silent	SNP	ENST00000359511.4	37	CCDS1133.1																																																																																			.	.	none		0.572	SLC25A44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040856.1	NM_014655		C	156182902	T	C	156182902	1	2	47	0	1	0	0	0	0	0	0	0	12142	1829	64	3		3	PMF1	1	156182902	IGR	SNP	T	TCGA-RQ-AAAT-01A-11D-A38X-10	962451	156182902	93067719	9	15743											
GPATCH4	54865	hgsc.bcm.edu	37	chr1	156565049	156565049	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tccctggttccaccacctaaAagtttcctcacctctatctt	8	14	3	16	0	3	0	1	0	2	0	6	0	6	0	6	1	0	2	6	1	3	5	rs77528517|rs72559129	byFrequency	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:156565049A>C	ENST00000438976.2	-	8	1114	c.1084T>G	c.(1084-1086)Ttt>Gtt	p.F362V	GPATCH4_ENST00000497287.1_5'Flank|GPATCH4_ENST00000368232.4_Missense_Mutation_p.F357V			Q5T3I0	GPTC4_HUMAN	G patch domain containing 4	357							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)					CACCACCTAAAAGTTTCCTCA	0.507																																					p.F362V		Atlas-SNP	.											.	GPATCH4	34	.	0			c.T1084G						PASS	.						192	192	192					1																	156565049		2203	4300	6503	SO:0001583	missense	54865	exon8			ACCTAAAAGTTTC	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.1084T>G	1.37:g.156565049A>C	ENSP00000396441:p.Phe362Val	333	0	0		280	14	0.05	NM_015590	Q5T3I1|Q6ZUE7|Q8IWG8|Q9NXH4	Missense_Mutation	SNP	ENST00000438976.2	37	CCDS44245.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	0.368|0.368	-0.935701|-0.935701	0.02340|0.02340	.|.	.|.	ENSG00000160818|ENSG00000160818	ENST00000368229|ENST00000368232;ENST00000438976	.|.	.|.	.|.	3.86|3.86	-2.77|-2.77	0.05877|0.05877	.|.	.|.	.|.	.|.	.|.	.|T	.|0.03220	.|0.0094	.|.	.|.	.|.	0.09310|0.09310	N|N	0.999999|0.999999	.|B	.|0.13594	.|0.008	.|B	.|0.14023	.|0.01	.|T	.|0.41980	.|-0.9478	.|7	.|0.02654	.|T	.|1	.|.	6.2915|6.2915	0.21063|0.21063	0.4516:0.0:0.4207:0.1278|0.4516:0.0:0.4207:0.1278	.|.	.|362	.|E9PAV9	.|.	.|V	-1|357;362	.|.	.|ENSP00000357215:F357V	.|F	-|-	.|1	.|0	GPATCH4|GPATCH4	154831673|154831673	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.008000|0.008000	0.06430|0.06430	0.130000|0.130000	0.15850|0.15850	-0.571000|-0.571000	0.06014|0.06014	-0.379000|-0.379000	0.06801|0.06801	.|TTT	A|0.333;C|0.333;G|0.333	0.333	strong		0.507	GPATCH4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386947.1	NM_017725		C	156565049	A	C	156565049	3	2	47	1	0	0	0	0	1	0	0	0	6601	14	1	5	47	5	GPATCH4	1	156565049	Missense_Mutation	SNP	A	TCGA-RQ-AAAT-01A-11D-A38X-10	382147	156565049	92685572	10	15744											
OR6N1	128372	hgsc.bcm.edu	37	chr1	158735736	158735736	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catagaagatgagaaccacaGtgaagtgggaggcacacgtg	15	5	14	7	1	0	4	0	2	0	3	0	6	0	5	1	2	1	1	1	2	4	1			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:158735736G>A	ENST00000335094.2	-	1	756	c.737C>T	c.(736-738)aCt>aTt	p.T246I		NM_001005185.1	NP_001005185.1	Q8NGY5	OR6N1_HUMAN	olfactory receptor, family 6, subfamily N, member 1	246						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)					GAGAACCACAGTGAAGTGGGA	0.532																																					p.T246I		Atlas-SNP	.											.	OR6N1	96	.	0			c.C737T						PASS	.						170	159	163					1																	158735736		2203	4300	6503	SO:0001583	missense	128372	exon1			ACCACAGTGAAGT	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.737C>T	1.37:g.158735736G>A	ENSP00000335535:p.Thr246Ile	99	0	0		94	35	0.37234	NM_001005185	Q5VUU8|Q96R35	Missense_Mutation	SNP	ENST00000335094.2	37	CCDS30905.1	.	.	.	.	.	.	.	.	.	.	G	7.489	0.650179	0.14516	.	.	ENSG00000197403	ENST00000335094	T	0.00350	7.98	4.74	3.8	0.43715	GPCR, rhodopsin-like superfamily (1);	0.159979	0.30227	N	0.010102	T	0.00073	0.0002	L	0.38692	1.165	0.26491	N	0.974945	B	0.22080	0.064	B	0.22152	0.038	T	0.27191	-1.0081	10	0.38643	T	0.18	-6.181	11.135	0.48368	0.0962:0.0:0.9038:0.0	.	246	Q8NGY5	OR6N1_HUMAN	I	246	ENSP00000335535:T246I	ENSP00000335535:T246I	T	-	2	0	OR6N1	157002360	0.000000	0.05858	0.998000	0.56505	0.513000	0.34164	0.272000	0.18644	1.129000	0.42072	0.655000	0.94253	ACT	.	.	none		0.532	OR6N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059067.1	NM_001005185		A	158735736	G	A	158735736	3	1	47	1	0	0	0	0	1	0	0	0	11215	1029	36	2	204	2	OR6N1	1	158735736	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	2170687	158735736	90514885	11	15745											
HMCN1	83872	hgsc.bcm.edu	37	chr1	186007087	186007087	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accacctagtctggaagatgCtggaaaaatgctgaatgaga	15	8	11	7	0	1	3	0	2	1	2	1	6	1	5	2	2	2	2	2	2	5	1			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:186007087C>G	ENST00000271588.4	+	37	6000	c.5771C>G	c.(5770-5772)gCt>gGt	p.A1924G	HMCN1_ENST00000367492.2_Missense_Mutation_p.A1924G	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	1924	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						CTGGAAGATGCTGGAAAAATG	0.383																																					p.A1924G		Atlas-SNP	.											.	HMCN1	797	.	0			c.C5771G						PASS	.						135	127	130					1																	186007087		2203	4300	6503	SO:0001583	missense	83872	exon37			AAGATGCTGGAAA	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.5771C>G	1.37:g.186007087C>G	ENSP00000271588:p.Ala1924Gly	118	0	0		88	16	0.181818	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	2.881	-0.231818	0.05983	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.66099	-0.18;-0.19	5.52	4.6	0.57074	Immunoglobulin-like (1);	0.233532	0.43747	N	0.000525	T	0.35913	0.0948	N	0.01705	-0.755	0.37687	D	0.923692	B	0.09022	0.002	B	0.09377	0.004	T	0.22871	-1.0204	10	0.18710	T	0.47	.	16.2196	0.82251	0.0:0.867:0.133:0.0	.	1924	Q96RW7	HMCN1_HUMAN	G	1924	ENSP00000271588:A1924G;ENSP00000356462:A1924G	ENSP00000271588:A1924G	A	+	2	0	HMCN1	184273710	0.820000	0.29190	0.096000	0.21009	0.007000	0.05969	3.307000	0.51888	1.306000	0.44926	0.555000	0.69702	GCT	.	.	none		0.383	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935		G	186007087	C	G	186007087	3	3	47	1	0	0	0	0	1	0	0	0	7229	797	28	4	5917	4	HMCN1	1	186007087	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	27271351	186007087	63243534	12	15746											
BTG2	7832	hgsc.bcm.edu	37	chr1	203274827	203274827	+	Missense_Mutation	SNP	C	C	G																															aggacccggggctgcgtgagCgagcagaggcttaaggtctt																										TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:203274827C>G	ENST00000290551.4	+	1	164	c.93C>G	c.(91-93)agC>agG	p.S31R	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	31					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			GCTGCGTGAGCGAGCAGAGGC	0.711																																					p.S31R		Atlas-SNP	.											.	BTG2	16	.	0			c.C93G						PASS	.						16	16	16					1																	203274827		2157	4235	6392	SO:0001583	missense	7832	exon1			CGTGAGCGAGCAG		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.93C>G	1.37:g.203274827C>G	ENSP00000290551:p.Ser31Arg	85	0	0		66	13	0.19697	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	C	14.94	2.683961	0.47991	.	.	ENSG00000159388	ENST00000290551	T	0.23754	1.89	4.66	3.75	0.43078	Anti-proliferative protein (3);	0.175253	0.47455	D	0.000221	T	0.26304	0.0642	L	0.59436	1.845	0.37789	D	0.92728	B	0.16802	0.019	B	0.28916	0.096	T	0.14980	-1.0453	10	0.54805	T	0.06	-0.1987	7.4459	0.27211	0.0:0.7394:0.1689:0.0917	.	31	P78543	BTG2_HUMAN	R	31	ENSP00000290551:S31R	ENSP00000290551:S31R	S	+	3	2	BTG2	201541450	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	0.692000	0.25482	1.191000	0.43056	0.478000	0.44815	AGC	.	.	none		0.711	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		G	203274827	C	G	203274827	3	3	47	1	0	0	0	0	1	0	0	0	1556	767	27	4	95	4	BTG2	1	203274827	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	17267740	203274827	45975794	13	15747	208	2									
BTG2	7832	hgsc.bcm.edu	37	chr1	203274831	203274831	+	Missense_Mutation	SNP	C	C	A																															cccggggctgcgtgagcgagCagaggcttaaggtcttcagc																								rs530501274		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:203274831C>A	ENST00000290551.4	+	1	168	c.97C>A	c.(97-99)Cag>Aag	p.Q33K	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	33					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			CGTGAGCGAGCAGAGGCTTAA	0.706																																					p.Q33K		Atlas-SNP	.											.	BTG2	16	.	0			c.C97A						PASS	.						15	16	16					1																	203274831		2150	4221	6371	SO:0001583	missense	7832	exon1			AGCGAGCAGAGGC		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.97C>A	1.37:g.203274831C>A	ENSP00000290551:p.Gln33Lys	84	0	0		66	41	0.621212	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	C	16.25	3.070481	0.55539	.	.	ENSG00000159388	ENST00000290551	T	0.22134	1.97	4.66	3.72	0.42706	Anti-proliferative protein (3);	0.270105	0.31145	N	0.008179	T	0.17959	0.0431	L	0.45581	1.43	0.42010	D	0.99093	B	0.24533	0.105	B	0.26094	0.066	T	0.05099	-1.0906	10	0.28530	T	0.3	-10.9891	8.7243	0.34460	0.1715:0.6626:0.1659:0.0	.	33	P78543	BTG2_HUMAN	K	33	ENSP00000290551:Q33K	ENSP00000290551:Q33K	Q	+	1	0	BTG2	201541454	1.000000	0.71417	0.994000	0.49952	0.847000	0.48162	2.921000	0.48852	1.144000	0.42321	0.478000	0.44815	CAG	.	.	none		0.706	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		A	203274831	C	A	203274831	3	1	47	1	0	0	0	0	1	0	0	0	1556	711	25	4	99	4	BTG2	1	203274831	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	4	203274831	45975790	14	15748	208	2									
BTG2	7832	hgsc.bcm.edu	37	chr1	203274867	203274867	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	tcagcggggcgctccaggagGcactcacaggtgagcgcatg	8	5	16	12	3	2	1	2	1	0	0	3	2	3	2	1	5	2	3	1	5	0	0			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:203274867G>C	ENST00000290551.4	+	1	204	c.133G>C	c.(133-135)Gca>Cca	p.A45P	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	45					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.A45T(1)		haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			GCTCCAGGAGGCACTCACAGG	0.706																																					p.A45P		Atlas-SNP	.											BTG2,lymph_node,lymphoid_neoplasm,-1,2	BTG2	16	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G133C						PASS	.						11	13	13					1																	203274867		2020	3950	5970	SO:0001583	missense	7832	exon1			CAGGAGGCACTCA		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.133G>C	1.37:g.203274867G>C	ENSP00000290551:p.Ala45Pro	69	0	0		53	14	0.264151	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.163593	0.78226	.	.	ENSG00000159388	ENST00000290551	T	0.25085	1.82	4.4	4.4	0.53042	Anti-proliferative protein (3);	0.078518	0.49916	D	0.000121	T	0.52008	0.1708	M	0.82630	2.6	0.47374	D	0.999406	D	0.62365	0.991	D	0.64687	0.928	T	0.58222	-0.7674	10	0.51188	T	0.08	-33.413	15.7078	0.77598	0.0:0.0:1.0:0.0	.	45	P78543	BTG2_HUMAN	P	45	ENSP00000290551:A45P	ENSP00000290551:A45P	A	+	1	0	BTG2	201541490	1.000000	0.71417	0.991000	0.47740	0.943000	0.58893	4.326000	0.59241	2.282000	0.76494	0.471000	0.43371	GCA	.	.	none		0.706	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		C	203274867	G	C	203274867	3	2	47	1	0	0	0	0	1	0	0	0	1556	1203	42	4	135	4	BTG2	1	203274867	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	36	203274867	45975754	15	15749											
ITPKB	3707	hgsc.bcm.edu	37	chr1	226925103	226925103	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	gggccgccgccgctcttcatCtcgttggcgctattcatgat	4	12	11	14	5	4	1	2	1	2	0	5	1	4	1	3	2	0	3	3	2	1	4			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr1:226925103C>T	ENST00000272117.3	-	1	56	c.57G>A	c.(55-57)gaG>gaA	p.E19E	ITPKB_ENST00000429204.1_Silent_p.E19E|ITPKB_ENST00000366784.1_Silent_p.E19E			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	19					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)				CGCTCTTCATCTCGTTGGCGC	0.697																																					p.E19E	Colon(84;110 1851 5306 33547)	Atlas-SNP	.											ITPKB_ENST00000429204,scalp,carcinoma,-2,1	ITPKB	158	1	0			c.G57A						PASS	.						15	18	17					1																	226925103		2084	4139	6223	SO:0001819	synonymous_variant	3707	exon2			CTTCATCTCGTTG	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.57G>A	1.37:g.226925103C>T		57	0	0		39	13	0.333333	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Silent	SNP	ENST00000272117.3	37	CCDS1555.1																																																																																			.	.	none		0.697	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221		T	226925103	C	T	226925103	2	4	47	1	0	0	0	0	0	0	0	1	7927	912	32	2		2	ITPKB	1	226925103	Silent	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	23650236	226925103	22325518	16	15750											
C2orf71	388939	hgsc.bcm.edu	37	chr2	29296353	29296353	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atttggctgctcctggggctCtcttttcttcaaaggccaag	6	14	10	11	0	3	0	1	0	2	0	5	0	4	0	2	4	1	3	2	4	2	4			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr2:29296353C>T	ENST00000331664.5	-	1	774	c.775G>A	c.(775-777)Gag>Aag	p.E259K		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	259					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						TCCTGGGGCTCTCTTTTCTTC	0.562																																					p.E259K		Atlas-SNP	.											.	C2orf71	146	.	0			c.G775A						PASS	.						64	66	65					2																	29296353		1984	4173	6157	SO:0001583	missense	388939	exon1			GGGGCTCTCTTTT		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.775G>A	2.37:g.29296353C>T	ENSP00000332809:p.Glu259Lys	89	0	0		53	8	0.150943	NM_001029883		Missense_Mutation	SNP	ENST00000331664.5	37	CCDS42669.1	.	.	.	.	.	.	.	.	.	.	C	11.24	1.581641	0.28180	.	.	ENSG00000179270	ENST00000331664	T	0.21932	1.98	5.62	5.62	0.85841	.	0.385689	0.28560	N	0.014902	T	0.22627	0.0546	L	0.45581	1.43	0.09310	N	1	P	0.39022	0.655	B	0.34452	0.183	T	0.13202	-1.0518	10	0.51188	T	0.08	-17.6579	19.6596	0.95859	0.0:1.0:0.0:0.0	.	259	A6NGG8	CB071_HUMAN	K	259	ENSP00000332809:E259K	ENSP00000332809:E259K	E	-	1	0	C2orf71	29149857	0.502000	0.26107	0.409000	0.26459	0.181000	0.23173	1.766000	0.38491	2.648000	0.89879	0.561000	0.74099	GAG	.	.	none		0.562	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883		T	29296353	C	T	29296353	3	4	47	1	0	0	0	0	1	0	0	0	2193	922	32	2	3099	2	C2orf71	2	29296353	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10		29296353	213903020	17	15751											
PIGF	5281	hgsc.bcm.edu	37	chr2	46839367	46839367	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	aatataaaattaaaacttacCcatttctactgaacactctt	17	14	1	9	0	2	1	0	1	2	0	2	1	2	1	1	0	4	0	1	0	9	7			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr2:46839367C>T	ENST00000281382.6	-	4	607	c.437G>A	c.(436-438)gGa>gAa	p.G146E	PIGF_ENST00000495933.1_5'UTR|PIGF_ENST00000306465.4_Splice_Site_p.G146E	NM_002643.3	NP_002634.1	Q07326	PIGF_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class F	146					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)			taaaaCTTACCCATTTCTACT	0.284																																					p.G146E		Atlas-SNP	.											.	PIGF	9	.	0			c.G437A						PASS	.						15	13	14					2																	46839367		2052	4024	6076	SO:0001630	splice_region_variant	5281	exon4			ACTTACCCATTTC		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.437+1G>A	2.37:g.46839367C>T		309	1	0.00323625		206	81	0.393204	NM_002643	Q8WW20	Missense_Mutation	SNP	ENST00000281382.6	37	CCDS1827.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.693759	0.88735	.	.	ENSG00000151665	ENST00000281382;ENST00000306465	.	.	.	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.79323	0.4426	M	0.70595	2.14	0.80722	D	1	D;D	0.76494	0.999;0.991	D;P	0.72982	0.979;0.895	T	0.76892	-0.2791	8	.	.	.	-9.518	19.9893	0.97361	0.0:1.0:0.0:0.0	.	146;146	Q07326;Q07326-2	PIGF_HUMAN;.	E	146	.	.	G	-	2	0	PIGF	46692871	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.336000	0.72954	2.826000	0.97356	0.563000	0.77884	GGA	.	.	none		0.284	PIGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250749.2	NM_173074	Missense_Mutation	T	46839367	C	T	46839367	5	4	47	1	0	0	0	0	0	0	1	0	11896	637	22	2	313	2	PIGF	2	46839367	Splice_Site	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	17543014	46839367	196360006	18	15752											
BCL11A	53335	hgsc.bcm.edu	37	chr2	60688036	60688036	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	tccgaagctaaggaagggatCtttgagctgcctggaggccg	9	8	15	9	2	1	1	0	1	1	0	2	5	2	4	3	4	3	2	3	4	3	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr2:60688036C>T	ENST00000335712.6	-	4	2238	c.2011G>A	c.(2011-2013)Gat>Aat	p.D671N	BCL11A_ENST00000537768.1_Missense_Mutation_p.D340N|BCL11A_ENST00000359629.5_Intron|BCL11A_ENST00000356842.4_Missense_Mutation_p.D671N|BCL11A_ENST00000538214.1_Missense_Mutation_p.D637N|BCL11A_ENST00000477659.1_5'UTR|BCL11A_ENST00000358510.4_Missense_Mutation_p.D637N	NM_022893.3	NP_075044.2	Q9H165	BC11A_HUMAN	B-cell CLL/lymphoma 11A (zinc finger protein)	671					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)			AGGAAGGGATCTTTGAGCTGC	0.637			T	IGH@	B-CLL																																p.D671N		Atlas-SNP	.		Dom	yes		2	2p13	53335	B-cell CLL/lymphoma 11A		L	.	BCL11A	298	.	0			c.G2011A						PASS	.						39	48	45					2																	60688036		2202	4295	6497	SO:0001583	missense	53335	exon4			AGGGATCTTTGAG	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.2011G>A	2.37:g.60688036C>T	ENSP00000338774:p.Asp671Asn	59	0	0		68	7	0.102941	NM_018014	D6W5D7|Q86W14|Q8WU92|Q96JL6|Q9H163|Q9H164|Q9H3G9|Q9NWA7	Missense_Mutation	SNP	ENST00000335712.6	37	CCDS1862.1	.	.	.	.	.	.	.	.	.	.	C	15.22	2.768661	0.49680	.	.	ENSG00000119866	ENST00000356842;ENST00000378117;ENST00000538214;ENST00000537768;ENST00000335712;ENST00000358510	T;T;T;T;T	0.13307	2.6;3.28;2.72;3.32;3.23	5.93	5.93	0.95920	.	0.125598	0.51477	D	0.000100	T	0.30070	0.0753	L	0.50333	1.59	0.58432	D	0.999998	D;P;P;P;D	0.61697	0.99;0.805;0.61;0.947;0.969	P;B;B;P;P	0.61940	0.794;0.26;0.328;0.798;0.896	T	0.00677	-1.1614	10	0.16896	T	0.51	-2.2696	20.3465	0.98790	0.0:1.0:0.0:0.0	.	637;340;637;671;671	F5H2Y4;B4DT16;Q9H165-6;Q9H165;D9YZV9	.;.;.;BC11A_HUMAN;.	N	671;696;637;340;671;637	ENSP00000349300:D671N;ENSP00000438303:D637N;ENSP00000443712:D340N;ENSP00000338774:D671N;ENSP00000351307:D637N	ENSP00000338774:D671N	D	-	1	0	BCL11A	60541540	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.798000	0.96311	0.655000	0.94253	GAT	.	.	none		0.637	BCL11A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251579.2	NM_022893		T	60688036	C	T	60688036	3	4	47	1	0	0	0	0	1	0	0	0	1363	913	32	2	606	2	BCL11A	2	60688036	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	13848669	60688036	182511337	19	15753											
ETAA1	54465	hgsc.bcm.edu	37	chr2	67631813	67631813	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agacatcagaaagtatatgtGagatcaataataattccgaa	19	10	7	5	1	2	3	2	1	0	3	3	5	3	3	1	0	0	1	1	0	7	5			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr2:67631813G>A	ENST00000272342.5	+	5	2129	c.1999G>A	c.(1999-2001)Gag>Aag	p.E667K	ETAA1_ENST00000462772.1_Intron	NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	667						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						AAGTATATGTGAGATCAATAA	0.343																																					p.E667K		Atlas-SNP	.											.	ETAA1	88	.	0			c.G1999A						PASS	.						83	88	86					2																	67631813		2202	4295	6497	SO:0001583	missense	54465	exon5			ATATGTGAGATCA	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.1999G>A	2.37:g.67631813G>A	ENSP00000272342:p.Glu667Lys	99	0	0		100	42	0.42	NM_019002	Q05BT7|Q53SC4	Missense_Mutation	SNP	ENST00000272342.5	37	CCDS1882.1	.	.	.	.	.	.	.	.	.	.	-	11.45	1.642910	0.29246	.	.	ENSG00000143971	ENST00000272342	T	0.18960	2.18	4.65	-1.19	0.09585	.	1.031440	0.07617	N	0.926447	T	0.12603	0.0306	L	0.41236	1.265	0.09310	N	1	B	0.13145	0.007	B	0.14578	0.011	T	0.38090	-0.9677	10	0.02654	T	1	-1.0365	5.2166	0.15346	0.4149:0.148:0.4372:0.0	.	667	Q9NY74	ETAA1_HUMAN	K	667	ENSP00000272342:E667K	ENSP00000272342:E667K	E	+	1	0	ETAA1	67485317	0.362000	0.24980	0.000000	0.03702	0.424000	0.31475	0.779000	0.26746	-0.078000	0.12730	0.467000	0.42956	GAG	.	.	none		0.343	ETAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251735.1	NM_019002		A	67631813	G	A	67631813	3	1	47	1	0	0	0	0	1	0	0	0	5269	1291	45	2	2017	2	ETAA1	2	67631813	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	6943777	67631813	175567560	20	15754											
POU3F3	5455	hgsc.bcm.edu	37	chr2	105473228	105473228	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gaggtgagcgtcaagggcgcGctggagagccacttcctcaa	9	6	15	11	3	2	2	2	1	0	1	3	4	3	2	2	3	2	1	2	3	2	1			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr2:105473228G>A	ENST00000361360.2	+	1	1260	c.1260G>A	c.(1258-1260)gcG>gcA	p.A420A	RP11-13J10.1_ENST00000598623.1_RNA	NM_006236.1	NP_006227.1	P20264	PO3F3_HUMAN	POU class 3 homeobox 3	420					central nervous system development (GO:0007417)|cerebral cortex radially oriented cell migration (GO:0021799)|forebrain ventricular zone progenitor cell division (GO:0021869)|metanephric ascending thin limb development (GO:0072218)|metanephric DCT cell differentiation (GO:0072240)|metanephric loop of Henle development (GO:0072236)|metanephric macula densa development (GO:0072227)|metanephric thick ascending limb development (GO:0072233)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|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)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	12						TCAAGGGCGCGCTGGAGAGCC	0.657																																					p.A420A		Atlas-SNP	.											.	POU3F3	43	.	0			c.G1260A						PASS	.						36	37	37					2																	105473228		2203	4300	6503	SO:0001819	synonymous_variant	5455	exon1			GGGCGCGCTGGAG		CCDS33265.1	2q12.1	2011-06-20	2007-07-13		ENSG00000198914	ENSG00000198914		"Homeoboxes / POU class"	9216	protein-coding gene	gene with protein product		602480	"POU domain class 3, transcription factor 3"				Standard	NM_006236		Approved	BRN1, OTF8	uc010ywg.2	P20264	OTTHUMG00000153067	ENST00000361360.2:c.1260G>A	2.37:g.105473228G>A		74	0	0		87	33	0.37931	NM_006236	P78379|Q4ZG25	Silent	SNP	ENST00000361360.2	37	CCDS33265.1																																																																																			.	.	none		0.657	POU3F3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329335.2			A	105473228	G	A	105473228	2	1	47	1	0	0	0	0	0	0	0	1	12285	1074	38	1		1	POU3F3	2	105473228	Silent	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	37841415	105473228	137726145	21	15755											
LRP2	4036	hgsc.bcm.edu	37	chr2	170060578	170060578	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggttcttcacaacagtgttgAttcccctgggctgggagagc	7	11	13	10	0	2	2	1	1	1	1	3	3	3	2	2	3	2	3	2	3	1	4			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr2:170060578A>G	ENST00000263816.3	-	42	8204	c.7919T>C	c.(7918-7920)aTc>aCc	p.I2640T		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2640					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)"	AACAGTGTTGATTCCCCTGGG	0.463																																					p.I2640T		Atlas-SNP	.											.	LRP2	751	.	0			c.T7919C						PASS	.						186	189	188					2																	170060578		2203	4300	6503	SO:0001583	missense	4036	exon42			GTGTTGATTCCCC		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.7919T>C	2.37:g.170060578A>G	ENSP00000263816:p.Ile2640Thr	234	0	0		151	84	0.556291	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	A	15.68	2.906247	0.52333	.	.	ENSG00000081479	ENST00000263816	D	0.91295	-2.82	5.58	5.58	0.84498	Six-bladed beta-propeller, TolB-like (1);	0.163861	0.52532	D	0.000062	D	0.94548	0.8244	H	0.97340	3.985	0.80722	D	1	P	0.47762	0.9	B	0.43225	0.412	D	0.95521	0.8594	10	0.51188	T	0.08	.	15.7383	0.77863	1.0:0.0:0.0:0.0	.	2640	P98164	LRP2_HUMAN	T	2640	ENSP00000263816:I2640T	ENSP00000263816:I2640T	I	-	2	0	LRP2	169768824	1.000000	0.71417	0.006000	0.13384	0.007000	0.05969	9.238000	0.95380	2.116000	0.64780	0.533000	0.62120	ATC	.	.	none		0.463	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525		G	170060578	A	G	170060578	3	3	47	1	0	0	0	0	1	0	0	0	8965	333	12	3	6200	3	LRP2	2	170060578	Missense_Mutation	SNP	A	TCGA-RQ-AAAT-01A-11D-A38X-10	64587350	170060578	73138795	22	15756											
MFSD6	54842	hgsc.bcm.edu	37	chr2	191301341	191301341	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcaccatatcaccaaaaatgCgtgagaaaagaaaccttttg	17	9	6	9	1	2	2	2	1	0	2	2	3	2	2	3	0	2	0	3	0	6	3			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr2:191301341C>T	ENST00000392328.1	+	3	910	c.586C>T	c.(586-588)Cgt>Tgt	p.R196C	MFSD6_ENST00000281416.7_Missense_Mutation_p.R196C	NM_017694.3	NP_060164.3	Q6ZSS7	MFSD6_HUMAN	major facilitator superfamily domain containing 6	196					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						ACCAAAAATGCGTGAGAAAAG	0.458																																					p.R196C		Atlas-SNP	.											MFSD6,caecum,carcinoma,0,1	MFSD6	58	1	0			c.C586T						PASS	.						76	83	81					2																	191301341		2203	4300	6503	SO:0001583	missense	54842	exon3			AAAATGCGTGAGA		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.586C>T	2.37:g.191301341C>T	ENSP00000376141:p.Arg196Cys	140	0	0		99	63	0.636364	NM_017694	D3KSZ4|Q86TH2|Q9NXM3	Missense_Mutation	SNP	ENST00000392328.1	37	CCDS2306.1	.	.	.	.	.	.	.	.	.	.	C	9.956	1.221465	0.22457	.	.	ENSG00000151690	ENST00000392328;ENST00000281416	T;T	0.35048	1.33;1.33	5.39	3.57	0.40892	Major facilitator superfamily domain, general substrate transporter (1);	0.219617	0.41605	D	0.000844	T	0.37758	0.1015	L	0.48642	1.525	0.41426	D	0.987836	D	0.71674	0.998	P	0.49528	0.614	T	0.18272	-1.0342	10	0.54805	T	0.06	-5.0941	10.2208	0.43196	0.154:0.6982:0.1478:0.0	.	196	Q6ZSS7	MFSD6_HUMAN	C	196	ENSP00000376141:R196C;ENSP00000281416:R196C	ENSP00000281416:R196C	R	+	1	0	MFSD6	191009586	0.045000	0.20229	0.002000	0.10522	0.075000	0.17131	1.907000	0.39897	0.823000	0.34589	-0.133000	0.14855	CGT	.	.	none		0.458	MFSD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255931.1			T	191301341	C	T	191301341	3	4	47	1	0	0	0	0	1	0	0	0	9544	768	27	1	588	1	MFSD6	2	191301341	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	21240763	191301341	51898032	23	15757											
STAT4	6775	hgsc.bcm.edu	37	chr2	191905872	191905872	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tcttcagtcaccatgtgacaGccctaaggaagagagaaata	15	8	9	9	0	3	3	2	1	1	2	3	5	3	4	2	1	1	0	2	1	4	3			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr2:191905872G>T	ENST00000392320.2	-	15	1568	c.1254C>A	c.(1252-1254)ggC>ggA	p.G418G	STAT4_ENST00000470708.1_5'UTR|STAT4_ENST00000358470.4_Silent_p.G418G	NM_003151.3	NP_003142.1	Q14765	STAT4_HUMAN	signal transducer and activator of transcription 4	418					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)	p.G418G(1)		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)			CCATGTGACAGCCCTAAGGAA	0.333																																					p.G418G		Atlas-SNP	.											STAT4,rectum,carcinoma,0,1	STAT4	85	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C1254A						PASS	.						103	97	99					2																	191905872		2203	4300	6503	SO:0001819	synonymous_variant	6775	exon15			GTGACAGCCCTAA		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.1254C>A	2.37:g.191905872G>T		171	0	0		158	32	0.202532	NM_001243835	Q96NZ6	Silent	SNP	ENST00000392320.2	37	CCDS2310.1																																																																																			.	.	none		0.333	STAT4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335586.1	NM_003151		T	191905872	G	T	191905872	2	4	47	1	0	0	0	0	0	0	0	1	15282	958	34	4		4	STAT4	2	191905872	Silent	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	604531	191905872	51293501	24	15758											
ERBB4	2066	hgsc.bcm.edu	37	chr2	212587162	212587162	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctccatatgtgtactttgcaTtgaaattgtgctccagttga	9	16	8	8	0	0	2	0	2	0	0	2	2	2	2	2	0	3	4	2	0	3	6			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr2:212587162T>G	ENST00000342788.4	-	7	1149	c.839A>C	c.(838-840)aAt>aCt	p.N280T	ERBB4_ENST00000436443.1_Missense_Mutation_p.N280T|ERBB4_ENST00000484474.1_5'Flank|ERBB4_ENST00000402597.1_Missense_Mutation_p.N280T	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	280	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)	GTACTTTGCATTGAAATTGTG	0.378										TSP Lung(8;0.080)																											p.N280T		Atlas-SNP	.											.	ERBB4	480	.	0			c.A839C						PASS	.						180	164	170					2																	212587162		2203	4300	6503	SO:0001583	missense	2066	exon7			TTTGCATTGAAAT	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.839A>C	2.37:g.212587162T>G	ENSP00000342235:p.Asn280Thr	165	0	0		128	21	0.164062	NM_001042599	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	37	CCDS2394.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.24|14.24	2.476435|2.476435	0.44044|0.44044	.|.	.|.	ENSG00000178568|ENSG00000178568	ENST00000260943|ENST00000342788;ENST00000436443;ENST00000402597	.|T;T;T	.|0.28255	.|1.62;1.62;1.62	5.83|5.83	5.83|5.83	0.93111|0.93111	.|Growth factor, receptor (1);Furin-like cysteine-rich domain (1);	.|0.175798	.|0.64402	.|D	.|0.000007	T|T	0.44519|0.44519	0.1297|0.1297	L|L	0.58428|0.58428	1.81|1.81	0.37517|0.37517	D|D	0.917396|0.917396	.|B;B;B;B;B	.|0.26635	.|0.021;0.15;0.155;0.021;0.026	.|B;B;B;B;B	.|0.43386	.|0.03;0.418;0.257;0.03;0.056	T|T	0.47005|0.47005	-0.9150|-0.9150	5|10	.|0.35671	.|T	.|0.21	.|.	16.1946|16.1946	0.82018|0.82018	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|280;280;139;280;280	.|Q15303-4;Q15303-2;Q53QS8;Q15303-3;Q15303	.|.;.;.;.;ERBB4_HUMAN	L|T	280|280	.|ENSP00000342235:N280T;ENSP00000403204:N280T;ENSP00000385565:N280T	.|ENSP00000342235:N280T	M|N	-|-	1|2	0|0	ERBB4|ERBB4	212295407|212295407	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.971000|0.971000	0.66376|0.66376	6.018000|6.018000	0.70811|0.70811	2.228000|2.228000	0.72767|0.72767	0.528000|0.528000	0.53228|0.53228	ATG|AAT	.	.	none		0.378	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599		G	212587162	T	G	212587162	3	3	47	1	0	0	0	0	1	0	0	0	5211	1493	52	5	3175	5	ERBB4	2	212587162	Missense_Mutation	SNP	T	TCGA-RQ-AAAT-01A-11D-A38X-10	20681290	212587162	30612211	25	15759											
GBX2	2637	hgsc.bcm.edu	37	chr2	237076128	237076128	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgtctcggccgcggagaaggCgagcagcgagccctctttgg	6	6	16	13	6	2	1	0	0	2	1	3	4	2	1	2	4	3	1	2	4	1	1			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr2:237076128C>T	ENST00000306318.4	-	1	884	c.487G>A	c.(487-489)Gcc>Acc	p.A163T	GBX2_ENST00000465889.1_5'Flank|AC079135.1_ENST00000483218.1_RNA|GBX2_ENST00000551105.1_Missense_Mutation_p.A163T|AC079135.1_ENST00000415226.1_RNA	NM_001485.2	NP_001476.2	P52951	GBX2_HUMAN	gastrulation brain homeobox 2	163				LPPAHPHHQIPSLPTGFCSSLAQGMALTSTLMATLPGGFSA SPQHQEAAAARKFAPQPLPGGGNFDKAEALQADAEDGKGFL AKEGSLLAFSAAETVQASLVGAVRGQGKDESKVEDDPKG -> CRPHTLTTRSPACPQASAPAWRRAWRSPLRSWPRSPAA SPRRPSTRRRQRPASSRRSRCPAAVTSTRRRRCRLTRRTAK ASWPKRARCSPSPRPRRCRLRSSGLSEGKGKTSQRWKTTRS (in Ref. 1; AAC03241). {ECO:0000305}.	autonomic nervous system development (GO:0048483)|axon guidance (GO:0007411)|cerebellar granule cell precursor proliferation (GO:0021930)|cerebellum development (GO:0021549)|forebrain neuron development (GO:0021884)|inner ear morphogenesis (GO:0042472)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|patterning of blood vessels (GO:0001569)|rhombomere 2 development (GO:0021568)|thalamus development (GO:0021794)|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)|kidney(1)|large_intestine(1)|lung(4)	7		Breast(86;0.00235)|Renal(207;0.00339)|all_hematologic(139;0.00357)|all_lung(227;0.0616)|Acute lymphoblastic leukemia(138;0.0775)|Ovarian(221;0.089)|Lung NSC(271;0.179)		Epithelial(121;4.5e-25)|OV - Ovarian serous cystadenocarcinoma(60;5.16e-11)|BRCA - Breast invasive adenocarcinoma(100;3.4e-05)|Lung(119;0.00195)|LUSC - Lung squamous cell carcinoma(224;0.00471)		GCGGAGAAGGCGAGCAGCGAG	0.756																																					p.A163T		Atlas-SNP	.											.	GBX2	20	.	0			c.G487A						PASS	.						13	13	13					2																	237076128		2138	4210	6348	SO:0001583	missense	2637	exon1			AGAAGGCGAGCAG	AF118452	CCDS2515.1	2q37.2	2012-03-09	2005-12-22		ENSG00000168505	ENSG00000168505		"Homeoboxes / ANTP class : HOXL subclass"	4186	protein-coding gene	gene with protein product		601135	"gastrulation brain homeo box 2"			9346236, 8838315	Standard	XM_005246071		Approved		uc002vvw.1	P52951	OTTHUMG00000133294	ENST00000306318.4:c.487G>A	2.37:g.237076128C>T	ENSP00000302251:p.Ala163Thr	69	0	0		38	18	0.473684	NM_001485	B2RPH7|O43833|Q53RX5|Q9Y5Y1	Missense_Mutation	SNP	ENST00000306318.4	37	CCDS2515.1	.	.	.	.	.	.	.	.	.	.	C	15.80	2.940228	0.52972	.	.	ENSG00000168505	ENST00000306318;ENST00000551105	D	0.91894	-2.93	4.6	2.48	0.30137	.	0.334685	0.28360	N	0.015636	T	0.79112	0.4391	N	0.08118	0	0.32887	D	0.511398	B;B	0.30824	0.296;0.146	B;B	0.22601	0.04;0.011	T	0.77955	-0.2393	10	0.33141	T	0.24	-9.731	8.0352	0.30488	0.384:0.4985:0.1175:0.0	.	163;163	F8VY47;P52951	.;GBX2_HUMAN	T	163	ENSP00000302251:A163T	ENSP00000302251:A163T	A	-	1	0	GBX2	236740867	0.032000	0.19561	1.000000	0.80357	0.974000	0.67602	0.010000	0.13242	0.890000	0.36211	0.462000	0.41574	GCC	.	.	none		0.756	GBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257078.3	NM_001485		T	237076128	C	T	237076128	3	4	47	1	0	0	0	0	1	0	0	0	6289	768	27	1	567	1	GBX2	2	237076128	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	24488966	237076128	6123245	26	15760											
NGLY1	55768	hgsc.bcm.edu	37	chr3	25781094	25781094	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aatcgattgctgaactggcaGgcatcacagtaatgatcttc	12	11	9	9	1	2	2	1	2	1	0	4	3	2	2	0	2	2	4	0	2	3	3			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr3:25781094G>A	ENST00000280700.5	-	5	1015	c.855C>T	c.(853-855)gcC>gcT	p.A285A	NGLY1_ENST00000417874.2_Silent_p.A243A|NGLY1_ENST00000396649.3_Silent_p.A285A|NGLY1_ENST00000428257.1_Silent_p.A285A|NGLY1_ENST00000422724.2_Intron	NM_018297.3	NP_060767.2	Q96IV0	NGLY1_HUMAN	N-glycanase 1	285					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						TGAACTGGCAGGCATCACAGT	0.423																																					p.A285A		Atlas-SNP	.											.	NGLY1	57	.	0			c.C855T						PASS	.						154	121	132					3																	25781094		2203	4300	6503	SO:0001819	synonymous_variant	55768	exon5			CTGGCAGGCATCA	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.855C>T	3.37:g.25781094G>A		107	0	0		155	14	0.0903226	NM_018297	B4DJE9|Q59FB1|Q6PJD8|Q9BVR8|Q9NR70	Silent	SNP	ENST00000280700.5	37	CCDS33719.1																																																																																			.	.	none		0.423	NGLY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340832.2			A	25781094	G	A	25781094	2	1	47	1	0	0	0	0	0	0	0	1	10407	987	35	2		2	NGLY1	3	25781094	Silent	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10		25781094	172241336	27	15761											
MYD88	4615	hgsc.bcm.edu	37	chr3	38182641	38182641	+	Nonstop_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggtgcccatcagaagcgacTgatccccatcaagtacaagg	13	6	10	12	1	2	2	2	1	0	1	3	3	3	2	3	2	3	1	3	2	4	1	rs387907272		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr3:38182641T>C	ENST00000495303.1	+	3	483	c.478T>C	c.(478-480)Tga>Cga	p.*160R	MYD88_ENST00000417037.2_Missense_Mutation_p.L273P|MYD88_ENST00000424893.1_Missense_Mutation_p.L220P|MYD88_ENST00000481122.1_3'UTR|MYD88_ENST00000443433.2_Nonstop_Mutation_p.*205R|MYD88_ENST00000396334.3_Missense_Mutation_p.L265P	NM_001172566.1	NP_001166037.1	Q99836	MYD88_HUMAN	myeloid differentiation primary response 88	0	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|cell surface receptor signaling pathway (GO:0007166)|cellular response to mechanical stimulus (GO:0071260)|cytokine-mediated signaling pathway (GO:0019221)|defense response to Gram-positive bacterium (GO:0050830)|establishment of endothelial intestinal barrier (GO:0090557)|immunoglobulin mediated immune response (GO:0016064)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of apoptotic process (GO:0043066)|negative regulation of growth of symbiont in host (GO:0044130)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-23 production (GO:0032747)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of lymphocyte proliferation (GO:0050671)|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 tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon production (GO:0032481)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)|response to molecule of fungal origin (GO:0002238)|response to peptidoglycan (GO:0032494)|response to virus (GO:0009615)|signal transduction (GO:0007165)|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)|type I interferon biosynthetic process (GO:0045351)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)	death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|TIR domain binding (GO:0070976)	p.L265P(188)		breast(1)|haematopoietic_and_lymphoid_tissue(226)|large_intestine(3)|lung(6)|upper_aerodigestive_tract(1)	237				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		CAGAAGCGACTGATCCCCATC	0.552			Mis		ABC-DLBCL								T|||	1	0.000199681	0.0	0.0	5008	,	,		22034	0.0		0.001	False		,,,				2504	0.0				p.X205R		Atlas-SNP	.		Dom	yes		3	3p22	4615	myeloid differentiation primary response gene (88)		L	MYD88,NS,lymphoid_neoplasm,0,828	MYD88	900	828	188	Substitution - Missense(188)	haematopoietic_and_lymphoid_tissue(188)	c.T613C						PASS	.						148	119	129					3																	38182641		2203	4300	6503	SO:0001578	stop_lost	4615	exon4			AGCGACTGATCCC	U84408	CCDS2674.2, CCDS54565.1, CCDS54566.1, CCDS54567.1, CCDS54568.1	3p22	2014-09-17	2012-11-15		ENSG00000172936	ENSG00000172936			7562	protein-coding gene	gene with protein product		602170	"myeloid differentiation primary response gene (88)"			9013863	Standard	NM_002468		Approved		uc003chx.3	Q99836	OTTHUMG00000131083	ENST00000495303.1:c.478T>C	3.37:g.38182641T>C	ENSP00000417848:p.*160Argext*8	62	0	0		92	76	0.826087	NM_001172569	B4DKH8|B4DKU4|B4DQ60|B4DQ72|J3KPU4|J3KQ87|J3KQJ6|P78397|Q53XS7	Missense_Mutation	SNP	ENST00000495303.1	37	CCDS54568.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	18.85|18.85	3.710754|3.710754	0.68730|0.68730	.|.	.|.	ENSG00000172936|ENSG00000172936	ENST00000417037;ENST00000396334;ENST00000424893;ENST00000421516;ENST00000415158|ENST00000495303;ENST00000443433	T;T;T;T|.	0.15487|.	2.42;2.42;2.42;2.42|.	5.74|5.74	5.74|5.74	0.90152|0.90152	Toll/interleukin-1 receptor homology (TIR) domain (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.71676|.	0.3368|.	.|.	.|.	.|.	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;0.999;0.999|.	T|.	0.70626|.	-0.4820|.	9|.	0.87932|.	D|.	0|.	-17.9268|-17.9268	15.535|15.535	0.75996|0.75996	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	207;252;241|.	Q99836-2;Q99836;B4E3D6|.	.;MYD88_HUMAN;.|.	P|R	273;265;220;272;241|160;205	ENSP00000401399:L273P;ENSP00000379625:L265P;ENSP00000389979:L220P;ENSP00000391753:L272P|.	ENSP00000379625:L265P|.	L|X	+|+	2|1	0|0	MYD88|MYD88	38157645|38157645	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.639000|7.639000	0.83342|0.83342	2.326000|2.326000	0.78906|0.78906	0.533000|0.533000	0.62120|0.62120	CTG|TGA	.	.	none		0.552	MYD88-008	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000342700.1	NM_002468		C	38182641	T	C	38182641	4	2	47	1	0	0	0	0	0	0	0	0	10032	1593	55	3	836	3	MYD88	3	38182641	Nonstop_Mutation	SNP	T	TCGA-RQ-AAAT-01A-11D-A38X-10	12401547	38182641	159839789	28	15762											
CACNA2D3	55799	hgsc.bcm.edu	37	chr3	54798316	54798316	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aataccttcacgtgcttagcCggcccaaagtcatcgaccag	11	8	8	14	3	2	0	2	0	0	0	3	1	2	0	4	1	3	1	4	1	4	3			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr3:54798316C>T	ENST00000474759.1	+	13	1366	c.1318C>T	c.(1318-1320)Cgg>Tgg	p.R440W	CACNA2D3_ENST00000490478.1_Missense_Mutation_p.R346W|CACNA2D3_ENST00000288197.5_Missense_Mutation_p.R440W|CACNA2D3_ENST00000415676.2_Missense_Mutation_p.R440W	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	440						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)	CGTGCTTAGCCGGCCCAAAGT	0.517																																					p.R440W		Atlas-SNP	.											CACNA2D3,caecum,carcinoma,-2,1	CACNA2D3	159	1	0			c.C1318T						PASS	.						136	132	133					3																	54798316		2065	4199	6264	SO:0001583	missense	55799	exon13			CTTAGCCGGCCCA	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.1318C>T	3.37:g.54798316C>T	ENSP00000419101:p.Arg440Trp	74	0	0		46	12	0.26087	NM_018398	B2RPL6|Q9NY16|Q9NY18	Missense_Mutation	SNP	ENST00000474759.1	37	CCDS54598.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.857144	0.91433	.	.	ENSG00000157445	ENST00000415676;ENST00000474759;ENST00000288197;ENST00000490478;ENST00000398624;ENST00000438476	T;T;T;T	0.14391	2.51;2.51;2.51;2.56	5.95	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.28034	0.0691	L	0.32530	0.975	0.58432	D	0.999998	D	0.89917	1.0	D	0.75020	0.985	T	0.03296	-1.1051	10	0.87932	D	0	.	16.492	0.84203	0.1322:0.8678:0.0:0.0	.	440	Q8IZS8	CA2D3_HUMAN	W	440;440;440;346;346;345	ENSP00000389506:R440W;ENSP00000419101:R440W;ENSP00000288197:R440W;ENSP00000417279:R346W	ENSP00000288197:R440W	R	+	1	2	CACNA2D3	54773356	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.348000	0.59379	1.502000	0.48669	0.650000	0.86243	CGG	.	.	none		0.517	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1			T	54798316	C	T	54798316	3	4	47	1	0	0	0	0	1	0	0	0	2552	643	23	1	1368	1	CACNA2D3	3	54798316	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	16615675	54798316	143224114	29	15763											
MAGI1	9223	hgsc.bcm.edu	37	chr3	65415776	65415776	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	caacttgagcatgtgtgtgtCccaaaacacaggtgtcattc	11	11	9	10	0	1	1	1	1	0	0	3	1	2	1	1	1	3	1	1	1	3	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr3:65415776C>T	ENST00000497477.2	-	12	1585	c.1586G>A	c.(1585-1587)gGa>gAa	p.G529E	MAGI1_ENST00000483466.1_Missense_Mutation_p.G529E|MAGI1_ENST00000402939.2_Missense_Mutation_p.G529E|MAGI1_ENST00000330909.8_Missense_Mutation_p.G529E|MAGI1_ENST00000470990.1_5'UTR			Q96QZ7	MAGI1_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 1	529	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)		ATGTGTGTGTCCCAAAACACA	0.468																																					p.G529E		Atlas-SNP	.											.	MAGI1	481	.	0			c.G1586A						PASS	.						87	72	77					3																	65415776		2203	4300	6503	SO:0001583	missense	9223	exon12			GTGTGTCCCAAAA	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.1586G>A	3.37:g.65415776C>T	ENSP00000424369:p.Gly529Glu	70	0	0		49	30	0.612245	NM_001033057	A8K188|O00309|O43863|O75085|Q96QZ8|Q96QZ9	Missense_Mutation	SNP	ENST00000497477.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.210525|5.210525	0.95069|0.95069	.|.	.|.	ENSG00000151276|ENSG00000151276	ENST00000460329|ENST00000402939;ENST00000330909;ENST00000422949;ENST00000463103;ENST00000483466;ENST00000497477;ENST00000472257	.|T;T;T;T;T;T	.|0.54479	.|0.57;0.57;0.57;0.57;0.57;0.57	5.92|5.92	5.92|5.92	0.95590|0.95590	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.78375|0.78375	0.4273|0.4273	M|M	0.87038|0.87038	2.855|2.855	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;0.999;1.0;1.0;1.0	T|T	0.80271|0.80271	-0.1452|-0.1452	5|10	.|0.66056	.|D	.|0.02	-12.8008|-12.8008	20.3065|20.3065	0.98633|0.98633	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|529;529;529;529;529	.|Q96QZ7-6;Q96QZ7-4;Q96QZ7-3;Q96QZ7-2;Q96QZ7-5	.|.;.;.;.;.	N|E	410|529;529;425;404;529;529;315	.|ENSP00000385450:G529E;ENSP00000331157:G529E;ENSP00000418177:G404E;ENSP00000420323:G529E;ENSP00000424369:G529E;ENSP00000420796:G315E	.|ENSP00000331157:G529E	D|G	-|-	1|2	0|0	MAGI1|MAGI1	65390816|65390816	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	2.809000|2.809000	0.96659|0.96659	0.650000|0.650000	0.86243|0.86243	GAC|GGA	.	.	none		0.468	MAGI1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000349132.2	NM_004742		T	65415776	C	T	65415776	3	4	47	1	0	0	0	0	1	0	0	0	9199	855	30	2	3084	2	MAGI1	3	65415776	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	10617460	65415776	132606654	30	15764											
CHMP2B	25978	hgsc.bcm.edu	37	chr3	87295015	87295015	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tacacaaacaaaagtgatgaAttcccaaatgaagatggctg	18	8	8	7	0	0	4	0	3	0	1	1	4	1	4	1	1	2	1	1	1	7	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr3:87295015A>G	ENST00000263780.4	+	3	516	c.278A>G	c.(277-279)aAt>aGt	p.N93S	CHMP2B_ENST00000471660.1_Missense_Mutation_p.N52S|CHMP2B_ENST00000472024.1_3'UTR|CHMP2B_ENST00000494980.1_Intron	NM_014043.3	NP_054762.2	Q9UQN3	CHM2B_HUMAN	charged multivesicular body protein 2B	93					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)		AAAGTGATGAATTCCCAAATG	0.323																																					p.N93S		Atlas-SNP	.											.	CHMP2B	28	.	0			c.A278G						PASS	.						81	87	85					3																	87295015		2203	4300	6503	SO:0001583	missense	25978	exon3			TGATGAATTCCCA	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.278A>G	3.37:g.87295015A>G	ENSP00000263780:p.Asn93Ser	187	0	0		159	27	0.169811	NM_014043	B4DJG8|Q53HC7|Q9Y4U6	Missense_Mutation	SNP	ENST00000263780.4	37	CCDS2918.1	.	.	.	.	.	.	.	.	.	.	A	12.59	1.983107	0.34942	.	.	ENSG00000083937	ENST00000471660;ENST00000263780	T;T	0.71817	-0.6;-0.6	5.02	5.02	0.67125	.	0.142259	0.64402	D	0.000006	T	0.57755	0.2075	L	0.40543	1.245	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.52411	-0.8579	10	0.18710	T	0.47	-9.1359	9.2981	0.37829	0.9186:0.0:0.0814:0.0	.	52;93	B4DJG8;Q9UQN3	.;CHM2B_HUMAN	S	52;93	ENSP00000419998:N52S;ENSP00000263780:N93S	ENSP00000263780:N93S	N	+	2	0	CHMP2B	87377705	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.039000	0.70972	1.861000	0.53984	0.533000	0.62120	AAT	.	.	none		0.323	CHMP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352779.2	NM_014043		G	87295015	A	G	87295015	3	3	47	1	0	0	0	0	1	0	0	0	3357	101	4	3	288	3	CHMP2B	3	87295015	Missense_Mutation	SNP	A	TCGA-RQ-AAAT-01A-11D-A38X-10	21879239	87295015	110727415	31	15765											
IGSF11	152404	hgsc.bcm.edu	37	chr3	118649074	118649074	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgctggctgaccccgggccAcctggatactcccagggctc	5	7	12	17	1	0	1	0	1	0	0	2	2	1	2	5	4	2	3	5	4	1	1			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr3:118649074A>G	ENST00000393775.2	-	2	406	c.101T>C	c.(100-102)gTg>gCg	p.V34A	IGSF11_ENST00000489689.1_Missense_Mutation_p.V34A|IGSF11_ENST00000354673.2_Missense_Mutation_p.V33A|IGSF11_ENST00000459718.1_5'UTR|IGSF11_ENST00000491903.1_Missense_Mutation_p.V34A|IGSF11_ENST00000425327.2_Missense_Mutation_p.V33A|IGSF11_ENST00000441144.2_Missense_Mutation_p.V33A	NM_001015887.1	NP_001015887.1	Q5DX21	IGS11_HUMAN	immunoglobulin superfamily, member 11	34	Ig-like V-type.				cell adhesion (GO:0007155)|regulation of growth (GO:0040008)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						ACCCCGGGCCACCTGGATACT	0.557																																					p.V34A		Atlas-SNP	.											.	IGSF11	122	.	0			c.T101C						PASS	.						104	104	104					3																	118649074		2203	4300	6503	SO:0001583	missense	152404	exon2			CGGGCCACCTGGA	AB079879	CCDS2983.1, CCDS46891.1	3q21.2	2013-01-11			ENSG00000144847	ENSG00000144847		"Immunoglobulin superfamily / I-set domain containing"	16669	protein-coding gene	gene with protein product	"cancer/testis antigen 119"	608351				12207903	Standard	XM_006713516		Approved	BT-IgSF, MGC35227, Igsf13, VSIG3, CT119	uc003ebw.3	Q5DX21	OTTHUMG00000159387	ENST00000393775.2:c.101T>C	3.37:g.118649074A>G	ENSP00000377370:p.Val34Ala	87	0	0		66	14	0.212121	NM_001015887	C9JZN0|Q8N4F1|Q8N7T8|Q8NDD2	Missense_Mutation	SNP	ENST00000393775.2	37	CCDS46891.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.357979	0.82243	.	.	ENSG00000144847	ENST00000425327;ENST00000393775;ENST00000489689;ENST00000354673;ENST00000441144;ENST00000491903	T;T;T;T;T;T	0.68903	-0.36;-0.36;-0.36;-0.36;-0.36;-0.36	5.27	5.27	0.74061	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.72867	0.3514	L	0.37697	1.125	0.58432	D	0.999999	D;D;D;D;D	0.89917	1.0;0.998;1.0;1.0;0.999	D;D;D;D;D	0.87578	0.998;0.99;0.997;0.998;0.994	T	0.69045	-0.5249	10	0.23891	T	0.37	.	14.5182	0.67833	1.0:0.0:0.0:0.0	.	34;33;33;34;34	C9JBA5;Q5DX21-3;Q5DX21-2;C9JMW0;Q5DX21	.;.;.;.;IGS11_HUMAN	A	33;34;34;33;33;34	ENSP00000406092:V33A;ENSP00000377370:V34A;ENSP00000420486:V34A;ENSP00000346700:V33A;ENSP00000401240:V33A;ENSP00000417413:V34A	ENSP00000346700:V33A	V	-	2	0	IGSF11	120131764	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.692000	0.91284	2.207000	0.71202	0.533000	0.62120	GTG	.	.	none		0.557	IGSF11-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355075.2			G	118649074	A	G	118649074	3	3	47	1	0	0	0	0	1	0	0	0	7607	159	6	3	1218	3	IGSF11	3	118649074	Missense_Mutation	SNP	A	TCGA-RQ-AAAT-01A-11D-A38X-10	31354059	118649074	79373356	32	15766											
COL6A5	256076	hgsc.bcm.edu	37	chr3	130116569	130116569	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	atcaagggggtgagctgtggGgctggcacagaggcacaggt	9	6	19	7	0	1	2	1	1	0	1	1	2	1	2	0	7	1	4	0	7	1	0			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr3:130116569G>A	ENST00000432398.2	+	9	4205	c.3711G>A	c.(3709-3711)ggG>ggA	p.G1237G	COL6A5_ENST00000265379.6_Silent_p.G1237G	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1237	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 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						TGAGCTGTGGGGCTGGCACAG	0.542																																					p.G1237G		Atlas-SNP	.											.	COL6A5	205	.	0			c.G3711A						PASS	.						103	94	97					3																	130116569		692	1591	2283	SO:0001819	synonymous_variant	256076	exon9			CTGTGGGGCTGGC	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.3711G>A	3.37:g.130116569G>A		110	0	0		94	42	0.446809	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Silent	SNP	ENST00000432398.2	37																																																																																				.	.	none		0.542	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264		A	130116569	G	A	130116569	2	1	47	1	0	0	0	0	0	0	0	1	3704	1219	43	2		2	COL6A5	3	130116569	Silent	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	11467495	130116569	67905861	33	15767											
POLN	353497	hgsc.bcm.edu	37	chr4	2097647	2097647	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcgtgtgtcacctgttccaCgggcacatccttcctgcatg	5	12	10	14	2	1	0	1	0	0	0	4	0	4	0	4	1	2	3	4	1	0	2	rs571169469		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr4:2097647C>T	ENST00000511885.2	-	20	2349	c.1996G>A	c.(1996-1998)Gtg>Atg	p.V666M	POLN_ENST00000382865.1_Missense_Mutation_p.V666M			Q7Z5Q5	DPOLN_HUMAN	polymerase (DNA directed) nu	666					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)			ACCTGTTCCACGGGCACATCC	0.597								DNA polymerases (catalytic subunits)																													p.V666M		Atlas-SNP	.											.	POLN	82	.	0			c.G1996A						PASS	.						225	169	187					4																	2097647		2203	4300	6503	SO:0001583	missense	353497	exon18			GTTCCACGGGCAC	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.1996G>A	4.37:g.2097647C>T	ENSP00000435506:p.Val666Met	108	0	0		108	17	0.157407	NM_181808	A2A336|B4E158|Q4TTW4|Q6ZNF4	Missense_Mutation	SNP	ENST00000511885.2	37	CCDS3360.1	.	.	.	.	.	.	.	.	.	.	C	5.125	0.208765	0.09757	.	.	ENSG00000130997	ENST00000511885;ENST00000382865;ENST00000253313;ENST00000382857	D;D	0.96651	-4.08;-4.08	3.68	-6.39	0.01951	DNA-directed DNA polymerase, family A, palm domain (2);	1.857100	0.02434	N	0.083837	D	0.89574	0.6754	L	0.39085	1.19	0.09310	N	1	B;P;B	0.35807	0.025;0.522;0.007	B;B;B	0.18561	0.022;0.021;0.01	D	0.84221	0.0461	10	0.39692	T	0.17	0.6846	2.5723	0.04798	0.1033:0.4161:0.1645:0.3161	.	197;357;666	C9JDP8;E9PE06;Q7Z5Q5	.;.;DPOLN_HUMAN	M	666;666;357;197	ENSP00000435506:V666M;ENSP00000372316:V666M	ENSP00000253313:V357M	V	-	1	0	POLN	2067445	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.471000	0.00990	-1.765000	0.01303	-1.332000	0.01269	GTG	.	.	none		0.597	POLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000205684.2	NM_181808		T	2097647	C	T	2097647	3	4	47	1	0	0	0	0	1	0	0	0	12216	536	19	1	734	1	POLN	4	2097647	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10		2097647	189056629	34	15768											
MAN2B2	23324	hgsc.bcm.edu	37	chr4	6612851	6612851	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	ctgtggaacaacttcgactgGgacctgggctacaacctcac	10	8	10	13	1	1	0	1	0	0	0	2	3	1	2	2	3	4	1	2	3	4	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr4:6612851G>C	ENST00000285599.3	+	15	2445	c.2409G>C	c.(2407-2409)tgG>tgC	p.W803C	MAN2B2_ENST00000504248.1_Missense_Mutation_p.W752C	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	803					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						ACTTCGACTGGGACCTGGGCT	0.652																																					p.W803C		Atlas-SNP	.											.	MAN2B2	80	.	0			c.G2409C						PASS	.						58	58	58					4																	6612851		2203	4300	6503	SO:0001583	missense	23324	exon15			CGACTGGGACCTG	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.2409G>C	4.37:g.6612851G>C	ENSP00000285599:p.Trp803Cys	91	0	0		61	40	0.655738	NM_015274	Q66MP2|Q86T67	Missense_Mutation	SNP	ENST00000285599.3	37	CCDS33951.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.50|14.50	2.554295|2.554295	0.45487|0.45487	.|.	.|.	ENSG00000013288|ENSG00000013288	ENST00000505907|ENST00000285599;ENST00000504248	.|D;D	.|0.83591	.|-1.74;-1.74	4.87|4.87	4.87|4.87	0.63330|0.63330	.|Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	.|0.126763	.|0.56097	.|D	.|0.000023	D|D	0.90164|0.90164	0.6926|0.6926	M|M	0.78801|0.78801	2.425|2.425	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.76494	.|0.999;0.999;0.996	.|D;D;D	.|0.74348	.|0.974;0.983;0.917	D|D	0.90939|0.90939	0.4796|0.4796	5|10	.|0.59425	.|D	.|0.04	-9.7275|-9.7275	13.6149|13.6149	0.62101|0.62101	0.0:0.0:0.8445:0.1555|0.0:0.0:0.8445:0.1555	.|.	.|752;803;803	.|E9PCD7;Q9Y2E5;Q9Y2E5-2	.|.;MA2B2_HUMAN;.	A|C	802|803;752	.|ENSP00000285599:W803C;ENSP00000423129:W752C	.|ENSP00000285599:W803C	G|W	+|+	2|3	0|0	MAN2B2|MAN2B2	6663752|6663752	1.000000|1.000000	0.71417|0.71417	0.019000|0.019000	0.16419|0.16419	0.679000|0.679000	0.39708|0.39708	6.770000|6.770000	0.74990|0.74990	2.260000|2.260000	0.74910|0.74910	0.555000|0.555000	0.69702|0.69702	GGG|TGG	.	.	none		0.652	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274		C	6612851	G	C	6612851	3	2	47	1	0	0	0	0	1	0	0	0	9226	1241	43	4	2467	4	MAN2B2	4	6612851	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	4515204	6612851	184541425	35	15769											
TAPT1	202018	hgsc.bcm.edu	37	chr4	16165117	16165117	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttttccttttgatgaataggTtgtttggtgatggaggcaga	8	17	13	3	0	0	4	0	3	0	1	1	5	1	5	1	4	0	3	1	4	2	7			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr4:16165117T>C	ENST00000405303.2	-	14	1601	c.1518A>G	c.(1516-1518)caA>caG	p.Q506Q	TAPT1_ENST00000304584.8_3'UTR|TAPT1_ENST00000399920.3_Silent_p.Q395Q	NM_153365.2	NP_699196.2	Q6NXT6	TAPT1_HUMAN	transmembrane anterior posterior transformation 1	506					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						GATGAATAGGTTGTTTGGTGA	0.363																																					p.Q506Q		Atlas-SNP	.											.	TAPT1	31	.	0			c.A1518G						PASS	.						92	87	88					4																	16165117		1875	4124	5999	SO:0001819	synonymous_variant	202018	exon14			AATAGGTTGTTTG	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.1518A>G	4.37:g.16165117T>C		234	0	0		209	45	0.215311	NM_153365	Q8N2S3|Q9NZK9	Silent	SNP	ENST00000405303.2	37	CCDS47030.1																																																																																			.	.	none		0.363	TAPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359568.1	NM_153365		C	16165117	T	C	16165117	2	2	47	1	0	0	0	0	0	0	0	1	15569	1722	60	3		3	TAPT1	4	16165117	Silent	SNP	T	TCGA-RQ-AAAT-01A-11D-A38X-10	9552266	16165117	174989159	36	15770											
TAPT1	202018	hgsc.bcm.edu	37	chr4	16165144	16165144	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtgatggaggcagacaggttTtcttctgtggaaaggcctgt	8	12	15	6	0	2	2	0	1	2	1	2	4	2	4	1	5	0	2	1	5	1	3			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr4:16165144T>C	ENST00000405303.2	-	14	1574	c.1491A>G	c.(1489-1491)gaA>gaG	p.E497E	TAPT1_ENST00000304584.8_3'UTR|TAPT1_ENST00000399920.3_Silent_p.E386E	NM_153365.2	NP_699196.2	Q6NXT6	TAPT1_HUMAN	transmembrane anterior posterior transformation 1	497					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						CAGACAGGTTTTCTTCTGTGG	0.348																																					p.E497E		Atlas-SNP	.											.	TAPT1	31	.	0			c.A1491G						PASS	.						63	59	60					4																	16165144		1856	4112	5968	SO:0001819	synonymous_variant	202018	exon14			CAGGTTTTCTTCT	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.1491A>G	4.37:g.16165144T>C		203	0	0		177	43	0.242938	NM_153365	Q8N2S3|Q9NZK9	Silent	SNP	ENST00000405303.2	37	CCDS47030.1																																																																																			.	.	none		0.348	TAPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359568.1	NM_153365		C	16165144	T	C	16165144	2	2	47	1	0	0	0	0	0	0	0	1	15569	1838	64	3		3	TAPT1	4	16165144	Silent	SNP	T	TCGA-RQ-AAAT-01A-11D-A38X-10	27	16165144	174989132	37	15771											
GUF1	60558	hgsc.bcm.edu	37	chr4	44680787	44680787	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggctaccgacaggctctacAgctccgcagaattcaaggtg	10	7	12	12	2	2	1	1	0	1	1	3	2	3	1	2	3	3	4	2	3	4	3			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr4:44680787A>G	ENST00000281543.5	+	1	342	c.148A>G	c.(148-150)Agc>Ggc	p.S50G	GUF1_ENST00000506793.1_Intron	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						CAGGCTCTACAGCTCCGCAGA	0.622																																					p.S50G		Atlas-SNP	.											.	GUF1	72	.	0			c.A148G						PASS	.						13	15	15					4																	44680787		2199	4292	6491	SO:0001583	missense	60558	exon1			CTCTACAGCTCCG		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.148A>G	4.37:g.44680787A>G	ENSP00000281543:p.Ser50Gly	278	0	0		242	37	0.152893	NM_021927		Missense_Mutation	SNP	ENST00000281543.5	37	CCDS3468.1	.	.	.	.	.	.	.	.	.	.	A	11.33	1.607169	0.28623	.	.	ENSG00000151806	ENST00000281543	T	0.70164	-0.46	4.01	-5.1	0.02911	.	1.118960	0.06514	N	0.738611	T	0.36026	0.0952	N	0.08118	0	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.09207	-1.0685	10	0.32370	T	0.25	0.5496	0.4147	0.00447	0.2657:0.1519:0.2865:0.296	.	50	Q8N442	GUF1_HUMAN	G	50	ENSP00000281543:S50G	ENSP00000281543:S50G	S	+	1	0	GUF1	44375544	0.004000	0.15560	0.002000	0.10522	0.081000	0.17604	-0.295000	0.08298	-0.969000	0.03573	0.533000	0.62120	AGC	.	.	none		0.622	GUF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250469.3	NM_021927		G	44680787	A	G	44680787	3	3	47	1	0	0	0	0	1	0	0	0	6908	188	7	3	150	3	GUF1	4	44680787	Missense_Mutation	SNP	A	TCGA-RQ-AAAT-01A-11D-A38X-10	28515643	44680787	146473489	38	15772											
PDLIM5	10611	hgsc.bcm.edu	37	chr4	95575792	95575792	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gccaaaggaagatccttggaGtaagtattggaaacgttttt	13	12	11	5	1	0	1	0	0	0	1	1	4	1	4	2	3	1	3	2	3	5	6			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr4:95575792G>A	ENST00000317968.4	+	10	1600		c.e10+1		PDLIM5_ENST00000437932.1_Splice_Site|PDLIM5_ENST00000514743.1_Splice_Site|PDLIM5_ENST00000380176.3_Splice_Site|PDLIM5_ENST00000542407.1_Splice_Site	NM_001256428.1|NM_006457.4	NP_001243357.1|NP_006448	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5						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)		GATCCTTGGAGTAAGTATTGG	0.348																																					.		Atlas-SNP	.											.	PDLIM5	76	.	0			c.1464+1G>A						PASS	.						110	112	111					4																	95575792		2203	4300	6503	SO:0001630	splice_region_variant	10611	exon10			CTTGGAGTAAGTA	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.1464+1G>A	4.37:g.95575792G>A		172	0	0		200	45	0.225	NM_006457	A8K6F9|D6RB78|E9PBF5|O60705|Q56VN4|Q5UW38|Q8WVK0	Splice_Site	SNP	ENST00000317968.4	37	CCDS3641.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.666750	0.88251	.	.	ENSG00000163110	ENST00000437932;ENST00000317968;ENST00000503974;ENST00000542407;ENST00000514743	.	.	.	5.98	5.98	0.97165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.452	0.99131	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PDLIM5	95794815	1.000000	0.71417	1.000000	0.80357	0.919000	0.55068	9.832000	0.99423	2.838000	0.97847	0.591000	0.81541	.	.	.	none		0.348	PDLIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253586.1		Intron	A	95575792	G	A	95575792	5	1	47	1	0	0	0	0	0	0	1	0	11692	1043	36	2	1659	2	PDLIM5	4	95575792	Splice_Site	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	50895005	95575792	95578484	39	15773											
DKK2	27123	hgsc.bcm.edu	37	chr4	107845787	107845787	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	taatgaccgtggtttcgatcTctgtgccgagtaccatccag	8	12	10	11	3	1	1	0	1	1	0	4	3	2	1	4	1	2	2	4	1	2	3			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr4:107845787T>C	ENST00000285311.3	-	3	1149	c.444A>G	c.(442-444)agA>agG	p.R148R	DKK2_ENST00000513208.1_Silent_p.R48R|DKK2_ENST00000510463.1_Silent_p.R102R	NM_014421.2	NP_055236.1	Q9UBU2	DKK2_HUMAN	dickkopf WNT signaling pathway inhibitor 2	148					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)		GGTTTCGATCTCTGTGCCGAG	0.443																																					p.R148R		Atlas-SNP	.											.	DKK2	96	.	0			c.A444G						PASS	.						236	214	222					4																	107845787		2203	4300	6503	SO:0001819	synonymous_variant	27123	exon3			TCGATCTCTGTGC	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.444A>G	4.37:g.107845787T>C		294	0	0		224	152	0.678571	NM_014421	A0AVE9|B2R6S7|Q9UIU3	Silent	SNP	ENST00000285311.3	37	CCDS3675.1																																																																																			.	.	none		0.443	DKK2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253959.4			C	107845787	T	C	107845787	2	2	47	1	0	0	0	0	0	0	0	1	4547	1548	54	3		3	DKK2	4	107845787	Silent	SNP	T	TCGA-RQ-AAAT-01A-11D-A38X-10	12269995	107845787	83308489	40	15774											
SEC24B	10427	hgsc.bcm.edu	37	chr4	110384430	110384430	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gccatgtactctgccagctcTtctgttgcgtctcagggatt	5	14	10	12	1	4	0	1	0	4	0	5	1	4	1	2	1	4	3	2	1	1	4			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr4:110384430T>C	ENST00000265175.5	+	2	562	c.507T>C	c.(505-507)tcT>tcC	p.S169S	SEC24B_ENST00000504968.2_Silent_p.S200S|SEC24B_ENST00000399100.2_Silent_p.S169S	NM_006323.2	NP_006314.2	O95487	SC24B_HUMAN	SEC24 family member B	169					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)		CTGCCAGCTCTTCTGTTGCGT	0.478																																					p.S169S		Atlas-SNP	.											.	SEC24B	186	.	0			c.T507C						PASS	.						328	314	318					4																	110384430		2031	4188	6219	SO:0001819	synonymous_variant	10427	exon2			CAGCTCTTCTGTT	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.507T>C	4.37:g.110384430T>C		205	0	0		187	38	0.203209	NM_006323	B7ZKM8|B7ZKN4|Q0VG08	Silent	SNP	ENST00000265175.5	37	CCDS47124.1																																																																																			.	.	none		0.478	SEC24B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364693.2			C	110384430	T	C	110384430	2	2	47	1	0	0	0	0	0	0	0	1	14010	1596	56	3		3	SEC24B	4	110384430	Silent	SNP	T	TCGA-RQ-AAAT-01A-11D-A38X-10	2538643	110384430	80769846	41	15775											
FGG	2266	hgsc.bcm.edu	37	chr4	155526109	155526109	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	attgtgagtctgttgaatggGattatcttcatagtggtttt	8	19	11	3	0	3	2	1	2	2	0	3	3	3	3	0	2	0	2	0	2	3	7			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr4:155526109G>T	ENST00000336098.3	-	9	1277	c.1239C>A	c.(1237-1239)atC>atA	p.I413I	FGG_ENST00000405164.1_Silent_p.I421I|FGG_ENST00000404648.3_Silent_p.I413I|FGG_ENST00000407946.1_Silent_p.I421I	NM_021870.2	NP_068656.2	P02679	FIBG_HUMAN	fibrinogen gamma chain	413	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.|Gamma-chain polymerization, binding amino end of another fibrin alpha chain.				blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|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)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|receptor binding (GO:0005102)|structural molecule activity (GO:0005198)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(9)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27	all_hematologic(180;0.215)	Renal(120;0.0458)			Sucralfate(DB00364)	TGTTGAATGGGATTATCTTCA	0.458																																					p.I413I		Atlas-SNP	.											.	FGG	71	.	0			c.C1239A						PASS	.						202	184	190					4																	155526109		2203	4300	6503	SO:0001819	synonymous_variant	2266	exon9			GAATGGGATTATC		CCDS3788.1, CCDS47153.1	4q28	2014-09-17			ENSG00000171557	ENSG00000171557		"Fibrinogen C domain containing", "Endogenous ligands"	3694	protein-coding gene	gene with protein product		134850	"fibrinogen, gamma polypeptide"				Standard	NM_000509		Approved		uc003ioj.3	P02679	OTTHUMG00000150329	ENST00000336098.3:c.1239C>A	4.37:g.155526109G>T		213	0	0		164	34	0.207317	NM_000509	A8K057|P04469|P04470|Q53Y18|Q96A14|Q96KJ3|Q9UC62|Q9UC63|Q9UCF3	Silent	SNP	ENST00000336098.3	37	CCDS3788.1																																																																																			.	.	none		0.458	FGG-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317581.1	NM_021870		T	155526109	G	T	155526109	2	4	47	1	0	0	0	0	0	0	0	1	5878	1164	41	4		4	FGG	4	155526109	Silent	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	45141679	155526109	35628167	42	15776											
GRIA2	2891	hgsc.bcm.edu	37	chr4	158142838	158142838	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggggggctatttcctaggggCgccgatcaagaatacagtgc	9	8	15	9	2	1	1	1	0	0	1	2	2	2	1	2	5	2	1	2	5	5	4	rs371935251		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr4:158142838C>T	ENST00000264426.9	+	2	387	c.108C>T	c.(106-108)ggC>ggT	p.G36G	GRIA2_ENST00000449365.1_5'UTR|GRIA2_ENST00000296526.7_Silent_p.G36G|GRIA2_ENST00000504801.1_Intron|GRIA2_ENST00000507898.1_5'UTR|GRIA2_ENST00000393815.2_5'UTR	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	36					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)	p.G36G(2)		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)	TTCCTAGGGGCGCCGATCAAG	0.537																																					p.G36G		Atlas-SNP	.											GRIA2_ENST00000264426,NS,carcinoma,0,2	GRIA2	358	2	2	Substitution - coding silent(2)	kidney(2)	c.C108T						PASS	.						95	99	98					4																	158142838		2203	4300	6503	SO:0001819	synonymous_variant	2891	exon2			TAGGGGCGCCGAT		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.108C>T	4.37:g.158142838C>T		100	0	0		83	17	0.204819	NM_000826	A8MT92|I6L997|Q96FP6	Silent	SNP	ENST00000264426.9	37	CCDS43274.1																																																																																			.	.	alt		0.537	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2			T	158142838	C	T	158142838	2	4	47	1	0	0	0	0	0	0	0	1	6777	755	27	1		1	GRIA2	4	158142838	Silent	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	2616729	158142838	33011438	43	15777											
ETFDH	2110	hgsc.bcm.edu	37	chr4	159601621	159601621	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcgtaatttttgtgcagcaTatcagtgctttcatgcctta	8	18	7	8	1	2	0	2	0	0	0	3	0	2	0	1	0	4	4	1	0	3	7			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr4:159601621T>G	ENST00000511912.1	+	2	369	c.37T>G	c.(37-39)Tat>Gat	p.Y13D	ETFDH_ENST00000307738.5_Intron	NM_001281738.1|NM_004453.2	NP_001268667.1|NP_004444.2	Q16134	ETFD_HUMAN	electron-transferring-flavoprotein dehydrogenase	13					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)		TTGTGCAGCATATCAGTGCTT	0.308																																					p.Y13D		Atlas-SNP	.											.	ETFDH	57	.	0			c.T37G						PASS	.						69	65	66					4																	159601621		2203	4300	6503	SO:0001583	missense	2110	exon2			GCAGCATATCAGT	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.37T>G	4.37:g.159601621T>G	ENSP00000426638:p.Tyr13Asp	374	0	0		339	209	0.616519	NM_004453	B4E3R9|J3KND9|Q7Z347	Missense_Mutation	SNP	ENST00000511912.1	37	CCDS3800.1	.	.	.	.	.	.	.	.	.	.	T	12.61	1.990778	0.35131	.	.	ENSG00000171503	ENST00000511912	D	0.97186	-4.28	5.63	1.57	0.23409	.	0.343116	0.34435	N	0.003961	D	0.92237	0.7538	L	0.29908	0.895	0.80722	D	1	B	0.10296	0.003	B	0.11329	0.006	D	0.85706	0.1316	10	0.36615	T	0.2	0.1782	7.7593	0.28942	0.0:0.403:0.0:0.597	.	13	Q16134	ETFD_HUMAN	D	13	ENSP00000426638:Y13D	ENSP00000426638:Y13D	Y	+	1	0	ETFDH	159821071	0.697000	0.27767	0.728000	0.30774	0.906000	0.53458	0.223000	0.17719	0.503000	0.28060	-0.376000	0.06991	TAT	.	.	none		0.308	ETFDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365718.2			G	159601621	T	G	159601621	3	3	47	1	0	0	0	0	1	0	0	0	5273	1406	49	5	43	5	ETFDH	4	159601621	Missense_Mutation	SNP	T	TCGA-RQ-AAAT-01A-11D-A38X-10	1458783	159601621	31552655	44	15778											
ODZ3	55714	hgsc.bcm.edu	37	chr4	183650276	183650276	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccttttatgatcgaatcagtTtccttataggatctgatagc	10	16	7	8	1	2	2	1	2	1	0	4	4	3	3	2	1	1	1	2	1	5	6			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr4:183650276T>G	ENST00000511685.1	+	14	2650	c.2527T>G	c.(2527-2529)Ttc>Gtc	p.F843V	TENM3_ENST00000502950.1_3'UTR|TENM3_ENST00000406950.2_Missense_Mutation_p.F843V			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	843					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)										TCGAATCAGTTTCCTTATAGG	0.418																																					p.F843V		Atlas-SNP	.											.	.	.	.	0			c.T2527G						PASS	.						113	110	111					4																	183650276		1918	4133	6051	SO:0001583	missense	55714	exon13			ATCAGTTTCCTTA	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.2527T>G	4.37:g.183650276T>G	ENSP00000424226:p.Phe843Val	144	0	0		136	17	0.125	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	T	13.87	2.367200	0.41902	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.89810	-2.57;-2.57	4.84	4.84	0.62591	.	.	.	.	.	D	0.94291	0.8166	M	0.85710	2.77	0.80722	D	1	D	0.57899	0.981	D	0.65140	0.932	D	0.95185	0.8303	9	0.87932	D	0	.	14.8669	0.70422	0.0:0.0:0.0:1.0	.	843	Q9P273	TEN3_HUMAN	V	843	ENSP00000424226:F843V;ENSP00000385276:F843V	ENSP00000385276:F843V	F	+	1	0	ODZ3	183887270	1.000000	0.71417	0.946000	0.38457	0.603000	0.37013	5.991000	0.70602	2.154000	0.67381	0.460000	0.39030	TTC	.	.	none		0.418	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1			G	183650276	T	G	183650276	3	3	47	1	0	0	0	0	1	0	0	0	10845	1841	64	5	2577	5	ODZ3	4	183650276	Missense_Mutation	SNP	T	TCGA-RQ-AAAT-01A-11D-A38X-10	24048655	183650276	7504000	45	15779											
FAM105B	90268	hgsc.bcm.edu	37	chr5	14681631	14681631	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gcgagtccgtggtgataattActgtgcactgagggccacgc	8	9	14	10	3	0	2	0	2	0	0	1	3	1	2	2	2	2	1	2	2	2	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr5:14681631A>T	ENST00000284274.4	+	4	461	c.383A>T	c.(382-384)tAc>tTc	p.Y128F		NM_138348.4	NP_612357.4	Q96BN8	OTUL_HUMAN		128	OTU.				canonical Wnt signaling pathway (GO:0060070)|innate immune response (GO:0045087)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|protein linear deubiquitination (GO:1990108)|sprouting angiogenesis (GO:0002040)	cytoplasm (GO:0005737)|LUBAC complex (GO:0071797)	cysteine-type peptidase activity (GO:0008234)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	14	Lung NSC(4;0.00696)					GGTGATAATTACTGTGCACTG	0.562																																					p.Y128F		Atlas-SNP	.											.	FAM105B	36	.	0			c.A383T						PASS	.						76	83	81					5																	14681631		2080	4218	6298	SO:0001583	missense	90268	exon4			ATAATTACTGTGC																												ENST00000284274.4:c.383A>T	5.37:g.14681631A>T	ENSP00000284274:p.Tyr128Phe	194	0	0		116	36	0.310345	NM_138348	D3DTD3|Q8NAS0|Q96IA3	Missense_Mutation	SNP	ENST00000284274.4	37	CCDS43302.1	.	.	.	.	.	.	.	.	.	.	A	24.5	4.542953	0.86022	.	.	ENSG00000154124	ENST00000284274	T	0.19532	2.14	5.82	5.82	0.92795	.	0.061315	0.64402	D	0.000002	T	0.41143	0.1146	M	0.68317	2.08	0.50813	D	0.999894	D	0.71674	0.998	D	0.63488	0.915	T	0.31558	-0.9939	10	0.87932	D	0	-16.5211	11.3113	0.49366	0.9272:0.0:0.0728:0.0	.	128	Q96BN8	F105B_HUMAN	F	128	ENSP00000284274:Y128F	ENSP00000284274:Y128F	Y	+	2	0	FAM105B	14734631	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.027000	0.93706	2.225000	0.72522	0.460000	0.39030	TAC	.	.	none		0.562	FAM105B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366012.1			T	14681631	A	T	14681631	3	4	47	1	0	0	0	0	1	0	0	0	5393	391	14	5	397	5	FAM105B	5	14681631	Missense_Mutation	SNP	A	TCGA-RQ-AAAT-01A-11D-A38X-10		14681631	166233629	46	15780											
MAP1B	4131	hgsc.bcm.edu	37	chr5	71492363	71492363	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aggctggtggtgccgaggagCagtatggattcctcaccaca	9	8	14	10	1	1	0	1	0	0	0	2	3	2	2	3	5	2	3	3	5	1	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr5:71492363C>A	ENST00000296755.7	+	5	3479	c.3181C>A	c.(3181-3183)Cag>Aag	p.Q1061K		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	1061					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)		TGCCGAGGAGCAGTATGGATT	0.527																																					p.Q1061K	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.C3181A						PASS	.						102	106	104					5																	71492363		2203	4300	6503	SO:0001583	missense	4131	exon5			GAGGAGCAGTATG	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.3181C>A	5.37:g.71492363C>A	ENSP00000296755:p.Gln1061Lys	50	0	0		36	14	0.388889	NM_005909	A2BDK5	Missense_Mutation	SNP	ENST00000296755.7	37	CCDS4012.1	.	.	.	.	.	.	.	.	.	.	C	0.783	-0.761567	0.02996	.	.	ENSG00000131711	ENST00000296755	T	0.03386	3.95	5.86	4.91	0.64330	.	0.186043	0.38164	N	0.001796	T	0.01730	0.0055	N	0.01874	-0.695	0.33778	D	0.623966	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.44651	-0.9314	10	0.12430	T	0.62	-19.5589	13.6838	0.62504	0.2629:0.7371:0.0:0.0	.	935;1061	A2BDK6;P46821	.;MAP1B_HUMAN	K	1061	ENSP00000296755:Q1061K	ENSP00000296755:Q1061K	Q	+	1	0	MAP1B	71528119	0.918000	0.31147	0.998000	0.56505	0.626000	0.37791	1.922000	0.40045	2.784000	0.95788	0.655000	0.94253	CAG	.	.	none		0.527	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909		A	71492363	C	A	71492363	3	1	47	1	0	0	0	0	1	0	0	0	9237	711	25	4	3199	4	MAP1B	5	71492363	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	56810732	71492363	109422897	47	15781											
MCC	4163	hgsc.bcm.edu	37	chr5	112419851	112419851	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccgatcagatgatgacgattCggaccttgtctttgatagct	9	13	10	9	3	2	4	1	3	1	1	3	7	2	5	2	1	1	1	2	1	1	4	rs373730711		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr5:112419851C>T	ENST00000302475.4	-	8	1575	c.1012G>A	c.(1012-1014)Gaa>Aaa	p.E338K	MCC_ENST00000515367.2_Missense_Mutation_p.E275K|MCC_ENST00000408903.3_Missense_Mutation_p.E528K|MCC_ENST00000514701.3_5'UTR	NM_002387.2	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers	338					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)		GATGACGATTCGGACCTTGTC	0.448													C|||	1	0.000199681	0.0	0.0	5008	,	,		19552	0.0		0.0	False		,,,				2504	0.001				p.E528K		Atlas-SNP	.											.	MCC	234	.	0			c.G1582A						PASS	.	C	LYS/GLU,LYS/GLU	1,4403	2.1+/-5.4	0,1,2201	178	162	168		1582,1012	5.5	0.6	5		168	0,8600		0,0,4300	no	missense,missense	MCC	NM_001085377.1,NM_002387.2	56,56	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	528/1020,338/830	112419851	1,13003	2202	4300	6502	SO:0001583	missense	4163	exon10			ACGATTCGGACCT		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.1012G>A	5.37:g.112419851C>T	ENSP00000305617:p.Glu338Lys	142	0	0		94	30	0.319149	NM_001085377	D3DT05|Q6ZR04	Missense_Mutation	SNP	ENST00000302475.4	37	CCDS4111.1	.	.	.	.	.	.	.	.	.	.	C	15.45	2.836563	0.50951	2.27E-4	0.0	ENSG00000171444	ENST00000302475;ENST00000515367;ENST00000408903	T;T;T	0.33865	2.56;2.57;1.39	5.47	5.47	0.80525	.	0.060761	0.64402	D	0.000007	T	0.29976	0.0750	N	0.14661	0.345	0.58432	D	0.999998	P;P;D;P	0.56521	0.892;0.738;0.976;0.817	B;B;P;B	0.45856	0.099;0.139;0.495;0.099	T	0.05225	-1.0898	10	0.35671	T	0.21	-5.0905	19.3251	0.94258	0.0:1.0:0.0:0.0	.	338;300;528;338	B7Z6G0;B3KTX0;P23508-2;P23508	.;.;.;CRCM_HUMAN	K	338;275;528	ENSP00000305617:E338K;ENSP00000421615:E275K;ENSP00000386227:E528K	ENSP00000305617:E338K	E	-	1	0	MCC	112447750	1.000000	0.71417	0.619000	0.29118	0.283000	0.27025	5.961000	0.70356	2.574000	0.86865	0.563000	0.77884	GAA	.	.	weak		0.448	MCC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250736.3	NM_001085377		T	112419851	C	T	112419851	3	4	47	1	0	0	0	0	1	0	0	0	9382	893	31	1	1517	1	MCC	5	112419851	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	40927488	112419851	68495409	48	15782											
LMNB1	4001	hgsc.bcm.edu	37	chr5	126113530	126113530	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cagatcgagctgggcaagtgCaaggcggaacacgaccagct	12	4	14	11	3	0	1	0	0	0	1	1	4	0	2	1	3	4	4	1	3	3	0			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr5:126113530C>T	ENST00000261366.5	+	1	691	c.330C>T	c.(328-330)tgC>tgT	p.C110C	LMNB1_ENST00000460265.1_3'UTR|RP11-434D11.4_ENST00000509185.2_lincRNA|LMNB1_ENST00000395354.1_Silent_p.C110C	NM_001198557.1|NM_005573.3	NP_001185486.1|NP_005564.1	P20700	LMNB1_HUMAN	lamin B1	110	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)		TGGGCAAGTGCAAGGCGGAAC	0.711																																					p.C110C		Atlas-SNP	.											.	LMNB1	49	.	0			c.C330T						PASS	.						4	4	4					5																	126113530		1956	3851	5807	SO:0001819	synonymous_variant	4001	exon1			CAAGTGCAAGGCG	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.330C>T	5.37:g.126113530C>T		37	0	0		24	10	0.416667	NM_005573	B2R6J6|Q3SYN7|Q96EI6	Silent	SNP	ENST00000261366.5	37	CCDS4140.1																																																																																			.	.	none		0.711	LMNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250956.2	NM_005573		T	126113530	C	T	126113530	2	4	47	1	0	0	0	0	0	0	0	1	8858	718	25	2		2	LMNB1	5	126113530	Silent	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	13693679	126113530	54801730	49	15783											
PCDHA4	56144	hgsc.bcm.edu	37	chr5	140186856	140186856	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gcagcctgggaggcagggaaCggtcagctccactactcggt	8	6	15	12	2	1	0	1	0	0	0	3	2	2	2	2	5	4	3	2	5	2	1			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr5:140186856C>T	ENST00000530339.1	+	1	84	c.84C>T	c.(82-84)aaC>aaT	p.N28N	PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Silent_p.N28N|PCDHA4_ENST00000356878.4_Silent_p.N28N|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	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)	p.N28N(1)		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)			AGGCAGGGAACGGTCAGCTCC	0.627																																					p.N28N		Atlas-SNP	.											PCDHA4_ENST00000530339,colon,carcinoma,+1,5	PCDHA4	419	5	1	Substitution - coding silent(1)	ovary(1)	c.C84T						scavenged	.						64	71	69					5																	140186856		2203	4300	6503	SO:0001819	synonymous_variant	56144	exon1			AGGGAACGGTCAG	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.84C>T	5.37:g.140186856C>T		110	1	0.00909091		92	30	0.326087	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			.	.	none		0.627	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907		T	140186856	C	T	140186856	2	4	47	1	0	0	0	0	0	0	0	1	11535	535	19	1		1	PCDHA4	5	140186856	Silent	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	14073326	140186856	40728404	50	15784											
PCDHB5	26167	hgsc.bcm.edu	37	chr5	140517068	140517068	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcccaggcccaggccgactcGctcactgtctacctggtggt	5	8	12	16	2	2	0	1	0	1	0	3	1	2	0	4	4	1	1	4	4	1	1			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr5:140517068G>A	ENST00000231134.5	+	1	2269	c.2052G>A	c.(2050-2052)tcG>tcA	p.S684S		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	684					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)			AGGCCGACTCGCTCACTGTCT	0.697																																					p.S684S		Atlas-SNP	.											PCDHB5,NS,carcinoma,+1,1	PCDHB5	184	1	0			c.G2052A						PASS	.						68	72	70					5																	140517068		2199	4295	6494	SO:0001819	synonymous_variant	26167	exon1			CGACTCGCTCACT	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.2052G>A	5.37:g.140517068G>A		85	0	0		56	24	0.428571	NM_015669	Q549F4|Q9UFU9	Silent	SNP	ENST00000231134.5	37	CCDS4247.1																																																																																			.	.	none		0.697	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669		A	140517068	G	A	140517068	2	1	47	1	0	0	0	0	0	0	0	1	11554	1074	38	1		1	PCDHB5	5	140517068	Silent	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	330212	140517068	40398192	51	15785											
HIST1H1C	3006	hgsc.bcm.edu	37	chr6	26056330	26056330	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gcttccccggaggctgccttCttgttgagtttaaaggagcc	6	12	12	11	1	1	1	0	1	1	0	2	3	2	3	4	3	2	4	4	3	2	6			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:26056330C>G	ENST00000343677.2	-	1	369	c.327G>C	c.(325-327)aaG>aaC	p.K109N		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	109	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				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)	p.K109N(1)		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						AGGCTGCCTTCTTGTTGAGTT	0.557																																					p.K109N		Atlas-SNP	.											HIST1H1C,colon,carcinoma,0,2	HIST1H1C	80	2	1	Substitution - Missense(1)	ovary(1)	c.G327C						PASS	.						80	87	85					6																	26056330		2203	4300	6503	SO:0001583	missense	3006	exon1			TGCCTTCTTGTTG	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.327G>C	6.37:g.26056330C>G	ENSP00000339566:p.Lys109Asn	183	0	0		180	38	0.211111	NM_005319	A8K4I2	Missense_Mutation	SNP	ENST00000343677.2	37	CCDS4577.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.746067	0.89663	.	.	ENSG00000187837	ENST00000343677	T	0.11821	2.74	5.54	5.54	0.83059	Histone H1/H5 (2);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.107876	0.64402	D	0.000008	T	0.49029	0.1533	H	0.96604	3.85	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.66524	-0.5902	10	0.87932	D	0	-3.6427	18.8173	0.92081	0.0:1.0:0.0:0.0	.	109	P16403	H12_HUMAN	N	109	ENSP00000339566:K109N	ENSP00000339566:K109N	K	-	3	2	HIST1H1C	26164309	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	3.924000	0.56476	2.763000	0.94921	0.655000	0.94253	AAG	.	.	none		0.557	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319		G	26056330	C	G	26056330	3	3	47	1	0	0	0	0	1	0	0	0	7133	912	32	4	318	4	HIST1H1C	6	26056330	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10		26056330	145058737	52	15786											
HIST1H1E	3008	hgsc.bcm.edu	37	chr6	26156900	26156900	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtgagcaagggcaccctggtGcagaccaagggcaccggcgc	9	3	16	13	2	0	2	0	1	0	1	0	2	0	2	3	4	2	4	3	4	2	0	rs549787183		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:26156900G>A	ENST00000304218.3	+	1	342	c.282G>A	c.(280-282)gtG>gtA	p.V94V	HIST1H2BD_ENST00000289316.2_5'Flank|HIST1H2BD_ENST00000377777.4_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	94	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						GCACCCTGGTGCAGACCAAGG	0.607													G|||	1	0.000199681	0.0	0.0	5008	,	,		15327	0.0		0.001	False		,,,				2504	0.0				p.V94V		Atlas-SNP	.											HIST1H1E,NS,carcinoma,+2,1	HIST1H1E	69	1	0			c.G282A						PASS	.						51	55	53					6																	26156900		2203	4300	6503	SO:0001819	synonymous_variant	3008	exon1			CCTGGTGCAGACC	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.282G>A	6.37:g.26156900G>A		117	0	0		104	41	0.394231	NM_005321	Q4VB25	Silent	SNP	ENST00000304218.3	37	CCDS4586.1																																																																																			.	.	none		0.607	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321		A	26156900	G	A	26156900	2	1	47	1	0	0	0	0	0	0	0	1	7135	1306	46	2		2	HIST1H1E	6	26156900	Silent	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	100570	26156900	144958167	53	15787			1	76		3	3	1627	N	G_C	2.650645e-05
HIST1H1E	3008	hgsc.bcm.edu	37	chr6	26156969	26156969	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggcctctggggaagccaaGcctaaggctaaaaaggcagg	12	4	15	10	1	1	0	0	0	1	0	1	1	1	1	3	6	2	2	3	6	6	2	rs376044340		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:26156969G>A	ENST00000304218.3	+	1	411	c.351G>A	c.(349-351)aaG>aaA	p.K117K	HIST1H2BD_ENST00000289316.2_5'Flank|HIST1H2BD_ENST00000377777.4_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	117					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						GGGAAGCCAAGCCTAAGGCTA	0.642																																					p.K117K		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.G351A						PASS	.	G		0,4404		0,0,2202	24	31	29		351	1.7	1	6		29	2,8598		0,2,4298	no	coding-synonymous	HIST1H1E	NM_005321.2		0,2,6500	AA,AG,GG		0.0233,0.0,0.0154		117/220	26156969	2,13002	2202	4300	6502	SO:0001819	synonymous_variant	3008	exon1			AGCCAAGCCTAAG	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.351G>A	6.37:g.26156969G>A		96	0	0		88	23	0.261364	NM_005321	Q4VB25	Silent	SNP	ENST00000304218.3	37	CCDS4586.1																																																																																			.	.	weak		0.642	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321		A	26156969	G	A	26156969	2	1	47	1	0	0	0	0	0	0	0	1	7135	962	34	2		2	HIST1H1E	6	26156969	Silent	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	69	26156969	144958098	54	15788			1	76		3	3	1627	N	G_C	2.650645e-05
HIST1H2BD	3017	hgsc.bcm.edu	37	chr6	26158526	26158526	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agctattcagtgtatgtgtaCaaggtgctgaagcaggtcca	11	11	12	7	0	1	1	1	1	0	0	2	1	2	1	1	2	4	5	1	2	5	4			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:26158526C>T	ENST00000289316.2	+	1	153	c.129C>T	c.(127-129)taC>taT	p.Y43Y	HIST1H2BD_ENST00000377777.4_Silent_p.Y43Y	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.Y43Y		Atlas-SNP	.											.	HIST1H2BD	45	.	0			c.C129T						PASS	.						203	188	193					6																	26158526		2203	4300	6503	SO:0001819	synonymous_variant	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>T	6.37:g.26158526C>T		112	0	0		121	20	0.165289	NM_021063		Silent	SNP	ENST00000289316.2	37	CCDS4587.1																																																																																			.	.	none		0.557	HIST1H2BD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040088.1	NM_021063		T	26158526	C	T	26158526	2	4	47	1	0	0	0	0	0	0	0	1	7152	489	17	2		2	HIST1H2BD	6	26158526	Silent	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	1557	26158526	144956541	55	15789			1	76		3	3	1627	N	G_C	2.650645e-05
LTB	4050	hgsc.bcm.edu	37	chr6	31549597	31549597	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagtctgctcttacccagtcCttgctgggcctgtgccccgg	3	11	11	16	1	2	0	0	0	2	0	3	0	3	0	5	2	4	2	5	2	1	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:31549597C>T	ENST00000429299.2	-	2	209	c.202G>A	c.(202-204)Gga>Aga	p.G68R	LTB_ENST00000483972.1_Intron|LTB_ENST00000446745.2_Intron	NM_002341.1	NP_002332.1	Q06643	TNFC_HUMAN	lymphotoxin beta (TNF superfamily, member 3)	68				DPGAQAQQGL -> GLSAPGSGRT (in Ref. 2; AAB37342). {ECO:0000305}.	cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|signal transduction (GO:0007165)|skin development (GO:0043588)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	9						TTACCCAGTCCTTGCTGGGCC	0.622																																					p.G68R		Atlas-SNP	.											LTB,NS,lymphoid_neoplasm,0,1	LTB	19	1	0			c.G202A						PASS	.						93	102	99					6																	31549597		1510	2708	4218	SO:0001583	missense	4050	exon2			CCAGTCCTTGCTG	L11015	CCDS4703.1, CCDS4704.1	6p21.3	2013-05-22			ENSG00000227507	ENSG00000227507		"Tumor necrosis factor (ligand) superfamily"	6711	protein-coding gene	gene with protein product		600978		TNFC		7916655, 1714477	Standard	NM_002341		Approved	p33, TNFSF3	uc003nuk.3	Q06643	OTTHUMG00000031136	ENST00000429299.2:c.202G>A	6.37:g.31549597C>T	ENSP00000410481:p.Gly68Arg	101	0	0		83	34	0.409639	NM_002341	P78370|Q52LU8|Q99761	Missense_Mutation	SNP	ENST00000429299.2	37	CCDS4703.1	.	.	.	.	.	.	.	.	.	.	C	10.61	1.398347	0.25205	.	.	ENSG00000227507	ENST00000429299	T	0.20200	2.09	5.45	2.51	0.30379	.	1.717780	0.03086	N	0.159154	T	0.02230	0.0069	N	0.01668	-0.77	0.09310	N	0.999994	B	0.06786	0.001	B	0.08055	0.003	T	0.34725	-0.9817	10	0.15952	T	0.53	1.0706	8.1037	0.30872	0.0:0.5863:0.2923:0.1214	.	68	Q06643	TNFC_HUMAN	R	68	ENSP00000410481:G68R	ENSP00000410481:G68R	G	-	1	0	LTB	31657576	0.038000	0.19896	0.101000	0.21167	0.840000	0.47671	0.893000	0.28336	0.656000	0.30886	0.655000	0.94253	GGA	.	.	none		0.622	LTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076239.3			T	31549597	C	T	31549597	3	4	47	1	0	0	0	0	1	0	0	0	9079	690	24	2	544	2	LTB	6	31549597	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	5391071	31549597	139565470	56	15790											
HLA-DPA1	3113	hgsc.bcm.edu	37	chr6	33041313	33041313	+	Missense_Mutation	SNP	G	G	C																															agagggctctcaagatcacaGctctgatatggaacattctg																										TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:33041313G>C	ENST00000419277.1	-	2	164	c.35C>G	c.(34-36)gCt>gGt	p.A12G	HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.A12G|HLA-DPB1_ENST00000418931.2_5'Flank|HLA-DPB1_ENST00000535465.1_5'Flank|HLA-DPA1_ENST00000463066.1_5'UTR	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	12					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|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)|integral component of plasma membrane (GO:0005887)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						CAAGATCACAGCTCTGATATG	0.557																																					p.A12G		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.C35G						PASS	.						191	175	181					6																	33041313		1511	2709	4220	SO:0001583	missense	3113	exon1			ATCACAGCTCTGA	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.35C>G	6.37:g.33041313G>C	ENSP00000393566:p.Ala12Gly	75	0	0		49	18	0.367347	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Missense_Mutation	SNP	ENST00000419277.1	37	CCDS4764.1	.	.	.	.	.	.	.	.	.	.	G	11.25	1.582133	0.28180	.	.	ENSG00000231389	ENST00000419277;ENST00000428995;ENST00000448544;ENST00000453337;ENST00000417724	T;T;T	0.02656	4.56;4.56;4.21	4.1	1.19	0.21007	.	0.640274	0.14756	U	0.300279	T	0.00875	0.0029	L	0.41710	1.295	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.47235	-0.9133	10	0.87932	D	0	.	3.6194	0.08090	0.2214:0.0:0.5695:0.2091	.	12	P20036	DPA1_HUMAN	G	12	ENSP00000393566:A12G;ENSP00000402872:A12G;ENSP00000390929:A12G	ENSP00000398134:A12G	A	-	2	0	HLA-DPA1	33149291	0.000000	0.05858	0.000000	0.03702	0.126000	0.20510	-0.331000	0.07914	-0.010000	0.14271	-0.148000	0.13756	GCT	.	.	none		0.557	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554		C	33041313	G	C	33041313	3	2	47	1	0	0	0	0	1	0	0	0	7211	971	34	4	763	4	HLA-DPA1	6	33041313	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	1491716	33041313	138073754	57	15791	209	2									
HLA-DPA1	3113	hgsc.bcm.edu	37	chr6	33041314	33041314	+	Missense_Mutation	SNP	C	C	T																															gagggctctcaagatcacagCtctgatatggaacattctgt																										TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:33041314C>T	ENST00000419277.1	-	2	163	c.34G>A	c.(34-36)Gct>Act	p.A12T	HLA-DPA1_ENST00000428995.1_Missense_Mutation_p.A12T|HLA-DPB1_ENST00000418931.2_5'Flank|HLA-DPB1_ENST00000535465.1_5'Flank|HLA-DPA1_ENST00000463066.1_5'UTR	NM_001242524.1|NM_001242525.1	NP_001229453.1|NP_001229454.1	P20036	DPA1_HUMAN	major histocompatibility complex, class II, DP alpha 1	12					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cellular response to interferon-gamma (GO:0071346)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|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)|integral component of plasma membrane (GO:0005887)|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)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			kidney(5)|large_intestine(1)|lung(6)|prostate(1)|skin(2)	15						AAGATCACAGCTCTGATATGG	0.557																																					p.A12T		Atlas-SNP	.											.	HLA-DPA1	20	.	0			c.G34A						PASS	.						190	174	180					6																	33041314		1511	2709	4220	SO:0001583	missense	3113	exon1			TCACAGCTCTGAT	X00457	CCDS4764.1	6p21.3	2013-01-11			ENSG00000231389	ENSG00000231389		"Histocompatibility complex", "Immunoglobulin superfamily / C1-set domain containing"	4938	protein-coding gene	gene with protein product		142880		HLA-DP1A		6584734	Standard	NM_033554		Approved		uc003ocs.2	P20036	OTTHUMG00000031058	ENST00000419277.1:c.34G>A	6.37:g.33041314C>T	ENSP00000393566:p.Ala12Thr	74	0	0		47	17	0.361702	NM_033554	A9YWH7|B9UKH4|O19722|O46883|P01905|P79554|Q2Q060|Q2Q061|Q5EY03|Q5STP1|Q6DQK4|Q9BCQ1|Q9TPX3|Q9XS10	Missense_Mutation	SNP	ENST00000419277.1	37	CCDS4764.1	.	.	.	.	.	.	.	.	.	.	C	13.96	2.392417	0.42410	.	.	ENSG00000231389	ENST00000419277;ENST00000428995;ENST00000448544;ENST00000453337;ENST00000417724	T;T;T	0.02552	4.6;4.6;4.25	4.1	-1.87	0.07737	.	0.640274	0.14756	N	0.300279	T	0.00998	0.0033	L	0.59436	1.845	0.09310	N	1	B	0.32717	0.381	B	0.32624	0.149	T	0.44483	-0.9325	10	0.87932	D	0	.	1.319	0.02112	0.1483:0.409:0.146:0.2967	.	12	P20036	DPA1_HUMAN	T	12	ENSP00000393566:A12T;ENSP00000402872:A12T;ENSP00000390929:A12T	ENSP00000398134:A12T	A	-	1	0	HLA-DPA1	33149292	0.000000	0.05858	0.000000	0.03702	0.122000	0.20287	0.524000	0.22940	-0.286000	0.09076	0.643000	0.83706	GCT	.	.	none		0.557	HLA-DPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076071.3	NM_033554		T	33041314	C	T	33041314	3	4	47	1	0	0	0	0	1	0	0	0	7211	797	28	2	764	2	HLA-DPA1	6	33041314	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	1	33041314	138073753	58	15792	209	2									
PIM1	5292	hgsc.bcm.edu	37	chr6	37138402	37138402	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	cacctgcgcgccgcgccctgCaacgacctgcacgccaccaa	8	3	9	21	6	0	0	0	0	0	0	0	1	0	0	6	0	4	2	6	0	2	0			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:37138402C>T	ENST00000373509.5	+	1	424	c.51C>T	c.(49-51)tgC>tgT	p.C17C		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	108					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)	CCGCGCCCTGCAACGACCTGC	0.721			T	BCL6	NHL																																p.C108C		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C324T						PASS	.						27	28	28					6																	37138402		2201	4296	6497	SO:0001819	synonymous_variant	5292	exon1			GCCCTGCAACGAC		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.51C>T	6.37:g.37138402C>T		89	0	0		60	16	0.266667	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.721	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37138402	C	T	37138402	2	4	47	1	0	0	0	0	0	0	0	1	11936	718	25	2		2	PIM1	6	37138402	Silent	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	4097088	37138402	133976665	59	15793			2	77	10979876	5	5	802	N	G_C	6.900079e-12
PIM1	5292	hgsc.bcm.edu	37	chr6	37138423	37138423	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aacgacctgcacgccaccaaGctggcgcccggtgagagcac	10	3	12	16	4	0	1	0	1	0	1	0	3	0	1	4	2	4	3	4	2	2	0			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:37138423G>C	ENST00000373509.5	+	1	445	c.72G>C	c.(70-72)aaG>aaC	p.K24N		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	115					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)	p.K24N(1)		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)	ACGCCACCAAGCTGGCGCCCG	0.726			T	BCL6	NHL																																p.K115N		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,0,1	PIM1	71	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G345C						PASS	.						22	25	24					6																	37138423		2197	4289	6486	SO:0001583	missense	5292	exon1			CACCAAGCTGGCG		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.72G>C	6.37:g.37138423G>C	ENSP00000362608:p.Lys24Asn	79	0	0		59	15	0.254237	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	G	9.145	1.014762	0.19355	.	.	ENSG00000137193	ENST00000373509	T	0.69685	-0.42	4.2	2.33	0.28932	Protein kinase-like domain (1);	0.226724	0.29775	N	0.011236	T	0.17280	0.0415	N	0.08118	0	0.26025	N	0.981812	B	0.33266	0.404	B	0.25759	0.063	T	0.21552	-1.0242	10	0.18276	T	0.48	.	8.2558	0.31756	0.2022:0.0:0.7978:0.0	.	115	P11309	PIM1_HUMAN	N	24	ENSP00000362608:K24N	ENSP00000362608:K24N	K	+	3	2	PIM1	37246401	1.000000	0.71417	1.000000	0.80357	0.879000	0.50718	1.199000	0.32235	0.461000	0.27071	-0.284000	0.09977	AAG	.	.	none		0.726	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			C	37138423	G	C	37138423	3	2	47	1	0	0	0	0	1	0	0	0	11936	962	34	4	74	4	PIM1	6	37138423	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	21	37138423	133976644	60	15794			2	77	10979876	5	5	802	N	G_C	6.900079e-12
PIM1	5292	hgsc.bcm.edu	37	chr6	37138563	37138563	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	tcctaggcaaggagaaggagCccctggagtcgcagtaccag	11	5	14	11	1	0	1	0	0	0	1	2	4	1	3	4	4	2	3	4	4	4	2	rs34095970		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:37138563C>A	ENST00000373509.5	+	2	470	c.97C>A	c.(97-99)Ccc>Acc	p.P33T		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	124					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)	GGAGAAGGAGCCCCTGGAGTC	0.701			T	BCL6	NHL																																p.P124T		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C370A						PASS	.						21	31	28					6																	37138563		2155	4262	6417	SO:0001583	missense	5292	exon2			AAGGAGCCCCTGG		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.97C>A	6.37:g.37138563C>A	ENSP00000362608:p.Pro33Thr	52	0	0		73	15	0.205479	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	C	14.38	2.517268	0.44763	.	.	ENSG00000137193	ENST00000373509	T	0.69040	-0.37	4.64	3.75	0.43078	Protein kinase-like domain (1);	0.000000	0.64402	D	0.000001	T	0.27419	0.0673	N	0.08118	0	0.48571	D	0.999676	B	0.09022	0.002	B	0.06405	0.002	T	0.11060	-1.0603	10	0.23302	T	0.38	.	12.1438	0.54012	0.0:0.9152:0.0:0.0848	.	124	P11309	PIM1_HUMAN	T	33	ENSP00000362608:P33T	ENSP00000362608:P33T	P	+	1	0	PIM1	37246541	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.980000	0.40618	2.294000	0.77228	0.549000	0.68633	CCC	.	.	none		0.701	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			A	37138563	C	A	37138563	3	1	47	1	0	0	0	0	1	0	0	0	11936	739	26	4	103	4	PIM1	6	37138563	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	140	37138563	133976504	61	15795			2	77	10979876	5	5	802	N	G_C	6.900079e-12
PIM1	5292	hgsc.bcm.edu	37	chr6	37139086	37139086	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggggagccctgcaagaggaGctggcccgcagcttcttctg	7	7	15	12	1	2	1	0	0	2	1	2	3	2	3	2	4	4	4	2	4	1	2	rs33989191	byFrequency	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:37139086G>C	ENST00000373509.5	+	4	799	c.426G>C	c.(424-426)gaG>gaC	p.E142D		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	233	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)	TGCAAGAGGAGCTGGCCCGCA	0.617			T	BCL6	NHL								G|||	11	0.00219649	0.0083	0.0	5008	,	,		16103	0.0		0.0	False		,,,				2504	0.0				p.E233D		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.G699C						PASS	.	G	ASP/GLU	38,4368	40.8+/-73.8	0,38,2165	59	70	66		426	3.3	1	6	dbSNP_126	66	0,8600		0,0,4300	yes	missense	PIM1	NM_002648.3	45	0,38,6465	CC,CG,GG		0.0,0.8625,0.2922	benign	142/314	37139086	38,12968	2203	4300	6503	SO:0001583	missense	5292	exon4			AGAGGAGCTGGCC		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.426G>C	6.37:g.37139086G>C	ENSP00000362608:p.Glu142Asp	114	0	0		80	14	0.175	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	2.740	-0.262501	0.05791	0.008625	0.0	ENSG00000137193	ENST00000373509	T	0.65916	-0.18	4.19	3.31	0.37934	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.376195	0.26224	N	0.025611	T	0.17959	0.0431	N	0.04373	-0.215	0.38312	D	0.943293	B	0.02656	0.0	B	0.04013	0.001	T	0.07986	-1.0744	10	0.10902	T	0.67	.	13.2969	0.60303	0.0:0.4445:0.5555:0.0	rs33989191	233	P11309	PIM1_HUMAN	D	142	ENSP00000362608:E142D	ENSP00000362608:E142D	E	+	3	2	PIM1	37247064	1.000000	0.71417	1.000000	0.80357	0.416000	0.31233	2.500000	0.45381	0.949000	0.37715	0.448000	0.29417	GAG	G|0.998;C|0.002	0.002	strong		0.617	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			C	37139086	G	C	37139086	3	2	47	1	0	0	0	0	1	0	0	0	11936	962	34	4	440	4	PIM1	6	37139086	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	523	37139086	133975981	62	15796			2	77	10979876	5	5	802	N	G_C	6.900079e-12
PIM1	5292	hgsc.bcm.edu	37	chr6	37139203	37139203	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	atcgacctcaatcgcggcgaGctcaagctcatcgacttcgg	9	8	10	14	6	3	0	3	0	0	0	7	3	3	0	1	2	2	2	1	2	2	1			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:37139203G>C	ENST00000373509.5	+	4	916	c.543G>C	c.(541-543)gaG>gaC	p.E181D		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	272	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)	p.E181D(1)		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)	ATCGCGGCGAGCTCAAGCTCA	0.637			T	BCL6	NHL																																p.E272D		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	PIM1,NS,lymphoid_neoplasm,0,1	PIM1	71	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G816C						PASS	.						32	33	32					6																	37139203		2203	4300	6503	SO:0001583	missense	5292	exon4			CGGCGAGCTCAAG		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.543G>C	6.37:g.37139203G>C	ENSP00000362608:p.Glu181Asp	71	0	0		64	10	0.15625	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Missense_Mutation	SNP	ENST00000373509.5	37	CCDS4830.1	.	.	.	.	.	.	.	.	.	.	G	10.45	1.354972	0.24512	.	.	ENSG00000137193	ENST00000373509	T	0.66099	-0.19	4.36	3.47	0.39725	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.207237	0.40554	N	0.001073	T	0.26412	0.0645	L	0.45698	1.435	0.33559	D	0.597158	B	0.13594	0.008	B	0.19946	0.027	T	0.07558	-1.0766	10	0.08837	T	0.75	.	5.5129	0.16890	0.3296:0.0:0.6704:0.0	.	272	P11309	PIM1_HUMAN	D	181	ENSP00000362608:E181D	ENSP00000362608:E181D	E	+	3	2	PIM1	37247181	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.006000	0.40874	1.020000	0.39573	0.448000	0.29417	GAG	.	.	none		0.637	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			C	37139203	G	C	37139203	3	2	47	1	0	0	0	0	1	0	0	0	11936	962	34	4	557	4	PIM1	6	37139203	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	117	37139203	133975864	63	15797			2	77	10979876	5	5	802	N	G_C	6.900079e-12
KIF6	221458	hgsc.bcm.edu	37	chr6	39607449	39607449	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atgcctctgtcactgtaacgCtctgcaccccctgtgatagt	7	12	8	14	1	3	1	1	1	2	0	3	1	3	1	3	0	3	3	3	0	2	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:39607449C>T	ENST00000287152.7	-	4	430	c.336G>A	c.(334-336)gaG>gaA	p.E112E	KIF6_ENST00000373215.3_Silent_p.E112E|KIF6_ENST00000373216.3_Silent_p.E112E|KIF6_ENST00000538893.1_Silent_p.E112E	NM_145027.4	NP_659464.3	Q6ZMV9	KIF6_HUMAN	kinesin family member 6	112	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						CACTGTAACGCTCTGCACCCC	0.413																																					p.E112E		Atlas-SNP	.											.	KIF6	233	.	0			c.G336A						PASS	.						184	137	153					6																	39607449		2203	4300	6503	SO:0001819	synonymous_variant	221458	exon4			GTAACGCTCTGCA	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.336G>A	6.37:g.39607449C>T		151	0	0		126	48	0.380952	NM_145027	Q2MDE3|Q2MDE4|Q5T8J6|Q6ZWE3|Q86T87|Q8WTV4	Silent	SNP	ENST00000287152.7	37	CCDS4844.1	.	.	.	.	.	.	.	.	.	.	C	9.295	1.051571	0.19827	.	.	ENSG00000164627	ENST00000458470	.	.	.	5.67	-0.341	0.12639	.	.	.	.	.	T	0.43612	0.1255	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41980	-0.9478	4	.	.	.	.	10.5753	0.45223	0.0:0.4399:0.0:0.5601	.	.	.	.	N	4	.	.	S	-	2	0	KIF6	39715427	0.985000	0.35326	0.989000	0.46669	0.921000	0.55340	0.304000	0.19228	-0.138000	0.11434	-0.736000	0.03550	AGC	.	.	none		0.413	KIF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040455.2	NM_145027		T	39607449	C	T	39607449	2	4	47	1	0	0	0	0	0	0	0	1	8317	796	28	2		2	KIF6	6	39607449	Silent	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	2468246	39607449	131507618	64	15798											
PKHD1	5314	hgsc.bcm.edu	37	chr6	51523890	51523890	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	ttgttacttgataaggatgaAatcattccagtgctccttac	11	15	7	8	0	1	2	1	2	0	0	3	3	3	3	2	1	3	2	2	1	4	6			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:51523890A>G	ENST00000371117.3	-	61	11309	c.11034T>C	c.(11032-11034)atT>atC	p.I3678I		NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3678					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)					ATAAGGATGAAATCATTCCAG	0.418																																					p.I3678I		Atlas-SNP	.											.	PKHD1	927	.	0			c.T11034C						PASS	.						173	161	165					6																	51523890		2203	4300	6503	SO:0001819	synonymous_variant	5314	exon61			GGATGAAATCATT	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.11034T>C	6.37:g.51523890A>G		84	0	0		88	15	0.170455	NM_138694	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			.	.	none		0.418	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694		G	51523890	A	G	51523890	2	3	47	1	0	0	0	0	0	0	0	1	11980	10	1	3		3	PKHD1	6	51523890	Silent	SNP	A	TCGA-RQ-AAAT-01A-11D-A38X-10	11916441	51523890	119591177	65	15799											
LCA5	167691	hgsc.bcm.edu	37	chr6	80223259	80223259	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ttcaaagatttattttctttTagcagctcagctaacttgac	11	17	5	8	0	3	2	2	1	1	1	3	2	3	2	0	0	4	3	0	0	4	9			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:80223259T>G	ENST00000392959.1	-	4	1001	c.390A>C	c.(388-390)ctA>ctC	p.L130L	LCA5_ENST00000467898.3_Silent_p.L130L|LCA5_ENST00000369846.4_Silent_p.L130L	NM_181714.3	NP_859065.2	Q86VQ0	LCA5_HUMAN	Leber congenital amaurosis 5	130					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)		TATTTTCTTTTAGCAGCTCAG	0.373																																					p.L130L		Atlas-SNP	.											.	LCA5	71	.	0			c.A390C						PASS	.						74	76	75					6																	80223259		2203	4299	6502	SO:0001819	synonymous_variant	167691	exon3			TTCTTTTAGCAGC		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.390A>C	6.37:g.80223259T>G		282	0	0		165	113	0.684848	NM_001122769	E1P542|Q9BWX7	Silent	SNP	ENST00000392959.1	37	CCDS4990.1																																																																																			.	.	none		0.373	LCA5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259269.1	NM_181714		G	80223259	T	G	80223259	2	3	47	1	0	0	0	0	0	0	0	1	8665	1741	61	5		5	LCA5	6	80223259	Silent	SNP	T	TCGA-RQ-AAAT-01A-11D-A38X-10	28699369	80223259	90891808	66	15800											
AIM1	202	hgsc.bcm.edu	37	chr6	106968969	106968969	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	agggtgccccgccctgtggtTtgaacaaagaacagtcaaat	12	8	11	10	1	1	2	1	1	0	1	1	2	1	2	3	2	3	1	3	2	4	1			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:106968969T>G	ENST00000369066.3	+	2	3149	c.2662T>G	c.(2662-2664)Ttg>Gtg	p.L888V		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)		GCCCTGTGGTTTGAACAAAGA	0.478																																					p.L888V		Atlas-SNP	.											.	AIM1	161	.	0			c.T2662G						PASS	.						79	84	83					6																	106968969		2203	4300	6503	SO:0001583	missense	202	exon2			TGTGGTTTGAACA	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.2662T>G	6.37:g.106968969T>G	ENSP00000358062:p.Leu888Val	130	0	0		65	56	0.861538	NM_001624	Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	37	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	T	0.856	-0.736842	0.03111	.	.	ENSG00000112297	ENST00000285105;ENST00000369066	T	0.71341	-0.56	5.99	0.485	0.16830	.	1.843970	0.02402	N	0.080812	T	0.33089	0.0851	N	0.22421	0.69	0.09310	N	0.99999	B	0.17667	0.023	B	0.14023	0.01	T	0.08146	-1.0736	10	0.32370	T	0.25	.	5.9215	0.19084	0.2723:0.0:0.2831:0.4446	.	888	Q9Y4K1	AIM1_HUMAN	V	1296;888	ENSP00000358062:L888V	ENSP00000285105:L1296V	L	+	1	2	AIM1	107075662	0.951000	0.32395	0.000000	0.03702	0.986000	0.74619	0.678000	0.25277	-0.127000	0.11661	0.533000	0.62120	TTG	.	.	none		0.478	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			G	106968969	T	G	106968969	3	3	47	1	0	0	0	0	1	0	0	0	430	1838	64	5	2668	5	AIM1	6	106968969	Missense_Mutation	SNP	T	TCGA-RQ-AAAT-01A-11D-A38X-10	26745710	106968969	64146098	67	15801											
ALDH8A1	64577	hgsc.bcm.edu	37	chr6	135239666	135239666	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaaaggaaggttcagctcccTgatgagccagcagttggtcc	10	8	13	10	0	1	2	1	2	0	0	3	4	3	3	3	3	3	4	3	3	2	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:135239666T>A	ENST00000265605.2	-	7	1419	c.1351A>T	c.(1351-1353)Agg>Tgg	p.R451W	ALDH8A1_ENST00000367845.2_Missense_Mutation_p.R397W|ALDH8A1_ENST00000367847.2_Missense_Mutation_p.R401W	NM_022568.3	NP_072090.1	Q9H2A2	AL8A1_HUMAN	aldehyde dehydrogenase 8 family, member A1	451					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)		TTCAGCTCCCTGATGAGCCAG	0.567																																					p.R451W		Atlas-SNP	.											.	ALDH8A1	68	.	0			c.A1351T						PASS	.						86	74	78					6																	135239666		2203	4300	6503	SO:0001583	missense	64577	exon7			GCTCCCTGATGAG	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.1351A>T	6.37:g.135239666T>A	ENSP00000265605:p.Arg451Trp	115	0	0		51	39	0.764706	NM_022568	B7Z521|O60793|Q24JS9|Q53GT3|Q5TI80	Missense_Mutation	SNP	ENST00000265605.2	37	CCDS5171.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.709287	0.89018	.	.	ENSG00000118514	ENST00000265605;ENST00000367845;ENST00000367847	T;T;T	0.76709	-1.04;1.54;-1.04	6.07	4.88	0.63580	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.000000	0.85682	D	0.000000	T	0.82051	0.4953	M	0.64404	1.975	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	0.84435	0.0579	10	0.66056	D	0.02	.	13.3589	0.60644	0.0:0.0:0.1316:0.8684	.	401;397;451	B7Z521;Q9H2A2-2;Q9H2A2	.;.;AL8A1_HUMAN	W	451;397;401	ENSP00000265605:R451W;ENSP00000356819:R397W;ENSP00000356821:R401W	ENSP00000265605:R451W	R	-	1	2	ALDH8A1	135281359	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.074000	0.41529	1.081000	0.41110	0.533000	0.62120	AGG	.	.	none		0.567	ALDH8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042334.2			A	135239666	T	A	135239666	3	1	47	1	0	0	0	0	1	0	0	0	505	1579	55	5	116	5	ALDH8A1	6	135239666	Missense_Mutation	SNP	T	TCGA-RQ-AAAT-01A-11D-A38X-10	28270697	135239666	35875401	68	15802											
REPS1	85021	hgsc.bcm.edu	37	chr6	139262508	139262508	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	atcaatcagtttgggcattaAgctttcaggaagtttttctg	10	16	9	6	0	4	0	3	0	1	0	4	1	4	1	0	2	1	4	0	2	3	5			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr6:139262508A>G	ENST00000450536.2	-	8	1673	c.1099T>C	c.(1099-1101)Tta>Cta	p.L367L	REPS1_ENST00000415951.2_Silent_p.L367L|REPS1_ENST00000258062.5_Silent_p.L367L|REPS1_ENST00000409812.2_Silent_p.L367L|REPS1_ENST00000367663.4_Silent_p.L367L			Q96D71	REPS1_HUMAN	RALBP1 associated Eps domain containing 1	367	EH 2. {ECO:0000255|PROSITE- ProRule:PRU00077}.				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)		TTGGGCATTAAGCTTTCAGGA	0.398																																					p.L367L		Atlas-SNP	.											.	REPS1	58	.	0			c.T1099C						PASS	.						177	180	179					6																	139262508		2203	4300	6503	SO:0001819	synonymous_variant	85021	exon8			GCATTAAGCTTTC		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.1099T>C	6.37:g.139262508A>G		156	0	0		69	51	0.73913	NM_001128617	B7ZBZ8|B7ZBZ9|B7ZC00|J3KP76|Q5JWJ5|Q5JWJ6|Q5JWJ7|Q8NDR7|Q8WU62|Q9BXY9	Silent	SNP	ENST00000450536.2	37																																																																																				.	.	none		0.398	REPS1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000042447.3			G	139262508	A	G	139262508	2	3	47	1	0	0	0	0	0	0	0	1	13243	69	3	3		3	REPS1	6	139262508	Silent	SNP	A	TCGA-RQ-AAAT-01A-11D-A38X-10	4022842	139262508	31852559	69	15803											
EIF3B	8662	hgsc.bcm.edu	37	chr7	2409105	2409105	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attttattttcctgttctgcAgagacttttcttggtctcct	5	21	6	9	0	3	1	0	0	3	1	5	2	4	1	2	1	1	2	2	1	1	8			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr7:2409105A>C	ENST00000360876.4	+	10	1459		c.e10-1		EIF3B_ENST00000397011.2_Splice_Site	NM_001037283.1	NP_001032360.1			eukaryotic translation initiation factor 3, subunit B											breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(11)|ovary(1)|skin(1)	24		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0833)|OV - Ovarian serous cystadenocarcinoma(56;7.76e-14)		CCTGTTCTGCAGAGACTTTTC	0.423																																					.		Atlas-SNP	.											.	EIF3B	54	.	0			c.1404-2A>C						PASS	.						186	199	194					7																	2409105		2203	4300	6503	SO:0001630	splice_region_variant	8662	exon10			TTCTGCAGAGACT	U62583	CCDS5332.1	7p22	2013-02-12	2007-07-27	2007-07-27	ENSG00000106263	ENSG00000106263		"RNA binding motif (RRM) containing"	3280	protein-coding gene	gene with protein product		603917	"eukaryotic translation initiation factor 3, subunit 9 eta, 116kDa"	EIF3S9		8995410	Standard	NM_001037283		Approved	PRT1, eIF3b	uc003sly.3	P55884	OTTHUMG00000022839	ENST00000360876.4:c.1404-1A>C	7.37:g.2409105A>C		484	0	0		366	128	0.349727	NM_003751		Splice_Site	SNP	ENST00000360876.4	37	CCDS5332.1	.	.	.	.	.	.	.	.	.	.	A	16.26	3.071841	0.55646	.	.	ENSG00000106263	ENST00000314800;ENST00000360876;ENST00000397011;ENST00000489558	.	.	.	5.45	5.45	0.79879	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8091	0.78543	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	EIF3B	2375631	1.000000	0.71417	0.958000	0.39756	0.625000	0.37756	9.048000	0.93830	2.192000	0.70111	0.459000	0.35465	.	.	.	none		0.423	EIF3B-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207006.1		Intron	C	2409105	A	C	2409105	5	2	47	1	0	0	0	0	0	0	1	0	5015	202	7	5	1440	5	EIF3B	7	2409105	Splice_Site	SNP	A	TCGA-RQ-AAAT-01A-11D-A38X-10		2409105	156729558	70	15804											
BMPER	168667	hgsc.bcm.edu	37	chr7	33945290	33945290	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccgccgctcgcctgggattaCgtgctgcgtcttgctgctac	3	11	12	15	5	1	0	0	0	1	0	2	1	1	1	3	1	6	4	3	1	2	3			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr7:33945290C>T	ENST00000297161.2	+	2	439	c.65C>T	c.(64-66)aCg>aTg	p.T22M	BMPER_ENST00000426693.1_Missense_Mutation_p.T22M	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	22					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						CCTGGGATTACGTGCTGCGTC	0.657																																					p.T22M		Atlas-SNP	.											BMPER,NS,carcinoma,-1,1	BMPER	131	1	0			c.C65T						PASS	.						53	49	50					7																	33945290		2203	4300	6503	SO:0001583	missense	168667	exon2			GGATTACGTGCTG		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.65C>T	7.37:g.33945290C>T	ENSP00000297161:p.Thr22Met	79	0	0		83	15	0.180723	NM_133468	A8K1P8|Q8TF36	Missense_Mutation	SNP	ENST00000297161.2	37	CCDS5442.1	.	.	.	.	.	.	.	.	.	.	C	17.42	3.386045	0.61956	.	.	ENSG00000164619	ENST00000297161;ENST00000426693;ENST00000436222	T;T	0.19532	2.14;2.14	3.65	3.65	0.41850	.	0.272984	0.29119	N	0.013098	T	0.21427	0.0516	L	0.39898	1.24	0.29655	N	0.843626	D	0.63046	0.992	P	0.47044	0.535	T	0.06935	-1.0799	10	0.66056	D	0.02	.	10.617	0.45456	0.1929:0.8071:0.0:0.0	.	22	Q8N8U9	BMPER_HUMAN	M	22	ENSP00000297161:T22M;ENSP00000393950:T22M	ENSP00000297161:T22M	T	+	2	0	BMPER	33911815	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	3.575000	0.53870	2.014000	0.59158	0.557000	0.71058	ACG	.	.	none		0.657	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2	NM_133468		T	33945290	C	T	33945290	3	4	47	1	0	0	0	0	1	0	0	0	1468	536	19	1	67	1	BMPER	7	33945290	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	31536185	33945290	125193373	71	15805											
FZD1	8321	hgsc.bcm.edu	37	chr7	90894950	90894950	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gttctggaccagcaaccctcAgcacggcggcggagggcacc	8	4	14	15	3	2	0	1	0	1	0	2	2	2	2	3	5	3	4	3	5	1	1			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr7:90894950A>G	ENST00000287934.2	+	1	1168	c.755A>G	c.(754-756)cAg>cGg	p.Q252R		NM_003505.1	NP_003496.1	Q9UP38	FZD1_HUMAN	frizzled class receptor 1	252					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)			AGCAACCCTCAGCACGGCGGC	0.736																																					p.Q252R		Atlas-SNP	.											.	FZD1	64	.	0			c.A755G						PASS	.						8	9	8					7																	90894950		2150	4250	6400	SO:0001583	missense	8321	exon1			ACCCTCAGCACGG	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.755A>G	7.37:g.90894950A>G	ENSP00000287934:p.Gln252Arg	37	0	0		60	13	0.216667	NM_003505	A4D1E8|O94815|Q549T8	Missense_Mutation	SNP	ENST00000287934.2	37	CCDS5620.1	.	.	.	.	.	.	.	.	.	.	A	12.20	1.866343	0.32977	.	.	ENSG00000157240	ENST00000287934	T	0.76316	-1.01	4.73	4.73	0.59995	.	0.781766	0.10486	N	0.668960	T	0.55721	0.1938	N	0.02539	-0.55	0.41784	D	0.989832	B	0.02656	0.0	B	0.04013	0.001	T	0.47394	-0.9121	10	0.17369	T	0.5	.	14.0288	0.64601	1.0:0.0:0.0:0.0	.	252	Q9UP38	FZD1_HUMAN	R	252	ENSP00000287934:Q252R	ENSP00000287934:Q252R	Q	+	2	0	FZD1	90732886	0.733000	0.28132	1.000000	0.80357	0.985000	0.73830	0.944000	0.29043	1.985000	0.57927	0.418000	0.28097	CAG	.	.	none		0.736	FZD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059367.2	NM_003505		G	90894950	A	G	90894950	3	3	47	1	0	0	0	0	1	0	0	0	6136	188	7	3	757	3	FZD1	7	90894950	Missense_Mutation	SNP	A	TCGA-RQ-AAAT-01A-11D-A38X-10	56949660	90894950	68243713	72	15806											
LAMB1	3912	hgsc.bcm.edu	37	chr7	107603364	107603364	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctttacctgtggctcgtagcGaattaggatgtcgtactcca	8	13	10	10	3	0	0	0	0	0	0	3	2	1	1	2	2	3	3	2	2	5	5			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr7:107603364G>A	ENST00000222399.6	-	15	2073	c.1843C>T	c.(1843-1845)Cgc>Tgc	p.R615C	LAMB1_ENST00000393560.1_Missense_Mutation_p.R615C|LAMB1_ENST00000393561.1_Missense_Mutation_p.R639C	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	615	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)	p.R615C(1)		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						GGCTCGTAGCGAATTAGGATG	0.453																																					p.R615C		Atlas-SNP	.											LAMB1,NS,carcinoma,0,1	LAMB1	185	1	1	Substitution - Missense(1)	lung(1)	c.C1843T						scavenged	.						83	83	83					7																	107603364		2203	4300	6503	SO:0001583	missense	3912	exon15			CGTAGCGAATTAG	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.1843C>T	7.37:g.107603364G>A	ENSP00000222399:p.Arg615Cys	216	2	0.00925926		203	51	0.251232	NM_002291	Q14D91	Missense_Mutation	SNP	ENST00000222399.6	37	CCDS5750.1	.	.	.	.	.	.	.	.	.	.	G	18.74	3.688937	0.68271	.	.	ENSG00000091136	ENST00000393561;ENST00000222399;ENST00000393560	T;T;T	0.52295	0.82;0.83;0.67	4.72	4.72	0.59763	Laminin IV (1);	.	.	.	.	T	0.68485	0.3006	M	0.77103	2.36	0.80722	D	1	D;P;B	0.89917	1.0;0.682;0.296	D;B;B	0.63488	0.915;0.107;0.055	T	0.74714	-0.3572	9	0.87932	D	0	.	17.7011	0.88295	0.0:0.0:1.0:0.0	.	615;615;639	E7EPA6;P07942;G3XAI2	.;LAMB1_HUMAN;.	C	639;615;615	ENSP00000377191:R639C;ENSP00000222399:R615C;ENSP00000377190:R615C	ENSP00000222399:R615C	R	-	1	0	LAMB1	107390600	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.480000	0.81109	2.181000	0.69327	0.563000	0.77884	CGC	.	.	none		0.453	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291		A	107603364	G	A	107603364	3	1	47	1	0	0	0	0	1	0	0	0	8619	1058	37	1	3597	1	LAMB1	7	107603364	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	16708414	107603364	51535299	73	15807											
KCND2	3751	hgsc.bcm.edu	37	chr7	119915438	119915438	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tttgcttcgcctggctgcagCgcctagtcgttaccgttttg	3	15	11	12	4	0	0	0	0	0	0	2	0	0	0	3	1	4	5	3	1	2	6			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr7:119915438C>T	ENST00000331113.4	+	1	1717	c.752C>T	c.(751-753)gCg>gTg	p.A251V		NM_012281.2	NP_036413.1	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 2	251					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)	CTGGCTGCAGCGCCTAGTCGT	0.532																																					p.A251V		Atlas-SNP	.											.	KCND2	194	.	0			c.C752T						PASS	.						183	151	162					7																	119915438		2203	4300	6503	SO:0001583	missense	3751	exon1			CTGCAGCGCCTAG	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.752C>T	7.37:g.119915438C>T	ENSP00000333496:p.Ala251Val	127	0	0		183	27	0.147541	NM_012281	O95012|O95021|Q2TBD3|Q9UBY7|Q9UN98|Q9UNH9	Missense_Mutation	SNP	ENST00000331113.4	37	CCDS5776.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.143439	0.77888	.	.	ENSG00000184408	ENST00000331113	D	0.97831	-4.56	5.57	5.57	0.84162	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98463	0.9488	M	0.67625	2.065	0.54753	D	0.999986	D	0.89917	1.0	D	0.78314	0.991	D	0.98623	1.0668	9	.	.	.	.	19.5635	0.95382	0.0:1.0:0.0:0.0	.	251	Q9NZV8	KCND2_HUMAN	V	251	ENSP00000333496:A251V	.	A	+	2	0	KCND2	119702674	1.000000	0.71417	0.195000	0.23364	0.955000	0.61496	5.999000	0.70665	2.636000	0.89361	0.557000	0.71058	GCG	.	.	none		0.532	KCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346996.1	NM_012281		T	119915438	C	T	119915438	3	4	47	1	0	0	0	0	1	0	0	0	8028	768	27	1	754	1	KCND2	7	119915438	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	12312074	119915438	39223225	74	15808											
RBM33	155435	hgsc.bcm.edu	37	chr7	155532534	155532545	+	In_Frame_Del	DEL	CCCACCCCAGCA	CCCACCCCAGCA	-																															cccccgccccagcaccagccCccaccccagcacccaccaca																										TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	CCCACCCCAGCA	CCCACCCCAGCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr7:155532534_155532545delCCCACCCCAGCA	ENST00000401878.3	+	12	2061_2072	c.1863_1874delCCCACCCCAGCA	c.(1861-1875)cccccaccccagcac>ccc	p.PPQH630del		NM_053043.2	NP_444271.2	Q96EV2	RBM33_HUMAN	RNA binding motif protein 33	630	His-rich.|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)		agcaccagcccccaccccagcacccaccacag	0.708																																					p.621_625del		Atlas-Indel	.											.	RBM33	157	.	0			c.1862_1873del						PASS	.			77,2879		15,47,1416						5.1	0.2			6	120,5272		26,68,2602	no	coding	RBM33	NM_053043.2		41,115,4018	A1A1,A1R,RR		2.2255,2.6049,2.3598				197,8151				SO:0001651	inframe_deletion	155435	exon12			.	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.1863_1874delCCCACCCCAGCA	7.37:g.155532534_155532545delCCCACCCCAGCA	ENSP00000384160:p.Pro630_His633del	41	0	0		25	13	0.52	NM_053043	A4D244|B5MC24|Q52LF5|Q75LN9|Q75ML5|Q9NSV0	In_Frame_Del	DEL	ENST00000401878.3	37	CCDS5941.2																																																																																			.	.	none		0.708	RBM33-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317225.3	NM_001008408		-	155532545	CCCACCCCAGCA	-	155532534	7	5	47	1	0	1	0	1	0	0	0	0	13145	610	22	0	1909	0	RBM33	7	155532534	In_Frame_Del	DEL	CCCACCCCAGCA	TCGA-RQ-AAAT-01A-11D-A38X-10	35617096	155532534	3606129	75	15809											
DLGAP2	9228	hgsc.bcm.edu	37	chr8	1497114	1497114	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agcaccttcccgcggatgcaCtacagctcgcactacgacac	10	6	8	17	4	0	0	0	0	0	0	2	2	1	1	2	1	5	4	2	1	2	3			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr8:1497114C>A	ENST00000421627.2	+	2	389	c.255C>A	c.(253-255)caC>caA	p.H85Q		NM_004745.3	NP_004736.2	Q9P1A6	DLGP2_HUMAN	discs, large (Drosophila) homolog-associated protein 2	164					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)		CGCGGATGCACTACAGCTCGC	0.682																																					p.H85Q		Atlas-SNP	.											.	DLGAP2	292	.	0			c.C255A						PASS	.						18	20	19					8																	1497114		2176	4269	6445	SO:0001583	missense	9228	exon2			GATGCACTACAGC	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.255C>A	8.37:g.1497114C>A	ENSP00000400258:p.His85Gln	33	0	0		21	7	0.333333	NM_004745	A1QCF8|A1QCF9|A5D8Y2|O14488|O14664|Q9P1A7	Missense_Mutation	SNP	ENST00000421627.2	37	CCDS47760.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.1|25.1	4.604713|4.604713	0.87157|0.87157	.|.	.|.	ENSG00000198010|ENSG00000198010	ENST00000356067;ENST00000421627|ENST00000520901	T|.	0.16743|.	2.32|.	5.43|5.43	4.56|4.56	0.56223|0.56223	.|.	0.101563|.	0.85682|.	D|.	0.000000|.	T|T	0.75339|0.75339	0.3836|0.3836	M|M	0.79926|0.79926	2.475|2.475	0.45806|0.45806	D|D	0.998684|0.998684	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.87578|.	0.998;0.996|.	T|T	0.76889|0.76889	-0.2792|-0.2792	10|5	0.87932|.	D|.	0|.	-18.5305|-18.5305	14.0129|14.0129	0.64507|0.64507	0.0:0.9271:0.0:0.0729|0.0:0.9271:0.0:0.0729	.|.	164;164|.	Q9P1A6-2;Q9P1A6|.	.;DLGP2_HUMAN|.	Q|N	130;85|102	ENSP00000400258:H85Q|.	ENSP00000348366:H130Q|.	H|T	+|+	3|2	2|0	DLGAP2|DLGAP2	1484521|1484521	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.967000|0.967000	0.64934|0.64934	1.532000|1.532000	0.36029|0.36029	1.292000|1.292000	0.44672|0.44672	0.561000|0.561000	0.74099|0.74099	CAC|ACT	.	.	none		0.682	DLGAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374478.1	NM_004745		A	1497114	C	A	1497114	3	1	47	1	0	0	0	0	1	0	0	0	4562	564	20	4	257	4	DLGAP2	8	1497114	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10		1497114	144866908	76	15810											
SOX7	83595	hgsc.bcm.edu	37	chr8	10587841	10587841	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggagcccttgtcccccggggGccgggggacggccggcggcg	2	3	21	15	6	0	0	0	0	0	0	1	2	1	2	5	8	1	0	5	8	0	1			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr8:10587841G>A	ENST00000304501.1	-	1	181	c.103C>T	c.(103-105)Ccc>Tcc	p.P35S	CTD-2135J3.3_ENST00000506149.2_RNA|CTD-2135J3.3_ENST00000519568.1_RNA|SOX7_ENST00000554914.1_Intron|SOX7_ENST00000553390.1_Intron	NM_031439.2	NP_113627.1	Q9BT81	SOX7_HUMAN	SRY (sex determining region Y)-box 7	35					endoderm formation (GO:0001706)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|regulation of canonical Wnt signaling pathway (GO:0060828)|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)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20				COAD - Colon adenocarcinoma(149;0.0732)		Tcccccgggggccgggggacg	0.701																																					p.P35S		Atlas-SNP	.											.	SOX7	50	.	0			c.C103T						PASS	.						10	14	13					8																	10587841		2170	4260	6430	SO:0001583	missense	83595	exon1			CCGGGGGCCGGGG	AJ409320	CCDS5977.1	8p22	2013-01-25			ENSG00000171056	ENSG00000171056		"SRY (sex determining region Y)-boxes"	18196	protein-coding gene	gene with protein product		612202				11691915	Standard	NM_031439		Approved		uc003wtf.3	Q9BT81	OTTHUMG00000090585	ENST00000304501.1:c.103C>T	8.37:g.10587841G>A	ENSP00000301921:p.Pro35Ser	110	0	0		84	31	0.369048	NM_031439	B4DKV0|Q53YD0	Missense_Mutation	SNP	ENST00000304501.1	37	CCDS5977.1	.	.	.	.	.	.	.	.	.	.	g	3.164	-0.171510	0.06421	.	.	ENSG00000171056	ENST00000304501	D	0.98531	-4.98	3.47	1.26	0.21427	High mobility group, superfamily (1);	0.278361	0.35407	U	0.003229	D	0.91294	0.7255	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	D	0.83684	0.0173	10	0.08837	T	0.75	.	6.9316	0.24444	0.0:0.1745:0.6208:0.2047	.	35	Q9BT81	SOX7_HUMAN	S	35	ENSP00000301921:P35S	ENSP00000301921:P35S	P	-	1	0	SOX7	10625251	0.001000	0.12720	0.029000	0.17559	0.300000	0.27592	0.569000	0.23638	0.616000	0.30141	0.450000	0.29827	CCC	.	.	none		0.701	SOX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207131.1			A	10587841	G	A	10587841	3	1	47	1	0	0	0	0	1	0	0	0	14971	1203	42	2	1071	2	SOX7	8	10587841	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	9090727	10587841	135776181	77	15811											
CHD7	55636	hgsc.bcm.edu	37	chr8	61714117	61714118	+	Frame_Shift_Ins	INS	-	-	A																															tgcagaaggcccagtggtagINSaaaaaattatgagcagtcgt																										TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr8:61714117_61714118insA	ENST00000423902.2	+	6	2886_2887	c.2407_2408insA	c.(2407-2409)gaafs	p.E803fs	CHD7_ENST00000525508.1_Frame_Shift_Ins_p.E803fs|CHD7_ENST00000524602.1_Intron	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	803	Chromo 1. {ECO:0000255|PROSITE- ProRule:PRU00053}.				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)	p.556_871dup(1)		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)			CCCAGTGGTAGAAAAAATTATG	0.391																																					p.E803fs		Pindel,Atlas-Indel	.											.	CHD7	534	.	1	Insertion - In frame(1)	lung(1)	c.2407_2408insA						PASS	.																																			SO:0001589	frameshift_variant	55636	exon6			.	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.2413dupA	8.37:g.61714123_61714123dupA	ENSP00000392028:p.Glu803fs	138	0	.		164	28	0.171	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Frame_Shift_Ins	INS	ENST00000423902.2	37	CCDS47865.1																																																																																			.	.	none		0.391	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762		A	61714118	-	A	61714117	7	5	47	1	0	1	1	0	0	0	0	0	3332	943	33	0	2425	0	CHD7	8	61714117	Frame_Shift_Ins	INS	-	TCGA-RQ-AAAT-01A-11D-A38X-10	51126276	61714117	84649905	78	15812											
PABPC1	26986	hgsc.bcm.edu	37	chr8	101730000	101730000	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agctagatatttataacttaCactttgcgatcatttaggag	13	15	7	6	1	1	1	1	0	0	1	1	3	1	2	0	1	4	1	0	1	6	9			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr8:101730000C>A	ENST00000318607.5	-	3	1632		c.e3+1		PABPC1_ENST00000519596.1_5'Flank|PABPC1_ENST00000519004.1_Splice_Site|PABPC1_ENST00000522387.1_Splice_Site	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1						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)			TTATAACTTACACTTTGCGAT	0.323																																					.		Atlas-SNP	.											.	PABPC1	76	.	0			c.503+1G>T						PASS	.						47	45	46					8																	101730000		2203	4299	6502	SO:0001630	splice_region_variant	26986	exon4			AACTTACACTTTG	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.503+1G>T	8.37:g.101730000C>A		385	1	0.0025974		334	117	0.350299	NM_002568	Q15097|Q93004	Splice_Site	SNP	ENST00000318607.5	37	CCDS6289.1	.	.	.	.	.	.	.	.	.	.	C	17.89	3.499709	0.64298	.	.	ENSG00000070756	ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387;ENST00000519100;ENST00000523555	.	.	.	4.95	4.95	0.65309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.5422	0.91033	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PABPC1	101799176	1.000000	0.71417	1.000000	0.80357	0.755000	0.42902	7.756000	0.85195	2.456000	0.83038	0.563000	0.77884	.	.	.	none		0.323	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	Intron	A	101730000	C	A	101730000	5	1	47	1	0	0	0	0	0	0	1	0	11372	492	17	4	1454	4	PABPC1	8	101730000	Splice_Site	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	40015883	101730000	44634022	79	15813											
PABPC1	26986	hgsc.bcm.edu	37	chr8	101730422	101730422	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	gttgcctactccacttttgcGaagtgatggatcacgctgag	8	12	11	10	2	1	2	1	2	0	0	2	4	2	3	2	1	3	2	2	1	2	4			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr8:101730422G>C	ENST00000318607.5	-	2	1408	c.280C>G	c.(280-282)Cgc>Ggc	p.R94G	PABPC1_ENST00000519596.1_5'Flank|PABPC1_ENST00000519004.1_Missense_Mutation_p.R49G|PABPC1_ENST00000522387.1_Missense_Mutation_p.R94G	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	94					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)			CCACTTTTGCGAAGTGATGGA	0.413																																					p.R94G		Atlas-SNP	.											PABPC1,NS,carcinoma,+2,2	PABPC1	76	2	0			c.C280G						scavenged	.						94	88	90					8																	101730422		2203	4300	6503	SO:0001583	missense	26986	exon2			TTTTGCGAAGTGA	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.280C>G	8.37:g.101730422G>C	ENSP00000313007:p.Arg94Gly	109	1	0.00917431		107	38	0.35514	NM_002568	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.	.	.	.	.	.	.	.	.	.	g	19.43	3.826868	0.71143	.	.	ENSG00000070756	ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387;ENST00000518196;ENST00000521865;ENST00000520142	T;T;T;T;T;T	0.05786	3.39;3.39;3.39;3.39;3.39;3.39	5.37	4.5	0.54988	.	0.086607	0.49916	N	0.000131	T	0.37237	0.0996	H	0.96889	3.9	0.47994	D	0.99956	D;D;D	0.76494	0.999;0.998;0.998	D;P;P	0.63597	0.916;0.845;0.845	T	0.62412	-0.6860	10	0.87932	D	0	.	16.6119	0.84885	0.0:0.1303:0.8697:0.0	.	94;94;94	E7ERJ7;B3KT93;P11940	.;.;PABP1_HUMAN	G	94;94;49;94;49;94;94	ENSP00000313007:R94G;ENSP00000429594:R49G;ENSP00000429395:R94G;ENSP00000430159:R49G;ENSP00000429119:R94G;ENSP00000430012:R94G	ENSP00000313007:R94G	R	-	1	0	PABPC1	101799598	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.090000	0.57693	1.421000	0.47157	-0.127000	0.14921	CGC	.	.	none		0.413	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568		C	101730422	G	C	101730422	3	2	47	1	0	0	0	0	1	0	0	0	11372	1058	37	4	1682	4	PABPC1	8	101730422	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	422	101730422	44633600	80	15814											
ENPP2	5168	hgsc.bcm.edu	37	chr8	120631489	120631489	+	Silent	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ataaaatacacttaccctgcAgggcattctgcggcctttat	11	12	7	11	1	1	0	0	0	1	0	1	0	1	0	2	2	4	2	2	2	5	6			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr8:120631489A>T	ENST00000075322.6	-	5	532	c.474T>A	c.(472-474)ccT>ccA	p.P158P	ENPP2_ENST00000259486.6_Silent_p.P158P|ENPP2_ENST00000427067.2_Silent_p.P154P|ENPP2_ENST00000522826.1_Silent_p.P158P	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	158					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)			CTTACCCTGCAGGGCATTCTG	0.348																																					p.P158P	Melanoma(20;305 879 2501 4818 31020)	Atlas-SNP	.											.	ENPP2	254	.	0			c.T474A						PASS	.						98	92	94					8																	120631489		2203	4300	6503	SO:0001819	synonymous_variant	5168	exon5			CCCTGCAGGGCAT	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.474T>A	8.37:g.120631489A>T		137	0	0		120	53	0.441667	NM_001130863	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Silent	SNP	ENST00000075322.6	37	CCDS34936.1																																																																																			.	.	none		0.348	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1			T	120631489	A	T	120631489	2	4	47	1	0	0	0	0	0	0	0	1	5132	175	7	5		5	ENPP2	8	120631489	Silent	SNP	A	TCGA-RQ-AAAT-01A-11D-A38X-10	18901067	120631489	25732533	81	15815											
GML	2765	hgsc.bcm.edu	37	chr8	143927837	143927837	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attctcgtgaactacttgttTataagaactgtacaaacaac	15	13	5	8	1	1	2	0	1	1	1	2	2	1	2	0	0	6	2	0	0	8	7	rs527963435		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr8:143927837T>C	ENST00000220940.1	+	4	298	c.208T>C	c.(208-210)Tat>Cat	p.Y70H		NM_002066.2	NP_002057.1	Q99445	GML_HUMAN	glycosylphosphatidylinositol anchored molecule like	70	UPAR/Ly6.				apoptotic process (GO:0006915)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|negative regulation of cell proliferation (GO:0008285)	anchored component of membrane (GO:0031225)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(2)|endometrium(1)|large_intestine(6)|lung(8)	18	all_cancers(97;4.26e-11)|all_epithelial(106;1.85e-08)|Lung NSC(106;0.000274)|all_lung(105;0.000755)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					ACTACTTGTTTATAAGAACTG	0.358																																					p.Y70H		Atlas-SNP	.											.	GML	34	.	0			c.T208C						PASS	.						47	50	49					8																	143927837		2203	4300	6503	SO:0001583	missense	2765	exon4			CTTGTTTATAAGA	D84290	CCDS6391.1	8q24.3	2014-05-14	2012-11-02						4375	protein-coding gene	gene with protein product		602370	"GPI anchored molecule like protein", "glycosylphosphatidylinositol anchored molecule like protein"			8934543, 9169150	Standard	NM_002066		Approved	LY6DL	uc003yxg.3	Q99445		ENST00000220940.1:c.208T>C	8.37:g.143927837T>C	ENSP00000220940:p.Tyr70His	184	0	0		162	67	0.41358	NM_002066	A0AVF6|O00686|O00731	Missense_Mutation	SNP	ENST00000220940.1	37	CCDS6391.1	.	.	.	.	.	.	.	.	.	.	N	12.72	2.021959	0.35701	.	.	ENSG00000104499	ENST00000220940	T	0.22134	1.97	3.52	0.822	0.18806	Ly-6 antigen / uPA receptor -like (1);CD59 antigen, conserved site (1);	0.882556	0.09431	N	0.803024	T	0.31857	0.0810	L	0.56769	1.78	0.09310	N	1	D	0.64830	0.994	P	0.61477	0.889	T	0.15464	-1.0436	10	0.38643	T	0.18	-9.9934	2.9907	0.05982	0.2121:0.122:0.0:0.6659	.	70	Q99445	GML_HUMAN	H	70	ENSP00000220940:Y70H	ENSP00000220940:Y70H	Y	+	1	0	GML	143924839	0.415000	0.25416	0.010000	0.14722	0.004000	0.04260	0.819000	0.27308	0.158000	0.19367	0.455000	0.32223	TAT	.	.	none		0.358	GML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379659.1	NM_002066		C	143927837	T	C	143927837	3	2	47	1	0	0	0	0	1	0	0	0	6500	1754	61	3	218	3	GML	8	143927837	Missense_Mutation	SNP	T	TCGA-RQ-AAAT-01A-11D-A38X-10	23296348	143927837	2436185	82	15816											
FOXD4	2298	hgsc.bcm.edu	37	chr9	117303	117303	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cttcggtgccccggcataggCgggggccgagagcagtaggt	6	6	18	11	4	0	1	0	0	0	1	1	2	0	1	3	6	2	3	3	6	2	3			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr9:117303C>T	ENST00000382500.2	-	1	1114	c.817G>A	c.(817-819)Gcc>Acc	p.A273T		NM_207305.4	NP_997188.2	Q12950	FOXD4_HUMAN	forkhead box D4	273	Pro-rich.				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)			endometrium(5)|large_intestine(2)|lung(3)|prostate(1)|skin(3)	14	all_lung(41;0.218)	all_cancers(5;0.0395)|Acute lymphoblastic leukemia(5;1.91e-07)|all_hematologic(5;1.95e-06)	Kidney(42;0.112)|KIRC - Kidney renal clear cell carcinoma(5;0.157)	all cancers(5;0.000704)|Lung(218;0.00755)|GBM - Glioblastoma multiforme(5;0.0149)|Epithelial(6;0.0154)		CCGGCATAGGCGGGGGCCGAG	0.701																																					p.A273T		Atlas-SNP	.											.	FOXD4	75	.	0			c.G817A						PASS	.						21	29	26					9																	117303		1510	3118	4628	SO:0001583	missense	2298	exon1			CATAGGCGGGGGC	U13223	CCDS34975.1	9p24.3	2014-09-17			ENSG00000170122	ENSG00000170122		"Forkhead boxes"	3805	protein-coding gene	gene with protein product		601092		FKHL9		7957066, 8825632, 12234674	Standard	NM_207305		Approved	FREAC5, FOXD4a	uc003zfz.4	Q12950	OTTHUMG00000021015	ENST00000382500.2:c.817G>A	9.37:g.117303C>T	ENSP00000371940:p.Ala273Thr	20	0	0		16	5	0.3125	NM_207305	B2RN05|B9EGL7|Q5VVK1|Q8WXT6	Missense_Mutation	SNP	ENST00000382500.2	37	CCDS34975.1	.	.	.	.	.	.	.	.	.	.	.	9.647	1.140578	0.21205	.	.	ENSG00000170122	ENST00000382500	D	0.95035	-3.59	2.41	0.42	0.16444	.	0.439500	0.16007	U	0.234007	D	0.86372	0.5917	N	0.20986	0.625	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.75025	-0.3463	10	0.45353	T	0.12	.	3.4329	0.07434	0.0:0.5061:0.2126:0.2813	.	273	Q12950	FOXD4_HUMAN	T	273	ENSP00000371940:A273T	ENSP00000371940:A273T	A	-	1	0	FOXD4	107303	0.006000	0.16342	0.009000	0.14445	0.007000	0.05969	-0.062000	0.11674	-0.061000	0.13110	-0.751000	0.03497	GCC	.	.	none		0.701	FOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055433.1	NM_207305		T	117303	C	T	117303	3	4	47	1	0	0	0	0	1	0	0	0	6007	768	27	1	506	1	FOXD4	9	117303	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10		117303	141096128	83	15817											
BNC2	54796	hgsc.bcm.edu	37	chr9	16727796	16727796	+	Splice_Site	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagaaagaaagtaacttaccTgttgggacattctgaataag	17	10	9	5	0	1	3	0	1	1	2	1	4	1	4	1	1	2	2	1	1	7	5			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr9:16727796T>A	ENST00000380672.4	-	3	386	c.329A>T	c.(328-330)cAg>cTg	p.Q110L	BNC2_ENST00000545497.1_Intron|BNC2_ENST00000380667.2_Intron|BNC2_ENST00000380666.2_Splice_Site_p.Q110L|RP11-62F24.2_ENST00000450445.1_RNA	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)		GTAACTTACCTGTTGGGACAT	0.373																																					p.Q110L		Atlas-SNP	.											.	BNC2	166	.	0			c.A329T						PASS	.						176	168	171					9																	16727796		2203	4300	6503	SO:0001630	splice_region_variant	54796	exon3			CTTACCTGTTGGG	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.330+1A>T	9.37:g.16727796T>A		152	0	0		99	45	0.454545	NM_017637		Missense_Mutation	SNP	ENST00000380672.4	37	CCDS6482.2	.	.	.	.	.	.	.	.	.	.	T	21.0	4.089390	0.76756	.	.	ENSG00000173068	ENST00000380672;ENST00000418777;ENST00000456672;ENST00000436939;ENST00000380666;ENST00000540340	T;T;T	0.04015	3.73;3.73;3.73	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.17066	0.0410	L	0.47716	1.5	0.80722	D	1	D;D;D;D	0.63046	0.992;0.981;0.967;0.967	D;D;P;D	0.72982	0.979;0.969;0.901;0.932	T	0.00071	-1.2131	10	0.72032	D	0.01	-18.987	16.8222	0.85835	0.0:0.0:0.0:1.0	.	110;110;68;110	Q06HC4;Q6ZN30-2;Q5H9S4;Q6ZN30	.;.;.;BNC2_HUMAN	L	110;67;110;110;110;110	ENSP00000370047:Q110L;ENSP00000408370:Q67L;ENSP00000370041:Q110L	ENSP00000370041:Q110L	Q	-	2	0	BNC2	16717796	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.470000	0.80973	2.371000	0.80710	0.533000	0.62120	CAG	.	.	none		0.373	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637	Missense_Mutation	A	16727796	T	A	16727796	5	1	47	1	0	0	0	0	0	0	1	0	1475	1594	55	5	2990	5	BNC2	9	16727796	Splice_Site	SNP	T	TCGA-RQ-AAAT-01A-11D-A38X-10	16610493	16727796	124485635	84	15818											
ADAMTSL1	92949	hgsc.bcm.edu	37	chr9	18680514	18680514	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ctggcacaggagtggtctccGgtaactgtgccttctttctt	5	14	11	11	1	3	0	0	0	3	0	4	1	3	1	2	4	2	2	2	4	1	4			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr9:18680514G>A	ENST00000380548.4	+	11	1680	c.1341G>A	c.(1339-1341)ccG>ccA	p.P447P	ADAMTSL1_ENST00000327883.7_Splice_Site_p.P447P|ADAMTSL1_ENST00000380566.4_Silent_p.P430P|ADAMTSL1_ENST00000276935.6_Splice_Site_p.P447P	NM_001040272.5	NP_001035362.3	Q8N6G6	ATL1_HUMAN	ADAMTS-like 1	447	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.					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)		AGTGGTCTCCGGTAACTGTGC	0.527																																					p.P447P		Atlas-SNP	.											.	ADAMTSL1	306	.	0			c.G1341A						PASS	.						116	112	114					9																	18680514		2203	4300	6503	SO:0001630	splice_region_variant	92949	exon11			GTCTCCGGTAACT	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.1341+1G>A	9.37:g.18680514G>A		50	0	0		45	16	0.355556	NM_052866	A6PVN1|A8K7E1|Q496M6|Q496M8|Q5T708|Q5VZT8|Q8NAI9|Q96RW4|Q9BXY3	Silent	SNP	ENST00000380548.4	37	CCDS47954.1																																																																																			.	.	none		0.527	ADAMTSL1-012	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401206.1		Silent	A	18680514	G	A	18680514	5	1	47	1	0	0	0	0	0	0	1	0	274	1130	39	1	1383	1	ADAMTSL1	9	18680514	Splice_Site	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	1952718	18680514	122532917	85	15819											
GCNT1	2650	hgsc.bcm.edu	37	chr9	79118237	79118237	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	agttgatggagtgggcacaaGacacatacagccctgatgag	13	7	13	8	0	0	4	0	3	0	1	0	5	0	5	1	2	2	2	1	2	2	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr9:79118237G>A	ENST00000376730.4	+	4	1423	c.940G>A	c.(940-942)Gac>Aac	p.D314N	GCNT1_ENST00000536223.1_Missense_Mutation_p.D314N|GCNT1_ENST00000444201.2_Missense_Mutation_p.D314N|GCNT1_ENST00000442371.1_Missense_Mutation_p.D314N	NM_001097636.1|NM_001490.4	NP_001091105.1|NP_001481.2	Q02742	GCNT1_HUMAN	glucosaminyl (N-acetyl) transferase 1, core 2	314	Catalytic. {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						GTGGGCACAAGACACATACAG	0.488																																					p.D314N		Atlas-SNP	.											.	GCNT1	52	.	0			c.G940A						PASS	.						74	74	74					9																	79118237		2203	4300	6503	SO:0001583	missense	2650	exon4			GCACAAGACACAT	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.940G>A	9.37:g.79118237G>A	ENSP00000365920:p.Asp314Asn	120	0	0		116	53	0.456897	NM_001490	Q6DJZ4	Missense_Mutation	SNP	ENST00000376730.4	37	CCDS6653.1	.	.	.	.	.	.	.	.	.	.	g	33	5.233247	0.95207	.	.	ENSG00000187210	ENST00000536223;ENST00000442371;ENST00000444201;ENST00000376730	T;T;T;T	0.11277	2.79;2.79;2.79;2.79	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.42720	0.1215	M	0.86805	2.84	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.21621	-1.0240	9	.	.	.	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	314	Q02742	GCNT1_HUMAN	N	314	ENSP00000440883:D314N;ENSP00000415454:D314N;ENSP00000390703:D314N;ENSP00000365920:D314N	.	D	+	1	0	GCNT1	78308057	1.000000	0.71417	0.995000	0.50966	0.957000	0.61999	9.869000	0.99810	2.941000	0.99782	0.655000	0.94253	GAC	.	.	none		0.488	GCNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052725.1	NM_001097634		A	79118237	G	A	79118237	3	1	47	1	0	0	0	0	1	0	0	0	6308	942	33	2	942	2	GCNT1	9	79118237	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	60437723	79118237	62095194	86	15820											
FLJ46321	389763	hgsc.bcm.edu	37	chr9	84609323	84609323	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggggatgcagggctggggaCatcccaacgcaggagaaaga	13	3	17	8	1	0	2	0	0	0	2	1	5	1	4	1	6	2	3	1	6	2	0			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr9:84609323C>T	ENST00000344803.2	+	4	3985	c.3938C>T	c.(3937-3939)aCa>aTa	p.T1313I		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	1313					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GGGCTGGGGACATCCCAACGC	0.527																																					p.T1313I		Atlas-SNP	.											.	.	.	.	0			c.C3938T						PASS	.						30	30	30					9																	84609323		1936	4134	6070	SO:0001583	missense	389763	exon4			TGGGGACATCCCA		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.3938C>T	9.37:g.84609323C>T	ENSP00000341988:p.Thr1313Ile	74	0	0		77	43	0.558442	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	C	10.60	1.396019	0.25205	.	.	ENSG00000214929	ENST00000344803	T	0.18016	2.24	3.02	-0.0902	0.13666	.	0.543984	0.13848	U	0.358549	T	0.08133	0.0203	N	0.24115	0.695	0.09310	N	1	P	0.37101	0.582	B	0.33339	0.162	T	0.23762	-1.0179	10	0.35671	T	0.21	-4.7927	3.1663	0.06536	0.0:0.4943:0.229:0.2767	.	1313	Q6ZQQ2	F75D1_HUMAN	I	1313	ENSP00000341988:T1313I	ENSP00000341988:T1313I	T	+	2	0	FAM75D1	83799143	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.381000	0.07417	-0.010000	0.14271	0.655000	0.94253	ACA	.	.	none		0.527	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670		T	84609323	C	T	84609323	3	4	47	1	0	0	0	0	1	0	0	0	5940	478	17	2	3952	2	FLJ46321	9	84609323	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	5491086	84609323	56604108	87	15821											
GRID1	2894	hgsc.bcm.edu	37	chr10	87614258	87614258	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagcctgaggcttaccttgcGcatgtctttgccaaaagtct	8	12	10	11	1	2	1	0	1	2	0	2	2	2	1	3	1	4	2	3	1	3	3			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr10:87614258G>A	ENST00000327946.7	-	8	1313	c.1228C>T	c.(1228-1230)Cgc>Tgc	p.R410C		NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	410					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.R410S(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						CTTACCTTGCGCATGTCTTTG	0.512										Multiple Myeloma(13;0.14)																											p.R410C		Atlas-SNP	.											GRID1,right_upper_lobe,carcinoma,0,2	GRID1	204	2	1	Substitution - Missense(1)	lung(1)	c.C1228T						PASS	.						129	112	118					10																	87614258		2203	4300	6503	SO:0001583	missense	2894	exon8			CCTTGCGCATGTC	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.1228C>T	10.37:g.87614258G>A	ENSP00000330148:p.Arg410Cys	45	0	0		34	13	0.382353	NM_017551	B3KXD5|B7Z7L0|Q8IXT3	Missense_Mutation	SNP	ENST00000327946.7	37	CCDS31236.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.055667	0.75960	.	.	ENSG00000182771	ENST00000327946	D	0.86694	-2.16	5.79	3.93	0.45458	.	0.558823	0.17213	N	0.182625	T	0.78786	0.4338	N	0.24115	0.695	0.80722	D	1	B	0.15719	0.014	B	0.06405	0.002	T	0.72769	-0.4193	10	0.87932	D	0	.	10.416	0.44322	0.0696:0.0:0.7963:0.1341	.	410	Q9ULK0	GRID1_HUMAN	C	410	ENSP00000330148:R410C	ENSP00000330148:R410C	R	-	1	0	GRID1	87604238	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.806000	0.62569	0.782000	0.33613	0.563000	0.77884	CGC	.	.	none		0.512	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613		A	87614258	G	A	87614258	3	1	47	1	0	0	0	0	1	0	0	0	6780	1087	38	1	1837	1	GRID1	10	87614258	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10		87614258	47920489	88	15822											
OR52R1	119695	hgsc.bcm.edu	37	chr11	4825232	4825232	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gagtgggaagcagatagccaCgtagcagtccagggccatag	12	5	15	9	1	0	1	0	0	0	1	1	3	1	2	3	2	3	3	3	2	4	3			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:4825232C>T	ENST00000356069.2	-	1	378	c.379G>A	c.(379-381)Gtg>Atg	p.V127M	MMP26_ENST00000380390.1_Intron|OR52R1_ENST00000380382.1_Missense_Mutation_p.V206M|MMP26_ENST00000477339.1_Intron	NM_001005177.3	NP_001005177.3	Q8NGF1	O52R1_HUMAN	olfactory receptor, family 52, subfamily R, 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)			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)		CAGATAGCCACGTAGCAGTCC	0.557																																					p.V127M		Atlas-SNP	.											.	OR52R1	81	.	0			c.G379A						PASS	.						127	113	118					11																	4825232		2201	4298	6499	SO:0001583	missense	119695	exon1			TAGCCACGTAGCA	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.379G>A	11.37:g.4825232C>T	ENSP00000348368:p.Val127Met	31	0	0		36	12	0.333333	NM_001005177	Q6IFI0	Missense_Mutation	SNP	ENST00000356069.2	37	CCDS31360.2	.	.	.	.	.	.	.	.	.	.	C	14.11	2.438113	0.43326	.	.	ENSG00000176937	ENST00000356069;ENST00000380382	T;T	0.00366	7.79;7.79	5.42	4.49	0.54785	GPCR, rhodopsin-like superfamily (1);	0.182661	0.26731	N	0.022798	T	0.00936	0.0031	M	0.84773	2.715	0.29270	N	0.870731	D	0.89917	1.0	D	0.72338	0.977	T	0.15292	-1.0442	10	0.72032	D	0.01	.	9.1316	0.36848	0.1468:0.7743:0.0:0.079	.	127	Q8NGF1	O52R1_HUMAN	M	127;206	ENSP00000348368:V127M;ENSP00000369742:V206M	ENSP00000348368:V127M	V	-	1	0	OR52R1	4781808	0.001000	0.12720	0.999000	0.59377	0.167000	0.22549	0.028000	0.13644	2.826000	0.97356	0.650000	0.86243	GTG	.	.	none		0.557	OR52R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142183.1	NM_001005177		T	4825232	C	T	4825232	3	4	47	1	0	0	0	0	1	0	0	0	11140	536	19	1	571	1	OR52R1	11	4825232	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10		4825232	130181284	89	15823											
OR51I2	390064	hgsc.bcm.edu	37	chr11	5475352	5475352	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ccacctttggcatggacctgTtttttatcttcctctcctat	5	18	5	13	0	2	0	0	0	2	0	4	1	3	1	5	2	0	2	5	2	2	6			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:5475352T>C	ENST00000341449.2	+	1	715	c.634T>C	c.(634-636)Ttt>Ctt	p.F212L	HBE1_ENST00000380237.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380252.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001004754.2	NP_001004754.1	Q9H344	O51I2_HUMAN	olfactory receptor, family 51, subfamily I, member 2	212					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)		CATGGACCTGTTTTTTATCTT	0.478																																					p.F212L		Atlas-SNP	.											.	OR51I2	76	.	0			c.T634C						PASS	.						382	325	345					11																	5475352		2201	4297	6498	SO:0001583	missense	390064	exon1			GACCTGTTTTTTA	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.634T>C	11.37:g.5475352T>C	ENSP00000341987:p.Phe212Leu	359	0	0		338	51	0.150888	NM_001004754	Q6IF81	Missense_Mutation	SNP	ENST00000341449.2	37	CCDS31383.1	.	.	.	.	.	.	.	.	.	.	T	0.009	-1.840977	0.00573	.	.	ENSG00000187918	ENST00000341449	T	0.32515	1.45	5.58	-10.1	0.00402	GPCR, rhodopsin-like superfamily (1);	1.199250	0.06023	N	0.651698	T	0.04363	0.0120	N	0.00358	-1.6	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.17289	-1.0374	10	0.02654	T	1	.	3.6162	0.08078	0.2624:0.4828:0.0785:0.1763	.	212	Q9H344	O51I2_HUMAN	L	212	ENSP00000341987:F212L	ENSP00000341987:F212L	F	+	1	0	OR51I2	5431928	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-5.134000	0.00148	-1.504000	0.01810	-0.256000	0.11100	TTT	.	.	none		0.478	OR51I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143385.1	NM_001004754		C	5475352	T	C	5475352	3	2	47	1	0	0	0	0	1	0	0	0	11110	1725	60	3	636	3	OR51I2	11	5475352	Missense_Mutation	SNP	T	TCGA-RQ-AAAT-01A-11D-A38X-10	650120	5475352	129531164	90	15824											
IPO7	10527	hgsc.bcm.edu	37	chr11	9459505	9459505	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttacacagtggcttaatgatGttgactgtttcttggggtaa	9	16	11	5	0	1	2	0	2	1	0	1	2	1	2	0	3	1	4	0	3	3	6			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:9459505G>A	ENST00000379719.3	+	21	2615	c.2473G>A	c.(2473-2475)Gtt>Att	p.V825I		NM_006391.2	NP_006382.1	O95373	IPO7_HUMAN	importin 7	825					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)		GCTTAATGATGTTGACTGTTT	0.313																																					p.V825I		Atlas-SNP	.											IPO7,NS,carcinoma,-1,1	IPO7	72	1	0			c.G2473A						PASS	.						79	76	77					11																	9459505		2201	4294	6495	SO:0001583	missense	10527	exon21			AATGATGTTGACT	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.2473G>A	11.37:g.9459505G>A	ENSP00000369042:p.Val825Ile	227	0	0		218	23	0.105505	NM_006391	A6NNM5|B2R786|Q1RMF7|Q9H177|Q9NTE3	Missense_Mutation	SNP	ENST00000379719.3	37	CCDS31425.1	.	.	.	.	.	.	.	.	.	.	G	12.57	1.978231	0.34942	.	.	ENSG00000205339	ENST00000379719	T	0.64260	-0.09	4.93	4.93	0.64822	Armadillo-like helical (1);Armadillo-type fold (1);	0.058434	0.64402	D	0.000002	T	0.34106	0.0886	N	0.01438	-0.865	0.48830	D	0.99971	B	0.09022	0.002	B	0.10450	0.005	T	0.37407	-0.9707	10	0.07325	T	0.83	.	18.1413	0.89641	0.0:0.0:1.0:0.0	.	825	O95373	IPO7_HUMAN	I	825	ENSP00000369042:V825I	ENSP00000369042:V825I	V	+	1	0	IPO7	9416081	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.085000	0.64468	2.270000	0.75569	0.460000	0.39030	GTT	.	.	none		0.313	IPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386022.1	NM_006391		A	9459505	G	A	9459505	3	1	47	1	0	0	0	0	1	0	0	0	7806	1377	48	2	2555	2	IPO7	11	9459505	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	3984153	9459505	125547011	91	15825											
OR8K5	219453	hgsc.bcm.edu	37	chr11	55927085	55927085	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	ggaaccacatgtggagaaagCctttttcctgccctctgcag	9	10	10	12	0	1	1	0	0	1	1	2	3	2	2	4	2	4	1	4	2	2	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:55927085C>G	ENST00000313447.1	-	1	708	c.709G>C	c.(709-711)Gct>Cct	p.A237P		NM_001004058.2	NP_001004058.2	Q8NH50	OR8K5_HUMAN	olfactory receptor, family 8, subfamily K, member 5	237						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.A237T(1)		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)				GTGGAGAAAGCCTTTTTCCTG	0.408																																					p.A237P		Atlas-SNP	.											OR8K5,NS,carcinoma,0,2	OR8K5	82	2	1	Substitution - Missense(1)	lung(1)	c.G709C						PASS	.						85	80	82					11																	55927085		2201	4296	6497	SO:0001583	missense	219453	exon1			AGAAAGCCTTTTT	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.709G>C	11.37:g.55927085C>G	ENSP00000323853:p.Ala237Pro	96	0	0		143	16	0.111888	NM_001004058	Q6IFB5	Missense_Mutation	SNP	ENST00000313447.1	37	CCDS31521.1	.	.	.	.	.	.	.	.	.	.	c	14.32	2.500187	0.44455	.	.	ENSG00000181752	ENST00000313447	T	0.00363	7.83	3.98	3.06	0.35304	GPCR, rhodopsin-like superfamily (1);	0.351885	0.24431	N	0.038600	T	0.01592	0.0051	H	0.99454	4.575	0.32250	N	0.571499	D	0.69078	0.997	D	0.67231	0.95	T	0.02766	-1.1113	10	0.87932	D	0	.	11.6173	0.51096	0.1805:0.8195:0.0:0.0	.	237	Q8NH50	OR8K5_HUMAN	P	237	ENSP00000323853:A237P	ENSP00000323853:A237P	A	-	1	0	OR8K5	55683661	0.994000	0.37717	0.954000	0.39281	0.155000	0.21991	3.064000	0.49986	1.019000	0.39547	-0.377000	0.06932	GCT	.	.	none		0.408	OR8K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391543.1	NM_001004058		G	55927085	C	G	55927085	3	3	47	1	0	0	0	0	1	0	0	0	11254	739	26	4	217	4	OR8K5	11	55927085	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	46467580	55927085	79079431	92	15826											
SHANK2	22941	hgsc.bcm.edu	37	chr11	70505972	70505972	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtccttagtccggcttgccaCgccaccccaccttcatccac	6	9	6	20	2	1	0	1	0	0	0	4	0	4	0	8	1	1	1	8	1	1	3	rs141960453		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:70505972C>T	ENST00000423696.2	-	7	921	c.885G>A	c.(883-885)gcG>gcA	p.A295A	SHANK2_ENST00000357171.3_Silent_p.A86A|SHANK2_ENST00000449833.2_Silent_p.A86A|SHANK2_ENST00000338508.4_Silent_p.A675A|SHANK2_ENST00000409530.1_Silent_p.A85A|SHANK2_ENST00000449116.2_Silent_p.A86A|SHANK2_ENST00000409161.1_Silent_p.A85A			Q9UPX8	SHAN2_HUMAN	SH3 and multiple ankyrin repeat domains 2	295	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)			CGGCTTGCCACGCCACCCCAC	0.577																																					p.A86A		Atlas-SNP	.											.	SHANK2	340	.	0			c.G258A						PASS	.	T	,	4,4396	8.1+/-20.4	0,4,2196	129	105	113		1876,258	-10	0.2	11	dbSNP_134	113	0,8588		0,0,4294	no	coding-synonymous,coding-synonymous	SHANK2	NM_012309.3,NM_133266.3	,	0,4,6490	TT,TC,CC		0.0,0.0909,0.0308	,	674/1850,86/1262	70505972	4,12984	2200	4294	6494	SO:0001819	synonymous_variant	22941	exon2			TTGCCACGCCACC	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.885G>A	11.37:g.70505972C>T		113	0	0		139	83	0.597122	NM_133266	C0SPG8|C0SPG9|Q3Y8G9|Q52LK2|Q9UKP1	Silent	SNP	ENST00000423696.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	9.731|9.731	1.162196|1.162196	0.21538|0.21538	9.09E-4|9.09E-4	0.0|0.0	ENSG00000162105|ENSG00000162105	ENST00000426687|ENST00000412252	.|.	.|.	.|.	5.0|5.0	-9.99|-9.99	0.00435|0.00435	.|.	.|.	.|.	.|.	.|.	T|T	0.35595|0.35595	0.0937|0.0937	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.45920|0.45920	-0.9228|-0.9228	4|4	.|.	.|.	.|.	.|.	3.5758|3.5758	0.07934|0.07934	0.1331:0.0985:0.2003:0.5681|0.1331:0.0985:0.2003:0.5681	.|.	.|.	.|.	.|.	H|M	84|85	.|.	.|.	R|V	-|-	2|1	0|0	SHANK2|SHANK2	70183620|70183620	0.000000|0.000000	0.05858|0.05858	0.244000|0.244000	0.24202|0.24202	0.980000|0.980000	0.70556|0.70556	-1.990000|-1.990000	0.01479|0.01479	-3.107000|-3.107000	0.00243|0.00243	-0.733000|-0.733000	0.03571|0.03571	CGT|GTG	C|1.000;T|0.000	0.000	weak		0.577	SHANK2-203	KNOWN	basic	protein_coding	protein_coding		NM_012309		T	70505972	C	T	70505972	2	4	47	1	0	0	0	0	0	0	0	1	14280	523	19	1		1	SHANK2	11	70505972	Silent	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	14578887	70505972	64500544	93	15827											
FAM181B	220382	hgsc.bcm.edu	37	chr11	82444591	82444591	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gagtagatcgcgggtggcctCgcgcacgtcccctccttcgg	4	8	14	15	6	0	1	0	0	0	1	5	2	2	1	4	3	0	2	4	3	1	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:82444591C>T	ENST00000329203.3	-	1	315	c.181G>A	c.(181-183)Gag>Aag	p.E61K		NM_175885.3	NP_787081.2	A6NEQ2	F181B_HUMAN	family with sequence similarity 181, member B	61										large_intestine(1)|lung(2)|prostate(1)	4						CGGGTGGCCTCGCGCACGTCC	0.662																																					p.E61K		Atlas-SNP	.											.	FAM181B	14	.	0			c.G181A						PASS	.						25	22	23					11																	82444591		2202	4300	6502	SO:0001583	missense	220382	exon1			TGGCCTCGCGCAC	AK095054, BC039262	CCDS31648.1	11q14.1	2011-11-30			ENSG00000182103	ENSG00000182103			28512	protein-coding gene	gene with protein product						12477932	Standard	NM_175885		Approved	LOC220382, MGC33846	uc001ozp.3	A6NEQ2	OTTHUMG00000166869	ENST00000329203.3:c.181G>A	11.37:g.82444591C>T	ENSP00000365295:p.Glu61Lys	50	0	0		64	42	0.65625	NM_175885	B2RWP1	Missense_Mutation	SNP	ENST00000329203.3	37	CCDS31648.1	.	.	.	.	.	.	.	.	.	.	C	16.91	3.253538	0.59212	.	.	ENSG00000182103	ENST00000329203	T	0.34275	1.37	3.79	2.88	0.33553	.	0.080008	0.48767	N	0.000165	T	0.31263	0.0791	L	0.50333	1.59	0.50632	D	0.999889	P	0.45902	0.868	B	0.40677	0.337	T	0.05468	-1.0883	9	.	.	.	.	11.2366	0.48944	0.0:0.9085:0.0:0.0915	.	61	A6NEQ2	F181B_HUMAN	K	61	ENSP00000365295:E61K	.	E	-	1	0	FAM181B	82122239	1.000000	0.71417	1.000000	0.80357	0.003000	0.03518	6.310000	0.72830	0.794000	0.33899	-0.391000	0.06502	GAG	.	.	none		0.662	FAM181B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391626.1	NM_175885		T	82444591	C	T	82444591	3	4	47	1	0	0	0	0	1	0	0	0	5514	893	31	1	1103	1	FAM181B	11	82444591	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	11938619	82444591	52561925	94	15828											
DLG2	1740	hgsc.bcm.edu	37	chr11	83770527	83770527	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	cgcaagatacaatcattgacCctgcaaggaaggaaaagagt	17	6	10	8	1	1	3	1	1	0	2	1	5	1	5	1	2	2	2	1	2	7	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:83770527C>T	ENST00000532653.1	-	6	737	c.435G>A	c.(433-435)agG>agA	p.R145R	DLG2_ENST00000398309.2_Splice_Site_p.R145R|DLG2_ENST00000531015.1_Splice_Site_p.R112R|DLG2_ENST00000376104.2_Splice_Site_p.R250R|DLG2_ENST00000524982.1_Splice_Site_p.R145R|DLG2_ENST00000376106.3_5'UTR|DLG2_ENST00000280241.8_Splice_Site_p.R184R|DLG2_ENST00000543673.1_Splice_Site_p.R250R|DLG2_ENST00000418306.2_Splice_Site_p.R94R|DLG2_ENST00000330014.6_Splice_Site_p.R84R|DLG2_ENST00000398301.2_Splice_Site_p.R184R|DLG2_ENST00000537455.1_5'UTR			Q14168	MPP2_HUMAN	discs, large homolog 2 (Drosophila)	0					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)				AATCATTGACCCTGCAAGGAA	0.433																																					p.R250R		Atlas-SNP	.											.	DLG2	448	.	0			c.G750A						PASS	.						54	48	50					11																	83770527		1878	4117	5995	SO:0001630	splice_region_variant	1740	exon11			ATTGACCCTGCAA	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.435-1G>A	11.37:g.83770527C>T		81	0	0		84	20	0.238095	NM_001142699	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Silent	SNP	ENST00000532653.1	37																																																																																				.	.	none		0.433	DLG2-009	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000259253.2	NM_001364	Silent	T	83770527	C	T	83770527	5	4	47	1	0	0	0	0	0	0	1	0	4557	637	22	2	2299	2	DLG2	11	83770527	Splice_Site	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	1325936	83770527	51235989	95	15829											
CTSC	1075	hgsc.bcm.edu	37	chr11	88070757	88070757	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggtcaagataggtgcagttGgcaggtgtgtcgcagcgcac	9	8	16	8	2	1	1	1	0	0	1	2	1	1	1	0	4	2	5	0	4	2	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:88070757G>A	ENST00000227266.5	-	1	198	c.84C>T	c.(82-84)gcC>gcT	p.A28A	CTSC_ENST00000524463.1_Silent_p.A28A|CTSC_ENST00000393301.4_5'UTR|CTSC_ENST00000529974.1_Silent_p.A28A	NM_001814.4	NP_001805	P53634	CATC_HUMAN	cathepsin C	28					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)				AGGTGCAGTTGGCAGGTGTGT	0.667																																					p.A28A		Atlas-SNP	.											.	CTSC	46	.	0			c.C84T						PASS	.						19	19	19					11																	88070757		2196	4287	6483	SO:0001819	synonymous_variant	1075	exon1			GCAGTTGGCAGGT	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.84C>T	11.37:g.88070757G>A		165	0	0		194	23	0.118557	NM_148170	A8K7V2|B5MDD5|Q2HIY8|Q53G93|Q71E75|Q71E76|Q7M4N9|Q7Z3G7|Q7Z5U7|Q8WY99|Q8WYA7|Q8WYA8	Silent	SNP	ENST00000227266.5	37	CCDS8282.1																																																																																			.	.	none		0.667	CTSC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394019.2	NM_001814		A	88070757	G	A	88070757	2	1	47	1	0	0	0	0	0	0	0	1	4033	1335	47	2		2	CTSC	11	88070757	Silent	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	4300230	88070757	46935759	96	15830											
ABCG4	64137	hgsc.bcm.edu	37	chr11	119031694	119031694	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggagccacagagcatcctcCgagcgctggatgtggaggat	9	6	16	10	2	0	1	0	0	0	1	2	6	2	5	3	4	3	2	3	4	0	0			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:119031694C>T	ENST00000449422.2	+	15	2007	c.1819C>T	c.(1819-1821)Cga>Tga	p.R607*	ABCG4_ENST00000531739.1_Nonsense_Mutation_p.R607*|ABCG4_ENST00000307417.3_Nonsense_Mutation_p.R607*	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	607	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)		GAGCATCCTCCGAGCGCTGGA	0.577																																					p.R607X		Atlas-SNP	.											.	ABCG4	77	.	0			c.C1819T						PASS	.						109	95	99					11																	119031694		2200	4295	6495	SO:0001587	stop_gained	64137	exon15			ATCCTCCGAGCGC	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.1819C>T	11.37:g.119031694C>T	ENSP00000406874:p.Arg607*	138	0	0		164	41	0.25	NM_022169	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Nonsense_Mutation	SNP	ENST00000449422.2	37	CCDS8415.1	.	.	.	.	.	.	.	.	.	.	C	40	8.193064	0.98699	.	.	ENSG00000172350	ENST00000307417;ENST00000449422;ENST00000531739	.	.	.	5.42	5.42	0.78866	.	0.245301	0.41605	D	0.000850	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08599	T	0.76	-1.6587	14.8887	0.70590	0.144:0.856:0.0:0.0	.	.	.	.	X	607	.	ENSP00000304111:R607X	R	+	1	2	ABCG4	118536904	1.000000	0.71417	0.989000	0.46669	0.998000	0.95712	3.098000	0.50259	2.552000	0.86080	0.561000	0.74099	CGA	.	.	none		0.577	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169		T	119031694	C	T	119031694	4	4	47	1	0	0	0	0	0	1	0	0	70	644	23	1	1873	1	ABCG4	11	119031694	Nonsense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	30960937	119031694	15974822	97	15831											
RPUSD4	84881	hgsc.bcm.edu	37	chr11	126081386	126081386	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttcccgtttctgggctcggaGcttctccgctaatctctggg	3	14	11	13	3	3	0	0	0	3	0	7	1	4	1	2	3	1	4	2	3	1	4			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:126081386G>A	ENST00000298317.4	-	1	201	c.148C>T	c.(148-150)Ctc>Ttc	p.L50F	FAM118B_ENST00000360194.4_5'Flank|RPUSD4_ENST00000534393.1_5'Flank|RPUSD4_ENST00000533628.1_Missense_Mutation_p.L50F|FAM118B_ENST00000529731.1_5'Flank|RP11-50B3.4_ENST00000532866.1_RNA|FAM118B_ENST00000533050.1_5'UTR|RNU4-86P_ENST00000410135.1_RNA	NM_032795.2	NP_116184.2	Q96CM3	RUSD4_HUMAN	RNA pseudouridylate synthase domain containing 4	50					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)		TGGGCTCGGAGCTTCTCCGCT	0.572																																					p.L50F		Atlas-SNP	.											.	RPUSD4	36	.	0			c.C148T						PASS	.						147	156	153					11																	126081386		2201	4299	6500	SO:0001583	missense	84881	exon1			CTCGGAGCTTCTC	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.148C>T	11.37:g.126081386G>A	ENSP00000298317:p.Leu50Phe	80	0	0		74	36	0.486486	NM_001144827	E9PML2|Q96K56	Missense_Mutation	SNP	ENST00000298317.4	37	CCDS8469.1	.	.	.	.	.	.	.	.	.	.	G	14.30	2.493570	0.44352	.	.	ENSG00000165526	ENST00000298317;ENST00000533628;ENST00000532674	T;T;T	0.43688	2.69;2.49;0.94	5.31	3.44	0.39384	.	0.671765	0.14801	N	0.297611	T	0.60090	0.2242	M	0.77616	2.38	0.80722	D	1	D;D	0.76494	0.99;0.999	P;D	0.68943	0.866;0.961	T	0.56390	-0.7987	10	0.45353	T	0.12	-22.2246	7.8321	0.29349	0.1845:0.0:0.8155:0.0	.	50;50	E9PML2;Q96CM3	.;RUSD4_HUMAN	F	50	ENSP00000298317:L50F;ENSP00000433065:L50F;ENSP00000433709:L50F	ENSP00000298317:L50F	L	-	1	0	RPUSD4	125586596	0.960000	0.32886	0.643000	0.29450	0.026000	0.11368	1.570000	0.36439	0.809000	0.34255	0.650000	0.86243	CTC	.	.	none		0.572	RPUSD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386336.1	NM_032795		A	126081386	G	A	126081386	3	1	47	1	0	0	0	0	1	0	0	0	13684	971	34	2	1013	2	RPUSD4	11	126081386	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	7049692	126081386	8925130	98	15832											
SRPR	6734	hgsc.bcm.edu	37	chr11	126134971	126134971	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtgtagggcactcaaacgccGggtgtgtgtacgcagctgct	7	9	15	10	3	1	0	1	0	0	0	1	0	1	0	1	2	4	6	1	2	3	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:126134971G>A	ENST00000332118.6	-	11	1562	c.1408C>T	c.(1408-1410)Cgg>Tgg	p.R470W	SRPR_ENST00000532259.1_Missense_Mutation_p.R442W|SRPR_ENST00000530680.1_5'Flank	NM_003139.3	NP_003130.2	P08240	SRPR_HUMAN	signal recognition particle receptor (docking protein)	470					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)		CTCAAACGCCGGGTGTGTGTA	0.542																																					p.R470W		Atlas-SNP	.											.	SRPR	60	.	0			c.C1408T						PASS	.						67	61	63					11																	126134971		2201	4299	6500	SO:0001583	missense	6734	exon11			AACGCCGGGTGTG	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.1408C>T	11.37:g.126134971G>A	ENSP00000328023:p.Arg470Trp	59	0	0		68	17	0.25	NM_003139	A6NIB3|B2R5Z8|B4E0H3|E9PJS4|Q9BVJ4	Missense_Mutation	SNP	ENST00000332118.6	37	CCDS31717.1	.	.	.	.	.	.	.	.	.	.	G	34	5.364665	0.95877	.	.	ENSG00000182934	ENST00000332118;ENST00000532259	.	.	.	5.26	5.26	0.73747	ATPase, AAA+ type, core (1);Signal recognition particle, SRP54 subunit, GTPase (2);	0.112768	0.64402	D	0.000006	D	0.85596	0.5733	M	0.90082	3.085	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	D	0.88160	0.2857	9	0.87932	D	0	-12.8572	19.0619	0.93096	0.0:0.0:1.0:0.0	.	442;470	E9PJS4;P08240	.;SRPR_HUMAN	W	470;442	.	ENSP00000328023:R470W	R	-	1	2	SRPR	125640181	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.411000	0.97342	2.744000	0.94065	0.650000	0.86243	CGG	.	.	none		0.542	SRPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386425.2	NM_003139		A	126134971	G	A	126134971	3	1	47	1	0	0	0	0	1	0	0	0	15177	1115	39	1	524	1	SRPR	11	126134971	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	53585	126134971	8871545	99	15833											
KIRREL3	84623	hgsc.bcm.edu	37	chr11	126299147	126299147	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ccttgtggacaatttccactCggatatcatttttggctgac	8	15	8	10	1	1	1	1	1	0	0	3	3	2	3	2	3	0	1	2	3	2	5			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr11:126299147C>T	ENST00000525144.2	-	15	1982	c.1733G>A	c.(1732-1734)cGa>cAa	p.R578Q	KIRREL3_ENST00000416561.2_Missense_Mutation_p.R45Q|KIRREL3_ENST00000529097.2_Missense_Mutation_p.R566Q	NM_032531.3	NP_115920.1	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 (Drosophila)	578					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)		AATTTCCACTCGGATATCATT	0.453																																					p.R578Q		Atlas-SNP	.											.	KIRREL3	183	.	0			c.G1733A						PASS	.						97	101	99					11																	126299147		1946	4141	6087	SO:0001583	missense	84623	exon15			TCCACTCGGATAT	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.1733G>A	11.37:g.126299147C>T	ENSP00000435466:p.Arg578Gln	110	0	0		108	19	0.175926	NM_032531	Q3MIJ7|Q6UWJ9|Q6UWL5|Q96JG0	Missense_Mutation	SNP	ENST00000525144.2	37	CCDS53723.1	.	.	.	.	.	.	.	.	.	.	C	36	5.627850	0.96671	.	.	ENSG00000149571	ENST00000525144;ENST00000529097;ENST00000416561	T;T;T	0.79554	-0.67;-0.42;-1.28	5.66	5.66	0.87406	.	0.000000	0.64402	D	0.000001	D	0.86871	0.6037	L	0.46157	1.445	0.58432	D	0.999999	D;D	0.71674	0.998;0.995	D;P	0.66602	0.945;0.837	D	0.87215	0.2250	10	0.66056	D	0.02	-4.7594	19.7415	0.96232	0.0:1.0:0.0:0.0	.	566;578	E9PRX9;Q8IZU9	.;KIRR3_HUMAN	Q	578;566;45	ENSP00000435466:R578Q;ENSP00000434081:R566Q;ENSP00000408692:R45Q	ENSP00000408692:R45Q	R	-	2	0	KIRREL3	125804357	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.487000	0.81328	2.668000	0.90789	0.561000	0.74099	CGA	.	.	none		0.453	KIRREL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386479.2	NM_032531		T	126299147	C	T	126299147	3	4	47	1	0	0	0	0	1	0	0	0	8335	884	31	1	615	1	KIRREL3	11	126299147	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	164176	126299147	8707369	100	15834											
SCNN1A	6337	hgsc.bcm.edu	37	chr12	6457289	6457289	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	accagtatcggcttcggaacCttcggagcagcatgaggaac	11	7	12	11	3	0	1	0	1	0	0	3	4	0	4	2	4	4	4	2	4	3	3			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr12:6457289C>T	ENST00000228916.2	-	13	1858	c.1760G>A	c.(1759-1761)aGg>aAg	p.R587K	SCNN1A_ENST00000358945.3_Missense_Mutation_p.R609K|SCNN1A_ENST00000396966.2_3'UTR|SCNN1A_ENST00000540037.1_Missense_Mutation_p.R287K|SCNN1A_ENST00000360168.3_Missense_Mutation_p.R646K|SCNN1A_ENST00000543768.1_Missense_Mutation_p.R610K	NM_001038.5	NP_001029.1	P37088	SCNNA_HUMAN	sodium channel, non-voltage-gated 1 alpha subunit	587					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)	apical plasma membrane (GO:0016324)|ciliary membrane (GO:0060170)|cortical actin cytoskeleton (GO:0030864)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(2)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Amiloride(DB00594)|Triamterene(DB00384)	GCTTCGGAACCTTCGGAGCAG	0.622																																					p.R646K		Atlas-SNP	.											.	SCNN1A	54	.	0			c.G1937A						PASS	.						53	53	53					12																	6457289		2203	4300	6503	SO:0001583	missense	6337	exon12			CGGAACCTTCGGA	Z92978	CCDS8543.1, CCDS53738.1, CCDS53739.1	12p13	2012-02-28	2012-02-28		ENSG00000111319	ENSG00000111319		"Ion channels / Sodium channel, nonvoltage-gated", "Sodium channels"	10599	protein-coding gene	gene with protein product		600228	"sodium channel, nonvoltage-gated 1 alpha", "sodium channel, non-voltage-gated 1 alpha"	SCNN1		7896277	Standard	NM_001038		Approved	ENaCalpha	uc001qnw.3	P37088	OTTHUMG00000168268	ENST00000228916.2:c.1760G>A	12.37:g.6457289C>T	ENSP00000228916:p.Arg587Lys	71	0	0		107	49	0.457944	NM_001159576	A5X2U9|B4E2Q5|C5HTZ0|O43271|Q6GSQ6|Q9UM64	Missense_Mutation	SNP	ENST00000228916.2	37	CCDS8543.1	.	.	.	.	.	.	.	.	.	.	C	15.36	2.810468	0.50421	.	.	ENSG00000111319	ENST00000360168;ENST00000358945;ENST00000540037;ENST00000228916;ENST00000543768	T;T;T;T;T	0.71817	-0.54;-0.6;-0.33;-0.5;-0.53	4.54	3.63	0.41609	.	0.092333	0.44688	D	0.000423	T	0.64789	0.2630	M	0.74881	2.28	0.25856	N	0.983882	B;B;B	0.28512	0.214;0.214;0.208	B;B;B	0.22152	0.031;0.018;0.038	T	0.58662	-0.7597	10	0.40728	T	0.16	-30.2911	7.5852	0.27989	0.0:0.7999:0.0:0.2001	.	610;587;646	B4E2Q5;P37088;P37088-2	.;SCNNA_HUMAN;.	K	646;609;287;587;610	ENSP00000353292:R646K;ENSP00000351825:R609K;ENSP00000440876:R287K;ENSP00000228916:R587K;ENSP00000438739:R610K	ENSP00000228916:R587K	R	-	2	0	SCNN1A	6327550	1.000000	0.71417	0.998000	0.56505	0.888000	0.51559	2.385000	0.44371	2.090000	0.63153	0.561000	0.74099	AGG	.	.	none		0.622	SCNN1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399055.1			T	6457289	C	T	6457289	3	4	47	1	0	0	0	0	1	0	0	0	13942	681	24	2	253	2	SCNN1A	12	6457289	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10		6457289	127394606	101	15835											
C1S	716	hgsc.bcm.edu	37	chr12	7172542	7172542	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccaagtggtggtgaccttgcGgagagaagattttgatgtgg	9	11	16	5	1	0	4	0	2	0	2	0	6	0	5	2	4	1	0	2	4	2	3	rs147341600		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr12:7172542G>A	ENST00000406697.1	+	9	1284	c.656G>A	c.(655-657)cGg>cAg	p.R219Q	C1S_ENST00000328916.3_Missense_Mutation_p.R219Q|C1S_ENST00000402681.3_Missense_Mutation_p.R52Q|C1S_ENST00000360817.5_Missense_Mutation_p.R219Q			P09871	C1S_HUMAN	complement component 1, s subcomponent	219	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				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)	GTGACCTTGCGGAGAGAAGAT	0.468																																					p.R219Q	GBM(156;750 1943 12971 24779 31015)	Atlas-SNP	.											.	C1S	93	.	0			c.G656A						PASS	.	G	GLN/ARG,GLN/ARG	0,4406		0,0,2203	135	138	137		656,656	-2.4	0.1	12	dbSNP_134	137	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	C1S	NM_001734.3,NM_201442.2	43,43	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	benign,benign	219/689,219/689	7172542	3,13003	2203	4300	6503	SO:0001583	missense	716	exon6			CCTTGCGGAGAGA		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.656G>A	12.37:g.7172542G>A	ENSP00000385035:p.Arg219Gln	130	0	0		129	20	0.155039	NM_201442	D3DUT4|Q9UCU7|Q9UCU8|Q9UCU9|Q9UCV0|Q9UCV1|Q9UCV2|Q9UCV3|Q9UCV4|Q9UCV5|Q9UM14	Missense_Mutation	SNP	ENST00000406697.1	37	CCDS31735.1	.	.	.	.	.	.	.	.	.	.	G	0.179	-1.063860	0.01934	0.0	3.49E-4	ENSG00000182326	ENST00000406697;ENST00000328916;ENST00000360817;ENST00000402681;ENST00000542978	T;T;T;T;T	0.17213	2.29;2.29;2.29;2.29;2.29	6.17	-2.39	0.06602	CUB (5);	0.630882	0.13151	N	0.409855	T	0.07279	0.0184	N	0.12611	0.24	0.09310	N	1	B	0.18013	0.025	B	0.14023	0.01	T	0.40194	-0.9576	10	0.02654	T	1	.	12.9992	0.58666	0.6693:0.0:0.3307:0.0	.	219	P09871	C1S_HUMAN	Q	219;219;219;52;52	ENSP00000385035:R219Q;ENSP00000328173:R219Q;ENSP00000354057:R219Q;ENSP00000384171:R52Q;ENSP00000442298:R52Q	ENSP00000328173:R219Q	R	+	2	0	C1S	7042803	0.001000	0.12720	0.060000	0.19600	0.161000	0.22273	-0.248000	0.08854	-0.286000	0.09076	-0.345000	0.07892	CGG	G|1.000;A|0.000	0.000	weak		0.468	C1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317481.1	NM_001734		A	7172542	G	A	7172542	3	1	47	1	0	0	0	0	1	0	0	0	1976	1116	39	1	674	1	C1S	12	7172542	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	715253	7172542	126679353	102	15836											
NAV3	89795	hgsc.bcm.edu	37	chr12	78400358	78400358	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acacagtgccacctccaccaTgttgactgtaaagcagtcaa	13	8	7	13	0	1	1	1	1	0	0	2	1	2	1	4	0	2	3	4	0	3	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr12:78400358T>A	ENST00000397909.2	+	8	1213	c.1040T>A	c.(1039-1041)aTg>aAg	p.M347K	NAV3_ENST00000228327.6_Missense_Mutation_p.M347K|NAV3_ENST00000266692.7_Missense_Mutation_p.M347K|NAV3_ENST00000536525.2_Missense_Mutation_p.M347K			Q8IVL0	NAV3_HUMAN	neuron navigator 3	347						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						ACCTCCACCATGTTGACTGTA	0.562										HNSCC(70;0.22)																											p.M347K		Atlas-SNP	.											.	NAV3	506	.	0			c.T1040A						PASS	.						61	63	62					12																	78400358		2101	4221	6322	SO:0001583	missense	89795	exon8			CCACCATGTTGAC	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.1040T>A	12.37:g.78400358T>A	ENSP00000381007:p.Met347Lys	99	0	0		89	16	0.179775	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.57|17.57	3.423239|3.423239	0.62733|0.62733	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000550503|ENST00000549464;ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692	.|T;T;T;T;T	.|0.39592	.|1.07;1.07;1.07;1.07;1.07	5.61|5.61	5.61|5.61	0.85477|0.85477	.|.	.|0.000000	.|0.48767	.|U	.|0.000174	T|T	0.57621|0.57621	0.2066|0.2066	L|L	0.52011|0.52011	1.625|1.625	0.80722|0.80722	D|D	1|1	.|D;D	.|0.62365	.|0.973;0.991	.|D;P	.|0.64042	.|0.921;0.73	T|T	0.60255|0.60255	-0.7299|-0.7299	5|10	.|0.72032	.|D	.|0.01	-19.3128|-19.3128	15.804|15.804	0.78477|0.78477	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|347;347	.|Q8IVL0;Q8IVL0-2	.|NAV3_HUMAN;.	Q|K	170|347	.|ENSP00000446628:M347K;ENSP00000446132:M347K;ENSP00000381007:M347K;ENSP00000228327:M347K;ENSP00000266692:M347K	.|ENSP00000228327:M347K	H|M	+|+	3|2	2|0	NAV3|NAV3	76924489|76924489	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.632000|0.632000	0.37999|0.37999	5.998000|5.998000	0.70653|0.70653	2.138000|2.138000	0.66242|0.66242	0.459000|0.459000	0.35465|0.35465	CAT|ATG	.	.	none		0.562	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383		A	78400358	T	A	78400358	3	1	47	1	0	0	0	0	1	0	0	0	10194	1464	51	5	1070	5	NAV3	12	78400358	Missense_Mutation	SNP	T	TCGA-RQ-AAAT-01A-11D-A38X-10	71227816	78400358	55451537	103	15837											
LRRIQ1	84125	hgsc.bcm.edu	37	chr12	85459141	85459141	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	cttcgacgctgtggattaacTtctttgcacagcctgagtaa	9	13	9	10	2	1	1	0	1	1	0	2	3	1	2	1	1	3	3	1	1	2	5			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr12:85459141T>G	ENST00000393217.2	+	9	2554	c.2493T>G	c.(2491-2493)acT>acG	p.T831T		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	831										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)		GTGGATTAACTTCTTTGCACA	0.363																																					p.T831T		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.T2493G						PASS	.						126	121	123					12																	85459141		2203	4300	6503	SO:0001819	synonymous_variant	84125	exon9			ATTAACTTCTTTG	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.2493T>G	12.37:g.85459141T>G		118	0	0		96	28	0.291667	NM_001079910	Q567P4|Q9BS17|Q9HA36	Silent	SNP	ENST00000393217.2	37	CCDS41816.1																																																																																			.	.	none		0.363	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165		G	85459141	T	G	85459141	2	3	47	1	0	0	0	0	0	0	0	1	9038	1596	56	5		5	LRRIQ1	12	85459141	Silent	SNP	T	TCGA-RQ-AAAT-01A-11D-A38X-10	7058783	85459141	48392754	104	15838											
BTG1	694	hgsc.bcm.edu	37	chr12	92539203	92539203	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gctctggctgaaggtctgcaGctgtcgctcgctcgtgagcc	4	10	14	13	3	2	2	0	2	2	0	5	2	2	2	1	2	3	6	1	2	1	0	rs369374957		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr12:92539203G>A	ENST00000256015.3	-	1	470	c.109C>T	c.(109-111)Ctg>Ttg	p.L37L	C12orf79_ENST00000551563.2_5'Flank|C12orf79_ENST00000546975.1_5'Flank|C12orf79_ENST00000549802.1_5'Flank|RP11-796E2.4_ENST00000499685.2_RNA|RP11-796E2.4_ENST00000501008.2_RNA	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	37					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)	p.L37L(1)		haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				AAGGTCTGCAGCTGTCGCTCG	0.677			T	MYC	BCLL																																p.L37L		Atlas-SNP	.		Dom	yes		12	12q22	694	"B-cell translocation gene 1, anti-proliferative"		L	BTG1,NS,lymphoid_neoplasm,0,3	BTG1	30	3	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C109T						PASS	.						38	41	40					12																	92539203		2203	4300	6503	SO:0001819	synonymous_variant	694	exon1			TCTGCAGCTGTCG		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.109C>T	12.37:g.92539203G>A		161	0	0		141	65	0.460993	NM_001731	P31607	Silent	SNP	ENST00000256015.3	37	CCDS9043.1																																																																																			.	.	alt		0.677	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1			A	92539203	G	A	92539203	2	1	47	1	0	0	0	0	0	0	0	1	1555	962	34	2		2	BTG1	12	92539203	Silent	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	7080062	92539203	41312692	105	15839											
DTX1	1840	hgsc.bcm.edu	37	chr12	113496024	113496024	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	cggccaggccacggtgggctGatgcctgtgaatggtctggg	5	8	18	10	2	1	2	0	2	1	0	1	2	1	2	3	6	1	1	3	6	1	0			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr12:113496024G>C	ENST00000257600.3	+	1	530	c.27G>C	c.(25-27)ctG>ctC	p.L9L		NM_004416.2	NP_004407.2	Q86Y01	DTX1_HUMAN	deltex 1, E3 ubiquitin ligase	9					cell surface receptor signaling pathway (GO:0007166)|glial cell differentiation (GO:0010001)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of T cell differentiation (GO:0045581)|Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)|regulation of Notch signaling pathway (GO:0008593)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Notch binding (GO:0005112)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	32						ACGGTGGGCTGATGCCTGTGA	0.697																																					p.L9L		Atlas-SNP	.											.	DTX1	83	.	0			c.G27C						PASS	.						48	39	42					12																	113496024		2200	4298	6498	SO:0001819	synonymous_variant	1840	exon1			TGGGCTGATGCCT	AF053700	CCDS9164.1	12q24	2014-01-28	2014-01-28			ENSG00000135144			3060	protein-coding gene	gene with protein product		602582	"deltex homolog 1 (Drosophila)"			9590294, 12670957	Standard	NM_004416		Approved	hDx-1	uc001tuk.1	Q86Y01	OTTHUMG00000169610	ENST00000257600.3:c.27G>C	12.37:g.113496024G>C		101	0	0		71	26	0.366197	NM_004416	O60630|Q9BS04	Silent	SNP	ENST00000257600.3	37	CCDS9164.1																																																																																			.	.	none		0.697	DTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405045.2			C	113496024	G	C	113496024	2	2	47	1	0	0	0	0	0	0	0	1	4795	1277	45	4		4	DTX1	12	113496024	Silent	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	20956821	113496024	20355871	106	15840			3	78		3	3	178	N	G_A	3.138677e-07
DTX1	1840	hgsc.bcm.edu	37	chr12	113496139	113496139	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cggccaccgtgtgccaccacAttgagaacgtgctgaaggag	10	6	13	12	3	0	2	0	2	0	1	0	4	0	3	4	2	3	1	4	2	2	1			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr12:113496139A>T	ENST00000257600.3	+	1	645	c.142A>T	c.(142-144)Att>Ttt	p.I48F		NM_004416.2	NP_004407.2	Q86Y01	DTX1_HUMAN	deltex 1, E3 ubiquitin ligase	48	WWE 1. {ECO:0000255|PROSITE- ProRule:PRU00248}.				cell surface receptor signaling pathway (GO:0007166)|glial cell differentiation (GO:0010001)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of T cell differentiation (GO:0045581)|Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)|regulation of Notch signaling pathway (GO:0008593)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Notch binding (GO:0005112)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	32						GTGCCACCACATTGAGAACGT	0.652																																					p.I48F		Atlas-SNP	.											.	DTX1	83	.	0			c.A142T						PASS	.						110	96	100					12																	113496139		2203	4300	6503	SO:0001583	missense	1840	exon1			CACCACATTGAGA	AF053700	CCDS9164.1	12q24	2014-01-28	2014-01-28			ENSG00000135144			3060	protein-coding gene	gene with protein product		602582	"deltex homolog 1 (Drosophila)"			9590294, 12670957	Standard	NM_004416		Approved	hDx-1	uc001tuk.1	Q86Y01	OTTHUMG00000169610	ENST00000257600.3:c.142A>T	12.37:g.113496139A>T	ENSP00000257600:p.Ile48Phe	79	0	0		61	19	0.311475	NM_004416	O60630|Q9BS04	Missense_Mutation	SNP	ENST00000257600.3	37	CCDS9164.1	.	.	.	.	.	.	.	.	.	.	A	27.4	4.824981	0.90955	.	.	ENSG00000135144	ENST00000257600	T	0.64438	-0.1	3.9	3.9	0.45041	WWE domain (2);WWE domain, subgroup (1);	0.000000	0.64402	U	0.000001	T	0.79275	0.4418	M	0.84683	2.71	0.53688	D	0.999976	D	0.69078	0.997	D	0.79108	0.992	T	0.82697	-0.0329	10	0.87932	D	0	-2.9711	11.9027	0.52692	1.0:0.0:0.0:0.0	.	48	Q86Y01	DTX1_HUMAN	F	48	ENSP00000257600:I48F	ENSP00000257600:I48F	I	+	1	0	DTX1	111980522	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	8.407000	0.90218	1.644000	0.50603	0.454000	0.30748	ATT	.	.	none		0.652	DTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405045.2			T	113496139	A	T	113496139	3	4	47	1	0	0	0	0	1	0	0	0	4795	217	8	5	144	5	DTX1	12	113496139	Missense_Mutation	SNP	A	TCGA-RQ-AAAT-01A-11D-A38X-10	115	113496139	20355756	107	15841			3	78		3	3	178	N	G_A	3.138677e-07
DTX1	1840	hgsc.bcm.edu	37	chr12	113496201	113496201	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctggggcaggtggacgcccaGcttgtgccctacatcatcga	7	8	13	13	2	1	0	1	0	0	0	2	2	1	1	2	4	3	2	2	4	1	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr12:113496201G>A	ENST00000257600.3	+	1	707	c.204G>A	c.(202-204)caG>caA	p.Q68Q		NM_004416.2	NP_004407.2	Q86Y01	DTX1_HUMAN	deltex 1, E3 ubiquitin ligase	68	WWE 1. {ECO:0000255|PROSITE- ProRule:PRU00248}.				cell surface receptor signaling pathway (GO:0007166)|glial cell differentiation (GO:0010001)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of T cell differentiation (GO:0045581)|Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)|regulation of Notch signaling pathway (GO:0008593)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ligase activity (GO:0016874)|Notch binding (GO:0005112)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	32						TGGACGCCCAGCTTGTGCCCT	0.662																																					p.Q68Q		Atlas-SNP	.											DTX1,NS,lymphoid_neoplasm,+1,1	DTX1	83	1	0			c.G204A						PASS	.						124	114	117					12																	113496201		2203	4300	6503	SO:0001819	synonymous_variant	1840	exon1			CGCCCAGCTTGTG	AF053700	CCDS9164.1	12q24	2014-01-28	2014-01-28			ENSG00000135144			3060	protein-coding gene	gene with protein product		602582	"deltex homolog 1 (Drosophila)"			9590294, 12670957	Standard	NM_004416		Approved	hDx-1	uc001tuk.1	Q86Y01	OTTHUMG00000169610	ENST00000257600.3:c.204G>A	12.37:g.113496201G>A		31	0	0		32	11	0.34375	NM_004416	O60630|Q9BS04	Silent	SNP	ENST00000257600.3	37	CCDS9164.1																																																																																			.	.	none		0.662	DTX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405045.2			A	113496201	G	A	113496201	2	1	47	1	0	0	0	0	0	0	0	1	4795	962	34	2		2	DTX1	12	113496201	Silent	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	62	113496201	20355694	108	15842			3	78		3	3	178	N	G_A	3.138677e-07
PUS1	80324	hgsc.bcm.edu	37	chr12	132426407	132426407	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cgcagccttcaaggaggagcAcatctaccccaccatcatcg	11	6	8	16	2	3	0	2	0	1	0	4	2	3	2	4	2	3	2	4	2	2	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr12:132426407A>G	ENST00000376649.3	+	5	1615	c.1115A>G	c.(1114-1116)cAc>cGc	p.H372R	PUS1_ENST00000535067.1_Intron|PUS1_ENST00000542167.2_Missense_Mutation_p.H319R|PUS1_ENST00000440818.2_Missense_Mutation_p.H344R|PUS1_ENST00000443358.2_Missense_Mutation_p.H344R	NM_025215.5	NP_079491.2	Q9Y606	TRUA_HUMAN	pseudouridylate synthase 1	372					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)		AAGGAGGAGCACATCTACCCC	0.612																																					p.H372R	Esophageal Squamous(102;671 2009 17384 45666)	Atlas-SNP	.											.	PUS1	47	.	0			c.A1115G						PASS	.						93	66	75					12																	132426407		2203	4300	6503	SO:0001583	missense	80324	exon5			AGGAGCACATCTA	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.1115A>G	12.37:g.132426407A>G	ENSP00000365837:p.His372Arg	103	0	0		89	37	0.41573	NM_025215	A8K877|B3KQC1|Q8WYT2|Q9BU44	Missense_Mutation	SNP	ENST00000376649.3	37	CCDS9275.2	.	.	.	.	.	.	.	.	.	.	A	12.24	1.877457	0.33162	.	.	ENSG00000177192	ENST00000443358;ENST00000376649;ENST00000322060;ENST00000440818;ENST00000542167	T;T;T;T;T	0.54675	0.57;0.56;0.57;0.57;0.56	5.17	5.17	0.71159	.	0.357746	0.33075	N	0.005309	T	0.49321	0.1550	L	0.51914	1.62	0.37582	D	0.919854	B;B	0.19073	0.016;0.033	B;B	0.19946	0.026;0.027	T	0.53005	-0.8499	10	0.48119	T	0.1	-8.4957	14.9932	0.71406	1.0:0.0:0.0:0.0	.	319;372	F5H1S9;Q9Y606	.;TRUA_HUMAN	R	344;372;344;344;319	ENSP00000392451:H344R;ENSP00000365837:H372R;ENSP00000324726:H344R;ENSP00000400032:H344R;ENSP00000438948:H319R	ENSP00000324726:H344R	H	+	2	0	PUS1	130992360	1.000000	0.71417	0.999000	0.59377	0.825000	0.46686	7.383000	0.79741	1.947000	0.56498	0.402000	0.26972	CAC	.	.	none		0.612	PUS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250313.2	NM_025215		G	132426407	A	G	132426407	3	3	47	1	0	0	0	0	1	0	0	0	12845	159	6	3	1133	3	PUS1	12	132426407	Missense_Mutation	SNP	A	TCGA-RQ-AAAT-01A-11D-A38X-10	18930206	132426407	1425488	109	15843											
SACS	26278	hgsc.bcm.edu	37	chr13	23913163	23913163	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tacatctataaatggtttgaActgattaggaaattttctaa	15	16	6	4	0	2	2	0	2	2	0	2	3	2	3	0	2	2	1	0	2	8	8			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr13:23913163A>G	ENST00000382292.3	-	9	5125	c.4852T>C	c.(4852-4854)Ttc>Ctc	p.F1618L	SACS_ENST00000382298.3_Missense_Mutation_p.F1618L|SACS_ENST00000402364.1_Missense_Mutation_p.F868L			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	1618					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)		AATGGTTTGAACTGATTAGGA	0.338																																					p.F1618L		Atlas-SNP	.											.	SACS	871	.	0			c.T4852C						PASS	.						91	88	89					13																	23913163		2203	4299	6502	SO:0001583	missense	26278	exon10			GTTTGAACTGATT	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.4852T>C	13.37:g.23913163A>G	ENSP00000371729:p.Phe1618Leu	77	0	0		65	24	0.369231	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	A	20.8	4.058297	0.76074	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.94793	-3.52;-3.52;-3.52	5.84	5.84	0.93424	ATPase-like, ATP-binding domain (2);	0.000000	0.85682	D	0.000000	D	0.94804	0.8322	L	0.55481	1.735	0.53688	D	0.999977	P	0.39717	0.684	P	0.48334	0.574	D	0.94681	0.7865	10	0.52906	T	0.07	.	16.2302	0.82332	1.0:0.0:0.0:0.0	.	1618	Q9NZJ4	SACS_HUMAN	L	1618;868;1618	ENSP00000371729:F1618L;ENSP00000385844:F868L;ENSP00000371735:F1618L	ENSP00000371729:F1618L	F	-	1	0	SACS	22811163	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	8.962000	0.93254	2.228000	0.72767	0.533000	0.62120	TTC	.	.	none		0.338	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		G	23913163	A	G	23913163	3	3	47	1	0	0	0	0	1	0	0	0	13819	43	2	3	8891	3	SACS	13	23913163	Missense_Mutation	SNP	A	TCGA-RQ-AAAT-01A-11D-A38X-10		23913163	91256715	110	15844											
SLITRK1	114798	hgsc.bcm.edu	37	chr13	84454425	84454425	+	Silent	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gtagcgatgttattgttgccCagatccaacagaatgaggtt	11	12	11	7	1	0	3	0	1	0	2	1	4	1	3	2	1	3	4	2	1	4	5			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr13:84454425C>A	ENST00000377084.2	-	1	2103	c.1218G>T	c.(1216-1218)ctG>ctT	p.L406L		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	406					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)		TATTGTTGCCCAGATCCAACA	0.453																																					p.L406L		Atlas-SNP	.											.	SLITRK1	196	.	0			c.G1218T						PASS	.						235	228	231					13																	84454425		2203	4300	6503	SO:0001819	synonymous_variant	114798	exon1			GTTGCCCAGATCC	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.1218G>T	13.37:g.84454425C>A		111	0	0		106	33	0.311321	NM_052910	Q5U5I6|Q96SF9	Silent	SNP	ENST00000377084.2	37	CCDS9464.1																																																																																			.	.	none		0.453	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910		A	84454425	C	A	84454425	2	1	47	1	0	0	0	0	0	0	0	1	14757	581	21	4		4	SLITRK1	13	84454425	Silent	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	60541262	84454425	30715453	111	15845											
VPS13C	54832	hgsc.bcm.edu	37	chr15	62256044	62256044	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gaacttttaccttgaatcttGatttcggcgatattgttctt	8	19	7	7	2	2	2	0	2	2	0	3	4	2	2	1	1	2	1	1	1	4	9			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr15:62256044G>C	ENST00000261517.5	-	32	3394	c.3321C>G	c.(3319-3321)atC>atG	p.I1107M	VPS13C_ENST00000395896.4_Missense_Mutation_p.I1107M|VPS13C_ENST00000249837.3_Missense_Mutation_p.I1064M|VPS13C_ENST00000395898.3_Missense_Mutation_p.I1064M	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						CTTGAATCTTGATTTCGGCGA	0.343																																					p.I1107M		Atlas-SNP	.											.	VPS13C	506	.	0			c.C3321G						PASS	.						117	107	110					15																	62256044		2202	4300	6502	SO:0001583	missense	54832	exon32			AATCTTGATTTCG	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.3321C>G	15.37:g.62256044G>C	ENSP00000261517:p.Ile1107Met	207	0	0		149	127	0.852349	NM_020821		Missense_Mutation	SNP	ENST00000261517.5	37	CCDS32257.1	.	.	.	.	.	.	.	.	.	.	G	15.81	2.941870	0.53079	.	.	ENSG00000129003	ENST00000249837;ENST00000261517;ENST00000395896;ENST00000395898	T;T;T	0.46819	0.86;0.86;0.86	5.66	4.67	0.58626	.	0.000000	0.85682	D	0.000000	T	0.67979	0.2951	M	0.70595	2.14	0.51012	D	0.999901	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.85130	0.976;0.986;0.99;0.997	T	0.68704	-0.5338	10	0.48119	T	0.1	.	17.3263	0.87248	0.0:0.0:0.8664:0.1336	.	1064;1107;1064;1107	Q709C8-4;Q709C8-2;Q709C8-3;Q709C8	.;.;.;VP13C_HUMAN	M	1064;1107;1107;1107	ENSP00000249837:I1064M;ENSP00000261517:I1107M;ENSP00000379233:I1107M	ENSP00000249837:I1064M	I	-	3	3	VPS13C	60043336	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	2.484000	0.45242	2.656000	0.90262	0.655000	0.94253	ATC	.	.	none		0.343	VPS13C-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415997.1	NM_017684		C	62256044	G	C	62256044	3	2	47	1	0	0	0	0	1	0	0	0	17206	1280	45	4	8184	4	VPS13C	15	62256044	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10		62256044	40275348	112	15846											
CACNA1H	8912	hgsc.bcm.edu	37	chr16	1255246	1255246	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acccgtacaacatcttcgacGgcatcatcgtggtcatcagg	10	9	9	13	4	4	0	3	0	1	0	6	1	4	0	1	3	2	2	1	3	2	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr16:1255246G>A	ENST00000348261.5	+	11	2832	c.2584G>A	c.(2584-2586)Ggc>Agc	p.G862S	CACNA1H_ENST00000565831.1_Missense_Mutation_p.G862S|CACNA1H_ENST00000358590.4_Missense_Mutation_p.G862S|RP11-616M22.3_ENST00000564700.1_RNA	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	862					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)	CATCTTCGACGGCATCATCGT	0.602																																					p.G862S		Atlas-SNP	.											.	CACNA1H	317	.	0			c.G2584A						PASS	.						85	88	87					16																	1255246		2054	4196	6250	SO:0001583	missense	8912	exon11			TTCGACGGCATCA	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.2584G>A	16.37:g.1255246G>A	ENSP00000334198:p.Gly862Ser	47	0	0		35	16	0.457143	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	G	11.35	1.612304	0.28712	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.98362	-4.89;-4.89	3.93	3.93	0.45458	Ion transport (1);	0.179382	0.49305	D	0.000150	D	0.97145	0.9067	L	0.47716	1.5	0.44302	D	0.997171	P;D	0.58268	0.808;0.982	B;P	0.50270	0.17;0.636	D	0.96334	0.9246	10	0.33940	T	0.23	.	15.1309	0.72523	0.0:0.0:1.0:0.0	.	862;862	O95180-2;O95180	.;CAC1H_HUMAN	S	862	ENSP00000334198:G862S;ENSP00000351401:G862S	ENSP00000334198:G862S	G	+	1	0	CACNA1H	1195247	0.999000	0.42202	0.721000	0.30653	0.300000	0.27592	2.892000	0.48625	2.034000	0.60081	0.655000	0.94253	GGC	.	.	none		0.602	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407		A	1255246	G	A	1255246	3	1	47	1	0	0	0	0	1	0	0	0	2547	1116	39	1	2622	1	CACNA1H	16	1255246	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10		1255246	89099507	113	15847											
DNASE1L2	1775	hgsc.bcm.edu	37	chr16	2287821	2287821	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgcagctatgtgcgggcgcaGgactgggccgccatccgtct	5	8	15	13	4	1	0	0	0	1	0	2	1	2	1	3	3	3	3	3	3	1	1			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr16:2287821G>A	ENST00000564065.1	+	5	1646	c.645G>A	c.(643-645)caG>caA	p.Q215Q	DNASE1L2_ENST00000320700.5_Silent_p.Q215Q|DNASE1L2_ENST00000382437.4_Silent_p.Q194Q|RP11-304L19.11_ENST00000565709.1_RNA|RP11-304L19.12_ENST00000564055.1_lincRNA|DNASE1L2_ENST00000567494.1_Silent_p.Q215Q			Q92874	DNSL2_HUMAN	deoxyribonuclease I-like 2	215					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						TGCGGGCGCAGGACTGGGCCG	0.672																																					p.Q215Q		Atlas-SNP	.											.	DNASE1L2	14	.	0			c.G645A						PASS	.						19	24	22					16																	2287821		2092	4205	6297	SO:0001819	synonymous_variant	1775	exon6			GGCGCAGGACTGG	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.645G>A	16.37:g.2287821G>A		71	0	0		50	20	0.4	NM_001374	E9PBY4|Q6JVM2|Q6JVM3	Silent	SNP	ENST00000564065.1	37	CCDS42105.1																																																																																			.	.	none		0.672	DNASE1L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435236.1	NM_001374		A	2287821	G	A	2287821	2	1	47	1	0	0	0	0	0	0	0	1	4664	991	35	2		2	DNASE1L2	16	2287821	Silent	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	1032575	2287821	88066932	114	15848											
TRIM72	260434	hgsc.bcm.edu	37	chr16	31230671	31230671	+	5'Flank	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcaagatgcgggtgttccTggctgcactggagggctcct	5	9	17	10	1	0	1	0	0	0	1	2	2	2	2	2	5	2	5	2	5	1	1			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr16:31230671T>C	ENST00000302964.3	-	0	0				TRIM72_ENST00000322122.3_Missense_Mutation_p.L183P|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						CGGGTGTTCCTGGCTGCACTG	0.652																																					p.L183P		Atlas-SNP	.											.	TRIM72	32	.	0			c.T548C						PASS	.						51	54	53					16																	31230671		2197	4299	6496	SO:0001631	upstream_gene_variant	493829	exon4			TGTTCCTGGCTGC		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		16.37:g.31230671T>C	Exception_encountered	99	0	0		62	11	0.177419	NM_001008274	B2R8L4|Q8NFP8	Missense_Mutation	SNP	ENST00000302964.3	37	CCDS10710.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.242510	0.79912	.	.	ENSG00000177238	ENST00000322122	T	0.72725	-0.68	5.37	5.37	0.77165	.	0.117745	0.36893	N	0.002344	T	0.80470	0.4629	M	0.61703	1.905	0.80722	D	1	D	0.71674	0.998	P	0.62649	0.905	T	0.82806	-0.0275	10	0.87932	D	0	.	14.3504	0.66697	0.0:0.0:0.0:1.0	.	183	Q6ZMU5	TRI72_HUMAN	P	183	ENSP00000312675:L183P	ENSP00000312675:L183P	L	+	2	0	TRIM72	31138172	1.000000	0.71417	0.996000	0.52242	0.745000	0.42441	4.888000	0.63164	2.024000	0.59613	0.533000	0.62120	CTG	.	.	none		0.652	PYDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255543.2	NM_152901		C	31230671	T	C	31230671	1	2	47	0	1	0	0	0	0	0	0	0	16560	1580	55	3		3	TRIM72	16	31230671	5'Flank	SNP	T	TCGA-RQ-AAAT-01A-11D-A38X-10	28942850	31230671	59124082	115	15849											
ADAMTS18	170692	hgsc.bcm.edu	37	chr16	77401400	77401400	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	gatggtgatactctgtctctCgactctgagatgcatgggga	8	12	13	8	1	3	2	0	2	3	1	5	6	3	3	0	3	2	1	0	3	1	1			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr16:77401400C>T	ENST00000282849.5	-	4	1134	c.716G>A	c.(715-717)cGa>cAa	p.R239Q	ADAMTS18_ENST00000567121.1_5'UTR	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	239					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						CTCTGTCTCTCGACTCTGAGA	0.478																																					p.R239Q		Atlas-SNP	.											.	ADAMTS18	270	.	0			c.G716A						PASS	.						87	81	83					16																	77401400		2198	4300	6498	SO:0001583	missense	170692	exon4			GTCTCTCGACTCT	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.716G>A	16.37:g.77401400C>T	ENSP00000282849:p.Arg239Gln	126	0	0		127	63	0.496063	NM_199355	Q6P4R5|Q6ZWJ9	Missense_Mutation	SNP	ENST00000282849.5	37	CCDS10926.1	.	.	.	.	.	.	.	.	.	.	C	0.260	-1.000444	0.02128	.	.	ENSG00000140873	ENST00000282849;ENST00000449265	T;T	0.60171	0.21;2.84	4.72	-5.52	0.02560	.	0.875294	0.10159	N	0.708571	T	0.16514	0.0397	N	0.01048	-1.04	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.36065	-0.9763	10	0.05436	T	0.98	.	4.9243	0.13885	0.0857:0.2003:0.4601:0.2538	.	239	Q8TE60	ATS18_HUMAN	Q	239	ENSP00000282849:R239Q;ENSP00000392540:R239Q	ENSP00000282849:R239Q	R	-	2	0	ADAMTS18	75958901	0.001000	0.12720	0.013000	0.15412	0.205000	0.24178	-0.509000	0.06336	-0.592000	0.05851	-3.097000	0.00064	CGA	.	.	none		0.478	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1			T	77401400	C	T	77401400	3	4	47	1	0	0	0	0	1	0	0	0	263	884	31	1	3029	1	ADAMTS18	16	77401400	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	46170729	77401400	12953353	116	15850											
TP53	7157	hgsc.bcm.edu	37	chr17	7577539	7577539	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gatggtgaggatgggcctccGgttcatgccgcccatgcagg	6	8	16	11	2	1	1	1	1	0	0	2	3	2	2	4	5	2	2	4	5	0	1	rs397516437|rs121912651		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr17:7577539G>A	ENST00000269305.4	-	7	931	c.742C>T	c.(742-744)Cgg>Tgg	p.R248W	TP53_ENST00000455263.2_Missense_Mutation_p.R248W|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000359597.4_Missense_Mutation_p.R248W|TP53_ENST00000445888.2_Missense_Mutation_p.R248W|TP53_ENST00000413465.2_Missense_Mutation_p.R248W|TP53_ENST00000420246.2_Missense_Mutation_p.R248W	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,+1,1635	TP53	33396	1635	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	PASS	.						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	17.37:g.7577539G>A	ENSP00000269305:p.Arg248Trp	95	0	0		44	30	0.681818	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	37	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	.	.	weak		0.577	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546		A	7577539	G	A	7577539	3	1	47	1	0	0	0	0	1	0	0	0	16396	1115	39	1	548	1	TP53	17	7577539	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10		7577539	73617671	117	15851											
PER1	5187	hgsc.bcm.edu	37	chr17	8053822	8053822	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaggagctgtgtgagctcCgctgagatgcgcctctagac	8	8	15	10	2	1	3	0	2	1	2	2	6	2	5	2	2	3	3	2	2	1	1			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr17:8053822C>T	ENST00000317276.4	-	2	440	c.203G>A	c.(202-204)cGg>cAg	p.R68Q	PER1_ENST00000581082.1_Missense_Mutation_p.R68Q|PER1_ENST00000354903.5_Missense_Mutation_p.R52Q	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	68	Interaction with BTRC. {ECO:0000269|PubMed:15917222}.|Ser-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						GTGTGAGCTCCGCTGAGATGC	0.582			T	ETV6	"AML, CMML"			Other conserved DNA damage response genes																													p.R68Q		Atlas-SNP	.		Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	.	PER1	104	.	0			c.G203A						PASS	.						114	103	106					17																	8053822		2203	4300	6503	SO:0001583	missense	5187	exon2			GAGCTCCGCTGAG	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.203G>A	17.37:g.8053822C>T	ENSP00000314420:p.Arg68Gln	76	0	0		44	25	0.568182	NM_002616	B2RPA8|B4DI49|D3DTR3	Missense_Mutation	SNP	ENST00000317276.4	37	CCDS11131.1	.	.	.	.	.	.	.	.	.	.	C	16.05	3.013101	0.54468	.	.	ENSG00000179094	ENST00000317276;ENST00000354903	T;T	0.36699	2.65;1.24	5.16	3.97	0.46021	.	0.063176	0.64402	D	0.000013	T	0.14013	0.0339	N	0.11064	0.09	0.38309	D	0.943193	B;P;B	0.48640	0.028;0.913;0.44	B;B;B	0.36378	0.006;0.223;0.022	T	0.06789	-1.0807	10	0.13470	T	0.59	-18.8514	7.9228	0.29857	0.0:0.8031:0.0:0.1969	.	68;52;68	Q6IN51;B4DI49;O15534	.;.;PER1_HUMAN	Q	68;52	ENSP00000314420:R68Q;ENSP00000346979:R52Q	ENSP00000314420:R68Q	R	-	2	0	PER1	7994547	1.000000	0.71417	1.000000	0.80357	0.715000	0.41141	1.762000	0.38451	2.405000	0.81733	0.563000	0.77884	CGG	.	.	none		0.582	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2			T	8053822	C	T	8053822	3	4	47	1	0	0	0	0	1	0	0	0	11738	652	23	1	3757	1	PER1	17	8053822	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	476283	8053822	73141388	118	15852											
STAT3	6774	hgsc.bcm.edu	37	chr17	40475063	40475063	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aagtgaaagtgacgcctcctTctttgctgctttcactgaat	9	14	8	10	1	2	3	1	3	1	0	3	3	3	3	2	0	2	2	2	0	3	3			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr17:40475063T>C	ENST00000264657.5	-	20	2159	c.1847A>G	c.(1846-1848)gAa>gGa	p.E616G	STAT3_ENST00000585517.1_Missense_Mutation_p.E616G|STAT3_ENST00000588969.1_Missense_Mutation_p.E616G|STAT3_ENST00000404395.3_Missense_Mutation_p.E616G|STAT3_ENST00000389272.3_Missense_Mutation_p.E518G	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)	616	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)		GACGCCTCCTTCTTTGCTGCT	0.562									Hyperimmunoglobulin E Recurrent Infection Syndrome		OREG0024421	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E616G		Atlas-SNP	.											STAT3,NS,lymphoid_neoplasm,-1,1	STAT3	268	1	0			c.A1847G						PASS	.						129	120	123					17																	40475063		2203	4300	6503	SO:0001583	missense	6774	exon20	Familial Cancer Database	HIES, Hyper IgE syndrome, autosomal dominant (Job syndrome) / recessive	CCTCCTTCTTTGC	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.1847A>G	17.37:g.40475063T>C	ENSP00000264657:p.Glu616Gly	87	0	0	893	76	25	0.328947	NM_003150	A8K7B8|K7ENL3|O14916|Q9BW54	Missense_Mutation	SNP	ENST00000264657.5	37	CCDS32656.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.175244	0.78564	.	.	ENSG00000168610	ENST00000264657;ENST00000389272;ENST00000404395	D;D;D	0.89343	-2.5;-2.5;-2.5	5.29	5.29	0.74685	SH2 motif (4);	0.000000	0.85682	D	0.000000	D	0.86016	0.5832	L	0.49126	1.545	0.80722	D	1	P;P;P	0.44344	0.8;0.833;0.833	B;B;B	0.39258	0.195;0.295;0.295	D	0.87270	0.2285	10	0.52906	T	0.07	-26.4272	15.3873	0.74711	0.0:0.0:0.0:1.0	.	616;616;616	P40763-2;P40763;B5BTZ6	.;STAT3_HUMAN;.	G	616;518;616	ENSP00000264657:E616G;ENSP00000373923:E518G;ENSP00000384943:E616G	ENSP00000264657:E616G	E	-	2	0	STAT3	37728589	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.846000	0.86887	2.221000	0.72209	0.533000	0.62120	GAA	.	.	none		0.562	STAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319353.3	NM_139276, NM_003150		C	40475063	T	C	40475063	3	2	47	1	0	0	0	0	1	0	0	0	15281	1783	62	3	485	3	STAT3	17	40475063	Missense_Mutation	SNP	T	TCGA-RQ-AAAT-01A-11D-A38X-10	32421241	40475063	40720147	119	15853											
ITGB3	3690	hgsc.bcm.edu	37	chr17	45369814	45369814	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtcagcccgtctgcagccagCggggcgagtgcctctgtggt	4	8	16	13	3	3	0	1	0	2	0	3	1	3	0	3	3	5	1	3	3	0	0	rs145572861	byFrequency	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr17:45369814C>T	ENST00000559488.1	+	10	1586	c.1570C>T	c.(1570-1572)Cgg>Tgg	p.R524W	ITGB3_ENST00000435993.2_Missense_Mutation_p.R477W|ITGB3_ENST00000560629.1_Missense_Mutation_p.A512V	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	524	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)	CTGCAGCCAGCGGGGCGAGTG	0.617													C|||	2	0.000399361	0.0008	0.0	5008	,	,		18639	0.001		0.0	False		,,,				2504	0.0				p.R524W		Atlas-SNP	.											.	ITGB3	157	.	0			c.C1570T						PASS	.	C	TRP/ARG	5,4401	9.9+/-24.2	0,5,2198	88	81	84		1570	4.4	1	17	dbSNP_134	84	0,8600		0,0,4300	yes	missense	ITGB3	NM_000212.2	101	0,5,6498	TT,TC,CC		0.0,0.1135,0.0384	probably-damaging	524/789	45369814	5,13001	2203	4300	6503	SO:0001583	missense	3690	exon10			AGCCAGCGGGGCG		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.1570C>T	17.37:g.45369814C>T	ENSP00000452786:p.Arg524Trp	50	0	0		41	17	0.414634	NM_000212	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Missense_Mutation	SNP	ENST00000559488.1	37	CCDS11511.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	19.68	3.872407	0.72180	0.001135	0.0	ENSG00000178852	ENST00000262017;ENST00000435993	D	0.99329	-5.75	5.38	4.39	0.52855	EGF, extracellular (1);	0.055231	0.64402	D	0.000002	D	0.99450	0.9805	M	0.91140	3.18	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98771	1.0728	10	0.87932	D	0	.	11.7475	0.51828	0.4384:0.5616:0.0:0.0	.	524	P05106	ITB3_HUMAN	W	524;477	ENSP00000407801:R477W	ENSP00000262017:R524W	R	+	1	2	C17orf57	42724813	0.931000	0.31567	1.000000	0.80357	0.940000	0.58332	0.075000	0.14686	1.240000	0.43803	0.462000	0.41574	CGG	C|1.000;T|0.000	0.000	strong		0.617	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212		T	45369814	C	T	45369814	3	4	47	1	0	0	0	0	1	0	0	0	7904	759	27	1	1608	1	ITGB3	17	45369814	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	4894751	45369814	35825396	120	15854											
SPATA20	64847	hgsc.bcm.edu	37	chr17	48631644	48631644	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagagcccagcgccaattccGtgtcagcccacaacctgctc	9	6	8	18	2	1	1	1	0	0	1	3	1	2	1	5	0	5	1	5	0	2	1	rs200274697		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr17:48631644G>A	ENST00000356488.4	+	14	2025	c.1942G>A	c.(1942-1944)Gtg>Atg	p.V648M	CACNA1G-AS1_ENST00000505793.1_RNA|SPATA20_ENST00000393244.3_Missense_Mutation_p.V604M|CACNA1G-AS1_ENST00000505495.1_RNA|SPATA20_ENST00000511937.1_3'UTR|CACNA1G-AS1_ENST00000508920.1_RNA|SPATA20_ENST00000006658.6_Missense_Mutation_p.V664M	NM_001258372.1	NP_001245301.1	Q8TB22	SPT20_HUMAN	spermatogenesis associated 20	648					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)			CGCCAATTCCGTGTCAGCCCA	0.627																																					p.V664M		Atlas-SNP	.											.	SPATA20	59	.	0			c.G1990A						PASS	.						109	77	88					17																	48631644		2203	4300	6503	SO:0001583	missense	64847	exon15			AATTCCGTGTCAG		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.1942G>A	17.37:g.48631644G>A	ENSP00000348878:p.Val648Met	99	0	0		75	38	0.506667	NM_022827	Q2TA99|Q2XUZ6|Q6P0P1|Q8WVW3|Q9H747	Missense_Mutation	SNP	ENST00000356488.4	37	CCDS58563.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	26.5	4.744792	0.89663	.	.	ENSG00000006282	ENST00000006658;ENST00000356488;ENST00000393244	T;T;T	0.64085	-0.08;-0.08;-0.08	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.77485	0.4137	M	0.83774	2.66	0.80722	D	1	D;D	0.65815	0.995;0.972	P;P	0.55713	0.781;0.782	T	0.80865	-0.1191	10	0.56958	D	0.05	-22.9431	18.4943	0.90858	0.0:0.0:1.0:0.0	.	648;664	Q8TB22;Q8TB22-2	SPT20_HUMAN;.	M	664;648;604	ENSP00000006658:V664M;ENSP00000348878:V648M;ENSP00000376935:V604M	ENSP00000006658:V664M	V	+	1	0	SPATA20	45986643	1.000000	0.71417	0.853000	0.33588	0.785000	0.44390	7.586000	0.82596	2.467000	0.83353	0.561000	0.74099	GTG	G|1.000;A|0.000	0.000	strong		0.627	SPATA20-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367651.1	NM_022827		A	48631644	G	A	48631644	3	1	47	1	0	0	0	0	1	0	0	0	15021	1145	40	1	2048	1	SPATA20	17	48631644	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	3261830	48631644	32563566	121	15855											
CD79B	974	hgsc.bcm.edu	37	chr17	62006798	62006798	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgcccctctccttacctcgTaggtgtgatcttcctccatg	4	14	7	16	1	2	1	0	1	2	0	6	1	4	1	6	1	2	1	6	1	2	3			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr17:62006798T>A	ENST00000006750.3	-	5	679	c.587A>T	c.(586-588)tAc>tTc	p.Y196F	CD79B_ENST00000392795.3_Missense_Mutation_p.Y197F|CD79B_ENST00000349817.2_Missense_Mutation_p.Y92F	NM_000626.2|NM_021602.2	NP_000617.1|NP_067613.1	P40259	CD79B_HUMAN	CD79b molecule, immunoglobulin-associated beta	196	ITAM. {ECO:0000255|PROSITE- ProRule:PRU00379}.				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)	p.Y196C(1)|p.Y196F(1)|p.Y196S(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	15						CCTTACCTCGTAGGTGTGATC	0.632			"Mis, O"		DLBCL																																p.Y197F		Atlas-SNP	.		Dom	yes		17	17q23	974	"CD79b molecule, immunoglobulin-associated beta"		L	CD79B,NS,lymphoid_neoplasm,-1,13	CD79B	38	13	3	Substitution - Missense(3)	haematopoietic_and_lymphoid_tissue(3)	c.A590T						scavenged	.						93	74	81					17																	62006798		2203	4300	6503	SO:0001583	missense	974	exon5			ACCTCGTAGGTGT	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.587A>T	17.37:g.62006798T>A	ENSP00000006750:p.Tyr196Phe	84	1	0.0119048		51	40	0.784314	NM_001039933	Q53FS2|Q9BU06	Missense_Mutation	SNP	ENST00000006750.3	37	CCDS11655.1	.	.	.	.	.	.	.	.	.	.	T	15.77	2.930227	0.52866	.	.	ENSG00000007312	ENST00000349817;ENST00000392795;ENST00000006750	D;D;D	0.96587	-4.06;-4.06;-4.06	4.2	4.2	0.49525	.	0.000000	0.64402	D	0.000002	D	0.95601	0.8570	N	0.24115	0.695	0.43426	D	0.995588	D;D	0.76494	0.996;0.999	D;D	0.85130	0.986;0.997	D	0.95387	0.8478	10	0.87932	D	0	-12.4743	9.5968	0.39578	0.0:0.0:0.0:1.0	.	92;196	P40259-2;P40259	.;CD79B_HUMAN	F	92;197;196	ENSP00000245862:Y92F;ENSP00000376544:Y197F;ENSP00000006750:Y196F	ENSP00000006750:Y196F	Y	-	2	0	CD79B	59360530	0.997000	0.39634	0.977000	0.42913	0.245000	0.25701	3.902000	0.56310	1.782000	0.52362	0.358000	0.22013	TAC	.	.	none		0.632	CD79B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417711.1			A	62006798	T	A	62006798	3	1	47	1	0	0	0	0	1	0	0	0	3039	1638	57	5	110	5	CD79B	17	62006798	Missense_Mutation	SNP	T	TCGA-RQ-AAAT-01A-11D-A38X-10	13375154	62006798	19188412	122	15856											
CCDC46	201134	hgsc.bcm.edu	37	chr17	64125942	64125942	+	Splice_Site	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gattttttcgaataaacttcCtgaaatacaaaagggaaaaa	19	11	6	5	1	0	1	0	1	0	0	2	4	1	2	1	1	2	0	1	1	9	6			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr17:64125942C>A	ENST00000392769.2	-	6	783		c.e6-1		CEP112_ENST00000535342.2_Splice_Site|CEP112_ENST00000537949.1_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						AATAAACTTCCTGAAATACAa	0.333																																					.		Atlas-SNP	.											.	CEP112	192	.	0			c.565-1G>T						PASS	.						59	60	60					17																	64125942		2202	4299	6501	SO:0001630	splice_region_variant	201134	exon7			AACTTCCTGAAAT	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.565-1G>T	17.37:g.64125942C>A		349	0	0		290	141	0.486207	NM_001199165	Q6PIB5|Q8NCR4|Q8NFR4	Splice_Site	SNP	ENST00000392769.2	37	CCDS32710.1	.	.	.	.	.	.	.	.	.	.	C	12.12	1.843859	0.32606	.	.	ENSG00000154240	ENST00000535342;ENST00000392769;ENST00000537949	.	.	.	5.32	5.32	0.75619	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5104	0.67784	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CEP112	61556404	1.000000	0.71417	1.000000	0.80357	0.233000	0.25261	4.453000	0.60061	2.493000	0.84123	0.650000	0.86243	.	.	.	none		0.333	CEP112-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446582.1	NM_145036	Intron	A	64125942	C	A	64125942	5	1	47	1	0	0	0	0	0	0	1	0	2819	695	24	4	2557	4	CCDC46	17	64125942	Splice_Site	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	2119144	64125942	17069268	123	15857											
SDK2	54549	hgsc.bcm.edu	37	chr17	71434182	71434182	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcctcacactcgtagtagccGgcgtcactgccggtggggtt	5	9	14	13	4	2	0	2	0	0	0	3	0	2	0	3	4	2	3	3	4	2	3			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr17:71434182G>A	ENST00000392650.3	-	7	837	c.837C>T	c.(835-837)gcC>gcT	p.A279A	SDK2_ENST00000388726.3_Silent_p.A279A	NM_001144952.1	NP_001138424.1	Q58EX2	SDK2_HUMAN	sidekick cell adhesion molecule 2	279	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						CGTAGTAGCCGGCGTCACTGC	0.632																																					p.A279A		Atlas-SNP	.											.	SDK2	219	.	0			c.C837T						PASS	.						28	38	35					17																	71434182		692	1591	2283	SO:0001819	synonymous_variant	54549	exon7			GTAGCCGGCGTCA	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.837C>T	17.37:g.71434182G>A		80	0	0		48	20	0.416667	NM_001144952	A6NMR8|C9JA57|Q86VY3|Q9NTD2|Q9NVB3|Q9P214	Silent	SNP	ENST00000392650.3	37	CCDS45769.1	.	.	.	.	.	.	.	.	.	.	G	2.222	-0.378123	0.05000	.	.	ENSG00000069188	ENST00000416616	.	.	.	5.05	-0.688	0.11317	.	.	.	.	.	T	0.53802	0.1819	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44421	-0.9329	4	.	.	.	.	7.8147	0.29252	0.3879:0.104:0.5081:0.0	.	.	.	.	W	184	.	.	R	-	1	2	SDK2	68945777	0.123000	0.22298	0.968000	0.41197	0.041000	0.13682	-0.401000	0.07232	-0.292000	0.08999	-2.620000	0.00156	CGG	.	.	none		0.632	SDK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327598.2	NM_019064		A	71434182	G	A	71434182	2	1	47	1	0	0	0	0	0	0	0	1	13984	1103	39	1		1	SDK2	17	71434182	Silent	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	7308240	71434182	9761028	124	15858											
NFATC1	4772	hgsc.bcm.edu	37	chr18	77156301	77156301	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggtcttcgggagaggagaaaCtttggggcccgcgccgcgcg	6	6	18	11	6	1	2	0	0	1	2	2	4	1	2	2	5	1	0	2	5	1	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr18:77156301C>G	ENST00000427363.2	+	1	77	c.77C>G	c.(76-78)aCt>aGt	p.T26S	NFATC1_ENST00000587635.1_Missense_Mutation_p.T26S|NFATC1_ENST00000591814.1_Missense_Mutation_p.T26S|NFATC1_ENST00000397790.2_5'UTR|NFATC1_ENST00000542384.1_Missense_Mutation_p.T26S|NFATC1_ENST00000253506.5_Missense_Mutation_p.T26S			O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1	26					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)	AGAGGAGAAACTTTggggccc	0.731																																					p.T26S	GBM(151;1210 2593 28719 45011)	Atlas-SNP	.											.	NFATC1	105	.	0			c.C77G						PASS	.						6	6	6					18																	77156301		2092	4172	6264	SO:0001583	missense	4772	exon1			GAGAAACTTTGGG	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.77C>G	18.37:g.77156301C>G	ENSP00000389377:p.Thr26Ser	121	0	0		96	23	0.239583	NM_172390	B5B2M4|B5B2M5|B5B2M6|B5B2M7|B5B2M8|B5B2M9|B5B2N1|Q12865|Q15793|Q2M1S3	Missense_Mutation	SNP	ENST00000427363.2	37		.	.	.	.	.	.	.	.	.	.	-	3.969	-0.008806	0.07727	.	.	ENSG00000131196	ENST00000318065;ENST00000253506;ENST00000542384	T;T	0.13538	3.0;2.58	2.46	-0.0619	0.13783	.	.	.	.	.	T	0.06050	0.0157	N	0.08118	0	0.80722	D	1	B;B;B;B	0.06786	0.0;0.001;0.001;0.0	B;B;B;B	0.06405	0.001;0.002;0.002;0.001	T	0.36432	-0.9748	9	0.22706	T	0.39	.	9.1199	0.36780	0.0:0.5714:0.4286:0.0	.	26;26;26;26	B5B2M6;O95644;B5B2M4;Q2M1S3	.;NFAC1_HUMAN;.;.	S	26	ENSP00000253506:T26S;ENSP00000442435:T26S	ENSP00000253506:T26S	T	+	2	0	NFATC1	75257289	0.998000	0.40836	1.000000	0.80357	0.974000	0.67602	0.909000	0.28558	0.139000	0.18822	0.437000	0.28790	ACT	.	.	none		0.731	NFATC1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000450507.1	NM_172390		G	77156301	C	G	77156301	3	3	47	1	0	0	0	0	1	0	0	0	10370	565	20	4	79	4	NFATC1	18	77156301	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10		77156301	920947	125	15859											
ZNRF4	148066	hgsc.bcm.edu	37	chr19	5455866	5455866	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	atctgccggcgctgttcggcGtccccctggcccccgagggc	2	7	14	18	5	1	0	0	0	1	0	3	1	2	0	5	4	1	2	5	4	0	1	rs375118147		TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr19:5455866G>A	ENST00000222033.4	+	1	441	c.364G>A	c.(364-366)Gtc>Atc	p.V122I		NM_181710.3	NP_859061.3	Q8WWF5	ZNRF4_HUMAN	zinc and ring finger 4	122						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)		GCTGTTCGGCGTCCCCCTGGC	0.682																																					p.V122I		Atlas-SNP	.											.	ZNRF4	59	.	0			c.G364A						PASS	.	G	ILE/VAL	0,4210		0,0,2105	47	55	53		364	-0.8	0	19		53	1,8419		0,1,4209	no	missense	ZNRF4	NM_181710.3	29	0,1,6314	AA,AG,GG		0.0119,0.0,0.0079	benign	122/430	5455866	1,12629	2105	4210	6315	SO:0001583	missense	148066	exon1			TTCGGCGTCCCCC	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.364G>A	19.37:g.5455866G>A	ENSP00000222033:p.Val122Ile	34	0	0		26	7	0.269231	NM_181710	A8K886|O75866	Missense_Mutation	SNP	ENST00000222033.4	37	CCDS42475.1	.	.	.	.	.	.	.	.	.	.	G	2.855	-0.237362	0.05944	0.0	1.19E-4	ENSG00000105428	ENST00000222033	T	0.04862	3.54	4.55	-0.827	0.10802	.	0.557882	0.16640	U	0.205677	T	0.04048	0.0113	L	0.40543	1.245	0.09310	N	1	B	0.30211	0.273	B	0.17722	0.019	T	0.35943	-0.9768	10	0.37606	T	0.19	.	3.753	0.08573	0.0962:0.4131:0.3402:0.1505	.	122	Q8WWF5	ZNRF4_HUMAN	I	122	ENSP00000222033:V122I	ENSP00000222033:V122I	V	+	1	0	ZNRF4	5406866	0.073000	0.21202	0.001000	0.08648	0.045000	0.14185	0.594000	0.24014	0.004000	0.14682	-0.424000	0.05967	GTC	.	.	weak		0.682	ZNRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450924.1	NM_181710		A	5455866	G	A	5455866	3	1	47	1	0	0	0	0	1	0	0	0	18229	1145	40	1	366	1	ZNRF4	19	5455866	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10		5455866	53673117	126	15860											
MCOLN1	57192	hgsc.bcm.edu	37	chr19	7593558	7593558	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gtccttcctcctctgcgcccGctcactccttcgaggcttcc	2	12	7	20	3	2	0	1	0	1	0	8	1	7	0	6	1	1	2	6	1	0	3			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr19:7593558G>A	ENST00000264079.6	+	8	1078	c.953G>A	c.(952-954)cGc>cAc	p.R318H		NM_020533.2	NP_065394.1	Q9GZU1	MCLN1_HUMAN	mucolipin 1	318					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|cellular iron ion homeostasis (GO:0006879)|ion transmembrane transport (GO:0034220)|release of sequestered calcium ion into cytosol (GO:0051209)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cation channel activity (GO:0005261)|NAADP-sensitive calcium-release channel activity (GO:0072345)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CTCTGCGCCCGCTCACTCCTT	0.637																																					p.R318H		Atlas-SNP	.											MCOLN1,colon,carcinoma,+1,1	MCOLN1	54	1	0			c.G953A						PASS	.						151	94	113					19																	7593558		2203	4300	6503	SO:0001583	missense	57192	exon8			GCGCCCGCTCACT	AF249319	CCDS12180.1	19p13.2	2011-12-16				ENSG00000090674		"Voltage-gated ion channels / Transient receptor potential cation channels"	13356	protein-coding gene	gene with protein product		605248				16382100	Standard	NM_020533		Approved	TRPML1, ML4, MLIV, MST080, MSTP080, TRPM-L1	uc002mgo.3	Q9GZU1		ENST00000264079.6:c.953G>A	19.37:g.7593558G>A	ENSP00000264079:p.Arg318His	153	0	0		118	52	0.440678	NM_020533	D6W647|Q7Z4F7|Q9H292|Q9H4B3|Q9H4B5	Missense_Mutation	SNP	ENST00000264079.6	37	CCDS12180.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.170229	0.78452	.	.	ENSG00000090674	ENST00000264079;ENST00000394321	D	0.83992	-1.79	5.32	5.32	0.75619	.	0.050554	0.85682	D	0.000000	D	0.91436	0.7297	M	0.87682	2.9	0.80722	D	1	D;D	0.63880	0.993;0.976	D;P	0.63381	0.914;0.717	D	0.92856	0.6301	10	0.87932	D	0	.	16.4854	0.84183	0.0:0.0:1.0:0.0	.	283;318	Q9GZU1-2;Q9GZU1	.;MCLN1_HUMAN	H	318;283	ENSP00000264079:R318H	ENSP00000264079:R318H	R	+	2	0	MCOLN1	7499558	1.000000	0.71417	1.000000	0.80357	0.197000	0.23852	7.602000	0.82796	2.492000	0.84095	0.563000	0.77884	CGC	.	.	none		0.637	MCOLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458974.2	NM_020533		A	7593558	G	A	7593558	3	1	47	1	0	0	0	0	1	0	0	0	9404	1087	38	1	983	1	MCOLN1	19	7593558	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	2137692	7593558	51535425	127	15861											
CD97	976	hgsc.bcm.edu	37	chr19	14512523	14512523	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtcactatgggtcagagcagCgcacgcatgaagctgaattg	11	8	13	9	2	2	3	2	2	0	1	2	3	2	3	0	1	3	4	0	1	3	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr19:14512523C>T	ENST00000242786.5	+	11	1214	c.1134C>T	c.(1132-1134)agC>agT	p.S378S	CD97_ENST00000357355.3_Silent_p.S329S|CD97_ENST00000358600.3_Silent_p.S285S|CTC-548K16.5_ENST00000590626.1_RNA	NM_078481.3	NP_510966.1	P48960	CD97_HUMAN	CD97 molecule	378					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						GTCAGAGCAGCGCACGCATGA	0.622																																					p.S378S		Atlas-SNP	.											.	CD97	86	.	0			c.C1134T						PASS	.						66	54	58					19																	14512523		2203	4300	6503	SO:0001819	synonymous_variant	976	exon11			GAGCAGCGCACGC		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.1134C>T	19.37:g.14512523C>T		65	0	0		57	22	0.385965	NM_078481	A8K7Z4|B2RBJ9|O00718|O76101|Q8NG72|Q8TBQ7	Silent	SNP	ENST00000242786.5	37	CCDS32929.1																																																																																			.	.	none		0.622	CD97-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459821.2	NM_078481		T	14512523	C	T	14512523	2	4	47	1	0	0	0	0	0	0	0	1	3051	767	27	1		1	CD97	19	14512523	Silent	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	6918965	14512523	44616460	128	15862											
SLC1A6	6511	hgsc.bcm.edu	37	chr19	15073065	15073065	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctggttccgttctccactgaGaatggaggaggcatggaggc	8	9	15	9	1	1	1	0	1	1	1	3	5	2	4	2	6	0	3	2	6	1	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr19:15073065G>T	ENST00000221742.3	-	5	691	c.684C>A	c.(682-684)ttC>ttA	p.F228L	SLC1A6_ENST00000544886.2_Missense_Mutation_p.F228L|SLC1A6_ENST00000430939.2_Missense_Mutation_p.F164L|SLC1A6_ENST00000600144.1_Missense_Mutation_p.F228L|SLC1A6_ENST00000598504.1_Missense_Mutation_p.F228L	NM_005071.1	NP_005062.1	P48664	EAA4_HUMAN	solute carrier family 1 (high affinity aspartate/glutamate transporter), member 6	228					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						TCTCCACTGAGAATGGAGGAG	0.567																																					p.F228L		Atlas-SNP	.											.	SLC1A6	111	.	0			c.C684A						PASS	.						111	105	107					19																	15073065		2203	4300	6503	SO:0001583	missense	6511	exon8			CACTGAGAATGGA		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.684C>A	19.37:g.15073065G>T	ENSP00000221742:p.Phe228Leu	90	0	0		70	30	0.428571	NM_001272087	Q8N753	Missense_Mutation	SNP	ENST00000221742.3	37	CCDS12321.1	.	.	.	.	.	.	.	.	.	.	g	3.890	-0.024160	0.07634	.	.	ENSG00000105143	ENST00000430939;ENST00000221742;ENST00000544886	T;T;T	0.69306	-0.39;0.67;1.4	4.42	0.947	0.19555	.	0.359970	0.28332	N	0.015725	T	0.31009	0.0783	N	0.02539	-0.55	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.17098	0.017;0.0;0.0	T	0.25012	-1.0144	10	0.08179	T	0.78	-12.7775	5.5234	0.16945	0.3711:0.0:0.6289:0.0	.	164;228;228	E7EV13;Q8N753;P48664	.;.;EAA4_HUMAN	L	164;228;228	ENSP00000409386:F164L;ENSP00000221742:F228L;ENSP00000446175:F228L	ENSP00000221742:F228L	F	-	3	2	SLC1A6	14934065	0.812000	0.29077	0.300000	0.25030	0.783000	0.44284	0.099000	0.15210	0.513000	0.28278	0.454000	0.30748	TTC	.	.	none		0.567	SLC1A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466283.1	NM_005071		T	15073065	G	T	15073065	3	4	47	1	0	0	0	0	1	0	0	0	14451	933	33	4	1030	4	SLC1A6	19	15073065	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	560542	15073065	44055918	129	15863											
MAP1S	55201	hgsc.bcm.edu	37	chr19	17838807	17838807	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccctggcccgccccaactcaCgcgctgccgcccccaaagcc	6	3	8	24	4	1	0	1	0	0	0	1	0	1	0	8	1	3	1	8	1	2	0			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr19:17838807C>T	ENST00000324096.4	+	5	2765	c.2614C>T	c.(2614-2616)Cgc>Tgc	p.R872C	MAP1S_ENST00000597681.1_3'UTR|MAP1S_ENST00000544059.2_Missense_Mutation_p.R846C|CTD-3149D2.4_ENST00000595363.1_RNA	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	872	Necessary for association with microtubules.|Necessary for interaction with RASSF1 isoform A and isoform C.				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						CCCCAACTCACGCGCTGCCGC	0.682																																					p.R872C		Atlas-SNP	.											.	MAP1S	74	.	0			c.C2614T						PASS	.						8	10	10					19																	17838807		2151	4207	6358	SO:0001583	missense	55201	exon5			AACTCACGCGCTG	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.2614C>T	19.37:g.17838807C>T	ENSP00000325313:p.Arg872Cys	89	0	0		68	20	0.294118	NM_018174	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Missense_Mutation	SNP	ENST00000324096.4	37	CCDS32954.1	.	.	.	.	.	.	.	.	.	.	C	14.21	2.467034	0.43839	.	.	ENSG00000130479	ENST00000324096;ENST00000544059	T;T	0.19105	2.17;2.17	4.99	-3.27	0.05048	.	2.214490	0.01791	N	0.032329	T	0.12220	0.0297	N	0.14661	0.345	0.09310	N	1	P;P	0.52692	0.955;0.955	B;B	0.41723	0.365;0.365	T	0.20874	-1.0262	10	0.56958	D	0.05	-1.5835	4.9983	0.14251	0.3404:0.2807:0.3789:0.0	.	846;872	B4DH53;Q66K74	.;MAP1S_HUMAN	C	872;846	ENSP00000325313:R872C;ENSP00000439243:R846C	ENSP00000325313:R872C	R	+	1	0	MAP1S	17699807	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.283000	0.18846	-0.338000	0.08413	-1.053000	0.02334	CGC	.	.	none		0.682	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174		T	17838807	C	T	17838807	3	4	47	1	0	0	0	0	1	0	0	0	9243	536	19	1	2632	1	MAP1S	19	17838807	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	2765742	17838807	41290176	130	15864											
CILP2	148113	hgsc.bcm.edu	37	chr19	19651184	19651184	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gccgtccgccgtcggcgagcGcgtgcacttgaaccccacgc	5	5	13	18	8	0	1	0	1	0	0	2	2	1	1	5	1	3	1	5	1	1	1			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr19:19651184G>A	ENST00000291495.5	+	3	420	c.335G>A	c.(334-336)cGc>cAc	p.R112H	CILP2_ENST00000586018.1_Missense_Mutation_p.R118H	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	112						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						GTCGGCGAGCGCGTGCACTTG	0.721																																					p.R112H		Atlas-SNP	.											.	CILP2	84	.	0			c.G335A						PASS	.						5	6	6					19																	19651184		2017	4033	6050	SO:0001583	missense	148113	exon3			GCGAGCGCGTGCA	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.335G>A	19.37:g.19651184G>A	ENSP00000291495:p.Arg112His	56	0	0		35	15	0.428571	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Missense_Mutation	SNP	ENST00000291495.5	37	CCDS12405.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.615674	0.87359	.	.	ENSG00000160161	ENST00000291495	T	0.17370	2.28	4.27	4.27	0.50696	.	0.142510	0.44097	D	0.000481	T	0.28632	0.0709	L	0.42245	1.32	0.35344	D	0.786743	D;D	0.71674	0.994;0.998	P;D	0.66716	0.866;0.946	T	0.25984	-1.0116	10	0.42905	T	0.14	-2.4888	9.6583	0.39939	0.0:0.0:0.7916:0.2083	.	112;112	B2RAJ0;Q8IUL8	.;CILP2_HUMAN	H	112	ENSP00000291495:R112H	ENSP00000291495:R112H	R	+	2	0	CILP2	19512184	1.000000	0.71417	0.998000	0.56505	0.940000	0.58332	3.229000	0.51278	1.937000	0.56155	0.306000	0.20318	CGC	.	.	none		0.721	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221		A	19651184	G	A	19651184	3	1	47	1	0	0	0	0	1	0	0	0	3432	1087	38	1	345	1	CILP2	19	19651184	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	1812377	19651184	39477799	131	15865											
LGALS13	29124	hgsc.bcm.edu	37	chr19	40095831	40095831	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccctcagcaatgacccacagCtgcaggtggatttctacact	10	9	8	14	0	2	1	1	1	1	0	2	2	2	2	2	2	4	3	2	2	2	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr19:40095831C>A	ENST00000221797.4	+	3	151	c.106C>A	c.(106-108)Ctg>Atg	p.L36M		NM_013268.2	NP_037400.1	Q9UHV8	PP13_HUMAN	lectin, galactoside-binding, soluble, 13	36	Galectin. {ECO:0000255|PROSITE- ProRule:PRU00639}.				apoptotic process (GO:0006915)|phospholipid metabolic process (GO:0006644)		carbohydrate binding (GO:0030246)|lysophospholipase activity (GO:0004622)			lung(5)|ovary(1)|urinary_tract(1)	7	all_cancers(60;1.77e-05)|all_lung(34;5.38e-08)|Lung NSC(34;6.37e-08)|Ovarian(47;0.116)		Epithelial(26;3.28e-26)|OV - Ovarian serous cystadenocarcinoma(5;7.31e-25)|all cancers(26;1.15e-23)|LUSC - Lung squamous cell carcinoma(53;0.00281)			TGACCCACAGCTGCAGGTGGA	0.517																																					p.L36M		Atlas-SNP	.											.	LGALS13	22	.	0			c.C106A						PASS	.						143	112	122					19																	40095831		2203	4300	6503	SO:0001583	missense	29124	exon3			CCACAGCTGCAGG	AF117383	CCDS33024.1	19q13.2	2014-03-19	2008-07-25		ENSG00000105198	ENSG00000105198		"Lectins, galactoside-binding"	15449	protein-coding gene	gene with protein product	"galectin 13"	608717				6856484, 10527825	Standard	NM_013268		Approved	PP13, PLAC8	uc002omb.3	Q9UHV8	OTTHUMG00000183073	ENST00000221797.4:c.106C>A	19.37:g.40095831C>A	ENSP00000221797:p.Leu36Met	94	0	0		78	19	0.24359	NM_013268	C5HZ15	Missense_Mutation	SNP	ENST00000221797.4	37	CCDS33024.1	.	.	.	.	.	.	.	.	.	.	.	11.18	1.562868	0.27915	.	.	ENSG00000105198	ENST00000221797	T	0.05996	3.36	0.744	-1.35	0.09114	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	.	.	.	.	T	0.15998	0.0385	M	0.66506	2.035	0.19775	N	0.99996	D	0.60160	0.987	D	0.65874	0.939	T	0.09015	-1.0694	8	0.56958	D	0.05	.	.	.	.	.	36	Q9UHV8	PP13_HUMAN	M	36	ENSP00000221797:L36M	ENSP00000221797:L36M	L	+	1	2	LGALS13	44787671	0.038000	0.19896	0.434000	0.26772	0.452000	0.32318	-1.528000	0.02225	-0.386000	0.07821	0.305000	0.20034	CTG	.	.	none		0.517	LGALS13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464968.1	NM_013268		A	40095831	C	A	40095831	3	1	47	1	0	0	0	0	1	0	0	0	8749	796	28	4	116	4	LGALS13	19	40095831	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	20444647	40095831	19033152	132	15866											
ATP1A3	478	hgsc.bcm.edu	37	chr19	42485704	42485704	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ctcagccactttcttgttgcGttcacgcatcagcttcacgg	6	13	8	14	3	5	0	4	0	1	0	5	0	5	0	1	1	3	4	1	1	0	5	rs150785666	byFrequency	TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr19:42485704G>A	ENST00000302102.5	-	11	1537	c.1387C>T	c.(1387-1389)Cgc>Tgc	p.R463C	ATP1A3_ENST00000543770.1_Missense_Mutation_p.R474C|ATP1A3_ENST00000602133.1_Missense_Mutation_p.R433C|ATP1A3_ENST00000545399.1_Missense_Mutation_p.R476C	NM_152296.4	NP_689509.1	P13637	AT1A3_HUMAN	ATPase, Na+/K+ transporting, alpha 3 polypeptide	463					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						TTCTTGTTGCGTTCACGCATC	0.552																																					p.R476C		Atlas-SNP	.											.	ATP1A3	117	.	0			c.C1426T						PASS	.	G	CYS/ARG	3,4403	6.2+/-15.9	0,3,2200	113	96	102		1387	3.9	1	19	dbSNP_134	102	7,8593	5.7+/-21.5	0,7,4293	yes	missense	ATP1A3	NM_152296.3	180	0,10,6493	AA,AG,GG		0.0814,0.0681,0.0769	possibly-damaging	463/1014	42485704	10,12996	2203	4300	6503	SO:0001583	missense	478	exon11			TGTTGCGTTCACG		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.1387C>T	19.37:g.42485704G>A	ENSP00000302397:p.Arg463Cys	112	0	0		78	34	0.435897	NM_001256214	B7Z2T0|B7Z401|F5H6J6|Q16732|Q16735|Q969K5	Missense_Mutation	SNP	ENST00000302102.5	37	CCDS12594.1	.	.	.	.	.	.	.	.	.	.	G	19.42	3.824059	0.71143	6.81E-4	8.14E-4	ENSG00000105409	ENST00000302102;ENST00000441343;ENST00000545399;ENST00000368080;ENST00000535899;ENST00000543770	D;D;D;D	0.96073	-3.9;-3.9;-3.9;-3.9	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);	0.240845	0.39834	N	0.001256	D	0.94896	0.8350	L	0.37750	1.13	0.54753	D	0.999989	P;P;D;P	0.71674	0.951;0.628;0.998;0.679	P;P;P;P	0.62813	0.762;0.483;0.907;0.617	D	0.94166	0.7419	10	0.87932	D	0	.	9.0984	0.36653	0.0:0.0:0.7817:0.2183	.	476;474;463;463	B7Z2T0;F5H6J6;E9PC51;P13637	.;.;.;AT1A3_HUMAN	C	463;463;476;433;207;474	ENSP00000302397:R463C;ENSP00000411503:R463C;ENSP00000444688:R476C;ENSP00000437577:R474C	ENSP00000302397:R463C	R	-	1	0	ATP1A3	47177544	0.309000	0.24518	0.966000	0.40874	0.990000	0.78478	2.548000	0.45794	2.449000	0.82847	0.561000	0.74099	CGC	G|0.999;A|0.001	0.001	strong		0.552	ATP1A3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268107.1	NM_152296		A	42485704	G	A	42485704	3	1	47	1	0	0	0	0	1	0	0	0	1130	1145	40	1	1706	1	ATP1A3	19	42485704	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	2389873	42485704	16643279	133	15867											
C20orf3	57136	hgsc.bcm.edu	37	chr20	24959519	24959519	+	Splice_Site	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	agagcgggggttctttgaagCtgcaaaataatgcaattcca	13	10	11	7	1	1	2	0	1	1	1	2	2	2	2	1	2	4	4	1	2	5	4			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr20:24959519C>T	ENST00000217456.2	-	3	503		c.e3-1		APMAP_ENST00000447138.1_Splice_Site	NM_020531.2	NP_065392.1	Q9HDC9	APMAP_HUMAN	adipocyte plasma membrane associated protein						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)										TTCTTTGAAGCTGCAAAATAA	0.438																																					.		Atlas-SNP	.											.	APMAP	3	.	0			c.213-1G>A						PASS	.						45	48	47					20																	24959519		2203	4300	6503	SO:0001630	splice_region_variant	57136	exon4			TTGAAGCTGCAAA	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.213-1G>A	20.37:g.24959519C>T		63	0	0		44	21	0.477273	NM_020531	A8K514|B4DXG1|Q6UVZ8|Q9GZS8|Q9NUB2	Splice_Site	SNP	ENST00000217456.2	37	CCDS13166.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.116208	0.77323	.	.	ENSG00000101474	ENST00000451442;ENST00000217456;ENST00000447138	.	.	.	5.08	5.08	0.68730	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0204	0.80478	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C20orf3	24907519	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.018000	0.76406	2.642000	0.89623	0.561000	0.74099	.	.	.	none		0.438	APMAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078380.2	NM_020531	Intron	T	24959519	C	T	24959519	5	4	47	1	0	0	0	0	0	0	1	0	2111	811	28	2	1066	2	C20orf3	20	24959519	Splice_Site	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10		24959519	38066001	134	15868											
RAB22A	57403	hgsc.bcm.edu	37	chr20	56928537	56928537	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	gaaagagcttcgacagcatgGcccacctaatattgtagttg	12	10	10	9	1	0	1	0	0	0	1	1	3	0	1	2	1	2	4	2	1	4	6			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr20:56928537G>A	ENST00000244040.3	+	5	601	c.320G>A	c.(319-321)gGc>gAc	p.G107D		NM_020673.2	NP_065724.1	Q9UL26	RB22A_HUMAN	RAB22A, member RAS oncogene family	107					endocytosis (GO:0006897)|endosome organization (GO:0007032)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(2)|kidney(1)|large_intestine(2)|pancreas(1)	6	all_epithelial(3;5.09e-14)|Lung NSC(12;0.000122)|all_lung(29;0.00042)		BRCA - Breast invasive adenocarcinoma(13;6.2e-12)|Epithelial(14;4.73e-08)|all cancers(14;4.83e-07)			CGACAGCATGGCCCACCTAAT	0.368																																					p.G107D		Atlas-SNP	.											.	RAB22A	15	.	0			c.G320A						PASS	.						116	110	112					20																	56928537		2203	4300	6503	SO:0001583	missense	57403	exon5			AGCATGGCCCACC	AF091034	CCDS33497.1	20q13	2008-07-03			ENSG00000124209	ENSG00000124209		"RAB, member RAS oncogene"	9764	protein-coding gene	gene with protein product		612966					Standard	NM_020673		Approved		uc002xyz.3	Q9UL26	OTTHUMG00000032844	ENST00000244040.3:c.320G>A	20.37:g.56928537G>A	ENSP00000244040:p.Gly107Asp	213	0	0		207	84	0.405797	NM_020673	B3KR86|E1P605|Q8TF12|Q9H4E6	Missense_Mutation	SNP	ENST00000244040.3	37	CCDS33497.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.970755	0.92919	.	.	ENSG00000124209	ENST00000244040	T	0.76448	-1.02	5.92	5.92	0.95590	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.84665	0.5522	L	0.37466	1.105	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85299	0.1072	10	0.87932	D	0	-23.3447	20.3081	0.98638	0.0:0.0:1.0:0.0	.	107	Q9UL26	RB22A_HUMAN	D	107	ENSP00000244040:G107D	ENSP00000244040:G107D	G	+	2	0	RAB22A	56361943	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.476000	0.97823	2.795000	0.96236	0.655000	0.94253	GGC	.	.	none		0.368	RAB22A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079880.2			A	56928537	G	A	56928537	3	1	47	1	0	0	0	0	1	0	0	0	12924	1203	42	2	338	2	RAB22A	20	56928537	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	31969018	56928537	6096983	135	15869											
NPEPL1	79716	hgsc.bcm.edu	37	chr20	57269609	57269609	+	Silent	SNP	G	G	A																															accgtggagtttttcctggtGggacaagacaacgggccggt																										TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr20:57269609G>A	ENST00000356091.6	+	3	756	c.468G>A	c.(466-468)gtG>gtA	p.V156V	NPEPL1_ENST00000525817.1_Silent_p.V108V|STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525967.1_Silent_p.V128V	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	156						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)			TTTTCCTGGTGGGACAAGACA	0.667																																					p.V156V		Atlas-SNP	.											.	NPEPL1	36	.	0			c.G468A						PASS	.						30	32	32					20																	57269609		1950	4143	6093	SO:0001819	synonymous_variant	79716	exon3			CCTGGTGGGACAA	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.468G>A	20.37:g.57269609G>A		84	0	0		72	31	0.430556	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Silent	SNP	ENST00000356091.6	37	CCDS46621.1																																																																																			.	.	none		0.667	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663		A	57269609	G	A	57269609	2	1	47	1	0	0	0	0	0	0	0	1	10583	1335	47	2		2	NPEPL1	20	57269609	Silent	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	341072	57269609	5755911	136	15870	210	2									
NPEPL1	79716	hgsc.bcm.edu	37	chr20	57269610	57269610	+	Missense_Mutation	SNP	G	G	A																															ccgtggagtttttcctggtgGgacaagacaacgggccggtg																										TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr20:57269610G>A	ENST00000356091.6	+	3	757	c.469G>A	c.(469-471)Gga>Aga	p.G157R	NPEPL1_ENST00000525817.1_Missense_Mutation_p.G109R|STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525967.1_Missense_Mutation_p.G129R	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	157						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)			TTTCCTGGTGGGACAAGACAA	0.667																																					p.G157R		Atlas-SNP	.											.	NPEPL1	36	.	0			c.G469A						PASS	.						30	32	31					20																	57269610		1953	4145	6098	SO:0001583	missense	79716	exon3			CTGGTGGGACAAG	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.469G>A	20.37:g.57269610G>A	ENSP00000348395:p.Gly157Arg	84	0	0		71	31	0.43662	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Missense_Mutation	SNP	ENST00000356091.6	37	CCDS46621.1	.	.	.	.	.	.	.	.	.	.	G	15.13	2.742333	0.49151	.	.	ENSG00000215440	ENST00000525967;ENST00000525817;ENST00000356091	T;T;T	0.32023	1.47;1.49;1.48	4.62	3.66	0.41972	.	0.052273	0.85682	D	0.000000	T	0.46639	0.1403	M	0.76328	2.33	0.51233	D	0.999914	P;P;P;D	0.54207	0.823;0.839;0.848;0.965	B;P;B;P	0.57283	0.374;0.583;0.374;0.817	T	0.41858	-0.9485	10	0.18710	T	0.47	-9.0519	13.1398	0.59428	0.0:0.0:0.8389:0.1611	.	157;109;129;157	Q8NDH3;G5EA34;E9PN47;Q8NDH3-3	PEPL1_HUMAN;.;.;.	R	129;109;157	ENSP00000434810:G129R;ENSP00000437112:G109R;ENSP00000348395:G157R	ENSP00000348395:G157R	G	+	1	0	NPEPL1	56703017	1.000000	0.71417	0.995000	0.50966	0.107000	0.19398	9.409000	0.97331	0.931000	0.37242	-0.320000	0.08662	GGA	.	.	none		0.667	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663		A	57269610	G	A	57269610	3	1	47	1	0	0	0	0	1	0	0	0	10583	1233	43	2	325	2	NPEPL1	20	57269610	Missense_Mutation	SNP	G	TCGA-RQ-AAAT-01A-11D-A38X-10	1	57269610	5755910	137	15871	210	2									
SON	6651	hgsc.bcm.edu	37	chr21	34922547	34922547	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtcatctgcaattgaagcgcTaagattgccagagcagcctg	11	9	11	10	1	2	3	1	1	1	2	2	3	2	3	2	0	5	3	2	0	3	3			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr21:34922547T>C	ENST00000356577.4	+	3	1485	c.1010T>C	c.(1009-1011)cTa>cCa	p.L337P	SON_ENST00000300278.4_Missense_Mutation_p.L337P|SON_ENST00000290239.6_Missense_Mutation_p.L337P|SON_ENST00000381679.4_Missense_Mutation_p.L337P|SON_ENST00000381692.2_Intron	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	337					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						ATTGAAGCGCTAAGATTGCCA	0.502											OREG0003564	type=REGULATORY REGION|Gene=AK074269|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.L337P		Atlas-SNP	.											.	SON	343	.	0			c.T1010C						PASS	.						105	110	108					21																	34922547		2203	4300	6503	SO:0001583	missense	6651	exon3			AAGCGCTAAGATT	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.1010T>C	21.37:g.34922547T>C	ENSP00000348984:p.Leu337Pro	70	0	0	851	67	21	0.313433	NM_032195	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	37	CCDS13629.1	.	.	.	.	.	.	.	.	.	.	T	11.55	1.672860	0.29693	.	.	ENSG00000159140	ENST00000356577;ENST00000290239;ENST00000300278;ENST00000381679	T;T;T;T	0.16597	2.52;2.5;2.49;2.33	5.54	0.00568	0.14064	.	0.517188	0.16322	N	0.219526	T	0.21062	0.0507	L	0.29908	0.895	0.30562	N	0.764394	D;D;B	0.89917	0.999;1.0;0.126	D;D;B	0.69824	0.925;0.966;0.069	T	0.13872	-1.0493	10	0.36615	T	0.2	.	4.9548	0.14033	0.463:0.0843:0.0:0.4526	.	337;337;337	P18583;P18583-3;P18583-6	SON_HUMAN;.;.	P	337	ENSP00000348984:L337P;ENSP00000290239:L337P;ENSP00000300278:L337P;ENSP00000371095:L337P	ENSP00000290239:L337P	L	+	2	0	SON	33844417	0.001000	0.12720	0.908000	0.35775	0.992000	0.81027	-0.017000	0.12590	0.059000	0.16252	-0.527000	0.04329	CTA	.	.	none		0.502	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927		C	34922547	T	C	34922547	3	2	47	1	0	0	0	0	1	0	0	0	14941	1522	53	3	1020	3	SON	21	34922547	Missense_Mutation	SNP	T	TCGA-RQ-AAAT-01A-11D-A38X-10		34922547	13207348	138	15872											
DEPDC5	9681	hgsc.bcm.edu	37	chr22	32257381	32257381	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccttctttatggagtttgtcCgcagcccacgcacagcatcg	7	11	9	14	3	1	0	0	0	1	0	3	1	2	1	3	1	2	4	3	1	1	4			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chr22:32257381C>T	ENST00000382112.3	+	32	3335	c.3265C>T	c.(3265-3267)Cgc>Tgc	p.R1089C	DEPDC5_ENST00000400248.2_Intron|DEPDC5_ENST00000400249.2_Intron|DEPDC5_ENST00000539165.1_Intron|DEPDC5_ENST00000382105.2_Missense_Mutation_p.R1020C|DEPDC5_ENST00000266091.3_Intron|DEPDC5_ENST00000494060.1_Intron|DEPDC5_ENST00000535622.1_Intron|DEPDC5_ENST00000382111.2_Missense_Mutation_p.R1098C|DEPDC5_ENST00000400246.1_Missense_Mutation_p.R1098C	NM_001136029.2|NM_001242896.1	NP_001129501.1|NP_001229825.1	O75140	DEPD5_HUMAN	DEP domain containing 5	1098					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						GGAGTTTGTCCGCAGCCCACG	0.577																																					p.R1098C		Atlas-SNP	.											.	DEPDC5	266	.	0			c.C3292T						PASS	.						80	71	73					22																	32257381		692	1591	2283	SO:0001583	missense	9681	exon33			TTTGTCCGCAGCC	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.3265C>T	22.37:g.32257381C>T	ENSP00000371546:p.Arg1089Cys	109	0	0		115	38	0.330435	NM_001242896	A6H8V6|A8MPX9|B4DH93|B9EGN9|Q5K3V5|Q5THY9|Q5THZ0|Q5THZ1|Q5THZ3|Q68DR1|Q6MZX3|Q6PEZ1|Q9UGV8|Q9UH13	Missense_Mutation	SNP	ENST00000382112.3	37	CCDS46692.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.671763	0.88348	.	.	ENSG00000100150	ENST00000400246;ENST00000382105;ENST00000382112;ENST00000382111	T;T;T;T	0.35973	1.73;1.28;1.77;1.73	5.51	5.51	0.81932	.	0.000000	0.37437	U	0.002098	T	0.44456	0.1294	L	0.29908	0.895	0.80722	D	1	D;D;D;D	0.71674	0.994;0.993;0.998;0.993	P;B;P;B	0.56700	0.731;0.446;0.804;0.348	T	0.36939	-0.9727	10	0.59425	D	0.04	.	17.9698	0.89110	0.0:1.0:0.0:0.0	.	419;1098;484;1089	B4DSS1;B9EGN9;O75140-7;A8MPX9	.;.;.;.	C	1098;1020;1089;1098	ENSP00000383105:R1098C;ENSP00000371539:R1020C;ENSP00000371546:R1089C;ENSP00000371545:R1098C	ENSP00000371539:R1020C	R	+	1	0	DEPDC5	30587381	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.620000	0.61226	2.598000	0.87819	0.650000	0.86243	CGC	.	.	none		0.577	DEPDC5-006	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129087.1	NM_014662		T	32257381	C	T	32257381	3	4	47	1	0	0	0	0	1	0	0	0	4444	652	23	1	3409	1	DEPDC5	22	32257381	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10		32257381	19047185	139	15873											
AKAP4	8852	hgsc.bcm.edu	37	chrX	49957130	49957130	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	gatagttctgtggcattgcaCcactgtgaatgcatctggtg	8	13	12	8	0	2	1	0	1	2	0	2	2	2	1	1	2	2	4	1	2	2	3			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chrX:49957130C>G	ENST00000376056.2	-	5	2357	c.2207G>C	c.(2206-2208)gGt>gCt	p.G736A	AKAP4_ENST00000481402.1_5'UTR|AKAP4_ENST00000376058.2_Missense_Mutation_p.G362A|AKAP4_ENST00000358526.2_Missense_Mutation_p.G745A|AKAP4_ENST00000376064.3_Missense_Mutation_p.G736A					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)					TGGCATTGCACCACTGTGAAT	0.483																																					p.G745A		Atlas-SNP	.											.	AKAP4	131	.	0			c.G2234C						PASS	.						103	68	80					X																	49957130		2203	4300	6503	SO:0001583	missense	8852	exon5			ATTGCACCACTGT	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.2207G>C	X.37:g.49957130C>G	ENSP00000365224:p.Gly736Ala	204	0	0		133	97	0.729323	NM_003886		Missense_Mutation	SNP	ENST00000376056.2	37	CCDS14330.1	.	.	.	.	.	.	.	.	.	.	C	5.691	0.311971	0.10789	.	.	ENSG00000147081	ENST00000376056;ENST00000376058;ENST00000358526;ENST00000376064	T;T;T;T	0.04551	3.6;3.6;3.6;3.6	4.3	-5.82	0.02333	A-kinase anchor 110kDa, C-terminal (1);	1.644940	0.03577	N	0.229552	T	0.01800	0.0057	N	0.01874	-0.695	0.09310	N	1	B;B	0.30326	0.001;0.276	B;B	0.32393	0.001;0.145	T	0.41142	-0.9525	9	.	.	.	1.0666	5.0654	0.14580	0.1045:0.144:0.5559:0.1956	.	745;362	Q5JQC9;A6ND82	AKAP4_HUMAN;.	A	736;362;745;736	ENSP00000365224:G736A;ENSP00000365226:G362A;ENSP00000351327:G745A;ENSP00000365232:G736A	.	G	-	2	0	AKAP4	49843870	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.084000	0.01363	-1.165000	0.02786	-0.295000	0.09555	GGT	.	.	none		0.483	AKAP4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056552.1	NM_003886		G	49957130	C	G	49957130	3	3	47	1	0	0	0	0	1	0	0	0	453	507	18	4	338	4	AKAP4	23	49957130	Missense_Mutation	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10		49957130	105313430	140	15874											
TEX13A	56157	hgsc.bcm.edu	37	chrX	104464743	104464743	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gtctcctgctgctccctgagCttcttcaggtctgatgccaa	5	13	9	14	0	4	2	1	2	3	0	6	2	5	2	3	1	4	3	3	1	1	2			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chrX:104464743C>T	ENST00000413579.1	-	2	450	c.339G>A	c.(337-339)aaG>aaA	p.K113K	IL1RAPL2_ENST00000344799.4_Intron|TEX13A_ENST00000372578.3_Silent_p.K113K|IL1RAPL2_ENST00000372582.1_Intron|TEX13A_ENST00000372575.1_Silent_p.K113K			Q9BXU3	TX13A_HUMAN	testis expressed 13A	113							zinc ion binding (GO:0008270)			large_intestine(5)|ovary(2)|upper_aerodigestive_tract(1)	8						GCTCCCTGAGCTTCTTCAGGT	0.607																																					p.K113K		Atlas-SNP	.											.	TEX13A	55	.	0			c.G339A						PASS	.						33	34	34					X																	104464743		2169	4253	6422	SO:0001819	synonymous_variant	56157	exon2			CCTGAGCTTCTTC	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.339G>A	X.37:g.104464743C>T		110	0	0		60	25	0.416667	NM_031274	B1B1G8|Q32NB6	Silent	SNP	ENST00000413579.1	37																																																																																				.	.	none		0.607	TEX13A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_031274		T	104464743	C	T	104464743	2	4	47	1	0	0	0	0	0	0	0	1	15791	796	28	2		2	TEX13A	23	104464743	Silent	SNP	C	TCGA-RQ-AAAT-01A-11D-A38X-10	54507613	104464743	50805817	141	15875											
UBE2A	7319	hgsc.bcm.edu	37	chrX	118717088	118717088	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	attttaaaaattgtctctttAgtctctgttggatgaaccca	11	17	6	7	0	2	1	0	1	2	0	4	2	2	2	1	1	1	1	1	1	5	6			TCGA-RQ-AAAT-01A-11D-A38X-10	TCGA-RQ-AAAT-10A-01D-A38X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	e19f833b-db2a-411f-99fd-bd14d8527305	1a234e98-37da-4bcb-a68f-c1c5136ddf26	g.chrX:118717088A>C	ENST00000371558.2	+	6	504		c.e6-1		UBE2A_ENST00000371569.5_Splice_Site|UBE2A_ENST00000346330.3_Splice_Site	NM_001282161.1|NM_003336.2|NM_181762.1	NP_001269090.1|NP_003327.2|NP_861427.1	P49459	UBE2A_HUMAN	ubiquitin-conjugating enzyme E2A						antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|DNA repair (GO:0006281)|histone H2A ubiquitination (GO:0033522)|in utero embryonic development (GO:0001701)|maternal process involved in female pregnancy (GO:0060135)|positive regulation of cell proliferation (GO:0008284)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein polyubiquitination (GO:0000209)|response to UV (GO:0009411)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|cytosol (GO:0005829)|HULC complex (GO:0033503)|nuclear chromatin (GO:0000790)|XY body (GO:0001741)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)			haematopoietic_and_lymphoid_tissue(1)|lung(7)	8						TTGTCTCTTTAGTCTCTGTTG	0.388								Rad6 pathway																													.		Atlas-SNP	.											.	UBE2A	43	.	0			c.241-2A>C						PASS	.						99	89	93					X																	118717088		2203	4300	6503	SO:0001630	splice_region_variant	7319	exon5			CTCTTTAGTCTCT	AK223045	CCDS14580.1, CCDS14581.1	Xq24	2011-05-19	2011-05-19		ENSG00000077721	ENSG00000077721		"Ubiquitin-conjugating enzymes E2"	12472	protein-coding gene	gene with protein product		312180	"ubiquitin-conjugating enzyme E2A (RAD6 homolog)"			1559696	Standard	NM_003336		Approved	UBC2, HHR6A, RAD6A	uc004erl.3	P49459	OTTHUMG00000022275	ENST00000371558.2:c.331-1A>C	X.37:g.118717088A>C		71	0	0		42	34	0.809524	NM_181762	A6NFE9|A6NGR2|A6NMF5|B2R7R9|D3DWI1|Q4TTG1|Q96FX4	Splice_Site	SNP	ENST00000371558.2	37	CCDS14580.1	.	.	.	.	.	.	.	.	.	.	A	13.86	2.362521	0.41902	.	.	ENSG00000077721	ENST00000371558;ENST00000346330;ENST00000371569	.	.	.	5.91	5.91	0.95273	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3672	0.66815	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UBE2A	118601116	1.000000	0.71417	0.966000	0.40874	0.444000	0.32077	9.329000	0.96413	1.992000	0.58205	0.412000	0.27726	.	.	.	none		0.388	UBE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058036.1	NM_003336	Intron	C	118717088	A	C	118717088	5	2	47	1	0	0	0	0	0	0	1	0	16859	434	15	5	351	5	UBE2A	23	118717088	Splice_Site	SNP	A	TCGA-RQ-AAAT-01A-11D-A38X-10	14252345	118717088	36553472	142	15876											
CDK11A	728642	hgsc.bcm.edu	37	chr1	1647901	1647901	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgttcgtgctctctttctttCactctagcatgcttccctaa	5	17	5	14	2	4	0	1	0	3	0	7	0	5	0	1	0	3	4	1	0	2	6			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:1647901C>T	ENST00000378633.1	-	5	421	c.342G>A	c.(340-342)gtG>gtA	p.V114V	CDK11A_ENST00000404249.3_Silent_p.V124V|CDK11A_ENST00000358779.5_Silent_p.V114V|RP1-283E3.8_ENST00000598846.1_RNA|CDK11A_ENST00000378635.3_Silent_p.V114V|CDK11A_ENST00000378638.2_Silent_p.V90V|CDK11A_ENST00000356200.3_Silent_p.V90V|CDK11A_ENST00000357760.2_Silent_p.V114V			Q9UQ88	CD11A_HUMAN	cyclin-dependent kinase 11A	114	Glu-rich.				apoptotic process (GO:0006915)|mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(4)|stomach(1)|urinary_tract(1)	18						CTCTTTCTTTCACTCTAGCAT	0.483																																					p.V124V	Pancreas(186;965 2119 30274 40311 50569)	Atlas-SNP	.											.	CDK11B	37	.	0			c.G372A						PASS	.						124	116	118					1																	1647901		1896	4118	6014	SO:0001819	synonymous_variant	984	exon5			TTCTTTCACTCTA	AF067522	CCDS44042.1, CCDS44043.1	1p36.33	2011-11-08	2009-12-16	2009-12-16	ENSG00000008128	ENSG00000008128		"Cyclin-dependent kinases"	1730	protein-coding gene	gene with protein product		116951	"cell division cycle 2-like 2", "cell division cycle 2-like 2 (PITSLRE proteins)"	CDC2L3, CDC2L2		7920654, 9750192, 19884882	Standard	NM_033529		Approved	PITSLRE, CDK11-p110, CDK11-p58, CDK11-p46, p58GTA		Q9UQ88	OTTHUMG00000000703	ENST00000378633.1:c.342G>A	1.37:g.1647901C>T		212	0	0		238	14	0.0588235	NM_033486	O95227|O95228|O96012|Q12821|Q12853|Q12854|Q2TAJ0|Q5QPR0|Q5QPR1|Q5QPR2|Q9UBC4|Q9UBI3|Q9UEI1|Q9UEI2|Q9UP53|Q9UP54|Q9UP55|Q9UP56|Q9UQ86|Q9UQ87|Q9UQ89	Silent	SNP	ENST00000378633.1	37																																																																																				.	.	none		0.483	CDK11A-005	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000001735.1	NM_024011		T	1647901	C	T	1647901	2	4	48	1	0	0	0	0	0	0	0	1	3128	813	29	2		2	CDK11A	1	1647901	Silent	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10		1647901	247602720	1	15877											
NOL9	79707	hgsc.bcm.edu	37	chr1	6614339	6614339	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	tcgcggtgttgggtctccggGccgccgccgcgcgcgacacc	2	6	16	17	9	1	0	0	0	1	0	3	1	1	0	5	3	0	1	5	3	0	1			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:6614339G>C	ENST00000377705.5	-	1	256	c.224C>G	c.(223-225)gCc>gGc	p.A75G	TAS1R1_ENST00000328191.4_5'Flank|TAS1R1_ENST00000351136.3_5'Flank|TAS1R1_ENST00000333172.6_5'Flank	NM_024654.4	NP_078930	Q5SY16	NOL9_HUMAN	nucleolar protein 9	75					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)		GGGTCTCCGGGCCGCCGCCGC	0.736																																					p.A75G		Atlas-SNP	.											.	NOL9	49	.	0			c.C224G						PASS	.						7	5	5					1																	6614339		1475	3019	4494	SO:0001583	missense	79707	exon1			CTCCGGGCCGCCG	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.224C>G	1.37:g.6614339G>C	ENSP00000366934:p.Ala75Gly	117	0	0		131	37	0.282443	NM_024654	Q2NL84|Q4VBY3|Q6P472|Q7L4D6|Q96EE0|Q9H5L4	Missense_Mutation	SNP	ENST00000377705.5	37	CCDS80.1	.	.	.	.	.	.	.	.	.	.	G	11.00	1.509501	0.27036	.	.	ENSG00000162408	ENST00000377705	T	0.18502	2.21	3.31	1.37	0.22104	.	7.427200	0.00166	N	0.000002	T	0.08670	0.0215	N	0.08118	0	0.09310	N	1	B	0.30068	0.267	B	0.25291	0.059	T	0.20273	-1.0280	10	0.23891	T	0.37	1.8366	3.9684	0.09443	0.1269:0.0:0.6398:0.2332	.	75	Q5SY16	NOL9_HUMAN	G	75	ENSP00000366934:A75G	ENSP00000366934:A75G	A	-	2	0	NOL9	6536926	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.197000	0.09518	0.388000	0.25054	0.407000	0.27541	GCC	.	.	none		0.736	NOL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002625.1	NM_024654		C	6614339	G	C	6614339	3	2	48	1	0	0	0	0	1	0	0	0	10537	1203	42	4	1932	4	NOL9	1	6614339	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	4966438	6614339	242636282	2	15878											
VPS13D	55187	hgsc.bcm.edu	37	chr1	12398337	12398337	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	agtacagccagtctgactaaCctagagcaccagatctatgc	13	8	8	12	0	2	3	0	1	2	2	2	3	2	3	3	0	5	2	3	0	4	4			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:12398337C>T	ENST00000358136.3	+	40	8731	c.8601C>T	c.(8599-8601)aaC>aaT	p.N2867N	VPS13D_ENST00000356315.4_Intron	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)		GTCTGACTAACCTAGAGCACC	0.408																																					p.N2867N		Atlas-SNP	.											.	VPS13D	316	.	0			c.C8601T						PASS	.						178	171	174					1																	12398337		2203	4300	6503	SO:0001819	synonymous_variant	55187	exon40			GACTAACCTAGAG	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.8601C>T	1.37:g.12398337C>T		69	0	0		74	22	0.297297	NM_015378		Silent	SNP	ENST00000358136.3	37	CCDS30588.1	.	.	.	.	.	.	.	.	.	.	C	9.489	1.100178	0.20552	.	.	ENSG00000048707	ENST00000011700	.	.	.	5.99	5.08	0.68730	.	.	.	.	.	T	0.71091	0.3299	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.70550	-0.4841	4	.	.	.	.	15.2099	0.73214	0.0:0.933:0.0:0.067	.	.	.	.	I	1690	.	.	T	+	2	0	VPS13D	12320924	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.973000	0.49264	1.549000	0.49425	-0.136000	0.14681	ACC	.	.	none		0.408	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378		T	12398337	C	T	12398337	2	4	48	1	0	0	0	0	0	0	0	1	17207	506	18	2		2	VPS13D	1	12398337	Silent	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	5783998	12398337	236852284	3	15879											
SPEN	23013	hgsc.bcm.edu	37	chr1	16256987	16256987	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagaagacaagctacgtgagCgagatgaaagactctctagt	15	7	12	7	2	1	6	0	2	1	4	2	8	1	6	0	0	3	1	0	0	5	2			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:16256987C>T	ENST00000375759.3	+	11	4456	c.4252C>T	c.(4252-4254)Cga>Tga	p.R1418*		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1418					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)		GCTACGTGAGCGAGATGAAAG	0.398																																					p.R1418X		Atlas-SNP	.											.	SPEN	374	.	0			c.C4252T						PASS	.						88	88	88					1																	16256987		2203	4300	6503	SO:0001587	stop_gained	23013	exon11			CGTGAGCGAGATG		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.4252C>T	1.37:g.16256987C>T	ENSP00000364912:p.Arg1418*	79	0	0		74	15	0.202703	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Nonsense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	.	.	.	.	.	.	.	.	.	.	C	42	9.732756	0.99251	.	.	ENSG00000065526	ENST00000375759	.	.	.	4.42	3.49	0.39957	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	-8.429	11.7282	0.51722	0.1906:0.8094:0.0:0.0	.	.	.	.	X	1418	.	ENSP00000364912:R1418X	R	+	1	2	SPEN	16129574	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.391000	0.34475	1.427000	0.47276	0.563000	0.77884	CGA	.	.	none		0.398	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001		T	16256987	C	T	16256987	4	4	48	1	0	0	0	0	0	1	0	0	15053	760	27	1	4294	1	SPEN	1	16256987	Nonsense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	3858650	16256987	232993634	4	15880											
C1orf64	149563	hgsc.bcm.edu	37	chr1	16332643	16332643	+	Silent	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	atgggtgggggatgccttgcCcaggccagggccaccctgcc	5	6	16	14	0	0	0	0	0	0	0	0	1	0	1	6	5	3	0	6	5	0	1			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:16332643C>G	ENST00000329454.2	+	2	380	c.312C>G	c.(310-312)gcC>gcG	p.A104A	RP11-5P18.5_ENST00000437156.1_RNA	NM_178840.2	NP_849162.1	Q8NEQ6	CA064_HUMAN	chromosome 1 open reading frame 64	104										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)		GATGCCTTGCCCAGGCCAGGG	0.647																																					p.A104A		Atlas-SNP	.											.	C1orf64	16	.	0			c.C312G						PASS	.						50	51	51					1																	16332643		2203	4300	6503	SO:0001819	synonymous_variant	149563	exon2			CCTTGCCCAGGCC	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.312C>G	1.37:g.16332643C>G		73	0	0		94	16	0.170213	NM_178840	B3KXI9	Silent	SNP	ENST00000329454.2	37	CCDS166.1																																																																																			.	.	none		0.647	C1orf64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026317.1	NM_178840		G	16332643	C	G	16332643	2	3	48	1	0	0	0	0	0	0	0	1	2056	610	22	4		4	C1orf64	1	16332643	Silent	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	75656	16332643	232917978	5	15881											
PAX7	5081	hgsc.bcm.edu	37	chr1	18962816	18962816	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcggacaagaaggaggacgaCggcgaaaagaaggccaaaca	18	0	15	8	4	0	2	0	0	0	2	0	7	0	5	1	5	1	0	1	5	6	0	rs372598486		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:18962816C>T	ENST00000375375.3	+	4	1135	c.537C>T	c.(535-537)gaC>gaT	p.D179D	PAX7_ENST00000400661.3_Silent_p.D177D|PAX7_ENST00000420770.2_Silent_p.D179D	NM_002584.2|NM_013945.2	NP_002575.1|NP_039236.1	P23759	PAX7_HUMAN	paired box 7	179	Sufficient to mediate interaction with PAXBP1. {ECO:0000250}.				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)		aggaggacgacggcgaaaaga	0.557			T	FOXO1A	alveolar rhabdomyosarcoma																																p.D179D		Atlas-SNP	.		Dom	yes		1	1p36.2-p36.12	5081	paired box gene 7		M	.	PAX7	127	.	0			c.C537T						PASS	.						232	198	209					1																	18962816		2203	4300	6503	SO:0001819	synonymous_variant	5081	exon4			GGACGACGGCGAA	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.537C>T	1.37:g.18962816C>T		77	0	0		90	21	0.233333	NM_002584	E9PFV9|Q0VA99|Q2PJS5	Silent	SNP	ENST00000375375.3	37	CCDS186.1																																																																																			.	.	none		0.557	PAX7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000006928.1	NM_002584		T	18962816	C	T	18962816	2	4	48	1	0	0	0	0	0	0	0	1	11493	535	19	1		1	PAX7	1	18962816	Silent	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	2630173	18962816	230287805	6	15882											
WDTC1	23038	hgsc.bcm.edu	37	chr1	27608772	27608772	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtctggagtggaatgagaaaGgagagtaagtatgagctaga	15	8	16	2	0	1	4	0	2	1	3	1	8	1	6	0	3	1	3	0	3	5	3			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:27608772G>A	ENST00000319394.3	+	4	710	c.175G>A	c.(175-177)Gga>Aga	p.G59R	WDTC1_ENST00000361771.3_Missense_Mutation_p.G59R	NM_001276252.1|NM_015023.3	NP_001263181.1|NP_055838.2	Q8N5D0	WDTC1_HUMAN	WD and tetratricopeptide repeats 1	59					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)		GAATGAGAAAGGAGAGTAAGT	0.517																																					p.G59R		Atlas-SNP	.											.	WDTC1	69	.	0			c.G175A						PASS	.						103	91	95					1																	27608772		2203	4300	6503	SO:0001583	missense	23038	exon4			GAGAAAGGAGAGT	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.175G>A	1.37:g.27608772G>A	ENSP00000317971:p.Gly59Arg	43	0	0		44	17	0.386364	NM_015023	D3DPL5|Q5SSC5|Q9NV87|Q9UPW4	Missense_Mutation	SNP	ENST00000319394.3	37		.	.	.	.	.	.	.	.	.	.	G	28.8	4.949156	0.92660	.	.	ENSG00000142784	ENST00000319394;ENST00000361771	T;T	0.65549	-0.16;-0.16	4.7	4.7	0.59300	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	0.81912	0.4923	M	0.86740	2.835	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.85399	0.1130	10	0.87932	D	0	.	17.1641	0.86810	0.0:0.0:1.0:0.0	.	59;59	Q8N5D0;Q8N5D0-4	WDTC1_HUMAN;.	R	59	ENSP00000317971:G59R;ENSP00000355317:G59R	ENSP00000317971:G59R	G	+	1	0	WDTC1	27481359	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.976000	0.93442	2.612000	0.88384	0.655000	0.94253	GGA	.	.	none		0.517	WDTC1-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015023		A	27608772	G	A	27608772	3	1	48	1	0	0	0	0	1	0	0	0	17357	1001	35	2	185	2	WDTC1	1	27608772	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	8645956	27608772	221641849	7	15883											
SMPDL3B	27293	hgsc.bcm.edu	37	chr1	28282207	28282207	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ccttgtaggtgtacattgtcGgccacgtgcccccggggttc	4	11	13	13	3	0	0	0	0	0	0	2	0	0	0	4	4	2	3	4	4	2	5			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:28282207G>A	ENST00000373894.3	+	6	894	c.703G>A	c.(703-705)Ggc>Agc	p.G235S	SMPDL3B_ENST00000549094.1_Missense_Mutation_p.G187S|SMPDL3B_ENST00000373888.4_Missense_Mutation_p.G235S|RP11-460I13.2_ENST00000448015.1_RNA	NM_014474.2	NP_055289.2	Q92485	ASM3B_HUMAN	sphingomyelin phosphodiesterase, acid-like 3B	235					sphingomyelin catabolic process (GO:0006685)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	16		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000431)|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;5.68e-24)|Colorectal(126;1.65e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00587)|READ - Rectum adenocarcinoma(331;0.055)		GTACATTGTCGGCCACGTGCC	0.527																																					p.G235S		Atlas-SNP	.											.	SMPDL3B	54	.	0			c.G703A						PASS	.						75	77	76					1																	28282207		2203	4300	6503	SO:0001583	missense	27293	exon6			ATTGTCGGCCACG	Y08134	CCDS30655.1, CCDS30656.1	1p35.3	2008-02-05			ENSG00000130768	ENSG00000130768			21416	protein-coding gene	gene with protein product							Standard	NM_014474		Approved	ASML3B	uc001bpg.3	Q92485	OTTHUMG00000003910	ENST00000373894.3:c.703G>A	1.37:g.28282207G>A	ENSP00000363001:p.Gly235Ser	67	0	0		68	16	0.235294	NM_001009568	B7ZB35|Q5T0Z0|Q96CB7	Missense_Mutation	SNP	ENST00000373894.3	37	CCDS30655.1	.	.	.	.	.	.	.	.	.	.	G	19.84	3.901958	0.72754	.	.	ENSG00000130768	ENST00000373894;ENST00000373890;ENST00000411604;ENST00000373888;ENST00000549094;ENST00000412515	D;D;D;D	0.96427	-4.01;-4.01;-4.01;-4.01	5.22	5.22	0.72569	Metallophosphoesterase domain (1);	0.000000	0.85682	D	0.000000	D	0.97904	0.9311	M	0.73430	2.235	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.996;0.998;0.996	D	0.97750	1.0214	10	0.40728	T	0.16	-37.9539	18.7635	0.91862	0.0:0.0:1.0:0.0	.	187;235;235	F8VWW8;Q92485;Q92485-2	.;ASM3B_HUMAN;.	S	235;265;265;235;187;187	ENSP00000363001:G235S;ENSP00000388092:G265S;ENSP00000362995:G235S;ENSP00000449450:G187S	ENSP00000362995:G235S	G	+	1	0	SMPDL3B	28154794	1.000000	0.71417	0.977000	0.42913	0.008000	0.06430	9.756000	0.98918	2.417000	0.82017	0.462000	0.41574	GGC	.	.	none		0.527	SMPDL3B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011170.1	NM_014474		A	28282207	G	A	28282207	3	1	48	1	0	0	0	0	1	0	0	0	14824	1116	39	1	725	1	SMPDL3B	1	28282207	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	673435	28282207	220968414	8	15884											
MACF1	23499	hgsc.bcm.edu	37	chr1	39908411	39908411	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaaaaatgatgttttggctcAtcaagccacagtggaaacag	16	9	9	7	0	2	1	2	1	0	0	2	2	2	2	1	2	2	2	1	2	5	2			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:39908411A>G	ENST00000372915.3	+	77	18914	c.18827A>G	c.(18826-18828)cAt>cGt	p.H6276R	MACF1_ENST00000361689.2_Missense_Mutation_p.H4318R|MACF1_ENST00000539005.1_Missense_Mutation_p.H4188R|MACF1_ENST00000564288.1_Missense_Mutation_p.H6377R|MACF1_ENST00000289893.4_Missense_Mutation_p.H4820R|MACF1_ENST00000545844.1_Missense_Mutation_p.H4318R|MACF1_ENST00000567887.1_Missense_Mutation_p.H6414R|MACF1_ENST00000317713.7_Missense_Mutation_p.H4318R			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	6276					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)			GTTTTGGCTCATCAAGCCACA	0.398																																					p.H4318R		Atlas-SNP	.											.	MACF1	909	.	0			c.A12953G						PASS	.						51	49	50					1																	39908411		2203	4300	6503	SO:0001583	missense	23499	exon75			TGGCTCATCAAGC	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.18827A>G	1.37:g.39908411A>G	ENSP00000362006:p.His6276Arg	112	0	0		113	30	0.265487	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	A	23.5	4.423174	0.83559	.	.	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893	T;T;T;T;T;T	0.50813	1.3;0.73;1.3;1.3;1.3;0.73	5.82	5.82	0.92795	.	0.000000	0.64402	D	0.000005	T	0.61689	0.2367	L	0.41079	1.255	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	T	0.64145	-0.6476	10	0.72032	D	0.01	.	16.1839	0.81934	1.0:0.0:0.0:0.0	.	6276;4318	Q9UPN3;F8W8Q1	MACF1_HUMAN;.	R	4318;6276;4318;4318;4188;4820	ENSP00000439537:H4318R;ENSP00000362006:H6276R;ENSP00000354573:H4318R;ENSP00000313438:H4318R;ENSP00000444364:H4188R;ENSP00000289893:H4820R	ENSP00000289893:H4820R	H	+	2	0	MACF1	39680998	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.962000	0.93254	2.222000	0.72286	0.533000	0.62120	CAT	.	.	none		0.398	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044		G	39908411	A	G	39908411	3	3	48	1	0	0	0	0	1	0	0	0	9153	217	8	3	19398	3	MACF1	1	39908411	Missense_Mutation	SNP	A	TCGA-VB-A8QN-01A-11D-A382-10	11626204	39908411	209342210	9	15885											
ST6GALNAC5	81849	hgsc.bcm.edu	37	chr1	77334232	77334232	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	accaccatgtgcaccagcttGttgctagtgtacagcagcct	9	10	9	13	0	0	0	0	0	0	0	0	0	0	0	4	0	6	6	4	0	2	4			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:77334232G>A	ENST00000477717.1	+	2	301	c.66G>A	c.(64-66)ttG>ttA	p.L22L	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	22					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						GCACCAGCTTGTTGCTAGTGT	0.672																																					p.L22L		Atlas-SNP	.											.	ST6GALNAC5	59	.	0			c.G66A						PASS	.						34	32	32					1																	77334232		2203	4299	6502	SO:0001819	synonymous_variant	81849	exon2			CAGCTTGTTGCTA		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.66G>A	1.37:g.77334232G>A		203	0	0		210	50	0.238095	NM_030965	B1AK82	Silent	SNP	ENST00000477717.1	37	CCDS673.1																																																																																			.	.	none		0.672	ST6GALNAC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026692.2	NM_030965		A	77334232	G	A	77334232	2	1	48	1	0	0	0	0	0	0	0	1	15242	1368	48	2		2	ST6GALNAC5	1	77334232	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	37425821	77334232	171916389	10	15886											
LPHN2	23266	hgsc.bcm.edu	37	chr1	82409302	82409302	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	atttataatacccgattaaaCcgaggagaatatgtagatgt	16	12	8	5	2	0	2	0	0	0	2	0	5	0	2	2	1	2	1	2	1	8	7			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:82409302C>A	ENST00000370728.1	+	8	1692	c.1047C>A	c.(1045-1047)aaC>aaA	p.N349K	LPHN2_ENST00000335786.5_Missense_Mutation_p.N349K|LPHN2_ENST00000370715.1_Missense_Mutation_p.N349K|LPHN2_ENST00000469377.2_Intron|LPHN2_ENST00000370713.1_Missense_Mutation_p.N349K|LPHN2_ENST00000359929.3_Missense_Mutation_p.N349K|LPHN2_ENST00000370725.1_Missense_Mutation_p.N349K|LPHN2_ENST00000370717.2_Missense_Mutation_p.N349K|LPHN2_ENST00000370723.1_Missense_Mutation_p.N349K|LPHN2_ENST00000370730.1_Missense_Mutation_p.N349K|LPHN2_ENST00000394879.1_Missense_Mutation_p.N349K|LPHN2_ENST00000319517.6_Missense_Mutation_p.N349K|LPHN2_ENST00000370721.1_Missense_Mutation_p.N353K|LPHN2_ENST00000370727.1_Missense_Mutation_p.N349K|LPHN2_ENST00000271029.4_Missense_Mutation_p.N349K			O95490	LPHN2_HUMAN	latrophilin 2	349	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)|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)		CCCGATTAAACCGAGGAGAAT	0.383																																					p.N349K		Atlas-SNP	.											.	LPHN2	464	.	0			c.C1047A						PASS	.						155	154	154					1																	82409302		2203	4299	6502	SO:0001583	missense	23266	exon5			ATTAAACCGAGGA	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.1047C>A	1.37:g.82409302C>A	ENSP00000359763:p.Asn349Lys	87	0	0		120	33	0.275	NM_012302	A5XEI2|B1ALT8|B1ALT9|B1ALU0|B1ALU2|B1ALU4|B1ALU5|B1ALU6|O94882|Q5VX76|Q9UKY5|Q9UKY6	Missense_Mutation	SNP	ENST00000370728.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.791|9.791	1.177918|1.177918	0.21787|0.21787	.|.	.|.	ENSG00000117114|ENSG00000117114	ENST00000370721;ENST00000370728;ENST00000370730;ENST00000370727;ENST00000370725;ENST00000370723;ENST00000359929;ENST00000370715;ENST00000370713;ENST00000319517;ENST00000370717;ENST00000394879;ENST00000271029;ENST00000335786|ENST00000449420	D;D;D;D;D;D;D;D;D;D;D;D;D;D|.	0.88664|.	-2.41;-2.41;-2.41;-2.41;-2.41;-2.41;-2.41;-2.41;-2.41;-2.41;-2.41;-2.41;-2.41;-2.41|.	5.54|5.54	4.62|4.62	0.57501|0.57501	.|.	0.160030|.	0.53938|.	D|.	0.000042|.	T|T	0.45337|0.45337	0.1337|0.1337	L|L	0.56396|0.56396	1.775|1.775	0.36629|0.36629	D|D	0.876203|0.876203	B;B;B|.	0.06786|.	0.001;0.001;0.0|.	B;B;B|.	0.08055|.	0.003;0.002;0.001|.	T|T	0.50276|0.50276	-0.8847|-0.8847	10|5	0.62326|.	D|.	0.03|.	.|.	6.8169|6.8169	0.23835|0.23835	0.1426:0.7106:0.0:0.1468|0.1426:0.7106:0.0:0.1468	.|.	349;349;349|.	O95490-3;O95490-4;O95490-2|.	.;.;.|.	K|N	353;349;349;349;349;349;349;349;349;349;349;349;349;349|217	ENSP00000359756:N353K;ENSP00000359763:N349K;ENSP00000359765:N349K;ENSP00000359762:N349K;ENSP00000359760:N349K;ENSP00000359758:N349K;ENSP00000353006:N349K;ENSP00000359750:N349K;ENSP00000359748:N349K;ENSP00000322270:N349K;ENSP00000359752:N349K;ENSP00000378344:N349K;ENSP00000271029:N349K;ENSP00000337306:N349K|.	ENSP00000271029:N349K|.	N|T	+|+	3|2	2|0	LPHN2|LPHN2	82181890|82181890	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.940000|0.940000	0.58332|0.58332	1.052000|1.052000	0.30429|0.30429	1.302000|1.302000	0.44855|0.44855	0.557000|0.557000	0.71058|0.71058	AAC|ACC	.	.	none		0.383	LPHN2-007	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000027188.1	NM_012302		A	82409302	C	A	82409302	3	1	48	1	0	0	0	0	1	0	0	0	8925	506	18	4	1061	4	LPHN2	1	82409302	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	5075070	82409302	166841319	11	15887											
NBPF10	100132406	hgsc.bcm.edu	37	chr1	145293535	145293535	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	acctcaaagagaaatgttttCtaactcaactggccggcttc	12	11	7	11	1	3	1	2	0	1	1	4	2	3	1	2	2	2	2	2	2	4	4	rs55936365		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:145293535C>G	ENST00000369339.3	+	3	383	c.130C>G	c.(130-132)Cta>Gta	p.L44V	RP11-458D21.5_ENST00000468030.1_3'UTR|NBPF10_ENST00000342960.5_Missense_Mutation_p.L44V|NBPF10_ENST00000369338.1_Intron			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	315						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.L44V(2)		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)		GAAATGTTTTCTAACTCAACT	0.443																																					p.L44V		Atlas-SNP	.											NBPF10,NS,carcinoma,0,2	NBPF10	221	2	2	Substitution - Missense(2)	kidney(2)	c.C130G						scavenged	.																																			SO:0001583	missense	100132406	exon1			TGTTTTCTAACTC	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.130C>G	1.37:g.145293535C>G	ENSP00000358345:p.Leu44Val	62	0	0		86	7	0.0813954	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000369339.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.027|0.027	-1.360141|-1.360141	0.01245|0.01245	.|.	.|.	ENSG00000163386|ENSG00000163386	ENST00000369339;ENST00000342960|ENST00000448873	T|.	0.02837|.	4.14|.	0.687|0.687	-1.37|-1.37	0.09056|0.09056	.|.	.|.	.|.	.|.	.|.	T|T	0.01765|0.01765	0.0056|0.0056	N|N	0.01122|0.01122	-1.005|-1.005	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.33007|0.33007	-0.9885|-0.9885	9|6	0.02654|0.33141	T|T	1|0.24	.|.	3.2142|3.2142	0.06692|0.06692	0.3787:0.2355:0.3858:0.0|0.3787:0.2355:0.3858:0.0	rs55936365|rs55936365	44|.	A8MQ30|.	.|.	V|C	44|3	ENSP00000345684:L44V|.	ENSP00000345684:L44V|ENSP00000414194:S3C	L|S	+|+	1|2	2|0	NBPF10|NBPF10	144004892|144004892	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-3.451000|-3.451000	0.00466|0.00466	-3.626000|-3.626000	0.00130|0.00130	-3.729000|-3.729000	0.00022|0.00022	CTA|TCT	.	.	weak		0.443	NBPF10-001	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038550.3	NM_001039703		G	145293535	C	G	145293535	3	3	48	1	0	0	0	0	1	0	0	0	10202	912	32	4	132	4	NBPF10	1	145293535	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	62884233	145293535	103957086	12	15888											
HIST2H2BE	8349	hgsc.bcm.edu	37	chr1	149858047	149858047	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	atgccggtgtcggggtggacCtgcttcagcaccttgtacac	6	10	13	12	2	1	0	1	0	0	0	2	1	1	1	3	4	4	3	3	4	1	3			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:149858047C>T	ENST00000369155.2	-	1	185	c.144G>A	c.(142-144)caG>caA	p.Q48Q	HIST2H2AC_ENST00000331380.2_5'Flank|BOLA1_ENST00000369153.2_5'Flank	NM_003528.2	NP_003519.1	Q16778	H2B2E_HUMAN	histone cluster 2, H2be	48					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)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	14	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			CGGGGTGGACCTGCTTCAGCA	0.587																																					p.Q48Q		Atlas-SNP	.											.	HIST2H2BE	33	.	0			c.G144A						PASS	.						200	187	191					1																	149858047		2203	4300	6503	SO:0001819	synonymous_variant	8349	exon1			GTGGACCTGCTTC	AY131979	CCDS936.1	1q21.2	2011-01-27	2006-10-11	2003-03-07	ENSG00000184678	ENSG00000184678		"Histones / Replication-dependent"	4760	protein-coding gene	gene with protein product		601831	"H2B histone family, member Q", "histone 2, H2be"	H2B, H2BFQ		1469070, 12408966	Standard	NM_003528		Approved	H2B/q, H2B.1	uc001etc.3	Q16778	OTTHUMG00000012095	ENST00000369155.2:c.144G>A	1.37:g.149858047C>T		100	0	0		159	35	0.220126	NM_003528	A3KMC7|A8K110|Q4KMY1|Q5QNX0|Q9UE88	Silent	SNP	ENST00000369155.2	37	CCDS936.1																																																																																			.	.	none		0.587	HIST2H2BE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033455.1	NM_003528		T	149858047	C	T	149858047	2	4	48	1	0	0	0	0	0	0	0	1	7188	680	24	2		2	HIST2H2BE	1	149858047	Silent	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	4564512	149858047	99392574	13	15889											
MCL1	4170	hgsc.bcm.edu	37	chr1	150551347	150551347	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gccgtctcgtggttgcgctgCacgccatccccaacccgtcg	4	8	11	18	6	1	0	0	0	1	0	4	0	2	0	5	1	3	3	5	1	1	1			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:150551347C>T	ENST00000369026.2	-	1	719	c.660G>A	c.(658-660)gtG>gtA	p.V220V	MCL1_ENST00000307940.3_Silent_p.V220V|MCL1_ENST00000464132.1_5'Flank	NM_001197320.1|NM_021960.4	NP_001184249.1|NP_068779.1	Q07820	MCL1_HUMAN	myeloid cell leukemia 1	220					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)			GGTTGCGCTGCACGCCATCCC	0.632																																					p.V220V		Atlas-SNP	.											MCL1,NS,carcinoma,0,1	MCL1	27	1	0			c.G660A						PASS	.						59	65	63					1																	150551347		2203	4300	6503	SO:0001819	synonymous_variant	4170	exon1			GCGCTGCACGCCA	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.660G>A	1.37:g.150551347C>T		52	0	0		63	15	0.238095	NM_182763	B2R6B2|D3DV03|D3DV04|Q9HD91|Q9NRQ3|Q9NRQ4|Q9UHR7|Q9UHR8|Q9UHR9|Q9UNJ1	Silent	SNP	ENST00000369026.2	37	CCDS957.1																																																																																			.	.	none		0.632	MCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084402.1	NM_021960		T	150551347	C	T	150551347	2	4	48	1	0	0	0	0	0	0	0	1	9393	697	25	2		2	MCL1	1	150551347	Silent	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	693300	150551347	98699274	14	15890											
RPTN	126638	hgsc.bcm.edu	37	chr1	152128876	152128876	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taatgagaatcctgaattggTttttcacaccgatttaaggc	12	14	8	7	1	1	2	1	2	0	1	2	4	2	2	2	2	0	1	2	2	4	6			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:152128876T>G	ENST00000316073.3	-	3	763	c.699A>C	c.(697-699)aaA>aaC	p.K233N		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	233	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						CCTGAATTGGTTTTTCACACC	0.403																																					p.K233N		Atlas-SNP	.											RPTN,colon,carcinoma,0,1	RPTN	123	1	0			c.A699C						scavenged	.						253	212	224					1																	152128876		1568	3582	5150	SO:0001583	missense	126638	exon3			AATTGGTTTTTCA	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.699A>C	1.37:g.152128876T>G	ENSP00000317895:p.Lys233Asn	259	1	0.003861		280	51	0.182143	NM_001122965	B7ZBZ3	Missense_Mutation	SNP	ENST00000316073.3	37	CCDS41397.1	.	.	.	.	.	.	.	.	.	.	T	9.469	1.095250	0.20471	.	.	ENSG00000215853	ENST00000316073	T	0.13538	2.58	4.17	-1.53	0.08611	.	.	.	.	.	T	0.01976	0.0062	L	0.39020	1.185	0.09310	N	1	B	0.22146	0.065	B	0.14023	0.01	T	0.47142	-0.9140	9	0.18710	T	0.47	-3.9643	0.1266	0.00069	0.3014:0.1795:0.1654:0.3537	.	233	Q6XPR3	RPTN_HUMAN	N	233	ENSP00000317895:K233N	ENSP00000317895:K233N	K	-	3	2	RPTN	150395500	0.013000	0.17824	0.017000	0.16124	0.577000	0.36160	0.088000	0.14979	-0.152000	0.11156	0.363000	0.22086	AAA	.	.	none		0.403	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312		G	152128876	T	G	152128876	3	3	48	1	0	0	0	0	1	0	0	0	13679	1722	60	5	1659	5	RPTN	1	152128876	Missense_Mutation	SNP	T	TCGA-VB-A8QN-01A-11D-A382-10	1577529	152128876	97121745	15	15891											
LCE1A	353131	hgsc.bcm.edu	37	chr1	152800123	152800123	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gtggctccagctctgggggcGgctgcagctctgggggaggt	3	8	20	10	1	2	0	0	0	2	0	3	1	3	1	1	7	3	5	1	7	0	0	rs141081392	byFrequency	TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:152800123G>A	ENST00000335123.2	+	1	175	c.175G>A	c.(175-177)Ggc>Agc	p.G59S		NM_178348.2	NP_848125.1	Q5T7P2	LCE1A_HUMAN	late cornified envelope 1A	59	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)			CTCTGGGGGCGGCTGCAGCTC	0.667																																					p.G59S		Atlas-SNP	.											.	LCE1A	23	.	0			c.G175A						PASS	.	T	SER/GLY	0,4406		0,0,2203	35	41	39		175	-3.2	0.7	1	dbSNP_134	39	2,8598		0,2,4298	no	missense	LCE1A	NM_178348.2	56	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	possibly-damaging	59/111	152800123	2,13004	2203	4300	6503	SO:0001583	missense	353131	exon1			GGGGGCGGCTGCA		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.175G>A	1.37:g.152800123G>A	ENSP00000334869:p.Gly59Ser	142	0	0		162	34	0.209877	NM_178348		Missense_Mutation	SNP	ENST00000335123.2	37	CCDS1028.1	.	.	.	.	.	.	.	.	.	.	T	12.19	1.864213	0.32977	0.0	2.33E-4	ENSG00000186844	ENST00000368766;ENST00000335123	T;T	0.02944	4.1;4.1	1.63	-3.25	0.05079	.	0.000000	0.38663	N	0.001619	T	0.00468	0.0015	N	0.14661	0.345	0.09310	N	1	P	0.35780	0.52	B	0.20767	0.031	T	0.49643	-0.8918	10	0.87932	D	0	.	7.2939	0.26383	0.0:0.0:0.4666:0.5334	.	59	Q5T7P2	LCE1A_HUMAN	S	59	ENSP00000357755:G59S;ENSP00000334869:G59S	ENSP00000334869:G59S	G	+	1	0	LCE1A	151066747	0.001000	0.12720	0.686000	0.30086	0.613000	0.37349	-0.661000	0.05311	-0.857000	0.04115	-1.275000	0.01399	GGC	A|0.000;G|0.999;T|0.000	0.000	strong		0.667	LCE1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034660.2	NM_178348		A	152800123	G	A	152800123	3	1	48	1	0	0	0	0	1	0	0	0	8668	1116	39	1	177	1	LCE1A	1	152800123	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	671247	152800123	96450498	16	15892											
FDPS	2224	hgsc.bcm.edu	37	chr1	155288031	155288031	+	Silent	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atctaccgcctgctgaagctCtattgccgggagcagcccta	8	9	10	14	2	2	1	0	1	2	0	2	2	2	2	4	1	6	3	4	1	4	4			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:155288031C>T	ENST00000356657.6	+	6	795	c.633C>T	c.(631-633)ctC>ctT	p.L211L	RUSC1-AS1_ENST00000443642.1_RNA|FDPS_ENST00000368356.4_Silent_p.L211L|RUSC1_ENST00000368352.5_5'Flank|FDPS_ENST00000447866.1_Silent_p.L145L|RUSC1_ENST00000368354.3_5'Flank|RUSC1-AS1_ENST00000543656.1_RNA|RUSC1-AS1_ENST00000450199.1_RNA|RUSC1-AS1_ENST00000446880.1_RNA	NM_001135821.1	NP_001129293.1	P14324	FPPS_HUMAN	farnesyl diphosphate synthase	211					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)	TGCTGAAGCTCTATTGCCGGG	0.542																																					p.L211L		Atlas-SNP	.											FDPS,right_lower_lobe,carcinoma,0,1	FDPS	41	1	0			c.C633T						PASS	.						77	73	74					1																	155288031		2203	4300	6503	SO:0001819	synonymous_variant	2224	exon6			GAAGCTCTATTGC	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.633C>T	1.37:g.155288031C>T		36	0	0		73	20	0.273973	NM_001135821	D3DV91|E9PCI9|Q96G29	Silent	SNP	ENST00000356657.6	37	CCDS1110.1																																																																																			.	.	none		0.542	FDPS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039053.1	NM_002004		T	155288031	C	T	155288031	2	4	48	1	0	0	0	0	0	0	0	1	5811	900	32	2		2	FDPS	1	155288031	Silent	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	2487908	155288031	93962590	17	15893											
UAP1	6675	hgsc.bcm.edu	37	chr1	162549371	162549371	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	aaaattattttggaagagaaGaacaaagtttctatggctcc	16	12	8	5	0	1	2	0	0	1	2	2	4	2	3	1	2	1	2	1	2	8	5			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:162549371G>A	ENST00000367925.1	+	3	671	c.639G>A	c.(637-639)aaG>aaA	p.K213K	UAP1_ENST00000367924.1_Silent_p.K213K|UAP1_ENST00000271469.3_Silent_p.K213K|UAP1_ENST00000367926.4_Silent_p.K213K			Q16222	UAP1_HUMAN	UDP-N-acetylglucosamine pyrophosphorylase 1	213					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)			TGGAAGAGAAGAACAAAGTTT	0.323																																					p.K213K		Atlas-SNP	.											.	UAP1	47	.	0			c.G639A						PASS	.						67	71	70					1																	162549371		2200	4300	6500	SO:0001819	synonymous_variant	6675	exon4			AGAGAAGAACAAA	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.639G>A	1.37:g.162549371G>A		23	0	0		38	10	0.263158	NM_003115	B2R6R8|Q5VTA9|Q5VTB0|Q5VTB1|Q96GM2	Silent	SNP	ENST00000367925.1	37																																																																																				.	.	none		0.323	UAP1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000083203.1	NM_003115		A	162549371	G	A	162549371	2	1	48	1	0	0	0	0	0	0	0	1	16840	933	33	2		2	UAP1	1	162549371	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	7261340	162549371	86701250	18	15894											
DUSP27	92235	hgsc.bcm.edu	37	chr1	167096795	167096795	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	accacactgagctcacccgcGgaaagttgcagaagcaaagt	14	5	10	12	2	1	2	1	1	0	1	1	3	1	3	2	1	3	4	2	1	3	1	rs142434634	byFrequency	TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:167096795G>A	ENST00000361200.2	+	6	2593	c.2427G>A	c.(2425-2427)gcG>gcA	p.A809A	DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000271385.5_Silent_p.A809A|DUSP27_ENST00000443333.1_Silent_p.A809A			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	809					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						GCTCACCCGCGGAAAGTTGCA	0.572													G|||	2	0.000399361	0.0	0.0029	5008	,	,		22206	0.0		0.0	False		,,,				2504	0.0				p.A809A		Atlas-SNP	.											DUSP27,right_upper_lobe,carcinoma,0,1	DUSP27	235	1	0			c.G2427A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	83	76	78		2427	-10.1	0	1	dbSNP_134	78	3,8597	3.7+/-12.6	0,3,4297	no	coding-synonymous	DUSP27	NM_001080426.1		0,4,6499	AA,AG,GG		0.0349,0.0227,0.0308		809/1159	167096795	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	92235	exon5			ACCCGCGGAAAGT	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.2427G>A	1.37:g.167096795G>A		72	0	0		81	15	0.185185	NM_001080426	A0AUM4|Q9C074	Silent	SNP	ENST00000361200.2	37	CCDS30932.1																																																																																			G|0.999;A|0.001	0.001	strong		0.572	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426		A	167096795	G	A	167096795	2	1	48	1	0	0	0	0	0	0	0	1	4826	1103	39	1		1	DUSP27	1	167096795	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	4547424	167096795	82153826	19	15895											
C1orf114	57821	hgsc.bcm.edu	37	chr1	169391492	169391492	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gaatgccgtttggtgtgctcCattactgtctcattctcttt	5	18	8	10	1	2	0	1	0	2	0	5	1	3	0	2	1	3	2	2	1	2	4			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:169391492C>T	ENST00000367806.3	-	3	329	c.177G>A	c.(175-177)atG>atA	p.M59I	CCDC181_ENST00000367805.3_Missense_Mutation_p.M59I|CCDC181_ENST00000545005.1_Missense_Mutation_p.M59I|CCDC181_ENST00000491570.1_5'UTR	NM_021179.1	NP_067002.1	Q5TID7	CC181_HUMAN	coiled-coil domain containing 181	59						nucleus (GO:0005634)											TGGTGTGCTCCATTACTGTCT	0.373																																					p.M59I		Atlas-SNP	.											.	C1orf114	67	.	0			c.G177A						PASS	.						107	98	101					1																	169391492		2202	4300	6502	SO:0001583	missense	57821	exon3			GTGCTCCATTACT	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.177G>A	1.37:g.169391492C>T	ENSP00000356780:p.Met59Ile	357	0	0		441	87	0.197279	NM_021179	O60780|Q53FD5|Q5TID9|Q8TC48	Missense_Mutation	SNP	ENST00000367806.3	37		.	.	.	.	.	.	.	.	.	.	C	2.193	-0.384829	0.04966	.	.	ENSG00000117477	ENST00000367805;ENST00000367806;ENST00000545005;ENST00000456107	T;T;T;T	0.21031	2.04;2.04;2.04;2.03	5.27	-1.78	0.07957	.	1.412370	0.04011	N	0.298187	T	0.02267	0.0070	N	0.02011	-0.69	0.09310	N	0.999991	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	0.36615	T	0.2	0.0962	6.7625	0.23548	0.0:0.1371:0.3585:0.5044	.	59;59;59	Q5TID7-2;Q5TID7;Q5TID7-3	.;CA114_HUMAN;.	I	59	ENSP00000356779:M59I;ENSP00000356780:M59I;ENSP00000442297:M59I;ENSP00000411000:M59I	ENSP00000356779:M59I	M	-	3	0	C1orf114	167658116	0.731000	0.28111	0.094000	0.20943	0.052000	0.14988	0.854000	0.27791	-0.002000	0.14469	-0.414000	0.06135	ATG	.	.	none		0.373	CCDC181-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000086099.1	NM_021179		T	169391492	C	T	169391492	3	4	48	1	0	0	0	0	1	0	0	0	1989	594	21	2	1365	2	C1orf114	1	169391492	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	2294697	169391492	79859129	20	15896											
FMO2	2327	hgsc.bcm.edu	37	chr1	171174750	171174750	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aactgctgaacttcaagctcGttgggtgacaagagttttca	11	12	10	8	1	2	3	2	2	0	1	3	3	2	3	0	1	4	4	0	1	4	4	rs72549336|rs187393653		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:171174750G>A	ENST00000209929.7	+	7	1318	c.1160G>A	c.(1159-1161)cGt>cAt	p.R387H	RP1-127D3.4_ENST00000445909.1_RNA|FMO2_ENST00000441535.1_Missense_Mutation_p.R387H|FMO2_ENST00000529935.1_3'UTR|RP1-127D3.4_ENST00000422841.1_RNA|RP1-127D3.4_ENST00000445290.1_RNA			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	386					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)					CTTCAAGCTCGTTGGGTGACA	0.468																																					p.R387H		Atlas-SNP	.											FMO2,NS,carcinoma,0,2	FMO2	66	2	0			c.G1160A						PASS	.						43	42	42					1																	171174750		2203	4299	6502	SO:0001583	missense	2327	exon7			AAGCTCGTTGGGT	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.1160G>A	1.37:g.171174750G>A	ENSP00000209929:p.Arg387His	51	0	0		57	11	0.192982	NM_001460	Q53XR0	Missense_Mutation	SNP	ENST00000209929.7	37	CCDS1293.1	.	.	.	.	.	.	.	.	.	.	G	35	5.460870	0.96240	.	.	ENSG00000094963	ENST00000209929;ENST00000441535	T;T	0.63580	-0.05;-0.05	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.81009	0.4734	H	0.94385	3.53	0.80722	D	1	D	0.61697	0.99	P	0.58577	0.841	D	0.85749	0.1342	10	0.72032	D	0.01	-17.9497	18.6468	0.91413	0.0:0.0:1.0:0.0	.	387	Q99518	FMO2_HUMAN	H	387	ENSP00000209929:R387H;ENSP00000405905:R387H	ENSP00000209929:R387H	R	+	2	0	FMO2	169441374	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.732000	0.74790	2.768000	0.95171	0.655000	0.94253	CGT	G|1.000;T|0.000	.	alt		0.468	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460		A	171174750	G	A	171174750	3	1	48	1	0	0	0	0	1	0	0	0	5963	1145	40	1	1182	1	FMO2	1	171174750	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	1783258	171174750	78075871	21	15897											
GPR52	9293	hgsc.bcm.edu	37	chr1	174418186	174418209	+	In_Frame_Del	DEL	AACTGTGTAATATACAGCCTCTCC	AACTGTGTAATATACAGCCTCTCC	-																															caataagtaatagtttttgtAactgtgtaatatacagcctc																								rs75331361|rs560667623		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	AACTGTGTAATATACAGCCTCTCC	AACTGTGTAATATACAGCCTCTCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:174418186_174418209delAACTGTGTAATATACAGCCTCTCC	ENST00000367685.2	+	1	975_998	c.937_960delAACTGTGTAATATACAGCCTCTCC	c.(937-960)aactgtgtaatatacagcctctccdel	p.NCVIYSLS313del	RABGAP1L_ENST00000367689.3_Intron|RABGAP1L_ENST00000357444.6_Intron|RABGAP1L_ENST00000251507.4_Intron	NM_005684.4	NP_005675.3	Q9Y2T5	GPR52_HUMAN	G protein-coupled receptor 52	313					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						TAGTTTTTGTAACTGTGTAATATACAGCCTCTCCAACAGCGTTT	0.442																																					p.312_320del	Ovarian(92;924 1390 1930 16467 40583)	Atlas-Indel	.											.	GPR52	40	.	0			c.936_959del						PASS	.																																			SO:0001651	inframe_deletion	9293	exon1			.	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.937_960delAACTGTGTAATATACAGCCTCTCC	1.37:g.174418186_174418209delAACTGTGTAATATACAGCCTCTCC	ENSP00000356658:p.Asn313_Ser320del	115	0	0		143	17	0.118881	NM_005684	O75654|Q4VBL6|Q6ISM0	In_Frame_Del	DEL	ENST00000367685.2	37	CCDS30941.1																																																																																			.	.	none		0.442	GPR52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084511.1	NM_005684		-	174418209	AACTGTGTAATATACAGCCTCTCC	-	174418186	7	5	48	1	0	1	0	1	0	0	0	0	6706	362	13	0	939	0	GPR52	1	174418186	In_Frame_Del	DEL	AACTGTGTAATATACAGCCTCTCC	TCGA-VB-A8QN-01A-11D-A382-10	3243436	174418186	74832435	22	15898											
RGS8	85397	hgsc.bcm.edu	37	chr1	182638779	182638779	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgcgtggcatcagtaaggcCgccatacaggcatcagctta	10	8	11	12	2	2	0	2	0	0	0	2	0	2	0	2	3	3	4	2	3	3	3			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:182638779C>T	ENST00000483095.2	-	3	263	c.6G>A	c.(4-6)gcG>gcA	p.A2A	RGS8_ENST00000367557.4_Silent_p.A2A|RGS8_ENST00000491420.2_5'UTR|RGS8_ENST00000367556.1_Silent_p.A2A|RGS8_ENST00000258302.4_Intron			P57771	RGS8_HUMAN	regulator of G-protein signaling 8	2					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						TCAGTAAGGCCGCCATACAGG	0.517																																					p.A2A	Ovarian(189;1262 3804 41973)	Atlas-SNP	.											.	RGS8	51	.	0			c.G6A						PASS	.						134	143	140					1																	182638779		1971	4154	6125	SO:0001819	synonymous_variant	85397	exon3			TAAGGCCGCCATA	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.6G>A	1.37:g.182638779C>T		85	0	0		103	22	0.213592	NM_001102450	B4DGL9|Q3SYD2	Silent	SNP	ENST00000483095.2	37	CCDS41443.1																																																																																			.	.	none		0.517	RGS8-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358979.1	NM_033345		T	182638779	C	T	182638779	2	4	48	1	0	0	0	0	0	0	0	1	13327	639	23	1		1	RGS8	1	182638779	Silent	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	8220593	182638779	66611842	23	15899											
CFH	3075	hgsc.bcm.edu	37	chr1	196716285	196716285	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ttatggaaaattataacataGcattaaggtggacagccaaa	18	10	8	5	0	0	0	0	0	0	0	0	2	0	2	1	3	3	1	1	3	8	5			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:196716285G>A	ENST00000367429.4	+	22	3778	c.3538G>A	c.(3538-3540)Gca>Aca	p.A1180T		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	1180	Sushi 20. {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						TTATAACATAGCATTAAGGTG	0.343																																					p.A1180T		Atlas-SNP	.											.	CFH	251	.	0			c.G3538A						PASS	.						140	138	138					1																	196716285		2203	4300	6503	SO:0001583	missense	3075	exon22			AACATAGCATTAA	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.3538G>A	1.37:g.196716285G>A	ENSP00000356399:p.Ala1180Thr	409	0	0		576	99	0.171875	NM_000186	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Missense_Mutation	SNP	ENST00000367429.4	37	CCDS1385.1	.	.	.	.	.	.	.	.	.	.	.	3.487	-0.104608	0.06967	.	.	ENSG00000000971	ENST00000367429	D	0.82984	-1.67	4.48	-8.97	0.00758	Complement control module (1);Sushi/SCR/CCP (1);	.	.	.	.	T	0.53834	0.1821	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.54016	-0.8356	9	0.13853	T	0.58	.	13.2549	0.60073	0.1389:0.2653:0.5958:0.0	.	1180	P08603	CFAH_HUMAN	T	1180	ENSP00000356399:A1180T	ENSP00000356399:A1180T	A	+	1	0	CFH	194982908	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.592000	0.00421	-2.554000	0.00477	-0.417000	0.06048	GCA	.	.	none		0.343	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186		A	196716285	G	A	196716285	3	1	48	1	0	0	0	0	1	0	0	0	3285	971	34	2	3642	2	CFH	1	196716285	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	14077506	196716285	52534336	24	15900											
IGFN1	91156	hgsc.bcm.edu	37	chr1	201182456	201182456	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tgggaggtcaggcaggaggcCtggctcactcaggagcaggt	8	6	18	9	0	3	0	3	0	0	0	3	3	3	3	1	8	1	3	1	8	0	0			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:201182456C>T	ENST00000335211.4	+	12	8565	c.8435C>T	c.(8434-8436)cCt>cTt	p.P2812L	IGFN1_ENST00000451870.2_Intron|IGFN1_ENST00000295591.8_5'UTR	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						GGCAGGAGGCCTGGCTCACTC	0.637																																					p.P2812L		Atlas-SNP	.											.	IGFN1	220	.	0			c.C8435T						PASS	.						45	52	50					1																	201182456		692	1591	2283	SO:0001583	missense	91156	exon12			GGAGGCCTGGCTC	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.8435C>T	1.37:g.201182456C>T	ENSP00000334714:p.Pro2812Leu	88	0	0		135	25	0.185185	NM_001164586	F8WAI1|Q9NT72	Missense_Mutation	SNP	ENST00000335211.4	37	CCDS53455.1	.	.	.	.	.	.	.	.	.	.	C	10.52	1.372301	0.24857	.	.	ENSG00000163395	ENST00000335211	T	0.54071	0.59	3.54	-3.87	0.04218	.	.	.	.	.	T	0.34164	0.0888	N	0.22421	0.69	0.09310	N	0.999999	.	.	.	.	.	.	T	0.32929	-0.9888	7	0.48119	T	0.1	.	4.4927	0.11820	0.0:0.3952:0.2935:0.3113	.	.	.	.	L	2812	ENSP00000334714:P2812L	ENSP00000334714:P2812L	P	+	2	0	IGFN1	199449079	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-1.317000	0.02707	-0.920000	0.03799	-0.424000	0.05967	CCT	.	.	none		0.637	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275		T	201182456	C	T	201182456	3	4	48	1	0	0	0	0	1	0	0	0	7599	681	24	2	8477	2	IGFN1	1	201182456	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	4466171	201182456	48068165	25	15901											
ADIPOR1	51094	hgsc.bcm.edu	37	chr1	202915676	202915676	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tgaccatgtagcagatagtcGttgtcctttagccagtcagg	9	12	11	9	1	1	2	1	1	0	1	3	2	2	2	3	1	2	3	3	1	3	5	rs377163409		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:202915676G>A	ENST00000340990.5	-	4	619	c.321C>T	c.(319-321)aaC>aaT	p.N107N	ADIPOR1_ENST00000436244.1_Silent_p.N107N|ADIPOR1_ENST00000367254.3_Silent_p.N107N	NM_015999.4	NP_057083.2	Q96A54	ADR1_HUMAN	adiponectin receptor 1	107					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)			GCAGATAGTCGTTGTCCTTTA	0.507													G|||	1	0.000199681	0.0	0.0	5008	,	,		21433	0.0		0.0	False		,,,				2504	0.001				p.N107N		Atlas-SNP	.											ADIPOR1,NS,carcinoma,0,1	ADIPOR1	32	1	0			c.C321T						PASS	.						224	170	188					1																	202915676		2203	4300	6503	SO:0001819	synonymous_variant	51094	exon4			ATAGTCGTTGTCC		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.321C>T	1.37:g.202915676G>A		74	0	0		109	17	0.155963	NM_015999	B3KMB0|Q53HS7|Q53YY6|Q9Y360	Silent	SNP	ENST00000340990.5	37	CCDS1430.1																																																																																			.	.	none		0.507	ADIPOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099160.2	NM_015999		A	202915676	G	A	202915676	2	1	48	1	0	0	0	0	0	0	0	1	318	1136	40	1		1	ADIPOR1	1	202915676	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	1733220	202915676	46334945	26	15902											
BTG2	7832	hgsc.bcm.edu	37	chr1	203276387	203276387	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	accagctgctgcccagcgagCtgaccctgtgggtggacccc	6	6	13	16	1	0	1	0	1	0	0	0	3	0	2	5	2	5	3	5	2	0	0			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:203276387C>T	ENST00000290551.4	+	2	369	c.298C>T	c.(298-300)Ctg>Ttg	p.L100L	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	100					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			GCCCAGCGAGCTGACCCTGTG	0.642																																					p.L100L		Atlas-SNP	.											.	BTG2	16	.	0			c.C298T						PASS	.						47	49	48					1																	203276387		2203	4300	6503	SO:0001819	synonymous_variant	7832	exon2			AGCGAGCTGACCC		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"B-cell translocation gene 2", "pheochromacytoma cell-3", "NGF-inducible anti-proliferative protein PC3", "nerve growth factor-inducible anti-proliferative"	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.298C>T	1.37:g.203276387C>T		47	0	0		57	8	0.140351	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Silent	SNP	ENST00000290551.4	37	CCDS1437.1																																																																																			.	.	none		0.642	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763		T	203276387	C	T	203276387	2	4	48	1	0	0	0	0	0	0	0	1	1556	796	28	2		2	BTG2	1	203276387	Silent	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	360711	203276387	45974234	27	15903											
OBSCN	84033	hgsc.bcm.edu	37	chr1	228557697	228557697	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gaccgtgccaccctcctgaaCgtcctggaggggcgcgtgtc	5	7	14	15	4	0	1	0	1	0	0	3	3	2	2	5	3	2	0	5	3	1	0	rs200703788	byFrequency	TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:228557697C>T	ENST00000422127.1	+	91	20066	c.20022C>T	c.(20020-20022)aaC>aaT	p.N6674N	OBSCN_ENST00000366707.4_Silent_p.N4308N|OBSCN_ENST00000570156.2_Silent_p.N7631N	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	6674	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)				CCCTCCTGAACGTCCTGGAGG	0.637																																					p.N7631N		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C22893T						PASS	.						67	69	68					1																	228557697		2005	4157	6162	SO:0001819	synonymous_variant	84033	exon102			CCTGAACGTCCTG	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.20022C>T	1.37:g.228557697C>T		56	0	0		73	17	0.232877	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	C	6.857	0.527360	0.13066	.	.	ENSG00000154358	ENST00000441106	.	.	.	4.72	-7.4	0.01397	.	.	.	.	.	T	0.42314	0.1197	.	.	.	0.26941	N	0.966244	.	.	.	.	.	.	T	0.42916	-0.9423	4	.	.	.	.	16.4815	0.84159	0.0:0.2737:0.0:0.7263	.	.	.	.	C	1291	.	.	R	+	1	0	OBSCN	226624320	0.001000	0.12720	0.001000	0.08648	0.084000	0.17831	-1.550000	0.02180	-1.617000	0.01570	-0.463000	0.05309	CGT	C|0.996;G|0.004	.	alt		0.637	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843		T	228557697	C	T	228557697	2	4	48	1	0	0	0	0	0	0	0	1	10821	535	19	1		1	OBSCN	1	228557697	Silent	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	25281310	228557697	20692924	28	15904											
DISC1	27185	hgsc.bcm.edu	37	chr1	231931010	231931010	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tccaggaaagaataaaatccCtcaacttgtcacttaaagaa	18	9	5	9	0	2	2	2	0	0	2	4	3	4	3	2	1	1	0	2	1	8	3			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:231931010C>A	ENST00000602281.1	+	7	1710	c.1657C>A	c.(1657-1659)Ctc>Atc	p.L553I	DISC1_ENST00000537876.1_Intron|DISC1_ENST00000535983.1_Missense_Mutation_p.L553I|DISC1_ENST00000366636.4_Missense_Mutation_p.L553I|DISC1_ENST00000539444.1_Missense_Mutation_p.L553I|DISC1_ENST00000366633.3_Missense_Mutation_p.L553I|DISC1_ENST00000602873.1_Intron|DISC1_ENST00000366637.3_5'UTR|TSNAX-DISC1_ENST00000602962.1_3'UTR|DISC1_ENST00000439617.2_Missense_Mutation_p.L553I	NM_001164542.1|NM_001164544.1	NP_001158014.1|NP_001158016.1	Q9NRI5	DISC1_HUMAN	disrupted in schizophrenia 1	553	Interaction with TRAF3IP1.|Necessary and sufficient for interaction with PCNT and localization at the centrosome.|Required for localization to punctate cytoplasmic foci.				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)				AATAAAATCCCTCAACTTGTC	0.353																																					p.L585I		Atlas-SNP	.											.	DISC1	207	.	0			c.C1753A						PASS	.						84	85	85					1																	231931010		2203	4300	6503	SO:0001583	missense	27185	exon8			AAATCCCTCAACT	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.1657C>A	1.37:g.231931010C>A	ENSP00000473425:p.Leu553Ile	77	0	0		102	24	0.235294	NM_001164537	A6NLH2|C4P091|C4P095|C4P0A1|C4P0A3|C4P0B3|C4P0B6|C4P0C1|C9J6D0|O75045|Q5VT44|Q5VT45|Q8IXJ0|Q8IXJ1|Q9BX19|Q9NRI3|Q9NRI4	Missense_Mutation	SNP	ENST00000602281.1	37	CCDS59205.1	.	.	.	.	.	.	.	.	.	.	C	16.61	3.171714	0.57584	.	.	ENSG00000162946	ENST00000439617;ENST00000366637;ENST00000366636;ENST00000366638;ENST00000532576;ENST00000535983;ENST00000366633;ENST00000539444	D;D;D;D;D	0.83163	-1.69;-1.69;-1.69;-1.69;-1.69	4.72	3.8	0.43715	.	0.079041	0.51477	D	0.000093	D	0.86760	0.6010	L	0.54323	1.7	0.80722	D	1	D;D;D;P;D;D;P;D;D;P;P;D;P;D;P;P	0.76494	0.986;0.999;0.989;0.75;0.972;0.998;0.513;0.972;0.972;0.754;0.75;0.986;0.859;0.986;0.859;0.754	P;D;P;B;P;P;B;P;P;B;B;P;B;P;P;B	0.67725	0.799;0.953;0.846;0.292;0.536;0.885;0.191;0.536;0.536;0.37;0.292;0.683;0.435;0.683;0.586;0.37	D	0.86889	0.2047	10	0.72032	D	0.01	-7.753	9.8129	0.40835	0.0:0.8338:0.0:0.1662	.	585;431;585;553;553;431;553;553;553;553;553;553;553;553;553;553	C4P096;C4P094;E2QRA4;C4P0A3;C4P098;F5H1F1;C4P0A4;A6NLH2;C4P095;C4P0B6;C4P0B1;A7E2W8;Q5T409;Q9NRI5-2;Q9NRI5;Q9NRI5-3	.;.;.;.;.;.;.;.;.;.;.;.;.;.;DISC1_HUMAN;.	I	553;553;553;585;431;553;553;553	ENSP00000403888:L553I;ENSP00000355596:L553I;ENSP00000443996:L553I;ENSP00000355593:L553I;ENSP00000440953:L553I	ENSP00000355593:L553I	L	+	1	0	DISC1	229997633	0.837000	0.29446	0.983000	0.44433	0.993000	0.82548	1.489000	0.35562	1.312000	0.45043	0.557000	0.71058	CTC	.	.	none		0.353	DISC1-019	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000467451.1	NM_018662		A	231931010	C	A	231931010	3	1	48	1	0	0	0	0	1	0	0	0	4540	681	24	4	2056	4	DISC1	1	231931010	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	3373313	231931010	17319611	29	15905											
FMN2	56776	hgsc.bcm.edu	37	chr1	240371409	240371409	+	Silent	SNP	G	G	T	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggagcgggcataccccctccGccccctctacccggagtggg	5	5	13	18	3	1	0	0	0	1	0	2	2	2	2	6	4	3	1	6	4	2	2	rs373533409	byFrequency	TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:240371409G>T	ENST00000319653.9	+	5	3527	c.3297G>T	c.(3295-3297)ccG>ccT	p.P1099P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1099	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)			TACCCCCTCCGCCCCCTCTAC	0.731																																					p.P1099P		Atlas-SNP	.											FMN2,NS,neuroblastoma,0,1	FMN2	451	1	0			c.G3297T						scavenged	.						6	8	8					1																	240371409		2016	4072	6088	SO:0001819	synonymous_variant	56776	exon5			CCCTCCGCCCCCT	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.3297G>T	1.37:g.240371409G>T		23	2	0.0869565		49	4	0.0816327	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			.	.	none		0.731	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		T	240371409	G	T	240371409	2	4	48	1	0	0	0	0	0	0	0	1	5958	1074	38	4		4	FMN2	1	240371409	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	8440399	240371409	8879212	30	15906											
FMN2	56776	hgsc.bcm.edu	37	chr1	240635709	240635709	+	Nonsense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	aggtgtgtagacagaagaaaGgaaaatcactttataaaata	20	9	9	3	0	1	3	1	0	0	3	1	4	1	4	0	2	0	1	0	2	9	5			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:240635709G>T	ENST00000319653.9	+	17	5328	c.5098G>T	c.(5098-5100)Gga>Tga	p.G1700*	FMN2_ENST00000543681.1_Nonsense_Mutation_p.G20*|FMN2_ENST00000545751.1_Nonsense_Mutation_p.G296*|AL646016.1_ENST00000596886.1_Intron|FMN2_ENST00000496950.1_3'UTR	NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1700					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)			ACAGAAGAAAGGAAAATCACT	0.318																																					p.G1700X		Atlas-SNP	.											.	FMN2	451	.	0			c.G5098T						PASS	.						77	85	82					1																	240635709		2203	4298	6501	SO:0001587	stop_gained	56776	exon17			AAGAAAGGAAAAT	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.5098G>T	1.37:g.240635709G>T	ENSP00000318884:p.Gly1700*	151	0	0		172	32	0.186047	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Nonsense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	.	.	.	.	.	.	.	.	.	.	G	40	8.160609	0.98683	.	.	ENSG00000155816	ENST00000319653;ENST00000545751;ENST00000537355;ENST00000406993;ENST00000543681	.	.	.	5.83	5.83	0.93111	.	0.192599	0.35555	N	0.003121	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.31617	T	0.26	.	18.3013	0.90164	0.0:0.0:1.0:0.0	.	.	.	.	X	1700;296;327;176;20	.	ENSP00000318884:G1700X	G	+	1	0	FMN2	238702332	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	6.247000	0.72411	2.758000	0.94735	0.655000	0.94253	GGA	.	.	none		0.318	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352		T	240635709	G	T	240635709	4	4	48	1	0	0	0	0	0	1	0	0	5958	1001	35	4	5164	4	FMN2	1	240635709	Nonsense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	264300	240635709	8614912	31	15907											
C1orf101	257044	hgsc.bcm.edu	37	chr1	244769022	244769022	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atgataatggctatgttaaaGacgttgaagcaaatttcata	16	13	8	4	1	1	3	1	2	0	1	1	3	1	3	0	1	1	4	0	1	7	6			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr1:244769022G>A	ENST00000366534.4	+	18	2383	c.2329G>A	c.(2329-2331)Gac>Aac	p.D777N	C1orf101_ENST00000473875.1_3'UTR|C1orf101_ENST00000366531.3_Missense_Mutation_p.D626N|C1orf101_ENST00000366533.4_Missense_Mutation_p.D777N	NM_001130957.1	NP_001124429.1	Q5SY80	CA101_HUMAN	chromosome 1 open reading frame 101	777						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)			CTATGTTAAAGACGTTGAAGC	0.353																																					p.D777N		Atlas-SNP	.											.	C1orf101	158	.	0			c.G2329A						PASS	.						127	124	125					1																	244769022		2203	4300	6503	SO:0001583	missense	257044	exon18			GTTAAAGACGTTG	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.2329G>A	1.37:g.244769022G>A	ENSP00000355492:p.Asp777Asn	133	0	0		135	33	0.244444	NM_173807	B4DZR4|B7Z7X5|E9PEA3|Q8IYZ6	Missense_Mutation	SNP	ENST00000366534.4	37	CCDS44340.1	.	.	.	.	.	.	.	.	.	.	G	12.85	2.060538	0.36373	.	.	ENSG00000179397	ENST00000391841;ENST00000366534;ENST00000366533;ENST00000428042;ENST00000366531	T;T;T;T	0.23552	1.9;1.9;1.9;1.9	5.36	0.0116	0.14088	.	1.258880	0.05240	N	0.511932	T	0.40694	0.1127	L	0.53249	1.67	0.09310	N	1	B;P;D;D	0.76494	0.1;0.872;0.999;0.991	B;P;D;P	0.66351	0.046;0.529;0.943;0.883	T	0.20371	-1.0277	10	0.62326	D	0.03	.	4.3263	0.11041	0.2737:0.3237:0.4026:0.0	.	697;777;777;626	B1AQM6;Q5SY80;Q5SY80-2;B4DZR4	.;CA101_HUMAN;.;.	N	777;777;777;697;626	ENSP00000355492:D777N;ENSP00000355491:D777N;ENSP00000395796:D697N;ENSP00000355489:D626N	ENSP00000355489:D626N	D	+	1	0	C1orf101	242835645	0.865000	0.29922	0.001000	0.08648	0.005000	0.04900	0.641000	0.24720	-0.030000	0.13804	0.585000	0.79938	GAC	.	.	none		0.353	C1orf101-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096701.1	NM_173807		A	244769022	G	A	244769022	3	1	48	1	0	0	0	0	1	0	0	0	1978	942	33	2	2399	2	C1orf101	1	244769022	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	4133313	244769022	4481599	32	15908											
TSSC1	7260	hgsc.bcm.edu	37	chr2	3261073	3261073	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	aatatgcaaaatcctaccagGccatgttgccatgggctgtg	11	10	10	10	0	0	0	0	0	0	0	1	0	1	0	4	2	3	3	4	2	5	3			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr2:3261073G>C	ENST00000382125.4	-	4	605	c.413C>G	c.(412-414)gCc>gGc	p.A138G	TSSC1_ENST00000398659.4_Missense_Mutation_p.A165G|TSSC1_ENST00000443925.2_Missense_Mutation_p.A138G|TSSC1_ENST00000478754.1_5'UTR	NM_003310.2	NP_003301.1	Q53HC9	TSSC1_HUMAN	tumor suppressing subtransferable candidate 1	138										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)		ATCCTACCAGGCCATGTTGCC	0.562																																					p.A138G	Colon(140;1261 1762 4183 34270 49743)	Atlas-SNP	.											.	TSSC1	39	.	0			c.C413G						PASS	.						89	80	83					2																	3261073		2203	4300	6503	SO:0001583	missense	7260	exon4			TACCAGGCCATGT	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.413C>G	2.37:g.3261073G>C	ENSP00000371559:p.Ala138Gly	90	0	0		60	13	0.216667	NM_003310	D6W4Y1|O43179|Q53S19|Q53SG2	Missense_Mutation	SNP	ENST00000382125.4	37	CCDS1651.1	.	.	.	.	.	.	.	.	.	.	G	19.91	3.914595	0.72983	.	.	ENSG00000032389	ENST00000382125;ENST00000398659;ENST00000443925	T;T;T	0.13657	2.57;2.57;2.57	5.59	5.59	0.84812	WD40/YVTN repeat-like-containing domain (1);	0.049431	0.85682	D	0.000000	T	0.15825	0.0381	L	0.60455	1.87	0.80722	D	1	P	0.45902	0.868	B	0.37692	0.256	T	0.08289	-1.0729	10	0.18276	T	0.48	.	18.6315	0.91361	0.0:0.0:1.0:0.0	.	138	Q53HC9	TSSC1_HUMAN	G	138;165;138	ENSP00000371559:A138G;ENSP00000381652:A165G;ENSP00000389080:A138G	ENSP00000371559:A138G	A	-	2	0	TSSC1	3240080	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.643000	0.98464	2.626000	0.88956	0.650000	0.86243	GCC	.	.	none		0.562	TSSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206694.2	NM_003310		C	3261073	G	C	3261073	3	2	48	1	0	0	0	0	1	0	0	0	16681	1203	42	4	774	4	TSSC1	2	3261073	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10		3261073	239938300	33	15909											
RHOB	388	hgsc.bcm.edu	37	chr2	20647760	20647760	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagacggccacgcgcgccgcGctgcagaagcgctacggctc	7	3	15	16	8	0	2	0	0	0	2	1	3	0	2	2	2	3	4	2	2	2	1			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr2:20647760G>A	ENST00000272233.4	+	1	926	c.534G>A	c.(532-534)gcG>gcA	p.A178A		NM_004040.2	NP_004031.1	P62745	RHOB_HUMAN	ras homolog family member B	178					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)	CGCGCGCCGCGCTGCAGAAGC	0.697																																					p.A178A		Atlas-SNP	.											.	RHOB	18	.	0			c.G534A						PASS	.						45	48	47					2																	20647760		2181	4268	6449	SO:0001819	synonymous_variant	388	exon1			CGCCGCGCTGCAG		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.534G>A	2.37:g.20647760G>A		50	0	0		56	16	0.285714	NM_004040	B2R692|P01121|Q5U0H6|Q7RTN5|Q7RTR9|Q9CUV7	Silent	SNP	ENST00000272233.4	37	CCDS1699.1																																																																																			.	.	none		0.697	RHOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207500.1	NM_004040		A	20647760	G	A	20647760	2	1	48	1	0	0	0	0	0	0	0	1	13347	1074	38	1		1	RHOB	2	20647760	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	17386687	20647760	222551613	34	15910											
TMEM214	54867	hgsc.bcm.edu	37	chr2	27260571	27260571	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	cccctgagatgaagaaagagGtgaggatatggtgggaggct	12	7	17	5	0	0	5	0	3	0	3	0	8	0	7	2	5	0	1	2	5	3	1			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr2:27260571G>A	ENST00000238788.9	+	9	1214		c.e9+1		TMEM214_ENST00000404032.3_Splice_Site	NM_017727.4	NP_060197.4	Q6NUQ4	TM214_HUMAN	transmembrane protein 214						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						GAAGAAAGAGGTGAGGATATG	0.557																																					.		Atlas-SNP	.											.	TMEM214	41	.	0			c.1017+1G>A						PASS	.						87	87	87					2																	27260571		1896	4122	6018	SO:0001630	splice_region_variant	54867	exon8			AAAGAGGTGAGGA		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.1152+1G>A	2.37:g.27260571G>A		145	0	0		150	40	0.266667	NM_001083590	A6NNF2|B3KUI9|B5MCD8|D6W547|Q53SW1|Q69YH4|Q8NC45|Q8WZ37|Q9NXH2	Splice_Site	SNP	ENST00000238788.9	37	CCDS42664.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.175815	0.78564	.	.	ENSG00000119777	ENST00000238788;ENST00000404032;ENST00000537397;ENST00000425720	.	.	.	5.39	5.39	0.77823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.2941	0.87166	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TMEM214	27114075	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	9.222000	0.95196	2.700000	0.92200	0.561000	0.74099	.	.	.	none		0.557	TMEM214-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324748.1	NM_017727	Intron	A	27260571	G	A	27260571	5	1	48	1	0	0	0	0	0	0	1	0	16152	1275	44	2	1187	2	TMEM214	2	27260571	Splice_Site	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	6612811	27260571	215938802	35	15911											
DNAH6	1768	hgsc.bcm.edu	37	chr2	84921393	84921393	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gattgctcggatgatacgtcAagaaagaggcaatgccctgc	12	8	12	9	2	1	3	1	1	0	2	2	5	1	4	1	2	4	2	1	2	4	2			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr2:84921393A>G	ENST00000237449.6	+	45	7321	c.7313A>G	c.(7312-7314)cAa>cGa	p.Q2438R	DNAH6_ENST00000398278.2_Missense_Mutation_p.Q2389R|DNAH6_ENST00000602588.1_Missense_Mutation_p.Q410R|DNAH6_ENST00000389394.3_Missense_Mutation_p.Q2438R			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	2438	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						ATGATACGTCAAGAAAGAGGC	0.493																																					p.Q2438R		Atlas-SNP	.											.	DNAH6	194	.	0			c.A7313G						PASS	.						127	107	113					2																	84921393		692	1591	2283	SO:0001583	missense	1768	exon46			TACGTCAAGAAAG	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.7313A>G	2.37:g.84921393A>G	ENSP00000237449:p.Gln2438Arg	101	0	0		103	35	0.339806	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	37	CCDS46348.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.645427	0.87859	.	.	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.41400	1.0;1.0;1.0	5.47	5.47	0.80525	Dynein heavy chain, P-loop containing D4 domain (1);	.	.	.	.	T	0.72104	0.3419	M	0.92833	3.35	0.49130	D	0.999757	D;D	0.89917	1.0;0.995	D;D	0.83275	0.996;0.975	T	0.79550	-0.1757	9	0.66056	D	0.02	.	14.5287	0.67909	1.0:0.0:0.0:0.0	.	2438;2389	Q9C0G6;Q9C0G6-4	DYH6_HUMAN;.	R	2438;2389;2438	ENSP00000374045:Q2438R;ENSP00000381326:Q2389R;ENSP00000237449:Q2438R	ENSP00000237449:Q2438R	Q	+	2	0	DNAH6	84774904	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.088000	0.89523	2.074000	0.62210	0.533000	0.62120	CAA	.	.	none		0.493	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370		G	84921393	A	G	84921393	3	3	48	1	0	0	0	0	1	0	0	0	4607	130	5	3	7491	3	DNAH6	2	84921393	Missense_Mutation	SNP	A	TCGA-VB-A8QN-01A-11D-A382-10	57660822	84921393	158277980	36	15912											
NCKAP5	344148	hgsc.bcm.edu	37	chr2	133636475	133636475	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ttttcattctccaaagccaaCgctgaattctctgcctgcag	9	13	6	13	1	3	1	1	1	2	0	5	1	3	1	3	0	4	2	3	0	3	4	rs200896980	byFrequency	TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr2:133636475C>T	ENST00000409261.1	-	9	967	c.594G>A	c.(592-594)gcG>gcA	p.A198A	NCKAP5_ENST00000409213.1_Silent_p.A198A|NCKAP5_ENST00000317721.6_Silent_p.A198A|NCKAP5_ENST00000405974.3_Silent_p.A198A	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	198										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						CCAAAGCCAACGCTGAATTCT	0.388													C|||	2	0.000399361	0.0015	0.0	5008	,	,		19695	0.0		0.0	False		,,,				2504	0.0				p.A198A		Atlas-SNP	.											NCKAP5_ENST00000405974,colon,carcinoma,-1,2	NCKAP5	322	2	0			c.G594A						PASS	.	C	,	5,3941		0,5,1968	159	149	152		594,594	-11.1	0.7	2		152	0,8296		0,0,4148	no	coding-synonymous,coding-synonymous	NCKAP5	NM_207363.2,NM_207481.3	,	0,5,6116	TT,TC,CC		0.0,0.1267,0.0408	,	198/1910,198/591	133636475	5,12237	1973	4148	6121	SO:0001819	synonymous_variant	344148	exon9			AGCCAACGCTGAA	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.594G>A	2.37:g.133636475C>T		86	0	0		94	25	0.265957	NM_207481	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Silent	SNP	ENST00000409261.1	37	CCDS46418.1																																																																																			C|1.000;T|0.000	0.000	strong		0.388	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481		T	133636475	C	T	133636475	2	4	48	1	0	0	0	0	0	0	0	1	10232	523	19	1		1	NCKAP5	2	133636475	Silent	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	48715082	133636475	109562898	37	15913											
KCNJ3	3760	hgsc.bcm.edu	37	chr2	155566166	155566166	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	0	1	0	0	0	cccttgaccaacttgaactgGatgtaggttttagtacaggg	10	12	11	8	0	0	2	0	2	0	0	0	3	0	3	2	3	3	3	2	3	5	6			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr2:155566166G>A	ENST00000295101.2	+	2	1231	c.754G>A	c.(754-756)Gat>Aat	p.D252N	KCNJ3_ENST00000544049.1_Intron|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	252					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)	ACTTGAACTGGATGTAGGTTT	0.463																																					p.D252N		Atlas-SNP	.											KCNJ3,NS,carcinoma,0,2	KCNJ3	126	2	0			c.G754A						PASS	.						118	113	115					2																	155566166		2203	4300	6503	SO:0001583	missense	3760	exon2			GAACTGGATGTAG	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.754G>A	2.37:g.155566166G>A	ENSP00000295101:p.Asp252Asn	248	0	0		239	54	0.225941	NM_001260509	B4DEW7|Q8TBI0	Missense_Mutation	SNP	ENST00000295101.2	37	CCDS2200.1	.	.	.	.	.	.	.	.	.	.	G	12.42	1.933079	0.34096	.	.	ENSG00000162989	ENST00000295101	D	0.93604	-3.25	5.96	5.96	0.96718	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.045255	0.85682	D	0.000000	D	0.83238	0.5211	N	0.01800	-0.715	0.80722	D	1	B	0.18166	0.026	B	0.26416	0.069	T	0.79322	-0.1851	10	0.07030	T	0.85	.	19.4074	0.94653	0.0:0.0:1.0:0.0	.	252	P48549	IRK3_HUMAN	N	252	ENSP00000295101:D252N	ENSP00000295101:D252N	D	+	1	0	KCNJ3	155274412	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.864000	0.99589	2.831000	0.97527	0.650000	0.86243	GAT	.	.	none		0.463	KCNJ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254890.2	NM_002239		A	155566166	G	A	155566166	3	1	48	1	0	0	0	0	1	0	0	0	8061	1174	41	2	760	2	KCNJ3	2	155566166	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	21929691	155566166	87633207	38	15914											
TTC30B	150737	hgsc.bcm.edu	37	chr2	178415820	178415820	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	aataccaaagtcataatttcCtttggcacaataaagagttc	16	12	5	8	0	1	1	1	0	0	1	3	1	2	1	2	1	1	2	2	1	7	6			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr2:178415820C>T	ENST00000408939.3	-	1	1922	c.1672G>A	c.(1672-1674)Gga>Aga	p.G558R		NM_152517.2	NP_689730.2	Q8N4P2	TT30B_HUMAN	tetratricopeptide repeat domain 30B	558					cilium assembly (GO:0042384)|intraciliary transport (GO:0042073)	cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)				cervix(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|urinary_tract(1)	23			OV - Ovarian serous cystadenocarcinoma(117;0.00151)|Epithelial(96;0.00931)|all cancers(119;0.0362)			TCATAATTTCCTTTGGCACAA	0.388																																					p.G558R		Atlas-SNP	.											.	TTC30B	44	.	0			c.G1672A						PASS	.						183	193	189					2																	178415820		2203	4300	6503	SO:0001583	missense	150737	exon1			AATTTCCTTTGGC	AK055552	CCDS42784.1	2q31.2	2014-02-21			ENSG00000196659	ENSG00000196659		"Tetratricopeptide (TTC) repeat domain containing", "Intraflagellar transport homologs"	26425	protein-coding gene	gene with protein product						12477932	Standard	NM_152517		Approved	FLJ30990, fleer, IFT70	uc002uln.3	Q8N4P2	OTTHUMG00000154166	ENST00000408939.3:c.1672G>A	2.37:g.178415820C>T	ENSP00000386181:p.Gly558Arg	239	0	0		291	76	0.261168	NM_152517	Q63HQ1|Q96NE6	Missense_Mutation	SNP	ENST00000408939.3	37	CCDS42784.1	.	.	.	.	.	.	.	.	.	.	C	17.29	3.352187	0.61183	.	.	ENSG00000196659	ENST00000500357;ENST00000408939	T	0.21031	2.03	4.87	4.87	0.63330	.	0.000000	0.85682	D	0.000000	T	0.56485	0.1988	M	0.91872	3.25	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.67465	-0.5664	10	0.87932	D	0	.	18.5618	0.91102	0.0:1.0:0.0:0.0	.	558	Q8N4P2	TT30B_HUMAN	R	511;558	ENSP00000386181:G558R	ENSP00000386181:G558R	G	-	1	0	TTC30B	178124066	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	6.918000	0.75788	2.675000	0.91044	0.655000	0.94253	GGA	.	.	none		0.388	TTC30B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334193.2	NM_152517		T	178415820	C	T	178415820	3	4	48	1	0	0	0	0	1	0	0	0	16714	690	24	2	329	2	TTC30B	2	178415820	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	22849654	178415820	64783553	39	15915											
COL6A3	1293	hgsc.bcm.edu	37	chr2	238249705	238249705	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tctaagatgaaagccatgtcGatgtccacatcgctccctgc	10	10	8	13	2	1	2	0	1	1	1	5	3	3	2	3	0	2	1	3	0	2	1			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr2:238249705G>A	ENST00000295550.4	-	38	8306	c.7854C>T	c.(7852-7854)atC>atT	p.I2618I	COL6A3_ENST00000472056.1_Silent_p.I2011I|COL6A3_ENST00000346358.4_Silent_p.I2418I|COL6A3_ENST00000409809.1_Silent_p.I2412I|COL6A3_ENST00000347401.3_Silent_p.I2417I|COL6A3_ENST00000353578.4_Silent_p.I2412I	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2618	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)		AAGCCATGTCGATGTCCACAT	0.517																																					p.I2618I		Atlas-SNP	.											.	COL6A3	608	.	0			c.C7854T						PASS	.						175	171	172					2																	238249705		2203	4300	6503	SO:0001819	synonymous_variant	1293	exon38			CATGTCGATGTCC	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.7854C>T	2.37:g.238249705G>A		80	0	0		105	39	0.371429	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			.	.	none		0.517	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369		A	238249705	G	A	238249705	2	1	48	1	0	0	0	0	0	0	0	1	3703	1048	37	1		1	COL6A3	2	238249705	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	59833885	238249705	4949668	40	15916											
SCN5A	6331	hgsc.bcm.edu	37	chr3	38620946	38620946	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ggctccaggtcctggaatccGgaggggcctctgggccaccg	5	6	16	14	2	1	0	0	0	1	0	4	2	4	2	6	7	0	1	6	7	1	0	rs1805125	byFrequency	TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr3:38620946G>A	ENST00000333535.4	-	18	3418	c.3269C>T	c.(3268-3270)cCg>cTg	p.P1090L	SCN5A_ENST00000455624.2_Missense_Mutation_p.P1089L|SCN5A_ENST00000449557.2_Intron|SCN5A_ENST00000443581.1_Missense_Mutation_p.P1089L|SCN5A_ENST00000425664.1_Missense_Mutation_p.P1090L|SCN5A_ENST00000450102.2_Intron|SCN5A_ENST00000414099.2_Missense_Mutation_p.P1090L|SCN5A_ENST00000451551.2_Intron|SCN5A_ENST00000413689.1_Missense_Mutation_p.P1090L|SCN5A_ENST00000423572.2_Missense_Mutation_p.P1089L			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	1090			P -> L (in dbSNP:rs1805125). {ECO:0000269|PubMed:18368697}.		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)	CCTGGAATCCGGAGGGGCCTC	0.657													G|||	22	0.00439297	0.0	0.0	5008	,	,		17928	0.0198		0.001	False		,,,				2504	0.001				p.P1090L		Atlas-SNP	.											SCN5A,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,1	SCN5A	634	1	0			c.C3269T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,,LEU/PRO	1,4049		0,1,2024	18	21	20		3266,3269,3269,3266,,3269	-0.6	0	3	dbSNP_89	20	0,8396		0,0,4198	yes	missense,missense,missense,missense,intron,missense	SCN5A	NM_000335.4,NM_001099404.1,NM_001099405.1,NM_001160160.1,NM_001160161.1,NM_198056.2	98,98,98,98,,98	0,1,6222	AA,AG,GG		0.0,0.0247,0.0080	,,,,,	1089/2016,1090/2017,1090/1999,1089/1984,,1090/2017	38620946	1,12445	2025	4198	6223	SO:0001583	missense	6331	exon18			GAATCCGGAGGGG	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.3269C>T	3.37:g.38620946G>A	ENSP00000328968:p.Pro1090Leu	54	0	0		66	19	0.287879	NM_198056	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Missense_Mutation	SNP	ENST00000333535.4	37	CCDS46796.1	12	0.005494505494505495	0	0.0	0	0.0	12	0.02097902097902098	0	0.0	G	4.704	0.130956	0.08981	2.47E-4	0.0	ENSG00000183873	ENST00000414099;ENST00000423572;ENST00000413689;ENST00000443581;ENST00000425664;ENST00000333535;ENST00000455624	D;D;D;D;D;D;D	0.95690	-3.68;-3.72;-3.7;-3.72;-3.68;-3.7;-3.78	4.3	-0.553	0.11815	Sodium ion transport-associated (1);	1.922100	0.02137	N	0.056824	D	0.86932	0.6052	L	0.53249	1.67	0.09310	N	1	B;B;B;B;B;B	0.21452	0.056;0.046;0.056;0.056;0.031;0.046	B;B;B;B;B;B	0.19946	0.027;0.024;0.027;0.027;0.014;0.016	T	0.74940	-0.3493	10	0.40728	T	0.16	.	0.7669	0.01016	0.1995:0.1546:0.3682:0.2777	rs1805125	1089;1090;1090;1090;1089;1090	E9PHB6;Q14524-6;E9PG18;Q14524;Q14524-2;E9PEK2	.;.;.;SCN5A_HUMAN;.;.	L	1090;1089;1090;1089;1090;1090;1089	ENSP00000398962:P1090L;ENSP00000398266:P1089L;ENSP00000410257:P1090L;ENSP00000397915:P1089L;ENSP00000416634:P1090L;ENSP00000328968:P1090L;ENSP00000399524:P1089L	ENSP00000328968:P1090L	P	-	2	0	SCN5A	38595950	0.020000	0.18652	0.007000	0.13788	0.179000	0.23085	-0.113000	0.10774	-0.096000	0.12329	-0.123000	0.14984	CCG	G|0.994;A|0.006	0.006	strong		0.657	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056		A	38620946	G	A	38620946	3	1	48	1	0	0	0	0	1	0	0	0	13937	1116	39	1	2825	1	SCN5A	3	38620946	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10		38620946	159401484	41	15917											
ULK4	54986	hgsc.bcm.edu	37	chr3	41954353	41954353	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ctgctccagcaaaagctttcTtccaaaatgaatgctgcagt	12	11	7	11	0	1	1	0	1	1	0	3	1	3	1	2	0	5	5	2	0	5	2			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr3:41954353T>C	ENST00000301831.4	-	9	1304	c.842A>G	c.(841-843)aAg>aGg	p.K281R	ULK4_ENST00000420927.1_Missense_Mutation_p.K281R	NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	281					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)		AAAAGCTTTCTTCCAAAATGA	0.373																																					p.K281R		Atlas-SNP	.											.	ULK4	150	.	0			c.A842G						PASS	.						91	86	87					3																	41954353		1872	4096	5968	SO:0001583	missense	54986	exon9			GCTTTCTTCCAAA	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.842A>G	3.37:g.41954353T>C	ENSP00000301831:p.Lys281Arg	72	0	0		88	24	0.272727	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	.	.	.	.	.	.	.	.	.	.	T	9.925	1.213261	0.22289	.	.	ENSG00000168038	ENST00000301831;ENST00000420927	T;T	0.74106	-0.81;1.87	5.17	3.97	0.46021	Protein kinase-like domain (1);	0.592998	0.19166	N	0.121075	T	0.65984	0.2744	L	0.55103	1.725	0.80722	D	1	B;B	0.16396	0.017;0.007	B;B	0.12156	0.007;0.007	T	0.57888	-0.7733	10	0.29301	T	0.29	.	7.7383	0.28827	0.0:0.1693:0.0:0.8307	.	281;281	B4E2M4;Q96C45	.;ULK4_HUMAN	R	281	ENSP00000301831:K281R;ENSP00000412187:K281R	ENSP00000301831:K281R	K	-	2	0	ULK4	41929357	1.000000	0.71417	0.858000	0.33744	0.931000	0.56810	2.876000	0.48498	0.784000	0.33661	0.533000	0.62120	AAG	.	.	none		0.373	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989		C	41954353	T	C	41954353	3	2	48	1	0	0	0	0	1	0	0	0	16993	1609	56	3	3101	3	ULK4	3	41954353	Missense_Mutation	SNP	T	TCGA-VB-A8QN-01A-11D-A382-10	3333407	41954353	156068077	42	15918											
CAMP	820	hgsc.bcm.edu	37	chr3	48265112	48265112	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	caggtcctcagctacaaggaAgctgtgcttcgtgctataga	10	10	11	10	1	1	1	1	0	0	1	3	2	2	2	1	2	5	4	1	2	5	4			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr3:48265112A>G	ENST00000576243.1	+	1	251	c.111A>G	c.(109-111)gaA>gaG	p.E37E	CAMP_ENST00000296435.2_Silent_p.E40E			P49913	CAMP_HUMAN	cathelicidin antimicrobial peptide	37					antibacterial humoral response (GO:0019731)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to peptidoglycan (GO:0071224)|cellular response to tumor necrosis factor (GO:0071356)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|killing by host of symbiont cells (GO:0051873)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of growth of symbiont on or near host surface (GO:0044140)|phagosome maturation (GO:0090382)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein phosphorylation (GO:0001934)	cell projection (GO:0042995)|cell wall (GO:0005618)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|specific granule (GO:0042581)				endometrium(2)|large_intestine(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6				BRCA - Breast invasive adenocarcinoma(193;0.000614)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		GCTACAAGGAAGCTGTGCTTC	0.612																																					p.E40E		Atlas-SNP	.											.	CAMP	12	.	0			c.A120G						PASS	.						96	78	84					3																	48265112		2203	4300	6503	SO:0001819	synonymous_variant	820	exon1			CAAGGAAGCTGTG	BC055089	CCDS2762.1, CCDS2762.2	3p21.3	2014-01-30			ENSG00000164047	ENSG00000164047		"Endogenous ligands"	1472	protein-coding gene	gene with protein product		600474				7624374	Standard	NM_004345		Approved	CAP18, FALL39, FALL-39, LL37	uc003csj.3	P49913	OTTHUMG00000133526	ENST00000576243.1:c.111A>G	3.37:g.48265112A>G		65	0	0		78	18	0.230769	NM_004345	Q71SN9	Silent	SNP	ENST00000576243.1	37																																																																																				.	.	none		0.612	CAMP-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_004345		G	48265112	A	G	48265112	2	3	48	1	0	0	0	0	0	0	0	1	2612	69	3	3		3	CAMP	3	48265112	Silent	SNP	A	TCGA-VB-A8QN-01A-11D-A382-10	6310759	48265112	149757318	43	15919											
EPHA3	2042	hgsc.bcm.edu	37	chr3	89480468	89480468	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tttctgatttcggactttcgCgtgtcctggaggatgaccca	6	14	11	10	3	1	2	0	2	1	0	4	5	2	5	2	3	0	0	2	3	0	3			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr3:89480468C>T	ENST00000336596.2	+	13	2530	c.2305C>T	c.(2305-2307)Cgt>Tgt	p.R769C	EPHA3_ENST00000494014.1_Missense_Mutation_p.R769C	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	769	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)		CGGACTTTCGCGTGTCCTGGA	0.428										TSP Lung(6;0.00050)																											p.R769C		Atlas-SNP	.											EPHA3,colon,carcinoma,-1,5	EPHA3	501	5	0			c.C2305T						PASS	.						129	122	124					3																	89480468		2203	4300	6503	SO:0001583	missense	2042	exon13			CTTTCGCGTGTCC	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.2305C>T	3.37:g.89480468C>T	ENSP00000337451:p.Arg769Cys	93	0	0		94	23	0.244681	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	C	16.54	3.152892	0.57259	.	.	ENSG00000044524	ENST00000336596;ENST00000494014	D;D	0.85484	-1.99;-1.99	5.33	4.4	0.53042	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	0.93864	0.8037	M	0.92459	3.31	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.94943	0.8093	9	.	.	.	.	15.9138	0.79496	0.1354:0.8646:0.0:0.0	.	769	P29320	EPHA3_HUMAN	C	769	ENSP00000337451:R769C;ENSP00000419190:R769C	.	R	+	1	0	EPHA3	89563158	0.992000	0.36948	0.994000	0.49952	0.272000	0.26649	3.027000	0.49697	2.648000	0.89879	0.585000	0.79938	CGT	.	.	none		0.428	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233		T	89480468	C	T	89480468	3	4	48	1	0	0	0	0	1	0	0	0	5170	768	27	1	2381	1	EPHA3	3	89480468	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	41215356	89480468	108541962	44	15920											
EPHA6	285220	hgsc.bcm.edu	37	chr3	97466293	97466293	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	agagtcccctggtgaagttcCggaatatcctttgtttgtca	8	14	10	9	1	1	2	1	1	0	1	4	3	4	3	4	2	0	2	4	2	3	4			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr3:97466293C>T	ENST00000389672.5	+	17	3193	c.3155C>T	c.(3154-3156)cCg>cTg	p.P1052L		NM_001080448.2	NP_001073917.2	Q9UF33	EPHA6_HUMAN	EPH receptor A6	958						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						GGTGAAGTTCCGGAATATCCT	0.393																																					p.P1052L		Atlas-SNP	.											.	EPHA6	439	.	0			c.C3155T						PASS	.						80	72	75					3																	97466293		1838	4102	5940	SO:0001583	missense	285220	exon17			AAGTTCCGGAATA	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.3155C>T	3.37:g.97466293C>T	ENSP00000374323:p.Pro1052Leu	99	0	0		123	19	0.154472	NM_001080448	D6RAL5	Missense_Mutation	SNP	ENST00000389672.5	37	CCDS46876.1	.	.	.	.	.	.	.	.	.	.	C	13.90	2.375336	0.42105	.	.	ENSG00000080224	ENST00000389672	T	0.74737	-0.87	5.39	5.39	0.77823	.	.	.	.	.	T	0.75561	0.3866	N	0.25485	0.75	0.80722	D	1	.	.	.	.	.	.	T	0.77755	-0.2469	7	0.66056	D	0.02	.	19.5176	0.95170	0.0:1.0:0.0:0.0	.	.	.	.	L	1052	ENSP00000374323:P1052L	ENSP00000374323:P1052L	P	+	2	0	EPHA6	98948983	0.119000	0.22226	0.891000	0.34965	0.612000	0.37316	2.873000	0.48475	2.688000	0.91661	0.585000	0.79938	CCG	.	.	none		0.393	EPHA6-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353845.3	NM_001080448		T	97466293	C	T	97466293	3	4	48	1	0	0	0	0	1	0	0	0	5173	652	23	1	3338	1	EPHA6	3	97466293	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	7985825	97466293	100556137	45	15921											
ZNF80	7634	hgsc.bcm.edu	37	chr3	113955390	113955390	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	agtgtgaatcttcatgtgccGggttaaggaagagttgtagt	10	13	14	4	1	2	2	1	1	1	1	2	3	2	3	1	2	1	3	1	2	4	4			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr3:113955390G>A	ENST00000482457.2	-	1	1035	c.532C>T	c.(532-534)Cgg>Tgg	p.R178W	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	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)			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)				TTCATGTGCCGGGTTAAGGAA	0.478																																					p.R178W	GBM(23;986 1114 21716)	Atlas-SNP	.											ZNF80,colon,carcinoma,+1,1	ZNF80	75	1	0			c.C532T						PASS	.						122	125	124					3																	113955390		2203	4300	6503	SO:0001583	missense	7634	exon1			TGTGCCGGGTTAA	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.532C>T	3.37:g.113955390G>A	ENSP00000417192:p.Arg178Trp	51	0	0		71	15	0.211268	NM_007136	Q6NSW4|Q6NT14	Missense_Mutation	SNP	ENST00000482457.2	37	CCDS2979.1	.	.	.	.	.	.	.	.	.	.	G	16.87	3.243323	0.58995	.	.	ENSG00000174255	ENST00000482457	T	0.26660	1.72	2.81	0.881	0.19166	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.43809	0.1264	M	0.76574	2.34	0.09310	N	1	D	0.89917	1.0	D	0.71414	0.973	T	0.18587	-1.0332	9	0.72032	D	0.01	.	5.0015	0.14266	0.0:0.2352:0.3717:0.3931	.	178	P51504	ZNF80_HUMAN	W	178	ENSP00000417192:R178W	ENSP00000309812:R178W	R	-	1	2	ZNF80	115438080	0.000000	0.05858	0.000000	0.03702	0.781000	0.44180	-5.966000	0.00088	0.205000	0.20568	-0.314000	0.08810	CGG	.	.	none		0.478	ZNF80-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354696.2	NM_007136		A	113955390	G	A	113955390	3	1	48	1	0	0	0	0	1	0	0	0	18183	1115	39	1	293	1	ZNF80	3	113955390	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	16489097	113955390	84067040	46	15922											
KALRN	8997	hgsc.bcm.edu	37	chr3	124165041	124165041	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gctcctgcagagggagaatcGcgtgctgcatttctggacct	7	10	13	11	2	1	2	0	0	1	2	3	4	2	3	2	2	3	4	2	2	1	1	rs375081975		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr3:124165041G>A	ENST00000240874.3	+	20	3498	c.3341G>A	c.(3340-3342)cGc>cAc	p.R1114H	KALRN_ENST00000360013.3_Missense_Mutation_p.R1114H|KALRN_ENST00000460856.1_Missense_Mutation_p.R1105H	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1114					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						AGGGAGAATCGCGTGCTGCAT	0.557																																					p.R1114H		Atlas-SNP	.											.	KALRN	556	.	0			c.G3341A						PASS	.	G	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	109	99	102		3341,3341	5.2	0.8	3		102	0,8600		0,0,4300	no	missense,missense	KALRN	NM_001024660.3,NM_003947.4	29,29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	1114/2987,1114/1664	124165041	1,13005	2203	4300	6503	SO:0001583	missense	8997	exon20			AGAATCGCGTGCT	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.3341G>A	3.37:g.124165041G>A	ENSP00000240874:p.Arg1114His	61	0	0		59	10	0.169492	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Missense_Mutation	SNP	ENST00000240874.3	37	CCDS3027.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	34|34	5.325430|5.325430	0.95708|0.95708	2.27E-4|2.27E-4	0.0|0.0	ENSG00000160145|ENSG00000160145	ENST00000354186|ENST00000460856;ENST00000240874;ENST00000360013	.|T;T;T	.|0.42131	.|0.98;0.98;0.98	5.22|5.22	5.22|5.22	0.72569|0.72569	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.61022|0.61022	0.2314|0.2314	L|L	0.54323|0.54323	1.7|1.7	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;0.999;0.999;1.0	.|D;D;D;D	.|0.91635	.|0.999;0.925;0.987;0.999	T|T	0.54873|0.54873	-0.8228|-0.8228	5|10	.|0.33940	.|T	.|0.23	.|.	18.9721|18.9721	0.92719|0.92719	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1105;460;1114;1114	.|C9IZQ6;F2Z3Q6;O60229;O60229-2	.|.;.;KALRN_HUMAN;.	T|H	1083|1105;1114;1114	.|ENSP00000418611:R1105H;ENSP00000240874:R1114H;ENSP00000353109:R1114H	.|ENSP00000240874:R1114H	A|R	+|+	1|2	0|0	KALRN|KALRN	125647731|125647731	1.000000|1.000000	0.71417|0.71417	0.839000|0.839000	0.33178|0.33178	0.945000|0.945000	0.59286|0.59286	9.611000|9.611000	0.98342|0.98342	2.721000|2.721000	0.93114|0.93114	0.561000|0.561000	0.74099|0.74099	GCG|CGC	.	.	weak		0.557	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		A	124165041	G	A	124165041	3	1	48	1	0	0	0	0	1	0	0	0	7984	1087	38	1	3419	1	KALRN	3	124165041	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	10209651	124165041	73857389	47	15923											
TFDP2	7029	hgsc.bcm.edu	37	chr3	141688919	141688921	+	In_Frame_Del	DEL	AGG	AGG	-																															atctcggtatctttacctgtAggagaagttcttgcagctgg																										TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr3:141688919_141688921delAGG	ENST00000489671.1	-	9	1156_1158	c.726_728delCCT	c.(724-729)ctccta>cta	p.242_243LL>L	TFDP2_ENST00000486111.1_In_Frame_Del_p.182_183LL>L|TFDP2_ENST00000310282.6_In_Frame_Del_p.182_183LL>L|TFDP2_ENST00000479040.1_In_Frame_Del_p.181_182LL>L|TFDP2_ENST00000495310.1_In_Frame_Del_p.145_146LL>L|TFDP2_ENST00000499676.2_In_Frame_Del_p.182_183LL>L|TFDP2_ENST00000317104.7_In_Frame_Del_p.166_167LL>L|TFDP2_ENST00000397991.4_In_Frame_Del_p.214_215LL>L|TFDP2_ENST00000467072.1_In_Frame_Del_p.182_183LL>L|TFDP2_ENST00000477292.1_In_Frame_Del_p.106_107LL>L			Q14188	TFDP2_HUMAN	transcription factor Dp-2 (E2F dimerization partner 2)	242	DCB1.|Dimerization. {ECO:0000255}.				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						CTTTACCTGTAGGAGAAGTTCTT	0.429																																					p.243_243del		Pindel,Atlas-Indel	.											.	TFDP2	44	.	0			c.727_729del						PASS	.																																			SO:0001651	inframe_deletion	7029	exon9			.	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.726_728delCCT	3.37:g.141688919_141688921delAGG	ENSP00000420616:p.Leu243del	164	0	.		165	31	0.188	NM_001178139	B7Z8C8|B7Z8L5|D3DNG1|E9PFC3|F8WAI2|Q13331|Q14187|Q6R754|Q8WU88|Q9UG28	In_Frame_Del	DEL	ENST00000489671.1	37	CCDS54650.1																																																																																			.	.	none		0.429	TFDP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353294.4	NM_006286		-	141688921	AGG	-	141688919	7	5	48	1	0	1	0	1	0	0	0	0	15813	420	15	0	632	0	TFDP2	3	141688919	In_Frame_Del	DEL	AGG	TCGA-VB-A8QN-01A-11D-A382-10	17523878	141688919	56333511	48	15924											
PAQR9	344838	hgsc.bcm.edu	37	chr3	142681479	142681479	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gaacgggtaggtacaccagtCggtacggctcttgcagcagg	9	7	15	10	3	1	0	0	0	1	0	2	1	1	0	1	5	5	6	1	5	4	4			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr3:142681479C>A	ENST00000340634.3	-	1	699	c.700G>T	c.(700-702)Gac>Tac	p.D234Y	RP11-372E1.6_ENST00000607937.1_RNA|RP11-372E1.6_ENST00000598787.1_RNA|RP11-372E1.6_ENST00000493825.1_RNA|RP11-372E1.6_ENST00000478823.1_RNA|RP11-372E1.6_ENST00000593321.1_RNA|RP11-372E1.6_ENST00000598139.1_RNA|RP11-372E1.6_ENST00000594095.1_RNA|RP11-372E1.6_ENST00000497652.1_RNA|RP11-372E1.6_ENST00000608686.1_RNA|RP11-372E1.6_ENST00000595248.1_RNA|RP11-372E1.6_ENST00000595774.1_RNA|RP11-372E1.6_ENST00000608349.1_RNA	NM_198504.2	NP_940906.1	Q6ZVX9	PAQR9_HUMAN	progestin and adipoQ receptor family member IX	234						integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			endometrium(2)|large_intestine(7)|lung(12)|prostate(1)	22						GTACACCAGTCGGTACGGCTC	0.657																																					p.D234Y		Atlas-SNP	.											.	PAQR9	57	.	0			c.G700T						PASS	.						63	59	60					3																	142681479		2203	4300	6503	SO:0001583	missense	344838	exon1			ACCAGTCGGTACG	AY424287	CCDS3128.1	3q23	2008-05-02			ENSG00000188582	ENSG00000188582			30131	protein-coding gene	gene with protein product		614580					Standard	NM_198504		Approved	FLJ41938	uc003evg.3	Q6ZVX9	OTTHUMG00000159313	ENST00000340634.3:c.700G>T	3.37:g.142681479C>A	ENSP00000341564:p.Asp234Tyr	58	0	0		79	25	0.316456	NM_198504	Q147T6	Missense_Mutation	SNP	ENST00000340634.3	37	CCDS3128.1	.	.	.	.	.	.	.	.	.	.	C	14.65	2.599051	0.46318	.	.	ENSG00000188582	ENST00000340634	T	0.22945	1.93	5.22	5.22	0.72569	.	0.297111	0.29745	N	0.011320	T	0.15955	0.0384	N	0.04508	-0.205	0.21499	N	0.99967	B	0.14805	0.011	B	0.13407	0.009	T	0.23797	-1.0178	10	0.51188	T	0.08	-30.7356	19.1774	0.93607	0.0:1.0:0.0:0.0	.	234	Q6ZVX9	PAQR9_HUMAN	Y	234	ENSP00000341564:D234Y	ENSP00000341564:D234Y	D	-	1	0	PAQR9	144164169	0.989000	0.36119	0.990000	0.47175	0.896000	0.52359	2.616000	0.46376	2.595000	0.87683	0.655000	0.94253	GAC	.	.	none		0.657	PAQR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354538.1	NM_198504		A	142681479	C	A	142681479	3	1	48	1	0	0	0	0	1	0	0	0	11451	884	31	4	437	4	PAQR9	3	142681479	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	992560	142681479	55340951	49	15925											
GPR149	344758	hgsc.bcm.edu	37	chr3	154139035	154139035	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gtaatatcagtatttgtgcaTttgttgatgcctctttgtgt	7	20	9	5	0	2	1	1	1	1	0	2	1	2	1	1	0	2	4	1	0	3	7			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr3:154139035T>C	ENST00000389740.2	-	3	1515	c.1416A>G	c.(1414-1416)aaA>aaG	p.K472K		NM_001038705.1	NP_001033794.1	Q86SP6	GP149_HUMAN	G protein-coupled receptor 149	472					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)			TATTTGTGCATTTGTTGATGC	0.398																																					p.K472K		Atlas-SNP	.											.	GPR149	134	.	0			c.A1416G						PASS	.						303	289	293					3																	154139035		1965	4147	6112	SO:0001819	synonymous_variant	344758	exon3			TGTGCATTTGTTG	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.1416A>G	3.37:g.154139035T>C		240	0	0		251	66	0.262948	NM_001038705		Silent	SNP	ENST00000389740.2	37	CCDS43162.1																																																																																			.	.	none		0.398	GPR149-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353430.1	XM_293580		C	154139035	T	C	154139035	2	2	48	1	0	0	0	0	0	0	0	1	6662	1490	52	3		3	GPR149	3	154139035	Silent	SNP	T	TCGA-VB-A8QN-01A-11D-A382-10	11457556	154139035	43883395	50	15926											
C3orf59	151963	hgsc.bcm.edu	37	chr3	192516412	192516412	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gccttgacatgctcaatggcGgtgcgcaagtgctctgccgg	6	9	14	12	3	2	1	1	1	1	0	2	1	2	1	2	3	4	3	2	3	2	1	rs138837641	byFrequency	TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr3:192516412G>A	ENST00000392452.2	-	2	1559	c.1239C>T	c.(1237-1239)acC>acT	p.T413T		NM_178496.3	NP_848591.2	Q8IYB1	M21D2_HUMAN	Mab-21 domain containing 2	413							protein complex binding (GO:0032403)			endometrium(3)|kidney(1)|large_intestine(4)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)	31						GCTCAATGGCGGTGCGCAAGT	0.612													G|||	2	0.000399361	0.0008	0.0	5008	,	,		18319	0.001		0.0	False		,,,				2504	0.0				p.T413T		Atlas-SNP	.											MB21D2,NS,carcinoma,0,1	MB21D2	75	1	0			c.C1239T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	53	50	51		1239	-10.5	0.1	3	dbSNP_134	51	0,8600		0,0,4300	no	coding-synonymous	MB21D2	NM_178496.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		413/492	192516412	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	151963	exon2			AATGGCGGTGCGC	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.1239C>T	3.37:g.192516412G>A		62	0	0		59	21	0.355932	NM_178496	Q86VD8	Silent	SNP	ENST00000392452.2	37	CCDS3302.2																																																																																			G|1.000;A|0.000	0.000	strong		0.612	MB21D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341543.1	NM_178496		A	192516412	G	A	192516412	2	1	48	1	0	0	0	0	0	0	0	1	2239	1103	39	1		1	C3orf59	3	192516412	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	38377377	192516412	5506018	51	15927											
RGS12	6002	hgsc.bcm.edu	37	chr4	3418713	3418713	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gtaccaggaatgcatcctggCggaagtggagggccgtgcac	9	6	16	10	2	0	0	0	0	0	0	1	3	1	3	3	5	3	3	3	5	3	1			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr4:3418713C>T	ENST00000344733.5	+	8	3405	c.2501C>T	c.(2500-2502)gCg>gTg	p.A834V	RGS12_ENST00000382788.3_Missense_Mutation_p.A834V|RGS12_ENST00000338806.4_Missense_Mutation_p.A186V|RGS12_ENST00000538395.1_Missense_Mutation_p.A176V|RGS12_ENST00000508158.1_3'UTR|RGS12_ENST00000336727.3_Missense_Mutation_p.A834V|RGS12_ENST00000306648.7_Missense_Mutation_p.A232V|RGS12_ENST00000543385.1_3'UTR	NM_198229.2	NP_937872.1	O14924	RGS12_HUMAN	regulator of G-protein signaling 12	834					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)		TGCATCCTGGCGGAAGTGGAG	0.582																																					p.A834V		Atlas-SNP	.											RGS12,NS,carcinoma,-1,2	RGS12	128	2	0			c.C2501T						PASS	.						63	68	66					4																	3418713		2203	4300	6503	SO:0001583	missense	6002	exon8			TCCTGGCGGAAGT	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.2501C>T	4.37:g.3418713C>T	ENSP00000339381:p.Ala834Val	103	0	0		113	32	0.283186	NM_002926	B1AQ30|B1AQ31|B1AQ32|B7Z764|E7EMN9|O14922|O14923|O43510|O75338|Q147X0|Q8WX95	Missense_Mutation	SNP	ENST00000344733.5	37	CCDS3366.1	.	.	.	.	.	.	.	.	.	.	C	25.0	4.595185	0.86953	.	.	ENSG00000159788	ENST00000344733;ENST00000336727;ENST00000382788;ENST00000306648;ENST00000338806;ENST00000538395	T;T;T;T;T;T	0.02258	4.37;4.37;4.37;4.37;4.37;4.37	4.54	4.54	0.55810	Regulator of G protein signalling superfamily (1);	0.000000	0.85682	D	0.000000	T	0.13200	0.0320	M	0.82630	2.6	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.76494	0.999;0.998;0.999;0.998;0.999;0.999;0.999;0.987;0.997	P;P;D;P;D;D;D;P;P	0.65773	0.9;0.844;0.936;0.844;0.938;0.938;0.93;0.712;0.902	T	0.00802	-1.1560	10	0.66056	D	0.02	-27.9321	16.6416	0.85128	0.0:1.0:0.0:0.0	.	176;33;176;33;176;186;232;834;834	B7Z764;B3KVS7;B7Z8B8;A8K440;O14924-2;O14924-3;Q8WX95;O14924;O14924-4	.;.;.;.;.;.;.;RGS12_HUMAN;.	V	834;834;834;232;186;176	ENSP00000339381:A834V;ENSP00000338509:A834V;ENSP00000372238:A834V;ENSP00000304459:A232V;ENSP00000342133:A186V;ENSP00000438888:A176V	ENSP00000304459:A232V	A	+	2	0	RGS12	3388511	1.000000	0.71417	0.923000	0.36655	0.346000	0.29079	7.443000	0.80521	2.247000	0.74100	0.609000	0.83330	GCG	.	.	none		0.582	RGS12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206602.1	NM_002926		T	3418713	C	T	3418713	3	4	48	1	0	0	0	0	1	0	0	0	13310	768	27	1	2585	1	RGS12	4	3418713	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10		3418713	187735563	52	15928											
LNX1	84708	hgsc.bcm.edu	37	chr4	54362377	54362377	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttccaagctgctcctcggggCtacttttgttgagaatcaca	8	13	9	11	1	1	1	1	1	0	1	4	2	3	1	2	2	3	4	2	2	3	5			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr4:54362377C>A	ENST00000263925.7	-	6	1477	c.1163G>T	c.(1162-1164)aGc>aTc	p.S388I	LNX1_ENST00000306888.2_Missense_Mutation_p.S292I|LNX1-AS1_ENST00000502373.1_RNA|FIP1L1_ENST00000507166.1_Intron	NM_001126328.2	NP_001119800.1	Q8TBB1	LNX1_HUMAN	ligand of numb-protein X 1, E3 ubiquitin protein ligase	388	PDZ 2. {ECO:0000255|PROSITE- ProRule:PRU00143}.				protein homooligomerization (GO:0051260)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(1)|central_nervous_system(3)|endometrium(3)|large_intestine(11)|lung(6)|ovary(3)|urinary_tract(4)	32	all_neural(26;0.153)		GBM - Glioblastoma multiforme(3;8.2e-46)|LUSC - Lung squamous cell carcinoma(32;0.0134)			CTCCTCGGGGCTACTTTTGTT	0.527																																					p.S388I		Atlas-SNP	.											.	LNX1	139	.	0			c.G1163T						PASS	.						102	99	100					4																	54362377		2203	4300	6503	SO:0001583	missense	84708	exon6			TCGGGGCTACTTT	AF237782	CCDS3492.1, CCDS47057.1	4q12	2013-01-09	2012-02-23	2005-11-04	ENSG00000072201	ENSG00000072201		"RING-type (C3HC4) zinc fingers"	6657	protein-coding gene	gene with protein product		609732	"ligand of numb-protein X", "ligand of numb-protein X 1"	LNX		11521506, 11782429	Standard	NM_032622		Approved	MPDZ, PDZRN2	uc003hag.5	Q8TBB1	OTTHUMG00000102099	ENST00000263925.7:c.1163G>T	4.37:g.54362377C>A	ENSP00000263925:p.Ser388Ile	84	0	0		89	24	0.269663	NM_001126328	Q4W5K7|Q8N4C2|Q96MJ7|Q9BY20	Missense_Mutation	SNP	ENST00000263925.7	37	CCDS47057.1	.	.	.	.	.	.	.	.	.	.	C	12.81	2.049759	0.36181	.	.	ENSG00000072201	ENST00000306888;ENST00000538207;ENST00000263925	T;T	0.32272	1.46;1.46	5.29	3.51	0.40186	PDZ/DHR/GLGF (3);	0.321656	0.41712	D	0.000835	T	0.46776	0.1410	M	0.76170	2.325	0.46774	D	0.999198	D;P	0.53745	0.962;0.696	P;B	0.53146	0.719;0.355	T	0.48445	-0.9035	10	0.38643	T	0.18	.	15.5056	0.75739	0.0:0.7374:0.2626:0.0	.	388;292	Q8TBB1;Q8TBB1-2	LNX1_HUMAN;.	I	292;226;388	ENSP00000302879:S292I;ENSP00000263925:S388I	ENSP00000263925:S388I	S	-	2	0	LNX1	54057134	1.000000	0.71417	0.991000	0.47740	0.492000	0.33523	0.964000	0.29306	0.759000	0.33084	0.561000	0.74099	AGC	.	.	none		0.527	LNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219934.2			A	54362377	C	A	54362377	3	1	48	1	0	0	0	0	1	0	0	0	8874	797	28	4	1047	4	LNX1	4	54362377	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	50943664	54362377	136791899	53	15929											
UGT2B7	7364	hgsc.bcm.edu	37	chr4	69962771	69962771	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	tctcagcttctctcctggctAcacttttgaaaagcatagtg	9	14	7	11	0	2	1	1	1	2	0	5	1	3	1	1	1	3	3	1	1	4	5			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr4:69962771A>G	ENST00000508661.1	+	1	560	c.533A>G	c.(532-534)tAc>tGc	p.Y178C	UGT2B7_ENST00000509763.1_Intron|UGT2B7_ENST00000305231.7_Missense_Mutation_p.Y178C			P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	178					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)	TCTCCTGGCTACACTTTTGAA	0.408																																					p.Y178C		Atlas-SNP	.											.	UGT2B7	79	.	0			c.A533G						PASS	.						126	125	126					4																	69962771		2203	4298	6501	SO:0001583	missense	7364	exon1			CTGGCTACACTTT	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.533A>G	4.37:g.69962771A>G	ENSP00000427659:p.Tyr178Cys	165	0	0		205	48	0.234146	NM_001074	B2R810|Q6GTW0	Missense_Mutation	SNP	ENST00000508661.1	37		.	.	.	.	.	.	.	.	.	.	A	9.009	0.981926	0.18812	.	.	ENSG00000171234	ENST00000305231;ENST00000508661	T;T	0.60548	0.18;0.18	2.54	2.54	0.30619	.	0.423820	0.17969	U	0.155940	T	0.61413	0.2345	L	0.37466	1.105	0.09310	N	1	D;B	0.67145	0.996;0.11	D;B	0.70016	0.967;0.292	T	0.47509	-0.9112	9	.	.	.	.	8.5583	0.33494	1.0:0.0:0.0:0.0	.	178;178	E9PBP8;P16662	.;UD2B7_HUMAN	C	178	ENSP00000304811:Y178C;ENSP00000427659:Y178C	.	Y	+	2	0	UGT2B7	69997360	0.008000	0.16893	0.002000	0.10522	0.005000	0.04900	2.511000	0.45476	1.157000	0.42530	0.260000	0.18958	TAC	.	.	none		0.408	UGT2B7-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000362103.1	NM_001074		G	69962771	A	G	69962771	3	3	48	1	0	0	0	0	1	0	0	0	16977	391	14	3	535	3	UGT2B7	4	69962771	Missense_Mutation	SNP	A	TCGA-VB-A8QN-01A-11D-A382-10	15600394	69962771	121191505	54	15930											
OTUD4	54726	hgsc.bcm.edu	37	chr4	146059393	146059393	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gaactgggcctaagaatggaTtgggtccaaaagatggctgg	12	8	15	6	0	0	2	0	0	0	2	1	4	1	3	2	5	1	1	2	5	5	2			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr4:146059393T>C	ENST00000447906.2	-	21	2721	c.2534A>G	c.(2533-2535)aAt>aGt	p.N845S	OTUD4_ENST00000454497.2_Missense_Mutation_p.N780S|OTUD4_ENST00000455611.2_Intron			Q01804	OTUD4_HUMAN	OTU deubiquitinase 4	845					protein K48-linked deubiquitination (GO:0071108)		poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(180;0.151)					TAAGAATGGATTGGGTCCAAA	0.463																																					p.N780S		Atlas-SNP	.											.	OTUD4	120	.	0			c.A2339G						PASS	.						64	60	61					4																	146059393		2203	4298	6501	SO:0001583	missense	54726	exon21			AATGGATTGGGTC		CCDS3764.1, CCDS47139.1	4q31.21	2014-02-24	2014-02-24		ENSG00000164164	ENSG00000164164		"OTU domain containing"	24949	protein-coding gene	gene with protein product		611744	"OTU domain containing 4"			1475186, 12727813, 19996094	Standard	NM_001102653		Approved	HSHIN1, KIAA1046, DUBA6	uc003ika.4	Q01804	OTTHUMG00000161480	ENST00000447906.2:c.2534A>G	4.37:g.146059393T>C	ENSP00000395487:p.Asn845Ser	152	0	0		140	45	0.321429	NM_001102653	B4DYS4|Q147U2|Q1ZYK1|Q6PG39|Q96MQ5|Q9NT94|Q9UPV6	Missense_Mutation	SNP	ENST00000447906.2	37		.	.	.	.	.	.	.	.	.	.	T	3.667	-0.068360	0.07228	.	.	ENSG00000164164	ENST00000454497;ENST00000447906	T;T	0.30981	1.51;1.51	5.89	-0.53	0.11898	.	0.310609	0.31188	N	0.008087	T	0.15349	0.0370	N	0.17082	0.46	0.21064	N	0.999798	B;B	0.29378	0.243;0.157	B;B	0.26310	0.068;0.031	T	0.26018	-1.0115	10	0.17832	T	0.49	-11.1144	11.9038	0.52699	0.0:0.4566:0.0:0.5433	.	845;844	G3V0I6;Q01804	.;OTUD4_HUMAN	S	780;845	ENSP00000409279:N780S;ENSP00000395487:N845S	ENSP00000395487:N845S	N	-	2	0	OTUD4	146278843	0.782000	0.28689	0.680000	0.29994	0.501000	0.33797	0.126000	0.15769	-0.066000	0.12998	-0.400000	0.06385	AAT	.	.	none		0.463	OTUD4-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000365117.2	NM_017493		C	146059393	T	C	146059393	3	2	48	1	0	0	0	0	1	0	0	0	11323	1493	52	3	814	3	OTUD4	4	146059393	Missense_Mutation	SNP	T	TCGA-VB-A8QN-01A-11D-A382-10	76096622	146059393	45094883	55	15931											
LRAT	9227	hgsc.bcm.edu	37	chr4	155665953	155665953	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccctacagcctgctgtggAacaactgcgagcacttcgtg	8	8	10	15	2	0	0	0	0	0	0	1	2	0	1	3	1	7	2	3	1	3	2			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr4:155665953A>C	ENST00000336356.3	+	2	728	c.475A>C	c.(475-477)Aac>Cac	p.N159H	LRAT_ENST00000507827.1_Missense_Mutation_p.N159H	NM_004744.3	NP_004735.2	O95237	LRAT_HUMAN	lecithin retinol acyltransferase (phosphatidylcholine--retinol O-acyltransferase)	159					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)	CCTGCTGTGGAACAACTGCGA	0.592																																					p.N159H		Atlas-SNP	.											.	LRAT	29	.	0			c.A475C						PASS	.						73	78	76					4																	155665953		2203	4300	6503	SO:0001583	missense	9227	exon2			CTGTGGAACAACT	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.475A>C	4.37:g.155665953A>C	ENSP00000337224:p.Asn159His	51	0	0		35	9	0.257143	NM_004744	A8K983|Q8N716	Missense_Mutation	SNP	ENST00000336356.3	37	CCDS3789.1	.	.	.	.	.	.	.	.	.	.	A	19.03	3.748540	0.69533	.	.	ENSG00000121207	ENST00000507827;ENST00000336356	T;T	0.27402	1.67;1.67	5.5	4.31	0.51392	NC (1);	0.082456	0.85682	D	0.000000	T	0.51295	0.1666	M	0.91510	3.215	0.48975	D	0.999739	P	0.43578	0.811	P	0.49561	0.615	T	0.56589	-0.7954	10	0.42905	T	0.14	-23.6927	11.4728	0.50280	0.9293:0.0:0.0707:0.0	.	159	O95237	LRAT_HUMAN	H	159	ENSP00000426761:N159H;ENSP00000337224:N159H	ENSP00000337224:N159H	N	+	1	0	LRAT	155885403	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	7.228000	0.78079	0.925000	0.37094	-0.462000	0.05337	AAC	.	.	none		0.592	LRAT-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365246.1	NM_004744		C	155665953	A	C	155665953	3	2	48	1	0	0	0	0	1	0	0	0	8939	246	9	5	477	5	LRAT	4	155665953	Missense_Mutation	SNP	A	TCGA-VB-A8QN-01A-11D-A382-10	9606560	155665953	35488323	56	15932											
GHR	2690	hgsc.bcm.edu	37	chr5	42689036	42689036	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ccaagtgccgttcacctgagCgagagactttttcatgccac	9	10	9	13	2	2	2	2	1	0	1	2	4	2	2	4	0	3	1	4	0	1	3	rs121909358		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr5:42689036C>T	ENST00000230882.4	+	4	371	c.181C>T	c.(181-183)Cga>Tga	p.R61*	GHR_ENST00000537449.1_Intron|GHR_ENST00000357703.3_Nonsense_Mutation_p.R39*	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	61					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)	TTCACCTGAGCGAGAGACTTT	0.448																																					p.R68X		Atlas-SNP	.											.	GHR	94	.	0			c.C202T	GRCh37	CM910179	GHR	M	rs121909358	PASS	.						275	254	261					5																	42689036		2203	4300	6503	SO:0001587	stop_gained	2690	exon4			CCTGAGCGAGAGA		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.181C>T	5.37:g.42689036C>T	ENSP00000230882:p.Arg61*	129	0	0		134	31	0.231343	NM_001242399	Q9HCX2	Nonsense_Mutation	SNP	ENST00000230882.4	37	CCDS3940.1	.	.	.	.	.	.	.	.	.	.	C	37	6.363108	0.97507	.	.	ENSG00000112964	ENST00000230882;ENST00000357703;ENST00000356276	.	.	.	5.66	5.66	0.87406	.	0.207702	0.41712	D	0.000835	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.45353	T	0.12	-6.9137	15.027	0.71677	0.1429:0.8571:0.0:0.0	.	.	.	.	X	61;39;61	.	ENSP00000230882:R61X	R	+	1	2	GHR	42724793	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.554000	0.36266	2.657000	0.90304	0.655000	0.94253	CGA	.	.	weak		0.448	GHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211605.2	NM_000163		T	42689036	C	T	42689036	4	4	48	1	0	0	0	0	0	1	0	0	6379	760	27	1	191	1	GHR	5	42689036	Nonsense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10		42689036	138226224	57	15933											
MSH3	4437	hgsc.bcm.edu	37	chr5	79950750	79950750	+	Silent	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcgcccccagcgcccccagcTcccgccttcccgccccagct	3	4	8	26	4	0	0	0	0	0	0	2	0	2	0	9	0	3	2	9	0	0	1	rs144629981|rs3045983|rs1047489	byFrequency	TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr5:79950750T>G	ENST00000265081.6	+	1	284	c.204T>G	c.(202-204)gcT>gcG	p.A68A	DHFR_ENST00000505337.1_5'Flank|DHFR_ENST00000439211.2_5'UTR|DHFR_ENST00000511032.1_5'Flank|DHFR_ENST00000513048.1_5'Flank|DHFR_ENST00000504396.1_5'Flank	NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	68					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)		CGCCCCCAGCTCCCGCCTTCC	0.741								Mismatch excision repair (MMR)																													p.A68A	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											.	MSH3	129	.	0			c.T204G						PASS	.						3	3	3					5																	79950750		1568	3264	4832	SO:0001819	synonymous_variant	4437	exon1			CCCAGCTCCCGCC	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.204T>G	5.37:g.79950750T>G		0	0	.		16	16	1	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Silent	SNP	ENST00000265081.6	37	CCDS34195.1																																																																																			.	.	weak		0.741	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439		G	79950750	T	G	79950750	2	3	48	1	0	0	0	0	0	0	0	1	9880	1538	54	5		5	MSH3	5	79950750	Silent	SNP	T	TCGA-VB-A8QN-01A-11D-A382-10	37261714	79950750	100964510	58	15934											
WDR36	134430	hgsc.bcm.edu	37	chr5	110428002	110428002	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	actttatgtgttgcactgagGgcagtctccggaaacgcgat	9	11	12	9	3	1	1	0	1	1	0	2	3	1	2	1	2	2	3	1	2	2	3			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr5:110428002G>T	ENST00000513710.2	+	1	20	c.16G>T	c.(16-18)Ggc>Tgc	p.G6C	WDR36_ENST00000506538.2_Missense_Mutation_p.G6C|WDR36_ENST00000505303.1_5'Flank|CTC-551A13.2_ENST00000507269.3_RNA			Q8NI36	WDR36_HUMAN	WD repeat domain 36	6					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)		TTGCACTGAGGGCAGTCTCCG	0.592																																					p.G6C		Atlas-SNP	.											.	WDR36	111	.	0			c.G16T						PASS	.						80	85	84					5																	110428002		2202	4300	6502	SO:0001583	missense	134430	exon1			ACTGAGGGCAGTC	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.16G>T	5.37:g.110428002G>T	ENSP00000424628:p.Gly6Cys	78	0	0		83	12	0.144578	NM_139281	A2RUS4|Q68E02|Q8N1Q2	Missense_Mutation	SNP	ENST00000513710.2	37	CCDS4102.1	.	.	.	.	.	.	.	.	.	.	G	12.28	1.890516	0.33348	.	.	ENSG00000134987	ENST00000506538;ENST00000513710	T;T	0.66815	-0.23;-0.23	5.33	-0.223	0.13118	.	2.121900	0.01992	N	0.045560	T	0.44871	0.1314	N	0.08118	0	0.09310	N	0.999995	P	0.35527	0.507	B	0.30105	0.111	T	0.44757	-0.9307	10	0.87932	D	0	5.157	6.0246	0.19648	0.3214:0.128:0.5506:0.0	.	6	Q8NI36	WDR36_HUMAN	C	6	ENSP00000423067:G6C;ENSP00000424628:G6C	ENSP00000423067:G6C	G	+	1	0	WDR36	110455901	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	0.161000	0.16481	-0.142000	0.11354	0.655000	0.94253	GGC	.	.	none		0.592	WDR36-008	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000373504.3	NM_139281		T	110428002	G	T	110428002	3	4	48	1	0	0	0	0	1	0	0	0	17305	1232	43	4	18	4	WDR36	5	110428002	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	30477252	110428002	70487258	59	15935											
KCNN2	3781	hgsc.bcm.edu	37	chr5	113698763	113698763	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggaggaggcggcggcggtggCgggagcgggcacggcagcag	6	1	25	9	6	0	0	0	0	0	0	0	3	0	3	0	10	2	3	0	10	0	0	rs368298090	byFrequency	TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr5:113698763C>T	ENST00000512097.3	+	2	1309	c.291C>T	c.(289-291)ggC>ggT	p.G97G	KCNN2_ENST00000264773.3_Silent_p.G97G			Q9H2S1	KCNN2_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	97	Poly-Gly.				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)	gcggcggtggcgggagcgggc	0.637													C|||	3	0.000599042	0.0	0.0	5008	,	,		12844	0.0		0.0	False		,,,				2504	0.0031				p.G97G		Atlas-SNP	.											.	KCNN2	144	.	0			c.C291T						PASS	.	C		0,4384		0,0,2192	23	24	24		291	-2.4	1	5		24	1,8587		0,1,4293	no	coding-synonymous	KCNN2	NM_021614.2		0,1,6485	TT,TC,CC		0.0116,0.0,0.0077		97/580	113698763	1,12971	2192	4294	6486	SO:0001819	synonymous_variant	3781	exon1			CGGTGGCGGGAGC	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.291C>T	5.37:g.113698763C>T		29	0	0		49	9	0.183673	NM_021614	A6NF94|Q0VFZ4|Q6PJI0|Q6X2Y2	Silent	SNP	ENST00000512097.3	37	CCDS4114.1																																																																																			.	.	weak		0.637	KCNN2-001	KNOWN	not_organism_supported|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250775.2	NM_021614		T	113698763	C	T	113698763	2	4	48	1	0	0	0	0	0	0	0	1	8088	755	27	1		1	KCNN2	5	113698763	Silent	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	3270761	113698763	67216497	60	15936											
PCDHA2	56146	hgsc.bcm.edu	37	chr5	140175767	140175767	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	accttcaagaattactactcGttggtgctggacagcgccct	9	11	9	12	2	1	1	1	0	0	1	2	2	1	2	2	2	4	2	2	2	4	4			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr5:140175767G>A	ENST00000526136.1	+	1	1218	c.1218G>A	c.(1216-1218)tcG>tcA	p.S406S	PCDHA2_ENST00000520672.2_Silent_p.S406S|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000378132.1_Silent_p.S406S|PCDHA1_ENST00000394633.3_Intron	NM_018905.2	NP_061728.1	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2	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(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)			ATTACTACTCGTTGGTGCTGG	0.622																																					p.S406S		Atlas-SNP	.											.	PCDHA2	404	.	0			c.G1218A						PASS	.						157	139	145					5																	140175767		2203	4300	6503	SO:0001819	synonymous_variant	56146	exon1			CTACTCGTTGGTG	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.1218G>A	5.37:g.140175767G>A		79	0	0		81	20	0.246914	NM_031495	O75287|Q9BTV3	Silent	SNP	ENST00000526136.1	37	CCDS54914.1																																																																																			.	.	none		0.622	PCDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372877.3	NM_018905		A	140175767	G	A	140175767	2	1	48	1	0	0	0	0	0	0	0	1	11533	1132	40	1		1	PCDHA2	5	140175767	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	26477004	140175767	40739493	61	15937											
PCDHA9	9752	hgsc.bcm.edu	37	chr5	140229661	140229661	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cagccgttggaccacgaggaGctggagctgctacagttcca	9	7	13	12	2	0	0	0	0	0	0	1	4	1	3	3	3	5	5	3	3	1	3			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr5:140229661G>C	ENST00000532602.1	+	1	2614	c.1581G>C	c.(1579-1581)gaG>gaC	p.E527D	PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA9_ENST00000378122.3_Missense_Mutation_p.E527D|PCDHA6_ENST00000529310.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA3_ENST00000522353.2_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	527	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(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)			ACCACGAGGAGCTGGAGCTGC	0.677																																					p.E527D	Melanoma(55;1800 1972 14909)	Atlas-SNP	.											.	PCDHA9	373	.	0			c.G1581C						PASS	.						61	69	66					5																	140229661		2194	4269	6463	SO:0001583	missense	9752	exon1			CGAGGAGCTGGAG	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.1581G>C	5.37:g.140229661G>C	ENSP00000436042:p.Glu527Asp	76	0	0		74	24	0.324324	NM_031857	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	37	CCDS54920.1	.	.	.	.	.	.	.	.	.	.	G	17.94	3.511932	0.64522	.	.	ENSG00000204961	ENST00000532602;ENST00000378122	T;T	0.53857	0.6;0.6	3.56	3.56	0.40772	Cadherin (5);Cadherin-like (1);	0.265650	0.18860	U	0.129149	T	0.62319	0.2418	L	0.46567	1.45	0.21105	N	0.99979	B;D	0.71674	0.383;0.998	B;D	0.77557	0.151;0.99	T	0.50566	-0.8813	10	0.87932	D	0	.	9.3017	0.37849	0.1035:0.0:0.8965:0.0	.	527;527	Q9Y5H5;Q9Y5H5-2	PCDA9_HUMAN;.	D	527	ENSP00000436042:E527D;ENSP00000367362:E527D	ENSP00000367362:E527D	E	+	3	2	PCDHA9	140209845	0.000000	0.05858	1.000000	0.80357	0.957000	0.61999	0.283000	0.18846	1.973000	0.57446	0.306000	0.20318	GAG	.	.	none		0.677	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857		C	140229661	G	C	140229661	3	2	48	1	0	0	0	0	1	0	0	0	11540	962	34	4	1583	4	PCDHA9	5	140229661	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	53894	140229661	40685599	62	15938											
PCDHA11	56138	hgsc.bcm.edu	37	chr5	140251070	140251070	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	caggagccagggtcaaatcaCcccggacaggtgagttttct	10	8	12	11	1	3	1	2	1	1	0	3	3	3	3	3	4	1	1	3	4	1	2			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr5:140251070C>T	ENST00000398640.2	+	1	2382	c.2382C>T	c.(2380-2382)caC>caT	p.H794H	PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA8_ENST00000531613.1_Intron	NM_018902.3	NP_061725.1	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11	794	6 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)			breast(1)|lung(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTCAAATCACCCCGGACAGG	0.453																																					p.H794H		Atlas-SNP	.											.	PCDHA11	209	.	0			c.C2382T						PASS	.						14	17	16					5																	140251070		2169	4291	6460	SO:0001819	synonymous_variant	56138	exon1			AAATCACCCCGGA	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.2382C>T	5.37:g.140251070C>T		221	0	0		247	62	0.251012	NM_018902	B2RN58|O75279	Silent	SNP	ENST00000398640.2	37	CCDS47284.1																																																																																			.	.	none		0.453	PCDHA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372885.2	NM_018902		T	140251070	C	T	140251070	2	4	48	1	0	0	0	0	0	0	0	1	11530	506	18	2		2	PCDHA11	5	140251070	Silent	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	21409	140251070	40664190	63	15939											
PCDHGA7	56108	hgsc.bcm.edu	37	chr5	140764414	140764414	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tggtggccgtccaggaccacGgtcagcctcctctgtcagcc	5	8	12	16	2	3	0	2	0	1	0	5	1	5	1	6	4	2	0	6	4	0	0			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr5:140764414G>A	ENST00000518325.1	+	1	1948	c.1948G>A	c.(1948-1950)Ggt>Agt	p.G650S	PCDHGA3_ENST00000253812.6_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA5_ENST00000518069.1_Intron	NM_018920.2	NP_061743.1	Q9Y5G6	PCDG7_HUMAN	protocadherin gamma subfamily A, 7	650	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)			CCAGGACCACGGTCAGCCTCC	0.672																																					p.G650S		Atlas-SNP	.											PCDHGA7,NS,carcinoma,0,1	PCDHGA7	130	1	0			c.G1948A						PASS	.						35	42	40					5																	140764414		2198	4298	6496	SO:0001583	missense	56108	exon1			GACCACGGTCAGC	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.1948G>A	5.37:g.140764414G>A	ENSP00000430024:p.Gly650Ser	57	0	0		81	23	0.283951	NM_032087	B2RN87|Q9Y5D0	Missense_Mutation	SNP	ENST00000518325.1	37	CCDS54927.1	.	.	.	.	.	.	.	.	.	.	.	23.0	4.362272	0.82353	.	.	ENSG00000253537	ENST00000518325	T	0.64260	-0.09	4.9	4.9	0.64082	Cadherin (4);Cadherin-like (1);	.	.	.	.	D	0.85932	0.5812	H	0.96301	3.8	0.42286	D	0.992115	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.994	D	0.90975	0.4823	9	0.87932	D	0	.	18.0791	0.89437	0.0:0.0:1.0:0.0	.	650;650	Q9Y5G6;Q9Y5G6-2	PCDG7_HUMAN;.	S	650	ENSP00000430024:G650S	ENSP00000430024:G650S	G	+	1	0	PCDHGA7	140744598	1.000000	0.71417	0.726000	0.30738	0.831000	0.47069	7.575000	0.82447	2.413000	0.81919	0.655000	0.94253	GGT	.	.	none		0.672	PCDHGA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374744.1	NM_018920		A	140764414	G	A	140764414	3	1	48	1	0	0	0	0	1	0	0	0	11568	1116	39	1	1950	1	PCDHGA7	5	140764414	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	513344	140764414	40150846	64	15940											
GABRA1	2554	hgsc.bcm.edu	37	chr5	161317976	161317976	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctttgttattcaaacataccTgccatgcataatgacagtga	13	13	6	9	0	1	2	1	2	0	0	1	2	1	2	2	0	4	2	2	0	4	5			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr5:161317976T>A	ENST00000428797.2	+	9	1131	c.776T>A	c.(775-777)cTg>cAg	p.L259Q	GABRA1_ENST00000444819.1_Missense_Mutation_p.L259Q|GABRA1_ENST00000023897.6_Missense_Mutation_p.L259Q|GABRA1_ENST00000420560.1_Missense_Mutation_p.L259Q|GABRA1_ENST00000393943.4_Missense_Mutation_p.L259Q|GABRA1_ENST00000437025.2_Missense_Mutation_p.L259Q	NM_001127643.1	NP_001121115.1	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 1	259					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)	CAAACATACCTGCCATGCATA	0.398																																					p.L259Q		Atlas-SNP	.											.	GABRA1	132	.	0			c.T776A						PASS	.						139	132	134					5																	161317976		2203	4300	6503	SO:0001583	missense	2554	exon9			CATACCTGCCATG		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.776T>A	5.37:g.161317976T>A	ENSP00000393097:p.Leu259Gln	88	0	0		101	18	0.178218	NM_001127643	D3DQK6|Q8N629	Missense_Mutation	SNP	ENST00000428797.2	37	CCDS4357.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.341635	0.81911	.	.	ENSG00000022355	ENST00000023897;ENST00000428797;ENST00000393943;ENST00000437025;ENST00000420560;ENST00000444819	D;D;D;D;D;D	0.86627	-2.15;-2.15;-2.15;-2.15;-2.15;-2.15	5.52	5.52	0.82312	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.64402	D	0.000002	D	0.92987	0.7768	M	0.75615	2.305	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.93811	0.7110	10	0.87932	D	0	.	15.6517	0.77099	0.0:0.0:0.0:1.0	.	259	P14867	GBRA1_HUMAN	Q	259	ENSP00000023897:L259Q;ENSP00000393097:L259Q;ENSP00000377517:L259Q;ENSP00000415441:L259Q;ENSP00000408041:L259Q;ENSP00000414232:L259Q	ENSP00000023897:L259Q	L	+	2	0	GABRA1	161250554	1.000000	0.71417	1.000000	0.80357	0.590000	0.36582	7.903000	0.87398	2.105000	0.64084	0.528000	0.53228	CTG	.	.	none		0.398	GABRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252702.2	NM_000806.5		A	161317976	T	A	161317976	3	1	48	1	0	0	0	0	1	0	0	0	6168	1580	55	5	802	5	GABRA1	5	161317976	Missense_Mutation	SNP	T	TCGA-VB-A8QN-01A-11D-A382-10	20553562	161317976	19597284	65	15941											
ADAMTS2	9509	hgsc.bcm.edu	37	chr5	178549748	178549748	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cagagcactggccgctcctgGgtgccgttgccacaggttac	6	8	13	14	2	0	1	0	0	0	1	1	1	1	1	4	3	4	4	4	3	1	2			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr5:178549748G>T	ENST00000251582.7	-	20	3086	c.2985C>A	c.(2983-2985)acC>acA	p.T995T		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	995	TSP type-1 4. {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)		GCCGCTCCTGGGTGCCGTTGC	0.682																																					p.T995T		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.C2985A						PASS	.						17	18	18					5																	178549748		2147	4234	6381	SO:0001819	synonymous_variant	9509	exon20			CTCCTGGGTGCCG	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.2985C>A	5.37:g.178549748G>T		55	0	0		79	17	0.21519	NM_014244		Silent	SNP	ENST00000251582.7	37	CCDS4444.1																																																																																			.	.	none		0.682	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244		T	178549748	G	T	178549748	2	4	48	1	0	0	0	0	0	0	0	1	265	1219	43	4		4	ADAMTS2	5	178549748	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	17231772	178549748	2365512	66	15942											
HIST1H1C	3006	hgsc.bcm.edu	37	chr6	26056471	26056471	+	Silent	SNP	C	C	G	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	gcggcagccaacgcttttttCagagcagccagagaaactcc	11	7	10	13	2	1	2	1	0	0	2	2	3	2	2	3	1	5	3	3	1	2	3			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr6:26056471C>G	ENST00000343677.2	-	1	228	c.186G>C	c.(184-186)ctG>ctC	p.L62L		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	62	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				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						ACGCTTTTTTCAGAGCAGCCA	0.567																																					p.L62L		Atlas-SNP	.											.	HIST1H1C	80	.	0			c.G186C						PASS	.						81	90	87					6																	26056471		2203	4300	6503	SO:0001819	synonymous_variant	3006	exon1			TTTTTTCAGAGCA	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.186G>C	6.37:g.26056471C>G		120	0	0		119	36	0.302521	NM_005319	A8K4I2	Silent	SNP	ENST00000343677.2	37	CCDS4577.1																																																																																			.	.	none		0.567	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043372.1	NM_005319		G	26056471	C	G	26056471	2	3	48	1	0	0	0	0	0	0	0	1	7133	813	29	4		4	HIST1H1C	6	26056471	Silent	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10		26056471	145058596	67	15943											
HIST1H1E	3008	hgsc.bcm.edu	37	chr6	26156985	26156985	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	ccaagcctaaggctaaaaagGcaggcgcggccaaggccaag	14	2	13	12	2	0	0	0	0	0	0	0	0	0	0	4	5	1	2	4	5	7	2	rs199659170	byFrequency	TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr6:26156985G>C	ENST00000304218.3	+	1	427	c.367G>C	c.(367-369)Gca>Cca	p.A123P	HIST1H2BD_ENST00000377777.4_5'Flank|HIST1H2BD_ENST00000289316.2_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	123					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						GGCTAAAAAGGCAGGCGCGGC	0.637																																					p.A123P		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.G367C						PASS	.						20	27	25					6																	26156985		2203	4300	6503	SO:0001583	missense	3008	exon1			AAAAAGGCAGGCG	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.367G>C	6.37:g.26156985G>C	ENSP00000307705:p.Ala123Pro	67	0	0		88	24	0.272727	NM_005321	Q4VB25	Missense_Mutation	SNP	ENST00000304218.3	37	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	4.950	0.176497	0.09443	.	.	ENSG00000168298	ENST00000304218	T	0.15487	2.42	5.51	2.52	0.30459	.	0.795350	0.11485	N	0.559313	T	0.02767	0.0083	N	0.19112	0.55	0.31036	N	0.71687	B	0.02656	0.0	B	0.01281	0.0	T	0.40757	-0.9546	10	0.33141	T	0.24	-0.0758	1.85	0.03167	0.1645:0.1346:0.4251:0.2758	.	123	P10412	H14_HUMAN	P	123	ENSP00000307705:A123P	ENSP00000307705:A123P	A	+	1	0	HIST1H1E	26264964	0.000000	0.05858	0.840000	0.33206	0.022000	0.10575	-0.096000	0.11059	0.756000	0.33013	0.561000	0.74099	GCA	G|1.000;A|0.000	.	alt		0.637	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321		C	26156985	G	C	26156985	3	2	48	1	0	0	0	0	1	0	0	0	7135	1203	42	4	369	4	HIST1H1E	6	26156985	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	100514	26156985	144958082	68	15944											
HIST1H1E	3008	hgsc.bcm.edu	37	chr6	26157108	26157108	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aggcgaagaagccggctgcaGctgctggagccaaaaaagcg	13	3	15	10	3	0	1	0	0	0	1	0	3	0	2	2	3	6	4	2	3	5	0	rs201935674	byFrequency	TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr6:26157108G>A	ENST00000304218.3	+	1	550	c.490G>A	c.(490-492)Gct>Act	p.A164T	HIST1H2BD_ENST00000377777.4_5'Flank|HIST1H2BD_ENST00000289316.2_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	164					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)	p.A164P(1)		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						GCCGGCTGCAGCTGCTGGAGC	0.597													G|||	2	0.000399361	0.0	0.0	5008	,	,		12111	0.0		0.002	False		,,,				2504	0.0				p.A164T		Atlas-SNP	.											HIST1H1E,NS,lymphoid_neoplasm,-1,3	HIST1H1E	69	3	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G490A						PASS	.						15	21	19					6																	26157108		2192	4287	6479	SO:0001583	missense	3008	exon1			GCTGCAGCTGCTG	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.490G>A	6.37:g.26157108G>A	ENSP00000307705:p.Ala164Thr	54	0	0		63	18	0.285714	NM_005321	Q4VB25	Missense_Mutation	SNP	ENST00000304218.3	37	CCDS4586.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	.	13.33	2.206374	0.39003	.	.	ENSG00000168298	ENST00000304218	T	0.04862	3.54	5.49	5.49	0.81192	.	0.133164	0.49916	D	0.000129	T	0.04543	0.0124	L	0.37697	1.125	0.49798	D	0.99982	P	0.48911	0.917	P	0.51297	0.665	T	0.11324	-1.0592	10	0.02654	T	1	-2.5382	18.7205	0.91691	0.0:0.0:1.0:0.0	.	164	P10412	H14_HUMAN	T	164	ENSP00000307705:A164T	ENSP00000307705:A164T	A	+	1	0	HIST1H1E	26265087	0.970000	0.33590	0.822000	0.32727	0.970000	0.65996	2.285000	0.43487	2.723000	0.93209	0.655000	0.94253	GCT	G|0.999;A|0.001	0.001	strong		0.597	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321		A	26157108	G	A	26157108	3	1	48	1	0	0	0	0	1	0	0	0	7135	971	34	2	492	2	HIST1H1E	6	26157108	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	123	26157108	144957959	69	15945											
HIST1H1D	3007	hgsc.bcm.edu	37	chr6	26234976	26234976	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gccgcaagcgctttcttaagCgcggccagagaaacgccgct	9	6	12	14	6	1	1	0	0	1	1	1	2	1	1	3	1	3	3	3	1	3	2	rs150400552		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr6:26234976C>T	ENST00000244534.5	-	1	240	c.186G>A	c.(184-186)gcG>gcA	p.A62A		NM_005320.2	NP_005311.1	P16402	H13_HUMAN	histone cluster 1, H1d	62	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				CTTTCTTAAGCGCGGCCAGAG	0.547																																					p.A62A		Atlas-SNP	.											.	HIST1H1D	40	.	0			c.G186A						PASS	.						82	89	87					6																	26234976		2203	4300	6503	SO:0001819	synonymous_variant	3007	exon1			CTTAAGCGCGGCC	M60747	CCDS4597.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000124575	ENSG00000124575		"Histones / Replication-dependent"	4717	protein-coding gene	gene with protein product		142210	"H1 histone family, member 3", "histone 1, H1d"	H1F3		1916825, 12408966	Standard	NM_005320		Approved	H1.3, H1d, H1s-2	uc003nhd.3	P16402	OTTHUMG00000014432	ENST00000244534.5:c.186G>A	6.37:g.26234976C>T		161	0	0		179	53	0.296089	NM_005320	B2R751|Q2M2I2	Silent	SNP	ENST00000244534.5	37	CCDS4597.1																																																																																			C|1.000;A|0.000	.	alt		0.547	HIST1H1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040095.1	NM_005320		T	26234976	C	T	26234976	2	4	48	1	0	0	0	0	0	0	0	1	7134	755	27	1		1	HIST1H1D	6	26234976	Silent	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	77868	26234976	144880091	70	15946											
HIST1H2AG	8969	hgsc.bcm.edu	37	chr6	27101120	27101120	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctccaactggccatccgcaaCgacgaggagctcaacaagct	12	5	9	15	3	1	0	1	0	0	0	3	3	3	1	3	2	5	3	3	2	4	0			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr6:27101120C>T	ENST00000359193.2	+	1	289	c.270C>T	c.(268-270)aaC>aaT	p.N90N	HIST1H2BJ_ENST00000541790.1_5'Flank|HIST1H2BJ_ENST00000339812.2_5'Flank|HIST1H2BJ_ENST00000607124.1_5'Flank	NM_021064.4	NP_066408.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2ag	90						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						CCATCCGCAACGACGAGGAGC	0.612																																					p.N90N		Atlas-SNP	.											.	HIST1H2AG	37	.	0			c.C270T						PASS	.						115	110	111					6																	27101120		2203	4300	6503	SO:0001819	synonymous_variant	8969	exon1			CCGCAACGACGAG	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.270C>T	6.37:g.27101120C>T		129	0	0		156	36	0.230769	NM_021064	P02261|Q2M1R2|Q76PA6	Silent	SNP	ENST00000359193.2	37	CCDS4619.1																																																																																			.	.	none		0.612	HIST1H2AG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040137.1	NM_021064		T	27101120	C	T	27101120	2	4	48	1	0	0	0	0	0	0	0	1	7142	535	19	1		1	HIST1H2AG	6	27101120	Silent	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	866144	27101120	144013947	71	15947											
HIST1H2BK	85236	hgsc.bcm.edu	37	chr6	27114200	27114200	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	acgcttacttggcaagtttaCttagcgctggtgtacttggt	7	15	11	8	2	0	0	0	0	0	0	0	0	0	0	0	3	4	5	0	3	5	7			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr6:27114200C>T	ENST00000356950.1	-	1	377	c.378G>A	c.(376-378)aaG>aaA	p.K126K	HIST1H2AH_ENST00000377459.1_5'Flank|HIST1H2BK_ENST00000396891.4_Silent_p.K126K|MIR3143_ENST00000584253.1_RNA			O60814	H2B1K_HUMAN	histone cluster 1, H2bk	126					antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)	extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	13						GGCAAGTTTACTTAGCGCTGG	0.542																																					p.K126K		Atlas-SNP	.											.	HIST1H2BK	68	.	0			c.G378A						PASS	.						82	89	87					6																	27114200		2202	4299	6501	SO:0001819	synonymous_variant	85236	exon1			AGTTTACTTAGCG	AJ223352	CCDS4621.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000197903	ENSG00000197903		"Histones / Replication-dependent"	13954	protein-coding gene	gene with protein product		615045	"H2B histone family, member T", "histone 1, H2bk"	H2BFT		12408966	Standard	NM_080593		Approved	H2BFAiii	uc003nix.2	O60814	OTTHUMG00000014473	ENST00000356950.1:c.378G>A	6.37:g.27114200C>T		135	0	0		137	49	0.357664	NM_080593	A8K7P7|Q2VPI7	Silent	SNP	ENST00000356950.1	37	CCDS4621.1																																																																																			.	.	none		0.542	HIST1H2BK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040141.1	NM_080593		T	27114200	C	T	27114200	2	4	48	1	0	0	0	0	0	0	0	1	7159	564	20	2		2	HIST1H2BK	6	27114200	Silent	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	13080	27114200	144000867	72	15948											
HIST1H1B	3009	hgsc.bcm.edu	37	chr6	27834916	27834916	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tggcccccgcgggcttcttaGctttagcggcgcctgccttc	2	11	12	16	4	1	0	0	0	1	0	2	0	1	0	4	3	3	2	4	3	2	5	rs199758872		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr6:27834916G>A	ENST00000331442.3	-	1	443	c.392C>T	c.(391-393)gCt>gTt	p.A131V		NM_005322.2	NP_005313.1	P16401	H15_HUMAN	histone cluster 1, H1b	131					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						GGGCTTCTTAGCTTTAGCGGC	0.607																																					p.A131V		Atlas-SNP	.											.	HIST1H1B	54	.	0			c.C392T						PASS	.						81	96	91					6																	27834916		2203	4299	6502	SO:0001583	missense	3009	exon1			TTCTTAGCTTTAG	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.392C>T	6.37:g.27834916G>A	ENSP00000330074:p.Ala131Val	108	0	0		136	40	0.294118	NM_005322	Q14529|Q3MJ42	Missense_Mutation	SNP	ENST00000331442.3	37	CCDS4635.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	14.95	2.687908	0.48097	.	.	ENSG00000184357	ENST00000331442	T	0.16897	2.31	5.19	5.19	0.71726	.	0.194604	0.42548	D	0.000695	T	0.06096	0.0158	N	0.08118	0	0.50313	D	0.999862	B	0.23316	0.083	B	0.32090	0.14	T	0.32955	-0.9887	10	0.34782	T	0.22	-2.5827	18.087	0.89461	0.0:0.0:1.0:0.0	.	131	P16401	H15_HUMAN	V	131	ENSP00000330074:A131V	ENSP00000330074:A131V	A	-	2	0	HIST1H1B	27942895	0.843000	0.29541	0.031000	0.17742	0.597000	0.36814	4.678000	0.61641	2.600000	0.87896	0.655000	0.94253	GCT	G|1.000;A|0.000	0.000	strong		0.607	HIST1H1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043371.1	NM_005322		A	27834916	G	A	27834916	3	1	48	1	0	0	0	0	1	0	0	0	7132	971	34	2	292	2	HIST1H1B	6	27834916	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	720716	27834916	143280151	73	15949											
HLA-B	3106	hgsc.bcm.edu	37	chr6	31324576	31324576	+	Nonsense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ccaatactccggcccctcctGctctatccacggcgcccgcg	5	7	8	21	5	1	0	0	0	1	0	4	0	4	0	7	2	2	1	7	2	3	2	rs151341159|rs281864598|rs41553618		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr6:31324576G>A	ENST00000412585.2	-	2	260	c.232C>T	c.(232-234)Cag>Tag	p.Q78*		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	78	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						GGCCCCTCCTGCTCTATCCAC	0.637									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.Q78X		Atlas-SNP	.											.	HLA-B	54	.	0			c.C232T						PASS	.						49	48	48					6																	31324576		2149	4170	6319	SO:0001587	stop_gained	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	CCTCCTGCTCTAT	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.232C>T	6.37:g.31324576G>A	ENSP00000399168:p.Gln78*	84	0	0		75	18	0.24	NM_005514	Q29764	Nonsense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	14.19	2.460322	0.43736	.	.	ENSG00000234745	ENST00000412585;ENST00000434333	.	.	.	3.16	3.16	0.36331	.	1.312210	0.06463	U	0.729762	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	12.2525	0.54605	0.0:0.0:1.0:0.0	.	.	.	.	X	78;89	.	ENSP00000399168:Q78X	Q	-	1	0	HLA-B	31432555	0.000000	0.05858	0.581000	0.28614	0.013000	0.08279	-0.147000	0.10234	1.804000	0.52760	0.442000	0.29010	CAG	.	.	weak		0.637	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514		A	31324576	G	A	31324576	4	1	48	1	0	0	0	0	0	1	0	0	7205	1328	46	2	880	2	HLA-B	6	31324576	Nonsense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	3489660	31324576	139790491	74	15950											
PIM1	5292	hgsc.bcm.edu	37	chr6	37138372	37138372	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	atgctcttgtccaaaatcaaCtcgcttgcccacctgcgcgc	8	10	7	16	3	2	0	1	0	1	0	4	0	3	0	3	0	4	2	3	0	3	2			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr6:37138372C>T	ENST00000373509.5	+	1	394	c.21C>T	c.(19-21)aaC>aaT	p.N7N		NM_001243186.1|NM_002648.3	NP_001230115.1|NP_002639.1	P11309	PIM1_HUMAN	Pim-1 proto-oncogene, serine/threonine kinase	98					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)	CCAAAATCAACTCGCTTGCCC	0.721			T	BCL6	NHL																																p.N98N		Atlas-SNP	.		Dom	yes		6	6p21.2	5292	pim-1 oncogene		L	.	PIM1	71	.	0			c.C294T						PASS	.						31	31	31					6																	37138372		2202	4298	6500	SO:0001819	synonymous_variant	5292	exon1			AATCAACTCGCTT		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.21C>T	6.37:g.37138372C>T		58	0	0		44	10	0.227273	NM_001243186	Q38RT9|Q5T7H7|Q96RG3	Silent	SNP	ENST00000373509.5	37	CCDS4830.1																																																																																			.	.	none		0.721	PIM1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043903.1			T	37138372	C	T	37138372	2	4	48	1	0	0	0	0	0	0	0	1	11936	564	20	2		2	PIM1	6	37138372	Silent	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	5813796	37138372	133976695	75	15951											
C6orf138	442213	hgsc.bcm.edu	37	chr6	47976501	47976501	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ggcccaggaagggcttactgCgcaagcagtccttcatggag	9	7	14	11	1	1	0	1	0	0	0	2	2	2	2	2	4	3	3	2	4	3	2	rs143420847	byFrequency	TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr6:47976501C>T	ENST00000339488.4	-	2	809	c.776G>A	c.(775-777)cGc>cAc	p.R259H	PTCHD4_ENST00000543600.1_Missense_Mutation_p.R242H	NM_001013732.3	NP_001013754.3	Q6ZW05	PTHD4_HUMAN	patched domain containing 4	259	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.					integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)										GGGCTTACTGCGCAAGCAGTC	0.557													C|||	2	0.000399361	0.0008	0.0	5008	,	,		18423	0.0		0.001	False		,,,				2504	0.0				p.R259H		Atlas-SNP	.											.	.	.	.	0			c.G776A						PASS	.	C	HIS/ARG,HIS/ARG	1,4045		0,1,2022	58	59	59		776,776	6.2	1	6	dbSNP_134	59	0,8406		0,0,4203	no	missense,missense	C6orf138	NM_001013732.3,NM_207499.2	29,29	0,1,6225	TT,TC,CC		0.0,0.0247,0.0080	probably-damaging,probably-damaging	259/847,259/312	47976501	1,12451	2023	4203	6226	SO:0001583	missense	442213	exon2			TTACTGCGCAAGC		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.776G>A	6.37:g.47976501C>T	ENSP00000341914:p.Arg259His	90	0	0		116	34	0.293103	NM_001013732	B0QZ29|B4DRK3|Q5T884	Missense_Mutation	SNP	ENST00000339488.4	37	CCDS34473.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	29.8	5.039983	0.93630	2.47E-4	0.0	ENSG00000244694	ENST00000339488;ENST00000543600	D;D	0.86230	-2.09;-2.09	6.16	6.16	0.99307	Sterol-sensing domain (1);	0.049562	0.85682	D	0.000000	D	0.93051	0.7788	M	0.74881	2.28	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	D	0.91320	0.5081	10	0.49607	T	0.09	.	20.8598	0.99761	0.0:1.0:0.0:0.0	.	259;242	Q6ZW05;B0QZ29	CF138_HUMAN;.	H	259;242	ENSP00000341914:R259H;ENSP00000439864:R242H	ENSP00000341914:R259H	R	-	2	0	C6orf138	48084460	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.487000	0.81328	2.937000	0.99478	0.650000	0.86243	CGC	C|1.000;T|0.000	0.000	strong		0.557	PTCHD4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317987.2	NM_001013732		T	47976501	C	T	47976501	3	4	48	1	0	0	0	0	1	0	0	0	2334	768	27	1	1772	1	C6orf138	6	47976501	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	10838129	47976501	123138566	76	15952											
EFHC1	114327	hgsc.bcm.edu	37	chr6	52288818	52288818	+	Silent	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	1	1	0	0	0	0	gttcgacgtccaacagttggGataggcggagaccggctcca	9	7	14	11	4	0	1	0	0	0	1	3	4	2	2	3	4	1	3	3	4	2	3			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr6:52288818G>C	ENST00000371068.5	+	2	241	c.138G>C	c.(136-138)ggG>ggC	p.G46G	EFHC1_ENST00000433625.2_5'UTR|EFHC1_ENST00000491749.1_3'UTR|EFHC1_ENST00000538167.1_Silent_p.G27G	NM_018100.3	NP_060570.2	Q5JVL4	EFHC1_HUMAN	EF-hand domain (C-terminal) containing 1	46						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)					CAACAGTTGGGATAGGCGGAG	0.498																																					p.G46G		Atlas-SNP	.											EFHC1,right_lower_lobe,carcinoma,0,1	EFHC1	68	1	0			c.G138C						PASS	.						99	92	94					6																	52288818		2203	4300	6503	SO:0001819	synonymous_variant	114327	exon2			AGTTGGGATAGGC	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.138G>C	6.37:g.52288818G>C		47	0	0		58	13	0.224138	NM_018100	B4DMU3|F5GZD8|Q5XKM4|Q6E1U7|Q6E1U8|Q8WUL2|Q9NVW6	Silent	SNP	ENST00000371068.5	37	CCDS4942.1																																																																																			.	.	none		0.498	EFHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040905.2	NM_018100		C	52288818	G	C	52288818	2	2	48	1	0	0	0	0	0	0	0	1	4948	1161	41	4		4	EFHC1	6	52288818	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	4312317	52288818	118826249	77	15953											
DST	667	hgsc.bcm.edu	37	chr6	56483209	56483209	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	atctggtttgaaggtacagtCtttggctgtgctcttttttt	5	20	10	6	0	3	1	0	1	3	0	3	1	3	1	0	3	2	4	0	3	2	6			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr6:56483209C>T	ENST00000370765.6	-	23	5730	c.5623G>A	c.(5623-5625)Gac>Aac	p.D1875N	DST_ENST00000361203.3_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000370788.2_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000244364.6_Intron|DST_ENST00000370769.4_Intron|DST_ENST00000446842.2_Intron|DST_ENST00000370754.5_Intron	NM_001723.5	NP_001714.1	Q03001	DYST_HUMAN	dystonin	0					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)			AAGGTACAGTCTTTGGCTGTG	0.438																																					p.D1875N		Atlas-SNP	.											.	DST	1427	.	0			c.G5623A						PASS	.						71	72	71					6																	56483209		2203	4300	6503	SO:0001583	missense	667	exon23			TACAGTCTTTGGC	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.5623G>A	6.37:g.56483209C>T	ENSP00000359801:p.Asp1875Asn	134	0	0		155	35	0.225806	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	37	CCDS4959.1	.	.	.	.	.	.	.	.	.	.	C	13.14	2.147806	0.37923	.	.	ENSG00000151914	ENST00000370765	T	0.34667	1.35	4.87	3.09	0.35607	.	.	.	.	.	T	0.12305	0.0299	.	.	.	0.22835	N	0.998678	B	0.02656	0.0	B	0.01281	0.0	T	0.07121	-1.0789	7	0.52906	T	0.07	.	7.8725	0.29573	0.0:0.7476:0.0:0.2524	.	1875	Q03001-3	.	N	1875	ENSP00000359801:D1875N	ENSP00000359801:D1875N	D	-	1	0	DST	56591168	0.918000	0.31147	0.006000	0.13384	0.844000	0.47949	0.808000	0.27154	0.583000	0.29574	0.650000	0.86243	GAC	.	.	none		0.438	DST-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041027.2	NM_001723		T	56483209	C	T	56483209	3	4	48	1	0	0	0	0	1	0	0	0	4785	913	32	2	14780	2	DST	6	56483209	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	4194391	56483209	114631858	78	15954											
KHDRBS2	202559	hgsc.bcm.edu	37	chr6	62887168	62887168	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ctgatgacatcaagatacttCttttcttcgtcttccttttt	7	20	4	10	1	4	3	1	2	3	1	6	3	5	3	1	0	1	0	1	0	2	8			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr6:62887168C>A	ENST00000281156.4	-	2	419	c.141G>T	c.(139-141)aaG>aaT	p.K47N		NM_152688.2	NP_689901.2	Q5VWX1	KHDR2_HUMAN	KH domain containing, RNA binding, signal transduction associated 2	47					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)	p.K47N(1)		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)		CAAGATACTTCTTTTCTTCGT	0.338																																					p.K47N		Atlas-SNP	.											KHDRBS2,NS,carcinoma,0,1	KHDRBS2	103	1	1	Substitution - Missense(1)	endometrium(1)	c.G141T						PASS	.						130	119	123					6																	62887168		2200	4299	6499	SO:0001583	missense	202559	exon2			ATACTTCTTTTCT	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.141G>T	6.37:g.62887168C>A	ENSP00000281156:p.Lys47Asn	142	0	0		83	31	0.373494	NM_152688	A8K7M8|Q8N4I4|Q8TCZ4	Missense_Mutation	SNP	ENST00000281156.4	37	CCDS4963.1	.	.	.	.	.	.	.	.	.	.	C	10.49	1.364326	0.24684	.	.	ENSG00000112232	ENST00000281156;ENST00000539571	T	0.15952	2.38	5.25	4.38	0.52667	.	0.265109	0.42172	D	0.000744	T	0.06781	0.0173	L	0.51422	1.61	0.58432	D	0.999994	P	0.36683	0.565	B	0.33454	0.164	T	0.15636	-1.0430	10	0.19147	T	0.46	-3.2222	12.7929	0.57545	0.0:0.9205:0.0:0.0794	.	47	Q5VWX1	KHDR2_HUMAN	N	47	ENSP00000281156:K47N	ENSP00000281156:K47N	K	-	3	2	KHDRBS2	62945127	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	3.714000	0.54889	1.211000	0.43351	0.460000	0.39030	AAG	.	.	none		0.338	KHDRBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041066.2	NM_152688		A	62887168	C	A	62887168	3	1	48	1	0	0	0	0	1	0	0	0	8156	912	32	4	940	4	KHDRBS2	6	62887168	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	6403959	62887168	108227899	79	15955											
MDN1	23195	hgsc.bcm.edu	37	chr6	90466006	90466006	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggaacctactttatgattcCttgcactgtattcttgttca	8	17	7	9	0	2	1	1	1	1	0	3	2	3	2	2	1	3	3	2	1	4	9			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr6:90466006C>T	ENST00000369393.3	-	20	2921	c.2806G>A	c.(2806-2808)Gga>Aga	p.G936R	MDN1_ENST00000428876.1_Missense_Mutation_p.G936R			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	936					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)		TTTATGATTCCTTGCACTGTA	0.333																																					p.G936R		Atlas-SNP	.											MDN1,NS,carcinoma,0,1	MDN1	478	1	0			c.G2806A						PASS	.						199	193	195					6																	90466006		2202	4296	6498	SO:0001583	missense	23195	exon20			TGATTCCTTGCAC	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.2806G>A	6.37:g.90466006C>T	ENSP00000358400:p.Gly936Arg	126	0	0		129	34	0.263566	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	C	17.49	3.402192	0.62288	.	.	ENSG00000112159	ENST00000369393;ENST00000428876;ENST00000439638	T;T;T	0.38240	1.15;1.15;1.15	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.22244	0.0536	L	0.39085	1.19	0.80722	D	1	B;B	0.33345	0.409;0.308	B;B	0.37550	0.168;0.253	T	0.04400	-1.0954	10	0.17832	T	0.49	.	20.3789	0.98926	0.0:1.0:0.0:0.0	.	863;936	Q5T795;Q9NU22	.;MDN1_HUMAN	R	936;936;863	ENSP00000358400:G936R;ENSP00000413970:G936R;ENSP00000409664:G863R	ENSP00000358400:G936R	G	-	1	0	MDN1	90522727	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.949000	0.75971	2.826000	0.97356	0.563000	0.77884	GGA	.	.	none		0.333	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2			T	90466006	C	T	90466006	3	4	48	1	0	0	0	0	1	0	0	0	9424	690	24	2	14316	2	MDN1	6	90466006	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	27578838	90466006	80649061	80	15956											
FAM120B	84498	hgsc.bcm.edu	37	chr6	170704591	170704591	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	acagggaggtggggaagacaGggctccagctaccacaggac	12	3	16	10	0	0	1	0	0	0	1	1	4	1	4	2	6	2	2	2	6	2	1			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr6:170704591G>A	ENST00000476287.1	+	9	2724	c.2616G>A	c.(2614-2616)caG>caA	p.Q872Q	FAM120B_ENST00000540480.1_Silent_p.Q884Q|FAM120B_ENST00000252510.9_Silent_p.Q204Q|FAM120B_ENST00000537664.1_Silent_p.Q895Q	NM_032448.1	NP_115824.1	Q96EK7	F120B_HUMAN	family with sequence similarity 120B	872					cell differentiation (GO:0030154)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|liver(1)|lung(15)|ovary(1)|prostate(2)|skin(2)	44		Breast(66;0.000338)|Esophageal squamous(34;0.241)		OV - Ovarian serous cystadenocarcinoma(33;3.94e-22)|BRCA - Breast invasive adenocarcinoma(81;6.47e-06)|GBM - Glioblastoma multiforme(31;0.0899)		GGGGAAGACAGGGCTCCAGCT	0.542																																					p.Q872Q		Atlas-SNP	.											.	FAM120B	108	.	0			c.G2616A						PASS	.						45	37	40					6																	170704591		2196	4293	6489	SO:0001819	synonymous_variant	84498	exon9			AAGACAGGGCTCC	AB058741	CCDS5314.1, CCDS75555.1	6q27	2011-04-13	2006-07-04	2006-07-04	ENSG00000112584	ENSG00000112584			21109	protein-coding gene	gene with protein product	"PPARgamma constitutive coactivator 1", "constitutive coactivator of PPAR-gamma"	612266	"KIAA1838"	KIAA1838		14585507	Standard	NM_032448		Approved	PGCC1, CCPG	uc003qxp.3	Q96EK7	OTTHUMG00000016080	ENST00000476287.1:c.2616G>A	6.37:g.170704591G>A		46	0	0		61	20	0.327869	NM_032448	B4DL34|Q86V68|Q96JI9	Silent	SNP	ENST00000476287.1	37	CCDS5314.1																																																																																			.	.	none		0.542	FAM120B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000043259.2	NM_032448		A	170704591	G	A	170704591	2	1	48	1	0	0	0	0	0	0	0	1	5422	991	35	2		2	FAM120B	6	170704591	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	80238585	170704591	410476	81	15957											
ZNF273	10793	hgsc.bcm.edu	37	chr7	64388883	64388883	+	Missense_Mutation	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cctcaacccttactagacatAagatagttcatactggagag	14	10	7	10	0	2	3	2	0	0	3	2	4	2	3	2	1	3	1	2	1	6	6			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr7:64388883A>C	ENST00000476120.1	+	4	1248	c.1177A>C	c.(1177-1179)Aag>Cag	p.K393Q	ZNF273_ENST00000319636.5_Missense_Mutation_p.K328Q|ZNF273_ENST00000527278.1_3'UTR	NM_021148.2	NP_066971.2	Q14593	ZN273_HUMAN	zinc finger protein 273	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)|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)				TACTAGACATAAGATAGTTCA	0.353																																					p.K393Q	Ovarian(154;605 895 6696 7659 15316 19321 21716 23848 32322 36932)	Atlas-SNP	.											.	ZNF273	45	.	0			c.A1177C						PASS	.						49	53	52					7																	64388883		2201	4298	6499	SO:0001583	missense	10793	exon4			AGACATAAGATAG	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.1177A>C	7.37:g.64388883A>C	ENSP00000418719:p.Lys393Gln	61	0	0		65	13	0.2	NM_021148	B3KQZ5|Q6P3V4	Missense_Mutation	SNP	ENST00000476120.1	37	CCDS5528.2	.	.	.	.	.	.	.	.	.	.	.	13.59	2.283312	0.40394	.	.	ENSG00000198039	ENST00000476120;ENST00000319636	T;T	0.07567	3.18;3.18	1.16	-0.975	0.10289	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08670	0.0215	N	0.11789	0.175	0.21105	N	0.999781	D	0.76494	0.999	D	0.74023	0.982	T	0.35076	-0.9803	9	0.13108	T	0.6	.	4.7908	0.13248	0.3721:0.6278:0.0:0.0	.	393	Q14593	ZN273_HUMAN	Q	393;328	ENSP00000418719:K393Q;ENSP00000324518:K328Q	ENSP00000324518:K328Q	K	+	1	0	ZNF273	64026318	0.000000	0.05858	0.786000	0.31890	0.785000	0.44390	-0.741000	0.04855	0.175000	0.19841	0.172000	0.16884	AAG	.	.	none		0.353	ZNF273-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313502.1			C	64388883	A	C	64388883	3	2	48	1	0	0	0	0	1	0	0	0	17823	363	13	5	1191	5	ZNF273	7	64388883	Missense_Mutation	SNP	A	TCGA-VB-A8QN-01A-11D-A382-10		64388883	94749780	82	15958											
SEMA3E	9723	hgsc.bcm.edu	37	chr7	83036446	83036446	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccgaccctggtgtaaattgcGtgagcattgttttctgcctc	6	14	10	11	2	1	1	0	1	1	0	2	2	1	1	3	1	3	3	3	1	2	5	rs533306215		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr7:83036446G>A	ENST00000307792.3	-	7	1247	c.780C>T	c.(778-780)caC>caT	p.H260H	SEMA3E_ENST00000427262.1_Silent_p.H200H	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	260	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)				TGTAAATTGCGTGAGCATTGT	0.403																																					p.H260H		Atlas-SNP	.											.	SEMA3E	125	.	0			c.C780T						PASS	.						116	108	111					7																	83036446		2203	4300	6503	SO:0001819	synonymous_variant	9723	exon7			AATTGCGTGAGCA	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.780C>T	7.37:g.83036446G>A		48	0	0		54	14	0.259259	NM_012431	B4E1P1|Q75M94|Q75M97	Silent	SNP	ENST00000307792.3	37	CCDS34674.1																																																																																			.	.	none		0.403	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431		A	83036446	G	A	83036446	2	1	48	1	0	0	0	0	0	0	0	1	14043	1136	40	1		1	SEMA3E	7	83036446	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	18647563	83036446	76102217	83	15959											
MUC17	140453	hgsc.bcm.edu	37	chr7	100682814	100682814	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	cagcaccacgctgttggccaAttctgaggctagcacccttt	8	10	9	14	1	1	1	0	1	1	0	1	1	1	1	3	2	2	5	3	2	2	4	rs201007776		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr7:100682814A>G	ENST00000306151.4	+	3	8181	c.8117A>G	c.(8116-8118)aAt>aGt	p.N2706S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2706	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)					CTGTTGGCCAATTCTGAGGCT	0.493																																					p.N2706S		Atlas-SNP	.											MUC17,NS,carcinoma,0,1	MUC17	804	1	0			c.A8117G						scavenged	.						245	255	251					7																	100682814		2203	4300	6503	SO:0001583	missense	140453	exon3			TGGCCAATTCTGA	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.8117A>G	7.37:g.100682814A>G	ENSP00000302716:p.Asn2706Ser	55	2	0.0363636		76	5	0.0657895	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	0.044	-1.274581	0.01410	.	.	ENSG00000169876	ENST00000306151	T	0.02015	4.5	0.37	-0.741	0.11112	.	.	.	.	.	T	0.00754	0.0025	N	0.02539	-0.55	0.09310	N	1	B	0.17667	0.023	B	0.08055	0.003	T	0.43065	-0.9414	9	0.06236	T	0.91	.	0.1449	0.00087	0.2508:0.246:0.2581:0.2451	.	2706	Q685J3	MUC17_HUMAN	S	2706	ENSP00000302716:N2706S	ENSP00000302716:N2706S	N	+	2	0	MUC17	100469534	0.000000	0.05858	0.001000	0.08648	0.021000	0.10359	-0.783000	0.04638	-2.048000	0.00907	-1.389000	0.01157	AAT	A|0.999;G|0.001	0.001	weak		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105		G	100682814	A	G	100682814	3	3	48	1	0	0	0	0	1	0	0	0	9983	101	4	3	8127	3	MUC17	7	100682814	Missense_Mutation	SNP	A	TCGA-VB-A8QN-01A-11D-A382-10	17646368	100682814	58455849	84	15960											
LRRN3	54674	hgsc.bcm.edu	37	chr7	110764565	110764565	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgatgtcaaggtatataaTcttactcatctgaatccatc	12	15	5	9	0	5	2	2	2	3	0	7	2	6	2	1	1	1	1	1	1	6	4			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr7:110764565T>C	ENST00000422987.3	+	2	2568	c.1737T>C	c.(1735-1737)aaT>aaC	p.N579N	IMMP2L_ENST00000331762.3_Intron|LRRN3_ENST00000451085.1_Silent_p.N579N|LRRN3_ENST00000308478.5_Silent_p.N579N|IMMP2L_ENST00000489381.1_Intron|IMMP2L_ENST00000415362.1_Intron|IMMP2L_ENST00000405709.2_Intron|IMMP2L_ENST00000452895.1_Intron|IMMP2L_ENST00000437687.1_Intron|IMMP2L_ENST00000450877.1_Intron|IMMP2L_ENST00000447215.1_Intron	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	579	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)		AGGTATATAATCTTACTCATC	0.343																																					p.N579N		Atlas-SNP	.											.	LRRN3	132	.	0			c.T1737C						PASS	.						52	49	50					7																	110764565		2203	4300	6503	SO:0001819	synonymous_variant	54674	exon2			ATATAATCTTACT	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.1737T>C	7.37:g.110764565T>C		48	0	0		48	16	0.333333	NM_018334	O43377|Q6I9V8|Q8IYQ6	Silent	SNP	ENST00000422987.3	37	CCDS5754.1																																																																																			.	.	none		0.343	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334		C	110764565	T	C	110764565	2	2	48	1	0	0	0	0	0	0	0	1	9045	1432	50	3		3	LRRN3	7	110764565	Silent	SNP	T	TCGA-VB-A8QN-01A-11D-A382-10	10081751	110764565	48374098	85	15961											
PPP1R3A	5506	hgsc.bcm.edu	37	chr7	113517882	113517882	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattaagtcataatggtagaCagttataagaaatatcagaa	19	11	7	4	0	2	3	2	0	0	3	2	3	2	3	0	1	0	2	0	1	8	6			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr7:113517882C>T	ENST00000284601.3	-	4	3333	c.3265G>A	c.(3265-3267)Gtc>Atc	p.V1089I		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	1089					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						TAATGGTAGACAGTTATAAGA	0.348																																					p.V1089I		Atlas-SNP	.											PPP1R3A,caecum,carcinoma,+1,1	PPP1R3A	317	1	0			c.G3265A						PASS	.						84	86	86					7																	113517882		2202	4299	6501	SO:0001583	missense	5506	exon4			GGTAGACAGTTAT	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.3265G>A	7.37:g.113517882C>T	ENSP00000284601:p.Val1089Ile	92	0	0		81	20	0.246914	NM_002711	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Missense_Mutation	SNP	ENST00000284601.3	37	CCDS5759.1	.	.	.	.	.	.	.	.	.	.	C	0.010	-1.782052	0.00634	.	.	ENSG00000154415	ENST00000284601	T	0.15256	2.44	5.85	-0.598	0.11649	.	0.641150	0.15224	N	0.273777	T	0.05410	0.0143	N	0.05510	-0.035	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36456	-0.9747	10	0.12766	T	0.61	0.3076	1.0196	0.01515	0.2055:0.2575:0.1164:0.4207	.	1089	Q16821	PPR3A_HUMAN	I	1089	ENSP00000284601:V1089I	ENSP00000284601:V1089I	V	-	1	0	PPP1R3A	113305118	0.942000	0.31987	0.951000	0.38953	0.577000	0.36160	0.348000	0.20031	-0.316000	0.08690	-0.247000	0.11927	GTC	.	.	none		0.348	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711		T	113517882	C	T	113517882	3	4	48	1	0	0	0	0	1	0	0	0	12383	478	17	2	107	2	PPP1R3A	7	113517882	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	2753317	113517882	45620781	86	15962											
TAS2R16	50833	hgsc.bcm.edu	37	chr7	122634896	122634896	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cattaagatgaaagcatagaCaaaagcttcccagacccata	18	7	6	10	0	0	4	0	1	0	3	1	4	1	4	2	0	2	2	2	0	6	4			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr7:122634896C>G	ENST00000249284.2	-	1	858	c.793G>C	c.(793-795)Gtc>Ctc	p.V265L		NM_016945.2	NP_058641.1	Q9NYV7	T2R16_HUMAN	taste receptor, type 2, member 16	265					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						AAAGCATAGACAAAAGCTTCC	0.398																																					p.V265L		Atlas-SNP	.											.	TAS2R16	57	.	0			c.G793C						PASS	.						128	126	127					7																	122634896		2203	4300	6503	SO:0001583	missense	50833	exon1			CATAGACAAAAGC	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.793G>C	7.37:g.122634896C>G	ENSP00000249284:p.Val265Leu	70	0	0		69	29	0.42029	NM_016945	A4D0X2|Q502V3|Q549U8|Q645W1	Missense_Mutation	SNP	ENST00000249284.2	37	CCDS5785.1	.	.	.	.	.	.	.	.	.	.	C	10.21	1.288649	0.23478	.	.	ENSG00000128519	ENST00000249284	T	0.35973	1.28	4.68	2.13	0.27403	.	0.443137	0.20257	N	0.095949	T	0.21509	0.0518	L	0.27053	0.805	0.09310	N	1	B	0.10296	0.003	B	0.13407	0.009	T	0.16305	-1.0407	10	0.28530	T	0.3	.	6.2548	0.20867	0.0:0.2053:0.0:0.7947	.	265	Q9NYV7	T2R16_HUMAN	L	265	ENSP00000249284:V265L	ENSP00000249284:V265L	V	-	1	0	TAS2R16	122422132	0.933000	0.31639	0.003000	0.11579	0.021000	0.10359	2.498000	0.45363	0.385000	0.24970	-0.423000	0.05987	GTC	.	.	none		0.398	TAS2R16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347409.1	NM_016945		G	122634896	C	G	122634896	3	3	48	1	0	0	0	0	1	0	0	0	15584	478	17	4	86	4	TAS2R16	7	122634896	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	9117014	122634896	36503767	87	15963											
MYST3	7994	hgsc.bcm.edu	37	chr8	41834600	41834600	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	attgctcagagtagtccaccActtccccccgagctttccgc	7	10	7	17	2	1	1	1	0	0	1	4	2	4	1	6	0	2	3	6	0	1	4			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr8:41834600A>G	ENST00000396930.3	-	8	1832	c.1289T>C	c.(1288-1290)gTg>gCg	p.V430A	KAT6A_ENST00000265713.2_Missense_Mutation_p.V430A|KAT6A_ENST00000406337.1_Missense_Mutation_p.V430A|KAT6A_ENST00000485568.1_Missense_Mutation_p.V430A	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	430	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)										GTAGTCCACCACTTCCCCCCG	0.458																																					p.V430A		Atlas-SNP	.											.	.	.	.	0			c.T1289C						PASS	.						121	116	118					8																	41834600		2203	4300	6503	SO:0001583	missense	7994	exon8			TCCACCACTTCCC	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.1289T>C	8.37:g.41834600A>G	ENSP00000380136:p.Val430Ala	169	0	0		221	64	0.289593	NM_001099412	Q76L81	Missense_Mutation	SNP	ENST00000396930.3	37	CCDS6124.1	.	.	.	.	.	.	.	.	.	.	A	13.35	2.211518	0.39102	.	.	ENSG00000083168	ENST00000265713;ENST00000406337;ENST00000396930;ENST00000485568	T;T;T;D	0.84730	0.11;0.11;0.11;-1.89	5.52	3.07	0.35406	.	0.274720	0.30732	N	0.008981	T	0.75177	0.3814	L	0.34521	1.04	0.37487	D	0.916244	B;B	0.06786	0.001;0.001	B;B	0.09377	0.001;0.004	T	0.66598	-0.5883	10	0.33940	T	0.23	-8.0183	8.4599	0.32921	0.7849:0.0:0.2151:0.0	.	430;430	A5PLL3;Q92794	.;KAT6A_HUMAN	A	430	ENSP00000265713:V430A;ENSP00000385888:V430A;ENSP00000380136:V430A;ENSP00000430606:V430A	ENSP00000265713:V430A	V	-	2	0	KAT6A	41953757	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	5.017000	0.64047	0.359000	0.24239	0.529000	0.55759	GTG	.	.	none		0.458	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766		G	41834600	A	G	41834600	3	3	48	1	0	0	0	0	1	0	0	0	10113	159	6	3	4769	3	MYST3	8	41834600	Missense_Mutation	SNP	A	TCGA-VB-A8QN-01A-11D-A382-10		41834600	104529422	88	15964											
EYA1	2138	hgsc.bcm.edu	37	chr8	72267114	72267114	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	ctaccactcagacggctatgCgggctggttagatcctgcat	8	10	11	12	2	1	2	1	0	0	2	2	2	2	2	2	3	3	4	2	3	3	3			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr8:72267114C>T	ENST00000340726.3	-	3	666	c.27G>A	c.(25-27)ccG>ccA	p.P9P	EYA1_ENST00000388742.4_Silent_p.P9P|EYA1_ENST00000388743.2_Silent_p.P9P|EYA1_ENST00000303824.7_Silent_p.P9P|EYA1_ENST00000388740.3_Intron|EYA1_ENST00000388741.2_Intron|EYA1_ENST00000419131.1_Silent_p.P9P	NM_000503.4	NP_000494.2	Q99502	EYA1_HUMAN	EYA transcriptional coactivator and phosphatase 1	9					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)			GACGGCTATGCGGGCTGGTTA	0.453																																					p.P9P		Atlas-SNP	.											.	EYA1	108	.	0			c.G27A						PASS	.						171	168	169					8																	72267114		2203	4300	6503	SO:0001819	synonymous_variant	2138	exon2			GCTATGCGGGCTG	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.27G>A	8.37:g.72267114C>T		78	0	0		90	23	0.255556	NM_172059	A6NHQ0|G5E9R4|Q0P516|Q8WX80	Silent	SNP	ENST00000340726.3	37	CCDS34906.1																																																																																			.	.	none		0.453	EYA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313788.2	NM_000503, NM_172060		T	72267114	C	T	72267114	2	4	48	1	0	0	0	0	0	0	0	1	5330	755	27	1		1	EYA1	8	72267114	Silent	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	30432514	72267114	74096908	89	15965											
ZFAT	57623	hgsc.bcm.edu	37	chr8	135612768	135612768	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ggtgggacacttcagcaagaTgttactgtgtttctgaatta	10	14	11	6	0	2	2	1	1	1	1	2	3	2	3	0	2	2	3	0	2	4	4			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr8:135612768T>C	ENST00000377838.3	-	7	2560	c.2386A>G	c.(2386-2388)Atc>Gtc	p.I796V	ZFAT-AS1_ENST00000505776.1_RNA|ZFAT_ENST00000523399.1_Missense_Mutation_p.I734V|ZFAT_ENST00000520356.1_Missense_Mutation_p.I784V|ZFAT_ENST00000520214.1_Missense_Mutation_p.I784V|ZFAT_ENST00000429442.2_Missense_Mutation_p.I784V|ZFAT_ENST00000520727.1_Missense_Mutation_p.I784V	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	796					hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|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)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			TTCAGCAAGATGTTACTGTGT	0.433																																					p.I796V		Atlas-SNP	.											.	ZFAT	265	.	0			c.A2386G						PASS	.						177	174	175					8																	135612768		1978	4157	6135	SO:0001583	missense	57623	exon7			GCAAGATGTTACT	BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827		"Zinc fingers, C2H2-type"	19899	protein-coding gene	gene with protein product		610931	"zinc finger protein 406"	ZNF406, ZFAT1		10819331, 18329245	Standard	NM_020863		Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.2386A>G	8.37:g.135612768T>C	ENSP00000367069:p.Ile796Val	139	0	0		159	33	0.207547	NM_020863	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Missense_Mutation	SNP	ENST00000377838.3	37	CCDS47924.1	.	.	.	.	.	.	.	.	.	.	T	14.91	2.675100	0.47781	.	.	ENSG00000066827	ENST00000520356;ENST00000520727;ENST00000429442;ENST00000377838;ENST00000520214;ENST00000318135;ENST00000523399;ENST00000398946	T;T;T;T;T;T	0.14766	2.48;2.48;2.48;2.48;2.48;2.48	5.61	1.97	0.26223	.	0.297381	0.35805	N	0.002965	T	0.04137	0.0115	N	0.03917	-0.325	0.29344	N	0.865847	P;B;B;B	0.36412	0.552;0.192;0.009;0.001	B;B;B;B	0.27076	0.064;0.076;0.013;0.003	T	0.24154	-1.0168	10	0.66056	D	0.02	-19.3815	4.2442	0.10663	0.1385:0.2253:0.0:0.6362	.	734;784;784;796	E9PER3;E9PBN4;Q9P243-3;Q9P243	.;.;.;ZFAT_HUMAN	V	784;784;784;796;784;683;734;784	ENSP00000427879:I784V;ENSP00000427831:I784V;ENSP00000394501:I784V;ENSP00000367069:I796V;ENSP00000428483:I784V;ENSP00000429091:I734V	ENSP00000326997:I683V	I	-	1	0	ZFAT	135681950	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.914000	0.28624	0.502000	0.28037	0.533000	0.62120	ATC	.	.	none		0.433	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939		C	135612768	T	C	135612768	3	2	48	1	0	0	0	0	1	0	0	0	17647	1464	51	3	1385	3	ZFAT	8	135612768	Missense_Mutation	SNP	T	TCGA-VB-A8QN-01A-11D-A382-10	63345654	135612768	10751254	90	15966											
PLEC	5339	hgsc.bcm.edu	37	chr8	144997818	144997818	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gcctgcacccgggcctcctcCgcctcctcagccgcccgccg	2	5	10	24	5	1	0	1	0	0	0	4	0	4	0	10	1	2	1	10	1	0	0	rs539190005		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr8:144997818C>T	ENST00000322810.4	-	31	6859	c.6690G>A	c.(6688-6690)gcG>gcA	p.A2230A	PLEC_ENST00000356346.3_Silent_p.A2079A|PLEC_ENST00000398774.2_Silent_p.A2061A|PLEC_ENST00000436759.2_Silent_p.A2120A|PLEC_ENST00000354958.2_Silent_p.A2071A|PLEC_ENST00000527096.1_Silent_p.A2116A|PLEC_ENST00000357649.2_Silent_p.A2097A|PLEC_ENST00000345136.3_Silent_p.A2093A|PLEC_ENST00000354589.3_Silent_p.A2093A	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	2230	Central fibrous rod domain.				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						GGGCCTCCTCCGCCTCCTCAG	0.736																																					p.A2230A		Atlas-SNP	.											.	PLEC	1144	.	0			c.G6690A						PASS	.						3	4	4					8																	144997818		1654	3519	5173	SO:0001819	synonymous_variant	5339	exon31			CTCCTCCGCCTCC	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.6690G>A	8.37:g.144997818C>T		23	0	0		41	9	0.219512	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			.	.	none		0.736	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445		T	144997818	C	T	144997818	2	4	48	1	0	0	0	0	0	0	0	1	12061	639	23	1		1	PLEC	8	144997818	Silent	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	9385050	144997818	1366204	91	15967											
TYRP1	7306	hgsc.bcm.edu	37	chr9	12694262	12694262	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggcagagatgatcgggaggTctggcccttgcgcttcttca	6	11	14	10	2	3	2	1	1	2	1	4	4	3	3	1	4	1	2	1	4	0	3			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr9:12694262T>A	ENST00000388918.5	+	2	395	c.266T>A	c.(265-267)gTc>gAc	p.V89D	TYRP1_ENST00000381137.2_De_novo_Start_InFrame|TYRP1_ENST00000381136.2_5'Flank	NM_000550.2	NP_000541.1	P17643	TYRP1_HUMAN	tyrosinase-related protein 1	89					acetoacetic acid metabolic process (GO:0043438)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome organization (GO:0032438)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|melanosome (GO:0042470)|melanosome membrane (GO:0033162)	copper ion binding (GO:0005507)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, another compound as one donor, and incorporation of one atom of oxygen (GO:0016716)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|stomach(1)	22		all_cancers(3;3.1e-05)|all_lung(3;1.7e-06)|Lung NSC(3;2.09e-06)|all_epithelial(3;0.000695)|all_hematologic(3;0.0033)|Acute lymphoblastic leukemia(23;0.0744)		GBM - Glioblastoma multiforme(50;9.85e-06)		GATCGGGAGGTCTGGCCCTTG	0.587									Oculocutaneous Albinism																												p.V89D		Atlas-SNP	.											.	TYRP1	60	.	0			c.T266A						PASS	.						48	42	44					9																	12694262		2203	4300	6503	SO:0001583	missense	7306	exon2	Familial Cancer Database		GGGAGGTCTGGCC	L33830	CCDS34990.1	9p23	2013-01-08			ENSG00000107165	ENSG00000107165			12450	protein-coding gene	gene with protein product		115501		TYRP, CAS2		9434945	Standard	NM_000550		Approved	GP75, CATB, TRP, b-PROTEIN, OCA3	uc003zkv.4	P17643	OTTHUMG00000021034	ENST00000388918.5:c.266T>A	9.37:g.12694262T>A	ENSP00000373570:p.Val89Asp	63	0	0		41	11	0.268293	NM_000550	P78468|P78469|Q13721|Q15679	Missense_Mutation	SNP	ENST00000388918.5	37	CCDS34990.1	.	.	.	.	.	.	.	.	.	.	t	4.240	0.043527	0.08196	.	.	ENSG00000107165	ENST00000473763;ENST00000388918	T;D	0.83992	2.37;-1.79	5.5	-11.0	0.00169	Uncharacterised domain, di-copper centre (1);	0.887861	0.09965	N	0.732931	T	0.43077	0.1231	N	0.00771	-1.2	0.09310	N	1	B	0.17038	0.02	B	0.22386	0.039	T	0.49380	-0.8946	10	0.15499	T	0.54	-8.1282	2.5154	0.04667	0.2616:0.3919:0.1284:0.218	.	89	P17643	TYRP1_HUMAN	D	89	ENSP00000419006:V89D;ENSP00000373570:V89D	ENSP00000373570:V89D	V	+	2	0	TYRP1	12684262	0.000000	0.05858	0.000000	0.03702	0.127000	0.20565	-0.596000	0.05720	-2.394000	0.00583	-2.484000	0.00197	GTC	.	.	none		0.587	TYRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055502.3	NM_000550		A	12694262	T	A	12694262	3	1	48	1	0	0	0	0	1	0	0	0	16831	1667	58	5	268	5	TYRP1	9	12694262	Missense_Mutation	SNP	T	TCGA-VB-A8QN-01A-11D-A382-10		12694262	128519169	92	15968											
DCAF12	25853	hgsc.bcm.edu	37	chr9	34125210	34125210	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	acttcccggttcttcaagtaGtatactaaggatctcttcac	10	14	6	11	1	4	0	2	0	2	0	6	1	5	1	1	2	1	3	1	2	5	8			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr9:34125210G>A	ENST00000361264.4	-	2	485	c.144C>T	c.(142-144)taC>taT	p.Y48Y	DCAF12_ENST00000463286.1_5'UTR	NM_015397.3	NP_056212.1	Q5T6F0	DCA12_HUMAN	DDB1 and CUL4 associated factor 12	48					protein ubiquitination (GO:0016567)	centrosome (GO:0005813)|Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)				breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)	11						TCTTCAAGTAGTATACTAAGG	0.463																																					p.Y48Y		Atlas-SNP	.											.	DCAF12	37	.	0			c.C144T						PASS	.						90	85	86					9																	34125210		2203	4300	6503	SO:0001819	synonymous_variant	25853	exon2			CAAGTAGTATACT	AB067479	CCDS6549.1	9p11.2	2013-01-09	2009-07-17	2009-07-17	ENSG00000198876	ENSG00000198876		"WD repeat domain containing", "DDB1 and CUL4 associated factors"	19911	protein-coding gene	gene with protein product	"cancer/testis antigen 102"		"KIAA1892", "WD repeat domain 40A"	KIAA1892, WDR40A		11572484, 9110174	Standard	NM_015397		Approved	DKFZP434O125, MGC1058, CT102, TCC52	uc003ztt.2	Q5T6F0	OTTHUMG00000019806	ENST00000361264.4:c.144C>T	9.37:g.34125210G>A		83	0	0		83	24	0.289157	NM_015397	A8KA70|D3DRL6|Q5T6E9|Q5T6F1|Q6P3V0|Q7L4F8|Q96PZ5|Q9NXA9|Q9UFJ1	Silent	SNP	ENST00000361264.4	37	CCDS6549.1																																																																																			.	.	none		0.463	DCAF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052133.2	NM_015397		A	34125210	G	A	34125210	2	1	48	1	0	0	0	0	0	0	0	1	4265	1024	36	2		2	DCAF12	9	34125210	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	21430948	34125210	107088221	93	15969											
ADARB2	105	hgsc.bcm.edu	37	chr10	1230952	1230952	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tgaaggggggcgacttccccGgctggcgcgcctcggcgtca	4	6	17	14	6	1	1	1	1	0	0	3	2	2	1	3	6	0	1	3	6	1	1	rs138785387		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr10:1230952G>A	ENST00000381312.1	-	9	2217	c.1892C>T	c.(1891-1893)cCg>cTg	p.P631L	ADARB2_ENST00000381310.3_Missense_Mutation_p.P140L|ADARB2_ENST00000381305.1_Missense_Mutation_p.P33L	NM_018702.3	NP_061172.1	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2 (non-functional)	631	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				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)		CGACTTCCCCGGCTGGCGCGC	0.682																																					p.P631L		Atlas-SNP	.											.	ADARB2	95	.	0			c.C1892T						PASS	.	G	LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	27	27	27		1892	4.8	0.9	10	dbSNP_134	27	2,8594	2.2+/-6.3	0,2,4296	yes	missense	ADARB2	NM_018702.3	98	0,3,6498	AA,AG,GG		0.0233,0.0227,0.0231	probably-damaging	631/740	1230952	3,12999	2203	4298	6501	SO:0001583	missense	105	exon9			TTCCCCGGCTGGC	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.1892C>T	10.37:g.1230952G>A	ENSP00000370713:p.Pro631Leu	47	0	0		73	24	0.328767	NM_018702	B2RPJ5|Q5VUT6|Q5VW42	Missense_Mutation	SNP	ENST00000381312.1	37	CCDS7058.1	.	.	.	.	.	.	.	.	.	.	G	15.04	2.714870	0.48622	2.27E-4	2.33E-4	ENSG00000185736	ENST00000381312;ENST00000381310;ENST00000381305	D;D;D	0.93659	-3.26;-3.26;-3.26	4.81	4.81	0.61882	Adenosine deaminase/editase (3);	0.222293	0.46758	D	0.000264	D	0.94706	0.8292	M	0.78049	2.395	0.58432	D	0.999994	P;P;D	0.59767	0.933;0.932;0.986	P;P;P	0.49085	0.537;0.6;0.475	D	0.95484	0.8563	10	0.72032	D	0.01	-27.7191	17.8992	0.88898	0.0:0.0:1.0:0.0	.	631;33;140	Q9NS39;Q5VW43;Q5VW42	RED2_HUMAN;.;.	L	631;140;33	ENSP00000370713:P631L;ENSP00000370711:P140L;ENSP00000370706:P33L	ENSP00000370706:P33L	P	-	2	0	ADARB2	1220952	1.000000	0.71417	0.920000	0.36463	0.080000	0.17528	4.341000	0.59335	2.220000	0.72140	0.561000	0.74099	CCG	G|1.000;A|0.000	0.000	weak		0.682	ADARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046426.1	NM_018702		A	1230952	G	A	1230952	3	1	48	1	0	0	0	0	1	0	0	0	283	1116	39	1	335	1	ADARB2	10	1230952	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10		1230952	134303795	94	15970											
ST8SIA6	338596	hgsc.bcm.edu	37	chr10	17363320	17363320	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aatgtcctccagaaatagggCttttttttcctttaagttcc	9	17	6	9	0	0	1	0	0	0	1	4	1	4	1	4	1	0	2	4	1	4	8			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr10:17363320C>T	ENST00000377602.4	-	8	828	c.754G>A	c.(754-756)Gcc>Acc	p.A252T		NM_001004470.1	NP_001004470.1	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	252					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						AGAAATAGGGCTTTTTTTTCC	0.348																																					p.A252T		Atlas-SNP	.											.	ST8SIA6	85	.	0			c.G754A						PASS	.						37	41	40					10																	17363320		2195	4298	6493	SO:0001583	missense	338596	exon8			ATAGGGCTTTTTT		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.754G>A	10.37:g.17363320C>T	ENSP00000366827:p.Ala252Thr	63	0	0		70	17	0.242857	NM_001004470	B0YJ97|B9EH72|Q5VZH4	Missense_Mutation	SNP	ENST00000377602.4	37	CCDS31158.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.129|0.129	-1.116296|-1.116296	0.01799|0.01799	.|.	.|.	ENSG00000148488|ENSG00000148488	ENST00000377610;ENST00000377602|ENST00000440449	T|.	0.29142|.	1.58|.	5.18|5.18	2.08|2.08	0.27032|0.27032	.|.	0.599365|.	0.19535|.	N|.	0.111928|.	T|T	0.22513|0.22513	0.0543|0.0543	N|N	0.25094|0.25094	0.71|0.71	0.09310|0.09310	N|N	1|1	B|.	0.18461|.	0.028|.	B|.	0.19666|.	0.026|.	T|T	0.19614|0.19614	-1.0300|-1.0300	10|5	0.19590|.	T|.	0.45|.	-9.7736|-9.7736	4.24|4.24	0.10643|0.10643	0.2922:0.4836:0.0:0.2242|0.2922:0.4836:0.0:0.2242	.|.	252|.	P61647|.	SIA8F_HUMAN|.	T|N	82;252|72	ENSP00000366827:A252T|.	ENSP00000366827:A252T|.	A|S	-|-	1|2	0|0	ST8SIA6|ST8SIA6	17403326|17403326	0.002000|0.002000	0.14202|0.14202	0.014000|0.014000	0.15608|0.15608	0.041000|0.041000	0.13682|0.13682	-0.286000|-0.286000	0.08399|0.08399	0.850000|0.850000	0.35239|0.35239	-0.142000|-0.142000	0.14014|0.14014	GCC|AGC	.	.	none		0.348	ST8SIA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047036.1	NM_001004470		T	17363320	C	T	17363320	3	4	48	1	0	0	0	0	1	0	0	0	15251	797	28	2	446	2	ST8SIA6	10	17363320	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	16132368	17363320	118171427	95	15971											
ARID5B	84159	hgsc.bcm.edu	37	chr10	63661942	63661942	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tcggctcaccgtgtggcttgCacggaccttacattttctac	6	13	9	13	3	2	0	1	0	1	0	3	1	2	1	2	3	3	3	2	3	2	5			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr10:63661942C>T	ENST00000279873.7	+	2	456	c.46C>T	c.(46-48)Cac>Tac	p.H16Y		NM_032199.2	NP_115575.1	Q14865	ARI5B_HUMAN	AT rich interactive domain 5B (MRF1-like)	16					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)					GTGTGGCTTGCACGGACCTTA	0.438																																					p.H16Y		Atlas-SNP	.											.	ARID5B	125	.	0			c.C46T						PASS	.						95	103	100					10																	63661942		2203	4300	6503	SO:0001583	missense	84159	exon2			GGCTTGCACGGAC	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.46C>T	10.37:g.63661942C>T	ENSP00000279873:p.His16Tyr	155	0	0		133	30	0.225564	NM_032199	B4DLB3|Q05DG6|Q32Q59|Q5VST4|Q6NZ42|Q7Z3M4|Q8N421|Q9H786	Missense_Mutation	SNP	ENST00000279873.7	37	CCDS31208.1	.	.	.	.	.	.	.	.	.	.	C	19.01	3.742927	0.69418	.	.	ENSG00000150347	ENST00000279873	T	0.53640	0.61	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.68760	0.3036	M	0.65498	2.005	0.80722	D	1	D;D	0.71674	0.996;0.998	D;D	0.78314	0.991;0.983	T	0.70310	-0.4907	10	0.87932	D	0	-19.9629	18.7117	0.91659	0.0:1.0:0.0:0.0	.	16;16	Q14865-3;Q14865	.;ARI5B_HUMAN	Y	16	ENSP00000279873:H16Y	ENSP00000279873:H16Y	H	+	1	0	ARID5B	63331948	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.809000	0.75211	2.712000	0.92718	0.650000	0.86243	CAC	.	.	none		0.438	ARID5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048233.1	XM_084482		T	63661942	C	T	63661942	3	4	48	1	0	0	0	0	1	0	0	0	922	710	25	2	52	2	ARID5B	10	63661942	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	46298622	63661942	71872805	96	15972											
UNC5B	219699	hgsc.bcm.edu	37	chr10	73050831	73050831	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	atctgctgccctgactggtgGtttccaccccgtcaacttta	6	13	8	14	1	2	1	1	1	1	0	3	1	3	1	4	2	3	2	4	2	2	3			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr10:73050831G>T	ENST00000335350.6	+	9	1675	c.1259G>T	c.(1258-1260)gGt>gTt	p.G420V	UNC5B_ENST00000373192.4_Missense_Mutation_p.G409V	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	420					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						CTGACTGGTGGTTTCCACCCC	0.597																																					p.G420V		Atlas-SNP	.											UNC5B,NS,neuroblastoma,+1,2	UNC5B	123	2	0			c.G1259T						PASS	.						240	226	231					10																	73050831		2203	4300	6503	SO:0001583	missense	219699	exon9			CTGGTGGTTTCCA	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.1259G>T	10.37:g.73050831G>T	ENSP00000334329:p.Gly420Val	66	0	0		50	15	0.3	NM_170744	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Missense_Mutation	SNP	ENST00000335350.6	37	CCDS7309.1	.	.	.	.	.	.	.	.	.	.	G	16.05	3.013898	0.54468	.	.	ENSG00000107731	ENST00000335350;ENST00000373192	T;T	0.56275	0.58;0.47	5.39	5.39	0.77823	.	0.108387	0.64402	D	0.000005	T	0.74061	0.3667	M	0.82823	2.61	0.80722	D	1	D;D	0.64830	0.994;0.99	P;P	0.62382	0.901;0.743	T	0.77656	-0.2506	10	0.62326	D	0.03	-29.0247	19.1392	0.93441	0.0:0.0:1.0:0.0	.	409;420	Q8IZJ1-2;Q8IZJ1	.;UNC5B_HUMAN	V	420;409	ENSP00000334329:G420V;ENSP00000362288:G409V	ENSP00000334329:G420V	G	+	2	0	UNC5B	72720837	1.000000	0.71417	0.961000	0.40146	0.094000	0.18550	7.387000	0.79785	2.535000	0.85469	0.655000	0.94253	GGT	.	.	none		0.597	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744		T	73050831	G	T	73050831	3	4	48	1	0	0	0	0	1	0	0	0	17007	1261	44	4	1293	4	UNC5B	10	73050831	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	9388889	73050831	62483916	97	15973											
PTEN	5728	hgsc.bcm.edu	37	chr10	89720852	89720852	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	caaataaagacaaagccaacCgatacttttctccaaatttt	17	11	3	10	1	1	1	0	0	1	1	2	2	1	1	3	0	3	0	3	0	7	6	rs121909231		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr10:89720852C>T	ENST00000371953.3	+	8	2360	c.1003C>T	c.(1003-1005)Cga>Tga	p.R335*	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	335	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.R335*(25)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.R335G(1)|p.W274_F341del(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)		CAAAGCCAACCGATACTTTTC	0.333		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.R335X		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,-1,27	PTEN	3652	27	77	Whole gene deletion(37)|Substitution - Nonsense(25)|Deletion - Frameshift(9)|Deletion - In frame(3)|Unknown(2)|Substitution - Missense(1)	central_nervous_system(25)|prostate(16)|skin(8)|haematopoietic_and_lymphoid_tissue(7)|endometrium(6)|lung(4)|breast(3)|ovary(3)|urinary_tract(2)|upper_aerodigestive_tract(1)|stomach(1)|soft_tissue(1)	c.C1003T	GRCh37	CM971278	PTEN	M	rs121909231	PASS	.						60	63	62					10																	89720852		2203	4298	6501	SO:0001587	stop_gained	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.	GCCAACCGATACT	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.1003C>T	10.37:g.89720852C>T	ENSP00000361021:p.Arg335*	157	0	0		160	28	0.175	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Nonsense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	C	48	14.209601	0.99784	.	.	ENSG00000171862	ENST00000371953	.	.	.	5.37	4.39	0.52855	.	0.053988	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	0.4934	12.825	0.57714	0.2831:0.7169:0.0:0.0	.	.	.	.	X	335	.	.	R	+	1	2	PTEN	89710832	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.629000	0.46485	2.516000	0.84829	0.591000	0.81541	CGA	.	.	weak		0.333	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314		T	89720852	C	T	89720852	4	4	48	1	0	0	0	0	0	1	0	0	12750	644	23	1	1033	1	PTEN	10	89720852	Nonsense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	16670021	89720852	45813895	98	15974											
TH	7054	hgsc.bcm.edu	37	chr11	2189155	2189155	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cgctggcggtacacctggtcCgagaagccctgagggcagag	8	5	16	12	3	0	3	0	1	0	2	1	4	1	3	3	4	2	3	3	4	2	1	rs376615793		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr11:2189155C>T	ENST00000381178.1	-	6	696	c.678G>A	c.(676-678)tcG>tcA	p.S226S	TH_ENST00000333684.5_Silent_p.S199S|TH_ENST00000381175.1_Silent_p.S222S|TH_ENST00000352909.3_Silent_p.S195S	NM_199292.2	NP_954986.2	P07101	TY3H_HUMAN	tyrosine hydroxylase	226					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)	ACACCTGGTCCGAGAAGCCCT	0.672																																					p.S226S		Atlas-SNP	.											TH,colon,carcinoma,-1,1	TH	43	1	0			c.G678A						PASS	.	C	,,	0,4388		0,0,2194	34	28	30		585,678,666	-7.2	0.8	11		30	2,8594	2.2+/-6.3	0,2,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	TH	NM_000360.3,NM_199292.2,NM_199293.2	,,	0,2,6490	TT,TC,CC		0.0233,0.0,0.0154	,,	195/498,226/529,222/525	2189155	2,12982	2194	4298	6492	SO:0001819	synonymous_variant	7054	exon6			CTGGTCCGAGAAG	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.678G>A	11.37:g.2189155C>T		92	0	0		95	48	0.505263	NM_199292	B7ZL70|B7ZL73|Q0PWM2|Q0PWM3|Q15585|Q15588|Q15589|Q2M3B4	Silent	SNP	ENST00000381178.1	37	CCDS7731.1	.	.	.	.	.	.	.	.	.	.	C	9.938	1.216711	0.22373	0.0	2.33E-4	ENSG00000180176	ENST00000412076	.	.	.	3.59	-7.18	0.01505	.	.	.	.	.	T	0.33614	0.0869	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38866	-0.9641	4	.	.	.	-27.0867	0.3619	0.00366	0.2736:0.2138:0.2712:0.2415	.	.	.	.	R	9	.	.	G	-	1	0	TH	2145731	0.000000	0.05858	0.835000	0.33067	0.819000	0.46315	-2.626000	0.00874	-1.699000	0.01416	-0.802000	0.03209	GGA	.	.	weak		0.672	TH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026597.1	NM_000360		T	2189155	C	T	2189155	2	4	48	1	0	0	0	0	0	0	0	1	15853	639	23	1		1	TH	11	2189155	Silent	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10		2189155	132817361	99	15975											
SLC17A6	57084	hgsc.bcm.edu	37	chr11	22364888	22364888	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	cagattccgggaggctacatCgcgtctcggctggcagccaa	8	7	13	13	4	1	1	0	0	1	1	4	2	2	2	2	4	2	3	2	4	2	2	rs557561735		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr11:22364888C>T	ENST00000263160.3	+	3	872	c.435C>T	c.(433-435)atC>atT	p.I145I		NM_020346.2	NP_065079.1	Q9P2U8	VGLU2_HUMAN	solute carrier family 17 (vesicular glutamate transporter), member 6	145					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						GAGGCTACATCGCGTCTCGGC	0.587													C|||	1	0.000199681	0.0008	0.0	5008	,	,		15895	0.0		0.0	False		,,,				2504	0.0				p.I145I		Atlas-SNP	.											.	SLC17A6	135	.	0			c.C435T						PASS	.						64	67	66					11																	22364888		2203	4300	6503	SO:0001819	synonymous_variant	57084	exon3			CTACATCGCGTCT	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.435C>T	11.37:g.22364888C>T		22	0	0		27	8	0.296296	NM_020346	A6NKS2	Silent	SNP	ENST00000263160.3	37	CCDS7856.1																																																																																			.	.	none		0.587	SLC17A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387671.1	NM_020346		T	22364888	C	T	22364888	2	4	48	1	0	0	0	0	0	0	0	1	14436	874	31	1		1	SLC17A6	11	22364888	Silent	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	20175733	22364888	112641628	100	15976											
ANO3	63982	hgsc.bcm.edu	37	chr11	26664763	26664763	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	tttaccaccatctttgttgcGgcttttcctctagcccctct	4	17	5	15	1	3	0	0	0	3	0	4	0	4	0	5	1	3	2	5	1	2	7			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr11:26664763G>A	ENST00000256737.3	+	23	3162	c.2310G>A	c.(2308-2310)gcG>gcA	p.A770A	ANO3_ENST00000537978.1_Silent_p.A754A|ANO3_ENST00000525139.1_Silent_p.A754A|ANO3_ENST00000531568.1_Silent_p.A624A	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						TCTTTGTTGCGGCTTTTCCTC	0.383																																					p.A770A		Atlas-SNP	.											ANO3,right_upper_lobe,carcinoma,0,1	ANO3	145	1	0			c.G2310A						PASS	.						123	111	115					11																	26664763		2203	4299	6502	SO:0001819	synonymous_variant	63982	exon23			TGTTGCGGCTTTT	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.2310G>A	11.37:g.26664763G>A		190	0	0		200	59	0.295	NM_031418	B7Z3F5	Silent	SNP	ENST00000256737.3	37	CCDS31447.1																																																																																			.	.	none		0.383	ANO3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387806.1	NM_031418		A	26664763	G	A	26664763	2	1	48	1	0	0	0	0	0	0	0	1	698	1103	39	1		1	ANO3	11	26664763	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	4299875	26664763	108341753	101	15977											
QSER1	79832	hgsc.bcm.edu	37	chr11	32975559	32975559	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	aagctcttcagaatcctcaaAgcccattgaacttgatggtc	12	11	7	11	0	3	3	2	2	1	1	5	3	4	3	2	1	3	1	2	1	4	3			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr11:32975559A>T	ENST00000399302.2	+	5	4282	c.3947A>T	c.(3946-3948)aAg>aTg	p.K1316M	QSER1_ENST00000527788.1_Missense_Mutation_p.K1077M	NM_001076786.1	NP_001070254.1	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	1316										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)					GAATCCTCAAAGCCCATTGAA	0.433																																					p.K1316M		Atlas-SNP	.											.	QSER1	153	.	0			c.A3947T						PASS	.						84	80	81					11																	32975559		1891	4106	5997	SO:0001583	missense	79832	exon5			CCTCAAAGCCCAT	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.3947A>T	11.37:g.32975559A>T	ENSP00000382241:p.Lys1316Met	87	0	0		78	19	0.24359	NM_001076786	Q6ZU30|Q6ZUR5	Missense_Mutation	SNP	ENST00000399302.2	37	CCDS41631.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.99|11.99	1.804089|1.804089	0.31869|0.31869	.|.	.|.	ENSG00000060749|ENSG00000060749	ENST00000399302;ENST00000078652;ENST00000527788|ENST00000524678	T;T|.	0.27557|.	1.99;1.66|.	5.92|5.92	3.59|3.59	0.41128|0.41128	.|.	0.000000|.	0.64402|.	D|.	0.000003|.	T|T	0.54498|0.54498	0.1862|0.1862	L|L	0.57536|0.57536	1.79|1.79	0.33676|0.33676	D|D	0.611481|0.611481	D;D;D|.	0.71674|.	0.998;0.969;0.983|.	D;P;P|.	0.63113|.	0.911;0.719;0.62|.	T|T	0.61744|0.61744	-0.7000|-0.7000	10|5	0.72032|.	D|.	0.01|.	.|.	8.6295|8.6295	0.33911|0.33911	0.798:0.1346:0.0675:0.0|0.798:0.1346:0.0675:0.0	.|.	1077;1077;1316|.	C9JJ88;Q2KHR3-2;Q2KHR3|.	.;.;QSER1_HUMAN|.	M|C	1316;1077;1077|337	ENSP00000382241:K1316M;ENSP00000432766:K1077M|.	ENSP00000078652:K1077M|.	K|S	+|+	2|1	0|0	QSER1|QSER1	32932135|32932135	0.990000|0.990000	0.36364|0.36364	0.149000|0.149000	0.22428|0.22428	0.006000|0.006000	0.05464|0.05464	3.184000|3.184000	0.50926|0.50926	0.488000|0.488000	0.27723|0.27723	-0.361000|-0.361000	0.07541|0.07541	AAG|AGC	.	.	none		0.433	QSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388448.1	NM_024774		T	32975559	A	T	32975559	3	4	48	1	0	0	0	0	1	0	0	0	12897	72	3	5	3957	5	QSER1	11	32975559	Missense_Mutation	SNP	A	TCGA-VB-A8QN-01A-11D-A382-10	6310796	32975559	102030957	102	15978											
C11orf41	25758	hgsc.bcm.edu	37	chr11	33667498	33667498	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggtggtgaccagcgctccGgggaccatgacgcggcccag	7	4	17	13	4	0	2	0	2	0	0	1	4	1	3	4	5	1	1	4	5	0	0			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr11:33667498G>A	ENST00000321505.4	+	16	4965	c.4785G>A	c.(4783-4785)ccG>ccA	p.P1595P	KIAA1549L_ENST00000389726.3_Silent_p.P1601P			Q6ZVL6	K154L_HUMAN	KIAA1549-like	1595						integral component of membrane (GO:0016021)											CCAGCGCTCCGGGGACCATGA	0.672																																					p.P1595P		Atlas-SNP	.											.	.	.	.	0			c.G4785A						PASS	.						17	20	19					11																	33667498		2000	4159	6159	SO:0001819	synonymous_variant	25758	exon16			CGCTCCGGGGACC	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.4785G>A	11.37:g.33667498G>A		78	0	0		108	26	0.240741	NM_012194	B0QYU0	Silent	SNP	ENST00000321505.4	37	CCDS44565.2																																																																																			.	.	none		0.672	KIAA1549L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317998.1	NM_012194		A	33667498	G	A	33667498	2	1	48	1	0	0	0	0	0	0	0	1	1642	1103	39	1		1	C11orf41	11	33667498	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	691939	33667498	101339018	103	15979											
OR5AP2	338675	hgsc.bcm.edu	37	chr11	56409003	56409003	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	taagatcttctttagggcctTttttacatccttatttttta	8	22	4	7	0	2	1	0	0	2	1	3	1	3	1	2	1	1	0	2	1	5	11			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr11:56409003T>G	ENST00000302981.1	-	1	912	c.913A>C	c.(913-915)Aag>Cag	p.K305Q	OR5AP2_ENST00000544374.1_Missense_Mutation_p.K306Q	NM_001002925.1	NP_001002925.1	Q8NGF4	O5AP2_HUMAN	olfactory receptor, family 5, subfamily AP, member 2	305						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						TTTAGGGCCTTTTTTACATCC	0.343																																					p.K305Q		Atlas-SNP	.											OR5AP2,NS,carcinoma,+2,1	OR5AP2	69	1	0			c.A913C						PASS	.						76	75	75					11																	56409003		2201	4296	6497	SO:0001583	missense	338675	exon1			GGGCCTTTTTTAC	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.913A>C	11.37:g.56409003T>G	ENSP00000303111:p.Lys305Gln	116	0	0		127	21	0.165354	NM_001002925	B2RNM8	Missense_Mutation	SNP	ENST00000302981.1	37	CCDS31534.1	.	.	.	.	.	.	.	.	.	.	T	2.710	-0.269067	0.05716	.	.	ENSG00000172464	ENST00000544374;ENST00000302981	T;T	0.38722	1.12;1.12	4.94	-0.595	0.11660	.	1.447480	0.04221	N	0.333544	T	0.25419	0.0618	N	0.11201	0.11	0.09310	N	1	B	0.11235	0.004	B	0.09377	0.004	T	0.22034	-1.0228	10	0.31617	T	0.26	.	9.4414	0.38670	0.0:0.4066:0.0:0.5934	.	305	Q8NGF4	O5AP2_HUMAN	Q	306;305	ENSP00000442701:K306Q;ENSP00000303111:K305Q	ENSP00000303111:K305Q	K	-	1	0	OR5AP2	56165579	0.000000	0.05858	0.029000	0.17559	0.238000	0.25445	-0.462000	0.06704	0.018000	0.15052	-0.192000	0.12808	AAG	.	.	none		0.343	OR5AP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391613.1	NM_001002925		G	56409003	T	G	56409003	3	3	48	1	0	0	0	0	1	0	0	0	11153	1850	64	5	41	5	OR5AP2	11	56409003	Missense_Mutation	SNP	T	TCGA-VB-A8QN-01A-11D-A382-10	22741505	56409003	78597513	104	15980											
MTA2	9219	hgsc.bcm.edu	37	chr11	62368098	62368098	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	attctgctccactcaccttgTtgagctcctcaatccgtcta	7	14	5	15	1	4	1	2	1	2	0	7	1	7	1	4	0	2	3	4	0	2	4			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr11:62368098T>C	ENST00000278823.2	-	2	481	c.92A>G	c.(91-93)aAc>aGc	p.N31S	MTA2_ENST00000524902.1_5'Flank|MTA2_ENST00000527204.1_5'UTR	NM_004739.3	NP_004730.2	O94776	MTA2_HUMAN	metastasis associated 1 family, member 2	31	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						ACTCACCTTGTTGAGCTCCTC	0.498																																					p.N31S		Atlas-SNP	.											MTA2,NS,carcinoma,0,1	MTA2	54	1	0			c.A92G						PASS	.						81	70	74					11																	62368098		2202	4299	6501	SO:0001583	missense	9219	exon2			ACCTTGTTGAGCT	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.92A>G	11.37:g.62368098T>C	ENSP00000278823:p.Asn31Ser	65	0	0		72	14	0.194444	NM_004739	Q68DB1|Q9UQB5	Missense_Mutation	SNP	ENST00000278823.2	37	CCDS8022.1	.	.	.	.	.	.	.	.	.	.	T	32	5.182718	0.94885	.	.	ENSG00000149480	ENST00000278823	D	0.85411	-1.98	4.85	4.85	0.62838	Bromo adjacent homology (BAH) domain (3);	0.000000	0.85682	D	0.000000	D	0.90896	0.7139	M	0.71296	2.17	0.80722	D	1	P	0.51057	0.941	D	0.71414	0.973	D	0.91635	0.5322	10	0.72032	D	0.01	-8.0007	12.3694	0.55246	0.0:0.0:0.0:1.0	.	31	O94776	MTA2_HUMAN	S	31	ENSP00000278823:N31S	ENSP00000278823:N31S	N	-	2	0	MTA2	62124674	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.192000	0.77771	1.806000	0.52798	0.460000	0.39030	AAC	.	.	none		0.498	MTA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395578.1	NM_004739		C	62368098	T	C	62368098	3	2	48	1	0	0	0	0	1	0	0	0	9918	1725	60	3	1982	3	MTA2	11	62368098	Missense_Mutation	SNP	T	TCGA-VB-A8QN-01A-11D-A382-10	5959095	62368098	72638418	105	15981											
PC	5091	hgsc.bcm.edu	37	chr11	66636367	66636367	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acctgcaggcgggagttgacCtcgatgaagtagtgcttgcc	8	9	14	10	2	0	2	0	2	0	0	1	4	0	3	3	2	3	4	3	2	2	3			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr11:66636367C>G	ENST00000393958.2	-	9	1065	c.972G>C	c.(970-972)gaG>gaC	p.E324D	PC_ENST00000524491.1_Missense_Mutation_p.E284D|PC_ENST00000393955.2_Missense_Mutation_p.E324D|PC_ENST00000393960.1_Missense_Mutation_p.E324D|PC_ENST00000355677.3_Missense_Mutation_p.E324D	NM_000920.3	NP_000911.2	P11498	PYC_HUMAN	pyruvate carboxylase	324	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)	GGGAGTTGACCTCGATGAAGT	0.667																																					p.E324D		Atlas-SNP	.											.	PC	116	.	0			c.G972C						PASS	.						85	76	79					11																	66636367		2200	4295	6495	SO:0001583	missense	5091	exon9			GTTGACCTCGATG	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.972G>C	11.37:g.66636367C>G	ENSP00000377530:p.Glu324Asp	123	0	0		92	8	0.0869565	NM_000920	B4DN00|Q16705	Missense_Mutation	SNP	ENST00000393958.2	37	CCDS8152.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.222436	0.79464	.	.	ENSG00000173599	ENST00000393955;ENST00000393958;ENST00000393960;ENST00000524491;ENST00000355677	D;D;D;D;D	0.99663	-6.33;-6.33;-6.33;-6.33;-6.33	4.65	3.74	0.42951	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);Biotin carboxylation domain (1);	0.000000	0.64402	D	0.000001	D	0.99771	0.9906	H	0.99498	4.595	0.53688	D	0.999978	D	0.89917	1.0	D	0.91635	0.999	D	0.97749	1.0213	10	0.87932	D	0	-29.5504	7.0636	0.25139	0.0:0.7935:0.0:0.2065	.	324	P11498	PYC_HUMAN	D	324;324;324;284;324	ENSP00000377527:E324D;ENSP00000377530:E324D;ENSP00000377532:E324D;ENSP00000434192:E284D;ENSP00000347900:E324D	ENSP00000347900:E324D	E	-	3	2	PC	66392943	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.402000	0.34600	0.949000	0.37715	0.561000	0.74099	GAG	.	.	none		0.667	PC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393115.1	NM_001040716		G	66636367	C	G	66636367	3	3	48	1	0	0	0	0	1	0	0	0	11506	680	24	4	2620	4	PC	11	66636367	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	4268269	66636367	68370149	106	15982											
P2RY6	5031	hgsc.bcm.edu	37	chr11	73008491	73008491	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	tcacccagaagaagttccgcCggcgaccacatgagctccta	11	6	9	15	3	1	3	1	1	0	2	3	4	3	3	5	1	1	2	5	1	3	2	rs139336490		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr11:73008491C>T	ENST00000393590.2	+	2	1227	c.928C>T	c.(928-930)Cgg>Tgg	p.R310W	P2RY6_ENST00000349767.2_Missense_Mutation_p.R310W|P2RY6_ENST00000393591.1_Missense_Mutation_p.R310W|P2RY6_ENST00000540342.1_Missense_Mutation_p.R310W|P2RY6_ENST00000540124.1_Missense_Mutation_p.R310W|P2RY6_ENST00000538328.1_Missense_Mutation_p.R310W|P2RY6_ENST00000542092.1_Missense_Mutation_p.R310W|P2RY6_ENST00000393592.2_Missense_Mutation_p.R310W	NM_001277207.1|NM_001277208.1	NP_001264136.1|NP_001264137.1	Q15077	P2RY6_HUMAN	pyrimidinergic receptor P2Y, G-protein coupled, 6	310					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						GAAGTTCCGCCGGCGACCACA	0.587																																					p.R310W		Atlas-SNP	.											.	P2RY6	45	.	0			c.C928T						PASS	.						31	33	32					11																	73008491		2190	4275	6465	SO:0001583	missense	5031	exon4			TTCCGCCGGCGAC		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.928C>T	11.37:g.73008491C>T	ENSP00000377215:p.Arg310Trp	32	0	0		31	13	0.419355	NM_176796	Q15754	Missense_Mutation	SNP	ENST00000393590.2	37	CCDS8220.1	.	.	.	.	.	.	.	.	.	.	C	13.40	2.225220	0.39300	.	.	ENSG00000171631	ENST00000540342;ENST00000542092;ENST00000349767;ENST00000393592;ENST00000393591;ENST00000540124;ENST00000393590;ENST00000538328	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	4.92	4.92	0.64577	.	0.440844	0.23032	N	0.052725	T	0.32793	0.0841	M	0.76002	2.32	0.39492	D	0.968068	P	0.49635	0.926	B	0.36504	0.226	T	0.47623	-0.9103	10	0.87932	D	0	.	14.0296	0.64606	0.0:0.8365:0.1635:0.0	.	310	Q15077	P2RY6_HUMAN	W	310	ENSP00000443427:R310W;ENSP00000445652:R310W;ENSP00000309771:R310W;ENSP00000377217:R310W;ENSP00000377216:R310W;ENSP00000442551:R310W;ENSP00000377215:R310W;ENSP00000442990:R310W	ENSP00000309771:R310W	R	+	1	2	P2RY6	72686139	0.841000	0.29509	0.911000	0.35937	0.283000	0.27025	2.411000	0.44600	2.696000	0.92011	0.655000	0.94253	CGG	C|1.000;A|0.000	.	alt		0.587	P2RY6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397349.1			T	73008491	C	T	73008491	3	4	48	1	0	0	0	0	1	0	0	0	11363	643	23	1	930	1	P2RY6	11	73008491	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	6372124	73008491	61998025	107	15983											
PGR	5241	hgsc.bcm.edu	37	chr11	100999588	100999588	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgctggtcctgcgtcttttCgtcggaggggtcctgtccct	1	14	13	13	3	1	0	0	0	1	0	6	1	4	1	3	4	2	1	3	4	0	2			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr11:100999588C>T	ENST00000325455.5	-	1	1667	c.214G>A	c.(214-216)Gaa>Aaa	p.E72K	PGR_ENST00000534013.1_Intron|PGR_ENST00000263463.5_Missense_Mutation_p.E72K	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	72	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)	TGCGTCTTTTCGTCGGAGGGG	0.617																																					p.E72K	Pancreas(124;2271 2354 21954 22882)	Atlas-SNP	.											.	PGR	115	.	0			c.G214A						PASS	.						63	54	57					11																	100999588		2203	4300	6503	SO:0001583	missense	5241	exon1			TCTTTTCGTCGGA	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.214G>A	11.37:g.100999588C>T	ENSP00000325120:p.Glu72Lys	56	0	0		49	15	0.306122	NM_000926	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Missense_Mutation	SNP	ENST00000325455.5	37	CCDS8310.1	.	.	.	.	.	.	.	.	.	.	C	2.430	-0.331127	0.05314	.	.	ENSG00000082175	ENST00000325455;ENST00000263463;ENST00000537623	T;T	0.09723	2.95;2.95	4.0	2.06	0.26882	.	1.260700	0.05663	N	0.587210	T	0.08447	0.0210	N	0.22421	0.69	0.09310	N	1	B;B	0.31581	0.329;0.197	B;B	0.20577	0.03;0.03	T	0.40213	-0.9575	10	0.38643	T	0.18	.	11.1299	0.48341	0.0:0.6386:0.3614:0.0	.	72;72	Q8TDS3;P06401	.;PRGR_HUMAN	K	72	ENSP00000325120:E72K;ENSP00000263463:E72K	ENSP00000263463:E72K	E	-	1	0	PGR	100504798	0.000000	0.05858	0.003000	0.11579	0.059000	0.15707	-0.197000	0.09518	0.329000	0.23460	0.561000	0.74099	GAA	.	.	none		0.617	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1			T	100999588	C	T	100999588	3	4	48	1	0	0	0	0	1	0	0	0	11814	893	31	1	2619	1	PGR	11	100999588	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	27991097	100999588	34006928	108	15984											
DIXDC1	85458	hgsc.bcm.edu	37	chr11	111851576	111851576	+	Splice_Site	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	ggaatagagaacagaacaggTactatctctacgcctgcctg	13	8	10	10	1	1	2	0	0	1	2	2	4	1	3	2	2	5	1	2	2	7	4			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr11:111851576T>C	ENST00000389821.4	+	6	1066		c.e6+2		DIXDC1_ENST00000440460.2_Splice_Site|DIXDC1_ENST00000315253.5_Splice_Site			Q155Q3	DIXC1_HUMAN	DIX domain containing 1						camera-type eye development (GO:0043010)|cell cycle (GO:0007049)|cerebellar cortex development (GO:0021695)|cerebral cortex radially oriented cell migration (GO:0021799)|forebrain development (GO:0030900)|forebrain ventricular zone progenitor cell division (GO:0021869)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of axonogenesis (GO:0050772)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JNK cascade (GO:0046330)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of JNK cascade (GO:0046328)|regulation of microtubule cytoskeleton organization (GO:0070507)|Wnt signaling pathway (GO:0016055)	axon terminus (GO:0043679)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cytosol (GO:0005829)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	gamma-tubulin binding (GO:0043015)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)			cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	17		all_cancers(61;7.58e-15)|all_epithelial(67;5.42e-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;2.99e-07)|BRCA - Breast invasive adenocarcinoma(274;6.72e-07)|all cancers(92;6.25e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0548)		ACAGAACAGGTACTATCTCTA	0.483																																					.		Atlas-SNP	.											.	DIXDC1	50	.	0			c.769+2T>C						PASS	.						85	80	81					11																	111851576		1923	4122	6045	SO:0001630	splice_region_variant	85458	exon6			AACAGGTACTATC	AB051522	CCDS60957.1, CCDS73381.1, CCDS73382.1	11q23.1	2014-03-20			ENSG00000150764	ENSG00000150764			23695	protein-coding gene	gene with protein product		610493				12792787	Standard	NM_001037954		Approved	KIAA1735, Dixin	uc001pmm.3	Q155Q3	OTTHUMG00000166912	ENST00000389821.4:c.1066+2T>C	11.37:g.111851576T>C		51	0	0		64	13	0.203125	NM_001037954	A1A5D8|E9PRV4|Q6P2J8|Q6PIK4|Q86SR7|Q8IVY4|Q96N69|Q9C0C8	Splice_Site	SNP	ENST00000389821.4	37		.	.	.	.	.	.	.	.	.	.	T	21.3	4.123010	0.77436	.	.	ENSG00000150764	ENST00000440460;ENST00000315253	.	.	.	5.71	5.71	0.89125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1587	0.72764	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	DIXDC1	111356786	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	5.091000	0.64505	2.182000	0.69389	0.533000	0.62120	.	.	.	none		0.483	DIXDC1-001	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000391833.1	NM_001037954	Intron	C	111851576	T	C	111851576	5	2	48	1	0	0	0	0	0	0	1	0	4543	1652	57	3	820	3	DIXDC1	11	111851576	Splice_Site	SNP	T	TCGA-VB-A8QN-01A-11D-A382-10	10851988	111851576	23154940	109	15985											
CRTAM	56253	hgsc.bcm.edu	37	chr11	122726409	122726409	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	aaattgctacataggtggaaCgctccatgaatttgaaactg	14	11	9	7	1	0	2	0	2	0	0	1	3	1	3	1	2	4	2	1	2	6	4			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr11:122726409C>T	ENST00000227348.4	+	5	544	c.497C>T	c.(496-498)aCg>aTg	p.T166M		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)		ATAGGTGGAACGCTCCATGAA	0.408																																					p.T166M		Atlas-SNP	.											.	CRTAM	50	.	0			c.C497T						PASS	.						96	92	93					11																	122726409		2202	4299	6501	SO:0001583	missense	56253	exon5			GTGGAACGCTCCA	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.497C>T	11.37:g.122726409C>T	ENSP00000227348:p.Thr166Met	66	0	0		116	20	0.172414	NM_019604		Missense_Mutation	SNP	ENST00000227348.4	37	CCDS8437.1	.	.	.	.	.	.	.	.	.	.	C	15.91	2.972531	0.53614	.	.	ENSG00000109943	ENST00000227348	T	0.78364	-1.17	4.86	0.531	0.17108	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.419648	0.24831	N	0.035252	T	0.78444	0.4284	M	0.63843	1.955	0.09310	N	1	D	0.76494	0.999	P	0.56398	0.797	T	0.68492	-0.5394	10	0.62326	D	0.03	.	4.9511	0.14015	0.3121:0.5166:0.0:0.1712	.	166	O95727	CRTAM_HUMAN	M	166	ENSP00000227348:T166M	ENSP00000227348:T166M	T	+	2	0	CRTAM	122231619	0.001000	0.12720	0.000000	0.03702	0.357000	0.29423	0.155000	0.16362	-0.090000	0.12462	0.462000	0.41574	ACG	.	.	none		0.408	CRTAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387507.1	NM_019604		T	122726409	C	T	122726409	3	4	48	1	0	0	0	0	1	0	0	0	3899	536	19	1	515	1	CRTAM	11	122726409	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	10874833	122726409	12280107	110	15986											
DDX25	29118	hgsc.bcm.edu	37	chr11	125774440	125774440	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	cgttactgtggggaggcgacGcaggggcggcggagagcgag	7	4	22	8	6	0	1	0	0	0	1	0	5	0	2	0	7	2	2	0	7	1	1			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr11:125774440G>A	ENST00000263576.6	+	1	183	c.28G>A	c.(28-30)Gca>Aca	p.A10T	DDX25_ENST00000525943.1_Intron|PUS3_ENST00000227474.3_5'Flank|RP11-680F20.9_ENST00000533033.2_RNA	NM_013264.4	NP_037396.3	Q9UHL0	DDX25_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 25	10					mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|ovary(2)|upper_aerodigestive_tract(1)	10	all_hematologic(175;0.177)	Breast(109;0.0021)|all_lung(97;0.0203)|Lung NSC(97;0.0203)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.14e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.046)		GGGAGGCGACGCAGGGGCGGC	0.726																																					p.A10T		Atlas-SNP	.											.	DDX25	65	.	0			c.G28A						PASS	.						4	11	9					11																	125774440		584	1438	2022	SO:0001583	missense	29118	exon1			GGCGACGCAGGGG	AF155140	CCDS44766.1	11q24	2012-02-23	2012-02-23		ENSG00000109832	ENSG00000109832		"DEAD-boxes"	18698	protein-coding gene	gene with protein product	"gonadotropin-regulated testicular RNA helicase"	607663	"DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 25", "DEAD (Asp-Glu-Ala-Asp) box polypeptide 25"			10608860, 15096601	Standard	NM_013264		Approved	GRTH	uc001qcz.5	Q9UHL0	OTTHUMG00000165859	ENST00000263576.6:c.28G>A	11.37:g.125774440G>A	ENSP00000263576:p.Ala10Thr	37	0	0		71	38	0.535211	NM_013264	B2R6Z0|Q5XVN2|Q86W81|Q8IYP1	Missense_Mutation	SNP	ENST00000263576.6	37	CCDS44766.1	.	.	.	.	.	.	.	.	.	.	G	14.50	2.554398	0.45487	.	.	ENSG00000109832	ENST00000263576	T	0.03413	3.94	4.15	3.23	0.37069	.	0.279248	0.25458	N	0.030527	T	0.02304	0.0071	N	0.22421	0.69	0.28701	N	0.904047	P;P	0.35551	0.509;0.509	B;B	0.27887	0.084;0.084	T	0.43376	-0.9395	10	0.17369	T	0.5	1.0E-4	9.6226	0.39730	0.0:0.2478:0.7522:0.0	.	10;10	B4DHI6;Q9UHL0	.;DDX25_HUMAN	T	10	ENSP00000263576:A10T	ENSP00000263576:A10T	A	+	1	0	DDX25	125279650	0.995000	0.38212	0.972000	0.41901	0.908000	0.53690	2.400000	0.44504	0.905000	0.36596	0.462000	0.41574	GCA	.	.	none		0.726	DDX25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386736.3	NM_013264		A	125774440	G	A	125774440	3	1	48	1	0	0	0	0	1	0	0	0	4354	1087	38	1	30	1	DDX25	11	125774440	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	3048031	125774440	9232076	111	15987											
PTPN6	5777	hgsc.bcm.edu	37	chr12	7061261	7061261	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tggagtactacactcagcagCagggtgtcctgcaggaccgc	9	7	13	12	1	1	0	1	0	0	0	2	2	2	2	2	3	5	4	2	3	2	2			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr12:7061261C>T	ENST00000318974.9	+	3	491	c.247C>T	c.(247-249)Cag>Tag	p.Q83*	PTPN6_ENST00000447931.2_Nonsense_Mutation_p.Q44*|PTPN6_ENST00000456013.1_Nonsense_Mutation_p.Q83*|PTPN6_ENST00000399448.1_Nonsense_Mutation_p.Q85*	NM_002831.5	NP_002822.2	P29350	PTN6_HUMAN	protein tyrosine phosphatase, non-receptor type 6	83	SH2 1. {ECO:0000255|PROSITE- ProRule:PRU00191}.				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						CACTCAGCAGCAGGGTGTCCT	0.582																																					p.Q85X		Atlas-SNP	.											.	PTPN6	42	.	0			c.C253T						PASS	.						109	128	122					12																	7061261		2199	4299	6498	SO:0001587	stop_gained	5777	exon3			CAGCAGCAGGGTG		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.247C>T	12.37:g.7061261C>T	ENSP00000326010:p.Gln83*	77	0	0		77	26	0.337662	NM_080548	A8K306|G3V0F8|Q969V8|Q9UK67	Nonsense_Mutation	SNP	ENST00000318974.9	37	CCDS44820.1	.	.	.	.	.	.	.	.	.	.	C	37	6.099851	0.97281	.	.	ENSG00000111679	ENST00000543115;ENST00000399448;ENST00000447931;ENST00000538715;ENST00000318974;ENST00000456013;ENST00000536521;ENST00000541698;ENST00000542462	.	.	.	4.68	4.68	0.58851	.	0.198796	0.43747	D	0.000523	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.3729	0.60723	0.0:0.842:0.158:0.0	.	.	.	.	X	104;85;44;83;83;83;83;83;42	.	ENSP00000326010:Q83X	Q	+	1	0	PTPN6	6931522	1.000000	0.71417	0.862000	0.33874	0.890000	0.51754	4.947000	0.63583	2.149000	0.67028	0.561000	0.74099	CAG	.	.	none		0.582	PTPN6-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400023.1	NM_002831		T	7061261	C	T	7061261	4	4	48	1	0	0	0	0	0	1	0	0	12807	711	25	2	275	2	PTPN6	12	7061261	Nonsense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10		7061261	126790634	112	15988											
PTPN6	5777	hgsc.bcm.edu	37	chr12	7067131	7067131	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccagtacctgagctggcccgAccatggggtccccagtgagc	7	6	13	15	1	0	2	0	2	0	0	1	3	1	2	6	3	3	2	6	3	1	1			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr12:7067131A>G	ENST00000318974.9	+	11	1500	c.1256A>G	c.(1255-1257)gAc>gGc	p.D419G	PTPN6_ENST00000447931.2_Missense_Mutation_p.D380G|PTPN6_ENST00000456013.1_Missense_Mutation_p.D419G|PTPN6_ENST00000399448.1_Missense_Mutation_p.D421G	NM_002831.5	NP_002822.2	P29350	PTN6_HUMAN	protein tyrosine phosphatase, non-receptor type 6	419	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						AGCTGGCCCGACCATGGGGTC	0.612																																					p.D421G		Atlas-SNP	.											.	PTPN6	42	.	0			c.A1262G						PASS	.						65	71	69					12																	7067131		1956	4143	6099	SO:0001583	missense	5777	exon11			GGCCCGACCATGG		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.1256A>G	12.37:g.7067131A>G	ENSP00000326010:p.Asp419Gly	39	0	0		42	20	0.47619	NM_080548	A8K306|G3V0F8|Q969V8|Q9UK67	Missense_Mutation	SNP	ENST00000318974.9	37	CCDS44820.1	.	.	.	.	.	.	.	.	.	.	A	27.5	4.834452	0.91036	.	.	ENSG00000111679	ENST00000399448;ENST00000447931;ENST00000318974;ENST00000456013	D;D;D;D	0.86230	-2.09;-2.09;-2.09;-2.09	5.08	5.08	0.68730	Protein-tyrosine phosphatase, receptor/non-receptor type (4);	0.000000	0.85682	D	0.000000	D	0.96303	0.8794	H	0.98849	4.35	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;0.996	D;D;D;D;D	0.97110	1.0;0.998;0.997;0.999;0.96	D	0.97996	1.0357	10	0.87932	D	0	.	14.8457	0.70259	1.0:0.0:0.0:0.0	.	407;380;419;419;421	B4DPS0;P29350-2;G3V0F8;P29350;Q53XS4	.;.;.;PTN6_HUMAN;.	G	421;380;419;419	ENSP00000382376:D421G;ENSP00000415979:D380G;ENSP00000326010:D419G;ENSP00000391592:D419G	ENSP00000326010:D419G	D	+	2	0	PTPN6	6937392	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.307000	0.96226	1.901000	0.55032	0.459000	0.35465	GAC	.	.	none		0.612	PTPN6-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400023.1	NM_002831		G	7067131	A	G	7067131	3	3	48	1	0	0	0	0	1	0	0	0	12807	275	10	3	1316	3	PTPN6	12	7067131	Missense_Mutation	SNP	A	TCGA-VB-A8QN-01A-11D-A382-10	5870	7067131	126784764	113	15989											
PDE3A	5139	hgsc.bcm.edu	37	chr12	20522508	20522508	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcagtgtaaggaggcggcggCggcggaggaggaggaagcag	10	2	23	6	4	0	0	0	0	0	0	0	5	0	5	0	9	1	3	0	9	2	1			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr12:20522508C>T	ENST00000359062.3	+	1	330	c.290C>T	c.(289-291)gCg>gTg	p.A97V	RP11-284H19.1_ENST00000535755.1_RNA	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	97	Poly-Ala.				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)	GAGGCGGCGGCGGCGGAGGAG	0.746																																					p.A97V		Atlas-SNP	.											.	PDE3A	184	.	0			c.C290T						PASS	.						4	4	4					12																	20522508		2044	4045	6089	SO:0001583	missense	5139	exon1			CGGCGGCGGCGGA		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.290C>T	12.37:g.20522508C>T	ENSP00000351957:p.Ala97Val	58	0	0		63	17	0.269841	NM_000921	O60865|Q13348|Q17RD1	Missense_Mutation	SNP	ENST00000359062.3	37	CCDS31754.1	.	.	.	.	.	.	.	.	.	.	C	13.39	2.224155	0.39300	.	.	ENSG00000172572	ENST00000359062	T	0.66099	-0.19	4.9	2.78	0.32641	.	1.198670	0.06095	N	0.664382	T	0.41119	0.1145	N	0.08118	0	0.26441	N	0.975772	P	0.51351	0.944	B	0.40228	0.323	T	0.34054	-0.9844	10	0.56958	D	0.05	.	6.2375	0.20772	0.3302:0.5183:0.1515:0.0	.	97	Q14432	PDE3A_HUMAN	V	97	ENSP00000351957:A97V	ENSP00000351957:A97V	A	+	2	0	PDE3A	20413775	0.766000	0.28496	0.988000	0.46212	0.517000	0.34286	0.127000	0.15790	1.002000	0.39104	0.449000	0.29647	GCG	.	.	none		0.746	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2			T	20522508	C	T	20522508	3	4	48	1	0	0	0	0	1	0	0	0	11646	768	27	1	292	1	PDE3A	12	20522508	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	13455377	20522508	113329387	114	15990											
LST-3TM12	338821	hgsc.bcm.edu	37	chr12	21201645	21201645	+	Splice_Site	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcttttttctcttatttctaGgagtcctcgccctacctgct	4	18	6	13	1	2	0	0	0	2	0	5	1	3	1	3	1	2	2	3	1	3	7			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr12:21201645G>A	ENST00000421593.2	+	8	994		c.e8-1		SLCO1B7_ENST00000554957.1_Splice_Site|LST3_ENST00000540229.1_Intron|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						CTTATTTCTAGGAGTCCTCGC	0.333																																					.		Atlas-SNP	.											.	SLCO1B7	85	.	0			c.995-1G>A						PASS	.						25	23	24					12																	21201645		1917	4160	6077	SO:0001630	splice_region_variant	338821	exon8			TTTCTAGGAGTCC	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	ENST00000421593.2:c.995-1G>A	12.37:g.21201645G>A		145	0	0		143	34	0.237762	NM_001009562	Q71QF0	Splice_Site	SNP	ENST00000421593.2	37	CCDS44843.1	.	.	.	.	.	.	.	.	.	.	.	8.546	0.874312	0.17395	.	.	ENSG00000257046;ENSG00000205754;ENSG00000205754	ENST00000381541;ENST00000554957;ENST00000421593	.	.	.	3.45	3.45	0.39498	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2399	0.54536	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLCO1B7;RP11-545J16.1	21092912	1.000000	0.71417	0.997000	0.53966	0.177000	0.22998	6.639000	0.74314	1.909000	0.55274	0.508000	0.49915	.	.	.	none		0.333	SLCO1B7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402066.1	NM_001009562	Intron	A	21201645	G	A	21201645	5	1	48	1	0	0	0	0	0	0	1	0	9075	1014	35	2	1024	2	LST-3TM12	12	21201645	Splice_Site	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	679137	21201645	112650250	115	15991											
KRAS	3845	hgsc.bcm.edu	37	chr12	25398262	25398262	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ttctgaattagctgtatcgtCaaggcactcttgcctacgcc	8	13	8	12	2	3	1	1	1	2	0	4	1	3	1	2	1	3	3	2	1	5	5	rs121913538		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr12:25398262C>A	ENST00000256078.4	-	2	120	c.57G>T	c.(55-57)ttG>ttT	p.L19F	KRAS_ENST00000311936.3_Missense_Mutation_p.L19F|KRAS_ENST00000557334.1_Missense_Mutation_p.L19F|KRAS_ENST00000556131.1_Missense_Mutation_p.L19F	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	19					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.L19F(15)	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)			GCTGTATCGTCAAGGCACTCT	0.358		119	Mis		"pancreatic, colorectal, lung, thyroid, AML, others"				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.L19F	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,colon,carcinoma,0,22	KRAS	30930	22	15	Substitution - Missense(15)	large_intestine(10)|haematopoietic_and_lymphoid_tissue(5)	c.G57T						PASS	.						89	78	82					12																	25398262		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	TATCGTCAAGGCA	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.57G>T	12.37:g.25398262C>A	ENSP00000256078:p.Leu19Phe	179	0	0		173	41	0.236994	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.992040	0.74703	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	D;T;T;T	0.86562	-2.14;-1.3;-1.3;-1.3	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.94364	0.8188	M	0.89840	3.065	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.94992	0.8135	10	0.87932	D	0	.	14.0395	0.64665	0.0:0.8488:0.1512:0.0	.	19;19	P01116-2;P01116	.;RASK_HUMAN	F	19	ENSP00000308495:L19F;ENSP00000452512:L19F;ENSP00000256078:L19F;ENSP00000451856:L19F	ENSP00000256078:L19F	L	-	3	2	KRAS	25289529	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.986000	0.40677	2.668000	0.90789	0.563000	0.77884	TTG	.	.	weak		0.358	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360		A	25398262	C	A	25398262	3	1	48	1	0	0	0	0	1	0	0	0	8447	825	29	4	649	4	KRAS	12	25398262	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	4196617	25398262	108453633	116	15992											
FGD4	121512	hgsc.bcm.edu	37	chr12	32734984	32734984	+	Silent	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggcatggattgacaaccacAcctcaacaaaaactcctctc	15	7	5	14	0	2	1	1	1	1	0	4	2	3	2	3	2	3	1	3	2	4	1			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr12:32734984A>G	ENST00000427716.2	+	4	607	c.183A>G	c.(181-183)acA>acG	p.T61T	FGD4_ENST00000546442.1_5'UTR|FGD4_ENST00000531134.1_Silent_p.T146T|FGD4_ENST00000534526.2_Silent_p.T198T|FGD4_ENST00000266482.3_5'UTR|FGD4_ENST00000472289.1_Silent_p.T61T|FGD4_ENST00000525053.1_Silent_p.T173T	NM_139241.2	NP_640334.2	Q96M96	FGD4_HUMAN	FYVE, RhoGEF and PH domain containing 4	61	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)					TGACAACCACACCTCAACAAA	0.448																																					p.T61T		Atlas-SNP	.											.	FGD4	86	.	0			c.A183G						PASS	.						117	117	117					12																	32734984		2203	4300	6503	SO:0001819	synonymous_variant	121512	exon4			AACCACACCTCAA	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.183A>G	12.37:g.32734984A>G		113	0	0		114	28	0.245614	NM_139241	Q6ULS2|Q8TCP6	Silent	SNP	ENST00000427716.2	37	CCDS8727.1																																																																																			.	.	none		0.448	FGD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268017.1	NM_139241		G	32734984	A	G	32734984	2	3	48	1	0	0	0	0	0	0	0	1	5843	146	6	3		3	FGD4	12	32734984	Silent	SNP	A	TCGA-VB-A8QN-01A-11D-A382-10	7336722	32734984	101116911	117	15993											
DIP2B	57609	hgsc.bcm.edu	37	chr12	51126265	51126265	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aaagacatcgggctgtccccGcgggctgtcagcaccacttt	8	8	11	14	3	1	1	1	0	0	1	3	1	2	1	3	2	1	3	3	2	1	1			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr12:51126265G>A	ENST00000301180.5	+	32	3961	c.3927G>A	c.(3925-3927)ccG>ccA	p.P1309P		NM_173602.2	NP_775873.2	Q9P265	DIP2B_HUMAN	DIP2 disco-interacting protein 2 homolog B (Drosophila)	1309						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						GGCTGTCCCCGCGGGCTGTCA	0.532																																					p.P1309P		Atlas-SNP	.											.	DIP2B	167	.	0			c.G3927A						PASS	.						88	79	82					12																	51126265		2203	4300	6503	SO:0001819	synonymous_variant	57609	exon32			GTCCCCGCGGGCT	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.3927G>A	12.37:g.51126265G>A		57	0	0		46	6	0.130435	NM_173602	Q6B011|Q8N1L5|Q8NB38	Silent	SNP	ENST00000301180.5	37	CCDS31799.1																																																																																			.	.	none		0.532	DIP2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404243.1	NM_173602		A	51126265	G	A	51126265	2	1	48	1	0	0	0	0	0	0	0	1	4530	1074	38	1		1	DIP2B	12	51126265	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	18391281	51126265	82725630	118	15994											
CTDSP2	10106	hgsc.bcm.edu	37	chr12	58217705	58217705	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	actgcattctcggggtggaaTatgtaagaagcaggcgagtt	11	10	14	6	2	1	1	0	0	1	1	2	3	1	2	0	4	2	4	0	4	4	4	rs78662830		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr12:58217705T>C	ENST00000398073.2	-	7	975	c.672A>G	c.(670-672)atA>atG	p.I224M	CTDSP2_ENST00000547701.1_Missense_Mutation_p.I72M|MIR26A2_ENST00000385054.1_RNA|CTDSP2_ENST00000548823.1_Missense_Mutation_p.I51M	NM_005730.3	NP_005721.3	O14595	CTDS2_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 2	224	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.				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)					CGGGGTGGAATATGTAAGAAG	0.577																																					p.I224M		Atlas-SNP	.											.	CTDSP2	25	.	0			c.A672G						PASS	.						42	44	43					12																	58217705		2042	4196	6238	SO:0001583	missense	10106	exon7			GTGGAATATGTAA	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.672A>G	12.37:g.58217705T>C	ENSP00000381148:p.Ile224Met	23	0	0		29	8	0.275862	NM_005730	A8K5H4|Q53ZR2|Q6NZY3|Q9UEX1	Missense_Mutation	SNP	ENST00000398073.2	37	CCDS41801.1	.	.	.	.	.	.	.	.	.	.	T	14.56	2.572529	0.45798	.	.	ENSG00000175215	ENST00000398073;ENST00000548823;ENST00000549039;ENST00000547701	T;T;T;T	0.17213	2.29;2.29;2.29;2.29	5.43	3.62	0.41486	NLI interacting factor (3);Dullard phosphatase domain, eukaryotic (1);HAD-like domain (2);	0.044888	0.85682	D	0.000000	T	0.27663	0.0680	L	0.36672	1.1	0.58432	D	0.999997	B;D;P	0.69078	0.124;0.997;0.844	P;D;P	0.69479	0.482;0.964;0.749	T	0.01341	-1.1380	10	0.66056	D	0.02	-14.9731	9.633	0.39791	0.0745:0.0:0.7823:0.1432	.	98;51;224	B4DH48;F8W1I1;O14595	.;.;CTDS2_HUMAN	M	224;51;78;72	ENSP00000381148:I224M;ENSP00000447046:I51M;ENSP00000448386:I78M;ENSP00000446705:I72M	ENSP00000381148:I224M	I	-	3	3	CTDSP2	56503972	1.000000	0.71417	1.000000	0.80357	0.257000	0.26127	3.225000	0.51246	0.866000	0.35629	-1.048000	0.02349	ATA	.	.	alt		0.577	CTDSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409353.1	NM_005730		C	58217705	T	C	58217705	3	2	48	1	0	0	0	0	1	0	0	0	4006	1396	49	3	151	3	CTDSP2	12	58217705	Missense_Mutation	SNP	T	TCGA-VB-A8QN-01A-11D-A382-10	7091440	58217705	75634190	119	15995											
TCTN1	79600	hgsc.bcm.edu	37	chr12	111082831	111082831	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggtgaagagcctgctgtgggGccagggcttcccagattacg	7	8	16	10	1	0	3	0	1	0	2	1	3	1	3	3	4	3	2	3	4	2	2			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr12:111082831G>T	ENST00000551590.1	+	12	1547	c.1391G>T	c.(1390-1392)gGc>gTc	p.G464V	TCTN1_ENST00000397659.4_Missense_Mutation_p.G464V|TCTN1_ENST00000397655.3_Missense_Mutation_p.G450V|HVCN1_ENST00000548312.1_Intron|TCTN1_ENST00000377654.3_Silent_p.G210G			Q2MV58	TECT1_HUMAN	tectonic family member 1	464					central nervous system interneuron axonogenesis (GO:0021956)|cilium morphogenesis (GO:0060271)|dorsal/ventral neural tube patterning (GO:0021904)|in utero embryonic development (GO:0001701)|neural tube formation (GO:0001841)|regulation of smoothened signaling pathway (GO:0008589)|somatic motor neuron differentiation (GO:0021523)|telencephalon development (GO:0021537)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|membrane (GO:0016020)|TCTN-B9D complex (GO:0036038)				NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(9)|urinary_tract(1)	15						CTGCTGTGGGGCCAGGGCTTC	0.547																																					p.G464V		Atlas-SNP	.											.	TCTN1	37	.	0			c.G1391T						PASS	.						78	78	78					12																	111082831		1878	4104	5982	SO:0001583	missense	79600	exon12			TGTGGGGCCAGGG	AK055891	CCDS41833.1, CCDS41834.1, CCDS41835.1	12q24.11	2011-09-07			ENSG00000204852	ENSG00000204852		"Tectonic proteins"	26113	protein-coding gene	gene with protein product		609863				16357211	Standard	NM_001082537		Approved	FLJ21127, TECT1, JBTS13	uc001trn.4	Q2MV58	OTTHUMG00000150051	ENST00000551590.1:c.1391G>T	12.37:g.111082831G>T	ENSP00000448735:p.Gly464Val	49	0	0		49	12	0.244898	NM_001082537	A8MX11|Q49A60|Q6P5X1|Q6UXW2|Q8NAE9|Q96N72|Q9H798	Missense_Mutation	SNP	ENST00000551590.1	37	CCDS41835.1	.	.	.	.	.	.	.	.	.	.	G	17.53	3.412968	0.62511	.	.	ENSG00000204852	ENST00000397650;ENST00000551590;ENST00000397655;ENST00000397657;ENST00000397659;ENST00000397652;ENST00000547461;ENST00000552038	T;T;T	0.80566	-1.38;-1.39;-1.37	5.66	5.66	0.87406	.	1.378350	0.04967	N	0.463180	D	0.92169	0.7517	M	0.80183	2.485	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	0.83235	-0.0061	10	0.44086	T	0.13	-8.2873	20.1253	0.97977	0.0:0.0:1.0:0.0	.	464;450;464	Q2MV58;Q2MV58-3;Q2MV58-2	TECT1_HUMAN;.;.	V	355;464;450;286;464;408;25;68	ENSP00000448735:G464V;ENSP00000380775:G450V;ENSP00000380779:G464V	ENSP00000380771:G355V	G	+	2	0	TCTN1	109567214	1.000000	0.71417	1.000000	0.80357	0.126000	0.20510	5.516000	0.67055	2.832000	0.97577	0.655000	0.94253	GGC	.	.	none		0.547	TCTN1-001	KNOWN	non_canonical_TEC|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000316016.2	NM_024549		T	111082831	G	T	111082831	3	4	48	1	0	0	0	0	1	0	0	0	15737	1203	42	4	1609	4	TCTN1	12	111082831	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	52865126	111082831	22769064	120	15996											
ACAD10	80724	hgsc.bcm.edu	37	chr12	112182836	112182836	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggagcccctccccactgatcGaagacctcaaggtaaagcag	12	5	10	14	1	1	2	1	1	0	1	3	4	2	3	5	2	2	2	5	2	4	1	rs147958599		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr12:112182836G>A	ENST00000313698.4	+	13	2259	c.2104G>A	c.(2104-2106)Gaa>Aaa	p.E702K	ACAD10_ENST00000413681.3_3'UTR|ACAD10_ENST00000549590.1_Missense_Mutation_p.E702K|ACAD10_ENST00000392636.2_Missense_Mutation_p.E304K|ACAD10_ENST00000455480.2_Missense_Mutation_p.E733K	NM_025247.5	NP_079523.3	Q6JQN1	ACD10_HUMAN	acyl-CoA dehydrogenase family, member 10	702						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						CCCACTGATCGAAGACCTCAA	0.612																																					p.E733K		Atlas-SNP	.											.	ACAD10	93	.	0			c.G2197A						PASS	.	G	LYS/GLU,LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	42	45	44		2197,2104	4.4	0.4	12	dbSNP_134	44	0,8600		0,0,4300	no	missense,missense	ACAD10	NM_001136538.1,NM_025247.5	56,56	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	733/1091,702/1060	112182836	1,13005	2203	4300	6503	SO:0001583	missense	80724	exon14			CTGATCGAAGACC	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.2104G>A	12.37:g.112182836G>A	ENSP00000325137:p.Glu702Lys	26	0	0		27	5	0.185185	NM_001136538	G3XAJ0|Q8N828|Q8NAP2|Q96BX5	Missense_Mutation	SNP	ENST00000313698.4	37	CCDS31903.1	.	.	.	.	.	.	.	.	.	.	G	18.93	3.727387	0.69074	2.27E-4	0.0	ENSG00000111271	ENST00000392636;ENST00000413681;ENST00000549590;ENST00000455480;ENST00000515283;ENST00000313698	D;T;D;D	0.99704	-6.46;2.87;-6.46;-6.46	5.31	4.42	0.53409	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA dehydrogenase, N-terminal (1);Acyl-CoA dehydrogenase/oxidase, N-terminal (1);	0.294003	0.30311	N	0.009911	D	0.99566	0.9844	M	0.83312	2.635	0.45150	D	0.998164	D;D;P	0.60575	0.979;0.988;0.948	P;P;B	0.60012	0.689;0.867;0.397	D	0.97992	1.0355	10	0.62326	D	0.03	.	13.3098	0.60374	0.0786:0.0:0.9214:0.0	.	733;702;702	G3XAJ0;Q6JQN1;Q6JQN1-2	.;ACD10_HUMAN;.	K	304;702;702;733;95;702	ENSP00000376411:E304K;ENSP00000446959:E702K;ENSP00000389813:E733K;ENSP00000325137:E702K	ENSP00000325137:E702K	E	+	1	0	ACAD10	110667219	1.000000	0.71417	0.439000	0.26833	0.268000	0.26511	3.485000	0.53208	1.378000	0.46305	0.655000	0.94253	GAA	G|1.000;A|0.000	0.000	weak		0.612	ACAD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368307.1	NM_025247		A	112182836	G	A	112182836	3	1	48	1	0	0	0	0	1	0	0	0	108	1059	37	1	2247	1	ACAD10	12	112182836	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	1100005	112182836	21669059	121	15997											
TBX3	6926	hgsc.bcm.edu	37	chr12	115112370	115112370	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gcgctgtgccctcgcgaaccGggctcctgcgctcctccgcg	2	7	13	19	7	0	0	0	0	0	0	4	1	3	0	5	1	3	3	5	1	1	0	rs371891930		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr12:115112370G>A	ENST00000257566.3	-	7	1759	c.1370C>T	c.(1369-1371)cCg>cTg	p.P457L	TBX3_ENST00000349155.2_Missense_Mutation_p.P437L	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	457					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)		CTCGCGAACCGGGCTCCTGCG	0.751																																					p.P457L		Atlas-SNP	.											TBX3,NS,carcinoma,+1,1	TBX3	106	1	0			c.C1370T						PASS	.	G	LEU/PRO,LEU/PRO	0,4302		0,0,2151	8	11	10		1310,1370	5.1	0.9	12		10	1,8327		0,1,4163	no	missense,missense	TBX3	NM_005996.3,NM_016569.3	98,98	0,1,6314	AA,AG,GG		0.012,0.0,0.0079	probably-damaging,probably-damaging	437/724,457/744	115112370	1,12629	2151	4164	6315	SO:0001583	missense	6926	exon7			CGAACCGGGCTCC	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.1370C>T	12.37:g.115112370G>A	ENSP00000257566:p.Pro457Leu	35	0	0		46	9	0.195652	NM_016569	Q8TB20|Q9UKF8	Missense_Mutation	SNP	ENST00000257566.3	37	CCDS9176.1	.	.	.	.	.	.	.	.	.	.	G	14.47	2.543547	0.45280	0.0	1.2E-4	ENSG00000135111	ENST00000349155;ENST00000257566;ENST00000361100	D;D	0.87412	-2.25;-2.24	5.14	5.14	0.70334	.	3.995250	0.00465	N	0.000108	D	0.94341	0.8181	M	0.71581	2.175	0.80722	D	1	P;D	0.89917	0.807;1.0	B;D	0.87578	0.375;0.998	T	0.82827	-0.0265	10	0.29301	T	0.29	.	17.5833	0.87973	0.0:0.0:1.0:0.0	.	437;457	O15119-2;O15119	.;TBX3_HUMAN	L	437;457;457	ENSP00000257567:P437L;ENSP00000257566:P457L	ENSP00000257566:P457L	P	-	2	0	TBX3	113596753	1.000000	0.71417	0.871000	0.34182	0.016000	0.09150	8.587000	0.90810	2.391000	0.81399	0.591000	0.81541	CCG	.	.	weak		0.751	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404947.2	NM_016569, NM_005996		A	115112370	G	A	115112370	3	1	48	1	0	0	0	0	1	0	0	0	15674	1116	39	1	869	1	TBX3	12	115112370	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	2929534	115112370	18739525	122	15998											
P2RX4	5025	hgsc.bcm.edu	37	chr12	121670290	121670290	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	aggcctatggcatccgcttcGacatcattgtgtttgggaag	8	12	12	9	2	1	0	1	0	0	0	3	2	2	1	2	3	0	3	2	3	2	4			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr12:121670290G>A	ENST00000337233.4	+	9	1266	c.958G>A	c.(958-960)Gac>Aac	p.D320N	P2RX4_ENST00000543171.1_Missense_Mutation_p.D219N|P2RX4_ENST00000541532.1_3'UTR|P2RX4_ENST00000359949.7_Missense_Mutation_p.D336N	NM_001261397.1|NM_001261398.1|NM_002560.2	NP_001248326.1|NP_001248327.1|NP_002551.2	Q99571	P2RX4_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 4	320					apoptotic signaling pathway (GO:0097190)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cellular response to ATP (GO:0071318)|endothelial cell activation (GO:0042118)|ion transmembrane transport (GO:0034220)|membrane depolarization (GO:0051899)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|neuronal action potential (GO:0019228)|nitric oxide biosynthetic process (GO:0006809)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of prostaglandin secretion (GO:0032308)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction (GO:0055117)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sodium ion transport (GO:0002028)|relaxation of cardiac muscle (GO:0055119)|response to ATP (GO:0033198)|response to fluid shear stress (GO:0034405)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|tissue homeostasis (GO:0001894)|transport (GO:0006810)|vasodilation (GO:0042311)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|cadherin binding (GO:0045296)|copper ion binding (GO:0005507)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)|zinc ion binding (GO:0008270)			breast(1)|kidney(4)|large_intestine(4)|lung(7)|prostate(1)	17	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CATCCGCTTCGACATCATTGT	0.597																																					p.D336N		Atlas-SNP	.											.	P2RX4	27	.	0			c.G1006A						PASS	.						98	81	87					12																	121670290		2203	4300	6503	SO:0001583	missense	5025	exon10			CGCTTCGACATCA	Y07684	CCDS9214.1, CCDS58282.1	12q24.32	2012-01-17			ENSG00000135124	ENSG00000135124		"Purinergic receptors", "Ligand-gated ion channels / Purinergic receptors, ionotropic"	8535	protein-coding gene	gene with protein product		600846				9016352	Standard	NM_002560		Approved	P2X4	uc031qjt.1	Q99571	OTTHUMG00000169155	ENST00000337233.4:c.958G>A	12.37:g.121670290G>A	ENSP00000336607:p.Asp320Asn	59	0	0		56	13	0.232143	NM_001256796	E7EPF7|F6RU17|O00450|O14722|Q5U089|Q5U090|Q8N4N1|Q9UBG9	Missense_Mutation	SNP	ENST00000337233.4	37	CCDS9214.1	.	.	.	.	.	.	.	.	.	.	G	34	5.311696	0.95655	.	.	ENSG00000135124	ENST00000337233;ENST00000359949;ENST00000543171;ENST00000542067	T;T;T;T	0.05139	3.49;3.49;3.49;3.49	5.02	5.02	0.67125	.	0.090749	0.64402	D	0.000001	T	0.29061	0.0722	M	0.90369	3.11	0.58432	D	0.999997	P;P;P	0.52316	0.604;0.952;0.918	B;P;P	0.58266	0.261;0.836;0.735	T	0.22730	-1.0208	10	0.87932	D	0	-30.6984	17.3156	0.87222	0.0:0.0:1.0:0.0	.	293;336;320	F6RU17;E7EPF7;Q99571	.;.;P2RX4_HUMAN	N	320;336;219;293	ENSP00000336607:D320N;ENSP00000353032:D336N;ENSP00000438131:D219N;ENSP00000438329:D293N	ENSP00000336607:D320N	D	+	1	0	P2RX4	120154673	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	6.337000	0.72958	2.329000	0.79093	0.462000	0.41574	GAC	.	.	none		0.597	P2RX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402545.1	NM_175567		A	121670290	G	A	121670290	3	1	48	1	0	0	0	0	1	0	0	0	11351	1058	37	1	992	1	P2RX4	12	121670290	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	6557920	121670290	12181605	123	15999											
FOXO1	2308	hgsc.bcm.edu	37	chr13	41239864	41239864	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	atgaggtcggcgtaggacagGttgccccacgcgttgcggcg	6	7	17	11	6	0	1	0	1	0	0	1	2	0	2	2	5	2	3	2	5	1	3			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr13:41239864G>C	ENST00000379561.5	-	1	870	c.486C>G	c.(484-486)aaC>aaG	p.N162K		NM_002015.3	NP_002006.2	Q12778	FOXO1_HUMAN	forkhead box O1	162					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)		CGTAGGACAGGTTGCCCCACG	0.716																																					p.N162K		Atlas-SNP	.											.	FOXO1	110	.	0			c.C486G						PASS	.						22	19	20					13																	41239864		2203	4300	6503	SO:0001583	missense	2308	exon1			GGACAGGTTGCCC		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.486C>G	13.37:g.41239864G>C	ENSP00000368880:p.Asn162Lys	31	0	0		32	14	0.4375	NM_002015	O43523|Q5VYC7|Q6NSK6	Missense_Mutation	SNP	ENST00000379561.5	37	CCDS9371.1	.	.	.	.	.	.	.	.	.	.	G	16.74	3.206797	0.58343	.	.	ENSG00000150907	ENST00000379561	D	0.94650	-3.48	3.56	3.56	0.40772	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.85682	D	0.000000	D	0.96390	0.8822	M	0.66378	2.025	0.58432	D	0.99999	D	0.89917	1.0	D	0.91635	0.999	D	0.96689	0.9509	10	0.66056	D	0.02	-10.4108	14.0952	0.65016	0.0:0.0:1.0:0.0	.	162	Q12778	FOXO1_HUMAN	K	162	ENSP00000368880:N162K	ENSP00000368880:N162K	N	-	3	2	FOXO1	40137864	.	.	1.000000	0.80357	0.511000	0.34104	.	.	1.693000	0.51124	0.563000	0.77884	AAC	.	.	none		0.716	FOXO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044634.3	NM_002015		C	41239864	G	C	41239864	3	2	48	1	0	0	0	0	1	0	0	0	6031	1252	44	4	1489	4	FOXO1	13	41239864	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10		41239864	73930014	124	16000											
OR4N2	390429	hgsc.bcm.edu	37	chr14	20295818	20295818	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gcaacttggccttcctggatGcatcctactccttcattgtg	6	14	8	13	0	1	0	1	0	0	0	4	1	4	1	4	2	3	2	4	2	2	5			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr14:20295818G>A	ENST00000315947.1	+	1	211	c.211G>A	c.(211-213)Gca>Aca	p.A71T	OR4N2_ENST00000568211.1_Missense_Mutation_p.A71T	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	71						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)		CTTCCTGGATGCATCCTACTC	0.488																																					p.A71T		Atlas-SNP	.											OR4N2,NS,carcinoma,-2,2	OR4N2	125	2	0			c.G211A						PASS	.						159	188	178					14																	20295818		2203	4297	6500	SO:0001583	missense	390429	exon1			CTGGATGCATCCT		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.211G>A	14.37:g.20295818G>A	ENSP00000319601:p.Ala71Thr	154	0	0		163	39	0.239264	NM_001004723	Q6IEY9|Q6IFA2	Missense_Mutation	SNP	ENST00000315947.1	37	CCDS32022.1	.	.	.	.	.	.	.	.	.	.	.	13.07	2.127186	0.37533	.	.	ENSG00000176294	ENST00000557677;ENST00000315947	T;T	0.03004	4.08;4.08	4.3	3.33	0.38152	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000184	T	0.01695	0.0054	N	0.04768	-0.165	0.24707	N	0.993226	B	0.34264	0.446	B	0.32677	0.15	T	0.48864	-0.8997	10	0.26408	T	0.33	-9.1401	4.864	0.13598	0.1096:0.0:0.6794:0.211	.	71	Q8NGD1	OR4N2_HUMAN	T	71	ENSP00000452022:A71T;ENSP00000319601:A71T	ENSP00000319601:A71T	A	+	1	0	OR4N2	19365658	0.000000	0.05858	1.000000	0.80357	0.944000	0.59088	-0.921000	0.04008	2.374000	0.81015	0.591000	0.81541	GCA	.	.	none		0.488	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2			A	20295818	G	A	20295818	3	1	48	1	0	0	0	0	1	0	0	0	11086	1319	46	2	213	2	OR4N2	14	20295818	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10		20295818	87053722	125	16001											
GMPR2	51292	hgsc.bcm.edu	37	chr14	24702483	24702483	+	Silent	SNP	G	G	T	0	0	1	0	0	0	0	1	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cctcatattgacaacgatgtGaaactggacttcaaggatgt	13	11	9	8	1	2	2	2	2	0	0	2	5	2	4	1	2	2	0	1	2	4	3			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr14:24702483G>T	ENST00000355299.4	+	2	485	c.24G>T	c.(22-24)gtG>gtT	p.V8V	GMPR2_ENST00000456667.3_Silent_p.V8V|NEDD8-MDP1_ENST00000534348.1_5'Flank|GMPR2_ENST00000420554.2_Silent_p.V26V|NEDD8-MDP1_ENST00000604306.1_5'Flank|NEDD8_ENST00000250495.5_5'Flank|NEDD8_ENST00000533242.1_5'Flank|GMPR2_ENST00000348719.7_Silent_p.V8V|NEDD8_ENST00000524927.1_5'Flank|GMPR2_ENST00000559104.1_Silent_p.V26V|GMPR2_ENST00000399440.2_Silent_p.V8V|GMPR2_ENST00000559910.1_Silent_p.V8V|GMPR2_ENST00000557854.1_Silent_p.V26V|GMPR2_ENST00000559836.1_Silent_p.V8V	NM_001002000.1	NP_001002000.1	Q9P2T1	GMPR2_HUMAN	guanosine monophosphate reductase 2	8					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)			large_intestine(4)|lung(3)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	12				GBM - Glioblastoma multiforme(265;0.0181)		ACAACGATGTGAAACTGGACT	0.512																																					p.V26V		Atlas-SNP	.											.	GMPR2	37	.	0			c.G78T						PASS	.						296	285	288					14																	24702483		2026	4179	6205	SO:0001819	synonymous_variant	51292	exon1			CGATGTGAAACTG		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.24G>T	14.37:g.24702483G>T		53	0	0		57	19	0.333333	NM_016576	D3DS66|Q567T0|Q6IAJ8|Q86T14	Silent	SNP	ENST00000355299.4	37	CCDS41935.1																																																																																			.	.	none		0.512	GMPR2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415821.2	NM_016576		T	24702483	G	T	24702483	2	4	48	1	0	0	0	0	0	0	0	1	6505	1277	45	4		4	GMPR2	14	24702483	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	4406665	24702483	82647057	126	16002											
HEATR5A	25938	hgsc.bcm.edu	37	chr14	31819064	31819064	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	ccacttgggctaatctagccCatgactctgcagctgcacat	9	10	8	14	0	2	1	0	1	2	0	2	1	2	1	2	1	4	4	2	1	2	3			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr14:31819064C>T	ENST00000389961.3	-	17	2620	c.2621G>A	c.(2620-2622)tGg>tAg	p.W874*	HEATR5A_ENST00000543095.2_Nonsense_Mutation_p.W880*|HEATR5A_ENST00000404677.3_Nonsense_Mutation_p.W880*|HEATR5A_ENST00000439348.1_Nonsense_Mutation_p.W874*|HEATR5A_ENST00000439727.1_Nonsense_Mutation_p.W587*			Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	874										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)		TAATCTAGCCCATGACTCTGC	0.418																																					p.W880X		Atlas-SNP	.											.	HEATR5A	181	.	0			c.G2639A						PASS	.						54	53	54					14																	31819064		1882	4119	6001	SO:0001587	stop_gained	25938	exon18			CTAGCCCATGACT	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.2621G>A	14.37:g.31819064C>T	ENSP00000374611:p.Trp874*	94	0	0		76	22	0.289474	NM_015473	Q68DD8|Q6P3S5|Q6P5R9|Q9H8D7|Q9NXB7|Q9P2N0|Q9UFQ3	Nonsense_Mutation	SNP	ENST00000389961.3	37		.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	38|38|38	6.641922|6.641922|6.641922	0.97726|0.97726|0.97726	.|.|.	.|.|.	ENSG00000129493|ENSG00000129493|ENSG00000129493	ENST00000538864|ENST00000550366|ENST00000389961;ENST00000439348;ENST00000439727;ENST00000543095;ENST00000404677	.|.|.	.|.|.	.|.|.	5.48|5.48|5.48	4.52|4.52|4.52	0.55395|0.55395|0.55395	.|.|.	.|.|0.237405	.|.|0.36101	.|.|N	.|.|0.002798	T|T|.	0.62405|0.62405|.	0.2425|0.2425|.	.|.|.	.|.|.	.|.|.	0.80722|0.80722|0.80722	A|A|A	1|1|1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|.	0.68157|0.68157|.	-0.5483|-0.5483|.	3|3|.	.|.|0.33940	.|.|T	.|.|0.23	.|.|.	13.1556|13.1556|13.1556	0.59516|0.59516|0.59516	0.3025:0.6975:0.0:0.0|0.3025:0.6975:0.0:0.0|0.3025:0.6975:0.0:0.0	.|.|.	.|.|.	.|.|.	.|.|.	R|I|X	508|522|874;874;587;880;880	.|.|.	.|.|ENSP00000374611:W874X	G|M|W	-|-|-	1|3|2	0|0|0	HEATR5A|HEATR5A|HEATR5A	30888815|30888815|30888815	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.998000|0.998000|0.998000	0.56505|0.56505|0.56505	0.897000|0.897000|0.897000	0.52465|0.52465|0.52465	4.312000|4.312000|4.312000	0.59154|0.59154|0.59154	2.587000|2.587000|2.587000	0.87381|0.87381|0.87381	0.655000|0.655000|0.655000	0.94253|0.94253|0.94253	GGG|ATG|TGG	.	.	none		0.418	HEATR5A-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015473		T	31819064	C	T	31819064	4	4	48	1	0	0	0	0	0	1	0	0	7040	595	21	2	3577	2	HEATR5A	14	31819064	Nonsense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	7116581	31819064	75530476	127	16003											
FSCB	84075	hgsc.bcm.edu	37	chr14	44973798	44973798	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cctgtccatcattggtattaGacaaatctttaaggacagaa	14	12	7	8	0	2	2	1	0	1	2	3	3	3	3	2	2	0	1	2	2	5	5			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr14:44973798G>A	ENST00000340446.4	-	1	2684	c.2393C>T	c.(2392-2394)tCt>tTt	p.S798F	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	798						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)		ATTGGTATTAGACAAATCTTT	0.368																																					p.S798F		Atlas-SNP	.											FSCB,NS,carcinoma,0,1	FSCB	173	1	0			c.C2393T						PASS	.						72	77	76					14																	44973798		2202	4300	6502	SO:0001583	missense	84075	exon1			GTATTAGACAAAT	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.2393C>T	14.37:g.44973798G>A	ENSP00000344579:p.Ser798Phe	148	0	0		122	27	0.221311	NM_032135	Q5H9U7|Q86YI2|Q9H0J3	Missense_Mutation	SNP	ENST00000340446.4	37	CCDS9679.1	.	.	.	.	.	.	.	.	.	.	G	13.77	2.335252	0.41398	.	.	ENSG00000189139	ENST00000340446;ENST00000537803	T	0.17691	2.26	3.72	2.82	0.32997	.	.	.	.	.	T	0.27349	0.0671	L	0.46157	1.445	0.09310	N	1	D	0.69078	0.997	P	0.62184	0.899	T	0.05750	-1.0866	9	0.87932	D	0	-0.5539	5.8233	0.18540	0.2368:0.0:0.7632:0.0	.	798	Q5H9T9	FSCB_HUMAN	F	798;691	ENSP00000344579:S798F	ENSP00000344579:S798F	S	-	2	0	FSCB	44043548	0.011000	0.17503	0.003000	0.11579	0.091000	0.18340	1.756000	0.38390	1.136000	0.42199	0.484000	0.47621	TCT	.	.	none		0.368	FSCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276788.1	NM_032135		A	44973798	G	A	44973798	3	1	48	1	0	0	0	0	1	0	0	0	6074	942	33	2	88	2	FSCB	14	44973798	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	13154734	44973798	62375742	128	16004											
ADAM21	8747	hgsc.bcm.edu	37	chr14	70926009	70926009	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gggtattgactatcatttaaGgatgaacatatctgacattg	13	14	9	5	0	2	3	1	3	1	0	2	4	2	4	0	2	1	1	0	2	5	7			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr14:70926009G>A	ENST00000603540.1	+	2	2051	c.1793G>A	c.(1792-1794)aGg>aAg	p.R598K	RP11-486O13.4_ENST00000556646.1_lincRNA|ADAM21_ENST00000267499.3_Missense_Mutation_p.R598K	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	598	Cys-rich.				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)		TATCATTTAAGGATGAACATA	0.423																																					p.R598K		Atlas-SNP	.											.	ADAM21	181	.	0			c.G1793A						PASS	.						153	139	144					14																	70926009		2203	4300	6503	SO:0001583	missense	8747	exon2			ATTTAAGGATGAA	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.1793G>A	14.37:g.70926009G>A	ENSP00000474385:p.Arg598Lys	205	0	0		234	66	0.282051	NM_003813	O43507|Q2VPC6|Q32MR0	Missense_Mutation	SNP	ENST00000603540.1	37	CCDS9804.1	.	.	.	.	.	.	.	.	.	.	G	5.870	0.344640	0.11126	.	.	ENSG00000139985	ENST00000267499	T	0.20738	2.05	4.49	2.62	0.31277	ADAM, cysteine-rich (2);	0.545816	0.14800	U	0.297713	T	0.12220	0.0297	N	0.11560	0.145	0.09310	N	1	B	0.12630	0.006	B	0.10450	0.005	T	0.25257	-1.0137	10	0.72032	D	0.01	.	11.0101	0.47657	0.1552:0.0:0.8448:0.0	.	598	Q9UKJ8	ADA21_HUMAN	K	598	ENSP00000267499:R598K	ENSP00000267499:R598K	R	+	2	0	ADAM21	69995762	0.999000	0.42202	0.011000	0.14972	0.043000	0.13939	3.198000	0.51035	0.608000	0.30000	0.563000	0.77884	AGG	.	.	none		0.423	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3			A	70926009	G	A	70926009	3	1	48	1	0	0	0	0	1	0	0	0	243	1000	35	2	1795	2	ADAM21	14	70926009	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	25952211	70926009	36423531	129	16005											
ABCD4	5826	hgsc.bcm.edu	37	chr14	74762572	74762572	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cacacctaaaatctccctccAgcttctcctgatgcaccagc	10	9	4	18	0	2	1	0	1	2	0	5	1	3	1	5	0	3	2	5	0	2	2			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr14:74762572A>T	ENST00000356924.4	-	6	796	c.653T>A	c.(652-654)cTg>cAg	p.L218Q	ABCD4_ENST00000557588.1_Intron|ABCD4_ENST00000298816.7_Missense_Mutation_p.L131Q|ABCD4_ENST00000557554.1_Intron|AC005519.4_ENST00000554532.2_RNA	NM_005050.3	NP_005041.1	O14678	ABCD4_HUMAN	ATP-binding cassette, sub-family D (ALD), member 4	218	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cobalamin metabolic process (GO:0009235)|transmembrane transport (GO:0055085)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			cervix(2)|endometrium(3)|kidney(3)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00153)		ATCTCCCTCCAGCTTCTCCTG	0.502																																					p.L218Q		Atlas-SNP	.											.	ABCD4	54	.	0			c.T653A						PASS	.						91	84	86					14																	74762572		2203	4300	6503	SO:0001583	missense	5826	exon6			CCCTCCAGCTTCT	AF009746	CCDS9828.1	14q24	2012-03-14			ENSG00000119688	ENSG00000119688		"ATP binding cassette transporters / subfamily D"	68	protein-coding gene	gene with protein product		603214		PXMP1L		9266848, 9302272	Standard	NR_003256		Approved	PMP69, P70R, EST352188	uc001xpr.2	O14678	OTTHUMG00000171207	ENST00000356924.4:c.653T>A	14.37:g.74762572A>T	ENSP00000349396:p.Leu218Gln	61	0	0		72	21	0.291667	NM_005050	A8K5L7|Q6IAQ0|Q96E75	Missense_Mutation	SNP	ENST00000356924.4	37	CCDS9828.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.2|20.2	3.957277|3.957277	0.73902|0.73902	.|.	.|.	ENSG00000119688|ENSG00000119688	ENST00000356924;ENST00000298816|ENST00000556971	D;D|.	0.99745|.	-6.61;-6.61|.	5.46|5.46	5.46|5.46	0.80206|0.80206	ABC transporter, N-terminal (1);ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.74913|0.74913	0.3779|0.3779	M|M	0.74546|0.74546	2.27|2.27	0.80722|0.80722	D|D	1|1	B;P;P|.	0.38677|.	0.39;0.642;0.642|.	B;P;P|.	0.48334|.	0.372;0.574;0.574|.	T|T	0.75608|0.75608	-0.3259|-0.3259	10|5	0.52906|.	T|.	0.07|.	.|.	15.55|15.55	0.76141|0.76141	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	131;218;218|.	F8W7M4;A8K5L7;O14678|.	.;.;ABCD4_HUMAN|.	Q|R	218;131|178	ENSP00000349396:L218Q;ENSP00000298816:L131Q|.	ENSP00000298816:L131Q|.	L|W	-|-	2|1	0|0	ABCD4|ABCD4	73832325|73832325	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	9.198000|9.198000	0.94994|0.94994	2.062000|2.062000	0.61559|0.61559	0.533000|0.533000	0.62120|0.62120	CTG|TGG	.	.	none		0.502	ABCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314382.1	NM_005050		T	74762572	A	T	74762572	3	4	48	1	0	0	0	0	1	0	0	0	63	188	7	5	1223	5	ABCD4	14	74762572	Missense_Mutation	SNP	A	TCGA-VB-A8QN-01A-11D-A382-10	3836563	74762572	32586968	130	16006											
C14orf4	64207	hgsc.bcm.edu	37	chr14	77493827	77493827	+	Silent	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgctgctgttgctgttgctgTtgcgcggcggcggcggcggc	0	11	19	11	6	0	0	0	0	0	0	0	0	0	0	0	5	5	7	0	5	0	3			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr14:77493827T>C	ENST00000238647.3	-	1	1207	c.309A>G	c.(307-309)caA>caG	p.Q103Q		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	103	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						gctgttgctgttgcgcggcgg	0.701																																					p.Q103Q		Atlas-SNP	.											.	IRF2BPL	40	.	0			c.A309G						PASS	.						1	1	1					14																	77493827		1045	1849	2894	SO:0001819	synonymous_variant	64207	exon1			TTGCTGTTGCGCG	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.309A>G	14.37:g.77493827T>C		25	0	0		27	5	0.185185	NM_024496	Q8NDQ2|Q96JG2|Q9H3I7	Silent	SNP	ENST00000238647.3	37	CCDS9854.1																																																																																			.	.	none		0.701	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1	NM_024496		C	77493827	T	C	77493827	2	2	48	1	0	0	0	0	0	0	0	1	1775	1722	60	3		3	C14orf4	14	77493827	Silent	SNP	T	TCGA-VB-A8QN-01A-11D-A382-10	2731255	77493827	29855713	131	16007											
MAGEL2	54551	hgsc.bcm.edu	37	chr15	23890158	23890158	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttagattctcccagggccttGggccctgccagtcatgaaag	8	10	11	12	0	2	2	1	1	1	1	3	2	2	2	4	2	1	0	4	2	2	3			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr15:23890158G>T	ENST00000532292.1	-	1	1017	c.923C>A	c.(922-924)cCa>cAa	p.P308Q		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2	191	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				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)		CCAGGGCCTTGGGCCCTGCCA	0.627																																					p.P911Q		Atlas-SNP	.											.	MAGEL2	108	.	0			c.C2732A						PASS	.						40	50	47					15																	23890158		2108	4257	6365	SO:0001583	missense	54551	exon1			GGCCTTGGGCCCT	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.923C>A	15.37:g.23890158G>T	ENSP00000433433:p.Pro308Gln	92	0	0		85	14	0.164706	NM_019066		Missense_Mutation	SNP	ENST00000532292.1	37		.	.	.	.	.	.	.	.	.	.	G	7.264	0.605704	0.14002	.	.	ENSG00000254585	ENST00000532292	.	.	.	3.7	0.729	0.18266	.	.	.	.	.	T	0.20700	0.0498	N	0.24115	0.695	0.09310	N	1	.	.	.	.	.	.	T	0.22941	-1.0202	5	.	.	.	.	2.9645	0.05903	0.2333:0.0:0.5271:0.2396	.	.	.	.	K	340	.	.	Q	-	1	0	MAGEL2	21441251	0.079000	0.21365	0.005000	0.12908	0.204000	0.24138	1.099000	0.31013	0.163000	0.19507	-0.274000	0.10170	CAA	.	.	none		0.627	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395182.2	NM_019066		T	23890158	G	T	23890158	3	4	48	1	0	0	0	0	1	0	0	0	9198	1348	47	4	1021	4	MAGEL2	15	23890158	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10		23890158	78641234	132	16008											
GABRB3	2562	hgsc.bcm.edu	37	chr15	26806091	26806091	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	gagcctacccggttgctttcGctctttgaacggtcattctt	5	15	9	12	3	3	1	1	1	2	0	4	2	3	1	2	2	4	3	2	2	2	6	rs369761963		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr15:26806091G>A	ENST00000311550.5	-	8	1179	c.1068C>T	c.(1066-1068)agC>agT	p.S356S	GABRB3_ENST00000541819.2_Silent_p.S412S|GABRB3_ENST00000299267.4_Silent_p.S356S|GABRB3_ENST00000400188.3_Silent_p.S285S|GABRB3_ENST00000545868.1_Silent_p.S271S	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	356					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)	GGTTGCTTTCGCTCTTTGAAC	0.478																																					p.S356S		Atlas-SNP	.											GABRB3_ENST00000541819,colon,carcinoma,-1,4	GABRB3	338	4	0			c.C1068T						PASS	.	G	,,,	1,4405	2.1+/-5.4	0,1,2202	247	267	260		1068,813,855,1068	-8.1	0.4	15		260	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GABRB3	NM_000814.5,NM_001191320.1,NM_001191321.1,NM_021912.4	,,,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,,,	356/474,271/389,285/403,356/474	26806091	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2562	exon8			GCTTTCGCTCTTT		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.1068C>T	15.37:g.26806091G>A		253	0	0		279	60	0.215054	NM_021912	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Silent	SNP	ENST00000311550.5	37	CCDS10019.1																																																																																			.	.	weak		0.478	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2			A	26806091	G	A	26806091	2	1	48	1	0	0	0	0	0	0	0	1	6176	1078	38	1		1	GABRB3	15	26806091	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	2915933	26806091	75725301	133	16009											
OCA2	4948	hgsc.bcm.edu	37	chr15	28202854	28202854	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgatgcgctgagcagtcaggCgccagacgtgaatctcgtgc	8	8	14	11	4	2	4	1	3	1	1	3	4	2	4	1	1	3	2	1	1	1	0			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr15:28202854C>T	ENST00000354638.3	-	16	1819	c.1664G>A	c.(1663-1665)cGc>cAc	p.R555H	OCA2_ENST00000353809.5_Missense_Mutation_p.R531H|OCA2_ENST00000382996.2_Missense_Mutation_p.R555H	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II	555					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)			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)		AGCAGTCAGGCGCCAGACGTG	0.632									Oculocutaneous Albinism																												p.R555H		Atlas-SNP	.											.	OCA2	173	.	0			c.G1664A						PASS	.						26	27	27					15																	28202854		2202	4298	6500	SO:0001583	missense	4948	exon16	Familial Cancer Database		GTCAGGCGCCAGA		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.1664G>A	15.37:g.28202854C>T	ENSP00000346659:p.Arg555His	42	0	0		43	16	0.372093	NM_000275	Q15211|Q15212|Q96EN1|Q9UMI5	Missense_Mutation	SNP	ENST00000354638.3	37	CCDS10020.1	.	.	.	.	.	.	.	.	.	.	C	18.60	3.659379	0.67586	.	.	ENSG00000104044	ENST00000354638;ENST00000353809;ENST00000382996	D;D;D	0.91577	-2.84;-2.64;-2.87	5.8	3.72	0.42706	Divalent ion symporter (1);	0.050853	0.64402	D	0.000001	D	0.91915	0.7440	L	0.46157	1.445	0.38391	D	0.945402	D;D	0.89917	0.996;1.0	P;D	0.72338	0.781;0.977	D	0.92105	0.5691	10	0.72032	D	0.01	-12.7964	8.1247	0.30992	0.0:0.7696:0.0:0.2304	.	531;555	Q04671-2;Q04671	.;P_HUMAN	H	555;531;555	ENSP00000346659:R555H;ENSP00000261276:R531H;ENSP00000372457:R555H	ENSP00000261276:R531H	R	-	2	0	OCA2	25876449	1.000000	0.71417	1.000000	0.80357	0.483000	0.33249	3.318000	0.51975	1.468000	0.48064	-0.229000	0.12294	CGC	.	.	none		0.632	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	NM_000275		T	28202854	C	T	28202854	3	4	48	1	0	0	0	0	1	0	0	0	10824	768	27	1	888	1	OCA2	15	28202854	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	1396763	28202854	74328538	134	16010											
APBA2	321	hgsc.bcm.edu	37	chr15	29346718	29346718	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	acaccggcgcctccccctacCgcctgaggcgtggggatggg	5	5	15	16	4	0	1	0	1	0	0	1	2	1	2	6	5	1	0	6	5	1	1	rs149847107		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr15:29346718C>T	ENST00000558402.1	+	5	1230	c.631C>T	c.(631-633)Cgc>Tgc	p.R211C	APBA2_ENST00000558330.1_Missense_Mutation_p.R211C|APBA2_ENST00000561069.1_Missense_Mutation_p.R211C|APBA2_ENST00000411764.1_Missense_Mutation_p.R211C|APBA2_ENST00000558259.1_Missense_Mutation_p.R211C			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	211	STXBP1-binding.			DEPSVLEAHDQEEDGHYCASKEGYQDYYPEEANGNTGASPY RLRR -> MSPPSLRPMTRKKMVTMCQQRGLPGLLPRGGQR EHRRLPLPPEA (in Ref. 1; AAC39767). {ECO:0000305}.	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)		CTCCCCCTACCGCCTGAGGCG	0.602													C|||	1	0.000199681	0.0	0.0	5008	,	,		20367	0.0		0.001	False		,,,				2504	0.0				p.R211C		Atlas-SNP	.											APBA2,caecum,carcinoma,-1,1	APBA2	132	1	0			c.C631T						PASS	.	C	CYS/ARG,CYS/ARG	0,4402		0,0,2201	44	34	37		631,631	2.9	0.1	15	dbSNP_134	37	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	APBA2	NM_001130414.1,NM_005503.3	180,180	0,1,6500	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	211/738,211/750	29346718	1,13001	2201	4300	6501	SO:0001583	missense	321	exon3			CCCTACCGCCTGA	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.631C>T	15.37:g.29346718C>T	ENSP00000453293:p.Arg211Cys	42	0	0		67	19	0.283582	NM_005503	E9PGI4|O60571|Q5XKC0	Missense_Mutation	SNP	ENST00000558402.1	37	CCDS10022.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	12.31	1.898247	0.33535	0.0	1.16E-4	ENSG00000034053	ENST00000411764;ENST00000219865	T	0.47177	0.85	4.77	2.89	0.33648	.	0.517876	0.20604	N	0.089082	T	0.42720	0.1215	L	0.54323	1.7	0.18873	N	0.999985	B;D;B	0.63046	0.122;0.992;0.06	B;B;B	0.42916	0.008;0.402;0.006	T	0.35895	-0.9770	10	0.72032	D	0.01	.	10.2679	0.43466	0.0:0.8387:0.0:0.1613	.	211;211;211	Q5XKC0;E9PGI4;Q99767	.;.;APBA2_HUMAN	C	211	ENSP00000409312:R211C	ENSP00000219865:R211C	R	+	1	0	APBA2	27134010	0.000000	0.05858	0.085000	0.20634	0.465000	0.32709	0.245000	0.18142	0.541000	0.28827	-0.142000	0.14014	CGC	C|1.000;T|0.000	0.000	strong		0.602	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503		T	29346718	C	T	29346718	3	4	48	1	0	0	0	0	1	0	0	0	757	652	23	1	633	1	APBA2	15	29346718	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	1143864	29346718	73184674	135	16011											
TMEM62	80021	hgsc.bcm.edu	37	chr15	43476576	43476576	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	atacttgaaaattatgcctgTtcacctacttatgctactgc	11	15	5	10	0	1	1	1	1	0	0	1	1	1	1	2	0	6	2	2	0	7	7			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr15:43476576T>C	ENST00000260403.2	+	14	2003	c.1724T>C	c.(1723-1725)gTt>gCt	p.V575A	CCNDBP1_ENST00000356633.5_5'Flank|EPB42_ENST00000563128.1_Intron|TMEM62_ENST00000569369.1_3'UTR|CCNDBP1_ENST00000300213.4_5'Flank|RP11-473C18.3_ENST00000565685.1_RNA	NM_024956.3	NP_079232.3	Q0P6H9	TMM62_HUMAN	transmembrane protein 62	575						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)		ATTATGCCTGTTCACCTACTT	0.443																																					p.V575A		Atlas-SNP	.											.	TMEM62	47	.	0			c.T1724C						PASS	.						246	235	239					15																	43476576		2203	4299	6502	SO:0001583	missense	80021	exon14			TGCCTGTTCACCT	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.1724T>C	15.37:g.43476576T>C	ENSP00000260403:p.Val575Ala	216	0	0		239	66	0.276151	NM_024956	Q6I9Y5|Q9H5J6	Missense_Mutation	SNP	ENST00000260403.2	37	CCDS32210.1	.	.	.	.	.	.	.	.	.	.	T	17.60	3.430817	0.62844	.	.	ENSG00000137842	ENST00000260403	.	.	.	5.13	3.95	0.45737	.	0.244558	0.41500	D	0.000868	T	0.59595	0.2205	L	0.50333	1.59	0.41888	D	0.990353	P	0.52316	0.952	P	0.50860	0.652	T	0.64093	-0.6488	9	0.56958	D	0.05	-6.2758	12.2964	0.54849	0.0:0.0:0.1408:0.8592	.	575	Q0P6H9	TMM62_HUMAN	A	575	.	ENSP00000260403:V575A	V	+	2	0	TMEM62	41263868	0.994000	0.37717	1.000000	0.80357	0.918000	0.54935	4.208000	0.58486	2.153000	0.67306	0.459000	0.35465	GTT	.	.	none		0.443	TMEM62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432227.1	NM_024956		C	43476576	T	C	43476576	3	2	48	1	0	0	0	0	1	0	0	0	16204	1725	60	3	1778	3	TMEM62	15	43476576	Missense_Mutation	SNP	T	TCGA-VB-A8QN-01A-11D-A382-10	14129858	43476576	59054816	136	16012											
TGM7	116179	hgsc.bcm.edu	37	chr15	43577071	43577071	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	tttcggtcatagtacgtatcGatggtcaagttcctatccac	9	14	8	10	3	2	0	2	0	0	0	6	1	4	0	2	2	1	3	2	2	5	6			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr15:43577071G>A	ENST00000452443.2	-	7	949	c.945C>T	c.(943-945)atC>atT	p.I315I		NM_052955.2	NP_443187.1	Q96PF1	TGM7_HUMAN	transglutaminase 7	315					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)	AGTACGTATCGATGGTCAAGT	0.443																																					p.I315I		Atlas-SNP	.											.	TGM7	86	.	0			c.C945T						PASS	.						242	196	212					15																	43577071		2202	4299	6501	SO:0001819	synonymous_variant	116179	exon7			CGTATCGATGGTC	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.945C>T	15.37:g.43577071G>A		84	0	0		95	38	0.4	NM_052955		Silent	SNP	ENST00000452443.2	37	CCDS32213.1																																																																																			.	.	none		0.443	TGM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432489.1	NM_052955		A	43577071	G	A	43577071	2	1	48	1	0	0	0	0	0	0	0	1	15850	1048	37	1		1	TGM7	15	43577071	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	100495	43577071	58954321	137	16013											
FOXB1	27023	hgsc.bcm.edu	37	chr15	60297267	60297267	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	tctcccgagaagatgctgccGctgagcgagatctacaagtt	10	9	11	11	3	2	4	0	1	2	3	3	6	2	4	2	0	4	3	2	0	3	2			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr15:60297267G>A	ENST00000396057.4	+	2	584	c.105G>A	c.(103-105)ccG>ccA	p.P35P	FOXB1_ENST00000560857.1_Intron	NM_012182.2	NP_036314.2	Q99853	FOXB1_HUMAN	forkhead box B1	35					axon target recognition (GO:0007412)|cell migration in diencephalon (GO:0061381)|epithelial cell differentiation involved in mammary gland alveolus development (GO:0061030)|floor plate development (GO:0033504)|hypothalamus cell migration (GO:0021855)|inferior colliculus development (GO:0061379)|lactation (GO:0007595)|mammary gland lobule development (GO:0061377)|mammillary body development (GO:0021767)|mammillothalamic axonal tract development (GO:0061374)|midbrain development (GO:0030901)|negative regulation of neuron apoptotic process (GO:0043524)|somitogenesis (GO:0001756)|spinal cord development (GO:0021510)|telencephalon cell migration (GO:0022029)|thalamus development (GO:0021794)|transcription, DNA-templated (GO:0006351)|urogenital system development (GO:0001655)|visual learning (GO:0008542)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(1)|lung(3)|ovary(1)	6						AGATGCTGCCGCTGAGCGAGA	0.602																																					p.P35P		Atlas-SNP	.											.	FOXB1	29	.	0			c.G105A						PASS	.						98	96	97					15																	60297267		2203	4300	6503	SO:0001819	synonymous_variant	27023	exon2			GCTGCCGCTGAGC	AF055080	CCDS32255.1	15q22.2	2014-09-09			ENSG00000171956	ENSG00000171956		"Forkhead boxes"	3799	protein-coding gene	gene with protein product							Standard	NM_012182		Approved	HFKH-5, FKH5	uc002agj.1	Q99853	OTTHUMG00000172011	ENST00000396057.4:c.105G>A	15.37:g.60297267G>A		35	0	0		42	9	0.214286	NM_012182	O60652|O75917|Q14CL2	Silent	SNP	ENST00000396057.4	37	CCDS32255.1																																																																																			.	.	none		0.602	FOXB1-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416378.1			A	60297267	G	A	60297267	2	1	48	1	0	0	0	0	0	0	0	1	6000	1074	38	1		1	FOXB1	15	60297267	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	16720196	60297267	42234125	138	16014											
MAN2C1	4123	hgsc.bcm.edu	37	chr15	75660458	75660458	+	Silent	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tgcgcggggcggaagtcccgCtggactgcctcctggtaggg	4	7	18	12	4	0	0	0	0	0	0	2	2	2	2	3	6	2	2	3	6	2	1			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr15:75660458C>T	ENST00000267978.5	-	2	229	c.183G>A	c.(181-183)caG>caA	p.Q61Q	MAN2C1_ENST00000565683.1_Silent_p.Q61Q|MAN2C1_ENST00000563622.1_Silent_p.Q61Q|MAN2C1_ENST00000569482.1_Silent_p.Q61Q|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	61					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						GGAAGTCCCGCTGGACTGCCT	0.692																																					p.Q61Q		Atlas-SNP	.											.	MAN2C1	76	.	0			c.G183A						PASS	.						10	13	12					15																	75660458		2188	4278	6466	SO:0001819	synonymous_variant	4123	exon2			GTCCCGCTGGACT	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.183G>A	15.37:g.75660458C>T		51	0	0		61	16	0.262295	NM_001256494	H3BMX2|H3BQY8|H3BUT6|Q13358|Q68EM8|Q9UL64	Silent	SNP	ENST00000267978.5	37	CCDS32298.1																																																																																			.	.	none		0.692	MAN2C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419965.1			T	75660458	C	T	75660458	2	4	48	1	0	0	0	0	0	0	0	1	9227	796	28	2		2	MAN2C1	15	75660458	Silent	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	15363191	75660458	26870934	139	16015											
MSLN	10232	hgsc.bcm.edu	37	chr16	815722	815722	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	0	1	1	0	1	cgcgtggcggcaacgctcctCtcgggacccatcctggcggc	4	6	14	17	6	1	0	0	0	1	0	4	1	3	1	3	5	1	2	3	5	1	0			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr16:815722C>T	ENST00000382862.3	+	10	922	c.827C>T	c.(826-828)tCt>tTt	p.S276F	MSLN_ENST00000566549.1_Missense_Mutation_p.S276F|MSLN_ENST00000563941.1_Missense_Mutation_p.S276F|MSLN_ENST00000545450.2_Missense_Mutation_p.S276F	NM_013404.4	NP_037536.2	Q13421	MSLN_HUMAN	mesothelin	276	Required for megakaryocyte-potentiating factor activity.				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)		p.S276F(2)		breast(2)|kidney(2)|lung(11)|pancreas(1)|prostate(1)|skin(3)	20		Hepatocellular(780;0.00335)				CAACGCTCCTCTCGGGACCCA	0.716																																					p.S276F		Atlas-SNP	.											MSLN_ENST00000446427,NS,carcinoma,0,2	MSLN	109	2	2	Substitution - Missense(2)	lung(2)	c.C827T						scavenged	.						21	25	24					16																	815722		2176	4279	6455	SO:0001583	missense	10232	exon11			GCTCCTCTCGGGA	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.827C>T	16.37:g.815722C>T	ENSP00000372313:p.Ser276Phe	81	2	0.0246914		76	16	0.210526	NM_005823	D3DU65|Q14859|Q4VQD5|Q96GR6|Q96KJ5|Q9BR17|Q9BTR2|Q9UCB2|Q9UK57	Missense_Mutation	SNP	ENST00000382862.3	37	CCDS32356.1	.	.	.	.	.	.	.	.	.	.	C	14.73	2.621508	0.46736	.	.	ENSG00000102854	ENST00000446427;ENST00000445361;ENST00000545450;ENST00000382862	T;T	0.17854	2.25;2.25	4.67	-1.77	0.07982	.	1.359800	0.04991	U	0.467355	T	0.29256	0.0728	L	0.59436	1.845	0.09310	N	1	D;D;D;D	0.59357	0.981;0.985;0.981;0.981	P;D;P;P	0.63877	0.867;0.919;0.867;0.867	T	0.26883	-1.0090	10	0.38643	T	0.18	-7.6659	2.6096	0.04887	0.3551:0.2859:0.0:0.3591	.	275;276;276;276	Q13421-4;Q13421;Q13421-2;Q13421-3	.;MSLN_HUMAN;.;.	F	276	ENSP00000442965:S276F;ENSP00000372313:S276F	ENSP00000372313:S276F	S	+	2	0	MSLN	755723	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.874000	0.04210	-0.094000	0.12374	-1.167000	0.01749	TCT	.	.	none		0.716	MSLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109253.2			T	815722	C	T	815722	3	4	48	1	0	0	0	0	1	0	0	0	9890	913	32	2	861	2	MSLN	16	815722	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10		815722	89539031	140	16016											
ABCA3	21	hgsc.bcm.edu	37	chr16	2374447	2374447	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ctgtggttgaaggggtgctcGaagaccacggcggccagcac	8	6	16	11	3	0	2	0	1	0	1	1	3	0	2	2	5	2	3	2	5	2	1			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr16:2374447G>A	ENST00000301732.5	-	6	1105	c.405C>T	c.(403-405)ttC>ttT	p.F135F	ABCA3_ENST00000567910.1_Silent_p.F135F|ABCA3_ENST00000382381.3_Silent_p.F135F	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	135					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)	p.F135L(1)		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)	AGGGGTGCTCGAAGACCACGG	0.637																																					p.F135F		Atlas-SNP	.											ABCA3,NS,carcinoma,0,1	ABCA3	176	1	1	Substitution - Missense(1)	lung(1)	c.C405T						PASS	.						37	31	33					16																	2374447		2198	4300	6498	SO:0001819	synonymous_variant	21	exon6			GTGCTCGAAGACC	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.405C>T	16.37:g.2374447G>A		20	0	0		13	5	0.384615	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Silent	SNP	ENST00000301732.5	37	CCDS10466.1																																																																																			.	.	none		0.637	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089		A	2374447	G	A	2374447	2	1	48	1	0	0	0	0	0	0	0	1	33	1049	37	1		1	ABCA3	16	2374447	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	1558725	2374447	87980306	141	16017											
SOCS1	8651	hgsc.bcm.edu	37	chr16	11349190	11349190	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	ggaagtgcgtgtcgccggggGccggggccgggaccgcgggg	3	3	24	11	7	0	0	0	0	0	0	1	2	0	2	4	8	1	0	4	8	1	0	rs587778691		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr16:11349190G>A	ENST00000332029.2	-	2	296	c.146C>T	c.(145-147)gCc>gTc	p.A49V	RMI2_ENST00000572173.1_Intron	NM_003745.1	NP_003736.1	O15524	SOCS1_HUMAN	suppressor of cytokine signaling 1	49					cellular response to amino acid stimulus (GO:0071230)|cytokine-mediated signaling pathway (GO:0019221)|fat cell differentiation (GO:0045444)|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 insulin receptor signaling pathway (GO:0046627)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of protein phosphorylation (GO:0001932)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)	insulin-like growth factor receptor binding (GO:0005159)|kinase inhibitor activity (GO:0019210)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)	p.A37fs*27(2)|p.A49fs*66(1)|p.0?(1)		breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(66)|lung(3)	71						GTcgccgggggccggggccgg	0.761			"F, O"		"Hodgkin Lymphoma, PMBL"																																p.A49V	Colon(177;456 3548 27231)	Atlas-SNP	.		Rec	yes		16	16p13.13	8651	suppressor of cytokine signaling 1		L	.	SOCS1	84	.	4	Deletion - Frameshift(3)|Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(4)	c.C146T						PASS	.						1	1	1					16																	11349190		979	2206	3185	SO:0001583	missense	8651	exon2			CCGGGGGCCGGGG	U88326	CCDS10546.1	16p13.13	2013-02-14			ENSG00000185338	ENSG00000185338		"Suppressors of cytokine signaling", "SH2 domain containing"	19383	protein-coding gene	gene with protein product		603597				7796808, 9266833	Standard	NM_003745		Approved	SOCS-1, SSI-1, JAB, TIP3, Cish1	uc002dar.1	O15524	OTTHUMG00000129792	ENST00000332029.2:c.146C>T	16.37:g.11349190G>A	ENSP00000329418:p.Ala49Val	23	0	0		27	12	0.444444	NM_003745	O15097|Q9NSA7	Missense_Mutation	SNP	ENST00000332029.2	37	CCDS10546.1	.	.	.	.	.	.	.	.	.	.	G	8.597	0.885981	0.17540	.	.	ENSG00000185338	ENST00000332029	T	0.23552	1.9	3.98	1.87	0.25490	.	0.795116	0.11431	N	0.564788	T	0.12220	0.0297	N	0.22421	0.69	0.20638	N	0.999874	B	0.34103	0.437	B	0.27500	0.08	T	0.22765	-1.0207	10	0.10636	T	0.68	-23.3662	6.1919	0.20528	0.2106:0.2012:0.5882:0.0	.	49	O15524	SOCS1_HUMAN	V	49	ENSP00000329418:A49V	ENSP00000329418:A49V	A	-	2	0	SOCS1	11256691	0.952000	0.32445	0.995000	0.50966	0.324000	0.28378	3.694000	0.54742	0.652000	0.30806	-0.448000	0.05591	GCC	.	.	none		0.761	SOCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252018.1			A	11349190	G	A	11349190	3	1	48	1	0	0	0	0	1	0	0	0	14928	1203	42	2	493	2	SOCS1	16	11349190	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	8974743	11349190	79005563	142	16018											
RNF40	9810	hgsc.bcm.edu	37	chr16	30778068	30778068	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	acatcaacccacagagcgacGagctggggctgcagaagaag	14	3	13	11	2	1	3	1	0	0	3	1	5	1	3	1	2	4	3	1	2	3	0			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr16:30778068G>A	ENST00000324685.6	+	11	1735	c.1300G>A	c.(1300-1302)Gag>Aag	p.E434K	RNF40_ENST00000357890.5_Missense_Mutation_p.E334K|RNF40_ENST00000402121.3_Missense_Mutation_p.E126K|RNF40_ENST00000563683.1_Missense_Mutation_p.E394K	NM_001207033.1|NM_014771.3	NP_001193962.1|NP_055586	O75150	BRE1B_HUMAN	ring finger protein 40, E3 ubiquitin protein ligase	434					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)			ACAGAGCGACGAGCTGGGGCT	0.572																																					p.E434K		Atlas-SNP	.											.	RNF40	83	.	0			c.G1300A						PASS	.						60	44	50					16																	30778068		2197	4300	6497	SO:0001583	missense	9810	exon11			AGCGACGAGCTGG	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.1300G>A	16.37:g.30778068G>A	ENSP00000325677:p.Glu434Lys	32	0	0		30	9	0.3	NM_014771	Q6AHZ6|Q6N005|Q7L3T6|Q8N615|Q96T18|Q9BSV9|Q9HC82	Missense_Mutation	SNP	ENST00000324685.6	37	CCDS10691.1	.	.	.	.	.	.	.	.	.	.	G	35	5.422441	0.96111	.	.	ENSG00000103549	ENST00000324685;ENST00000357890;ENST00000402121	T;T;T	0.58210	0.93;0.76;0.35	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.76962	0.4061	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	0.999;0.997;0.998;0.998	T	0.76252	-0.3027	10	0.45353	T	0.12	-15.5499	19.4154	0.94694	0.0:0.0:1.0:0.0	.	126;334;434;434	F8W8Z4;O75150-4;A8K6K1;O75150	.;.;.;BRE1B_HUMAN	K	434;334;126	ENSP00000325677:E434K;ENSP00000350563:E334K;ENSP00000384942:E126K	ENSP00000325677:E434K	E	+	1	0	RNF40	30685569	1.000000	0.71417	0.994000	0.49952	0.770000	0.43624	9.164000	0.94755	2.884000	0.98904	0.655000	0.94253	GAG	.	.	none		0.572	RNF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255524.2	NM_014771		A	30778068	G	A	30778068	3	1	48	1	0	0	0	0	1	0	0	0	13508	1059	37	1	1338	1	RNF40	16	30778068	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	19428878	30778068	59576685	143	16019											
TMEM102	284114	hgsc.bcm.edu	37	chr17	7339603	7339603	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	cgagggctccctggatctggGgcatgcacccctgggtccct	4	8	14	15	1	1	0	0	0	1	0	3	2	3	1	4	5	1	3	4	5	0	0			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr17:7339603G>C	ENST00000323206.1	+	3	578	c.305G>C	c.(304-306)gGg>gCg	p.G102A	RP11-104H15.9_ENST00000570444.1_RNA|FGF11_ENST00000293829.4_5'Flank|FGF11_ENST00000575235.1_5'Flank|TMEM102_ENST00000396568.1_Missense_Mutation_p.G102A|RP11-104H15.7_ENST00000575310.1_RNA|RP11-104H15.8_ENST00000576615.1_RNA	NM_178518.2	NP_848613.1	Q8N9M5	TM102_HUMAN	transmembrane protein 102	102					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)				CTGGATCTGGGGCATGCACCC	0.607																																					p.G102A		Atlas-SNP	.											.	TMEM102	11	.	0			c.G305C						PASS	.						46	50	49					17																	7339603		2203	4300	6503	SO:0001583	missense	284114	exon3			ATCTGGGGCATGC	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.305G>C	17.37:g.7339603G>C	ENSP00000315387:p.Gly102Ala	29	0	0		36	8	0.222222	NM_178518	D3DTP8	Missense_Mutation	SNP	ENST00000323206.1	37	CCDS11104.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.175575	0.78564	.	.	ENSG00000181284	ENST00000323206;ENST00000396568	T;T	0.44083	0.93;0.93	5.36	5.36	0.76844	.	0.000000	0.53938	D	0.000049	T	0.61098	0.2320	M	0.65975	2.015	0.38711	D	0.953215	D	0.76494	0.999	D	0.68039	0.955	T	0.65911	-0.6053	10	0.59425	D	0.04	-10.7966	14.5838	0.68310	0.0:0.0:1.0:0.0	.	102	Q8N9M5	TM102_HUMAN	A	102	ENSP00000315387:G102A;ENSP00000379815:G102A	ENSP00000315387:G102A	G	+	2	0	TMEM102	7280327	0.998000	0.40836	0.998000	0.56505	0.994000	0.84299	3.066000	0.50002	2.498000	0.84270	0.655000	0.94253	GGG	.	.	none		0.607	TMEM102-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256405.1	NM_178518		C	7339603	G	C	7339603	3	2	48	1	0	0	0	0	1	0	0	0	16032	1232	43	4	311	4	TMEM102	17	7339603	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10		7339603	73855607	144	16020											
AURKB	9212	hgsc.bcm.edu	37	chr17	8108608	8108608	+	Missense_Mutation	SNP	A	A	T	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	ccccaccagcagctcatagcAaagcactccaatgcaccaca	14	4	5	18	0	1	0	1	0	0	0	2	0	2	0	5	0	5	5	5	0	3	1			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr17:8108608A>T	ENST00000585124.1	-	8	880	c.787T>A	c.(787-789)Tgc>Agc	p.C263S	AURKB_ENST00000316199.6_Missense_Mutation_p.C264S|AURKB_ENST00000534871.1_Missense_Mutation_p.C222S|AURKB_ENST00000578549.1_Missense_Mutation_p.C231S|AURKB_ENST00000535053.1_3'UTR	NM_004217.3	NP_004208.2	Q96GD4	AURKB_HUMAN	aurora kinase B	263	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				abscission (GO:0009838)|aging (GO:0007568)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|attachment of spindle microtubules to kinetochore (GO:0008608)|cell proliferation (GO:0008283)|cellular response to UV (GO:0034644)|cleavage furrow formation (GO:0036089)|cytokinesis checkpoint (GO:0031565)|histone H3-S28 phosphorylation (GO:0043988)|histone modification (GO:0016570)|mitotic cell cycle (GO:0000278)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of cytokinesis (GO:0032466)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cytokinesis (GO:0032467)|protein autophosphorylation (GO:0046777)|protein localization to kinetochore (GO:0034501)|protein phosphorylation (GO:0006468)|regulation of chromosome segregation (GO:0051983)|spindle checkpoint (GO:0031577)|spindle midzone assembly involved in mitosis (GO:0051256)|spindle stabilization (GO:0043146)	chromocenter (GO:0010369)|chromosome passenger complex (GO:0032133)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|histone serine kinase activity (GO:0035174)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			breast(1)|central_nervous_system(1)|lung(2)	4						AGCTCATAGCAAAGCACTCCA	0.582																																					p.C263S	NSCLC(134;1161 2470 43664 51568)	Atlas-SNP	.											.	AURKB	47	.	0			c.T787A						PASS	.						156	118	131					17																	8108608		2203	4300	6503	SO:0001583	missense	9212	exon8			CATAGCAAAGCAC	AF004022	CCDS11134.1, CCDS58514.1, CCDS67162.1	17p13.1	2013-01-17	2003-07-21	2003-07-23	ENSG00000178999	ENSG00000178999		"Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"	11390	protein-coding gene	gene with protein product	"aurora-B", "aurora-1", "protein phosphatase 1, regulatory subunit 48"	604970	"serine/threonine kinase 12"	STK12		9858806	Standard	NM_001256834		Approved	Aik2, IPL1, AurB, AIM-1, ARK2, STK5, PPP1R48	uc002gkm.4	Q96GD4	OTTHUMG00000108189	ENST00000585124.1:c.787T>A	17.37:g.8108608A>T	ENSP00000463999:p.Cys263Ser	52	0	0		65	20	0.307692	NM_004217	B4DNM4|C7G533|C7G534|C7G535|D3DTR4|J9JID1|O14630|O60446|O95083|Q96DV5|Q9UQ46	Missense_Mutation	SNP	ENST00000585124.1	37	CCDS11134.1	.	.	.	.	.	.	.	.	.	.	A	27.4	4.832058	0.91036	.	.	ENSG00000178999	ENST00000316199;ENST00000534871	T	0.64991	-0.13	5.33	5.33	0.75918	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	0.62588	0.2440	N	0.16790	0.44	0.80722	D	1	D;D	0.71674	0.998;0.998	P;P	0.61592	0.891;0.891	T	0.68330	-0.5437	10	0.87932	D	0	-22.5833	13.3096	0.60371	1.0:0.0:0.0:0.0	.	263;263	C7G533;Q96GD4	.;AURKB_HUMAN	S	263;222	ENSP00000443869:C222S	ENSP00000313950:C263S	C	-	1	0	AURKB	8049333	1.000000	0.71417	0.999000	0.59377	0.746000	0.42486	9.088000	0.94132	2.249000	0.74217	0.528000	0.53228	TGC	.	.	none		0.582	AURKB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000226995.2	NM_004217		T	8108608	A	T	8108608	3	4	48	1	0	0	0	0	1	0	0	0	1223	130	5	5	255	5	AURKB	17	8108608	Missense_Mutation	SNP	A	TCGA-VB-A8QN-01A-11D-A382-10	769005	8108608	73086602	145	16021											
MYH1	4619	hgsc.bcm.edu	37	chr17	10400708	10400708	+	Missense_Mutation	SNP	T	T	G	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	tgctgagtgagcgggattccTtttgagaagcttcaagttca	9	13	12	7	1	2	3	2	3	0	1	3	5	3	4	1	1	3	3	1	1	2	5			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr17:10400708T>G	ENST00000226207.5	-	32	4521	c.4427A>C	c.(4426-4428)aAg>aCg	p.K1476T	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	1476					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						GCGGGATTCCTTTTGAGAAGC	0.383																																					p.K1476T		Atlas-SNP	.											.	MYH1	403	.	0			c.A4427C						PASS	.						79	77	77					17																	10400708		2203	4300	6503	SO:0001583	missense	4619	exon32			GATTCCTTTTGAG		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.4427A>C	17.37:g.10400708T>G	ENSP00000226207:p.Lys1476Thr	124	0	0		134	35	0.261194	NM_005963	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	37	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.182577	0.78677	.	.	ENSG00000109061	ENST00000226207;ENST00000379814	T	0.80214	-1.35	5.7	5.7	0.88788	Myosin tail (1);	0.000000	0.45361	U	0.000378	D	0.88621	0.6486	M	0.84585	2.705	0.58432	D	0.999999	D	0.55385	0.971	P	0.55508	0.777	D	0.90399	0.4401	10	0.72032	D	0.01	.	16.2494	0.82473	0.0:0.0:0.0:1.0	.	1476	P12882	MYH1_HUMAN	T	1476;565	ENSP00000226207:K1476T	ENSP00000226207:K1476T	K	-	2	0	MYH1	10341433	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.991000	0.88244	2.287000	0.76781	0.533000	0.62120	AAG	.	.	none		0.383	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963		G	10400708	T	G	10400708	3	3	48	1	0	0	0	0	1	0	0	0	10038	1609	56	5	1428	5	MYH1	17	10400708	Missense_Mutation	SNP	T	TCGA-VB-A8QN-01A-11D-A382-10	2292100	10400708	70794502	146	16022											
MYH2	4620	hgsc.bcm.edu	37	chr17	10428151	10428151	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	ggcatggttcagctggatttCcatttcattgaggtctccct	6	15	10	10	0	3	1	2	1	1	0	5	2	4	2	2	4	1	3	2	4	0	4			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr17:10428151C>T	ENST00000245503.5	-	34	5278	c.4894G>A	c.(4894-4896)Gaa>Aaa	p.E1632K	RP11-799N11.1_ENST00000399342.2_RNA|MYH2_ENST00000532183.2_Intron|RP11-799N11.1_ENST00000581304.1_RNA|MYH2_ENST00000397183.2_Missense_Mutation_p.E1632K|CTC-297N7.11_ENST00000587182.2_RNA	NM_017534.5	NP_060004.3	Q9UKX2	MYH2_HUMAN	myosin, heavy chain 2, skeletal muscle, adult	1632					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						AGCTGGATTTCCATTTCATTG	0.507																																					p.E1632K		Atlas-SNP	.											.	MYH2	390	.	0			c.G4894A						PASS	.						206	179	188					17																	10428151		2203	4297	6500	SO:0001583	missense	4620	exon34			GGATTTCCATTTC		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.4894G>A	17.37:g.10428151C>T	ENSP00000245503:p.Glu1632Lys	271	0	0		267	73	0.273408	NM_017534	A0AVL4|Q14322|Q16229|Q567P6|Q86T56	Missense_Mutation	SNP	ENST00000245503.5	37	CCDS11156.1	.	.	.	.	.	.	.	.	.	.	C	34	5.331921	0.95733	.	.	ENSG00000125414	ENST00000245503;ENST00000397183	D;D	0.84146	-1.81;-1.81	5.44	5.44	0.79542	Myosin tail (1);	0.000000	0.39834	U	0.001251	D	0.95570	0.8560	H	0.98238	4.18	0.80722	D	1	D	0.55172	0.97	D	0.66847	0.947	D	0.96775	0.9571	10	0.87932	D	0	.	19.4557	0.94886	0.0:1.0:0.0:0.0	.	1632	Q9UKX2	MYH2_HUMAN	K	1632	ENSP00000245503:E1632K;ENSP00000380367:E1632K	ENSP00000245503:E1632K	E	-	1	0	MYH2	10368876	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.563000	0.82314	2.823000	0.97156	0.591000	0.81541	GAA	.	.	none		0.507	MYH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252726.3	NM_017534		T	10428151	C	T	10428151	3	4	48	1	0	0	0	0	1	0	0	0	10044	864	30	2	959	2	MYH2	17	10428151	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	27443	10428151	70767059	147	16023											
CYTSB	92521	hgsc.bcm.edu	37	chr17	20107645	20107645	+	Splice_Site	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	ttttcttcttctgtctttaaGgggcctttacaacaactaaa	10	17	5	9	0	4	0	0	0	4	0	4	0	4	0	1	2	3	0	1	2	6	9			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr17:20107645G>T	ENST00000261503.5	+	4	334		c.e4-1		SPECC1_ENST00000536879.1_Intron|SPECC1_ENST00000584527.1_5'Flank|AC004702.2_ENST00000580225.1_lincRNA|SPECC1_ENST00000395527.4_Splice_Site|SPECC1_ENST00000395530.2_Splice_Site|SPECC1_ENST00000472876.1_Intron|SPECC1_ENST00000395525.3_Splice_Site|SPECC1_ENST00000395529.3_Splice_Site|SPECC1_ENST00000395522.2_Splice_Site	NM_001033553.2	NP_001028725.1	Q5M775	CYTSB_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1						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)		CTGTCTTTAAGGGGCCTTTAC	0.438																																					.		Atlas-SNP	.											.	SPECC1	100	.	0			c.284-1G>T						PASS	.						118	130	126					17																	20107645		2203	4300	6503	SO:0001630	splice_region_variant	92521	exon4			CTTTAAGGGGCCT	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.284-1G>T	17.37:g.20107645G>T		33	0	0		51	11	0.215686	NM_001243439	B4DHH0|B7WNS8|Q5IBP1|Q5IBP2|Q5IBP3|Q5IBP4|Q5M772|Q5M773|Q5M774|Q86XT8|Q8N4U4|Q8WU84|Q9HCQ3	Splice_Site	SNP	ENST00000261503.5	37	CCDS32590.1	.	.	.	.	.	.	.	.	.	.	G	11.62	1.691542	0.30052	.	.	ENSG00000128487	ENST00000395530;ENST00000261503;ENST00000395529;ENST00000395522;ENST00000395527;ENST00000395525	.	.	.	5.13	5.13	0.70059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.4284	0.83832	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SPECC1	20048237	1.000000	0.71417	0.747000	0.31113	0.277000	0.26821	6.642000	0.74329	2.558000	0.86282	0.591000	0.81541	.	.	.	none		0.438	SPECC1-018	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441206.1	NM_152904	Intron	T	20107645	G	T	20107645	5	4	48	1	0	0	0	0	0	0	1	0	4212	1014	35	4	337	4	CYTSB	17	20107645	Splice_Site	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	9679494	20107645	61087565	148	16024											
STAT3	6774	hgsc.bcm.edu	37	chr17	40475068	40475068	+	Missense_Mutation	SNP	G	G	C	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	aaagtgacgcctccttctttGctgctttcactgaatcttag	8	15	7	11	1	3	2	1	2	2	0	4	2	4	2	2	0	2	2	2	0	3	4			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr17:40475068G>C	ENST00000264657.5	-	20	2154	c.1842C>G	c.(1840-1842)agC>agG	p.S614R	STAT3_ENST00000404395.3_Missense_Mutation_p.S614R|STAT3_ENST00000588969.1_Missense_Mutation_p.S614R|STAT3_ENST00000389272.3_Missense_Mutation_p.S516R|STAT3_ENST00000585517.1_Missense_Mutation_p.S614R	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)	614	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)	p.S614R(1)		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)		CTCCTTCTTTGCTGCTTTCAC	0.572									Hyperimmunoglobulin E Recurrent Infection Syndrome		OREG0024421	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S614R		Atlas-SNP	.											STAT3,lymph_node,lymphoid_neoplasm,0,4	STAT3	268	4	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C1842G						PASS	.						134	125	128					17																	40475068		2203	4300	6503	SO:0001583	missense	6774	exon20	Familial Cancer Database	HIES, Hyper IgE syndrome, autosomal dominant (Job syndrome) / recessive	TTCTTTGCTGCTT	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.1842C>G	17.37:g.40475068G>C	ENSP00000264657:p.Ser614Arg	74	0	0	893	70	19	0.271429	NM_003150	A8K7B8|K7ENL3|O14916|Q9BW54	Missense_Mutation	SNP	ENST00000264657.5	37	CCDS32656.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.393161	0.83011	.	.	ENSG00000168610	ENST00000264657;ENST00000389272;ENST00000404395	D;D;D	0.96522	-4.04;-4.04;-4.04	5.29	5.29	0.74685	SH2 motif (4);	0.000000	0.85682	D	0.000000	D	0.97244	0.9099	L	0.43923	1.385	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	D	0.97931	1.0320	10	0.87932	D	0	-10.2909	19.12	0.93358	0.0:0.0:1.0:0.0	.	614;614;614	P40763-2;P40763;B5BTZ6	.;STAT3_HUMAN;.	R	614;516;614	ENSP00000264657:S614R;ENSP00000373923:S516R;ENSP00000384943:S614R	ENSP00000264657:S614R	S	-	3	2	STAT3	37728594	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.477000	0.66799	2.752000	0.94435	0.655000	0.94253	AGC	.	.	none		0.572	STAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319353.3	NM_139276, NM_003150		C	40475068	G	C	40475068	3	2	48	1	0	0	0	0	1	0	0	0	15281	1310	46	4	490	4	STAT3	17	40475068	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	20367423	40475068	40720142	149	16025											
SEPT4	5414	hgsc.bcm.edu	37	chr17	56599357	56599357	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	aagggtgagatgaagtacagGcagcagtgcaccctgttgtc	11	8	14	8	0	0	2	0	2	0	1	1	3	0	2	1	2	3	5	1	2	3	2	rs144640338		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr17:56599357G>A	ENST00000317268.3	-	6	944	c.768C>T	c.(766-768)tgC>tgT	p.C256C	RP11-112H10.4_ENST00000580589.1_RNA|SEPT4_ENST00000393086.1_Silent_p.C237C|SEPT4_ENST00000580809.1_Silent_p.C138C|SEPT4_ENST00000583114.1_Silent_p.C109C|SEPT4_ENST00000412945.3_Silent_p.C248C|SEPT4_ENST00000457347.2_Silent_p.C271C|SEPT4_ENST00000317256.6_Silent_p.C237C|SEPT4_ENST00000426861.1_Silent_p.C237C|SEPT4_ENST00000579371.1_Silent_p.C157C|SEPT4_ENST00000580844.1_Silent_p.C157C	NM_004574.3	NP_004565.1	O43236	SEPT4_HUMAN	septin 4	256	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)					TGAAGTACAGGCAGCAGTGCA	0.562																																					p.C271C		Atlas-SNP	.											.	SEPT4	48	.	0			c.C813T						PASS	.	G	,,,	0,4406		0,0,2203	175	145	155		744,768,711,711	4.9	1	17	dbSNP_134	155	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEPT4	NM_001198713.1,NM_004574.3,NM_080415.2,NM_080416.2	,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,	248/471,256/479,237/275,237/460	56599357	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	5414	exon7			GTACAGGCAGCAG	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.768C>T	17.37:g.56599357G>A		126	0	0		135	36	0.266667	NM_001256782	B2RD42|B3KSX9|B4DXC6|B4DXV5|Q6IAP3|Q9H315|Q9UM58	Silent	SNP	ENST00000317268.3	37	CCDS11610.1																																																																																			G|1.000;A|0.000	0.000	weak		0.562	SEPT4-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445420.1	NM_080417		A	56599357	G	A	56599357	2	1	48	1	0	0	0	0	0	0	0	1	14081	1195	42	2		2	SEPT4	17	56599357	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	16124289	56599357	24595853	150	16026											
DNAH17	8632	hgsc.bcm.edu	37	chr17	76450728	76450728	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tggttgttccaggtggccacGtccgcgtcatctgtcagcag	5	11	13	12	3	3	0	2	0	1	0	5	0	5	0	3	3	1	3	3	3	0	2	rs148972892		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr17:76450728G>A	ENST00000585328.1	-	64	10339	c.10215C>T	c.(10213-10215)gaC>gaT	p.D3405D	DNAH17_ENST00000586052.1_5'UTR|DNAH17_ENST00000389840.5_Silent_p.D3396D	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	3396	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)			AGGTGGCCACGTCCGCGTCAT	0.637													G|||	1	0.000199681	0.0	0.0	5008	,	,		17233	0.0		0.001	False		,,,				2504	0.0				p.D3410D		Atlas-SNP	.											.	DNAH17	347	.	0			c.C10230T						PASS	.	G		0,4406		0,0,2203	104	83	90		10230	-0.2	0.8	17	dbSNP_134	90	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	DNAH17	NM_173628.3		0,4,6499	AA,AG,GG		0.0465,0.0,0.0308		3410/4463	76450728	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	8632	exon64			GGCCACGTCCGCG	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.10215C>T	17.37:g.76450728G>A		42	0	0		64	19	0.296875	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				G|1.000;A|0.000	0.000	strong		0.637	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		A	76450728	G	A	76450728	2	1	48	1	0	0	0	0	0	0	0	1	4603	1136	40	1		1	DNAH17	17	76450728	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	19851371	76450728	4744482	151	16027											
DSG1	1828	hgsc.bcm.edu	37	chr18	28926102	28926102	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	gaacattaagaagaaattctAtgagggaatgtagagaagga	19	8	12	2	0	1	4	0	1	1	3	1	8	1	6	0	2	1	1	0	2	8	4			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr18:28926102A>G	ENST00000257192.4	+	14	2253	c.2041A>G	c.(2041-2043)Atg>Gtg	p.M681V	RP11-534N16.1_ENST00000578477.1_RNA|RP11-534N16.1_ENST00000581856.1_RNA|RP11-534N16.1_ENST00000578119.1_RNA|RNU6-167P_ENST00000384292.1_RNA|DSG1_ENST00000462981.2_Missense_Mutation_p.M40V	NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	681					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)			AAGAAATTCTATGAGGGAATG	0.418																																					p.M681V		Atlas-SNP	.											DSG1,bladder,carcinoma,-2,1	DSG1	176	1	0			c.A2041G						PASS	.						101	103	103					18																	28926102		2203	4300	6503	SO:0001583	missense	1828	exon14			AATTCTATGAGGG	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.2041A>G	18.37:g.28926102A>G	ENSP00000257192:p.Met681Val	83	0	0		71	12	0.169014	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	.	.	.	.	.	.	.	.	.	.	A	11.54	1.670182	0.29693	.	.	ENSG00000134760	ENST00000257192	T	0.55760	0.5	6.06	4.9	0.64082	Cadherin, cytoplasmic domain (1);	0.061477	0.64402	D	0.000002	T	0.36303	0.0962	N	0.19112	0.55	0.32403	N	0.551713	P	0.40578	0.722	B	0.38921	0.285	T	0.47661	-0.9100	10	0.34782	T	0.22	.	10.3501	0.43929	0.9261:0.0:0.0739:0.0	.	681	Q02413	DSG1_HUMAN	V	681	ENSP00000257192:M681V	ENSP00000257192:M681V	M	+	1	0	DSG1	27180100	0.996000	0.38824	1.000000	0.80357	0.996000	0.88848	1.100000	0.31025	1.100000	0.41517	0.533000	0.62120	ATG	.	.	none		0.418	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942		G	28926102	A	G	28926102	3	3	48	1	0	0	0	0	1	0	0	0	4778	449	16	3	2095	3	DSG1	18	28926102	Missense_Mutation	SNP	A	TCGA-VB-A8QN-01A-11D-A382-10		28926102	49151146	152	16028											
DSG4	147409	hgsc.bcm.edu	37	chr18	28966774	28966774	+	Missense_Mutation	SNP	A	A	G	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	acaactcgaagaggaaccccAttgccaaagtaagtgatgaa	17	6	9	9	1	0	3	0	2	0	1	1	5	0	4	3	1	3	1	3	1	6	2			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr18:28966774A>G	ENST00000308128.4	+	3	343	c.208A>G	c.(208-210)Att>Gtt	p.I70V	RP11-534N16.1_ENST00000578477.1_RNA|DSG4_ENST00000359747.4_Missense_Mutation_p.I70V|RP11-534N16.1_ENST00000581856.1_RNA|RP11-534N16.1_ENST00000581452.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	70	Cadherin 1. {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)			GAGGAACCCCATTGCCAAAGT	0.473																																					p.I70V		Atlas-SNP	.											.	DSG4	343	.	0			c.A208G						PASS	.						93	84	87					18																	28966774		2203	4300	6503	SO:0001583	missense	147409	exon3			AACCCCATTGCCA	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.208A>G	18.37:g.28966774A>G	ENSP00000311859:p.Ile70Val	74	0	0		64	15	0.234375	NM_001134453	A2RUI1|Q6Y9L9|Q8IXV4	Missense_Mutation	SNP	ENST00000308128.4	37	CCDS11897.1	.	.	.	.	.	.	.	.	.	.	A	17.74	3.465033	0.63513	.	.	ENSG00000175065	ENST00000308128;ENST00000359747	T;T	0.42131	0.98;0.98	5.22	5.22	0.72569	Cadherin (3);	0.000000	0.35207	N	0.003361	T	0.53417	0.1795	L	0.42487	1.325	0.39467	D	0.967666	D;D	0.67145	0.996;0.988	D;D	0.85130	0.997;0.923	T	0.48410	-0.9038	10	0.16896	T	0.51	.	13.9536	0.64133	1.0:0.0:0.0:0.0	.	70;70	Q86SJ6-2;Q86SJ6	.;DSG4_HUMAN	V	70	ENSP00000311859:I70V;ENSP00000352785:I70V	ENSP00000311859:I70V	I	+	1	0	DSG4	27220772	1.000000	0.71417	0.912000	0.35992	0.601000	0.36947	6.122000	0.71608	2.092000	0.63282	0.528000	0.53228	ATT	.	.	none		0.473	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986		G	28966774	A	G	28966774	3	3	48	1	0	0	0	0	1	0	0	0	4781	217	8	3	218	3	DSG4	18	28966774	Missense_Mutation	SNP	A	TCGA-VB-A8QN-01A-11D-A382-10	40672	28966774	49110474	153	16029											
CBLN2	147381	hgsc.bcm.edu	37	chr18	70205920	70205920	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	tctgttatacactttgaccaCgtggaagctgaagctataaa	13	12	8	8	1	1	2	0	2	1	0	1	3	1	3	1	1	3	3	1	1	7	5			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr18:70205920C>T	ENST00000269503.4	-	4	1218	c.445G>A	c.(445-447)Gtg>Atg	p.V149M	CBLN2_ENST00000584764.1_Missense_Mutation_p.V33M|CBLN2_ENST00000581073.1_Missense_Mutation_p.V35M|CBLN2_ENST00000585159.1_Missense_Mutation_p.V149M|CBLN2_ENST00000583651.1_5'UTR	NM_182511.3	NP_872317.1	Q8IUK8	CBLN2_HUMAN	cerebellin 2 precursor	149	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)				ACTTTGACCACGTGGAAGCTG	0.403																																					p.V149M		Atlas-SNP	.											.	CBLN2	41	.	0			c.G445A						PASS	.						121	115	117					18																	70205920		2203	4300	6503	SO:0001583	missense	147381	exon4			TGACCACGTGGAA	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.445G>A	18.37:g.70205920C>T	ENSP00000269503:p.Val149Met	83	0	0		96	33	0.34375	NM_182511	Q53Z56	Missense_Mutation	SNP	ENST00000269503.4	37	CCDS11999.1	.	.	.	.	.	.	.	.	.	.	C	15.83	2.948914	0.53186	.	.	ENSG00000141668	ENST00000269503	T	0.76839	-1.05	5.51	5.51	0.81932	Tumour necrosis factor-like (2);Complement C1q protein (4);	0.000000	0.85682	D	0.000000	D	0.87569	0.6210	M	0.70275	2.135	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	D	0.85208	0.1019	10	0.34782	T	0.22	-27.0636	19.7945	0.96474	0.0:1.0:0.0:0.0	.	149	Q8IUK8	CBLN2_HUMAN	M	149	ENSP00000269503:V149M	ENSP00000269503:V149M	V	-	1	0	CBLN2	68356900	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.769000	0.85360	2.746000	0.94184	0.591000	0.81541	GTG	.	.	none		0.403	CBLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256288.1	NM_182511		T	70205920	C	T	70205920	3	4	48	1	0	0	0	0	1	0	0	0	2707	536	19	1	237	1	CBLN2	18	70205920	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	41239146	70205920	7871328	154	16030											
SALL3	27164	hgsc.bcm.edu	37	chr18	76756928	76756928	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	catgtggaataacgcccccgCgagacgcggccgccgcctgt	7	5	13	16	7	0	1	0	0	0	1	0	3	0	2	5	2	1	0	5	2	2	1	rs533436270		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr18:76756928C>T	ENST00000537592.2	+	3	3509	c.3509C>T	c.(3508-3510)gCg>gTg	p.A1170V	SALL3_ENST00000536229.3_Missense_Mutation_p.A965V|SALL3_ENST00000575389.2_Missense_Mutation_p.A1098V	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	1170					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)		AACGCCCCCGCGAGACGCGGC	0.627																																					p.A1170V		Atlas-SNP	.											SALL3,colon,carcinoma,0,1	SALL3	162	1	0			c.C3509T						scavenged	.						21	24	23					18																	76756928		2203	4300	6503	SO:0001583	missense	27164	exon3			CCCCCGCGAGACG	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.3509C>T	18.37:g.76756928C>T	ENSP00000441823:p.Ala1170Val	47	0	0		53	9	0.169811	NM_171999	Q9UGH1	Missense_Mutation	SNP	ENST00000537592.2	37	CCDS12013.1	.	.	.	.	.	.	.	.	.	.	C	13.20	2.165258	0.38217	.	.	ENSG00000256463	ENST00000537592;ENST00000536229;ENST00000543056	T	0.10573	2.86	4.79	4.79	0.61399	.	0.000000	0.56097	D	0.000028	T	0.40570	0.1122	M	0.87180	2.865	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.962	T	0.49351	-0.8949	10	0.72032	D	0.01	-43.6667	18.2244	0.89913	0.0:1.0:0.0:0.0	.	830;1170	F5GXY4;Q9BXA9	.;SALL3_HUMAN	V	1170;1098;830	ENSP00000441823:A1170V	ENSP00000299466:A1170V	A	+	2	0	SALL3	74857916	1.000000	0.71417	0.370000	0.25965	0.778000	0.44026	5.940000	0.70187	2.351000	0.79841	0.561000	0.74099	GCG	.	.	none		0.627	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999		T	76756928	C	T	76756928	3	4	48	1	0	0	0	0	1	0	0	0	13827	768	27	1	3519	1	SALL3	18	76756928	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	6551008	76756928	1320320	155	16031											
TCF3	6929	hgsc.bcm.edu	37	chr19	1650209	1650209	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	aggaggtcactgagctccttGtctgtgcccacaggcgccat	7	9	12	13	1	2	1	1	1	1	0	3	2	3	2	3	3	2	1	3	3	0	1	rs373351484		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr19:1650209G>A	ENST00000262965.5	-	2	383	c.39C>T	c.(37-39)gaC>gaT	p.D13D	TCF3_ENST00000344749.5_Silent_p.D13D|TCF3_ENST00000588136.1_Silent_p.D13D|TCF3_ENST00000395423.3_Silent_p.D13D	NM_003200.3	NP_003191.1	Q9HCS4	TF7L1_HUMAN	transcription factor 3	0	CTNNB1-binding. {ECO:0000250}.|Gly-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)		TGAGCTCCTTGTCTGTGCCCA	0.642			T	"PBX1, HLF, TFPT"	pre B-ALL																																p.D13D		Atlas-SNP	.		Dom	yes		19	19p13.3	6929	transcription factor 3 (E2A immunoglobulin enhancer binding factors E12/E47)		L	.	TCF3	72	.	0			c.C39T						PASS	.						42	43	43					19																	1650209		2179	4269	6448	SO:0001819	synonymous_variant	6929	exon2			CTCCTTGTCTGTG	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.39C>T	19.37:g.1650209G>A		22	0	0		37	11	0.297297	NM_003200	Q53R97|Q6PD70|Q9NP00	Silent	SNP	ENST00000262965.5	37	CCDS12074.1																																																																																			.	.	alt		0.642	TCF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449367.1	NM_003200		A	1650209	G	A	1650209	2	1	48	1	0	0	0	0	0	0	0	1	15709	1368	48	2		2	TCF3	19	1650209	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10		1650209	57478774	156	16032											
MUC16	94025	hgsc.bcm.edu	37	chr19	9062349	9062349	+	Missense_Mutation	SNP	T	T	A	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	agtcagataggacagaagatTgtgattcatgtccagaaatg	15	10	11	5	0	2	5	2	1	0	4	3	6	3	6	1	1	0	0	1	1	3	3			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr19:9062349T>A	ENST00000397910.4	-	3	25300	c.25097A>T	c.(25096-25098)cAa>cTa	p.Q8366L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	8368	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						GACAGAAGATTGTGATTCATG	0.488																																					p.Q8366L		Atlas-SNP	.											.	MUC16	4315	.	0			c.A25097T						PASS	.						192	187	189					19																	9062349		2104	4217	6321	SO:0001583	missense	94025	exon3			GAAGATTGTGATT	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.25097A>T	19.37:g.9062349T>A	ENSP00000381008:p.Gln8366Leu	123	0	0		111	24	0.216216	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	t	2.473	-0.321332	0.05386	.	.	ENSG00000181143	ENST00000397910	T	0.24538	1.85	1.67	-3.34	0.04943	.	.	.	.	.	T	0.17959	0.0431	L	0.43152	1.355	.	.	.	B	0.21071	0.051	B	0.13407	0.009	T	0.12372	-1.0550	8	0.87932	D	0	.	5.1877	0.15193	0.1893:0.0:0.5705:0.2401	.	8366	B5ME49	.	L	8366	ENSP00000381008:Q8366L	ENSP00000381008:Q8366L	Q	-	2	0	MUC16	8923349	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.791000	0.01758	-1.768000	0.01298	-0.842000	0.03052	CAA	.	.	none		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690		A	9062349	T	A	9062349	3	1	48	1	0	0	0	0	1	0	0	0	9982	1812	63	5	18754	5	MUC16	19	9062349	Missense_Mutation	SNP	T	TCGA-VB-A8QN-01A-11D-A382-10	7412140	9062349	50066634	157	16033											
PRKCSH	5589	hgsc.bcm.edu	37	chr19	11558370	11558370	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gaggaggaggaggaggaggaGgaagaagaggctgaagaaga	17	1	22	1	0	0	5	0	1	0	4	0	13	0	12	0	8	0	1	0	8	4	0	rs77563879		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr19:11558370G>A	ENST00000589838.1	+	10	966	c.966G>A	c.(964-966)gaG>gaA	p.E322E	PRKCSH_ENST00000252455.2_Silent_p.E322E|PRKCSH_ENST00000592741.1_Silent_p.E322E|PRKCSH_ENST00000412601.1_Silent_p.E322E|PRKCSH_ENST00000591462.1_Silent_p.E322E|PRKCSH_ENST00000587327.1_Silent_p.E322E			P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H	322	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						aggaggaggaggaagaagagg	0.632																																					p.E322E		Atlas-SNP	.											PRKCSH,caecum,carcinoma,0,1	PRKCSH	55	1	1	Deletion - In frame(1)	central_nervous_system(1)	c.G966A						scavenged	.						27	27	27					19																	11558370		2200	4298	6498	SO:0001819	synonymous_variant	5589	exon11			GGAGGAGGAAGAA		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.966G>A	19.37:g.11558370G>A		49	1	0.0204082		57	5	0.0877193	NM_001001329	A8K318|Q96BU9|Q96D06|Q9P0W9	Silent	SNP	ENST00000589838.1	37	CCDS32911.1																																																																																			.	.	weak		0.632	PRKCSH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458817.1			A	11558370	G	A	11558370	2	1	48	1	0	0	0	0	0	0	0	1	12528	991	35	2		2	PRKCSH	19	11558370	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	2496021	11558370	47570613	158	16034											
SLC5A5	6528	hgsc.bcm.edu	37	chr19	17984984	17984984	+	Missense_Mutation	SNP	G	G	T	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	cagccgcgcagtgcggctctGcgggactttgcagtacattg	6	9	14	12	4	1	0	0	0	1	0	1	1	1	1	1	2	5	4	1	2	1	3			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr19:17984984G>T	ENST00000222248.3	+	2	742	c.395G>T	c.(394-396)tGc>tTc	p.C132F		NM_000453.2	NP_000444.1	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium/iodide cotransporter), member 5	132					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						GTGCGGCTCTGCGGGACTTTG	0.672																																					p.C132F	Melanoma(65;1008 1708 7910 46650)	Atlas-SNP	.											.	SLC5A5	67	.	0			c.G395T						PASS	.						39	38	38					19																	17984984		2203	4300	6503	SO:0001583	missense	6528	exon2			GGCTCTGCGGGAC		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.395G>T	19.37:g.17984984G>T	ENSP00000222248:p.Cys132Phe	76	0	0		62	16	0.258065	NM_000453	O43702|Q2M335|Q9NYB6	Missense_Mutation	SNP	ENST00000222248.3	37	CCDS12368.1	.	.	.	.	.	.	.	.	.	.	G	10.59	1.392224	0.25118	.	.	ENSG00000105641	ENST00000222248	D	0.86865	-2.18	4.27	4.27	0.50696	.	0.202043	0.44285	D	0.000469	T	0.76357	0.3976	N	0.17564	0.495	0.32638	N	0.521147	B	0.02656	0.0	B	0.12156	0.007	T	0.74481	-0.3651	10	0.23302	T	0.38	.	12.5512	0.56227	0.0:0.0:1.0:0.0	.	132	Q92911	SC5A5_HUMAN	F	132	ENSP00000222248:C132F	ENSP00000222248:C132F	C	+	2	0	SLC5A5	17845984	1.000000	0.71417	1.000000	0.80357	0.054000	0.15201	2.837000	0.48191	2.107000	0.64212	0.436000	0.28706	TGC	.	.	none		0.672	SLC5A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466690.1			T	17984984	G	T	17984984	3	4	48	1	0	0	0	0	1	0	0	0	14683	1319	46	4	401	4	SLC5A5	19	17984984	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	6426614	17984984	41143999	159	16035											
ZNF208	7757	hgsc.bcm.edu	37	chr19	22156863	22156863	+	Missense_Mutation	SNP	C	C	A	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	atgtgtaataagggttgagaCcttactgaaggctttgccac	11	12	11	7	0	0	2	0	2	0	1	0	3	0	2	2	2	2	3	2	2	4	5	rs202200782		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr19:22156863C>A	ENST00000397126.4	-	4	1121	c.973G>T	c.(973-975)Gtc>Ttc	p.V325F	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	325					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.V325F(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)				AGGGTTGAGACCTTACTGAAG	0.403																																					p.V325F		Atlas-SNP	.											ZNF208_ENST00000428290,NS,carcinoma,0,7	ZNF208	817	7	1	Substitution - Missense(1)	NS(1)	c.G973T						scavenged	.						66	68	67					19																	22156863		1946	3920	5866	SO:0001583	missense	7757	exon4			TTGAGACCTTACT	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.973G>T	19.37:g.22156863C>A	ENSP00000380315:p.Val325Phe	72	1	0.0138889		25	4	0.16	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	C	0.040	-1.286883	0.01387	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.38560	1.13	2.93	-5.86	0.02304	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.21962	0.0529	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.10428	-1.0630	8	0.39692	T	0.17	.	0.9385	0.01350	0.2555:0.1041:0.2969:0.3435	.	325	O43345	ZN208_HUMAN	F	325	ENSP00000380315:V325F	ENSP00000380315:V325F	V	-	1	0	ZNF208	21948703	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.688000	0.00392	-2.968000	0.00287	-2.283000	0.00269	GTC	C|0.996;A|0.004	0.004	weak		0.403	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		A	22156863	C	A	22156863	3	1	48	1	0	0	0	0	1	0	0	0	17781	507	18	4	2873	4	ZNF208	19	22156863	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	4171879	22156863	36972120	160	16036											
ZNF208	7757	hgsc.bcm.edu	37	chr19	22157288	22157288	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	gagataggtgtgaaagcatgCaaaatgatctgacgtattct	14	11	11	5	1	2	4	0	3	2	1	2	5	2	4	0	1	2	3	0	1	5	3			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr19:22157288C>T	ENST00000397126.4	-	4	696	c.548G>A	c.(547-549)tGc>tAc	p.C183Y	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	183					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)				TGAAAGCATGCAAAATGATCT	0.333																																					p.C183Y		Atlas-SNP	.											.	ZNF208	817	.	0			c.G548A						PASS	.						86	84	85					19																	22157288		2038	4222	6260	SO:0001583	missense	7757	exon4			AGCATGCAAAATG	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.548G>A	19.37:g.22157288C>T	ENSP00000380315:p.Cys183Tyr	135	0	0		94	28	0.297872	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	.	.	.	.	.	.	.	.	.	.	C	0	-2.664133	0.00107	.	.	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.14516	2.5	1.62	0.204	0.15199	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13628	0.0330	.	.	.	0.09310	N	1	D	0.69078	0.997	P	0.61070	0.883	T	0.13899	-1.0492	8	0.06494	T	0.89	.	6.1001	0.20043	0.0:0.4968:0.5032:0.0	.	183	O43345	ZN208_HUMAN	Y	183	ENSP00000380315:C183Y	ENSP00000380315:C183Y	C	-	2	0	ZNF208	21949128	0.000000	0.05858	0.005000	0.12908	0.755000	0.42902	-0.498000	0.06420	0.904000	0.36572	0.298000	0.19748	TGC	.	.	none		0.333	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153		T	22157288	C	T	22157288	3	4	48	1	0	0	0	0	1	0	0	0	17781	710	25	2	3298	2	ZNF208	19	22157288	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	425	22157288	36971695	161	16037											
GGN	199720	hgsc.bcm.edu	37	chr19	38876581	38876583	+	In_Frame_Del	DEL	GCA	GCA	-																															gggcggcggtgtgggcggtgGcagcggtggtaactcctgca																										TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	GCA	GCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr19:38876581_38876583delGCA	ENST00000334928.6	-	3	1451_1453	c.1319_1321delTGC	c.(1318-1323)ctgcca>cca	p.L440del	AC005789.9_ENST00000585411.1_RNA|GGN_ENST00000591809.1_Intron|SPRED3_ENST00000587013.1_5'Flank	NM_152657.3	NP_689870.3	Q86UU5	GGN_HUMAN	gametogenetin	440	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)			gtgggcggtggcagcggtggTAA	0.724																																					p.440_441del		Atlas-Indel	.											.	GGN	50	.	0			c.1320_1322del						PASS	.																																			SO:0001651	inframe_deletion	199720	exon3			.	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.1319_1321delTGC	19.37:g.38876581_38876583delGCA	ENSP00000334940:p.Leu440del	68	0	0		72	11	0.152778	NM_152657	Q7RTU6|Q86UU4|Q8NAA1	In_Frame_Del	DEL	ENST00000334928.6	37	CCDS12516.1																																																																																			.	.	none		0.724	GGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459205.1	NM_152657		-	38876583	GCA	-	38876581	7	5	48	1	0	1	0	1	0	0	0	0	6366	1203	42	0	645	0	GGN	19	38876581	In_Frame_Del	DEL	GCA	TCGA-VB-A8QN-01A-11D-A382-10	16719293	38876581	20252402	162	16038											
ZNF841	284371	hgsc.bcm.edu	37	chr19	52569180	52569180	+	Missense_Mutation	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	cacaatcattacatttataaGgtttctctccggtatgaatt	12	16	5	8	1	2	1	1	1	1	0	4	1	3	1	1	2	1	2	1	2	6	7			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr19:52569180G>A	ENST00000426391.2	-	5	2158	c.1607C>T	c.(1606-1608)cCt>cTt	p.P536L	ZNF841_ENST00000594295.1_Missense_Mutation_p.P652L|ZNF841_ENST00000389534.4_Missense_Mutation_p.P652L|ZNF432_ENST00000598446.1_Intron|ZNF841_ENST00000359973.2_Intron|CTC-471J1.2_ENST00000569091.1_RNA			Q6ZN19	ZN841_HUMAN	zinc finger protein 841	536					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						ACATTTATAAGGTTTCTCTCC	0.428																																					p.P652L		Atlas-SNP	.											.	ZNF841	183	.	0			c.C1955T						PASS	.						100	94	96					19																	52569180		692	1591	2283	SO:0001583	missense	284371	exon7			TTATAAGGTTTCT	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.1607C>T	19.37:g.52569180G>A	ENSP00000415453:p.Pro536Leu	123	0	0		142	35	0.246479	NM_001136499	B9EG58|Q6ZN82|Q6ZP71|Q8N9U7	Missense_Mutation	SNP	ENST00000426391.2	37		.	.	.	.	.	.	.	.	.	.	G	18.27	3.587926	0.66105	.	.	ENSG00000197608	ENST00000389534;ENST00000426391	T;T	0.17054	2.3;2.3	1.88	0.814	0.18756	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.36248	0.0960	M	0.74546	2.27	0.31539	N	0.660191	D;P	0.89917	1.0;0.908	D;B	0.87578	0.998;0.368	T	0.36817	-0.9732	9	0.54805	T	0.06	.	7.6369	0.28272	0.1609:0.0:0.8391:0.0	.	652;536	Q6ZN19-3;Q6ZN19	.;ZN841_HUMAN	L	652;536	ENSP00000374185:P652L;ENSP00000415453:P536L	ENSP00000374185:P652L	P	-	2	0	ZNF841	57260992	0.000000	0.05858	0.004000	0.12327	0.887000	0.51463	-0.138000	0.10374	1.025000	0.39708	0.313000	0.20887	CCT	.	.	none		0.428	ZNF841-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000462435.1	XM_209155		A	52569180	G	A	52569180	3	1	48	1	0	0	0	0	1	0	0	0	18204	1000	35	2	823	2	ZNF841	19	52569180	Missense_Mutation	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	13692599	52569180	6559803	163	16039											
ZNF841	284371	hgsc.bcm.edu	37	chr19	52569959	52569959	+	Missense_Mutation	SNP	C	C	G	0	0	0	1	0	0	1	0	0	0	1	0	1	0	1	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	ttgtctccagtatgaactgtCtgatgagttgcaagagagga	11	12	12	6	0	2	4	0	3	2	1	3	6	2	5	1	1	2	3	1	1	3	3			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr19:52569959C>G	ENST00000426391.2	-	5	1379	c.828G>C	c.(826-828)caG>caC	p.Q276H	ZNF841_ENST00000594295.1_Missense_Mutation_p.Q392H|ZNF841_ENST00000389534.4_Missense_Mutation_p.Q392H|ZNF432_ENST00000598446.1_Intron|ZNF841_ENST00000359973.2_Missense_Mutation_p.Q276H			Q6ZN19	ZN841_HUMAN	zinc finger protein 841	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)			breast(1)|endometrium(4)|kidney(3)|lung(3)	11						TATGAACTGTCTGATGAGTTG	0.403																																					p.Q392H		Atlas-SNP	.											.	ZNF841	183	.	0			c.G1176C						PASS	.						121	109	112					19																	52569959		692	1591	2283	SO:0001583	missense	284371	exon7			AACTGTCTGATGA	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.828G>C	19.37:g.52569959C>G	ENSP00000415453:p.Gln276His	107	0	0		96	27	0.28125	NM_001136499	B9EG58|Q6ZN82|Q6ZP71|Q8N9U7	Missense_Mutation	SNP	ENST00000426391.2	37		.	.	.	.	.	.	.	.	.	.	C	16.68	3.190664	0.58017	.	.	ENSG00000197608	ENST00000389534;ENST00000426391;ENST00000359973	T;T;T	0.36520	1.25;1.25;1.25	2.26	-2.37	0.06643	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.39462	0.1079	L	0.43757	1.38	0.09310	N	1	D;B;D	0.58970	0.984;0.234;0.974	D;B;D	0.65987	0.94;0.049;0.912	T	0.26052	-1.0114	9	0.51188	T	0.08	.	0.9063	0.01285	0.1624:0.3178:0.2785:0.2414	.	392;276;276	Q6ZN19-3;Q6ZN19-2;Q6ZN19	.;.;ZN841_HUMAN	H	392;276;276	ENSP00000374185:Q392H;ENSP00000415453:Q276H;ENSP00000353060:Q276H	ENSP00000353060:Q276H	Q	-	3	2	ZNF841	57261771	0.000000	0.05858	0.000000	0.03702	0.936000	0.57629	-0.278000	0.08490	-0.564000	0.06070	0.313000	0.20887	CAG	.	.	none		0.403	ZNF841-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000462435.1	XM_209155		G	52569959	C	G	52569959	3	3	48	1	0	0	0	0	1	0	0	0	18204	912	32	4	1602	4	ZNF841	19	52569959	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	779	52569959	6559024	164	16040											
ZNF135	7694	hgsc.bcm.edu	37	chr19	58574874	58574874	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	gcaagaggcagagctgtgggCggtggagtctagacttcccc	8	7	16	10	1	1	3	0	0	1	3	2	4	2	4	2	4	1	3	2	4	2	2			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr19:58574874C>T	ENST00000313434.5	+	4	322	c.221C>T	c.(220-222)gCg>gTg	p.A74V	ZNF135_ENST00000401053.4_Missense_Mutation_p.A86V|ZNF135_ENST00000439855.2_Missense_Mutation_p.A74V|ZNF135_ENST00000359978.6_Missense_Mutation_p.A86V|ZNF135_ENST00000506786.1_Missense_Mutation_p.A32V|ZNF135_ENST00000511556.1_Missense_Mutation_p.A74V	NM_003436.3	NP_003427.3	P52742	ZN135_HUMAN	zinc finger protein 135	74	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)		GAGCTGTGGGCGGTGGAGTCT	0.572																																					p.A86V		Atlas-SNP	.											.	ZNF135	159	.	0			c.C257T						PASS	.						112	98	103					19																	58574874		2203	4300	6503	SO:0001583	missense	7694	exon3			TGTGGGCGGTGGA	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.221C>T	19.37:g.58574874C>T	ENSP00000321406:p.Ala74Val	71	0	0		73	13	0.178082	NM_007134	B4DHH9|E9PEV2|F5GYY9|I3L0B3|Q5U5L3|Q8N1I7	Missense_Mutation	SNP	ENST00000313434.5	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	0.024|0.024	-1.388368|-1.388368	0.01185|0.01185	.|.	.|.	ENSG00000176293|ENSG00000176293	ENST00000504540;ENST00000401053;ENST00000359978;ENST00000439855;ENST00000313434;ENST00000511556;ENST00000506786|ENST00000391699	T;T;T;T;T;T|.	0.26067|.	1.76;1.76;1.76;1.76;1.76;1.76|.	2.51|2.51	-0.893|-0.893	0.10567|0.10567	Krueppel-associated box (2);|.	.|.	.|.	.|.	.|.	T|T	0.07999|0.07999	0.0200|0.0200	N|N	0.00894|0.00894	-1.105|-1.105	0.09310|0.09310	N|N	1|1	B;B;B|.	0.11235|.	0.001;0.001;0.004|.	B;B;B|.	0.04013|.	0.001;0.001;0.001|.	T|T	0.36866|0.36866	-0.9730|-0.9730	9|5	0.20519|.	T|.	0.43|.	.|.	5.1902|5.1902	0.15205|0.15205	0.0:0.5554:0.0:0.4446|0.0:0.5554:0.0:0.4446	.|.	74;74;86|.	E9PEV2;P52742;Q8N1I7|.	.;ZN135_HUMAN;.|.	V|W	86;86;86;74;74;74;32|80	ENSP00000441410:A86V;ENSP00000369437:A86V;ENSP00000444828:A74V;ENSP00000321406:A74V;ENSP00000422074:A74V;ENSP00000427691:A32V|.	ENSP00000321406:A74V|.	A|R	+|+	2|1	0|2	ZNF135|ZNF135	63266686|63266686	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-1.546000|-1.546000	0.02188|0.02188	-0.094000|-0.094000	0.12374|0.12374	-0.251000|-0.251000	0.11542|0.11542	GCG|CGG	.	.	none		0.572	ZNF135-003	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000361899.2	NM_003436		T	58574874	C	T	58574874	3	4	48	1	0	0	0	0	1	0	0	0	17740	768	27	1	304	1	ZNF135	19	58574874	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	6004915	58574874	554109	165	16041											
JAG1	182	hgsc.bcm.edu	37	chr20	10633195	10633195	+	Silent	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	cagatgccgtggacgcatccCgggtgtgggatgcacttatc	7	9	14	11	3	0	1	0	0	0	1	2	3	1	3	2	3	2	2	2	3	1	1			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr20:10633195C>T	ENST00000254958.5	-	6	1322	c.807G>A	c.(805-807)ccG>ccA	p.P269P	JAG1_ENST00000423891.2_Silent_p.P110P	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	269	EGF-like 2; atypical. {ECO:0000255|PROSITE-ProRule:PRU00076}.		P -> L (in ALGS1). {ECO:0000269|PubMed:12497640}.		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						GGACGCATCCCGGGTGTGGGA	0.567									Alagille Syndrome																												p.P269P		Atlas-SNP	.											JAG1_ENST00000254958,colon,carcinoma,0,2	JAG1	213	2	0			c.G807A						PASS	.						60	53	55					20																	10633195		2203	4300	6503	SO:0001819	synonymous_variant	182	exon6	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	GCATCCCGGGTGT	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.807G>A	20.37:g.10633195C>T		88	0	0		66	16	0.242424	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Silent	SNP	ENST00000254958.5	37	CCDS13112.1																																																																																			.	.	none		0.567	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214		T	10633195	C	T	10633195	2	4	48	1	0	0	0	0	0	0	0	1	7943	639	23	1		1	JAG1	20	10633195	Silent	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10		10633195	52392325	166	16042											
PLUNC	51297	hgsc.bcm.edu	37	chr20	31825915	31825915	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	gggcattctggaaaaccttcCgctcctggacatcctgaagc	9	9	10	13	1	1	1	0	1	1	0	4	3	4	3	4	3	2	2	4	3	3	2			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr20:31825915C>T	ENST00000354297.4	+	3	286	c.215C>T	c.(214-216)cCg>cTg	p.P72L	BPIFA1_ENST00000375422.2_Missense_Mutation_p.P72L|BPIFA1_ENST00000375413.4_Missense_Mutation_p.P72L	NM_130852.2	NP_570913.1	Q9NP55	BPIA1_HUMAN	BPI fold containing family A, member 1	72					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)										GAAAACCTTCCGCTCCTGGAC	0.562																																					p.P72L		Atlas-SNP	.											PLUNC,NS,carcinoma,-1,1	.	.	1	0			c.C215T						PASS	.						66	65	65					20																	31825915		2203	4300	6503	SO:0001583	missense	51297	exon3			ACCTTCCGCTCCT	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.215C>T	20.37:g.31825915C>T	ENSP00000346251:p.Pro72Leu	41	0	0		48	14	0.291667	NM_016583	A8K9R3|E1P5M9|Q9NZT0	Missense_Mutation	SNP	ENST00000354297.4	37	CCDS13217.1	.	.	.	.	.	.	.	.	.	.	C	13.94	2.385566	0.42308	.	.	ENSG00000198183	ENST00000375422;ENST00000354297;ENST00000375413;ENST00000544328	T;T;T	0.05717	3.4;3.4;3.4	5.43	5.43	0.79202	.	0.091687	0.48767	D	0.000170	T	0.25382	0.0617	M	0.82323	2.585	0.25290	N	0.989361	D	0.76494	0.999	D	0.65010	0.931	T	0.04708	-1.0932	10	0.51188	T	0.08	-13.9534	14.6064	0.68481	0.0:1.0:0.0:0.0	.	72	Q9NP55	BPIA1_HUMAN	L	72;72;72;58	ENSP00000364571:P72L;ENSP00000346251:P72L;ENSP00000364562:P72L	ENSP00000346251:P72L	P	+	2	0	BPIFA1	31289576	0.722000	0.28017	0.101000	0.21167	0.001000	0.01503	1.938000	0.40203	2.813000	0.96785	0.655000	0.94253	CCG	.	.	none		0.562	BPIFA1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078667.2	NM_130852		T	31825915	C	T	31825915	3	4	48	1	0	0	0	0	1	0	0	0	12124	652	23	1	221	1	PLUNC	20	31825915	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	21192720	31825915	31199605	167	16043											
TPD52L2	7165	hgsc.bcm.edu	37	chr20	62521256	62521256	+	Silent	SNP	G	G	A	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	gacaacctcccttcctcagcGgggagtggtgacaagcccct	8	7	11	15	1	1	1	1	1	0	0	3	3	3	2	5	3	3	0	5	3	2	1	rs143876889		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr20:62521256G>A	ENST00000346249.4	+	7	655	c.579G>A	c.(577-579)gcG>gcA	p.A193A	TPD52L2_ENST00000358548.4_Silent_p.A187A|TPD52L2_ENST00000369927.4_Silent_p.A150A|TPD52L2_ENST00000217121.5_Silent_p.A216A|TPD52L2_ENST00000352482.4_Silent_p.A207A|TPD52L2_ENST00000351424.4_Silent_p.A196A|TPD52L2_ENST00000348257.5_Silent_p.A173A	NM_001243891.1|NM_003288.3	NP_001230820.1|NP_003279.2	O43399	TPD54_HUMAN	tumor protein D52-like 2	193					regulation of cell proliferation (GO:0042127)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	8	all_cancers(38;1.3e-12)|all_epithelial(29;2.23e-14)|Lung NSC(23;5.92e-10)|all_lung(23;2.08e-09)					CTTCCTCAGCGGGGAGTGGTG	0.557																																					p.R177Q		Atlas-SNP	.											.	TPD52L2	20	.	0			c.G530A						PASS	.	G	,,,,,	0,4406		0,0,2203	81	71	75		579,519,648,588,621,561	-10	0	20	dbSNP_134	75	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TPD52L2	NM_003288.3,NM_199359.2,NM_199360.2,NM_199361.2,NM_199362.2,NM_199363.2	,,,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,,	193/207,173/187,216/230,196/210,207/221,187/201	62521256	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	7165	exon6			CTCAGCGGGGAGT	AF004430	CCDS13540.1, CCDS13541.1, CCDS13542.1, CCDS13543.1, CCDS13544.1, CCDS13545.1, CCDS58785.1, CCDS74752.1, CCDS74753.1	20q13.2-q13.3	2007-12-19			ENSG00000101150	ENSG00000101150			12007	protein-coding gene	gene with protein product		603747				9484778	Standard	NM_199360		Approved	D54, hD54	uc002ygy.3	O43399	OTTHUMG00000033009	ENST00000346249.4:c.579G>A	20.37:g.62521256G>A		55	0	0		32	11	0.34375	NM_001243895	B4DPJ6|E1P5G7|O43398|Q5JWU5|Q5JWU6|Q5JWU8|Q5U0E0|Q9H3Z6	Missense_Mutation	SNP	ENST00000346249.4	37	CCDS13540.1																																																																																			G|1.000;A|0.000	0.000	weak		0.557	TPD52L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080248.1			A	62521256	G	A	62521256	2	1	48	1	0	0	0	0	0	0	0	1	16414	1103	39	1		1	TPD52L2	20	62521256	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10	30695341	62521256	504264	168	16044											
DNMT3L	29947	hgsc.bcm.edu	37	chr21	45680710	45680710	+	Missense_Mutation	SNP	T	T	C	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	gctggttagccttgacttcaTatgcaataagatctggaaag	12	12	10	7	0	2	2	1	1	1	1	2	3	2	3	1	2	2	3	1	2	5	5			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr21:45680710T>C	ENST00000418993.1	-	3	602	c.119A>G	c.(118-120)tAt>tGt	p.Y40C	DNMT3L_ENST00000270172.3_Missense_Mutation_p.Y40C	NM_175867.2	NP_787063.1	Q9UJW3	DNM3L_HUMAN	DNA (cytosine-5-)-methyltransferase 3-like	40					chorionic trophoblast cell differentiation (GO:0060718)|DNA methylation (GO:0006306)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|placenta development (GO:0001890)|positive regulation of catalytic activity (GO:0043085)|regulation of gene expression by genetic imprinting (GO:0006349)|spermatogenesis (GO:0007283)	condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(3)	11				Colorectal(79;0.0165)|READ - Rectum adenocarcinoma(84;0.0781)		CTTGACTTCATATGCAATAAG	0.438																																					p.Y40C		Atlas-SNP	.											.	DNMT3L	33	.	0			c.A119G						PASS	.						174	164	168					21																	45680710		2203	4299	6502	SO:0001583	missense	29947	exon3			ACTTCATATGCAA	AF194032	CCDS13705.1	21q22.3	2008-07-31			ENSG00000142182	ENSG00000142182			2980	protein-coding gene	gene with protein product	"cytosine-5-methyltransferase 3-like protein", "human cytosine-5-methyltransferase 3-like protein"	606588				10857753	Standard	NM_013369		Approved	MGC1090	uc002zeh.2	Q9UJW3	OTTHUMG00000086914	ENST00000418993.1:c.119A>G	21.37:g.45680710T>C	ENSP00000412862:p.Tyr40Cys	131	0	0		133	31	0.233083	NM_013369	E9PB42|Q9BUJ4	Missense_Mutation	SNP	ENST00000418993.1	37	CCDS46650.1	.	.	.	.	.	.	.	.	.	.	T	7.270	0.606979	0.14002	.	.	ENSG00000142182	ENST00000270172;ENST00000418993	D;D	0.83075	-1.68;-1.68	3.6	2.36	0.29203	.	0.342864	0.27375	N	0.019645	D	0.86318	0.5904	M	0.65975	2.015	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.66847	0.947;0.947	T	0.75274	-0.3375	10	0.42905	T	0.14	-17.0402	5.8846	0.18874	0.2344:0.0:0.0:0.7656	.	40;40	Q9UJW3-2;Q9UJW3	.;DNM3L_HUMAN	C	40	ENSP00000270172:Y40C;ENSP00000412862:Y40C	ENSP00000270172:Y40C	Y	-	2	0	DNMT3L	44505138	0.975000	0.34042	0.019000	0.16419	0.019000	0.09904	4.241000	0.58707	0.511000	0.28236	0.379000	0.24179	TAT	.	.	none		0.438	DNMT3L-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000195820.1	NM_013369		C	45680710	T	C	45680710	3	2	48	1	0	0	0	0	1	0	0	0	4680	1406	49	3	1084	3	DNMT3L	21	45680710	Missense_Mutation	SNP	T	TCGA-VB-A8QN-01A-11D-A382-10		45680710	2449185	169	16045											
IGLL5	100423062	hgsc.bcm.edu	37	chr22	23230278	23230278	+	Silent	SNP	G	G	A	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	ggttgtgagacccctgaggaGctgggccctggtcccaggca	6	7	16	12	0	0	2	0	2	0	1	1	4	1	3	4	5	1	3	4	5	0	1	rs544778929	byFrequency	TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr22:23230278G>A	ENST00000526893.1	+	1	319	c.45G>A	c.(43-45)gaG>gaA	p.E15E	IGLL5_ENST00000532223.2_Silent_p.E15E|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000531372.1_Silent_p.E15E	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	15						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CCCCTGAGGAGCTGGGCCCTG	0.672													G|||	6	0.00119808	0.0023	0.0029	5008	,	,		13267	0.0		0.0	False		,,,				2504	0.001				p.E15E		Atlas-SNP	.											IGLL5,NS,lymphoid_neoplasm,0,1	IGLL5	26	1	0			c.G45A						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			TGAGGAGCTGGGC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"Immunoglobulin superfamily / C1-set domain containing"	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.45G>A	22.37:g.23230278G>A		136	0	0		108	30	0.277778	NM_001178126		Silent	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.672	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126		A	23230278	G	A	23230278	2	1	48	1	0	0	0	0	0	0	0	1	7603	962	34	2		2	IGLL5	22	23230278	Silent	SNP	G	TCGA-VB-A8QN-01A-11D-A382-10		23230278	28074288	170	16046											
CABIN1	23523	hgsc.bcm.edu	37	chr22	24447360	24447360	+	Nonsense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	tagatgaggccttggggctgCgaaaaaagaggcaagcgctg	12	6	16	7	2	0	3	0	1	0	2	0	4	0	3	1	4	2	3	1	4	5	2	rs556308783		TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chr22:24447360C>T	ENST00000398319.2	+	8	1115	c.730C>T	c.(730-732)Cga>Tga	p.R244*	CABIN1_ENST00000405822.2_Intron|CABIN1_ENST00000263119.5_Nonsense_Mutation_p.R244*	NM_001199281.1	NP_001186210.1	Q9Y6J0	CABIN_HUMAN	calcineurin binding protein 1	244					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						CTTGGGGCTGCGAAAAAAGAG	0.517																																					p.R244X		Atlas-SNP	.											.	CABIN1	153	.	0			c.C730T						PASS	.						117	103	108					22																	24447360		2203	4300	6503	SO:0001587	stop_gained	23523	exon8			GGGCTGCGAAAAA	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.730C>T	22.37:g.24447360C>T	ENSP00000381364:p.Arg244*	93	0	0		92	26	0.282609	NM_001199281	G5E9F3|Q6PHY0|Q9Y460	Nonsense_Mutation	SNP	ENST00000398319.2	37	CCDS13823.1	.	.	.	.	.	.	.	.	.	.	C	28.2	4.901417	0.92035	.	.	ENSG00000099991	ENST00000454754;ENST00000263119;ENST00000445422;ENST00000398319;ENST00000536026	.	.	.	5.21	4.18	0.49190	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	14.5723	0.68220	0.1475:0.8525:0.0:0.0	.	.	.	.	X	199;244;199;244;244	.	ENSP00000263119:R244X	R	+	1	2	CABIN1	22777360	1.000000	0.71417	0.999000	0.59377	0.013000	0.08279	2.687000	0.46976	1.326000	0.45319	-0.329000	0.08387	CGA	.	.	none		0.517	CABIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320161.2	NM_012295		T	24447360	C	T	24447360	4	4	48	1	0	0	0	0	0	1	0	0	2530	760	27	1	756	1	CABIN1	22	24447360	Nonsense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10	1217082	24447360	26857206	171	16047											
FAM47B	170062	hgsc.bcm.edu	37	chrX	34961271	34961271	+	Missense_Mutation	SNP	C	C	T	0	0	0	1	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	ggccctattttccgagctctCgccagtacagccagcacgga	8	8	10	15	3	1	0	0	0	1	0	3	2	2	1	4	2	4	3	4	2	2	4			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chrX:34961271C>T	ENST00000329357.5	+	1	359	c.323C>T	c.(322-324)tCg>tTg	p.S108L		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	108										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						TCCGAGCTCTCGCCAGTACAG	0.517																																					p.S108L		Atlas-SNP	.											.	FAM47B	209	.	0			c.C323T						PASS	.						89	82	84					X																	34961271		2202	4300	6502	SO:0001583	missense	170062	exon1			AGCTCTCGCCAGT	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.323C>T	X.37:g.34961271C>T	ENSP00000328307:p.Ser108Leu	80	0	0		89	37	0.41573	NM_152631	Q5JQN5|Q6PIG3	Missense_Mutation	SNP	ENST00000329357.5	37	CCDS14236.1	.	.	.	.	.	.	.	.	.	.	C	7.692	0.691313	0.15039	.	.	ENSG00000189132	ENST00000329357	T	0.19806	2.12	0.843	-0.305	0.12784	.	.	.	.	.	T	0.15912	0.0383	M	0.64997	1.995	0.09310	N	1	P	0.36535	0.557	B	0.28465	0.09	T	0.13764	-1.0497	9	0.34782	T	0.22	.	5.1951	0.15232	0.0:0.743:0.0:0.257	.	108	Q8NA70	FA47B_HUMAN	L	108	ENSP00000328307:S108L	ENSP00000328307:S108L	S	+	2	0	FAM47B	34871192	0.002000	0.14202	0.004000	0.12327	0.005000	0.04900	0.123000	0.15708	-0.184000	0.10567	0.292000	0.19580	TCG	.	.	none		0.517	FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056211.1	NM_152631		T	34961271	C	T	34961271	3	4	48	1	0	0	0	0	1	0	0	0	5578	893	31	1	325	1	FAM47B	23	34961271	Missense_Mutation	SNP	C	TCGA-VB-A8QN-01A-11D-A382-10		34961271	120309289	172	16048											
UBE2A	7319	hgsc.bcm.edu	37	chrX	118708862	118708862	+	Splice_Site	SNP	A	A	C	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	acccctgtctgtcttcccgaAggttgcaggaggatcctcca	7	10	10	14	1	2	0	0	0	2	0	5	3	5	2	5	3	1	2	5	3	1	2			TCGA-VB-A8QN-01A-11D-A382-10	TCGA-VB-A8QN-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	9f0d2750-df3a-4483-a914-016ced90bcfb	3bb2b474-51e0-48eb-b243-4ddd53fb1cda	g.chrX:118708862A>C	ENST00000371558.2	+	2	218		c.e2-1		UBE2A_ENST00000346330.3_Splice_Site|UBE2A_ENST00000469205.1_Splice_Site	NM_001282161.1|NM_003336.2|NM_181762.1	NP_001269090.1|NP_003327.2|NP_861427.1	P49459	UBE2A_HUMAN	ubiquitin-conjugating enzyme E2A						antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|DNA repair (GO:0006281)|histone H2A ubiquitination (GO:0033522)|in utero embryonic development (GO:0001701)|maternal process involved in female pregnancy (GO:0060135)|positive regulation of cell proliferation (GO:0008284)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein polyubiquitination (GO:0000209)|response to UV (GO:0009411)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|cytosol (GO:0005829)|HULC complex (GO:0033503)|nuclear chromatin (GO:0000790)|XY body (GO:0001741)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)			haematopoietic_and_lymphoid_tissue(1)|lung(7)	8						GTCTTCCCGAAGGTTGCAGGA	0.697								Rad6 pathway																													.		Atlas-SNP	.											.	UBE2A	43	.	0			c.45-2A>C						PASS	.						129	105	113					X																	118708862		2203	4300	6503	SO:0001630	splice_region_variant	7319	exon2			TCCCGAAGGTTGC	AK223045	CCDS14580.1, CCDS14581.1	Xq24	2011-05-19	2011-05-19		ENSG00000077721	ENSG00000077721		"Ubiquitin-conjugating enzymes E2"	12472	protein-coding gene	gene with protein product		312180	"ubiquitin-conjugating enzyme E2A (RAD6 homolog)"			1559696	Standard	NM_003336		Approved	UBC2, HHR6A, RAD6A	uc004erl.3	P49459	OTTHUMG00000022275	ENST00000371558.2:c.45-1A>C	X.37:g.118708862A>C		152	0	0		167	74	0.443114	NM_181762	A6NFE9|A6NGR2|A6NMF5|B2R7R9|D3DWI1|Q4TTG1|Q96FX4	Splice_Site	SNP	ENST00000371558.2	37	CCDS14580.1	.	.	.	.	.	.	.	.	.	.	A	13.89	2.371271	0.42003	.	.	ENSG00000077721	ENST00000371558;ENST00000346330	.	.	.	4.6	4.6	0.57074	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.22	0.37370	0.8043:0.1957:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UBE2A	118592890	1.000000	0.71417	0.966000	0.40874	0.394000	0.30568	8.517000	0.90555	1.709000	0.51313	0.430000	0.28490	.	.	.	none		0.697	UBE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058036.1	NM_003336	Intron	C	118708862	A	C	118708862	5	2	48	1	0	0	0	0	0	0	1	0	16859	86	3	5	49	5	UBE2A	23	118708862	Splice_Site	SNP	A	TCGA-VB-A8QN-01A-11D-A382-10	83747591	118708862	36561698	173	16049											
